From 358347602cfd43673f4cc64f598440cd5417baeb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Dec 2021 12:26:52 +0100
Subject: [PATCH 0001/1827] Switch hermite_spline_xz to index

Might help with performance
---
 include/interpolation_xz.hxx                  |  2 +-
 src/mesh/interpolation/hermite_spline_xz.cxx  | 86 +++++++++----------
 .../monotonic_hermite_spline_xz.cxx           | 61 ++++++-------
 3 files changed, 65 insertions(+), 84 deletions(-)

diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx
index 47474ad39c..04269a830d 100644
--- a/include/interpolation_xz.hxx
+++ b/include/interpolation_xz.hxx
@@ -95,7 +95,7 @@ protected:
   /// This is protected rather than private so that it can be
   /// extended and used by HermiteSplineMonotonic
 
-  Tensor<int> i_corner; // x-index of bottom-left grid point
+  Tensor<SpecificInd<IND_TYPE::IND_3D>> i_corner; // index of bottom-left grid point
   Tensor<int> k_corner; // z-index of bottom-left grid point
 
   // Basis functions for cubic Hermite spline interpolation
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index f5ce3357cb..9f14d4b836 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -38,7 +38,6 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
 
   // Initialise in order to avoid 'uninitialized value' errors from Valgrind when using
   // guard-cell values
-  i_corner = -1;
   k_corner = -1;
 
   // Allocate Field3D members
@@ -55,6 +54,8 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
 void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                                   const std::string& region) {
 
+  const int ny = localmesh->LocalNy;
+  const int nz = localmesh->LocalNz;
   BOUT_FOR(i, delta_x.getRegion(region)) {
     const int x = i.x();
     const int y = i.y();
@@ -65,29 +66,29 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
 
     // The integer part of xt_prime, zt_prime are the indices of the cell
     // containing the field line end-point
-    i_corner(x, y, z) = static_cast<int>(floor(delta_x(x, y, z)));
+    int i_corn = static_cast<int>(floor(delta_x(x, y, z)));
     k_corner(x, y, z) = static_cast<int>(floor(delta_z(x, y, z)));
 
     // t_x, t_z are the normalised coordinates \in [0,1) within the cell
     // calculated by taking the remainder of the floating point index
-    BoutReal t_x = delta_x(x, y, z) - static_cast<BoutReal>(i_corner(x, y, z));
+    BoutReal t_x = delta_x(x, y, z) - static_cast<BoutReal>(i_corn);
     BoutReal t_z = delta_z(x, y, z) - static_cast<BoutReal>(k_corner(x, y, z));
 
     // NOTE: A (small) hack to avoid one-sided differences
-    if (i_corner(x, y, z) >= localmesh->xend) {
-      i_corner(x, y, z) = localmesh->xend - 1;
+    if (i_corn >= localmesh->xend) {
+      i_corn = localmesh->xend - 1;
       t_x = 1.0;
     }
-    if (i_corner(x, y, z) < localmesh->xstart) {
-      i_corner(x, y, z) = localmesh->xstart;
+    if (i_corn < localmesh->xstart) {
+      i_corn = localmesh->xstart;
       t_x = 0.0;
     }
 
     // Check that t_x and t_z are in range
     if ((t_x < 0.0) || (t_x > 1.0)) {
       throw BoutException(
-          "t_x={:e} out of range at ({:d},{:d},{:d}) (delta_x={:e}, i_corner={:d})", t_x,
-          x, y, z, delta_x(x, y, z), i_corner(x, y, z));
+          "t_x={:e} out of range at ({:d},{:d},{:d}) (delta_x={:e}, i_corn={:d})", t_x,
+          x, y, z, delta_x(x, y, z), i_corn);
     }
 
     if ((t_z < 0.0) || (t_z > 1.0)) {
@@ -96,17 +97,20 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
           x, y, z, delta_z(x, y, z), k_corner(x, y, z));
     }
 
-    h00_x(x, y, z) = (2. * t_x * t_x * t_x) - (3. * t_x * t_x) + 1.;
-    h00_z(x, y, z) = (2. * t_z * t_z * t_z) - (3. * t_z * t_z) + 1.;
+    i_corner[i] = SpecificInd<IND_TYPE::IND_3D>(
+        (((i_corn * ny) + (y + y_offset)) * nz + k_corner(x, y, z)), ny, nz);
 
-    h01_x(x, y, z) = (-2. * t_x * t_x * t_x) + (3. * t_x * t_x);
-    h01_z(x, y, z) = (-2. * t_z * t_z * t_z) + (3. * t_z * t_z);
+    h00_x[i] = (2. * t_x * t_x * t_x) - (3. * t_x * t_x) + 1.;
+    h00_z[i] = (2. * t_z * t_z * t_z) - (3. * t_z * t_z) + 1.;
 
-    h10_x(x, y, z) = t_x * (1. - t_x) * (1. - t_x);
-    h10_z(x, y, z) = t_z * (1. - t_z) * (1. - t_z);
+    h01_x[i] = (-2. * t_x * t_x * t_x) + (3. * t_x * t_x);
+    h01_z[i] = (-2. * t_z * t_z * t_z) + (3. * t_z * t_z);
 
-    h11_x(x, y, z) = (t_x * t_x * t_x) - (t_x * t_x);
-    h11_z(x, y, z) = (t_z * t_z * t_z) - (t_z * t_z);
+    h10_x[i] = t_x * (1. - t_x) * (1. - t_x);
+    h10_z[i] = t_z * (1. - t_z) * (1. - t_z);
+
+    h11_x[i] = (t_x * t_x * t_x) - (t_x * t_x);
+    h11_z[i] = (t_z * t_z * t_z) - (t_z * t_z);
   }
 }
 
@@ -137,8 +141,8 @@ XZHermiteSpline::getWeightsForYApproximation(int i, int j, int k, int yoffset) {
   const int ncz = localmesh->LocalNz;
   const int k_mod = ((k_corner(i, j, k) % ncz) + ncz) % ncz;
   const int k_mod_m1 = (k_mod > 0) ? (k_mod - 1) : (ncz - 1);
-  const int k_mod_p1 = (k_mod + 1) % ncz;
-  const int k_mod_p2 = (k_mod + 2) % ncz;
+  const int k_mod_p1 = (k_mod == ncz) ? 0 : k_mod + 1;
+  const int k_mod_p2 = (k_mod_p1 == ncz) ? 0 : k_mod_p1 + 1;
 
   return {{i, j + yoffset, k_mod_m1, -0.5 * h10_z(i, j, k)},
           {i, j + yoffset, k_mod,    h00_z(i, j, k) - 0.5 * h11_z(i, j, k)},
@@ -183,45 +187,35 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
     if (skip_mask(x, y, z))
       continue;
 
-    // Due to lack of guard cells in z-direction, we need to ensure z-index
-    // wraps around
-    const int ncz = localmesh->LocalNz;
-    const int z_mod = ((k_corner(x, y, z) % ncz) + ncz) % ncz;
-    const int z_mod_p1 = (z_mod + 1) % ncz;
+    const auto iyp = i.yp(y_offset);
 
-    const int y_next = y + y_offset;
+    const auto ic = i_corner[i];
+    const auto iczp = ic.zp();
+    const auto icxp = ic.xp();
+    const auto icxpzp = iczp.xp();
 
     // Interpolate f in X at Z
-    const BoutReal f_z = f(i_corner(x, y, z), y_next, z_mod) * h00_x(x, y, z)
-                         + f(i_corner(x, y, z) + 1, y_next, z_mod) * h01_x(x, y, z)
-                         + fx(i_corner(x, y, z), y_next, z_mod) * h10_x(x, y, z)
-                         + fx(i_corner(x, y, z) + 1, y_next, z_mod) * h11_x(x, y, z);
+    const BoutReal f_z =
+        f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
 
     // Interpolate f in X at Z+1
-    const BoutReal f_zp1 = f(i_corner(x, y, z), y_next, z_mod_p1) * h00_x(x, y, z)
-                           + f(i_corner(x, y, z) + 1, y_next, z_mod_p1) * h01_x(x, y, z)
-                           + fx(i_corner(x, y, z), y_next, z_mod_p1) * h10_x(x, y, z)
-                           + fx(i_corner(x, y, z) + 1, y_next, z_mod_p1) * h11_x(x, y, z);
+    const BoutReal f_zp1 = f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] + fx[iczp] * h10_x[i]
+                           + fx[icxpzp] * h11_x[i];
 
     // Interpolate fz in X at Z
-    const BoutReal fz_z = fz(i_corner(x, y, z), y_next, z_mod) * h00_x(x, y, z)
-                          + fz(i_corner(x, y, z) + 1, y_next, z_mod) * h01_x(x, y, z)
-                          + fxz(i_corner(x, y, z), y_next, z_mod) * h10_x(x, y, z)
-                          + fxz(i_corner(x, y, z) + 1, y_next, z_mod) * h11_x(x, y, z);
+    const BoutReal fz_z = fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] + fxz[ic] * h10_x[i]
+                          + fxz[icxp] * h11_x[i];
 
     // Interpolate fz in X at Z+1
-    const BoutReal fz_zp1 =
-        fz(i_corner(x, y, z), y_next, z_mod_p1) * h00_x(x, y, z)
-        + fz(i_corner(x, y, z) + 1, y_next, z_mod_p1) * h01_x(x, y, z)
-        + fxz(i_corner(x, y, z), y_next, z_mod_p1) * h10_x(x, y, z)
-        + fxz(i_corner(x, y, z) + 1, y_next, z_mod_p1) * h11_x(x, y, z);
+    const BoutReal fz_zp1 = fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i]
+                            + fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
 
     // Interpolate in Z
-    f_interp(x, y_next, z) = +f_z * h00_z(x, y, z) + f_zp1 * h01_z(x, y, z)
-                             + fz_z * h10_z(x, y, z) + fz_zp1 * h11_z(x, y, z);
+    f_interp[iyp] =
+        +f_z * h00_z[i] + f_zp1 * h01_z[i] + fz_z * h10_z[i] + fz_zp1 * h11_z[i];
 
-    ASSERT2(std::isfinite(f_interp(x, y_next, z)) || x < localmesh->xstart
-            || x > localmesh->xend);
+    ASSERT2(std::isfinite(f_interp[iyp]) || i.x() < localmesh->xstart
+            || i.x() > localmesh->xend);
   }
   return f_interp;
 }
diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
index bcf402231b..b2cfdb9515 100644
--- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
@@ -66,44 +66,35 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
     if (skip_mask(x, y, z))
       continue;
 
-    // Due to lack of guard cells in z-direction, we need to ensure z-index
-    // wraps around
-    const int ncz = localmesh->LocalNz;
-    const int z_mod = ((k_corner(x, y, z) % ncz) + ncz) % ncz;
-    const int z_mod_p1 = (z_mod + 1) % ncz;
+    const auto iyp = i.yp(y_offset);
 
-    const int y_next = y + y_offset;
+    const auto ic = i_corner[i];
+    const auto iczp = ic.zp();
+    const auto icxp = ic.xp();
+    const auto icxpzp = iczp.xp();
 
     // Interpolate f in X at Z
-    const BoutReal f_z = f(i_corner(x, y, z), y_next, z_mod) * h00_x(x, y, z)
-                         + f(i_corner(x, y, z) + 1, y_next, z_mod) * h01_x(x, y, z)
-                         + fx(i_corner(x, y, z), y_next, z_mod) * h10_x(x, y, z)
-                         + fx(i_corner(x, y, z) + 1, y_next, z_mod) * h11_x(x, y, z);
+    const BoutReal f_z =
+        f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
 
     // Interpolate f in X at Z+1
-    const BoutReal f_zp1 = f(i_corner(x, y, z), y_next, z_mod_p1) * h00_x(x, y, z)
-                           + f(i_corner(x, y, z) + 1, y_next, z_mod_p1) * h01_x(x, y, z)
-                           + fx(i_corner(x, y, z), y_next, z_mod_p1) * h10_x(x, y, z)
-                           + fx(i_corner(x, y, z) + 1, y_next, z_mod_p1) * h11_x(x, y, z);
+    const BoutReal f_zp1 = f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] + fx[iczp] * h10_x[i]
+                           + fx[icxpzp] * h11_x[i];
 
     // Interpolate fz in X at Z
-    const BoutReal fz_z = fz(i_corner(x, y, z), y_next, z_mod) * h00_x(x, y, z)
-                          + fz(i_corner(x, y, z) + 1, y_next, z_mod) * h01_x(x, y, z)
-                          + fxz(i_corner(x, y, z), y_next, z_mod) * h10_x(x, y, z)
-                          + fxz(i_corner(x, y, z) + 1, y_next, z_mod) * h11_x(x, y, z);
+    const BoutReal fz_z = fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] + fxz[ic] * h10_x[i]
+                          + fxz[icxp] * h11_x[i];
 
     // Interpolate fz in X at Z+1
-    const BoutReal fz_zp1 =
-        fz(i_corner(x, y, z), y_next, z_mod_p1) * h00_x(x, y, z)
-        + fz(i_corner(x, y, z) + 1, y_next, z_mod_p1) * h01_x(x, y, z)
-        + fxz(i_corner(x, y, z), y_next, z_mod_p1) * h10_x(x, y, z)
-        + fxz(i_corner(x, y, z) + 1, y_next, z_mod_p1) * h11_x(x, y, z);
+    const BoutReal fz_zp1 = fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i]
+                            + fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
 
     // Interpolate in Z
-    BoutReal result = +f_z * h00_z(x, y, z) + f_zp1 * h01_z(x, y, z)
-                      + fz_z * h10_z(x, y, z) + fz_zp1 * h11_z(x, y, z);
+    BoutReal result =
+        +f_z * h00_z[i] + f_zp1 * h01_z[i] + fz_z * h10_z[i] + fz_zp1 * h11_z[i];
 
-    ASSERT2(std::isfinite(result) || x < localmesh->xstart || x > localmesh->xend);
+    ASSERT2(std::isfinite(result) || i.x() < localmesh->xstart
+            || i.x() > localmesh->xend);
 
     // Monotonicity
     // Force the interpolated result to be in the range of the
@@ -111,18 +102,14 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
     // but also degrades accuracy near maxima and minima.
     // Perhaps should only impose near boundaries, since that is where
     // problems most obviously occur.
-    const BoutReal localmax = BOUTMAX(f(i_corner(x, y, z), y_next, z_mod),
-                                      f(i_corner(x, y, z) + 1, y_next, z_mod),
-                                      f(i_corner(x, y, z), y_next, z_mod_p1),
-                                      f(i_corner(x, y, z) + 1, y_next, z_mod_p1));
+    const BoutReal localmax = BOUTMAX(f[ic], f[icxp], f[iczp], f[icxpzp]);
 
-    const BoutReal localmin = BOUTMIN(f(i_corner(x, y, z), y_next, z_mod),
-                                      f(i_corner(x, y, z) + 1, y_next, z_mod),
-                                      f(i_corner(x, y, z), y_next, z_mod_p1),
-                                      f(i_corner(x, y, z) + 1, y_next, z_mod_p1));
+    const BoutReal localmin = BOUTMIN(f[ic], f[icxp], f[iczp], f[icxpzp]);
 
-    ASSERT2(std::isfinite(localmax) || x < localmesh->xstart || x > localmesh->xend);
-    ASSERT2(std::isfinite(localmin) || x < localmesh->xstart || x > localmesh->xend);
+    ASSERT2(std::isfinite(localmax) || i.x() < localmesh->xstart
+            || i.x() > localmesh->xend);
+    ASSERT2(std::isfinite(localmin) || i.x() < localmesh->xstart
+            || i.x() > localmesh->xend);
 
     if (result > localmax) {
       result = localmax;
@@ -131,7 +118,7 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
       result = localmin;
     }
 
-    f_interp(x, y_next, z) = result;
+    f_interp[iyp] = result;
   }
   return f_interp;
 }

From 4ec74efcead5f2aabdac00ea950f166d17c92176 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20Schw=C3=B6rer?= <dave@ipp.mpg.de>
Date: Wed, 22 Sep 2021 11:28:45 +0200
Subject: [PATCH 0002/1827] Switch toward regions

---
 include/interpolation_xz.hxx                  | 53 +++++++++++++++----
 include/mask.hxx                              | 10 ++++
 src/mesh/interpolation/bilinear_xz.cxx        | 12 ++---
 src/mesh/interpolation/hermite_spline_xz.cxx  | 18 ++-----
 src/mesh/interpolation/lagrange_4pt_xz.cxx    | 15 ++----
 .../monotonic_hermite_spline_xz.cxx           |  7 +--
 6 files changed, 65 insertions(+), 50 deletions(-)

diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx
index 04269a830d..7a58ce3346 100644
--- a/include/interpolation_xz.hxx
+++ b/include/interpolation_xz.hxx
@@ -37,24 +37,56 @@ const Field3D interpolate(const Field2D &f, const Field3D &delta_x,
 const Field3D interpolate(const Field2D &f, const Field3D &delta_x);
 
 class XZInterpolation {
+public:
+  int y_offset;
+
 protected:
   Mesh* localmesh{nullptr};
 
-  // 3D vector of points to skip (true -> skip this point)
-  BoutMask skip_mask;
+  std::string region_name{""};
+  std::shared_ptr<Region<Ind3D>> region{nullptr};
 
 public:
   XZInterpolation(int y_offset = 0, Mesh* localmeshIn = nullptr)
-      : localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn),
-        skip_mask(*localmesh, false), y_offset(y_offset) {}
+      : y_offset(y_offset),
+        localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn),
+        region_name("RGN_ALL") {}
   XZInterpolation(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr)
       : XZInterpolation(y_offset, mesh) {
-    skip_mask = mask;
+    region = regionFromMask(mask, localmesh);
   }
+  XZInterpolation(const std::string& region_name, int y_offset = 0, Mesh* mesh = nullptr)
+      : y_offset(y_offset), localmesh(mesh), region_name(region_name) {}
+  XZInterpolation(std::shared_ptr<Region<Ind3D>> region, int y_offset = 0,
+                  Mesh* mesh = nullptr)
+      : y_offset(y_offset), localmesh(mesh), region(region) {}
   virtual ~XZInterpolation() = default;
 
-
-  void setMask(const BoutMask &mask) { skip_mask = mask; }
+  void setMask(const BoutMask& mask) {
+    region = regionFromMask(mask, localmesh);
+    region_name = "";
+  }
+  void setRegion(const std::string& region_name) {
+    this->region_name = region_name;
+    this->region = nullptr;
+  }
+  void setRegion(const std::shared_ptr<Region<Ind3D>>& region) {
+    this->region_name = "";
+    this->region = region;
+  }
+  Region<Ind3D> getRegion() const {
+    if (region_name != "") {
+      return localmesh->getRegion(region_name);
+    }
+    ASSERT1(region != nullptr);
+    return *region;
+  }
+  Region<Ind3D> getRegion(const std::string& region) const {
+    if (region != "" and region != "RGN_ALL") {
+      return getIntersection(localmesh->getRegion(region), getRegion());
+    }
+    return getRegion();
+  }
   virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                            const std::string& region = "RGN_NOBNDRY") = 0;
   virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
@@ -71,7 +103,6 @@ public:
                               const std::string& region = "RGN_NOBNDRY") = 0;
 
   // Interpolate using the field at (x,y+y_offset,z), rather than (x,y,z)
-  int y_offset;
   void setYOffset(int offset) { y_offset = offset; }
 
   virtual std::vector<ParallelTransform::PositionsAndWeights>
@@ -119,7 +150,7 @@ public:
   XZHermiteSpline(int y_offset = 0, Mesh *mesh = nullptr);
   XZHermiteSpline(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr)
       : XZHermiteSpline(y_offset, mesh) {
-    skip_mask = mask;
+    region = regionFromMask(mask, localmesh);
   }
 
   void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
@@ -177,7 +208,7 @@ public:
   XZLagrange4pt(int y_offset = 0, Mesh *mesh = nullptr);
   XZLagrange4pt(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr)
       : XZLagrange4pt(y_offset, mesh) {
-    skip_mask = mask;
+    region = regionFromMask(mask, localmesh);
   }
 
   void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
@@ -210,7 +241,7 @@ public:
   XZBilinear(int y_offset = 0, Mesh *mesh = nullptr);
   XZBilinear(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr)
       : XZBilinear(y_offset, mesh) {
-    skip_mask = mask;
+    region = regionFromMask(mask, localmesh);
   }
 
   void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
diff --git a/include/mask.hxx b/include/mask.hxx
index 8940edbb16..c26bf31d61 100644
--- a/include/mask.hxx
+++ b/include/mask.hxx
@@ -72,4 +72,14 @@ public:
   }
 };
 
+inline std::unique_ptr<Region<Ind3D>> regionFromMask(const BoutMask& mask,
+                                                     const Mesh* mesh) {
+  std::vector<Ind3D> indices;
+  for (auto i : mesh->getRegion("RGN_ALL")) {
+    if (not mask(i.x(), i.y(), i.z())) {
+      indices.push_back(i);
+    }
+  }
+  return std::make_unique<Region<Ind3D>>(indices);
+}
 #endif //__MASK_H__
diff --git a/src/mesh/interpolation/bilinear_xz.cxx b/src/mesh/interpolation/bilinear_xz.cxx
index 7819fafe6f..1869df3218 100644
--- a/src/mesh/interpolation/bilinear_xz.cxx
+++ b/src/mesh/interpolation/bilinear_xz.cxx
@@ -45,14 +45,11 @@ XZBilinear::XZBilinear(int y_offset, Mesh *mesh)
 void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                              const std::string& region) {
 
-  BOUT_FOR(i, delta_x.getRegion(region)) {
+  BOUT_FOR(i, getRegion(region)) {
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();
 
-    if (skip_mask(x, y, z))
-      continue;
-
     // The integer part of xt_prime, zt_prime are the indices of the cell
     // containing the field line end-point
     i_corner(x, y, z) = static_cast<int>(floor(delta_x(x, y, z)));
@@ -87,7 +84,7 @@ void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
 
 void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                              const BoutMask& mask, const std::string& region) {
-  skip_mask = mask;
+  setMask(mask);
   calcWeights(delta_x, delta_z, region);
 }
 
@@ -95,14 +92,11 @@ Field3D XZBilinear::interpolate(const Field3D& f, const std::string& region) con
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
 
-  BOUT_FOR(i, f.getRegion(region)) {
+  BOUT_FOR(i, this->getRegion(region)) {
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();
 
-    if (skip_mask(x, y, z))
-      continue;
-
     const int y_next = y + y_offset;
     // Due to lack of guard cells in z-direction, we need to ensure z-index
     // wraps around
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 9f14d4b836..a682c58839 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -56,14 +56,11 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
 
   const int ny = localmesh->LocalNy;
   const int nz = localmesh->LocalNz;
-  BOUT_FOR(i, delta_x.getRegion(region)) {
+  BOUT_FOR(i, getRegion(region)) {
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();
 
-    if (skip_mask(x, y, z))
-      continue;
-
     // The integer part of xt_prime, zt_prime are the indices of the cell
     // containing the field line end-point
     int i_corn = static_cast<int>(floor(delta_x(x, y, z)));
@@ -116,7 +113,7 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
 
 void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                                   const BoutMask& mask, const std::string& region) {
-  skip_mask = mask;
+  setMask(mask);
   calcWeights(delta_x, delta_z, region);
 }
 
@@ -179,16 +176,7 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
     localmesh->wait(h);
   }
 
-  BOUT_FOR(i, f.getRegion(region)) {
-    const int x = i.x();
-    const int y = i.y();
-    const int z = i.z();
-
-    if (skip_mask(x, y, z))
-      continue;
-
-    const auto iyp = i.yp(y_offset);
-
+  BOUT_FOR(i, getRegion(region)) {
     const auto ic = i_corner[i];
     const auto iczp = ic.zp();
     const auto icxp = ic.xp();
diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx
index 3a5de28e59..7c79a3f713 100644
--- a/src/mesh/interpolation/lagrange_4pt_xz.cxx
+++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx
@@ -39,15 +39,12 @@ XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh *mesh)
 
 void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                                 const std::string& region) {
-
-  BOUT_FOR(i, delta_x.getRegion(region)) {
+  const auto curregion = getRegion(region);
+  BOUT_FOR(i, curregion) {
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();
 
-    if (skip_mask(x, y, z))
-      continue;
-
     // The integer part of xt_prime, zt_prime are the indices of the cell
     // containing the field line end-point
     i_corner(x, y, z) = static_cast<int>(floor(delta_x(x, y, z)));
@@ -80,7 +77,7 @@ void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
 
 void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                                 const BoutMask& mask, const std::string& region) {
-  skip_mask = mask;
+  setMask(mask);
   calcWeights(delta_x, delta_z, region);
 }
 
@@ -89,14 +86,12 @@ Field3D XZLagrange4pt::interpolate(const Field3D& f, const std::string& region)
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
 
-  BOUT_FOR(i, f.getRegion(region)) {
+  const auto curregion{getRegion(region)};
+  BOUT_FOR(i, curregion) {
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();
 
-    if (skip_mask(x, y, z))
-      continue;
-
     const int jx = i_corner(x, y, z);
     const int jx2mnew = (jx == 0) ? 0 : (jx - 1);
     const int jxpnew = jx + 1;
diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
index b2cfdb9515..47eeb2df20 100644
--- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
@@ -22,7 +22,7 @@
 
 #include "globals.hxx"
 #include "interpolation_xz.hxx"
-#include "output.hxx"
+//#include "output.hxx"
 #include "bout/index_derivs_interface.hxx"
 #include "bout/mesh.hxx"
 
@@ -58,14 +58,11 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
     localmesh->wait(h);
   }
 
-  BOUT_FOR(i, f.getRegion(region)) {
+  BOUT_FOR(i, getRegion(region)) {
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();
 
-    if (skip_mask(x, y, z))
-      continue;
-
     const auto iyp = i.yp(y_offset);
 
     const auto ic = i_corner[i];

From d0960204c870dc52cfe5315de22a8e5a4607b4eb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20Schw=C3=B6rer?= <dave@ipp.mpg.de>
Date: Fri, 24 Sep 2021 11:19:50 +0200
Subject: [PATCH 0003/1827] Switch to regions for FCI regions

---
 include/bout/region.hxx                       | 23 +++++
 include/interpolation_xz.hxx                  | 14 ++-
 include/mask.hxx                              |  1 +
 include/utils.hxx                             |  9 ++
 src/mesh/interpolation/bilinear_xz.cxx        |  6 +-
 src/mesh/interpolation/lagrange_4pt_xz.cxx    |  2 +-
 .../monotonic_hermite_spline_xz.cxx           |  3 +-
 src/mesh/parallel/fci.cxx                     | 89 +++++++++----------
 src/mesh/parallel/fci.hxx                     |  7 +-
 9 files changed, 98 insertions(+), 56 deletions(-)

diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index f84c058814..4d0cb51159 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -51,6 +51,7 @@
 #include "bout_types.hxx"
 #include "bout/assert.hxx"
 #include "bout/openmpwrap.hxx"
+class BoutMask;
 
 /// The MAXREGIONBLOCKSIZE value can be tuned to try to optimise
 /// performance on specific hardware. It determines what the largest
@@ -644,6 +645,28 @@ public:
     return *this; // To allow command chaining
   };
 
+  /// Return a new region equivalent to *this but with indices contained
+  /// in mask Region removed
+  Region<T> mask(const BoutMask& mask) {
+    // Get the current set of indices that we're going to mask and then
+    // use to create the result region.
+    auto currentIndices = getIndices();
+
+    // Lambda that returns true/false depending if the passed value is in maskIndices
+    // With C++14 T can be auto instead
+    auto isInVector = [&](T val) { return mask[val]; };
+
+    // Erase elements of currentIndices that are in maskIndices
+    currentIndices.erase(
+        std::remove_if(std::begin(currentIndices), std::end(currentIndices), isInVector),
+        std::end(currentIndices));
+
+    // Update indices
+    setIndices(currentIndices);
+
+    return *this; // To allow command chaining
+  };
+
   /// Returns a new region including only indices contained in both
   /// this region and the other.
   Region<T> getIntersection(const Region<T>& otherRegion) {
diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx
index 7a58ce3346..915b5a8478 100644
--- a/include/interpolation_xz.hxx
+++ b/include/interpolation_xz.hxx
@@ -49,8 +49,7 @@ protected:
 public:
   XZInterpolation(int y_offset = 0, Mesh* localmeshIn = nullptr)
       : y_offset(y_offset),
-        localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn),
-        region_name("RGN_ALL") {}
+        localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn) {}
   XZInterpolation(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr)
       : XZInterpolation(y_offset, mesh) {
     region = regionFromMask(mask, localmesh);
@@ -74,6 +73,10 @@ public:
     this->region_name = "";
     this->region = region;
   }
+  void setRegion(const Region<Ind3D>& region) {
+    this->region_name = "";
+    this->region = std::make_shared<Region<Ind3D>>(region);
+  }
   Region<Ind3D> getRegion() const {
     if (region_name != "") {
       return localmesh->getRegion(region_name);
@@ -82,9 +85,14 @@ public:
     return *region;
   }
   Region<Ind3D> getRegion(const std::string& region) const {
+    const bool has_region = region_name != "" or this->region != nullptr;
     if (region != "" and region != "RGN_ALL") {
-      return getIntersection(localmesh->getRegion(region), getRegion());
+      if (has_region) {
+        return getIntersection(localmesh->getRegion(region), getRegion());
+      }
+      return localmesh->getRegion(region);
     }
+    ASSERT1(has_region);
     return getRegion();
   }
   virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
diff --git a/include/mask.hxx b/include/mask.hxx
index c26bf31d61..6113e94d63 100644
--- a/include/mask.hxx
+++ b/include/mask.hxx
@@ -70,6 +70,7 @@ public:
   inline const bool& operator()(int jx, int jy, int jz) const {
     return mask(jx, jy, jz);
   }
+  inline const bool& operator[](const Ind3D& i) const { return mask[i]; }
 };
 
 inline std::unique_ptr<Region<Ind3D>> regionFromMask(const BoutMask& mask,
diff --git a/include/utils.hxx b/include/utils.hxx
index 9de4628358..ea293f7bf8 100644
--- a/include/utils.hxx
+++ b/include/utils.hxx
@@ -38,6 +38,7 @@
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/build_config.hxx"
+#include "bout/region.hxx"
 
 #include <algorithm>
 #include <cmath>
@@ -348,6 +349,14 @@ public:
     return data[(i1*n2+i2)*n3 + i3];
   }
 
+  const T& operator[](Ind3D i) const {
+    // ny and nz are private :-(
+    // ASSERT2(i.nz == n3);
+    // ASSERT2(i.ny == n2);
+    ASSERT2(0 <= i.ind && i.ind < n1 * n2 * n3);
+    return data[i.ind];
+  }
+
   Tensor& operator=(const T&val){
     for(auto &i: data){
       i = val;
diff --git a/src/mesh/interpolation/bilinear_xz.cxx b/src/mesh/interpolation/bilinear_xz.cxx
index 1869df3218..e36527e765 100644
--- a/src/mesh/interpolation/bilinear_xz.cxx
+++ b/src/mesh/interpolation/bilinear_xz.cxx
@@ -45,7 +45,8 @@ XZBilinear::XZBilinear(int y_offset, Mesh *mesh)
 void XZBilinear::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                              const std::string& region) {
 
-  BOUT_FOR(i, getRegion(region)) {
+  const auto curregion{getRegion(region)};
+  BOUT_FOR(i, curregion) {
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();
@@ -92,7 +93,8 @@ Field3D XZBilinear::interpolate(const Field3D& f, const std::string& region) con
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
 
-  BOUT_FOR(i, this->getRegion(region)) {
+  const auto curregion{getRegion(region)};
+  BOUT_FOR(i, curregion) {
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();
diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx
index 7c79a3f713..caf4ce45eb 100644
--- a/src/mesh/interpolation/lagrange_4pt_xz.cxx
+++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx
@@ -39,7 +39,7 @@ XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh *mesh)
 
 void XZLagrange4pt::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                                 const std::string& region) {
-  const auto curregion = getRegion(region);
+  const auto curregion{getRegion(region)};
   BOUT_FOR(i, curregion) {
     const int x = i.x();
     const int y = i.y();
diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
index 47eeb2df20..fbffc0b1fd 100644
--- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
@@ -58,7 +58,8 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
     localmesh->wait(h);
   }
 
-  BOUT_FOR(i, getRegion(region)) {
+  const auto curregion{getRegion(region)};
+  BOUT_FOR(i, curregion) {
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index c25765852e..77f34fd282 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -50,7 +50,8 @@
 FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
                int offset_, BoundaryRegionPar* inner_boundary,
                BoundaryRegionPar* outer_boundary, bool zperiodic)
-    : map_mesh(mesh), offset(offset_), boundary_mask(map_mesh),
+    : map_mesh(mesh), offset(offset_),
+      region_no_boundary(map_mesh.getRegion("RGN_NOBNDRY")),
       corner_boundary_mask(map_mesh) {
 
   TRACE("Creating FCIMAP for direction {:d}", offset);
@@ -156,6 +157,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
 
   const int ncz = map_mesh.LocalNz;
 
+  BoutMask to_remove(map_mesh);
   // Serial loop because call to BoundaryRegionPar::addPoint
   // (probably?) can't be done in parallel
   BOUT_FOR_SERIAL(i, xt_prime.getRegion("RGN_NOBNDRY")) {
@@ -185,7 +187,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
     // indices (forward/backward_xt_prime and forward/backward_zt_prime)
     // are set to -1
 
-    boundary_mask(x, y, z) = true;
+    to_remove(x, y, z) = true;
 
     // Need to specify the index of the boundary intersection, but
     // this may not be defined in general.
@@ -200,13 +202,11 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
     // and the gradients dR/dx etc. are evaluated at (x,y,z)
 
     // Cache the offsets
-    const auto i_xp = i.xp();
-    const auto i_xm = i.xm();
     const auto i_zp = i.zp();
     const auto i_zm = i.zm();
 
-    const BoutReal dR_dx = 0.5 * (R[i_xp] - R[i_xm]);
-    const BoutReal dZ_dx = 0.5 * (Z[i_xp] - Z[i_xm]);
+    const BoutReal dR_dx = 0.5 * (R[i.xp()] - R[i.xm()]);
+    const BoutReal dZ_dx = 0.5 * (Z[i.xp()] - Z[i.xm()]);
 
     BoutReal dR_dz, dZ_dz;
     // Handle the edge cases in Z
@@ -241,8 +241,17 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
                         PI           // Right-angle intersection
     );
   }
-
-  interp->setMask(boundary_mask);
+  region_no_boundary = region_no_boundary.mask(to_remove);
+
+  const auto region = fmt::format("RGN_YPAR_{:+d}", offset);
+  if (not map_mesh.hasRegion3D(region)) {
+    // The valid region for this slice
+    map_mesh.addRegion3D(region,
+			 Region<Ind3D>(map_mesh.xstart, map_mesh.xend,
+				       map_mesh.ystart+offset, map_mesh.yend+offset,
+				       0, map_mesh.LocalNz-1,
+				       map_mesh.LocalNy, map_mesh.LocalNz));
+  }
 }
 
 Field3D FCIMap::integrate(Field3D &f) const {
@@ -265,45 +274,33 @@ Field3D FCIMap::integrate(Field3D &f) const {
 
   int nz = map_mesh.LocalNz;
 
-  for(int x = map_mesh.xstart; x <= map_mesh.xend; x++) {
-    for(int y = map_mesh.ystart; y <= map_mesh.yend; y++) {
-
-      int ynext = y+offset;
-
-      for(int z = 0; z < nz; z++) {
-        if (boundary_mask(x,y,z))
-          continue;
-
-        int zm = z - 1;
-        if (z == 0) {
-          zm = nz-1;
-        }
-
-        BoutReal f_c  = centre(x,ynext,z);
-
-        if (corner_boundary_mask(x, y, z) || corner_boundary_mask(x - 1, y, z) ||
-            corner_boundary_mask(x, y, zm) || corner_boundary_mask(x - 1, y, zm) ||
-            (x == map_mesh.xstart)) {
-          // One of the corners leaves the domain.
-          // Use the cell centre value, since boundary conditions are not
-          // currently applied to corners.
-          result(x, ynext, z) = f_c;
-
-        } else {
-          BoutReal f_pp = corner(x, ynext, z);      // (x+1/2, z+1/2)
-          BoutReal f_mp = corner(x - 1, ynext, z);  // (x-1/2, z+1/2)
-          BoutReal f_pm = corner(x, ynext, zm);     // (x+1/2, z-1/2)
-          BoutReal f_mm = corner(x - 1, ynext, zm); // (x-1/2, z-1/2)
-
-          // This uses a simple weighted average of centre and corners
-          // A more sophisticated approach might be to use e.g. Gauss-Lobatto points
-          // which would include cell edges and corners
-          result(x, ynext, z) = 0.5 * (f_c + 0.25 * (f_pp + f_mp + f_pm + f_mm));
-
-          ASSERT2(std::isfinite(result(x,ynext,z)));
-        }
-      }
+  BOUT_FOR(i, region_no_boundary) {
+    const auto inext = i.yp(offset);
+    BoutReal f_c = centre[inext];
+    const auto izm = i.zm();
+    const int x = i.x();
+    const int y = i.y();
+    const int z = i.z();
+    const int zm = izm.z();
+    if (corner_boundary_mask(x, y, z) || corner_boundary_mask(x - 1, y, z)
+        || corner_boundary_mask(x, y, zm) || corner_boundary_mask(x - 1, y, zm)
+        || (x == map_mesh.xstart)) {
+      // One of the corners leaves the domain.
+      // Use the cell centre value, since boundary conditions are not
+      // currently applied to corners.
+      result[inext] = f_c;
+    } else {
+      BoutReal f_pp = corner[inext];           // (x+1/2, z+1/2)
+      BoutReal f_mp = corner[inext.xm()];      // (x-1/2, z+1/2)
+      BoutReal f_pm = corner[inext.zm()];      // (x+1/2, z-1/2)
+      BoutReal f_mm = corner[inext.xm().zm()]; // (x-1/2, z-1/2)
+
+      // This uses a simple weighted average of centre and corners
+      // A more sophisticated approach might be to use e.g. Gauss-Lobatto points
+      // which would include cell edges and corners
+      result[inext] = 0.5 * (f_c + 0.25 * (f_pp + f_mp + f_pm + f_mm));
     }
+    ASSERT2(finite(result[inext]));
   }
   return result;
 }
diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx
index 3ecd964bfa..ef7c98693e 100644
--- a/src/mesh/parallel/fci.hxx
+++ b/src/mesh/parallel/fci.hxx
@@ -54,11 +54,12 @@ public:
   /// Direction of map
   const int offset;
 
-  /// boundary mask - has the field line left the domain
-  BoutMask boundary_mask;
+  /// region containing all points where the field line has not left the
+  /// domain
+  Region<Ind3D> region_no_boundary;
   /// If any of the integration area has left the domain
   BoutMask corner_boundary_mask;
-  
+
   Field3D interpolate(Field3D& f) const {
     ASSERT1(&map_mesh == f.getMesh());
     return interp->interpolate(f);

From d2a81bf142eea4e05fe5bb9c925290586a05fde6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20Schw=C3=B6rer?= <dave@ipp.mpg.de>
Date: Fri, 19 Nov 2021 13:38:21 +0100
Subject: [PATCH 0004/1827] Use region_id in interpolation

Otherwise the regions aren't cached.
---
 include/interpolation_xz.hxx | 61 +++++++++++++++++-------------------
 include/mask.hxx             |  4 +--
 2 files changed, 30 insertions(+), 35 deletions(-)

diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx
index 915b5a8478..df58d5b70e 100644
--- a/include/interpolation_xz.hxx
+++ b/include/interpolation_xz.hxx
@@ -43,8 +43,7 @@ public:
 protected:
   Mesh* localmesh{nullptr};
 
-  std::string region_name{""};
-  std::shared_ptr<Region<Ind3D>> region{nullptr};
+  int region_id{-1};
 
 public:
   XZInterpolation(int y_offset = 0, Mesh* localmeshIn = nullptr)
@@ -52,48 +51,44 @@ public:
         localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn) {}
   XZInterpolation(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr)
       : XZInterpolation(y_offset, mesh) {
-    region = regionFromMask(mask, localmesh);
+    setMask(mask);
   }
   XZInterpolation(const std::string& region_name, int y_offset = 0, Mesh* mesh = nullptr)
-      : y_offset(y_offset), localmesh(mesh), region_name(region_name) {}
-  XZInterpolation(std::shared_ptr<Region<Ind3D>> region, int y_offset = 0,
+    : y_offset(y_offset), localmesh(mesh), region_id(localmesh->getRegionID(region_name)) {}
+  XZInterpolation(const Region<Ind3D>& region, int y_offset = 0,
                   Mesh* mesh = nullptr)
-      : y_offset(y_offset), localmesh(mesh), region(region) {}
+      : y_offset(y_offset), localmesh(mesh){
+    setRegion(region);
+  }
   virtual ~XZInterpolation() = default;
 
   void setMask(const BoutMask& mask) {
-    region = regionFromMask(mask, localmesh);
-    region_name = "";
+    setRegion(regionFromMask(mask, localmesh));
   }
   void setRegion(const std::string& region_name) {
-    this->region_name = region_name;
-    this->region = nullptr;
-  }
-  void setRegion(const std::shared_ptr<Region<Ind3D>>& region) {
-    this->region_name = "";
-    this->region = region;
+    this->region_id = localmesh->getRegionID(region_name);
   }
   void setRegion(const Region<Ind3D>& region) {
-    this->region_name = "";
-    this->region = std::make_shared<Region<Ind3D>>(region);
+    std::string name;
+    int i=0;
+    do {
+      name = fmt::format("unsec_reg_xz_interp_{:d}",i++);
+    } while (localmesh->hasRegion3D(name));
+    localmesh->addRegion(name, region);
+    this->region_id = localmesh->getRegionID(name);
   }
-  Region<Ind3D> getRegion() const {
-    if (region_name != "") {
-      return localmesh->getRegion(region_name);
-    }
-    ASSERT1(region != nullptr);
-    return *region;
+  const Region<Ind3D>& getRegion() const {
+    ASSERT2(region_id != -1);
+    return localmesh->getRegion(region_id);
   }
-  Region<Ind3D> getRegion(const std::string& region) const {
-    const bool has_region = region_name != "" or this->region != nullptr;
-    if (region != "" and region != "RGN_ALL") {
-      if (has_region) {
-        return getIntersection(localmesh->getRegion(region), getRegion());
-      }
+  const Region<Ind3D>& getRegion(const std::string& region) const {
+    if (region_id == -1) {
       return localmesh->getRegion(region);
     }
-    ASSERT1(has_region);
-    return getRegion();
+    if (region == "" or region == "RGN_ALL"){
+      return getRegion();
+    }
+    return localmesh->getRegion(localmesh->getCommonRegion(localmesh->getRegionID(region), region_id));
   }
   virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                            const std::string& region = "RGN_NOBNDRY") = 0;
@@ -158,7 +153,7 @@ public:
   XZHermiteSpline(int y_offset = 0, Mesh *mesh = nullptr);
   XZHermiteSpline(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr)
       : XZHermiteSpline(y_offset, mesh) {
-    region = regionFromMask(mask, localmesh);
+    setRegion(regionFromMask(mask, localmesh));
   }
 
   void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
@@ -216,7 +211,7 @@ public:
   XZLagrange4pt(int y_offset = 0, Mesh *mesh = nullptr);
   XZLagrange4pt(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr)
       : XZLagrange4pt(y_offset, mesh) {
-    region = regionFromMask(mask, localmesh);
+    setRegion(regionFromMask(mask, localmesh));
   }
 
   void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
@@ -249,7 +244,7 @@ public:
   XZBilinear(int y_offset = 0, Mesh *mesh = nullptr);
   XZBilinear(const BoutMask &mask, int y_offset = 0, Mesh *mesh = nullptr)
       : XZBilinear(y_offset, mesh) {
-    region = regionFromMask(mask, localmesh);
+    setRegion(regionFromMask(mask, localmesh));
   }
 
   void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
diff --git a/include/mask.hxx b/include/mask.hxx
index 6113e94d63..96d2c99ac3 100644
--- a/include/mask.hxx
+++ b/include/mask.hxx
@@ -73,7 +73,7 @@ public:
   inline const bool& operator[](const Ind3D& i) const { return mask[i]; }
 };
 
-inline std::unique_ptr<Region<Ind3D>> regionFromMask(const BoutMask& mask,
+inline Region<Ind3D> regionFromMask(const BoutMask& mask,
                                                      const Mesh* mesh) {
   std::vector<Ind3D> indices;
   for (auto i : mesh->getRegion("RGN_ALL")) {
@@ -81,6 +81,6 @@ inline std::unique_ptr<Region<Ind3D>> regionFromMask(const BoutMask& mask,
       indices.push_back(i);
     }
   }
-  return std::make_unique<Region<Ind3D>>(indices);
+  return Region<Ind3D>{indices};
 }
 #endif //__MASK_H__

From ea5640f1b661ab2978deff9084d56f3184b513ad Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Dec 2021 12:26:52 +0100
Subject: [PATCH 0005/1827] Switch hermite_spline_xz to index

Might help with performance
---
 src/mesh/interpolation/hermite_spline_xz.cxx           | 2 ++
 src/mesh/interpolation/monotonic_hermite_spline_xz.cxx | 4 ----
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index a682c58839..1319f7532d 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -177,6 +177,8 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   }
 
   BOUT_FOR(i, getRegion(region)) {
+    const auto iyp = i.yp(y_offset);
+
     const auto ic = i_corner[i];
     const auto iczp = ic.zp();
     const auto icxp = ic.xp();
diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
index fbffc0b1fd..e0cdf91ac8 100644
--- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
@@ -60,10 +60,6 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
 
   const auto curregion{getRegion(region)};
   BOUT_FOR(i, curregion) {
-    const int x = i.x();
-    const int y = i.y();
-    const int z = i.z();
-
     const auto iyp = i.yp(y_offset);
 
     const auto ic = i_corner[i];

From 089ddfa8413948f1fa8b1c759c64b05ce77e2468 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 16 Nov 2022 10:33:57 +0100
Subject: [PATCH 0006/1827] Improve hermitesplinesXZ

Precalculate the matrix. This hard-codes the DDX and DDZ derivative to
C2.

Rather than taking derivatives, this first does the matrix-matrix
multiplication and then does only a single matrix-vector operation,
rather than 4.

Retains a switch to go back to the old version.
---
 include/interpolation_xz.hxx                 |   2 +
 src/mesh/interpolation/hermite_spline_xz.cxx | 161 ++++++++++++++++---
 2 files changed, 142 insertions(+), 21 deletions(-)

diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx
index df58d5b70e..e6eb8c3078 100644
--- a/include/interpolation_xz.hxx
+++ b/include/interpolation_xz.hxx
@@ -147,6 +147,8 @@ protected:
   Field3D h10_z;
   Field3D h11_z;
 
+  std::vector<Field3D> newWeights;
+
 public:
   XZHermiteSpline(Mesh *mesh = nullptr)
       : XZHermiteSpline(0, mesh) {}
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 1319f7532d..08515c7056 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -49,6 +49,13 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
   h01_z.allocate();
   h10_z.allocate();
   h11_z.allocate();
+
+
+  newWeights.reserve(16);
+  for (int w=0; w<16;++w){
+    newWeights.emplace_back(localmesh);
+    newWeights[w].allocate();
+  }
 }
 
 void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
@@ -108,6 +115,115 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
 
     h11_x[i] = (t_x * t_x * t_x) - (t_x * t_x);
     h11_z[i] = (t_z * t_z * t_z) - (t_z * t_z);
+
+#define USE_NEW_WEIGHTS 1
+#if USE_NEW_WEIGHTS
+
+    for (int w =0; w<16;++w){
+      newWeights[w][i]=0;
+    }
+    // The distribution of our weights:
+    //  0   4   8    12
+    //  1   5   9    13
+    //  2   6   10   14
+    //  3   7   11   15
+    // e.g. 1 == ic.xm(); 4 == ic.zm(); 5 == ic;  7 == ic.zp(2);
+
+    // f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
+    newWeights[5][i]  += h00_x[i] * h00_z[i];
+    newWeights[9][i]  += h01_x[i] * h00_z[i];
+    newWeights[9][i]  += h10_x[i] * h00_z[i] / 2;
+    newWeights[1][i]  -= h10_x[i] * h00_z[i] / 2;
+    newWeights[13][i] += h11_x[i] * h00_z[i] / 2;
+    newWeights[5][i]  -= h11_x[i] * h00_z[i] / 2;
+
+    // f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] +
+    // fx[iczp] * h10_x[i] + fx[icxpzp] * h11_x[i];
+    newWeights[6][i]  += h00_x[i] * h01_z[i];
+    newWeights[10][i] += h01_x[i] * h01_z[i];
+    newWeights[10][i] += h10_x[i] * h01_z[i] / 2;
+    newWeights[2][i]  -= h10_x[i] * h01_z[i] / 2;
+    newWeights[14][i] += h11_x[i] * h01_z[i] / 2;
+    newWeights[6][i]  -= h11_x[i] * h01_z[i] / 2;
+
+    // fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] +
+    // fxz[ic] * h10_x[i]+ fxz[icxp] * h11_x[i];
+    newWeights[6][i]  += h00_x[i] * h10_z[i] / 2;
+    newWeights[4][i]  -= h00_x[i] * h10_z[i] / 2;
+    newWeights[10][i] += h01_x[i] * h10_z[i] / 2;
+    newWeights[8][i]  -= h01_x[i] * h10_z[i] / 2;
+    newWeights[10][i] += h10_x[i] * h10_z[i] / 4;
+    newWeights[8][i]  -= h10_x[i] * h10_z[i] / 4;
+    newWeights[2][i]  -= h10_x[i] * h10_z[i] / 4;
+    newWeights[0][i]  += h10_x[i] * h10_z[i] / 4;
+    newWeights[14][i] += h11_x[i] * h10_z[i] / 4;
+    newWeights[12][i] -= h11_x[i] * h10_z[i] / 4;
+    newWeights[6][i] -= h11_x[i] * h10_z[i] / 4;
+    newWeights[4][i]  += h11_x[i] * h10_z[i] / 4;
+
+    // fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i] +
+    // fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
+    newWeights[7][i]  += h00_x[i] * h11_z[i] / 2;
+    newWeights[5][i]  -= h00_x[i] * h11_z[i] / 2;
+    newWeights[11][i] += h01_x[i] * h11_z[i] / 2;
+    newWeights[9][i]  -= h01_x[i] * h11_z[i] / 2;
+    newWeights[11][i] += h10_x[i] * h11_z[i] / 4;
+    newWeights[9][i]  -= h10_x[i] * h11_z[i] / 4;
+    newWeights[3][i]  -= h10_x[i] * h11_z[i] / 4;
+    newWeights[1][i]  += h10_x[i] * h11_z[i] / 4;
+    newWeights[15][i] += h11_x[i] * h11_z[i] / 4;
+    newWeights[13][i] -= h11_x[i] * h11_z[i] / 4;
+    newWeights[7][i]  -= h11_x[i] * h11_z[i] / 4;
+    newWeights[5][i]  += h11_x[i] * h11_z[i] / 4;
+
+
+    //   // f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
+    // newWeights[5][i]  += h00_x[i] * h00_z[i];
+    // newWeights[9][i]  += h01_x[i] * h00_z[i];
+    // newWeights[9][i]  += h10_x[i] * h00_z[i] / 2 / localmesh->dx[ic];
+    // newWeights[1][i]  -= h10_x[i] * h00_z[i] / 2 / localmesh->dx[ic];
+    // newWeights[13][i] += h11_x[i] * h00_z[i] / 2 / localmesh->dx[ic.xp()];
+    // newWeights[5][i]  -= h11_x[i] * h00_z[i] / 2 / localmesh->dx[ic.xp()];
+
+    // // f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] +
+    // // fx[iczp] * h10_x[i] + fx[icxpzp] * h11_x[i];
+    // newWeights[6][i]  += h00_x[i] * h01_z[i];
+    // newWeights[10][i]  += h01_x[i] * h01_z[i];
+    // newWeights[10][i]  += h10_x[i] * h01_z[i] / 2/ localmesh->dx[ic.zp()];
+    // newWeights[2][i]  -= h10_x[i] * h01_z[i] / 2/ localmesh->dx[ic.zp()];
+    // newWeights[14][i] += h11_x[i] * h01_z[i] / 2/ localmesh->dx[ic.zp().xp()];
+    // newWeights[6][i]  -= h11_x[i] * h01_z[i] / 2/ localmesh->dx[ic.zp().xp()];
+
+    // // fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] +
+    // // fxz[ic] * h10_x[i]+ fxz[icxp] * h11_x[i];
+    // newWeights[6][i]  += h00_x[i] * h10_z[i] / 2 / localmesh->dz[ic];
+    // newWeights[4][i]  -= h00_x[i] * h10_z[i] / 2 / localmesh->dz[ic];
+    // newWeights[10][i] += h01_x[i] * h10_z[i] / 2 / localmesh->dz[ic.xp()];
+    // newWeights[8][i]  -= h01_x[i] * h10_z[i] / 2 / localmesh->dz[ic.xp()];
+    // newWeights[10][i] += h10_x[i] * h10_z[i] / 4 / localmesh->dz[ic] / localmesh->dx[ic];
+    // newWeights[8][i]  -= h10_x[i] * h10_z[i] / 4 / localmesh->dz[ic] / localmesh->dx[ic];
+    // newWeights[2][i]  -= h10_x[i] * h10_z[i] / 4 / localmesh->dz[ic] / localmesh->dx[ic];
+    // newWeights[0][i]  += h10_x[i] * h10_z[i] / 4 / localmesh->dz[ic] / localmesh->dx[ic];
+    // newWeights[14][i] += h11_x[i] * h10_z[i] / 4 / localmesh->dz[ic.xp()] / localmesh->dx[ic.xp()];
+    // newWeights[12][i] -= h11_x[i] * h10_z[i] / 4 / localmesh->dz[ic.xp()] / localmesh->dx[ic.xp()];
+    // newWeights[6][i] -= h11_x[i] * h10_z[i] / 4 / localmesh->dz[ic.xp()] / localmesh->dx[ic.xp()];
+    // newWeights[4][i]  += h11_x[i] * h10_z[i] / 4 / localmesh->dz[ic.xp()] / localmesh->dx[ic.xp()];
+
+    // // fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i] +
+    // // fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
+    // newWeights[7][i]  += h00_x[i] * h11_z[i] / 2 / localmesh->dz[ic.zp()];
+    // newWeights[5][i]  -= h00_x[i] * h11_z[i] / 2 / localmesh->dz[ic.zp()];
+    // newWeights[11][i] += h01_x[i] * h11_z[i] / 2 / localmesh->dz[ic.zp().xp()];
+    // newWeights[9][i]  -= h01_x[i] * h11_z[i] / 2 / localmesh->dz[ic.zp().xp()];
+    // newWeights[11][i] += h10_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp()] / localmesh->dx[ic.zp()];
+    // newWeights[9][i]  -= h10_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp()] / localmesh->dx[ic.zp()];
+    // newWeights[3][i]  -= h10_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp()] / localmesh->dx[ic.zp()];
+    // newWeights[1][i]  += h10_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp()] / localmesh->dx[ic.zp()];
+    // newWeights[15][i] += h11_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp().xp()] / localmesh->dx[ic.zp().xp()];
+    // newWeights[13][i] -= h11_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp().xp()] / localmesh->dx[ic.zp().xp()];
+    // newWeights[7][i]  -= h11_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp().xp()] / localmesh->dx[ic.zp().xp()];
+    // newWeights[5][i]  += h11_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp().xp()] / localmesh->dx[ic.zp().xp()];
+#endif
   }
 }
 
@@ -152,29 +268,31 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
 
+
+#if USE_NEW_WEIGHTS
+  BOUT_FOR(i, getRegion(region)) {
+    auto ic =  i_corner[i];
+    auto iyp = i.yp(y_offset);
+
+    f_interp[iyp]=0;
+    for (int w = 0; w < 4; ++w){
+      f_interp[iyp] += newWeights[w*4+0][i] * f[ic.zm().xp(w-1)];
+      f_interp[iyp] += newWeights[w*4+1][i] * f[ic.xp(w-1)];
+      f_interp[iyp] += newWeights[w*4+2][i] * f[ic.zp().xp(w-1)];
+      f_interp[iyp] += newWeights[w*4+3][i] * f[ic.zp(2).xp(w-1)];
+    }
+  }
+  return f_interp;
+#else
   // Derivatives are used for tension and need to be on dimensionless
   // coordinates
-  Field3D fx = bout::derivatives::index::DDX(f, CELL_DEFAULT, "DEFAULT");
-  localmesh->communicateXZ(fx);
-  // communicate in y, but do not calculate parallel slices
-  {
-    auto h = localmesh->sendY(fx);
-    localmesh->wait(h);
-  }
-  Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", "RGN_ALL");
-  localmesh->communicateXZ(fz);
-  // communicate in y, but do not calculate parallel slices
-  {
-    auto h = localmesh->sendY(fz);
-    localmesh->wait(h);
-  }
-  Field3D fxz = bout::derivatives::index::DDX(fz, CELL_DEFAULT, "DEFAULT");
-  localmesh->communicateXZ(fxz);
-  // communicate in y, but do not calculate parallel slices
-  {
-    auto h = localmesh->sendY(fxz);
-    localmesh->wait(h);
-  }
+  const auto region2 = fmt::format("RGN_YPAR_{:+d}", y_offset);
+  // f has been communcated, and thus we can assume that the x-boundaries are
+  // also valid in the y-boundary.  Thus the differentiated field needs no
+  // extra comms.
+  Field3D fx = bout::derivatives::index::DDX(f, CELL_DEFAULT, "DEFAULT", region2);
+  Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", region2);
+  Field3D fxz = bout::derivatives::index::DDZ(fx, CELL_DEFAULT, "DEFAULT", region2);
 
   BOUT_FOR(i, getRegion(region)) {
     const auto iyp = i.yp(y_offset);
@@ -208,6 +326,7 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
             || i.x() > localmesh->xend);
   }
   return f_interp;
+# endif
 }
 
 Field3D XZHermiteSpline::interpolate(const Field3D& f, const Field3D& delta_x,

From de7d1deab6a419bf974fb8df5074fba4514175e3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 17 Nov 2022 10:36:29 +0100
Subject: [PATCH 0007/1827] Cleanup

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 50 +-------------------
 1 file changed, 1 insertion(+), 49 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 08515c7056..22da552125 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -158,7 +158,7 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     newWeights[0][i]  += h10_x[i] * h10_z[i] / 4;
     newWeights[14][i] += h11_x[i] * h10_z[i] / 4;
     newWeights[12][i] -= h11_x[i] * h10_z[i] / 4;
-    newWeights[6][i] -= h11_x[i] * h10_z[i] / 4;
+    newWeights[6][i]  -= h11_x[i] * h10_z[i] / 4;
     newWeights[4][i]  += h11_x[i] * h10_z[i] / 4;
 
     // fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i] +
@@ -175,54 +175,6 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     newWeights[13][i] -= h11_x[i] * h11_z[i] / 4;
     newWeights[7][i]  -= h11_x[i] * h11_z[i] / 4;
     newWeights[5][i]  += h11_x[i] * h11_z[i] / 4;
-
-
-    //   // f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
-    // newWeights[5][i]  += h00_x[i] * h00_z[i];
-    // newWeights[9][i]  += h01_x[i] * h00_z[i];
-    // newWeights[9][i]  += h10_x[i] * h00_z[i] / 2 / localmesh->dx[ic];
-    // newWeights[1][i]  -= h10_x[i] * h00_z[i] / 2 / localmesh->dx[ic];
-    // newWeights[13][i] += h11_x[i] * h00_z[i] / 2 / localmesh->dx[ic.xp()];
-    // newWeights[5][i]  -= h11_x[i] * h00_z[i] / 2 / localmesh->dx[ic.xp()];
-
-    // // f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] +
-    // // fx[iczp] * h10_x[i] + fx[icxpzp] * h11_x[i];
-    // newWeights[6][i]  += h00_x[i] * h01_z[i];
-    // newWeights[10][i]  += h01_x[i] * h01_z[i];
-    // newWeights[10][i]  += h10_x[i] * h01_z[i] / 2/ localmesh->dx[ic.zp()];
-    // newWeights[2][i]  -= h10_x[i] * h01_z[i] / 2/ localmesh->dx[ic.zp()];
-    // newWeights[14][i] += h11_x[i] * h01_z[i] / 2/ localmesh->dx[ic.zp().xp()];
-    // newWeights[6][i]  -= h11_x[i] * h01_z[i] / 2/ localmesh->dx[ic.zp().xp()];
-
-    // // fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] +
-    // // fxz[ic] * h10_x[i]+ fxz[icxp] * h11_x[i];
-    // newWeights[6][i]  += h00_x[i] * h10_z[i] / 2 / localmesh->dz[ic];
-    // newWeights[4][i]  -= h00_x[i] * h10_z[i] / 2 / localmesh->dz[ic];
-    // newWeights[10][i] += h01_x[i] * h10_z[i] / 2 / localmesh->dz[ic.xp()];
-    // newWeights[8][i]  -= h01_x[i] * h10_z[i] / 2 / localmesh->dz[ic.xp()];
-    // newWeights[10][i] += h10_x[i] * h10_z[i] / 4 / localmesh->dz[ic] / localmesh->dx[ic];
-    // newWeights[8][i]  -= h10_x[i] * h10_z[i] / 4 / localmesh->dz[ic] / localmesh->dx[ic];
-    // newWeights[2][i]  -= h10_x[i] * h10_z[i] / 4 / localmesh->dz[ic] / localmesh->dx[ic];
-    // newWeights[0][i]  += h10_x[i] * h10_z[i] / 4 / localmesh->dz[ic] / localmesh->dx[ic];
-    // newWeights[14][i] += h11_x[i] * h10_z[i] / 4 / localmesh->dz[ic.xp()] / localmesh->dx[ic.xp()];
-    // newWeights[12][i] -= h11_x[i] * h10_z[i] / 4 / localmesh->dz[ic.xp()] / localmesh->dx[ic.xp()];
-    // newWeights[6][i] -= h11_x[i] * h10_z[i] / 4 / localmesh->dz[ic.xp()] / localmesh->dx[ic.xp()];
-    // newWeights[4][i]  += h11_x[i] * h10_z[i] / 4 / localmesh->dz[ic.xp()] / localmesh->dx[ic.xp()];
-
-    // // fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i] +
-    // // fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
-    // newWeights[7][i]  += h00_x[i] * h11_z[i] / 2 / localmesh->dz[ic.zp()];
-    // newWeights[5][i]  -= h00_x[i] * h11_z[i] / 2 / localmesh->dz[ic.zp()];
-    // newWeights[11][i] += h01_x[i] * h11_z[i] / 2 / localmesh->dz[ic.zp().xp()];
-    // newWeights[9][i]  -= h01_x[i] * h11_z[i] / 2 / localmesh->dz[ic.zp().xp()];
-    // newWeights[11][i] += h10_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp()] / localmesh->dx[ic.zp()];
-    // newWeights[9][i]  -= h10_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp()] / localmesh->dx[ic.zp()];
-    // newWeights[3][i]  -= h10_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp()] / localmesh->dx[ic.zp()];
-    // newWeights[1][i]  += h10_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp()] / localmesh->dx[ic.zp()];
-    // newWeights[15][i] += h11_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp().xp()] / localmesh->dx[ic.zp().xp()];
-    // newWeights[13][i] -= h11_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp().xp()] / localmesh->dx[ic.zp().xp()];
-    // newWeights[7][i]  -= h11_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp().xp()] / localmesh->dx[ic.zp().xp()];
-    // newWeights[5][i]  += h11_x[i] * h11_z[i] / 4 / localmesh->dz[ic.zp().xp()] / localmesh->dx[ic.zp().xp()];
 #endif
   }
 }

From 8a1c2306b9496a09d768fe4fe990352f5fb34936 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Feb 2023 10:55:01 +0100
Subject: [PATCH 0008/1827] Enable splitting in X using PETSc

---
 include/interpolation_xz.hxx                 |  27 ++++
 src/mesh/interpolation/hermite_spline_xz.cxx | 140 ++++++++++++++++++-
 2 files changed, 161 insertions(+), 6 deletions(-)

diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx
index e6eb8c3078..620d146edf 100644
--- a/include/interpolation_xz.hxx
+++ b/include/interpolation_xz.hxx
@@ -26,6 +26,15 @@
 
 #include "mask.hxx"
 
+#define USE_NEW_WEIGHTS 1
+#if BOUT_HAS_PETSC
+#define HS_USE_PETSC 1
+#endif
+
+#ifdef HS_USE_PETSC
+#include "bout/petsclib.hxx"
+#endif
+
 class Options;
 
 /// Interpolate a field onto a perturbed set of points
@@ -149,6 +158,13 @@ protected:
 
   std::vector<Field3D> newWeights;
 
+#if HS_USE_PETSC
+  PetscLib* petsclib;
+  bool isInit{false};
+  Mat petscWeights;
+  Vec rhs, result;
+#endif
+
 public:
   XZHermiteSpline(Mesh *mesh = nullptr)
       : XZHermiteSpline(0, mesh) {}
@@ -157,6 +173,17 @@ public:
       : XZHermiteSpline(y_offset, mesh) {
     setRegion(regionFromMask(mask, localmesh));
   }
+  ~XZHermiteSpline() {
+#if HS_USE_PETSC
+    if (isInit) {
+      MatDestroy(&petscWeights);
+      VecDestroy(&rhs);
+      VecDestroy(&result);
+      isInit = false;
+      delete petsclib;
+    }
+#endif
+  }
 
   void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                    const std::string& region = "RGN_NOBNDRY") override;
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 22da552125..1b63c84231 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -23,10 +23,84 @@
 #include "globals.hxx"
 #include "interpolation_xz.hxx"
 #include "bout/index_derivs_interface.hxx"
-#include "bout/mesh.hxx"
+#include "../impls/bout/boutmesh.hxx"
 
 #include <vector>
 
+class IndConverter {
+public:
+  IndConverter(Mesh* mesh)
+      : mesh(dynamic_cast<BoutMesh*>(mesh)), nxpe(mesh->getNXPE()), nype(mesh->getNYPE()),
+        xstart(mesh->xstart), ystart(mesh->ystart), zstart(0),
+        lnx(mesh->LocalNx - 2 * xstart), lny(mesh->LocalNy - 2 * ystart),
+        lnz(mesh->LocalNz - 2 * zstart) {}
+  // ix and iy are global indices
+  // iy is local
+  int fromMeshToGlobal(int ix, int iy, int iz) {
+    const int xstart = mesh->xstart;
+    const int lnx = mesh->LocalNx - xstart * 2;
+    // x-proc-id
+    int pex = divToNeg(ix - xstart, lnx);
+    if (pex < 0) {
+      pex = 0;
+    }
+    if (pex >= nxpe) {
+      pex = nxpe - 1;
+    }
+    const int zstart = 0;
+    const int lnz = mesh->LocalNz - zstart * 2;
+    // z-proc-id
+    // pez only for wrapping around ; later needs similar treatment than pey
+    const int pez = divToNeg(iz - zstart, lnz);
+    // y proc-id - y is already local
+    const int ystart = mesh->ystart;
+    const int lny = mesh->LocalNy - ystart * 2;
+    const int pey_offset = divToNeg(iy - ystart, lny);
+    int pey = pey_offset + mesh->getYProcIndex();
+    while (pey < 0) {
+      pey += nype;
+    }
+    while (pey >= nype) {
+      pey -= nype;
+    }
+    ASSERT2(pex >= 0);
+    ASSERT2(pex < nxpe);
+    ASSERT2(pey >= 0);
+    ASSERT2(pey < nype);
+    return fromLocalToGlobal(ix - pex * lnx, iy - pey_offset * lny, iz - pez * lnz, pex,
+                             pey, 0);
+  }
+  int fromLocalToGlobal(const int ilocalx, const int ilocaly, const int ilocalz) {
+    return fromLocalToGlobal(ilocalx, ilocaly, ilocalz, mesh->getXProcIndex(),
+                             mesh->getYProcIndex(), 0);
+  }
+  int fromLocalToGlobal(const int ilocalx, const int ilocaly, const int ilocalz,
+                        const int pex, const int pey, const int pez) {
+    ASSERT3(ilocalx >= 0);
+    ASSERT3(ilocaly >= 0);
+    ASSERT3(ilocalz >= 0);
+    const int ilocal = ((ilocalx * mesh->LocalNy) + ilocaly) * mesh->LocalNz + ilocalz;
+    const int ret = ilocal
+                    + mesh->LocalNx * mesh->LocalNy * mesh->LocalNz
+                          * ((pey * nxpe + pex) * nzpe + pez);
+    ASSERT3(ret >= 0);
+    ASSERT3(ret < nxpe * nype * mesh->LocalNx * mesh->LocalNy * mesh->LocalNz);
+    return ret;
+  }
+
+private:
+  // number of procs
+  BoutMesh* mesh;
+  const int nxpe;
+  const int nype;
+  const int nzpe{1};
+  const int xstart, ystart, zstart;
+  const int lnx, lny, lnz;
+  static int divToNeg(const int n, const int d) {
+    return (n < 0) ? ((n - d + 1) / d) : (n / d);
+  }
+};
+
 XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
     : XZInterpolation(y_offset, mesh),
       h00_x(localmesh), h01_x(localmesh), h10_x(localmesh), h11_x(localmesh),
@@ -50,12 +124,27 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
   h10_z.allocate();
   h11_z.allocate();
 
-
+#if USE_NEW_WEIGHTS
   newWeights.reserve(16);
   for (int w=0; w<16;++w){
     newWeights.emplace_back(localmesh);
     newWeights[w].allocate();
   }
+#ifdef HS_USE_PETSC
+  petsclib = new PetscLib(
+      &Options::root()["mesh:paralleltransform:xzinterpolation:hermitespline"]);
+  // MatCreate(MPI_Comm comm,Mat *A)
+  // MatCreate(MPI_COMM_WORLD, &petscWeights);
+  //  MatSetSizes(petscWeights, m, m, M, M);
+  // PetscErrorCode MatCreateAIJ(MPI_Comm comm, PetscInt m, PetscInt n, PetscInt M,
+  // PetscInt N, 			      PetscInt d_nz, const PetscInt d_nnz[], PetscInt o_nz, const PetscInt
+  //o_nnz[], Mat *A)
+  //  MatSetSizes(Mat A,PetscInt m,PetscInt n,PetscInt M,PetscInt N)
+  const int m = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz;
+  const int M = m * mesh->getNXPE() * mesh->getNYPE();
+  MatCreateAIJ(MPI_COMM_WORLD, m, m, M, M, 16, nullptr, 16, nullptr, &petscWeights);
+#endif
+#endif
 }
 
 void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
@@ -63,6 +152,11 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
 
   const int ny = localmesh->LocalNy;
   const int nz = localmesh->LocalNz;
+  const int xend = (localmesh->xend - localmesh->xstart + 1) * localmesh->getNXPE()
+                   + localmesh->xstart - 1;
+#ifdef HS_USE_PETSC
+  IndConverter conv{localmesh};
+#endif
   BOUT_FOR(i, getRegion(region)) {
     const int x = i.x();
     const int y = i.y();
@@ -79,8 +173,8 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     BoutReal t_z = delta_z(x, y, z) - static_cast<BoutReal>(k_corner(x, y, z));
 
     // NOTE: A (small) hack to avoid one-sided differences
-    if (i_corn >= localmesh->xend) {
-      i_corn = localmesh->xend - 1;
+    if (i_corn >= xend) {
+      i_corn = xend - 1;
       t_x = 1.0;
     }
     if (i_corn < localmesh->xstart) {
@@ -116,7 +210,6 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     h11_x[i] = (t_x * t_x * t_x) - (t_x * t_x);
     h11_z[i] = (t_z * t_z * t_z) - (t_z * t_z);
 
-#define USE_NEW_WEIGHTS 1
 #if USE_NEW_WEIGHTS
 
     for (int w =0; w<16;++w){
@@ -175,8 +268,28 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     newWeights[13][i] -= h11_x[i] * h11_z[i] / 4;
     newWeights[7][i]  -= h11_x[i] * h11_z[i] / 4;
     newWeights[5][i]  += h11_x[i] * h11_z[i] / 4;
+#ifdef HS_USE_PETSC
+    PetscInt idxn[1] = {/* ;  idxn[0] = */ conv.fromLocalToGlobal(x, y + y_offset, z)};
+    // ixstep = mesh->LocalNx * mesh->LocalNz;
+    for (int j = 0; j < 4; ++j) {
+      PetscInt idxm[4];
+      PetscScalar vals[4];
+      for (int k = 0; k < 4; ++k) {
+        idxm[k] = conv.fromMeshToGlobal(i_corn - 1 + j, y + y_offset,
+                                        k_corner(x, y, z) - 1 + k);
+        vals[k] = newWeights[j * 4 + k][i];
+      }
+      MatSetValues(petscWeights, 1, idxn, 4, idxm, vals, INSERT_VALUES);
+    }
+#endif
 #endif
   }
+#ifdef HS_USE_PETSC
+  isInit = true;
+  MatAssemblyBegin(petscWeights, MAT_FINAL_ASSEMBLY);
+  MatAssemblyEnd(petscWeights, MAT_FINAL_ASSEMBLY);
+  MatCreateVecs(petscWeights, &rhs, &result);
+#endif
 }
 
 void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
@@ -220,8 +333,22 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
 
-
 #if USE_NEW_WEIGHTS
+#ifdef HS_USE_PETSC
+  BoutReal* ptr;
+  const BoutReal* cptr;
+  VecGetArray(rhs, &ptr);
+  BOUT_FOR(i, f.getRegion("RGN_NOY")) { ptr[int(i)] = f[i]; }
+  VecRestoreArray(rhs, &ptr);
+  MatMult(petscWeights, rhs, result);
+  VecGetArrayRead(result, &cptr);
+  const auto region2 = fmt::format("RGN_YPAR_{:+d}", y_offset);
+  BOUT_FOR(i, f.getRegion(region2)) {
+    f_interp[i] = cptr[int(i)];
+    ASSERT2(std::isfinite(cptr[int(i)]));
+  }
+  VecRestoreArrayRead(result, &cptr);
+#else
   BOUT_FOR(i, getRegion(region)) {
     auto ic =  i_corner[i];
     auto iyp = i.yp(y_offset);
@@ -234,6 +361,7 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
       f_interp[iyp] += newWeights[w*4+3][i] * f[ic.zp(2).xp(w-1)];
     }
   }
+#endif
   return f_interp;
 #else
   // Derivatives are used for tension and need to be on dimensionless

From 8234ccf92a8725f05453b22e874ec989c4e52121 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Feb 2023 10:56:08 +0100
Subject: [PATCH 0009/1827] Test parallised interpolation if PETSc is found

---
 tests/MMS/spatial/fci/data/BOUT.inp |  2 +-
 tests/MMS/spatial/fci/runtest       | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index 5f377bbb56..b845e22012 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -20,4 +20,4 @@ y_periodic = true
 z_periodic = true
 
 [mesh:paralleltransform:xzinterpolation]
-type = lagrange4pt
+type = hermitespline
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 1613155ed2..afff928087 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -19,13 +19,13 @@ from sys import stdout
 
 import zoidberg as zb
 
-nx = 3  # Not changed for these tests
+nx = 4  # Not changed for these tests
 
 # Resolution in y and z
 nlist = [8, 16, 32, 64, 128]
 
 # Number of parallel slices (in each direction)
-nslices = [1, 2]
+nslices = [1]  # , 2]
 
 directory = "data"
 
@@ -59,7 +59,7 @@ for nslice in nslices:
         # Note that the Bz and Bzprime parameters here must be the same as in mms.py
         field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
         # Create rectangular poloidal grids
-        poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(nx, n, 0.1, 1.0)
+        poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(nx, n, 0.1, 1.0, MXG=1)
         # Set the ylength and y locations
         ylength = 10.0
 
@@ -72,12 +72,12 @@ for nslice in nslices:
         # Create the grid
         grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
         # Make and write maps
-        maps = zb.make_maps(grid, field, nslice=nslice, quiet=True)
+        maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
         zb.write_maps(
             grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True
         )
 
-        args = " MZ={} MYG={} mesh:paralleltransform:y_periodic={} mesh:ddy:first={}".format(
+        args = " MZ={} MYG={} mesh:paralleltransform:y_periodic={} mesh:ddy:first={} NXPE=2".format(
             n, nslice, yperiodic, method_orders[nslice]["name"]
         )
 

From 9525e2cb7ccdbfe4d888e9f0e0f019e29936d1de Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Feb 2023 12:43:13 +0100
Subject: [PATCH 0010/1827] Fall back to region if not shifted

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 1b63c84231..37dc48662f 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -342,7 +342,7 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   VecRestoreArray(rhs, &ptr);
   MatMult(petscWeights, rhs, result);
   VecGetArrayRead(result, &cptr);
-  const auto region2 = fmt::format("RGN_YPAR_{:+d}", y_offset);
+  const auto region2 = y_offset == 0 ? region : fmt::format("RGN_YPAR_{:+d}", y_offset);
   BOUT_FOR(i, f.getRegion(region2)) {
     f_interp[i] = cptr[int(i)];
     ASSERT2(std::isfinite(cptr[int(i)]));

From b62082c8cf680deb391fbeaab2184a56d178177b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Feb 2023 14:05:56 +0100
Subject: [PATCH 0011/1827] Split in X only if we have PETSc

---
 tests/MMS/spatial/fci/runtest | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index afff928087..7a54b87ccf 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -77,8 +77,12 @@ for nslice in nslices:
             grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True
         )
 
-        args = " MZ={} MYG={} mesh:paralleltransform:y_periodic={} mesh:ddy:first={} NXPE=2".format(
-            n, nslice, yperiodic, method_orders[nslice]["name"]
+        args = " MZ={} MYG={} mesh:paralleltransform:y_periodic={} mesh:ddy:first={} NXPE={}".format(
+            n,
+            nslice,
+            yperiodic,
+            method_orders[nslice]["name"],
+            2 if conf.has["petsc"] else 1,
         )
 
         # Command to run

From e147bc5fa3151726a1b9281993c40ba19b6cfbdc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Feb 2023 18:32:55 +0100
Subject: [PATCH 0012/1827] Add test-interpolate for splitting in X

---
 .../integrated/test-interpolate/data/BOUT.inp |  1 -
 tests/integrated/test-interpolate/runtest     | 22 ++++++++++++++-----
 .../test-interpolate/test_interpolate.cxx     |  3 ++-
 3 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/tests/integrated/test-interpolate/data/BOUT.inp b/tests/integrated/test-interpolate/data/BOUT.inp
index 101c63f3c7..804e780bbe 100644
--- a/tests/integrated/test-interpolate/data/BOUT.inp
+++ b/tests/integrated/test-interpolate/data/BOUT.inp
@@ -4,7 +4,6 @@
 #
 
 MZ = 4   # Z size
-NXPE = 1
 
 ZMAX = 1
 MXG = 2
diff --git a/tests/integrated/test-interpolate/runtest b/tests/integrated/test-interpolate/runtest
index 08975cfd33..3e8f2c5bc6 100755
--- a/tests/integrated/test-interpolate/runtest
+++ b/tests/integrated/test-interpolate/runtest
@@ -6,6 +6,7 @@
 
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata import collect
+import boutconfig
 from numpy import sqrt, max, abs, mean, array, log, polyfit
 from sys import stdout, exit
 
@@ -16,7 +17,7 @@ show_plot = False
 nxlist = [16, 32, 64, 128]
 
 # Only testing 2D (x, z) slices, so only need one processor
-nproc = 1
+nproc = 2
 
 # Variables to compare
 varlist = ["a", "b", "c"]
@@ -48,11 +49,9 @@ for method in methods:
     for nx in nxlist:
         dx = 1.0 / (nx)
 
-        args = (
-            " mesh:nx={nx4} mesh:dx={dx} MZ={nx} xzinterpolation:type={method}".format(
-                nx4=nx + 4, dx=dx, nx=nx, method=method
-            )
-        )
+        args = f" mesh:nx={nx + 4} mesh:dx={dx} MZ={nx} xzinterpolation:type={method}"
+        NXPE = 2 if method == "hermitespline" and boutconfig.has["petsc"] else 1
+        args += f" NXPE={NXPE}"
 
         cmd = "./test_interpolate" + args
 
@@ -71,6 +70,17 @@ for method in methods:
 
             E = interp - solution
 
+            if False:
+                import matplotlib.pyplot as plt
+
+                def myplot(f, lbl=None):
+                    plt.plot(f[:, 0, 6], label=lbl)
+
+                myplot(interp, "interp")
+                myplot(solution, "sol")
+                plt.legend()
+                plt.show()
+
             l2 = float(sqrt(mean(E**2)))
             linf = float(max(abs(E)))
 
diff --git a/tests/integrated/test-interpolate/test_interpolate.cxx b/tests/integrated/test-interpolate/test_interpolate.cxx
index 958409bbc1..8f19cd2a28 100644
--- a/tests/integrated/test-interpolate/test_interpolate.cxx
+++ b/tests/integrated/test-interpolate/test_interpolate.cxx
@@ -72,7 +72,7 @@ int main(int argc, char **argv) {
     BoutReal dz = index.z() + dice();
     // For the last point, put the displacement inwards
     // Otherwise we try to interpolate in the guard cells, which doesn't work so well
-    if (index.x() >= mesh->xend) {
+    if (index.x() >= mesh->xend && mesh->getNXPE() - 1 == mesh->getXProcIndex()) {
       dx = index.x() - dice();
     }
     deltax[index] = dx;
@@ -87,6 +87,7 @@ int main(int argc, char **argv) {
     c_solution[index] = c_gen->generate(pos);
   }
 
+  deltax += (mesh->LocalNx - mesh->xstart * 2) * mesh->getXProcIndex();
   // Create the interpolation object from the input options
   auto interp = XZInterpolationFactory::getInstance().create();
 

From 62d5bbec211127ffa6aeb6c06a8abaeee237b85d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Feb 2023 18:41:27 +0100
Subject: [PATCH 0013/1827] Cleanup

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 37dc48662f..e41dfa4d03 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -269,7 +269,10 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     newWeights[7][i]  -= h11_x[i] * h11_z[i] / 4;
     newWeights[5][i]  += h11_x[i] * h11_z[i] / 4;
 #ifdef HS_USE_PETSC
-    PetscInt idxn[1] = {/* ;  idxn[0] = */ conv.fromLocalToGlobal(x, y + y_offset, z)};
+    PetscInt idxn[1] = {conv.fromLocalToGlobal(x, y + y_offset, z)};
+    // output.write("debug: {:d} -> {:d}: {:d}:{:d} -> {:d}:{:d}\n", conv.fromLocalToGlobal(x, y + y_offset, z),
+    //     conv.fromMeshToGlobal(i_corn, y + y_offset, k_corner(x, y, z)),
+    //     x, z, i_corn, k_corner(x, y, z));
     // ixstep = mesh->LocalNx * mesh->LocalNz;
     for (int j = 0; j < 4; ++j) {
       PetscInt idxm[4];

From 5c324157ca1d2f3eb241eac68e5f55feaef889ae Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Feb 2023 19:44:17 +0100
Subject: [PATCH 0014/1827] Only run in parallel if we split in X

---
 tests/integrated/test-interpolate/runtest | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/tests/integrated/test-interpolate/runtest b/tests/integrated/test-interpolate/runtest
index 3e8f2c5bc6..f5460aff2a 100755
--- a/tests/integrated/test-interpolate/runtest
+++ b/tests/integrated/test-interpolate/runtest
@@ -16,9 +16,6 @@ show_plot = False
 # List of NX values to use
 nxlist = [16, 32, 64, 128]
 
-# Only testing 2D (x, z) slices, so only need one processor
-nproc = 2
-
 # Variables to compare
 varlist = ["a", "b", "c"]
 markers = ["bo", "r^", "kx"]
@@ -50,8 +47,8 @@ for method in methods:
         dx = 1.0 / (nx)
 
         args = f" mesh:nx={nx + 4} mesh:dx={dx} MZ={nx} xzinterpolation:type={method}"
-        NXPE = 2 if method == "hermitespline" and boutconfig.has["petsc"] else 1
-        args += f" NXPE={NXPE}"
+        nproc = 2 if method == "hermitespline" and boutconfig.has["petsc"] else 1
+        args += f" NXPE={nproc}"
 
         cmd = "./test_interpolate" + args
 

From a4a28c6e3c4025500f7a8bbbc0b0e474720703e0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 3 Feb 2023 13:10:21 +0100
Subject: [PATCH 0015/1827] Delete object

release leaks the pointer, reset free's the object.
---
 tests/integrated/test-interpolate/test_interpolate.cxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/integrated/test-interpolate/test_interpolate.cxx b/tests/integrated/test-interpolate/test_interpolate.cxx
index 8f19cd2a28..ed8e80f43f 100644
--- a/tests/integrated/test-interpolate/test_interpolate.cxx
+++ b/tests/integrated/test-interpolate/test_interpolate.cxx
@@ -113,6 +113,7 @@ int main(int argc, char **argv) {
   bout::writeDefaultOutputFile(dump);
 
   bout::checkForUnusedOptions();
+  interp.reset();
   BoutFinalise();
 
   return 0;

From 0e28dc1c5dbaa8c5e73bb09020ac2d01924aa850 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 3 Feb 2023 14:05:38 +0100
Subject: [PATCH 0016/1827] Create PetscVecs only once

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index e41dfa4d03..4e6fc8320c 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -288,10 +288,12 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
 #endif
   }
 #ifdef HS_USE_PETSC
-  isInit = true;
   MatAssemblyBegin(petscWeights, MAT_FINAL_ASSEMBLY);
   MatAssemblyEnd(petscWeights, MAT_FINAL_ASSEMBLY);
-  MatCreateVecs(petscWeights, &rhs, &result);
+  if (!isInit) {
+    MatCreateVecs(petscWeights, &rhs, &result);
+  }
+  isInit = true;
 #endif
 }
 

From 66bde042f6553e372465eb47be0ede532a815bde Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 3 Feb 2023 14:06:09 +0100
Subject: [PATCH 0017/1827] Be more general about cleaning up before
 BoutFinialise

---
 tests/integrated/test-interpolate/test_interpolate.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-interpolate/test_interpolate.cxx b/tests/integrated/test-interpolate/test_interpolate.cxx
index ed8e80f43f..517d9c2445 100644
--- a/tests/integrated/test-interpolate/test_interpolate.cxx
+++ b/tests/integrated/test-interpolate/test_interpolate.cxx
@@ -30,7 +30,7 @@ std::shared_ptr<FieldGenerator> getGeneratorFromOptions(const std::string& varna
 
 int main(int argc, char **argv) {
   BoutInitialise(argc, argv);
-
+  {
   // Random number generator
   std::default_random_engine generator;
   // Uniform distribution of BoutReals from 0 to 1
@@ -113,7 +113,7 @@ int main(int argc, char **argv) {
   bout::writeDefaultOutputFile(dump);
 
   bout::checkForUnusedOptions();
-  interp.reset();
+  }
   BoutFinalise();
 
   return 0;

From adba8774b274073e07eb13cd8165a7594dd99bd0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 3 Feb 2023 14:56:13 +0100
Subject: [PATCH 0018/1827] Run different interpolations in the fci test

---
 tests/MMS/spatial/fci/runtest | 197 +++++++++++++++++++---------------
 1 file changed, 108 insertions(+), 89 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 7a54b87ccf..d68b6c6ca1 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -47,96 +47,115 @@ failures = []
 build_and_log("FCI MMS test")
 
 for nslice in nslices:
-    error_2[nslice] = []
-    error_inf[nslice] = []
-
-    # Which central difference scheme to use and its expected order
-    order = nslice * 2
-    method_orders[nslice] = {"name": "C{}".format(order), "order": order}
-
-    for n in nlist:
-        # Define the magnetic field using new poloidal gridding method
-        # Note that the Bz and Bzprime parameters here must be the same as in mms.py
-        field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
-        # Create rectangular poloidal grids
-        poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(nx, n, 0.1, 1.0, MXG=1)
-        # Set the ylength and y locations
-        ylength = 10.0
-
-        if yperiodic:
-            ycoords = linspace(0.0, ylength, n, endpoint=False)
+    for method in [
+        "hermitespline",
+        "lagrange4pt",
+        "bilinear",
+        # "monotonichermitespline",
+    ]:
+        error_2[nslice] = []
+        error_inf[nslice] = []
+
+        # Which central difference scheme to use and its expected order
+        order = nslice * 2
+        method_orders[nslice] = {"name": "C{}".format(order), "order": order}
+
+        for n in nlist:
+            # Define the magnetic field using new poloidal gridding method
+            # Note that the Bz and Bzprime parameters here must be the same as in mms.py
+            field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
+            # Create rectangular poloidal grids
+            poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(
+                nx, n, 0.1, 1.0, MXG=1
+            )
+            # Set the ylength and y locations
+            ylength = 10.0
+
+            if yperiodic:
+                ycoords = linspace(0.0, ylength, n, endpoint=False)
+            else:
+                # Doesn't include the end points
+                ycoords = (arange(n) + 0.5) * ylength / float(n)
+
+            # Create the grid
+            grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
+            # Make and write maps
+            maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
+            zb.write_maps(
+                grid,
+                field,
+                maps,
+                new_names=False,
+                metric2d=conf.isMetric2D(),
+                quiet=True,
+            )
+
+            args = " MZ={} MYG={} mesh:paralleltransform:y_periodic={} mesh:ddy:first={} NXPE={}".format(
+                n,
+                nslice,
+                yperiodic,
+                method_orders[nslice]["name"],
+                2 if conf.has["petsc"] and method == "hermitespline" else 1,
+            )
+            args += f" mesh:paralleltransform:xzinterpolation:type={method}"
+
+            # Command to run
+            cmd = "./fci_mms " + args
+
+            print("Running command: " + cmd)
+
+            # Launch using MPI
+            s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
+
+            # Save output to log file
+            with open("run.log." + str(n), "w") as f:
+                f.write(out)
+
+            if s:
+                print("Run failed!\nOutput was:\n")
+                print(out)
+                exit(s)
+
+            # Collect data
+            l_2 = collect(
+                "l_2",
+                tind=[1, 1],
+                info=False,
+                path=directory,
+                xguards=False,
+                yguards=False,
+            )
+            l_inf = collect(
+                "l_inf",
+                tind=[1, 1],
+                info=False,
+                path=directory,
+                xguards=False,
+                yguards=False,
+            )
+
+            error_2[nslice].append(l_2)
+            error_inf[nslice].append(l_inf)
+
+            print("Errors : l-2 {:f} l-inf {:f}".format(l_2, l_inf))
+
+        dx = 1.0 / array(nlist)
+
+        # Calculate convergence order
+        fit = polyfit(log(dx), log(error_2[nslice]), 1)
+        order = fit[0]
+        stdout.write("Convergence order = {:f} (fit)".format(order))
+
+        order = log(error_2[nslice][-2] / error_2[nslice][-1]) / log(dx[-2] / dx[-1])
+        stdout.write(", {:f} (small spacing)".format(order))
+
+        # Should be close to the expected order
+        if order > method_orders[nslice]["order"] * 0.95:
+            print("............ PASS\n")
         else:
-            # Doesn't include the end points
-            ycoords = (arange(n) + 0.5) * ylength / float(n)
-
-        # Create the grid
-        grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
-        # Make and write maps
-        maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
-        zb.write_maps(
-            grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True
-        )
-
-        args = " MZ={} MYG={} mesh:paralleltransform:y_periodic={} mesh:ddy:first={} NXPE={}".format(
-            n,
-            nslice,
-            yperiodic,
-            method_orders[nslice]["name"],
-            2 if conf.has["petsc"] else 1,
-        )
-
-        # Command to run
-        cmd = "./fci_mms " + args
-
-        print("Running command: " + cmd)
-
-        # Launch using MPI
-        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-
-        # Save output to log file
-        with open("run.log." + str(n), "w") as f:
-            f.write(out)
-
-        if s:
-            print("Run failed!\nOutput was:\n")
-            print(out)
-            exit(s)
-
-        # Collect data
-        l_2 = collect(
-            "l_2", tind=[1, 1], info=False, path=directory, xguards=False, yguards=False
-        )
-        l_inf = collect(
-            "l_inf",
-            tind=[1, 1],
-            info=False,
-            path=directory,
-            xguards=False,
-            yguards=False,
-        )
-
-        error_2[nslice].append(l_2)
-        error_inf[nslice].append(l_inf)
-
-        print("Errors : l-2 {:f} l-inf {:f}".format(l_2, l_inf))
-
-    dx = 1.0 / array(nlist)
-
-    # Calculate convergence order
-    fit = polyfit(log(dx), log(error_2[nslice]), 1)
-    order = fit[0]
-    stdout.write("Convergence order = {:f} (fit)".format(order))
-
-    order = log(error_2[nslice][-2] / error_2[nslice][-1]) / log(dx[-2] / dx[-1])
-    stdout.write(", {:f} (small spacing)".format(order))
-
-    # Should be close to the expected order
-    if order > method_orders[nslice]["order"] * 0.95:
-        print("............ PASS\n")
-    else:
-        print("............ FAIL\n")
-        success = False
-        failures.append(method_orders[nslice]["name"])
+            print("............ FAIL\n")
+            success = False
+            failures.append(method_orders[nslice]["name"])
 
 
 with open("fci_mms.pkl", "wb") as output:

From cbaf894b2b77b09111f0b38d17653476b3263c35 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 7 Feb 2023 14:06:13 +0100
Subject: [PATCH 0019/1827] Fix parallel boundary region with x splitting

---
 src/mesh/parallel/fci.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 77f34fd282..baf0f3fc6b 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -158,6 +158,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
   const int ncz = map_mesh.LocalNz;
 
   BoutMask to_remove(map_mesh);
+  const int xend = map_mesh.xstart + (map_mesh.xend - map_mesh.xstart + 1) * map_mesh.getNXPE() - 1;
   // Serial loop because call to BoundaryRegionPar::addPoint
   // (probably?) can't be done in parallel
   BOUT_FOR_SERIAL(i, xt_prime.getRegion("RGN_NOBNDRY")) {
@@ -171,7 +172,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
       }
     }
 
-    if ((xt_prime[i] >= map_mesh.xstart) and (xt_prime[i] <= map_mesh.xend)) {
+    if ((xt_prime[i] >= map_mesh.xstart) and (xt_prime[i] <= xend)) {
       // Not a boundary
       continue;
     }

From 5673f0c2ea8ecef929b99fb473cc25bc393a76e7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 7 Feb 2023 14:12:52 +0100
Subject: [PATCH 0020/1827] Add integrated test for FCI X splitting

* helped finding the bug for the boundary
* rather slow (around 1 minute)
* needs internet connectivity
---
 cmake/BOUT++functions.cmake                  | 16 +++++-
 tests/integrated/CMakeLists.txt              |  2 +
 tests/integrated/test-fci-mpi/CMakeLists.txt |  8 +++
 tests/integrated/test-fci-mpi/data/BOUT.inp  | 28 ++++++++++
 tests/integrated/test-fci-mpi/fci_mpi.cxx    | 37 +++++++++++++
 tests/integrated/test-fci-mpi/runtest        | 58 ++++++++++++++++++++
 6 files changed, 148 insertions(+), 1 deletion(-)
 create mode 100644 tests/integrated/test-fci-mpi/CMakeLists.txt
 create mode 100644 tests/integrated/test-fci-mpi/data/BOUT.inp
 create mode 100644 tests/integrated/test-fci-mpi/fci_mpi.cxx
 create mode 100755 tests/integrated/test-fci-mpi/runtest

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 40e45f99be..77279dfd4b 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -162,7 +162,7 @@ endfunction()
 #
 function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
   set(options USE_RUNTEST USE_DATA_BOUT_INP)
-  set(oneValueArgs EXECUTABLE_NAME PROCESSORS)
+  set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME)
   set(multiValueArgs SOURCES EXTRA_FILES REQUIRES CONFLICTS TESTARGS EXTRA_DEPENDS)
   cmake_parse_arguments(BOUT_TEST_OPTIONS "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
 
@@ -202,6 +202,20 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
     add_custom_target(${TESTNAME})
   endif()
 
+  if (BOUT_TEST_OPTIONS_DOWNLOAD)
+    if (NOT BOUT_TEST_OPTIONS_DOWNLOAD_NAME)
+      message(FATAL_ERROR "We need DOWNLOAD_NAME if we should DOWNLOAD!")
+    endif()
+    set(output )
+    add_custom_command(OUTPUT ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
+      COMMAND wget ${BOUT_TEST_OPTIONS_DOWNLOAD} -O ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMENT "Downloading ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}"
+      )
+    add_custom_target(download_test_data DEPENDS ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME})
+    add_dependencies(${TESTNAME} download_test_data)
+  endif()
+
   if (BOUT_TEST_OPTIONS_EXTRA_DEPENDS)
     add_dependencies(${TESTNAME} ${BOUT_TEST_OPTIONS_EXTRA_DEPENDS})
   endif()
diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt
index 2fe72dfe2d..89cbf6ffe6 100644
--- a/tests/integrated/CMakeLists.txt
+++ b/tests/integrated/CMakeLists.txt
@@ -9,6 +9,8 @@ add_subdirectory(test-cyclic)
 add_subdirectory(test-delp2)
 add_subdirectory(test-drift-instability)
 add_subdirectory(test-drift-instability-staggered)
+add_subdirectory(test-fci-boundary)
+add_subdirectory(test-fci-mpi)
 add_subdirectory(test-fieldgroupComm)
 add_subdirectory(test-griddata)
 add_subdirectory(test-griddata-yboundary-guards)
diff --git a/tests/integrated/test-fci-mpi/CMakeLists.txt b/tests/integrated/test-fci-mpi/CMakeLists.txt
new file mode 100644
index 0000000000..6a1ec33ac6
--- /dev/null
+++ b/tests/integrated/test-fci-mpi/CMakeLists.txt
@@ -0,0 +1,8 @@
+bout_add_mms_test(test-fci-mpi
+  SOURCES fci_mpi.cxx
+  USE_RUNTEST
+  USE_DATA_BOUT_INP
+  PROCESSORS 6
+  DOWNLOAD https://zenodo.org/record/7614499/files/W7X-conf4-36x8x128.fci.nc?download=1
+  DOWNLOAD_NAME grid.fci.nc
+)
diff --git a/tests/integrated/test-fci-mpi/data/BOUT.inp b/tests/integrated/test-fci-mpi/data/BOUT.inp
new file mode 100644
index 0000000000..47272dab61
--- /dev/null
+++ b/tests/integrated/test-fci-mpi/data/BOUT.inp
@@ -0,0 +1,28 @@
+grid = grid.fci.nc
+
+[mesh]
+symmetricglobalx = true
+
+[mesh:ddy]
+first = C2
+second = C2
+
+[mesh:paralleltransform]
+type = fci
+y_periodic = true
+z_periodic = true
+
+[mesh:paralleltransform:xzinterpolation]
+type = hermitespline
+
+[input_0]
+function = sin(z)
+
+[input_1]
+function = cos(y)
+
+[input_2]
+function = sin(x)
+
+[input_3]
+function = sin(x) * sin(z) * cos(y)
diff --git a/tests/integrated/test-fci-mpi/fci_mpi.cxx b/tests/integrated/test-fci-mpi/fci_mpi.cxx
new file mode 100644
index 0000000000..b353493dda
--- /dev/null
+++ b/tests/integrated/test-fci-mpi/fci_mpi.cxx
@@ -0,0 +1,37 @@
+#include "bout.hxx"
+#include "derivs.hxx"
+#include "field_factory.hxx"
+
+int main(int argc, char** argv) {
+  BoutInitialise(argc, argv);
+  {
+    using bout::globals::mesh;
+    Options *options = Options::getRoot();
+    int i=0;
+    std::string default_str {"not_set"};
+    Options dump;
+    while (true) {
+      std::string temp_str;
+      options->get(fmt::format("input_{:d}:function", i), temp_str, default_str);
+      if (temp_str == default_str) {
+	break;
+      }
+      Field3D input{FieldFactory::get()->create3D(fmt::format("input_{:d}:function", i), Options::getRoot(), mesh)};
+      //options->get(fmt::format("input_{:d}:boundary_perp", i), temp_str, s"free_o3");
+      mesh->communicate(input);
+      input.applyParallelBoundary("parallel_neumann_o2");
+      for (int slice = -mesh->ystart; slice <= mesh->ystart; ++slice) {
+	if (slice) {
+	  Field3D tmp{0.};
+	  BOUT_FOR(i, tmp.getRegion("RGN_NOBNDRY")) {
+	    tmp[i] = input.ynext(slice)[i.yp(slice)];
+	  }
+	  dump[fmt::format("output_{:d}_{:+d}", i, slice)] = tmp;
+	}
+      }
+      ++i;
+    }
+    bout::writeDefaultOutputFile(dump);
+  }
+  BoutFinalise();
+}
diff --git a/tests/integrated/test-fci-mpi/runtest b/tests/integrated/test-fci-mpi/runtest
new file mode 100755
index 0000000000..4ac0e43460
--- /dev/null
+++ b/tests/integrated/test-fci-mpi/runtest
@@ -0,0 +1,58 @@
+#!/usr/bin/env python3
+#
+# Python script to run and analyse MMS test
+#
+
+# Cores: 8
+# requires: metric_3d
+
+from boututils.run_wrapper import build_and_log, launch_safe, shell_safe
+from boutdata.collect import collect
+import boutconfig as conf
+import itertools
+
+import numpy as np
+
+# Resolution in x and y
+nlist = [1, 2, 4]
+
+maxcores = 8
+
+nslices = [1]
+
+success = True
+
+build_and_log("FCI MMS test")
+
+for nslice in nslices:
+    for NXPE, NYPE in itertools.product(nlist, nlist):
+
+        if NXPE * NYPE > maxcores:
+            continue
+
+        args = f"NXPE={NXPE} NYPE={NYPE}"
+        # Command to run
+        cmd = f"./fci_mpi {args}"
+
+        print(f"Running command: {cmd}")
+
+        mthread = maxcores // (NXPE * NYPE)
+        # Launch using MPI
+        _, out = launch_safe(cmd, nproc=NXPE * NYPE, mthread=mthread, pipe=True)
+
+        # Save output to log file
+        with open("run.log.{NXPE}.{NYPE}.{nslice}.log", "w") as f:
+            f.write(out)
+
+        collect_kw = dict(info=False, xguards=False, yguards=False, path="data")
+        if NXPE == NYPE == 1:
+            # reference data!
+            ref = {}
+            for i in range(4):
+                for yp in range(1, nslice + 1):
+                    for y in [-yp, yp]:
+                        name = f"output_{i}_{y:+d}"
+                        ref[name] = collect(name, **collect_kw)
+        else:
+            for name, val in ref.items():
+                assert np.allclose(val, collect(name, **collect_kw))

From 9149bf406fe01a98966095455757f71c0305272c Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Wed, 8 Feb 2023 09:20:18 +0000
Subject: [PATCH 0021/1827] Apply black changes

---
 bin/bout-v5-xzinterpolation-upgrader.py                    | 3 ---
 bin/bout_3to4.py                                           | 1 -
 src/field/gen_fieldops.py                                  | 2 --
 tests/MMS/GBS/circle.py                                    | 1 -
 tests/MMS/GBS/mms-slab3d.py                                | 1 -
 tests/MMS/GBS/runtest-slab3d                               | 1 -
 tests/integrated/test-drift-instability/runtest            | 1 -
 tests/integrated/test-fci-mpi/runtest                      | 1 -
 tests/integrated/test-multigrid_laplace/runtest            | 1 -
 .../test-multigrid_laplace/runtest_multiple_grids          | 1 -
 tests/integrated/test-multigrid_laplace/runtest_unsheared  | 1 -
 tests/integrated/test-naulin-laplace/runtest               | 1 -
 .../integrated/test-naulin-laplace/runtest_multiple_grids  | 1 -
 tests/integrated/test-naulin-laplace/runtest_unsheared     | 1 -
 tests/integrated/test-petsc_laplace_MAST-grid/runtest      | 1 -
 tests/integrated/test-twistshift-staggered/runtest         | 1 +
 tests/integrated/test-twistshift/runtest                   | 2 ++
 tests/integrated/test-yupdown-weights/runtest              | 1 -
 tests/integrated/test-yupdown/runtest                      | 1 -
 tests/integrated/test_suite                                | 1 +
 tools/pylib/post_bout/__init__.py                          | 1 -
 tools/pylib/post_bout/basic_info.py                        | 3 ---
 tools/pylib/post_bout/grate2.py                            | 2 --
 tools/pylib/post_bout/pb_corral.py                         | 4 ----
 tools/pylib/post_bout/pb_draw.py                           | 7 -------
 tools/pylib/post_bout/pb_nonlinear.py                      | 1 -
 tools/pylib/post_bout/pb_present.py                        | 1 -
 tools/pylib/post_bout/read_cxx.py                          | 1 -
 tools/pylib/post_bout/read_inp.py                          | 3 ---
 tools/pylib/post_bout/rms.py                               | 1 -
 tools/tokamak_grids/elite/elite2nc                         | 1 +
 tools/tokamak_grids/gato/gato2nc                           | 1 +
 32 files changed, 6 insertions(+), 44 deletions(-)

diff --git a/bin/bout-v5-xzinterpolation-upgrader.py b/bin/bout-v5-xzinterpolation-upgrader.py
index 1e19c6a034..37c79e0de8 100755
--- a/bin/bout-v5-xzinterpolation-upgrader.py
+++ b/bin/bout-v5-xzinterpolation-upgrader.py
@@ -64,7 +64,6 @@ def fix_header_includes(old_header, new_header, source):
 
 
 def fix_interpolations(old_interpolation, new_interpolation, source):
-
     return re.sub(
         r"""
         \b{}\b
@@ -118,7 +117,6 @@ def clang_fix_interpolation(old_interpolation, new_interpolation, node, source):
 
 
 def fix_factories(old_factory, new_factory, source):
-
     return re.sub(
         r"""
         \b{}\b
@@ -186,7 +184,6 @@ def apply_fixes(headers, interpolations, factories, source):
 
 
 def clang_apply_fixes(headers, interpolations, factories, filename, source):
-
     # translation unit
     tu = clang_parse(filename, source)
 
diff --git a/bin/bout_3to4.py b/bin/bout_3to4.py
index 02481fcf6e..d41db36fbb 100755
--- a/bin/bout_3to4.py
+++ b/bin/bout_3to4.py
@@ -195,7 +195,6 @@ def throw_warnings(line_text, filename, line_num):
 
 
 if __name__ == "__main__":
-
     epilog = """
     Currently bout_3to4 can detect the following transformations are needed:
         - Triple square brackets instead of round brackets for subscripts
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 646580559f..68a3a1b059 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -189,7 +189,6 @@ def returnType(f1, f2):
 
 
 if __name__ == "__main__":
-
     parser = argparse.ArgumentParser(
         description="Generate code for the Field arithmetic operators"
     )
@@ -274,7 +273,6 @@ def returnType(f1, f2):
         rhs.name = "rhs"
 
         for operator, operator_name in operators.items():
-
             template_args = {
                 "operator": operator,
                 "operator_name": operator_name,
diff --git a/tests/MMS/GBS/circle.py b/tests/MMS/GBS/circle.py
index b2553f47c3..b33cc77d8c 100644
--- a/tests/MMS/GBS/circle.py
+++ b/tests/MMS/GBS/circle.py
@@ -30,7 +30,6 @@ def generate(
     mxg=2,
     file="circle.nc",
 ):
-
     # q = rBt / RBp
     Bp = r * Bt / (R * q)
 
diff --git a/tests/MMS/GBS/mms-slab3d.py b/tests/MMS/GBS/mms-slab3d.py
index f88a897c98..2f958cfa69 100644
--- a/tests/MMS/GBS/mms-slab3d.py
+++ b/tests/MMS/GBS/mms-slab3d.py
@@ -277,7 +277,6 @@ def C(f):
 # print "\n\nDelp2 phi = ", Delp2(phi, metric).subs(replace)
 
 if not estatic:
-
     Spsi = Delp2(psi, metric) - 0.5 * Ne * mi_me * beta_e * psi - Ne * (Vi - VePsi)
     print("\n[psi]")
     print("\nsolution = " + exprToStr(psi.subs(replace)))
diff --git a/tests/MMS/GBS/runtest-slab3d b/tests/MMS/GBS/runtest-slab3d
index cdcde3e1b3..f193583e47 100755
--- a/tests/MMS/GBS/runtest-slab3d
+++ b/tests/MMS/GBS/runtest-slab3d
@@ -95,7 +95,6 @@ with open("mms-slab3d.pkl", "wb") as output:
 # plot errors
 
 for var, mark in zip(varlist, markers):
-
     order = log(error_2[var][-1] / error_2[var][-2]) / log(dx[-1] / dx[-2])
     print("%s Convergence order = %f" % (var, order))
     if 1.9 < order < 2.1:
diff --git a/tests/integrated/test-drift-instability/runtest b/tests/integrated/test-drift-instability/runtest
index 16b35d69d9..e8ddddc11d 100755
--- a/tests/integrated/test-drift-instability/runtest
+++ b/tests/integrated/test-drift-instability/runtest
@@ -197,7 +197,6 @@ def run_zeff_case(zeff):
 
 
 if __name__ == "__main__":
-
     parser = argparse.ArgumentParser("Run drift-instability test")
     parser.add_argument(
         "-Z",
diff --git a/tests/integrated/test-fci-mpi/runtest b/tests/integrated/test-fci-mpi/runtest
index 4ac0e43460..e12b330326 100755
--- a/tests/integrated/test-fci-mpi/runtest
+++ b/tests/integrated/test-fci-mpi/runtest
@@ -26,7 +26,6 @@ build_and_log("FCI MMS test")
 
 for nslice in nslices:
     for NXPE, NYPE in itertools.product(nlist, nlist):
-
         if NXPE * NYPE > maxcores:
             continue
 
diff --git a/tests/integrated/test-multigrid_laplace/runtest b/tests/integrated/test-multigrid_laplace/runtest
index 76914d19e4..4a7455f80b 100755
--- a/tests/integrated/test-multigrid_laplace/runtest
+++ b/tests/integrated/test-multigrid_laplace/runtest
@@ -29,7 +29,6 @@ print("Running multigrid Laplacian inversion test")
 success = True
 
 for nproc in [1, 3]:
-
     # Make sure we don't use too many cores:
     # Reduce number of OpenMP threads when using multiple MPI processes
     mthread = 2
diff --git a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
index 26cdd96ff6..6817120b13 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
+++ b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
@@ -26,7 +26,6 @@ success = True
 
 for nproc in [1, 2, 4]:
     for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]:
-
         # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
         cmd = "./test_multigrid_laplace -f " + inputfile + " NXPE=" + str(nproc)
 
diff --git a/tests/integrated/test-multigrid_laplace/runtest_unsheared b/tests/integrated/test-multigrid_laplace/runtest_unsheared
index fd0e11fbbf..cda68f2167 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_unsheared
+++ b/tests/integrated/test-multigrid_laplace/runtest_unsheared
@@ -25,7 +25,6 @@ print("Running multigrid Laplacian inversion test")
 success = True
 
 for nproc in [1, 3]:
-
     # Make sure we don't use too many cores:
     # Reduce number of OpenMP threads when using multiple MPI processes
     mthread = 2
diff --git a/tests/integrated/test-naulin-laplace/runtest b/tests/integrated/test-naulin-laplace/runtest
index 82dd22776e..f972eab6cc 100755
--- a/tests/integrated/test-naulin-laplace/runtest
+++ b/tests/integrated/test-naulin-laplace/runtest
@@ -29,7 +29,6 @@ print("Running LaplaceNaulin inversion test")
 success = True
 
 for nproc in [1, 3]:
-
     # Make sure we don't use too many cores:
     # Reduce number of OpenMP threads when using multiple MPI processes
     mthread = 2
diff --git a/tests/integrated/test-naulin-laplace/runtest_multiple_grids b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
index 2d583fd1b8..c0281c3a4e 100755
--- a/tests/integrated/test-naulin-laplace/runtest_multiple_grids
+++ b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
@@ -26,7 +26,6 @@ success = True
 
 for nproc in [1, 2, 4]:
     for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]:
-
         # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver)
         cmd = "./test_naulin_laplace -f " + inputfile + " NXPE=" + str(nproc)
 
diff --git a/tests/integrated/test-naulin-laplace/runtest_unsheared b/tests/integrated/test-naulin-laplace/runtest_unsheared
index ec956686ef..8f47f33026 100755
--- a/tests/integrated/test-naulin-laplace/runtest_unsheared
+++ b/tests/integrated/test-naulin-laplace/runtest_unsheared
@@ -25,7 +25,6 @@ print("Running LaplaceNaulin inversion test")
 success = True
 
 for nproc in [1, 3]:
-
     # Make sure we don't use too many cores:
     # Reduce number of OpenMP threads when using multiple MPI processes
     mthread = 2
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/runtest b/tests/integrated/test-petsc_laplace_MAST-grid/runtest
index c1c973e3b2..bf6656fbf2 100755
--- a/tests/integrated/test-petsc_laplace_MAST-grid/runtest
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/runtest
@@ -43,7 +43,6 @@ for nproc in [1, 2, 4]:
     #  if nproc > 2:
     #    nxpe = 2
     for jy in [2, 34, 65, 81, 113]:
-
         cmd = (
             "./test_petsc_laplace_MAST_grid grid=grids/grid_MAST_SOL_jyis{}.nc".format(
                 jy
diff --git a/tests/integrated/test-twistshift-staggered/runtest b/tests/integrated/test-twistshift-staggered/runtest
index 2976a80ecd..5bb9963db7 100755
--- a/tests/integrated/test-twistshift-staggered/runtest
+++ b/tests/integrated/test-twistshift-staggered/runtest
@@ -24,6 +24,7 @@ check = collect("check", path=datapath, yguards=True, info=False)
 
 success = True
 
+
 # Check test_aligned is *not* periodic in y
 def test1(ylower, yupper):
     global success
diff --git a/tests/integrated/test-twistshift/runtest b/tests/integrated/test-twistshift/runtest
index 26b5c2b135..c4858970c4 100755
--- a/tests/integrated/test-twistshift/runtest
+++ b/tests/integrated/test-twistshift/runtest
@@ -24,6 +24,7 @@ result = collect("result", path=datapath, yguards=True, info=False)
 
 success = True
 
+
 # Check test_aligned is *not* periodic in y
 def test1(ylower, yupper):
     global success
@@ -49,6 +50,7 @@ if numpy.any(numpy.abs(result - test) > tol):
     print("Fail - result has not been communicated correctly - is different from input")
     success = False
 
+
 # Check result is periodic in y
 def test2(ylower, yupper):
     global success
diff --git a/tests/integrated/test-yupdown-weights/runtest b/tests/integrated/test-yupdown-weights/runtest
index e40b81368f..4b59d08cb0 100755
--- a/tests/integrated/test-yupdown-weights/runtest
+++ b/tests/integrated/test-yupdown-weights/runtest
@@ -10,7 +10,6 @@ build_and_log("parallel slices and weights test")
 
 failed = False
 for shifttype in ["shiftedinterp"]:
-
     s, out = launch_safe(
         "./test_yupdown_weights mesh:paralleltransform:type=" + shifttype,
         nproc=1,
diff --git a/tests/integrated/test-yupdown/runtest b/tests/integrated/test-yupdown/runtest
index 1b24f86327..34fcd36496 100755
--- a/tests/integrated/test-yupdown/runtest
+++ b/tests/integrated/test-yupdown/runtest
@@ -12,7 +12,6 @@ build_and_log("parallel slices test")
 failed = False
 
 for shifttype in ["shifted", "shiftedinterp"]:
-
     s, out = launch_safe(
         "./test_yupdown mesh:paralleltransform:type=" + shifttype,
         nproc=1,
diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite
index e6012e3869..307a8d84b3 100755
--- a/tests/integrated/test_suite
+++ b/tests/integrated/test_suite
@@ -241,6 +241,7 @@ if args.get_list:
             print(test)
     sys.exit(0)
 
+
 # A function to get more threads from the job server
 def get_threads():
     global js_read
diff --git a/tools/pylib/post_bout/__init__.py b/tools/pylib/post_bout/__init__.py
index a06792ed41..069ae3e85b 100644
--- a/tools/pylib/post_bout/__init__.py
+++ b/tools/pylib/post_bout/__init__.py
@@ -15,7 +15,6 @@
 import os
 
 try:
-
     boutpath = os.environ["BOUT_TOP"]
     pylibpath = boutpath + "/tools/pylib"
     boutdatapath = pylibpath + "/boutdata"
diff --git a/tools/pylib/post_bout/basic_info.py b/tools/pylib/post_bout/basic_info.py
index 28660c39bc..563bfe6e98 100644
--- a/tools/pylib/post_bout/basic_info.py
+++ b/tools/pylib/post_bout/basic_info.py
@@ -10,7 +10,6 @@
 
 
 def basic_info(data, meta, rescale=True, rotate=False, user_peak=0, nonlinear=None):
-
     print("in basic_info")
     # from . import read_grid,parse_inp,read_inp,show
 
@@ -227,7 +226,6 @@ def fft_info(
             jumps = np.where(abs(phase_r) > old_div(np.pi, 32))
             # print jumps
             if len(jumps[0]) != 0:
-
                 all_pts = np.array(list(range(0, nt)))
                 good_pts = (np.where(abs(phase_r) < old_div(np.pi, 3)))[0]
                 # print good_pts,good_pts
@@ -363,7 +361,6 @@ def fft_info(
 
 # return a 2d array fof boolean values, a very simple boolian filter
 def local_maxima(array2d, user_peak, index=False, count=4, floor=0, bug=False):
-
     from operator import itemgetter, attrgetter
 
     if user_peak == 0:
diff --git a/tools/pylib/post_bout/grate2.py b/tools/pylib/post_bout/grate2.py
index 58f5a47e2b..5157863cc2 100644
--- a/tools/pylib/post_bout/grate2.py
+++ b/tools/pylib/post_bout/grate2.py
@@ -13,7 +13,6 @@
 
 
 def avgrate(p, y=None, tind=None):
-
     if tind is None:
         tind = 0
 
@@ -25,7 +24,6 @@ def avgrate(p, y=None, tind=None):
     growth = np.zeros((ni, nj))
 
     with np.errstate(divide="ignore"):
-
         for i in range(ni):
             for j in range(nj):
                 growth[i, j] = np.gradient(np.log(rmsp_f[tind::, i, j]))[-1]
diff --git a/tools/pylib/post_bout/pb_corral.py b/tools/pylib/post_bout/pb_corral.py
index 412a677921..df9a9b00b6 100644
--- a/tools/pylib/post_bout/pb_corral.py
+++ b/tools/pylib/post_bout/pb_corral.py
@@ -40,7 +40,6 @@
 def corral(
     cached=True, refresh=False, debug=False, IConly=1, logname="status.log", skew=False
 ):
-
     print("in corral")
     log = read_log(logname=logname)
     # done = log['done']
@@ -53,7 +52,6 @@ def corral(
     print("current:", current)
 
     if refresh == True:
-
         for i, path in enumerate(runs):
             print(i, path)
             a = post_bout.save(path=path, IConly=IConly)  # re post-process a run
@@ -61,7 +59,6 @@ def corral(
     elif (
         cached == False
     ):  # if all the ind. simulation pkl files are in place skip this part
-
         a = post_bout.save(path=current)  # save to current dir
         # here is really where you shoudl write to status.log
         # write_log('status.log',
@@ -111,7 +108,6 @@ def islist(input):
 
 class LinRes(object):
     def __init__(self, all_modes):
-
         self.mode_db = all_modes
         self.db = all_modes
         # self.ave_db = all_ave
diff --git a/tools/pylib/post_bout/pb_draw.py b/tools/pylib/post_bout/pb_draw.py
index 75bca03a15..272aab9c35 100644
--- a/tools/pylib/post_bout/pb_draw.py
+++ b/tools/pylib/post_bout/pb_draw.py
@@ -140,7 +140,6 @@ def plottheory(
             fig1.savefig(pp, format="pdf")
             plt.close(fig1)
         else:  # if not plot its probably plotted iwth sim data, print chi somewhere
-
             for i, m in enumerate(s.models):
                 textstr = r"$\chi^2$" + "$=%.2f$" % (m.chi[comp].sum())
                 print(textstr)
@@ -173,7 +172,6 @@ def plotomega(
         trans=False,
         infobox=True,
     ):
-
         colors = [
             "b.",
             "r.",
@@ -1064,7 +1062,6 @@ def plotmodes(
         linestyle="-",
         summary=True,
     ):
-
         Nplots = self.nrun
 
         colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
@@ -1265,7 +1262,6 @@ def plotmodes(
     def plotradeigen(
         self, pp, field="Ni", comp="amp", yscale="linear", xscale="linear"
     ):
-
         Nplots = self.nrun
         colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
         fig1 = plt.figure()
@@ -1368,7 +1364,6 @@ def plotmodes2(
         xrange=1,
         debug=False,
     ):
-
         Nplots = self.nrun
         Modes = subset(self.db, "field", [field])  # pick  field
         colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
@@ -1464,7 +1459,6 @@ def plotMacroDep(
     def savemovie(
         self, field="Ni", yscale="log", xscale="log", moviename="spectrum.avi"
     ):
-
         print("Making movie animation.mpg - this make take a while")
         files = []
 
@@ -1504,7 +1498,6 @@ def savemovie(
         os.system("rm *png")
 
     def printmeta(self, pp, filename="output2.pdf", debug=False):
-
         import os
         from pyPdf import PdfFileWriter, PdfFileReader
 
diff --git a/tools/pylib/post_bout/pb_nonlinear.py b/tools/pylib/post_bout/pb_nonlinear.py
index c14072cff5..3fb726d4f8 100644
--- a/tools/pylib/post_bout/pb_nonlinear.py
+++ b/tools/pylib/post_bout/pb_nonlinear.py
@@ -46,7 +46,6 @@ def plotnlrhs(
         xscale="linear",
         xrange=1,
     ):
-
         colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
 
         Modes = subset(self.db, "field", [field])  # pick  field
diff --git a/tools/pylib/post_bout/pb_present.py b/tools/pylib/post_bout/pb_present.py
index e1fc92ea6d..64fcaf1ec6 100644
--- a/tools/pylib/post_bout/pb_present.py
+++ b/tools/pylib/post_bout/pb_present.py
@@ -96,7 +96,6 @@ def show(
         for j in list(
             set(s.dz).union()
         ):  # looping over runs, over unique 'dz' key values
-
             ss = subset(s.db, "dz", [j])  # subset where dz = j
             plt.scatter(ss.MN[:, 1], ss.MN[:, 0], c=colors[i])
             plt.annotate(str(j), (ss.MN[0, 1], ss.MN[0, 0]))
diff --git a/tools/pylib/post_bout/read_cxx.py b/tools/pylib/post_bout/read_cxx.py
index 907edc48a7..eda88aac5b 100644
--- a/tools/pylib/post_bout/read_cxx.py
+++ b/tools/pylib/post_bout/read_cxx.py
@@ -98,7 +98,6 @@ def get_evolved_cxx(cxxfile=None):
 
 
 def read_cxx(path=".", boutcxx="physics_code.cxx.ref", evolved=""):
-
     # print path, boutcxx
     boutcxx = path + "/" + boutcxx
     # boutcxx = open(boutcxx,'r').readlines()
diff --git a/tools/pylib/post_bout/read_inp.py b/tools/pylib/post_bout/read_inp.py
index 40a60774af..87de7ddf3a 100644
--- a/tools/pylib/post_bout/read_inp.py
+++ b/tools/pylib/post_bout/read_inp.py
@@ -12,7 +12,6 @@
 
 
 def read_inp(path="", boutinp="BOUT.inp"):
-
     boutfile = path + "/" + boutinp
     boutinp = open(boutfile, "r").readlines()
 
@@ -29,7 +28,6 @@ def read_inp(path="", boutinp="BOUT.inp"):
 
 
 def parse_inp(boutlist):
-
     import re
     from ordereddict import OrderedDict
 
@@ -67,7 +65,6 @@ def parse_inp(boutlist):
 
 
 def read_log(path=".", logname="status.log"):
-
     print("in read_log")
     import re
     from ordereddict import OrderedDict
diff --git a/tools/pylib/post_bout/rms.py b/tools/pylib/post_bout/rms.py
index 9ec23d9f90..6a9bdb1929 100644
--- a/tools/pylib/post_bout/rms.py
+++ b/tools/pylib/post_bout/rms.py
@@ -14,7 +14,6 @@
 
 
 def rms(f):
-
     nt = f.shape[0]
 
     ns = f.shape[1]
diff --git a/tools/tokamak_grids/elite/elite2nc b/tools/tokamak_grids/elite/elite2nc
index eb17c13bd9..669c36aef9 100755
--- a/tools/tokamak_grids/elite/elite2nc
+++ b/tools/tokamak_grids/elite/elite2nc
@@ -57,6 +57,7 @@ if not desc:
 
 print("Description: " + desc)
 
+
 # Define a generator to get the next token from the file
 def file_tokens(fp):
     toklist = []
diff --git a/tools/tokamak_grids/gato/gato2nc b/tools/tokamak_grids/gato/gato2nc
index ba4cdc6e69..4ed2b2d632 100755
--- a/tools/tokamak_grids/gato/gato2nc
+++ b/tools/tokamak_grids/gato/gato2nc
@@ -68,6 +68,7 @@ print("Date: " + date)
 desc = f.readline()
 print("Description: " + desc)
 
+
 # Define a generator to get the next token from the file
 def file_tokens(fp):
     """Generator to get numbers from a text file"""

From a088700cd86a4a1244a9159b0f15dd4f62fa40da Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Wed, 8 Feb 2023 10:19:40 +0000
Subject: [PATCH 0022/1827] Apply clang-format changes

---
 include/interpolation_xz.hxx                  |  21 ++-
 include/mask.hxx                              |   3 +-
 src/mesh/interpolation/hermite_spline_xz.cxx  |  84 +++++-----
 src/mesh/parallel/fci.cxx                     |  12 +-
 tests/integrated/test-fci-mpi/fci_mpi.cxx     |  27 ++--
 .../test-interpolate/test_interpolate.cxx     | 146 +++++++++---------
 6 files changed, 147 insertions(+), 146 deletions(-)

diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx
index 620d146edf..df4c7fc61a 100644
--- a/include/interpolation_xz.hxx
+++ b/include/interpolation_xz.hxx
@@ -63,25 +63,23 @@ public:
     setMask(mask);
   }
   XZInterpolation(const std::string& region_name, int y_offset = 0, Mesh* mesh = nullptr)
-    : y_offset(y_offset), localmesh(mesh), region_id(localmesh->getRegionID(region_name)) {}
-  XZInterpolation(const Region<Ind3D>& region, int y_offset = 0,
-                  Mesh* mesh = nullptr)
-      : y_offset(y_offset), localmesh(mesh){
+      : y_offset(y_offset), localmesh(mesh),
+        region_id(localmesh->getRegionID(region_name)) {}
+  XZInterpolation(const Region<Ind3D>& region, int y_offset = 0, Mesh* mesh = nullptr)
+      : y_offset(y_offset), localmesh(mesh) {
     setRegion(region);
   }
   virtual ~XZInterpolation() = default;
 
-  void setMask(const BoutMask& mask) {
-    setRegion(regionFromMask(mask, localmesh));
-  }
+  void setMask(const BoutMask& mask) { setRegion(regionFromMask(mask, localmesh)); }
   void setRegion(const std::string& region_name) {
     this->region_id = localmesh->getRegionID(region_name);
   }
   void setRegion(const Region<Ind3D>& region) {
     std::string name;
-    int i=0;
+    int i = 0;
     do {
-      name = fmt::format("unsec_reg_xz_interp_{:d}",i++);
+      name = fmt::format("unsec_reg_xz_interp_{:d}", i++);
     } while (localmesh->hasRegion3D(name));
     localmesh->addRegion(name, region);
     this->region_id = localmesh->getRegionID(name);
@@ -94,10 +92,11 @@ public:
     if (region_id == -1) {
       return localmesh->getRegion(region);
     }
-    if (region == "" or region == "RGN_ALL"){
+    if (region == "" or region == "RGN_ALL") {
       return getRegion();
     }
-    return localmesh->getRegion(localmesh->getCommonRegion(localmesh->getRegionID(region), region_id));
+    return localmesh->getRegion(
+        localmesh->getCommonRegion(localmesh->getRegionID(region), region_id));
   }
   virtual void calcWeights(const Field3D& delta_x, const Field3D& delta_z,
                            const std::string& region = "RGN_NOBNDRY") = 0;
diff --git a/include/mask.hxx b/include/mask.hxx
index 96d2c99ac3..20211b5d02 100644
--- a/include/mask.hxx
+++ b/include/mask.hxx
@@ -73,8 +73,7 @@ public:
   inline const bool& operator[](const Ind3D& i) const { return mask[i]; }
 };
 
-inline Region<Ind3D> regionFromMask(const BoutMask& mask,
-                                                     const Mesh* mesh) {
+inline Region<Ind3D> regionFromMask(const BoutMask& mask, const Mesh* mesh) {
   std::vector<Ind3D> indices;
   for (auto i : mesh->getRegion("RGN_ALL")) {
     if (not mask(i.x(), i.y(), i.z())) {
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 4e6fc8320c..a5b9c8bd05 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -20,10 +20,10 @@
  *
  **************************************************************************/
 
+#include "../impls/bout/boutmesh.hxx"
 #include "globals.hxx"
 #include "interpolation_xz.hxx"
 #include "bout/index_derivs_interface.hxx"
-#include "../impls/bout/boutmesh.hxx"
 
 #include <vector>
 
@@ -126,7 +126,7 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
 
 #if USE_NEW_WEIGHTS
   newWeights.reserve(16);
-  for (int w=0; w<16;++w){
+  for (int w = 0; w < 16; ++w) {
     newWeights.emplace_back(localmesh);
     newWeights[w].allocate();
   }
@@ -137,8 +137,9 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
   // MatCreate(MPI_COMM_WORLD, &petscWeights);
   //  MatSetSizes(petscWeights, m, m, M, M);
   // PetscErrorCode MatCreateAIJ(MPI_Comm comm, PetscInt m, PetscInt n, PetscInt M,
-  // PetscInt N, 			      PetscInt d_nz, const PetscInt d_nnz[], PetscInt o_nz, const PetscInt
-  //o_nnz[], Mat *A)
+  // PetscInt N, 			      PetscInt d_nz, const PetscInt d_nnz[], PetscInt o_nz,
+  // const PetscInt
+  // o_nnz[], Mat *A)
   //  MatSetSizes(Mat A,PetscInt m,PetscInt n,PetscInt M,PetscInt N)
   const int m = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz;
   const int M = m * mesh->getNXPE() * mesh->getNYPE();
@@ -185,8 +186,8 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     // Check that t_x and t_z are in range
     if ((t_x < 0.0) || (t_x > 1.0)) {
       throw BoutException(
-          "t_x={:e} out of range at ({:d},{:d},{:d}) (delta_x={:e}, i_corn={:d})", t_x,
-          x, y, z, delta_x(x, y, z), i_corn);
+          "t_x={:e} out of range at ({:d},{:d},{:d}) (delta_x={:e}, i_corn={:d})", t_x, x,
+          y, z, delta_x(x, y, z), i_corn);
     }
 
     if ((t_z < 0.0) || (t_z > 1.0)) {
@@ -212,8 +213,8 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
 
 #if USE_NEW_WEIGHTS
 
-    for (int w =0; w<16;++w){
-      newWeights[w][i]=0;
+    for (int w = 0; w < 16; ++w) {
+      newWeights[w][i] = 0;
     }
     // The distribution of our weights:
     //  0   4   8    12
@@ -223,54 +224,55 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     // e.g. 1 == ic.xm(); 4 == ic.zm(); 5 == ic;  7 == ic.zp(2);
 
     // f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
-    newWeights[5][i]  += h00_x[i] * h00_z[i];
-    newWeights[9][i]  += h01_x[i] * h00_z[i];
-    newWeights[9][i]  += h10_x[i] * h00_z[i] / 2;
-    newWeights[1][i]  -= h10_x[i] * h00_z[i] / 2;
+    newWeights[5][i] += h00_x[i] * h00_z[i];
+    newWeights[9][i] += h01_x[i] * h00_z[i];
+    newWeights[9][i] += h10_x[i] * h00_z[i] / 2;
+    newWeights[1][i] -= h10_x[i] * h00_z[i] / 2;
     newWeights[13][i] += h11_x[i] * h00_z[i] / 2;
-    newWeights[5][i]  -= h11_x[i] * h00_z[i] / 2;
+    newWeights[5][i] -= h11_x[i] * h00_z[i] / 2;
 
     // f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] +
     // fx[iczp] * h10_x[i] + fx[icxpzp] * h11_x[i];
-    newWeights[6][i]  += h00_x[i] * h01_z[i];
+    newWeights[6][i] += h00_x[i] * h01_z[i];
     newWeights[10][i] += h01_x[i] * h01_z[i];
     newWeights[10][i] += h10_x[i] * h01_z[i] / 2;
-    newWeights[2][i]  -= h10_x[i] * h01_z[i] / 2;
+    newWeights[2][i] -= h10_x[i] * h01_z[i] / 2;
     newWeights[14][i] += h11_x[i] * h01_z[i] / 2;
-    newWeights[6][i]  -= h11_x[i] * h01_z[i] / 2;
+    newWeights[6][i] -= h11_x[i] * h01_z[i] / 2;
 
     // fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] +
     // fxz[ic] * h10_x[i]+ fxz[icxp] * h11_x[i];
-    newWeights[6][i]  += h00_x[i] * h10_z[i] / 2;
-    newWeights[4][i]  -= h00_x[i] * h10_z[i] / 2;
+    newWeights[6][i] += h00_x[i] * h10_z[i] / 2;
+    newWeights[4][i] -= h00_x[i] * h10_z[i] / 2;
     newWeights[10][i] += h01_x[i] * h10_z[i] / 2;
-    newWeights[8][i]  -= h01_x[i] * h10_z[i] / 2;
+    newWeights[8][i] -= h01_x[i] * h10_z[i] / 2;
     newWeights[10][i] += h10_x[i] * h10_z[i] / 4;
-    newWeights[8][i]  -= h10_x[i] * h10_z[i] / 4;
-    newWeights[2][i]  -= h10_x[i] * h10_z[i] / 4;
-    newWeights[0][i]  += h10_x[i] * h10_z[i] / 4;
+    newWeights[8][i] -= h10_x[i] * h10_z[i] / 4;
+    newWeights[2][i] -= h10_x[i] * h10_z[i] / 4;
+    newWeights[0][i] += h10_x[i] * h10_z[i] / 4;
     newWeights[14][i] += h11_x[i] * h10_z[i] / 4;
     newWeights[12][i] -= h11_x[i] * h10_z[i] / 4;
-    newWeights[6][i]  -= h11_x[i] * h10_z[i] / 4;
-    newWeights[4][i]  += h11_x[i] * h10_z[i] / 4;
+    newWeights[6][i] -= h11_x[i] * h10_z[i] / 4;
+    newWeights[4][i] += h11_x[i] * h10_z[i] / 4;
 
     // fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i] +
     // fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
-    newWeights[7][i]  += h00_x[i] * h11_z[i] / 2;
-    newWeights[5][i]  -= h00_x[i] * h11_z[i] / 2;
+    newWeights[7][i] += h00_x[i] * h11_z[i] / 2;
+    newWeights[5][i] -= h00_x[i] * h11_z[i] / 2;
     newWeights[11][i] += h01_x[i] * h11_z[i] / 2;
-    newWeights[9][i]  -= h01_x[i] * h11_z[i] / 2;
+    newWeights[9][i] -= h01_x[i] * h11_z[i] / 2;
     newWeights[11][i] += h10_x[i] * h11_z[i] / 4;
-    newWeights[9][i]  -= h10_x[i] * h11_z[i] / 4;
-    newWeights[3][i]  -= h10_x[i] * h11_z[i] / 4;
-    newWeights[1][i]  += h10_x[i] * h11_z[i] / 4;
+    newWeights[9][i] -= h10_x[i] * h11_z[i] / 4;
+    newWeights[3][i] -= h10_x[i] * h11_z[i] / 4;
+    newWeights[1][i] += h10_x[i] * h11_z[i] / 4;
     newWeights[15][i] += h11_x[i] * h11_z[i] / 4;
     newWeights[13][i] -= h11_x[i] * h11_z[i] / 4;
-    newWeights[7][i]  -= h11_x[i] * h11_z[i] / 4;
-    newWeights[5][i]  += h11_x[i] * h11_z[i] / 4;
+    newWeights[7][i] -= h11_x[i] * h11_z[i] / 4;
+    newWeights[5][i] += h11_x[i] * h11_z[i] / 4;
 #ifdef HS_USE_PETSC
     PetscInt idxn[1] = {conv.fromLocalToGlobal(x, y + y_offset, z)};
-    // output.write("debug: {:d} -> {:d}: {:d}:{:d} -> {:d}:{:d}\n", conv.fromLocalToGlobal(x, y + y_offset, z),
+    // output.write("debug: {:d} -> {:d}: {:d}:{:d} -> {:d}:{:d}\n",
+    // conv.fromLocalToGlobal(x, y + y_offset, z),
     //     conv.fromMeshToGlobal(i_corn, y + y_offset, k_corner(x, y, z)),
     //     x, z, i_corn, k_corner(x, y, z));
     // ixstep = mesh->LocalNx * mesh->LocalNz;
@@ -355,15 +357,15 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   VecRestoreArrayRead(result, &cptr);
 #else
   BOUT_FOR(i, getRegion(region)) {
-    auto ic =  i_corner[i];
+    auto ic = i_corner[i];
     auto iyp = i.yp(y_offset);
 
-    f_interp[iyp]=0;
-    for (int w = 0; w < 4; ++w){
-      f_interp[iyp] += newWeights[w*4+0][i] * f[ic.zm().xp(w-1)];
-      f_interp[iyp] += newWeights[w*4+1][i] * f[ic.xp(w-1)];
-      f_interp[iyp] += newWeights[w*4+2][i] * f[ic.zp().xp(w-1)];
-      f_interp[iyp] += newWeights[w*4+3][i] * f[ic.zp(2).xp(w-1)];
+    f_interp[iyp] = 0;
+    for (int w = 0; w < 4; ++w) {
+      f_interp[iyp] += newWeights[w * 4 + 0][i] * f[ic.zm().xp(w - 1)];
+      f_interp[iyp] += newWeights[w * 4 + 1][i] * f[ic.xp(w - 1)];
+      f_interp[iyp] += newWeights[w * 4 + 2][i] * f[ic.zp().xp(w - 1)];
+      f_interp[iyp] += newWeights[w * 4 + 3][i] * f[ic.zp(2).xp(w - 1)];
     }
   }
 #endif
@@ -411,7 +413,7 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
             || i.x() > localmesh->xend);
   }
   return f_interp;
-# endif
+#endif
 }
 
 Field3D XZHermiteSpline::interpolate(const Field3D& f, const Field3D& delta_x,
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index baf0f3fc6b..4b964ae0fa 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -158,7 +158,8 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
   const int ncz = map_mesh.LocalNz;
 
   BoutMask to_remove(map_mesh);
-  const int xend = map_mesh.xstart + (map_mesh.xend - map_mesh.xstart + 1) * map_mesh.getNXPE() - 1;
+  const int xend =
+      map_mesh.xstart + (map_mesh.xend - map_mesh.xstart + 1) * map_mesh.getNXPE() - 1;
   // Serial loop because call to BoundaryRegionPar::addPoint
   // (probably?) can't be done in parallel
   BOUT_FOR_SERIAL(i, xt_prime.getRegion("RGN_NOBNDRY")) {
@@ -247,11 +248,10 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
   const auto region = fmt::format("RGN_YPAR_{:+d}", offset);
   if (not map_mesh.hasRegion3D(region)) {
     // The valid region for this slice
-    map_mesh.addRegion3D(region,
-			 Region<Ind3D>(map_mesh.xstart, map_mesh.xend,
-				       map_mesh.ystart+offset, map_mesh.yend+offset,
-				       0, map_mesh.LocalNz-1,
-				       map_mesh.LocalNy, map_mesh.LocalNz));
+    map_mesh.addRegion3D(
+        region, Region<Ind3D>(map_mesh.xstart, map_mesh.xend, map_mesh.ystart + offset,
+                              map_mesh.yend + offset, 0, map_mesh.LocalNz - 1,
+                              map_mesh.LocalNy, map_mesh.LocalNz));
   }
 }
 
diff --git a/tests/integrated/test-fci-mpi/fci_mpi.cxx b/tests/integrated/test-fci-mpi/fci_mpi.cxx
index b353493dda..6ae711351e 100644
--- a/tests/integrated/test-fci-mpi/fci_mpi.cxx
+++ b/tests/integrated/test-fci-mpi/fci_mpi.cxx
@@ -6,28 +6,29 @@ int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
   {
     using bout::globals::mesh;
-    Options *options = Options::getRoot();
-    int i=0;
-    std::string default_str {"not_set"};
+    Options* options = Options::getRoot();
+    int i = 0;
+    std::string default_str{"not_set"};
     Options dump;
     while (true) {
       std::string temp_str;
       options->get(fmt::format("input_{:d}:function", i), temp_str, default_str);
       if (temp_str == default_str) {
-	break;
+        break;
       }
-      Field3D input{FieldFactory::get()->create3D(fmt::format("input_{:d}:function", i), Options::getRoot(), mesh)};
-      //options->get(fmt::format("input_{:d}:boundary_perp", i), temp_str, s"free_o3");
+      Field3D input{FieldFactory::get()->create3D(fmt::format("input_{:d}:function", i),
+                                                  Options::getRoot(), mesh)};
+      // options->get(fmt::format("input_{:d}:boundary_perp", i), temp_str, s"free_o3");
       mesh->communicate(input);
       input.applyParallelBoundary("parallel_neumann_o2");
       for (int slice = -mesh->ystart; slice <= mesh->ystart; ++slice) {
-	if (slice) {
-	  Field3D tmp{0.};
-	  BOUT_FOR(i, tmp.getRegion("RGN_NOBNDRY")) {
-	    tmp[i] = input.ynext(slice)[i.yp(slice)];
-	  }
-	  dump[fmt::format("output_{:d}_{:+d}", i, slice)] = tmp;
-	}
+        if (slice) {
+          Field3D tmp{0.};
+          BOUT_FOR(i, tmp.getRegion("RGN_NOBNDRY")) {
+            tmp[i] = input.ynext(slice)[i.yp(slice)];
+          }
+          dump[fmt::format("output_{:d}_{:+d}", i, slice)] = tmp;
+        }
       }
       ++i;
     }
diff --git a/tests/integrated/test-interpolate/test_interpolate.cxx b/tests/integrated/test-interpolate/test_interpolate.cxx
index 517d9c2445..a14208e7b3 100644
--- a/tests/integrated/test-interpolate/test_interpolate.cxx
+++ b/tests/integrated/test-interpolate/test_interpolate.cxx
@@ -31,88 +31,88 @@ std::shared_ptr<FieldGenerator> getGeneratorFromOptions(const std::string& varna
 int main(int argc, char **argv) {
   BoutInitialise(argc, argv);
   {
-  // Random number generator
-  std::default_random_engine generator;
-  // Uniform distribution of BoutReals from 0 to 1
-  std::uniform_real_distribution<BoutReal> distribution{0.0, 1.0};
-
-  using bout::globals::mesh;
-
-  FieldFactory f(mesh);
-
-  // Set up generators and solutions for three different analtyic functions
-  std::string a_func;
-  auto a_gen = getGeneratorFromOptions("a", a_func);
-  Field3D a = f.create3D(a_func);
-  Field3D a_solution = 0.0;
-  Field3D a_interp = 0.0;
-
-  std::string b_func;
-  auto b_gen = getGeneratorFromOptions("b", b_func);
-  Field3D b = f.create3D(b_func);
-  Field3D b_solution = 0.0;
-  Field3D b_interp = 0.0;
-
-  std::string c_func;
-  auto c_gen = getGeneratorFromOptions("c", c_func);
-  Field3D c = f.create3D(c_func);
-  Field3D c_solution = 0.0;
-  Field3D c_interp = 0.0;
-
-  // x and z displacements
-  Field3D deltax = 0.0;
-  Field3D deltaz = 0.0;
-
-  // Bind the random number generator and distribution into a single function
-  auto dice = std::bind(distribution, generator);
-
-  for (const auto &index : deltax) {
-    // Get some random displacements
-    BoutReal dx = index.x() + dice();
-    BoutReal dz = index.z() + dice();
-    // For the last point, put the displacement inwards
-    // Otherwise we try to interpolate in the guard cells, which doesn't work so well
-    if (index.x() >= mesh->xend && mesh->getNXPE() - 1 == mesh->getXProcIndex()) {
-      dx = index.x() - dice();
+    // Random number generator
+    std::default_random_engine generator;
+    // Uniform distribution of BoutReals from 0 to 1
+    std::uniform_real_distribution<BoutReal> distribution{0.0, 1.0};
+
+    using bout::globals::mesh;
+
+    FieldFactory f(mesh);
+
+    // Set up generators and solutions for three different analtyic functions
+    std::string a_func;
+    auto a_gen = getGeneratorFromOptions("a", a_func);
+    Field3D a = f.create3D(a_func);
+    Field3D a_solution = 0.0;
+    Field3D a_interp = 0.0;
+
+    std::string b_func;
+    auto b_gen = getGeneratorFromOptions("b", b_func);
+    Field3D b = f.create3D(b_func);
+    Field3D b_solution = 0.0;
+    Field3D b_interp = 0.0;
+
+    std::string c_func;
+    auto c_gen = getGeneratorFromOptions("c", c_func);
+    Field3D c = f.create3D(c_func);
+    Field3D c_solution = 0.0;
+    Field3D c_interp = 0.0;
+
+    // x and z displacements
+    Field3D deltax = 0.0;
+    Field3D deltaz = 0.0;
+
+    // Bind the random number generator and distribution into a single function
+    auto dice = std::bind(distribution, generator);
+
+    for (const auto& index : deltax) {
+      // Get some random displacements
+      BoutReal dx = index.x() + dice();
+      BoutReal dz = index.z() + dice();
+      // For the last point, put the displacement inwards
+      // Otherwise we try to interpolate in the guard cells, which doesn't work so well
+      if (index.x() >= mesh->xend && mesh->getNXPE() - 1 == mesh->getXProcIndex()) {
+        dx = index.x() - dice();
+      }
+      deltax[index] = dx;
+      deltaz[index] = dz;
+      // Get the global indices
+      bout::generator::Context pos{index, CELL_CENTRE, deltax.getMesh(), 0.0};
+      pos.set("x", mesh->GlobalX(dx), "z",
+              TWOPI * static_cast<BoutReal>(dz) / static_cast<BoutReal>(mesh->LocalNz));
+      // Generate the analytic solution at the displacements
+      a_solution[index] = a_gen->generate(pos);
+      b_solution[index] = b_gen->generate(pos);
+      c_solution[index] = c_gen->generate(pos);
     }
-    deltax[index] = dx;
-    deltaz[index] = dz;
-    // Get the global indices
-    bout::generator::Context pos{index, CELL_CENTRE, deltax.getMesh(), 0.0};
-    pos.set("x", mesh->GlobalX(dx),
-            "z", TWOPI * static_cast<BoutReal>(dz) / static_cast<BoutReal>(mesh->LocalNz));
-    // Generate the analytic solution at the displacements
-    a_solution[index] = a_gen->generate(pos);
-    b_solution[index] = b_gen->generate(pos);
-    c_solution[index] = c_gen->generate(pos);
-  }
 
-  deltax += (mesh->LocalNx - mesh->xstart * 2) * mesh->getXProcIndex();
-  // Create the interpolation object from the input options
-  auto interp = XZInterpolationFactory::getInstance().create();
+    deltax += (mesh->LocalNx - mesh->xstart * 2) * mesh->getXProcIndex();
+    // Create the interpolation object from the input options
+    auto interp = XZInterpolationFactory::getInstance().create();
 
-  // Interpolate the analytic functions at the displacements
-  a_interp = interp->interpolate(a, deltax, deltaz);
-  b_interp = interp->interpolate(b, deltax, deltaz);
-  c_interp = interp->interpolate(c, deltax, deltaz);
+    // Interpolate the analytic functions at the displacements
+    a_interp = interp->interpolate(a, deltax, deltaz);
+    b_interp = interp->interpolate(b, deltax, deltaz);
+    c_interp = interp->interpolate(c, deltax, deltaz);
 
-  Options dump;
+    Options dump;
 
-  dump["a"] = a;
-  dump["a_interp"] = a_interp;
-  dump["a_solution"] = a_solution;
+    dump["a"] = a;
+    dump["a_interp"] = a_interp;
+    dump["a_solution"] = a_solution;
 
-  dump["b"] = b;
-  dump["b_interp"] = b_interp;
-  dump["b_solution"] = b_solution;
+    dump["b"] = b;
+    dump["b_interp"] = b_interp;
+    dump["b_solution"] = b_solution;
 
-  dump["c"] = c;
-  dump["c_interp"] = c_interp;
-  dump["c_solution"] = c_solution;
+    dump["c"] = c;
+    dump["c_interp"] = c_interp;
+    dump["c_solution"] = c_solution;
 
-  bout::writeDefaultOutputFile(dump);
+    bout::writeDefaultOutputFile(dump);
 
-  bout::checkForUnusedOptions();
+    bout::checkForUnusedOptions();
   }
   BoutFinalise();
 

From 32ea2fdcf7a10efb86e9c8541d6dcb47aaa1f538 Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Wed, 8 Feb 2023 13:10:31 +0000
Subject: [PATCH 0023/1827] Apply clang-format changes

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index a5b9c8bd05..2d1649a7c1 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -137,9 +137,8 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
   // MatCreate(MPI_COMM_WORLD, &petscWeights);
   //  MatSetSizes(petscWeights, m, m, M, M);
   // PetscErrorCode MatCreateAIJ(MPI_Comm comm, PetscInt m, PetscInt n, PetscInt M,
-  // PetscInt N, 			      PetscInt d_nz, const PetscInt d_nnz[], PetscInt o_nz,
-  // const PetscInt
-  // o_nnz[], Mat *A)
+  // PetscInt N, 			      PetscInt d_nz, const PetscInt d_nnz[], PetscInt
+  // o_nz, const PetscInt o_nnz[], Mat *A)
   //  MatSetSizes(Mat A,PetscInt m,PetscInt n,PetscInt M,PetscInt N)
   const int m = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz;
   const int M = m * mesh->getNXPE() * mesh->getNYPE();

From faac69c321c957d542b7631e900d34e690238f02 Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Wed, 8 Feb 2023 13:10:52 +0000
Subject: [PATCH 0024/1827] Apply clang-format changes

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 2d1649a7c1..93f1c326e8 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -137,8 +137,8 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
   // MatCreate(MPI_COMM_WORLD, &petscWeights);
   //  MatSetSizes(petscWeights, m, m, M, M);
   // PetscErrorCode MatCreateAIJ(MPI_Comm comm, PetscInt m, PetscInt n, PetscInt M,
-  // PetscInt N, 			      PetscInt d_nz, const PetscInt d_nnz[], PetscInt
-  // o_nz, const PetscInt o_nnz[], Mat *A)
+  // PetscInt N, 			      PetscInt d_nz, const PetscInt d_nnz[],
+  // PetscInt o_nz, const PetscInt o_nnz[], Mat *A)
   //  MatSetSizes(Mat A,PetscInt m,PetscInt n,PetscInt M,PetscInt N)
   const int m = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz;
   const int M = m * mesh->getNXPE() * mesh->getNYPE();

From cc1672d1b9e28af98089fcdff59d6c2f8aa8594d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 14 Jun 2023 12:06:27 -0700
Subject: [PATCH 0025/1827] Add Array<int> to Options

Enable 1D arrays of integers to be read from NetCDF files,
and made available via `Mesh::get()`. Mainly useful for
mesh construction.
---
 include/bout/options.hxx           |  6 +++++-
 include/bout/utils.hxx             |  4 ++--
 src/mesh/data/gridfromfile.cxx     | 20 +++++++++++++------
 src/sys/options.cxx                | 31 ++++++++++++++++++++++++++++++
 src/sys/options/options_netcdf.cxx |  4 ++++
 5 files changed, 56 insertions(+), 9 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index bf1704100f..fae05b8ecc 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -196,7 +196,7 @@ public:
   /// The type used to store values
   using ValueType =
       bout::utils::variant<bool, int, BoutReal, std::string, Field2D, Field3D, FieldPerp,
-                           Array<BoutReal>, Matrix<BoutReal>, Tensor<BoutReal>>;
+                           Array<BoutReal>, Array<int>, Matrix<BoutReal>, Tensor<BoutReal>>;
 
   /// The type used to store attributes
   /// Extends the variant class so that cast operator can be implemented
@@ -874,6 +874,8 @@ void Options::assign<>(FieldPerp val, std::string source);
 template <>
 void Options::assign<>(Array<BoutReal> val, std::string source);
 template <>
+void Options::assign<>(Array<int> val, std::string source);
+template <>
 void Options::assign<>(Matrix<BoutReal> val, std::string source);
 template <>
 void Options::assign<>(Tensor<BoutReal> val, std::string source);
@@ -902,6 +904,8 @@ FieldPerp Options::as<FieldPerp>(const FieldPerp& similar_to) const;
 template <>
 Array<BoutReal> Options::as<Array<BoutReal>>(const Array<BoutReal>& similar_to) const;
 template <>
+Array<int> Options::as<Array<int>>(const Array<int>& similar_to) const;
+template <>
 Matrix<BoutReal> Options::as<Matrix<BoutReal>>(const Matrix<BoutReal>& similar_to) const;
 template <>
 Tensor<BoutReal> Options::as<Tensor<BoutReal>>(const Tensor<BoutReal>& similar_to) const;
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 450d3eaf87..e2ec5b24db 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -543,8 +543,8 @@ std::string toString(const T& val) {
 /// where the type may be std::string.
 inline std::string toString(const std::string& val) { return val; }
 
-template <>
-inline std::string toString<>(const Array<BoutReal>& UNUSED(val)) {
+template <typename T>
+inline std::string toString(const Array<T>& UNUSED(val)) {
   return "<Array>";
 }
 
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 7e875bd109..7fab486e54 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -138,7 +138,8 @@ struct GetDimensions {
   std::vector<int> operator()(MAYBE_UNUSED(int value)) { return {1}; }
   std::vector<int> operator()(MAYBE_UNUSED(BoutReal value)) { return {1}; }
   std::vector<int> operator()(MAYBE_UNUSED(const std::string& value)) { return {1}; }
-  std::vector<int> operator()(const Array<BoutReal>& array) { return {array.size()}; }
+  template<typename T>
+  std::vector<int> operator()(const Array<T>& array) { return {array.size()}; }
   std::vector<int> operator()(const Matrix<BoutReal>& array) {
     const auto shape = array.shape();
     return {std::get<0>(shape), std::get<1>(shape)};
@@ -471,13 +472,20 @@ void GridFile::readField(Mesh* m, const std::string& name, int UNUSED(ys), int U
   }
 }
 
-bool GridFile::get(MAYBE_UNUSED(Mesh* m), MAYBE_UNUSED(std::vector<int>& var),
-                   MAYBE_UNUSED(const std::string& name), MAYBE_UNUSED(int len),
-                   MAYBE_UNUSED(int offset),
-                   MAYBE_UNUSED(GridDataSource::Direction dir)) {
+bool GridFile::get(Mesh* UNUSED(m), std::vector<int>& var, const std::string& name,
+                   int len, int offset, GridDataSource::Direction UNUSED(dir)) {
   TRACE("GridFile::get(vector<int>)");
 
-  return false;
+  if (not data.isSet(name)) {
+    return false;
+  }
+
+  const auto full_var = data[name].as<Array<int>>();
+  const auto* it = std::begin(full_var);
+  std::advance(it, offset);
+  std::copy_n(it, len, std::begin(var));
+
+  return true;
 }
 
 bool GridFile::get(Mesh* UNUSED(m), std::vector<BoutReal>& var, const std::string& name,
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 8b49b1f3f1..fec4073682 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -288,6 +288,10 @@ void Options::assign<>(Array<BoutReal> val, std::string source) {
   _set_no_check(std::move(val), std::move(source));
 }
 template <>
+void Options::assign<>(Array<int> val, std::string source) {
+  _set_no_check(std::move(val), std::move(source));
+}
+template <>
 void Options::assign<>(Matrix<BoutReal> val, std::string source) {
   _set_no_check(std::move(val), std::move(source));
 }
@@ -723,6 +727,33 @@ Array<BoutReal> Options::as<Array<BoutReal>>(const Array<BoutReal>& similar_to)
   return result;
 }
 
+template <>
+Array<int> Options::as<Array<int>>(const Array<int>& similar_to) const {
+  if (is_section) {
+    throw BoutException(_("Option {:s} has no value"), full_name);
+  }
+
+  Array<int> result = bout::utils::visit(
+      ConvertContainer<Array<int>>{
+          fmt::format(
+              _("Value for option {:s} cannot be converted to an Array<int>"),
+              full_name),
+          similar_to},
+      value);
+
+  // Mark this option as used
+  value_used = true;
+
+  output_info << _("\tOption ") << full_name << " = Array<int>";
+  if (hasAttribute("source")) {
+    // Specify the source of the setting
+    output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
+  }
+  output_info << endl;
+
+  return result;
+}
+
 template <>
 Matrix<BoutReal> Options::as<Matrix<BoutReal>>(const Matrix<BoutReal>& similar_to) const {
   if (is_section) {
diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx
index d7ceeaea60..7c21b309bc 100644
--- a/src/sys/options/options_netcdf.cxx
+++ b/src/sys/options/options_netcdf.cxx
@@ -88,6 +88,10 @@ void readGroup(const std::string& filename, const NcGroup& group, Options& resul
         Array<double> value(static_cast<int>(dims[0].getSize()));
         var.getVar(value.begin());
         result[var_name] = value;
+      } else if (var_type == ncInt or var_type == ncShort) {
+        Array<int> value(static_cast<int>(dims[0].getSize()));
+        var.getVar(value.begin());
+        result[var_name] = value;
       } else if ((var_type == ncString) or (var_type == ncChar)) {
         std::string value;
         value.resize(dims[0].getSize());

From e654af65c6ea32a0ee4f6f07659e246ac70ac88b Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 14 Jun 2023 18:06:49 -0700
Subject: [PATCH 0026/1827] GridFile: Check sizes, allocate vector ints

When reading 1D vector of ints, check that the input is long enough,
and resize the output vector.
---
 src/mesh/data/gridfromfile.cxx | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 7fab486e54..7c02cf4ab7 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -481,6 +481,16 @@ bool GridFile::get(Mesh* UNUSED(m), std::vector<int>& var, const std::string& na
   }
 
   const auto full_var = data[name].as<Array<int>>();
+
+  // Check size
+  if (full_var.size() < len + offset) {
+    throw BoutException("{} has length {}. Expected {} elements + {} offset",
+                        name, full_var.size(), len, offset);
+  }
+
+  // Ensure that output variable has the correct size
+  var.resize(len);
+
   const auto* it = std::begin(full_var);
   std::advance(it, offset);
   std::copy_n(it, len, std::begin(var));

From 359766313a8b878f056008358192cb4653130384 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 14 Jun 2023 18:08:32 -0700
Subject: [PATCH 0027/1827] Add limiters in input mesh

A short-term fix, allowing extra limiters to be added with inputs:

limiter_count : int
limiter_yinds : [int], length limiter_count
limiter_xstarts : [int], length limiter_count
limiter_xends : [int], length limiter_count

The limiter(s) are added between yinds[i] and yinds[i] + 1
---
 src/mesh/impls/bout/boutmesh.cxx | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index a802d3f5b3..448832ea57 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -2073,6 +2073,32 @@ void BoutMesh::topology() {
     add_target(ny_inner - 1, 0, nx);
   }
 
+  // Additional limiters
+  // Each limiter needs 3 indices: A Y index, start and end X indices
+  int limiter_count = 0;
+  Mesh::get(limiter_count, "limiter_count", 0);
+  if (limiter_count > 0) {
+    std::vector<int> limiter_yinds, limiter_xstarts, limiter_xends;
+    if (!source->get(this, limiter_yinds, "limiter_yinds", limiter_count)) {
+      throw BoutException("Couldn't read limiter_yinds vector of length {} from mesh", limiter_count);
+    }
+    if (!source->get(this, limiter_xstarts, "limiter_xstarts", limiter_count)) {
+      throw BoutException("Couldn't read limiter_xstarts vector of length {} from mesh", limiter_count);
+    }
+    if (!source->get(this, limiter_xends, "limiter_xends", limiter_count)) {
+      throw BoutException("Couldn't read limiter_xend vector of length {} from mesh", limiter_count);
+    }
+
+    for (int i = 0; i < limiter_count; ++i) {
+      int yind = limiter_yinds[i];
+      int xstart = limiter_xstarts[i];
+      int xend = limiter_xends[i];
+      output_info.write("Adding a limiter between y={} and {}. X indices {} to {}\n",
+                        yind, yind+1, xstart, xend);
+      add_target(yind, xstart, xend);
+    }
+  }
+
   if ((ixseps_inner > 0)
       && (((PE_YIND * MYSUB > jyseps1_1) && (PE_YIND * MYSUB <= jyseps2_1))
           || ((PE_YIND * MYSUB > jyseps1_2) && (PE_YIND * MYSUB <= jyseps2_2)))) {

From 1c1d834c822857239efa5f8189b187845cebe073 Mon Sep 17 00:00:00 2001
From: bendudson <bendudson@users.noreply.github.com>
Date: Thu, 15 Jun 2023 01:17:21 +0000
Subject: [PATCH 0028/1827] Apply clang-format changes

---
 include/bout/options.hxx         |  6 +++---
 src/mesh/data/gridfromfile.cxx   | 10 ++++++----
 src/mesh/impls/bout/boutmesh.cxx | 11 +++++++----
 src/sys/options.cxx              |  5 ++---
 4 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index fae05b8ecc..e790b405b5 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -194,9 +194,9 @@ public:
   static void cleanup();
 
   /// The type used to store values
-  using ValueType =
-      bout::utils::variant<bool, int, BoutReal, std::string, Field2D, Field3D, FieldPerp,
-                           Array<BoutReal>, Array<int>, Matrix<BoutReal>, Tensor<BoutReal>>;
+  using ValueType = bout::utils::variant<bool, int, BoutReal, std::string, Field2D,
+                                         Field3D, FieldPerp, Array<BoutReal>, Array<int>,
+                                         Matrix<BoutReal>, Tensor<BoutReal>>;
 
   /// The type used to store attributes
   /// Extends the variant class so that cast operator can be implemented
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 7c02cf4ab7..eed70776b3 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -138,8 +138,10 @@ struct GetDimensions {
   std::vector<int> operator()(MAYBE_UNUSED(int value)) { return {1}; }
   std::vector<int> operator()(MAYBE_UNUSED(BoutReal value)) { return {1}; }
   std::vector<int> operator()(MAYBE_UNUSED(const std::string& value)) { return {1}; }
-  template<typename T>
-  std::vector<int> operator()(const Array<T>& array) { return {array.size()}; }
+  template <typename T>
+  std::vector<int> operator()(const Array<T>& array) {
+    return {array.size()};
+  }
   std::vector<int> operator()(const Matrix<BoutReal>& array) {
     const auto shape = array.shape();
     return {std::get<0>(shape), std::get<1>(shape)};
@@ -484,8 +486,8 @@ bool GridFile::get(Mesh* UNUSED(m), std::vector<int>& var, const std::string& na
 
   // Check size
   if (full_var.size() < len + offset) {
-    throw BoutException("{} has length {}. Expected {} elements + {} offset",
-                        name, full_var.size(), len, offset);
+    throw BoutException("{} has length {}. Expected {} elements + {} offset", name,
+                        full_var.size(), len, offset);
   }
 
   // Ensure that output variable has the correct size
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 448832ea57..c2c9b51ba3 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -2080,13 +2080,16 @@ void BoutMesh::topology() {
   if (limiter_count > 0) {
     std::vector<int> limiter_yinds, limiter_xstarts, limiter_xends;
     if (!source->get(this, limiter_yinds, "limiter_yinds", limiter_count)) {
-      throw BoutException("Couldn't read limiter_yinds vector of length {} from mesh", limiter_count);
+      throw BoutException("Couldn't read limiter_yinds vector of length {} from mesh",
+                          limiter_count);
     }
     if (!source->get(this, limiter_xstarts, "limiter_xstarts", limiter_count)) {
-      throw BoutException("Couldn't read limiter_xstarts vector of length {} from mesh", limiter_count);
+      throw BoutException("Couldn't read limiter_xstarts vector of length {} from mesh",
+                          limiter_count);
     }
     if (!source->get(this, limiter_xends, "limiter_xends", limiter_count)) {
-      throw BoutException("Couldn't read limiter_xend vector of length {} from mesh", limiter_count);
+      throw BoutException("Couldn't read limiter_xend vector of length {} from mesh",
+                          limiter_count);
     }
 
     for (int i = 0; i < limiter_count; ++i) {
@@ -2094,7 +2097,7 @@ void BoutMesh::topology() {
       int xstart = limiter_xstarts[i];
       int xend = limiter_xends[i];
       output_info.write("Adding a limiter between y={} and {}. X indices {} to {}\n",
-                        yind, yind+1, xstart, xend);
+                        yind, yind + 1, xstart, xend);
       add_target(yind, xstart, xend);
     }
   }
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index fec4073682..1c50db5896 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -735,9 +735,8 @@ Array<int> Options::as<Array<int>>(const Array<int>& similar_to) const {
 
   Array<int> result = bout::utils::visit(
       ConvertContainer<Array<int>>{
-          fmt::format(
-              _("Value for option {:s} cannot be converted to an Array<int>"),
-              full_name),
+          fmt::format(_("Value for option {:s} cannot be converted to an Array<int>"),
+                      full_name),
           similar_to},
       value);
 

From 3f311e0896799974a154638ef0ff62b85401becb Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 14:04:00 +0000
Subject: [PATCH 0029/1827] Docs: Fix some double-backtick issues

---
 manual/sphinx/user_docs/bout_options.rst | 30 ++++++++++++------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst
index 85a8a17d59..f63e65b6df 100644
--- a/manual/sphinx/user_docs/bout_options.rst
+++ b/manual/sphinx/user_docs/bout_options.rst
@@ -139,10 +139,10 @@ Boolean expressions
 Boolean values must be "true", "false", "True", "False", "1" or
 "0". All lowercase ("true"/"false") is preferred, but the uppercase
 versions are allowed to support Python string conversions. Booleans
-can be combined into expressions using binary operators `&` (logical
-AND), `|` (logical OR), and unary operator `!` (logical NOT). For
-example "true & false" evaluates to `false`; "!false" evaluates to
-`true`.  Like real values and integers, boolean expressions can refer
+can be combined into expressions using binary operators ``&`` (logical
+AND), ``|`` (logical OR), and unary operator ``!`` (logical NOT). For
+example "true & false" evaluates to ``false``; "!false" evaluates to
+``true``. Like real values and integers, boolean expressions can refer
 to other variables:
 
 .. code-block:: cfg
@@ -150,8 +150,8 @@ to other variables:
    switch = true
    other_switch = !switch
 
-Boolean expressions can be formed by comparing real values using
-`>` and `<` comparison operators:
+Boolean expressions can be formed by comparing real values using ``>``
+and ``<`` comparison operators:
 
 .. code-block:: cfg
 
@@ -160,15 +160,15 @@ Boolean expressions can be formed by comparing real values using
    is_false = value < 2
 
 .. note::
-   Previous BOUT++ versions (v5.1.0 and earlier) were case
-   insensitive when reading boolean values, so would read "True" or
-   "yEs" as `true`, and "False" or "No" as `false`. These earlier
-   versions did not allow boolean expressions.
-
-Internally, booleans are evaluated as real values, with `true` being 1
-and `false` being 0. Logical operators (`&`, `|`, `!`) check that
-their left and right arguments are either close to 0 or close to 1
-(like integers, "close to" is within 1e-3).
+   Previous BOUT++ versions (v5.1.0 and earlier) were case insensitive
+   when reading boolean values, so would read "True" or "yEs" as
+   ``true``, and "False" or "No" as ``false``. These earlier versions
+   did not allow boolean expressions.
+
+Internally, booleans are evaluated as real values, with ``true`` being
+1 and ``false`` being 0. Logical operators (``&``, ``|``, ``!``) check
+that their left and right arguments are either close to 0 or close to
+1 (like integers, "close to" is within 1e-3).
 
 Special symbols in Option names
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

From 0bc5206ed28aa41ab43e9f32707aa524318386eb Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 15:07:54 +0000
Subject: [PATCH 0030/1827] Docs: Update code layout

Prefer linking to sections rather than specific files, as these have
changed a fair bit
---
 manual/sphinx/developer_docs/code_layout.rst | 294 ++++---------------
 manual/sphinx/developer_docs/mesh.rst        |   4 +
 manual/sphinx/user_docs/variable_init.rst    |   2 +
 3 files changed, 58 insertions(+), 242 deletions(-)

diff --git a/manual/sphinx/developer_docs/code_layout.rst b/manual/sphinx/developer_docs/code_layout.rst
index 7605355d7f..e79245cde3 100644
--- a/manual/sphinx/developer_docs/code_layout.rst
+++ b/manual/sphinx/developer_docs/code_layout.rst
@@ -49,275 +49,85 @@ Directories
 -----------
 
 The source code for the core of BOUT++ is divided into include files
-(which can be used in physics models) in ``bout++/include``, and source
-code and low-level includes in ``bout++/src``. Many parts of the code
-are defined by their interface, and can have multiple different
-implementations. An example is the time-integration solvers: many
-different implementations are available, some of which use external
-libraries, but all have the same interface and can be used
+(which can be used in physics models) in ``bout++/include/bout``, and
+source code and low-level includes in ``bout++/src``. Many parts of
+the code are defined by their interface, and can have multiple
+different implementations. An example is the time-integration solvers:
+many different implementations are available, some of which use
+external libraries, but all have the same interface and can be used
 interchangeably. This is reflected in the directory structure inside
-``bout++/src``. A common pattern is to store individual implementations
-of an interface in a subdirectory called ``impls``.
+``bout++/src``. A common pattern is to store individual
+implementations of an interface in a subdirectory called ``impls``.
 
 ::
 
-    include/foo.hxx
+    include/bout/foo.hxx
     src/.../foo.cxx
-    src/.../foo_factory.hxx
-    src/.../foo_factory.cxx
     src/.../impls/one/one.hxx
     src/.../impls/one/one.cxx
 
 where ``foo.hxx`` defines the interface, ``foo.cxx`` implements common
-functions used in several implementations. ``foo_factory`` creates new
-implementations, and is the only file which includes all the
-implementations. Individual implementations are stored in their own
-subdirectories of ``impls``. Components which follow this pattern
-include ``fileio`` formats, ``invert/laplace`` and ``invert/parderiv``
-inversion codes, ``mesh``, and ``solver``.
+functions used in several implementations. Individual implementations
+are stored in their own subdirectories of ``impls``. Components which
+follow this pattern include ``invert/laplace`` and ``invert/parderiv``
+inversions, ``mesh``, and ``solver``.
 
-The current source code files are:
+The layout of the ``src/`` directory is as follows:
 
-- :doc:`bout++.cxx<../_breathe_autogen/file/bout_09_09_8cxx>`: Main
-  file which initialises, runs and finalises BOUT++. Currently
-  contains a `main()` function, though this is being removed shortly.
+- :doc:`src/bout++.cxx<../_breathe_autogen/file/bout_09_09_8cxx>`: Main
+  file which initialises, runs and finalises BOUT++.
 
-- field
+- ``src/field``
 
-   - :doc:`field2d.cxx<../_breathe_autogen/file/field2d_8cxx>`
-     implements the `Field2D` class. This is a scalar field which
-     varies only in :math:`x` and :math:`y` and is used for things
-     like metric tensor components and initial profiles. It supplies
-     lots of overloaded operators and functions on these objects.
+  - Implementations of "fields" (the scalars `Field2D`, `Field3D`,
+    `FieldPerp`, and vectors `Vector2D`, `Vector3D`), as well as basic
+    operations (arithmetic, :ref:`sec-algebraic-ops`, and vector
+    calculus), and :ref:`initialisation <sec-variable-init>`.
 
-   - :doc:`field3d.cxx<../_breathe_autogen/file/field3d_8cxx>`
-     implements the `Field3D` class, which varies in :math:`x`,
-     :math:`y` and :math:`z`. Since these handle a lot more memory
-     than Field2D objects, the memory management is more complicated
-     and includes reference counting. See section
-     :ref:`sec-memorymanage` for more details.
+- ``src/invert``
 
-   - :doc:`field_data.cxx<../_breathe_autogen/file/field__data_8cxx>`
-     Implements some functions in the `FieldData` class. This is a
-     mainly pure virtual interface class which is inherited by
-     `Field2D` and `Field3D`.
+  - Implementations of different inverse operators, including Fourier
+    transforms (via an interface to `FFTW <http://www.fftw.org>`_, see
+    `bout::fft::rfft` and `bout::fft::irfft`).
 
-   - :doc:`fieldperp.cxx<../_breathe_autogen/file/fieldperp_8cxx>`
-     implements a `FieldPerp` class to store slices perpendicular to
-     the magnetic field i.e. they are a function of :math:`x` and
-     :math:`z` only. This is mainly used for Laplacian inversion
-     routines, and needs to be integrated with the other fields
-     better.
+- ``src/invert/laplace``
 
-   - :doc:`initialprofiles.cxx<../_breathe_autogen/file/initialprofiles_8cxx>`
-     routines to set the initial values of fields when a simulation
-     first starts. Reads settings from the option file based on the name
-     of the variable.
+  - Implementations of some inverse generalised Laplacian operator
+    variations, where some directions may be constant. See
+    :ref:`sec-laplacian` for more details.
 
-   - :doc:`vecops.cxx<../_breathe_autogen/file/vecops_8cxx>` a
-     collection of function to operate on vectors.  Contains things
-     like ``Grad``, ``Div`` and ``Curl``, and uses a combination of
-     field differential operators (in
-     :doc:`difops.cxx<../_breathe_autogen/file/difops_8cxx>`) and
-     metric tensor components (in `Mesh`).
+- ``src/invert/parderiv``
 
-   - :doc:`vector2d.cxx<../_breathe_autogen/file/vector2d_8cxx>`
-     implements the `Vector2D` class, which uses a `Field2D` object
-     for each of its 3 components. Overloads operators to supply
-     things like dot and cross products.
+  - Inversion of parallel derivatives, intended for use in
+    preconditioners. See `InvertPar`
 
-   - :doc:`vector3d.cxx<../_breathe_autogen/file/vector3d_8cxx>`
-     implements `Vector3D` by using a `Field3D`
-     object for each component.
+- ``src/invert/pardiv``
 
-   - :doc:`where.cxx<../_breathe_autogen/file/where_8cxx>` supplies
-     functions for choosing between values based on selection
-     criteria.
+  - Inversion of parallel divergence, intended for use in
+    :ref:`sec-nonlocal-heatflux`.
 
-- invert
+- ``src/mesh``
 
-   - :doc:`fft_fftw.cxx<../_breathe_autogen/file/fft__fftw_8cxx>`
-     implements the :doc:`fft.hxx<../_breathe_autogen/file/fft_8hxx>`
-     interface by calling the Fastest Fourier Transform in the West
-     (FFTW) library.
+  - Implementations of low-level numerical routines. This includes
+    things like the :ref:`inter-process communications
+    <sec-communications>`, :ref:`boundary conditions <sec-bndryopts>`,
+    :ref:`derivative operators <sec-diffops>`, interpolation, the
+    coordinate system (including :ref:`sec-parallel-transforms`), and
+    the :ref:`sec-mesh` itself.
 
-- invert / laplace
+- ``src/physics``
 
-   - :doc:`invert_laplace.cxx<../_breathe_autogen/file/invert__laplace_8cxx>` uses Fourier
-      decomposition in :math:`z` combined with tri- and band-diagonal
-      solvers in :math:`x` to solve Laplacian problems.
+  - This contains some specialised physics operators and routines,
+    such as gyro-averaging and :ref:`sec-nonlocal-heatflux`.
 
-   - impls
+- ``src/solver``
 
-      - serial\_tri
+  - Implementations of :ref:`time integration solvers
+    <sec-time-integration>`
 
-         - :doc:`serial_tri.hxx<../_breathe_autogen/file/serial__tri_8hxx>`
+- ``src/sys``
 
-         - :doc:`serial_tri.cxx<../_breathe_autogen/file/serial__tri_8cxx>`
-
-      - serial\_band
-
-         - :doc:`serial_band.hxx<../_breathe_autogen/file/serial__band_8hxx>`
-
-         - :doc:`serial_band.cxx<../_breathe_autogen/file/serial__band_8cxx>`
-
-      - spt
-
-         - :doc:`spt.hxx<../_breathe_autogen/file/spt_8hxx>`
-
-         - :doc:`spt.cxx<../_breathe_autogen/file/spt_8cxx>`
-
-- invert / parderiv
-
-   -
-     :doc:`invert_parderiv.cxx<../_breathe_autogen/file/invert__parderiv_8cxx>`
-     inverts a problem involving only parallel :math:`y`
-     derivatives. Intended for use in some preconditioners.
-
-   - impls
-
-      - cyclic
-
-         - :doc:`cyclic.cxx<../_breathe_autogen/file/cyclic_8cxx>`
-
-         - :doc:`cyclic.hxx<../_breathe_autogen/file/cyclic_8hxx>`
-
-- :doc:`lapack_routines.cxx<../_breathe_autogen/file/lapack__routines_8cxx>` supplies an
-   interface to the LAPACK linear solvers, which are used by the
-   ``invert_laplace`` routines.
-
-- mesh
-
-   - :doc:`boundary_factory.cxx<../_breathe_autogen/file/boundary__factory_8cxx>` creates boundary
-     condition operators which can then be applied to
-     fields. Described in section :ref:`sec-BoundaryFactory`.
-
-   - :doc:`boundary_region.cxx<../_breathe_autogen/file/boundary__region_8cxx>` implements a way
-     to describe and iterate over boundary regions. Created by the
-     mesh, and then used by boundary conditions. See
-     section :ref:`sec-BoundaryRegion` for more details.
-
-   - :doc:`boundary_standard.cxx<../_breathe_autogen/file/boundary__standard_8cxx>` implements some
-     standard boundary operations and modifiers such as ``Neumann``
-     and ``Dirichlet``.
-
-   - :doc:`difops.cxx<../_breathe_autogen/file/difops_8cxx>` is a
-     collection of differential operators on scalar fields. It uses
-     the differential methods in :doc:`derivs.cxx<../_breathe_autogen/file/derivs_8cxx>` and the metric tensor
-     components in `Mesh` to compute operators.
-
-   - :doc:`interpolation.cxx<../_breathe_autogen/file/interpolation_8cxx>` contains functions
-     for interpolating fields
-
-   - :doc:`mesh.cxx<../_breathe_autogen/file/mesh_8cxx>` is the base
-     class for the `Mesh` object. Contains routines useful
-     for all `Mesh` implementations.
-
-   - impls
-
-      - bout
-
-         - :doc:`boutmesh.cxx<../_breathe_autogen/file/boutmesh_8cxx>`
-           implements a mesh interface which is compatible with BOUT
-           grid files.
-
-         - :doc:`boutmesh.hxx<../_breathe_autogen/file/boutmesh_8hxx>`
-
-- physics
-
-   - :doc:`gyro_average.cxx<../_breathe_autogen/file/gyro__average_8cxx>`
-      gyro-averaging operators
-
-   - :doc:`smoothing.cxx<../_breathe_autogen/file/smoothing_8cxx>`
-     provides smoothing routines on scalar fields
-
-   - :doc:`sourcex.cxx<../_breathe_autogen/file/sourcex_8cxx>` contains
-     some useful routines for creating sources and sinks in physics
-     equations.
-
-- solver
-
-   - :doc:`solver.cxx<../_breathe_autogen/file/solver_8cxx>` is the
-     interface for all solvers
-
-   - impls
-
-      - cvode
-
-         - :doc:`cvode.cxx<../_breathe_autogen/file/cvode_8cxx>` is the
-           implementation of `Solver` which interfaces with
-           the SUNDIALS CVODE library.
-
-         - :doc:`cvode.hxx<../_breathe_autogen/file/cvode_8hxx>`
-
-      - ida
-
-         - :doc:`ida.cxx<../_breathe_autogen/file/ida_8cxx>` is the
-           implementation which interfaces with the SUNDIALS IDA
-           library
-
-         - :doc:`ida.hxx<../_breathe_autogen/file/ida_8hxx>`
-
-      - petsc
-
-         - :doc:`petsc.cxx<../_breathe_autogen/file/petsc_8cxx>` is the
-           interface to the PETSc time integration routines
-
-         - :doc:`petsc.hxx<../_breathe_autogen/file/petsc_8hxx>`
-
-      - pvode
-
-         - :doc:`pvode.cxx<../_breathe_autogen/file/pvode_8cxx>`
-           interfaces with the 1998 (pre-SUNDIALS) version of PVODE
-           (which became CVODE).
-
-         - :doc:`pvode.hxx<../_breathe_autogen/file/pvode_8hxx>`
-
-- sys
-
-   - :doc:`boutcomm.cxx<../_breathe_autogen/file/boutcomm_8cxx>`
-
-   - :doc:`boutexception.cxx<../_breathe_autogen/file/boutexception_8cxx>`
-     is an exception class which are used for error handling
-
-   - :doc:`derivs.cxx<../_breathe_autogen/file/derivs_8cxx>` contains
-     basic derivative methods such as upwinding, central difference
-     and WENO methods. These are then used by
-     :doc:`difops.cxx<../_breathe_autogen/file/difops_8cxx>`. Details are
-     given in section :ref:`sec-diffops`.
-
-   - :doc:`msg_stack.cxx<../_breathe_autogen/file/msg__stack_8cxx>` is
-     part of the error handling system. It maintains a stack of
-     messages which can be pushed onto the stack at the start of a
-     function, then removed (popped) at the end. If an error occurs or
-     a segmentation fault is caught then this stack is printed out and
-     can help to find errors.
-
-   - :doc:`options.cxx<../_breathe_autogen/file/options_8cxx>` provides
-     an interface to the BOUT.inp option file and the command-line
-     options.
-
-   - :doc:`optionsreader.cxx<../_breathe_autogen/file/optionsreader_8cxx>`
-
-   - :doc:`output.cxx<../_breathe_autogen/file/output_8cxx>`
-
-   - :doc:`range.cxx<../_breathe_autogen/file/range_8cxx>` Provides the
-     RangeIterator class, used to iterate over a set of
-     ranges. Described in section :ref:`sec-rangeiterator`
-
-   - :doc:`timer.cxx<../_breathe_autogen/file/timer_8cxx>` a class for
-     timing parts of the code like communications and file
-     I/O. Described in section :ref:`sec-timerclass`
-
-   - :doc:`utils.cxx<../_breathe_autogen/file/utils_8cxx>` contains
-     miscellaneous small useful routines such as allocating and
-     freeing arrays.
-
-   - options
-
-      - :doc:`optionparser.hxx<../_breathe_autogen/file/optionparser_8hxx>`
-
-      - :doc:`options_ini.cxx<../_breathe_autogen/file/options__ini_8cxx>`
-
-      - :doc:`options_ini.hxx<../_breathe_autogen/file/options__ini_8hxx>`
+  - General purpose utilities used throughout the library, such as
+    `BoutException`, wrappers for C libraries like ``PETSc`` and
+    ``HYPRE``, screen and file input and output.
 
diff --git a/manual/sphinx/developer_docs/mesh.rst b/manual/sphinx/developer_docs/mesh.rst
index ff3e40d4b0..c592773324 100644
--- a/manual/sphinx/developer_docs/mesh.rst
+++ b/manual/sphinx/developer_docs/mesh.rst
@@ -1,3 +1,5 @@
+.. _sec-mesh:
+
 Mesh
 ====
 
@@ -99,6 +101,8 @@ it::
 
 To read 2D and 3D fields, the branch-cuts need to be taken into account.
 
+.. _sec-communications:
+
 Communications
 --------------
 
diff --git a/manual/sphinx/user_docs/variable_init.rst b/manual/sphinx/user_docs/variable_init.rst
index 4ac13e0ead..ebe989c233 100644
--- a/manual/sphinx/user_docs/variable_init.rst
+++ b/manual/sphinx/user_docs/variable_init.rst
@@ -1,3 +1,5 @@
+.. _sec-variable-init:
+
 Variable initialisation
 =======================
 

From 297b28430988b871815947071e4bdd7ae461eca2 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 15:08:31 +0000
Subject: [PATCH 0031/1827] Docs: Fix underline too short

---
 manual/sphinx/user_docs/installing.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst
index eb155909bf..22fc3e724f 100644
--- a/manual/sphinx/user_docs/installing.rst
+++ b/manual/sphinx/user_docs/installing.rst
@@ -397,7 +397,7 @@ installation for that.
 
 
 Working with an active ``conda`` environment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 When ``conda`` is used, it installs separate versions of several libraries. These
 can cause warnings or even failures when linking BOUT++ executables. There are

From e6bc5c5d0e85b5e895b124b066bbf62aed6c45b1 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 15:12:09 +0000
Subject: [PATCH 0032/1827] Docs: Don't include boutdata/boututils in docs

---
 manual/sphinx/conf.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 29c0985841..d8ab76cf23 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -31,7 +31,8 @@
 import subprocess
 import sys
 
-sys.path.append("../../tools/pylib")
+sys.path.append("../../tools/pylib/boutpp")
+sys.path.append("../../tools/pylib/boutconfig")
 
 # Are we running on readthedocs?
 on_readthedocs = os.environ.get("READTHEDOCS") == "True"

From 41da8a816f3217c608ca3739330f9f3fc9186902 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 15:35:11 +0000
Subject: [PATCH 0033/1827] Docs: Fix reference link

---
 manual/sphinx/user_docs/physics_models.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manual/sphinx/user_docs/physics_models.rst b/manual/sphinx/user_docs/physics_models.rst
index 56e3b719b4..fa62541f3d 100644
--- a/manual/sphinx/user_docs/physics_models.rst
+++ b/manual/sphinx/user_docs/physics_models.rst
@@ -28,7 +28,7 @@ either physics models (e.g. ``test-delp2`` and
 Building Physics Models
 -----------------------
 
-After building the library (see :ref:`sec-cmake`), you can build a
+After building the library (see :ref:`sec-config-bout`), you can build a
 physics model in several different ways.
 
 For the bundled examples, perhaps the easiest is to build it directly

From 96723d088369ad73e8e74329a860a1775395da6c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 15:47:00 +0000
Subject: [PATCH 0034/1827] Docs: Fix bullet points (require blank line before
 start)

---
 manual/sphinx/user_docs/installing.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst
index 22fc3e724f..4f47255d2e 100644
--- a/manual/sphinx/user_docs/installing.rst
+++ b/manual/sphinx/user_docs/installing.rst
@@ -402,14 +402,17 @@ Working with an active ``conda`` environment
 When ``conda`` is used, it installs separate versions of several libraries. These
 can cause warnings or even failures when linking BOUT++ executables. There are
 several alternatives to deal with this problem:
+
 * The simplest but least convenient option is to use ``conda deactivate`` before
   configuring, compiling, or running any BOUT++ program.
+
 * You might sometimes want to link to the conda-installed libraries. This is
   probably not ideal for production runs on an HPC system (as conda downloads
   binary packages that will not be optimized for specific hardware), but can be
   a simple way to get packages for testing or on a personal computer. In this
   case just keep your ``conda`` environment active, and with luck the libraries
   should be picked up by the standard search mechanisms.
+
 * In case you do want a fully optimized and as-stable-as-possible build for
   production runs, it is probably best not to depend on any conda packages for
   compiling or running BOUT++ executables (restrict ``conda`` to providing Python

From 82c0708b6be5a2db608b5a1b884c76178404c89a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 15:47:46 +0000
Subject: [PATCH 0035/1827] Docs: Fix wrong start of literal block

---
 manual/sphinx/user_docs/running_bout.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manual/sphinx/user_docs/running_bout.rst b/manual/sphinx/user_docs/running_bout.rst
index 59c5b53828..5ee7a9bfb3 100644
--- a/manual/sphinx/user_docs/running_bout.rst
+++ b/manual/sphinx/user_docs/running_bout.rst
@@ -457,7 +457,7 @@ values loaded, the solver can be started::
         3d fields = 2, 2d fields = 0 neq=100, local_N=100
 
 This last line gives the number of equations being evolved (in this case
-100), and the number of these on this processor (here 100).::
+100), and the number of these on this processor (here 100).
 
 The absolute and relative tolerances come next::
 

From e1591bcda65b93788e42392c470461a690307726 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 15:55:24 +0000
Subject: [PATCH 0036/1827] Docs: Fix snippet for Scorep

---
 .../developer_docs/performance_profiling.rst      | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/manual/sphinx/developer_docs/performance_profiling.rst b/manual/sphinx/developer_docs/performance_profiling.rst
index d93c1e904b..de14d695da 100644
--- a/manual/sphinx/developer_docs/performance_profiling.rst
+++ b/manual/sphinx/developer_docs/performance_profiling.rst
@@ -85,9 +85,7 @@ Configure and build
 Configure with ``-BOUT_USE_SCOREP`` to enable Scorep instrumentation,
 then build as normal.  This option can be combined with other options,
 but it is usually desirable to profile the optimized code, configuring
-with the flags ````. Build the code with ``make`` as normal.
-
-With CMake:
+with the flags:
 
 .. code-block:: bash
 
@@ -95,14 +93,13 @@ With CMake:
       -DCMAKE_C_COMPILER=scorep-mpicc \
       -DCMAKE_CXX_COMPILER=scorep-mpicxx \
       -DCMAKE_CXX_FLAGS=-O3 -DCHECK=0 \
+      -DCMAKE_BUILD_TYPE=RelWithDebInfo \
       <other CMake options>
 
-This will turn off the instrumentation during the configure
-step. Please be aware that if you change ``CMakeLists.txt``, CMake
-will try to automatically reconfigure the build, which the Score-P
-wrappers interfere with. In this case you will need to restart the
-configure step from scratch (i.e. remove the build directory and start
-again).
+``SCOREP_WRAPPER=off`` is used turn off the instrumentation during the
+configure step. You probably want to use a fresh build directory to
+prevent any issues from cached results when setting the compilers like
+this.
 
 Run and analysis
 ~~~~~~~~~~~~~~~~

From dcb33f44a215a267f98a8dcb69a3056e9a4dac5a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 15:58:41 +0000
Subject: [PATCH 0037/1827] Docs: Fix unknown role

---
 manual/sphinx/developer_docs/file_io.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manual/sphinx/developer_docs/file_io.rst b/manual/sphinx/developer_docs/file_io.rst
index aece8cfb1e..0d13e70cfc 100644
--- a/manual/sphinx/developer_docs/file_io.rst
+++ b/manual/sphinx/developer_docs/file_io.rst
@@ -114,5 +114,5 @@ in the first output file, which `collect` uses to get its type and dimensions.
 .. [2] Actually, the C++ I/O code should work fine even if a `FieldPerp` object is defined
        with different y-indices on different processors. This may be useful for diagnostic
        or debugging purposes. However, Python routines like `collect` and
-       :py:`boutdata.restart.redistribute` will fail because they find inconsistent
+       `boutdata.restart.redistribute` will fail because they find inconsistent
        `yindex_global` values.

From aa4a6553394f9420564d12ff8df681a8ba6d0618 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 16:07:44 +0000
Subject: [PATCH 0038/1827] Docs: Fix syntax for footnote

---
 manual/sphinx/user_docs/boundary_options.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 57c6658891..d5e1b9199c 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -108,7 +108,7 @@ Boundary conditions for non-orthogonal grids
 
 If non-orthogonal grids are used (meaning that the x- and y-directions are not orthogonal,
 so ``g12 != 0.``), then corner cells may be required. The boundary conditions are applied
-in corner cells[#disablecorners]_ by applying the y-boundary condition using x-boundary
+in corner cells [#disablecorners]_ by applying the y-boundary condition using x-boundary
 values. This requires that x-boundary conditions are applied before y-boundary conditions.
 The ordering is taken care of by the methods described in this section, but also needs to
 be respected by any custom boundary conditions in user code (e.g. sheath boundary

From 6640e940e350c3636d83026f2ee2a60322fb9440 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 17:00:55 +0000
Subject: [PATCH 0039/1827] Fix a couple of "most vexing parse" that doxygen
 doesn't like

---
 include/bout/dcomplex.hxx | 4 +++-
 include/bout/sys/uuid.h   | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/include/bout/dcomplex.hxx b/include/bout/dcomplex.hxx
index 569b5f2c13..3bb360b055 100644
--- a/include/bout/dcomplex.hxx
+++ b/include/bout/dcomplex.hxx
@@ -37,7 +37,9 @@
 
 using dcomplex = std::complex<BoutReal>;
 
-const dcomplex Im(0, 1); // 1i
+/// Imaginary unit, ``1i``
+//NOLINTNEXTLINE(readability-identifier-length)
+constexpr dcomplex Im{0, 1};
 
 /// Complex type for passing data to/from FORTRAN
 struct fcmplx {
diff --git a/include/bout/sys/uuid.h b/include/bout/sys/uuid.h
index d043ea780e..edc252bb44 100644
--- a/include/bout/sys/uuid.h
+++ b/include/bout/sys/uuid.h
@@ -261,7 +261,7 @@ class sha1 {
   size_t m_byteCount;
 };
 
-static std::mt19937 clock_gen(std::random_device{}());
+static std::mt19937 clock_gen{std::random_device{}()};
 static std::uniform_int_distribution<short> clock_dis{-32768, 32767};
 static std::atomic_short clock_sequence{clock_dis(clock_gen)};
 } // namespace detail

From 534fe4db38604369f111e1f2020f93e3f005edd6 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 17:07:50 +0000
Subject: [PATCH 0040/1827] Docs: Don't keep separate doxygen config for
 readthedocs

---
 manual/doxygen/Doxyfile             | 1390 +--------------------------
 manual/doxygen/Doxyfile_readthedocs | 1119 ---------------------
 manual/sphinx/conf.py               |    5 +-
 3 files changed, 19 insertions(+), 2495 deletions(-)
 delete mode 100644 manual/doxygen/Doxyfile_readthedocs

diff --git a/manual/doxygen/Doxyfile b/manual/doxygen/Doxyfile
index 216ef60915..e27df586ec 100644
--- a/manual/doxygen/Doxyfile
+++ b/manual/doxygen/Doxyfile
@@ -246,34 +246,6 @@ ALIASES                =
 
 TCL_SUBST              =
 
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
-# only. Doxygen will then generate output that is more tailored for C. For
-# instance, some of the names that are used will be different. The list of all
-# members will be omitted, etc.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_FOR_C  = NO
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
-# Python sources only. Doxygen will then generate output that is more tailored
-# for that language. For instance, namespaces will be presented as packages,
-# qualified scopes will look different, etc.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_JAVA   = NO
-
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-# sources. Doxygen will then generate output that is tailored for Fortran.
-# The default value is: NO.
-
-OPTIMIZE_FOR_FORTRAN   = NO
-
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-# sources. Doxygen will then generate output that is tailored for VHDL.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_VHDL   = NO
-
 # Doxygen selects the parser to use depending on the extension of the files it
 # parses. With this tag you can assign which parser to use for a given
 # extension. Doxygen has a built-in mapping, but you can override or extend it
@@ -328,21 +300,7 @@ AUTOLINK_SUPPORT       = YES
 # diagrams that involve STL classes more complete and accurate.
 # The default value is: NO.
 
-BUILTIN_STL_SUPPORT    = NO
-
-# If you use Microsoft's C++/CLI language, you should set this option to YES to
-# enable parsing support.
-# The default value is: NO.
-
-CPP_CLI_SUPPORT        = NO
-
-# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
-# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
-# will parse them like normal C++ but will assume all classes use public instead
-# of private inheritance when no explicit protection keyword is present.
-# The default value is: NO.
-
-SIP_SUPPORT            = NO
+BUILTIN_STL_SUPPORT    = YES
 
 # For Microsoft's IDL there are propget and propput attributes to indicate
 # getter and setter methods for a property. Setting this option to YES will make
@@ -352,7 +310,7 @@ SIP_SUPPORT            = NO
 # should set this option to NO.
 # The default value is: YES.
 
-IDL_PROPERTY_SUPPORT   = YES
+IDL_PROPERTY_SUPPORT   = NO
 
 # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
 # tag is set to YES then doxygen will reuse the documentation of the first
@@ -435,13 +393,13 @@ LOOKUP_CACHE_SIZE      = 0
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = YES
+EXTRACT_ALL            = NO
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIVATE        = YES
+EXTRACT_PRIVATE        = NO
 
 # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
@@ -463,14 +421,6 @@ EXTRACT_STATIC         = YES
 
 EXTRACT_LOCAL_CLASSES  = YES
 
-# This flag is only useful for Objective-C code. If set to YES, local methods,
-# which are defined in the implementation section but not in the interface are
-# included in the documentation. If set to NO, only methods in the interface are
-# included.
-# The default value is: NO.
-
-EXTRACT_LOCAL_METHODS  = YES
-
 # If this flag is set to YES, the members of anonymous namespaces will be
 # extracted and appear in the documentation as a namespace called
 # 'anonymous_namespace{file}', where file will be replaced with the base name of
@@ -508,7 +458,7 @@ HIDE_FRIEND_COMPOUNDS  = NO
 # blocks will be appended to the function's detailed documentation block.
 # The default value is: NO.
 
-HIDE_IN_BODY_DOCS      = NO
+HIDE_IN_BODY_DOCS      = YES
 
 # The INTERNAL_DOCS tag determines if documentation that is typed after a
 # \internal command is included. If the tag is set to NO then the documentation
@@ -590,7 +540,7 @@ SORT_BRIEF_DOCS        = NO
 # detailed member documentation.
 # The default value is: NO.
 
-SORT_MEMBERS_CTORS_1ST = NO
+SORT_MEMBERS_CTORS_1ST = YES
 
 # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
 # of group names into alphabetical order. If set to NO the group names will
@@ -623,19 +573,19 @@ STRICT_PROTO_MATCHING  = NO
 # list. This list is created by putting \todo commands in the documentation.
 # The default value is: YES.
 
-GENERATE_TODOLIST      = YES
+GENERATE_TODOLIST      = NO
 
 # The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
 # list. This list is created by putting \test commands in the documentation.
 # The default value is: YES.
 
-GENERATE_TESTLIST      = YES
+GENERATE_TESTLIST      = NO
 
 # The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
 # list. This list is created by putting \bug commands in the documentation.
 # The default value is: YES.
 
-GENERATE_BUGLIST       = YES
+GENERATE_BUGLIST       = NO
 
 # The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
 # the deprecated list. This list is created by putting \deprecated commands in
@@ -673,7 +623,7 @@ SHOW_USED_FILES        = YES
 # (if specified).
 # The default value is: YES.
 
-SHOW_FILES             = YES
+SHOW_FILES             = NO
 
 # Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
 # page. This will remove the Namespaces entry from the Quick Index and from the
@@ -791,7 +741,7 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = ../../include/bout \
-                         ../../src/
+                         ../../src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -858,99 +808,6 @@ EXCLUDE_SYMLINKS       = NO
 
 EXCLUDE_PATTERNS       =
 
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
-# (namespaces, classes, functions, etc.) that should be excluded from the
-# output. The symbol name can be a fully qualified name, a word, or if the
-# wildcard * is used, a substring. Examples: ANamespace, AClass,
-# AClass::ANamespace, ANamespace::*Test
-#
-# Note that the wildcards are matched against the file with absolute path, so to
-# exclude all test directories use the pattern */test/*
-
-EXCLUDE_SYMBOLS        =
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or directories
-# that contain example code fragments that are included (see the \include
-# command).
-
-EXAMPLE_PATH           =
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
-# *.h) to filter out the source-files in the directories. If left blank all
-# files are included.
-
-EXAMPLE_PATTERNS       = *
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude commands
-# irrespective of the value of the RECURSIVE tag.
-# The default value is: NO.
-
-EXAMPLE_RECURSIVE      = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or directories
-# that contain images that are to be included in the documentation (see the
-# \image command).
-
-IMAGE_PATH             =
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command:
-#
-# <filter> <input-file>
-#
-# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
-# name of an input file. Doxygen will then use the output that the filter
-# program writes to standard output. If FILTER_PATTERNS is specified, this tag
-# will be ignored.
-#
-# Note that the filter must not add or remove lines; it is applied before the
-# code is scanned, but not when the output code is generated. If lines are added
-# or removed, the anchors will not be placed correctly.
-#
-# Note that for custom extensions or not directly supported extensions you also
-# need to set EXTENSION_MAPPING for the extension otherwise the files are not
-# properly processed by doxygen.
-
-INPUT_FILTER           =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form: pattern=filter
-# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
-# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
-# patterns match the file name, INPUT_FILTER is applied.
-#
-# Note that for custom extensions or not directly supported extensions you also
-# need to set EXTENSION_MAPPING for the extension otherwise the files are not
-# properly processed by doxygen.
-
-FILTER_PATTERNS        =
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will also be used to filter the input files that are used for
-# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
-# The default value is: NO.
-
-FILTER_SOURCE_FILES    = NO
-
-# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
-# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
-# it is also possible to disable source filtering for a specific pattern using
-# *.ext= (so without naming a filter).
-# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
-
-FILTER_SOURCE_PATTERNS =
-
-# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
-# is part of the input, its contents will be placed on the main page
-# (index.html). This can be useful if you have a project on for instance GitHub
-# and want to reuse the introduction page also for the doxygen output.
-
-USE_MDFILE_AS_MAINPAGE =
-
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
 #---------------------------------------------------------------------------
@@ -1005,7 +862,7 @@ REFERENCES_LINK_SOURCE = YES
 # The default value is: YES.
 # This tag requires that the tag SOURCE_BROWSER is set to YES.
 
-SOURCE_TOOLTIPS        = YES
+SOURCE_TOOLTIPS        = NO
 
 # If the USE_HTAGS tag is set to YES then the references to source code will
 # point to the HTML generated by the htags(1) tool instead of doxygen built-in
@@ -1048,21 +905,6 @@ VERBATIM_HEADERS       = NO
 
 ALPHABETICAL_INDEX     = NO
 
-# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
-# which the alphabetical index list will be split.
-# Minimum value: 1, maximum value: 20, default value: 5.
-# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
-
-COLS_IN_ALPHA_INDEX    = 5
-
-# In case all classes in a project start with a common prefix, all classes will
-# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
-# can be used to specify a prefix (or a list of prefixes) that should be ignored
-# while generating the index headers.
-# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
-
-IGNORE_PREFIX          =
-
 #---------------------------------------------------------------------------
 # Configuration options related to the HTML output
 #---------------------------------------------------------------------------
@@ -1070,542 +912,7 @@ IGNORE_PREFIX          =
 # If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
 # The default value is: YES.
 
-GENERATE_HTML          = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: html.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_OUTPUT            = html
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
-# generated HTML page (for example: .htm, .php, .asp).
-# The default value is: .html.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_FILE_EXTENSION    = .html
-
-# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
-# each generated HTML page. If the tag is left blank doxygen will generate a
-# standard header.
-#
-# To get valid HTML the header file that includes any scripts and style sheets
-# that doxygen needs, which is dependent on the configuration options used (e.g.
-# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
-# default header using
-# doxygen -w html new_header.html new_footer.html new_stylesheet.css
-# YourConfigFile
-# and then modify the file new_header.html. See also section "Doxygen usage"
-# for information on how to generate the default header that doxygen normally
-# uses.
-# Note: The header is subject to change so you typically have to regenerate the
-# default header when upgrading to a newer version of doxygen. For a description
-# of the possible markers and block names see the documentation.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_HEADER            =
-
-# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
-# generated HTML page. If the tag is left blank doxygen will generate a standard
-# footer. See HTML_HEADER for more information on how to generate a default
-# footer and what special commands can be used inside the footer. See also
-# section "Doxygen usage" for information on how to generate the default footer
-# that doxygen normally uses.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_FOOTER            =
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
-# sheet that is used by each HTML page. It can be used to fine-tune the look of
-# the HTML output. If left blank doxygen will generate a default style sheet.
-# See also section "Doxygen usage" for information on how to generate the style
-# sheet that doxygen normally uses.
-# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
-# it is more robust and this tag (HTML_STYLESHEET) will in the future become
-# obsolete.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_STYLESHEET        =
-
-# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
-# cascading style sheets that are included after the standard style sheets
-# created by doxygen. Using this option one can overrule certain style aspects.
-# This is preferred over using HTML_STYLESHEET since it does not replace the
-# standard style sheet and is therefore more robust against future updates.
-# Doxygen will copy the style sheet files to the output directory.
-# Note: The order of the extra style sheet files is of importance (e.g. the last
-# style sheet in the list overrules the setting of the previous ones in the
-# list). For an example see the documentation.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_EXTRA_STYLESHEET  =
-
-# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
-# other source files which should be copied to the HTML output directory. Note
-# that these files will be copied to the base HTML output directory. Use the
-# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
-# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
-# files will be copied as-is; there are no commands or markers available.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_EXTRA_FILES       =
-
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
-# will adjust the colors in the style sheet and background images according to
-# this color. Hue is specified as an angle on a colorwheel, see
-# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
-# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
-# purple, and 360 is red again.
-# Minimum value: 0, maximum value: 359, default value: 220.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_HUE    = 220
-
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
-# in the HTML output. For a value of 0 the output will use grayscales only. A
-# value of 255 will produce the most vivid colors.
-# Minimum value: 0, maximum value: 255, default value: 100.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_SAT    = 100
-
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
-# luminance component of the colors in the HTML output. Values below 100
-# gradually make the output lighter, whereas values above 100 make the output
-# darker. The value divided by 100 is the actual gamma applied, so 80 represents
-# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
-# change the gamma.
-# Minimum value: 40, maximum value: 240, default value: 80.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_GAMMA  = 80
-
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting this
-# to YES can help to show when doxygen was last run and thus if the
-# documentation is up to date.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_TIMESTAMP         = NO
-
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
-# documentation will contain sections that can be hidden and shown after the
-# page has loaded.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_DYNAMIC_SECTIONS  = NO
-
-# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
-# shown in the various tree structured indices initially; the user can expand
-# and collapse entries dynamically later on. Doxygen will expand the tree to
-# such a level that at most the specified number of entries are visible (unless
-# a fully collapsed tree already exceeds this amount). So setting the number of
-# entries 1 will produce a full collapsed tree by default. 0 is a special value
-# representing an infinite number of entries and will result in a full expanded
-# tree by default.
-# Minimum value: 0, maximum value: 9999, default value: 100.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_INDEX_NUM_ENTRIES = 100
-
-# If the GENERATE_DOCSET tag is set to YES, additional index files will be
-# generated that can be used as input for Apple's Xcode 3 integrated development
-# environment (see: http://developer.apple.com/tools/xcode/), introduced with
-# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
-# Makefile in the HTML output directory. Running make will produce the docset in
-# that directory and running make install will install the docset in
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
-# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
-# for more information.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_DOCSET        = NO
-
-# This tag determines the name of the docset feed. A documentation feed provides
-# an umbrella under which multiple documentation sets from a single provider
-# (such as a company or product suite) can be grouped.
-# The default value is: Doxygen generated docs.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_FEEDNAME        = "Doxygen generated docs"
-
-# This tag specifies a string that should uniquely identify the documentation
-# set bundle. This should be a reverse domain-name style string, e.g.
-# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
-# The default value is: org.doxygen.Project.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_BUNDLE_ID       = org.doxygen.Project
-
-# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
-# the documentation publisher. This should be a reverse domain-name style
-# string, e.g. com.mycompany.MyDocSet.documentation.
-# The default value is: org.doxygen.Publisher.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
-
-# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
-# The default value is: Publisher.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_PUBLISHER_NAME  = Publisher
-
-# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
-# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
-# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
-# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
-# Windows.
-#
-# The HTML Help Workshop contains a compiler that can convert all HTML output
-# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
-# files are now used as the Windows 98 help format, and will replace the old
-# Windows help format (.hlp) on all Windows platforms in the future. Compressed
-# HTML files also contain an index, a table of contents, and you can search for
-# words in the documentation. The HTML workshop also contains a viewer for
-# compressed HTML files.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_HTMLHELP      = NO
-
-# The CHM_FILE tag can be used to specify the file name of the resulting .chm
-# file. You can add a path in front of the file if the result should not be
-# written to the html output directory.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-CHM_FILE               =
-
-# The HHC_LOCATION tag can be used to specify the location (absolute path
-# including file name) of the HTML help compiler (hhc.exe). If non-empty,
-# doxygen will try to run the HTML help compiler on the generated index.hhp.
-# The file has to be specified with full path.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-HHC_LOCATION           =
-
-# The GENERATE_CHI flag controls if a separate .chi index file is generated
-# (YES) or that it should be included in the master .chm file (NO).
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-GENERATE_CHI           = NO
-
-# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
-# and project file content.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-CHM_INDEX_ENCODING     =
-
-# The BINARY_TOC flag controls whether a binary table of contents is generated
-# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
-# enables the Previous and Next buttons.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-BINARY_TOC             = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members to
-# the table of contents of the HTML help documentation and to the tree view.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-TOC_EXPAND             = NO
-
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
-# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
-# (.qch) of the generated HTML documentation.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_QHP           = NO
-
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
-# the file name of the resulting .qch file. The path specified is relative to
-# the HTML output folder.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QCH_FILE               =
-
-# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
-# Project output. For more information please see Qt Help Project / Namespace
-# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
-# The default value is: org.doxygen.Project.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_NAMESPACE          = org.doxygen.Project
-
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
-# Help Project output. For more information please see Qt Help Project / Virtual
-# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
-# folders).
-# The default value is: doc.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_VIRTUAL_FOLDER     = doc
-
-# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
-# filter to add. For more information please see Qt Help Project / Custom
-# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
-# filters).
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_CUST_FILTER_NAME   =
-
-# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
-# custom filter to add. For more information please see Qt Help Project / Custom
-# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
-# filters).
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_CUST_FILTER_ATTRS  =
-
-# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
-# project's filter section matches. Qt Help Project / Filter Attributes (see:
-# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_SECT_FILTER_ATTRS  =
-
-# The QHG_LOCATION tag can be used to specify the location of Qt's
-# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
-# generated .qhp file.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHG_LOCATION           =
-
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
-# generated, together with the HTML files, they form an Eclipse help plugin. To
-# install this plugin and make it available under the help contents menu in
-# Eclipse, the contents of the directory containing the HTML and XML files needs
-# to be copied into the plugins directory of eclipse. The name of the directory
-# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
-# After copying Eclipse needs to be restarted before the help appears.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_ECLIPSEHELP   = NO
-
-# A unique identifier for the Eclipse help plugin. When installing the plugin
-# the directory name containing the HTML and XML files should also have this
-# name. Each documentation set should have its own identifier.
-# The default value is: org.doxygen.Project.
-# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
-
-ECLIPSE_DOC_ID         = org.doxygen.Project
-
-# If you want full control over the layout of the generated HTML pages it might
-# be necessary to disable the index and replace it with your own. The
-# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
-# of each HTML page. A value of NO enables the index and the value YES disables
-# it. Since the tabs in the index contain the same information as the navigation
-# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-DISABLE_INDEX          = NO
-
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information. If the tag
-# value is set to YES, a side panel will be generated containing a tree-like
-# index structure (just like the one that is generated for HTML Help). For this
-# to work a browser that supports JavaScript, DHTML, CSS and frames is required
-# (i.e. any modern browser). Windows users are probably better off using the
-# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
-# further fine-tune the look of the index. As an example, the default style
-# sheet generated by doxygen has an example that shows how to put an image at
-# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
-# the same information as the tab index, you could consider setting
-# DISABLE_INDEX to YES when enabling this option.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_TREEVIEW      = NO
-
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
-# doxygen will group on one line in the generated HTML documentation.
-#
-# Note that a value of 0 will completely suppress the enum values from appearing
-# in the overview section.
-# Minimum value: 0, maximum value: 20, default value: 4.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-ENUM_VALUES_PER_LINE   = 4
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
-# to set the initial width (in pixels) of the frame in which the tree is shown.
-# Minimum value: 0, maximum value: 1500, default value: 250.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-TREEVIEW_WIDTH         = 250
-
-# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
-# external symbols imported via tag files in a separate window.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-EXT_LINKS_IN_WINDOW    = NO
-
-# Use this tag to change the font size of LaTeX formulas included as images in
-# the HTML documentation. When you change the font size after a successful
-# doxygen run you need to manually remove any form_*.png images from the HTML
-# output directory to force them to be regenerated.
-# Minimum value: 8, maximum value: 50, default value: 10.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-FORMULA_FONTSIZE       = 10
-
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are not
-# supported properly for IE 6.0, but are supported on all modern browsers.
-#
-# Note that when changing this option you need to delete any form_*.png files in
-# the HTML output directory before the changes have effect.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-FORMULA_TRANSPARENT    = YES
-
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
-# http://www.mathjax.org) which uses client side Javascript for the rendering
-# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
-# installed or if you want to formulas look prettier in the HTML output. When
-# enabled you may also need to install MathJax separately and configure the path
-# to it using the MATHJAX_RELPATH option.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-USE_MATHJAX            = NO
-
-# When MathJax is enabled you can set the default output format to be used for
-# the MathJax output. See the MathJax site (see:
-# http://docs.mathjax.org/en/latest/output.html) for more details.
-# Possible values are: HTML-CSS (which is slower, but has the best
-# compatibility), NativeMML (i.e. MathML) and SVG.
-# The default value is: HTML-CSS.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_FORMAT         = HTML-CSS
-
-# When MathJax is enabled you need to specify the location relative to the HTML
-# output directory using the MATHJAX_RELPATH option. The destination directory
-# should contain the MathJax.js script. For instance, if the mathjax directory
-# is located at the same level as the HTML output directory, then
-# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
-# Content Delivery Network so you can quickly see the result without installing
-# MathJax. However, it is strongly recommended to install a local copy of
-# MathJax from http://www.mathjax.org before deployment.
-# The default value is: http://cdn.mathjax.org/mathjax/latest.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
-
-# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
-# extension names that should be enabled during MathJax rendering. For example
-# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_EXTENSIONS     =
-
-# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
-# of code that will be used on startup of the MathJax code. See the MathJax site
-# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
-# example see the documentation.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_CODEFILE       =
-
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
-# the HTML output. The underlying search engine uses javascript and DHTML and
-# should work on any modern browser. Note that when using HTML help
-# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
-# there is already a search function so this one should typically be disabled.
-# For large projects the javascript based search engine can be slow, then
-# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
-# search using the keyboard; to jump to the search box use <access key> + S
-# (what the <access key> is depends on the OS and browser, but it is typically
-# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
-# key> to jump into the search results window, the results can be navigated
-# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
-# the search. The filter options can be selected when the cursor is inside the
-# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
-# to select a filter and <Enter> or <escape> to activate or cancel the filter
-# option.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-SEARCHENGINE           = NO
-
-# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a web server instead of a web client using Javascript. There
-# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
-# setting. When disabled, doxygen will generate a PHP script for searching and
-# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
-# and searching needs to be provided by external tools. See the section
-# "External Indexing and Searching" for details.
-# The default value is: NO.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-SERVER_BASED_SEARCH    = NO
-
-# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
-# script for searching. Instead the search results are written to an XML file
-# which needs to be processed by an external indexer. Doxygen will invoke an
-# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
-# search results.
-#
-# Doxygen ships with an example indexer (doxyindexer) and search engine
-# (doxysearch.cgi) which are based on the open source search engine library
-# Xapian (see: http://xapian.org/).
-#
-# See the section "External Indexing and Searching" for details.
-# The default value is: NO.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-EXTERNAL_SEARCH        = NO
-
-# The SEARCHENGINE_URL should point to a search engine hosted by a web server
-# which will return the search results when EXTERNAL_SEARCH is enabled.
-#
-# Doxygen ships with an example indexer (doxyindexer) and search engine
-# (doxysearch.cgi) which are based on the open source search engine library
-# Xapian (see: http://xapian.org/). See the section "External Indexing and
-# Searching" for details.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-SEARCHENGINE_URL       =
-
-# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
-# search data is written to a file for indexing by an external tool. With the
-# SEARCHDATA_FILE tag the name of this file can be specified.
-# The default file is: searchdata.xml.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-SEARCHDATA_FILE        = searchdata.xml
-
-# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
-# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
-# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
-# projects and redirect the results back to the right project.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-EXTERNAL_SEARCH_ID     =
-
-# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
-# projects other than the one defined by this configuration file, but that are
-# all added to the same external search index. Each project needs to have a
-# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
-# to a relative location where the documentation can be found. The format is:
-# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-EXTRA_SEARCH_MAPPINGS  =
+GENERATE_HTML          = NO
 
 #---------------------------------------------------------------------------
 # Configuration options related to the LaTeX output
@@ -1614,277 +921,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = YES
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: latex.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_OUTPUT           = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked.
-#
-# Note that when enabling USE_PDFLATEX this option is only used for generating
-# bitmaps for formulas in the HTML output, but not in the Makefile that is
-# written to the output directory.
-# The default file is: latex.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_CMD_NAME         = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
-# index for LaTeX.
-# The default file is: makeindex.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-MAKEINDEX_CMD_NAME     = makeindex
-
-# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
-# documents. This may be useful for small projects and may help to save some
-# trees in general.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-COMPACT_LATEX          = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used by the
-# printer.
-# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
-# 14 inches) and executive (7.25 x 10.5 inches).
-# The default value is: a4.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-PAPER_TYPE             = a4wide
-
-# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
-# that should be included in the LaTeX output. The package can be specified just
-# by its name or with the correct syntax as to be used with the LaTeX
-# \usepackage command. To get the times font for instance you can specify :
-# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
-# To use the option intlimits with the amsmath package you can specify:
-# EXTRA_PACKAGES=[intlimits]{amsmath}
-# If left blank no extra packages will be included.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-EXTRA_PACKAGES         =
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
-# generated LaTeX document. The header should contain everything until the first
-# chapter. If it is left blank doxygen will generate a standard header. See
-# section "Doxygen usage" for information on how to let doxygen write the
-# default header to a separate file.
-#
-# Note: Only use a user-defined header if you know what you are doing! The
-# following commands have a special meaning inside the header: $title,
-# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
-# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
-# string, for the replacement values of the other commands the user is referred
-# to HTML_HEADER.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_HEADER           =
-
-# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
-# generated LaTeX document. The footer should contain everything after the last
-# chapter. If it is left blank doxygen will generate a standard footer. See
-# LATEX_HEADER for more information on how to generate a default footer and what
-# special commands can be used inside the footer.
-#
-# Note: Only use a user-defined footer if you know what you are doing!
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_FOOTER           =
-
-# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
-# LaTeX style sheets that are included after the standard style sheets created
-# by doxygen. Using this option one can overrule certain style aspects. Doxygen
-# will copy the style sheet files to the output directory.
-# Note: The order of the extra style sheet files is of importance (e.g. the last
-# style sheet in the list overrules the setting of the previous ones in the
-# list).
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_EXTRA_STYLESHEET =
-
-# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
-# other source files which should be copied to the LATEX_OUTPUT output
-# directory. Note that the files will be copied as-is; there are no commands or
-# markers available.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_EXTRA_FILES      =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
-# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
-# contain links (just like the HTML output) instead of page references. This
-# makes the output suitable for online browsing using a PDF viewer.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-PDF_HYPERLINKS         = NO
-
-# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
-# the PDF file directly from the LaTeX files. Set this option to YES, to get a
-# higher quality PDF documentation.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-USE_PDFLATEX           = NO
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
-# command to the generated LaTeX files. This will instruct LaTeX to keep running
-# if errors occur, instead of asking the user for help. This option is also used
-# when generating formulas in HTML.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_BATCHMODE        = NO
-
-# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
-# index chapters (such as File Index, Compound Index, etc.) in the output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_HIDE_INDICES     = NO
-
-# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
-# code with syntax highlighting in the LaTeX output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_SOURCE_CODE      = NO
-
-# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
-# bibliography, e.g. plainnat, or ieeetr. See
-# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
-# The default value is: plain.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_BIB_STYLE        = plain
-
-# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
-# page will contain the date and time when the page was generated. Setting this
-# to NO can help when comparing the output of multiple runs.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_TIMESTAMP        = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
-# RTF output is optimized for Word 97 and may not look too pretty with other RTF
-# readers/editors.
-# The default value is: NO.
-
-GENERATE_RTF           = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: rtf.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_OUTPUT             = rtf
-
-# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
-# documents. This may be useful for small projects and may help to save some
-# trees in general.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-COMPACT_RTF            = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
-# contain hyperlink fields. The RTF file will contain links (just like the HTML
-# output) instead of page references. This makes the output suitable for online
-# browsing using Word or some other Word compatible readers that support those
-# fields.
-#
-# Note: WordPad (write) and others do not support links.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_HYPERLINKS         = NO
-
-# Load stylesheet definitions from file. Syntax is similar to doxygen's config
-# file, i.e. a series of assignments. You only have to provide replacements,
-# missing definitions are set to their default value.
-#
-# See also section "Doxygen usage" for information on how to generate the
-# default style sheet that doxygen normally uses.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_STYLESHEET_FILE    =
-
-# Set optional variables used in the generation of an RTF document. Syntax is
-# similar to doxygen's config file. A template extensions file can be generated
-# using doxygen -e rtf extensionFile.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_EXTENSIONS_FILE    =
-
-# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
-# with syntax highlighting in the RTF output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_SOURCE_CODE        = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
-# classes and files.
-# The default value is: NO.
-
-GENERATE_MAN           = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it. A directory man3 will be created inside the directory specified by
-# MAN_OUTPUT.
-# The default directory is: man.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-MAN_OUTPUT             = man
-
-# The MAN_EXTENSION tag determines the extension that is added to the generated
-# man pages. In case the manual section does not start with a number, the number
-# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
-# optional.
-# The default value is: .3.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-MAN_EXTENSION          = .3
-
-# The MAN_SUBDIR tag determines the name of the directory created within
-# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
-# MAN_EXTENSION with the initial . removed.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-MAN_SUBDIR             =
-
-# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
-# will generate one additional man file for each entity documented in the real
-# man page(s). These additional files only source the real man page, but without
-# them the man command would be unable to find the correct page.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-MAN_LINKS              = NO
+GENERATE_LATEX         = NO
 
 #---------------------------------------------------------------------------
 # Configuration options related to the XML output
@@ -1911,84 +948,7 @@ XML_OUTPUT             = xml
 # The default value is: YES.
 # This tag requires that the tag GENERATE_XML is set to YES.
 
-XML_PROGRAMLISTING     = YES
-
-#---------------------------------------------------------------------------
-# Configuration options related to the DOCBOOK output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
-# that can be used to generate PDF.
-# The default value is: NO.
-
-GENERATE_DOCBOOK       = NO
-
-# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
-# front of it.
-# The default directory is: docbook.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_OUTPUT         = docbook
-
-# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
-# program listings (including syntax highlighting and cross-referencing
-# information) to the DOCBOOK output. Note that enabling this will significantly
-# increase the size of the DOCBOOK output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_PROGRAMLISTING = NO
-
-#---------------------------------------------------------------------------
-# Configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
-# AutoGen Definitions (see http://autogen.sf.net) file that captures the
-# structure of the code including all documentation. Note that this feature is
-# still experimental and incomplete at the moment.
-# The default value is: NO.
-
-GENERATE_AUTOGEN_DEF   = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
-# file that captures the structure of the code including all documentation.
-#
-# Note that this feature is still experimental and incomplete at the moment.
-# The default value is: NO.
-
-GENERATE_PERLMOD       = NO
-
-# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
-# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
-# output from the Perl module output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-
-PERLMOD_LATEX          = NO
-
-# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
-# formatted so it can be parsed by a human reader. This is useful if you want to
-# understand what is going on. On the other hand, if this tag is set to NO, the
-# size of the Perl module output will be much smaller and Perl will parse it
-# just the same.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-
-PERLMOD_PRETTY         = YES
-
-# The names of the make variables in the generated doxyrules.make file are
-# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
-# so different doxyrules.make files included by the same Makefile don't
-# overwrite each other's variables.
-# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-
-PERLMOD_MAKEVAR_PREFIX =
+XML_PROGRAMLISTING     = NO
 
 #---------------------------------------------------------------------------
 # Configuration options related to the preprocessor
@@ -2110,47 +1070,19 @@ SKIP_FUNCTION_MACROS   = YES
 # Configuration options related to external references
 #---------------------------------------------------------------------------
 
-# The TAGFILES tag can be used to specify one or more tag files. For each tag
-# file the location of the external documentation should be added. The format of
-# a tag file without this location is as follows:
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where loc1 and loc2 can be relative or absolute paths or URLs. See the
-# section "Linking to external documentation" for more information about the use
-# of tag files.
-# Note: Each tag file must have a unique name (where the name does NOT include
-# the path). If a tag file is not located in the directory in which doxygen is
-# run, you must also specify the path to the tagfile here.
-
-TAGFILES               =
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
-# tag file that is based on the input files it reads. See section "Linking to
-# external documentation" for more information about the usage of tag files.
-
-GENERATE_TAGFILE       =
-
-# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
-# the class index. If set to NO, only the inherited external classes will be
-# listed.
-# The default value is: NO.
-
-ALLEXTERNALS           = NO
-
 # If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
 # in the modules index. If set to NO, only the current project's groups will be
 # listed.
 # The default value is: YES.
 
-EXTERNAL_GROUPS        = YES
+EXTERNAL_GROUPS        = NO
 
 # If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
 # the related pages index. If set to NO, only the current project's pages will
 # be listed.
 # The default value is: YES.
 
-EXTERNAL_PAGES         = YES
+EXTERNAL_PAGES         = NO
 
 # The PERL_PATH should be the absolute path and name of the perl script
 # interpreter (i.e. the result of 'which perl').
@@ -2169,23 +1101,7 @@ PERL_PATH              = /usr/bin/perl
 # powerful graphs.
 # The default value is: YES.
 
-CLASS_DIAGRAMS         = YES
-
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see:
-# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
-# the mscgen tool resides. If left empty the tool is assumed to be found in the
-# default search path.
-
-MSCGEN_PATH            =
-
-# You can include diagrams made with dia in doxygen documentation. Doxygen will
-# then run dia to produce the diagram and insert it in the documentation. The
-# DIA_PATH tag allows you to specify the directory where the dia binary resides.
-# If left empty dia is assumed to be found in the default search path.
-
-DIA_PATH               =
+CLASS_DIAGRAMS         = NO
 
 # If set to YES the inheritance and collaboration graphs will hide inheritance
 # and usage relations if the target is undocumented or is not a class.
@@ -2201,273 +1117,3 @@ HIDE_UNDOC_RELATIONS   = YES
 # The default value is: NO.
 
 HAVE_DOT               = NO
-
-# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
-# to run in parallel. When set to 0 doxygen will base this on the number of
-# processors available in the system. You can set it explicitly to a value
-# larger than 0 to get control over the balance between CPU load and processing
-# speed.
-# Minimum value: 0, maximum value: 32, default value: 0.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_NUM_THREADS        = 0
-
-# When you want a differently looking font in the dot files that doxygen
-# generates you can specify the font name using DOT_FONTNAME. You need to make
-# sure dot is able to find the font, which can be done by putting it in a
-# standard location or by setting the DOTFONTPATH environment variable or by
-# setting DOT_FONTPATH to the directory containing the font.
-# The default value is: Helvetica.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_FONTNAME           = Helvetica
-
-# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
-# dot graphs.
-# Minimum value: 4, maximum value: 24, default value: 10.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_FONTSIZE           = 10
-
-# By default doxygen will tell dot to use the default font as specified with
-# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
-# the path where dot can find it using this tag.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_FONTPATH           =
-
-# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
-# each documented class showing the direct and indirect inheritance relations.
-# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-CLASS_GRAPH            = YES
-
-# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
-# graph for each documented class showing the direct and indirect implementation
-# dependencies (inheritance, containment, and class references variables) of the
-# class with other documented classes.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-COLLABORATION_GRAPH    = YES
-
-# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
-# groups, showing the direct groups dependencies.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-GROUP_GRAPHS           = YES
-
-# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
-# Language.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-UML_LOOK               = NO
-
-# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
-# class node. If there are many fields or methods and many nodes the graph may
-# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
-# number of items for each type to make the size more manageable. Set this to 0
-# for no limit. Note that the threshold may be exceeded by 50% before the limit
-# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
-# but if the number exceeds 15, the total amount of fields shown is limited to
-# 10.
-# Minimum value: 0, maximum value: 100, default value: 10.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-UML_LIMIT_NUM_FIELDS   = 10
-
-# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
-# collaboration graphs will show the relations between templates and their
-# instances.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-TEMPLATE_RELATIONS     = NO
-
-# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
-# YES then doxygen will generate a graph for each documented file showing the
-# direct and indirect include dependencies of the file with other documented
-# files.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-INCLUDE_GRAPH          = YES
-
-# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
-# set to YES then doxygen will generate a graph for each documented file showing
-# the direct and indirect include dependencies of the file with other documented
-# files.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-INCLUDED_BY_GRAPH      = YES
-
-# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
-# dependency graph for every global function or class method.
-#
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command. Disabling a call graph can be
-# accomplished by means of the command \hidecallgraph.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-CALL_GRAPH             = NO
-
-# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
-# dependency graph for every global function or class method.
-#
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable caller graphs for selected
-# functions only using the \callergraph command. Disabling a caller graph can be
-# accomplished by means of the command \hidecallergraph.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-CALLER_GRAPH           = NO
-
-# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
-# hierarchy of all classes instead of a textual one.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-GRAPHICAL_HIERARCHY    = YES
-
-# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
-# dependencies a directory has on other directories in a graphical way. The
-# dependency relations are determined by the #include relations between the
-# files in the directories.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DIRECTORY_GRAPH        = YES
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. For an explanation of the image formats see the section
-# output formats in the documentation of the dot tool (Graphviz (see:
-# http://www.graphviz.org/)).
-# Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
-# to make the SVG files visible in IE 9+ (other browsers do not have this
-# requirement).
-# Possible values are: png, jpg, gif, svg, png:gd, png:gd:gd, png:cairo,
-# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
-# png:gdiplus:gdiplus.
-# The default value is: png.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_IMAGE_FORMAT       = png
-
-# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
-# enable generation of interactive SVG images that allow zooming and panning.
-#
-# Note that this requires a modern browser other than Internet Explorer. Tested
-# and working are Firefox, Chrome, Safari, and Opera.
-# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
-# the SVG files visible. Older versions of IE do not have SVG support.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-INTERACTIVE_SVG        = NO
-
-# The DOT_PATH tag can be used to specify the path where the dot tool can be
-# found. If left blank, it is assumed the dot tool can be found in the path.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_PATH               =
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the \dotfile
-# command).
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOTFILE_DIRS           =
-
-# The MSCFILE_DIRS tag can be used to specify one or more directories that
-# contain msc files that are included in the documentation (see the \mscfile
-# command).
-
-MSCFILE_DIRS           =
-
-# The DIAFILE_DIRS tag can be used to specify one or more directories that
-# contain dia files that are included in the documentation (see the \diafile
-# command).
-
-DIAFILE_DIRS           =
-
-# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
-# path where java can find the plantuml.jar file. If left blank, it is assumed
-# PlantUML is not used or called during a preprocessing step. Doxygen will
-# generate a warning when it encounters a \startuml command in this case and
-# will not generate output for the diagram.
-
-PLANTUML_JAR_PATH      =
-
-# When using plantuml, the specified paths are searched for files specified by
-# the !include statement in a plantuml block.
-
-PLANTUML_INCLUDE_PATH  =
-
-# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
-# that will be shown in the graph. If the number of nodes in a graph becomes
-# larger than this value, doxygen will truncate the graph, which is visualized
-# by representing a node as a red box. Note that doxygen if the number of direct
-# children of the root node in a graph is already larger than
-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
-# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
-# Minimum value: 0, maximum value: 10000, default value: 50.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_GRAPH_MAX_NODES    = 50
-
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
-# generated by dot. A depth value of 3 means that only nodes reachable from the
-# root by following a path via at most 3 edges will be shown. Nodes that lay
-# further from the root node will be omitted. Note that setting this option to 1
-# or 2 may greatly reduce the computation time needed for large code bases. Also
-# note that the size of a graph can be further restricted by
-# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
-# Minimum value: 0, maximum value: 1000, default value: 0.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-MAX_DOT_GRAPH_DEPTH    = 1000
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not seem
-# to support this out of the box.
-#
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_TRANSPARENT        = NO
-
-# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
-# files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10) support
-# this, this feature is disabled by default.
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_MULTI_TARGETS      = NO
-
-# If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
-# explaining the meaning of the various boxes and arrows in the dot generated
-# graphs.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-GENERATE_LEGEND        = YES
-
-# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot
-# files that are used to generate the various graphs.
-# The default value is: YES.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_CLEANUP            = YES
diff --git a/manual/doxygen/Doxyfile_readthedocs b/manual/doxygen/Doxyfile_readthedocs
deleted file mode 100644
index e27df586ec..0000000000
--- a/manual/doxygen/Doxyfile_readthedocs
+++ /dev/null
@@ -1,1119 +0,0 @@
-# Doxyfile 1.8.12
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project.
-#
-# All text after a double hash (##) is considered a comment and is placed in
-# front of the TAG it is preceding.
-#
-# All text after a single hash (#) is considered a comment and will be ignored.
-# The format is:
-# TAG = value [value, ...]
-# For lists, items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (\" \").
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-
-# This tag specifies the encoding used for all characters in the config file
-# that follow. The default is UTF-8 which is also the encoding used for all text
-# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
-# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
-# for the list of possible encodings.
-# The default value is: UTF-8.
-
-DOXYFILE_ENCODING      = UTF-8
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
-# double-quotes, unless you are using Doxywizard) that should identify the
-# project for which the documentation is generated. This name is used in the
-# title of most generated pages and in a few other places.
-# The default value is: My Project.
-
-PROJECT_NAME           = BOUT++
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
-# could be handy for archiving the generated documentation or if some version
-# control system is used.
-
-PROJECT_NUMBER         = 5.1.0
-
-# Using the PROJECT_BRIEF tag one can provide an optional one line description
-# for a project that appears at the top of each page and should give viewer a
-# quick idea about the purpose of the project. Keep the description short.
-
-PROJECT_BRIEF          =
-
-# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
-# in the documentation. The maximum height of the logo should not exceed 55
-# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
-# the logo to the output directory.
-
-PROJECT_LOGO           =
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
-# into which the generated documentation will be written. If a relative path is
-# entered, it will be relative to the location where doxygen was started. If
-# left blank the current directory will be used.
-
-OUTPUT_DIRECTORY       = bout
-
-# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
-# directories (in 2 levels) under the output directory of each output format and
-# will distribute the generated files over these directories. Enabling this
-# option can be useful when feeding doxygen a huge amount of source files, where
-# putting all generated files in the same directory would otherwise causes
-# performance problems for the file system.
-# The default value is: NO.
-
-CREATE_SUBDIRS         = NO
-
-# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
-# characters to appear in the names of generated files. If set to NO, non-ASCII
-# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
-# U+3044.
-# The default value is: NO.
-
-ALLOW_UNICODE_NAMES    = NO
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
-# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
-# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
-# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
-# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
-# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
-# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
-# Ukrainian and Vietnamese.
-# The default value is: English.
-
-OUTPUT_LANGUAGE        = English
-
-# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
-# descriptions after the members that are listed in the file and class
-# documentation (similar to Javadoc). Set to NO to disable this.
-# The default value is: YES.
-
-BRIEF_MEMBER_DESC      = YES
-
-# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
-# description of a member or function before the detailed description
-#
-# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
-# brief descriptions will be completely suppressed.
-# The default value is: YES.
-
-REPEAT_BRIEF           = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator that is
-# used to form the text in various listings. Each string in this list, if found
-# as the leading text of the brief description, will be stripped from the text
-# and the result, after processing the whole list, is used as the annotated
-# text. Otherwise, the brief description is used as-is. If left blank, the
-# following values are used ($name is automatically replaced with the name of
-# the entity):The $name class, The $name widget, The $name file, is, provides,
-# specifies, contains, represents, a, an and the.
-
-ABBREVIATE_BRIEF       = "The $name class " \
-                         "The $name widget " \
-                         "The $name file " \
-                         is \
-                         provides \
-                         specifies \
-                         contains \
-                         represents \
-                         a \
-                         an \
-                         the
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# doxygen will generate a detailed section even if there is only a brief
-# description.
-# The default value is: NO.
-
-ALWAYS_DETAILED_SEC    = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-# The default value is: NO.
-
-INLINE_INHERITED_MEMB  = NO
-
-# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
-# before files name in the file list and in the header files. If set to NO the
-# shortest path that makes the file name unique will be used
-# The default value is: YES.
-
-FULL_PATH_NAMES        = YES
-
-# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
-# Stripping is only done if one of the specified strings matches the left-hand
-# part of the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the path to
-# strip.
-#
-# Note that you can specify absolute paths here, but also relative paths, which
-# will be relative from the directory where doxygen is started.
-# This tag requires that the tag FULL_PATH_NAMES is set to YES.
-
-STRIP_FROM_PATH        =
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
-# path mentioned in the documentation of a class, which tells the reader which
-# header file to include in order to use a class. If left blank only the name of
-# the header file containing the class definition is used. Otherwise one should
-# specify the list of include paths that are normally passed to the compiler
-# using the -I flag.
-
-STRIP_FROM_INC_PATH    =
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
-# less readable) file names. This can be useful is your file systems doesn't
-# support long names like on DOS, Mac, or CD-ROM.
-# The default value is: NO.
-
-SHORT_NAMES            = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
-# first line (until the first dot) of a Javadoc-style comment as the brief
-# description. If set to NO, the Javadoc-style will behave just like regular Qt-
-# style comments (thus requiring an explicit @brief command for a brief
-# description.)
-# The default value is: NO.
-
-JAVADOC_AUTOBRIEF      = NO
-
-# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
-# line (until the first dot) of a Qt-style comment as the brief description. If
-# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
-# requiring an explicit \brief command for a brief description.)
-# The default value is: NO.
-
-QT_AUTOBRIEF           = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
-# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
-# a brief description. This used to be the default behavior. The new default is
-# to treat a multi-line C++ comment block as a detailed description. Set this
-# tag to YES if you prefer the old behavior instead.
-#
-# Note that setting this tag to YES also means that rational rose comments are
-# not recognized any more.
-# The default value is: NO.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
-# documentation from any documented member that it re-implements.
-# The default value is: YES.
-
-INHERIT_DOCS           = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
-# page for each member. If set to NO, the documentation of a member will be part
-# of the file/class/namespace that contains it.
-# The default value is: NO.
-
-SEPARATE_MEMBER_PAGES  = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
-# uses this value to replace tabs by spaces in code fragments.
-# Minimum value: 1, maximum value: 16, default value: 4.
-
-TAB_SIZE               = 8
-
-# This tag can be used to specify a number of aliases that act as commands in
-# the documentation. An alias has the form:
-# name=value
-# For example adding
-# "sideeffect=@par Side Effects:\n"
-# will allow you to put the command \sideeffect (or @sideeffect) in the
-# documentation, which will result in a user-defined paragraph with heading
-# "Side Effects:". You can put \n's in the value part of an alias to insert
-# newlines.
-
-ALIASES                =
-
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding "class=itcl::class"
-# will allow you to use the command class in the itcl::class meaning.
-
-TCL_SUBST              =
-
-# Doxygen selects the parser to use depending on the extension of the files it
-# parses. With this tag you can assign which parser to use for a given
-# extension. Doxygen has a built-in mapping, but you can override or extend it
-# using this tag. The format is ext=language, where ext is a file extension, and
-# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
-# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
-# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
-# Fortran. In the later case the parser tries to guess whether the code is fixed
-# or free formatted code, this is the default for Fortran type files), VHDL. For
-# instance to make doxygen treat .inc files as Fortran files (default is PHP),
-# and .f files as C (default is Fortran), use: inc=Fortran f=C.
-#
-# Note: For files without extension you can use no_extension as a placeholder.
-#
-# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
-# the files are not read by doxygen.
-
-EXTENSION_MAPPING      =
-
-# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
-# according to the Markdown format, which allows for more readable
-# documentation. See http://daringfireball.net/projects/markdown/ for details.
-# The output of markdown processing is further processed by doxygen, so you can
-# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
-# case of backward compatibilities issues.
-# The default value is: YES.
-
-MARKDOWN_SUPPORT       = YES
-
-# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
-# to that level are automatically included in the table of contents, even if
-# they do not have an id attribute.
-# Note: This feature currently applies only to Markdown headings.
-# Minimum value: 0, maximum value: 99, default value: 0.
-# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
-
-TOC_INCLUDE_HEADINGS   = 0
-
-# When enabled doxygen tries to link words that correspond to documented
-# classes, or namespaces to their corresponding documentation. Such a link can
-# be prevented in individual cases by putting a % sign in front of the word or
-# globally by setting AUTOLINK_SUPPORT to NO.
-# The default value is: YES.
-
-AUTOLINK_SUPPORT       = YES
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
-# to include (a tag file for) the STL sources as input, then you should set this
-# tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string);
-# versus func(std::string) {}). This also make the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-# The default value is: NO.
-
-BUILTIN_STL_SUPPORT    = YES
-
-# For Microsoft's IDL there are propget and propput attributes to indicate
-# getter and setter methods for a property. Setting this option to YES will make
-# doxygen to replace the get and set methods by a property in the documentation.
-# This will only work if the methods are indeed getting or setting a simple
-# type. If this is not the case, or you want to show the methods anyway, you
-# should set this option to NO.
-# The default value is: YES.
-
-IDL_PROPERTY_SUPPORT   = NO
-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
-# all members of a group must be documented explicitly.
-# The default value is: NO.
-
-DISTRIBUTE_GROUP_DOC   = NO
-
-# If one adds a struct or class to a group and this option is enabled, then also
-# any nested class or struct is added to the same group. By default this option
-# is disabled and one has to add nested compounds explicitly via \ingroup.
-# The default value is: NO.
-
-GROUP_NESTED_COMPOUNDS = NO
-
-# Set the SUBGROUPING tag to YES to allow class member groups of the same type
-# (for instance a group of public functions) to be put as a subgroup of that
-# type (e.g. under the Public Functions section). Set it to NO to prevent
-# subgrouping. Alternatively, this can be done per class using the
-# \nosubgrouping command.
-# The default value is: YES.
-
-SUBGROUPING            = YES
-
-# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
-# are shown inside the group in which they are included (e.g. using \ingroup)
-# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
-# and RTF).
-#
-# Note that this feature does not work in combination with
-# SEPARATE_MEMBER_PAGES.
-# The default value is: NO.
-
-INLINE_GROUPED_CLASSES = NO
-
-# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
-# with only public data fields or simple typedef fields will be shown inline in
-# the documentation of the scope in which they are defined (i.e. file,
-# namespace, or group documentation), provided this scope is documented. If set
-# to NO, structs, classes, and unions are shown on a separate page (for HTML and
-# Man pages) or section (for LaTeX and RTF).
-# The default value is: NO.
-
-INLINE_SIMPLE_STRUCTS  = NO
-
-# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
-# enum is documented as struct, union, or enum with the name of the typedef. So
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
-# with name TypeT. When disabled the typedef will appear as a member of a file,
-# namespace, or class. And the struct will be named TypeS. This can typically be
-# useful for C code in case the coding convention dictates that all compound
-# types are typedef'ed and only the typedef is referenced, never the tag name.
-# The default value is: NO.
-
-TYPEDEF_HIDES_STRUCT   = NO
-
-# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
-# cache is used to resolve symbols given their name and scope. Since this can be
-# an expensive process and often the same symbol appears multiple times in the
-# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
-# doxygen will become slower. If the cache is too large, memory is wasted. The
-# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
-# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
-# symbols. At the end of a run doxygen will report the cache usage and suggest
-# the optimal cache size from a speed point of view.
-# Minimum value: 0, maximum value: 9, default value: 0.
-
-LOOKUP_CACHE_SIZE      = 0
-
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
-# documentation are documented, even if no documentation was available. Private
-# class members and static file members will be hidden unless the
-# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
-# Note: This will also disable the warnings about undocumented members that are
-# normally produced when WARNINGS is set to YES.
-# The default value is: NO.
-
-EXTRACT_ALL            = NO
-
-# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
-# be included in the documentation.
-# The default value is: NO.
-
-EXTRACT_PRIVATE        = NO
-
-# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
-# scope will be included in the documentation.
-# The default value is: NO.
-
-EXTRACT_PACKAGE        = NO
-
-# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
-# included in the documentation.
-# The default value is: NO.
-
-EXTRACT_STATIC         = YES
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
-# locally in source files will be included in the documentation. If set to NO,
-# only classes defined in header files are included. Does not have any effect
-# for Java sources.
-# The default value is: YES.
-
-EXTRACT_LOCAL_CLASSES  = YES
-
-# If this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base name of
-# the file that contains the anonymous namespace. By default anonymous namespace
-# are hidden.
-# The default value is: NO.
-
-EXTRACT_ANON_NSPACES   = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
-# undocumented members inside documented classes or files. If set to NO these
-# members will be included in the various overviews, but no documentation
-# section is generated. This option has no effect if EXTRACT_ALL is enabled.
-# The default value is: NO.
-
-HIDE_UNDOC_MEMBERS     = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy. If set
-# to NO, these classes will be included in the various overviews. This option
-# has no effect if EXTRACT_ALL is enabled.
-# The default value is: NO.
-
-HIDE_UNDOC_CLASSES     = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
-# (class|struct|union) declarations. If set to NO, these declarations will be
-# included in the documentation.
-# The default value is: NO.
-
-HIDE_FRIEND_COMPOUNDS  = NO
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
-# documentation blocks found inside the body of a function. If set to NO, these
-# blocks will be appended to the function's detailed documentation block.
-# The default value is: NO.
-
-HIDE_IN_BODY_DOCS      = YES
-
-# The INTERNAL_DOCS tag determines if documentation that is typed after a
-# \internal command is included. If the tag is set to NO then the documentation
-# will be excluded. Set it to YES to include the internal documentation.
-# The default value is: NO.
-
-INTERNAL_DOCS          = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
-# names in lower-case letters. If set to YES, upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
-# The default value is: system dependent.
-
-CASE_SENSE_NAMES       = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
-# their full class and namespace scopes in the documentation. If set to YES, the
-# scope will be hidden.
-# The default value is: NO.
-
-HIDE_SCOPE_NAMES       = NO
-
-# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
-# append additional text to a page's title, such as Class Reference. If set to
-# YES the compound reference will be hidden.
-# The default value is: NO.
-
-HIDE_COMPOUND_REFERENCE= NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
-# the files that are included by a file in the documentation of that file.
-# The default value is: YES.
-
-SHOW_INCLUDE_FILES     = YES
-
-# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
-# grouped member an include statement to the documentation, telling the reader
-# which file to include in order to use the member.
-# The default value is: NO.
-
-SHOW_GROUPED_MEMB_INC  = NO
-
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
-# files with double quotes in the documentation rather than with sharp brackets.
-# The default value is: NO.
-
-FORCE_LOCAL_INCLUDES   = NO
-
-# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
-# documentation for inline members.
-# The default value is: YES.
-
-INLINE_INFO            = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
-# (detailed) documentation of file and class members alphabetically by member
-# name. If set to NO, the members will appear in declaration order.
-# The default value is: YES.
-
-SORT_MEMBER_DOCS       = YES
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
-# descriptions of file, namespace and class members alphabetically by member
-# name. If set to NO, the members will appear in declaration order. Note that
-# this will also influence the order of the classes in the class list.
-# The default value is: NO.
-
-SORT_BRIEF_DOCS        = NO
-
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
-# (brief and detailed) documentation of class members so that constructors and
-# destructors are listed first. If set to NO the constructors will appear in the
-# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
-# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
-# member documentation.
-# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
-# detailed member documentation.
-# The default value is: NO.
-
-SORT_MEMBERS_CTORS_1ST = YES
-
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
-# of group names into alphabetical order. If set to NO the group names will
-# appear in their defined order.
-# The default value is: NO.
-
-SORT_GROUP_NAMES       = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
-# fully-qualified names, including namespaces. If set to NO, the class list will
-# be sorted only by class name, not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the alphabetical
-# list.
-# The default value is: NO.
-
-SORT_BY_SCOPE_NAME     = NO
-
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
-# type resolution of all parameters of a function it will reject a match between
-# the prototype and the implementation of a member function even if there is
-# only one candidate or it is obvious which candidate to choose by doing a
-# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
-# accept a match between prototype and implementation in such cases.
-# The default value is: NO.
-
-STRICT_PROTO_MATCHING  = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
-# list. This list is created by putting \todo commands in the documentation.
-# The default value is: YES.
-
-GENERATE_TODOLIST      = NO
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
-# list. This list is created by putting \test commands in the documentation.
-# The default value is: YES.
-
-GENERATE_TESTLIST      = NO
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
-# list. This list is created by putting \bug commands in the documentation.
-# The default value is: YES.
-
-GENERATE_BUGLIST       = NO
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
-# the deprecated list. This list is created by putting \deprecated commands in
-# the documentation.
-# The default value is: YES.
-
-GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional documentation
-# sections, marked by \if <section_label> ... \endif and \cond <section_label>
-# ... \endcond blocks.
-
-ENABLED_SECTIONS       =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
-# initial value of a variable or macro / define can have for it to appear in the
-# documentation. If the initializer consists of more lines than specified here
-# it will be hidden. Use a value of 0 to hide initializers completely. The
-# appearance of the value of individual variables and macros / defines can be
-# controlled using \showinitializer or \hideinitializer command in the
-# documentation regardless of this setting.
-# Minimum value: 0, maximum value: 10000, default value: 30.
-
-MAX_INITIALIZER_LINES  = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
-# the bottom of the documentation of classes and structs. If set to YES, the
-# list will mention the files that were used to generate the documentation.
-# The default value is: YES.
-
-SHOW_USED_FILES        = YES
-
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
-# will remove the Files entry from the Quick Index and from the Folder Tree View
-# (if specified).
-# The default value is: YES.
-
-SHOW_FILES             = NO
-
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
-# page. This will remove the Namespaces entry from the Quick Index and from the
-# Folder Tree View (if specified).
-# The default value is: YES.
-
-SHOW_NAMESPACES        = YES
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from
-# the version control system). Doxygen will invoke the program by executing (via
-# popen()) the command command input-file, where command is the value of the
-# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
-# by doxygen. Whatever the program writes to standard output is used as the file
-# version. For an example see the documentation.
-
-FILE_VERSION_FILTER    =
-
-# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
-# by doxygen. The layout file controls the global structure of the generated
-# output files in an output format independent way. To create the layout file
-# that represents doxygen's defaults, run doxygen with the -l option. You can
-# optionally specify a file name after the option, if omitted DoxygenLayout.xml
-# will be used as the name of the layout file.
-#
-# Note that if you run doxygen from a directory containing a file called
-# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
-# tag is left empty.
-
-LAYOUT_FILE            =
-
-# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
-# the reference definitions. This must be a list of .bib files. The .bib
-# extension is automatically appended if omitted. This requires the bibtex tool
-# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
-# For LaTeX the style of the bibliography can be controlled using
-# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
-# search path. See also \cite for info how to create references.
-
-CITE_BIB_FILES         =
-
-#---------------------------------------------------------------------------
-# Configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated to
-# standard output by doxygen. If QUIET is set to YES this implies that the
-# messages are off.
-# The default value is: NO.
-
-QUIET                  = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
-# this implies that the warnings are on.
-#
-# Tip: Turn warnings on while writing the documentation.
-# The default value is: YES.
-
-WARNINGS               = YES
-
-# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
-# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
-# will automatically be disabled.
-# The default value is: YES.
-
-WARN_IF_UNDOCUMENTED   = YES
-
-# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some parameters
-# in a documented function, or documenting parameters that don't exist or using
-# markup commands wrongly.
-# The default value is: YES.
-
-WARN_IF_DOC_ERROR      = YES
-
-# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
-# are documented, but have no documentation for their parameters or return
-# value. If set to NO, doxygen will only warn about wrong or incomplete
-# parameter documentation, but not about the absence of documentation.
-# The default value is: NO.
-
-WARN_NO_PARAMDOC       = NO
-
-# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
-# a warning is encountered.
-# The default value is: NO.
-
-WARN_AS_ERROR          = NO
-
-# The WARN_FORMAT tag determines the format of the warning messages that doxygen
-# can produce. The string should contain the $file, $line, and $text tags, which
-# will be replaced by the file and line number from which the warning originated
-# and the warning text. Optionally the format may contain $version, which will
-# be replaced by the version of the file (if it could be obtained via
-# FILE_VERSION_FILTER)
-# The default value is: $file:$line: $text.
-
-WARN_FORMAT            = "$file:$line: $text "
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning and error
-# messages should be written. If left blank the output is written to standard
-# error (stderr).
-
-WARN_LOGFILE           =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# The INPUT tag is used to specify the files and/or directories that contain
-# documented source files. You may enter file names like myfile.cpp or
-# directories like /usr/src/myproject. Separate the files or directories with
-# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
-# Note: If this tag is empty the current directory is searched.
-
-INPUT                  = ../../include/bout \
-                         ../../src
-
-# This tag can be used to specify the character encoding of the source files
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
-# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
-# documentation (see: http://www.gnu.org/software/libiconv) for the list of
-# possible encodings.
-# The default value is: UTF-8.
-
-INPUT_ENCODING         = UTF-8
-
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
-# *.h) to filter out the source-files in the directories.
-#
-# Note that for custom extensions or not directly supported extensions you also
-# need to set EXTENSION_MAPPING for the extension otherwise the files are not
-# read by doxygen.
-#
-# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
-# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
-# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
-# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
-# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
-
-FILE_PATTERNS          = *.c \
-                         *.cxx \
-                         *.h \
-                         *.hxx \
-                         *.py
-
-# The RECURSIVE tag can be used to specify whether or not subdirectories should
-# be searched for input files as well.
-# The default value is: NO.
-
-RECURSIVE              = YES
-
-# The EXCLUDE tag can be used to specify files and/or directories that should be
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-#
-# Note that relative paths are relative to the directory from which doxygen is
-# run.
-
-EXCLUDE                = ../../examples \
-                         ../../tools/ \
-                         ../../manual/ \
-                         ../../bin/ \
-                         ../../externalpackages/googletest/ \
-                         ../../tests/
-
-# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
-# directories that are symbolic links (a Unix file system feature) are excluded
-# from the input.
-# The default value is: NO.
-
-EXCLUDE_SYMLINKS       = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories.
-#
-# Note that the wildcards are matched against the file with absolute path, so to
-# exclude all test directories for example use the pattern */test/*
-
-EXCLUDE_PATTERNS       =
-
-#---------------------------------------------------------------------------
-# Configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
-# generated. Documented entities will be cross-referenced with these sources.
-#
-# Note: To get rid of all source code in the generated output, make sure that
-# also VERBATIM_HEADERS is set to NO.
-# The default value is: NO.
-
-SOURCE_BROWSER         = NO
-
-# Setting the INLINE_SOURCES tag to YES will include the body of functions,
-# classes and enums directly into the documentation.
-# The default value is: NO.
-
-INLINE_SOURCES         = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
-# special comment blocks from generated source code fragments. Normal C, C++ and
-# Fortran comments will always remain visible.
-# The default value is: YES.
-
-STRIP_CODE_COMMENTS    = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
-# function all documented functions referencing it will be listed.
-# The default value is: NO.
-
-REFERENCED_BY_RELATION = NO
-
-# If the REFERENCES_RELATION tag is set to YES then for each documented function
-# all documented entities called/used by that function will be listed.
-# The default value is: NO.
-
-REFERENCES_RELATION    = NO
-
-# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
-# to YES then the hyperlinks from functions in REFERENCES_RELATION and
-# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
-# link to the documentation.
-# The default value is: YES.
-
-REFERENCES_LINK_SOURCE = YES
-
-# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
-# source code will show a tooltip with additional information such as prototype,
-# brief description and links to the definition and documentation. Since this
-# will make the HTML file larger and loading of large files a bit slower, you
-# can opt to disable this feature.
-# The default value is: YES.
-# This tag requires that the tag SOURCE_BROWSER is set to YES.
-
-SOURCE_TOOLTIPS        = NO
-
-# If the USE_HTAGS tag is set to YES then the references to source code will
-# point to the HTML generated by the htags(1) tool instead of doxygen built-in
-# source browser. The htags tool is part of GNU's global source tagging system
-# (see http://www.gnu.org/software/global/global.html). You will need version
-# 4.8.6 or higher.
-#
-# To use it do the following:
-# - Install the latest version of global
-# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
-# - Make sure the INPUT points to the root of the source tree
-# - Run doxygen as normal
-#
-# Doxygen will invoke htags (and that will in turn invoke gtags), so these
-# tools must be available from the command line (i.e. in the search path).
-#
-# The result: instead of the source browser generated by doxygen, the links to
-# source code will now point to the output of htags.
-# The default value is: NO.
-# This tag requires that the tag SOURCE_BROWSER is set to YES.
-
-USE_HTAGS              = NO
-
-# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
-# verbatim copy of the header file for each class for which an include is
-# specified. Set to NO to disable this.
-# See also: Section \class.
-# The default value is: YES.
-
-VERBATIM_HEADERS       = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
-# compounds will be generated. Enable this if the project contains a lot of
-# classes, structs, unions or interfaces.
-# The default value is: YES.
-
-ALPHABETICAL_INDEX     = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
-# The default value is: YES.
-
-GENERATE_HTML          = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
-# The default value is: YES.
-
-GENERATE_LATEX         = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the XML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
-# captures the structure of the code including all documentation.
-# The default value is: NO.
-
-GENERATE_XML           = YES
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: xml.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_OUTPUT             = xml
-
-# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
-# listings (including syntax highlighting and cross-referencing information) to
-# the XML output. Note that enabling this will significantly increase the size
-# of the XML output.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_PROGRAMLISTING     = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
-#---------------------------------------------------------------------------
-
-# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
-# C-preprocessor directives found in the sources and include files.
-# The default value is: YES.
-
-ENABLE_PREPROCESSING   = YES
-
-# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
-# in the source code. If set to NO, only conditional compilation will be
-# performed. Macro expansion can be done in a controlled way by setting
-# EXPAND_ONLY_PREDEF to YES.
-# The default value is: NO.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-MACRO_EXPANSION        = YES
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
-# the macro expansion is limited to the macros specified with the PREDEFINED and
-# EXPAND_AS_DEFINED tags.
-# The default value is: NO.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-EXPAND_ONLY_PREDEF     = NO
-
-# If the SEARCH_INCLUDES tag is set to YES, the include files in the
-# INCLUDE_PATH will be searched if a #include is found.
-# The default value is: YES.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-SEARCH_INCLUDES        = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by the
-# preprocessor.
-# This tag requires that the tag SEARCH_INCLUDES is set to YES.
-
-INCLUDE_PATH           =
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will be
-# used.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-INCLUDE_FILE_PATTERNS  =
-
-# The PREDEFINED tag can be used to specify one or more macro names that are
-# defined before the preprocessor is started (similar to the -D option of e.g.
-# gcc). The argument of the tag is a list of macros of the form: name or
-# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
-# is assumed. To prevent a macro definition from being undefined via #undef or
-# recursively expanded use the := operator instead of the = operator.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-PREDEFINED             = BACKTRACE \
-                         BOUT_FPE \
-                         BOUT_CHECK_LEVEL=3 \
-                         BOUT_HAS_ARKODE \
-                         BOUT_HAS_CVODE \
-                         BOUT_HAS_FFTW \
-                         BOUT_HAS_GETTEXT \
-                         BOUT_HAS_HYPRE \
-                         BOUT_HAS_IDA \
-                         BOUT_HAS_LAPACK \
-                         BOUT_HAS_NETCDF \
-                         BOUT_HAS_PETSC \
-                         BOUT_HAS_PRETTY_FUNCTION \
-                         BOUT_HAS_PVODE \
-                         BOUT_HAS_SCOREP \
-                         BOUT_HAS_SLEPC \
-                         BOUT_HAS_SUNDIALS \
-                         BOUT_HAS_UUID_SYSTEM_GENERATOR \
-                         BOUT_USE_BACKTRACE \
-                         BOUT_USE_COLOR \
-                         BOUT_USE_OPENMP \
-                         BOUT_USE_OUTPUT_DEBUG \
-                         BOUT_USE_SIGFPE \
-                         BOUT_USE_SIGNAL \
-                         BOUT_USE_TRACK \
-                         BOUT_HAS_UMPIRE \
-                         BOUT_HAS_CALIPER \
-                         BOUT_HAS_RAJA \
-                         BOUT_USE_CUDA \
-                         BOUT_METRIC_TYPE=2D \
-                         BOUT_USE_METRIC_3D \
-                         BOUT_USE_MSGSTACK \
-                         CHECK=3 \
-                         LOGCOLOR \
-                         PETSC_HAS_SUNDIALS \
-                         PETSC_RELEASE \
-                         PETSC_VERSION=3.8 \
-                         UNUSED(x)=x \
-                         _OPENMP
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
-# tag can be used to specify a list of macro names that should be expanded. The
-# macro definition that is found in the sources will be used. Use the PREDEFINED
-# tag if you want to use a different macro definition that overrules the
-# definition found in the source code.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-EXPAND_AS_DEFINED      =
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
-# remove all references to function-like macros that are alone on a line, have
-# an all uppercase name, and do not end with a semicolon. Such function macros
-# are typically used for boiler-plate code, and will confuse the parser if not
-# removed.
-# The default value is: YES.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-SKIP_FUNCTION_MACROS   = YES
-
-#---------------------------------------------------------------------------
-# Configuration options related to external references
-#---------------------------------------------------------------------------
-
-# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will be
-# listed.
-# The default value is: YES.
-
-EXTERNAL_GROUPS        = NO
-
-# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
-# the related pages index. If set to NO, only the current project's pages will
-# be listed.
-# The default value is: YES.
-
-EXTERNAL_PAGES         = NO
-
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of 'which perl').
-# The default file (with absolute path) is: /usr/bin/perl.
-
-PERL_PATH              = /usr/bin/perl
-
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
-# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
-# NO turns the diagrams off. Note that this option also works with HAVE_DOT
-# disabled, but it is recommended to install and use dot, since it yields more
-# powerful graphs.
-# The default value is: YES.
-
-CLASS_DIAGRAMS         = NO
-
-# If set to YES the inheritance and collaboration graphs will hide inheritance
-# and usage relations if the target is undocumented or is not a class.
-# The default value is: YES.
-
-HIDE_UNDOC_RELATIONS   = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz (see:
-# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
-# Bell Labs. The other options in this section have no effect if this option is
-# set to NO
-# The default value is: NO.
-
-HAVE_DOT               = NO
diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index d8ab76cf23..9d8f1cc4f4 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -104,10 +104,7 @@ def __getattr__(cls, name):
 # readthedocs currently runs out of memory if we actually dare to try to do this
 if has_breathe:
     # Run doxygen to generate the XML sources
-    if on_readthedocs:
-        subprocess.call("cd ../doxygen; doxygen Doxyfile_readthedocs", shell=True)
-    else:
-        subprocess.call("cd ../doxygen; doxygen Doxyfile", shell=True)
+    subprocess.run(["doxygen", "Doxyfile"], cwd="../doxygen", check=True)
     # Now use breathe.apidoc to autogen rst files for each XML file
     apidoc_args = argparse.Namespace(
         destdir="_breathe_autogen/",

From 87ec9b094103b9a846b5c6d75a4f37d176a04875 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 17:18:49 +0000
Subject: [PATCH 0041/1827] Remove unused `#define` from petsc/slepc solvers

---
 src/solver/impls/petsc/petsc.hxx | 1 -
 src/solver/impls/slepc/slepc.hxx | 2 --
 2 files changed, 3 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index 349f40bad8..2b2b5de67a 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -56,7 +56,6 @@ RegisterSolver<PetscSolver> registersolverpetsc("petsc");
 }
 
 using BoutReal = PetscScalar;
-#define OPT_SIZE 40
 
 using rhsfunc = int (*)(BoutReal);
 
diff --git a/src/solver/impls/slepc/slepc.hxx b/src/solver/impls/slepc/slepc.hxx
index 88f35a04f9..6872248675 100644
--- a/src/solver/impls/slepc/slepc.hxx
+++ b/src/solver/impls/slepc/slepc.hxx
@@ -53,8 +53,6 @@ class SlepcSolver;
 
 #include <vector>
 
-#define OPT_SIZE 40
-
 // Define a name to use with SolverType to indicate SlepcSolver
 // is in charge of advancing fields
 #define SOLVERSLEPCSELF "self"

From 1eb0c4fd10b9093816694d682ec1cdcd7ebaaa83 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 17:21:10 +0000
Subject: [PATCH 0042/1827] Remove duplicate function pointer alias

---
 src/solver/impls/petsc/petsc.hxx | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index 2b2b5de67a..30c954f62d 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -57,8 +57,6 @@ RegisterSolver<PetscSolver> registersolverpetsc("petsc");
 
 using BoutReal = PetscScalar;
 
-using rhsfunc = int (*)(BoutReal);
-
 extern BoutReal simtime;
 
 /// Monitor function called on every internal timestep

From f47847ce574b3aa5cb493cba2c2fc373cd2a359a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 17:21:38 +0000
Subject: [PATCH 0043/1827] Remove unnecessary type alias

We might want some check that `BoutReal == PetscScalar` but this type
alias would just cover up any problem. At best, this wouldn't compile,
but it's possible it would just lead to link time problems
---
 src/solver/impls/petsc/petsc.hxx | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index 30c954f62d..7b4e9caeab 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -55,8 +55,6 @@ namespace {
 RegisterSolver<PetscSolver> registersolverpetsc("petsc");
 }
 
-using BoutReal = PetscScalar;
-
 extern BoutReal simtime;
 
 /// Monitor function called on every internal timestep

From 3ee4153a7d2aec62c985fd1883b8113eba1e9400 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 17:34:25 +0000
Subject: [PATCH 0044/1827] Docs: Add a couple of macros that doxygen should
 ignore

---
 manual/doxygen/Doxyfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/manual/doxygen/Doxyfile b/manual/doxygen/Doxyfile
index e27df586ec..ad49544189 100644
--- a/manual/doxygen/Doxyfile
+++ b/manual/doxygen/Doxyfile
@@ -1045,7 +1045,9 @@ PREDEFINED             = BACKTRACE \
                          PETSC_RELEASE \
                          PETSC_VERSION=3.8 \
                          UNUSED(x)=x \
-                         _OPENMP
+                         _OPENMP \
+                         BOUT_HOST_DEVICE \
+                         MAYBE_UNUSED(x)=x
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The

From bc4345647995a29e2d12b84132673be77982b4fd Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 22 Jan 2024 17:36:35 +0000
Subject: [PATCH 0045/1827] Docs: Don't process .cxx files

---
 manual/doxygen/Doxyfile | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/manual/doxygen/Doxyfile b/manual/doxygen/Doxyfile
index ad49544189..7698ac363d 100644
--- a/manual/doxygen/Doxyfile
+++ b/manual/doxygen/Doxyfile
@@ -766,9 +766,7 @@ INPUT_ENCODING         = UTF-8
 # *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
 # *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
 
-FILE_PATTERNS          = *.c \
-                         *.cxx \
-                         *.h \
+FILE_PATTERNS          = *.h \
                          *.hxx \
                          *.py
 

From 37fea9184ff9a02afc56c7dd8260948bac74ffd4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 23 Jan 2024 15:31:08 +0000
Subject: [PATCH 0046/1827] Docs: Fix some latex equations in docstrings

---
 include/bout/field.hxx        |  2 +-
 include/bout/gyro_average.hxx | 14 +++++++++++---
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 9a425942c1..5ee164e958 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -565,7 +565,7 @@ FIELD_FUNC(exp, ::exp)
 /// Natural logarithm of \p f over region \p rgn, inverse of
 /// exponential
 ///
-///     \f$\ln(\exp(f)) = f\f$
+/// \f[\ln(\exp(f)) = f\f]
 ///
 /// This loops over the entire domain, including guard/boundary cells by
 /// default (can be changed using the rgn argument)
diff --git a/include/bout/gyro_average.hxx b/include/bout/gyro_average.hxx
index 0f9f2a13f7..413b2a4627 100644
--- a/include/bout/gyro_average.hxx
+++ b/include/bout/gyro_average.hxx
@@ -41,7 +41,9 @@ constexpr int GYRO_FLAGS = INVERT_BNDRY_ONE + INVERT_RHS;
 
 /// Gyro-average using Taylor series approximation
 ///
-///     \f$ \Gamma(f) = f + \rho^2 \nabla_\perp^2(f)\f$
+/// \f[
+///    \Gamma(f) = f + \rho^2 \nabla_\perp^2(f)
+/// \f]
 ///
 /// Note: Faster, but less robust than Pade approximations
 ///
@@ -51,7 +53,9 @@ Field3D gyroTaylor0(const Field3D& f, const Field3D& rho);
 
 /// Gyro-average using Pade approximation
 ///
-///     \f$ \Gamma_0 = (1 - \rho^2 \nabla_\perp^2)g = f\f$
+/// \f[
+///    \Gamma_0 = (1 - \rho^2 \nabla_\perp^2)g = f
+/// \f]
 ///
 /// NOTE: Uses Z average of rho for efficient inversion
 ///
@@ -70,7 +74,11 @@ Field3D gyroPade0(const Field3D& f, const Field2D& rho,
 Field3D gyroPade0(const Field3D& f, BoutReal rho, int inner_boundary_flags = GYRO_FLAGS,
                   int outer_boundary_flags = GYRO_FLAGS);
 
-/// Pade approximation \f$Gamma_1 = (1 - \frac{1}{2} \rho^2 \nabla_\perp^2)g = f\f$
+/// Pade approximation
+///
+/// \f[
+///    \Gamma_1 = (1 - \frac{1}{2} \rho^2 \nabla_\perp^2)g = f
+/// \f]
 ///
 /// Note: Have to use Z average of rho for efficient inversion
 ///

From f61651514d479431b62d5f25147c883dc0f637de Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 24 Jan 2024 14:11:31 +0000
Subject: [PATCH 0047/1827] Tweak `HypreLib` docs

Fixes formatting of example, and ensures file docstring doesn't get
attached to the `bout` namespace and so appear in every single file
that has the namespace!
---
 include/bout/hyprelib.hxx | 38 ++++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/include/bout/hyprelib.hxx b/include/bout/hyprelib.hxx
index 407b0eacda..07daa0b641 100644
--- a/include/bout/hyprelib.hxx
+++ b/include/bout/hyprelib.hxx
@@ -1,24 +1,24 @@
-/*!************************************************************************
+/*! \file ******************************************************************
  * Provides access to the Hypre library, handling initialisation and
  * finalisation.
  *
  * Usage
  * -----
  *
- * #include <bout/hyprelib.hxx>
+ *     #include <bout/hyprelib.hxx>
  *
- * class MyClass {
- *   public:
+ *     class MyClass {
+ *       HypreLib lib;
+ *     public:
+ *       // ...
+ *     };
  *
- *   private:
- *     HypreLib lib;
- * };
  *
- *
- * This will then automatically initialise Hypre the first time an object
- * is created, and finalise it when the last object is destroyed.
- *
- **************************************************************************
+ * This will then automatically ensure Hypre is initialised the first
+ * time an instance is created, and finalise it when the last instances is
+ * destroyed (across all objects using `HypreLib`)
+ */
+/**************************************************************************
  * Copyright 2012 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
@@ -43,16 +43,17 @@
 #ifndef BOUT_HYPRELIB_H
 #define BOUT_HYPRELIB_H
 
-#include "bout/build_config.hxx"
+#include "bout/build_defines.hxx"
 
 namespace bout {
-#if BOUT_HAS_HYPRE
 /*!
  * Handles initialisation and finalisation of Hypre library.
- * The first instance which is created initialises Hypre.
- * Keeps a count of the number of how many instances exist
- * when the last instance is destroyed it finalises Hypre.
+ *
+ * The first instance which is created initialises Hypre. Keeps a
+ * count of the number of how many instances exist, and when the last
+ * instance is destroyed it finalises Hypre.
  */
+#if BOUT_HAS_HYPRE
 class HypreLib {
 public:
   explicit HypreLib();
@@ -64,10 +65,11 @@ public:
 
   ~HypreLib();
 
+  /// Immediately finalise Hypre library
   static void cleanup();
 
 private:
-  static int count; ///< How many instances?
+  static int count; ///< Current number of instances
 };
 
 #else // BOUT_HAS_HYPRE

From de2599d7ff260fede3ce3bf487d3e38023ec3b61 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 24 Jan 2024 14:12:56 +0000
Subject: [PATCH 0048/1827] Docs: Always set breathe config even if not
 generating files

---
 manual/sphinx/conf.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 9d8f1cc4f4..a7c4b27578 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -126,11 +126,12 @@ def __getattr__(cls, name):
     for key, value in apidoc.TYPEDICT.items():
         apidoc.create_modules_toc_file(key, value, apidoc_args)
 
-    # -- Options for breathe extension ----------------------------------------
 
-    breathe_projects = {"BOUT++": "../doxygen/bout/xml"}
-    breathe_default_project = "BOUT++"
-    breathe_default_members = ("members",)
+# -- Options for breathe extension ----------------------------------------
+
+breathe_projects = {"BOUT++": "../doxygen/bout/xml"}
+breathe_default_project = "BOUT++"
+breathe_default_members = ("members",)
 
 # -- General configuration ------------------------------------------------
 

From e30da8cb646eac146cb60a6b18f10fd013881e27 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 24 Jan 2024 14:25:58 +0000
Subject: [PATCH 0049/1827] Docs: Don't show header to include in docs

---
 manual/sphinx/conf.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index a7c4b27578..67507633b6 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -132,6 +132,7 @@ def __getattr__(cls, name):
 breathe_projects = {"BOUT++": "../doxygen/bout/xml"}
 breathe_default_project = "BOUT++"
 breathe_default_members = ("members",)
+breathe_show_include = False
 
 # -- General configuration ------------------------------------------------
 

From 8e6c93d9a6752636c59a8de44c5796761c960379 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 24 Jan 2024 14:26:31 +0000
Subject: [PATCH 0050/1827] Docs: Don't run doxygen on python files

---
 manual/doxygen/Doxyfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/manual/doxygen/Doxyfile b/manual/doxygen/Doxyfile
index 7698ac363d..1cc235558a 100644
--- a/manual/doxygen/Doxyfile
+++ b/manual/doxygen/Doxyfile
@@ -767,8 +767,7 @@ INPUT_ENCODING         = UTF-8
 # *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
 
 FILE_PATTERNS          = *.h \
-                         *.hxx \
-                         *.py
+                         *.hxx
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.

From 709de64e11e06d7b4e0e06e40cd5c9559e708191 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 24 Jan 2024 17:06:01 +0000
Subject: [PATCH 0051/1827] Docs: Fix some egregiously outdated solver docs

---
 manual/sphinx/user_docs/time_integration.rst | 58 ++++++++++----------
 1 file changed, 28 insertions(+), 30 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 7d0b56abcc..5a33b85e08 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -987,28 +987,33 @@ This may in some cases be less efficient.
 Implementation internals
 ------------------------
 
+.. todo:: Update these docs for modern API
+
 The solver is the interface between BOUT++ and the time-integration
-code such as SUNDIALS. All solvers implement the `Solver`
-class interface (see ``src/solver/generic_solver.hxx``).
+code such as SUNDIALS. All solvers implement the `Solver` class
+interface.
 
 First all the fields which are to be evolved need to be added to the
-solver. These are always done in pairs, the first specifying the field,
-and the second the time-derivative::
+solver with `Solver::add`::
+
+    virtual void add(Field2D &v, const std::string& name);
 
-    void add(Field2D &v, Field2D &F_v, const char* name);
+This is normally called in the `PhysicsModel::init` initialisation
+routine. This is a virtual function so that individual solver
+implementations can keep track of additional information if required.
 
-This is normally called in the `PhysicsModel::init` initialisation routine.
-Some solvers (e.g. IDA) can support constraints, which need to be added
-in the same way as evolving fields::
+Some solvers (e.g. IDA) can support constraints, which need
+to be added in the same way as evolving fields::
 
-    bool constraints();
-    void constraint(Field2D &v, Field2D &C_v, const char* name);
+    virtual bool constraints();
+    virtual void constraint(Field2D &v, Field2D &C_v, std::string name);
 
-The ``constraints()`` function tests whether or not the current solver
-supports constraints. The format of ``constraint(...)`` is the same as
-``add``, except that now the solver will attempt to make ``C_v`` zero.
-If ``constraint`` is called when the solver doesn’t support them then an
-error should occur.
+The `Solver::constraints` function tests whether or not the current
+solver supports constraints. The format of `Solver::constraint`
+similar to `Solver::add`, except that it takes a second argument,
+``C_v``, which the solver will attempt to make zero. If ``constraint``
+is called when the solver doesn’t support them then an error will
+occur.
 
 If the physics model implements a preconditioner or Jacobian-vector
 multiplication routine, these can be passed to the solver during
@@ -1025,23 +1030,16 @@ be ignored.
 Once the problem to be solved has been specified, the solver can be
 initialised using::
 
-    int init();
+    virtual int init();
 
-which returns an error code (0 on success). This is currently called in
-:doc:`bout++.cxx<../_breathe_autogen/file/bout_09_09_8cxx>`::
-
-    if (solver.init()) {
-      output.write("Failed to initialise solver. Aborting\n");
-      return(1);
-    }
-
-which passes the (physics module) RHS function `PhysicsModel::rhs` to the
-solver along with the number and size of the output steps.
-
-::
+which returns an error code (0 on success). This is function is
+essential for implementations that must allocate memory based on the
+total number of fields being evolved, as this won't be known until
+after all calls to `Solver::add` and `Solver::constraint` have been
+handled. One of the very first things overrides for ``init`` should do
+is to call the base implementation `Solver::init` to handle the
+generic initialisation.
 
-    typedef int (*MonitorFunc)(BoutReal simtime, int iter, int NOUT);
-    int run(MonitorFunc f);
 
 .. [1]
    Taken from a talk by L.Chacon available here

From 3ed4c7ccff07675eaafa3e4c2a26525768529391 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 24 Jan 2024 17:44:34 +0000
Subject: [PATCH 0052/1827] Docs: Fix some broken links now `.cxx` files aren't
 included

---
 manual/sphinx/developer_docs/mesh.rst              | 6 +++---
 manual/sphinx/user_docs/differential_operators.rst | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/manual/sphinx/developer_docs/mesh.rst b/manual/sphinx/developer_docs/mesh.rst
index c592773324..908b883737 100644
--- a/manual/sphinx/developer_docs/mesh.rst
+++ b/manual/sphinx/developer_docs/mesh.rst
@@ -34,9 +34,9 @@ The `Mesh constructor <Mesh::Mesh>` takes `GridDataSource` and
 `Options` objects. You can also call `Mesh::create` with just one of
 these objects, which will call out to the `MeshFactory` singleton to
 create a mesh "automatically". This is the way that it is done in
-:doc:`bout++.cxx <../_breathe_autogen/file/bout_09_09_8cxx>`. Once you
-have instantiated a `Mesh` object, you can then call `Mesh::load` to
-read in all the appropriate variables from the `GridDataSource`::
+`BoutInitialise`. Once you have instantiated a `Mesh` object, you can
+then call `Mesh::load` to read in all the appropriate variables from
+the `GridDataSource`::
 
     mesh = Mesh::create();  ///< Create the mesh
     mesh->load();           ///< Load from sources. Required for Field initialisation
diff --git a/manual/sphinx/user_docs/differential_operators.rst b/manual/sphinx/user_docs/differential_operators.rst
index 50a795f7ff..25abc15e70 100644
--- a/manual/sphinx/user_docs/differential_operators.rst
+++ b/manual/sphinx/user_docs/differential_operators.rst
@@ -528,7 +528,7 @@ cell is added to another. There are several caveats to this:
   precision.
 
 The methods can be used by including the
-:doc:`header<../_breathe_autogen/file/fv__ops_8cxx>`::
+:doc:`header<../_breathe_autogen/file/fv__ops_8hxx>`::
 
    #include "bout/fv_ops.hxx"
 
@@ -536,7 +536,7 @@ The methods can be used by including the
 **Note** The methods are defined in a namespace ``FV``.
 
 Some methods (those with templates) are defined in the header, but others
-are defined in :doc:`src/mesh/fv_ops.cxx<../_breathe_autogen/file/fv__ops_8cxx>`.
+are defined in the ``.cxx`` file.
 
 
 Parallel divergence ``Div_par``

From d4559e3eee253356c33bbf33839e3bfb439bdf7b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 25 Jan 2024 15:46:22 +0000
Subject: [PATCH 0053/1827] Docs: Fix file-level docstrings not rendering
 correctly

---
 include/bout/adios_object.hxx                 |   2 +-
 include/bout/assert.hxx                       |   2 +-
 include/bout/field_accessor.hxx               |   3 +-
 include/bout/generic_factory.hxx              |   4 +
 include/bout/invert/laplacexy2.hxx            |  12 +-
 include/bout/lapack_routines.hxx              |  16 ++-
 include/bout/openmpwrap.hxx                   |   8 +-
 include/bout/options_io.hxx                   |   1 +
 include/bout/optionsreader.hxx                |   6 +-
 include/bout/output.hxx                       |   6 +-
 include/bout/rajalib.hxx                      |   2 +-
 include/bout/sys/gettext.hxx                  |   1 +
 include/bout/sys/uuid.h                       |  23 ++--
 include/bout/sys/variant.hxx                  |  16 +--
 include/bout/vectormetric.hxx                 |   4 +
 src/invert/lapack_routines.cxx                |  16 +--
 .../laplace/impls/cyclic/cyclic_laplace.cxx   |  15 +--
 .../laplace/impls/cyclic/cyclic_laplace.hxx   |   9 +-
 .../laplace/impls/naulin/naulin_laplace.cxx   | 120 +----------------
 .../laplace/impls/naulin/naulin_laplace.hxx   | 125 +++++++++++++++++-
 src/invert/laplace/impls/pcr/pcr.hxx          |   8 +-
 .../laplace/impls/pcr_thomas/pcr_thomas.hxx   |   8 +-
 .../laplace/impls/petsc/petsc_laplace.hxx     |  13 +-
 src/solver/impls/imex-bdf2/imex-bdf2.hxx      |   2 +-
 src/solver/impls/petsc/petsc.hxx              |   8 +-
 25 files changed, 214 insertions(+), 216 deletions(-)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 9d2f545b46..f3cd2d5d0a 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -1,4 +1,4 @@
-/*!************************************************************************
+/*!\file*******************************************************************
  * Provides access to the ADIOS library, handling initialisation and
  * finalisation.
  *
diff --git a/include/bout/assert.hxx b/include/bout/assert.hxx
index 233641966b..d5dc07723b 100644
--- a/include/bout/assert.hxx
+++ b/include/bout/assert.hxx
@@ -1,4 +1,4 @@
-/*!
+/*!\file
  * Defines a macro ASSERT which throws a BoutException if a given
  * condition is false. Whether the assertion is tested depends on
  * the checking level, so assetions can be removed for optimised runs.
diff --git a/include/bout/field_accessor.hxx b/include/bout/field_accessor.hxx
index 69b58da979..eea705b8c4 100644
--- a/include/bout/field_accessor.hxx
+++ b/include/bout/field_accessor.hxx
@@ -1,7 +1,8 @@
+/// \file
+///
 /// FieldAccessor
 ///
 /// Provides quick but unsafe access to field and coordinate system data
-///
 
 #pragma once
 #ifndef FIELD_ACCESSOR_H__
diff --git a/include/bout/generic_factory.hxx b/include/bout/generic_factory.hxx
index f7a0692af8..56e19b1114 100644
--- a/include/bout/generic_factory.hxx
+++ b/include/bout/generic_factory.hxx
@@ -1,5 +1,9 @@
+/// \file
 /// Base type for factories
 
+// Copyright 2018-2022 Peter Hill, BOUT++ Team
+// SPDX-License-Identifier: MIT
+
 #pragma once
 #ifndef BOUT_GENERIC_FACTORY_H
 #define BOUT_GENERIC_FACTORY_H
diff --git a/include/bout/invert/laplacexy2.hxx b/include/bout/invert/laplacexy2.hxx
index 6945de7b99..43a66d4a0b 100644
--- a/include/bout/invert/laplacexy2.hxx
+++ b/include/bout/invert/laplacexy2.hxx
@@ -1,14 +1,16 @@
 /**************************************************************************
+ * \file
  * Laplacian solver in 2D (X-Y)
  *
  * Equation solved is:
+ * \f[
+ *   \nabla(A \cdot \nabla_\perp(x)) + B x = b
+ * \f]
  *
- * Div( A * Grad_perp(x) ) + B*x = b
- *
- * Intended for use in solving n = 0 component of potential
+ * Intended for use in solving ``n = 0`` component of potential
  * from inversion of vorticity equation
- *
- **************************************************************************
+ */
+/**************************************************************************
  * Copyright 2015 B.Dudson
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/include/bout/lapack_routines.hxx b/include/bout/lapack_routines.hxx
index 70a3128f81..c8ca4a3b35 100644
--- a/include/bout/lapack_routines.hxx
+++ b/include/bout/lapack_routines.hxx
@@ -1,8 +1,22 @@
+/// \file
+///
+/// Serial code to invert a complex tridiagonal system
+///
+/// Solves a banded matrix given the matrix in compact form:
+///
+///     a[0...(n-1)][0...(m1+m2)]
+///
+/// and the rhs vector:
+///
+///     b[0...(n-1)]
+///
+/// ``a`` is overwritten, and ``b`` is replaced by the solution
+
 /**************************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx
index 032705e61a..506f257cbc 100644
--- a/include/bout/openmpwrap.hxx
+++ b/include/bout/openmpwrap.hxx
@@ -1,8 +1,6 @@
-/************************************************************************/ /**
- * \brief Openmp utilitiy wrappers
- * 
- * 
- **************************************************************************
+/// \file
+///  Openmp utilitiy wrappers
+/**************************************************************************
  * Copyright 2017
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index 65c3cb7dd1..977b13631a 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -1,3 +1,4 @@
+/// \file
 /// Parent class for IO to binary files and streams
 ///
 ///
diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx
index 428c7a8c8f..a54bee6f96 100644
--- a/include/bout/optionsreader.hxx
+++ b/include/bout/optionsreader.hxx
@@ -1,4 +1,4 @@
-/*!************************************************************************
+/*! \file
 * Singleton class for reading options files
 *
 * Uses a bridge pattern to access OptionParser classes to parse
@@ -6,8 +6,8 @@
 *
 * Handles the command-line parsing
 * 
-*
-**************************************************************************
+*/
+/*************************************************************************
 * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
 *
 * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index ef09aa7ee5..768fc39454 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -1,7 +1,7 @@
+/// \file
+/// Logging, for printing messages/errors etc.
+
 /**************************************************************************
- * Output, for printing messages/errors etc.
- *
- **************************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/include/bout/rajalib.hxx b/include/bout/rajalib.hxx
index b9f6913459..83be632d48 100644
--- a/include/bout/rajalib.hxx
+++ b/include/bout/rajalib.hxx
@@ -1,4 +1,4 @@
-/*!
+/*! \file
  * RAJA library utilities and wrappers
  *
  * Defines:
diff --git a/include/bout/sys/gettext.hxx b/include/bout/sys/gettext.hxx
index 2ada87ab63..45d31a275a 100644
--- a/include/bout/sys/gettext.hxx
+++ b/include/bout/sys/gettext.hxx
@@ -1,3 +1,4 @@
+/// \file
 /// Support for i18n using GNU gettext
 
 #ifndef __BOUT_GETTEXT_H__
diff --git a/include/bout/sys/uuid.h b/include/bout/sys/uuid.h
index edc252bb44..9cff7727f2 100644
--- a/include/bout/sys/uuid.h
+++ b/include/bout/sys/uuid.h
@@ -1,14 +1,15 @@
-// Based on stduuid by Marius Bancila: https://github.com/mariusbancila/stduuid
-// Originially copied from version at commit 5890c94bfac2f00f22a1c1481e5839c51d6a6f3f
-// This version hacked by J. Omotani to make it C++14 compatible:
-//   - remove uses of span
-//   - brace-initialise std::atomic_short clock_sequence to avoid deleted
-//     move-constructor error
-//   - remove use of std::optional. Throw exceptions instead.
-//   - replace std::bytes with char
-//   - replace 'if constexpr' with plain 'if'
-//   - replace 'is_same_v<>' with 'is_same<>::value'
-//   - replace std::copy with strncpy in uuid_name_generator::reset()
+/// Based on stduuid by Marius Bancila: https://github.com/mariusbancila/stduuid
+///
+/// Originially copied from version at commit 5890c94bfac2f00f22a1c1481e5839c51d6a6f3f
+/// This version hacked by J. Omotani to make it C++14 compatible:
+///   - remove uses of span
+///   - brace-initialise std::atomic_short clock_sequence to avoid deleted
+///     move-constructor error
+///   - remove use of std::optional. Throw exceptions instead.
+///   - replace std::bytes with char
+///   - replace 'if constexpr' with plain 'if'
+///   - replace 'is_same_v<>' with 'is_same<>::value'
+///   - replace std::copy with strncpy in uuid_name_generator::reset()
 //
 // Copyright (c) 2017
 //
diff --git a/include/bout/sys/variant.hxx b/include/bout/sys/variant.hxx
index f47d67e229..1b541f096d 100644
--- a/include/bout/sys/variant.hxx
+++ b/include/bout/sys/variant.hxx
@@ -1,15 +1,15 @@
-///
+/// \file
 /// Variant utilities
 ///
 /// All in namespace bout::utils
-///    variant
-///    visit
-///    holds_alternative
-///    get
 ///
-///    variantEqualTo
-///    variantStaticCastOrThrow
-///    variantToString
+/// - `variant`
+/// - `visit`
+/// - `holds_alternative`
+/// - `get`
+/// - `variantEqualTo`
+/// - `variantStaticCastOrThrow`
+/// - `variantToString`
 ///
 /// Internal implementation in bout::utils::details
 
diff --git a/include/bout/vectormetric.hxx b/include/bout/vectormetric.hxx
index 3ac31c2a45..1c4907ff43 100644
--- a/include/bout/vectormetric.hxx
+++ b/include/bout/vectormetric.hxx
@@ -1,3 +1,7 @@
+/// \file
+/// Header to simplify using `Vector2D`/`Vector3D` when switching
+/// between 2D and 3D metrics in user code
+
 #pragma once
 
 #include "bout/build_config.hxx"
diff --git a/src/invert/lapack_routines.cxx b/src/invert/lapack_routines.cxx
index 144a478b65..08a58a367a 100644
--- a/src/invert/lapack_routines.cxx
+++ b/src/invert/lapack_routines.cxx
@@ -1,18 +1,4 @@
-/*!
- * \file lapack_routines.cxx
- *
- * Serial code to invert a complex tridiagonal system
- *
- * Complex banded matrix solver
- *
- * Solves a banded matrix given the matrix in compact form
- * a[0...(n-1)][0...(m1+m2)]
- * and the rhs vector
- * b[0...(n-1)]
- * 
- * a is overwritten, and b is replaced by the solution
- *
- **************************************************************************
+/**************************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
index 2687bf7187..c1db7d522b 100644
--- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
+++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
@@ -1,17 +1,4 @@
-/*!
- * \file cyclic.cxx
- *
- * \brief FFT + Tridiagonal solver in serial or parallel
- *
- * Not particularly optimised: Each y slice is solved sequentially
- *
- * CHANGELOG
- * =========
- *
- * Jan 2014: Brendan Shanahan <bws502@york.ac.uk>
- *         * Added DST option
- *
- **************************************************************************
+/**************************************************************************
  * Copyright 2013 B.D.Dudson
  *
  * Contact: Ben Dudson, benjamin.dudson@york.ac.uk
diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
index 841f0a4e05..8b5539be38 100644
--- a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
+++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
@@ -1,10 +1,10 @@
-/**************************************************************************
+/*!\file
  * Perpendicular Laplacian inversion in serial or parallel
  * 
  * Simplified version of serial_tri and spt algorithms. Uses FFTs and
  * the cyclic reduction class to solve tridiagonal systems.
- *
- **************************************************************************
+ */
+/**************************************************************************
  * Copyright 2013 B.D.Dudson
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
@@ -54,9 +54,6 @@ RegisterLaplace<LaplaceCyclic> registerlaplacecycle(LAPLACE_CYCLIC);
 }
 
 /// Solves the 2D Laplacian equation using the CyclicReduce class
-/*!
- * 
- */
 class LaplaceCyclic : public Laplacian {
 public:
   LaplaceCyclic(Options* opt = nullptr, const CELL_LOC loc = CELL_CENTRE,
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index d82f874cbb..d9093c4c5f 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -1,23 +1,4 @@
-// clang-format off
-/*!
- * \file naulin_laplace.cxx
- *
- * \brief Iterative solver to handle non-constant-in-z coefficients
- *
- * Scheme suggested by Volker Naulin: solve
- * Delp2(phi[i+1]) + 1/DC(C1*D)*Grad_perp(DC(C2))*Grad_perp(phi[i+1]) + DC(A/D)*phi[i+1]
- *   = rhs(phi[i]) + 1/DC(C1*D)*Grad_perp(DC(C2))*Grad_perp(phi[i]) + DC(A/D)*phi[i]
- * using standard FFT-based solver, iterating to include other terms by
- * evaluating them on rhs using phi from previous iteration.
- * DC part (i.e. Field2D part) of C1*D, C2 and A/D is kept in the FFT inversion
- * to improve convergence by including as much as possible in the direct solve
- * and so that all Neumann boundary conditions can be used at least when
- * DC(A/D)!=0.
- *
- * CHANGELOG
- * =========
- *
- **************************************************************************
+/**************************************************************************
  * Copyright 2018 B.D.Dudson, M. Loiten, J. Omotani
  *
  * Contact: Ben Dudson, benjamin.dudson@york.ac.uk
@@ -37,106 +18,7 @@
  * You should have received a copy of the GNU Lesser General Public License
  * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
  *
- * ## Explanation of the procedure:
- * A way to invert the equation
- * \f$\Omega^D = \nabla\cdot(n\nabla_\perp \phi)\f$
- * invented by Naulin, V.
- * In an orthogonal system, we have that:
- *
- * \f{eqnarray}{
- * \Omega^D &=& \nabla\cdot(n\nabla_\perp \phi)\\
- *       &=& n \nabla_\perp^2 \phi + \nabla n\cdot\nabla_\perp \phi\\
- *       &=& n \Omega + \nabla n\cdot\nabla_\perp \phi\\
- *       &=& n \Omega + \nabla_\perp n\cdot\nabla_\perp \phi
- * \f}
- *
- * Rearranging gives
- *
- * \f{eqnarray}{
- * \Omega  &=& \frac{\Omega^D}{n} - \nabla_\perp \ln(n)\cdot\nabla_\perp \phi\\
- * \nabla_\perp^2 \phi
- * &=& \frac{\Omega^D}{n} - \nabla_\perp \ln(n)\cdot\nabla_\perp \phi
- * \f}
- *
- * In fact we allow for the slightly more general form
- *
- * \f{eqnarray}{
- * \nabla_\perp^2 \phi + <\frac{A}{D}>\phi
- * &=& rhs/D - \frac{1}{D\,C1} \nabla_\perp C2\cdot\nabla_\perp \phi - (\frac{A}{D} - <\frac{A}{D}>)*\phi
- * \f}
- *
- * The iteration can be under-relaxed to help it converge. Amount of under-relaxation is
- * set by the parameter 'underrelax_factor'. 0<underrelax_factor<=1, with
- * underrelax_factor=1 corresponding to no under-relaxation. The amount of
- * under-relaxation is temporarily increased if the iteration starts diverging, the
- * starting value uof underrelax_factor can be set with the initial_underrelax_factor
- * option.
- *
- * The iteration now works as follows:
- *      1. Get the vorticity from
- *         \code{.cpp}
- *         vort = (vortD/n) - grad_perp(ln_n)*grad_perp(phiCur)
- *         [Delp2(phiNext) + 1/DC(C2*D)*grad_perp(DC(C2))*grad_perp(phiNext) + DC(A/D)*phiNext
- *          = b(phiCur)
- *          = (rhs/D) - (1/C1/D*grad_perp(C2)*grad_perp(phiCur) - 1/DC(C2*D)*grad_perp(DC(C2))*grad_perp(phiCur)) - (A/D - DC(A/D))*phiCur]
- *         \endcode
- *         where phiCur is phi of the current iteration
- *         [and DC(f) is the constant-in-z component of f]
- *      2. Invert \f$phi\f$ to find the voricity using
- *         \code{.cpp}
- *         phiNext = invert_laplace_perp(vort)
- *         [set Acoef of laplace_perp solver to DC(A/D)
- *          and C1coef of laplace_perp solver to DC(C1*D)
- *          and C2coef of laplace_perp solver to DC(C2)
- *          then phiNext = invert_laplace_perp(underrelax_factor*b(phiCur) - (1-underrelax_factor)*b(phiPrev))]
- *          where b(phiPrev) is the previous rhs value, which (up to rounding errors) is
- *          the same as the lhs of the direct solver applied to phiCur.
- *         \endcode
- *         where phiNext is the newly obtained \f$phi\f$
- *      3. Calculate the error at phi=phiNext
- *         \code{.cpp}
- *         error3D = Delp2(phiNext) + 1/C1*grad_perp(C2)*grad_perp(phiNext) + A/D*phiNext - rhs/D
- *                 = b(phiCur) - b(phiNext)
- *         as b(phiCur) = Delp2(phiNext) + 1/DC(C2*D)*grad_perp(DC(C2))*grad_perp(phiNext) + DC(A/D)*phiNext
- *         up to rounding errors
- *         \endcode
- *      4. Calculate the infinity norms of the error
- *         \code{.cpp}
- *         EAbsLInf = max(error3D)
- *         ERelLInf = EAbsLInf/sqrt( max((rhs/D)^2) )
- *         \endcode
- *      5. Check whether
- *         \code{.cpp}
- *         EAbsLInf > atol
- *         \endcode
- *          * If yes
- *              * Check whether
- *                \code{.cpp}
- *                ERelLInf > rtol
- *                \endcode
- *              * If yes
- *                  * Check whether
- *                  \code{.cpp}
- *                  EAbsLInf > EAbsLInf(previous step)
- *                  \endcode
- *                    * If yes
- *                      \code{.cpp}
- *                      underrelax_factor *= 0.9
- *                      \endcode
- *                      Restart iteration
- *                    * If no
- *                      * Set
- *                        \code{.cpp}
- *                        phiCur = phiNext
- *                        \endcode
- *                        increase curCount and start from step 1
- *                      * If number of iteration is above maxit, throw exception
- *              * If no
- *                  * Stop: Function returns phiNext
- *          * if no
- *              * Stop: Function returns phiNext
  */
-// clang-format on
 
 #include <bout/boutexception.hxx>
 #include <bout/coordinates.hxx>
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.hxx b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
index f544e74336..81890a899f 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.hxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
@@ -1,7 +1,126 @@
+/// \file
+/// Iterative solver to handle non-constant-in-z coefficients
+///
+/// Scheme suggested by Volker Naulin: solve
+/// \f[
+///   \nabla^2(\phi[i+1])
+///      + 1/DC(C_1 D)\nabla_\perp(DC(C_2))\nalba_\perp(\phi[i+1])
+///      + DC(A/D)*phi[i+1]
+///   = rhs(\phi[i])
+///        + 1/DC(C_1 D)\nabla_\perp(DC(C_2))\nabla_\perp(\phi[i])
+///        + DC(A/D)*\phi[i]
+/// \f]
+///
+/// using standard FFT-based solver, iterating to include other terms
+/// by evaluating them on ``rhs`` using \f$\phi\f$ from previous
+/// iteration.  DC part (i.e. `Field2D` part) of \f$C_1 D\f$,
+/// \f$C_2\f$ and \f$A,D\f$ is kept in the FFT inversion to improve
+/// convergence by including as much as possible in the direct solve
+/// and so that all Neumann boundary conditions can be used at least
+/// when \f$DC(A/D)!=0\f$
+///
+/// Explanation of the procedure
+/// ----------------------------
+///
+/// A way to invert the equation
+/// \f$\Omega^D = \nabla\cdot(n\nabla_\perp \phi)\f$
+/// invented by Naulin, V.
+/// In an orthogonal system, we have that:
+///
+/// \f{eqnarray}{
+/// \Omega^D &=& \nabla\cdot(n\nabla_\perp \phi)\                    \
+///       &=& n \nabla_\perp^2 \phi + \nabla n\cdot\nabla_\perp \phi\\
+///       &=& n \Omega + \nabla n\cdot\nabla_\perp \phi\\
+///       &=& n \Omega + \nabla_\perp n\cdot\nabla_\perp \phi
+/// \f}
+///
+/// Rearranging gives
+///
+/// \f{eqnarray}{
+/// \Omega  &=& \frac{\Omega^D}{n} - \nabla_\perp \ln(n)\cdot\nabla_\perp \phi\ \
+/// \nabla_\perp^2 \phi
+/// &=& \frac{\Omega^D}{n} - \nabla_\perp \ln(n)\cdot\nabla_\perp \phi
+/// \f}
+///
+/// In fact we allow for the slightly more general form
+///
+/// \f{eqnarray}{
+/// \nabla_\perp^2 \phi + <\frac{A}{D}>\phi
+/// &=& rhs/D - \frac{1}{D\,C1} \nabla_\perp C2\cdot\nabla_\perp \phi - (\frac{A}{D} - <\frac{A}{D}>)*\phi
+/// \f}
+///
+/// The iteration can be under-relaxed to help it converge. Amount of under-relaxation is
+/// set by the parameter 'underrelax_factor'. 0<underrelax_factor<=1, with
+/// underrelax_factor=1 corresponding to no under-relaxation. The amount of
+/// under-relaxation is temporarily increased if the iteration starts diverging, the
+/// starting value uof underrelax_factor can be set with the initial_underrelax_factor
+/// option.
+///
+/// The iteration now works as follows:
+///  1. Get the vorticity from
+///     \code{.cpp}
+///     vort = (vortD/n) - grad_perp(ln_n)*grad_perp(phiCur)
+///     [Delp2(phiNext) + 1/DC(C2*D)*grad_perp(DC(C2))*grad_perp(phiNext) + DC(A/D)*phiNext
+///      = b(phiCur)
+///      = (rhs/D) - (1/C1/D*grad_perp(C2)*grad_perp(phiCur) - 1/DC(C2*D)*grad_perp(DC(C2))*grad_perp(phiCur)) - (A/D - DC(A/D))*phiCur]
+///    \endcode
+///    where phiCur is phi of the current iteration
+///    [and DC(f) is the constant-in-z component of f]
+/// 2. Invert \f$phi\f$ to find the voricity using
+///    \code{.cpp}
+///    phiNext = invert_laplace_perp(vort)
+///    [set Acoef of laplace_perp solver to DC(A/D)
+///     and C1coef of laplace_perp solver to DC(C1*D)
+///     and C2coef of laplace_perp solver to DC(C2)
+///     then phiNext = invert_laplace_perp(underrelax_factor*b(phiCur) - (1-underrelax_factor)*b(phiPrev))]
+///     where b(phiPrev) is the previous rhs value, which (up to rounding errors) is
+///     the same as the lhs of the direct solver applied to phiCur.
+///    \endcode
+///    where phiNext is the newly obtained \f$phi\f$
+/// 3. Calculate the error at phi=phiNext
+///    \code{.cpp}
+///    error3D = Delp2(phiNext) + 1/C1*grad_perp(C2)*grad_perp(phiNext) + A/D*phiNext - rhs/D
+///            = b(phiCur) - b(phiNext)
+///    as b(phiCur) = Delp2(phiNext) + 1/DC(C2*D)*grad_perp(DC(C2))*grad_perp(phiNext) + DC(A/D)*phiNext
+///    up to rounding errors
+///    \endcode
+/// 4. Calculate the infinity norms of the error
+///    \code{.cpp}
+///    EAbsLInf = max(error3D)
+///    ERelLInf = EAbsLInf/sqrt( max((rhs/D)^2) )
+///    \endcode
+/// 5. Check whether
+///    \code{.cpp}
+///    EAbsLInf > atol
+///    \endcode
+///     * If yes
+///         * Check whether
+///           \code{.cpp}
+///           ERelLInf > rtol
+///           \endcode
+///         * If yes
+///             * Check whether
+///             \code{.cpp}
+///             EAbsLInf > EAbsLInf(previous step)
+///             \endcode
+///               * If yes
+///                 \code{.cpp}
+///                 underrelax_factor *= 0.9
+///                 \endcode
+///                 Restart iteration
+///               * If no
+///                 * Set
+///                   \code{.cpp}
+///                   phiCur = phiNext
+///                   \endcode
+///                   increase curCount and start from step 1
+///                 * If number of iteration is above maxit, throw exception
+///         * If no
+///             * Stop: Function returns phiNext
+///     * if no
+///         * Stop: Function returns phiNext
+
 /**************************************************************************
- * Iterative solver to handle non-constant-in-z coefficients
- * 
- **************************************************************************
  * Copyright 2018 B.D.Dudson, M. Loiten, J. Omotani
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/src/invert/laplace/impls/pcr/pcr.hxx b/src/invert/laplace/impls/pcr/pcr.hxx
index 38b7c356d3..28a08b2008 100644
--- a/src/invert/laplace/impls/pcr/pcr.hxx
+++ b/src/invert/laplace/impls/pcr/pcr.hxx
@@ -1,8 +1,8 @@
+/// \file
+/// Perpendicular Laplacian inversion. Parallel code using FFT
+/// and tridiagonal solver.
+
 /**************************************************************************
- * Perpendicular Laplacian inversion. Parallel code using FFT
- * and tridiagonal solver.
- *
- **************************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx
index 009a1def2b..9e2a60d740 100644
--- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx
+++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx
@@ -1,8 +1,8 @@
+/// \file
+/// Perpendicular Laplacian inversion. Parallel code using FFT
+/// and tridiagonal solver.
+
 /**************************************************************************
- * Perpendicular Laplacian inversion. Parallel code using FFT
- * and tridiagonal solver.
- *
- **************************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.hxx b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
index 3b1d3bcb49..4fc4158eee 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.hxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
@@ -1,10 +1,11 @@
+/// \file
+/// Perpendicular Laplacian inversion using PETSc Solvers
+///
+/// Equation solved is:
+/// \f[
+/// d\nabla^2_\perp x + (1/c1)\nabla_perp c2\cdot\nabla_\perp x + ex\nabla_x x + ez\nabla_z x + a x = b
+/// \f]
 /**************************************************************************
- * Perpendicular Laplacian inversion.
- *                           Using PETSc Solvers
- *
- * Equation solved is: \f$d\nabla^2_\perp x + (1/c1)\nabla_perp c2\cdot\nabla_\perp x + ex\nabla_x x + ez\nabla_z x + a x = b\f$
- *
- **************************************************************************
  * Copyright 2013 J. Buchanan, J. Omotani
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.hxx b/src/solver/impls/imex-bdf2/imex-bdf2.hxx
index 4126c48265..12540c3ea3 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.hxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.hxx
@@ -1,5 +1,5 @@
 /*!*************************************************************************
- * \file imex-bdf2.cxx
+ * \file
  *
  * 2nd order IMEX-BDF scheme
  *
diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index 7b4e9caeab..2f0aeba2ba 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -1,8 +1,8 @@
+/// \file
+/// Interface to PETSc solver
+/// NOTE: This class needs tidying, generalising to use FieldData interface
+
 /**************************************************************************
- * Interface to PETSc solver
- * NOTE: This class needs tidying, generalising to use FieldData interface
- *
- **************************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk

From 8feddbbc54d5ecf39a11758d625abf16615729ba Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 25 Jan 2024 15:47:31 +0000
Subject: [PATCH 0054/1827] Docs: Fix a bunch of LaTeX/codeblock rendering
 issues

---
 include/bout/bout.hxx                         |  9 ++
 include/bout/difops.hxx                       |  4 +-
 include/bout/field_accessor.hxx               |  4 +-
 include/bout/fv_ops.hxx                       | 95 ++++++++++---------
 include/bout/generic_factory.hxx              |  2 +-
 include/bout/initialprofiles.hxx              | 22 ++---
 include/bout/invert_laplace.hxx               |  9 +-
 include/bout/lapack_routines.hxx              | 37 ++++----
 include/bout/openmpwrap.hxx                   |  4 +-
 include/bout/options_io.hxx                   | 16 ++--
 include/bout/optionsreader.hxx                |  8 +-
 include/bout/output.hxx                       | 25 +++--
 include/bout/physicsmodel.hxx                 | 15 ++-
 src/bout++.cxx                                | 17 ----
 .../laplace/impls/naulin/naulin_laplace.hxx   | 12 +--
 src/mesh/fv_ops.cxx                           |  1 -
 16 files changed, 139 insertions(+), 141 deletions(-)

diff --git a/include/bout/bout.hxx b/include/bout/bout.hxx
index d929a19c2f..f7b63a88c6 100644
--- a/include/bout/bout.hxx
+++ b/include/bout/bout.hxx
@@ -34,6 +34,7 @@
 #ifndef BOUT_H
 #define BOUT_H
 
+//NOLINTBEGIN(unused-includes)
 #include "bout/build_config.hxx"
 
 #include "bout/boutcomm.hxx"
@@ -53,6 +54,7 @@
 #include "bout/vector3d.hxx"
 #include "bout/version.hxx"
 #include "bout/where.hxx"
+//NOLINTEND(unused-includes)
 
 // BOUT++ main functions
 
@@ -79,6 +81,13 @@
  * either by including boutmain.hxx or by including bout/physicsmodel.hxx
  * and using the BOUTMAIN macro.
  *
+ * Outputs
+ * -------
+ *
+ * Any non-zero return value should halt the simulation. If the return value is
+ * less than zero, the exit status from BOUT++ is 0, otherwise it is the return
+ * value of BoutInitialise.
+ *
  */
 int BoutInitialise(int& argc, char**& argv);
 
diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 2b5c6746fd..6a264009db 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -148,9 +148,9 @@ inline Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
 }
 
 /*!
- * second parallel derivative
+ * Second parallel derivative:
  * \f[
- *    (\mathbf{b} dot \nabla)(\mathbf{b} dot \nabla)
+ *    (\mathbf{b} \cdot \nabla)(\mathbf{b} \cdot \nabla)
  * \f]
  *
  * Note: For parallel Laplacian use LaplacePar
diff --git a/include/bout/field_accessor.hxx b/include/bout/field_accessor.hxx
index eea705b8c4..f942f38a11 100644
--- a/include/bout/field_accessor.hxx
+++ b/include/bout/field_accessor.hxx
@@ -120,9 +120,9 @@ using Field2DAccessor = FieldAccessor<location, Field2D>;
 ///
 /// Usage:
 ///
-///   ddt(fa)[i] =
+///     ddt(fa)[i] = /* expression */
 ///
-///  where fa is a FieldAccessor, and i is an int
+/// where ``fa`` is a FieldAccessor, and ``i`` is an int
 ///
 template <CELL_LOC location, class FieldType>
 BOUT_HOST_DEVICE inline BoutRealArray& ddt(const FieldAccessor<location, FieldType>& fa) {
diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 5f1e688bd8..f32613b549 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -13,9 +13,10 @@
 #include <bout/mesh.hxx>
 
 namespace FV {
-/*!
- * Div ( a Grad_perp(f) ) -- ∇⊥ ( a ⋅ ∇⊥ f) -- Vorticity
- */
+/// Vorticity:
+/// \f[
+///   \nabla_\perp (a \cdot \nabla_\perp(f))
+/// \f]
 Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& x);
 
 [[deprecated("Please use Div_a_Grad_perp instead")]] inline Field3D
@@ -23,50 +24,56 @@ Div_a_Laplace_perp(const Field3D& a, const Field3D& x) {
   return Div_a_Grad_perp(a, x);
 }
 
-/*!
-   * Divergence of a parallel diffusion Div( k * Grad_par(f) )
-   */
+/// Divergence of a parallel diffusion
+/// \f[
+///   \nabla_\parallel(k \cdot \nabla_\parallel(f) )
+/// \f]
 const Field3D Div_par_K_Grad_par(const Field3D& k, const Field3D& f,
                                  bool bndry_flux = true);
 
-/*!
-   * 4th-order derivative in Y, using derivatives
-   * on cell boundaries.
-   *
-   * A one-sided 3rd-order derivative, given a value
-   * at a boundary is:
-   *
-   * d3f/dx3 ~= 16/5 f_b - 6 f_0 + 4 f_1 - 6/5 f_2
-   *
-   * where f_b is the value on the boundary; f_0 is the cell
-   * to the left of the boundary; f_1 to the left of f_0 and f_2
-   * to the left of f_1
-   *
-   *    f_2 | f_1 | f_0 |
-   *                   f_b
-   *
-   * NB: Uses to/from FieldAligned coordinates
-   *
-   * No fluxes through domain boundaries
-   */
+/// 4th-order derivative in Y, using derivatives
+/// on cell boundaries.
+///
+/// A one-sided 3rd-order derivative, given a value
+/// at a boundary is:
+///
+/// \f[
+/// \frac{d^3f}{dx^3} \simeq \tfrac{16}{5} f_b - 6 f_0 + 4 f_1 - \tfrac{6}{5} f_2
+/// \f]
+///
+/// where:
+///
+/// - \f$f_b\f$ is the value on the boundary,
+/// - \f$f_0\f$ is the cell to the left of the boundary,
+/// - \f$f_1\f$ to the left of \f$f_0\f$, and
+/// - \f$f_2\f$ to the left of f_1:
+///
+/// .. code:: text
+///    f_2 | f_1 | f_0 |
+///                   f_b
+///
+/// NB: Uses to/from FieldAligned coordinates
+///
+/// No fluxes through domain boundaries
 const Field3D D4DY4(const Field3D& d, const Field3D& f);
 
-/*!
-   * 4th-order dissipation term
-   *
-   *
-   * A one-sided 3rd-order derivative, given a value
-   * at a boundary is:
-   *
-   * d3f/dx3 ~= 16/5 f_b - 6 f_0 + 4 f_1 - 6/5 f_2
-   *
-   * where f_b is the value on the boundary; f_0 is the cell
-   * to the left of the boundary; f_1 to the left of f_0 and f_2
-   * to the left of f_1
-   *
-   *    f_2 | f_1 | f_0 |
-   *                   f_b
-   */
+
+/// 4th-order dissipation term
+///
+/// \f[
+/// \frac{d^3f}{dx^3} \simeq \tfrac{16}{5} f_b - 6 f_0 + 4 f_1 - \tfrac{6}{5} f_2
+/// \f]
+///
+/// where:
+///
+/// - \f$f_b\f$ is the value on the boundary,
+/// - \f$f_0\f$ is the cell to the left of the boundary,
+/// - \f$f_1\f$ to the left of \f$f_0\f$, and
+/// - \f$f_2\f$ to the left of f_1:
+///
+/// .. code:: text
+///    f_2 | f_1 | f_0 |
+///                   f_b
 const Field3D D4DY4_Index(const Field3D& f, bool bndry_flux = true);
 
 /*!
@@ -74,10 +81,10 @@ const Field3D D4DY4_Index(const Field3D& f, bool bndry_flux = true);
    * which includes cell face values L and R
    */
 struct Stencil1D {
-  // Cell centre values
+  /// Cell centre values
   BoutReal c, m, p, mm, pp;
 
-  // Left and right cell face values
+  /// Left and right cell face values
   BoutReal L, R;
 };
 
diff --git a/include/bout/generic_factory.hxx b/include/bout/generic_factory.hxx
index 56e19b1114..589431bc2a 100644
--- a/include/bout/generic_factory.hxx
+++ b/include/bout/generic_factory.hxx
@@ -52,7 +52,7 @@
 ///     RegisterInFactory<Base, Derived, MyFactory, Options*> register("derived_type");
 ///     auto foo = MyFactory::getInstance().create("derived_type");
 ///
-///   In a .cxx file the static members should be declared:
+/// In a .cxx file the static members should be declared:
 ///
 ///     constexpr decltype(MyFactory::type_name) MyFactory::type_name;
 ///     constexpr decltype(MyFactory::section_name) MyFactory::section_name;
diff --git a/include/bout/initialprofiles.hxx b/include/bout/initialprofiles.hxx
index 71cab22431..cbceef4b25 100644
--- a/include/bout/initialprofiles.hxx
+++ b/include/bout/initialprofiles.hxx
@@ -58,22 +58,22 @@ class Vector3D;
  * -------
  * Given the input file:
  *
- * [All]
- * function = sin(y)
+ *     [all]
+ *     function = sin(y)
  *
- * [pressure]
+ *     [pressure]
  *
- * [density]
- * scale = 0.2
+ *     [density]
+ *     scale = 0.2
  *
- * [vorticity]
- * function = cos(y)
+ *     [vorticity]
+ *     function = cos(y)
  *
- * initial_profile would generate:
+ * `initial_profile` would generate:
  *
- * o pressure -> sin(y)
- * o density  -> 0.2*sin(y)
- * o vorticity -> cos(y)
+ * - ``pressure -> sin(y)``
+ * - ``density  -> 0.2*sin(y)``
+ * - ``vorticity -> cos(y)``
  *
  */
 void initial_profile(const std::string& name, Field3D& var);
diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx
index c4ae5efdf8..5a88de5231 100644
--- a/include/bout/invert_laplace.hxx
+++ b/include/bout/invert_laplace.hxx
@@ -3,11 +3,14 @@
  *
  * Perpendicular Laplacian inversion using FFT and Tridiagonal solver
  *
- * Equation solved is: \f$d*\nabla^2_\perp x + (1/c)\nabla_perp c\cdot\nabla_\perp x + a x = b\f$
+ * Equation solved is:
+ * \f[
+ *   d \nabla^2_\perp x + (1/c)\nabla_\perp c\cdot\nabla_\perp x + a x = b
+ * \f]
  * 
  * Where a, c and d are functions of x and y only (not z)
- *
- **************************************************************************
+ */
+/**************************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
diff --git a/include/bout/lapack_routines.hxx b/include/bout/lapack_routines.hxx
index c8ca4a3b35..14c4bdc353 100644
--- a/include/bout/lapack_routines.hxx
+++ b/include/bout/lapack_routines.hxx
@@ -39,35 +39,34 @@
 
 #include <bout/utils.hxx>
 
-/* Tridiagonal inversion
- *
- * a = Left of diagonal (so a[0] not used)
- * b = diagonal terms
- * c = Right of diagonal (so c[n-1] not used)
- * r = RHS vector
- * u = Result vector
- * n = Length of vectors
- *
- * 
- * b[0]   c[0]
- * a[1]   b[1]   c[1]
- *         .       .    . 
- * 
- */
-
-// Tri-diagonal solvers
+/// Tridiagonal inversion
+///
+/// \param a Left of diagonal (so a[0] not used)
+/// \param b diagonal terms
+/// \param c Right of diagonal (so c[n-1] not used)
+/// \param r RHS vector
+/// \param u Result vector
+/// \param n Length of vectors
+///
+///     b[0]   c[0]
+///     a[1]   b[1]   c[1]
+///             .       .    .
+///
+/// Uses LAPACK routine ZGTSV
 int tridag(const dcomplex* a, const dcomplex* b, const dcomplex* c, const dcomplex* r,
            dcomplex* u, int n);
 bool tridag(const BoutReal* a, const BoutReal* b, const BoutReal* c, const BoutReal* r,
             BoutReal* x, int n);
 
-// Cyclic tridiagonal
+/// Cyclic tridiagonal
+///
+/// Uses Sherman-Morrison formula
 void cyclic_tridag(BoutReal* a, BoutReal* b, BoutReal* c, BoutReal* r, BoutReal* x,
                    int n);
 void cyclic_tridag(dcomplex* a, dcomplex* b, dcomplex* c, dcomplex* r, dcomplex* x,
                    int n);
 
-/// Complex band matrix solver
+/// Complex band matrix solver using ZGBSV
 void cband_solve(Matrix<dcomplex>& a, int n, int m1, int m2, Array<dcomplex>& b);
 
 #endif // __LAPACK_ROUTINES_H__
diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx
index 506f257cbc..6a298970db 100644
--- a/include/bout/openmpwrap.hxx
+++ b/include/bout/openmpwrap.hxx
@@ -31,8 +31,8 @@
 #define INDIRECT1(a) INDIRECT0(omp a)
 #define INDIRECT2(b) INDIRECT1(b)
 
-//Define a macro wrapper to the use of `#pragma omp` to avoid unknown pragma
-//warnings when compiling without openmp support.
+/// Wrapper to use `#pragma omp` while avoiding unknown pragma
+/// warnings when compiling without openmp support.
 #if BOUT_USE_OPENMP
 #define BOUT_OMP(...) _Pragma(INDIRECT2(__VA_ARGS__))
 #else
diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index 977b13631a..35c7b44a36 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -6,8 +6,8 @@
 ///
 /// 1. Dump files, containing time history:
 ///
-///       auto dump = OptionsIOFactory::getInstance().createOutput();
-///       dump->write(data);
+///        auto dump = OptionsIOFactory::getInstance().createOutput();
+///        dump->write(data);
 ///
 ///    where data is an Options tree. By default dump files are configured
 ///    with the root `output` section, or an Option tree can be passed to
@@ -15,19 +15,19 @@
 ///
 /// 2. Restart files:
 ///
-///       auto restart = OptionsIOFactory::getInstance().createOutput();
-///       restart->write(data);
+///        auto restart = OptionsIOFactory::getInstance().createOutput();
+///        restart->write(data);
 ///
 ///    where data is an Options tree. By default restart files are configured
 ///    with the root `restart_files` section, or an Option tree can be passed to
 ///    `createRestart`.
 ///
 /// 3. Ad-hoc single files
-///   Note: The caller should consider how multiple processors interact with the file.
+///    Note: The caller should consider how multiple processors interact with the file.
 ///
-///       auto file = OptionsIOFactory::getInstance().createFile("some_file.nc");
-///   or
-///       auto file = OptionsIO::create("some_file.nc");
+///        auto file = OptionsIOFactory::getInstance().createFile("some_file.nc");
+///        // or
+///        auto file = OptionsIO::create("some_file.nc");
 ///
 ///
 
diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx
index a54bee6f96..98f6848412 100644
--- a/include/bout/optionsreader.hxx
+++ b/include/bout/optionsreader.hxx
@@ -47,11 +47,11 @@ class OptionsReader;
 /// Example
 /// -------
 ///
-/// Options opt;
-/// OptionsReader::getInstance()->read(&opt, "somefile.inp");
-///
-/// opt now contains a tree of sections and options from the input file "somefile.inp"
+///     Options opt;
+///     OptionsReader::getInstance()->read(&opt, "somefile.inp");
 ///
+/// ``opt`` now contains a tree of sections and options from the input
+/// file "somefile.inp"
 class OptionsReader {
 public:
   /// Return a pointer to the instance singleton
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index 768fc39454..fbb48f9e07 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -46,19 +46,18 @@ class Output;
 using std::endl;
 
 /// Class for text output to stdout and/or log file
-/*!
-  This class can be used to output either in fmt format:
-
-    output.write("A string {:s} and number {:d}\n", str, i);
-
-  or as a C++ stream buffer:
-
-    output << "A string " << str << " and number " << i << endl;
-
-  If a file has been opened (i.e. the processor's log file) then the string
-  will be written to the file. In addition, output to stdout can be enabled
-  and disabled.
-*/
+///
+/// This class can be used to output either in ``fmt`` format:
+///
+///     output.write("A string {:s} and number {:d}\n", str, i);
+///
+/// or as a C++ stream buffer:
+///
+///     output << "A string " << str << " and number " << i << endl;
+///
+/// If a file has been opened (i.e. the processor's log file) then the string
+/// will be written to the file. In addition, output to stdout can be enabled
+/// and disabled.
 class Output : private multioutbuf_init<char, std::char_traits<char>>,
                public std::basic_ostream<char, std::char_traits<char>> {
 
diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index e0f046eb1f..3f8f5b6132 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -402,19 +402,18 @@ private:
 };
 
 /*!
- * Macro to define a simple main() which creates
- * the given model and runs it. This should be sufficient
- * for most use cases, but a user can define their own
- * main() function if needed.
+ * Macro to define a simple ``main()`` which creates the given model
+ * and runs it. This should be sufficient for most use cases, but a
+ * user can define their own ``main()`` function if needed.
  *
  * Example
  * -------
  *
- * class MyModel : public PhysicsModel {
- *   ..
- * };
+ *     class MyModel : public PhysicsModel {
+ *       // ...
+ *     };
  *
- * BOUTMAIN(MyModel);
+ *     BOUTMAIN(MyModel);
  */
 #define BOUTMAIN(ModelClass)                                       \
   int main(int argc, char** argv) {                                \
diff --git a/src/bout++.cxx b/src/bout++.cxx
index 1dc93dc76d..a0296fc663 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -114,24 +114,7 @@ namespace {
 constexpr auto is_enabled(bool enabled) { return enabled ? "enabled" : "disabled"; }
 } // namespace
 
-/*!
-  Initialise BOUT++
 
-  Inputs
-  ------
-
-  The command-line arguments argc and argv are passed by
-  reference, and pointers to these will be stored in various
-  places in BOUT++.
-
-  Outputs
-  -------
-
-  Any non-zero return value should halt the simulation. If the return value is
-  less than zero, the exit status from BOUT++ is 0, otherwise it is the return
-  value of BoutInitialise.
-
- */
 int BoutInitialise(int& argc, char**& argv) {
 
   using namespace bout::experimental;
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.hxx b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
index 81890a899f..383ac069af 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.hxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
@@ -2,14 +2,14 @@
 /// Iterative solver to handle non-constant-in-z coefficients
 ///
 /// Scheme suggested by Volker Naulin: solve
-/// \f[
+/// \f{eqnarray}
 ///   \nabla^2(\phi[i+1])
-///      + 1/DC(C_1 D)\nabla_\perp(DC(C_2))\nalba_\perp(\phi[i+1])
-///      + DC(A/D)*phi[i+1]
+///      + 1/DC(C_1 D)\nabla_\perp(DC(C_2))\nabla_\perp(\phi[i+1])
+///      + DC(A/D)\phi[i+1] \\
 ///   = rhs(\phi[i])
 ///        + 1/DC(C_1 D)\nabla_\perp(DC(C_2))\nabla_\perp(\phi[i])
-///        + DC(A/D)*\phi[i]
-/// \f]
+///        + DC(A/D)\phi[i]
+/// \f}
 ///
 /// using standard FFT-based solver, iterating to include other terms
 /// by evaluating them on ``rhs`` using \f$\phi\f$ from previous
@@ -46,7 +46,7 @@
 ///
 /// \f{eqnarray}{
 /// \nabla_\perp^2 \phi + <\frac{A}{D}>\phi
-/// &=& rhs/D - \frac{1}{D\,C1} \nabla_\perp C2\cdot\nabla_\perp \phi - (\frac{A}{D} - <\frac{A}{D}>)*\phi
+/// &=& rhs/D - \frac{1}{D\,C1} \nabla_\perp C2\cdot\nabla_\perp \phi - (\frac{A}{D} - <\frac{A}{D}>)\phi
 /// \f}
 ///
 /// The iteration can be under-relaxed to help it converge. Amount of under-relaxation is
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index 0a5d5f9624..f6e427232c 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -22,7 +22,6 @@ Slices<T> makeslices(bool use_slices, const T& field) {
 
 namespace FV {
 
-// Div ( a Grad_perp(f) ) -- ∇⊥ ( a ⋅ ∇⊥ f) --  Vorticity
 Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
   ASSERT2(a.getLocation() == f.getLocation());
 

From 678b41e81440a5c26ff373a596d2e4990dbf0ffe Mon Sep 17 00:00:00 2001
From: ZedThree <ZedThree@users.noreply.github.com>
Date: Thu, 25 Jan 2024 16:51:56 +0000
Subject: [PATCH 0055/1827] Apply clang-format changes

---
 include/bout/fv_ops.hxx | 1 -
 src/bout++.cxx          | 1 -
 2 files changed, 2 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index f32613b549..3dd8ec3325 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -57,7 +57,6 @@ const Field3D Div_par_K_Grad_par(const Field3D& k, const Field3D& f,
 /// No fluxes through domain boundaries
 const Field3D D4DY4(const Field3D& d, const Field3D& f);
 
-
 /// 4th-order dissipation term
 ///
 /// \f[
diff --git a/src/bout++.cxx b/src/bout++.cxx
index a0296fc663..f0d94ab1aa 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -114,7 +114,6 @@ namespace {
 constexpr auto is_enabled(bool enabled) { return enabled ? "enabled" : "disabled"; }
 } // namespace
 
-
 int BoutInitialise(int& argc, char**& argv) {
 
   using namespace bout::experimental;

From 49cd98582a5048c779d93c223fa014b855abb5c7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Sun, 4 Feb 2024 21:26:20 +0100
Subject: [PATCH 0056/1827] Merge remote-tracking branch 'origin/next' into
 fci-splitting

---
 .build_adios2_for_ci.sh                       |   62 +
 .clang-tidy                                   |    2 +-
 .github/workflows/clang-tidy-review.yml       |    2 +-
 .github/workflows/tests.yml                   |    8 +-
 CHANGELOG.md                                  |    2 +
 CMakeLists.txt                                |   12 +-
 README.md                                     |   77 +-
 bin/bout-config.in                            |    7 +
 bout++Config.cmake.in                         |    1 +
 cmake/SetupBOUTThirdParty.cmake               |   39 +
 cmake_build_defines.hxx.in                    |    1 +
 examples/elm-pb-outerloop/data/BOUT.inp       |    6 -
 .../elm-pb-outerloop/elm_pb_outerloop.cxx     |   37 +-
 examples/elm-pb/data/BOUT.inp                 |   12 +-
 examples/elm-pb/elm_pb.cxx                    |   12 +-
 examples/elm-pb/plot_linear.py                |   85 +
 examples/make-script/makefile                 |    4 +-
 .../performance/arithmetic/arithmetic.cxx     |   14 +-
 examples/shear-alfven-wave/orig_test.idl.dat  |  Bin 2436 -> 0 bytes
 examples/uedge-benchmark/result_080917.idl    |  Bin 268684 -> 0 bytes
 examples/uedge-benchmark/ue_bmk.idl           |  Bin 324156 -> 0 bytes
 include/bout/adios_object.hxx                 |   83 +
 include/bout/boundary_op.hxx                  |    5 +-
 include/bout/bout.hxx                         |   10 +-
 include/bout/boutexception.hxx                |    2 -
 include/bout/build_config.hxx                 |    1 +
 include/bout/field.hxx                        |    2 +-
 include/bout/field2d.hxx                      |    5 +-
 include/bout/field3d.hxx                      |   11 +
 include/bout/field_data.hxx                   |    2 -
 include/bout/fieldperp.hxx                    |    3 +
 include/bout/format.hxx                       |   16 -
 include/bout/generic_factory.hxx              |   14 +-
 include/bout/globalindexer.hxx                |    8 +-
 include/bout/index_derivs.hxx                 |    7 -
 include/bout/interpolation_xz.hxx             |    5 +-
 include/bout/interpolation_z.hxx              |    2 +-
 include/bout/invert_laplace.hxx               |    4 +-
 include/bout/mask.hxx                         |    5 +-
 include/bout/mesh.hxx                         |   26 +-
 include/bout/monitor.hxx                      |    4 +-
 include/bout/msg_stack.hxx                    |    3 +-
 include/bout/options.hxx                      |  107 +-
 include/bout/options_io.hxx                   |  178 ++
 include/bout/options_netcdf.hxx               |  118 --
 include/bout/optionsreader.hxx                |    1 -
 include/bout/output.hxx                       |    3 +-
 include/bout/paralleltransform.hxx            |    2 +-
 include/bout/physicsmodel.hxx                 |   11 +-
 include/bout/region.hxx                       |    9 +-
 include/bout/revision.hxx.in                  |    6 +-
 include/bout/solver.hxx                       |    9 +-
 include/bout/sundials_backports.hxx           |   14 +-
 include/bout/sys/expressionparser.hxx         |   13 +-
 include/bout/sys/generator_context.hxx        |   16 +-
 include/bout/unused.hxx                       |   20 -
 include/bout/utils.hxx                        |   13 +
 include/bout/vector2d.hxx                     |    2 +-
 include/bout/vector3d.hxx                     |    5 +-
 include/bout/version.hxx.in                   |   14 +-
 manual/sphinx/index.rst                       |    1 +
 manual/sphinx/user_docs/adios2.rst            |   45 +
 manual/sphinx/user_docs/advanced_install.rst  |    6 +-
 manual/sphinx/user_docs/bout_options.rst      |  109 +-
 manual/sphinx/user_docs/installing.rst        |    4 +
 src/bout++.cxx                                |   23 +-
 src/field/field.cxx                           |    2 -
 src/field/field3d.cxx                         |   16 +-
 src/field/field_factory.cxx                   |   24 +-
 src/field/gen_fieldops.jinja                  |   20 +-
 src/field/generated_fieldops.cxx              |  168 +-
 src/invert/fft_fftw.cxx                       |   24 +-
 .../laplace/impls/multigrid/multigrid_alg.cxx |    2 +-
 src/invert/laplace/invert_laplace.cxx         |   11 +-
 src/invert/laplacexz/laplacexz.cxx            |    5 -
 src/invert/parderiv/invert_parderiv.cxx       |    4 -
 src/invert/pardiv/invert_pardiv.cxx           |    4 -
 src/mesh/coordinates.cxx                      |    8 +-
 src/mesh/data/gridfromfile.cxx                |   20 +-
 src/mesh/difops.cxx                           |    4 +-
 src/mesh/impls/bout/boutmesh.cxx              |   47 +-
 src/mesh/index_derivs.cxx                     |    5 +-
 src/mesh/interpolation/hermite_spline_xz.cxx  |   12 +-
 src/mesh/interpolation/hermite_spline_z.cxx   |    7 -
 src/mesh/interpolation_xz.cxx                 |    8 -
 src/mesh/mesh.cxx                             |  114 +-
 src/mesh/parallel/fci.cxx                     |   23 +-
 src/mesh/parallel/fci.hxx                     |    2 +-
 src/physics/physicsmodel.cxx                  |   50 +-
 src/solver/impls/arkode/arkode.cxx            |    2 +-
 src/solver/impls/cvode/cvode.cxx              |    3 +-
 src/solver/impls/ida/ida.cxx                  |    2 +-
 src/solver/impls/imex-bdf2/imex-bdf2.cxx      |    3 -
 src/solver/impls/petsc/petsc.cxx              |   14 +-
 src/solver/impls/rkgeneric/rkscheme.cxx       |    5 -
 src/solver/impls/slepc/slepc.cxx              |    2 +-
 src/solver/solver.cxx                         |    7 +-
 src/sys/adios_object.cxx                      |   98 +
 src/sys/derivs.cxx                            |   18 +-
 src/sys/expressionparser.cxx                  |   44 +
 src/sys/hyprelib.cxx                          |    4 +-
 src/sys/options.cxx                           |  264 +--
 src/sys/options/options_adios.cxx             |  548 ++++++
 src/sys/options/options_adios.hxx             |   83 +
 src/sys/options/options_ini.cxx               |    2 +-
 src/sys/options/options_io.cxx                |   58 +
 src/sys/options/options_netcdf.cxx            |   62 +-
 src/sys/options/options_netcdf.hxx            |   84 +
 tests/MMS/spatial/fci/data/BOUT.inp           |    1 +
 tests/MMS/spatial/fci/fci_mms.cxx             |    2 +
 tests/MMS/spatial/fci/mms.py                  |    3 -
 tests/MMS/spatial/fci/runtest                 |    2 +-
 tests/MMS/time/time.cxx                       |    8 +-
 tests/integrated/CMakeLists.txt               |    1 +
 tests/integrated/test-beuler/test_beuler.cxx  |    3 -
 .../collect-staggered/data/BOUT.inp           |    2 +-
 .../test-boutpp/collect/input/BOUT.inp        |    2 +-
 .../test-boutpp/legacy-model/data/BOUT.inp    |    2 +-
 .../test-boutpp/mms-ddz/data/BOUT.inp         |    2 +-
 .../test-boutpp/slicing/basics.indexing.html  | 1368 +++++++++++++
 .../test-boutpp/slicing/basics.indexing.txt   |  687 +++++++
 .../test-boutpp/slicing/slicingexamples       |    1 +
 tests/integrated/test-boutpp/slicing/test.py  |    4 +
 .../test-griddata/test_griddata.cxx           |    2 +-
 .../orig_test.idl.dat                         |  Bin 2612 -> 0 bytes
 .../test-options-adios/CMakeLists.txt         |    6 +
 .../test-options-adios/data/BOUT.inp          |    6 +
 tests/integrated/test-options-adios/makefile  |    6 +
 tests/integrated/test-options-adios/runtest   |   74 +
 .../test-options-adios/test-options-adios.cxx |  111 ++
 .../test-options-netcdf.cxx                   |   24 +-
 tests/integrated/test-solver/test_solver.cxx  |    2 -
 .../test-twistshift.cxx                       |   10 +-
 .../test-twistshift/test-twistshift.cxx       |    2 +-
 .../test_yupdown_weights.cxx                  |    2 +-
 tests/unit/CMakeLists.txt                     |    3 +
 tests/unit/field/test_vector2d.cxx            |    4 -
 .../include/bout/test_generic_factory.cxx     |    9 -
 tests/unit/include/bout/test_region.cxx       |   18 +
 tests/unit/mesh/data/test_gridfromoptions.cxx |   13 +-
 tests/unit/sys/test_expressionparser.cxx      |   39 +-
 tests/unit/sys/test_options.cxx               |   79 +-
 tests/unit/sys/test_options_netcdf.cxx        |   77 +-
 tests/unit/test_extras.cxx                    |    5 -
 tests/unit/test_extras.hxx                    |   24 +-
 tools/pylib/_boutpp_build/bout_options.pxd    |   17 +-
 tools/pylib/_boutpp_build/boutcpp.pxd.jinja   |    2 +-
 tools/pylib/_boutpp_build/boutpp.pyx.jinja    |    1 -
 tools/pylib/post_bout/ListDict.py             |   61 -
 tools/pylib/post_bout/__init__.py             |   95 -
 tools/pylib/post_bout/basic_info.py           |  421 ----
 tools/pylib/post_bout/grate2.py               |   52 -
 tools/pylib/post_bout/pb_corral.py            |  540 ------
 tools/pylib/post_bout/pb_draw.py              | 1692 -----------------
 tools/pylib/post_bout/pb_nonlinear.py         |   99 -
 tools/pylib/post_bout/pb_present.py           |  213 ---
 tools/pylib/post_bout/read_cxx.py             |  139 --
 tools/pylib/post_bout/read_inp.py             |  433 -----
 tools/pylib/post_bout/rms.py                  |   55 -
 159 files changed, 4839 insertions(+), 4798 deletions(-)
 create mode 100755 .build_adios2_for_ci.sh
 create mode 100644 examples/elm-pb/plot_linear.py
 delete mode 100644 examples/shear-alfven-wave/orig_test.idl.dat
 delete mode 100644 examples/uedge-benchmark/result_080917.idl
 delete mode 100644 examples/uedge-benchmark/ue_bmk.idl
 create mode 100755 include/bout/adios_object.hxx
 delete mode 100644 include/bout/format.hxx
 create mode 100644 include/bout/options_io.hxx
 delete mode 100644 include/bout/options_netcdf.hxx
 create mode 100644 manual/sphinx/user_docs/adios2.rst
 create mode 100644 src/sys/adios_object.cxx
 create mode 100644 src/sys/options/options_adios.cxx
 create mode 100644 src/sys/options/options_adios.hxx
 create mode 100644 src/sys/options/options_io.cxx
 create mode 100644 src/sys/options/options_netcdf.hxx
 create mode 100644 tests/integrated/test-boutpp/slicing/basics.indexing.html
 create mode 100644 tests/integrated/test-boutpp/slicing/basics.indexing.txt
 create mode 100644 tests/integrated/test-boutpp/slicing/slicingexamples
 create mode 100644 tests/integrated/test-boutpp/slicing/test.py
 delete mode 100644 tests/integrated/test-interchange-instability/orig_test.idl.dat
 create mode 100644 tests/integrated/test-options-adios/CMakeLists.txt
 create mode 100644 tests/integrated/test-options-adios/data/BOUT.inp
 create mode 100644 tests/integrated/test-options-adios/makefile
 create mode 100755 tests/integrated/test-options-adios/runtest
 create mode 100644 tests/integrated/test-options-adios/test-options-adios.cxx
 delete mode 100644 tools/pylib/post_bout/ListDict.py
 delete mode 100644 tools/pylib/post_bout/__init__.py
 delete mode 100644 tools/pylib/post_bout/basic_info.py
 delete mode 100644 tools/pylib/post_bout/grate2.py
 delete mode 100644 tools/pylib/post_bout/pb_corral.py
 delete mode 100644 tools/pylib/post_bout/pb_draw.py
 delete mode 100644 tools/pylib/post_bout/pb_nonlinear.py
 delete mode 100644 tools/pylib/post_bout/pb_present.py
 delete mode 100644 tools/pylib/post_bout/read_cxx.py
 delete mode 100644 tools/pylib/post_bout/read_inp.py
 delete mode 100644 tools/pylib/post_bout/rms.py

diff --git a/.build_adios2_for_ci.sh b/.build_adios2_for_ci.sh
new file mode 100755
index 0000000000..c6d4178884
--- /dev/null
+++ b/.build_adios2_for_ci.sh
@@ -0,0 +1,62 @@
+#!/bin/bash
+
+set -e
+
+if test $BUILD_ADIOS2 ; then
+    if [[ ! -d $HOME/local/adios/include/adios2.h ]] || test $1 ; then
+	echo "****************************************"
+	echo "Building ADIOS2"
+	echo "****************************************"
+
+	branch=${1:-release_29}
+    if [ ! -d adios2 ]; then
+    	git clone -b $branch https://github.com/ornladios/ADIOS2.git adios2 --depth=1
+    fi
+
+	pushd adios2
+    rm -rf build
+    mkdir -p build
+    pushd build
+
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=$HOME/local \
+        -DADIOS2_USE_MPI=ON \
+        -DADIOS2_USE_Fortran=OFF \
+        -DADIOS2_USE_Python=OFF \
+        -DADIOS2_BUILD_EXAMPLES=OFF \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+        -DBUILD_TESTING=OFF \
+        -DADIOS2_USE_SST=OFF \
+        -DADIOS2_USE_MGARD=OFF \
+        -DADIOS2_USE_HDF5=OFF \
+        -DADIOS2_USE_BZip2=OFF \
+        -DADIOS2_USE_Blosc2=OFF \
+        -DADIOS2_USE_SZ=OFF \
+        -DADIOS2_USE_ZFP=OFF \
+        -DADIOS2_USE_DAOS=OFF \
+        -DADIOS2_USE_UCX=OFF \
+        -DADIOS2_USE_LIBPRESSIO=OFF \
+        -DADIOS2_USE_Sodium=OFF \
+        -DADIOS2_USE_ZeroMQ=OFF \
+        -DADIOS2_USE_MHS=OFF \
+        -DADIOS2_USE_DataMan=OFF
+
+	make -j 4 && make install
+	popd
+
+	echo "****************************************"
+	echo " Finished building ADIOS2"
+	echo "****************************************"
+
+    else
+
+	echo "****************************************"
+	echo " ADIOS2 already installed"
+	echo "****************************************"
+    fi
+else
+    echo "****************************************"
+    echo " ADIOS2 not requested"
+    echo "****************************************"
+fi
diff --git a/.clang-tidy b/.clang-tidy
index b52a287a8d..48a434bc14 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -1,5 +1,5 @@
 ---
-Checks:          'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity'
+Checks:          'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
 AnalyzeTemporaryDtors: false
diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index d546ce3af2..f50d5aeff7 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -32,7 +32,7 @@ jobs:
           # the unit tests until they're fixed or ignored upstream
           exclude: "tests/unit/*cxx"
           cmake_command: |
-            pip install cmake && \
+            pip install --break-system-packages cmake && \
             cmake --version && \
             git config --global --add safe.directory "$GITHUB_WORKSPACE" && \
             cmake . -B build -DBUILD_SHARED_LIBS=ON \
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 1083c5e059..c449beb4ca 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -39,7 +39,7 @@ jobs:
         is_cron:
           - ${{ github.event_name == 'cron' }}
         config:
-          - name: "CMake, PETSc unreleased"
+          - name: "CMake, PETSc unreleased, ADIOS"
             os: ubuntu-20.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
@@ -47,12 +47,15 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_ADIOS2=ON
                             -DBOUT_ENABLE_PYTHON=ON
+                            -DADIOS2_ROOT=/home/runner/local/adios2
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
                             -DSLEPC_DIR=/home/runner/local/slepc"
             build_petsc: -petsc-main
             build_petsc_branch: main
+            build_adios2: true
             on_cron: true
 
           - name: "Default options, Ubuntu 20.04"
@@ -201,6 +204,9 @@ jobs:
       - name: Build PETSc
         run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh ${{ matrix.config.build_petsc_branch }}
 
+      - name: Build ADIOS2
+        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh 
+
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 656b284b9d..d71dc470e9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@
 ### Breaking changes
 
 - The autotools `./configure` build system has been removed
+- Parsing of booleans has changed [\#2828][https://github.com/boutproject/BOUT-dev/pull/2828] ([bendudson][https://github.com/bendudson]).
+  See the [manual page](https://bout-dev.readthedocs.io/en/stable/user_docs/bout_options.html#boolean-expressions) for details.
 
 
 ## [v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7199bb376a..483672fb67 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -83,6 +83,7 @@ function(bout_update_submodules)
 endfunction()
 
 set(BOUT_SOURCES
+  ./include/bout/adios_object.hxx
   ./include/bout/array.hxx
   ./include/bout/assert.hxx
   ./include/bout/boundary_factory.hxx
@@ -114,7 +115,6 @@ set(BOUT_SOURCES
   ./include/bout/field_factory.hxx
   ./include/bout/fieldgroup.hxx
   ./include/bout/fieldperp.hxx
-  ./include/bout/format.hxx
   ./include/bout/fv_ops.hxx
   ./include/bout/generic_factory.hxx
   ./include/bout/globalfield.hxx
@@ -146,7 +146,7 @@ set(BOUT_SOURCES
   ./include/bout/openmpwrap.hxx
   ./include/bout/operatorstencil.hxx
   ./include/bout/options.hxx
-  ./include/bout/options_netcdf.hxx
+  ./include/bout/options_io.hxx
   ./include/bout/optionsreader.hxx
   ./include/bout/output.hxx
   ./include/bout/output_bout_types.hxx
@@ -325,6 +325,7 @@ set(BOUT_SOURCES
   ./src/solver/impls/split-rk/split-rk.cxx
   ./src/solver/impls/split-rk/split-rk.hxx
   ./src/solver/solver.cxx
+  ./src/sys/adios_object.cxx
   ./src/sys/bout_types.cxx
   ./src/sys/boutcomm.cxx
   ./src/sys/boutexception.cxx
@@ -338,7 +339,11 @@ set(BOUT_SOURCES
   ./src/sys/options/optionparser.hxx
   ./src/sys/options/options_ini.cxx
   ./src/sys/options/options_ini.hxx
+  ./src/sys/options/options_io.cxx
   ./src/sys/options/options_netcdf.cxx
+  ./src/sys/options/options_netcdf.hxx
+  ./src/sys/options/options_adios.cxx
+  ./src/sys/options/options_adios.hxx
   ./src/sys/optionsreader.cxx
   ./src/sys/output.cxx
   ./src/sys/petsclib.cxx
@@ -462,7 +467,7 @@ set_target_properties(bout++ PROPERTIES
 # Set some variables for the bout-config script
 set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -L\$BOUT_LIB_PATH -lbout++")
 set(BOUT_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/include")
-set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS}")
+set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS} -std=c++17")
 
 target_compile_features(bout++ PUBLIC cxx_std_17)
 set_target_properties(bout++ PROPERTIES CXX_EXTENSIONS OFF)
@@ -930,6 +935,7 @@ message("
    SUNDIALS support         : ${BOUT_HAS_SUNDIALS}
    HYPRE support            : ${BOUT_HAS_HYPRE}
    NetCDF support           : ${BOUT_HAS_NETCDF}
+   ADIOS support            : ${BOUT_HAS_ADIOS}
    FFTW support             : ${BOUT_HAS_FFTW}
    LAPACK support           : ${BOUT_HAS_LAPACK}
    OpenMP support           : ${BOUT_USE_OPENMP}
diff --git a/README.md b/README.md
index fd9e6931ab..5f774ad337 100644
--- a/README.md
+++ b/README.md
@@ -26,8 +26,11 @@ For example, the following set of equations for magnetohydrodynamics
 (MHD):
 
 ![ddt_rho](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Crho%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Crho%20-%20%5Crho%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)
+
 ![ddt_p](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20p%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%20p%20-%20%5Cgamma%20p%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)
+
 ![ddt_v](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Cmathbf%7Bv%7D%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Cmathbf%7Bv%7D%20&plus;%20%5Cfrac%7B1%7D%7B%5Crho%7D%28-%5Cnabla%20p%20&plus;%20%28%5Cnabla%5Ctimes%5Cmathbf%7BB%7D%29%5Ctimes%5Cmathbf%7BB%7D%29)
+
 ![ddt_B](http://latex.codecogs.com/png.latex?%7B%7B%5Cfrac%7B%5Cpartial%20%5Cmathbf%7BB%7D%7D%7B%5Cpartial%20t%7D%7D%7D%20%3D%20%5Cnabla%5Ctimes%28%5Cmathbf%7Bv%7D%5Ctimes%5Cmathbf%7BB%7D%29)
 
 can be written simply as:
@@ -43,7 +46,7 @@ The full code for this example can be found in the [orszag-tang
 example](examples/orszag-tang/mhd.cxx).
 
 Jointly developed by University of York (UK), LLNL, CCFE, DCU, DTU,
-and other international partners.
+and other international partners. See the Git logs for author details.
 
 
 Homepage found at [http://boutproject.github.io/](http://boutproject.github.io/)
@@ -52,7 +55,6 @@ Homepage found at [http://boutproject.github.io/](http://boutproject.github.io/)
 * [Requirements](#requirements)
 * [Usage and installation](#usage-and-installation)
 * [Terms of use](#terms-of-use)
-* [Overview of files](#overview-of-files)
 * [Contributing](#contributing)
 * [License](#license)
 
@@ -66,18 +68,17 @@ BOUT++ needs the following:
 
 BOUT++ has the following optional dependencies:
 
-* FFTW3 (strongly recommended!)
-* OpenMP
-* PETSc
-* SLEPc
-* ARKODE
-* IDA
-* CVODE
+* [FFTW3](https://www.fftw.org/) (strongly recommended!)
+* [SUNDIALS](https://computing.llnl.gov/projects/sundials): CVODE, IDA, ARKODE
+* [PETSc](https://petsc.org)
+* [ADIOS2](https://adios2.readthedocs.io/)
+* [SLEPc](https://slepc.upv.es/)
 * LAPACK
+* OpenMP
 * Score-p (for performance diagnostics)
 
 ## Usage and installation
-Please see the [users manual](http://bout-dev.readthedocs.io)
+Please see the [users manual](http://bout-dev.readthedocs.io).
 
 ## Terms of use
 
@@ -105,58 +106,14 @@ You can convert the CITATION.cff file into a Bibtex file as follows:
     pip3 install --user cffconvert
     cffconvert -if CITATION.cff -f bibtex -of CITATION.bib
 
-## Overview of files
-
-This directory contains
-
-* **bin**                   Files for setting the BOUT++ configuration
-* **examples**              Example models and test codes
-* **externalpackages**      External packages needed for installing BOUT++
-* **include**               Header files used in BOUT++
-* **manual**                Manuals and documentation (also [doxygen](http://www.stack.nl/~dimitri/doxygen/) documentation)
-* **src**                   The main code directory
-* **CITATION**              Contains the paper citation for BOUT++
-* **LICENSE**               LGPL license
-* **LICENSE.GPL**           GPL license
-* **tools**                 Tools for helping with analysis, mesh generation, and data managment
-
-  * **archiving**               Routines for managing input/output files e.g. compressing data, converting formats, and managing runs
-  * **cyl_and_helimak_grids**   IDL codes for generating cylindrical and helimak grids
-  * **eigensolver**             Matlab routines for solving eigenmodes
-  * **idllib**                  Analysis codes in IDL. Add this to your IDL_PATH environment variable
-  * **line_tracing**            IDL routines for line tracing of field lines
-  * **line_tracing_v2**         Newer version of the IDL routines for line tracing of field lines
-  * **mathematicalib**          Library for post processing using Mathematica
-  * **matlablib**               Library for post processing using MATLAB
-  * **numlib**                  Numerical IDL routines
-  * **octave**                  Routines for post processing using octave
-  * **plasmalib**               IDL routines for calculation of plasma parameters
-  * **pdb2idl**                 Library to read Portable Data Binary (PDB) files into IDL
-  * **pylib**                   Analysis codes in Python
-
-    * **boutdata**        Routines to simplify accessing BOUT++ output
-    * **boututils**       Some useful routines for accessing and plotting data
-    * **post_bout**       Routines for post processing in BOUT++
-
-  * **slab**              IDL routine for grid generation of a slab
-  * **tokamak_grids**     Code to generate input grids for tokamak equilibria
-
-    * **gridgen**         Grid generator in IDL. Hypnotoad GUI for converting G-EQDSK files into a flux-aligned orthogonal grid.
-    * **elite**           Convert ELITE .eqin files into an intermediate binary file
-    * **gato**            Convert DSKGATO files into intermediate binary format
-    * **all**             Convert the intermediate binary file into BOUT++ input grid
-    * **coils**           Routines for calculating the field due to external RMP coils and adding to existing equilibria
-    * **cyclone**         Generate cyclone test cases (concentric circle "equilibrium" for local flux-surface calculations)
-    * **py_gridgen**      Translation" into python of the corresponding IDL routines in the folder gridgen
-    * **shifted_circle**  Produce shifted cirle equilibria input grids
 
 
 ## Contributing
 
-See [CONTRIBUTING.md](CONTRIBUTING.md).
+See [CONTRIBUTING.md](CONTRIBUTING.md) and the [manual page](https://bout-dev.readthedocs.io/en/stable/developer_docs/contributing.html)
 
 ## License
-Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+Copyright 2010-2024 BOUT++ contributors
 
 BOUT++ is free software: you can redistribute it and/or modify
 it under the terms of the GNU Lesser General Public License as published by
@@ -171,15 +128,7 @@ GNU Lesser General Public License for more details.
 A copy of the LGPL license is in [LICENSE](LICENSE). Since this is based
 on (and refers to) the GPL, this is included in [LICENSE.GPL](LICENSE.GPL).
 
-Some of the autoconf macros under [m4](m4) are licensed under
-GPLv3. These are not necessary to either build or run BOUT++, but are
-used in the creation of [configure](configure) from
-[configure.ac](configure.ac), and are provided as a courtesy to
-developers. You are free to substitute them with other autoconf macros
-that provide equivalent functionality.
-
 BOUT++ links by default with some GPL licensed libraries. Thus if you
 compile BOUT++ with any of them, BOUT++ will automatically be licensed
 as GPL. Thus if you want to use BOUT++ with GPL non-compatible code,
 make sure to compile without GPLed code.
-
diff --git a/bin/bout-config.in b/bin/bout-config.in
index 697d3ddc71..a9045fff39 100755
--- a/bin/bout-config.in
+++ b/bin/bout-config.in
@@ -29,6 +29,7 @@ idlpath="@IDLCONFIGPATH@"
 pythonpath="@PYTHONCONFIGPATH@"
 
 has_netcdf="@BOUT_HAS_NETCDF@"
+has_adios="@BOUT_HAS_ADIOS@"
 has_legacy_netcdf="@BOUT_HAS_LEGACY_NETCDF@"
 has_pnetcdf="@BOUT_HAS_PNETCDF@"
 has_pvode="@BOUT_HAS_PVODE@"
@@ -71,6 +72,7 @@ Available values for OPTION include:
   --python       Python path
 
   --has-netcdf  NetCDF file support
+  --has-adios   ADIOS file support
   --has-legacy-netcdf  Legacy NetCDF file support
   --has-pnetcdf Parallel NetCDF file support
   --has-pvode   PVODE solver support
@@ -109,6 +111,7 @@ all()
         echo "  --python      -> $pythonpath"
         echo
         echo "  --has-netcdf  -> $has_netcdf"
+        echo "  --has-adios   -> $has_adios"
         echo "  --has-legacy-netcdf  -> $has_legacy_netcdf"
         echo "  --has-pnetcdf -> $has_pnetcdf"
         echo "  --has-pvode   -> $has_pvode"
@@ -197,6 +200,10 @@ while test $# -gt 0; do
         echo $has_netcdf
         ;;
 
+    --has-adios)
+        echo $has_adios
+        ;;
+
     --has-legacy-netcdf)
         echo $has_legacy_netcdf
         ;;
diff --git a/bout++Config.cmake.in b/bout++Config.cmake.in
index e33e950e6f..3d824e455f 100644
--- a/bout++Config.cmake.in
+++ b/bout++Config.cmake.in
@@ -15,6 +15,7 @@ set(BOUT_USE_METRIC_3D @BOUT_USE_METRIC_3D@)
 
 set(BOUT_HAS_PVODE @BOUT_HAS_PVODE@)
 set(BOUT_HAS_NETCDF @BOUT_HAS_NETCDF@)
+set(BOUT_HAS_ADIOS @BOUT_HAS_ADIOS@)
 set(BOUT_HAS_FFTW @BOUT_HAS_FFTW@)
 set(BOUT_HAS_LAPACK @BOUT_HAS_LAPACK@)
 set(BOUT_HAS_PETSC @BOUT_HAS_PETSC@)
diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 55f201bdad..e1d6f00cb4 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -156,6 +156,7 @@ option(BOUT_USE_NETCDF "Enable support for NetCDF output" ON)
 option(BOUT_DOWNLOAD_NETCDF_CXX4 "Download and build netCDF-cxx4" OFF)
 if (BOUT_USE_NETCDF)
   if (BOUT_DOWNLOAD_NETCDF_CXX4)
+    message(STATUS "Downloading and configuring NetCDF-cxx4")
     include(FetchContent)
     FetchContent_Declare(
       netcdf-cxx4
@@ -185,6 +186,44 @@ endif()
 message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}")
 set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})
 
+option(BOUT_USE_ADIOS "Enable support for ADIOS output" ON)
+option(BOUT_DOWNLOAD_ADIOS "Download and build ADIOS2" OFF)
+if (BOUT_USE_ADIOS)
+  if (BOUT_DOWNLOAD_ADIOS)
+    message(STATUS "Downloading and configuring ADIOS2")
+    include(FetchContent)
+    FetchContent_Declare(
+      adios2
+      GIT_REPOSITORY https://github.com/ornladios/ADIOS2.git
+      GIT_TAG origin/master
+      GIT_SHALLOW 1
+      )
+    set(ADIOS2_USE_MPI ON CACHE BOOL "" FORCE)
+    set(ADIOS2_USE_Fortran OFF CACHE BOOL "" FORCE)
+    set(ADIOS2_USE_Python OFF CACHE BOOL "" FORCE)
+    set(ADIOS2_BUILD_EXAMPLES OFF CACHE BOOL "" FORCE)
+    # Disable testing, or ADIOS will try to find or install GTEST
+    set(BUILD_TESTING OFF CACHE BOOL "" FORCE)
+    # Note: SST requires <rdma/fabric.h> but doesn't check at configure time
+    set(ADIOS2_USE_SST OFF CACHE BOOL "" FORCE)
+    FetchContent_MakeAvailable(adios2)
+    target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi)
+    message(STATUS "ADIOS2 done configuring")
+  else()
+    find_package(ADIOS2)
+    if (ADIOS2_FOUND)
+      ENABLE_LANGUAGE(C)
+      find_package(MPI REQUIRED COMPONENTS C)
+      target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C)
+    else()
+      set(BOUT_USE_ADIOS OFF)
+    endif()
+  endif()
+endif()
+message(STATUS "ADIOS support: ${BOUT_USE_ADIOS}")
+set(BOUT_HAS_ADIOS ${BOUT_USE_ADIOS})
+
+
 option(BOUT_USE_FFTW "Enable support for FFTW" ON)
 if (BOUT_USE_FFTW)
   find_package(FFTW REQUIRED)
diff --git a/cmake_build_defines.hxx.in b/cmake_build_defines.hxx.in
index a637dbc46a..ed6e8685f6 100644
--- a/cmake_build_defines.hxx.in
+++ b/cmake_build_defines.hxx.in
@@ -13,6 +13,7 @@
 #cmakedefine01 BOUT_HAS_IDA
 #cmakedefine01 BOUT_HAS_LAPACK
 #cmakedefine01 BOUT_HAS_NETCDF
+#cmakedefine01 BOUT_HAS_ADIOS
 #cmakedefine01 BOUT_HAS_PETSC
 #cmakedefine01 BOUT_HAS_PRETTY_FUNCTION
 #cmakedefine01 BOUT_HAS_PVODE
diff --git a/examples/elm-pb-outerloop/data/BOUT.inp b/examples/elm-pb-outerloop/data/BOUT.inp
index d06073f838..6c9f268057 100644
--- a/examples/elm-pb-outerloop/data/BOUT.inp
+++ b/examples/elm-pb-outerloop/data/BOUT.inp
@@ -13,9 +13,6 @@ MZ = 16             # Number of points in Z
 
 grid = "cbm18_dens8.grid_nx68ny64.nc"  # Grid file
 
-dump_format = "nc"      # Dump file format. "nc" = NetCDF, "pdb" = PDB
-restart_format = "nc"   # Restart file format
-
 [mesh]
 
 staggergrids = false    # Use staggered grids
@@ -44,9 +41,6 @@ first = C4  # Z derivatives can be done using FFT
 second = C4
 upwind = W3
 
-[output]
-shiftoutput = true  # Put the output into field-aligned coordinates
-
 ##################################################
 # FFTs
 
diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index 691f4303f4..8e84901806 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -1576,7 +1576,17 @@ class ELMpb : public PhysicsModel {
     Field3D B0U = B0 * U;
     mesh->communicate(B0U);
     auto B0U_acc = FieldAccessor<>(B0U);
-#endif
+#else
+    Field3D B0phi = B0 * phi;
+    mesh->communicate(B0phi);
+    auto B0phi_acc = FieldAccessor<>(B0phi);
+
+#if EHALL
+    Field3D B0P = B0 * P;
+    mesh->communicate(B0 * P);
+    auto B0P_acc = FieldAccessor<>(B0P);
+#endif // EHALL
+#endif // EVOLVE_JPAR
 
 #if RELAX_J_VAC
     auto vac_mask_acc = FieldAccessor<>(vac_mask);
@@ -1612,23 +1622,24 @@ class ELMpb : public PhysicsModel {
 
 #else
       // Evolve vector potential ddt(psi)
-      ddt(Psi_acc)[i] =
-          -GRAD_PARP(phi_acc) + eta_acc[i] * Jpar_acc[i]
+      ddt(Psi_acc)[i] = -GRAD_PARP(B0phi_acc) / B0_acc[i2d] + eta_acc[i] * Jpar_acc[i]
 
-          + EVAL_IF(EHALL, // electron parallel pressure
-                    0.25 * delta_i * (GRAD_PARP(P_acc) + bracket(P0_acc, Psi_acc, i)))
+                        + EVAL_IF(EHALL, // electron parallel pressure
+                                  0.25 * delta_i
+                                      * (GRAD_PARP(B0P_acc) / B0_acc[i2d]
+                                         + bracket(P0_acc, Psi_acc, i) * B0_acc[i2d]))
 
-          - EVAL_IF(DIAMAG_PHI0, // Equilibrium flow
-                    bracket(phi0_acc, Psi_acc, i))
+                        - EVAL_IF(DIAMAG_PHI0, // Equilibrium flow
+                                  bracket(phi0_acc, Psi_acc, i) * B0_acc[i2d])
 
-          + EVAL_IF(DIAMAG_GRAD_T, // grad_par(T_e) correction
-                    1.71 * dnorm * 0.5 * GRAD_PARP(P_acc) / B0_acc[i2d])
+                        + EVAL_IF(DIAMAG_GRAD_T, // grad_par(T_e) correction
+                                  1.71 * dnorm * 0.5 * GRAD_PARP(P_acc) / B0_acc[i2d])
 
-          - EVAL_IF(HYPERRESIST, // Hyper-resistivity
-                    eta_acc[i] * hyperresist * Delp2(Jpar_acc, i))
+                        - EVAL_IF(HYPERRESIST, // Hyper-resistivity
+                                  eta_acc[i] * hyperresist * Delp2(Jpar_acc, i))
 
-          - EVAL_IF(EHYPERVISCOS, // electron Hyper-viscosity
-                    eta_acc[i] * ehyperviscos * Delp2(Jpar2_acc, i));
+                        - EVAL_IF(EHYPERVISCOS, // electron Hyper-viscosity
+                                  eta_acc[i] * ehyperviscos * Delp2(Jpar2_acc, i));
 #endif
 
       ////////////////////////////////////////////////////
diff --git a/examples/elm-pb/data/BOUT.inp b/examples/elm-pb/data/BOUT.inp
index 69d8bb0976..55a4a30c06 100644
--- a/examples/elm-pb/data/BOUT.inp
+++ b/examples/elm-pb/data/BOUT.inp
@@ -12,21 +12,18 @@ zperiod = 15        # Fraction of a torus to simulate
 MZ = 16             # Number of points in Z
 
 grid = "cbm18_dens8.grid_nx68ny64.nc"  # Grid file
-restart_format = "nc"   # Restart file format
 
 [mesh]
 
 staggergrids = false    # Use staggered grids
 
 [mesh:paralleltransform]
-
 type = shifted # Use shifted metric method
 
 ##################################################
 # derivative methods
 
 [mesh:ddx]
-
 first = C4  # order of first x derivatives
 second = C4 # order of second x derivatives
 upwind = W3 # order of upwinding method W3 = Weno3
@@ -42,9 +39,6 @@ first = C4  # Z derivatives can be done using FFT
 second = C4
 upwind = W3
 
-[output]
-shiftoutput = true  # Put the output into field-aligned coordinates
-
 ##################################################
 # FFTs
 
@@ -58,8 +52,8 @@ fft_measurement_flag = measure  # If using FFTW, perform tests to determine fast
 [solver]
 
 # mudq, mldq, mukeep, mlkeep preconditioner options
-atol = 1e-08 # absolute tolerance
-rtol = 1e-05  # relative tolerance
+atol = 1.0e-8 # absolute tolerance
+rtol = 1.0e-5  # relative tolerance
 
 use_precon = false    # Use preconditioner: User-supplied or BBD
 
@@ -160,7 +154,7 @@ damp_t_const = 1e-2  # Damping time constant
 
 diffusion_par = -1.0   # Parallel pressure diffusion (< 0 = none)
 diffusion_p4 = -1e-05   # parallel hyper-viscous diffusion for pressure (< 0 = none)
-diffusion_u4 = 1e-05    # parallel hyper-viscous diffusion for vorticity (< 0 = none)
+diffusion_u4 = -1e-05    # parallel hyper-viscous diffusion for vorticity (< 0 = none)
 diffusion_a4 = -1e-05   # parallel hyper-viscous diffusion for vector potential (< 0 = none)
 
 ## heat source in pressure in watts
diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx
index 6232c72d52..e81742747a 100644
--- a/examples/elm-pb/elm_pb.cxx
+++ b/examples/elm-pb/elm_pb.cxx
@@ -371,8 +371,9 @@ class ELMpb : public PhysicsModel {
 
     density = options["density"].doc("Number density [m^-3]").withDefault(1.0e19);
 
-    evolve_jpar =
-        options["evolve_jpar"].doc("If true, evolve J raher than Psi").withDefault(false);
+    evolve_jpar = options["evolve_jpar"]
+                      .doc("If true, evolve J rather than Psi")
+                      .withDefault(false);
     phi_constraint = options["phi_constraint"]
                          .doc("Use solver constraint for phi?")
                          .withDefault(false);
@@ -1487,15 +1488,16 @@ class ELMpb : public PhysicsModel {
       }
     } else {
       // Vector potential
-      ddt(Psi) = -Grad_parP(phi, loc) + eta * Jpar;
+      ddt(Psi) = -Grad_parP(phi * B0, loc) / B0 + eta * Jpar;
 
       if (eHall) { // electron parallel pressure
         ddt(Psi) += 0.25 * delta_i
-                    * (Grad_parP(P, loc) + bracket(interp_to(P0, loc), Psi, bm_mag));
+                    * (Grad_parP(B0 * P, loc) / B0
+                       + bracket(interp_to(P0, loc), Psi, bm_mag) * B0);
       }
 
       if (diamag_phi0) { // Equilibrium flow
-        ddt(Psi) -= bracket(interp_to(phi0, loc), Psi, bm_exb);
+        ddt(Psi) -= bracket(interp_to(phi0, loc), Psi, bm_exb) * B0;
       }
 
       if (withflow) { // net flow
diff --git a/examples/elm-pb/plot_linear.py b/examples/elm-pb/plot_linear.py
new file mode 100644
index 0000000000..42047ec5dc
--- /dev/null
+++ b/examples/elm-pb/plot_linear.py
@@ -0,0 +1,85 @@
+# Plots an analysis of the linear growth rate
+#
+# Input argument is the directory containing data files.
+#
+# Example:
+#     $ python plot_linear.py data/
+#
+
+from boutdata import collect
+import numpy as np
+import matplotlib.pyplot as plt
+import os
+import sys
+
+if len(sys.argv) != 2:
+    raise ValueError(f"Usage: {sys.argv[0]} path")
+
+# Path to the data
+path = sys.argv[1]
+
+# Read pressure at last time point, to find peak
+p = collect("P", path=path, tind=-1).squeeze()
+prms = np.sqrt(np.mean(p**2, axis=-1))
+
+pyprof = np.amax(prms, axis=0)
+yind = np.argmax(pyprof)
+pxprof = prms[:, yind]
+xind = np.argmax(pxprof)
+print(f"Peak amplitude at x = {xind}, y = {yind}")
+
+# Read pressure time history at index of peak amplitude
+p = collect("P", path=path, xind=xind, yind=yind).squeeze()
+
+# p = p[:,:-1] # Remove point in Z
+
+prms = np.sqrt(np.mean(p**2, axis=-1))
+
+t = collect("t_array", path=path)
+dt = t[1] - t[0]
+
+gamma = np.gradient(np.log(prms)) / dt
+growth_rate = np.mean(gamma[len(gamma) // 2 :])
+growth_rate_std = np.std(gamma[len(gamma) // 2 :])
+
+print(f"Mean growth rate: {growth_rate} +/- {growth_rate_std}")
+
+fig, axs = plt.subplots(2, 2)
+
+ax = axs[0, 0]
+ax.plot(pyprof)
+ax.set_xlabel("Y index")
+ax.set_ylabel("RMS pressure")
+ax.axvline(yind, linestyle="--", color="k")
+ax.text(yind, 0.5 * pyprof[yind], f"y = {yind}")
+
+ax = axs[0, 1]
+ax.plot(pxprof)
+ax.set_xlabel("X index")
+ax.set_ylabel("RMS pressure")
+ax.axvline(xind, linestyle="--", color="k")
+ax.text(xind, 0.5 * pxprof[xind], f"x = {xind}")
+
+ax = axs[1, 0]
+ax.plot(t, prms)
+ax.set_xlabel(r"Time [$\tau_A$]")
+ax.set_ylabel("RMS pressure")
+ax.set_yscale("log")
+ax.plot(t, prms[-1] * np.exp(growth_rate * (t - t[-1])), "--k")
+
+ax = axs[1, 1]
+ax.plot(t, gamma)
+ax.set_xlabel(r"Time [$\tau_A$]")
+ax.set_ylabel("Growth rate [$\omega_A$]")
+ax.axhline(growth_rate, linestyle="--", color="k")
+ax.text(
+    (t[-1] + t[0]) / 4,
+    growth_rate * 1.2,
+    rf"$\gamma = {growth_rate:.3f}\pm {growth_rate_std:.3f} \omega_A$",
+)
+
+plt.savefig(os.path.join(path, "linear_growth.pdf"))
+plt.savefig(os.path.join(path, "linear_growth.png"))
+
+plt.tight_layout()
+plt.show()
diff --git a/examples/make-script/makefile b/examples/make-script/makefile
index ac5f4e96a4..b941125bce 100644
--- a/examples/make-script/makefile
+++ b/examples/make-script/makefile
@@ -22,11 +22,11 @@ LDFLAGS:=$(shell bout-config --libs)
 
 $(TARGET): makefile $(OBJ)
 	@echo "  Linking" $(TARGET)
-	@$(LD) -o $(TARGET) $(OBJ) $(LDFLAGS)
+	$(LD) -o $(TARGET) $(OBJ) $(LDFLAGS)
 
 %.o: %.cxx
 	@echo "  Compiling " $(@F:.o=.cxx)
-	@$(CXX) $(CFLAGS) -c $(@F:.o=.cxx) -o $@
+	$(CXX) $(CFLAGS) -c $(@F:.o=.cxx) -o $@
 
 .PHONY: clean
 clean:
diff --git a/examples/performance/arithmetic/arithmetic.cxx b/examples/performance/arithmetic/arithmetic.cxx
index 583c857e28..fc2357978a 100644
--- a/examples/performance/arithmetic/arithmetic.cxx
+++ b/examples/performance/arithmetic/arithmetic.cxx
@@ -18,6 +18,7 @@ using namespace std::chrono;
     SteadyClock start = steady_clock::now();                                     \
     { __VA_ARGS__; }                                                             \
     Duration diff = steady_clock::now() - start;                                 \
+    diff *= 1000 * 1000;                                                         \
     elapsed.min = diff > elapsed.min ? elapsed.min : diff;                       \
     elapsed.max = diff < elapsed.max ? elapsed.max : diff;                       \
     elapsed.count++;                                                             \
@@ -38,6 +39,8 @@ class Arithmetic : public PhysicsModel {
     Field3D a = 1.0;
     Field3D b = 2.0;
     Field3D c = 3.0;
+    a.setRegion("RGN_ALL");
+    b.setRegion("RGN_NOBNDRY");
 
     Field3D result1, result2, result3, result4;
 
@@ -48,7 +51,7 @@ class Arithmetic : public PhysicsModel {
     Durations elapsed1 = dur_init, elapsed2 = dur_init, elapsed3 = dur_init,
               elapsed4 = dur_init;
 
-    for (int ik = 0; ik < 1e2; ++ik) {
+    for (int ik = 0; ik < 1e3; ++ik) {
       TIMEIT(elapsed1, result1 = 2. * a + b * c;);
 
       // Using C loops
@@ -77,12 +80,13 @@ class Arithmetic : public PhysicsModel {
     }
 
     output.enable();
-    output << "TIMING\n======\n";
+    output << "TIMING      |    minimum |       mean |    maximum\n"
+           << "----------- | ---------- | ---------- | ----------\n";
     //#define PRINT(str,elapsed)   output << str << elapsed.min.count()<<
     //elapsed.avg.count()<< elapsed.max.count() << endl;
-#define PRINT(str, elapsed)                                                \
-  output.write("{:s} {:8.3g} {:8.3g} {:8.3g}\n", str, elapsed.min.count(), \
-               elapsed.avg.count(), elapsed.max.count())
+#define PRINT(str, elapsed)                                          \
+  output.write("{:s} | {:7.3f} us | {:7.3f} us | {:7.3f} us\n", str, \
+               elapsed.min.count(), elapsed.avg.count(), elapsed.max.count())
     PRINT("Fields:    ", elapsed1);
     PRINT("C loop:    ", elapsed2);
     PRINT("Templates: ", elapsed3);
diff --git a/examples/shear-alfven-wave/orig_test.idl.dat b/examples/shear-alfven-wave/orig_test.idl.dat
deleted file mode 100644
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diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
new file mode 100755
index 0000000000..9d2f545b46
--- /dev/null
+++ b/include/bout/adios_object.hxx
@@ -0,0 +1,83 @@
+/*!************************************************************************
+ * Provides access to the ADIOS library, handling initialisation and
+ * finalisation.
+ *
+ * Usage
+ * -----
+ *
+ * #include <bout/adios_object.hxx>
+ *
+ **************************************************************************/
+
+#ifndef ADIOS_OBJECT_HXX
+#define ADIOS_OBJECT_HXX
+
+#include "bout/build_config.hxx"
+
+#if BOUT_HAS_ADIOS
+
+#include <adios2.h>
+#include <memory>
+#include <mpi.h>
+
+namespace bout {
+
+void ADIOSInit(MPI_Comm comm);
+void ADIOSInit(const std::string configFile, MPI_Comm comm);
+void ADIOSFinalize();
+
+using ADIOSPtr = std::shared_ptr<adios2::ADIOS>;
+using EnginePtr = std::shared_ptr<adios2::Engine>;
+using IOPtr = std::shared_ptr<adios2::IO>;
+
+ADIOSPtr GetADIOSPtr();
+IOPtr GetIOPtr(const std::string IOName);
+
+class ADIOSStream {
+public:
+  adios2::IO io;
+  adios2::Engine engine;
+  adios2::Variable<double> vTime;
+  adios2::Variable<int> vStep;
+  int adiosStep = 0;
+  bool isInStep = false; // true if BeginStep was called and EndStep was not yet called
+
+  /** create or return the ADIOSStream based on the target file name */
+  static ADIOSStream& ADIOSGetStream(const std::string& fname);
+
+  ~ADIOSStream();
+
+  template <class T>
+  adios2::Variable<T> GetValueVariable(const std::string& varname) {
+    auto v = io.InquireVariable<T>(varname);
+    if (!v) {
+      v = io.DefineVariable<T>(varname);
+    }
+    return v;
+  }
+
+  template <class T>
+  adios2::Variable<T> GetArrayVariable(const std::string& varname, adios2::Dims& shape) {
+    adios2::Variable<T> v = io.InquireVariable<T>(varname);
+    if (!v) {
+      adios2::Dims start(shape.size());
+      v = io.DefineVariable<T>(varname, shape, start, shape);
+    } else {
+      v.SetShape(shape);
+    }
+    return v;
+  }
+
+private:
+  ADIOSStream(const std::string fname) : fname(fname){};
+  std::string fname;
+};
+
+/** Set user parameters for an IO group */
+void ADIOSSetParameters(const std::string& input, const char delimKeyValue,
+                        const char delimItem, adios2::IO& io);
+
+} // namespace bout
+
+#endif //BOUT_HAS_ADIOS
+#endif //ADIOS_OBJECT_HXX
diff --git a/include/bout/boundary_op.hxx b/include/bout/boundary_op.hxx
index 035caa2778..1a9aa1ad68 100644
--- a/include/bout/boundary_op.hxx
+++ b/include/bout/boundary_op.hxx
@@ -78,8 +78,9 @@ public:
   virtual void apply_ddt(Vector3D& f) { apply(ddt(f)); }
 
   BoundaryRegion* bndry;
-  bool
-      apply_to_ddt; // True if this boundary condition should be applied on the time derivatives, false if it should be applied to the field values
+  // True if this boundary condition should be applied on the time derivatives
+  // false if it should be applied to the field values
+  bool apply_to_ddt;
 };
 
 class BoundaryModifier : public BoundaryOp {
diff --git a/include/bout/bout.hxx b/include/bout/bout.hxx
index 5e718dde33..d929a19c2f 100644
--- a/include/bout/bout.hxx
+++ b/include/bout/bout.hxx
@@ -2,8 +2,6 @@
  *
  * @mainpage BOUT++
  *
- * @version 3.0
- *
  * @par Description
  * Framework for the solution of partial differential
  * equations, in particular fluid models in plasma physics.
@@ -33,8 +31,8 @@
  *
  **************************************************************************/
 
-#ifndef __BOUT_H__
-#define __BOUT_H__
+#ifndef BOUT_H
+#define BOUT_H
 
 #include "bout/build_config.hxx"
 
@@ -44,7 +42,7 @@
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
-#include "bout/options_netcdf.hxx"
+#include "bout/options_io.hxx"
 #include "bout/output.hxx"
 #include "bout/smoothing.hxx" // Smoothing functions
 #include "bout/solver.hxx"
@@ -206,4 +204,4 @@ private:
  */
 int BoutFinalise(bool write_settings = true);
 
-#endif // __BOUT_H__
+#endif // BOUT_H
diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx
index 5b8a421692..243b819961 100644
--- a/include/bout/boutexception.hxx
+++ b/include/bout/boutexception.hxx
@@ -10,8 +10,6 @@ class BoutException;
 #include <string>
 #include <utility>
 
-#include "bout/format.hxx"
-
 #include "fmt/core.h"
 
 /// Throw BoutRhsFail with \p message if any one process has non-zero
diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx
index a98c615c77..c97962f7cf 100644
--- a/include/bout/build_config.hxx
+++ b/include/bout/build_config.hxx
@@ -17,6 +17,7 @@ constexpr auto has_gettext = static_cast<bool>(BOUT_HAS_GETTEXT);
 constexpr auto has_lapack = static_cast<bool>(BOUT_HAS_LAPACK);
 constexpr auto has_legacy_netcdf = static_cast<bool>(BOUT_HAS_LEGACY_NETCDF);
 constexpr auto has_netcdf = static_cast<bool>(BOUT_HAS_NETCDF);
+constexpr auto has_adios = static_cast<bool>(BOUT_HAS_ADIOS);
 constexpr auto has_petsc = static_cast<bool>(BOUT_HAS_PETSC);
 constexpr auto has_hypre = static_cast<bool>(BOUT_HAS_HYPRE);
 constexpr auto has_umpire = static_cast<bool>(BOUT_HAS_UMPIRE);
diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 9a425942c1..a4f4f52803 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -370,7 +370,7 @@ inline bool isUniform(const T& f, bool allpe = false,
 /// @param[in] allpe   Check over all processors
 /// @param[in] region  The region to assume is uniform
 template <typename T, typename = bout::utils::EnableIfField<T>>
-inline BoutReal getUniform(const T& f, MAYBE_UNUSED(bool allpe) = false,
+inline BoutReal getUniform(const T& f, [[maybe_unused]] bool allpe = false,
                            const std::string& region = "RGN_ALL") {
 #if CHECK > 1
   if (not isUniform(f, allpe, region)) {
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index a36f899692..5bac67beb2 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -33,7 +33,7 @@ class Field2D;
 class Mesh;
 #include "bout/field.hxx"
 #include "bout/field_data.hxx"
-class Field3D; //#include "bout/field3d.hxx"
+class Field3D;
 #include "bout/fieldperp.hxx"
 #include "bout/stencils.hxx"
 
@@ -174,6 +174,9 @@ public:
   /// Return a Region<Ind2D> reference to use to iterate over this field
   const Region<Ind2D>& getRegion(REGION region) const;
   const Region<Ind2D>& getRegion(const std::string& region_name) const;
+  const Region<Ind2D>& getValidRegionWithDefault(const std::string& region_name) const {
+    return getRegion(region_name);
+  }
 
   Region<Ind2D>::RegionIndices::const_iterator begin() const {
     return std::begin(getRegion("RGN_ALL"));
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 4e6510f8a6..9f5326253d 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -40,6 +40,7 @@ class Mesh; // #include "bout/mesh.hxx"
 
 #include "bout/utils.hxx"
 
+#include <optional>
 #include <vector>
 
 /// Class for 3D X-Y-Z scalar fields
@@ -313,6 +314,13 @@ public:
   ///
   const Region<Ind3D>& getRegion(REGION region) const;
   const Region<Ind3D>& getRegion(const std::string& region_name) const;
+  /// Use region provided by the default, and if none is set, use the provided one
+  const Region<Ind3D>& getValidRegionWithDefault(const std::string& region_name) const;
+  void setRegion(const std::string& region_name);
+  void resetRegion() { regionID.reset(); };
+  void setRegion(size_t id) { regionID = id; };
+  void setRegion(std::optional<size_t> id) { regionID = id; };
+  std::optional<size_t> getRegionID() const { return regionID; };
 
   /// Return a Region<Ind2D> reference to use to iterate over the x- and
   /// y-indices of this field
@@ -503,6 +511,9 @@ private:
 
   /// Fields containing values along Y
   std::vector<Field3D> yup_fields{}, ydown_fields{};
+
+  /// RegionID over which the field is valid
+  std::optional<size_t> regionID;
 };
 
 // Non-member overloaded operators
diff --git a/include/bout/field_data.hxx b/include/bout/field_data.hxx
index 59bd751fc4..03b9d6759b 100644
--- a/include/bout/field_data.hxx
+++ b/include/bout/field_data.hxx
@@ -38,8 +38,6 @@ class FieldData;
 #include <string>
 #include <vector>
 
-// Including the next line leads to compiler errors
-//#include "bout/boundary_op.hxx"
 class BoundaryOp;
 class BoundaryOpPar;
 class Coordinates;
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 3b6e0567d8..3b8ed45db6 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -98,6 +98,9 @@ public:
   /// Return a Region<IndPerp> reference to use to iterate over this field
   const Region<IndPerp>& getRegion(REGION region) const;
   const Region<IndPerp>& getRegion(const std::string& region_name) const;
+  const Region<IndPerp>& getValidRegionWithDefault(const std::string& region_name) const {
+    return getRegion(region_name);
+  }
 
   Region<IndPerp>::RegionIndices::const_iterator begin() const {
     return std::begin(getRegion("RGN_ALL"));
diff --git a/include/bout/format.hxx b/include/bout/format.hxx
deleted file mode 100644
index 846303a3fd..0000000000
--- a/include/bout/format.hxx
+++ /dev/null
@@ -1,16 +0,0 @@
-#ifndef __BOUT_FORMAT_H__
-#define __BOUT_FORMAT_H__
-
-/// Tell GCC that a function has a printf-style like argument
-/// The first argument is the position of format string, and the
-/// second is the position of the first variadic argument
-/// Note that it seems to start counting from 1, and also counts a
-/// *this pointer, as the first argument, so often 2 would be the
-/// first argument.
-#if defined(__GNUC__)
-#define BOUT_FORMAT_ARGS(i, j) __attribute__((format(printf, i, j)))
-#else
-#define BOUT_FORMAT_ARGS(i, j)
-#endif
-
-#endif //__BOUT_FORMAT_H__
diff --git a/include/bout/generic_factory.hxx b/include/bout/generic_factory.hxx
index 3a2a63c94c..9493ef77f1 100644
--- a/include/bout/generic_factory.hxx
+++ b/include/bout/generic_factory.hxx
@@ -1,8 +1,8 @@
 /// Base type for factories
 
 #pragma once
-#ifndef __BOUT_GENERIC_FACTORY_H__
-#define __BOUT_GENERIC_FACTORY_H__
+#ifndef BOUT_GENERIC_FACTORY_H
+#define BOUT_GENERIC_FACTORY_H
 
 #include "bout/boutexception.hxx"
 #include "bout/options.hxx"
@@ -48,14 +48,6 @@
 ///     RegisterInFactory<Base, Derived, MyFactory, Options*> register("derived_type");
 ///     auto foo = MyFactory::getInstance().create("derived_type");
 ///
-///   In a .cxx file the static members should be declared:
-///
-///     constexpr decltype(MyFactory::type_name) MyFactory::type_name;
-///     constexpr decltype(MyFactory::section_name) MyFactory::section_name;
-///     constexpr decltype(MyFactory::option_name) MyFactory::option_name;
-///     constexpr decltype(MyFactory::default_type) MyFactory::default_type;
-///
-///
 /// @tparam BaseType       The base class that this factory creates
 /// @tparam DerivedFactory The derived factory inheriting from this class
 /// @tparam TypeCreator    The function signature for creating a new BaseType
@@ -259,4 +251,4 @@ public:
   };
 };
 
-#endif // __BOUT_GENERIC_FACTORY_H__
+#endif // BOUT_GENERIC_FACTORY_H
diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx
index 3d0ef21cea..ab1c927832 100644
--- a/include/bout/globalindexer.hxx
+++ b/include/bout/globalindexer.hxx
@@ -70,14 +70,14 @@ public:
 
     bndryCandidate = mask(allCandidate, getRegionNobndry());
 
-    regionInnerX = getIntersection(bndryCandidate, indices.getRegion("RGN_INNER_X"));
-    regionOuterX = getIntersection(bndryCandidate, indices.getRegion("RGN_OUTER_X"));
+    regionInnerX = intersection(bndryCandidate, indices.getRegion("RGN_INNER_X"));
+    regionOuterX = intersection(bndryCandidate, indices.getRegion("RGN_OUTER_X"));
     if (std::is_same<T, FieldPerp>::value) {
       regionLowerY = Region<ind_type>({});
       regionUpperY = Region<ind_type>({});
     } else {
-      regionLowerY = getIntersection(bndryCandidate, indices.getRegion("RGN_LOWER_Y"));
-      regionUpperY = getIntersection(bndryCandidate, indices.getRegion("RGN_UPPER_Y"));
+      regionLowerY = intersection(bndryCandidate, indices.getRegion("RGN_LOWER_Y"));
+      regionUpperY = intersection(bndryCandidate, indices.getRegion("RGN_UPPER_Y"));
     }
     regionBndry = regionLowerY + regionInnerX + regionOuterX + regionUpperY;
     regionAll = getRegionNobndry() + regionBndry;
diff --git a/include/bout/index_derivs.hxx b/include/bout/index_derivs.hxx
index 8cb5c88aff..456f98f8c2 100644
--- a/include/bout/index_derivs.hxx
+++ b/include/bout/index_derivs.hxx
@@ -124,13 +124,6 @@ public:
   BoutReal apply(const stencil& v, const stencil& f) const { return func(v, f); }
 };
 
-// Redundant definitions because C++
-// Not necessary in C++17
-template <class FF>
-constexpr FF DerivativeType<FF>::func;
-template <class FF>
-constexpr metaData DerivativeType<FF>::meta;
-
 /////////////////////////////////////////////////////////////////////////////////
 /// Following code is for dealing with registering a method/methods for all
 /// template combinations, in conjunction with the template_combinations code.
diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 04b1ad0cdb..46f64256a8 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -75,6 +75,9 @@ public:
   void setRegion(const std::string& region_name) {
     this->region_id = localmesh->getRegionID(region_name);
   }
+  void setRegion(const std::unique_ptr<Region<Ind3D>> region){
+    setRegion(*region);
+  }
   void setRegion(const Region<Ind3D>& region) {
     std::string name;
     int i = 0;
@@ -299,7 +302,7 @@ public:
   ReturnType create(Options* options = nullptr, Mesh* mesh = nullptr) const {
     return Factory::create(getType(options), mesh);
   }
-  ReturnType create(const std::string& type, MAYBE_UNUSED(Options* options)) const {
+  ReturnType create(const std::string& type, [[maybe_unused]] Options* options) const {
     return Factory::create(type, nullptr);
   }
 
diff --git a/include/bout/interpolation_z.hxx b/include/bout/interpolation_z.hxx
index 596b2634fb..b11d7ff5b6 100644
--- a/include/bout/interpolation_z.hxx
+++ b/include/bout/interpolation_z.hxx
@@ -82,7 +82,7 @@ public:
                     Region<Ind3D> region_in = {}) const {
     return Factory::create(getType(nullptr), y_offset, mesh, region_in);
   }
-  ReturnType create(const std::string& type, MAYBE_UNUSED(Options* options)) const {
+  ReturnType create(const std::string& type, [[maybe_unused]] Options* options) const {
     return Factory::create(type, 0, nullptr, Region<Ind3D>{});
   }
 
diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx
index c4ae5efdf8..78417b9fce 100644
--- a/include/bout/invert_laplace.hxx
+++ b/include/bout/invert_laplace.hxx
@@ -275,8 +275,8 @@ public:
   /// performance information, with optional name for the time
   /// dimension
   void outputVars(Options& output_options) const { outputVars(output_options, "t"); }
-  virtual void outputVars(MAYBE_UNUSED(Options& output_options),
-                          MAYBE_UNUSED(const std::string& time_dimension)) const {}
+  virtual void outputVars([[maybe_unused]] Options& output_options,
+                          [[maybe_unused]] const std::string& time_dimension) const {}
 
   /// Register performance monitor with \p solver, prefix output with
   /// `Options` section name
diff --git a/include/bout/mask.hxx b/include/bout/mask.hxx
index 9c8c4b96dc..89197ddcf2 100644
--- a/include/bout/mask.hxx
+++ b/include/bout/mask.hxx
@@ -69,13 +69,14 @@ public:
   inline const bool& operator[](const Ind3D& i) const { return mask[i]; }
 };
 
-inline Region<Ind3D> regionFromMask(const BoutMask& mask, const Mesh* mesh) {
+inline std::unique_ptr<Region<Ind3D>> regionFromMask(const BoutMask& mask,
+                                                     const Mesh* mesh) {
   std::vector<Ind3D> indices;
   for (auto i : mesh->getRegion("RGN_ALL")) {
     if (not mask(i.x(), i.y(), i.z())) {
       indices.push_back(i);
     }
   }
-  return Region<Ind3D>{indices};
+  return std::make_unique<Region<Ind3D>>(indices);
 }
 #endif //__MASK_H__
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 45ea392482..8f73552ea5 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -74,6 +74,7 @@ class Mesh;
 #include <list>
 #include <map>
 #include <memory>
+#include <optional>
 #include <set>
 #include <string>
 
@@ -134,7 +135,7 @@ public:
 
   /// Add output variables to \p output_options
   /// These are used for post-processing
-  virtual void outputVars(MAYBE_UNUSED(Options& output_options)) {}
+  virtual void outputVars([[maybe_unused]] Options& output_options) {}
 
   // Get routines to request data from mesh file
 
@@ -503,9 +504,20 @@ public:
   int GlobalNx, GlobalNy, GlobalNz; ///< Size of the global arrays. Note: can have holes
   /// Size of the global arrays excluding boundary points.
   int GlobalNxNoBoundaries, GlobalNyNoBoundaries, GlobalNzNoBoundaries;
+
+  /// Note: These offsets only correct if Y guards are not included in the global array
+  ///       and are corrected in gridfromfile.cxx
   int OffsetX, OffsetY, OffsetZ; ///< Offset of this mesh within the global array
                                  ///< so startx on this processor is OffsetX in global
 
+  /// Map between local and global indices
+  /// (MapGlobalX, MapGlobalY, MapGlobalZ) in the global index space maps to (MapLocalX, MapLocalY, MapLocalZ) locally.
+  /// Note that boundary cells are included in the global index space, but communication
+  /// guard cells are not.
+  int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices
+  int MapLocalX, MapLocalY, MapLocalZ;    ///< Start local indices
+  int MapCountX, MapCountY, MapCountZ;    ///< Size of the mapped region
+
   /// Returns the number of unique cells (i.e., ones not used for
   /// communication) on this processor for 3D fields. Boundaries
   /// are only included to a depth of 1.
@@ -795,6 +807,14 @@ public:
   // Switch for communication of corner guard and boundary cells
   const bool include_corner_cells;
 
+  std::optional<size_t> getCommonRegion(std::optional<size_t>, std::optional<size_t>);
+  size_t getRegionID(const std::string& region) const;
+  const Region<Ind3D>& getRegion(size_t RegionID) const { return region3D[RegionID]; }
+  const Region<Ind3D>& getRegion(std::optional<size_t> RegionID) const {
+    ASSERT1(RegionID.has_value());
+    return region3D[RegionID.value()];
+  }
+
 private:
   /// Allocates default Coordinates objects
   /// By default attempts to read staggered Coordinates from grid data source,
@@ -807,7 +827,9 @@ private:
                            bool force_interpolate_from_centre = false);
 
   //Internal region related information
-  std::map<std::string, Region<Ind3D>> regionMap3D;
+  std::map<std::string, size_t> regionMap3D;
+  std::vector<Region<Ind3D>> region3D;
+  std::vector<std::optional<size_t>> region3Dintersect;
   std::map<std::string, Region<Ind2D>> regionMap2D;
   std::map<std::string, Region<IndPerp>> regionMapPerp;
   Array<int> indexLookup3Dto2D;
diff --git a/include/bout/monitor.hxx b/include/bout/monitor.hxx
index eb86c01554..5bc4fc7e12 100644
--- a/include/bout/monitor.hxx
+++ b/include/bout/monitor.hxx
@@ -50,8 +50,8 @@ public:
   /// Callback function for when a clean shutdown is initiated
   virtual void cleanup(){};
 
-  virtual void outputVars(MAYBE_UNUSED(Options& options),
-                          MAYBE_UNUSED(const std::string& time_dimension)) {}
+  virtual void outputVars([[maybe_unused]] Options& options,
+                          [[maybe_unused]] const std::string& time_dimension) {}
 
 protected:
   /// Get the currently set timestep for this monitor
diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx
index cc19a7b9f6..993d8adb75 100644
--- a/include/bout/msg_stack.hxx
+++ b/include/bout/msg_stack.hxx
@@ -31,7 +31,6 @@ class MsgStack;
 
 #include "bout/build_config.hxx"
 
-#include "bout/format.hxx"
 #include "bout/unused.hxx"
 
 #include "fmt/core.h"
@@ -201,7 +200,7 @@ private:
    arguments and the optional arguments follow from there.
  */
 #define TRACE(...) \
-  MsgStackItem CONCATENATE(msgTrace_, __LINE__)(__FILE__, __LINE__, __VA_ARGS__)
+  const MsgStackItem CONCATENATE(msgTrace_, __LINE__)(__FILE__, __LINE__, __VA_ARGS__)
 #else
 #define TRACE(...)
 #endif
diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index bf1704100f..c45149cbdd 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -53,7 +53,6 @@ class Options;
 #include <fmt/core.h>
 
 #include <cmath>
-#include <iomanip>
 #include <map>
 #include <ostream>
 #include <set>
@@ -182,9 +181,20 @@ public:
   /// Example:  { {"key1", 42}, {"key2", field} }
   Options(std::initializer_list<std::pair<std::string, Options>> values);
 
-  /// Copy constructor
   Options(const Options& other);
 
+  /// Copy assignment
+  ///
+  /// This replaces the value, attributes and all children
+  ///
+  /// Note that if only the value is desired, then that can be copied using
+  /// the value member directly e.g. option2.value = option1.value;
+  ///
+  Options& operator=(const Options& other);
+
+  Options(Options&& other) noexcept;
+  Options& operator=(Options&& other) noexcept;
+
   ~Options() = default;
 
   /// Get a reference to the only root instance
@@ -210,14 +220,11 @@ public:
   public:
     using Base = bout::utils::variant<bool, int, BoutReal, std::string>;
 
-    /// Constructor
     AttributeType() = default;
-    /// Copy constructor
     AttributeType(const AttributeType& other) = default;
-    /// Move constructor
-    AttributeType(AttributeType&& other) : Base(std::move(other)) {}
-
-    /// Destructor
+    AttributeType(AttributeType&& other) = default;
+    AttributeType& operator=(const AttributeType& other) = default;
+    AttributeType& operator=(AttributeType&& other) = default;
     ~AttributeType() = default;
 
     /// Assignment operator, including move assignment
@@ -229,9 +236,6 @@ public:
       return *this;
     }
 
-    /// Copy assignment operator
-    AttributeType& operator=(const AttributeType& other) = default;
-
     /// Initialise with a value
     /// This enables AttributeTypes to be constructed using initializer lists
     template <typename T>
@@ -362,15 +366,6 @@ public:
     return inputvalue;
   }
 
-  /// Copy assignment
-  ///
-  /// This replaces the value, attributes and all children
-  ///
-  /// Note that if only the value is desired, then that can be copied using
-  /// the value member directly e.g. option2.value = option1.value;
-  ///
-  Options& operator=(const Options& other);
-
   /// Assign a value to the option.
   /// This will throw an exception if already has a value
   ///
@@ -382,9 +377,9 @@ public:
   /// Note: Specialised versions for types stored in ValueType
   template <typename T>
   void assign(T val, std::string source = "") {
-    std::stringstream ss;
-    ss << val;
-    _set(ss.str(), std::move(source), false);
+    std::stringstream as_str;
+    as_str << val;
+    _set(as_str.str(), std::move(source), false);
   }
 
   /// Force to a value
@@ -462,20 +457,20 @@ public:
       // If the variant is a string then we may be able to parse it
 
       if (bout::utils::holds_alternative<std::string>(value)) {
-        std::stringstream ss(bout::utils::get<std::string>(value));
-        ss >> val;
+        std::stringstream as_str(bout::utils::get<std::string>(value));
+        as_str >> val;
 
         // Check if the parse failed
-        if (ss.fail()) {
+        if (as_str.fail()) {
           throw BoutException("Option {:s} could not be parsed ('{:s}')", full_name,
                               bout::utils::variantToString(value));
         }
 
         // Check if there are characters remaining
         std::string remainder;
-        std::getline(ss, remainder);
-        for (const char& ch : remainder) {
-          if (!std::isspace(static_cast<unsigned char>(ch))) {
+        std::getline(as_str, remainder);
+        for (const unsigned char chr : remainder) {
+          if (!std::isspace(chr)) {
             // Meaningful character not parsed
             throw BoutException("Option {:s} could not be parsed", full_name);
           }
@@ -495,7 +490,7 @@ public:
       // Specify the source of the setting
       output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
     }
-    output_info << endl;
+    output_info << '\n';
 
     return val;
   }
@@ -514,7 +509,7 @@ public:
       value_used = true; // Mark the option as used
 
       output_info << _("\tOption ") << full_name << " = " << def << " (" << DEFAULT_SOURCE
-                  << ")" << std::endl;
+                  << ")\n";
       return def;
     }
     T val = as<T>(def);
@@ -547,7 +542,7 @@ public:
       *this = def;
 
       output_info << _("\tOption ") << full_name << " = " << def.full_name << " ("
-                  << DEFAULT_SOURCE << ")" << std::endl;
+                  << DEFAULT_SOURCE << ")\n";
     } else {
       // Check if this was previously set as a default option
       if (bout::utils::variantEqualTo(attributes.at("source"), DEFAULT_SOURCE)) {
@@ -571,7 +566,7 @@ public:
     if (is_section) {
       // Option not found
       output_info << _("\tOption ") << full_name << " = " << def << " (" << DEFAULT_SOURCE
-                  << ")" << std::endl;
+                  << ")\n";
       return def;
     }
     T val = as<T>(def);
@@ -657,8 +652,8 @@ public:
 
   // Setting options
   template <typename T>
-  void forceSet(const std::string& key, T t, const std::string& source = "") {
-    (*this)[key].force(t, source);
+  void forceSet(const std::string& key, T val, const std::string& source = "") {
+    (*this)[key].force(val, source);
   }
 
   /*!
@@ -670,11 +665,11 @@ public:
     if (!is_section) {
       return false;
     }
-    auto it = children.find(key);
-    if (it == children.end()) {
+    auto child = children.find(key);
+    if (child == children.end()) {
       return false;
     }
-    return it->second.isSet();
+    return child->second.isSet();
   }
 
   /// Get options, passing in a reference to a variable
@@ -702,13 +697,12 @@ public:
 
   /// Print just the name of this object without parent sections
   std::string name() const {
-    auto pos = full_name.rfind(":");
+    auto pos = full_name.rfind(':');
     if (pos == std::string::npos) {
       // No parent section or sections
       return full_name;
-    } else {
-      return full_name.substr(pos + 1);
     }
+    return full_name.substr(pos + 1);
   }
 
   /// Return a new Options instance which contains all the values
@@ -731,21 +725,6 @@ public:
   /// clean the cache of parsed options
   static void cleanCache();
 
-  /*!
-   * Class used to store values, together with
-   * information about their origin and usage
-   */
-  struct OptionValue {
-    std::string value;
-    std::string source;        // Source of the setting
-    mutable bool used = false; // Set to true when used
-
-    /// This constructor needed for map::emplace
-    /// Can be removed in C++17 with map::insert and brace initialisation
-    OptionValue(std::string value, std::string source, bool used)
-        : value(std::move(value)), source(std::move(source)), used(used) {}
-  };
-
   /// Read-only access to internal options and sections
   /// to allow iteration over the tree
   std::map<std::string, const Options*> subsections() const;
@@ -784,8 +763,6 @@ private:
   /// The source label given to default values
   static const std::string DEFAULT_SOURCE;
 
-  static Options* root_instance; ///< Only instance of the root section
-
   Options* parent_instance{nullptr};
   std::string full_name; // full path name for logging only
 
@@ -837,8 +814,8 @@ private:
 
   /// Tests if two values are similar.
   template <typename T>
-  bool similar(T a, T b) const {
-    return a == b;
+  bool similar(T lhs, T rhs) const {
+    return lhs == rhs;
   }
 };
 
@@ -862,7 +839,7 @@ inline void Options::assign<>(std::string val, std::string source) {
 // Note: const char* version needed to avoid conversion to bool
 template <>
 inline void Options::assign<>(const char* val, std::string source) {
-  _set(std::string(val), source, false);
+  _set(std::string(val), std::move(source), false);
 }
 // Note: Field assignments don't check for previous assignment (always force)
 template <>
@@ -880,8 +857,8 @@ void Options::assign<>(Tensor<BoutReal> val, std::string source);
 
 /// Specialised similar comparison methods
 template <>
-inline bool Options::similar<BoutReal>(BoutReal a, BoutReal b) const {
-  return fabs(a - b) < 1e-10;
+inline bool Options::similar<BoutReal>(BoutReal lhs, BoutReal rhs) const {
+  return fabs(lhs - rhs) < 1e-10;
 }
 
 /// Specialised as routines
@@ -972,6 +949,8 @@ private:
 template <>
 struct fmt::formatter<Options> : public bout::details::OptionsFormatterBase {};
 
+// NOLINTBEGIN(cppcoreguidelines-macro-usage)
+
 /// Define for reading options which passes the variable name
 #define OPTION(options, var, def) pointer(options)->get(#var, var, def)
 
@@ -1032,4 +1011,6 @@ struct fmt::formatter<Options> : public bout::details::OptionsFormatterBase {};
                          __LINE__) = Options::root()[name].overrideDefault(value); \
   }
 
+// NOLINTEND(cppcoreguidelines-macro-usage)
+
 #endif // __OPTIONS_H__
diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
new file mode 100644
index 0000000000..65c3cb7dd1
--- /dev/null
+++ b/include/bout/options_io.hxx
@@ -0,0 +1,178 @@
+/// Parent class for IO to binary files and streams
+///
+///
+/// Usage:
+///
+/// 1. Dump files, containing time history:
+///
+///       auto dump = OptionsIOFactory::getInstance().createOutput();
+///       dump->write(data);
+///
+///    where data is an Options tree. By default dump files are configured
+///    with the root `output` section, or an Option tree can be passed to
+///    `createOutput`.
+///
+/// 2. Restart files:
+///
+///       auto restart = OptionsIOFactory::getInstance().createOutput();
+///       restart->write(data);
+///
+///    where data is an Options tree. By default restart files are configured
+///    with the root `restart_files` section, or an Option tree can be passed to
+///    `createRestart`.
+///
+/// 3. Ad-hoc single files
+///   Note: The caller should consider how multiple processors interact with the file.
+///
+///       auto file = OptionsIOFactory::getInstance().createFile("some_file.nc");
+///   or
+///       auto file = OptionsIO::create("some_file.nc");
+///
+///
+
+#pragma once
+
+#ifndef OPTIONS_IO_H
+#define OPTIONS_IO_H
+
+#include "bout/build_config.hxx"
+#include "bout/generic_factory.hxx"
+#include "bout/options.hxx"
+
+#include <memory>
+#include <string>
+
+namespace bout {
+
+class OptionsIO {
+public:
+  /// No default constructor, as settings are required
+  OptionsIO() = delete;
+
+  /// Constructor specifies the kind of file, and options to control
+  /// the name of file, mode of operation etc.
+  OptionsIO(Options&) {}
+
+  virtual ~OptionsIO() = default;
+
+  OptionsIO(const OptionsIO&) = delete;
+  OptionsIO(OptionsIO&&) noexcept = default;
+  OptionsIO& operator=(const OptionsIO&) = delete;
+  OptionsIO& operator=(OptionsIO&&) noexcept = default;
+
+  /// Read options from file
+  virtual Options read() = 0;
+
+  /// Write options to file
+  void write(const Options& options) { write(options, "t"); }
+  virtual void write(const Options& options, const std::string& time_dim) = 0;
+
+  /// NetCDF: Check that all variables with the same time dimension have the
+  /// same size in that dimension. Throws BoutException if there are
+  /// any differences, otherwise is silent.
+  /// ADIOS: Indicate completion of an output step.
+  virtual void verifyTimesteps() const = 0;
+
+  /// Create an OptionsIO for I/O to the given file.
+  /// This uses the default file type and default options.
+  static std::unique_ptr<OptionsIO> create(const std::string& file);
+
+  /// Create an OptionsIO for I/O to the given file.
+  /// The file will be configured using the given `config` options:
+  ///  - "type" : string   The file type e.g. "netcdf" or "adios"
+  ///  - "file" : string   Name of the file
+  ///  - "append" : bool   Append to existing data (Default is false)
+  static std::unique_ptr<OptionsIO> create(Options& config);
+
+  /// Create an OptionsIO for I/O to the given file.
+  /// The file will be configured using the given `config` options:
+  ///  - "type" : string   The file type e.g. "netcdf" or "adios"
+  ///  - "file" : string   Name of the file
+  ///  - "append" : bool   Append to existing data (Default is false)
+  ///
+  /// Example:
+  ///
+  ///     auto file = OptionsIO::create({
+  ///         {"file", "some_file.nc"},
+  ///         {"type", "netcdf"},
+  ///         {"append", false}
+  ///     });
+  static std::unique_ptr<OptionsIO>
+  create(std::initializer_list<std::pair<std::string, Options>> config_list) {
+    Options config(config_list); // Construct an Options to pass by reference
+    return create(config);
+  }
+};
+
+class OptionsIOFactory : public Factory<OptionsIO, OptionsIOFactory, Options&> {
+public:
+  static constexpr auto type_name = "OptionsIO";
+  static constexpr auto section_name = "io";
+  static constexpr auto option_name = "type";
+  static constexpr auto default_type =
+#if BOUT_HAS_NETCDF
+      "netcdf";
+#elif BOUT_HAS_ADIOS
+      "adios";
+#else
+      "invalid";
+#endif
+
+  /// Create a restart file, configured with options (if given),
+  /// or root "restart_files" section.
+  ///
+  /// Options:
+  ///  - "type"    The type of file e.g "netcdf" or "adios"
+  ///  - "file"    Name of the file. Default is <path>/<prefix>.[type-dependent]
+  ///  - "path"    Path to restart files. Default is root "datadir" option,
+  ///              that defaults to "data"
+  ///  - "prefix"  Default is "BOUT.restart"
+  ReturnType createRestart(Options* optionsptr = nullptr) const;
+
+  /// Create an output file for writing time history.
+  /// Configure with options (if given), or root "output" section.
+  ///
+  /// Options:
+  ///  - "type"    The type of file e.g "netcdf" or "adios"
+  ///  - "file"    Name of the file. Default is <path>/<prefix>.[type]
+  ///  - "path"    Path to output files. Default is root "datadir" option,
+  ///              that defaults to "data"
+  ///  - "prefix"  Default is "BOUT.dmp"
+  ///  - "append"  Append to existing file? Default is root "append" option,
+  ///              that defaults to false.
+  ReturnType createOutput(Options* optionsptr = nullptr) const;
+
+  /// Create a single file (e.g. mesh file) of the default type
+  ReturnType createFile(const std::string& file) const;
+};
+
+/// Simpler name for Factory registration helper class
+///
+/// Usage:
+///
+///     #include <bout/options_io.hxx>
+///     namespace {
+///     RegisterOptionsIO<MyOptionsIO> registeroptionsiomine("myoptionsio");
+///     }
+template <typename DerivedType>
+using RegisterOptionsIO = OptionsIOFactory::RegisterInFactory<DerivedType>;
+
+/// Simpler name for indicating that an OptionsIO implementation
+/// is unavailable.
+///
+/// Usage:
+///
+///     namespace {
+///     RegisterUnavailableOptionsIO
+///         unavailablemyoptionsio("myoptiosio", "BOUT++ was not configured with MyOptionsIO");
+///     }
+using RegisterUnavailableOptionsIO = OptionsIOFactory::RegisterUnavailableInFactory;
+
+/// Convenient wrapper function around OptionsIOFactory::createOutput
+/// Opens a dump file configured with the `output` root section,
+/// and writes the given `data` to the file.
+void writeDefaultOutputFile(Options& data);
+
+} // namespace bout
+
+#endif //  OPTIONS_IO_H
diff --git a/include/bout/options_netcdf.hxx b/include/bout/options_netcdf.hxx
deleted file mode 100644
index 2fdb71c6d4..0000000000
--- a/include/bout/options_netcdf.hxx
+++ /dev/null
@@ -1,118 +0,0 @@
-
-#pragma once
-
-#ifndef __OPTIONS_NETCDF_H__
-#define __OPTIONS_NETCDF_H__
-
-#include "bout/build_config.hxx"
-
-#if !BOUT_HAS_NETCDF || BOUT_HAS_LEGACY_NETCDF
-
-#include <string>
-
-#include "bout/boutexception.hxx"
-#include "bout/options.hxx"
-
-namespace bout {
-
-class OptionsNetCDF {
-public:
-  enum class FileMode {
-    replace, ///< Overwrite file when writing
-    append   ///< Append to file when writing
-  };
-
-  OptionsNetCDF(const std::string& filename, FileMode mode = FileMode::replace) {}
-  OptionsNetCDF(const OptionsNetCDF&) = default;
-  OptionsNetCDF(OptionsNetCDF&&) = default;
-  OptionsNetCDF& operator=(const OptionsNetCDF&) = default;
-  OptionsNetCDF& operator=(OptionsNetCDF&&) = default;
-
-  /// Read options from file
-  Options read() { throw BoutException("OptionsNetCDF not available\n"); }
-
-  /// Write options to file
-  void write(const Options& options) {
-    throw BoutException("OptionsNetCDF not available\n");
-  }
-};
-
-} // namespace bout
-
-#else
-
-#include <memory>
-#include <string>
-
-#include "bout/options.hxx"
-
-/// Forward declare netCDF file type so we don't need to depend
-/// directly on netCDF
-namespace netCDF {
-class NcFile;
-}
-
-namespace bout {
-
-class OptionsNetCDF {
-public:
-  enum class FileMode {
-    replace, ///< Overwrite file when writing
-    append   ///< Append to file when writing
-  };
-
-  // Constructors need to be defined in implementation due to forward
-  // declaration of NcFile
-  OptionsNetCDF();
-  explicit OptionsNetCDF(std::string filename, FileMode mode = FileMode::replace);
-  ~OptionsNetCDF();
-  OptionsNetCDF(const OptionsNetCDF&) = delete;
-  OptionsNetCDF(OptionsNetCDF&&) noexcept;
-  OptionsNetCDF& operator=(const OptionsNetCDF&) = delete;
-  OptionsNetCDF& operator=(OptionsNetCDF&&) noexcept;
-
-  /// Read options from file
-  Options read();
-
-  /// Write options to file
-  void write(const Options& options) { write(options, "t"); }
-  void write(const Options& options, const std::string& time_dim);
-
-  /// Check that all variables with the same time dimension have the
-  /// same size in that dimension. Throws BoutException if there are
-  /// any differences, otherwise is silent
-  void verifyTimesteps() const;
-
-private:
-  /// Name of the file on disk
-  std::string filename;
-  /// How to open the file for writing
-  FileMode file_mode{FileMode::replace};
-  /// Pointer to netCDF file so we don't introduce direct dependence
-  std::unique_ptr<netCDF::NcFile> data_file;
-};
-
-} // namespace bout
-
-#endif
-
-namespace bout {
-/// Name of the directory for restart files
-std::string getRestartDirectoryName(Options& options);
-/// Name of the restart file on this rank
-std::string getRestartFilename(Options& options);
-/// Name of the restart file on \p rank
-std::string getRestartFilename(Options& options, int rank);
-/// Name of the main output file on this rank
-std::string getOutputFilename(Options& options);
-/// Name of the main output file on \p rank
-std::string getOutputFilename(Options& options, int rank);
-/// Write `Options::root()` to the main output file, overwriting any
-/// existing files
-void writeDefaultOutputFile();
-/// Write \p options to the main output file, overwriting any existing
-/// files
-void writeDefaultOutputFile(Options& options);
-} // namespace bout
-
-#endif //  __OPTIONS_NETCDF_H__
diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx
index 428c7a8c8f..32c302a3f7 100644
--- a/include/bout/optionsreader.hxx
+++ b/include/bout/optionsreader.hxx
@@ -34,7 +34,6 @@ class OptionsReader;
 #ifndef __OPTIONSREADER_H__
 #define __OPTIONSREADER_H__
 
-#include "bout/format.hxx"
 #include "bout/options.hxx"
 
 #include "fmt/core.h"
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index ef09aa7ee5..a44e987197 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -37,7 +37,6 @@ class Output;
 
 #include "bout/assert.hxx"
 #include "bout/boutexception.hxx"
-#include "bout/format.hxx"
 #include "bout/sys/gettext.hxx" // for gettext _() macro
 #include "bout/unused.hxx"
 
@@ -144,7 +143,7 @@ public:
   void print([[maybe_unused]] const std::string& message) override{};
   void enable() override{};
   void disable() override{};
-  void enable(MAYBE_UNUSED(bool enable)){};
+  void enable([[maybe_unused]] bool enable){};
   bool isEnabled() override { return false; }
 };
 
diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx
index bb00dcbd45..4a7e4989c8 100644
--- a/include/bout/paralleltransform.hxx
+++ b/include/bout/paralleltransform.hxx
@@ -83,7 +83,7 @@ public:
   }
 
   /// Output variables used by a ParallelTransform instance to \p output_options
-  virtual void outputVars(MAYBE_UNUSED(Options& output_options)) {}
+  virtual void outputVars([[maybe_unused]] Options& output_options) {}
 
   /// If \p twist_shift_enabled is true, does a `Field3D` with Y direction \p ytype
   /// require a twist-shift at branch cuts on closed field lines?
diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index a9a7d7344d..e0f046eb1f 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -42,7 +42,7 @@ class PhysicsModel;
 #include "bout/macro_for_each.hxx"
 #include "bout/msg_stack.hxx"
 #include "bout/options.hxx"
-#include "bout/options_netcdf.hxx"
+#include "bout/options_io.hxx"
 #include "bout/sys/variant.hxx"
 #include "bout/unused.hxx"
 #include "bout/utils.hxx"
@@ -88,9 +88,6 @@ public:
   void add(Vector2D* value, const std::string& name, bool save_repeat = false);
   void add(Vector3D* value, const std::string& name, bool save_repeat = false);
 
-  /// Write stored data to file immediately
-  bool write();
-
 private:
   /// Helper struct to save enough information so that we can save an
   /// object to file later
@@ -148,7 +145,7 @@ public:
   bout::DataFileFacade restart{};
 
   /*!
-   * Initialse the model, calling the init() and postInit() methods
+   * Initialise the model, calling the init() and postInit() methods
    *
    * Note: this is usually only called by the Solver
    */
@@ -383,13 +380,13 @@ private:
   /// State for outputs
   Options output_options;
   /// File to write the outputs to
-  bout::OptionsNetCDF output_file;
+  std::unique_ptr<bout::OptionsIO> output_file;
   /// Should we write output files
   bool output_enabled{true};
   /// Stores the state for restarting
   Options restart_options;
   /// File to write the restart-state to
-  bout::OptionsNetCDF restart_file;
+  std::unique_ptr<bout::OptionsIO> restart_file;
   /// Should we write restart files
   bool restart_enabled{true};
   /// Split operator model?
diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index 541280420b..13c4a137fa 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -566,6 +566,10 @@ public:
 
   Region<T>(ContiguousBlocks& blocks) : blocks(blocks) { indices = getRegionIndices(); };
 
+  bool operator==(const Region<T>& other) const {
+    return std::equal(this->begin(), this->end(), other.begin(), other.end());
+  }
+
   /// Destructor
   ~Region() = default;
 
@@ -683,8 +687,7 @@ public:
     return *this; // To allow command chaining
   };
 
-  /// Returns a new region including only indices contained in both
-  /// this region and the other.
+  /// Get a new region including only indices that are in both regions.
   Region<T> getIntersection(const Region<T>& otherRegion) {
     // Get other indices and sort as we're going to be searching through
     // this vector so if it's sorted we can be more efficient
@@ -941,7 +944,7 @@ Region<T> mask(const Region<T>& region, const Region<T>& mask) {
 
 /// Return the intersection of two regions
 template <typename T>
-Region<T> getIntersection(const Region<T>& region, const Region<T>& otherRegion) {
+Region<T> intersection(const Region<T>& region, const Region<T>& otherRegion) {
   auto result = region;
   return result.getIntersection(otherRegion);
 }
diff --git a/include/bout/revision.hxx.in b/include/bout/revision.hxx.in
index f0e3abdb8b..393e8cc34f 100644
--- a/include/bout/revision.hxx.in
+++ b/include/bout/revision.hxx.in
@@ -7,18 +7,16 @@
 #ifndef BOUT_REVISION_H
 #define BOUT_REVISION_H
 
-// TODO: Make these all `inline` when we upgrade to C++17
-
 namespace bout {
 namespace version {
 /// The git commit hash
 #ifndef BOUT_REVISION
-constexpr auto revision = "@BOUT_REVISION@";
+inline constexpr auto revision = "@BOUT_REVISION@";
 #else
 // Stringify value passed at compile time
 #define BUILDFLAG1_(x) #x
 #define BUILDFLAG(x) BUILDFLAG1_(x)
-constexpr auto revision = BUILDFLAG(BOUT_REVISION);
+inline constexpr auto revision = BUILDFLAG(BOUT_REVISION);
 #undef BUILDFLAG1
 #undef BUILDFLAG
 #endif
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 8a3f07c27a..d110d7ff17 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -33,8 +33,8 @@
  *
  **************************************************************************/
 
-#ifndef __SOLVER_H__
-#define __SOLVER_H__
+#ifndef SOLVER_H
+#define SOLVER_H
 
 #include "bout/build_config.hxx"
 
@@ -63,7 +63,6 @@ using Jacobian = int (*)(BoutReal t);
 /// Solution monitor, called each timestep
 using TimestepMonitorFunc = int (*)(Solver* solver, BoutReal simtime, BoutReal lastdt);
 
-//#include "bout/globals.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/generic_factory.hxx"
@@ -270,7 +269,7 @@ public:
   virtual void constraint(Vector3D& v, Vector3D& C_v, std::string name);
 
   /// Set a maximum internal timestep (only for explicit schemes)
-  virtual void setMaxTimestep(MAYBE_UNUSED(BoutReal dt)) {}
+  virtual void setMaxTimestep([[maybe_unused]] BoutReal dt) {}
   /// Return the current internal timestep
   virtual BoutReal getCurrentTimestep() { return 0.0; }
 
@@ -597,4 +596,4 @@ private:
   BoutReal output_timestep;
 };
 
-#endif // __SOLVER_H__
+#endif // SOLVER_H
diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx
index c5e0f3ab15..c4f4aa59ef 100644
--- a/include/bout/sundials_backports.hxx
+++ b/include/bout/sundials_backports.hxx
@@ -27,19 +27,19 @@
 
 #if SUNDIALS_VERSION_MAJOR < 3
 using SUNLinearSolver = int*;
-inline void SUNLinSolFree(MAYBE_UNUSED(SUNLinearSolver solver)) {}
+inline void SUNLinSolFree([[maybe_unused]] SUNLinearSolver solver) {}
 using sunindextype = long int;
 #endif
 
 #if SUNDIALS_VERSION_MAJOR < 4
 using SUNNonlinearSolver = int*;
-inline void SUNNonlinSolFree(MAYBE_UNUSED(SUNNonlinearSolver solver)) {}
+inline void SUNNonlinSolFree([[maybe_unused]] SUNNonlinearSolver solver) {}
 #endif
 
 #if SUNDIALS_VERSION_MAJOR < 6
 namespace sundials {
 struct Context {
-  Context(void* comm MAYBE_UNUSED()) {}
+  Context(void* comm [[maybe_unused]]) {}
 };
 } // namespace sundials
 
@@ -51,13 +51,13 @@ constexpr auto SUN_PREC_NONE = PREC_NONE;
 
 inline N_Vector N_VNew_Parallel(MPI_Comm comm, sunindextype local_length,
                                 sunindextype global_length,
-                                MAYBE_UNUSED(SUNContext sunctx)) {
+                                [[maybe_unused]] SUNContext sunctx) {
   return N_VNew_Parallel(comm, local_length, global_length);
 }
 
 #if SUNDIALS_VERSION_MAJOR >= 3
 inline SUNLinearSolver SUNLinSol_SPGMR(N_Vector y, int pretype, int maxl,
-                                       MAYBE_UNUSED(SUNContext sunctx)) {
+                                       [[maybe_unused]] SUNContext sunctx) {
 #if SUNDIALS_VERSION_MAJOR == 3
   return SUNSPGMR(y, pretype, maxl);
 #else
@@ -66,12 +66,12 @@ inline SUNLinearSolver SUNLinSol_SPGMR(N_Vector y, int pretype, int maxl,
 }
 #if SUNDIALS_VERSION_MAJOR >= 4
 inline SUNNonlinearSolver SUNNonlinSol_FixedPoint(N_Vector y, int m,
-                                                  MAYBE_UNUSED(SUNContext sunctx)) {
+                                                  [[maybe_unused]] SUNContext sunctx) {
   return SUNNonlinSol_FixedPoint(y, m);
 }
 
 inline SUNNonlinearSolver SUNNonlinSol_Newton(N_Vector y,
-                                              MAYBE_UNUSED(SUNContext sunctx)) {
+                                              [[maybe_unused]] SUNContext sunctx) {
   return SUNNonlinSol_Newton(y);
 }
 #endif // SUNDIALS_VERSION_MAJOR >= 4
diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx
index 0ee3a7f97b..660ad20ab3 100644
--- a/include/bout/sys/expressionparser.hxx
+++ b/include/bout/sys/expressionparser.hxx
@@ -3,9 +3,9 @@
  *
  * Parses strings containing expressions, returning a tree of generators
  *
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010-2024 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -24,10 +24,9 @@
  *
  **************************************************************************/
 
-#ifndef __EXPRESSION_PARSER_H__
-#define __EXPRESSION_PARSER_H__
+#ifndef EXPRESSION_PARSER_H
+#define EXPRESSION_PARSER_H
 
-#include "bout/format.hxx"
 #include "bout/unused.hxx"
 
 #include "fmt/core.h"
@@ -158,7 +157,7 @@ protected:
   /// Characters which cannot be used in symbols without escaping;
   /// all other allowed. In addition, whitespace cannot be used.
   /// Adding a binary operator adds its symbol to this string
-  std::string reserved_chars = "+-*/^[](){},=";
+  std::string reserved_chars = "+-*/^[](){},=!";
 
 private:
   std::map<std::string, FieldGeneratorPtr> gen; ///< Generators, addressed by name
@@ -260,4 +259,4 @@ private:
   std::string message;
 };
 
-#endif // __EXPRESSION_PARSER_H__
+#endif // EXPRESSION_PARSER_H
diff --git a/include/bout/sys/generator_context.hxx b/include/bout/sys/generator_context.hxx
index 3f912ec1da..528b96113d 100644
--- a/include/bout/sys/generator_context.hxx
+++ b/include/bout/sys/generator_context.hxx
@@ -28,10 +28,7 @@ public:
   Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t);
 
   /// If constructed without parameters, contains no values (null).
-  /// Requesting x,y,z or t should throw an exception
-  ///
-  /// NOTE: For backward compatibility, all locations are set to zero.
-  /// This should be changed in a future release.
+  /// Requesting x,y,z or t throws an exception
   Context() = default;
 
   /// The location on the boundary
@@ -60,7 +57,13 @@ public:
   }
 
   /// Retrieve a value previously set
-  BoutReal get(const std::string& name) const { return parameters.at(name); }
+  BoutReal get(const std::string& name) const {
+    auto it = parameters.find(name);
+    if (it != parameters.end()) {
+      return it->second;
+    }
+    throw BoutException("Generator context doesn't contain '{:s}'", name);
+  }
 
   /// Get the mesh for this context (position)
   /// If the mesh is null this will throw a BoutException (if CHECK >= 1)
@@ -73,8 +76,7 @@ private:
   Mesh* localmesh{nullptr}; ///< The mesh on which the position is defined
 
   /// Contains user-set values which can be set and retrieved
-  std::map<std::string, BoutReal> parameters{
-      {"x", 0.0}, {"y", 0.0}, {"z", 0.0}, {"t", 0.0}};
+  std::map<std::string, BoutReal> parameters{};
 };
 
 } // namespace generator
diff --git a/include/bout/unused.hxx b/include/bout/unused.hxx
index 6e7a46c7c0..74fd3c2f98 100644
--- a/include/bout/unused.hxx
+++ b/include/bout/unused.hxx
@@ -37,24 +37,4 @@
 #define UNUSED(x) x
 #endif
 
-/// Mark a function parameter as possibly unused in the function body
-///
-/// Unlike `UNUSED`, this has to go around the type as well:
-///
-///    MAYBE_UNUSED(int foo);
-#ifdef __has_cpp_attribute
-#if __has_cpp_attribute(maybe_unused)
-#define MAYBE_UNUSED(x) [[maybe_unused]] x
-#endif
-#endif
-#ifndef MAYBE_UNUSED
-#if defined(__GNUC__)
-#define MAYBE_UNUSED(x) [[gnu::unused]] x
-#elif defined(_MSC_VER)
-#define MAYBE_UNUSED(x) __pragma(warning(suppress : 4100)) x
-#else
-#define MAYBE_UNUSED(x) x
-#endif
-#endif
-
 #endif //__UNUSED_H__
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 3e02b74c39..c650293c40 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -205,6 +205,8 @@ public:
   using size_type = int;
 
   Matrix() = default;
+  Matrix(Matrix&&) noexcept = default;
+  Matrix& operator=(Matrix&&) noexcept = default;
   Matrix(size_type n1, size_type n2) : n1(n1), n2(n2) {
     ASSERT2(n1 >= 0);
     ASSERT2(n2 >= 0);
@@ -215,6 +217,7 @@ public:
     // Prevent copy on write for Matrix
     data.ensureUnique();
   }
+  ~Matrix() = default;
 
   /// Reallocate the Matrix to shape \p new_size_1 by \p new_size_2
   ///
@@ -299,6 +302,8 @@ public:
   using size_type = int;
 
   Tensor() = default;
+  Tensor(Tensor&&) noexcept = default;
+  Tensor& operator=(Tensor&&) noexcept = default;
   Tensor(size_type n1, size_type n2, size_type n3) : n1(n1), n2(n2), n3(n3) {
     ASSERT2(n1 >= 0);
     ASSERT2(n2 >= 0);
@@ -310,6 +315,7 @@ public:
     // Prevent copy on write for Tensor
     data.ensureUnique();
   }
+  ~Tensor() = default;
 
   /// Reallocate the Tensor with shape \p new_size_1 by \p new_size_2 by \p new_size_3
   ///
@@ -355,6 +361,13 @@ public:
     ASSERT2(0 <= i.ind && i.ind < n1 * n2 * n3);
     return data[i.ind];
   }
+  T& operator[](Ind3D i) {
+    // ny and nz are private :-(
+    // ASSERT2(i.nz == n3);
+    // ASSERT2(i.ny == n2);
+    ASSERT2(0 <= i.ind && i.ind < n1 * n2 * n3);
+    return data[i.ind];
+  }
 
   Tensor& operator=(const T& val) {
     for (auto& i : data) {
diff --git a/include/bout/vector2d.hxx b/include/bout/vector2d.hxx
index 9ff4a69ba8..974c5f81db 100644
--- a/include/bout/vector2d.hxx
+++ b/include/bout/vector2d.hxx
@@ -39,7 +39,7 @@ class Vector2D;
 
 class Field2D;
 class Field3D;
-class Vector3D; //#include "bout/vector3d.hxx"
+class Vector3D;
 
 #include <bout/coordinates.hxx>
 
diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx
index f3adf41ae8..93ee798663 100644
--- a/include/bout/vector3d.hxx
+++ b/include/bout/vector3d.hxx
@@ -33,11 +33,10 @@ class Vector3D;
 #ifndef __VECTOR3D_H__
 #define __VECTOR3D_H__
 
-class Field2D; //#include "bout/field2d.hxx"
+class Field2D;
+class Vector2D;
 #include "bout/field3d.hxx"
 
-class Vector2D; //#include "bout/vector2d.hxx"
-
 /*!
  * Represents a 3D vector, with x,y,z components
  * stored as separate Field3D objects
diff --git a/include/bout/version.hxx.in b/include/bout/version.hxx.in
index 06a32808af..3eaf40dbd7 100644
--- a/include/bout/version.hxx.in
+++ b/include/bout/version.hxx.in
@@ -5,22 +5,20 @@
 #ifndef BOUT_VERSION_H
 #define BOUT_VERSION_H
 
-// TODO: Make these all `inline` when we upgrade to C++17
-
 namespace bout {
 namespace version {
 /// The full version number
-constexpr auto full = "@BOUT_VERSION@";
+inline constexpr auto full = "@BOUT_VERSION@";
 /// The major version number
-constexpr int major = @BOUT_VERSION_MAJOR@;
+inline constexpr int major = @BOUT_VERSION_MAJOR@;
 /// The minor version number
-constexpr int minor = @BOUT_VERSION_MINOR@;
+inline constexpr int minor = @BOUT_VERSION_MINOR@;
 /// The patch version number
-constexpr int patch = @BOUT_VERSION_PATCH@;
+inline constexpr int patch = @BOUT_VERSION_PATCH@;
 /// The version pre-release identifier
-constexpr auto prerelease = "@BOUT_VERSION_TAG@";
+inline constexpr auto prerelease = "@BOUT_VERSION_TAG@";
 /// The full version number as a double
-constexpr double as_double = @BOUT_VERSION_MAJOR@.@BOUT_VERSION_MINOR@@BOUT_VERSION_PATCH@;
+inline constexpr double as_double = @BOUT_VERSION_MAJOR@.@BOUT_VERSION_MINOR@@BOUT_VERSION_PATCH@;
 } // namespace version
 } // namespace bout
 
diff --git a/manual/sphinx/index.rst b/manual/sphinx/index.rst
index 46728c7119..9f661ca187 100644
--- a/manual/sphinx/index.rst
+++ b/manual/sphinx/index.rst
@@ -42,6 +42,7 @@ The documentation is divided into the following sections:
    user_docs/boundary_options
    user_docs/testing
    user_docs/gpu_support
+   user_docs/adios2
    
 .. toctree::
    :maxdepth: 2
diff --git a/manual/sphinx/user_docs/adios2.rst b/manual/sphinx/user_docs/adios2.rst
new file mode 100644
index 0000000000..8a6228cd3a
--- /dev/null
+++ b/manual/sphinx/user_docs/adios2.rst
@@ -0,0 +1,45 @@
+.. _sec-adios2:
+
+ADIOS2 support
+==============
+
+This section summarises the use of `ADIOS2 <https://adios2.readthedocs.io/>`_ in BOUT++.
+
+Installation
+------------
+
+The easiest way to configure BOUT++ with ADIOS2 is to tell CMake to download and build it
+with this flag::
+
+  -DBOUT_DOWNLOAD_ADIOS=ON
+
+The ``master`` branch will be downloaded from `Github <https://github.com/ornladios/ADIOS2>`_,
+configured and built with BOUT++.
+
+Alternatively, if ADIOS is already installed then the following flags can be used::
+
+  -DBOUT_USE_ADIOS=ON -DADIOS2_ROOT=/path/to/adios2
+
+Output files
+------------
+
+The output (dump) files are controlled with the root ``output`` options.
+By default the output format is NetCDF, so to use ADIOS2 instead set
+the output type in BOUT.inp::
+
+  [output]
+  type = adios
+
+or on the BOUT++ command line set ``output:type=adios``. The default
+prefix is "BOUT.dmp" so the ADIOS file will be called "BOUT.dmp.bp". To change this,
+set the ``output:prefix`` option.
+
+Restart files
+-------------
+
+The restart files are contolled with the root ``restart_files`` options,
+so to read and write restarts from an ADIOS dataset, put in BOUT.inp::
+
+  [restart_files]
+  type = adios
+
diff --git a/manual/sphinx/user_docs/advanced_install.rst b/manual/sphinx/user_docs/advanced_install.rst
index 957173b820..e25be12b4b 100644
--- a/manual/sphinx/user_docs/advanced_install.rst
+++ b/manual/sphinx/user_docs/advanced_install.rst
@@ -170,8 +170,10 @@ for a production run use:
 File formats
 ------------
 
-BOUT++ can currently use the NetCDF-4_ file format, with experimental
-support for the parallel flavour. NetCDF is a widely used format and
+BOUT++ can currently use the NetCDF-4_ file format and the ADIOS2 library
+for high-performance parallel output.
+
+NetCDF is a widely used format and
 has many tools for viewing and manipulating files.
 
 .. _NetCDF-4: https://www.unidata.ucar.edu/software/netcdf/
diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst
index 5422558ff9..85a8a17d59 100644
--- a/manual/sphinx/user_docs/bout_options.rst
+++ b/manual/sphinx/user_docs/bout_options.rst
@@ -48,9 +48,10 @@ name in square brackets.
 
 Option names can contain almost any character except ’=’ and ’:’,
 including unicode.  If they start with a number or ``.``, contain
-arithmetic symbols (``+-*/^``), brackets (``(){}[]``), equality
-(``=``), whitespace or comma ``,``, then these will need to be escaped
-in expressions. See below for how this is done.
+arithmetic/boolean operator symbols (``+-*/^&|!<>``), brackets
+(``(){}[]``), equality (``=``), whitespace or comma ``,``, then these
+will need to be escaped in expressions. See below for how this is
+done.
 
 Subsections can also be used, separated by colons ’:’, e.g.
 
@@ -87,6 +88,13 @@ operators, with the usual precedence rules. In addition to ``π``,
 expressions can use predefined variables ``x``, ``y``, ``z`` and ``t``
 to refer to the spatial and time coordinates (for definitions of the values
 these variables take see :ref:`sec-expressions`).
+
+.. note:: The variables ``x``, ``y``, ``z`` should only be defined
+   when reading a 3D field; ``t`` should only be defined when reading
+   a time-dependent value. Earlier BOUT++ versions (v5.1.0 and earler)
+   defined all of these to be 0 by default e.g. when reading scalar
+   inputs.
+
 A number of functions are defined, listed in table
 :numref:`tab-initexprfunc`. One slightly unusual feature (borrowed from `Julia <https://julialang.org/>`_)
 is that if a number comes before a symbol or an opening bracket (``(``)
@@ -109,11 +117,11 @@ The convention is the same as in `Python <https://www.python.org/>`_:
 If brackets are not balanced (closed) then the expression continues on the next line.
 
 All expressions are calculated in floating point and then converted to
-an integer if needed when read inside BOUT++. The conversion is done by rounding
-to the nearest integer, but throws an error if the floating point
-value is not within :math:`1e-3` of an integer. This is to minimise
-unexpected behaviour. If you want to round any result to an integer,
-use the ``round`` function:
+an integer (or boolean) if needed when read inside BOUT++. The
+conversion is done by rounding to the nearest integer, but throws an
+error if the floating point value is not within :math:`1e-3` of an
+integer. This is to minimise unexpected behaviour. If you want to
+round any result to an integer, use the ``round`` function:
 
 .. code-block:: cfg
 
@@ -125,6 +133,43 @@ number, since the type is determined by how it is used.
 
 Have a look through the examples to see how the options are used.
 
+Boolean expressions
+~~~~~~~~~~~~~~~~~~~
+
+Boolean values must be "true", "false", "True", "False", "1" or
+"0". All lowercase ("true"/"false") is preferred, but the uppercase
+versions are allowed to support Python string conversions. Booleans
+can be combined into expressions using binary operators `&` (logical
+AND), `|` (logical OR), and unary operator `!` (logical NOT). For
+example "true & false" evaluates to `false`; "!false" evaluates to
+`true`.  Like real values and integers, boolean expressions can refer
+to other variables:
+
+.. code-block:: cfg
+
+   switch = true
+   other_switch = !switch
+
+Boolean expressions can be formed by comparing real values using
+`>` and `<` comparison operators:
+
+.. code-block:: cfg
+
+   value = 3.2
+   is_true = value > 3
+   is_false = value < 2
+
+.. note::
+   Previous BOUT++ versions (v5.1.0 and earlier) were case
+   insensitive when reading boolean values, so would read "True" or
+   "yEs" as `true`, and "False" or "No" as `false`. These earlier
+   versions did not allow boolean expressions.
+
+Internally, booleans are evaluated as real values, with `true` being 1
+and `false` being 0. Logical operators (`&`, `|`, `!`) check that
+their left and right arguments are either close to 0 or close to 1
+(like integers, "close to" is within 1e-3).
+
 Special symbols in Option names
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -523,6 +568,12 @@ options available are listed in table :numref:`tab-outputopts`.
    +-------------+----------------------------------------------------+--------------+
    | enabled     | Writing is enabled                                 | true         |
    +-------------+----------------------------------------------------+--------------+
+   | type        | File type e.g. "netcdf" or "adios"                 | "netcdf"     |
+   +-------------+----------------------------------------------------+--------------+
+   | prefix      | File name prefix                                   | "BOUT.dmp"   |
+   +-------------+----------------------------------------------------+--------------+
+   | path        | Directory to write the file into                   | ``datadir``  |
+   +-------------+----------------------------------------------------+--------------+
    | floats      | Write floats rather than doubles                   | false        |
    +-------------+----------------------------------------------------+--------------+
    | flush       | Flush the file to disk after each write            | true         |
@@ -531,8 +582,6 @@ options available are listed in table :numref:`tab-outputopts`.
    +-------------+----------------------------------------------------+--------------+
    | openclose   | Re-open the file for each write, and close after   | true         |
    +-------------+----------------------------------------------------+--------------+
-   | parallel    | Use parallel I/O                                   | false        |
-   +-------------+----------------------------------------------------+--------------+
 
 |
 
@@ -541,20 +590,6 @@ want to exclude I/O from the timings. **floats** can be used to reduce the size
 of the output files: files are stored as double by default, but setting
 **floats = true** changes the output to single-precision floats.
 
-To enable parallel I/O for either output or restart files, set
-
-.. code-block:: cfg
-
-    parallel = true
-
-in the output or restart section. If you have compiled BOUT++ with a
-parallel I/O library such as pnetcdf (see
-:ref:`sec-advancedinstall`), then rather than outputting one file per
-processor, all processors will output to the same file. For restart
-files this is particularly useful, as it means that you can restart a
-job with a different number of processors. Note that this feature is
-still experimental, and incomplete: output dump files are not yet
-supported by the collect routines.
 
 Implementation
 --------------
@@ -833,30 +868,30 @@ This is currently quite rudimentary and needs improving.
 
 .. _sec-options-netcdf:
 
-Reading and writing to NetCDF
------------------------------
+Reading and writing to binary formats
+-------------------------------------
 
-The `bout::OptionsNetCDF` class provides an interface to read and
-write options. Examples are in integrated test
+The `bout::OptionsIO` class provides an interface to read and
+write options to binary files. Examples are in integrated test
 ``tests/integrated/test-options-netcdf/``
 
 To write the current `Options` tree (e.g. from ``BOUT.inp``) to a
 NetCDF file::
 
-  bout::OptionsNetCDF("settings.nc").write(Options::root());
+  bout::OptionsIO::create("settings.nc")->write(Options::root());
 
 and to read it in again::
 
-  Options data = bout::OptionsNetCDF("settings.nc").read();
+  Options data = bout::OptionsIO::create("settings.nc")->read();
 
 Fields can also be stored and written::
 
   Options fields;
   fields["f2d"] = Field2D(1.0);
   fields["f3d"] = Field3D(2.0);
-  bout::OptionsNetCDF("fields.nc").write(fields);
+  bout::OptionsIO::create("fields.nc").write(fields);
 
-This should allow the input settings and evolving variables to be
+This allows the input settings and evolving variables to be
 combined into a single tree (see above on joining trees) and written
 to the output dump or restart files.
 
@@ -865,7 +900,7 @@ an ``Array<BoutReal>``, 2D as ``Matrix<BoutReal>`` and 3D as
 ``Tensor<BoutReal>``. These can be extracted directly from the
 ``Options`` tree, or converted to a Field::
 
-  Options fields_in = bout::OptionsNetCDF("fields.nc").read();
+  Options fields_in = bout::OptionsIO::create("fields.nc")->read();
   Field2D f2d = fields_in["f2d"].as<Field2D>();
   Field3D f3d = fields_in["f3d"].as<Field3D>();
 
@@ -907,7 +942,7 @@ automatically set the ``"time_dimension"`` attribute::
   // Or use `assignRepeat` to do it automatically:
   data["field"].assignRepeat(Field3D(2.0));
   
-  bout::OptionsNetCDF("time.nc").write(data);
+  bout::OptionsIO::create("time.nc")->write(data);
   
   // Update time-dependent values. This can be done without `force` if the time_dimension
   // attribute is set
@@ -915,13 +950,13 @@ automatically set the ``"time_dimension"`` attribute::
   data["field"] = Field3D(3.0);
   
   // Append data to file
-  bout::OptionsNetCDF("time.nc", bout::OptionsNetCDF::FileMode::append).write(data);
+  bout::OptionsIO({{"file", "time.nc"}, {"append", true}})->write(data);
 
-.. note:: By default, `bout::OptionsNetCDF::write` will only write variables
+.. note:: By default, `bout::OptionsIO::write` will only write variables
           with a ``"time_dimension"`` of ``"t"``. You can write
           variables with a different time dimension by passing it as
           the second argument:
-          ``OptionsNetCDF(filename).write(options, "t2")`` for example.
+          ``OptionsIO::create(filename)->write(options, "t2")`` for example.
 
 
 FFT
diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst
index fc1b2ce2da..eb155909bf 100644
--- a/manual/sphinx/user_docs/installing.rst
+++ b/manual/sphinx/user_docs/installing.rst
@@ -373,6 +373,10 @@ For SUNDIALS, use ``-DBOUT_DOWNLOAD_SUNDIALS=ON``. If using ``ccmake`` this opti
 may not appear initially. This automatically sets ``BOUT_USE_SUNDIALS=ON``, and
 configures SUNDIALS to use MPI.
 
+For ADIOS2, use ``-DBOUT_DOWNLOAD_ADIOS=ON``. This will download and
+configure `ADIOS2 <https://adios2.readthedocs.io/>`_, enabling BOUT++
+to read and write this high-performance parallel file format.
+
 Bundled Dependencies
 ~~~~~~~~~~~~~~~~~~~~
 
diff --git a/src/bout++.cxx b/src/bout++.cxx
index 127cb6ff4a..481a928bec 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -4,9 +4,9 @@
  * Adapted from the BOUT code by B.Dudson, University of York, Oct 2007
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010-2023 BOUT++ contributors
  *
- * Contact Ben Dudson, bd512@york.ac.uk
+ * Contact Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -59,6 +59,10 @@ const char DEFAULT_DIR[] = "data";
 #include "bout/bout.hxx"
 #undef BOUT_NO_USING_NAMESPACE_BOUTGLOBALS
 
+#if BOUT_HAS_ADIOS
+#include "bout/adios_object.hxx"
+#endif
+
 #include <fmt/format.h>
 
 #include <csignal>
@@ -161,6 +165,10 @@ int BoutInitialise(int& argc, char**& argv) {
 
     savePIDtoFile(args.data_dir, MYPE);
 
+#if BOUT_HAS_ADIOS
+    bout::ADIOSInit(BoutComm::get());
+#endif
+
     // Print the different parts of the startup info
     printStartupHeader(MYPE, BoutComm::size());
     printCompileTimeOptions();
@@ -182,8 +190,7 @@ int BoutInitialise(int& argc, char**& argv) {
     // but it's possible that only happens in BoutFinalise, which is
     // too late for that check.
     const auto datadir = Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
-    MAYBE_UNUSED()
-    const auto optionfile =
+    [[maybe_unused]] const auto optionfile =
         Options::root()["optionfile"].withDefault<std::string>(args.opt_file);
     const auto settingsfile =
         Options::root()["settingsfile"].withDefault<std::string>(args.set_file);
@@ -565,6 +572,7 @@ void printCompileTimeOptions() {
   constexpr auto netcdf_flavour =
       has_netcdf ? (has_legacy_netcdf ? " (Legacy)" : " (NetCDF4)") : "";
   output_info.write(_("\tNetCDF support {}{}\n"), is_enabled(has_netcdf), netcdf_flavour);
+  output_info.write(_("\tADIOS support {}\n"), is_enabled(has_adios));
   output_info.write(_("\tPETSc support {}\n"), is_enabled(has_petsc));
   output_info.write(_("\tPretty function name support {}\n"),
                     is_enabled(has_pretty_function));
@@ -693,6 +701,7 @@ void addBuildFlagsToOptions(Options& options) {
   options["has_gettext"].force(bout::build::has_gettext);
   options["has_lapack"].force(bout::build::has_lapack);
   options["has_netcdf"].force(bout::build::has_netcdf);
+  options["has_adios"].force(bout::build::has_adios);
   options["has_petsc"].force(bout::build::has_petsc);
   options["has_hypre"].force(bout::build::has_hypre);
   options["has_umpire"].force(bout::build::has_umpire);
@@ -788,6 +797,10 @@ int BoutFinalise(bool write_settings) {
   // Call HYPER_Finalize if not already called
   bout::HypreLib::cleanup();
 
+#if BOUT_HAS_ADIOS
+  bout::ADIOSFinalize();
+#endif
+
   // MPI communicator, including MPI_Finalize()
   BoutComm::cleanup();
 
@@ -823,7 +836,7 @@ BoutMonitor::BoutMonitor(BoutReal timestep, Options& options)
                           .doc(_("Name of file whose existence triggers a stop"))
                           .withDefault("BOUT.stop"))) {}
 
-int BoutMonitor::call(Solver* solver, BoutReal t, MAYBE_UNUSED(int iter), int NOUT) {
+int BoutMonitor::call(Solver* solver, BoutReal t, [[maybe_unused]] int iter, int NOUT) {
   TRACE("BoutMonitor::call({:e}, {:d}, {:d})", t, iter, NOUT);
 
   // Increment Solver's iteration counter, and set the global `iteration`
diff --git a/src/field/field.cxx b/src/field/field.cxx
index 54883c506c..e48a8f3ef7 100644
--- a/src/field/field.cxx
+++ b/src/field/field.cxx
@@ -23,8 +23,6 @@
  *
  **************************************************************************/
 
-//#include <bout/globals.hxx>
-
 #include <bout/boutexception.hxx>
 #include <bout/coordinates.hxx>
 #include <bout/field.hxx>
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 0bd9e66fc4..b4bb0d394f 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -173,7 +173,7 @@ const Field3D& Field3D::ynext(int dir) const {
   if (dir > 0) {
     return yup(dir - 1);
   } else if (dir < 0) {
-    return ydown(std::abs(dir) - 1);
+    return ydown(-dir - 1);
   } else {
     return *this;
   }
@@ -742,7 +742,7 @@ namespace {
 #if CHECK > 2
 void checkDataIsFiniteOnRegion(const Field3D& f, const std::string& region) {
   // Do full checks
-  BOUT_FOR_SERIAL(i, f.getRegion(region)) {
+  BOUT_FOR_SERIAL(i, f.getValidRegionWithDefault(region)) {
     if (!finite(f[i])) {
       throw BoutException("Field3D: Operation on non-finite data at [{:d}][{:d}][{:d}]\n",
                           i.x(), i.y(), i.z());
@@ -819,3 +819,15 @@ void swap(Field3D& first, Field3D& second) noexcept {
   swap(first.yup_fields, second.yup_fields);
   swap(first.ydown_fields, second.ydown_fields);
 }
+
+const Region<Ind3D>&
+Field3D::getValidRegionWithDefault(const std::string& region_name) const {
+  if (regionID.has_value()) {
+    return fieldmesh->getRegion(regionID.value());
+  }
+  return fieldmesh->getRegion(region_name);
+}
+
+void Field3D::setRegion(const std::string& region_name) {
+  regionID = fieldmesh->getRegionID(region_name);
+}
diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index fb03c3b174..f65f2e7f55 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -93,8 +93,20 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
   // Note: don't use 'options' here because 'options' is a 'const Options*'
   // pointer, so this would fail if the "input" section is not present.
   Options& nonconst_options{opt == nullptr ? Options::root() : *opt};
-  transform_from_field_aligned =
-      nonconst_options["input"]["transform_from_field_aligned"].withDefault(true);
+
+  // Convert from string, or FieldFactory is used to parse the string
+  auto str =
+      nonconst_options["input"]["transform_from_field_aligned"].withDefault<std::string>(
+          "true");
+  if ((str == "true") or (str == "True")) {
+    transform_from_field_aligned = true;
+  } else if ((str == "false") or (str == "False")) {
+    transform_from_field_aligned = false;
+  } else {
+    throw ParseException(
+        "Invalid boolean given as input:transform_from_field_aligned: '{:s}'",
+        nonconst_options["input"]["transform_from_field_aligned"].as<std::string>());
+  }
 
   // Convert using stoi rather than Options, or a FieldFactory is used to parse
   // the string, leading to infinite loop.
@@ -114,6 +126,14 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
   addGenerator("pi", std::make_shared<FieldValue>(PI));
   addGenerator("π", std::make_shared<FieldValue>(PI));
 
+  // Boolean values
+  addGenerator("true", std::make_shared<FieldValue>(1));
+  addGenerator("false", std::make_shared<FieldValue>(0));
+
+  // Python converts booleans to True/False
+  addGenerator("True", std::make_shared<FieldValue>(1));
+  addGenerator("False", std::make_shared<FieldValue>(0));
+
   // Some standard functions
   addGenerator("sin", std::make_shared<FieldGenOneArg<sin>>(nullptr, "sin"));
   addGenerator("cos", std::make_shared<FieldGenOneArg<cos>>(nullptr, "cos"));
diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index 249245b21c..ecd4e628cc 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -8,6 +8,17 @@
   checkData({{lhs.name}});
   checkData({{rhs.name}});
 
+  {% if out == "Field3D" %}
+    {% if lhs == rhs == "Field3D" %}
+      {{out.name}}.setRegion({{lhs.name}}.getMesh()->getCommonRegion({{lhs.name}}.getRegionID(),
+                                                                     {{rhs.name}}.getRegionID()));
+    {% elif lhs == "Field3D" %}
+      {{out.name}}.setRegion({{lhs.name}}.getRegionID());
+    {% elif rhs == "Field3D" %}
+      {{out.name}}.setRegion({{rhs.name}}.getRegionID());
+    {% endif %}
+  {% endif %}
+
   {% if (out == "Field3D") and ((lhs == "Field2D") or (rhs =="Field2D")) %}
     Mesh *localmesh = {{lhs.name if lhs.field_type != "BoutReal" else rhs.name}}.getMesh();
 
@@ -41,11 +52,11 @@
 	}
   {% elif (operator == "/") and (rhs == "BoutReal") %}
       const auto tmp = 1.0 / {{rhs.index}};
-      {{region_loop}}({{index_var}}, {{out.name}}.getRegion({{region_name}})) {
+      {{region_loop}}({{index_var}}, {{out.name}}.getValidRegionWithDefault({{region_name}})) {
          {{out.index}} = {{lhs.index}} * tmp;
       }
   {% else %}
-    {{region_loop}}({{index_var}}, {{out.name}}.getRegion({{region_name}})) {
+    {{region_loop}}({{index_var}}, {{out.name}}.getValidRegionWithDefault({{region_name}})) {
 	    {{out.index}} = {{lhs.index}} {{operator}} {{rhs.index}};
 	}
   {% endif %}
@@ -73,6 +84,11 @@
     checkData(*this);
     checkData({{rhs.name}});
 
+    {% if lhs == rhs == "Field3D" %}
+      regionID = fieldmesh->getCommonRegion(regionID, {{rhs.name}}.regionID);
+    {% endif %}
+
+
   {% if (lhs == "Field3D") and (rhs =="Field2D") %}
     {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) {
 	const auto {{mixed_base_ind}} = fieldmesh->ind2Dto3D({{index_var}});
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index a3613eca3e..6b778acee3 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -14,7 +14,9 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] * rhs[index];
   }
 
@@ -36,6 +38,8 @@ Field3D& Field3D::operator*=(const Field3D& rhs) {
     checkData(*this);
     checkData(rhs);
 
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
 
     checkData(*this);
@@ -54,7 +58,9 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] / rhs[index];
   }
 
@@ -76,6 +82,8 @@ Field3D& Field3D::operator/=(const Field3D& rhs) {
     checkData(*this);
     checkData(rhs);
 
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
 
     checkData(*this);
@@ -94,7 +102,9 @@ Field3D operator+(const Field3D& lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] + rhs[index];
   }
 
@@ -116,6 +126,8 @@ Field3D& Field3D::operator+=(const Field3D& rhs) {
     checkData(*this);
     checkData(rhs);
 
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
 
     checkData(*this);
@@ -134,7 +146,9 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] - rhs[index];
   }
 
@@ -156,6 +170,8 @@ Field3D& Field3D::operator-=(const Field3D& rhs) {
     checkData(*this);
     checkData(rhs);
 
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
 
     checkData(*this);
@@ -174,6 +190,8 @@ Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
+  result.setRegion(lhs.getRegionID());
+
   Mesh* localmesh = lhs.getMesh();
 
   BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
@@ -224,6 +242,8 @@ Field3D operator/(const Field3D& lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
+  result.setRegion(lhs.getRegionID());
+
   Mesh* localmesh = lhs.getMesh();
 
   BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
@@ -276,6 +296,8 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
+  result.setRegion(lhs.getRegionID());
+
   Mesh* localmesh = lhs.getMesh();
 
   BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
@@ -326,6 +348,8 @@ Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
+  result.setRegion(lhs.getRegionID());
+
   Mesh* localmesh = lhs.getMesh();
 
   BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
@@ -455,7 +479,11 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; }
+  result.setRegion(lhs.getRegionID());
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * rhs;
+  }
 
   checkData(result);
   return result;
@@ -491,8 +519,12 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
+  result.setRegion(lhs.getRegionID());
+
   const auto tmp = 1.0 / rhs;
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * tmp;
+  }
 
   checkData(result);
   return result;
@@ -529,7 +561,11 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; }
+  result.setRegion(lhs.getRegionID());
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] + rhs;
+  }
 
   checkData(result);
   return result;
@@ -565,7 +601,11 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; }
+  result.setRegion(lhs.getRegionID());
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] - rhs;
+  }
 
   checkData(result);
   return result;
@@ -602,6 +642,8 @@ Field3D operator*(const Field2D& lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
+  result.setRegion(rhs.getRegionID());
+
   Mesh* localmesh = lhs.getMesh();
 
   BOUT_FOR(index, lhs.getRegion("RGN_ALL")) {
@@ -623,6 +665,8 @@ Field3D operator/(const Field2D& lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
+  result.setRegion(rhs.getRegionID());
+
   Mesh* localmesh = lhs.getMesh();
 
   BOUT_FOR(index, lhs.getRegion("RGN_ALL")) {
@@ -644,6 +688,8 @@ Field3D operator+(const Field2D& lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
+  result.setRegion(rhs.getRegionID());
+
   Mesh* localmesh = lhs.getMesh();
 
   BOUT_FOR(index, lhs.getRegion("RGN_ALL")) {
@@ -665,6 +711,8 @@ Field3D operator-(const Field2D& lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
+  result.setRegion(rhs.getRegionID());
+
   Mesh* localmesh = lhs.getMesh();
 
   BOUT_FOR(index, lhs.getRegion("RGN_ALL")) {
@@ -686,7 +734,7 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] * rhs[index];
   }
 
@@ -722,7 +770,7 @@ Field2D operator/(const Field2D& lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] / rhs[index];
   }
 
@@ -758,7 +806,7 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] + rhs[index];
   }
 
@@ -794,7 +842,7 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] - rhs[index];
   }
 
@@ -909,7 +957,9 @@ Field2D operator*(const Field2D& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * rhs;
+  }
 
   checkData(result);
   return result;
@@ -942,7 +992,9 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
   checkData(rhs);
 
   const auto tmp = 1.0 / rhs;
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * tmp;
+  }
 
   checkData(result);
   return result;
@@ -975,7 +1027,9 @@ Field2D operator+(const Field2D& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] + rhs;
+  }
 
   checkData(result);
   return result;
@@ -1007,7 +1061,9 @@ Field2D operator-(const Field2D& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] - rhs;
+  }
 
   checkData(result);
   return result;
@@ -1408,7 +1464,7 @@ FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] * rhs[index];
   }
 
@@ -1444,7 +1500,7 @@ FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] / rhs[index];
   }
 
@@ -1480,7 +1536,7 @@ FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] + rhs[index];
   }
 
@@ -1516,7 +1572,7 @@ FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) {
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] - rhs[index];
   }
 
@@ -1551,7 +1607,9 @@ FieldPerp operator*(const FieldPerp& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * rhs; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * rhs;
+  }
 
   checkData(result);
   return result;
@@ -1584,7 +1642,9 @@ FieldPerp operator/(const FieldPerp& lhs, const BoutReal rhs) {
   checkData(rhs);
 
   const auto tmp = 1.0 / rhs;
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] * tmp; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * tmp;
+  }
 
   checkData(result);
   return result;
@@ -1616,7 +1676,9 @@ FieldPerp operator+(const FieldPerp& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] + rhs; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] + rhs;
+  }
 
   checkData(result);
   return result;
@@ -1648,7 +1710,9 @@ FieldPerp operator-(const FieldPerp& lhs, const BoutReal rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs[index] - rhs; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] - rhs;
+  }
 
   checkData(result);
   return result;
@@ -1680,7 +1744,11 @@ Field3D operator*(const BoutReal lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; }
+  result.setRegion(rhs.getRegionID());
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs * rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1693,7 +1761,11 @@ Field3D operator/(const BoutReal lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; }
+  result.setRegion(rhs.getRegionID());
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs / rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1706,7 +1778,11 @@ Field3D operator+(const BoutReal lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; }
+  result.setRegion(rhs.getRegionID());
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs + rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1719,7 +1795,11 @@ Field3D operator-(const BoutReal lhs, const Field3D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; }
+  result.setRegion(rhs.getRegionID());
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs - rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1732,7 +1812,9 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs * rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1745,7 +1827,9 @@ Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs / rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1758,7 +1842,9 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs + rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1771,7 +1857,9 @@ Field2D operator-(const BoutReal lhs, const Field2D& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs - rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1784,7 +1872,9 @@ FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs * rhs[index]; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs * rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1797,7 +1887,9 @@ FieldPerp operator/(const BoutReal lhs, const FieldPerp& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs / rhs[index]; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs / rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1810,7 +1902,9 @@ FieldPerp operator+(const BoutReal lhs, const FieldPerp& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs + rhs[index]; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs + rhs[index];
+  }
 
   checkData(result);
   return result;
@@ -1823,7 +1917,9 @@ FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) {
   checkData(lhs);
   checkData(rhs);
 
-  BOUT_FOR(index, result.getRegion("RGN_ALL")) { result[index] = lhs - rhs[index]; }
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs - rhs[index];
+  }
 
   checkData(result);
   return result;
diff --git a/src/invert/fft_fftw.cxx b/src/invert/fft_fftw.cxx
index f158fa3d7a..514396c828 100644
--- a/src/invert/fft_fftw.cxx
+++ b/src/invert/fft_fftw.cxx
@@ -106,8 +106,8 @@ void fft_init(bool fft_measure) {
 
 #if !BOUT_USE_OPENMP
 // Serial code
-void rfft(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length),
-          MAYBE_UNUSED(dcomplex* out)) {
+void rfft([[maybe_unused]] const BoutReal* in, [[maybe_unused]] int length,
+          [[maybe_unused]] dcomplex* out) {
 #if !BOUT_HAS_FFTW
   throw BoutException("This instance of BOUT++ has been compiled without fftw support.");
 #else
@@ -170,8 +170,8 @@ void rfft(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length),
 #endif
 }
 
-void irfft(MAYBE_UNUSED(const dcomplex* in), MAYBE_UNUSED(int length),
-           MAYBE_UNUSED(BoutReal* out)) {
+void irfft([[maybe_unused]] const dcomplex* in, [[maybe_unused]] int length,
+           [[maybe_unused]] BoutReal* out) {
 #if !BOUT_HAS_FFTW
   throw BoutException("This instance of BOUT++ has been compiled without fftw support.");
 #else
@@ -233,8 +233,8 @@ void irfft(MAYBE_UNUSED(const dcomplex* in), MAYBE_UNUSED(int length),
 }
 #else
 // Parallel thread-safe version of rfft and irfft
-void rfft(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length),
-          MAYBE_UNUSED(dcomplex* out)) {
+void rfft([[maybe_unused]] const BoutReal* in, [[maybe_unused]] int length,
+          [[maybe_unused]] dcomplex* out) {
 #if !BOUT_HAS_FFTW
   throw BoutException("This instance of BOUT++ has been compiled without fftw support.");
 #else
@@ -312,8 +312,8 @@ void rfft(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length),
 #endif
 }
 
-void irfft(MAYBE_UNUSED(const dcomplex* in), MAYBE_UNUSED(int length),
-           MAYBE_UNUSED(BoutReal* out)) {
+void irfft([[maybe_unused]] const dcomplex* in, [[maybe_unused]] int length,
+           [[maybe_unused]] BoutReal* out) {
 #if !BOUT_HAS_FFTW
   throw BoutException("This instance of BOUT++ has been compiled without fftw support.");
 #else
@@ -388,8 +388,8 @@ void irfft(MAYBE_UNUSED(const dcomplex* in), MAYBE_UNUSED(int length),
 #endif
 //  Discrete sine transforms (B Shanahan)
 
-void DST(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length),
-         MAYBE_UNUSED(dcomplex* out)) {
+void DST([[maybe_unused]] const BoutReal* in, [[maybe_unused]] int length,
+         [[maybe_unused]] dcomplex* out) {
 #if !BOUT_HAS_FFTW
   throw BoutException("This instance of BOUT++ has been compiled without fftw support.");
 #else
@@ -446,8 +446,8 @@ void DST(MAYBE_UNUSED(const BoutReal* in), MAYBE_UNUSED(int length),
 #endif
 }
 
-void DST_rev(MAYBE_UNUSED(dcomplex* in), MAYBE_UNUSED(int length),
-             MAYBE_UNUSED(BoutReal* out)) {
+void DST_rev([[maybe_unused]] dcomplex* in, [[maybe_unused]] int length,
+             [[maybe_unused]] BoutReal* out) {
 #if !BOUT_HAS_FFTW
   throw BoutException("This instance of BOUT++ has been compiled without fftw support.");
 #else
diff --git a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx
index 0043c95d18..88556e02ad 100644
--- a/src/invert/laplace/impls/multigrid/multigrid_alg.cxx
+++ b/src/invert/laplace/impls/multigrid/multigrid_alg.cxx
@@ -704,7 +704,7 @@ void MultigridAlg::communications(BoutReal* x, int level) {
 
   MPI_Status status[4];
   int stag, rtag;
-  MAYBE_UNUSED(int ierr);
+  [[maybe_unused]] int ierr;
 
   if (zNP > 1) {
     MPI_Request requests[] = {MPI_REQUEST_NULL, MPI_REQUEST_NULL, MPI_REQUEST_NULL,
diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx
index dc3d1a3c3f..505b04cc4f 100644
--- a/src/invert/laplace/invert_laplace.cxx
+++ b/src/invert/laplace/invert_laplace.cxx
@@ -782,9 +782,10 @@ void Laplacian::savePerformance(Solver& solver, const std::string& name) {
   solver.addMonitor(&monitor, Solver::BACK);
 }
 
-int Laplacian::LaplacianMonitor::call(MAYBE_UNUSED(Solver* solver),
-                                      MAYBE_UNUSED(BoutReal time), MAYBE_UNUSED(int iter),
-                                      MAYBE_UNUSED(int nout)) {
+int Laplacian::LaplacianMonitor::call([[maybe_unused]] Solver* solver,
+                                      [[maybe_unused]] BoutReal time,
+                                      [[maybe_unused]] int iter,
+                                      [[maybe_unused]] int nout) {
   // Nothing to do, values are always calculated
   return 0;
 }
@@ -805,7 +806,3 @@ void laplace_tridag_coefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dcom
                           const Field2D* ccoef, const Field2D* d, CELL_LOC loc) {
   Laplacian::defaultInstance()->tridagCoefs(jx, jy, jz, a, b, c, ccoef, d, loc);
 }
-constexpr decltype(LaplaceFactory::type_name) LaplaceFactory::type_name;
-constexpr decltype(LaplaceFactory::section_name) LaplaceFactory::section_name;
-constexpr decltype(LaplaceFactory::option_name) LaplaceFactory::option_name;
-constexpr decltype(LaplaceFactory::default_type) LaplaceFactory::default_type;
diff --git a/src/invert/laplacexz/laplacexz.cxx b/src/invert/laplacexz/laplacexz.cxx
index a2b99280e6..d064f62104 100644
--- a/src/invert/laplacexz/laplacexz.cxx
+++ b/src/invert/laplacexz/laplacexz.cxx
@@ -5,8 +5,3 @@
 
 // DO NOT REMOVE: ensures linker keeps all symbols in this TU
 void LaplaceXZFactory::ensureRegistered() {}
-
-constexpr decltype(LaplaceXZFactory::type_name) LaplaceXZFactory::type_name;
-constexpr decltype(LaplaceXZFactory::section_name) LaplaceXZFactory::section_name;
-constexpr decltype(LaplaceXZFactory::option_name) LaplaceXZFactory::option_name;
-constexpr decltype(LaplaceXZFactory::default_type) LaplaceXZFactory::default_type;
diff --git a/src/invert/parderiv/invert_parderiv.cxx b/src/invert/parderiv/invert_parderiv.cxx
index bc8ad8669f..e14c0ee1d2 100644
--- a/src/invert/parderiv/invert_parderiv.cxx
+++ b/src/invert/parderiv/invert_parderiv.cxx
@@ -39,7 +39,3 @@ const Field2D InvertPar::solve(const Field2D& f) {
 
 // DO NOT REMOVE: ensures linker keeps all symbols in this TU
 void InvertParFactory::ensureRegistered() {}
-constexpr decltype(InvertParFactory::type_name) InvertParFactory::type_name;
-constexpr decltype(InvertParFactory::section_name) InvertParFactory::section_name;
-constexpr decltype(InvertParFactory::option_name) InvertParFactory::option_name;
-constexpr decltype(InvertParFactory::default_type) InvertParFactory::default_type;
diff --git a/src/invert/pardiv/invert_pardiv.cxx b/src/invert/pardiv/invert_pardiv.cxx
index d05b594aa1..30e421edd8 100644
--- a/src/invert/pardiv/invert_pardiv.cxx
+++ b/src/invert/pardiv/invert_pardiv.cxx
@@ -39,7 +39,3 @@ Field2D InvertParDiv::solve(const Field2D& f) {
 
 // DO NOT REMOVE: ensures linker keeps all symbols in this TU
 void InvertParDivFactory::ensureRegistered() {}
-constexpr decltype(InvertParDivFactory::type_name) InvertParDivFactory::type_name;
-constexpr decltype(InvertParDivFactory::section_name) InvertParDivFactory::section_name;
-constexpr decltype(InvertParDivFactory::option_name) InvertParDivFactory::option_name;
-constexpr decltype(InvertParDivFactory::default_type) InvertParDivFactory::default_type;
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 25d623aad8..5ec0bb79e1 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1528,7 +1528,7 @@ Field3D Coordinates::DDZ(const Field3D& f, CELL_LOC outloc, const std::string& m
 // Parallel gradient
 
 Coordinates::FieldMetric Coordinates::Grad_par(const Field2D& var,
-                                               MAYBE_UNUSED(CELL_LOC outloc),
+                                               [[maybe_unused]] CELL_LOC outloc,
                                                const std::string& UNUSED(method)) {
   TRACE("Coordinates::Grad_par( Field2D )");
   ASSERT1(location == outloc
@@ -1550,7 +1550,7 @@ Field3D Coordinates::Grad_par(const Field3D& var, CELL_LOC outloc,
 // vparallel times the parallel derivative along unperturbed B-field
 
 Coordinates::FieldMetric Coordinates::Vpar_Grad_par(const Field2D& v, const Field2D& f,
-                                                    MAYBE_UNUSED(CELL_LOC outloc),
+                                                    [[maybe_unused]] CELL_LOC outloc,
                                                     const std::string& UNUSED(method)) {
   ASSERT1(location == outloc || (outloc == CELL_DEFAULT && location == f.getLocation()));
 
@@ -1829,8 +1829,8 @@ Field3D Coordinates::Laplace(const Field3D& f, CELL_LOC outloc,
 
 // Full perpendicular Laplacian, in form of inverse of Laplacian operator in LaplaceXY
 // solver
-Field2D Coordinates::Laplace_perpXY(MAYBE_UNUSED(const Field2D& A),
-                                    MAYBE_UNUSED(const Field2D& f)) {
+Field2D Coordinates::Laplace_perpXY([[maybe_unused]] const Field2D& A,
+                                    [[maybe_unused]] const Field2D& f) {
   TRACE("Coordinates::Laplace_perpXY( Field2D )");
 #if not(BOUT_USE_METRIC_3D)
   Field2D result;
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 7e875bd109..41147ba76c 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -6,7 +6,7 @@
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
 #include <bout/msg_stack.hxx>
-#include <bout/options_netcdf.hxx>
+#include <bout/options_io.hxx>
 #include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/unused.hxx>
@@ -14,7 +14,7 @@
 #include <utility>
 
 GridFile::GridFile(std::string gridfilename)
-    : GridDataSource(true), data(bout::OptionsNetCDF(gridfilename).read()),
+    : GridDataSource(true), data(bout::OptionsIO::create(gridfilename)->read()),
       filename(std::move(gridfilename)) {
   TRACE("GridFile constructor");
 
@@ -134,10 +134,10 @@ bool GridFile::get(Mesh* m, Field3D& var, const std::string& name, BoutReal def,
 namespace {
 /// Visitor that returns the shape of its argument
 struct GetDimensions {
-  std::vector<int> operator()(MAYBE_UNUSED(bool value)) { return {1}; }
-  std::vector<int> operator()(MAYBE_UNUSED(int value)) { return {1}; }
-  std::vector<int> operator()(MAYBE_UNUSED(BoutReal value)) { return {1}; }
-  std::vector<int> operator()(MAYBE_UNUSED(const std::string& value)) { return {1}; }
+  std::vector<int> operator()([[maybe_unused]] bool value) { return {1}; }
+  std::vector<int> operator()([[maybe_unused]] int value) { return {1}; }
+  std::vector<int> operator()([[maybe_unused]] BoutReal value) { return {1}; }
+  std::vector<int> operator()([[maybe_unused]] const std::string& value) { return {1}; }
   std::vector<int> operator()(const Array<BoutReal>& array) { return {array.size()}; }
   std::vector<int> operator()(const Matrix<BoutReal>& array) {
     const auto shape = array.shape();
@@ -471,10 +471,10 @@ void GridFile::readField(Mesh* m, const std::string& name, int UNUSED(ys), int U
   }
 }
 
-bool GridFile::get(MAYBE_UNUSED(Mesh* m), MAYBE_UNUSED(std::vector<int>& var),
-                   MAYBE_UNUSED(const std::string& name), MAYBE_UNUSED(int len),
-                   MAYBE_UNUSED(int offset),
-                   MAYBE_UNUSED(GridDataSource::Direction dir)) {
+bool GridFile::get([[maybe_unused]] Mesh* m, [[maybe_unused]] std::vector<int>& var,
+                   [[maybe_unused]] const std::string& name, [[maybe_unused]] int len,
+                   [[maybe_unused]] int offset,
+                   [[maybe_unused]] GridDataSource::Direction dir) {
   TRACE("GridFile::get(vector<int>)");
 
   return false;
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 9b7665ad30..f252abe0ea 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -645,7 +645,7 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
   }
   ASSERT1(outloc == g.getLocation());
 
-  MAYBE_UNUSED(Mesh * mesh) = f.getMesh();
+  [[maybe_unused]] Mesh* mesh = f.getMesh();
 
   Field3D result{emptyFrom(f).setLocation(outloc)};
 
@@ -862,7 +862,7 @@ Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method,
 }
 
 Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
-                CELL_LOC outloc, MAYBE_UNUSED(Solver* solver)) {
+                CELL_LOC outloc, [[maybe_unused]] Solver* solver) {
   TRACE("Field3D, Field3D");
 
   ASSERT1_FIELDS_COMPATIBLE(f, g);
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index a802d3f5b3..956aba0f79 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -333,7 +333,9 @@ void BoutMesh::setDerivedGridSizes() {
   }
 
   GlobalNx = nx;
-  GlobalNy = ny + 2 * MYG;
+  GlobalNy =
+      ny
+      + 2 * MYG; // Note: For double null this should be be 4 * MYG if boundary cells are stored
   GlobalNz = nz;
 
   // If we've got a second pair of diverator legs, we need an extra
@@ -374,6 +376,7 @@ void BoutMesh::setDerivedGridSizes() {
   }
 
   // Set global offsets
+  // Note: These don't properly include guard/boundary cells
   OffsetX = PE_XIND * MXSUB;
   OffsetY = PE_YIND * MYSUB;
   OffsetZ = 0;
@@ -392,6 +395,48 @@ void BoutMesh::setDerivedGridSizes() {
 
   zstart = MZG;
   zend = MZG + MZSUB - 1;
+
+  // Mapping local to global indices
+  if (periodicX) {
+    // No boundary cells in X
+    MapGlobalX = PE_XIND * MXSUB;
+    MapLocalX = MXG;
+    MapCountX = MXSUB;
+  } else {
+    // X boundaries stored for firstX and lastX processors
+    if (firstX()) {
+      MapGlobalX = 0;
+      MapLocalX = 0;
+      MapCountX = MXG + MXSUB;
+    } else {
+      MapGlobalX = MXG + PE_XIND * MXSUB;
+      MapLocalX = MXG; // Guard cells not included
+      MapCountX = MXSUB;
+    }
+    if (lastX()) {
+      // Doesn't change the origin, but adds outer X boundary cells
+      MapCountX += MXG;
+    }
+  }
+
+  if (PE_YIND == 0) {
+    // Include Y boundary cells
+    MapGlobalY = 0;
+    MapLocalY = 0;
+    MapCountY = MYG + MYSUB;
+  } else {
+    MapGlobalY = MYG + PE_YIND * MYSUB;
+    MapLocalY = MYG;
+    MapCountY = MYSUB;
+  }
+  if (PE_YIND == NYPE - 1) {
+    // Include Y upper boundary region.
+    MapCountY += MYG;
+  }
+
+  MapGlobalZ = 0;
+  MapLocalZ = MZG; // Omit boundary cells
+  MapCountZ = MZSUB;
 }
 
 int BoutMesh::load() {
diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx
index 769315ca68..d84f5ced37 100644
--- a/src/mesh/index_derivs.cxx
+++ b/src/mesh/index_derivs.cxx
@@ -59,7 +59,7 @@ STAGGER Mesh::getStagger(const CELL_LOC inloc, const CELL_LOC outloc,
   }
 }
 
-STAGGER Mesh::getStagger(const CELL_LOC vloc, MAYBE_UNUSED(const CELL_LOC inloc),
+STAGGER Mesh::getStagger(const CELL_LOC vloc, [[maybe_unused]] const CELL_LOC inloc,
                          const CELL_LOC outloc, const CELL_LOC allowedStaggerLoc) const {
   TRACE("Mesh::getStagger -- four arguments");
   ASSERT1(inloc == outloc);
@@ -485,7 +485,6 @@ class FFTDerivativeType {
   }
   static constexpr metaData meta{"FFT", 0, DERIV::Standard};
 };
-constexpr metaData FFTDerivativeType::meta;
 
 class FFT2ndDerivativeType {
 public:
@@ -544,7 +543,6 @@ class FFT2ndDerivativeType {
   }
   static constexpr metaData meta{"FFT", 0, DERIV::StandardSecond};
 };
-constexpr metaData FFT2ndDerivativeType::meta;
 
 produceCombinations<Set<WRAP_ENUM(DIRECTION, Z)>, Set<WRAP_ENUM(STAGGER, None)>,
                     Set<TypeContainer<Field3D>>,
@@ -574,7 +572,6 @@ class SplitFluxDerivativeType {
   }
   static constexpr metaData meta{"SPLIT", 2, DERIV::Flux};
 };
-constexpr metaData SplitFluxDerivativeType::meta;
 
 produceCombinations<
     Set<WRAP_ENUM(DIRECTION, X), WRAP_ENUM(DIRECTION, Y),
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 2a540a0bc4..9e41bac191 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -182,7 +182,7 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
       t_x = 0.0;
     }
 
-    k_corner(x, y, z) = ((k_corner(x, y, z) % ncz) + ncz) % ncz;
+    k_corner(x, y, z) = ((k_corner(x, y, z) % nz) + nz) % nz;
 
     // Check that t_x and t_z are in range
     if ((t_x < 0.0) || (t_x > 1.0)) {
@@ -198,7 +198,7 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     }
 
     i_corner[i] = SpecificInd<IND_TYPE::IND_3D>(
-        (((i_corn * ny) + (y + y_offset)) * nz + k_corner(x, y, z)), ny, nz);
+					   (((i_corn * ny) + (y + y_offset)) * nz + k_corner(x, y, z)), ny, nz);
 
     h00_x[i] = (2. * t_x * t_x * t_x) - (3. * t_x * t_x) + 1.;
     h00_z[i] = (2. * t_z * t_z * t_z) - (3. * t_z * t_z) + 1.;
@@ -324,11 +324,11 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
  */
 std::vector<ParallelTransform::PositionsAndWeights>
 XZHermiteSpline::getWeightsForYApproximation(int i, int j, int k, int yoffset) {
-  const int ncz = localmesh->LocalNz;
+  const int nz = localmesh->LocalNz;
   const int k_mod = k_corner(i, j, k);
-  const int k_mod_m1 = (k_mod > 0) ? (k_mod - 1) : (ncz - 1);
-  const int k_mod_p1 = (k_mod == ncz) ? 0 : k_mod + 1;
-  const int k_mod_p2 = (k_mod_p1 == ncz) ? 0 : k_mod_p1 + 1;
+  const int k_mod_m1 = (k_mod > 0) ? (k_mod - 1) : (nz - 1);
+  const int k_mod_p1 = (k_mod == nz) ? 0 : k_mod + 1;
+  const int k_mod_p2 = (k_mod_p1 == nz) ? 0 : k_mod_p1 + 1;
 
   return {{i, j + yoffset, k_mod_m1, -0.5 * h10_z(i, j, k)},
           {i, j + yoffset, k_mod, h00_z(i, j, k) - 0.5 * h11_z(i, j, k)},
diff --git a/src/mesh/interpolation/hermite_spline_z.cxx b/src/mesh/interpolation/hermite_spline_z.cxx
index 921094af73..c4c44cb7b4 100644
--- a/src/mesh/interpolation/hermite_spline_z.cxx
+++ b/src/mesh/interpolation/hermite_spline_z.cxx
@@ -192,10 +192,3 @@ void ZInterpolationFactory::ensureRegistered() {}
 namespace {
 RegisterZInterpolation<ZHermiteSpline> registerzinterphermitespline{"hermitespline"};
 } // namespace
-
-constexpr decltype(ZInterpolationFactory::type_name) ZInterpolationFactory::type_name;
-constexpr decltype(ZInterpolationFactory::section_name)
-    ZInterpolationFactory::section_name;
-constexpr decltype(ZInterpolationFactory::option_name) ZInterpolationFactory::option_name;
-constexpr decltype(ZInterpolationFactory::default_type)
-    ZInterpolationFactory::default_type;
diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx
index 11dbdc215d..f7f0b457f2 100644
--- a/src/mesh/interpolation_xz.cxx
+++ b/src/mesh/interpolation_xz.cxx
@@ -93,11 +93,3 @@ RegisterXZInterpolation<XZMonotonicHermiteSpline> registerinterpmonotonichermite
 RegisterXZInterpolation<XZLagrange4pt> registerinterplagrange4pt{"lagrange4pt"};
 RegisterXZInterpolation<XZBilinear> registerinterpbilinear{"bilinear"};
 } // namespace
-
-constexpr decltype(XZInterpolationFactory::type_name) XZInterpolationFactory::type_name;
-constexpr decltype(XZInterpolationFactory::section_name)
-    XZInterpolationFactory::section_name;
-constexpr decltype(XZInterpolationFactory::option_name)
-    XZInterpolationFactory::option_name;
-constexpr decltype(XZInterpolationFactory::default_type)
-    XZInterpolationFactory::default_type;
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index e754b4fe43..0f6315a987 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -555,6 +555,14 @@ Mesh::createDefaultCoordinates(const CELL_LOC location,
 }
 
 const Region<>& Mesh::getRegion3D(const std::string& region_name) const {
+  const auto found = regionMap3D.find(region_name);
+  if (found == end(regionMap3D)) {
+    throw BoutException(_("Couldn't find region {:s} in regionMap3D"), region_name);
+  }
+  return region3D[found->second];
+}
+
+size_t Mesh::getRegionID(const std::string& region_name) const {
   const auto found = regionMap3D.find(region_name);
   if (found == end(regionMap3D)) {
     throw BoutException(_("Couldn't find region {:s} in regionMap3D"), region_name);
@@ -595,7 +603,21 @@ void Mesh::addRegion3D(const std::string& region_name, const Region<>& region) {
     throw BoutException(_("Trying to add an already existing region {:s} to regionMap3D"),
                         region_name);
   }
-  regionMap3D[region_name] = region;
+
+  std::optional<size_t> id;
+  for (size_t i = 0; i < region3D.size(); ++i) {
+    if (region3D[i] == region) {
+      id = i;
+      break;
+    }
+  }
+  if (!id.has_value()) {
+    id = region3D.size();
+    region3D.push_back(region);
+  }
+
+  regionMap3D[region_name] = id.value();
+
   output_verbose.write(_("Registered region 3D {:s}"), region_name);
   output_verbose << "\n:\t" << region.getStats() << "\n";
 }
@@ -734,7 +756,89 @@ void Mesh::recalculateStaggeredCoordinates() {
   }
 }
 
-constexpr decltype(MeshFactory::type_name) MeshFactory::type_name;
-constexpr decltype(MeshFactory::section_name) MeshFactory::section_name;
-constexpr decltype(MeshFactory::option_name) MeshFactory::option_name;
-constexpr decltype(MeshFactory::default_type) MeshFactory::default_type;
+std::optional<size_t> Mesh::getCommonRegion(std::optional<size_t> lhs,
+                                            std::optional<size_t> rhs) {
+  if (!lhs.has_value()) {
+    return rhs;
+  }
+  if (!rhs.has_value()) {
+    return lhs;
+  }
+  if (lhs.value() == rhs.value()) {
+    return lhs;
+  }
+  const size_t low = std::min(lhs.value(), rhs.value());
+  const size_t high = std::max(lhs.value(), rhs.value());
+
+  /* This function finds the ID of the region corresponding to the
+     intersection of two regions, and caches the result. The cache is a
+     vector, indexed by some function of the two input IDs. Because the
+     intersection of two regions doesn't depend on the order, and the
+     intersection of a region with itself is the identity operation, we can
+     order the IDs numerically and use a generalised triangle number:
+     $[n (n - 1) / 2] + m$ to construct the cache index. This diagram shows
+     the result for the first few numbers:
+       |  0  1  2  3
+     ----------------
+     0 |
+     1 |  0
+     2 |  1  2
+     3 |  3  4  5
+     4 |  6  7  8  9
+
+     These indices might be sparse, but presumably we don't expect to store
+     very many intersections so this shouldn't give much overhead.
+
+     After calculating the cache index, we look it up in the cache (possibly
+     reallocating to ensure it's large enough). If the index is in the cache,
+     we can just return it as-is, otherwise we need to do a bit more work.
+
+     First, we need to fully compute the intersection of the two regions. We
+     then check if this corresponds to an existing region. If so, we cache the
+     ID of that region and return it. Otherwise, we need to store this new
+     region in `region3D` -- the index in this vector is the ID we need to
+     cache and return here.
+   */
+  const size_t pos = (high * (high - 1)) / 2 + low;
+  if (region3Dintersect.size() <= pos) {
+    BOUT_OMP(critical(mesh_intersection_realloc))
+    // By default this function does not need the mutex, however, if we are
+    // going to allocate global memory, we need to use a mutex.
+    // Now that we have the mutex, we need to check again whether a
+    // different thread was faster and already allocated.
+    // BOUT_OMP(single) would work in most cases, but it would fail if the
+    // function is called in parallel with different arguments. While BOUT++
+    // is not currently doing it, other openmp parallised projects might be
+    // calling BOUT++ in this way.
+#if BOUT_USE_OPENMP
+    if (region3Dintersect.size() <= pos)
+#endif
+    {
+      region3Dintersect.resize(pos + 1, std::nullopt);
+    }
+  }
+  if (region3Dintersect[pos].has_value()) {
+    return region3Dintersect[pos];
+  }
+  {
+    BOUT_OMP(critical(mesh_intersection))
+    // See comment above why we need to check again in case of OpenMP
+#if BOUT_USE_OPENMP
+    if (!region3Dintersect[pos].has_value())
+#endif
+    {
+      auto common = intersection(region3D[low], region3D[high]);
+      for (size_t i = 0; i < region3D.size(); ++i) {
+        if (common == region3D[i]) {
+          region3Dintersect[pos] = i;
+          break;
+        }
+      }
+      if (!region3Dintersect[pos].has_value()) {
+        region3Dintersect[pos] = region3D.size();
+        region3D.push_back(common);
+      }
+    }
+  }
+  return region3Dintersect[pos];
+}
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 6ac2e3533f..bc8f3a54db 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -212,20 +212,8 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
     const BoutReal dR_dx = 0.5 * (R[i.xp()] - R[i.xm()]);
     const BoutReal dZ_dx = 0.5 * (Z[i.xp()] - Z[i.xm()]);
 
-    BoutReal dR_dz, dZ_dz;
-    // Handle the edge cases in Z
-    if (z == 0) {
-      dR_dz = R[i_zp] - R[i];
-      dZ_dz = Z[i_zp] - Z[i];
-
-    } else if (z == map_mesh.LocalNz - 1) {
-      dR_dz = R[i] - R[i_zm];
-      dZ_dz = Z[i] - Z[i_zm];
-
-    } else {
-      dR_dz = 0.5 * (R[i_zp] - R[i_zm]);
-      dZ_dz = 0.5 * (Z[i_zp] - Z[i_zm]);
-    }
+    const BoutReal dR_dz = 0.5 * (R[i_zp] - R[i_zm]);
+    const BoutReal dZ_dz = 0.5 * (Z[i_zp] - Z[i_zm]);
 
     const BoutReal det = dR_dx * dZ_dz - dR_dz * dZ_dx; // Determinant of 2x2 matrix
 
@@ -238,7 +226,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
 
     // Negative xt_prime means we've hit the inner boundary, otherwise
     // the outer boundary
-    auto* boundary = (xt_prime[i] < 0.0) ? inner_boundary : outer_boundary;
+    auto* boundary = (xt_prime[i] < map_mesh.xstart) ? inner_boundary : outer_boundary;
     boundary->add_point(x, y, z, x + dx, y + 0.5 * offset,
                         z + dz,      // Intersection point in local index space
                         0.5 * dy[i], // Distance to intersection
@@ -247,6 +235,8 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options,
   }
   region_no_boundary = region_no_boundary.mask(to_remove);
 
+  interp->setRegion(region_no_boundary);
+
   const auto region = fmt::format("RGN_YPAR_{:+d}", offset);
   if (not map_mesh.hasRegion3D(region)) {
     // The valid region for this slice
@@ -275,8 +265,6 @@ Field3D FCIMap::integrate(Field3D& f) const {
   result = BoutNaN;
 #endif
 
-  int nz = map_mesh.LocalNz;
-
   BOUT_FOR(i, region_no_boundary) {
     const auto inext = i.yp(offset);
     BoutReal f_c = centre[inext];
@@ -337,6 +325,7 @@ void FCITransform::calcParallelSlices(Field3D& f) {
   // Interpolate f onto yup and ydown fields
   for (const auto& map : field_line_maps) {
     f.ynext(map.offset) = map.interpolate(f);
+    f.ynext(map.offset).setRegion(fmt::format("RGN_YPAR_{:+d}", map.offset));
   }
 }
 
diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx
index 6d7c3d14e2..a749c084cc 100644
--- a/src/mesh/parallel/fci.hxx
+++ b/src/mesh/parallel/fci.hxx
@@ -127,7 +127,7 @@ public:
   bool canToFromFieldAligned() const override { return false; }
 
   bool requiresTwistShift(bool UNUSED(twist_shift_enabled),
-                          MAYBE_UNUSED(YDirectionType ytype)) override {
+                          [[maybe_unused]] YDirectionType ytype) override {
     // No Field3Ds require twist-shift, because they cannot be field-aligned
     ASSERT1(ytype == YDirectionType::Standard);
 
diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx
index cac4bda5cc..9f538895ed 100644
--- a/src/physics/physicsmodel.cxx
+++ b/src/physics/physicsmodel.cxx
@@ -58,35 +58,25 @@ void DataFileFacade::add(Vector3D* value, const std::string& name, bool save_rep
   add(value->y, name_prefix + "y"s, save_repeat);
   add(value->z, name_prefix + "z"s, save_repeat);
 }
-
-bool DataFileFacade::write() {
-  for (const auto& item : data) {
-    bout::utils::visit(bout::OptionsConversionVisitor{Options::root(), item.name},
-                       item.value);
-    if (item.repeat) {
-      Options::root()[item.name].attributes["time_dimension"] = "t";
-    }
-  }
-  writeDefaultOutputFile();
-  return true;
-}
 } // namespace bout
 
 PhysicsModel::PhysicsModel()
-    : mesh(bout::globals::mesh),
-      output_file(bout::getOutputFilename(Options::root()),
-                  Options::root()["append"]
-                          .doc("Add output data to existing (dump) files?")
-                          .withDefault(false)
-                      ? bout::OptionsNetCDF::FileMode::append
-                      : bout::OptionsNetCDF::FileMode::replace),
-      output_enabled(Options::root()["output"]["enabled"]
-                         .doc("Write output files")
-                         .withDefault(true)),
-      restart_file(bout::getRestartFilename(Options::root())),
+    : mesh(bout::globals::mesh), output_enabled(Options::root()["output"]["enabled"]
+                                                    .doc("Write output files")
+                                                    .withDefault(true)),
       restart_enabled(Options::root()["restart_files"]["enabled"]
                           .doc("Write restart files")
-                          .withDefault(true)) {}
+                          .withDefault(true))
+
+{
+  if (output_enabled) {
+    output_file = bout::OptionsIOFactory::getInstance().createOutput();
+  }
+
+  if (restart_enabled) {
+    restart_file = bout::OptionsIOFactory::getInstance().createRestart();
+  }
+}
 
 void PhysicsModel::initialise(Solver* s) {
   if (initialised) {
@@ -104,7 +94,7 @@ void PhysicsModel::initialise(Solver* s) {
   const bool restarting = Options::root()["restart"].withDefault(false);
 
   if (restarting) {
-    restart_options = restart_file.read();
+    restart_options = restart_file->read();
   }
 
   // Call user init code to specify evolving variables
@@ -187,7 +177,7 @@ int PhysicsModel::postInit(bool restarting) {
     restart_options["BOUT_VERSION"].force(bout::version::as_double, "PhysicsModel");
 
     // Write _everything_ to restart file
-    restart_file.write(restart_options);
+    restart_file->write(restart_options);
   }
 
   // Add monitor to the solver which calls restart.write() and
@@ -219,7 +209,7 @@ void PhysicsModel::restartVars(Options& options) {
 
 void PhysicsModel::writeRestartFile() {
   if (restart_enabled) {
-    restart_file.write(restart_options);
+    restart_file->write(restart_options);
   }
 }
 
@@ -227,20 +217,20 @@ void PhysicsModel::writeOutputFile() { writeOutputFile(output_options); }
 
 void PhysicsModel::writeOutputFile(const Options& options) {
   if (output_enabled) {
-    output_file.write(options, "t");
+    output_file->write(options, "t");
   }
 }
 
 void PhysicsModel::writeOutputFile(const Options& options,
                                    const std::string& time_dimension) {
   if (output_enabled) {
-    output_file.write(options, time_dimension);
+    output_file->write(options, time_dimension);
   }
 }
 
 void PhysicsModel::finishOutputTimestep() const {
   if (output_enabled) {
-    output_file.verifyTimesteps();
+    output_file->verifyTimesteps();
   }
 }
 
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 13e0dd817e..9691f2f7da 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -161,7 +161,7 @@ constexpr auto& ARKStepSetUserData = ARKodeSetUserData;
 
 #if SUNDIALS_VERSION_MAJOR < 6
 void* ARKStepCreate(ARKRhsFn fe, ARKRhsFn fi, BoutReal t0, N_Vector y0,
-                    MAYBE_UNUSED(SUNContext context)) {
+                    [[maybe_unused]] SUNContext context) {
   return ARKStepCreate(fe, fi, t0, y0);
 }
 #endif
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 70eb3b8841..f35ae680d5 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -112,7 +112,8 @@ constexpr auto CV_NEWTON = 0;
 #endif
 
 #if SUNDIALS_VERSION_MAJOR >= 3
-void* CVodeCreate(int lmm, MAYBE_UNUSED(int iter), MAYBE_UNUSED(SUNContext context)) {
+void* CVodeCreate(int lmm, [[maybe_unused]] int iter,
+                  [[maybe_unused]] SUNContext context) {
 #if SUNDIALS_VERSION_MAJOR == 3
   return CVodeCreate(lmm, iter);
 #elif SUNDIALS_VERSION_MAJOR == 4 || SUNDIALS_VERSION_MAJOR == 5
diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx
index b008ebf903..189a103bbe 100644
--- a/src/solver/impls/ida/ida.cxx
+++ b/src/solver/impls/ida/ida.cxx
@@ -85,7 +85,7 @@ constexpr auto& ida_pre_shim = ida_pre;
 #endif
 
 #if SUNDIALS_VERSION_MAJOR < 6
-void* IDACreate(MAYBE_UNUSED(SUNContext)) { return IDACreate(); }
+void* IDACreate([[maybe_unused]] SUNContext) { return IDACreate(); }
 #endif
 
 IdaSolver::IdaSolver(Options* opts)
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
index adafbb71c5..da62e9b8bb 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
@@ -18,9 +18,6 @@
 #include "petscmat.h"
 #include "petscsnes.h"
 
-// Redundent definition because < C++17
-constexpr int IMEXBDF2::MAX_SUPPORTED_ORDER;
-
 IMEXBDF2::IMEXBDF2(Options* opt)
     : Solver(opt), maxOrder((*options)["maxOrder"]
                                 .doc("Maximum order of the scheme (1/2/3)")
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 1b81ca36b6..7a2b2cf3de 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -29,7 +29,6 @@
 
 #if BOUT_HAS_PETSC
 
-//#include <private/tsimpl.h>
 #include <petsc.h>
 
 #include <bout/boutcomm.hxx>
@@ -750,10 +749,10 @@ PetscErrorCode solver_rhsjacobian(TS UNUSED(ts), BoutReal UNUSED(t), Vec UNUSED(
   PetscFunctionReturn(0);
 }
 #else
-PetscErrorCode solver_rhsjacobian(MAYBE_UNUSED(TS ts), MAYBE_UNUSED(BoutReal t),
-                                  MAYBE_UNUSED(Vec globalin), Mat* J, Mat* Jpre,
-                                  MAYBE_UNUSED(MatStructure* str),
-                                  MAYBE_UNUSED(void* f_data)) {
+PetscErrorCode solver_rhsjacobian([[maybe_unused]] TS ts, [[maybe_unused]] BoutReal t,
+                                  [[maybe_unused]] Vec globalin, Mat* J, Mat* Jpre,
+                                  [[maybe_unused]] MatStructure* str,
+                                  [[maybe_unused]] void* f_data) {
   PetscErrorCode ierr;
 
   PetscFunctionBegin;
@@ -798,8 +797,9 @@ PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin, Vec UNUSED(glob
 }
 #else
 PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin,
-                                MAYBE_UNUSED(Vec globalindot), MAYBE_UNUSED(PetscReal a),
-                                Mat* J, Mat* Jpre, MatStructure* str, void* f_data) {
+                                [[maybe_unused]] Vec globalindot,
+                                [[maybe_unused]] PetscReal a, Mat* J, Mat* Jpre,
+                                MatStructure* str, void* f_data) {
   PetscErrorCode ierr;
 
   PetscFunctionBegin;
diff --git a/src/solver/impls/rkgeneric/rkscheme.cxx b/src/solver/impls/rkgeneric/rkscheme.cxx
index 740adec909..25de364533 100644
--- a/src/solver/impls/rkgeneric/rkscheme.cxx
+++ b/src/solver/impls/rkgeneric/rkscheme.cxx
@@ -308,8 +308,3 @@ void RKScheme::zeroSteps() {
     }
   }
 }
-
-constexpr decltype(RKSchemeFactory::type_name) RKSchemeFactory::type_name;
-constexpr decltype(RKSchemeFactory::section_name) RKSchemeFactory::section_name;
-constexpr decltype(RKSchemeFactory::option_name) RKSchemeFactory::option_name;
-constexpr decltype(RKSchemeFactory::default_type) RKSchemeFactory::default_type;
diff --git a/src/solver/impls/slepc/slepc.cxx b/src/solver/impls/slepc/slepc.cxx
index f90afe717e..8cbb002d11 100644
--- a/src/solver/impls/slepc/slepc.cxx
+++ b/src/solver/impls/slepc/slepc.cxx
@@ -572,7 +572,7 @@ void SlepcSolver::monitor(PetscInt its, PetscInt nconv, PetscScalar eigr[],
   static int nConvPrev = 0;
 
   // Disable floating-point exceptions for the duration of this function
-  MAYBE_UNUSED(QuietFPE quiet_fpe{});
+  [[maybe_unused]] QuietFPE quiet_fpe{};
 
   // No output until after first iteration
   if (its < 1) {
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 9dd31f011e..02e6ec6d04 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1498,7 +1498,7 @@ void Solver::post_rhs(BoutReal UNUSED(t)) {
   }
 
   // Make sure 3D fields are at the correct cell location, etc.
-  for (MAYBE_UNUSED(const auto& f) : f3d) {
+  for ([[maybe_unused]] const auto& f : f3d) {
     ASSERT1_FIELDS_COMPATIBLE(*f.var, *f.F_var);
   }
 
@@ -1571,8 +1571,3 @@ void Solver::calculate_mms_error(BoutReal t) {
     *(f.MMS_err) = *(f.var) - solution;
   }
 }
-
-constexpr decltype(SolverFactory::type_name) SolverFactory::type_name;
-constexpr decltype(SolverFactory::section_name) SolverFactory::section_name;
-constexpr decltype(SolverFactory::option_name) SolverFactory::option_name;
-constexpr decltype(SolverFactory::default_type) SolverFactory::default_type;
diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx
new file mode 100644
index 0000000000..c7d6dab9aa
--- /dev/null
+++ b/src/sys/adios_object.cxx
@@ -0,0 +1,98 @@
+#include "bout/build_config.hxx"
+
+#if BOUT_HAS_ADIOS
+
+#include "bout/adios_object.hxx"
+#include "bout/boutexception.hxx"
+
+#include <exception>
+#include <iostream>
+#include <unordered_map>
+
+namespace bout {
+
+static ADIOSPtr adios = nullptr;
+static std::unordered_map<std::string, ADIOSStream> adiosStreams;
+
+void ADIOSInit(MPI_Comm comm) { adios = std::make_shared<adios2::ADIOS>(comm); }
+
+void ADIOSInit(const std::string configFile, MPI_Comm comm) {
+  adios = std::make_shared<adios2::ADIOS>(configFile, comm);
+}
+
+void ADIOSFinalize() {
+  if (adios == nullptr) {
+    throw BoutException(
+        "ADIOS needs to be initialized first before calling ADIOSFinalize()");
+  }
+  adiosStreams.clear();
+  adios.reset();
+}
+
+ADIOSPtr GetADIOSPtr() {
+  if (adios == nullptr) {
+    throw BoutException(
+        "ADIOS needs to be initialized first before calling GetADIOSPtr()");
+  }
+  return adios;
+}
+
+IOPtr GetIOPtr(const std::string IOName) {
+  auto adios = GetADIOSPtr();
+  IOPtr io = nullptr;
+  try {
+    io = std::make_shared<adios2::IO>(adios->AtIO(IOName));
+  } catch (std::invalid_argument& e) {
+  }
+  return io;
+}
+
+ADIOSStream::~ADIOSStream() {
+  if (engine) {
+    if (isInStep) {
+      engine.EndStep();
+      isInStep = false;
+    }
+    engine.Close();
+  }
+}
+
+ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname) {
+  auto it = adiosStreams.find(fname);
+  if (it == adiosStreams.end()) {
+    it = adiosStreams.emplace(fname, ADIOSStream(fname)).first;
+  }
+  return it->second;
+}
+
+void ADIOSSetParameters(const std::string& input, const char delimKeyValue,
+                        const char delimItem, adios2::IO& io) {
+  auto lf_Trim = [](std::string& input) {
+    input.erase(0, input.find_first_not_of(" \n\r\t")); // prefixing spaces
+    input.erase(input.find_last_not_of(" \n\r\t") + 1); // suffixing spaces
+  };
+
+  std::istringstream inputSS(input);
+  std::string parameter;
+  while (std::getline(inputSS, parameter, delimItem)) {
+    const size_t position = parameter.find(delimKeyValue);
+    if (position == parameter.npos) {
+      throw BoutException("ADIOSSetParameters(): wrong format for IO parameter "
+                          + parameter + ", format must be key" + delimKeyValue
+                          + "value for each entry");
+    }
+
+    std::string key = parameter.substr(0, position);
+    lf_Trim(key);
+    std::string value = parameter.substr(position + 1);
+    lf_Trim(value);
+    if (value.length() == 0) {
+      throw BoutException("ADIOS2SetParameters: empty value in IO parameter " + parameter
+                          + ", format must be key" + delimKeyValue + "value");
+    }
+    io.SetParameter(key, value);
+  }
+}
+
+} // namespace bout
+#endif //BOUT_HAS_ADIOS
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index 7f629cfbb5..ee9bcbcc2c 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -331,8 +331,8 @@ Field3D D2DXDY(const Field3D& f, CELL_LOC outloc, const std::string& method,
 }
 
 Coordinates::FieldMetric D2DXDZ(const Field2D& f, CELL_LOC outloc,
-                                MAYBE_UNUSED(const std::string& method),
-                                MAYBE_UNUSED(const std::string& region)) {
+                                [[maybe_unused]] const std::string& method,
+                                [[maybe_unused]] const std::string& region) {
 #if BOUT_USE_METRIC_3D
   Field3D tmp{f};
   return D2DXDZ(tmp, outloc, method, region);
@@ -356,8 +356,8 @@ Field3D D2DXDZ(const Field3D& f, CELL_LOC outloc, const std::string& method,
 }
 
 Coordinates::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc,
-                                MAYBE_UNUSED(const std::string& method),
-                                MAYBE_UNUSED(const std::string& region)) {
+                                [[maybe_unused]] const std::string& method,
+                                [[maybe_unused]] const std::string& region) {
 #if BOUT_USE_METRIC_3D
   Field3D tmp{f};
   return D2DYDZ(tmp, outloc, method, region);
@@ -369,8 +369,8 @@ Coordinates::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc,
 #endif
 }
 
-Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc, MAYBE_UNUSED(const std::string& method),
-               const std::string& region) {
+Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc,
+               [[maybe_unused]] const std::string& method, const std::string& region) {
   // If staggering in z, take y-derivative at f's location.
   const auto y_location =
       (outloc == CELL_ZLOW or f.getLocation() == CELL_ZLOW) ? CELL_DEFAULT : outloc;
@@ -426,9 +426,9 @@ Coordinates::FieldMetric VDDZ(const Field2D& v, const Field2D& f, CELL_LOC outlo
 }
 
 // Note that this is zero because no compression is included
-Coordinates::FieldMetric VDDZ(MAYBE_UNUSED(const Field3D& v), const Field2D& f,
-                              CELL_LOC outloc, MAYBE_UNUSED(const std::string& method),
-                              MAYBE_UNUSED(const std::string& region)) {
+Coordinates::FieldMetric VDDZ([[maybe_unused]] const Field3D& v, const Field2D& f,
+                              CELL_LOC outloc, [[maybe_unused]] const std::string& method,
+                              [[maybe_unused]] const std::string& region) {
 #if BOUT_USE_METRIC_3D
   Field3D tmp{f};
   return bout::derivatives::index::VDDZ(v, tmp, outloc, method, region)
diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx
index 39f8d3bb71..8290a4cae0 100644
--- a/src/sys/expressionparser.cxx
+++ b/src/sys/expressionparser.cxx
@@ -184,10 +184,29 @@ FieldGeneratorPtr FieldBinary::clone(const list<FieldGeneratorPtr> args) {
   return std::make_shared<FieldBinary>(args.front(), args.back(), op);
 }
 
+/// Convert a real value to a Boolean
+/// Throw exception if `rval` isn't close to 0 or 1
+bool toBool(BoutReal rval) {
+  int ival = ROUND(rval);
+  if ((fabs(rval - static_cast<BoutReal>(ival)) > 1e-3) or (ival < 0) or (ival > 1)) {
+    throw BoutException(_("Boolean operator argument {:e} is not a bool"), rval);
+  }
+  return ival == 1;
+}
+
 BoutReal FieldBinary::generate(const Context& ctx) {
   BoutReal lval = lhs->generate(ctx);
   BoutReal rval = rhs->generate(ctx);
+
   switch (op) {
+  case '|': // Logical OR
+    return (toBool(lval) or toBool(rval)) ? 1.0 : 0.0;
+  case '&': // Logical AND
+    return (toBool(lval) and toBool(rval)) ? 1.0 : 0.0;
+  case '>': // Comparison
+    return (lval > rval) ? 1.0 : 0.0;
+  case '<':
+    return (lval < rval) ? 1.0 : 0.0;
   case '+':
     return lval + rval;
   case '-':
@@ -203,10 +222,30 @@ BoutReal FieldBinary::generate(const Context& ctx) {
   throw ParseException("Unknown binary operator '{:c}'", op);
 }
 
+class LogicalNot : public FieldGenerator {
+public:
+  /// Logically negate a boolean expression
+  LogicalNot(FieldGeneratorPtr expr) : expr(expr) {}
+
+  /// Evaluate expression, check it's a bool, and return 1 or 0
+  double generate(const Context& ctx) override {
+    return toBool(expr->generate(ctx)) ? 0.0 : 1.0;
+  }
+
+  std::string str() const override { return "!"s + expr->str(); }
+
+private:
+  FieldGeneratorPtr expr;
+};
+
 /////////////////////////////////////////////
 
 ExpressionParser::ExpressionParser() {
   // Add standard binary operations
+  addBinaryOp('|', std::make_shared<FieldBinary>(nullptr, nullptr, '|'), 3);
+  addBinaryOp('&', std::make_shared<FieldBinary>(nullptr, nullptr, '&'), 5);
+  addBinaryOp('<', std::make_shared<FieldBinary>(nullptr, nullptr, '<'), 7);
+  addBinaryOp('>', std::make_shared<FieldBinary>(nullptr, nullptr, '>'), 7);
   addBinaryOp('+', std::make_shared<FieldBinary>(nullptr, nullptr, '+'), 10);
   addBinaryOp('-', std::make_shared<FieldBinary>(nullptr, nullptr, '-'), 10);
   addBinaryOp('*', std::make_shared<FieldBinary>(nullptr, nullptr, '*'), 20);
@@ -482,6 +521,11 @@ FieldGeneratorPtr ExpressionParser::parsePrimary(LexInfo& lex) const {
     // Don't eat the minus, and return an implicit zero
     return std::make_shared<FieldValue>(0.0);
   }
+  case '!': {
+    // Logical not
+    lex.nextToken(); // Eat '!'
+    return std::make_shared<LogicalNot>(parsePrimary(lex));
+  }
   case '(': {
     return parseParenExpr(lex);
   }
diff --git a/src/sys/hyprelib.cxx b/src/sys/hyprelib.cxx
index e833162726..691e53230f 100644
--- a/src/sys/hyprelib.cxx
+++ b/src/sys/hyprelib.cxx
@@ -39,7 +39,7 @@ HypreLib::HypreLib() {
   }
 }
 
-HypreLib::HypreLib(MAYBE_UNUSED() const HypreLib& other) noexcept {
+HypreLib::HypreLib([[maybe_unused]] const HypreLib& other) noexcept {
   BOUT_OMP(critical(HypreLib))
   {
     // No need to initialise Hypre, because it must already be initialised
@@ -47,7 +47,7 @@ HypreLib::HypreLib(MAYBE_UNUSED() const HypreLib& other) noexcept {
   }
 }
 
-HypreLib::HypreLib(MAYBE_UNUSED() HypreLib&& other) noexcept {
+HypreLib::HypreLib([[maybe_unused]] HypreLib&& other) noexcept {
   BOUT_OMP(critical(HypreLib))
   {
     // No need to initialise Hypre, because it must already be initialised
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 8b49b1f3f1..14d9e47d91 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -1,14 +1,34 @@
-#include <bout/boutexception.hxx>
-#include <bout/field_factory.hxx> // Used for parsing expressions
-#include <bout/options.hxx>
-#include <bout/output.hxx>
-#include <bout/utils.hxx>
-
+#include "bout/options.hxx"
+
+#include "bout/array.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/field_factory.hxx" // Used for parsing expressions
+#include "bout/fieldperp.hxx"
+#include "bout/output.hxx"
+#include "bout/sys/expressionparser.hxx"
+#include "bout/sys/gettext.hxx"
+#include "bout/sys/type_name.hxx"
+#include "bout/sys/variant.hxx"
+#include "bout/traits.hxx"
+#include "bout/unused.hxx"
+#include "bout/utils.hxx"
+
+#include <fmt/core.h>
 #include <fmt/format.h>
 
 #include <algorithm>
-#include <iomanip>
-#include <sstream>
+#include <cmath>
+#include <initializer_list>
+#include <iterator>
+#include <map>
+#include <set>
+#include <string>
+#include <tuple>
+#include <utility>
+#include <vector>
 
 /// The source label given to default values
 const std::string Options::DEFAULT_SOURCE{_("default")};
@@ -19,23 +39,12 @@ std::string Options::getDefaultSource() { return DEFAULT_SOURCE; }
 /// having been used
 constexpr auto conditionally_used_attribute = "conditionally used";
 
-Options* Options::root_instance{nullptr};
-
 Options& Options::root() {
-  if (root_instance == nullptr) {
-    // Create the singleton
-    root_instance = new Options();
-  }
-  return *root_instance;
+  static Options root_instance;
+  return root_instance;
 }
 
-void Options::cleanup() {
-  if (root_instance == nullptr) {
-    return;
-  }
-  delete root_instance;
-  root_instance = nullptr;
-}
+void Options::cleanup() { root() = Options{}; }
 
 Options::Options(const Options& other)
     : value(other.value), attributes(other.attributes),
@@ -50,6 +59,19 @@ Options::Options(const Options& other)
   }
 }
 
+Options::Options(Options&& other) noexcept
+    : value(std::move(other.value)), attributes(std::move(other.attributes)),
+      parent_instance(other.parent_instance), full_name(std::move(other.full_name)),
+      is_section(other.is_section), children(std::move(other.children)),
+      value_used(other.value_used) {
+
+  // Ensure that this is the parent of all children,
+  // otherwise will point to the original Options instance
+  for (auto& child : children) {
+    child.second.parent_instance = this;
+  }
+}
+
 template <>
 Options::Options(const char* value) {
   assign<std::string>(value);
@@ -80,7 +102,7 @@ Options::Options(std::initializer_list<std::pair<std::string, Options>> values)
     append_impl(children, section_name, append_impl);
   };
 
-  for (auto& value : values) {
+  for (const auto& value : values) {
     (*this)[value.first] = value.second;
     // value.second was constructed from the "bare" `Options<T>(T)` so
     // doesn't have `full_name` set. This clobbers
@@ -107,15 +129,15 @@ Options& Options::operator[](const std::string& name) {
   }
 
   // If name is compound, e.g. "section:subsection", then split the name
-  auto subsection_split = name.find(":");
+  auto subsection_split = name.find(':');
   if (subsection_split != std::string::npos) {
     return (*this)[name.substr(0, subsection_split)][name.substr(subsection_split + 1)];
   }
 
   // Find and return if already exists
-  auto it = children.find(name);
-  if (it != children.end()) {
-    return it->second;
+  auto child = children.find(name);
+  if (child != children.end()) {
+    return child->second;
   }
 
   // Doesn't exist yet, so add
@@ -146,19 +168,19 @@ const Options& Options::operator[](const std::string& name) const {
   }
 
   // If name is compound, e.g. "section:subsection", then split the name
-  auto subsection_split = name.find(":");
+  auto subsection_split = name.find(':');
   if (subsection_split != std::string::npos) {
     return (*this)[name.substr(0, subsection_split)][name.substr(subsection_split + 1)];
   }
 
   // Find and return if already exists
-  auto it = children.find(name);
-  if (it == children.end()) {
+  auto child = children.find(name);
+  if (child == children.end()) {
     // Doesn't exist
     throw BoutException(_("Option {:s}:{:s} does not exist"), full_name, name);
   }
 
-  return it->second;
+  return child->second;
 }
 
 std::multiset<Options::FuzzyMatch>
@@ -209,6 +231,10 @@ Options::fuzzyFind(const std::string& name, std::string::size_type distance) con
 }
 
 Options& Options::operator=(const Options& other) {
+  if (this == &other) {
+    return *this;
+  }
+
   // Note: Here can't do copy-and-swap because pointers to parents are stored
 
   value = other.value;
@@ -232,6 +258,28 @@ Options& Options::operator=(const Options& other) {
   return *this;
 }
 
+Options& Options::operator=(Options&& other) noexcept {
+  if (this == &other) {
+    return *this;
+  }
+
+  // Note: Here can't do copy-and-swap because pointers to parents are stored
+
+  value = std::move(other.value);
+  attributes = std::move(other.attributes);
+  full_name = std::move(other.full_name);
+  is_section = other.is_section;
+  children = std::move(other.children);
+  value_used = other.value_used;
+
+  // Ensure that this is the parent of all children,
+  // otherwise will point to the original Options instance
+  for (auto& child : children) {
+    child.second.parent_instance = this;
+  }
+  return *this;
+}
+
 bool Options::isSet() const {
   // Only values can be set/unset
   if (is_section) {
@@ -247,18 +295,17 @@ bool Options::isSet() const {
 }
 
 bool Options::isSection(const std::string& name) const {
-  if (name == "") {
+  if (name.empty()) {
     // Test this object
     return is_section;
   }
 
   // Is there a child section?
-  auto it = children.find(name);
-  if (it == children.end()) {
+  const auto child = children.find(name);
+  if (child == children.end()) {
     return false;
-  } else {
-    return it->second.isSection();
   }
+  return child->second.isSection();
 }
 
 template <>
@@ -296,27 +343,6 @@ void Options::assign<>(Tensor<BoutReal> val, std::string source) {
   _set_no_check(std::move(val), std::move(source));
 }
 
-template <>
-std::string Options::as<std::string>(const std::string& UNUSED(similar_to)) const {
-  if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
-  }
-
-  // Mark this option as used
-  value_used = true;
-
-  std::string result = bout::utils::variantToString(value);
-
-  output_info << _("\tOption ") << full_name << " = " << result;
-  if (attributes.count("source")) {
-    // Specify the source of the setting
-    output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
-  }
-  output_info << endl;
-
-  return result;
-}
-
 namespace {
 /// Use FieldFactory to evaluate expression
 double parseExpression(const Options::ValueType& value, const Options* options,
@@ -336,22 +362,50 @@ double parseExpression(const Options::ValueType& value, const Options* options,
                         full_name, bout::utils::variantToString(value), error.what());
   }
 }
+
+/// Helper function to print `key = value` with optional source
+template <class T>
+void printNameValueSourceLine(const Options& option, const T& value) {
+  output_info.write(_("\tOption {} = {}"), option.str(), value);
+  if (option.hasAttribute("source")) {
+    // Specify the source of the setting
+    output_info.write(" ({})",
+                      bout::utils::variantToString(option.attributes.at("source")));
+  }
+  output_info.write("\n");
+}
 } // namespace
 
+template <>
+std::string Options::as<std::string>(const std::string& UNUSED(similar_to)) const {
+  if (is_section) {
+    throw BoutException(_("Option {:s} has no value"), full_name);
+  }
+
+  // Mark this option as used
+  value_used = true;
+
+  std::string result = bout::utils::variantToString(value);
+
+  printNameValueSourceLine(*this, result);
+
+  return result;
+}
+
 template <>
 int Options::as<int>(const int& UNUSED(similar_to)) const {
   if (is_section) {
     throw BoutException(_("Option {:s} has no value"), full_name);
   }
 
-  int result;
+  int result = 0;
 
   if (bout::utils::holds_alternative<int>(value)) {
     result = bout::utils::get<int>(value);
 
   } else {
     // Cases which get a BoutReal then check if close to an integer
-    BoutReal rval;
+    BoutReal rval = BoutNaN;
 
     if (bout::utils::holds_alternative<BoutReal>(value)) {
       rval = bout::utils::get<BoutReal>(value);
@@ -376,12 +430,7 @@ int Options::as<int>(const int& UNUSED(similar_to)) const {
 
   value_used = true;
 
-  output_info << _("\tOption ") << full_name << " = " << result;
-  if (attributes.count("source")) {
-    // Specify the source of the setting
-    output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
-  }
-  output_info << endl;
+  printNameValueSourceLine(*this, result);
 
   return result;
 }
@@ -392,7 +441,7 @@ BoutReal Options::as<BoutReal>(const BoutReal& UNUSED(similar_to)) const {
     throw BoutException(_("Option {:s} has no value"), full_name);
   }
 
-  BoutReal result;
+  BoutReal result = BoutNaN;
 
   if (bout::utils::holds_alternative<int>(value)) {
     result = static_cast<BoutReal>(bout::utils::get<int>(value));
@@ -411,12 +460,7 @@ BoutReal Options::as<BoutReal>(const BoutReal& UNUSED(similar_to)) const {
   // Mark this option as used
   value_used = true;
 
-  output_info << _("\tOption ") << full_name << " = " << result;
-  if (attributes.count("source")) {
-    // Specify the source of the setting
-    output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
-  }
-  output_info << endl;
+  printNameValueSourceLine(*this, result);
 
   return result;
 }
@@ -427,25 +471,22 @@ bool Options::as<bool>(const bool& UNUSED(similar_to)) const {
     throw BoutException(_("Option {:s} has no value"), full_name);
   }
 
-  bool result;
+  bool result = false;
 
   if (bout::utils::holds_alternative<bool>(value)) {
     result = bout::utils::get<bool>(value);
 
   } else if (bout::utils::holds_alternative<std::string>(value)) {
-    // case-insensitve check, so convert string to lower case
-    const auto strvalue = lowercase(bout::utils::get<std::string>(value));
-
-    if ((strvalue == "y") or (strvalue == "yes") or (strvalue == "t")
-        or (strvalue == "true") or (strvalue == "1")) {
-      result = true;
-    } else if ((strvalue == "n") or (strvalue == "no") or (strvalue == "f")
-               or (strvalue == "false") or (strvalue == "0")) {
-      result = false;
-    } else {
-      throw BoutException(_("\tOption '{:s}': Boolean expected. Got '{:s}'\n"), full_name,
-                          strvalue);
+    // Parse as floating point because that's the only type the parser understands
+    const BoutReal rval = parseExpression(value, this, "bool", full_name);
+
+    // Check that the result is either close to 1 (true) or close to 0 (false)
+    const int ival = ROUND(rval);
+    if ((fabs(rval - static_cast<BoutReal>(ival)) > 1e-3) or (ival < 0) or (ival > 1)) {
+      throw BoutException(_("Value for option {:s} = {:e} is not a bool"), full_name,
+                          rval);
     }
+    result = ival == 1;
   } else {
     throw BoutException(_("Value for option {:s} cannot be converted to a bool"),
                         full_name);
@@ -453,13 +494,7 @@ bool Options::as<bool>(const bool& UNUSED(similar_to)) const {
 
   value_used = true;
 
-  output_info << _("\tOption ") << full_name << " = " << toString(result);
-
-  if (attributes.count("source")) {
-    // Specify the source of the setting
-    output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
-  }
-  output_info << endl;
+  printNameValueSourceLine(*this, toString(result));
 
   return result;
 }
@@ -493,7 +528,7 @@ Field3D Options::as<Field3D>(const Field3D& similar_to) const {
 
   if (bout::utils::holds_alternative<BoutReal>(value)
       or bout::utils::holds_alternative<int>(value)) {
-    BoutReal scalar_value =
+    const BoutReal scalar_value =
         bout::utils::variantStaticCastOrThrow<ValueType, BoutReal>(value);
 
     // Get metadata from similar_to, fill field with scalar_value
@@ -549,7 +584,7 @@ Field2D Options::as<Field2D>(const Field2D& similar_to) const {
 
   if (bout::utils::holds_alternative<BoutReal>(value)
       or bout::utils::holds_alternative<int>(value)) {
-    BoutReal scalar_value =
+    const BoutReal scalar_value =
         bout::utils::variantStaticCastOrThrow<ValueType, BoutReal>(value);
 
     // Get metadata from similar_to, fill field with scalar_value
@@ -601,7 +636,7 @@ FieldPerp Options::as<FieldPerp>(const FieldPerp& similar_to) const {
 
   if (bout::utils::holds_alternative<BoutReal>(value)
       or bout::utils::holds_alternative<int>(value)) {
-    BoutReal scalar_value =
+    const BoutReal scalar_value =
         bout::utils::variantStaticCastOrThrow<ValueType, BoutReal>(value);
 
     // Get metadata from similar_to, fill field with scalar_value
@@ -686,7 +721,7 @@ struct ConvertContainer {
   Container operator()(const Container& value) { return value; }
 
   template <class Other>
-  Container operator()(MAYBE_UNUSED(const Other& value)) {
+  Container operator()([[maybe_unused]] const Other& value) {
     throw BoutException(error_message);
   }
 
@@ -713,12 +748,7 @@ Array<BoutReal> Options::as<Array<BoutReal>>(const Array<BoutReal>& similar_to)
   // Mark this option as used
   value_used = true;
 
-  output_info << _("\tOption ") << full_name << " = Array<BoutReal>";
-  if (hasAttribute("source")) {
-    // Specify the source of the setting
-    output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
-  }
-  output_info << endl;
+  printNameValueSourceLine(*this, "Array<BoutReal>");
 
   return result;
 }
@@ -740,12 +770,7 @@ Matrix<BoutReal> Options::as<Matrix<BoutReal>>(const Matrix<BoutReal>& similar_t
   // Mark this option as used
   value_used = true;
 
-  output_info << _("\tOption ") << full_name << " = Matrix<BoutReal>";
-  if (hasAttribute("source")) {
-    // Specify the source of the setting
-    output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
-  }
-  output_info << endl;
+  printNameValueSourceLine(*this, "Matrix<BoutReal>");
 
   return result;
 }
@@ -767,12 +792,7 @@ Tensor<BoutReal> Options::as<Tensor<BoutReal>>(const Tensor<BoutReal>& similar_t
   // Mark this option as used
   value_used = true;
 
-  output_info << _("\tOption ") << full_name << " = Tensor<BoutReal>";
-  if (hasAttribute("source")) {
-    // Specify the source of the setting
-    output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
-  }
-  output_info << endl;
+  printNameValueSourceLine(*this, "Tensor<BoutReal>");
 
   return result;
 }
@@ -858,7 +878,7 @@ Options Options::getUnused(const std::vector<std::string>& exclude_sources) cons
 }
 
 void Options::printUnused() const {
-  Options unused = getUnused();
+  const Options unused = getUnused();
 
   // Two cases: single value, or a section.  If it's a single value,
   // we can check it directly. If it's a section, we can see if it has
@@ -882,9 +902,9 @@ void Options::cleanCache() { FieldFactory::get()->cleanCache(); }
 
 std::map<std::string, const Options*> Options::subsections() const {
   std::map<std::string, const Options*> sections;
-  for (const auto& it : children) {
-    if (it.second.is_section) {
-      sections[it.first] = &it.second;
+  for (const auto& child : children) {
+    if (child.second.is_section) {
+      sections[child.first] = &child.second;
     }
   }
   return sections;
@@ -915,8 +935,8 @@ fmt::format_parse_context::iterator
 bout::details::OptionsFormatterBase::parse(fmt::format_parse_context& ctx) {
 
   const auto* closing_brace = std::find(ctx.begin(), ctx.end(), '}');
-  std::for_each(ctx.begin(), closing_brace, [&](auto it) {
-    switch (it) {
+  std::for_each(ctx.begin(), closing_brace, [&](auto ctx_opt) {
+    switch (ctx_opt) {
     case 'd':
       docstrings = true;
       break;
@@ -1014,7 +1034,7 @@ bout::details::OptionsFormatterBase::format(const Options& options,
 
   // Only print section headers if the section has a name and it has
   // non-section children
-  const auto children = options.getChildren();
+  const auto& children = options.getChildren();
   const bool has_child_values =
       std::any_of(children.begin(), children.end(),
                   [](const auto& child) { return child.second.isValue(); });
@@ -1059,7 +1079,7 @@ void checkForUnusedOptions() {
 
 void checkForUnusedOptions(const Options& options, const std::string& data_dir,
                            const std::string& option_file) {
-  Options unused = options.getUnused();
+  const Options unused = options.getUnused();
   if (not unused.getChildren().empty()) {
 
     // Construct a string with all the fuzzy matches for each unused option
diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
new file mode 100644
index 0000000000..e93a1fea94
--- /dev/null
+++ b/src/sys/options/options_adios.cxx
@@ -0,0 +1,548 @@
+#include "bout/build_config.hxx"
+
+#if BOUT_HAS_ADIOS
+
+#include "options_adios.hxx"
+#include "bout/adios_object.hxx"
+
+#include "bout/bout.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/globals.hxx"
+#include "bout/mesh.hxx"
+#include "bout/sys/timer.hxx"
+
+#include "adios2.h"
+#include <exception>
+#include <iostream>
+#include <vector>
+
+namespace bout {
+/// Name of the attribute used to track individual variable's time indices
+constexpr auto current_time_index_name = "current_time_index";
+
+OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) {
+  if (options["file"].doc("File name. Defaults to <path>/<prefix>.pb").isSet()) {
+    filename = options["file"].as<std::string>();
+  } else {
+    // Both path and prefix must be set
+    filename = fmt::format("{}/{}.bp", options["path"].as<std::string>(),
+                           options["prefix"].as<std::string>());
+  }
+
+  file_mode = (options["append"].doc("Append to existing file?").withDefault<bool>(false))
+                  ? FileMode::append
+                  : FileMode::replace;
+
+  singleWriteFile = options["singleWriteFile"].withDefault<bool>(false);
+}
+
+template <class T>
+Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name,
+                     const std::string& type) {
+  std::vector<T> data;
+  adios2::Variable<T> variable = io.InquireVariable<T>(name);
+
+  if (variable.ShapeID() == adios2::ShapeID::GlobalValue) {
+    T value;
+    reader.Get<T>(variable, &value, adios2::Mode::Sync);
+    return Options(value);
+  }
+
+  if (variable.ShapeID() == adios2::ShapeID::LocalArray) {
+    throw std::invalid_argument(
+        "ADIOS reader did not implement reading local arrays like " + type + " " + name
+        + " in file " + reader.Name());
+  }
+
+  if (type != "double" && type != "float") {
+    throw std::invalid_argument(
+        "ADIOS reader did not implement reading arrays that are not double/float type. "
+        "Found "
+        + type + " " + name + " in file " + reader.Name());
+  }
+
+  if (type == "double" && sizeof(BoutReal) != sizeof(double)) {
+    throw std::invalid_argument(
+        "ADIOS does not allow for implicit type conversions. BoutReal type is "
+        "float but found "
+        + type + " " + name + " in file " + reader.Name());
+  }
+
+  if (type == "float" && sizeof(BoutReal) != sizeof(float)) {
+    throw std::invalid_argument(
+        "ADIOS reader does not allow for implicit type conversions. BoutReal type is "
+        "double but found "
+        + type + " " + name + " in file " + reader.Name());
+  }
+
+  auto dims = variable.Shape();
+  auto ndims = dims.size();
+  adios2::Variable<BoutReal> variableD = io.InquireVariable<BoutReal>(name);
+
+  switch (ndims) {
+  case 1: {
+    Array<BoutReal> value(static_cast<int>(dims[0]));
+    BoutReal* data = value.begin();
+    reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
+    return Options(value);
+  }
+  case 2: {
+    Matrix<BoutReal> value(static_cast<int>(dims[0]), static_cast<int>(dims[1]));
+    BoutReal* data = value.begin();
+    reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
+    return Options(value);
+  }
+  case 3: {
+    Tensor<BoutReal> value(static_cast<int>(dims[0]), static_cast<int>(dims[1]),
+                           static_cast<int>(dims[2]));
+    BoutReal* data = value.begin();
+    reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
+    return Options(value);
+  }
+  }
+  throw BoutException("ADIOS reader failed to read '{}' of dimension {} in file '{}'",
+                      name, ndims, reader.Name());
+}
+
+Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name,
+                     const std::string& type) {
+#define declare_template_instantiation(T)           \
+  if (type == adios2::GetType<T>()) {               \
+    return readVariable<T>(reader, io, name, type); \
+  }
+  ADIOS2_FOREACH_ATTRIBUTE_PRIMITIVE_STDTYPE_1ARG(declare_template_instantiation)
+  declare_template_instantiation(std::string)
+#undef declare_template_instantiation
+      output_warn.write("ADIOS readVariable can't read type '{}' (variable '{}')", type,
+                        name);
+  return Options{};
+}
+
+bool readAttribute(adios2::IO& io, const std::string& name, const std::string& type,
+                   Options& result) {
+  // Attribute is the part of 'name' after the last '/' separator
+  std::string attrname;
+  auto pos = name.find_last_of('/');
+  if (pos == std::string::npos) {
+    attrname = name;
+  } else {
+    attrname = name.substr(pos + 1);
+  }
+
+#define declare_template_instantiation(T)                  \
+  if (type == adios2::GetType<T>()) {                      \
+    adios2::Attribute<T> a = io.InquireAttribute<T>(name); \
+    result.attributes[attrname] = *a.Data().data();        \
+    return true;                                           \
+  }
+  // Only some types of attributes are supported
+  //declare_template_instantiation(bool)
+  declare_template_instantiation(int) declare_template_instantiation(BoutReal)
+      declare_template_instantiation(std::string)
+#undef declare_template_instantiation
+          output_warn.write("ADIOS readAttribute can't read type '{}' (variable '{}')",
+                            type, name);
+  return false;
+}
+
+Options OptionsADIOS::read() {
+  Timer timer("io");
+
+  // Open file
+  ADIOSPtr adiosp = GetADIOSPtr();
+  adios2::IO io;
+  std::string ioname = "read_" + filename;
+  try {
+    io = adiosp->AtIO(ioname);
+  } catch (const std::invalid_argument& e) {
+    io = adiosp->DeclareIO(ioname);
+  }
+
+  adios2::Engine reader = io.Open(filename, adios2::Mode::ReadRandomAccess);
+  if (!reader) {
+    throw BoutException("Could not open ADIOS file '{:s}' for reading", filename);
+  }
+
+  Options result;
+
+  // Iterate over all variables
+  for (const auto& varpair : io.AvailableVariables()) {
+    const auto& var_name = varpair.first; // Name of the variable
+
+    auto it = varpair.second.find("Type");
+    const std::string& var_type = it->second;
+
+    Options* varptr = &result;
+    for (const auto& piece : strsplit(var_name, '/')) {
+      varptr = &(*varptr)[piece]; // Navigate to subsection if needed
+    }
+    Options& var = *varptr;
+
+    // Note: Copying the value rather than simple assignment is used
+    // because the Options assignment operator overwrites full_name.
+    var = 0; // Setting is_section to false
+    var.value = readVariable(reader, io, var_name, var_type).value;
+    var.attributes["source"] = filename;
+
+    // Get variable attributes
+    for (const auto& attpair : io.AvailableAttributes(var_name, "/", true)) {
+      const auto& att_name = attpair.first; // Attribute name
+      const auto& att = attpair.second;     // attribute params
+
+      auto it = att.find("Type");
+      const std::string& att_type = it->second;
+      readAttribute(io, att_name, att_type, var);
+    }
+  }
+
+  reader.Close();
+
+  return result;
+}
+
+void OptionsADIOS::verifyTimesteps() const {
+  ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename);
+  stream.engine.EndStep();
+  stream.isInStep = false;
+  return;
+}
+
+/// Visit a variant type, and put the data into a NcVar
+struct ADIOSPutVarVisitor {
+  ADIOSPutVarVisitor(const std::string& name, ADIOSStream& stream)
+      : varname(name), stream(stream) {}
+  template <typename T>
+  void operator()(const T& value) {
+    adios2::Variable<T> var = stream.GetValueVariable<T>(varname);
+    stream.engine.Put(var, value);
+  }
+
+private:
+  const std::string& varname;
+  ADIOSStream& stream;
+};
+
+template <>
+void ADIOSPutVarVisitor::operator()<bool>(const bool& value) {
+  // Scalars are only written from processor 0
+  if (BoutComm::rank() != 0) {
+    return;
+  }
+  adios2::Variable<int> var = stream.GetValueVariable<int>(varname);
+  stream.engine.Put<int>(var, static_cast<int>(value));
+}
+
+template <>
+void ADIOSPutVarVisitor::operator()<int>(const int& value) {
+  // Scalars are only written from processor 0
+  if (BoutComm::rank() != 0) {
+    return;
+  }
+  adios2::Variable<int> var = stream.GetValueVariable<int>(varname);
+  stream.engine.Put<int>(var, value);
+}
+
+template <>
+void ADIOSPutVarVisitor::operator()<BoutReal>(const BoutReal& value) {
+  // Scalars are only written from processor 0
+  if (BoutComm::rank() != 0) {
+    return;
+  }
+  adios2::Variable<BoutReal> var = stream.GetValueVariable<BoutReal>(varname);
+  stream.engine.Put<BoutReal>(var, value);
+}
+
+template <>
+void ADIOSPutVarVisitor::operator()<std::string>(const std::string& value) {
+  // Scalars are only written from processor 0
+  if (BoutComm::rank() != 0) {
+    return;
+  }
+  adios2::Variable<std::string> var = stream.GetValueVariable<std::string>(varname);
+  stream.engine.Put<std::string>(var, value, adios2::Mode::Sync);
+}
+
+template <>
+void ADIOSPutVarVisitor::operator()<Field2D>(const Field2D& value) {
+  // Get the mesh that describes how local data relates to global arrays
+  auto mesh = value.getMesh();
+
+  // The global size of this array includes boundary cells but not communication guard cells.
+  // In general this array will be sparse because it may have gaps.
+  adios2::Dims shape = {static_cast<size_t>(mesh->GlobalNx),
+                        static_cast<size_t>(mesh->GlobalNy)};
+
+  // Offset of this processor's data into the global array
+  adios2::Dims start = {static_cast<size_t>(mesh->MapGlobalX),
+                        static_cast<size_t>(mesh->MapGlobalY)};
+
+  // The size of the mapped region
+  adios2::Dims count = {static_cast<size_t>(mesh->MapCountX),
+                        static_cast<size_t>(mesh->MapCountY)};
+
+  // Where the actual data starts in data pointer (to exclude ghost cells)
+  adios2::Dims memStart = {static_cast<size_t>(mesh->MapLocalX),
+                           static_cast<size_t>(mesh->MapLocalY)};
+
+  // The actual size of data pointer in memory (including ghost cells)
+  adios2::Dims memCount = {static_cast<size_t>(value.getNx()),
+                           static_cast<size_t>(value.getNy())};
+
+  adios2::Variable<BoutReal> var = stream.GetArrayVariable<BoutReal>(varname, shape);
+  /* std::cout << "PutVar Field2D rank " << BoutComm::rank() << " var = " << varname
+            << " shape = " << shape[0] << "x" << shape[1] << " count = " << count[0]
+            << "x" << count[1] << " Nx*Ny = " << value.getNx() << "x" << value.getNy()
+            << " memStart = " << memStart[0] << "x" << memStart[1]
+            << " memCount = " << memCount[0] << "x" << memCount[1] << std::endl;*/
+  var.SetSelection({start, count});
+  var.SetMemorySelection({memStart, memCount});
+  stream.engine.Put<BoutReal>(var, &value(0, 0));
+}
+
+template <>
+void ADIOSPutVarVisitor::operator()<Field3D>(const Field3D& value) {
+  // Get the mesh that describes how local data relates to global arrays
+  auto mesh = value.getMesh();
+
+  // The global size of this array includes boundary cells but not communication guard cells.
+  // In general this array will be sparse because it may have gaps.
+  adios2::Dims shape = {static_cast<size_t>(mesh->GlobalNx),
+                        static_cast<size_t>(mesh->GlobalNy),
+                        static_cast<size_t>(mesh->GlobalNz)};
+
+  // Offset of this processor's data into the global array
+  adios2::Dims start = {static_cast<size_t>(mesh->MapGlobalX),
+                        static_cast<size_t>(mesh->MapGlobalY),
+                        static_cast<size_t>(mesh->MapGlobalZ)};
+
+  // The size of the mapped region
+  adios2::Dims count = {static_cast<size_t>(mesh->MapCountX),
+                        static_cast<size_t>(mesh->MapCountY),
+                        static_cast<size_t>(mesh->MapCountZ)};
+
+  // Where the actual data starts in data pointer (to exclude ghost cells)
+  adios2::Dims memStart = {static_cast<size_t>(mesh->MapLocalX),
+                           static_cast<size_t>(mesh->MapLocalY),
+                           static_cast<size_t>(mesh->MapLocalZ)};
+
+  // The actual size of data pointer in memory (including ghost cells)
+  adios2::Dims memCount = {static_cast<size_t>(value.getNx()),
+                           static_cast<size_t>(value.getNy()),
+                           static_cast<size_t>(value.getNz())};
+
+  adios2::Variable<BoutReal> var = stream.GetArrayVariable<BoutReal>(varname, shape);
+  /*std::cout << "PutVar Field3D rank " << BoutComm::rank() << " var = " << varname
+            << " shape = " << shape[0] << "x" << shape[1] << "x" << shape[2]
+            << " count = " << count[0] << "x" << count[1] << "x" << count[2]
+            << " Nx*Ny = " << value.getNx() << "x" << value.getNy() << "x"
+            << value.getNz() << " memStart = " << memStart[0] << "x" << memStart[1] << "x"
+            << memStart[2] << " memCount = " << memCount[0] << "x" << memCount[1] << "x"
+            << memCount[2] << std::endl;*/
+  var.SetSelection({start, count});
+  var.SetMemorySelection({memStart, memCount});
+  stream.engine.Put<BoutReal>(var, &value(0, 0, 0));
+}
+
+template <>
+void ADIOSPutVarVisitor::operator()<FieldPerp>(const FieldPerp& value) {
+  // Get the mesh that describes how local data relates to global arrays
+  auto mesh = value.getMesh();
+
+  // The global size of this array includes boundary cells but not communication guard cells.
+  // In general this array will be sparse because it may have gaps.
+  adios2::Dims shape = {static_cast<size_t>(mesh->GlobalNx),
+                        static_cast<size_t>(mesh->GlobalNz)};
+
+  // Offset of this processor's data into the global array
+  adios2::Dims start = {static_cast<size_t>(mesh->MapGlobalX),
+                        static_cast<size_t>(mesh->MapGlobalZ)};
+
+  // The size of the mapped region
+  adios2::Dims count = {static_cast<size_t>(mesh->MapCountX),
+                        static_cast<size_t>(mesh->MapCountZ)};
+
+  // Where the actual data starts in data pointer (to exclude ghost cells)
+  adios2::Dims memStart = {static_cast<size_t>(mesh->MapLocalX),
+                           static_cast<size_t>(mesh->MapLocalZ)};
+
+  // The actual size of data pointer in memory (including ghost cells)
+  adios2::Dims memCount = {static_cast<size_t>(value.getNx()),
+                           static_cast<size_t>(value.getNz())};
+
+  adios2::Variable<BoutReal> var = stream.GetArrayVariable<BoutReal>(varname, shape);
+  /* std::cout << "PutVar FieldPerp rank " << BoutComm::rank() << " var = " << varname
+            << " shape = " << shape[0] << "x" << shape[1] << " count = " << count[0]
+            << "x" << count[1] << " Nx*Ny = " << value.getNx() << "x" << value.getNy()
+            << " memStart = " << memStart[0] << "x" << memStart[1]
+            << " memCount = " << memCount[0] << "x" << memCount[1] << std::endl; */
+  var.SetSelection({start, count});
+  var.SetMemorySelection({memStart, memCount});
+  stream.engine.Put<BoutReal>(var, &value(0, 0));
+}
+
+template <>
+void ADIOSPutVarVisitor::operator()<Array<BoutReal>>(const Array<BoutReal>& value) {
+  // Pointer to data. Assumed to be contiguous array
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.size()};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0};
+  adios2::Dims count = {1, shape[1]};
+  adios2::Variable<BoutReal> var = stream.GetArrayVariable<BoutReal>(varname, shape);
+  var.SetSelection({start, count});
+  stream.engine.Put<BoutReal>(var, value.begin());
+}
+
+template <>
+void ADIOSPutVarVisitor::operator()<Matrix<BoutReal>>(const Matrix<BoutReal>& value) {
+  // Pointer to data. Assumed to be contiguous array
+  auto s = value.shape();
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s),
+                        (size_t)std::get<1>(s)};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0};
+  adios2::Dims count = {1, shape[1], shape[2]};
+  adios2::Variable<BoutReal> var = stream.GetArrayVariable<BoutReal>(varname, shape);
+  var.SetSelection({start, count});
+  stream.engine.Put<BoutReal>(var, value.begin());
+}
+
+template <>
+void ADIOSPutVarVisitor::operator()<Tensor<BoutReal>>(const Tensor<BoutReal>& value) {
+  // Pointer to data. Assumed to be contiguous array
+  auto s = value.shape();
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s),
+                        (size_t)std::get<1>(s), (size_t)std::get<2>(s)};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0};
+  adios2::Dims count = {1, shape[1], shape[2], shape[3]};
+  adios2::Variable<BoutReal> var = stream.GetArrayVariable<BoutReal>(varname, shape);
+  var.SetSelection({start, count});
+  stream.engine.Put<BoutReal>(var, value.begin());
+}
+
+/// Visit a variant type, and put the data into a NcVar
+struct ADIOSPutAttVisitor {
+  ADIOSPutAttVisitor(const std::string& varname, const std::string& attrname,
+                     ADIOSStream& stream)
+      : varname(varname), attrname(attrname), stream(stream) {}
+  template <typename T>
+  void operator()(const T& value) {
+    stream.io.DefineAttribute<T>(attrname, value, varname, "/", false);
+  }
+
+private:
+  const std::string& varname;
+  const std::string& attrname;
+  ADIOSStream& stream;
+};
+
+template <>
+void ADIOSPutAttVisitor::operator()<bool>(const bool& value) {
+  stream.io.DefineAttribute<int>(attrname, (int)value, varname, "/", false);
+}
+
+void writeGroup(const Options& options, ADIOSStream& stream, const std::string& groupname,
+                const std::string& time_dimension) {
+
+  for (const auto& childpair : options.getChildren()) {
+    const auto& name = childpair.first;
+    const auto& child = childpair.second;
+
+    if (child.isSection()) {
+      TRACE("Writing group '{:s}'", name);
+      writeGroup(child, stream, name, time_dimension);
+      continue;
+    }
+
+    if (child.isValue()) {
+      try {
+        auto time_it = child.attributes.find("time_dimension");
+        if (time_it == child.attributes.end()) {
+          if (stream.adiosStep > 0) {
+            // we should only write the non-varying values in the first step
+            continue;
+          }
+        } else {
+          // Has a time dimension
+
+          const auto& time_name = bout::utils::get<std::string>(time_it->second);
+
+          // Only write time-varying values that match current time
+          // dimension being written
+          if (time_name != time_dimension) {
+            continue;
+          }
+        }
+
+        // Write the variable
+        // Note: ADIOS2 uses '/' to as a group separator; BOUT++ uses ':'
+        std::string varname = groupname.empty() ? name : groupname + "/" + name;
+        bout::utils::visit(ADIOSPutVarVisitor(varname, stream), child.value);
+
+        // Write attributes
+        if (!BoutComm::rank()) {
+          for (const auto& attribute : child.attributes) {
+            const std::string& att_name = attribute.first;
+            const auto& att = attribute.second;
+
+            bout::utils::visit(ADIOSPutAttVisitor(varname, att_name, stream), att);
+          }
+        }
+
+      } catch (const std::exception& e) {
+        throw BoutException("Error while writing value '{:s}' : {:s}", name, e.what());
+      }
+    }
+  }
+}
+
+/// Write options to file
+void OptionsADIOS::write(const Options& options, const std::string& time_dim) {
+  Timer timer("io");
+
+  // ADIOSStream is just a BOUT++ object, it does not create anything inside ADIOS
+  ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename);
+
+  // Need to have an adios2::IO object first, which can only be created once.
+  if (!stream.io) {
+    ADIOSPtr adiosp = GetADIOSPtr();
+    std::string ioname = "write_" + filename;
+    try {
+      stream.io = adiosp->AtIO(ioname);
+    } catch (const std::invalid_argument& e) {
+      stream.io = adiosp->DeclareIO(ioname);
+      stream.io.SetEngine("BP5");
+    }
+  }
+
+  /* Open file once and keep it open, close in stream desctructor
+     or close after writing if singleWriteFile == true
+    */
+  if (!stream.engine) {
+    adios2::Mode amode =
+        (file_mode == FileMode::append ? adios2::Mode::Append : adios2::Mode::Write);
+    stream.engine = stream.io.Open(filename, amode);
+    if (!stream.engine) {
+      throw BoutException("Could not open ADIOS file '{:s}' for writing", filename);
+    }
+  }
+
+  /* Multiple write() calls allowed in a single adios step to output multiple
+     Options objects in the same step. verifyTimesteps() will indicate the 
+     completion of the step (and adios will publish the step).
+  */
+  if (!stream.isInStep) {
+    stream.engine.BeginStep();
+    stream.isInStep = true;
+    stream.adiosStep = stream.engine.CurrentStep();
+  }
+
+  writeGroup(options, stream, "", time_dim);
+
+  /* In singleWriteFile mode, we complete the step and close the file */
+  if (singleWriteFile) {
+    stream.engine.EndStep();
+    stream.engine.Close();
+  }
+}
+
+} // namespace bout
+
+#endif // BOUT_HAS_ADIOS
diff --git a/src/sys/options/options_adios.hxx b/src/sys/options/options_adios.hxx
new file mode 100644
index 0000000000..eddb3976ff
--- /dev/null
+++ b/src/sys/options/options_adios.hxx
@@ -0,0 +1,83 @@
+
+#pragma once
+
+#ifndef OPTIONS_ADIOS_H
+#define OPTIONS_ADIOS_H
+
+#include "bout/build_config.hxx"
+#include "bout/options.hxx"
+#include "bout/options_io.hxx"
+
+#if !BOUT_HAS_ADIOS
+
+namespace {
+bout::RegisterUnavailableOptionsIO
+    registerunavailableoptionsadios("adios", "BOUT++ was not configured with ADIOS2");
+}
+
+#else
+
+#include <memory>
+#include <string>
+
+namespace bout {
+
+/// Forward declare ADIOS file type so we don't need to depend
+/// directly on ADIOS
+struct ADIOSStream;
+
+class OptionsADIOS : public OptionsIO {
+public:
+  // Constructors need to be defined in implementation due to forward
+  // declaration of ADIOSStream
+  OptionsADIOS() = delete;
+
+  /// Create an OptionsADIOS
+  ///
+  /// Options:
+  ///  - "file"   The name of the file
+  ///    If not set then "path" and "prefix" must be set,
+  ///    and file is set to {path}/{prefix}.bp
+  ///  - "append"
+  ///  - "singleWriteFile"
+  OptionsADIOS(Options& options);
+
+  OptionsADIOS(const OptionsADIOS&) = delete;
+  OptionsADIOS(OptionsADIOS&&) noexcept = default;
+  ~OptionsADIOS() = default;
+
+  OptionsADIOS& operator=(const OptionsADIOS&) = delete;
+  OptionsADIOS& operator=(OptionsADIOS&&) noexcept = default;
+
+  /// Read options from file
+  Options read() override;
+
+  /// Write options to file
+  void write(const Options& options, const std::string& time_dim) override;
+
+  /// Check that all variables with the same time dimension have the
+  /// same size in that dimension. Throws BoutException if there are
+  /// any differences, otherwise is silent
+  void verifyTimesteps() const override;
+
+private:
+  enum class FileMode {
+    replace, ///< Overwrite file when writing
+    append   ///< Append to file when writing
+  };
+
+  /// Name of the file on disk
+  std::string filename;
+  /// How to open the file for writing
+  FileMode file_mode{FileMode::replace};
+  bool singleWriteFile = false;
+};
+
+namespace {
+RegisterOptionsIO<OptionsADIOS> registeroptionsadios("adios");
+}
+
+} // namespace bout
+
+#endif // BOUT_HAS_ADIOS
+#endif // OPTIONS_ADIOS_H
diff --git a/src/sys/options/options_ini.cxx b/src/sys/options/options_ini.cxx
index a1e9bcaeb1..d1889f993b 100644
--- a/src/sys/options/options_ini.cxx
+++ b/src/sys/options/options_ini.cxx
@@ -189,7 +189,7 @@ void OptionINI::parse(const string& buffer, string& key, string& value) {
     // Just set a flag to true
     // e.g. "restart" or "append" on command line
     key = buffer;
-    value = string("TRUE");
+    value = string("true");
     return;
   }
 
diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx
new file mode 100644
index 0000000000..6717b6b07d
--- /dev/null
+++ b/src/sys/options/options_io.cxx
@@ -0,0 +1,58 @@
+#include "bout/options_io.hxx"
+#include "bout/bout.hxx"
+#include "bout/globals.hxx"
+#include "bout/mesh.hxx"
+
+#include "options_adios.hxx"
+#include "options_netcdf.hxx"
+
+namespace bout {
+std::unique_ptr<OptionsIO> OptionsIO::create(const std::string& file) {
+  return OptionsIOFactory::getInstance().createFile(file);
+}
+
+std::unique_ptr<OptionsIO> OptionsIO::create(Options& config) {
+  auto& factory = OptionsIOFactory::getInstance();
+  return factory.create(factory.getType(&config), config);
+}
+
+OptionsIOFactory::ReturnType OptionsIOFactory::createRestart(Options* optionsptr) const {
+  Options& options = optionsptr ? *optionsptr : Options::root()["restart_files"];
+
+  // Set defaults
+  options["path"].overrideDefault(
+      Options::root()["datadir"].withDefault<std::string>("data"));
+  options["prefix"].overrideDefault("BOUT.restart");
+  options["append"].overrideDefault(false);
+  options["singleWriteFile"].overrideDefault(true);
+  return create(getType(&options), options);
+}
+
+OptionsIOFactory::ReturnType OptionsIOFactory::createOutput(Options* optionsptr) const {
+  Options& options = optionsptr ? *optionsptr : Options::root()["output"];
+
+  // Set defaults
+  options["path"].overrideDefault(
+      Options::root()["datadir"].withDefault<std::string>("data"));
+  options["prefix"].overrideDefault("BOUT.dmp");
+  options["append"].overrideDefault(Options::root()["append"]
+                                        .doc("Add output data to existing (dump) files?")
+                                        .withDefault<bool>(false));
+  return create(getType(&options), options);
+}
+
+OptionsIOFactory::ReturnType OptionsIOFactory::createFile(const std::string& file) const {
+  Options options{{"file", file}};
+  return create(getDefaultType(), options);
+}
+
+void writeDefaultOutputFile(Options& data) {
+  // Add BOUT++ version and flags
+  bout::experimental::addBuildFlagsToOptions(data);
+  // Add mesh information
+  bout::globals::mesh->outputVars(data);
+  // Write to the default output file
+  OptionsIOFactory::getInstance().createOutput()->write(data);
+}
+
+} // namespace bout
diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx
index d7ceeaea60..65fbca14c0 100644
--- a/src/sys/options/options_netcdf.cxx
+++ b/src/sys/options/options_netcdf.cxx
@@ -2,7 +2,7 @@
 
 #if BOUT_HAS_NETCDF && !BOUT_HAS_LEGACY_NETCDF
 
-#include "bout/options_netcdf.hxx"
+#include "options_netcdf.hxx"
 
 #include "bout/bout.hxx"
 #include "bout/globals.hxx"
@@ -196,8 +196,7 @@ NcType NcTypeVisitor::operator()<double>(const double& UNUSED(t)) {
 }
 
 template <>
-MAYBE_UNUSED()
-NcType NcTypeVisitor::operator()<float>(const float& UNUSED(t)) {
+[[maybe_unused]] NcType NcTypeVisitor::operator()<float>(const float& UNUSED(t)) {
   return ncFloat;
 }
 
@@ -403,8 +402,7 @@ void NcPutAttVisitor::operator()(const double& value) {
   var.putAtt(name, ncDouble, value);
 }
 template <>
-MAYBE_UNUSED()
-void NcPutAttVisitor::operator()(const float& value) {
+[[maybe_unused]] void NcPutAttVisitor::operator()(const float& value) {
   var.putAtt(name, ncFloat, value);
 }
 template <>
@@ -643,14 +641,19 @@ std::vector<TimeDimensionError> verifyTimesteps(const NcGroup& group) {
 
 namespace bout {
 
-OptionsNetCDF::OptionsNetCDF() : data_file(nullptr) {}
-
-OptionsNetCDF::OptionsNetCDF(std::string filename, FileMode mode)
-    : filename(std::move(filename)), file_mode(mode), data_file(nullptr) {}
+OptionsNetCDF::OptionsNetCDF(Options& options) : OptionsIO(options) {
+  if (options["file"].doc("File name. Defaults to <path>/<prefix>.<rank>.nc").isSet()) {
+    filename = options["file"].as<std::string>();
+  } else {
+    // Both path and prefix must be set
+    filename = fmt::format("{}/{}.{}.nc", options["path"].as<std::string>(),
+                           options["prefix"].as<std::string>(), BoutComm::rank());
+  }
 
-OptionsNetCDF::~OptionsNetCDF() = default;
-OptionsNetCDF::OptionsNetCDF(OptionsNetCDF&&) noexcept = default;
-OptionsNetCDF& OptionsNetCDF::operator=(OptionsNetCDF&&) noexcept = default;
+  file_mode = (options["append"].doc("Append to existing file?").withDefault<bool>(false))
+                  ? FileMode::append
+                  : FileMode::replace;
+}
 
 void OptionsNetCDF::verifyTimesteps() const {
   NcFile dataFile(filename, NcFile::read);
@@ -699,41 +702,6 @@ void OptionsNetCDF::write(const Options& options, const std::string& time_dim) {
   data_file->sync();
 }
 
-std::string getRestartDirectoryName(Options& options) {
-  if (options["restartdir"].isSet()) {
-    // Solver-specific restart directory
-    return options["restartdir"].withDefault<std::string>("data");
-  }
-  // Use the root data directory
-  return options["datadir"].withDefault<std::string>("data");
-}
-
-std::string getRestartFilename(Options& options) {
-  return getRestartFilename(options, BoutComm::rank());
-}
-
-std::string getRestartFilename(Options& options, int rank) {
-  return fmt::format("{}/BOUT.restart.{}.nc", bout::getRestartDirectoryName(options),
-                     rank);
-}
-
-std::string getOutputFilename(Options& options) {
-  return getOutputFilename(options, BoutComm::rank());
-}
-
-std::string getOutputFilename(Options& options, int rank) {
-  return fmt::format("{}/BOUT.dmp.{}.nc",
-                     options["datadir"].withDefault<std::string>("data"), rank);
-}
-
-void writeDefaultOutputFile() { writeDefaultOutputFile(Options::root()); }
-
-void writeDefaultOutputFile(Options& options) {
-  bout::experimental::addBuildFlagsToOptions(options);
-  bout::globals::mesh->outputVars(options);
-  OptionsNetCDF(getOutputFilename(Options::root())).write(options);
-}
-
 } // namespace bout
 
 #endif // BOUT_HAS_NETCDF
diff --git a/src/sys/options/options_netcdf.hxx b/src/sys/options/options_netcdf.hxx
new file mode 100644
index 0000000000..8f195c9d92
--- /dev/null
+++ b/src/sys/options/options_netcdf.hxx
@@ -0,0 +1,84 @@
+
+#pragma once
+
+#ifndef OPTIONS_NETCDF_H
+#define OPTIONS_NETCDF_H
+
+#include "bout/build_config.hxx"
+
+#include "bout/options.hxx"
+#include "bout/options_io.hxx"
+
+#if !BOUT_HAS_NETCDF || BOUT_HAS_LEGACY_NETCDF
+
+namespace {
+RegisterUnavailableOptionsIO
+    registerunavailableoptionsnetcdf("netcdf", "BOUT++ was not configured with NetCDF");
+}
+
+#else
+
+#include <memory>
+#include <netcdf>
+#include <string>
+
+namespace bout {
+
+class OptionsNetCDF : public OptionsIO {
+public:
+  // Constructors need to be defined in implementation due to forward
+  // declaration of NcFile
+  OptionsNetCDF() = delete;
+
+  /// Create an OptionsNetCDF
+  ///
+  /// Options:
+  ///  - "file"   The name of the file
+  ///    If not set then "path" and "prefix" options must be set,
+  ///    and file is set to {path}/{prefix}.{rank}.nc
+  ///  - "append"  File mode, default is false
+  OptionsNetCDF(Options& options);
+
+  ~OptionsNetCDF() {}
+
+  OptionsNetCDF(const OptionsNetCDF&) = delete;
+  OptionsNetCDF(OptionsNetCDF&&) noexcept = default;
+  OptionsNetCDF& operator=(const OptionsNetCDF&) = delete;
+  OptionsNetCDF& operator=(OptionsNetCDF&&) noexcept = default;
+
+  /// Read options from file
+  Options read();
+
+  /// Write options to file
+  void write(const Options& options) { write(options, "t"); }
+  void write(const Options& options, const std::string& time_dim);
+
+  /// Check that all variables with the same time dimension have the
+  /// same size in that dimension. Throws BoutException if there are
+  /// any differences, otherwise is silent
+  void verifyTimesteps() const;
+
+private:
+  enum class FileMode {
+    replace, ///< Overwrite file when writing
+    append   ///< Append to file when writing
+  };
+
+  /// Pointer to netCDF file so we don't introduce direct dependence
+  std::unique_ptr<netCDF::NcFile> data_file = nullptr;
+
+  /// Name of the file on disk
+  std::string filename;
+  /// How to open the file for writing
+  FileMode file_mode{FileMode::replace};
+};
+
+namespace {
+RegisterOptionsIO<OptionsNetCDF> registeroptionsnetcdf("netcdf");
+}
+
+} // namespace bout
+
+#endif
+
+#endif //  OPTIONS_NETCDF_H
diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index b845e22012..b4825c6207 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -5,6 +5,7 @@ input_field = sin(y - 2*z) + sin(y - z)
 solution = (6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0)
 
 MXG = 1
+MYG = 1
 NXPE = 1
 
 [mesh]
diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index 5a2599368e..18405a7f88 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -17,6 +17,8 @@ int main(int argc, char** argv) {
   Field3D error{result - solution};
 
   Options dump;
+  // Add mesh geometry variables
+  mesh->outputVars(dump);
 
   dump["l_2"] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
   dump["l_inf"] = max(abs(error), true, "RGN_NOBNDRY");
diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index 806441b330..1e71135c90 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -3,9 +3,6 @@
 # Generate manufactured solution and sources for FCI test
 #
 
-from __future__ import division
-from __future__ import print_function
-
 from boutdata.mms import *
 
 from sympy import sin, cos, sqrt
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 0ec8b70e9f..542cefa07e 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -187,7 +187,7 @@ if False:
                 dx,
                 error_inf[nslice],
                 "--",
-                label="{} $l_\inf$".format(method_orders[nslice]["name"]),
+                label="{} $l_\\inf$".format(method_orders[nslice]["name"]),
             )
         ax.legend(loc="upper left")
         ax.grid()
diff --git a/tests/MMS/time/time.cxx b/tests/MMS/time/time.cxx
index 346662a8e3..17e1f547ab 100644
--- a/tests/MMS/time/time.cxx
+++ b/tests/MMS/time/time.cxx
@@ -10,7 +10,7 @@
 
 class TimeTest : public PhysicsModel {
 public:
-  int init(MAYBE_UNUSED(bool restart)) {
+  int init([[maybe_unused]] bool restart) override {
     solver->add(f, "f"); // Solve a single 3D field
 
     setSplitOperator();
@@ -18,16 +18,16 @@ class TimeTest : public PhysicsModel {
     return 0;
   }
 
-  int rhs(MAYBE_UNUSED(BoutReal time)) {
+  int rhs([[maybe_unused]] BoutReal time) override {
     ddt(f) = f;
     return 0;
   }
 
-  int convective(MAYBE_UNUSED(BoutReal time)) {
+  int convective([[maybe_unused]] BoutReal time) {
     ddt(f) = 0.5 * f;
     return 0;
   }
-  int diffusive(MAYBE_UNUSED(BoutReal time)) {
+  int diffusive([[maybe_unused]] BoutReal time) {
     ddt(f) = 0.5 * f;
     return 0;
   }
diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt
index 1fe0e13b2d..8c4f096f83 100644
--- a/tests/integrated/CMakeLists.txt
+++ b/tests/integrated/CMakeLists.txt
@@ -31,6 +31,7 @@ add_subdirectory(test-laplacexz)
 add_subdirectory(test-multigrid_laplace)
 add_subdirectory(test-naulin-laplace)
 add_subdirectory(test-options-netcdf)
+add_subdirectory(test-options-adios)
 add_subdirectory(test-petsc_laplace)
 add_subdirectory(test-petsc_laplace_MAST-grid)
 add_subdirectory(test-restart-io)
diff --git a/tests/integrated/test-beuler/test_beuler.cxx b/tests/integrated/test-beuler/test_beuler.cxx
index cfdae89eb2..5a080767dd 100644
--- a/tests/integrated/test-beuler/test_beuler.cxx
+++ b/tests/integrated/test-beuler/test_beuler.cxx
@@ -41,7 +41,6 @@ class TestSolver : public PhysicsModel {
 };
 
 int main(int argc, char** argv) {
-
   // Absolute tolerance for difference between the actual value and the
   // expected value
   constexpr BoutReal tolerance = 1.e-5;
@@ -87,8 +86,6 @@ int main(int argc, char** argv) {
 
   solver->solve();
 
-  BoutFinalise(false);
-
   if (model.check_solution(tolerance)) {
     output_test << " PASSED\n";
     return 0;
diff --git a/tests/integrated/test-boutpp/collect-staggered/data/BOUT.inp b/tests/integrated/test-boutpp/collect-staggered/data/BOUT.inp
index 6dc68a7e8b..cb1d1ec7f6 100644
--- a/tests/integrated/test-boutpp/collect-staggered/data/BOUT.inp
+++ b/tests/integrated/test-boutpp/collect-staggered/data/BOUT.inp
@@ -2,7 +2,7 @@ nout = 10
 timestep = 0.1
 
 [mesh]
-staggergrids = True
+staggergrids = true
 n = 1
 nx = n+2*MXG
 ny = 16
diff --git a/tests/integrated/test-boutpp/collect/input/BOUT.inp b/tests/integrated/test-boutpp/collect/input/BOUT.inp
index a390bb1891..cad2f17c52 100644
--- a/tests/integrated/test-boutpp/collect/input/BOUT.inp
+++ b/tests/integrated/test-boutpp/collect/input/BOUT.inp
@@ -5,7 +5,7 @@ MXG = 2
 MYG = 2
 
 [mesh]
-staggergrids = True
+staggergrids = true
 n = 1
 nx = n+2*MXG
 ny = n
diff --git a/tests/integrated/test-boutpp/legacy-model/data/BOUT.inp b/tests/integrated/test-boutpp/legacy-model/data/BOUT.inp
index c6dd2fd761..b6b44502f6 100644
--- a/tests/integrated/test-boutpp/legacy-model/data/BOUT.inp
+++ b/tests/integrated/test-boutpp/legacy-model/data/BOUT.inp
@@ -2,7 +2,7 @@ nout = 10
 timestep = 0.1
 
 [mesh]
-staggergrids = True
+staggergrids = true
 n = 1
 nx = n+2*MXG
 ny = n
diff --git a/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp b/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp
index a390bb1891..cad2f17c52 100644
--- a/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp
+++ b/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp
@@ -5,7 +5,7 @@ MXG = 2
 MYG = 2
 
 [mesh]
-staggergrids = True
+staggergrids = true
 n = 1
 nx = n+2*MXG
 ny = n
diff --git a/tests/integrated/test-boutpp/slicing/basics.indexing.html b/tests/integrated/test-boutpp/slicing/basics.indexing.html
new file mode 100644
index 0000000000..180f39c6ed
--- /dev/null
+++ b/tests/integrated/test-boutpp/slicing/basics.indexing.html
@@ -0,0 +1,1368 @@
+
+<!DOCTYPE html>
+
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
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+            
+              
+              <div class="toc-item">
+                
+<div class="tocsection onthispage mt-5 pt-1 pb-3">
+    <i class="fas fa-list"></i> On this page
+</div>
+
+<nav id="bd-toc-nav">
+    <ul class="visible nav section-nav flex-column">
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#basic-indexing">
+   Basic indexing
+  </a>
+  <ul class="nav section-nav flex-column">
+   <li class="toc-h3 nav-item toc-entry">
+    <a class="reference internal nav-link" href="#single-element-indexing">
+     Single element indexing
+    </a>
+   </li>
+   <li class="toc-h3 nav-item toc-entry">
+    <a class="reference internal nav-link" href="#slicing-and-striding">
+     Slicing and striding
+    </a>
+   </li>
+   <li class="toc-h3 nav-item toc-entry">
+    <a class="reference internal nav-link" href="#dimensional-indexing-tools">
+     Dimensional indexing tools
+    </a>
+   </li>
+  </ul>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#advanced-indexing">
+   Advanced indexing
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+  <ul class="nav section-nav flex-column">
+   <li class="toc-h3 nav-item toc-entry">
+    <a class="reference internal nav-link" href="#integer-array-indexing">
+     Integer array indexing
+    </a>
+   </li>
+   <li class="toc-h3 nav-item toc-entry">
+    <a class="reference internal nav-link" href="#boolean-array-indexing">
+     Boolean array indexing
+    </a>
+   </li>
+   <li class="toc-h3 nav-item toc-entry">
+    <a class="reference internal nav-link" href="#combining-advanced-and-basic-indexing">
+     Combining advanced and basic indexing
+    </a>
+   </li>
+  </ul>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#field-access">
+   Field access
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#flat-iterator-indexing">
+   Flat Iterator indexing
+  </a>
+ </li>
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+  <a class="reference internal nav-link" href="#assigning-values-to-indexed-arrays">
+   Assigning values to indexed arrays
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#dealing-with-variable-numbers-of-indices-within-programs">
+   Dealing with variable numbers of indices within programs
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#detailed-notes">
+   Detailed notes
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+              
+              <div>
+                
+  <section id="indexing-on-ndarrays">
+<span id="basics-indexing"></span><h1>Indexing on <a class="reference internal" href="../reference/generated/numpy.ndarray.html#numpy.ndarray" title="numpy.ndarray"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarrays</span></code></a><a class="headerlink" href="#indexing-on-ndarrays" title="Permalink to this headline">#</a></h1>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="../reference/arrays.indexing.html#routines-indexing"><span class="std std-ref">Indexing routines</span></a></p>
+</div>
+<p id="index-0"><a class="reference internal" href="../reference/generated/numpy.ndarray.html#numpy.ndarray" title="numpy.ndarray"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarrays</span></code></a> can be indexed using the standard Python
+<code class="docutils literal notranslate"><span class="pre">x[obj]</span></code> syntax, where <em>x</em> is the array and <em>obj</em> the selection.
+There are different kinds of indexing available depending on <em>obj</em>:
+basic indexing, advanced indexing and field access.</p>
+<p>Most of the following examples show the use of indexing when
+referencing data in an array. The examples work just as well
+when assigning to an array. See <a class="reference internal" href="#assigning-values-to-indexed-arrays"><span class="std std-ref">Assigning values to indexed arrays</span></a> for
+specific examples and explanations on how assignments work.</p>
+<p>Note that in Python, <code class="docutils literal notranslate"><span class="pre">x[(exp1,</span> <span class="pre">exp2,</span> <span class="pre">...,</span> <span class="pre">expN)]</span></code> is equivalent to
+<code class="docutils literal notranslate"><span class="pre">x[exp1,</span> <span class="pre">exp2,</span> <span class="pre">...,</span> <span class="pre">expN]</span></code>; the latter is just syntactic sugar
+for the former.</p>
+<section id="basic-indexing">
+<span id="id1"></span><h2>Basic indexing<a class="headerlink" href="#basic-indexing" title="Permalink to this headline">#</a></h2>
+<section id="single-element-indexing">
+<span id="id2"></span><h3>Single element indexing<a class="headerlink" href="#single-element-indexing" title="Permalink to this headline">#</a></h3>
+<p>Single element indexing works
+exactly like that for other standard Python sequences. It is 0-based,
+and accepts negative indices for indexing from the end of the array.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+<span class="go">2</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">]</span>
+<span class="go">8</span>
+</pre></div>
+</div>
+<p>It is not necessary to
+separate each dimension’s index into its own set of square brackets.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="o">.</span><span class="n">shape</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>  <span class="c1"># now x is 2-dimensional</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span>
+<span class="go">8</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+<span class="go">9</span>
+</pre></div>
+</div>
+<p>Note that if one indexes a multidimensional array with fewer indices
+than dimensions, one gets a subdimensional array. For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+<span class="go">array([0, 1, 2, 3, 4])</span>
+</pre></div>
+</div>
+<p>That is, each index specified selects the array corresponding to the
+rest of the dimensions selected. In the above example, choosing 0
+means that the remaining dimension of length 5 is being left unspecified,
+and that what is returned is an array of that dimensionality and size.
+It must be noted that the returned array is a <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">view</span></a>, i.e., it is not a
+copy of the original, but points to the same values in memory as does the
+original array.
+In  this case, the 1-D array at the first position (0) is returned.
+So using a single index on the returned array, results in a single
+element being returned. That is:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span>
+<span class="go">2</span>
+</pre></div>
+</div>
+<p>So note that <code class="docutils literal notranslate"><span class="pre">x[0,</span> <span class="pre">2]</span> <span class="pre">==</span> <span class="pre">x[0][2]</span></code> though the second case is more
+inefficient as a new temporary array is created after the first index
+that is subsequently indexed by 2.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>NumPy uses C-order indexing. That means that the last
+index usually represents the most rapidly changing memory location,
+unlike Fortran or IDL, where the first index represents the most
+rapidly changing location in memory. This difference represents a
+great potential for confusion.</p>
+</div>
+</section>
+<section id="slicing-and-striding">
+<span id="id3"></span><h3>Slicing and striding<a class="headerlink" href="#slicing-and-striding" title="Permalink to this headline">#</a></h3>
+<p>Basic slicing extends Python’s basic concept of slicing to N
+dimensions. Basic slicing occurs when <em>obj</em> is a <a class="reference external" href="https://docs.python.org/3/library/functions.html#slice" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">slice</span></code></a> object
+(constructed by <code class="docutils literal notranslate"><span class="pre">start:stop:step</span></code> notation inside of brackets), an
+integer, or a tuple of slice objects and integers. <a class="reference external" href="https://docs.python.org/3/library/constants.html#Ellipsis" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Ellipsis</span></code></a>
+and <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a> objects can be interspersed with these as
+well.</p>
+<p id="index-1">The simplest case of indexing with <em>N</em> integers returns an <a class="reference internal" href="../reference/arrays.scalars.html#arrays-scalars"><span class="std std-ref">array
+scalar</span></a> representing the corresponding item.  As in
+Python, all indices are zero-based: for the <em>i</em>-th index <span class="math notranslate nohighlight">\(n_i\)</span>,
+the valid range is <span class="math notranslate nohighlight">\(0 \le n_i &lt; d_i\)</span> where <span class="math notranslate nohighlight">\(d_i\)</span> is the
+<em>i</em>-th element of the shape of the array.  Negative indices are
+interpreted as counting from the end of the array (<em>i.e.</em>, if
+<span class="math notranslate nohighlight">\(n_i &lt; 0\)</span>, it means <span class="math notranslate nohighlight">\(n_i + d_i\)</span>).</p>
+<p>All arrays generated by basic slicing are always <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">views</span></a>
+of the original array.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>NumPy slicing creates a <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">view</span></a> instead of a copy as in the case of
+built-in Python sequences such as string, tuple and list.
+Care must be taken when extracting
+a small portion from a large array which becomes useless after the
+extraction, because the small portion extracted contains a reference
+to the large original array whose memory will not be released until
+all arrays derived from it are garbage-collected. In such cases an
+explicit <code class="docutils literal notranslate"><span class="pre">copy()</span></code> is recommended.</p>
+</div>
+<p>The standard rules of sequence slicing apply to basic slicing on a
+per-dimension basis (including using a step index). Some useful
+concepts to remember include:</p>
+<ul>
+<li><p>The basic slice syntax is <code class="docutils literal notranslate"><span class="pre">i:j:k</span></code> where <em>i</em> is the starting index,
+<em>j</em> is the stopping index, and <em>k</em> is the step (<span class="math notranslate nohighlight">\(k\neq0\)</span>).
+This selects the <em>m</em> elements (in the corresponding dimension) with
+index values <em>i</em>, <em>i + k</em>, …, <em>i + (m - 1) k</em> where
+<span class="math notranslate nohighlight">\(m = q + (r\neq0)\)</span> and <em>q</em> and <em>r</em> are the quotient and remainder
+obtained by dividing <em>j - i</em> by <em>k</em>: <em>j - i = q k + r</em>, so that
+<em>i + (m - 1) k &lt; j</em>.
+For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="mi">7</span><span class="p">,</span> <span class="mi">8</span><span class="p">,</span> <span class="mi">9</span><span class="p">])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">7</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
+<span class="go">array([1, 3, 5])</span>
+</pre></div>
+</div>
+</li>
+<li><p>Negative <em>i</em> and <em>j</em> are interpreted as <em>n + i</em> and <em>n + j</em> where
+<em>n</em> is the number of elements in the corresponding dimension.
+Negative <em>k</em> makes stepping go towards smaller indices.
+From the above example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">:</span><span class="mi">10</span><span class="p">]</span>
+<span class="go">array([8, 9])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">3</span><span class="p">:</span><span class="mi">3</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+<span class="go">array([7, 6, 5, 4])</span>
+</pre></div>
+</div>
+</li>
+<li><p>Assume <em>n</em> is the number of elements in the dimension being
+sliced. Then, if <em>i</em> is not given it defaults to 0 for <em>k &gt; 0</em> and
+<em>n - 1</em> for <em>k &lt; 0</em> . If <em>j</em> is not given it defaults to <em>n</em> for <em>k &gt; 0</em>
+and <em>-n-1</em> for <em>k &lt; 0</em> . If <em>k</em> is not given it defaults to 1. Note that
+<code class="docutils literal notranslate"><span class="pre">::</span></code> is the same as <code class="docutils literal notranslate"><span class="pre">:</span></code> and means select all indices along this
+axis.
+From the above example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">5</span><span class="p">:]</span>
+<span class="go">array([5, 6, 7, 8, 9])</span>
+</pre></div>
+</div>
+</li>
+<li><p>If the number of objects in the selection tuple is less than
+<em>N</em>, then <code class="docutils literal notranslate"><span class="pre">:</span></code> is assumed for any subsequent dimensions.
+For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[[</span><span class="mi">1</span><span class="p">],[</span><span class="mi">2</span><span class="p">],[</span><span class="mi">3</span><span class="p">]],</span> <span class="p">[[</span><span class="mi">4</span><span class="p">],[</span><span class="mi">5</span><span class="p">],[</span><span class="mi">6</span><span class="p">]]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="o">.</span><span class="n">shape</span>
+<span class="go">(2, 3, 1)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
+<span class="go">array([[[4],</span>
+<span class="go">        [5],</span>
+<span class="go">        [6]]])</span>
+</pre></div>
+</div>
+</li>
+<li><p>An integer, <em>i</em>, returns the same values as <code class="docutils literal notranslate"><span class="pre">i:i+1</span></code>
+<strong>except</strong> the dimensionality of the returned object is reduced by
+1. In particular, a selection tuple with the <em>p</em>-th
+element an integer (and all other entries <code class="docutils literal notranslate"><span class="pre">:</span></code>) returns the
+corresponding sub-array with dimension <em>N - 1</em>. If <em>N = 1</em>
+then the returned object is an array scalar. These objects are
+explained in <a class="reference internal" href="../reference/arrays.scalars.html#arrays-scalars"><span class="std std-ref">Scalars</span></a>.</p></li>
+<li><p>If the selection tuple has all entries <code class="docutils literal notranslate"><span class="pre">:</span></code> except the
+<em>p</em>-th entry which is a slice object <code class="docutils literal notranslate"><span class="pre">i:j:k</span></code>,
+then the returned array has dimension <em>N</em> formed by
+concatenating the sub-arrays returned by integer indexing of
+elements <em>i</em>, <em>i+k</em>, …, <em>i + (m - 1) k &lt; j</em>,</p></li>
+<li><p>Basic slicing with more than one non-<code class="docutils literal notranslate"><span class="pre">:</span></code> entry in the slicing
+tuple, acts like repeated application of slicing using a single
+non-<code class="docutils literal notranslate"><span class="pre">:</span></code> entry, where the non-<code class="docutils literal notranslate"><span class="pre">:</span></code> entries are successively taken
+(with all other non-<code class="docutils literal notranslate"><span class="pre">:</span></code> entries replaced by <code class="docutils literal notranslate"><span class="pre">:</span></code>). Thus,
+<code class="docutils literal notranslate"><span class="pre">x[ind1,</span> <span class="pre">...,</span> <span class="pre">ind2,:]</span></code> acts like <code class="docutils literal notranslate"><span class="pre">x[ind1][...,</span> <span class="pre">ind2,</span> <span class="pre">:]</span></code> under basic
+slicing.</p>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>The above is <strong>not</strong> true for advanced indexing.</p>
+</div>
+</li>
+<li><p>You may use slicing to set values in the array, but (unlike lists) you
+can never grow the array. The size of the value to be set in
+<code class="docutils literal notranslate"><span class="pre">x[obj]</span> <span class="pre">=</span> <span class="pre">value</span></code> must be (broadcastable) to the same shape as
+<code class="docutils literal notranslate"><span class="pre">x[obj]</span></code>.</p></li>
+<li><p>A slicing tuple can always be constructed as <em>obj</em>
+and used in the <code class="docutils literal notranslate"><span class="pre">x[obj]</span></code> notation. Slice objects can be used in
+the construction in place of the <code class="docutils literal notranslate"><span class="pre">[start:stop:step]</span></code>
+notation. For example, <code class="docutils literal notranslate"><span class="pre">x[1:10:5,</span> <span class="pre">::-1]</span></code> can also be implemented
+as <code class="docutils literal notranslate"><span class="pre">obj</span> <span class="pre">=</span> <span class="pre">(slice(1,</span> <span class="pre">10,</span> <span class="pre">5),</span> <span class="pre">slice(None,</span> <span class="pre">None,</span> <span class="pre">-1));</span> <span class="pre">x[obj]</span></code> . This
+can be useful for constructing generic code that works on arrays
+of arbitrary dimensions. See <a class="reference internal" href="#dealing-with-variable-indices"><span class="std std-ref">Dealing with variable numbers of indices within programs</span></a>
+for more information.</p></li>
+</ul>
+</section>
+<section id="dimensional-indexing-tools">
+<span id="index-2"></span><span id="id4"></span><h3>Dimensional indexing tools<a class="headerlink" href="#dimensional-indexing-tools" title="Permalink to this headline">#</a></h3>
+<p>There are some tools to facilitate the easy matching of array shapes with
+expressions and in assignments.</p>
+<p><a class="reference external" href="https://docs.python.org/3/library/constants.html#Ellipsis" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Ellipsis</span></code></a> expands to the number of <code class="docutils literal notranslate"><span class="pre">:</span></code> objects needed for the
+selection tuple to index all dimensions. In most cases, this means that the
+length of the expanded selection tuple is <code class="docutils literal notranslate"><span class="pre">x.ndim</span></code>. There may only be a
+single ellipsis present.
+From the above example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">...</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
+<span class="go">array([[1, 2, 3],</span>
+<span class="go">      [4, 5, 6]])</span>
+</pre></div>
+</div>
+<p>This is equivalent to:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[:,</span> <span class="p">:,</span> <span class="mi">0</span><span class="p">]</span>
+<span class="go">array([[1, 2, 3],</span>
+<span class="go">      [4, 5, 6]])</span>
+</pre></div>
+</div>
+<p>Each <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a> object in the selection tuple serves to expand
+the dimensions of the resulting selection by one unit-length
+dimension.  The added dimension is the position of the <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a>
+object in the selection tuple. <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a> is an alias for
+<code class="docutils literal notranslate"><span class="pre">None</span></code>, and <code class="docutils literal notranslate"><span class="pre">None</span></code> can be used in place of this with the same result.
+From the above example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:,</span> <span class="p">:]</span><span class="o">.</span><span class="n">shape</span>
+<span class="go">(2, 1, 3, 1)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[:,</span> <span class="kc">None</span><span class="p">,</span> <span class="p">:,</span> <span class="p">:]</span><span class="o">.</span><span class="n">shape</span>
+<span class="go">(2, 1, 3, 1)</span>
+</pre></div>
+</div>
+<p>This can be handy to combine two
+arrays in a way that otherwise would require explicit reshaping
+operations. For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">]</span> <span class="o">+</span> <span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:]</span>
+<span class="go">array([[0, 1, 2, 3, 4],</span>
+<span class="go">      [1, 2, 3, 4, 5],</span>
+<span class="go">      [2, 3, 4, 5, 6],</span>
+<span class="go">      [3, 4, 5, 6, 7],</span>
+<span class="go">      [4, 5, 6, 7, 8]])</span>
+</pre></div>
+</div>
+</section>
+</section>
+<section id="advanced-indexing">
+<span id="id5"></span><h2>Advanced indexing<a class="headerlink" href="#advanced-indexing" title="Permalink to this headline">#</a></h2>
+<p>Advanced indexing is triggered when the selection object, <em>obj</em>, is a
+non-tuple sequence object, an <a class="reference internal" href="../reference/generated/numpy.ndarray.html#numpy.ndarray" title="numpy.ndarray"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> (of data type integer or bool),
+or a tuple with at least one sequence object or ndarray (of data type
+integer or bool). There are two types of advanced indexing: integer
+and Boolean.</p>
+<p>Advanced indexing always returns a <em>copy</em> of the data (contrast with
+basic slicing that returns a <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">view</span></a>).</p>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>The definition of advanced indexing means that <code class="docutils literal notranslate"><span class="pre">x[(1,</span> <span class="pre">2,</span> <span class="pre">3),]</span></code> is
+fundamentally different than <code class="docutils literal notranslate"><span class="pre">x[(1,</span> <span class="pre">2,</span> <span class="pre">3)]</span></code>. The latter is
+equivalent to <code class="docutils literal notranslate"><span class="pre">x[1,</span> <span class="pre">2,</span> <span class="pre">3]</span></code> which will trigger basic selection while
+the former will trigger advanced indexing. Be sure to understand
+why this occurs.</p>
+<p>Also recognize that <code class="docutils literal notranslate"><span class="pre">x[[1,</span> <span class="pre">2,</span> <span class="pre">3]]</span></code> will trigger advanced indexing,
+whereas due to the deprecated Numeric compatibility mentioned above,
+<code class="docutils literal notranslate"><span class="pre">x[[1,</span> <span class="pre">2,</span> <span class="pre">slice(None)]]</span></code> will trigger basic slicing.</p>
+</div>
+<section id="integer-array-indexing">
+<h3>Integer array indexing<a class="headerlink" href="#integer-array-indexing" title="Permalink to this headline">#</a></h3>
+<p>Integer array indexing allows selection of arbitrary items in the array
+based on their <em>N</em>-dimensional index. Each integer array represents a number
+of indices into that dimension.</p>
+<p>Negative values are permitted in the index arrays and work as they do with
+single indices or slices:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
+<span class="go">array([10,  9,  8,  7,  6,  5,  4,  3,  2])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">8</span><span class="p">])]</span>
+<span class="go">array([7, 7, 9, 2])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="o">-</span><span class="mi">3</span><span class="p">,</span> <span class="mi">8</span><span class="p">])]</span>
+<span class="go">array([7, 7, 4, 2])</span>
+</pre></div>
+</div>
+<p>If the index values are out of bounds then an <code class="docutils literal notranslate"><span class="pre">IndexError</span></code> is thrown:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="p">[</span><span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">])]</span>
+<span class="go">array([[3, 4],</span>
+<span class="go">      [5, 6]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">])]</span>
+<span class="gt">Traceback (most recent call last):</span>
+  <span class="c">...</span>
+<span class="gr">IndexError</span>: <span class="n">index 3 is out of bounds for axis 0 with size 3</span>
+</pre></div>
+</div>
+<p>When the index consists of as many integer arrays as dimensions of the array
+being indexed, the indexing is straightforward, but different from slicing.</p>
+<p>Advanced indices always are <a class="reference internal" href="basics.broadcasting.html#basics-broadcasting"><span class="std std-ref">broadcast</span></a> and
+iterated as <em>one</em>:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">result</span><span class="p">[</span><span class="n">i_1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">i_M</span><span class="p">]</span> <span class="o">==</span> <span class="n">x</span><span class="p">[</span><span class="n">ind_1</span><span class="p">[</span><span class="n">i_1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">i_M</span><span class="p">],</span> <span class="n">ind_2</span><span class="p">[</span><span class="n">i_1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">i_M</span><span class="p">],</span>
+                           <span class="o">...</span><span class="p">,</span> <span class="n">ind_N</span><span class="p">[</span><span class="n">i_1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">i_M</span><span class="p">]]</span>
+</pre></div>
+</div>
+<p>Note that the resulting shape is identical to the (broadcast) indexing array
+shapes <code class="docutils literal notranslate"><span class="pre">ind_1,</span> <span class="pre">...,</span> <span class="pre">ind_N</span></code>. If the indices cannot be broadcast to the
+same shape, an exception <code class="docutils literal notranslate"><span class="pre">IndexError:</span> <span class="pre">shape</span> <span class="pre">mismatch:</span> <span class="pre">indexing</span> <span class="pre">arrays</span> <span class="pre">could</span>
+<span class="pre">not</span> <span class="pre">be</span> <span class="pre">broadcast</span> <span class="pre">together</span> <span class="pre">with</span> <span class="pre">shapes...</span></code> is raised.</p>
+<p>Indexing with multidimensional index arrays tend
+to be more unusual uses, but they are permitted, and they are useful for some
+problems. We’ll start with the simplest multidimensional case:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">35</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">y</span>
+<span class="go">array([[ 0,  1,  2,  3,  4,  5,  6],</span>
+<span class="go">       [ 7,  8,  9, 10, 11, 12, 13],</span>
+<span class="go">       [14, 15, 16, 17, 18, 19, 20],</span>
+<span class="go">       [21, 22, 23, 24, 25, 26, 27],</span>
+<span class="go">       [28, 29, 30, 31, 32, 33, 34]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">])]</span>
+<span class="go">array([ 0, 15, 30])</span>
+</pre></div>
+</div>
+<p>In this case, if the index arrays have a matching shape, and there is an
+index array for each dimension of the array being indexed, the resultant
+array has the same shape as the index arrays, and the values correspond
+to the index set for each position in the index arrays. In this example,
+the first index value is 0 for both index arrays, and thus the first value
+of the resultant array is <code class="docutils literal notranslate"><span class="pre">y[0,</span> <span class="pre">0]</span></code>. The next value is <code class="docutils literal notranslate"><span class="pre">y[2,</span> <span class="pre">1]</span></code>, and
+the last is <code class="docutils literal notranslate"><span class="pre">y[4,</span> <span class="pre">2]</span></code>.</p>
+<p>If the index arrays do not have the same shape, there is an attempt to
+broadcast them to the same shape. If they cannot be broadcast to the same
+shape, an exception is raised:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">])]</span>
+<span class="gt">Traceback (most recent call last):</span>
+  <span class="c">...</span>
+<span class="gr">IndexError</span>: <span class="n">shape mismatch: indexing arrays could not be broadcast</span>
+<span class="go">together with shapes (3,) (2,)</span>
+</pre></div>
+</div>
+<p>The broadcasting mechanism permits index arrays to be combined with
+scalars for other indices. The effect is that the scalar value is used
+for all the corresponding values of the index arrays:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="mi">1</span><span class="p">]</span>
+<span class="go">array([ 1, 15, 29])</span>
+</pre></div>
+</div>
+<p>Jumping to the next level of complexity, it is possible to only partially
+index an array with index arrays. It takes a bit of thought to understand
+what happens in such cases. For example if we just use one index array
+with y:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">])]</span>
+<span class="go">array([[ 0,  1,  2,  3,  4,  5,  6],</span>
+<span class="go">      [14, 15, 16, 17, 18, 19, 20],</span>
+<span class="go">      [28, 29, 30, 31, 32, 33, 34]])</span>
+</pre></div>
+</div>
+<p>It results in the construction of a new array where each value of the
+index array selects one row from the array being indexed and the resultant
+array has the resulting shape (number of index elements, size of row).</p>
+<p>In general, the shape of the resultant array will be the concatenation of
+the shape of the index array (or the shape that all the index arrays were
+broadcast to) with the shape of any unused dimensions (those not indexed)
+in the array being indexed.</p>
+<p class="rubric">Example</p>
+<p>From each row, a specific element should be selected. The row index is just
+<code class="docutils literal notranslate"><span class="pre">[0,</span> <span class="pre">1,</span> <span class="pre">2]</span></code> and the column index specifies the element to choose for the
+corresponding row, here <code class="docutils literal notranslate"><span class="pre">[0,</span> <span class="pre">1,</span> <span class="pre">0]</span></code>. Using both together the task
+can be solved using advanced indexing:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="p">[</span><span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]]</span>
+<span class="go">array([1, 4, 5])</span>
+</pre></div>
+</div>
+<p>To achieve a behaviour similar to the basic slicing above, broadcasting can be
+used. The function <a class="reference internal" href="../reference/generated/numpy.ix_.html#numpy.ix_" title="numpy.ix_"><code class="xref py py-func docutils literal notranslate"><span class="pre">ix_</span></code></a> can help with this broadcasting. This is best
+understood with an example.</p>
+<p class="rubric">Example</p>
+<p>From a 4x3 array the corner elements should be selected using advanced
+indexing. Thus all elements for which the column is one of <code class="docutils literal notranslate"><span class="pre">[0,</span> <span class="pre">2]</span></code> and
+the row is one of <code class="docutils literal notranslate"><span class="pre">[0,</span> <span class="pre">3]</span></code> need to be selected. To use advanced indexing
+one needs to select all elements <em>explicitly</em>. Using the method explained
+previously one could write:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span> <span class="mi">0</span><span class="p">,</span>  <span class="mi">1</span><span class="p">,</span>  <span class="mi">2</span><span class="p">],</span>
+<span class="gp">... </span>              <span class="p">[</span> <span class="mi">3</span><span class="p">,</span>  <span class="mi">4</span><span class="p">,</span>  <span class="mi">5</span><span class="p">],</span>
+<span class="gp">... </span>              <span class="p">[</span> <span class="mi">6</span><span class="p">,</span>  <span class="mi">7</span><span class="p">,</span>  <span class="mi">8</span><span class="p">],</span>
+<span class="gp">... </span>              <span class="p">[</span> <span class="mi">9</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">11</span><span class="p">]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span>
+<span class="gp">... </span>                 <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">intp</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">columns</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span>
+<span class="gp">... </span>                    <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">intp</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rows</span><span class="p">,</span> <span class="n">columns</span><span class="p">]</span>
+<span class="go">array([[ 0,  2],</span>
+<span class="go">       [ 9, 11]])</span>
+</pre></div>
+</div>
+<p>However, since the indexing arrays above just repeat themselves,
+broadcasting can be used (compare operations such as
+<code class="docutils literal notranslate"><span class="pre">rows[:,</span> <span class="pre">np.newaxis]</span> <span class="pre">+</span> <span class="pre">columns</span></code>) to simplify this:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">intp</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">columns</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">intp</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">]</span>
+<span class="go">array([[0],</span>
+<span class="go">       [3]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rows</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span> <span class="n">columns</span><span class="p">]</span>
+<span class="go">array([[ 0,  2],</span>
+<span class="go">       [ 9, 11]])</span>
+</pre></div>
+</div>
+<p>This broadcasting can also be achieved using the function <a class="reference internal" href="../reference/generated/numpy.ix_.html#numpy.ix_" title="numpy.ix_"><code class="xref py py-func docutils literal notranslate"><span class="pre">ix_</span></code></a>:</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ix_</span><span class="p">(</span><span class="n">rows</span><span class="p">,</span> <span class="n">columns</span><span class="p">)]</span>
+<span class="go">array([[ 0,  2],</span>
+<span class="go">       [ 9, 11]])</span>
+</pre></div>
+</div>
+<p>Note that without the <code class="docutils literal notranslate"><span class="pre">np.ix_</span></code> call, only the diagonal elements would
+be selected:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rows</span><span class="p">,</span> <span class="n">columns</span><span class="p">]</span>
+<span class="go">array([ 0, 11])</span>
+</pre></div>
+</div>
+<p>This difference is the most important thing to remember about
+indexing with multiple advanced indices.</p>
+<p class="rubric">Example</p>
+<p>A real-life example of where advanced indexing may be useful is for a color
+lookup table where we want to map the values of an image into RGB triples for
+display. The lookup table could have a shape (nlookup, 3). Indexing
+such an array with an image with shape (ny, nx) with dtype=np.uint8
+(or any integer type so long as values are with the bounds of the
+lookup table) will result in an array of shape (ny, nx, 3) where a
+triple of RGB values is associated with each pixel location.</p>
+</section>
+<section id="boolean-array-indexing">
+<span id="boolean-indexing"></span><h3>Boolean array indexing<a class="headerlink" href="#boolean-array-indexing" title="Permalink to this headline">#</a></h3>
+<p>This advanced indexing occurs when <em>obj</em> is an array object of Boolean
+type, such as may be returned from comparison operators. A single
+boolean index array is practically identical to <code class="docutils literal notranslate"><span class="pre">x[obj.nonzero()]</span></code> where,
+as described above, <a class="reference internal" href="../reference/generated/numpy.ndarray.nonzero.html#numpy.ndarray.nonzero" title="numpy.ndarray.nonzero"><code class="xref py py-meth docutils literal notranslate"><span class="pre">obj.nonzero()</span></code></a> returns a
+tuple (of length <a class="reference internal" href="../reference/generated/numpy.ndarray.ndim.html#numpy.ndarray.ndim" title="numpy.ndarray.ndim"><code class="xref py py-attr docutils literal notranslate"><span class="pre">obj.ndim</span></code></a>) of integer index
+arrays showing the <a class="reference external" href="https://docs.python.org/3/library/constants.html#True" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">True</span></code></a> elements of <em>obj</em>. However, it is
+faster when <code class="docutils literal notranslate"><span class="pre">obj.shape</span> <span class="pre">==</span> <span class="pre">x.shape</span></code>.</p>
+<p>If <code class="docutils literal notranslate"><span class="pre">obj.ndim</span> <span class="pre">==</span> <span class="pre">x.ndim</span></code>, <code class="docutils literal notranslate"><span class="pre">x[obj]</span></code> returns a 1-dimensional array
+filled with the elements of <em>x</em> corresponding to the <a class="reference external" href="https://docs.python.org/3/library/constants.html#True" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">True</span></code></a>
+values of <em>obj</em>.  The search order will be <a class="reference internal" href="../glossary.html#term-row-major"><span class="xref std std-term">row-major</span></a>,
+C-style. If <em>obj</em> has <a class="reference external" href="https://docs.python.org/3/library/constants.html#True" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">True</span></code></a> values at entries that are outside
+of the bounds of <em>x</em>, then an index error will be raised. If <em>obj</em> is
+smaller than <em>x</em> it is identical to filling it with <a class="reference external" href="https://docs.python.org/3/library/constants.html#False" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">False</span></code></a>.</p>
+<p>A common use case for this is filtering for desired element values.
+For example, one may wish to select all entries from an array which
+are not <a class="reference internal" href="../reference/constants.html#numpy.NaN" title="numpy.NaN"><code class="xref py py-const docutils literal notranslate"><span class="pre">NaN</span></code></a>:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">2.</span><span class="p">],</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="mf">3.</span><span class="p">],</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">~</span><span class="n">np</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">x</span><span class="p">)]</span>
+<span class="go">array([1., 2., 3.])</span>
+</pre></div>
+</div>
+<p>Or wish to add a constant to all negative elements:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mf">1.</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.</span><span class="p">,</span> <span class="o">-</span><span class="mf">2.</span><span class="p">,</span> <span class="mi">3</span><span class="p">])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">x</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">20</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
+<span class="go">array([ 1., 19., 18., 3.])</span>
+</pre></div>
+</div>
+<p>In general if an index includes a Boolean array, the result will be
+identical to inserting <code class="docutils literal notranslate"><span class="pre">obj.nonzero()</span></code> into the same position
+and using the integer array indexing mechanism described above.
+<code class="docutils literal notranslate"><span class="pre">x[ind_1,</span> <span class="pre">boolean_array,</span> <span class="pre">ind_2]</span></code> is equivalent to
+<code class="docutils literal notranslate"><span class="pre">x[(ind_1,)</span> <span class="pre">+</span> <span class="pre">boolean_array.nonzero()</span> <span class="pre">+</span> <span class="pre">(ind_2,)]</span></code>.</p>
+<p>If there is only one Boolean array and no integer indexing array present,
+this is straightforward. Care must only be taken to make sure that the
+boolean index has <em>exactly</em> as many dimensions as it is supposed to work
+with.</p>
+<p>In general, when the boolean array has fewer dimensions than the array being
+indexed, this is equivalent to <code class="docutils literal notranslate"><span class="pre">x[b,</span> <span class="pre">...]</span></code>, which means x is indexed by b
+followed by as many <code class="docutils literal notranslate"><span class="pre">:</span></code> as are needed to fill out the rank of x. Thus the
+shape of the result is one dimension containing the number of True elements of
+the boolean array, followed by the remaining dimensions of the array being
+indexed:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">35</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span> <span class="o">=</span> <span class="n">x</span> <span class="o">&gt;</span> <span class="mi">20</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span><span class="p">[:,</span> <span class="mi">5</span><span class="p">]</span>
+<span class="go">array([False, False, False,  True,  True])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">b</span><span class="p">[:,</span> <span class="mi">5</span><span class="p">]]</span>
+<span class="go">array([[21, 22, 23, 24, 25, 26, 27],</span>
+<span class="go">      [28, 29, 30, 31, 32, 33, 34]])</span>
+</pre></div>
+</div>
+<p>Here the 4th and 5th rows are selected from the indexed array and
+combined to make a 2-D array.</p>
+<p class="rubric">Example</p>
+<p>From an array, select all rows which sum up to less or equal two:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">rowsum</span> <span class="o">=</span> <span class="n">x</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rowsum</span> <span class="o">&lt;=</span> <span class="mi">2</span><span class="p">,</span> <span class="p">:]</span>
+<span class="go">array([[0, 1],</span>
+<span class="go">       [1, 1]])</span>
+</pre></div>
+</div>
+<p>Combining multiple Boolean indexing arrays or a Boolean with an integer
+indexing array can best be understood with the
+<a class="reference internal" href="../reference/generated/numpy.ndarray.nonzero.html#numpy.ndarray.nonzero" title="numpy.ndarray.nonzero"><code class="xref py py-meth docutils literal notranslate"><span class="pre">obj.nonzero()</span></code></a> analogy. The function <a class="reference internal" href="../reference/generated/numpy.ix_.html#numpy.ix_" title="numpy.ix_"><code class="xref py py-func docutils literal notranslate"><span class="pre">ix_</span></code></a>
+also supports boolean arrays and will work without any surprises.</p>
+<p class="rubric">Example</p>
+<p>Use boolean indexing to select all rows adding up to an even
+number. At the same time columns 0 and 2 should be selected with an
+advanced integer index. Using the <a class="reference internal" href="../reference/generated/numpy.ix_.html#numpy.ix_" title="numpy.ix_"><code class="xref py py-func docutils literal notranslate"><span class="pre">ix_</span></code></a> function this can be done
+with:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span> <span class="mi">0</span><span class="p">,</span>  <span class="mi">1</span><span class="p">,</span>  <span class="mi">2</span><span class="p">],</span>
+<span class="gp">... </span>              <span class="p">[</span> <span class="mi">3</span><span class="p">,</span>  <span class="mi">4</span><span class="p">,</span>  <span class="mi">5</span><span class="p">],</span>
+<span class="gp">... </span>              <span class="p">[</span> <span class="mi">6</span><span class="p">,</span>  <span class="mi">7</span><span class="p">,</span>  <span class="mi">8</span><span class="p">],</span>
+<span class="gp">... </span>              <span class="p">[</span> <span class="mi">9</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">11</span><span class="p">]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span> <span class="o">=</span> <span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="o">%</span> <span class="mi">2</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span>
+<span class="go">array([False,  True, False,  True])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ix_</span><span class="p">(</span><span class="n">rows</span><span class="p">,</span> <span class="n">columns</span><span class="p">)]</span>
+<span class="go">array([[ 3,  5],</span>
+<span class="go">       [ 9, 11]])</span>
+</pre></div>
+</div>
+<p>Without the <code class="docutils literal notranslate"><span class="pre">np.ix_</span></code> call, only the diagonal elements would be
+selected.</p>
+<p>Or without <code class="docutils literal notranslate"><span class="pre">np.ix_</span></code> (compare the integer array examples):</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span> <span class="o">=</span> <span class="n">rows</span><span class="o">.</span><span class="n">nonzero</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rows</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span> <span class="n">columns</span><span class="p">]</span>
+<span class="go">array([[ 3,  5],</span>
+<span class="go">       [ 9, 11]])</span>
+</pre></div>
+</div>
+<p class="rubric">Example</p>
+<p>Use a 2-D boolean array of shape (2, 3)
+with four True elements to select rows from a 3-D array of shape
+(2, 3, 5) results in a 2-D result of shape (4, 5):</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">30</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
+<span class="go">array([[[ 0,  1,  2,  3,  4],</span>
+<span class="go">        [ 5,  6,  7,  8,  9],</span>
+<span class="go">        [10, 11, 12, 13, 14]],</span>
+<span class="go">      [[15, 16, 17, 18, 19],</span>
+<span class="go">        [20, 21, 22, 23, 24],</span>
+<span class="go">        [25, 26, 27, 28, 29]]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="kc">True</span><span class="p">,</span> <span class="kc">True</span><span class="p">,</span> <span class="kc">False</span><span class="p">],</span> <span class="p">[</span><span class="kc">False</span><span class="p">,</span> <span class="kc">True</span><span class="p">,</span> <span class="kc">True</span><span class="p">]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">b</span><span class="p">]</span>
+<span class="go">array([[ 0,  1,  2,  3,  4],</span>
+<span class="go">      [ 5,  6,  7,  8,  9],</span>
+<span class="go">      [20, 21, 22, 23, 24],</span>
+<span class="go">      [25, 26, 27, 28, 29]])</span>
+</pre></div>
+</div>
+</section>
+<section id="combining-advanced-and-basic-indexing">
+<span id="id6"></span><h3>Combining advanced and basic indexing<a class="headerlink" href="#combining-advanced-and-basic-indexing" title="Permalink to this headline">#</a></h3>
+<p>When there is at least one slice (<code class="docutils literal notranslate"><span class="pre">:</span></code>), ellipsis (<code class="docutils literal notranslate"><span class="pre">...</span></code>) or <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a>
+in the index (or the array has more dimensions than there are advanced indices),
+then the behaviour can be more complicated. It is like concatenating the
+indexing result for each advanced index element.</p>
+<p>In the simplest case, there is only a <em>single</em> advanced index combined with
+a slice. For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">35</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span><span class="mi">7</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span>
+<span class="go">array([[ 1,  2],</span>
+<span class="go">       [15, 16],</span>
+<span class="go">       [29, 30]])</span>
+</pre></div>
+</div>
+<p>In effect, the slice and index array operation are independent. The slice
+operation extracts columns with index 1 and 2, (i.e. the 2nd and 3rd columns),
+followed by the index array operation which extracts rows with index 0, 2 and 4
+(i.e the first, third and fifth rows). This is equivalent to:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">][</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="p">:]</span>
+<span class="go">array([[ 1,  2],</span>
+<span class="go">       [15, 16],</span>
+<span class="go">       [29, 30]])</span>
+</pre></div>
+</div>
+<p>A single advanced index can, for example, replace a slice and the result array
+will be the same. However, it is a copy and may have a different memory layout.
+A slice is preferable when it is possible.
+For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span> <span class="mi">0</span><span class="p">,</span>  <span class="mi">1</span><span class="p">,</span>  <span class="mi">2</span><span class="p">],</span>
+<span class="gp">... </span>              <span class="p">[</span> <span class="mi">3</span><span class="p">,</span>  <span class="mi">4</span><span class="p">,</span>  <span class="mi">5</span><span class="p">],</span>
+<span class="gp">... </span>              <span class="p">[</span> <span class="mi">6</span><span class="p">,</span>  <span class="mi">7</span><span class="p">,</span>  <span class="mi">8</span><span class="p">],</span>
+<span class="gp">... </span>              <span class="p">[</span> <span class="mi">9</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">11</span><span class="p">]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span>
+<span class="go">array([[4, 5]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">2</span><span class="p">,</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]]</span>
+<span class="go">array([[4, 5]])</span>
+</pre></div>
+</div>
+<p>The easiest way to understand a combination of <em>multiple</em> advanced indices may
+be to think in terms of the resulting shape. There are two parts to the indexing
+operation, the subspace defined by the basic indexing (excluding integers) and
+the subspace from the advanced indexing part. Two cases of index combination
+need to be distinguished:</p>
+<ul class="simple">
+<li><p>The advanced indices are separated by a slice, <a class="reference external" href="https://docs.python.org/3/library/constants.html#Ellipsis" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Ellipsis</span></code></a> or
+<a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a>. For example <code class="docutils literal notranslate"><span class="pre">x[arr1,</span> <span class="pre">:,</span> <span class="pre">arr2]</span></code>.</p></li>
+<li><p>The advanced indices are all next to each other.
+For example <code class="docutils literal notranslate"><span class="pre">x[...,</span> <span class="pre">arr1,</span> <span class="pre">arr2,</span> <span class="pre">:]</span></code> but <em>not</em> <code class="docutils literal notranslate"><span class="pre">x[arr1,</span> <span class="pre">:,</span> <span class="pre">1]</span></code>
+since <code class="docutils literal notranslate"><span class="pre">1</span></code> is an advanced index in this regard.</p></li>
+</ul>
+<p>In the first case, the dimensions resulting from the advanced indexing
+operation come first in the result array, and the subspace dimensions after
+that.
+In the second case, the dimensions from the advanced indexing operations
+are inserted into the result array at the same spot as they were in the
+initial array (the latter logic is what makes simple advanced indexing
+behave just like slicing).</p>
+<p class="rubric">Example</p>
+<p>Suppose <code class="docutils literal notranslate"><span class="pre">x.shape</span></code> is (10, 20, 30) and <code class="docutils literal notranslate"><span class="pre">ind</span></code> is a (2, 3, 4)-shaped
+indexing <a class="reference internal" href="../reference/arrays.scalars.html#numpy.intp" title="numpy.intp"><code class="xref py py-class docutils literal notranslate"><span class="pre">intp</span></code></a> array, then <code class="docutils literal notranslate"><span class="pre">result</span> <span class="pre">=</span> <span class="pre">x[...,</span> <span class="pre">ind,</span> <span class="pre">:]</span></code> has
+shape (10, 2, 3, 4, 30) because the (20,)-shaped subspace has been
+replaced with a (2, 3, 4)-shaped broadcasted indexing subspace. If
+we let <em>i, j, k</em> loop over the (2, 3, 4)-shaped subspace then
+<code class="docutils literal notranslate"><span class="pre">result[...,</span> <span class="pre">i,</span> <span class="pre">j,</span> <span class="pre">k,</span> <span class="pre">:]</span> <span class="pre">=</span> <span class="pre">x[...,</span> <span class="pre">ind[i,</span> <span class="pre">j,</span> <span class="pre">k],</span> <span class="pre">:]</span></code>. This example
+produces the same result as <a class="reference internal" href="../reference/generated/numpy.ndarray.take.html#numpy.ndarray.take" title="numpy.ndarray.take"><code class="xref py py-meth docutils literal notranslate"><span class="pre">x.take(ind,</span> <span class="pre">axis=-2)</span></code></a>.</p>
+<p class="rubric">Example</p>
+<p>Let <code class="docutils literal notranslate"><span class="pre">x.shape</span></code> be (10, 20, 30, 40, 50) and suppose <code class="docutils literal notranslate"><span class="pre">ind_1</span></code>
+and <code class="docutils literal notranslate"><span class="pre">ind_2</span></code> can be broadcast to the shape (2, 3, 4). Then
+<code class="docutils literal notranslate"><span class="pre">x[:,</span> <span class="pre">ind_1,</span> <span class="pre">ind_2]</span></code> has shape (10, 2, 3, 4, 40, 50) because the
+(20, 30)-shaped subspace from X has been replaced with the
+(2, 3, 4) subspace from the indices. However,
+<code class="docutils literal notranslate"><span class="pre">x[:,</span> <span class="pre">ind_1,</span> <span class="pre">:,</span> <span class="pre">ind_2]</span></code> has shape (2, 3, 4, 10, 30, 50) because there
+is no unambiguous place to drop in the indexing subspace, thus
+it is tacked-on to the beginning. It is always possible to use
+<a class="reference internal" href="../reference/generated/numpy.ndarray.transpose.html#numpy.ndarray.transpose" title="numpy.ndarray.transpose"><code class="xref py py-meth docutils literal notranslate"><span class="pre">.transpose()</span></code></a> to move the subspace
+anywhere desired. Note that this example cannot be replicated
+using <a class="reference internal" href="../reference/generated/numpy.take.html#numpy.take" title="numpy.take"><code class="xref py py-func docutils literal notranslate"><span class="pre">take</span></code></a>.</p>
+<p class="rubric">Example</p>
+<p>Slicing can be combined with broadcasted boolean indices:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">35</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span> <span class="o">=</span> <span class="n">x</span> <span class="o">&gt;</span> <span class="mi">20</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span>
+<span class="go">array([[False, False, False, False, False, False, False],</span>
+<span class="go">      [False, False, False, False, False, False, False],</span>
+<span class="go">      [False, False, False, False, False, False, False],</span>
+<span class="go">      [ True,  True,  True,  True,  True,  True,  True],</span>
+<span class="go">      [ True,  True,  True,  True,  True,  True,  True]])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">b</span><span class="p">[:,</span> <span class="mi">5</span><span class="p">],</span> <span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span>
+<span class="go">array([[22, 23],</span>
+<span class="go">      [29, 30]])</span>
+</pre></div>
+</div>
+</section>
+</section>
+<section id="field-access">
+<span id="arrays-indexing-fields"></span><h2>Field access<a class="headerlink" href="#field-access" title="Permalink to this headline">#</a></h2>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="basics.rec.html#structured-arrays"><span class="std std-ref">Structured arrays</span></a></p>
+</div>
+<p>If the <a class="reference internal" href="../reference/generated/numpy.ndarray.html#numpy.ndarray" title="numpy.ndarray"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> object is a structured array the <a class="reference internal" href="../glossary.html#term-field"><span class="xref std std-term">fields</span></a>
+of the array can be accessed by indexing the array with strings,
+dictionary-like.</p>
+<p>Indexing <code class="docutils literal notranslate"><span class="pre">x['field-name']</span></code> returns a new <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">view</span></a> to the array,
+which is of the same shape as <em>x</em> (except when the field is a
+sub-array) but of data type <code class="docutils literal notranslate"><span class="pre">x.dtype['field-name']</span></code> and contains
+only the part of the data in the specified field. Also,
+<a class="reference internal" href="../reference/arrays.classes.html#arrays-classes-rec"><span class="std std-ref">record array</span></a> scalars can be “indexed” this way.</p>
+<p>Indexing into a structured array can also be done with a list of field names,
+e.g. <code class="docutils literal notranslate"><span class="pre">x[['field-name1',</span> <span class="pre">'field-name2']]</span></code>. As of NumPy 1.16, this returns a
+view containing only those fields. In older versions of NumPy, it returned a
+copy. See the user guide section on <a class="reference internal" href="basics.rec.html#structured-arrays"><span class="std std-ref">Structured arrays</span></a> for more
+information on multifield indexing.</p>
+<p>If the accessed field is a sub-array, the dimensions of the sub-array
+are appended to the shape of the result.
+For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="p">[(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">),</span> <span class="p">(</span><span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">,</span> <span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="s1">&#39;a&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span>
+<span class="go">(2, 2)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="s1">&#39;a&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">dtype</span>
+<span class="go">dtype(&#39;int32&#39;)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="s1">&#39;b&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span>
+<span class="go">(2, 2, 3, 3)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="s1">&#39;b&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">dtype</span>
+<span class="go">dtype(&#39;float64&#39;)</span>
+</pre></div>
+</div>
+</section>
+<section id="flat-iterator-indexing">
+<span id="id7"></span><h2>Flat Iterator indexing<a class="headerlink" href="#flat-iterator-indexing" title="Permalink to this headline">#</a></h2>
+<p><a class="reference internal" href="../reference/generated/numpy.ndarray.flat.html#numpy.ndarray.flat" title="numpy.ndarray.flat"><code class="xref py py-attr docutils literal notranslate"><span class="pre">x.flat</span></code></a> returns an iterator that will iterate
+over the entire array (in C-contiguous style with the last index
+varying the fastest). This iterator object can also be indexed using
+basic slicing or advanced indexing as long as the selection object is
+not a tuple. This should be clear from the fact that <a class="reference internal" href="../reference/generated/numpy.ndarray.flat.html#numpy.ndarray.flat" title="numpy.ndarray.flat"><code class="xref py py-attr docutils literal notranslate"><span class="pre">x.flat</span></code></a> is a 1-dimensional view. It can be used for integer
+indexing with 1-dimensional C-style-flat indices. The shape of any
+returned array is therefore the shape of the integer indexing object.</p>
+</section>
+<section id="assigning-values-to-indexed-arrays">
+<span id="index-3"></span><span id="id8"></span><h2>Assigning values to indexed arrays<a class="headerlink" href="#assigning-values-to-indexed-arrays" title="Permalink to this headline">#</a></h2>
+<p>As mentioned, one can select a subset of an array to assign to using
+a single index, slices, and index and mask arrays. The value being
+assigned to the indexed array must be shape consistent (the same shape
+or broadcastable to the shape the index produces). For example, it is
+permitted to assign a constant to a slice:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">:</span><span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+</pre></div>
+</div>
+<p>or an array of the right size:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">:</span><span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Note that assignments may result in changes if assigning
+higher types to lower types (like floats to ints) or even
+exceptions (assigning complex to floats or ints):</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.2</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<span class="go">1</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.2</span><span class="n">j</span>
+<span class="gt">Traceback (most recent call last):</span>
+  <span class="c">...</span>
+<span class="gr">TypeError</span>: <span class="n">can&#39;t convert complex to int</span>
+</pre></div>
+</div>
+<p>Unlike some of the references (such as array and mask indices)
+assignments are always made to the original data in the array
+(indeed, nothing else would make sense!). Note though, that some
+actions may not work as one may naively expect. This particular
+example is often surprising to people:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">50</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
+<span class="go">array([ 0, 10, 20, 30, 40])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">])]</span> <span class="o">+=</span> <span class="mi">1</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
+<span class="go">array([ 0, 11, 20, 31, 40])</span>
+</pre></div>
+</div>
+<p>Where people expect that the 1st location will be incremented by 3.
+In fact, it will only be incremented by 1. The reason is that
+a new array is extracted from the original (as a temporary) containing
+the values at 1, 1, 3, 1, then the value 1 is added to the temporary,
+and then the temporary is assigned back to the original array. Thus
+the value of the array at <code class="docutils literal notranslate"><span class="pre">x[1]</span> <span class="pre">+</span> <span class="pre">1</span></code> is assigned to <code class="docutils literal notranslate"><span class="pre">x[1]</span></code> three times,
+rather than being incremented 3 times.</p>
+</section>
+<section id="dealing-with-variable-numbers-of-indices-within-programs">
+<span id="dealing-with-variable-indices"></span><h2>Dealing with variable numbers of indices within programs<a class="headerlink" href="#dealing-with-variable-numbers-of-indices-within-programs" title="Permalink to this headline">#</a></h2>
+<p>The indexing syntax is very powerful but limiting when dealing with
+a variable number of indices. For example, if you want to write
+a function that can handle arguments with various numbers of
+dimensions without having to write special case code for each
+number of possible dimensions, how can that be done? If one
+supplies to the index a tuple, the tuple will be interpreted
+as a list of indices. For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">81</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">indices</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[</span><span class="n">indices</span><span class="p">]</span>
+<span class="go">40</span>
+</pre></div>
+</div>
+<p>So one can use code to construct tuples of any number of indices
+and then use these within an index.</p>
+<p>Slices can be specified within programs by using the slice() function
+in Python. For example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">indices</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="nb">slice</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>  <span class="c1"># same as [1, 1, 1, 0:2]</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[</span><span class="n">indices</span><span class="p">]</span>
+<span class="go">array([39, 40])</span>
+</pre></div>
+</div>
+<p>Likewise, ellipsis can be specified by code by using the Ellipsis
+object:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">indices</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="bp">Ellipsis</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>  <span class="c1"># same as [1, ..., 1]</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[</span><span class="n">indices</span><span class="p">]</span>
+<span class="go">array([[28, 31, 34],</span>
+<span class="go">       [37, 40, 43],</span>
+<span class="go">       [46, 49, 52]])</span>
+</pre></div>
+</div>
+<p>For this reason, it is possible to use the output from the
+<a class="reference internal" href="../reference/generated/numpy.ndarray.nonzero.html#numpy.ndarray.nonzero" title="numpy.ndarray.nonzero"><code class="xref py py-meth docutils literal notranslate"><span class="pre">np.nonzero()</span></code></a> function directly as an index since
+it always returns a tuple of index arrays.</p>
+<p>Because of the special treatment of tuples, they are not automatically
+converted to an array as a list would be. As an example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">]]</span>  <span class="c1"># produces a large array</span>
+<span class="go">array([[[[27, 28, 29],</span>
+<span class="go">         [30, 31, 32], ...</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)]</span>  <span class="c1"># returns a single value</span>
+<span class="go">40</span>
+</pre></div>
+</div>
+</section>
+<section id="detailed-notes">
+<h2>Detailed notes<a class="headerlink" href="#detailed-notes" title="Permalink to this headline">#</a></h2>
+<p>These are some detailed notes, which are not of importance for day to day
+indexing (in no particular order):</p>
+<ul class="simple">
+<li><p>The native NumPy indexing type is <code class="docutils literal notranslate"><span class="pre">intp</span></code> and may differ from the
+default integer array type. <code class="docutils literal notranslate"><span class="pre">intp</span></code> is the smallest data type
+sufficient to safely index any array; for advanced indexing it may be
+faster than other types.</p></li>
+<li><p>For advanced assignments, there is in general no guarantee for the
+iteration order. This means that if an element is set more than once,
+it is not possible to predict the final result.</p></li>
+<li><p>An empty (tuple) index is a full scalar index into a zero-dimensional array.
+<code class="docutils literal notranslate"><span class="pre">x[()]</span></code> returns a <em>scalar</em> if <code class="docutils literal notranslate"><span class="pre">x</span></code> is zero-dimensional and a view
+otherwise. On the other hand, <code class="docutils literal notranslate"><span class="pre">x[...]</span></code> always returns a view.</p></li>
+<li><p>If a zero-dimensional array is present in the index <em>and</em> it is a full
+integer index the result will be a <em>scalar</em> and not a zero-dimensional array.
+(Advanced indexing is not triggered.)</p></li>
+<li><p>When an ellipsis (<code class="docutils literal notranslate"><span class="pre">...</span></code>) is present but has no size (i.e. replaces zero
+<code class="docutils literal notranslate"><span class="pre">:</span></code>) the result will still always be an array. A view if no advanced index
+is present, otherwise a copy.</p></li>
+<li><p>The <code class="docutils literal notranslate"><span class="pre">nonzero</span></code> equivalence for Boolean arrays does not hold for zero
+dimensional boolean arrays.</p></li>
+<li><p>When the result of an advanced indexing operation has no elements but an
+individual index is out of bounds, whether or not an <code class="docutils literal notranslate"><span class="pre">IndexError</span></code> is
+raised is undefined (e.g. <code class="docutils literal notranslate"><span class="pre">x[[],</span> <span class="pre">[123]]</span></code> with <code class="docutils literal notranslate"><span class="pre">123</span></code> being out of bounds).</p></li>
+<li><p>When a <em>casting</em> error occurs during assignment (for example updating a
+numerical array using a sequence of strings), the array being assigned
+to may end up in an unpredictable partially updated state.
+However, if any other error (such as an out of bounds index) occurs, the
+array will remain unchanged.</p></li>
+<li><p>The memory layout of an advanced indexing result is optimized for each
+indexing operation and no particular memory order can be assumed.</p></li>
+<li><p>When using a subclass (especially one which manipulates its shape), the
+default <code class="docutils literal notranslate"><span class="pre">ndarray.__setitem__</span></code> behaviour will call <code class="docutils literal notranslate"><span class="pre">__getitem__</span></code> for
+<em>basic</em> indexing but not for <em>advanced</em> indexing. For such a subclass it may
+be preferable to call <code class="docutils literal notranslate"><span class="pre">ndarray.__setitem__</span></code> with a <em>base class</em> ndarray
+view on the data. This <em>must</em> be done if the subclasses <code class="docutils literal notranslate"><span class="pre">__getitem__</span></code> does
+not return views.</p></li>
+</ul>
+</section>
+</section>
+
+
+              </div>
+              
+              
+              <!-- Previous / next buttons -->
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+    <a class='left-prev' id="prev-link" href="basics.creation.html" title="previous page">
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diff --git a/tests/integrated/test-boutpp/slicing/basics.indexing.txt b/tests/integrated/test-boutpp/slicing/basics.indexing.txt
new file mode 100644
index 0000000000..eba782d5e2
--- /dev/null
+++ b/tests/integrated/test-boutpp/slicing/basics.indexing.txt
@@ -0,0 +1,687 @@
+
+logo
+
+    User Guide
+    API reference
+    Development
+    Release notes
+    Learn
+
+    GitHub
+    Twitter
+
+    What is NumPy?
+    Installation
+    NumPy quickstart
+    NumPy: the absolute basics for beginners
+    NumPy fundamentals
+        Array creation
+        Indexing on ndarrays
+        I/O with NumPy
+        Data types
+        Broadcasting
+        Byte-swapping
+        Structured arrays
+        Writing custom array containers
+        Subclassing ndarray
+        Universal functions ( ufunc ) basics
+        Copies and views
+        Interoperability with NumPy
+    Miscellaneous
+    NumPy for MATLAB users
+    Building from source
+    Using NumPy C-API
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+    For downstream package authors
+
+    F2PY user guide and reference manual
+    Glossary
+    Under-the-hood Documentation for developers
+    Reporting bugs
+    Release notes
+    NumPy license
+
+On this page
+
+    Basic indexing
+        Single element indexing
+        Slicing and striding
+        Dimensional indexing tools
+    Advanced indexing
+    Field access
+    Flat Iterator indexing
+    Assigning values to indexed arrays
+    Dealing with variable numbers of indices within programs
+    Detailed notes
+
+Indexing on ndarrays
+
+See also
+
+Indexing routines
+
+ndarrays can be indexed using the standard Python x[obj] syntax, where x is the array and obj the selection. There are different kinds of indexing available depending on obj: basic indexing, advanced indexing and field access.
+
+Most of the following examples show the use of indexing when referencing data in an array. The examples work just as well when assigning to an array. See Assigning values to indexed arrays for specific examples and explanations on how assignments work.
+
+Note that in Python, x[(exp1, exp2, ..., expN)] is equivalent to x[exp1, exp2, ..., expN]; the latter is just syntactic sugar for the former.
+Basic indexing
+Single element indexing
+
+Single element indexing works exactly like that for other standard Python sequences. It is 0-based, and accepts negative indices for indexing from the end of the array.
+
+x = np.arange(10)
+
+x[2]
+2
+
+x[-2]
+8
+
+It is not necessary to separate each dimension’s index into its own set of square brackets.
+
+x.shape = (2, 5)  # now x is 2-dimensional
+
+x[1, 3]
+8
+
+x[1, -1]
+9
+
+Note that if one indexes a multidimensional array with fewer indices than dimensions, one gets a subdimensional array. For example:
+
+x[0]
+array([0, 1, 2, 3, 4])
+
+That is, each index specified selects the array corresponding to the rest of the dimensions selected. In the above example, choosing 0 means that the remaining dimension of length 5 is being left unspecified, and that what is returned is an array of that dimensionality and size. It must be noted that the returned array is a view, i.e., it is not a copy of the original, but points to the same values in memory as does the original array. In this case, the 1-D array at the first position (0) is returned. So using a single index on the returned array, results in a single element being returned. That is:
+
+x[0][2]
+2
+
+So note that x[0, 2] == x[0][2] though the second case is more inefficient as a new temporary array is created after the first index that is subsequently indexed by 2.
+
+Note
+
+NumPy uses C-order indexing. That means that the last index usually represents the most rapidly changing memory location, unlike Fortran or IDL, where the first index represents the most rapidly changing location in memory. This difference represents a great potential for confusion.
+Slicing and striding
+
+Basic slicing extends Python’s basic concept of slicing to N dimensions. Basic slicing occurs when obj is a slice object (constructed by start:stop:step notation inside of brackets), an integer, or a tuple of slice objects and integers. Ellipsis and newaxis objects can be interspersed with these as well.
+
+The simplest case of indexing with N integers returns an array scalar representing the corresponding item. As in Python, all indices are zero-based: for the i-th index
+, the valid range is where is the i-th element of the shape of the array. Negative indices are interpreted as counting from the end of the array (i.e., if , it means
+
+).
+
+All arrays generated by basic slicing are always views of the original array.
+
+Note
+
+NumPy slicing creates a view instead of a copy as in the case of built-in Python sequences such as string, tuple and list. Care must be taken when extracting a small portion from a large array which becomes useless after the extraction, because the small portion extracted contains a reference to the large original array whose memory will not be released until all arrays derived from it are garbage-collected. In such cases an explicit copy() is recommended.
+
+The standard rules of sequence slicing apply to basic slicing on a per-dimension basis (including using a step index). Some useful concepts to remember include:
+
+    The basic slice syntax is i:j:k where i is the starting index, j is the stopping index, and k is the step (
+
+). This selects the m elements (in the corresponding dimension) with index values i, i + k, …, i + (m - 1) k where
+
+and q and r are the quotient and remainder obtained by dividing j - i by k: j - i = q k + r, so that i + (m - 1) k < j. For example:
+
+x = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
+
+x[1:7:2]
+array([1, 3, 5])
+
+Negative i and j are interpreted as n + i and n + j where n is the number of elements in the corresponding dimension. Negative k makes stepping go towards smaller indices. From the above example:
+
+x[-2:10]
+array([8, 9])
+
+x[-3:3:-1]
+array([7, 6, 5, 4])
+
+Assume n is the number of elements in the dimension being sliced. Then, if i is not given it defaults to 0 for k > 0 and n - 1 for k < 0 . If j is not given it defaults to n for k > 0 and -n-1 for k < 0 . If k is not given it defaults to 1. Note that :: is the same as : and means select all indices along this axis. From the above example:
+
+x[5:]
+array([5, 6, 7, 8, 9])
+
+If the number of objects in the selection tuple is less than N, then : is assumed for any subsequent dimensions. For example:
+
+x = np.array([[[1],[2],[3]], [[4],[5],[6]]])
+
+x.shape
+(2, 3, 1)
+
+    x[1:2]
+    array([[[4],
+            [5],
+            [6]]])
+
+    An integer, i, returns the same values as i:i+1 except the dimensionality of the returned object is reduced by 1. In particular, a selection tuple with the p-th element an integer (and all other entries :) returns the corresponding sub-array with dimension N - 1. If N = 1 then the returned object is an array scalar. These objects are explained in Scalars.
+
+    If the selection tuple has all entries : except the p-th entry which is a slice object i:j:k, then the returned array has dimension N formed by concatenating the sub-arrays returned by integer indexing of elements i, i+k, …, i + (m - 1) k < j,
+
+    Basic slicing with more than one non-: entry in the slicing tuple, acts like repeated application of slicing using a single non-: entry, where the non-: entries are successively taken (with all other non-: entries replaced by :). Thus, x[ind1, ..., ind2,:] acts like x[ind1][..., ind2, :] under basic slicing.
+
+    Warning
+
+    The above is not true for advanced indexing.
+
+    You may use slicing to set values in the array, but (unlike lists) you can never grow the array. The size of the value to be set in x[obj] = value must be (broadcastable) to the same shape as x[obj].
+
+    A slicing tuple can always be constructed as obj and used in the x[obj] notation. Slice objects can be used in the construction in place of the [start:stop:step] notation. For example, x[1:10:5, ::-1] can also be implemented as obj = (slice(1, 10, 5), slice(None, None, -1)); x[obj] . This can be useful for constructing generic code that works on arrays of arbitrary dimensions. See Dealing with variable numbers of indices within programs for more information.
+
+Dimensional indexing tools
+
+There are some tools to facilitate the easy matching of array shapes with expressions and in assignments.
+
+Ellipsis expands to the number of : objects needed for the selection tuple to index all dimensions. In most cases, this means that the length of the expanded selection tuple is x.ndim. There may only be a single ellipsis present. From the above example:
+
+x[..., 0]
+array([[1, 2, 3],
+      [4, 5, 6]])
+
+This is equivalent to:
+
+x[:, :, 0]
+array([[1, 2, 3],
+      [4, 5, 6]])
+
+Each newaxis object in the selection tuple serves to expand the dimensions of the resulting selection by one unit-length dimension. The added dimension is the position of the newaxis object in the selection tuple. newaxis is an alias for None, and None can be used in place of this with the same result. From the above example:
+
+x[:, np.newaxis, :, :].shape
+(2, 1, 3, 1)
+
+x[:, None, :, :].shape
+(2, 1, 3, 1)
+
+This can be handy to combine two arrays in a way that otherwise would require explicit reshaping operations. For example:
+
+x = np.arange(5)
+
+x[:, np.newaxis] + x[np.newaxis, :]
+array([[0, 1, 2, 3, 4],
+      [1, 2, 3, 4, 5],
+      [2, 3, 4, 5, 6],
+      [3, 4, 5, 6, 7],
+      [4, 5, 6, 7, 8]])
+
+Advanced indexing
+
+Advanced indexing is triggered when the selection object, obj, is a non-tuple sequence object, an ndarray (of data type integer or bool), or a tuple with at least one sequence object or ndarray (of data type integer or bool). There are two types of advanced indexing: integer and Boolean.
+
+Advanced indexing always returns a copy of the data (contrast with basic slicing that returns a view).
+
+Warning
+
+The definition of advanced indexing means that x[(1, 2, 3),] is fundamentally different than x[(1, 2, 3)]. The latter is equivalent to x[1, 2, 3] which will trigger basic selection while the former will trigger advanced indexing. Be sure to understand why this occurs.
+
+Also recognize that x[[1, 2, 3]] will trigger advanced indexing, whereas due to the deprecated Numeric compatibility mentioned above, x[[1, 2, slice(None)]] will trigger basic slicing.
+Integer array indexing
+
+Integer array indexing allows selection of arbitrary items in the array based on their N-dimensional index. Each integer array represents a number of indices into that dimension.
+
+Negative values are permitted in the index arrays and work as they do with single indices or slices:
+
+x = np.arange(10, 1, -1)
+
+x
+array([10,  9,  8,  7,  6,  5,  4,  3,  2])
+
+x[np.array([3, 3, 1, 8])]
+array([7, 7, 9, 2])
+
+x[np.array([3, 3, -3, 8])]
+array([7, 7, 4, 2])
+
+If the index values are out of bounds then an IndexError is thrown:
+
+x = np.array([[1, 2], [3, 4], [5, 6]])
+
+x[np.array([1, -1])]
+array([[3, 4],
+      [5, 6]])
+
+x[np.array([3, 4])]
+Traceback (most recent call last):
+  ...
+IndexError: index 3 is out of bounds for axis 0 with size 3
+
+When the index consists of as many integer arrays as dimensions of the array being indexed, the indexing is straightforward, but different from slicing.
+
+Advanced indices always are broadcast and iterated as one:
+
+result[i_1, ..., i_M] == x[ind_1[i_1, ..., i_M], ind_2[i_1, ..., i_M],
+                           ..., ind_N[i_1, ..., i_M]]
+
+Note that the resulting shape is identical to the (broadcast) indexing array shapes ind_1, ..., ind_N. If the indices cannot be broadcast to the same shape, an exception IndexError: shape mismatch: indexing arrays could not be broadcast together with shapes... is raised.
+
+Indexing with multidimensional index arrays tend to be more unusual uses, but they are permitted, and they are useful for some problems. We’ll start with the simplest multidimensional case:
+
+y = np.arange(35).reshape(5, 7)
+
+y
+array([[ 0,  1,  2,  3,  4,  5,  6],
+       [ 7,  8,  9, 10, 11, 12, 13],
+       [14, 15, 16, 17, 18, 19, 20],
+       [21, 22, 23, 24, 25, 26, 27],
+       [28, 29, 30, 31, 32, 33, 34]])
+
+y[np.array([0, 2, 4]), np.array([0, 1, 2])]
+array([ 0, 15, 30])
+
+In this case, if the index arrays have a matching shape, and there is an index array for each dimension of the array being indexed, the resultant array has the same shape as the index arrays, and the values correspond to the index set for each position in the index arrays. In this example, the first index value is 0 for both index arrays, and thus the first value of the resultant array is y[0, 0]. The next value is y[2, 1], and the last is y[4, 2].
+
+If the index arrays do not have the same shape, there is an attempt to broadcast them to the same shape. If they cannot be broadcast to the same shape, an exception is raised:
+
+y[np.array([0, 2, 4]), np.array([0, 1])]
+Traceback (most recent call last):
+  ...
+IndexError: shape mismatch: indexing arrays could not be broadcast
+together with shapes (3,) (2,)
+
+The broadcasting mechanism permits index arrays to be combined with scalars for other indices. The effect is that the scalar value is used for all the corresponding values of the index arrays:
+
+y[np.array([0, 2, 4]), 1]
+array([ 1, 15, 29])
+
+Jumping to the next level of complexity, it is possible to only partially index an array with index arrays. It takes a bit of thought to understand what happens in such cases. For example if we just use one index array with y:
+
+y[np.array([0, 2, 4])]
+array([[ 0,  1,  2,  3,  4,  5,  6],
+      [14, 15, 16, 17, 18, 19, 20],
+      [28, 29, 30, 31, 32, 33, 34]])
+
+It results in the construction of a new array where each value of the index array selects one row from the array being indexed and the resultant array has the resulting shape (number of index elements, size of row).
+
+In general, the shape of the resultant array will be the concatenation of the shape of the index array (or the shape that all the index arrays were broadcast to) with the shape of any unused dimensions (those not indexed) in the array being indexed.
+
+Example
+
+From each row, a specific element should be selected. The row index is just [0, 1, 2] and the column index specifies the element to choose for the corresponding row, here [0, 1, 0]. Using both together the task can be solved using advanced indexing:
+
+x = np.array([[1, 2], [3, 4], [5, 6]])
+
+x[[0, 1, 2], [0, 1, 0]]
+array([1, 4, 5])
+
+To achieve a behaviour similar to the basic slicing above, broadcasting can be used. The function ix_ can help with this broadcasting. This is best understood with an example.
+
+Example
+
+From a 4x3 array the corner elements should be selected using advanced indexing. Thus all elements for which the column is one of [0, 2] and the row is one of [0, 3] need to be selected. To use advanced indexing one needs to select all elements explicitly. Using the method explained previously one could write:
+
+x = np.array([[ 0,  1,  2],
+
+              [ 3,  4,  5],
+
+              [ 6,  7,  8],
+
+              [ 9, 10, 11]])
+
+rows = np.array([[0, 0],
+
+                 [3, 3]], dtype=np.intp)
+
+columns = np.array([[0, 2],
+
+                    [0, 2]], dtype=np.intp)
+
+x[rows, columns]
+array([[ 0,  2],
+       [ 9, 11]])
+
+However, since the indexing arrays above just repeat themselves, broadcasting can be used (compare operations such as rows[:, np.newaxis] + columns) to simplify this:
+
+rows = np.array([0, 3], dtype=np.intp)
+
+columns = np.array([0, 2], dtype=np.intp)
+
+rows[:, np.newaxis]
+array([[0],
+       [3]])
+
+x[rows[:, np.newaxis], columns]
+array([[ 0,  2],
+       [ 9, 11]])
+
+This broadcasting can also be achieved using the function ix_:
+
+x[np.ix_(rows, columns)]
+array([[ 0,  2],
+       [ 9, 11]])
+
+Note that without the np.ix_ call, only the diagonal elements would be selected:
+
+x[rows, columns]
+array([ 0, 11])
+
+This difference is the most important thing to remember about indexing with multiple advanced indices.
+
+Example
+
+A real-life example of where advanced indexing may be useful is for a color lookup table where we want to map the values of an image into RGB triples for display. The lookup table could have a shape (nlookup, 3). Indexing such an array with an image with shape (ny, nx) with dtype=np.uint8 (or any integer type so long as values are with the bounds of the lookup table) will result in an array of shape (ny, nx, 3) where a triple of RGB values is associated with each pixel location.
+Boolean array indexing
+
+This advanced indexing occurs when obj is an array object of Boolean type, such as may be returned from comparison operators. A single boolean index array is practically identical to x[obj.nonzero()] where, as described above, obj.nonzero() returns a tuple (of length obj.ndim) of integer index arrays showing the True elements of obj. However, it is faster when obj.shape == x.shape.
+
+If obj.ndim == x.ndim, x[obj] returns a 1-dimensional array filled with the elements of x corresponding to the True values of obj. The search order will be row-major, C-style. If obj has True values at entries that are outside of the bounds of x, then an index error will be raised. If obj is smaller than x it is identical to filling it with False.
+
+A common use case for this is filtering for desired element values. For example, one may wish to select all entries from an array which are not NaN:
+
+x = np.array([[1., 2.], [np.nan, 3.], [np.nan, np.nan]])
+
+x[~np.isnan(x)]
+array([1., 2., 3.])
+
+Or wish to add a constant to all negative elements:
+
+x = np.array([1., -1., -2., 3])
+
+x[x < 0] += 20
+
+x
+array([ 1., 19., 18., 3.])
+
+In general if an index includes a Boolean array, the result will be identical to inserting obj.nonzero() into the same position and using the integer array indexing mechanism described above. x[ind_1, boolean_array, ind_2] is equivalent to x[(ind_1,) + boolean_array.nonzero() + (ind_2,)].
+
+If there is only one Boolean array and no integer indexing array present, this is straightforward. Care must only be taken to make sure that the boolean index has exactly as many dimensions as it is supposed to work with.
+
+In general, when the boolean array has fewer dimensions than the array being indexed, this is equivalent to x[b, ...], which means x is indexed by b followed by as many : as are needed to fill out the rank of x. Thus the shape of the result is one dimension containing the number of True elements of the boolean array, followed by the remaining dimensions of the array being indexed:
+
+x = np.arange(35).reshape(5, 7)
+
+b = x > 20
+
+b[:, 5]
+array([False, False, False,  True,  True])
+
+x[b[:, 5]]
+array([[21, 22, 23, 24, 25, 26, 27],
+      [28, 29, 30, 31, 32, 33, 34]])
+
+Here the 4th and 5th rows are selected from the indexed array and combined to make a 2-D array.
+
+Example
+
+From an array, select all rows which sum up to less or equal two:
+
+x = np.array([[0, 1], [1, 1], [2, 2]])
+
+rowsum = x.sum(-1)
+
+x[rowsum <= 2, :]
+array([[0, 1],
+       [1, 1]])
+
+Combining multiple Boolean indexing arrays or a Boolean with an integer indexing array can best be understood with the obj.nonzero() analogy. The function ix_ also supports boolean arrays and will work without any surprises.
+
+Example
+
+Use boolean indexing to select all rows adding up to an even number. At the same time columns 0 and 2 should be selected with an advanced integer index. Using the ix_ function this can be done with:
+
+x = np.array([[ 0,  1,  2],
+
+              [ 3,  4,  5],
+
+              [ 6,  7,  8],
+
+              [ 9, 10, 11]])
+
+rows = (x.sum(-1) % 2) == 0
+
+rows
+array([False,  True, False,  True])
+
+columns = [0, 2]
+
+x[np.ix_(rows, columns)]
+array([[ 3,  5],
+       [ 9, 11]])
+
+Without the np.ix_ call, only the diagonal elements would be selected.
+
+Or without np.ix_ (compare the integer array examples):
+
+rows = rows.nonzero()[0]
+
+x[rows[:, np.newaxis], columns]
+array([[ 3,  5],
+       [ 9, 11]])
+
+Example
+
+Use a 2-D boolean array of shape (2, 3) with four True elements to select rows from a 3-D array of shape (2, 3, 5) results in a 2-D result of shape (4, 5):
+
+x = np.arange(30).reshape(2, 3, 5)
+
+x
+array([[[ 0,  1,  2,  3,  4],
+        [ 5,  6,  7,  8,  9],
+        [10, 11, 12, 13, 14]],
+      [[15, 16, 17, 18, 19],
+        [20, 21, 22, 23, 24],
+        [25, 26, 27, 28, 29]]])
+
+b = np.array([[True, True, False], [False, True, True]])
+
+x[b]
+array([[ 0,  1,  2,  3,  4],
+      [ 5,  6,  7,  8,  9],
+      [20, 21, 22, 23, 24],
+      [25, 26, 27, 28, 29]])
+
+Combining advanced and basic indexing
+
+When there is at least one slice (:), ellipsis (...) or newaxis in the index (or the array has more dimensions than there are advanced indices), then the behaviour can be more complicated. It is like concatenating the indexing result for each advanced index element.
+
+In the simplest case, there is only a single advanced index combined with a slice. For example:
+
+y = np.arange(35).reshape(5,7)
+
+y[np.array([0, 2, 4]), 1:3]
+array([[ 1,  2],
+       [15, 16],
+       [29, 30]])
+
+In effect, the slice and index array operation are independent. The slice operation extracts columns with index 1 and 2, (i.e. the 2nd and 3rd columns), followed by the index array operation which extracts rows with index 0, 2 and 4 (i.e the first, third and fifth rows). This is equivalent to:
+
+y[:, 1:3][np.array([0, 2, 4]), :]
+array([[ 1,  2],
+       [15, 16],
+       [29, 30]])
+
+A single advanced index can, for example, replace a slice and the result array will be the same. However, it is a copy and may have a different memory layout. A slice is preferable when it is possible. For example:
+
+x = np.array([[ 0,  1,  2],
+
+              [ 3,  4,  5],
+
+              [ 6,  7,  8],
+
+              [ 9, 10, 11]])
+
+x[1:2, 1:3]
+array([[4, 5]])
+
+x[1:2, [1, 2]]
+array([[4, 5]])
+
+The easiest way to understand a combination of multiple advanced indices may be to think in terms of the resulting shape. There are two parts to the indexing operation, the subspace defined by the basic indexing (excluding integers) and the subspace from the advanced indexing part. Two cases of index combination need to be distinguished:
+
+    The advanced indices are separated by a slice, Ellipsis or newaxis. For example x[arr1, :, arr2].
+
+    The advanced indices are all next to each other. For example x[..., arr1, arr2, :] but not x[arr1, :, 1] since 1 is an advanced index in this regard.
+
+In the first case, the dimensions resulting from the advanced indexing operation come first in the result array, and the subspace dimensions after that. In the second case, the dimensions from the advanced indexing operations are inserted into the result array at the same spot as they were in the initial array (the latter logic is what makes simple advanced indexing behave just like slicing).
+
+Example
+
+Suppose x.shape is (10, 20, 30) and ind is a (2, 3, 4)-shaped indexing intp array, then result = x[..., ind, :] has shape (10, 2, 3, 4, 30) because the (20,)-shaped subspace has been replaced with a (2, 3, 4)-shaped broadcasted indexing subspace. If we let i, j, k loop over the (2, 3, 4)-shaped subspace then result[..., i, j, k, :] = x[..., ind[i, j, k], :]. This example produces the same result as x.take(ind, axis=-2).
+
+Example
+
+Let x.shape be (10, 20, 30, 40, 50) and suppose ind_1 and ind_2 can be broadcast to the shape (2, 3, 4). Then x[:, ind_1, ind_2] has shape (10, 2, 3, 4, 40, 50) because the (20, 30)-shaped subspace from X has been replaced with the (2, 3, 4) subspace from the indices. However, x[:, ind_1, :, ind_2] has shape (2, 3, 4, 10, 30, 50) because there is no unambiguous place to drop in the indexing subspace, thus it is tacked-on to the beginning. It is always possible to use .transpose() to move the subspace anywhere desired. Note that this example cannot be replicated using take.
+
+Example
+
+Slicing can be combined with broadcasted boolean indices:
+
+x = np.arange(35).reshape(5, 7)
+
+b = x > 20
+
+b
+array([[False, False, False, False, False, False, False],
+      [False, False, False, False, False, False, False],
+      [False, False, False, False, False, False, False],
+      [ True,  True,  True,  True,  True,  True,  True],
+      [ True,  True,  True,  True,  True,  True,  True]])
+
+x[b[:, 5], 1:3]
+array([[22, 23],
+      [29, 30]])
+
+Field access
+
+See also
+
+Structured arrays
+
+If the ndarray object is a structured array the fields of the array can be accessed by indexing the array with strings, dictionary-like.
+
+Indexing x['field-name'] returns a new view to the array, which is of the same shape as x (except when the field is a sub-array) but of data type x.dtype['field-name'] and contains only the part of the data in the specified field. Also, record array scalars can be “indexed” this way.
+
+Indexing into a structured array can also be done with a list of field names, e.g. x[['field-name1', 'field-name2']]. As of NumPy 1.16, this returns a view containing only those fields. In older versions of NumPy, it returned a copy. See the user guide section on Structured arrays for more information on multifield indexing.
+
+If the accessed field is a sub-array, the dimensions of the sub-array are appended to the shape of the result. For example:
+
+x = np.zeros((2, 2), dtype=[('a', np.int32), ('b', np.float64, (3, 3))])
+
+x['a'].shape
+(2, 2)
+
+x['a'].dtype
+dtype('int32')
+
+x['b'].shape
+(2, 2, 3, 3)
+
+x['b'].dtype
+dtype('float64')
+
+Flat Iterator indexing
+
+x.flat returns an iterator that will iterate over the entire array (in C-contiguous style with the last index varying the fastest). This iterator object can also be indexed using basic slicing or advanced indexing as long as the selection object is not a tuple. This should be clear from the fact that x.flat is a 1-dimensional view. It can be used for integer indexing with 1-dimensional C-style-flat indices. The shape of any returned array is therefore the shape of the integer indexing object.
+Assigning values to indexed arrays
+
+As mentioned, one can select a subset of an array to assign to using a single index, slices, and index and mask arrays. The value being assigned to the indexed array must be shape consistent (the same shape or broadcastable to the shape the index produces). For example, it is permitted to assign a constant to a slice:
+
+x = np.arange(10)
+
+x[2:7] = 1
+
+or an array of the right size:
+
+x[2:7] = np.arange(5)
+
+Note that assignments may result in changes if assigning higher types to lower types (like floats to ints) or even exceptions (assigning complex to floats or ints):
+
+x[1] = 1.2
+
+x[1]
+1
+
+x[1] = 1.2j
+Traceback (most recent call last):
+  ...
+TypeError: can't convert complex to int
+
+Unlike some of the references (such as array and mask indices) assignments are always made to the original data in the array (indeed, nothing else would make sense!). Note though, that some actions may not work as one may naively expect. This particular example is often surprising to people:
+
+x = np.arange(0, 50, 10)
+
+x
+array([ 0, 10, 20, 30, 40])
+
+x[np.array([1, 1, 3, 1])] += 1
+
+x
+array([ 0, 11, 20, 31, 40])
+
+Where people expect that the 1st location will be incremented by 3. In fact, it will only be incremented by 1. The reason is that a new array is extracted from the original (as a temporary) containing the values at 1, 1, 3, 1, then the value 1 is added to the temporary, and then the temporary is assigned back to the original array. Thus the value of the array at x[1] + 1 is assigned to x[1] three times, rather than being incremented 3 times.
+Dealing with variable numbers of indices within programs
+
+The indexing syntax is very powerful but limiting when dealing with a variable number of indices. For example, if you want to write a function that can handle arguments with various numbers of dimensions without having to write special case code for each number of possible dimensions, how can that be done? If one supplies to the index a tuple, the tuple will be interpreted as a list of indices. For example:
+
+z = np.arange(81).reshape(3, 3, 3, 3)
+
+indices = (1, 1, 1, 1)
+
+z[indices]
+40
+
+So one can use code to construct tuples of any number of indices and then use these within an index.
+
+Slices can be specified within programs by using the slice() function in Python. For example:
+
+indices = (1, 1, 1, slice(0, 2))  # same as [1, 1, 1, 0:2]
+
+z[indices]
+array([39, 40])
+
+Likewise, ellipsis can be specified by code by using the Ellipsis object:
+
+indices = (1, Ellipsis, 1)  # same as [1, ..., 1]
+
+z[indices]
+array([[28, 31, 34],
+       [37, 40, 43],
+       [46, 49, 52]])
+
+For this reason, it is possible to use the output from the np.nonzero() function directly as an index since it always returns a tuple of index arrays.
+
+Because of the special treatment of tuples, they are not automatically converted to an array as a list would be. As an example:
+
+z[[1, 1, 1, 1]]  # produces a large array
+array([[[[27, 28, 29],
+         [30, 31, 32], ...
+
+z[(1, 1, 1, 1)]  # returns a single value
+40
+
+Detailed notes
+
+These are some detailed notes, which are not of importance for day to day indexing (in no particular order):
+
+    The native NumPy indexing type is intp and may differ from the default integer array type. intp is the smallest data type sufficient to safely index any array; for advanced indexing it may be faster than other types.
+
+    For advanced assignments, there is in general no guarantee for the iteration order. This means that if an element is set more than once, it is not possible to predict the final result.
+
+    An empty (tuple) index is a full scalar index into a zero-dimensional array. x[()] returns a scalar if x is zero-dimensional and a view otherwise. On the other hand, x[...] always returns a view.
+
+    If a zero-dimensional array is present in the index and it is a full integer index the result will be a scalar and not a zero-dimensional array. (Advanced indexing is not triggered.)
+
+    When an ellipsis (...) is present but has no size (i.e. replaces zero :) the result will still always be an array. A view if no advanced index is present, otherwise a copy.
+
+    The nonzero equivalence for Boolean arrays does not hold for zero dimensional boolean arrays.
+
+    When the result of an advanced indexing operation has no elements but an individual index is out of bounds, whether or not an IndexError is raised is undefined (e.g. x[[], [123]] with 123 being out of bounds).
+
+    When a casting error occurs during assignment (for example updating a numerical array using a sequence of strings), the array being assigned to may end up in an unpredictable partially updated state. However, if any other error (such as an out of bounds index) occurs, the array will remain unchanged.
+
+    The memory layout of an advanced indexing result is optimized for each indexing operation and no particular memory order can be assumed.
+
+    When using a subclass (especially one which manipulates its shape), the default ndarray.__setitem__ behaviour will call __getitem__ for basic indexing but not for advanced indexing. For such a subclass it may be preferable to call ndarray.__setitem__ with a base class ndarray view on the data. This must be done if the subclasses __getitem__ does not return views.
+
+previous
+
+Array creation
+
+next
+
+I/O with NumPy
+
+© Copyright 2008-2022, NumPy Developers.
+
+Created using Sphinx 4.5.0.
diff --git a/tests/integrated/test-boutpp/slicing/slicingexamples b/tests/integrated/test-boutpp/slicing/slicingexamples
new file mode 100644
index 0000000000..7edb2fa5bc
--- /dev/null
+++ b/tests/integrated/test-boutpp/slicing/slicingexamples
@@ -0,0 +1 @@
+,
diff --git a/tests/integrated/test-boutpp/slicing/test.py b/tests/integrated/test-boutpp/slicing/test.py
new file mode 100644
index 0000000000..2f36b362cb
--- /dev/null
+++ b/tests/integrated/test-boutpp/slicing/test.py
@@ -0,0 +1,4 @@
+import boutcore as bc
+
+bc.init("-d test")
+bc.print("We can print to the log from python 🎉")
diff --git a/tests/integrated/test-griddata/test_griddata.cxx b/tests/integrated/test-griddata/test_griddata.cxx
index 9f12d48d9d..0277f9e001 100644
--- a/tests/integrated/test-griddata/test_griddata.cxx
+++ b/tests/integrated/test-griddata/test_griddata.cxx
@@ -13,7 +13,7 @@ int main(int argc, char** argv) {
   dump["Bpxy"] = Bpxy;
   bout::experimental::addBuildFlagsToOptions(dump);
   bout::globals::mesh->outputVars(dump);
-  bout::OptionsNetCDF("data.nc").write(dump);
+  bout::OptionsIO::create("data.nc")->write(dump);
 
   BoutFinalise();
   return 0;
diff --git a/tests/integrated/test-interchange-instability/orig_test.idl.dat b/tests/integrated/test-interchange-instability/orig_test.idl.dat
deleted file mode 100644
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z3!W>dgo=iKq5epv5ZTQOTB=OgH*`Qaw*0Jc_GP#5byOC9@B2*j-o79{x&4yZ@Z0BN
t^yU|$ey>N|AMX&4FSLv2wpED>xKzA86lr<*UA3jMv=b1oT_K9vKLFhc!k7R6

diff --git a/tests/integrated/test-options-adios/CMakeLists.txt b/tests/integrated/test-options-adios/CMakeLists.txt
new file mode 100644
index 0000000000..110773d6fd
--- /dev/null
+++ b/tests/integrated/test-options-adios/CMakeLists.txt
@@ -0,0 +1,6 @@
+bout_add_integrated_test(test-options-adios
+  SOURCES test-options-adios.cxx
+  USE_RUNTEST
+  USE_DATA_BOUT_INP
+  REQUIRES BOUT_HAS_ADIOS
+  )
diff --git a/tests/integrated/test-options-adios/data/BOUT.inp b/tests/integrated/test-options-adios/data/BOUT.inp
new file mode 100644
index 0000000000..fa0f6d3681
--- /dev/null
+++ b/tests/integrated/test-options-adios/data/BOUT.inp
@@ -0,0 +1,6 @@
+
+
+[mesh]
+nx = 5
+ny = 2
+nz = 2
diff --git a/tests/integrated/test-options-adios/makefile b/tests/integrated/test-options-adios/makefile
new file mode 100644
index 0000000000..7dbbce8736
--- /dev/null
+++ b/tests/integrated/test-options-adios/makefile
@@ -0,0 +1,6 @@
+
+BOUT_TOP	= ../../..
+
+SOURCEC		= test-options-adios.cxx
+
+include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-options-adios/runtest b/tests/integrated/test-options-adios/runtest
new file mode 100755
index 0000000000..1621c686a3
--- /dev/null
+++ b/tests/integrated/test-options-adios/runtest
@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+
+# Note: This test requires NCDF4, whereas on Travis NCDF is used
+# requires: netcdf
+# requires: adios
+# requires: not legacy_netcdf
+
+from boututils.datafile import DataFile
+from boututils.run_wrapper import build_and_log, shell, launch
+from boutdata.data import BoutOptionsFile
+
+import math
+import numpy as np
+
+build_and_log("options-netcdf test")
+shell("rm -f test-out.ini")
+shell("rm -f test-out.nc")
+
+# Create a NetCDF input file
+with DataFile("test.nc", create=True, format="NETCDF4") as f:
+    f.write("int", 42)
+    f.write("real", 3.1415)
+    f.write("string", "hello")
+
+# run BOUT++
+launch("./test-options-adios", nproc=1, mthread=1)
+
+# Check the output INI file
+result = BoutOptionsFile("test-out.ini")
+
+print(result)
+
+assert result["int"] == 42
+assert math.isclose(result["real"], 3.1415)
+assert result["string"] == "hello"
+
+print("Checking saved ADIOS test-out file -- Not implemented")
+
+# Check the output NetCDF file
+# with DataFile("test-out.nc") as f:
+#    assert f["int"] == 42
+#    assert math.isclose(f["real"], 3.1415)
+#    assert result["string"] == "hello"
+
+print("Checking saved settings.ini")
+
+# Check the settings.ini file, coming from BOUT.inp
+# which is converted to NetCDF, read in, then written again
+settings = BoutOptionsFile("settings.ini")
+
+assert settings["mesh"]["nx"] == 5
+assert settings["mesh"]["ny"] == 2
+
+print("Checking saved fields.bp -- Not implemented")
+
+# with DataFile("fields.nc") as f:
+#    assert f["f2d"].shape == (5, 6)  # Field2D
+#    assert f["f3d"].shape == (5, 6, 2)  # Field3D
+#    assert f["fperp"].shape == (5, 2)  # FieldPerp
+#    assert np.allclose(f["f2d"], 1.0)
+#    assert np.allclose(f["f3d"], 2.0)
+#    assert np.allclose(f["fperp"], 3.0)
+
+print("Checking saved fields2.bp -- Not implemented")
+
+# with DataFile("fields2.nc") as f:
+#    assert f["f2d"].shape == (5, 6)  # Field2D
+#    assert f["f3d"].shape == (5, 6, 2)  # Field3D
+#    assert f["fperp"].shape == (5, 2)  # FieldPerp
+#    assert np.allclose(f["f2d"], 1.0)
+#    assert np.allclose(f["f3d"], 2.0)
+#    assert np.allclose(f["fperp"], 3.0)
+
+print(" => Passed")
diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx
new file mode 100644
index 0000000000..60604e1aa3
--- /dev/null
+++ b/tests/integrated/test-options-adios/test-options-adios.cxx
@@ -0,0 +1,111 @@
+
+#include "bout/bout.hxx"
+
+#include "bout/options_io.hxx"
+#include "bout/optionsreader.hxx"
+
+using bout::OptionsIO;
+
+int main(int argc, char** argv) {
+  BoutInitialise(argc, argv);
+
+  // Read values from a NetCDF file
+  auto file = bout::OptionsIO::create("test.nc");
+
+  auto values = file->read();
+
+  values.printUnused();
+
+  // Write to an INI text file
+  OptionsReader* reader = OptionsReader::getInstance();
+  reader->write(&values, "test-out.ini");
+
+  // Write to ADIOS file, by setting file type "adios"
+  OptionsIO::create({{"file", "test-out.bp"},
+                     {"type", "adios"},
+                     {"append", false},
+                     {"singleWriteFile", true}})
+      ->write(values);
+
+  ///////////////////////////
+
+  // Write the BOUT.inp settings to ADIOS file
+  OptionsIO::create({{"file", "settings.bp"},
+                     {"type", "adios"},
+                     {"append", false},
+                     {"singleWriteFile", true}})
+      ->write(Options::root());
+
+  // Read back in
+  auto settings = OptionsIO::create({{"file", "settings.bp"}, {"type", "adios"}})->read();
+
+  // Write to INI file
+  reader->write(&settings, "settings.ini");
+
+  ///////////////////////////
+  // Write fields
+
+  Options fields;
+  fields["f2d"] = Field2D(1.0);
+  fields["f3d"] = Field3D(2.0);
+  fields["fperp"] = FieldPerp(3.0);
+  auto f = OptionsIO::create({{"file", "fields.bp"}, {"type", "adios"}});
+  /*
+     write() for adios only buffers data but does not guarantee writing to disk
+     unless singleWriteFile is set to true 
+     */
+  f->write(fields);
+  // indicate completion of step, required to get data on disk
+  f->verifyTimesteps();
+
+  ///////////////////////////
+  // Read fields
+
+  Options fields_in =
+      OptionsIO::create({{"file", "fields.bp"}, {"type", "adios"}})->read();
+
+  auto f2d = fields_in["f2d"].as<Field2D>(bout::globals::mesh);
+  auto f3d = fields_in["f3d"].as<Field3D>(bout::globals::mesh);
+  auto fperp = fields_in["fperp"].as<FieldPerp>(bout::globals::mesh);
+
+  Options fields2;
+  fields2["f2d"] = f2d;
+  fields2["f3d"] = f3d;
+  fields2["fperp"] = fperp;
+
+  // Write out again
+  auto f2 = OptionsIO::create({{"file", "fields2.bp"},
+                               {"type", "adios"},
+                               {"append", false},
+                               {"singleWriteFile", true}});
+  f2->write(fields2);
+
+  ///////////////////////////
+  // Time dependent values
+
+  Options data;
+  data["scalar"] = 1.0;
+  data["scalar"].attributes["time_dimension"] = "t";
+
+  data["field"] = Field3D(2.0);
+  data["field"].attributes["time_dimension"] = "t";
+
+  OptionsIO::create({{"file", "time.bp"},
+                     {"type", "adios"},
+                     {"append", false},
+                     {"singleWriteFile", true}})
+      ->write(data);
+
+  // Update time-dependent values
+  data["scalar"] = 2.0;
+  data["field"] = Field3D(3.0);
+
+  // Append data to file
+  OptionsIO::create({{"file", "time.bp"},
+                     {"type", "adios"},
+                     {"append", true},
+                     {"singleWriteFile", true}})
+      ->write(data);
+
+  BoutFinalise();
+};
diff --git a/tests/integrated/test-options-netcdf/test-options-netcdf.cxx b/tests/integrated/test-options-netcdf/test-options-netcdf.cxx
index 01c5749972..f5daf8919c 100644
--- a/tests/integrated/test-options-netcdf/test-options-netcdf.cxx
+++ b/tests/integrated/test-options-netcdf/test-options-netcdf.cxx
@@ -1,18 +1,18 @@
 
 #include "bout/bout.hxx"
 
-#include "bout/options_netcdf.hxx"
+#include "bout/options_io.hxx"
 #include "bout/optionsreader.hxx"
 
-using bout::OptionsNetCDF;
+using bout::OptionsIO;
 
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
   // Read values from a NetCDF file
-  OptionsNetCDF file("test.nc");
+  auto file = OptionsIO::create("test.nc");
 
-  auto values = file.read();
+  auto values = file->read();
 
   values.printUnused();
 
@@ -21,15 +21,15 @@ int main(int argc, char** argv) {
   reader->write(&values, "test-out.ini");
 
   // Write to a NetCDF file
-  OptionsNetCDF("test-out.nc").write(values);
+  OptionsIO::create("test-out.nc")->write(values);
 
   ///////////////////////////
 
   // Write the BOUT.inp settings to NetCDF file
-  OptionsNetCDF("settings.nc").write(Options::root());
+  OptionsIO::create("settings.nc")->write(Options::root());
 
   // Read back in
-  auto settings = OptionsNetCDF("settings.nc").read();
+  auto settings = OptionsIO::create("settings.nc")->read();
 
   // Write to INI file
   reader->write(&settings, "settings.ini");
@@ -41,12 +41,12 @@ int main(int argc, char** argv) {
   fields["f2d"] = Field2D(1.0);
   fields["f3d"] = Field3D(2.0);
   fields["fperp"] = FieldPerp(3.0);
-  OptionsNetCDF("fields.nc").write(fields);
+  OptionsIO::create("fields.nc")->write(fields);
 
   ///////////////////////////
   // Read fields
 
-  Options fields_in = OptionsNetCDF("fields.nc").read();
+  Options fields_in = OptionsIO::create("fields.nc")->read();
 
   auto f2d = fields_in["f2d"].as<Field2D>(bout::globals::mesh);
   auto f3d = fields_in["f3d"].as<Field3D>(bout::globals::mesh);
@@ -58,7 +58,7 @@ int main(int argc, char** argv) {
   fields2["fperp"] = fperp;
 
   // Write out again
-  OptionsNetCDF("fields2.nc").write(fields2);
+  OptionsIO::create("fields2.nc")->write(fields2);
 
   ///////////////////////////
   // Time dependent values
@@ -70,14 +70,14 @@ int main(int argc, char** argv) {
   data["field"] = Field3D(2.0);
   data["field"].attributes["time_dimension"] = "t";
 
-  OptionsNetCDF("time.nc").write(data);
+  OptionsIO::create("time.nc")->write(data);
 
   // Update time-dependent values
   data["scalar"] = 2.0;
   data["field"] = Field3D(3.0);
 
   // Append data to file
-  OptionsNetCDF("time.nc", OptionsNetCDF::FileMode::append).write(data);
+  OptionsIO::create({{"file", "time.nc"}, {"append", true}})->write(data);
 
   BoutFinalise();
 };
diff --git a/tests/integrated/test-solver/test_solver.cxx b/tests/integrated/test-solver/test_solver.cxx
index ee64c6097f..2e4345c8cc 100644
--- a/tests/integrated/test-solver/test_solver.cxx
+++ b/tests/integrated/test-solver/test_solver.cxx
@@ -146,8 +146,6 @@ int main(int argc, char** argv) {
     }
   }
 
-  BoutFinalise(false);
-
   if (!errors.empty()) {
     output_test << "\n => Some failed tests\n\n";
     for (auto& error : errors) {
diff --git a/tests/integrated/test-twistshift-staggered/test-twistshift.cxx b/tests/integrated/test-twistshift-staggered/test-twistshift.cxx
index 87b9e0a094..33b45b662d 100644
--- a/tests/integrated/test-twistshift-staggered/test-twistshift.cxx
+++ b/tests/integrated/test-twistshift-staggered/test-twistshift.cxx
@@ -4,11 +4,11 @@
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
-  Field3D test = FieldFactory::get()->create3D("test", nullptr, nullptr, CELL_YLOW);
+  using bout::globals::mesh;
 
-  Field3D test_aligned = toFieldAligned(test);
+  Field3D test = FieldFactory::get()->create3D("test", nullptr, mesh, CELL_YLOW);
 
-  using bout::globals::mesh;
+  Field3D test_aligned = toFieldAligned(test);
 
   // zero guard cells to check that communication is doing something
   for (int x = 0; x < mesh->LocalNx; x++) {
@@ -25,12 +25,12 @@ int main(int argc, char** argv) {
   mesh->communicate(test_aligned);
 
   Options::root()["check"] =
-      FieldFactory::get()->create3D("check", nullptr, nullptr, CELL_YLOW);
+      FieldFactory::get()->create3D("check", nullptr, mesh, CELL_YLOW);
 
   Options::root()["test"] = test;
   Options::root()["test_aligned"] = test_aligned;
 
-  bout::writeDefaultOutputFile();
+  bout::writeDefaultOutputFile(Options::root());
 
   BoutFinalise();
 }
diff --git a/tests/integrated/test-twistshift/test-twistshift.cxx b/tests/integrated/test-twistshift/test-twistshift.cxx
index ccde8b82b6..2c0fc79563 100644
--- a/tests/integrated/test-twistshift/test-twistshift.cxx
+++ b/tests/integrated/test-twistshift/test-twistshift.cxx
@@ -28,7 +28,7 @@ int main(int argc, char** argv) {
   Options::root()["test"] = test;
   Options::root()["test_aligned"] = test_aligned;
 
-  bout::writeDefaultOutputFile();
+  bout::writeDefaultOutputFile(Options::root());
 
   BoutFinalise();
 }
diff --git a/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx b/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx
index 22d1fb9e07..e8a2982bfd 100644
--- a/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx
+++ b/tests/integrated/test-yupdown-weights/test_yupdown_weights.cxx
@@ -70,7 +70,7 @@ int main(int argc, char** argv) {
 
   Options::root()["ddy"] = ddy;
   Options::root()["ddy2"] = ddy2;
-  bout::writeDefaultOutputFile();
+  bout::writeDefaultOutputFile(Options::root());
 
   BoutFinalise();
 
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index c0fd4a1e1f..c4ffa4fa75 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -19,6 +19,9 @@ if(NOT TARGET gtest)
   message(FATAL_ERROR "googletest not found! Have you disabled the git submodules (GIT_SUBMODULE)?")
 endif()
 
+# Some unit tests require GMOCK, so make sure we build it
+set(BUILD_GMOCK ON)
+
 mark_as_advanced(
   BUILD_GMOCK BUILD_GTEST BUILD_SHARED_LIBS
   gmock_build_tests gtest_build_samples gtest_build_tests
diff --git a/tests/unit/field/test_vector2d.cxx b/tests/unit/field/test_vector2d.cxx
index 263c8d6d11..838876c02b 100644
--- a/tests/unit/field/test_vector2d.cxx
+++ b/tests/unit/field/test_vector2d.cxx
@@ -85,10 +85,6 @@ class Vector2DTest : public ::testing::Test {
   Mesh* mesh_staggered = nullptr;
 };
 
-constexpr int Vector2DTest::nx;
-constexpr int Vector2DTest::ny;
-constexpr int Vector2DTest::nz;
-
 TEST_F(Vector2DTest, ApplyBoundaryString) {
   Vector2D v;
   v = 0.0;
diff --git a/tests/unit/include/bout/test_generic_factory.cxx b/tests/unit/include/bout/test_generic_factory.cxx
index 9368356151..f8a1e20bfa 100644
--- a/tests/unit/include/bout/test_generic_factory.cxx
+++ b/tests/unit/include/bout/test_generic_factory.cxx
@@ -37,10 +37,6 @@ class BaseFactory : public Factory<Base, BaseFactory, Options*> {
   static constexpr auto option_name = "type";
   static constexpr auto default_type = "base";
 };
-constexpr decltype(BaseFactory::type_name) BaseFactory::type_name;
-constexpr decltype(BaseFactory::section_name) BaseFactory::section_name;
-constexpr decltype(BaseFactory::option_name) BaseFactory::option_name;
-constexpr decltype(BaseFactory::default_type) BaseFactory::default_type;
 
 BaseFactory::RegisterInFactory<Base> registerme("base");
 BaseFactory::RegisterInFactory<Derived1> registerme1("derived1");
@@ -76,11 +72,6 @@ class ComplicatedFactory
   static constexpr auto default_type = "basecomplicated";
 };
 
-constexpr decltype(ComplicatedFactory::type_name) ComplicatedFactory::type_name;
-constexpr decltype(ComplicatedFactory::section_name) ComplicatedFactory::section_name;
-constexpr decltype(ComplicatedFactory::option_name) ComplicatedFactory::option_name;
-constexpr decltype(ComplicatedFactory::default_type) ComplicatedFactory::default_type;
-
 namespace {
 ComplicatedFactory::RegisterInFactory<BaseComplicated> registerme3("basecomplicated");
 ComplicatedFactory::RegisterInFactory<DerivedComplicated1>
diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx
index f13fe8bd78..fa46fed769 100644
--- a/tests/unit/include/bout/test_region.cxx
+++ b/tests/unit/include/bout/test_region.cxx
@@ -274,6 +274,24 @@ TEST_F(RegionTest, regionLoopAllSection) {
   EXPECT_EQ(count, nmesh);
 }
 
+TEST_F(RegionTest, regionIntersection) {
+  auto& region1 = mesh->getRegion3D("RGN_ALL");
+
+  auto& region2 = mesh->getRegion3D("RGN_NOBNDRY");
+
+  const int nmesh = RegionTest::nx * RegionTest::ny * RegionTest::nz;
+
+  EXPECT_EQ(region1.size(), nmesh);
+  EXPECT_GT(region1.size(), region2.size());
+
+  const auto& region3 = intersection(region1, region2);
+
+  EXPECT_EQ(region2.size(), region3.size());
+  // Ensure this did not change
+  EXPECT_EQ(region1.size(), nmesh);
+  EXPECT_EQ(mesh->getRegion3D("RGN_ALL").size(), nmesh);
+}
+
 TEST_F(RegionTest, regionLoopNoBndrySection) {
   const auto& region = mesh->getRegion3D("RGN_NOBNDRY");
 
diff --git a/tests/unit/mesh/data/test_gridfromoptions.cxx b/tests/unit/mesh/data/test_gridfromoptions.cxx
index d2a038cb93..84f08ff47b 100644
--- a/tests/unit/mesh/data/test_gridfromoptions.cxx
+++ b/tests/unit/mesh/data/test_gridfromoptions.cxx
@@ -33,6 +33,8 @@ class GridFromOptionsTest : public ::testing::Test {
     output_progress.disable();
     output_warn.disable();
     options["f"] = expected_string;
+    options["n"] = 12;
+    options["r"] = 3.14;
 
     // modify mesh section in global options
     options["dx"] = "1.";
@@ -116,10 +118,11 @@ TEST_F(GridFromOptionsTest, GetStringNone) {
 
 TEST_F(GridFromOptionsTest, GetInt) {
   int result{-1};
-  int expected{3};
 
-  EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f"));
-  EXPECT_EQ(result, expected);
+  // The expression must not depend on x,y,z or t
+  EXPECT_THROW(griddata->get(&mesh_from_options, result, "f"), BoutException);
+  griddata->get(&mesh_from_options, result, "n");
+  EXPECT_EQ(result, 12);
 }
 
 TEST_F(GridFromOptionsTest, GetIntNone) {
@@ -132,9 +135,9 @@ TEST_F(GridFromOptionsTest, GetIntNone) {
 
 TEST_F(GridFromOptionsTest, GetBoutReal) {
   BoutReal result{-1.};
-  BoutReal expected{3.};
+  BoutReal expected{3.14};
 
-  EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f"));
+  EXPECT_TRUE(griddata->get(&mesh_from_options, result, "r"));
   EXPECT_EQ(result, expected);
 }
 
diff --git a/tests/unit/sys/test_expressionparser.cxx b/tests/unit/sys/test_expressionparser.cxx
index 00cb23c042..c4f0ebfcf3 100644
--- a/tests/unit/sys/test_expressionparser.cxx
+++ b/tests/unit/sys/test_expressionparser.cxx
@@ -379,9 +379,9 @@ TEST_F(ExpressionParserTest, BadBinaryOp) {
 
 TEST_F(ExpressionParserTest, AddBinaryOp) {
   // Add a synonym for multiply with a lower precedence than addition
-  parser.addBinaryOp('&', std::make_shared<FieldBinary>(nullptr, nullptr, '*'), 5);
+  parser.addBinaryOp('$', std::make_shared<FieldBinary>(nullptr, nullptr, '*'), 5);
 
-  auto fieldgen = parser.parseString("2 & x + 3");
+  auto fieldgen = parser.parseString("2 $ x + 3");
   EXPECT_EQ(fieldgen->str(), "(2*(x+3))");
 
   for (auto x : x_array) {
@@ -679,3 +679,38 @@ TEST_F(ExpressionParserTest, FuzzyFind) {
   EXPECT_EQ(first_CAPS_match->name, "multiply");
   EXPECT_EQ(first_CAPS_match->distance, 1);
 }
+
+TEST_F(ExpressionParserTest, LogicalOR) {
+  EXPECT_DOUBLE_EQ(parser.parseString("1 | 0")->generate({}), 1.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("0 | 1")->generate({}), 1.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("1 | 1")->generate({}), 1.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("0 | 0")->generate({}), 0.0);
+}
+
+TEST_F(ExpressionParserTest, LogicalAND) {
+  EXPECT_DOUBLE_EQ(parser.parseString("1 & 0")->generate({}), 0.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("0 & 1")->generate({}), 0.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("1 & 1")->generate({}), 1.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("0 & 0")->generate({}), 0.0);
+}
+
+TEST_F(ExpressionParserTest, LogicalNOT) {
+  EXPECT_DOUBLE_EQ(parser.parseString("!0")->generate({}), 1.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("!1")->generate({}), 0.0);
+}
+
+TEST_F(ExpressionParserTest, LogicalNOTprecedence) {
+  // Should bind more strongly than all binary operators
+  EXPECT_DOUBLE_EQ(parser.parseString("!1 & 0")->generate({}), 0.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("1 & !0")->generate({}), 1.0);
+}
+
+TEST_F(ExpressionParserTest, CompareGT) {
+  EXPECT_DOUBLE_EQ(parser.parseString("1 > 0")->generate({}), 1.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("3 > 5")->generate({}), 0.0);
+}
+
+TEST_F(ExpressionParserTest, CompareLT) {
+  EXPECT_DOUBLE_EQ(parser.parseString("1 < 0")->generate({}), 0.0);
+  EXPECT_DOUBLE_EQ(parser.parseString("3 < 5")->generate({}), 1.0);
+}
diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx
index a357923053..1f0ae92ed2 100644
--- a/tests/unit/sys/test_options.cxx
+++ b/tests/unit/sys/test_options.cxx
@@ -232,10 +232,9 @@ TEST_F(OptionsTest, GetBoolFromString) {
 
   EXPECT_EQ(value, true);
 
+  // "yes" is not an acceptable bool
   bool value2;
-  options.get("bool_key2", value2, false, false);
-
-  EXPECT_EQ(value2, true);
+  EXPECT_THROW(options.get("bool_key2", value2, false, false), BoutException);
 }
 
 TEST_F(OptionsTest, DefaultValueBool) {
@@ -327,7 +326,7 @@ TEST_F(OptionsTest, ValueUsed) {
   Options options;
   options["key1"] = 1;
   EXPECT_FALSE(options["key1"].valueUsed());
-  MAYBE_UNUSED(const int value) = options["key1"];
+  [[maybe_unused]] const int value = options["key1"];
   EXPECT_TRUE(options["key1"].valueUsed());
 }
 
@@ -1246,17 +1245,17 @@ TEST_F(OptionsTest, GetUnused) {
   // This shouldn't count as unused
   option["section2"]["value5"].attributes["source"] = "Output";
 
-  MAYBE_UNUSED(auto value1) = option["section1"]["value1"].as<int>();
-  MAYBE_UNUSED(auto value3) = option["section2"]["subsection1"]["value3"].as<bool>();
+  [[maybe_unused]] auto value1 = option["section1"]["value1"].as<int>();
+  [[maybe_unused]] auto value3 = option["section2"]["subsection1"]["value3"].as<bool>();
 
   Options expected_unused{{"section1", {{"value2", "hello"}}},
                           {"section2", {{"subsection1", {{"value4", 3.2}}}}}};
 
   EXPECT_EQ(option.getUnused(), expected_unused);
 
-  MAYBE_UNUSED(auto value2) = option["section1"]["value2"].as<std::string>();
-  MAYBE_UNUSED(auto value4) = option["section2"]["subsection1"]["value4"].as<double>();
-  MAYBE_UNUSED(auto value5) = option["section2"]["value5"].as<int>();
+  [[maybe_unused]] auto value2 = option["section1"]["value2"].as<std::string>();
+  [[maybe_unused]] auto value4 = option["section2"]["subsection1"]["value4"].as<double>();
+  [[maybe_unused]] auto value5 = option["section2"]["value5"].as<int>();
 
   Options expected_empty{};
 
@@ -1334,8 +1333,8 @@ TEST_F(OptionsTest, CheckForUnusedOptions) {
   // This shouldn't count as unused
   option["section2"]["value5"].attributes["source"] = "Output";
 
-  MAYBE_UNUSED(auto value1) = option["section1"]["value1"].as<int>();
-  MAYBE_UNUSED(auto value3) = option["section2"]["subsection1"]["value3"].as<bool>();
+  [[maybe_unused]] auto value1 = option["section1"]["value1"].as<int>();
+  [[maybe_unused]] auto value3 = option["section2"]["subsection1"]["value3"].as<bool>();
 
   EXPECT_THROW(bout::checkForUnusedOptions(option, "data", "BOUT.inp"), BoutException);
 }
@@ -1361,8 +1360,7 @@ TEST_P(BoolTrueTestParametrized, BoolTrueFromString) {
 }
 
 INSTANTIATE_TEST_CASE_P(BoolTrueTests, BoolTrueTestParametrized,
-                        ::testing::Values("y", "Y", "yes", "Yes", "yeS", "t", "true", "T",
-                                          "True", "tRuE", "1"));
+                        ::testing::Values("true", "True", "1"));
 
 class BoolFalseTestParametrized : public OptionsTest,
                                   public ::testing::WithParamInterface<std::string> {};
@@ -1376,8 +1374,7 @@ TEST_P(BoolFalseTestParametrized, BoolFalseFromString) {
 }
 
 INSTANTIATE_TEST_CASE_P(BoolFalseTests, BoolFalseTestParametrized,
-                        ::testing::Values("n", "N", "no", "No", "nO", "f", "false", "F",
-                                          "False", "fAlSe", "0"));
+                        ::testing::Values("false", "False", "0"));
 
 class BoolInvalidTestParametrized : public OptionsTest,
                                     public ::testing::WithParamInterface<std::string> {};
@@ -1391,6 +1388,52 @@ TEST_P(BoolInvalidTestParametrized, BoolInvalidFromString) {
 }
 
 INSTANTIATE_TEST_CASE_P(BoolInvalidTests, BoolInvalidTestParametrized,
-                        ::testing::Values("a", "B", "yellow", "Yogi", "test", "truelong",
-                                          "Tim", "2", "not", "No bool", "nOno",
-                                          "falsebuttoolong", "-1"));
+                        ::testing::Values("yes", "no", "y", "n", "a", "B", "yellow",
+                                          "Yogi", "test", "truelong", "Tim", "2", "not",
+                                          "No bool", "nOno", "falsebuttoolong", "-1",
+                                          "1.1"));
+
+TEST_F(OptionsTest, BoolLogicalOR) {
+  ASSERT_TRUE(Options("true | false").as<bool>());
+  ASSERT_TRUE(Options("false | true").as<bool>());
+  ASSERT_TRUE(Options("true | true").as<bool>());
+  ASSERT_FALSE(Options("false | false").as<bool>());
+  ASSERT_TRUE(Options("true | false | true").as<bool>());
+}
+
+TEST_F(OptionsTest, BoolLogicalAND) {
+  ASSERT_FALSE(Options("true & false").as<bool>());
+  ASSERT_FALSE(Options("false & true").as<bool>());
+  ASSERT_TRUE(Options("true & true").as<bool>());
+  ASSERT_FALSE(Options("false & false").as<bool>());
+  ASSERT_FALSE(Options("true & false & true").as<bool>());
+
+  EXPECT_THROW(Options("true & 1.3").as<bool>(), BoutException);
+  EXPECT_THROW(Options("2 & false").as<bool>(), BoutException);
+}
+
+TEST_F(OptionsTest, BoolLogicalNOT) {
+  ASSERT_FALSE(Options("!true").as<bool>());
+  ASSERT_TRUE(Options("!false").as<bool>());
+  ASSERT_FALSE(Options("!true & false").as<bool>());
+  ASSERT_TRUE(Options("!(true & false)").as<bool>());
+  ASSERT_TRUE(Options("true & !false").as<bool>());
+
+  EXPECT_THROW(Options("!2").as<bool>(), BoutException);
+  EXPECT_THROW(Options("!1.2").as<bool>(), BoutException);
+}
+
+TEST_F(OptionsTest, BoolComparisonGT) {
+  ASSERT_TRUE(Options("2 > 1").as<bool>());
+  ASSERT_FALSE(Options("2 > 3").as<bool>());
+}
+
+TEST_F(OptionsTest, BoolComparisonLT) {
+  ASSERT_FALSE(Options("2 < 1").as<bool>());
+  ASSERT_TRUE(Options("2 < 3").as<bool>());
+}
+
+TEST_F(OptionsTest, BoolCompound) {
+  ASSERT_TRUE(Options("true & !false").as<bool>());
+  ASSERT_TRUE(Options("2 > 1 & 2 < 3").as<bool>());
+}
diff --git a/tests/unit/sys/test_options_netcdf.cxx b/tests/unit/sys/test_options_netcdf.cxx
index b086043822..5869cf4932 100644
--- a/tests/unit/sys/test_options_netcdf.cxx
+++ b/tests/unit/sys/test_options_netcdf.cxx
@@ -9,9 +9,9 @@
 #include "test_extras.hxx"
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
-#include "bout/options_netcdf.hxx"
+#include "bout/options_io.hxx"
 
-using bout::OptionsNetCDF;
+using bout::OptionsIO;
 
 #include <cstdio>
 
@@ -39,11 +39,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteInt) {
     options["test"] = 42;
 
     // Write the file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read again
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   EXPECT_EQ(data["test"], 42);
 }
@@ -54,11 +54,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteString) {
     options["test"] = std::string{"hello"};
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   EXPECT_EQ(data["test"], std::string("hello"));
 }
@@ -69,11 +69,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteField2D) {
     options["test"] = Field2D(1.0);
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   Field2D value = data["test"].as<Field2D>(bout::globals::mesh);
 
@@ -87,11 +87,11 @@ TEST_F(OptionsNetCDFTest, ReadWriteField3D) {
     options["test"] = Field3D(2.4);
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   Field3D value = data["test"].as<Field3D>(bout::globals::mesh);
 
@@ -106,11 +106,11 @@ TEST_F(OptionsNetCDFTest, Groups) {
     options["test"]["key"] = 42;
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
   EXPECT_EQ(data["test"]["key"], 42);
 }
 
@@ -121,11 +121,11 @@ TEST_F(OptionsNetCDFTest, AttributeInt) {
     options["test"].attributes["thing"] = 4;
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
   EXPECT_EQ(data["test"].attributes["thing"].as<int>(), 4);
 }
 
@@ -136,11 +136,11 @@ TEST_F(OptionsNetCDFTest, AttributeBoutReal) {
     options["test"].attributes["thing"] = 3.14;
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
   EXPECT_DOUBLE_EQ(data["test"].attributes["thing"].as<BoutReal>(), 3.14);
 }
 
@@ -151,11 +151,11 @@ TEST_F(OptionsNetCDFTest, AttributeString) {
     options["test"].attributes["thing"] = "hello";
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
   EXPECT_EQ(data["test"].attributes["thing"].as<std::string>(), "hello");
 }
 
@@ -165,11 +165,11 @@ TEST_F(OptionsNetCDFTest, Field2DWriteCellCentre) {
     options["f2d"] = Field2D(2.0);
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   EXPECT_EQ(data["f2d"].attributes["cell_location"].as<std::string>(),
             toString(CELL_CENTRE));
@@ -181,11 +181,11 @@ TEST_F(OptionsNetCDFTest, Field2DWriteCellYLow) {
     options["f2d"] = Field2D(2.0, mesh_staggered).setLocation(CELL_YLOW);
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   EXPECT_EQ(data["f2d"].attributes["cell_location"].as<std::string>(),
             toString(CELL_YLOW));
@@ -197,11 +197,11 @@ TEST_F(OptionsNetCDFTest, Field3DWriteCellCentre) {
     options["f3d"] = Field3D(2.0);
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   EXPECT_EQ(data["f3d"].attributes["cell_location"].as<std::string>(),
             toString(CELL_CENTRE));
@@ -213,11 +213,11 @@ TEST_F(OptionsNetCDFTest, Field3DWriteCellYLow) {
     options["f3d"] = Field3D(2.0, mesh_staggered).setLocation(CELL_YLOW);
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   EXPECT_EQ(data["f3d"].attributes["cell_location"].as<std::string>(),
             toString(CELL_YLOW));
@@ -235,11 +235,11 @@ TEST_F(OptionsNetCDFTest, FieldPerpWriteCellCentre) {
     fperp.getMesh()->getXcomm();
 
     // Write file
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
   // Read file
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   EXPECT_EQ(data["fperp"].attributes["cell_location"].as<std::string>(),
             toString(CELL_CENTRE));
@@ -252,10 +252,10 @@ TEST_F(OptionsNetCDFTest, VerifyTimesteps) {
     options["thing1"] = 1.0;
     options["thing1"].attributes["time_dimension"] = "t";
 
-    OptionsNetCDF(filename).write(options);
+    OptionsIO::create(filename)->write(options);
   }
 
-  EXPECT_NO_THROW(OptionsNetCDF(filename).verifyTimesteps());
+  EXPECT_NO_THROW(OptionsIO::create(filename)->verifyTimesteps());
 
   {
     Options options;
@@ -265,10 +265,11 @@ TEST_F(OptionsNetCDFTest, VerifyTimesteps) {
     options["thing2"] = 3.0;
     options["thing2"].attributes["time_dimension"] = "t";
 
-    OptionsNetCDF(filename, OptionsNetCDF::FileMode::append).write(options);
+    OptionsIO::create({{"type", "netcdf"}, {"file", filename}, {"append", true}})
+        ->write(options);
   }
 
-  EXPECT_THROW(OptionsNetCDF(filename).verifyTimesteps(), BoutException);
+  EXPECT_THROW(OptionsIO::create(filename)->verifyTimesteps(), BoutException);
 }
 
 TEST_F(OptionsNetCDFTest, WriteTimeDimension) {
@@ -278,10 +279,10 @@ TEST_F(OptionsNetCDFTest, WriteTimeDimension) {
     options["thing2"].assignRepeat(2.0, "t2"); // non-default
 
     // Only write non-default time dim
-    OptionsNetCDF(filename).write(options, "t2");
+    OptionsIO::create(filename)->write(options, "t2");
   }
 
-  Options data = OptionsNetCDF(filename).read();
+  Options data = OptionsIO::create(filename)->read();
 
   EXPECT_FALSE(data.isSet("thing1"));
   EXPECT_TRUE(data.isSet("thing2"));
@@ -297,12 +298,12 @@ TEST_F(OptionsNetCDFTest, WriteMultipleTimeDimensions) {
     options["thing4_t2"].assignRepeat(2.0, "t2"); // non-default
 
     // Write the non-default time dim twice
-    OptionsNetCDF(filename).write(options, "t2");
-    OptionsNetCDF(filename).write(options, "t2");
-    OptionsNetCDF(filename).write(options, "t");
+    OptionsIO::create(filename)->write(options, "t2");
+    OptionsIO::create(filename)->write(options, "t2");
+    OptionsIO::create(filename)->write(options, "t");
   }
 
-  EXPECT_NO_THROW(OptionsNetCDF(filename).verifyTimesteps());
+  EXPECT_NO_THROW(OptionsIO::create(filename)->verifyTimesteps());
 }
 
 #endif // BOUT_HAS_NETCDF
diff --git a/tests/unit/test_extras.cxx b/tests/unit/test_extras.cxx
index a4c51ac3c4..491dd189fc 100644
--- a/tests/unit/test_extras.cxx
+++ b/tests/unit/test_extras.cxx
@@ -3,11 +3,6 @@
 
 #include <cmath>
 
-// Need to provide a redundant declaration because C++
-constexpr int FakeMeshFixture::nx;
-constexpr int FakeMeshFixture::ny;
-constexpr int FakeMeshFixture::nz;
-
 ::testing::AssertionResult IsSubString(const std::string& str,
                                        const std::string& substring) {
   if (str.find(substring) != std::string::npos) {
diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx
index f0868ddf49..845ea4f255 100644
--- a/tests/unit/test_extras.hxx
+++ b/tests/unit/test_extras.hxx
@@ -51,13 +51,13 @@ inline std::ostream& operator<<(std::ostream& out, const SpecificInd<N>& index)
 }
 
 /// Helpers to get the type of a Field as a string
-auto inline getFieldType(MAYBE_UNUSED(const Field2D& field)) -> std::string {
+auto inline getFieldType([[maybe_unused]] const Field2D& field) -> std::string {
   return "Field2D";
 }
-auto inline getFieldType(MAYBE_UNUSED(const Field3D& field)) -> std::string {
+auto inline getFieldType([[maybe_unused]] const Field3D& field) -> std::string {
   return "Field3D";
 }
-auto inline getFieldType(MAYBE_UNUSED(const FieldPerp& field)) -> std::string {
+auto inline getFieldType([[maybe_unused]] const FieldPerp& field) -> std::string {
   return "FieldPerp";
 }
 
@@ -339,7 +339,7 @@ public:
 
   bool hasVar(const std::string& UNUSED(name)) override { return false; }
 
-  bool get(MAYBE_UNUSED(Mesh* m), std::string& sval, const std::string& name,
+  bool get([[maybe_unused]] Mesh* m, std::string& sval, const std::string& name,
            const std::string& def = "") override {
     if (values[name].isSet()) {
       sval = values[name].as<std::string>();
@@ -348,7 +348,7 @@ public:
     sval = def;
     return false;
   }
-  bool get(MAYBE_UNUSED(Mesh* m), int& ival, const std::string& name,
+  bool get([[maybe_unused]] Mesh* m, int& ival, const std::string& name,
            int def = 0) override {
     if (values[name].isSet()) {
       ival = values[name].as<int>();
@@ -357,7 +357,7 @@ public:
     ival = def;
     return false;
   }
-  bool get(MAYBE_UNUSED(Mesh* m), BoutReal& rval, const std::string& name,
+  bool get([[maybe_unused]] Mesh* m, BoutReal& rval, const std::string& name,
            BoutReal def = 0.0) override {
     if (values[name].isSet()) {
       rval = values[name].as<BoutReal>();
@@ -394,15 +394,15 @@ public:
     return false;
   }
 
-  bool get(MAYBE_UNUSED(Mesh* m), MAYBE_UNUSED(std::vector<int>& var),
-           MAYBE_UNUSED(const std::string& name), MAYBE_UNUSED(int len),
-           MAYBE_UNUSED(int def) = 0, Direction = GridDataSource::X) override {
+  bool get([[maybe_unused]] Mesh* m, [[maybe_unused]] std::vector<int>& var,
+           [[maybe_unused]] const std::string& name, [[maybe_unused]] int len,
+           [[maybe_unused]] int def = 0, Direction = GridDataSource::X) override {
     throw BoutException("Not Implemented");
     return false;
   }
-  bool get(MAYBE_UNUSED(Mesh* m), MAYBE_UNUSED(std::vector<BoutReal>& var),
-           MAYBE_UNUSED(const std::string& name), MAYBE_UNUSED(int len),
-           MAYBE_UNUSED(int def) = 0,
+  bool get([[maybe_unused]] Mesh* m, [[maybe_unused]] std::vector<BoutReal>& var,
+           [[maybe_unused]] const std::string& name, [[maybe_unused]] int len,
+           [[maybe_unused]] int def = 0,
            Direction UNUSED(dir) = GridDataSource::X) override {
     throw BoutException("Not Implemented");
     return false;
diff --git a/tools/pylib/_boutpp_build/bout_options.pxd b/tools/pylib/_boutpp_build/bout_options.pxd
index ba5e64c8e3..be17608cea 100644
--- a/tools/pylib/_boutpp_build/bout_options.pxd
+++ b/tools/pylib/_boutpp_build/bout_options.pxd
@@ -8,20 +8,11 @@ cdef extern from "boutexception_helper.hxx":
      cdef void raise_bout_py_error()
 
 
-cdef extern from "bout/options_netcdf.hxx" namespace "bout":
-    cdef void writeDefaultOutputFile();
+cdef extern from "bout/options_io.hxx" namespace "bout":
     cdef void writeDefaultOutputFile(Options& options);
-    cppclass OptionsNetCDF:
-        enum FileMode:
-             replace
-             append
-        OptionsNetCDF() except +raise_bout_py_error
-        OptionsNetCDF(string filename) except +raise_bout_py_error
-        OptionsNetCDF(string filename, FileMode mode) except +raise_bout_py_error
-        OptionsNetCDF(const OptionsNetCDF&);
-        OptionsNetCDF(OptionsNetCDF&&);
-        OptionsNetCDF& operator=(const OptionsNetCDF&);
-        OptionsNetCDF& operator=(OptionsNetCDF&&);
+    cppclass OptionsIO:
+        @staticmethod
+        OptionsIO * create(string filename)
         Options read();
         void write(const Options& options);
         void write(const Options& options, string time_dim);
diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
index c94fd14a17..12e210a5b5 100644
--- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
+++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
@@ -5,7 +5,7 @@ from libcpp.memory cimport unique_ptr
 from libcpp.string cimport string
 
 cimport resolve_enum as benum
-from bout_options cimport Options, OptionsReader, OptionsNetCDF, writeDefaultOutputFile
+from bout_options cimport Options, OptionsReader, OptionsIO, writeDefaultOutputFile
 
 cdef extern from "boutexception_helper.hxx":
      cdef void raise_bout_py_error()
diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 657e2f28c1..3aeb1428eb 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -1723,7 +1723,6 @@ cdef class Options:
             del self.cobj
             self.cobj = NULL
 
-
 def writeDefaultOutputFile(options: Options):
     c.writeDefaultOutputFile(deref(options.cobj))
 
diff --git a/tools/pylib/post_bout/ListDict.py b/tools/pylib/post_bout/ListDict.py
deleted file mode 100644
index f500825651..0000000000
--- a/tools/pylib/post_bout/ListDict.py
+++ /dev/null
@@ -1,61 +0,0 @@
-from __future__ import print_function
-import sys
-import os
-
-try:
-    boutpath = os.environ["BOUT_TOP"]
-    pylibpath = boutpath + "/pylib"
-    pbpath = pylibpath + "/post_bout"
-    boutdatapath = pylibpath + "/boutdata"
-    boututilpath = pylibpath + "/boututils"
-
-    allpath = [boutpath, pylibpath, pbpath, boutdatapath, boututilpath]
-    [sys.path.append(elem) for elem in allpath]
-except:
-    print("meh")
-
-import numpy as np
-
-
-def ListDictKey(input, key):
-    # given a key and a list of dictionaries this method returns an ordered
-    # list of requested key values
-    output = []
-    for x in input:
-        try:
-            # print x[key]
-            output.append(x[key])
-        except:
-            print("Key not found")
-            return 1
-
-    return output
-
-
-def ListDictFilt(input, key, valuelist):
-    # given a key,value pair and a list of dictionaries this
-    # method returns an ordered list of dictionaries where (dict(key)==value) = True
-    # http://stackoverflow.com/questions/5762643/how-to-filter-list-of-dictionaries-with-matching-values-for-a-given-key
-    try:
-        x = copyf(input, key, valuelist)
-        return x
-    except:
-        return []
-
-
-def copyf(dictlist, key, valuelist):
-    return [dictio for dictio in dictlist if dictio[key] in valuelist]
-
-
-# def subset(obj):
-#     #def __init__(self,alldb,key,valuelist,model=False):
-#     selection = ListDictFilt(obj.mode_db,obj.key,valuelist)
-#     if len(selection) !=0:
-#         LinRes.__init__(obj,selection)
-#         self.skey = key
-#         if model==True:
-#             self.model()
-#         else:
-#             LinRes.__init__(self,alldb)
-#             if model==True:
-#                 self.model()
diff --git a/tools/pylib/post_bout/__init__.py b/tools/pylib/post_bout/__init__.py
deleted file mode 100644
index 069ae3e85b..0000000000
--- a/tools/pylib/post_bout/__init__.py
+++ /dev/null
@@ -1,95 +0,0 @@
-from __future__ import print_function
-from __future__ import absolute_import
-
-##################################################
-#            BOUT++ data package
-#
-# Routines for examining simulation results for BOUT++
-#
-##################################################
-
-print("Loading BOUT++ post processing routines")
-
-# Load routines from separate files
-import sys
-import os
-
-try:
-    boutpath = os.environ["BOUT_TOP"]
-    pylibpath = boutpath + "/tools/pylib"
-    boutdatapath = pylibpath + "/boutdata"
-    boututilpath = pylibpath + "/boututils"
-    allpath = [boutpath, pylibpath, boutdatapath, boututilpath]
-    [sys.path.append(elem) for elem in allpath]
-    print(sys.path)
-
-    # sys.path.append('/home/cryosphere/BOUT/tools/pylib')
-    # sys.path.append('/home/cryosphere/BOUT/tools/pylib/boutdata')
-    # sys.path.append('/home/cryosphere/BOUT/tools/pylib/boututils')
-
-    print("in post_bout/__init__.py")
-
-    import matplotlib
-
-    matplotlib.use("pdf")  # savemovie must be called as a diff. sesssion
-
-    import gobject
-    import numpy as np
-except ImportError:
-    print("can't find the modules I need, you fail")
-    sys.exit()  # no point in going on
-
-
-# import some bout specific modules
-try:
-    import boutdata
-    import boututils
-except:
-    print("can't find bout related modules, you fail")
-
-# import some home-brewed modules
-
-
-# create some aliases
-
-
-try:
-    from read_grid import read_grid
-except:
-    print("Sorry, no read_grid")
-
-try:
-    from .read_inp import parse_inp, read_inp, read_log, metadata
-except:
-    print("Sorry no parse_inp")
-
-try:
-    from .read_cxx import read_cxx, get_evolved_cxx, no_comment_cxx
-except:
-    print("Sorry no read_cxx")
-
-try:
-    from post_bout import save, read
-except:
-    print("Sorry, no show")
-
-try:
-    from .basic_info import basic_info, fft_info
-except:
-    print("Sorry, no basic_info")
-
-try:
-    from .pb_corral import corral, LinRes, subset
-except:
-    print("No corral")
-
-try:
-    from . import ListDict
-except:
-    print("No ListDict")
-
-try:
-    # from rotate_mp import rotate
-    from rotate2 import rotate
-except:
-    print("No rotate")
diff --git a/tools/pylib/post_bout/basic_info.py b/tools/pylib/post_bout/basic_info.py
deleted file mode 100644
index 563bfe6e98..0000000000
--- a/tools/pylib/post_bout/basic_info.py
+++ /dev/null
@@ -1,421 +0,0 @@
-from __future__ import print_function
-from __future__ import division
-from builtins import zip
-from builtins import range
-from past.utils import old_div
-
-# basic_info return some statistical averages and harmonic info
-import numpy as np
-import math
-
-
-def basic_info(data, meta, rescale=True, rotate=False, user_peak=0, nonlinear=None):
-    print("in basic_info")
-    # from . import read_grid,parse_inp,read_inp,show
-
-    dims = data.shape
-    ndims = len(dims)
-
-    mxg = meta["MXG"]["v"]
-
-    if ndims == 4:
-        nt, nx, ny, nz = data.shape
-        print(nt, nx, ny)
-    else:
-        print("something with dimesions")
-
-    dc = (
-        data.mean(1).mean(1).mean(1)
-    )  # there MUST be a way to indicate all axis at once
-    amp = abs(data).max(1).max(1).max(1)
-    dt = meta["dt"]["v"]
-
-    if rescale:
-        amp_o = amp - dc
-        fourDamp = np.repeat(amp_o, nx * ny * nz)
-        fourDamp = fourDamp.reshape(nt, nx, ny, nz)
-        dc_n = old_div(dc, amp_o)
-        data_n = old_div(data, fourDamp)
-
-        print(data.shape)
-        dfdt = np.gradient(data)[0]
-        dfdt = abs(dfdt).max(1).max(1).max(1)
-
-        ave = {"amp": amp, "dc": dc, "amp_o": amp_o, "dfdt": dfdt}
-
-    else:
-        print("no rescaling")
-        ave = {"amp": amp, "dc": dc}
-
-    if nonlinear is not None:  # add nonlinear part if user provides
-        nl = abs(nonlinear[:, mxg : -1.0 * mxg, :, :]).max(1).max(1).max(1)
-        nl_norm = (old_div(nl, dfdt)) * dt
-
-        ave["nl"] = nl
-        ave["nl_norm"] = nl_norm
-
-    if rotate:
-        print("rotate stuff")
-        # will need to provide some grid geometry to do this one
-    else:
-        print("or not")
-
-    # let's identify the dominant modes, for now at every [t,x] slice
-    # if the data set is too large we can average over x
-    peaks_db = fft_info(
-        data, user_peak, meta=meta
-    )  # Nt X Nx X (# of loc. max) list of dict
-
-    # print peaks[0]['gamma']
-    return peaks_db, ave
-
-
-def fft_info(
-    data,
-    user_peak,
-    dimension=[3, 4],
-    rescale=False,
-    wavelet=False,
-    show=False,
-    meta=0,
-    edgefix=False,
-):
-    import numpy as np
-    import math
-
-    print("in fft_inf0")
-
-    dims = data.shape
-    ndims = len(dims)
-
-    if ndims == 4:
-        nt, nx, ny, nz = data.shape
-        print(data.shape)
-    else:
-        print("something with dimesions")
-
-    # data2 = data
-    # if edgefix:
-    #     data2 = np.zeros((nt,nx,ny+1,nz+1))
-
-    #     for t in range(nt):
-    #         for x in range(nx):
-    #             temp = np.append(data[t,x,:,:],[data[t,x,0,:]],0)
-    #             data2[t,x,:,:] = np.append(temp,
-    #                                        np.transpose([temp[:,0]]),1)
-
-    # dt, k labels for the revelant dimensions
-
-    dt = meta["dt"]["v"]
-    dz = meta["dz"]
-    # IC = meta['IC']
-    ky_max = old_div(ny, 2)
-    kz_max = old_div(nz, 2)
-    amp = abs(data).max(2).max(2)  # nt x nx
-
-    print("dt: ", dt)
-
-    # print data[0,2,:,:]
-
-    IC = amp[0, :].max()  # intial condition, set
-    print(IC)
-
-    fft_data = np.fft.fft2(data)[
-        :, :, 0:ky_max, 0:kz_max
-    ]  # by default the last 2 dimensions
-
-    power = fft_data.conj() * fft_data
-    # print power[0].max(), (IC*(ky_max)*(kz_max))**2
-
-    cross_pow = old_div((fft_data * (np.roll(fft_data, 1, axis=0)).conj()), (ny * nz))
-
-    if rescale:
-        fft_data_n = np.fft.fft2(data_n)[:, :, 0:ky_max, 0:kz_max]
-        pow_n = np.sqrt((fft_data_n.conj() * fft_data_n).real)
-
-    peaks = [[[] for i in range(nx)] for j in range(nt)]  # a list of dictionaries
-    peaks_db = []
-
-    peak_hist = [[0 for i in range(kz_max)] for j in range(ky_max)]  # a 2d bin array
-
-    # for now using a lame 2x loop method
-
-    if user_peak != 0:
-        for mem in user_peak:
-            print(mem)
-            peak_hist[int(mem[0])][int(mem[1])] = abs(
-                power.mean(0).mean(0)[int(mem[0]), int(mem[1])]
-            )
-
-        # floor =  ((IC*(kz_max*ky_max))**2)/10000
-
-    else:
-        for t in range(nt):
-            for x in range(nx):
-                peaks[t][x] = local_maxima(
-                    power[t, x, :, :], 0, floor=(IC * (kz_max * ky_max)) ** 2
-                )
-                for p in peaks[t][
-                    x
-                ]:  # looping over each returned peakset at some fixed t,x pair
-                    peak_hist[p["y_i"]][
-                        p["z_i"]
-                    ] += 1  # average across t and x, at least exclude pad
-        floor = 0
-
-    # this array is usefull for determining what the dominant modes are
-    # but we want to retain the option of observing how the amplitude
-    # of any give harmonic varies in space
-
-    peak_hist = np.array(peak_hist)
-
-    # let's find the top N overall powerfull harmnonics
-    net_peak = local_maxima(peak_hist, user_peak, bug=False)
-
-    print("net_peak: ", net_peak, user_peak != 0)
-    # dom_mode = [{'amp':[],'amp_n':[],'phase':[],'freq':[],'gamma':[]} for x in net_peak]
-    dom_mode_db = []
-
-    Bp = meta["Bpxy"]["v"][:, old_div(ny, 2)]
-    B = meta["Bxy"]["v"][:, old_div(ny, 2)]
-    Bt = meta["Btxy"]["v"][:, old_div(ny, 2)]
-
-    rho_s = meta["rho_s"]["v"]
-
-    L_z = old_div(meta["L_z"], rho_s)
-    # L_z =
-    L_y = meta["lpar"]  # already normalized earlier in read_inp.py
-    L_norm = old_div(meta["lbNorm"], rho_s)
-
-    hthe0_n = 1e2 * meta["hthe0"]["v"] / rho_s  # no x dep
-    hthe0_n_x = old_div(L_y, (2 * np.pi))  # no x dep
-
-    print("L_z,Ly: ", L_z, L_y)
-
-    # if user provides the harmo    nic info overide the found peaks
-
-    # thi is where all the good stuff is picked up
-
-    # look at each mode annd pull out some usefull linear measures
-    for i, p in enumerate(net_peak):
-        # print i,p['y_i'],p['z_i'],fft_data.shape,fft_data[:,:,p['y_i'],p['z_i']].shape
-
-        amp = (
-            old_div(np.sqrt(power[:, :, p["y_i"], p["z_i"]]), (kz_max * ky_max))
-        ).real
-
-        # print (np.angle(fft_data[:,:,p['y_i'],p['z_i']],deg=False)).real
-
-        phase = -np.array(
-            np.gradient(
-                np.squeeze(np.angle(fft_data[:, :, p["y_i"], p["z_i"]], deg=False))
-            )[0].real
-        )  # nt x nx
-
-        gamma_instant = np.array(np.gradient(np.log(np.squeeze(amp)))[0])
-
-        # loop over radaii
-        phasenew = []
-        gammanew = []
-        from scipy.interpolate import interp2d, interp1d
-        from scipy import interp
-
-        gamma_t = np.transpose(gamma_instant)
-        for i, phase_r in enumerate(np.transpose(phase)):
-            gamma_r = gamma_t[i]
-            jumps = np.where(abs(phase_r) > old_div(np.pi, 32))
-            # print jumps
-            if len(jumps[0]) != 0:
-                all_pts = np.array(list(range(0, nt)))
-                good_pts = (np.where(abs(phase_r) < old_div(np.pi, 3)))[0]
-                # print good_pts,good_pts
-                # f = interp1d(good_pts,phase_r[good_pts],fill_value=.001)
-                # print max(all_pts), max(good_pts)
-                # phasenew.append(f(all_pts))
-                try:
-                    phase_r = interp(all_pts, good_pts, phase_r[good_pts])
-                    gamma_r = interp(all_pts, good_pts, gamma_r[good_pts])
-                except:
-                    "no phase smoothing"
-            phasenew.append(phase_r)
-            gammanew.append(gamma_r)
-
-        phase = old_div(np.transpose(phasenew), dt)
-
-        gamma_i = old_div(np.transpose(gammanew), dt)
-
-        amp_n = (
-            old_div(np.sqrt(power[:, :, p["y_i"], p["z_i"]]), (kz_max * ky_max * amp))
-        ).real
-        # amp_n = dom_mode[i]['amp_n'] #nt x nx
-
-        # let just look over the nx range
-        # lnamp = np.log(amp[nt/2:,2:-2])
-        try:
-            lnamp = np.log(amp[old_div(nt, 2) :, :])
-        except:
-            print("some log(0) stuff in basic_info")
-
-        t = dt * np.array(list(range(nt)))  # dt matters obviouslyww
-        r = np.polyfit(t[old_div(nt, 2) :], lnamp, 1, full=True)
-
-        gamma_est = r[0][0]  # nx
-        f0 = np.exp(r[0][1])  # nx
-        res = r[1]
-        pad = [0, 0]
-        # gamma_est = np.concatenate([pad,gamma_est,pad])
-        # f0 = np.concatenate([pad,f0,pad])
-        # res = np.concatenate([pad,res,pad])
-
-        # sig = res/np.sqrt((x['nt']-2))
-        sig = np.sqrt(old_div(res, (nt - 2)))
-        # sig0 = sig*np.sqrt(1/(x['nt'])+ ) # who cares
-        sig1 = sig * np.sqrt(old_div(1.0, (nt * t.var())))
-        nt = np.array(nt)
-        print("shapes ", nt.shape, nt, lnamp.shape, res.shape, gamma_est)
-        # print r
-        res = 1 - old_div(res, (nt * lnamp.var(0)))  # nx
-        res[0:2] = 0
-        res[-2:] = 0
-
-        gamma = [gamma_est, sig1, f0, res]
-
-        # gamma_est2 = np.gradient(amp)[0]/(amp[:,:]*dt)
-        # gamma_w =  np.gradient(gamma_est2)[0]
-
-        # gamma_i = np.abs(gamma_w).argmin(0) #index of the minimum for any given run
-        # for j in range(nx):
-        #     gamma_w[0:max([gamma_i[j],nt/3]),j] = np.average(gamma_w)*100000.0
-
-        freq = np.array(
-            weighted_avg_and_std(phase[-10:, :], weights=np.ones(phase[-10:, :].shape))
-        )
-
-        # gamma = weighted_avg_and_std(
-        #         gamma_est2[-5:,:],weights=np.ones(gamma_est2[-5:,:].shape))
-
-        k = [
-            [p["y_i"], p["z_i"]],
-            [2 * math.pi * float(p["y_i"]) / L_y, 2 * math.pi * p["z_i"] / L_z],
-        ]
-        # L_y is normalized
-
-        # simple k def, works in drift-instability fine
-        # k = [[p['y_i'],p['z_i']],
-        #      [(B/Bp)**-1*2*math.pi*float(p['y_i'])/(L_y),(B/Bp)*2*math.pi*p['z_i']/L_z]]
-
-        # k_r = [[p['y_i'],p['z_i']],
-        #      [(Bp/B)*2*math.pi*float(p['y_i'])/(L_y),
-        #       (B/Bp)*2*math.pi*p['z_i']/L_z]]
-
-        k_r = [
-            [p["y_i"], p["z_i"]],
-            [
-                2 * math.pi * float(p["y_i"]) / (L_y),
-                (old_div(B, Bp)) * 2 * math.pi * p["z_i"] / L_z
-                + (old_div(Bt, B)) * 2 * math.pi * float(p["y_i"]) / (L_y),
-            ],
-        ]
-
-        # revised
-        # k_r = [[p['y_i'],p['z_i']],
-        #      [2*math.pi*float(p['y_i'])/(L_y),
-        #       (Bp/B)*2*math.pi*p['z_i']/L_z
-        #       - (Bt/Bp)*2*math.pi*float(p['y_i'])/(L_y)]]
-        # revised
-
-        # what I think is the most general one, works in drift-instability again
-        # seems to work for Bz only helimak, now trying Bp = Bt
-        # k = [[p['y_i'],p['z_i']],
-        #      [((Bp/B)*float(p['y_i'])/(hthe0_n)) +
-        #       2*np.pi*p['z_i']*np.sqrt(1-(Bp/B)**2)/L_z,
-        #       2*math.pi*p['z_i']/L_norm -
-        #       float(p['y_i'])*np.sqrt(1-(Bp/B)**2)/(hthe0_n)]]
-        # k = [[p['y_i'],p['z_i']],
-        #      [((Bp/B)*float(p['y_i'])/(hthe0_n)),
-        #       2*math.pi*p['z_i']/L_norm]]
-        # BOTH SEEM TO PRODOCE SAME RESULTS
-
-        # k = [[p['y_i'],p['z_i']],
-        #      [(float(p['y_i'])/(hthe0_n_x)),
-        #       2*math.pi*float(p['z_i'])/L_norm]]
-
-        dom_mode_db.append(
-            {
-                "modeid": i,
-                "k": k[1],
-                "gamma": gamma,
-                "freq": freq,
-                "amp": amp,
-                "amp_n": amp_n,
-                "phase": phase,
-                "mn": k[0],
-                "nt": nt,
-                "k_r": k_r[1],
-                "gamma_i": gamma_i,
-            }
-        )
-
-    return dom_mode_db
-
-
-# return a 2d array fof boolean values, a very simple boolian filter
-def local_maxima(array2d, user_peak, index=False, count=4, floor=0, bug=False):
-    from operator import itemgetter, attrgetter
-
-    if user_peak == 0:
-        where = (
-            (array2d >= np.roll(array2d, 1, 0))
-            & (array2d >= np.roll(array2d, -1, 0))
-            & (array2d >= np.roll(array2d, 0, 1))
-            & (array2d >= np.roll(array2d, 0, -1))
-            & (array2d >= old_div(array2d.max(), 5.0))
-            & (array2d > floor * np.ones(array2d.shape))
-            & (array2d >= array2d.mean())
-        )
-    else:  # some simpler filter if user indicated some modes
-        where = array2d > floor
-
-    # ignore the lesser local maxima, throw out anything with a ZERO
-    if bug == True:
-        print(array2d, array2d[where.nonzero()], where.nonzero()[0])
-
-    peaks = list(zip(where.nonzero()[0], where.nonzero()[1], array2d[where.nonzero()]))
-
-    peaks = sorted(peaks, key=itemgetter(2), reverse=True)
-
-    if len(peaks) > count and user_peak == 0:
-        peaks = peaks[0:count]
-
-    keys = ["y_i", "z_i", "amp"]
-
-    peaks = [dict(list(zip(keys, peaks[x]))) for x in range(len(peaks))]
-
-    return peaks
-    # return np.array(peak_dic)
-
-
-def weighted_avg_and_std(values, weights):
-    """
-    Returns the weighted average and standard deviation.
-
-    values, weights -- Numpy ndarrays with the same shape.
-    """
-
-    if len(values.shape) == 2:
-        average = np.average(values, 0)  # , weights=weights)
-        variance = old_div(
-            (
-                np.inner(
-                    weights.transpose(), ((values - average) ** 2).transpose()
-                ).diagonal()
-            ),
-            weights.sum(0),
-        )
-    else:
-        average = np.average(values, weights=weights)
-        variance = old_div(
-            np.dot(weights, (values - average) ** 2), weights.sum()
-        )  # Fast and numerically precise
-
-    return [average, variance]
diff --git a/tools/pylib/post_bout/grate2.py b/tools/pylib/post_bout/grate2.py
deleted file mode 100644
index 5157863cc2..0000000000
--- a/tools/pylib/post_bout/grate2.py
+++ /dev/null
@@ -1,52 +0,0 @@
-from __future__ import print_function
-from builtins import range
-
-###
-# compute average growth rate bout variable f and plane y
-# prints value in plane y and total average
-# optional tind excludes initial 'tind' time steps
-# Note it masks the values != Inf
-###
-import numpy as np
-from boutdata.collect import collect
-from boututils.moment_xyzt import moment_xyzt
-
-
-def avgrate(p, y=None, tind=None):
-    if tind is None:
-        tind = 0
-
-    rmsp_f = moment_xyzt(p, "RMS").rms
-
-    ni = np.shape(rmsp_f)[1]
-    nj = np.shape(rmsp_f)[2]
-
-    growth = np.zeros((ni, nj))
-
-    with np.errstate(divide="ignore"):
-        for i in range(ni):
-            for j in range(nj):
-                growth[i, j] = np.gradient(np.log(rmsp_f[tind::, i, j]))[-1]
-
-    d = np.ma.masked_array(growth, np.isnan(growth))
-
-    # masked arrays
-    # http://stackoverflow.com/questions/5480694/numpy-calculate-averages-with-nans-removed
-
-    print("Total average growth rate= ", np.mean(np.ma.masked_array(d, np.isinf(d))))
-    if y is not None:
-        print(
-            "Growth rate in plane",
-            y,
-            "= ",
-            np.mean(np.ma.masked_array(growth[:, y], np.isnan(growth[:, y]))),
-        )
-
-
-# test
-if __name__ == "__main__":
-    path = "/Users/brey/BOUT/bout/examples/elm-pb/data"
-
-    data = collect("P", path=path)
-
-    avgrate(data, 32)
diff --git a/tools/pylib/post_bout/pb_corral.py b/tools/pylib/post_bout/pb_corral.py
deleted file mode 100644
index df9a9b00b6..0000000000
--- a/tools/pylib/post_bout/pb_corral.py
+++ /dev/null
@@ -1,540 +0,0 @@
-# note - these commands are only run by default in interactive mode
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import division
-from builtins import filter
-from builtins import range
-from past.utils import old_div
-from builtins import object
-import os
-import sys
-
-try:
-    boutpath = os.environ["BOUT_TOP"]
-    pylibpath = boutpath + "tools/pylib"
-    pbpath = pylibpath + "/post_bout"
-    boutdatapath = pylibpath + "/boutdata"
-    boututilpath = pylibpath + "/boututils"
-
-    allpath = [boutpath, pylibpath, pbpath, boutdatapath, boututilpath]
-    [sys.path.append(elem) for elem in allpath]
-
-except:
-    print("unable to append needed .py files")
-
-sys.path.append("/usr/local/pylib")
-
-import post_bout as post_bout
-from .ListDict import ListDictKey, ListDictFilt
-from .read_inp import parse_inp, read_inp, read_log
-from .basic_info import weighted_avg_and_std
-from .read_cxx import read_cxx, findlowpass
-
-
-import os
-import numpy as np
-import pickle
-import subprocess
-
-
-def corral(
-    cached=True, refresh=False, debug=False, IConly=1, logname="status.log", skew=False
-):
-    print("in corral")
-    log = read_log(logname=logname)
-    # done = log['done']
-    runs = log["runs"]  # a list of all directories, we need this,
-    # only need 'runs' if the simulation is done
-
-    current = log["current"]  # always return the last data_dir
-
-    print(log)
-    print("current:", current)
-
-    if refresh == True:
-        for i, path in enumerate(runs):
-            print(i, path)
-            a = post_bout.save(path=path, IConly=IConly)  # re post-process a run
-
-    elif (
-        cached == False
-    ):  # if all the ind. simulation pkl files are in place skip this part
-        a = post_bout.save(path=current)  # save to current dir
-        # here is really where you shoudl write to status.log
-        # write_log('status.log',
-        cached = True
-
-    # if done:
-
-    all_ave = []
-    all_modes = []
-    print("last_one: ")
-    for i, val in enumerate(runs):
-        print(val)
-        mode_db, ave_db = post_bout.read(path=val)
-        # alldata.append(array)
-        all_modes.append(mode_db)
-        all_ave.append(ave_db)
-
-        # build the end database
-
-        # remove the read in pickle
-
-    # return alldb
-    def islist(input):
-        return isinstance(input, list)
-
-    all_modes = list(filter(islist, all_modes))
-    # all_ave = filter(islist,all_ave)
-
-    # alldb = sum(alldb,[])
-    # alldata = np.array(alldata)
-    all_modes = sum(all_modes, [])
-
-    nt = []
-    for mode in all_modes:
-        nt.append(len(mode["amp"]))
-        nt = [max(nt)]
-
-    nt = nt[0]
-    t = list(range(nt))
-    i = 0
-
-    if debug:
-        return all_modes, all_ave
-    else:
-        return LinRes(all_modes)
-
-
-class LinRes(object):
-    def __init__(self, all_modes):
-        self.mode_db = all_modes
-        self.db = all_modes
-        # self.ave_db = all_ave
-
-        alldb = self.db
-        # self.modekeys = data[0]['fields']['Ni']['modes'][0].keys()
-        # print len(alldb)
-
-        self.meta = np.array(ListDictKey(self.db, "meta"))[0]
-
-        self.keys = list((self.mode_db)[0].keys())
-        # self.avekeys = data[0]['fields']['Ni']['ave'].keys()
-
-        # self.nrun = len(alldb) #number of runs
-
-        self.path = np.array(ListDictKey(self.db, "path"))
-        self.cxx = []
-        self.maxN = []
-
-        self.ave = np.array(ListDictKey(alldb, "ave"))
-
-        # [self.cxx.append(read_cxx(path=elem,boutcxx='2fluid.cxx.ref')) for elem in self.path]
-        # [self.maxN.append(findlowpass(elem)) for elem in self.cxx]
-        [
-            self.cxx.append(read_cxx(path=elem, boutcxx="physics_code.cxx.ref"))
-            for elem in self.path
-        ]
-
-        self.maxZ = np.array(ListDictKey(alldb, "maxZ"))
-        self.maxN = self.maxZ
-        # self.maxN = findlowpass(self.cxx) #low pass filt from .cxx
-
-        self.nx = np.array(ListDictKey(alldb, "nx"))[0]
-        self.ny = np.array(ListDictKey(alldb, "ny"))[0]
-        self.nz = np.array(ListDictKey(alldb, "nz"))[0]
-
-        # self.nt = int(data[0]['meta']['NOUT']['v']+1)
-        self.Rxy = np.array(ListDictKey(alldb, "Rxy"))
-        self.Rxynorm = np.array(ListDictKey(alldb, "Rxynorm"))
-        self.nt = np.array(ListDictKey(alldb, "nt"))
-
-        self.dt = np.array(ListDictKey(alldb, "dt"))
-        self.nfields = np.array(ListDictKey(alldb, "nfields"))
-
-        self.field = np.array(ListDictKey(alldb, "field"))
-
-        self.k = np.array(ListDictKey(alldb, "k"))
-        self.k_r = np.array(ListDictKey(alldb, "k_r"))
-
-        self.mn = np.array(ListDictKey(alldb, "mn"))
-
-        # return ListDictKey(alldb,'phase')
-
-        # self.phase = np.array(ListDictKey(alldb,'phase'))
-        self.phase = ListDictKey(alldb, "phase")
-
-        # self.amp= np.array(ListDictKey(alldb,'amp'))
-        # self.amp_n=np.array(ListDictKey(alldb,'amp_n'))
-        # self.dc= []
-        # self.freq = np.array(ListDictKey(alldb,'k'))
-        # self.gamma = np.array(ListDictKey(alldb,'gamma'))
-
-        self.amp = ListDictKey(alldb, "amp")
-        self.amp_n = ListDictKey(alldb, "amp_n")
-        self.dc = []
-        # self.freq = np.array(ListDictKey(alldb,'k'))
-        self.gamma = np.array(ListDictKey(alldb, "gamma"))
-        self.gamma_i = np.array(ListDictKey(alldb, "gamma_i"))
-
-        self.freq = np.array(ListDictKey(alldb, "freq"))
-
-        self.IC = np.array(ListDictKey(alldb, "IC"))
-        self.dz = np.array(ListDictKey(alldb, "dz"))
-        self.meta["dz"] = np.array(list(set(self.dz).union()))
-
-        self.nmodes = self.dz.size
-
-        self.MN = np.array(ListDictKey(alldb, "MN"))
-        # self.MN = np.float32(self.mn)
-        # self.MN[:,1] = self.mn[:,1]/self.dz
-        self.nrun = len(set(self.path).union())
-        self.L = np.array(ListDictKey(alldb, "L"))
-        # self.C_s =
-        self.modeid = np.array(ListDictKey(alldb, "modeid"))
-
-        self.trans = np.array(ListDictKey(alldb, "transform"))
-
-        if np.any(self.trans):
-            self.phase_r = ListDictKey(alldb, "phase_r")
-            self.gamma_r = np.array(ListDictKey(alldb, "gamma_r"))
-            self.amp_r = ListDictKey(alldb, "amp_r")
-            self.freq_r = np.array(ListDictKey(alldb, "freq_r"))
-
-        # try:
-        #     self.model(haswak=False) #
-        # except:
-        #     self.M = 0
-
-        # try:
-        try:  # analytic model based on simple matrix
-            self.models = []
-            # self.models.append(_model(self)) #create a list to contain models
-            self.models.append(
-                _model(self, haswak=True, name="haswak")
-            )  # another model
-        # self.models.append(_model(self,haswak=True,name='haswak_0',m=0))
-        # for Ln in range(10):
-        #     Lval = 10**((.2*Ln -1)/10)
-        #     #Lval = 10**(Ln-1)
-        #     #Lval =
-        #     print Lval
-        #     self.models.append(_model(self,varL=True,name='varL'+str(Lval),Lval=Lval,haswak=True))
-
-        except:
-            self.M = 0
-
-        try:  # analytic models based on user defined complex omega
-            self.ref = []
-            self.ref.append(_ref(self))
-        # self.ref.append(_ref(self,haswak=False,name='drift'))
-        # demand a complex omega to compare
-        # self.ref.append(_ref(self,haswas=True,name='haswak'))
-        except:
-            self.ref = 0
-
-    # self.models.append(_model(self,haswak2=True,name='haswak2'))
-
-    # except:
-    #     print 'FAIL'
-
-    def _amp(self, tind, xind):
-        # first select modes that actually have valid (tind,xind)
-        # indecies
-        # s = subset(self.db,'modeid',modelist)
-        return np.array([self.amp[i][tind, xind] for i in range(self.nmodes)])
-
-    # def model(self,field='Ni',plot=False,haswak=False):
-
-    #    #enrich the object
-    #    allk = self.k_r[:,1,self.nx/2] #one location for now
-    #    allkpar = self.k_r[:,0,self.nx/2] #one location for now
-
-    #    self.M = []
-    #    self.eigsys = []
-    #    self.gammaA = []
-    #    self.omegaA = []
-    #    self.eigvec = []
-    #    self.gammamax = []
-    #    self.omegamax = []
-
-    #    #allk = np.arange(0.1,100.0,.1)
-    #    #allk=  np.sort(list(set(allk).union()))
-
-    #    for i,k in enumerate(allk):
-    #       #print i
-    #       #M =np.matrix(np.random.rand(3,3),dtype=complex)
-    #       M = np.zeros([3,3],dtype=complex)
-    #       M[0,0] = 0
-    #       M[0,1] = k/(self.L[i,self.nx/2,self.ny/2])
-    #       M[1,0] = (2*np.pi/self.meta['lpar'][self.nx/2])**2 * self.meta['sig_par'][0]*complex(0,k**-2)
-    #       M[1,1]= -(2*np.pi/self.meta['lpar'][self.nx/2])**2 * self.meta['sig_par'][0]*complex(0,k**-2)
-
-    #       if haswak:
-    #           M[0,0] = M[0,0] + M[1,1]*complex(0,k**2)
-    #           M[0,1] = M[0,1] + M[1,0]*complex(0,k**2)
-
-    #       #if rho_conv:
-
-    #       #M[1,0] = (allkpar[i])**2 * self.meta['sig_par'][0]*complex(0,k**-2)
-    #       #M[1,1]= -(allkpar[i])**2 * self.meta['sig_par'][0]*complex(0,k**-2)
-
-    #       eigsys= np.linalg.eig(M)
-    #       gamma = (eigsys)[0].imag
-    #       omega =(eigsys)[0].real
-    #       eigvec = eigsys[1]
-
-    #       self.M.append(M)
-    #       self.eigsys.append(eigsys)
-    #       self.gammaA.append(gamma)
-    #       self.gammamax.append(max(gamma))
-    #       where = ((gamma == gamma.max()) & (omega != 0))
-    #       self.omegamax.append(omega[where[0]])
-    #       self.eigvec.append(eigvec)
-    #       self.omegaA.append(omega)
-
-    class __model__(object):
-        def __init__(self):
-            self.M = 0
-
-
-class subset(LinRes):
-    def __init__(self, alldb, key, valuelist, model=False):
-        selection = ListDictFilt(alldb, key, valuelist)
-        if len(selection) != 0:
-            LinRes.__init__(self, selection)
-            self.skey = key
-            if model == True:
-                self.model()
-        else:
-            LinRes.__init__(self, alldb)
-            if model == True:
-                self.model()
-
-
-# class subset(originClass):
-#     def __init__(self,alldb,key,valuelist,model=False):
-#       selection = ListDictFilt(alldb,key,valuelist)
-#       if len(selection) !=0:
-#          originClass.__init__(self,selection,input_obj.ave_db)
-#          self.skey = key
-#          if model==True:
-#             self.model()
-#       else:
-#          origin.__init__(self,alldb)
-#          if model==True:
-#             self.model()
-
-# not sure if this is the best way . . .
-
-
-# class subset(object):
-#     def __init__(self,input_obj,key,valuelist,model=False):
-#         selection = ListDictFilt(input_obj.mode_db,key,valuelist)
-#         if len(selection) !=0:
-#             import copy
-#             self = copy.copy(input_obj)
-#             self.__init__(selection,input_obj.ave_db)
-#             self.skey = key
-#             if model==True:
-#                 self.model()
-#         else:
-#             self = input_obj
-#             if model==True:
-#                 self.model()
-
-
-class _ref(object):  # NOT a derived obj, just takes one as a var
-    def __init__(self, input_obj, name="haswak", haswak=True):
-        allk = input_obj.k_r[:, 1, old_div(input_obj.nx, 2)]  # one location for now
-        allkpar = input_obj.k_r[:, 0, old_div(input_obj.nx, 2)]  # one location for now
-        self.name = name
-
-        self.gamma = []
-        self.omega = []
-        self.soln = {}
-        self.soln["gamma"] = []
-        self.soln["freq"] = []
-
-        for i, k in enumerate(allk):
-            omega_star = old_div(
-                -(k),
-                (input_obj.L[i, old_div(input_obj.nx, 2), old_div(input_obj.ny, 2)]),
-            )
-
-            nu = (
-                2 * np.pi / input_obj.meta["lpar"][old_div(input_obj.nx, 2)]
-            ) ** 2 * input_obj.meta["sig_par"][0]
-
-            if haswak:
-                omega = old_div(-omega_star, (1 + (k) ** 2))
-                gamma = old_div(((k**2) * omega_star**2), (nu * (1 + k**2) ** 3))
-            else:
-                # omega = -np.sqrt(nu*omega_star)/(np.sqrt(2)*k) + nu**(3/2)/(8*np.sqrt(2*omega_star)*k**3)
-                # gamma = np.sqrt(nu*omega_star)/(np.sqrt(2)*k) - nu/(2* k**2) + nu**(3/2)/(8*np.sqrt(2*omega_star)*k**3)
-                omega = -omega_star + old_div((2 * k**4 * omega_star**3), nu**2)
-                gamma = old_div((k * omega_star) ** 2, nu) - (
-                    5 * (k**6 * omega_star * 4 / nu**3)
-                )
-            self.gamma.append(gamma)
-            self.omega.append(omega)
-
-        self.soln["freq"] = np.transpose(np.array(self.omega))
-        self.soln["gamma"] = np.transpose(np.array(self.gamma))
-
-
-class _model(object):  # NOT a derived class,but one that takes a class as input
-    def __init__(
-        self,
-        input_obj,
-        name="drift",
-        haswak=False,
-        rho_conv=False,
-        haswak2=False,
-        varL=False,
-        Lval=1.0,
-        m=1,
-    ):
-        allk = input_obj.k_r[:, 1, old_div(input_obj.nx, 2)]  # one location for now
-        allkpar = input_obj.k_r[:, 0, old_div(input_obj.nx, 2)]  # one location for now
-
-        # numerical value to compare against
-
-        numgam = input_obj.gamma[:, 0, old_div(input_obj.nx, 2)]
-        numfreq = input_obj.freq[:, 0, old_div(input_obj.nx, 2)]
-        self.name = name
-
-        self.M = []
-        self.eigsys = []
-        self.gammaA = []
-        self.omegaA = []
-        self.eigvec = []
-        self.gammamax = []
-        self.omegamax = []
-        self.k = []
-        self.m = m
-
-        self.soln = {}
-        self.soln["freq"] = []
-        self.soln["gamma"] = []
-        self.soln["gammamax"] = []
-        self.soln["freqmax"] = []
-
-        self.chi = {}
-        self.chi["freq"] = []
-        self.chi["gamma"] = []
-
-        for i, k in enumerate(allk):
-            # print i
-            # M =np.matrix(np.random.rand(3,3),dtype=complex)
-            M = np.zeros([4, 4], dtype=complex)
-            M[0, 0] = 0
-            # k = k/np.sqrt(10)
-            # L = (input_obj.L)*np.sqrt(10)
-
-            if k == 0:
-                k = 1e-5
-
-            # print k {n,phi,v,ajpar}
-            M[0, 1] = old_div(
-                k, (input_obj.L[i, old_div(input_obj.nx, 2), old_div(input_obj.ny, 2)])
-            )
-            M[1, 0] = (
-                (2 * m * np.pi / input_obj.meta["lpar"][old_div(input_obj.nx, 2)]) ** 2
-                * input_obj.meta["sig_par"][0]
-                * complex(0, (k) ** -2)
-            )
-            M[1, 1] = (
-                -(
-                    (2 * m * np.pi / input_obj.meta["lpar"][old_div(input_obj.nx, 2)])
-                    ** 2
-                )
-                * input_obj.meta["sig_par"][0]
-                * complex(0, (k) ** -2)
-            )
-
-            # parallel dynamics
-            # M[2,2] = k/(input_obj.L[i,input_obj.nx/2,input_obj.ny/2])
-            # M[2,0] = -(2*m*np.pi/input_obj.meta['lpar'][input_obj.nx/2])
-            # M[0,2] = -(2*m*np.pi/input_obj.meta['lpar'][input_obj.nx/2])
-
-            # M[1,0] = (2*m*np.pi/input_obj.meta['lpar'][input_obj.nx/2])**2 * input_obj.meta['sig_par'][0]
-            # M[1,1]= -(2*m*np.pi/input_obj.meta['lpar'][input_obj.nx/2])**2 * input_obj.meta['sig_par'][0]
-
-            # ajpar dynamics - effectively parallel electron dynamics instead of
-
-            if haswak:
-                M[0, 0] = (
-                    -(
-                        (
-                            2
-                            * m
-                            * np.pi
-                            / input_obj.meta["lpar"][old_div(input_obj.nx, 2)]
-                        )
-                        ** 2
-                    )
-                    * input_obj.meta["sig_par"][0]
-                    * complex(0, 1)
-                )
-                M[0, 1] = (
-                    2 * m * np.pi / input_obj.meta["lpar"][old_div(input_obj.nx, 2)]
-                ) ** 2 * input_obj.meta["sig_par"][0] * complex(0, 1) + M[0, 1]
-
-            if varL:
-                M[0, 1] = Lval * M[0, 1]
-
-            if rho_conv:  # not used
-                M[1, 0] = (
-                    (allkpar[i]) ** 2
-                    * input_obj.meta["sig_par"][0]
-                    * complex(0, (k) ** -2)
-                )
-                M[1, 1] = (
-                    -((allkpar[i]) ** 2)
-                    * input_obj.meta["sig_par"][0]
-                    * complex(0, (k) ** -2)
-                )
-
-            eigsys = np.linalg.eig(M)
-            gamma = (eigsys)[0].imag
-            omega = (eigsys)[0].real
-            eigvec = eigsys[1]
-            self.k.append(k)
-
-            self.M.append(M)
-            self.eigsys.append(eigsys)
-
-            self.gammaA.append(gamma)
-            self.soln["gamma"].append(gamma)
-
-            self.gammamax.append(max(gamma))
-            self.soln["gammamax"].append(max(gamma))
-
-            where = (gamma == gamma.max()) & (omega != 0)
-            # if len(where) > 1:
-            #     where = where[0]
-            self.omegamax.append(omega[where])
-            self.soln["freqmax"].append(omega[where])
-
-            # print k,gamma,where,M,omega
-            chigam = old_div(((numgam - max(gamma)) ** 2), max(gamma))
-            chifreq = old_div(((numfreq - omega[where]) ** 2), omega[where])
-
-            self.eigvec.append(eigvec)
-            self.omegaA.append(omega)
-            self.soln["freq"].append(omega)
-
-            self.chi["freq"].append(chifreq[i])
-
-            self.chi["gamma"].append(chigam[i])
-
-        self.dim = M.shape[0]
-        self.soln["freq"] = np.transpose(np.array(self.soln["freq"]))
-        self.soln["gamma"] = np.transpose(np.array(self.soln["gamma"]))
-        self.chi["freq"] = np.transpose(np.array(self.chi["freq"]))
-        self.chi["gamma"] = np.transpose(np.array(self.chi["gamma"]))
-
-        # self.soln = {}
-        # self.soln['freq'] = self.omegaA
-        # self.soln['gamma'] = self.gammaA
diff --git a/tools/pylib/post_bout/pb_draw.py b/tools/pylib/post_bout/pb_draw.py
deleted file mode 100644
index 272aab9c35..0000000000
--- a/tools/pylib/post_bout/pb_draw.py
+++ /dev/null
@@ -1,1692 +0,0 @@
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import division
-from builtins import str
-from builtins import range
-from past.utils import old_div
-
-# some standard analytic stuff to plot, if appending just overplot gam or omeg
-from .pb_corral import LinRes
-from .ListDict import ListDictKey, ListDictFilt
-import numpy as np
-
-import matplotlib.pyplot as plt
-from matplotlib import cm
-import matplotlib.artist as artist
-import matplotlib.ticker as ticker
-import matplotlib.pyplot as plt
-import matplotlib.patches as patches
-from matplotlib.figure import Figure
-from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
-from matplotlib.backends.backend_pdf import PdfPages
-
-from reportlab.platypus import *
-from reportlab.lib.styles import getSampleStyleSheet
-from reportlab.rl_config import defaultPageSize
-from reportlab.lib.units import inch
-from reportlab.graphics.charts.linecharts import HorizontalLineChart
-from reportlab.graphics.shapes import Drawing
-from reportlab.graphics.charts.lineplots import LinePlot
-from reportlab.graphics.widgets.markers import makeMarker
-from reportlab.lib import colors
-
-from replab_x_vs_y import RL_Plot
-from matplotlib.ticker import ScalarFormatter, FormatStrFormatter, MultipleLocator
-
-
-class LinResDraw(LinRes):
-    def __init__(self, alldb):
-        LinRes.__init__(self, alldb)
-
-    def plottheory(
-        self, pp, m=1, canvas=None, comp="gamma", field="Ni", allroots=False
-    ):
-        if len(self.models) == 0:
-            try:
-                self.models = []
-                self.models.append(_model(self))  # create a list to contain models
-                self.models.append(
-                    _model(self, haswak=True, name="haswak")
-                )  # another model
-            except:
-                return 0
-
-        s = subset(self.db, "field", [field])
-
-        modelist = []
-
-        [modelist.append([m, n + 1]) for n in range(min(s.maxN) - 1)]
-
-        s = subset(s.db, "mn", modelist)
-
-        allk = s.k[:, 1, old_div(s.nx, 2)]
-        ki = np.argsort(allk)
-
-        ownpage = False
-        if canvas is None:
-            ownpage = True
-
-        if ownpage:  # if not an overplot
-            fig1 = plt.figure()
-            canvas = fig1.add_subplot(1, 1, 1)
-
-        label = "gamma analytic"
-
-        # if comp=='gamma':
-        #     y = np.array(s.gammamax)[ki]
-        # else:
-        #     y = np.array(s.omegamax)[ki]
-
-        for m in s.models:
-            print(m.name)
-
-        for i, m in enumerate(s.models):
-            print(m.name, comp, m.soln[comp].shape)
-
-            if allroots:
-                for elem in m.soln[comp]:
-                    # y = []
-                    # elem has 2 or more elements
-                    y = (np.array(elem)[ki]).flatten()  # n values
-                    # y = y.astype('float')
-                    print(y.shape)
-                    canvas.plot(
-                        (allk[ki]).flatten(), y, ",", label=label, c=cm.jet(0.2 * i)
-                    )
-            try:
-                ymax = (np.array(m.soln[comp + "max"])[ki]).flatten()
-                # ymax =  (np.array(m.gammamax)[ki]).flatten()
-                ymax = ymax.astype("float")
-                print(comp, " ymax:", ymax)
-                canvas.plot(
-                    (allk[ki]).flatten(), ymax, "-", label=label, c=cm.jet(0.2 * i)
-                )
-                # if comp=='gamma':
-                #     y = (np.array(m.gammamax)[ki]).flatten()
-
-                # else:
-                #     y = (np.array(m.omegamax)[ki]).flatten()
-
-            # print m.name, ':' ,y.astype('float')
-
-            except:
-                print("fail to add theory curve")
-
-            canvas.annotate(m.name, (allk[ki[0]], 1.1 * ymax[0]), fontsize=8)
-            canvas.annotate(m.name, (1.1 * allk[ki[-1]], 1.1 * ymax[-1]), fontsize=8)
-
-            try:
-                for i, m in enumerate(s.ref):
-                    if not allroots:
-                        y = (np.array(m.soln[comp])[ki]).flatten()
-                        y = y.astype("float")
-                        canvas.plot(
-                            (allk[ki]).flatten(),
-                            y,
-                            "--",
-                            label=label,
-                            c=cm.jet(0.2 * i),
-                        )
-            except:
-                print("no reference curve")
-
-        if ownpage:  # set scales if this is its own plot
-            # canvas.set_yscale('symlog',linthreshy=1e-13)
-            # canvas.set_xscale('log')
-
-            canvas.axis("tight")
-            canvas.set_xscale("log")
-            canvas.set_yscale("symlog")
-            fig1.savefig(pp, format="pdf")
-            plt.close(fig1)
-        else:  # if not plot its probably plotted iwth sim data, print chi somewhere
-            for i, m in enumerate(s.models):
-                textstr = r"$\chi^2$" + "$=%.2f$" % (m.chi[comp].sum())
-                print(textstr)
-                # textstr = '$\L=%.2f$'%(m.chi[comp].sum())
-                props = dict(boxstyle="square", facecolor="white", alpha=0.3)
-                textbox = canvas.text(
-                    0.1,
-                    0.1,
-                    textstr,
-                    transform=canvas.transAxes,
-                    fontsize=10,
-                    verticalalignment="top",
-                    bbox=props,
-                )
-
-    def plotomega(
-        self,
-        pp,
-        canvas=None,
-        field="Ni",
-        yscale="linear",
-        clip=0,
-        xaxis="t",
-        xscale="linear",
-        xrange=1,
-        comp="gamma",
-        pltlegend="both",
-        overplot=False,
-        gridON=True,
-        trans=False,
-        infobox=True,
-    ):
-        colors = [
-            "b.",
-            "r.",
-            "k.",
-            "c.",
-            "g.",
-            "y.",
-            "m.",
-            "b.",
-            "r.",
-            "k.",
-            "c.",
-            "g.",
-            "y.",
-            "m.",
-        ]
-        colordash = [
-            "b",
-            "r",
-            "k",
-            "c",
-            "g",
-            "y",
-            "m",
-            "b",
-            "r",
-            "k",
-            "c",
-            "g",
-            "y",
-            "m",
-        ]
-
-        if canvas is None:
-            ownpage = True
-        else:
-            ownpage = False
-
-        if ownpage:
-            fig1 = plt.figure()
-            fig1.subplots_adjust(bottom=0.12)
-            fig1.subplots_adjust(top=0.80)
-            fig1.subplots_adjust(right=0.83)
-            fig1.subplots_adjust(left=0.17)
-            canvas = fig1.add_subplot(1, 1, 1)
-            clonex = canvas.twinx()
-            # if trans:
-            #     cloney = canvas.twiny()
-
-        dzhandles = []
-        parhandles = []
-        parlabels = []
-        dzlabels = []
-
-        m_shift = 1
-        for q in np.array(list(range(1))) + m_shift:
-            s = subset(self.db, "field", [field])  # pick  field
-            maxZ = min(s.maxN)
-            modelist = []
-            [modelist.append([q, p + 1]) for p in range(maxZ - 1)]
-            print(modelist)
-            print(q, "in plotgamma")
-
-        s = subset(s.db, "mn", modelist)
-
-        xrange = old_div(s.nx, 2) - 2
-
-        xrange = [old_div(s.nx, 2), old_div(s.nx, 2) + xrange]
-
-        y = np.array(ListDictKey(s.db, comp))
-
-        # y = s.gamma #nmodes x 2 x nx ndarray
-        k = s.k  ##nmodes x 2 x nx ndarray k_zeta
-
-        kfactor = np.mean(
-            old_div(s.k_r[:, 1, old_div(s.nx, 2)], s.k[:, 1, old_div(s.nx, 2)])
-        )  # good enough for now
-
-        print(
-            k[:, 1, old_div(s.nx, 2)].shape,
-            y[:, 0, old_div(s.nx, 2)].shape,
-            len(colors),
-            ownpage,
-        )  # ,k[:,1,s.nx/2],y[:,0,s.nx/2]
-
-        parhandles.append(
-            canvas.errorbar(
-                np.squeeze(k[:, 1, old_div(s.nx, 2)]),
-                np.squeeze(y[:, 0, old_div(s.nx, 2)]),
-                yerr=np.squeeze(y[:, 1, old_div(s.nx, 2)]),
-                fmt=colors[q],
-            )
-        )
-
-        parlabels.append("m " + str(q))
-
-        # loop over dz sets and connect with dotted line  . . .
-        jj = 0
-
-        ymin_data = np.max(np.array(ListDictKey(s.db, comp)))
-        ymax_data = 0  # for bookeeping
-
-        for p in list(set(s.path).union()):
-            print(p, "in plotomega")
-
-            sub_s = subset(s.db, "path", [p])
-            j = sub_s.dz[0]
-            # print sub_s.amp.shape
-            s_i = np.argsort(sub_s.mn[:, 1])  # sort by 'local' m, global m is ok also
-            # print s_i, sub_s.mn, sub_s.nx, jj
-            y = np.array(ListDictKey(sub_s.db, comp))
-            y_alt = 2.0 * np.array(ListDictKey(sub_s.db, comp))
-
-            k = sub_s.k  ##
-            if q == m_shift:  # fix the parallel mode
-                dzhandles.append(
-                    canvas.plot(
-                        k[s_i, 1, old_div(sub_s.nx, 2)],
-                        y[s_i, 0, old_div(sub_s.nx, 2)],
-                        color=colordash[jj],
-                        alpha=0.5,
-                    )
-                )
-                # clonex.plot(k[s_i,1,sub_s.nx/2],
-                # y_alt[s_i,0,sub_s.nx/2],color=colordash[jj],alpha=.5)
-                # if np.any(sub_s.trans) and trans:
-                #     comp_r = comp+'_r'
-                #     k_r =  sub_s.k_r
-                #     y2 = np.array(ListDictKey(sub_s.db,comp_r))
-                #     cloney.plot(k[s_i,1,sub_s.nx/2],
-                #                 y2[s_i,0,sub_s.nx/2],'k.',ms = 3)
-
-                ymin_data = np.min([np.min(y[s_i, 0, old_div(sub_s.nx, 2)]), ymin_data])
-                ymax_data = np.max([np.max(y[s_i, 0, old_div(sub_s.nx, 2)]), ymax_data])
-
-                print("dzhandle color", jj)
-                # dzlabels.append("DZ: "+ str(2*j)+r'$\pi$')
-                dzlabels.append(j)
-
-                if yscale == "log":
-                    factor = 10
-                else:
-                    factor = 2
-                print("annotating")
-                canvas.annotate(
-                    str(j),
-                    (
-                        k[s_i[0], 1, old_div(sub_s.nx, 2)],
-                        y[s_i[0], 0, old_div(sub_s.nx, 2)],
-                    ),
-                    fontsize=8,
-                )
-                p = canvas.axvspan(
-                    k[s_i[0], 1, old_div(sub_s.nx, 2)],
-                    k[s_i[-1], 1, old_div(sub_s.nx, 2)],
-                    facecolor=colordash[jj],
-                    alpha=0.01,
-                )
-                print("done annotating")
-            else:
-                canvas.plot(
-                    k[s_i, 1, old_div(sub_s.nx, 2)],
-                    y[s_i, 0, old_div(sub_s.nx, 2)],
-                    color=colordash[jj],
-                    alpha=0.3,
-                )
-
-            jj = jj + 1
-
-        dzhandles = np.array(dzhandles).flatten()
-        dzlabels = np.array(dzlabels).flatten()
-
-        dzlabels = list(set(dzlabels).union())
-
-        dz_i = np.argsort(dzlabels)
-
-        dzhandles = dzhandles[dz_i]
-        dzlabels_cp = np.array(dzlabels)[dz_i]
-
-        print(type(dzlabels), np.size(dzlabels))
-        for i in range(np.size(dzlabels)):
-            dzlabels[i] = "DZ: " + str(dzlabels_cp[i])  # +r"$\pi$"
-
-        parlabels = np.array(parlabels).flatten()
-
-        # if pltlegend =='both':    #
-
-        print("legends")
-
-        # l1 = legend(parhandles,parlabels,loc = 3,prop={'size':6})
-        # l2 = legend(dzhandles,dzlabels,loc = 1,prop={'size':6})
-        # plt.gca().add_artist(l1)
-
-        # else:
-        #    legend(dzhandles,dzlabels,loc=3,prop={'size':6})
-        if overplot == True:
-            try:
-                self.plottheory(pp, canvas=canvas, comp=comp, field=field)
-                # self.plottheory(pp,comp=comp)
-            except:
-                print("no theory plot")
-        if infobox:
-            textstr = "$\L_{\parallel}=%.2f$\n$\L_{\partial_r n}=%.2f$\n$B=%.2f$" % (
-                s.meta["lpar"][old_div(s.nx, 2)],
-                s.meta["L"][old_div(s.nx, 2), old_div(s.ny, 2)],
-                s.meta["Bpxy"]["v"][old_div(s.nx, 2), old_div(s.ny, 2)],
-            )
-            props = dict(boxstyle="square", facecolor="white", alpha=0.3)
-            textbox = canvas.text(
-                0.82,
-                0.95,
-                textstr,
-                transform=canvas.transAxes,
-                fontsize=10,
-                verticalalignment="top",
-                bbox=props,
-            )
-            # leg = canvas.legend(handles,labels,ncol=2,loc='best',prop={'size':4},fancybox=True)
-            # textbox.get_frame().set_alpha(0.3)
-            # matplotlib.patches.Rectangle
-            # p = patches.Rectangle((0, 0), 1, 1, fc="r")
-            # p = str('L_par')
-            # leg = canvas.legend([p], ["Red Rectangle"],loc='best',prop={'size':4})
-            # leg.get_frame().set_alpha(0.3)
-
-        # cloney.set_xlim(xmin,xmax)
-        try:
-            canvas.set_yscale(yscale)
-            canvas.set_xscale(xscale)
-
-            if yscale == "symlog":
-                canvas.set_yscale(yscale, linthreshy=1e-13)
-            if xscale == "symlog":
-                canvas.set_xscale(xscale, linthreshy=1e-13)
-
-            if gridON:
-                canvas.grid()
-        except:
-            try:
-                canvas.set_yscale("symlog")
-            except:
-                print("scaling failed completely")
-
-        # print '[xmin, xmax, ymin, ymax]: ',[xmin, xmax, ymin, ymax]
-
-        clonex.set_yscale(yscale)  # must be called before limits are set
-
-        try:
-            if yscale == "linear":
-                formatter = ticker.ScalarFormatter()
-                formatter.set_powerlimits((-2, 2))  # force scientific notation
-                canvas.yaxis.set_major_formatter(formatter)
-                clonex.yaxis.set_major_formatter(formatter)
-                # canvas.useOffset=False
-        except:
-            print("fail 1")
-        [xmin, xmax, ymin, ymax] = canvas.axis()
-
-        if yscale == "symlog":
-            clonex.set_yscale(yscale, linthreshy=1e-9)
-        if xscale == "symlog":
-            clonex.set_xscale(xscale, linthreshy=1e-9)
-            # if np.any(s.trans) and trans:
-        [xmin1, xmax1, ymin1, ymax1] = canvas.axis()
-        if trans:
-            try:
-                cloney = canvas.twiny()
-                # cloney.set_yscale(yscale)
-                cloney.set_xscale(xscale)
-                [xmin1, xmax1, ymin2, ymax2] = canvas.axis()
-
-                if xscale == "symlog":
-                    cloney.set_xscale(xscale, linthreshy=1e-9)
-                if yscale == "symlog":
-                    cloney.set_yscale(yscale, linthreshy=1e-9)
-                if yscale == "linear":
-                    cloney.yaxis.set_major_formatter(formatter)
-            except:
-                print("fail trans")
-                #     cloney.useOffset=False
-
-            # if xscale =='symlog' and trans:
-            #     cloney.set_yscale(yscale,linthreshy=1e-9)
-            #     cloney.set_xscale(xscale,linthreshy=1e-9)
-
-        Ln_drive_scale = s.meta["w_Ln"][0] ** -1
-        # Ln_drive_scale = 2.1e3
-        clonex.set_ylim(Ln_drive_scale * ymin, Ln_drive_scale * ymax)
-
-        try:
-            if trans:
-                # k_factor = #scales from k_zeta to k_perp
-                cloney.set_xlim(kfactor * xmin, kfactor * xmax)
-                # if np.any(sub_s.trans) and trans:
-                #     comp_r = comp+'_r'
-                #     y2 = np.array(ListDictKey(sub_s.db,comp_r))
-                #    #canvas.plot(k[s_i,1,sub_s.nx/2],
-                #    #           y2[s_i,0,sub_s.nx/2],'k.',ms = 3)
-
-                #     cloney.plot(k_r[s_i,1,sub_s.nx/2],
-                #                y2[s_i,0,sub_s.nx/2],'k.',ms = 3)
-                #     print 'np.sum(np.abs(y-y2)): ',np.sum(np.abs(y-y2)),comp_r
-                # kfactor =1.0
-                # cloney.set_xlim(xmin,xmax)
-                cloney.set_ylim(
-                    ymin, ymax
-                )  # because cloney shares the yaxis with canvas it may overide them, this fixes that
-                cloney.set_xlabel(r"$k_{\perp} \rho_{ci}$", fontsize=18)
-        except:
-            print("moar fail")
-            # clonex.set_xscale(xscale)
-
-        # except:
-        #     #canvas.set_xscale('symlog', linthreshx=0.1)
-        #     print 'extra axis FAIL'
-
-        # if yscale == 'linear':
-        # canvas.yaxis.set_major_locator(ticker.LinearLocator(numticks=8))
-
-        # minorLocator   = MultipleLocator(.005)
-        # canvas.yaxis.set_minor_locator(minorLocator)
-        # spawn another y label
-
-        # clone = canvas.twinx()
-        # s2 = np.sin(2*np.pi*t)
-        # ax2.plot(x, s2, 'r.')
-
-        # ion_acoust_str = r"$\frac{c_s}{L_{\partial_r n}}}$"
-
-        if comp == "gamma":
-            canvas.set_ylabel(
-                r"$\frac{\gamma}{\omega_{ci}}$", fontsize=18, rotation="horizontal"
-            )
-            clonex.set_ylabel(
-                r"$\frac{\gamma}{\frac{c_s}{L_n}}$",
-                color="k",
-                fontsize=18,
-                rotation="horizontal",
-            )
-        if comp == "freq":
-            canvas.set_ylabel(
-                r"$\frac{\omega}{\omega_{ci}}$", fontsize=18, rotation="horizontal"
-            )
-            clonex.set_ylabel(
-                r"$\frac{\omega}{\frac{c_s}{L_n}}$",
-                color="k",
-                fontsize=18,
-                rotation="horizontal",
-            )
-
-        if comp == "amp":
-            canvas.set_ylabel(r"$A_k$", fontsize=18, rotation="horizontal")
-            clonex.set_ylabel(
-                r"$\frac{A_k}{A_{max}}$", color="k", fontsize=18, rotation="horizontal"
-            )
-
-        canvas.set_xlabel(r"$k_{\zeta} \rho_{ci}$", fontsize=18)
-
-        title = comp + " computed from " + field
-        # canvas.set_title(title,fontsize=14)
-        fig1.suptitle(title, fontsize=14)
-
-        if ownpage:
-            try:
-                fig1.savefig(pp, format="pdf")
-            except:
-                print("pyplt doesnt like you")
-            plt.close(fig1)
-
-    def plotfreq(
-        self, pp, field="Ni", clip=0, xaxis="t", xscale="linear", yscale="linear"
-    ):
-        # colors = ['b','g','r','c','m','y','k','b','g','r','c','m','y','k']
-        colors = [
-            "b.",
-            "g.",
-            "r.",
-            "c.",
-            "m.",
-            "y.",
-            "k.",
-            "b.",
-            "g.",
-            "r.",
-            "c.",
-            "m.",
-            "y",
-            "k",
-        ]
-        plt.figure()
-
-        # s = subset(self.db,'field',[field]) #pick  field
-
-        for q in range(4):
-            s = subset(self.db, "field", [field])  # pick  field across all dz sets
-            modelist = []
-            [modelist.append([q + 1, p + 1]) for p in range(5)]
-            print(q, "in plotgamma")
-            s = subset(s.db, "mn", modelist)
-
-            gamma = s.freq  # nmodes x 2 x nx ndarray
-            k = s.k  ##nmodes x 2 x nx ndarray
-
-            plt.errorbar(
-                k[:, 1, old_div(s.nx, 2)],
-                gamma[:, 0, old_div(s.nx, 2)],
-                yerr=gamma[:, 1, old_div(s.nx, 2)],
-                fmt=colors[q],
-            )
-            plt.plot(
-                k[:, 1, old_div(s.nx, 2)],
-                gamma[:, 0, old_div(s.nx, 2)],
-                "k:",
-                alpha=0.3,
-            )
-
-            # loop over dz sets and connect with dotted line  . . .
-            for j in list(set(s.dz).union()):
-                # print j,len(s.mn)
-                sub_s = subset(s.db, "dz", [j])
-                gamma = sub_s.gamma
-                k = sub_s.k  ##
-                plt.plot(
-                    k[:, 1, old_div(sub_s.nx, 2)],
-                    gamma[:, 0, old_div(sub_s.nx, 2)],
-                    "k:",
-                    alpha=0.1,
-                )
-
-        try:
-            plt.yscale(yscale)
-        except:
-            print("yscale fail")
-
-        try:
-            plt.xscale(yscale)
-        except:
-            plt.xscale("symlog")
-        plt.xlabel(r"$k \rho_{ci}$", fontsize=14)
-        plt.ylabel(r"$\frac{\omega}{\omega_{ci}}$", fontsize=14)
-        # plt.title(r'$\frac{\omega}\{\omega_{ci}}$ '+ 'computed from'+field+ 'field',fontsize=10)
-
-        plt.savefig(pp, format="pdf")
-        plt.close()
-
-    def plotgamma(
-        self,
-        pp,
-        field="Ni",
-        yscale="symlog",
-        clip=0,
-        xaxis="t",
-        xscale="linear",
-        xrange=1,
-        comp="gamma",
-        overplot=False,
-        trans=True,
-    ):
-        self.plotomega(
-            pp,
-            field=field,
-            yscale=yscale,
-            clip=clip,
-            xaxis=xaxis,
-            xscale=xscale,
-            xrange=xrange,
-            comp=comp,
-            overplot=overplot,
-            trans=trans,
-        )
-
-    def plotfreq2(
-        self,
-        pp,
-        field="Ni",
-        yscale="symlog",
-        clip=0,
-        xaxis="t",
-        xscale="linear",
-        xrange=1,
-        comp="freq",
-        overplot=False,
-        trans=True,
-    ):
-        self.plotomega(
-            pp,
-            field=field,
-            yscale=yscale,
-            clip=clip,
-            xaxis=xaxis,
-            xscale=xscale,
-            xrange=xrange,
-            comp=comp,
-            overplot=overplot,
-            trans=trans,
-        )
-
-    def plotvsK(
-        self,
-        pp,
-        rootfig=None,
-        field="Ni",
-        yscale="log",
-        clip=0,
-        xaxis="t",
-        xscale="linear",
-        xrange=1,
-        comp="amp",
-        pltlegend="both",
-        overplot=False,
-        gridON=True,
-        trans=False,
-        infobox=True,
-        m=1,
-        t=[0],
-        file=None,
-        save=True,
-    ):
-        colors = [
-            "b.",
-            "r.",
-            "k.",
-            "c.",
-            "g.",
-            "y.",
-            "m.",
-            "b.",
-            "r.",
-            "k.",
-            "c.",
-            "g.",
-            "y.",
-            "m.",
-        ]
-        colordash = [
-            "b",
-            "r",
-            "k",
-            "c",
-            "g",
-            "y",
-            "m",
-            "b",
-            "r",
-            "k",
-            "c",
-            "g",
-            "y",
-            "m",
-        ]
-
-        if rootfig is None:
-            ownpage = True
-        else:
-            ownpage = False
-
-        if ownpage:
-            fig1 = plt.figure()
-            fig1.subplots_adjust(bottom=0.12)
-            fig1.subplots_adjust(top=0.80)
-            fig1.subplots_adjust(right=0.83)
-            fig1.subplots_adjust(left=0.17)
-            canvas = fig1.add_subplot(1, 1, 1)
-            clonex = canvas.twinx()
-            # if trans:
-            #     cloney = canvas.twiny()
-        else:
-            canvas = rootfig.add_subplot(1, 1, 1)
-
-        dzhandles = []
-        parhandles = []
-        parlabels = []
-        dzlabels = []
-
-        # pick the modes
-        m_shift = m
-        for q in np.array(list(range(1))) + m_shift:
-            s = subset(self.db, "field", [field])  # pick  field
-            maxZ = min(s.maxN)
-            modelist = []
-            [modelist.append([q, p + 1]) for p in range(maxZ - 1)]
-        # print q,'in plotgamma'
-        s = subset(s.db, "mn", modelist)
-
-        # set x-range
-        xrange = old_div(s.nx, 2) - 2
-        xrange = [old_div(s.nx, 2), old_div(s.nx, 2) + xrange]
-
-        # pull up the data
-        y = np.array(ListDictKey(s.db, comp))
-        print("y.shape", y.shape)
-
-        # in case multiple timesteps are indicated
-        all_y = []
-        all_yerr = []
-        if comp == "amp":
-            for elem in t:
-                all_y.append(np.squeeze(y[:, elem, :]))
-                all_yerr.append(np.squeeze(0 * y[:, elem, :]))
-            ynorm = np.max(all_y)
-            # all_y = np.array(np.squeeze(all_y))
-            # all_yerr = np.array(np.squeeze(all_yerr))
-
-        else:
-            all_y.append(np.squeeze(y[:, 0, :]))
-            all_yerr.append(np.squeeze(y[:, 1, :]))
-            ynorm = s.meta["w_Ln"][0]
-
-        k = s.k  ##nmodes x 2 x nx ndarray k_zeta
-
-        kfactor = np.mean(
-            old_div(s.k_r[:, 1, old_div(s.nx, 2)], s.k[:, 1, old_div(s.nx, 2)])
-        )  # good enough for now
-
-        for elem in range(np.size(t)):
-            # print 'printing line' , elem
-            errorline = parhandles.append(
-                canvas.errorbar(
-                    k[:, 1, old_div(s.nx, 2)],
-                    all_y[elem][:, old_div(s.nx, 2)],
-                    yerr=all_yerr[elem][:, old_div(s.nx, 2)],
-                    fmt=colors[q],
-                )
-            )
-
-        parlabels.append("m " + str(q))
-
-        # loop over dz sets and connect with dotted line  . . .
-        jj = 0  # will reference dz color
-
-        ymin_data = np.max(np.array(ListDictKey(s.db, comp)))
-        ymax_data = 0  # for bookeeping
-
-        for p in list(set(s.path).union()):
-            sub_s = subset(s.db, "path", [p])
-            j = sub_s.dz[0]
-            # print sub_s.amp.shape
-            s_i = np.argsort(sub_s.mn[:, 1])  # sort by 'local' m, global m is ok also
-            # print s_i, sub_s.mn, sub_s.nx, jj
-            y = np.array(ListDictKey(sub_s.db, comp))
-            y_alt = 2.0 * np.array(ListDictKey(sub_s.db, comp))
-            all_y = []
-            all_yerr = []
-            if comp == "amp":
-                for elem in t:
-                    all_y.append(np.squeeze(y[:, elem, :]))
-                    all_yerr.append(np.squeeze(0 * y[:, elem, :]))
-            else:
-                all_y.append(np.squeeze(y[:, 0, :]))
-                all_yerr.append(np.squeeze(y[:, 1, :]))
-
-            k = sub_s.k  ##
-
-            for elem in range(np.size(t)):
-                if q == m_shift:  # fix the parallel mode
-                    dzhandles.append(
-                        canvas.plot(
-                            k[s_i, 1, old_div(sub_s.nx, 2)],
-                            all_y[elem][s_i, old_div(sub_s.nx, 2)],
-                            color=colordash[jj],
-                            alpha=0.5,
-                        )
-                    )
-
-                    ymin_data = np.min(
-                        [np.min(y[s_i, old_div(sub_s.nx, 2)]), ymin_data]
-                    )
-                    ymax_data = np.max(
-                        [np.max(y[s_i, old_div(sub_s.nx, 2)]), ymax_data]
-                    )
-
-                    dzlabels.append(j)
-
-                    if yscale == "log":
-                        factor = 10
-                    else:
-                        factor = 2
-                    # print 'annotating'
-                    canvas.annotate(
-                        str(j),
-                        (
-                            k[s_i[0], 1, old_div(sub_s.nx, 2)],
-                            y[elem][s_i[0], old_div(sub_s.nx, 2)],
-                        ),
-                        fontsize=8,
-                    )
-                    # p = canvas.axvspan(k[s_i[0],1,sub_s.nx/2], k[s_i[-1],1,sub_s.nx/2],
-                    #               facecolor=colordash[jj], alpha=0.01)
-                    print("done annotating")
-                else:
-                    canvas.plot(
-                        k[s_i, 1, old_div(sub_s.nx, 2)],
-                        y[elem][s_i, old_div(sub_s.nx, 2)],
-                        color=colordash[jj],
-                        alpha=0.3,
-                    )
-
-                jj = jj + 1
-
-        dzhandles = np.array(dzhandles).flatten()
-        dzlabels = np.array(dzlabels).flatten()
-
-        dzlabels = list(set(dzlabels).union())
-
-        dz_i = np.argsort(dzlabels)
-
-        dzhandles = dzhandles[dz_i]
-        dzlabels_cp = np.array(dzlabels)[dz_i]
-
-        # print type(dzlabels), np.size(dzlabels)
-        for i in range(np.size(dzlabels)):
-            dzlabels[i] = "DZ: " + str(dzlabels_cp[i])  # +r"$\pi$"
-
-        parlabels = np.array(parlabels).flatten()
-
-        if overplot == True:
-            try:
-                self.plottheory(pp, canvas=canvas, comp=comp, field=field)
-                # self.plottheory(pp,comp=comp)
-            except:
-                print("no theory plot")
-        if infobox:
-            textstr = "$\L_{\parallel}=%.2f$\n$\L_{\partial_r n}=%.2f$\n$B=%.2f$" % (
-                s.meta["lpar"][old_div(s.nx, 2)],
-                s.meta["L"][old_div(s.nx, 2), old_div(s.ny, 2)],
-                s.meta["Bpxy"]["v"][old_div(s.nx, 2), old_div(s.ny, 2)],
-            )
-            props = dict(boxstyle="square", facecolor="white", alpha=0.3)
-            textbox = canvas.text(
-                0.82,
-                0.95,
-                textstr,
-                transform=canvas.transAxes,
-                fontsize=10,
-                verticalalignment="top",
-                bbox=props,
-            )
-            # leg = canvas.legend(handles,labels,ncol=2,loc='best',prop={'size':4},fancybox=True)
-
-        # cloney.set_xlim(xmin,xmax)
-        try:
-            canvas.set_yscale(yscale)
-            canvas.set_xscale(xscale)
-
-            if yscale == "symlog":
-                canvas.set_yscale(yscale, linthreshy=1e-13)
-            if xscale == "symlog":
-                canvas.set_xscale(xscale, linthreshy=1e-13)
-
-            if gridON:
-                canvas.grid()
-        except:
-            try:
-                canvas.set_yscale("symlog")
-            except:
-                print("scaling failed completely")
-
-        ##################################################################
-
-        if ownpage and rootfig is None:
-            clonex.set_yscale(yscale)  # must be called before limits are set
-
-            try:
-                if yscale == "linear":
-                    formatter = ticker.ScalarFormatter()
-                    formatter.set_powerlimits((-2, 2))  # force scientific notation
-                    canvas.yaxis.set_major_formatter(formatter)
-                    clonex.yaxis.set_major_formatter(formatter)
-                # canvas.useOffset=False
-            except:
-                print("fail 1")
-            [xmin, xmax, ymin, ymax] = canvas.axis()
-
-            if yscale == "symlog":
-                clonex.set_yscale(yscale, linthreshy=1e-9)
-            if xscale == "symlog":
-                clonex.set_xscale(xscale, linthreshy=1e-9)
-            # if np.any(s.trans) and trans:
-            [xmin1, xmax1, ymin1, ymax1] = canvas.axis()
-            if trans:
-                try:
-                    cloney = canvas.twiny()
-                    # cloney.set_yscale(yscale)
-                    cloney.set_xscale(xscale)
-                    [xmin1, xmax1, ymin2, ymax2] = canvas.axis()
-
-                    if xscale == "symlog":
-                        cloney.set_xscale(xscale, linthreshy=1e-9)
-                    if yscale == "symlog":
-                        cloney.set_yscale(yscale, linthreshy=1e-9)
-                    if yscale == "linear":
-                        cloney.yaxis.set_major_formatter(formatter)
-                except:
-                    print("fail trans")
-
-            Ln_drive_scale = s.meta["w_Ln"][0] ** -1
-            # Ln_drive_scale = 2.1e3
-            # clonex.set_ylim(Ln_drive_scale*ymin, Ln_drive_scale*ymax)
-            clonex.set_ylim(ynorm**-1 * ymin, ynorm**-1 * ymax)
-
-            try:
-                if trans:
-                    # k_factor = #scales from k_zeta to k_perp
-                    cloney.set_xlim(kfactor * xmin, kfactor * xmax)
-
-                    cloney.set_ylim(
-                        ymin, ymax
-                    )  # because cloney shares the yaxis with canvas it may overide them, this fixes that
-                    cloney.set_xlabel(r"$k_{\perp} \rho_{ci}$", fontsize=18)
-            except:
-                print("moar fail")
-            # clonex.set_xscale(xscale)
-
-            # ion_acoust_str = r"$\frac{c_s}{L_{\partial_r n}}}$"
-
-            if comp == "gamma":
-                canvas.set_ylabel(
-                    r"$\frac{\gamma}{\omega_{ci}}$", fontsize=18, rotation="horizontal"
-                )
-                clonex.set_ylabel(
-                    r"$\frac{\gamma}{\frac{c_s}{L_n}}$",
-                    color="k",
-                    fontsize=18,
-                    rotation="horizontal",
-                )
-            if comp == "freq":
-                canvas.set_ylabel(
-                    r"$\frac{\omega}{\omega_{ci}}$", fontsize=18, rotation="horizontal"
-                )
-                clonex.set_ylabel(
-                    r"$\frac{\omega}{\frac{c_s}{L_n}}$",
-                    color="k",
-                    fontsize=18,
-                    rotation="horizontal",
-                )
-
-            if comp == "amp":
-                canvas.set_ylabel(r"$A_k$", fontsize=18, rotation="horizontal")
-                clonex.set_ylabel(
-                    r"$\frac{A_k}{A_{max}}$",
-                    color="k",
-                    fontsize=18,
-                    rotation="horizontal",
-                )
-
-            canvas.set_xlabel(r"$k_{\zeta} \rho_{ci}$", fontsize=18)
-
-            title = comp + " computed from " + field
-            # canvas.set_title(title,fontsize=14)
-            fig1.suptitle(title, fontsize=14)
-
-        if not ownpage:
-            print("probably for a movie")
-            fig1 = rootfig
-            # canvasjunk = fig1.add_subplot(1,1,1)
-            # canvasjunk = canvas
-
-        if save:
-            if file is None:
-                try:
-                    fig1.savefig(pp, format="pdf")
-                except:
-                    print("pyplt doesnt like you")
-            else:
-                try:
-                    fig1.savefig(file, dpi=200)
-                except:
-                    print("no movie for you ;(")
-
-        if ownpage:
-            # fig1.close()
-            plt.close(fig1)
-
-    def plotmodes(
-        self,
-        pp,
-        field="Ni",
-        comp="amp",
-        math="1",
-        ylim=1,
-        yscale="symlog",
-        clip=False,
-        xaxis="t",
-        xscale="linear",
-        xrange=1,
-        debug=False,
-        yaxis=r"$\frac{Ni}{Ni_0}$",
-        linestyle="-",
-        summary=True,
-    ):
-        Nplots = self.nrun
-
-        colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
-        styles = ["^", "s"]
-
-        fig1 = plt.figure()
-
-        fig2 = plt.figure()
-
-        Modes = subset(self.db, "field", [field])  # pick  field
-
-        adj = fig2.subplots_adjust(hspace=0.4, wspace=0.4)
-        fig2.suptitle("Dominant mode " + comp + " for  " + field)
-        props = dict(alpha=0.8, edgecolors="none")
-
-        allcurves = fig1.add_subplot(1, 1, 1)
-        fig1.suptitle("Dominant mode behavior for  " + field)
-
-        modenames = []
-        k = 0
-
-        for j in list(set(Modes.path).union()):  #
-            s = subset(Modes.db, "path", [j])  # pick run
-            dz = s.dz[0]
-            xr = list(
-                range(
-                    old_div(s.nx, 2) - old_div(xrange, 2),
-                    old_div(s.nx, 2) + old_div(xrange, 2) + 1,
-                )
-            )
-            data = np.array(
-                ListDictKey(s.db, comp)
-            )  # pick component should be ok for a fixed dz key
-
-            data = data  # + 1e-32 #hacky way to deal with buggy scaling
-            ax = fig2.add_subplot(round(old_div(Nplots, 3.0) + 1.0), 3, k + 1)
-
-            ax.grid(True, linestyle="-", color=".75")
-            handles = []
-            # modenames.append(str(j))
-
-            # find the "biggest" mode for this dz
-            d = data[:, s.nt[0] - 1, :]  # nmode X nx array
-            # d = s.gamma[:,2,:]
-            where = d == np.nanmax(d)
-            z = where.nonzero()  # mode index and n index
-            imax = z[0][0]
-            # xi_max = z[1][0]
-            xi_max = old_div(s.nx, 2)
-
-            if debug and yscale == "log":
-                gamma = np.array(ListDictKey(s.db, "gamma"))  # nmodes x 2 x nx
-
-            for i in range(s.nmodes):
-                if math == "gamma":
-                    out = old_div(np.gradient(data[i, :, xr])[1], data[i, :, xr])
-                else:
-                    out = data[i, 2:, xi_max]  # skip the first 2 points
-
-                if xaxis == "t":
-                    # print 'out.size', out.size, out.shape
-                    x = np.array(list(range(out.size)))
-                    # plt.plot(x,out.flatten(),c=colors[k])
-                    label = str(s.mn[i])
-                    # handles.append(ax.plot(x,out.flatten(),
-                    #                 c=cm.jet(1.*k),label = label))
-                    ax.plot(
-                        x, out.flatten(), c=cm.jet(0.2 * i), label=label, linestyle="-"
-                    )
-
-                else:
-                    x = np.array(ListDictKey(s.db, xaxis))[i, :, xr]
-                    # x #an N? by nx array
-                    print(x[:, 1], out[:, 0])
-                    plt.scatter(x[:, 1], out[:, 0])  # ,c=colors[k])
-                    ax.scatter(
-                        x[:, 1], out[:, 0]
-                    )  # ,c=colors[k])#,alpha = (1 +i)/s.nmodes)
-
-                    # detect error (bar data
-                    print("error bars:", x, out)
-
-            # ax.legend(handles,labels,loc='best',prop={'size':6})
-
-            formatter = ticker.ScalarFormatter()
-            formatter.set_powerlimits((0, 0))
-            ax.xaxis.set_major_formatter(formatter)
-            # ax.axis('tight')
-            if yscale == "linear":
-                ax.yaxis.set_major_formatter(formatter)
-            if yscale == "symlog":
-                ax.set_yscale("symlog", linthreshy=1e-13)
-            else:
-                try:
-                    ax.set_yscale(yscale)
-                except:
-                    print("may get weird axis")
-                    ax.set_yscale("symlog")
-            # if comp=='phase' or yscale=='linear':
-            #         ax.set_xscale('symlog',linthreshx=1.0)
-
-            ax.set_xscale(xscale)
-
-            ax.axis("tight")
-            artist.setp(ax.axes.get_xticklabels(), fontsize=6)
-            artist.setp(ax.axes.get_yticklabels(), fontsize=8)
-            # artist.setp(ax.axes.get_yscale(), fontsize=8)
-            ax.set_title(str(dz), fontsize=10)
-            ax.set_xlabel(xaxis)
-            handles, labels = ax.get_legend_handles_labels()
-            leg = ax.legend(
-                handles, labels, ncol=2, loc="best", prop={"size": 4}, fancybox=True
-            )
-            leg.get_frame().set_alpha(0.3)
-            # x = s.Rxy[imax,:,s.ny/2]
-
-            t0 = 2
-            if clip == True:
-                t0 = round(old_div(s.nt[0], 3))
-            y = np.squeeze(data[imax, t0:, xi_max])
-            x = np.array(list(range(y.size)))
-
-            print(imax, xi_max)
-
-            label = (
-                str([round(elem, 3) for elem in s.MN[imax]])
-                + str(s.mn[imax])
-                + " at x= "
-                + str(xi_max)
-                + " ,"
-                + str(
-                    round(
-                        old_div(s.gamma[imax, 2, xi_max], s.gamma[imax, 0, xi_max]), 3
-                    )
-                )
-                + "%  "
-                + str(round(s.gamma[imax, 0, xi_max], 4))
-            )
-
-            short_label = str(dz)
-            print(short_label, x.shape, y.shape)
-            allcurves.plot(x, y, ".", c=cm.jet(1.0 * k / len(x)), label=label)
-            # print len(x), k*len(x)/(Nplots+2),s.nrun
-            allcurves.annotate(
-                short_label,
-                (x[k * len(x) / (Nplots + 1)], y[k * len(x) / (Nplots + 1)]),
-                fontsize=8,
-            )
-
-            # modenames.append(str([round(elem,3) for elem in s.MN[imax]])
-            #        +str(s.mn[imax])+' at x= '+str(xi_max)+' ,'+str(s.gamma[imax,2,xi_max]))
-
-            if debug and yscale == "log":
-                gam = gamma[imax, 0, xi_max]
-                f0 = gamma[imax, 1, xi_max]
-                allcurves.plot(x, f0 * np.exp(gam * s.dt[imax] * x), "k:")
-
-            k += 1
-
-        # if ylim:
-        #    allcurves.set_ylim(data[,xi_max].min(),5*data[:,xi_max].max())
-
-        fig2.savefig(pp, format="pdf")
-
-        handles, labels = allcurves.get_legend_handles_labels()
-        allcurves.legend(handles, labels, loc="best", prop={"size": 6})
-        # allcurves.legend(modenames,loc='best',prop={'size':6})
-        allcurves.set_title(
-            field + " " + comp + ", all runs, " + yscale + " yscale", fontsize=10
-        )
-        allcurves.set_ylabel(yaxis)
-        allcurves.set_xlabel(xaxis)
-
-        if yscale == "linear":
-            allcurves.yaxis.set_major_formatter(formatter)
-        else:
-            try:
-                allcurves.set_yscale(yscale)
-            except:
-                print("may get weird axis scaling")
-            if yscale == "log":
-                allcurves.axis("tight")
-            # allcurves.set_ylim(data.min(),data.max())
-        # allcurves.set_yscale(yscale,nonposy='mask')
-
-        # plt.xscale(xscale)
-
-        # plt.legend(modenames,loc='best')
-        if summary:
-            fig1.savefig(pp, format="pdf")
-            plt.close(fig1)
-
-        plt.close(fig2)
-
-    # except:
-    #   print "Sorry you fail"
-
-    def plotradeigen(
-        self, pp, field="Ni", comp="amp", yscale="linear", xscale="linear"
-    ):
-        Nplots = self.nrun
-        colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
-        fig1 = plt.figure()
-
-        fig2 = plt.figure()
-        adj = fig2.subplots_adjust(hspace=0.4, wspace=0.4)
-
-        # canvas = FigureCanvas(fig)
-
-        Modes = subset(self.db, "field", [field])
-
-        k = 0
-        fig2.suptitle("Dominant mode behavior for  " + field)
-        props = dict(alpha=0.8, edgecolors="none")
-
-        allcurves = fig1.add_subplot(1, 1, 1)
-        fig1.suptitle("Dominant mode behavior for  " + field)
-
-        modeleg = []
-
-        for p in list(set(Modes.path).union()):
-            print(p)
-            s = subset(Modes.db, "path", [p])  # pick run
-            # data = np.array(ListDictKey(s.db,comp)) #pick component
-            j = s.dz[0]
-            ax = fig2.add_subplot(round(old_div(Nplots, 3.0) + 1.0), 3, k + 1)
-            ax.grid(True, linestyle="-", color=".75")
-            data = np.array(ListDictKey(s.db, comp))  # pick component
-            handles = []
-
-            # find the "biggest" mode for this dz
-            d = data[:, s.nt[0] - 1, :]  # nmode X nx array
-            where = d == d.max()
-            z = where.nonzero()  # mode index and n index
-            imax = z[0][0]
-            modeleg.append(
-                str([round(elem, 3) for elem in s.MN[imax]]) + str(s.mn[imax])
-            )
-
-            # str(s.k[:,1,:][z])
-
-            for i in range(s.nmodes):
-                # out = mode[mode.ny/2,:]
-                # print i,s.Rxynorm.shape,s.ny
-                x = np.squeeze(s.Rxynorm[i, :, old_div(s.ny, 2)])
-                y = data[i, s.nt[0] - 1, :]
-
-                handles.append(ax.plot(x, y, c=cm.jet(1.0 * k / len(x))))
-
-            formatter = ticker.ScalarFormatter()
-            formatter.set_powerlimits((0, 0))
-            ax.xaxis.set_major_formatter(formatter)
-
-            if yscale == "linear":
-                ax.yaxis.set_major_formatter(formatter)
-            else:
-                ax.set_yscale(yscale)
-
-            artist.setp(ax.axes.get_xticklabels(), fontsize=6)
-            artist.setp(ax.axes.get_yticklabels(), fontsize=8)
-            # artist.setp(ax.axes.get_yscale(), fontsize=8)
-            ax.set_title(str(j), fontsize=10)
-
-            x = np.squeeze(s.Rxynorm[imax, :, old_div(s.ny, 2)])
-            y = data[imax, s.nt[0] - 1, :]
-            # allcurves.plot(x,y,c= colors[k])
-            allcurves.plot(x, y, c=cm.jet(0.1 * k / len(x)))
-            print(k)
-            k = k + 1
-
-        fig2.savefig(pp, format="pdf")
-        if yscale == "linear":
-            allcurves.yaxis.set_major_formatter(formatter)
-        else:
-            allcurves.set_yscale(yscale)
-        try:
-            allcurves.set_xscale(xscale)
-        except:
-            allcurves.set_xscale("symlog")
-
-        # allcurves.xaxis.set_major_formatter(ticker.NullFormatter())
-        allcurves.legend(modeleg, loc="best", prop={"size": 6})
-        allcurves.set_xlabel(r"$\frac{x}{\rho_{ci}}$")
-        allcurves.set_ylabel(r"$\frac{Ni}{Ni_0}$")
-        fig1.savefig(pp, format="pdf")
-        plt.close(fig1)
-        plt.close(fig2)
-
-    def plotmodes2(
-        self,
-        pp,
-        field="Ni",
-        comp="amp",
-        math="1",
-        ylim=1,
-        yscale="symlog",
-        clip=0,
-        xaxis="t",
-        xscale="linear",
-        xrange=1,
-        debug=False,
-    ):
-        Nplots = self.nrun
-        Modes = subset(self.db, "field", [field])  # pick  field
-        colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
-
-        fig = Figure()
-        plt.figure()
-
-        canvas = FigureCanvas(fig)
-        k = 0
-        nrow = round(old_div(Nplots, 3.0) + 1.0)
-        ncol = 3
-        # nrow = round(Nplots/3.0 + 1.0)
-        # ncol = round(Nplots/3.0 + 1.0)
-        f, axarr = plt.subplots(int(nrow), int(ncol))
-
-        for p in list(set(Modes.path).union()):  #
-            s = subset(Modes.db, "path", [p])  # pick run
-            j = s.dz[0]
-            xr = list(
-                range(
-                    old_div(s.nx, 2) - old_div(xrange, 2),
-                    old_div(s.nx, 2) + old_div(xrange, 2) + 1,
-                )
-            )
-            data = np.array(ListDictKey(s.db, comp))  # pick component
-            # ax =fig.add_subplot(round(Nplots/3.0 + 1.0),3,k+1)
-
-            for i in range(s.nmodes):
-                out = data[i, :, xr]
-
-            print(j, i)
-            if xaxis == "t":
-                x = list(range(out.size))
-                # plt.scatter(x,out.flatten(),c=colors[k])
-                plt.scatter(x, out.flatten(), c=cm.jet(1.0 * k / len(x)))
-                # axarr[j%(ncol),j/ncol].scatter(x,out.flatten(),c=colors[k])#,alpha = (1 +i)/s.nmodes)
-                axarr[old_div(j, ncol), j % (ncol)].scatter(
-                    x, out.flatten(), c=cm.jet(1.0 * k / len(x))
-                )  #
-
-            else:
-                x = np.array(ListDictKey(s.db, xaxis))[i, :, xr]
-                # x #an N? by nx array
-                print(x[:, 1], out[:, 0])
-                plt.scatter(x[:, 1], out[:, 0])  # ,c=colors[k])
-                axarr[j % (col), old_div(j, col)].scatter(
-                    x[:, 1], out[:, 0]
-                )  # ,c=colors[k])#,alpha = (1 +i)/s.nmodes)
-
-                # detect error (bar data
-                print("error bars:", x, out)
-
-            axarr[old_div(j, ncol), j % (ncol)].set_yscale(yscale)
-            axarr[old_div(j, ncol), j % (ncol)].set_xscale(xscale)
-            axarr[old_div(j, ncol), j % (ncol)].set_title(str(j), fontsize=10)
-            axarr[old_div(j, ncol), j % (ncol)].set_xlabel(xaxis)
-
-            plt.setp([a.get_xticklabels() for a in axarr[0, :]], visible=False)
-            plt.setp([a.get_yticklabels() for a in axarr[:, ncol - 1]], visible=False)
-
-            if ylim:
-                axarr[j % (ncol), old_div(j, ncol)].set_ylim(data.min(), 5 * data.max())
-            k += 1
-
-        plt.title(field + " " + comp + ", all runs, " + yscale + " yscale", fontsize=10)
-        plt.xlabel(xaxis)
-        if ylim:
-            plt.ylim(data.min(), 10 * data.max())
-
-        plt.yscale(yscale, nonposy="mask")
-        plt.xscale(xscale)
-
-        fig.savefig(pp, format="pdf")
-        plt.savefig(pp, format="pdf")
-
-        plt.close()
-
-        return 0
-
-    def plotMacroDep(
-        self,
-        pp,
-        field="Ni",
-        yscale="symlog",
-        clip=0,
-        xaxis="t",
-        xscale="linear",
-        xrange=1,
-    ):
-        colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
-        plt.figure()
-
-    def savemovie(
-        self, field="Ni", yscale="log", xscale="log", moviename="spectrum.avi"
-    ):
-        print("Making movie animation.mpg - this make take a while")
-        files = []
-
-        for t in range(self.nt[0] - 3):
-            print(t)
-            filename = str("%03d" % (t + 1) + ".png")
-            self.plotvsK(
-                "dont need pp",
-                yscale="log",
-                t=[1, t + 2],
-                xscale="log",
-                overplot=False,
-                comp="amp",
-                trans=True,
-                file=filename,
-            )
-            files.append(filename)
-
-        command = (
-            "mencoder",
-            "mf://*.png",
-            "-mf",
-            "type=png:w=800:h=600:fps=10",
-            "-ovc",
-            "lavc",
-            "-lavcopts",
-            "vcodec=mpeg4",
-            "-oac",
-            "copy",
-            "-o",
-            moviename,
-        )
-
-        import subprocess, os
-
-        subprocess.check_call(command)
-        os.system("rm *png")
-
-    def printmeta(self, pp, filename="output2.pdf", debug=False):
-        import os
-        from pyPdf import PdfFileWriter, PdfFileReader
-
-        PAGE_HEIGHT = defaultPageSize[1]
-        styles = getSampleStyleSheet()
-        Title = "BOUT++ Results"
-        Author = "Dmitry Meyerson"
-        URL = ""
-        email = "dmitry.meyerson@gmail.com"
-        Abstract = """This document highlights some results from BOUT++ simulation"""
-        Elements = []
-        HeaderStyle = styles["Heading1"]
-        ParaStyle = styles["Normal"]
-        PreStyle = styles["Code"]
-
-        def header(
-            txt, style=HeaderStyle, klass=Paragraph, sep=0.3
-        ):  # return styled text with a space
-            s = Spacer(0.2 * inch, sep * inch)
-            para = klass(txt, style)
-            sect = [s, para]
-            result = KeepTogether(sect)
-            return result
-
-        def p(txt):  # wrapper for header
-            return header(txt, style=ParaStyle, sep=0.1)
-
-        def pre(txt):  # return styled text with a space
-            s = Spacer(0.1 * inch, 0.1 * inch)
-            p = Preformatted(txt, PreStyle)
-            precomps = [s, p]
-            result = KeepTogether(precomps)
-            return result
-
-        def graphout(name, datain, xaxis=None):
-            if xaxis is None:
-                xaxis = list(range(datain.size))
-            if xlabel is None:
-                xlabel = ""
-            if ylabel is None:
-                ylabel = ""
-
-            drawing = Drawing(400, 200)
-            # data = [
-            #    ((1,1), (2,2), (2.5,1), (3,3), (4,5)),
-            #    ((1,2), (2,3), (2.5,2), (3.5,5), (4,6))
-            #    ]
-            dataview = [tuple([(xaxis[i], datain[i]) for i in range(datain.size)])]
-            lp = LinePlot()
-            lp.x = 50
-            lp.y = 50
-            lp.height = 125
-            lp.width = 300
-            lp.data = dataview
-            lp.xValueAxis.xLabelFormat = "{mmm} {yy}"
-            lp.lineLabels.fontSize = 6
-            lp.lineLabels.boxStrokeWidth = 0.5
-            lp.lineLabels.visible = 1
-            lp.lineLabels.boxAnchor = "c"
-            # lp.joinedLines = 1
-            # lp.lines[0].symbol = makeMarker('FilledCircle')
-            # lp.lines[1].symbol = makeMarker('Circle')
-            # lp.lineLabelFormat = '%2.0f'
-            # lp.strokeColor = colors.black
-            # lp.xValueAxis.valueMin = min(xaxis)
-            # lp.xValueAxis.valueMax = max(xaxis)
-            # lp.xValueAxis.valueSteps = xaxis
-            # lp.xValueAxis.labelTextFormat = '%2.1f'
-            # lp.yValueAxis.valueMin = min(datain)
-            # lp.yValueAxis.valueMax = max(datain)
-            # lp.yValueAxis.valueSteps = [1, 2, 3, 5, 6]
-            drawing.add(lp)
-            return drawing
-
-        def go():
-            doc = SimpleDocTemplate("meta.pdf")
-            doc.build(Elements)
-
-        mytitle = header(Title)
-        myname = header(Author, sep=0.1, style=ParaStyle)
-        mysite = header(URL, sep=0.1, style=ParaStyle)
-        mymail = header(email, sep=0.1, style=ParaStyle)
-        abstract_title = header("ABSTRACT")
-        myabstract = p(Abstract)
-        head_info = [mytitle, myname, mysite, mymail, abstract_title, myabstract]
-        Elements.extend(head_info)
-
-        meta_title = header("metadata", sep=0)
-        metasection = []
-        metasection.append(meta_title)
-
-        for i, elem in enumerate(self.meta):
-            # if type(self.meta[elem]) != type(np.array([])):
-
-            print(elem, type(self.meta[elem]))
-
-            if type(self.meta[elem]) == type({}):
-                print("{}")
-                data = np.array(self.meta[elem]["v"])
-                unit_label = str(self.meta[elem]["u"])
-            else:
-                data = np.array(self.meta[elem])
-                unit_label = ""
-
-            xaxis = np.squeeze(self.meta["Rxy"]["v"][:, old_div(self.ny, 2)])
-
-            if data.shape == (self.nx, self.ny):
-                datastr = np.squeeze(data[:, old_div(self.ny, 2)])
-                # metasection.append(graphout('stuff',datastr,xaxis=xaxis))
-                # metasection.append(RL_Plot(datastr,xaxis))
-
-                metasection.append(RL_Plot(datastr, xaxis, linelabel=str(elem)))
-            # metasection.append(RL_Plot(datastr,xaxis,xlabel='xlabel'))
-            elif data.shape == self.nx:
-                datastr = data
-            # metasection.append(graphout('stuff',datastr,xaxis=xaxis))
-            # metasection.append(RL_Plot(datastr,xaxis,linelabel=str(elem)))
-            elif data.shape == (1,):
-                data = data[0]
-                metasection.append(
-                    header(
-                        str(elem) + ": " + str(data) + " " + unit_label,
-                        sep=0.1,
-                        style=ParaStyle,
-                    )
-                )
-            else:
-                print(elem, data, data.shape)
-                metasection.append(
-                    header(
-                        str(elem) + ": " + str(data) + " " + unit_label,
-                        sep=0.1,
-                        style=ParaStyle,
-                    )
-                )
-
-        src = KeepTogether(metasection)
-        Elements.append(src)
-
-        cxxtitle = header("Equations in CXX")
-        cxxsection = []
-        # print self.cxx
-        cxxsection.append(header(self.cxx[0], sep=0.1, style=ParaStyle))
-        cxxsrc = KeepTogether(cxxsection)
-
-        Elements.append(cxxsrc)
-        # for i,elem in enumerate(self.cxx):
-        #    if type(self.meta[elem])== type({}):
-        #       print elem #np.array(self.meta[elem]['v']).shape()
-        #       if np.array(self.meta[elem]['v']).shape == (self.nx,self.ny):
-        #          datastr = str(self.meta[elem]['v'][:,self.ny/2])
-        #          metasection.append(graphout('stuff',
-        #                                      self.meta[elem]['v'][:,self.ny/2]))
-        #       else:
-        #          datastr = str(self.meta[elem]['v'])
-        #       metasection.append(header(str(elem)+': '+datastr
-        #                                    + ' '+ str(self.meta[elem]['u']),
-        #                                    sep=0.1, style=ParaStyle))
-
-        if debug:
-            return Elements
-        go()
-
-        output = PdfFileWriter()
-        metapdf = PdfFileReader(file("meta.pdf", "rb"))
-        mainpdf = PdfFileReader(file("output.pdf", "rb"))
-
-        for i in range(0, metapdf.getNumPages()):
-            output.addPage(metapdf.getPage(i))
-
-        for i in range(0, mainpdf.getNumPages()):
-            output.addPage(mainpdf.getPage(i))
-
-        outputFile = filename
-        outputStream = file(outputFile, "wb")
-        output.write(outputStream)
-        outputStream.close()
-        print("Consolidation complete.")
-
-
-class subset(LinResDraw):
-    def __init__(self, alldb, key, valuelist, model=False):
-        selection = ListDictFilt(alldb, key, valuelist)
-        if len(selection) != 0:
-            LinRes.__init__(self, selection)
-            self.skey = key
-            if model == True:
-                self.model()
-        else:
-            LinRes.__init__(self, alldb)
-            if model == True:
-                self.model()
diff --git a/tools/pylib/post_bout/pb_nonlinear.py b/tools/pylib/post_bout/pb_nonlinear.py
deleted file mode 100644
index 3fb726d4f8..0000000000
--- a/tools/pylib/post_bout/pb_nonlinear.py
+++ /dev/null
@@ -1,99 +0,0 @@
-from __future__ import absolute_import
-from __future__ import division
-from builtins import range
-from past.utils import old_div
-
-# some function to plot nonlinear stuff
-from .pb_corral import LinRes
-from .ListDict import ListDictKey, ListDictFilt
-import numpy as np
-
-import matplotlib.pyplot as plt
-from matplotlib import cm
-import matplotlib.artist as artist
-import matplotlib.ticker as ticker
-import matplotlib.pyplot as plt
-import matplotlib.patches as patches
-from matplotlib.figure import Figure
-from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
-from matplotlib.backends.backend_pdf import PdfPages
-
-from reportlab.platypus import *
-from reportlab.lib.styles import getSampleStyleSheet
-from reportlab.rl_config import defaultPageSize
-from reportlab.lib.units import inch
-from reportlab.graphics.charts.linecharts import HorizontalLineChart
-from reportlab.graphics.shapes import Drawing
-from reportlab.graphics.charts.lineplots import LinePlot
-from reportlab.graphics.widgets.markers import makeMarker
-from reportlab.lib import colors
-
-from replab_x_vs_y import RL_Plot
-from matplotlib.ticker import ScalarFormatter, FormatStrFormatter, MultipleLocator
-
-
-class NLinResDraw(LinRes):
-    def __init__(self, alldb):
-        LinRes.__init__(self, alldb)
-
-    def plotnlrhs(
-        self,
-        pp,
-        field="Ni",
-        yscale="linear",
-        clip=0,
-        xaxis="t",
-        xscale="linear",
-        xrange=1,
-    ):
-        colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
-
-        Modes = subset(self.db, "field", [field])  # pick  field
-        comp = "ave"
-
-        fig1 = plt.figure()
-        adj = fig1.subplots_adjust(hspace=0.4, wspace=0.4)
-        fig1.suptitle("Nonlinear contribution for " + field)
-        props = dict(alpha=0.8, edgecolors="none")
-        Nplots = self.nrun
-
-        k = 0
-        for j in list(set(Modes.path).union()):
-            s = subset(Modes.db, "path", [j])  # pick a run folder - many modes
-            dz = s.dz[0]
-            data = s.ave[0]["nl"]
-            x = np.array(list(range(data.size)))
-
-            ax = fig1.add_subplot(round(old_div(Nplots, 2.0) + 1.0), 2, k + 1)
-            ax.set_ylabel(r"$\frac{ddt_N}{ddt}$", fontsize=12, rotation="horizontal")
-            k += 1
-            ax.grid(True, linestyle="-", color=".75")
-            try:
-                ax.set_yscale(yscale, linthreshy=1e-13)
-            except:
-                ax.set_yscale("linear")
-            i = 1
-            ax.plot(x, data.flatten(), c=cm.jet(0.2 * i), linestyle="-")
-
-            # data = np.array(ListDictKey(s.db,comp)) #pick component should be ok for a fixed dz key
-
-            # we are not interested in looping over all modes
-
-        fig1.savefig(pp, format="pdf")
-        plt.close(fig1)
-
-    # return 0
-
-
-class subset(NLinResDraw):
-    def __init__(self, alldb, key, valuelist, model=False):
-        selection = ListDictFilt(alldb, key, valuelist)
-        if len(selection) != 0:
-            LinRes.__init__(self, selection)
-            self.skey = key
-            if model == True:
-                self.model()
-        else:
-            LinRes.__init__(self, alldb)
-            if model == True:
-                self.model()
diff --git a/tools/pylib/post_bout/pb_present.py b/tools/pylib/post_bout/pb_present.py
deleted file mode 100644
index 64fcaf1ec6..0000000000
--- a/tools/pylib/post_bout/pb_present.py
+++ /dev/null
@@ -1,213 +0,0 @@
-from __future__ import print_function
-from __future__ import absolute_import
-from builtins import str
-from builtins import range
-from .pb_draw import LinResDraw, subset
-from .pb_corral import LinRes
-from .pb_nonlinear import NLinResDraw
-from pb_transport import Transport
-
-import numpy as np
-import matplotlib.pyplot as plt
-
-import matplotlib.pyplot as plt
-from matplotlib.figure import Figure
-from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
-from matplotlib.backends.backend_pdf import PdfPages
-import matplotlib.artist as artist
-import matplotlib.ticker as ticker
-
-# from matplotlib.ticker import FuncFormatter
-# from matplotlib.ticker import ScalarFormatter
-
-from reportlab.platypus import *
-from reportlab.lib.styles import getSampleStyleSheet
-from reportlab.rl_config import defaultPageSize
-from reportlab.lib.units import inch
-from reportlab.graphics.charts.linecharts import HorizontalLineChart
-from reportlab.graphics.shapes import Drawing
-from reportlab.graphics.charts.lineplots import LinePlot
-from reportlab.graphics.widgets.markers import makeMarker
-from reportlab.lib import colors
-
-from replab_x_vs_y import RL_Plot
-
-# for movie making
-from multiprocessing import Queue, Pool
-import multiprocessing
-import subprocess
-
-# uses  LinResDraw to make a pdf
-
-
-class LinResPresent(LinResDraw, NLinResDraw, Transport):
-    def __init__(self, alldb):
-        LinResDraw.__init__(self, alldb)
-        NLinResDraw.__init__(self, alldb)
-        Transport.__init__(self, alldb)
-
-    def show(
-        self,
-        filter=True,
-        quick=False,
-        pdfname="output2.pdf",
-        debug=False,
-        spectrum_movie=False,
-    ):
-        colors = ["b", "g", "r", "c", "m", "y", "k", "b", "g", "r", "c", "m", "y", "k"]
-        pp = PdfPages("output.pdf")
-
-        # start by removing modes above the maxN threshold
-        modelist = []
-        [
-            modelist.append(list(self.modeid[p]))
-            for p in range(self.nmodes)
-            if self.mn[p][1] <= self.maxN[p]
-        ]
-
-        s = subset(self.db, "modeid", modelist)
-
-        try:
-            # fig = Figure(figsize=(6,6))
-            # fig = plt.figure()
-            dz0 = list(set(s.dz).union())[0]
-            ss = subset(s.db, "dz", [dz0])
-
-            # show initial condition and the first step after
-            s.plotvsK(
-                pp,
-                yscale="log",
-                xscale="log",
-                t=[0, 1, -1],
-                overplot=False,
-                comp="amp",
-                trans=True,
-            )
-
-            if spectrum_movie:
-                ss.savemovie()
-
-        except:
-            print("no scatter")
-        # 2D true NM spectrum with color code and boxes around spectral res regions log scale
-
-        plt.figure()
-        i = 0
-        for j in list(
-            set(s.dz).union()
-        ):  # looping over runs, over unique 'dz' key values
-            ss = subset(s.db, "dz", [j])  # subset where dz = j
-            plt.scatter(ss.MN[:, 1], ss.MN[:, 0], c=colors[i])
-            plt.annotate(str(j), (ss.MN[0, 1], ss.MN[0, 0]))
-            i += 1
-
-        plt.title(" Ni spectrum at t=0, all x")
-        plt.ylabel("M -parallel")
-        plt.xlabel("N -  axisymmteric")
-        plt.xscale("log")
-        plt.grid(True, linestyle="-", color=".75")
-
-        try:
-            plt.savefig(pp, format="pdf")
-        except:
-            print("FAILED TO save 1st part")
-
-        plt.close()
-
-        # for elem in self.meta['evolved']['v']:
-        #    s.plotnl(pp
-
-        if self.meta["nonlinear"]["v"] == "true":
-            self.plotnlrhs(pp)
-
-        if self.meta["transport"] == "true":
-            self.plotnlrms(pp)
-
-        for elem in self.meta["evolved"]:
-            s.plotmodes(
-                pp,
-                yscale="symlog",
-                comp="phase",
-                linestyle=".",
-                field=elem,
-                summary=False,
-            )
-            s.plotmodes(pp, yscale="symlog", field=elem, summary=False)
-            print(elem)
-            try:
-                s.plotmodes(
-                    pp, yscale="symlog", field=elem, comp="gamma_i", summary=False
-                )
-            except:
-                print("gamma_i plot for " + elem + " failed")
-
-        # s.plotmodes(pp,yscale='symlog',summary=False)
-
-        modelist = []
-        # maxZ =
-        # [modelist.append([1,p+1]) for p in range(maxZ-1)]
-        [
-            modelist.append(list(self.modeid[p]))
-            for p in range(self.nmodes)
-            if self.mn[p][1] <= self.maxN[p]
-        ]
-        ss = subset(s.db, "mn", modelist)
-
-        if debug:  # just a few problematic slides
-            fig1 = plt.figure()
-            pp_bug = PdfPages("debug.pdf")
-            # ss.plotmodes(pp_bug,yscale='symlog',comp='phase',summary=False)
-            s.plotfreq2(pp_bug, xscale="log", yscale="symlog", overplot=True)
-            ss.plotgamma(pp_bug, xscale="log", yscale="symlog", overplot=True)
-            ss.plottheory(pp_bug)
-            ss.plottheory(pp_bug, comp="freq")
-            fig1.savefig(pp_bug, format="pdf")
-            pp_bug.close()
-            pp.close()
-            return 0
-
-        dir(ss)
-        ss.plotmodes(pp, yscale="log", debug=True, summary=False)
-        ss.plotmodes(pp, yscale="symlog", comp="phase", summary=False)
-        ss.plotmodes(pp, yscale="symlog", comp="phase", field="rho", summary=False)
-        print(dir(ss))
-
-        # ss.plotmodes(pp,yscale='log',comp='phase',clip=True)
-
-        # ss.plotfreq2(pp,xscale='log',yscale='linear',overplot=False)
-        for elem in self.meta["evolved"]:
-            ss.plotfreq2(
-                pp, xscale="log", yscale="symlog", field=elem, overplot=True, trans=True
-            )
-
-        # ss.plotfreq2(pp,xscale='log',yscale='symlog',field='rho',overplot=True)
-
-        if quick == True:
-            pp.close()
-            s.printmeta(pp)
-
-            # plt.savefig(pp, format='pdf')
-            return 0
-
-        all_fields = list(set(s.field).union())
-
-        s.plotgamma(pp, xscale="log", yscale="linear", overplot=True, trans=True)
-
-        s.plotgamma(pp, yscale="symlog", xscale="log", overplot=True)
-        s.plotgamma(pp, yscale="symlog", xscale="log", field="rho", overplot=True)
-
-        try:
-            s.plotfreq2(pp, xscale="log", yscale="linear", overplot=True)
-            # s.plotfreq2(pp,xscale='log',yscale='symlog',overplot=False)
-            s.plotfreq2(pp, xscale="log", yscale="symlog", field="rho", overplot=True)
-
-            # s.plotfreq2(pp,xscale='log',yscale='linear')
-        except:
-            print("something terrible")
-
-        s.plotradeigen(pp, yscale="linear")
-        # s.plotradeigen(pp,field ='Vi',yscale='linear')
-        s.plotradeigen(pp, field="rho", yscale="log")
-
-        pp.close()
-        s.printmeta(pp, filename=pdfname)  # append a metadata header
diff --git a/tools/pylib/post_bout/read_cxx.py b/tools/pylib/post_bout/read_cxx.py
deleted file mode 100644
index eda88aac5b..0000000000
--- a/tools/pylib/post_bout/read_cxx.py
+++ /dev/null
@@ -1,139 +0,0 @@
-from builtins import range
-from read_grid import read_grid
-from ordereddict import OrderedDict
-import numpy as np
-import string
-import re
-
-
-def findlowpass(cxxstring):
-    ##p1="lowPass\(.*\)"
-    p1 = "lowPass\(.*\,(.*)\)"
-    maxN = np.array(re.findall(p1, cxxstring))
-    # print substrings
-
-    # p2=("[0-9]")
-
-    # maxN = np.array([re.findall(p2,elem) for elem in substrings]).flatten()
-
-    if maxN.size == 0:
-        return 100
-    else:
-        output = int(min(maxN))
-        if output == 0:
-            return 20
-        else:
-            return output
-
-
-def no_comment_cxx(path=".", boutcxx="physics_code.cxx.ref"):
-    # print 'no_comment'
-    boutcxx = path + "/" + boutcxx
-    # boutcxx = open(boutcxx,'r').readlines()
-    f = open(boutcxx, "r")
-    boutcxx = f.read()
-    f.close()
-
-    start = string.find(boutcxx, "/*")
-    end = string.find(boutcxx, "*/") + 2
-
-    s = boutcxx[0:start]
-    for i in range(string.count(boutcxx, "/*")):
-        start = string.find(boutcxx, "/*", end)
-        s = s + boutcxx[end + 1 : start - 1]
-
-        end = string.find(boutcxx, "*/", end) + 2
-
-        s = s + boutcxx[end + 1 :]
-
-    # pattern = "\n \s* \(//)* .* \n" #pattern for a section start [All],[Ni], etc
-    pattern = "\n+.*;"  # everythin
-    pattern = re.compile(pattern)
-    result = re.findall(pattern, s)
-
-    # print result
-
-    nocomment = []
-    for elem in result:
-        # print elem
-        elem = elem.lstrip()
-        stop = elem.find("//")
-        # print start,stop
-
-        if stop > 0:
-            nocomment.append(elem[0:stop])
-        elif stop == -1:
-            nocomment.append(elem)
-
-    # result = pattern.match(val)
-    # start = string.find(z,'\n  //')
-    # end =string.find(boutcxx,'*/')+2
-    # print nocomment
-
-    return nocomment
-
-
-def get_evolved_cxx(cxxfile=None):
-    if cxxfile is None:
-        cxxfile = no_comment_cxx()
-
-    # s = cxxfile
-    # section_0 = string.find(s,'int physics_run(BoutReal t)')
-    # section_1 = string.find(s,'return',section_0)
-    # s =  s[section_0:section_1]
-    temp = []
-
-    for x in cxxfile:
-        i = x.find("bout_solve(")
-        # print i,x
-        if i != -1:
-            comma_i = x[i::].find('"')
-            comma_j = x[i::].rfind('"')
-            # print x[i+comma_i:i+comma_j+1]
-            temp.append(x[i + comma_i + 1 : i + comma_j])
-
-    evolved = []
-    [evolved.append(x) for x in set(temp)]
-    return np.array(evolved)
-
-
-def read_cxx(path=".", boutcxx="physics_code.cxx.ref", evolved=""):
-    # print path, boutcxx
-    boutcxx = path + "/" + boutcxx
-    # boutcxx = open(boutcxx,'r').readlines()
-    f = open(boutcxx, "r")
-    boutcxx = f.read()
-    f.close()
-
-    # start by stripping out all comments
-    # look at the 1st character of all list elements
-    # for now use a gross loop, vectorize later
-
-    start = string.find(boutcxx, "/*")
-    end = string.find(boutcxx, "*/") + 2
-
-    s = boutcxx[0:start]
-    for i in range(string.count(boutcxx, "/*")):
-        start = string.find(boutcxx, "/*", end)
-        s = s + boutcxx[end + 1 : start - 1]
-
-        end = string.find(boutcxx, "*/", end) + 2
-
-        s = s + boutcxx[end + 1 :]
-
-    section_0 = string.find(s, "int physics_run(BoutReal t)")
-    section_1 = string.find(s, "return", section_0)
-    s = s[section_0:section_1]
-
-    tmp = open("./read_cxx.tmp", "w")
-    tmp.write(s)
-    tmp.close()
-    tmp = open("./read_cxx.tmp", "r")
-
-    cxxlist = ""
-
-    for line in tmp:
-        if line[0] != "//" and line.isspace() == False:
-            cxxlist = cxxlist + line.split("//")[0]
-
-    return cxxlist
diff --git a/tools/pylib/post_bout/read_inp.py b/tools/pylib/post_bout/read_inp.py
deleted file mode 100644
index 87de7ddf3a..0000000000
--- a/tools/pylib/post_bout/read_inp.py
+++ /dev/null
@@ -1,433 +0,0 @@
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import division
-from builtins import str
-from past.utils import old_div
-from builtins import object
-from read_grid import read_grid
-from ordereddict import OrderedDict
-import numpy as np
-from boututils.file_import import file_import
-from .read_cxx import *
-
-
-def read_inp(path="", boutinp="BOUT.inp"):
-    boutfile = path + "/" + boutinp
-    boutinp = open(boutfile, "r").readlines()
-
-    # start by stripping out all comments
-    # look at the 1st character of all list elements
-    # for now use a gross loop, vectorize later
-    boutlist = []
-
-    for i, val in enumerate(boutinp):
-        if val[0] != "#" and val.isspace() == False:
-            boutlist.append(val.split("#")[0])
-
-    return boutlist
-
-
-def parse_inp(boutlist):
-    import re
-    from ordereddict import OrderedDict
-
-    if not boutlist:
-        return 0
-
-    # boutdic={} unordered standard dict
-    boutdic = OrderedDict()
-
-    # regex is messy see http://docs.python.org/howto/regex.html#regex-howto
-    pattern = "\[\S*\]"  # pattern for a section start [All],[Ni], etc
-
-    pattern = re.compile(pattern)
-
-    boutdic["[main]"] = {}
-    current = "[main]"
-
-    for i, val in enumerate(boutlist):
-        # print i,val
-        result = pattern.match(val)
-        # while the current value is not a new section name add everything to the current section
-
-        if result is None:
-            # print val
-            key, value = val.split("=")
-            value = value.replace('"', "")
-            # print current, key,value
-
-            boutdic[current][key.strip()] = value.strip()
-        else:
-            boutdic[result.group()] = {}
-            current = result.group()
-
-    return boutdic
-
-
-def read_log(path=".", logname="status.log"):
-    print("in read_log")
-    import re
-    from ordereddict import OrderedDict
-
-    # logfile = path+'/'+logname
-    logfile = logname
-    print(logfile)
-    logcase = open(logfile, "r").readlines()
-
-    # start by stripping out all comments
-    # look at the 1st character of all list elements
-    # for now use a gross loop, vectorize later
-    loglist = []
-
-    for i, val in enumerate(logcase):
-        if val[0] != "#" and val.isspace() == False:
-            loglist.append(val.split("#")[0])
-
-    if not loglist:
-        return 0
-
-    logdict = OrderedDict()
-    logdict["runs"] = []
-    # print len(loglist)
-    print(loglist)
-    # print loglist[len(loglist)-1] == 'last one\n'
-
-    # last = loglist.pop().rstrip()
-
-    # logdict['done'] = last == 'done'
-
-    logdict["current"] = loglist.pop().rstrip()
-    for i, val in enumerate(loglist):
-        print(val)
-        logdict["runs"].append(val.rstrip())
-
-    logdict["runs"].append(logdict["current"])
-
-    # print logdict
-    return logdict
-
-
-def metadata(inpfile="BOUT.inp", path=".", v=False):
-    filepath = path + "/" + inpfile
-    print(filepath)
-    inp = read_inp(path=path, boutinp=inpfile)
-    inp = parse_inp(inp)  # inp file
-    print(path)
-    outinfo = file_import(path + "/BOUT.dmp.0.nc")  # output data
-
-    try:
-        print(path)
-        cxxinfo = no_comment_cxx(path=path, boutcxx="physics_code.cxx.ref")
-        # evolved = get_evolved_cxx(cxxinfo)
-        fieldkeys = get_evolved_cxx(cxxinfo)
-        fieldkeys = ["[" + elem + "]" for elem in fieldkeys]
-    except:
-        print("cant find the cxx file")
-
-    # gridoptions = {'grid':grid,'mesh':mesh}
-    if "[mesh]" in list(inp.keys()):
-        # IC = outinfo
-        IC = read_grid(path + "/BOUT.dmp.0.nc")  # output data again
-    elif "grid" in inp["[main]"]:
-        gridname = inp["[main]"]["grid"]
-        try:
-            IC = read_grid(gridname)  # have to be an ansoulte file path for now
-            print("IC: ", type(IC))
-        # print IC.variables
-        # print gridname
-        except:
-            # print gridname
-            print("Fail to load the grid file")
-    # print IC
-
-    # print gridname
-    # print len(IC)
-    # print IC
-
-    evolved = []
-    collected = []
-    ICscale = []
-
-    # fieldkeys = ['[Ni]','[Te]','[Ti]','[Vi]','[rho]',
-    #              '[Ajpar]','[Apar]','[vEBx]','[vEBy]','[vEBz]',
-    #              '[jpar]','[phi]']
-
-    # construct fieldkeys from cxx info
-    # fieldkeys = ['['+x+']' for x in evolved]
-    # fieldkeys = evolved
-
-    # just look ahead and see what 3D fields have been output
-    available = np.array([str(x) for x in outinfo])
-    a = np.array([(len(outinfo[x].shape) == 4) for x in available])
-    available = available[a]
-
-    defaultIC = float(inp["[All]"].get("scale", 0.0))
-
-    # print inp.keys()
-
-    # figure out which fields are evolved
-    print(fieldkeys)
-
-    for section in list(inp.keys()):  # loop over section keys
-        print("section: ", section)
-        if section in fieldkeys:  # pick the relevant sections
-            print(section)
-            # print inp[section].get('evolve','True')
-            # rint (inp[section].get('evolve','True')).lower().strip()
-            if (
-                inp[section].get("evolve", "True").lower().strip() == "true"
-            ):  # and section[1:-1] in available :
-                print("ok reading")
-                evolved.append(section.strip("[]"))
-                ICscale.append(float(inp[section].get("scale", defaultIC)))
-
-        if inp[section].get("collect", "False").lower().strip() == "true":
-            collected.append(section.strip("[]"))
-
-    try:
-        if inp["[physics]"].get("transport", "False").lower().strip() == "true":
-            vEBstr = ["vEBx", "vEBy", "vEBz", "vEBrms"]
-            [collected.append(item) for item in vEBstr]
-    except:
-        print("no [physics] key")
-
-    meta = OrderedDict()
-
-    class ValUnit(object):
-        def __init__(self, value=0, units=""):
-            self.u = units
-            self.v = value
-
-        def todict(self):
-            return {"u": self.u, "v": self.v}
-
-    # def decode_valunit(d):
-
-    def ToFloat(metaString):
-        try:
-            return float(metaString)
-        except ValueError:
-            return metaString
-
-    # meta['evolved'] = ValUnit(evolved,'')
-    meta["evolved"] = evolved
-    meta["collected"] = collected
-    meta["IC"] = np.array(ICscale)
-    d = {}
-
-    print("evolved: ", evolved)
-
-    # read meta data from .inp file, this is whre most metadata get written
-    for section in list(inp.keys()):
-        if ("evolve" not in inp[section]) and (
-            "first" not in inp[section]
-        ):  # hacky way to exclude some less relevant metadata
-            for elem in list(inp[section].keys()):
-                meta[elem] = ValUnit(ToFloat(inp[section][elem]))
-                d[elem] = np.array(ToFloat(inp[section][elem]))
-
-    # read in some values from the grid(IC) and scale them as needed
-    norms = {
-        "Ni0": ValUnit(1.0e14, "cm^-3"),
-        "bmag": ValUnit(1.0e4, "gauss"),
-        "Ni_x": ValUnit(1.0e14, "cm^-3"),
-        "Te_x": ValUnit(1.0, "eV"),
-        "Ti_x": ValUnit(1.0, "eV"),
-        "Rxy": ValUnit(1, "m"),
-        "Bxy": ValUnit(1.0e4, "gauss"),
-        "Bpxy": ValUnit(1.0e4, "gauss"),
-        "Btxy": ValUnit(1.0e4, "gauss"),
-        "Zxy": ValUnit(1, "m"),
-        "dlthe": ValUnit(1, "m"),
-        "dx": ValUnit(1, "m"),
-        "hthe0": ValUnit(1, "m"),
-    }
-
-    availkeys = np.array([str(x) for x in outinfo])
-    tmp1 = np.array([x for x in availkeys])
-    # b = np.array([x if x not in available for x in a])
-    tmp2 = np.array([x for x in tmp1 if x not in available])
-    static_fields = np.array([x for x in tmp2 if x in list(norms.keys())])
-    # static_fields = tmp2
-
-    # print availkeys
-    # print meta.keys()
-    # print IC.variables.keys()
-    # print tmp1
-    # print tmp2
-
-    for elem in static_fields:
-        print("elem: ", elem)
-        meta[elem] = ValUnit(IC.variables[elem][:] * norms[elem].v, norms[elem].u)
-        d[elem] = np.array(IC.variables[elem][:] * norms[elem].v)
-
-    for elem in IC.variables:
-        if elem not in meta:
-            if elem in list(norms.keys()):
-                meta[elem] = ValUnit(
-                    IC.variables[elem][:] * norms[elem].v, norms[elem].u
-                )
-                d[elem] = np.array(IC.variables[elem][:] * norms[elem].v)
-            else:
-                meta[elem] = IC.variables[elem][:]
-                d[elem] = IC.variables[elem][:]
-
-    # print d.keys()
-
-    # if case some values are missing
-    default = {
-        "bmag": 1,
-        "Ni_x": 1,
-        "NOUT": 100,
-        "TIMESTEP": 1,
-        "MZ": 32,
-        "AA": 1,
-        "Zeff": ValUnit(1, ""),
-        "ZZ": 1,
-        "zlowpass": 0.0,
-        "transport": False,
-    }
-    diff = set(default.keys()).difference(set(d.keys()))
-
-    for elem in diff:
-        # print 'diff: ',elem
-        meta[elem] = default[elem]
-        d[elem] = np.array(default[elem])
-
-    # print meta.keys()
-    # print d.keys()
-
-    # print meta['zlowpass']
-
-    if meta["zlowpass"] != 0:
-        print(meta["MZ"].v, meta["zlowpass"].v)
-        meta["maxZ"] = int(np.floor(meta["MZ"].v * meta["zlowpass"].v))
-    else:
-        meta["maxZ"] = 5
-
-    # meta['nx'] = nx
-    # meta['ny']= ny
-    meta["dt"] = meta["TIMESTEP"]
-
-    # nx,ny  = d['Rxy'].shape
-
-    # print meta['AA'].v
-
-    meta["rho_s"] = ValUnit(
-        1.02e2 * np.sqrt(d["AA"] * d["Te_x"]) / (d["ZZ"] * d["bmag"]), "cm"
-    )  # ion gyrorad at T_e, in cm
-    meta["rho_i"] = ValUnit(
-        1.02e2 * np.sqrt(d["AA"] * d["Ti_x"]) / (d["ZZ"] * d["bmag"]), "cm"
-    )
-    meta["rho_e"] = ValUnit(2.38 * np.sqrt(d["Te_x"]) / (d["bmag"]), "cm")
-
-    meta["fmei"] = ValUnit(1.0 / 1836.2 / d["AA"])
-
-    meta["lambda_ei"] = 24.0 - np.log(old_div(np.sqrt(d["Ni_x"]), d["Te_x"]))
-    meta["lambda_ii"] = 23.0 - np.log(
-        d["ZZ"] ** 3 * np.sqrt(2.0 * d["Ni_x"]) / (d["Ti_x"] ** 1.5)
-    )  #
-
-    meta["wci"] = 1.0 * 9.58e3 * d["ZZ"] * d["bmag"] / d["AA"]  # ion gyrofrteq
-    meta["wpi"] = (
-        1.32e3 * d["ZZ"] * np.sqrt(old_div(d["Ni_x"], d["AA"]))
-    )  # ion plasma freq
-
-    meta["wce"] = 1.78e7 * d["bmag"]  # electron gyrofreq
-    meta["wpe"] = 5.64e4 * np.sqrt(d["Ni_x"])  # electron plasma freq
-
-    meta["v_the"] = 4.19e7 * np.sqrt(d["Te_x"])  # cm/s
-    meta["v_thi"] = 9.79e5 * np.sqrt(old_div(d["Ti_x"], d["AA"]))  # cm/s
-    meta["c_s"] = 9.79e5 * np.sqrt(5.0 / 3.0 * d["ZZ"] * d["Te_x"] / d["AA"])  #
-    meta["v_A"] = 2.18e11 * np.sqrt(old_div(1.0, (d["AA"] * d["Ni_x"])))
-
-    meta["nueix"] = 2.91e-6 * d["Ni_x"] * meta["lambda_ei"] / d["Te_x"] ** 1.5  #
-    meta["nuiix"] = (
-        4.78e-8
-        * d["ZZ"] ** 4.0
-        * d["Ni_x"]
-        * meta["lambda_ii"]
-        / d["Ti_x"] ** 1.5
-        / np.sqrt(d["AA"])
-    )  #
-    meta["nu_hat"] = meta["Zeff"].v * meta["nueix"] / meta["wci"]
-
-    meta["L_d"] = 7.43e2 * np.sqrt(old_div(d["Te_x"], d["Ni_x"]))
-    meta["L_i_inrt"] = (
-        2.28e7 * np.sqrt(old_div(d["AA"], d["Ni_x"])) / d["ZZ"]
-    )  # ion inertial length in cm
-    meta["L_e_inrt"] = 5.31e5 * np.sqrt(d["Ni_x"])  # elec inertial length in cm
-
-    meta["Ve_x"] = 4.19e7 * d["Te_x"]
-
-    meta["R0"] = old_div((d["Rxy"].max() + d["Rxy"].min()), 2.0)
-
-    print(d["Rxy"].mean(1))
-    print(d["ZMAX"])
-    print(d["ZMIN"])
-    meta["L_z"] = (
-        1e2 * 2 * np.pi * d["Rxy"].mean(1) * (d["ZMAX"] - d["ZMIN"])
-    )  # in cm toroidal range
-    meta["dz"] = d["ZMAX"] - d["ZMIN"]
-
-    # meta['lbNorm']=meta['L_z']*(d['Bpxy']/d['Bxy']).mean(1)     #-binormal coord range [cm]
-    meta["lbNorm"] = meta["L_z"] * (old_div(d["Bxy"], d["Bpxy"])).mean(1)
-
-    # meta['zPerp']=np.array(meta['lbNorm']).mean*np.array(range(d['MZ']))/(d['MZ']-1)
-    # let's calculate some profile properties
-    dx = np.gradient(d["Rxy"])[0]
-    meta["L"] = (
-        1.0
-        * 1e2
-        * dx
-        * (meta["Ni0"].v)
-        / np.gradient(meta["Ni0"].v)[0]
-        / meta["rho_s"].v
-    )
-
-    meta["w_Ln"] = old_div(
-        meta["c_s"], (np.min(abs(meta["L"])) * meta["wci"] * meta["rho_s"].v)
-    )  # normed to wci
-
-    AA = meta["AA"].v
-    ZZ = d["ZZ"]
-    Te_x = d["Te_x"]
-    Ti_x = d["Ti_x"]
-    fmei = meta["fmei"].v
-
-    meta["lpar"] = (
-        1e2 * ((old_div(d["Bxy"], d["Bpxy"])) * d["dlthe"]).sum(1) / meta["rho_s"].v
-    )  # -[normed], average over flux surfaces, parallel length
-
-    # yes dlthe is always the vertical displacement
-    # dlthe = (hthe0*2 pi)/nz
-    # meta['lpar']=1e2*(d['Bxy']/d['Bpxy']).mean(1)*d['dlthe'].mean(1) #function of x
-    meta["sig_par"] = old_div(1.0, (fmei * 0.51 * meta["nu_hat"]))
-    # meta['heat_nue'] = ((2*np.pi/meta['lpar'])**2)/(fmei*meta['nu_hat'])
-    # kz_e = kz_i*(rho_e/rho_i)
-    # kz_s = kz_i*(rho_s/rho_i)
-    # kz_i = (TWOPI/L_z)*(indgen((*current_str).fft.nz+1))*rho_i
-
-    # knorm = (TWOPI/lbNorm)*(indgen((*current_str).fft.nz+1))*rho_s
-
-    # for now just translate
-    for elem in meta:
-        if type(meta[elem]).__name__ == "ValUnit":
-            meta[elem] = {"u": meta[elem].u, "v": meta[elem].v}
-
-    print("meta: ", type(meta))
-    return meta
-
-    # meta['DZ'] =inp['[main]']['ZMAX']#-b['[main]']['ZMIN']
-    # AA = inp['[2fluid]']['AA']
-    # Ni0 = IC.variables['Ni0'][:]*1.e14
-    # bmag = IC.variables['bmag'][:]*1.e4 #to cgs
-    # Ni_x = IC.variables['Ni_x'][:]*1.e14 # cm^-3
-    # Te_x
-
-    # rho_s = 1.02e2*sqrt(AA.v*Te_x.v)/ZZ.v/bmag.v
-    # rho_i
-    # rho_e
-
-
-# for i,val in enumerate(boutlist):
diff --git a/tools/pylib/post_bout/rms.py b/tools/pylib/post_bout/rms.py
deleted file mode 100644
index 6a9bdb1929..0000000000
--- a/tools/pylib/post_bout/rms.py
+++ /dev/null
@@ -1,55 +0,0 @@
-from __future__ import division
-from builtins import range
-from past.utils import old_div
-
-###
-# rms(f) : compute growth rate vs. time based on rms of bout variable f for all grid points
-# plot_rms (x,y): plots the graph growth_rate vs. time for grid point x,y
-###
-
-
-import numpy as np
-from pylab import plot, show, xlabel, ylabel, tight_layout
-from boutdata.collect import collect
-
-
-def rms(f):
-    nt = f.shape[0]
-
-    ns = f.shape[1]
-    ne = f.shape[2]
-    nz = f.shape[3]
-
-    ar = np.zeros([nz])
-
-    rms = np.zeros([nt, ns, ne])
-
-    for i in range(nt):
-        for j in range(ns):
-            for k in range(ne):
-                ar = f[i, j, k, :]
-                valav = np.sum(ar)
-                tot = np.sum(old_div(np.power(ar - valav, 2), nz))
-                rms[i, j, k] = np.sqrt(tot)
-    return rms
-
-
-def plot_rms(x, y):
-    s = plot(np.gradient(np.log(rmsp[:, x, y])))
-    ylabel("$\gamma / \omega_A$", fontsize=25)
-    xlabel("Time$(\\tau_A)$", fontsize=25)
-    tight_layout()
-    return s
-
-
-# test
-if __name__ == "__main__":
-    path = "../../../examples/elm-pb/data"
-
-    data = collect("P", path=path)
-
-    rmsp = rms(data)
-
-    plot_rms(34, 32)
-    tight_layout()
-    show()

From 4566405dfb88c8ca6564a769ea37aa07ba3c8eb1 Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Sun, 4 Feb 2024 20:27:11 +0000
Subject: [PATCH 0057/1827] Apply black changes

---
 tests/MMS/diffusion2/runtest         | 2 +-
 tools/tokamak_grids/all/grid2bout.py | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/MMS/diffusion2/runtest b/tests/MMS/diffusion2/runtest
index d915018d8d..6039c6faa6 100755
--- a/tests/MMS/diffusion2/runtest
+++ b/tests/MMS/diffusion2/runtest
@@ -27,7 +27,7 @@ build_and_log("MMS diffusion test")
 inputs = [
     ("X", ["mesh:nx"]),
     ("Y", ["mesh:ny"]),
-    ("Z", ["MZ"])  # ,
+    ("Z", ["MZ"]),  # ,
     # ("XYZ", ["mesh:nx", "mesh:ny", "MZ"])
 ]
 
diff --git a/tools/tokamak_grids/all/grid2bout.py b/tools/tokamak_grids/all/grid2bout.py
index da62a37aeb..6520e8f116 100644
--- a/tools/tokamak_grids/all/grid2bout.py
+++ b/tools/tokamak_grids/all/grid2bout.py
@@ -3,6 +3,7 @@
 
 
 """
+
 from __future__ import print_function
 
 from numpy import max

From 4935742c6075583067c5909fe82d292d233cc4f4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Sun, 4 Feb 2024 21:39:39 +0100
Subject: [PATCH 0058/1827] CI: install wget

---
 .ci_fedora.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 452afb4b7e..18b86467fb 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -41,7 +41,7 @@ then
     # Ignore weak depencies
     echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
     time dnf -y install dnf5
-    time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort
+    time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort wget
     # Allow to override packages - see #2073
     time dnf5 copr enable -y davidsch/fixes4bout || :
     time dnf5 -y upgrade

From 147a872cc4fc2056268d57d43d947cbe6605a8c0 Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Sun, 4 Feb 2024 20:53:06 +0000
Subject: [PATCH 0059/1827] Apply clang-format changes

---
 include/bout/interpolation_xz.hxx            |  4 +---
 src/mesh/interpolation/hermite_spline_xz.cxx | 12 ++++++------
 2 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 46f64256a8..3b45498595 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -75,9 +75,7 @@ public:
   void setRegion(const std::string& region_name) {
     this->region_id = localmesh->getRegionID(region_name);
   }
-  void setRegion(const std::unique_ptr<Region<Ind3D>> region){
-    setRegion(*region);
-  }
+  void setRegion(const std::unique_ptr<Region<Ind3D>> region) { setRegion(*region); }
   void setRegion(const Region<Ind3D>& region) {
     std::string name;
     int i = 0;
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 9e41bac191..782a701c2e 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -22,8 +22,8 @@
 
 #include "../impls/bout/boutmesh.hxx"
 #include "bout/globals.hxx"
-#include "bout/interpolation_xz.hxx"
 #include "bout/index_derivs_interface.hxx"
+#include "bout/interpolation_xz.hxx"
 
 #include <vector>
 
@@ -101,10 +101,10 @@ class IndConverter {
   }
 };
 
-XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh *mesh)
-    : XZInterpolation(y_offset, mesh),
-      h00_x(localmesh), h01_x(localmesh), h10_x(localmesh), h11_x(localmesh),
-      h00_z(localmesh), h01_z(localmesh), h10_z(localmesh), h11_z(localmesh) {
+XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* mesh)
+    : XZInterpolation(y_offset, mesh), h00_x(localmesh), h01_x(localmesh),
+      h10_x(localmesh), h11_x(localmesh), h00_z(localmesh), h01_z(localmesh),
+      h10_z(localmesh), h11_z(localmesh) {
 
   // Index arrays contain guard cells in order to get subscripts right
   i_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
@@ -198,7 +198,7 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     }
 
     i_corner[i] = SpecificInd<IND_TYPE::IND_3D>(
-					   (((i_corn * ny) + (y + y_offset)) * nz + k_corner(x, y, z)), ny, nz);
+        (((i_corn * ny) + (y + y_offset)) * nz + k_corner(x, y, z)), ny, nz);
 
     h00_x[i] = (2. * t_x * t_x * t_x) - (3. * t_x * t_x) + 1.;
     h00_z[i] = (2. * t_z * t_z * t_z) - (3. * t_z * t_z) + 1.;

From cee68f2aa24f1cac7605cc5326de70a3491dc81c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 7 Feb 2024 14:20:26 +0100
Subject: [PATCH 0060/1827] Add asserts to serial methods to avoid using in
 parallel

---
 include/bout/interpolation_xz.hxx            | 21 ++++++++++++++++----
 src/mesh/interpolation/hermite_spline_xz.cxx |  5 +++++
 2 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 3b45498595..3dee48fedb 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -212,11 +212,24 @@ public:
 /// problems most obviously occur.
 class XZMonotonicHermiteSpline : public XZHermiteSpline {
 public:
-  XZMonotonicHermiteSpline(Mesh* mesh = nullptr) : XZHermiteSpline(0, mesh) {}
+  XZMonotonicHermiteSpline(Mesh* mesh = nullptr)
+      : XZHermiteSpline(0, mesh) {
+    if (localmesh->getNXPE() > 1){
+      throw BoutException("Do not support MPI splitting in X");
+    }
+  }
   XZMonotonicHermiteSpline(int y_offset = 0, Mesh* mesh = nullptr)
-      : XZHermiteSpline(y_offset, mesh) {}
-  XZMonotonicHermiteSpline(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr)
-      : XZHermiteSpline(mask, y_offset, mesh) {}
+      : XZHermiteSpline(y_offset, mesh) {
+    if (localmesh->getNXPE() > 1){
+      throw BoutException("Do not support MPI splitting in X");
+    }
+  }
+  XZMonotonicHermiteSpline(const BoutMask &mask, int y_offset = 0, Mesh* mesh = nullptr)
+      : XZHermiteSpline(mask, y_offset, mesh) {
+    if (localmesh->getNXPE() > 1){
+      throw BoutException("Do not support MPI splitting in X");
+    }
+  }
 
   using XZHermiteSpline::interpolate;
   /// Interpolate using precalculated weights.
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 782a701c2e..b5093a2da9 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -145,6 +145,11 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* mesh)
   MatCreateAIJ(MPI_COMM_WORLD, m, m, M, M, 16, nullptr, 16, nullptr, &petscWeights);
 #endif
 #endif
+#ifndef HS_USE_PETSC
+  if (localmesh->getNXPE() > 1){
+    throw BoutException("Require PETSc for MPI splitting in X");
+  }
+#endif
 }
 
 void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z,

From 15aaa055ad424e63194123c1f81aa6a1a5f38ca6 Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Wed, 7 Feb 2024 13:25:23 +0000
Subject: [PATCH 0061/1827] Apply clang-format changes

---
 include/bout/interpolation_xz.hxx            | 11 +++++------
 src/mesh/interpolation/hermite_spline_xz.cxx |  2 +-
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 3dee48fedb..4f171e3420 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -212,21 +212,20 @@ public:
 /// problems most obviously occur.
 class XZMonotonicHermiteSpline : public XZHermiteSpline {
 public:
-  XZMonotonicHermiteSpline(Mesh* mesh = nullptr)
-      : XZHermiteSpline(0, mesh) {
-    if (localmesh->getNXPE() > 1){
+  XZMonotonicHermiteSpline(Mesh* mesh = nullptr) : XZHermiteSpline(0, mesh) {
+    if (localmesh->getNXPE() > 1) {
       throw BoutException("Do not support MPI splitting in X");
     }
   }
   XZMonotonicHermiteSpline(int y_offset = 0, Mesh* mesh = nullptr)
       : XZHermiteSpline(y_offset, mesh) {
-    if (localmesh->getNXPE() > 1){
+    if (localmesh->getNXPE() > 1) {
       throw BoutException("Do not support MPI splitting in X");
     }
   }
-  XZMonotonicHermiteSpline(const BoutMask &mask, int y_offset = 0, Mesh* mesh = nullptr)
+  XZMonotonicHermiteSpline(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr)
       : XZHermiteSpline(mask, y_offset, mesh) {
-    if (localmesh->getNXPE() > 1){
+    if (localmesh->getNXPE() > 1) {
       throw BoutException("Do not support MPI splitting in X");
     }
   }
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index b5093a2da9..f167a7576d 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -146,7 +146,7 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* mesh)
 #endif
 #endif
 #ifndef HS_USE_PETSC
-  if (localmesh->getNXPE() > 1){
+  if (localmesh->getNXPE() > 1) {
     throw BoutException("Require PETSc for MPI splitting in X");
   }
 #endif

From 30ea7e397d9e6c78625ba33102fb49a3493ffde9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 13 Feb 2024 14:30:50 +0100
Subject: [PATCH 0062/1827] Remove accidentially added files

---
 .../test-boutpp/slicing/basics.indexing.html  | 1368 -----------------
 .../test-boutpp/slicing/basics.indexing.txt   |  687 ---------
 .../test-boutpp/slicing/slicingexamples       |    1 -
 tests/integrated/test-boutpp/slicing/test.py  |    4 -
 4 files changed, 2060 deletions(-)
 delete mode 100644 tests/integrated/test-boutpp/slicing/basics.indexing.html
 delete mode 100644 tests/integrated/test-boutpp/slicing/basics.indexing.txt
 delete mode 100644 tests/integrated/test-boutpp/slicing/slicingexamples
 delete mode 100644 tests/integrated/test-boutpp/slicing/test.py

diff --git a/tests/integrated/test-boutpp/slicing/basics.indexing.html b/tests/integrated/test-boutpp/slicing/basics.indexing.html
deleted file mode 100644
index 180f39c6ed..0000000000
--- a/tests/integrated/test-boutpp/slicing/basics.indexing.html
+++ /dev/null
@@ -1,1368 +0,0 @@
-
-<!DOCTYPE html>
-
-<html>
-  <head>
-    <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
-
-    <title>Indexing on ndarrays &#8212; NumPy v1.23 Manual</title>
-    
-  <!-- Loaded before other Sphinx assets -->
-  <link href="../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
-<link href="../_static/styles/pydata-sphinx-theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
-
-    
-  <link rel="stylesheet"
-    href="../_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
-
-    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/graphviz.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/numpy.css" />
-    
-  <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf">
-
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-    <script src="../_static/jquery.js"></script>
-    <script src="../_static/underscore.js"></script>
-    <script src="../_static/doctools.js"></script>
-    <script async="async" src="../_static/scipy-mathjax/MathJax.js?config=scipy-mathjax"></script>
-    <link rel="shortcut icon" href="../_static/favicon.ico"/>
-    <link rel="index" title="Index" href="../genindex.html" />
-    <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="I/O with NumPy" href="basics.io.html" />
-    <link rel="prev" title="Array creation" href="basics.creation.html" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
-    
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-    <!-- Google Analytics -->
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-  </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="60">
-    
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-        <span class="caret"></span>
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-    });
-    // this prevents the browser from following the href of the clicked node
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-        const currentFilePath = "user/basics.indexing.html";
-        // create links to the corresponding page in the other docs versions
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-            const node = document.createElement("a");
-            node.setAttribute("class", "list-group-item list-group-item-action py-1");
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-            if (entry.version == "doc/1.23") {
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-  <section id="indexing-on-ndarrays">
-<span id="basics-indexing"></span><h1>Indexing on <a class="reference internal" href="../reference/generated/numpy.ndarray.html#numpy.ndarray" title="numpy.ndarray"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarrays</span></code></a><a class="headerlink" href="#indexing-on-ndarrays" title="Permalink to this headline">#</a></h1>
-<div class="admonition seealso">
-<p class="admonition-title">See also</p>
-<p><a class="reference internal" href="../reference/arrays.indexing.html#routines-indexing"><span class="std std-ref">Indexing routines</span></a></p>
-</div>
-<p id="index-0"><a class="reference internal" href="../reference/generated/numpy.ndarray.html#numpy.ndarray" title="numpy.ndarray"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarrays</span></code></a> can be indexed using the standard Python
-<code class="docutils literal notranslate"><span class="pre">x[obj]</span></code> syntax, where <em>x</em> is the array and <em>obj</em> the selection.
-There are different kinds of indexing available depending on <em>obj</em>:
-basic indexing, advanced indexing and field access.</p>
-<p>Most of the following examples show the use of indexing when
-referencing data in an array. The examples work just as well
-when assigning to an array. See <a class="reference internal" href="#assigning-values-to-indexed-arrays"><span class="std std-ref">Assigning values to indexed arrays</span></a> for
-specific examples and explanations on how assignments work.</p>
-<p>Note that in Python, <code class="docutils literal notranslate"><span class="pre">x[(exp1,</span> <span class="pre">exp2,</span> <span class="pre">...,</span> <span class="pre">expN)]</span></code> is equivalent to
-<code class="docutils literal notranslate"><span class="pre">x[exp1,</span> <span class="pre">exp2,</span> <span class="pre">...,</span> <span class="pre">expN]</span></code>; the latter is just syntactic sugar
-for the former.</p>
-<section id="basic-indexing">
-<span id="id1"></span><h2>Basic indexing<a class="headerlink" href="#basic-indexing" title="Permalink to this headline">#</a></h2>
-<section id="single-element-indexing">
-<span id="id2"></span><h3>Single element indexing<a class="headerlink" href="#single-element-indexing" title="Permalink to this headline">#</a></h3>
-<p>Single element indexing works
-exactly like that for other standard Python sequences. It is 0-based,
-and accepts negative indices for indexing from the end of the array.</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-<span class="go">2</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">]</span>
-<span class="go">8</span>
-</pre></div>
-</div>
-<p>It is not necessary to
-separate each dimension’s index into its own set of square brackets.</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="o">.</span><span class="n">shape</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>  <span class="c1"># now x is 2-dimensional</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span>
-<span class="go">8</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">]</span>
-<span class="go">9</span>
-</pre></div>
-</div>
-<p>Note that if one indexes a multidimensional array with fewer indices
-than dimensions, one gets a subdimensional array. For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-<span class="go">array([0, 1, 2, 3, 4])</span>
-</pre></div>
-</div>
-<p>That is, each index specified selects the array corresponding to the
-rest of the dimensions selected. In the above example, choosing 0
-means that the remaining dimension of length 5 is being left unspecified,
-and that what is returned is an array of that dimensionality and size.
-It must be noted that the returned array is a <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">view</span></a>, i.e., it is not a
-copy of the original, but points to the same values in memory as does the
-original array.
-In  this case, the 1-D array at the first position (0) is returned.
-So using a single index on the returned array, results in a single
-element being returned. That is:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span>
-<span class="go">2</span>
-</pre></div>
-</div>
-<p>So note that <code class="docutils literal notranslate"><span class="pre">x[0,</span> <span class="pre">2]</span> <span class="pre">==</span> <span class="pre">x[0][2]</span></code> though the second case is more
-inefficient as a new temporary array is created after the first index
-that is subsequently indexed by 2.</p>
-<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p>NumPy uses C-order indexing. That means that the last
-index usually represents the most rapidly changing memory location,
-unlike Fortran or IDL, where the first index represents the most
-rapidly changing location in memory. This difference represents a
-great potential for confusion.</p>
-</div>
-</section>
-<section id="slicing-and-striding">
-<span id="id3"></span><h3>Slicing and striding<a class="headerlink" href="#slicing-and-striding" title="Permalink to this headline">#</a></h3>
-<p>Basic slicing extends Python’s basic concept of slicing to N
-dimensions. Basic slicing occurs when <em>obj</em> is a <a class="reference external" href="https://docs.python.org/3/library/functions.html#slice" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">slice</span></code></a> object
-(constructed by <code class="docutils literal notranslate"><span class="pre">start:stop:step</span></code> notation inside of brackets), an
-integer, or a tuple of slice objects and integers. <a class="reference external" href="https://docs.python.org/3/library/constants.html#Ellipsis" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Ellipsis</span></code></a>
-and <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a> objects can be interspersed with these as
-well.</p>
-<p id="index-1">The simplest case of indexing with <em>N</em> integers returns an <a class="reference internal" href="../reference/arrays.scalars.html#arrays-scalars"><span class="std std-ref">array
-scalar</span></a> representing the corresponding item.  As in
-Python, all indices are zero-based: for the <em>i</em>-th index <span class="math notranslate nohighlight">\(n_i\)</span>,
-the valid range is <span class="math notranslate nohighlight">\(0 \le n_i &lt; d_i\)</span> where <span class="math notranslate nohighlight">\(d_i\)</span> is the
-<em>i</em>-th element of the shape of the array.  Negative indices are
-interpreted as counting from the end of the array (<em>i.e.</em>, if
-<span class="math notranslate nohighlight">\(n_i &lt; 0\)</span>, it means <span class="math notranslate nohighlight">\(n_i + d_i\)</span>).</p>
-<p>All arrays generated by basic slicing are always <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">views</span></a>
-of the original array.</p>
-<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p>NumPy slicing creates a <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">view</span></a> instead of a copy as in the case of
-built-in Python sequences such as string, tuple and list.
-Care must be taken when extracting
-a small portion from a large array which becomes useless after the
-extraction, because the small portion extracted contains a reference
-to the large original array whose memory will not be released until
-all arrays derived from it are garbage-collected. In such cases an
-explicit <code class="docutils literal notranslate"><span class="pre">copy()</span></code> is recommended.</p>
-</div>
-<p>The standard rules of sequence slicing apply to basic slicing on a
-per-dimension basis (including using a step index). Some useful
-concepts to remember include:</p>
-<ul>
-<li><p>The basic slice syntax is <code class="docutils literal notranslate"><span class="pre">i:j:k</span></code> where <em>i</em> is the starting index,
-<em>j</em> is the stopping index, and <em>k</em> is the step (<span class="math notranslate nohighlight">\(k\neq0\)</span>).
-This selects the <em>m</em> elements (in the corresponding dimension) with
-index values <em>i</em>, <em>i + k</em>, …, <em>i + (m - 1) k</em> where
-<span class="math notranslate nohighlight">\(m = q + (r\neq0)\)</span> and <em>q</em> and <em>r</em> are the quotient and remainder
-obtained by dividing <em>j - i</em> by <em>k</em>: <em>j - i = q k + r</em>, so that
-<em>i + (m - 1) k &lt; j</em>.
-For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="mi">7</span><span class="p">,</span> <span class="mi">8</span><span class="p">,</span> <span class="mi">9</span><span class="p">])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">7</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
-<span class="go">array([1, 3, 5])</span>
-</pre></div>
-</div>
-</li>
-<li><p>Negative <em>i</em> and <em>j</em> are interpreted as <em>n + i</em> and <em>n + j</em> where
-<em>n</em> is the number of elements in the corresponding dimension.
-Negative <em>k</em> makes stepping go towards smaller indices.
-From the above example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">:</span><span class="mi">10</span><span class="p">]</span>
-<span class="go">array([8, 9])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">3</span><span class="p">:</span><span class="mi">3</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
-<span class="go">array([7, 6, 5, 4])</span>
-</pre></div>
-</div>
-</li>
-<li><p>Assume <em>n</em> is the number of elements in the dimension being
-sliced. Then, if <em>i</em> is not given it defaults to 0 for <em>k &gt; 0</em> and
-<em>n - 1</em> for <em>k &lt; 0</em> . If <em>j</em> is not given it defaults to <em>n</em> for <em>k &gt; 0</em>
-and <em>-n-1</em> for <em>k &lt; 0</em> . If <em>k</em> is not given it defaults to 1. Note that
-<code class="docutils literal notranslate"><span class="pre">::</span></code> is the same as <code class="docutils literal notranslate"><span class="pre">:</span></code> and means select all indices along this
-axis.
-From the above example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">5</span><span class="p">:]</span>
-<span class="go">array([5, 6, 7, 8, 9])</span>
-</pre></div>
-</div>
-</li>
-<li><p>If the number of objects in the selection tuple is less than
-<em>N</em>, then <code class="docutils literal notranslate"><span class="pre">:</span></code> is assumed for any subsequent dimensions.
-For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[[</span><span class="mi">1</span><span class="p">],[</span><span class="mi">2</span><span class="p">],[</span><span class="mi">3</span><span class="p">]],</span> <span class="p">[[</span><span class="mi">4</span><span class="p">],[</span><span class="mi">5</span><span class="p">],[</span><span class="mi">6</span><span class="p">]]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="o">.</span><span class="n">shape</span>
-<span class="go">(2, 3, 1)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
-<span class="go">array([[[4],</span>
-<span class="go">        [5],</span>
-<span class="go">        [6]]])</span>
-</pre></div>
-</div>
-</li>
-<li><p>An integer, <em>i</em>, returns the same values as <code class="docutils literal notranslate"><span class="pre">i:i+1</span></code>
-<strong>except</strong> the dimensionality of the returned object is reduced by
-1. In particular, a selection tuple with the <em>p</em>-th
-element an integer (and all other entries <code class="docutils literal notranslate"><span class="pre">:</span></code>) returns the
-corresponding sub-array with dimension <em>N - 1</em>. If <em>N = 1</em>
-then the returned object is an array scalar. These objects are
-explained in <a class="reference internal" href="../reference/arrays.scalars.html#arrays-scalars"><span class="std std-ref">Scalars</span></a>.</p></li>
-<li><p>If the selection tuple has all entries <code class="docutils literal notranslate"><span class="pre">:</span></code> except the
-<em>p</em>-th entry which is a slice object <code class="docutils literal notranslate"><span class="pre">i:j:k</span></code>,
-then the returned array has dimension <em>N</em> formed by
-concatenating the sub-arrays returned by integer indexing of
-elements <em>i</em>, <em>i+k</em>, …, <em>i + (m - 1) k &lt; j</em>,</p></li>
-<li><p>Basic slicing with more than one non-<code class="docutils literal notranslate"><span class="pre">:</span></code> entry in the slicing
-tuple, acts like repeated application of slicing using a single
-non-<code class="docutils literal notranslate"><span class="pre">:</span></code> entry, where the non-<code class="docutils literal notranslate"><span class="pre">:</span></code> entries are successively taken
-(with all other non-<code class="docutils literal notranslate"><span class="pre">:</span></code> entries replaced by <code class="docutils literal notranslate"><span class="pre">:</span></code>). Thus,
-<code class="docutils literal notranslate"><span class="pre">x[ind1,</span> <span class="pre">...,</span> <span class="pre">ind2,:]</span></code> acts like <code class="docutils literal notranslate"><span class="pre">x[ind1][...,</span> <span class="pre">ind2,</span> <span class="pre">:]</span></code> under basic
-slicing.</p>
-<div class="admonition warning">
-<p class="admonition-title">Warning</p>
-<p>The above is <strong>not</strong> true for advanced indexing.</p>
-</div>
-</li>
-<li><p>You may use slicing to set values in the array, but (unlike lists) you
-can never grow the array. The size of the value to be set in
-<code class="docutils literal notranslate"><span class="pre">x[obj]</span> <span class="pre">=</span> <span class="pre">value</span></code> must be (broadcastable) to the same shape as
-<code class="docutils literal notranslate"><span class="pre">x[obj]</span></code>.</p></li>
-<li><p>A slicing tuple can always be constructed as <em>obj</em>
-and used in the <code class="docutils literal notranslate"><span class="pre">x[obj]</span></code> notation. Slice objects can be used in
-the construction in place of the <code class="docutils literal notranslate"><span class="pre">[start:stop:step]</span></code>
-notation. For example, <code class="docutils literal notranslate"><span class="pre">x[1:10:5,</span> <span class="pre">::-1]</span></code> can also be implemented
-as <code class="docutils literal notranslate"><span class="pre">obj</span> <span class="pre">=</span> <span class="pre">(slice(1,</span> <span class="pre">10,</span> <span class="pre">5),</span> <span class="pre">slice(None,</span> <span class="pre">None,</span> <span class="pre">-1));</span> <span class="pre">x[obj]</span></code> . This
-can be useful for constructing generic code that works on arrays
-of arbitrary dimensions. See <a class="reference internal" href="#dealing-with-variable-indices"><span class="std std-ref">Dealing with variable numbers of indices within programs</span></a>
-for more information.</p></li>
-</ul>
-</section>
-<section id="dimensional-indexing-tools">
-<span id="index-2"></span><span id="id4"></span><h3>Dimensional indexing tools<a class="headerlink" href="#dimensional-indexing-tools" title="Permalink to this headline">#</a></h3>
-<p>There are some tools to facilitate the easy matching of array shapes with
-expressions and in assignments.</p>
-<p><a class="reference external" href="https://docs.python.org/3/library/constants.html#Ellipsis" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Ellipsis</span></code></a> expands to the number of <code class="docutils literal notranslate"><span class="pre">:</span></code> objects needed for the
-selection tuple to index all dimensions. In most cases, this means that the
-length of the expanded selection tuple is <code class="docutils literal notranslate"><span class="pre">x.ndim</span></code>. There may only be a
-single ellipsis present.
-From the above example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">...</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
-<span class="go">array([[1, 2, 3],</span>
-<span class="go">      [4, 5, 6]])</span>
-</pre></div>
-</div>
-<p>This is equivalent to:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[:,</span> <span class="p">:,</span> <span class="mi">0</span><span class="p">]</span>
-<span class="go">array([[1, 2, 3],</span>
-<span class="go">      [4, 5, 6]])</span>
-</pre></div>
-</div>
-<p>Each <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a> object in the selection tuple serves to expand
-the dimensions of the resulting selection by one unit-length
-dimension.  The added dimension is the position of the <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a>
-object in the selection tuple. <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a> is an alias for
-<code class="docutils literal notranslate"><span class="pre">None</span></code>, and <code class="docutils literal notranslate"><span class="pre">None</span></code> can be used in place of this with the same result.
-From the above example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:,</span> <span class="p">:]</span><span class="o">.</span><span class="n">shape</span>
-<span class="go">(2, 1, 3, 1)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[:,</span> <span class="kc">None</span><span class="p">,</span> <span class="p">:,</span> <span class="p">:]</span><span class="o">.</span><span class="n">shape</span>
-<span class="go">(2, 1, 3, 1)</span>
-</pre></div>
-</div>
-<p>This can be handy to combine two
-arrays in a way that otherwise would require explicit reshaping
-operations. For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">]</span> <span class="o">+</span> <span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,</span> <span class="p">:]</span>
-<span class="go">array([[0, 1, 2, 3, 4],</span>
-<span class="go">      [1, 2, 3, 4, 5],</span>
-<span class="go">      [2, 3, 4, 5, 6],</span>
-<span class="go">      [3, 4, 5, 6, 7],</span>
-<span class="go">      [4, 5, 6, 7, 8]])</span>
-</pre></div>
-</div>
-</section>
-</section>
-<section id="advanced-indexing">
-<span id="id5"></span><h2>Advanced indexing<a class="headerlink" href="#advanced-indexing" title="Permalink to this headline">#</a></h2>
-<p>Advanced indexing is triggered when the selection object, <em>obj</em>, is a
-non-tuple sequence object, an <a class="reference internal" href="../reference/generated/numpy.ndarray.html#numpy.ndarray" title="numpy.ndarray"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> (of data type integer or bool),
-or a tuple with at least one sequence object or ndarray (of data type
-integer or bool). There are two types of advanced indexing: integer
-and Boolean.</p>
-<p>Advanced indexing always returns a <em>copy</em> of the data (contrast with
-basic slicing that returns a <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">view</span></a>).</p>
-<div class="admonition warning">
-<p class="admonition-title">Warning</p>
-<p>The definition of advanced indexing means that <code class="docutils literal notranslate"><span class="pre">x[(1,</span> <span class="pre">2,</span> <span class="pre">3),]</span></code> is
-fundamentally different than <code class="docutils literal notranslate"><span class="pre">x[(1,</span> <span class="pre">2,</span> <span class="pre">3)]</span></code>. The latter is
-equivalent to <code class="docutils literal notranslate"><span class="pre">x[1,</span> <span class="pre">2,</span> <span class="pre">3]</span></code> which will trigger basic selection while
-the former will trigger advanced indexing. Be sure to understand
-why this occurs.</p>
-<p>Also recognize that <code class="docutils literal notranslate"><span class="pre">x[[1,</span> <span class="pre">2,</span> <span class="pre">3]]</span></code> will trigger advanced indexing,
-whereas due to the deprecated Numeric compatibility mentioned above,
-<code class="docutils literal notranslate"><span class="pre">x[[1,</span> <span class="pre">2,</span> <span class="pre">slice(None)]]</span></code> will trigger basic slicing.</p>
-</div>
-<section id="integer-array-indexing">
-<h3>Integer array indexing<a class="headerlink" href="#integer-array-indexing" title="Permalink to this headline">#</a></h3>
-<p>Integer array indexing allows selection of arbitrary items in the array
-based on their <em>N</em>-dimensional index. Each integer array represents a number
-of indices into that dimension.</p>
-<p>Negative values are permitted in the index arrays and work as they do with
-single indices or slices:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
-<span class="go">array([10,  9,  8,  7,  6,  5,  4,  3,  2])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">8</span><span class="p">])]</span>
-<span class="go">array([7, 7, 9, 2])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="o">-</span><span class="mi">3</span><span class="p">,</span> <span class="mi">8</span><span class="p">])]</span>
-<span class="go">array([7, 7, 4, 2])</span>
-</pre></div>
-</div>
-<p>If the index values are out of bounds then an <code class="docutils literal notranslate"><span class="pre">IndexError</span></code> is thrown:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="p">[</span><span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">])]</span>
-<span class="go">array([[3, 4],</span>
-<span class="go">      [5, 6]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">])]</span>
-<span class="gt">Traceback (most recent call last):</span>
-  <span class="c">...</span>
-<span class="gr">IndexError</span>: <span class="n">index 3 is out of bounds for axis 0 with size 3</span>
-</pre></div>
-</div>
-<p>When the index consists of as many integer arrays as dimensions of the array
-being indexed, the indexing is straightforward, but different from slicing.</p>
-<p>Advanced indices always are <a class="reference internal" href="basics.broadcasting.html#basics-broadcasting"><span class="std std-ref">broadcast</span></a> and
-iterated as <em>one</em>:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">result</span><span class="p">[</span><span class="n">i_1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">i_M</span><span class="p">]</span> <span class="o">==</span> <span class="n">x</span><span class="p">[</span><span class="n">ind_1</span><span class="p">[</span><span class="n">i_1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">i_M</span><span class="p">],</span> <span class="n">ind_2</span><span class="p">[</span><span class="n">i_1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">i_M</span><span class="p">],</span>
-                           <span class="o">...</span><span class="p">,</span> <span class="n">ind_N</span><span class="p">[</span><span class="n">i_1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">i_M</span><span class="p">]]</span>
-</pre></div>
-</div>
-<p>Note that the resulting shape is identical to the (broadcast) indexing array
-shapes <code class="docutils literal notranslate"><span class="pre">ind_1,</span> <span class="pre">...,</span> <span class="pre">ind_N</span></code>. If the indices cannot be broadcast to the
-same shape, an exception <code class="docutils literal notranslate"><span class="pre">IndexError:</span> <span class="pre">shape</span> <span class="pre">mismatch:</span> <span class="pre">indexing</span> <span class="pre">arrays</span> <span class="pre">could</span>
-<span class="pre">not</span> <span class="pre">be</span> <span class="pre">broadcast</span> <span class="pre">together</span> <span class="pre">with</span> <span class="pre">shapes...</span></code> is raised.</p>
-<p>Indexing with multidimensional index arrays tend
-to be more unusual uses, but they are permitted, and they are useful for some
-problems. We’ll start with the simplest multidimensional case:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">35</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">y</span>
-<span class="go">array([[ 0,  1,  2,  3,  4,  5,  6],</span>
-<span class="go">       [ 7,  8,  9, 10, 11, 12, 13],</span>
-<span class="go">       [14, 15, 16, 17, 18, 19, 20],</span>
-<span class="go">       [21, 22, 23, 24, 25, 26, 27],</span>
-<span class="go">       [28, 29, 30, 31, 32, 33, 34]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">])]</span>
-<span class="go">array([ 0, 15, 30])</span>
-</pre></div>
-</div>
-<p>In this case, if the index arrays have a matching shape, and there is an
-index array for each dimension of the array being indexed, the resultant
-array has the same shape as the index arrays, and the values correspond
-to the index set for each position in the index arrays. In this example,
-the first index value is 0 for both index arrays, and thus the first value
-of the resultant array is <code class="docutils literal notranslate"><span class="pre">y[0,</span> <span class="pre">0]</span></code>. The next value is <code class="docutils literal notranslate"><span class="pre">y[2,</span> <span class="pre">1]</span></code>, and
-the last is <code class="docutils literal notranslate"><span class="pre">y[4,</span> <span class="pre">2]</span></code>.</p>
-<p>If the index arrays do not have the same shape, there is an attempt to
-broadcast them to the same shape. If they cannot be broadcast to the same
-shape, an exception is raised:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">])]</span>
-<span class="gt">Traceback (most recent call last):</span>
-  <span class="c">...</span>
-<span class="gr">IndexError</span>: <span class="n">shape mismatch: indexing arrays could not be broadcast</span>
-<span class="go">together with shapes (3,) (2,)</span>
-</pre></div>
-</div>
-<p>The broadcasting mechanism permits index arrays to be combined with
-scalars for other indices. The effect is that the scalar value is used
-for all the corresponding values of the index arrays:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="mi">1</span><span class="p">]</span>
-<span class="go">array([ 1, 15, 29])</span>
-</pre></div>
-</div>
-<p>Jumping to the next level of complexity, it is possible to only partially
-index an array with index arrays. It takes a bit of thought to understand
-what happens in such cases. For example if we just use one index array
-with y:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">])]</span>
-<span class="go">array([[ 0,  1,  2,  3,  4,  5,  6],</span>
-<span class="go">      [14, 15, 16, 17, 18, 19, 20],</span>
-<span class="go">      [28, 29, 30, 31, 32, 33, 34]])</span>
-</pre></div>
-</div>
-<p>It results in the construction of a new array where each value of the
-index array selects one row from the array being indexed and the resultant
-array has the resulting shape (number of index elements, size of row).</p>
-<p>In general, the shape of the resultant array will be the concatenation of
-the shape of the index array (or the shape that all the index arrays were
-broadcast to) with the shape of any unused dimensions (those not indexed)
-in the array being indexed.</p>
-<p class="rubric">Example</p>
-<p>From each row, a specific element should be selected. The row index is just
-<code class="docutils literal notranslate"><span class="pre">[0,</span> <span class="pre">1,</span> <span class="pre">2]</span></code> and the column index specifies the element to choose for the
-corresponding row, here <code class="docutils literal notranslate"><span class="pre">[0,</span> <span class="pre">1,</span> <span class="pre">0]</span></code>. Using both together the task
-can be solved using advanced indexing:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="p">[</span><span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]]</span>
-<span class="go">array([1, 4, 5])</span>
-</pre></div>
-</div>
-<p>To achieve a behaviour similar to the basic slicing above, broadcasting can be
-used. The function <a class="reference internal" href="../reference/generated/numpy.ix_.html#numpy.ix_" title="numpy.ix_"><code class="xref py py-func docutils literal notranslate"><span class="pre">ix_</span></code></a> can help with this broadcasting. This is best
-understood with an example.</p>
-<p class="rubric">Example</p>
-<p>From a 4x3 array the corner elements should be selected using advanced
-indexing. Thus all elements for which the column is one of <code class="docutils literal notranslate"><span class="pre">[0,</span> <span class="pre">2]</span></code> and
-the row is one of <code class="docutils literal notranslate"><span class="pre">[0,</span> <span class="pre">3]</span></code> need to be selected. To use advanced indexing
-one needs to select all elements <em>explicitly</em>. Using the method explained
-previously one could write:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span> <span class="mi">0</span><span class="p">,</span>  <span class="mi">1</span><span class="p">,</span>  <span class="mi">2</span><span class="p">],</span>
-<span class="gp">... </span>              <span class="p">[</span> <span class="mi">3</span><span class="p">,</span>  <span class="mi">4</span><span class="p">,</span>  <span class="mi">5</span><span class="p">],</span>
-<span class="gp">... </span>              <span class="p">[</span> <span class="mi">6</span><span class="p">,</span>  <span class="mi">7</span><span class="p">,</span>  <span class="mi">8</span><span class="p">],</span>
-<span class="gp">... </span>              <span class="p">[</span> <span class="mi">9</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">11</span><span class="p">]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span>
-<span class="gp">... </span>                 <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">intp</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">columns</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span>
-<span class="gp">... </span>                    <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">intp</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rows</span><span class="p">,</span> <span class="n">columns</span><span class="p">]</span>
-<span class="go">array([[ 0,  2],</span>
-<span class="go">       [ 9, 11]])</span>
-</pre></div>
-</div>
-<p>However, since the indexing arrays above just repeat themselves,
-broadcasting can be used (compare operations such as
-<code class="docutils literal notranslate"><span class="pre">rows[:,</span> <span class="pre">np.newaxis]</span> <span class="pre">+</span> <span class="pre">columns</span></code>) to simplify this:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">intp</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">columns</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">intp</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">]</span>
-<span class="go">array([[0],</span>
-<span class="go">       [3]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rows</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span> <span class="n">columns</span><span class="p">]</span>
-<span class="go">array([[ 0,  2],</span>
-<span class="go">       [ 9, 11]])</span>
-</pre></div>
-</div>
-<p>This broadcasting can also be achieved using the function <a class="reference internal" href="../reference/generated/numpy.ix_.html#numpy.ix_" title="numpy.ix_"><code class="xref py py-func docutils literal notranslate"><span class="pre">ix_</span></code></a>:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ix_</span><span class="p">(</span><span class="n">rows</span><span class="p">,</span> <span class="n">columns</span><span class="p">)]</span>
-<span class="go">array([[ 0,  2],</span>
-<span class="go">       [ 9, 11]])</span>
-</pre></div>
-</div>
-<p>Note that without the <code class="docutils literal notranslate"><span class="pre">np.ix_</span></code> call, only the diagonal elements would
-be selected:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rows</span><span class="p">,</span> <span class="n">columns</span><span class="p">]</span>
-<span class="go">array([ 0, 11])</span>
-</pre></div>
-</div>
-<p>This difference is the most important thing to remember about
-indexing with multiple advanced indices.</p>
-<p class="rubric">Example</p>
-<p>A real-life example of where advanced indexing may be useful is for a color
-lookup table where we want to map the values of an image into RGB triples for
-display. The lookup table could have a shape (nlookup, 3). Indexing
-such an array with an image with shape (ny, nx) with dtype=np.uint8
-(or any integer type so long as values are with the bounds of the
-lookup table) will result in an array of shape (ny, nx, 3) where a
-triple of RGB values is associated with each pixel location.</p>
-</section>
-<section id="boolean-array-indexing">
-<span id="boolean-indexing"></span><h3>Boolean array indexing<a class="headerlink" href="#boolean-array-indexing" title="Permalink to this headline">#</a></h3>
-<p>This advanced indexing occurs when <em>obj</em> is an array object of Boolean
-type, such as may be returned from comparison operators. A single
-boolean index array is practically identical to <code class="docutils literal notranslate"><span class="pre">x[obj.nonzero()]</span></code> where,
-as described above, <a class="reference internal" href="../reference/generated/numpy.ndarray.nonzero.html#numpy.ndarray.nonzero" title="numpy.ndarray.nonzero"><code class="xref py py-meth docutils literal notranslate"><span class="pre">obj.nonzero()</span></code></a> returns a
-tuple (of length <a class="reference internal" href="../reference/generated/numpy.ndarray.ndim.html#numpy.ndarray.ndim" title="numpy.ndarray.ndim"><code class="xref py py-attr docutils literal notranslate"><span class="pre">obj.ndim</span></code></a>) of integer index
-arrays showing the <a class="reference external" href="https://docs.python.org/3/library/constants.html#True" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">True</span></code></a> elements of <em>obj</em>. However, it is
-faster when <code class="docutils literal notranslate"><span class="pre">obj.shape</span> <span class="pre">==</span> <span class="pre">x.shape</span></code>.</p>
-<p>If <code class="docutils literal notranslate"><span class="pre">obj.ndim</span> <span class="pre">==</span> <span class="pre">x.ndim</span></code>, <code class="docutils literal notranslate"><span class="pre">x[obj]</span></code> returns a 1-dimensional array
-filled with the elements of <em>x</em> corresponding to the <a class="reference external" href="https://docs.python.org/3/library/constants.html#True" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">True</span></code></a>
-values of <em>obj</em>.  The search order will be <a class="reference internal" href="../glossary.html#term-row-major"><span class="xref std std-term">row-major</span></a>,
-C-style. If <em>obj</em> has <a class="reference external" href="https://docs.python.org/3/library/constants.html#True" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">True</span></code></a> values at entries that are outside
-of the bounds of <em>x</em>, then an index error will be raised. If <em>obj</em> is
-smaller than <em>x</em> it is identical to filling it with <a class="reference external" href="https://docs.python.org/3/library/constants.html#False" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">False</span></code></a>.</p>
-<p>A common use case for this is filtering for desired element values.
-For example, one may wish to select all entries from an array which
-are not <a class="reference internal" href="../reference/constants.html#numpy.NaN" title="numpy.NaN"><code class="xref py py-const docutils literal notranslate"><span class="pre">NaN</span></code></a>:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">2.</span><span class="p">],</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="mf">3.</span><span class="p">],</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="o">~</span><span class="n">np</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">x</span><span class="p">)]</span>
-<span class="go">array([1., 2., 3.])</span>
-</pre></div>
-</div>
-<p>Or wish to add a constant to all negative elements:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mf">1.</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.</span><span class="p">,</span> <span class="o">-</span><span class="mf">2.</span><span class="p">,</span> <span class="mi">3</span><span class="p">])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">x</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">20</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
-<span class="go">array([ 1., 19., 18., 3.])</span>
-</pre></div>
-</div>
-<p>In general if an index includes a Boolean array, the result will be
-identical to inserting <code class="docutils literal notranslate"><span class="pre">obj.nonzero()</span></code> into the same position
-and using the integer array indexing mechanism described above.
-<code class="docutils literal notranslate"><span class="pre">x[ind_1,</span> <span class="pre">boolean_array,</span> <span class="pre">ind_2]</span></code> is equivalent to
-<code class="docutils literal notranslate"><span class="pre">x[(ind_1,)</span> <span class="pre">+</span> <span class="pre">boolean_array.nonzero()</span> <span class="pre">+</span> <span class="pre">(ind_2,)]</span></code>.</p>
-<p>If there is only one Boolean array and no integer indexing array present,
-this is straightforward. Care must only be taken to make sure that the
-boolean index has <em>exactly</em> as many dimensions as it is supposed to work
-with.</p>
-<p>In general, when the boolean array has fewer dimensions than the array being
-indexed, this is equivalent to <code class="docutils literal notranslate"><span class="pre">x[b,</span> <span class="pre">...]</span></code>, which means x is indexed by b
-followed by as many <code class="docutils literal notranslate"><span class="pre">:</span></code> as are needed to fill out the rank of x. Thus the
-shape of the result is one dimension containing the number of True elements of
-the boolean array, followed by the remaining dimensions of the array being
-indexed:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">35</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span> <span class="o">=</span> <span class="n">x</span> <span class="o">&gt;</span> <span class="mi">20</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span><span class="p">[:,</span> <span class="mi">5</span><span class="p">]</span>
-<span class="go">array([False, False, False,  True,  True])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">b</span><span class="p">[:,</span> <span class="mi">5</span><span class="p">]]</span>
-<span class="go">array([[21, 22, 23, 24, 25, 26, 27],</span>
-<span class="go">      [28, 29, 30, 31, 32, 33, 34]])</span>
-</pre></div>
-</div>
-<p>Here the 4th and 5th rows are selected from the indexed array and
-combined to make a 2-D array.</p>
-<p class="rubric">Example</p>
-<p>From an array, select all rows which sum up to less or equal two:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">rowsum</span> <span class="o">=</span> <span class="n">x</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rowsum</span> <span class="o">&lt;=</span> <span class="mi">2</span><span class="p">,</span> <span class="p">:]</span>
-<span class="go">array([[0, 1],</span>
-<span class="go">       [1, 1]])</span>
-</pre></div>
-</div>
-<p>Combining multiple Boolean indexing arrays or a Boolean with an integer
-indexing array can best be understood with the
-<a class="reference internal" href="../reference/generated/numpy.ndarray.nonzero.html#numpy.ndarray.nonzero" title="numpy.ndarray.nonzero"><code class="xref py py-meth docutils literal notranslate"><span class="pre">obj.nonzero()</span></code></a> analogy. The function <a class="reference internal" href="../reference/generated/numpy.ix_.html#numpy.ix_" title="numpy.ix_"><code class="xref py py-func docutils literal notranslate"><span class="pre">ix_</span></code></a>
-also supports boolean arrays and will work without any surprises.</p>
-<p class="rubric">Example</p>
-<p>Use boolean indexing to select all rows adding up to an even
-number. At the same time columns 0 and 2 should be selected with an
-advanced integer index. Using the <a class="reference internal" href="../reference/generated/numpy.ix_.html#numpy.ix_" title="numpy.ix_"><code class="xref py py-func docutils literal notranslate"><span class="pre">ix_</span></code></a> function this can be done
-with:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span> <span class="mi">0</span><span class="p">,</span>  <span class="mi">1</span><span class="p">,</span>  <span class="mi">2</span><span class="p">],</span>
-<span class="gp">... </span>              <span class="p">[</span> <span class="mi">3</span><span class="p">,</span>  <span class="mi">4</span><span class="p">,</span>  <span class="mi">5</span><span class="p">],</span>
-<span class="gp">... </span>              <span class="p">[</span> <span class="mi">6</span><span class="p">,</span>  <span class="mi">7</span><span class="p">,</span>  <span class="mi">8</span><span class="p">],</span>
-<span class="gp">... </span>              <span class="p">[</span> <span class="mi">9</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">11</span><span class="p">]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span> <span class="o">=</span> <span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="o">%</span> <span class="mi">2</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span>
-<span class="go">array([False,  True, False,  True])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ix_</span><span class="p">(</span><span class="n">rows</span><span class="p">,</span> <span class="n">columns</span><span class="p">)]</span>
-<span class="go">array([[ 3,  5],</span>
-<span class="go">       [ 9, 11]])</span>
-</pre></div>
-</div>
-<p>Without the <code class="docutils literal notranslate"><span class="pre">np.ix_</span></code> call, only the diagonal elements would be
-selected.</p>
-<p>Or without <code class="docutils literal notranslate"><span class="pre">np.ix_</span></code> (compare the integer array examples):</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span> <span class="o">=</span> <span class="n">rows</span><span class="o">.</span><span class="n">nonzero</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">rows</span><span class="p">[:,</span> <span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span> <span class="n">columns</span><span class="p">]</span>
-<span class="go">array([[ 3,  5],</span>
-<span class="go">       [ 9, 11]])</span>
-</pre></div>
-</div>
-<p class="rubric">Example</p>
-<p>Use a 2-D boolean array of shape (2, 3)
-with four True elements to select rows from a 3-D array of shape
-(2, 3, 5) results in a 2-D result of shape (4, 5):</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">30</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
-<span class="go">array([[[ 0,  1,  2,  3,  4],</span>
-<span class="go">        [ 5,  6,  7,  8,  9],</span>
-<span class="go">        [10, 11, 12, 13, 14]],</span>
-<span class="go">      [[15, 16, 17, 18, 19],</span>
-<span class="go">        [20, 21, 22, 23, 24],</span>
-<span class="go">        [25, 26, 27, 28, 29]]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="kc">True</span><span class="p">,</span> <span class="kc">True</span><span class="p">,</span> <span class="kc">False</span><span class="p">],</span> <span class="p">[</span><span class="kc">False</span><span class="p">,</span> <span class="kc">True</span><span class="p">,</span> <span class="kc">True</span><span class="p">]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">b</span><span class="p">]</span>
-<span class="go">array([[ 0,  1,  2,  3,  4],</span>
-<span class="go">      [ 5,  6,  7,  8,  9],</span>
-<span class="go">      [20, 21, 22, 23, 24],</span>
-<span class="go">      [25, 26, 27, 28, 29]])</span>
-</pre></div>
-</div>
-</section>
-<section id="combining-advanced-and-basic-indexing">
-<span id="id6"></span><h3>Combining advanced and basic indexing<a class="headerlink" href="#combining-advanced-and-basic-indexing" title="Permalink to this headline">#</a></h3>
-<p>When there is at least one slice (<code class="docutils literal notranslate"><span class="pre">:</span></code>), ellipsis (<code class="docutils literal notranslate"><span class="pre">...</span></code>) or <a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a>
-in the index (or the array has more dimensions than there are advanced indices),
-then the behaviour can be more complicated. It is like concatenating the
-indexing result for each advanced index element.</p>
-<p>In the simplest case, there is only a <em>single</em> advanced index combined with
-a slice. For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">35</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span><span class="mi">7</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span>
-<span class="go">array([[ 1,  2],</span>
-<span class="go">       [15, 16],</span>
-<span class="go">       [29, 30]])</span>
-</pre></div>
-</div>
-<p>In effect, the slice and index array operation are independent. The slice
-operation extracts columns with index 1 and 2, (i.e. the 2nd and 3rd columns),
-followed by the index array operation which extracts rows with index 0, 2 and 4
-(i.e the first, third and fifth rows). This is equivalent to:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">y</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">][</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">]),</span> <span class="p">:]</span>
-<span class="go">array([[ 1,  2],</span>
-<span class="go">       [15, 16],</span>
-<span class="go">       [29, 30]])</span>
-</pre></div>
-</div>
-<p>A single advanced index can, for example, replace a slice and the result array
-will be the same. However, it is a copy and may have a different memory layout.
-A slice is preferable when it is possible.
-For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span> <span class="mi">0</span><span class="p">,</span>  <span class="mi">1</span><span class="p">,</span>  <span class="mi">2</span><span class="p">],</span>
-<span class="gp">... </span>              <span class="p">[</span> <span class="mi">3</span><span class="p">,</span>  <span class="mi">4</span><span class="p">,</span>  <span class="mi">5</span><span class="p">],</span>
-<span class="gp">... </span>              <span class="p">[</span> <span class="mi">6</span><span class="p">,</span>  <span class="mi">7</span><span class="p">,</span>  <span class="mi">8</span><span class="p">],</span>
-<span class="gp">... </span>              <span class="p">[</span> <span class="mi">9</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">11</span><span class="p">]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span>
-<span class="go">array([[4, 5]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">2</span><span class="p">,</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]]</span>
-<span class="go">array([[4, 5]])</span>
-</pre></div>
-</div>
-<p>The easiest way to understand a combination of <em>multiple</em> advanced indices may
-be to think in terms of the resulting shape. There are two parts to the indexing
-operation, the subspace defined by the basic indexing (excluding integers) and
-the subspace from the advanced indexing part. Two cases of index combination
-need to be distinguished:</p>
-<ul class="simple">
-<li><p>The advanced indices are separated by a slice, <a class="reference external" href="https://docs.python.org/3/library/constants.html#Ellipsis" title="(in Python v3.10)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Ellipsis</span></code></a> or
-<a class="reference internal" href="../reference/constants.html#numpy.newaxis" title="numpy.newaxis"><code class="xref py py-const docutils literal notranslate"><span class="pre">newaxis</span></code></a>. For example <code class="docutils literal notranslate"><span class="pre">x[arr1,</span> <span class="pre">:,</span> <span class="pre">arr2]</span></code>.</p></li>
-<li><p>The advanced indices are all next to each other.
-For example <code class="docutils literal notranslate"><span class="pre">x[...,</span> <span class="pre">arr1,</span> <span class="pre">arr2,</span> <span class="pre">:]</span></code> but <em>not</em> <code class="docutils literal notranslate"><span class="pre">x[arr1,</span> <span class="pre">:,</span> <span class="pre">1]</span></code>
-since <code class="docutils literal notranslate"><span class="pre">1</span></code> is an advanced index in this regard.</p></li>
-</ul>
-<p>In the first case, the dimensions resulting from the advanced indexing
-operation come first in the result array, and the subspace dimensions after
-that.
-In the second case, the dimensions from the advanced indexing operations
-are inserted into the result array at the same spot as they were in the
-initial array (the latter logic is what makes simple advanced indexing
-behave just like slicing).</p>
-<p class="rubric">Example</p>
-<p>Suppose <code class="docutils literal notranslate"><span class="pre">x.shape</span></code> is (10, 20, 30) and <code class="docutils literal notranslate"><span class="pre">ind</span></code> is a (2, 3, 4)-shaped
-indexing <a class="reference internal" href="../reference/arrays.scalars.html#numpy.intp" title="numpy.intp"><code class="xref py py-class docutils literal notranslate"><span class="pre">intp</span></code></a> array, then <code class="docutils literal notranslate"><span class="pre">result</span> <span class="pre">=</span> <span class="pre">x[...,</span> <span class="pre">ind,</span> <span class="pre">:]</span></code> has
-shape (10, 2, 3, 4, 30) because the (20,)-shaped subspace has been
-replaced with a (2, 3, 4)-shaped broadcasted indexing subspace. If
-we let <em>i, j, k</em> loop over the (2, 3, 4)-shaped subspace then
-<code class="docutils literal notranslate"><span class="pre">result[...,</span> <span class="pre">i,</span> <span class="pre">j,</span> <span class="pre">k,</span> <span class="pre">:]</span> <span class="pre">=</span> <span class="pre">x[...,</span> <span class="pre">ind[i,</span> <span class="pre">j,</span> <span class="pre">k],</span> <span class="pre">:]</span></code>. This example
-produces the same result as <a class="reference internal" href="../reference/generated/numpy.ndarray.take.html#numpy.ndarray.take" title="numpy.ndarray.take"><code class="xref py py-meth docutils literal notranslate"><span class="pre">x.take(ind,</span> <span class="pre">axis=-2)</span></code></a>.</p>
-<p class="rubric">Example</p>
-<p>Let <code class="docutils literal notranslate"><span class="pre">x.shape</span></code> be (10, 20, 30, 40, 50) and suppose <code class="docutils literal notranslate"><span class="pre">ind_1</span></code>
-and <code class="docutils literal notranslate"><span class="pre">ind_2</span></code> can be broadcast to the shape (2, 3, 4). Then
-<code class="docutils literal notranslate"><span class="pre">x[:,</span> <span class="pre">ind_1,</span> <span class="pre">ind_2]</span></code> has shape (10, 2, 3, 4, 40, 50) because the
-(20, 30)-shaped subspace from X has been replaced with the
-(2, 3, 4) subspace from the indices. However,
-<code class="docutils literal notranslate"><span class="pre">x[:,</span> <span class="pre">ind_1,</span> <span class="pre">:,</span> <span class="pre">ind_2]</span></code> has shape (2, 3, 4, 10, 30, 50) because there
-is no unambiguous place to drop in the indexing subspace, thus
-it is tacked-on to the beginning. It is always possible to use
-<a class="reference internal" href="../reference/generated/numpy.ndarray.transpose.html#numpy.ndarray.transpose" title="numpy.ndarray.transpose"><code class="xref py py-meth docutils literal notranslate"><span class="pre">.transpose()</span></code></a> to move the subspace
-anywhere desired. Note that this example cannot be replicated
-using <a class="reference internal" href="../reference/generated/numpy.take.html#numpy.take" title="numpy.take"><code class="xref py py-func docutils literal notranslate"><span class="pre">take</span></code></a>.</p>
-<p class="rubric">Example</p>
-<p>Slicing can be combined with broadcasted boolean indices:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">35</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span> <span class="o">=</span> <span class="n">x</span> <span class="o">&gt;</span> <span class="mi">20</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span>
-<span class="go">array([[False, False, False, False, False, False, False],</span>
-<span class="go">      [False, False, False, False, False, False, False],</span>
-<span class="go">      [False, False, False, False, False, False, False],</span>
-<span class="go">      [ True,  True,  True,  True,  True,  True,  True],</span>
-<span class="go">      [ True,  True,  True,  True,  True,  True,  True]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">b</span><span class="p">[:,</span> <span class="mi">5</span><span class="p">],</span> <span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span>
-<span class="go">array([[22, 23],</span>
-<span class="go">      [29, 30]])</span>
-</pre></div>
-</div>
-</section>
-</section>
-<section id="field-access">
-<span id="arrays-indexing-fields"></span><h2>Field access<a class="headerlink" href="#field-access" title="Permalink to this headline">#</a></h2>
-<div class="admonition seealso">
-<p class="admonition-title">See also</p>
-<p><a class="reference internal" href="basics.rec.html#structured-arrays"><span class="std std-ref">Structured arrays</span></a></p>
-</div>
-<p>If the <a class="reference internal" href="../reference/generated/numpy.ndarray.html#numpy.ndarray" title="numpy.ndarray"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> object is a structured array the <a class="reference internal" href="../glossary.html#term-field"><span class="xref std std-term">fields</span></a>
-of the array can be accessed by indexing the array with strings,
-dictionary-like.</p>
-<p>Indexing <code class="docutils literal notranslate"><span class="pre">x['field-name']</span></code> returns a new <a class="reference internal" href="../glossary.html#term-view"><span class="xref std std-term">view</span></a> to the array,
-which is of the same shape as <em>x</em> (except when the field is a
-sub-array) but of data type <code class="docutils literal notranslate"><span class="pre">x.dtype['field-name']</span></code> and contains
-only the part of the data in the specified field. Also,
-<a class="reference internal" href="../reference/arrays.classes.html#arrays-classes-rec"><span class="std std-ref">record array</span></a> scalars can be “indexed” this way.</p>
-<p>Indexing into a structured array can also be done with a list of field names,
-e.g. <code class="docutils literal notranslate"><span class="pre">x[['field-name1',</span> <span class="pre">'field-name2']]</span></code>. As of NumPy 1.16, this returns a
-view containing only those fields. In older versions of NumPy, it returned a
-copy. See the user guide section on <a class="reference internal" href="basics.rec.html#structured-arrays"><span class="std std-ref">Structured arrays</span></a> for more
-information on multifield indexing.</p>
-<p>If the accessed field is a sub-array, the dimensions of the sub-array
-are appended to the shape of the result.
-For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="p">[(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">),</span> <span class="p">(</span><span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">,</span> <span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="s1">&#39;a&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span>
-<span class="go">(2, 2)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="s1">&#39;a&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">dtype</span>
-<span class="go">dtype(&#39;int32&#39;)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="s1">&#39;b&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span>
-<span class="go">(2, 2, 3, 3)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="s1">&#39;b&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">dtype</span>
-<span class="go">dtype(&#39;float64&#39;)</span>
-</pre></div>
-</div>
-</section>
-<section id="flat-iterator-indexing">
-<span id="id7"></span><h2>Flat Iterator indexing<a class="headerlink" href="#flat-iterator-indexing" title="Permalink to this headline">#</a></h2>
-<p><a class="reference internal" href="../reference/generated/numpy.ndarray.flat.html#numpy.ndarray.flat" title="numpy.ndarray.flat"><code class="xref py py-attr docutils literal notranslate"><span class="pre">x.flat</span></code></a> returns an iterator that will iterate
-over the entire array (in C-contiguous style with the last index
-varying the fastest). This iterator object can also be indexed using
-basic slicing or advanced indexing as long as the selection object is
-not a tuple. This should be clear from the fact that <a class="reference internal" href="../reference/generated/numpy.ndarray.flat.html#numpy.ndarray.flat" title="numpy.ndarray.flat"><code class="xref py py-attr docutils literal notranslate"><span class="pre">x.flat</span></code></a> is a 1-dimensional view. It can be used for integer
-indexing with 1-dimensional C-style-flat indices. The shape of any
-returned array is therefore the shape of the integer indexing object.</p>
-</section>
-<section id="assigning-values-to-indexed-arrays">
-<span id="index-3"></span><span id="id8"></span><h2>Assigning values to indexed arrays<a class="headerlink" href="#assigning-values-to-indexed-arrays" title="Permalink to this headline">#</a></h2>
-<p>As mentioned, one can select a subset of an array to assign to using
-a single index, slices, and index and mask arrays. The value being
-assigned to the indexed array must be shape consistent (the same shape
-or broadcastable to the shape the index produces). For example, it is
-permitted to assign a constant to a slice:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">:</span><span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
-</pre></div>
-</div>
-<p>or an array of the right size:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">:</span><span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>Note that assignments may result in changes if assigning
-higher types to lower types (like floats to ints) or even
-exceptions (assigning complex to floats or ints):</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.2</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<span class="go">1</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.2</span><span class="n">j</span>
-<span class="gt">Traceback (most recent call last):</span>
-  <span class="c">...</span>
-<span class="gr">TypeError</span>: <span class="n">can&#39;t convert complex to int</span>
-</pre></div>
-</div>
-<p>Unlike some of the references (such as array and mask indices)
-assignments are always made to the original data in the array
-(indeed, nothing else would make sense!). Note though, that some
-actions may not work as one may naively expect. This particular
-example is often surprising to people:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">50</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
-<span class="go">array([ 0, 10, 20, 30, 40])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">])]</span> <span class="o">+=</span> <span class="mi">1</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span>
-<span class="go">array([ 0, 11, 20, 31, 40])</span>
-</pre></div>
-</div>
-<p>Where people expect that the 1st location will be incremented by 3.
-In fact, it will only be incremented by 1. The reason is that
-a new array is extracted from the original (as a temporary) containing
-the values at 1, 1, 3, 1, then the value 1 is added to the temporary,
-and then the temporary is assigned back to the original array. Thus
-the value of the array at <code class="docutils literal notranslate"><span class="pre">x[1]</span> <span class="pre">+</span> <span class="pre">1</span></code> is assigned to <code class="docutils literal notranslate"><span class="pre">x[1]</span></code> three times,
-rather than being incremented 3 times.</p>
-</section>
-<section id="dealing-with-variable-numbers-of-indices-within-programs">
-<span id="dealing-with-variable-indices"></span><h2>Dealing with variable numbers of indices within programs<a class="headerlink" href="#dealing-with-variable-numbers-of-indices-within-programs" title="Permalink to this headline">#</a></h2>
-<p>The indexing syntax is very powerful but limiting when dealing with
-a variable number of indices. For example, if you want to write
-a function that can handle arguments with various numbers of
-dimensions without having to write special case code for each
-number of possible dimensions, how can that be done? If one
-supplies to the index a tuple, the tuple will be interpreted
-as a list of indices. For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">81</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">indices</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[</span><span class="n">indices</span><span class="p">]</span>
-<span class="go">40</span>
-</pre></div>
-</div>
-<p>So one can use code to construct tuples of any number of indices
-and then use these within an index.</p>
-<p>Slices can be specified within programs by using the slice() function
-in Python. For example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">indices</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="nb">slice</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>  <span class="c1"># same as [1, 1, 1, 0:2]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[</span><span class="n">indices</span><span class="p">]</span>
-<span class="go">array([39, 40])</span>
-</pre></div>
-</div>
-<p>Likewise, ellipsis can be specified by code by using the Ellipsis
-object:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">indices</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="bp">Ellipsis</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>  <span class="c1"># same as [1, ..., 1]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[</span><span class="n">indices</span><span class="p">]</span>
-<span class="go">array([[28, 31, 34],</span>
-<span class="go">       [37, 40, 43],</span>
-<span class="go">       [46, 49, 52]])</span>
-</pre></div>
-</div>
-<p>For this reason, it is possible to use the output from the
-<a class="reference internal" href="../reference/generated/numpy.ndarray.nonzero.html#numpy.ndarray.nonzero" title="numpy.ndarray.nonzero"><code class="xref py py-meth docutils literal notranslate"><span class="pre">np.nonzero()</span></code></a> function directly as an index since
-it always returns a tuple of index arrays.</p>
-<p>Because of the special treatment of tuples, they are not automatically
-converted to an array as a list would be. As an example:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">]]</span>  <span class="c1"># produces a large array</span>
-<span class="go">array([[[[27, 28, 29],</span>
-<span class="go">         [30, 31, 32], ...</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">z</span><span class="p">[(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)]</span>  <span class="c1"># returns a single value</span>
-<span class="go">40</span>
-</pre></div>
-</div>
-</section>
-<section id="detailed-notes">
-<h2>Detailed notes<a class="headerlink" href="#detailed-notes" title="Permalink to this headline">#</a></h2>
-<p>These are some detailed notes, which are not of importance for day to day
-indexing (in no particular order):</p>
-<ul class="simple">
-<li><p>The native NumPy indexing type is <code class="docutils literal notranslate"><span class="pre">intp</span></code> and may differ from the
-default integer array type. <code class="docutils literal notranslate"><span class="pre">intp</span></code> is the smallest data type
-sufficient to safely index any array; for advanced indexing it may be
-faster than other types.</p></li>
-<li><p>For advanced assignments, there is in general no guarantee for the
-iteration order. This means that if an element is set more than once,
-it is not possible to predict the final result.</p></li>
-<li><p>An empty (tuple) index is a full scalar index into a zero-dimensional array.
-<code class="docutils literal notranslate"><span class="pre">x[()]</span></code> returns a <em>scalar</em> if <code class="docutils literal notranslate"><span class="pre">x</span></code> is zero-dimensional and a view
-otherwise. On the other hand, <code class="docutils literal notranslate"><span class="pre">x[...]</span></code> always returns a view.</p></li>
-<li><p>If a zero-dimensional array is present in the index <em>and</em> it is a full
-integer index the result will be a <em>scalar</em> and not a zero-dimensional array.
-(Advanced indexing is not triggered.)</p></li>
-<li><p>When an ellipsis (<code class="docutils literal notranslate"><span class="pre">...</span></code>) is present but has no size (i.e. replaces zero
-<code class="docutils literal notranslate"><span class="pre">:</span></code>) the result will still always be an array. A view if no advanced index
-is present, otherwise a copy.</p></li>
-<li><p>The <code class="docutils literal notranslate"><span class="pre">nonzero</span></code> equivalence for Boolean arrays does not hold for zero
-dimensional boolean arrays.</p></li>
-<li><p>When the result of an advanced indexing operation has no elements but an
-individual index is out of bounds, whether or not an <code class="docutils literal notranslate"><span class="pre">IndexError</span></code> is
-raised is undefined (e.g. <code class="docutils literal notranslate"><span class="pre">x[[],</span> <span class="pre">[123]]</span></code> with <code class="docutils literal notranslate"><span class="pre">123</span></code> being out of bounds).</p></li>
-<li><p>When a <em>casting</em> error occurs during assignment (for example updating a
-numerical array using a sequence of strings), the array being assigned
-to may end up in an unpredictable partially updated state.
-However, if any other error (such as an out of bounds index) occurs, the
-array will remain unchanged.</p></li>
-<li><p>The memory layout of an advanced indexing result is optimized for each
-indexing operation and no particular memory order can be assumed.</p></li>
-<li><p>When using a subclass (especially one which manipulates its shape), the
-default <code class="docutils literal notranslate"><span class="pre">ndarray.__setitem__</span></code> behaviour will call <code class="docutils literal notranslate"><span class="pre">__getitem__</span></code> for
-<em>basic</em> indexing but not for <em>advanced</em> indexing. For such a subclass it may
-be preferable to call <code class="docutils literal notranslate"><span class="pre">ndarray.__setitem__</span></code> with a <em>base class</em> ndarray
-view on the data. This <em>must</em> be done if the subclasses <code class="docutils literal notranslate"><span class="pre">__getitem__</span></code> does
-not return views.</p></li>
-</ul>
-</section>
-</section>
-
-
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diff --git a/tests/integrated/test-boutpp/slicing/basics.indexing.txt b/tests/integrated/test-boutpp/slicing/basics.indexing.txt
deleted file mode 100644
index eba782d5e2..0000000000
--- a/tests/integrated/test-boutpp/slicing/basics.indexing.txt
+++ /dev/null
@@ -1,687 +0,0 @@
-
-logo
-
-    User Guide
-    API reference
-    Development
-    Release notes
-    Learn
-
-    GitHub
-    Twitter
-
-    What is NumPy?
-    Installation
-    NumPy quickstart
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-    NumPy fundamentals
-        Array creation
-        Indexing on ndarrays
-        I/O with NumPy
-        Data types
-        Broadcasting
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-On this page
-
-    Basic indexing
-        Single element indexing
-        Slicing and striding
-        Dimensional indexing tools
-    Advanced indexing
-    Field access
-    Flat Iterator indexing
-    Assigning values to indexed arrays
-    Dealing with variable numbers of indices within programs
-    Detailed notes
-
-Indexing on ndarrays
-
-See also
-
-Indexing routines
-
-ndarrays can be indexed using the standard Python x[obj] syntax, where x is the array and obj the selection. There are different kinds of indexing available depending on obj: basic indexing, advanced indexing and field access.
-
-Most of the following examples show the use of indexing when referencing data in an array. The examples work just as well when assigning to an array. See Assigning values to indexed arrays for specific examples and explanations on how assignments work.
-
-Note that in Python, x[(exp1, exp2, ..., expN)] is equivalent to x[exp1, exp2, ..., expN]; the latter is just syntactic sugar for the former.
-Basic indexing
-Single element indexing
-
-Single element indexing works exactly like that for other standard Python sequences. It is 0-based, and accepts negative indices for indexing from the end of the array.
-
-x = np.arange(10)
-
-x[2]
-2
-
-x[-2]
-8
-
-It is not necessary to separate each dimension’s index into its own set of square brackets.
-
-x.shape = (2, 5)  # now x is 2-dimensional
-
-x[1, 3]
-8
-
-x[1, -1]
-9
-
-Note that if one indexes a multidimensional array with fewer indices than dimensions, one gets a subdimensional array. For example:
-
-x[0]
-array([0, 1, 2, 3, 4])
-
-That is, each index specified selects the array corresponding to the rest of the dimensions selected. In the above example, choosing 0 means that the remaining dimension of length 5 is being left unspecified, and that what is returned is an array of that dimensionality and size. It must be noted that the returned array is a view, i.e., it is not a copy of the original, but points to the same values in memory as does the original array. In this case, the 1-D array at the first position (0) is returned. So using a single index on the returned array, results in a single element being returned. That is:
-
-x[0][2]
-2
-
-So note that x[0, 2] == x[0][2] though the second case is more inefficient as a new temporary array is created after the first index that is subsequently indexed by 2.
-
-Note
-
-NumPy uses C-order indexing. That means that the last index usually represents the most rapidly changing memory location, unlike Fortran or IDL, where the first index represents the most rapidly changing location in memory. This difference represents a great potential for confusion.
-Slicing and striding
-
-Basic slicing extends Python’s basic concept of slicing to N dimensions. Basic slicing occurs when obj is a slice object (constructed by start:stop:step notation inside of brackets), an integer, or a tuple of slice objects and integers. Ellipsis and newaxis objects can be interspersed with these as well.
-
-The simplest case of indexing with N integers returns an array scalar representing the corresponding item. As in Python, all indices are zero-based: for the i-th index
-, the valid range is where is the i-th element of the shape of the array. Negative indices are interpreted as counting from the end of the array (i.e., if , it means
-
-).
-
-All arrays generated by basic slicing are always views of the original array.
-
-Note
-
-NumPy slicing creates a view instead of a copy as in the case of built-in Python sequences such as string, tuple and list. Care must be taken when extracting a small portion from a large array which becomes useless after the extraction, because the small portion extracted contains a reference to the large original array whose memory will not be released until all arrays derived from it are garbage-collected. In such cases an explicit copy() is recommended.
-
-The standard rules of sequence slicing apply to basic slicing on a per-dimension basis (including using a step index). Some useful concepts to remember include:
-
-    The basic slice syntax is i:j:k where i is the starting index, j is the stopping index, and k is the step (
-
-). This selects the m elements (in the corresponding dimension) with index values i, i + k, …, i + (m - 1) k where
-
-and q and r are the quotient and remainder obtained by dividing j - i by k: j - i = q k + r, so that i + (m - 1) k < j. For example:
-
-x = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
-
-x[1:7:2]
-array([1, 3, 5])
-
-Negative i and j are interpreted as n + i and n + j where n is the number of elements in the corresponding dimension. Negative k makes stepping go towards smaller indices. From the above example:
-
-x[-2:10]
-array([8, 9])
-
-x[-3:3:-1]
-array([7, 6, 5, 4])
-
-Assume n is the number of elements in the dimension being sliced. Then, if i is not given it defaults to 0 for k > 0 and n - 1 for k < 0 . If j is not given it defaults to n for k > 0 and -n-1 for k < 0 . If k is not given it defaults to 1. Note that :: is the same as : and means select all indices along this axis. From the above example:
-
-x[5:]
-array([5, 6, 7, 8, 9])
-
-If the number of objects in the selection tuple is less than N, then : is assumed for any subsequent dimensions. For example:
-
-x = np.array([[[1],[2],[3]], [[4],[5],[6]]])
-
-x.shape
-(2, 3, 1)
-
-    x[1:2]
-    array([[[4],
-            [5],
-            [6]]])
-
-    An integer, i, returns the same values as i:i+1 except the dimensionality of the returned object is reduced by 1. In particular, a selection tuple with the p-th element an integer (and all other entries :) returns the corresponding sub-array with dimension N - 1. If N = 1 then the returned object is an array scalar. These objects are explained in Scalars.
-
-    If the selection tuple has all entries : except the p-th entry which is a slice object i:j:k, then the returned array has dimension N formed by concatenating the sub-arrays returned by integer indexing of elements i, i+k, …, i + (m - 1) k < j,
-
-    Basic slicing with more than one non-: entry in the slicing tuple, acts like repeated application of slicing using a single non-: entry, where the non-: entries are successively taken (with all other non-: entries replaced by :). Thus, x[ind1, ..., ind2,:] acts like x[ind1][..., ind2, :] under basic slicing.
-
-    Warning
-
-    The above is not true for advanced indexing.
-
-    You may use slicing to set values in the array, but (unlike lists) you can never grow the array. The size of the value to be set in x[obj] = value must be (broadcastable) to the same shape as x[obj].
-
-    A slicing tuple can always be constructed as obj and used in the x[obj] notation. Slice objects can be used in the construction in place of the [start:stop:step] notation. For example, x[1:10:5, ::-1] can also be implemented as obj = (slice(1, 10, 5), slice(None, None, -1)); x[obj] . This can be useful for constructing generic code that works on arrays of arbitrary dimensions. See Dealing with variable numbers of indices within programs for more information.
-
-Dimensional indexing tools
-
-There are some tools to facilitate the easy matching of array shapes with expressions and in assignments.
-
-Ellipsis expands to the number of : objects needed for the selection tuple to index all dimensions. In most cases, this means that the length of the expanded selection tuple is x.ndim. There may only be a single ellipsis present. From the above example:
-
-x[..., 0]
-array([[1, 2, 3],
-      [4, 5, 6]])
-
-This is equivalent to:
-
-x[:, :, 0]
-array([[1, 2, 3],
-      [4, 5, 6]])
-
-Each newaxis object in the selection tuple serves to expand the dimensions of the resulting selection by one unit-length dimension. The added dimension is the position of the newaxis object in the selection tuple. newaxis is an alias for None, and None can be used in place of this with the same result. From the above example:
-
-x[:, np.newaxis, :, :].shape
-(2, 1, 3, 1)
-
-x[:, None, :, :].shape
-(2, 1, 3, 1)
-
-This can be handy to combine two arrays in a way that otherwise would require explicit reshaping operations. For example:
-
-x = np.arange(5)
-
-x[:, np.newaxis] + x[np.newaxis, :]
-array([[0, 1, 2, 3, 4],
-      [1, 2, 3, 4, 5],
-      [2, 3, 4, 5, 6],
-      [3, 4, 5, 6, 7],
-      [4, 5, 6, 7, 8]])
-
-Advanced indexing
-
-Advanced indexing is triggered when the selection object, obj, is a non-tuple sequence object, an ndarray (of data type integer or bool), or a tuple with at least one sequence object or ndarray (of data type integer or bool). There are two types of advanced indexing: integer and Boolean.
-
-Advanced indexing always returns a copy of the data (contrast with basic slicing that returns a view).
-
-Warning
-
-The definition of advanced indexing means that x[(1, 2, 3),] is fundamentally different than x[(1, 2, 3)]. The latter is equivalent to x[1, 2, 3] which will trigger basic selection while the former will trigger advanced indexing. Be sure to understand why this occurs.
-
-Also recognize that x[[1, 2, 3]] will trigger advanced indexing, whereas due to the deprecated Numeric compatibility mentioned above, x[[1, 2, slice(None)]] will trigger basic slicing.
-Integer array indexing
-
-Integer array indexing allows selection of arbitrary items in the array based on their N-dimensional index. Each integer array represents a number of indices into that dimension.
-
-Negative values are permitted in the index arrays and work as they do with single indices or slices:
-
-x = np.arange(10, 1, -1)
-
-x
-array([10,  9,  8,  7,  6,  5,  4,  3,  2])
-
-x[np.array([3, 3, 1, 8])]
-array([7, 7, 9, 2])
-
-x[np.array([3, 3, -3, 8])]
-array([7, 7, 4, 2])
-
-If the index values are out of bounds then an IndexError is thrown:
-
-x = np.array([[1, 2], [3, 4], [5, 6]])
-
-x[np.array([1, -1])]
-array([[3, 4],
-      [5, 6]])
-
-x[np.array([3, 4])]
-Traceback (most recent call last):
-  ...
-IndexError: index 3 is out of bounds for axis 0 with size 3
-
-When the index consists of as many integer arrays as dimensions of the array being indexed, the indexing is straightforward, but different from slicing.
-
-Advanced indices always are broadcast and iterated as one:
-
-result[i_1, ..., i_M] == x[ind_1[i_1, ..., i_M], ind_2[i_1, ..., i_M],
-                           ..., ind_N[i_1, ..., i_M]]
-
-Note that the resulting shape is identical to the (broadcast) indexing array shapes ind_1, ..., ind_N. If the indices cannot be broadcast to the same shape, an exception IndexError: shape mismatch: indexing arrays could not be broadcast together with shapes... is raised.
-
-Indexing with multidimensional index arrays tend to be more unusual uses, but they are permitted, and they are useful for some problems. We’ll start with the simplest multidimensional case:
-
-y = np.arange(35).reshape(5, 7)
-
-y
-array([[ 0,  1,  2,  3,  4,  5,  6],
-       [ 7,  8,  9, 10, 11, 12, 13],
-       [14, 15, 16, 17, 18, 19, 20],
-       [21, 22, 23, 24, 25, 26, 27],
-       [28, 29, 30, 31, 32, 33, 34]])
-
-y[np.array([0, 2, 4]), np.array([0, 1, 2])]
-array([ 0, 15, 30])
-
-In this case, if the index arrays have a matching shape, and there is an index array for each dimension of the array being indexed, the resultant array has the same shape as the index arrays, and the values correspond to the index set for each position in the index arrays. In this example, the first index value is 0 for both index arrays, and thus the first value of the resultant array is y[0, 0]. The next value is y[2, 1], and the last is y[4, 2].
-
-If the index arrays do not have the same shape, there is an attempt to broadcast them to the same shape. If they cannot be broadcast to the same shape, an exception is raised:
-
-y[np.array([0, 2, 4]), np.array([0, 1])]
-Traceback (most recent call last):
-  ...
-IndexError: shape mismatch: indexing arrays could not be broadcast
-together with shapes (3,) (2,)
-
-The broadcasting mechanism permits index arrays to be combined with scalars for other indices. The effect is that the scalar value is used for all the corresponding values of the index arrays:
-
-y[np.array([0, 2, 4]), 1]
-array([ 1, 15, 29])
-
-Jumping to the next level of complexity, it is possible to only partially index an array with index arrays. It takes a bit of thought to understand what happens in such cases. For example if we just use one index array with y:
-
-y[np.array([0, 2, 4])]
-array([[ 0,  1,  2,  3,  4,  5,  6],
-      [14, 15, 16, 17, 18, 19, 20],
-      [28, 29, 30, 31, 32, 33, 34]])
-
-It results in the construction of a new array where each value of the index array selects one row from the array being indexed and the resultant array has the resulting shape (number of index elements, size of row).
-
-In general, the shape of the resultant array will be the concatenation of the shape of the index array (or the shape that all the index arrays were broadcast to) with the shape of any unused dimensions (those not indexed) in the array being indexed.
-
-Example
-
-From each row, a specific element should be selected. The row index is just [0, 1, 2] and the column index specifies the element to choose for the corresponding row, here [0, 1, 0]. Using both together the task can be solved using advanced indexing:
-
-x = np.array([[1, 2], [3, 4], [5, 6]])
-
-x[[0, 1, 2], [0, 1, 0]]
-array([1, 4, 5])
-
-To achieve a behaviour similar to the basic slicing above, broadcasting can be used. The function ix_ can help with this broadcasting. This is best understood with an example.
-
-Example
-
-From a 4x3 array the corner elements should be selected using advanced indexing. Thus all elements for which the column is one of [0, 2] and the row is one of [0, 3] need to be selected. To use advanced indexing one needs to select all elements explicitly. Using the method explained previously one could write:
-
-x = np.array([[ 0,  1,  2],
-
-              [ 3,  4,  5],
-
-              [ 6,  7,  8],
-
-              [ 9, 10, 11]])
-
-rows = np.array([[0, 0],
-
-                 [3, 3]], dtype=np.intp)
-
-columns = np.array([[0, 2],
-
-                    [0, 2]], dtype=np.intp)
-
-x[rows, columns]
-array([[ 0,  2],
-       [ 9, 11]])
-
-However, since the indexing arrays above just repeat themselves, broadcasting can be used (compare operations such as rows[:, np.newaxis] + columns) to simplify this:
-
-rows = np.array([0, 3], dtype=np.intp)
-
-columns = np.array([0, 2], dtype=np.intp)
-
-rows[:, np.newaxis]
-array([[0],
-       [3]])
-
-x[rows[:, np.newaxis], columns]
-array([[ 0,  2],
-       [ 9, 11]])
-
-This broadcasting can also be achieved using the function ix_:
-
-x[np.ix_(rows, columns)]
-array([[ 0,  2],
-       [ 9, 11]])
-
-Note that without the np.ix_ call, only the diagonal elements would be selected:
-
-x[rows, columns]
-array([ 0, 11])
-
-This difference is the most important thing to remember about indexing with multiple advanced indices.
-
-Example
-
-A real-life example of where advanced indexing may be useful is for a color lookup table where we want to map the values of an image into RGB triples for display. The lookup table could have a shape (nlookup, 3). Indexing such an array with an image with shape (ny, nx) with dtype=np.uint8 (or any integer type so long as values are with the bounds of the lookup table) will result in an array of shape (ny, nx, 3) where a triple of RGB values is associated with each pixel location.
-Boolean array indexing
-
-This advanced indexing occurs when obj is an array object of Boolean type, such as may be returned from comparison operators. A single boolean index array is practically identical to x[obj.nonzero()] where, as described above, obj.nonzero() returns a tuple (of length obj.ndim) of integer index arrays showing the True elements of obj. However, it is faster when obj.shape == x.shape.
-
-If obj.ndim == x.ndim, x[obj] returns a 1-dimensional array filled with the elements of x corresponding to the True values of obj. The search order will be row-major, C-style. If obj has True values at entries that are outside of the bounds of x, then an index error will be raised. If obj is smaller than x it is identical to filling it with False.
-
-A common use case for this is filtering for desired element values. For example, one may wish to select all entries from an array which are not NaN:
-
-x = np.array([[1., 2.], [np.nan, 3.], [np.nan, np.nan]])
-
-x[~np.isnan(x)]
-array([1., 2., 3.])
-
-Or wish to add a constant to all negative elements:
-
-x = np.array([1., -1., -2., 3])
-
-x[x < 0] += 20
-
-x
-array([ 1., 19., 18., 3.])
-
-In general if an index includes a Boolean array, the result will be identical to inserting obj.nonzero() into the same position and using the integer array indexing mechanism described above. x[ind_1, boolean_array, ind_2] is equivalent to x[(ind_1,) + boolean_array.nonzero() + (ind_2,)].
-
-If there is only one Boolean array and no integer indexing array present, this is straightforward. Care must only be taken to make sure that the boolean index has exactly as many dimensions as it is supposed to work with.
-
-In general, when the boolean array has fewer dimensions than the array being indexed, this is equivalent to x[b, ...], which means x is indexed by b followed by as many : as are needed to fill out the rank of x. Thus the shape of the result is one dimension containing the number of True elements of the boolean array, followed by the remaining dimensions of the array being indexed:
-
-x = np.arange(35).reshape(5, 7)
-
-b = x > 20
-
-b[:, 5]
-array([False, False, False,  True,  True])
-
-x[b[:, 5]]
-array([[21, 22, 23, 24, 25, 26, 27],
-      [28, 29, 30, 31, 32, 33, 34]])
-
-Here the 4th and 5th rows are selected from the indexed array and combined to make a 2-D array.
-
-Example
-
-From an array, select all rows which sum up to less or equal two:
-
-x = np.array([[0, 1], [1, 1], [2, 2]])
-
-rowsum = x.sum(-1)
-
-x[rowsum <= 2, :]
-array([[0, 1],
-       [1, 1]])
-
-Combining multiple Boolean indexing arrays or a Boolean with an integer indexing array can best be understood with the obj.nonzero() analogy. The function ix_ also supports boolean arrays and will work without any surprises.
-
-Example
-
-Use boolean indexing to select all rows adding up to an even number. At the same time columns 0 and 2 should be selected with an advanced integer index. Using the ix_ function this can be done with:
-
-x = np.array([[ 0,  1,  2],
-
-              [ 3,  4,  5],
-
-              [ 6,  7,  8],
-
-              [ 9, 10, 11]])
-
-rows = (x.sum(-1) % 2) == 0
-
-rows
-array([False,  True, False,  True])
-
-columns = [0, 2]
-
-x[np.ix_(rows, columns)]
-array([[ 3,  5],
-       [ 9, 11]])
-
-Without the np.ix_ call, only the diagonal elements would be selected.
-
-Or without np.ix_ (compare the integer array examples):
-
-rows = rows.nonzero()[0]
-
-x[rows[:, np.newaxis], columns]
-array([[ 3,  5],
-       [ 9, 11]])
-
-Example
-
-Use a 2-D boolean array of shape (2, 3) with four True elements to select rows from a 3-D array of shape (2, 3, 5) results in a 2-D result of shape (4, 5):
-
-x = np.arange(30).reshape(2, 3, 5)
-
-x
-array([[[ 0,  1,  2,  3,  4],
-        [ 5,  6,  7,  8,  9],
-        [10, 11, 12, 13, 14]],
-      [[15, 16, 17, 18, 19],
-        [20, 21, 22, 23, 24],
-        [25, 26, 27, 28, 29]]])
-
-b = np.array([[True, True, False], [False, True, True]])
-
-x[b]
-array([[ 0,  1,  2,  3,  4],
-      [ 5,  6,  7,  8,  9],
-      [20, 21, 22, 23, 24],
-      [25, 26, 27, 28, 29]])
-
-Combining advanced and basic indexing
-
-When there is at least one slice (:), ellipsis (...) or newaxis in the index (or the array has more dimensions than there are advanced indices), then the behaviour can be more complicated. It is like concatenating the indexing result for each advanced index element.
-
-In the simplest case, there is only a single advanced index combined with a slice. For example:
-
-y = np.arange(35).reshape(5,7)
-
-y[np.array([0, 2, 4]), 1:3]
-array([[ 1,  2],
-       [15, 16],
-       [29, 30]])
-
-In effect, the slice and index array operation are independent. The slice operation extracts columns with index 1 and 2, (i.e. the 2nd and 3rd columns), followed by the index array operation which extracts rows with index 0, 2 and 4 (i.e the first, third and fifth rows). This is equivalent to:
-
-y[:, 1:3][np.array([0, 2, 4]), :]
-array([[ 1,  2],
-       [15, 16],
-       [29, 30]])
-
-A single advanced index can, for example, replace a slice and the result array will be the same. However, it is a copy and may have a different memory layout. A slice is preferable when it is possible. For example:
-
-x = np.array([[ 0,  1,  2],
-
-              [ 3,  4,  5],
-
-              [ 6,  7,  8],
-
-              [ 9, 10, 11]])
-
-x[1:2, 1:3]
-array([[4, 5]])
-
-x[1:2, [1, 2]]
-array([[4, 5]])
-
-The easiest way to understand a combination of multiple advanced indices may be to think in terms of the resulting shape. There are two parts to the indexing operation, the subspace defined by the basic indexing (excluding integers) and the subspace from the advanced indexing part. Two cases of index combination need to be distinguished:
-
-    The advanced indices are separated by a slice, Ellipsis or newaxis. For example x[arr1, :, arr2].
-
-    The advanced indices are all next to each other. For example x[..., arr1, arr2, :] but not x[arr1, :, 1] since 1 is an advanced index in this regard.
-
-In the first case, the dimensions resulting from the advanced indexing operation come first in the result array, and the subspace dimensions after that. In the second case, the dimensions from the advanced indexing operations are inserted into the result array at the same spot as they were in the initial array (the latter logic is what makes simple advanced indexing behave just like slicing).
-
-Example
-
-Suppose x.shape is (10, 20, 30) and ind is a (2, 3, 4)-shaped indexing intp array, then result = x[..., ind, :] has shape (10, 2, 3, 4, 30) because the (20,)-shaped subspace has been replaced with a (2, 3, 4)-shaped broadcasted indexing subspace. If we let i, j, k loop over the (2, 3, 4)-shaped subspace then result[..., i, j, k, :] = x[..., ind[i, j, k], :]. This example produces the same result as x.take(ind, axis=-2).
-
-Example
-
-Let x.shape be (10, 20, 30, 40, 50) and suppose ind_1 and ind_2 can be broadcast to the shape (2, 3, 4). Then x[:, ind_1, ind_2] has shape (10, 2, 3, 4, 40, 50) because the (20, 30)-shaped subspace from X has been replaced with the (2, 3, 4) subspace from the indices. However, x[:, ind_1, :, ind_2] has shape (2, 3, 4, 10, 30, 50) because there is no unambiguous place to drop in the indexing subspace, thus it is tacked-on to the beginning. It is always possible to use .transpose() to move the subspace anywhere desired. Note that this example cannot be replicated using take.
-
-Example
-
-Slicing can be combined with broadcasted boolean indices:
-
-x = np.arange(35).reshape(5, 7)
-
-b = x > 20
-
-b
-array([[False, False, False, False, False, False, False],
-      [False, False, False, False, False, False, False],
-      [False, False, False, False, False, False, False],
-      [ True,  True,  True,  True,  True,  True,  True],
-      [ True,  True,  True,  True,  True,  True,  True]])
-
-x[b[:, 5], 1:3]
-array([[22, 23],
-      [29, 30]])
-
-Field access
-
-See also
-
-Structured arrays
-
-If the ndarray object is a structured array the fields of the array can be accessed by indexing the array with strings, dictionary-like.
-
-Indexing x['field-name'] returns a new view to the array, which is of the same shape as x (except when the field is a sub-array) but of data type x.dtype['field-name'] and contains only the part of the data in the specified field. Also, record array scalars can be “indexed” this way.
-
-Indexing into a structured array can also be done with a list of field names, e.g. x[['field-name1', 'field-name2']]. As of NumPy 1.16, this returns a view containing only those fields. In older versions of NumPy, it returned a copy. See the user guide section on Structured arrays for more information on multifield indexing.
-
-If the accessed field is a sub-array, the dimensions of the sub-array are appended to the shape of the result. For example:
-
-x = np.zeros((2, 2), dtype=[('a', np.int32), ('b', np.float64, (3, 3))])
-
-x['a'].shape
-(2, 2)
-
-x['a'].dtype
-dtype('int32')
-
-x['b'].shape
-(2, 2, 3, 3)
-
-x['b'].dtype
-dtype('float64')
-
-Flat Iterator indexing
-
-x.flat returns an iterator that will iterate over the entire array (in C-contiguous style with the last index varying the fastest). This iterator object can also be indexed using basic slicing or advanced indexing as long as the selection object is not a tuple. This should be clear from the fact that x.flat is a 1-dimensional view. It can be used for integer indexing with 1-dimensional C-style-flat indices. The shape of any returned array is therefore the shape of the integer indexing object.
-Assigning values to indexed arrays
-
-As mentioned, one can select a subset of an array to assign to using a single index, slices, and index and mask arrays. The value being assigned to the indexed array must be shape consistent (the same shape or broadcastable to the shape the index produces). For example, it is permitted to assign a constant to a slice:
-
-x = np.arange(10)
-
-x[2:7] = 1
-
-or an array of the right size:
-
-x[2:7] = np.arange(5)
-
-Note that assignments may result in changes if assigning higher types to lower types (like floats to ints) or even exceptions (assigning complex to floats or ints):
-
-x[1] = 1.2
-
-x[1]
-1
-
-x[1] = 1.2j
-Traceback (most recent call last):
-  ...
-TypeError: can't convert complex to int
-
-Unlike some of the references (such as array and mask indices) assignments are always made to the original data in the array (indeed, nothing else would make sense!). Note though, that some actions may not work as one may naively expect. This particular example is often surprising to people:
-
-x = np.arange(0, 50, 10)
-
-x
-array([ 0, 10, 20, 30, 40])
-
-x[np.array([1, 1, 3, 1])] += 1
-
-x
-array([ 0, 11, 20, 31, 40])
-
-Where people expect that the 1st location will be incremented by 3. In fact, it will only be incremented by 1. The reason is that a new array is extracted from the original (as a temporary) containing the values at 1, 1, 3, 1, then the value 1 is added to the temporary, and then the temporary is assigned back to the original array. Thus the value of the array at x[1] + 1 is assigned to x[1] three times, rather than being incremented 3 times.
-Dealing with variable numbers of indices within programs
-
-The indexing syntax is very powerful but limiting when dealing with a variable number of indices. For example, if you want to write a function that can handle arguments with various numbers of dimensions without having to write special case code for each number of possible dimensions, how can that be done? If one supplies to the index a tuple, the tuple will be interpreted as a list of indices. For example:
-
-z = np.arange(81).reshape(3, 3, 3, 3)
-
-indices = (1, 1, 1, 1)
-
-z[indices]
-40
-
-So one can use code to construct tuples of any number of indices and then use these within an index.
-
-Slices can be specified within programs by using the slice() function in Python. For example:
-
-indices = (1, 1, 1, slice(0, 2))  # same as [1, 1, 1, 0:2]
-
-z[indices]
-array([39, 40])
-
-Likewise, ellipsis can be specified by code by using the Ellipsis object:
-
-indices = (1, Ellipsis, 1)  # same as [1, ..., 1]
-
-z[indices]
-array([[28, 31, 34],
-       [37, 40, 43],
-       [46, 49, 52]])
-
-For this reason, it is possible to use the output from the np.nonzero() function directly as an index since it always returns a tuple of index arrays.
-
-Because of the special treatment of tuples, they are not automatically converted to an array as a list would be. As an example:
-
-z[[1, 1, 1, 1]]  # produces a large array
-array([[[[27, 28, 29],
-         [30, 31, 32], ...
-
-z[(1, 1, 1, 1)]  # returns a single value
-40
-
-Detailed notes
-
-These are some detailed notes, which are not of importance for day to day indexing (in no particular order):
-
-    The native NumPy indexing type is intp and may differ from the default integer array type. intp is the smallest data type sufficient to safely index any array; for advanced indexing it may be faster than other types.
-
-    For advanced assignments, there is in general no guarantee for the iteration order. This means that if an element is set more than once, it is not possible to predict the final result.
-
-    An empty (tuple) index is a full scalar index into a zero-dimensional array. x[()] returns a scalar if x is zero-dimensional and a view otherwise. On the other hand, x[...] always returns a view.
-
-    If a zero-dimensional array is present in the index and it is a full integer index the result will be a scalar and not a zero-dimensional array. (Advanced indexing is not triggered.)
-
-    When an ellipsis (...) is present but has no size (i.e. replaces zero :) the result will still always be an array. A view if no advanced index is present, otherwise a copy.
-
-    The nonzero equivalence for Boolean arrays does not hold for zero dimensional boolean arrays.
-
-    When the result of an advanced indexing operation has no elements but an individual index is out of bounds, whether or not an IndexError is raised is undefined (e.g. x[[], [123]] with 123 being out of bounds).
-
-    When a casting error occurs during assignment (for example updating a numerical array using a sequence of strings), the array being assigned to may end up in an unpredictable partially updated state. However, if any other error (such as an out of bounds index) occurs, the array will remain unchanged.
-
-    The memory layout of an advanced indexing result is optimized for each indexing operation and no particular memory order can be assumed.
-
-    When using a subclass (especially one which manipulates its shape), the default ndarray.__setitem__ behaviour will call __getitem__ for basic indexing but not for advanced indexing. For such a subclass it may be preferable to call ndarray.__setitem__ with a base class ndarray view on the data. This must be done if the subclasses __getitem__ does not return views.
-
-previous
-
-Array creation
-
-next
-
-I/O with NumPy
-
-© Copyright 2008-2022, NumPy Developers.
-
-Created using Sphinx 4.5.0.
diff --git a/tests/integrated/test-boutpp/slicing/slicingexamples b/tests/integrated/test-boutpp/slicing/slicingexamples
deleted file mode 100644
index 7edb2fa5bc..0000000000
--- a/tests/integrated/test-boutpp/slicing/slicingexamples
+++ /dev/null
@@ -1 +0,0 @@
-,
diff --git a/tests/integrated/test-boutpp/slicing/test.py b/tests/integrated/test-boutpp/slicing/test.py
deleted file mode 100644
index 2f36b362cb..0000000000
--- a/tests/integrated/test-boutpp/slicing/test.py
+++ /dev/null
@@ -1,4 +0,0 @@
-import boutcore as bc
-
-bc.init("-d test")
-bc.print("We can print to the log from python 🎉")

From 10d320f700ed1fc8da6d356e52aaacfa23a8c665 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 15 Feb 2024 22:04:49 +0100
Subject: [PATCH 0063/1827] Use parallel_neumann as BC

---
 tests/integrated/test-fci-mpi/fci_mpi.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-fci-mpi/fci_mpi.cxx b/tests/integrated/test-fci-mpi/fci_mpi.cxx
index 6ae711351e..e19572c52c 100644
--- a/tests/integrated/test-fci-mpi/fci_mpi.cxx
+++ b/tests/integrated/test-fci-mpi/fci_mpi.cxx
@@ -20,7 +20,7 @@ int main(int argc, char** argv) {
                                                   Options::getRoot(), mesh)};
       // options->get(fmt::format("input_{:d}:boundary_perp", i), temp_str, s"free_o3");
       mesh->communicate(input);
-      input.applyParallelBoundary("parallel_neumann_o2");
+      input.applyParallelBoundary("parallel_neumann");
       for (int slice = -mesh->ystart; slice <= mesh->ystart; ++slice) {
         if (slice) {
           Field3D tmp{0.};

From 4b05708bb5def102ff83920a38e4396542c36901 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 15 Feb 2024 22:05:04 +0100
Subject: [PATCH 0064/1827] fix usage of f-string

---
 tests/integrated/test-fci-mpi/runtest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-fci-mpi/runtest b/tests/integrated/test-fci-mpi/runtest
index e12b330326..6676f8f7a5 100755
--- a/tests/integrated/test-fci-mpi/runtest
+++ b/tests/integrated/test-fci-mpi/runtest
@@ -40,7 +40,7 @@ for nslice in nslices:
         _, out = launch_safe(cmd, nproc=NXPE * NYPE, mthread=mthread, pipe=True)
 
         # Save output to log file
-        with open("run.log.{NXPE}.{NYPE}.{nslice}.log", "w") as f:
+        with open(f"run.log.{NXPE}.{NYPE}.{nslice}.log", "w") as f:
             f.write(out)
 
         collect_kw = dict(info=False, xguards=False, yguards=False, path="data")

From 60224e4292254f2a7954550fc03002fde165d303 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 19 Feb 2024 14:05:26 +0100
Subject: [PATCH 0065/1827] Use localmesh

mesh may not be initialised or be a different mesh
---
 src/mesh/interpolation/hermite_spline_xz.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index f167a7576d..c0040d096e 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -140,8 +140,8 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* mesh)
   // PetscInt N, 			      PetscInt d_nz, const PetscInt d_nnz[],
   // PetscInt o_nz, const PetscInt o_nnz[], Mat *A)
   //  MatSetSizes(Mat A,PetscInt m,PetscInt n,PetscInt M,PetscInt N)
-  const int m = mesh->LocalNx * mesh->LocalNy * mesh->LocalNz;
-  const int M = m * mesh->getNXPE() * mesh->getNYPE();
+  const int m = localmesh->LocalNx * localmesh->LocalNy * localmesh->LocalNz;
+  const int M = m * localmesh->getNXPE() * localmesh->getNYPE();
   MatCreateAIJ(MPI_COMM_WORLD, m, m, M, M, 16, nullptr, 16, nullptr, &petscWeights);
 #endif
 #endif

From 608bb5d15575236589d4956dd4c241a493067f15 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 19 Feb 2024 14:52:48 +0100
Subject: [PATCH 0066/1827] add PETSc requirement for MPI test

---
 tests/integrated/test-fci-mpi/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/integrated/test-fci-mpi/CMakeLists.txt b/tests/integrated/test-fci-mpi/CMakeLists.txt
index 6a1ec33ac6..0dd38487a3 100644
--- a/tests/integrated/test-fci-mpi/CMakeLists.txt
+++ b/tests/integrated/test-fci-mpi/CMakeLists.txt
@@ -5,4 +5,5 @@ bout_add_mms_test(test-fci-mpi
   PROCESSORS 6
   DOWNLOAD https://zenodo.org/record/7614499/files/W7X-conf4-36x8x128.fci.nc?download=1
   DOWNLOAD_NAME grid.fci.nc
+  REQUIRES BOUT_HAS_PETSC
 )

From 88741c5b26e1b318e1d4d167a595814b4eac041f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 19 Feb 2024 14:53:06 +0100
Subject: [PATCH 0067/1827] Update header location

---
 tests/integrated/test-fci-mpi/fci_mpi.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/integrated/test-fci-mpi/fci_mpi.cxx b/tests/integrated/test-fci-mpi/fci_mpi.cxx
index e19572c52c..d102a7c8e3 100644
--- a/tests/integrated/test-fci-mpi/fci_mpi.cxx
+++ b/tests/integrated/test-fci-mpi/fci_mpi.cxx
@@ -1,6 +1,6 @@
-#include "bout.hxx"
-#include "derivs.hxx"
-#include "field_factory.hxx"
+#include "bout/bout.hxx"
+#include "bout/derivs.hxx"
+#include "bout/field_factory.hxx"
 
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);

From 09f609b96a42e0e3df3a701472236d2c516c4b68 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 19 Feb 2024 17:29:18 +0100
Subject: [PATCH 0068/1827] More const correctness

---
 tests/integrated/test-fci-mpi/fci_mpi.cxx            |  4 ++--
 .../integrated/test-interpolate/test_interpolate.cxx | 12 ++++++------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/integrated/test-fci-mpi/fci_mpi.cxx b/tests/integrated/test-fci-mpi/fci_mpi.cxx
index d102a7c8e3..f4c26adc96 100644
--- a/tests/integrated/test-fci-mpi/fci_mpi.cxx
+++ b/tests/integrated/test-fci-mpi/fci_mpi.cxx
@@ -8,7 +8,7 @@ int main(int argc, char** argv) {
     using bout::globals::mesh;
     Options* options = Options::getRoot();
     int i = 0;
-    std::string default_str{"not_set"};
+    const std::string default_str{"not_set"};
     Options dump;
     while (true) {
       std::string temp_str;
@@ -22,7 +22,7 @@ int main(int argc, char** argv) {
       mesh->communicate(input);
       input.applyParallelBoundary("parallel_neumann");
       for (int slice = -mesh->ystart; slice <= mesh->ystart; ++slice) {
-        if (slice) {
+        if (slice != 0) {
           Field3D tmp{0.};
           BOUT_FOR(i, tmp.getRegion("RGN_NOBNDRY")) {
             tmp[i] = input.ynext(slice)[i.yp(slice)];
diff --git a/tests/integrated/test-interpolate/test_interpolate.cxx b/tests/integrated/test-interpolate/test_interpolate.cxx
index 7b0ced5a21..33963dbb9e 100644
--- a/tests/integrated/test-interpolate/test_interpolate.cxx
+++ b/tests/integrated/test-interpolate/test_interpolate.cxx
@@ -32,30 +32,30 @@ int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
   {
     // Random number generator
-    std::default_random_engine generator;
+    const std::default_random_engine generator;
     // Uniform distribution of BoutReals from 0 to 1
-    std::uniform_real_distribution<BoutReal> distribution{0.0, 1.0};
+    const std::uniform_real_distribution<BoutReal> distribution{0.0, 1.0};
 
     using bout::globals::mesh;
 
-    FieldFactory f(mesh);
+    const FieldFactory fieldfact(mesh);
 
     // Set up generators and solutions for three different analtyic functions
     std::string a_func;
     auto a_gen = getGeneratorFromOptions("a", a_func);
-    Field3D a = f.create3D(a_func);
+    const Field3D a = fieldfact.create3D(a_func);
     Field3D a_solution = 0.0;
     Field3D a_interp = 0.0;
 
     std::string b_func;
     auto b_gen = getGeneratorFromOptions("b", b_func);
-    Field3D b = f.create3D(b_func);
+    const Field3D b = fieldfact.create3D(b_func);
     Field3D b_solution = 0.0;
     Field3D b_interp = 0.0;
 
     std::string c_func;
     auto c_gen = getGeneratorFromOptions("c", c_func);
-    Field3D c = f.create3D(c_func);
+    const Field3D c = fieldfact.create3D(c_func);
     Field3D c_solution = 0.0;
     Field3D c_interp = 0.0;
 

From f6ae060d4a0e38e37968a6ff21ee13cd21d0a50f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 1 Mar 2024 20:46:47 +0100
Subject: [PATCH 0069/1827] Add MIT License text

include/bout/generic_factory.hxx is licensed under the MIT License
based on Modern C++ Design/Loki by A. Alexandrescu
---
 LICENSE.MIT | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 LICENSE.MIT

diff --git a/LICENSE.MIT b/LICENSE.MIT
new file mode 100644
index 0000000000..14e2e075df
--- /dev/null
+++ b/LICENSE.MIT
@@ -0,0 +1,19 @@
+Copyright (c) <year> <copyright holders>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

From d344f421d6234df0eb44c3362d36004d6f537d84 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 14 Mar 2024 13:57:27 +0100
Subject: [PATCH 0070/1827] Revert "Docs: Don't include boutdata/boututils in
 docs"

This reverts commit e6bc5c5d0e85b5e895b124b066bbf62aed6c45b1.

The commit tried to make boutuitls and boutdata non-importable for the
documentation tool.  If those modules should be remove from the
documentation, this can be achieved by removing them from
manual/sphinx/_apidoc/. This should not break the documentation fro
boutpp or boutconfig.
---
 manual/sphinx/conf.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 67507633b6..62f7b1c06f 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -31,8 +31,7 @@
 import subprocess
 import sys
 
-sys.path.append("../../tools/pylib/boutpp")
-sys.path.append("../../tools/pylib/boutconfig")
+sys.path.append("../../tools/pylib")
 
 # Are we running on readthedocs?
 on_readthedocs = os.environ.get("READTHEDOCS") == "True"

From fee27c95cbf1ac53eb2e7612293e90716548f761 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 3 Nov 2023 11:51:03 +0100
Subject: [PATCH 0071/1827] Dump field before and after rhs evaluation for
 debugging

---
 src/solver/impls/pvode/pvode.cxx | 43 ++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index b2cfd233a9..8a51a9cb19 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -293,6 +293,49 @@ BoutReal PvodeSolver::run(BoutReal tout) {
   // Check return flag
   if (flag != SUCCESS) {
     output_error.write("ERROR CVODE step failed, flag = {:d}\n", flag);
+    CVodeMemRec* cv_mem = (CVodeMem)cvode_mem;
+    if (f2d.empty() and v2d.empty() and v3d.empty()) {
+      Options debug{};
+      using namespace std::string_literals;
+      Mesh* mesh{};
+      for (const auto& prefix : {"pre_"s, "residuum_"s}) {
+        std::vector<Field3D> ffs{};
+        std::vector<bool> evolve_bndrys{};
+        for (const auto& f : f3d) {
+          Field3D ff{0.};
+          ff.allocate();
+          ff.setLocation(f.location);
+          mesh = ff.getMesh();
+          debug[fmt::format("{:s}{:s}", prefix, f.name)] = ff;
+          ffs.push_back(ff);
+          evolve_bndrys.push_back(f.evolve_bndry);
+        }
+        pvode_load_data_f3d(evolve_bndrys, ffs,
+                            prefix == "pre_"s ? udata : N_VDATA(cv_mem->cv_acor));
+      }
+
+      for (auto& f : f3d) {
+        f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug);
+	setName(f.var, f.name);
+      }
+      run_rhs(simtime);
+
+      for (auto& f : f3d) {
+	debug[f.name] = *f.var;
+      }
+
+      if (mesh) {
+        mesh->outputVars(debug);
+        debug["BOUT_VERSION"].force(bout::version::as_double);
+      }
+
+      std::string outname = fmt::format(
+          "{}/BOUT.debug.{}.nc",
+          Options::root()["datadir"].withDefault<std::string>("data"), BoutComm::rank());
+
+      bout::OptionsNetCDF(outname).write(debug);
+      MPI_Barrier(BoutComm::get());
+    }
     return (-1.0);
   }
 

From 96da2e9f88e313f4dd388b2c83d701046aedf96c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 3 Nov 2023 11:49:32 +0100
Subject: [PATCH 0072/1827] Add setName function

---
 include/bout/field.hxx | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index c0693ec0fb..0867560c3b 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -683,4 +683,12 @@ inline T floor(const T& var, BoutReal f, const std::string& rgn = "RGN_ALL") {
 
 #undef FIELD_FUNC
 
+template <typename T, typename = bout::utils::EnableIfField<T>, class... Types>
+inline T setName(T&& f, const std::string& name, Types... args) {
+#if BOUT_USE_TRACK
+  f.name = fmt::format(name, args...);
+#endif
+  return f;
+}
+
 #endif /* FIELD_H */

From e56981ceeb0409d7d48d81e1225e7332c0346519 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 19 Jun 2023 09:33:00 +0200
Subject: [PATCH 0073/1827] Set div_par and grad_par names

---
 src/mesh/coordinates.cxx | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 01f0fe46ca..3948c75b94 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1542,7 +1542,11 @@ Field3D Coordinates::Grad_par(const Field3D& var, CELL_LOC outloc,
   TRACE("Coordinates::Grad_par( Field3D )");
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
-  return ::DDY(var, outloc, method) * invSg();
+  if (invSg == nullptr) {
+    invSg = std::make_unique<FieldMetric>();
+    (*invSg) = 1.0 / sqrt(g_22);
+  }
+  return setName(::DDY(var, outloc, method) * invSg(), "Grad_par({:s})", var.name);
 }
 
 /////////////////////////////////////////////////////////
@@ -1601,7 +1605,7 @@ Field3D Coordinates::Div_par(const Field3D& f, CELL_LOC outloc,
     f_B.yup(i) = f.yup(i) / Bxy_floc.yup(i);
     f_B.ydown(i) = f.ydown(i) / Bxy_floc.ydown(i);
   }
-  return Bxy * Grad_par(f_B, outloc, method);
+  return setName(Bxy * Grad_par(f_B, outloc, method), "Div_par({:s})", f.name);
 }
 
 /////////////////////////////////////////////////////////

From 6b2c132e3db61fa4f453e43a6988e8534f6c0a43 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 19 Jun 2023 09:32:25 +0200
Subject: [PATCH 0074/1827] Dump debug file if PVODE fails

Use the new track feature (better name required) to dump the different
components of the ddt() as well as the residuum for the evolved fields.
---
 src/solver/impls/pvode/pvode.cxx | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 8a51a9cb19..7283b7d0eb 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -42,12 +42,39 @@
 #include <pvode/iterativ.h> // contains the enum for types of preconditioning
 #include <pvode/pvbbdpre.h> // band preconditioner function prototypes
 
+#include <string>
+
 using namespace pvode;
 
 void solver_f(integer N, BoutReal t, N_Vector u, N_Vector udot, void* f_data);
 void solver_gloc(integer N, BoutReal t, BoutReal* u, BoutReal* udot, void* f_data);
 void solver_cfn(integer N, BoutReal t, N_Vector u, void* f_data);
 
+namespace {
+// local only
+void pvode_load_data_f3d(const std::vector<bool>& evolve_bndrys,
+                         std::vector<Field3D>& ffs, BoutReal* udata) {
+  int p = 0;
+  Mesh* mesh = ffs[0].getMesh();
+  const int nz = mesh->LocalNz;
+  for (const auto& bndry : {true, false}) {
+    for (const auto& i2d : mesh->getRegion2D(bndry ? "RGN_BNDRY" : "RGN_NOBNDRY")) {
+      for (int jz = 0; jz < nz; jz++) {
+        // Loop over 3D variables
+        std::vector<bool>::const_iterator evolve_bndry = evolve_bndrys.begin();
+        for (std::vector<Field3D>::iterator ff = ffs.begin(); ff != ffs.end(); ++ff) {
+          if (bndry && !*evolve_bndry)
+            continue;
+          (*ff)[mesh->ind2Dto3D(i2d, jz)] = udata[p];
+          p++;
+        }
+        ++evolve_bndry;
+      }
+    }
+  }
+}
+} // namespace
+
 const BoutReal ZERO = 0.0;
 
 long int iopt[OPT_SIZE];

From df2d66189f4d2e87cc024521ad287936b9c0ba85 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 19 Jun 2023 09:27:19 +0200
Subject: [PATCH 0075/1827] Add tracking to Field3D

This keeps track of all the changes done to the field and stores them to
a OptionsObject.
---
 include/bout/field3d.hxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index ba8c8e879e..8992575be6 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -514,6 +514,13 @@ private:
 
   /// RegionID over which the field is valid
   std::optional<size_t> regionID;
+
+  int tracking_state{0};
+  Options* tracking{nullptr};
+  std::string selfname{""};
+  template <class T>
+  Options* track(const T& change, std::string op);
+  Options* track(const BoutReal& change, std::string op);
 };
 
 // Non-member overloaded operators

From 263f9fedaad854832bfdbf6a5ac9322eb492c71e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 19 Jun 2023 09:27:19 +0200
Subject: [PATCH 0076/1827] Add tracking to Field3D

This keeps track of all the changes done to the field and stores them to
a OptionsObject.
---
 include/bout/field3d.hxx         |   4 +
 src/field/field3d.cxx            |  44 ++++
 src/field/gen_fieldops.jinja     |  14 ++
 src/field/generated_fieldops.cxx | 348 +++++++++++++++++++++++++++++++
 4 files changed, 410 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 8992575be6..bf7a9cc180 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -295,6 +295,10 @@ public:
   /// cuts on closed field lines?
   bool requiresTwistShift(bool twist_shift_enabled);
 
+  /// Enable a special tracking mode for debugging
+  /// Save all changes that, are done to the field, to tracking
+  Field3D& enableTracking(const std::string& name, Options& tracking);
+
   /////////////////////////////////////////////////////////
   // Data access
 
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 011353f34a..f0f088b656 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -243,6 +243,7 @@ Field3D& Field3D::operator=(const Field3D& rhs) {
   }
 
   TRACE("Field3D: Assignment from Field3D");
+  track(rhs, "operator=");
 
   // Copy base slice
   Field::operator=(rhs);
@@ -263,6 +264,7 @@ Field3D& Field3D::operator=(const Field3D& rhs) {
 
 Field3D& Field3D::operator=(Field3D&& rhs) {
   TRACE("Field3D: Assignment from Field3D");
+  track(rhs, "operator=");
 
   // Move parallel slices or delete existing ones.
   yup_fields = std::move(rhs.yup_fields);
@@ -283,6 +285,7 @@ Field3D& Field3D::operator=(Field3D&& rhs) {
 
 Field3D& Field3D::operator=(const Field2D& rhs) {
   TRACE("Field3D = Field2D");
+  track(rhs, "operator=");
 
   /// Check that the data is allocated
   ASSERT1(rhs.isAllocated());
@@ -327,6 +330,7 @@ void Field3D::operator=(const FieldPerp& rhs) {
 
 Field3D& Field3D::operator=(const BoutReal val) {
   TRACE("Field3D = BoutReal");
+  track(val, "operator=");
 
   // Delete existing parallel slices. We don't copy parallel slices, so any
   // that currently exist will be incorrect.
@@ -831,3 +835,43 @@ Field3D::getValidRegionWithDefault(const std::string& region_name) const {
 void Field3D::setRegion(const std::string& region_name) {
   regionID = fieldmesh->getRegionID(region_name);
 }
+
+Field3D& Field3D::enableTracking(const std::string& name, Options& _tracking) {
+  tracking = &_tracking;
+  tracking_state = 1;
+  selfname = name;
+  return *this;
+}
+
+template <class T>
+Options* Field3D::track(const T& change, std::string op) {
+  if (tracking and tracking_state) {
+    const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
+    tracking->set(outname, change, "tracking");
+    (*tracking)[outname].setAttributes({
+      {"operation", op},
+#if BOUT_USE_TRACK
+          {"rhs.name", change.name},
+#endif
+    });
+    return &(*tracking)[outname];
+  }
+  return nullptr;
+}
+
+template Options* Field3D::track<Field3D>(const Field3D&, std::string);
+template Options* Field3D::track<Field2D>(const Field2D&, std::string);
+template Options* Field3D::track<FieldPerp>(const FieldPerp&, std::string);
+
+Options* Field3D::track(const BoutReal& change, std::string op) {
+  if (tracking and tracking_state) {
+    const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
+    tracking->set(outname, change, "tracking");
+    (*tracking)[outname].setAttributes({
+        {"operation", op},
+        {"rhs.name", "BR"},
+    });
+    return &(*tracking)[outname];
+  }
+  return nullptr;
+}
diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index ecd4e628cc..58b1ae28ba 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -61,6 +61,10 @@
 	}
   {% endif %}
 
+#if BOUT_USE_TRACK
+  {{out.name}}.name = fmt::format("{:s} {{operator}} {:s}", {{'"BR"' if lhs == "BoutReal" else lhs.name + ".name"}}
+  		      				     	  , {{'"BR"' if rhs == "BoutReal" else rhs.name + ".name"}});
+#endif
   checkData({{out.name}});
   return {{out.name}};
 }
@@ -129,9 +133,19 @@
     }
   {% endif %}
 
+  {% if lhs == "Field3D" %}
+    track(rhs, "operator{{operator}}=");
+  {% endif %}
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} {{operator}}= {:s}", this->name, {{'"BR"' if rhs == "BoutReal" else rhs.name + ".name"}});
+#endif
+
     checkData(*this);
 
   } else {
+  {% if lhs == "Field3D" %}
+    track(rhs, "operator{{operator}}=");
+  {% endif %}
     (*this) = (*this) {{operator}} {{rhs.name}};
   }
   return *this;
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 6b778acee3..3495d87dbc 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -20,6 +20,9 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] * rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -42,9 +45,15 @@ Field3D& Field3D::operator*=(const Field3D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
 
+    track(rhs, "operator*=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator*=");
     (*this) = (*this) * rhs;
   }
   return *this;
@@ -64,6 +73,9 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] / rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -86,9 +98,15 @@ Field3D& Field3D::operator/=(const Field3D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
 
+    track(rhs, "operator/=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator/=");
     (*this) = (*this) / rhs;
   }
   return *this;
@@ -108,6 +126,9 @@ Field3D operator+(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] + rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -130,9 +151,15 @@ Field3D& Field3D::operator+=(const Field3D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
 
+    track(rhs, "operator+=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator+=");
     (*this) = (*this) + rhs;
   }
   return *this;
@@ -152,6 +179,9 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] - rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -174,9 +204,15 @@ Field3D& Field3D::operator-=(const Field3D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
 
+    track(rhs, "operator-=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator-=");
     (*this) = (*this) - rhs;
   }
   return *this;
@@ -201,6 +237,9 @@ Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
     }
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -226,9 +265,15 @@ Field3D& Field3D::operator*=(const Field2D& rhs) {
       }
     }
 
+    track(rhs, "operator*=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator*=");
     (*this) = (*this) * rhs;
   }
   return *this;
@@ -254,6 +299,9 @@ Field3D operator/(const Field3D& lhs, const Field2D& rhs) {
     }
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -280,9 +328,15 @@ Field3D& Field3D::operator/=(const Field2D& rhs) {
       }
     }
 
+    track(rhs, "operator/=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator/=");
     (*this) = (*this) / rhs;
   }
   return *this;
@@ -307,6 +361,9 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
     }
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -332,9 +389,15 @@ Field3D& Field3D::operator+=(const Field2D& rhs) {
       }
     }
 
+    track(rhs, "operator+=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator+=");
     (*this) = (*this) + rhs;
   }
   return *this;
@@ -359,6 +422,9 @@ Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
     }
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -384,9 +450,15 @@ Field3D& Field3D::operator-=(const Field2D& rhs) {
       }
     }
 
+    track(rhs, "operator-=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator-=");
     (*this) = (*this) - rhs;
   }
   return *this;
@@ -408,6 +480,9 @@ FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] * rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -428,6 +503,9 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] / rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -448,6 +526,9 @@ FieldPerp operator+(const Field3D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] + rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -468,6 +549,9 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] - rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -485,6 +569,9 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * rhs;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -504,9 +591,15 @@ Field3D& Field3D::operator*=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
 
+    track(rhs, "operator*=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator*=");
     (*this) = (*this) * rhs;
   }
   return *this;
@@ -526,6 +619,9 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * tmp;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -546,9 +642,15 @@ Field3D& Field3D::operator/=(const BoutReal rhs) {
     const auto tmp = 1.0 / rhs;
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; }
 
+    track(rhs, "operator/=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator/=");
     (*this) = (*this) / rhs;
   }
   return *this;
@@ -567,6 +669,9 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] + rhs;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -586,9 +691,15 @@ Field3D& Field3D::operator+=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
 
+    track(rhs, "operator+=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator+=");
     (*this) = (*this) + rhs;
   }
   return *this;
@@ -607,6 +718,9 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] - rhs;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -626,9 +740,15 @@ Field3D& Field3D::operator-=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
 
+    track(rhs, "operator-=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
+    track(rhs, "operator-=");
     (*this) = (*this) - rhs;
   }
   return *this;
@@ -653,6 +773,9 @@ Field3D operator*(const Field2D& lhs, const Field3D& rhs) {
     }
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -676,6 +799,9 @@ Field3D operator/(const Field2D& lhs, const Field3D& rhs) {
     }
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -699,6 +825,9 @@ Field3D operator+(const Field2D& lhs, const Field3D& rhs) {
     }
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -722,6 +851,9 @@ Field3D operator-(const Field2D& lhs, const Field3D& rhs) {
     }
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -738,6 +870,9 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
     result[index] = lhs[index] * rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -754,6 +889,10 @@ Field2D& Field2D::operator*=(const Field2D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -774,6 +913,9 @@ Field2D operator/(const Field2D& lhs, const Field2D& rhs) {
     result[index] = lhs[index] / rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -790,6 +932,10 @@ Field2D& Field2D::operator/=(const Field2D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -810,6 +956,9 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
     result[index] = lhs[index] + rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -826,6 +975,10 @@ Field2D& Field2D::operator+=(const Field2D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -846,6 +999,9 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
     result[index] = lhs[index] - rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -862,6 +1018,10 @@ Field2D& Field2D::operator-=(const Field2D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -886,6 +1046,9 @@ FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] * rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -906,6 +1069,9 @@ FieldPerp operator/(const Field2D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] / rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -926,6 +1092,9 @@ FieldPerp operator+(const Field2D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] + rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -946,6 +1115,9 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] - rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -961,6 +1133,9 @@ Field2D operator*(const Field2D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * rhs;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -976,6 +1151,10 @@ Field2D& Field2D::operator*=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
@@ -996,6 +1175,9 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * tmp;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -1012,6 +1194,10 @@ Field2D& Field2D::operator/=(const BoutReal rhs) {
     const auto tmp = 1.0 / rhs;
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
@@ -1031,6 +1217,9 @@ Field2D operator+(const Field2D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] + rhs;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -1046,6 +1235,10 @@ Field2D& Field2D::operator+=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
@@ -1065,6 +1258,9 @@ Field2D operator-(const Field2D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] - rhs;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -1080,6 +1276,10 @@ Field2D& Field2D::operator-=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
@@ -1104,6 +1304,9 @@ FieldPerp operator*(const FieldPerp& lhs, const Field3D& rhs) {
     result[index] = lhs[index] * rhs[base_ind];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1126,6 +1329,10 @@ FieldPerp& FieldPerp::operator*=(const Field3D& rhs) {
       (*this)[index] *= rhs[base_ind];
     }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1150,6 +1357,9 @@ FieldPerp operator/(const FieldPerp& lhs, const Field3D& rhs) {
     result[index] = lhs[index] / rhs[base_ind];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1172,6 +1382,10 @@ FieldPerp& FieldPerp::operator/=(const Field3D& rhs) {
       (*this)[index] /= rhs[base_ind];
     }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1196,6 +1410,9 @@ FieldPerp operator+(const FieldPerp& lhs, const Field3D& rhs) {
     result[index] = lhs[index] + rhs[base_ind];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1218,6 +1435,10 @@ FieldPerp& FieldPerp::operator+=(const Field3D& rhs) {
       (*this)[index] += rhs[base_ind];
     }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1242,6 +1463,9 @@ FieldPerp operator-(const FieldPerp& lhs, const Field3D& rhs) {
     result[index] = lhs[index] - rhs[base_ind];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1264,6 +1488,10 @@ FieldPerp& FieldPerp::operator-=(const Field3D& rhs) {
       (*this)[index] -= rhs[base_ind];
     }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1288,6 +1516,9 @@ FieldPerp operator*(const FieldPerp& lhs, const Field2D& rhs) {
     result[index] = lhs[index] * rhs[base_ind];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1310,6 +1541,10 @@ FieldPerp& FieldPerp::operator*=(const Field2D& rhs) {
       (*this)[index] *= rhs[base_ind];
     }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1334,6 +1569,9 @@ FieldPerp operator/(const FieldPerp& lhs, const Field2D& rhs) {
     result[index] = lhs[index] / rhs[base_ind];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1356,6 +1594,10 @@ FieldPerp& FieldPerp::operator/=(const Field2D& rhs) {
       (*this)[index] /= rhs[base_ind];
     }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1380,6 +1622,9 @@ FieldPerp operator+(const FieldPerp& lhs, const Field2D& rhs) {
     result[index] = lhs[index] + rhs[base_ind];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1402,6 +1647,10 @@ FieldPerp& FieldPerp::operator+=(const Field2D& rhs) {
       (*this)[index] += rhs[base_ind];
     }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1426,6 +1675,9 @@ FieldPerp operator-(const FieldPerp& lhs, const Field2D& rhs) {
     result[index] = lhs[index] - rhs[base_ind];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1448,6 +1700,10 @@ FieldPerp& FieldPerp::operator-=(const Field2D& rhs) {
       (*this)[index] -= rhs[base_ind];
     }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1468,6 +1724,9 @@ FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs) {
     result[index] = lhs[index] * rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1484,6 +1743,10 @@ FieldPerp& FieldPerp::operator*=(const FieldPerp& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1504,6 +1767,9 @@ FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs) {
     result[index] = lhs[index] / rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1520,6 +1786,10 @@ FieldPerp& FieldPerp::operator/=(const FieldPerp& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1540,6 +1810,9 @@ FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs) {
     result[index] = lhs[index] + rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1556,6 +1829,10 @@ FieldPerp& FieldPerp::operator+=(const FieldPerp& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1576,6 +1853,9 @@ FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs) {
     result[index] = lhs[index] - rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1592,6 +1872,10 @@ FieldPerp& FieldPerp::operator-=(const FieldPerp& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
+#endif
+
     checkData(*this);
 
   } else {
@@ -1611,6 +1895,9 @@ FieldPerp operator*(const FieldPerp& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * rhs;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -1626,6 +1913,10 @@ FieldPerp& FieldPerp::operator*=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
@@ -1646,6 +1937,9 @@ FieldPerp operator/(const FieldPerp& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * tmp;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -1661,6 +1955,10 @@ FieldPerp& FieldPerp::operator/=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
@@ -1680,6 +1978,9 @@ FieldPerp operator+(const FieldPerp& lhs, const BoutReal rhs) {
     result[index] = lhs[index] + rhs;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -1695,6 +1996,10 @@ FieldPerp& FieldPerp::operator+=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
@@ -1714,6 +2019,9 @@ FieldPerp operator-(const FieldPerp& lhs, const BoutReal rhs) {
     result[index] = lhs[index] - rhs;
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, "BR");
+#endif
   checkData(result);
   return result;
 }
@@ -1729,6 +2037,10 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
 
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, "BR");
+#endif
+
     checkData(*this);
 
   } else {
@@ -1750,6 +2062,9 @@ Field3D operator*(const BoutReal lhs, const Field3D& rhs) {
     result[index] = lhs * rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1767,6 +2082,9 @@ Field3D operator/(const BoutReal lhs, const Field3D& rhs) {
     result[index] = lhs / rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1784,6 +2102,9 @@ Field3D operator+(const BoutReal lhs, const Field3D& rhs) {
     result[index] = lhs + rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1801,6 +2122,9 @@ Field3D operator-(const BoutReal lhs, const Field3D& rhs) {
     result[index] = lhs - rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1816,6 +2140,9 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
     result[index] = lhs * rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1831,6 +2158,9 @@ Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
     result[index] = lhs / rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1846,6 +2176,9 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
     result[index] = lhs + rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1861,6 +2194,9 @@ Field2D operator-(const BoutReal lhs, const Field2D& rhs) {
     result[index] = lhs - rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1876,6 +2212,9 @@ FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {
     result[index] = lhs * rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1891,6 +2230,9 @@ FieldPerp operator/(const BoutReal lhs, const FieldPerp& rhs) {
     result[index] = lhs / rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1906,6 +2248,9 @@ FieldPerp operator+(const BoutReal lhs, const FieldPerp& rhs) {
     result[index] = lhs + rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }
@@ -1921,6 +2266,9 @@ FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) {
     result[index] = lhs - rhs[index];
   }
 
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", "BR", rhs.name);
+#endif
   checkData(result);
   return result;
 }

From bac4ca92a31b60c40e87dd47b2ef764f571a58be Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 25 Apr 2023 09:16:38 +0200
Subject: [PATCH 0077/1827] cvode: Add option to use Adams Moulton solver
 instead of BDF

---
 src/solver/impls/pvode/pvode.cxx | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 7283b7d0eb..ae5cd783a8 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -214,7 +214,34 @@ int PvodeSolver::init() {
   }
   iopt[MXSTEP] = pvode_mxstep;
 
-  cvode_mem = CVodeMalloc(neq, solver_f, simtime, u, BDF, NEWTON, SS, &reltol, &abstol,
+  {
+    /* ropt[H0]      : initial step size. Optional input.             */
+
+    /* ropt[HMAX]    : maximum absolute value of step size allowed.   *
+     *                 Optional input. (Default is infinity).         */
+    const BoutReal hmax(
+        (*options)["max_timestep"].doc("Maximum internal timestep").withDefault(-1.));
+    if (hmax > 0) {
+      ropt[HMAX] = hmax;
+    }
+    /* ropt[HMIN]    : minimum absolute value of step size allowed.   *
+     *                 Optional input. (Default is 0.0).              */
+    const BoutReal hmin(
+        (*options)["min_timestep"].doc("Minimum internal timestep").withDefault(-1.));
+    if (hmin > 0) {
+      ropt[HMIN] = hmin;
+    }
+    /* iopt[MAXORD] : maximum lmm order to be used by the solver.     *
+     *                Optional input. (Default = 12 for ADAMS, 5 for  *
+     *                BDF).                                           */
+    const int maxOrder((*options)["max_order"].doc("Maximum order").withDefault(-1));
+    if (maxOrder > 0) {
+      iopt[MAXORD] = maxOrder;
+    }
+  }
+  const bool use_adam((*options)["adams_moulton"].doc("Use Adams Moulton solver instead of BDF").withDefault(false));
+
+  cvode_mem = CVodeMalloc(neq, solver_f, simtime, u, use_adam ? ADAMS : BDF, NEWTON, SS, &reltol, &abstol,
                           this, nullptr, optIn, iopt, ropt, machEnv);
 
   if (cvode_mem == nullptr) {

From 708bdcb2ff0a5c346edb43f7e609949b7c7afbd9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Mar 2023 12:59:22 +0200
Subject: [PATCH 0078/1827] Expose more pvode option to user

---
 src/solver/impls/pvode/pvode.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index ae5cd783a8..ac6e981b50 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -212,6 +212,9 @@ int PvodeSolver::init() {
   for (i = 0; i < OPT_SIZE; i++) {
     ropt[i] = ZERO;
   }
+  /* iopt[MXSTEP] : maximum number of internal steps to be taken by *
+   *                the solver in its attempt to reach tout.        *
+   *                Optional input. (Default = 500).                */
   iopt[MXSTEP] = pvode_mxstep;
 
   {

From d88b454aa2b2924a26a180440f956911c05a0abc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 19 Mar 2024 16:04:48 +0100
Subject: [PATCH 0079/1827] Fix bad cherry-pick

---
 src/mesh/coordinates.cxx | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 3948c75b94..32774d6229 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1542,10 +1542,6 @@ Field3D Coordinates::Grad_par(const Field3D& var, CELL_LOC outloc,
   TRACE("Coordinates::Grad_par( Field3D )");
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
-  if (invSg == nullptr) {
-    invSg = std::make_unique<FieldMetric>();
-    (*invSg) = 1.0 / sqrt(g_22);
-  }
   return setName(::DDY(var, outloc, method) * invSg(), "Grad_par({:s})", var.name);
 }
 

From 023bc41730de39040a50ae245363945d2447d63b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 19 Mar 2024 16:35:43 +0100
Subject: [PATCH 0080/1827] Update to new API

---
 include/bout/field.hxx           | 7 +++++++
 src/solver/impls/pvode/pvode.cxx | 4 ++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 0867560c3b..04035f5b76 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -683,6 +683,13 @@ inline T floor(const T& var, BoutReal f, const std::string& rgn = "RGN_ALL") {
 
 #undef FIELD_FUNC
 
+template <typename T, typename = bout::utils::EnableIfField<T>, class... Types>
+inline void setName(T& f, const std::string& name, Types... args) {
+#if BOUT_USE_TRACK
+  f.name = fmt::format(name, args...);
+#endif
+}
+
 template <typename T, typename = bout::utils::EnableIfField<T>, class... Types>
 inline T setName(T&& f, const std::string& name, Types... args) {
 #if BOUT_USE_TRACK
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index ac6e981b50..762fba32d1 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -373,7 +373,7 @@ BoutReal PvodeSolver::run(BoutReal tout) {
 
       for (auto& f : f3d) {
         f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug);
-	setName(f.var, f.name);
+	setName(*f.var, f.name);
       }
       run_rhs(simtime);
 
@@ -390,7 +390,7 @@ BoutReal PvodeSolver::run(BoutReal tout) {
           "{}/BOUT.debug.{}.nc",
           Options::root()["datadir"].withDefault<std::string>("data"), BoutComm::rank());
 
-      bout::OptionsNetCDF(outname).write(debug);
+      bout::OptionsIO::create(outname)->write(debug);
       MPI_Barrier(BoutComm::get());
     }
     return (-1.0);

From affc995c4ba482c79677c890cc44ccb47d45b648 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 19 Mar 2024 16:35:53 +0100
Subject: [PATCH 0081/1827] Fix documentation

---
 manual/sphinx/user_docs/bout_options.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst
index 85a8a17d59..330a0dad7e 100644
--- a/manual/sphinx/user_docs/bout_options.rst
+++ b/manual/sphinx/user_docs/bout_options.rst
@@ -889,7 +889,7 @@ Fields can also be stored and written::
   Options fields;
   fields["f2d"] = Field2D(1.0);
   fields["f3d"] = Field3D(2.0);
-  bout::OptionsIO::create("fields.nc").write(fields);
+  bout::OptionsIO::create("fields.nc")->write(fields);
 
 This allows the input settings and evolving variables to be
 combined into a single tree (see above on joining trees) and written

From 71f5b6adb6a8ad7b8941ba783773897906d870d2 Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Tue, 19 Mar 2024 15:50:33 +0000
Subject: [PATCH 0082/1827] Apply clang-format changes

---
 src/solver/impls/pvode/pvode.cxx | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 762fba32d1..a12f330964 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -242,10 +242,12 @@ int PvodeSolver::init() {
       iopt[MAXORD] = maxOrder;
     }
   }
-  const bool use_adam((*options)["adams_moulton"].doc("Use Adams Moulton solver instead of BDF").withDefault(false));
+  const bool use_adam((*options)["adams_moulton"]
+                          .doc("Use Adams Moulton solver instead of BDF")
+                          .withDefault(false));
 
-  cvode_mem = CVodeMalloc(neq, solver_f, simtime, u, use_adam ? ADAMS : BDF, NEWTON, SS, &reltol, &abstol,
-                          this, nullptr, optIn, iopt, ropt, machEnv);
+  cvode_mem = CVodeMalloc(neq, solver_f, simtime, u, use_adam ? ADAMS : BDF, NEWTON, SS,
+                          &reltol, &abstol, this, nullptr, optIn, iopt, ropt, machEnv);
 
   if (cvode_mem == nullptr) {
     throw BoutException("\tError: CVodeMalloc failed.\n");
@@ -373,12 +375,12 @@ BoutReal PvodeSolver::run(BoutReal tout) {
 
       for (auto& f : f3d) {
         f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug);
-	setName(*f.var, f.name);
+        setName(*f.var, f.name);
       }
       run_rhs(simtime);
 
       for (auto& f : f3d) {
-	debug[f.name] = *f.var;
+        debug[f.name] = *f.var;
       }
 
       if (mesh) {

From 31fd46153fad6977524394179d0b83ac51f26b9e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 20 Mar 2024 09:59:13 +0100
Subject: [PATCH 0083/1827] Apply recomendations from code-review

---
 include/bout/field3d.hxx         |  6 +++---
 src/field/field3d.cxx            | 10 +++++-----
 src/solver/impls/pvode/pvode.cxx |  5 +++--
 3 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index bf7a9cc180..cfde9e5328 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -521,10 +521,10 @@ private:
 
   int tracking_state{0};
   Options* tracking{nullptr};
-  std::string selfname{""};
+  std::string selfname;
   template <class T>
-  Options* track(const T& change, std::string op);
-  Options* track(const BoutReal& change, std::string op);
+  Options* track(const T& change, std::string operation);
+  Options* track(const BoutReal& change, std::string operation);
 };
 
 // Non-member overloaded operators
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index f0f088b656..2196d6eea4 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -844,12 +844,12 @@ Field3D& Field3D::enableTracking(const std::string& name, Options& _tracking) {
 }
 
 template <class T>
-Options* Field3D::track(const T& change, std::string op) {
-  if (tracking and tracking_state) {
+Options* Field3D::track(const T& change, std::string operation) {
+  if (tracking != nullptr and tracking_state != 0) {
     const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
     tracking->set(outname, change, "tracking");
     (*tracking)[outname].setAttributes({
-      {"operation", op},
+      {"operation", operation},
 #if BOUT_USE_TRACK
           {"rhs.name", change.name},
 #endif
@@ -863,12 +863,12 @@ template Options* Field3D::track<Field3D>(const Field3D&, std::string);
 template Options* Field3D::track<Field2D>(const Field2D&, std::string);
 template Options* Field3D::track<FieldPerp>(const FieldPerp&, std::string);
 
-Options* Field3D::track(const BoutReal& change, std::string op) {
+Options* Field3D::track(const BoutReal& change, std::string operation) {
   if (tracking and tracking_state) {
     const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
     tracking->set(outname, change, "tracking");
     (*tracking)[outname].setAttributes({
-        {"operation", op},
+        {"operation", operation},
         {"rhs.name", "BR"},
     });
     return &(*tracking)[outname];
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index a12f330964..f3a96b03af 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -53,7 +53,7 @@ void solver_cfn(integer N, BoutReal t, N_Vector u, void* f_data);
 namespace {
 // local only
 void pvode_load_data_f3d(const std::vector<bool>& evolve_bndrys,
-                         std::vector<Field3D>& ffs, BoutReal* udata) {
+                         std::vector<Field3D>& ffs, const BoutReal* udata) {
   int p = 0;
   Mesh* mesh = ffs[0].getMesh();
   const int nz = mesh->LocalNz;
@@ -63,8 +63,9 @@ void pvode_load_data_f3d(const std::vector<bool>& evolve_bndrys,
         // Loop over 3D variables
         std::vector<bool>::const_iterator evolve_bndry = evolve_bndrys.begin();
         for (std::vector<Field3D>::iterator ff = ffs.begin(); ff != ffs.end(); ++ff) {
-          if (bndry && !*evolve_bndry)
+          if (bndry && !*evolve_bndry) {
             continue;
+	  }
           (*ff)[mesh->ind2Dto3D(i2d, jz)] = udata[p];
           p++;
         }

From 17e46cfc1c0a835fea474ac68f64a9addbf4379f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 20 Mar 2024 10:02:28 +0100
Subject: [PATCH 0084/1827] Use more meaningful names

---
 src/solver/impls/pvode/pvode.cxx | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index f3a96b03af..c389a3c0d1 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -359,18 +359,18 @@ BoutReal PvodeSolver::run(BoutReal tout) {
       using namespace std::string_literals;
       Mesh* mesh{};
       for (const auto& prefix : {"pre_"s, "residuum_"s}) {
-        std::vector<Field3D> ffs{};
+        std::vector<Field3D> list_of_fields{};
         std::vector<bool> evolve_bndrys{};
         for (const auto& f : f3d) {
-          Field3D ff{0.};
-          ff.allocate();
-          ff.setLocation(f.location);
-          mesh = ff.getMesh();
-          debug[fmt::format("{:s}{:s}", prefix, f.name)] = ff;
-          ffs.push_back(ff);
+          mesh = f.var->getMesh();
+          Field3D to_load{0., mesh};
+          to_load.allocate();
+          to_load.setLocation(f.location);
+          debug[fmt::format("{:s}{:s}", prefix, f.name)] = to_load;
+          list_of_fields.push_back(to_load);
           evolve_bndrys.push_back(f.evolve_bndry);
         }
-        pvode_load_data_f3d(evolve_bndrys, ffs,
+        pvode_load_data_f3d(evolve_bndrys, list_of_fields,
                             prefix == "pre_"s ? udata : N_VDATA(cv_mem->cv_acor));
       }
 

From 9c0ae16ed905588b50f3e4fe634dcedf47de22b5 Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Wed, 20 Mar 2024 09:03:10 +0000
Subject: [PATCH 0085/1827] Apply clang-format changes

---
 src/solver/impls/pvode/pvode.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index c389a3c0d1..fe231e1086 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -65,7 +65,7 @@ void pvode_load_data_f3d(const std::vector<bool>& evolve_bndrys,
         for (std::vector<Field3D>::iterator ff = ffs.begin(); ff != ffs.end(); ++ff) {
           if (bndry && !*evolve_bndry) {
             continue;
-	  }
+          }
           (*ff)[mesh->ind2Dto3D(i2d, jz)] = udata[p];
           p++;
         }

From 4a17b4982df9788fc26407db70f14d0ce16098e3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 20 Mar 2024 10:04:52 +0100
Subject: [PATCH 0086/1827] Apply suggestions from code review

---
 src/solver/impls/pvode/pvode.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index fe231e1086..db28f64d86 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -384,12 +384,12 @@ BoutReal PvodeSolver::run(BoutReal tout) {
         debug[f.name] = *f.var;
       }
 
-      if (mesh) {
+      if (mesh != nullptr) {
         mesh->outputVars(debug);
         debug["BOUT_VERSION"].force(bout::version::as_double);
       }
 
-      std::string outname = fmt::format(
+      const std::string outname = fmt::format(
           "{}/BOUT.debug.{}.nc",
           Options::root()["datadir"].withDefault<std::string>("data"), BoutComm::rank());
 

From 2f7c3c0664c954c016b949ea8c199f6f35ac289f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 20 Mar 2024 16:02:22 +0100
Subject: [PATCH 0087/1827] Workaround for gcc 9.4

gcc 9.4 is unable to correctly parse the construction for the function
argument, if name.change is used directly. First making a copy seems to work
around that issue.
---
 src/field/field3d.cxx | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 2196d6eea4..e0d4dda01d 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -848,10 +848,14 @@ Options* Field3D::track(const T& change, std::string operation) {
   if (tracking != nullptr and tracking_state != 0) {
     const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
     tracking->set(outname, change, "tracking");
+    // Workaround for bug in gcc9.4
+#if BOUT_USE_TRACK
+    const std::string changename = change.name;
+#endif
     (*tracking)[outname].setAttributes({
       {"operation", operation},
 #if BOUT_USE_TRACK
-          {"rhs.name", change.name},
+          {"rhs.name", changename},
 #endif
     });
     return &(*tracking)[outname];

From d611758ae6b02a93e51eeeaebe025b628a23c9b3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 9 Apr 2024 15:15:30 +0200
Subject: [PATCH 0088/1827] Add option to debug on failure

---
 src/solver/impls/pvode/pvode.cxx | 80 ++++++++++++++++++--------------
 src/solver/impls/pvode/pvode.hxx |  9 +++-
 2 files changed, 52 insertions(+), 37 deletions(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index db28f64d86..9dce5d357f 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -247,6 +247,11 @@ int PvodeSolver::init() {
                           .doc("Use Adams Moulton solver instead of BDF")
                           .withDefault(false));
 
+  debug_on_failure =
+      (*options)["debug_on_failure"]
+          .doc("Run an aditional rhs if the solver fails with extra tracking")
+          .withDefault(false);
+
   cvode_mem = CVodeMalloc(neq, solver_f, simtime, u, use_adam ? ADAMS : BDF, NEWTON, SS,
                           &reltol, &abstol, this, nullptr, optIn, iopt, ropt, machEnv);
 
@@ -354,47 +359,52 @@ BoutReal PvodeSolver::run(BoutReal tout) {
   if (flag != SUCCESS) {
     output_error.write("ERROR CVODE step failed, flag = {:d}\n", flag);
     CVodeMemRec* cv_mem = (CVodeMem)cvode_mem;
-    if (f2d.empty() and v2d.empty() and v3d.empty()) {
-      Options debug{};
-      using namespace std::string_literals;
-      Mesh* mesh{};
-      for (const auto& prefix : {"pre_"s, "residuum_"s}) {
-        std::vector<Field3D> list_of_fields{};
-        std::vector<bool> evolve_bndrys{};
-        for (const auto& f : f3d) {
-          mesh = f.var->getMesh();
-          Field3D to_load{0., mesh};
-          to_load.allocate();
-          to_load.setLocation(f.location);
-          debug[fmt::format("{:s}{:s}", prefix, f.name)] = to_load;
-          list_of_fields.push_back(to_load);
-          evolve_bndrys.push_back(f.evolve_bndry);
+    if (debug_on_failure) {
+      if (f2d.empty() and v2d.empty() and v3d.empty()) {
+        Options debug{};
+        using namespace std::string_literals;
+        Mesh* mesh{};
+        for (const auto& prefix : {"pre_"s, "residuum_"s}) {
+          std::vector<Field3D> list_of_fields{};
+          std::vector<bool> evolve_bndrys{};
+          for (const auto& f : f3d) {
+            mesh = f.var->getMesh();
+            Field3D to_load{0., mesh};
+            to_load.allocate();
+            to_load.setLocation(f.location);
+            debug[fmt::format("{:s}{:s}", prefix, f.name)] = to_load;
+            list_of_fields.push_back(to_load);
+            evolve_bndrys.push_back(f.evolve_bndry);
+          }
+          pvode_load_data_f3d(evolve_bndrys, list_of_fields,
+                              prefix == "pre_"s ? udata : N_VDATA(cv_mem->cv_acor));
         }
-        pvode_load_data_f3d(evolve_bndrys, list_of_fields,
-                            prefix == "pre_"s ? udata : N_VDATA(cv_mem->cv_acor));
-      }
 
-      for (auto& f : f3d) {
-        f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug);
-        setName(*f.var, f.name);
-      }
-      run_rhs(simtime);
+        for (auto& f : f3d) {
+          f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug);
+          setName(*f.var, f.name);
+        }
+        run_rhs(simtime);
 
-      for (auto& f : f3d) {
-        debug[f.name] = *f.var;
-      }
+        for (auto& f : f3d) {
+          debug[f.name] = *f.var;
+        }
 
-      if (mesh != nullptr) {
-        mesh->outputVars(debug);
-        debug["BOUT_VERSION"].force(bout::version::as_double);
-      }
+        if (mesh != nullptr) {
+          mesh->outputVars(debug);
+          debug["BOUT_VERSION"].force(bout::version::as_double);
+        }
 
-      const std::string outname = fmt::format(
-          "{}/BOUT.debug.{}.nc",
-          Options::root()["datadir"].withDefault<std::string>("data"), BoutComm::rank());
+        const std::string outname =
+            fmt::format("{}/BOUT.debug.{}.nc",
+                        Options::root()["datadir"].withDefault<std::string>("data"),
+                        BoutComm::rank());
 
-      bout::OptionsIO::create(outname)->write(debug);
-      MPI_Barrier(BoutComm::get());
+        bout::OptionsIO::create(outname)->write(debug);
+        MPI_Barrier(BoutComm::get());
+      } else {
+        output_warn.write("debug_on_failure is currently only supported for Field3Ds");
+      }
     }
     return (-1.0);
   }
diff --git a/src/solver/impls/pvode/pvode.hxx b/src/solver/impls/pvode/pvode.hxx
index d29135d02e..3b385af99d 100644
--- a/src/solver/impls/pvode/pvode.hxx
+++ b/src/solver/impls/pvode/pvode.hxx
@@ -75,10 +75,15 @@ private:
   pvode::machEnvType machEnv{nullptr};
   void* cvode_mem{nullptr};
 
-  BoutReal abstol, reltol; // addresses passed in init must be preserved
+  BoutReal abstol, reltol;
+  // addresses passed in init must be preserved
   pvode::PVBBDData pdata{nullptr};
 
-  bool pvode_initialised = false;
+  /// is pvode already initialised?
+  bool pvode_initialised{false};
+
+  /// Add debugging data if solver fails
+  bool debug_on_failure{false};
 };
 
 #endif // BOUT_PVODE_SOLVER_H

From db96b7ecc3df8613a80203d59a421bf4186f25d1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 9 Apr 2024 15:56:25 +0200
Subject: [PATCH 0089/1827] Add option to euler solver to dump debug info

---
 src/solver/impls/euler/euler.cxx | 36 +++++++++++++++++++++++++++++++-
 src/solver/impls/euler/euler.hxx |  2 ++
 2 files changed, 37 insertions(+), 1 deletion(-)

diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 3976f4402c..45ba5ccdbf 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -20,7 +20,10 @@ EulerSolver::EulerSolver(Options* options)
                      .withDefault(2.)),
       timestep((*options)["timestep"]
                    .doc("Internal timestep (defaults to output timestep)")
-                   .withDefault(getOutputTimestep())) {}
+                   .withDefault(getOutputTimestep())),
+      dump_at_time((*options)["dump_at_time"]
+                       .doc("Dump debug info about the simulation")
+                       .withDefault(-1)) {}
 
 void EulerSolver::setMaxTimestep(BoutReal dt) {
   if (dt >= cfl_factor * timestep) {
@@ -141,7 +144,38 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
                             Array<BoutReal>& result) {
 
   load_vars(std::begin(start));
+  const bool dump_now = dump_at_time > 0 && std::abs(dump_at_time - curtime) < dt;
+  std::unique_ptr<Options> debug_ptr;
+  if (dump_now) {
+    debug_ptr = std::make_unique<Options>();
+    Options& debug = *debug_ptr;
+    for (auto& f : f3d) {
+      f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug);
+      setName(*f.var, f.name);
+    }
+  }
+
   run_rhs(curtime);
+  if (dump_now) {
+    Options& debug = *debug_ptr;
+    Mesh* mesh;
+    for (auto& f : f3d) {
+      debug[f.name] = *f.var;
+      mesh = f.var->getMesh();
+    }
+
+    if (mesh != nullptr) {
+      mesh->outputVars(debug);
+      debug["BOUT_VERSION"].force(bout::version::as_double);
+    }
+
+    const std::string outname = fmt::format(
+        "{}/BOUT.debug.{}.nc",
+        Options::root()["datadir"].withDefault<std::string>("data"), BoutComm::rank());
+
+    bout::OptionsIO::create(outname)->write(debug);
+    MPI_Barrier(BoutComm::get());
+  }
   save_derivs(std::begin(result));
 
   BOUT_OMP_PERF(parallel for)
diff --git a/src/solver/impls/euler/euler.hxx b/src/solver/impls/euler/euler.hxx
index 0ee81a3d33..4b6dc60a62 100644
--- a/src/solver/impls/euler/euler.hxx
+++ b/src/solver/impls/euler/euler.hxx
@@ -64,6 +64,8 @@ private:
   /// Take a single step to calculate f1
   void take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& start,
                  Array<BoutReal>& result);
+
+  BoutReal dump_at_time{-1.};
 };
 
 #endif // BOUT_KARNIADAKIS_SOLVER_H

From 84bfcef2d10dc2dabf280c792a548519158414df Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 15 Apr 2024 11:25:59 +0200
Subject: [PATCH 0090/1827] Disable tracking once we are done

---
 include/bout/field3d.hxx         | 7 +++++++
 src/solver/impls/euler/euler.cxx | 5 ++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index cfde9e5328..97118cb70a 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -299,6 +299,13 @@ public:
   /// Save all changes that, are done to the field, to tracking
   Field3D& enableTracking(const std::string& name, Options& tracking);
 
+  /// Disable tracking
+  Field3D& disableTracking(){
+    tracking = nullptr;
+    tracking_state = 0;
+    return *this;
+  }
+
   /////////////////////////////////////////////////////////
   // Data access
 
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 45ba5ccdbf..227d7ba454 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -158,7 +158,7 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
   run_rhs(curtime);
   if (dump_now) {
     Options& debug = *debug_ptr;
-    Mesh* mesh;
+    Mesh* mesh{nullptr};
     for (auto& f : f3d) {
       debug[f.name] = *f.var;
       mesh = f.var->getMesh();
@@ -175,6 +175,9 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
 
     bout::OptionsIO::create(outname)->write(debug);
     MPI_Barrier(BoutComm::get());
+    for (auto& f : f3d) {
+      f.F_var->disableTracking();
+    }
   }
   save_derivs(std::begin(result));
 

From 73265df7ebafd0a4d63763765977dd90cda2ce69 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 15 Apr 2024 11:27:07 +0200
Subject: [PATCH 0091/1827] Allow to dump every timestep with euler

---
 src/solver/impls/euler/euler.cxx | 14 ++++++++++----
 src/solver/impls/euler/euler.hxx |  1 +
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 227d7ba454..ded28984aa 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -144,7 +144,8 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
                             Array<BoutReal>& result) {
 
   load_vars(std::begin(start));
-  const bool dump_now = dump_at_time > 0 && std::abs(dump_at_time - curtime) < dt;
+  const bool dump_now =
+      (dump_at_time >= 0 && std::abs(dump_at_time - curtime) < dt) || dump_at_time < -3;
   std::unique_ptr<Options> debug_ptr;
   if (dump_now) {
     debug_ptr = std::make_unique<Options>();
@@ -152,6 +153,8 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
     for (auto& f : f3d) {
       f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug);
       setName(*f.var, f.name);
+      debug[fmt::format("pre_{:s}", f.name)] = *f.var;
+      f.var->allocate();
     }
   }
 
@@ -169,9 +172,12 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
       debug["BOUT_VERSION"].force(bout::version::as_double);
     }
 
-    const std::string outname = fmt::format(
-        "{}/BOUT.debug.{}.nc",
-        Options::root()["datadir"].withDefault<std::string>("data"), BoutComm::rank());
+    const std::string outnumber =
+        dump_at_time < -3 ? fmt::format(".{}", debug_counter++) : "";
+    const std::string outname =
+        fmt::format("{}/BOUT.debug{}.{}.nc",
+                    Options::root()["datadir"].withDefault<std::string>("data"),
+                    outnumber, BoutComm::rank());
 
     bout::OptionsIO::create(outname)->write(debug);
     MPI_Barrier(BoutComm::get());
diff --git a/src/solver/impls/euler/euler.hxx b/src/solver/impls/euler/euler.hxx
index 4b6dc60a62..fc9b7f53bb 100644
--- a/src/solver/impls/euler/euler.hxx
+++ b/src/solver/impls/euler/euler.hxx
@@ -66,6 +66,7 @@ private:
                  Array<BoutReal>& result);
 
   BoutReal dump_at_time{-1.};
+  int debug_counter{0};
 };
 
 #endif // BOUT_KARNIADAKIS_SOLVER_H

From 8ff388aeb9f74c23fb6cc8a073565cc19276d268 Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Mon, 15 Apr 2024 09:30:12 +0000
Subject: [PATCH 0092/1827] Apply clang-format changes

---
 include/bout/field3d.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 97118cb70a..395e3201e4 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -300,7 +300,7 @@ public:
   Field3D& enableTracking(const std::string& name, Options& tracking);
 
   /// Disable tracking
-  Field3D& disableTracking(){
+  Field3D& disableTracking() {
     tracking = nullptr;
     tracking_state = 0;
     return *this;

From e5157adbbd31921c3597b004b557f22f5cc99f78 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Apr 2024 10:45:27 +0200
Subject: [PATCH 0093/1827] Fix bad merge

---
 include/bout/utils.hxx | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 12f438c7d3..e965c5d433 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -369,14 +369,6 @@ public:
     return data[i.ind];
   }
 
-  T& operator[](Ind3D i) {
-    // ny and nz are private :-(
-    // ASSERT2(i.nz == n3);
-    // ASSERT2(i.ny == n2);
-    ASSERT2(0 <= i.ind && i.ind < n1 * n2 * n3);
-    return data[i.ind];
-  }
-
   Tensor& operator=(const T& val) {
     for (auto& i : data) {
       i = val;

From efd623720723f21071fdcbb72d805995afa894e7 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 6 May 2024 17:27:11 -0700
Subject: [PATCH 0094/1827] Start N_Vector implementation

---
 CMakeLists.txt         |   1 +
 src/solver/nvector.hxx | 159 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 160 insertions(+)
 create mode 100644 src/solver/nvector.hxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f57a78a14a..0a8358edd8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -325,6 +325,7 @@ set(BOUT_SOURCES
   ./src/solver/impls/split-rk/split-rk.cxx
   ./src/solver/impls/split-rk/split-rk.hxx
   ./src/solver/solver.cxx
+  ./src/solver/nvector.hxx
   ./src/sys/adios_object.cxx
   ./src/sys/bout_types.cxx
   ./src/sys/boutcomm.cxx
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
new file mode 100644
index 0000000000..8d45e38e9f
--- /dev/null
+++ b/src/solver/nvector.hxx
@@ -0,0 +1,159 @@
+/**************************************************************************
+ * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ *
+ * Contact: Ben Dudson, bd512@york.ac.uk
+ * 
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#ifndef BOUT_SUNDIAL_SOLVER_H
+#define BOUT_SUNDIAL_SOLVER_H
+
+#include <bout/field.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/vector2d.hxx>
+#include <bout/vector3d.hxx>
+#include <nvector/nvector_manyvector.h>
+#include <sundials/sundials_nvector.h>
+
+#include "bout/sundials_backports.hxx"
+
+template <typename T, typename = bout::utils::EnableIfField<T>>
+T& N_VContent_Bout(N_Vector v) {
+  return *static_cast<T*>(v->content);
+}
+
+template <typename T, typename = bout::utils::EnableIfField<T>>
+N_Vector N_VNew_Bout(sundials::Context& ctx, T& field) {
+  N_Vector v = callWithSUNContext(N_VNewEmpty, ctx);
+  if (v == nullptr) {
+    throw BoutException("N_VNewEmpty failed\n");
+  }
+
+  // TODO: double check ownership of the field. This is probably ok, though
+  v->content = static_cast<void*>(&field);
+
+  v->ops->nvgetvectorid = []([[maybe_unused]] N_Vector x) {
+    return SUNDIALS_NVEC_CUSTOM;
+  };
+
+  v->ops->nvclone = [](N_Vector x) {
+    // TODO
+    return x;
+  };
+
+  v->ops->nvdestroy = [](N_Vector x) { N_VFreeEmpty(x); };
+
+  v->ops->nvgetlength = [](N_Vector x) -> sunindextype {
+    // Is the the full domain size or just the subset fo the MPI process?
+    return N_VContent_Bout<T>(x).size();
+  };
+
+  v->ops->nvconst = [](sunrealtype c, N_Vector x) {
+    N_VContent_Bout<T>(x) = c;
+  };
+
+  v->ops->nvprod = [](N_Vector x, N_Vector y, N_Vector z) {
+    // TODO: make sure this is the most efficient way
+    N_VContent_Bout<T>(z) = N_VContent_Bout<T>(x) * N_VContent_Bout<T>(y);
+  };
+
+  v->ops->nvabs = [](N_Vector x, N_Vector y) {
+    N_VContent_Bout<T>(y) = abs(N_VContent_Bout<T>(x));
+  };
+
+  /* Other functions to implement (most optional)
+  N_Vector (*nvcloneempty)(N_Vector);
+   void (*nvdestroy)(N_Vector);
+   void (*nvspace)(N_Vector, sunindextype*, sunindextype*);
+   sunrealtype* (*nvgetarraypointer)(N_Vector);
+   sunrealtype* (*nvgetdevicearraypointer)(N_Vector);
+   void (*nvsetarraypointer)(sunrealtype*, N_Vector);
+   SUNComm (*nvgetcommunicator)(N_Vector);
+   sunindextype (*nvgetlength)(N_Vector);
+   sunindextype (*nvgetlocallength)(N_Vector);
+   void (*nvlinearsum)(sunrealtype, N_Vector, sunrealtype, N_Vector, N_Vector);
+   void (*nvconst)(sunrealtype, N_Vector);
+   void (*nvprod)(N_Vector, N_Vector, N_Vector);
+   void (*nvdiv)(N_Vector, N_Vector, N_Vector);
+   void (*nvscale)(sunrealtype, N_Vector, N_Vector);
+   void (*nvabs)(N_Vector, N_Vector);
+   void (*nvinv)(N_Vector, N_Vector);
+   void (*nvaddconst)(N_Vector, sunrealtype, N_Vector);
+   sunrealtype (*nvdotprod)(N_Vector, N_Vector);
+   sunrealtype (*nvmaxnorm)(N_Vector);
+   sunrealtype (*nvwrmsnorm)(N_Vector, N_Vector);
+   sunrealtype (*nvwrmsnormmask)(N_Vector, N_Vector, N_Vector);
+   sunrealtype (*nvmin)(N_Vector);
+   sunrealtype (*nvwl2norm)(N_Vector, N_Vector);
+   sunrealtype (*nvl1norm)(N_Vector);
+   void (*nvcompare)(sunrealtype, N_Vector, N_Vector);
+   sunbooleantype (*nvinvtest)(N_Vector, N_Vector);
+   sunbooleantype (*nvconstrmask)(N_Vector, N_Vector, N_Vector);
+   sunrealtype (*nvminquotient)(N_Vector, N_Vector);
+   SUNErrCode (*nvlinearcombination)(int, sunrealtype*, N_Vector*, N_Vector);
+   SUNErrCode (*nvscaleaddmulti)(int, sunrealtype*, N_Vector, N_Vector*,
+                                 N_Vector*);
+   SUNErrCode (*nvdotprodmulti)(int, N_Vector, N_Vector*, sunrealtype*);
+   SUNErrCode (*nvlinearsumvectorarray)(int, sunrealtype, N_Vector*, sunrealtype,
+                                          N_Vector*, N_Vector*);
+   SUNErrCode (*nvscalevectorarray)(int, sunrealtype*, N_Vector*, N_Vector*);
+   SUNErrCode (*nvconstvectorarray)(int, sunrealtype, N_Vector*);
+   SUNErrCode (*nvwrmsnormvectorarray)(int, N_Vector*, N_Vector*, sunrealtype*);
+   SUNErrCode (*nvwrmsnormmaskvectorarray)(int, N_Vector*, N_Vector*, N_Vector,
+                                             sunrealtype*);
+   SUNErrCode (*nvscaleaddmultivectorarray)(int, int, sunrealtype*, N_Vector*,
+                                             N_Vector**, N_Vector**);
+   SUNErrCode (*nvlinearcombinationvectorarray)(int, int, sunrealtype*,
+                                                N_Vector**, N_Vector*);
+   sunrealtype (*nvdotprodlocal)(N_Vector, N_Vector);
+   sunrealtype (*nvmaxnormlocal)(N_Vector);
+   sunrealtype (*nvminlocal)(N_Vector);
+   sunrealtype (*nvl1normlocal)(N_Vector);
+   sunbooleantype (*nvinvtestlocal)(N_Vector, N_Vector);
+   sunbooleantype (*nvconstrmasklocal)(N_Vector, N_Vector, N_Vector);
+   sunrealtype (*nvminquotientlocal)(N_Vector, N_Vector);
+   sunrealtype (*nvwsqrsumlocal)(N_Vector, N_Vector);
+   sunrealtype (*nvwsqrsummasklocal)(N_Vector, N_Vector, N_Vector);
+   SUNErrCode (*nvdotprodmultilocal)(int, N_Vector, N_Vector*, sunrealtype*);
+   SUNErrCode (*nvdotprodmultiallreduce)(int, N_Vector, sunrealtype*);
+   SUNErrCode (*nvbufsize)(N_Vector, sunindextype*);
+   SUNErrCode (*nvbufpack)(N_Vector, void*);
+   SUNErrCode (*nvbufunpack)(N_Vector, void*);
+   void (*nvprint)(N_Vector);
+   void (*nvprintfile)(N_Vector, FILE*);
+   */
+
+  return v;
+}
+
+template <typename... Args>
+N_Vector N_VNew_Bout(sundials::Context& ctx, Args&... args) {
+  N_Vector vecs[] = {N_VNew_Bout(ctx, args)...};
+  return N_VNew_ManyVector(sizeof...(Args), vecs, ctx);
+}
+
+N_Vector N_VNew_Bout(sundials::Context& ctx, Vector2D& vec) {
+  return N_VNew_Bout<Field2D, Field2D>(ctx, vec.x, vec.y);
+}
+
+N_Vector N_VNew_Bout(sundials::Context& ctx, Vector3D& vec) {
+  return N_VNew_Bout(ctx, vec.x, vec.y, vec.z);
+}
+
+#endif

From aaac3726185cfe137d5897c15313f269a38e8e52 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 6 May 2024 18:45:43 -0700
Subject: [PATCH 0095/1827] Add clone operation

---
 include/bout/sundials_backports.hxx |  2 +-
 src/solver/nvector.hxx              | 53 ++++++++++++++++++++---------
 2 files changed, 38 insertions(+), 17 deletions(-)

diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx
index 4ec334f4d4..9143bff495 100644
--- a/include/bout/sundials_backports.hxx
+++ b/include/bout/sundials_backports.hxx
@@ -62,7 +62,7 @@ inline sundials::Context createSUNContext([[maybe_unused]] MPI_Comm& comm) {
 }
 
 template <typename Func, typename... Args>
-inline decltype(auto) callWithSUNContext(Func f, [[maybe_unused]] sundials::Context& ctx,
+inline decltype(auto) callWithSUNContext(Func f, [[maybe_unused]] const SUNContext ctx,
                                          Args&&... args) {
 #if SUNDIALS_VERSION_MAJOR < 6
   return f(std::forward<Args>(args)...);
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 8d45e38e9f..b271b93750 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -33,48 +33,69 @@
 
 #include "bout/sundials_backports.hxx"
 
+namespace {
+  template <typename T>
+  struct Content {
+    T& field;
+    const bool own;
+  };
+
+  template <typename T>
+  Content<T>& N_VContent_Bout(const N_Vector v) {
+    return *static_cast<Content<T>*>(v->content);
+  }
+}
+
 template <typename T, typename = bout::utils::EnableIfField<T>>
-T& N_VContent_Bout(N_Vector v) {
-  return *static_cast<T*>(v->content);
+T& N_VField_Bout(const N_Vector v) {
+  return N_VContent_Bout<T>(v).field;
 }
 
 template <typename T, typename = bout::utils::EnableIfField<T>>
-N_Vector N_VNew_Bout(sundials::Context& ctx, T& field) {
+N_Vector N_VNew_Bout(const SUNContext ctx, T& field, const bool own = false) {
   N_Vector v = callWithSUNContext(N_VNewEmpty, ctx);
   if (v == nullptr) {
     throw BoutException("N_VNewEmpty failed\n");
   }
 
-  // TODO: double check ownership of the field. This is probably ok, though
-  v->content = static_cast<void*>(&field);
+  v->content = static_cast<void*>(new Content<T>({field, own}));
 
   v->ops->nvgetvectorid = []([[maybe_unused]] N_Vector x) {
     return SUNDIALS_NVEC_CUSTOM;
   };
 
   v->ops->nvclone = [](N_Vector x) {
-    // TODO
-    return x;
+    T* field = new T(N_VField_Bout<T>(x));
+    return N_VNew_Bout<T>(x->sunctx, *field, true);
   };
 
-  v->ops->nvdestroy = [](N_Vector x) { N_VFreeEmpty(x); };
+  v->ops->nvdestroy = [](N_Vector x) {
+    if (x == nullptr) {
+      return;
+    }
+    if (x->content != nullptr && N_VContent_Bout<T>(x).own) {
+      delete &N_VField_Bout<T>(x);
+    }
+    delete &N_VContent_Bout<T>(x);
+    N_VFreeEmpty(x);
+  };
 
   v->ops->nvgetlength = [](N_Vector x) -> sunindextype {
     // Is the the full domain size or just the subset fo the MPI process?
-    return N_VContent_Bout<T>(x).size();
+    return N_VField_Bout<T>(x).size();
   };
 
   v->ops->nvconst = [](sunrealtype c, N_Vector x) {
-    N_VContent_Bout<T>(x) = c;
+    N_VField_Bout<T>(x) = c;
   };
 
   v->ops->nvprod = [](N_Vector x, N_Vector y, N_Vector z) {
     // TODO: make sure this is the most efficient way
-    N_VContent_Bout<T>(z) = N_VContent_Bout<T>(x) * N_VContent_Bout<T>(y);
+    N_VField_Bout<T>(z) = N_VField_Bout<T>(x) * N_VField_Bout<T>(y);
   };
 
   v->ops->nvabs = [](N_Vector x, N_Vector y) {
-    N_VContent_Bout<T>(y) = abs(N_VContent_Bout<T>(x));
+    N_VField_Bout<T>(y) = abs(N_VField_Bout<T>(x));
   };
 
   /* Other functions to implement (most optional)
@@ -143,16 +164,16 @@ N_Vector N_VNew_Bout(sundials::Context& ctx, T& field) {
 }
 
 template <typename... Args>
-N_Vector N_VNew_Bout(sundials::Context& ctx, Args&... args) {
+N_Vector N_VNew_Bout(const SUNContext ctx, Args&... args) {
   N_Vector vecs[] = {N_VNew_Bout(ctx, args)...};
   return N_VNew_ManyVector(sizeof...(Args), vecs, ctx);
 }
 
-N_Vector N_VNew_Bout(sundials::Context& ctx, Vector2D& vec) {
-  return N_VNew_Bout<Field2D, Field2D>(ctx, vec.x, vec.y);
+N_Vector N_VNew_Bout(const SUNContext ctx, Vector2D& vec) {
+  return N_VNew_Bout(ctx, vec.x, vec.y);
 }
 
-N_Vector N_VNew_Bout(sundials::Context& ctx, Vector3D& vec) {
+N_Vector N_VNew_Bout(const SUNContext ctx, Vector3D& vec) {
   return N_VNew_Bout(ctx, vec.x, vec.y, vec.z);
 }
 

From 8a0615934448e9a7ae6029a34321b6d0b9d1cd4f Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 6 May 2024 23:50:47 -0700
Subject: [PATCH 0096/1827] Allow N_Vector template type to be
 Vector2D/Vector3D

---
 src/solver/nvector.hxx | 200 ++++++++++++++++++++++-------------------
 1 file changed, 109 insertions(+), 91 deletions(-)

diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index b271b93750..175a366761 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -34,147 +34,165 @@
 #include "bout/sundials_backports.hxx"
 
 namespace {
-  template <typename T>
-  struct Content {
-    T& field;
-    const bool own;
-  };
-
-  template <typename T>
-  Content<T>& N_VContent_Bout(const N_Vector v) {
-    return *static_cast<Content<T>*>(v->content);
+template <typename T>
+struct Content {
+  T& data; // A vector or field
+  const bool own;
+
+  ~Content() {
+    if (own) {
+      delete &data;
+    }
   }
+};
+} // namespace
+
+template <typename T>
+T& N_VData_Bout(const N_Vector v) {
+  return static_cast<Content<T>*>(v->content)->data;
 }
 
-template <typename T, typename = bout::utils::EnableIfField<T>>
-T& N_VField_Bout(const N_Vector v) {
-  return N_VContent_Bout<T>(v).field;
+namespace {
+  template <typename T, typename F, typename... Args>
+  std::enable_if_t<bout::utils::is_Field_v<T>, void> mapFields(F f, Args ... vectors) {
+    f(N_VData_Bout<T>(vectors)...);
+  }
+
+  template <typename T, typename F, typename... Args>
+  std::enable_if_t<std::is_base_of_v<Vector2D, T>, void> mapFields(F f, Args ... vectors) {
+    f(N_VData_Bout<T>(vectors).x...);
+    f(N_VData_Bout<T>(vectors).y...);
+  }
+
+  template <typename T, typename F, typename... Args>
+  std::enable_if_t<std::is_base_of_v<Vector3D, T>, void> mapFields(F f, Args ... vectors) {
+    f(N_VData_Bout<T>(vectors).x...);
+    f(N_VData_Bout<T>(vectors).y...);
+    f(N_VData_Bout<T>(vectors).z...);
+  }
 }
 
-template <typename T, typename = bout::utils::EnableIfField<T>>
-N_Vector N_VNew_Bout(const SUNContext ctx, T& field, const bool own = false) {
+template <typename T>
+N_Vector N_VNew_Bout(const SUNContext ctx, T& data, const bool own = false) {
   N_Vector v = callWithSUNContext(N_VNewEmpty, ctx);
   if (v == nullptr) {
     throw BoutException("N_VNewEmpty failed\n");
   }
 
-  v->content = static_cast<void*>(new Content<T>({field, own}));
+  v->content = static_cast<void*>(new Content<T>({data, own}));
 
   v->ops->nvgetvectorid = []([[maybe_unused]] N_Vector x) {
     return SUNDIALS_NVEC_CUSTOM;
   };
 
   v->ops->nvclone = [](N_Vector x) {
-    T* field = new T(N_VField_Bout<T>(x));
-    return N_VNew_Bout<T>(x->sunctx, *field, true);
+    T* data = new T(N_VData_Bout<T>(x));
+    return N_VNew_Bout<T>(x->sunctx, *data, true);
   };
 
   v->ops->nvdestroy = [](N_Vector x) {
     if (x == nullptr) {
       return;
     }
-    if (x->content != nullptr && N_VContent_Bout<T>(x).own) {
-      delete &N_VField_Bout<T>(x);
-    }
-    delete &N_VContent_Bout<T>(x);
+    delete static_cast<Content<T>*>(x->content);
     N_VFreeEmpty(x);
   };
 
-  v->ops->nvgetlength = [](N_Vector x) -> sunindextype {
-    // Is the the full domain size or just the subset fo the MPI process?
-    return N_VField_Bout<T>(x).size();
+  v->ops->nvgetlength = [](N_Vector x) {
+    sunindextype len = 0;
+    mapFields<T>([&len] (auto & fx) {
+      len += fx.size(); // TODO: check this isn't the MPI local size
+    }, x);
+    return len;
   };
 
   v->ops->nvconst = [](sunrealtype c, N_Vector x) {
-    N_VField_Bout<T>(x) = c;
+    mapFields<T>([c] (auto & f) {
+      f = c;
+    }, x);
   };
 
   v->ops->nvprod = [](N_Vector x, N_Vector y, N_Vector z) {
-    // TODO: make sure this is the most efficient way
-    N_VField_Bout<T>(z) = N_VField_Bout<T>(x) * N_VField_Bout<T>(y);
+    mapFields<T>([] (auto & fx, auto & fy, auto & fz) {
+      fz = fx * fy;
+    }, x, y, z);
   };
 
   v->ops->nvabs = [](N_Vector x, N_Vector y) {
-    N_VField_Bout<T>(y) = abs(N_VField_Bout<T>(x));
+    mapFields<T>([] (auto & fx, auto & fy) {
+      fy = abs(fx);
+    }, x, y);
   };
 
   /* Other functions to implement (most optional)
-  N_Vector (*nvcloneempty)(N_Vector);
-   void (*nvdestroy)(N_Vector);
-   void (*nvspace)(N_Vector, sunindextype*, sunindextype*);
-   sunrealtype* (*nvgetarraypointer)(N_Vector);
-   sunrealtype* (*nvgetdevicearraypointer)(N_Vector);
-   void (*nvsetarraypointer)(sunrealtype*, N_Vector);
-   SUNComm (*nvgetcommunicator)(N_Vector);
-   sunindextype (*nvgetlength)(N_Vector);
-   sunindextype (*nvgetlocallength)(N_Vector);
-   void (*nvlinearsum)(sunrealtype, N_Vector, sunrealtype, N_Vector, N_Vector);
-   void (*nvconst)(sunrealtype, N_Vector);
-   void (*nvprod)(N_Vector, N_Vector, N_Vector);
-   void (*nvdiv)(N_Vector, N_Vector, N_Vector);
-   void (*nvscale)(sunrealtype, N_Vector, N_Vector);
-   void (*nvabs)(N_Vector, N_Vector);
-   void (*nvinv)(N_Vector, N_Vector);
-   void (*nvaddconst)(N_Vector, sunrealtype, N_Vector);
-   sunrealtype (*nvdotprod)(N_Vector, N_Vector);
-   sunrealtype (*nvmaxnorm)(N_Vector);
-   sunrealtype (*nvwrmsnorm)(N_Vector, N_Vector);
-   sunrealtype (*nvwrmsnormmask)(N_Vector, N_Vector, N_Vector);
-   sunrealtype (*nvmin)(N_Vector);
-   sunrealtype (*nvwl2norm)(N_Vector, N_Vector);
-   sunrealtype (*nvl1norm)(N_Vector);
-   void (*nvcompare)(sunrealtype, N_Vector, N_Vector);
-   sunbooleantype (*nvinvtest)(N_Vector, N_Vector);
-   sunbooleantype (*nvconstrmask)(N_Vector, N_Vector, N_Vector);
-   sunrealtype (*nvminquotient)(N_Vector, N_Vector);
-   SUNErrCode (*nvlinearcombination)(int, sunrealtype*, N_Vector*, N_Vector);
+  N_Vector (*nvcloneempty)(N_Vector); // Probably not needed
+   void (*nvdestroy)(N_Vector); // Implemented
+   void (*nvspace)(N_Vector, sunindextype*, sunindextype*); // Probably not needed
+   sunrealtype* (*nvgetarraypointer)(N_Vector); // Probably not needed
+   sunrealtype* (*nvgetdevicearraypointer)(N_Vector); // Probably not needed
+   void (*nvsetarraypointer)(sunrealtype*, N_Vector); // Probably not needed
+   SUNComm (*nvgetcommunicator)(N_Vector); // Probably not needed
+   sunindextype (*nvgetlength)(N_Vector); // Implemented
+   sunindextype (*nvgetlocallength)(N_Vector);  // Probably not needed
+   void (*nvlinearsum)(sunrealtype, N_Vector, sunrealtype, N_Vector, N_Vector); // TODO
+   void (*nvconst)(sunrealtype, N_Vector); // Implemented
+   void (*nvprod)(N_Vector, N_Vector, N_Vector); // Implemented
+   void (*nvdiv)(N_Vector, N_Vector, N_Vector); // TODO
+   void (*nvscale)(sunrealtype, N_Vector, N_Vector); // TODO
+   void (*nvabs)(N_Vector, N_Vector); // Implemented
+   void (*nvinv)(N_Vector, N_Vector); // TODO
+   void (*nvaddconst)(N_Vector, sunrealtype, N_Vector); // TODO
+   sunrealtype (*nvdotprod)(N_Vector, N_Vector); // TODO
+   sunrealtype (*nvmaxnorm)(N_Vector); // TODO
+   sunrealtype (*nvwrmsnorm)(N_Vector, N_Vector); // TODO
+   sunrealtype (*nvwrmsnormmask)(N_Vector, N_Vector, N_Vector); // TODO
+   sunrealtype (*nvmin)(N_Vector); // TODO
+   sunrealtype (*nvwl2norm)(N_Vector, N_Vector); // TODO
+   sunrealtype (*nvl1norm)(N_Vector); // TODO
+   void (*nvcompare)(sunrealtype, N_Vector, N_Vector); // TODO
+   sunbooleantype (*nvinvtest)(N_Vector, N_Vector); // TODO
+   sunbooleantype (*nvconstrmask)(N_Vector, N_Vector, N_Vector); // TODO
+   sunrealtype (*nvminquotient)(N_Vector, N_Vector); // TODO
+   SUNErrCode (*nvlinearcombination)(int, sunrealtype*, N_Vector*, N_Vector); // TODO
    SUNErrCode (*nvscaleaddmulti)(int, sunrealtype*, N_Vector, N_Vector*,
-                                 N_Vector*);
-   SUNErrCode (*nvdotprodmulti)(int, N_Vector, N_Vector*, sunrealtype*);
+                                 N_Vector*); // Probably not needed
+   SUNErrCode (*nvdotprodmulti)(int, N_Vector, N_Vector*, sunrealtype*); // Probably not needed
    SUNErrCode (*nvlinearsumvectorarray)(int, sunrealtype, N_Vector*, sunrealtype,
-                                          N_Vector*, N_Vector*);
-   SUNErrCode (*nvscalevectorarray)(int, sunrealtype*, N_Vector*, N_Vector*);
-   SUNErrCode (*nvconstvectorarray)(int, sunrealtype, N_Vector*);
-   SUNErrCode (*nvwrmsnormvectorarray)(int, N_Vector*, N_Vector*, sunrealtype*);
+                                          N_Vector*, N_Vector*); // Probably not needed
+   SUNErrCode (*nvscalevectorarray)(int, sunrealtype*, N_Vector*, N_Vector*); // Probably not needed
+   SUNErrCode (*nvconstvectorarray)(int, sunrealtype, N_Vector*); // Probably not needed
+   SUNErrCode (*nvwrmsnormvectorarray)(int, N_Vector*, N_Vector*, sunrealtype*); // Probably not needed
    SUNErrCode (*nvwrmsnormmaskvectorarray)(int, N_Vector*, N_Vector*, N_Vector,
-                                             sunrealtype*);
+                                             sunrealtype*); // Probably not needed
    SUNErrCode (*nvscaleaddmultivectorarray)(int, int, sunrealtype*, N_Vector*,
-                                             N_Vector**, N_Vector**);
+                                             N_Vector**, N_Vector**); // Probably not needed
    SUNErrCode (*nvlinearcombinationvectorarray)(int, int, sunrealtype*,
-                                                N_Vector**, N_Vector*);
-   sunrealtype (*nvdotprodlocal)(N_Vector, N_Vector);
-   sunrealtype (*nvmaxnormlocal)(N_Vector);
-   sunrealtype (*nvminlocal)(N_Vector);
-   sunrealtype (*nvl1normlocal)(N_Vector);
-   sunbooleantype (*nvinvtestlocal)(N_Vector, N_Vector);
-   sunbooleantype (*nvconstrmasklocal)(N_Vector, N_Vector, N_Vector);
-   sunrealtype (*nvminquotientlocal)(N_Vector, N_Vector);
-   sunrealtype (*nvwsqrsumlocal)(N_Vector, N_Vector);
-   sunrealtype (*nvwsqrsummasklocal)(N_Vector, N_Vector, N_Vector);
-   SUNErrCode (*nvdotprodmultilocal)(int, N_Vector, N_Vector*, sunrealtype*);
-   SUNErrCode (*nvdotprodmultiallreduce)(int, N_Vector, sunrealtype*);
-   SUNErrCode (*nvbufsize)(N_Vector, sunindextype*);
-   SUNErrCode (*nvbufpack)(N_Vector, void*);
-   SUNErrCode (*nvbufunpack)(N_Vector, void*);
-   void (*nvprint)(N_Vector);
-   void (*nvprintfile)(N_Vector, FILE*);
+                                                N_Vector**, N_Vector*); // Probably not needed
+   sunrealtype (*nvdotprodlocal)(N_Vector, N_Vector); // Probably not needed
+   sunrealtype (*nvmaxnormlocal)(N_Vector); // Probably not needed
+   sunrealtype (*nvminlocal)(N_Vector); // Probably not needed
+   sunrealtype (*nvl1normlocal)(N_Vector); // Probably not needed
+   sunbooleantype (*nvinvtestlocal)(N_Vector, N_Vector); // Probably not needed
+   sunbooleantype (*nvconstrmasklocal)(N_Vector, N_Vector, N_Vector); // Probably not needed
+   sunrealtype (*nvminquotientlocal)(N_Vector, N_Vector); // Probably not needed
+   sunrealtype (*nvwsqrsumlocal)(N_Vector, N_Vector); // Probably not needed
+   sunrealtype (*nvwsqrsummasklocal)(N_Vector, N_Vector, N_Vector); // Probably not needed
+   SUNErrCode (*nvdotprodmultilocal)(int, N_Vector, N_Vector*, sunrealtype*); // Probably not needed
+   SUNErrCode (*nvdotprodmultiallreduce)(int, N_Vector, sunrealtype*); // Probably not needed
+   SUNErrCode (*nvbufsize)(N_Vector, sunindextype*); // Probably not needed
+   SUNErrCode (*nvbufpack)(N_Vector, void*); // Probably not needed
+   SUNErrCode (*nvbufunpack)(N_Vector, void*); // Probably not needed
+   void (*nvprint)(N_Vector); // Nice, but optional
+   void (*nvprintfile)(N_Vector, FILE*); // Probably not needed
    */
 
   return v;
 }
 
 template <typename... Args>
-N_Vector N_VNew_Bout(const SUNContext ctx, Args&... args) {
+N_Vector N_VNew_Bout(SUNContext ctx, Args&... args) {
   N_Vector vecs[] = {N_VNew_Bout(ctx, args)...};
   return N_VNew_ManyVector(sizeof...(Args), vecs, ctx);
 }
 
-N_Vector N_VNew_Bout(const SUNContext ctx, Vector2D& vec) {
-  return N_VNew_Bout(ctx, vec.x, vec.y);
-}
-
-N_Vector N_VNew_Bout(const SUNContext ctx, Vector3D& vec) {
-  return N_VNew_Bout(ctx, vec.x, vec.y, vec.z);
-}
-
 #endif

From a49253a1e0a28b88c1aeefad72b35123df0d7ea7 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 6 May 2024 23:51:37 -0700
Subject: [PATCH 0097/1827] Apply formatter

---
 src/solver/nvector.hxx | 50 +++++++++++++++++++-----------------------
 1 file changed, 23 insertions(+), 27 deletions(-)

diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 175a366761..70903d9b81 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -53,24 +53,24 @@ T& N_VData_Bout(const N_Vector v) {
 }
 
 namespace {
-  template <typename T, typename F, typename... Args>
-  std::enable_if_t<bout::utils::is_Field_v<T>, void> mapFields(F f, Args ... vectors) {
-    f(N_VData_Bout<T>(vectors)...);
-  }
+template <typename T, typename F, typename... Args>
+std::enable_if_t<bout::utils::is_Field_v<T>, void> mapFields(F f, Args... vectors) {
+  f(N_VData_Bout<T>(vectors)...);
+}
 
-  template <typename T, typename F, typename... Args>
-  std::enable_if_t<std::is_base_of_v<Vector2D, T>, void> mapFields(F f, Args ... vectors) {
-    f(N_VData_Bout<T>(vectors).x...);
-    f(N_VData_Bout<T>(vectors).y...);
-  }
+template <typename T, typename F, typename... Args>
+std::enable_if_t<std::is_base_of_v<Vector2D, T>, void> mapFields(F f, Args... vectors) {
+  f(N_VData_Bout<T>(vectors).x...);
+  f(N_VData_Bout<T>(vectors).y...);
+}
 
-  template <typename T, typename F, typename... Args>
-  std::enable_if_t<std::is_base_of_v<Vector3D, T>, void> mapFields(F f, Args ... vectors) {
-    f(N_VData_Bout<T>(vectors).x...);
-    f(N_VData_Bout<T>(vectors).y...);
-    f(N_VData_Bout<T>(vectors).z...);
-  }
+template <typename T, typename F, typename... Args>
+std::enable_if_t<std::is_base_of_v<Vector3D, T>, void> mapFields(F f, Args... vectors) {
+  f(N_VData_Bout<T>(vectors).x...);
+  f(N_VData_Bout<T>(vectors).y...);
+  f(N_VData_Bout<T>(vectors).z...);
 }
+} // namespace
 
 template <typename T>
 N_Vector N_VNew_Bout(const SUNContext ctx, T& data, const bool own = false) {
@@ -100,28 +100,24 @@ N_Vector N_VNew_Bout(const SUNContext ctx, T& data, const bool own = false) {
 
   v->ops->nvgetlength = [](N_Vector x) {
     sunindextype len = 0;
-    mapFields<T>([&len] (auto & fx) {
-      len += fx.size(); // TODO: check this isn't the MPI local size
-    }, x);
+    mapFields<T>(
+        [&len](auto& fx) {
+          len += fx.size(); // TODO: check this isn't the MPI local size
+        },
+        x);
     return len;
   };
 
   v->ops->nvconst = [](sunrealtype c, N_Vector x) {
-    mapFields<T>([c] (auto & f) {
-      f = c;
-    }, x);
+    mapFields<T>([c](auto& f) { f = c; }, x);
   };
 
   v->ops->nvprod = [](N_Vector x, N_Vector y, N_Vector z) {
-    mapFields<T>([] (auto & fx, auto & fy, auto & fz) {
-      fz = fx * fy;
-    }, x, y, z);
+    mapFields<T>([](auto& fx, auto& fy, auto& fz) { fz = fx * fy; }, x, y, z);
   };
 
   v->ops->nvabs = [](N_Vector x, N_Vector y) {
-    mapFields<T>([] (auto & fx, auto & fy) {
-      fy = abs(fx);
-    }, x, y);
+    mapFields<T>([](auto& fx, auto& fy) { fy = abs(fx); }, x, y);
   };
 
   /* Other functions to implement (most optional)

From 184b7e94c47d576669737be3ba055fff0d42c08c Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 20 May 2024 17:51:19 -0700
Subject: [PATCH 0098/1827] Add remaining basic operations

---
 src/solver/nvector.hxx | 170 +++++++++++++++++++++++++++++------------
 1 file changed, 121 insertions(+), 49 deletions(-)

diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 70903d9b81..f72f63790b 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -36,58 +36,74 @@
 namespace {
 template <typename T>
 struct Content {
-  T& data; // A vector or field
+  T& field; // A Field2D or Field3D
   const bool own;
 
   ~Content() {
     if (own) {
-      delete &data;
+      delete &field;
     }
   }
 };
-} // namespace
 
-template <typename T>
-T& N_VData_Bout(const N_Vector v) {
-  return static_cast<Content<T>*>(v->content)->data;
+template <typename R, typename T, typename... U>
+BoutReal fieldReduce(R reduce, bool allpe, const std::string& rgn, const T& f1,
+                     const U&... f2) {
+  BoutReal result = 0;
+  const auto region = f1.getRegion(rgn);
+    BOUT_FOR_OMP(i, region, parallel for reduction(+:result)) {
+      result += reduce(f1[i], f2[i]...);
+    }
+
+    if (allpe) {
+      BoutReal localresult = result;
+      MPI_Allreduce(&localresult, &result, 1, MPI_DOUBLE, MPI_MAX, BoutComm::get());
+    }
+    return result;
 }
 
-namespace {
-template <typename T, typename F, typename... Args>
-std::enable_if_t<bout::utils::is_Field_v<T>, void> mapFields(F f, Args... vectors) {
-  f(N_VData_Bout<T>(vectors)...);
+template <typename T>
+BoutReal dotProd(const T& f1, const T& f2, bool allpe = false,
+                 const std::string& rgn = "RGN_NOBNDRY") {
+  return fieldReduce(std::multiplies(), allpe, rgn, f1, f2);
 }
 
-template <typename T, typename F, typename... Args>
-std::enable_if_t<std::is_base_of_v<Vector2D, T>, void> mapFields(F f, Args... vectors) {
-  f(N_VData_Bout<T>(vectors).x...);
-  f(N_VData_Bout<T>(vectors).y...);
+template <typename T>
+BoutReal weightedL2Norm(const T& f, const T& w, bool allpe = false,
+                        const std::string& rgn = "RGN_NOBNDRY") {
+  return fieldReduce(
+      [](const BoutReal v1, const BoutReal v2) { return std::pow(v1 * v2, 2); }, allpe,
+      rgn, f, w);
 }
 
-template <typename T, typename F, typename... Args>
-std::enable_if_t<std::is_base_of_v<Vector3D, T>, void> mapFields(F f, Args... vectors) {
-  f(N_VData_Bout<T>(vectors).x...);
-  f(N_VData_Bout<T>(vectors).y...);
-  f(N_VData_Bout<T>(vectors).z...);
+template <typename T>
+BoutReal l1Norm(const T& f, bool allpe = false, const std::string& rgn = "RGN_NOBNDRY") {
+  return fieldReduce(std::abs<BoutReal>, allpe, rgn, f);
 }
 } // namespace
 
 template <typename T>
-N_Vector N_VNew_Bout(const SUNContext ctx, T& data, const bool own = false) {
+T& N_VField_Bout(const N_Vector v) {
+  return static_cast<Content<T>*>(v->content)->field;
+}
+
+template <typename T, typename = bout::utils::EnableIfField<T>>
+N_Vector N_VNew_Bout(const SUNContext ctx, T& field, const bool own = false) {
   N_Vector v = callWithSUNContext(N_VNewEmpty, ctx);
   if (v == nullptr) {
     throw BoutException("N_VNewEmpty failed\n");
   }
 
-  v->content = static_cast<void*>(new Content<T>({data, own}));
+  v->content = static_cast<void*>(new Content<T>({field, own}));
 
   v->ops->nvgetvectorid = []([[maybe_unused]] N_Vector x) {
     return SUNDIALS_NVEC_CUSTOM;
   };
 
   v->ops->nvclone = [](N_Vector x) {
-    T* data = new T(N_VData_Bout<T>(x));
-    return N_VNew_Bout<T>(x->sunctx, *data, true);
+    T* const fieldClone = new T(N_VField_Bout<T>(x));
+    fieldClone->allocate();
+    return N_VNew_Bout(x->sunctx, *fieldClone, true);
   };
 
   v->ops->nvdestroy = [](N_Vector x) {
@@ -99,27 +115,60 @@ N_Vector N_VNew_Bout(const SUNContext ctx, T& data, const bool own = false) {
   };
 
   v->ops->nvgetlength = [](N_Vector x) {
-    sunindextype len = 0;
-    mapFields<T>(
-        [&len](auto& fx) {
-          len += fx.size(); // TODO: check this isn't the MPI local size
-        },
-        x);
-    return len;
+    // Is this correct with MPI?
+    return static_cast<sunindextype>(N_VField_Bout<T>(x).size());
   };
 
-  v->ops->nvconst = [](sunrealtype c, N_Vector x) {
-    mapFields<T>([c](auto& f) { f = c; }, x);
+  v->ops->nvlinearsum = [](sunrealtype a, N_Vector x, sunrealtype b, N_Vector y,
+                           N_Vector z) {
+    N_VField_Bout<T>(z) = a * N_VField_Bout<T>(x) + b * N_VField_Bout<T>(y);
   };
 
+  v->ops->nvconst = [](sunrealtype c, N_Vector x) { N_VField_Bout<T>(x) = c; };
+
   v->ops->nvprod = [](N_Vector x, N_Vector y, N_Vector z) {
-    mapFields<T>([](auto& fx, auto& fy, auto& fz) { fz = fx * fy; }, x, y, z);
+    N_VField_Bout<T>(z) = N_VField_Bout<T>(x) * N_VField_Bout<T>(y);
+  };
+
+  v->ops->nvdiv = [](N_Vector x, N_Vector y, N_Vector z) {
+    N_VField_Bout<T>(z) = N_VField_Bout<T>(x) / N_VField_Bout<T>(y);
+  };
+
+  v->ops->nvscale = [](sunrealtype a, N_Vector x, N_Vector y) {
+    N_VField_Bout<T>(y) = a * N_VField_Bout<T>(x);
   };
 
   v->ops->nvabs = [](N_Vector x, N_Vector y) {
-    mapFields<T>([](auto& fx, auto& fy) { fy = abs(fx); }, x, y);
+    N_VField_Bout<T>(y) = abs(N_VField_Bout<T>(x));
+  };
+
+  v->ops->nvinv = [](N_Vector x, N_Vector y) {
+    N_VField_Bout<T>(y) = 1 / N_VField_Bout<T>(x);
   };
 
+  v->ops->nvaddconst = [](N_Vector x, sunrealtype a, N_Vector y) {
+    N_VField_Bout<T>(y) = a + N_VField_Bout<T>(x);
+  };
+
+  v->ops->nvdotprod = [](N_Vector x, N_Vector y) {
+    return dotProd(N_VField_Bout<T>(x), N_VField_Bout<T>(y), true);
+  };
+
+  v->ops->nvmaxnorm = [](N_Vector x) { return max(abs(N_VField_Bout<T>(x)), true); };
+
+  v->ops->nvwrmsnorm = [](N_Vector x, N_Vector y) {
+    const auto sqrtLen = std::sqrt(static_cast<BoutReal>(N_VGetLength(x)));
+    return weightedL2Norm(N_VField_Bout<T>(x), N_VField_Bout<T>(y), true) / sqrtLen;
+  };
+
+  v->ops->nvmin = [](N_Vector x) { return min(N_VField_Bout<T>(x), true); };
+
+  v->ops->nvwl2norm = [](N_Vector x, N_Vector y) {
+    return weightedL2Norm(N_VField_Bout<T>(x), N_VField_Bout<T>(y), true);
+  };
+
+  v->ops->nvl1norm = [](N_Vector x) { return l1Norm(N_VField_Bout<T>(x), true); };
+
   /* Other functions to implement (most optional)
   N_Vector (*nvcloneempty)(N_Vector); // Probably not needed
    void (*nvdestroy)(N_Vector); // Implemented
@@ -130,21 +179,21 @@ N_Vector N_VNew_Bout(const SUNContext ctx, T& data, const bool own = false) {
    SUNComm (*nvgetcommunicator)(N_Vector); // Probably not needed
    sunindextype (*nvgetlength)(N_Vector); // Implemented
    sunindextype (*nvgetlocallength)(N_Vector);  // Probably not needed
-   void (*nvlinearsum)(sunrealtype, N_Vector, sunrealtype, N_Vector, N_Vector); // TODO
+   void (*nvlinearsum)(sunrealtype, N_Vector, sunrealtype, N_Vector, N_Vector); // Implemented
    void (*nvconst)(sunrealtype, N_Vector); // Implemented
    void (*nvprod)(N_Vector, N_Vector, N_Vector); // Implemented
-   void (*nvdiv)(N_Vector, N_Vector, N_Vector); // TODO
-   void (*nvscale)(sunrealtype, N_Vector, N_Vector); // TODO
+   void (*nvdiv)(N_Vector, N_Vector, N_Vector); // Implemented
+   void (*nvscale)(sunrealtype, N_Vector, N_Vector); // Implemented
    void (*nvabs)(N_Vector, N_Vector); // Implemented
-   void (*nvinv)(N_Vector, N_Vector); // TODO
-   void (*nvaddconst)(N_Vector, sunrealtype, N_Vector); // TODO
-   sunrealtype (*nvdotprod)(N_Vector, N_Vector); // TODO
-   sunrealtype (*nvmaxnorm)(N_Vector); // TODO
-   sunrealtype (*nvwrmsnorm)(N_Vector, N_Vector); // TODO
+   void (*nvinv)(N_Vector, N_Vector); // Implemented
+   void (*nvaddconst)(N_Vector, sunrealtype, N_Vector); // Implemented
+   sunrealtype (*nvdotprod)(N_Vector, N_Vector); // Implemented
+   sunrealtype (*nvmaxnorm)(N_Vector); // Implemented
+   sunrealtype (*nvwrmsnorm)(N_Vector, N_Vector); // Implemented
    sunrealtype (*nvwrmsnormmask)(N_Vector, N_Vector, N_Vector); // TODO
-   sunrealtype (*nvmin)(N_Vector); // TODO
-   sunrealtype (*nvwl2norm)(N_Vector, N_Vector); // TODO
-   sunrealtype (*nvl1norm)(N_Vector); // TODO
+   sunrealtype (*nvmin)(N_Vector); // Implemented
+   sunrealtype (*nvwl2norm)(N_Vector, N_Vector); // Implemented
+   sunrealtype (*nvl1norm)(N_Vector); // Implemented
    void (*nvcompare)(sunrealtype, N_Vector, N_Vector); // TODO
    sunbooleantype (*nvinvtest)(N_Vector, N_Vector); // TODO
    sunbooleantype (*nvconstrmask)(N_Vector, N_Vector, N_Vector); // TODO
@@ -185,10 +234,33 @@ N_Vector N_VNew_Bout(const SUNContext ctx, T& data, const bool own = false) {
   return v;
 }
 
-template <typename... Args>
-N_Vector N_VNew_Bout(SUNContext ctx, Args&... args) {
-  N_Vector vecs[] = {N_VNew_Bout(ctx, args)...};
-  return N_VNew_ManyVector(sizeof...(Args), vecs, ctx);
+N_Vector N_VNew_Bout(const SUNContext ctx, Vector2D& vec, const bool own = false) {
+  N_Vector vecs[] = {N_VNew_Bout(ctx, vec.x, own), N_VNew_Bout(ctx, vec.y, own)};
+  return N_VNew_ManyVector(2, vecs, ctx);
+}
+
+N_Vector N_VNew_Bout(const SUNContext ctx, Vector3D& vec, const bool own = false) {
+  N_Vector vecs[] = {N_VNew_Bout(ctx, vec.x, own), N_VNew_Bout(ctx, vec.y, own),
+                     N_VNew_Bout(ctx, vec.z, own)};
+  return N_VNew_ManyVector(3, vecs, ctx);
+}
+
+template <typename... T>
+N_Vector N_VNew_Bout(const SUNContext ctx, std::vector<T>&... args) {
+  std::vector<N_Vector> vecs((args.size() + ...));
+  auto vecsBegin = vecs.begin();
+  ((std::transform(args.begin(), args.end(), vecsBegin,
+                   [ctx](T& field) { return N_VNew_Bout(ctx, field); }),
+    vecsBegin += args.size()),
+   ...);
+  return N_VNew_ManyVector(vecs.size(), vecs.data(), ctx);
+}
+
+auto test() {
+  Vector3D* f = nullptr;
+  sundials::Context ctx;
+  std::vector v{*f, *f};
+  return N_VNew_Bout(ctx, v, v, v);
 }
 
 #endif

From 25667e4f8bd6eca17219a3ed3225b6d86c62bd8a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 30 May 2024 15:18:11 +0200
Subject: [PATCH 0099/1827] Update docs

---
 manual/sphinx/user_docs/boundary_options.rst | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 57c6658891..a3cdf0078b 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -147,8 +147,10 @@ shifted``, see :ref:`sec-shifted-metric`), the recommended method is
 to apply boundary conditions directly to the ``yup`` and ``ydown``
 parallel slices. This can be done by setting ``bndry_par_yup`` and
 ``bndry_par_ydown``, or ``bndry_par_all`` to set both at once. The
-possible values are ``parallel_dirichlet``, ``parallel_dirichlet_O3``
-and ``parallel_neumann``. The stencils used are the same as for the
+possible values are ``parallel_dirichlet_o1``,
+``parallel_dirichlet_o2``, ``parallel_dirichlet_o3``
+and ``parallel_neumann_o1``, ``parallel_neumann_o2``,
+``parallel_neumann_o3``. The stencils used are the same as for the
 standard boundary conditions without the ``parallel_`` prefix, but are
 applied directly to parallel slices. The boundary condition can only
 be applied after the parallel slices are calculated, which is usually
@@ -168,7 +170,7 @@ For example, for an evolving variable ``f``, put a section in the
     [f]
     bndry_xin = dirichlet
     bndry_xout = dirichlet
-    bndry_par_all = parallel_neumann
+    bndry_par_all = parallel_neumann_o2
     bndry_ydown = none
     bndry_yup = none
 
@@ -278,7 +280,7 @@ cells of the base variable. For example, for an evolving variable
     [f]
     bndry_xin = dirichlet
     bndry_xout = dirichlet
-    bndry_par_all = parallel_dirichlet
+    bndry_par_all = parallel_dirichlet_o2
     bndry_ydown = none
     bndry_yup = none
 
@@ -289,7 +291,7 @@ communication, while the perpendicular ones before:
 
     f.applyBoundary();
     mesh->communicate(f);
-    f.applyParallelBoundary("parallel_neumann");
+    f.applyParallelBoundary("parallel_neumann_o2");
 
 Note that during grid generation care has to be taken to ensure that there are
 no "short" connection lengths. Otherwise it can happen that for a point on a

From 1c31c299ce4f2c8de6bb6a3922bc556b0421e6cc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 30 May 2024 15:18:19 +0200
Subject: [PATCH 0100/1827] Update test

---
 tests/integrated/test-fci-mpi/fci_mpi.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-fci-mpi/fci_mpi.cxx b/tests/integrated/test-fci-mpi/fci_mpi.cxx
index f4c26adc96..94520dd4a6 100644
--- a/tests/integrated/test-fci-mpi/fci_mpi.cxx
+++ b/tests/integrated/test-fci-mpi/fci_mpi.cxx
@@ -20,7 +20,7 @@ int main(int argc, char** argv) {
                                                   Options::getRoot(), mesh)};
       // options->get(fmt::format("input_{:d}:boundary_perp", i), temp_str, s"free_o3");
       mesh->communicate(input);
-      input.applyParallelBoundary("parallel_neumann");
+      input.applyParallelBoundary("parallel_neumann_o2");
       for (int slice = -mesh->ystart; slice <= mesh->ystart; ++slice) {
         if (slice != 0) {
           Field3D tmp{0.};

From bfdf9ec88f4ab6efc62f928420f1f0e485db7346 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 10 Jun 2024 15:06:19 -0700
Subject: [PATCH 0101/1827] Add missing sqrt

---
 src/solver/nvector.hxx | 4 ++--
 src/solver/solver.cxx  | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index f72f63790b..7c35e3cc55 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -71,9 +71,9 @@ BoutReal dotProd(const T& f1, const T& f2, bool allpe = false,
 template <typename T>
 BoutReal weightedL2Norm(const T& f, const T& w, bool allpe = false,
                         const std::string& rgn = "RGN_NOBNDRY") {
-  return fieldReduce(
+  return std::sqrt(fieldReduce(
       [](const BoutReal v1, const BoutReal v2) { return std::pow(v1 * v2, 2); }, allpe,
-      rgn, f, w);
+      rgn, f, w));
 }
 
 template <typename T>
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 1b7ec1fd74..8aab466f66 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -22,6 +22,8 @@
 
 #include "bout/build_config.hxx"
 
+#include "nvector.hxx"
+
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/boutcomm.hxx"

From b4ebb73d275b46541b2708515e0bf7f07b13ae5e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Sep 2024 21:34:27 +0000
Subject: [PATCH 0102/1827] Update numpy requirement from ~=2.0.0 to ~=2.1.1

Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.0...v2.1.1)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index bc3d31de2b..a6e578ff69 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 Jinja2~=3.1.4
-numpy~=2.0.0
+numpy~=2.1.1
 scipy>=1.11.0
 netcdf4~=1.7.1
 matplotlib>=3.7.0

From 58d2b3aa4f571c686ed4949fda88ed31ca095e0a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 23 Sep 2024 19:27:53 +0000
Subject: [PATCH 0103/1827] Bump externalpackages/googletest from `0953a17` to
 `6dae7eb`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `0953a17` to `6dae7eb`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/0953a17a4281fc26831da647ad3fcd5e21e6473b...6dae7eb4a5c3a169f3e298392bff4680224aa94a)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 0953a17a42..6dae7eb4a5 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 0953a17a4281fc26831da647ad3fcd5e21e6473b
+Subproject commit 6dae7eb4a5c3a169f3e298392bff4680224aa94a

From d36debf2b1e960fef22da44ab17c81a9bd016e1e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2024 19:12:09 +0000
Subject: [PATCH 0104/1827] Update numpy requirement from ~=2.1.1 to ~=2.1.2

Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index a6e578ff69..3fe0712381 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 Jinja2~=3.1.4
-numpy~=2.1.1
+numpy~=2.1.2
 scipy>=1.11.0
 netcdf4~=1.7.1
 matplotlib>=3.7.0

From 6ead1ae9eb3efd2157363baccf8ba360a306d900 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 17 Oct 2024 09:41:39 -0700
Subject: [PATCH 0105/1827] Start adding vector to arkode integrator

---
 cmake/SetupBOUTThirdParty.cmake    |  4 +-
 src/solver/impls/arkode/arkode.cxx | 12 +++--
 src/solver/nvector.hxx             | 86 ++++++++++++++++++------------
 src/solver/solver.cxx              |  2 -
 4 files changed, 64 insertions(+), 40 deletions(-)

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 127fbda765..ae62f7e0e0 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -297,9 +297,11 @@ if (BOUT_USE_SUNDIALS)
     FetchContent_MakeAvailable(sundials)
     message(STATUS "SUNDIALS done configuring")
   else()
-    find_package(SUNDIALS 4 REQUIRED)
+    enable_language(C)
+    find_package(SUNDIALS REQUIRED)
   endif()
   target_link_libraries(bout++ PUBLIC SUNDIALS::nvecparallel)
+  target_link_libraries(bout++ PUBLIC SUNDIALS::nvecmanyvector)
   target_link_libraries(bout++ PUBLIC SUNDIALS::cvode)
   target_link_libraries(bout++ PUBLIC SUNDIALS::ida)
   target_link_libraries(bout++ PUBLIC SUNDIALS::arkode)
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index bc3be6f80a..ae02739b8b 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -40,6 +40,7 @@
 #include "bout/output.hxx"
 #include "bout/unused.hxx"
 #include "bout/utils.hxx"
+#include "../../nvector.hxx"
 
 #include <arkode/arkode_arkstep.h>
 #include <arkode/arkode_bbdpre.h>
@@ -187,13 +188,18 @@ int ArkodeSolver::init() {
                n2Dvars(), neq, local_N);
 
   // Allocate memory
-  uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
+  // uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
+  // if (uvec == nullptr) {
+  //   throw BoutException("SUNDIALS memory allocation failed\n");
+  // }
+
+  uvec = N_VNew_Bout(suncontext, *f3d.back().var, false);
   if (uvec == nullptr) {
-    throw BoutException("SUNDIALS memory allocation failed\n");
+    throw BoutException("BOUT N_Vector failed\n");
   }
 
   // Put the variables into uvec
-  save_vars(N_VGetArrayPointer(uvec));
+  // save_vars(N_VGetArrayPointer(uvec));
 
   ASSERT1(solve_explicit or solve_implicit);
 
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 7c35e3cc55..a103b71a5b 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -34,10 +34,32 @@
 #include "bout/sundials_backports.hxx"
 
 namespace {
+template <typename T>
+T allReduce(const T local, const MPI_Op op = MPI_SUM) {
+  T global;
+  constexpr auto type = []() {
+    if constexpr (std::is_same_v<T, double>) {
+      return MPI_DOUBLE;
+    } else if constexpr (std::is_same_v<T, unsigned int>) {
+      return MPI_UNSIGNED;
+    }
+  }();
+  MPI_Allreduce(&local, &global, 1, type, op, BoutComm::get());
+  return global;
+}
+
 template <typename T>
 struct Content {
   T& field; // A Field2D or Field3D
   const bool own;
+  const bool evolve_bndry;
+  const sunindextype length;
+
+  Content(T& field, const bool own, const bool evolve_bndry)
+      : field(field), own(own), evolve_bndry(evolve_bndry),
+        length(allReduce(getRegion().size())) {}
+
+  auto getRegion() const { return field.getRegion(evolve_bndry ? RGN_ALL : RGN_NOBNDRY); }
 
   ~Content() {
     if (own) {
@@ -46,57 +68,56 @@ struct Content {
   }
 };
 
-template <typename R, typename T, typename... U>
-BoutReal fieldReduce(R reduce, bool allpe, const std::string& rgn, const T& f1,
-                     const U&... f2) {
+template <typename R, typename C, typename... D>
+BoutReal fieldReduce(const R reduce, const bool allpe, const C& c1, const D&... c2) {
   BoutReal result = 0;
-  const auto region = f1.getRegion(rgn);
-    BOUT_FOR_OMP(i, region, parallel for reduction(+:result)) {
-      result += reduce(f1[i], f2[i]...);
-    }
+  const auto region = c1.getRegion();
+  BOUT_FOR_OMP(i, region, parallel for reduction(+:result)) {
+    result += reduce(c1.field[i], c2.field[i]...);
+  }
 
-    if (allpe) {
-      BoutReal localresult = result;
-      MPI_Allreduce(&localresult, &result, 1, MPI_DOUBLE, MPI_MAX, BoutComm::get());
-    }
-    return result;
+  return allpe ? allReduce(result) : result;
 }
 
 template <typename T>
-BoutReal dotProd(const T& f1, const T& f2, bool allpe = false,
-                 const std::string& rgn = "RGN_NOBNDRY") {
-  return fieldReduce(std::multiplies(), allpe, rgn, f1, f2);
+BoutReal dotProd(const Content<T>& c1, const Content<T>& c2, const bool allpe) {
+  return fieldReduce(std::multiplies<BoutReal>(), allpe, c1, c2);
 }
 
 template <typename T>
-BoutReal weightedL2Norm(const T& f, const T& w, bool allpe = false,
-                        const std::string& rgn = "RGN_NOBNDRY") {
+BoutReal weightedL2Norm(const Content<T>& c1, const Content<T>& c2, const bool allpe) {
   return std::sqrt(fieldReduce(
-      [](const BoutReal v1, const BoutReal v2) { return std::pow(v1 * v2, 2); }, allpe,
-      rgn, f, w));
+      [](const auto v1, const auto v2) { return std::pow(v1 * v2, 2); }, allpe,
+      c1, c2));
+}
+
+template <typename T>
+BoutReal l1Norm(const Content<T>& c, const bool allpe) {
+  return fieldReduce(std::abs<BoutReal>, allpe, c);
 }
 
 template <typename T>
-BoutReal l1Norm(const T& f, bool allpe = false, const std::string& rgn = "RGN_NOBNDRY") {
-  return fieldReduce(std::abs<BoutReal>, allpe, rgn, f);
+Content<T>& N_VContent_Bout(const N_Vector v) {
+  return *static_cast<Content<T>*>(v->content);
 }
 } // namespace
 
 template <typename T>
 T& N_VField_Bout(const N_Vector v) {
-  return static_cast<Content<T>*>(v->content)->field;
+  return N_VContent_Bout<T>(v).field;
 }
 
 template <typename T, typename = bout::utils::EnableIfField<T>>
-N_Vector N_VNew_Bout(const SUNContext ctx, T& field, const bool own = false) {
+N_Vector N_VNew_Bout(const SUNContext ctx, T& field, const bool evolve_bndry,
+                     const bool own = false) {N_VNew_Bout
   N_Vector v = callWithSUNContext(N_VNewEmpty, ctx);
   if (v == nullptr) {
     throw BoutException("N_VNewEmpty failed\n");
   }
 
-  v->content = static_cast<void*>(new Content<T>({field, own}));
+  v->content = static_cast<void*>(new Content<T>(field, own, evolve_bndry));
 
-  v->ops->nvgetvectorid = []([[maybe_unused]] N_Vector x) {
+  v->ops->nvgetvectorid = [](N_Vector) {
     return SUNDIALS_NVEC_CUSTOM;
   };
 
@@ -110,14 +131,11 @@ N_Vector N_VNew_Bout(const SUNContext ctx, T& field, const bool own = false) {
     if (x == nullptr) {
       return;
     }
-    delete static_cast<Content<T>*>(x->content);
+    delete &N_VContent_Bout<T>(x);
     N_VFreeEmpty(x);
   };
 
-  v->ops->nvgetlength = [](N_Vector x) {
-    // Is this correct with MPI?
-    return static_cast<sunindextype>(N_VField_Bout<T>(x).size());
-  };
+  v->ops->nvgetlength = [](N_Vector x) { return N_VContent_Bout<T>(x).length; };
 
   v->ops->nvlinearsum = [](sunrealtype a, N_Vector x, sunrealtype b, N_Vector y,
                            N_Vector z) {
@@ -151,23 +169,23 @@ N_Vector N_VNew_Bout(const SUNContext ctx, T& field, const bool own = false) {
   };
 
   v->ops->nvdotprod = [](N_Vector x, N_Vector y) {
-    return dotProd(N_VField_Bout<T>(x), N_VField_Bout<T>(y), true);
+    return dotProd(N_VContent_Bout<T>(x), N_VContent_Bout<T>(y), true);
   };
 
   v->ops->nvmaxnorm = [](N_Vector x) { return max(abs(N_VField_Bout<T>(x)), true); };
 
   v->ops->nvwrmsnorm = [](N_Vector x, N_Vector y) {
     const auto sqrtLen = std::sqrt(static_cast<BoutReal>(N_VGetLength(x)));
-    return weightedL2Norm(N_VField_Bout<T>(x), N_VField_Bout<T>(y), true) / sqrtLen;
+    return weightedL2Norm(N_VContent_Bout<T>(x), N_VContent_Bout<T>(y), true) / sqrtLen;
   };
 
   v->ops->nvmin = [](N_Vector x) { return min(N_VField_Bout<T>(x), true); };
 
   v->ops->nvwl2norm = [](N_Vector x, N_Vector y) {
-    return weightedL2Norm(N_VField_Bout<T>(x), N_VField_Bout<T>(y), true);
+    return weightedL2Norm(N_VContent_Bout<T>(x), N_VContent_Bout<T>(y), true);
   };
 
-  v->ops->nvl1norm = [](N_Vector x) { return l1Norm(N_VField_Bout<T>(x), true); };
+  v->ops->nvl1norm = [](N_Vector x) { return l1Norm(N_VContent_Bout<T>(x), true); };
 
   /* Other functions to implement (most optional)
   N_Vector (*nvcloneempty)(N_Vector); // Probably not needed
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 8aab466f66..1b7ec1fd74 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -22,8 +22,6 @@
 
 #include "bout/build_config.hxx"
 
-#include "nvector.hxx"
-
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/boutcomm.hxx"

From c200e2f0cbc5be4bcece466820c716fb85b13f10 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Fri, 18 Oct 2024 21:18:49 -0700
Subject: [PATCH 0106/1827] Add functions to swap state

---
 src/solver/impls/arkode/arkode.cxx |   4 +-
 src/solver/impls/arkode/arkode.hxx |  27 ++
 src/solver/nvector.hxx             | 426 ++++++++++++++---------------
 3 files changed, 229 insertions(+), 228 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 25e2a1adbe..0e10755fa3 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -39,7 +39,6 @@
 #include "bout/output.hxx"
 #include "bout/unused.hxx"
 #include "bout/utils.hxx"
-#include "../../nvector.hxx"
 
 #include <arkode/arkode_arkstep.h>
 #include <arkode/arkode_bbdpre.h>
@@ -191,7 +190,8 @@ int ArkodeSolver::init() {
   //   throw BoutException("SUNDIALS memory allocation failed\n");
   // }
 
-  uvec = N_VNew_Bout(suncontext, *f3d.back().var, false);
+  // uvec = N_VNew_Bout(suncontext, *f3d.back().var, false);
+  uvec = nullptr;
   if (uvec == nullptr) {
     throw BoutException("BOUT N_Vector failed\n");
   }
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 4050ed377f..6ce1af9565 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -44,6 +44,7 @@ RegisterUnavailableSolver
 #include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/sundials_backports.hxx"
+#include "../../nvector.hxx"
 
 #include <nvector/nvector_parallel.h>
 #include <sundials/sundials_config.h>
@@ -158,6 +159,32 @@ private:
                              std::vector<BoutReal>& f2dtols,
                              std::vector<BoutReal>& f3dtols, bool bndry);
 
+  N_Vector nvector_from_state(const SUNContext ctx) {
+    std::vector<N_Vector> subvectors;
+    subvectors.reserve(f2d.size() + f3d.size());
+    const auto inserter = std::back_inserter(subvectors);
+
+    const auto var_str_to_nvector = [ctx](auto &var_str) {
+      return BoutNVector::create(ctx, var_str.var, var_str.evolve_bndry);
+    };
+    std::transform(f2d.begin(), f2d.end(), inserter, var_str_to_nvector);
+    std::transform(f3d.begin(), f3d.end(), inserter, var_str_to_nvector);
+    return BoutNVector::create(ctx, subvectors);
+  }
+
+  void swap_rhs_state(const N_Vector v) {
+    std::size_t i = 0;
+    for (auto &var_str : f2d) {
+      BoutNVector::swap(v, var_str.F_var, i);
+      i++;
+    }
+
+    for (auto &var_str : f3d) {
+      BoutNVector::swap(v, var_str.F_var, i);
+      i++;
+    }
+  }
+
   /// SPGMR solver structure
   SUNLinearSolver sun_solver{nullptr};
   /// Solver for implicit stages
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index a103b71a5b..9ecc247412 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -20,265 +20,239 @@
  *
  **************************************************************************/
 
-#ifndef BOUT_SUNDIAL_SOLVER_H
-#define BOUT_SUNDIAL_SOLVER_H
+#ifndef BOUT_NVECTOR_H
+#define BOUT_NVECTOR_H
 
 #include <bout/field.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
-#include <bout/vector2d.hxx>
-#include <bout/vector3d.hxx>
 #include <nvector/nvector_manyvector.h>
 #include <sundials/sundials_nvector.h>
 
 #include "bout/sundials_backports.hxx"
 
-namespace {
-template <typename T>
-T allReduce(const T local, const MPI_Op op = MPI_SUM) {
-  T global;
-  constexpr auto type = []() {
-    if constexpr (std::is_same_v<T, double>) {
-      return MPI_DOUBLE;
-    } else if constexpr (std::is_same_v<T, unsigned int>) {
-      return MPI_UNSIGNED;
-    }
-  }();
-  MPI_Allreduce(&local, &global, 1, type, op, BoutComm::get());
-  return global;
-}
-
-template <typename T>
-struct Content {
-  T& field; // A Field2D or Field3D
-  const bool own;
-  const bool evolve_bndry;
-  const sunindextype length;
-
-  Content(T& field, const bool own, const bool evolve_bndry)
-      : field(field), own(own), evolve_bndry(evolve_bndry),
-        length(allReduce(getRegion().size())) {}
-
-  auto getRegion() const { return field.getRegion(evolve_bndry ? RGN_ALL : RGN_NOBNDRY); }
-
-  ~Content() {
-    if (own) {
-      delete &field;
+class BoutNVector {
+private:
+  template <typename V>
+  static V all_reduce(const V local, const MPI_Op op = MPI_SUM) {
+    V global;
+    static constexpr auto type = []() {
+      if constexpr (std::is_same_v<V, double>) {
+        return MPI_DOUBLE;
+      } else if constexpr (std::is_same_v<V, unsigned int>) {
+        return MPI_UNSIGNED;
+      }
+    }();
+    MPI_Allreduce(&local, &global, 1, type, op, BoutComm::get());
+    return global;
+  }
+  
+  template <typename T>
+  struct Content {
+    T* field;
+    const bool own;
+    const bool evolve_bndry;
+    const sunindextype length;
+
+    Content(T* const field, const bool own, const bool evolve_bndry)
+        : field(field), own(own), evolve_bndry(evolve_bndry),
+          length(all_reduce(getRegion().size())) {}
+
+    auto getRegion() const { return field->getRegion(evolve_bndry ? RGN_ALL : RGN_NOBNDRY); }
+
+    ~Content() {
+      if (own) {
+        delete &field;
+      }
     }
+  };
+
+  template <typename T>
+  static Content<T>& get_content(const N_Vector v) {
+    return *static_cast<Content<T>*>(v->content);
   }
-};
 
-template <typename R, typename C, typename... D>
-BoutReal fieldReduce(const R reduce, const bool allpe, const C& c1, const D&... c2) {
-  BoutReal result = 0;
-  const auto region = c1.getRegion();
-  BOUT_FOR_OMP(i, region, parallel for reduction(+:result)) {
-    result += reduce(c1.field[i], c2.field[i]...);
+  template <typename T>
+  static T& get_field(const N_Vector v) {
+    return *get_content<T>(v).field;
   }
 
-  return allpe ? allReduce(result) : result;
-}
-
-template <typename T>
-BoutReal dotProd(const Content<T>& c1, const Content<T>& c2, const bool allpe) {
-  return fieldReduce(std::multiplies<BoutReal>(), allpe, c1, c2);
-}
-
-template <typename T>
-BoutReal weightedL2Norm(const Content<T>& c1, const Content<T>& c2, const bool allpe) {
-  return std::sqrt(fieldReduce(
-      [](const auto v1, const auto v2) { return std::pow(v1 * v2, 2); }, allpe,
-      c1, c2));
-}
-
-template <typename T>
-BoutReal l1Norm(const Content<T>& c, const bool allpe) {
-  return fieldReduce(std::abs<BoutReal>, allpe, c);
-}
-
-template <typename T>
-Content<T>& N_VContent_Bout(const N_Vector v) {
-  return *static_cast<Content<T>*>(v->content);
-}
-} // namespace
-
-template <typename T>
-T& N_VField_Bout(const N_Vector v) {
-  return N_VContent_Bout<T>(v).field;
-}
-
-template <typename T, typename = bout::utils::EnableIfField<T>>
-N_Vector N_VNew_Bout(const SUNContext ctx, T& field, const bool evolve_bndry,
-                     const bool own = false) {N_VNew_Bout
-  N_Vector v = callWithSUNContext(N_VNewEmpty, ctx);
-  if (v == nullptr) {
-    throw BoutException("N_VNewEmpty failed\n");
+  template <typename T, typename R, typename ... V>
+  static BoutReal reduce_field(const R reduce, const bool allpe, const N_Vector v1, const V... v2) {
+      BoutReal result = 0;
+      const auto region = get_content<T>(v1).getRegion();
+      BOUT_FOR_OMP(i, region, parallel for reduction(+:result)) {
+        result += reduce(get_field<T>(v1)[i], get_field<T>(v2)[i]...);
+      }
+
+      return allpe ? all_reduce(result) : result;
   }
 
-  v->content = static_cast<void*>(new Content<T>(field, own, evolve_bndry));
+public:
+  // NVector() = delete; // Enforce static access only
+  
+  template <typename T, typename = bout::utils::EnableIfField<T>>
+  static N_Vector create(const SUNContext ctx, T *const field, const bool evolve_bndry,
+                      const bool own = false) {
+    N_Vector v = callWithSUNContext(N_VNewEmpty, ctx);
+    if (v == nullptr) {
+      throw BoutException("N_VNewEmpty failed\n");
+    }
 
-  v->ops->nvgetvectorid = [](N_Vector) {
-    return SUNDIALS_NVEC_CUSTOM;
-  };
+    v->content = static_cast<void*>(new Content<T>(field, own, evolve_bndry));
 
-  v->ops->nvclone = [](N_Vector x) {
-    T* const fieldClone = new T(N_VField_Bout<T>(x));
-    fieldClone->allocate();
-    return N_VNew_Bout(x->sunctx, *fieldClone, true);
-  };
+    v->ops->nvgetvectorid = [](N_Vector) { return SUNDIALS_NVEC_CUSTOM; };
 
-  v->ops->nvdestroy = [](N_Vector x) {
-    if (x == nullptr) {
-      return;
-    }
-    delete &N_VContent_Bout<T>(x);
-    N_VFreeEmpty(x);
-  };
+    v->ops->nvclone = [](N_Vector x) {
+      Content<T> content = get_content<T>(x);
+      T* field_clone = new T(*content.field);
+      field_clone->allocate();
+      return create(x->sunctx, field_clone, content.evolve_bndry, true);
+    };
 
-  v->ops->nvgetlength = [](N_Vector x) { return N_VContent_Bout<T>(x).length; };
+    v->ops->nvdestroy = [](N_Vector x) {
+      if (x == nullptr) {
+        return;
+      }
+      delete &get_content<T>(x);
+      N_VFreeEmpty(x);
+    };
 
-  v->ops->nvlinearsum = [](sunrealtype a, N_Vector x, sunrealtype b, N_Vector y,
-                           N_Vector z) {
-    N_VField_Bout<T>(z) = a * N_VField_Bout<T>(x) + b * N_VField_Bout<T>(y);
-  };
+    v->ops->nvgetlength = [](N_Vector x) { return get_content<T>(x).length; };
 
-  v->ops->nvconst = [](sunrealtype c, N_Vector x) { N_VField_Bout<T>(x) = c; };
+    v->ops->nvlinearsum = [](sunrealtype a, N_Vector x, sunrealtype b, N_Vector y,
+                            N_Vector z) {
+      get_field<T>(z) = a * get_field<T>(x) + b * get_field<T>(y);
+    };
 
-  v->ops->nvprod = [](N_Vector x, N_Vector y, N_Vector z) {
-    N_VField_Bout<T>(z) = N_VField_Bout<T>(x) * N_VField_Bout<T>(y);
-  };
+    v->ops->nvconst = [](sunrealtype c, N_Vector x) { get_field<T>(x) = c; };
 
-  v->ops->nvdiv = [](N_Vector x, N_Vector y, N_Vector z) {
-    N_VField_Bout<T>(z) = N_VField_Bout<T>(x) / N_VField_Bout<T>(y);
-  };
+    v->ops->nvprod = [](N_Vector x, N_Vector y, N_Vector z) {
+      get_field<T>(z) = get_field<T>(x) * get_field<T>(y);
+    };
 
-  v->ops->nvscale = [](sunrealtype a, N_Vector x, N_Vector y) {
-    N_VField_Bout<T>(y) = a * N_VField_Bout<T>(x);
-  };
+    v->ops->nvdiv = [](N_Vector x, N_Vector y, N_Vector z) {
+      get_field<T>(z) = get_field<T>(x) / get_field<T>(y);
+    };
 
-  v->ops->nvabs = [](N_Vector x, N_Vector y) {
-    N_VField_Bout<T>(y) = abs(N_VField_Bout<T>(x));
-  };
+    v->ops->nvscale = [](sunrealtype a, N_Vector x, N_Vector y) {
+      get_field<T>(y) = a * get_field<T>(x);
+    };
 
-  v->ops->nvinv = [](N_Vector x, N_Vector y) {
-    N_VField_Bout<T>(y) = 1 / N_VField_Bout<T>(x);
-  };
+    v->ops->nvabs = [](N_Vector x, N_Vector y) {
+      get_field<T>(y) = abs(get_field<T>(x));
+    };
 
-  v->ops->nvaddconst = [](N_Vector x, sunrealtype a, N_Vector y) {
-    N_VField_Bout<T>(y) = a + N_VField_Bout<T>(x);
-  };
+    v->ops->nvinv = [](N_Vector x, N_Vector y) {
+      get_field<T>(y) = 1 / get_field<T>(x);
+    };
 
-  v->ops->nvdotprod = [](N_Vector x, N_Vector y) {
-    return dotProd(N_VContent_Bout<T>(x), N_VContent_Bout<T>(y), true);
-  };
+    v->ops->nvaddconst = [](N_Vector x, sunrealtype a, N_Vector y) {
+      get_field<T>(y) = a + get_field<T>(x);
+    };
 
-  v->ops->nvmaxnorm = [](N_Vector x) { return max(abs(N_VField_Bout<T>(x)), true); };
+    v->ops->nvdotprod = [](N_Vector x, N_Vector y) {
+      return reduce_field<T>(std::multiplies<BoutReal>(), true, x, y);
+    };
 
-  v->ops->nvwrmsnorm = [](N_Vector x, N_Vector y) {
-    const auto sqrtLen = std::sqrt(static_cast<BoutReal>(N_VGetLength(x)));
-    return weightedL2Norm(N_VContent_Bout<T>(x), N_VContent_Bout<T>(y), true) / sqrtLen;
-  };
+    v->ops->nvmaxnorm = [](N_Vector x) { return max(abs(get_field<T>(x)), true); };
 
-  v->ops->nvmin = [](N_Vector x) { return min(N_VField_Bout<T>(x), true); };
+    v->ops->nvwrmsnorm = [](N_Vector x, N_Vector y) {
+      return N_VWL2Norm(x, y) / std::sqrt(static_cast<BoutReal>(N_VGetLength(x)));
+    };
 
-  v->ops->nvwl2norm = [](N_Vector x, N_Vector y) {
-    return weightedL2Norm(N_VContent_Bout<T>(x), N_VContent_Bout<T>(y), true);
-  };
+    v->ops->nvmin = [](N_Vector x) { return min(get_field<T>(x), true); };
+
+    v->ops->nvwl2norm = [](N_Vector x, N_Vector y) {
+      return std::sqrt(reduce_field<T>([](const auto v1, const auto v2) {
+        return std::pow(v1 * v2, 2);
+      }, true, x, y));
+    };
+
+    v->ops->nvl1norm = [](N_Vector x) {
+      return reduce_field<T>(std::abs<BoutReal>, true, x);
+    };
+
+    return v;
+  }
+
+  template <typename V>
+  static N_Vector create(const SUNContext ctx, V& subvectors) {
+    return callWithSUNContext(N_VNew_ManyVector, ctx, std::size(subvectors),
+                              std::data(subvectors));
+  }
+
+  template <typename T, typename = bout::utils::EnableIfField<T>>
+  static void swap(const N_Vector v, T* &field) {
+    std::swap(get_content<T>(v).field, field);
+  }
 
-  v->ops->nvl1norm = [](N_Vector x) { return l1Norm(N_VContent_Bout<T>(x), true); };
-
-  /* Other functions to implement (most optional)
-  N_Vector (*nvcloneempty)(N_Vector); // Probably not needed
-   void (*nvdestroy)(N_Vector); // Implemented
-   void (*nvspace)(N_Vector, sunindextype*, sunindextype*); // Probably not needed
-   sunrealtype* (*nvgetarraypointer)(N_Vector); // Probably not needed
-   sunrealtype* (*nvgetdevicearraypointer)(N_Vector); // Probably not needed
-   void (*nvsetarraypointer)(sunrealtype*, N_Vector); // Probably not needed
-   SUNComm (*nvgetcommunicator)(N_Vector); // Probably not needed
-   sunindextype (*nvgetlength)(N_Vector); // Implemented
-   sunindextype (*nvgetlocallength)(N_Vector);  // Probably not needed
-   void (*nvlinearsum)(sunrealtype, N_Vector, sunrealtype, N_Vector, N_Vector); // Implemented
-   void (*nvconst)(sunrealtype, N_Vector); // Implemented
-   void (*nvprod)(N_Vector, N_Vector, N_Vector); // Implemented
-   void (*nvdiv)(N_Vector, N_Vector, N_Vector); // Implemented
-   void (*nvscale)(sunrealtype, N_Vector, N_Vector); // Implemented
-   void (*nvabs)(N_Vector, N_Vector); // Implemented
-   void (*nvinv)(N_Vector, N_Vector); // Implemented
-   void (*nvaddconst)(N_Vector, sunrealtype, N_Vector); // Implemented
-   sunrealtype (*nvdotprod)(N_Vector, N_Vector); // Implemented
-   sunrealtype (*nvmaxnorm)(N_Vector); // Implemented
-   sunrealtype (*nvwrmsnorm)(N_Vector, N_Vector); // Implemented
-   sunrealtype (*nvwrmsnormmask)(N_Vector, N_Vector, N_Vector); // TODO
-   sunrealtype (*nvmin)(N_Vector); // Implemented
-   sunrealtype (*nvwl2norm)(N_Vector, N_Vector); // Implemented
-   sunrealtype (*nvl1norm)(N_Vector); // Implemented
-   void (*nvcompare)(sunrealtype, N_Vector, N_Vector); // TODO
-   sunbooleantype (*nvinvtest)(N_Vector, N_Vector); // TODO
-   sunbooleantype (*nvconstrmask)(N_Vector, N_Vector, N_Vector); // TODO
-   sunrealtype (*nvminquotient)(N_Vector, N_Vector); // TODO
-   SUNErrCode (*nvlinearcombination)(int, sunrealtype*, N_Vector*, N_Vector); // TODO
-   SUNErrCode (*nvscaleaddmulti)(int, sunrealtype*, N_Vector, N_Vector*,
-                                 N_Vector*); // Probably not needed
-   SUNErrCode (*nvdotprodmulti)(int, N_Vector, N_Vector*, sunrealtype*); // Probably not needed
-   SUNErrCode (*nvlinearsumvectorarray)(int, sunrealtype, N_Vector*, sunrealtype,
-                                          N_Vector*, N_Vector*); // Probably not needed
-   SUNErrCode (*nvscalevectorarray)(int, sunrealtype*, N_Vector*, N_Vector*); // Probably not needed
-   SUNErrCode (*nvconstvectorarray)(int, sunrealtype, N_Vector*); // Probably not needed
-   SUNErrCode (*nvwrmsnormvectorarray)(int, N_Vector*, N_Vector*, sunrealtype*); // Probably not needed
-   SUNErrCode (*nvwrmsnormmaskvectorarray)(int, N_Vector*, N_Vector*, N_Vector,
-                                             sunrealtype*); // Probably not needed
-   SUNErrCode (*nvscaleaddmultivectorarray)(int, int, sunrealtype*, N_Vector*,
-                                             N_Vector**, N_Vector**); // Probably not needed
-   SUNErrCode (*nvlinearcombinationvectorarray)(int, int, sunrealtype*,
-                                                N_Vector**, N_Vector*); // Probably not needed
-   sunrealtype (*nvdotprodlocal)(N_Vector, N_Vector); // Probably not needed
-   sunrealtype (*nvmaxnormlocal)(N_Vector); // Probably not needed
-   sunrealtype (*nvminlocal)(N_Vector); // Probably not needed
-   sunrealtype (*nvl1normlocal)(N_Vector); // Probably not needed
-   sunbooleantype (*nvinvtestlocal)(N_Vector, N_Vector); // Probably not needed
-   sunbooleantype (*nvconstrmasklocal)(N_Vector, N_Vector, N_Vector); // Probably not needed
-   sunrealtype (*nvminquotientlocal)(N_Vector, N_Vector); // Probably not needed
-   sunrealtype (*nvwsqrsumlocal)(N_Vector, N_Vector); // Probably not needed
-   sunrealtype (*nvwsqrsummasklocal)(N_Vector, N_Vector, N_Vector); // Probably not needed
-   SUNErrCode (*nvdotprodmultilocal)(int, N_Vector, N_Vector*, sunrealtype*); // Probably not needed
-   SUNErrCode (*nvdotprodmultiallreduce)(int, N_Vector, sunrealtype*); // Probably not needed
-   SUNErrCode (*nvbufsize)(N_Vector, sunindextype*); // Probably not needed
-   SUNErrCode (*nvbufpack)(N_Vector, void*); // Probably not needed
-   SUNErrCode (*nvbufunpack)(N_Vector, void*); // Probably not needed
-   void (*nvprint)(N_Vector); // Nice, but optional
-   void (*nvprintfile)(N_Vector, FILE*); // Probably not needed
-   */
-
-  return v;
-}
-
-N_Vector N_VNew_Bout(const SUNContext ctx, Vector2D& vec, const bool own = false) {
-  N_Vector vecs[] = {N_VNew_Bout(ctx, vec.x, own), N_VNew_Bout(ctx, vec.y, own)};
-  return N_VNew_ManyVector(2, vecs, ctx);
-}
-
-N_Vector N_VNew_Bout(const SUNContext ctx, Vector3D& vec, const bool own = false) {
-  N_Vector vecs[] = {N_VNew_Bout(ctx, vec.x, own), N_VNew_Bout(ctx, vec.y, own),
-                     N_VNew_Bout(ctx, vec.z, own)};
-  return N_VNew_ManyVector(3, vecs, ctx);
-}
-
-template <typename... T>
-N_Vector N_VNew_Bout(const SUNContext ctx, std::vector<T>&... args) {
-  std::vector<N_Vector> vecs((args.size() + ...));
-  auto vecsBegin = vecs.begin();
-  ((std::transform(args.begin(), args.end(), vecsBegin,
-                   [ctx](T& field) { return N_VNew_Bout(ctx, field); }),
-    vecsBegin += args.size()),
-   ...);
-  return N_VNew_ManyVector(vecs.size(), vecs.data(), ctx);
-}
-
-auto test() {
-  Vector3D* f = nullptr;
-  sundials::Context ctx;
-  std::vector v{*f, *f};
-  return N_VNew_Bout(ctx, v, v, v);
-}
+  template <typename T, typename = bout::utils::EnableIfField<T>>
+  static void swap(const N_Vector v, T* &field, std::size_t subvector) {
+    return swap(N_VGetSubvector_ManyVector(v, subvector), field);
+  }
+};
 
 #endif
+
+/* Other functions to implement (most optional)
+N_Vector (*nvcloneempty)(N_Vector); // Probably not needed
+void (*nvdestroy)(N_Vector); // Implemented
+void (*nvspace)(N_Vector, sunindextype*, sunindextype*); // Not needed
+sunrealtype* (*nvgetarraypointer)(N_Vector); // Probably not needed
+sunrealtype* (*nvgetdevicearraypointer)(N_Vector); // Probably not needed
+void (*nvsetarraypointer)(sunrealtype*, N_Vector); // Probably not needed
+SUNComm (*nvgetcommunicator)(N_Vector); // Probably not needed
+sunindextype (*nvgetlength)(N_Vector); // Implemented
+sunindextype (*nvgetlocallength)(N_Vector);  // Probably not needed
+void (*nvlinearsum)(sunrealtype, N_Vector, sunrealtype, N_Vector, N_Vector); // Implemented
+void (*nvconst)(sunrealtype, N_Vector); // Implemented
+void (*nvprod)(N_Vector, N_Vector, N_Vector); // Implemented
+void (*nvdiv)(N_Vector, N_Vector, N_Vector); // Implemented
+void (*nvscale)(sunrealtype, N_Vector, N_Vector); // Implemented
+void (*nvabs)(N_Vector, N_Vector); // Implemented
+void (*nvinv)(N_Vector, N_Vector); // Implemented
+void (*nvaddconst)(N_Vector, sunrealtype, N_Vector); // Implemented
+sunrealtype (*nvdotprod)(N_Vector, N_Vector); // Implemented
+sunrealtype (*nvmaxnorm)(N_Vector); // Implemented
+sunrealtype (*nvwrmsnorm)(N_Vector, N_Vector); // Implemented
+sunrealtype (*nvwrmsnormmask)(N_Vector, N_Vector, N_Vector); // TODO
+sunrealtype (*nvmin)(N_Vector); // Implemented
+sunrealtype (*nvwl2norm)(N_Vector, N_Vector); // Implemented
+sunrealtype (*nvl1norm)(N_Vector); // Implemented
+void (*nvcompare)(sunrealtype, N_Vector, N_Vector); // TODO
+sunbooleantype (*nvinvtest)(N_Vector, N_Vector); // TODO
+sunbooleantype (*nvconstrmask)(N_Vector, N_Vector, N_Vector); // TODO
+sunrealtype (*nvminquotient)(N_Vector, N_Vector); // TODO
+SUNErrCode (*nvlinearcombination)(int, sunrealtype*, N_Vector*, N_Vector); // TODO
+SUNErrCode (*nvscaleaddmulti)(int, sunrealtype*, N_Vector, N_Vector*,
+                          N_Vector*); // Probably not needed
+SUNErrCode (*nvdotprodmulti)(int, N_Vector, N_Vector*, sunrealtype*); // Probably not needed
+SUNErrCode (*nvlinearsumvectorarray)(int, sunrealtype, N_Vector*, sunrealtype,
+                                    N_Vector*, N_Vector*); // Probably not needed
+SUNErrCode (*nvscalevectorarray)(int, sunrealtype*, N_Vector*, N_Vector*); // Probably not needed
+SUNErrCode (*nvconstvectorarray)(int, sunrealtype, N_Vector*); // Probably not needed
+SUNErrCode (*nvwrmsnormvectorarray)(int, N_Vector*, N_Vector*, sunrealtype*); // Probably not needed
+SUNErrCode (*nvwrmsnormmaskvectorarray)(int, N_Vector*, N_Vector*, N_Vector,
+                                      sunrealtype*); // Probably not needed
+SUNErrCode (*nvscaleaddmultivectorarray)(int, int, sunrealtype*, N_Vector*,
+                                      N_Vector**, N_Vector**); // Probably not needed
+SUNErrCode (*nvlinearcombinationvectorarray)(int, int, sunrealtype*,
+                                          N_Vector**, N_Vector*); // Probably not needed
+sunrealtype (*nvdotprodlocal)(N_Vector, N_Vector); // Probably not needed
+sunrealtype (*nvmaxnormlocal)(N_Vector); // Probably not needed
+sunrealtype (*nvminlocal)(N_Vector); // Probably not needed
+sunrealtype (*nvl1normlocal)(N_Vector); // Probably not needed
+sunbooleantype (*nvinvtestlocal)(N_Vector, N_Vector); // Probably not needed
+sunbooleantype (*nvconstrmasklocal)(N_Vector, N_Vector, N_Vector); // Probably not needed
+sunrealtype (*nvminquotientlocal)(N_Vector, N_Vector); // Probably not needed
+sunrealtype (*nvwsqrsumlocal)(N_Vector, N_Vector); // Probably not needed
+sunrealtype (*nvwsqrsummasklocal)(N_Vector, N_Vector, N_Vector); // Probably not needed
+SUNErrCode (*nvdotprodmultilocal)(int, N_Vector, N_Vector*, sunrealtype*); // Probably not needed
+SUNErrCode (*nvdotprodmultiall_reduce)(int, N_Vector, sunrealtype*); // Probably not needed
+SUNErrCode (*nvbufsize)(N_Vector, sunindextype*); // Probably not needed
+SUNErrCode (*nvbufpack)(N_Vector, void*); // Probably not needed
+SUNErrCode (*nvbufunpack)(N_Vector, void*); // Probably not needed
+void (*nvprint)(N_Vector); // Nice, but optional
+void (*nvprintfile)(N_Vector, FILE*); // Probably not needed
+*/

From 94962f13ff0f2fd7e400f775e05714c748ba1b41 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 21 Oct 2024 13:49:03 +0200
Subject: [PATCH 0107/1827] master branch will be 5.1.2 not 5.2.0

---
 CMakeLists.txt                       | 2 +-
 tools/pylib/_boutpp_build/backend.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3c2a26a07b..60d34e1ad7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -26,7 +26,7 @@ endif()
 # Set the version here, strip any extra tags to use in `project`
 # We try to use git to get a full description, inspired by setuptools_scm
 set(_bout_previous_version "5.1.1")
-set(_bout_next_version "5.2.0")
+set(_bout_next_version "5.1.2")
 execute_process(
   COMMAND "git" describe --tags --match=v${_bout_previous_version}
   COMMAND sed -e s/${_bout_previous_version}-/${_bout_next_version}.dev/ -e s/-/+/
diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index e89f37bb42..23e60fc583 100644
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -34,7 +34,7 @@ def getversion():
             return version
 
         _bout_previous_version = "v5.1.1"
-        _bout_next_version = "v5.2.0"
+        _bout_next_version = "v5.1.2"
 
         try:
             try:

From 6724e7548bf88a7824845a9caf1c77c49bef269b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 12:02:43 +0200
Subject: [PATCH 0108/1827] Dump also parallel fields by default

---
 src/solver/impls/pvode/pvode.cxx | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 9dce5d357f..66344f7cde 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -358,8 +358,8 @@ BoutReal PvodeSolver::run(BoutReal tout) {
   // Check return flag
   if (flag != SUCCESS) {
     output_error.write("ERROR CVODE step failed, flag = {:d}\n", flag);
-    CVodeMemRec* cv_mem = (CVodeMem)cvode_mem;
     if (debug_on_failure) {
+      CVodeMemRec* cv_mem = (CVodeMem)cvode_mem;
       if (f2d.empty() and v2d.empty() and v3d.empty()) {
         Options debug{};
         using namespace std::string_literals;
@@ -388,6 +388,9 @@ BoutReal PvodeSolver::run(BoutReal tout) {
 
         for (auto& f : f3d) {
           debug[f.name] = *f.var;
+	  if (f.var->hasParallelSlices()) {
+	    saveParallel(debug, f.name, *f.var);
+	  }
         }
 
         if (mesh != nullptr) {

From 28212c2e97c725f20099fd302fb17efc86243c7b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 12:01:16 +0200
Subject: [PATCH 0109/1827] Also dump parallel fields

---
 src/solver/impls/euler/euler.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index ded28984aa..5477b5760b 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -163,7 +163,7 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
     Options& debug = *debug_ptr;
     Mesh* mesh{nullptr};
     for (auto& f : f3d) {
-      debug[f.name] = *f.var;
+      saveParallel(debug, f.name, *f.var);
       mesh = f.var->getMesh();
     }
 

From 9cf0fba6971c1c6367b3aee3c5d68f9bcf4121ed Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 11:53:26 +0200
Subject: [PATCH 0110/1827] Clarify which div_par has been used

---
 src/mesh/coordinates.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 32774d6229..483b3e458c 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1601,7 +1601,7 @@ Field3D Coordinates::Div_par(const Field3D& f, CELL_LOC outloc,
     f_B.yup(i) = f.yup(i) / Bxy_floc.yup(i);
     f_B.ydown(i) = f.ydown(i) / Bxy_floc.ydown(i);
   }
-  return setName(Bxy * Grad_par(f_B, outloc, method), "Div_par({:s})", f.name);
+  return setName(Bxy * Grad_par(f_B, outloc, method), "C:Div_par({:s})", f.name);
 }
 
 /////////////////////////////////////////////////////////

From 97b67e187149d5c7e6624ffd1222ef8d242d5270 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 10:30:32 +0200
Subject: [PATCH 0111/1827] Expose tracking

Useful for physics module to record additional data if the solver is
failing
---
 include/bout/field3d.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 395e3201e4..0f227a8da3 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -510,6 +510,8 @@ public:
 
   int size() const override { return nx * ny * nz; };
 
+  Options* getTracking() { return tracking; };
+
 private:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
   int nx{-1}, ny{-1}, nz{-1};

From 77e08ec6f7e4e38978e1ec85218af8475991ce4b Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Tue, 22 Oct 2024 09:57:45 +0000
Subject: [PATCH 0112/1827] Apply clang-format changes

---
 src/solver/impls/pvode/pvode.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 66344f7cde..d4ac14fef2 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -388,9 +388,9 @@ BoutReal PvodeSolver::run(BoutReal tout) {
 
         for (auto& f : f3d) {
           debug[f.name] = *f.var;
-	  if (f.var->hasParallelSlices()) {
-	    saveParallel(debug, f.name, *f.var);
-	  }
+          if (f.var->hasParallelSlices()) {
+            saveParallel(debug, f.name, *f.var);
+          }
         }
 
         if (mesh != nullptr) {

From ba6fc6cea816d0c2163dcbd3af4f64824a25f446 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 10:32:17 +0200
Subject: [PATCH 0113/1827] Add simple interface to store parallel fields

Just dumping the parallel slices does in general not work, as then
collect discards that, especially if NYPE==ny
---
 include/bout/options.hxx |  3 +++
 src/sys/options.cxx      | 16 ++++++++++++++++
 2 files changed, 19 insertions(+)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 839c847289..e1f5ae68fa 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -946,6 +946,9 @@ Tensor<BoutReal> Options::as<Tensor<BoutReal>>(const Tensor<BoutReal>& similar_t
 /// Convert \p value to string
 std::string toString(const Options& value);
 
+/// Save the parallel fields
+void saveParallel(Options& opt, const std::string name, const Field3D& tosave);
+
 /// Output a stringified \p value to a stream
 ///
 /// This is templated to avoid implict casting: anything is
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 49a81cfa88..71339b6089 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -306,6 +306,22 @@ void Options::assign<>(Tensor<BoutReal> val, std::string source) {
   _set_no_check(std::move(val), std::move(source));
 }
 
+void saveParallel(Options& opt, const std::string name, const Field3D& tosave){
+  ASSERT2(tosave.hasParallelSlices());
+  opt[name] = tosave;
+  for (size_t i0=1 ;  i0 <= tosave.numberParallelSlices(); ++i0) {
+    for (int i: {i0, -i0} ) {
+      Field3D tmp;
+      tmp.allocate();
+      const auto& fpar = tosave.ynext(i);
+      for (auto j: fpar.getValidRegionWithDefault("RGN_NO_BOUNDARY")){
+	tmp[j.yp(-i)] = fpar[j];
+      }
+      opt[fmt::format("{}_y{:+d}", name, i)] = tmp;
+    }
+  }
+}
+
 namespace {
 /// Use FieldFactory to evaluate expression
 double parseExpression(const Options::ValueType& value, const Options* options,

From 3c0d6a8f6a4d20bdee9d140b9f90af9432a6810c Mon Sep 17 00:00:00 2001
From: dschwoerer <dschwoerer@users.noreply.github.com>
Date: Tue, 22 Oct 2024 10:26:41 +0000
Subject: [PATCH 0114/1827] Apply clang-format changes

---
 src/sys/options.cxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 71339b6089..1193deb013 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -306,16 +306,16 @@ void Options::assign<>(Tensor<BoutReal> val, std::string source) {
   _set_no_check(std::move(val), std::move(source));
 }
 
-void saveParallel(Options& opt, const std::string name, const Field3D& tosave){
+void saveParallel(Options& opt, const std::string name, const Field3D& tosave) {
   ASSERT2(tosave.hasParallelSlices());
   opt[name] = tosave;
-  for (size_t i0=1 ;  i0 <= tosave.numberParallelSlices(); ++i0) {
-    for (int i: {i0, -i0} ) {
+  for (size_t i0 = 1; i0 <= tosave.numberParallelSlices(); ++i0) {
+    for (int i : {i0, -i0}) {
       Field3D tmp;
       tmp.allocate();
       const auto& fpar = tosave.ynext(i);
-      for (auto j: fpar.getValidRegionWithDefault("RGN_NO_BOUNDARY")){
-	tmp[j.yp(-i)] = fpar[j];
+      for (auto j : fpar.getValidRegionWithDefault("RGN_NO_BOUNDARY")) {
+        tmp[j.yp(-i)] = fpar[j];
       }
       opt[fmt::format("{}_y{:+d}", name, i)] = tmp;
     }

From d0669cdcafa76bec00116abb2d934e05405eae35 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 22 Oct 2024 15:37:56 +0200
Subject: [PATCH 0115/1827] Do not use numberParallelSlices()

---
 src/sys/options.cxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index df1dee56f4..3f7a0c4071 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -338,9 +338,10 @@ void Options::assign<>(Tensor<BoutReal> val, std::string source) {
 }
 
 void saveParallel(Options& opt, const std::string name, const Field3D& tosave) {
-  ASSERT2(tosave.hasParallelSlices());
   opt[name] = tosave;
-  for (size_t i0 = 1; i0 <= tosave.numberParallelSlices(); ++i0) {
+  const size_t numberParallelSlices =
+      tosave.hasParallelSlices() ? 0 : tosave.getMesh()->ystart;
+  for (size_t i0 = 1; i0 <= numberParallelSlices; ++i0) {
     for (int i : {i0, -i0}) {
       Field3D tmp;
       tmp.allocate();

From 2435b00f1c404efa809c55c8f3c2337f68570ba5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Nov 2024 19:43:01 +0000
Subject: [PATCH 0116/1827] Bump externalpackages/googletest from `6dae7eb` to
 `d144031`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `6dae7eb` to `d144031`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/6dae7eb4a5c3a169f3e298392bff4680224aa94a...d144031940543e15423a25ae5a8a74141044862f)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 6dae7eb4a5..d144031940 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 6dae7eb4a5c3a169f3e298392bff4680224aa94a
+Subproject commit d144031940543e15423a25ae5a8a74141044862f

From 3518b5604d6bd6d5d678e710d4466c422f647808 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 4 Nov 2024 14:35:01 -0800
Subject: [PATCH 0117/1827] Finish swap state after evolve

---
 src/solver/impls/arkode/arkode.cxx | 21 ++++++++-------
 src/solver/impls/arkode/arkode.hxx | 16 +++++++-----
 src/solver/nvector.hxx             | 42 +++++++++++++++---------------
 3 files changed, 43 insertions(+), 36 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 0e10755fa3..d725a983bf 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -191,7 +191,7 @@ int ArkodeSolver::init() {
   // }
 
   // uvec = N_VNew_Bout(suncontext, *f3d.back().var, false);
-  uvec = nullptr;
+  uvec = nvector_from_state(suncontext);
   if (uvec == nullptr) {
     throw BoutException("BOUT N_Vector failed\n");
   }
@@ -602,7 +602,8 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   }
 
   // Copy variables
-  load_vars(N_VGetArrayPointer(uvec));
+  // load_vars(N_VGetArrayPointer(uvec));
+  set_state(uvec);
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
   // run_diffusive(simtime);
@@ -653,14 +654,16 @@ void ArkodeSolver::rhs_i(BoutReal t, BoutReal* udata, BoutReal* dudata) {
 /**************************************************************************
  *   Full  RHS function du = F(t, u)
  **************************************************************************/
-void ArkodeSolver::rhs(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+void ArkodeSolver::rhs(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs({:e})", t);
 
-  load_vars(udata);
+  // load_vars(udata);
+  set_state(u, du);
   ARKStepGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs(t);
-  save_derivs(dudata);
+  // save_derivs(dudata);
+  set_state(u, du);
 }
 
 /**************************************************************************
@@ -675,7 +678,7 @@ void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* uda
 
   if (!hasPreconditioner()) {
     // Identity (but should never happen)
-    const auto length = N_VGetLocalLength_Parallel(uvec);
+    const auto length = N_VGetLocalLength(uvec);
     std::copy(rvec, rvec + length, zvec);
     return;
   }
@@ -759,14 +762,14 @@ int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
 
 int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
 
-  BoutReal* udata = N_VGetArrayPointer(u);
-  BoutReal* dudata = N_VGetArrayPointer(du);
+  // BoutReal* udata = N_VGetArrayPointer(u);
+  // BoutReal* dudata = N_VGetArrayPointer(du);
 
   auto* s = static_cast<ArkodeSolver*>(user_data);
 
   // Calculate RHS function
   try {
-    s->rhs(t, udata, dudata);
+    s->rhs(t, u, du);
   } catch (BoutRhsFail& error) {
     return 1;
   }
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 6ce1af9565..082fa38b57 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -85,7 +85,7 @@ public:
   // These functions used internally (but need to be public)
   void rhs_e(BoutReal t, BoutReal* udata, BoutReal* dudata);
   void rhs_i(BoutReal t, BoutReal* udata, BoutReal* dudata);
-  void rhs(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs(BoutReal t, N_Vector u, N_Vector du);
   void pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec,
            BoutReal* zvec);
   void jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
@@ -172,16 +172,20 @@ private:
     return BoutNVector::create(ctx, subvectors);
   }
 
-  void swap_rhs_state(const N_Vector v) {
+  void set_state(const N_Vector u, const N_Vector du = nullptr) {
     std::size_t i = 0;
     for (auto &var_str : f2d) {
-      BoutNVector::swap(v, var_str.F_var, i);
+      BoutNVector::swap(u, var_str.var, i);
+      BoutNVector::swap(du, var_str.F_var, i);
       i++;
     }
 
-    for (auto &var_str : f3d) {
-      BoutNVector::swap(v, var_str.F_var, i);
-      i++;
+    if (du != nullptr) {
+      for (auto &var_str : f3d) {
+        BoutNVector::swap(u, var_str.var, i);
+        BoutNVector::swap(du, var_str.F_var, i);
+        i++;
+      }
     }
   }
 
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 9ecc247412..b83b35a6c7 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -46,7 +46,7 @@ private:
     MPI_Allreduce(&local, &global, 1, type, op, BoutComm::get());
     return global;
   }
-  
+
   template <typename T>
   struct Content {
     T* field;
@@ -58,11 +58,13 @@ private:
         : field(field), own(own), evolve_bndry(evolve_bndry),
           length(all_reduce(getRegion().size())) {}
 
-    auto getRegion() const { return field->getRegion(evolve_bndry ? RGN_ALL : RGN_NOBNDRY); }
+    auto getRegion() const {
+      return field->getRegion(evolve_bndry ? RGN_ALL : RGN_NOBNDRY);
+    }
 
     ~Content() {
       if (own) {
-        delete &field;
+        delete field;
       }
     }
   };
@@ -77,10 +79,11 @@ private:
     return *get_content<T>(v).field;
   }
 
-  template <typename T, typename R, typename ... V>
-  static BoutReal reduce_field(const R reduce, const bool allpe, const N_Vector v1, const V... v2) {
-      BoutReal result = 0;
-      const auto region = get_content<T>(v1).getRegion();
+  template <typename T, typename R, typename... V>
+  static BoutReal reduce_field(const R reduce, const bool allpe, const N_Vector v1,
+                               const V... v2) {
+    BoutReal result = 0;
+    const auto region = get_content<T>(v1).getRegion();
       BOUT_FOR_OMP(i, region, parallel for reduction(+:result)) {
         result += reduce(get_field<T>(v1)[i], get_field<T>(v2)[i]...);
       }
@@ -89,11 +92,11 @@ private:
   }
 
 public:
-  // NVector() = delete; // Enforce static access only
-  
+  BoutNVector() = delete; // Enforce static access only
+
   template <typename T, typename = bout::utils::EnableIfField<T>>
-  static N_Vector create(const SUNContext ctx, T *const field, const bool evolve_bndry,
-                      const bool own = false) {
+  static N_Vector create(const SUNContext ctx, T* const field, const bool evolve_bndry,
+                         const bool own = false) {
     N_Vector v = callWithSUNContext(N_VNewEmpty, ctx);
     if (v == nullptr) {
       throw BoutException("N_VNewEmpty failed\n");
@@ -104,7 +107,7 @@ public:
     v->ops->nvgetvectorid = [](N_Vector) { return SUNDIALS_NVEC_CUSTOM; };
 
     v->ops->nvclone = [](N_Vector x) {
-      Content<T> content = get_content<T>(x);
+      const Content<T>& content = get_content<T>(x);
       T* field_clone = new T(*content.field);
       field_clone->allocate();
       return create(x->sunctx, field_clone, content.evolve_bndry, true);
@@ -121,7 +124,7 @@ public:
     v->ops->nvgetlength = [](N_Vector x) { return get_content<T>(x).length; };
 
     v->ops->nvlinearsum = [](sunrealtype a, N_Vector x, sunrealtype b, N_Vector y,
-                            N_Vector z) {
+                             N_Vector z) {
       get_field<T>(z) = a * get_field<T>(x) + b * get_field<T>(y);
     };
 
@@ -143,9 +146,7 @@ public:
       get_field<T>(y) = abs(get_field<T>(x));
     };
 
-    v->ops->nvinv = [](N_Vector x, N_Vector y) {
-      get_field<T>(y) = 1 / get_field<T>(x);
-    };
+    v->ops->nvinv = [](N_Vector x, N_Vector y) { get_field<T>(y) = 1 / get_field<T>(x); };
 
     v->ops->nvaddconst = [](N_Vector x, sunrealtype a, N_Vector y) {
       get_field<T>(y) = a + get_field<T>(x);
@@ -164,9 +165,8 @@ public:
     v->ops->nvmin = [](N_Vector x) { return min(get_field<T>(x), true); };
 
     v->ops->nvwl2norm = [](N_Vector x, N_Vector y) {
-      return std::sqrt(reduce_field<T>([](const auto v1, const auto v2) {
-        return std::pow(v1 * v2, 2);
-      }, true, x, y));
+      return std::sqrt(reduce_field<T>(
+          [](const auto v1, const auto v2) { return std::pow(v1 * v2, 2); }, true, x, y));
     };
 
     v->ops->nvl1norm = [](N_Vector x) {
@@ -183,12 +183,12 @@ public:
   }
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
-  static void swap(const N_Vector v, T* &field) {
+  static void swap(const N_Vector v, T*& field) {
     std::swap(get_content<T>(v).field, field);
   }
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
-  static void swap(const N_Vector v, T* &field, std::size_t subvector) {
+  static void swap(const N_Vector v, T*& field, std::size_t subvector) {
     return swap(N_VGetSubvector_ManyVector(v, subvector), field);
   }
 };

From 6206d88ab5beef5099cc56e853b05cb73fda66d7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Nov 2024 19:21:55 +0000
Subject: [PATCH 0118/1827] Bump ZedThree/clang-tidy-review from 0.19.0 to
 0.20.1

Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.19.0 to 0.20.1.
- [Release notes](https://github.com/zedthree/clang-tidy-review/releases)
- [Changelog](https://github.com/ZedThree/clang-tidy-review/blob/master/CHANGELOG.md)
- [Commits](https://github.com/zedthree/clang-tidy-review/compare/v0.19.0...v0.20.1)

---
updated-dependencies:
- dependency-name: ZedThree/clang-tidy-review
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/clang-tidy-review.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 4cdec88c83..b2f9bd7573 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -22,7 +22,7 @@ jobs:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.19.0
+        uses: ZedThree/clang-tidy-review@v0.20.1
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.19.0
+        uses: ZedThree/clang-tidy-review/upload@v0.20.1

From 67a282fb23f9fea0035ba43811754ed7cb9957b3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Nov 2024 19:21:58 +0000
Subject: [PATCH 0119/1827] Bump codecov/codecov-action from 4 to 5

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v4...v5)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 7ca76cc7aa..c316ba4db1 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -218,7 +218,7 @@ jobs:
 
       - name: Upload coverage
         if: ${{ matrix.config.name == 'Coverage' }}
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
 
   Fedora:
     # This is its own job as it doesn't use most of the steps of the

From c9318740652d2a61351270e3ff8b86a9cf4a78f7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 Nov 2024 10:00:17 +0100
Subject: [PATCH 0120/1827] Use PEP 625 compatible archive name

---
 tools/pylib/_boutpp_build/backend.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 23e60fc583..1fba557cdc 100644
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -198,7 +198,7 @@ def build_sdist(sdist_directory, config_settings=None):
             if k == "nightly":
                 useLocalVersion = False
                 pkgname = "boutpp-nightly"
-    prefix = f"{pkgname}-{getversion()}"
+    prefix = f"{pkgname.replace('-', '_')}-{getversion()}"
     fname = f"{prefix}.tar"
     run(f"git archive HEAD --prefix {prefix}/ -o {sdist_directory}/{fname}")
     _, tmp = tempfile.mkstemp(suffix=".tar")

From 0f2630aa2be8d9ce4b3fe496fc541757617574e6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 23 Dec 2024 19:35:15 +0000
Subject: [PATCH 0121/1827] Update numpy requirement from ~=2.1.2 to ~=2.2.1

Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.2...v2.2.1)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 3fe0712381..e7bd77a1c4 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 Jinja2~=3.1.4
-numpy~=2.1.2
+numpy~=2.2.1
 scipy>=1.11.0
 netcdf4~=1.7.1
 matplotlib>=3.7.0

From d3ced6f10e5ee7a8fcee53fda89dffd9be4fa6b1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Jan 2025 19:10:18 +0000
Subject: [PATCH 0122/1827] Bump externalpackages/googletest from `d144031` to
 `504ea69`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `d144031` to `504ea69`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/d144031940543e15423a25ae5a8a74141044862f...504ea69cf7e9947be54f808a09b7b08988e84b5f)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index d144031940..504ea69cf7 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit d144031940543e15423a25ae5a8a74141044862f
+Subproject commit 504ea69cf7e9947be54f808a09b7b08988e84b5f

From 42fc8ff5350b8da32518a0bd449b8e3dc149bb9f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Jan 2025 12:25:13 +0100
Subject: [PATCH 0123/1827] prefer const ref

---
 include/bout/options.hxx | 2 +-
 src/sys/options.cxx      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index e207c6b4d4..bc43bda3ef 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -991,7 +991,7 @@ Tensor<BoutReal> Options::as<Tensor<BoutReal>>(const Tensor<BoutReal>& similar_t
 std::string toString(const Options& value);
 
 /// Save the parallel fields
-void saveParallel(Options& opt, const std::string name, const Field3D& tosave);
+void saveParallel(Options& opt, const std::string& name, const Field3D& tosave);
 
 /// Output a stringified \p value to a stream
 ///
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index d49f014f25..e674667d7b 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -343,7 +343,7 @@ Options& Options::assign<>(Tensor<BoutReal> val, std::string source) {
   return *this;
 }
 
-void saveParallel(Options& opt, const std::string name, const Field3D& tosave) {
+void saveParallel(Options& opt, const std::string& name, const Field3D& tosave) {
   opt[name] = tosave;
   const size_t numberParallelSlices =
       tosave.hasParallelSlices() ? 0 : tosave.getMesh()->ystart;

From c9c13d4ee451234385be78ff3159b9a82a4ee3dd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Jan 2025 12:25:53 +0100
Subject: [PATCH 0124/1827] Update for move of bout/version.hxx

---
 src/solver/impls/euler/euler.cxx | 1 +
 src/solver/impls/pvode/pvode.cxx | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 5477b5760b..ce2a594cb8 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -1,6 +1,7 @@
 
 #include "euler.hxx"
 
+#include "bout/version.hxx"
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/msg_stack.hxx>
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 5cc41e31c5..6db3b6ccfe 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -35,8 +35,8 @@
 #include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
-
-#include "bout/unused.hxx"
+#include <bout/unused.hxx>
+#include <bout/version.hxx>
 
 #include <pvode/cvspgmr.h>  // use CVSPGMR linear solver each internal step
 #include <pvode/iterativ.h> // contains the enum for types of preconditioning

From ff93406d32ec28d84c6957191d787db5c25a16fb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Jan 2025 12:26:07 +0100
Subject: [PATCH 0125/1827] Prefer auto

---
 src/solver/impls/pvode/pvode.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 6db3b6ccfe..3fc6b6866c 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -61,8 +61,8 @@ void pvode_load_data_f3d(const std::vector<bool>& evolve_bndrys,
     for (const auto& i2d : mesh->getRegion2D(bndry ? "RGN_BNDRY" : "RGN_NOBNDRY")) {
       for (int jz = 0; jz < nz; jz++) {
         // Loop over 3D variables
-        std::vector<bool>::const_iterator evolve_bndry = evolve_bndrys.begin();
-        for (std::vector<Field3D>::iterator ff = ffs.begin(); ff != ffs.end(); ++ff) {
+        auto evolve_bndry = evolve_bndrys.cbegin();
+        for (auto ff = ffs.begin(); ff != ffs.end(); ++ff) {
           if (bndry && !*evolve_bndry) {
             continue;
           }

From a096cc5f812509857617529523727a96a17bc1ef Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Jan 2025 12:26:29 +0100
Subject: [PATCH 0126/1827] Avoid warning for 3d metrics

---
 src/physics/smoothing.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/physics/smoothing.cxx b/src/physics/smoothing.cxx
index 0a1391907f..036c475cd7 100644
--- a/src/physics/smoothing.cxx
+++ b/src/physics/smoothing.cxx
@@ -350,7 +350,7 @@ BoutReal Average_XY(const Field2D& var) {
   return Vol_Glb;
 }
 
-BoutReal Vol_Integral(const Field2D& var) {
+BoutReal Vol_Integral([[maybe_unused]] const Field2D& var) {
 #if BOUT_USE_METRIC_3D
   AUTO_TRACE();
   throw BoutException("Vol_Intregral currently incompatible with 3D metrics");

From 27db46d503b98eb0fe8682595cd1cb7a115367d9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Jan 2025 12:29:36 +0100
Subject: [PATCH 0127/1827] Apply recommendations from code review

* switch to std::weak_ptr
* reorder branches in pvode debug
* make track a trivial inline function
* ensure _track template is only used for fields
---
 include/bout/field3d.hxx         | 20 +++++---
 src/field/field3d.cxx            | 66 ++++++++++++++-----------
 src/solver/impls/euler/euler.cxx |  6 +--
 src/solver/impls/pvode/pvode.cxx | 83 +++++++++++++++-----------------
 4 files changed, 94 insertions(+), 81 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index d1b5a0813d..90ea7020db 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -293,11 +293,11 @@ public:
 
   /// Enable a special tracking mode for debugging
   /// Save all changes that, are done to the field, to tracking
-  Field3D& enableTracking(const std::string& name, Options& tracking);
+  Field3D& enableTracking(const std::string& name, std::weak_ptr<Options> tracking);
 
   /// Disable tracking
   Field3D& disableTracking() {
-    tracking = nullptr;
+    tracking.reset();
     tracking_state = 0;
     return *this;
   }
@@ -506,7 +506,7 @@ public:
 
   int size() const override { return nx * ny * nz; };
 
-  Options* getTracking() { return tracking; };
+  std::weak_ptr<Options> getTracking() { return tracking; };
 
 private:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
@@ -525,11 +525,17 @@ private:
   std::optional<size_t> regionID;
 
   int tracking_state{0};
-  Options* tracking{nullptr};
+  std::weak_ptr<Options> tracking;
   std::string selfname;
-  template <class T>
-  Options* track(const T& change, std::string operation);
-  Options* track(const BoutReal& change, std::string operation);
+  template <typename T>
+  inline void track(const T& change, const std::string& operation) {
+    if (tracking_state != 0) {
+      _track(change, operation);
+    }
+  }
+  template <typename T, typename = bout::utils::EnableIfField<T>>
+  void _track(const T& change, std::string operation);
+  void _track(const BoutReal& change, std::string operation);
 };
 
 // Non-member overloaded operators
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 3807b54314..17571ea4c1 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -844,46 +844,56 @@ void Field3D::setRegion(const std::string& region_name) {
   regionID = fieldmesh->getRegionID(region_name);
 }
 
-Field3D& Field3D::enableTracking(const std::string& name, Options& _tracking) {
-  tracking = &_tracking;
+Field3D& Field3D::enableTracking(const std::string& name,
+                                 std::weak_ptr<Options> _tracking) {
+  tracking = _tracking;
   tracking_state = 1;
   selfname = name;
   return *this;
 }
 
-template <class T>
-Options* Field3D::track(const T& change, std::string operation) {
-  if (tracking != nullptr and tracking_state != 0) {
-    const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
-    tracking->set(outname, change, "tracking");
-    // Workaround for bug in gcc9.4
+template <typename T, typename>
+void Field3D::_track(const T& change, std::string operation) {
+  if (tracking_state == 0) {
+    return;
+  }
+  auto locked = tracking.lock();
+  if (locked == nullptr) {
+    return;
+  }
+  const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
+
+  locked->set(outname, change, "tracking");
+  // Workaround for bug in gcc9.4
 #if BOUT_USE_TRACK
-    const std::string changename = change.name;
+  const std::string changename = change.name;
 #endif
-    (*tracking)[outname].setAttributes({
+  (*locked)[outname].setAttributes({
       {"operation", operation},
 #if BOUT_USE_TRACK
-          {"rhs.name", changename},
+      {"rhs.name", changename},
 #endif
-    });
-    return &(*tracking)[outname];
-  }
-  return nullptr;
+  });
 }
 
-template Options* Field3D::track<Field3D>(const Field3D&, std::string);
-template Options* Field3D::track<Field2D>(const Field2D&, std::string);
-template Options* Field3D::track<FieldPerp>(const FieldPerp&, std::string);
+template void
+Field3D::_track<Field3D, bout::utils::EnableIfField<Field3D>>(const Field3D&,
+                                                              std::string);
+template void Field3D::_track<Field2D>(const Field2D&, std::string);
+template void Field3D::_track<>(const FieldPerp&, std::string);
 
-Options* Field3D::track(const BoutReal& change, std::string operation) {
-  if (tracking and tracking_state) {
-    const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
-    tracking->set(outname, change, "tracking");
-    (*tracking)[outname].setAttributes({
-        {"operation", operation},
-        {"rhs.name", "BR"},
-    });
-    return &(*tracking)[outname];
+void Field3D::_track(const BoutReal& change, std::string operation) {
+  if (tracking_state == 0) {
+    return;
   }
-  return nullptr;
+  auto locked = tracking.lock();
+  if (locked == nullptr) {
+    return;
+  }
+  const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
+  locked->set(outname, change, "tracking");
+  (*locked)[outname].setAttributes({
+      {"operation", operation},
+      {"rhs.name", "BoutReal"},
+  });
 }
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index ce2a594cb8..110331eeb1 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -147,12 +147,12 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
   load_vars(std::begin(start));
   const bool dump_now =
       (dump_at_time >= 0 && std::abs(dump_at_time - curtime) < dt) || dump_at_time < -3;
-  std::unique_ptr<Options> debug_ptr;
+  std::shared_ptr<Options> debug_ptr;
   if (dump_now) {
-    debug_ptr = std::make_unique<Options>();
+    debug_ptr = std::make_shared<Options>();
     Options& debug = *debug_ptr;
     for (auto& f : f3d) {
-      f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug);
+      f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug_ptr);
       setName(*f.var, f.name);
       debug[fmt::format("pre_{:s}", f.name)] = *f.var;
       f.var->allocate();
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 3fc6b6866c..4815f0153b 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -360,56 +360,53 @@ BoutReal PvodeSolver::run(BoutReal tout) {
     output_error.write("ERROR CVODE step failed, flag = {:d}\n", flag);
     if (debug_on_failure) {
       CVodeMemRec* cv_mem = (CVodeMem)cvode_mem;
-      if (f2d.empty() and v2d.empty() and v3d.empty()) {
-        Options debug{};
-        using namespace std::string_literals;
-        Mesh* mesh{};
-        for (const auto& prefix : {"pre_"s, "residuum_"s}) {
-          std::vector<Field3D> list_of_fields{};
-          std::vector<bool> evolve_bndrys{};
-          for (const auto& f : f3d) {
-            mesh = f.var->getMesh();
-            Field3D to_load{0., mesh};
-            to_load.allocate();
-            to_load.setLocation(f.location);
-            debug[fmt::format("{:s}{:s}", prefix, f.name)] = to_load;
-            list_of_fields.push_back(to_load);
-            evolve_bndrys.push_back(f.evolve_bndry);
-          }
-          pvode_load_data_f3d(evolve_bndrys, list_of_fields,
-                              prefix == "pre_"s ? udata : N_VDATA(cv_mem->cv_acor));
+      if (!(f2d.empty() and v2d.empty() and v3d.empty())) {
+        output_warn.write("debug_on_failure is currently only supported for Field3Ds");
+        return -1.0;
+      }
+      auto debug_ptr = std::make_shared<Options>();
+      Options& debug = *debug_ptr;
+      using namespace std::string_literals;
+      Mesh* mesh{};
+      for (const auto& prefix : {"pre_"s, "residuum_"s}) {
+        std::vector<Field3D> list_of_fields{};
+        std::vector<bool> evolve_bndrys{};
+        for (const auto& f : f3d) {
+          mesh = f.var->getMesh();
+          Field3D to_load{0., mesh};
+          to_load.allocate();
+          to_load.setLocation(f.location);
+          debug[fmt::format("{:s}{:s}", prefix, f.name)] = to_load;
+          list_of_fields.push_back(to_load);
+          evolve_bndrys.push_back(f.evolve_bndry);
         }
+        pvode_load_data_f3d(evolve_bndrys, list_of_fields,
+                            prefix == "pre_"s ? udata : N_VDATA(cv_mem->cv_acor));
+      }
 
-        for (auto& f : f3d) {
-          f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug);
-          setName(*f.var, f.name);
-        }
-        run_rhs(simtime);
+      for (auto& f : f3d) {
+        f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug_ptr);
+        setName(*f.var, f.name);
+      }
+      run_rhs(simtime);
 
-        for (auto& f : f3d) {
-          debug[f.name] = *f.var;
-          if (f.var->hasParallelSlices()) {
-            saveParallel(debug, f.name, *f.var);
-          }
-        }
+      for (auto& f : f3d) {
+        saveParallel(debug, f.name, *f.var);
+      }
 
-        if (mesh != nullptr) {
-          mesh->outputVars(debug);
-          debug["BOUT_VERSION"].force(bout::version::as_double);
-        }
+      if (mesh != nullptr) {
+        mesh->outputVars(debug);
+        debug["BOUT_VERSION"].force(bout::version::as_double);
+      }
 
-        const std::string outname =
-            fmt::format("{}/BOUT.debug.{}.nc",
-                        Options::root()["datadir"].withDefault<std::string>("data"),
-                        BoutComm::rank());
+      const std::string outname = fmt::format(
+          "{}/BOUT.debug.{}.nc",
+          Options::root()["datadir"].withDefault<std::string>("data"), BoutComm::rank());
 
-        bout::OptionsIO::create(outname)->write(debug);
-        MPI_Barrier(BoutComm::get());
-      } else {
-        output_warn.write("debug_on_failure is currently only supported for Field3Ds");
-      }
+      bout::OptionsIO::create(outname)->write(debug);
+      MPI_Barrier(BoutComm::get());
     }
-    return (-1.0);
+    return -1.0;
   }
 
   return simtime;

From 24610c3682c43934e6560c73130d2030da234218 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Jan 2025 12:29:52 +0100
Subject: [PATCH 0128/1827] Explain purpose of variables

---
 include/bout/field3d.hxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 90ea7020db..8866f17b49 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -524,8 +524,11 @@ private:
   /// RegionID over which the field is valid
   std::optional<size_t> regionID;
 
+  /// counter for tracking, to assign unique names to the variable names
   int tracking_state{0};
   std::weak_ptr<Options> tracking;
+  // name is changed if we assign to the variable, while selfname is a
+  // non-changing copy that is used for the variable names in the dump files
   std::string selfname;
   template <typename T>
   inline void track(const T& change, const std::string& operation) {

From f6db2df5dc97f1f2047e3328503f8728a337977b Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Thu, 16 Jan 2025 11:30:30 +0000
Subject: [PATCH 0129/1827] Apply clang-format changes

---
 src/field/field3d.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 17571ea4c1..1eeb0dd344 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -869,9 +869,9 @@ void Field3D::_track(const T& change, std::string operation) {
   const std::string changename = change.name;
 #endif
   (*locked)[outname].setAttributes({
-      {"operation", operation},
+    {"operation", operation},
 #if BOUT_USE_TRACK
-      {"rhs.name", changename},
+        {"rhs.name", changename},
 #endif
   });
 }

From e047a677bca5a26f894e60470591bcd2b9477d10 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 20 Jan 2025 19:50:11 +0000
Subject: [PATCH 0130/1827] Bump externalpackages/googletest from `504ea69` to
 `2b6b042`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `504ea69` to `2b6b042`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/504ea69cf7e9947be54f808a09b7b08988e84b5f...2b6b042a77446ff322cd7522ca068d9f2a21c1d1)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 504ea69cf7..2b6b042a77 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 504ea69cf7e9947be54f808a09b7b08988e84b5f
+Subproject commit 2b6b042a77446ff322cd7522ca068d9f2a21c1d1

From 937a3c472b9a7df0a2bff6cab3418ad017719c7d Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Fri, 24 Jan 2025 11:22:31 -0800
Subject: [PATCH 0131/1827] Get prototype running

---
 .vscode/settings.json              | 78 ++++++++++++++++++++++++++++++
 include/bout/field2d.hxx           |  2 +
 include/bout/field3d.hxx           |  2 +
 src/field/field3d.cxx              |  2 +-
 src/solver/impls/arkode/arkode.cxx |  6 +--
 src/solver/impls/arkode/arkode.hxx | 19 +++++---
 src/solver/nvector.hxx             | 14 ++++--
 tests/unit/solver/test_nvector.cxx |  0
 8 files changed, 106 insertions(+), 17 deletions(-)
 create mode 100644 .vscode/settings.json
 create mode 100644 tests/unit/solver/test_nvector.cxx

diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000000..7dce96283d
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,78 @@
+{
+  "files.associations": {
+    "array": "cpp",
+    "limits": "cpp",
+    "complex": "cpp",
+    "cwchar": "cpp",
+    "list": "cpp",
+    "vector": "cpp",
+    "exception": "cpp",
+    "fstream": "cpp",
+    "functional": "cpp",
+    "initializer_list": "cpp",
+    "iosfwd": "cpp",
+    "istream": "cpp",
+    "new": "cpp",
+    "ostream": "cpp",
+    "sstream": "cpp",
+    "stdexcept": "cpp",
+    "streambuf": "cpp",
+    "tuple": "cpp",
+    "type_traits": "cpp",
+    "any": "cpp",
+    "atomic": "cpp",
+    "bit": "cpp",
+    "*.tcc": "cpp",
+    "bitset": "cpp",
+    "cctype": "cpp",
+    "charconv": "cpp",
+    "chrono": "cpp",
+    "clocale": "cpp",
+    "cmath": "cpp",
+    "codecvt": "cpp",
+    "compare": "cpp",
+    "concepts": "cpp",
+    "condition_variable": "cpp",
+    "csignal": "cpp",
+    "cstdarg": "cpp",
+    "cstddef": "cpp",
+    "cstdint": "cpp",
+    "cstdio": "cpp",
+    "cstdlib": "cpp",
+    "cstring": "cpp",
+    "ctime": "cpp",
+    "cwctype": "cpp",
+    "deque": "cpp",
+    "forward_list": "cpp",
+    "map": "cpp",
+    "set": "cpp",
+    "string": "cpp",
+    "unordered_map": "cpp",
+    "unordered_set": "cpp",
+    "algorithm": "cpp",
+    "iterator": "cpp",
+    "memory": "cpp",
+    "memory_resource": "cpp",
+    "numeric": "cpp",
+    "optional": "cpp",
+    "random": "cpp",
+    "ratio": "cpp",
+    "string_view": "cpp",
+    "system_error": "cpp",
+    "utility": "cpp",
+    "format": "cpp",
+    "iomanip": "cpp",
+    "iostream": "cpp",
+    "mutex": "cpp",
+    "numbers": "cpp",
+    "semaphore": "cpp",
+    "span": "cpp",
+    "stop_token": "cpp",
+    "thread": "cpp",
+    "cfenv": "cpp",
+    "cinttypes": "cpp",
+    "typeindex": "cpp",
+    "typeinfo": "cpp",
+    "variant": "cpp"
+  }
+}
\ No newline at end of file
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 28ad106c88..990c14927b 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -287,6 +287,8 @@ private:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
   int nx{-1}, ny{-1};
 
+public:
+
   /// Time-derivative, can be nullptr
   Field2D* deriv{nullptr};
 };
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 3989b5f62a..c27a02c623 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -502,9 +502,11 @@ private:
   /// Internal data array. Handles allocation/freeing of memory
   Array<BoutReal> data;
 
+public:
   /// Time derivative (may be nullptr)
   Field3D* deriv{nullptr};
 
+private:
   /// Fields containing values along Y
   std::vector<Field3D> yup_fields{}, ydown_fields{};
 
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 7eda5d0266..2dd0a07e67 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -106,7 +106,7 @@ Field3D::Field3D(Array<BoutReal> data_in, Mesh* localmesh, CELL_LOC datalocation
   ASSERT1(data.size() == nx * ny * nz);
 }
 
-Field3D::~Field3D() { delete deriv; }
+Field3D::~Field3D() {  } // TODO: fix
 
 Field3D& Field3D::allocate() {
   if (data.empty()) {
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 35c73f1159..3e7f1d7f6d 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -595,7 +595,7 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
 
   // Copy variables
   // load_vars(N_VGetArrayPointer(uvec));
-  set_state(uvec);
+  swap_state(uvec);
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
   // run_diffusive(simtime);
@@ -650,12 +650,12 @@ void ArkodeSolver::rhs(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs({:e})", t);
 
   // load_vars(udata);
-  set_state(u, du);
+  swap_state(u, du);
   ARKodeGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs(t);
   // save_derivs(dudata);
-  set_state(u, du);
+  swap_state(u, du);
 }
 
 /**************************************************************************
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 62e27cbda3..5524b1d5d1 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -214,20 +214,23 @@ private:
     return BoutNVector::create(ctx, subvectors);
   }
 
-  void set_state(const N_Vector u, const N_Vector du = nullptr) {
+  void swap_state(const N_Vector u, const N_Vector du = nullptr) {
     std::size_t i = 0;
     for (auto &var_str : f2d) {
-      BoutNVector::swap(u, var_str.var, i);
-      BoutNVector::swap(du, var_str.F_var, i);
+      BoutNVector::swap_qqq(u, *var_str.var, i);
+      if (du != nullptr) {
+        BoutNVector::swap_qqq(du, *var_str.F_var, i);
+      }
       i++;
     }
 
-    if (du != nullptr) {
-      for (auto &var_str : f3d) {
-        BoutNVector::swap(u, var_str.var, i);
-        BoutNVector::swap(du, var_str.F_var, i);
-        i++;
+    for (auto &var_str : f3d) {
+      BoutNVector::swap_qqq(u, *var_str.var, i);
+      if (du != nullptr) {
+        BoutNVector::swap_qqq(du, *var_str.F_var, i);
       }
+      var_str.var->deriv = var_str.F_var;
+      i++;
     }
   }
 
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index b83b35a6c7..69d5018739 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -108,8 +108,12 @@ public:
 
     v->ops->nvclone = [](N_Vector x) {
       const Content<T>& content = get_content<T>(x);
-      T* field_clone = new T(*content.field);
+      // TODO: ensure no memory leaks
+      // T* field_clone = new T(*content.field);
+      T* field_clone = new T(content.field->getMesh(), content.field->getLocation(), content.field->getDirections());
       field_clone->allocate();
+      field_clone->copyBoundary(*content.field);
+      (*field_clone) = 42;
       return create(x->sunctx, field_clone, content.evolve_bndry, true);
     };
 
@@ -183,13 +187,13 @@ public:
   }
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
-  static void swap(const N_Vector v, T*& field) {
-    std::swap(get_content<T>(v).field, field);
+  static void swap_qqq(const N_Vector v, T& field) {
+    swap(get_field<T>(v), field);
   }
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
-  static void swap(const N_Vector v, T*& field, std::size_t subvector) {
-    return swap(N_VGetSubvector_ManyVector(v, subvector), field);
+  static void swap_qqq(const N_Vector v, T& field, std::size_t subvector) {
+    return swap_qqq(N_VGetSubvector_ManyVector(v, subvector), field);
   }
 };
 
diff --git a/tests/unit/solver/test_nvector.cxx b/tests/unit/solver/test_nvector.cxx
new file mode 100644
index 0000000000..e69de29bb2

From 81d929d7fc37697ad791e4334a7f16f372491a70 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Jan 2025 17:17:04 +0100
Subject: [PATCH 0132/1827] Add delay on error

---
 include/bout/physicsmodel.hxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index 9fa25d8b0f..876f51940d 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -47,6 +47,8 @@ class PhysicsModel;
 #include "bout/unused.hxx"
 #include "bout/utils.hxx"
 
+#include <chrono>
+#include <thread>
 #include <type_traits>
 #include <vector>
 
@@ -435,6 +437,7 @@ private:
     } catch (const BoutException& e) {                             \
       output << "Error encountered: " << e.what();                 \
       output << e.getBacktrace() << endl;                          \
+      std::this_thread::sleep_for(std::chrono::milliseconds(100)); \
       MPI_Abort(BoutComm::get(), 1);                               \
     }                                                              \
     BoutFinalise();                                                \

From 5bcdd6d4c23cf3e0648174582df733a8033caa74 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 14 Feb 2025 11:19:46 +0000
Subject: [PATCH 0133/1827] Fix docstring and argument name for
 `Div_a_Grad_perp`

---
 include/bout/fv_ops.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 0e0d78fda5..52edde4bda 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -15,9 +15,9 @@
 namespace FV {
 /// Vorticity:
 /// \f[
-///   \nabla_\perp (a \cdot \nabla_\perp(f))
+///   \nabla (a \cdot \nabla_\perp(f))
 /// \f]
-Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& x);
+Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f);
 
 [[deprecated("Please use Div_a_Grad_perp instead")]] inline Field3D
 Div_a_Laplace_perp(const Field3D& a, const Field3D& x) {

From c1b48372c25050231ca2bc43ee930cf45ae763eb Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 14 Feb 2025 11:40:34 +0000
Subject: [PATCH 0134/1827] docs: Fix some links to python docs

---
 manual/sphinx/developer_docs/file_io.rst | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/manual/sphinx/developer_docs/file_io.rst b/manual/sphinx/developer_docs/file_io.rst
index 0d13e70cfc..361dd5f949 100644
--- a/manual/sphinx/developer_docs/file_io.rst
+++ b/manual/sphinx/developer_docs/file_io.rst
@@ -108,11 +108,12 @@ y-index. The expectation is that the other processors would all save an invalid
 `FieldPerp` variable, with a `yindex_global` that is more negative than the
 lowest y-boundary guard cell [2]_. The reason for saving the invalid `FieldPerp` variables
 is so that all variables are present in every dump file (even if they are not allocated or
-used); in particular the Python `collect` routine assumes that any variable will be found
-in the first output file, which `collect` uses to get its type and dimensions.
+used); in particular the Python :py:func:`boutdata.collect.collect` routine assumes that
+any variable will be found in the first output file, which
+:py:func:`boutdata.collect.collect` uses to get its type and dimensions.
 
 .. [2] Actually, the C++ I/O code should work fine even if a `FieldPerp` object is defined
        with different y-indices on different processors. This may be useful for diagnostic
-       or debugging purposes. However, Python routines like `collect` and
-       `boutdata.restart.redistribute` will fail because they find inconsistent
+       or debugging purposes. However, Python routines like :py:func:`collect` and
+       :py:func:`boutdata.restart.redistribute` will fail because they find inconsistent
        `yindex_global` values.

From 54535bd814db35ac9710a78f01ad758e230a9c0c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 14 Feb 2025 11:59:53 +0000
Subject: [PATCH 0135/1827] docs: Fix a couple of links to no longer included
 `.cxx` files

---
 manual/sphinx/developer_docs/code_layout.rst | 5 +++--
 manual/sphinx/user_docs/laplacian.rst        | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/manual/sphinx/developer_docs/code_layout.rst b/manual/sphinx/developer_docs/code_layout.rst
index e79245cde3..833b763ce9 100644
--- a/manual/sphinx/developer_docs/code_layout.rst
+++ b/manual/sphinx/developer_docs/code_layout.rst
@@ -74,8 +74,9 @@ inversions, ``mesh``, and ``solver``.
 
 The layout of the ``src/`` directory is as follows:
 
-- :doc:`src/bout++.cxx<../_breathe_autogen/file/bout_09_09_8cxx>`: Main
-  file which initialises, runs and finalises BOUT++.
+- ``src/bout++.cxx``: Main file which initialises, runs and finalises
+  BOUT++. The two most important public functions are `BoutInitialise`
+  and `BoutFinalise` for starting/stopping the library.
 
 - ``src/field``
 
diff --git a/manual/sphinx/user_docs/laplacian.rst b/manual/sphinx/user_docs/laplacian.rst
index 5365ba14a7..1529149726 100644
--- a/manual/sphinx/user_docs/laplacian.rst
+++ b/manual/sphinx/user_docs/laplacian.rst
@@ -183,7 +183,7 @@ within the physics module using ``setGlobalFlags``,
    +--------------------------+-------------------------------------------------------------------------+----------------------------------------------+
    | ``flags``                | DEPRECATED. Sets global solver options and boundary                     | ``0``                                        |
    |                          | conditions. See :ref:`Laplace flags<tab-laplaceflags>` or               |                                              |
-   |                          | :doc:`invert_laplace.cxx<../_breathe_autogen/file/invert__laplace_8cxx>`|                                              |
+   |                          | :doc:`invert_laplace.hxx<../_breathe_autogen/file/invert__laplace_8hxx>`|                                              |
    +--------------------------+-------------------------------------------------------------------------+----------------------------------------------+
    | ``include_yguards``      | Perform inversion in :math:`y`\ -boundary guard cells                   | ``false``                                    |
    +--------------------------+-------------------------------------------------------------------------+----------------------------------------------+

From 6ea22a07e46f0b0b64f8e95903da981e88799fee Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Fri, 14 Feb 2025 12:01:10 +0000
Subject: [PATCH 0136/1827] Apply black changes

---
 tests/integrated/test_suite | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite
index 307a8d84b3..77ad7882c4 100755
--- a/tests/integrated/test_suite
+++ b/tests/integrated/test_suite
@@ -188,7 +188,7 @@ class Test(threading.Thread):
                 self.output += "\n(It is likely that a timeout occured)"
             else:
                 # ❌ Failed
-                print("\u274C", end="")  # No newline
+                print("\u274c", end="")  # No newline
             print(" %7.3f s" % (time.time() - self.local.start_time), flush=True)
 
     def _cost(self):

From c2344046a767145c19c8b8d8cc6d6dd34d352ecc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 17 Feb 2025 19:18:09 +0000
Subject: [PATCH 0137/1827] Bump externalpackages/boutdata from `e458cf0` to
 `0aaef41`

Bumps [externalpackages/boutdata](https://github.com/boutproject/boutdata) from `e458cf0` to `0aaef41`.
- [Release notes](https://github.com/boutproject/boutdata/releases)
- [Commits](https://github.com/boutproject/boutdata/compare/e458cf0cf2af6ff68db91da39ef3e15a7e9e6b3d...0aaef417af092882ac295c4d84e4532e4a10e01f)

---
updated-dependencies:
- dependency-name: externalpackages/boutdata
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/boutdata | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/boutdata b/externalpackages/boutdata
index e458cf0cf2..0aaef417af 160000
--- a/externalpackages/boutdata
+++ b/externalpackages/boutdata
@@ -1 +1 @@
-Subproject commit e458cf0cf2af6ff68db91da39ef3e15a7e9e6b3d
+Subproject commit 0aaef417af092882ac295c4d84e4532e4a10e01f

From 0e328fc4f2e4d3e8242fda37230f87118b0c847a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 17 Feb 2025 19:56:15 +0000
Subject: [PATCH 0138/1827] Update pygithub requirement from ~=2.4 to ~=2.6

Updates the requirements on [pygithub](https://github.com/pygithub/pygithub) to permit the latest version.
- [Release notes](https://github.com/pygithub/pygithub/releases)
- [Changelog](https://github.com/PyGithub/PyGithub/blob/main/doc/changes.rst)
- [Commits](https://github.com/pygithub/pygithub/compare/v2.4.0...v2.6.0)

---
updated-dependencies:
- dependency-name: pygithub
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements_maint.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements_maint.txt b/requirements_maint.txt
index 9f4ddc3699..e6ba00ce48 100644
--- a/requirements_maint.txt
+++ b/requirements_maint.txt
@@ -1,3 +1,3 @@
-pygithub~=2.4
+pygithub~=2.6
 ruamel-yaml~=0.18
 Unidecode~=1.3

From bfc8ed87892cab19dbcb7c2a9021b563be8e000b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 7 Jan 2025 11:06:30 +0100
Subject: [PATCH 0139/1827] CI: Install zoidberg and new versions

---
 requirements.txt | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index e7bd77a1c4..52d3076d58 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,8 +1,9 @@
-Jinja2~=3.1.4
-numpy~=2.2.1
-scipy>=1.11.0
-netcdf4~=1.7.1
+Jinja2>=3.1.4
+numpy>=2.0.0
+scipy>=1.14.1
+netcdf4>=1.7.1
 matplotlib>=3.7.0
-Cython~=3.0.0
-boututils~=0.2.1
-boutdata~=0.2.1
+Cython>=3.0.0
+boututils>=0.2.1
+boutdata>=0.2.1
+zoidberg>=0.2.2

From 33067dd40f96e91085b51a9dc49b5379216c53e8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 7 Jan 2025 13:13:15 +0100
Subject: [PATCH 0140/1827] DEBUG: monkey patch zoidberg

---
 tests/MMS/spatial/fci/runtest | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 3db54a3870..fd6e0899d8 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -74,6 +74,16 @@ for nslice in nslices:
         # Create the grid
         grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
         # Make and write maps
+        from scipy.interpolate import RectBivariateSpline as RBS
+
+        def myRBS(a, b, c):
+            mx, my = c.shape
+            kx = max(mx - 1, 1)
+            kx = min(kx, 3)
+            print(c.shape, kx)
+            return RBS(a, b, c, kx=kx)
+
+        zb.poloidal_grid.RectBivariateSpline = myRBS
         maps = zb.make_maps(grid, field, nslice=nslice, quiet=True)
         zb.write_maps(
             grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True

From 0416ba3cb43d0a16b38d79b740751203a5080ccc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 7 Jan 2025 13:58:17 +0100
Subject: [PATCH 0141/1827] Specify MXG=1

---
 tests/MMS/spatial/fci/runtest | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index fd6e0899d8..a588c6800a 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -61,7 +61,7 @@ for nslice in nslices:
         # Note that the Bz and Bzprime parameters here must be the same as in mms.py
         field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
         # Create rectangular poloidal grids
-        poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(nx, n, 0.1, 1.0)
+        poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(nx, n, 0.1, 1.0, MXG=1)
         # Set the ylength and y locations
         ylength = 10.0
 
@@ -84,7 +84,7 @@ for nslice in nslices:
             return RBS(a, b, c, kx=kx)
 
         zb.poloidal_grid.RectBivariateSpline = myRBS
-        maps = zb.make_maps(grid, field, nslice=nslice, quiet=True)
+        maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
         zb.write_maps(
             grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True
         )

From bea060e4cb687f797ae42473a46631e09f004ef4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 7 Jan 2025 17:05:02 +0100
Subject: [PATCH 0142/1827] Remove debug statement

---
 tests/MMS/spatial/fci/runtest | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index a588c6800a..1b7b74a867 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -80,7 +80,6 @@ for nslice in nslices:
             mx, my = c.shape
             kx = max(mx - 1, 1)
             kx = min(kx, 3)
-            print(c.shape, kx)
             return RBS(a, b, c, kx=kx)
 
         zb.poloidal_grid.RectBivariateSpline = myRBS

From a1df60915efe150902c1858f7e3b5b21ff749c3d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 7 Jan 2025 17:05:11 +0100
Subject: [PATCH 0143/1827] Remove python2 compat

---
 tests/MMS/spatial/fci/runtest | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 1b7b74a867..b5ca2db5c5 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -6,9 +6,6 @@
 # Cores: 2
 # requires: zoidberg
 
-from __future__ import division
-from __future__ import print_function
-
 from boututils.run_wrapper import build_and_log, launch_safe
 from boutdata.collect import collect
 import boutconfig as conf

From b6a91b81979c0b5fc3addf1eb99dd9d33e3b21d0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 8 Jan 2025 09:26:26 +0100
Subject: [PATCH 0144/1827] CI: Try limiting multithreading

---
 .ci_fedora.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 974a23a362..77e7f45055 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -59,7 +59,11 @@ else
     export OMPI_MCA_rmaps_base_oversubscribe=yes
     export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
     export TRAVIS=true
+    # Try limiting openmp threads
     export FLEXIBLAS=NETLIB
+    export MKL_NUM_THREADS=1
+    export NUMEXPR_NUM_THREADS=1
+    export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
     echo "starting configure"

From 05f030c771b00f8bc6b3d17680c41f2847e8c7bd Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Wed, 19 Feb 2025 09:13:59 +0000
Subject: [PATCH 0145/1827] Apply black changes

---
 tests/integrated/test_suite | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite
index 307a8d84b3..77ad7882c4 100755
--- a/tests/integrated/test_suite
+++ b/tests/integrated/test_suite
@@ -188,7 +188,7 @@ class Test(threading.Thread):
                 self.output += "\n(It is likely that a timeout occured)"
             else:
                 # ❌ Failed
-                print("\u274C", end="")  # No newline
+                print("\u274c", end="")  # No newline
             print(" %7.3f s" % (time.time() - self.local.start_time), flush=True)
 
     def _cost(self):

From 8132089ec8154036b827712192ff6182900e5109 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 3 Mar 2022 15:51:50 +0100
Subject: [PATCH 0146/1827] Always use python3

---
 cmake/FindCython.cmake                   |  2 +-
 cmake/FindNumpy.cmake                    | 16 ++++++++--------
 manual/sphinx/conf.py                    |  2 +-
 tools/pylib/_boutpp_build/CMakeLists.txt | 12 ++++++------
 4 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/cmake/FindCython.cmake b/cmake/FindCython.cmake
index 76f43480d9..3b98cde89e 100644
--- a/cmake/FindCython.cmake
+++ b/cmake/FindCython.cmake
@@ -10,7 +10,7 @@
 #   CYTHON_FOUND - true if Cython was found
 #   CYTHON_VERSION - Cython version
 
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import cython ; print(cython.__version__)"
+execute_process(COMMAND ${Python3_EXECUTABLE} -c "import cython ; print(cython.__version__)"
   RESULT_VARIABLE _cython_runs
   OUTPUT_VARIABLE CYTHON_VERSION
   OUTPUT_STRIP_TRAILING_WHITESPACE
diff --git a/cmake/FindNumpy.cmake b/cmake/FindNumpy.cmake
index 201bc19221..250eff5959 100644
--- a/cmake/FindNumpy.cmake
+++ b/cmake/FindNumpy.cmake
@@ -12,32 +12,32 @@
 #   Numpy_INCLUDE_DIR
 
 
-find_package(Python 3.6 COMPONENTS Interpreter Development)
+find_package(Python3 3.6 COMPONENTS Interpreter Development)
 
-if (NOT Python_FOUND)
-  message(STATUS "Could not find numpy as python was not found. Maybe the developement package is missing?")
-  set(Numpy_FOUND ${Python_FOUND})
+if (NOT Python3_FOUND)
+  message(STATUS "Could not find numpy as python3 was not found. Maybe the developement package is missing?")
+  set(Numpy_FOUND ${Python3_FOUND})
   return()
 endif()
 
 if (NOT Numpy_FOUND)
-  execute_process(COMMAND ${Python_EXECUTABLE} -c "import numpy ; print(numpy.__version__)"
+  execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.__version__)"
     OUTPUT_STRIP_TRAILING_WHITESPACE
     OUTPUT_VARIABLE Numpy_VERSION
     )
-  execute_process(COMMAND ${Python_EXECUTABLE} -c "import numpy ; print(numpy.get_include())"
+  execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.get_include())"
     OUTPUT_STRIP_TRAILING_WHITESPACE
     OUTPUT_VARIABLE _numpy_include_dirs
     )
 endif()
 
 if (Numpy_DEBUG)
-  message(STATUS "Looking for numpy headers in: ${_numpy_include_dirs} ${PYTHON_INCLUDE_DIR}")
+  message(STATUS "Looking for numpy headers in: ${_numpy_include_dirs} ${Python3_INCLUDE_DIRS}")
 endif()
 
 find_path(Numpy_INCLUDE_DIR
   numpy/arrayobject.h
-  PATHS "${_numpy_include_dirs}" "${PYTHON_INCLUDE_DIR}"
+  PATHS "${_numpy_include_dirs}" "${Python3_INCLUDE_DIRS}"
   PATH_SUFFIXES numpy/core/include
   )
 
diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 5adf3c3633..55d059feba 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -88,7 +88,7 @@ def __getattr__(cls, name):
         + " -DBOUT_UPDATE_GIT_SUBMODULE=OFF"
         + " -DBOUT_TESTS=OFF"
         + " -DBOUT_ALLOW_INSOURCE_BUILD=ON"
-        + f" -DPython_ROOT_DIR={pydir}"
+        + f" -DPython3_ROOT_DIR={pydir}"
         + f" -Dmpark_variant_DIR={pwd}/externalpackages/mpark.variant/"
         + f" -Dfmt_DIR={pwd}/externalpackages/fmt/"
     )
diff --git a/tools/pylib/_boutpp_build/CMakeLists.txt b/tools/pylib/_boutpp_build/CMakeLists.txt
index 6b88986a28..3be2a5d2aa 100644
--- a/tools/pylib/_boutpp_build/CMakeLists.txt
+++ b/tools/pylib/_boutpp_build/CMakeLists.txt
@@ -25,7 +25,7 @@ bout_python_maybe_error(${Cython_FOUND} Cython)
 find_package(Bash)
 bout_python_maybe_error(${Bash_FOUND} Bash)
 
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import jinja2"
+execute_process(COMMAND ${Python3_EXECUTABLE} -c "import jinja2"
   RESULT_VARIABLE jinja2_FOUND)
 if (jinja2_FOUND EQUAL 0)
   # We have jinja2 - all good
@@ -33,7 +33,7 @@ else()
   bout_python_maybe_error(OFF jinja2)
 endif()
 
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX')[:-3])"
+execute_process(COMMAND ${Python3_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX')[:-3])"
   RESULT_VARIABLE PYTHON_WORKING
   OUTPUT_VARIABLE PYTHON_EXT_SUFFIX
   OUTPUT_STRIP_TRAILING_WHITESPACE
@@ -73,7 +73,7 @@ foreach(file IN LISTS files)
   #message(FATAL_ERROR "${gen} ${src}/${file}.jinja")
   add_custom_command(OUTPUT ${gen}
 	COMMAND ${CMAKE_COMMAND} -E make_directory ${tar}
-	COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${tar}/..:\${PYTHONPATH} ${Python_EXECUTABLE} generate.py ${file}.jinja ${gen}
+	COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${tar}/..:\${PYTHONPATH} ${Python3_EXECUTABLE} generate.py ${file}.jinja ${gen}
 	DEPENDS ${src}/${file}.jinja
 	DEPENDS ${src}/helper.py
 	DEPENDS ${src}/resolve_enum_inv.pyx.jinja
@@ -93,8 +93,7 @@ endforeach()
 
 add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libboutpp.cpp
   COMMAND ${CMAKE_COMMAND} -E copy boutpp.pyx libboutpp.pyx
-  COMMAND ${Python_EXECUTABLE} -m cython libboutpp.pyx --cplus -3  -X binding=True -X embedsignature=True
-  COMMENT "Cythonizing python interface"
+  COMMAND ${Python3_EXECUTABLE} -m cython libboutpp.pyx --cplus -3  -X binding=True -X embedsignature=True
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   DEPENDS ${boutpp_depends}
   )
@@ -120,5 +119,6 @@ install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/boutpp.py
   DESTINATION ${CMAKE_INSTALL_PYTHON_SITEARCH}/boutpp/
   RENAME __init__.py
   )
+
 target_link_libraries(boutpp${PYTHON_EXT_SUFFIX} bout++)
-target_include_directories(boutpp${PYTHON_EXT_SUFFIX} PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}> ${Numpy_INCLUDE_DIRS} ${Python_INCLUDE_DIRS})
+target_include_directories(boutpp${PYTHON_EXT_SUFFIX} PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}> ${Numpy_INCLUDE_DIRS} ${Python3_INCLUDE_DIRS})

From 401319b0653b775fa6caf97844c21574b11e62c5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 22 Mar 2024 12:43:51 +0100
Subject: [PATCH 0147/1827] expose setConditionallyUsed

---
 tools/pylib/_boutpp_build/bout_options.pxd |  1 +
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 14 ++++++++++++--
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/tools/pylib/_boutpp_build/bout_options.pxd b/tools/pylib/_boutpp_build/bout_options.pxd
index ba5e64c8e3..c4de2a9d37 100644
--- a/tools/pylib/_boutpp_build/bout_options.pxd
+++ b/tools/pylib/_boutpp_build/bout_options.pxd
@@ -52,6 +52,7 @@ cdef extern from "bout/options.hxx":
         void get(string, double&, double)
         void get(string, bool&, bool)
         void cleanCache()
+        void setConditionallyUsed()
 
 
 cdef extern from "bout/optionsreader.hxx":
diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 657e2f28c1..ae4d9212a8 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -1209,8 +1209,9 @@ def finalise():
             else:
                 for ourClass in ourClasses:
                     if isinstance(obj, ourClass):
-                         ourClass.__boutpp_dealloc(obj)
-                         break
+                        if hasattr(ourClass, "__boutpp_dealloc"):
+                            ourClass.__boutpp_dealloc(obj)
+                            break
     del objects
     # Actually finalise
     if wasInit:
@@ -1715,6 +1716,15 @@ cdef class Options:
             opt.get(key, ret_str, default_)
             return ret_str.decode()
 
+    def setConditionallyUsed(self):
+        """Set the attribute "conditionally used" to be true for \p options
+        and all its children/sections, causing `Options::getUnused` to
+        assume those options have been used. This is useful to ignore
+        options when checking for typos etc.
+        """
+        cdef c.Options* opt = self.cobj
+        opt.setConditionallyUsed()
+
     def __dealloc__(self):
         self.__boutpp_dealloc()
 

From b1251bb281977c138c24ba2425da94c1679ec786 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 22 Mar 2024 12:46:01 +0100
Subject: [PATCH 0148/1827] Ensure errors in solve and rhs are catchable

Fixes GH#2890
---
 tools/pylib/_boutpp_build/boutcpp.pxd.jinja | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
index c94fd14a17..dafdd51c5f 100644
--- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
+++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
@@ -148,10 +148,10 @@ cdef extern from "bout/physicsmodel.hxx":
 ctypedef void (*Method)(void *param, void *user_data)
 cdef extern from "helper.h":
     cppclass PythonModel(PhysicsModel):
-        int rhs(double t)
+        int rhs(double t) except +raise_bout_py_error
         void pyinit()
         void free()
-        void solve()
+        void solve() except +raise_bout_py_error
         Solver * getSolver()
         void set_rhs_func(PythonModelCallback*)
         void set_init_func(PythonModelCallback*)

From d619adf26b7134ad7f4dd7396beb6db8d832bcc4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 25 Mar 2024 09:29:16 +0100
Subject: [PATCH 0149/1827] Do not use python preserved __ prefix

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 48 +++++++++++-----------
 1 file changed, 24 insertions(+), 24 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index ae4d9212a8..de01748b6f 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -583,9 +583,9 @@ cdef class {{ field.field_type }}:
 
 {% endfor %}
     def __dealloc__(self):
-        self.__boutpp_dealloc()
+        self._boutpp_dealloc()
 
-    def __boutpp_dealloc(self):
+    def _boutpp_dealloc(self):
         if self.isSelfOwned and self.cobj != NULL:
             del self.cobj
             self.cobj = NULL
@@ -645,9 +645,9 @@ cdef class {{ vec }}:
 
 
     def __dealloc__(self):
-        self.__boutpp_dealloc()
+        self._boutpp_dealloc()
 
-    def __boutpp_dealloc(self):
+    def _boutpp_dealloc(self):
         if self.isSelfOwned and self.cobj != NULL:
             del self.cobj
             self.cobj=NULL
@@ -742,9 +742,9 @@ cdef class Mesh:
         return msh
 
     def __dealloc__(self):
-        self.__boutpp_dealloc()
+        self._boutpp_dealloc()
 
-    def __boutpp_dealloc(self):
+    def _boutpp_dealloc(self):
         if self.cobj and self.isSelfOwned:
             del self.cobj
             self.cobj = NULL
@@ -850,9 +850,9 @@ cdef class Coordinates:
 {% endfor %}
 
     def __dealloc__(self):
-        self.__boutpp_dealloc()
+        self._boutpp_dealloc()
 
-    def __boutpp_dealloc(self):
+    def _boutpp_dealloc(self):
         if self.cobj and self.isSelfOwned:
             del self.cobj
             self.cobj = NULL
@@ -931,9 +931,9 @@ cdef class FieldFactory:
         checkInit()
         cobj=< c.FieldFactory*>0
     def __dealloc__(self):
-        self.__boutpp_dealloc()
+        self._boutpp_dealloc()
 
-    def __boutpp_dealloc(self):
+    def _boutpp_dealloc(self):
         if self.cobj != NULL:
             del self.cobj
             self.cobj = NULL
@@ -965,9 +965,9 @@ cdef class PythonModelCallback:
         self.cobj = new c.PythonModelCallback(callback, <void*>method)
 
     def __dealloc__(self):
-        self.__boutpp_dealloc()
+        self._boutpp_dealloc()
 
-    def __boutpp_dealloc(self):
+    def _boutpp_dealloc(self):
         if self.cobj:
             del self.cobj
             self.cobj = NULL
@@ -1037,12 +1037,12 @@ cdef class PhysicsModelBase(object):
         self.cmodel.set_init_func(self.callbackinit)
 
     def __dealloc__(self):
-        if hasattr(self, "__boutpp_dealloc"):
-            self.__boutpp_dealloc()
+        if hasattr(self, "_boutpp_dealloc"):
+            self._boutpp_dealloc()
         else:
-            PhysicsModelBase.__boutpp_dealloc(self)
+            PhysicsModelBase._boutpp_dealloc(self)
 
-    def __boutpp_dealloc(self):
+    def _boutpp_dealloc(self):
         if self.cmodel != <c.PythonModel *> 0:
             self.cmodel.free()
             del self.cmodel
@@ -1123,8 +1123,8 @@ class PhysicsModel(PhysicsModelBase):
     def __dealloc__(self):
         super(PhysicsModel,self).__dealloc__()
 
-    def __boutpp_dealloc(self):
-        super(PhysicsModel,self).__boutpp_dealloc()
+    def _boutpp_dealloc(self):
+        super(PhysicsModel,self)._boutpp_dealloc()
 
 cdef extern from "bout/bout.hxx":
     int BoutInitialise(int&, char **&) except +raise_bout_py_error
@@ -1204,13 +1204,13 @@ def finalise():
                   PythonModelCallback)
     for obj in objects:
         if isinstance(obj, ourClasses):
-            if hasattr(obj, "__boutpp_dealloc"):
-                obj.__boutpp_dealloc()
+            if hasattr(obj, "_boutpp_dealloc"):
+                obj._boutpp_dealloc()
             else:
                 for ourClass in ourClasses:
                     if isinstance(obj, ourClass):
-                        if hasattr(ourClass, "__boutpp_dealloc"):
-                            ourClass.__boutpp_dealloc(obj)
+                        if hasattr(ourClass, "_boutpp_dealloc"):
+                            ourClass._boutpp_dealloc(obj)
                             break
     del objects
     # Actually finalise
@@ -1726,9 +1726,9 @@ cdef class Options:
         opt.setConditionallyUsed()
 
     def __dealloc__(self):
-        self.__boutpp_dealloc()
+        self._boutpp_dealloc()
 
-    def __boutpp_dealloc(self):
+    def _boutpp_dealloc(self):
         if self.isSelfOwned and self.cobj != NULL:
             del self.cobj
             self.cobj = NULL

From c5789dafb9c5a8b04ec17c74b5a3caa2feb785fe Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Dec 2024 15:42:13 +0100
Subject: [PATCH 0150/1827] make backend executable

---
 tools/pylib/_boutpp_build/backend.py | 2 ++
 1 file changed, 2 insertions(+)
 mode change 100644 => 100755 tools/pylib/_boutpp_build/backend.py

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
old mode 100644
new mode 100755
index 1fba557cdc..02aeb22b7e
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -1,3 +1,5 @@
+#!/bin/python3
+
 import os  # corelib
 import glob  # corelib
 import hashlib  # corelib

From e6a02c6b0a464c0bddc049d63ec78fef731cf835 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Dec 2024 15:41:53 +0100
Subject: [PATCH 0151/1827] Print the help if an invalid argument is given

---
 tools/pylib/_boutpp_build/backend.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 02aeb22b7e..b367a4bdf8 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -370,4 +370,7 @@ def help():
     import sys
 
     for todo in sys.argv[1:]:
+        if todo not in todos:
+            help()
+            sys.exit(1)
         todos[todo]()

From fd25df7bd95cf670ded169285b442a2b110ec0b2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Dec 2024 15:41:18 +0100
Subject: [PATCH 0152/1827] Make printVersion a function

This ensures we have documentation for it
---
 tools/pylib/_boutpp_build/backend.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index b367a4bdf8..0c1e611a2f 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -350,12 +350,19 @@ def help():
         print(fmt % row)
 
 
+def printVersion():
+    """
+    print the version
+    """
+    print(getversion())
+
+
 todos = dict(
     nightly=nightly,
     sdist=sdist,
     wheel=wheel,
     dist=dist,
-    version=lambda: print(getversion()),
+    version=printVersion,
     help=help,
 )
 todos.update(

From 4b078626b16a2f57e1ec07a85755f12b9eecda83 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Dec 2024 10:52:40 +0100
Subject: [PATCH 0153/1827] Add delay to python interface

This is to ensure that all MPI routines are called before MPI_Finalise
is called.

Resolves: gh#3041
---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 149 +++++++++++----------
 1 file changed, 81 insertions(+), 68 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index de01748b6f..6ffecd3596 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -16,11 +16,49 @@ from cython.operator import dereference as deref
 import numbers
 import sys
 import gc
+from time import sleep
 
 size_t = np.uint
 
 cdef extern from "boutexception_helper.hxx":
-     cdef void raise_bout_py_error()
+    cdef void raise_bout_py_error()
+
+cdef class BOUTppBase:
+    """
+    Base class that provides some mechanism for deallocation
+    """
+    cdef c.bool _is_freed
+    cdef c.bool _is_init
+    def __cinit__(self, c.bool init=True):
+        self._is_freed = False
+        self._is_init = init
+
+    def _boutpp_dealloc(self):
+        self._is_freed = True
+
+    def _boutpp_wait_freed(self):
+        while not self._is_freed:
+            sleep(0.001)
+
+{% macro dealloc(self=False, uniquePtr=False) %}
+    def __dealloc__(self):
+        self._boutpp_dealloc()
+
+    def _boutpp_dealloc(self):
+{% if self %}
+        if self.isSelfOwned and self.cobj != NULL:
+{% else %}
+        if self.cobj != NULL:
+{% endif %}
+{% if uniquePtr %}
+            self.cobj.release()
+{% else %}
+            del self.cobj
+            self.cobj = NULL
+{% endif %}
+        super()._boutpp_dealloc()
+{% endmacro %}
+
 {% for field in fields %}
 
 cdef extern from "helper.h":
@@ -60,7 +98,7 @@ cdef {{ field.field_type }} {{ field.fdd }}FromPtr(c.{{ field.field_type }}* i):
     f.isSelfOwned = False
     return f
 
-cdef class {{ field.field_type }}:
+cdef class {{ field.field_type }}(BOUTppBase):
     """
     The {{ field.field_type }} class
     """
@@ -228,6 +266,7 @@ cdef class {{ field.field_type }}:
         if obj:
             self.cobj = obj.cobj
         self.isSelfOwned=True
+        super().__cinit__()
 
     def set(self, data, ignoreDataType=False):
         """
@@ -582,23 +621,18 @@ cdef class {{ field.field_type }}:
             self.cobj.{{ boundaryMethod }}()
 
 {% endfor %}
-    def __dealloc__(self):
-        self._boutpp_dealloc()
-
-    def _boutpp_dealloc(self):
-        if self.isSelfOwned and self.cobj != NULL:
-            del self.cobj
-            self.cobj = NULL
+{{ dealloc(True) }}
 
     @property
     def shape(self):
         return {{ field.makelist("self.cobj.getN$d()") }}
 {% endfor %}
+
 {% for vec in vecs %}
 cdef extern from "helper.h":
     c.{{ vec.field }} c_mul_{{ vec }}_{{ vec }}(c.{{ vec }} *, c.{{ vec }} *) except +
 
-cdef class {{ vec }}:
+cdef class {{ vec }}(BOUTppBase):
     """
     {{ vec }} class
 
@@ -642,16 +676,7 @@ cdef class {{ vec }}:
 {% endfor %}
         return data_
 
-
-
-    def __dealloc__(self):
-        self._boutpp_dealloc()
-
-    def _boutpp_dealloc(self):
-        if self.isSelfOwned and self.cobj != NULL:
-            del self.cobj
-            self.cobj=NULL
-
+{{ dealloc(True) }}
 
 cdef {{ vec }} {{ vec.vdd }}FromObj(c.{{ vec }} i):
     v={{ vec }}()
@@ -667,7 +692,7 @@ cdef extern from "helper.h":
     c.Field3D c_Grad_perp_dot_Grad_perp(c.Field3D,c.Field3D);
     void c_mesh_normalise(c.Mesh* , double)
 
-cdef class Mesh:
+cdef class Mesh(BOUTppBase):
     """
     Mesh class
 
@@ -741,13 +766,7 @@ cdef class Mesh:
         msh.isSelfOwned = False
         return msh
 
-    def __dealloc__(self):
-        self._boutpp_dealloc()
-
-    def _boutpp_dealloc(self):
-        if self.cobj and self.isSelfOwned:
-            del self.cobj
-            self.cobj = NULL
+{{ dealloc(True) }}
 
     cdef getFactory(self):
         """
@@ -822,7 +841,7 @@ cdef Coordinates coordsFromPtr(c.Coordinates * obj):
     coords.isSelfOwned = False
     return coords
 
-cdef class Coordinates:
+cdef class Coordinates(BOUTppBase):
     """
     Contains information about geometry, such as metric tensors
     """
@@ -849,15 +868,9 @@ cdef class Coordinates:
         self.{{f}} = {{ metric_field.fdd }}FromPtr(&self.cobj.{{f}})
 {% endfor %}
 
-    def __dealloc__(self):
-        self._boutpp_dealloc()
-
-    def _boutpp_dealloc(self):
-        if self.cobj and self.isSelfOwned:
-            del self.cobj
-            self.cobj = NULL
+{{ dealloc(True) }}
 
-cdef class Laplacian:
+cdef class Laplacian(BOUTppBase):
     """
     Laplacian inversion solver
 
@@ -867,7 +880,7 @@ cdef class Laplacian:
     """
     cdef unique_ptr[c.Laplacian] cobj
     cdef c.bool isSelfOwned
-    def __init__(self,section=None):
+    def __init__(self, section=None):
         """
         Initialiase a Laplacian solver
 
@@ -882,7 +895,8 @@ cdef class Laplacian:
         else:
            self.cobj = c.Laplacian.create(NULL)
         self.isSelfOwned = True
-    def solve(self,Field3D x, Field3D guess):
+
+    def solve(self, Field3D x, Field3D guess):
         """
         Calculate the Laplacian inversion
 
@@ -925,18 +939,15 @@ cdef class Laplacian:
         deref(self.cobj).setCoef{{ coeff }}({{ coeff }}.cobj[0])
 {% endfor %}
 
-cdef class FieldFactory:
+{{ dealloc(True, uniquePtr=True) }}
+
+cdef class FieldFactory(BOUTppBase):
     cdef c.FieldFactory * cobj
     def __init__(self):
         checkInit()
         cobj=< c.FieldFactory*>0
-    def __dealloc__(self):
-        self._boutpp_dealloc()
 
-    def _boutpp_dealloc(self):
-        if self.cobj != NULL:
-            del self.cobj
-            self.cobj = NULL
+{{ dealloc() }}
 
 cdef void callback(void * parameter, void * method) with gil:
     cdef double time = (<double*>parameter)[0]
@@ -953,7 +964,7 @@ cdef void callback(void * parameter, void * method) with gil:
 
 ctypedef void (*Method)(void *param)
 
-cdef class PythonModelCallback:
+cdef class PythonModelCallback(BOUTppBase):
     """Needed for callbacks from C++ to python"""
     cdef c.PythonModelCallback * cobj
 
@@ -963,21 +974,16 @@ cdef class PythonModelCallback:
         # "method"   :: The effective method passed by the Python user
         checkInit()
         self.cobj = new c.PythonModelCallback(callback, <void*>method)
+        self.__cinit__()
 
-    def __dealloc__(self):
-        self._boutpp_dealloc()
-
-    def _boutpp_dealloc(self):
-        if self.cobj:
-            del self.cobj
-            self.cobj = NULL
+{{ dealloc() }}
 
     cpdef void execute(self, parameter):
         # "parameter" :: The parameter to be passed to the "method"
         self.cobj.cy_execute(<void*>parameter)
 
 
-cdef class PhysicsModelBase(object):
+cdef class PhysicsModelBase(BOUTppBase):
     """The PhysicsModelBase in python - better use the PhysicsModel class"""
     cdef c.PythonModel * cmodel
     cdef c.PythonModelCallback * callback
@@ -1049,6 +1055,7 @@ cdef class PhysicsModelBase(object):
             del self.callback
             del self.callbackinit
             self.cmodel = <c.PythonModel *> 0
+        super()._boutpp_dealloc()
 
 class PhysicsModel(PhysicsModelBase):
     """
@@ -1121,10 +1128,10 @@ class PhysicsModel(PhysicsModelBase):
         pass
 
     def __dealloc__(self):
-        super(PhysicsModel,self).__dealloc__()
+        super().__dealloc__()
 
     def _boutpp_dealloc(self):
-        super(PhysicsModel,self)._boutpp_dealloc()
+        super()._boutpp_dealloc()
 
 cdef extern from "bout/bout.hxx":
     int BoutInitialise(int&, char **&) except +raise_bout_py_error
@@ -1199,9 +1206,11 @@ def finalise():
     wasInit = _isInit
     _isInit = False
     objects = gc.get_objects()
-    ourClasses = (Coordinates, Field2D, Field3D, Mesh, Options,
-                  PhysicsModel, PhysicsModelBase, Vector2D, Vector3D,
-                  PythonModelCallback)
+    ourClasses = (
+        Field2D, Field3D, Vector2D, Vector3D, Mesh, Coordinates,
+        Laplacian, FieldFactory, PythonModelCallback, PhysicsModel,
+        PhysicsModelBase, PythonModelCallback, Options, BOUTppBase,
+    )
     for obj in objects:
         if isinstance(obj, ourClasses):
             if hasattr(obj, "_boutpp_dealloc"):
@@ -1212,6 +1221,16 @@ def finalise():
                         if hasattr(ourClass, "_boutpp_dealloc"):
                             ourClass._boutpp_dealloc(obj)
                             break
+    for obj in objects:
+        if isinstance(obj, ourClasses):
+            if hasattr(obj, "_boutpp_wait_dealloc"):
+                obj._boutpp_wait_dealloc()
+            else:
+                for ourClass in ourClasses:
+                    if isinstance(obj, ourClass):
+                        if hasattr(ourClass, "_boutpp_wait_dealloc"):
+                            ourClass._boutpp_wait_dealloc(obj)
+                            break
     del objects
     # Actually finalise
     if wasInit:
@@ -1522,7 +1541,7 @@ def setOption(name, value, source="PyInterface", force=False):
     root = Options.root()
     root.set(name, value, source, force)
 
-cdef class Options:
+cdef class Options(BOUTppBase):
     """
     The Options class
     """
@@ -1725,13 +1744,7 @@ cdef class Options:
         cdef c.Options* opt = self.cobj
         opt.setConditionallyUsed()
 
-    def __dealloc__(self):
-        self._boutpp_dealloc()
-
-    def _boutpp_dealloc(self):
-        if self.isSelfOwned and self.cobj != NULL:
-            del self.cobj
-            self.cobj = NULL
+{{ dealloc(True) }}
 
 
 def writeDefaultOutputFile(options: Options):

From ec45eb5ca4a1f62edb4634496a3f7954e8a65f83 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Dec 2024 11:12:59 +0100
Subject: [PATCH 0154/1827] Allow abitrary arguments to base __cinit__

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 6ffecd3596..639d4ea4dd 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -28,10 +28,8 @@ cdef class BOUTppBase:
     Base class that provides some mechanism for deallocation
     """
     cdef c.bool _is_freed
-    cdef c.bool _is_init
-    def __cinit__(self, c.bool init=True):
+    def __cinit__(self, *args, **kwargs):
         self._is_freed = False
-        self._is_init = init
 
     def _boutpp_dealloc(self):
         self._is_freed = True

From 536bd2403962043ef5cf0281c7cc5d1fbdb7a557 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Dec 2024 11:15:08 +0100
Subject: [PATCH 0155/1827] cinit is always called, do not need to call it

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 639d4ea4dd..083dae4688 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -259,12 +259,11 @@ cdef class {{ field.field_type }}(BOUTppBase):
         f.setAll(data, ignoreDataType=ignoreDataType)
         return f
 
-    def __cinit__(self,{{ field.field_type }} obj=None):
+    def __cinit__(self, {{ field.field_type }} obj=None):
         self.cobj = NULL
         if obj:
             self.cobj = obj.cobj
-        self.isSelfOwned=True
-        super().__cinit__()
+        self.isSelfOwned = True
 
     def set(self, data, ignoreDataType=False):
         """

From 8daff5b139c9bb3e0e2ec5757f256155795f59a0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Dec 2024 15:37:58 +0100
Subject: [PATCH 0156/1827] Use generated code, to avoid having to deal with
 inheritance

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 239 +++++++++------------
 1 file changed, 105 insertions(+), 134 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 083dae4688..3ae6dfc47d 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -23,38 +23,52 @@ size_t = np.uint
 cdef extern from "boutexception_helper.hxx":
     cdef void raise_bout_py_error()
 
-cdef class BOUTppBase:
-    """
-    Base class that provides some mechanism for deallocation
-    """
-    cdef c.bool _is_freed
-    def __cinit__(self, *args, **kwargs):
-        self._is_freed = False
-
-    def _boutpp_dealloc(self):
-        self._is_freed = True
-
+{% macro wait() %}
     def _boutpp_wait_freed(self):
         while not self._is_freed:
             sleep(0.001)
+{% endmacro %}
 
-{% macro dealloc(self=False, uniquePtr=False) %}
+{% macro dealloc(extra_dealloc='', uniquePtr=False) %}
     def __dealloc__(self):
         self._boutpp_dealloc()
 
     def _boutpp_dealloc(self):
-{% if self %}
+{{ extra_dealloc | indent(width=8) }}
         if self.isSelfOwned and self.cobj != NULL:
-{% else %}
-        if self.cobj != NULL:
-{% endif %}
 {% if uniquePtr %}
             self.cobj.release()
 {% else %}
             del self.cobj
             self.cobj = NULL
 {% endif %}
-        super()._boutpp_dealloc()
+
+{{ wait() }}
+{% endmacro %}
+
+{% macro class(name, init="", extra_dealloc="", defaultSO=True, data="", uniquePtr=False, init_args="*args, **kwargs",
+               comment="") %}
+cdef class {{ name }}{{ "(" ~ base ~ ")" if base else "" }}:
+    """
+{% if comment %}
+{{ comment | indent }}
+{% else %}
+    The {{ name }} class
+{% endif %}
+    """
+    cdef {{ "unique_ptr[c." ~ name ~ "]" if uniquePtr else "c." ~ name ~ "* " }} cobj
+    cdef c.bool isSelfOwned
+    cdef c.bool _is_freed
+    {{ data | indent }}
+    def __cinit__(self, {{ init_args}}):
+        self._is_freed = False
+{% if not uniquePtr and cobj %}
+        self.isSelfOwned = {{ defaultSO }}
+        self.cobj = NULL
+{% endif %}
+{{ init | indent(width=8) }}
+
+{{ dealloc(extra_dealloc=extra_dealloc, uniquePtr=uniquePtr) }}
 {% endmacro %}
 
 {% for field in fields %}
@@ -96,12 +110,8 @@ cdef {{ field.field_type }} {{ field.fdd }}FromPtr(c.{{ field.field_type }}* i):
     f.isSelfOwned = False
     return f
 
-cdef class {{ field.field_type }}(BOUTppBase):
-    """
-    The {{ field.field_type }} class
-    """
-    cdef c.{{ field.field_type }} * cobj
-    cdef c.bool isSelfOwned
+
+{{ class(field.field_type) }}
 
     @classmethod
     def fromMesh(cls, mesh=None):
@@ -259,12 +269,6 @@ cdef class {{ field.field_type }}(BOUTppBase):
         f.setAll(data, ignoreDataType=ignoreDataType)
         return f
 
-    def __cinit__(self, {{ field.field_type }} obj=None):
-        self.cobj = NULL
-        if obj:
-            self.cobj = obj.cobj
-        self.isSelfOwned = True
-
     def set(self, data, ignoreDataType=False):
         """
         Set all data of the {{ field.field_type }}
@@ -400,7 +404,7 @@ cdef class {{ field.field_type }}(BOUTppBase):
 
         Returns
         -------
-	{{ field.field_type }}
+        {{ field.field_type }}
             exponential of the field to the power of the exponential
         """
         if other is not None:
@@ -618,7 +622,6 @@ cdef class {{ field.field_type }}(BOUTppBase):
             self.cobj.{{ boundaryMethod }}()
 
 {% endfor %}
-{{ dealloc(True) }}
 
     @property
     def shape(self):
@@ -629,14 +632,8 @@ cdef class {{ field.field_type }}(BOUTppBase):
 cdef extern from "helper.h":
     c.{{ vec.field }} c_mul_{{ vec }}_{{ vec }}(c.{{ vec }} *, c.{{ vec }} *) except +
 
-cdef class {{ vec }}(BOUTppBase):
-    """
-    {{ vec }} class
+{{ class(vec) }}
 
-    A vector of {{ vec.field }}
-    """
-    cdef c.{{ vec }} * cobj
-    cdef c.bool isSelfOwned
 {% for d in "xyz" %}
     @property
     def {{ d }}(self):
@@ -673,8 +670,6 @@ cdef class {{ vec }}(BOUTppBase):
 {% endfor %}
         return data_
 
-{{ dealloc(True) }}
-
 cdef {{ vec }} {{ vec.vdd }}FromObj(c.{{ vec }} i):
     v={{ vec }}()
     v.cobj = new c.{{ vec }}(<const c.{{ vec }} & ?> i)
@@ -689,19 +684,18 @@ cdef extern from "helper.h":
     c.Field3D c_Grad_perp_dot_Grad_perp(c.Field3D,c.Field3D);
     void c_mesh_normalise(c.Mesh* , double)
 
-cdef class Mesh(BOUTppBase):
-    """
-    Mesh class
 
-    Contains information about geometry.
-    It contains also the coordinates and is responsible for taking deriavtives.
-    """
-    cdef c.Mesh * cobj;
-    cdef c.bool isSelfOwned
-    cdef double isNormalised
-    cdef FieldFactory factory
-    cdef Coordinates _coords
-    cdef options
+{{ class("Mesh", comment="""
+Mesh class
+
+Contains information about geometry.
+It contains also the coordinates and is responsible for taking deriavtives.
+""", data="""
+cdef double isNormalised
+cdef FieldFactory factory
+cdef Coordinates _coords
+cdef options
+""") }}
 
     def __init__(self, create=True, section=None, options=None):
         """
@@ -723,7 +717,7 @@ cdef class Mesh(BOUTppBase):
             global Options object is used.
         """
         checkInit()
-        self.cobj=<c.Mesh*>0
+        self.cobj = <c.Mesh*>0
         cdef c.string tmp
         cdef c.Options * opt = NULL
         self.isSelfOwned = False
@@ -763,8 +757,6 @@ cdef class Mesh(BOUTppBase):
         msh.isSelfOwned = False
         return msh
 
-{{ dealloc(True) }}
-
     cdef getFactory(self):
         """
         Get the FieldFactory of the mesh
@@ -835,48 +827,36 @@ cdef Coordinates coordsFromPtr(c.Coordinates * obj):
     coords = Coordinates()
     coords.cobj = obj
     coords._setmembers()
-    coords.isSelfOwned = False
     return coords
 
-cdef class Coordinates(BOUTppBase):
-    """
-    Contains information about geometry, such as metric tensors
-    """
-    cdef c.Coordinates * cobj
-    cdef c.bool isSelfOwned
-    cdef public {{ metric_field }} dx, dy, dz
-    cdef public {{ metric_field }} J
-    cdef public {{ metric_field }} Bxy
-    cdef public {{ metric_field }} g11, g22, g33, g12, g13, g23
-    cdef public {{ metric_field }} g_11, g_22, g_33, g_12, g_13, g_23
-    cdef public {{ metric_field }} G1_11, G1_22, G1_33, G1_12, G1_13, G1_23
-    cdef public {{ metric_field }} G2_11, G2_22, G2_33, G2_12, G2_13, G2_23
-    cdef public {{ metric_field }} G3_11, G3_22, G3_33, G3_12, G3_13, G3_23
-    cdef public {{ metric_field }} G1, G2, G3
-    cdef public {{ metric_field }} ShiftTorsion
-    cdef public {{ metric_field }} IntShiftTorsion
-
-    def __init__(self):
-        self.cobj = NULL
-        self.isSelfOwned = False
+{% set data %}
+cdef public {{ metric_field }} dx, dy, dz
+cdef public {{ metric_field }} J
+cdef public {{ metric_field }} Bxy
+cdef public {{ metric_field }} g11, g22, g33, g12, g13, g23
+cdef public {{ metric_field }} g_11, g_22, g_33, g_12, g_13, g_23
+cdef public {{ metric_field }} G1_11, G1_22, G1_33, G1_12, G1_13, G1_23
+cdef public {{ metric_field }} G2_11, G2_22, G2_33, G2_12, G2_13, G2_23
+cdef public {{ metric_field }} G3_11, G3_22, G3_33, G3_12, G3_13, G3_23
+cdef public {{ metric_field }} G1, G2, G3
+cdef public {{ metric_field }} ShiftTorsion
+cdef public {{ metric_field }} IntShiftTorsion
+{% endset %}
+{{ class("Coordinates", comment="Contains information about geometry, such as metric tensors", data=data, defaultSO=False) }}
 
     def _setmembers(self):
 {% for f in "dx", "dy", "dz", "J", "Bxy", "g11", "g22", "g33", "g12", "g13", "g23", "g_11", "g_22", "g_33", "g_12", "g_13", "g_23", "G1_11", "G1_22", "G1_33", "G1_12", "G1_13", "G1_23", "G2_11", "G2_22", "G2_33", "G2_12", "G2_13", "G2_23", "G3_11", "G3_22", "G3_33", "G3_12", "G3_13", "G3_23", "G1", "G2", "G3", "ShiftTorsion", "IntShiftTorsion" %}
         self.{{f}} = {{ metric_field.fdd }}FromPtr(&self.cobj.{{f}})
 {% endfor %}
 
-{{ dealloc(True) }}
+{{ class("Laplacian", comment="""
+Laplacian inversion solver
 
-cdef class Laplacian(BOUTppBase):
-    """
-    Laplacian inversion solver
+Compute the Laplacian inversion of objects.
 
-    Compute the Laplacian inversion of objects.
+Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\perp x + ex\\nabla_x x + ez\\nabla_z x + a x = b
+""", uniquePtr=True) }}
 
-    Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\perp x + ex\\nabla_x x + ez\\nabla_z x + a x = b
-    """
-    cdef unique_ptr[c.Laplacian] cobj
-    cdef c.bool isSelfOwned
     def __init__(self, section=None):
         """
         Initialiase a Laplacian solver
@@ -936,15 +916,8 @@ cdef class Laplacian(BOUTppBase):
         deref(self.cobj).setCoef{{ coeff }}({{ coeff }}.cobj[0])
 {% endfor %}
 
-{{ dealloc(True, uniquePtr=True) }}
 
-cdef class FieldFactory(BOUTppBase):
-    cdef c.FieldFactory * cobj
-    def __init__(self):
-        checkInit()
-        cobj=< c.FieldFactory*>0
-
-{{ dealloc() }}
+{{ class("FieldFactory", defaultSO=False) }}
 
 cdef void callback(void * parameter, void * method) with gil:
     cdef double time = (<double*>parameter)[0]
@@ -961,14 +934,20 @@ cdef void callback(void * parameter, void * method) with gil:
 
 ctypedef void (*Method)(void *param)
 
-cdef class PythonModelCallback(BOUTppBase):
-    """Needed for callbacks from C++ to python"""
+cdef class PythonModelCallback:
+    """
+    Needed for callbacks from C++ to python
+    """
     cdef c.PythonModelCallback * cobj
+    cdef c.bool _is_freed
+    cdef c.bool isSelfOwned
 
     def __cinit__(self, method):
         # "callback" :: The pattern/converter method to fire a Python
         #               object method from C typed infos
         # "method"   :: The effective method passed by the Python user
+        self._is_freed = False
+        self.isSelfOwned = True
         checkInit()
         self.cobj = new c.PythonModelCallback(callback, <void*>method)
         self.__cinit__()
@@ -980,18 +959,24 @@ cdef class PythonModelCallback(BOUTppBase):
         self.cobj.cy_execute(<void*>parameter)
 
 
-cdef class PhysicsModelBase(BOUTppBase):
+cdef class PhysicsModelBase:
     """The PhysicsModelBase in python - better use the PhysicsModel class"""
     cdef c.PythonModel * cmodel
     cdef c.PythonModelCallback * callback
     cdef c.PythonModelCallback * callbackinit
     cdef c.bool _done_pyinit
-    def __init__(self):
+    cdef c.bool _is_freed
+    cdef c.bool isSelfOwned
+
+    def __cinit__(self):
         checkInit()
-        self.cmodel  = new c.PythonModel()
-        self.callback= <c.PythonModelCallback*> 0
-        self.callbackinit= <c.PythonModelCallback*> 0
+        self.cmodel = new c.PythonModel()
+        self.callback = NULL
+        self.callbackinit = NULL
         self._done_pyinit = False
+        self._is_freed = False
+        self.isSelfOwned = True
+
     def solve(self):
         if self._done_pyinit == False:
             self._done_pyinit = True
@@ -1011,7 +996,7 @@ cdef class PhysicsModelBase(BOUTppBase):
             f3d = (<Field3D?>kwargs[key]).cobj
             self.cmodel.getSolver().add(f3d[0],tmp)
 
-    def setRhs(self,rhs):
+    def setRhs(self, rhs):
         """
         set the rhs function to be called
 
@@ -1020,7 +1005,7 @@ cdef class PhysicsModelBase(BOUTppBase):
         rhs : function
             Must not be a method, and must accept an double (time) as argument
         """
-        if self.callback != <c.PythonModelCallback*>0:
+        if self.callback != NULL:
             del self.callback
         self.callback = new c.PythonModelCallback(callback, <void*> rhs)
         self.cmodel.set_rhs_func(self.callback)
@@ -1046,13 +1031,16 @@ cdef class PhysicsModelBase(BOUTppBase):
             PhysicsModelBase._boutpp_dealloc(self)
 
     def _boutpp_dealloc(self):
-        if self.cmodel != <c.PythonModel *> 0:
+        if self.cmodel != NULL:
             self.cmodel.free()
             del self.cmodel
             del self.callback
             del self.callbackinit
             self.cmodel = <c.PythonModel *> 0
-        super()._boutpp_dealloc()
+        self._is_freed = True
+
+{{ wait() }}
+
 
 class PhysicsModel(PhysicsModelBase):
     """
@@ -1081,18 +1069,11 @@ class PhysicsModel(PhysicsModelBase):
     model.solve()
     """
 
-    def __init__(self):
-        super(PhysicsModel,self).__init__()
-        self._super_is_initialised=True
     def solve(self):
         """
         Call the solver.
         This makes sure that self.init(restart) and self.rhs(time) are called from the solver.
         """
-        try:
-            self._super_is_initialised
-        except:
-            raise RuntimeError("PhysicsModel is not initialized")
         def _rhs(time):
            self.rhs(time)
         self.myrhs=_rhs
@@ -1102,6 +1083,7 @@ class PhysicsModel(PhysicsModelBase):
         self.myinit=_init
         self.setInit(self.myinit)
         super(PhysicsModel,self).solve()
+
     def solve_for(self,*args,**kwargs):
         """
         Add Field3D's to be solved for.
@@ -1113,11 +1095,8 @@ class PhysicsModel(PhysicsModelBase):
         kwargs : dictionary of Field2D or Field3D
             Keys must be strings, and value of dict must be the Field3D which should be evolved.
         """
-        try:
-            self._super_is_initialised
-        except:
-            raise RuntimeError("PhysicsModel is not initialized")
         super(PhysicsModel,self).solve_for(*args,**kwargs)
+
     def init(self,restart):
         """
         This can be overwritten to do model specific initialization
@@ -1206,7 +1185,7 @@ def finalise():
     ourClasses = (
         Field2D, Field3D, Vector2D, Vector3D, Mesh, Coordinates,
         Laplacian, FieldFactory, PythonModelCallback, PhysicsModel,
-        PhysicsModelBase, PythonModelCallback, Options, BOUTppBase,
+        PhysicsModelBase, PythonModelCallback, Options,
     )
     for obj in objects:
         if isinstance(obj, ourClasses):
@@ -1220,14 +1199,16 @@ def finalise():
                             break
     for obj in objects:
         if isinstance(obj, ourClasses):
-            if hasattr(obj, "_boutpp_wait_dealloc"):
-                obj._boutpp_wait_dealloc()
+            if hasattr(obj, "_boutpp_wait_freed"):
+                obj._boutpp_wait_freed()
             else:
                 for ourClass in ourClasses:
                     if isinstance(obj, ourClass):
-                        if hasattr(ourClass, "_boutpp_wait_dealloc"):
-                            ourClass._boutpp_wait_dealloc(obj)
+                        if hasattr(ourClass, "_boutpp_wait_freed"):
+                            ourClass._boutpp_wait_freed(obj)
                             break
+                        else:
+                            print(f"{obj} of type {ourClass} cannot wait!")
     del objects
     # Actually finalise
     if wasInit:
@@ -1538,12 +1519,7 @@ def setOption(name, value, source="PyInterface", force=False):
     root = Options.root()
     root.set(name, value, source, force)
 
-cdef class Options(BOUTppBase):
-    """
-    The Options class
-    """
-    cdef c.Options * cobj
-    cdef c.bool isSelfOwned
+{{ class("Options") }}
 
     def __init__(self, **kwargs):
         """Construct an Options from keywords or dict"""
@@ -1595,13 +1571,11 @@ cdef class Options(BOUTppBase):
             The Options object
         """
         checkInit()
-        opt = Options("")
-        opt.cobj = new c.Options()
-        opt.isSelfOwned = True
+        opt = Options()
         cdef char * file_
         file__ = file.encode()
         file_ = file__
-        c.OptionsReader.getInstance().read(opt.cobj, "%s", file_)
+        c.OptionsReader.getInstance().read(opt.cobj, file_)
         return opt
 
     @staticmethod
@@ -1741,9 +1715,6 @@ cdef class Options(BOUTppBase):
         cdef c.Options* opt = self.cobj
         opt.setConditionallyUsed()
 
-{{ dealloc(True) }}
-
-
 def writeDefaultOutputFile(options: Options):
     c.writeDefaultOutputFile(deref(options.cobj))
 

From 74134842766f7f53c54c13db61287412e628b5c3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Dec 2024 15:40:52 +0100
Subject: [PATCH 0157/1827] Track references in boutpp

The list from gc was incomplete.
Using a custom weakref list ensures we can free all objects before
MPI_Finalize is called.

This reverts 0e4314c449581, which was not working as it relied on the
same, incomplete, list of objects.

Resolves: gh#3041
---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 66 +++++++++-------------
 1 file changed, 26 insertions(+), 40 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 3ae6dfc47d..d6f0601f1c 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -15,20 +15,16 @@ from libcpp.memory cimport unique_ptr
 from cython.operator import dereference as deref
 import numbers
 import sys
-import gc
 from time import sleep
+import weakref
+
+_allobjects = []
 
 size_t = np.uint
 
 cdef extern from "boutexception_helper.hxx":
     cdef void raise_bout_py_error()
 
-{% macro wait() %}
-    def _boutpp_wait_freed(self):
-        while not self._is_freed:
-            sleep(0.001)
-{% endmacro %}
-
 {% macro dealloc(extra_dealloc='', uniquePtr=False) %}
     def __dealloc__(self):
         self._boutpp_dealloc()
@@ -43,7 +39,6 @@ cdef extern from "boutexception_helper.hxx":
             self.cobj = NULL
 {% endif %}
 
-{{ wait() }}
 {% endmacro %}
 
 {% macro class(name, init="", extra_dealloc="", defaultSO=True, data="", uniquePtr=False, init_args="*args, **kwargs",
@@ -58,10 +53,11 @@ cdef class {{ name }}{{ "(" ~ base ~ ")" if base else "" }}:
     """
     cdef {{ "unique_ptr[c." ~ name ~ "]" if uniquePtr else "c." ~ name ~ "* " }} cobj
     cdef c.bool isSelfOwned
-    cdef c.bool _is_freed
+    cdef object __weakref__
     {{ data | indent }}
     def __cinit__(self, {{ init_args}}):
-        self._is_freed = False
+        global _allobjects
+        _allobjects.append(weakref.ref(self))
 {% if not uniquePtr and cobj %}
         self.isSelfOwned = {{ defaultSO }}
         self.cobj = NULL
@@ -939,14 +935,15 @@ cdef class PythonModelCallback:
     Needed for callbacks from C++ to python
     """
     cdef c.PythonModelCallback * cobj
-    cdef c.bool _is_freed
     cdef c.bool isSelfOwned
+    cdef object __weakref__
 
     def __cinit__(self, method):
         # "callback" :: The pattern/converter method to fire a Python
         #               object method from C typed infos
         # "method"   :: The effective method passed by the Python user
-        self._is_freed = False
+        global _allobjects
+        _allobjects.append(weakref.ref(self))
         self.isSelfOwned = True
         checkInit()
         self.cobj = new c.PythonModelCallback(callback, <void*>method)
@@ -965,16 +962,17 @@ cdef class PhysicsModelBase:
     cdef c.PythonModelCallback * callback
     cdef c.PythonModelCallback * callbackinit
     cdef c.bool _done_pyinit
-    cdef c.bool _is_freed
     cdef c.bool isSelfOwned
+    cdef object __weakref__
 
     def __cinit__(self):
         checkInit()
+        global _allobjects
+        _allobjects.append(weakref.ref(self))
         self.cmodel = new c.PythonModel()
         self.callback = NULL
         self.callbackinit = NULL
         self._done_pyinit = False
-        self._is_freed = False
         self.isSelfOwned = True
 
     def solve(self):
@@ -1037,9 +1035,6 @@ cdef class PhysicsModelBase:
             del self.callback
             del self.callbackinit
             self.cmodel = <c.PythonModel *> 0
-        self._is_freed = True
-
-{{ wait() }}
 
 
 class PhysicsModel(PhysicsModelBase):
@@ -1181,34 +1176,25 @@ def finalise():
     global _isInit
     wasInit = _isInit
     _isInit = False
-    objects = gc.get_objects()
+    objects = _allobjects #gc.get_objects()
     ourClasses = (
         Field2D, Field3D, Vector2D, Vector3D, Mesh, Coordinates,
         Laplacian, FieldFactory, PythonModelCallback, PhysicsModel,
         PhysicsModelBase, PythonModelCallback, Options,
     )
-    for obj in objects:
-        if isinstance(obj, ourClasses):
-            if hasattr(obj, "_boutpp_dealloc"):
-                obj._boutpp_dealloc()
-            else:
-                for ourClass in ourClasses:
-                    if isinstance(obj, ourClass):
-                        if hasattr(ourClass, "_boutpp_dealloc"):
-                            ourClass._boutpp_dealloc(obj)
-                            break
-    for obj in objects:
-        if isinstance(obj, ourClasses):
-            if hasattr(obj, "_boutpp_wait_freed"):
-                obj._boutpp_wait_freed()
-            else:
-                for ourClass in ourClasses:
-                    if isinstance(obj, ourClass):
-                        if hasattr(ourClass, "_boutpp_wait_freed"):
-                            ourClass._boutpp_wait_freed(obj)
-                            break
-                        else:
-                            print(f"{obj} of type {ourClass} cannot wait!")
+    for objr in objects:
+        obj = objr()
+        if obj is None:
+            continue
+        if hasattr(obj, "_boutpp_dealloc"):
+            obj._boutpp_dealloc()
+        else:
+            for ourClass in ourClasses:
+                if isinstance(obj, ourClass):
+                    if hasattr(ourClass, "_boutpp_dealloc"):
+                        ourClass._boutpp_dealloc(obj)
+                        break
+
     del objects
     # Actually finalise
     if wasInit:

From cb083c0bda420c49fb7dacc3b0c4eaaa3f7644b2 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Wed, 19 Feb 2025 10:08:22 +0000
Subject: [PATCH 0158/1827] Apply black changes

---
 tests/integrated/test_suite | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite
index 307a8d84b3..77ad7882c4 100755
--- a/tests/integrated/test_suite
+++ b/tests/integrated/test_suite
@@ -188,7 +188,7 @@ class Test(threading.Thread):
                 self.output += "\n(It is likely that a timeout occured)"
             else:
                 # ❌ Failed
-                print("\u274C", end="")  # No newline
+                print("\u274c", end="")  # No newline
             print(" %7.3f s" % (time.time() - self.local.start_time), flush=True)
 
     def _cost(self):

From dc932cc56bdefce5f81dfa31fecf08fedcd0c4c6 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Tue, 25 Feb 2025 13:57:25 -0800
Subject: [PATCH 0159/1827] Support BOUT_FOR_RAJA GPU field operators

---
 CMakeLists.txt                        |   9 +-
 include/bout/coordinates_accessor.hxx |   2 +-
 include/bout/field_accessor.hxx       |  40 +++++-
 include/bout/mesh.hxx                 |   5 +
 include/bout/rajalib.hxx              |  13 +-
 include/bout/single_index_ops.hxx     |  11 --
 src/field/gen_fieldops.jinja          | 200 +++++++++++++++++++++-----
 src/field/gen_fieldops.py             |  58 +++++++-
 src/mesh/coordinates.cxx              |   5 +-
 src/mesh/coordinates_accessor.cxx     |  18 ++-
 10 files changed, 294 insertions(+), 67 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c45fca3b72..f0a657fe94 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -386,8 +386,15 @@ if (BOUT_GENERATE_FIELDOPS)
   if (NOT ClangFormat_FOUND)
     message(FATAL_ERROR "clang-format not found, but you have requested to generate code!")
   endif()
+  if (BOUT_ENABLE_RAJA)
+    set(GEN_LOOP_EXEC "raja")
+  elseif (BOUT_ENABLE_OPENMP)
+    set(GEN_LOOP_EXEC "openmp")
+  else()
+    set(GEN_LOOP_EXEC "serial")
+  endif()
   add_custom_command( OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/src/field/generated_fieldops.cxx
-    COMMAND ${Python3_EXECUTABLE} gen_fieldops.py --filename generated_fieldops.cxx.tmp
+    COMMAND ${Python3_EXECUTABLE} gen_fieldops.py --loop-exec ${GEN_LOOP_EXEC} --filename generated_fieldops.cxx.tmp
     COMMAND ${ClangFormat_BIN} generated_fieldops.cxx.tmp -i
     COMMAND ${CMAKE_COMMAND} -E rename generated_fieldops.cxx.tmp generated_fieldops.cxx
     DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/src/field/gen_fieldops.jinja  ${CMAKE_CURRENT_SOURCE_DIR}/src/field/gen_fieldops.py
diff --git a/include/bout/coordinates_accessor.hxx b/include/bout/coordinates_accessor.hxx
index 532351d57a..2376ab5039 100644
--- a/include/bout/coordinates_accessor.hxx
+++ b/include/bout/coordinates_accessor.hxx
@@ -31,7 +31,7 @@
 ///    -> If Coordinates data is changed, the cache should be cleared
 ///    by calling CoordinatesAccessor::clear()
 struct CoordinatesAccessor {
-  CoordinatesAccessor() = delete;
+  CoordinatesAccessor() {}
 
   /// Constructor from Coordinates
   /// Copies data from coords, doesn't modify it
diff --git a/include/bout/field_accessor.hxx b/include/bout/field_accessor.hxx
index 69b58da979..71d0537d9e 100644
--- a/include/bout/field_accessor.hxx
+++ b/include/bout/field_accessor.hxx
@@ -57,10 +57,17 @@ struct FieldAccessor {
   /// Constructor from Field3D
   ///
   /// @param[in] f    The field to access. Must already be allocated
-  explicit FieldAccessor(FieldType& f) : coords(f.getCoordinates()) {
+  explicit FieldAccessor(FieldType& f) {
     ASSERT0(f.getLocation() == location);
     ASSERT0(f.isAllocated());
 
+    if (auto* Coords = f.getCoordinates()) {
+      coords = CoordinatesAccessor{Coords};
+    }
+    else {
+      coords = CoordinatesAccessor{};
+    }
+
     data = BoutRealArray{&f(0, 0, 0)};
 
     // Field size
@@ -81,15 +88,19 @@ struct FieldAccessor {
     ddt = BoutRealArray{&(f.timeDeriv()->operator()(0, 0, 0))};
   }
 
+  explicit FieldAccessor(const FieldType& f) : FieldAccessor(const_cast<FieldType&>(f)) {}
+
   /// Provide shorthand for access to field data.
   /// Does not convert between 3D and 2D indices,
   /// so fa[i] is equivalent to fa.data[i].
   ///
   BOUT_HOST_DEVICE inline const BoutReal& operator[](int ind) const { return data[ind]; }
+  BOUT_HOST_DEVICE inline BoutReal& operator[](int ind) { return data[ind]; }
 
   BOUT_HOST_DEVICE inline const BoutReal& operator[](const Ind3D& ind) const {
     return data[ind.ind];
   }
+  BOUT_HOST_DEVICE inline BoutReal& operator[](const Ind3D& ind) { return data[ind.ind]; }
 
   // Pointers to the field data arrays
   // These are wrapped in BoutRealArray types so they can be indexed with Ind3D or int
@@ -115,6 +126,9 @@ struct FieldAccessor {
 template <CELL_LOC location = CELL_CENTRE>
 using Field2DAccessor = FieldAccessor<location, Field2D>;
 
+template <CELL_LOC location = CELL_CENTRE>
+using Field3DAccessor = FieldAccessor<location, Field3D>;
+
 /// Syntactic sugar for time derivative of a field
 ///
 /// Usage:
@@ -130,4 +144,28 @@ BOUT_HOST_DEVICE inline BoutRealArray& ddt(const FieldAccessor<location, FieldTy
   return const_cast<BoutRealArray&>(fa.ddt);
 }
 
+struct FieldPerpAccessor {
+  FieldPerpAccessor() = delete;
+
+  int nx, nz;
+  int yindex;
+  BoutReal* data;
+
+  explicit FieldPerpAccessor(const FieldPerp& f) {
+    ASSERT0(f.isAllocated());
+
+    data = BoutRealArray{const_cast<BoutReal*>(&f(0, 0, 0))};
+
+    // Field size
+    nx = f.getNx();
+    nz = f.getNz();
+
+    yindex = f.getIndex();
+  }
+
+  BOUT_HOST_DEVICE int getIndex() const { return yindex; }
+  BOUT_HOST_DEVICE inline const BoutReal& operator[](int ind) const { return data[ind]; }
+  BOUT_HOST_DEVICE inline BoutReal& operator[](int ind) { return data[ind]; }
+};
+
 #endif
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index a1c88a2634..b6553d06ec 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -762,6 +762,11 @@ public:
     return {(indPerp.ind - jz) * LocalNy + LocalNz * jy + jz, LocalNy, LocalNz};
   }
 
+  BOUT_HOST_DEVICE int flatIndPerpto3D(const int& flatIndPerp, const int nz, int jy = 0) const {
+    int jz = flatIndPerp % nz;
+    return (flatIndPerp - jz) * LocalNy + LocalNz * jy + jz;
+  }
+
   /// Converts an Ind3D to an Ind2D representing a 2D index using a lookup -- to be used with care
   Ind2D map3Dto2D(const Ind3D& ind3D) {
     return {indexLookup3Dto2D[ind3D.ind], LocalNy, 1};
diff --git a/include/bout/rajalib.hxx b/include/bout/rajalib.hxx
index b9f6913459..92eae68858 100644
--- a/include/bout/rajalib.hxx
+++ b/include/bout/rajalib.hxx
@@ -23,6 +23,15 @@
 
 #include "RAJA/RAJA.hpp" // using RAJA lib
 
+#if BOUT_HAS_CUDA
+// TODO: Make configurable
+const int CUDA_BLOCK_SIZE = 256;
+using EXEC_POL = RAJA::cuda_exec<CUDA_BLOCK_SIZE>;
+//using EXEC_POL = RAJA::loop_exec;
+#else  // not BOUT_USE_CUDA
+using EXEC_POL = RAJA::loop_exec;
+#endif // end BOUT_USE_CUDA
+
 /// Wrapper around RAJA::forall
 /// Enables computations to be done on CPU or GPU (CUDA).
 ///
@@ -81,7 +90,7 @@ struct RajaForAll {
     // Note: must be a local variable
     const int* _ob_i_ind_raw = &_ob_i_ind[0];
     RAJA::forall<EXEC_POL>(RAJA::RangeSegment(0, _ob_i_ind.size()),
-                           [=] RAJA_DEVICE(int id) {
+                           [=] RAJA_DEVICE(int id) mutable {
                              // Look up index and call user function
                              f(_ob_i_ind_raw[id]);
                            });
@@ -127,7 +136,7 @@ private:
 /// to create variables which shadow the class members.
 ///
 #define BOUT_FOR_RAJA(index, region, ...) \
-  RajaForAll(region) << [ =, ##__VA_ARGS__ ] RAJA_DEVICE(int index)
+RajaForAll(region) << [ =, ##__VA_ARGS__ ] RAJA_DEVICE(int index) mutable
 
 #else // BOUT_HAS_RAJA
 
diff --git a/include/bout/single_index_ops.hxx b/include/bout/single_index_ops.hxx
index 60bd78bc36..c29d1a471f 100644
--- a/include/bout/single_index_ops.hxx
+++ b/include/bout/single_index_ops.hxx
@@ -7,17 +7,6 @@
 
 #include "field_accessor.hxx"
 
-#if BOUT_HAS_RAJA
-//--  RAJA CUDA settings--------------------------------------------------------start
-#if BOUT_HAS_CUDA
-const int CUDA_BLOCK_SIZE = 256; // TODO: Make configurable
-using EXEC_POL = RAJA::cuda_exec<CUDA_BLOCK_SIZE>;
-#else  // not BOUT_USE_CUDA
-using EXEC_POL = RAJA::loop_exec;
-#endif // end BOUT_USE_CUDA
-////-----------CUDA settings------------------------------------------------------end
-#endif // end BOUT_HAS_RAJA
-
 // Ind3D: i.zp():
 BOUT_HOST_DEVICE inline int i_zp(const int id, const int nz) {
   int jz = id % nz;
diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index ecd4e628cc..60f9cbbd7e 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -8,6 +8,26 @@
   checkData({{lhs.name}});
   checkData({{rhs.name}});
 
+  {% if (region_loop == "BOUT_FOR_RAJA") %}
+    {% if out.field_type == "FieldPerp" %}
+      auto {{out.name}}_acc = FieldPerpAccessor{ {{out.name}} };
+    {% else %}
+      auto {{out.name}}_acc = FieldAccessor({{out.name}});
+    {% endif %}
+    {% if lhs.field_type == "FieldPerp" %}
+      auto {{lhs.name}}_acc = FieldPerpAccessor{ {{lhs.name}} };
+    {% elif lhs.field_type == "BoutReal" %}
+    {% else %}
+      auto {{lhs.name}}_acc = FieldAccessor({{lhs.name}});
+    {% endif %}
+    {% if rhs.field_type == "FieldPerp" %}
+      auto {{rhs.name}}_acc = FieldPerpAccessor{ {{rhs.name}} };
+    {% elif rhs.field_type == "BoutReal" %}
+    {% else %}
+      auto {{rhs.name}}_acc = FieldAccessor({{rhs.name}});
+    {% endif %}
+  {% endif %}
+
   {% if out == "Field3D" %}
     {% if lhs == rhs == "Field3D" %}
       {{out.name}}.setRegion({{lhs.name}}.getMesh()->getCommonRegion({{lhs.name}}.getRegionID(),
@@ -20,45 +40,98 @@
   {% endif %}
 
   {% if (out == "Field3D") and ((lhs == "Field2D") or (rhs =="Field2D")) %}
+    {% if (region_loop == "BOUT_FOR_RAJA") %}
+    int mesh_nz = {{lhs.name if lhs.field_type != "BoutReal" else rhs.name}}_acc.mesh_nz;
+    {% else %}
     Mesh *localmesh = {{lhs.name if lhs.field_type != "BoutReal" else rhs.name}}.getMesh();
+    {% endif %}
 
     {% if (lhs == "Field2D") %}
     {{region_loop}}({{index_var}}, {{lhs.name}}.getRegion({{region_name}})) {
     {% else %}
     {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) {
     {% endif %}
-	const auto {{mixed_base_ind}} = localmesh->ind2Dto3D({{index_var}});
-	{% if (operator == "/") and (rhs == "Field2D") %}
-           const auto tmp = 1.0 / {{rhs.mixed_index}};
-	   for (int {{jz_var}} = 0; {{jz_var}} < localmesh->LocalNz; ++{{jz_var}}){
-         	   {{out.mixed_index}} = {{lhs.mixed_index}} * tmp;
+      {% if (region_loop == "BOUT_FOR_RAJA") %}
+        const auto {{mixed_base_ind}} = {{index_var}} * mesh_nz;
+      {% else %}
+        const auto {{mixed_base_ind}} = localmesh->ind2Dto3D({{index_var}});
+      {% endif %}
+	    {% if (operator == "/") and (rhs == "Field2D") %}
+        {% if (region_loop == "BOUT_FOR_RAJA") %}
+          const auto tmp = 1.0 / {{rhs.mixed_index_acc}};
         {% else %}
-	   for (int {{jz_var}} = 0; {{jz_var}} < localmesh->LocalNz; ++{{jz_var}}){
-	           {{out.mixed_index}} = {{lhs.mixed_index}} {{operator}} {{rhs.mixed_index}};
+          const auto tmp = 1.0 / {{rhs.mixed_index}};
         {% endif %}
+        {% if (region_loop == "BOUT_FOR_RAJA") %}
+	      for (int {{jz_var}} = 0; {{jz_var}} < mesh_nz; ++{{jz_var}}){
+        {% else %}
+	      for (int {{jz_var}} = 0; {{jz_var}} < localmesh->LocalNz; ++{{jz_var}}){
+        {% endif %}
+          {% if (region_loop == "BOUT_FOR_RAJA") %}
+            {{out.mixed_index_acc}} = {{lhs.mixed_index_acc}} * tmp;
+          {% else %}
+            {{out.mixed_index}} = {{lhs.mixed_index}} * tmp;
+          {% endif %}
+      {% else %}
+        {% if (region_loop == "BOUT_FOR_RAJA") %}
+	      for (int {{jz_var}} = 0; {{jz_var}} < mesh_nz; ++{{jz_var}}){
+        {% else %}
+	      for (int {{jz_var}} = 0; {{jz_var}} < localmesh->LocalNz; ++{{jz_var}}){
+        {% endif %}
+          {% if (region_loop == "BOUT_FOR_RAJA") %}
+            {{out.mixed_index_acc}} = {{lhs.mixed_index_acc}} {{operator}} {{rhs.mixed_index_acc}};
+          {% else %}
+            {{out.mixed_index}} = {{lhs.mixed_index}} {{operator}} {{rhs.mixed_index}};
+          {% endif %}
+      {% endif %}
 	}
-	}
+	}{% if (region_loop == "BOUT_FOR_RAJA") %};{% endif %}
   {% elif out == "FieldPerp" and (lhs == "Field2D" or lhs == "Field3D" or rhs == "Field2D" or rhs == "Field3D")%}
     Mesh *localmesh = {{lhs.name if lhs.field_type != "BoutReal" else rhs.name}}.getMesh();
 
     {{region_loop}}({{index_var}}, {{out.name}}.getRegion({{region_name}})) {
-            int yind = {{lhs.name if lhs == "FieldPerp" else rhs.name}}.getIndex();
-            const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
+            {% if (region_loop == "BOUT_FOR_RAJA") %}
+              int yind = {{lhs.name if lhs == "FieldPerp" else rhs.name}}_acc.getIndex();
+            {% else %}
+              int yind = {{lhs.name if lhs == "FieldPerp" else rhs.name}}.getIndex();
+            {% endif %}
+            {% if (region_loop == "BOUT_FOR_RAJA") %}
+              ; // DONE2
+              const auto {{mixed_base_ind}} = localmesh->flatIndPerpto3D({{index_var}}, result_acc.nz, yind);
+            {% else %}
+              const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
+            {% endif %}
             {% if lhs != "FieldPerp" %}
-	    {{out.index}} = {{lhs.base_index}} {{operator}} {{rhs.index}};
+              {% if (region_loop == "BOUT_FOR_RAJA") %}
+                {{out.index_acc}} = {{lhs.base_index_acc}} {{operator}} {{rhs.index_acc}};
+              {% else %}
+                {{out.index}} = {{lhs.base_index}} {{operator}} {{rhs.index}};
+              {% endif %}
             {% else %}
-	    {{out.index}} = {{lhs.index}} {{operator}} {{rhs.base_index}};
+              {% if (region_loop == "BOUT_FOR_RAJA") %}
+                {{out.index_acc}} = {{lhs.index_acc}} {{operator}} {{rhs.base_index_acc}};
+              {% else %}
+                {{out.index}} = {{lhs.index}} {{operator}} {{rhs.base_index}};
+              {% endif %}
             {% endif %}
-	}
+	}{% if (region_loop == "BOUT_FOR_RAJA") %};{% endif %}
   {% elif (operator == "/") and (rhs == "BoutReal") %}
       const auto tmp = 1.0 / {{rhs.index}};
       {{region_loop}}({{index_var}}, {{out.name}}.getValidRegionWithDefault({{region_name}})) {
-         {{out.index}} = {{lhs.index}} * tmp;
-      }
+        {% if (region_loop == "BOUT_FOR_RAJA") %}
+          {{out.index_acc}} = {{lhs.index_acc}} * tmp;
+        {% else %}
+          {{out.index}} = {{lhs.index}} * tmp;
+        {% endif %}
+      }{% if (region_loop == "BOUT_FOR_RAJA") %};{% endif %}
   {% else %}
     {{region_loop}}({{index_var}}, {{out.name}}.getValidRegionWithDefault({{region_name}})) {
-	    {{out.index}} = {{lhs.index}} {{operator}} {{rhs.index}};
-	}
+    {% if (region_loop == "BOUT_FOR_RAJA") %}
+      {{out.index_acc}} = {{lhs.index_acc}} {{operator}} {{rhs.index_acc}};
+    {% else %}
+        {{out.index}} = {{lhs.index}} {{operator}} {{rhs.index}};
+    {% endif %}
+	}{% if (region_loop == "BOUT_FOR_RAJA") %};{% endif %}
   {% endif %}
 
   checkData({{out.name}});
@@ -84,49 +157,102 @@
     checkData(*this);
     checkData({{rhs.name}});
 
+    {% if (region_loop == "BOUT_FOR_RAJA") %}
+      {% if lhs.field_type == "FieldPerp" %}
+        auto this_acc = FieldPerpAccessor{(*this)};
+      {% else %}
+        auto this_acc = FieldAccessor(*this);
+      {% endif %}
+      {% if rhs.field_type == "FieldPerp" %}
+        auto {{rhs.name}}_acc = FieldPerpAccessor{ {{rhs.name}} };
+      {% elif rhs.field_type == "BoutReal" %}
+      {% else %}
+        auto {{rhs.name}}_acc = FieldAccessor({{rhs.name}});
+      {% endif %}
+    {% endif %}
+
     {% if lhs == rhs == "Field3D" %}
       regionID = fieldmesh->getCommonRegion(regionID, {{rhs.name}}.regionID);
     {% endif %}
 
-
   {% if (lhs == "Field3D") and (rhs =="Field2D") %}
+    {% if (region_loop == "BOUT_FOR_RAJA") %}
+    int mesh_nz = fieldmesh->LocalNz;
+    {% endif %}
     {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) {
-	const auto {{mixed_base_ind}} = fieldmesh->ind2Dto3D({{index_var}});
-	{% if (operator == "/") and (rhs == "Field2D") %}
-           const auto tmp = 1.0 / {{rhs.mixed_index}};
-	   for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
-		   (*this)[{{mixed_base_ind}} + {{jz_var}}] *= tmp;
+      {% if (region_loop == "BOUT_FOR_RAJA") %}
+        const auto {{mixed_base_ind}} = {{index_var}} * mesh_nz;
+      {% else %}
+        const auto {{mixed_base_ind}} = fieldmesh->ind2Dto3D({{index_var}});
+      {% endif %}
+      {% if (operator == "/") and (rhs == "Field2D") %}
+        {% if (region_loop == "BOUT_FOR_RAJA") %}
+          const auto tmp = 1.0 / {{rhs.mixed_index_acc}};
+          for (int {{jz_var}} = 0; {{jz_var}} < mesh_nz; ++{{jz_var}}){
+            this_acc[{{mixed_base_ind}} + {{jz_var}}] *= tmp;
         {% else %}
-           for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
-	           (*this)[{{mixed_base_ind}} + {{jz_var}}] {{operator}}= {{rhs.index}};
+          const auto tmp = 1.0 / {{rhs.mixed_index}};
+          for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
+            (*this)[{{mixed_base_ind}} + {{jz_var}}] *= tmp;
         {% endif %}
+      {% else %}
+        {% if (region_loop == "BOUT_FOR_RAJA") %}
+          for (int {{jz_var}} = 0; {{jz_var}} < mesh_nz; ++{{jz_var}}){
+            this_acc[{{mixed_base_ind}} + {{jz_var}}] {{operator}}= {{rhs.index_acc}};
+        {% else %}
+          for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
+            (*this)[{{mixed_base_ind}} + {{jz_var}}] {{operator}}= {{rhs.index}};
+        {% endif %}
+      {% endif %}
 	}
-	}
+  }{% if (region_loop == "BOUT_FOR_RAJA") %};{% endif %}
   {% elif lhs == "FieldPerp" and (rhs == "Field3D" or rhs == "Field2D")%}
     Mesh *localmesh = this->getMesh();
+    {% if (region_loop == "BOUT_FOR_RAJA") %}
+    int yind = this->getIndex();
+  {% endif %}
 
     {{region_loop}}({{index_var}}, this->getRegion({{region_name}})) {
-            int yind = this->getIndex();
-            const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
-            (*this)[{{index_var}}] {{operator}}= {{rhs.base_index}};
-	}
+            {% if (region_loop == "BOUT_FOR_RAJA") %}
+              const auto {{mixed_base_ind}} = localmesh->flatIndPerpto3D({{index_var}}, yind);
+              this_acc[{{index_var}}] {{operator}}= {{rhs.base_index_acc}};
+            {% else %}
+              int yind = this->getIndex();
+              const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
+              (*this)[{{index_var}}] {{operator}}= {{rhs.base_index}};
+            {% endif %}
+	}{% if (region_loop == "BOUT_FOR_RAJA") %};{% endif %}
   {% elif rhs == "FieldPerp" and (lhs == "Field3D" or lhs == "Field2D")%}
     Mesh *localmesh = this->getMesh();
 
     {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) {
-            int yind = {{rhs.name}}.getIndex();
-            const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
-            (*this)[{{base_ind_var}}] {{operator}}= {{rhs.index}};
-	}
+            {% if (region_loop == "BOUT_FOR_RAJA") %}
+              int yind = {{rhs.name}}.getIndex();
+              const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
+              this_acc[{{base_ind_var}}] {{operator}}= {{rhs.index}};
+            {% else %}
+              int yind = {{rhs.name}}.getIndex();
+              const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
+              (*this)[{{base_ind_var}}] {{operator}}= {{rhs.index}};
+            {% endif %}
+	}{% if (region_loop == "BOUT_FOR_RAJA") %};{% endif %}
   {% elif (operator == "/") and (lhs == "Field3D" or lhs == "Field2D") and (rhs =="BoutReal") %}
     const auto tmp = 1.0 / {{rhs.index}};
     {{region_loop}}({{index_var}}, this->getRegion({{region_name}})) {
+      {% if (region_loop == "BOUT_FOR_RAJA") %}
+        this_acc[{{index_var}}] *= tmp;
+      {% else %}
         (*this)[{{index_var}}] *= tmp;
-    }
+      {% endif %}
+    }{% if (region_loop == "BOUT_FOR_RAJA") %};{% endif %}
   {% else %}
     {{region_loop}}({{index_var}}, this->getRegion({{region_name}})) {
-      (*this)[{{index_var}}] {{operator}}= {{rhs.index}};
-    }
+      {% if (region_loop == "BOUT_FOR_RAJA") %}
+        this_acc[{{index_var}}] {{operator}}= {{rhs.index_acc}};
+      {% else %}
+        (*this)[{{index_var}}] {{operator}}= {{rhs.index}};
+      {% endif %}
+    }{% if (region_loop == "BOUT_FOR_RAJA") %};{% endif %}
   {% endif %}
 
     checkData(*this);
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 29631ff7aa..bf06a8ea5c 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -132,6 +132,17 @@ def index(self):
         else:
             return "{self.name}[{self.index_var}]".format(self=self)
 
+    @property
+    def index_acc(self):
+        """Returns "_acc[{index_var}]" for an accessor-based index, except if
+        field_type is BoutReal, in which case just returns ""
+
+        """
+        if self.field_type == "BoutReal":
+            return "{self.name}".format(self=self)
+        else:
+            return "{self.name}_acc[{self.index_var}]".format(self=self)
+
     @property
     def mixed_index(self):
         """Returns "[{index_var} + {jz_var}]" if field_type is Field3D,
@@ -147,6 +158,21 @@ def mixed_index(self):
         else:  # Field2D
             return "{self.name}[{self.index_var}]".format(self=self)
 
+    @property
+    def mixed_index_acc(self):
+        """Returns "_acc[{index_var} + {jz_var}]" for an accessor if field_type
+        is Field3D, self.index if Field2D or just returns "" for BoutReal
+
+        """
+        if self.field_type == "BoutReal":
+            return "{self.name}_acc".format(self=self)
+        elif self.field_type == "Field3D":
+            return "{self.name}_acc[{self.mixed_base_ind_var} + {self.jz_var}]".format(
+                self=self
+            )
+        else:  # Field2D
+            return "{self.name}_acc[{self.index_var}]".format(self=self)
+
     @property
     def base_index(self):
         """Returns "[{mixed_base_ind_var}]" if field_type is Field3D, Field2D or FieldPerp
@@ -158,6 +184,18 @@ def base_index(self):
         else:
             return "{self.name}[{self.mixed_base_ind_var}]".format(self=self)
 
+    @property
+    def base_index_acc(self):
+        """Returns "_acc[{mixed_base_ind_var}]" for an accessor if field_type is
+        Field3D, Field2D or FieldPerp or just returns "" for BoutReal
+
+        """
+        if self.field_type == "BoutReal":
+            return "{self.name}".format(self=self)
+        else:
+            return "{self.name}_acc[{self.mixed_base_ind_var}]".format(self=self)
+
+
     def __eq__(self, other):
         try:
             return self.field_type == other.field_type
@@ -198,11 +236,11 @@ def returnType(f1, f2):
     )
     # By default use OpenMP enabled loops but allow to disable
     parser.add_argument(
-        "--no-openmp",
-        action="store_false",
-        default=False,
-        dest="noOpenMP",
-        help="Don't use OpenMP compatible loops",
+        "--loop-exec",
+        default="openmp",
+        dest="loop_exec",
+        choices=["serial", "openmp", "raja"],
+        help="Choose the loop execution method. Default is OpenMP",
     )
 
     args = parser.parse_args()
@@ -213,10 +251,16 @@ def returnType(f1, f2):
     mixed_base_ind_var = "base_ind"
     region_name = '"RGN_ALL"'
 
-    if args.noOpenMP:
+    if args.loop_exec == "openmp":
+        region_loop = "BOUT_FOR"
+    elif args.loop_exec == "raja":
+        region_loop = "BOUT_FOR_RAJA"
+        header += "#include <bout/rajalib.hxx>\n"
+        header += "#include <bout/field_accessor.hxx>\n"
+    elif args.loop_exec == "serial":
         region_loop = "BOUT_FOR_SERIAL"
     else:
-        region_loop = "BOUT_FOR"
+        raise ValueError("Unknown loop execution method")
 
     # Declare what fields we currently support:
     # Field perp is currently missing
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 34c524d1e7..8123720144 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -23,6 +23,8 @@
 #include "parallel/fci.hxx"
 #include "parallel/shiftedmetricinterp.hxx"
 
+#include "bout/coordinates_accessor.hxx"
+
 // use anonymous namespace so this utility function is not available outside this file
 namespace {
 template <typename T, typename... Ts>
@@ -1203,10 +1205,11 @@ int Coordinates::geometry(bool recalculate_staggered,
     localmesh->recalculateStaggeredCoordinates();
   }
 
-  // Invalidate and recalculate cached variables
+  // Invalidate and recalculate cached variables and any accessor
   zlength_cache.reset();
   Grad2_par2_DDY_invSgCache.clear();
   invSgCache.reset();
+  CoordinatesAccessor::clear(this);
 
   return 0;
 }
diff --git a/src/mesh/coordinates_accessor.cxx b/src/mesh/coordinates_accessor.cxx
index aff546c2b0..196234d999 100644
--- a/src/mesh/coordinates_accessor.cxx
+++ b/src/mesh/coordinates_accessor.cxx
@@ -40,8 +40,9 @@ CoordinatesAccessor::CoordinatesAccessor(const Coordinates* coords) {
 
   // Copy data from Coordinates variable into data array
   // Uses the symbol to look up the corresponding Offset
-#define COPY_STRIPE1(symbol) \
-  data[stripe_size * ind.ind + static_cast<int>(Offset::symbol)] = coords->symbol[ind];
+#define COPY_STRIPE1(symbol)        \
+  if (coords->symbol.isAllocated()) \
+    data[stripe_size * ind.ind + static_cast<int>(Offset::symbol)] = coords->symbol[ind];
 
   // Implement copy for each argument
 #define COPY_STRIPE(...) \
@@ -54,10 +55,15 @@ CoordinatesAccessor::CoordinatesAccessor(const Coordinates* coords) {
     COPY_STRIPE(d1_dx, d1_dy, d1_dz);
     COPY_STRIPE(J);
 
-    data[stripe_size * ind.ind + static_cast<int>(Offset::B)] = coords->Bxy[ind];
-    data[stripe_size * ind.ind + static_cast<int>(Offset::Byup)] = coords->Bxy.yup()[ind];
-    data[stripe_size * ind.ind + static_cast<int>(Offset::Bydown)] =
-        coords->Bxy.ydown()[ind];
+    if (coords->Bxy.isAllocated()) {
+      data[stripe_size * ind.ind + static_cast<int>(Offset::B)] = coords->Bxy[ind];
+      if (coords->Bxy.yup().isAllocated())
+        data[stripe_size * ind.ind + static_cast<int>(Offset::Byup)] =
+            coords->Bxy.yup()[ind];
+      if (coords->Bxy.ydown().isAllocated())
+        data[stripe_size * ind.ind + static_cast<int>(Offset::Bydown)] =
+            coords->Bxy.ydown()[ind];
+    }
 
     COPY_STRIPE(G1, G3);
     COPY_STRIPE(g11, g12, g13, g22, g23, g33);

From 3fc19142c14c3e976be0c2e0f3f304c2d292cf2e Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 14 Apr 2025 13:16:33 -0700
Subject: [PATCH 0160/1827] Switch to sundials::Context

---
 include/bout/sundials_backports.hxx | 6 +++---
 src/solver/impls/arkode/arkode.hxx  | 4 ++--
 src/solver/nvector.hxx              | 9 ++++-----
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx
index c407289fac..3fcb87f6e2 100644
--- a/include/bout/sundials_backports.hxx
+++ b/include/bout/sundials_backports.hxx
@@ -77,13 +77,13 @@ inline sundials::Context createSUNContext([[maybe_unused]] MPI_Comm& comm) {
 #endif
 }
 
-template <typename Func, typename... Args>
-inline decltype(auto) callWithSUNContext(Func f, [[maybe_unused]] const SUNContext ctx,
+template <typename Func, typename Ctx, typename... Args>
+inline decltype(auto) callWithSUNContext(Func f, [[maybe_unused]] Ctx&& ctx,
                                          Args&&... args) {
 #if SUNDIALS_VERSION_LESS_THAN(6, 0, 0)
   return f(std::forward<Args>(args)...);
 #else
-  return f(std::forward<Args>(args)..., ctx);
+  return f(std::forward<Args>(args)..., std::forward<Ctx>(ctx));
 #endif
 }
 
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 5524b1d5d1..7c95a6ce46 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -201,12 +201,12 @@ private:
                              std::vector<BoutReal>& f2dtols,
                              std::vector<BoutReal>& f3dtols, bool bndry);
 
-  N_Vector nvector_from_state(const SUNContext ctx) {
+  N_Vector nvector_from_state(const sundials::Context& ctx) {
     std::vector<N_Vector> subvectors;
     subvectors.reserve(f2d.size() + f3d.size());
     const auto inserter = std::back_inserter(subvectors);
 
-    const auto var_str_to_nvector = [ctx](auto &var_str) {
+    const auto var_str_to_nvector = [&ctx](auto &var_str) {
       return BoutNVector::create(ctx, var_str.var, var_str.evolve_bndry);
     };
     std::transform(f2d.begin(), f2d.end(), inserter, var_str_to_nvector);
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 69d5018739..de4dd8d410 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -94,10 +94,10 @@ private:
 public:
   BoutNVector() = delete; // Enforce static access only
 
-  template <typename T, typename = bout::utils::EnableIfField<T>>
-  static N_Vector create(const SUNContext ctx, T* const field, const bool evolve_bndry,
+  template <typename T, typename Ctx, typename = bout::utils::EnableIfField<T>>
+  static N_Vector create(Ctx&& ctx, T* const field, const bool evolve_bndry,
                          const bool own = false) {
-    N_Vector v = callWithSUNContext(N_VNewEmpty, ctx);
+    N_Vector v = callWithSUNContext(N_VNewEmpty, std::forward<Ctx>(ctx));
     if (v == nullptr) {
       throw BoutException("N_VNewEmpty failed\n");
     }
@@ -113,7 +113,6 @@ public:
       T* field_clone = new T(content.field->getMesh(), content.field->getLocation(), content.field->getDirections());
       field_clone->allocate();
       field_clone->copyBoundary(*content.field);
-      (*field_clone) = 42;
       return create(x->sunctx, field_clone, content.evolve_bndry, true);
     };
 
@@ -181,7 +180,7 @@ public:
   }
 
   template <typename V>
-  static N_Vector create(const SUNContext ctx, V& subvectors) {
+  static N_Vector create(const sundials::Context& ctx, V& subvectors) {
     return callWithSUNContext(N_VNew_ManyVector, ctx, std::size(subvectors),
                               std::data(subvectors));
   }

From d38a8f1af24cbe57a40fb7a889cbb257e81b2896 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 14 Apr 2025 20:22:11 +0000
Subject: [PATCH 0161/1827] Bump ZedThree/clang-tidy-review from 0.20.1 to
 0.21.0

Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.20.1 to 0.21.0.
- [Release notes](https://github.com/zedthree/clang-tidy-review/releases)
- [Changelog](https://github.com/ZedThree/clang-tidy-review/blob/master/CHANGELOG.md)
- [Commits](https://github.com/zedthree/clang-tidy-review/compare/v0.20.1...v0.21.0)

---
updated-dependencies:
- dependency-name: ZedThree/clang-tidy-review
  dependency-version: 0.21.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/clang-tidy-review.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index b2f9bd7573..9746075b1a 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -22,7 +22,7 @@ jobs:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.20.1
+        uses: ZedThree/clang-tidy-review@v0.21.0
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.20.1
+        uses: ZedThree/clang-tidy-review/upload@v0.21.0

From 7253298aad03d70ca50ce3d439fad8c79b191ce8 Mon Sep 17 00:00:00 2001
From: Tom Body <116750897+tbody-cfs@users.noreply.github.com>
Date: Wed, 16 Apr 2025 20:27:18 -0400
Subject: [PATCH 0162/1827] Update CMakeLists.txt

Address #2945
---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 60d34e1ad7..9dc804d50f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -51,7 +51,7 @@ message(STATUS "Configuring BOUT++ version ${BOUT_FULL_VERSION}")
 project(BOUT++
   DESCRIPTION "Fluid PDE solver framework"
   VERSION ${BOUT_CMAKE_ACCEPTABLE_VERSION}
-  LANGUAGES CXX)
+  LANGUAGES C CXX)
 
 include(CMakeDependentOption)
 

From 3c3aca61377e8c7576c912a5bb9597c5768103d0 Mon Sep 17 00:00:00 2001
From: Tom Body <tbody@cfs.energy>
Date: Fri, 18 Apr 2025 16:18:09 +0000
Subject: [PATCH 0163/1827] Move enable C to NetCDF

---
 cmake/FindnetCDF.cmake          | 1 +
 cmake/SetupBOUTThirdParty.cmake | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/FindnetCDF.cmake b/cmake/FindnetCDF.cmake
index 393c57549b..361095954e 100644
--- a/cmake/FindnetCDF.cmake
+++ b/cmake/FindnetCDF.cmake
@@ -32,6 +32,7 @@ if (NOT netCDF_ROOT AND EXISTS "${BOUT_USE_NETCDF}")
   set(netCDF_ROOT "${BOUT_USE_NETCDF}")
 endif()
 
+enable_language(C)
 find_package(netCDF QUIET CONFIG)
 
 if (netCDF_FOUND)
diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 43067ad9e0..65be28334b 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -254,7 +254,6 @@ if (BOUT_USE_SUNDIALS)
     FetchContent_MakeAvailable(sundials)
     message(STATUS "SUNDIALS done configuring")
   else()
-    enable_language(C)
     find_package(SUNDIALS REQUIRED)
     if (SUNDIALS_VERSION VERSION_LESS 4.0.0)
       message(FATAL_ERROR "SUNDIALS_VERSION 4.0.0 or newer is required. Found version ${SUNDIALS_VERSION}.")

From 2c9b3e2432a4e35f74c7aec02ebc218577118e71 Mon Sep 17 00:00:00 2001
From: Tom Body <tbody@cfs.energy>
Date: Fri, 18 Apr 2025 17:36:08 +0000
Subject: [PATCH 0164/1827] Remove top-level C

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9dc804d50f..60d34e1ad7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -51,7 +51,7 @@ message(STATUS "Configuring BOUT++ version ${BOUT_FULL_VERSION}")
 project(BOUT++
   DESCRIPTION "Fluid PDE solver framework"
   VERSION ${BOUT_CMAKE_ACCEPTABLE_VERSION}
-  LANGUAGES C CXX)
+  LANGUAGES CXX)
 
 include(CMakeDependentOption)
 

From 36c17409858bf90538a829d49a992f4211f947a0 Mon Sep 17 00:00:00 2001
From: Tom Body <tbody@cfs.energy>
Date: Fri, 18 Apr 2025 18:47:12 +0000
Subject: [PATCH 0165/1827] Add back in C language for SUNDIALS

---
 cmake/SetupBOUTThirdParty.cmake | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 65be28334b..eefe513a3d 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -233,6 +233,7 @@ option(BOUT_DOWNLOAD_SUNDIALS "Download and build SUNDIALS" OFF)
 cmake_dependent_option(BOUT_USE_SUNDIALS "Enable support for SUNDIALS time solvers" OFF
   "NOT BOUT_DOWNLOAD_SUNDIALS" ON)
 if (BOUT_USE_SUNDIALS)
+  enable_language(C)
   if (BOUT_DOWNLOAD_SUNDIALS)
     message(STATUS "Downloading and configuring SUNDIALS")
     include(FetchContent)

From 1552269fcf65b722f5dc8175d93950ff8fa19028 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 19 May 2025 19:43:02 +0000
Subject: [PATCH 0166/1827] Bump externalpackages/googletest from `2b6b042` to
 `bac6a8f`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `2b6b042` to `bac6a8f`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/2b6b042a77446ff322cd7522ca068d9f2a21c1d1...bac6a8fd8a729eef0d1b2d1a4625f4de62c60220)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: bac6a8fd8a729eef0d1b2d1a4625f4de62c60220
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 2b6b042a77..bac6a8fd8a 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 2b6b042a77446ff322cd7522ca068d9f2a21c1d1
+Subproject commit bac6a8fd8a729eef0d1b2d1a4625f4de62c60220

From d7db014335200cf49ddc78dac3493e282450b2d7 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 19 May 2025 14:08:12 -0700
Subject: [PATCH 0167/1827] Use move assignment rather than pointer swapping

---
 .vscode/settings.json              | 78 ------------------------------
 src/field/field3d.cxx              |  2 +-
 src/solver/impls/arkode/arkode.hxx |  4 +-
 src/solver/nvector.hxx             | 26 +++++-----
 4 files changed, 17 insertions(+), 93 deletions(-)
 delete mode 100644 .vscode/settings.json

diff --git a/.vscode/settings.json b/.vscode/settings.json
deleted file mode 100644
index 7dce96283d..0000000000
--- a/.vscode/settings.json
+++ /dev/null
@@ -1,78 +0,0 @@
-{
-  "files.associations": {
-    "array": "cpp",
-    "limits": "cpp",
-    "complex": "cpp",
-    "cwchar": "cpp",
-    "list": "cpp",
-    "vector": "cpp",
-    "exception": "cpp",
-    "fstream": "cpp",
-    "functional": "cpp",
-    "initializer_list": "cpp",
-    "iosfwd": "cpp",
-    "istream": "cpp",
-    "new": "cpp",
-    "ostream": "cpp",
-    "sstream": "cpp",
-    "stdexcept": "cpp",
-    "streambuf": "cpp",
-    "tuple": "cpp",
-    "type_traits": "cpp",
-    "any": "cpp",
-    "atomic": "cpp",
-    "bit": "cpp",
-    "*.tcc": "cpp",
-    "bitset": "cpp",
-    "cctype": "cpp",
-    "charconv": "cpp",
-    "chrono": "cpp",
-    "clocale": "cpp",
-    "cmath": "cpp",
-    "codecvt": "cpp",
-    "compare": "cpp",
-    "concepts": "cpp",
-    "condition_variable": "cpp",
-    "csignal": "cpp",
-    "cstdarg": "cpp",
-    "cstddef": "cpp",
-    "cstdint": "cpp",
-    "cstdio": "cpp",
-    "cstdlib": "cpp",
-    "cstring": "cpp",
-    "ctime": "cpp",
-    "cwctype": "cpp",
-    "deque": "cpp",
-    "forward_list": "cpp",
-    "map": "cpp",
-    "set": "cpp",
-    "string": "cpp",
-    "unordered_map": "cpp",
-    "unordered_set": "cpp",
-    "algorithm": "cpp",
-    "iterator": "cpp",
-    "memory": "cpp",
-    "memory_resource": "cpp",
-    "numeric": "cpp",
-    "optional": "cpp",
-    "random": "cpp",
-    "ratio": "cpp",
-    "string_view": "cpp",
-    "system_error": "cpp",
-    "utility": "cpp",
-    "format": "cpp",
-    "iomanip": "cpp",
-    "iostream": "cpp",
-    "mutex": "cpp",
-    "numbers": "cpp",
-    "semaphore": "cpp",
-    "span": "cpp",
-    "stop_token": "cpp",
-    "thread": "cpp",
-    "cfenv": "cpp",
-    "cinttypes": "cpp",
-    "typeindex": "cpp",
-    "typeinfo": "cpp",
-    "variant": "cpp"
-  }
-}
\ No newline at end of file
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index af29c98425..0d2bc0694e 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -106,7 +106,7 @@ Field3D::Field3D(Array<BoutReal> data_in, Mesh* localmesh, CELL_LOC datalocation
   ASSERT1(data.size() == nx * ny * nz);
 }
 
-Field3D::~Field3D() {  } // TODO: fix
+Field3D::~Field3D() { delete deriv; }
 
 Field3D& Field3D::allocate() {
   if (data.empty()) {
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 7c95a6ce46..1a422b6a13 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -207,7 +207,7 @@ private:
     const auto inserter = std::back_inserter(subvectors);
 
     const auto var_str_to_nvector = [&ctx](auto &var_str) {
-      return BoutNVector::create(ctx, var_str.var, var_str.evolve_bndry);
+      return BoutNVector::create(ctx, *var_str.var, var_str.evolve_bndry);
     };
     std::transform(f2d.begin(), f2d.end(), inserter, var_str_to_nvector);
     std::transform(f3d.begin(), f3d.end(), inserter, var_str_to_nvector);
@@ -229,7 +229,7 @@ private:
       if (du != nullptr) {
         BoutNVector::swap_qqq(du, *var_str.F_var, i);
       }
-      var_str.var->deriv = var_str.F_var;
+      // var_str.var->deriv = var_str.F_var;
       i++;
     }
   }
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index de4dd8d410..7ed0e60fa1 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -49,22 +49,22 @@ private:
 
   template <typename T>
   struct Content {
-    T* field;
+    T& field;
     const bool own;
     const bool evolve_bndry;
     const sunindextype length;
 
-    Content(T* const field, const bool own, const bool evolve_bndry)
+    Content(T& field, const bool own, const bool evolve_bndry)
         : field(field), own(own), evolve_bndry(evolve_bndry),
           length(all_reduce(getRegion().size())) {}
 
     auto getRegion() const {
-      return field->getRegion(evolve_bndry ? RGN_ALL : RGN_NOBNDRY);
+      return field.getRegion(evolve_bndry ? RGN_ALL : RGN_NOBNDRY);
     }
 
     ~Content() {
       if (own) {
-        delete field;
+        delete &field;
       }
     }
   };
@@ -76,7 +76,7 @@ private:
 
   template <typename T>
   static T& get_field(const N_Vector v) {
-    return *get_content<T>(v).field;
+    return get_content<T>(v).field;
   }
 
   template <typename T, typename R, typename... V>
@@ -95,7 +95,7 @@ public:
   BoutNVector() = delete; // Enforce static access only
 
   template <typename T, typename Ctx, typename = bout::utils::EnableIfField<T>>
-  static N_Vector create(Ctx&& ctx, T* const field, const bool evolve_bndry,
+  static N_Vector create(Ctx&& ctx, T& field, const bool evolve_bndry,
                          const bool own = false) {
     N_Vector v = callWithSUNContext(N_VNewEmpty, std::forward<Ctx>(ctx));
     if (v == nullptr) {
@@ -110,10 +110,10 @@ public:
       const Content<T>& content = get_content<T>(x);
       // TODO: ensure no memory leaks
       // T* field_clone = new T(*content.field);
-      T* field_clone = new T(content.field->getMesh(), content.field->getLocation(), content.field->getDirections());
+      T* field_clone = new T(content.field.getMesh(), content.field.getLocation(), content.field.getDirections());
       field_clone->allocate();
-      field_clone->copyBoundary(*content.field);
-      return create(x->sunctx, field_clone, content.evolve_bndry, true);
+      field_clone->copyBoundary(content.field);
+      return create(x->sunctx, *field_clone, content.evolve_bndry, true);
     };
 
     v->ops->nvdestroy = [](N_Vector x) {
@@ -181,8 +181,10 @@ public:
 
   template <typename V>
   static N_Vector create(const sundials::Context& ctx, V& subvectors) {
-    return callWithSUNContext(N_VNew_ManyVector, ctx, std::size(subvectors),
-                              std::data(subvectors));
+    const auto v =  callWithSUNContext(N_VNew_ManyVector, ctx, std::size(subvectors),
+                                       std::data(subvectors));
+    ((N_VectorContent_ManyVector)v->content)->own_data = true;
+    return v;
   }
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
@@ -192,7 +194,7 @@ public:
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
   static void swap_qqq(const N_Vector v, T& field, std::size_t subvector) {
-    return swap_qqq(N_VGetSubvector_ManyVector(v, subvector), field);
+    return BoutNVector::swap_qqq(N_VGetSubvector_ManyVector(v, subvector), field);
   }
 };
 

From a0eeb2605dfea4e6af2ede38c4e0a1b58b1e5029 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 19 May 2025 14:11:28 -0700
Subject: [PATCH 0168/1827] Fix access to deriv field

---
 include/bout/field2d.hxx | 2 --
 include/bout/field3d.hxx | 2 --
 2 files changed, 4 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 1cedeb949f..92658f1bbf 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -283,8 +283,6 @@ private:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
   int nx{-1}, ny{-1};
 
-public:
-
   /// Time-derivative, can be nullptr
   Field2D* deriv{nullptr};
 };
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index ca6b9951c0..a75e38df36 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -500,11 +500,9 @@ private:
   /// Internal data array. Handles allocation/freeing of memory
   Array<BoutReal> data;
 
-public:
   /// Time derivative (may be nullptr)
   Field3D* deriv{nullptr};
 
-private:
   /// Fields containing values along Y
   std::vector<Field3D> yup_fields{}, ydown_fields{};
 

From 88dfb29e315dab93524f14b1b428817ba9e60ad1 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 19 May 2025 18:35:30 -0700
Subject: [PATCH 0169/1827] Get things working with implicit and IMEX methods

---
 src/solver/impls/arkode/arkode.cxx | 78 +++++++++++-------------------
 src/solver/impls/arkode/arkode.hxx | 36 ++++++++------
 src/solver/nvector.hxx             |  7 +--
 3 files changed, 54 insertions(+), 67 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 3e7f1d7f6d..f1e6faed29 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -612,11 +612,12 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
  * Explicit RHS function du = F_E(t, u)
  **************************************************************************/
 
-void ArkodeSolver::rhs_e(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs_e({:e})", t);
 
   // Load state from udata
-  load_vars(udata);
+  swap_state(u);
+  swap_deriv(du);
 
   // Get the current timestep
   // Note: ARKodeGetCurrentStep updated too late in older versions
@@ -626,21 +627,24 @@ void ArkodeSolver::rhs_e(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   run_convective(t);
 
   // Save derivatives to dudata
-  save_derivs(dudata);
+  swap_state(u);
+  swap_deriv(du);
 }
 
 /**************************************************************************
  *   Implicit RHS function du = F_I(t, u)
  **************************************************************************/
 
-void ArkodeSolver::rhs_i(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+void ArkodeSolver::rhs_i(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs_i({:e})", t);
 
-  load_vars(udata);
+  swap_state(u);
+  swap_deriv(du);
   ARKodeGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_diffusive(t);
-  save_derivs(dudata);
+  swap_state(u);
+  swap_deriv(du);
 }
 
 /**************************************************************************
@@ -649,42 +653,40 @@ void ArkodeSolver::rhs_i(BoutReal t, BoutReal* udata, BoutReal* dudata) {
 void ArkodeSolver::rhs(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs({:e})", t);
 
-  // load_vars(udata);
-  swap_state(u, du);
+  swap_state(u);
+  swap_deriv(du);
   ARKodeGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs(t);
-  // save_derivs(dudata);
-  swap_state(u, du);
+  swap_state(u);
+  swap_deriv(du);
 }
 
 /**************************************************************************
  * Preconditioner function
  **************************************************************************/
 
-void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata,
-                       BoutReal* rvec, BoutReal* zvec) {
+void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u,
+                       N_Vector rvec, N_Vector zvec) {
   TRACE("Running preconditioner: ArkodeSolver::pre({:e})", t);
 
   const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
 
   if (!hasPreconditioner()) {
     // Identity (but should never happen)
-    const auto length = N_VGetLocalLength(uvec);
-    std::copy(rvec, rvec + length, zvec);
+    N_VScale(1, rvec, zvec);
     return;
   }
 
   // Load state from udata (as with res function)
-  load_vars(udata);
-
-  // Load vector to be inverted into F_vars
-  load_derivs(rvec);
+  swap_state(u);
+  swap_deriv(rvec);
 
   runPreconditioner(t, gamma, delta);
 
   // Save the solution from F_vars
-  save_derivs(zvec);
+  // TODO: only need to swap zvec not u
+  swap_deriv(zvec);
 
   pre_Wtime += bout::globals::mpi->MPI_Wtime() - tstart;
   pre_ncalls++;
@@ -694,7 +696,7 @@ void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* uda
  * Jacobian-vector multiplication function
  **************************************************************************/
 
-void ArkodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata) {
+void ArkodeSolver::jac(BoutReal t, N_Vector y, N_Vector v, N_Vector Jv) {
   TRACE("Running Jacobian: ArkodeSolver::jac({:e})", t);
 
   if (not hasJacobian()) {
@@ -702,16 +704,14 @@ void ArkodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* J
   }
 
   // Load state from ydate
-  load_vars(ydata);
-
-  // Load vector to be multiplied into F_vars
-  load_derivs(vdata);
+  swap_state(y);
+  swap_deriv(v);
 
   // Call function
   runJacobian(t);
 
   // Save Jv from vars
-  save_derivs(Jvdata);
+  swap_deriv(Jv);
 }
 
 /**************************************************************************
@@ -721,15 +721,11 @@ void ArkodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* J
 // NOLINTBEGIN(readability-identifier-length)
 namespace {
 int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
-
-  BoutReal* udata = N_VGetArrayPointer(u);
-  BoutReal* dudata = N_VGetArrayPointer(du);
-
   auto* s = static_cast<ArkodeSolver*>(user_data);
 
   // Calculate RHS function
   try {
-    s->rhs_e(t, udata, dudata);
+    s->rhs_e(t, u, du);
   } catch (BoutRhsFail& error) {
     return 1;
   }
@@ -737,15 +733,11 @@ int arkode_rhs_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
 }
 
 int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
-
-  BoutReal* udata = N_VGetArrayPointer(u);
-  BoutReal* dudata = N_VGetArrayPointer(du);
-
   auto* s = static_cast<ArkodeSolver*>(user_data);
 
   // Calculate RHS function
   try {
-    s->rhs_i(t, udata, dudata);
+    s->rhs_i(t, u, du);
   } catch (BoutRhsFail& error) {
     return 1;
   }
@@ -753,10 +745,6 @@ int arkode_rhs_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
 }
 
 int arkode_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
-
-  // BoutReal* udata = N_VGetArrayPointer(u);
-  // BoutReal* dudata = N_VGetArrayPointer(du);
-
   auto* s = static_cast<ArkodeSolver*>(user_data);
 
   // Calculate RHS function
@@ -777,14 +765,10 @@ int arkode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector
 /// Preconditioner function
 int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec,
                BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) {
-  BoutReal* udata = N_VGetArrayPointer(yy);
-  BoutReal* rdata = N_VGetArrayPointer(rvec);
-  BoutReal* zdata = N_VGetArrayPointer(zvec);
-
   auto* s = static_cast<ArkodeSolver*>(user_data);
 
   // Calculate residuals
-  s->pre(t, gamma, delta, udata, rdata, zdata);
+  s->pre(t, gamma, delta, yy, rvec, zvec);
 
   return 0;
 }
@@ -792,13 +776,9 @@ int arkode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Ve
 /// Jacobian-vector multiplication function
 int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy),
                void* user_data, N_Vector UNUSED(tmp)) {
-  BoutReal* ydata = N_VGetArrayPointer(y);   ///< System state
-  BoutReal* vdata = N_VGetArrayPointer(v);   ///< Input vector
-  BoutReal* Jvdata = N_VGetArrayPointer(Jv); ///< Jacobian*vector output
-
   auto* s = static_cast<ArkodeSolver*>(user_data);
 
-  s->jac(t, ydata, vdata, Jvdata);
+  s->jac(t, y, v, Jv);
 
   return 0;
 }
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 1a422b6a13..4766d8a741 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -123,12 +123,12 @@ public:
   BoutReal run(BoutReal tout);
 
   // These functions used internally (but need to be public)
-  void rhs_e(BoutReal t, BoutReal* udata, BoutReal* dudata);
-  void rhs_i(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_e(BoutReal t, N_Vector u, N_Vector du);
+  void rhs_i(BoutReal t, N_Vector u, N_Vector du);
   void rhs(BoutReal t, N_Vector u, N_Vector du);
-  void pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec,
-           BoutReal* zvec);
-  void jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
+  void pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u, N_Vector rvec,
+           N_Vector zvec);
+  void jac(BoutReal t, N_Vector y, N_Vector v, N_Vector Jv);
 
 private:
   BoutReal hcur; //< Current internal timestep
@@ -214,22 +214,28 @@ private:
     return BoutNVector::create(ctx, subvectors);
   }
 
-  void swap_state(const N_Vector u, const N_Vector du = nullptr) {
+  void swap_state(const N_Vector u) {
     std::size_t i = 0;
     for (auto &var_str : f2d) {
-      BoutNVector::swap_qqq(u, *var_str.var, i);
-      if (du != nullptr) {
-        BoutNVector::swap_qqq(du, *var_str.F_var, i);
-      }
+      BoutNVector::swap(u, *var_str.var, i);
       i++;
     }
 
     for (auto &var_str : f3d) {
-      BoutNVector::swap_qqq(u, *var_str.var, i);
-      if (du != nullptr) {
-        BoutNVector::swap_qqq(du, *var_str.F_var, i);
-      }
-      // var_str.var->deriv = var_str.F_var;
+      BoutNVector::swap(u, *var_str.var, i);
+      i++;
+    }
+  }
+
+  void swap_deriv(const N_Vector du) {
+    std::size_t i = 0;
+    for (auto &var_str : f2d) {
+      BoutNVector::swap(du, *var_str.F_var, i);
+      i++;
+    }
+
+    for (auto &var_str : f3d) {
+      BoutNVector::swap(du, *var_str.F_var, i);
       i++;
     }
   }
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 7ed0e60fa1..7f2973b36c 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -188,13 +188,14 @@ public:
   }
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
-  static void swap_qqq(const N_Vector v, T& field) {
+  static void swap(const N_Vector v, T& field) {
+    using ::swap;
     swap(get_field<T>(v), field);
   }
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
-  static void swap_qqq(const N_Vector v, T& field, std::size_t subvector) {
-    return BoutNVector::swap_qqq(N_VGetSubvector_ManyVector(v, subvector), field);
+  static void swap(const N_Vector v, T& field, std::size_t subvector) {
+    return BoutNVector::swap(N_VGetSubvector_ManyVector(v, subvector), field);
   }
 };
 

From fa7f651298781299b616b3f511a18ae976a6c6aa Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Tue, 20 May 2025 14:02:57 -0700
Subject: [PATCH 0170/1827] Fix iterator const

---
 src/solver/impls/arkode/arkode.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 4766d8a741..57d386e821 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -209,8 +209,8 @@ private:
     const auto var_str_to_nvector = [&ctx](auto &var_str) {
       return BoutNVector::create(ctx, *var_str.var, var_str.evolve_bndry);
     };
-    std::transform(f2d.begin(), f2d.end(), inserter, var_str_to_nvector);
-    std::transform(f3d.begin(), f3d.end(), inserter, var_str_to_nvector);
+    std::transform(f2d.cbegin(), f2d.cend(), inserter, var_str_to_nvector);
+    std::transform(f3d.cbegin(), f3d.cend(), inserter, var_str_to_nvector);
     return BoutNVector::create(ctx, subvectors);
   }
 

From b83d2b5286ab5f56e4ca257bf86dc952f84daf57 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Mon, 26 May 2025 18:57:31 -0700
Subject: [PATCH 0171/1827] Working WIP

---
 include/bout/field3d.hxx                      |  5 +-
 include/bout/field_accessor.hxx               |  1 +
 include/bout/fieldops.hxx                     | 67 +++++++++++++++
 include/bout/rajalib.hxx                      | 15 ++++
 include/bout/vector3d.hxx                     |  1 +
 src/field/field3d.cxx                         |  3 +-
 src/field/generated_fieldops.cxx              | 86 +++++++++++++++++--
 src/field/vecops.cxx                          |  1 +
 .../laplace/impls/naulin/naulin_laplace.cxx   |  1 +
 src/sys/derivs.cxx                            |  1 +
 10 files changed, 173 insertions(+), 8 deletions(-)
 create mode 100644 include/bout/fieldops.hxx

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index a75e38df36..6d0624ff73 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -38,6 +38,7 @@ class Field3D;
 #include <vector>
 
 class Mesh;
+class BinaryExpr;
 
 /// Class for 3D X-Y-Z scalar fields
 /*!
@@ -183,6 +184,7 @@ public:
   Field3D(Array<BoutReal> data, Mesh* localmesh, CELL_LOC location = CELL_CENTRE,
           DirectionTypes directions_in = {YDirectionType::Standard,
                                           ZDirectionType::Standard});
+  Field3D(const BinaryExpr& expr);
   /// Destructor
   ~Field3D() override;
 
@@ -424,6 +426,7 @@ public:
   /// return void, as only part initialised
   void operator=(const FieldPerp& rhs);
   Field3D& operator=(BoutReal val);
+  Field3D& operator=(BinaryExpr expr);
   ///@}
 
   /// Addition operators
@@ -518,7 +521,7 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs);
 FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs);
 FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
 
-Field3D operator+(const Field3D& lhs, const Field3D& rhs);
+BinaryExpr operator+(const Field3D& lhs, const Field3D& rhs);
 Field3D operator-(const Field3D& lhs, const Field3D& rhs);
 Field3D operator*(const Field3D& lhs, const Field3D& rhs);
 Field3D operator/(const Field3D& lhs, const Field3D& rhs);
diff --git a/include/bout/field_accessor.hxx b/include/bout/field_accessor.hxx
index 71d0537d9e..a43420d6b3 100644
--- a/include/bout/field_accessor.hxx
+++ b/include/bout/field_accessor.hxx
@@ -96,6 +96,7 @@ struct FieldAccessor {
   ///
   BOUT_HOST_DEVICE inline const BoutReal& operator[](int ind) const { return data[ind]; }
   BOUT_HOST_DEVICE inline BoutReal& operator[](int ind) { return data[ind]; }
+  __device__ inline BoutReal operator()(int i) const { return data[i]; }
 
   BOUT_HOST_DEVICE inline const BoutReal& operator[](const Ind3D& ind) const {
     return data[ind.ind];
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
new file mode 100644
index 0000000000..b80aaec446
--- /dev/null
+++ b/include/bout/fieldops.hxx
@@ -0,0 +1,67 @@
+#pragma once
+#ifndef BOUT_FIELDOPS_HXX
+#define BOUT_FIELDOPS_HXX
+
+#include "bout/bout_types.hxx"
+#include "bout/field_accessor.hxx"
+
+struct Add {
+  __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a + b; }
+};
+struct Sub {
+  __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a - b; }
+};
+struct Mul {
+  __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a * b; }
+};
+struct Div {
+  __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a / b; }
+};
+
+struct BinaryExpr {
+  struct RegionIndices {
+    int* data;
+    int size;
+
+    RegionIndices(int n) : size(n) {
+      cudaMallocManaged(&data, n * sizeof(int));
+      for (int i = 0; i < n; ++i)
+        data[i] = 0;
+    }
+    ~RegionIndices() { cudaFree(data); }
+
+    __device__ inline int operator()(int idx) const { return data[idx]; }
+  };
+
+  using FieldType = FieldAccessor<CELL_CENTRE, Field3D>;
+
+  FieldType lhs;
+  FieldType rhs;
+  RegionIndices indices;
+  Add op;
+
+  Mesh* mesh;
+  CELL_LOC location = CELL_CENTRE;
+  DirectionTypes directions;
+
+  template <typename IndType>
+  BinaryExpr(FieldType lhs, FieldType rhs, Mesh* mesh, CELL_LOC location,
+             DirectionTypes directions, const Region<IndType>& region)
+      : lhs(lhs), rhs(rhs), mesh(mesh), location(location), directions(directions),
+        indices(region.getIndices().size()) {
+    // Copy the region indices into the managed array
+    for (int i = 0; i < indices.size; ++i) {
+      indices.data[i] = region.getIndices()[i].ind;
+    }
+  }
+
+  __host__ __device__ inline int getSize() const { return indices.size; }
+  __device__ inline int regionIdx(int idx) const { return indices(idx); }
+  __device__ inline BoutReal operator()(int idx) const { return op(lhs(idx), rhs(idx)); }
+
+  Mesh* getMesh() const { return mesh; }
+  CELL_LOC getLocation() const { return location; }
+  DirectionTypes getDirections() const { return directions; }
+};
+
+#endif // BOUT_EXPRESSION_HXX
\ No newline at end of file
diff --git a/include/bout/rajalib.hxx b/include/bout/rajalib.hxx
index 92eae68858..b3da46da50 100644
--- a/include/bout/rajalib.hxx
+++ b/include/bout/rajalib.hxx
@@ -14,6 +14,7 @@
  */
 
 #pragma once
+#include "bout/array.hxx"
 #ifndef RAJALIB_H
 #define RAJALIB_H
 
@@ -138,6 +139,20 @@ private:
 #define BOUT_FOR_RAJA(index, region, ...) \
 RajaForAll(region) << [ =, ##__VA_ARGS__ ] RAJA_DEVICE(int index) mutable
 
+// NEW STUFF
+
+template <typename Expr>
+__global__ void evaluator(BoutReal *out, Expr &expr) {
+  int tid = threadIdx.x + blockIdx.x * blockDim.x;
+  int stride = blockDim.x * gridDim.x;
+  for (int i = tid; i < expr.getSize(); i += stride) {
+    out[expr.regionIdx(i)] = expr(expr.regionIdx(i)); // single‐pass fusion
+  }
+}
+
+// END OF NEW STUFF
+
+
 #else // BOUT_HAS_RAJA
 
 #warning RAJA not enabled. BOUT_FOR_RAJA falling back to BOUT_FOR.
diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx
index 0c71dcffa5..ad68dc17ee 100644
--- a/include/bout/vector3d.hxx
+++ b/include/bout/vector3d.hxx
@@ -36,6 +36,7 @@ class Vector3D;
 class Field2D;
 class Vector2D;
 #include "bout/field3d.hxx"
+#include "bout/fieldops.hxx"
 
 /*!
  * Represents a 3D vector, with x,y,z components
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 0d2bc0694e..9ea488d8f1 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -805,7 +805,8 @@ bool operator==(const Field3D& a, const Field3D& b) {
   if (!a.isAllocated() || !b.isAllocated()) {
     return false;
   }
-  return min(abs(a - b)) < 1e-10;
+  Field3D Sub = a - b;
+  return min(Sub) < 1e-10;
 }
 
 std::ostream& operator<<(std::ostream& out, const Field3D& value) {
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 6b778acee3..b1b99caaa9 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -1,11 +1,73 @@
 // This file is autogenerated - see gen_fieldops.py
+#include "bout/rajalib.hxx"
+#include "bout/fieldops.hxx"
+
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
+#include <bout/field_accessor.hxx>
 #include <bout/globals.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 
+template <typename T>
+struct ExprFor {
+  using type = T;
+};
+
+template <>
+struct ExprFor<Field3D> {
+  using type = FieldAccessor<CELL_CENTRE, Field3D>;
+};
+
+template <typename T>
+using ExprFor_t = typename ExprFor<std::decay_t<T>>::type;
+
+//template<typename Op>
+//class ExpressionExpr : public ExprBase {
+//private:
+//  const Expression& lhs;
+//  const Expression& rhs;
+//  Op op;
+//
+//public:
+//  ExpressionExpr(const Expression& lhs, const Expression& rhs, Op op)
+//      : lhs(lhs), rhs(rhs), op(op),
+//        ExprBase(lhs.getMesh(), lhs.getLocation(), lhs.getDirections()) {}
+//
+//  __device__ BoutReal operator()(int idx) const override {
+//    return op(lhs(idx), rhs(idx));
+//  }
+//
+//  __host__ __device__ int getSize() const override {
+//    return lhs.getSize(); // Assume same size
+//  }
+//
+//  __device__ int regionIdx(int idx) const override {
+//    return lhs.regionIdx(idx); // Use lhs indexing
+//  }
+//};
+
+Field3D& Field3D::operator=(BinaryExpr expr) {
+  constexpr int THREADS = 256;
+  int blocks = (size() + THREADS - 1) / THREADS;
+
+  // one kernel launch that writes each element exactly once
+  evaluator<<<blocks, THREADS>>>(&data[0], expr);
+  cudaDeviceSynchronize();
+  return *this;
+}
+//
+Field3D::Field3D(const BinaryExpr& expr) {
+  Array<BoutReal> data{expr.getSize()};
+
+  constexpr int THREADS = 256;
+  int blocks = (expr.getSize() + THREADS - 1) / THREADS;
+  evaluator<<<blocks, THREADS>>>(&data[0], expr);
+  cudaDeviceSynchronize();
+  *this = Field3D{data, expr.getMesh(), expr.getLocation(), expr.getDirections()};
+}
+
 // Provide the C++ wrapper for multiplication of Field3D and Field3D
 Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
@@ -21,6 +83,8 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
   }
 
   checkData(result);
+  std::cout << "operator*\n";
+  getchar();
   return result;
 }
 
@@ -65,6 +129,8 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
   }
 
   checkData(result);
+  std::cout << "operator/\n";
+  getchar();
   return result;
 }
 
@@ -95,7 +161,7 @@ Field3D& Field3D::operator/=(const Field3D& rhs) {
 }
 
 // Provide the C++ wrapper for addition of Field3D and Field3D
-Field3D operator+(const Field3D& lhs, const Field3D& rhs) {
+BinaryExpr operator+(const Field3D& lhs, const Field3D& rhs) {
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(lhs)};
@@ -104,12 +170,18 @@ Field3D operator+(const Field3D& lhs, const Field3D& rhs) {
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
 
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs[index];
-  }
+  std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
+  return BinaryExpr{static_cast<ExprFor_t<Field3D>>(lhs),
+                    static_cast<ExprFor_t<Field3D>>(rhs),
+                    lhs.getMesh(),
+                    lhs.getLocation(),
+                    lhs.getDirections(),
+                    result.getValidRegionWithDefault("RGN_ALL")};
 
-  checkData(result);
-  return result;
+  //constexpr int THREADS = 256;
+  //int blocks = (BE.getSize() + THREADS - 1) / THREADS;
+  //evaluator<<<blocks, THREADS>>>(&result(0, 0, 0), BE);
+  //return result;
 }
 
 // Provide the C++ operator to update Field3D by addition with Field3D
@@ -152,6 +224,8 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] - rhs[index];
   }
 
+  std::cout << "operator-\n";
+  getchar();
   checkData(result);
   return result;
 }
diff --git a/src/field/vecops.cxx b/src/field/vecops.cxx
index 5f34e2af02..9b1105e7aa 100644
--- a/src/field/vecops.cxx
+++ b/src/field/vecops.cxx
@@ -28,6 +28,7 @@
 #include <bout/scorepwrapper.hxx>
 
 #include <bout/derivs.hxx>
+#include <bout/fieldops.hxx>
 #include <bout/globals.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/unused.hxx>
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index e6f68d850d..74ec68dae9 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -142,6 +142,7 @@
 #include <bout/coordinates.hxx>
 #include <bout/derivs.hxx>
 #include <bout/difops.hxx>
+#include <bout/fieldops.hxx>
 #include <bout/globals.hxx>
 #include <bout/mesh.hxx>
 #include <bout/sys/timer.hxx>
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index ee9bcbcc2c..55e2c77a29 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -49,6 +49,7 @@
 
 #include <cmath>
 
+#include <bout/fieldops.hxx>
 #include <bout/output.hxx>
 #include <bout/unused.hxx>
 

From 970870958f390587c1c1dff9ae3ee1493aa74c8a Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Tue, 27 May 2025 17:12:14 -0700
Subject: [PATCH 0172/1827] WIP 2

- Compiles but crashes. I suspect it's because nested operators copy
Field3D on the device (rhs)
---
 include/bout/array.hxx           |  2 +-
 include/bout/field3d.hxx         | 52 +++++++++++++++++++--
 include/bout/fieldops.hxx        | 79 ++++++++++++++++++++++++++-----
 src/field/generated_fieldops.cxx | 80 +++++++++-----------------------
 4 files changed, 140 insertions(+), 73 deletions(-)

diff --git a/include/bout/array.hxx b/include/bout/array.hxx
index 2c42f15aad..b83c29c51d 100644
--- a/include/bout/array.hxx
+++ b/include/bout/array.hxx
@@ -66,7 +66,7 @@ struct ArrayData {
 #if BOUT_HAS_UMPIRE
     auto& rm = umpire::ResourceManager::getInstance();
 #if BOUT_HAS_CUDA
-    auto allocator = rm.getAllocator(umpire::resource::Pinned);
+    auto allocator = rm.getAllocator(umpire::resource::Unified);
 #else
     auto allocator = rm.getAllocator("HOST");
 #endif
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 6d0624ff73..b03730ddfa 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -38,7 +38,10 @@ class Field3D;
 #include <vector>
 
 class Mesh;
-class BinaryExpr;
+
+//template <typename L, typename R>
+//class BinaryExpr;
+#include "bout/fieldops.hxx"
 
 /// Class for 3D X-Y-Z scalar fields
 /*!
@@ -184,7 +187,15 @@ public:
   Field3D(Array<BoutReal> data, Mesh* localmesh, CELL_LOC location = CELL_CENTRE,
           DirectionTypes directions_in = {YDirectionType::Standard,
                                           ZDirectionType::Standard});
-  Field3D(const BinaryExpr& expr);
+  template <typename L, typename R>
+  Field3D(const BinaryExpr<L, R>& expr) {
+    Array<BoutReal> data{expr.getSize()};
+    constexpr int THREADS = 256;
+    int blocks = (expr.getSize() + THREADS - 1) / THREADS;
+    evaluatorExpr<<<blocks, THREADS>>>(&data[0], expr);
+    cudaDeviceSynchronize();
+    *this = Field3D{data, expr.getMesh(), expr.getLocation(), expr.getDirections()};
+  }
   /// Destructor
   ~Field3D() override;
 
@@ -415,6 +426,15 @@ public:
     return &data[(jx * ny + jy) * nz];
   }
 
+  struct View {
+    BoutReal* data;
+    __device__ inline BoutReal operator()(int idx) const { return data[idx]; }
+  };
+  operator View() { return View{&data[0]}; }
+
+  __device__ inline BoutReal operator()(int i) { return View()(i); }
+  __device__ inline BoutReal operator()(int i) const { return View()(i); }
+
   /////////////////////////////////////////////////////////
   // Operators
 
@@ -426,7 +446,15 @@ public:
   /// return void, as only part initialised
   void operator=(const FieldPerp& rhs);
   Field3D& operator=(BoutReal val);
-  Field3D& operator=(BinaryExpr expr);
+  template <typename L, typename R>
+  Field3D& operator=(BinaryExpr<L, R> expr) {
+    constexpr int THREADS = 256;
+    int blocks = (expr.getSize() + THREADS - 1) / THREADS;
+    evaluatorExpr<<<blocks, THREADS>>>(&data[0], expr);
+    cudaDeviceSynchronize();
+    return *this;
+  }
+
   ///@}
 
   /// Addition operators
@@ -521,7 +549,23 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs);
 FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs);
 FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
 
-BinaryExpr operator+(const Field3D& lhs, const Field3D& rhs);
+template <typename L, typename R,
+          typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
+BinaryExpr<L, R> operator+(const L& lhs, const R& rhs) {
+  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
+
+  std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
+  return BinaryExpr{lhs,
+                    rhs,
+                    BinaryExpr<L, R>::Op::ADD,
+                    lhs.getMesh(),
+                    lhs.getLocation(),
+                    lhs.getDirections(),
+                    regionID,
+                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
+                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
+}
+
 Field3D operator-(const Field3D& lhs, const Field3D& rhs);
 Field3D operator*(const Field3D& lhs, const Field3D& rhs);
 Field3D operator/(const Field3D& lhs, const Field3D& rhs);
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index b80aaec446..7cdb339854 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -3,7 +3,14 @@
 #define BOUT_FIELDOPS_HXX
 
 #include "bout/bout_types.hxx"
-#include "bout/field_accessor.hxx"
+
+#include <cuda_runtime.h>
+#include <optional>
+
+class Mesh;
+class Field3D;
+
+#include <type_traits>
 
 struct Add {
   __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a + b; }
@@ -18,7 +25,18 @@ struct Div {
   __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a / b; }
 };
 
+template <typename Expr>
+__global__ static void evaluatorExpr(BoutReal* out, Expr& expr) {
+  int tid = threadIdx.x + blockIdx.x * blockDim.x;
+  int stride = blockDim.x * gridDim.x;
+  for (int i = tid; i < expr.getSize(); i += stride) {
+    out[expr.regionIdx(i)] = expr(expr.regionIdx(i)); // single‐pass fusion
+  }
+}
+
+template <typename L, typename R>
 struct BinaryExpr {
+  enum class Op { ADD, SUB, MUL, DIV };
   struct RegionIndices {
     int* data;
     int size;
@@ -33,22 +51,22 @@ struct BinaryExpr {
     __device__ inline int operator()(int idx) const { return data[idx]; }
   };
 
-  using FieldType = FieldAccessor<CELL_CENTRE, Field3D>;
-
-  FieldType lhs;
-  FieldType rhs;
+  L lhs;
+  R rhs;
   RegionIndices indices;
-  Add op;
+  Op op;
 
   Mesh* mesh;
   CELL_LOC location = CELL_CENTRE;
   DirectionTypes directions;
+  std::optional<size_t> regionID;
 
   template <typename IndType>
-  BinaryExpr(FieldType lhs, FieldType rhs, Mesh* mesh, CELL_LOC location,
-             DirectionTypes directions, const Region<IndType>& region)
-      : lhs(lhs), rhs(rhs), mesh(mesh), location(location), directions(directions),
-        indices(region.getIndices().size()) {
+  BinaryExpr(L lhs, R rhs, Op op, Mesh* mesh, CELL_LOC location,
+             DirectionTypes directions, std::optional<size_t> regionID,
+             const Region<IndType>& region)
+      : lhs(lhs), rhs(rhs), op(op), mesh(mesh), location(location),
+        directions(directions), regionID(regionID), indices(region.getIndices().size()) {
     // Copy the region indices into the managed array
     for (int i = 0; i < indices.size; ++i) {
       indices.data[i] = region.getIndices()[i].ind;
@@ -57,11 +75,50 @@ struct BinaryExpr {
 
   __host__ __device__ inline int getSize() const { return indices.size; }
   __device__ inline int regionIdx(int idx) const { return indices(idx); }
-  __device__ inline BoutReal operator()(int idx) const { return op(lhs(idx), rhs(idx)); }
+  __device__ inline BoutReal operator()(int idx) const {
+    switch (op) {
+    case Op::ADD:
+      return Add{}(lhs(idx), rhs(idx));
+    case Op::SUB:
+      return Sub{}(lhs(idx), rhs(idx));
+    case Op::MUL:
+      return Mul{}(lhs(idx), rhs(idx));
+    case Op::DIV:
+      return Div{}(lhs(idx), rhs(idx));
+    }
+  }
+
+  void evaluate(BoutReal* data) const {}
 
   Mesh* getMesh() const { return mesh; }
   CELL_LOC getLocation() const { return location; }
   DirectionTypes getDirections() const { return directions; }
+  std::optional<size_t> getRegionID() const { return regionID; };
 };
 
+//template <typename T>
+//struct Expr {
+//  using type = T;
+//};
+//
+//template <>
+//struct Expr<Field3D> {
+//  using type = Field3D::View;
+//};
+
+// 1) detect our BinaryExpr<T,U> template
+template <typename>
+struct is_binary_expr : std::false_type {};
+template <typename A, typename B>
+struct is_binary_expr<BinaryExpr<A, B>> : std::true_type {};
+
+// 2) detect “any subclass of Field”
+//    assuming Field is your common base class
+template <typename T>
+constexpr bool is_field_v = std::is_base_of<Field3D, std::decay_t<T>>::value;
+
+// 3) combine into “is one of our expression types”
+template <typename T>
+constexpr bool is_expr_v = is_field_v<T> || is_binary_expr<std::decay_t<T>>::value;
+
 #endif // BOUT_EXPRESSION_HXX
\ No newline at end of file
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index b1b99caaa9..2c414c8dde 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -10,45 +10,9 @@
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 
-template <typename T>
-struct ExprFor {
-  using type = T;
-};
-
-template <>
-struct ExprFor<Field3D> {
-  using type = FieldAccessor<CELL_CENTRE, Field3D>;
-};
-
-template <typename T>
-using ExprFor_t = typename ExprFor<std::decay_t<T>>::type;
-
-//template<typename Op>
-//class ExpressionExpr : public ExprBase {
-//private:
-//  const Expression& lhs;
-//  const Expression& rhs;
-//  Op op;
-//
-//public:
-//  ExpressionExpr(const Expression& lhs, const Expression& rhs, Op op)
-//      : lhs(lhs), rhs(rhs), op(op),
-//        ExprBase(lhs.getMesh(), lhs.getLocation(), lhs.getDirections()) {}
-//
-//  __device__ BoutReal operator()(int idx) const override {
-//    return op(lhs(idx), rhs(idx));
-//  }
-//
-//  __host__ __device__ int getSize() const override {
-//    return lhs.getSize(); // Assume same size
-//  }
-//
-//  __device__ int regionIdx(int idx) const override {
-//    return lhs.regionIdx(idx); // Use lhs indexing
-//  }
-//};
-
-Field3D& Field3D::operator=(BinaryExpr expr) {
+#if 0
+template <typename L, typename R>
+Field3D& Field3D::operator=(BinaryExpr<L, R> expr) {
   constexpr int THREADS = 256;
   int blocks = (size() + THREADS - 1) / THREADS;
 
@@ -57,8 +21,12 @@ Field3D& Field3D::operator=(BinaryExpr expr) {
   cudaDeviceSynchronize();
   return *this;
 }
-//
-Field3D::Field3D(const BinaryExpr& expr) {
+template Field3D&
+    Field3D::operator= <Field3D, Field3D>(BinaryExpr<Field3D, Field3D> expr);
+#endif
+
+#if 0
+Field3D::Field3D(const BinaryExpr<Field3D, Field3D>& expr) {
   Array<BoutReal> data{expr.getSize()};
 
   constexpr int THREADS = 256;
@@ -67,6 +35,7 @@ Field3D::Field3D(const BinaryExpr& expr) {
   cudaDeviceSynchronize();
   *this = Field3D{data, expr.getMesh(), expr.getLocation(), expr.getDirections()};
 }
+#endif
 
 // Provide the C++ wrapper for multiplication of Field3D and Field3D
 Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
@@ -83,8 +52,6 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
   }
 
   checkData(result);
-  std::cout << "operator*\n";
-  getchar();
   return result;
 }
 
@@ -129,8 +96,6 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
   }
 
   checkData(result);
-  std::cout << "operator/\n";
-  getchar();
   return result;
 }
 
@@ -160,29 +125,32 @@ Field3D& Field3D::operator/=(const Field3D& rhs) {
   return *this;
 }
 
+#if 0
 // Provide the C++ wrapper for addition of Field3D and Field3D
-BinaryExpr operator+(const Field3D& lhs, const Field3D& rhs) {
+template <typename L, typename R, typename>
+BinaryExpr<L, R> operator+(const L& lhs, const R& rhs) {
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(lhs)};
   checkData(lhs);
   checkData(rhs);
 
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{static_cast<ExprFor_t<Field3D>>(lhs),
-                    static_cast<ExprFor_t<Field3D>>(rhs),
+  return BinaryExpr{lhs,
+                    rhs,
+                    BinaryExpr<L, R>::Op::ADD,
                     lhs.getMesh(),
                     lhs.getLocation(),
                     lhs.getDirections(),
-                    result.getValidRegionWithDefault("RGN_ALL")};
-
-  //constexpr int THREADS = 256;
-  //int blocks = (BE.getSize() + THREADS - 1) / THREADS;
-  //evaluator<<<blocks, THREADS>>>(&result(0, 0, 0), BE);
-  //return result;
+                    regionID,
+                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
+                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
 }
+template BinaryExpr<Field3D, Field3D> operator+ <Field3D, Field3D>(const Field3D& lhs,
+                                                                   const Field3D& rhs);
+#endif
 
 // Provide the C++ operator to update Field3D by addition with Field3D
 Field3D& Field3D::operator+=(const Field3D& rhs) {
@@ -224,8 +192,6 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] - rhs[index];
   }
 
-  std::cout << "operator-\n";
-  getchar();
   checkData(result);
   return result;
 }

From e20da9d606a4eaee7581ad3d5ae6ac54f6e7a382 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Tue, 27 May 2025 19:24:41 -0700
Subject: [PATCH 0173/1827] Working - WIP 3

- Uses Views to avoid copying uncopyable stuff
---
 include/bout/field3d.hxx  | 17 +++++++++-------
 include/bout/fieldops.hxx | 41 ++++++++++++++++++++++++++-------------
 2 files changed, 37 insertions(+), 21 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index b03730ddfa..ca62885fdf 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -192,7 +192,8 @@ public:
     Array<BoutReal> data{expr.getSize()};
     constexpr int THREADS = 256;
     int blocks = (expr.getSize() + THREADS - 1) / THREADS;
-    evaluatorExpr<<<blocks, THREADS>>>(&data[0], expr);
+    evaluatorExpr<<<blocks, THREADS>>>(
+        &data[0], static_cast<typename BinaryExpr<L, R>::View>(expr));
     cudaDeviceSynchronize();
     *this = Field3D{data, expr.getMesh(), expr.getLocation(), expr.getDirections()};
   }
@@ -427,10 +428,11 @@ public:
   }
 
   struct View {
-    BoutReal* data;
+    const BoutReal* data;
     __device__ inline BoutReal operator()(int idx) const { return data[idx]; }
   };
   operator View() { return View{&data[0]}; }
+  operator View() const { return View{&data[0]}; }
 
   __device__ inline BoutReal operator()(int i) { return View()(i); }
   __device__ inline BoutReal operator()(int i) const { return View()(i); }
@@ -450,7 +452,8 @@ public:
   Field3D& operator=(BinaryExpr<L, R> expr) {
     constexpr int THREADS = 256;
     int blocks = (expr.getSize() + THREADS - 1) / THREADS;
-    evaluatorExpr<<<blocks, THREADS>>>(&data[0], expr);
+    evaluatorExpr<<<blocks, THREADS>>>(
+        &data[0], static_cast<typename BinaryExpr<L, R>::View>(expr));
     cudaDeviceSynchronize();
     return *this;
   }
@@ -551,13 +554,13 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
 
 template <typename L, typename R,
           typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
-BinaryExpr<L, R> operator+(const L& lhs, const R& rhs) {
+BinaryExpr<typename L::View, typename R::View> operator+(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{lhs,
-                    rhs,
-                    BinaryExpr<L, R>::Op::ADD,
+  return BinaryExpr{static_cast<typename L::View>(lhs),
+                    static_cast<typename R::View>(rhs),
+                    BinaryExpr<typename L::View, typename R::View>::Op::ADD,
                     lhs.getMesh(),
                     lhs.getLocation(),
                     lhs.getDirections(),
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 7cdb339854..359177f3fc 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -26,7 +26,7 @@ struct Div {
 };
 
 template <typename Expr>
-__global__ static void evaluatorExpr(BoutReal* out, Expr& expr) {
+__global__ static void evaluatorExpr(BoutReal* out, const Expr& expr) {
   int tid = threadIdx.x + blockIdx.x * blockDim.x;
   int stride = blockDim.x * gridDim.x;
   for (int i = tid; i < expr.getSize(); i += stride) {
@@ -73,20 +73,33 @@ struct BinaryExpr {
     }
   }
 
-  __host__ __device__ inline int getSize() const { return indices.size; }
-  __device__ inline int regionIdx(int idx) const { return indices(idx); }
-  __device__ inline BoutReal operator()(int idx) const {
-    switch (op) {
-    case Op::ADD:
-      return Add{}(lhs(idx), rhs(idx));
-    case Op::SUB:
-      return Sub{}(lhs(idx), rhs(idx));
-    case Op::MUL:
-      return Mul{}(lhs(idx), rhs(idx));
-    case Op::DIV:
-      return Div{}(lhs(idx), rhs(idx));
+  __host__ inline int getSize() const { return indices.size; }
+
+  struct View {
+    L lhs;
+    R rhs;
+    int* indices;
+    int size;
+    Op op;
+
+    __host__ __device__ inline int getSize() const { return size; }
+    __device__ inline int regionIdx(int idx) const { return indices[idx]; }
+    __device__ inline BoutReal operator()(int idx) const {
+      switch (op) {
+      case Op::ADD:
+        return Add{}(lhs(idx), rhs(idx));
+      case Op::SUB:
+        return Sub{}(lhs(idx), rhs(idx));
+      case Op::MUL:
+        return Mul{}(lhs(idx), rhs(idx));
+      case Op::DIV:
+        return Div{}(lhs(idx), rhs(idx));
+      }
     }
-  }
+  };
+
+  operator View() { return View{lhs, rhs, indices.data, indices.size, op}; }
+  operator View() const { return View{lhs, rhs, indices.data, indices.size, op}; }
 
   void evaluate(BoutReal* data) const {}
 

From 096f57637216f9133d69a06b6aa8a8b6bdd82f7b Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Tue, 27 May 2025 23:54:55 -0700
Subject: [PATCH 0174/1827] WIP 3

- operatorors +=, -=, *=, /= are working
---
 include/bout/field3d.hxx         | 105 ++++++++++++---
 include/bout/fieldops.hxx        |   7 +-
 src/field/generated_fieldops.cxx | 214 +------------------------------
 3 files changed, 96 insertions(+), 230 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index ca62885fdf..a299f5bfdc 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -190,11 +190,7 @@ public:
   template <typename L, typename R>
   Field3D(const BinaryExpr<L, R>& expr) {
     Array<BoutReal> data{expr.getSize()};
-    constexpr int THREADS = 256;
-    int blocks = (expr.getSize() + THREADS - 1) / THREADS;
-    evaluatorExpr<<<blocks, THREADS>>>(
-        &data[0], static_cast<typename BinaryExpr<L, R>::View>(expr));
-    cudaDeviceSynchronize();
+    expr.evaluate(&data[0]);
     *this = Field3D{data, expr.getMesh(), expr.getLocation(), expr.getDirections()};
   }
   /// Destructor
@@ -450,11 +446,7 @@ public:
   Field3D& operator=(BoutReal val);
   template <typename L, typename R>
   Field3D& operator=(BinaryExpr<L, R> expr) {
-    constexpr int THREADS = 256;
-    int blocks = (expr.getSize() + THREADS - 1) / THREADS;
-    evaluatorExpr<<<blocks, THREADS>>>(
-        &data[0], static_cast<typename BinaryExpr<L, R>::View>(expr));
-    cudaDeviceSynchronize();
+    expr.evaluate(&data[0]);
     return *this;
   }
 
@@ -462,28 +454,56 @@ public:
 
   /// Addition operators
   ///@{
-  Field3D& operator+=(const Field3D& rhs);
+  //Field3D& operator+=(const Field3D& rhs);
+  template <typename R, typename = std::enable_if_t<is_expr_v<R>>>
+  Field3D& operator+=(const R& rhs) {
+    printf("Running operator+= with CUDA\n");
+    data.ensureUnique();
+    (*this) = (*this) + rhs;
+    return *this;
+  }
   Field3D& operator+=(const Field2D& rhs);
   Field3D& operator+=(BoutReal rhs);
   ///@}
 
   /// Subtraction operators
   ///@{
-  Field3D& operator-=(const Field3D& rhs);
+  //Field3D& operator-=(const Field3D& rhs);
+  template <typename R, typename = std::enable_if_t<is_expr_v<R>>>
+  Field3D& operator-=(const R& rhs) {
+    printf("Running operator-= with CUDA\n");
+    data.ensureUnique();
+    (*this) = (*this) - rhs;
+    return *this;
+  }
   Field3D& operator-=(const Field2D& rhs);
   Field3D& operator-=(BoutReal rhs);
   ///@}
 
   /// Multiplication operators
   ///@{
-  Field3D& operator*=(const Field3D& rhs);
+  //Field3D& operator*=(const Field3D& rhs);
+    template <typename R, typename = std::enable_if_t<is_expr_v<R>>>
+  Field3D& operator*=(const R& rhs) {
+    printf("Running operator*= with CUDA\n");
+    data.ensureUnique();
+    (*this) = (*this) * rhs;
+    return *this;
+  }
   Field3D& operator*=(const Field2D& rhs);
   Field3D& operator*=(BoutReal rhs);
   ///@}
 
   /// Division operators
   ///@{
-  Field3D& operator/=(const Field3D& rhs);
+      template <typename R, typename = std::enable_if_t<is_expr_v<R>>>
+  Field3D& operator/=(const R& rhs) {
+    printf("Running operator/= with CUDA\n");
+    data.ensureUnique();
+    (*this) = (*this) * rhs;
+    return *this;
+  }
+  //Field3D& operator/=(const Field3D& rhs);
   Field3D& operator/=(const Field2D& rhs);
   Field3D& operator/=(BoutReal rhs);
   ///@}
@@ -546,6 +566,10 @@ private:
 
 // Non-member overloaded operators
 
+template<typename T>
+constexpr bool always_false = false;
+
+
 // Binary operators
 FieldPerp operator+(const Field3D& lhs, const FieldPerp& rhs);
 FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs);
@@ -569,9 +593,56 @@ BinaryExpr<typename L::View, typename R::View> operator+(const L& lhs, const R&
                                           : lhs.getMesh()->getRegion("RGN_ALL"))};
 }
 
-Field3D operator-(const Field3D& lhs, const Field3D& rhs);
-Field3D operator*(const Field3D& lhs, const Field3D& rhs);
-Field3D operator/(const Field3D& lhs, const Field3D& rhs);
+template <typename L, typename R,
+          typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
+BinaryExpr<typename L::View, typename R::View> operator-(const L& lhs, const R& rhs) {
+  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
+
+  std::cout << "RUNNING operator- using BinaryExpr with CUDA" << "\n";
+  return BinaryExpr{static_cast<typename L::View>(lhs),
+                    static_cast<typename R::View>(rhs),
+                    BinaryExpr<typename L::View, typename R::View>::Op::SUB,
+                    lhs.getMesh(),
+                    lhs.getLocation(),
+                    lhs.getDirections(),
+                    regionID,
+                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
+                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
+}
+
+template <typename L, typename R,
+          typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
+BinaryExpr<typename L::View, typename R::View> operator*(const L& lhs, const R& rhs) {
+  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
+
+  std::cout << "RUNNING operator* using BinaryExpr with CUDA" << "\n";
+  return BinaryExpr{static_cast<typename L::View>(lhs),
+                    static_cast<typename R::View>(rhs),
+                    BinaryExpr<typename L::View, typename R::View>::Op::MUL,
+                    lhs.getMesh(),
+                    lhs.getLocation(),
+                    lhs.getDirections(),
+                    regionID,
+                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
+                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
+}
+
+template <typename L, typename R,
+          typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
+BinaryExpr<typename L::View, typename R::View> operator/(const L& lhs, const R& rhs) {
+  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
+
+  std::cout << "RUNNING operator/ using BinaryExpr with CUDA" << "\n";
+  return BinaryExpr{static_cast<typename L::View>(lhs),
+                    static_cast<typename R::View>(rhs),
+                    BinaryExpr<typename L::View, typename R::View>::Op::DIV,
+                    lhs.getMesh(),
+                    lhs.getLocation(),
+                    lhs.getDirections(),
+                    regionID,
+                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
+                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
+}
 
 Field3D operator+(const Field3D& lhs, const Field2D& rhs);
 Field3D operator-(const Field3D& lhs, const Field2D& rhs);
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 359177f3fc..2ef7161f6d 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -101,7 +101,12 @@ struct BinaryExpr {
   operator View() { return View{lhs, rhs, indices.data, indices.size, op}; }
   operator View() const { return View{lhs, rhs, indices.data, indices.size, op}; }
 
-  void evaluate(BoutReal* data) const {}
+  void evaluate(BoutReal* data) const {
+    constexpr int THREADS = 256;
+    int blocks = (getSize() + THREADS - 1) / THREADS;
+    evaluatorExpr<<<blocks, THREADS>>>(&data[0], static_cast<View>(*this));
+    cudaDeviceSynchronize();
+  }
 
   Mesh* getMesh() const { return mesh; }
   CELL_LOC getLocation() const { return location; }
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 2c414c8dde..63cbf9b847 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -10,218 +10,6 @@
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 
-#if 0
-template <typename L, typename R>
-Field3D& Field3D::operator=(BinaryExpr<L, R> expr) {
-  constexpr int THREADS = 256;
-  int blocks = (size() + THREADS - 1) / THREADS;
-
-  // one kernel launch that writes each element exactly once
-  evaluator<<<blocks, THREADS>>>(&data[0], expr);
-  cudaDeviceSynchronize();
-  return *this;
-}
-template Field3D&
-    Field3D::operator= <Field3D, Field3D>(BinaryExpr<Field3D, Field3D> expr);
-#endif
-
-#if 0
-Field3D::Field3D(const BinaryExpr<Field3D, Field3D>& expr) {
-  Array<BoutReal> data{expr.getSize()};
-
-  constexpr int THREADS = 256;
-  int blocks = (expr.getSize() + THREADS - 1) / THREADS;
-  evaluator<<<blocks, THREADS>>>(&data[0], expr);
-  cudaDeviceSynchronize();
-  *this = Field3D{data, expr.getMesh(), expr.getLocation(), expr.getDirections()};
-}
-#endif
-
-// Provide the C++ wrapper for multiplication of Field3D and Field3D
-Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ operator to update Field3D by multiplication with Field3D
-Field3D& Field3D::operator*=(const Field3D& rhs) {
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) * rhs;
-  }
-  return *this;
-}
-
-// Provide the C++ wrapper for division of Field3D and Field3D
-Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] / rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ operator to update Field3D by division with Field3D
-Field3D& Field3D::operator/=(const Field3D& rhs) {
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) / rhs;
-  }
-  return *this;
-}
-
-#if 0
-// Provide the C++ wrapper for addition of Field3D and Field3D
-template <typename L, typename R, typename>
-BinaryExpr<L, R> operator+(const L& lhs, const R& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
-
-  std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{lhs,
-                    rhs,
-                    BinaryExpr<L, R>::Op::ADD,
-                    lhs.getMesh(),
-                    lhs.getLocation(),
-                    lhs.getDirections(),
-                    regionID,
-                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
-                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
-}
-template BinaryExpr<Field3D, Field3D> operator+ <Field3D, Field3D>(const Field3D& lhs,
-                                                                   const Field3D& rhs);
-#endif
-
-// Provide the C++ operator to update Field3D by addition with Field3D
-Field3D& Field3D::operator+=(const Field3D& rhs) {
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) + rhs;
-  }
-  return *this;
-}
-
-// Provide the C++ wrapper for subtraction of Field3D and Field3D
-Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ operator to update Field3D by subtraction with Field3D
-Field3D& Field3D::operator-=(const Field3D& rhs) {
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) - rhs;
-  }
-  return *this;
-}
-
 // Provide the C++ wrapper for multiplication of Field3D and Field2D
 Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
@@ -328,6 +116,7 @@ Field3D& Field3D::operator/=(const Field2D& rhs) {
   return *this;
 }
 
+#if 1
 // Provide the C++ wrapper for addition of Field3D and Field2D
 Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
@@ -350,6 +139,7 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field3D by addition with Field2D
 Field3D& Field3D::operator+=(const Field2D& rhs) {

From 34cba4d30879dcfbe76e0dfb9bba43af965342d6 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Wed, 28 May 2025 00:19:27 -0700
Subject: [PATCH 0175/1827] WIP 4

- Use functor template parameter for operation
---
 include/bout/field3d.hxx  | 26 +++++++++----------
 include/bout/fieldops.hxx | 53 ++++++++++++++++++---------------------
 2 files changed, 36 insertions(+), 43 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index a299f5bfdc..9696fce77d 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -39,8 +39,6 @@ class Field3D;
 
 class Mesh;
 
-//template <typename L, typename R>
-//class BinaryExpr;
 #include "bout/fieldops.hxx"
 
 /// Class for 3D X-Y-Z scalar fields
@@ -187,8 +185,8 @@ public:
   Field3D(Array<BoutReal> data, Mesh* localmesh, CELL_LOC location = CELL_CENTRE,
           DirectionTypes directions_in = {YDirectionType::Standard,
                                           ZDirectionType::Standard});
-  template <typename L, typename R>
-  Field3D(const BinaryExpr<L, R>& expr) {
+  template <typename L, typename R, typename Func>
+  Field3D(const BinaryExpr<L, R, Func>& expr) {
     Array<BoutReal> data{expr.getSize()};
     expr.evaluate(&data[0]);
     *this = Field3D{data, expr.getMesh(), expr.getLocation(), expr.getDirections()};
@@ -444,8 +442,8 @@ public:
   /// return void, as only part initialised
   void operator=(const FieldPerp& rhs);
   Field3D& operator=(BoutReal val);
-  template <typename L, typename R>
-  Field3D& operator=(BinaryExpr<L, R> expr) {
+  template <typename L, typename R, typename Func>
+  Field3D& operator=(BinaryExpr<L, R, Func> expr) {
     expr.evaluate(&data[0]);
     return *this;
   }
@@ -578,13 +576,13 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
 
 template <typename L, typename R,
           typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
-BinaryExpr<typename L::View, typename R::View> operator+(const L& lhs, const R& rhs) {
+BinaryExpr<typename L::View, typename R::View, bout::op::Add> operator+(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
   return BinaryExpr{static_cast<typename L::View>(lhs),
                     static_cast<typename R::View>(rhs),
-                    BinaryExpr<typename L::View, typename R::View>::Op::ADD,
+                    bout::op::Add{},
                     lhs.getMesh(),
                     lhs.getLocation(),
                     lhs.getDirections(),
@@ -595,13 +593,13 @@ BinaryExpr<typename L::View, typename R::View> operator+(const L& lhs, const R&
 
 template <typename L, typename R,
           typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
-BinaryExpr<typename L::View, typename R::View> operator-(const L& lhs, const R& rhs) {
+BinaryExpr<typename L::View, typename R::View, bout::op::Sub> operator-(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator- using BinaryExpr with CUDA" << "\n";
   return BinaryExpr{static_cast<typename L::View>(lhs),
                     static_cast<typename R::View>(rhs),
-                    BinaryExpr<typename L::View, typename R::View>::Op::SUB,
+                    bout::op::Sub{},
                     lhs.getMesh(),
                     lhs.getLocation(),
                     lhs.getDirections(),
@@ -612,13 +610,13 @@ BinaryExpr<typename L::View, typename R::View> operator-(const L& lhs, const R&
 
 template <typename L, typename R,
           typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
-BinaryExpr<typename L::View, typename R::View> operator*(const L& lhs, const R& rhs) {
+BinaryExpr<typename L::View, typename R::View, bout::op::Mul> operator*(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator* using BinaryExpr with CUDA" << "\n";
   return BinaryExpr{static_cast<typename L::View>(lhs),
                     static_cast<typename R::View>(rhs),
-                    BinaryExpr<typename L::View, typename R::View>::Op::MUL,
+                    bout::op::Mul{},
                     lhs.getMesh(),
                     lhs.getLocation(),
                     lhs.getDirections(),
@@ -629,13 +627,13 @@ BinaryExpr<typename L::View, typename R::View> operator*(const L& lhs, const R&
 
 template <typename L, typename R,
           typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
-BinaryExpr<typename L::View, typename R::View> operator/(const L& lhs, const R& rhs) {
+BinaryExpr<typename L::View, typename R::View, bout::op::Div> operator/(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator/ using BinaryExpr with CUDA" << "\n";
   return BinaryExpr{static_cast<typename L::View>(lhs),
                     static_cast<typename R::View>(rhs),
-                    BinaryExpr<typename L::View, typename R::View>::Op::DIV,
+                    bout::op::Div{},
                     lhs.getMesh(),
                     lhs.getLocation(),
                     lhs.getDirections(),
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 2ef7161f6d..b2052b12a1 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -12,17 +12,21 @@ class Field3D;
 
 #include <type_traits>
 
-struct Add {
-  __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a + b; }
-};
-struct Sub {
-  __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a - b; }
-};
-struct Mul {
-  __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a * b; }
+namespace bout {
+namespace op {
+  struct Add {
+    __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a + b; }
+  };
+  struct Sub {
+    __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a - b; }
+  };
+  struct Mul {
+    __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a * b; }
+  };
+  struct Div {
+    __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a / b; }
+  };
 };
-struct Div {
-  __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a / b; }
 };
 
 template <typename Expr>
@@ -34,7 +38,7 @@ __global__ static void evaluatorExpr(BoutReal* out, const Expr& expr) {
   }
 }
 
-template <typename L, typename R>
+template <typename L, typename R, typename Func>
 struct BinaryExpr {
   enum class Op { ADD, SUB, MUL, DIV };
   struct RegionIndices {
@@ -54,7 +58,7 @@ struct BinaryExpr {
   L lhs;
   R rhs;
   RegionIndices indices;
-  Op op;
+  Func f;
 
   Mesh* mesh;
   CELL_LOC location = CELL_CENTRE;
@@ -62,10 +66,10 @@ struct BinaryExpr {
   std::optional<size_t> regionID;
 
   template <typename IndType>
-  BinaryExpr(L lhs, R rhs, Op op, Mesh* mesh, CELL_LOC location,
+  BinaryExpr(L lhs, R rhs, Func f, Mesh* mesh, CELL_LOC location,
              DirectionTypes directions, std::optional<size_t> regionID,
              const Region<IndType>& region)
-      : lhs(lhs), rhs(rhs), op(op), mesh(mesh), location(location),
+      : lhs(lhs), rhs(rhs), f(f), mesh(mesh), location(location),
         directions(directions), regionID(regionID), indices(region.getIndices().size()) {
     // Copy the region indices into the managed array
     for (int i = 0; i < indices.size; ++i) {
@@ -80,26 +84,17 @@ struct BinaryExpr {
     R rhs;
     int* indices;
     int size;
-    Op op;
+    Func f;
 
     __host__ __device__ inline int getSize() const { return size; }
     __device__ inline int regionIdx(int idx) const { return indices[idx]; }
     __device__ inline BoutReal operator()(int idx) const {
-      switch (op) {
-      case Op::ADD:
-        return Add{}(lhs(idx), rhs(idx));
-      case Op::SUB:
-        return Sub{}(lhs(idx), rhs(idx));
-      case Op::MUL:
-        return Mul{}(lhs(idx), rhs(idx));
-      case Op::DIV:
-        return Div{}(lhs(idx), rhs(idx));
-      }
+      f(lhs(idx), rhs(idx)); // single‐pass fusion
     }
   };
 
-  operator View() { return View{lhs, rhs, indices.data, indices.size, op}; }
-  operator View() const { return View{lhs, rhs, indices.data, indices.size, op}; }
+  operator View() { return View{lhs, rhs, indices.data, indices.size, f}; }
+  operator View() const { return View{lhs, rhs, indices.data, indices.size, f}; }
 
   void evaluate(BoutReal* data) const {
     constexpr int THREADS = 256;
@@ -127,8 +122,8 @@ struct BinaryExpr {
 // 1) detect our BinaryExpr<T,U> template
 template <typename>
 struct is_binary_expr : std::false_type {};
-template <typename A, typename B>
-struct is_binary_expr<BinaryExpr<A, B>> : std::true_type {};
+template <typename A, typename B, typename F>
+struct is_binary_expr<BinaryExpr<A, B, F>> : std::true_type {};
 
 // 2) detect “any subclass of Field”
 //    assuming Field is your common base class

From 7d75b9db770db6ab7a30d3b7c27151e817e82086 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Wed, 28 May 2025 00:29:57 -0700
Subject: [PATCH 0176/1827] Used managed array for indices

---
 include/bout/fieldops.hxx | 28 +++++++---------------------
 1 file changed, 7 insertions(+), 21 deletions(-)

diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index b2052b12a1..2ea6ac44a6 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -41,23 +41,9 @@ __global__ static void evaluatorExpr(BoutReal* out, const Expr& expr) {
 template <typename L, typename R, typename Func>
 struct BinaryExpr {
   enum class Op { ADD, SUB, MUL, DIV };
-  struct RegionIndices {
-    int* data;
-    int size;
-
-    RegionIndices(int n) : size(n) {
-      cudaMallocManaged(&data, n * sizeof(int));
-      for (int i = 0; i < n; ++i)
-        data[i] = 0;
-    }
-    ~RegionIndices() { cudaFree(data); }
-
-    __device__ inline int operator()(int idx) const { return data[idx]; }
-  };
-
   L lhs;
   R rhs;
-  RegionIndices indices;
+  Array<int> indices;
   Func f;
 
   Mesh* mesh;
@@ -72,17 +58,17 @@ struct BinaryExpr {
       : lhs(lhs), rhs(rhs), f(f), mesh(mesh), location(location),
         directions(directions), regionID(regionID), indices(region.getIndices().size()) {
     // Copy the region indices into the managed array
-    for (int i = 0; i < indices.size; ++i) {
-      indices.data[i] = region.getIndices()[i].ind;
+    for (int i = 0; i < indices.size(); ++i) {
+      indices[i] = region.getIndices()[i].ind;
     }
   }
 
-  __host__ inline int getSize() const { return indices.size; }
+  __host__ inline int getSize() const { return indices.size(); }
 
   struct View {
     L lhs;
     R rhs;
-    int* indices;
+    const int* indices;
     int size;
     Func f;
 
@@ -93,8 +79,8 @@ struct BinaryExpr {
     }
   };
 
-  operator View() { return View{lhs, rhs, indices.data, indices.size, f}; }
-  operator View() const { return View{lhs, rhs, indices.data, indices.size, f}; }
+  operator View() { return View{lhs, rhs, &indices[0], indices.size(), f}; }
+  operator View() const { return View{lhs, rhs, &indices[0], indices.size(), f}; }
 
   void evaluate(BoutReal* data) const {
     constexpr int THREADS = 256;

From b8e7e973e0a4a245c1aa1be2933a0c830a2818e6 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Wed, 28 May 2025 02:03:25 -0700
Subject: [PATCH 0177/1827] Better SFINAE for specializations

---
 include/bout/field3d.hxx  | 67 ++++++++++++++++++++++++++++++++-------
 include/bout/fieldops.hxx | 21 +++++-------
 2 files changed, 63 insertions(+), 25 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 9696fce77d..cd981ff60d 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -40,6 +40,13 @@ class Field3D;
 class Mesh;
 
 #include "bout/fieldops.hxx"
+// Base template: nothing is an expression by default
+template <typename T>
+struct is_expr_field3d : std::false_type {};
+
+// Helper variable template
+template <typename T>
+inline constexpr bool is_expr_field3d_v = is_expr_field3d<std::decay_t<T>>::value;
 
 /// Class for 3D X-Y-Z scalar fields
 /*!
@@ -453,7 +460,7 @@ public:
   /// Addition operators
   ///@{
   //Field3D& operator+=(const Field3D& rhs);
-  template <typename R, typename = std::enable_if_t<is_expr_v<R>>>
+  template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator+=(const R& rhs) {
     printf("Running operator+= with CUDA\n");
     data.ensureUnique();
@@ -467,7 +474,7 @@ public:
   /// Subtraction operators
   ///@{
   //Field3D& operator-=(const Field3D& rhs);
-  template <typename R, typename = std::enable_if_t<is_expr_v<R>>>
+  template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator-=(const R& rhs) {
     printf("Running operator-= with CUDA\n");
     data.ensureUnique();
@@ -481,7 +488,7 @@ public:
   /// Multiplication operators
   ///@{
   //Field3D& operator*=(const Field3D& rhs);
-    template <typename R, typename = std::enable_if_t<is_expr_v<R>>>
+  template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator*=(const R& rhs) {
     printf("Running operator*= with CUDA\n");
     data.ensureUnique();
@@ -494,7 +501,7 @@ public:
 
   /// Division operators
   ///@{
-      template <typename R, typename = std::enable_if_t<is_expr_v<R>>>
+  template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator/=(const R& rhs) {
     printf("Running operator/= with CUDA\n");
     data.ensureUnique();
@@ -575,8 +582,9 @@ FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs);
 FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
 
 template <typename L, typename R,
-          typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
-BinaryExpr<typename L::View, typename R::View, bout::op::Add> operator+(const L& lhs, const R& rhs) {
+          typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
+BinaryExpr<typename L::View, typename R::View, bout::op::Add> operator+(const L& lhs,
+                                                                        const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
@@ -592,8 +600,9 @@ BinaryExpr<typename L::View, typename R::View, bout::op::Add> operator+(const L&
 }
 
 template <typename L, typename R,
-          typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
-BinaryExpr<typename L::View, typename R::View, bout::op::Sub> operator-(const L& lhs, const R& rhs) {
+          typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
+BinaryExpr<typename L::View, typename R::View, bout::op::Sub> operator-(const L& lhs,
+                                                                        const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator- using BinaryExpr with CUDA" << "\n";
@@ -609,8 +618,9 @@ BinaryExpr<typename L::View, typename R::View, bout::op::Sub> operator-(const L&
 }
 
 template <typename L, typename R,
-          typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
-BinaryExpr<typename L::View, typename R::View, bout::op::Mul> operator*(const L& lhs, const R& rhs) {
+          typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
+BinaryExpr<typename L::View, typename R::View, bout::op::Mul> operator*(const L& lhs,
+                                                                        const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator* using BinaryExpr with CUDA" << "\n";
@@ -626,8 +636,9 @@ BinaryExpr<typename L::View, typename R::View, bout::op::Mul> operator*(const L&
 }
 
 template <typename L, typename R,
-          typename = std::enable_if_t<is_expr_v<L> && is_expr_v<R>>>
-BinaryExpr<typename L::View, typename R::View, bout::op::Div> operator/(const L& lhs, const R& rhs) {
+          typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
+BinaryExpr<typename L::View, typename R::View, bout::op::Div> operator/(const L& lhs,
+                                                                        const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator/ using BinaryExpr with CUDA" << "\n";
@@ -643,6 +654,22 @@ BinaryExpr<typename L::View, typename R::View, bout::op::Div> operator/(const L&
 }
 
 Field3D operator+(const Field3D& lhs, const Field2D& rhs);
+// template <typename L, typename R,
+// typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>>>
+// BinaryExpr<typename L::View, typename R::View, bout::op::Add> operator+(const L& lhs, const R& rhs) {
+// auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
+//
+// std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
+// return BinaryExpr{static_cast<typename L::View>(lhs),
+// static_cast<typename R::View>(rhs),
+// bout::op::Add{},
+// lhs.getMesh(),
+// lhs.getLocation(),
+// lhs.getDirections(),
+// regionID,
+// (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
+// : lhs.getMesh()->getRegion("RGN_ALL"))};
+// }
 Field3D operator-(const Field3D& lhs, const Field2D& rhs);
 Field3D operator*(const Field3D& lhs, const Field2D& rhs);
 Field3D operator/(const Field3D& lhs, const Field2D& rhs);
@@ -769,4 +796,20 @@ bool operator==(const Field3D& a, const Field3D& b);
 /// Output a string describing a Field3D to a stream
 std::ostream& operator<<(std::ostream& out, const Field3D& value);
 
+// A raw Field3D is an expression leaf
+template <>
+struct is_expr_field3d<Field3D> : std::true_type {};
+template <>
+struct is_expr_field3d<Field3D::View> : std::true_type {};
+
+// Any nested BinaryExpr<L,R,Fun> is an expression iff L is
+template <typename L, typename R, typename Fun>
+struct is_expr_field3d<BinaryExpr<L, R, Fun>>
+    : std::true_type {};
+
+//template<typename L,typename R,typename Fun>
+//struct is_expr_field3d< typename BinaryExpr<L,R,Fun>::View >
+//  : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value> {};
+//  //: is_expr_field3d<std::decay_t<L>> {};
+
 #endif /* BOUT_FIELD3D_H */
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 2ea6ac44a6..7c7f511cc3 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -40,7 +40,6 @@ __global__ static void evaluatorExpr(BoutReal* out, const Expr& expr) {
 
 template <typename L, typename R, typename Func>
 struct BinaryExpr {
-  enum class Op { ADD, SUB, MUL, DIV };
   L lhs;
   R rhs;
   Array<int> indices;
@@ -95,16 +94,7 @@ struct BinaryExpr {
   std::optional<size_t> getRegionID() const { return regionID; };
 };
 
-//template <typename T>
-//struct Expr {
-//  using type = T;
-//};
-//
-//template <>
-//struct Expr<Field3D> {
-//  using type = Field3D::View;
-//};
-
+#if 0
 // 1) detect our BinaryExpr<T,U> template
 template <typename>
 struct is_binary_expr : std::false_type {};
@@ -114,10 +104,15 @@ struct is_binary_expr<BinaryExpr<A, B, F>> : std::true_type {};
 // 2) detect “any subclass of Field”
 //    assuming Field is your common base class
 template <typename T>
-constexpr bool is_field_v = std::is_base_of<Field3D, std::decay_t<T>>::value;
+constexpr bool is_field3d_v = std::is_base_of<Field3D, std::decay_t<T>>::value;
 
 // 3) combine into “is one of our expression types”
 template <typename T>
-constexpr bool is_expr_v = is_field_v<T> || is_binary_expr<std::decay_t<T>>::value;
+constexpr bool is_expr_field3d_v =
+    is_field3d_v<T> || is_binary_expr<std::decay_t<T>>::value;
+#endif
+
+#if 1
 
+#endif
 #endif // BOUT_EXPRESSION_HXX
\ No newline at end of file

From d830f8d781c48921a9f6ce5ec5a519d162c9fa3a Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Wed, 28 May 2025 23:15:30 -0700
Subject: [PATCH 0178/1827] Fix major bug in the binary expr operator() and add
 operators

- Working version
---
 include/bout/field2d.hxx                      |  10 +
 include/bout/field3d.hxx                      | 163 ++++++++++-----
 include/bout/fieldops.hxx                     |  84 ++++----
 include/bout/rajalib.hxx                      |   2 +-
 include/bout/vector3d.hxx                     |   1 -
 src/field/generated_fieldops.cxx              | 193 +++++++++++++++++-
 src/field/vecops.cxx                          |   1 -
 .../laplace/impls/naulin/naulin_laplace.cxx   |   1 -
 src/sys/derivs.cxx                            |   1 -
 9 files changed, 348 insertions(+), 108 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 92658f1bbf..5f0901ac67 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -276,6 +276,16 @@ public:
 
   int size() const override { return nx * ny; };
 
+  struct View {
+    const BoutReal* data;
+    __device__ inline BoutReal operator()(int idx) const { return data[idx]; }
+  };
+  operator View() { return View{&data[0]}; }
+  operator View() const { return View{&data[0]}; }
+
+  __device__ inline BoutReal operator()(int i) { return View()(i); }
+  __device__ inline BoutReal operator()(int i) const { return View()(i); }
+
 private:
   /// Internal data array. Handles allocation/freeing of memory
   Array<BoutReal> data;
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index cd981ff60d..c6bc02faf9 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -44,10 +44,16 @@ class Mesh;
 template <typename T>
 struct is_expr_field3d : std::false_type {};
 
+template <typename T>
+struct is_expr_field2d : std::false_type {};
+
 // Helper variable template
 template <typename T>
 inline constexpr bool is_expr_field3d_v = is_expr_field3d<std::decay_t<T>>::value;
 
+template <typename T>
+inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::valuen;
+
 /// Class for 3D X-Y-Z scalar fields
 /*!
   This class represents a scalar field defined over the mesh.
@@ -194,9 +200,12 @@ public:
                                           ZDirectionType::Standard});
   template <typename L, typename R, typename Func>
   Field3D(const BinaryExpr<L, R, Func>& expr) {
-    Array<BoutReal> data{expr.getSize()};
+    std::cout << "RUNNING constructor from BinaryExpr\n";
+    Array<BoutReal> data{expr.size()};
     expr.evaluate(&data[0]);
-    *this = Field3D{data, expr.getMesh(), expr.getLocation(), expr.getDirections()};
+    *this = std::move(Field3D{std::move(data), expr.getMesh(), expr.getLocation(),
+                              expr.getDirections()});
+    setRegion(expr.getRegionID());
   }
   /// Destructor
   ~Field3D() override;
@@ -430,13 +439,12 @@ public:
 
   struct View {
     const BoutReal* data;
-    __device__ inline BoutReal operator()(int idx) const { return data[idx]; }
+    __host__ __device__ inline BoutReal operator()(int idx) const { return data[idx]; }
+    //__device__ inline const BoutReal* operator()() const { return data; }
   };
   operator View() { return View{&data[0]}; }
   operator View() const { return View{&data[0]}; }
 
-  __device__ inline BoutReal operator()(int i) { return View()(i); }
-  __device__ inline BoutReal operator()(int i) const { return View()(i); }
 
   /////////////////////////////////////////////////////////
   // Operators
@@ -450,7 +458,9 @@ public:
   void operator=(const FieldPerp& rhs);
   Field3D& operator=(BoutReal val);
   template <typename L, typename R, typename Func>
-  Field3D& operator=(BinaryExpr<L, R, Func> expr) {
+  Field3D& operator=(BinaryExpr<L, R, Func>& expr) {
+    std::cout << "RUNNING operator= with CUDA\n";
+    regionID = expr.getRegionID();
     expr.evaluate(&data[0]);
     return *this;
   }
@@ -462,9 +472,19 @@ public:
   //Field3D& operator+=(const Field3D& rhs);
   template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator+=(const R& rhs) {
-    printf("Running operator+= with CUDA\n");
-    data.ensureUnique();
-    (*this) = (*this) + rhs;
+    printf("RUNNING operator+= with CUDA\n");
+    if (data.unique()) {
+      // Delete existing parallel slices. We don't copy parallel slices, so any
+      // that currently exist will be incorrect.
+      clearParallelSlices();
+
+      auto BE = (*this) + rhs;
+      regionID = BE.getRegionID();
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) + rhs;
+    }
+
     return *this;
   }
   Field3D& operator+=(const Field2D& rhs);
@@ -476,9 +496,18 @@ public:
   //Field3D& operator-=(const Field3D& rhs);
   template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator-=(const R& rhs) {
-    printf("Running operator-= with CUDA\n");
-    data.ensureUnique();
-    (*this) = (*this) - rhs;
+    if (data.unique()) {
+      printf("RUNNING operator-= with CUDA with BE\n");
+      // Delete existing parallel slices. We don't copy parallel slices, so any
+      // that currently exist will be incorrect.
+      clearParallelSlices();
+      auto BE = (*this) - rhs;
+      BE.evaluate(&data[0]);
+    } else {
+      printf("RUNNING operator-= with CUDA with operation\n");
+      (*this) = (*this) - rhs;
+    }
+
     return *this;
   }
   Field3D& operator-=(const Field2D& rhs);
@@ -490,9 +519,19 @@ public:
   //Field3D& operator*=(const Field3D& rhs);
   template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator*=(const R& rhs) {
-    printf("Running operator*= with CUDA\n");
-    data.ensureUnique();
-    (*this) = (*this) * rhs;
+    printf("RUNNING operator*= with CUDA\n");
+    if (data.unique()) {
+      // Delete existing parallel slices. We don't copy parallel slices, so any
+      // that currently exist will be incorrect.
+      clearParallelSlices();
+
+      auto BE = (*this) * rhs;
+      regionID = BE.getRegionID();
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) * rhs;
+    }
+
     return *this;
   }
   Field3D& operator*=(const Field2D& rhs);
@@ -501,14 +540,24 @@ public:
 
   /// Division operators
   ///@{
+  //Field3D& operator/=(const Field3D& rhs);
   template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator/=(const R& rhs) {
-    printf("Running operator/= with CUDA\n");
-    data.ensureUnique();
-    (*this) = (*this) * rhs;
+    printf("RUNNING operator/= with CUDA\n");
+    if (data.unique()) {
+      // Delete existing parallel slices. We don't copy parallel slices, so any
+      // that currently exist will be incorrect.
+      clearParallelSlices();
+
+      auto BE = (*this) / rhs;
+      regionID = BE.getRegionID();
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) / rhs;
+    }
+
     return *this;
   }
-  //Field3D& operator/=(const Field3D& rhs);
   Field3D& operator/=(const Field2D& rhs);
   Field3D& operator/=(BoutReal rhs);
   ///@}
@@ -571,10 +620,9 @@ private:
 
 // Non-member overloaded operators
 
-template<typename T>
+template <typename T>
 constexpr bool always_false = false;
 
-
 // Binary operators
 FieldPerp operator+(const Field3D& lhs, const FieldPerp& rhs);
 FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs);
@@ -583,13 +631,12 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
 
 template <typename L, typename R,
           typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
-BinaryExpr<typename L::View, typename R::View, bout::op::Add> operator+(const L& lhs,
-                                                                        const R& rhs) {
+BinaryExpr<L, R, bout::op::Add> operator+(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{static_cast<typename L::View>(lhs),
-                    static_cast<typename R::View>(rhs),
+  return BinaryExpr{(lhs),
+                    (rhs),
                     bout::op::Add{},
                     lhs.getMesh(),
                     lhs.getLocation(),
@@ -601,13 +648,12 @@ BinaryExpr<typename L::View, typename R::View, bout::op::Add> operator+(const L&
 
 template <typename L, typename R,
           typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
-BinaryExpr<typename L::View, typename R::View, bout::op::Sub> operator-(const L& lhs,
-                                                                        const R& rhs) {
+BinaryExpr<L, R, bout::op::Sub> operator-(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator- using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{static_cast<typename L::View>(lhs),
-                    static_cast<typename R::View>(rhs),
+  return BinaryExpr{(lhs),
+                    (rhs),
                     bout::op::Sub{},
                     lhs.getMesh(),
                     lhs.getLocation(),
@@ -619,13 +665,12 @@ BinaryExpr<typename L::View, typename R::View, bout::op::Sub> operator-(const L&
 
 template <typename L, typename R,
           typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
-BinaryExpr<typename L::View, typename R::View, bout::op::Mul> operator*(const L& lhs,
-                                                                        const R& rhs) {
+BinaryExpr<L, R, bout::op::Mul> operator*(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator* using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{static_cast<typename L::View>(lhs),
-                    static_cast<typename R::View>(rhs),
+  return BinaryExpr{(lhs),
+                    (rhs),
                     bout::op::Mul{},
                     lhs.getMesh(),
                     lhs.getLocation(),
@@ -637,13 +682,12 @@ BinaryExpr<typename L::View, typename R::View, bout::op::Mul> operator*(const L&
 
 template <typename L, typename R,
           typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
-BinaryExpr<typename L::View, typename R::View, bout::op::Div> operator/(const L& lhs,
-                                                                        const R& rhs) {
+BinaryExpr<L, R, bout::op::Div> operator/(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
   std::cout << "RUNNING operator/ using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{static_cast<typename L::View>(lhs),
-                    static_cast<typename R::View>(rhs),
+  return BinaryExpr{(lhs),
+                    (rhs),
                     bout::op::Div{},
                     lhs.getMesh(),
                     lhs.getLocation(),
@@ -654,22 +698,26 @@ BinaryExpr<typename L::View, typename R::View, bout::op::Div> operator/(const L&
 }
 
 Field3D operator+(const Field3D& lhs, const Field2D& rhs);
-// template <typename L, typename R,
-// typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>>>
-// BinaryExpr<typename L::View, typename R::View, bout::op::Add> operator+(const L& lhs, const R& rhs) {
-// auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
+//template <typename L, typename R>
+//auto operator+(const L& lhs, const R& rhs)
+//    -> std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
+//                        BinaryExpr<L, R, bout::op::Add>> {
+//  static_assert(always_false<L> || always_false<R>, "Hello");
+//  auto regionID = lhs.getRegionID();
 //
-// std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
-// return BinaryExpr{static_cast<typename L::View>(lhs),
-// static_cast<typename R::View>(rhs),
-// bout::op::Add{},
-// lhs.getMesh(),
-// lhs.getLocation(),
-// lhs.getDirections(),
-// regionID,
-// (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
-// : lhs.getMesh()->getRegion("RGN_ALL"))};
-// }
+//  std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
+//  int mesh_nz = lhs.getMesh()->LocalNz;
+//  auto LambdaOp = [mesh_nz]() {
+//  };
+//  return BinaryExpr{(lhs),
+//          (rhs),
+//          bout::op::Add{},
+//          lhs.getMesh(),
+//          lhs.getLocation(),
+//          lhs.getDirections(),
+//          regionID,
+//          rhs.getRegion("RGN_ALL")};
+//}
 Field3D operator-(const Field3D& lhs, const Field2D& rhs);
 Field3D operator*(const Field3D& lhs, const Field2D& rhs);
 Field3D operator/(const Field3D& lhs, const Field2D& rhs);
@@ -713,7 +761,7 @@ void checkData(const Field3D& f, const std::string& region = "RGN_NOBNDRY");
 /// Ignored with disabled CHECK; Throw an exception if \p f is not
 /// allocated or if any elements are non-finite (for CHECK > 2)
 inline void checkData(const Field3D& UNUSED(f),
-                      const std::string& UNUSED(region) = "RGN_NOBNDRY"){};
+                      const std::string& UNUSED(region) = "RGN_NOBNDRY") {};
 #endif
 
 /// Fourier filtering, removes all except one mode
@@ -799,13 +847,18 @@ std::ostream& operator<<(std::ostream& out, const Field3D& value);
 // A raw Field3D is an expression leaf
 template <>
 struct is_expr_field3d<Field3D> : std::true_type {};
+
 template <>
-struct is_expr_field3d<Field3D::View> : std::true_type {};
+struct is_expr_field2d<Field2D> : std::true_type {};
 
 // Any nested BinaryExpr<L,R,Fun> is an expression iff L is
+//template <typename L, typename R, typename Fun>
+//struct is_expr_field3d<BinaryExpr<L, R, Fun>>
+//    : std::true_type {};
+
 template <typename L, typename R, typename Fun>
 struct is_expr_field3d<BinaryExpr<L, R, Fun>>
-    : std::true_type {};
+    : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value> {};
 
 //template<typename L,typename R,typename Fun>
 //struct is_expr_field3d< typename BinaryExpr<L,R,Fun>::View >
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 7c7f511cc3..e9c87f242f 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -15,16 +15,26 @@ class Field3D;
 namespace bout {
 namespace op {
   struct Add {
-    __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a + b; }
+    template<typename LView, typename RView>
+    __host__ __device__ inline BoutReal operator()(int idx, const LView &L, const RView &R) const {
+      return L(idx) + R(idx);
+    }
+    __host__ __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a + b; }
   };
   struct Sub {
-    __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a - b; }
-  };
-  struct Mul {
-    __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a * b; }
-  };
-  struct Div {
-    __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a / b; }
+    template<typename LView, typename RView>
+    __host__ __device__ inline BoutReal operator()(int idx, const LView &L, const RView &R) const { return L(idx) - R(idx); }
+    __host__ __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a - b; }
+  };                                                                                                
+  struct Mul {                                                                                      
+    template<typename LView, typename RView>
+    __host__ __device__ inline BoutReal operator()(int idx, const LView &L, const RView &R) const { return L(idx) * R(idx); }
+    __host__ __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a * b; }
+  };                                                                                                
+  struct Div {                                                                                      
+    template<typename LView, typename RView>
+    __host__ __device__ inline BoutReal operator()(int idx, const LView &L, const RView &R) const { return L(idx) / R(idx); }
+    __host__ __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a / b; }
   };
 };
 };
@@ -33,15 +43,17 @@ template <typename Expr>
 __global__ static void evaluatorExpr(BoutReal* out, const Expr& expr) {
   int tid = threadIdx.x + blockIdx.x * blockDim.x;
   int stride = blockDim.x * gridDim.x;
-  for (int i = tid; i < expr.getSize(); i += stride) {
+  for (int i = tid; i < expr.size(); i += stride) {
     out[expr.regionIdx(i)] = expr(expr.regionIdx(i)); // single‐pass fusion
   }
 }
 
 template <typename L, typename R, typename Func>
 struct BinaryExpr {
-  L lhs;
-  R rhs;
+  const L &LHS;
+  const R &RHS;
+  typename L::View lhs;
+  typename R::View rhs;
   Array<int> indices;
   Func f;
 
@@ -51,30 +63,36 @@ struct BinaryExpr {
   std::optional<size_t> regionID;
 
   template <typename IndType>
-  BinaryExpr(L lhs, R rhs, Func f, Mesh* mesh, CELL_LOC location,
+  BinaryExpr(const L &lhs, const R &rhs, Func f, Mesh* mesh, CELL_LOC location,
              DirectionTypes directions, std::optional<size_t> regionID,
              const Region<IndType>& region)
-      : lhs(lhs), rhs(rhs), f(f), mesh(mesh), location(location),
-        directions(directions), regionID(regionID), indices(region.getIndices().size()) {
+      : LHS(lhs), RHS(rhs), lhs(static_cast<typename L::View>(lhs)), rhs(static_cast<typename R::View>(rhs)),
+        f(f), mesh(mesh), location(location), directions(directions), regionID(regionID),
+        indices(region.getIndices().size()) {
     // Copy the region indices into the managed array
     for (int i = 0; i < indices.size(); ++i) {
       indices[i] = region.getIndices()[i].ind;
     }
   }
 
-  __host__ inline int getSize() const { return indices.size(); }
+  inline int size() const { return indices.size(); }
+  inline BoutReal operator()(int idx) const {
+    return f(idx, lhs, rhs); // single‐pass fusion
+  }
+  inline int regionIdx(int idx) const { return indices[idx]; }
 
   struct View {
-    L lhs;
-    R rhs;
+    typename L::View lhs;
+    typename R::View rhs;
     const int* indices;
-    int size;
+    int num_indices;
     Func f;
 
-    __host__ __device__ inline int getSize() const { return size; }
+    __device__ inline int size() const { return num_indices; }
     __device__ inline int regionIdx(int idx) const { return indices[idx]; }
     __device__ inline BoutReal operator()(int idx) const {
-      f(lhs(idx), rhs(idx)); // single‐pass fusion
+      return f(idx, lhs, rhs); // single‐pass fusion
+      //return f(lhs(idx), rhs(idx)); // single‐pass fusion
     }
   };
 
@@ -83,9 +101,12 @@ struct BinaryExpr {
 
   void evaluate(BoutReal* data) const {
     constexpr int THREADS = 256;
-    int blocks = (getSize() + THREADS - 1) / THREADS;
+    int blocks = (size() + THREADS - 1) / THREADS;
     evaluatorExpr<<<blocks, THREADS>>>(&data[0], static_cast<View>(*this));
     cudaDeviceSynchronize();
+    //for(int i=0; i<size(); ++i) {
+    //  data[regionIdx(i)] = f(i, lhs, rhs); // single‐pass fusion
+    //}
   }
 
   Mesh* getMesh() const { return mesh; }
@@ -94,25 +115,4 @@ struct BinaryExpr {
   std::optional<size_t> getRegionID() const { return regionID; };
 };
 
-#if 0
-// 1) detect our BinaryExpr<T,U> template
-template <typename>
-struct is_binary_expr : std::false_type {};
-template <typename A, typename B, typename F>
-struct is_binary_expr<BinaryExpr<A, B, F>> : std::true_type {};
-
-// 2) detect “any subclass of Field”
-//    assuming Field is your common base class
-template <typename T>
-constexpr bool is_field3d_v = std::is_base_of<Field3D, std::decay_t<T>>::value;
-
-// 3) combine into “is one of our expression types”
-template <typename T>
-constexpr bool is_expr_field3d_v =
-    is_field3d_v<T> || is_binary_expr<std::decay_t<T>>::value;
-#endif
-
-#if 1
-
-#endif
 #endif // BOUT_EXPRESSION_HXX
\ No newline at end of file
diff --git a/include/bout/rajalib.hxx b/include/bout/rajalib.hxx
index b3da46da50..d61a58e0d8 100644
--- a/include/bout/rajalib.hxx
+++ b/include/bout/rajalib.hxx
@@ -145,7 +145,7 @@ template <typename Expr>
 __global__ void evaluator(BoutReal *out, Expr &expr) {
   int tid = threadIdx.x + blockIdx.x * blockDim.x;
   int stride = blockDim.x * gridDim.x;
-  for (int i = tid; i < expr.getSize(); i += stride) {
+  for (int i = tid; i < expr.size(); i += stride) {
     out[expr.regionIdx(i)] = expr(expr.regionIdx(i)); // single‐pass fusion
   }
 }
diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx
index ad68dc17ee..0c71dcffa5 100644
--- a/include/bout/vector3d.hxx
+++ b/include/bout/vector3d.hxx
@@ -36,7 +36,6 @@ class Vector3D;
 class Field2D;
 class Vector2D;
 #include "bout/field3d.hxx"
-#include "bout/fieldops.hxx"
 
 /*!
  * Represents a 3D vector, with x,y,z components
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 63cbf9b847..c35ae2e866 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -1,15 +1,198 @@
 // This file is autogenerated - see gen_fieldops.py
-#include "bout/rajalib.hxx"
-#include "bout/fieldops.hxx"
-
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
-#include <bout/field_accessor.hxx>
 #include <bout/globals.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 
+// Provide the C++ wrapper for multiplication of Field3D and Field3D
+Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3D result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3D by multiplication with Field3D
+#if 0
+Field3D& Field3D::operator*=(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // that currently exist will be incorrect.
+    clearParallelSlices();
+
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
+
+    checkData(*this);
+
+  } else {
+    (*this) = (*this) * rhs;
+  }
+  return *this;
+}
+#endif
+
+// Provide the C++ wrapper for division of Field3D and Field3D
+Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3D result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] / rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3D by division with Field3D
+#if 0
+Field3D& Field3D::operator/=(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // that currently exist will be incorrect.
+    clearParallelSlices();
+
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
+
+    checkData(*this);
+
+  } else {
+    (*this) = (*this) / rhs;
+  }
+  return *this;
+}
+#endif
+
+// Provide the C++ wrapper for addition of Field3D and Field3D
+Field3D operator+(const Field3D& lhs, const Field3D& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3D result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] + rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+#if 0
+// Provide the C++ operator to update Field3D by addition with Field3D
+Field3D& Field3D::operator+=(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // that currently exist will be incorrect.
+    clearParallelSlices();
+
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
+
+    checkData(*this);
+
+  } else {
+    (*this) = (*this) + rhs;
+  }
+  return *this;
+}
+#endif
+
+// Provide the C++ wrapper for subtraction of Field3D and Field3D
+Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3D result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] - rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3D by subtraction with Field3D
+#if 0
+Field3D& Field3D::operator-=(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // that currently exist will be incorrect.
+    clearParallelSlices();
+
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { 
+      (*this)[index] -= rhs[index]; 
+      printf("[golden] val[%d] %lf\n", index, (*this)[index]);
+    }
+
+    checkData(*this);
+
+  } else {
+    (*this) = (*this) - rhs;
+  }
+  return *this;
+}
+#endif
+
 // Provide the C++ wrapper for multiplication of Field3D and Field2D
 Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
@@ -116,7 +299,6 @@ Field3D& Field3D::operator/=(const Field2D& rhs) {
   return *this;
 }
 
-#if 1
 // Provide the C++ wrapper for addition of Field3D and Field2D
 Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
@@ -139,7 +321,6 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
-#endif
 
 // Provide the C++ operator to update Field3D by addition with Field2D
 Field3D& Field3D::operator+=(const Field2D& rhs) {
diff --git a/src/field/vecops.cxx b/src/field/vecops.cxx
index 9b1105e7aa..5f34e2af02 100644
--- a/src/field/vecops.cxx
+++ b/src/field/vecops.cxx
@@ -28,7 +28,6 @@
 #include <bout/scorepwrapper.hxx>
 
 #include <bout/derivs.hxx>
-#include <bout/fieldops.hxx>
 #include <bout/globals.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/unused.hxx>
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index 74ec68dae9..e6f68d850d 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -142,7 +142,6 @@
 #include <bout/coordinates.hxx>
 #include <bout/derivs.hxx>
 #include <bout/difops.hxx>
-#include <bout/fieldops.hxx>
 #include <bout/globals.hxx>
 #include <bout/mesh.hxx>
 #include <bout/sys/timer.hxx>
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index 55e2c77a29..ee9bcbcc2c 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -49,7 +49,6 @@
 
 #include <cmath>
 
-#include <bout/fieldops.hxx>
 #include <bout/output.hxx>
 #include <bout/unused.hxx>
 

From c5f9fd668138b61cbd3ce6542177d538ac7becec Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Thu, 29 May 2025 22:40:53 -0700
Subject: [PATCH 0179/1827] WIP

- More operators
---
 include/bout/array.hxx           |   2 +-
 include/bout/field2d.hxx         |  33 +++-
 include/bout/field3d.hxx         | 254 ++++++++++++++++++----------
 include/bout/fieldops.hxx        | 157 +++++++++++++----
 src/field/generated_fieldops.cxx | 281 +++++++++++--------------------
 5 files changed, 418 insertions(+), 309 deletions(-)

diff --git a/include/bout/array.hxx b/include/bout/array.hxx
index b83c29c51d..2c42f15aad 100644
--- a/include/bout/array.hxx
+++ b/include/bout/array.hxx
@@ -66,7 +66,7 @@ struct ArrayData {
 #if BOUT_HAS_UMPIRE
     auto& rm = umpire::ResourceManager::getInstance();
 #if BOUT_HAS_CUDA
-    auto allocator = rm.getAllocator(umpire::resource::Unified);
+    auto allocator = rm.getAllocator(umpire::resource::Pinned);
 #else
     auto allocator = rm.getAllocator("HOST");
 #endif
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 5f0901ac67..db2ce194f8 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -277,11 +277,22 @@ public:
   int size() const override { return nx * ny; };
 
   struct View {
-    const BoutReal* data;
-    __device__ inline BoutReal operator()(int idx) const { return data[idx]; }
+    BoutReal* data;
+    int mul = 1;
+    int div = 1;
+    __device__ inline BoutReal operator()(int idx) const { return data[(idx*mul/div)]; }
+    __device__ inline BoutReal& operator[](int idx) const {
+      return data[(idx * mul)/div];
+    }
+
+    View& setScale(int mul, int div) {
+      this->mul = mul;
+      this->div = div;
+      return *this;
+    }
   };
   operator View() { return View{&data[0]}; }
-  operator View() const { return View{&data[0]}; }
+  operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
 
   __device__ inline BoutReal operator()(int i) { return View()(i); }
   __device__ inline BoutReal operator()(int i) const { return View()(i); }
@@ -302,6 +313,22 @@ private:
 Field2D operator+(const Field2D& lhs, const Field2D& rhs);
 Field2D operator-(const Field2D& lhs, const Field2D& rhs);
 Field2D operator*(const Field2D& lhs, const Field2D& rhs);
+#if 0
+template <typename L, typename R,
+          typename = std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>>>
+BinaryExpr<L, R, bout::op::Mul> operator*(const L& lhs, const R& rhs) {
+  return BinaryExpr<L, R, bout::op::Mul>{static_cast<typename L::View>(lhs),
+                                         static_cast<typename R::View>(rhs),
+                                         bout::op::Mul{},
+                                         lhs.getMesh(),
+                                         lhs.getLocation(),
+                                         lhs.getDirections(),
+                                         lhs.getRegionID(),
+                                         (regionID.has_value()
+                                              ? lhs.getMesh()->getRegion(regionID.value())
+                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
+}
+#endif
 Field2D operator/(const Field2D& lhs, const Field2D& rhs);
 
 Field3D operator+(const Field2D& lhs, const Field3D& rhs);
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index c6bc02faf9..33e42cccbb 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -52,7 +52,7 @@ template <typename T>
 inline constexpr bool is_expr_field3d_v = is_expr_field3d<std::decay_t<T>>::value;
 
 template <typename T>
-inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::valuen;
+inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::value;
 
 /// Class for 3D X-Y-Z scalar fields
 /*!
@@ -200,7 +200,7 @@ public:
                                           ZDirectionType::Standard});
   template <typename L, typename R, typename Func>
   Field3D(const BinaryExpr<L, R, Func>& expr) {
-    std::cout << "RUNNING constructor from BinaryExpr\n";
+    //std::cout << "RUNNING constructor from BinaryExpr\n";
     Array<BoutReal> data{expr.size()};
     expr.evaluate(&data[0]);
     *this = std::move(Field3D{std::move(data), expr.getMesh(), expr.getLocation(),
@@ -438,13 +438,30 @@ public:
   }
 
   struct View {
-    const BoutReal* data;
-    __host__ __device__ inline BoutReal operator()(int idx) const { return data[idx]; }
-    //__device__ inline const BoutReal* operator()() const { return data; }
+    BoutReal* data;
+    int mul = 1;
+    int div = 1;
+    int offset = 0;
+    __host__ __device__ inline BoutReal operator()(int idx) const {
+      return data[(idx * mul) / div + offset];
+    }
+    __device__ inline BoutReal& operator[](int idx) const {
+      return data[(idx * mul) / div + offset];
+    }
+
+    View& setScale(int mul, int div) {
+      this->mul = mul;
+      this->div = div;
+      return *this;
+    }
+    View& setOffset(int o) {
+      offset = o;
+      return *this;
+    }
   };
   operator View() { return View{&data[0]}; }
-  operator View() const { return View{&data[0]}; }
-
+  operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
+  //operator View() const { return View{&data[0]}; }
 
   /////////////////////////////////////////////////////////
   // Operators
@@ -461,7 +478,8 @@ public:
   Field3D& operator=(BinaryExpr<L, R, Func>& expr) {
     std::cout << "RUNNING operator= with CUDA\n";
     regionID = expr.getRegionID();
-    expr.evaluate(&data[0]);
+    //expr.evaluate(&data[0]);
+    expr.evaluateWithResult(static_cast<View>(*this));
     return *this;
   }
 
@@ -472,15 +490,17 @@ public:
   //Field3D& operator+=(const Field3D& rhs);
   template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator+=(const R& rhs) {
-    printf("RUNNING operator+= with CUDA\n");
+    //printf("RUNNING operator+= with CUDA\n");
     if (data.unique()) {
+      printf("RUNNING operator+= with CUDA with evaluateWithResult\n");
       // Delete existing parallel slices. We don't copy parallel slices, so any
       // that currently exist will be incorrect.
       clearParallelSlices();
 
       auto BE = (*this) + rhs;
       regionID = BE.getRegionID();
-      BE.evaluate(&data[0]);
+      //BE.evaluate(&data[0]);
+      BE.evaluateWithResult(static_cast<View>(*this));
     } else {
       (*this) = (*this) + rhs;
     }
@@ -497,14 +517,14 @@ public:
   template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator-=(const R& rhs) {
     if (data.unique()) {
-      printf("RUNNING operator-= with CUDA with BE\n");
+      //printf("RUNNING operator-= with CUDA with BE\n");
       // Delete existing parallel slices. We don't copy parallel slices, so any
       // that currently exist will be incorrect.
       clearParallelSlices();
       auto BE = (*this) - rhs;
       BE.evaluate(&data[0]);
     } else {
-      printf("RUNNING operator-= with CUDA with operation\n");
+      //printf("RUNNING operator-= with CUDA with operation\n");
       (*this) = (*this) - rhs;
     }
 
@@ -519,7 +539,7 @@ public:
   //Field3D& operator*=(const Field3D& rhs);
   template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
   Field3D& operator*=(const R& rhs) {
-    printf("RUNNING operator*= with CUDA\n");
+    //printf("RUNNING operator*= with CUDA\n");
     if (data.unique()) {
       // Delete existing parallel slices. We don't copy parallel slices, so any
       // that currently exist will be incorrect.
@@ -541,9 +561,9 @@ public:
   /// Division operators
   ///@{
   //Field3D& operator/=(const Field3D& rhs);
-  template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
-  Field3D& operator/=(const R& rhs) {
-    printf("RUNNING operator/= with CUDA\n");
+  template <typename R>
+ std::enable_if_t<is_expr_field3d_v<R>,Field3D&> operator/=(const R& rhs) {
+    //printf("RUNNING operator/= with CUDA\n");
     if (data.unique()) {
       // Delete existing parallel slices. We don't copy parallel slices, so any
       // that currently exist will be incorrect.
@@ -558,7 +578,23 @@ public:
 
     return *this;
   }
-  Field3D& operator/=(const Field2D& rhs);
+  //Field3D& operator/=(const Field2D& rhs);
+  template <typename R>
+std::enable_if_t<is_expr_field2d_v<R>, Field3D&> operator/=(const R& rhs) {
+    //printf("RUNNING operator/= with CUDA\n");
+    if (data.unique()) {
+      // Delete existing parallel slices. We don't copy parallel slices, so any
+      // that currently exist will be incorrect.
+      clearParallelSlices();
+
+      auto BE = (*this) / rhs;
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) / rhs;
+    }
+
+    return *this;
+  }
   Field3D& operator/=(BoutReal rhs);
   ///@}
 
@@ -634,16 +670,17 @@ template <typename L, typename R,
 BinaryExpr<L, R, bout::op::Add> operator+(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
-  std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{(lhs),
-                    (rhs),
-                    bout::op::Add{},
-                    lhs.getMesh(),
-                    lhs.getLocation(),
-                    lhs.getDirections(),
-                    regionID,
-                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
-                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
+  //std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
+  return BinaryExpr<L, R, bout::op::Add>{static_cast<typename L::View>(lhs),
+                                         static_cast<typename R::View>(rhs),
+                                         bout::op::Add{},
+                                         lhs.getMesh(),
+                                         lhs.getLocation(),
+                                         lhs.getDirections(),
+                                         regionID,
+                                         (regionID.has_value()
+                                              ? lhs.getMesh()->getRegion(regionID.value())
+                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
 }
 
 template <typename L, typename R,
@@ -651,33 +688,36 @@ template <typename L, typename R,
 BinaryExpr<L, R, bout::op::Sub> operator-(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
-  std::cout << "RUNNING operator- using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{(lhs),
-                    (rhs),
-                    bout::op::Sub{},
-                    lhs.getMesh(),
-                    lhs.getLocation(),
-                    lhs.getDirections(),
-                    regionID,
-                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
-                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
+  //std::cout << "RUNNING operator- using BinaryExpr with CUDA" << "\n";
+  return BinaryExpr<L, R, bout::op::Sub>{static_cast<typename L::View>(lhs),
+                                         static_cast<typename R::View>(rhs),
+                                         bout::op::Sub{},
+                                         lhs.getMesh(),
+                                         lhs.getLocation(),
+                                         lhs.getDirections(),
+                                         regionID,
+                                         (regionID.has_value()
+                                              ? lhs.getMesh()->getRegion(regionID.value())
+                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
 }
 
-template <typename L, typename R,
-          typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
-BinaryExpr<L, R, bout::op::Mul> operator*(const L& lhs, const R& rhs) {
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<L, R, bout::op::Mul>>
+operator*(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
-  std::cout << "RUNNING operator* using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{(lhs),
-                    (rhs),
-                    bout::op::Mul{},
-                    lhs.getMesh(),
-                    lhs.getLocation(),
-                    lhs.getDirections(),
-                    regionID,
-                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
-                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
+  //std::cout << "RUNNING operator* using BinaryExpr with CUDA" << "\n";
+  return BinaryExpr<L, R, bout::op::Mul>{static_cast<typename L::View>(lhs),
+                                         static_cast<typename R::View>(rhs),
+                                         bout::op::Mul{},
+                                         lhs.getMesh(),
+                                         lhs.getLocation(),
+                                         lhs.getDirections(),
+                                         regionID,
+                                         (regionID.has_value()
+                                              ? lhs.getMesh()->getRegion(regionID.value())
+                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
 }
 
 template <typename L, typename R,
@@ -685,42 +725,84 @@ template <typename L, typename R,
 BinaryExpr<L, R, bout::op::Div> operator/(const L& lhs, const R& rhs) {
   auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
 
-  std::cout << "RUNNING operator/ using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr{(lhs),
-                    (rhs),
-                    bout::op::Div{},
+  //std::cout << "RUNNING operator/ using BinaryExpr with CUDA" << "\n";
+  return BinaryExpr<L, R, bout::op::Div>{static_cast<typename L::View>(lhs),
+                                         static_cast<typename R::View>(rhs),
+                                         bout::op::Div{},
+                                         lhs.getMesh(),
+                                         lhs.getLocation(),
+                                         lhs.getDirections(),
+                                         regionID,
+                                         (regionID.has_value()
+                                              ? lhs.getMesh()->getRegion(regionID.value())
+                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
+}
+
+Field3D operator+(const Field3D& lhs, const Field2D& rhs);
+#if 0
+template <typename L, typename R,
+          std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
+                           BinaryExpr<L, R, bout::op::Add>>>
+BinaryExpr<L, R, bout::op::Add> operator+(const L& lhs, const R& rhs) {
+  //static_assert(always_false<L> || always_false<R>, "Hello");
+  auto regionID = lhs.getRegionID();
+
+  std::cout << "RUNNING Field3D + Field2D using BinaryExpr with CUDA" << "\n";
+  int mesh_nz = lhs.getMesh()->LocalNz;
+
+  return BinaryExpr{static_cast<typename L::View>(lhs),
+                    static_cast<typename R::View>(rhs).setScale(1, mesh_nz),
+                    bout::op::Add{},
                     lhs.getMesh(),
                     lhs.getLocation(),
                     lhs.getDirections(),
                     regionID,
-                    (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
-                                          : lhs.getMesh()->getRegion("RGN_ALL"))};
+                    rhs.getRegion("RGN_ALL")};
 }
-
-Field3D operator+(const Field3D& lhs, const Field2D& rhs);
-//template <typename L, typename R>
-//auto operator+(const L& lhs, const R& rhs)
-//    -> std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
-//                        BinaryExpr<L, R, bout::op::Add>> {
-//  static_assert(always_false<L> || always_false<R>, "Hello");
-//  auto regionID = lhs.getRegionID();
-//
-//  std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
-//  int mesh_nz = lhs.getMesh()->LocalNz;
-//  auto LambdaOp = [mesh_nz]() {
-//  };
-//  return BinaryExpr{(lhs),
-//          (rhs),
-//          bout::op::Add{},
-//          lhs.getMesh(),
-//          lhs.getLocation(),
-//          lhs.getDirections(),
-//          regionID,
-//          rhs.getRegion("RGN_ALL")};
-//}
+#endif
 Field3D operator-(const Field3D& lhs, const Field2D& rhs);
-Field3D operator*(const Field3D& lhs, const Field2D& rhs);
-Field3D operator/(const Field3D& lhs, const Field2D& rhs);
+//Field3D operator*(const Field3D& lhs, const Field2D& rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<L, R, bout::op::Mul>>
+operator*(const L& lhs, const R& rhs) {
+  //static_assert(always_false<L> || always_false<R>, "Hello");
+  auto regionID = lhs.getRegionID();
+
+  //std::cout << "RUNNING Field3D * Field2D using BinaryExpr with CUDA" << "\n";
+  int mesh_nz = lhs.getMesh()->LocalNz;
+
+  return BinaryExpr<L, R, bout::op::Mul>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename R::View>(rhs).setScale(1, mesh_nz),
+      bout::op::Mul{},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      regionID,
+      lhs.getMesh()->getRegion("RGN_ALL")};
+}
+//Field3D operator/(const Field3D& lhs, const Field2D& rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<L, R, bout::op::Div>>
+operator/(const L& lhs, const R& rhs) {
+  //static_assert(always_false<L> || always_false<R>, "Hello");
+  auto regionID = lhs.getRegionID();
+
+  //std::cout << "RUNNING Field3D * Field2D using BinaryExpr with CUDA" << "\n";
+  int mesh_nz = lhs.getMesh()->LocalNz;
+
+  return BinaryExpr<L, R, bout::op::Div>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename R::View>(rhs).setScale(1, mesh_nz),
+      bout::op::Div{},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      regionID,
+      lhs.getMesh()->getRegion("RGN_ALL")};
+}
 
 Field3D operator+(const Field3D& lhs, BoutReal rhs);
 Field3D operator-(const Field3D& lhs, BoutReal rhs);
@@ -851,15 +933,17 @@ struct is_expr_field3d<Field3D> : std::true_type {};
 template <>
 struct is_expr_field2d<Field2D> : std::true_type {};
 
-// Any nested BinaryExpr<L,R,Fun> is an expression iff L is
-//template <typename L, typename R, typename Fun>
-//struct is_expr_field3d<BinaryExpr<L, R, Fun>>
-//    : std::true_type {};
-
 template <typename L, typename R, typename Fun>
 struct is_expr_field3d<BinaryExpr<L, R, Fun>>
     : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value> {};
 
+template <typename L, typename R, typename Fun>
+struct is_expr_field2d<BinaryExpr<L, R, Fun>>
+    : std::integral_constant<bool, is_expr_field2d<std::decay_t<L>>::value> {};
+
+//template <typename L, typename R, typename Fun>
+//struct is_expr_field3d<typename BinaryExpr<L, R, Fun>::View> : is_expr_field3d<L> {};
+
 //template<typename L,typename R,typename Fun>
 //struct is_expr_field3d< typename BinaryExpr<L,R,Fun>::View >
 //  : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value> {};
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index e9c87f242f..d83d1eedd1 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -1,4 +1,6 @@
 #pragma once
+#include "bout/array.hxx"
+#include <unordered_map>
 #ifndef BOUT_FIELDOPS_HXX
 #define BOUT_FIELDOPS_HXX
 
@@ -14,44 +16,96 @@ class Field3D;
 
 namespace bout {
 namespace op {
-  struct Add {
-    template<typename LView, typename RView>
-    __host__ __device__ inline BoutReal operator()(int idx, const LView &L, const RView &R) const {
-      return L(idx) + R(idx);
+struct Assign {
+  int scale = 1;
+  int offset = 0;
+  template <typename Expr>
+  __device__ void operator()(int idx, BoutReal* out, const Expr& expr) const {
+    out[(idx * scale) + offset] = expr.lhs(idx) + expr.rhs(idx);
+  }
+};
+
+struct Add {
+  template <typename LView, typename RView>
+  __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
+                                                 const RView& R) const {
+    return L(idx) + R(idx);
+  }
+  __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
+    return a + b;
+  }
+};
+  struct Sub {
+    template <typename LView, typename RView>
+    __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
+                                                   const RView& R) const {
+      return L(idx) - R(idx);
+    }
+    __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
+      return a - b;
     }
-    __host__ __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a + b; }
   };
-  struct Sub {
-    template<typename LView, typename RView>
-    __host__ __device__ inline BoutReal operator()(int idx, const LView &L, const RView &R) const { return L(idx) - R(idx); }
-    __host__ __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a - b; }
-  };                                                                                                
-  struct Mul {                                                                                      
-    template<typename LView, typename RView>
-    __host__ __device__ inline BoutReal operator()(int idx, const LView &L, const RView &R) const { return L(idx) * R(idx); }
-    __host__ __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a * b; }
-  };                                                                                                
-  struct Div {                                                                                      
-    template<typename LView, typename RView>
-    __host__ __device__ inline BoutReal operator()(int idx, const LView &L, const RView &R) const { return L(idx) / R(idx); }
-    __host__ __device__ inline BoutReal operator()(BoutReal a, BoutReal b) const { return a / b; }
+  struct Mul {
+    template <typename LView, typename RView>
+    __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
+                                                   const RView& R) const {
+      return L(idx) * R(idx);
+    }
+    __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
+      return a * b;
+    }
+  };
+  struct Div {
+    template <typename LView, typename RView>
+    __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
+                                                   const RView& R) const {
+      return L(idx) / R(idx);
+    }
+    __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
+      return a / b;
+    }
   };
 };
 };
 
 template <typename Expr>
-__global__ static void evaluatorExpr(BoutReal* out, const Expr& expr) {
+__global__ __launch_bounds__(256) static void evaluatorExpr(BoutReal* out,
+                                                            const Expr expr) {
   int tid = threadIdx.x + blockIdx.x * blockDim.x;
-  int stride = blockDim.x * gridDim.x;
-  for (int i = tid; i < expr.size(); i += stride) {
-    out[expr.regionIdx(i)] = expr(expr.regionIdx(i)); // single‐pass fusion
+  if (tid >= expr.size()) {
+    return; // Out of bounds
   }
+  int idx = expr.regionIdx(tid);
+  out[idx] = expr(idx); // single‐pass fusion
+  //int stride = blockDim.x * gridDim.x;
+  //for (int i = tid, e = expr.size(); i < e; i += stride) {
+  //  int idx = expr.regionIdx(i);
+  //  out[idx] = expr(idx); // single‐pass fusion
+  //}
 }
 
+template <typename Result, typename Expr>
+__global__ __launch_bounds__(256) static void evaluatorExprWithResult(Result res,
+                                                                      const Expr expr) {
+  int tid = threadIdx.x + blockIdx.x * blockDim.x;
+  if (tid >= expr.size()) {
+    return; // Out of bounds
+  }
+  int idx = expr.regionIdx(tid);
+  res[idx] = expr(idx); // single‐pass fusion
+  //res(idx, expr(idx)); // single‐pass fusion
+  //res(idx) = expr(idx); // single‐pass fusion
+  //int stride = blockDim.x * gridDim.x;
+  //for (int i = tid, e = expr.size(); i < e; i += stride) {
+  //  int idx = expr.regionIdx(i);
+  //  out[idx] = expr(idx); // single‐pass fusion
+  //}
+}
+
+inline std::unordered_map<void*, Array<int>> regionIndicesCache;
+
 template <typename L, typename R, typename Func>
 struct BinaryExpr {
-  const L &LHS;
-  const R &RHS;
   typename L::View lhs;
   typename R::View rhs;
   Array<int> indices;
@@ -63,16 +117,31 @@ struct BinaryExpr {
   std::optional<size_t> regionID;
 
   template <typename IndType>
-  BinaryExpr(const L &lhs, const R &rhs, Func f, Mesh* mesh, CELL_LOC location,
-             DirectionTypes directions, std::optional<size_t> regionID,
+  BinaryExpr(const typename L::View& lhs, const typename R::View& rhs, Func f, Mesh* mesh,
+             CELL_LOC location, DirectionTypes directions, std::optional<size_t> regionID,
              const Region<IndType>& region)
-      : LHS(lhs), RHS(rhs), lhs(static_cast<typename L::View>(lhs)), rhs(static_cast<typename R::View>(rhs)),
-        f(f), mesh(mesh), location(location), directions(directions), regionID(regionID),
-        indices(region.getIndices().size()) {
+      //: lhs(static_cast<typename L::View>(lhs)), rhs(static_cast<typename R::View>(rhs)),
+      : lhs(lhs), rhs(rhs), f(f), mesh(mesh), location(location), directions(directions),
+        regionID(regionID), indices(region.getIndices().size()) {
     // Copy the region indices into the managed array
     for (int i = 0; i < indices.size(); ++i) {
       indices[i] = region.getIndices()[i].ind;
     }
+    //if (regionIndicesCache.find(static_cast<void*>(const_cast<Region<IndType>*>(&region)))
+    //    != regionIndicesCache.end()) {
+    //  // If we have already computed the indices for this region, use them
+    //  indices =
+    //      regionIndicesCache[static_cast<void*>(const_cast<Region<IndType>*>(&region))];
+    //} else {
+    //  // Otherwise, compute the indices and store them in the cache
+    //  indices = Array<int>(region.getIndices().size());
+    //  // Copy the region indices into the managed array
+    //  for (int i = 0; i < indices.size(); ++i) {
+    //    indices[i] = region.getIndices()[i].ind;
+    //  }
+    //  regionIndicesCache[static_cast<void*>(const_cast<Region<IndType>*>(&region))] =
+    //      indices;
+    //}
   }
 
   inline int size() const { return indices.size(); }
@@ -87,10 +156,21 @@ struct BinaryExpr {
     const int* indices;
     int num_indices;
     Func f;
+    int scale = 1;
+    int offset = 0;
 
-    __device__ inline int size() const { return num_indices; }
-    __device__ inline int regionIdx(int idx) const { return indices[idx]; }
-    __device__ inline BoutReal operator()(int idx) const {
+    View& setScale(int s) {
+      scale = s;
+      return *this;
+    }
+    View& setOffset(int o) {
+      offset = o;
+      return *this;
+    }
+
+    __device__ __forceinline__ int size() const { return num_indices; }
+    __device__ __forceinline__ int regionIdx(int idx) const { return indices[idx]; }
+    __device__ __forceinline__ BoutReal operator()(int idx) const {
       return f(idx, lhs, rhs); // single‐pass fusion
       //return f(lhs(idx), rhs(idx)); // single‐pass fusion
     }
@@ -109,6 +189,17 @@ struct BinaryExpr {
     //}
   }
 
+  template <typename Result>
+  void evaluateWithResult(const Result& res) const {
+    constexpr int THREADS = 256;
+    int blocks = (size() + THREADS - 1) / THREADS;
+    evaluatorExprWithResult<<<blocks, THREADS>>>(res, static_cast<View>(*this));
+    cudaDeviceSynchronize();
+    //for(int i=0; i<size(); ++i) {
+    //  data[regionIdx(i)] = f(i, lhs, rhs); // single‐pass fusion
+    //}
+  }
+
   Mesh* getMesh() const { return mesh; }
   CELL_LOC getLocation() const { return location; }
   DirectionTypes getDirections() const { return directions; }
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index c35ae2e866..691e450b0c 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -6,195 +6,10 @@
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 
-// Provide the C++ wrapper for multiplication of Field3D and Field3D
-Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ operator to update Field3D by multiplication with Field3D
-#if 0
-Field3D& Field3D::operator*=(const Field3D& rhs) {
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) * rhs;
-  }
-  return *this;
-}
-#endif
-
-// Provide the C++ wrapper for division of Field3D and Field3D
-Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] / rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ operator to update Field3D by division with Field3D
-#if 0
-Field3D& Field3D::operator/=(const Field3D& rhs) {
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) / rhs;
-  }
-  return *this;
-}
-#endif
-
-// Provide the C++ wrapper for addition of Field3D and Field3D
-Field3D operator+(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-
-#if 0
-// Provide the C++ operator to update Field3D by addition with Field3D
-Field3D& Field3D::operator+=(const Field3D& rhs) {
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) + rhs;
-  }
-  return *this;
-}
-#endif
-
-// Provide the C++ wrapper for subtraction of Field3D and Field3D
-Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ operator to update Field3D by subtraction with Field3D
-#if 0
-Field3D& Field3D::operator-=(const Field3D& rhs) {
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { 
-      (*this)[index] -= rhs[index]; 
-      printf("[golden] val[%d] %lf\n", index, (*this)[index]);
-    }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) - rhs;
-  }
-  return *this;
-}
-#endif
-
 // Provide the C++ wrapper for multiplication of Field3D and Field2D
+#if 0
 Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator "<< __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(lhs)};
@@ -215,9 +30,11 @@ Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field3D by multiplication with Field2D
 Field3D& Field3D::operator*=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -245,8 +62,10 @@ Field3D& Field3D::operator*=(const Field2D& rhs) {
   return *this;
 }
 
+#if 1
 // Provide the C++ wrapper for division of Field3D and Field2D
 Field3D operator/(const Field3D& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator "<< __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(lhs)};
@@ -268,9 +87,12 @@ Field3D operator/(const Field3D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
+#if 0
 // Provide the C++ operator to update Field3D by division with Field2D
 Field3D& Field3D::operator/=(const Field2D& rhs) {
+  std::cout << "RUNNING operator "<< __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -298,9 +120,11 @@ Field3D& Field3D::operator/=(const Field2D& rhs) {
   }
   return *this;
 }
+#endif
 
 // Provide the C++ wrapper for addition of Field3D and Field2D
 Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(lhs)};
@@ -324,6 +148,7 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update Field3D by addition with Field2D
 Field3D& Field3D::operator+=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -353,6 +178,7 @@ Field3D& Field3D::operator+=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for subtraction of Field3D and Field2D
 Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(lhs)};
@@ -376,6 +202,7 @@ Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update Field3D by subtraction with Field2D
 Field3D& Field3D::operator-=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -405,6 +232,7 @@ Field3D& Field3D::operator-=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for multiplication of Field3D and FieldPerp
 FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(rhs)};
@@ -425,6 +253,7 @@ FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for division of Field3D and FieldPerp
 FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(rhs)};
@@ -445,6 +274,7 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for addition of Field3D and FieldPerp
 FieldPerp operator+(const Field3D& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(rhs)};
@@ -465,6 +295,7 @@ FieldPerp operator+(const Field3D& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for subtraction of Field3D and FieldPerp
 FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(rhs)};
@@ -485,6 +316,7 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for multiplication of Field3D and BoutReal
 Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field3D result{emptyFrom(lhs)};
   checkData(lhs);
@@ -502,6 +334,7 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update Field3D by multiplication with BoutReal
 Field3D& Field3D::operator*=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -525,6 +358,7 @@ Field3D& Field3D::operator*=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for division of Field3D and BoutReal
 Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field3D result{emptyFrom(lhs)};
   checkData(lhs);
@@ -543,6 +377,7 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update Field3D by division with BoutReal
 Field3D& Field3D::operator/=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -567,6 +402,7 @@ Field3D& Field3D::operator/=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for addition of Field3D and BoutReal
 Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field3D result{emptyFrom(lhs)};
   checkData(lhs);
@@ -584,6 +420,7 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update Field3D by addition with BoutReal
 Field3D& Field3D::operator+=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -607,6 +444,7 @@ Field3D& Field3D::operator+=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for subtraction of Field3D and BoutReal
 Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field3D result{emptyFrom(lhs)};
   checkData(lhs);
@@ -624,6 +462,7 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update Field3D by subtraction with BoutReal
 Field3D& Field3D::operator-=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -647,6 +486,7 @@ Field3D& Field3D::operator-=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for multiplication of Field2D and Field3D
 Field3D operator*(const Field2D& lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(rhs)};
@@ -670,6 +510,7 @@ Field3D operator*(const Field2D& lhs, const Field3D& rhs) {
 
 // Provide the C++ wrapper for division of Field2D and Field3D
 Field3D operator/(const Field2D& lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(rhs)};
@@ -693,6 +534,7 @@ Field3D operator/(const Field2D& lhs, const Field3D& rhs) {
 
 // Provide the C++ wrapper for addition of Field2D and Field3D
 Field3D operator+(const Field2D& lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(rhs)};
@@ -716,6 +558,7 @@ Field3D operator+(const Field2D& lhs, const Field3D& rhs) {
 
 // Provide the C++ wrapper for subtraction of Field2D and Field3D
 Field3D operator-(const Field2D& lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field3D result{emptyFrom(rhs)};
@@ -739,6 +582,7 @@ Field3D operator-(const Field2D& lhs, const Field3D& rhs) {
 
 // Provide the C++ wrapper for multiplication of Field2D and Field2D
 Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field2D result{emptyFrom(lhs)};
@@ -755,6 +599,7 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update Field2D by multiplication with Field2D
 Field2D& Field2D::operator*=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -775,6 +620,7 @@ Field2D& Field2D::operator*=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for division of Field2D and Field2D
 Field2D operator/(const Field2D& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field2D result{emptyFrom(lhs)};
@@ -791,6 +637,7 @@ Field2D operator/(const Field2D& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update Field2D by division with Field2D
 Field2D& Field2D::operator/=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -811,6 +658,7 @@ Field2D& Field2D::operator/=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for addition of Field2D and Field2D
 Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field2D result{emptyFrom(lhs)};
@@ -827,6 +675,7 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update Field2D by addition with Field2D
 Field2D& Field2D::operator+=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -847,6 +696,7 @@ Field2D& Field2D::operator+=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for subtraction of Field2D and Field2D
 Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   Field2D result{emptyFrom(lhs)};
@@ -863,6 +713,7 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update Field2D by subtraction with Field2D
 Field2D& Field2D::operator-=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -883,6 +734,7 @@ Field2D& Field2D::operator-=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for multiplication of Field2D and FieldPerp
 FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(rhs)};
@@ -903,6 +755,7 @@ FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for division of Field2D and FieldPerp
 FieldPerp operator/(const Field2D& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(rhs)};
@@ -923,6 +776,7 @@ FieldPerp operator/(const Field2D& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for addition of Field2D and FieldPerp
 FieldPerp operator+(const Field2D& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(rhs)};
@@ -943,6 +797,7 @@ FieldPerp operator+(const Field2D& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for subtraction of Field2D and FieldPerp
 FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(rhs)};
@@ -963,6 +818,7 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for multiplication of Field2D and BoutReal
 Field2D operator*(const Field2D& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field2D result{emptyFrom(lhs)};
   checkData(lhs);
@@ -978,6 +834,7 @@ Field2D operator*(const Field2D& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update Field2D by multiplication with BoutReal
 Field2D& Field2D::operator*=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -997,6 +854,7 @@ Field2D& Field2D::operator*=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for division of Field2D and BoutReal
 Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field2D result{emptyFrom(lhs)};
   checkData(lhs);
@@ -1013,6 +871,7 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update Field2D by division with BoutReal
 Field2D& Field2D::operator/=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1033,6 +892,7 @@ Field2D& Field2D::operator/=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for addition of Field2D and BoutReal
 Field2D operator+(const Field2D& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field2D result{emptyFrom(lhs)};
   checkData(lhs);
@@ -1048,6 +908,7 @@ Field2D operator+(const Field2D& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update Field2D by addition with BoutReal
 Field2D& Field2D::operator+=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1067,6 +928,7 @@ Field2D& Field2D::operator+=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for subtraction of Field2D and BoutReal
 Field2D operator-(const Field2D& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field2D result{emptyFrom(lhs)};
   checkData(lhs);
@@ -1082,6 +944,7 @@ Field2D operator-(const Field2D& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update Field2D by subtraction with BoutReal
 Field2D& Field2D::operator-=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1101,6 +964,7 @@ Field2D& Field2D::operator-=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for multiplication of FieldPerp and Field3D
 FieldPerp operator*(const FieldPerp& lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1121,6 +985,7 @@ FieldPerp operator*(const FieldPerp& lhs, const Field3D& rhs) {
 
 // Provide the C++ operator to update FieldPerp by multiplication with Field3D
 FieldPerp& FieldPerp::operator*=(const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1147,6 +1012,7 @@ FieldPerp& FieldPerp::operator*=(const Field3D& rhs) {
 
 // Provide the C++ wrapper for division of FieldPerp and Field3D
 FieldPerp operator/(const FieldPerp& lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1167,6 +1033,7 @@ FieldPerp operator/(const FieldPerp& lhs, const Field3D& rhs) {
 
 // Provide the C++ operator to update FieldPerp by division with Field3D
 FieldPerp& FieldPerp::operator/=(const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1193,6 +1060,7 @@ FieldPerp& FieldPerp::operator/=(const Field3D& rhs) {
 
 // Provide the C++ wrapper for addition of FieldPerp and Field3D
 FieldPerp operator+(const FieldPerp& lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1213,6 +1081,7 @@ FieldPerp operator+(const FieldPerp& lhs, const Field3D& rhs) {
 
 // Provide the C++ operator to update FieldPerp by addition with Field3D
 FieldPerp& FieldPerp::operator+=(const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1239,6 +1108,7 @@ FieldPerp& FieldPerp::operator+=(const Field3D& rhs) {
 
 // Provide the C++ wrapper for subtraction of FieldPerp and Field3D
 FieldPerp operator-(const FieldPerp& lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1259,6 +1129,7 @@ FieldPerp operator-(const FieldPerp& lhs, const Field3D& rhs) {
 
 // Provide the C++ operator to update FieldPerp by subtraction with Field3D
 FieldPerp& FieldPerp::operator-=(const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1285,6 +1156,7 @@ FieldPerp& FieldPerp::operator-=(const Field3D& rhs) {
 
 // Provide the C++ wrapper for multiplication of FieldPerp and Field2D
 FieldPerp operator*(const FieldPerp& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1305,6 +1177,7 @@ FieldPerp operator*(const FieldPerp& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update FieldPerp by multiplication with Field2D
 FieldPerp& FieldPerp::operator*=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1331,6 +1204,7 @@ FieldPerp& FieldPerp::operator*=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for division of FieldPerp and Field2D
 FieldPerp operator/(const FieldPerp& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1351,6 +1225,7 @@ FieldPerp operator/(const FieldPerp& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update FieldPerp by division with Field2D
 FieldPerp& FieldPerp::operator/=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1377,6 +1252,7 @@ FieldPerp& FieldPerp::operator/=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for addition of FieldPerp and Field2D
 FieldPerp operator+(const FieldPerp& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1397,6 +1273,7 @@ FieldPerp operator+(const FieldPerp& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update FieldPerp by addition with Field2D
 FieldPerp& FieldPerp::operator+=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1423,6 +1300,7 @@ FieldPerp& FieldPerp::operator+=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for subtraction of FieldPerp and Field2D
 FieldPerp operator-(const FieldPerp& lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1443,6 +1321,7 @@ FieldPerp operator-(const FieldPerp& lhs, const Field2D& rhs) {
 
 // Provide the C++ operator to update FieldPerp by subtraction with Field2D
 FieldPerp& FieldPerp::operator-=(const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1469,6 +1348,7 @@ FieldPerp& FieldPerp::operator-=(const Field2D& rhs) {
 
 // Provide the C++ wrapper for multiplication of FieldPerp and FieldPerp
 FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1485,6 +1365,7 @@ FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ operator to update FieldPerp by multiplication with FieldPerp
 FieldPerp& FieldPerp::operator*=(const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1505,6 +1386,7 @@ FieldPerp& FieldPerp::operator*=(const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for division of FieldPerp and FieldPerp
 FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1521,6 +1403,7 @@ FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ operator to update FieldPerp by division with FieldPerp
 FieldPerp& FieldPerp::operator/=(const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1541,6 +1424,7 @@ FieldPerp& FieldPerp::operator/=(const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for addition of FieldPerp and FieldPerp
 FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1557,6 +1441,7 @@ FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ operator to update FieldPerp by addition with FieldPerp
 FieldPerp& FieldPerp::operator+=(const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1577,6 +1462,7 @@ FieldPerp& FieldPerp::operator+=(const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for subtraction of FieldPerp and FieldPerp
 FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
 
   FieldPerp result{emptyFrom(lhs)};
@@ -1593,6 +1479,7 @@ FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs) {
 
 // Provide the C++ operator to update FieldPerp by subtraction with FieldPerp
 FieldPerp& FieldPerp::operator-=(const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1613,6 +1500,7 @@ FieldPerp& FieldPerp::operator-=(const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for multiplication of FieldPerp and BoutReal
 FieldPerp operator*(const FieldPerp& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   FieldPerp result{emptyFrom(lhs)};
   checkData(lhs);
@@ -1628,6 +1516,7 @@ FieldPerp operator*(const FieldPerp& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update FieldPerp by multiplication with BoutReal
 FieldPerp& FieldPerp::operator*=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1647,6 +1536,7 @@ FieldPerp& FieldPerp::operator*=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for division of FieldPerp and BoutReal
 FieldPerp operator/(const FieldPerp& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   FieldPerp result{emptyFrom(lhs)};
   checkData(lhs);
@@ -1663,6 +1553,7 @@ FieldPerp operator/(const FieldPerp& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update FieldPerp by division with BoutReal
 FieldPerp& FieldPerp::operator/=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1682,6 +1573,7 @@ FieldPerp& FieldPerp::operator/=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for addition of FieldPerp and BoutReal
 FieldPerp operator+(const FieldPerp& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   FieldPerp result{emptyFrom(lhs)};
   checkData(lhs);
@@ -1697,6 +1589,7 @@ FieldPerp operator+(const FieldPerp& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update FieldPerp by addition with BoutReal
 FieldPerp& FieldPerp::operator+=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1716,6 +1609,7 @@ FieldPerp& FieldPerp::operator+=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for subtraction of FieldPerp and BoutReal
 FieldPerp operator-(const FieldPerp& lhs, const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   FieldPerp result{emptyFrom(lhs)};
   checkData(lhs);
@@ -1731,6 +1625,7 @@ FieldPerp operator-(const FieldPerp& lhs, const BoutReal rhs) {
 
 // Provide the C++ operator to update FieldPerp by subtraction with BoutReal
 FieldPerp& FieldPerp::operator-=(const BoutReal rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
   if (data.unique()) {
@@ -1750,6 +1645,7 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) {
 
 // Provide the C++ wrapper for multiplication of BoutReal and Field3D
 Field3D operator*(const BoutReal lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field3D result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1767,6 +1663,7 @@ Field3D operator*(const BoutReal lhs, const Field3D& rhs) {
 
 // Provide the C++ wrapper for division of BoutReal and Field3D
 Field3D operator/(const BoutReal lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field3D result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1784,6 +1681,7 @@ Field3D operator/(const BoutReal lhs, const Field3D& rhs) {
 
 // Provide the C++ wrapper for addition of BoutReal and Field3D
 Field3D operator+(const BoutReal lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field3D result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1801,6 +1699,7 @@ Field3D operator+(const BoutReal lhs, const Field3D& rhs) {
 
 // Provide the C++ wrapper for subtraction of BoutReal and Field3D
 Field3D operator-(const BoutReal lhs, const Field3D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field3D result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1818,6 +1717,7 @@ Field3D operator-(const BoutReal lhs, const Field3D& rhs) {
 
 // Provide the C++ wrapper for multiplication of BoutReal and Field2D
 Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field2D result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1833,6 +1733,7 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
 
 // Provide the C++ wrapper for division of BoutReal and Field2D
 Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field2D result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1848,6 +1749,7 @@ Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
 
 // Provide the C++ wrapper for addition of BoutReal and Field2D
 Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field2D result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1863,6 +1765,7 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
 
 // Provide the C++ wrapper for subtraction of BoutReal and Field2D
 Field2D operator-(const BoutReal lhs, const Field2D& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   Field2D result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1878,6 +1781,7 @@ Field2D operator-(const BoutReal lhs, const Field2D& rhs) {
 
 // Provide the C++ wrapper for multiplication of BoutReal and FieldPerp
 FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   FieldPerp result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1893,6 +1797,7 @@ FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for division of BoutReal and FieldPerp
 FieldPerp operator/(const BoutReal lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   FieldPerp result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1908,6 +1813,7 @@ FieldPerp operator/(const BoutReal lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for addition of BoutReal and FieldPerp
 FieldPerp operator+(const BoutReal lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   FieldPerp result{emptyFrom(rhs)};
   checkData(lhs);
@@ -1923,6 +1829,7 @@ FieldPerp operator+(const BoutReal lhs, const FieldPerp& rhs) {
 
 // Provide the C++ wrapper for subtraction of BoutReal and FieldPerp
 FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) {
+  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
   FieldPerp result{emptyFrom(rhs)};
   checkData(lhs);

From eeb3426aebeed2cb7735e2605c36fd977930eb17 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 30 May 2025 11:35:00 -0700
Subject: [PATCH 0180/1827] Options: Add Matrix<int> and Tensor<int>

Enable Options to store index arrays
---
 include/bout/options.hxx | 21 ++++++++------
 include/bout/utils.hxx   | 12 ++++----
 src/sys/options.cxx      | 63 ++++++++++++++++++++++++++++++++++++++--
 3 files changed, 78 insertions(+), 18 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index d6f0e460e2..6ee9beeb6d 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -12,7 +12,7 @@
 * options and allows access to all sub-sections
 *
 **************************************************************************
-* Copyright 2010-2024 BOUT++ contributors
+* Copyright 2010-2025 BOUT++ contributors
 *
 * Contact: Ben Dudson, dudson2@llnl.gov
 *
@@ -201,9 +201,9 @@ public:
   }
 
   /// The type used to store values
-  using ValueType =
-      bout::utils::variant<bool, int, BoutReal, std::string, Field2D, Field3D, FieldPerp,
-                           Array<BoutReal>, Matrix<BoutReal>, Tensor<BoutReal>>;
+  using ValueType = bout::utils::variant<bool, int, BoutReal, std::string, Field2D,
+                                         Field3D, FieldPerp, Array<BoutReal>, Array<int>,
+                                         Matrix<BoutReal>, Matrix<int>, Tensor<BoutReal>, Tensor<int>>;
 
   /// A tree representation with leaves containing ValueType.
   /// Used to construct Options from initializer lists.
@@ -271,11 +271,6 @@ public:
   /// Free all memory
   static void cleanup();
 
-  /// The type used to store values
-  using ValueType = bout::utils::variant<bool, int, BoutReal, std::string, Field2D,
-                                         Field3D, FieldPerp, Array<BoutReal>, Array<int>,
-                                         Matrix<BoutReal>, Tensor<BoutReal>>;
-
   /// The type used to store attributes
   /// Extends the variant class so that cast operator can be implemented
   /// and assignment operator overloaded
@@ -964,7 +959,11 @@ Options& Options::assign<>(Array<int> val, std::string source);
 template <>
 Options& Options::assign<>(Matrix<BoutReal> val, std::string source);
 template <>
+Options& Options::assign<>(Matrix<int> val, std::string source);
+template <>
 Options& Options::assign<>(Tensor<BoutReal> val, std::string source);
+template <>
+Options& Options::assign<>(Tensor<int> val, std::string source);
 
 /// Specialised similar comparison methods
 template <>
@@ -994,7 +993,11 @@ Array<int> Options::as<Array<int>>(const Array<int>& similar_to) const;
 template <>
 Matrix<BoutReal> Options::as<Matrix<BoutReal>>(const Matrix<BoutReal>& similar_to) const;
 template <>
+Matrix<int> Options::as<Matrix<int>>(const Matrix<int>& similar_to) const;
+template <>
 Tensor<BoutReal> Options::as<Tensor<BoutReal>>(const Tensor<BoutReal>& similar_to) const;
+template <>
+Tensor<int> Options::as<Tensor<int>>(const Tensor<int>& similar_to) const;
 
 /// Convert \p value to string
 std::string toString(const Options& value);
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 343631691c..d933129ea7 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -5,9 +5,9 @@
  * simple but common calculations
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2025 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  * 
  * This file is part of BOUT++.
  *
@@ -523,13 +523,13 @@ inline std::string toString(const Array<T>& UNUSED(val)) {
   return "<Array>";
 }
 
-template <>
-inline std::string toString<>(const Matrix<BoutReal>& UNUSED(val)) {
+template <typename T>
+inline std::string toString(const Matrix<T>& UNUSED(val)) {
   return "<Matrix>";
 }
 
-template <>
-inline std::string toString<>(const Tensor<BoutReal>& UNUSED(val)) {
+template <typename T>
+inline std::string toString(const Tensor<T>& UNUSED(val)) {
   return "<Tensor>";
 }
 
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 027724eba6..951a46aca4 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -343,10 +343,20 @@ Options& Options::assign<>(Matrix<BoutReal> val, std::string source) {
   return *this;
 }
 template <>
+Options& Options::assign<>(Matrix<int> val, std::string source) {
+  _set_no_check(std::move(val), std::move(source));
+  return *this;
+}
+template <>
 Options& Options::assign<>(Tensor<BoutReal> val, std::string source) {
   _set_no_check(std::move(val), std::move(source));
   return *this;
 }
+template <>
+Options& Options::assign<>(Tensor<int> val, std::string source) {
+  _set_no_check(std::move(val), std::move(source));
+  return *this;
+}
 
 namespace {
 /// Use FieldFactory to evaluate expression
@@ -814,6 +824,28 @@ Matrix<BoutReal> Options::as<Matrix<BoutReal>>(const Matrix<BoutReal>& similar_t
   return result;
 }
 
+template <>
+Matrix<int> Options::as<Matrix<int>>(const Matrix<int>& similar_to) const {
+  if (is_section) {
+    throw BoutException(_("Option {:s} has no value"), full_name);
+  }
+
+  auto result = bout::utils::visit(
+      ConvertContainer<Matrix<int>>{
+          fmt::format(
+              _("Value for option {:s} cannot be converted to an Matrix<int>"),
+              full_name),
+          similar_to},
+      value);
+
+  // Mark this option as used
+  value_used = true;
+
+  printNameValueSourceLine(*this, "Matrix<int>");
+
+  return result;
+}
+
 template <>
 Tensor<BoutReal> Options::as<Tensor<BoutReal>>(const Tensor<BoutReal>& similar_to) const {
   if (is_section) {
@@ -836,6 +868,28 @@ Tensor<BoutReal> Options::as<Tensor<BoutReal>>(const Tensor<BoutReal>& similar_t
   return result;
 }
 
+template <>
+Tensor<int> Options::as<Tensor<int>>(const Tensor<int>& similar_to) const {
+  if (is_section) {
+    throw BoutException(_("Option {:s} has no value"), full_name);
+  }
+
+  auto result = bout::utils::visit(
+      ConvertContainer<Tensor<int>>{
+          fmt::format(
+              _("Value for option {:s} cannot be converted to an Tensor<int>"),
+              full_name),
+          similar_to},
+      value);
+
+  // Mark this option as used
+  value_used = true;
+
+  printNameValueSourceLine(*this, "Tensor<int>");
+
+  return result;
+}
+
 // Note: This is defined here rather than in the header
 // to avoid using as<string> before specialising it.
 bool Options::operator==(const char* other) const {
@@ -977,12 +1031,15 @@ struct GetDimensions {
   std::vector<int> operator()([[maybe_unused]] int value) { return {1}; }
   std::vector<int> operator()([[maybe_unused]] BoutReal value) { return {1}; }
   std::vector<int> operator()([[maybe_unused]] const std::string& value) { return {1}; }
-  std::vector<int> operator()(const Array<BoutReal>& array) { return {array.size()}; }
-  std::vector<int> operator()(const Matrix<BoutReal>& array) {
+  template <typename T>
+  std::vector<int> operator()(const Array<T>& array) { return {array.size()}; }
+  template <typename T>
+  std::vector<int> operator()(const Matrix<T>& array) {
     const auto shape = array.shape();
     return {std::get<0>(shape), std::get<1>(shape)};
   }
-  std::vector<int> operator()(const Tensor<BoutReal>& array) {
+  template <typename T>
+  std::vector<int> operator()(const Tensor<T>& array) {
     const auto shape = array.shape();
     return {std::get<0>(shape), std::get<1>(shape), std::get<2>(shape)};
   }

From 979cce8dce3c46f580f6ca11b929034579b120dd Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Fri, 30 May 2025 18:55:28 +0000
Subject: [PATCH 0181/1827] Apply black changes

---
 tests/integrated/test_suite | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite
index 307a8d84b3..77ad7882c4 100755
--- a/tests/integrated/test_suite
+++ b/tests/integrated/test_suite
@@ -188,7 +188,7 @@ class Test(threading.Thread):
                 self.output += "\n(It is likely that a timeout occured)"
             else:
                 # ❌ Failed
-                print("\u274C", end="")  # No newline
+                print("\u274c", end="")  # No newline
             print(" %7.3f s" % (time.time() - self.local.start_time), flush=True)
 
     def _cost(self):

From 4d64ad2bbbd7bb1f717cf27b91cb85105dd6723d Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 30 May 2025 17:37:58 -0700
Subject: [PATCH 0182/1827] More operators

- Working version
---
 .../elm-pb-outerloop/elm_pb_outerloop.cxx     |   5 +-
 include/bout/assert.hxx                       |   1 +
 include/bout/bout_types.hxx                   |  11 ++
 include/bout/field2d.hxx                      | 114 ++++++++++++++++--
 include/bout/field3d.hxx                      |  53 ++++----
 include/bout/fieldops.hxx                     |  47 ++++++--
 include/bout/interpolation.hxx                |  16 ++-
 include/bout/utils.hxx                        |   4 +-
 src/field/field2d.cxx                         |   3 +-
 src/field/generated_fieldops.cxx              |  14 ++-
 src/field/vecops.cxx                          |   2 +-
 .../laplace/impls/naulin/naulin_laplace.cxx   |   3 +-
 src/mesh/coordinates.cxx                      |  32 ++---
 src/sys/derivs.cxx                            |   4 +-
 14 files changed, 235 insertions(+), 74 deletions(-)

diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index 8e84901806..d985c3ef9d 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -1793,7 +1793,7 @@ class ELMpb : public PhysicsModel {
       // Calculate coefficient.
 
       hyper_mu_x = hyperviscos * metric->g_11 * SQ(metric->dx)
-                   * abs(metric->g11 * D2DX2(U)) / (abs(U) + 1e-3);
+                   * abs(Field3D{metric->g11 * D2DX2(U)}) / (abs(U) + 1e-3);
       hyper_mu_x.applyBoundary("dirichlet"); // Set to zero on all boundaries
 
       ddt(U) += hyper_mu_x * metric->g11 * D2DX2(U);
@@ -1840,7 +1840,8 @@ class ELMpb : public PhysicsModel {
       ddt(U) -= 0.5 * Upara2 * bracket(Pi0, Dperp2Phi, bm_exb) / B0;
       Field3D B0phi = B0 * phi;
       mesh->communicate(B0phi);
-      Field3D B0phi0 = B0 * phi0;
+      Field2D res = B0 * phi0;
+      Field3D B0phi0 = res;
       mesh->communicate(B0phi0);
       ddt(U) += 0.5 * Upara2 * bracket(B0phi, Dperp2Pi0, bm_exb) / B0;
       ddt(U) += 0.5 * Upara2 * bracket(B0phi0, Dperp2Pi, bm_exb) / B0;
diff --git a/include/bout/assert.hxx b/include/bout/assert.hxx
index 653c44ed42..2909cfc3c3 100644
--- a/include/bout/assert.hxx
+++ b/include/bout/assert.hxx
@@ -38,6 +38,7 @@
 #if CHECKLEVEL >= 1
 #define ASSERT1(condition)                                                               \
   if (!(condition)) {                                                                    \
+    abort();                                                                             \
     throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \
                         #condition);                                                     \
   }
diff --git a/include/bout/bout_types.hxx b/include/bout/bout_types.hxx
index c1f06fca7c..b2f38b61aa 100644
--- a/include/bout/bout_types.hxx
+++ b/include/bout/bout_types.hxx
@@ -140,4 +140,15 @@ struct enumWrapper {
 /// Boundary condition function
 using FuncPtr = BoutReal (*)(BoutReal t, BoutReal x, BoutReal y, BoutReal z);
 
+template<typename T>
+struct Constant {
+  T val;
+  struct View {
+    T v;
+   View(T v) : v(v) {}
+    __device__ T operator()(int) const { return v; }
+  };
+  operator View() const { return {val}; }
+};
+
 #endif // BOUT_TYPES_H
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index db2ce194f8..9d9948296e 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -38,6 +38,8 @@ class Field2D;
 #include "bout/region.hxx"
 #include "bout/unused.hxx"
 
+#include "bout/fieldops.hxx"
+
 #if BOUT_HAS_RAJA
 #include "RAJA/RAJA.hpp" // using RAJA lib
 #endif
@@ -45,6 +47,16 @@ class Field2D;
 class Field3D;
 class Mesh;
 
+//template <typename T>
+//struct is_expr_field2d : std::false_type {};
+
+//template <typename T>
+//inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::value;
+
+template <typename L, typename R, typename Fun>
+struct is_expr_field2d<BinaryExpr<L, R, Fun>>
+    : std::integral_constant<bool, is_expr_field2d<std::decay_t<L>>::value && is_expr_field2d_v<std::decay_t<R>>> {};
+
 /*!
  * \brief 2D X-Y scalar fields
  *
@@ -91,6 +103,14 @@ public:
           DirectionTypes directions_in = {YDirectionType::Standard,
                                           ZDirectionType::Average});
 
+  template <typename L, typename R, typename Func,
+            typename = std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>>>
+  Field2D(const BinaryExpr<L, R, Func>& expr) {
+    Array<BoutReal> data{expr.size()};
+    expr.evaluate(&data[0]);
+    *this = std::move(Field2D{std::move(data), expr.getMesh(), expr.getLocation(),
+                              expr.getDirections()});
+  }
   /*!
    * Destructor
    */
@@ -166,6 +186,14 @@ public:
    */
   Field2D& operator=(BoutReal rhs);
 
+  template <typename L, typename R, typename Func>
+  std::enable_if_t<is_expr_field2d_v<L>, Field2D&>
+  operator=(BinaryExpr<L, R, Func>& expr) {
+    std::cout << "RUNNING Field2D operator= with CUDA\n";
+    expr.evaluate(&data[0]);
+    return *this;
+  }
+
   /////////////////////////////////////////////////////////
   // Data access
 
@@ -310,30 +338,90 @@ private:
 
 // Non-member overloaded operators
 
-Field2D operator+(const Field2D& lhs, const Field2D& rhs);
-Field2D operator-(const Field2D& lhs, const Field2D& rhs);
-Field2D operator*(const Field2D& lhs, const Field2D& rhs);
-#if 0
-template <typename L, typename R,
-          typename = std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>>>
-BinaryExpr<L, R, bout::op::Mul> operator*(const L& lhs, const R& rhs) {
+//Field2D operator+(const Field2D& lhs, const Field2D& rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<L, R, bout::op::Add>>
+operator+(const L& lhs, const R& rhs) {
+  return BinaryExpr<L, R, bout::op::Add>{static_cast<typename L::View>(lhs),
+                                         static_cast<typename R::View>(rhs),
+                                         bout::op::Add{},
+                                         lhs.getMesh(),
+                                         lhs.getLocation(),
+                                         lhs.getDirections(),
+                                         std::nullopt,
+                                         lhs.getMesh()->getRegion2D("RGN_ALL")};
+}
+//Field2D operator-(const Field2D& lhs, const Field2D& rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<L, R, bout::op::Sub>>
+operator-(const L& lhs, const R& rhs) {
+  return BinaryExpr<L, R, bout::op::Sub>{static_cast<typename L::View>(lhs),
+                                         static_cast<typename R::View>(rhs),
+                                         bout::op::Sub{},
+                                         lhs.getMesh(),
+                                         lhs.getLocation(),
+                                         lhs.getDirections(),
+                                         std::nullopt,
+                                         lhs.getMesh()->getRegion2D("RGN_ALL")};
+}
+//Field2D operator*(const Field2D& lhs, const Field2D& rhs);
+#if 1
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<L, R, bout::op::Mul>>
+operator*(const L& lhs, const R& rhs) {
   return BinaryExpr<L, R, bout::op::Mul>{static_cast<typename L::View>(lhs),
                                          static_cast<typename R::View>(rhs),
                                          bout::op::Mul{},
                                          lhs.getMesh(),
                                          lhs.getLocation(),
                                          lhs.getDirections(),
-                                         lhs.getRegionID(),
-                                         (regionID.has_value()
-                                              ? lhs.getMesh()->getRegion(regionID.value())
-                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
+                                         std::nullopt,
+                                         lhs.getMesh()->getRegion2D("RGN_ALL")};
+}
+#endif
+//Field2D operator/(const Field2D& lhs, const Field2D& rhs);
+#if 1
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<L, R, bout::op::Div>>
+operator/(const L& lhs, const R& rhs) {
+  return BinaryExpr<L, R, bout::op::Div>{static_cast<typename L::View>(lhs),
+                                         static_cast<typename R::View>(rhs),
+                                         bout::op::Div{},
+                                         lhs.getMesh(),
+                                         lhs.getLocation(),
+                                         lhs.getDirections(),
+                                         std::nullopt,
+                                         lhs.getMesh()->getRegion2D("RGN_ALL")};
 }
 #endif
-Field2D operator/(const Field2D& lhs, const Field2D& rhs);
 
 Field3D operator+(const Field2D& lhs, const Field3D& rhs);
 Field3D operator-(const Field2D& lhs, const Field3D& rhs);
-Field3D operator*(const Field2D& lhs, const Field3D& rhs);
+//Field3D operator*(const Field2D& lhs, const Field3D& rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<L, R, bout::op::Mul>>
+operator*(const L& lhs, const R& rhs) {
+  //static_assert(always_false<L> || always_false<R>, "Hello");
+  auto regionID = rhs.getRegionID();
+
+  //std::cout << "RUNNING Field3D * Field2D using BinaryExpr with CUDA" << "\n";
+  int mesh_nz = rhs.getMesh()->LocalNz;
+
+  return BinaryExpr<L, R, bout::op::Mul>{
+      static_cast<typename L::View>(lhs).setScale(1, mesh_nz),
+      static_cast<typename R::View>(rhs),
+      bout::op::Mul{},
+      rhs.getMesh(),
+      rhs.getLocation(),
+      rhs.getDirections(),
+      regionID,
+      rhs.getMesh()->getRegion("RGN_ALL")};
+}
 Field3D operator/(const Field2D& lhs, const Field3D& rhs);
 
 Field2D operator+(const Field2D& lhs, BoutReal rhs);
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 33e42cccbb..80956cd6f9 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -40,19 +40,6 @@ class Field3D;
 class Mesh;
 
 #include "bout/fieldops.hxx"
-// Base template: nothing is an expression by default
-template <typename T>
-struct is_expr_field3d : std::false_type {};
-
-template <typename T>
-struct is_expr_field2d : std::false_type {};
-
-// Helper variable template
-template <typename T>
-inline constexpr bool is_expr_field3d_v = is_expr_field3d<std::decay_t<T>>::value;
-
-template <typename T>
-inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::value;
 
 /// Class for 3D X-Y-Z scalar fields
 /*!
@@ -198,7 +185,8 @@ public:
   Field3D(Array<BoutReal> data, Mesh* localmesh, CELL_LOC location = CELL_CENTRE,
           DirectionTypes directions_in = {YDirectionType::Standard,
                                           ZDirectionType::Standard});
-  template <typename L, typename R, typename Func>
+  template <typename L, typename R, typename Func,
+            typename = std::enable_if_t<is_expr_field3d_v<L> || is_expr_field3d_v<R>>>
   Field3D(const BinaryExpr<L, R, Func>& expr) {
     //std::cout << "RUNNING constructor from BinaryExpr\n";
     Array<BoutReal> data{expr.size()};
@@ -475,7 +463,8 @@ public:
   void operator=(const FieldPerp& rhs);
   Field3D& operator=(BoutReal val);
   template <typename L, typename R, typename Func>
-  Field3D& operator=(BinaryExpr<L, R, Func>& expr) {
+  std::enable_if_t<is_expr_field3d_v<L>, Field3D&>
+  operator=(BinaryExpr<L, R, Func>& expr) {
     std::cout << "RUNNING operator= with CUDA\n";
     regionID = expr.getRegionID();
     //expr.evaluate(&data[0]);
@@ -811,7 +800,25 @@ Field3D operator/(const Field3D& lhs, BoutReal rhs);
 
 Field3D operator+(BoutReal lhs, const Field3D& rhs);
 Field3D operator-(BoutReal lhs, const Field3D& rhs);
-Field3D operator*(BoutReal lhs, const Field3D& rhs);
+//Field3D operator*(BoutReal lhs, const Field3D& rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_boutreal_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Constant<L>, R, bout::op::Mul>>
+operator*(const L& lhs, const R& rhs) {
+  //static_assert(always_false<L> || always_false<R>, "Hello");
+  auto regionID = rhs.getRegionID();
+
+  return BinaryExpr<Constant<L>, R, bout::op::Mul>{
+      static_cast<typename Constant<L>::View>(lhs),
+      static_cast<typename R::View>(rhs),
+      bout::op::Mul{},
+      rhs.getMesh(),
+      rhs.getLocation(),
+      rhs.getDirections(),
+      regionID,
+      rhs.getMesh()->getRegion("RGN_ALL")};
+}
+
 Field3D operator/(BoutReal lhs, const Field3D& rhs);
 
 /*!
@@ -935,18 +942,6 @@ struct is_expr_field2d<Field2D> : std::true_type {};
 
 template <typename L, typename R, typename Fun>
 struct is_expr_field3d<BinaryExpr<L, R, Fun>>
-    : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value> {};
-
-template <typename L, typename R, typename Fun>
-struct is_expr_field2d<BinaryExpr<L, R, Fun>>
-    : std::integral_constant<bool, is_expr_field2d<std::decay_t<L>>::value> {};
-
-//template <typename L, typename R, typename Fun>
-//struct is_expr_field3d<typename BinaryExpr<L, R, Fun>::View> : is_expr_field3d<L> {};
-
-//template<typename L,typename R,typename Fun>
-//struct is_expr_field3d< typename BinaryExpr<L,R,Fun>::View >
-//  : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value> {};
-//  //: is_expr_field3d<std::decay_t<L>> {};
+    : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value || is_expr_field3d_v<std::decay_t<R>>> {};
 
 #endif /* BOUT_FIELD3D_H */
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index d83d1eedd1..b78dadc315 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -1,18 +1,46 @@
 #pragma once
-#include "bout/array.hxx"
-#include <unordered_map>
 #ifndef BOUT_FIELDOPS_HXX
 #define BOUT_FIELDOPS_HXX
 
+#include "bout/array.hxx"
 #include "bout/bout_types.hxx"
 
 #include <cuda_runtime.h>
 #include <optional>
+#include <type_traits>
+#include <unordered_map>
 
 class Mesh;
 class Field3D;
+class Field2D;
+
+template <typename T>
+struct is_expr_field2d : std::false_type {};
+
+template <typename T>
+inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::value;
+
+// Base template: nothing is an expression by default
+template <typename T>
+struct is_expr_field3d : std::false_type {};
+
+// Helper variable template
+template <typename T>
+inline constexpr bool is_expr_field3d_v = is_expr_field3d<std::decay_t<T>>::value;
+
+template <typename T>
+struct is_expr_boutreal : std::false_type {};
+
+template <typename T>
+inline constexpr bool is_expr_boutreal_v = is_expr_boutreal<std::decay_t<T>>::value;
+
+template <>
+struct is_expr_boutreal<BoutReal> : std::true_type {};
+
+template <typename T>
+struct is_expr_boutreal<Constant<T>>
+    : std::integral_constant<bool, is_expr_boutreal_v<std::decay_t<T>>> {};
 
-#include <type_traits>
 
 namespace bout {
 namespace op {
@@ -144,6 +172,9 @@ struct BinaryExpr {
     //}
   }
 
+  BinaryExpr& operator=(BinaryExpr const&) = delete;
+  BinaryExpr& operator=(BinaryExpr&&) = delete;
+
   inline int size() const { return indices.size(); }
   inline BoutReal operator()(int idx) const {
     return f(idx, lhs, rhs); // single‐pass fusion
@@ -156,11 +187,13 @@ struct BinaryExpr {
     const int* indices;
     int num_indices;
     Func f;
-    int scale = 1;
+    int mul = 1;
+    int div = 1;
     int offset = 0;
 
-    View& setScale(int s) {
-      scale = s;
+    View& setScale(int mul, int div) {
+      this->mul = mul;
+      this->div = div;
       return *this;
     }
     View& setOffset(int o) {
@@ -171,7 +204,7 @@ struct BinaryExpr {
     __device__ __forceinline__ int size() const { return num_indices; }
     __device__ __forceinline__ int regionIdx(int idx) const { return indices[idx]; }
     __device__ __forceinline__ BoutReal operator()(int idx) const {
-      return f(idx, lhs, rhs); // single‐pass fusion
+      return f((idx * mul) / div, lhs, rhs); // single‐pass fusion
       //return f(lhs(idx), rhs(idx)); // single‐pass fusion
     }
   };
diff --git a/include/bout/interpolation.hxx b/include/bout/interpolation.hxx
index 2c7df4472d..85c04cf897 100644
--- a/include/bout/interpolation.hxx
+++ b/include/bout/interpolation.hxx
@@ -55,7 +55,8 @@ inline BoutReal interp(const stencil& s) {
   @param[in]   region  Region where output will be calculated
 */
 template <typename T>
-const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_ALL") {
+std::enable_if_t<bout::utils::is_Field2D_v<T> || bout::utils::is_Field3D_v<T>, const T>
+interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_ALL") {
   AUTO_TRACE();
   static_assert(bout::utils::is_Field2D_v<T> || bout::utils::is_Field3D_v<T>,
                 "interp_to must be templated with one of Field2D or Field3D.");
@@ -203,4 +204,17 @@ const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_AL
   return result;
 }
 
+
+template<typename E>
+std::enable_if_t<is_expr_field3d_v<E> && !bout::utils::is_Field3D_v<E>, const Field3D> 
+interp_to(const E &expr, CELL_LOC loc, const std::string rgn = "RGN_ALL") {
+  return interp_to( Field3D{expr}, loc, std::move(rgn) );
+}
+
+template<typename E>
+std::enable_if_t<is_expr_field2d_v<E> && !bout::utils::is_Field2D_v<E>, const Field2D> 
+interp_to(const E &expr, CELL_LOC loc, const std::string rgn = "RGN_ALL") {
+  return interp_to( Field2D{expr}, loc, std::move(rgn) );
+}
+
 #endif // BOUT_INTERP_H
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index e2ac814e53..42aa761886 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -422,12 +422,12 @@ inline BoutReal randomu() {
  * i.e. t * t
  */
 template <typename T>
-inline T SQ(const T& t) {
+inline auto SQ(const T& t) {
   return t * t;
 }
 
 template <>
-BOUT_HOST_DEVICE inline BoutReal SQ(const BoutReal& t) {
+BOUT_HOST_DEVICE inline auto SQ(const BoutReal& t) {
   return t * t;
 }
 
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index c8b9ebb689..e5c1d466b7 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -389,7 +389,8 @@ bool operator==(const Field2D& a, const Field2D& b) {
   if (!a.isAllocated() || !b.isAllocated()) {
     return false;
   }
-  return min(abs(a - b)) < 1e-10;
+  Field2D diff = a - b;
+  return min(abs(diff)) < 1e-10;
 }
 
 std::ostream& operator<<(std::ostream& out, const Field2D& value) {
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 691e450b0c..439320b0ae 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -62,7 +62,7 @@ Field3D& Field3D::operator*=(const Field2D& rhs) {
   return *this;
 }
 
-#if 1
+#if 0
 // Provide the C++ wrapper for division of Field3D and Field2D
 Field3D operator/(const Field3D& lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator "<< __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -485,6 +485,7 @@ Field3D& Field3D::operator-=(const BoutReal rhs) {
 }
 
 // Provide the C++ wrapper for multiplication of Field2D and Field3D
+#if 0
 Field3D operator*(const Field2D& lhs, const Field3D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
@@ -507,6 +508,7 @@ Field3D operator*(const Field2D& lhs, const Field3D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ wrapper for division of Field2D and Field3D
 Field3D operator/(const Field2D& lhs, const Field3D& rhs) {
@@ -581,6 +583,7 @@ Field3D operator-(const Field2D& lhs, const Field3D& rhs) {
 }
 
 // Provide the C++ wrapper for multiplication of Field2D and Field2D
+#if 0
 Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
@@ -596,6 +599,7 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field2D by multiplication with Field2D
 Field2D& Field2D::operator*=(const Field2D& rhs) {
@@ -618,6 +622,7 @@ Field2D& Field2D::operator*=(const Field2D& rhs) {
   return *this;
 }
 
+#if 0
 // Provide the C++ wrapper for division of Field2D and Field2D
 Field2D operator/(const Field2D& lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -634,6 +639,7 @@ Field2D operator/(const Field2D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field2D by division with Field2D
 Field2D& Field2D::operator/=(const Field2D& rhs) {
@@ -657,6 +663,7 @@ Field2D& Field2D::operator/=(const Field2D& rhs) {
 }
 
 // Provide the C++ wrapper for addition of Field2D and Field2D
+#if 0
 Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
@@ -672,6 +679,7 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field2D by addition with Field2D
 Field2D& Field2D::operator+=(const Field2D& rhs) {
@@ -695,6 +703,7 @@ Field2D& Field2D::operator+=(const Field2D& rhs) {
 }
 
 // Provide the C++ wrapper for subtraction of Field2D and Field2D
+#if 0
 Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
@@ -710,6 +719,7 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field2D by subtraction with Field2D
 Field2D& Field2D::operator-=(const Field2D& rhs) {
@@ -1643,6 +1653,7 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) {
   return *this;
 }
 
+#if 0
 // Provide the C++ wrapper for multiplication of BoutReal and Field3D
 Field3D operator*(const BoutReal lhs, const Field3D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -1660,6 +1671,7 @@ Field3D operator*(const BoutReal lhs, const Field3D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ wrapper for division of BoutReal and Field3D
 Field3D operator/(const BoutReal lhs, const Field3D& rhs) {
diff --git a/src/field/vecops.cxx b/src/field/vecops.cxx
index 5f34e2af02..95409963f6 100644
--- a/src/field/vecops.cxx
+++ b/src/field/vecops.cxx
@@ -187,7 +187,7 @@ Field3D Div(const Vector3D& v, CELL_LOC outloc, const std::string& method) {
   Vector3D vcn = v;
   vcn.toContravariant();
 
-  auto vcnJy = vcn.y.getCoordinates()->J * vcn.y;
+  Field3D vcnJy = vcn.y.getCoordinates()->J * vcn.y;
   if (v.y.hasParallelSlices()) {
     // If v.y has parallel slices then we are using ShiftedMetric (with
     // mesh:calcParallelSlices_on_communicate=true) or FCI, so we should calculate
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index e6f68d850d..203b0c0abd 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -269,8 +269,9 @@ Field3D LaplaceNaulin::solve(const Field3D& rhs, const Field3D& x0) {
   delp2solver->setCoefC2(C2coef_DC);
 
   // Use this below to normalize error for relative error estimate
+  Field3D SQField = SQ(rhsOverD);
   BoutReal RMS_rhsOverD = sqrt(mean(
-      SQ(rhsOverD), true,
+      SQField, true,
       "RGN_NOBNDRY")); // use sqrt(mean(SQ)) to make sure we do not divide by zero at a point
 
   BoutReal error_rel = 1e20, error_abs = 1e20, last_error = error_abs;
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 8123720144..9861fe58bf 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -553,7 +553,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
                                   transform.get());
 
     // Compare calculated and loaded values
-    output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(J - Jcalc)));
+    Field2D diff = J - Jcalc;
+    output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(diff)));
 
     communicate(J);
 
@@ -578,7 +579,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
 
     Bxy = interpolateAndExtrapolate(Bxy, location, extrapolate_x, extrapolate_y, false,
                                     transform.get());
-    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
+    FieldMetric diff = Bxy - Bcalc;
+    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(diff)));
   }
 
   // Check Bxy
@@ -759,8 +761,9 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
       J = interpolateAndExtrapolate(J, location, extrapolate_x, extrapolate_y, false,
                                     transform.get());
 
+      FieldMetric diff = J - Jcalc;
       // Compare calculated and loaded values
-      output_warn.write("\tMaximum difference in J is %e\n", max(abs(J - Jcalc)));
+      output_warn.write("\tMaximum difference in J is %e\n", max(abs(diff)));
 
       // Re-evaluate Bxy using new J
       Bxy = sqrt(g_22) / J;
@@ -785,7 +788,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
       Bxy = interpolateAndExtrapolate(Bxy, location, extrapolate_x, extrapolate_y, false,
                                       transform.get());
 
-      output_warn.write("\tMaximum difference in Bxy is %e\n", max(abs(Bxy - Bcalc)));
+      FieldMetric diff = Bxy - Bcalc;
+      output_warn.write("\tMaximum difference in Bxy is %e\n", max(abs(diff)));
     }
 
     // Check Bxy
@@ -1029,7 +1033,7 @@ int Coordinates::geometry(bool recalculate_staggered,
   G3_23 = 0.5 * g13 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g23 * DDZ(g_22)
           + 0.5 * g33 * DDY(g_33);
 
-  auto tmp = J * g12;
+  FieldMetric tmp = J * g12;
   communicate(tmp);
   G1 = (DDX(J * g11) + DDY(tmp) + DDZ(J * g13)) / J;
   tmp = J * g22;
@@ -1268,9 +1272,9 @@ int Coordinates::calcCovariant(const std::string& region) {
 
   output_info.write("\tLocal maximum error in diagonal inversion is {:e}\n", maxerr);
 
-  maxerr = BOUTMAX(max(abs(g_11 * g12 + g_12 * g22 + g_13 * g23)),
-                   max(abs(g_11 * g13 + g_12 * g23 + g_13 * g33)),
-                   max(abs(g_12 * g13 + g_22 * g23 + g_23 * g33)));
+  maxerr = BOUTMAX(max(abs(FieldMetric{g_11 * g12 + g_12 * g22 + g_13 * g23})),
+                   max(abs(FieldMetric{g_11 * g13 + g_12 * g23 + g_13 * g33})),
+                   max(abs(FieldMetric{g_12 * g13 + g_22 * g23 + g_23 * g33})));
 
   output_info.write("\tLocal maximum error in off-diagonal inversion is {:e}\n", maxerr);
 
@@ -1324,9 +1328,9 @@ int Coordinates::calcContravariant(const std::string& region) {
 
   output_info.write("\tMaximum error in diagonal inversion is {:e}\n", maxerr);
 
-  maxerr = BOUTMAX(max(abs(g_11 * g12 + g_12 * g22 + g_13 * g23)),
-                   max(abs(g_11 * g13 + g_12 * g23 + g_13 * g33)),
-                   max(abs(g_12 * g13 + g_22 * g23 + g_23 * g33)));
+  maxerr = BOUTMAX(max(abs(FieldMetric{g_11 * g12 + g_12 * g22 + g_13 * g23})),
+                   max(abs(FieldMetric{g_11 * g13 + g_12 * g23 + g_13 * g33})),
+                   max(abs(FieldMetric{g_12 * g13 + g_22 * g23 + g_23 * g33})));
 
   output_info.write("\tMaximum error in off-diagonal inversion is {:e}\n", maxerr);
   return 0;
@@ -1339,13 +1343,13 @@ int Coordinates::jacobian() {
   const bool extrapolate_x = not localmesh->sourceHasXBoundaryGuards();
   const bool extrapolate_y = not localmesh->sourceHasYBoundaryGuards();
 
-  auto g = g11 * g22 * g33 + 2.0 * g12 * g13 * g23 - g11 * g23 * g23 - g22 * g13 * g13
-           - g33 * g12 * g12;
+  auto g = FieldMetric{g11 * g22 * g33 + 2.0 * g12 * g13 * g23 - g11 * g23 * g23
+                       - g22 * g13 * g13 - g33 * g12 * g12};
 
   // Check that g is positive
   bout::checkPositive(g, "The determinant of g^ij", "RGN_NOBNDRY");
 
-  J = 1. / sqrt(g);
+  J = 1. / sqrt(Field2D{g});
   // More robust to extrapolate derived quantities directly, rather than
   // deriving from extrapolated covariant metric components
   J = interpolateAndExtrapolate(J, location, extrapolate_x, extrapolate_y, false,
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index ee9bcbcc2c..f12c517f82 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -173,7 +173,7 @@ Coordinates::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc,
                                const std::string& method, const std::string& region) {
   Coordinates* coords = f.getCoordinates(outloc);
 
-  auto result =
+  Field2D result =
       bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx);
 
   if (coords->non_uniform) {
@@ -210,7 +210,7 @@ Coordinates::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc,
                                const std::string& method, const std::string& region) {
   Coordinates* coords = f.getCoordinates(outloc);
 
-  auto result =
+  Field2D result =
       bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy);
   if (coords->non_uniform) {
     // Correction for non-uniform f.getMesh()

From 5dfa66a75cba94f47aade6c6c63ca29afc0eb099 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Sat, 31 May 2025 08:13:20 -0700
Subject: [PATCH 0183/1827] Add more operators

---
 .../elm-pb-outerloop/elm_pb_outerloop.cxx     |  4 +-
 include/bout/assert.hxx                       |  2 +-
 include/bout/field2d.hxx                      | 80 +++++++++++++++----
 include/bout/field3d.hxx                      | 16 ++--
 include/bout/fieldops.hxx                     | 49 +++---------
 src/field/generated_fieldops.cxx              |  6 ++
 src/mesh/coordinates.cxx                      | 12 +--
 7 files changed, 102 insertions(+), 67 deletions(-)

diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index d985c3ef9d..ec2ab8e2a7 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -713,7 +713,7 @@ class ELMpb : public PhysicsModel {
       diamag_phi0 = false;
       K_H_term = false;
     } else {
-      Dphi0 = -D_min - 0.5 * D_0 * (1.0 - tanh(D_s * (x - x0)));
+      Dphi0 = -D_min - 0.5 * D_0 * (1.0 - tanh(Field2D{D_s * (x - x0)}));
     }
 
     if (sign < 0) { // change flow direction
@@ -1213,7 +1213,7 @@ class ELMpb : public PhysicsModel {
       // Only if not restarting: Check initial perturbation
 
       // Set U to zero where P0 < vacuum_pressure
-      U = where(P0 - vacuum_pressure, U, 0.0);
+      U = where(Field2D{P0 - vacuum_pressure}, U, 0.0);
 
       if (constn0) {
         ubyn = U;
diff --git a/include/bout/assert.hxx b/include/bout/assert.hxx
index 2909cfc3c3..954ae8dba0 100644
--- a/include/bout/assert.hxx
+++ b/include/bout/assert.hxx
@@ -38,9 +38,9 @@
 #if CHECKLEVEL >= 1
 #define ASSERT1(condition)                                                               \
   if (!(condition)) {                                                                    \
-    abort();                                                                             \
     throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \
                         #condition);                                                     \
+    abort();                                                                             \
   }
 #else // CHECKLEVEL >= 1
 #define ASSERT1(condition)
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 9d9948296e..baff508331 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -47,15 +47,14 @@ class Field2D;
 class Field3D;
 class Mesh;
 
-//template <typename T>
-//struct is_expr_field2d : std::false_type {};
-
-//template <typename T>
-//inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::value;
-
 template <typename L, typename R, typename Fun>
 struct is_expr_field2d<BinaryExpr<L, R, Fun>>
-    : std::integral_constant<bool, is_expr_field2d<std::decay_t<L>>::value && is_expr_field2d_v<std::decay_t<R>>> {};
+    : std::integral_constant<bool, (is_expr_field2d_v<std::decay_t<L>>
+                                    && is_expr_field2d_v<std::decay_t<R>>)
+                                       || (is_expr_constant_v<std::decay_t<L>>
+                                           && is_expr_field2d_v<std::decay_t<R>>)
+                                       || (is_expr_field2d_v<std::decay_t<L>>
+                                           && is_expr_constant_v<std::decay_t<R>>)> {};
 
 /*!
  * \brief 2D X-Y scalar fields
@@ -103,8 +102,11 @@ public:
           DirectionTypes directions_in = {YDirectionType::Standard,
                                           ZDirectionType::Average});
 
-  template <typename L, typename R, typename Func,
-            typename = std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>>>
+  template <
+      typename L, typename R, typename Func,
+      typename = std::enable_if_t<(is_expr_field2d_v<L> && is_expr_field2d_v<R>)
+                                  || (is_expr_constant_v<L> && is_expr_field2d_v<R>)
+                                  || (is_expr_field2d_v<L> && is_expr_constant_v<R>)>>
   Field2D(const BinaryExpr<L, R, Func>& expr) {
     Array<BoutReal> data{expr.size()};
     expr.evaluate(&data[0]);
@@ -188,9 +190,13 @@ public:
 
   template <typename L, typename R, typename Func>
   std::enable_if_t<is_expr_field2d_v<L>, Field2D&>
-  operator=(BinaryExpr<L, R, Func>& expr) {
+  operator=(const BinaryExpr<L, R, Func>& expr) {
     std::cout << "RUNNING Field2D operator= with CUDA\n";
-    expr.evaluate(&data[0]);
+    if (isAllocated()) {
+      expr.evaluate(&data[0]);
+    } else {
+      *this = Field2D{expr};
+    }
     return *this;
   }
 
@@ -278,7 +284,19 @@ public:
   /// In-place division. Copy-on-write used if data is shared
   Field2D& operator/=(const Field2D& rhs);
   /// In-place division. Copy-on-write used if data is shared
-  Field2D& operator/=(BoutReal rhs);
+  //Field2D& operator/=(BoutReal rhs);
+    template <typename R, typename = std::enable_if_t<is_expr_constant_v<R>>>
+  Field2D& operator/=(R rhs) {
+    //printf("RUNNING operator+= with CUDA\n");
+    if (data.unique()) {
+      auto BE = (*this) / rhs;
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) / rhs;
+    }
+
+    return *this;
+  }
 
   // FieldData virtual functions
 
@@ -425,13 +443,47 @@ operator*(const L& lhs, const R& rhs) {
 Field3D operator/(const Field2D& lhs, const Field3D& rhs);
 
 Field2D operator+(const Field2D& lhs, BoutReal rhs);
-Field2D operator-(const Field2D& lhs, BoutReal rhs);
+//Field2D operator-(const Field2D& lhs, BoutReal rhs);
+#if 1
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<L, Constant<R>, bout::op::Sub>>
+operator-(const L& lhs, R rhs) {
+  return BinaryExpr<L, Constant<R>, bout::op::Sub>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename Constant<R>::View>(rhs),
+      bout::op::Sub{},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      std::nullopt,
+      lhs.getMesh()->getRegion2D("RGN_ALL")};
+}
+#endif
 Field2D operator*(const Field2D& lhs, BoutReal rhs);
 Field2D operator/(const Field2D& lhs, BoutReal rhs);
 
 Field2D operator+(BoutReal lhs, const Field2D& rhs);
 Field2D operator-(BoutReal lhs, const Field2D& rhs);
-Field2D operator*(BoutReal lhs, const Field2D& rhs);
+//Field2D operator*(BoutReal lhs, const Field2D& rhs);
+#if 1
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Constant<L>, R, bout::op::Mul>>
+operator*(L lhs, const R& rhs) {
+  //static_assert(always_false<L> || always_false<R>, "Hello");
+
+  return BinaryExpr<Constant<L>, R, bout::op::Mul>{
+      static_cast<typename Constant<L>::View>(lhs),
+      static_cast<typename R::View>(rhs),
+      bout::op::Mul{},
+      rhs.getMesh(),
+      rhs.getLocation(),
+      rhs.getDirections(),
+      std::nullopt,
+      rhs.getMesh()->getRegion2D("RGN_ALL")};
+}
+#endif
 Field2D operator/(BoutReal lhs, const Field2D& rhs);
 
 /*!
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 80956cd6f9..c11bab0599 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -467,8 +467,12 @@ public:
   operator=(BinaryExpr<L, R, Func>& expr) {
     std::cout << "RUNNING operator= with CUDA\n";
     regionID = expr.getRegionID();
-    //expr.evaluate(&data[0]);
-    expr.evaluateWithResult(static_cast<View>(*this));
+    if(isAllocated()) {
+      expr.evaluate(&data[0]);
+    }
+    else {
+      *this = Field3D{expr};
+    }
     return *this;
   }
 
@@ -481,15 +485,15 @@ public:
   Field3D& operator+=(const R& rhs) {
     //printf("RUNNING operator+= with CUDA\n");
     if (data.unique()) {
-      printf("RUNNING operator+= with CUDA with evaluateWithResult\n");
+      //std::cout << "RUNNING Field3D operator+=  w/ CUDA" << __FILE__ << " "
+      //          << std::to_string(__LINE__) << "\n";
       // Delete existing parallel slices. We don't copy parallel slices, so any
       // that currently exist will be incorrect.
       clearParallelSlices();
 
       auto BE = (*this) + rhs;
       regionID = BE.getRegionID();
-      //BE.evaluate(&data[0]);
-      BE.evaluateWithResult(static_cast<View>(*this));
+      BE.evaluate(&data[0]);
     } else {
       (*this) = (*this) + rhs;
     }
@@ -802,7 +806,7 @@ Field3D operator+(BoutReal lhs, const Field3D& rhs);
 Field3D operator-(BoutReal lhs, const Field3D& rhs);
 //Field3D operator*(BoutReal lhs, const Field3D& rhs);
 template <typename L, typename R>
-std::enable_if_t<is_expr_boutreal_v<L> && is_expr_field3d_v<R>,
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,
                  BinaryExpr<Constant<L>, R, bout::op::Mul>>
 operator*(const L& lhs, const R& rhs) {
   //static_assert(always_false<L> || always_false<R>, "Hello");
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index b78dadc315..6ec7947be4 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -29,18 +29,20 @@ template <typename T>
 inline constexpr bool is_expr_field3d_v = is_expr_field3d<std::decay_t<T>>::value;
 
 template <typename T>
-struct is_expr_boutreal : std::false_type {};
+struct is_expr_constant : std::bool_constant<std::is_arithmetic_v<T>> {};
 
 template <typename T>
-inline constexpr bool is_expr_boutreal_v = is_expr_boutreal<std::decay_t<T>>::value;
-
-template <>
-struct is_expr_boutreal<BoutReal> : std::true_type {};
+inline constexpr bool is_expr_constant_v = is_expr_constant<std::decay_t<T>>::value;
 
 template <typename T>
-struct is_expr_boutreal<Constant<T>>
-    : std::integral_constant<bool, is_expr_boutreal_v<std::decay_t<T>>> {};
+struct is_expr_constant<Constant<T>>
+    : std::integral_constant<bool, is_expr_constant_v<std::decay_t<T>>> {};
 
+// After the specialization…
+static_assert(is_expr_constant_v<Constant<int>> == true,
+              "Constant<int> should be recognized as an expr_constant!");
+static_assert(is_expr_constant_v<Constant<float>> == true,
+              "Constant<float> should be recognized as an expr_constant!");
 
 namespace bout {
 namespace op {
@@ -101,7 +103,7 @@ __global__ __launch_bounds__(256) static void evaluatorExpr(BoutReal* out,
                                                             const Expr expr) {
   int tid = threadIdx.x + blockIdx.x * blockDim.x;
   if (tid >= expr.size()) {
-    return; // Out of bounds
+    return;
   }
   int idx = expr.regionIdx(tid);
   out[idx] = expr(idx); // single‐pass fusion
@@ -112,24 +114,6 @@ __global__ __launch_bounds__(256) static void evaluatorExpr(BoutReal* out,
   //}
 }
 
-template <typename Result, typename Expr>
-__global__ __launch_bounds__(256) static void evaluatorExprWithResult(Result res,
-                                                                      const Expr expr) {
-  int tid = threadIdx.x + blockIdx.x * blockDim.x;
-  if (tid >= expr.size()) {
-    return; // Out of bounds
-  }
-  int idx = expr.regionIdx(tid);
-  res[idx] = expr(idx); // single‐pass fusion
-  //res(idx, expr(idx)); // single‐pass fusion
-  //res(idx) = expr(idx); // single‐pass fusion
-  //int stride = blockDim.x * gridDim.x;
-  //for (int i = tid, e = expr.size(); i < e; i += stride) {
-  //  int idx = expr.regionIdx(i);
-  //  out[idx] = expr(idx); // single‐pass fusion
-  //}
-}
-
 inline std::unordered_map<void*, Array<int>> regionIndicesCache;
 
 template <typename L, typename R, typename Func>
@@ -222,21 +206,10 @@ struct BinaryExpr {
     //}
   }
 
-  template <typename Result>
-  void evaluateWithResult(const Result& res) const {
-    constexpr int THREADS = 256;
-    int blocks = (size() + THREADS - 1) / THREADS;
-    evaluatorExprWithResult<<<blocks, THREADS>>>(res, static_cast<View>(*this));
-    cudaDeviceSynchronize();
-    //for(int i=0; i<size(); ++i) {
-    //  data[regionIdx(i)] = f(i, lhs, rhs); // single‐pass fusion
-    //}
-  }
-
   Mesh* getMesh() const { return mesh; }
   CELL_LOC getLocation() const { return location; }
   DirectionTypes getDirections() const { return directions; }
   std::optional<size_t> getRegionID() const { return regionID; };
 };
 
-#endif // BOUT_EXPRESSION_HXX
\ No newline at end of file
+#endif // BOUT_EXPRESSION_HX
\ No newline at end of file
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 439320b0ae..9ae40ba41b 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -879,6 +879,7 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
   return result;
 }
 
+#if 0
 // Provide the C++ operator to update Field2D by division with BoutReal
 Field2D& Field2D::operator/=(const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -899,6 +900,7 @@ Field2D& Field2D::operator/=(const BoutReal rhs) {
   }
   return *this;
 }
+#endif
 
 // Provide the C++ wrapper for addition of Field2D and BoutReal
 Field2D operator+(const Field2D& lhs, const BoutReal rhs) {
@@ -937,6 +939,7 @@ Field2D& Field2D::operator+=(const BoutReal rhs) {
 }
 
 // Provide the C++ wrapper for subtraction of Field2D and BoutReal
+#if 0
 Field2D operator-(const Field2D& lhs, const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
@@ -951,6 +954,7 @@ Field2D operator-(const Field2D& lhs, const BoutReal rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field2D by subtraction with BoutReal
 Field2D& Field2D::operator-=(const BoutReal rhs) {
@@ -1727,6 +1731,7 @@ Field3D operator-(const BoutReal lhs, const Field3D& rhs) {
   return result;
 }
 
+#if 0
 // Provide the C++ wrapper for multiplication of BoutReal and Field2D
 Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -1742,6 +1747,7 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ wrapper for division of BoutReal and Field2D
 Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 9861fe58bf..8bded7fee5 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1266,9 +1266,9 @@ int Coordinates::calcCovariant(const std::string& region) {
   }
 
   BoutReal maxerr;
-  maxerr = BOUTMAX(max(abs((g_11 * g11 + g_12 * g12 + g_13 * g13) - 1)),
-                   max(abs((g_12 * g12 + g_22 * g22 + g_23 * g23) - 1)),
-                   max(abs((g_13 * g13 + g_23 * g23 + g_33 * g33) - 1)));
+  maxerr = BOUTMAX(max(abs(FieldMetric{(g_11 * g11 + g_12 * g12 + g_13 * g13) - 1})),
+                   max(abs(FieldMetric{(g_12 * g12 + g_22 * g22 + g_23 * g23) - 1})),
+                   max(abs(FieldMetric{(g_13 * g13 + g_23 * g23 + g_33 * g33) - 1})));
 
   output_info.write("\tLocal maximum error in diagonal inversion is {:e}\n", maxerr);
 
@@ -1322,9 +1322,9 @@ int Coordinates::calcContravariant(const std::string& region) {
   }
 
   BoutReal maxerr;
-  maxerr = BOUTMAX(max(abs((g_11 * g11 + g_12 * g12 + g_13 * g13) - 1)),
-                   max(abs((g_12 * g12 + g_22 * g22 + g_23 * g23) - 1)),
-                   max(abs((g_13 * g13 + g_23 * g23 + g_33 * g33) - 1)));
+  maxerr = BOUTMAX(max(abs(FieldMetric{(g_11 * g11 + g_12 * g12 + g_13 * g13) - 1})),
+                   max(abs(FieldMetric{(g_12 * g12 + g_22 * g22 + g_23 * g23) - 1})),
+                   max(abs(FieldMetric{(g_13 * g13 + g_23 * g23 + g_33 * g33) - 1})));
 
   output_info.write("\tMaximum error in diagonal inversion is {:e}\n", maxerr);
 

From 026645a47a43e7f9f0cb748dac893313c2a3ba2f Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Sat, 31 May 2025 18:30:17 -0700
Subject: [PATCH 0184/1827] More operators

macro for dedup definition per operator
---
 .../elm-pb-outerloop/elm_pb_outerloop.cxx     |   3 +-
 include/bout/field2d.hxx                      | 127 ++++++++++++++++--
 include/bout/field3d.hxx                      |  80 ++++++++++-
 include/bout/utils.hxx                        |   5 +-
 src/field/generated_fieldops.cxx              |  24 ++++
 src/mesh/coordinates.cxx                      |   4 +-
 src/physics/snb.cxx                           |   2 +-
 7 files changed, 221 insertions(+), 24 deletions(-)

diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index ec2ab8e2a7..7d38780814 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -1031,7 +1031,8 @@ class ELMpb : public PhysicsModel {
     vacuum_trans *= pnorm;
 
     // Transitions from 0 in core to 1 in vacuum
-    vac_mask = (1.0 - tanh((P0 - vacuum_pressure) / vacuum_trans)) / 2.0;
+    Field2D tanh_res = tanh(Field2D{(P0 - vacuum_pressure) / vacuum_trans});
+    vac_mask = (1.0 - tanh_res) / 2.0;
 
     if (spitzer_resist) {
       // Use Spitzer resistivity
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index baff508331..97946ee713 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -270,17 +270,66 @@ public:
   }
 
   /// In-place addition. Copy-on-write used if data is shared
-  Field2D& operator+=(const Field2D& rhs);
+  //Field2D& operator+=(const Field2D& rhs);
+  template <typename R, typename = std::enable_if_t<is_expr_field2d_v<R>>>
+  Field2D& operator+=(const R& rhs) {
+    //printf("RUNNING operator+= with CUDA\n");
+    if (data.unique()) {
+      auto BE = (*this) + rhs;
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) * rhs;
+    }
+
+    return *this;
+  }
   /// In-place addition. Copy-on-write used if data is shared
   Field2D& operator+=(BoutReal rhs);
   /// In-place subtraction. Copy-on-write used if data is shared
-  Field2D& operator-=(const Field2D& rhs);
+  //Field2D& operator-=(const Field2D& rhs);
+  //here1
+  template <typename R, typename = std::enable_if_t<is_expr_field2d_v<R>>>
+  Field2D& operator-=(const R& rhs) {
+    //printf("RUNNING operator+= with CUDA\n");
+    if (data.unique()) {
+      auto BE = (*this) - rhs;
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) * rhs;
+    }
+
+    return *this;
+  }
   /// In-place subtraction. Copy-on-write used if data is shared
   Field2D& operator-=(BoutReal rhs);
   /// In-place multiplication. Copy-on-write used if data is shared
-  Field2D& operator*=(const Field2D& rhs);
+  //Field2D& operator*=(const Field2D& rhs);
+  template <typename R, typename = std::enable_if_t<is_expr_field2d_v<R>>>
+  Field2D& operator*=(const R& rhs) {
+    //printf("RUNNING operator+= with CUDA\n");
+    if (data.unique()) {
+      auto BE = (*this) * rhs;
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) * rhs;
+    }
+
+    return *this;
+  }
   /// In-place multiplication. Copy-on-write used if data is shared
-  Field2D& operator*=(BoutReal rhs);
+  //Field2D& operator*=(BoutReal rhs);
+  template <typename R, typename = std::enable_if_t<is_expr_constant_v<R>>>
+  Field2D& operator*=(R rhs) {
+    //printf("RUNNING operator+= with CUDA\n");
+    if (data.unique()) {
+      auto BE = (*this) * rhs;
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) * rhs;
+    }
+
+    return *this;
+  }
   /// In-place division. Copy-on-write used if data is shared
   Field2D& operator/=(const Field2D& rhs);
   /// In-place division. Copy-on-write used if data is shared
@@ -444,7 +493,6 @@ Field3D operator/(const Field2D& lhs, const Field3D& rhs);
 
 Field2D operator+(const Field2D& lhs, BoutReal rhs);
 //Field2D operator-(const Field2D& lhs, BoutReal rhs);
-#if 1
 template <typename L, typename R>
 std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
                  BinaryExpr<L, Constant<R>, bout::op::Sub>>
@@ -459,14 +507,56 @@ operator-(const L& lhs, R rhs) {
       std::nullopt,
       lhs.getMesh()->getRegion2D("RGN_ALL")};
 }
-#endif
-Field2D operator*(const Field2D& lhs, BoutReal rhs);
-Field2D operator/(const Field2D& lhs, BoutReal rhs);
+//Field2D operator*(const Field2D& lhs, BoutReal rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<L, Constant<R>, bout::op::Mul>>
+operator*(const L& lhs, R rhs) {
+  return BinaryExpr<L, Constant<R>, bout::op::Mul>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename Constant<R>::View>(rhs),
+      bout::op::Mul{},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      std::nullopt,
+      lhs.getMesh()->getRegion2D("RGN_ALL")};
+}
+//Field2D operator/(const Field2D& lhs, BoutReal rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<L, Constant<R>, bout::op::Div>>
+operator/(const L& lhs, R rhs) {
+  return BinaryExpr<L, Constant<R>, bout::op::Div>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename Constant<R>::View>(rhs),
+      bout::op::Div{},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      std::nullopt,
+      lhs.getMesh()->getRegion2D("RGN_ALL")};
+}
 
 Field2D operator+(BoutReal lhs, const Field2D& rhs);
-Field2D operator-(BoutReal lhs, const Field2D& rhs);
+//Field2D operator-(BoutReal lhs, const Field2D& rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Constant<L>, R, bout::op::Sub>>
+operator-(L lhs, const R& rhs) {
+  //static_assert(always_false<L> || always_false<R>, "Hello");
+
+  return BinaryExpr<Constant<L>, R, bout::op::Sub>{
+      static_cast<typename Constant<L>::View>(lhs),
+      static_cast<typename R::View>(rhs),
+      bout::op::Sub{},
+      rhs.getMesh(),
+      rhs.getLocation(),
+      rhs.getDirections(),
+      std::nullopt,
+      rhs.getMesh()->getRegion2D("RGN_ALL")};
+}
 //Field2D operator*(BoutReal lhs, const Field2D& rhs);
-#if 1
 template <typename L, typename R>
 std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
                  BinaryExpr<Constant<L>, R, bout::op::Mul>>
@@ -483,8 +573,21 @@ operator*(L lhs, const R& rhs) {
       std::nullopt,
       rhs.getMesh()->getRegion2D("RGN_ALL")};
 }
-#endif
-Field2D operator/(BoutReal lhs, const Field2D& rhs);
+//Field2D operator/(BoutReal lhs, const Field2D& rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Constant<L>, R, bout::op::Div>>
+operator/(L lhs, const R& rhs) {
+  return BinaryExpr<Constant<L>, R, bout::op::Div>{
+      static_cast<typename Constant<L>::View>(lhs),
+      static_cast<typename R::View>(rhs),
+      bout::op::Div{},
+      rhs.getMesh(),
+      rhs.getLocation(),
+      rhs.getDirections(),
+      std::nullopt,
+      rhs.getMesh()->getRegion2D("RGN_ALL")};
+}
 
 /*!
  * Unary minus. Returns the negative of given field,
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index c11bab0599..cab156db79 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -548,7 +548,25 @@ public:
     return *this;
   }
   Field3D& operator*=(const Field2D& rhs);
-  Field3D& operator*=(BoutReal rhs);
+  //Field3D& operator*=(BoutReal rhs);
+  // here1
+  template <typename R, typename = std::enable_if_t<is_expr_constant_v<R>>>
+  Field3D& operator*=(R rhs) {
+    //printf("RUNNING operator*= with CUDA\n");
+    if (data.unique()) {
+      // Delete existing parallel slices. We don't copy parallel slices, so any
+      // that currently exist will be incorrect.
+      clearParallelSlices();
+
+      auto BE = (*this) * rhs;
+      regionID = BE.getRegionID();
+      BE.evaluate(&data[0]);
+    } else {
+      (*this) = (*this) * rhs;
+    }
+
+    return *this;
+  }
   ///@}
 
   /// Division operators
@@ -799,17 +817,51 @@ operator/(const L& lhs, const R& rhs) {
 
 Field3D operator+(const Field3D& lhs, BoutReal rhs);
 Field3D operator-(const Field3D& lhs, BoutReal rhs);
-Field3D operator*(const Field3D& lhs, BoutReal rhs);
+//Field3D operator*(const Field3D& lhs, BoutReal rhs);
+//here2
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<L, Constant<R>, bout::op::Mul>>
+operator*(const L& lhs, R rhs) {
+  //static_assert(always_false<L> || always_false<R>, "Hello");
+  auto regionID = lhs.getRegionID();
+
+  return BinaryExpr<L, Constant<R>, bout::op::Mul>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename Constant<R>::View>(rhs),
+      bout::op::Mul{},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      regionID,
+      lhs.getMesh()->getRegion("RGN_ALL")};
+}
 Field3D operator/(const Field3D& lhs, BoutReal rhs);
 
-Field3D operator+(BoutReal lhs, const Field3D& rhs);
+//Field3D operator+(BoutReal lhs, const Field3D& rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Constant<L>, R, bout::op::Add>>
+operator+(const L& lhs, const R& rhs) {
+  auto regionID = rhs.getRegionID();
+
+  return BinaryExpr<Constant<L>, R, bout::op::Add>{
+      static_cast<typename Constant<L>::View>(lhs),
+      static_cast<typename R::View>(rhs),
+      bout::op::Add{},
+      rhs.getMesh(),
+      rhs.getLocation(),
+      rhs.getDirections(),
+      regionID,
+      rhs.getMesh()->getRegion("RGN_ALL")};
+}
 Field3D operator-(BoutReal lhs, const Field3D& rhs);
+#if 0
 //Field3D operator*(BoutReal lhs, const Field3D& rhs);
 template <typename L, typename R>
 std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,
                  BinaryExpr<Constant<L>, R, bout::op::Mul>>
 operator*(const L& lhs, const R& rhs) {
-  //static_assert(always_false<L> || always_false<R>, "Hello");
   auto regionID = rhs.getRegionID();
 
   return BinaryExpr<Constant<L>, R, bout::op::Mul>{
@@ -822,9 +874,29 @@ operator*(const L& lhs, const R& rhs) {
       regionID,
       rhs.getMesh()->getRegion("RGN_ALL")};
 }
+#endif
 
 Field3D operator/(BoutReal lhs, const Field3D& rhs);
 
+#define FIELD3D_BOUTREAL_OP(OP_SYM, OP_KIND)                      \
+  template <typename L, typename R>                               \
+  std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>, \
+                   BinaryExpr<Constant<L>, R, bout::op::OP_KIND>> \
+  operator OP_SYM(const L & lhs, const R & rhs) {                \
+    auto regionID = rhs.getRegionID();                            \
+    return BinaryExpr<Constant<L>, R, bout::op::OP_KIND>{         \
+        static_cast<typename Constant<L>::View>(lhs),             \
+        static_cast<typename R::View>(rhs),                       \
+        bout::op::OP_KIND{},                                      \
+        rhs.getMesh(),                                            \
+        rhs.getLocation(),                                        \
+        rhs.getDirections(),                                      \
+        regionID,                                                 \
+        rhs.getMesh()->getRegion("RGN_ALL")};                     \
+  }
+
+FIELD3D_BOUTREAL_OP(*, Mul)
+
 /*!
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 42aa761886..c8383b12fa 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -426,10 +426,7 @@ inline auto SQ(const T& t) {
   return t * t;
 }
 
-template <>
-BOUT_HOST_DEVICE inline auto SQ(const BoutReal& t) {
-  return t * t;
-}
+BOUT_HOST_DEVICE inline BoutReal SQ(const BoutReal& t) { return t * t; }
 
 /*!
  * Round \p x to the nearest integer
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 9ae40ba41b..4040f8a175 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -315,6 +315,8 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) {
 }
 
 // Provide the C++ wrapper for multiplication of Field3D and BoutReal
+// here2
+#if 0
 Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
 
@@ -331,8 +333,11 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field3D by multiplication with BoutReal
+// here1
+#if 0
 Field3D& Field3D::operator*=(const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
   // only if data is unique we update the field
@@ -355,6 +360,7 @@ Field3D& Field3D::operator*=(const BoutReal rhs) {
   }
   return *this;
 }
+#endif
 
 // Provide the C++ wrapper for division of Field3D and BoutReal
 Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
@@ -601,6 +607,7 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
 }
 #endif
 
+#if 0
 // Provide the C++ operator to update Field2D by multiplication with Field2D
 Field2D& Field2D::operator*=(const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -621,6 +628,7 @@ Field2D& Field2D::operator*=(const Field2D& rhs) {
   }
   return *this;
 }
+#endif
 
 #if 0
 // Provide the C++ wrapper for division of Field2D and Field2D
@@ -681,6 +689,7 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
 }
 #endif
 
+#if 0
 // Provide the C++ operator to update Field2D by addition with Field2D
 Field2D& Field2D::operator+=(const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -701,6 +710,7 @@ Field2D& Field2D::operator+=(const Field2D& rhs) {
   }
   return *this;
 }
+#endif
 
 // Provide the C++ wrapper for subtraction of Field2D and Field2D
 #if 0
@@ -721,6 +731,7 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
 }
 #endif
 
+#if 0
 // Provide the C++ operator to update Field2D by subtraction with Field2D
 Field2D& Field2D::operator-=(const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -741,6 +752,7 @@ Field2D& Field2D::operator-=(const Field2D& rhs) {
   }
   return *this;
 }
+#endif
 
 // Provide the C++ wrapper for multiplication of Field2D and FieldPerp
 FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) {
@@ -826,6 +838,7 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) {
   return result;
 }
 
+#if 0
 // Provide the C++ wrapper for multiplication of Field2D and BoutReal
 Field2D operator*(const Field2D& lhs, const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -841,7 +854,9 @@ Field2D operator*(const Field2D& lhs, const BoutReal rhs) {
   checkData(result);
   return result;
 }
+#endif
 
+#if 0
 // Provide the C++ operator to update Field2D by multiplication with BoutReal
 Field2D& Field2D::operator*=(const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -861,7 +876,9 @@ Field2D& Field2D::operator*=(const BoutReal rhs) {
   }
   return *this;
 }
+#endif
 
+#if 0
 // Provide the C++ wrapper for division of Field2D and BoutReal
 Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -878,6 +895,7 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 #if 0
 // Provide the C++ operator to update Field2D by division with BoutReal
@@ -1695,6 +1713,7 @@ Field3D operator/(const BoutReal lhs, const Field3D& rhs) {
   return result;
 }
 
+#if 0
 // Provide the C++ wrapper for addition of BoutReal and Field3D
 Field3D operator+(const BoutReal lhs, const Field3D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -1712,6 +1731,7 @@ Field3D operator+(const BoutReal lhs, const Field3D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ wrapper for subtraction of BoutReal and Field3D
 Field3D operator-(const BoutReal lhs, const Field3D& rhs) {
@@ -1749,6 +1769,7 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
 }
 #endif
 
+#if 0
 // Provide the C++ wrapper for division of BoutReal and Field2D
 Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -1764,6 +1785,7 @@ Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ wrapper for addition of BoutReal and Field2D
 Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
@@ -1781,6 +1803,7 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
   return result;
 }
 
+#if 0
 // Provide the C++ wrapper for subtraction of BoutReal and Field2D
 Field2D operator-(const BoutReal lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -1796,6 +1819,7 @@ Field2D operator-(const BoutReal lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ wrapper for multiplication of BoutReal and FieldPerp
 FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 8bded7fee5..b8fd33c019 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1102,7 +1102,7 @@ int Coordinates::geometry(bool recalculate_staggered,
     if (localmesh->get(d2x, "d2x" + suffix, 0.0, false, location)) {
       output_warn.write(
           "\tWARNING: differencing quantity 'd2x' not found. Calculating from dx\n");
-      d1_dx = bout::derivatives::index::DDX(1. / dx); // d/di(1/dx)
+      d1_dx = bout::derivatives::index::DDX(FieldMetric{1. / dx}); // d/di(1/dx)
 
       communicate(d1_dx);
       d1_dx =
@@ -1156,7 +1156,7 @@ int Coordinates::geometry(bool recalculate_staggered,
     if (localmesh->get(d2x, "d2x", 0.0, false)) {
       output_warn.write(
           "\tWARNING: differencing quantity 'd2x' not found. Calculating from dx\n");
-      d1_dx = bout::derivatives::index::DDX(1. / dx); // d/di(1/dx)
+      d1_dx = bout::derivatives::index::DDX(FieldMetric{1. / dx}); // d/di(1/dx)
 
       communicate(d1_dx);
       d1_dx =
diff --git a/src/physics/snb.cxx b/src/physics/snb.cxx
index 80da9e1bf8..475b12ca1a 100644
--- a/src/physics/snb.cxx
+++ b/src/physics/snb.cxx
@@ -14,7 +14,7 @@ Field3D HeatFluxSNB::divHeatFlux(const Field3D& Te, const Field3D& Ne,
   Field3D thermal_speed = sqrt(2. * SI::qe * Te / SI::Me);
 
   BoutReal Y = SQ(SQ(SI::qe) / (SI::e0 * SI::Me)) / (4 * PI);
-  Field3D coulomb_log = 6.6 - 0.5 * log(Ne * 1e-20) + 1.5 * log(Te);
+  Field3D coulomb_log = 6.6 - 0.5 * log(Field3D{Ne * 1e-20}) + 1.5 * log(Te);
 
   // Thermal electron-electron mean free path [m]
   Field3D lambda_ee_T = pow(thermal_speed, 4) / (Y * Ne * coulomb_log);

From 338920e284e39ae7f9954a0adcd3e87cb6444992 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Sat, 31 May 2025 21:17:34 -0700
Subject: [PATCH 0185/1827] More operators

---
 .../elm-pb-outerloop/elm_pb_outerloop.cxx     |   2 +-
 include/bout/field3d.hxx                      | 129 +++--
 include/bout/fieldops.hxx                     |  14 +-
 src/field/generated_fieldops.cxx              | 541 +-----------------
 src/physics/snb.cxx                           |   2 +-
 5 files changed, 76 insertions(+), 612 deletions(-)

diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index 7d38780814..901e57bf97 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -1283,7 +1283,7 @@ class ELMpb : public PhysicsModel {
     ////////////////////////////////////////////
     // Transitions from 0 in core to 1 in vacuum
     if (nonlinear) {
-      vac_mask = (1.0 - tanh(((P0 + P) - vacuum_pressure) / vacuum_trans)) / 2.0;
+      vac_mask = (1.0 - tanh(Field3D{((P0 + P) - vacuum_pressure) / vacuum_trans})) / 2.0;
 
       // Update resistivity
       if (spitzer_resist) {
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index cab156db79..d4dd1397a7 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -749,7 +749,7 @@ BinaryExpr<L, R, bout::op::Div> operator/(const L& lhs, const R& rhs) {
                                               : lhs.getMesh()->getRegion("RGN_ALL"))};
 }
 
-Field3D operator+(const Field3D& lhs, const Field2D& rhs);
+//Field3D operator+(const Field3D& lhs, const Field2D& rhs);
 #if 0
 template <typename L, typename R,
           std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
@@ -771,8 +771,9 @@ BinaryExpr<L, R, bout::op::Add> operator+(const L& lhs, const R& rhs) {
                     rhs.getRegion("RGN_ALL")};
 }
 #endif
-Field3D operator-(const Field3D& lhs, const Field2D& rhs);
+//Field3D operator-(const Field3D& lhs, const Field2D& rhs);
 //Field3D operator*(const Field3D& lhs, const Field2D& rhs);
+#if 0
 template <typename L, typename R>
 std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
                  BinaryExpr<L, R, bout::op::Mul>>
@@ -793,7 +794,9 @@ operator*(const L& lhs, const R& rhs) {
       regionID,
       lhs.getMesh()->getRegion("RGN_ALL")};
 }
+#endif
 //Field3D operator/(const Field3D& lhs, const Field2D& rhs);
+#if 0
 template <typename L, typename R>
 std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
                  BinaryExpr<L, R, bout::op::Div>>
@@ -814,80 +817,73 @@ operator/(const L& lhs, const R& rhs) {
       regionID,
       lhs.getMesh()->getRegion("RGN_ALL")};
 }
+#endif
 
-Field3D operator+(const Field3D& lhs, BoutReal rhs);
-Field3D operator-(const Field3D& lhs, BoutReal rhs);
+#define FIELD3D_FIELD3D_FIELD2D_OP(OP_SYM, OP_TYPE)                                      \
+  template <typename L, typename R>                                                      \
+  std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,                         \
+                   BinaryExpr<L, R, bout::op::OP_TYPE>> operator OP_SYM(const L & lhs,   \
+                                                                        const R & rhs) { \
+    auto regionID = lhs.getRegionID();                                                   \
+    int mesh_nz = lhs.getMesh()->LocalNz;                                                \
+    return BinaryExpr<L, R, bout::op::OP_TYPE>{                                          \
+        static_cast<typename L::View>(lhs),                                              \
+        static_cast<typename R::View>(rhs).setScale(1, mesh_nz),                         \
+        bout::op::OP_TYPE{},                                                             \
+        lhs.getMesh(),                                                                   \
+        lhs.getLocation(),                                                               \
+        lhs.getDirections(),                                                             \
+        regionID,                                                                        \
+        lhs.getMesh()->getRegion("RGN_ALL")};                                            \
+  }
+
+FIELD3D_FIELD3D_FIELD2D_OP(+, Add)
+FIELD3D_FIELD3D_FIELD2D_OP(-, Sub)
+FIELD3D_FIELD3D_FIELD2D_OP(*, Mul)
+FIELD3D_FIELD3D_FIELD2D_OP(/, Div)
+
+//Field3D operator+(const Field3D& lhs, BoutReal rhs);
+//Field3D operator-(const Field3D& lhs, BoutReal rhs);
 //Field3D operator*(const Field3D& lhs, BoutReal rhs);
-//here2
-template <typename L, typename R>
-std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>,
-                 BinaryExpr<L, Constant<R>, bout::op::Mul>>
-operator*(const L& lhs, R rhs) {
-  //static_assert(always_false<L> || always_false<R>, "Hello");
-  auto regionID = lhs.getRegionID();
+//Field3D operator/(const Field3D& lhs, BoutReal rhs);
 
-  return BinaryExpr<L, Constant<R>, bout::op::Mul>{
-      static_cast<typename L::View>(lhs),
-      static_cast<typename Constant<R>::View>(rhs),
-      bout::op::Mul{},
-      lhs.getMesh(),
-      lhs.getLocation(),
-      lhs.getDirections(),
-      regionID,
-      lhs.getMesh()->getRegion("RGN_ALL")};
-}
-Field3D operator/(const Field3D& lhs, BoutReal rhs);
+#define FIELD3D_FIELD3D_BOUTREAL_OP(OP_SYM, OP_TYPE)              \
+  template <typename L, typename R>                               \
+  std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>, \
+                   BinaryExpr<L, Constant<R>, bout::op::OP_TYPE>> \
+  operator OP_SYM(const L & lhs, R rhs) {                         \
+    auto regionID = lhs.getRegionID();                            \
+    return BinaryExpr<L, Constant<R>, bout::op::OP_TYPE>{         \
+        static_cast<typename L::View>(lhs),                       \
+        static_cast<typename Constant<R>::View>(rhs),             \
+        bout::op::OP_TYPE{},                                      \
+        lhs.getMesh(),                                            \
+        lhs.getLocation(),                                        \
+        lhs.getDirections(),                                      \
+        regionID,                                                 \
+        lhs.getMesh()->getRegion("RGN_ALL")};                     \
+  }
+
+FIELD3D_FIELD3D_BOUTREAL_OP(+, Add)
+FIELD3D_FIELD3D_BOUTREAL_OP(-, Sub)
+FIELD3D_FIELD3D_BOUTREAL_OP(*, Mul)
+FIELD3D_FIELD3D_BOUTREAL_OP(/, Div)
 
 //Field3D operator+(BoutReal lhs, const Field3D& rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,
-                 BinaryExpr<Constant<L>, R, bout::op::Add>>
-operator+(const L& lhs, const R& rhs) {
-  auto regionID = rhs.getRegionID();
-
-  return BinaryExpr<Constant<L>, R, bout::op::Add>{
-      static_cast<typename Constant<L>::View>(lhs),
-      static_cast<typename R::View>(rhs),
-      bout::op::Add{},
-      rhs.getMesh(),
-      rhs.getLocation(),
-      rhs.getDirections(),
-      regionID,
-      rhs.getMesh()->getRegion("RGN_ALL")};
-}
-Field3D operator-(BoutReal lhs, const Field3D& rhs);
-#if 0
+//Field3D operator-(BoutReal lhs, const Field3D& rhs);
 //Field3D operator*(BoutReal lhs, const Field3D& rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,
-                 BinaryExpr<Constant<L>, R, bout::op::Mul>>
-operator*(const L& lhs, const R& rhs) {
-  auto regionID = rhs.getRegionID();
-
-  return BinaryExpr<Constant<L>, R, bout::op::Mul>{
-      static_cast<typename Constant<L>::View>(lhs),
-      static_cast<typename R::View>(rhs),
-      bout::op::Mul{},
-      rhs.getMesh(),
-      rhs.getLocation(),
-      rhs.getDirections(),
-      regionID,
-      rhs.getMesh()->getRegion("RGN_ALL")};
-}
-#endif
-
-Field3D operator/(BoutReal lhs, const Field3D& rhs);
+//Field3D operator/(BoutReal lhs, const Field3D& rhs);
 
-#define FIELD3D_BOUTREAL_OP(OP_SYM, OP_KIND)                      \
+#define FIELD3D_BOUTREAL_FIELD3D_OP(OP_SYM, OP_TYPE)              \
   template <typename L, typename R>                               \
   std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>, \
-                   BinaryExpr<Constant<L>, R, bout::op::OP_KIND>> \
-  operator OP_SYM(const L & lhs, const R & rhs) {                \
+                   BinaryExpr<Constant<L>, R, bout::op::OP_TYPE>> \
+  operator OP_SYM(const L & lhs, const R & rhs) {                 \
     auto regionID = rhs.getRegionID();                            \
-    return BinaryExpr<Constant<L>, R, bout::op::OP_KIND>{         \
+    return BinaryExpr<Constant<L>, R, bout::op::OP_TYPE>{         \
         static_cast<typename Constant<L>::View>(lhs),             \
         static_cast<typename R::View>(rhs),                       \
-        bout::op::OP_KIND{},                                      \
+        bout::op::OP_TYPE{},                                      \
         rhs.getMesh(),                                            \
         rhs.getLocation(),                                        \
         rhs.getDirections(),                                      \
@@ -895,7 +891,10 @@ Field3D operator/(BoutReal lhs, const Field3D& rhs);
         rhs.getMesh()->getRegion("RGN_ALL")};                     \
   }
 
-FIELD3D_BOUTREAL_OP(*, Mul)
+FIELD3D_BOUTREAL_FIELD3D_OP(+, Add)
+FIELD3D_BOUTREAL_FIELD3D_OP(-, Sub)
+FIELD3D_BOUTREAL_FIELD3D_OP(*, Mul)
+FIELD3D_BOUTREAL_FIELD3D_OP(/, Div)
 
 /*!
  * Unary minus. Returns the negative of given field,
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 6ec7947be4..0de73d1205 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -38,12 +38,7 @@ template <typename T>
 struct is_expr_constant<Constant<T>>
     : std::integral_constant<bool, is_expr_constant_v<std::decay_t<T>>> {};
 
-// After the specialization…
-static_assert(is_expr_constant_v<Constant<int>> == true,
-              "Constant<int> should be recognized as an expr_constant!");
-static_assert(is_expr_constant_v<Constant<float>> == true,
-              "Constant<float> should be recognized as an expr_constant!");
-
+constexpr int THREADS = 256;
 namespace bout {
 namespace op {
 struct Assign {
@@ -99,8 +94,7 @@ struct Add {
 };
 
 template <typename Expr>
-__global__ __launch_bounds__(256) static void evaluatorExpr(BoutReal* out,
-                                                            const Expr expr) {
+__global__ void __launch_bounds__(THREADS) evaluatorExpr(BoutReal* out, const Expr expr) {
   int tid = threadIdx.x + blockIdx.x * blockDim.x;
   if (tid >= expr.size()) {
     return;
@@ -197,13 +191,9 @@ struct BinaryExpr {
   operator View() const { return View{lhs, rhs, &indices[0], indices.size(), f}; }
 
   void evaluate(BoutReal* data) const {
-    constexpr int THREADS = 256;
     int blocks = (size() + THREADS - 1) / THREADS;
     evaluatorExpr<<<blocks, THREADS>>>(&data[0], static_cast<View>(*this));
     cudaDeviceSynchronize();
-    //for(int i=0; i<size(); ++i) {
-    //  data[regionIdx(i)] = f(i, lhs, rhs); // single‐pass fusion
-    //}
   }
 
   Mesh* getMesh() const { return mesh; }
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 4040f8a175..c69597c8db 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -6,32 +6,6 @@
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 
-// Provide the C++ wrapper for multiplication of Field3D and Field2D
-#if 0
-Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator "<< __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[base_ind + jz] * rhs[index];
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
 // Provide the C++ operator to update Field3D by multiplication with Field2D
 Field3D& Field3D::operator*=(const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -63,65 +37,6 @@ Field3D& Field3D::operator*=(const Field2D& rhs) {
 }
 
 #if 0
-// Provide the C++ wrapper for division of Field3D and Field2D
-Field3D operator/(const Field3D& lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator "<< __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    const auto tmp = 1.0 / rhs[index];
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[base_ind + jz] * tmp;
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-#if 0
-// Provide the C++ operator to update Field3D by division with Field2D
-Field3D& Field3D::operator/=(const Field2D& rhs) {
-  std::cout << "RUNNING operator "<< __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
-      const auto base_ind = fieldmesh->ind2Dto3D(index);
-      const auto tmp = 1.0 / rhs[index];
-      for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) {
-        (*this)[base_ind + jz] *= tmp;
-      }
-    }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) / rhs;
-  }
-  return *this;
-}
-#endif
-
 // Provide the C++ wrapper for addition of Field3D and Field2D
 Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -145,6 +60,7 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field3D by addition with Field2D
 Field3D& Field3D::operator+=(const Field2D& rhs) {
@@ -176,6 +92,7 @@ Field3D& Field3D::operator+=(const Field2D& rhs) {
   return *this;
 }
 
+#if 0
 // Provide the C++ wrapper for subtraction of Field3D and Field2D
 Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -199,6 +116,7 @@ Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field3D by subtraction with Field2D
 Field3D& Field3D::operator-=(const Field2D& rhs) {
@@ -314,54 +232,7 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) {
   return result;
 }
 
-// Provide the C++ wrapper for multiplication of Field3D and BoutReal
-// here2
-#if 0
-Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs;
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-// Provide the C++ operator to update Field3D by multiplication with BoutReal
-// here1
 #if 0
-Field3D& Field3D::operator*=(const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) * rhs;
-  }
-  return *this;
-}
-#endif
-
 // Provide the C++ wrapper for division of Field3D and BoutReal
 Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -380,6 +251,7 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field3D by division with BoutReal
 Field3D& Field3D::operator/=(const BoutReal rhs) {
@@ -406,6 +278,7 @@ Field3D& Field3D::operator/=(const BoutReal rhs) {
   return *this;
 }
 
+#if 0
 // Provide the C++ wrapper for addition of Field3D and BoutReal
 Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -423,6 +296,7 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field3D by addition with BoutReal
 Field3D& Field3D::operator+=(const BoutReal rhs) {
@@ -448,6 +322,7 @@ Field3D& Field3D::operator+=(const BoutReal rhs) {
   return *this;
 }
 
+#if 0
 // Provide the C++ wrapper for subtraction of Field3D and BoutReal
 Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -465,6 +340,7 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ operator to update Field3D by subtraction with BoutReal
 Field3D& Field3D::operator-=(const BoutReal rhs) {
@@ -490,32 +366,6 @@ Field3D& Field3D::operator-=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for multiplication of Field2D and Field3D
-#if 0
-Field3D operator*(const Field2D& lhs, const Field3D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR(index, lhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[index] * rhs[base_ind + jz];
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
 // Provide the C++ wrapper for division of Field2D and Field3D
 Field3D operator/(const Field2D& lhs, const Field3D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -588,67 +438,6 @@ Field3D operator-(const Field2D& lhs, const Field3D& rhs) {
   return result;
 }
 
-// Provide the C++ wrapper for multiplication of Field2D and Field2D
-#if 0
-Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-#if 0
-// Provide the C++ operator to update Field2D by multiplication with Field2D
-Field2D& Field2D::operator*=(const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) * rhs;
-  }
-  return *this;
-}
-#endif
-
-#if 0
-// Provide the C++ wrapper for division of Field2D and Field2D
-Field2D operator/(const Field2D& lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] / rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
 // Provide the C++ operator to update Field2D by division with Field2D
 Field2D& Field2D::operator/=(const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -670,90 +459,6 @@ Field2D& Field2D::operator/=(const Field2D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for addition of Field2D and Field2D
-#if 0
-Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-#if 0
-// Provide the C++ operator to update Field2D by addition with Field2D
-Field2D& Field2D::operator+=(const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) + rhs;
-  }
-  return *this;
-}
-#endif
-
-// Provide the C++ wrapper for subtraction of Field2D and Field2D
-#if 0
-Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-#if 0
-// Provide the C++ operator to update Field2D by subtraction with Field2D
-Field2D& Field2D::operator-=(const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) - rhs;
-  }
-  return *this;
-}
-#endif
-
 // Provide the C++ wrapper for multiplication of Field2D and FieldPerp
 FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -838,88 +543,6 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) {
   return result;
 }
 
-#if 0
-// Provide the C++ wrapper for multiplication of Field2D and BoutReal
-Field2D operator*(const Field2D& lhs, const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs;
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-#if 0
-// Provide the C++ operator to update Field2D by multiplication with BoutReal
-Field2D& Field2D::operator*=(const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) * rhs;
-  }
-  return *this;
-}
-#endif
-
-#if 0
-// Provide the C++ wrapper for division of Field2D and BoutReal
-Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  const auto tmp = 1.0 / rhs;
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * tmp;
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-#if 0
-// Provide the C++ operator to update Field2D by division with BoutReal
-Field2D& Field2D::operator/=(const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-
-    checkData(*this);
-    checkData(rhs);
-
-    const auto tmp = 1.0 / rhs;
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) / rhs;
-  }
-  return *this;
-}
-#endif
-
 // Provide the C++ wrapper for addition of Field2D and BoutReal
 Field2D operator+(const Field2D& lhs, const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -956,24 +579,6 @@ Field2D& Field2D::operator+=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for subtraction of Field2D and BoutReal
-#if 0
-Field2D operator-(const Field2D& lhs, const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs;
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
 // Provide the C++ operator to update Field2D by subtraction with BoutReal
 Field2D& Field2D::operator-=(const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -1675,118 +1280,6 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) {
   return *this;
 }
 
-#if 0
-// Provide the C++ wrapper for multiplication of BoutReal and Field3D
-Field3D operator*(const BoutReal lhs, const Field3D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs * rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-// Provide the C++ wrapper for division of BoutReal and Field3D
-Field3D operator/(const BoutReal lhs, const Field3D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs / rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-
-#if 0
-// Provide the C++ wrapper for addition of BoutReal and Field3D
-Field3D operator+(const BoutReal lhs, const Field3D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs + rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-// Provide the C++ wrapper for subtraction of BoutReal and Field3D
-Field3D operator-(const BoutReal lhs, const Field3D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs - rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-
-#if 0
-// Provide the C++ wrapper for multiplication of BoutReal and Field2D
-Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field2D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs * rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-#if 0
-// Provide the C++ wrapper for division of BoutReal and Field2D
-Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field2D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs / rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
 // Provide the C++ wrapper for addition of BoutReal and Field2D
 Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -1803,24 +1296,6 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
   return result;
 }
 
-#if 0
-// Provide the C++ wrapper for subtraction of BoutReal and Field2D
-Field2D operator-(const BoutReal lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field2D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs - rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
 // Provide the C++ wrapper for multiplication of BoutReal and FieldPerp
 FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
diff --git a/src/physics/snb.cxx b/src/physics/snb.cxx
index 475b12ca1a..f21bfb7ee0 100644
--- a/src/physics/snb.cxx
+++ b/src/physics/snb.cxx
@@ -11,7 +11,7 @@ namespace bout {
 Field3D HeatFluxSNB::divHeatFlux(const Field3D& Te, const Field3D& Ne,
                                  Field3D* Div_Q_SH_out) {
 
-  Field3D thermal_speed = sqrt(2. * SI::qe * Te / SI::Me);
+  Field3D thermal_speed = sqrt(Field3D{2. * SI::qe * Te / SI::Me});
 
   BoutReal Y = SQ(SQ(SI::qe) / (SI::e0 * SI::Me)) / (4 * PI);
   Field3D coulomb_log = 6.6 - 0.5 * log(Field3D{Ne * 1e-20}) + 1.5 * log(Te);

From 6e8818114e398258ca548d3b85e061d92c78264e Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Sat, 31 May 2025 23:25:47 -0700
Subject: [PATCH 0186/1827] More operators and cleanup

---
 include/bout/field2d.hxx         |  25 ++++-
 include/bout/field3d.hxx         | 157 +++++--------------------------
 src/field/generated_fieldops.cxx |   2 +
 3 files changed, 47 insertions(+), 137 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 97946ee713..b7911b7e76 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -538,7 +538,8 @@ operator/(const L& lhs, R rhs) {
       lhs.getMesh()->getRegion2D("RGN_ALL")};
 }
 
-Field2D operator+(BoutReal lhs, const Field2D& rhs);
+#if 0
+//Field2D operator+(BoutReal lhs, const Field2D& rhs);
 //Field2D operator-(BoutReal lhs, const Field2D& rhs);
 template <typename L, typename R>
 std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
@@ -588,6 +589,28 @@ operator/(L lhs, const R& rhs) {
       std::nullopt,
       rhs.getMesh()->getRegion2D("RGN_ALL")};
 }
+#endif
+
+#define FIELD2D_BOUTREAL_FIELD2D_OP(OP_SYM, OP_TYPE)              \
+  template <typename L, typename R>                               \
+  std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>, \
+                   BinaryExpr<Constant<L>, R, bout::op::OP_TYPE>> \
+  operator OP_SYM(L lhs, const R & rhs) {                         \
+    return BinaryExpr<Constant<L>, R, bout::op::OP_TYPE>{         \
+        static_cast<typename Constant<L>::View>(lhs),             \
+        static_cast<typename R::View>(rhs),                       \
+        bout::op::OP_TYPE{},                                      \
+        rhs.getMesh(),                                            \
+        rhs.getLocation(),                                        \
+        rhs.getDirections(),                                      \
+        std::nullopt,                                             \
+        rhs.getMesh()->getRegion2D("RGN_ALL")};                   \
+  }
+
+FIELD2D_BOUTREAL_FIELD2D_OP(+, Add)
+FIELD2D_BOUTREAL_FIELD2D_OP(-, Sub)
+FIELD2D_BOUTREAL_FIELD2D_OP(*, Mul)
+FIELD2D_BOUTREAL_FIELD2D_OP(/, Div)
 
 /*!
  * Unary minus. Returns the negative of given field,
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index d4dd1397a7..8f433909f9 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -676,148 +676,33 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs);
 FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs);
 FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
 
-template <typename L, typename R,
-          typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
-BinaryExpr<L, R, bout::op::Add> operator+(const L& lhs, const R& rhs) {
-  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
-
-  //std::cout << "RUNNING operator+ using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr<L, R, bout::op::Add>{static_cast<typename L::View>(lhs),
-                                         static_cast<typename R::View>(rhs),
-                                         bout::op::Add{},
-                                         lhs.getMesh(),
-                                         lhs.getLocation(),
-                                         lhs.getDirections(),
-                                         regionID,
-                                         (regionID.has_value()
-                                              ? lhs.getMesh()->getRegion(regionID.value())
-                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
-}
-
-template <typename L, typename R,
-          typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
-BinaryExpr<L, R, bout::op::Sub> operator-(const L& lhs, const R& rhs) {
-  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
-
-  //std::cout << "RUNNING operator- using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr<L, R, bout::op::Sub>{static_cast<typename L::View>(lhs),
-                                         static_cast<typename R::View>(rhs),
-                                         bout::op::Sub{},
-                                         lhs.getMesh(),
-                                         lhs.getLocation(),
-                                         lhs.getDirections(),
-                                         regionID,
-                                         (regionID.has_value()
-                                              ? lhs.getMesh()->getRegion(regionID.value())
-                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
-}
-
-template <typename L, typename R>
-std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>,
-                 BinaryExpr<L, R, bout::op::Mul>>
-operator*(const L& lhs, const R& rhs) {
-  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
-
-  //std::cout << "RUNNING operator* using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr<L, R, bout::op::Mul>{static_cast<typename L::View>(lhs),
-                                         static_cast<typename R::View>(rhs),
-                                         bout::op::Mul{},
-                                         lhs.getMesh(),
-                                         lhs.getLocation(),
-                                         lhs.getDirections(),
-                                         regionID,
-                                         (regionID.has_value()
-                                              ? lhs.getMesh()->getRegion(regionID.value())
-                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
-}
+#define FIELD3D_FIELD3D_FIELD3D_OP(OP_SYM, OP_TYPE)                                    \
+  template <typename L, typename R,                                                    \
+            typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>> \
+  BinaryExpr<L, R, bout::op::OP_TYPE> operator OP_SYM(const L & lhs, const R & rhs) {  \
+    auto regionID =                                                                    \
+        lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());          \
+    return BinaryExpr<L, R, bout::op::OP_TYPE>{                                        \
+        static_cast<typename L::View>(lhs),                                            \
+        static_cast<typename R::View>(rhs),                                            \
+        bout::op::OP_TYPE{},                                                           \
+        lhs.getMesh(),                                                                 \
+        lhs.getLocation(),                                                             \
+        lhs.getDirections(),                                                           \
+        regionID,                                                                      \
+        (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())             \
+                              : lhs.getMesh()->getRegion("RGN_ALL"))};                 \
+  }
 
-template <typename L, typename R,
-          typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
-BinaryExpr<L, R, bout::op::Div> operator/(const L& lhs, const R& rhs) {
-  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
-
-  //std::cout << "RUNNING operator/ using BinaryExpr with CUDA" << "\n";
-  return BinaryExpr<L, R, bout::op::Div>{static_cast<typename L::View>(lhs),
-                                         static_cast<typename R::View>(rhs),
-                                         bout::op::Div{},
-                                         lhs.getMesh(),
-                                         lhs.getLocation(),
-                                         lhs.getDirections(),
-                                         regionID,
-                                         (regionID.has_value()
-                                              ? lhs.getMesh()->getRegion(regionID.value())
-                                              : lhs.getMesh()->getRegion("RGN_ALL"))};
-}
+FIELD3D_FIELD3D_FIELD3D_OP(+, Add)
+FIELD3D_FIELD3D_FIELD3D_OP(-, Sub)
+FIELD3D_FIELD3D_FIELD3D_OP(*, Mul)
+FIELD3D_FIELD3D_FIELD3D_OP(/, Div)
 
 //Field3D operator+(const Field3D& lhs, const Field2D& rhs);
-#if 0
-template <typename L, typename R,
-          std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
-                           BinaryExpr<L, R, bout::op::Add>>>
-BinaryExpr<L, R, bout::op::Add> operator+(const L& lhs, const R& rhs) {
-  //static_assert(always_false<L> || always_false<R>, "Hello");
-  auto regionID = lhs.getRegionID();
-
-  std::cout << "RUNNING Field3D + Field2D using BinaryExpr with CUDA" << "\n";
-  int mesh_nz = lhs.getMesh()->LocalNz;
-
-  return BinaryExpr{static_cast<typename L::View>(lhs),
-                    static_cast<typename R::View>(rhs).setScale(1, mesh_nz),
-                    bout::op::Add{},
-                    lhs.getMesh(),
-                    lhs.getLocation(),
-                    lhs.getDirections(),
-                    regionID,
-                    rhs.getRegion("RGN_ALL")};
-}
-#endif
 //Field3D operator-(const Field3D& lhs, const Field2D& rhs);
 //Field3D operator*(const Field3D& lhs, const Field2D& rhs);
-#if 0
-template <typename L, typename R>
-std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
-                 BinaryExpr<L, R, bout::op::Mul>>
-operator*(const L& lhs, const R& rhs) {
-  //static_assert(always_false<L> || always_false<R>, "Hello");
-  auto regionID = lhs.getRegionID();
-
-  //std::cout << "RUNNING Field3D * Field2D using BinaryExpr with CUDA" << "\n";
-  int mesh_nz = lhs.getMesh()->LocalNz;
-
-  return BinaryExpr<L, R, bout::op::Mul>{
-      static_cast<typename L::View>(lhs),
-      static_cast<typename R::View>(rhs).setScale(1, mesh_nz),
-      bout::op::Mul{},
-      lhs.getMesh(),
-      lhs.getLocation(),
-      lhs.getDirections(),
-      regionID,
-      lhs.getMesh()->getRegion("RGN_ALL")};
-}
-#endif
 //Field3D operator/(const Field3D& lhs, const Field2D& rhs);
-#if 0
-template <typename L, typename R>
-std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
-                 BinaryExpr<L, R, bout::op::Div>>
-operator/(const L& lhs, const R& rhs) {
-  //static_assert(always_false<L> || always_false<R>, "Hello");
-  auto regionID = lhs.getRegionID();
-
-  //std::cout << "RUNNING Field3D * Field2D using BinaryExpr with CUDA" << "\n";
-  int mesh_nz = lhs.getMesh()->LocalNz;
-
-  return BinaryExpr<L, R, bout::op::Div>{
-      static_cast<typename L::View>(lhs),
-      static_cast<typename R::View>(rhs).setScale(1, mesh_nz),
-      bout::op::Div{},
-      lhs.getMesh(),
-      lhs.getLocation(),
-      lhs.getDirections(),
-      regionID,
-      lhs.getMesh()->getRegion("RGN_ALL")};
-}
-#endif
 
 #define FIELD3D_FIELD3D_FIELD2D_OP(OP_SYM, OP_TYPE)                                      \
   template <typename L, typename R>                                                      \
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index c69597c8db..dca1605b91 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -1280,6 +1280,7 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) {
   return *this;
 }
 
+#if 0
 // Provide the C++ wrapper for addition of BoutReal and Field2D
 Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -1295,6 +1296,7 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
   checkData(result);
   return result;
 }
+#endif
 
 // Provide the C++ wrapper for multiplication of BoutReal and FieldPerp
 FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {

From 25d1272acdae941d8141fb671a97a790438cb0b5 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Sun, 1 Jun 2025 00:42:44 -0700
Subject: [PATCH 0187/1827] More operators and cleanup

---
 include/bout/field2d.hxx         | 334 ++++++--------------------
 include/bout/field3d.hxx         | 158 ++-----------
 src/field/generated_fieldops.cxx | 386 +------------------------------
 3 files changed, 98 insertions(+), 780 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index b7911b7e76..f430b98c6c 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -269,83 +269,23 @@ public:
     return operator()(jx, jy);
   }
 
-  /// In-place addition. Copy-on-write used if data is shared
-  //Field2D& operator+=(const Field2D& rhs);
-  template <typename R, typename = std::enable_if_t<is_expr_field2d_v<R>>>
-  Field2D& operator+=(const R& rhs) {
-    //printf("RUNNING operator+= with CUDA\n");
-    if (data.unique()) {
-      auto BE = (*this) + rhs;
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) * rhs;
-    }
-
-    return *this;
-  }
-  /// In-place addition. Copy-on-write used if data is shared
-  Field2D& operator+=(BoutReal rhs);
-  /// In-place subtraction. Copy-on-write used if data is shared
-  //Field2D& operator-=(const Field2D& rhs);
-  //here1
-  template <typename R, typename = std::enable_if_t<is_expr_field2d_v<R>>>
-  Field2D& operator-=(const R& rhs) {
-    //printf("RUNNING operator+= with CUDA\n");
-    if (data.unique()) {
-      auto BE = (*this) - rhs;
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) * rhs;
-    }
-
-    return *this;
+#define FIELD2D_OP_EQUALS(OP_SYM)                                           \
+  template <typename R>                                                     \
+  std::enable_if_t<is_expr_field2d_v<R> || is_expr_constant_v<R>, Field2D&> \
+  operator OP_SYM##=(R rhs) {                                               \
+    if (data.unique()) {                                                    \
+      auto BE = (*this)OP_SYM rhs;                                          \
+      BE.evaluate(&data[0]);                                                \
+    } else {                                                                \
+      (*this) = (*this)OP_SYM rhs;                                          \
+    }                                                                       \
+    return *this;                                                           \
   }
-  /// In-place subtraction. Copy-on-write used if data is shared
-  Field2D& operator-=(BoutReal rhs);
-  /// In-place multiplication. Copy-on-write used if data is shared
-  //Field2D& operator*=(const Field2D& rhs);
-  template <typename R, typename = std::enable_if_t<is_expr_field2d_v<R>>>
-  Field2D& operator*=(const R& rhs) {
-    //printf("RUNNING operator+= with CUDA\n");
-    if (data.unique()) {
-      auto BE = (*this) * rhs;
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) * rhs;
-    }
 
-    return *this;
-  }
-  /// In-place multiplication. Copy-on-write used if data is shared
-  //Field2D& operator*=(BoutReal rhs);
-  template <typename R, typename = std::enable_if_t<is_expr_constant_v<R>>>
-  Field2D& operator*=(R rhs) {
-    //printf("RUNNING operator+= with CUDA\n");
-    if (data.unique()) {
-      auto BE = (*this) * rhs;
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) * rhs;
-    }
-
-    return *this;
-  }
-  /// In-place division. Copy-on-write used if data is shared
-  Field2D& operator/=(const Field2D& rhs);
-  /// In-place division. Copy-on-write used if data is shared
-  //Field2D& operator/=(BoutReal rhs);
-    template <typename R, typename = std::enable_if_t<is_expr_constant_v<R>>>
-  Field2D& operator/=(R rhs) {
-    //printf("RUNNING operator+= with CUDA\n");
-    if (data.unique()) {
-      auto BE = (*this) / rhs;
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) / rhs;
-    }
-
-    return *this;
-  }
+  FIELD2D_OP_EQUALS(+)
+  FIELD2D_OP_EQUALS(-)
+  FIELD2D_OP_EQUALS(*)
+  FIELD2D_OP_EQUALS(/)
 
   // FieldData virtual functions
 
@@ -405,191 +345,69 @@ private:
 
 // Non-member overloaded operators
 
-//Field2D operator+(const Field2D& lhs, const Field2D& rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
-                 BinaryExpr<L, R, bout::op::Add>>
-operator+(const L& lhs, const R& rhs) {
-  return BinaryExpr<L, R, bout::op::Add>{static_cast<typename L::View>(lhs),
-                                         static_cast<typename R::View>(rhs),
-                                         bout::op::Add{},
-                                         lhs.getMesh(),
-                                         lhs.getLocation(),
-                                         lhs.getDirections(),
-                                         std::nullopt,
-                                         lhs.getMesh()->getRegion2D("RGN_ALL")};
-}
-//Field2D operator-(const Field2D& lhs, const Field2D& rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
-                 BinaryExpr<L, R, bout::op::Sub>>
-operator-(const L& lhs, const R& rhs) {
-  return BinaryExpr<L, R, bout::op::Sub>{static_cast<typename L::View>(lhs),
-                                         static_cast<typename R::View>(rhs),
-                                         bout::op::Sub{},
-                                         lhs.getMesh(),
-                                         lhs.getLocation(),
-                                         lhs.getDirections(),
-                                         std::nullopt,
-                                         lhs.getMesh()->getRegion2D("RGN_ALL")};
-}
-//Field2D operator*(const Field2D& lhs, const Field2D& rhs);
-#if 1
-template <typename L, typename R>
-std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
-                 BinaryExpr<L, R, bout::op::Mul>>
-operator*(const L& lhs, const R& rhs) {
-  return BinaryExpr<L, R, bout::op::Mul>{static_cast<typename L::View>(lhs),
-                                         static_cast<typename R::View>(rhs),
-                                         bout::op::Mul{},
-                                         lhs.getMesh(),
-                                         lhs.getLocation(),
-                                         lhs.getDirections(),
-                                         std::nullopt,
-                                         lhs.getMesh()->getRegion2D("RGN_ALL")};
-}
-#endif
-//Field2D operator/(const Field2D& lhs, const Field2D& rhs);
-#if 1
-template <typename L, typename R>
-std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
-                 BinaryExpr<L, R, bout::op::Div>>
-operator/(const L& lhs, const R& rhs) {
-  return BinaryExpr<L, R, bout::op::Div>{static_cast<typename L::View>(lhs),
-                                         static_cast<typename R::View>(rhs),
-                                         bout::op::Div{},
-                                         lhs.getMesh(),
-                                         lhs.getLocation(),
-                                         lhs.getDirections(),
-                                         std::nullopt,
-                                         lhs.getMesh()->getRegion2D("RGN_ALL")};
-}
-#endif
+#define FIELD2D_FIELD2D_FIELD2D_OP(OP_SYM, OP_TYPE)                                      \
+  template <typename L, typename R>                                                      \
+  std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,                         \
+                   BinaryExpr<L, R, bout::op::OP_TYPE>> operator OP_SYM(const L & lhs,   \
+                                                                        const R & rhs) { \
+    return BinaryExpr<L, R, bout::op::OP_TYPE>{static_cast<typename L::View>(lhs),       \
+                                               static_cast<typename R::View>(rhs),       \
+                                               bout::op::OP_TYPE{},                      \
+                                               lhs.getMesh(),                            \
+                                               lhs.getLocation(),                        \
+                                               lhs.getDirections(),                      \
+                                               std::nullopt,                             \
+                                               lhs.getMesh()->getRegion2D("RGN_ALL")};   \
+  }
 
-Field3D operator+(const Field2D& lhs, const Field3D& rhs);
-Field3D operator-(const Field2D& lhs, const Field3D& rhs);
-//Field3D operator*(const Field2D& lhs, const Field3D& rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_field2d_v<L> && is_expr_field3d_v<R>,
-                 BinaryExpr<L, R, bout::op::Mul>>
-operator*(const L& lhs, const R& rhs) {
-  //static_assert(always_false<L> || always_false<R>, "Hello");
-  auto regionID = rhs.getRegionID();
-
-  //std::cout << "RUNNING Field3D * Field2D using BinaryExpr with CUDA" << "\n";
-  int mesh_nz = rhs.getMesh()->LocalNz;
-
-  return BinaryExpr<L, R, bout::op::Mul>{
-      static_cast<typename L::View>(lhs).setScale(1, mesh_nz),
-      static_cast<typename R::View>(rhs),
-      bout::op::Mul{},
-      rhs.getMesh(),
-      rhs.getLocation(),
-      rhs.getDirections(),
-      regionID,
-      rhs.getMesh()->getRegion("RGN_ALL")};
-}
-Field3D operator/(const Field2D& lhs, const Field3D& rhs);
-
-Field2D operator+(const Field2D& lhs, BoutReal rhs);
-//Field2D operator-(const Field2D& lhs, BoutReal rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
-                 BinaryExpr<L, Constant<R>, bout::op::Sub>>
-operator-(const L& lhs, R rhs) {
-  return BinaryExpr<L, Constant<R>, bout::op::Sub>{
-      static_cast<typename L::View>(lhs),
-      static_cast<typename Constant<R>::View>(rhs),
-      bout::op::Sub{},
-      lhs.getMesh(),
-      lhs.getLocation(),
-      lhs.getDirections(),
-      std::nullopt,
-      lhs.getMesh()->getRegion2D("RGN_ALL")};
-}
-//Field2D operator*(const Field2D& lhs, BoutReal rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
-                 BinaryExpr<L, Constant<R>, bout::op::Mul>>
-operator*(const L& lhs, R rhs) {
-  return BinaryExpr<L, Constant<R>, bout::op::Mul>{
-      static_cast<typename L::View>(lhs),
-      static_cast<typename Constant<R>::View>(rhs),
-      bout::op::Mul{},
-      lhs.getMesh(),
-      lhs.getLocation(),
-      lhs.getDirections(),
-      std::nullopt,
-      lhs.getMesh()->getRegion2D("RGN_ALL")};
-}
-//Field2D operator/(const Field2D& lhs, BoutReal rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
-                 BinaryExpr<L, Constant<R>, bout::op::Div>>
-operator/(const L& lhs, R rhs) {
-  return BinaryExpr<L, Constant<R>, bout::op::Div>{
-      static_cast<typename L::View>(lhs),
-      static_cast<typename Constant<R>::View>(rhs),
-      bout::op::Div{},
-      lhs.getMesh(),
-      lhs.getLocation(),
-      lhs.getDirections(),
-      std::nullopt,
-      lhs.getMesh()->getRegion2D("RGN_ALL")};
-}
+FIELD2D_FIELD2D_FIELD2D_OP(+, Add)
+FIELD2D_FIELD2D_FIELD2D_OP(-, Sub)
+FIELD2D_FIELD2D_FIELD2D_OP(*, Mul)
+FIELD2D_FIELD2D_FIELD2D_OP(/, Div)
+
+#define FIELD3D_FIELD2D_FIELD3D_OP(OP_SYM, OP_TYPE)                                      \
+  template <typename L, typename R>                                                      \
+  std::enable_if_t<is_expr_field2d_v<L> && is_expr_field3d_v<R>,                         \
+                   BinaryExpr<L, R, bout::op::OP_TYPE>> operator OP_SYM(const L & lhs,   \
+                                                                        const R & rhs) { \
+    auto regionID = rhs.getRegionID();                                                   \
+    int mesh_nz = rhs.getMesh()->LocalNz;                                                \
+    return BinaryExpr<L, R, bout::op::OP_TYPE>{                                          \
+        static_cast<typename L::View>(lhs).setScale(1, mesh_nz),                         \
+        static_cast<typename R::View>(rhs),                                              \
+        bout::op::OP_TYPE{},                                                             \
+        rhs.getMesh(),                                                                   \
+        rhs.getLocation(),                                                               \
+        rhs.getDirections(),                                                             \
+        regionID,                                                                        \
+        rhs.getMesh()->getRegion("RGN_ALL")};                                            \
+  }
 
-#if 0
-//Field2D operator+(BoutReal lhs, const Field2D& rhs);
-//Field2D operator-(BoutReal lhs, const Field2D& rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
-                 BinaryExpr<Constant<L>, R, bout::op::Sub>>
-operator-(L lhs, const R& rhs) {
-  //static_assert(always_false<L> || always_false<R>, "Hello");
-
-  return BinaryExpr<Constant<L>, R, bout::op::Sub>{
-      static_cast<typename Constant<L>::View>(lhs),
-      static_cast<typename R::View>(rhs),
-      bout::op::Sub{},
-      rhs.getMesh(),
-      rhs.getLocation(),
-      rhs.getDirections(),
-      std::nullopt,
-      rhs.getMesh()->getRegion2D("RGN_ALL")};
-}
-//Field2D operator*(BoutReal lhs, const Field2D& rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
-                 BinaryExpr<Constant<L>, R, bout::op::Mul>>
-operator*(L lhs, const R& rhs) {
-  //static_assert(always_false<L> || always_false<R>, "Hello");
-
-  return BinaryExpr<Constant<L>, R, bout::op::Mul>{
-      static_cast<typename Constant<L>::View>(lhs),
-      static_cast<typename R::View>(rhs),
-      bout::op::Mul{},
-      rhs.getMesh(),
-      rhs.getLocation(),
-      rhs.getDirections(),
-      std::nullopt,
-      rhs.getMesh()->getRegion2D("RGN_ALL")};
-}
-//Field2D operator/(BoutReal lhs, const Field2D& rhs);
-template <typename L, typename R>
-std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
-                 BinaryExpr<Constant<L>, R, bout::op::Div>>
-operator/(L lhs, const R& rhs) {
-  return BinaryExpr<Constant<L>, R, bout::op::Div>{
-      static_cast<typename Constant<L>::View>(lhs),
-      static_cast<typename R::View>(rhs),
-      bout::op::Div{},
-      rhs.getMesh(),
-      rhs.getLocation(),
-      rhs.getDirections(),
-      std::nullopt,
-      rhs.getMesh()->getRegion2D("RGN_ALL")};
-}
-#endif
+FIELD3D_FIELD2D_FIELD3D_OP(+, Add)
+FIELD3D_FIELD2D_FIELD3D_OP(-, Sub)
+FIELD3D_FIELD2D_FIELD3D_OP(*, Mul)
+FIELD3D_FIELD2D_FIELD3D_OP(/, Div)
+
+#define FIELD2D_FIELD2D_BOUTREAL_OP(OP_SYM, OP_TYPE)              \
+  template <typename L, typename R>                               \
+  std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>, \
+                   BinaryExpr<L, Constant<R>, bout::op::OP_TYPE>> \
+  operator OP_SYM(const L & lhs, R rhs) {                         \
+    return BinaryExpr<L, Constant<R>, bout::op::OP_TYPE>{         \
+        static_cast<typename L::View>(lhs),                       \
+        static_cast<typename Constant<R>::View>(rhs),             \
+        bout::op::OP_TYPE{},                                      \
+        lhs.getMesh(),                                            \
+        lhs.getLocation(),                                        \
+        lhs.getDirections(),                                      \
+        std::nullopt,                                             \
+        lhs.getMesh()->getRegion2D("RGN_ALL")};                   \
+  }
+
+FIELD2D_FIELD2D_BOUTREAL_OP(+, Add)
+FIELD2D_FIELD2D_BOUTREAL_OP(-, Sub)
+FIELD2D_FIELD2D_BOUTREAL_OP(*, Mul)
+FIELD2D_FIELD2D_BOUTREAL_OP(/, Div)
 
 #define FIELD2D_BOUTREAL_FIELD2D_OP(OP_SYM, OP_TYPE)              \
   template <typename L, typename R>                               \
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 8f433909f9..fac2adc337 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -478,135 +478,26 @@ public:
 
   ///@}
 
-  /// Addition operators
-  ///@{
-  //Field3D& operator+=(const Field3D& rhs);
-  template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
-  Field3D& operator+=(const R& rhs) {
-    //printf("RUNNING operator+= with CUDA\n");
-    if (data.unique()) {
-      //std::cout << "RUNNING Field3D operator+=  w/ CUDA" << __FILE__ << " "
-      //          << std::to_string(__LINE__) << "\n";
-      // Delete existing parallel slices. We don't copy parallel slices, so any
-      // that currently exist will be incorrect.
-      clearParallelSlices();
-
-      auto BE = (*this) + rhs;
-      regionID = BE.getRegionID();
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) + rhs;
-    }
-
-    return *this;
-  }
-  Field3D& operator+=(const Field2D& rhs);
-  Field3D& operator+=(BoutReal rhs);
-  ///@}
-
-  /// Subtraction operators
-  ///@{
-  //Field3D& operator-=(const Field3D& rhs);
-  template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
-  Field3D& operator-=(const R& rhs) {
-    if (data.unique()) {
-      //printf("RUNNING operator-= with CUDA with BE\n");
-      // Delete existing parallel slices. We don't copy parallel slices, so any
-      // that currently exist will be incorrect.
-      clearParallelSlices();
-      auto BE = (*this) - rhs;
-      BE.evaluate(&data[0]);
-    } else {
-      //printf("RUNNING operator-= with CUDA with operation\n");
-      (*this) = (*this) - rhs;
-    }
-
-    return *this;
-  }
-  Field3D& operator-=(const Field2D& rhs);
-  Field3D& operator-=(BoutReal rhs);
-  ///@}
-
-  /// Multiplication operators
-  ///@{
-  //Field3D& operator*=(const Field3D& rhs);
-  template <typename R, typename = std::enable_if_t<is_expr_field3d_v<R>>>
-  Field3D& operator*=(const R& rhs) {
-    //printf("RUNNING operator*= with CUDA\n");
-    if (data.unique()) {
-      // Delete existing parallel slices. We don't copy parallel slices, so any
-      // that currently exist will be incorrect.
-      clearParallelSlices();
-
-      auto BE = (*this) * rhs;
-      regionID = BE.getRegionID();
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) * rhs;
-    }
-
-    return *this;
+#define FIELD3D_OP_EQUALS(OP_SYM)                                \
+  template <typename R>                                          \
+  std::enable_if_t<is_expr_field3d_v<R> || is_expr_field2d_v<R>  \
+                       || is_expr_constant_v<R>,                 \
+                   Field3D&> operator OP_SYM##=(const R & rhs) { \
+    if (data.unique()) {                                         \
+      clearParallelSlices();                                     \
+      auto Expr = (*this)OP_SYM rhs;                             \
+      Expr.evaluate(&data[0]);                                   \
+    } else {                                                     \
+      (*this) = (*this)OP_SYM rhs;                               \
+    }                                                            \
+    return *this;                                                \
   }
-  Field3D& operator*=(const Field2D& rhs);
-  //Field3D& operator*=(BoutReal rhs);
-  // here1
-  template <typename R, typename = std::enable_if_t<is_expr_constant_v<R>>>
-  Field3D& operator*=(R rhs) {
-    //printf("RUNNING operator*= with CUDA\n");
-    if (data.unique()) {
-      // Delete existing parallel slices. We don't copy parallel slices, so any
-      // that currently exist will be incorrect.
-      clearParallelSlices();
-
-      auto BE = (*this) * rhs;
-      regionID = BE.getRegionID();
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) * rhs;
-    }
 
-    return *this;
-  }
-  ///@}
+  FIELD3D_OP_EQUALS(+)
+  FIELD3D_OP_EQUALS(-)
+  FIELD3D_OP_EQUALS(*)
+  FIELD3D_OP_EQUALS(/)
 
-  /// Division operators
-  ///@{
-  //Field3D& operator/=(const Field3D& rhs);
-  template <typename R>
- std::enable_if_t<is_expr_field3d_v<R>,Field3D&> operator/=(const R& rhs) {
-    //printf("RUNNING operator/= with CUDA\n");
-    if (data.unique()) {
-      // Delete existing parallel slices. We don't copy parallel slices, so any
-      // that currently exist will be incorrect.
-      clearParallelSlices();
-
-      auto BE = (*this) / rhs;
-      regionID = BE.getRegionID();
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) / rhs;
-    }
-
-    return *this;
-  }
-  //Field3D& operator/=(const Field2D& rhs);
-  template <typename R>
-std::enable_if_t<is_expr_field2d_v<R>, Field3D&> operator/=(const R& rhs) {
-    //printf("RUNNING operator/= with CUDA\n");
-    if (data.unique()) {
-      // Delete existing parallel slices. We don't copy parallel slices, so any
-      // that currently exist will be incorrect.
-      clearParallelSlices();
-
-      auto BE = (*this) / rhs;
-      BE.evaluate(&data[0]);
-    } else {
-      (*this) = (*this) / rhs;
-    }
-
-    return *this;
-  }
-  Field3D& operator/=(BoutReal rhs);
   ///@}
 
   // FieldData virtual functions
@@ -699,11 +590,6 @@ FIELD3D_FIELD3D_FIELD3D_OP(-, Sub)
 FIELD3D_FIELD3D_FIELD3D_OP(*, Mul)
 FIELD3D_FIELD3D_FIELD3D_OP(/, Div)
 
-//Field3D operator+(const Field3D& lhs, const Field2D& rhs);
-//Field3D operator-(const Field3D& lhs, const Field2D& rhs);
-//Field3D operator*(const Field3D& lhs, const Field2D& rhs);
-//Field3D operator/(const Field3D& lhs, const Field2D& rhs);
-
 #define FIELD3D_FIELD3D_FIELD2D_OP(OP_SYM, OP_TYPE)                                      \
   template <typename L, typename R>                                                      \
   std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,                         \
@@ -727,11 +613,6 @@ FIELD3D_FIELD3D_FIELD2D_OP(-, Sub)
 FIELD3D_FIELD3D_FIELD2D_OP(*, Mul)
 FIELD3D_FIELD3D_FIELD2D_OP(/, Div)
 
-//Field3D operator+(const Field3D& lhs, BoutReal rhs);
-//Field3D operator-(const Field3D& lhs, BoutReal rhs);
-//Field3D operator*(const Field3D& lhs, BoutReal rhs);
-//Field3D operator/(const Field3D& lhs, BoutReal rhs);
-
 #define FIELD3D_FIELD3D_BOUTREAL_OP(OP_SYM, OP_TYPE)              \
   template <typename L, typename R>                               \
   std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>, \
@@ -754,11 +635,6 @@ FIELD3D_FIELD3D_BOUTREAL_OP(-, Sub)
 FIELD3D_FIELD3D_BOUTREAL_OP(*, Mul)
 FIELD3D_FIELD3D_BOUTREAL_OP(/, Div)
 
-//Field3D operator+(BoutReal lhs, const Field3D& rhs);
-//Field3D operator-(BoutReal lhs, const Field3D& rhs);
-//Field3D operator*(BoutReal lhs, const Field3D& rhs);
-//Field3D operator/(BoutReal lhs, const Field3D& rhs);
-
 #define FIELD3D_BOUTREAL_FIELD3D_OP(OP_SYM, OP_TYPE)              \
   template <typename L, typename R>                               \
   std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>, \
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index dca1605b91..c78a9ed7b7 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -6,148 +6,6 @@
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 
-// Provide the C++ operator to update Field3D by multiplication with Field2D
-Field3D& Field3D::operator*=(const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
-      const auto base_ind = fieldmesh->ind2Dto3D(index);
-      for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) {
-        (*this)[base_ind + jz] *= rhs[index];
-      }
-    }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) * rhs;
-  }
-  return *this;
-}
-
-#if 0
-// Provide the C++ wrapper for addition of Field3D and Field2D
-Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[base_ind + jz] + rhs[index];
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-// Provide the C++ operator to update Field3D by addition with Field2D
-Field3D& Field3D::operator+=(const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
-      const auto base_ind = fieldmesh->ind2Dto3D(index);
-      for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) {
-        (*this)[base_ind + jz] += rhs[index];
-      }
-    }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) + rhs;
-  }
-  return *this;
-}
-
-#if 0
-// Provide the C++ wrapper for subtraction of Field3D and Field2D
-Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[base_ind + jz] - rhs[index];
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-// Provide the C++ operator to update Field3D by subtraction with Field2D
-Field3D& Field3D::operator-=(const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
-      const auto base_ind = fieldmesh->ind2Dto3D(index);
-      for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) {
-        (*this)[base_ind + jz] -= rhs[index];
-      }
-    }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) - rhs;
-  }
-  return *this;
-}
-
 // Provide the C++ wrapper for multiplication of Field3D and FieldPerp
 FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -233,211 +91,6 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) {
 }
 
 #if 0
-// Provide the C++ wrapper for division of Field3D and BoutReal
-Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  const auto tmp = 1.0 / rhs;
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * tmp;
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-// Provide the C++ operator to update Field3D by division with BoutReal
-Field3D& Field3D::operator/=(const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    const auto tmp = 1.0 / rhs;
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) / rhs;
-  }
-  return *this;
-}
-
-#if 0
-// Provide the C++ wrapper for addition of Field3D and BoutReal
-Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs;
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-// Provide the C++ operator to update Field3D by addition with BoutReal
-Field3D& Field3D::operator+=(const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) + rhs;
-  }
-  return *this;
-}
-
-#if 0
-// Provide the C++ wrapper for subtraction of Field3D and BoutReal
-Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs;
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
-// Provide the C++ operator to update Field3D by subtraction with BoutReal
-Field3D& Field3D::operator-=(const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-
-    // Delete existing parallel slices. We don't copy parallel slices, so any
-    // that currently exist will be incorrect.
-    clearParallelSlices();
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) - rhs;
-  }
-  return *this;
-}
-
-// Provide the C++ wrapper for division of Field2D and Field3D
-Field3D operator/(const Field2D& lhs, const Field3D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR(index, lhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[index] / rhs[base_ind + jz];
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for addition of Field2D and Field3D
-Field3D operator+(const Field2D& lhs, const Field3D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR(index, lhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[index] + rhs[base_ind + jz];
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for subtraction of Field2D and Field3D
-Field3D operator-(const Field2D& lhs, const Field3D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR(index, lhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[index] - rhs[base_ind + jz];
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field2D by division with Field2D
 Field2D& Field2D::operator/=(const Field2D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -458,6 +111,7 @@ Field2D& Field2D::operator/=(const Field2D& rhs) {
   }
   return *this;
 }
+#endif
 
 // Provide the C++ wrapper for multiplication of Field2D and FieldPerp
 FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) {
@@ -543,22 +197,7 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) {
   return result;
 }
 
-// Provide the C++ wrapper for addition of Field2D and BoutReal
-Field2D operator+(const Field2D& lhs, const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs;
-  }
-
-  checkData(result);
-  return result;
-}
-
+#if 0
 // Provide the C++ operator to update Field2D by addition with BoutReal
 Field2D& Field2D::operator+=(const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -578,7 +217,9 @@ Field2D& Field2D::operator+=(const BoutReal rhs) {
   }
   return *this;
 }
+#endif
 
+#if 0
 // Provide the C++ operator to update Field2D by subtraction with BoutReal
 Field2D& Field2D::operator-=(const BoutReal rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -598,6 +239,7 @@ Field2D& Field2D::operator-=(const BoutReal rhs) {
   }
   return *this;
 }
+#endif
 
 // Provide the C++ wrapper for multiplication of FieldPerp and Field3D
 FieldPerp operator*(const FieldPerp& lhs, const Field3D& rhs) {
@@ -1280,24 +922,6 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) {
   return *this;
 }
 
-#if 0
-// Provide the C++ wrapper for addition of BoutReal and Field2D
-Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-
-  Field2D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs + rhs[index];
-  }
-
-  checkData(result);
-  return result;
-}
-#endif
-
 // Provide the C++ wrapper for multiplication of BoutReal and FieldPerp
 FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";

From 56a8678fb275fd6035e99bb1d506f047817a6d8d Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Sun, 1 Jun 2025 06:30:58 -0700
Subject: [PATCH 0188/1827] Cleanup

---
 src/field/generated_fieldops.cxx | 67 --------------------------------
 1 file changed, 67 deletions(-)

diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index c78a9ed7b7..022fedbd17 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -90,29 +90,6 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) {
   return result;
 }
 
-#if 0
-// Provide the C++ operator to update Field2D by division with Field2D
-Field2D& Field2D::operator/=(const Field2D& rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) / rhs;
-  }
-  return *this;
-}
-#endif
-
 // Provide the C++ wrapper for multiplication of Field2D and FieldPerp
 FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
@@ -197,50 +174,6 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) {
   return result;
 }
 
-#if 0
-// Provide the C++ operator to update Field2D by addition with BoutReal
-Field2D& Field2D::operator+=(const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) + rhs;
-  }
-  return *this;
-}
-#endif
-
-#if 0
-// Provide the C++ operator to update Field2D by subtraction with BoutReal
-Field2D& Field2D::operator-=(const BoutReal rhs) {
-  std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";
-  // only if data is unique we update the field
-  // otherwise just call the non-inplace version
-  if (data.unique()) {
-
-    checkData(*this);
-    checkData(rhs);
-
-    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
-
-    checkData(*this);
-
-  } else {
-    (*this) = (*this) - rhs;
-  }
-  return *this;
-}
-#endif
-
 // Provide the C++ wrapper for multiplication of FieldPerp and Field3D
 FieldPerp operator*(const FieldPerp& lhs, const Field3D& rhs) {
   std::cout << "RUNNING operator " << __FILE__ << " " << std::to_string(__LINE__) << "\n";

From 3e3a0ea3973f222a31091ae42c1c360ebb34da3f Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Mon, 2 Jun 2025 20:09:40 -0700
Subject: [PATCH 0189/1827] Add __host__ to make evaluator host-callable,
 remove offset

---
 include/bout/bout_types.hxx |  2 +-
 include/bout/field2d.hxx    |  7 +++-
 include/bout/field3d.hxx    | 11 ++---
 include/bout/fieldops.hxx   | 81 +++++++++++++++++++++++++------------
 4 files changed, 64 insertions(+), 37 deletions(-)

diff --git a/include/bout/bout_types.hxx b/include/bout/bout_types.hxx
index b2f38b61aa..c725c281d3 100644
--- a/include/bout/bout_types.hxx
+++ b/include/bout/bout_types.hxx
@@ -146,7 +146,7 @@ struct Constant {
   struct View {
     T v;
    View(T v) : v(v) {}
-    __device__ T operator()(int) const { return v; }
+   __host__ __device__ T operator()(int) const { return v; }
   };
   operator View() const { return {val}; }
 };
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index f430b98c6c..88f67f277b 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -108,6 +108,7 @@ public:
                                   || (is_expr_constant_v<L> && is_expr_field2d_v<R>)
                                   || (is_expr_field2d_v<L> && is_expr_constant_v<R>)>>
   Field2D(const BinaryExpr<L, R, Func>& expr) {
+    std::cout << "RUNNING Field2D constructor with CUDA\n";
     Array<BoutReal> data{expr.size()};
     expr.evaluate(&data[0]);
     *this = std::move(Field2D{std::move(data), expr.getMesh(), expr.getLocation(),
@@ -315,8 +316,10 @@ public:
     BoutReal* data;
     int mul = 1;
     int div = 1;
-    __device__ inline BoutReal operator()(int idx) const { return data[(idx*mul/div)]; }
-    __device__ inline BoutReal& operator[](int idx) const {
+    __host__ __device__ inline BoutReal operator()(int idx) const {
+      return data[(idx * mul / div)];
+    }
+    __host__ __device__ inline BoutReal& operator[](int idx) const {
       return data[(idx * mul)/div];
     }
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index fac2adc337..5056a4128b 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -429,12 +429,11 @@ public:
     BoutReal* data;
     int mul = 1;
     int div = 1;
-    int offset = 0;
     __host__ __device__ inline BoutReal operator()(int idx) const {
-      return data[(idx * mul) / div + offset];
+      return data[(idx * mul) / div];
     }
-    __device__ inline BoutReal& operator[](int idx) const {
-      return data[(idx * mul) / div + offset];
+    __host__ __device__ inline BoutReal& operator[](int idx) const {
+      return data[(idx * mul) / div];
     }
 
     View& setScale(int mul, int div) {
@@ -442,10 +441,6 @@ public:
       this->div = div;
       return *this;
     }
-    View& setOffset(int o) {
-      offset = o;
-      return *this;
-    }
   };
   operator View() { return View{&data[0]}; }
   operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 0de73d1205..9346b55e48 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -38,55 +38,58 @@ template <typename T>
 struct is_expr_constant<Constant<T>>
     : std::integral_constant<bool, is_expr_constant_v<std::decay_t<T>>> {};
 
-constexpr int THREADS = 256;
+constexpr int THREADS = 128;
 namespace bout {
 namespace op {
 struct Assign {
   int scale = 1;
   int offset = 0;
   template <typename Expr>
-  __device__ void operator()(int idx, BoutReal* out, const Expr& expr) const {
+  __host__ __device__ void operator()(int idx, BoutReal* out, const Expr& expr) const {
     out[(idx * scale) + offset] = expr.lhs(idx) + expr.rhs(idx);
   }
 };
 
 struct Add {
   template <typename LView, typename RView>
-  __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
-                                                 const RView& R) const {
+  __host__ __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
+                                                          const RView& R) const {
     return L(idx) + R(idx);
   }
-  __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
+  __host__ __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
     return a + b;
   }
 };
   struct Sub {
     template <typename LView, typename RView>
-    __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
-                                                   const RView& R) const {
+    __host__ __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
+                                                            const RView& R) const {
       return L(idx) - R(idx);
     }
-    __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
+    __host__ __device__ __forceinline__ BoutReal operator()(BoutReal a,
+                                                            BoutReal b) const {
       return a - b;
     }
   };
   struct Mul {
     template <typename LView, typename RView>
-    __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
-                                                   const RView& R) const {
+    __host__ __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
+                                                            const RView& R) const {
       return L(idx) * R(idx);
     }
-    __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
+    __host__ __device__ __forceinline__ BoutReal operator()(BoutReal a,
+                                                            BoutReal b) const {
       return a * b;
     }
   };
   struct Div {
     template <typename LView, typename RView>
-    __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
-                                                   const RView& R) const {
+    __host__ __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
+                                                            const RView& R) const {
       return L(idx) / R(idx);
     }
-    __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
+    __host__ __device__ __forceinline__ BoutReal operator()(BoutReal a,
+                                                            BoutReal b) const {
       return a / b;
     }
   };
@@ -96,13 +99,24 @@ struct Add {
 template <typename Expr>
 __global__ void __launch_bounds__(THREADS) evaluatorExpr(BoutReal* out, const Expr expr) {
   int tid = threadIdx.x + blockIdx.x * blockDim.x;
-  if (tid >= expr.size()) {
+  int e = expr.size();
+
+  // In-bounds version
+  //if (tid < e) {
+  //  int idx = expr.regionIdx(tid);
+  //  out[idx] = expr(idx); // single‐pass fusion
+  //}
+
+  // Out-of-bounds version
+  if (tid >= e) {
     return;
   }
   int idx = expr.regionIdx(tid);
   out[idx] = expr(idx); // single‐pass fusion
+
+  // Grid-strided loop
   //int stride = blockDim.x * gridDim.x;
-  //for (int i = tid, e = expr.size(); i < e; i += stride) {
+  //for (int i = tid; i < e; i += stride) {
   //  int idx = expr.regionIdx(i);
   //  out[idx] = expr(idx); // single‐pass fusion
   //}
@@ -133,6 +147,18 @@ struct BinaryExpr {
     for (int i = 0; i < indices.size(); ++i) {
       indices[i] = region.getIndices()[i].ind;
     }
+    //std::cout << "===PRE-sorting indices\n";
+    //for (auto& ind : indices) {
+    //  std::cout << ind << " ";
+    //}
+    //std::cout << "===end PRE\n";
+    //std::sort(indices.begin(), indices.end(),
+    //          [](const auto& a, const auto& b) { return a < b; });
+    //std::cout << "===POST-sorting indices\n";
+    //for (auto& ind : indices) {
+    //  std::cout << ind << " ";
+    //}
+    //std::cout << "===end POST\n";
     //if (regionIndicesCache.find(static_cast<void*>(const_cast<Region<IndType>*>(&region)))
     //    != regionIndicesCache.end()) {
     //  // If we have already computed the indices for this region, use them
@@ -167,23 +193,19 @@ struct BinaryExpr {
     Func f;
     int mul = 1;
     int div = 1;
-    int offset = 0;
 
     View& setScale(int mul, int div) {
       this->mul = mul;
       this->div = div;
       return *this;
     }
-    View& setOffset(int o) {
-      offset = o;
-      return *this;
+    __host__ __device__ __forceinline__ int size() const { return num_indices; }
+    __host__ __device__ __forceinline__ int regionIdx(int idx) const {
+      return indices[idx];
     }
-
-    __device__ __forceinline__ int size() const { return num_indices; }
-    __device__ __forceinline__ int regionIdx(int idx) const { return indices[idx]; }
-    __device__ __forceinline__ BoutReal operator()(int idx) const {
-      return f((idx * mul) / div, lhs, rhs); // single‐pass fusion
-      //return f(lhs(idx), rhs(idx)); // single‐pass fusion
+    __host__ __device__ __forceinline__ BoutReal operator()(int idx) const {
+      //return f((idx * mul) / div, lhs, rhs); // single‐pass fusion
+      return f(lhs((idx * mul) / div), rhs((idx * mul) / div)); // single‐pass fusion
     }
   };
 
@@ -194,6 +216,13 @@ struct BinaryExpr {
     int blocks = (size() + THREADS - 1) / THREADS;
     evaluatorExpr<<<blocks, THREADS>>>(&data[0], static_cast<View>(*this));
     cudaDeviceSynchronize();
+    // OpenMP impl.
+    //int e = size();
+    //#pragma omp parallel for
+    //for (int i = 0; i < e; ++i) {
+    //  int idx = regionIdx(i);
+    //  data[idx] = operator()(idx); // single‐pass fusion
+    //}
   }
 
   Mesh* getMesh() const { return mesh; }

From 56fe675a77441ec3f447b54d97ea49f7069e8375 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Wed, 4 Jun 2025 01:18:13 -0700
Subject: [PATCH 0190/1827] Update

- Add field functions (sqrt, abs, etc.)
- Add ResT template parameter to BinaryExpr for future use
- Update some operators (min, max, etc.) to take as input a BinaryExpr
  and evaluate it before apply
---
 .../elm-pb-outerloop/elm_pb_outerloop.cxx     |   8 +-
 include/bout/field.hxx                        |  52 +++++--
 include/bout/field2d.hxx                      | 127 +++++++++---------
 include/bout/field3d.hxx                      | 110 +++++++--------
 include/bout/fieldops.hxx                     |  13 +-
 include/bout/fieldperp.hxx                    |  39 ++++++
 src/field/field2d.cxx                         |   3 +-
 src/field/fieldperp.cxx                       |   2 +-
 src/mesh/coordinates.cxx                      |   2 +-
 src/physics/snb.cxx                           |   4 +-
 10 files changed, 219 insertions(+), 141 deletions(-)

diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index 901e57bf97..96c28bab12 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -713,7 +713,7 @@ class ELMpb : public PhysicsModel {
       diamag_phi0 = false;
       K_H_term = false;
     } else {
-      Dphi0 = -D_min - 0.5 * D_0 * (1.0 - tanh(Field2D{D_s * (x - x0)}));
+      Dphi0 = -D_min - 0.5 * D_0 * (1.0 - tanh(D_s * (x - x0)));
     }
 
     if (sign < 0) { // change flow direction
@@ -1031,7 +1031,7 @@ class ELMpb : public PhysicsModel {
     vacuum_trans *= pnorm;
 
     // Transitions from 0 in core to 1 in vacuum
-    Field2D tanh_res = tanh(Field2D{(P0 - vacuum_pressure) / vacuum_trans});
+    Field2D tanh_res = tanh((P0 - vacuum_pressure) / vacuum_trans);
     vac_mask = (1.0 - tanh_res) / 2.0;
 
     if (spitzer_resist) {
@@ -1283,7 +1283,7 @@ class ELMpb : public PhysicsModel {
     ////////////////////////////////////////////
     // Transitions from 0 in core to 1 in vacuum
     if (nonlinear) {
-      vac_mask = (1.0 - tanh(Field3D{((P0 + P) - vacuum_pressure) / vacuum_trans})) / 2.0;
+      vac_mask = (1.0 - tanh(((P0 + P) - vacuum_pressure) / vacuum_trans)) / 2.0;
 
       // Update resistivity
       if (spitzer_resist) {
@@ -1794,7 +1794,7 @@ class ELMpb : public PhysicsModel {
       // Calculate coefficient.
 
       hyper_mu_x = hyperviscos * metric->g_11 * SQ(metric->dx)
-                   * abs(Field3D{metric->g11 * D2DX2(U)}) / (abs(U) + 1e-3);
+                   * abs(metric->g11 * D2DX2(U)) / (abs(U) + 1e-3);
       hyper_mu_x.applyBoundary("dirichlet"); // Set to zero on all boundaries
 
       ddt(U) += hyper_mu_x * metric->g11 * D2DX2(U);
diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 188d529ef0..fe2b4767d2 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -44,6 +44,8 @@ class Field;
 #include <bout/globals.hxx>
 #include <bout/rvec.hxx>
 
+#include "bout/fieldops.hxx"
+
 class Mesh;
 
 /// Base class for scalar fields
@@ -327,6 +329,12 @@ inline BoutReal min(const T& f, bool allpe = false,
   return result;
 }
 
+template <typename ResT, typename L, typename R, typename Func>
+inline BoutReal min(const BinaryExpr<ResT, L, R, Func>& f, bool allpe = false,
+                    const std::string& rgn = "RGN_NOBNDRY") {
+  return min(ResT{f}, allpe, rgn);
+}
+
 /// Returns true if all elements of \p f over \p region are equal. By
 /// default only checks the local processor, use \p allpe to check
 /// globally
@@ -412,6 +420,12 @@ inline BoutReal max(const T& f, bool allpe = false,
   return result;
 }
 
+template <typename ResT, typename L, typename R, typename Func>
+inline BoutReal max(const BinaryExpr<ResT, L, R, Func>& f, bool allpe = false,
+                    const std::string& rgn = "RGN_NOBNDRY") {
+  return max(ResT{f}, allpe, rgn);
+}
+
 /// Mean of \p f, excluding the boundary/guard cells by default (can
 /// be changed with \p rgn argument).
 ///
@@ -519,17 +533,33 @@ T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
 #ifdef FIELD_FUNC
 #error This macro has already been defined
 #else
-#define FIELD_FUNC(name, func)                                     \
-  template <typename T, typename = bout::utils::EnableIfField<T>>  \
-  inline T name(const T& f, const std::string& rgn = "RGN_ALL") {  \
-    AUTO_TRACE();                                                  \
-    /* Check if the input is allocated */                          \
-    checkData(f);                                                  \
-    /* Define and allocate the output result */                    \
-    T result{emptyFrom(f)};                                        \
-    BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); } \
-    checkData(result);                                             \
-    return result;                                                 \
+#define FIELD_FUNC(name, func)                                                          \
+  namespace bout::op {                                                                  \
+  struct name {                                                                         \
+    template <typename LView, typename RView>                                           \
+    __host__ __device__ BoutReal operator()(int idx, const LView& L,                    \
+                                            const RView& R) const {                     \
+      return func(L(idx));                                                              \
+    }                                                                                   \
+  };                                                                                    \
+  };                                                                                    \
+  template <typename T, typename = bout::utils::EnableIfField<T>>                       \
+  inline BinaryExpr<T, T, T, bout::op::name> name(const T& f,                           \
+                                                  const std::string& rgn = "RGN_ALL") { \
+    std::cout << "RUNNING " #name " with CUDA\n";                                       \
+    return BinaryExpr<T, T, T, bout::op::name>{static_cast<typename T::View>(f),        \
+                                               static_cast<typename T::View>(f),        \
+                                               bout::op::name{},                        \
+                                               f.getMesh(),                             \
+                                               f.getLocation(),                         \
+                                               f.getDirections(),                       \
+                                               std::nullopt,                            \
+                                               f.getRegion(rgn)};                       \
+  }                                                                                     \
+  template <typename ResT, typename L, typename R, typename Func>                       \
+  inline BinaryExpr<ResT, ResT, ResT, bout::op::name> name(                             \
+      const BinaryExpr<ResT, L, R, Func>& f, const std::string& rgn = "RGN_ALL") {      \
+    return name(ResT{f}, rgn);                                                          \
   }
 #endif
 
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 88f67f277b..da8de551ad 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -47,8 +47,8 @@ class Field2D;
 class Field3D;
 class Mesh;
 
-template <typename L, typename R, typename Fun>
-struct is_expr_field2d<BinaryExpr<L, R, Fun>>
+template <typename ResT, typename L, typename R, typename Fun>
+struct is_expr_field2d<BinaryExpr<ResT, L, R, Fun>>
     : std::integral_constant<bool, (is_expr_field2d_v<std::decay_t<L>>
                                     && is_expr_field2d_v<std::decay_t<R>>)
                                        || (is_expr_constant_v<std::decay_t<L>>
@@ -103,11 +103,11 @@ public:
                                           ZDirectionType::Average});
 
   template <
-      typename L, typename R, typename Func,
+      typename ResT, typename L, typename R, typename Func,
       typename = std::enable_if_t<(is_expr_field2d_v<L> && is_expr_field2d_v<R>)
                                   || (is_expr_constant_v<L> && is_expr_field2d_v<R>)
                                   || (is_expr_field2d_v<L> && is_expr_constant_v<R>)>>
-  Field2D(const BinaryExpr<L, R, Func>& expr) {
+  Field2D(const BinaryExpr<ResT, L, R, Func>& expr) {
     std::cout << "RUNNING Field2D constructor with CUDA\n";
     Array<BoutReal> data{expr.size()};
     expr.evaluate(&data[0]);
@@ -189,9 +189,9 @@ public:
    */
   Field2D& operator=(BoutReal rhs);
 
-  template <typename L, typename R, typename Func>
+  template <typename ResT, typename L, typename R, typename Func>
   std::enable_if_t<is_expr_field2d_v<L>, Field2D&>
-  operator=(const BinaryExpr<L, R, Func>& expr) {
+  operator=(const BinaryExpr<ResT, L, R, Func>& expr) {
     std::cout << "RUNNING Field2D operator= with CUDA\n";
     if (isAllocated()) {
       expr.evaluate(&data[0]);
@@ -348,19 +348,20 @@ private:
 
 // Non-member overloaded operators
 
-#define FIELD2D_FIELD2D_FIELD2D_OP(OP_SYM, OP_TYPE)                                      \
-  template <typename L, typename R>                                                      \
-  std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,                         \
-                   BinaryExpr<L, R, bout::op::OP_TYPE>> operator OP_SYM(const L & lhs,   \
-                                                                        const R & rhs) { \
-    return BinaryExpr<L, R, bout::op::OP_TYPE>{static_cast<typename L::View>(lhs),       \
-                                               static_cast<typename R::View>(rhs),       \
-                                               bout::op::OP_TYPE{},                      \
-                                               lhs.getMesh(),                            \
-                                               lhs.getLocation(),                        \
-                                               lhs.getDirections(),                      \
-                                               std::nullopt,                             \
-                                               lhs.getMesh()->getRegion2D("RGN_ALL")};   \
+#define FIELD2D_FIELD2D_FIELD2D_OP(OP_SYM, OP_TYPE)              \
+  template <typename L, typename R>                              \
+  std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>, \
+                   BinaryExpr<Field2D, L, R, bout::op::OP_TYPE>> \
+  operator OP_SYM(const L & lhs, const R & rhs) {                \
+    return BinaryExpr<Field2D, L, R, bout::op::OP_TYPE>{         \
+        static_cast<typename L::View>(lhs),                      \
+        static_cast<typename R::View>(rhs),                      \
+        bout::op::OP_TYPE{},                                     \
+        lhs.getMesh(),                                           \
+        lhs.getLocation(),                                       \
+        lhs.getDirections(),                                     \
+        std::nullopt,                                            \
+        lhs.getMesh()->getRegion2D("RGN_ALL")};                  \
   }
 
 FIELD2D_FIELD2D_FIELD2D_OP(+, Add)
@@ -368,22 +369,22 @@ FIELD2D_FIELD2D_FIELD2D_OP(-, Sub)
 FIELD2D_FIELD2D_FIELD2D_OP(*, Mul)
 FIELD2D_FIELD2D_FIELD2D_OP(/, Div)
 
-#define FIELD3D_FIELD2D_FIELD3D_OP(OP_SYM, OP_TYPE)                                      \
-  template <typename L, typename R>                                                      \
-  std::enable_if_t<is_expr_field2d_v<L> && is_expr_field3d_v<R>,                         \
-                   BinaryExpr<L, R, bout::op::OP_TYPE>> operator OP_SYM(const L & lhs,   \
-                                                                        const R & rhs) { \
-    auto regionID = rhs.getRegionID();                                                   \
-    int mesh_nz = rhs.getMesh()->LocalNz;                                                \
-    return BinaryExpr<L, R, bout::op::OP_TYPE>{                                          \
-        static_cast<typename L::View>(lhs).setScale(1, mesh_nz),                         \
-        static_cast<typename R::View>(rhs),                                              \
-        bout::op::OP_TYPE{},                                                             \
-        rhs.getMesh(),                                                                   \
-        rhs.getLocation(),                                                               \
-        rhs.getDirections(),                                                             \
-        regionID,                                                                        \
-        rhs.getMesh()->getRegion("RGN_ALL")};                                            \
+#define FIELD3D_FIELD2D_FIELD3D_OP(OP_SYM, OP_TYPE)              \
+  template <typename L, typename R>                              \
+  std::enable_if_t<is_expr_field2d_v<L> && is_expr_field3d_v<R>, \
+                   BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>> \
+  operator OP_SYM(const L & lhs, const R & rhs) {                \
+    auto regionID = rhs.getRegionID();                           \
+    int mesh_nz = rhs.getMesh()->LocalNz;                        \
+    return BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>{         \
+        static_cast<typename L::View>(lhs).setScale(1, mesh_nz), \
+        static_cast<typename R::View>(rhs),                      \
+        bout::op::OP_TYPE{},                                     \
+        rhs.getMesh(),                                           \
+        rhs.getLocation(),                                       \
+        rhs.getDirections(),                                     \
+        regionID,                                                \
+        rhs.getMesh()->getRegion("RGN_ALL")};                    \
   }
 
 FIELD3D_FIELD2D_FIELD3D_OP(+, Add)
@@ -391,20 +392,20 @@ FIELD3D_FIELD2D_FIELD3D_OP(-, Sub)
 FIELD3D_FIELD2D_FIELD3D_OP(*, Mul)
 FIELD3D_FIELD2D_FIELD3D_OP(/, Div)
 
-#define FIELD2D_FIELD2D_BOUTREAL_OP(OP_SYM, OP_TYPE)              \
-  template <typename L, typename R>                               \
-  std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>, \
-                   BinaryExpr<L, Constant<R>, bout::op::OP_TYPE>> \
-  operator OP_SYM(const L & lhs, R rhs) {                         \
-    return BinaryExpr<L, Constant<R>, bout::op::OP_TYPE>{         \
-        static_cast<typename L::View>(lhs),                       \
-        static_cast<typename Constant<R>::View>(rhs),             \
-        bout::op::OP_TYPE{},                                      \
-        lhs.getMesh(),                                            \
-        lhs.getLocation(),                                        \
-        lhs.getDirections(),                                      \
-        std::nullopt,                                             \
-        lhs.getMesh()->getRegion2D("RGN_ALL")};                   \
+#define FIELD2D_FIELD2D_BOUTREAL_OP(OP_SYM, OP_TYPE)                       \
+  template <typename L, typename R>                                        \
+  std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,          \
+                   BinaryExpr<Field2D, L, Constant<R>, bout::op::OP_TYPE>> \
+  operator OP_SYM(const L & lhs, R rhs) {                                  \
+    return BinaryExpr<Field2D, L, Constant<R>, bout::op::OP_TYPE>{         \
+        static_cast<typename L::View>(lhs),                                \
+        static_cast<typename Constant<R>::View>(rhs),                      \
+        bout::op::OP_TYPE{},                                               \
+        lhs.getMesh(),                                                     \
+        lhs.getLocation(),                                                 \
+        lhs.getDirections(),                                               \
+        std::nullopt,                                                      \
+        lhs.getMesh()->getRegion2D("RGN_ALL")};                            \
   }
 
 FIELD2D_FIELD2D_BOUTREAL_OP(+, Add)
@@ -412,20 +413,20 @@ FIELD2D_FIELD2D_BOUTREAL_OP(-, Sub)
 FIELD2D_FIELD2D_BOUTREAL_OP(*, Mul)
 FIELD2D_FIELD2D_BOUTREAL_OP(/, Div)
 
-#define FIELD2D_BOUTREAL_FIELD2D_OP(OP_SYM, OP_TYPE)              \
-  template <typename L, typename R>                               \
-  std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>, \
-                   BinaryExpr<Constant<L>, R, bout::op::OP_TYPE>> \
-  operator OP_SYM(L lhs, const R & rhs) {                         \
-    return BinaryExpr<Constant<L>, R, bout::op::OP_TYPE>{         \
-        static_cast<typename Constant<L>::View>(lhs),             \
-        static_cast<typename R::View>(rhs),                       \
-        bout::op::OP_TYPE{},                                      \
-        rhs.getMesh(),                                            \
-        rhs.getLocation(),                                        \
-        rhs.getDirections(),                                      \
-        std::nullopt,                                             \
-        rhs.getMesh()->getRegion2D("RGN_ALL")};                   \
+#define FIELD2D_BOUTREAL_FIELD2D_OP(OP_SYM, OP_TYPE)                       \
+  template <typename L, typename R>                                        \
+  std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,          \
+                   BinaryExpr<Field2D, Constant<L>, R, bout::op::OP_TYPE>> \
+  operator OP_SYM(L lhs, const R & rhs) {                                  \
+    return BinaryExpr<Field2D, Constant<L>, R, bout::op::OP_TYPE>{         \
+        static_cast<typename Constant<L>::View>(lhs),                      \
+        static_cast<typename R::View>(rhs),                                \
+        bout::op::OP_TYPE{},                                               \
+        rhs.getMesh(),                                                     \
+        rhs.getLocation(),                                                 \
+        rhs.getDirections(),                                               \
+        std::nullopt,                                                      \
+        rhs.getMesh()->getRegion2D("RGN_ALL")};                            \
   }
 
 FIELD2D_BOUTREAL_FIELD2D_OP(+, Add)
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 5056a4128b..62b299bc48 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -187,7 +187,7 @@ public:
                                           ZDirectionType::Standard});
   template <typename L, typename R, typename Func,
             typename = std::enable_if_t<is_expr_field3d_v<L> || is_expr_field3d_v<R>>>
-  Field3D(const BinaryExpr<L, R, Func>& expr) {
+  Field3D(const BinaryExpr<Field3D, L, R, Func>& expr) {
     //std::cout << "RUNNING constructor from BinaryExpr\n";
     Array<BoutReal> data{expr.size()};
     expr.evaluate(&data[0]);
@@ -457,9 +457,9 @@ public:
   /// return void, as only part initialised
   void operator=(const FieldPerp& rhs);
   Field3D& operator=(BoutReal val);
-  template <typename L, typename R, typename Func>
+  template <typename ResT, typename L, typename R, typename Func>
   std::enable_if_t<is_expr_field3d_v<L>, Field3D&>
-  operator=(BinaryExpr<L, R, Func>& expr) {
+  operator=(BinaryExpr<ResT, L, R, Func>& expr) {
     std::cout << "RUNNING operator= with CUDA\n";
     regionID = expr.getRegionID();
     if(isAllocated()) {
@@ -565,10 +565,11 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
 #define FIELD3D_FIELD3D_FIELD3D_OP(OP_SYM, OP_TYPE)                                    \
   template <typename L, typename R,                                                    \
             typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>> \
-  BinaryExpr<L, R, bout::op::OP_TYPE> operator OP_SYM(const L & lhs, const R & rhs) {  \
+  BinaryExpr<Field3D, L, R, bout::op::OP_TYPE> operator OP_SYM(const L & lhs,          \
+                                                               const R & rhs) {        \
     auto regionID =                                                                    \
         lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());          \
-    return BinaryExpr<L, R, bout::op::OP_TYPE>{                                        \
+    return BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>{                               \
         static_cast<typename L::View>(lhs),                                            \
         static_cast<typename R::View>(rhs),                                            \
         bout::op::OP_TYPE{},                                                           \
@@ -585,22 +586,22 @@ FIELD3D_FIELD3D_FIELD3D_OP(-, Sub)
 FIELD3D_FIELD3D_FIELD3D_OP(*, Mul)
 FIELD3D_FIELD3D_FIELD3D_OP(/, Div)
 
-#define FIELD3D_FIELD3D_FIELD2D_OP(OP_SYM, OP_TYPE)                                      \
-  template <typename L, typename R>                                                      \
-  std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,                         \
-                   BinaryExpr<L, R, bout::op::OP_TYPE>> operator OP_SYM(const L & lhs,   \
-                                                                        const R & rhs) { \
-    auto regionID = lhs.getRegionID();                                                   \
-    int mesh_nz = lhs.getMesh()->LocalNz;                                                \
-    return BinaryExpr<L, R, bout::op::OP_TYPE>{                                          \
-        static_cast<typename L::View>(lhs),                                              \
-        static_cast<typename R::View>(rhs).setScale(1, mesh_nz),                         \
-        bout::op::OP_TYPE{},                                                             \
-        lhs.getMesh(),                                                                   \
-        lhs.getLocation(),                                                               \
-        lhs.getDirections(),                                                             \
-        regionID,                                                                        \
-        lhs.getMesh()->getRegion("RGN_ALL")};                                            \
+#define FIELD3D_FIELD3D_FIELD2D_OP(OP_SYM, OP_TYPE)              \
+  template <typename L, typename R>                              \
+  std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>, \
+                   BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>> \
+  operator OP_SYM(const L & lhs, const R & rhs) {                \
+    auto regionID = lhs.getRegionID();                           \
+    int mesh_nz = lhs.getMesh()->LocalNz;                        \
+    return BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>{         \
+        static_cast<typename L::View>(lhs),                      \
+        static_cast<typename R::View>(rhs).setScale(1, mesh_nz), \
+        bout::op::OP_TYPE{},                                     \
+        lhs.getMesh(),                                           \
+        lhs.getLocation(),                                       \
+        lhs.getDirections(),                                     \
+        regionID,                                                \
+        lhs.getMesh()->getRegion("RGN_ALL")};                    \
   }
 
 FIELD3D_FIELD3D_FIELD2D_OP(+, Add)
@@ -608,21 +609,21 @@ FIELD3D_FIELD3D_FIELD2D_OP(-, Sub)
 FIELD3D_FIELD3D_FIELD2D_OP(*, Mul)
 FIELD3D_FIELD3D_FIELD2D_OP(/, Div)
 
-#define FIELD3D_FIELD3D_BOUTREAL_OP(OP_SYM, OP_TYPE)              \
-  template <typename L, typename R>                               \
-  std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>, \
-                   BinaryExpr<L, Constant<R>, bout::op::OP_TYPE>> \
-  operator OP_SYM(const L & lhs, R rhs) {                         \
-    auto regionID = lhs.getRegionID();                            \
-    return BinaryExpr<L, Constant<R>, bout::op::OP_TYPE>{         \
-        static_cast<typename L::View>(lhs),                       \
-        static_cast<typename Constant<R>::View>(rhs),             \
-        bout::op::OP_TYPE{},                                      \
-        lhs.getMesh(),                                            \
-        lhs.getLocation(),                                        \
-        lhs.getDirections(),                                      \
-        regionID,                                                 \
-        lhs.getMesh()->getRegion("RGN_ALL")};                     \
+#define FIELD3D_FIELD3D_BOUTREAL_OP(OP_SYM, OP_TYPE)                       \
+  template <typename L, typename R>                                        \
+  std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>,          \
+                   BinaryExpr<Field3D, L, Constant<R>, bout::op::OP_TYPE>> \
+  operator OP_SYM(const L & lhs, R rhs) {                                  \
+    auto regionID = lhs.getRegionID();                                     \
+    return BinaryExpr<Field3D, L, Constant<R>, bout::op::OP_TYPE>{         \
+        static_cast<typename L::View>(lhs),                                \
+        static_cast<typename Constant<R>::View>(rhs),                      \
+        bout::op::OP_TYPE{},                                               \
+        lhs.getMesh(),                                                     \
+        lhs.getLocation(),                                                 \
+        lhs.getDirections(),                                               \
+        regionID,                                                          \
+        lhs.getMesh()->getRegion("RGN_ALL")};                              \
   }
 
 FIELD3D_FIELD3D_BOUTREAL_OP(+, Add)
@@ -630,21 +631,21 @@ FIELD3D_FIELD3D_BOUTREAL_OP(-, Sub)
 FIELD3D_FIELD3D_BOUTREAL_OP(*, Mul)
 FIELD3D_FIELD3D_BOUTREAL_OP(/, Div)
 
-#define FIELD3D_BOUTREAL_FIELD3D_OP(OP_SYM, OP_TYPE)              \
-  template <typename L, typename R>                               \
-  std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>, \
-                   BinaryExpr<Constant<L>, R, bout::op::OP_TYPE>> \
-  operator OP_SYM(const L & lhs, const R & rhs) {                 \
-    auto regionID = rhs.getRegionID();                            \
-    return BinaryExpr<Constant<L>, R, bout::op::OP_TYPE>{         \
-        static_cast<typename Constant<L>::View>(lhs),             \
-        static_cast<typename R::View>(rhs),                       \
-        bout::op::OP_TYPE{},                                      \
-        rhs.getMesh(),                                            \
-        rhs.getLocation(),                                        \
-        rhs.getDirections(),                                      \
-        regionID,                                                 \
-        rhs.getMesh()->getRegion("RGN_ALL")};                     \
+#define FIELD3D_BOUTREAL_FIELD3D_OP(OP_SYM, OP_TYPE)                       \
+  template <typename L, typename R>                                        \
+  std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,          \
+                   BinaryExpr<Field3D, Constant<L>, R, bout::op::OP_TYPE>> \
+  operator OP_SYM(const L & lhs, const R & rhs) {                          \
+    auto regionID = rhs.getRegionID();                                     \
+    return BinaryExpr<Field3D, Constant<L>, R, bout::op::OP_TYPE>{         \
+        static_cast<typename Constant<L>::View>(lhs),                      \
+        static_cast<typename R::View>(rhs),                                \
+        bout::op::OP_TYPE{},                                               \
+        rhs.getMesh(),                                                     \
+        rhs.getLocation(),                                                 \
+        rhs.getDirections(),                                               \
+        regionID,                                                          \
+        rhs.getMesh()->getRegion("RGN_ALL")};                              \
   }
 
 FIELD3D_BOUTREAL_FIELD3D_OP(+, Add)
@@ -771,8 +772,9 @@ struct is_expr_field3d<Field3D> : std::true_type {};
 template <>
 struct is_expr_field2d<Field2D> : std::true_type {};
 
-template <typename L, typename R, typename Fun>
-struct is_expr_field3d<BinaryExpr<L, R, Fun>>
-    : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value || is_expr_field3d_v<std::decay_t<R>>> {};
+template <typename ResT, typename L, typename R, typename Fun>
+struct is_expr_field3d<BinaryExpr<ResT, L, R, Fun>>
+    : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value
+                                       || is_expr_field3d_v<std::decay_t<R>>> {};
 
 #endif /* BOUT_FIELD3D_H */
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 9346b55e48..48d104e3ea 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -24,6 +24,12 @@ inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::valu
 template <typename T>
 struct is_expr_field3d : std::false_type {};
 
+template <typename T>
+struct is_expr_fieldperp : std::false_type {};
+
+template <typename T>
+inline constexpr bool is_expr_fieldperp_v = is_expr_fieldperp<std::decay_t<T>>::value;
+
 // Helper variable template
 template <typename T>
 inline constexpr bool is_expr_field3d_v = is_expr_field3d<std::decay_t<T>>::value;
@@ -124,7 +130,7 @@ __global__ void __launch_bounds__(THREADS) evaluatorExpr(BoutReal* out, const Ex
 
 inline std::unordered_map<void*, Array<int>> regionIndicesCache;
 
-template <typename L, typename R, typename Func>
+template <typename ResT, typename L, typename R, typename Func>
 struct BinaryExpr {
   typename L::View lhs;
   typename R::View rhs;
@@ -185,6 +191,7 @@ struct BinaryExpr {
   }
   inline int regionIdx(int idx) const { return indices[idx]; }
 
+  //operator ResT() { return ResT{*this}; }
   struct View {
     typename L::View lhs;
     typename R::View rhs;
@@ -204,8 +211,8 @@ struct BinaryExpr {
       return indices[idx];
     }
     __host__ __device__ __forceinline__ BoutReal operator()(int idx) const {
-      //return f((idx * mul) / div, lhs, rhs); // single‐pass fusion
-      return f(lhs((idx * mul) / div), rhs((idx * mul) / div)); // single‐pass fusion
+      return f((idx * mul) / div, lhs, rhs); // single‐pass fusion
+      //return f(lhs((idx * mul) / div), rhs((idx * mul) / div)); // single‐pass fusion
     }
   };
 
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 6995308dbe..49d4fec1b7 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -86,6 +86,17 @@ public:
             DirectionTypes directions_in = {YDirectionType::Standard,
                                             ZDirectionType::Standard});
 
+  template <
+      typename ResT, typename L, typename R, typename Func,
+      typename = std::enable_if_t<(is_expr_fieldperp_v<L> && is_expr_fieldperp_v<R>)>>
+  FieldPerp(const BinaryExpr<ResT, L, R, Func>& expr) {
+    std::cout << "RUNNING FieldPerp constructor with CUDA\n";
+    Array<BoutReal> data{expr.size()};
+    expr.evaluate(&data[0]);
+    *this = std::move(FieldPerp{std::move(data), expr.getMesh(), expr.getLocation(),
+                                /* yindex */ -1, expr.getDirections()});
+  }
+
   ~FieldPerp() override = default;
 
   /*!
@@ -292,6 +303,26 @@ public:
 
   int size() const override { return nx * nz; };
 
+  struct View {
+    BoutReal* data;
+    int mul = 1;
+    int div = 1;
+    __host__ __device__ inline BoutReal operator()(int idx) const {
+      return data[(idx * mul) / div];
+    }
+    __host__ __device__ inline BoutReal& operator[](int idx) const {
+      return data[(idx * mul) / div];
+    }
+
+    View& setScale(int mul, int div) {
+      this->mul = mul;
+      this->div = div;
+      return *this;
+    }
+  };
+  operator View() { return View{&data[0]}; }
+  operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
+
 private:
   /// The Y index at which this FieldPerp is defined
   int yindex{-1};
@@ -379,4 +410,12 @@ bool operator==(const FieldPerp& a, const FieldPerp& b);
 /// Output a string describing a FieldPerp to a stream
 std::ostream& operator<<(std::ostream& out, const FieldPerp& value);
 
+template <>
+struct is_expr_fieldperp<FieldPerp> : std::true_type {};
+
+template <typename ResT, typename L, typename R, typename Fun>
+struct is_expr_fieldperp<BinaryExpr<ResT, L, R, Fun>>
+    : std::integral_constant<bool, is_expr_fieldperp_v<std::decay_t<L>>
+                                       && is_expr_fieldperp_v<std::decay_t<R>>> {};
+
 #endif
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index e5c1d466b7..c8b9ebb689 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -389,8 +389,7 @@ bool operator==(const Field2D& a, const Field2D& b) {
   if (!a.isAllocated() || !b.isAllocated()) {
     return false;
   }
-  Field2D diff = a - b;
-  return min(abs(diff)) < 1e-10;
+  return min(abs(a - b)) < 1e-10;
 }
 
 std::ostream& operator<<(std::ostream& out, const Field2D& value) {
diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index ca9bdc0397..9578aa0d9d 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -209,7 +209,7 @@ bool operator==(const FieldPerp& a, const FieldPerp& b) {
   if (!a.isAllocated() || !b.isAllocated()) {
     return false;
   }
-  return (a.getIndex() == b.getIndex()) and (min(abs(a - b)) < 1e-10);
+  return (a.getIndex() == b.getIndex()) and (min(FieldPerp{abs(a - b)}) < 1e-10);
 }
 
 std::ostream& operator<<(std::ostream& out, const FieldPerp& value) {
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index b8fd33c019..0139d21fd7 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1349,7 +1349,7 @@ int Coordinates::jacobian() {
   // Check that g is positive
   bout::checkPositive(g, "The determinant of g^ij", "RGN_NOBNDRY");
 
-  J = 1. / sqrt(Field2D{g});
+  J = 1. / sqrt(g);
   // More robust to extrapolate derived quantities directly, rather than
   // deriving from extrapolated covariant metric components
   J = interpolateAndExtrapolate(J, location, extrapolate_x, extrapolate_y, false,
diff --git a/src/physics/snb.cxx b/src/physics/snb.cxx
index f21bfb7ee0..80da9e1bf8 100644
--- a/src/physics/snb.cxx
+++ b/src/physics/snb.cxx
@@ -11,10 +11,10 @@ namespace bout {
 Field3D HeatFluxSNB::divHeatFlux(const Field3D& Te, const Field3D& Ne,
                                  Field3D* Div_Q_SH_out) {
 
-  Field3D thermal_speed = sqrt(Field3D{2. * SI::qe * Te / SI::Me});
+  Field3D thermal_speed = sqrt(2. * SI::qe * Te / SI::Me);
 
   BoutReal Y = SQ(SQ(SI::qe) / (SI::e0 * SI::Me)) / (4 * PI);
-  Field3D coulomb_log = 6.6 - 0.5 * log(Field3D{Ne * 1e-20}) + 1.5 * log(Te);
+  Field3D coulomb_log = 6.6 - 0.5 * log(Ne * 1e-20) + 1.5 * log(Te);
 
   // Thermal electron-electron mean free path [m]
   Field3D lambda_ee_T = pow(thermal_speed, 4) / (Y * Ne * coulomb_log);

From 21e964c8cf146a8ab67a1d224f543a279bfc5c56 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 4 Jun 2025 11:59:28 -0700
Subject: [PATCH 0191/1827] ADIOS2: Add Array/Matrix/Tensor<int> types

Without these the build fails at link time when building with ADIOS2.
---
 src/sys/options/options_adios.cxx | 40 +++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 09797647ed..06353a1de8 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -472,6 +472,18 @@ void ADIOSPutVarVisitor::operator()<FieldPerp>(const FieldPerp& value) {
   stream.engine.Put<BoutReal>(var, &value(0, 0));
 }
 
+template <>
+void ADIOSPutVarVisitor::operator()<Array<int>>(const Array<int>& value) {
+  // Pointer to data. Assumed to be contiguous array
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.size()};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0};
+  adios2::Dims count = {1, shape[1]};
+  adios2::Variable<int> var =
+      stream.GetArrayVariable<int>(varname, shape, DIMS_NONE, BoutComm::rank());
+  var.SetSelection({start, count});
+  stream.engine.Put<int>(var, value.begin());
+}
+
 template <>
 void ADIOSPutVarVisitor::operator()<Array<BoutReal>>(const Array<BoutReal>& value) {
   // Pointer to data. Assumed to be contiguous array
@@ -484,6 +496,20 @@ void ADIOSPutVarVisitor::operator()<Array<BoutReal>>(const Array<BoutReal>& valu
   stream.engine.Put<BoutReal>(var, value.begin());
 }
 
+template <>
+void ADIOSPutVarVisitor::operator()<Matrix<int>>(const Matrix<int>& value) {
+  // Pointer to data. Assumed to be contiguous array
+  auto s = value.shape();
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s),
+                        (size_t)std::get<1>(s)};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0};
+  adios2::Dims count = {1, shape[1], shape[2]};
+  adios2::Variable<int> var =
+      stream.GetArrayVariable<int>(varname, shape, DIMS_NONE, BoutComm::rank());
+  var.SetSelection({start, count});
+  stream.engine.Put<int>(var, value.begin());
+}
+
 template <>
 void ADIOSPutVarVisitor::operator()<Matrix<BoutReal>>(const Matrix<BoutReal>& value) {
   // Pointer to data. Assumed to be contiguous array
@@ -498,6 +524,20 @@ void ADIOSPutVarVisitor::operator()<Matrix<BoutReal>>(const Matrix<BoutReal>& va
   stream.engine.Put<BoutReal>(var, value.begin());
 }
 
+template <>
+void ADIOSPutVarVisitor::operator()<Tensor<int>>(const Tensor<int>& value) {
+  // Pointer to data. Assumed to be contiguous array
+  auto s = value.shape();
+  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s),
+                        (size_t)std::get<1>(s), (size_t)std::get<2>(s)};
+  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0};
+  adios2::Dims count = {1, shape[1], shape[2], shape[3]};
+  adios2::Variable<int> var =
+      stream.GetArrayVariable<int>(varname, shape, DIMS_NONE, BoutComm::rank());
+  var.SetSelection({start, count});
+  stream.engine.Put<int>(var, value.begin());
+}
+
 template <>
 void ADIOSPutVarVisitor::operator()<Tensor<BoutReal>>(const Tensor<BoutReal>& value) {
   // Pointer to data. Assumed to be contiguous array

From 020d8798eef05ec8141a033d3d7d5772db41236d Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Wed, 4 Jun 2025 19:01:57 +0000
Subject: [PATCH 0192/1827] Apply clang-format changes

---
 include/bout/options.hxx |  7 ++++---
 src/sys/options.cxx      | 14 +++++++-------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 6ee9beeb6d..273abdbaca 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -201,9 +201,10 @@ public:
   }
 
   /// The type used to store values
-  using ValueType = bout::utils::variant<bool, int, BoutReal, std::string, Field2D,
-                                         Field3D, FieldPerp, Array<BoutReal>, Array<int>,
-                                         Matrix<BoutReal>, Matrix<int>, Tensor<BoutReal>, Tensor<int>>;
+  using ValueType =
+      bout::utils::variant<bool, int, BoutReal, std::string, Field2D, Field3D, FieldPerp,
+                           Array<BoutReal>, Array<int>, Matrix<BoutReal>, Matrix<int>,
+                           Tensor<BoutReal>, Tensor<int>>;
 
   /// A tree representation with leaves containing ValueType.
   /// Used to construct Options from initializer lists.
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 951a46aca4..387a851f3b 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -832,9 +832,8 @@ Matrix<int> Options::as<Matrix<int>>(const Matrix<int>& similar_to) const {
 
   auto result = bout::utils::visit(
       ConvertContainer<Matrix<int>>{
-          fmt::format(
-              _("Value for option {:s} cannot be converted to an Matrix<int>"),
-              full_name),
+          fmt::format(_("Value for option {:s} cannot be converted to an Matrix<int>"),
+                      full_name),
           similar_to},
       value);
 
@@ -876,9 +875,8 @@ Tensor<int> Options::as<Tensor<int>>(const Tensor<int>& similar_to) const {
 
   auto result = bout::utils::visit(
       ConvertContainer<Tensor<int>>{
-          fmt::format(
-              _("Value for option {:s} cannot be converted to an Tensor<int>"),
-              full_name),
+          fmt::format(_("Value for option {:s} cannot be converted to an Tensor<int>"),
+                      full_name),
           similar_to},
       value);
 
@@ -1032,7 +1030,9 @@ struct GetDimensions {
   std::vector<int> operator()([[maybe_unused]] BoutReal value) { return {1}; }
   std::vector<int> operator()([[maybe_unused]] const std::string& value) { return {1}; }
   template <typename T>
-  std::vector<int> operator()(const Array<T>& array) { return {array.size()}; }
+  std::vector<int> operator()(const Array<T>& array) {
+    return {array.size()};
+  }
   template <typename T>
   std::vector<int> operator()(const Matrix<T>& array) {
     const auto shape = array.shape();

From a32390e282be43117b4add8313e08533833b298c Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 4 Jun 2025 14:45:05 -0700
Subject: [PATCH 0193/1827] Apply suggestions from code review

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 src/mesh/impls/bout/boutmesh.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 3ab30223f4..fe928f377d 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -2161,9 +2161,9 @@ void BoutMesh::topology() {
     }
 
     for (int i = 0; i < limiter_count; ++i) {
-      int yind = limiter_yinds[i];
-      int xstart = limiter_xstarts[i];
-      int xend = limiter_xends[i];
+      int const yind = limiter_yinds[i];
+      int const xstart = limiter_xstarts[i];
+      int const xend = limiter_xends[i];
       output_info.write("Adding a limiter between y={} and {}. X indices {} to {}\n",
                         yind, yind + 1, xstart, xend);
       add_target(yind, xstart, xend);

From bfedcc34369c5cad2590cd7b34abda80c67bee63 Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Wed, 4 Jun 2025 21:51:44 +0000
Subject: [PATCH 0194/1827] Apply clang-format changes

---
 src/solver/impls/arkode/arkode.cxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 23883cc043..514ff8671e 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -229,8 +229,7 @@ int ArkodeSolver::init() {
     throw BoutException("ARKodeSetUserData failed\n");
   }
 
-  if (ARKodeSetLinear(arkode_mem, static_cast<int>(set_linear))
-      != ARK_SUCCESS) {
+  if (ARKodeSetLinear(arkode_mem, static_cast<int>(set_linear)) != ARK_SUCCESS) {
     throw BoutException("ARKodeSetLinear failed\n");
   }
 

From 96cdee5b83aadc64304d1024ec84767e8e7c182b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Jun 2025 19:41:43 +0000
Subject: [PATCH 0195/1827] Bump externalpackages/boutdata from `0aaef41` to
 `a7a372d`

Bumps [externalpackages/boutdata](https://github.com/boutproject/boutdata) from `0aaef41` to `a7a372d`.
- [Release notes](https://github.com/boutproject/boutdata/releases)
- [Commits](https://github.com/boutproject/boutdata/compare/0aaef417af092882ac295c4d84e4532e4a10e01f...a7a372d5de7594cbe16381a3a82289ddaa58b6e7)

---
updated-dependencies:
- dependency-name: externalpackages/boutdata
  dependency-version: a7a372d5de7594cbe16381a3a82289ddaa58b6e7
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/boutdata | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/boutdata b/externalpackages/boutdata
index 0aaef417af..a7a372d5de 160000
--- a/externalpackages/boutdata
+++ b/externalpackages/boutdata
@@ -1 +1 @@
-Subproject commit 0aaef417af092882ac295c4d84e4532e4a10e01f
+Subproject commit a7a372d5de7594cbe16381a3a82289ddaa58b6e7

From 5d375970bcf2c99ca39077226c09e8ee0d802fcc Mon Sep 17 00:00:00 2001
From: Cristian Le <git@lecris.dev>
Date: Mon, 23 Jun 2025 15:04:37 +0200
Subject: [PATCH 0196/1827] Move the `EXCLUDE_FROM_ALL` inwards in the manual

---
 CMakeLists.txt        | 2 +-
 manual/CMakeLists.txt | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 60d34e1ad7..b3326c6742 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -733,7 +733,7 @@ endif()
 
 option(BOUT_BUILD_DOCS "Build the documentation" OFF)
 if (BOUT_BUILD_DOCS)
-  add_subdirectory(manual EXCLUDE_FROM_ALL)
+  add_subdirectory(manual)
 endif()
 
 
diff --git a/manual/CMakeLists.txt b/manual/CMakeLists.txt
index c8e22b1dcf..2e4e612d9f 100644
--- a/manual/CMakeLists.txt
+++ b/manual/CMakeLists.txt
@@ -24,10 +24,12 @@ set_target_properties(sphinx-html sphinx-pdf PROPERTIES
   ENVIRONMENT PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
 )
 
-add_custom_target(docs ALL)
+add_custom_target(docs)
 add_dependencies(docs sphinx-html)
 
 install(DIRECTORY ${BOUT_SPHINX_BUILD}/
   DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/doc/bout++/
+  EXCLUDE_FROM_ALL
+  COMPONENT docs
   PATTERN .* EXCLUDE
 )

From 51bef96fd6c7d1d1713389c72d2e9e3603b030d3 Mon Sep 17 00:00:00 2001
From: Cristian Le <git@lecris.dev>
Date: Mon, 23 Jun 2025 15:14:45 +0200
Subject: [PATCH 0197/1827] Fix the environment setting

---
 manual/CMakeLists.txt | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/manual/CMakeLists.txt b/manual/CMakeLists.txt
index 2e4e612d9f..b5224440bf 100644
--- a/manual/CMakeLists.txt
+++ b/manual/CMakeLists.txt
@@ -6,7 +6,13 @@ find_package(Sphinx REQUIRED)
 set(BOUT_SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/sphinx)
 set(BOUT_SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR}/docs)
 
+set(env_command
+    ${CMAKE_COMMAND} -E env
+    PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
+)
+
 add_custom_target(sphinx-html
+  COMMAND ${env_command}
   COMMAND ${SPHINX_EXECUTABLE} -b html ${BOUT_SPHINX_SOURCE} ${BOUT_SPHINX_BUILD}
   COMMAND ${CMAKE_COMMAND} -E echo "Generated HTML docs in file://${BOUT_SPHINX_BUILD}/index.html"
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -14,16 +20,13 @@ add_custom_target(sphinx-html
 )
 
 add_custom_target(sphinx-pdf
+  COMMAND ${env_command}
   COMMAND ${SPHINX_EXECUTABLE} -M latexpdf ${BOUT_SPHINX_SOURCE} ${BOUT_SPHINX_BUILD}
   COMMAND ${CMAKE_COMMAND} -E echo "Generated PDF docs in file://${BOUT_SPHINX_BUILD}"
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   COMMENT "Generating PDF documentation with Sphinx in ${BOUT_SPHINX_BUILD}"
 )
 
-set_target_properties(sphinx-html sphinx-pdf PROPERTIES
-  ENVIRONMENT PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
-)
-
 add_custom_target(docs)
 add_dependencies(docs sphinx-html)
 

From dd8e5ebca19c8fe38b2ad2cd6a9981ee85eac18f Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 30 Oct 2024 13:39:04 +0000
Subject: [PATCH 0198/1827] Replace deprecated `boututils.file_import`

---
 examples/elm-pb/Python/2dprofile.py             |  5 +++--
 examples/elm-pb/Python/plotcollapse.py          |  7 +++++--
 examples/elm-pb/Python/post.py                  |  5 +++--
 examples/elm-pb/Python/read_elmsize.py          |  5 +++--
 examples/elm-pb/Python/sprofiles.py             |  9 +++++----
 examples/elm-pb/Python/volume_int.py            | 14 ++++++++------
 tests/integrated/test-drift-instability/runtest |  8 ++++----
 7 files changed, 31 insertions(+), 22 deletions(-)

diff --git a/examples/elm-pb/Python/2dprofile.py b/examples/elm-pb/Python/2dprofile.py
index ea430a0fe1..5bb01972f9 100644
--- a/examples/elm-pb/Python/2dprofile.py
+++ b/examples/elm-pb/Python/2dprofile.py
@@ -3,10 +3,11 @@
 from past.utils import old_div
 import numpy as np
 import matplotlib.pyplot as plt
-from boututils.file_import import file_import
+from boututils.datafile import DataFile
 from matplotlib.ticker import FixedFormatter, FormatStrFormatter, AutoLocator, AutoMinorLocator
 
-g = file_import("./cbm18_dens8.grid_nx68ny64.nc")
+with DataFile("./cbm18_dens8.grid_nx68ny64.nc") as f:
+    g = {v: f.read(v) for v in f.keys()}
 
 majorLocator   = AutoLocator()
 majorFormatter = FormatStrFormatter('%3.0e')
diff --git a/examples/elm-pb/Python/plotcollapse.py b/examples/elm-pb/Python/plotcollapse.py
index 49858ae37e..ee64ca381f 100755
--- a/examples/elm-pb/Python/plotcollapse.py
+++ b/examples/elm-pb/Python/plotcollapse.py
@@ -5,9 +5,10 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from boututils.moment_xyzt import moment_xyzt
-from boututils.file_import import file_import
+from boututils.datafile import DataFile
 from boutdata.collect import collect
 import os
+from pathlib import Path
 
 #Dynamic matplotlib settings
 from matplotlib import rcParams
@@ -17,8 +18,10 @@
 
 if not os.path.exists('image'):
    os.makedirs('image')
+filename = Path(__file__).with_name("cbm18_dens8.grid_nx68ny64.nc")
+with DataFile(str(filename)) as f:
+    g = {v: f.read(v) for v in f.keys()}
 
-g = file_import(os.path.dirname(os.path.realpath(__file__))+'/../cbm18_dens8.grid_nx68ny64.nc')
 psi = old_div((g['psixy'][:, 32] - g['psi_axis']), (g['psi_bndry'] - g['psi_axis']))
 
 path = './data'
diff --git a/examples/elm-pb/Python/post.py b/examples/elm-pb/Python/post.py
index 2c2d3e2bde..9bb67347f0 100644
--- a/examples/elm-pb/Python/post.py
+++ b/examples/elm-pb/Python/post.py
@@ -5,7 +5,7 @@
 from __future__ import division
 from past.utils import old_div
 import numpy as np
-from boututils.file_import import file_import
+from boututils.datafile import DataFile
 from boutdata.collect import collect
 from pylab import plot, show, figure, xlabel, ylabel, annotate, xlim, ylim
 from boututils.moment_xyzt import moment_xyzt
@@ -23,7 +23,8 @@
 gfile='./cbm18_dens8.grid_nx68ny64.nc'
 
 
-g = file_import(gfile)
+with DataFile(gfile) as f:
+    g = {v: f.read(v) for v in f.keys()}
 
 
 Dphi0 = collect("Dphi0", path=path0)
diff --git a/examples/elm-pb/Python/read_elmsize.py b/examples/elm-pb/Python/read_elmsize.py
index b2ce7674a6..fcd3d24e53 100644
--- a/examples/elm-pb/Python/read_elmsize.py
+++ b/examples/elm-pb/Python/read_elmsize.py
@@ -1,6 +1,6 @@
 from boutdata.collect import collect
 from boututils.moment_xyzt import moment_xyzt
-from boututils.file_import import file_import
+from boututils.datafile import DataFile
 from pylab import save, figure, plot, title, xlabel, ylabel, show, tight_layout
 from elm_size import elm_size
 
@@ -19,7 +19,8 @@
 # te0=collect('te0', path=path)
 # save('te0.idl.dat', te0)
 
-gfile=file_import('./cbm18_dens8.grid_nx68ny64.nc')
+with DataFile("./cbm18_dens8.grid_nx68ny64.nc") as f:
+    gfile = {v: f.read(v) for v in f.keys()}
 
 p=collect('P', path=path)
 save('p.dat', p)
diff --git a/examples/elm-pb/Python/sprofiles.py b/examples/elm-pb/Python/sprofiles.py
index f118bce23c..9d8eea48de 100644
--- a/examples/elm-pb/Python/sprofiles.py
+++ b/examples/elm-pb/Python/sprofiles.py
@@ -3,17 +3,18 @@
 from builtins import range
 from past.utils import old_div
 import numpy as np
-from boututils.file_import import file_import
+from boututils.datafile import DataFile
 from boututils.surface_average import surface_average
 from boutdata.collect import collect
 from pylab import plot, show, xlabel, ylabel, figure, legend, gca
 
 
-path='./data'
+path = "./data"
 
-gfile='../cbm18_dens8.grid_nx68ny64.nc'
+gfile = "../cbm18_dens8.grid_nx68ny64.nc"
 
-g = file_import(gfile)
+with DataFile(gfile) as f:
+    g = {v: f.read(v) for v in f.keys()}
 
 var=collect("P", path=path)
 
diff --git a/examples/elm-pb/Python/volume_int.py b/examples/elm-pb/Python/volume_int.py
index 38775d37e0..e858f156d7 100644
--- a/examples/elm-pb/Python/volume_int.py
+++ b/examples/elm-pb/Python/volume_int.py
@@ -1,18 +1,20 @@
 from __future__ import print_function
-from boututils.file_import import file_import
+from boututils.datafile import DataFile
 from boututils.volume_integral import volume_integral
 from boutdata.collect import collect
+
 # Integrate over a volume
 
 
-path='./data/'
+path = "./data/"
 
-gfile='./cbm18_dens8.grid_nx68ny64.nc'
+gfile = "./cbm18_dens8.grid_nx68ny64.nc"
 
-g = file_import(gfile)
+with DataFile(gfile) as f:
+    g = {v: f.read(v) for v in f.keys()}
 
-var=collect("P", path=path)
+var = collect("P", path=path)
 
-sol=volume_integral(var, g)
+sol = volume_integral(var, g)
 
 print(sol)
diff --git a/tests/integrated/test-drift-instability/runtest b/tests/integrated/test-drift-instability/runtest
index e8ddddc11d..85aa8ea1f3 100755
--- a/tests/integrated/test-drift-instability/runtest
+++ b/tests/integrated/test-drift-instability/runtest
@@ -7,8 +7,8 @@
 # Requires: not metric_3d
 
 from boututils.run_wrapper import build_and_log, shell, launch_safe
-from boututils.file_import import file_import
 from boututils.calculus import deriv
+from boututils.datafile import DataFile
 from boututils.linear_regression import linear_regression
 
 from boutdata.collect import collect
@@ -94,6 +94,9 @@ def run_zeff_case(zeff):
     ny = dims[2]
     nz = dims[3]
 
+    with DataFile("uedge.grd_std.cdl") as f:
+        grid = {v: f.read(v) for v in f.keys()}
+
     # Calculate geometric and physical quantities
     lZeta = 1e2 * zmax * 2 * np.pi * grid["R0"]  # toroidal range [cm]
     lbNorm = lZeta * (
@@ -211,9 +214,6 @@ if __name__ == "__main__":
 
     build_and_log("resistive drift instability test")
 
-    # Import the grid file
-    grid = file_import("uedge.grd_std.cdl")
-
     return_code = 0
     for zeff in args.Zeff_list:
         success = run_zeff_case(zeff)

From 4ffb732409536618bc4422a8cfac81ff83760388 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Thu, 5 Jun 2025 10:03:47 +0000
Subject: [PATCH 0199/1827] Add PETSc version guards for function cast

---
 include/bout/petsc_interface.hxx         |  9 +++++++++
 src/solver/impls/imex-bdf2/imex-bdf2.cxx | 20 +++++++++++---------
 src/solver/impls/snes/snes.cxx           |  1 +
 3 files changed, 21 insertions(+), 9 deletions(-)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 8e7d44c67d..670d91b2ec 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -615,6 +615,15 @@ PetscVector<T> operator*(const PetscMatrix<T>& mat, const PetscVector<T>& vec) {
   return PetscVector<T>(vec, result);
 }
 
+// Compatibility wrappers
+// For < 3.24
+#if PETSC_VERSION_GE(3, 24, 0) \
+    || (PETSC_VERSION_GE(3, 23, 0) && PETSC_VERSION_RELEASE != 0)
+// Nothing to do
+#else
+using MatFDColoringFn = PetscErrorCode (*)();
+#endif
+
 #endif // BOUT_HAS_PETSC
 
 #endif // __PETSC_INTERFACE_H__
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
index adafbb71c5..3629965b87 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
@@ -9,6 +9,7 @@
 #include <bout/boutexception.hxx>
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
+#include <bout/petsc_interface.hxx>
 #include <bout/utils.hxx>
 
 #include <cmath>
@@ -116,7 +117,7 @@ static PetscErrorCode FormFunctionForDifferencing(void* ctx, Vec x, Vec f) {
  *
  * This can be a linearised and simplified form of FormFunction
  */
-static PetscErrorCode FormFunctionForColoring(SNES UNUSED(snes), Vec x, Vec f,
+static PetscErrorCode FormFunctionForColoring(void* UNUSED(snes), Vec x, Vec f,
                                               void* ctx) {
   return static_cast<IMEXBDF2*>(ctx)->snes_function(x, f, true);
 }
@@ -654,9 +655,15 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
       // Create data structure for SNESComputeJacobianDefaultColor
       MatFDColoringCreate(Jmf, iscoloring, &fdcoloring);
       // Set the function to difference
-      MatFDColoringSetFunction(
-          fdcoloring, reinterpret_cast<PetscErrorCode (*)()>(FormFunctionForColoring),
-          this);
+#if PETSC_VERSION_GE(3, 24, 0) \
+    || (PETSC_VERSION_GE(3, 23, 0) && PETSC_VERSION_RELEASE == 0)
+#define FUNC_MAYBE_CAST(func) func
+#else
+#define FUNC_MAYBE_CAST(func) reinterpret_cast<MatFDColoringFn>(func)
+#endif
+      MatFDColoringSetFunction(fdcoloring, FUNC_MAYBE_CAST(FormFunctionForColoring),
+                               this);
+#undef FUNC_MAYBE_CAST
       MatFDColoringSetFromOptions(fdcoloring);
       MatFDColoringSetUp(Jmf, iscoloring, fdcoloring);
       ISColoringDestroy(&iscoloring);
@@ -680,12 +687,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
           0, // Number of nonzeros per row in off-diagonal portion of local submatrix
           nullptr, &Jmf);
 
-#if PETSC_VERSION_GE(3, 4, 0)
       SNESSetJacobian(*snesIn, Jmf, Jmf, SNESComputeJacobianDefault, this);
-#else
-      // Before 3.4
-      SNESSetJacobian(*snesIn, Jmf, Jmf, SNESDefaultComputeJacobian, this);
-#endif
 
       MatSetOption(Jmf, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
     }
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 2143aad96a..b1db03f80a 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -7,6 +7,7 @@
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/msg_stack.hxx>
+#include <bout/petsc_interface.hxx>
 #include <bout/utils.hxx>
 
 #include <array>

From 1bc99e5c42ef94f4f93ccdbf651101417125611f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 6 Jun 2025 11:41:57 +0200
Subject: [PATCH 0200/1827] Update docs for what PETSc we support

3.23 has been tested in CI so is expected to work.
---
 manual/RELEASE_HOWTO.md                      | 1 +
 manual/sphinx/user_docs/advanced_install.rst | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/manual/RELEASE_HOWTO.md b/manual/RELEASE_HOWTO.md
index 4103e6f197..d8ced2afb5 100644
--- a/manual/RELEASE_HOWTO.md
+++ b/manual/RELEASE_HOWTO.md
@@ -51,6 +51,7 @@ Before merging PR:
     - [ ]  [`manual/doxygen/Doxyfile_readthedocs`][Doxyfile_readthedocs]: `PROJECT_NUMBER`
     - [ ]  [`manual/doxygen/Doxyfile`][Doxyfile]: `PROJECT_NUMBER`
     - [ ]  [`CMakeLists.txt`][CMakeLists]: `_bout_previous_version`, `_bout_next_version`
+- [ ] Update what version of PETSc and SUNDIALS we support (upper bound)
 
 
 After PR is merged:
diff --git a/manual/sphinx/user_docs/advanced_install.rst b/manual/sphinx/user_docs/advanced_install.rst
index 428666dbd7..91d2fa898b 100644
--- a/manual/sphinx/user_docs/advanced_install.rst
+++ b/manual/sphinx/user_docs/advanced_install.rst
@@ -480,7 +480,7 @@ BOUT++ can use PETSc https://www.mcs.anl.gov/petsc/ for time-integration
 and for solving elliptic problems, such as inverting Poisson and
 Helmholtz equations.
 
-Currently, BOUT++ supports PETSc versions 3.7 - 3.19. More recent versions may
+Currently, BOUT++ supports PETSc versions 3.7 - 3.23. More recent versions may
 well work, but the PETSc API does sometimes change in backward-incompatible
 ways, so this is not guaranteed. To install PETSc version 3.19, use the
 following steps::

From 63a868339eddcb8bb843b9fba66424eeb87fd08b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 17 Jun 2025 16:55:24 +0100
Subject: [PATCH 0201/1827] Fix PETSc version check for MatFDColoringFn typedef

---
 include/bout/petsc_interface.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 670d91b2ec..1538fb5b8e 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -618,7 +618,7 @@ PetscVector<T> operator*(const PetscMatrix<T>& mat, const PetscVector<T>& vec) {
 // Compatibility wrappers
 // For < 3.24
 #if PETSC_VERSION_GE(3, 24, 0) \
-    || (PETSC_VERSION_GE(3, 23, 0) && PETSC_VERSION_RELEASE != 0)
+    || (PETSC_VERSION_GE(3, 23, 0) && PETSC_VERSION_RELEASE == 0)
 // Nothing to do
 #else
 using MatFDColoringFn = PetscErrorCode (*)();

From 8e5a037b92f8a465a0bb00254ae7681725ae8565 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 17 Jun 2025 17:04:13 +0100
Subject: [PATCH 0202/1827] Move "maybe cast" macro to header for reuse

---
 include/bout/petsc_interface.hxx         |  3 ++-
 src/solver/impls/imex-bdf2/imex-bdf2.cxx | 11 ++---------
 src/solver/impls/snes/snes.cxx           |  2 +-
 3 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 1538fb5b8e..a38938488c 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -619,9 +619,10 @@ PetscVector<T> operator*(const PetscMatrix<T>& mat, const PetscVector<T>& vec) {
 // For < 3.24
 #if PETSC_VERSION_GE(3, 24, 0) \
     || (PETSC_VERSION_GE(3, 23, 0) && PETSC_VERSION_RELEASE == 0)
-// Nothing to do
+#define BOUT_CAST_MATFDCOLORINGFN(func) func
 #else
 using MatFDColoringFn = PetscErrorCode (*)();
+#define BOUT_CAST_MATFDCOLORINGFN(func) reinterpret_cast<MatFDColoringFn>(func)
 #endif
 
 #endif // BOUT_HAS_PETSC
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
index 3629965b87..f374d06356 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
@@ -655,15 +655,8 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
       // Create data structure for SNESComputeJacobianDefaultColor
       MatFDColoringCreate(Jmf, iscoloring, &fdcoloring);
       // Set the function to difference
-#if PETSC_VERSION_GE(3, 24, 0) \
-    || (PETSC_VERSION_GE(3, 23, 0) && PETSC_VERSION_RELEASE == 0)
-#define FUNC_MAYBE_CAST(func) func
-#else
-#define FUNC_MAYBE_CAST(func) reinterpret_cast<MatFDColoringFn>(func)
-#endif
-      MatFDColoringSetFunction(fdcoloring, FUNC_MAYBE_CAST(FormFunctionForColoring),
-                               this);
-#undef FUNC_MAYBE_CAST
+      MatFDColoringSetFunction(fdcoloring,
+                               BOUT_CAST_MATFDCOLORINGFN(FormFunctionForColoring), this);
       MatFDColoringSetFromOptions(fdcoloring);
       MatFDColoringSetUp(Jmf, iscoloring, fdcoloring);
       ISColoringDestroy(&iscoloring);
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index b1db03f80a..a2630ad56d 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -42,7 +42,7 @@ static PetscErrorCode FormFunctionForDifferencing(void* ctx, Vec x, Vec f) {
  *
  * This can be a linearised and simplified form of FormFunction
  */
-static PetscErrorCode FormFunctionForColoring(SNES UNUSED(snes), Vec x, Vec f,
+static PetscErrorCode FormFunctionForColoring(void* UNUSED(snes), Vec x, Vec f,
                                               void* ctx) {
   return static_cast<SNESSolver*>(ctx)->snes_function(x, f, true);
 }

From b5aa5d0ea2fe8d656a4921573efbdfd34acdddeb Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 17 Jun 2025 18:08:05 +0100
Subject: [PATCH 0203/1827] Convert macro to constexpr template function

Removes some clang-tidy warnings and silences one about reinterpret_cast
---
 include/bout/petsc_interface.hxx         | 14 ++++++++++++--
 src/solver/impls/imex-bdf2/imex-bdf2.cxx |  2 +-
 src/solver/impls/snes/snes.cxx           |  5 ++---
 3 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index a38938488c..2e55534e68 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -619,10 +619,20 @@ PetscVector<T> operator*(const PetscMatrix<T>& mat, const PetscVector<T>& vec) {
 // For < 3.24
 #if PETSC_VERSION_GE(3, 24, 0) \
     || (PETSC_VERSION_GE(3, 23, 0) && PETSC_VERSION_RELEASE == 0)
-#define BOUT_CAST_MATFDCOLORINGFN(func) func
+namespace bout {
+template <class T>
+constexpr auto cast_MatFDColoringFn(T func) {
+  return func;
+}
+} // namespace bout
 #else
 using MatFDColoringFn = PetscErrorCode (*)();
-#define BOUT_CAST_MATFDCOLORINGFN(func) reinterpret_cast<MatFDColoringFn>(func)
+namespace bout {
+template <class T>
+constexpr auto cast_MatFDColoringFn(T func) {
+  return reinterpret_cast<MatFDColoringFn>(func); // NOLINT(*-reinterpret-cast)
+}
+} // namespace bout
 #endif
 
 #endif // BOUT_HAS_PETSC
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
index f374d06356..dad9a8b3b0 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
@@ -656,7 +656,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
       MatFDColoringCreate(Jmf, iscoloring, &fdcoloring);
       // Set the function to difference
       MatFDColoringSetFunction(fdcoloring,
-                               BOUT_CAST_MATFDCOLORINGFN(FormFunctionForColoring), this);
+                               bout::cast_MatFDColoringFn(FormFunctionForColoring), this);
       MatFDColoringSetFromOptions(fdcoloring);
       MatFDColoringSetUp(Jmf, iscoloring, fdcoloring);
       ISColoringDestroy(&iscoloring);
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index a2630ad56d..a68aa43c38 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -585,9 +585,8 @@ int SNESSolver::init() {
       // Create data structure for SNESComputeJacobianDefaultColor
       MatFDColoringCreate(Jmf, iscoloring, &fdcoloring);
       // Set the function to difference
-      MatFDColoringSetFunction(
-          fdcoloring, reinterpret_cast<PetscErrorCode (*)()>(FormFunctionForColoring),
-          this);
+      MatFDColoringSetFunction(fdcoloring,
+                               bout::cast_MatFDColoringFn(FormFunctionForColoring), this);
       MatFDColoringSetFromOptions(fdcoloring);
       MatFDColoringSetUp(Jmf, iscoloring, fdcoloring);
       ISColoringDestroy(&iscoloring);

From 2d831da565f0af7628bbb8000b4c56cc8947e03a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 18 Sep 2024 16:35:25 +0100
Subject: [PATCH 0204/1827] CI: Bump all ubuntu images

---
 .github/workflows/tests.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index c316ba4db1..e30f55e0c9 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -40,7 +40,7 @@ jobs:
           - ${{ github.event_name == 'cron' }}
         config:
           - name: "CMake, PETSc unreleased"
-            os: ubuntu-20.04
+            os: ubuntu-24.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
                             -DBOUT_ENABLE_OPENMP=ON
@@ -55,13 +55,13 @@ jobs:
             build_petsc_branch: main
             on_cron: true
 
-          - name: "Default options, Ubuntu 20.04"
-            os: ubuntu-20.04
+          - name: "Default options, Ubuntu 22.04"
+            os: ubuntu-22.04
             cmake_options: ""
             on_cron: false
 
           - name: "Optimised, static"
-            os: ubuntu-20.04
+            os: ubuntu-latest
             cmake_options: "-DCHECK=0
                             -DBUILD_SHARED_LIBS=OFF
                             -DCMAKE_CXX_FLAGS=-Ofast
@@ -75,7 +75,7 @@ jobs:
             on_cron: false
 
           - name: "Debug, shared"
-            os: ubuntu-20.04
+            os: ubuntu-latest
             cmake_options: "-DCHECK=3
                             -DCMAKE_BUILD_TYPE=Debug
                             -DBOUT_ENABLE_SIGNAL=ON
@@ -86,8 +86,8 @@ jobs:
                             -DSUNDIALS_ROOT=/home/runner/local"
             on_cron: false
 
-          - name: "Shared, release, Ubuntu 20.04"
-            os: ubuntu-20.04
+          - name: "Shared, release"
+            os: ubuntu-latest
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_OPENMP=ON
                             -DCMAKE_BUILD_TYPE=Release
@@ -113,7 +113,7 @@ jobs:
             on_cron: false
 
           - name: "CMake, new PETSc"
-            os: ubuntu-20.04
+            os: ubuntu-latest
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
                             -DBOUT_ENABLE_OPENMP=ON
@@ -128,7 +128,7 @@ jobs:
             on_cron: false
 
           - name: "Coverage"
-            os: ubuntu-20.04
+            os: ubuntu-latest
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DCMAKE_BUILD_TYPE=Debug
                             -DCHECK=3

From 4f6b48fe733b25ce0d9f24b0a13735571b9179cd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 24 Jun 2025 11:37:26 +0200
Subject: [PATCH 0205/1827] CI: require python3-boututils

---
 .ci_fedora.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 77e7f45055..70ddbfb1ba 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -42,7 +42,7 @@ then
     echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
     echo "minrate=10M" >> /etc/dnf/dnf.conf
     time dnf -y install dnf5
-    time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort
+    time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort python3-boututils
     # Allow to override packages - see #2073
     time dnf5 copr enable -y davidsch/fixes4bout || :
     time dnf5 -y upgrade

From 9f6d7b003ad0f9e4891fa76714a20948f0010dbb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 24 Jun 2025 10:54:16 +0200
Subject: [PATCH 0206/1827] CI: Switch to released fedora

Resolves: #3127
---
 .github/workflows/tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index e30f55e0c9..d193337a28 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -229,8 +229,8 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: true
-      - name: Build Fedora rawhide
-        run: ./.ci_fedora.sh setup openmpi rawhide
+      - name: Build Fedora
+        run: ./.ci_fedora.sh setup openmpi latest
         shell: bash
         env:
           TRAVIS_BUILD_DIR: ${{ github.workspace }}

From 0dd6dfd1a37004ff4be195f1c0534d46716e3c23 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 5 Jun 2025 00:56:05 +0200
Subject: [PATCH 0207/1827] coloring for petsc solver is very likely broken

---
 src/solver/impls/petsc/petsc.cxx | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 1b81ca36b6..b502fcef10 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -515,9 +515,7 @@ int PetscSolver::init() {
   CHKERRQ(ierr);
   ierr = ISColoringDestroy(&iscoloring);
   CHKERRQ(ierr);
-  ierr = MatFDColoringSetFunction(matfdcoloring,
-                                  reinterpret_cast<PetscErrorCode (*)()>(solver_f), this);
-  CHKERRQ(ierr);
+  throw BoutException("Coloring is not working");
   ierr = SNESSetJacobian(snes, J, J, SNESComputeJacobianDefaultColor, matfdcoloring);
   CHKERRQ(ierr);
 

From ced312785cd2586b86b0c31c54ba84ad2dde14e4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 21 Oct 2024 14:13:10 +0200
Subject: [PATCH 0208/1827] Try to do the right thing for linking
 netCDF::netcdf

---
 CMakeLists.txt | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 60d34e1ad7..55b84cd765 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -789,8 +789,15 @@ foreach (flag ${CONFIG_LDFLAGS_LIST})
       # message("${flag} is a file")
       set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} ${flag}")
     else()
-      message("Fixing ${flag} to -l${flag}")
-      set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag}")
+      string(FIND "${flag}" "::" hascolcol)
+      if (${hascolcol} EQUAL -1)
+	message("Fixing ${flag} to -l${flag}")
+	set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag}")
+      else()
+	string(REGEX MATCH "[^:]*$" flag2 "${flag}")
+	message("Fixing ${flag} to -l${flag2}")
+	set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag2}")
+      endif()
     endif()
   endif()
 endforeach()

From 75768100b1dd4b7d55541d4c0cf0e65b2481e7ae Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 24 Jan 2025 11:23:42 -0800
Subject: [PATCH 0209/1827] Remove coverage test from github workflow

---
 .github/workflows/tests.yml | 34 ----------------------------------
 1 file changed, 34 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index d193337a28..ede53ef20d 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -127,25 +127,7 @@ jobs:
             build_petsc: -petsc
             on_cron: false
 
-          - name: "Coverage"
-            os: ubuntu-latest
-            cmake_options: "-DBUILD_SHARED_LIBS=ON
-                            -DCMAKE_BUILD_TYPE=Debug
-                            -DCHECK=3
-                            -DENABLE_COVERAGE=ON
-                            -DBOUT_USE_PETSC=ON
-                            -DBOUT_USE_SLEPC=ON
-                            -DBOUT_USE_HDF5=ON
-                            -DBOUT_USE_SUNDIALS=ON
-                            -DBOUT_ENABLE_PYTHON=ON
-                            -DSUNDIALS_ROOT=/home/runner/local"
-            unit_only: YES
-            on_cron: false
         exclude:
-          # Don't run the coverage tests if the branch isn't master or next
-          - is_master_or_next: false
-            config:
-              name: "Coverage"
           - is_cron: true
             config:
               on_cron: false
@@ -204,22 +186,6 @@ jobs:
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 
-      - name: Capture coverage
-        if: ${{ matrix.config.name == 'Coverage' }}
-        # Explicitly run the coverage capture target, because
-        # ci_script.sh also does the upload, and we're going to do
-        # that ourselves in the next step
-        run: |
-          # Ensure that there is a corresponding .gcda file for every .gcno file
-          # This is to try and make the coverage report slightly more accurate
-          # It still won't include, e.g. any solvers we don't build with though
-          find . -name "*.gcno" -exec sh -c 'touch -a "${1%.gcno}.gcda"' _ {} \;
-          make -C build code-coverage-capture
-
-      - name: Upload coverage
-        if: ${{ matrix.config.name == 'Coverage' }}
-        uses: codecov/codecov-action@v5
-
   Fedora:
     # This is its own job as it doesn't use most of the steps of the
     # standard_tests

From 8eafc089c623aa83ea3faba5d5afecae007e4c9a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 30 Jun 2025 22:32:47 +0000
Subject: [PATCH 0210/1827] Bump externalpackages/boutdata from `a7a372d` to
 `7164a89`

---
updated-dependencies:
- dependency-name: externalpackages/boutdata
  dependency-version: 7164a89c16dba1049d42e1715506b988c0af5926
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/boutdata | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/boutdata b/externalpackages/boutdata
index a7a372d5de..7164a89c16 160000
--- a/externalpackages/boutdata
+++ b/externalpackages/boutdata
@@ -1 +1 @@
-Subproject commit a7a372d5de7594cbe16381a3a82289ddaa58b6e7
+Subproject commit 7164a89c16dba1049d42e1715506b988c0af5926

From dc1d72d06b02068e44050c47e09fb32261b968d7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 31 Jul 2025 19:03:34 +0000
Subject: [PATCH 0211/1827] Update pygithub requirement from ~=2.6 to ~=2.7

Updates the requirements on [pygithub](https://github.com/pygithub/pygithub) to permit the latest version.
- [Release notes](https://github.com/pygithub/pygithub/releases)
- [Changelog](https://github.com/PyGithub/PyGithub/blob/main/doc/changes.rst)
- [Commits](https://github.com/pygithub/pygithub/compare/v2.6.0...v2.7.0)

---
updated-dependencies:
- dependency-name: pygithub
  dependency-version: 2.7.0
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements_maint.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements_maint.txt b/requirements_maint.txt
index e6ba00ce48..a5e94a0af5 100644
--- a/requirements_maint.txt
+++ b/requirements_maint.txt
@@ -1,3 +1,3 @@
-pygithub~=2.6
+pygithub~=2.7
 ruamel-yaml~=0.18
 Unidecode~=1.3

From c52fb5386ca1ef9811f8288a709f5e937b2f4c0e Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Mon, 4 Aug 2025 11:44:23 -0700
Subject: [PATCH 0212/1827] Add swapData function

---
 include/bout/field2d.hxx           |  3 ++-
 include/bout/field3d.hxx           |  3 ++-
 src/field/field2d.cxx              |  4 ++++
 src/field/field3d.cxx              |  4 ++++
 src/solver/nvector.hxx             | 23 ++++++++++-------------
 tests/unit/CMakeLists.txt          |  1 +
 tests/unit/solver/test_nvector.cxx | 16 ++++++++++++++++
 7 files changed, 39 insertions(+), 15 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 92658f1bbf..f1b8825931 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -271,7 +271,8 @@ public:
   void applyBoundary(const std::string& region, const std::string& condition);
   void applyTDerivBoundary() override;
   void setBoundaryTo(const Field2D& f2d); ///< Copy the boundary region
-
+  
+  void swapData(Field2D& other);
   friend void swap(Field2D& first, Field2D& second) noexcept;
 
   int size() const override { return nx * ny; };
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index a75e38df36..ab3b9b5a84 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -488,7 +488,8 @@ public:
                              const std::string& condition) override;
   void applyParallelBoundary(const std::string& region, const std::string& condition,
                              Field3D* f);
-
+  
+  void swapData(Field3D& other);
   friend void swap(Field3D& first, Field3D& second) noexcept;
 
   int size() const override { return nx * ny * nz; };
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index c8b9ebb689..5946f5e5f7 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -341,6 +341,10 @@ void Field2D::setBoundaryTo(const Field2D& f2d) {
   }
 }
 
+void Field2D::swapData(Field2D& other) {
+  std::swap(data, other.data);
+}
+
 ////////////// NON-MEMBER OVERLOADED OPERATORS //////////////
 
 // Unary minus
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 0d2bc0694e..2a1a1823f8 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -565,6 +565,10 @@ void Field3D::applyParallelBoundary(const std::string& region,
   }
 }
 
+void Field3D::swapData(Field3D& other) {
+  std::swap(data, other.data);
+}
+
 /***************************************************************
  *               NON-MEMBER OVERLOADED OPERATORS
  ***************************************************************/
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 7f2973b36c..4d38b24439 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -33,17 +33,15 @@
 
 class BoutNVector {
 private:
-  template <typename V>
-  static V all_reduce(const V local, const MPI_Op op = MPI_SUM) {
-    V global;
-    static constexpr auto type = []() {
-      if constexpr (std::is_same_v<V, double>) {
-        return MPI_DOUBLE;
-      } else if constexpr (std::is_same_v<V, unsigned int>) {
-        return MPI_UNSIGNED;
-      }
-    }();
-    MPI_Allreduce(&local, &global, 1, type, op, BoutComm::get());
+  static double all_reduce(const double local, const MPI_Op op = MPI_SUM) {
+    double global;
+    MPI_Allreduce(&local, &global, 1, MPI_DOUBLE, op, BoutComm::get());
+    return global;
+  }
+
+  static double all_reduce(const unsigned int local, const MPI_Op op = MPI_SUM) {
+    unsigned int global;
+    MPI_Allreduce(&local, &global, 1, MPI_UNSIGNED, op, BoutComm::get());
     return global;
   }
 
@@ -189,8 +187,7 @@ public:
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
   static void swap(const N_Vector v, T& field) {
-    using ::swap;
-    swap(get_field<T>(v), field);
+    field.swapData(get_field<T>(v));
   }
 
   template <typename T, typename = bout::utils::EnableIfField<T>>
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 47253c508f..7610147201 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -74,6 +74,7 @@ set(serial_tests_source
   ./mesh/test_paralleltransform.cxx
   ./solver/test_fakesolver.cxx
   ./solver/test_fakesolver.hxx
+  ./solver/test_nvector.cxx
   ./solver/test_solver.cxx
   ./solver/test_solverfactory.cxx
   ./sys/test_boutexception.cxx
diff --git a/tests/unit/solver/test_nvector.cxx b/tests/unit/solver/test_nvector.cxx
index e69de29bb2..9aa5a15178 100644
--- a/tests/unit/solver/test_nvector.cxx
+++ b/tests/unit/solver/test_nvector.cxx
@@ -0,0 +1,16 @@
+#include "gtest/gtest.h"
+#include <bout/mesh.hxx>
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+
+class NVectorFixture : public ::testing::Test {
+public:
+  Mesh mesh;
+  Field2D field1;
+
+  NVectorFixture() : field1{0} {}
+}
+
+TEST_F(NVectorFixture, Constructor) {
+
+}
\ No newline at end of file

From b192b6a1690dd361b34d3c9a8b5e8265b7e912c7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 12 Aug 2025 02:47:33 +0000
Subject: [PATCH 0213/1827] Bump externalpackages/googletest from `bac6a8f` to
 `244cec8`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `bac6a8f` to `244cec8`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/bac6a8fd8a729eef0d1b2d1a4625f4de62c60220...244cec869d12e53378fa0efb610cd4c32a454ec8)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: 244cec869d12e53378fa0efb610cd4c32a454ec8
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index bac6a8fd8a..244cec869d 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit bac6a8fd8a729eef0d1b2d1a4625f4de62c60220
+Subproject commit 244cec869d12e53378fa0efb610cd4c32a454ec8

From 424a2e5282810cba6239627b93634be5bc3519c1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 12 Aug 2025 04:47:47 +0000
Subject: [PATCH 0214/1827] Bump actions/checkout from 4 to 5

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/black-fix.yml         | 2 +-
 .github/workflows/clang-format.yml      | 2 +-
 .github/workflows/clang-tidy-review.yml | 2 +-
 .github/workflows/docker.yml            | 2 +-
 .github/workflows/python-package.yml    | 6 +++---
 .github/workflows/tests.yml             | 4 ++--
 6 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/black-fix.yml b/.github/workflows/black-fix.yml
index 92866dfcc2..6c1bfed4a5 100644
--- a/.github/workflows/black-fix.yml
+++ b/.github/workflows/black-fix.yml
@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: ${{ github.head_ref }}
 
diff --git a/.github/workflows/clang-format.yml b/.github/workflows/clang-format.yml
index 87f1947802..ed60dc9631 100644
--- a/.github/workflows/clang-format.yml
+++ b/.github/workflows/clang-format.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0
diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 9746075b1a..433204e492 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -17,7 +17,7 @@ jobs:
   review:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index a1dac41a6b..1380d0ea8e 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -52,7 +52,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Log in to the Container registry
         uses: docker/login-action@master
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index ea68e58c12..5a788f9eb0 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -17,7 +17,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         submodules: true
@@ -57,7 +57,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         submodules: true
@@ -106,7 +106,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         submodules: true
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ede53ef20d..aa3db3adc1 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -158,7 +158,7 @@ jobs:
                  liblapack-dev
                  libparpack2-dev
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
@@ -192,7 +192,7 @@ jobs:
     timeout-minutes: 60
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
       - name: Build Fedora

From 741b1df7c693db1c0970044206d25749801f4291 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 14 Aug 2025 20:51:21 -0700
Subject: [PATCH 0215/1827] PetscLib: Add setOptionsFromInputFile(TS& ts)

Sets options on a TS object using the options in the BOUT.inp
[petsc] section.
---
 include/bout/petsclib.hxx | 7 +++++--
 src/sys/petsclib.cxx      | 6 ++++++
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx
index 2008671286..760b18ff91 100644
--- a/include/bout/petsclib.hxx
+++ b/include/bout/petsclib.hxx
@@ -22,9 +22,9 @@
  * so it *must* be included before *any* PETSc header.
  * 
  **************************************************************************
- * Copyright 2012 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2012 - 2025 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  * 
  * This file is part of BOUT++.
  *
@@ -113,6 +113,9 @@ public:
   /// was passed to the constructor.
   void setOptionsFromInputFile(SNES& snes);
 
+  /// Set options for a TS time integrator
+  void setOptionsFromInputFile(TS& ts);
+
   /*!
    * Force cleanup. This will call PetscFinalize, printing a warning
    * if any instances of PetscLib still exist
diff --git a/src/sys/petsclib.cxx b/src/sys/petsclib.cxx
index f1cf1a9d1b..1830db89d9 100644
--- a/src/sys/petsclib.cxx
+++ b/src/sys/petsclib.cxx
@@ -119,6 +119,12 @@ void PetscLib::setOptionsFromInputFile(SNES& snes) {
   BOUT_DO_PETSC(SNESSetFromOptions(snes));
 }
 
+void PetscLib::setOptionsFromInputFile(TS& ts) {
+  BOUT_DO_PETSC(TSSetOptionsPrefix(ts, options_prefix.c_str()));
+
+  BOUT_DO_PETSC(TSSetFromOptions(ts));
+}
+
 void PetscLib::cleanup() {
   BOUT_OMP_SAFE(critical(PetscLib))
   {

From 33b984291a799a92466ddc284c2dd78776f94a06 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 14 Aug 2025 20:55:30 -0700
Subject: [PATCH 0216/1827] PETSc solver: Merge SNES Jacobian coloring with TS
 interface

Uses the TS interface https://petsc.org/release/manual/ts/
allowing many different time integration methods, timestep adaptation
methods etc. to be tried.
---
 src/solver/impls/petsc/petsc.cxx | 1518 +++++++++++++++---------------
 src/solver/impls/petsc/petsc.hxx |  102 +-
 2 files changed, 789 insertions(+), 831 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index dd63811f0f..22d8594c28 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -2,9 +2,9 @@
  * Interface to PETSc solver
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2025 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -32,53 +32,230 @@
 #include <petsc.h>
 
 #include <bout/boutcomm.hxx>
+#include <bout/boutexception.hxx>
+#include <bout/globals.hxx>
+#include <bout/msg_stack.hxx>
+#include <bout/petsc_interface.hxx>
+#include <bout/utils.hxx>
 
-#include <cstdlib>
+#include <cmath>
+#include <vector>
 
-#include <bout/interpolation.hxx> // Cell interpolation
-#include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 
-extern PetscErrorCode solver_f(TS ts, BoutReal t, Vec globalin, Vec globalout,
-                               void* f_data);
+#include "petscsnes.h"
+
+class ColoringStencil {
+private:
+  bool static isInSquare(int const i, int const j, int const n_square) {
+    return std::abs(i) <= n_square && std::abs(j) <= n_square;
+  }
+  bool static isInCross(int const i, int const j, int const n_cross) {
+    if (i == 0) {
+      return std::abs(j) <= n_cross;
+    }
+    if (j == 0) {
+      return std::abs(i) <= n_cross;
+    }
+    return false;
+  }
+  bool static isInTaxi(int const i, int const j, int const n_taxi) {
+    return std::abs(i) + std::abs(j) <= n_taxi;
+  }
+
+public:
+  auto static getOffsets(int n_square, int n_taxi, int n_cross) {
+    ASSERT2(n_square >= 0 && n_cross >= 0 && n_taxi >= 0
+            && n_square + n_cross + n_taxi > 0);
+    auto inside = [&](int i, int j) {
+      return isInSquare(i, j, n_square) || isInTaxi(i, j, n_taxi)
+             || isInCross(i, j, n_cross);
+    };
+    std::vector<std::pair<int, int>> xy_offsets;
+    auto loop_bound = std::max({n_square, n_taxi, n_cross});
+    for (int i = -loop_bound; i <= loop_bound; ++i) {
+      for (int j = -loop_bound; j <= loop_bound; ++j) {
+        if (inside(i, j)) {
+          xy_offsets.emplace_back(i, j);
+        }
+      }
+    }
+    return xy_offsets;
+  }
+};
+
+// PETSc callback function for matrix-free preconditioner
+static PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
+  // Get the context
+  void* ctx;
+  int ierr = PCShellGetContext(pc, &ctx);
+  CHKERRQ(ierr);
+  // Run the preconditioner
+  PetscFunctionReturn(static_cast<PetscSolver*>(ctx)->pre(x, y));
+}
+
+// PETSc callback function, that evaluates the nonlinear
+// function being integrated by TS.
+static PetscErrorCode solver_rhs(TS UNUSED(ts), BoutReal t, Vec globalin, Vec globalout,
+                                 void* f_data) {
+  PetscFunctionBegin;
+  auto* s = static_cast<PetscSolver*>(f_data);
+  s->rhs(t, globalin, globalout, false);
+  PetscFunctionReturn(0);
+}
+
+// PETSc callback function for finite differencing.
+// May use a linearised form of the RHS function.
+static PetscErrorCode solver_rhs_differencing(void* ctx, Vec globalin, Vec globalout) {
+  PetscFunctionBegin;
+  auto* s = static_cast<PetscSolver*>(ctx);
+  s->rhs_differencing(globalin, globalout);
+  PetscFunctionReturn(0);
+}
+
+// PETSc callback function for coloring.
+// May use a linearised form of the RHS function.
+static PetscErrorCode solver_rhs_coloring(void* UNUSED(snes), Vec globalin, Vec globalout,
+                                          void* ctx) {
+  PetscFunctionBegin;
+  auto* s = static_cast<PetscSolver*>(ctx);
+  s->rhs_differencing(globalin, globalout);
+  PetscFunctionReturn(0);
+}
 
-#if PETSC_VERSION_GE(3, 5, 0)
-extern PetscErrorCode solver_rhsjacobian(TS ts, BoutReal t, Vec globalin, Mat J, Mat Jpre,
-                                         void* f_data);
-extern PetscErrorCode solver_ijacobianfd(TS, PetscReal, Vec, Vec, PetscReal, Mat, Mat,
-                                         void*);
+// Compute IJacobian = dF/dU + a dF/dUdot
+// This is a dummy matrix that saves the shift.
+// The shift is later used in the matrix-free preconditioner
+PetscErrorCode solver_ijacobian(TS, BoutReal, Vec, Vec, PetscReal shift, Mat J, Mat Jpre,
+                                void* ctx) {
+  auto* solver = static_cast<PetscSolver*>(ctx);
+  solver->shift = shift;
+
+  PetscCall(MatAssemblyBegin(Jpre, MAT_FINAL_ASSEMBLY));
+  PetscCall(MatAssemblyEnd(Jpre, MAT_FINAL_ASSEMBLY));
+  if (J != Jpre) {
+    PetscCall(MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY));
+    PetscCall(MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY));
+  }
+
+  PetscFunctionReturn(0);
+}
+
+// This function is called by the TS object every internal timestep
+// It is responsible for triggering interpolation and output at
+// the output time interval.
+PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, void* ctx) {
+  PetscFunctionBegin;
+
+  auto* s = static_cast<PetscSolver*>(ctx);
+  if (t < s->next_output) {
+    // Not reached output time yet => return
+    PetscFunctionReturn(0);
+  }
+
+  PetscErrorCode ierr;
+  PetscReal tfinal;
+  static int i = 0;
+
+#if PETSC_VERSION_GE(3, 8, 0)
+  ierr = TSGetMaxTime(ts, &tfinal);
+  CHKERRQ(ierr);
 #else
-extern PetscErrorCode solver_rhsjacobian(TS ts, BoutReal t, Vec globalin, Mat* J,
-                                         Mat* Jpre, MatStructure* str, void* f_data);
-extern PetscErrorCode solver_ijacobianfd(TS, PetscReal, Vec, Vec, PetscReal, Mat*, Mat*,
-                                         MatStructure*, void*);
+  ierr = TSGetDuration(ts, nullptr, &tfinal);
+  CHKERRQ(ierr);
 #endif
 
-extern PetscErrorCode solver_if(TS, BoutReal, Vec, Vec, Vec, void*);
+  // Duplicate the solution vector X into a work vector
+  Vec interpolatedX;
+  ierr = VecDuplicate(X, &interpolatedX);
+  CHKERRQ(ierr);
 
-/// KSP preconditioner PCShell routines for physics preconditioners
-extern PetscErrorCode PhysicsPCApply(PC, Vec x, Vec y);
-extern PetscErrorCode PhysicsJacobianApply(Mat J, Vec x, Vec y);
-extern PetscErrorCode PhysicsSNESApply(SNES, Vec);
+  // The internal timestepper may have stepped over multiple output times
+  while (s->next_output <= t && s->next_output <= tfinal) {
+    if (s->interpolate) {
+      ierr = TSInterpolate(ts, s->next_output, interpolatedX);
+      CHKERRQ(ierr);
+    }
+
+    // Place the interpolated values into the global variables
+    const PetscScalar* x;
+    ierr = VecGetArrayRead(interpolatedX, &x);
+    CHKERRQ(ierr);
+    s->load_vars(const_cast<BoutReal*>(x));
+    ierr = VecRestoreArrayRead(interpolatedX, &x);
+    CHKERRQ(ierr);
+
+    if (s->call_monitors(s->next_output, i++, s->getNumberOutputSteps())) {
+      PetscFunctionReturn(1);
+    }
+
+    s->next_output += s->getOutputTimestep();
+  }
+
+  // Done with vector, so destroy it
+  ierr = VecDestroy(&interpolatedX);
+  CHKERRQ(ierr);
+
+  PetscFunctionReturn(0);
+}
 
 PetscSolver::PetscSolver(Options* opts)
     : Solver(opts),
       diagnose(
           (*options)["diagnose"].doc("Enable some diagnostic output").withDefault(false)),
-      adaptive(
-          (*options)["adaptive"].doc("Use adaptive timestepping").withDefault(false)),
-      use_precon((*options)["use_precon"]
-                     .doc("Use user-supplied preconditioning function")
-                     .withDefault(false)),
-      use_jacobian((*options)["use_jacobian"]
-                       .doc("Use user-supplied Jacobian function")
-                       .withDefault(false)),
-      abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
-      reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-5)),
-      adams_moulton((*options)["adams_moulton"]
-                        .doc("Use Adams-Moulton implicit multistep method instead of BDF "
-                             "(requires PETSc to have been built with SUNDIALS)")
-                        .withDefault(false)),
+      user_precon((*options)["user_precon"]
+                      .doc("Use user-supplied preconditioning function?")
+                      .withDefault(false)),
+      atol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
+      rtol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-5)),
+      stol((*options)["stol"]
+               .doc("Convergence tolerance in terms of the norm of the change in "
+                    "the solution between steps")
+               .withDefault(1e-8)),
+      maxnl((*options)["max_nonlinear_iterations"]
+                .doc("Maximum number of nonlinear iterations per SNES solve")
+                .withDefault(50)),
+      maxf((*options)["maxf"]
+               .doc("Maximum number of function evaluations per SNES solve")
+               .withDefault(10000)),
+      maxl((*options)["maxl"].doc("Maximum number of linear iterations").withDefault(20)),
+      ts_type(
+          (*options)["ts_type"].doc("PETSc time integrator type").withDefault("beuler")),
+      adapt_type((*options)["adapt_type"]
+                     .doc("PETSc TSAdaptType timestep adaptation method")
+                     .withDefault("basic")),
+      snes_type((*options)["snes_type"]
+                    .doc("PETSc nonlinear solver method to use")
+                    .withDefault("newtonls")),
+      ksp_type((*options)["ksp_type"]
+                   .doc("Linear solver type. By default let PETSc decide (gmres)")
+                   .withDefault("default")),
+      pc_type(
+          (*options)["pc_type"]
+              .doc("Preconditioner type. By default lets PETSc decide (ilu or bjacobi)")
+              .withDefault("default")),
+      pc_hypre_type((*options)["pc_hypre_type"]
+                        .doc("hypre preconditioner type: euclid, pilut, parasails, "
+                             "boomeramg, ams, ads")
+                        .withDefault("pilut")),
+      line_search_type((*options)["line_search_type"]
+                           .doc("Line search type: basic, bt, l2, cp, nleqerr")
+                           .withDefault("default")),
+      matrix_free((*options)["matrix_free"]
+                      .doc("Use matrix free Jacobian?")
+                      .withDefault<bool>(false)),
+      matrix_free_operator((*options)["matrix_free_operator"]
+                               .doc("Use matrix free Jacobian-vector operator?")
+                               .withDefault<bool>(false)),
+      lag_jacobian((*options)["lag_jacobian"]
+                       .doc("Re-use the Jacobian this number of SNES iterations")
+                       .withDefault(50)),
+      use_coloring((*options)["use_coloring"]
+                       .doc("Use matrix coloring to calculate Jacobian?")
+                       .withDefault<bool>(true)),
+      kspsetinitialguessnonzero((*options)["kspsetinitialguessnonzero"]
+                                    .doc("Set the initial guess to be non-zero")
+                                    .withDefault<bool>(false)),
       start_timestep((*options)["start_timestep"]
                          .doc("Initial internal timestep (defaults to output timestep)")
                          .withDefault(getOutputTimestep())),
@@ -87,9 +264,9 @@ PetscSolver::PetscSolver(Options* opts)
 
 PetscSolver::~PetscSolver() {
   VecDestroy(&u);
-  MatDestroy(&J);
+  MatDestroy(&Jfd);
   MatDestroy(&Jmf);
-  MatFDColoringDestroy(&matfdcoloring);
+  MatFDColoringDestroy(&fdcoloring);
   TSDestroy(&ts);
 }
 
@@ -99,74 +276,45 @@ PetscSolver::~PetscSolver() {
 
 int PetscSolver::init() {
   PetscErrorCode ierr;
-  int neq;
-  MPI_Comm comm = PETSC_COMM_WORLD;
-  PetscMPIInt rank;
 
   TRACE("Initialising PETSc-dev solver");
 
-  PetscFunctionBegin;
-  PetscLogEventRegister("PetscSolver::init", PETSC_VIEWER_CLASSID, &init_event);
-  PetscLogEventRegister("loop_vars", PETSC_VIEWER_CLASSID, &loop_event);
-  PetscLogEventRegister("solver_f", PETSC_VIEWER_CLASSID, &solver_event);
-
   Solver::init();
 
-  ierr = PetscLogEventBegin(init_event, 0, 0, 0, 0);
-  CHKERRQ(ierr);
-  output.write("Initialising PETSc-dev solver\n");
-  ierr = bout::globals::mpi->MPI_Comm_rank(comm, &rank);
-  CHKERRQ(ierr);
+  int nlocal = getLocalN(); // Number of evolving variables on this processor
 
-  PetscInt local_N = getLocalN(); // Number of evolving variables on this processor
-
-  /********** Get total problem size **********/
-  if (bout::globals::mpi->MPI_Allreduce(&local_N, &neq, 1, MPI_INT, MPI_SUM,
+  // Get total problem size
+  int neq;
+  if (bout::globals::mpi->MPI_Allreduce(&nlocal, &neq, 1, MPI_INT, MPI_SUM,
                                         BoutComm::get())) {
-    output_error.write("\tERROR: MPI_Allreduce failed!\n");
-    ierr = PetscLogEventEnd(init_event, 0, 0, 0, 0);
-    CHKERRQ(ierr);
-    PetscFunctionReturn(1);
+    throw BoutException("MPI_Allreduce failed!");
   }
 
-  ierr = VecCreate(BoutComm::get(), &u);
-  CHKERRQ(ierr);
-  ierr = VecSetSizes(u, local_N, PETSC_DECIDE);
+  output_info.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n",
+                    n3Dvars(), n2Dvars(), neq, nlocal);
+
+  // Create a vector to contain the state
+  PetscCall(VecCreate(BoutComm::get(), &u));
+  ierr = VecSetSizes(u, nlocal, PETSC_DECIDE);
   CHKERRQ(ierr);
   ierr = VecSetFromOptions(u);
   CHKERRQ(ierr);
 
-  ////////// SAVE INITIAL STATE TO PETSc VECTOR ///////////
-  // Set pointer to data array in vector u.
-  BoutReal* udata;
-
+  // Save initial state to PETSc Vec
+  BoutReal* udata; // Pointer to data array in vector u.
   ierr = VecGetArray(u, &udata);
   CHKERRQ(ierr);
   save_vars(udata);
   ierr = VecRestoreArray(u, &udata);
   CHKERRQ(ierr);
 
-  PetscReal norm;
-  ierr = VecNorm(u, NORM_1, &norm);
-  CHKERRQ(ierr);
-  output_info << "initial |u| = " << norm << "\n";
-
-  PetscBool J_load;
-  char load_file[PETSC_MAX_PATH_LEN]; /* jacobian input file name */
-  PetscBool J_write = PETSC_FALSE, J_slowfd = PETSC_FALSE;
-
   // Create timestepper
   ierr = TSCreate(BoutComm::get(), &ts);
   CHKERRQ(ierr);
   ierr = TSSetProblemType(ts, TS_NONLINEAR);
   CHKERRQ(ierr);
-#if PETSC_HAS_SUNDIALS
-  ierr = TSSetType(ts, TSSUNDIALS);
-  CHKERRQ(ierr);
-#else
-  ierr = TSSetType(ts, TSRK);
+  ierr = TSSetType(ts, ts_type.c_str());
   CHKERRQ(ierr);
-#endif
   ierr = TSSetApplicationContext(ts, this);
   CHKERRQ(ierr);
 
@@ -175,55 +323,38 @@ int PetscSolver::init() {
   Vec rhs_vec;
   ierr = VecDuplicate(u, &rhs_vec);
   CHKERRQ(ierr);
-  ierr = TSSetRHSFunction(ts, rhs_vec, solver_f, this);
-  CHKERRQ(ierr);
-  ierr = VecDestroy(&rhs_vec);
+  ierr = TSSetRHSFunction(ts, rhs_vec, solver_rhs, this);
   CHKERRQ(ierr);
 
   // Set up adaptive time-stepping
   TSAdapt adapt;
   ierr = TSGetAdapt(ts, &adapt);
   CHKERRQ(ierr);
-  if (adaptive) {
-    ierr = TSAdaptSetType(adapt, TSADAPTBASIC);
-    CHKERRQ(ierr);
-  } else {
-    ierr = TSAdaptSetType(adapt, TSADAPTNONE);
-    CHKERRQ(ierr);
-  }
-
-  // Set default absolute/relative tolerances
-  ierr = TSSetTolerances(ts, abstol, nullptr, reltol, nullptr);
+  ierr = TSAdaptSetType(adapt, adapt_type.c_str());
   CHKERRQ(ierr);
 
-#if PETSC_VERSION_LT(3, 5, 0)
-  ierr = TSRKSetTolerance(ts, reltol);
+  // Set default absolute/relative tolerances
+  // Note: Vector atol and rtol not given
+  ierr = TSSetTolerances(ts, atol, nullptr, rtol, nullptr);
   CHKERRQ(ierr);
-#endif
-
+  if (ts_type == TSSUNDIALS) {
 #if PETSC_HAS_SUNDIALS
-  // Set Sundials tolerances
-  ierr = TSSundialsSetTolerance(ts, abstol, reltol);
-  CHKERRQ(ierr);
-
-  // Select Sundials Adams-Moulton or BDF method
-  if (adams_moulton) {
-    output.write("\tUsing Adams-Moulton implicit multistep method\n");
-    ierr = TSSundialsSetType(ts, SUNDIALS_ADAMS);
-    CHKERRQ(ierr);
-  } else {
-    output.write("\tUsing BDF method\n");
-    ierr = TSSundialsSetType(ts, SUNDIALS_BDF);
-    CHKERRQ(ierr);
-  }
+    // The PETSc interface to SUNDIALS' CVODE
+    TSSundialsSetType(ts, SUNDIALS_BDF);
+    TSSundialsSetTolerance(ts, atol, rtol);
+#else
+    throw BoutException("PETSc was not built with SUNDIALS. Reconfigure and build PETSc "
+                        "with --download-sundials");
 #endif
+  }
 
-  // Initial time and timestep
+  // Initial time of the simulation state
   ierr = TSSetTime(ts, simtime);
   CHKERRQ(ierr);
+  next_output = simtime;
+
   ierr = TSSetTimeStep(ts, start_timestep);
   CHKERRQ(ierr);
-  next_output = simtime;
 
   // Total number of steps
   PetscInt total_steps = mxstep * getNumberOutputSteps();
@@ -245,377 +376,537 @@ int PetscSolver::init() {
   // Set the current solution
   ierr = TSSetSolution(ts, u);
   CHKERRQ(ierr);
-
-  // Create RHSJacobian J
-  SNES snes, psnes;
-  KSP ksp, nksp;
-  PC pc, npc;
-  PCType pctype;
-  TSType tstype;
-  PetscBool pcnone = PETSC_TRUE;
-
-  ierr = TSGetSNES(ts, &snes);
-  CHKERRQ(ierr);
+  // Allow TS to step over the final time
+  // Note: This does not affect intermediate outputs, that
+  //       are always interpolated (in PetscMonitor)
   ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_INTERPOLATE);
   CHKERRQ(ierr);
+  ierr = TSMonitorSet(ts, PetscMonitor, this, nullptr);
 
-#if PETSC_VERSION_GE(3, 7, 0)
-  ierr = PetscOptionsGetBool(nullptr, nullptr, "-interpolate", &interpolate, nullptr);
-  CHKERRQ(ierr);
-#else
-  ierr = PetscOptionsGetBool(nullptr, "-interpolate", &interpolate, nullptr);
-  CHKERRQ(ierr);
-#endif
+  if (ts_type != TSSUNDIALS) {
+    // Get and configure the SNES nonlinear solver
+    // Note: SUNDIALS does not use PETSc SNES or KSP
+    // https://petsc.org/release/manual/ts/#using-sundials-from-petsc
 
-  // Check for -output_name to see if user specified a "performance"
-  // run, if they didn't then use the standard monitor function. TODO:
-  // use PetscFList
-#if PETSC_VERSION_GE(3, 7, 0)
-  ierr = PetscOptionsGetString(nullptr, nullptr, "-output_name", this->output_name,
-                               sizeof this->output_name, &output_flag);
-  CHKERRQ(ierr);
-#else
-  ierr = PetscOptionsGetString(nullptr, "-output_name", this->output_name,
-                               sizeof this->output_name, &output_flag);
-  CHKERRQ(ierr);
-#endif
-
-  // If the output_name is not specified then use the standard monitor function
-  if (output_flag != 0U) {
-    ierr = SNESMonitorSet(snes, PetscSNESMonitor, this, nullptr);
+    ierr = TSGetSNES(ts, &snes);
     CHKERRQ(ierr);
-  } else {
-    ierr = TSMonitorSet(ts, PetscMonitor, this, nullptr);
-    CHKERRQ(ierr);
-  }
 
-  ierr = SNESSetTolerances(snes, abstol, reltol, PETSC_DEFAULT, PETSC_DEFAULT,
-                           PETSC_DEFAULT);
-  CHKERRQ(ierr);
-
-  // Matrix free Jacobian
-
-  if (use_jacobian and hasJacobian()) {
-    // Use a user-supplied Jacobian function
-    ierr = MatCreateShell(comm, local_N, local_N, neq, neq, this, &Jmf);
-    CHKERRQ(ierr);
-    ierr = MatShellSetOperation(Jmf, MATOP_MULT,
-                                reinterpret_cast<void (*)()>(PhysicsJacobianApply));
-    CHKERRQ(ierr);
-    ierr = TSSetIJacobian(ts, Jmf, Jmf, solver_ijacobian, this);
-    CHKERRQ(ierr);
-  } else {
-    // Use finite difference approximation
-    ierr = MatCreateSNESMF(snes, &Jmf);
-    CHKERRQ(ierr);
-    ierr = SNESSetJacobian(snes, Jmf, Jmf, MatMFFDComputeJacobian, this);
+    ierr = SNESSetType(snes, snes_type.c_str());
     CHKERRQ(ierr);
-  }
-
-  ierr = SNESGetKSP(snes, &ksp);
-  CHKERRQ(ierr);
 
-  ierr = KSPSetTolerances(ksp, reltol, abstol, PETSC_DEFAULT, PETSC_DEFAULT);
-  CHKERRQ(ierr);
-
-  ierr = KSPGetPC(ksp, &pc);
-  CHKERRQ(ierr);
+    // Line search
+    if (line_search_type != "default") {
+      SNESLineSearch linesearch;
+      SNESGetLineSearch(snes, &linesearch);
+      SNESLineSearchSetType(linesearch, line_search_type.c_str());
+    }
 
-  if (use_precon and hasPreconditioner()) {
+    // Set tolerances
+    // Note: TS should set SNES convergence tolerances
+    SNESSetTolerances(snes,
+                      PETSC_DETERMINE, // atol
+                      PETSC_DETERMINE, // rtol
+                      PETSC_DETERMINE, // stol
+                      maxnl, maxf);
 
-#if PETSC_VERSION_GE(3, 5, 0)
-    ierr = SNESGetNPC(snes, &psnes);
-    CHKERRQ(ierr);
-#else
-    ierr = SNESGetPC(snes, &psnes);
-    CHKERRQ(ierr);
+    // Force SNES to take at least one nonlinear iteration.
+    // This may prevent the solver from getting stuck in false steady state conditions
+#if PETSC_VERSION_GE(3, 8, 0)
+    SNESSetForceIteration(snes, PETSC_TRUE);
 #endif
-    ierr = SNESGetKSP(psnes, &nksp);
-    CHKERRQ(ierr);
-    ierr = KSPGetPC(nksp, &npc);
-    CHKERRQ(ierr);
-    ierr = SNESSetType(psnes, SNESSHELL);
-    CHKERRQ(ierr);
-    ierr = SNESShellSetSolve(psnes, PhysicsSNESApply);
-    CHKERRQ(ierr);
 
-    // Use a user-supplied preconditioner
+    // Re-use Jacobian
+    // Note: If the 'Amat' Jacobian is matrix free, SNESComputeJacobian
+    //       always updates its reference 'u' vector every nonlinear iteration
+    SNESSetLagJacobian(snes, lag_jacobian);
+    SNESSetLagJacobianPersists(snes, PETSC_FALSE);
 
-    // Tell PETSc we're using a "shell" preconditioner
-    ierr = PCSetType(pc, PCSHELL);
-    CHKERRQ(ierr);
-
-    // Set routine for applying preconditioner
-    ierr = PCShellSetApply(pc, PhysicsPCApply);
-    CHKERRQ(ierr);
+    SNESSetLagPreconditionerPersists(snes, PETSC_FALSE);
+    SNESSetLagPreconditioner(snes, 1); // Rebuild when Jacobian is rebuilt
 
-    // Set context to this solver object
-    ierr = PCShellSetContext(pc, this);
-    CHKERRQ(ierr);
+    // Get and configure the KSP linear solver
+    SNESGetKSP(snes, &ksp);
 
-    // Set name of preconditioner
-    ierr = PCShellSetName(pc, "PhysicsPreconditioner");
-    CHKERRQ(ierr);
-
-    // Need a callback for IJacobian to get shift 'alpha'
-    ierr = TSSetIJacobian(ts, Jmf, Jmf, solver_ijacobian, this);
-    CHKERRQ(ierr);
+    if (ksp_type != "default") {
+      KSPSetType(ksp, ksp_type.c_str());
+    }
 
-    // Use right preconditioner
-    ierr = KSPSetPCSide(ksp, PC_RIGHT);
-    CHKERRQ(ierr);
+    if (kspsetinitialguessnonzero) {
+      // Set the initial guess to be non-zero
+      KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
+    }
 
-  } else {
-    // Default to no preconditioner
-    ierr = PCSetType(pc, PCNONE);
-    CHKERRQ(ierr);
+    KSPSetTolerances(ksp,
+                     PETSC_DEFAULT, // rtol
+                     PETSC_DEFAULT, // abstol
+                     PETSC_DEFAULT, // dtol (divergence tolerance)
+                     maxl);         // Maximum number of iterations
+
+    // Set up the Jacobian
+    // Note: We can have both matrix-free Jacobian-vector operator (Jmf)
+    //       and a finite-difference Jacobian matrix (Jfd)
+    if (matrix_free or matrix_free_operator) {
+      /*
+        PETSc SNES matrix free Jacobian, using a different
+        operator for differencing.
+
+        See PETSc examples
+        http://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tests/ex7.c.html
+        and this thread:
+        http://lists.mcs.anl.gov/pipermail/petsc-users/2014-January/020075.html
+
+      */
+      MatCreateSNESMF(snes, &Jmf);
+
+      // Set a function to be called for differencing
+      // This can be a linearised form of the SNES function
+      // Note: Unsure if setting this will interfere with TS object
+      //       because the SNES Jacobian depends on the timestep
+      //MatMFFDSetFunction(Jmf, solver_rhs_differencing, this);
+    }
   }
-  ierr = TSSetFromOptions(ts);
-  CHKERRQ(ierr); // enable PETSc runtime options
-
-  ierr = PCGetType(pc, &pctype);
-  CHKERRQ(ierr);
-  ierr = TSGetType(ts, &tstype);
-  CHKERRQ(ierr);
-  output.write("\tTS type {:s}, PC type {:s}\n", tstype, pctype);
 
-  ierr = PetscObjectTypeCompare(reinterpret_cast<PetscObject>(pc), PCNONE, &pcnone);
-  CHKERRQ(ierr);
-  if (pcnone) {
-    ierr = PetscLogEventEnd(init_event, 0, 0, 0, 0);
-    CHKERRQ(ierr);
-    PetscFunctionReturn(0);
-  }
-  ierr = PetscObjectTypeCompare(reinterpret_cast<PetscObject>(pc), PCSHELL, &pcnone);
-  CHKERRQ(ierr);
-  if (pcnone) {
-    ierr = PetscLogEventEnd(init_event, 0, 0, 0, 0);
-    CHKERRQ(ierr);
-    PetscFunctionReturn(0);
+  // Configure preconditioner
+  PC pc;
+  if (ts_type == TSSUNDIALS) {
+#if PETSC_HAS_SUNDIALS
+    TSSundialsGetPC(ts, &pc);
+#endif
+  } else {
+    // Get PC context from KSP
+    KSPGetPC(ksp, &pc);
   }
+  if (matrix_free) {
+    // Matrix-free preconditioner
 
-  // Create Jacobian matrix to be used by preconditioner
-  output_info << " Get Jacobian matrix at simtime " << simtime << "\n";
-#if PETSC_VERSION_GE(3, 7, 0)
-  ierr = PetscOptionsGetString(nullptr, nullptr, "-J_load", load_file,
-                               PETSC_MAX_PATH_LEN - 1, &J_load);
-  CHKERRQ(ierr);
-#else
-  ierr = PetscOptionsGetString(nullptr, "-J_load", load_file, PETSC_MAX_PATH_LEN - 1,
-                               &J_load);
-  CHKERRQ(ierr);
-#endif
-  if (J_load) {
-    PetscViewer fd;
-    output_info << " Load Jmat ...local_N " << local_N << " neq " << neq << "\n";
-    ierr = PetscViewerBinaryOpen(comm, load_file, FILE_MODE_READ, &fd);
-    CHKERRQ(ierr);
-    ierr = MatCreate(PETSC_COMM_WORLD, &J);
-    CHKERRQ(ierr);
-    //ierr = MatSetType(J, MATBAIJ);CHKERRQ(ierr);
-    ierr = MatSetSizes(J, local_N, local_N, PETSC_DECIDE, PETSC_DECIDE);
-    CHKERRQ(ierr);
-    ierr = MatSetFromOptions(J);
-    CHKERRQ(ierr);
-    ierr = MatLoad(J, fd);
-    CHKERRQ(ierr);
-    ierr = PetscViewerDestroy(&fd);
-    CHKERRQ(ierr);
-  } else { // create Jacobian matrix
-
-    /* number of degrees (variables) at each grid point */
-    PetscInt dof = n3Dvars();
-
-    // Maximum allowable size of stencil in x is the number of guard cells
-    PetscInt stencil_width_estimate = options->operator[]("stencil_width_estimate")
-                                          .withDefault(bout::globals::mesh->xstart);
-    // This is the stencil in each direction (*2) along each dimension
-    // (*3), plus the point itself. Not sure if this is correct
-    // though, on several levels:
-    //   1. Ignores corner points used in e.g. brackets
-    //   2. Could have different stencil widths in each dimension
-    //   3. FFTs couple every single point together
-    PetscInt cols = stencil_width_estimate * 2 * 3 + 1;
-    PetscInt prealloc; // = cols*dof;
-
-    ierr = MatCreate(comm, &J);
-    CHKERRQ(ierr);
-    ierr = MatSetType(J, MATBAIJ);
-    CHKERRQ(ierr);
-    ierr = MatSetSizes(J, local_N, local_N, neq, neq);
-    CHKERRQ(ierr);
-    ierr = MatSetFromOptions(J);
-    CHKERRQ(ierr);
+    if (user_precon) {
+      output_info.write("\tUsing user-supplied preconditioner\n");
+      if (!hasPreconditioner()) {
+        throw BoutException("Model does not define a preconditioner");
+      }
+      // Set a Shell (matrix-free) preconditioner type
+      PCSetType(pc, PCSHELL);
 
-    // Get nonzero pattern of J - color_none !!!
-    prealloc = cols * dof * dof;
-    ierr = MatSeqAIJSetPreallocation(J, prealloc, nullptr);
-    CHKERRQ(ierr);
-    ierr = MatMPIAIJSetPreallocation(J, prealloc, nullptr, prealloc, nullptr);
-    CHKERRQ(ierr);
+      // Specify the preconditioner function
+      PCShellSetApply(pc, snesPCapply);
 
-    // why nonzeros=295900, allocated nonzeros=2816000/12800000 (*dof*dof), number of mallocs used during MatSetValues calls =256?
-    prealloc = cols;
-    ierr = MatSeqBAIJSetPreallocation(J, dof, prealloc, nullptr);
-    CHKERRQ(ierr);
-    ierr = MatMPIBAIJSetPreallocation(J, dof, prealloc, nullptr, prealloc, nullptr);
-    CHKERRQ(ierr);
-#if PETSC_VERSION_GE(3, 7, 0)
-    ierr = PetscOptionsHasName(nullptr, nullptr, "-J_slowfd", &J_slowfd);
-    CHKERRQ(ierr);
-#else
-    ierr = PetscOptionsHasName(nullptr, "-J_slowfd", &J_slowfd);
-    CHKERRQ(ierr);
-#endif
-    if (J_slowfd != 0U) { // create Jacobian matrix by slow fd
-      ierr = SNESSetJacobian(snes, J, J, SNESComputeJacobianDefault, nullptr);
-      CHKERRQ(ierr);
-      output_info << "SNESComputeJacobian J by slow fd...\n";
+      // Context used to supply object pointer
+      PCShellSetContext(pc, this);
 
-#if PETSC_VERSION_GE(3, 5, 0)
-      ierr = TSComputeRHSJacobian(ts, simtime, u, J, J);
+      // Set name of preconditioner
+      ierr = PCShellSetName(pc, "PhysicsPreconditioner");
       CHKERRQ(ierr);
-#else
-      MatStructure flg;
-      ierr = TSComputeRHSJacobian(ts, simtime, u, &J, &J, &flg);
-      CHKERRQ(ierr);
-#endif
-      output_info << "compute J by slow fd is done.\n";
-    } else { // get sparse pattern of the Jacobian
-      throw BoutException("Sorry, unimplemented way of setting PETSc preconditioner. "
-                          "Either set a preconditioner function with 'setPrecon' "
-                          "in your code, or load a matrix with '-Jload' on the "
-                          "command line, or calculate with finite differences "
-                          "with '-J_slowfd' (on command line)");
+    } else {
+      // Can't use preconditioner because no Jacobian matrix available
+      PCSetType(pc, PCNONE);
     }
-  }
-
-  // Create coloring context of J to be used during time stepping
 
-  output_info << " Create coloring ...\n";
+    // Callback to get the shift parameter
+    // Use matrix free for both operator and preconditioner
+    TSSetIJacobian(ts, Jmf, Jmf, solver_ijacobian, this);
 
-  ISColoring iscoloring;
-#if PETSC_VERSION_GE(3, 5, 0)
-  MatColoring coloring;
-  MatColoringCreate(Jmf, &coloring);
-  MatColoringSetType(coloring, MATCOLORINGSL);
-  MatColoringSetFromOptions(coloring);
-  // Calculate index sets
-  MatColoringApply(coloring, &iscoloring);
-  MatColoringDestroy(&coloring);
-#else
-  ierr = MatGetColoring(J, MATCOLORINGSL, &iscoloring);
-  CHKERRQ(ierr);
-#endif
-  ierr = MatFDColoringCreate(J, iscoloring, &matfdcoloring);
-  CHKERRQ(ierr);
-
-  ierr = MatFDColoringSetFromOptions(matfdcoloring);
-  CHKERRQ(ierr);
-  ierr = ISColoringDestroy(&iscoloring);
-  CHKERRQ(ierr);
-  throw BoutException("Coloring is not working");
-  ierr = SNESSetJacobian(snes, J, J, SNESComputeJacobianDefaultColor, matfdcoloring);
-  CHKERRQ(ierr);
-
-  // Write J in binary for study - see ~petsc/src/mat/examples/tests/ex124.c
-#if PETSC_VERSION_GE(3, 7, 0)
-  ierr = PetscOptionsHasName(nullptr, nullptr, "-J_write", &J_write);
-  CHKERRQ(ierr);
-#else
-  ierr = PetscOptionsHasName(nullptr, "-J_write", &J_write);
-  CHKERRQ(ierr);
-#endif
-  if (J_write != 0U) {
-    PetscViewer viewer = nullptr;
-    output_info.write("\n[{:d}] Test TSComputeRHSJacobian() ...\n", rank);
-#if PETSC_VERSION_GE(3, 5, 0)
-    ierr = TSComputeRHSJacobian(ts, simtime, u, J, J);
-    CHKERRQ(ierr);
+  } else {
+    // Set PC type from input
+    if (pc_type != "default") {
+      PCSetType(pc, pc_type.c_str());
+
+      if (pc_type == "hypre") {
+#if PETSC_HAVE_HYPRE
+        // Set the type of hypre preconditioner
+        PCHYPRESetType(pc, pc_hypre_type.c_str());
 #else
-    MatStructure J_structure;
-    ierr = TSComputeRHSJacobian(ts, simtime, u, &J, &J, &J_structure);
-    CHKERRQ(ierr);
+        throw BoutException("PETSc was not configured with Hypre.");
 #endif
+      }
+    }
 
-    output.write("[{:d}] TSComputeRHSJacobian is done\n", rank);
+    // Calculate a Jacobian matrix using finite differences. The finite
+    // difference Jacobian (Jfd) may be used for both operator and
+    // preconditioner or, if matrix_free_operator, in only the
+    // preconditioner.
+
+    if (use_coloring) {
+      // Use matrix coloring.  This greatly reduces the number of
+      // times the rhs() function needs to be evaluated when
+      // calculating the Jacobian, by identifying which quantities may
+      // be simultaneously perturbed.
+
+      // Use global mesh for now
+      Mesh* mesh = bout::globals::mesh;
+
+      //////////////////////////////////////////////////
+      // Get the local indices by starting at 0
+      Field3D index = globalIndex(0);
+
+      //////////////////////////////////////////////////
+      // Pre-allocate PETSc storage
+
+      output_progress.write("Setting Jacobian matrix sizes\n");
+
+      const int n2d = f2d.size();
+      const int n3d = f3d.size();
+
+      // Set size of Matrix on each processor to nlocal x nlocal
+      MatCreate(BoutComm::get(), &Jfd);
+      MatSetOption(Jfd, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
+      MatSetSizes(Jfd, nlocal, nlocal, PETSC_DETERMINE, PETSC_DETERMINE);
+      MatSetFromOptions(Jfd);
+      // Determine which row/columns of the matrix are locally owned
+      int Istart, Iend;
+      MatGetOwnershipRange(Jfd, &Istart, &Iend);
+      // Convert local into global indices
+      // Note: Not in the boundary cells, to keep -1 values
+      for (const auto& i : mesh->getRegion3D("RGN_NOBNDRY")) {
+        index[i] += Istart;
+      }
+      // Now communicate to fill guard cells
+      mesh->communicate(index);
+
+      // Non-zero elements on this processor
+      std::vector<PetscInt> d_nnz;
+      std::vector<PetscInt> o_nnz;
+      auto n_square = (*options)["stencil:square"]
+                          .doc("Extent of stencil (square)")
+                          .withDefault<int>(0);
+      auto n_taxi = (*options)["stencil:taxi"]
+                        .doc("Extent of stencil (taxi-cab norm)")
+                        .withDefault<int>(0);
+      auto n_cross = (*options)["stencil:cross"]
+                         .doc("Extent of stencil (cross)")
+                         .withDefault<int>(0);
+      // Set n_taxi 2 if nothing else is set
+      // Probably a better way to do this
+      if (n_square == 0 && n_taxi == 0 && n_cross == 0) {
+        output_info.write("Setting solver:stencil:taxi = 2\n");
+        n_taxi = 2;
+      }
+
+      auto const xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
+      {
+        // This is ugly but can't think of a better and robust way to
+        // count the non-zeros for some arbitrary stencil
+        // effectively the same loop as the one that sets the non-zeros below
+        std::vector<std::set<int>> d_nnz_map2d(nlocal);
+        std::vector<std::set<int>> o_nnz_map2d(nlocal);
+        std::vector<std::set<int>> d_nnz_map3d(nlocal);
+        std::vector<std::set<int>> o_nnz_map3d(nlocal);
+        // Loop over every element in 2D to count the *unique* non-zeros
+        for (int x = mesh->xstart; x <= mesh->xend; x++) {
+          for (int y = mesh->ystart; y <= mesh->yend; y++) {
+
+            const int ind0 = ROUND(index(x, y, 0)) - Istart;
+
+            // 2D fields
+            for (int i = 0; i < n2d; i++) {
+              const PetscInt row = ind0 + i;
+              // Loop through each point in the stencil
+              for (const auto& [x_off, y_off] : xy_offsets) {
+                const int xi = x + x_off;
+                const int yi = y + y_off;
+                if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
+                    || (yi >= mesh->LocalNy)) {
+                  continue;
+                }
+
+                const int ind2 = ROUND(index(xi, yi, 0));
+                if (ind2 < 0) {
+                  continue; // A boundary point
+                }
+
+                // Depends on all variables on this cell
+                for (int j = 0; j < n2d; j++) {
+                  const PetscInt col = ind2 + j;
+                  if (col >= Istart && col < Iend) {
+                    d_nnz_map2d[row].insert(col);
+                  } else {
+                    o_nnz_map2d[row].insert(col);
+                  }
+                }
+              }
+            }
+            // 3D fields
+            for (int z = 0; z < mesh->LocalNz; z++) {
+              const int ind = ROUND(index(x, y, z)) - Istart;
+
+              for (int i = 0; i < n3d; i++) {
+                PetscInt row = ind + i;
+                if (z == 0) {
+                  row += n2d;
+                }
+
+                // Depends on 2D fields
+                for (int j = 0; j < n2d; j++) {
+                  const PetscInt col = ind0 + j;
+                  if (col >= Istart && col < Iend) {
+                    d_nnz_map2d[row].insert(col);
+                  } else {
+                    o_nnz_map2d[row].insert(col);
+                  }
+                }
+
+                // Star pattern
+                for (const auto& [x_off, y_off] : xy_offsets) {
+                  const int xi = x + x_off;
+                  const int yi = y + y_off;
+
+                  if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
+                      || (yi >= mesh->LocalNy)) {
+                    continue;
+                  }
+
+                  int ind2 = ROUND(index(xi, yi, 0));
+                  if (ind2 < 0) {
+                    continue; // Boundary point
+                  }
+
+                  if (z == 0) {
+                    ind2 += n2d;
+                  }
+
+                  // 3D fields on this cell
+                  for (int j = 0; j < n3d; j++) {
+                    const PetscInt col = ind2 + j;
+                    if (col >= Istart && col < Iend) {
+                      d_nnz_map3d[row].insert(col);
+                    } else {
+                      o_nnz_map3d[row].insert(col);
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+
+        d_nnz.reserve(nlocal);
+        d_nnz.reserve(nlocal);
+
+        for (int i = 0; i < nlocal; ++i) {
+          // Assume all elements in the z direction are potentially coupled
+          d_nnz.emplace_back(d_nnz_map3d[i].size() * mesh->LocalNz
+                             + d_nnz_map2d[i].size());
+          o_nnz.emplace_back(o_nnz_map3d[i].size() * mesh->LocalNz
+                             + o_nnz_map2d[i].size());
+        }
+      }
+
+      output_progress.write("Pre-allocating Jacobian\n");
+      // Pre-allocate
+      MatMPIAIJSetPreallocation(Jfd, 0, d_nnz.data(), 0, o_nnz.data());
+      MatSeqAIJSetPreallocation(Jfd, 0, d_nnz.data());
+      MatSetUp(Jfd);
+      MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
+
+      //////////////////////////////////////////////////
+      // Mark non-zero entries
+
+      output_progress.write("Marking non-zero Jacobian entries\n");
+      PetscScalar val = 1.0;
+      for (int x = mesh->xstart; x <= mesh->xend; x++) {
+        for (int y = mesh->ystart; y <= mesh->yend; y++) {
+
+          const int ind0 = ROUND(index(x, y, 0));
+
+          // 2D fields
+          for (int i = 0; i < n2d; i++) {
+            const PetscInt row = ind0 + i;
+
+            // Loop through each point in the stencil
+            for (const auto& [x_off, y_off] : xy_offsets) {
+              const int xi = x + x_off;
+              const int yi = y + y_off;
+              if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
+                  || (yi >= mesh->LocalNy)) {
+                continue;
+              }
+
+              int ind2 = ROUND(index(xi, yi, 0));
+              if (ind2 < 0) {
+                continue; // A boundary point
+              }
+
+              // Depends on all variables on this cell
+              for (int j = 0; j < n2d; j++) {
+                PetscInt col = ind2 + j;
+                ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
+                CHKERRQ(ierr);
+              }
+            }
+          }
+          // 3D fields
+          for (int z = 0; z < mesh->LocalNz; z++) {
+            int ind = ROUND(index(x, y, z));
+
+            for (int i = 0; i < n3d; i++) {
+              PetscInt row = ind + i;
+              if (z == 0) {
+                row += n2d;
+              }
+
+              // Depends on 2D fields
+              for (int j = 0; j < n2d; j++) {
+                PetscInt col = ind0 + j;
+                ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
+                CHKERRQ(ierr);
+              }
+
+              // Star pattern
+              for (const auto& [x_off, y_off] : xy_offsets) {
+                int xi = x + x_off;
+                int yi = y + y_off;
+
+                if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
+                    || (yi >= mesh->LocalNy)) {
+                  continue;
+                }
+                for (int zi = 0; zi < mesh->LocalNz; ++zi) {
+                  int ind2 = ROUND(index(xi, yi, zi));
+                  if (ind2 < 0) {
+                    continue; // Boundary point
+                  }
+
+                  if (z == 0) {
+                    ind2 += n2d;
+                  }
+
+                  // 3D fields on this cell
+                  for (int j = 0; j < n3d; j++) {
+                    PetscInt col = ind2 + j;
+                    ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+                    if (ierr != 0) {
+                      output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n",
+                                   row, x, y, xi, yi, ind2, ind2 + n3d - 1);
+                    }
+                    CHKERRQ(ierr);
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+
+      // Finished marking non-zero entries
+
+      output_progress.write("Assembling Jacobian matrix\n");
+
+      // Assemble Matrix
+      MatAssemblyBegin(Jfd, MAT_FINAL_ASSEMBLY);
+      MatAssemblyEnd(Jfd, MAT_FINAL_ASSEMBLY);
+
+      {
+        // Test if the matrix is symmetric
+        // Values are 0 or 1 so tolerance (1e-5) shouldn't matter
+        PetscBool symmetric;
+        ierr = MatIsSymmetric(Jfd, 1e-5, &symmetric);
+        CHKERRQ(ierr);
+        if (!symmetric) {
+          output_warn.write("Jacobian pattern is not symmetric\n");
+        }
+      }
+
+      // The above can miss entries around the X-point branch cut:
+      // The diagonal terms are complicated because moving in X then Y
+      // is different from moving in Y then X at the X-point.
+      // Making sure the colouring matrix is symmetric does not
+      // necessarily give the correct stencil but may help.
+      if ((*options)["force_symmetric_coloring"]
+              .doc("Modifies coloring matrix to force it to be symmetric")
+              .withDefault<bool>(false)) {
+        Mat Jfd_T;
+        MatCreateTranspose(Jfd, &Jfd_T);
+        MatAXPY(Jfd, 1, Jfd_T, DIFFERENT_NONZERO_PATTERN);
+      }
+
+      output_progress.write("Creating Jacobian coloring\n");
+      updateColoring();
 
-    if (J_slowfd != 0U) {
-      output_info.write("[{:d}] writing J in binary to data/Jrhs_dense.dat...\n", rank);
-      ierr = PetscViewerBinaryOpen(comm, "data/Jrhs_dense.dat", FILE_MODE_WRITE, &viewer);
-      CHKERRQ(ierr);
     } else {
-      output_info.write("[{:d}] writing J in binary to data/Jrhs_sparse.dat...\n", rank);
-      ierr =
-          PetscViewerBinaryOpen(comm, "data/Jrhs_sparse.dat", FILE_MODE_WRITE, &viewer);
-      CHKERRQ(ierr);
+      // Brute force calculation
+      // There is usually no reason to use this, except as a check of
+      // the coloring calculation.
+
+      MatCreateAIJ(
+          BoutComm::get(), nlocal, nlocal,  // Local sizes
+          PETSC_DETERMINE, PETSC_DETERMINE, // Global sizes
+          3, // Number of nonzero entries in diagonal portion of local submatrix
+          nullptr,
+          0, // Number of nonzeros per row in off-diagonal portion of local submatrix
+          nullptr, &Jfd);
+
+      if (matrix_free_operator) {
+        SNESSetJacobian(snes, Jmf, Jfd, SNESComputeJacobianDefault, this);
+      } else {
+        SNESSetJacobian(snes, Jfd, Jfd, SNESComputeJacobianDefault, this);
+      }
+
+      MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
     }
-    ierr = MatView(J, viewer);
-    CHKERRQ(ierr);
-    ierr = PetscViewerDestroy(&viewer);
-    CHKERRQ(ierr);
   }
 
-  ierr = PetscLogEventEnd(init_event, 0, 0, 0, 0);
-  CHKERRQ(ierr);
-
-  PetscFunctionReturn(0);
+  // Get runtime options
+  lib.setOptionsFromInputFile(ts);
+
+  {
+    // Some reporting
+    TSType tstype;
+    TSGetType(ts, &tstype);
+    output_info.write("TS Type : {}\n", tstype);
+    TSAdaptType adapttype;
+    TSAdaptGetType(adapt, &adapttype);
+    output_info.write("TS Adapt Type : {}\n", adapttype);
+    SNESType snestype;
+    SNESGetType(snes, &snestype);
+    output_info.write("SNES Type : {}\n", snestype);
+    KSPType ksptype;
+    KSPGetType(ksp, &ksptype);
+    if (ksptype) {
+      output_info.write("KSP Type  : {}\n", ksptype);
+    }
+    PCType pctype;
+    PCGetType(pc, &pctype);
+    if (pctype) {
+      output_info.write("PC Type   : {}\n", pctype);
+    }
+  }
+  return 0;
 }
 
-/**************************************************************************
- * Run - Advance time
- **************************************************************************/
-
+// Starts the time integrator
 PetscErrorCode PetscSolver::run() {
-
   // Set when the next call to monitor is desired
   next_output = simtime + getOutputTimestep();
 
   PetscFunctionBegin;
 
-  if (this->output_flag) {
-    prev_linear_its = 0;
-    bout_snes_time = bout::globals::mpi->MPI_Wtime();
-  }
-
+  // Run the PETSc time integrator
+  // The PetscMonitor function is responsible for regular outputs
   CHKERRQ(TSSolve(ts, u));
 
-  // Gawd, everything is a hack
-  if ((this->output_flag != 0U) and (BoutComm::rank() == 0)) {
-    Output petsc_info(output_name);
-    // Don't write to stdout
-    petsc_info.disable();
-    petsc_info.write("SNES Iteration, KSP Iterations, Wall Time, Norm\n");
-    for (const auto& info : snes_list) {
-      petsc_info.write("{:d}, {:d}, {:e}, {:e}\n", info.it, info.linear_its, info.time,
-                       info.norm);
-    }
-  }
-
   PetscFunctionReturn(0);
 }
 
-/**************************************************************************
- * RHS function
- **************************************************************************/
-
-PetscErrorCode PetscSolver::rhs(TS UNUSED(ts), BoutReal t, Vec udata, Vec dudata) {
+// Evaluate the user-supplied RHS function
+// This method is called from the static PETSc callback functions
+PetscErrorCode PetscSolver::rhs(BoutReal t, Vec udata, Vec dudata, bool linear) {
   TRACE("Running RHS: PetscSolver::rhs({:e})", t);
 
-  const BoutReal* udata_array;
-  BoutReal* dudata_array;
+  simtime = t; // This will be used in rhs_differencing
 
   PetscFunctionBegin;
 
   // Load state from PETSc
+  const BoutReal* udata_array;
   VecGetArrayRead(udata, &udata_array);
   load_vars(const_cast<BoutReal*>(udata_array));
   VecRestoreArrayRead(udata, &udata_array);
 
   // Call RHS function
-  run_rhs(t);
+  run_rhs(t, linear);
 
   // Save derivatives to PETSc
+  BoutReal* dudata_array;
   VecGetArray(dudata, &dudata_array);
   save_derivs(dudata_array);
   VecRestoreArray(dudata, &dudata_array);
@@ -623,19 +914,17 @@ PetscErrorCode PetscSolver::rhs(TS UNUSED(ts), BoutReal t, Vec udata, Vec dudata
   PetscFunctionReturn(0);
 }
 
-/**************************************************************************
- * Preconditioner function
- **************************************************************************/
+// This is used for Jacobian-vector product and Jacobian coloring
+PetscErrorCode PetscSolver::rhs_differencing(Vec globalin, Vec globalout) {
+  return rhs(simtime, globalin, globalout, true);
+}
 
-PetscErrorCode PetscSolver::pre(PC UNUSED(pc), Vec x, Vec y) {
+// Matrix-free preconditioner function
+PetscErrorCode PetscSolver::pre(Vec x, Vec y) {
   TRACE("PetscSolver::pre()");
 
   BoutReal* data;
 
-  if (diagnose) {
-    output << "Preconditioning" << endl;
-  }
-
   // Load state
   VecGetArray(state, &data);
   load_vars(data);
@@ -654,355 +943,44 @@ PetscErrorCode PetscSolver::pre(PC UNUSED(pc), Vec x, Vec y) {
   save_derivs(data);
   VecRestoreArray(y, &data);
 
-  // Petsc's definition of Jacobian differs by a factor from Sundials'
+  // Petsc's definition of Jacobian differs by a factor from SUNDIALS'
+  // PETSc solves (scale + J)^-1
+  // SUNDIALS solves (I + gamma J)^-1
   PetscErrorCode ierr = VecScale(y, shift);
   CHKERRQ(ierr);
 
   return 0;
 }
 
-/**************************************************************************
- * User-supplied Jacobian function J(state) * x = y
- **************************************************************************/
-
-PetscErrorCode PetscSolver::jac(Vec x, Vec y) {
-  TRACE("PetscSolver::jac()");
-
-  BoutReal* data;
-
-  if (diagnose) {
-    output << "Jacobian evaluation\n";
-  }
-
-  // Load state
-  VecGetArray(state, &data);
-  load_vars(data);
-  VecRestoreArray(state, &data);
-
-  // Load vector to be operated on into F_vars
-  VecGetArray(x, &data);
-  load_derivs(data);
-  VecRestoreArray(x, &data);
-
-  // Call the Jacobian function
-  runJacobian(ts_time);
-
-  // Save the solution from time derivatives
-  VecGetArray(y, &data);
-  save_derivs(data);
-  VecRestoreArray(y, &data);
-
-  // y = a * x - y
-  PetscErrorCode ierr = VecAXPBY(y, shift, -1.0, x);
-  CHKERRQ(ierr);
-
-  return 0;
-}
-
-/**************************************************************************
- * Static functions which can be used for PETSc callbacks
- **************************************************************************/
-
-PetscErrorCode solver_f(TS ts, BoutReal t, Vec globalin, Vec globalout, void* f_data) {
-  PetscFunctionBegin;
-  auto* s = static_cast<PetscSolver*>(f_data);
-  PetscLogEventBegin(s->solver_event, 0, 0, 0, 0);
-  s->rhs(ts, t, globalin, globalout);
-  PetscLogEventEnd(s->solver_event, 0, 0, 0, 0);
-  PetscFunctionReturn(0);
-}
-
-/*
-  FormIFunction = Udot - RHSFunction
-*/
-PetscErrorCode solver_if(TS ts, BoutReal t, Vec globalin, Vec globalindot, Vec globalout,
-                         void* f_data) {
-  PetscErrorCode ierr;
-
-  PetscFunctionBegin;
-  ierr = solver_f(ts, t, globalin, globalout, f_data);
-  CHKERRQ(ierr);
-
-  ierr = VecAYPX(globalout, -1.0, globalindot);
-  CHKERRQ(ierr); // globalout = globalindot + (-1)globalout
-  PetscFunctionReturn(0);
-}
-
-#if PETSC_VERSION_GE(3, 5, 0)
-PetscErrorCode solver_rhsjacobian(TS UNUSED(ts), BoutReal UNUSED(t), Vec UNUSED(globalin),
-                                  Mat J, Mat Jpre, void* UNUSED(f_data)) {
-  PetscErrorCode ierr;
-
-  PetscFunctionBegin;
-  ierr = MatAssemblyBegin(Jpre, MAT_FINAL_ASSEMBLY);
-  CHKERRQ(ierr);
-  ierr = MatAssemblyEnd(Jpre, MAT_FINAL_ASSEMBLY);
-  CHKERRQ(ierr);
-  if (J != Jpre) {
-    ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);
-    CHKERRQ(ierr);
-    ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);
-    CHKERRQ(ierr);
-  }
-  PetscFunctionReturn(0);
-}
-#else
-PetscErrorCode solver_rhsjacobian([[maybe_unused]] TS ts, [[maybe_unused]] BoutReal t,
-                                  [[maybe_unused]] Vec globalin, Mat* J, Mat* Jpre,
-                                  [[maybe_unused]] MatStructure* str,
-                                  [[maybe_unused]] void* f_data) {
-  PetscErrorCode ierr;
-
-  PetscFunctionBegin;
-  ierr = MatAssemblyBegin(*Jpre, MAT_FINAL_ASSEMBLY);
-  CHKERRQ(ierr);
-  ierr = MatAssemblyEnd(*Jpre, MAT_FINAL_ASSEMBLY);
-  CHKERRQ(ierr);
-  if (*J != *Jpre) {
-    ierr = MatAssemblyBegin(*J, MAT_FINAL_ASSEMBLY);
-    CHKERRQ(ierr);
-    ierr = MatAssemblyEnd(*J, MAT_FINAL_ASSEMBLY);
-    CHKERRQ(ierr);
-  }
-  PetscFunctionReturn(0);
-}
-#endif
-
-/*
-  solver_ijacobian - Compute IJacobian = dF/dU + a dF/dUdot  - a dummy matrix used for pc=none
-*/
-#if PETSC_VERSION_GE(3, 5, 0)
-PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin, Vec UNUSED(globalindot),
-                                PetscReal a, Mat J, Mat Jpre, void* f_data) {
-  PetscErrorCode ierr;
-
-  PetscFunctionBegin;
-  ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, f_data);
-  CHKERRQ(ierr);
-
-  ////// Save data for preconditioner
-  auto* solver = static_cast<PetscSolver*>(f_data);
-
-  if (solver->diagnose) {
-    output << "Saving state, t = " << t << ", a = " << a << endl;
-  }
-
-  solver->shift = a;        // Save the shift 'a'
-  solver->state = globalin; // Save system state
-  solver->ts_time = t;
-
-  PetscFunctionReturn(0);
-}
-#else
-PetscErrorCode solver_ijacobian(TS ts, BoutReal t, Vec globalin,
-                                [[maybe_unused]] Vec globalindot,
-                                [[maybe_unused]] PetscReal a, Mat* J, Mat* Jpre,
-                                MatStructure* str, void* f_data) {
-  PetscErrorCode ierr;
-
-  PetscFunctionBegin;
-  ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, str, (void*)f_data);
-  CHKERRQ(ierr);
-
-  ////// Save data for preconditioner
-  PetscSolver* solver = (PetscSolver*)f_data;
-
-  if (solver->diagnose) {
-    output << "Saving state, t = " << t << ", a = " << a << endl;
-  }
-
-  solver->shift = a;        // Save the shift 'a'
-  solver->state = globalin; // Save system state
-  solver->ts_time = t;
-
-  PetscFunctionReturn(0);
-}
-#endif
-
-/*
-  solver_ijacobianfd - Compute IJacobian = dF/dU + a dF/dUdot  using finite deference - not implemented yet
-*/
-#if PETSC_VERSION_GE(3, 5, 0)
-PetscErrorCode solver_ijacobianfd(TS ts, BoutReal t, Vec globalin,
-                                  Vec UNUSED(globalindot), PetscReal UNUSED(a), Mat J,
-                                  Mat Jpre, void* f_data) {
-  PetscErrorCode ierr;
-
-  PetscFunctionBegin;
-  ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, f_data);
-  CHKERRQ(ierr);
-  //*Jpre + a
-  PetscFunctionReturn(0);
-}
-#else
-PetscErrorCode solver_ijacobianfd(TS ts, BoutReal t, Vec globalin, Vec globalindot,
-                                  PetscReal a, Mat* J, Mat* Jpre, MatStructure* str,
-                                  void* f_data) {
-  PetscErrorCode ierr;
-
-  PetscFunctionBegin;
-  ierr = solver_rhsjacobian(ts, t, globalin, J, Jpre, str, (void*)f_data);
-  CHKERRQ(ierr);
-  //*Jpre + a
-  PetscFunctionReturn(0);
-}
-#endif
-//-----------------------------------------
-
-PetscErrorCode PhysicsSNESApply(SNES snes, Vec x) {
-  PetscErrorCode ierr;
-  Vec F, Fout;
-  PetscReal fnorm = 0., foutnorm = 0., dot = 0.;
-  KSP ksp;
-  PC pc;
-  Mat A, B;
-
-  PetscFunctionBegin;
-  ierr = SNESGetJacobian(snes, &A, &B, nullptr, nullptr);
-  CHKERRQ(ierr);
-#if PETSC_VERSION_GE(3, 5, 0)
-  ierr = SNESComputeJacobian(snes, x, A, B);
-  CHKERRQ(ierr);
-#else
-  MatStructure diff = DIFFERENT_NONZERO_PATTERN;
-  ierr = SNESComputeJacobian(snes, x, &A, &B, &diff);
-  CHKERRQ(ierr);
-#endif
-  ierr = SNESGetKSP(snes, &ksp);
-  CHKERRQ(ierr);
-  ierr = KSPGetPC(ksp, &pc);
-  CHKERRQ(ierr);
-  ierr = SNESGetFunction(snes, &F, nullptr, nullptr);
-  CHKERRQ(ierr);
-  ierr = SNESComputeFunction(snes, x, F);
-  CHKERRQ(ierr);
-  ierr = SNESGetSolutionUpdate(snes, &Fout);
-  CHKERRQ(ierr);
-
-  ierr = PCApply(pc, F, Fout);
-  CHKERRQ(ierr);
-  ierr = VecNorm(Fout, NORM_2, &foutnorm);
-  CHKERRQ(ierr);
-  ierr = VecAXPY(x, -1., Fout);
-  CHKERRQ(ierr);
-  ierr = SNESComputeFunction(snes, x, F);
-  CHKERRQ(ierr);
-  ierr = VecNorm(F, NORM_2, &fnorm);
-  CHKERRQ(ierr);
-  ierr = VecDot(F, Fout, &dot);
-  CHKERRQ(ierr);
-  output_info << " (Debug) function norm: " << fnorm << ", P(f) norm " << foutnorm
-              << ", F \\cdot Fout " << dot << "  ";
-#if PETSC_VERSION_GE(3, 5, 0)
-  Vec func;
-  ierr = SNESGetFunction(snes, &func, nullptr, nullptr);
-  CHKERRQ(ierr);
-  ierr = VecNorm(func, NORM_2, &fnorm);
-  CHKERRQ(ierr);
-#else
-  ierr = SNESSetFunctionNorm(snes, fnorm);
-  CHKERRQ(ierr);
-#endif
-  ierr = SNESMonitor(snes, 0, fnorm);
-  CHKERRQ(ierr);
-
-  PetscFunctionReturn(0);
-}
-
-PetscErrorCode PhysicsPCApply(PC pc, Vec x, Vec y) {
-  int ierr;
-
-  // Get the context
-  PetscSolver* s;
-  ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&s));
-  CHKERRQ(ierr);
-
-  PetscFunctionReturn(s->pre(pc, x, y));
-}
-
-PetscErrorCode PhysicsJacobianApply(Mat J, Vec x, Vec y) {
-  // Get the context
-  PetscSolver* s;
-  int ierr = MatShellGetContext(J, reinterpret_cast<void**>(&s));
-  CHKERRQ(ierr);
-  PetscFunctionReturn(s->jac(x, y));
-}
-
-PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, void* ctx) {
-  PetscErrorCode ierr;
-  auto* s = static_cast<PetscSolver*>(ctx);
-  PetscReal tfinal, dt;
-  Vec interpolatedX;
-  const PetscScalar* x;
-  static int i = 0;
-
-  PetscFunctionBegin;
-  ierr = TSGetTimeStep(ts, &dt);
-  CHKERRQ(ierr);
-
-#if PETSC_VERSION_GE(3, 8, 0)
-  ierr = TSGetMaxTime(ts, &tfinal);
-  CHKERRQ(ierr);
-#else
-  ierr = TSGetDuration(ts, nullptr, &tfinal);
-  CHKERRQ(ierr);
-#endif
-
-  /* Duplicate the solution vector X into a work vector */
-  ierr = VecDuplicate(X, &interpolatedX);
-  CHKERRQ(ierr);
-  while (s->next_output <= t && s->next_output <= tfinal) {
-    if (s->interpolate) {
-      ierr = TSInterpolate(ts, s->next_output, interpolatedX);
-      CHKERRQ(ierr);
-    }
-
-    /* Place the interpolated values into the global variables */
-    ierr = VecGetArrayRead(interpolatedX, &x);
-    CHKERRQ(ierr);
-    s->load_vars(const_cast<BoutReal*>(x));
-    ierr = VecRestoreArrayRead(interpolatedX, &x);
-    CHKERRQ(ierr);
-
-    if (s->call_monitors(simtime, i++, s->getNumberOutputSteps())) {
-      PetscFunctionReturn(1);
-    }
-
-    s->next_output += s->getOutputTimestep();
-    simtime = s->next_output;
-  }
-
-  /* Done with vector, so destroy it */
-  ierr = VecDestroy(&interpolatedX);
-  CHKERRQ(ierr);
-
-  PetscFunctionReturn(0);
-}
-
-PetscErrorCode PetscSNESMonitor(SNES snes, PetscInt its, PetscReal norm, void* ctx) {
-  PetscErrorCode ierr;
-  PetscInt linear_its = 0;
-  BoutReal tmp = .0;
-  snes_info row;
-  auto* s = static_cast<PetscSolver*>(ctx);
+void PetscSolver::updateColoring() {
+  // Re-calculate the coloring
+  MatColoring coloring = NULL;
+  MatColoringCreate(Jfd, &coloring);
+  MatColoringSetType(coloring, MATCOLORINGGREEDY);
+  MatColoringSetFromOptions(coloring);
 
-  PetscFunctionBegin;
+  // Calculate new index sets
+  ISColoring iscoloring = NULL;
+  MatColoringApply(coloring, &iscoloring);
+  MatColoringDestroy(&coloring);
 
-  if (!its) {
-    s->prev_linear_its = 0;
+  // Replace the old coloring with the new one
+  MatFDColoringDestroy(&fdcoloring);
+  MatFDColoringCreate(Jfd, iscoloring, &fdcoloring);
+  MatFDColoringSetFunction(fdcoloring, bout::cast_MatFDColoringFn(solver_rhs_coloring),
+                           this);
+  MatFDColoringSetFromOptions(fdcoloring);
+  MatFDColoringSetUp(Jfd, iscoloring, fdcoloring);
+  ISColoringDestroy(&iscoloring);
+
+  // Replace the CTX pointer in SNES Jacobian
+  // Note: TSComputeIJacobianDefaultColor
+  if (matrix_free_operator) {
+    // Use matrix-free calculation for operator, finite difference for preconditioner
+    SNESSetJacobian(snes, Jmf, Jfd, SNESComputeJacobianDefaultColor, fdcoloring);
+  } else {
+    SNESSetJacobian(snes, Jfd, Jfd, SNESComputeJacobianDefaultColor, fdcoloring);
   }
-  ierr = SNESGetLinearSolveIterations(snes, &linear_its);
-  CHKERRQ(ierr);
-  tmp = bout::globals::mpi->MPI_Wtime();
-
-  row.it = its;
-  s->prev_linear_its = row.linear_its = linear_its - s->prev_linear_its;
-  row.time = tmp - s->bout_snes_time;
-  row.norm = norm;
-
-  s->snes_list.push_back(row);
-
-  PetscFunctionReturn(0);
 }
 
 #endif
diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index 686a7c6242..71a09ab61d 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -1,11 +1,10 @@
 /**************************************************************************
  * Interface to PETSc solver
- * NOTE: This class needs tidying, generalising to use FieldData interface
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2025 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -55,35 +54,6 @@ namespace {
 RegisterSolver<PetscSolver> registersolverpetsc("petsc");
 }
 
-using BoutReal = PetscScalar;
-#define OPT_SIZE 40
-
-using rhsfunc = int (*)(BoutReal);
-
-extern BoutReal simtime;
-
-/// Monitor function called on every internal timestep
-extern PetscErrorCode PetscMonitor(TS, PetscInt, PetscReal, Vec, void* ctx);
-/// Monitor function for SNES
-extern PetscErrorCode PetscSNESMonitor(SNES, PetscInt, PetscReal, void* ctx);
-
-/// Compute IJacobian = dF/dU + a dF/dUdot  - a dummy matrix used for pc=none
-#if PETSC_VERSION_GE(3, 5, 0)
-extern PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat, Mat,
-                                       void*);
-#else
-extern PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat*, Mat*,
-                                       MatStructure*, void*);
-#endif
-
-/// Data for SNES
-struct snes_info {
-  PetscInt it;
-  PetscInt linear_its;
-  PetscReal time;
-  PetscReal norm;
-};
-
 class PetscSolver : public Solver {
 public:
   PetscSolver(Options* opts = nullptr);
@@ -95,24 +65,17 @@ public:
   // These functions used internally (but need to be public)
 
   /// Wrapper for the RHS function
-  PetscErrorCode rhs(TS ts, PetscReal t, Vec globalin, Vec globalout);
+  PetscErrorCode rhs(PetscReal t, Vec globalin, Vec globalout, bool linear);
+  /// RHS function for differencing
+  PetscErrorCode rhs_differencing(Vec globalin, Vec globalout);
   /// Wrapper for the preconditioner
-  PetscErrorCode pre(PC pc, Vec x, Vec y);
-  /// Wrapper for the Jacobian function
-  PetscErrorCode jac(Vec x, Vec y);
+  PetscErrorCode pre(Vec x, Vec y);
 
   // Call back functions that need to access internal state
   friend PetscErrorCode PetscMonitor(TS, PetscInt, PetscReal, Vec, void* ctx);
-  friend PetscErrorCode PetscSNESMonitor(SNES, PetscInt, PetscReal, void* ctx);
-#if PETSC_VERSION_GE(3, 5, 0)
-  friend PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat, Mat,
-                                         void*);
-#else
-  friend PetscErrorCode solver_ijacobian(TS, PetscReal, Vec, Vec, PetscReal, Mat*, Mat*,
-                                         MatStructure*, void*);
-#endif
 
-  PetscLogEvent solver_event, loop_event, init_event;
+  friend PetscErrorCode solver_ijacobian(TS, BoutReal, Vec, Vec, PetscReal shift, Mat J,
+                                         Mat Jpre, void* ctx);
 
 private:
   BoutReal shift; ///< Shift (alpha) parameter from TS
@@ -121,28 +84,45 @@ private:
 
   PetscLib lib; ///< Handles initialising, finalising PETSc
 
-  Vec u{nullptr}; ///< PETSc solution vector
-  TS ts{nullptr}; ///< PETSc timestepper object
-  Mat J{nullptr}; ///< RHS Jacobian
-  Mat Jmf{nullptr};
-  MatFDColoring matfdcoloring{nullptr};
-
-  bool diagnose; ///< If true, print some information about current stage
+  Vec u{nullptr};                    ///< PETSc solution vector
+  TS ts{nullptr};                    ///< PETSc timestepper object
+  SNES snes{nullptr};                ///< PETSc nonlinear solver object
+  KSP ksp{nullptr};                  ///< PETSc linear solver
+  Mat Jmf{nullptr};                  ///< Matrix Free Jacobian
+  Mat Jfd{nullptr};                  ///< Finite Difference Jacobian
+  MatFDColoring fdcoloring{nullptr}; ///< Matrix coloring context
 
   BoutReal next_output; ///< When the monitor should be called next
 
   PetscBool interpolate{PETSC_TRUE}; ///< Whether to interpolate or not
 
-  char output_name[PETSC_MAX_PATH_LEN];
-  PetscBool output_flag{PETSC_FALSE};
-  PetscInt prev_linear_its;
-  BoutReal bout_snes_time{0.0};
-  std::vector<snes_info> snes_list;
+  bool diagnose;    ///< If true, print some information about current stage
+  bool user_precon; ///< Use user-supplied preconditioning function?
+
+  BoutReal atol; ///< Absolute tolerance
+  BoutReal rtol; ///< Relative tolerance
+  BoutReal stol; ///< Convergence tolerance
+
+  int maxnl; ///< Maximum nonlinear iterations per SNES solve
+  int maxf; ///< Maximum number of function evaluations allowed in the solver (default: 10000)
+  int maxl; ///< Maximum linear iterations
+
+  std::string ts_type;          ///< PETSc TS time solver type
+  std::string adapt_type;       ///< TSAdaptType timestep adaptation
+  std::string snes_type;        ///< PETSc SNES nonlinear solver type
+  std::string ksp_type;         ///< PETSc KSP linear solver type
+  std::string pc_type;          ///< Preconditioner type
+  std::string pc_hypre_type;    ///< Hypre preconditioner type
+  std::string line_search_type; ///< Line search type
+
+  bool matrix_free;          ///< Use matrix free Jacobian
+  bool matrix_free_operator; ///< Use matrix free Jacobian in the operator?
+  int lag_jacobian;          ///< Re-use Jacobian
+  bool use_coloring;         ///< Use matrix coloring
+  void updateColoring();     ///< Updates the coloring using Jfd
+
+  bool kspsetinitialguessnonzero; ///< Set initial guess to non-zero
 
-  bool adaptive; ///< Use adaptive timestepping
-  bool use_precon, use_jacobian;
-  BoutReal abstol, reltol;
-  bool adams_moulton;
   BoutReal start_timestep;
   int mxstep;
 };

From 46f7344592dcd9ceab4ac6d94093c95ec7b1aece Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 14 Aug 2025 21:56:16 -0700
Subject: [PATCH 0217/1827] petsc solver fixes

- Read `interpolate` option, allowing solution interpolation to
  be disabled for TS methods that don't support it (e.g. `pseudo`).

- Fix coloring method: The TS function should be used for coloring,
  not the RHS function directly. This is because SNES is solving
  a modified function that depends on the time step and TS method.
---
 src/solver/impls/petsc/petsc.cxx | 55 +++++++++++++-------------------
 src/solver/impls/petsc/petsc.hxx |  4 +--
 2 files changed, 23 insertions(+), 36 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 22d8594c28..fce7f1178f 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -104,25 +104,6 @@ static PetscErrorCode solver_rhs(TS UNUSED(ts), BoutReal t, Vec globalin, Vec gl
   PetscFunctionReturn(0);
 }
 
-// PETSc callback function for finite differencing.
-// May use a linearised form of the RHS function.
-static PetscErrorCode solver_rhs_differencing(void* ctx, Vec globalin, Vec globalout) {
-  PetscFunctionBegin;
-  auto* s = static_cast<PetscSolver*>(ctx);
-  s->rhs_differencing(globalin, globalout);
-  PetscFunctionReturn(0);
-}
-
-// PETSc callback function for coloring.
-// May use a linearised form of the RHS function.
-static PetscErrorCode solver_rhs_coloring(void* UNUSED(snes), Vec globalin, Vec globalout,
-                                          void* ctx) {
-  PetscFunctionBegin;
-  auto* s = static_cast<PetscSolver*>(ctx);
-  s->rhs_differencing(globalin, globalout);
-  PetscFunctionReturn(0);
-}
-
 // Compute IJacobian = dF/dU + a dF/dUdot
 // This is a dummy matrix that saves the shift.
 // The shift is later used in the matrix-free preconditioner
@@ -172,9 +153,14 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
 
   // The internal timestepper may have stepped over multiple output times
   while (s->next_output <= t && s->next_output <= tfinal) {
+    BoutReal output_time = t;
     if (s->interpolate) {
       ierr = TSInterpolate(ts, s->next_output, interpolatedX);
-      CHKERRQ(ierr);
+      if (ierr != PETSC_SUCCESS) {
+        throw BoutException("This PETSc TS does not support interpolation. Use a "
+                            "different method or set solver:interpolate=false");
+      }
+      output_time = s->next_output;
     }
 
     // Place the interpolated values into the global variables
@@ -185,11 +171,11 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
     ierr = VecRestoreArrayRead(interpolatedX, &x);
     CHKERRQ(ierr);
 
-    if (s->call_monitors(s->next_output, i++, s->getNumberOutputSteps())) {
+    if (s->call_monitors(output_time, i++, s->getNumberOutputSteps())) {
       PetscFunctionReturn(1);
     }
 
-    s->next_output += s->getOutputTimestep();
+    s->next_output = output_time + s->getOutputTimestep();
   }
 
   // Done with vector, so destroy it
@@ -200,7 +186,9 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
 }
 
 PetscSolver::PetscSolver(Options* opts)
-    : Solver(opts),
+    : Solver(opts), interpolate((*options)["interpolate"]
+                                    .doc("Interpolate to regular output times?")
+                                    .withDefault(true)),
       diagnose(
           (*options)["diagnose"].doc("Enable some diagnostic output").withDefault(false)),
       user_precon((*options)["user_precon"]
@@ -379,7 +367,11 @@ int PetscSolver::init() {
   // Allow TS to step over the final time
   // Note: This does not affect intermediate outputs, that
   //       are always interpolated (in PetscMonitor)
-  ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_INTERPOLATE);
+  if (interpolate) {
+    ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_INTERPOLATE);
+  } else {
+    ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_MATCHSTEP);
+  }
   CHKERRQ(ierr);
   ierr = TSMonitorSet(ts, PetscMonitor, this, nullptr);
 
@@ -892,7 +884,7 @@ PetscErrorCode PetscSolver::run() {
 PetscErrorCode PetscSolver::rhs(BoutReal t, Vec udata, Vec dudata, bool linear) {
   TRACE("Running RHS: PetscSolver::rhs({:e})", t);
 
-  simtime = t; // This will be used in rhs_differencing
+  simtime = t;
 
   PetscFunctionBegin;
 
@@ -914,11 +906,6 @@ PetscErrorCode PetscSolver::rhs(BoutReal t, Vec udata, Vec dudata, bool linear)
   PetscFunctionReturn(0);
 }
 
-// This is used for Jacobian-vector product and Jacobian coloring
-PetscErrorCode PetscSolver::rhs_differencing(Vec globalin, Vec globalout) {
-  return rhs(simtime, globalin, globalout, true);
-}
-
 // Matrix-free preconditioner function
 PetscErrorCode PetscSolver::pre(Vec x, Vec y) {
   TRACE("PetscSolver::pre()");
@@ -967,14 +954,16 @@ void PetscSolver::updateColoring() {
   // Replace the old coloring with the new one
   MatFDColoringDestroy(&fdcoloring);
   MatFDColoringCreate(Jfd, iscoloring, &fdcoloring);
-  MatFDColoringSetFunction(fdcoloring, bout::cast_MatFDColoringFn(solver_rhs_coloring),
-                           this);
+  // Use the SNES function that is defined by the TS method
+  // SNESTSFormFunction is defined in PETSc ts.c
+  // The ctx pointer should be the TS object
+  MatFDColoringSetFunction(fdcoloring, bout::cast_MatFDColoringFn(SNESTSFormFunction),
+                           ts);
   MatFDColoringSetFromOptions(fdcoloring);
   MatFDColoringSetUp(Jfd, iscoloring, fdcoloring);
   ISColoringDestroy(&iscoloring);
 
   // Replace the CTX pointer in SNES Jacobian
-  // Note: TSComputeIJacobianDefaultColor
   if (matrix_free_operator) {
     // Use matrix-free calculation for operator, finite difference for preconditioner
     SNESSetJacobian(snes, Jmf, Jfd, SNESComputeJacobianDefaultColor, fdcoloring);
diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index 71a09ab61d..5108e8cb30 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -66,8 +66,6 @@ public:
 
   /// Wrapper for the RHS function
   PetscErrorCode rhs(PetscReal t, Vec globalin, Vec globalout, bool linear);
-  /// RHS function for differencing
-  PetscErrorCode rhs_differencing(Vec globalin, Vec globalout);
   /// Wrapper for the preconditioner
   PetscErrorCode pre(Vec x, Vec y);
 
@@ -94,7 +92,7 @@ private:
 
   BoutReal next_output; ///< When the monitor should be called next
 
-  PetscBool interpolate{PETSC_TRUE}; ///< Whether to interpolate or not
+  bool interpolate; ///< Interpolate to regular times?
 
   bool diagnose;    ///< If true, print some information about current stage
   bool user_precon; ///< Use user-supplied preconditioning function?

From e4fe421de08e597ff0db426839d5b394247c1425 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 14 Aug 2025 22:31:31 -0700
Subject: [PATCH 0218/1827] petsc solver: Recover from SNES failures

Uses TSSetMaxSNESFailures, that can be overridden with a
petsc option.
---
 src/solver/impls/petsc/petsc.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index fce7f1178f..a6971c7270 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -361,6 +361,9 @@ int PetscSolver::init() {
   CHKERRQ(ierr);
 #endif
 
+  // Allow TS to recover from SNES failures
+  PetscCall(TSSetMaxSNESFailures(ts, PETSC_UNLIMITED));
+
   // Set the current solution
   ierr = TSSetSolution(ts, u);
   CHKERRQ(ierr);

From 3f67ac9ac22ee0c8b0a13ace14e98720d586d1f0 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 14 Aug 2025 22:34:24 -0700
Subject: [PATCH 0219/1827] petsc: Tidying with PetscCall

Replaces CHKERRQ macro call with a wrapper around the PETSc
function call.
---
 src/solver/impls/petsc/petsc.cxx | 59 +++++++++++---------------------
 1 file changed, 20 insertions(+), 39 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index a6971c7270..126aa46532 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -283,48 +283,35 @@ int PetscSolver::init() {
 
   // Create a vector to contain the state
   PetscCall(VecCreate(BoutComm::get(), &u));
-  ierr = VecSetSizes(u, nlocal, PETSC_DECIDE);
-  CHKERRQ(ierr);
-  ierr = VecSetFromOptions(u);
-  CHKERRQ(ierr);
+  PetscCall(VecSetSizes(u, nlocal, PETSC_DECIDE));
+  PetscCall(VecSetFromOptions(u));
 
   // Save initial state to PETSc Vec
   BoutReal* udata; // Pointer to data array in vector u.
-  ierr = VecGetArray(u, &udata);
-  CHKERRQ(ierr);
+  PetscCall(VecGetArray(u, &udata));
   save_vars(udata);
-  ierr = VecRestoreArray(u, &udata);
-  CHKERRQ(ierr);
+  PetscCall(VecRestoreArray(u, &udata));
 
   // Create timestepper
-  ierr = TSCreate(BoutComm::get(), &ts);
-  CHKERRQ(ierr);
-  ierr = TSSetProblemType(ts, TS_NONLINEAR);
-  CHKERRQ(ierr);
-  ierr = TSSetType(ts, ts_type.c_str());
-  CHKERRQ(ierr);
-  ierr = TSSetApplicationContext(ts, this);
-  CHKERRQ(ierr);
+  PetscCall(TSCreate(BoutComm::get(), &ts));
+  PetscCall(TSSetProblemType(ts, TS_NONLINEAR));
+  PetscCall(TSSetType(ts, ts_type.c_str()));
+  PetscCall(TSSetApplicationContext(ts, this));
 
   // Set user provided RHSFunction
   // Need to duplicate the solution vector for the residual
   Vec rhs_vec;
-  ierr = VecDuplicate(u, &rhs_vec);
-  CHKERRQ(ierr);
-  ierr = TSSetRHSFunction(ts, rhs_vec, solver_rhs, this);
-  CHKERRQ(ierr);
+  PetscCall(VecDuplicate(u, &rhs_vec));
+  PetscCall(TSSetRHSFunction(ts, rhs_vec, solver_rhs, this));
 
   // Set up adaptive time-stepping
   TSAdapt adapt;
-  ierr = TSGetAdapt(ts, &adapt);
-  CHKERRQ(ierr);
-  ierr = TSAdaptSetType(adapt, adapt_type.c_str());
-  CHKERRQ(ierr);
+  PetscCall(TSGetAdapt(ts, &adapt));
+  PetscCall(TSAdaptSetType(adapt, adapt_type.c_str()));
 
   // Set default absolute/relative tolerances
   // Note: Vector atol and rtol not given
-  ierr = TSSetTolerances(ts, atol, nullptr, rtol, nullptr);
-  CHKERRQ(ierr);
+  PetscCall(TSSetTolerances(ts, atol, nullptr, rtol, nullptr));
   if (ts_type == TSSUNDIALS) {
 #if PETSC_HAS_SUNDIALS
     // The PETSc interface to SUNDIALS' CVODE
@@ -337,12 +324,10 @@ int PetscSolver::init() {
   }
 
   // Initial time of the simulation state
-  ierr = TSSetTime(ts, simtime);
-  CHKERRQ(ierr);
+  PetscCall(TSSetTime(ts, simtime));
   next_output = simtime;
 
-  ierr = TSSetTimeStep(ts, start_timestep);
-  CHKERRQ(ierr);
+  PetscCall(TSSetTimeStep(ts, start_timestep));
 
   // Total number of steps
   PetscInt total_steps = mxstep * getNumberOutputSteps();
@@ -352,21 +337,17 @@ int PetscSolver::init() {
                simtime);
 
 #if PETSC_VERSION_GE(3, 8, 0)
-  ierr = TSSetMaxSteps(ts, total_steps);
-  CHKERRQ(ierr);
-  ierr = TSSetMaxTime(ts, tfinal);
-  CHKERRQ(ierr);
+  PetscCall(TSSetMaxSteps(ts, total_steps));
+  PetscCall(TSSetMaxTime(ts, tfinal));
 #else
-  ierr = TSSetDuration(ts, total_steps, tfinal);
-  CHKERRQ(ierr);
+  PetscCall(TSSetDuration(ts, total_steps, tfinal));
 #endif
 
   // Allow TS to recover from SNES failures
   PetscCall(TSSetMaxSNESFailures(ts, PETSC_UNLIMITED));
 
   // Set the current solution
-  ierr = TSSetSolution(ts, u);
-  CHKERRQ(ierr);
+  PetscCall(TSSetSolution(ts, u));
   // Allow TS to step over the final time
   // Note: This does not affect intermediate outputs, that
   //       are always interpolated (in PetscMonitor)
@@ -376,7 +357,7 @@ int PetscSolver::init() {
     ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_MATCHSTEP);
   }
   CHKERRQ(ierr);
-  ierr = TSMonitorSet(ts, PetscMonitor, this, nullptr);
+  PetscCall(TSMonitorSet(ts, PetscMonitor, this, nullptr));
 
   if (ts_type != TSSUNDIALS) {
     // Get and configure the SNES nonlinear solver

From 1aca504e46980c59d3ff77eeac4c2f13253eb90d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 14 Aug 2025 23:01:53 -0700
Subject: [PATCH 0220/1827] petsc solver improvements

- Allow Jacobian and preconditioner to persist across SNES solves.
  This is useful because many steps can typically be taken using
  the same preconditioner.

- Allow solver to recover from time step rejections
  by setting TSSetMaxStepRejections.
  This doesn't seem to work as expected with the `pseudo` TS method.
---
 src/solver/impls/petsc/petsc.cxx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 126aa46532..6154cf39cd 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -346,6 +346,9 @@ int PetscSolver::init() {
   // Allow TS to recover from SNES failures
   PetscCall(TSSetMaxSNESFailures(ts, PETSC_UNLIMITED));
 
+  // Recover from step rejections
+  PetscCall(TSSetMaxStepRejections(ts, PETSC_UNLIMITED));
+
   // Set the current solution
   PetscCall(TSSetSolution(ts, u));
   // Allow TS to step over the final time
@@ -395,9 +398,9 @@ int PetscSolver::init() {
     // Note: If the 'Amat' Jacobian is matrix free, SNESComputeJacobian
     //       always updates its reference 'u' vector every nonlinear iteration
     SNESSetLagJacobian(snes, lag_jacobian);
-    SNESSetLagJacobianPersists(snes, PETSC_FALSE);
+    SNESSetLagJacobianPersists(snes, PETSC_TRUE);
 
-    SNESSetLagPreconditionerPersists(snes, PETSC_FALSE);
+    SNESSetLagPreconditionerPersists(snes, PETSC_TRUE);
     SNESSetLagPreconditioner(snes, 1); // Rebuild when Jacobian is rebuilt
 
     // Get and configure the KSP linear solver

From e9025eed5a8e9f91d52795f232bb3483e9894320 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 14 Aug 2025 23:23:48 -0700
Subject: [PATCH 0221/1827] petsc: Add petsc headers and define PETSC_UNLIMITED

Introduced in PETSc 3.22 (probably), define PETSC_UNLIMITED
if it's undefined.

Include more headers for used PETSc functionality.
---
 src/solver/impls/petsc/petsc.cxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 6154cf39cd..7c09b7d2a4 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -43,8 +43,15 @@
 
 #include <bout/output.hxx>
 
+#include "petscsys.h"
+#include "petscts.h"
 #include "petscsnes.h"
 
+#ifndef PETSC_UNLIMITED
+// Introduced in PETSc 3.22
+#define PETSC_UNLIMITED -3
+#endif
+
 class ColoringStencil {
 private:
   bool static isInSquare(int const i, int const j, int const n_square) {

From 672172c7c7e72cb524b368d76519830e0954baf5 Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Fri, 15 Aug 2025 06:29:07 +0000
Subject: [PATCH 0222/1827] Apply clang-format changes

---
 src/solver/impls/petsc/petsc.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 7c09b7d2a4..051d6d3ee1 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -43,9 +43,9 @@
 
 #include <bout/output.hxx>
 
+#include "petscsnes.h"
 #include "petscsys.h"
 #include "petscts.h"
-#include "petscsnes.h"
 
 #ifndef PETSC_UNLIMITED
 // Introduced in PETSc 3.22

From a0b6cca1ace1b45ce48bb60566ad7336ddc86cee Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 15 Aug 2025 08:19:54 -0700
Subject: [PATCH 0223/1827] Apply suggestions from code review

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 src/solver/impls/petsc/petsc.cxx | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 051d6d3ee1..55dd948b8a 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -49,7 +49,7 @@
 
 #ifndef PETSC_UNLIMITED
 // Introduced in PETSc 3.22
-#define PETSC_UNLIMITED -3
+#define PETSC_UNLIMITED (-3)
 #endif
 
 class ColoringStencil {
@@ -94,7 +94,7 @@ class ColoringStencil {
 // PETSc callback function for matrix-free preconditioner
 static PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
   // Get the context
-  void* ctx;
+  void* ctx = nullptr;
   int ierr = PCShellGetContext(pc, &ctx);
   CHKERRQ(ierr);
   // Run the preconditioner
@@ -178,7 +178,7 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
     ierr = VecRestoreArrayRead(interpolatedX, &x);
     CHKERRQ(ierr);
 
-    if (s->call_monitors(output_time, i++, s->getNumberOutputSteps())) {
+    if (s->call_monitors(output_time, i++, s->getNumberOutputSteps()) != 0) {
       PetscFunctionReturn(1);
     }
 
@@ -669,9 +669,9 @@ int PetscSolver::init() {
 
         for (int i = 0; i < nlocal; ++i) {
           // Assume all elements in the z direction are potentially coupled
-          d_nnz.emplace_back(d_nnz_map3d[i].size() * mesh->LocalNz
+          d_nnz.emplace_back((d_nnz_map3d[i].size() * mesh->LocalNz)
                              + d_nnz_map2d[i].size());
-          o_nnz.emplace_back(o_nnz_map3d[i].size() * mesh->LocalNz
+          o_nnz.emplace_back((o_nnz_map3d[i].size() * mesh->LocalNz)
                              + o_nnz_map2d[i].size());
         }
       }
@@ -687,7 +687,7 @@ int PetscSolver::init() {
       // Mark non-zero entries
 
       output_progress.write("Marking non-zero Jacobian entries\n");
-      PetscScalar val = 1.0;
+      PetscScalar const val = 1.0;
       for (int x = mesh->xstart; x <= mesh->xend; x++) {
         for (int y = mesh->ystart; y <= mesh->yend; y++) {
 
@@ -706,14 +706,14 @@ int PetscSolver::init() {
                 continue;
               }
 
-              int ind2 = ROUND(index(xi, yi, 0));
+              int const ind2 = ROUND(index(xi, yi, 0));
               if (ind2 < 0) {
                 continue; // A boundary point
               }
 
               // Depends on all variables on this cell
               for (int j = 0; j < n2d; j++) {
-                PetscInt col = ind2 + j;
+                PetscInt const col = ind2 + j;
                 ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
                 CHKERRQ(ierr);
               }
@@ -721,7 +721,7 @@ int PetscSolver::init() {
           }
           // 3D fields
           for (int z = 0; z < mesh->LocalNz; z++) {
-            int ind = ROUND(index(x, y, z));
+            int const ind = ROUND(index(x, y, z));
 
             for (int i = 0; i < n3d; i++) {
               PetscInt row = ind + i;
@@ -731,7 +731,7 @@ int PetscSolver::init() {
 
               // Depends on 2D fields
               for (int j = 0; j < n2d; j++) {
-                PetscInt col = ind0 + j;
+                PetscInt const col = ind0 + j;
                 ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
                 CHKERRQ(ierr);
               }

From dbff5bfc9009d939cf1a34bae5da1be64d3bae4e Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 15 Aug 2025 12:24:12 -0700
Subject: [PATCH 0224/1827] petsc solver: Runs with SUNDIALS, some tidying

Runs SUNDIALS through PETSc, but preconditioning slows down the simulation.
Something wrong with the Jacobian calculation perhaps.

Some tidying, adding header files etc., to address Clang Tidy comments.
---
 src/solver/impls/petsc/petsc.cxx | 122 +++++++++++++++----------------
 src/solver/impls/petsc/petsc.hxx |   1 +
 2 files changed, 59 insertions(+), 64 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 55dd948b8a..df559af5bd 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -25,27 +25,30 @@
 
 #include "bout/build_defines.hxx"
 
-#include "petsc.hxx"
-
 #if BOUT_HAS_PETSC
 
-#include <petsc.h>
+#include "petsc.hxx"
+
+#include <algorithm>
+#include <cmath>
+#include <utility>
+#include <vector>
 
+#include <bout/assert.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/globals.hxx>
 #include <bout/msg_stack.hxx>
+#include <bout/output.hxx>
 #include <bout/petsc_interface.hxx>
 #include <bout/utils.hxx>
 
-#include <cmath>
-#include <vector>
-
-#include <bout/output.hxx>
-
-#include "petscsnes.h"
-#include "petscsys.h"
-#include "petscts.h"
+#include <petsc.h>
+#include <petscpctypes.h>
+#include <petscsnes.h>
+#include <petscsys.h>
+#include <petscts.h>
+#include <petscvec.h>
 
 #ifndef PETSC_UNLIMITED
 // Introduced in PETSc 3.22
@@ -95,8 +98,7 @@ class ColoringStencil {
 static PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
   // Get the context
   void* ctx = nullptr;
-  int ierr = PCShellGetContext(pc, &ctx);
-  CHKERRQ(ierr);
+  PetscCall(PCShellGetContext(pc, &ctx));
   // Run the preconditioner
   PetscFunctionReturn(static_cast<PetscSolver*>(ctx)->pre(x, y));
 }
@@ -141,28 +143,24 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
     PetscFunctionReturn(0);
   }
 
-  PetscErrorCode ierr;
   PetscReal tfinal;
   static int i = 0;
 
 #if PETSC_VERSION_GE(3, 8, 0)
-  ierr = TSGetMaxTime(ts, &tfinal);
-  CHKERRQ(ierr);
+  PetscCall(TSGetMaxTime(ts, &tfinal));
 #else
-  ierr = TSGetDuration(ts, nullptr, &tfinal);
-  CHKERRQ(ierr);
+  PetscCall(TSGetDuration(ts, nullptr, &tfinal));
 #endif
 
   // Duplicate the solution vector X into a work vector
   Vec interpolatedX;
-  ierr = VecDuplicate(X, &interpolatedX);
-  CHKERRQ(ierr);
+  PetscCall(VecDuplicate(X, &interpolatedX));
 
   // The internal timestepper may have stepped over multiple output times
   while (s->next_output <= t && s->next_output <= tfinal) {
     BoutReal output_time = t;
     if (s->interpolate) {
-      ierr = TSInterpolate(ts, s->next_output, interpolatedX);
+      int ierr = TSInterpolate(ts, s->next_output, interpolatedX);
       if (ierr != PETSC_SUCCESS) {
         throw BoutException("This PETSc TS does not support interpolation. Use a "
                             "different method or set solver:interpolate=false");
@@ -172,11 +170,9 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
 
     // Place the interpolated values into the global variables
     const PetscScalar* x;
-    ierr = VecGetArrayRead(interpolatedX, &x);
-    CHKERRQ(ierr);
+    PetscCall(VecGetArrayRead(interpolatedX, &x));
     s->load_vars(const_cast<BoutReal*>(x));
-    ierr = VecRestoreArrayRead(interpolatedX, &x);
-    CHKERRQ(ierr);
+    PetscCall(VecRestoreArrayRead(interpolatedX, &x));
 
     if (s->call_monitors(output_time, i++, s->getNumberOutputSteps()) != 0) {
       PetscFunctionReturn(1);
@@ -186,8 +182,7 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
   }
 
   // Done with vector, so destroy it
-  ierr = VecDestroy(&interpolatedX);
-  CHKERRQ(ierr);
+  PetscCall(VecDestroy(&interpolatedX));
 
   PetscFunctionReturn(0);
 }
@@ -214,8 +209,7 @@ PetscSolver::PetscSolver(Options* opts)
                .doc("Maximum number of function evaluations per SNES solve")
                .withDefault(10000)),
       maxl((*options)["maxl"].doc("Maximum number of linear iterations").withDefault(20)),
-      ts_type(
-          (*options)["ts_type"].doc("PETSc time integrator type").withDefault("beuler")),
+      ts_type((*options)["ts_type"].doc("PETSc time integrator type").withDefault("bdf")),
       adapt_type((*options)["adapt_type"]
                      .doc("PETSc TSAdaptType timestep adaptation method")
                      .withDefault("basic")),
@@ -270,7 +264,6 @@ PetscSolver::~PetscSolver() {
  **************************************************************************/
 
 int PetscSolver::init() {
-  PetscErrorCode ierr;
 
   TRACE("Initialising PETSc-dev solver");
 
@@ -320,7 +313,7 @@ int PetscSolver::init() {
   // Note: Vector atol and rtol not given
   PetscCall(TSSetTolerances(ts, atol, nullptr, rtol, nullptr));
   if (ts_type == TSSUNDIALS) {
-#if PETSC_HAS_SUNDIALS
+#if PETSC_HAVE_SUNDIALS2
     // The PETSc interface to SUNDIALS' CVODE
     TSSundialsSetType(ts, SUNDIALS_BDF);
     TSSundialsSetTolerance(ts, atol, rtol);
@@ -362,11 +355,10 @@ int PetscSolver::init() {
   // Note: This does not affect intermediate outputs, that
   //       are always interpolated (in PetscMonitor)
   if (interpolate) {
-    ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_INTERPOLATE);
+    PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_INTERPOLATE));
   } else {
-    ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_MATCHSTEP);
+    PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_MATCHSTEP));
   }
-  CHKERRQ(ierr);
   PetscCall(TSMonitorSet(ts, PetscMonitor, this, nullptr));
 
   if (ts_type != TSSUNDIALS) {
@@ -374,11 +366,8 @@ int PetscSolver::init() {
     // Note: SUNDIALS does not use PETSc SNES or KSP
     // https://petsc.org/release/manual/ts/#using-sundials-from-petsc
 
-    ierr = TSGetSNES(ts, &snes);
-    CHKERRQ(ierr);
-
-    ierr = SNESSetType(snes, snes_type.c_str());
-    CHKERRQ(ierr);
+    PetscCall(TSGetSNES(ts, &snes));
+    PetscCall(SNESSetType(snes, snes_type.c_str()));
 
     // Line search
     if (line_search_type != "default") {
@@ -455,7 +444,7 @@ int PetscSolver::init() {
   // Configure preconditioner
   PC pc;
   if (ts_type == TSSUNDIALS) {
-#if PETSC_HAS_SUNDIALS
+#if PETSC_HAVE_SUNDIALS2
     TSSundialsGetPC(ts, &pc);
 #endif
   } else {
@@ -480,8 +469,7 @@ int PetscSolver::init() {
       PCShellSetContext(pc, this);
 
       // Set name of preconditioner
-      ierr = PCShellSetName(pc, "PhysicsPreconditioner");
-      CHKERRQ(ierr);
+      PetscCall(PCShellSetName(pc, "PhysicsPreconditioner"));
     } else {
       // Can't use preconditioner because no Jacobian matrix available
       PCSetType(pc, PCNONE);
@@ -714,8 +702,7 @@ int PetscSolver::init() {
               // Depends on all variables on this cell
               for (int j = 0; j < n2d; j++) {
                 PetscInt const col = ind2 + j;
-                ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
-                CHKERRQ(ierr);
+                PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
               }
             }
           }
@@ -732,8 +719,7 @@ int PetscSolver::init() {
               // Depends on 2D fields
               for (int j = 0; j < n2d; j++) {
                 PetscInt const col = ind0 + j;
-                ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
-                CHKERRQ(ierr);
+                PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
               }
 
               // Star pattern
@@ -758,7 +744,7 @@ int PetscSolver::init() {
                   // 3D fields on this cell
                   for (int j = 0; j < n3d; j++) {
                     PetscInt col = ind2 + j;
-                    ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
+                    int ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
 
                     if (ierr != 0) {
                       output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n",
@@ -785,8 +771,7 @@ int PetscSolver::init() {
         // Test if the matrix is symmetric
         // Values are 0 or 1 so tolerance (1e-5) shouldn't matter
         PetscBool symmetric;
-        ierr = MatIsSymmetric(Jfd, 1e-5, &symmetric);
-        CHKERRQ(ierr);
+        PetscCall(MatIsSymmetric(Jfd, 1e-5, &symmetric));
         if (!symmetric) {
           output_warn.write("Jacobian pattern is not symmetric\n");
         }
@@ -842,13 +827,15 @@ int PetscSolver::init() {
     TSAdaptType adapttype;
     TSAdaptGetType(adapt, &adapttype);
     output_info.write("TS Adapt Type : {}\n", adapttype);
-    SNESType snestype;
-    SNESGetType(snes, &snestype);
-    output_info.write("SNES Type : {}\n", snestype);
-    KSPType ksptype;
-    KSPGetType(ksp, &ksptype);
-    if (ksptype) {
-      output_info.write("KSP Type  : {}\n", ksptype);
+    if (ts_type != TSSUNDIALS) {
+      SNESType snestype;
+      SNESGetType(snes, &snestype);
+      output_info.write("SNES Type : {}\n", snestype);
+      KSPType ksptype;
+      KSPGetType(ksp, &ksptype);
+      if (ksptype) {
+        output_info.write("KSP Type  : {}\n", ksptype);
+      }
     }
     PCType pctype;
     PCGetType(pc, &pctype);
@@ -927,8 +914,7 @@ PetscErrorCode PetscSolver::pre(Vec x, Vec y) {
   // Petsc's definition of Jacobian differs by a factor from SUNDIALS'
   // PETSc solves (scale + J)^-1
   // SUNDIALS solves (I + gamma J)^-1
-  PetscErrorCode ierr = VecScale(y, shift);
-  CHKERRQ(ierr);
+  PetscCall(VecScale(y, shift));
 
   return 0;
 }
@@ -951,18 +937,26 @@ void PetscSolver::updateColoring() {
   // Use the SNES function that is defined by the TS method
   // SNESTSFormFunction is defined in PETSc ts.c
   // The ctx pointer should be the TS object
-  MatFDColoringSetFunction(fdcoloring, bout::cast_MatFDColoringFn(SNESTSFormFunction),
-                           ts);
+  MatFDColoringSetFunction(fdcoloring,
+                           reinterpret_cast<MatFDColoringFn>(SNESTSFormFunction), ts);
   MatFDColoringSetFromOptions(fdcoloring);
   MatFDColoringSetUp(Jfd, iscoloring, fdcoloring);
   ISColoringDestroy(&iscoloring);
 
   // Replace the CTX pointer in SNES Jacobian
-  if (matrix_free_operator) {
-    // Use matrix-free calculation for operator, finite difference for preconditioner
-    SNESSetJacobian(snes, Jmf, Jfd, SNESComputeJacobianDefaultColor, fdcoloring);
+  if (ts_type == TSSUNDIALS) {
+#if PETSC_HAVE_SUNDIALS2
+    // The SUNDIALS interface calls TSGetIJacobian
+    // https://www.mcs.anl.gov/petsc/petsc-3.14/src/ts/impls/implicit/sundials/sundials.c
+    TSSetIJacobian(ts, Jfd, Jfd, solver_ijacobian, this);
+#endif
   } else {
-    SNESSetJacobian(snes, Jfd, Jfd, SNESComputeJacobianDefaultColor, fdcoloring);
+    if (matrix_free_operator) {
+      // Use matrix-free calculation for operator, finite difference for preconditioner
+      SNESSetJacobian(snes, Jmf, Jfd, SNESComputeJacobianDefaultColor, fdcoloring);
+    } else {
+      SNESSetJacobian(snes, Jfd, Jfd, SNESComputeJacobianDefaultColor, fdcoloring);
+    }
   }
 }
 
diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index 5108e8cb30..525ca93b40 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -47,6 +47,7 @@ class PetscSolver;
 #include <bout/vector3d.hxx>
 
 #include <petsc.h>
+#include <petscts.h>
 
 #include <vector>
 

From 720dd2ef2f70e61b23cc540e0ecaf4bf8512feef Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 15 Aug 2025 14:44:29 -0700
Subject: [PATCH 0225/1827] petsc solver: Fix Jacobian coloring with sundials
 method

This is fiddly because TS doesn't create a SNES object when TSType is
TSSUNDIALS. The nonlinear function being solved in sundials is similar
to the PETSc convention, but scaled by the "gamma" / shift factor.
---
 src/solver/impls/petsc/petsc.cxx | 56 +++++++++++++++++++++++++++-----
 src/solver/impls/petsc/petsc.hxx |  7 ++++
 2 files changed, 54 insertions(+), 9 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index df559af5bd..551552a9b4 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -94,8 +94,9 @@ class ColoringStencil {
   }
 };
 
+namespace {
 // PETSc callback function for matrix-free preconditioner
-static PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
+PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
   // Get the context
   void* ctx = nullptr;
   PetscCall(PCShellGetContext(pc, &ctx));
@@ -105,14 +106,25 @@ static PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
 
 // PETSc callback function, that evaluates the nonlinear
 // function being integrated by TS.
-static PetscErrorCode solver_rhs(TS UNUSED(ts), BoutReal t, Vec globalin, Vec globalout,
-                                 void* f_data) {
+PetscErrorCode solver_rhs(TS UNUSED(ts), BoutReal t, Vec globalin, Vec globalout,
+                          void* f_data) {
   PetscFunctionBegin;
   auto* s = static_cast<PetscSolver*>(f_data);
   s->rhs(t, globalin, globalout, false);
   PetscFunctionReturn(0);
 }
 
+// Form function for use with SUNDIALS.
+// This is needed because SNESTSFormFunction is not available
+// PETSc error: No method snesfunction for TS of type sundials
+PetscErrorCode solver_form_function(void* UNUSED(dummy), Vec U, Vec F, void* f_data) {
+  PetscFunctionBegin;
+  auto* s = static_cast<PetscSolver*>(f_data);
+  s->formFunction(U, F);
+  PetscFunctionReturn(0);
+}
+} // namespace
+
 // Compute IJacobian = dF/dU + a dF/dUdot
 // This is a dummy matrix that saves the shift.
 // The shift is later used in the matrix-free preconditioner
@@ -131,6 +143,14 @@ PetscErrorCode solver_ijacobian(TS, BoutReal, Vec, Vec, PetscReal shift, Mat J,
   PetscFunctionReturn(0);
 }
 
+PetscErrorCode solver_ijacobian_color(TS ts, PetscReal t, Vec U, Vec Udot,
+                                      PetscReal shift, Mat J, Mat B, void* ctx) {
+  auto* solver = static_cast<PetscSolver*>(ctx);
+  solver->shift = shift;
+
+  return TSComputeIJacobianDefaultColor(ts, t, U, Udot, shift, J, B, NULL);
+}
+
 // This function is called by the TS object every internal timestep
 // It is responsible for triggering interpolation and output at
 // the output time interval.
@@ -887,6 +907,15 @@ PetscErrorCode PetscSolver::rhs(BoutReal t, Vec udata, Vec dudata, bool linear)
   PetscFunctionReturn(0);
 }
 
+PetscErrorCode PetscSolver::formFunction(Vec U, Vec F) {
+  PetscFunctionBegin;
+  PetscCall(rhs(simtime, U, F, true)); // Can be linearised for coloring
+
+  // shift * U - dU/dt
+  PetscCall(VecAXPBY(F, shift, -1.0, U));
+  PetscFunctionReturn(0);
+}
+
 // Matrix-free preconditioner function
 PetscErrorCode PetscSolver::pre(Vec x, Vec y) {
   TRACE("PetscSolver::pre()");
@@ -934,11 +963,17 @@ void PetscSolver::updateColoring() {
   // Replace the old coloring with the new one
   MatFDColoringDestroy(&fdcoloring);
   MatFDColoringCreate(Jfd, iscoloring, &fdcoloring);
-  // Use the SNES function that is defined by the TS method
-  // SNESTSFormFunction is defined in PETSc ts.c
-  // The ctx pointer should be the TS object
-  MatFDColoringSetFunction(fdcoloring,
-                           reinterpret_cast<MatFDColoringFn>(SNESTSFormFunction), ts);
+  if (ts_type != TSSUNDIALS) {
+    // Use the SNES function that is defined by the TS method
+    // SNESTSFormFunction is defined in PETSc ts.c
+    // The ctx pointer should be the TS object
+    MatFDColoringSetFunction(fdcoloring,
+                             reinterpret_cast<MatFDColoringFn>(SNESTSFormFunction), ts);
+  } else {
+    // SNESTSFormFunction is not available for SUNDIALS
+    MatFDColoringSetFunction(
+        fdcoloring, reinterpret_cast<MatFDColoringFn>(solver_form_function), this);
+  }
   MatFDColoringSetFromOptions(fdcoloring);
   MatFDColoringSetUp(Jfd, iscoloring, fdcoloring);
   ISColoringDestroy(&iscoloring);
@@ -948,7 +983,10 @@ void PetscSolver::updateColoring() {
 #if PETSC_HAVE_SUNDIALS2
     // The SUNDIALS interface calls TSGetIJacobian
     // https://www.mcs.anl.gov/petsc/petsc-3.14/src/ts/impls/implicit/sundials/sundials.c
-    TSSetIJacobian(ts, Jfd, Jfd, solver_ijacobian, this);
+    // This sets the "TSMatFDColoring" property on the Jacobian, that is used in TSComputeIJacobianDefaultColor
+    PetscObjectCompose((PetscObject)Jfd, "TSMatFDColoring", (PetscObject)fdcoloring);
+    // Call a wrapper function that stores the shift in the PetscSolver
+    TSSetIJacobian(ts, Jfd, Jfd, solver_ijacobian_color, this);
 #endif
   } else {
     if (matrix_free_operator) {
diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index 525ca93b40..a9b41333f7 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -67,6 +67,8 @@ public:
 
   /// Wrapper for the RHS function
   PetscErrorCode rhs(PetscReal t, Vec globalin, Vec globalout, bool linear);
+  /// Residual calculation.
+  PetscErrorCode formFunction(Vec U, Vec F);
   /// Wrapper for the preconditioner
   PetscErrorCode pre(Vec x, Vec y);
 
@@ -76,6 +78,11 @@ public:
   friend PetscErrorCode solver_ijacobian(TS, BoutReal, Vec, Vec, PetscReal shift, Mat J,
                                          Mat Jpre, void* ctx);
 
+  // Wrapper around TSComputeIJacobianDefaultColor that saves the shift
+  // This is used to compute the Jacobian using coloring with SUNDIALS TS method.
+  friend PetscErrorCode solver_ijacobian_color(TS ts, PetscReal t, Vec U, Vec Udot,
+                                               PetscReal shift, Mat J, Mat B, void* ctx);
+
 private:
   BoutReal shift; ///< Shift (alpha) parameter from TS
   Vec state;

From 1e18bf23b15a93e9ec9a67b921582715bb72a469 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 15 Aug 2025 15:14:05 -0700
Subject: [PATCH 0226/1827] petsc: Use C-style cast for MatFDColoringFn

The function signature seems to vary between PETSc versions in
ways that break `reinterpret_cast` (and `bout::cast_MatFDColoringFn`
in `include/bout/petsc_interface.hxx`).
---
 src/solver/impls/petsc/petsc.cxx | 18 ++++++++++++------
 src/solver/impls/petsc/petsc.hxx |  3 +++
 src/sys/petsclib.cxx             |  1 +
 3 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 551552a9b4..ce33bc232c 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -44,6 +44,7 @@
 #include <bout/utils.hxx>
 
 #include <petsc.h>
+#include <petscmat.h>
 #include <petscpctypes.h>
 #include <petscsnes.h>
 #include <petscsys.h>
@@ -294,7 +295,8 @@ int PetscSolver::init() {
   // Get total problem size
   int neq;
   if (bout::globals::mpi->MPI_Allreduce(&nlocal, &neq, 1, MPI_INT, MPI_SUM,
-                                        BoutComm::get())) {
+                                        BoutComm::get())
+      != 0) {
     throw BoutException("MPI_Allreduce failed!");
   }
 
@@ -967,12 +969,16 @@ void PetscSolver::updateColoring() {
     // Use the SNES function that is defined by the TS method
     // SNESTSFormFunction is defined in PETSc ts.c
     // The ctx pointer should be the TS object
-    MatFDColoringSetFunction(fdcoloring,
-                             reinterpret_cast<MatFDColoringFn>(SNESTSFormFunction), ts);
+    //
+    // Note: The cast is horrible but the function signature
+    //       varies between PETSc versions in ways that break
+    //       reinterpret_cast.
+    MatFDColoringSetFunction(fdcoloring, (MatFDColoringFn)SNESTSFormFunction, ts);
   } else {
-    // SNESTSFormFunction is not available for SUNDIALS
-    MatFDColoringSetFunction(
-        fdcoloring, reinterpret_cast<MatFDColoringFn>(solver_form_function), this);
+    // SNESTSFormFunction is not available for SUNDIALS.
+    // This solver_form_function needs to know the shift
+    // (SUNDIALS' gamma) that we capture in solver_ijacobian_color.
+    MatFDColoringSetFunction(fdcoloring, (MatFDColoringFn)solver_form_function, this);
   }
   MatFDColoringSetFromOptions(fdcoloring);
   MatFDColoringSetUp(Jfd, iscoloring, fdcoloring);
diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index a9b41333f7..b7857c7afd 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -47,6 +47,9 @@ class PetscSolver;
 #include <bout/vector3d.hxx>
 
 #include <petsc.h>
+#include <petscksp.h>
+#include <petscpctypes.h>
+#include <petscsnes.h>
 #include <petscts.h>
 
 #include <vector>
diff --git a/src/sys/petsclib.cxx b/src/sys/petsclib.cxx
index 1830db89d9..bae53a8c7a 100644
--- a/src/sys/petsclib.cxx
+++ b/src/sys/petsclib.cxx
@@ -15,6 +15,7 @@
 #include <petscoptions.h>
 #include <petscsnes.h>
 #include <petscsys.h>
+#include <petscts.h>
 #include <petscversion.h>
 
 #include <string>

From ca355a8a0393fc0b7f56aeb47c9a34ca17642ae6 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 15 Aug 2025 15:44:40 -0700
Subject: [PATCH 0227/1827] petsc: Cast coloring function to void

This regrettable necessity follows the PETSc examples.

Function pointers are cast to `PetscErrorCode (*)(void)`, which
means that any future change to the signature will not be caught
but will give undefined behavior. May future maintainers forgive me.

Some drive-by tidying to appease Clang-tidy.
---
 include/bout/petsclib.hxx        |  1 +
 src/solver/impls/petsc/petsc.cxx | 25 +++++++++++++++++--------
 src/solver/impls/petsc/petsc.hxx |  4 ++--
 3 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx
index 760b18ff91..41d7618fd2 100644
--- a/include/bout/petsclib.hxx
+++ b/include/bout/petsclib.hxx
@@ -60,6 +60,7 @@ class Options;
 #define PETSC_HAVE_BROKEN_RECURSIVE_MACRO
 
 #include <petsc.h> // IWYU pragma: export
+#include <petscts.h>
 #include <petscversion.h>
 
 #include "bout/boutexception.hxx"
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index ce33bc232c..abd4fbf64b 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -35,19 +35,25 @@
 #include <vector>
 
 #include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/globals.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 #include <bout/petsc_interface.hxx>
+#include <bout/solver.hxx>
+#include <bout/unused.hxx>
 #include <bout/utils.hxx>
 
 #include <petsc.h>
+#include <petscerror.h>
+#include <petscistypes.h>
 #include <petscmat.h>
-#include <petscpctypes.h>
+#include <petscpc.h>
 #include <petscsnes.h>
 #include <petscsys.h>
+#include <petscsystypes.h>
 #include <petscts.h>
 #include <petscvec.h>
 
@@ -149,7 +155,7 @@ PetscErrorCode solver_ijacobian_color(TS ts, PetscReal t, Vec U, Vec Udot,
   auto* solver = static_cast<PetscSolver*>(ctx);
   solver->shift = shift;
 
-  return TSComputeIJacobianDefaultColor(ts, t, U, Udot, shift, J, B, NULL);
+  return TSComputeIJacobianDefaultColor(ts, t, U, Udot, shift, J, B, nullptr);
 }
 
 // This function is called by the TS object every internal timestep
@@ -765,7 +771,7 @@ int PetscSolver::init() {
 
                   // 3D fields on this cell
                   for (int j = 0; j < n3d; j++) {
-                    PetscInt col = ind2 + j;
+                    PetscInt const col = ind2 + j;
                     int ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
 
                     if (ierr != 0) {
@@ -952,13 +958,13 @@ PetscErrorCode PetscSolver::pre(Vec x, Vec y) {
 
 void PetscSolver::updateColoring() {
   // Re-calculate the coloring
-  MatColoring coloring = NULL;
+  MatColoring coloring{nullptr};
   MatColoringCreate(Jfd, &coloring);
   MatColoringSetType(coloring, MATCOLORINGGREEDY);
   MatColoringSetFromOptions(coloring);
 
   // Calculate new index sets
-  ISColoring iscoloring = NULL;
+  ISColoring iscoloring{nullptr};
   MatColoringApply(coloring, &iscoloring);
   MatColoringDestroy(&coloring);
 
@@ -972,13 +978,16 @@ void PetscSolver::updateColoring() {
     //
     // Note: The cast is horrible but the function signature
     //       varies between PETSc versions in ways that break
-    //       reinterpret_cast.
-    MatFDColoringSetFunction(fdcoloring, (MatFDColoringFn)SNESTSFormFunction, ts);
+    //       reinterpret_cast and a C cast to MatFDColoringFn.
+    //       This is the cast that PETSc examples use.
+    MatFDColoringSetFunction(fdcoloring, (PetscErrorCode (*)(void))SNESTSFormFunction,
+                             ts);
   } else {
     // SNESTSFormFunction is not available for SUNDIALS.
     // This solver_form_function needs to know the shift
     // (SUNDIALS' gamma) that we capture in solver_ijacobian_color.
-    MatFDColoringSetFunction(fdcoloring, (MatFDColoringFn)solver_form_function, this);
+    MatFDColoringSetFunction(fdcoloring, (PetscErrorCode (*)(void))solver_form_function,
+                             this);
   }
   MatFDColoringSetFromOptions(fdcoloring);
   MatFDColoringSetUp(Jfd, iscoloring, fdcoloring);
diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index b7857c7afd..78f7d1a1e4 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -48,7 +48,7 @@ class PetscSolver;
 
 #include <petsc.h>
 #include <petscksp.h>
-#include <petscpctypes.h>
+#include <petscmat.h>
 #include <petscsnes.h>
 #include <petscts.h>
 
@@ -69,7 +69,7 @@ public:
   // These functions used internally (but need to be public)
 
   /// Wrapper for the RHS function
-  PetscErrorCode rhs(PetscReal t, Vec globalin, Vec globalout, bool linear);
+  PetscErrorCode rhs(BoutReal t, Vec udata, Vec dudata, bool linear);
   /// Residual calculation.
   PetscErrorCode formFunction(Vec U, Vec F);
   /// Wrapper for the preconditioner

From f9179676563ea24ad7b963ca6a7e589a5dc3164f Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Fri, 15 Aug 2025 22:50:57 +0000
Subject: [PATCH 0228/1827] Apply clang-format changes

---
 src/solver/impls/petsc/petsc.cxx | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index abd4fbf64b..c0e3094481 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -980,13 +980,12 @@ void PetscSolver::updateColoring() {
     //       varies between PETSc versions in ways that break
     //       reinterpret_cast and a C cast to MatFDColoringFn.
     //       This is the cast that PETSc examples use.
-    MatFDColoringSetFunction(fdcoloring, (PetscErrorCode (*)(void))SNESTSFormFunction,
-                             ts);
+    MatFDColoringSetFunction(fdcoloring, (PetscErrorCode(*)(void))SNESTSFormFunction, ts);
   } else {
     // SNESTSFormFunction is not available for SUNDIALS.
     // This solver_form_function needs to know the shift
     // (SUNDIALS' gamma) that we capture in solver_ijacobian_color.
-    MatFDColoringSetFunction(fdcoloring, (PetscErrorCode (*)(void))solver_form_function,
+    MatFDColoringSetFunction(fdcoloring, (PetscErrorCode(*)(void))solver_form_function,
                              this);
   }
   MatFDColoringSetFromOptions(fdcoloring);

From 3da7deacd60d3595a231255a775fb4b0e9c97b8b Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 15 Aug 2025 16:19:03 -0700
Subject: [PATCH 0229/1827] Try bout::cast_MatFDColoringFn

Getting MatFDColoringSetFunction to work across PETSc versions
seems to be unreasonably difficult.
---
 src/solver/impls/petsc/petsc.cxx | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index c0e3094481..ed48d87312 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -976,16 +976,14 @@ void PetscSolver::updateColoring() {
     // SNESTSFormFunction is defined in PETSc ts.c
     // The ctx pointer should be the TS object
     //
-    // Note: The cast is horrible but the function signature
-    //       varies between PETSc versions in ways that break
-    //       reinterpret_cast and a C cast to MatFDColoringFn.
-    //       This is the cast that PETSc examples use.
-    MatFDColoringSetFunction(fdcoloring, (PetscErrorCode(*)(void))SNESTSFormFunction, ts);
+    // Note: The function type casting here is horrible but necessary
+    MatFDColoringSetFunction(fdcoloring, bout::cast_MatFDColoringFn(SNESTSFormFunction),
+                             ts);
   } else {
     // SNESTSFormFunction is not available for SUNDIALS.
     // This solver_form_function needs to know the shift
     // (SUNDIALS' gamma) that we capture in solver_ijacobian_color.
-    MatFDColoringSetFunction(fdcoloring, (PetscErrorCode(*)(void))solver_form_function,
+    MatFDColoringSetFunction(fdcoloring, bout::cast_MatFDColoringFn(solver_form_function),
                              this);
   }
   MatFDColoringSetFromOptions(fdcoloring);

From 64dd70e48adea2399c98cd1066bb9f4d7c92f386 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 15 Aug 2025 17:58:11 -0700
Subject: [PATCH 0230/1827] petsc: More function casting

I put on my robe and wizard hat...
---
 include/bout/petsc_interface.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 90dd188d8a..5c4f5ed0e8 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -573,7 +573,7 @@ PetscVector<T> operator*(const PetscMatrix<T>& mat, const PetscVector<T>& vec) {
 namespace bout {
 template <class T>
 constexpr auto cast_MatFDColoringFn(T func) {
-  return func;
+  return reinterpret_cast<MatFDColoringFn>(func); // NOLINT(*-reinterpret-cast)
 }
 } // namespace bout
 #else

From 0413697ab87423a750a42bd109838092891c71b0 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 15 Aug 2025 19:36:29 -0700
Subject: [PATCH 0231/1827] petsc: Yet more function casting

---
 include/bout/petsc_interface.hxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 5c4f5ed0e8..3ae02f41a6 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -6,9 +6,9 @@
  * up a linear system.
  *
  **************************************************************************
- * Copyright 2019 C. MacMackin
+ * Copyright 2019 - 2025 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -573,7 +573,7 @@ PetscVector<T> operator*(const PetscMatrix<T>& mat, const PetscVector<T>& vec) {
 namespace bout {
 template <class T>
 constexpr auto cast_MatFDColoringFn(T func) {
-  return reinterpret_cast<MatFDColoringFn>(func); // NOLINT(*-reinterpret-cast)
+  return reinterpret_cast<MatFDColoringFn*>(func); // NOLINT(*-reinterpret-cast)
 }
 } // namespace bout
 #else

From 56ad5e52dafaf1302a7b268b3d7cce7d122afc02 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 15 Aug 2025 20:11:30 -0700
Subject: [PATCH 0232/1827] petsc: Tighten tolerance in test-solver

Tests pass with beuler/bdf/cn ts_types if tolerance is sufficiently tight.
---
 tests/integrated/test-solver/test_solver.cxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/integrated/test-solver/test_solver.cxx b/tests/integrated/test-solver/test_solver.cxx
index 2e4345c8cc..a24db71750 100644
--- a/tests/integrated/test-solver/test_solver.cxx
+++ b/tests/integrated/test-solver/test_solver.cxx
@@ -100,8 +100,7 @@ int main(int argc, char** argv) {
   root["imexbdf2"]["adaptive"] = true;
   root["imexbdf2"]["adaptRtol"] = 1.e-5;
 
-  root["petsc"]["nout"] = 10000;
-  root["petsc"]["output_step"] = end / 10000;
+  root["petsc"]["rtol"] = 1e-7;
 
   root["snes"]["adaptive"] = true;
 

From fd49f9bb3f169c5627160027f6024a8ce2d1b3a6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 3 Sep 2025 13:50:04 +0000
Subject: [PATCH 0233/1827] Update pygithub requirement from ~=2.7 to ~=2.8

Updates the requirements on [pygithub](https://github.com/pygithub/pygithub) to permit the latest version.
- [Release notes](https://github.com/pygithub/pygithub/releases)
- [Changelog](https://github.com/PyGithub/PyGithub/blob/main/doc/changes.rst)
- [Commits](https://github.com/pygithub/pygithub/compare/v2.7.0...v2.8.1)

---
updated-dependencies:
- dependency-name: pygithub
  dependency-version: 2.8.1
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements_maint.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements_maint.txt b/requirements_maint.txt
index a5e94a0af5..b1d9db5ff8 100644
--- a/requirements_maint.txt
+++ b/requirements_maint.txt
@@ -1,3 +1,3 @@
-pygithub~=2.7
+pygithub~=2.8
 ruamel-yaml~=0.18
 Unidecode~=1.3

From 9cae0e58650ed4314642af015f0d22e91eb30365 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 4 Sep 2025 12:50:09 +0200
Subject: [PATCH 0234/1827] Remove License-File, add License and README

---
 tools/pylib/_boutpp_build/backend.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 3df29d276d..8d0b4f4015 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -216,9 +216,16 @@ def build_sdist(sdist_directory, config_settings=None):
             f"""Metadata-Version: 2.1
 Name: {pkgname}
 Version: {getversion()}
-License-File: COPYING
 """
         )
+        with open("LICENSE") as src:
+            pre = "License:"
+            for l in src:
+                f.write(f"{pre}{l}\n")
+                pre = "        "
+        f.write("\n\n")
+        with open("README.md") as src:
+            f.write(src.read())
     run(
         f"tar --append -f {sdist_directory}/{fname} _version.txt --xform='s\\_version.txt\\{prefix}/_version.txt\\'"
     )

From 97b0a882b334f60f0f5731d6a4652e2683e2e0a1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 4 Sep 2025 13:17:43 +0200
Subject: [PATCH 0235/1827] Fix spacing

---
 tools/pylib/_boutpp_build/backend.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 8d0b4f4015..c9db2f1b55 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -219,10 +219,10 @@ def build_sdist(sdist_directory, config_settings=None):
 """
         )
         with open("LICENSE") as src:
-            pre = "License:"
+            pre = "License: "
             for l in src:
-                f.write(f"{pre}{l}\n")
-                pre = "        "
+                f.write(f"{pre}{l}")
+                pre = "         "
         f.write("\n\n")
         with open("README.md") as src:
             f.write(src.read())

From 4803d54bda35086c8d721e1e19e0a56a3024bd09 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 4 Sep 2025 13:19:49 +0200
Subject: [PATCH 0236/1827] Add content type

---
 tools/pylib/_boutpp_build/backend.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index c9db2f1b55..98897ce126 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -223,7 +223,7 @@ def build_sdist(sdist_directory, config_settings=None):
             for l in src:
                 f.write(f"{pre}{l}")
                 pre = "         "
-        f.write("\n\n")
+        f.write("\nDescription-Content-Type: text/markdown\n\n")
         with open("README.md") as src:
             f.write(src.read())
     run(

From 89dc6fba5b1767f13bab0b38e489ae7aca86ce1c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 4 Sep 2025 13:22:32 +0200
Subject: [PATCH 0237/1827] Fix spacing

---
 tools/pylib/_boutpp_build/backend.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 98897ce126..6d341e6aaa 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -223,7 +223,7 @@ def build_sdist(sdist_directory, config_settings=None):
             for l in src:
                 f.write(f"{pre}{l}")
                 pre = "         "
-        f.write("\nDescription-Content-Type: text/markdown\n\n")
+        f.write("Description-Content-Type: text/markdown\n\n")
         with open("README.md") as src:
             f.write(src.read())
     run(

From a0657ef4b6bcca6e61b04a18d1af958735cae11e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 4 Sep 2025 12:50:09 +0200
Subject: [PATCH 0238/1827] Remove License-File, add License and README

---
 tools/pylib/_boutpp_build/backend.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 0c1e611a2f..c04f5111fc 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -216,9 +216,16 @@ def build_sdist(sdist_directory, config_settings=None):
             f"""Metadata-Version: 2.1
 Name: {pkgname}
 Version: {getversion()}
-License-File: COPYING
 """
         )
+        with open("LICENSE") as src:
+            pre = "License:"
+            for l in src:
+                f.write(f"{pre}{l}\n")
+                pre = "        "
+        f.write("\n\n")
+        with open("README.md") as src:
+            f.write(src.read())
     run(
         f"tar --append -f {sdist_directory}/{fname} _version.txt --xform='s\\_version.txt\\{prefix}/_version.txt\\'"
     )

From d01957421d8313d03d1d8f3ae8dec340204d8ca5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 4 Sep 2025 13:17:43 +0200
Subject: [PATCH 0239/1827] Fix spacing

---
 tools/pylib/_boutpp_build/backend.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index c04f5111fc..f854c4582f 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -219,10 +219,10 @@ def build_sdist(sdist_directory, config_settings=None):
 """
         )
         with open("LICENSE") as src:
-            pre = "License:"
+            pre = "License: "
             for l in src:
-                f.write(f"{pre}{l}\n")
-                pre = "        "
+                f.write(f"{pre}{l}")
+                pre = "         "
         f.write("\n\n")
         with open("README.md") as src:
             f.write(src.read())

From 7f79d21f82a27a050529bf5bcaa577a987112e96 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 4 Sep 2025 13:19:49 +0200
Subject: [PATCH 0240/1827] Add content type

---
 tools/pylib/_boutpp_build/backend.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index f854c4582f..6fd21c1506 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -223,7 +223,7 @@ def build_sdist(sdist_directory, config_settings=None):
             for l in src:
                 f.write(f"{pre}{l}")
                 pre = "         "
-        f.write("\n\n")
+        f.write("\nDescription-Content-Type: text/markdown\n\n")
         with open("README.md") as src:
             f.write(src.read())
     run(

From af37dff14f1875ad2ace70f3f260a246dc8ec010 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 4 Sep 2025 13:22:32 +0200
Subject: [PATCH 0241/1827] Fix spacing

---
 tools/pylib/_boutpp_build/backend.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 6fd21c1506..f105fadceb 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -223,7 +223,7 @@ def build_sdist(sdist_directory, config_settings=None):
             for l in src:
                 f.write(f"{pre}{l}")
                 pre = "         "
-        f.write("\nDescription-Content-Type: text/markdown\n\n")
+        f.write("Description-Content-Type: text/markdown\n\n")
         with open("README.md") as src:
             f.write(src.read())
     run(

From 921901511a8f5ffefe1144a8c63697d797aec4de Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 8 Sep 2025 19:40:35 +0000
Subject: [PATCH 0242/1827] Bump actions/setup-python from 5 to 6

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/python-package.yml | 6 +++---
 .github/workflows/tests.yml          | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 5a788f9eb0..fc5e84662c 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -22,7 +22,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -62,7 +62,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -111,7 +111,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index aa3db3adc1..0d73948d45 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -162,7 +162,7 @@ jobs:
         with:
           submodules: true
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.x'
 

From 78538d0dbc1fbc6226614065376a7fb3e3c09390 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 3 Oct 2025 09:39:42 -0700
Subject: [PATCH 0243/1827] Add a periodicY function to FieldFactory

Provides a variable "periodicY" that is 1 in the core and 0 outside.
---
 src/field/field_factory.cxx   |  7 +++++--
 src/field/fieldgenerators.hxx | 36 ++++++++++++++++++++++++++++++++---
 2 files changed, 38 insertions(+), 5 deletions(-)

diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index f65f2e7f55..c49106cc1d 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -1,7 +1,7 @@
 /**************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010-2025 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -176,6 +176,9 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
 
   // Where switch function
   addGenerator("where", std::make_shared<FieldWhere>(nullptr, nullptr, nullptr));
+
+  // Periodic in the Y direction?
+  addGenerator("periodicY", std::make_shared<FieldPeriodicY>(nullptr));
 }
 
 Field2D FieldFactory::create2D(const std::string& value, const Options* opt,
diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index 2485b4b82d..133d1d1e8a 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -1,4 +1,4 @@
-/*!
+/*!A
  * \file fieldgenerators.hxx
  *
  * These classes are used by FieldFactory
@@ -307,7 +307,7 @@ public:
   // Constructor
   FieldTanhHat(FieldGeneratorPtr xin, FieldGeneratorPtr widthin,
                FieldGeneratorPtr centerin, FieldGeneratorPtr steepnessin)
-      : X(xin), width(widthin), center(centerin), steepness(steepnessin){};
+      : X(xin), width(widthin), center(centerin), steepness(steepnessin) {};
   // Clone containing the list of arguments
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override;
   BoutReal generate(const bout::generator::Context& pos) override;
@@ -322,7 +322,7 @@ private:
 class FieldWhere : public FieldGenerator {
 public:
   FieldWhere(FieldGeneratorPtr test, FieldGeneratorPtr gt0, FieldGeneratorPtr lt0)
-      : test(test), gt0(gt0), lt0(lt0){};
+      : test(test), gt0(gt0), lt0(lt0) {};
 
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 3) {
@@ -352,4 +352,34 @@ private:
   FieldGeneratorPtr test, gt0, lt0;
 };
 
+/// Function that evaluates to 1 when Y is periodic (i.e. in the core), 0 otherwise
+class FieldPeriodicY : public FieldGenerator {
+public:
+  FieldPeriodicY(Mesh* mesh) : mesh(mesh) {
+    // Note: Assumes symmetricGlobalX
+    local_inner_boundary =
+        0.5 * (mesh->GlobalX(mesh->xstart - 1) + mesh->GlobalX(mesh->xstart));
+    local_outer_boundary =
+        0.5 * (mesh->GlobalX(mesh->xend + 1) + mesh->GlobalX(mesh->xend));
+  }
+  FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> UNUSED(args)) override {
+    return std::make_shared<FieldPeriodicY>(ctx.getMesh());
+  }
+  BoutReal generate(const bout::generator::Context& ctx) override {
+    int local_index = mesh->xstart
+                      + int(((ctx.x() - local_inner_boundary)
+                             / (local_outer_boundary - local_inner_boundary))
+                            * (mesh->xend - mesh->xstart + 1));
+    if (mesh->periodicY(local_index)) {
+      return 1.0;
+    }
+    return 0.0;
+  }
+
+private:
+  Mesh* mesh;
+  BoutReal local_inner_boundary;
+  BoutReal local_outer_boundary;
+};
+
 #endif // BOUT_FIELDGENERATORS_H

From 06c4599dae6d0201d5ce7f6f2641b9b0c4db39da Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Fri, 3 Oct 2025 16:41:58 +0000
Subject: [PATCH 0244/1827] Apply clang-format changes

---
 src/field/fieldgenerators.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index 133d1d1e8a..ea3682053a 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -307,7 +307,7 @@ public:
   // Constructor
   FieldTanhHat(FieldGeneratorPtr xin, FieldGeneratorPtr widthin,
                FieldGeneratorPtr centerin, FieldGeneratorPtr steepnessin)
-      : X(xin), width(widthin), center(centerin), steepness(steepnessin) {};
+      : X(xin), width(widthin), center(centerin), steepness(steepnessin){};
   // Clone containing the list of arguments
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override;
   BoutReal generate(const bout::generator::Context& pos) override;
@@ -322,7 +322,7 @@ private:
 class FieldWhere : public FieldGenerator {
 public:
   FieldWhere(FieldGeneratorPtr test, FieldGeneratorPtr gt0, FieldGeneratorPtr lt0)
-      : test(test), gt0(gt0), lt0(lt0) {};
+      : test(test), gt0(gt0), lt0(lt0){};
 
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 3) {

From a8512395bade559a6b7ae10ff3ad06bab4cacb66 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 3 Oct 2025 09:55:39 -0700
Subject: [PATCH 0245/1827] Fixes for periodicY field generator

---
 src/field/field_factory.cxx   |  2 +-
 src/field/fieldgenerators.hxx | 31 +++++++++++++------------------
 2 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index c49106cc1d..08a7f14fa3 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -178,7 +178,7 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
   addGenerator("where", std::make_shared<FieldWhere>(nullptr, nullptr, nullptr));
 
   // Periodic in the Y direction?
-  addGenerator("periodicY", std::make_shared<FieldPeriodicY>(nullptr));
+  addGenerator("periodicY", std::make_shared<FieldPeriodicY>());
 }
 
 Field2D FieldFactory::create2D(const std::string& value, const Options* opt,
diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index ea3682053a..050e335448 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -1,4 +1,4 @@
-/*!A
+/*!
  * \file fieldgenerators.hxx
  *
  * These classes are used by FieldFactory
@@ -353,33 +353,28 @@ private:
 };
 
 /// Function that evaluates to 1 when Y is periodic (i.e. in the core), 0 otherwise
+/// Note: Assumes symmetricGlobalX
 class FieldPeriodicY : public FieldGenerator {
 public:
-  FieldPeriodicY(Mesh* mesh) : mesh(mesh) {
-    // Note: Assumes symmetricGlobalX
-    local_inner_boundary =
-        0.5 * (mesh->GlobalX(mesh->xstart - 1) + mesh->GlobalX(mesh->xstart));
-    local_outer_boundary =
-        0.5 * (mesh->GlobalX(mesh->xend + 1) + mesh->GlobalX(mesh->xend));
-  }
+  FieldPeriodicY() = default;
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> UNUSED(args)) override {
-    return std::make_shared<FieldPeriodicY>(ctx.getMesh());
+    return std::make_shared<FieldPeriodicY>();
   }
   BoutReal generate(const bout::generator::Context& ctx) override {
-    int local_index = mesh->xstart
-                      + int(((ctx.x() - local_inner_boundary)
-                             / (local_outer_boundary - local_inner_boundary))
-                            * (mesh->xend - mesh->xstart + 1));
+    const Mesh* mesh = ctx.getMesh();
+    const BoutReal local_inner_boundary =
+        0.5 * (mesh->GlobalX(mesh->xstart - 1) + mesh->GlobalX(mesh->xstart));
+    const BoutReal local_outer_boundary =
+        0.5 * (mesh->GlobalX(mesh->xend + 1) + mesh->GlobalX(mesh->xend));
+    const int local_index = mesh->xstart
+                            + int(((ctx.x() - local_inner_boundary)
+                                   / (local_outer_boundary - local_inner_boundary))
+                                  * (mesh->xend - mesh->xstart + 1));
     if (mesh->periodicY(local_index)) {
       return 1.0;
     }
     return 0.0;
   }
-
-private:
-  Mesh* mesh;
-  BoutReal local_inner_boundary;
-  BoutReal local_outer_boundary;
 };
 
 #endif // BOUT_FIELDGENERATORS_H

From cfb22cfbd4ad82cad5e820f68ae6301e782a1a18 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 10:19:23 +0100
Subject: [PATCH 0246/1827] Update translations

---
 locale/de/libbout.po    | 346 +++++++++++++++++++++-------------------
 locale/es/libbout.po    | 344 ++++++++++++++++++++-------------------
 locale/fr/libbout.po    | 330 +++++++++++++++++++-------------------
 locale/libbout.pot      | 326 ++++++++++++++++++-------------------
 locale/zh_CN/libbout.po | 334 +++++++++++++++++++-------------------
 locale/zh_TW/libbout.po | 346 ++++++++++++++++++++--------------------
 6 files changed, 1031 insertions(+), 995 deletions(-)

diff --git a/locale/de/libbout.po b/locale/de/libbout.po
index 0e0773b5db..242beb45ca 100644
--- a/locale/de/libbout.po
+++ b/locale/de/libbout.po
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: BOUT++ 4.2.1\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2024-09-12 09:17+0100\n"
+"POT-Creation-Date: 2025-08-13 23:37+0100\n"
 "PO-Revision-Date: 2019-02-06 17:32+0000\n"
 "Last-Translator: David <schword2@mail.dcu.ie>\n"
 "Language-Team: German\n"
@@ -18,7 +18,7 @@ msgstr ""
 "Plural-Forms: nplurals=2; plural=(n != 1);\n"
 "X-Generator: Poedit 2.2.1\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:191
+#: ../src/mesh/impls/bout/boutmesh.cxx:182
 #, fuzzy, c++-format
 msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
@@ -27,7 +27,7 @@ msgstr ""
 "\t -> `Core` Region iyseps2_1-iyseps1_1 ({:d}-{:d} = {:d}) muss ein "
 "Vielfaches von MYSUB ({:d}) sein\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:224
+#: ../src/mesh/impls/bout/boutmesh.cxx:215
 #, fuzzy, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
@@ -36,7 +36,7 @@ msgstr ""
 "\t -> `Core` Region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) muss ein "
 "Vielfaches von MYSUB ({:d}) sein\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:199
+#: ../src/mesh/impls/bout/boutmesh.cxx:190
 #, fuzzy, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
@@ -45,11 +45,11 @@ msgstr ""
 "\t -> `Core` Region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) muss ein "
 "Vielfaches von MYSUB ({:d}) sein\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:309
+#: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
 msgstr "\t -> Wert OK\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:180
+#: ../src/mesh/impls/bout/boutmesh.cxx:171
 #, fuzzy, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
@@ -57,7 +57,7 @@ msgstr ""
 "\t -> `Leg` Region jyseps1_1+1 ({:d}) muss ein Vielfaches von MYSUB ({:d}) "
 "sein\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:215
+#: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, fuzzy, c++-format
 msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
@@ -66,7 +66,7 @@ msgstr ""
 "\t -> `Leg` Region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) muss ein "
 "Vielfaches von MYSUB ({:d}) sein\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:232
+#: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, fuzzy, c++-format
 msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
@@ -75,7 +75,7 @@ msgstr ""
 "\t -> `Leg` Region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) muss ein Vielfaches "
 "von MYSUB ({:d}) sein\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:208
+#: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, fuzzy, c++-format
 msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
@@ -84,12 +84,17 @@ msgstr ""
 "\t -> `Leg` Region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) muss ein "
 "Vielfaches von MYSUB ({:d}) sein\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:175
+#: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, fuzzy, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
 msgstr "\t -> ny/NYPE ({:d}/{:d} = {:d}) muss >= MYG ({:d}) sein\n"
 
 #: ../src/bout++.cxx:575
+#, fuzzy, c++-format
+msgid "\tADIOS2 support {}\n"
+msgstr "\tNetCDF Unterstützung ist aktiviert\n"
+
+#: ../src/bout++.cxx:583
 #, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
@@ -98,28 +103,28 @@ msgstr ""
 #. Processors divide equally
 #. Mesh in X divides equally
 #. Mesh in Y divides equally
-#: ../src/mesh/impls/bout/boutmesh.cxx:297
+#: ../src/mesh/impls/bout/boutmesh.cxx:288
 #, fuzzy, c++-format
 msgid "\tCandidate value: {:d}\n"
 msgstr "\tzu überprüfender Wert: {:d}\n"
 
-#: ../src/bout++.cxx:576
+#: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:594
+#: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
 msgstr "\tKommandozeilenoptionen für diese Ausführung: "
 
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
-#: ../src/bout++.cxx:590
+#: ../src/bout++.cxx:595
 #, fuzzy, c++-format
 msgid "\tCompiled with flags : {:s}\n"
 msgstr "\tWurde kompiliert mit den Optionen : {:s}\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:324
+#: ../src/mesh/impls/bout/boutmesh.cxx:315
 #, fuzzy, c++-format
 msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
@@ -128,14 +133,14 @@ msgstr ""
 "\tDas Gebiet wird in NXPE={:d} mal NYPE={:d} Gebiete der Größe localNx={:d} "
 "mal localNy={:d} aufgeteilt\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:364
+#: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, fuzzy, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
 "\tFEHLER: {:d} Punkte in der Y-Richtung können nicht gleichmässig zwischen "
 "{:d} Prozessen verteilt werden\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:372
+#: ../src/mesh/impls/bout/boutmesh.cxx:365
 #, fuzzy, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
@@ -156,31 +161,31 @@ msgstr ""
 msgid "\tEmpty key or value in command line '{:s}'\n"
 msgstr "\tSchlüssel (Key) oder Wert nicht gesetzt in der Befehlszeile '{:s}'\n"
 
-#: ../src/bout++.cxx:582
+#: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:561
+#: ../src/bout++.cxx:568
 #, fuzzy, c++-format
 msgid "\tFFT support {}\n"
 msgstr "\tNetCDF Unterstützung ist aktiviert\n"
 
-#: ../src/bout++.cxx:585
+#: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:583
+#: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:440
+#: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
 msgstr "\tGittergröße: "
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:463
+#: ../src/mesh/impls/bout/boutmesh.cxx:499
 #, fuzzy
 msgid "\tGuard cells (x,y,z): "
 msgstr "\tGuardzellen (x,y): "
@@ -194,17 +199,17 @@ msgstr ""
 "\tDer Schlüssel darf nicht ':' enthalten\n"
 "\tZeile: {:s}"
 
-#: ../src/bout++.cxx:563
+#: ../src/bout++.cxx:570
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:586
+#: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:560
+#: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
@@ -214,98 +219,94 @@ msgstr ""
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
 msgstr "\t'=' darf nicht mehrfach vorkommen: '{:s}'\n"
 
-#: ../src/bout++.cxx:562
+#: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:567
+#: ../src/bout++.cxx:574
 #, fuzzy, c++-format
 msgid "\tNetCDF support {}{}\n"
 msgstr "\tNetCDF Unterstützung ist aktiviert\n"
 
-#: ../src/bout++.cxx:577
+#: ../src/bout++.cxx:585
 #, fuzzy, c++-format
-msgid "\tOpenMP parallelisation {}"
-msgstr "\tOpenMP Parallelisierung ist deaktiviert\n"
+msgid "\tOpenMP parallelisation {}, using {} threads\n"
+msgstr "\tOpenMP Parallelisierung mit {:d} Threads ist aktiviert\n"
 
 #. Mark the option as used
 #. Option not found
-#: ../src/sys/options.cxx:311 ../src/sys/options.cxx:380
-#: ../src/sys/options.cxx:415 ../src/sys/options.cxx:457
-#: ../src/sys/options.cxx:717 ../src/sys/options.cxx:744
-#: ../src/sys/options.cxx:771 ../include/bout/options.hxx:516
-#: ../include/bout/options.hxx:549 ../include/bout/options.hxx:573
-#: ../include/bout/options.hxx:820
+#: ../include/bout/options.hxx:586 ../include/bout/options.hxx:619
+#: ../include/bout/options.hxx:643 ../include/bout/options.hxx:896
 msgid "\tOption "
 msgstr "\tOption "
 
-#: ../src/sys/options.cxx:447
+#: ../src/sys/options.cxx:369
 #, fuzzy, c++-format
-msgid "\tOption '{:s}': Boolean expected. Got '{:s}'\n"
-msgstr "\tOption '{:s}': Boolscherwert erwartet, '{:s}' gefunden\n"
+msgid "\tOption {} = {}"
+msgstr "\tOption "
 
 #: ../src/sys/options/options_ini.cxx:70
 #, fuzzy, c++-format
 msgid "\tOptions file '{:s}' not found\n"
 msgstr "\tDie Optionendatei '{:s}' konnte nicht gefunden werden\n"
 
-#: ../src/bout++.cxx:568
+#: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:571
+#: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:557
+#: ../src/bout++.cxx:564
 msgid "\tParallel NetCDF support disabled\n"
 msgstr "\tParallele-NetCDF Unterstützung ist deaktiviert\n"
 
-#: ../src/bout++.cxx:555
+#: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
 msgstr "\tParllele-NetCDF Unterstützung ist aktiviert\n"
 
-#: ../src/bout++.cxx:569
+#: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:437
+#: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
 msgstr "\tnz wird von der Griddatei gelesen\n"
 
-#: ../src/mesh/mesh.cxx:238
+#: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
 msgstr "\tKontravariantevektoren werden gelesen "
 
-#: ../src/mesh/mesh.cxx:231 ../src/mesh/mesh.cxx:252
+#: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
 msgstr "\tKovariantevektoren werden gelesen "
 
-#: ../src/bout++.cxx:548
+#: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
 msgstr ""
 
-#: ../src/bout++.cxx:573
+#: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:574
+#: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:572
+#: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:584
+#: ../src/bout++.cxx:589
 #, fuzzy, c++-format
 msgid "\tSignal handling support {}\n"
 msgstr "\tSignalverarbeitung ist deaktiviert\n"
@@ -315,7 +316,7 @@ msgstr "\tSignalverarbeitung ist deaktiviert\n"
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:577
+#: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
 msgstr "\tfertig\n"
 
@@ -325,7 +326,7 @@ msgid ""
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
 
-#: ../src/bout++.cxx:371
+#: ../src/bout++.cxx:378
 #, fuzzy
 msgid ""
 "\n"
@@ -345,7 +346,7 @@ msgstr ""
 "  -v, --verbose\t\tWortreicherer Ausgabe\n"
 "  -q, --quiet\t\tNur wichtigere Ausgaben anzeigen\n"
 
-#: ../src/sys/expressionparser.cxx:302
+#: ../src/sys/expressionparser.cxx:341
 #, c++-format
 msgid ""
 "\n"
@@ -353,7 +354,7 @@ msgid ""
 "  Did you mean '{0}'?"
 msgstr ""
 
-#: ../src/solver/solver.cxx:580
+#: ../src/solver/solver.cxx:586
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -362,7 +363,7 @@ msgstr ""
 "\n"
 "Simulation beendet um {:s}\n"
 
-#: ../src/solver/solver.cxx:532
+#: ../src/solver/solver.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -374,7 +375,7 @@ msgstr ""
 #. Raw string to help with the formatting of the message, and a
 #. separate variable so clang-format doesn't barf on the
 #. exception
-#: ../src/sys/options.cxx:1102
+#: ../src/sys/options.cxx:1158
 msgid ""
 "\n"
 "There were unused input options:\n"
@@ -402,7 +403,7 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/bout++.cxx:382
+#: ../src/bout++.cxx:389
 #, c++-format
 msgid ""
 "  --print-config\t\tPrint the compile-time configuration\n"
@@ -435,60 +436,60 @@ msgid ""
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
 
-#: ../src/bout++.cxx:379
+#: ../src/bout++.cxx:386
 #, fuzzy
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
 msgstr "  -c, --color\t\tFarbliche Ausgabe mit bout-log-color\n"
 
-#: ../include/bout/options.hxx:823
+#: ../include/bout/options.hxx:899
 #, fuzzy
 msgid ") overwritten with:"
 msgstr ") überschrieben mit {:s}"
 
-#: ../src/bout++.cxx:550
+#: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
 msgstr ""
 
-#: ../src/bout++.cxx:579
-#, c++-format
-msgid ", using {} threads"
-msgstr ""
-
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
 msgstr ""
 
-#: ../src/sys/options.cxx:868
+#: ../src/sys/options.cxx:895
 msgid "All options used\n"
 msgstr "Alle genutzten Optionen\n"
 
-#: ../src/bout++.cxx:528
+#: ../src/bout++.cxx:535
 #, fuzzy, c++-format
 msgid "BOUT++ version {:s}\n"
 msgstr "BOUT++ Version {:s}\n"
 
-#: ../src/bout++.cxx:143
+#: ../src/bout++.cxx:147
 #, fuzzy
 msgid "Bad command line arguments:\n"
 msgstr "\t'=' darf nicht mehrfach vorkommen: '{:s}'\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:559
+#: ../src/sys/expressionparser.cxx:192
+#, c++-format
+msgid "Boolean operator argument {:e} is not a bool"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
 msgstr "Randgebiete auf diesem Prozessor: "
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:355
+#: ../src/mesh/impls/bout/boutmesh.cxx:348
 #, fuzzy, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr ""
 "{:d} Punkte in der X-Richtung können nicht gleichmässig zwischen {:d} "
 "Prozessen verteilt werden\n"
 
-#: ../src/bout++.cxx:818
+#: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
 msgstr ""
 
-#: ../src/bout++.cxx:533
+#: ../src/bout++.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
@@ -501,7 +502,7 @@ msgstr ""
 msgid "Command line"
 msgstr "Befehlszeile"
 
-#: ../src/bout++.cxx:544 ../tests/unit/src/test_bout++.cxx:358
+#: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
 msgstr "Kompiliert mit:\n"
 
@@ -510,16 +511,16 @@ msgstr "Kompiliert mit:\n"
 msgid "Compiled with flags"
 msgstr "\tWurde kompiliert mit den Optionen : {:s}\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:568
+#: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
 msgstr "Standardregionen werden erstellt"
 
-#: ../src/bout++.cxx:520
+#: ../src/bout++.cxx:527
 #, fuzzy, c++-format
 msgid "Could not create PID file {:s}"
 msgstr "Die Ausgabedatei '{:s}' konnte nicht geöffnet werden\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:318
+#: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
 msgstr ""
@@ -531,32 +532,32 @@ msgstr ""
 msgid "Could not open output file '{:s}'\n"
 msgstr "Die Ausgabedatei '{:s}' konnte nicht geöffnet werden\n"
 
-#: ../src/bout++.cxx:652
+#: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
 msgstr ""
 
 #. Error reading
-#: ../src/mesh/mesh.cxx:532
+#: ../src/mesh/mesh.cxx:543
 #, fuzzy, c++-format
 msgid "Could not read integer array '{:s}'\n"
 msgstr "Der Ganzzahlen-Array '{:s}' konnte nicht gelesen werden\n"
 
 #. Failed . Probably not important enough to stop the simulation
-#: ../src/bout++.cxx:632
+#: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
 "Der Befehl 'bout-log-color' konnte nicht ausgeführt werden. Stellen Sie "
 "sicher, dass er sich in $PATH befindet.\n"
 
-#: ../src/solver/solver.cxx:765
+#: ../src/solver/solver.cxx:772
 #, fuzzy, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
 msgstr ""
 "'Monitor' konnte nicht hinzugefügt werden: {:g} ist nicht ein Vielfaches von "
 "{:g}!"
 
-#: ../src/sys/expressionparser.cxx:273
+#: ../src/sys/expressionparser.cxx:312
 #, c++-format
 msgid ""
 "Couldn't find generator '{}'. BOUT++ expressions are now case-sensitive, so "
@@ -565,73 +566,73 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:568
+#: ../src/mesh/mesh.cxx:587
 #, fuzzy, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
 msgstr "Die Region '{:s}' ist nicht in regionMap2D"
 
-#: ../src/mesh/mesh.cxx:560
+#: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
 #, fuzzy, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
 msgstr "Die Region '{:s}' ist nicht in regionMap3D"
 
-#: ../src/mesh/mesh.cxx:576
+#: ../src/mesh/mesh.cxx:595
 #, fuzzy, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
 msgstr "Die Region '{:s}' ist nicht in regionMapPerp"
 
 #. Convert any exceptions to something a bit more useful
-#: ../src/sys/options.cxx:336
+#: ../src/sys/options.cxx:361
 #, fuzzy, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
 msgstr ""
 "Die Option {:s} = '{:s}' konnte nicht als ganze Zahl interpretiert werden."
 
-#: ../src/bout++.cxx:508
+#: ../src/bout++.cxx:515
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
 msgstr "Der Datenordner \"{:s}\" existiert nicht oder ist nicht lesbar\n"
 
-#: ../src/bout++.cxx:505
+#: ../src/bout++.cxx:512
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
 msgstr ""
 "\"{:s}\" soll als Datenordner verwendet werden, ist jedoch kein Ordner\n"
 
-#: ../src/solver/solver.cxx:665
+#: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
 msgstr "FEHLER: Der Integrator ist bereits initialisiert.\n"
 
-#: ../src/bout++.cxx:209
+#: ../src/bout++.cxx:216
 #, fuzzy, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
 msgstr "Es wurde ein Fehler während der Initialisierung gefunden: {:s}\n"
 
-#: ../src/bout++.cxx:744
+#: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
 msgstr "Es wurde ein Fehler beim Schreiben der Einstellungsdatei gefunden"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:332
+#: ../src/mesh/impls/bout/boutmesh.cxx:323
 #, fuzzy, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
 msgstr "Fehler: nx muss größer als 2 mal MXG sein (2 * {:d})"
 
-#: ../src/solver/solver.cxx:512
+#: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
 msgstr ""
 "Der Integrator konnte nicht initialisiert werden. Der Prozess wird "
 "abgebrochen\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:290
+#: ../src/mesh/impls/bout/boutmesh.cxx:281
 #, fuzzy, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
 msgstr "Suche NXPE Wert (optimal = {:f})\n"
 
-#: ../src/solver/solver.cxx:668
+#: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
 msgstr "initialisiere den Integrator\n"
 
-#: ../src/bout++.cxx:494
+#: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
@@ -644,48 +645,48 @@ msgstr ""
 msgid "Invalid command line option '-' found - maybe check whitespace?"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:400
+#: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
 msgstr "Lade das Gitter"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:415
+#: ../src/mesh/impls/bout/boutmesh.cxx:451
 msgid "Mesh must contain nx"
 msgstr "Das Gitter muss nx enthalten"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:419
+#: ../src/mesh/impls/bout/boutmesh.cxx:455
 msgid "Mesh must contain ny"
 msgstr "Das Gitter muss ny enthalten"
 
 #. Not found
-#: ../src/mesh/mesh.cxx:536
+#: ../src/mesh/mesh.cxx:547
 #, fuzzy, c++-format
 msgid "Missing integer array {:s}\n"
 msgstr "Ganzzahlen-Array '{:s}' nicht gesetzt\n"
 
-#: ../src/solver/solver.cxx:905
+#: ../src/solver/solver.cxx:911
 #, fuzzy, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
 msgstr "Beendigung durch Monitor\n"
 
-#: ../src/solver/solver.cxx:883
+#: ../src/solver/solver.cxx:889
 #, fuzzy, c++-format
 msgid "Monitor signalled to quit (return code {})"
 msgstr "Der Monitor signaliserte die Beendigung"
 
-#: ../src/bout++.cxx:823
+#: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:565
+#: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
 msgstr "Keine Randregionen auf diesem Prozessor"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:550
+#: ../src/mesh/impls/bout/boutmesh.cxx:586
 #, fuzzy
 msgid "No boundary regions; domain is periodic\n"
 msgstr "Keine Randregionen auf diesem Prozessor"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:254
+#: ../src/mesh/impls/bout/boutmesh.cxx:245
 #, fuzzy, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
@@ -693,7 +694,7 @@ msgstr ""
 "Anzahl an Prozessoren ({:d}) nicht teilbar durch Anzahl in x Richtung "
 "({:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:267
+#: ../src/mesh/impls/bout/boutmesh.cxx:258
 #, fuzzy, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
@@ -702,26 +703,26 @@ msgstr ""
 "({:d})\n"
 
 #. Less than 2 time-steps left
-#: ../src/bout++.cxx:896
+#: ../src/bout++.cxx:908
 #, fuzzy, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
 msgstr "Nur noch {:e} Sekunden verfügbar. Abbruch\n"
 
-#: ../src/sys/options.cxx:303 ../src/sys/options.cxx:345
-#: ../src/sys/options.cxx:393 ../src/sys/options.cxx:428
-#: ../src/sys/options.cxx:703 ../src/sys/options.cxx:730
-#: ../src/sys/options.cxx:757
+#: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
+#: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
+#: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
+#: ../src/sys/options.cxx:789
 #, fuzzy, c++-format
 msgid "Option {:s} has no value"
 msgstr "Der Option '{:s}' wurde kein Wert zugewiesen"
 
 #. Doesn't exist
-#: ../src/sys/options.cxx:159
+#: ../src/sys/options.cxx:172
 #, fuzzy, c++-format
 msgid "Option {:s}:{:s} does not exist"
 msgstr "Die Option {:s}:{:s} exisitiert nicht"
 
-#: ../include/bout/options.hxx:828
+#: ../include/bout/options.hxx:904
 #, fuzzy, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
@@ -730,12 +731,12 @@ msgstr ""
 "Optionen: Der Wert {2:s} wird mit dem Wert {1:s} gleichen Ursprungs ({0:s}) "
 "überschrieben."
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:552
+#: ../src/mesh/impls/bout/boutmesh.cxx:588
 #, fuzzy
 msgid "Possible boundary regions are: "
 msgstr "Keine Randregionen auf diesem Prozessor"
 
-#: ../src/bout++.cxx:538
+#: ../src/bout++.cxx:545
 #, fuzzy, c++-format
 msgid ""
 "Processor number: {:d} of {:d}\n"
@@ -744,32 +745,32 @@ msgstr ""
 "Prozessorennummer: {:d} von {:d}\n"
 "\n"
 
-#: ../src/mesh/mesh.cxx:609
+#: ../src/mesh/mesh.cxx:642
 #, fuzzy, c++-format
 msgid "Registered region 2D {:s}"
 msgstr "2D Region '{:s}' hinzugefügt"
 
-#: ../src/mesh/mesh.cxx:599
+#: ../src/mesh/mesh.cxx:632
 #, fuzzy, c++-format
 msgid "Registered region 3D {:s}"
 msgstr "3D Region '{:s}' hinzugefügt"
 
-#: ../src/mesh/mesh.cxx:619
+#: ../src/mesh/mesh.cxx:652
 #, fuzzy, c++-format
 msgid "Registered region Perp {:s}"
 msgstr "Perp Region '{:s}' hinzugefügt"
 
-#: ../src/bout++.cxx:529
+#: ../src/bout++.cxx:536
 #, fuzzy, c++-format
 msgid "Revision: {:s}\n"
 msgstr "Revision: {:s}\n"
 
-#: ../src/solver/solver.cxx:581
+#: ../src/solver/solver.cxx:587
 msgid "Run time : "
 msgstr "Dauer: "
 
 #. / Run the solver
-#: ../src/solver/solver.cxx:525
+#: ../src/solver/solver.cxx:533
 msgid ""
 "Running simulation\n"
 "\n"
@@ -781,7 +782,7 @@ msgstr ""
 msgid "Signal"
 msgstr ""
 
-#: ../src/bout++.cxx:865
+#: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
@@ -790,7 +791,7 @@ msgstr ""
 "Integrator\n"
 "\n"
 
-#: ../src/bout++.cxx:868
+#: ../src/bout++.cxx:879
 msgid ""
 "Sim Time  |  RHS_e evals  | RHS_I evals  | Wall Time |  Calc    Inv   "
 "Comm    I/O   SOLVER\n"
@@ -800,18 +801,18 @@ msgstr ""
 "Komm    I/O   Integrator\n"
 "\n"
 
-#: ../src/solver/solver.cxx:506
+#: ../src/solver/solver.cxx:514
 #, fuzzy, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
 "Integriere mit einem `Monitor`-Zeitschritt von {1:e} für {0:d} Aufrufe.\n"
 
-#: ../src/solver/solver.cxx:502
+#: ../src/solver/solver.cxx:510
 #, fuzzy, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr "Integriere {:d} Zeitschritte von je {:e}\n"
 
-#: ../src/solver/solver.cxx:781
+#: ../src/solver/solver.cxx:788
 #, fuzzy, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
@@ -820,7 +821,7 @@ msgstr ""
 "Der Integrator kann den Zeitschritt nicht von {:g} auf {:g} reduzieren, "
 "nachdem er initialisiert wurde!"
 
-#: ../src/solver/solver.cxx:1281
+#: ../src/solver/solver.cxx:1289
 #, fuzzy, c++-format
 msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
@@ -829,27 +830,27 @@ msgstr ""
 "Die zeitliche Ableitung ist an der falschen Stelle. Das Feld '{2:s}' ist an "
 "Position {0:s}, während die Ableitung an Position {1:s} ist.\n"
 
-#: ../src/solver/solver.cxx:1480
+#: ../src/solver/solver.cxx:1494
 #, fuzzy, c++-format
 msgid "Time derivative for variable '{:s}' not set"
 msgstr "Zeitliche Ableitung für Variable '{:s}' nicht gesetzt"
 
-#: ../src/mesh/mesh.cxx:605
+#: ../src/mesh/mesh.cxx:638
 #, fuzzy, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
 msgstr "Die Region '{:s}' ist bereits vorhanden in der regionMap2D"
 
-#: ../src/mesh/mesh.cxx:595
+#: ../src/mesh/mesh.cxx:614
 #, fuzzy, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
 msgstr "Die Region '{:s}' ist bereits vorhanden in der regionMap3D"
 
-#: ../src/mesh/mesh.cxx:616
+#: ../src/mesh/mesh.cxx:649
 #, fuzzy, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
 msgstr "Die Region '{:s}' ist bereits vorhanden in der regionMapPerp"
 
-#: ../src/sys/options.cxx:99 ../src/sys/options.cxx:138
+#: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
 #, c++-format
 msgid ""
 "Trying to index Option '{0}' with '{1}', but '{0}' is a value, not a "
@@ -858,7 +859,7 @@ msgid ""
 "rename one of them.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:1462
+#: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
@@ -866,31 +867,31 @@ msgstr ""
 "Unbekannte Paralleltransformation\n"
 "Gültige Optionen sind 'identity', 'shifted', 'fci'"
 
-#: ../src/sys/options.cxx:872
+#: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
 msgstr "Ungenutzte Optionen:\n"
 
-#: ../src/bout++.cxx:439
+#: ../src/bout++.cxx:446
 #, fuzzy, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
 msgstr "Benutzung: {:s} -d <Datenordner>\n"
 
-#: ../src/bout++.cxx:448
+#: ../src/bout++.cxx:455
 #, fuzzy, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
 msgstr "Benutzung: {:s} -f <Optionendatei>\n"
 
-#: ../src/bout++.cxx:466
+#: ../src/bout++.cxx:473
 #, fuzzy, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
 msgstr "Benutzung: {:s} -f <Logdatei>\n"
 
-#: ../src/bout++.cxx:457
+#: ../src/bout++.cxx:464
 #, fuzzy, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
 msgstr "Benutzung: {:s} -f <Einstellungsdatei>\n"
 
-#: ../src/bout++.cxx:353
+#: ../src/bout++.cxx:360
 #, fuzzy, c++-format
 msgid "Usage is {} {} <name>\n"
 msgstr "Benutzung: {:s} -f <Logdatei>\n"
@@ -901,7 +902,7 @@ msgstr ""
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
-#: ../src/bout++.cxx:367
+#: ../src/bout++.cxx:374
 #, fuzzy, c++-format
 msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
@@ -911,68 +912,73 @@ msgstr ""
 "[VAR=WERT]\n"
 
 #. restart file should be written by physics model
-#: ../src/solver/solver.cxx:921
+#: ../src/solver/solver.cxx:927
 #, fuzzy
 msgid "User signalled to quit. Returning\n"
 msgstr "Beendigung durch Monitor\n"
 
-#: ../src/sys/options.cxx:373
+#: ../src/sys/options.cxx:486
+#, fuzzy, c++-format
+msgid "Value for option {:s} = {:e} is not a bool"
+msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
+
+#: ../src/sys/options.cxx:426
 #, fuzzy, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
-#: ../src/sys/options.cxx:408
+#: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
 msgstr ""
 
-#: ../src/sys/options.cxx:581
+#: ../src/sys/options.cxx:623
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
-#: ../src/sys/options.cxx:529
+#: ../src/sys/options.cxx:571
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
-#: ../src/sys/options.cxx:663
+#: ../src/sys/options.cxx:705
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
-#: ../src/sys/options.cxx:451
+#: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
 msgstr ""
 
-#: ../src/sys/options.cxx:709
+#: ../src/sys/options.cxx:751
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
-#: ../src/sys/options.cxx:736
+#: ../src/sys/options.cxx:773
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
-#: ../src/sys/options.cxx:763
+#: ../src/sys/options.cxx:795
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
 #. Another type which can't be converted
-#: ../src/sys/options.cxx:365
+#: ../src/sys/options.cxx:418
 #, fuzzy, c++-format
 msgid "Value for option {:s} is not an integer"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
-#: ../src/solver/solver.cxx:1232 ../src/solver/solver.cxx:1238
+#: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
 #, fuzzy, c++-format
 msgid "Variable '{:s}' not initialised"
 msgstr "Variable '{:s}' ist nicht initialisiert"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:431
+#: ../src/mesh/impls/bout/boutmesh.cxx:467
 #, fuzzy, c++-format
 msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
@@ -981,27 +987,27 @@ msgstr ""
 "WARNUNG: Anzahl der toroidalen Punkte sollte 2^n für effiziente FFTs sein. "
 "Ändere MZ falls FFTs verwendet werden\n"
 
-#: ../src/mesh/coordinates.cxx:633
+#: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:410
+#: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:638
+#: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:415
+#: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
 
-#: ../src/bout++.cxx:814
+#: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
 msgstr ""
 
@@ -1011,10 +1017,18 @@ msgid "Writing options to file {:s}\n"
 msgstr "Optionen werden in {:s} gespeichert\n"
 
 #. / The source label given to default values
-#: ../src/sys/options.cxx:15
+#: ../src/sys/options.cxx:34
 msgid "default"
 msgstr "Vorgabe"
 
+#, fuzzy, c++-format
+#~ msgid "\tOpenMP parallelisation {}"
+#~ msgstr "\tOpenMP Parallelisierung ist deaktiviert\n"
+
+#, fuzzy, c++-format
+#~ msgid "\tOption '{:s}': Boolean expected. Got '{:s}'\n"
+#~ msgstr "\tOption '{:s}': Boolscherwert erwartet, '{:s}' gefunden\n"
+
 #~ msgid "\tChecking disabled\n"
 #~ msgstr "\tChecks sind deaktiviert\n"
 
@@ -1022,10 +1036,6 @@ msgstr "Vorgabe"
 #~ msgid "\tChecking enabled, level {:d}\n"
 #~ msgstr "\tChecks der Stufe {:d} sind aktiviert\n"
 
-#, fuzzy
-#~ msgid "\tOpenMP parallelisation enabled, using {:d} threads\n"
-#~ msgstr "\tOpenMP Parallelisierung mit {:d} Threads ist aktiviert\n"
-
 #~ msgid "\tSignal handling enabled\n"
 #~ msgstr "\tSignalverarbeitung ist aktiviert\n"
 
@@ -1051,8 +1061,8 @@ msgstr "Vorgabe"
 #~ "überschrieben. Benötigt `restart`\n"
 #~ "  VAR=WERT  \t\tSetzt den Wert WERT für die Variable VAR\n"
 #~ "\n"
-#~ "Weitere Eingabeparameter sind in dem Manual und dem Quellcode (z.B. {:s}."
-#~ "cxx) des Physikmoduls definiert.\n"
+#~ "Weitere Eingabeparameter sind in dem Manual und dem Quellcode (z.B. "
+#~ "{:s}.cxx) des Physikmoduls definiert.\n"
 
 #, fuzzy
 #~ msgid "Couldn't get BoutReal from option {:s} = '{:s}'"
diff --git a/locale/es/libbout.po b/locale/es/libbout.po
index 8a3b22be61..68db78ada9 100644
--- a/locale/es/libbout.po
+++ b/locale/es/libbout.po
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: BOUT++ 4.2.1\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2024-09-12 09:17+0100\n"
+"POT-Creation-Date: 2025-08-13 23:37+0100\n"
 "PO-Revision-Date: 2019-02-11 12:46+0900\n"
 "Last-Translator: Marta <mpee500@york.ac.uk>\n"
 "Language-Team: Spanish\n"
@@ -16,7 +16,7 @@ msgstr ""
 "Content-Type: text/plain; charset=utf-8\n"
 "Content-Transfer-Encoding: 8bit\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:191
+#: ../src/mesh/impls/bout/boutmesh.cxx:182
 #, fuzzy, c++-format
 msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
@@ -25,7 +25,7 @@ msgstr ""
 "\t -> La región `Core` jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) debe ser un "
 "múltiplo de MYSUB ({:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:224
+#: ../src/mesh/impls/bout/boutmesh.cxx:215
 #, fuzzy, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
@@ -34,7 +34,7 @@ msgstr ""
 "\t -> La región `Core` jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) debe ser un "
 "múltiplo de MYSUB ({:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:199
+#: ../src/mesh/impls/bout/boutmesh.cxx:190
 #, fuzzy, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
@@ -43,11 +43,11 @@ msgstr ""
 "\t -> La región `Core` jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) debe ser un "
 "múltiplo de MYSUB ({:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:309
+#: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
 msgstr "\t -> El valor es bueno\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:180
+#: ../src/mesh/impls/bout/boutmesh.cxx:171
 #, fuzzy, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
@@ -55,7 +55,7 @@ msgstr ""
 "\t -> La región `Leg` jyseps1_1+1 ({:d}) debe ser un múltiplo de MYSUB "
 "({:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:215
+#: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, fuzzy, c++-format
 msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
@@ -64,7 +64,7 @@ msgstr ""
 "\t -> La región `Leg` jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) debe ser un "
 "múltiplo de MYSUB ({:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:232
+#: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, fuzzy, c++-format
 msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
@@ -73,7 +73,7 @@ msgstr ""
 "\t -> La región `Leg` ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) debe ser un "
 "múltiplo de MYSUB ({:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:208
+#: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, fuzzy, c++-format
 msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
@@ -82,12 +82,17 @@ msgstr ""
 "\t -> La región `Leg` ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) debe ser un "
 "múltiplo de MYSUB ({:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:175
+#: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, fuzzy, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
 msgstr "\t -> ny/NYPE ({:d}/{:d} = {:d}) debe ser >= MYG ({:d})\n"
 
 #: ../src/bout++.cxx:575
+#, fuzzy, c++-format
+msgid "\tADIOS2 support {}\n"
+msgstr "\tSoporte netCDF activado\n"
+
+#: ../src/bout++.cxx:583
 #, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
@@ -96,28 +101,28 @@ msgstr ""
 #. Processors divide equally
 #. Mesh in X divides equally
 #. Mesh in Y divides equally
-#: ../src/mesh/impls/bout/boutmesh.cxx:297
+#: ../src/mesh/impls/bout/boutmesh.cxx:288
 #, fuzzy, c++-format
 msgid "\tCandidate value: {:d}\n"
 msgstr "\tValor candidato: {:d}\n"
 
-#: ../src/bout++.cxx:576
+#: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:594
+#: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
 msgstr "\tParámetros de línea de comandos para esta ejecución :"
 
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
-#: ../src/bout++.cxx:590
+#: ../src/bout++.cxx:595
 #, fuzzy, c++-format
 msgid "\tCompiled with flags : {:s}\n"
 msgstr "\tCompilado con las opciones `flags` : {:s}\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:324
+#: ../src/mesh/impls/bout/boutmesh.cxx:315
 #, fuzzy, c++-format
 msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
@@ -126,14 +131,14 @@ msgstr ""
 "\tDominio separado (NXPE={:d}, NYPE={:d}) en los dominios (localNx={:d}, "
 "localNy={:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:364
+#: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, fuzzy, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
 "\tERROR: No se pueden separar {:d} Y puntos entre {:d} procesadores por "
 "igual\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:372
+#: ../src/mesh/impls/bout/boutmesh.cxx:365
 #, fuzzy, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
@@ -154,31 +159,31 @@ msgstr ""
 msgid "\tEmpty key or value in command line '{:s}'\n"
 msgstr "\tEntrada o valor vacío en la línea de comandos '{:s}'\n"
 
-#: ../src/bout++.cxx:582
+#: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:561
+#: ../src/bout++.cxx:568
 #, fuzzy, c++-format
 msgid "\tFFT support {}\n"
 msgstr "\tSoporte netCDF activado\n"
 
-#: ../src/bout++.cxx:585
+#: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:583
+#: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:440
+#: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
 msgstr "\tTamaño de la malla (`grid`): "
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:463
+#: ../src/mesh/impls/bout/boutmesh.cxx:499
 #, fuzzy
 msgid "\tGuard cells (x,y,z): "
 msgstr "\tProteger celdas (x,y): "
@@ -192,17 +197,17 @@ msgstr ""
 "\tLa entrada no debe contener el carácter ':'\n"
 "\tLínea: {:s}"
 
-#: ../src/bout++.cxx:563
+#: ../src/bout++.cxx:570
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:586
+#: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:560
+#: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
@@ -212,98 +217,95 @@ msgstr ""
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
 msgstr "\tMutilples '=' en el argumento de la línea de comandos '{:s}'\n"
 
-#: ../src/bout++.cxx:562
+#: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:567
+#: ../src/bout++.cxx:574
 #, fuzzy, c++-format
 msgid "\tNetCDF support {}{}\n"
 msgstr "\tSoporte netCDF activado\n"
 
-#: ../src/bout++.cxx:577
+#: ../src/bout++.cxx:585
 #, fuzzy, c++-format
-msgid "\tOpenMP parallelisation {}"
-msgstr "\tParalelización en OpenMP desactivada\n"
+msgid "\tOpenMP parallelisation {}, using {} threads\n"
+msgstr ""
+"\tParalelización en OpenMP activada, usando {:d} procesos (`threads`)\n"
 
 #. Mark the option as used
 #. Option not found
-#: ../src/sys/options.cxx:311 ../src/sys/options.cxx:380
-#: ../src/sys/options.cxx:415 ../src/sys/options.cxx:457
-#: ../src/sys/options.cxx:717 ../src/sys/options.cxx:744
-#: ../src/sys/options.cxx:771 ../include/bout/options.hxx:516
-#: ../include/bout/options.hxx:549 ../include/bout/options.hxx:573
-#: ../include/bout/options.hxx:820
+#: ../include/bout/options.hxx:586 ../include/bout/options.hxx:619
+#: ../include/bout/options.hxx:643 ../include/bout/options.hxx:896
 msgid "\tOption "
 msgstr "\tOpción "
 
-#: ../src/sys/options.cxx:447
+#: ../src/sys/options.cxx:369
 #, fuzzy, c++-format
-msgid "\tOption '{:s}': Boolean expected. Got '{:s}'\n"
-msgstr "\tOpción '{:s}': valor Booleano esperado. Se obtuvo '{:s}'\n"
+msgid "\tOption {} = {}"
+msgstr "\tOpción "
 
 #: ../src/sys/options/options_ini.cxx:70
 #, fuzzy, c++-format
 msgid "\tOptions file '{:s}' not found\n"
 msgstr "\tOpciones de archivo '{:s}' no encontrados\n"
 
-#: ../src/bout++.cxx:568
+#: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:571
+#: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:557
+#: ../src/bout++.cxx:564
 msgid "\tParallel NetCDF support disabled\n"
 msgstr "\tSoporte para NetCDF paralelo desactivado\n"
 
-#: ../src/bout++.cxx:555
+#: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
 msgstr "\tSoporte para NetCDF paralelo activado\n"
 
-#: ../src/bout++.cxx:569
+#: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:437
+#: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
 msgstr "\tLeer nz del archivo input de la malla `grid`\n"
 
-#: ../src/mesh/mesh.cxx:238
+#: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
 msgstr "\tLeyendo vector contravariante "
 
-#: ../src/mesh/mesh.cxx:231 ../src/mesh/mesh.cxx:252
+#: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
 msgstr "\tLeyendo vector covariante "
 
-#: ../src/bout++.cxx:548
+#: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
 msgstr ""
 
-#: ../src/bout++.cxx:573
+#: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:574
+#: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:572
+#: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:584
+#: ../src/bout++.cxx:589
 #, fuzzy, c++-format
 msgid "\tSignal handling support {}\n"
 msgstr "\tGestión de señal desactivada\n"
@@ -313,7 +315,7 @@ msgstr "\tGestión de señal desactivada\n"
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:577
+#: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
 msgstr "\tlisto\n"
 
@@ -323,7 +325,7 @@ msgid ""
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
 
-#: ../src/bout++.cxx:371
+#: ../src/bout++.cxx:378
 #, fuzzy
 msgid ""
 "\n"
@@ -343,7 +345,7 @@ msgstr ""
 "  -v, --verbose\t\tAumentar verbosidad\n"
 "  -q, --quiet\t\tDisminuir verbosidad\n"
 
-#: ../src/sys/expressionparser.cxx:302
+#: ../src/sys/expressionparser.cxx:341
 #, c++-format
 msgid ""
 "\n"
@@ -351,7 +353,7 @@ msgid ""
 "  Did you mean '{0}'?"
 msgstr ""
 
-#: ../src/solver/solver.cxx:580
+#: ../src/solver/solver.cxx:586
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -360,7 +362,7 @@ msgstr ""
 "\n"
 "Ejecución finalizada en  : {:s}\n"
 
-#: ../src/solver/solver.cxx:532
+#: ../src/solver/solver.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -372,7 +374,7 @@ msgstr ""
 #. Raw string to help with the formatting of the message, and a
 #. separate variable so clang-format doesn't barf on the
 #. exception
-#: ../src/sys/options.cxx:1102
+#: ../src/sys/options.cxx:1158
 msgid ""
 "\n"
 "There were unused input options:\n"
@@ -400,7 +402,7 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/bout++.cxx:382
+#: ../src/bout++.cxx:389
 #, c++-format
 msgid ""
 "  --print-config\t\tPrint the compile-time configuration\n"
@@ -433,57 +435,57 @@ msgid ""
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
 
-#: ../src/bout++.cxx:379
+#: ../src/bout++.cxx:386
 #, fuzzy
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
 msgstr "  -c, --color\t\tSalida de color usando bout-log-color\n"
 
-#: ../include/bout/options.hxx:823
+#: ../include/bout/options.hxx:899
 msgid ") overwritten with:"
 msgstr ""
 
-#: ../src/bout++.cxx:550
+#: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
 msgstr ""
 
-#: ../src/bout++.cxx:579
-#, c++-format
-msgid ", using {} threads"
-msgstr ""
-
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
 msgstr ""
 
-#: ../src/sys/options.cxx:868
+#: ../src/sys/options.cxx:895
 msgid "All options used\n"
 msgstr "Usando todas las opciones\n"
 
-#: ../src/bout++.cxx:528
+#: ../src/bout++.cxx:535
 #, fuzzy, c++-format
 msgid "BOUT++ version {:s}\n"
 msgstr "Versión de BOUT++ {:s}\n"
 
-#: ../src/bout++.cxx:143
+#: ../src/bout++.cxx:147
 #, fuzzy
 msgid "Bad command line arguments:\n"
 msgstr "\tMutilples '=' en el argumento de la línea de comandos '{:s}'\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:559
+#: ../src/sys/expressionparser.cxx:192
+#, c++-format
+msgid "Boolean operator argument {:e} is not a bool"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
 msgstr "Regiones frontera en este procesador: "
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:355
+#: ../src/mesh/impls/bout/boutmesh.cxx:348
 #, fuzzy, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr "No se pueden dividir {:d} X points entre {:d} procesadores por igual\n"
 
-#: ../src/bout++.cxx:818
+#: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
 msgstr ""
 
-#: ../src/bout++.cxx:533
+#: ../src/bout++.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
@@ -496,7 +498,7 @@ msgstr ""
 msgid "Command line"
 msgstr "Línea de comandos"
 
-#: ../src/bout++.cxx:544 ../tests/unit/src/test_bout++.cxx:358
+#: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
 msgstr "Opciones de tiempo de compilación:\n"
 
@@ -505,16 +507,16 @@ msgstr "Opciones de tiempo de compilación:\n"
 msgid "Compiled with flags"
 msgstr "\tCompilado con las opciones `flags` : {:s}\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:568
+#: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
 msgstr "Construyendo regiones por defecto"
 
-#: ../src/bout++.cxx:520
+#: ../src/bout++.cxx:527
 #, fuzzy, c++-format
 msgid "Could not create PID file {:s}"
 msgstr "No se pudo abrir el archivo de salida `output` '{:s}'\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:318
+#: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
 msgstr ""
@@ -526,30 +528,30 @@ msgstr ""
 msgid "Could not open output file '{:s}'\n"
 msgstr "No se pudo abrir el archivo de salida `output` '{:s}'\n"
 
-#: ../src/bout++.cxx:652
+#: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
 msgstr ""
 
 #. Error reading
-#: ../src/mesh/mesh.cxx:532
+#: ../src/mesh/mesh.cxx:543
 #, fuzzy, c++-format
 msgid "Could not read integer array '{:s}'\n"
 msgstr "No se pudo leer la matriz de enteros '{:s}'\n"
 
 #. Failed . Probably not important enough to stop the simulation
-#: ../src/bout++.cxx:632
+#: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
 "No se pudo ejecutar bout-log-color. Asegúrese de que se encuentre en su "
 "PATH\n"
 
-#: ../src/solver/solver.cxx:765
+#: ../src/solver/solver.cxx:772
 #, fuzzy, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
 msgstr "No se pudo añadir el Monitor: {:g} no és multiplo de {:g}!"
 
-#: ../src/sys/expressionparser.cxx:273
+#: ../src/sys/expressionparser.cxx:312
 #, c++-format
 msgid ""
 "Couldn't find generator '{}'. BOUT++ expressions are now case-sensitive, so "
@@ -558,69 +560,69 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:568
+#: ../src/mesh/mesh.cxx:587
 #, fuzzy, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
 msgstr "No se pudo encontrar la región {:s} en regionMap2D"
 
-#: ../src/mesh/mesh.cxx:560
+#: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
 #, fuzzy, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
 msgstr "No se pudo encontrar la región {:s} en regionMap2D"
 
-#: ../src/mesh/mesh.cxx:576
+#: ../src/mesh/mesh.cxx:595
 #, fuzzy, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
 msgstr "No se pudo encontrar la región {:s} en regionMapPerp"
 
 #. Convert any exceptions to something a bit more useful
-#: ../src/sys/options.cxx:336
+#: ../src/sys/options.cxx:361
 #, fuzzy, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
 msgstr "No se pudo recuperar el entero de la opción {:s} = '{:s}'"
 
-#: ../src/bout++.cxx:508
+#: ../src/bout++.cxx:515
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
 msgstr "DataDir \"{:s}\" no existe o no es accessible\n"
 
-#: ../src/bout++.cxx:505
+#: ../src/bout++.cxx:512
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
 msgstr "DataDir \"{:s}\" no es un directorio\n"
 
-#: ../src/solver/solver.cxx:665
+#: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
 msgstr "ERROR: el Solver ya se encuentra inicializado\n"
 
-#: ../src/bout++.cxx:209
+#: ../src/bout++.cxx:216
 #, fuzzy, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
 msgstr "Error encontrado durante la inicialización:{:s}\n"
 
-#: ../src/bout++.cxx:744
+#: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
 msgstr "Error durante el paso de opciones"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:332
+#: ../src/mesh/impls/bout/boutmesh.cxx:323
 #, fuzzy, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
 msgstr "Error: nx debe ser mayor que 2 veces MXG (2 * {:d})"
 
-#: ../src/solver/solver.cxx:512
+#: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
 msgstr "Fallo en inicializar el solver-> Abortando\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:290
+#: ../src/mesh/impls/bout/boutmesh.cxx:281
 #, fuzzy, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
 msgstr "Encontrando valor para NXPE (ideal = {:f})\n"
 
-#: ../src/solver/solver.cxx:668
+#: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
 msgstr "Initializando el solver\n"
 
-#: ../src/bout++.cxx:494
+#: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
@@ -633,48 +635,48 @@ msgstr ""
 msgid "Invalid command line option '-' found - maybe check whitespace?"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:400
+#: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
 msgstr "Cargando malla `mesh`"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:415
+#: ../src/mesh/impls/bout/boutmesh.cxx:451
 msgid "Mesh must contain nx"
 msgstr "La malla `mesh` debe contener nx"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:419
+#: ../src/mesh/impls/bout/boutmesh.cxx:455
 msgid "Mesh must contain ny"
 msgstr "La malla `mesh` debe contener ny"
 
 #. Not found
-#: ../src/mesh/mesh.cxx:536
+#: ../src/mesh/mesh.cxx:547
 #, fuzzy, c++-format
 msgid "Missing integer array {:s}\n"
 msgstr "Fala la matriz entera {:s}\n"
 
-#: ../src/solver/solver.cxx:905
+#: ../src/solver/solver.cxx:911
 #, fuzzy, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
 msgstr "Monitor indicó salir\n"
 
-#: ../src/solver/solver.cxx:883
+#: ../src/solver/solver.cxx:889
 #, fuzzy, c++-format
 msgid "Monitor signalled to quit (return code {})"
 msgstr "Monitor indicó salir"
 
-#: ../src/bout++.cxx:823
+#: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:565
+#: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
 msgstr "Sin regiones de frontera en este procesador"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:550
+#: ../src/mesh/impls/bout/boutmesh.cxx:586
 #, fuzzy
 msgid "No boundary regions; domain is periodic\n"
 msgstr "Sin regiones de frontera en este procesador"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:254
+#: ../src/mesh/impls/bout/boutmesh.cxx:245
 #, fuzzy, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
@@ -682,7 +684,7 @@ msgstr ""
 "Número de procesadores ({:d}) no divisible para NPs en la dirección x "
 "({:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:267
+#: ../src/mesh/impls/bout/boutmesh.cxx:258
 #, fuzzy, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
@@ -691,26 +693,26 @@ msgstr ""
 "({:d})\n"
 
 #. Less than 2 time-steps left
-#: ../src/bout++.cxx:896
+#: ../src/bout++.cxx:908
 #, fuzzy, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
 msgstr "Solo faltan {:e} segundos. Saliendo\n"
 
-#: ../src/sys/options.cxx:303 ../src/sys/options.cxx:345
-#: ../src/sys/options.cxx:393 ../src/sys/options.cxx:428
-#: ../src/sys/options.cxx:703 ../src/sys/options.cxx:730
-#: ../src/sys/options.cxx:757
+#: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
+#: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
+#: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
+#: ../src/sys/options.cxx:789
 #, fuzzy, c++-format
 msgid "Option {:s} has no value"
 msgstr "Opción {:s} sin valor"
 
 #. Doesn't exist
-#: ../src/sys/options.cxx:159
+#: ../src/sys/options.cxx:172
 #, fuzzy, c++-format
 msgid "Option {:s}:{:s} does not exist"
 msgstr "Opción {:s}:{:s} no existe"
 
-#: ../include/bout/options.hxx:828
+#: ../include/bout/options.hxx:904
 #, fuzzy, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
@@ -719,12 +721,12 @@ msgstr ""
 "Opciones: Cambiando valor de la misma fuente ({:s}) al valor nuevo '{:s}' - "
 "valor anterior era '{:s}'."
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:552
+#: ../src/mesh/impls/bout/boutmesh.cxx:588
 #, fuzzy
 msgid "Possible boundary regions are: "
 msgstr "Sin regiones de frontera en este procesador"
 
-#: ../src/bout++.cxx:538
+#: ../src/bout++.cxx:545
 #, fuzzy, c++-format
 msgid ""
 "Processor number: {:d} of {:d}\n"
@@ -733,32 +735,32 @@ msgstr ""
 "Procesador número: {:d} de {:d}\n"
 "\n"
 
-#: ../src/mesh/mesh.cxx:609
+#: ../src/mesh/mesh.cxx:642
 #, fuzzy, c++-format
 msgid "Registered region 2D {:s}"
 msgstr "Región 2D registrada {:s}"
 
-#: ../src/mesh/mesh.cxx:599
+#: ../src/mesh/mesh.cxx:632
 #, fuzzy, c++-format
 msgid "Registered region 3D {:s}"
 msgstr "Región 3D registrada {:s}"
 
-#: ../src/mesh/mesh.cxx:619
+#: ../src/mesh/mesh.cxx:652
 #, fuzzy, c++-format
 msgid "Registered region Perp {:s}"
 msgstr "Región Perp registrada {:s}"
 
-#: ../src/bout++.cxx:529
+#: ../src/bout++.cxx:536
 #, fuzzy, c++-format
 msgid "Revision: {:s}\n"
 msgstr "Revisión: {:s}\n"
 
-#: ../src/solver/solver.cxx:581
+#: ../src/solver/solver.cxx:587
 msgid "Run time : "
 msgstr "Tiempo de ejecución : "
 
 #. / Run the solver
-#: ../src/solver/solver.cxx:525
+#: ../src/solver/solver.cxx:533
 msgid ""
 "Running simulation\n"
 "\n"
@@ -770,7 +772,7 @@ msgstr ""
 msgid "Signal"
 msgstr ""
 
-#: ../src/bout++.cxx:865
+#: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
@@ -779,7 +781,7 @@ msgstr ""
 "SOLVER\n"
 "\n"
 
-#: ../src/bout++.cxx:868
+#: ../src/bout++.cxx:879
 msgid ""
 "Sim Time  |  RHS_e evals  | RHS_I evals  | Wall Time |  Calc    Inv   "
 "Comm    I/O   SOLVER\n"
@@ -789,21 +791,21 @@ msgstr ""
 "Com    I/O   SOLVER\n"
 "\n"
 
-#: ../src/solver/solver.cxx:506
+#: ../src/solver/solver.cxx:514
 #, fuzzy, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
 "Solver corriendo para {:d} outputs con intervalos de tiempo de monitor de "
 "{:e}\n"
 
-#: ../src/solver/solver.cxx:502
+#: ../src/solver/solver.cxx:510
 #, fuzzy, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr ""
 "Solver corriendo para {:d} outputs con intervalos de tiempo de output de "
 "{:e}\n"
 
-#: ../src/solver/solver.cxx:781
+#: ../src/solver/solver.cxx:788
 #, fuzzy, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
@@ -812,7 +814,7 @@ msgstr ""
 "Solver::addMonitor: No se puedo reducir el intervalo de tiempo (de {:g} a "
 "{:g}) después de que init fuera llamado!"
 
-#: ../src/solver/solver.cxx:1281
+#: ../src/solver/solver.cxx:1289
 #, fuzzy, c++-format
 msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
@@ -821,27 +823,27 @@ msgstr ""
 "Derivada del tiempo en lugar erróneo - El field se encuentra en  {:s}, la "
 "derivada se encuentra en {:s} para el field '{:s}'\n"
 
-#: ../src/solver/solver.cxx:1480
+#: ../src/solver/solver.cxx:1494
 #, fuzzy, c++-format
 msgid "Time derivative for variable '{:s}' not set"
 msgstr "Derivada del tiempo para la variable '{:s}' no fijada"
 
-#: ../src/mesh/mesh.cxx:605
+#: ../src/mesh/mesh.cxx:638
 #, fuzzy, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
 msgstr "Intentando añadir una región ya existente {:s} a regionMap2D"
 
-#: ../src/mesh/mesh.cxx:595
+#: ../src/mesh/mesh.cxx:614
 #, fuzzy, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
 msgstr "Intentando añadir una región ya existente {:s} a regionMap3D"
 
-#: ../src/mesh/mesh.cxx:616
+#: ../src/mesh/mesh.cxx:649
 #, fuzzy, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
 msgstr "Intentando añadir una región ya existente {:s} a regionMapPerp"
 
-#: ../src/sys/options.cxx:99 ../src/sys/options.cxx:138
+#: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
 #, c++-format
 msgid ""
 "Trying to index Option '{0}' with '{1}', but '{0}' is a value, not a "
@@ -850,7 +852,7 @@ msgid ""
 "rename one of them.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:1462
+#: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
@@ -858,31 +860,31 @@ msgstr ""
 "Opción paralleltransform desconocida.\n"
 "Opciones válidas son 'identity', 'shifted', 'fci'"
 
-#: ../src/sys/options.cxx:872
+#: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
 msgstr "Opciones sin usar:\n"
 
-#: ../src/bout++.cxx:439
+#: ../src/bout++.cxx:446
 #, fuzzy, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
 msgstr "Correcto uso es {:s} -d <data directory>\n"
 
-#: ../src/bout++.cxx:448
+#: ../src/bout++.cxx:455
 #, fuzzy, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
 msgstr "Correcto uso es {:s} -f <options filename>\n"
 
-#: ../src/bout++.cxx:466
+#: ../src/bout++.cxx:473
 #, fuzzy, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
 msgstr "Correcto uso es {:s} -l <log filename>\n"
 
-#: ../src/bout++.cxx:457
+#: ../src/bout++.cxx:464
 #, fuzzy, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
 msgstr "Correcto uso es {:s} -o <settings filename>\n"
 
-#: ../src/bout++.cxx:353
+#: ../src/bout++.cxx:360
 #, fuzzy, c++-format
 msgid "Usage is {} {} <name>\n"
 msgstr "Correcto uso es {:s} -l <log filename>\n"
@@ -893,7 +895,7 @@ msgstr ""
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
-#: ../src/bout++.cxx:367
+#: ../src/bout++.cxx:374
 #, fuzzy, c++-format
 msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
@@ -903,68 +905,73 @@ msgstr ""
 "[VAR=VALUE]\n"
 
 #. restart file should be written by physics model
-#: ../src/solver/solver.cxx:921
+#: ../src/solver/solver.cxx:927
 #, fuzzy
 msgid "User signalled to quit. Returning\n"
 msgstr "Monitor indicó salir\n"
 
-#: ../src/sys/options.cxx:373
+#: ../src/sys/options.cxx:486
+#, fuzzy, c++-format
+msgid "Value for option {:s} = {:e} is not a bool"
+msgstr "Valor para la opción {:s} = {:e} no es un entero"
+
+#: ../src/sys/options.cxx:426
 #, fuzzy, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
-#: ../src/sys/options.cxx:408
+#: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
 msgstr ""
 
-#: ../src/sys/options.cxx:581
+#: ../src/sys/options.cxx:623
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
-#: ../src/sys/options.cxx:529
+#: ../src/sys/options.cxx:571
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
-#: ../src/sys/options.cxx:663
+#: ../src/sys/options.cxx:705
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
-#: ../src/sys/options.cxx:451
+#: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
 msgstr ""
 
-#: ../src/sys/options.cxx:709
+#: ../src/sys/options.cxx:751
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
-#: ../src/sys/options.cxx:736
+#: ../src/sys/options.cxx:773
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
-#: ../src/sys/options.cxx:763
+#: ../src/sys/options.cxx:795
 #, fuzzy, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
 #. Another type which can't be converted
-#: ../src/sys/options.cxx:365
+#: ../src/sys/options.cxx:418
 #, fuzzy, c++-format
 msgid "Value for option {:s} is not an integer"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
-#: ../src/solver/solver.cxx:1232 ../src/solver/solver.cxx:1238
+#: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
 #, fuzzy, c++-format
 msgid "Variable '{:s}' not initialised"
 msgstr "Variable '{:s}' sin inicializar"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:431
+#: ../src/mesh/impls/bout/boutmesh.cxx:467
 #, fuzzy, c++-format
 msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
@@ -973,27 +980,27 @@ msgstr ""
 "WARNING: el número de puntos toroidales debería ser 2^n para una FFT "
 "eficiente -- considere cambiar MZ si se usan FFTs\n"
 
-#: ../src/mesh/coordinates.cxx:633
+#: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:410
+#: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:638
+#: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:415
+#: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
 
-#: ../src/bout++.cxx:814
+#: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
 msgstr ""
 
@@ -1003,10 +1010,18 @@ msgid "Writing options to file {:s}\n"
 msgstr "Escribiendo opciones a archivo {:s}\n"
 
 #. / The source label given to default values
-#: ../src/sys/options.cxx:15
+#: ../src/sys/options.cxx:34
 msgid "default"
 msgstr "por defecto"
 
+#, fuzzy, c++-format
+#~ msgid "\tOpenMP parallelisation {}"
+#~ msgstr "\tParalelización en OpenMP desactivada\n"
+
+#, fuzzy, c++-format
+#~ msgid "\tOption '{:s}': Boolean expected. Got '{:s}'\n"
+#~ msgstr "\tOpción '{:s}': valor Booleano esperado. Se obtuvo '{:s}'\n"
+
 #~ msgid "\tChecking disabled\n"
 #~ msgstr "\tComprobación desactivada\n"
 
@@ -1014,11 +1029,6 @@ msgstr "por defecto"
 #~ msgid "\tChecking enabled, level {:d}\n"
 #~ msgstr "\tComprobación activada, nivel {:d}\n"
 
-#, fuzzy
-#~ msgid "\tOpenMP parallelisation enabled, using {:d} threads\n"
-#~ msgstr ""
-#~ "\tParalelización en OpenMP activada, usando {:d} procesos (`threads`)\n"
-
 #~ msgid "\tSignal handling enabled\n"
 #~ msgstr "\tGestión de señal activada\n"
 
diff --git a/locale/fr/libbout.po b/locale/fr/libbout.po
index ae88b8953c..e9b5476696 100644
--- a/locale/fr/libbout.po
+++ b/locale/fr/libbout.po
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: BOUT++ 4.2.0\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2024-09-12 09:17+0100\n"
+"POT-Creation-Date: 2025-08-13 23:37+0100\n"
 "PO-Revision-Date: 2018-10-21 22:46+0100\n"
 "Last-Translator:  <benjamin.dudson@york.ac.uk>\n"
 "Language-Team: French\n"
@@ -17,65 +17,70 @@ msgstr ""
 "Content-Transfer-Encoding: 8bit\n"
 "Plural-Forms: nplurals=2; plural=(n > 1);\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:191
+#: ../src/mesh/impls/bout/boutmesh.cxx:182
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:224
+#: ../src/mesh/impls/bout/boutmesh.cxx:215
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:199
+#: ../src/mesh/impls/bout/boutmesh.cxx:190
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:309
+#: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:180
+#: ../src/mesh/impls/bout/boutmesh.cxx:171
 #, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:215
+#: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, c++-format
 msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:232
+#: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, c++-format
 msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:208
+#: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, c++-format
 msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:175
+#: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
 msgstr ""
 
 #: ../src/bout++.cxx:575
 #, c++-format
+msgid "\tADIOS2 support {}\n"
+msgstr ""
+
+#: ../src/bout++.cxx:583
+#, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
 
@@ -83,40 +88,40 @@ msgstr ""
 #. Processors divide equally
 #. Mesh in X divides equally
 #. Mesh in Y divides equally
-#: ../src/mesh/impls/bout/boutmesh.cxx:297
+#: ../src/mesh/impls/bout/boutmesh.cxx:288
 #, c++-format
 msgid "\tCandidate value: {:d}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:576
+#: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:594
+#: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
 msgstr ""
 
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
-#: ../src/bout++.cxx:590
+#: ../src/bout++.cxx:595
 #, c++-format
 msgid "\tCompiled with flags : {:s}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:324
+#: ../src/mesh/impls/bout/boutmesh.cxx:315
 #, c++-format
 msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:364
+#: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:372
+#: ../src/mesh/impls/bout/boutmesh.cxx:365
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
@@ -133,31 +138,31 @@ msgstr ""
 msgid "\tEmpty key or value in command line '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:582
+#: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:561
+#: ../src/bout++.cxx:568
 #, c++-format
 msgid "\tFFT support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:585
+#: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:583
+#: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:440
+#: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:463
+#: ../src/mesh/impls/bout/boutmesh.cxx:499
 msgid "\tGuard cells (x,y,z): "
 msgstr ""
 
@@ -168,17 +173,17 @@ msgid ""
 "\tLine: {:s}"
 msgstr ""
 
-#: ../src/bout++.cxx:563
+#: ../src/bout++.cxx:570
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:586
+#: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:560
+#: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
@@ -188,35 +193,31 @@ msgstr ""
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:562
+#: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:567
+#: ../src/bout++.cxx:574
 #, c++-format
 msgid "\tNetCDF support {}{}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:577
+#: ../src/bout++.cxx:585
 #, c++-format
-msgid "\tOpenMP parallelisation {}"
+msgid "\tOpenMP parallelisation {}, using {} threads\n"
 msgstr ""
 
 #. Mark the option as used
 #. Option not found
-#: ../src/sys/options.cxx:311 ../src/sys/options.cxx:380
-#: ../src/sys/options.cxx:415 ../src/sys/options.cxx:457
-#: ../src/sys/options.cxx:717 ../src/sys/options.cxx:744
-#: ../src/sys/options.cxx:771 ../include/bout/options.hxx:516
-#: ../include/bout/options.hxx:549 ../include/bout/options.hxx:573
-#: ../include/bout/options.hxx:820
+#: ../include/bout/options.hxx:586 ../include/bout/options.hxx:619
+#: ../include/bout/options.hxx:643 ../include/bout/options.hxx:896
 msgid "\tOption "
 msgstr ""
 
-#: ../src/sys/options.cxx:447
+#: ../src/sys/options.cxx:369
 #, c++-format
-msgid "\tOption '{:s}': Boolean expected. Got '{:s}'\n"
+msgid "\tOption {} = {}"
 msgstr ""
 
 #: ../src/sys/options/options_ini.cxx:70
@@ -224,62 +225,62 @@ msgstr ""
 msgid "\tOptions file '{:s}' not found\n"
 msgstr ""
 
-#: ../src/bout++.cxx:568
+#: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:571
+#: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:557
+#: ../src/bout++.cxx:564
 msgid "\tParallel NetCDF support disabled\n"
 msgstr ""
 
-#: ../src/bout++.cxx:555
+#: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
 msgstr ""
 
-#: ../src/bout++.cxx:569
+#: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:437
+#: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:238
+#: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:231 ../src/mesh/mesh.cxx:252
+#: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
 msgstr ""
 
-#: ../src/bout++.cxx:548
+#: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
 msgstr ""
 
-#: ../src/bout++.cxx:573
+#: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:574
+#: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:572
+#: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:584
+#: ../src/bout++.cxx:589
 #, fuzzy, c++-format
 msgid "\tSignal handling support {}\n"
 msgstr "\tTraitement du signal désactivé\n"
@@ -289,7 +290,7 @@ msgstr "\tTraitement du signal désactivé\n"
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:577
+#: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
 msgstr ""
 
@@ -299,7 +300,7 @@ msgid ""
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
 
-#: ../src/bout++.cxx:371
+#: ../src/bout++.cxx:378
 msgid ""
 "\n"
 "  -d <data directory>\t\tLook in <data directory> for input/output files\n"
@@ -310,7 +311,7 @@ msgid ""
 "  -q, --quiet\t\t\tDecrease verbosity\n"
 msgstr ""
 
-#: ../src/sys/expressionparser.cxx:302
+#: ../src/sys/expressionparser.cxx:341
 #, c++-format
 msgid ""
 "\n"
@@ -318,7 +319,7 @@ msgid ""
 "  Did you mean '{0}'?"
 msgstr ""
 
-#: ../src/solver/solver.cxx:580
+#: ../src/solver/solver.cxx:586
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -327,7 +328,7 @@ msgstr ""
 "\n"
 "L'exécution se termine à {:s}\n"
 
-#: ../src/solver/solver.cxx:532
+#: ../src/solver/solver.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -339,7 +340,7 @@ msgstr ""
 #. Raw string to help with the formatting of the message, and a
 #. separate variable so clang-format doesn't barf on the
 #. exception
-#: ../src/sys/options.cxx:1102
+#: ../src/sys/options.cxx:1158
 msgid ""
 "\n"
 "There were unused input options:\n"
@@ -367,7 +368,7 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/bout++.cxx:382
+#: ../src/bout++.cxx:389
 #, c++-format
 msgid ""
 "  --print-config\t\tPrint the compile-time configuration\n"
@@ -400,55 +401,55 @@ msgid ""
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
 
-#: ../src/bout++.cxx:379
+#: ../src/bout++.cxx:386
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
 msgstr ""
 
-#: ../include/bout/options.hxx:823
+#: ../include/bout/options.hxx:899
 msgid ") overwritten with:"
 msgstr ""
 
-#: ../src/bout++.cxx:550
+#: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
 msgstr ""
 
-#: ../src/bout++.cxx:579
-#, c++-format
-msgid ", using {} threads"
-msgstr ""
-
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
 msgstr ""
 
-#: ../src/sys/options.cxx:868
+#: ../src/sys/options.cxx:895
 msgid "All options used\n"
 msgstr ""
 
-#: ../src/bout++.cxx:528
+#: ../src/bout++.cxx:535
 #, c++-format
 msgid "BOUT++ version {:s}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:143
+#: ../src/bout++.cxx:147
 msgid "Bad command line arguments:\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:559
+#: ../src/sys/expressionparser.cxx:192
+#, c++-format
+msgid "Boolean operator argument {:e} is not a bool"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:355
+#: ../src/mesh/impls/bout/boutmesh.cxx:348
 #, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr ""
 
-#: ../src/bout++.cxx:818
+#: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
 msgstr ""
 
-#: ../src/bout++.cxx:533
+#: ../src/bout++.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
@@ -461,7 +462,7 @@ msgstr ""
 msgid "Command line"
 msgstr ""
 
-#: ../src/bout++.cxx:544 ../tests/unit/src/test_bout++.cxx:358
+#: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
 msgstr ""
 
@@ -469,16 +470,16 @@ msgstr ""
 msgid "Compiled with flags"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:568
+#: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
 msgstr ""
 
-#: ../src/bout++.cxx:520
+#: ../src/bout++.cxx:527
 #, c++-format
 msgid "Could not create PID file {:s}"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:318
+#: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
 msgstr ""
@@ -488,28 +489,28 @@ msgstr ""
 msgid "Could not open output file '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:652
+#: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
 msgstr ""
 
 #. Error reading
-#: ../src/mesh/mesh.cxx:532
+#: ../src/mesh/mesh.cxx:543
 #, c++-format
 msgid "Could not read integer array '{:s}'\n"
 msgstr ""
 
 #. Failed . Probably not important enough to stop the simulation
-#: ../src/bout++.cxx:632
+#: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:765
+#: ../src/solver/solver.cxx:772
 #, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
 msgstr ""
 
-#: ../src/sys/expressionparser.cxx:273
+#: ../src/sys/expressionparser.cxx:312
 #, c++-format
 msgid ""
 "Couldn't find generator '{}'. BOUT++ expressions are now case-sensitive, so "
@@ -518,70 +519,70 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:568
+#: ../src/mesh/mesh.cxx:587
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:560
+#: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:576
+#: ../src/mesh/mesh.cxx:595
 #, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
 msgstr ""
 
 #. Convert any exceptions to something a bit more useful
-#: ../src/sys/options.cxx:336
+#: ../src/sys/options.cxx:361
 #, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
 msgstr ""
 
-#: ../src/bout++.cxx:508
+#: ../src/bout++.cxx:515
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
 msgstr ""
 "Le répertoire de données \"{:s}\" n'existe pas ou n'est pas accessible\n"
 
-#: ../src/bout++.cxx:505
+#: ../src/bout++.cxx:512
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
 msgstr "\"{:s}\" n'est pas un répertoire\n"
 
-#: ../src/solver/solver.cxx:665
+#: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
 msgstr ""
 
-#: ../src/bout++.cxx:209
+#: ../src/bout++.cxx:216
 #, fuzzy, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
 msgstr "Erreur rencontrée lors de l'initialisation : {:s}\n"
 
-#: ../src/bout++.cxx:744
+#: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:332
+#: ../src/mesh/impls/bout/boutmesh.cxx:323
 #, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
 msgstr ""
 
-#: ../src/solver/solver.cxx:512
+#: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
 msgstr "Échec d'initialisation du solutionneur -> Abandonner\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:290
+#: ../src/mesh/impls/bout/boutmesh.cxx:281
 #, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:668
+#: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
 msgstr ""
 
-#: ../src/bout++.cxx:494
+#: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
@@ -591,122 +592,122 @@ msgstr ""
 msgid "Invalid command line option '-' found - maybe check whitespace?"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:400
+#: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:415
+#: ../src/mesh/impls/bout/boutmesh.cxx:451
 msgid "Mesh must contain nx"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:419
+#: ../src/mesh/impls/bout/boutmesh.cxx:455
 msgid "Mesh must contain ny"
 msgstr ""
 
 #. Not found
-#: ../src/mesh/mesh.cxx:536
+#: ../src/mesh/mesh.cxx:547
 #, c++-format
 msgid "Missing integer array {:s}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:905
+#: ../src/solver/solver.cxx:911
 #, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:883
+#: ../src/solver/solver.cxx:889
 #, c++-format
 msgid "Monitor signalled to quit (return code {})"
 msgstr ""
 
-#: ../src/bout++.cxx:823
+#: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:565
+#: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:550
+#: ../src/mesh/impls/bout/boutmesh.cxx:586
 msgid "No boundary regions; domain is periodic\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:254
+#: ../src/mesh/impls/bout/boutmesh.cxx:245
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:267
+#: ../src/mesh/impls/bout/boutmesh.cxx:258
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
 msgstr ""
 
 #. Less than 2 time-steps left
-#: ../src/bout++.cxx:896
+#: ../src/bout++.cxx:908
 #, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
 msgstr ""
 
-#: ../src/sys/options.cxx:303 ../src/sys/options.cxx:345
-#: ../src/sys/options.cxx:393 ../src/sys/options.cxx:428
-#: ../src/sys/options.cxx:703 ../src/sys/options.cxx:730
-#: ../src/sys/options.cxx:757
+#: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
+#: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
+#: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
+#: ../src/sys/options.cxx:789
 #, c++-format
 msgid "Option {:s} has no value"
 msgstr ""
 
 #. Doesn't exist
-#: ../src/sys/options.cxx:159
+#: ../src/sys/options.cxx:172
 #, c++-format
 msgid "Option {:s}:{:s} does not exist"
 msgstr ""
 
-#: ../include/bout/options.hxx:828
+#: ../include/bout/options.hxx:904
 #, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
 "value was '{:s}'."
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:552
+#: ../src/mesh/impls/bout/boutmesh.cxx:588
 msgid "Possible boundary regions are: "
 msgstr ""
 
-#: ../src/bout++.cxx:538
+#: ../src/bout++.cxx:545
 #, c++-format
 msgid ""
 "Processor number: {:d} of {:d}\n"
 "\n"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:609
+#: ../src/mesh/mesh.cxx:642
 #, c++-format
 msgid "Registered region 2D {:s}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:599
+#: ../src/mesh/mesh.cxx:632
 #, c++-format
 msgid "Registered region 3D {:s}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:619
+#: ../src/mesh/mesh.cxx:652
 #, c++-format
 msgid "Registered region Perp {:s}"
 msgstr ""
 
-#: ../src/bout++.cxx:529
+#: ../src/bout++.cxx:536
 #, c++-format
 msgid "Revision: {:s}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:581
+#: ../src/solver/solver.cxx:587
 msgid "Run time : "
 msgstr "Temps d'exécution : "
 
 #. / Run the solver
-#: ../src/solver/solver.cxx:525
+#: ../src/solver/solver.cxx:533
 msgid ""
 "Running simulation\n"
 "\n"
@@ -718,66 +719,66 @@ msgstr ""
 msgid "Signal"
 msgstr ""
 
-#: ../src/bout++.cxx:865
+#: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
 
-#: ../src/bout++.cxx:868
+#: ../src/bout++.cxx:879
 msgid ""
 "Sim Time  |  RHS_e evals  | RHS_I evals  | Wall Time |  Calc    Inv   "
 "Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:506
+#: ../src/solver/solver.cxx:514
 #, fuzzy, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
 "Le solveur fonctionne pour {:d} sorties avec un temps de moniteur de {:e}\n"
 
-#: ../src/solver/solver.cxx:502
+#: ../src/solver/solver.cxx:510
 #, fuzzy, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr ""
 "Le solveur fonctionne pour {:d} sorties avec un pas de sortie de {:e}\n"
 
-#: ../src/solver/solver.cxx:781
+#: ../src/solver/solver.cxx:788
 #, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
 "called!"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1281
+#: ../src/solver/solver.cxx:1289
 #, c++-format
 msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1480
+#: ../src/solver/solver.cxx:1494
 #, c++-format
 msgid "Time derivative for variable '{:s}' not set"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:605
+#: ../src/mesh/mesh.cxx:638
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:595
+#: ../src/mesh/mesh.cxx:614
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:616
+#: ../src/mesh/mesh.cxx:649
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
 msgstr ""
 
-#: ../src/sys/options.cxx:99 ../src/sys/options.cxx:138
+#: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
 #, c++-format
 msgid ""
 "Trying to index Option '{0}' with '{1}', but '{0}' is a value, not a "
@@ -786,37 +787,37 @@ msgid ""
 "rename one of them.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:1462
+#: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
 msgstr ""
 
-#: ../src/sys/options.cxx:872
+#: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
 msgstr ""
 
-#: ../src/bout++.cxx:439
+#: ../src/bout++.cxx:446
 #, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:448
+#: ../src/bout++.cxx:455
 #, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:466
+#: ../src/bout++.cxx:473
 #, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:457
+#: ../src/bout++.cxx:464
 #, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:353
+#: ../src/bout++.cxx:360
 #, c++-format
 msgid "Usage is {} {} <name>\n"
 msgstr ""
@@ -827,7 +828,7 @@ msgstr ""
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
-#: ../src/bout++.cxx:367
+#: ../src/bout++.cxx:374
 #, c++-format
 msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
@@ -835,94 +836,99 @@ msgid ""
 msgstr ""
 
 #. restart file should be written by physics model
-#: ../src/solver/solver.cxx:921
+#: ../src/solver/solver.cxx:927
 msgid "User signalled to quit. Returning\n"
 msgstr ""
 
-#: ../src/sys/options.cxx:373
+#: ../src/sys/options.cxx:486
+#, fuzzy, c++-format
+msgid "Value for option {:s} = {:e} is not a bool"
+msgstr "\"{:s}\" n'est pas un répertoire\n"
+
+#: ../src/sys/options.cxx:426
 #, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
 msgstr ""
 
-#: ../src/sys/options.cxx:408
+#: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
 msgstr ""
 
-#: ../src/sys/options.cxx:581
+#: ../src/sys/options.cxx:623
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
 msgstr ""
 
-#: ../src/sys/options.cxx:529
+#: ../src/sys/options.cxx:571
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
 msgstr ""
 
-#: ../src/sys/options.cxx:663
+#: ../src/sys/options.cxx:705
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
 msgstr ""
 
-#: ../src/sys/options.cxx:451
+#: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
 msgstr ""
 
-#: ../src/sys/options.cxx:709
+#: ../src/sys/options.cxx:751
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
 msgstr ""
 
-#: ../src/sys/options.cxx:736
+#: ../src/sys/options.cxx:773
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
 msgstr ""
 
-#: ../src/sys/options.cxx:763
+#: ../src/sys/options.cxx:795
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
 msgstr ""
 
 #. Another type which can't be converted
-#: ../src/sys/options.cxx:365
+#: ../src/sys/options.cxx:418
 #, c++-format
 msgid "Value for option {:s} is not an integer"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1232 ../src/solver/solver.cxx:1238
+#: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
 #, c++-format
 msgid "Variable '{:s}' not initialised"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:431
+#: ../src/mesh/impls/bout/boutmesh.cxx:467
 #, c++-format
 msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:633
+#: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:410
+#: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:638
+#: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:415
+#: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
 
-#: ../src/bout++.cxx:814
+#: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
 msgstr ""
 
@@ -932,7 +938,7 @@ msgid "Writing options to file {:s}\n"
 msgstr ""
 
 #. / The source label given to default values
-#: ../src/sys/options.cxx:15
+#: ../src/sys/options.cxx:34
 msgid "default"
 msgstr ""
 
@@ -946,10 +952,6 @@ msgstr ""
 #~ msgid "\tSignal handling enabled\n"
 #~ msgstr "\tTraitement du signal activé\n"
 
-#, fuzzy
-#~ msgid "Option {:s} is not a section"
-#~ msgstr "\"{:s}\" n'est pas un répertoire\n"
-
 #, fuzzy
 #~ msgid "Error encountered during initialisation\n"
 #~ msgstr "Erreur rencontrée lors de l'initialisation\n"
diff --git a/locale/libbout.pot b/locale/libbout.pot
index 3895001ba0..2ef0618dd0 100644
--- a/locale/libbout.pot
+++ b/locale/libbout.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2024-09-12 09:17+0100\n"
+"POT-Creation-Date: 2025-08-13 23:37+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -17,65 +17,70 @@ msgstr ""
 "Content-Type: text/plain; charset=CHARSET\n"
 "Content-Transfer-Encoding: 8bit\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:191
+#: ../src/mesh/impls/bout/boutmesh.cxx:182
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:224
+#: ../src/mesh/impls/bout/boutmesh.cxx:215
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:199
+#: ../src/mesh/impls/bout/boutmesh.cxx:190
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:309
+#: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:180
+#: ../src/mesh/impls/bout/boutmesh.cxx:171
 #, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:215
+#: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, c++-format
 msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:232
+#: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, c++-format
 msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:208
+#: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, c++-format
 msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:175
+#: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
 msgstr ""
 
 #: ../src/bout++.cxx:575
 #, c++-format
+msgid "\tADIOS2 support {}\n"
+msgstr ""
+
+#: ../src/bout++.cxx:583
+#, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
 
@@ -83,40 +88,40 @@ msgstr ""
 #. Processors divide equally
 #. Mesh in X divides equally
 #. Mesh in Y divides equally
-#: ../src/mesh/impls/bout/boutmesh.cxx:297
+#: ../src/mesh/impls/bout/boutmesh.cxx:288
 #, c++-format
 msgid "\tCandidate value: {:d}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:576
+#: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:594
+#: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
 msgstr ""
 
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
-#: ../src/bout++.cxx:590
+#: ../src/bout++.cxx:595
 #, c++-format
 msgid "\tCompiled with flags : {:s}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:324
+#: ../src/mesh/impls/bout/boutmesh.cxx:315
 #, c++-format
 msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:364
+#: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:372
+#: ../src/mesh/impls/bout/boutmesh.cxx:365
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
@@ -133,31 +138,31 @@ msgstr ""
 msgid "\tEmpty key or value in command line '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:582
+#: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:561
+#: ../src/bout++.cxx:568
 #, c++-format
 msgid "\tFFT support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:585
+#: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:583
+#: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:440
+#: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:463
+#: ../src/mesh/impls/bout/boutmesh.cxx:499
 msgid "\tGuard cells (x,y,z): "
 msgstr ""
 
@@ -168,17 +173,17 @@ msgid ""
 "\tLine: {:s}"
 msgstr ""
 
-#: ../src/bout++.cxx:563
+#: ../src/bout++.cxx:570
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:586
+#: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:560
+#: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
@@ -188,35 +193,31 @@ msgstr ""
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:562
+#: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:567
+#: ../src/bout++.cxx:574
 #, c++-format
 msgid "\tNetCDF support {}{}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:577
+#: ../src/bout++.cxx:585
 #, c++-format
-msgid "\tOpenMP parallelisation {}"
+msgid "\tOpenMP parallelisation {}, using {} threads\n"
 msgstr ""
 
 #. Mark the option as used
 #. Option not found
-#: ../src/sys/options.cxx:311 ../src/sys/options.cxx:380
-#: ../src/sys/options.cxx:415 ../src/sys/options.cxx:457
-#: ../src/sys/options.cxx:717 ../src/sys/options.cxx:744
-#: ../src/sys/options.cxx:771 ../include/bout/options.hxx:516
-#: ../include/bout/options.hxx:549 ../include/bout/options.hxx:573
-#: ../include/bout/options.hxx:820
+#: ../include/bout/options.hxx:586 ../include/bout/options.hxx:619
+#: ../include/bout/options.hxx:643 ../include/bout/options.hxx:896
 msgid "\tOption "
 msgstr ""
 
-#: ../src/sys/options.cxx:447
+#: ../src/sys/options.cxx:369
 #, c++-format
-msgid "\tOption '{:s}': Boolean expected. Got '{:s}'\n"
+msgid "\tOption {} = {}"
 msgstr ""
 
 #: ../src/sys/options/options_ini.cxx:70
@@ -224,62 +225,62 @@ msgstr ""
 msgid "\tOptions file '{:s}' not found\n"
 msgstr ""
 
-#: ../src/bout++.cxx:568
+#: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:571
+#: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:557
+#: ../src/bout++.cxx:564
 msgid "\tParallel NetCDF support disabled\n"
 msgstr ""
 
-#: ../src/bout++.cxx:555
+#: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
 msgstr ""
 
-#: ../src/bout++.cxx:569
+#: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:437
+#: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:238
+#: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:231 ../src/mesh/mesh.cxx:252
+#: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
 msgstr ""
 
-#: ../src/bout++.cxx:548
+#: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
 msgstr ""
 
-#: ../src/bout++.cxx:573
+#: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:574
+#: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:572
+#: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:584
+#: ../src/bout++.cxx:589
 #, c++-format
 msgid "\tSignal handling support {}\n"
 msgstr ""
@@ -289,7 +290,7 @@ msgstr ""
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:577
+#: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
 msgstr ""
 
@@ -299,7 +300,7 @@ msgid ""
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
 
-#: ../src/bout++.cxx:371
+#: ../src/bout++.cxx:378
 msgid ""
 "\n"
 "  -d <data directory>\t\tLook in <data directory> for input/output files\n"
@@ -310,7 +311,7 @@ msgid ""
 "  -q, --quiet\t\t\tDecrease verbosity\n"
 msgstr ""
 
-#: ../src/sys/expressionparser.cxx:302
+#: ../src/sys/expressionparser.cxx:341
 #, c++-format
 msgid ""
 "\n"
@@ -318,14 +319,14 @@ msgid ""
 "  Did you mean '{0}'?"
 msgstr ""
 
-#: ../src/solver/solver.cxx:580
+#: ../src/solver/solver.cxx:586
 #, c++-format
 msgid ""
 "\n"
 "Run finished at  : {:s}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:532
+#: ../src/solver/solver.cxx:540
 #, c++-format
 msgid ""
 "\n"
@@ -335,7 +336,7 @@ msgstr ""
 #. Raw string to help with the formatting of the message, and a
 #. separate variable so clang-format doesn't barf on the
 #. exception
-#: ../src/sys/options.cxx:1102
+#: ../src/sys/options.cxx:1158
 msgid ""
 "\n"
 "There were unused input options:\n"
@@ -363,7 +364,7 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/bout++.cxx:382
+#: ../src/bout++.cxx:389
 #, c++-format
 msgid ""
 "  --print-config\t\tPrint the compile-time configuration\n"
@@ -396,55 +397,55 @@ msgid ""
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
 
-#: ../src/bout++.cxx:379
+#: ../src/bout++.cxx:386
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
 msgstr ""
 
-#: ../include/bout/options.hxx:823
+#: ../include/bout/options.hxx:899
 msgid ") overwritten with:"
 msgstr ""
 
-#: ../src/bout++.cxx:550
+#: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
 msgstr ""
 
-#: ../src/bout++.cxx:579
-#, c++-format
-msgid ", using {} threads"
-msgstr ""
-
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
 msgstr ""
 
-#: ../src/sys/options.cxx:868
+#: ../src/sys/options.cxx:895
 msgid "All options used\n"
 msgstr ""
 
-#: ../src/bout++.cxx:528
+#: ../src/bout++.cxx:535
 #, c++-format
 msgid "BOUT++ version {:s}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:143
+#: ../src/bout++.cxx:147
 msgid "Bad command line arguments:\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:559
+#: ../src/sys/expressionparser.cxx:192
+#, c++-format
+msgid "Boolean operator argument {:e} is not a bool"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:355
+#: ../src/mesh/impls/bout/boutmesh.cxx:348
 #, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr ""
 
-#: ../src/bout++.cxx:818
+#: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
 msgstr ""
 
-#: ../src/bout++.cxx:533
+#: ../src/bout++.cxx:540
 #, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
@@ -455,7 +456,7 @@ msgstr ""
 msgid "Command line"
 msgstr ""
 
-#: ../src/bout++.cxx:544 ../tests/unit/src/test_bout++.cxx:358
+#: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
 msgstr ""
 
@@ -463,16 +464,16 @@ msgstr ""
 msgid "Compiled with flags"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:568
+#: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
 msgstr ""
 
-#: ../src/bout++.cxx:520
+#: ../src/bout++.cxx:527
 #, c++-format
 msgid "Could not create PID file {:s}"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:318
+#: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
 msgstr ""
@@ -482,28 +483,28 @@ msgstr ""
 msgid "Could not open output file '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:652
+#: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
 msgstr ""
 
 #. Error reading
-#: ../src/mesh/mesh.cxx:532
+#: ../src/mesh/mesh.cxx:543
 #, c++-format
 msgid "Could not read integer array '{:s}'\n"
 msgstr ""
 
 #. Failed . Probably not important enough to stop the simulation
-#: ../src/bout++.cxx:632
+#: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:765
+#: ../src/solver/solver.cxx:772
 #, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
 msgstr ""
 
-#: ../src/sys/expressionparser.cxx:273
+#: ../src/sys/expressionparser.cxx:312
 #, c++-format
 msgid ""
 "Couldn't find generator '{}'. BOUT++ expressions are now case-sensitive, so "
@@ -512,69 +513,69 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:568
+#: ../src/mesh/mesh.cxx:587
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:560
+#: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:576
+#: ../src/mesh/mesh.cxx:595
 #, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
 msgstr ""
 
 #. Convert any exceptions to something a bit more useful
-#: ../src/sys/options.cxx:336
+#: ../src/sys/options.cxx:361
 #, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
 msgstr ""
 
-#: ../src/bout++.cxx:508
+#: ../src/bout++.cxx:515
 #, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
 msgstr ""
 
-#: ../src/bout++.cxx:505
+#: ../src/bout++.cxx:512
 #, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:665
+#: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
 msgstr ""
 
-#: ../src/bout++.cxx:209
+#: ../src/bout++.cxx:216
 #, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:744
+#: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:332
+#: ../src/mesh/impls/bout/boutmesh.cxx:323
 #, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
 msgstr ""
 
-#: ../src/solver/solver.cxx:512
+#: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:290
+#: ../src/mesh/impls/bout/boutmesh.cxx:281
 #, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:668
+#: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
 msgstr ""
 
-#: ../src/bout++.cxx:494
+#: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
@@ -584,122 +585,122 @@ msgstr ""
 msgid "Invalid command line option '-' found - maybe check whitespace?"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:400
+#: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:415
+#: ../src/mesh/impls/bout/boutmesh.cxx:451
 msgid "Mesh must contain nx"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:419
+#: ../src/mesh/impls/bout/boutmesh.cxx:455
 msgid "Mesh must contain ny"
 msgstr ""
 
 #. Not found
-#: ../src/mesh/mesh.cxx:536
+#: ../src/mesh/mesh.cxx:547
 #, c++-format
 msgid "Missing integer array {:s}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:905
+#: ../src/solver/solver.cxx:911
 #, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:883
+#: ../src/solver/solver.cxx:889
 #, c++-format
 msgid "Monitor signalled to quit (return code {})"
 msgstr ""
 
-#: ../src/bout++.cxx:823
+#: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:565
+#: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:550
+#: ../src/mesh/impls/bout/boutmesh.cxx:586
 msgid "No boundary regions; domain is periodic\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:254
+#: ../src/mesh/impls/bout/boutmesh.cxx:245
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:267
+#: ../src/mesh/impls/bout/boutmesh.cxx:258
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
 msgstr ""
 
 #. Less than 2 time-steps left
-#: ../src/bout++.cxx:896
+#: ../src/bout++.cxx:908
 #, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
 msgstr ""
 
-#: ../src/sys/options.cxx:303 ../src/sys/options.cxx:345
-#: ../src/sys/options.cxx:393 ../src/sys/options.cxx:428
-#: ../src/sys/options.cxx:703 ../src/sys/options.cxx:730
-#: ../src/sys/options.cxx:757
+#: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
+#: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
+#: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
+#: ../src/sys/options.cxx:789
 #, c++-format
 msgid "Option {:s} has no value"
 msgstr ""
 
 #. Doesn't exist
-#: ../src/sys/options.cxx:159
+#: ../src/sys/options.cxx:172
 #, c++-format
 msgid "Option {:s}:{:s} does not exist"
 msgstr ""
 
-#: ../include/bout/options.hxx:828
+#: ../include/bout/options.hxx:904
 #, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
 "value was '{:s}'."
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:552
+#: ../src/mesh/impls/bout/boutmesh.cxx:588
 msgid "Possible boundary regions are: "
 msgstr ""
 
-#: ../src/bout++.cxx:538
+#: ../src/bout++.cxx:545
 #, c++-format
 msgid ""
 "Processor number: {:d} of {:d}\n"
 "\n"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:609
+#: ../src/mesh/mesh.cxx:642
 #, c++-format
 msgid "Registered region 2D {:s}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:599
+#: ../src/mesh/mesh.cxx:632
 #, c++-format
 msgid "Registered region 3D {:s}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:619
+#: ../src/mesh/mesh.cxx:652
 #, c++-format
 msgid "Registered region Perp {:s}"
 msgstr ""
 
-#: ../src/bout++.cxx:529
+#: ../src/bout++.cxx:536
 #, c++-format
 msgid "Revision: {:s}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:581
+#: ../src/solver/solver.cxx:587
 msgid "Run time : "
 msgstr ""
 
 #. / Run the solver
-#: ../src/solver/solver.cxx:525
+#: ../src/solver/solver.cxx:533
 msgid ""
 "Running simulation\n"
 "\n"
@@ -709,64 +710,64 @@ msgstr ""
 msgid "Signal"
 msgstr ""
 
-#: ../src/bout++.cxx:865
+#: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
 
-#: ../src/bout++.cxx:868
+#: ../src/bout++.cxx:879
 msgid ""
 "Sim Time  |  RHS_e evals  | RHS_I evals  | Wall Time |  Calc    Inv   "
 "Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:506
+#: ../src/solver/solver.cxx:514
 #, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:502
+#: ../src/solver/solver.cxx:510
 #, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:781
+#: ../src/solver/solver.cxx:788
 #, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
 "called!"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1281
+#: ../src/solver/solver.cxx:1289
 #, c++-format
 msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1480
+#: ../src/solver/solver.cxx:1494
 #, c++-format
 msgid "Time derivative for variable '{:s}' not set"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:605
+#: ../src/mesh/mesh.cxx:638
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:595
+#: ../src/mesh/mesh.cxx:614
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:616
+#: ../src/mesh/mesh.cxx:649
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
 msgstr ""
 
-#: ../src/sys/options.cxx:99 ../src/sys/options.cxx:138
+#: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
 #, c++-format
 msgid ""
 "Trying to index Option '{0}' with '{1}', but '{0}' is a value, not a "
@@ -775,37 +776,37 @@ msgid ""
 "rename one of them.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:1462
+#: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
 msgstr ""
 
-#: ../src/sys/options.cxx:872
+#: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
 msgstr ""
 
-#: ../src/bout++.cxx:439
+#: ../src/bout++.cxx:446
 #, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:448
+#: ../src/bout++.cxx:455
 #, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:466
+#: ../src/bout++.cxx:473
 #, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:457
+#: ../src/bout++.cxx:464
 #, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:353
+#: ../src/bout++.cxx:360
 #, c++-format
 msgid "Usage is {} {} <name>\n"
 msgstr ""
@@ -816,7 +817,7 @@ msgstr ""
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
-#: ../src/bout++.cxx:367
+#: ../src/bout++.cxx:374
 #, c++-format
 msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
@@ -824,94 +825,99 @@ msgid ""
 msgstr ""
 
 #. restart file should be written by physics model
-#: ../src/solver/solver.cxx:921
+#: ../src/solver/solver.cxx:927
 msgid "User signalled to quit. Returning\n"
 msgstr ""
 
-#: ../src/sys/options.cxx:373
+#: ../src/sys/options.cxx:486
+#, c++-format
+msgid "Value for option {:s} = {:e} is not a bool"
+msgstr ""
+
+#: ../src/sys/options.cxx:426
 #, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
 msgstr ""
 
-#: ../src/sys/options.cxx:408
+#: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
 msgstr ""
 
-#: ../src/sys/options.cxx:581
+#: ../src/sys/options.cxx:623
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
 msgstr ""
 
-#: ../src/sys/options.cxx:529
+#: ../src/sys/options.cxx:571
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
 msgstr ""
 
-#: ../src/sys/options.cxx:663
+#: ../src/sys/options.cxx:705
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
 msgstr ""
 
-#: ../src/sys/options.cxx:451
+#: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
 msgstr ""
 
-#: ../src/sys/options.cxx:709
+#: ../src/sys/options.cxx:751
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
 msgstr ""
 
-#: ../src/sys/options.cxx:736
+#: ../src/sys/options.cxx:773
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
 msgstr ""
 
-#: ../src/sys/options.cxx:763
+#: ../src/sys/options.cxx:795
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
 msgstr ""
 
 #. Another type which can't be converted
-#: ../src/sys/options.cxx:365
+#: ../src/sys/options.cxx:418
 #, c++-format
 msgid "Value for option {:s} is not an integer"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1232 ../src/solver/solver.cxx:1238
+#: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
 #, c++-format
 msgid "Variable '{:s}' not initialised"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:431
+#: ../src/mesh/impls/bout/boutmesh.cxx:467
 #, c++-format
 msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:633
+#: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:410
+#: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:638
+#: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:415
+#: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
 
-#: ../src/bout++.cxx:814
+#: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
 msgstr ""
 
@@ -921,6 +927,6 @@ msgid "Writing options to file {:s}\n"
 msgstr ""
 
 #. / The source label given to default values
-#: ../src/sys/options.cxx:15
+#: ../src/sys/options.cxx:34
 msgid "default"
 msgstr ""
diff --git a/locale/zh_CN/libbout.po b/locale/zh_CN/libbout.po
index 2c53b5392c..ecf8517d62 100644
--- a/locale/zh_CN/libbout.po
+++ b/locale/zh_CN/libbout.po
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: BOUT++ 4.2.0\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2024-09-12 09:17+0100\n"
+"POT-Creation-Date: 2025-08-13 23:37+0100\n"
 "PO-Revision-Date: 2018-10-22 22:56+0100\n"
 "Last-Translator:  <benjamin.dudson@york.ac.uk>\n"
 "Language-Team: Chinese (simplified)\n"
@@ -16,65 +16,70 @@ msgstr ""
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:191
+#: ../src/mesh/impls/bout/boutmesh.cxx:182
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:224
+#: ../src/mesh/impls/bout/boutmesh.cxx:215
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:199
+#: ../src/mesh/impls/bout/boutmesh.cxx:190
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:309
+#: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:180
+#: ../src/mesh/impls/bout/boutmesh.cxx:171
 #, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:215
+#: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, c++-format
 msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:232
+#: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, c++-format
 msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:208
+#: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, c++-format
 msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:175
+#: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
 msgstr ""
 
 #: ../src/bout++.cxx:575
 #, c++-format
+msgid "\tADIOS2 support {}\n"
+msgstr ""
+
+#: ../src/bout++.cxx:583
+#, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
 
@@ -82,40 +87,40 @@ msgstr ""
 #. Processors divide equally
 #. Mesh in X divides equally
 #. Mesh in Y divides equally
-#: ../src/mesh/impls/bout/boutmesh.cxx:297
+#: ../src/mesh/impls/bout/boutmesh.cxx:288
 #, c++-format
 msgid "\tCandidate value: {:d}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:576
+#: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:594
+#: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
 msgstr ""
 
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
-#: ../src/bout++.cxx:590
+#: ../src/bout++.cxx:595
 #, c++-format
 msgid "\tCompiled with flags : {:s}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:324
+#: ../src/mesh/impls/bout/boutmesh.cxx:315
 #, c++-format
 msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:364
+#: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:372
+#: ../src/mesh/impls/bout/boutmesh.cxx:365
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
@@ -132,31 +137,31 @@ msgstr ""
 msgid "\tEmpty key or value in command line '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:582
+#: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:561
+#: ../src/bout++.cxx:568
 #, c++-format
 msgid "\tFFT support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:585
+#: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:583
+#: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:440
+#: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:463
+#: ../src/mesh/impls/bout/boutmesh.cxx:499
 msgid "\tGuard cells (x,y,z): "
 msgstr ""
 
@@ -167,17 +172,17 @@ msgid ""
 "\tLine: {:s}"
 msgstr ""
 
-#: ../src/bout++.cxx:563
+#: ../src/bout++.cxx:570
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:586
+#: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:560
+#: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
@@ -187,98 +192,94 @@ msgstr ""
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:562
+#: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:567
+#: ../src/bout++.cxx:574
 #, c++-format
 msgid "\tNetCDF support {}{}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:577
+#: ../src/bout++.cxx:585
 #, c++-format
-msgid "\tOpenMP parallelisation {}"
+msgid "\tOpenMP parallelisation {}, using {} threads\n"
 msgstr ""
 
 #. Mark the option as used
 #. Option not found
-#: ../src/sys/options.cxx:311 ../src/sys/options.cxx:380
-#: ../src/sys/options.cxx:415 ../src/sys/options.cxx:457
-#: ../src/sys/options.cxx:717 ../src/sys/options.cxx:744
-#: ../src/sys/options.cxx:771 ../include/bout/options.hxx:516
-#: ../include/bout/options.hxx:549 ../include/bout/options.hxx:573
-#: ../include/bout/options.hxx:820
+#: ../include/bout/options.hxx:586 ../include/bout/options.hxx:619
+#: ../include/bout/options.hxx:643 ../include/bout/options.hxx:896
 msgid "\tOption "
 msgstr "\t选项 "
 
-#: ../src/sys/options.cxx:447
-#, c++-format
-msgid "\tOption '{:s}': Boolean expected. Got '{:s}'\n"
-msgstr ""
+#: ../src/sys/options.cxx:369
+#, fuzzy, c++-format
+msgid "\tOption {} = {}"
+msgstr "\t选项 "
 
 #: ../src/sys/options/options_ini.cxx:70
 #, c++-format
 msgid "\tOptions file '{:s}' not found\n"
 msgstr ""
 
-#: ../src/bout++.cxx:568
+#: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:571
+#: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:557
+#: ../src/bout++.cxx:564
 msgid "\tParallel NetCDF support disabled\n"
 msgstr ""
 
-#: ../src/bout++.cxx:555
+#: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
 msgstr ""
 
-#: ../src/bout++.cxx:569
+#: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:437
+#: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:238
+#: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:231 ../src/mesh/mesh.cxx:252
+#: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
 msgstr ""
 
-#: ../src/bout++.cxx:548
+#: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
 msgstr ""
 
-#: ../src/bout++.cxx:573
+#: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:574
+#: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:572
+#: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:584
+#: ../src/bout++.cxx:589
 #, fuzzy, c++-format
 msgid "\tSignal handling support {}\n"
 msgstr "\t测试关掉\n"
@@ -288,7 +289,7 @@ msgstr "\t测试关掉\n"
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:577
+#: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
 msgstr ""
 
@@ -298,7 +299,7 @@ msgid ""
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
 
-#: ../src/bout++.cxx:371
+#: ../src/bout++.cxx:378
 msgid ""
 "\n"
 "  -d <data directory>\t\tLook in <data directory> for input/output files\n"
@@ -309,7 +310,7 @@ msgid ""
 "  -q, --quiet\t\t\tDecrease verbosity\n"
 msgstr ""
 
-#: ../src/sys/expressionparser.cxx:302
+#: ../src/sys/expressionparser.cxx:341
 #, c++-format
 msgid ""
 "\n"
@@ -317,7 +318,7 @@ msgid ""
 "  Did you mean '{0}'?"
 msgstr ""
 
-#: ../src/solver/solver.cxx:580
+#: ../src/solver/solver.cxx:586
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -326,7 +327,7 @@ msgstr ""
 "\n"
 "计算结束于 {:s}\n"
 
-#: ../src/solver/solver.cxx:532
+#: ../src/solver/solver.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -338,7 +339,7 @@ msgstr ""
 #. Raw string to help with the formatting of the message, and a
 #. separate variable so clang-format doesn't barf on the
 #. exception
-#: ../src/sys/options.cxx:1102
+#: ../src/sys/options.cxx:1158
 msgid ""
 "\n"
 "There were unused input options:\n"
@@ -366,7 +367,7 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/bout++.cxx:382
+#: ../src/bout++.cxx:389
 #, c++-format
 msgid ""
 "  --print-config\t\tPrint the compile-time configuration\n"
@@ -399,55 +400,55 @@ msgid ""
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
 
-#: ../src/bout++.cxx:379
+#: ../src/bout++.cxx:386
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
 msgstr ""
 
-#: ../include/bout/options.hxx:823
+#: ../include/bout/options.hxx:899
 msgid ") overwritten with:"
 msgstr ""
 
-#: ../src/bout++.cxx:550
+#: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
 msgstr ""
 
-#: ../src/bout++.cxx:579
-#, c++-format
-msgid ", using {} threads"
-msgstr ""
-
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
 msgstr ""
 
-#: ../src/sys/options.cxx:868
+#: ../src/sys/options.cxx:895
 msgid "All options used\n"
 msgstr ""
 
-#: ../src/bout++.cxx:528
+#: ../src/bout++.cxx:535
 #, c++-format
 msgid "BOUT++ version {:s}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:143
+#: ../src/bout++.cxx:147
 msgid "Bad command line arguments:\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:559
+#: ../src/sys/expressionparser.cxx:192
+#, c++-format
+msgid "Boolean operator argument {:e} is not a bool"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:355
+#: ../src/mesh/impls/bout/boutmesh.cxx:348
 #, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr ""
 
-#: ../src/bout++.cxx:818
+#: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
 msgstr ""
 
-#: ../src/bout++.cxx:533
+#: ../src/bout++.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
@@ -460,7 +461,7 @@ msgstr ""
 msgid "Command line"
 msgstr ""
 
-#: ../src/bout++.cxx:544 ../tests/unit/src/test_bout++.cxx:358
+#: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
 msgstr ""
 
@@ -468,16 +469,16 @@ msgstr ""
 msgid "Compiled with flags"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:568
+#: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
 msgstr ""
 
-#: ../src/bout++.cxx:520
+#: ../src/bout++.cxx:527
 #, c++-format
 msgid "Could not create PID file {:s}"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:318
+#: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
 msgstr ""
@@ -487,28 +488,28 @@ msgstr ""
 msgid "Could not open output file '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:652
+#: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
 msgstr ""
 
 #. Error reading
-#: ../src/mesh/mesh.cxx:532
+#: ../src/mesh/mesh.cxx:543
 #, c++-format
 msgid "Could not read integer array '{:s}'\n"
 msgstr ""
 
 #. Failed . Probably not important enough to stop the simulation
-#: ../src/bout++.cxx:632
+#: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:765
+#: ../src/solver/solver.cxx:772
 #, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
 msgstr ""
 
-#: ../src/sys/expressionparser.cxx:273
+#: ../src/sys/expressionparser.cxx:312
 #, c++-format
 msgid ""
 "Couldn't find generator '{}'. BOUT++ expressions are now case-sensitive, so "
@@ -517,69 +518,69 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:568
+#: ../src/mesh/mesh.cxx:587
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:560
+#: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:576
+#: ../src/mesh/mesh.cxx:595
 #, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
 msgstr ""
 
 #. Convert any exceptions to something a bit more useful
-#: ../src/sys/options.cxx:336
+#: ../src/sys/options.cxx:361
 #, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
 msgstr ""
 
-#: ../src/bout++.cxx:508
+#: ../src/bout++.cxx:515
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
 msgstr "\"{:s}\" 不存在或不可访问\n"
 
-#: ../src/bout++.cxx:505
+#: ../src/bout++.cxx:512
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
 msgstr "\"{:s}\" 不是目录\n"
 
-#: ../src/solver/solver.cxx:665
+#: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
 msgstr ""
 
-#: ../src/bout++.cxx:209
+#: ../src/bout++.cxx:216
 #, fuzzy, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
 msgstr "启动时遇到错误 : {:s}\n"
 
-#: ../src/bout++.cxx:744
+#: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:332
+#: ../src/mesh/impls/bout/boutmesh.cxx:323
 #, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
 msgstr ""
 
-#: ../src/solver/solver.cxx:512
+#: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:290
+#: ../src/mesh/impls/bout/boutmesh.cxx:281
 #, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:668
+#: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
 msgstr ""
 
-#: ../src/bout++.cxx:494
+#: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
@@ -589,122 +590,122 @@ msgstr ""
 msgid "Invalid command line option '-' found - maybe check whitespace?"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:400
+#: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:415
+#: ../src/mesh/impls/bout/boutmesh.cxx:451
 msgid "Mesh must contain nx"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:419
+#: ../src/mesh/impls/bout/boutmesh.cxx:455
 msgid "Mesh must contain ny"
 msgstr ""
 
 #. Not found
-#: ../src/mesh/mesh.cxx:536
+#: ../src/mesh/mesh.cxx:547
 #, c++-format
 msgid "Missing integer array {:s}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:905
+#: ../src/solver/solver.cxx:911
 #, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:883
+#: ../src/solver/solver.cxx:889
 #, c++-format
 msgid "Monitor signalled to quit (return code {})"
 msgstr ""
 
-#: ../src/bout++.cxx:823
+#: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:565
+#: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:550
+#: ../src/mesh/impls/bout/boutmesh.cxx:586
 msgid "No boundary regions; domain is periodic\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:254
+#: ../src/mesh/impls/bout/boutmesh.cxx:245
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:267
+#: ../src/mesh/impls/bout/boutmesh.cxx:258
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
 msgstr ""
 
 #. Less than 2 time-steps left
-#: ../src/bout++.cxx:896
+#: ../src/bout++.cxx:908
 #, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
 msgstr ""
 
-#: ../src/sys/options.cxx:303 ../src/sys/options.cxx:345
-#: ../src/sys/options.cxx:393 ../src/sys/options.cxx:428
-#: ../src/sys/options.cxx:703 ../src/sys/options.cxx:730
-#: ../src/sys/options.cxx:757
+#: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
+#: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
+#: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
+#: ../src/sys/options.cxx:789
 #, c++-format
 msgid "Option {:s} has no value"
 msgstr ""
 
 #. Doesn't exist
-#: ../src/sys/options.cxx:159
+#: ../src/sys/options.cxx:172
 #, c++-format
 msgid "Option {:s}:{:s} does not exist"
 msgstr ""
 
-#: ../include/bout/options.hxx:828
+#: ../include/bout/options.hxx:904
 #, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
 "value was '{:s}'."
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:552
+#: ../src/mesh/impls/bout/boutmesh.cxx:588
 msgid "Possible boundary regions are: "
 msgstr ""
 
-#: ../src/bout++.cxx:538
+#: ../src/bout++.cxx:545
 #, c++-format
 msgid ""
 "Processor number: {:d} of {:d}\n"
 "\n"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:609
+#: ../src/mesh/mesh.cxx:642
 #, c++-format
 msgid "Registered region 2D {:s}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:599
+#: ../src/mesh/mesh.cxx:632
 #, c++-format
 msgid "Registered region 3D {:s}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:619
+#: ../src/mesh/mesh.cxx:652
 #, c++-format
 msgid "Registered region Perp {:s}"
 msgstr ""
 
-#: ../src/bout++.cxx:529
+#: ../src/bout++.cxx:536
 #, c++-format
 msgid "Revision: {:s}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:581
+#: ../src/solver/solver.cxx:587
 msgid "Run time : "
 msgstr "计算时间"
 
 #. / Run the solver
-#: ../src/solver/solver.cxx:525
+#: ../src/solver/solver.cxx:533
 msgid ""
 "Running simulation\n"
 "\n"
@@ -716,64 +717,64 @@ msgstr ""
 msgid "Signal"
 msgstr ""
 
-#: ../src/bout++.cxx:865
+#: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
 
-#: ../src/bout++.cxx:868
+#: ../src/bout++.cxx:879
 msgid ""
 "Sim Time  |  RHS_e evals  | RHS_I evals  | Wall Time |  Calc    Inv   "
 "Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:506
+#: ../src/solver/solver.cxx:514
 #, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:502
+#: ../src/solver/solver.cxx:510
 #, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:781
+#: ../src/solver/solver.cxx:788
 #, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
 "called!"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1281
+#: ../src/solver/solver.cxx:1289
 #, c++-format
 msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1480
+#: ../src/solver/solver.cxx:1494
 #, c++-format
 msgid "Time derivative for variable '{:s}' not set"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:605
+#: ../src/mesh/mesh.cxx:638
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:595
+#: ../src/mesh/mesh.cxx:614
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:616
+#: ../src/mesh/mesh.cxx:649
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
 msgstr ""
 
-#: ../src/sys/options.cxx:99 ../src/sys/options.cxx:138
+#: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
 #, c++-format
 msgid ""
 "Trying to index Option '{0}' with '{1}', but '{0}' is a value, not a "
@@ -782,37 +783,37 @@ msgid ""
 "rename one of them.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:1462
+#: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
 msgstr ""
 
-#: ../src/sys/options.cxx:872
+#: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
 msgstr ""
 
-#: ../src/bout++.cxx:439
+#: ../src/bout++.cxx:446
 #, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:448
+#: ../src/bout++.cxx:455
 #, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:466
+#: ../src/bout++.cxx:473
 #, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:457
+#: ../src/bout++.cxx:464
 #, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:353
+#: ../src/bout++.cxx:360
 #, c++-format
 msgid "Usage is {} {} <name>\n"
 msgstr ""
@@ -823,7 +824,7 @@ msgstr ""
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
-#: ../src/bout++.cxx:367
+#: ../src/bout++.cxx:374
 #, c++-format
 msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
@@ -831,94 +832,99 @@ msgid ""
 msgstr ""
 
 #. restart file should be written by physics model
-#: ../src/solver/solver.cxx:921
+#: ../src/solver/solver.cxx:927
 msgid "User signalled to quit. Returning\n"
 msgstr ""
 
-#: ../src/sys/options.cxx:373
+#: ../src/sys/options.cxx:486
+#, fuzzy, c++-format
+msgid "Value for option {:s} = {:e} is not a bool"
+msgstr "\"{:s}\" 不是目录\n"
+
+#: ../src/sys/options.cxx:426
 #, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
 msgstr ""
 
-#: ../src/sys/options.cxx:408
+#: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
 msgstr ""
 
-#: ../src/sys/options.cxx:581
+#: ../src/sys/options.cxx:623
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
 msgstr ""
 
-#: ../src/sys/options.cxx:529
+#: ../src/sys/options.cxx:571
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
 msgstr ""
 
-#: ../src/sys/options.cxx:663
+#: ../src/sys/options.cxx:705
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
 msgstr ""
 
-#: ../src/sys/options.cxx:451
+#: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
 msgstr ""
 
-#: ../src/sys/options.cxx:709
+#: ../src/sys/options.cxx:751
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
 msgstr ""
 
-#: ../src/sys/options.cxx:736
+#: ../src/sys/options.cxx:773
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
 msgstr ""
 
-#: ../src/sys/options.cxx:763
+#: ../src/sys/options.cxx:795
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
 msgstr ""
 
 #. Another type which can't be converted
-#: ../src/sys/options.cxx:365
+#: ../src/sys/options.cxx:418
 #, c++-format
 msgid "Value for option {:s} is not an integer"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1232 ../src/solver/solver.cxx:1238
+#: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
 #, c++-format
 msgid "Variable '{:s}' not initialised"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:431
+#: ../src/mesh/impls/bout/boutmesh.cxx:467
 #, c++-format
 msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:633
+#: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:410
+#: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:638
+#: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:415
+#: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
 
-#: ../src/bout++.cxx:814
+#: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
 msgstr ""
 
@@ -928,7 +934,7 @@ msgid "Writing options to file {:s}\n"
 msgstr ""
 
 #. / The source label given to default values
-#: ../src/sys/options.cxx:15
+#: ../src/sys/options.cxx:34
 msgid "default"
 msgstr ""
 
@@ -939,9 +945,5 @@ msgstr ""
 #~ msgid "\tChecking enabled, level {:d}\n"
 #~ msgstr "\t测试打开,级别 {:d}\n"
 
-#, fuzzy
-#~ msgid "Option {:s} is not a section"
-#~ msgstr "\"{:s}\" 不是目录\n"
-
 #~ msgid "Error encountered during initialisation\n"
 #~ msgstr "启动时遇到错误\n"
diff --git a/locale/zh_TW/libbout.po b/locale/zh_TW/libbout.po
index de0230d68d..abf44db51f 100644
--- a/locale/zh_TW/libbout.po
+++ b/locale/zh_TW/libbout.po
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: BOUT++ 4.2.0\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2024-09-12 09:17+0100\n"
+"POT-Creation-Date: 2025-08-13 23:37+0100\n"
 "PO-Revision-Date: 2018-10-22 22:56+0100\n"
 "Last-Translator:  <benjamin.dudson@york.ac.uk>\n"
 "Language-Team: Chinese (traditional)\n"
@@ -16,64 +16,69 @@ msgstr ""
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:191
+#: ../src/mesh/impls/bout/boutmesh.cxx:182
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:224
+#: ../src/mesh/impls/bout/boutmesh.cxx:215
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:199
+#: ../src/mesh/impls/bout/boutmesh.cxx:190
 #, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:309
+#: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
 msgstr "\t -> 好的號碼\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:180
+#: ../src/mesh/impls/bout/boutmesh.cxx:171
 #, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:215
+#: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, c++-format
 msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:232
+#: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, c++-format
 msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:208
+#: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, c++-format
 msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:175
+#: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
 msgstr ""
 
 #: ../src/bout++.cxx:575
+#, fuzzy, c++-format
+msgid "\tADIOS2 support {}\n"
+msgstr "\tOpenMP並行化已禁用\n"
+
+#: ../src/bout++.cxx:583
 #, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
@@ -82,40 +87,40 @@ msgstr ""
 #. Processors divide equally
 #. Mesh in X divides equally
 #. Mesh in Y divides equally
-#: ../src/mesh/impls/bout/boutmesh.cxx:297
+#: ../src/mesh/impls/bout/boutmesh.cxx:288
 #, fuzzy, c++-format
 msgid "\tCandidate value: {:d}\n"
 msgstr "\t候選人數目 {:d}\n"
 
-#: ../src/bout++.cxx:576
+#: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:594
+#: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
 msgstr ""
 
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
-#: ../src/bout++.cxx:590
+#: ../src/bout++.cxx:595
 #, fuzzy, c++-format
 msgid "\tCompiled with flags : {:s}\n"
 msgstr "\t用設置編譯: {:s}\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:324
+#: ../src/mesh/impls/bout/boutmesh.cxx:315
 #, fuzzy, c++-format
 msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
 msgstr "\t域 (NXPE={:d}, NYPE={:d}) 分裂成域 (localNx={:d}, localNy={:d})\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:364
+#: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:372
+#: ../src/mesh/impls/bout/boutmesh.cxx:365
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
@@ -132,31 +137,31 @@ msgstr ""
 msgid "\tEmpty key or value in command line '{:s}'\n"
 msgstr "\t命令行中的空鍵或值 '{:s}'\n"
 
-#: ../src/bout++.cxx:582
+#: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:561
+#: ../src/bout++.cxx:568
 #, c++-format
 msgid "\tFFT support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:585
+#: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:583
+#: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:440
+#: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
 msgstr "\t網格大小: "
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:463
+#: ../src/mesh/impls/bout/boutmesh.cxx:499
 msgid "\tGuard cells (x,y,z): "
 msgstr ""
 
@@ -167,17 +172,17 @@ msgid ""
 "\tLine: {:s}"
 msgstr ""
 
-#: ../src/bout++.cxx:563
+#: ../src/bout++.cxx:570
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:586
+#: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:560
+#: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
@@ -187,99 +192,95 @@ msgstr ""
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
 msgstr ""
 
-#: ../src/bout++.cxx:562
+#: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:567
+#: ../src/bout++.cxx:574
 #, fuzzy, c++-format
 msgid "\tNetCDF support {}{}\n"
 msgstr "\tOpenMP並行化已禁用\n"
 
-#: ../src/bout++.cxx:577
+#: ../src/bout++.cxx:585
 #, fuzzy, c++-format
-msgid "\tOpenMP parallelisation {}"
-msgstr "\tOpenMP並行化已禁用\n"
+msgid "\tOpenMP parallelisation {}, using {} threads\n"
+msgstr "\t啟用OpenMP並行化。 使用{:d}個線程\n"
 
 #. Mark the option as used
 #. Option not found
-#: ../src/sys/options.cxx:311 ../src/sys/options.cxx:380
-#: ../src/sys/options.cxx:415 ../src/sys/options.cxx:457
-#: ../src/sys/options.cxx:717 ../src/sys/options.cxx:744
-#: ../src/sys/options.cxx:771 ../include/bout/options.hxx:516
-#: ../include/bout/options.hxx:549 ../include/bout/options.hxx:573
-#: ../include/bout/options.hxx:820
+#: ../include/bout/options.hxx:586 ../include/bout/options.hxx:619
+#: ../include/bout/options.hxx:643 ../include/bout/options.hxx:896
 msgid "\tOption "
 msgstr "\t選項 "
 
-#: ../src/sys/options.cxx:447
+#: ../src/sys/options.cxx:369
 #, fuzzy, c++-format
-msgid "\tOption '{:s}': Boolean expected. Got '{:s}'\n"
-msgstr "\t選項 '{:s}': 布爾預期. 拿到 '{:s}'\n"
+msgid "\tOption {} = {}"
+msgstr "\t選項 "
 
 #: ../src/sys/options/options_ini.cxx:70
 #, fuzzy, c++-format
 msgid "\tOptions file '{:s}' not found\n"
 msgstr "\t找不到選項文件 '{:s}'\n"
 
-#: ../src/bout++.cxx:568
+#: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:571
+#: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:557
+#: ../src/bout++.cxx:564
 #, fuzzy
 msgid "\tParallel NetCDF support disabled\n"
 msgstr "\tOpenMP並行化已禁用\n"
 
-#: ../src/bout++.cxx:555
+#: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
 msgstr ""
 
-#: ../src/bout++.cxx:569
+#: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:437
+#: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:238
+#: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:231 ../src/mesh/mesh.cxx:252
+#: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
 msgstr ""
 
-#: ../src/bout++.cxx:548
+#: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
 msgstr ""
 
-#: ../src/bout++.cxx:573
+#: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:574
+#: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:572
+#: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
 
-#: ../src/bout++.cxx:584
+#: ../src/bout++.cxx:589
 #, fuzzy, c++-format
 msgid "\tSignal handling support {}\n"
 msgstr "\t測試關掉\n"
@@ -289,7 +290,7 @@ msgstr "\t測試關掉\n"
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:577
+#: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
 msgstr "\t完\n"
 
@@ -299,7 +300,7 @@ msgid ""
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
 
-#: ../src/bout++.cxx:371
+#: ../src/bout++.cxx:378
 msgid ""
 "\n"
 "  -d <data directory>\t\tLook in <data directory> for input/output files\n"
@@ -310,7 +311,7 @@ msgid ""
 "  -q, --quiet\t\t\tDecrease verbosity\n"
 msgstr ""
 
-#: ../src/sys/expressionparser.cxx:302
+#: ../src/sys/expressionparser.cxx:341
 #, c++-format
 msgid ""
 "\n"
@@ -318,7 +319,7 @@ msgid ""
 "  Did you mean '{0}'?"
 msgstr ""
 
-#: ../src/solver/solver.cxx:580
+#: ../src/solver/solver.cxx:586
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -327,7 +328,7 @@ msgstr ""
 "\n"
 "计算结束于 {:s}\n"
 
-#: ../src/solver/solver.cxx:532
+#: ../src/solver/solver.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "\n"
@@ -339,7 +340,7 @@ msgstr ""
 #. Raw string to help with the formatting of the message, and a
 #. separate variable so clang-format doesn't barf on the
 #. exception
-#: ../src/sys/options.cxx:1102
+#: ../src/sys/options.cxx:1158
 msgid ""
 "\n"
 "There were unused input options:\n"
@@ -367,7 +368,7 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/bout++.cxx:382
+#: ../src/bout++.cxx:389
 #, c++-format
 msgid ""
 "  --print-config\t\tPrint the compile-time configuration\n"
@@ -400,55 +401,55 @@ msgid ""
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
 
-#: ../src/bout++.cxx:379
+#: ../src/bout++.cxx:386
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
 msgstr ""
 
-#: ../include/bout/options.hxx:823
+#: ../include/bout/options.hxx:899
 msgid ") overwritten with:"
 msgstr ""
 
-#: ../src/bout++.cxx:550
+#: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
 msgstr ""
 
-#: ../src/bout++.cxx:579
-#, c++-format
-msgid ", using {} threads"
-msgstr ""
-
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
 msgstr ""
 
-#: ../src/sys/options.cxx:868
+#: ../src/sys/options.cxx:895
 msgid "All options used\n"
 msgstr ""
 
-#: ../src/bout++.cxx:528
+#: ../src/bout++.cxx:535
 #, fuzzy, c++-format
 msgid "BOUT++ version {:s}\n"
 msgstr "BOUT++ 版 {:s}\n"
 
-#: ../src/bout++.cxx:143
+#: ../src/bout++.cxx:147
 msgid "Bad command line arguments:\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:559
+#: ../src/sys/expressionparser.cxx:192
+#, c++-format
+msgid "Boolean operator argument {:e} is not a bool"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:355
+#: ../src/mesh/impls/bout/boutmesh.cxx:348
 #, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr ""
 
-#: ../src/bout++.cxx:818
+#: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
 msgstr ""
 
-#: ../src/bout++.cxx:533
+#: ../src/bout++.cxx:540
 #, fuzzy, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
@@ -461,7 +462,7 @@ msgstr ""
 msgid "Command line"
 msgstr ""
 
-#: ../src/bout++.cxx:544 ../tests/unit/src/test_bout++.cxx:358
+#: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
 msgstr "編譯選項:\n"
 
@@ -470,16 +471,16 @@ msgstr "編譯選項:\n"
 msgid "Compiled with flags"
 msgstr "\t用設置編譯: {:s}\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:568
+#: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
 msgstr ""
 
-#: ../src/bout++.cxx:520
+#: ../src/bout++.cxx:527
 #, fuzzy, c++-format
 msgid "Could not create PID file {:s}"
 msgstr "無法打開輸出文件 '{:s}'\n"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:318
+#: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
 msgstr "無法找到NXPE的有效值。 嘗試不同數量的處理器。"
@@ -489,28 +490,28 @@ msgstr "無法找到NXPE的有效值。 嘗試不同數量的處理器。"
 msgid "Could not open output file '{:s}'\n"
 msgstr "無法打開輸出文件 '{:s}'\n"
 
-#: ../src/bout++.cxx:652
+#: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
 msgstr ""
 
 #. Error reading
-#: ../src/mesh/mesh.cxx:532
+#: ../src/mesh/mesh.cxx:543
 #, c++-format
 msgid "Could not read integer array '{:s}'\n"
 msgstr ""
 
 #. Failed . Probably not important enough to stop the simulation
-#: ../src/bout++.cxx:632
+#: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:765
+#: ../src/solver/solver.cxx:772
 #, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
 msgstr ""
 
-#: ../src/sys/expressionparser.cxx:273
+#: ../src/sys/expressionparser.cxx:312
 #, c++-format
 msgid ""
 "Couldn't find generator '{}'. BOUT++ expressions are now case-sensitive, so "
@@ -519,69 +520,69 @@ msgid ""
 "{}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:568
+#: ../src/mesh/mesh.cxx:587
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:560
+#: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:576
+#: ../src/mesh/mesh.cxx:595
 #, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
 msgstr ""
 
 #. Convert any exceptions to something a bit more useful
-#: ../src/sys/options.cxx:336
+#: ../src/sys/options.cxx:361
 #, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
 msgstr ""
 
-#: ../src/bout++.cxx:508
+#: ../src/bout++.cxx:515
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
 msgstr "\"{:s}\" 不存在或不可訪問\n"
 
-#: ../src/bout++.cxx:505
+#: ../src/bout++.cxx:512
 #, fuzzy, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
 msgstr "\"{:s}\" 不是目錄\n"
 
-#: ../src/solver/solver.cxx:665
+#: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
 msgstr ""
 
-#: ../src/bout++.cxx:209
+#: ../src/bout++.cxx:216
 #, fuzzy, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
 msgstr "啟動時遇到錯誤 : {:s}\n"
 
-#: ../src/bout++.cxx:744
+#: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:332
+#: ../src/mesh/impls/bout/boutmesh.cxx:323
 #, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
 msgstr ""
 
-#: ../src/solver/solver.cxx:512
+#: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:290
+#: ../src/mesh/impls/bout/boutmesh.cxx:281
 #, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:668
+#: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
 msgstr "初始化求解器\n"
 
-#: ../src/bout++.cxx:494
+#: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
@@ -591,122 +592,122 @@ msgstr ""
 msgid "Invalid command line option '-' found - maybe check whitespace?"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:400
+#: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
 msgstr "加載網格"
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:415
+#: ../src/mesh/impls/bout/boutmesh.cxx:451
 msgid "Mesh must contain nx"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:419
+#: ../src/mesh/impls/bout/boutmesh.cxx:455
 msgid "Mesh must contain ny"
 msgstr ""
 
 #. Not found
-#: ../src/mesh/mesh.cxx:536
+#: ../src/mesh/mesh.cxx:547
 #, c++-format
 msgid "Missing integer array {:s}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:905
+#: ../src/solver/solver.cxx:911
 #, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:883
+#: ../src/solver/solver.cxx:889
 #, c++-format
 msgid "Monitor signalled to quit (return code {})"
 msgstr ""
 
-#: ../src/bout++.cxx:823
+#: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:565
+#: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:550
+#: ../src/mesh/impls/bout/boutmesh.cxx:586
 msgid "No boundary regions; domain is periodic\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:254
+#: ../src/mesh/impls/bout/boutmesh.cxx:245
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:267
+#: ../src/mesh/impls/bout/boutmesh.cxx:258
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
 msgstr ""
 
 #. Less than 2 time-steps left
-#: ../src/bout++.cxx:896
+#: ../src/bout++.cxx:908
 #, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
 msgstr ""
 
-#: ../src/sys/options.cxx:303 ../src/sys/options.cxx:345
-#: ../src/sys/options.cxx:393 ../src/sys/options.cxx:428
-#: ../src/sys/options.cxx:703 ../src/sys/options.cxx:730
-#: ../src/sys/options.cxx:757
+#: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
+#: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
+#: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
+#: ../src/sys/options.cxx:789
 #, fuzzy, c++-format
 msgid "Option {:s} has no value"
 msgstr "\"{:s}\" 不是目錄\n"
 
 #. Doesn't exist
-#: ../src/sys/options.cxx:159
+#: ../src/sys/options.cxx:172
 #, fuzzy, c++-format
 msgid "Option {:s}:{:s} does not exist"
 msgstr "選項{:s}:{:s}不存在"
 
-#: ../include/bout/options.hxx:828
+#: ../include/bout/options.hxx:904
 #, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
 "value was '{:s}'."
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:552
+#: ../src/mesh/impls/bout/boutmesh.cxx:588
 msgid "Possible boundary regions are: "
 msgstr ""
 
-#: ../src/bout++.cxx:538
+#: ../src/bout++.cxx:545
 #, c++-format
 msgid ""
 "Processor number: {:d} of {:d}\n"
 "\n"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:609
+#: ../src/mesh/mesh.cxx:642
 #, c++-format
 msgid "Registered region 2D {:s}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:599
+#: ../src/mesh/mesh.cxx:632
 #, c++-format
 msgid "Registered region 3D {:s}"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:619
+#: ../src/mesh/mesh.cxx:652
 #, c++-format
 msgid "Registered region Perp {:s}"
 msgstr ""
 
-#: ../src/bout++.cxx:529
+#: ../src/bout++.cxx:536
 #, fuzzy, c++-format
 msgid "Revision: {:s}\n"
 msgstr "版: {:s}\n"
 
-#: ../src/solver/solver.cxx:581
+#: ../src/solver/solver.cxx:587
 msgid "Run time : "
 msgstr "計算時間"
 
 #. / Run the solver
-#: ../src/solver/solver.cxx:525
+#: ../src/solver/solver.cxx:533
 msgid ""
 "Running simulation\n"
 "\n"
@@ -718,7 +719,7 @@ msgstr ""
 msgid "Signal"
 msgstr ""
 
-#: ../src/bout++.cxx:865
+#: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
@@ -727,7 +728,7 @@ msgstr ""
 "間整合\n"
 "\n"
 
-#: ../src/bout++.cxx:868
+#: ../src/bout++.cxx:879
 msgid ""
 "Sim Time  |  RHS_e evals  | RHS_I evals  | Wall Time |  Calc    Inv   "
 "Comm    I/O   SOLVER\n"
@@ -737,51 +738,51 @@ msgstr ""
 "通訊   輸入輸出  時間整合\n"
 "\n"
 
-#: ../src/solver/solver.cxx:506
+#: ../src/solver/solver.cxx:514
 #, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:502
+#: ../src/solver/solver.cxx:510
 #, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:781
+#: ../src/solver/solver.cxx:788
 #, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
 "called!"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1281
+#: ../src/solver/solver.cxx:1289
 #, c++-format
 msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1480
+#: ../src/solver/solver.cxx:1494
 #, c++-format
 msgid "Time derivative for variable '{:s}' not set"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:605
+#: ../src/mesh/mesh.cxx:638
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:595
+#: ../src/mesh/mesh.cxx:614
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
 msgstr ""
 
-#: ../src/mesh/mesh.cxx:616
+#: ../src/mesh/mesh.cxx:649
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
 msgstr ""
 
-#: ../src/sys/options.cxx:99 ../src/sys/options.cxx:138
+#: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
 #, c++-format
 msgid ""
 "Trying to index Option '{0}' with '{1}', but '{0}' is a value, not a "
@@ -790,37 +791,37 @@ msgid ""
 "rename one of them.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:1462
+#: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
 msgstr ""
 
-#: ../src/sys/options.cxx:872
+#: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
 msgstr ""
 
-#: ../src/bout++.cxx:439
+#: ../src/bout++.cxx:446
 #, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:448
+#: ../src/bout++.cxx:455
 #, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:466
+#: ../src/bout++.cxx:473
 #, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:457
+#: ../src/bout++.cxx:464
 #, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
 msgstr ""
 
-#: ../src/bout++.cxx:353
+#: ../src/bout++.cxx:360
 #, c++-format
 msgid "Usage is {} {} <name>\n"
 msgstr ""
@@ -831,7 +832,7 @@ msgstr ""
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
-#: ../src/bout++.cxx:367
+#: ../src/bout++.cxx:374
 #, c++-format
 msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
@@ -839,94 +840,99 @@ msgid ""
 msgstr ""
 
 #. restart file should be written by physics model
-#: ../src/solver/solver.cxx:921
+#: ../src/solver/solver.cxx:927
 msgid "User signalled to quit. Returning\n"
 msgstr ""
 
-#: ../src/sys/options.cxx:373
+#: ../src/sys/options.cxx:486
+#, fuzzy, c++-format
+msgid "Value for option {:s} = {:e} is not a bool"
+msgstr "\"{:s}\" 不是目錄\n"
+
+#: ../src/sys/options.cxx:426
 #, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
 msgstr ""
 
-#: ../src/sys/options.cxx:408
+#: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
 msgstr ""
 
-#: ../src/sys/options.cxx:581
+#: ../src/sys/options.cxx:623
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
 msgstr ""
 
-#: ../src/sys/options.cxx:529
+#: ../src/sys/options.cxx:571
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
 msgstr ""
 
-#: ../src/sys/options.cxx:663
+#: ../src/sys/options.cxx:705
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
 msgstr ""
 
-#: ../src/sys/options.cxx:451
+#: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
 msgstr ""
 
-#: ../src/sys/options.cxx:709
+#: ../src/sys/options.cxx:751
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
 msgstr ""
 
-#: ../src/sys/options.cxx:736
+#: ../src/sys/options.cxx:773
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
 msgstr ""
 
-#: ../src/sys/options.cxx:763
+#: ../src/sys/options.cxx:795
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
 msgstr ""
 
 #. Another type which can't be converted
-#: ../src/sys/options.cxx:365
+#: ../src/sys/options.cxx:418
 #, c++-format
 msgid "Value for option {:s} is not an integer"
 msgstr ""
 
-#: ../src/solver/solver.cxx:1232 ../src/solver/solver.cxx:1238
+#: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
 #, c++-format
 msgid "Variable '{:s}' not initialised"
 msgstr ""
 
-#: ../src/mesh/impls/bout/boutmesh.cxx:431
+#: ../src/mesh/impls/bout/boutmesh.cxx:467
 #, c++-format
 msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:633
+#: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:410
+#: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:638
+#: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
 
-#: ../src/mesh/coordinates.cxx:415
+#: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
 
-#: ../src/bout++.cxx:814
+#: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
 msgstr ""
 
@@ -936,10 +942,18 @@ msgid "Writing options to file {:s}\n"
 msgstr "寫選項到文件 "
 
 #. / The source label given to default values
-#: ../src/sys/options.cxx:15
+#: ../src/sys/options.cxx:34
 msgid "default"
 msgstr "默认设置"
 
+#, fuzzy, c++-format
+#~ msgid "\tOpenMP parallelisation {}"
+#~ msgstr "\tOpenMP並行化已禁用\n"
+
+#, fuzzy, c++-format
+#~ msgid "\tOption '{:s}': Boolean expected. Got '{:s}'\n"
+#~ msgstr "\t選項 '{:s}': 布爾預期. 拿到 '{:s}'\n"
+
 #~ msgid "\tChecking disabled\n"
 #~ msgstr "\t測試關掉\n"
 
@@ -947,13 +961,5 @@ msgstr "默认设置"
 #~ msgid "\tChecking enabled, level {:d}\n"
 #~ msgstr "\t測試打開,级别 {:d}\n"
 
-#, fuzzy
-#~ msgid "\tOpenMP parallelisation enabled, using {:d} threads\n"
-#~ msgstr "\t啟用OpenMP並行化。 使用{:d}個線程\n"
-
-#, fuzzy
-#~ msgid "Option {:s} is not a section"
-#~ msgstr "\"{:s}\" 不是目錄\n"
-
 #~ msgid "Error encountered during initialisation\n"
 #~ msgstr "啟動時遇到錯誤\n"

From 84f60c5d8497ee35882218b0f632913c89582fa1 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 10:49:46 +0100
Subject: [PATCH 0247/1827] Tweak citations updater, mention in docs

---
 bin/update_citations.py | 10 ++++++++++
 manual/RELEASE_HOWTO.md |  5 ++---
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/bin/update_citations.py b/bin/update_citations.py
index c7771a3611..63f597f588 100755
--- a/bin/update_citations.py
+++ b/bin/update_citations.py
@@ -1,4 +1,11 @@
 #!/usr/bin/env python3
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#     "ruamel-yaml",
+#     "unidecode",
+# ]
+# ///
 import argparse
 import subprocess
 from collections import defaultdict
@@ -242,6 +249,9 @@ def update_citations():
 
     new_authors = []
     for author in unrecognised_authors:
+        if " " not in author:
+            # This is just a GitHub handle, skip
+            continue
         first_name, last_name = author.rsplit(maxsplit=1)
         new_authors.append({"family-names": last_name, "given-names": first_name})
 
diff --git a/manual/RELEASE_HOWTO.md b/manual/RELEASE_HOWTO.md
index d8ced2afb5..72d1fb3f88 100644
--- a/manual/RELEASE_HOWTO.md
+++ b/manual/RELEASE_HOWTO.md
@@ -31,9 +31,8 @@ Before merging PR:
 - [ ] Update [`CHANGELOG.md`][changelog]:
     - Run [bout-changelog-generator.py LAST_RELEASE NEXT_RELEASE][bin/bout-changelog-generator.py]
         - See the docs for how to get the token
-- [ ] Get list of authors:
-    - [ ] `git log --format='%aN' | sort | uniq`
-    - [ ] Compare to list in [`CITATION.cff`][citation], add new authors
+- [ ] Run [`update_citations.py`][bin/update_citations.py] to add new
+      authors to [`CITATION.cff`](CITATION.cff)
 - [ ] Prep a new Zenodo release:
     - https://doi.org/10.5281/zenodo.1423212
     - "New Version"

From 265bbb9d2c4d3918f00d5999127a81c1775022b1 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 10:50:06 +0100
Subject: [PATCH 0248/1827] Add new authors

---
 CITATION.cff | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/CITATION.cff b/CITATION.cff
index 81f5c35e82..6a9881b379 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -197,6 +197,22 @@ authors:
   - family-names: Kryjak
     given-names: Mike
 
+  - family-names: Powell
+    given-names: Seimon
+  - family-names: Ağgül
+    given-names: Mustafa
+  - family-names: Parry
+    given-names: Owen
+  - family-names: Podhorszki
+    given-names: Norbert
+  - family-names: Falgout
+    given-names: Rob
+  - family-names: Li
+    given-names: Nami
+  - family-names: Body
+    given-names: Tom
+  - family-names: Tsagkaridis
+    given-names: Malamas
 version: 5.1.1
 date-released: 2023-04-10
 repository-code: https://github.com/boutproject/BOUT-dev

From 7e96b3f9609d34b8e5e75ce3de10047b9b584cfd Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 10:55:14 +0100
Subject: [PATCH 0249/1827] Add dependencies to changelog updater

---
 bin/bout-changelog-generator.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/bin/bout-changelog-generator.py b/bin/bout-changelog-generator.py
index cfb9a30bb0..d5ad11892e 100755
--- a/bin/bout-changelog-generator.py
+++ b/bin/bout-changelog-generator.py
@@ -1,4 +1,10 @@
 #! /usr/bin/env python3
+# /// script
+# requires-python = ">=3.12"
+# dependencies = [
+#     "pygithub",
+# ]
+# ///
 
 import argparse
 import os

From 7678b8ab7723ece7dcf3c48d2dd8b728e206d6f7 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 11:19:52 +0100
Subject: [PATCH 0250/1827] Tweak version updater, mention in docs

---
 bin/update_version_number_in_files.py |  5 -----
 manual/RELEASE_HOWTO.md               | 10 ++--------
 2 files changed, 2 insertions(+), 13 deletions(-)

diff --git a/bin/update_version_number_in_files.py b/bin/update_version_number_in_files.py
index 85df930aea..ec9a31bc32 100755
--- a/bin/update_version_number_in_files.py
+++ b/bin/update_version_number_in_files.py
@@ -66,11 +66,6 @@ def update_version_number_in_file(relative_filepath, pattern, new_version_number
 def bump_version_numbers(
     new_version_number: VersionNumber, next_version_number: VersionNumber
 ):
-    update_version_number_in_file(
-        "configure.ac",
-        r"^AC_INIT\(\[BOUT\+\+\],\[(\d+\.\d+\.\d+)\]",
-        new_version_number,
-    )
     update_version_number_in_file(
         "CITATION.cff", r"^version: (\d+\.\d+\.\d+)", new_version_number
     )
diff --git a/manual/RELEASE_HOWTO.md b/manual/RELEASE_HOWTO.md
index 72d1fb3f88..d0a6ddb231 100644
--- a/manual/RELEASE_HOWTO.md
+++ b/manual/RELEASE_HOWTO.md
@@ -29,7 +29,7 @@ Before merging PR:
     - Be aware that this *will* update the timestamps and *possibly*
       reorder file paths in the .po and .pot files
 - [ ] Update [`CHANGELOG.md`][changelog]:
-    - Run [bout-changelog-generator.py LAST_RELEASE NEXT_RELEASE][bin/bout-changelog-generator.py]
+    - Run [`bout-changelog-generator.py LAST_RELEASE NEXT_RELEASE`][bin/bout-changelog-generator.py]
         - See the docs for how to get the token
 - [ ] Run [`update_citations.py`][bin/update_citations.py] to add new
       authors to [`CITATION.cff`](CITATION.cff)
@@ -43,13 +43,7 @@ Before merging PR:
 - [ ] Change DOI in [`README.md`][README] to new DOI
 - [ ] Change date-released in [`CITATION.cff`][citation]
 - [ ] Check `abidiff` to see if `soname` needs bumping in `makefile`:
-- [ ] Change version number, removing prerelease tag in:
-    - [ ]  [`configure.ac`][configure]: `AC_INIT`
-    - [ ]  [`CITATION.cff`][citation]: `version`
-    - [ ]  [`manual/sphinx/conf.py`][sphinx_conf]: `version` and `release`
-    - [ ]  [`manual/doxygen/Doxyfile_readthedocs`][Doxyfile_readthedocs]: `PROJECT_NUMBER`
-    - [ ]  [`manual/doxygen/Doxyfile`][Doxyfile]: `PROJECT_NUMBER`
-    - [ ]  [`CMakeLists.txt`][CMakeLists]: `_bout_previous_version`, `_bout_next_version`
+- [ ] Run [`update_version_number.py LAST_RELEASE NEXT_RELEASE`][bin/update_version_number.py]
 - [ ] Update what version of PETSc and SUNDIALS we support (upper bound)
 
 

From ad1d5147894557608a6a28639fbed5256df7f2e8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 11:20:07 +0100
Subject: [PATCH 0251/1827] Bump version to 5.2.0

---
 CITATION.cff                         | 2 +-
 CMakeLists.txt                       | 4 ++--
 manual/doxygen/Doxyfile              | 2 +-
 manual/doxygen/Doxyfile_readthedocs  | 2 +-
 manual/sphinx/conf.py                | 4 ++--
 tools/pylib/_boutpp_build/backend.py | 4 ++--
 6 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 6a9881b379..496f8a3154 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -213,7 +213,7 @@ authors:
     given-names: Tom
   - family-names: Tsagkaridis
     given-names: Malamas
-version: 5.1.1
+version: 5.2.0
 date-released: 2023-04-10
 repository-code: https://github.com/boutproject/BOUT-dev
 url: http://boutproject.github.io/
diff --git a/CMakeLists.txt b/CMakeLists.txt
index c45fca3b72..5c49e434e4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,8 +25,8 @@ endif()
 # CMake currently doesn't support proper semver
 # Set the version here, strip any extra tags to use in `project`
 # We try to use git to get a full description, inspired by setuptools_scm
-set(_bout_previous_version "5.1.1")
-set(_bout_next_version "5.2.0")
+set(_bout_previous_version "5.2.0")
+set(_bout_next_version "5.2.1")
 execute_process(
   COMMAND "git" describe --tags --match=v${_bout_previous_version}
   COMMAND sed -e s/${_bout_previous_version}-/${_bout_next_version}.dev/ -e s/-/+/
diff --git a/manual/doxygen/Doxyfile b/manual/doxygen/Doxyfile
index 0e3c6f6945..e7998854b0 100644
--- a/manual/doxygen/Doxyfile
+++ b/manual/doxygen/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME           = BOUT++
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 5.1.1
+PROJECT_NUMBER         = 5.2.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
diff --git a/manual/doxygen/Doxyfile_readthedocs b/manual/doxygen/Doxyfile_readthedocs
index 5c67187248..73060bb6b4 100644
--- a/manual/doxygen/Doxyfile_readthedocs
+++ b/manual/doxygen/Doxyfile_readthedocs
@@ -38,7 +38,7 @@ PROJECT_NAME           = BOUT++
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 5.1.1
+PROJECT_NUMBER         = 5.2.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 55d059feba..3aa6e94dc3 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -184,9 +184,9 @@ def __getattr__(cls, name):
 # built documents.
 #
 # The short X.Y version.
-version = "5.1"
+version = "5.2"
 # The full version, including alpha/beta/rc tags.
-release = "5.1.1"
+release = "5.2.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 3df29d276d..ae3162cf11 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -35,8 +35,8 @@ def getversion():
             version = os.environ["BOUT_PRETEND_VERSION"]
             return version
 
-        _bout_previous_version = "v5.1.1"
-        _bout_next_version = "v5.2.0"
+        _bout_previous_version = "v5.2.0"
+        _bout_next_version = "v5.2.1"
 
         try:
             try:

From 0cb29717831fec0bf858a756261efaac34afbdef Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 11:26:20 +0100
Subject: [PATCH 0252/1827] Update changelog

---
 CHANGELOG.md | 66 ++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 64 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5d346d47e8..41e3e2c47b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,7 +1,8 @@
 # Changelog
 
-## [v6.0.0](https://github.com/boutproject/BOUT-dev/tree/next)
-[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.0...next)
+## [v5.2.0](https://github.com/boutproject/BOUT-dev/tree/v5.2.0
+
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.1...v5.2.0)
 
 ### Breaking changes
 
@@ -16,6 +17,67 @@
   confusing. Now, monitors are called with the current number of
   completed monitor-steps.
 
+## Changes
+
+- Fixes for FreeBSD [\#3172][https://github.com/boutproject/BOUT-dev/pull/3172] ([tomc271][https://github.com/tomc271])
+- snes: Print a warning if the coloring is non-symmetric. [\#3159][https://github.com/boutproject/BOUT-dev/pull/3159] ([bendudson][https://github.com/bendudson])
+- Cmake fix from master [\#3152][https://github.com/boutproject/BOUT-dev/pull/3152] ([oparry-ukaea][https://github.com/oparry-ukaea])
+- Bump ZedThree/clang-tidy-review from 0.20.1 to 0.21.0 [\#3150][https://github.com/boutproject/BOUT-dev/pull/3150] ([ZedThree][https://github.com/ZedThree])
+- SNES solver: Added a PID controller to update the timestep  [\#3146][https://github.com/boutproject/BOUT-dev/pull/3146] ([malamast][https://github.com/malamast])
+- Fix name clash in some examples and MMS tests  [\#3145][https://github.com/boutproject/BOUT-dev/pull/3145] ([ZedThree][https://github.com/ZedThree])
+- Handle absolute paths to options file [\#3142][https://github.com/boutproject/BOUT-dev/pull/3142] ([bendudson][https://github.com/bendudson])
+- Revert eliminate hypre boundary equations [\#3136][https://github.com/boutproject/BOUT-dev/pull/3136] ([ZedThree][https://github.com/ZedThree])
+- CI: Switch to released fedora [\#3134][https://github.com/boutproject/BOUT-dev/pull/3134] ([dschwoerer][https://github.com/dschwoerer])
+- Generalise FakeMeshFixture to allow configurable grid spacing via templating [\#3132][https://github.com/boutproject/BOUT-dev/pull/3132] ([tomc271][https://github.com/tomc271])
+- Fixes for ELM-PB preconditioner [\#3128][https://github.com/boutproject/BOUT-dev/pull/3128] ([Steven-Roberts][https://github.com/Steven-Roberts])
+- Fix cast for new petsc [\#3117][https://github.com/boutproject/BOUT-dev/pull/3117] ([dschwoerer][https://github.com/dschwoerer])
+- Fix bug where ARKODE considered all problems linear [\#3114][https://github.com/boutproject/BOUT-dev/pull/3114] ([Steven-Roberts][https://github.com/Steven-Roberts])
+- cvode: Add linear_solver option [\#3112][https://github.com/boutproject/BOUT-dev/pull/3112] ([bendudson][https://github.com/bendudson])
+- periodicX communication fixes [\#3109][https://github.com/boutproject/BOUT-dev/pull/3109] ([bendudson][https://github.com/bendudson])
+- beuler solver timestep and Jacobian calculation [\#3107][https://github.com/boutproject/BOUT-dev/pull/3107] ([bendudson][https://github.com/bendudson])
+- Feature/snes stencil [\#3104][https://github.com/boutproject/BOUT-dev/pull/3104] ([seimtpow][https://github.com/seimtpow])
+- Add attributes to ADIOS2 output to "define" dimensions as names. We n… [\#3098][https://github.com/boutproject/BOUT-dev/pull/3098] ([pnorbert][https://github.com/pnorbert])
+- CI: Avoid issues with special characters [\#3090][https://github.com/boutproject/BOUT-dev/pull/3090] ([dschwoerer][https://github.com/dschwoerer])
+- CI: Fix clang format [\#3086][https://github.com/boutproject/BOUT-dev/pull/3086] ([dschwoerer][https://github.com/dschwoerer])
+- Small updates for FCI output [\#3085][https://github.com/boutproject/BOUT-dev/pull/3085] ([bendudson][https://github.com/bendudson])
+- Eliminate boundary equations to improve HYPRE solves [\#3082][https://github.com/boutproject/BOUT-dev/pull/3082] ([rfalgout][https://github.com/rfalgout])
+- Elm-pb example with relaxing phi [\#3081][https://github.com/boutproject/BOUT-dev/pull/3081] ([bendudson][https://github.com/bendudson])
+- CI: Show more output of dnf5 to help debugging [\#3071][https://github.com/boutproject/BOUT-dev/pull/3071] ([dschwoerer][https://github.com/dschwoerer])
+- Fix clang tidy review [\#3070][https://github.com/boutproject/BOUT-dev/pull/3070] ([ZedThree][https://github.com/ZedThree])
+- CMake: Bump downloaded SUNDIALS version [\#3067][https://github.com/boutproject/BOUT-dev/pull/3067] ([ZedThree][https://github.com/ZedThree])
+- Use isfinite, fix pvode linking [\#3063][https://github.com/boutproject/BOUT-dev/pull/3063] ([bendudson][https://github.com/bendudson])
+- Make iteration more robust and give more options in LaplaceNaulin [\#3061][https://github.com/boutproject/BOUT-dev/pull/3061] ([johnomotani][https://github.com/johnomotani])
+- Fixes zoidberg [\#3054][https://github.com/boutproject/BOUT-dev/pull/3054] ([dschwoerer][https://github.com/dschwoerer])
+- Fix finalise in boutpp  [\#3053][https://github.com/boutproject/BOUT-dev/pull/3053] ([dschwoerer][https://github.com/dschwoerer])
+- Avoid some warnings for 3D Metrics [\#3052][https://github.com/boutproject/BOUT-dev/pull/3052] ([dschwoerer][https://github.com/dschwoerer])
+- Minor fixes for the python backend [\#3051][https://github.com/boutproject/BOUT-dev/pull/3051] ([dschwoerer][https://github.com/dschwoerer])
+- Cleanup BOUT_HOST_DEVICE qualifiers [\#3040][https://github.com/boutproject/BOUT-dev/pull/3040] ([ggeorgakoudis][https://github.com/ggeorgakoudis])
+- Deprecate options that are only used as default for other options [\#3038][https://github.com/boutproject/BOUT-dev/pull/3038] ([dschwoerer][https://github.com/dschwoerer])
+- Avoid using the wrong grid by accident [\#3036][https://github.com/boutproject/BOUT-dev/pull/3036] ([dschwoerer][https://github.com/dschwoerer])
+- Use PEP 625 compatible archive name (next) [\#3035][https://github.com/boutproject/BOUT-dev/pull/3035] ([dschwoerer][https://github.com/dschwoerer])
+- CI: Increase check level for debug run + unit test fixes [\#3033][https://github.com/boutproject/BOUT-dev/pull/3033] ([dschwoerer][https://github.com/dschwoerer])
+- Avoid `#define` conflict with sundials [\#3031][https://github.com/boutproject/BOUT-dev/pull/3031] ([dschwoerer][https://github.com/dschwoerer])
+- Ensure PETSc headers are included after `bout/petsclib.hxx` [\#3024][https://github.com/boutproject/BOUT-dev/pull/3024] ([ZedThree][https://github.com/ZedThree])
+- Fix minor HYPRE and ADIOS2 compilation issues [\#3022][https://github.com/boutproject/BOUT-dev/pull/3022] ([ZedThree][https://github.com/ZedThree])
+- Fix recompilation cascade [\#3021][https://github.com/boutproject/BOUT-dev/pull/3021] ([ZedThree][https://github.com/ZedThree])
+- Move `invert3x3` out of general purpose `utils.hxx` header [\#3018][https://github.com/boutproject/BOUT-dev/pull/3018] ([ZedThree][https://github.com/ZedThree])
+- Replace deprecated `boututils.file_import` [\#3017][https://github.com/boutproject/BOUT-dev/pull/3017] ([ZedThree][https://github.com/ZedThree])
+- CI: clang-tidy-review tweaks [\#3016][https://github.com/boutproject/BOUT-dev/pull/3016] ([ZedThree][https://github.com/ZedThree])
+- Backward Euler solver improvements [\#3009][https://github.com/boutproject/BOUT-dev/pull/3009] ([bendudson][https://github.com/bendudson])
+- Fix circular header dependency: mesh.hxx <-> griddata.hxx [\#3008][https://github.com/boutproject/BOUT-dev/pull/3008] ([ZedThree][https://github.com/ZedThree])
+- Fix exception message [\#3003][https://github.com/boutproject/BOUT-dev/pull/3003] ([dschwoerer][https://github.com/dschwoerer])
+- Ensure pointer is checked before dereferencing [\#3002][https://github.com/boutproject/BOUT-dev/pull/3002] ([dschwoerer][https://github.com/dschwoerer])
+- Fix: preserve regionID [\#3000][https://github.com/boutproject/BOUT-dev/pull/3000] ([dschwoerer][https://github.com/dschwoerer])
+- Lazy grid loading [\#2991][https://github.com/boutproject/BOUT-dev/pull/2991] ([dschwoerer][https://github.com/dschwoerer])
+- Fix compilation warnings with SUNDIALS 7.1.0 [\#2990][https://github.com/boutproject/BOUT-dev/pull/2990] ([Steven-Roberts][https://github.com/Steven-Roberts])
+- Add LC gitlab CI for GPU build/run tests [\#2989][https://github.com/boutproject/BOUT-dev/pull/2989] ([ggeorgakoudis][https://github.com/ggeorgakoudis])
+- BoutMask non-const operator[](Ind3D) [\#2988][https://github.com/boutproject/BOUT-dev/pull/2988] ([bendudson][https://github.com/bendudson])
+- Use consistently signed char [\#2987][https://github.com/boutproject/BOUT-dev/pull/2987] ([dschwoerer][https://github.com/dschwoerer])
+- naulin laplace: Acceptance tolerances after maxits [\#2983][https://github.com/boutproject/BOUT-dev/pull/2983] ([bendudson][https://github.com/bendudson])
+- Merge v5.1.1 into `next` [\#2978][https://github.com/boutproject/BOUT-dev/pull/2978] ([ZedThree][https://github.com/ZedThree])
+- CI: Bump all ubuntu images [\#2977][https://github.com/boutproject/BOUT-dev/pull/2977] ([ZedThree][https://github.com/ZedThree])
+- Read 2D variables into Field3D [\#2975][https://github.com/boutproject/BOUT-dev/pull/2975] ([bendudson][https://github.com/bendudson])
+
 ## [v5.1.1](https://github.com/boutproject/BOUT-dev/tree/v5.1.1)
 [Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.0...v5.1.1)
 

From 6e35ac05507c0f11bd5ccbcd955fd8b0a9860e3b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 13:50:13 +0100
Subject: [PATCH 0253/1827] CI: Don't run clang-{tidy,format} on RC branches

---
 .github/workflows/clang-format.yml      | 2 ++
 .github/workflows/clang-tidy-review.yml | 5 ++---
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/clang-format.yml b/.github/workflows/clang-format.yml
index 60cf5b6d6f..e32c959cb2 100644
--- a/.github/workflows/clang-format.yml
+++ b/.github/workflows/clang-format.yml
@@ -8,6 +8,8 @@ on:
 
 jobs:
   clang-format:
+    # Release candidate branches tend to have big PRs which causes all sorts of problems
+    if: ${{ !endsWith(github.head_ref, '-rc') }}
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 743eefe703..3f20db608f 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -5,9 +5,6 @@ on:
     paths:
       - '**.cxx'
       - '**.hxx'
-    branches-ignore:
-      # Release candidate branches tend to have big PRs which causes all sorts of problems
-      - 'v*rc'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -15,6 +12,8 @@ concurrency:
 
 jobs:
   review:
+    # Release candidate branches tend to have big PRs which causes all sorts of problems
+    if: ${{ !endsWith(github.head_ref, '-rc') }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5

From 6c78dc439884f66943842de574921367c9ffdd67 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 14:06:09 +0100
Subject: [PATCH 0254/1827] Fix reorder warning from snes

---
 src/solver/impls/snes/snes.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 2bb163f324..7965107b38 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -115,12 +115,12 @@ SNESSolver::SNESSolver(Options* opts)
                .doc("Convergence tolerance in terms of the norm of the change in "
                     "the solution between steps")
                .withDefault(1e-8)),
-      maxits((*options)["max_nonlinear_iterations"]
-                 .doc("Maximum number of nonlinear iterations per SNES solve")
-                 .withDefault(50)),
       maxf((*options)["maxf"]
                .doc("Maximum number of function evaluations per SNES solve")
                .withDefault(10000)),
+      maxits((*options)["max_nonlinear_iterations"]
+                 .doc("Maximum number of nonlinear iterations per SNES solve")
+                 .withDefault(50)),
       lower_its((*options)["lower_its"]
                     .doc("Iterations below which the next timestep is increased")
                     .withDefault(static_cast<int>(maxits * 0.5))),

From f1f014376ff22cb46734dec043ee23c507052ef1 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 14:06:27 +0100
Subject: [PATCH 0255/1827] Fix some easy clang-tidy snes warnings

---
 src/solver/impls/snes/snes.cxx | 14 +++++++-------
 src/solver/impls/snes/snes.hxx |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 7965107b38..de6c54388d 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -57,6 +57,7 @@ class ColoringStencil {
   }
 };
 
+namespace {
 /*
  * PETSc callback function, which evaluates the nonlinear
  * function to be solved by SNES.
@@ -64,7 +65,7 @@ class ColoringStencil {
  * This function assumes the context void pointer is a pointer
  * to an SNESSolver object.
  */
-static PetscErrorCode FormFunction(SNES UNUSED(snes), Vec x, Vec f, void* ctx) {
+PetscErrorCode FormFunction(SNES UNUSED(snes), Vec x, Vec f, void* ctx) {
   return static_cast<SNESSolver*>(ctx)->snes_function(x, f, false);
 }
 
@@ -73,7 +74,7 @@ static PetscErrorCode FormFunction(SNES UNUSED(snes), Vec x, Vec f, void* ctx) {
  *
  * This function can be a linearised form of FormFunction
  */
-static PetscErrorCode FormFunctionForDifferencing(void* ctx, Vec x, Vec f) {
+PetscErrorCode FormFunctionForDifferencing(void* ctx, Vec x, Vec f) {
   return static_cast<SNESSolver*>(ctx)->snes_function(x, f, true);
 }
 
@@ -82,21 +83,20 @@ static PetscErrorCode FormFunctionForDifferencing(void* ctx, Vec x, Vec f) {
  *
  * This can be a linearised and simplified form of FormFunction
  */
-static PetscErrorCode FormFunctionForColoring(void* UNUSED(snes), Vec x, Vec f,
+PetscErrorCode FormFunctionForColoring(void* UNUSED(snes), Vec x, Vec f,
                                               void* ctx) {
   return static_cast<SNESSolver*>(ctx)->snes_function(x, f, true);
 }
 
-static PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
-  int ierr;
-
+PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
   // Get the context
   SNESSolver* s;
-  ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&s));
+  int ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&s));
   CHKERRQ(ierr);
 
   PetscFunctionReturn(s->precon(x, y));
 }
+}
 
 SNESSolver::SNESSolver(Options* opts)
     : Solver(opts),
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index bd942f09ff..31deae6f06 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -57,7 +57,7 @@ BOUT_ENUM_CLASS(BoutSnesEquationForm, pseudo_transient, rearranged_backward_eule
 class SNESSolver : public Solver {
 public:
   explicit SNESSolver(Options* opts = nullptr);
-  ~SNESSolver() = default;
+  ~SNESSolver() override = default;
 
   int init() override;
   int run() override;

From 6380657813022478bf2870f4fbe6d6ecabe45259 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 14:06:51 +0100
Subject: [PATCH 0256/1827] Bump bundled fmt

---
 externalpackages/fmt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/fmt b/externalpackages/fmt
index 2ac6c5ca8b..486e7ba579 160000
--- a/externalpackages/fmt
+++ b/externalpackages/fmt
@@ -1 +1 @@
-Subproject commit 2ac6c5ca8b3dfbcb1cc5cf49a8cc121e3984559c
+Subproject commit 486e7ba579a2c677772d004ecd0311142ba481be

From 01c406823fed18c63a5745c72333999c82ef8364 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 16:16:30 +0100
Subject: [PATCH 0257/1827] Fix deprecation warning

---
 include/bout/invertable_operator.hxx | 56 +++++++++++++---------------
 1 file changed, 25 insertions(+), 31 deletions(-)

diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx
index fe139986be..9b9dbba41a 100644
--- a/include/bout/invertable_operator.hxx
+++ b/include/bout/invertable_operator.hxx
@@ -219,21 +219,18 @@ public:
                 localmesh->LocalNy, localmesh->LocalNz, localmesh->maxregionblocksize);
           }
         }
-        if (localmesh->firstY() or localmesh->lastY()) {
-          for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) {
-            if (not localmesh->periodicY(ix)) {
-              if (localmesh->firstY()) {
-                nocorner3D +=
-                    Region<Ind3D>(ix, ix, 0, localmesh->ystart - 1, 0,
-                                  localmesh->LocalNz - 1, localmesh->LocalNy,
-                                  localmesh->LocalNz, localmesh->maxregionblocksize);
-              }
-              if (localmesh->lastY()) {
-                nocorner3D += Region<Ind3D>(
-                    ix, ix, localmesh->LocalNy - localmesh->ystart,
-                    localmesh->LocalNy - 1, 0, localmesh->LocalNz - 1, localmesh->LocalNy,
-                    localmesh->LocalNz, localmesh->maxregionblocksize);
-              }
+        for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) {
+          if (not localmesh->periodicY(ix)) {
+            if (localmesh->firstY(ix)) {
+              nocorner3D += Region<Ind3D>(
+                  ix, ix, 0, localmesh->ystart - 1, 0, localmesh->LocalNz - 1,
+                  localmesh->LocalNy, localmesh->LocalNz, localmesh->maxregionblocksize);
+            }
+            if (localmesh->lastY(ix)) {
+              nocorner3D += Region<Ind3D>(
+                  ix, ix, localmesh->LocalNy - localmesh->ystart, localmesh->LocalNy - 1,
+                  0, localmesh->LocalNz - 1, localmesh->LocalNy, localmesh->LocalNz,
+                  localmesh->maxregionblocksize);
             }
           }
         }
@@ -259,20 +256,17 @@ public:
                               0, 0, localmesh->LocalNy, 1, localmesh->maxregionblocksize);
           }
         }
-        if (localmesh->firstY() or localmesh->lastY()) {
-          for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) {
-            if (not localmesh->periodicY(ix)) {
-              if (localmesh->firstY()) {
-                nocorner2D +=
-                    Region<Ind2D>(ix, ix, 0, localmesh->ystart - 1, 0, 0,
-                                  localmesh->LocalNy, 1, localmesh->maxregionblocksize);
-              }
-              if (localmesh->lastY()) {
-                nocorner2D +=
-                    Region<Ind2D>(ix, ix, localmesh->LocalNy - localmesh->ystart,
-                                  localmesh->LocalNy - 1, 0, 0, localmesh->LocalNy, 1,
-                                  localmesh->maxregionblocksize);
-              }
+        for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) {
+          if (not localmesh->periodicY(ix)) {
+            if (localmesh->firstY(ix)) {
+              nocorner2D +=
+                  Region<Ind2D>(ix, ix, 0, localmesh->ystart - 1, 0, 0,
+                                localmesh->LocalNy, 1, localmesh->maxregionblocksize);
+            }
+            if (localmesh->lastY(ix)) {
+              nocorner2D += Region<Ind2D>(
+                  ix, ix, localmesh->LocalNy - localmesh->ystart, localmesh->LocalNy - 1,
+                  0, 0, localmesh->LocalNy, 1, localmesh->maxregionblocksize);
             }
           }
         }
@@ -575,7 +569,7 @@ public:
 };
 
 #endif // PETSC
-};     // namespace inversion
-};     // namespace bout
+}; // namespace inversion
+}; // namespace bout
 
 #endif // HEADER GUARD

From e804d0978e3d33c3bf9e003aadb6ee83efefbc77 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 17:10:32 +0100
Subject: [PATCH 0258/1827] Remove `boututils` from requirements; bump
 `boutdata`

---
 requirements.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 52d3076d58..078eecac6d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,6 +4,5 @@ scipy>=1.14.1
 netcdf4>=1.7.1
 matplotlib>=3.7.0
 Cython>=3.0.0
-boututils>=0.2.1
-boutdata>=0.2.1
+boutdata>=0.3.0
 zoidberg>=0.2.2

From d5b92c70f2cf640b9e4ed80b8f0d0f79cf35bd09 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 17:13:57 +0100
Subject: [PATCH 0259/1827] Suppress warning from `nodiscard` function

---
 tests/unit/sys/test_options.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx
index 448b49fc19..a9a3bf4af4 100644
--- a/tests/unit/sys/test_options.cxx
+++ b/tests/unit/sys/test_options.cxx
@@ -1099,7 +1099,7 @@ value6 = 12
 }
 
 TEST_F(OptionsTest, InvalidFormat) {
-  EXPECT_THROW(fmt::format("{:nope}", Options{}), fmt::format_error);
+  EXPECT_THROW([[maybe_unused]] auto none = fmt::format("{:nope}", Options{}), fmt::format_error);
 }
 
 TEST_F(OptionsTest, FormatValue) {

From 87269806690664888e4a4a3c2469ebac59a4123b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 6 Oct 2025 17:42:20 +0100
Subject: [PATCH 0260/1827] Add shim for ARKodeGetNumRhsEvals

---
 src/solver/impls/arkode/arkode.cxx | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 6f20ce11a6..0151f90167 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -72,6 +72,18 @@ int arkode_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zve
 
 int arkode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector fy,
                void* user_data, N_Vector tmp);
+
+#if SUNDIALS_VERSION_LESS_THAN(7, 2, 0)
+// Shim for backwards compatibility
+int ARKodeGetNumRhsEvals(void* arkode_mem, int partition_index, long int* num_rhs_evals) {
+  long int temp = 0;
+  if (partition_index == 0) {
+    return ARKStepGetNumRhsEvals(arkode_mem, num_rhs_evals, &temp);
+  } else {
+    return ARKStepGetNumRhsEvals(arkode_mem, &temp, num_rhs_evals);
+  }
+}
+#endif
 } // namespace
 // NOLINTEND(readability-identifier-length)
 
@@ -417,8 +429,7 @@ int ArkodeSolver::init() {
         if (hasPreconditioner()) {
           output.write("\tUsing user-supplied preconditioner\n");
 
-          if (ARKodeSetPreconditioner(arkode_mem, nullptr, arkode_pre)
-              != ARKLS_SUCCESS) {
+          if (ARKodeSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARKLS_SUCCESS) {
             throw BoutException("ARKodeSetPreconditioner failed\n");
           }
         } else {
@@ -516,12 +527,13 @@ int ArkodeSolver::run() {
     }
 
     // Get additional diagnostics
-    long int temp_long_int, temp_long_int2;
+    long int temp_long_int = 0;
     ARKodeGetNumSteps(arkode_mem, &temp_long_int);
     nsteps = int(temp_long_int);
-    ARKStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2);
+    ARKodeGetNumRhsEvals(arkode_mem, 0, &temp_long_int);
     nfe_evals = int(temp_long_int);
-    nfi_evals = int(temp_long_int2);
+    ARKodeGetNumRhsEvals(arkode_mem, 1, &temp_long_int);
+    nfi_evals = int(temp_long_int);
     if (treatment == Treatment::ImEx or treatment == Treatment::Implicit) {
       ARKodeGetNumNonlinSolvIters(arkode_mem, &temp_long_int);
       nniters = int(temp_long_int);

From 466fa980d8fb7f80b14252adec8769ab4e98d55a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 10 Oct 2025 14:20:40 +0100
Subject: [PATCH 0261/1827] Bump DOI

---
 CITATION.cff | 4 ++--
 README.md    | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 496f8a3154..318fcd1406 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -214,10 +214,10 @@ authors:
   - family-names: Tsagkaridis
     given-names: Malamas
 version: 5.2.0
-date-released: 2023-04-10
+date-released: 2025-10-10
 repository-code: https://github.com/boutproject/BOUT-dev
 url: http://boutproject.github.io/
-doi: 10.5281/zenodo.13753882
+doi: 10.5281/zenodo.17313945
 license: 'LGPL-3.0-or-later'
 references:
   - type: article
diff --git a/README.md b/README.md
index c2e035e924..c9e76a1ff4 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@
 [![Build Status](https://github.com/boutproject/BOUT-dev/actions/workflows/tests.yml/badge.svg?branch=next)](https://github.com/boutproject/BOUT-dev/actions)
 [![License](https://img.shields.io/badge/license-LGPL-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0.en.html)
 [![py3comp](https://img.shields.io/badge/py3-compatible-brightgreen.svg)](https://img.shields.io/badge/py3-compatible-brightgreen.svg)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13753882.svg)](https://doi.org/10.5281/zenodo.8369888)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17313945.svg)](https://doi.org/10.5281/zenodo.17313945)
 
 ```
 .______     ______    __    __  .___________.

From dc3720f7b57aeb9cf0dde05374dffd664f0e37df Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 10 Oct 2025 11:36:51 -0700
Subject: [PATCH 0262/1827] snes solver: Consider timestep change at output

Previously the timestep adjustment was inside a conditional
`if (looping) {...`. The variable `looping` is false when the
simulation time reaches or exceeds the next output time.

This meant that when the internal timestep exceeded the output
step, `looping` was almost always `false` and so the internal
timestep would saturate.

With this change a timestep adjustment will be considered after
every successful internal timestep.

Note: There may have been a reason why timestep adjustments were
not considered, but I can't remember what it was and it was not
documented.
---
 src/solver/impls/snes/snes.cxx | 93 ++++++++++++++++------------------
 1 file changed, 45 insertions(+), 48 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index de6c54388d..c10095af53 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -1069,62 +1069,59 @@ int SNESSolver::run() {
       }
 #endif // PETSC_VERSION_GE(3,20,0)
 
-      if (looping) {
-
-        if (pid_controller) {
-          // Changing the timestep.
-          // Note: The preconditioner depends on the timestep,
-          // so we recalculate the jacobian and the preconditioner
-          //  every time the timestep changes
-
-          timestep = pid(timestep, nl_its);
-
-          // NOTE(malamast): Do we really need this?
-          // Recompute Jacobian (for now)
-          if (saved_jacobian_lag == 0) {
-            SNESGetLagJacobian(snes, &saved_jacobian_lag);
-            SNESSetLagJacobian(snes, 1);
-          }
+      if (pid_controller) {
+        // Changing the timestep.
+        // Note: The preconditioner depends on the timestep,
+        // so we recalculate the jacobian and the preconditioner
+        //  every time the timestep changes
 
-        } else {
+        timestep = pid(timestep, nl_its);
 
-          // Consider changing the timestep.
-          // Note: The preconditioner depends on the timestep,
-          // so if it is not recalculated the it will be less
-          // effective.
-          if ((nl_its <= lower_its) && (timestep < max_timestep)
-              && (steps_since_snes_failure > 2)) {
-            // Increase timestep slightly
-            timestep *= timestep_factor_on_lower_its;
-
-            timestep = std::min(timestep, max_timestep);
-
-            // Note: Setting the SNESJacobianFn to NULL retains
-            // previously set evaluation function.
-            //
-            // The SNES Jacobian is a combination of the RHS Jacobian
-            // and a factor involving the timestep.
-            // Depends on equation_form
-            // -> Probably call SNESSetJacobian(snes, Jfd, Jfd, NULL, fdcoloring);
-
-            if (static_cast<BoutReal>(lin_its) / nl_its > 4) {
-              // Recompute Jacobian (for now)
-              if (saved_jacobian_lag == 0) {
-                SNESGetLagJacobian(snes, &saved_jacobian_lag);
-                SNESSetLagJacobian(snes, 1);
-              }
-            }
+        // NOTE(malamast): Do we really need this?
+        // Recompute Jacobian (for now)
+        if (saved_jacobian_lag == 0) {
+          SNESGetLagJacobian(snes, &saved_jacobian_lag);
+          SNESSetLagJacobian(snes, 1);
+        }
 
-          } else if (nl_its >= upper_its) {
-            // Reduce timestep slightly
-            timestep *= timestep_factor_on_upper_its;
+      } else {
 
-            // Recompute Jacobian
+        // Consider changing the timestep.
+        // Note: The preconditioner depends on the timestep,
+        // so if it is not recalculated the it will be less
+        // effective.
+        if ((nl_its <= lower_its) && (timestep < max_timestep)
+            && (steps_since_snes_failure > 2)) {
+          // Increase timestep slightly
+          timestep *= timestep_factor_on_lower_its;
+
+          timestep = std::min(timestep, max_timestep);
+
+          // Note: Setting the SNESJacobianFn to NULL retains
+          // previously set evaluation function.
+          //
+          // The SNES Jacobian is a combination of the RHS Jacobian
+          // and a factor involving the timestep.
+          // Depends on equation_form
+          // -> Probably call SNESSetJacobian(snes, Jfd, Jfd, NULL, fdcoloring);
+
+          if (static_cast<BoutReal>(lin_its) / nl_its > 4) {
+            // Recompute Jacobian (for now)
             if (saved_jacobian_lag == 0) {
               SNESGetLagJacobian(snes, &saved_jacobian_lag);
               SNESSetLagJacobian(snes, 1);
             }
           }
+
+        } else if (nl_its >= upper_its) {
+          // Reduce timestep slightly
+          timestep *= timestep_factor_on_upper_its;
+
+          // Recompute Jacobian
+          if (saved_jacobian_lag == 0) {
+            SNESGetLagJacobian(snes, &saved_jacobian_lag);
+            SNESSetLagJacobian(snes, 1);
+          }
         }
       }
       snes_failures = 0;
@@ -1132,7 +1129,7 @@ int SNESSolver::run() {
 
     if (!matrix_free) {
       ASSERT2(simtime >= target);
-      ASSERT2(simtime - dt < target);
+      ASSERT2(simtime - dt <= target);
       // Stepped over output timestep => Interpolate
       // snes_x is the solution at t = simtime
       // x0 is the solution at t = simtime - dt

From 5ded72d4803f460e92b418040e9af58280c75acc Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sun, 12 Oct 2025 11:22:47 -0700
Subject: [PATCH 0263/1827] snes solver: Pseudo Transient Continuation method

Setting `pseudo_time = true` now enables Pseudo-timestepping,
in which each cell has a separate timestep.

The timestep in each cell is set inversely proportional to the
residual (RMS time-derivative of all quantities in cell).

Recommend enabling `pid_controller` that multiplies all timesteps
by the same factor, to control the number of nonlinear iterations.

Output time uses the minimum timestep in the domain, so simulations
shouldn't need to run for as long as when all cells are evolved at
the same speed.
---
 src/solver/impls/snes/snes.cxx | 522 +++++++++++++++++++++++++++------
 src/solver/impls/snes/snes.hxx |  22 +-
 2 files changed, 456 insertions(+), 88 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index de6c54388d..49650b7b97 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -8,6 +8,7 @@
 #include <bout/boutexception.hxx>
 #include <bout/globals.hxx>
 #include <bout/msg_stack.hxx>
+#include <bout/output_bout_types.hxx>
 #include <bout/petsc_interface.hxx>
 #include <bout/utils.hxx>
 
@@ -83,8 +84,7 @@ PetscErrorCode FormFunctionForDifferencing(void* ctx, Vec x, Vec f) {
  *
  * This can be a linearised and simplified form of FormFunction
  */
-PetscErrorCode FormFunctionForColoring(void* UNUSED(snes), Vec x, Vec f,
-                                              void* ctx) {
+PetscErrorCode FormFunctionForColoring(void* UNUSED(snes), Vec x, Vec f, void* ctx) {
   return static_cast<SNESSolver*>(ctx)->snes_function(x, f, true);
 }
 
@@ -96,7 +96,7 @@ PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
 
   PetscFunctionReturn(s->precon(x, y));
 }
-}
+} // namespace
 
 SNESSolver::SNESSolver(Options* opts)
     : Solver(opts),
@@ -138,6 +138,21 @@ SNESSolver::SNESSolver(Options* opts)
           (*options)["timestep_factor_on_lower_its"]
               .doc("Multiply timestep if iterations are below lower_its")
               .withDefault(1.4)),
+      pseudo_time((*options)["pseudo_time"]
+                      .doc("Pseudo-Transient Continuation method?")
+                      .withDefault<bool>(false)),
+      pseudo_alpha((*options)["pseudo_alpha"]
+                       .doc("Sets timestep using dt = alpha / residual")
+                       .withDefault(100. * atol * timestep)),
+      pseudo_growth_factor((*options)["pseudo_growth_factor"]
+                               .doc("PTC growth factor on success")
+                               .withDefault(1.1)),
+      pseudo_reduction_factor((*options)["pseudo_reduction_factor"]
+                                  .doc("PTC reduction factor on failure")
+                                  .withDefault(0.5)),
+      pseudo_max_ratio((*options)["pseudo_max_ratio"]
+                           .doc("PTC maximum timestep ratio between neighbors")
+                           .withDefault(2.)),
       pid_controller(
           (*options)["pid_controller"].doc("Use PID controller?").withDefault(false)),
       target_its((*options)["target_its"].doc("Target snes iterations").withDefault(7)),
@@ -277,6 +292,21 @@ int SNESSolver::init() {
     CHKERRQ(ierr);
   }
 
+  if (pseudo_time) {
+    // Storage for per-variable timestep
+    PetscCall(VecDuplicate(snes_x, &dt_vec));
+    // Starting timestep
+    PetscCall(VecSet(dt_vec, timestep));
+
+    // Storage for previous residual. Used to compare
+    // residuals before and after step, and adjust timestep accordingly
+    PetscCall(VecDuplicate(snes_x, &previous_f));
+
+    // Diagnostic outputs
+    pseudo_timestep = timestep;
+    pseudo_residual = 0.0;
+  }
+
   // Nonlinear solver interface (SNES)
   output_info.write("Create SNES\n");
   SNESCreate(BoutComm::get(), &snes);
@@ -767,6 +797,19 @@ int SNESSolver::run() {
     CHKERRQ(ierr);
   }
 
+  if (pseudo_time) {
+    // Calculate the initial residual in snes_f
+    run_rhs(simtime);
+    {
+      BoutReal* fdata = nullptr;
+      ierr = VecGetArray(snes_f, &fdata);
+      CHKERRQ(ierr);
+      save_derivs(fdata);
+      ierr = VecRestoreArray(snes_f, &fdata);
+      CHKERRQ(ierr);
+    }
+  }
+
   BoutReal target = simtime;
   for (int s = 0; s < getNumberOutputSteps(); s++) {
     target += getOutputTimestep();
@@ -837,46 +880,67 @@ int SNESSolver::run() {
       // Copy the state (snes_x) into initial values (x0)
       VecCopy(snes_x, x0);
 
-      if (timestep < dt_min_reset) {
-        // Hit the minimum timestep, probably through repeated failures
+      if (pseudo_time) {
+        // Pseudo-Transient Continuation
+        // Each evolving quantity may have its own timestep
+        // Set timestep and dt scalars to the minimum of dt_vec
+
+        PetscCall(VecMin(dt_vec, nullptr, &timestep));
+        dt = timestep;
 
-        if (saved_jacobian_lag != 0) {
-          // Already tried this and it didn't work
-          throw BoutException("Solver failed after many attempts");
+        // Copy residual from snes_f to previous_f
+        // The value of snes_f is set before the timestepping loop
+        // then calculated after the timestep
+        PetscCall(VecCopy(snes_f, previous_f));
+
+        looping = true;
+        if (simtime + timestep >= target) {
+          looping = false;
         }
+      } else {
+        // Timestepping
 
-        // Try resetting the preconditioner, turn off predictor, and use a large timestep
-        SNESGetLagJacobian(snes, &saved_jacobian_lag);
-        SNESSetLagJacobian(snes, 1);
-        timestep = getOutputTimestep();
-        predictor = false; // Predictor can cause problems in near steady-state.
-      }
+        if (timestep < dt_min_reset) {
+          // Hit the minimum timestep, probably through repeated failures
 
-      // Set the timestep
-      dt = timestep;
-      looping = true;
-      if (simtime + dt >= target) {
-        // Note: When the timestep is changed the preconditioner needs to be updated
-        // => Step over the output time and interpolate if not matrix free
-
-        if (matrix_free) {
-          // Ensure that the timestep goes to the next output time and then stops.
-          // This avoids the need to interpolate
-          dt = target - simtime;
+          if (saved_jacobian_lag != 0) {
+            // Already tried this and it didn't work
+            throw BoutException("Solver failed after many attempts");
+          }
+
+          // Try resetting the preconditioner, turn off predictor, and use a large timestep
+          SNESGetLagJacobian(snes, &saved_jacobian_lag);
+          SNESSetLagJacobian(snes, 1);
+          timestep = getOutputTimestep();
+          predictor = false; // Predictor can cause problems in near steady-state.
         }
-        looping = false;
-      }
 
-      if (predictor and (time1 > 0.0)) {
-        // Use (time1, x1) and (simtime, x0) to make prediction
-        // snes_x <- x0 + (dt / (simtime - time1)) * (x0 - x1)
-        // snes_x <- -β * x1 + (1 + β) * snes_x
-        BoutReal beta = dt / (simtime - time1);
-        VecAXPBY(snes_x, -beta, (1. + beta), x1);
-      }
+        // Set the timestep
+        dt = timestep;
+        looping = true;
+        if (simtime + dt >= target) {
+          // Note: When the timestep is changed the preconditioner needs to be updated
+          // => Step over the output time and interpolate if not matrix free
+
+          if (matrix_free) {
+            // Ensure that the timestep goes to the next output time and then stops.
+            // This avoids the need to interpolate
+            dt = target - simtime;
+          }
+          looping = false;
+        }
+
+        if (predictor and (time1 > 0.0)) {
+          // Use (time1, x1) and (simtime, x0) to make prediction
+          // snes_x <- x0 + (dt / (simtime - time1)) * (x0 - x1)
+          // snes_x <- -β * x1 + (1 + β) * snes_x
+          BoutReal beta = dt / (simtime - time1);
+          VecAXPBY(snes_x, -beta, (1. + beta), x1);
+        }
 
-      if (pid_controller) {
-        SNESSetLagJacobian(snes, lag_jacobian);
+        if (pid_controller) {
+          SNESSetLagJacobian(snes, lag_jacobian);
+        }
       }
 
       // Run the solver
@@ -917,8 +981,16 @@ int SNESSolver::run() {
         ++snes_failures;
         steps_since_snes_failure = 0;
 
-        // Try a smaller timestep
-        timestep *= timestep_factor_on_failure;
+        if (pseudo_time) {
+          // Global scaling of timesteps
+          // Note: A better strategy might be to reduce timesteps
+          //       in problematic cells.
+          PetscCall(VecScale(dt_vec, timestep_factor_on_failure));
+
+        } else {
+          // Try a smaller timestep
+          timestep *= timestep_factor_on_failure;
+        }
         // Restore state
         VecCopy(x0, snes_x);
 
@@ -972,7 +1044,8 @@ int SNESSolver::run() {
 
       if (nl_its == 0) {
         // This can occur even with SNESSetForceIteration
-        // Results in simulation state freezing and rapidly going to the end
+        // Results in simulation state freezing and rapidly going
+        // to the end
 
         if (scale_vars) {
           // scaled_x <- snes_x * var_scaling_factors
@@ -1016,8 +1089,14 @@ int SNESSolver::run() {
         // Gather and print diagnostic information
 
         output.print("\r"); // Carriage return for printing to screen
+
+        // if (pseudo_time) {
+        //   output.write("\tTime {} alpha {} min_timestep {} nl_iter {} lin_iter {} reason {}",
+        //                simtime, pseudo_alpha, timestep, nl_its, lin_its, static_cast<int>(reason));
+        // } else {
         output.write("Time: {}, timestep: {}, nl iter: {}, lin iter: {}, reason: {}",
                      simtime, timestep, nl_its, lin_its, static_cast<int>(reason));
+        // }
         if (snes_failures > 0) {
           output.write(", SNES failures: {}", snes_failures);
         }
@@ -1069,62 +1148,256 @@ int SNESSolver::run() {
       }
 #endif // PETSC_VERSION_GE(3,20,0)
 
-      if (looping) {
+      if (pseudo_time) {
+        // Adjust local timesteps
 
-        if (pid_controller) {
-          // Changing the timestep.
-          // Note: The preconditioner depends on the timestep,
-          // so we recalculate the jacobian and the preconditioner
-          //  every time the timestep changes
+        // Calculate residuals
+        if (scale_vars) {
+          // scaled_x <- snes_x * var_scaling_factors
+          PetscCall(VecPointwiseMult(scaled_x, snes_x, var_scaling_factors));
+          const BoutReal* xdata = nullptr;
+          PetscCall(VecGetArrayRead(scaled_x, &xdata));
+          load_vars(const_cast<BoutReal*>(xdata));
+          PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
+        } else {
+          const BoutReal* xdata = nullptr;
+          PetscCall(VecGetArrayRead(snes_x, &xdata));
+          load_vars(const_cast<BoutReal*>(xdata));
+          PetscCall(VecRestoreArrayRead(snes_x, &xdata));
+        }
+        run_rhs(simtime);
+        {
+          BoutReal* fdata = nullptr;
+          PetscCall(VecGetArray(snes_f, &fdata));
+          save_derivs(fdata);
+          PetscCall(VecRestoreArray(snes_f, &fdata));
+        }
 
-          timestep = pid(timestep, nl_its);
+        // Compare previous_f with snes_f
+        // Use a per-cell timestep so that e.g density and pressure
+        // evolve in a way consistent with the equation of state.
+
+        // Reading the residual vectors
+        const BoutReal* previous_residual = nullptr;
+        PetscCall(VecGetArrayRead(previous_f, &previous_residual));
+        const BoutReal* current_residual = nullptr;
+        PetscCall(VecGetArrayRead(snes_f, &current_residual));
+        // Modifying the dt_vec values
+        BoutReal* dt_data = nullptr;
+        PetscCall(VecGetArray(dt_vec, &dt_data));
+
+        // Note: The ordering of quantities in the PETSc vectors
+        // depends on the Solver::loop_vars function
+        Mesh* mesh = bout::globals::mesh;
+        int idx = 0; // Index into PETSc Vecs
+
+        // Boundary cells
+        for (const auto& i2d : mesh->getRegion2D("RGN_BNDRY")) {
+          // Field2D quantities evolved together
+          int count = 0;
+          BoutReal R0 = 0.0;
+          BoutReal R1 = 0.0;
 
-          // NOTE(malamast): Do we really need this?
-          // Recompute Jacobian (for now)
-          if (saved_jacobian_lag == 0) {
-            SNESGetLagJacobian(snes, &saved_jacobian_lag);
-            SNESSetLagJacobian(snes, 1);
+          for (const auto& f : f2d) {
+            if (!f.evolve_bndry) {
+              continue; // Not evolving boundary => Skip
+            }
+            R0 += SQ(previous_residual[idx + count]);
+            R1 += SQ(current_residual[idx + count]);
+            ++count;
+          }
+          if (count > 0) {
+            R0 = sqrt(R0 / count);
+            R1 = sqrt(R1 / count);
+
+            // Adjust timestep for these quantities
+            BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], R0, R1);
+            for (int i = 0; i != count; ++i) {
+              dt_data[idx++] = new_timestep;
+            }
           }
 
-        } else {
+          // Field3D quantities evolved together within a cell
+          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+            count = 0;
+            R0 = 0.0;
+            R1 = 0.0;
+            for (const auto& f : f3d) {
+              if (!f.evolve_bndry) {
+                continue; // Not evolving boundary => Skip
+              }
+              R0 += SQ(previous_residual[idx + count]);
+              R1 += SQ(current_residual[idx + count]);
+              ++count;
+            }
+            if (count > 0) {
+              R0 = sqrt(R0 / count);
+              R1 = sqrt(R1 / count);
+
+              BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], R0, R1);
+
+              auto i3d = mesh->ind2Dto3D(i2d, jz);
+              pseudo_residual[i3d] = R1;
+              pseudo_timestep[i3d] = new_timestep;
+
+              for (int i = 0; i != count; ++i) {
+                dt_data[idx++] = new_timestep;
+              }
+            }
+          }
+        }
+
+        // Bulk of domain.
+        // These loops don't check the boundary flags
+        for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) {
+          // Field2D quantities evolved together
+          if (f2d.size() > 0) {
+            BoutReal R0 = 0.0;
+            BoutReal R1 = 0.0;
+            for (std::size_t i = 0; i != f2d.size(); ++i) {
+              R0 += SQ(previous_residual[idx + i]);
+              R1 += SQ(current_residual[idx + i]);
+            }
+            R0 = sqrt(R0 / f2d.size());
+            R1 = sqrt(R1 / f2d.size());
+
+            // Adjust timestep for these quantities
+            BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], R0, R1);
+            for (std::size_t i = 0; i != f2d.size(); ++i) {
+              dt_data[idx++] = new_timestep;
+            }
+          }
 
-          // Consider changing the timestep.
-          // Note: The preconditioner depends on the timestep,
-          // so if it is not recalculated the it will be less
-          // effective.
-          if ((nl_its <= lower_its) && (timestep < max_timestep)
-              && (steps_since_snes_failure > 2)) {
-            // Increase timestep slightly
-            timestep *= timestep_factor_on_lower_its;
-
-            timestep = std::min(timestep, max_timestep);
-
-            // Note: Setting the SNESJacobianFn to NULL retains
-            // previously set evaluation function.
-            //
-            // The SNES Jacobian is a combination of the RHS Jacobian
-            // and a factor involving the timestep.
-            // Depends on equation_form
-            // -> Probably call SNESSetJacobian(snes, Jfd, Jfd, NULL, fdcoloring);
-
-            if (static_cast<BoutReal>(lin_its) / nl_its > 4) {
-              // Recompute Jacobian (for now)
-              if (saved_jacobian_lag == 0) {
-                SNESGetLagJacobian(snes, &saved_jacobian_lag);
-                SNESSetLagJacobian(snes, 1);
+          // Field3D quantities evolved together within a cell
+          if (f3d.size() > 0) {
+            for (int jz = 0; jz < mesh->LocalNz; jz++) {
+              BoutReal R0 = 0.0;
+              BoutReal R1 = 0.0;
+              for (std::size_t i = 0; i != f3d.size(); ++i) {
+                R0 += SQ(previous_residual[idx + i]);
+                R1 += SQ(current_residual[idx + i]);
+              }
+              R0 = sqrt(R0 / f3d.size());
+              R1 = sqrt(R1 / f3d.size());
+              BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], R0, R1);
+
+              auto i3d = mesh->ind2Dto3D(i2d, jz);
+              pseudo_residual[i3d] = R1;
+
+              // Compare to neighbors
+              BoutReal min_neighboring_dt = max_timestep;
+              BoutReal mean_neighboring_dt = 0.0;
+              int neighbor_count = 0;
+              if (i3d.x() != 0) {
+                BoutReal val = pseudo_timestep[i3d.xm()];
+                min_neighboring_dt = std::min(min_neighboring_dt, val);
+                mean_neighboring_dt += val;
+                ++neighbor_count;
+              }
+              if (i3d.x() != mesh->LocalNx - 1) {
+                BoutReal val = pseudo_timestep[i3d.xp()];
+                min_neighboring_dt = std::min(min_neighboring_dt, val);
+                mean_neighboring_dt += val;
+                ++neighbor_count;
+              }
+              if (i3d.y() != 0) {
+                BoutReal val = pseudo_timestep[i3d.ym()];
+                min_neighboring_dt = std::min(min_neighboring_dt, val);
+                mean_neighboring_dt += val;
+                ++neighbor_count;
+              }
+              if (i3d.x() != mesh->LocalNy - 1) {
+                BoutReal val = pseudo_timestep[i3d.yp()];
+                min_neighboring_dt = std::min(min_neighboring_dt, val);
+                mean_neighboring_dt += val;
+                ++neighbor_count;
+              }
+              mean_neighboring_dt /= neighbor_count;
+
+              // Smooth
+              //new_timestep = 0.1 * mean_neighboring_dt + 0.9 * new_timestep;
+
+              // Limit ratio of timestep between neighboring cells
+              new_timestep =
+                  std::min(new_timestep, pseudo_max_ratio * min_neighboring_dt);
+
+              pseudo_timestep[i3d] = new_timestep;
+
+              for (std::size_t i = 0; i != f3d.size(); ++i) {
+                dt_data[idx++] = new_timestep;
               }
             }
+          }
+        }
+
+        // Restore Vec data arrays
+        PetscCall(VecRestoreArrayRead(previous_f, &previous_residual));
+        PetscCall(VecRestoreArrayRead(snes_f, &current_residual));
+        PetscCall(VecRestoreArray(dt_vec, &dt_data));
+
+        // Need timesteps on neighboring processors
+        // to limit ratio
+        mesh->communicate(pseudo_timestep);
+        // Neumann boundary so timestep isn't pinned at boundaries
+        pseudo_timestep.applyBoundary("neumann");
+
+        if (pid_controller) {
+          // Adjust pseudo_alpha based on nonlinear iterations
+          pseudo_alpha = pid(pseudo_alpha, nl_its, max_timestep * atol * 100);
+        }
 
-          } else if (nl_its >= upper_its) {
-            // Reduce timestep slightly
-            timestep *= timestep_factor_on_upper_its;
+      } else if (pid_controller) {
+        // Changing the timestep using a PID controller.
+        // Note: The preconditioner depends on the timestep,
+        // so we recalculate the jacobian and the preconditioner
+        //  every time the timestep changes
 
-            // Recompute Jacobian
+        timestep = pid(timestep, nl_its, max_timestep);
+
+        // NOTE(malamast): Do we really need this?
+        // Recompute Jacobian (for now)
+        if (saved_jacobian_lag == 0) {
+          SNESGetLagJacobian(snes, &saved_jacobian_lag);
+          SNESSetLagJacobian(snes, 1);
+        }
+
+      } else {
+        // Consider changing the timestep.
+        // Note: The preconditioner depends on the timestep,
+        // so if it is not recalculated the it will be less
+        // effective.
+        if ((nl_its <= lower_its) && (timestep < max_timestep)
+            && (steps_since_snes_failure > 2)) {
+          // Increase timestep slightly
+          timestep *= timestep_factor_on_lower_its;
+
+          timestep = std::min(timestep, max_timestep);
+
+          // Note: Setting the SNESJacobianFn to NULL retains
+          // previously set evaluation function.
+          //
+          // The SNES Jacobian is a combination of the RHS Jacobian
+          // and a factor involving the timestep.
+          // Depends on equation_form
+          // -> Probably call SNESSetJacobian(snes, Jfd, Jfd, NULL, fdcoloring);
+
+          if (static_cast<BoutReal>(lin_its) / nl_its > 4) {
+            // Recompute Jacobian (for now)
             if (saved_jacobian_lag == 0) {
               SNESGetLagJacobian(snes, &saved_jacobian_lag);
               SNESSetLagJacobian(snes, 1);
             }
           }
+
+        } else if (nl_its >= upper_its) {
+          // Reduce timestep slightly
+          timestep *= timestep_factor_on_upper_its;
+
+          // Recompute Jacobian
+          if (saved_jacobian_lag == 0) {
+            SNESGetLagJacobian(snes, &saved_jacobian_lag);
+            SNESSetLagJacobian(snes, 1);
+          }
         }
       }
       snes_failures = 0;
@@ -1132,7 +1405,7 @@ int SNESSolver::run() {
 
     if (!matrix_free) {
       ASSERT2(simtime >= target);
-      ASSERT2(simtime - dt < target);
+      ASSERT2(simtime - dt <= target);
       // Stepped over output timestep => Interpolate
       // snes_x is the solution at t = simtime
       // x0 is the solution at t = simtime - dt
@@ -1181,6 +1454,56 @@ int SNESSolver::run() {
   return 0;
 }
 
+/// Switched Evolution Relaxation (SER)
+BoutReal SNESSolver::updatePseudoTimestep(BoutReal previous_timestep,
+                                          BoutReal previous_residual,
+                                          BoutReal current_residual) {
+
+  // Timestep inversely proportional to the residual, clipped to avoid
+  // rapid changes in timestep.
+  return std::min(
+      {std::max({pseudo_alpha / current_residual, previous_timestep / 1.5, dt_min_reset}),
+       1.5 * previous_timestep, max_timestep});
+
+  /*
+
+  // Alternative strategy based on history of residuals
+  // A hybrid strategy may be most effective, in which the timestep is
+  // inversely proportional to residual initially, or when residuals are large,
+  // and then the method transitions to being history-based
+
+  const BoutReal converged_threshold = 100 * atol;
+  const BoutReal transition_threshold = 1000 * atol;
+
+  if (current_residual < converged_threshold) {
+    return max_timestep;
+  }
+
+  // Smoothly transition from SER updates to frozen timestep
+  if (current_residual < transition_threshold) {
+    BoutReal reduction_ratio = current_residual / previous_residual;
+
+    if (reduction_ratio < 0.8) {
+      return std::min(0.5*(pseudo_growth_factor + 1.) * previous_timestep,
+                      max_timestep);
+    } else if (reduction_ratio > 1.2) {
+      return std::max(0.5*(pseudo_reduction_factor + 1) * previous_timestep, dt_min_reset);
+    }
+    // Leave unchanged if residual changes are small
+    return previous_timestep;
+  }
+
+  if (current_residual <= previous_residual) {
+    // Success
+    return std::min(pseudo_growth_factor * previous_timestep,
+                    max_timestep);
+  }
+  // Failed
+  // Consider rejecting the step
+  return std::max(pseudo_reduction_factor * previous_timestep, dt_min_reset);
+  */
+}
+
 // f = rhs
 PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
   // Get data from PETSc into BOUT++ fields
@@ -1240,13 +1563,24 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
     // f = (x0 - x)/Δt + f
     // First calculate x - x0 to minimise floating point issues
     VecWAXPY(delta_x, -1.0, x0, x); // delta_x = x - x0
-    VecAXPY(f, -1. / dt, delta_x);  // f <- f - delta_x / dt
+    if (pseudo_time) {
+      // dt can be different for each quantity
+      VecPointwiseDivide(delta_x, delta_x, dt_vec); // delta_x /= dt
+      VecAXPY(f, -1., delta_x);                     // f <- f - delta_x
+    } else {
+      VecAXPY(f, -1. / dt, delta_x); // f <- f - delta_x / dt
+    }
     break;
   }
   case BoutSnesEquationForm::backward_euler: {
     // Backward Euler
     // Set f = x - x0 - Δt*f
-    VecAYPX(f, -dt, x);   // f <- x - Δt*f
+    if (pseudo_time) {
+      VecPointwiseMult(f, f, dt_vec); // f <- Δt*f
+      VecAYPX(f, -1, x);              // f <- x - f
+    } else {
+      VecAYPX(f, -dt, x); // f <- x - Δt*f
+    }
     VecAXPY(f, -1.0, x0); // f <- f - x0
     break;
   }
@@ -1443,7 +1777,7 @@ void SNESSolver::updateColoring() {
   }
 }
 
-BoutReal SNESSolver::pid(BoutReal timestep, int nl_its) {
+BoutReal SNESSolver::pid(BoutReal timestep, int nl_its, BoutReal max_dt) {
 
   /* ---------- multiplicative PID factors ---------- */
   const BoutReal facP = std::pow(double(target_its) / double(nl_its), kP);
@@ -1452,11 +1786,11 @@ BoutReal SNESSolver::pid(BoutReal timestep, int nl_its) {
                                      / double(nl_its) / double(nl_its_prev2),
                                  kD);
 
-  // clamp groth factor to avoid huge changes
+  // clamp growth factor to avoid huge changes
   const BoutReal fac = std::clamp(facP * facI * facD, 0.2, 5.0);
 
   /* ---------- update timestep and history ---------- */
-  const BoutReal dt_new = std::min(timestep * fac, max_timestep);
+  const BoutReal dt_new = std::min(timestep * fac, max_dt);
 
   nl_its_prev2 = nl_its_prev;
   nl_its_prev = nl_its;
@@ -1464,4 +1798,20 @@ BoutReal SNESSolver::pid(BoutReal timestep, int nl_its) {
   return dt_new;
 }
 
+void SNESSolver::outputVars(Options& output_options, bool save_repeat) {
+  // Call base class function
+  Solver::outputVars(output_options, save_repeat);
+
+  if (!save_repeat) {
+    return; // Don't save diagnostics to restart files
+  }
+
+  if (pseudo_time) {
+    output_options["snes_pseudo_residual"].assignRepeat(pseudo_residual, "t", save_repeat,
+                                                        "SNESSolver");
+    output_options["snes_pseudo_timestep"].assignRepeat(pseudo_timestep, "t", save_repeat,
+                                                        "SNESSolver");
+  }
+}
+
 #endif // BOUT_HAS_PETSC
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 31deae6f06..c1bb3ecc56 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -39,6 +39,7 @@ class SNESSolver;
 
 #include <bout/bout_enum_class.hxx>
 #include <bout/bout_types.hxx>
+#include <bout/field3d.hxx>
 #include <bout/petsclib.hxx>
 
 #include <petsc.h>
@@ -88,9 +89,12 @@ public:
   /// finite difference approximated Jacobian.
   PetscErrorCode scaleJacobian(Mat B);
 
+  /// Save diagnostics to output
+  void outputVars(Options& output_options, bool save_repeat = true) override;
+
 private:
   BoutReal timestep;     ///< Internal timestep
-  BoutReal dt;           ///< Current timestep used in snes_function
+  BoutReal dt;           ///< Current timestep used in snes_function.
   BoutReal dt_min_reset; ///< If dt falls below this, reset solve
   BoutReal max_timestep; ///< Maximum timestep
 
@@ -107,6 +111,20 @@ private:
   BoutReal timestep_factor_on_upper_its;
   BoutReal timestep_factor_on_lower_its;
 
+  // Pseudo-Transient Continuation (PTC) variables
+  bool pseudo_time;                 ///< Use Pseudo time-stepping
+  BoutReal pseudo_alpha;            ///< dt = alpha / residual
+  BoutReal pseudo_growth_factor;    ///< Timestep increase 1.1 - 1.2
+  BoutReal pseudo_reduction_factor; ///< Timestep decrease 0.5
+  BoutReal pseudo_max_ratio;        ///< Maximum timestep ratio between neighboring cells
+  Vec dt_vec;                       ///< Each quantity can have its own timestep
+  Vec previous_f;                   ///< Previous residual
+  /// Decide the next pseudo-timestep
+  BoutReal updatePseudoTimestep(BoutReal previous_timestep, BoutReal previous_residual,
+                                BoutReal current_residual);
+  Field3D pseudo_residual; ///< Diagnostic output
+  Field3D pseudo_timestep;
+
   ///< PID controller parameters
   bool pid_controller; ///< Use PID controller?
   int target_its;      ///< Target number of nonlinear iterations for the PID controller.
@@ -118,7 +136,7 @@ private:
   int nl_its_prev;
   int nl_its_prev2;
 
-  BoutReal pid(BoutReal timestep, int nl_its); ///< Updates the timestep
+  BoutReal pid(BoutReal timestep, int nl_its, BoutReal max_dt); ///< Updates the timestep
 
   bool diagnose;          ///< Output additional diagnostics
   bool diagnose_failures; ///< Print diagnostics on SNES failures

From e9b8d12c45b8047f5b5c6a4da881db0c8df0f803 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 13 Oct 2025 10:16:15 -0700
Subject: [PATCH 0264/1827] snes: Remove pseudo_time switch, use
 equation_form=pseudo_transient

Rather than having a separate switch, just use equation_form to
select the Pseudo-Transient Continuation method.
---
 include/bout/mesh.hxx                        |   2 +-
 manual/sphinx/user_docs/time_integration.rst | 186 ++++++++++++++-----
 src/solver/impls/snes/snes.cxx               |  62 +++----
 src/solver/impls/snes/snes.hxx               |   8 +-
 4 files changed, 168 insertions(+), 90 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 02e2a23905..1db25adf78 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -757,7 +757,7 @@ public:
   void addRegionPerp(const std::string& region_name, const Region<IndPerp>& region);
 
   /// Converts an Ind2D to an Ind3D using calculation
-  Ind3D ind2Dto3D(const Ind2D& ind2D, int jz = 0) {
+  Ind3D ind2Dto3D(const Ind2D& ind2D, int jz = 0) const {
     return {ind2D.ind * LocalNz + jz, LocalNy, LocalNz};
   }
 
diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index c1526c14e2..373b5cdbe6 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -361,16 +361,145 @@ And the adaptive timestepping options:
 Backward Euler - SNES
 ---------------------
 
-The `beuler` or `snes` solver type (either name can be used) is
-intended mainly for solving steady-state problems, so integrates in
-time using a stable but low accuracy method (Backward Euler). It uses
-PETSc's SNES solvers to solve the nonlinear system at each timestep,
-and adjusts the internal timestep to keep the number of SNES
-iterations within a given range.
+The `beuler` or `snes` solver type (either name can be used) is a PETSc-based implicit
+solver for finding steady-state solutions to systems of partial differential equations.
+It supports multiple solution strategies including backward Euler timestepping,
+direct Newton iteration, and Pseudo-Transient Continuation (PTC) with Switched
+Evolution Relaxation (SER).
+
+Basic Configuration
+~~~~~~~~~~~~~~~~~~~
+
+The SNES solver is configured through the ``[solver]`` section of the input file:
+
+.. code-block:: ini
+
+   [solver]
+   type = snes
+
+   # Nonlinear solver settings
+   snes_type = newtonls          # anderson, newtonls, newtontr, nrichardson
+   atol = 1e-7                   # Absolute tolerance
+   rtol = 1e-6                   # Relative tolerance
+   stol = 1e-12                  # Solution change tolerance
+   max_nonlinear_iterations = 20 # Maximum SNES iterations per solve
+
+   # Linear solver settings
+   ksp_type = fgmres             # Linear solver: gmres, bicgstab, etc.
+   maxl = 20                     # Maximum linear iterations
+   pc_type = ilu                 # Preconditioner: ilu, bjacobi, hypre, etc.
+
+Timestepping Modes
+------------------
+
+The solver supports several timestepping strategies controlled by ``equation_form``:
+
+**Backward Euler (default)**
+   Standard implicit backward Euler method. Good for general timestepping.
+
+   .. code-block:: ini
+
+      equation_form = rearranged_backward_euler  # Default
+
+   This method has low accuracy in time but its dissipative properties
+   are helpful when evolving to steady state solutions.
+
+**Direct Newton**
+   Solves the steady-state problem F(u) = 0 directly without timestepping.
+
+   .. code-block:: ini
+
+      equation_form = direct_newton
+
+   This method is unlikely to converge unless the system is very close
+   to steady state.
+
+**Pseudo-Transient Continuation**
+   Uses pseudo-time to guide the solution to steady state. Recommended for
+   highly nonlinear problems where Newton's method fails.
+
+   .. code-block:: ini
+
+      equation_form = pseudo_transient
+
+   This uses the same form as rearranged_backward_euler, but the time step
+   can be different for each cell.
+
+
+Jacobian Finite Difference with Coloring
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The default and recommended approach for most problems:
+
+.. code-block:: ini
+
+   [solver]
+   use_coloring = true               # Enable (default)
+   lag_jacobian = 50                 # Reuse Jacobian for this many iterations
+
+   # Stencil shape (determines Jacobian sparsity pattern)
+   stencil:taxi = 2                  # Taxi-cab distance (default)
+   stencil:square = 0                # Square stencil extent
+   stencil:cross = 0                 # Cross stencil extent
+
+The coloring algorithm exploits the sparse structure of the Jacobian to reduce
+the number of function evaluations needed for finite differencing.
+
+Jacobian coloring stencil
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The stencil used to create the Jacobian colouring can be varied,
+depending on which numerical operators are in use.
+
+``solver:stencil:cross = N``
+e.g. for N == 2
+
+.. code-block:: bash
+
+        *
+        *
+    * * x * *
+        *
+        *
+
+
+``solver:stencil:square = N``
+e.g. for N == 2
+
+.. code-block:: bash
+
+    * * * * *
+    * * * * *
+    * * x * *
+    * * * * *
+    * * * * *
+
+``solver:stencil:taxi = N``
+e.g. for N == 2
+
+.. code-block:: bash
+
+        *
+      * * *
+    * * x * *
+      * * *
+        *
+
+Setting ``solver:force_symmetric_coloring = true``, will make sure
+that the jacobian colouring matrix is symmetric.  This will often
+include a few extra non-zeros that the stencil will miss otherwise
+
+
+
 
 +---------------------------+---------------+----------------------------------------------------+
 | Option                    | Default       |Description                                         |
 +===========================+===============+====================================================+
+| pseudo_time               | false         | Pseudo-Transient Continuation (PTC) method, using  |
+|                           |               | a different timestep for each cell.                |
++---------------------------+---------------+----------------------------------------------------+
+| pseudo_max_ratio          | 2.            | Maximum timestep ratio between neighboring cells   |
++---------------------------+---------------+----------------------------------------------------+
 | snes_type                 | newtonls      | PETSc SNES nonlinear solver (try anderson, qn)     |
 +---------------------------+---------------+----------------------------------------------------+
 | ksp_type                  | gmres         | PETSc KSP linear solver                            |
@@ -423,6 +552,8 @@ iterations within a given range.
 The predictor is linear extrapolation from the last two timesteps. It seems to be
 effective, but can be disabled by setting ``predictor = false``.
 
+
+
 The default `newtonls` SNES type can be very effective if combined
 with Jacobian coloring: The coloring enables the Jacobian to be
 calculated relatively efficiently; once a Jacobian matrix has been
@@ -456,50 +587,13 @@ Preconditioner types:
    Enable with command-line args ``-pc_type hypre -pc_hypre_type euclid -pc_hypre_euclid_levels k``
    where ``k`` is the level (1-8 typically).
 
-Jacobian coloring stencil
-~~~~~~~~~~~~~~~~~~~~~~~~~
-
-The stencil used to create the Jacobian colouring can be varied,
-depending on which numerical operators are in use.
-
-
-``solver:stencil:cross = N``
-e.g. for N == 2
-
-.. code-block:: bash
-
-        *
-        *
-    * * x * *
-        *
-        *
+Pseudo-Transient Continuation (PTC)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 
-``solver:stencil:square = N``
-e.g. for N == 2
 
-.. code-block:: bash
-
-    * * * * *
-    * * * * *
-    * * x * *
-    * * * * *
-    * * * * *
+Saves diagnostic ``Field3D`` output variables ``snes_pseudo_residual`` and ``snes_pseudo_timestep``.
 
-``solver:stencil:taxi = N``
-e.g. for N == 2
-
-.. code-block:: bash
-
-        *
-      * * *
-    * * x * *
-      * * *
-        *
-
-Setting ``solver:force_symmetric_coloring = true``, will make sure
-that the jacobian colouring matrix is symmetric.  This will often
-include a few extra non-zeros that the stencil will miss otherwise
 
 ODE integration
 ---------------
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 49650b7b97..b48afccc48 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -106,6 +106,11 @@ SNESSolver::SNESSolver(Options* opts)
                        .doc("If dt falls below this, reset to starting dt")
                        .withDefault(1e-6)),
       max_timestep((*options)["max_timestep"].doc("Maximum timestep").withDefault(1e37)),
+      equation_form(
+          (*options)["equation_form"]
+              .doc("Form of equation to solve: rearranged_backward_euler (default);"
+                   " pseudo_transient; backward_euler; direct_newton")
+              .withDefault(BoutSnesEquationForm::rearranged_backward_euler)),
       snes_type((*options)["snes_type"]
                     .doc("PETSc nonlinear solver method to use")
                     .withDefault("anderson")),
@@ -138,9 +143,6 @@ SNESSolver::SNESSolver(Options* opts)
           (*options)["timestep_factor_on_lower_its"]
               .doc("Multiply timestep if iterations are below lower_its")
               .withDefault(1.4)),
-      pseudo_time((*options)["pseudo_time"]
-                      .doc("Pseudo-Transient Continuation method?")
-                      .withDefault<bool>(false)),
       pseudo_alpha((*options)["pseudo_alpha"]
                        .doc("Sets timestep using dt = alpha / residual")
                        .withDefault(100. * atol * timestep)),
@@ -164,11 +166,6 @@ SNESSolver::SNESSolver(Options* opts)
       diagnose_failures((*options)["diagnose_failures"]
                             .doc("Print more diagnostics when SNES fails")
                             .withDefault<bool>(false)),
-      equation_form(
-          (*options)["equation_form"]
-              .doc("Form of equation to solve: rearranged_backward_euler (default);"
-                   " pseudo_transient; backward_euler; direct_newton")
-              .withDefault(BoutSnesEquationForm::rearranged_backward_euler)),
       predictor((*options)["predictor"].doc("Use linear predictor?").withDefault(true)),
       use_precon((*options)["use_precon"]
                      .doc("Use user-supplied preconditioner?")
@@ -292,7 +289,7 @@ int SNESSolver::init() {
     CHKERRQ(ierr);
   }
 
-  if (pseudo_time) {
+  if (equation_form == BoutSnesEquationForm::pseudo_transient) {
     // Storage for per-variable timestep
     PetscCall(VecDuplicate(snes_x, &dt_vec));
     // Starting timestep
@@ -797,7 +794,7 @@ int SNESSolver::run() {
     CHKERRQ(ierr);
   }
 
-  if (pseudo_time) {
+  if (equation_form == BoutSnesEquationForm::pseudo_transient) {
     // Calculate the initial residual in snes_f
     run_rhs(simtime);
     {
@@ -880,7 +877,7 @@ int SNESSolver::run() {
       // Copy the state (snes_x) into initial values (x0)
       VecCopy(snes_x, x0);
 
-      if (pseudo_time) {
+      if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Pseudo-Transient Continuation
         // Each evolving quantity may have its own timestep
         // Set timestep and dt scalars to the minimum of dt_vec
@@ -981,7 +978,7 @@ int SNESSolver::run() {
         ++snes_failures;
         steps_since_snes_failure = 0;
 
-        if (pseudo_time) {
+        if (equation_form == BoutSnesEquationForm::pseudo_transient) {
           // Global scaling of timesteps
           // Note: A better strategy might be to reduce timesteps
           //       in problematic cells.
@@ -1089,14 +1086,8 @@ int SNESSolver::run() {
         // Gather and print diagnostic information
 
         output.print("\r"); // Carriage return for printing to screen
-
-        // if (pseudo_time) {
-        //   output.write("\tTime {} alpha {} min_timestep {} nl_iter {} lin_iter {} reason {}",
-        //                simtime, pseudo_alpha, timestep, nl_its, lin_its, static_cast<int>(reason));
-        // } else {
         output.write("Time: {}, timestep: {}, nl iter: {}, lin iter: {}, reason: {}",
                      simtime, timestep, nl_its, lin_its, static_cast<int>(reason));
-        // }
         if (snes_failures > 0) {
           output.write(", SNES failures: {}", snes_failures);
         }
@@ -1148,7 +1139,7 @@ int SNESSolver::run() {
       }
 #endif // PETSC_VERSION_GE(3,20,0)
 
-      if (pseudo_time) {
+      if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Adjust local timesteps
 
         // Calculate residuals
@@ -1552,35 +1543,27 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
   CHKERRQ(ierr);
 
   switch (equation_form) {
-  case BoutSnesEquationForm::pseudo_transient: {
-    // Pseudo-transient timestepping (as in UEDGE)
-    // f <- f - x/Δt
-    VecAXPY(f, -1. / dt, x);
-    break;
-  }
   case BoutSnesEquationForm::rearranged_backward_euler: {
     // Rearranged Backward Euler
     // f = (x0 - x)/Δt + f
     // First calculate x - x0 to minimise floating point issues
     VecWAXPY(delta_x, -1.0, x0, x); // delta_x = x - x0
-    if (pseudo_time) {
-      // dt can be different for each quantity
-      VecPointwiseDivide(delta_x, delta_x, dt_vec); // delta_x /= dt
-      VecAXPY(f, -1., delta_x);                     // f <- f - delta_x
-    } else {
-      VecAXPY(f, -1. / dt, delta_x); // f <- f - delta_x / dt
-    }
+    VecAXPY(f, -1. / dt, delta_x); // f <- f - delta_x / dt
+    break;
+  }
+  case BoutSnesEquationForm::pseudo_transient: {
+    // Pseudo-transient timestepping. Same as Rearranged Backward Euler
+    // except that Δt is a vector
+    // f = (x0 - x)/Δt + f
+    VecWAXPY(delta_x, -1.0, x0, x);
+    VecPointwiseDivide(delta_x, delta_x, dt_vec); // delta_x /= dt
+    VecAXPY(f, -1., delta_x);                     // f <- f - delta_x
     break;
   }
   case BoutSnesEquationForm::backward_euler: {
     // Backward Euler
     // Set f = x - x0 - Δt*f
-    if (pseudo_time) {
-      VecPointwiseMult(f, f, dt_vec); // f <- Δt*f
-      VecAYPX(f, -1, x);              // f <- x - f
-    } else {
-      VecAYPX(f, -dt, x); // f <- x - Δt*f
-    }
+    VecAYPX(f, -dt, x); // f <- x - Δt*f
     VecAXPY(f, -1.0, x0); // f <- f - x0
     break;
   }
@@ -1806,7 +1789,8 @@ void SNESSolver::outputVars(Options& output_options, bool save_repeat) {
     return; // Don't save diagnostics to restart files
   }
 
-  if (pseudo_time) {
+  if (equation_form == BoutSnesEquationForm::pseudo_transient) {
+    output_options["snes_pseudo_alpha"].assignRepeat(pseudo_alpha, "t", save_repeat, "SNESSolver");
     output_options["snes_pseudo_residual"].assignRepeat(pseudo_residual, "t", save_repeat,
                                                         "SNESSolver");
     output_options["snes_pseudo_timestep"].assignRepeat(pseudo_timestep, "t", save_repeat,
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index c1bb3ecc56..257588e2a9 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -98,6 +98,9 @@ private:
   BoutReal dt_min_reset; ///< If dt falls below this, reset solve
   BoutReal max_timestep; ///< Maximum timestep
 
+  /// Form of the equation to solve
+  BoutSnesEquationForm equation_form;
+
   std::string snes_type;
   BoutReal atol; ///< Absolute tolerance
   BoutReal rtol; ///< Relative tolerance
@@ -112,7 +115,7 @@ private:
   BoutReal timestep_factor_on_lower_its;
 
   // Pseudo-Transient Continuation (PTC) variables
-  bool pseudo_time;                 ///< Use Pseudo time-stepping
+  // These are used if equation_form = pseudo_transient
   BoutReal pseudo_alpha;            ///< dt = alpha / residual
   BoutReal pseudo_growth_factor;    ///< Timestep increase 1.1 - 1.2
   BoutReal pseudo_reduction_factor; ///< Timestep decrease 0.5
@@ -144,9 +147,6 @@ private:
   int nlocal; ///< Number of variables on local processor
   int neq;    ///< Number of variables in total
 
-  /// Form of the equation to solve
-  BoutSnesEquationForm equation_form;
-
   PetscLib lib; ///< Handles initialising, finalising PETSc
   Vec snes_f;   ///< Used by SNES to store function
   Vec snes_x;   ///< Result of SNES

From a024d5858789f697c0a654e97dfcb99840a2b2ab Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 13 Oct 2025 11:14:11 -0700
Subject: [PATCH 0265/1827] snes: Refactoring, split rhs_function from
 snes_function

The rhs_function returns the time derivatives (residuals) that
are used in the PTC method.

The snes_function calls rhs_function, then modifies the function
depending on equation_form.
---
 src/solver/impls/snes/snes.cxx | 137 +++++++++++++--------------------
 src/solver/impls/snes/snes.hxx |   9 +++
 2 files changed, 63 insertions(+), 83 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index b48afccc48..cec0c3e058 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -18,6 +18,8 @@
 #include <bout/output.hxx>
 
 #include "petscsnes.h"
+#include "petscsys.h"
+#include "petscvec.h"
 
 class ColoringStencil {
 private:
@@ -253,8 +255,9 @@ int SNESSolver::init() {
   VecDuplicate(snes_x, &snes_f);
   VecDuplicate(snes_x, &x0);
 
-  if (equation_form == BoutSnesEquationForm::rearranged_backward_euler) {
-    // Need an intermediate vector for rearranged Backward Euler
+  if ((equation_form == BoutSnesEquationForm::rearranged_backward_euler)
+      || (equation_form == BoutSnesEquationForm::pseudo_transient)) {
+    // Need an intermediate vector for rearranged Backward Euler or Pseudo-Transient Continuation
     ierr = VecDuplicate(snes_x, &delta_x);
     CHKERRQ(ierr);
   }
@@ -931,7 +934,7 @@ int SNESSolver::run() {
           // Use (time1, x1) and (simtime, x0) to make prediction
           // snes_x <- x0 + (dt / (simtime - time1)) * (x0 - x1)
           // snes_x <- -β * x1 + (1 + β) * snes_x
-          BoutReal beta = dt / (simtime - time1);
+          const BoutReal beta = dt / (simtime - time1);
           VecAXPBY(snes_x, -beta, (1. + beta), x1);
         }
 
@@ -1142,27 +1145,7 @@ int SNESSolver::run() {
       if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Adjust local timesteps
 
-        // Calculate residuals
-        if (scale_vars) {
-          // scaled_x <- snes_x * var_scaling_factors
-          PetscCall(VecPointwiseMult(scaled_x, snes_x, var_scaling_factors));
-          const BoutReal* xdata = nullptr;
-          PetscCall(VecGetArrayRead(scaled_x, &xdata));
-          load_vars(const_cast<BoutReal*>(xdata));
-          PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
-        } else {
-          const BoutReal* xdata = nullptr;
-          PetscCall(VecGetArrayRead(snes_x, &xdata));
-          load_vars(const_cast<BoutReal*>(xdata));
-          PetscCall(VecRestoreArrayRead(snes_x, &xdata));
-        }
-        run_rhs(simtime);
-        {
-          BoutReal* fdata = nullptr;
-          PetscCall(VecGetArray(snes_f, &fdata));
-          save_derivs(fdata);
-          PetscCall(VecRestoreArray(snes_f, &fdata));
-        }
+        PetscCall(rhs_function(snes_x, snes_f, false));
 
         // Compare previous_f with snes_f
         // Use a per-cell timestep so that e.g density and pressure
@@ -1280,25 +1263,25 @@ int SNESSolver::run() {
               BoutReal mean_neighboring_dt = 0.0;
               int neighbor_count = 0;
               if (i3d.x() != 0) {
-                BoutReal val = pseudo_timestep[i3d.xm()];
+                const BoutReal val = pseudo_timestep[i3d.xm()];
                 min_neighboring_dt = std::min(min_neighboring_dt, val);
                 mean_neighboring_dt += val;
                 ++neighbor_count;
               }
               if (i3d.x() != mesh->LocalNx - 1) {
-                BoutReal val = pseudo_timestep[i3d.xp()];
+                const BoutReal val = pseudo_timestep[i3d.xp()];
                 min_neighboring_dt = std::min(min_neighboring_dt, val);
                 mean_neighboring_dt += val;
                 ++neighbor_count;
               }
               if (i3d.y() != 0) {
-                BoutReal val = pseudo_timestep[i3d.ym()];
+                const BoutReal val = pseudo_timestep[i3d.ym()];
                 min_neighboring_dt = std::min(min_neighboring_dt, val);
                 mean_neighboring_dt += val;
                 ++neighbor_count;
               }
               if (i3d.x() != mesh->LocalNy - 1) {
-                BoutReal val = pseudo_timestep[i3d.yp()];
+                const BoutReal val = pseudo_timestep[i3d.yp()];
                 min_neighboring_dt = std::min(min_neighboring_dt, val);
                 mean_neighboring_dt += val;
                 ++neighbor_count;
@@ -1495,29 +1478,23 @@ BoutReal SNESSolver::updatePseudoTimestep(BoutReal previous_timestep,
   */
 }
 
-// f = rhs
-PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
+PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
   // Get data from PETSc into BOUT++ fields
   if (scale_vars) {
     // scaled_x <- x * var_scaling_factors
-    int ierr = VecPointwiseMult(scaled_x, x, var_scaling_factors);
-    CHKERRQ(ierr);
+    PetscCall(VecPointwiseMult(scaled_x, x, var_scaling_factors));
 
     const BoutReal* xdata = nullptr;
-    ierr = VecGetArrayRead(scaled_x, &xdata);
-    CHKERRQ(ierr);
-    load_vars(const_cast<BoutReal*>(
-        xdata)); // const_cast needed due to load_vars API. Not writing to xdata.
-    ierr = VecRestoreArrayRead(scaled_x, &xdata);
-    CHKERRQ(ierr);
+    PetscCall(VecGetArrayRead(scaled_x, &xdata));
+    // const_cast needed due to load_vars API. Not writing to xdata.
+    load_vars(const_cast<BoutReal*>(xdata));
+    PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
   } else {
     const BoutReal* xdata = nullptr;
-    int ierr = VecGetArrayRead(x, &xdata);
-    CHKERRQ(ierr);
-    load_vars(const_cast<BoutReal*>(
-        xdata)); // const_cast needed due to load_vars API. Not writing to xdata.
-    ierr = VecRestoreArrayRead(x, &xdata);
-    CHKERRQ(ierr);
+    PetscCall(VecGetArrayRead(x, &xdata));
+    // const_cast needed due to load_vars API. Not writing to xdata.
+    load_vars(const_cast<BoutReal*>(xdata));
+    PetscCall(VecRestoreArrayRead(x, &xdata));
   }
 
   try {
@@ -1527,28 +1504,35 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
     // Simulation might fail, e.g. negative densities
     // if timestep too large
     output_warn.write("WARNING: BoutException thrown: {}\n", e.what());
+    return 2;
+  }
+
+  // Copy derivatives back
+  BoutReal* fdata = nullptr;
+  PetscCall(VecGetArray(f, &fdata));
+  save_derivs(fdata);
+  PetscCall(VecRestoreArray(f, &fdata));
+  return PETSC_SUCCESS;
+}
 
+// Result in f depends on equation_form
+PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
+
+  // Call the RHS function
+  if (rhs_function(x, f, linear) != PETSC_SUCCESS) {
     // Tell SNES that the input was out of domain
     SNESSetFunctionDomainError(snes);
     // Note: Returning non-zero error here leaves vectors in locked state
     return 0;
   }
 
-  // Copy derivatives back
-  BoutReal* fdata = nullptr;
-  int ierr = VecGetArray(f, &fdata);
-  CHKERRQ(ierr);
-  save_derivs(fdata);
-  ierr = VecRestoreArray(f, &fdata);
-  CHKERRQ(ierr);
-
   switch (equation_form) {
   case BoutSnesEquationForm::rearranged_backward_euler: {
     // Rearranged Backward Euler
     // f = (x0 - x)/Δt + f
     // First calculate x - x0 to minimise floating point issues
     VecWAXPY(delta_x, -1.0, x0, x); // delta_x = x - x0
-    VecAXPY(f, -1. / dt, delta_x); // f <- f - delta_x / dt
+    VecAXPY(f, -1. / dt, delta_x);  // f <- f - delta_x / dt
     break;
   }
   case BoutSnesEquationForm::pseudo_transient: {
@@ -1563,7 +1547,7 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
   case BoutSnesEquationForm::backward_euler: {
     // Backward Euler
     // Set f = x - x0 - Δt*f
-    VecAYPX(f, -dt, x); // f <- x - Δt*f
+    VecAYPX(f, -dt, x);   // f <- x - Δt*f
     VecAXPY(f, -1.0, x0); // f <- f - x0
     break;
   }
@@ -1578,8 +1562,7 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
 
   if (scale_rhs) {
     // f <- f * rhs_scaling_factors
-    ierr = VecPointwiseMult(f, f, rhs_scaling_factors);
-    CHKERRQ(ierr);
+    PetscCall(VecPointwiseMult(f, f, rhs_scaling_factors));
   }
 
   return 0;
@@ -1594,36 +1577,28 @@ PetscErrorCode SNESSolver::precon(Vec x, Vec f) {
     throw BoutException("No user preconditioner");
   }
 
-  int ierr;
-
   // Get data from PETSc into BOUT++ fields
   Vec solution;
-  SNESGetSolution(snes, &solution);
+  PetscCall(SNESGetSolution(snes, &solution));
   BoutReal* soldata;
-  ierr = VecGetArray(solution, &soldata);
-  CHKERRQ(ierr);
+  PetscCall(VecGetArray(solution, &soldata));
   load_vars(soldata);
-  ierr = VecRestoreArray(solution, &soldata);
-  CHKERRQ(ierr);
+  PetscCall(VecRestoreArray(solution, &soldata));
 
   // Load vector to be inverted into ddt() variables
   const BoutReal* xdata;
-  ierr = VecGetArrayRead(x, &xdata);
-  CHKERRQ(ierr);
+  PetscCall(VecGetArrayRead(x, &xdata));
   load_derivs(const_cast<BoutReal*>(xdata)); // Note: load_derivs does not modify data
-  ierr = VecRestoreArrayRead(x, &xdata);
-  CHKERRQ(ierr);
+  PetscCall(VecRestoreArrayRead(x, &xdata));
 
   // Run the preconditioner
   runPreconditioner(simtime + dt, dt, 0.0);
 
   // Save the solution from F_vars
   BoutReal* fdata;
-  ierr = VecGetArray(f, &fdata);
-  CHKERRQ(ierr);
+  PetscCall(VecGetArray(f, &fdata));
   save_derivs(fdata);
-  ierr = VecRestoreArray(f, &fdata);
-  CHKERRQ(ierr);
+  PetscCall(VecRestoreArray(f, &fdata));
 
   return 0;
 }
@@ -1635,8 +1610,6 @@ PetscErrorCode SNESSolver::scaleJacobian(Mat Jac_new) {
     return 0; // Not scaling the RHS values
   }
 
-  int ierr;
-
   // Get index of rows owned by this processor
   int rstart, rend;
   MatGetOwnershipRange(Jac_new, &rstart, &rend);
@@ -1651,8 +1624,7 @@ PetscErrorCode SNESSolver::scaleJacobian(Mat Jac_new) {
 
   // Calculate the norm of each row of the Jacobian
   PetscScalar* row_inv_norm_data;
-  ierr = VecGetArray(jac_row_inv_norms, &row_inv_norm_data);
-  CHKERRQ(ierr);
+  PetscCall(VecGetArray(jac_row_inv_norms, &row_inv_norm_data));
 
   PetscInt ncols;
   const PetscScalar* vals;
@@ -1676,12 +1648,11 @@ PetscErrorCode SNESSolver::scaleJacobian(Mat Jac_new) {
     MatRestoreRow(Jac_new, row, &ncols, nullptr, &vals);
   }
 
-  ierr = VecRestoreArray(jac_row_inv_norms, &row_inv_norm_data);
-  CHKERRQ(ierr);
+  PetscCall(VecRestoreArray(jac_row_inv_norms, &row_inv_norm_data));
 
   // Modify the RHS scaling: factor = factor / norm
-  ierr = VecPointwiseMult(rhs_scaling_factors, rhs_scaling_factors, jac_row_inv_norms);
-  CHKERRQ(ierr);
+  PetscCall(
+      VecPointwiseMult(rhs_scaling_factors, rhs_scaling_factors, jac_row_inv_norms));
 
   if (diagnose) {
     // Print maximum and minimum scaling factors
@@ -1692,10 +1663,9 @@ PetscErrorCode SNESSolver::scaleJacobian(Mat Jac_new) {
   }
 
   // Scale the Jacobian rows by multiplying on the left by 1/norm
-  ierr = MatDiagonalScale(Jac_new, jac_row_inv_norms, nullptr);
-  CHKERRQ(ierr);
+  PetscCall(MatDiagonalScale(Jac_new, jac_row_inv_norms, nullptr));
 
-  return 0;
+  return PETSC_SUCCESS;
 }
 
 ///
@@ -1790,7 +1760,8 @@ void SNESSolver::outputVars(Options& output_options, bool save_repeat) {
   }
 
   if (equation_form == BoutSnesEquationForm::pseudo_transient) {
-    output_options["snes_pseudo_alpha"].assignRepeat(pseudo_alpha, "t", save_repeat, "SNESSolver");
+    output_options["snes_pseudo_alpha"].assignRepeat(pseudo_alpha, "t", save_repeat,
+                                                     "SNESSolver");
     output_options["snes_pseudo_residual"].assignRepeat(pseudo_residual, "t", save_repeat,
                                                         "SNESSolver");
     output_options["snes_pseudo_timestep"].assignRepeat(pseudo_timestep, "t", save_repeat,
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 257588e2a9..53b87d6c28 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -69,6 +69,8 @@ public:
   ///
   ///     f = (x - gamma*G(x)) - rhs
   ///
+  /// The form depends on equation_form
+  ///
   ///
   /// @param[in] x  The state vector
   /// @param[out] f  The vector for the result f(x)
@@ -93,6 +95,13 @@ public:
   void outputVars(Options& output_options, bool save_repeat = true) override;
 
 private:
+  /// Call the physics model RHS function
+  ///
+  /// @param[in] x       The state vector. Will be scaled if scale_vars=true
+  /// @param[out] f      The vector for the result f(x)
+  /// @param[in] linear  Specifies that the SNES solver is in a linear (KSP) inner loop
+  PetscErrorCode rhs_function(Vec x, Vec f, bool linear);
+
   BoutReal timestep;     ///< Internal timestep
   BoutReal dt;           ///< Current timestep used in snes_function.
   BoutReal dt_min_reset; ///< If dt falls below this, reset solve

From 76c45c8508926e11bcfaeb61c082b50eff0636e6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Oct 2025 19:10:03 +0000
Subject: [PATCH 0266/1827] Bump stefanzweifel/git-auto-commit-action from 5 to
 7

Bumps [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action) from 5 to 7.
- [Release notes](https://github.com/stefanzweifel/git-auto-commit-action/releases)
- [Changelog](https://github.com/stefanzweifel/git-auto-commit-action/blob/master/CHANGELOG.md)
- [Commits](https://github.com/stefanzweifel/git-auto-commit-action/compare/v5...v7)

---
updated-dependencies:
- dependency-name: stefanzweifel/git-auto-commit-action
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/black-fix.yml    | 2 +-
 .github/workflows/clang-format.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/black-fix.yml b/.github/workflows/black-fix.yml
index 6c1bfed4a5..5cddbbfac6 100644
--- a/.github/workflows/black-fix.yml
+++ b/.github/workflows/black-fix.yml
@@ -41,6 +41,6 @@ jobs:
         ls
         $HOME/.local/bin/black tests/ tools/ $(grep -EIlr '^#!.*python.*$' bin/ tests/ tools/ src/ | grep -v _boutpp_build)
 
-    - uses: stefanzweifel/git-auto-commit-action@v5
+    - uses: stefanzweifel/git-auto-commit-action@v7
       with:
         commit_message: "Apply black changes"
diff --git a/.github/workflows/clang-format.yml b/.github/workflows/clang-format.yml
index e32c959cb2..4c1307d7c9 100644
--- a/.github/workflows/clang-format.yml
+++ b/.github/workflows/clang-format.yml
@@ -28,6 +28,6 @@ jobs:
           while ! git clang-format origin/${{ github.base_ref }} ; do git add . ; done
 
       - name: Commit to the PR branch
-        uses: stefanzweifel/git-auto-commit-action@v5
+        uses: stefanzweifel/git-auto-commit-action@v7
         with:
           commit_message: "Apply clang-format changes"

From bf62e5a3063ab68709f65e4256d357190a3f3828 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Oct 2025 19:11:14 +0000
Subject: [PATCH 0267/1827] Bump actions/checkout from 4 to 5

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index d6834eba6a..049a03664d 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -219,7 +219,7 @@ jobs:
     container: ghcr.io/ggeorgakoudis/boutdev-cuda:latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
       - name: Build minimal CUDA 12.2 @ GCC9.4.0 @ Ubuntu 20.04

From 37187e332893dea215871337258db3c1d812e314 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 13 Oct 2025 12:23:27 -0700
Subject: [PATCH 0268/1827] snes: Add pseudo_strategy option

Switches between different strategies for choosing cell time steps.
---
 src/solver/impls/snes/snes.cxx | 78 +++++++++++++++++++++-------------
 src/solver/impls/snes/snes.hxx | 11 +++++
 2 files changed, 59 insertions(+), 30 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index cec0c3e058..1adb2c4b46 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -12,6 +12,7 @@
 #include <bout/petsc_interface.hxx>
 #include <bout/utils.hxx>
 
+#include <algorithm>
 #include <cmath>
 #include <vector>
 
@@ -145,6 +146,9 @@ SNESSolver::SNESSolver(Options* opts)
           (*options)["timestep_factor_on_lower_its"]
               .doc("Multiply timestep if iterations are below lower_its")
               .withDefault(1.4)),
+      pseudo_strategy((*options)["pseudo_strategy"]
+                          .doc("PTC strategy to use when setting timesteps")
+                          .withDefault(BoutPTCStrategy::inverse_residual)),
       pseudo_alpha((*options)["pseudo_alpha"]
                        .doc("Sets timestep using dt = alpha / residual")
                        .withDefault(100. * atol * timestep)),
@@ -401,18 +405,13 @@ int SNESSolver::init() {
       auto n_square = (*options)["stencil:square"]
                           .doc("Extent of stencil (square)")
                           .withDefault<int>(0);
-      auto n_taxi = (*options)["stencil:taxi"]
-                        .doc("Extent of stencil (taxi-cab norm)")
-                        .withDefault<int>(0);
       auto n_cross = (*options)["stencil:cross"]
                          .doc("Extent of stencil (cross)")
                          .withDefault<int>(0);
       // Set n_taxi 2 if nothing else is set
-      // Probably a better way to do this
-      if (n_square == 0 && n_taxi == 0 && n_cross == 0) {
-        output_info.write("Setting solver:stencil:taxi = 2\n");
-        n_taxi = 2;
-      }
+      auto n_taxi = (*options)["stencil:taxi"]
+                        .doc("Extent of stencil (taxi-cab norm)")
+                        .withDefault<int>((n_square == 0 && n_cross == 0) ? 2 : 0);
 
       auto const xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
       {
@@ -1428,26 +1427,21 @@ int SNESSolver::run() {
   return 0;
 }
 
-/// Switched Evolution Relaxation (SER)
-BoutReal SNESSolver::updatePseudoTimestep(BoutReal previous_timestep,
-                                          BoutReal previous_residual,
-                                          BoutReal current_residual) {
-
-  // Timestep inversely proportional to the residual, clipped to avoid
-  // rapid changes in timestep.
+/// Timestep inversely proportional to the residual, clipped to avoid
+/// rapid changes in timestep.
+BoutReal SNESSolver::updatePseudoTimestep_inverse_residual(BoutReal previous_timestep,
+                                                           BoutReal current_residual) {
   return std::min(
       {std::max({pseudo_alpha / current_residual, previous_timestep / 1.5, dt_min_reset}),
        1.5 * previous_timestep, max_timestep});
+}
 
-  /*
-
-  // Alternative strategy based on history of residuals
-  // A hybrid strategy may be most effective, in which the timestep is
-  // inversely proportional to residual initially, or when residuals are large,
-  // and then the method transitions to being history-based
-
-  const BoutReal converged_threshold = 100 * atol;
-  const BoutReal transition_threshold = 1000 * atol;
+// Strategy based on history of residuals
+BoutReal SNESSolver::updatePseudoTimestep_history_based(BoutReal previous_timestep,
+                                                        BoutReal previous_residual,
+                                                        BoutReal current_residual) {
+  const BoutReal converged_threshold = 10 * atol;
+  const BoutReal transition_threshold = 100 * atol;
 
   if (current_residual < converged_threshold) {
     return max_timestep;
@@ -1455,13 +1449,14 @@ BoutReal SNESSolver::updatePseudoTimestep(BoutReal previous_timestep,
 
   // Smoothly transition from SER updates to frozen timestep
   if (current_residual < transition_threshold) {
-    BoutReal reduction_ratio = current_residual / previous_residual;
+    const BoutReal reduction_ratio = current_residual / previous_residual;
 
     if (reduction_ratio < 0.8) {
-      return std::min(0.5*(pseudo_growth_factor + 1.) * previous_timestep,
+      return std::min(0.5 * (pseudo_growth_factor + 1.) * previous_timestep,
                       max_timestep);
     } else if (reduction_ratio > 1.2) {
-      return std::max(0.5*(pseudo_reduction_factor + 1) * previous_timestep, dt_min_reset);
+      return std::max(0.5 * (pseudo_reduction_factor + 1) * previous_timestep,
+                      dt_min_reset);
     }
     // Leave unchanged if residual changes are small
     return previous_timestep;
@@ -1469,13 +1464,36 @@ BoutReal SNESSolver::updatePseudoTimestep(BoutReal previous_timestep,
 
   if (current_residual <= previous_residual) {
     // Success
-    return std::min(pseudo_growth_factor * previous_timestep,
-                    max_timestep);
+    return std::min(pseudo_growth_factor * previous_timestep, max_timestep);
   }
   // Failed
   // Consider rejecting the step
   return std::max(pseudo_reduction_factor * previous_timestep, dt_min_reset);
-  */
+}
+
+/// Switched Evolution Relaxation (SER)
+BoutReal SNESSolver::updatePseudoTimestep(BoutReal previous_timestep,
+                                          BoutReal previous_residual,
+                                          BoutReal current_residual) {
+  switch (pseudo_strategy) {
+  case BoutPTCStrategy::inverse_residual:
+    return updatePseudoTimestep_inverse_residual(previous_timestep, current_residual);
+
+  case BoutPTCStrategy::history_based:
+    return updatePseudoTimestep_history_based(previous_timestep, previous_residual,
+                                              current_residual);
+
+  case BoutPTCStrategy::hybrid:
+    // A hybrid strategy may be most effective, in which the timestep is
+    // inversely proportional to residual initially, or when residuals are large,
+    // and then the method transitions to being history-based
+    if (current_residual > 1000. * atol) {
+      return updatePseudoTimestep_inverse_residual(previous_timestep, current_residual);
+    } else {
+      return updatePseudoTimestep_history_based(previous_timestep, previous_residual,
+                                                current_residual);
+    }
+  };
 }
 
 PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 53b87d6c28..a7ed032a8f 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -53,6 +53,11 @@ RegisterSolver<SNESSolver> registersolverbeuler("beuler");
 BOUT_ENUM_CLASS(BoutSnesEquationForm, pseudo_transient, rearranged_backward_euler,
                 backward_euler, direct_newton);
 
+BOUT_ENUM_CLASS(BoutPTCStrategy,
+                inverse_residual, ///< dt = pseudo_alpha / residual
+                history_based,    ///< Grow/shrink dt based on residual decrease/increase
+                hybrid); ///< Combine inverse_residual and history_based strategies
+
 /// Uses PETSc's SNES interface to find a steady state solution to a
 /// nonlinear ODE by integrating in time with Backward Euler
 class SNESSolver : public Solver {
@@ -125,6 +130,7 @@ private:
 
   // Pseudo-Transient Continuation (PTC) variables
   // These are used if equation_form = pseudo_transient
+  BoutPTCStrategy pseudo_strategy;  ///< Strategy to use when setting timesteps
   BoutReal pseudo_alpha;            ///< dt = alpha / residual
   BoutReal pseudo_growth_factor;    ///< Timestep increase 1.1 - 1.2
   BoutReal pseudo_reduction_factor; ///< Timestep decrease 0.5
@@ -134,6 +140,11 @@ private:
   /// Decide the next pseudo-timestep
   BoutReal updatePseudoTimestep(BoutReal previous_timestep, BoutReal previous_residual,
                                 BoutReal current_residual);
+  BoutReal updatePseudoTimestep_inverse_residual(BoutReal previous_timestep,
+                                                 BoutReal current_residual);
+  BoutReal updatePseudoTimestep_history_based(BoutReal previous_timestep,
+                                              BoutReal previous_residual,
+                                              BoutReal current_residual);
   Field3D pseudo_residual; ///< Diagnostic output
   Field3D pseudo_timestep;
 

From 07c2882ef08b26b0f8f0c7405e372c0b47c9247e Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 13 Oct 2025 13:03:58 -0700
Subject: [PATCH 0269/1827] snes: Replace CHKERRQ with PetscCall macro

Minor tidying
---
 src/solver/impls/snes/snes.cxx | 135 ++++++++++++---------------------
 1 file changed, 47 insertions(+), 88 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 1adb2c4b46..dbcaa0fa6a 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -94,8 +94,7 @@ PetscErrorCode FormFunctionForColoring(void* UNUSED(snes), Vec x, Vec f, void* c
 PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
   // Get the context
   SNESSolver* s;
-  int ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&s));
-  CHKERRQ(ierr);
+  PetscCall(PCShellGetContext(pc, reinterpret_cast<void**>(&s)));
 
   PetscFunctionReturn(s->precon(x, y));
 }
@@ -245,55 +244,43 @@ int SNESSolver::init() {
                     n3Dvars(), n2Dvars(), neq, nlocal);
 
   // Initialise PETSc components
-  int ierr;
 
   // Vectors
   output_info.write("Creating vector\n");
-  ierr = VecCreate(BoutComm::get(), &snes_x);
-  CHKERRQ(ierr);
-  ierr = VecSetSizes(snes_x, nlocal, PETSC_DECIDE);
-  CHKERRQ(ierr);
-  ierr = VecSetFromOptions(snes_x);
-  CHKERRQ(ierr);
+  PetscCall(VecCreate(BoutComm::get(), &snes_x));
+  PetscCall(VecSetSizes(snes_x, nlocal, PETSC_DECIDE));
+  PetscCall(VecSetFromOptions(snes_x));
 
-  VecDuplicate(snes_x, &snes_f);
-  VecDuplicate(snes_x, &x0);
+  PetscCall(VecDuplicate(snes_x, &snes_f));
+  PetscCall(VecDuplicate(snes_x, &x0));
 
   if ((equation_form == BoutSnesEquationForm::rearranged_backward_euler)
       || (equation_form == BoutSnesEquationForm::pseudo_transient)) {
     // Need an intermediate vector for rearranged Backward Euler or Pseudo-Transient Continuation
-    ierr = VecDuplicate(snes_x, &delta_x);
-    CHKERRQ(ierr);
+    PetscCall(VecDuplicate(snes_x, &delta_x));
   }
 
   if (predictor) {
     // Storage for previous solution
-    ierr = VecDuplicate(snes_x, &x1);
-    CHKERRQ(ierr);
+    PetscCall(VecDuplicate(snes_x, &x1));
   }
 
   if (scale_rhs) {
     // Storage for rhs factors, one per evolving variable
-    ierr = VecDuplicate(snes_x, &rhs_scaling_factors);
-    CHKERRQ(ierr);
+    PetscCall(VecDuplicate(snes_x, &rhs_scaling_factors));
     // Set all factors to 1 to start with
-    ierr = VecSet(rhs_scaling_factors, 1.0);
-    CHKERRQ(ierr);
+    PetscCall(VecSet(rhs_scaling_factors, 1.0));
     // Array to store inverse Jacobian row norms
-    ierr = VecDuplicate(snes_x, &jac_row_inv_norms);
-    CHKERRQ(ierr);
+    PetscCall(VecDuplicate(snes_x, &jac_row_inv_norms));
   }
 
   if (scale_vars) {
     // Storage for var factors, one per evolving variable
-    ierr = VecDuplicate(snes_x, &var_scaling_factors);
-    CHKERRQ(ierr);
+    PetscCall(VecDuplicate(snes_x, &var_scaling_factors));
     // Set all factors to 1 to start with
-    ierr = VecSet(var_scaling_factors, 1.0);
-    CHKERRQ(ierr);
+    PetscCall(VecSet(var_scaling_factors, 1.0));
     // Storage for scaled 'x' state vectors
-    ierr = VecDuplicate(snes_x, &scaled_x);
-    CHKERRQ(ierr);
+    PetscCall(VecDuplicate(snes_x, &scaled_x));
   }
 
   if (equation_form == BoutSnesEquationForm::pseudo_transient) {
@@ -360,8 +347,7 @@ int SNESSolver::init() {
     // Create a vector to store interpolated output solution
     // Used so that the timestep does not have to be adjusted,
     // because that would require updating the preconditioner.
-    ierr = VecDuplicate(snes_x, &output_x);
-    CHKERRQ(ierr);
+    PetscCall(VecDuplicate(snes_x, &output_x));
 
     if (use_coloring) {
       // Use matrix coloring.
@@ -560,8 +546,7 @@ int SNESSolver::init() {
               // Depends on all variables on this cell
               for (int j = 0; j < n2d; j++) {
                 PetscInt col = ind2 + j;
-                ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
-                CHKERRQ(ierr);
+                PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
               }
             }
           }
@@ -578,8 +563,7 @@ int SNESSolver::init() {
               // Depends on 2D fields
               for (int j = 0; j < n2d; j++) {
                 PetscInt col = ind0 + j;
-                ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
-                CHKERRQ(ierr);
+                PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
               }
 
               // Star pattern
@@ -604,9 +588,9 @@ int SNESSolver::init() {
                   // 3D fields on this cell
                   for (int j = 0; j < n3d; j++) {
                     PetscInt col = ind2 + j;
-                    ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
+                    PetscErrorCode ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
 
-                    if (ierr != 0) {
+                    if (ierr != PETSC_SUCCESS) {
                       output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n",
                                    row, x, y, xi, yi, ind2, ind2 + n3d - 1);
                     }
@@ -631,8 +615,7 @@ int SNESSolver::init() {
         // Test if the matrix is symmetric
         // Values are 0 or 1 so tolerance (1e-5) shouldn't matter
         PetscBool symmetric;
-        ierr = MatIsSymmetric(Jfd, 1e-5, &symmetric);
-        CHKERRQ(ierr);
+        PetscCall(MatIsSymmetric(Jfd, 1e-5, &symmetric));
         if (!symmetric) {
           output_warn.write("Jacobian pattern is not symmetric\n");
         }
@@ -657,8 +640,7 @@ int SNESSolver::init() {
       if (prune_jacobian) {
         // Will remove small elements from the Jacobian.
         // Save a copy to recover from over-pruning
-        ierr = MatDuplicate(Jfd, MAT_SHARE_NONZERO_PATTERN, &Jfd_original);
-        CHKERRQ(ierr);
+        PetscCall(MatDuplicate(Jfd, MAT_SHARE_NONZERO_PATTERN, &Jfd_original));
       }
     } else {
       // Brute force calculation
@@ -785,15 +767,13 @@ int SNESSolver::init() {
 
 int SNESSolver::run() {
   TRACE("SNESSolver::run()");
-  int ierr;
+
   // Set initial guess at the solution from variables
   {
     BoutReal* xdata = nullptr;
-    int ierr = VecGetArray(snes_x, &xdata);
-    CHKERRQ(ierr);
+    PetscCall(VecGetArray(snes_x, &xdata));
     save_vars(xdata);
-    ierr = VecRestoreArray(snes_x, &xdata);
-    CHKERRQ(ierr);
+    PetscCall(VecRestoreArray(snes_x, &xdata));
   }
 
   if (equation_form == BoutSnesEquationForm::pseudo_transient) {
@@ -801,11 +781,9 @@ int SNESSolver::run() {
     run_rhs(simtime);
     {
       BoutReal* fdata = nullptr;
-      ierr = VecGetArray(snes_f, &fdata);
-      CHKERRQ(ierr);
+      PetscCall(VecGetArray(snes_f, &fdata));
       save_derivs(fdata);
-      ierr = VecRestoreArray(snes_f, &fdata);
-      CHKERRQ(ierr);
+      PetscCall(VecRestoreArray(snes_f, &fdata));
     }
   }
 
@@ -834,14 +812,11 @@ int SNESSolver::run() {
 
           // Take ownership of snes_x and var_scaling_factors data
           PetscScalar* snes_x_data = nullptr;
-          ierr = VecGetArray(snes_x, &snes_x_data);
-          CHKERRQ(ierr);
+          PetscCall(VecGetArray(snes_x, &snes_x_data));
           PetscScalar* x1_data;
-          ierr = VecGetArray(x1, &x1_data);
-          CHKERRQ(ierr);
+          PetscCall(VecGetArray(x1, &x1_data));
           PetscScalar* var_scaling_factors_data;
-          ierr = VecGetArray(var_scaling_factors, &var_scaling_factors_data);
-          CHKERRQ(ierr);
+          PetscCall(VecGetArray(var_scaling_factors, &var_scaling_factors_data));
 
           // Normalise each value in the state
           // Limit normalisation so scaling factor is never smaller than rtol
@@ -854,12 +829,9 @@ int SNESSolver::run() {
           }
 
           // Restore vector underlying data
-          ierr = VecRestoreArray(var_scaling_factors, &var_scaling_factors_data);
-          CHKERRQ(ierr);
-          ierr = VecRestoreArray(x1, &x1_data);
-          CHKERRQ(ierr);
-          ierr = VecRestoreArray(snes_x, &snes_x_data);
-          CHKERRQ(ierr);
+          PetscCall(VecRestoreArray(var_scaling_factors, &var_scaling_factors_data));
+          PetscCall(VecRestoreArray(x1, &x1_data));
+          PetscCall(VecRestoreArray(snes_x, &snes_x_data));
 
           if (diagnose) {
             // Print maximum and minimum scaling factors
@@ -955,7 +927,7 @@ int SNESSolver::run() {
       int lin_its;
       SNESGetLinearSolveIterations(snes, &lin_its);
 
-      if ((ierr != 0) or (reason < 0)) {
+      if ((ierr != PETSC_SUCCESS) or (reason < 0)) {
         // Diverged or SNES failed
 
         if (diagnose_failures) {
@@ -1001,8 +973,7 @@ int SNESSolver::run() {
           if (diagnose) {
             output.write("\nRestoring Jacobian\n");
           }
-          ierr = MatCopy(Jfd_original, Jfd, DIFFERENT_NONZERO_PATTERN);
-          CHKERRQ(ierr);
+          PetscCall(MatCopy(Jfd_original, Jfd, DIFFERENT_NONZERO_PATTERN));
           // The non-zero pattern has changed, so update coloring
           updateColoring();
           jacobian_pruned = false; // Reset flag. Will be set after pruning.
@@ -1048,33 +1019,26 @@ int SNESSolver::run() {
 
         if (scale_vars) {
           // scaled_x <- snes_x * var_scaling_factors
-          ierr = VecPointwiseMult(scaled_x, snes_x, var_scaling_factors);
-          CHKERRQ(ierr);
+          PetscCall(VecPointwiseMult(scaled_x, snes_x, var_scaling_factors));
 
           const BoutReal* xdata = nullptr;
-          ierr = VecGetArrayRead(scaled_x, &xdata);
-          CHKERRQ(ierr);
+          PetscCall(VecGetArrayRead(scaled_x, &xdata));
           load_vars(const_cast<BoutReal*>(xdata));
-          ierr = VecRestoreArrayRead(scaled_x, &xdata);
-          CHKERRQ(ierr);
+          PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
         } else {
           const BoutReal* xdata = nullptr;
-          ierr = VecGetArrayRead(snes_x, &xdata);
-          CHKERRQ(ierr);
+          PetscCall(VecGetArrayRead(snes_x, &xdata));
           load_vars(const_cast<BoutReal*>(xdata));
-          ierr = VecRestoreArrayRead(snes_x, &xdata);
-          CHKERRQ(ierr);
+          PetscCall(VecRestoreArrayRead(snes_x, &xdata));
         }
         run_rhs(simtime);
 
         // Copy derivatives back
         {
           BoutReal* fdata = nullptr;
-          ierr = VecGetArray(snes_f, &fdata);
-          CHKERRQ(ierr);
+          PetscCall(VecGetArray(snes_f, &fdata));
           save_derivs(fdata);
-          ierr = VecRestoreArray(snes_f, &fdata);
-          CHKERRQ(ierr);
+          PetscCall(VecRestoreArray(snes_f, &fdata));
         }
 
         // Forward Euler
@@ -1130,7 +1094,7 @@ int SNESSolver::run() {
           }
 
           // Prune Jacobian, keeping diagonal elements
-          ierr = MatFilter(Jfd, prune_abstol, PETSC_TRUE, PETSC_TRUE);
+          PetscCall(MatFilter(Jfd, prune_abstol, PETSC_TRUE, PETSC_TRUE));
 
           // Update the coloring from Jfd matrix
           updateColoring();
@@ -1400,22 +1364,17 @@ int SNESSolver::run() {
     // Put the result into variables
     if (scale_vars) {
       // scaled_x <- output_x * var_scaling_factors
-      int ierr = VecPointwiseMult(scaled_x, output_x, var_scaling_factors);
-      CHKERRQ(ierr);
+      PetscCall(VecPointwiseMult(scaled_x, output_x, var_scaling_factors));
 
       const BoutReal* xdata = nullptr;
-      ierr = VecGetArrayRead(scaled_x, &xdata);
-      CHKERRQ(ierr);
+      PetscCall(VecGetArrayRead(scaled_x, &xdata));
       load_vars(const_cast<BoutReal*>(xdata));
-      ierr = VecRestoreArrayRead(scaled_x, &xdata);
-      CHKERRQ(ierr);
+      PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
     } else {
       const BoutReal* xdata = nullptr;
-      int ierr = VecGetArrayRead(output_x, &xdata);
-      CHKERRQ(ierr);
+      PetscCall(VecGetArrayRead(output_x, &xdata));
       load_vars(const_cast<BoutReal*>(xdata));
-      ierr = VecRestoreArrayRead(output_x, &xdata);
-      CHKERRQ(ierr);
+      PetscCall(VecRestoreArrayRead(output_x, &xdata));
     }
     run_rhs(target); // Run RHS to calculate auxilliary variables
 

From cc58791f15881b4fdf722916f672029d28bee584 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 13 Oct 2025 15:06:10 -0700
Subject: [PATCH 0270/1827] snes: Split PTC implementation into separate
 functions

Trying to simplify the `run()` function by splitting out
pieces into separate functions.
---
 src/solver/impls/snes/snes.cxx | 353 +++++++++++++++------------------
 src/solver/impls/snes/snes.hxx |   9 +-
 2 files changed, 172 insertions(+), 190 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index dbcaa0fa6a..1840dd21c1 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -284,18 +284,7 @@ int SNESSolver::init() {
   }
 
   if (equation_form == BoutSnesEquationForm::pseudo_transient) {
-    // Storage for per-variable timestep
-    PetscCall(VecDuplicate(snes_x, &dt_vec));
-    // Starting timestep
-    PetscCall(VecSet(dt_vec, timestep));
-
-    // Storage for previous residual. Used to compare
-    // residuals before and after step, and adjust timestep accordingly
-    PetscCall(VecDuplicate(snes_x, &previous_f));
-
-    // Diagnostic outputs
-    pseudo_timestep = timestep;
-    pseudo_residual = 0.0;
+    PetscCall(initPseudoTimestepping());
   }
 
   // Nonlinear solver interface (SNES)
@@ -588,7 +577,8 @@ int SNESSolver::init() {
                   // 3D fields on this cell
                   for (int j = 0; j < n3d; j++) {
                     PetscInt col = ind2 + j;
-                    PetscErrorCode ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
+                    PetscErrorCode ierr =
+                        MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
 
                     if (ierr != PETSC_SUCCESS) {
                       output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n",
@@ -859,11 +849,6 @@ int SNESSolver::run() {
         PetscCall(VecMin(dt_vec, nullptr, &timestep));
         dt = timestep;
 
-        // Copy residual from snes_f to previous_f
-        // The value of snes_f is set before the timestepping loop
-        // then calculated after the timestep
-        PetscCall(VecCopy(snes_f, previous_f));
-
         looping = true;
         if (simtime + timestep >= target) {
           looping = false;
@@ -1107,176 +1092,7 @@ int SNESSolver::run() {
 
       if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Adjust local timesteps
-
-        PetscCall(rhs_function(snes_x, snes_f, false));
-
-        // Compare previous_f with snes_f
-        // Use a per-cell timestep so that e.g density and pressure
-        // evolve in a way consistent with the equation of state.
-
-        // Reading the residual vectors
-        const BoutReal* previous_residual = nullptr;
-        PetscCall(VecGetArrayRead(previous_f, &previous_residual));
-        const BoutReal* current_residual = nullptr;
-        PetscCall(VecGetArrayRead(snes_f, &current_residual));
-        // Modifying the dt_vec values
-        BoutReal* dt_data = nullptr;
-        PetscCall(VecGetArray(dt_vec, &dt_data));
-
-        // Note: The ordering of quantities in the PETSc vectors
-        // depends on the Solver::loop_vars function
-        Mesh* mesh = bout::globals::mesh;
-        int idx = 0; // Index into PETSc Vecs
-
-        // Boundary cells
-        for (const auto& i2d : mesh->getRegion2D("RGN_BNDRY")) {
-          // Field2D quantities evolved together
-          int count = 0;
-          BoutReal R0 = 0.0;
-          BoutReal R1 = 0.0;
-
-          for (const auto& f : f2d) {
-            if (!f.evolve_bndry) {
-              continue; // Not evolving boundary => Skip
-            }
-            R0 += SQ(previous_residual[idx + count]);
-            R1 += SQ(current_residual[idx + count]);
-            ++count;
-          }
-          if (count > 0) {
-            R0 = sqrt(R0 / count);
-            R1 = sqrt(R1 / count);
-
-            // Adjust timestep for these quantities
-            BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], R0, R1);
-            for (int i = 0; i != count; ++i) {
-              dt_data[idx++] = new_timestep;
-            }
-          }
-
-          // Field3D quantities evolved together within a cell
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
-            count = 0;
-            R0 = 0.0;
-            R1 = 0.0;
-            for (const auto& f : f3d) {
-              if (!f.evolve_bndry) {
-                continue; // Not evolving boundary => Skip
-              }
-              R0 += SQ(previous_residual[idx + count]);
-              R1 += SQ(current_residual[idx + count]);
-              ++count;
-            }
-            if (count > 0) {
-              R0 = sqrt(R0 / count);
-              R1 = sqrt(R1 / count);
-
-              BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], R0, R1);
-
-              auto i3d = mesh->ind2Dto3D(i2d, jz);
-              pseudo_residual[i3d] = R1;
-              pseudo_timestep[i3d] = new_timestep;
-
-              for (int i = 0; i != count; ++i) {
-                dt_data[idx++] = new_timestep;
-              }
-            }
-          }
-        }
-
-        // Bulk of domain.
-        // These loops don't check the boundary flags
-        for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) {
-          // Field2D quantities evolved together
-          if (f2d.size() > 0) {
-            BoutReal R0 = 0.0;
-            BoutReal R1 = 0.0;
-            for (std::size_t i = 0; i != f2d.size(); ++i) {
-              R0 += SQ(previous_residual[idx + i]);
-              R1 += SQ(current_residual[idx + i]);
-            }
-            R0 = sqrt(R0 / f2d.size());
-            R1 = sqrt(R1 / f2d.size());
-
-            // Adjust timestep for these quantities
-            BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], R0, R1);
-            for (std::size_t i = 0; i != f2d.size(); ++i) {
-              dt_data[idx++] = new_timestep;
-            }
-          }
-
-          // Field3D quantities evolved together within a cell
-          if (f3d.size() > 0) {
-            for (int jz = 0; jz < mesh->LocalNz; jz++) {
-              BoutReal R0 = 0.0;
-              BoutReal R1 = 0.0;
-              for (std::size_t i = 0; i != f3d.size(); ++i) {
-                R0 += SQ(previous_residual[idx + i]);
-                R1 += SQ(current_residual[idx + i]);
-              }
-              R0 = sqrt(R0 / f3d.size());
-              R1 = sqrt(R1 / f3d.size());
-              BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], R0, R1);
-
-              auto i3d = mesh->ind2Dto3D(i2d, jz);
-              pseudo_residual[i3d] = R1;
-
-              // Compare to neighbors
-              BoutReal min_neighboring_dt = max_timestep;
-              BoutReal mean_neighboring_dt = 0.0;
-              int neighbor_count = 0;
-              if (i3d.x() != 0) {
-                const BoutReal val = pseudo_timestep[i3d.xm()];
-                min_neighboring_dt = std::min(min_neighboring_dt, val);
-                mean_neighboring_dt += val;
-                ++neighbor_count;
-              }
-              if (i3d.x() != mesh->LocalNx - 1) {
-                const BoutReal val = pseudo_timestep[i3d.xp()];
-                min_neighboring_dt = std::min(min_neighboring_dt, val);
-                mean_neighboring_dt += val;
-                ++neighbor_count;
-              }
-              if (i3d.y() != 0) {
-                const BoutReal val = pseudo_timestep[i3d.ym()];
-                min_neighboring_dt = std::min(min_neighboring_dt, val);
-                mean_neighboring_dt += val;
-                ++neighbor_count;
-              }
-              if (i3d.x() != mesh->LocalNy - 1) {
-                const BoutReal val = pseudo_timestep[i3d.yp()];
-                min_neighboring_dt = std::min(min_neighboring_dt, val);
-                mean_neighboring_dt += val;
-                ++neighbor_count;
-              }
-              mean_neighboring_dt /= neighbor_count;
-
-              // Smooth
-              //new_timestep = 0.1 * mean_neighboring_dt + 0.9 * new_timestep;
-
-              // Limit ratio of timestep between neighboring cells
-              new_timestep =
-                  std::min(new_timestep, pseudo_max_ratio * min_neighboring_dt);
-
-              pseudo_timestep[i3d] = new_timestep;
-
-              for (std::size_t i = 0; i != f3d.size(); ++i) {
-                dt_data[idx++] = new_timestep;
-              }
-            }
-          }
-        }
-
-        // Restore Vec data arrays
-        PetscCall(VecRestoreArrayRead(previous_f, &previous_residual));
-        PetscCall(VecRestoreArrayRead(snes_f, &current_residual));
-        PetscCall(VecRestoreArray(dt_vec, &dt_data));
-
-        // Need timesteps on neighboring processors
-        // to limit ratio
-        mesh->communicate(pseudo_timestep);
-        // Neumann boundary so timestep isn't pinned at boundaries
-        pseudo_timestep.applyBoundary("neumann");
+        PetscCall(updatePseudoTimestepping(snes_x));
 
         if (pid_controller) {
           // Adjust pseudo_alpha based on nonlinear iterations
@@ -1386,6 +1202,167 @@ int SNESSolver::run() {
   return 0;
 }
 
+PetscErrorCode SNESSolver::initPseudoTimestepping() {
+  // Storage for per-variable timestep
+  PetscCall(VecDuplicate(snes_x, &dt_vec));
+  // Starting timestep
+  PetscCall(VecSet(dt_vec, timestep));
+
+  // Diagnostic outputs
+  pseudo_timestep = timestep;
+  pseudo_residual = 0.0;
+  pseudo_residual_2d = 0.0;
+
+  return PETSC_SUCCESS;
+}
+
+PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
+  // Call RHS function to get time derivatives
+  PetscCall(rhs_function(x, snes_f, false));
+
+  // Use a per-cell timestep so that e.g density and pressure
+  // evolve in a way consistent with the equation of state.
+
+  // Reading the residual vectors
+  const BoutReal* current_residual = nullptr;
+  PetscCall(VecGetArrayRead(snes_f, &current_residual));
+  // Modifying the dt_vec values
+  BoutReal* dt_data = nullptr;
+  PetscCall(VecGetArray(dt_vec, &dt_data));
+
+  // Note: The ordering of quantities in the PETSc vectors
+  // depends on the Solver::loop_vars function
+  Mesh* mesh = bout::globals::mesh;
+  int idx = 0; // Index into PETSc Vecs
+
+  // Boundary cells
+  for (const auto& i2d : mesh->getRegion2D("RGN_BNDRY")) {
+    // Field2D quantities evolved together
+    int count = 0;
+    BoutReal residual = 0.0;
+
+    for (const auto& f : f2d) {
+      if (!f.evolve_bndry) {
+        continue; // Not evolving boundary => Skip
+      }
+      residual += SQ(current_residual[idx + count]);
+      ++count;
+    }
+    if (count > 0) {
+      residual = sqrt(residual / count);
+
+      // Adjust timestep for these quantities
+      BoutReal new_timestep =
+          updatePseudoTimestep(dt_data[idx], pseudo_residual_2d[i2d], residual);
+      for (int i = 0; i != count; ++i) {
+        dt_data[idx++] = new_timestep;
+      }
+      pseudo_residual_2d[i2d] = residual;
+    }
+
+    // Field3D quantities evolved together within a cell
+    for (int jz = 0; jz < mesh->LocalNz; jz++) {
+      count = 0;
+      residual = 0.0;
+      for (const auto& f : f3d) {
+        if (!f.evolve_bndry) {
+          continue; // Not evolving boundary => Skip
+        }
+        residual += SQ(current_residual[idx + count]);
+        ++count;
+      }
+      if (count > 0) {
+        residual = sqrt(residual / count);
+
+        auto i3d = mesh->ind2Dto3D(i2d, jz);
+        BoutReal new_timestep =
+            updatePseudoTimestep(dt_data[idx], pseudo_residual[i3d], residual);
+
+        pseudo_residual[i3d] = residual;
+        pseudo_timestep[i3d] = new_timestep;
+
+        for (int i = 0; i != count; ++i) {
+          dt_data[idx++] = new_timestep;
+        }
+      }
+    }
+  }
+
+  // Bulk of domain.
+  // These loops don't check the boundary flags
+  for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) {
+    // Field2D quantities evolved together
+    if (f2d.size() > 0) {
+      BoutReal residual = 0.0;
+      for (std::size_t i = 0; i != f2d.size(); ++i) {
+        residual += SQ(current_residual[idx + i]);
+      }
+      residual = sqrt(residual / f2d.size());
+
+      // Adjust timestep for these quantities
+      BoutReal new_timestep =
+          updatePseudoTimestep(dt_data[idx], pseudo_residual_2d[i2d], residual);
+      for (std::size_t i = 0; i != f2d.size(); ++i) {
+        dt_data[idx++] = new_timestep;
+      }
+      pseudo_residual_2d[i2d] = residual;
+    }
+
+    // Field3D quantities evolved together within a cell
+    if (f3d.size() > 0) {
+      for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        auto i3d = mesh->ind2Dto3D(i2d, jz);
+
+        BoutReal residual = 0.0;
+        for (std::size_t i = 0; i != f3d.size(); ++i) {
+          residual += SQ(current_residual[idx + i]);
+        }
+        residual = sqrt(residual / f3d.size());
+        BoutReal new_timestep =
+            updatePseudoTimestep(dt_data[idx], pseudo_residual[i3d], residual);
+
+        pseudo_residual[i3d] = residual;
+
+        // Compare to neighbors
+        BoutReal min_neighboring_dt = max_timestep;
+        if (i3d.x() != 0) {
+          min_neighboring_dt = std::min(min_neighboring_dt, pseudo_timestep[i3d.xm()]);
+        }
+        if (i3d.x() != mesh->LocalNx - 1) {
+          min_neighboring_dt = std::min(min_neighboring_dt, pseudo_timestep[i3d.xp()]);
+        }
+        if (i3d.y() != 0) {
+          min_neighboring_dt = std::min(min_neighboring_dt, pseudo_timestep[i3d.ym()]);
+        }
+        if (i3d.x() != mesh->LocalNy - 1) {
+          min_neighboring_dt = std::min(min_neighboring_dt, pseudo_timestep[i3d.yp()]);
+        }
+
+        // Limit ratio of timestep between neighboring cells
+        new_timestep = std::min(new_timestep, pseudo_max_ratio * min_neighboring_dt);
+
+        pseudo_timestep[i3d] = new_timestep;
+
+        for (std::size_t i = 0; i != f3d.size(); ++i) {
+          dt_data[idx++] = new_timestep;
+        }
+      }
+    }
+  }
+
+  // Restore Vec data arrays
+  PetscCall(VecRestoreArrayRead(snes_f, &current_residual));
+  PetscCall(VecRestoreArray(dt_vec, &dt_data));
+
+  // Need timesteps on neighboring processors
+  // to limit ratio
+  mesh->communicate(pseudo_timestep);
+  // Neumann boundary so timestep isn't pinned at boundaries
+  pseudo_timestep.applyBoundary("neumann");
+
+  return PETSC_SUCCESS;
+}
+
 /// Timestep inversely proportional to the residual, clipped to avoid
 /// rapid changes in timestep.
 BoutReal SNESSolver::updatePseudoTimestep_inverse_residual(BoutReal previous_timestep,
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index a7ed032a8f..9086106ecd 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -136,8 +136,12 @@ private:
   BoutReal pseudo_reduction_factor; ///< Timestep decrease 0.5
   BoutReal pseudo_max_ratio;        ///< Maximum timestep ratio between neighboring cells
   Vec dt_vec;                       ///< Each quantity can have its own timestep
-  Vec previous_f;                   ///< Previous residual
-  /// Decide the next pseudo-timestep
+
+  /// Initialize the Pseudo-Transient Continuation method
+  PetscErrorCode initPseudoTimestepping();
+  /// Update dt_vec based on new solution x
+  PetscErrorCode updatePseudoTimestepping(Vec x);
+  /// Decide the next pseudo-timestep. Called by updatePseudoTimestepping
   BoutReal updatePseudoTimestep(BoutReal previous_timestep, BoutReal previous_residual,
                                 BoutReal current_residual);
   BoutReal updatePseudoTimestep_inverse_residual(BoutReal previous_timestep,
@@ -146,6 +150,7 @@ private:
                                               BoutReal previous_residual,
                                               BoutReal current_residual);
   Field3D pseudo_residual; ///< Diagnostic output
+  Field2D pseudo_residual_2d;
   Field3D pseudo_timestep;
 
   ///< PID controller parameters

From dcbdc5d13dcb4e44801a55d5ff6b27ce23679bf0 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 13 Oct 2025 19:45:56 -0700
Subject: [PATCH 0271/1827] snes: Refactoring Jacobian coloring and pruning

Moving Jacobian calculations into separate functions.
---
 src/solver/impls/snes/snes.cxx | 728 +++++++++++++++++----------------
 src/solver/impls/snes/snes.hxx |  11 +
 2 files changed, 380 insertions(+), 359 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 1840dd21c1..838da5fa5a 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -18,6 +18,7 @@
 
 #include <bout/output.hxx>
 
+#include "petscerror.h"
 #include "petscsnes.h"
 #include "petscsys.h"
 #include "petscvec.h"
@@ -100,6 +101,371 @@ PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
 }
 } // namespace
 
+PetscErrorCode SNESSolver::FDJinitialise() {
+  if (use_coloring) {
+    // Use matrix coloring.
+    // This greatly reduces the number of times the rhs() function
+    // needs to be evaluated when calculating the Jacobian.
+
+    // Use global mesh for now
+    Mesh* mesh = bout::globals::mesh;
+
+    //////////////////////////////////////////////////
+    // Get the local indices by starting at 0
+    Field3D index = globalIndex(0);
+
+    //////////////////////////////////////////////////
+    // Pre-allocate PETSc storage
+
+    output_progress.write("Setting Jacobian matrix sizes\n");
+
+    const int n2d = f2d.size();
+    const int n3d = f3d.size();
+
+    // Set size of Matrix on each processor to nlocal x nlocal
+    MatCreate(BoutComm::get(), &Jfd);
+    MatSetOption(Jfd, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
+    MatSetSizes(Jfd, nlocal, nlocal, PETSC_DETERMINE, PETSC_DETERMINE);
+    MatSetFromOptions(Jfd);
+    // Determine which row/columns of the matrix are locally owned
+    int Istart, Iend;
+    MatGetOwnershipRange(Jfd, &Istart, &Iend);
+    // Convert local into global indices
+    // Note: Not in the boundary cells, to keep -1 values
+    for (const auto& i : mesh->getRegion3D("RGN_NOBNDRY")) {
+      index[i] += Istart;
+    }
+    // Now communicate to fill guard cells
+    mesh->communicate(index);
+
+    // Non-zero elements on this processor
+    std::vector<PetscInt> d_nnz;
+    std::vector<PetscInt> o_nnz;
+    auto n_square = (*options)["stencil:square"]
+                        .doc("Extent of stencil (square)")
+                        .withDefault<int>(0);
+    auto n_cross =
+        (*options)["stencil:cross"].doc("Extent of stencil (cross)").withDefault<int>(0);
+    // Set n_taxi 2 if nothing else is set
+    auto n_taxi = (*options)["stencil:taxi"]
+                      .doc("Extent of stencil (taxi-cab norm)")
+                      .withDefault<int>((n_square == 0 && n_cross == 0) ? 2 : 0);
+
+    auto const xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
+    {
+      // This is ugly but can't think of a better and robust way to
+      // count the non-zeros for some arbitrary stencil
+      // effectively the same loop as the one that sets the non-zeros below
+      std::vector<std::set<int>> d_nnz_map2d(nlocal);
+      std::vector<std::set<int>> o_nnz_map2d(nlocal);
+      std::vector<std::set<int>> d_nnz_map3d(nlocal);
+      std::vector<std::set<int>> o_nnz_map3d(nlocal);
+      // Loop over every element in 2D to count the *unique* non-zeros
+      for (int x = mesh->xstart; x <= mesh->xend; x++) {
+        for (int y = mesh->ystart; y <= mesh->yend; y++) {
+
+          const int ind0 = ROUND(index(x, y, 0)) - Istart;
+
+          // 2D fields
+          for (int i = 0; i < n2d; i++) {
+            const PetscInt row = ind0 + i;
+            // Loop through each point in the stencil
+            for (const auto& [x_off, y_off] : xy_offsets) {
+              const int xi = x + x_off;
+              const int yi = y + y_off;
+              if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
+                  || (yi >= mesh->LocalNy)) {
+                continue;
+              }
+
+              const int ind2 = ROUND(index(xi, yi, 0));
+              if (ind2 < 0) {
+                continue; // A boundary point
+              }
+
+              // Depends on all variables on this cell
+              for (int j = 0; j < n2d; j++) {
+                const PetscInt col = ind2 + j;
+                if (col >= Istart && col < Iend) {
+                  d_nnz_map2d[row].insert(col);
+                } else {
+                  o_nnz_map2d[row].insert(col);
+                }
+              }
+            }
+          }
+          // 3D fields
+          for (int z = 0; z < mesh->LocalNz; z++) {
+            const int ind = ROUND(index(x, y, z)) - Istart;
+
+            for (int i = 0; i < n3d; i++) {
+              PetscInt row = ind + i;
+              if (z == 0) {
+                row += n2d;
+              }
+
+              // Depends on 2D fields
+              for (int j = 0; j < n2d; j++) {
+                const PetscInt col = ind0 + j;
+                if (col >= Istart && col < Iend) {
+                  d_nnz_map2d[row].insert(col);
+                } else {
+                  o_nnz_map2d[row].insert(col);
+                }
+              }
+
+              // Star pattern
+              for (const auto& [x_off, y_off] : xy_offsets) {
+                const int xi = x + x_off;
+                const int yi = y + y_off;
+
+                if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
+                    || (yi >= mesh->LocalNy)) {
+                  continue;
+                }
+
+                int ind2 = ROUND(index(xi, yi, 0));
+                if (ind2 < 0) {
+                  continue; // Boundary point
+                }
+
+                if (z == 0) {
+                  ind2 += n2d;
+                }
+
+                // 3D fields on this cell
+                for (int j = 0; j < n3d; j++) {
+                  const PetscInt col = ind2 + j;
+                  if (col >= Istart && col < Iend) {
+                    d_nnz_map3d[row].insert(col);
+                  } else {
+                    o_nnz_map3d[row].insert(col);
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+
+      d_nnz.reserve(nlocal);
+      d_nnz.reserve(nlocal);
+
+      for (int i = 0; i < nlocal; ++i) {
+        // Assume all elements in the z direction are potentially coupled
+        d_nnz.emplace_back(d_nnz_map3d[i].size() * mesh->LocalNz + d_nnz_map2d[i].size());
+        o_nnz.emplace_back(o_nnz_map3d[i].size() * mesh->LocalNz + o_nnz_map2d[i].size());
+      }
+    }
+
+    output_progress.write("Pre-allocating Jacobian\n");
+    // Pre-allocate
+    MatMPIAIJSetPreallocation(Jfd, 0, d_nnz.data(), 0, o_nnz.data());
+    MatSeqAIJSetPreallocation(Jfd, 0, d_nnz.data());
+    MatSetUp(Jfd);
+    MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
+
+    //////////////////////////////////////////////////
+    // Mark non-zero entries
+
+    output_progress.write("Marking non-zero Jacobian entries\n");
+    PetscScalar val = 1.0;
+    for (int x = mesh->xstart; x <= mesh->xend; x++) {
+      for (int y = mesh->ystart; y <= mesh->yend; y++) {
+
+        const int ind0 = ROUND(index(x, y, 0));
+
+        // 2D fields
+        for (int i = 0; i < n2d; i++) {
+          const PetscInt row = ind0 + i;
+
+          // Loop through each point in the stencil
+          for (const auto& [x_off, y_off] : xy_offsets) {
+            const int xi = x + x_off;
+            const int yi = y + y_off;
+            if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx) || (yi >= mesh->LocalNy)) {
+              continue;
+            }
+
+            int ind2 = ROUND(index(xi, yi, 0));
+            if (ind2 < 0) {
+              continue; // A boundary point
+            }
+
+            // Depends on all variables on this cell
+            for (int j = 0; j < n2d; j++) {
+              PetscInt col = ind2 + j;
+              PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
+            }
+          }
+        }
+        // 3D fields
+        for (int z = 0; z < mesh->LocalNz; z++) {
+          int ind = ROUND(index(x, y, z));
+
+          for (int i = 0; i < n3d; i++) {
+            PetscInt row = ind + i;
+            if (z == 0) {
+              row += n2d;
+            }
+
+            // Depends on 2D fields
+            for (int j = 0; j < n2d; j++) {
+              PetscInt col = ind0 + j;
+              PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
+            }
+
+            // Star pattern
+            for (const auto& [x_off, y_off] : xy_offsets) {
+              int xi = x + x_off;
+              int yi = y + y_off;
+
+              if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
+                  || (yi >= mesh->LocalNy)) {
+                continue;
+              }
+              for (int zi = 0; zi < mesh->LocalNz; ++zi) {
+                int ind2 = ROUND(index(xi, yi, zi));
+                if (ind2 < 0) {
+                  continue; // Boundary point
+                }
+
+                if (z == 0) {
+                  ind2 += n2d;
+                }
+
+                // 3D fields on this cell
+                for (int j = 0; j < n3d; j++) {
+                  PetscInt col = ind2 + j;
+                  PetscErrorCode ierr =
+                      MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+                  if (ierr != PETSC_SUCCESS) {
+                    output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n", row,
+                                 x, y, xi, yi, ind2, ind2 + n3d - 1);
+                  }
+                  CHKERRQ(ierr);
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+
+    // Finished marking non-zero entries
+
+    output_progress.write("Assembling Jacobian matrix\n");
+
+    // Assemble Matrix
+    MatAssemblyBegin(Jfd, MAT_FINAL_ASSEMBLY);
+    MatAssemblyEnd(Jfd, MAT_FINAL_ASSEMBLY);
+
+    {
+      // Test if the matrix is symmetric
+      // Values are 0 or 1 so tolerance (1e-5) shouldn't matter
+      PetscBool symmetric;
+      PetscCall(MatIsSymmetric(Jfd, 1e-5, &symmetric));
+      if (!symmetric) {
+        output_warn.write("Jacobian pattern is not symmetric\n");
+      }
+    }
+
+    // The above can miss entries around the X-point branch cut:
+    // The diagonal terms are complicated because moving in X then Y
+    // is different from moving in Y then X at the X-point.
+    // Making sure the colouring matrix is symmetric does not
+    // necessarily give the correct stencil but may help.
+    if ((*options)["force_symmetric_coloring"]
+            .doc("Modifies coloring matrix to force it to be symmetric")
+            .withDefault<bool>(false)) {
+      Mat Jfd_T;
+      MatCreateTranspose(Jfd, &Jfd_T);
+      MatAXPY(Jfd, 1, Jfd_T, DIFFERENT_NONZERO_PATTERN);
+    }
+
+    output_progress.write("Creating Jacobian coloring\n");
+    updateColoring();
+
+    if (prune_jacobian) {
+      // Will remove small elements from the Jacobian.
+      // Save a copy to recover from over-pruning
+      PetscCall(MatDuplicate(Jfd, MAT_SHARE_NONZERO_PATTERN, &Jfd_original));
+    }
+  } else {
+    // Brute force calculation
+    // There is usually no reason to use this, except as a check of
+    // the coloring calculation.
+
+    MatCreateAIJ(
+        BoutComm::get(), nlocal, nlocal,  // Local sizes
+        PETSC_DETERMINE, PETSC_DETERMINE, // Global sizes
+        3, // Number of nonzero entries in diagonal portion of local submatrix
+        nullptr,
+        0, // Number of nonzeros per row in off-diagonal portion of local submatrix
+        nullptr, &Jfd);
+
+    if (matrix_free_operator) {
+      SNESSetJacobian(snes, Jmf, Jfd, SNESComputeJacobianDefault, this);
+    } else {
+      SNESSetJacobian(snes, Jfd, Jfd, SNESComputeJacobianDefault, this);
+    }
+
+    MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
+  }
+}
+
+PetscErrorCode SNESSolver::FDJpruneJacobian() {
+#if PETSC_VERSION_GE(3, 20, 0)
+
+  // Remove small elements from the Jacobian and recompute the coloring
+  // Only do this if there are a significant number of small elements.
+  int small_elements = 0;
+  int total_elements = 0;
+
+  // Get index of rows owned by this processor
+  int rstart, rend;
+  MatGetOwnershipRange(Jfd, &rstart, &rend);
+
+  PetscInt ncols;
+  const PetscScalar* vals;
+  for (int row = rstart; row < rend; row++) {
+    MatGetRow(Jfd, row, &ncols, nullptr, &vals);
+    for (int col = 0; col < ncols; col++) {
+      if (std::abs(vals[col]) < prune_abstol) {
+        ++small_elements;
+      }
+      ++total_elements;
+    }
+    MatRestoreRow(Jfd, row, &ncols, nullptr, &vals);
+  }
+
+  if (small_elements > prune_fraction * total_elements) {
+    if (diagnose) {
+      output.write("\nPruning Jacobian elements: {} / {}\n", small_elements,
+                   total_elements);
+    }
+
+    // Prune Jacobian, keeping diagonal elements
+    PetscCall(MatFilter(Jfd, prune_abstol, PETSC_TRUE, PETSC_TRUE));
+
+    // Update the coloring from Jfd matrix
+    updateColoring();
+
+    // Mark the Jacobian as pruned. This is so that it is only restored if pruned.
+    jacobian_pruned = true;
+  }
+#endif // PETSC_VERSION_GE(3,20,0)
+}
+
+PetscErrorCode SNESSolver::FDJrestoreFromPruning() {
+  // Restore pruned non-zero elements
+  PetscCall(MatCopy(Jfd_original, Jfd, DIFFERENT_NONZERO_PATTERN));
+  // The non-zero pattern has changed, so update coloring
+  updateColoring();
+  jacobian_pruned = false; // Reset flag. Will be set after pruning.
+}
+
 SNESSolver::SNESSolver(Options* opts)
     : Solver(opts),
       timestep(
@@ -338,321 +704,7 @@ int SNESSolver::init() {
     // because that would require updating the preconditioner.
     PetscCall(VecDuplicate(snes_x, &output_x));
 
-    if (use_coloring) {
-      // Use matrix coloring.
-      // This greatly reduces the number of times the rhs() function
-      // needs to be evaluated when calculating the Jacobian.
-
-      // Use global mesh for now
-      Mesh* mesh = bout::globals::mesh;
-
-      //////////////////////////////////////////////////
-      // Get the local indices by starting at 0
-      Field3D index = globalIndex(0);
-
-      //////////////////////////////////////////////////
-      // Pre-allocate PETSc storage
-
-      output_progress.write("Setting Jacobian matrix sizes\n");
-
-      const int n2d = f2d.size();
-      const int n3d = f3d.size();
-
-      // Set size of Matrix on each processor to nlocal x nlocal
-      MatCreate(BoutComm::get(), &Jfd);
-      MatSetOption(Jfd, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
-      MatSetSizes(Jfd, nlocal, nlocal, PETSC_DETERMINE, PETSC_DETERMINE);
-      MatSetFromOptions(Jfd);
-      // Determine which row/columns of the matrix are locally owned
-      int Istart, Iend;
-      MatGetOwnershipRange(Jfd, &Istart, &Iend);
-      // Convert local into global indices
-      // Note: Not in the boundary cells, to keep -1 values
-      for (const auto& i : mesh->getRegion3D("RGN_NOBNDRY")) {
-        index[i] += Istart;
-      }
-      // Now communicate to fill guard cells
-      mesh->communicate(index);
-
-      // Non-zero elements on this processor
-      std::vector<PetscInt> d_nnz;
-      std::vector<PetscInt> o_nnz;
-      auto n_square = (*options)["stencil:square"]
-                          .doc("Extent of stencil (square)")
-                          .withDefault<int>(0);
-      auto n_cross = (*options)["stencil:cross"]
-                         .doc("Extent of stencil (cross)")
-                         .withDefault<int>(0);
-      // Set n_taxi 2 if nothing else is set
-      auto n_taxi = (*options)["stencil:taxi"]
-                        .doc("Extent of stencil (taxi-cab norm)")
-                        .withDefault<int>((n_square == 0 && n_cross == 0) ? 2 : 0);
-
-      auto const xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
-      {
-        // This is ugly but can't think of a better and robust way to
-        // count the non-zeros for some arbitrary stencil
-        // effectively the same loop as the one that sets the non-zeros below
-        std::vector<std::set<int>> d_nnz_map2d(nlocal);
-        std::vector<std::set<int>> o_nnz_map2d(nlocal);
-        std::vector<std::set<int>> d_nnz_map3d(nlocal);
-        std::vector<std::set<int>> o_nnz_map3d(nlocal);
-        // Loop over every element in 2D to count the *unique* non-zeros
-        for (int x = mesh->xstart; x <= mesh->xend; x++) {
-          for (int y = mesh->ystart; y <= mesh->yend; y++) {
-
-            const int ind0 = ROUND(index(x, y, 0)) - Istart;
-
-            // 2D fields
-            for (int i = 0; i < n2d; i++) {
-              const PetscInt row = ind0 + i;
-              // Loop through each point in the stencil
-              for (const auto& [x_off, y_off] : xy_offsets) {
-                const int xi = x + x_off;
-                const int yi = y + y_off;
-                if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                    || (yi >= mesh->LocalNy)) {
-                  continue;
-                }
-
-                const int ind2 = ROUND(index(xi, yi, 0));
-                if (ind2 < 0) {
-                  continue; // A boundary point
-                }
-
-                // Depends on all variables on this cell
-                for (int j = 0; j < n2d; j++) {
-                  const PetscInt col = ind2 + j;
-                  if (col >= Istart && col < Iend) {
-                    d_nnz_map2d[row].insert(col);
-                  } else {
-                    o_nnz_map2d[row].insert(col);
-                  }
-                }
-              }
-            }
-            // 3D fields
-            for (int z = 0; z < mesh->LocalNz; z++) {
-              const int ind = ROUND(index(x, y, z)) - Istart;
-
-              for (int i = 0; i < n3d; i++) {
-                PetscInt row = ind + i;
-                if (z == 0) {
-                  row += n2d;
-                }
-
-                // Depends on 2D fields
-                for (int j = 0; j < n2d; j++) {
-                  const PetscInt col = ind0 + j;
-                  if (col >= Istart && col < Iend) {
-                    d_nnz_map2d[row].insert(col);
-                  } else {
-                    o_nnz_map2d[row].insert(col);
-                  }
-                }
-
-                // Star pattern
-                for (const auto& [x_off, y_off] : xy_offsets) {
-                  const int xi = x + x_off;
-                  const int yi = y + y_off;
-
-                  if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                      || (yi >= mesh->LocalNy)) {
-                    continue;
-                  }
-
-                  int ind2 = ROUND(index(xi, yi, 0));
-                  if (ind2 < 0) {
-                    continue; // Boundary point
-                  }
-
-                  if (z == 0) {
-                    ind2 += n2d;
-                  }
-
-                  // 3D fields on this cell
-                  for (int j = 0; j < n3d; j++) {
-                    const PetscInt col = ind2 + j;
-                    if (col >= Istart && col < Iend) {
-                      d_nnz_map3d[row].insert(col);
-                    } else {
-                      o_nnz_map3d[row].insert(col);
-                    }
-                  }
-                }
-              }
-            }
-          }
-        }
-
-        d_nnz.reserve(nlocal);
-        d_nnz.reserve(nlocal);
-
-        for (int i = 0; i < nlocal; ++i) {
-          // Assume all elements in the z direction are potentially coupled
-          d_nnz.emplace_back(d_nnz_map3d[i].size() * mesh->LocalNz
-                             + d_nnz_map2d[i].size());
-          o_nnz.emplace_back(o_nnz_map3d[i].size() * mesh->LocalNz
-                             + o_nnz_map2d[i].size());
-        }
-      }
-
-      output_progress.write("Pre-allocating Jacobian\n");
-      // Pre-allocate
-      MatMPIAIJSetPreallocation(Jfd, 0, d_nnz.data(), 0, o_nnz.data());
-      MatSeqAIJSetPreallocation(Jfd, 0, d_nnz.data());
-      MatSetUp(Jfd);
-      MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
-
-      //////////////////////////////////////////////////
-      // Mark non-zero entries
-
-      output_progress.write("Marking non-zero Jacobian entries\n");
-      PetscScalar val = 1.0;
-      for (int x = mesh->xstart; x <= mesh->xend; x++) {
-        for (int y = mesh->ystart; y <= mesh->yend; y++) {
-
-          const int ind0 = ROUND(index(x, y, 0));
-
-          // 2D fields
-          for (int i = 0; i < n2d; i++) {
-            const PetscInt row = ind0 + i;
-
-            // Loop through each point in the stencil
-            for (const auto& [x_off, y_off] : xy_offsets) {
-              const int xi = x + x_off;
-              const int yi = y + y_off;
-              if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                  || (yi >= mesh->LocalNy)) {
-                continue;
-              }
-
-              int ind2 = ROUND(index(xi, yi, 0));
-              if (ind2 < 0) {
-                continue; // A boundary point
-              }
-
-              // Depends on all variables on this cell
-              for (int j = 0; j < n2d; j++) {
-                PetscInt col = ind2 + j;
-                PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
-              }
-            }
-          }
-          // 3D fields
-          for (int z = 0; z < mesh->LocalNz; z++) {
-            int ind = ROUND(index(x, y, z));
-
-            for (int i = 0; i < n3d; i++) {
-              PetscInt row = ind + i;
-              if (z == 0) {
-                row += n2d;
-              }
-
-              // Depends on 2D fields
-              for (int j = 0; j < n2d; j++) {
-                PetscInt col = ind0 + j;
-                PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
-              }
-
-              // Star pattern
-              for (const auto& [x_off, y_off] : xy_offsets) {
-                int xi = x + x_off;
-                int yi = y + y_off;
-
-                if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                    || (yi >= mesh->LocalNy)) {
-                  continue;
-                }
-                for (int zi = 0; zi < mesh->LocalNz; ++zi) {
-                  int ind2 = ROUND(index(xi, yi, zi));
-                  if (ind2 < 0) {
-                    continue; // Boundary point
-                  }
-
-                  if (z == 0) {
-                    ind2 += n2d;
-                  }
-
-                  // 3D fields on this cell
-                  for (int j = 0; j < n3d; j++) {
-                    PetscInt col = ind2 + j;
-                    PetscErrorCode ierr =
-                        MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-                    if (ierr != PETSC_SUCCESS) {
-                      output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n",
-                                   row, x, y, xi, yi, ind2, ind2 + n3d - 1);
-                    }
-                    CHKERRQ(ierr);
-                  }
-                }
-              }
-            }
-          }
-        }
-      }
-
-      // Finished marking non-zero entries
-
-      output_progress.write("Assembling Jacobian matrix\n");
-
-      // Assemble Matrix
-      MatAssemblyBegin(Jfd, MAT_FINAL_ASSEMBLY);
-      MatAssemblyEnd(Jfd, MAT_FINAL_ASSEMBLY);
-
-      {
-        // Test if the matrix is symmetric
-        // Values are 0 or 1 so tolerance (1e-5) shouldn't matter
-        PetscBool symmetric;
-        PetscCall(MatIsSymmetric(Jfd, 1e-5, &symmetric));
-        if (!symmetric) {
-          output_warn.write("Jacobian pattern is not symmetric\n");
-        }
-      }
-
-      // The above can miss entries around the X-point branch cut:
-      // The diagonal terms are complicated because moving in X then Y
-      // is different from moving in Y then X at the X-point.
-      // Making sure the colouring matrix is symmetric does not
-      // necessarily give the correct stencil but may help.
-      if ((*options)["force_symmetric_coloring"]
-              .doc("Modifies coloring matrix to force it to be symmetric")
-              .withDefault<bool>(false)) {
-        Mat Jfd_T;
-        MatCreateTranspose(Jfd, &Jfd_T);
-        MatAXPY(Jfd, 1, Jfd_T, DIFFERENT_NONZERO_PATTERN);
-      }
-
-      output_progress.write("Creating Jacobian coloring\n");
-      updateColoring();
-
-      if (prune_jacobian) {
-        // Will remove small elements from the Jacobian.
-        // Save a copy to recover from over-pruning
-        PetscCall(MatDuplicate(Jfd, MAT_SHARE_NONZERO_PATTERN, &Jfd_original));
-      }
-    } else {
-      // Brute force calculation
-      // There is usually no reason to use this, except as a check of
-      // the coloring calculation.
-
-      MatCreateAIJ(
-          BoutComm::get(), nlocal, nlocal,  // Local sizes
-          PETSC_DETERMINE, PETSC_DETERMINE, // Global sizes
-          3, // Number of nonzero entries in diagonal portion of local submatrix
-          nullptr,
-          0, // Number of nonzeros per row in off-diagonal portion of local submatrix
-          nullptr, &Jfd);
-
-      if (matrix_free_operator) {
-        SNESSetJacobian(snes, Jmf, Jfd, SNESComputeJacobianDefault, this);
-      } else {
-        SNESSetJacobian(snes, Jfd, Jfd, SNESComputeJacobianDefault, this);
-      }
-
-      MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
-    }
+    FDJinitialise();
 
     // Re-use Jacobian
     // Note: If the 'Amat' Jacobian is matrix free, SNESComputeJacobian
@@ -954,14 +1006,10 @@ int SNESSolver::run() {
         if (jacobian_pruned and (snes_failures > 2) and (4 * lin_its > 3 * maxl)) {
           // Taking 3/4 of maximum linear iterations on average per linear step
           // May indicate a preconditioner problem.
-          // Restore pruned non-zero elements
           if (diagnose) {
             output.write("\nRestoring Jacobian\n");
           }
-          PetscCall(MatCopy(Jfd_original, Jfd, DIFFERENT_NONZERO_PATTERN));
-          // The non-zero pattern has changed, so update coloring
-          updateColoring();
-          jacobian_pruned = false; // Reset flag. Will be set after pruning.
+          PetscCall(FDJrestoreFromPruning());
         }
 
         if (saved_jacobian_lag == 0) {
@@ -1045,50 +1093,12 @@ int SNESSolver::run() {
         output.write("\n");
       }
 
-#if PETSC_VERSION_GE(3, 20, 0)
       // MatFilter and MatEliminateZeros(Mat, bool) require PETSc >= 3.20
       if (jacobian_recalculated and prune_jacobian) {
         jacobian_recalculated = false; // Reset flag
 
-        // Remove small elements from the Jacobian and recompute the coloring
-        // Only do this if there are a significant number of small elements.
-        int small_elements = 0;
-        int total_elements = 0;
-
-        // Get index of rows owned by this processor
-        int rstart, rend;
-        MatGetOwnershipRange(Jfd, &rstart, &rend);
-
-        PetscInt ncols;
-        const PetscScalar* vals;
-        for (int row = rstart; row < rend; row++) {
-          MatGetRow(Jfd, row, &ncols, nullptr, &vals);
-          for (int col = 0; col < ncols; col++) {
-            if (std::abs(vals[col]) < prune_abstol) {
-              ++small_elements;
-            }
-            ++total_elements;
-          }
-          MatRestoreRow(Jfd, row, &ncols, nullptr, &vals);
-        }
-
-        if (small_elements > prune_fraction * total_elements) {
-          if (diagnose) {
-            output.write("\nPruning Jacobian elements: {} / {}\n", small_elements,
-                         total_elements);
-          }
-
-          // Prune Jacobian, keeping diagonal elements
-          PetscCall(MatFilter(Jfd, prune_abstol, PETSC_TRUE, PETSC_TRUE));
-
-          // Update the coloring from Jfd matrix
-          updateColoring();
-
-          // Mark the Jacobian as pruned. This is so that it is only restored if pruned.
-          jacobian_pruned = true;
-        }
+        FDJpruneJacobian();
       }
-#endif // PETSC_VERSION_GE(3,20,0)
 
       if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Adjust local timesteps
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 9086106ecd..98e96d3e4e 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -58,6 +58,13 @@ BOUT_ENUM_CLASS(BoutPTCStrategy,
                 history_based,    ///< Grow/shrink dt based on residual decrease/increase
                 hybrid); ///< Combine inverse_residual and history_based strategies
 
+// class FiniteDifferenceJacobian {
+// public:
+//   PetscError initialise();
+// private:
+
+// };
+
 /// Uses PETSc's SNES interface to find a steady state solution to a
 /// nonlinear ODE by integrating in time with Backward Euler
 class SNESSolver : public Solver {
@@ -100,6 +107,10 @@ public:
   void outputVars(Options& output_options, bool save_repeat = true) override;
 
 private:
+  PetscErrorCode FDJinitialise();
+  PetscErrorCode FDJpruneJacobian();
+  PetscErrorCode FDJrestoreFromPruning();
+
   /// Call the physics model RHS function
   ///
   /// @param[in] x       The state vector. Will be scaled if scale_vars=true

From 48c0b180f677183aaeb8ffa42e5a063b1a72c0b3 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 14 Oct 2025 11:03:06 -0700
Subject: [PATCH 0272/1827] snes: Expand manual and minor tidying

Add manual sections on adaptive timestepping and PTC method.

Minor tidying to address some Clang-Tidy comments.
---
 manual/sphinx/user_docs/time_integration.rst | 230 +++++++++++++++++--
 src/solver/impls/snes/snes.cxx               |   7 +-
 src/solver/impls/snes/snes.hxx               |   8 +-
 3 files changed, 214 insertions(+), 31 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 373b5cdbe6..7658602bc8 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -390,7 +390,7 @@ The SNES solver is configured through the ``[solver]`` section of the input file
    pc_type = ilu                 # Preconditioner: ilu, bjacobi, hypre, etc.
 
 Timestepping Modes
-------------------
+~~~~~~~~~~~~~~~~~~
 
 The solver supports several timestepping strategies controlled by ``equation_form``:
 
@@ -425,6 +425,183 @@ The solver supports several timestepping strategies controlled by ``equation_for
    This uses the same form as rearranged_backward_euler, but the time step
    can be different for each cell.
 
+Adaptive Timestepping
+~~~~~~~~~~~~~~~~~~~~~
+
+When ``equation_form = rearranged_backward_euler`` (default), the
+solver uses global timestepping with adaptive timestep control based
+on nonlinear iteration count.
+
+.. code-block:: ini
+
+   [solver]
+   type = snes
+   equation_form = rearranged_backward_euler
+
+   # Initial and maximum timesteps
+   timestep = 1.0                         # Initial timestep
+   max_timestep = 1e10                    # Upper limit on timestep
+   dt_min_reset = 1e-6                    # Reset the solver when timestep < this
+
+   # Timestep adaptation
+   lower_its = 3                          # Increase dt if iterations < this
+   upper_its = 10                         # Decrease dt if iterations > this
+   timestep_factor_on_lower_its = 1.4     # Growth factor
+   timestep_factor_on_upper_its = 0.9     # Reduction factor
+   timestep_factor_on_failure = 0.5       # Reduction on convergence failure
+
+PID Controller
+^^^^^^^^^^^^^^
+
+An alternative adaptive strategy using a PID controller:
+
+.. code-block:: ini
+
+   [solver]
+   pid_controller = true
+   target_its = 7        # Target number of nonlinear iterations
+   kP = 0.7              # Proportional gain
+   kI = 0.3              # Integral gain
+   kD = 0.2              # Derivative gain
+
+The PID controller adjusts the timestep to maintain approximately ``target_its``
+nonlinear iterations per solve, providing smoother adaptation than threshold-based
+methods.
+
+Pseudo-Transient Continuation and Switched Evolution Relaxation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+When ``equation_form = pseudo_transient`` the solver uses
+Pseudo-Transient Continuation (PTC). This is a robust numerical
+technique for solving steady-state problems that are too nonlinear for
+direct Newton iteration. Instead of solving the steady-state system
+**F(u) = 0** directly, PTC solves a modified time-dependent problem:
+
+.. math::
+
+   M(u) \frac{\partial u}{\partial \tau} + F(u) = 0
+
+where :math:`\tau` is a pseudo-time variable (not physical time) and :math:`M(u)`
+is a preconditioning matrix. As :math:`\tau \to \infty`, the solution converges
+to the steady state **F(u) = 0**.
+
+The key advantage of PTC is that it transforms a difficult root-finding problem
+into a sequence of easier initial value problems. Poor initial guesses that would
+cause Newton's method to diverge can still reach the solution via a stable
+pseudo-transient path.
+
+The Switched Evolution Relaxation (SER) method is a spatially adaptive
+variant of PTC that allows each cell to use a different
+pseudo-timestep :math:`\Delta\tau_i`. The timestep in each cell adapts
+based on the local residual, allowing the algorithm to take large
+timesteps in well-behaved regions (fast convergence), while taking
+small timesteps in difficult regions (stable advancement).  The the
+same :math:`\Delta\tau_i` is used for all equations (density,
+momentum, energy etc.) within each cell. This maintains coupling
+between temperature, pressure, and composition through the equation of
+state.
+
+**Key parameters:**
+
+``pseudo_max_ratio`` (default: 2.0)
+   Maximum allowed ratio of timesteps between neighboring cells. This prevents
+   sharp spatial gradients in convergence rate.
+
+**Example PTC configuration:**
+
+.. code-block:: ini
+
+   [solver]
+   type = snes
+   equation_form = pseudo_transient
+
+   timestep = 1.0                # Initial timestep
+
+   # SER parameters
+   pid_controller = true          # Scale timesteps based on iterations
+   pseudo_max_ratio = 2.0         # Limit neighbor timestep ratio
+
+   # Tolerances
+   atol = 1e-7
+   rtol = 1e-6
+   stol = 1e-12
+
+SER timestep strategy
+^^^^^^^^^^^^^^^^^^^^^
+
+After each nonlinear solve the timesteps in each cell are adjusted.
+The strategy used depends on the ``pseudo_strategy`` option:
+
+**inverse_residual** (default)
+
+If ``pseudo_strategy = inverse_residual`` then the timestep is inversely
+proportional to the RMS residual in each cell.
+``pseudo_alpha`` (default: 100 × atol × timestep)
+Controls the relationship between residual and timestep. The local timestep
+is computed as:
+
+.. math::
+
+   \Delta\tau_i = \frac{\alpha}{||R_i||}
+
+Larger values allow more aggressive timestepping. The default is to use
+a fixed ``pseudo_alpha`` but a better strategy is to enable the PID controller
+that adjusts this parameter based on the nonlinear solver convergence.
+
+The timestep is limited to be between ``dt_min_reset`` and
+``max_timestep``.  In addition the timestep is limited between 0.67 ×
+previous timestep and 1.5 × previous timestep, to limit sudden changes
+in timestep.
+
+In practice this strategy seems to work well, though problems could
+arise when residuals become very small.
+
+**history_based**
+
+When ``pseudo_strategy = history_based`` the history of residuals
+within each cell is used to adjust the timestep. The key parameters
+are:
+
+``pseudo_growth_factor`` (default: 1.1)
+   Factor by which timestep increases when residual decreases successfully.
+
+``pseudo_reduction_factor`` (default: 0.5)
+   Factor by which timestep decreases when residual increases (step rejected).
+
+This method may be less susceptible to fluctuations when residuals
+become small, but tends to be slower to converge when residuals are
+large.
+
+**hybrid**
+
+When ``pseudo_strategy = hybrid`` the ``inverse_residual`` and
+``history_based`` strategies are combined: When the residuals are
+large the ``inverse_residual`` method is used, and when residuals
+become small the method switches to ``history_based``.
+
+PID Controller
+^^^^^^^^^^^^^^
+
+When using the PTC method the PID controller can be used to dynamically
+adjust ``pseudo_alpha`` depending on the nonlinearity of the system:
+
+.. code-block:: ini
+
+   [solver]
+   pid_controller = true
+   target_its = 7        # Target number of nonlinear iterations
+   kP = 0.7              # Proportional gain
+   kI = 0.3              # Integral gain
+   kD = 0.2              # Derivative gain
+
+The PID controller adjusts ``pseudo_alpha``, scaling all cell
+timesteps together, to maintain approximately ``target_its`` nonlinear
+iterations per solve.
+
+With this enabled the solver uses the number of nonlinear iterations
+to scale timesteps globally, and residuals to scale timesteps locally.
+Note that the PID controller has no effect on the ``history_based``
+strategy because that strategy does not use ``pseudo_alpha``.
 
 Jacobian Finite Difference with Coloring
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -435,7 +612,7 @@ The default and recommended approach for most problems:
 
    [solver]
    use_coloring = true               # Enable (default)
-   lag_jacobian = 50                 # Reuse Jacobian for this many iterations
+   lag_jacobian = 5                  # Reuse Jacobian for this many iterations
 
    # Stencil shape (determines Jacobian sparsity pattern)
    stencil:taxi = 2                  # Taxi-cab distance (default)
@@ -449,7 +626,17 @@ Jacobian coloring stencil
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The stencil used to create the Jacobian colouring can be varied,
-depending on which numerical operators are in use.
+depending on which numerical operators are in use. It is important to
+note that the coloring won't work for every problem: It assumes that
+each evolving quantity is coupled to all other evolving quantities on
+the same grid cell, and on all the neighbouring grid cells. If the RHS
+function includes Fourier transforms, or matrix inversions
+(e.g. potential solves) then these will introduce longer-range
+coupling and the Jacobian calculation will give spurious
+results. Generally the method will then fail to converge. Two
+solutions are to a) switch to matrix-free (``matrix_free=true``),
+or b) solve the matrix inversion as a constraint.
+
 
 ``solver:stencil:cross = N``
 e.g. for N == 2
@@ -489,8 +676,26 @@ Setting ``solver:force_symmetric_coloring = true``, will make sure
 that the jacobian colouring matrix is symmetric.  This will often
 include a few extra non-zeros that the stencil will miss otherwise
 
+Diagnostics and Monitoring
+---------------------------
+
+.. code-block:: ini
+
+   [solver]
+   diagnose = true                # Print iteration info to screen
+   diagnose_failures = true       # Detailed diagnostics on failures
+
+When ``equation_form = pseudo_transient``, the solver saves additional diagnostic fields:
+
+- ``snes_pseudo_residual``: Local residual in each cell
+- ``snes_pseudo_timestep``: Local pseudo-timestep in each cell
+- ``snes_pseudo_alpha``: Global timestep scaling
 
+These can be visualized to understand convergence behavior and identify
+problematic regions.
 
+Summary of solver options
+~~~~~~~~~~~~~~~~~~~~~~~~~
 
 +---------------------------+---------------+----------------------------------------------------+
 | Option                    | Default       |Description                                         |
@@ -552,22 +757,11 @@ include a few extra non-zeros that the stencil will miss otherwise
 The predictor is linear extrapolation from the last two timesteps. It seems to be
 effective, but can be disabled by setting ``predictor = false``.
 
-
-
 The default `newtonls` SNES type can be very effective if combined
 with Jacobian coloring: The coloring enables the Jacobian to be
 calculated relatively efficiently; once a Jacobian matrix has been
 calculated, effective preconditioners can be used to speed up
-convergence.  It is important to note that the coloring assumes a star
-stencil and so won't work for every problem: It assumes that each
-evolving quantity is coupled to all other evolving quantities on the
-same grid cell, and on all the neighbouring grid cells. If the RHS
-function includes Fourier transforms, or matrix inversions
-(e.g. potential solves) then these will introduce longer-range
-coupling and the Jacobian calculation will give spurious
-results. Generally the method will then fail to converge. Two
-solutions are to a) switch to matrix-free (``matrix_free=true``), or b)
-solve the matrix inversion as a constraint.
+convergence.
 
 The `SNES type
 <https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/SNES/SNESType.html>`_
@@ -587,12 +781,6 @@ Preconditioner types:
    Enable with command-line args ``-pc_type hypre -pc_hypre_type euclid -pc_hypre_euclid_levels k``
    where ``k`` is the level (1-8 typically).
 
-Pseudo-Transient Continuation (PTC)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-
-
-Saves diagnostic ``Field3D`` output variables ``snes_pseudo_residual`` and ``snes_pseudo_timestep``.
 
 
 ODE integration
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 838da5fa5a..1207fcee1b 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -19,6 +19,7 @@
 #include <bout/output.hxx>
 
 #include "petscerror.h"
+#include "petscpc.h"
 #include "petscsnes.h"
 #include "petscsys.h"
 #include "petscvec.h"
@@ -1435,11 +1436,11 @@ BoutReal SNESSolver::updatePseudoTimestep(BoutReal previous_timestep,
     // and then the method transitions to being history-based
     if (current_residual > 1000. * atol) {
       return updatePseudoTimestep_inverse_residual(previous_timestep, current_residual);
-    } else {
-      return updatePseudoTimestep_history_based(previous_timestep, previous_residual,
-                                                current_residual);
     }
+    return updatePseudoTimestep_history_based(previous_timestep, previous_residual,
+                                              current_residual);
   };
+  throw BoutException("SNESSolver::updatePseudoTimestep invalid BoutPTCStrategy");
 }
 
 PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 98e96d3e4e..c37cc0b37a 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -39,6 +39,7 @@ class SNESSolver;
 
 #include <bout/bout_enum_class.hxx>
 #include <bout/bout_types.hxx>
+#include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/petsclib.hxx>
 
@@ -58,13 +59,6 @@ BOUT_ENUM_CLASS(BoutPTCStrategy,
                 history_based,    ///< Grow/shrink dt based on residual decrease/increase
                 hybrid); ///< Combine inverse_residual and history_based strategies
 
-// class FiniteDifferenceJacobian {
-// public:
-//   PetscError initialise();
-// private:
-
-// };
-
 /// Uses PETSc's SNES interface to find a steady state solution to a
 /// nonlinear ODE by integrating in time with Backward Euler
 class SNESSolver : public Solver {

From ca04bc81b374cbdd5a91f2e0a7843b9322a2a1f6 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 14 Oct 2025 15:17:58 -0700
Subject: [PATCH 0273/1827] snes: Add missing returns, clang tidying

---
 src/solver/impls/snes/snes.cxx | 32 ++++++++++++++++++++------------
 src/solver/impls/snes/snes.hxx |  6 +++---
 2 files changed, 23 insertions(+), 15 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 1207fcee1b..d349193ee4 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -14,14 +14,18 @@
 
 #include <algorithm>
 #include <cmath>
+#include <cstddef>
+#include <set>
 #include <vector>
 
 #include <bout/output.hxx>
 
 #include "petscerror.h"
+#include "petscmat.h"
 #include "petscpc.h"
 #include "petscsnes.h"
 #include "petscsys.h"
+#include "petscsystypes.h"
 #include "petscvec.h"
 
 class ColoringStencil {
@@ -270,7 +274,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
     // Mark non-zero entries
 
     output_progress.write("Marking non-zero Jacobian entries\n");
-    PetscScalar val = 1.0;
+    const PetscScalar val = 1.0;
     for (int x = mesh->xstart; x <= mesh->xend; x++) {
       for (int y = mesh->ystart; y <= mesh->yend; y++) {
 
@@ -288,14 +292,14 @@ PetscErrorCode SNESSolver::FDJinitialise() {
               continue;
             }
 
-            int ind2 = ROUND(index(xi, yi, 0));
+            const int ind2 = ROUND(index(xi, yi, 0));
             if (ind2 < 0) {
               continue; // A boundary point
             }
 
             // Depends on all variables on this cell
             for (int j = 0; j < n2d; j++) {
-              PetscInt col = ind2 + j;
+              const PetscInt col = ind2 + j;
               PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
             }
           }
@@ -312,7 +316,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
 
             // Depends on 2D fields
             for (int j = 0; j < n2d; j++) {
-              PetscInt col = ind0 + j;
+              const PetscInt col = ind0 + j;
               PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
             }
 
@@ -337,7 +341,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
 
                 // 3D fields on this cell
                 for (int j = 0; j < n3d; j++) {
-                  PetscInt col = ind2 + j;
+                  const PetscInt col = ind2 + j;
                   PetscErrorCode ierr =
                       MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
 
@@ -414,6 +418,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
 
     MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
   }
+  return PETSC_SUCCESS;
 }
 
 PetscErrorCode SNESSolver::FDJpruneJacobian() {
@@ -457,6 +462,7 @@ PetscErrorCode SNESSolver::FDJpruneJacobian() {
     jacobian_pruned = true;
   }
 #endif // PETSC_VERSION_GE(3,20,0)
+  return PETSC_SUCCESS;
 }
 
 PetscErrorCode SNESSolver::FDJrestoreFromPruning() {
@@ -465,6 +471,7 @@ PetscErrorCode SNESSolver::FDJrestoreFromPruning() {
   // The non-zero pattern has changed, so update coloring
   updateColoring();
   jacobian_pruned = false; // Reset flag. Will be set after pruning.
+  return PETSC_SUCCESS;
 }
 
 SNESSolver::SNESSolver(Options* opts)
@@ -705,7 +712,8 @@ int SNESSolver::init() {
     // because that would require updating the preconditioner.
     PetscCall(VecDuplicate(snes_x, &output_x));
 
-    FDJinitialise();
+    // Initialize the Finite Difference Jacobian
+    PetscCall(FDJinitialise());
 
     // Re-use Jacobian
     // Note: If the 'Amat' Jacobian is matrix free, SNESComputeJacobian
@@ -1286,7 +1294,7 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
         residual = sqrt(residual / count);
 
         auto i3d = mesh->ind2Dto3D(i2d, jz);
-        BoutReal new_timestep =
+        const BoutReal new_timestep =
             updatePseudoTimestep(dt_data[idx], pseudo_residual[i3d], residual);
 
         pseudo_residual[i3d] = residual;
@@ -1303,7 +1311,7 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
   // These loops don't check the boundary flags
   for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) {
     // Field2D quantities evolved together
-    if (f2d.size() > 0) {
+    if (!f2d.empty()) {
       BoutReal residual = 0.0;
       for (std::size_t i = 0; i != f2d.size(); ++i) {
         residual += SQ(current_residual[idx + i]);
@@ -1311,7 +1319,7 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
       residual = sqrt(residual / f2d.size());
 
       // Adjust timestep for these quantities
-      BoutReal new_timestep =
+      const BoutReal new_timestep =
           updatePseudoTimestep(dt_data[idx], pseudo_residual_2d[i2d], residual);
       for (std::size_t i = 0; i != f2d.size(); ++i) {
         dt_data[idx++] = new_timestep;
@@ -1320,7 +1328,7 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
     }
 
     // Field3D quantities evolved together within a cell
-    if (f3d.size() > 0) {
+    if (!f3d.empty()) {
       for (int jz = 0; jz < mesh->LocalNz; jz++) {
         auto i3d = mesh->ind2Dto3D(i2d, jz);
 
@@ -1530,7 +1538,7 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
     PetscCall(VecPointwiseMult(f, f, rhs_scaling_factors));
   }
 
-  return 0;
+  return PETSC_SUCCESS;
 }
 
 /*
@@ -1572,7 +1580,7 @@ PetscErrorCode SNESSolver::scaleJacobian(Mat Jac_new) {
   jacobian_recalculated = true;
 
   if (!scale_rhs) {
-    return 0; // Not scaling the RHS values
+    return PETSC_SUCCESS; // Not scaling the RHS values
   }
 
   // Get index of rows owned by this processor
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index c37cc0b37a..c988f2cc3f 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -101,9 +101,9 @@ public:
   void outputVars(Options& output_options, bool save_repeat = true) override;
 
 private:
-  PetscErrorCode FDJinitialise();
-  PetscErrorCode FDJpruneJacobian();
-  PetscErrorCode FDJrestoreFromPruning();
+  PetscErrorCode FDJinitialise();         ///< Finite Difference Jacobian initialise
+  PetscErrorCode FDJpruneJacobian();      ///< Remove small elements from the Jacobian
+  PetscErrorCode FDJrestoreFromPruning(); ///< Restore Jacobian to original pattern
 
   /// Call the physics model RHS function
   ///

From 9b1eb95f3d2dfb0f2a325fc938949ce33edc5362 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 15 Oct 2025 15:39:48 -0700
Subject: [PATCH 0274/1827] snes: pid_consider_failures and asinh_vars

Experimental features, off by default

1. pid_consider_failures (bool, default: false)

  If enabled, this reduces the magnitude of timestep increases
  when recent solves have frequently failed.
  Makes the solver more cautious so may reduce failures but also
  may not increase timesteps as quickly. Net effect on performance
  is likely problem dependent.

2. asinh_vars (bool, default: false)

  If enabled, evolves asinh() of all variables. This might be a
  good idea when variable magnitudes vary widely, either due to
  normalisation or strong variations across the mesh.

  - Behaves like log() for large values
  - Close to linear for small values, so the solver doesn't
    over-resolve e.g low density regions
  - Retains sign, unlike log: asinh(-x) = -asinh(x)
---
 src/solver/impls/snes/snes.cxx | 121 ++++++++++++++++++++++++---------
 src/solver/impls/snes/snes.hxx |   6 ++
 2 files changed, 96 insertions(+), 31 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index d349193ee4..4325a11250 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -540,6 +540,10 @@ SNESSolver::SNESSolver(Options* opts)
       kP((*options)["kP"].doc("Proportional PID parameter").withDefault(0.7)),
       kI((*options)["kI"].doc("Integral PID parameter").withDefault(0.3)),
       kD((*options)["kD"].doc("Derivative PID parameter").withDefault(0.2)),
+      pid_consider_failures(
+          (*options)["pid_consider_failures"]
+              .doc("Reduce timestep increases if recent solves have failed")
+              .withDefault<bool>(false)),
       diagnose(
           (*options)["diagnose"].doc("Print additional diagnostics").withDefault(false)),
       diagnose_failures((*options)["diagnose_failures"]
@@ -594,6 +598,9 @@ SNESSolver::SNESSolver(Options* opts)
                     .withDefault<bool>(false)),
       scale_vars((*options)["scale_vars"]
                      .doc("Scale variables (Jacobian column scaling)?")
+                     .withDefault<bool>(false)),
+      asinh_vars((*options)["asinh_vars"]
+                     .doc("Apply asinh() to all variables?")
                      .withDefault<bool>(false)) {}
 
 int SNESSolver::init() {
@@ -655,6 +662,8 @@ int SNESSolver::init() {
     PetscCall(VecSet(var_scaling_factors, 1.0));
     // Storage for scaled 'x' state vectors
     PetscCall(VecDuplicate(snes_x, &scaled_x));
+  } else if (asinh_vars) {
+    PetscCall(VecDuplicate(snes_x, &scaled_x));
   }
 
   if (equation_form == BoutSnesEquationForm::pseudo_transient) {
@@ -824,18 +833,17 @@ int SNESSolver::run() {
     BoutReal* xdata = nullptr;
     PetscCall(VecGetArray(snes_x, &xdata));
     save_vars(xdata);
-    PetscCall(VecRestoreArray(snes_x, &xdata));
-  }
 
-  if (equation_form == BoutSnesEquationForm::pseudo_transient) {
-    // Calculate the initial residual in snes_f
-    run_rhs(simtime);
-    {
-      BoutReal* fdata = nullptr;
-      PetscCall(VecGetArray(snes_f, &fdata));
-      save_derivs(fdata);
-      PetscCall(VecRestoreArray(snes_f, &fdata));
+    if (asinh_vars) {
+      // Evolving asinh(vars)
+      PetscInt size;
+      PetscCall(VecGetLocalSize(snes_x, &size));
+      for (PetscInt i = 0; i != size; ++i) {
+        xdata[i] = std::asinh(xdata[i] / asinh_scale);
+      }
     }
+
+    PetscCall(VecRestoreArray(snes_x, &xdata));
   }
 
   BoutReal target = simtime;
@@ -847,6 +855,7 @@ int SNESSolver::run() {
     int steps_since_snes_failure = 0;
     int saved_jacobian_lag = 0;
     int loop_count = 0;
+    recent_failure_rate = 0.0;
     do {
       if (simtime >= target)
         break; // Could happen if step over multiple outputs
@@ -973,9 +982,14 @@ int SNESSolver::run() {
       int lin_its;
       SNESGetLinearSolveIterations(snes, &lin_its);
 
+      // Rolling average of recent failures
+      recent_failure_rate *= 1. - inv_failure_window;
+
       if ((ierr != PETSC_SUCCESS) or (reason < 0)) {
         // Diverged or SNES failed
 
+        recent_failure_rate += inv_failure_window;
+
         if (diagnose_failures) {
           // Print diagnostics to help identify source of the problem
 
@@ -1200,17 +1214,29 @@ int SNESSolver::run() {
     if (scale_vars) {
       // scaled_x <- output_x * var_scaling_factors
       PetscCall(VecPointwiseMult(scaled_x, output_x, var_scaling_factors));
-
-      const BoutReal* xdata = nullptr;
-      PetscCall(VecGetArrayRead(scaled_x, &xdata));
-      load_vars(const_cast<BoutReal*>(xdata));
-      PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
+    } else if (asinh_vars) {
+      PetscCall(VecCopy(output_x, scaled_x));
     } else {
-      const BoutReal* xdata = nullptr;
-      PetscCall(VecGetArrayRead(output_x, &xdata));
-      load_vars(const_cast<BoutReal*>(xdata));
-      PetscCall(VecRestoreArrayRead(output_x, &xdata));
+      scaled_x = output_x;
+    }
+
+    if (asinh_vars) {
+      PetscInt size;
+      PetscCall(VecGetLocalSize(scaled_x, &size));
+
+      BoutReal* scaled_data = nullptr;
+      PetscCall(VecGetArray(scaled_x, &scaled_data));
+      for (PetscInt i = 0; i != size; ++i) {
+        scaled_data[i] = asinh_scale * std::sinh(scaled_data[i]);
+      }
+      PetscCall(VecRestoreArray(scaled_x, &scaled_data));
     }
+
+    const BoutReal* xdata = nullptr;
+    PetscCall(VecGetArrayRead(scaled_x, &xdata));
+    load_vars(const_cast<BoutReal*>(xdata));
+    PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
+
     run_rhs(target); // Run RHS to calculate auxilliary variables
 
     if (call_monitors(target, s, getNumberOutputSteps()) != 0) {
@@ -1456,20 +1482,30 @@ PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
   if (scale_vars) {
     // scaled_x <- x * var_scaling_factors
     PetscCall(VecPointwiseMult(scaled_x, x, var_scaling_factors));
-
-    const BoutReal* xdata = nullptr;
-    PetscCall(VecGetArrayRead(scaled_x, &xdata));
-    // const_cast needed due to load_vars API. Not writing to xdata.
-    load_vars(const_cast<BoutReal*>(xdata));
-    PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
+  } else if (asinh_vars) {
+    PetscCall(VecCopy(x, scaled_x));
   } else {
-    const BoutReal* xdata = nullptr;
-    PetscCall(VecGetArrayRead(x, &xdata));
-    // const_cast needed due to load_vars API. Not writing to xdata.
-    load_vars(const_cast<BoutReal*>(xdata));
-    PetscCall(VecRestoreArrayRead(x, &xdata));
+    scaled_x = x;
+  }
+
+  if (asinh_vars) {
+    PetscInt size;
+    PetscCall(VecGetLocalSize(scaled_x, &size));
+
+    BoutReal* scaled_data = nullptr;
+    PetscCall(VecGetArray(scaled_x, &scaled_data));
+    for (PetscInt i = 0; i != size; ++i) {
+      scaled_data[i] = asinh_scale * std::sinh(scaled_data[i]);
+    }
+    PetscCall(VecRestoreArray(scaled_x, &scaled_data));
   }
 
+  const BoutReal* xdata = nullptr;
+  PetscCall(VecGetArrayRead(scaled_x, &xdata));
+  // const_cast needed due to load_vars API. Not writing to xdata.
+  load_vars(const_cast<BoutReal*>(xdata));
+  PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
+
   try {
     // Call RHS function
     run_rhs(simtime + dt, linear);
@@ -1484,6 +1520,24 @@ PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
   BoutReal* fdata = nullptr;
   PetscCall(VecGetArray(f, &fdata));
   save_derivs(fdata);
+
+  if (asinh_vars) {
+    // Modify time-derivatives for asinh(var) using chain rule
+    // Evolving u = asinh(var / scale)
+    //
+    // du/dt = dvar/dt * du/dvar
+    //
+    // du/var = 1 / sqrt(var^2 + scale^2)
+    PetscInt size;
+    PetscCall(VecGetLocalSize(f, &size));
+    const BoutReal* scaled_data = nullptr;
+    PetscCall(VecGetArrayRead(scaled_x, &scaled_data));
+    for (PetscInt i = 0; i != size; ++i) {
+      fdata[i] /= std::sqrt(SQ(scaled_data[i]) + SQ(asinh_scale));
+    }
+    PetscCall(VecRestoreArrayRead(scaled_x, &scaled_data));
+  }
+
   PetscCall(VecRestoreArray(f, &fdata));
   return PETSC_SUCCESS;
 }
@@ -1713,7 +1767,12 @@ BoutReal SNESSolver::pid(BoutReal timestep, int nl_its, BoutReal max_dt) {
                                  kD);
 
   // clamp growth factor to avoid huge changes
-  const BoutReal fac = std::clamp(facP * facI * facD, 0.2, 5.0);
+  BoutReal fac = std::clamp(facP * facI * facD, 0.2, 5.0);
+
+  if (pid_consider_failures && (fac > 1.0)) {
+    // Reduce aggressiveness if recent steps have failed often
+    fac = pow(fac, std::max(0.3, 1.0 - 2.0 * recent_failure_rate));
+  }
 
   /* ---------- update timestep and history ---------- */
   const BoutReal dt_new = std::min(timestep * fac, max_dt);
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index c988f2cc3f..7039954418 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -165,6 +165,9 @@ private:
   BoutReal kP; ///< (0.6 - 0.8) Proportional parameter (main response to current step)
   BoutReal kI; ///< (0.2 - 0.4) Integral parameter (smooths history of changes)
   BoutReal kD; ///< (0.1 - 0.3) Derivative (dampens oscillation - optional)
+  bool pid_consider_failures; ///< Reduce timestep increases if recent solves have failed
+  BoutReal recent_failure_rate;            ///< Rolling average of recent failure rate
+  const BoutReal inv_failure_window = 0.1; ///< 1 / number of recent solves
 
   int nl_its_prev;
   int nl_its_prev2;
@@ -222,6 +225,9 @@ private:
   bool scale_vars;         ///< Scale individual variables?
   Vec var_scaling_factors; ///< Factors to multiply variables when passing to user
   Vec scaled_x;            ///< The values passed to the user RHS
+
+  bool asinh_vars; ///< Evolve asinh(vars) to compress magnitudes while preserving signs
+  const BoutReal asinh_scale = 1e-5; // Scale below which asinh response becomes ~linear
 };
 
 #else

From 8e211e2160eb0fc12232552e0e02dd7f584e7fcf Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 23 Oct 2025 17:04:28 +0100
Subject: [PATCH 0275/1827] Enable non-const iteration over `Options`

---
 include/bout/options.hxx           |  8 ++++++++
 src/sys/options/options_netcdf.cxx |  5 +----
 tests/unit/sys/test_options.cxx    | 11 +++++++++++
 3 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 9356326d0e..dbb926838a 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -205,6 +205,14 @@ public:
       bout::utils::variant<bool, int, BoutReal, std::string, Field2D, Field3D, FieldPerp,
                            Array<BoutReal>, Matrix<BoutReal>, Tensor<BoutReal>>;
 
+  /// Methods to iterate over `Options`
+  auto begin() { return std::begin(children); }
+  auto end() { return std::end(children); }
+  auto begin() const { return std::begin(children); }
+  auto end() const { return std::end(children); }
+  auto cbegin() const { return std::cbegin(children); }
+  auto cend() const { return std::cend(children); }
+
   /// A tree representation with leaves containing ValueType.
   /// Used to construct Options from initializer lists.
   ///
diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx
index 60dfba2102..94b62f0f02 100644
--- a/src/sys/options/options_netcdf.cxx
+++ b/src/sys/options/options_netcdf.cxx
@@ -448,10 +448,7 @@ void NcPutAttVisitor::operator()(const std::string& value) {
 void writeGroup(const Options& options, NcGroup group,
                 const std::string& time_dimension) {
 
-  for (const auto& childpair : options.getChildren()) {
-    const auto& name = childpair.first;
-    const auto& child = childpair.second;
-
+  for (const auto& [name, child] : options) {
     if (child.isValue()) {
       try {
         auto nctype = bout::utils::visit(NcTypeVisitor(), child.value);
diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx
index a9a3bf4af4..67e405953d 100644
--- a/tests/unit/sys/test_options.cxx
+++ b/tests/unit/sys/test_options.cxx
@@ -1439,3 +1439,14 @@ TEST_F(OptionsTest, BoolCompound) {
   ASSERT_TRUE(Options("true & !false").as<bool>());
   ASSERT_TRUE(Options("2 > 1 & 2 < 3").as<bool>());
 }
+
+TEST_F(OptionsTest, Iterate) {
+  Options option{{{"value1", 1}, {"value2", 2}}};
+
+  for (auto& [name, value] : option) {
+    value.force(value.as<int>() + 1);
+  }
+
+  ASSERT_EQ(option["value1"], 2);
+  ASSERT_EQ(option["value2"], 3);
+}

From 2792afd57d13dc1c0cddc6b2d3100373ebd08510 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 23 Oct 2025 18:15:05 +0100
Subject: [PATCH 0276/1827] Add factory for LaplaceXY, LaplaceXY2,
 LaplaceXY2Hypre

---
 CMakeLists.txt                                |   10 +-
 include/bout/invert/laplacexy.hxx             |  231 +-
 .../impls/hypre/laplacexy-hypre.cxx}          |   14 +-
 .../laplacexy/impls/hypre/laplacexy-hypre.hxx |   57 +-
 .../laplacexy/impls/petsc/laplacexy-petsc.cxx | 1891 ++++++++++++++++
 .../laplacexy/impls/petsc/laplacexy-petsc.hxx |  204 ++
 .../impls/petsc2/laplacexy-petsc2.cxx}        |   28 +-
 .../impls/petsc2/laplacexy-petsc2.hxx         |   74 +-
 src/invert/laplacexy/laplacexy.cxx            | 1893 +----------------
 .../test-laplacexy-fv/test-laplacexy.cxx      |    6 +-
 .../test-laplacexy-short/test-laplacexy.cxx   |   25 +-
 .../test-laplacexy/test-laplacexy.cxx         |    6 +-
 .../test-laplacexy2-hypre/test-laplacexy.cxx  |    8 +-
 13 files changed, 2258 insertions(+), 2189 deletions(-)
 rename src/invert/{laplacexy2/laplacexy2_hypre.cxx => laplacexy/impls/hypre/laplacexy-hypre.cxx} (97%)
 rename include/bout/invert/laplacexy2_hypre.hxx => src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx (70%)
 create mode 100644 src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
 create mode 100644 src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx
 rename src/invert/{laplacexy2/laplacexy2.cxx => laplacexy/impls/petsc2/laplacexy-petsc2.cxx} (94%)
 rename include/bout/invert/laplacexy2.hxx => src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx (64%)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5c49e434e4..cc368a3b32 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -235,11 +235,13 @@ set(BOUT_SOURCES
   ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
   ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx
   ./src/invert/laplace/invert_laplace.cxx
+  ./src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
+  ./src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
+  ./src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
+  ./src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx
+  ./src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
+  ./src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx
   ./src/invert/laplacexy/laplacexy.cxx
-  ./include/bout/invert/laplacexy2.hxx
-  ./src/invert/laplacexy2/laplacexy2.cxx
-  ./include/bout/invert/laplacexy2_hypre.hxx
-  ./src/invert/laplacexy2/laplacexy2_hypre.cxx 
   ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
   ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx
   ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
diff --git a/include/bout/invert/laplacexy.hxx b/include/bout/invert/laplacexy.hxx
index 5a4dd46512..7ec6901cee 100644
--- a/include/bout/invert/laplacexy.hxx
+++ b/include/bout/invert/laplacexy.hxx
@@ -1,18 +1,18 @@
 /**************************************************************************
- * Laplacian solver in 2D (X-Y)
+ * Perpendicular Laplacian inversion in X-Y
  *
- * Equation solved is: 
+ * Equation solved is:
  *
  * Div( A * Grad_perp(x) ) + B*x = b
  *
  * Intended for use in solving n = 0 component of potential
  * from inversion of vorticity equation
- * 
+ *
  **************************************************************************
- * Copyright 2015 B.Dudson
+ * Copyright 2015-2025 BOUT++ Team
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -30,196 +30,69 @@
  *
  **************************************************************************/
 
-#ifndef BOUT_LAPLACE_XY_H
-#define BOUT_LAPLACE_XY_H
-
-#include "bout/build_defines.hxx"
-
-#if !BOUT_HAS_PETSC
-// If no PETSc
-
-#warning LaplaceXY requires PETSc. No LaplaceXY available
+#ifndef BOUT_LAPLACEXY_H
+#define BOUT_LAPLACEXY_H
 
-#include <bout/boutexception.hxx>
+#include <bout/field2d.hxx>
+#include <bout/generic_factory.hxx>
+#include <bout/mesh.hxx>
+#include <bout/options.hxx>
 
-class Field2D;
-class Mesh;
-class Options;
+class LaplaceXY;
 class Solver;
 
-/*!
- * Create a dummy class so that code will compile
- * without PETSc, but will throw an exception if
- * LaplaceXY is used.
- */
-class LaplaceXY {
+class LaplaceXYFactory
+    : public Factory<LaplaceXY, LaplaceXYFactory, Mesh*, Options*, CELL_LOC> {
 public:
-  LaplaceXY(Mesh* UNUSED(m) = nullptr, Options* UNUSED(opt) = nullptr,
-            const CELL_LOC UNUSED(loc) = CELL_CENTRE) {
-    throw BoutException("LaplaceXY requires PETSc. No LaplaceXY available");
+  static constexpr auto type_name = "LaplaceXY";
+  static constexpr auto section_name = "laplacexy";
+  static constexpr auto option_name = "type";
+  static constexpr auto default_type = "petsc";
+
+  ReturnType create(Mesh* mesh = nullptr, Options* options = nullptr,
+                    CELL_LOC loc = CELL_CENTRE) const {
+    return Factory::create(getType(options), mesh, optionsOrDefaultSection(options), loc);
   }
-  void setCoefs(const Field2D& UNUSED(A), const Field2D& UNUSED(B)) {}
-  const Field2D solve(const Field2D& UNUSED(rhs), const Field2D& UNUSED(x0)) {
-    throw BoutException("LaplaceXY requires PETSc. No LaplaceXY available");
+  ReturnType create(const std::string& type, Options* options) const {
+    return Factory::create(type, nullptr, options, CELL_CENTRE);
   }
-  void savePerformance(Solver&, std::string) {
-    throw BoutException("LaplaceXY requires PETSc. No LaplaceXY available");
-  }
-};
 
-#else // BOUT_HAS_PETSC
+  static void ensureRegistered();
+};
 
-#include "bout/solver.hxx"
-#include "bout/utils.hxx"
-#include <bout/cyclic_reduction.hxx>
-#include <bout/mesh.hxx>
-#include <bout/petsclib.hxx>
+template <class DerivedType>
+using RegisterLaplaceXY = LaplaceXYFactory::RegisterInFactory<DerivedType>;
 
-class Options;
-class Solver;
+using RegisterUnavailableLaplaceXY = LaplaceXYFactory::RegisterUnavailableInFactory;
 
 class LaplaceXY {
 public:
-  /*! 
-   * Constructor
-   */
-  LaplaceXY(Mesh* m = nullptr, Options* opt = nullptr, const CELL_LOC loc = CELL_CENTRE);
-  /*!
-   * Destructor
-   */
-  ~LaplaceXY();
-
-  /*!
-   * Set coefficients (A, B) in equation:
-   * Div( A * Grad_perp(x) ) + B*x = b
-   */
-  void setCoefs(const Field2D& A, const Field2D& B);
-
-  /*!
-   * Solve Laplacian in X-Y
-   * 
-   * Inputs
-   * ======
-   *
-   * rhs  - The field to be inverted. This must be allocated
-   *        and contain valid data.
-   * x0   - Initial guess at the solution. If this is unallocated
-   *        then an initial guess of zero will be used.
-   * 
-   * Returns
-   * =======
-   * 
-   * The solution as a Field2D. On failure an exception will be raised
-   * 
-   */
-  const Field2D solve(const Field2D& rhs, const Field2D& x0);
-
-  /*!
-   * Preconditioner function
-   * This is called by PETSc via a static function.
-   * and should not be called by external users
-   */
-  int precon(Vec x, Vec y);
-
-  /*!
-   * If this method is called, save some performance monitoring information
-   */
-  void savePerformance(Solver& solver, const std::string& name = "");
+  LaplaceXY(Mesh* m = nullptr, [[maybe_unused]] Options* options = nullptr,
+            const CELL_LOC loc = CELL_CENTRE)
+      : localmesh(m == nullptr ? bout::globals::mesh : m), location(loc) {}
+  LaplaceXY(const LaplaceXY&) = default;
+  LaplaceXY(LaplaceXY&&) = delete;
+  LaplaceXY& operator=(const LaplaceXY&) = default;
+  LaplaceXY& operator=(LaplaceXY&&) = delete;
+  virtual ~LaplaceXY() = default;
+
+  virtual void setCoefs(const Field2D& A, const Field2D& B) = 0;
+
+  virtual Field2D solve(const Field2D& b, const Field2D& x0) = 0;
+
+  static std::unique_ptr<LaplaceXY> create(Mesh* m = nullptr, Options* opt = nullptr,
+                                           CELL_LOC loc = CELL_CENTRE) {
+    return LaplaceXYFactory::getInstance().create(m, opt, loc);
+  }
 
+protected:
+  static const int INVERT_DC_GRAD = 1;
+  static const int INVERT_AC_GRAD = 2; // Use zero neumann (NOTE: AC is a misnomer)
+  static const int INVERT_SET = 16;    // Set boundary to x0 value
+  static const int INVERT_RHS = 32;    // Set boundary to b value
 private:
-  PetscLib lib; ///< Requires PETSc library
-  Mat MatA;     ///< Matrix to be inverted
-  Vec xs, bs;   ///< Solution and RHS vectors
-  KSP ksp;      ///< Krylov Subspace solver
-  PC pc;        ///< Preconditioner
-
   Mesh* localmesh; ///< The mesh this operates on, provides metrics and communication
-
-  /// default prefix for writing performance logging variables
-  std::string default_prefix;
-
-  // Preconditioner
-  int xstart, xend;
-  int nloc, nsys;
-  Matrix<BoutReal> acoef, bcoef, ccoef, xvals, bvals;
-  std::unique_ptr<CyclicReduce<BoutReal>> cr; ///< Tridiagonal solver
-
-  // Use finite volume or finite difference discretization
-  bool finite_volume{true};
-
-  // Y derivatives
-  bool include_y_derivs; // Include Y derivative terms?
-
-  // Boundary conditions
-  bool x_inner_dirichlet;         // Dirichlet on inner X boundary?
-  bool x_outer_dirichlet;         // Dirichlet on outer X boundary?
-  std::string y_bndry{"neumann"}; // Boundary condition for y-boundary
-
-  // Location of the rhs and solution
   CELL_LOC location;
-
-  /*!
-   * Number of grid points on this processor
-   */
-  int localSize();
-
-  /*!
-   * Return the communicator for XY
-   */
-  MPI_Comm communicator();
-
-  /*!
-   * Return the global index of a local (x,y) coordinate
-   * including guard cells.
-   * Boundary cells have a global index of -1
-   *
-   * To do this, a Field2D (indexXY) is used to store
-   * the index as a floating point number which is then rounded
-   * to an integer. Guard cells are filled by communication
-   * so no additional logic is needed in Mesh.
-   */
-  int globalIndex(int x, int y);
-  Field2D indexXY; ///< Global index (integer stored as BoutReal)
-
-  // Save performance information?
-  bool save_performance = false;
-
-  // Running average of number of iterations taken for solve in each output timestep
-  BoutReal average_iterations = 0.;
-
-  // Variable to store the final result of average_iterations, since output is
-  // written after all other monitors have been called, and average_iterations
-  // must be reset in the monitor
-  BoutReal output_average_iterations = 0.;
-
-  // Running total of number of calls to the solver in each output timestep
-  int n_calls = 0;
-
-  // Utility methods
-  void setPreallocationFiniteVolume(PetscInt* d_nnz, PetscInt* o_nnz);
-  void setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nnz);
-  void setMatrixElementsFiniteVolume(const Field2D& A, const Field2D& B);
-  void setMatrixElementsFiniteDifference(const Field2D& A, const Field2D& B);
-  void solveFiniteVolume(const Field2D& x0);
-  void solveFiniteDifference(const Field2D& x0);
-
-  // Monitor class used to reset performance-monitoring variables for a new
-  // output timestep
-  friend class LaplaceXYMonitor;
-  class LaplaceXYMonitor : public Monitor {
-  public:
-    LaplaceXYMonitor(LaplaceXY& owner) : laplacexy(owner) {}
-
-    int call(Solver* /*solver*/, BoutReal /*time*/, int /*iter*/, int /*nout*/) override;
-    void outputVars(Options& output_options, const std::string& time_dimension) override;
-
-  private:
-    // LaplaceXY object that this monitor belongs to
-    LaplaceXY& laplacexy;
-  };
-
-  LaplaceXYMonitor monitor;
 };
 
-#endif // BOUT_HAS_PETSC
-#endif // BOUT_LAPLACE_XY_H
+#endif // BOUT_LAPLACEXY_H
diff --git a/src/invert/laplacexy2/laplacexy2_hypre.cxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
similarity index 97%
rename from src/invert/laplacexy2/laplacexy2_hypre.cxx
rename to src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
index a5028169f8..950fcc4f8e 100644
--- a/src/invert/laplacexy2/laplacexy2_hypre.cxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
@@ -1,7 +1,9 @@
-#include <bout/invert/laplacexy2_hypre.hxx>
+#include "bout/build_defines.hxx"
 
 #if BOUT_HAS_HYPRE
 
+#include "laplacexy-hypre.hxx"
+
 #include "bout/assert.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/globals.hxx"
@@ -9,11 +11,11 @@
 #include "bout/output.hxx"
 #include "bout/sys/timer.hxx"
 
-#include <cmath>
-
 #if BOUT_HAS_CUDA && defined(__CUDACC__)
-#define gpuErrchk(ans) \
-  { gpuAssert((ans), __FILE__, __LINE__); }
+#define gpuErrchk(ans)                    \
+  {                                       \
+    gpuAssert((ans), __FILE__, __LINE__); \
+  }
 inline void gpuAssert(cudaError_t code, const char* file, int line, bool abort = true) {
   if (code != cudaSuccess) {
     fprintf(stderr, "GPUassert: %s %s %d\n", cudaGetErrorString(code), file, line);
@@ -226,7 +228,7 @@ void LaplaceXY2Hypre::setCoefs(const Field2D& A, const Field2D& B) {
   }
 }
 
-Field2D LaplaceXY2Hypre::solve(Field2D& rhs, Field2D& x0) {
+Field2D LaplaceXY2Hypre::solve(const Field2D& rhs, const Field2D& x0) {
   Timer timer("invert");
 
   ASSERT1(rhs.getMesh() == localmesh);
diff --git a/include/bout/invert/laplacexy2_hypre.hxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
similarity index 70%
rename from include/bout/invert/laplacexy2_hypre.hxx
rename to src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
index 1df0988d06..3950725a89 100644
--- a/include/bout/invert/laplacexy2_hypre.hxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
@@ -33,51 +33,36 @@
 #ifndef LAPLACE_XY2_HYPRE_H
 #define LAPLACE_XY2_HYPRE_H
 
-#include <bout/build_defines.hxx>
-
-#if not BOUT_HAS_HYPRE
-// If no Hypre
-
-#include "bout/globalindexer.hxx"
-#include <bout/boutexception.hxx>
-#include <bout/mesh.hxx>
-#include <bout/options.hxx>
-
-/*!
- * Create a dummy class so that code will compile
- * without Hypre, but will throw an exception if
- * LaplaceXY is used.
- */
-class LaplaceXY2Hypre {
-public:
-  LaplaceXY2Hypre(Mesh* UNUSED(m) = nullptr, Options* UNUSED(opt) = nullptr,
-                  const CELL_LOC UNUSED(loc) = CELL_CENTRE) {
-    throw BoutException("LaplaceXY requires Hypre. No LaplaceXY available");
-  }
-  void setCoefs(const Field2D& UNUSED(A), const Field2D& UNUSED(B)) {}
-  Field2D solve(const Field2D& UNUSED(rhs), const Field2D& UNUSED(x0)) {
-    throw BoutException("LaplaceXY requires Hypre. No LaplaceXY available");
-  }
-};
+#include "bout/build_defines.hxx"
+#include "bout/invert/laplacexy.hxx"
+
+#if !BOUT_HAS_PETSC
 
-#else // BOUT_HAS_HYPRE
+namespace {
+RegisterUnavailableLaplaceXY
+    registerlaplacexyhypre("hypre", "BOUT++ was not configured with HYPRE");
+}
+
+#else // BOUT_HAS_PETSC
 
 class Mesh;
 
-#include "bout/utils.hxx"
 #include <bout/hypre_interface.hxx>
 
-class LaplaceXY2Hypre {
+class LaplaceXY2Hypre : public LaplaceXY {
 public:
-  LaplaceXY2Hypre(Mesh* m = nullptr, Options* opt = nullptr,
-                  const CELL_LOC loc = CELL_CENTRE);
-  ~LaplaceXY2Hypre() = default;
+  LaplaceXY2Hypre(Mesh* m = nullptr, Options* opt = nullptr, CELL_LOC loc = CELL_CENTRE);
+  LaplaceXY2Hypre(const LaplaceXY2Hypre&) = delete;
+  LaplaceXY2Hypre(LaplaceXY2Hypre&&) = delete;
+  LaplaceXY2Hypre& operator=(const LaplaceXY2Hypre&) = delete;
+  LaplaceXY2Hypre& operator=(LaplaceXY2Hypre&&) = delete;
+  ~LaplaceXY2Hypre() override = default;
 
   /*!
    * Set coefficients (A, B) in equation:
    * Div( A * Grad_perp(x) ) + B*x = b
    */
-  void setCoefs(const Field2D& A, const Field2D& B);
+  void setCoefs(const Field2D& A, const Field2D& B) override;
 
   /*!
    * Solve Laplacian in X-Y
@@ -96,7 +81,7 @@ public:
    * The solution as a Field2D. On failure an exception will be raised
    *
    */
-  Field2D solve(Field2D& rhs, Field2D& x0);
+  Field2D solve(const Field2D& rhs, const Field2D& x0) override;
 
   /*!
    * Preconditioner function
@@ -131,5 +116,9 @@ private:
   MPI_Comm communicator();
 };
 
+namespace {
+const inline RegisterLaplaceXY<LaplaceXY2Hypre> registerlaplacexyhypre{"hypre"};
+}
+
 #endif // BOUT_HAS_HYPRE
 #endif // LAPLACE_XY_HYPRE_H
diff --git a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
new file mode 100644
index 0000000000..e80a2ca640
--- /dev/null
+++ b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
@@ -0,0 +1,1891 @@
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_PETSC
+
+#include "laplacexy-petsc.hxx"
+
+#include <bout/assert.hxx>
+#include <bout/boutcomm.hxx>
+#include <bout/derivs.hxx>
+#include <bout/globals.hxx>
+#include <bout/output.hxx>
+#include <bout/sys/timer.hxx>
+#include <bout/utils.hxx>
+
+#include <petscksp.h>
+
+#include <cmath>
+
+namespace {
+PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) {
+  // Get the context
+  LaplaceXYpetsc* s = nullptr;
+  const auto ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&s));
+  CHKERRQ(ierr);
+
+  PetscFunctionReturn(s->precon(x, y));
+}
+} // namespace
+
+LaplaceXYpetsc::LaplaceXYpetsc(Mesh* m, Options* opt, const CELL_LOC loc)
+    : lib(opt == nullptr ? &(Options::root()["laplacexy"]) : opt),
+      localmesh(m == nullptr ? bout::globals::mesh : m), location(loc), monitor(*this) {
+  Timer timer("invert");
+
+  if (opt == nullptr) {
+    // If no options supplied, use default
+    opt = &(Options::root()["laplacexy"]);
+  }
+
+  finite_volume =
+      (*opt)["finite_volume"]
+          .doc("Use finite volume rather than finite difference discretisation.")
+          .withDefault(true);
+
+  ///////////////////////////////////////////////////
+  // Boundary condititions options
+  if (localmesh->periodicY(localmesh->xstart)) {
+    // Periodic in Y, so in the core
+    x_inner_dirichlet = (*opt)["core_bndry_dirichlet"].withDefault(false);
+  } else {
+    // Non-periodic, so in the PF region
+    x_inner_dirichlet = (*opt)["pf_bndry_dirichlet"].withDefault(true);
+  }
+  if ((*opt)["y_bndry_dirichlet"].isSet()) {
+    throw BoutException("y_bndry_dirichlet has been deprecated. Use y_bndry=dirichlet "
+                        "instead.");
+  }
+  y_bndry = (*opt)["y_bndry"].withDefault("neumann");
+
+  // Check value of y_bndry is a supported option
+  if (not(y_bndry == "dirichlet" or y_bndry == "neumann" or y_bndry == "free_o3")) {
+
+    throw BoutException("Unrecognized option '{}' for laplacexy:ybndry", y_bndry);
+  }
+
+  if (not finite_volume) {
+    // Check we can use corner cells
+    if (not localmesh->include_corner_cells) {
+      throw BoutException(
+          "Finite difference form of LaplaceXYpetsc allows non-orthogonal x- and "
+          "y-directions, so requires mesh:include_corner_cells=true.");
+    }
+  }
+
+  // Use name of options section as the default prefix for performance logging variables
+  default_prefix = opt->name();
+
+  // Get MPI communicator
+  auto* comm = BoutComm::get();
+
+  // Local size
+  const int localN = localSize();
+
+  // Create Vectors
+  VecCreate(comm, &xs);
+  VecSetSizes(xs, localN, PETSC_DETERMINE);
+  VecSetFromOptions(xs);
+  VecDuplicate(xs, &bs);
+
+  // Set size of Matrix on each processor to localN x localN
+  MatCreate(comm, &MatA);
+  MatSetSizes(MatA, localN, localN, PETSC_DETERMINE, PETSC_DETERMINE);
+  MatSetFromOptions(MatA);
+
+  //////////////////////////////////////////////////
+  // Specify local indices. This creates a mapping
+  // from local indices to index, using a Field2D object
+
+  indexXY = -1; // Set all points to -1, indicating out of domain
+
+  int ind = 0;
+
+  // Y boundaries
+  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+    // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+      continue;
+    }
+    indexXY(it.ind, localmesh->ystart - 1) = ind++;
+  }
+  if ((not finite_volume) and localmesh->hasBndryLowerY()) {
+    // Corner boundary cells
+    if (localmesh->firstX()) {
+      indexXY(localmesh->xstart - 1, localmesh->ystart - 1) = ind++;
+    }
+    if (localmesh->lastX()) {
+      indexXY(localmesh->xend + 1, localmesh->ystart - 1) = ind++;
+    }
+  }
+  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+    // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+      continue;
+    }
+    indexXY(it.ind, localmesh->yend + 1) = ind++;
+  }
+  if ((not finite_volume) and localmesh->hasBndryUpperY()) {
+    // Corner boundary cells
+    if (localmesh->firstX()) {
+      indexXY(localmesh->xstart - 1, localmesh->yend + 1) = ind++;
+    }
+    if (localmesh->lastX()) {
+      indexXY(localmesh->xend + 1, localmesh->yend + 1) = ind++;
+    }
+  }
+
+  xstart = localmesh->xstart;
+  if (localmesh->firstX()) {
+    xstart -= 1; // Include X guard cells
+  }
+  xend = localmesh->xend;
+  if (localmesh->lastX()) {
+    xend += 1;
+  }
+  for (int x = xstart; x <= xend; x++) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      indexXY(x, y) = ind++;
+    }
+  }
+
+  ASSERT1(ind == localN); // Reached end of range
+
+  //////////////////////////////////////////////////
+  // Allocate storage for preconditioner
+
+  nloc = xend - xstart + 1;                       // Number of X points on this processor
+  nsys = localmesh->yend - localmesh->ystart + 1; // Number of separate Y slices
+
+  acoef.reallocate(nsys, nloc);
+  bcoef.reallocate(nsys, nloc);
+  ccoef.reallocate(nsys, nloc);
+  xvals.reallocate(nsys, nloc);
+  bvals.reallocate(nsys, nloc);
+
+  // Create a cyclic reduction object
+  cr = bout::utils::make_unique<CyclicReduce<BoutReal>>(localmesh->getXcomm(), nloc);
+
+  //////////////////////////////////////////////////
+  // Pre-allocate PETSc storage
+
+  PetscInt* d_nnz = nullptr;
+  PetscInt* o_nnz = nullptr;
+  PetscMalloc((localN) * sizeof(PetscInt), &d_nnz);
+  PetscMalloc((localN) * sizeof(PetscInt), &o_nnz);
+
+  if (finite_volume) {
+    setPreallocationFiniteVolume(d_nnz, o_nnz);
+  } else {
+    setPreallocationFiniteDifference(d_nnz, o_nnz);
+  }
+  // Pre-allocate
+  MatMPIAIJSetPreallocation(MatA, 0, d_nnz, 0, o_nnz);
+  MatSetUp(MatA);
+
+  PetscFree(d_nnz);
+  PetscFree(o_nnz);
+
+  // Determine which row/columns of the matrix are locally owned
+  int Istart = 0;
+  int Iend = 0;
+  MatGetOwnershipRange(MatA, &Istart, &Iend);
+
+  // Convert indexXY from local index to global index
+  indexXY += Istart;
+
+  // Now communicate to fill guard cells
+  // Note, this includes corner cells if necessary
+  localmesh->communicate(indexXY);
+
+  //////////////////////////////////////////////////
+  // Set up KSP
+
+  // Declare KSP Context
+  KSPCreate(comm, &ksp);
+
+  // Configure Linear Solver
+
+  const bool direct = (*opt)["direct"].doc("Use a direct LU solver").withDefault(false);
+
+  if (direct) {
+    KSPGetPC(ksp, &pc);
+    PCSetType(pc, PCLU);
+#if PETSC_VERSION_GE(3, 9, 0)
+    PCFactorSetMatSolverType(pc, "mumps");
+#else
+    PCFactorSetMatSolverPackage(pc, "mumps");
+#endif
+  } else {
+
+    // Convergence Parameters. Solution is considered converged if |r_k| < max( rtol * |b| , atol )
+    // where r_k = b - Ax_k. The solution is considered diverged if |r_k| > dtol * |b|.
+
+    const BoutReal rtol = (*opt)["rtol"].doc("Relative tolerance").withDefault(1e-5);
+    const BoutReal atol =
+        (*opt)["atol"]
+            .doc("Absolute tolerance. The solution is considered converged if |Ax-b| "
+                 "< max( rtol * |b| , atol )")
+            .withDefault(1e-10);
+    const BoutReal dtol =
+        (*opt)["dtol"]
+            .doc("The solution is considered diverged if |Ax-b| > dtol * |b|")
+            .withDefault(1e3);
+    const int maxits = (*opt)["maxits"].doc("Maximum iterations").withDefault(100000);
+
+    // Get KSP Solver Type
+    const std::string ksptype =
+        (*opt)["ksptype"].doc("KSP solver type").withDefault("gmres");
+
+    // Get PC type
+    const std::string pctype =
+        (*opt)["pctype"].doc("Preconditioner type").withDefault("none");
+
+    KSPSetType(ksp, ksptype.c_str());
+    KSPSetTolerances(ksp, rtol, atol, dtol, maxits);
+
+    KSPSetInitialGuessNonzero(ksp, static_cast<PetscBool>(true));
+
+    KSPGetPC(ksp, &pc);
+    PCSetType(pc, pctype.c_str());
+
+    if (pctype == "shell") {
+      // Using tridiagonal solver as preconditioner
+      PCShellSetApply(pc, laplacePCapply);
+      PCShellSetContext(pc, this);
+
+      const bool rightprec =
+          (*opt)["rightprec"].doc("Use right preconditioning?").withDefault(true);
+      if (rightprec) {
+        KSPSetPCSide(ksp, PC_RIGHT); // Right preconditioning
+      } else {
+        KSPSetPCSide(ksp, PC_LEFT); // Left preconditioning
+      }
+    }
+  }
+
+  lib.setOptionsFromInputFile(ksp);
+
+  ///////////////////////////////////////////////////
+  // Including Y derivatives?
+
+  include_y_derivs = (*opt)["include_y_derivs"]
+                         .doc("Include Y derivatives in operator to invert?")
+                         .withDefault(true);
+
+  ///////////////////////////////////////////////////
+  // Set the default coefficients
+  Field2D one(1., localmesh);
+  Field2D zero(0., localmesh);
+  one.setLocation(location);
+  zero.setLocation(location);
+  setCoefs(one, zero);
+}
+
+void LaplaceXYpetsc::setPreallocationFiniteVolume(PetscInt* d_nnz, PetscInt* o_nnz) {
+  const int localN = localSize();
+
+  // This discretisation uses a 5-point stencil
+  for (int i = 0; i < localN; i++) {
+    // Non-zero elements on this processor
+    d_nnz[i] = 5; // Star pattern in 2D
+    // Non-zero elements on neighboring processor
+    o_nnz[i] = 0;
+  }
+
+  // X boundaries
+  if (localmesh->firstX()) {
+    // Lower X boundary
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int localIndex = globalIndex(localmesh->xstart - 1, y);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+
+      d_nnz[localIndex] = 2; // Diagonal sub-matrix
+      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
+    }
+  } else {
+    // On another processor
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int localIndex = globalIndex(localmesh->xstart, y);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] -= 1;
+      o_nnz[localIndex] += 1;
+    }
+  }
+  if (localmesh->lastX()) {
+    // Upper X boundary
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int localIndex = globalIndex(localmesh->xend + 1, y);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] = 2; // Diagonal sub-matrix
+      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
+    }
+  } else {
+    // On another processor
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int localIndex = globalIndex(localmesh->xend, y);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] -= 1;
+      o_nnz[localIndex] += 1;
+    }
+  }
+  // Y boundaries
+
+  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
+    // Default to no boundary
+    // NOTE: This assumes that communications in Y are to other
+    //   processors. If Y is communicated with this processor (e.g. NYPE=1)
+    //   then this will result in PETSc warnings about out of range allocations
+    {
+      const int localIndex = globalIndex(x, localmesh->ystart);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      // d_nnz[localIndex] -= 1;  // Note: Slightly inefficient
+      o_nnz[localIndex] += 1;
+    }
+    {
+      const int localIndex = globalIndex(x, localmesh->yend);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      // d_nnz[localIndex] -= 1; // Note: Slightly inefficient
+      o_nnz[localIndex] += 1;
+    }
+  }
+
+  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+    // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+      continue;
+    }
+    {
+      const int localIndex = globalIndex(it.ind, localmesh->ystart - 1);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] = 2; // Diagonal sub-matrix
+      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
+    }
+    {
+      const int localIndex = globalIndex(it.ind, localmesh->ystart);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] += 1;
+      o_nnz[localIndex] -= 1;
+    }
+  }
+  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+    // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+      continue;
+    }
+    {
+      const int localIndex = globalIndex(it.ind, localmesh->yend + 1);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] = 2; // Diagonal sub-matrix
+      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
+    }
+    {
+      const int localIndex = globalIndex(it.ind, localmesh->yend);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] += 1;
+      o_nnz[localIndex] -= 1;
+    }
+  }
+}
+
+void LaplaceXYpetsc::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nnz) {
+  const int localN = localSize();
+
+  // This discretisation uses a 9-point stencil
+  for (int i = 0; i < localN; i++) {
+    // Non-zero elements on this processor
+    d_nnz[i] = 9; // Square pattern in 2D
+    // Non-zero elements on neighboring processor
+    o_nnz[i] = 0;
+  }
+
+  // X boundaries
+  if (localmesh->firstX()) {
+    // Lower X boundary
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int localIndex = globalIndex(localmesh->xstart - 1, y);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+
+      d_nnz[localIndex] = 2; // Diagonal sub-matrix
+      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
+    }
+  } else {
+    // On another processor
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int localIndex = globalIndex(localmesh->xstart, y);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] -= 3;
+      o_nnz[localIndex] += 3;
+    }
+  }
+  if (localmesh->lastX()) {
+    // Upper X boundary
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int localIndex = globalIndex(localmesh->xend + 1, y);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] = 2; // Diagonal sub-matrix
+      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
+    }
+  } else {
+    // On another processor
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int localIndex = globalIndex(localmesh->xend, y);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] -= 3;
+      o_nnz[localIndex] += 3;
+    }
+  }
+  // Y boundaries
+  const int y_bndry_stencil_size = (y_bndry == "free_o3") ? 4 : 2;
+
+  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
+    // Default to no boundary
+    // NOTE: This assumes that communications in Y are to other
+    //   processors. If Y is communicated with this processor (e.g. NYPE=1)
+    //   then this will result in PETSc warnings about out of range allocations
+    {
+      const int localIndex = globalIndex(x, localmesh->ystart);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      // d_nnz[localIndex] -= 3;  // Note: Slightly inefficient
+      o_nnz[localIndex] += 3;
+    }
+    {
+      const int localIndex = globalIndex(x, localmesh->yend);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      // d_nnz[localIndex] -= 3; // Note: Slightly inefficient
+      o_nnz[localIndex] += 3;
+    }
+  }
+
+  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+    // Should not go into corner cells, they are handled specially below
+    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+      continue;
+    }
+    {
+      const int localIndex = globalIndex(it.ind, localmesh->ystart - 1);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] = y_bndry_stencil_size; // Diagonal sub-matrix
+      o_nnz[localIndex] = 0;                    // Off-diagonal sub-matrix
+    }
+    {
+      const int localIndex = globalIndex(it.ind, localmesh->ystart);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      //d_nnz[localIndex] += 3;
+      o_nnz[localIndex] -= 3;
+    }
+  }
+  if (localmesh->hasBndryLowerY()) {
+    if (y_bndry == "dirichlet") {
+      // special handling for the corners, since we use a free_o3 y-boundary
+      // condition just in the corners when y_bndry=="dirichlet"
+      if (localmesh->firstX()) {
+        const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
+        ASSERT1((localIndex >= 0) && (localIndex < localN));
+        d_nnz[localIndex] = 4;
+      }
+      if (localmesh->lastX()) {
+        const int localIndex = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
+        ASSERT1((localIndex >= 0) && (localIndex < localN));
+        d_nnz[localIndex] = 4;
+      }
+    } else {
+      if (localmesh->firstX()) {
+        const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
+        ASSERT1((localIndex >= 0) && (localIndex < localN));
+        d_nnz[localIndex] = y_bndry_stencil_size;
+      }
+      if (localmesh->lastX()) {
+        const int localIndex = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
+        ASSERT1((localIndex >= 0) && (localIndex < localN));
+        d_nnz[localIndex] = y_bndry_stencil_size;
+      }
+    }
+  }
+  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+    // Should not go into corner cells, they are handled specially below
+    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+      continue;
+    }
+    {
+      const int localIndex = globalIndex(it.ind, localmesh->yend + 1);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      d_nnz[localIndex] = y_bndry_stencil_size; // Diagonal sub-matrix
+      o_nnz[localIndex] = 0;                    // Off-diagonal sub-matrix
+    }
+    {
+      const int localIndex = globalIndex(it.ind, localmesh->yend);
+      ASSERT1((localIndex >= 0) && (localIndex < localN));
+      //d_nnz[localIndex] += 3;
+      o_nnz[localIndex] -= 3;
+    }
+  }
+  if (localmesh->hasBndryUpperY()) {
+    if (y_bndry == "dirichlet") {
+      // special handling for the corners, since we use a free_o3 y-boundary
+      // condition just in the corners when y_bndry=="dirichlet"
+      if (localmesh->firstX()) {
+        const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
+        ASSERT1((localIndex >= 0) && (localIndex < localN));
+        d_nnz[localIndex] = 4;
+      }
+      if (localmesh->lastX()) {
+        const int localIndex = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
+        ASSERT1((localIndex >= 0) && (localIndex < localN));
+        d_nnz[localIndex] = 4;
+      }
+    } else {
+      if (localmesh->firstX()) {
+        const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
+        ASSERT1((localIndex >= 0) && (localIndex < localN));
+        d_nnz[localIndex] = y_bndry_stencil_size;
+      }
+      if (localmesh->lastX()) {
+        const int localIndex = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
+        ASSERT1((localIndex >= 0) && (localIndex < localN));
+        d_nnz[localIndex] = y_bndry_stencil_size;
+      }
+    }
+  }
+}
+
+void LaplaceXYpetsc::setCoefs(const Field2D& A, const Field2D& B) {
+  Timer timer("invert");
+
+  ASSERT1(A.getMesh() == localmesh);
+  ASSERT1(B.getMesh() == localmesh);
+  ASSERT1(A.getLocation() == location);
+  ASSERT1(B.getLocation() == location);
+
+  if (finite_volume) {
+    setMatrixElementsFiniteVolume(A, B);
+  } else {
+    setMatrixElementsFiniteDifference(A, B);
+  }
+
+  // X boundaries
+  if (localmesh->firstX()) {
+    if (x_inner_dirichlet) {
+
+      // Dirichlet on inner X boundary
+      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+        int row = globalIndex(localmesh->xstart - 1, y);
+        PetscScalar val = 0.5;
+        MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+        int col = globalIndex(localmesh->xstart, y);
+        MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+        // Preconditioner
+        bcoef(y - localmesh->ystart, 0) = 0.5;
+        ccoef(y - localmesh->ystart, 0) = 0.5;
+      }
+
+    } else {
+
+      // Neumann on inner X boundary
+      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+        int row = globalIndex(localmesh->xstart - 1, y);
+        PetscScalar val = 1.0;
+        MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+        int col = globalIndex(localmesh->xstart, y);
+        val = -1.0;
+        MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+        // Preconditioner
+        bcoef(y - localmesh->ystart, 0) = 1.0;
+        ccoef(y - localmesh->ystart, 0) = -1.0;
+      }
+    }
+  }
+  if (localmesh->lastX()) {
+    // Dirichlet on outer X boundary
+
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      int row = globalIndex(localmesh->xend + 1, y);
+      PetscScalar val = 0.5;
+      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+      int col = globalIndex(localmesh->xend, y);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+      // Preconditioner
+      acoef(y - localmesh->ystart, localmesh->xend + 1 - xstart) = 0.5;
+      bcoef(y - localmesh->ystart, localmesh->xend + 1 - xstart) = 0.5;
+    }
+  }
+
+  if (y_bndry == "dirichlet") {
+    // Dirichlet on Y boundaries
+    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int row = globalIndex(it.ind, localmesh->ystart - 1);
+      PetscScalar val = 0.5;
+      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+      int col = globalIndex(it.ind, localmesh->ystart);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+    }
+
+    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int row = globalIndex(it.ind, localmesh->yend + 1);
+      PetscScalar val = 0.5;
+      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+      int col = globalIndex(it.ind, localmesh->yend);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+    }
+  } else if (y_bndry == "neumann") {
+    // Neumann on Y boundaries
+    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int row = globalIndex(it.ind, localmesh->ystart - 1);
+      PetscScalar val = 1.0;
+      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+      val = -1.0;
+      int col = globalIndex(it.ind, localmesh->ystart);
+
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+    }
+
+    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int row = globalIndex(it.ind, localmesh->yend + 1);
+      PetscScalar val = 1.0;
+      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+      val = -1.0;
+      int col = globalIndex(it.ind, localmesh->yend);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+    }
+  } else if (y_bndry == "free_o3") {
+    // 'free_o3' extrapolating boundary condition on Y boundaries
+    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int row = globalIndex(it.ind, localmesh->ystart - 1);
+      PetscScalar val = 1.0;
+      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+      val = -3.0;
+      int col = globalIndex(it.ind, localmesh->ystart);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+      val = 3.0;
+      col = globalIndex(it.ind, localmesh->ystart + 1);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+      val = -1.0;
+      col = globalIndex(it.ind, localmesh->ystart + 2);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+    }
+
+    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int row = globalIndex(it.ind, localmesh->yend + 1);
+      PetscScalar val = 1.0;
+      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+      val = -3.0;
+      int col = globalIndex(it.ind, localmesh->yend);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+      val = 3.0;
+      col = globalIndex(it.ind, localmesh->yend - 1);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+      val = -1.0;
+      col = globalIndex(it.ind, localmesh->yend - 2);
+      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+    }
+  } else {
+    throw BoutException("Unsupported option for y_bndry");
+  }
+
+  if (not finite_volume) {
+    // Handle corner boundary cells in case we need to include D2DXDY
+    // Apply the y-boundary-condition to the cells in the x-boundary - this is an
+    // arbitrary choice, cf. connections around the X-point
+
+    if (localmesh->hasBndryLowerY()) {
+      if (localmesh->firstX()) {
+        if (y_bndry == "neumann") {
+          // Neumann y-bc
+          // f(xs-1,ys-1) = f(xs-1,ys)
+          PetscScalar val = 1.0;
+          int row = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
+          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+          val = -1.0;
+          int col = globalIndex(localmesh->xstart - 1, localmesh->ystart);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+        } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") {
+          // 'free_o3' extrapolating boundary condition on Y boundaries
+          // f(xs-1,ys-1) = 3*f(xs-1,ys) - 3*f(xs-1,ys+1) + f(xs-1,ys+2)
+          //
+          // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know
+          // what value to pass for the corner
+          PetscScalar val = 1.0;
+          int row = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
+          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+          val = -3.0;
+          int col = globalIndex(localmesh->xstart - 1, localmesh->ystart);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+          val = 3.0;
+          col = globalIndex(localmesh->xstart - 1, localmesh->ystart + 1);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+          val = -1.0;
+          col = globalIndex(localmesh->xstart - 1, localmesh->ystart + 2);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+        } else {
+          throw BoutException("Unsupported option for y_bndry");
+        }
+      }
+      if (localmesh->lastX()) {
+        if (y_bndry == "neumann") {
+          // Neumann y-bc
+          // f(xe+1,ys-1) = f(xe+1,ys)
+          PetscScalar val = 1.0;
+          int row = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
+          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+          val = -1.0;
+          int col = globalIndex(localmesh->xend + 1, localmesh->ystart);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+        } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") {
+          // 'free_o3' extrapolating boundary condition on Y boundaries
+          // f(xe+1,ys-1) = 3*f(xe+1,ys) - 3*f(xe+1,ys+1) + f(xe+1,ys+2)
+          //
+          // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know
+          // what value to pass for the corner
+          PetscScalar val = 1.0;
+          int row = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
+          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+          val = -3.0;
+          int col = globalIndex(localmesh->xend + 1, localmesh->ystart);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+          val = 3.0;
+          col = globalIndex(localmesh->xend + 1, localmesh->ystart + 1);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+          val = -1.0;
+          col = globalIndex(localmesh->xend + 1, localmesh->ystart + 2);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+        } else {
+          throw BoutException("Unsupported option for y_bndry");
+        }
+      }
+    }
+    if (localmesh->hasBndryUpperY()) {
+      if (localmesh->firstX()) {
+        if (y_bndry == "neumann") {
+          // Neumann y-bc
+          // f(xs-1,ys-1) = f(xs-1,ys)
+          PetscScalar val = 1.0;
+          int row = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
+          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+          val = -1.0;
+          int col = globalIndex(localmesh->xstart - 1, localmesh->yend);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+        } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") {
+          // 'free_o3' extrapolating boundary condition on Y boundaries
+          // f(xs-1,ys-1) = 3*f(xs-1,ys) - 3*f(xs-1,ys+1) + f(xs-1,ys+2)
+          //
+          // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know
+          // what value to pass for the corner
+          PetscScalar val = 1.0;
+          int row = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
+          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+          val = -3.0;
+          int col = globalIndex(localmesh->xstart - 1, localmesh->yend);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+          val = 3.0;
+          col = globalIndex(localmesh->xstart - 1, localmesh->yend - 1);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+          val = -1.0;
+          col = globalIndex(localmesh->xstart - 1, localmesh->yend - 2);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+        } else {
+          throw BoutException("Unsupported option for y_bndry");
+        }
+      }
+      if (localmesh->lastX()) {
+        if (y_bndry == "neumann") {
+          // Neumann y-bc
+          // f(xe+1,ys-1) = f(xe+1,ys)
+          PetscScalar val = 1.0;
+          int row = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
+          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+          val = -1.0;
+          int col = globalIndex(localmesh->xend + 1, localmesh->yend);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+        } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") {
+          // 'free_o3' extrapolating boundary condition on Y boundaries
+          // f(xe+1,ys-1) = 3*f(xe+1,ys) - 3*f(xe+1,ys+1) + f(xe+1,ys+2)
+          //
+          // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know
+          // what value to pass for the corner
+          PetscScalar val = 1.0;
+          int row = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
+          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
+
+          val = -3.0;
+          int col = globalIndex(localmesh->xend + 1, localmesh->yend);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+          val = 3.0;
+          col = globalIndex(localmesh->xend + 1, localmesh->yend - 1);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+
+          val = -1.0;
+          col = globalIndex(localmesh->xend + 1, localmesh->yend - 2);
+          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
+        } else {
+          throw BoutException("Unsupported option for y_bndry");
+        }
+      }
+    }
+  }
+
+  // Assemble Matrix
+  MatAssemblyBegin(MatA, MAT_FINAL_ASSEMBLY);
+  MatAssemblyEnd(MatA, MAT_FINAL_ASSEMBLY);
+
+  // Set the operator
+#if PETSC_VERSION_GE(3, 5, 0)
+  KSPSetOperators(ksp, MatA, MatA);
+#else
+  KSPSetOperators(ksp, MatA, MatA, DIFFERENT_NONZERO_PATTERN);
+#endif
+
+  // Set coefficients for preconditioner
+  cr->setCoefs(acoef, bcoef, ccoef);
+}
+
+void LaplaceXYpetsc::setMatrixElementsFiniteVolume(const Field2D& A, const Field2D& B) {
+  //////////////////////////////////////////////////
+  // Set Matrix elements
+  //
+  // (1/J) d/dx ( J * g11 d/dx ) + (1/J) d/dy ( J * g22 d/dy )
+
+  auto coords = localmesh->getCoordinates(location);
+  const Field2D J_DC = DC(coords->J);
+  const Field2D g11_DC = DC(coords->g11);
+  const Field2D dx_DC = DC(coords->dx);
+  const Field2D dy_DC = DC(coords->dy);
+  const Field2D g_22_DC = DC(coords->g_22);
+  const Field2D g_23_DC = DC(coords->g_23);
+  const Field2D g23_DC = DC(coords->g23);
+
+  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      // stencil entries
+      PetscScalar c, xm, xp, ym, yp;
+
+      // XX component
+
+      // Metrics on x+1/2 boundary
+      BoutReal J = 0.5 * (J_DC(x, y) + J_DC(x + 1, y));
+      BoutReal g11 = 0.5 * (g11_DC(x, y) + g11_DC(x + 1, y));
+      BoutReal dx = 0.5 * (dx_DC(x, y) + dx_DC(x + 1, y));
+      BoutReal Acoef = 0.5 * (A(x, y) + A(x + 1, y));
+
+      BoutReal val = Acoef * J * g11 / (J_DC(x, y) * dx * dx_DC(x, y));
+      xp = val;
+      c = -val;
+
+      // Metrics on x-1/2 boundary
+      J = 0.5 * (J_DC(x, y) + J_DC(x - 1, y));
+      g11 = 0.5 * (g11_DC(x, y) + g11_DC(x - 1, y));
+      dx = 0.5 * (dx_DC(x, y) + dx_DC(x - 1, y));
+      Acoef = 0.5 * (A(x, y) + A(x - 1, y));
+
+      val = Acoef * J * g11 / (J_DC(x, y) * dx * dx_DC(x, y));
+      xm = val;
+      c -= val;
+
+      c += B(x, y);
+
+      // Put values into the preconditioner, X derivatives only
+      acoef(y - localmesh->ystart, x - xstart) = xm;
+      bcoef(y - localmesh->ystart, x - xstart) = c;
+      ccoef(y - localmesh->ystart, x - xstart) = xp;
+
+      if (include_y_derivs) {
+        // YY component
+        // Metrics at y+1/2
+        J = 0.5 * (J_DC(x, y) + J_DC(x, y + 1));
+        BoutReal g_22 = 0.5 * (g_22_DC(x, y) + g_22_DC(x, y + 1));
+        BoutReal g23 = 0.5 * (g23_DC(x, y) + g23_DC(x, y + 1));
+        BoutReal g_23 = 0.5 * (g_23_DC(x, y) + g_23_DC(x, y + 1));
+        BoutReal dy = 0.5 * (dy_DC(x, y) + dy_DC(x, y + 1));
+        Acoef = 0.5 * (A(x, y + 1) + A(x, y));
+
+        val = -Acoef * J * g23 * g_23 / (g_22 * J_DC(x, y) * dy * dy_DC(x, y));
+        yp = val;
+        c -= val;
+
+        // Metrics at y-1/2
+        J = 0.5 * (J_DC(x, y) + J_DC(x, y - 1));
+        g_22 = 0.5 * (g_22_DC(x, y) + g_22_DC(x, y - 1));
+        g23 = 0.5 * (g23_DC(x, y) + g23_DC(x, y - 1));
+        g_23 = 0.5 * (g_23_DC(x, y) + g_23_DC(x, y - 1));
+        dy = 0.5 * (dy_DC(x, y) + dy_DC(x, y - 1));
+        Acoef = 0.5 * (A(x, y - 1) + A(x, y));
+
+        val = -Acoef * J * g23 * g_23 / (g_22 * J_DC(x, y) * dy * dy_DC(x, y));
+        ym = val;
+        c -= val;
+      }
+
+      /////////////////////////////////////////////////
+      // Now have a 5-point stencil for the Laplacian
+
+      int row = globalIndex(x, y);
+
+      // Set the centre (diagonal)
+      MatSetValues(MatA, 1, &row, 1, &row, &c, INSERT_VALUES);
+
+      // X + 1
+      int col = globalIndex(x + 1, y);
+      MatSetValues(MatA, 1, &row, 1, &col, &xp, INSERT_VALUES);
+
+      // X - 1
+      col = globalIndex(x - 1, y);
+      MatSetValues(MatA, 1, &row, 1, &col, &xm, INSERT_VALUES);
+
+      if (include_y_derivs) {
+        // Y + 1
+        col = globalIndex(x, y + 1);
+        MatSetValues(MatA, 1, &row, 1, &col, &yp, INSERT_VALUES);
+
+        // Y - 1
+        col = globalIndex(x, y - 1);
+        MatSetValues(MatA, 1, &row, 1, &col, &ym, INSERT_VALUES);
+      }
+    }
+  }
+}
+
+void LaplaceXYpetsc::setMatrixElementsFiniteDifference(const Field2D& A,
+                                                       const Field2D& B) {
+  //////////////////////////////////////////////////
+  // Set Matrix elements
+  //
+  // Div(A Grad(f)) + B f
+  // = A Laplace_perp(f) + Grad_perp(A).Grad_perp(f) + B f
+  // = A*(G1*dfdx + (G2-1/J*d/dy(J/g_22))*dfdy
+  //      + g11*d2fdx2 + (g22-1/g_22)*d2fdy2 + 2*g12*d2fdxdy)
+  //   + g11*dAdx*dfdx + (g22-1/g_22)*dAdy*dfdy + g12*(dAdx*dfdy + dAdy*dfdx)
+  //   + B*f
+
+  auto coords = localmesh->getCoordinates(location);
+  const Field2D G1_2D = DC(coords->G1);
+  const Field2D G2_2D = DC(coords->G2);
+  const Field2D J_2D = DC(coords->J);
+  const Field2D g11_2D = DC(coords->g11);
+  const Field2D g_22_2D = DC(coords->g_22);
+  const Field2D g22_2D = DC(coords->g22);
+  const Field2D g12_2D = DC(coords->g12);
+  const Field2D d1_dx_2D = DC(coords->d1_dx);
+  const Field2D d1_dy_2D = DC(coords->d1_dy);
+  const Field2D dx_2D = DC(coords->dx);
+  const Field2D dy_2D = DC(coords->dy);
+
+  const Field2D coef_dfdy = G2_2D - DC(DDY(J_2D / g_22_2D) / J_2D);
+
+  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      // stencil entries
+      PetscScalar c, xm, xp, ym, yp, xpyp, xpym, xmyp, xmym;
+
+      BoutReal dx = dx_2D(x, y);
+
+      // A*G1*dfdx
+      BoutReal val = A(x, y) * G1_2D(x, y) / (2. * dx);
+      xp = val;
+      xm = -val;
+
+      // A*g11*d2fdx2
+      val = A(x, y) * g11_2D(x, y) / SQ(dx);
+      xp += val;
+      c = -2. * val;
+      xm += val;
+      // Non-uniform grid correction
+      val = A(x, y) * g11_2D(x, y) * d1_dx_2D(x, y) / (2. * dx);
+      xp += val;
+      xm -= val;
+
+      // g11*dAdx*dfdx
+      val = g11_2D(x, y) * (A(x + 1, y) - A(x - 1, y)) / (4. * SQ(dx));
+      xp += val;
+      xm -= val;
+
+      // B*f
+      c += B(x, y);
+
+      // Put values into the preconditioner, X derivatives only
+      acoef(y - localmesh->ystart, x - xstart) = xm;
+      bcoef(y - localmesh->ystart, x - xstart) = c;
+      ccoef(y - localmesh->ystart, x - xstart) = xp;
+
+      if (include_y_derivs) {
+        BoutReal dy = dy_2D(x, y);
+        BoutReal dAdx = (A(x + 1, y) - A(x - 1, y)) / (2. * dx);
+        BoutReal dAdy = (A(x, y + 1) - A(x, y - 1)) / (2. * dy);
+
+        // A*(G2-1/J*d/dy(J/g_22))*dfdy
+        val = A(x, y) * coef_dfdy(x, y) / (2. * dy);
+        yp = val;
+        ym = -val;
+
+        // A*(g22-1/g_22)*d2fdy2
+        val = A(x, y) * (g22_2D(x, y) - 1. / g_22_2D(x, y)) / SQ(dy);
+        yp += val;
+        c -= 2. * val;
+        ym += val;
+        // Non-uniform mesh correction
+        val = A(x, y) * (g22_2D(x, y) - 1. / g_22_2D(x, y)) * d1_dy_2D(x, y) / (2. * dy);
+        yp += val;
+        ym -= val;
+
+        // 2*A*g12*d2dfdxdy
+        val = A(x, y) * g12_2D(x, y) / (2. * dx * dy);
+        xpyp = val;
+        xpym = -val;
+        xmyp = -val;
+        xmym = val;
+
+        // g22*dAdy*dfdy
+        val = (g22_2D(x, y) - 1. / g_22_2D(x, y)) * dAdy / (2. * dy);
+        yp += val;
+        ym -= val;
+
+        // g12*(dAdx*dfdy + dAdy*dfdx)
+        val = g12_2D(x, y) * dAdx / (2. * dy);
+        yp += val;
+        ym -= val;
+        val = g12_2D(x, y) * dAdy / (2. * dx);
+        xp += val;
+        xm -= val;
+      }
+
+      /////////////////////////////////////////////////
+      // Now have a 9-point stencil for the Laplacian
+
+      int row = globalIndex(x, y);
+
+      // Set the centre (diagonal)
+      MatSetValues(MatA, 1, &row, 1, &row, &c, INSERT_VALUES);
+
+      // X + 1
+      int col = globalIndex(x + 1, y);
+      MatSetValues(MatA, 1, &row, 1, &col, &xp, INSERT_VALUES);
+
+      // X - 1
+      col = globalIndex(x - 1, y);
+      MatSetValues(MatA, 1, &row, 1, &col, &xm, INSERT_VALUES);
+
+      if (include_y_derivs) {
+        // Y + 1
+        col = globalIndex(x, y + 1);
+        MatSetValues(MatA, 1, &row, 1, &col, &yp, INSERT_VALUES);
+
+        // Y - 1
+        col = globalIndex(x, y - 1);
+        MatSetValues(MatA, 1, &row, 1, &col, &ym, INSERT_VALUES);
+
+        // X + 1, Y + 1
+        col = globalIndex(x + 1, y + 1);
+        MatSetValues(MatA, 1, &row, 1, &col, &xpyp, INSERT_VALUES);
+
+        // X + 1, Y - 1
+        col = globalIndex(x + 1, y - 1);
+        MatSetValues(MatA, 1, &row, 1, &col, &xpym, INSERT_VALUES);
+
+        // X - 1, Y + 1
+        col = globalIndex(x - 1, y + 1);
+        MatSetValues(MatA, 1, &row, 1, &col, &xmyp, INSERT_VALUES);
+
+        // X - 1, Y - 1
+        col = globalIndex(x - 1, y - 1);
+        MatSetValues(MatA, 1, &row, 1, &col, &xmym, INSERT_VALUES);
+      }
+    }
+  }
+}
+
+LaplaceXYpetsc::~LaplaceXYpetsc() {
+  PetscBool is_finalised;
+  PetscFinalized(&is_finalised);
+
+  if (!is_finalised) {
+    // PetscFinalize may already have destroyed this object
+    KSPDestroy(&ksp);
+  }
+
+  VecDestroy(&xs);
+  VecDestroy(&bs);
+  MatDestroy(&MatA);
+}
+
+Field2D LaplaceXYpetsc::solve(const Field2D& rhs, const Field2D& x0) {
+  Timer timer("invert");
+
+  ASSERT1(rhs.getMesh() == localmesh);
+  ASSERT1(x0.getMesh() == localmesh);
+  ASSERT1(rhs.getLocation() == location);
+  ASSERT1(x0.getLocation() == location);
+
+  // Load initial guess x0 into xs and rhs into bs
+
+  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      int ind = globalIndex(x, y);
+
+      PetscScalar val = x0(x, y);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      val = rhs(x, y);
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+  }
+
+  if (finite_volume) {
+    solveFiniteVolume(x0);
+  } else {
+    solveFiniteDifference(x0);
+  }
+
+  // Assemble RHS Vector
+  VecAssemblyBegin(bs);
+  VecAssemblyEnd(bs);
+
+  // Assemble Trial Solution Vector
+  VecAssemblyBegin(xs);
+  VecAssemblyEnd(xs);
+
+  // Solve the system
+  KSPSolve(ksp, bs, xs);
+
+  KSPConvergedReason reason;
+  KSPGetConvergedReason(ksp, &reason);
+
+  if (reason <= 0) {
+    throw BoutException("LaplaceXYpetsc failed to converge. Reason {} ({:d})",
+                        KSPConvergedReasons[reason], static_cast<int>(reason));
+  }
+
+  if (save_performance) {
+    // Update performance monitoring information
+    n_calls++;
+
+    int iterations = 0;
+    KSPGetIterationNumber(ksp, &iterations);
+
+    average_iterations = BoutReal(n_calls - 1) / BoutReal(n_calls) * average_iterations
+                         + BoutReal(iterations) / BoutReal(n_calls);
+  }
+
+  //////////////////////////
+  // Copy data into result
+
+  Field2D result;
+  result.allocate();
+  result.setLocation(location);
+
+  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      int ind = globalIndex(x, y);
+
+      PetscScalar val;
+      VecGetValues(xs, 1, &ind, &val);
+      result(x, y) = val;
+    }
+  }
+
+  // Inner X boundary
+  if (localmesh->firstX()) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      int ind = globalIndex(localmesh->xstart - 1, y);
+      PetscScalar val;
+      VecGetValues(xs, 1, &ind, &val);
+      for (int x = localmesh->xstart - 1; x >= 0; x--) {
+        result(x, y) = val;
+      }
+    }
+  }
+
+  // Outer X boundary
+  if (localmesh->lastX()) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      int ind = globalIndex(localmesh->xend + 1, y);
+      PetscScalar val;
+      VecGetValues(xs, 1, &ind, &val);
+      for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
+        result(x, y) = val;
+      }
+    }
+  }
+
+  // Lower Y boundary
+  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+    if (
+        // Should not go into corner cells, finite-volume LaplaceXYpetsc stencil does not include
+        // them
+        (finite_volume and (it.ind < localmesh->xstart or it.ind > localmesh->xend))
+
+        // Only go into first corner cell for finite-difference
+        or (it.ind < localmesh->xstart - 1 or it.ind > localmesh->xend + 1)) {
+      continue;
+    }
+    int ind = globalIndex(it.ind, localmesh->ystart - 1);
+    PetscScalar val;
+    VecGetValues(xs, 1, &ind, &val);
+    for (int y = localmesh->ystart - 1; y >= 0; y--) {
+      result(it.ind, y) = val;
+    }
+  }
+
+  // Upper Y boundary
+  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+    if (
+        // Should not go into corner cells, finite-volume LaplaceXYpetsc stencil does not include
+        // them
+        (finite_volume and (it.ind < localmesh->xstart or it.ind > localmesh->xend))
+
+        // Only go into first corner cell for finite-difference
+        or (it.ind < localmesh->xstart - 1 or it.ind > localmesh->xend + 1)) {
+      continue;
+    }
+    int ind = globalIndex(it.ind, localmesh->yend + 1);
+    PetscScalar val;
+    VecGetValues(xs, 1, &ind, &val);
+    for (int y = localmesh->yend + 1; y < localmesh->LocalNy; y++) {
+      result(it.ind, y) = val;
+    }
+  }
+
+  return result;
+}
+
+void LaplaceXYpetsc::solveFiniteVolume(const Field2D& x0) {
+  // Use original LaplaceXYpetsc implementation of passing boundary values for backward
+  // compatibility
+  if (localmesh->firstX()) {
+    if (x_inner_dirichlet) {
+      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+        int ind = globalIndex(localmesh->xstart - 1, y);
+
+        PetscScalar val = x0(localmesh->xstart - 1, y);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        val = 0.5 * (x0(localmesh->xstart - 1, y) + x0(localmesh->xstart, y));
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    } else {
+      // Inner X boundary (Neumann)
+      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+        int ind = globalIndex(localmesh->xstart - 1, y);
+
+        PetscScalar val = x0(localmesh->xstart - 1, y);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        val = 0.0; // x0(localmesh->xstart-1,y) - x0(localmesh->xstart,y);
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    }
+  }
+
+  // Outer X boundary (Dirichlet)
+  if (localmesh->lastX()) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      int ind = globalIndex(localmesh->xend + 1, y);
+
+      PetscScalar val = x0(localmesh->xend + 1, y);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      val = 0.5 * (x0(localmesh->xend, y) + x0(localmesh->xend + 1, y));
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+  }
+
+  if (y_bndry == "dirichlet") {
+    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->ystart - 1);
+
+      PetscScalar val = x0(it.ind, localmesh->ystart - 1);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      val = 0.5 * (x0(it.ind, localmesh->ystart - 1) + x0(it.ind, localmesh->ystart));
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+
+    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->yend + 1);
+
+      PetscScalar val = x0(it.ind, localmesh->yend + 1);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      val = 0.5 * (x0(it.ind, localmesh->yend + 1) + x0(it.ind, localmesh->yend));
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+  } else if (y_bndry == "neumann" or y_bndry == "free_o3") {
+    // Y boundaries Neumann
+    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->ystart - 1);
+
+      PetscScalar val = x0(it.ind, localmesh->ystart - 1);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      val = 0.0;
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+
+    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+      // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->yend + 1);
+
+      PetscScalar val = x0(it.ind, localmesh->yend + 1);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      val = 0.0;
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+  } else {
+    throw BoutException("Unsupported option for y_bndry");
+  }
+}
+
+void LaplaceXYpetsc::solveFiniteDifference(const Field2D& x0) {
+  // For finite-difference implementation pass boundary values in the same way as for
+  // the 'Laplacian' solvers - the value to use (for Dirichlet boundary conditions) on
+  // the boundary (which is half way between grid cell and boundary cell) is passed as
+  // the value in the first boundary cell.
+  if (localmesh->firstX()) {
+    if (x_inner_dirichlet) {
+      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+        int ind = globalIndex(localmesh->xstart - 1, y);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = 2. * x0(localmesh->xstart - 1, y) - x0(localmesh->xstart, y);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Pass the value from boundary cell of x0 as the boundary condition to the rhs
+        val = x0(localmesh->xstart - 1, y);
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    } else {
+      // Inner X boundary (Neumann)
+      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+        int ind = globalIndex(localmesh->xstart - 1, y);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = x0(localmesh->xstart, y);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    }
+  }
+
+  // Outer X boundary (Dirichlet)
+  if (localmesh->lastX()) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      int ind = globalIndex(localmesh->xend + 1, y);
+
+      // For the boundary value of the initial guess, use the value that would be set by
+      // applying the boundary condition to the initial guess
+      PetscScalar val = 2. * x0(localmesh->xend + 1, y) - x0(localmesh->xend, y);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      // Pass the value from boundary cell of x0 as the boundary condition to the rhs
+      val = x0(localmesh->xend + 1, y);
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+  }
+
+  if (y_bndry == "dirichlet") {
+    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+      // Should not go into corner cells, they are treated specially below
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->ystart - 1);
+
+      // For the boundary value of the initial guess, use the value that would be set by
+      // applying the boundary condition to the initial guess
+      PetscScalar val =
+          2. * x0(it.ind, localmesh->ystart - 1) - x0(it.ind, localmesh->ystart);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      // Pass the value from boundary cell of x0 as the boundary condition to the rhs
+      val = x0(it.ind, localmesh->ystart - 1);
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+
+    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+      // Should not go into corner cells, they are treated specially below
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->yend + 1);
+
+      // For the boundary value of the initial guess, use the value that would be set by
+      // applying the boundary condition to the initial guess
+      PetscScalar val =
+          2. * x0(it.ind, localmesh->yend + 1) - x0(it.ind, localmesh->yend);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      // Pass the value from boundary cell of x0 as the boundary condition to the rhs
+      val = x0(it.ind, localmesh->yend + 1);
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+
+    // Use free_o3 for the corner boundary cells
+    if (localmesh->hasBndryLowerY()) {
+      if (localmesh->firstX()) {
+        int ind = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = 3. * x0(localmesh->xstart - 1, localmesh->ystart)
+                          - 3. * x0(localmesh->xstart - 1, localmesh->ystart + 1)
+                          + x0(localmesh->xstart - 1, localmesh->ystart + 2);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+      if (localmesh->lastX()) {
+        int ind = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = 3. * x0(localmesh->xend + 1, localmesh->ystart)
+                          - 3. * x0(localmesh->xend + 1, localmesh->ystart + 1)
+                          + x0(localmesh->xend + 1, localmesh->ystart + 2);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    }
+    if (localmesh->hasBndryUpperY()) {
+      if (localmesh->firstX()) {
+        int ind = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = 3. * x0(localmesh->xstart - 1, localmesh->yend)
+                          - 3. * x0(localmesh->xstart - 1, localmesh->yend - 1)
+                          + x0(localmesh->xstart - 1, localmesh->yend - 2);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+      if (localmesh->lastX()) {
+        int ind = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = 3. * x0(localmesh->xend + 1, localmesh->yend)
+                          - 3. * x0(localmesh->xend + 1, localmesh->yend - 1)
+                          + x0(localmesh->xend + 1, localmesh->yend - 2);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    }
+  } else if (y_bndry == "neumann") {
+    // Y boundaries Neumann
+    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+      // Should not go into corner cells, they are treated specially below
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->ystart - 1);
+
+      // For the boundary value of the initial guess, use the value that would be set by
+      // applying the boundary condition to the initial guess
+      PetscScalar val = x0(it.ind, localmesh->ystart);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      // Set the value for the rhs of the boundary condition to zero
+      val = 0.0;
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+    if (localmesh->hasBndryLowerY()) {
+      if (localmesh->firstX()) {
+        int ind = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = x0(localmesh->xstart - 1, localmesh->ystart);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+      if (localmesh->lastX()) {
+        int ind = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = x0(localmesh->xend + 1, localmesh->ystart);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    }
+
+    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+      // Should not go into corner cells, they are treated specially below
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->yend + 1);
+
+      // For the boundary value of the initial guess, use the value that would be set by
+      // applying the boundary condition to the initial guess
+      PetscScalar val = x0(it.ind, localmesh->yend);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      // Set the value for the rhs of the boundary condition to zero
+      val = 0.0;
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+    if (localmesh->hasBndryUpperY()) {
+      if (localmesh->firstX()) {
+        int ind = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = x0(localmesh->xstart - 1, localmesh->yend);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+      if (localmesh->lastX()) {
+        int ind = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = x0(localmesh->xend + 1, localmesh->yend);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    }
+  } else if (y_bndry == "free_o3") {
+    // Y boundaries free_o3
+    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+      // Should not go into corner cells, they are treated specially below
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->ystart - 1);
+
+      // For the boundary value of the initial guess, use the value that would be set by
+      // applying the boundary condition to the initial guess
+      PetscScalar val = 3. * x0(it.ind, localmesh->ystart)
+                        - 3. * x0(it.ind, localmesh->ystart + 1)
+                        + x0(it.ind, localmesh->ystart + 2);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      // Set the value for the rhs of the boundary condition to zero
+      val = 0.0;
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+    if (localmesh->hasBndryLowerY()) {
+      if (localmesh->firstX()) {
+        int ind = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = 3. * x0(localmesh->xstart - 1, localmesh->ystart)
+                          - 3. * x0(localmesh->xstart - 1, localmesh->ystart + 1)
+                          + x0(localmesh->xstart - 1, localmesh->ystart + 2);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+      if (localmesh->lastX()) {
+        int ind = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = 3. * x0(localmesh->xend + 1, localmesh->ystart)
+                          - 3. * x0(localmesh->xend + 1, localmesh->ystart + 1)
+                          + x0(localmesh->xend + 1, localmesh->ystart + 2);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    }
+
+    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+      // Should not go into corner cells, they are treated specially below
+      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+        continue;
+      }
+      int ind = globalIndex(it.ind, localmesh->yend + 1);
+
+      // For the boundary value of the initial guess, use the value that would be set by
+      // applying the boundary condition to the initial guess
+      PetscScalar val = 3. * x0(it.ind, localmesh->yend)
+                        - 3. * x0(it.ind, localmesh->yend - 1)
+                        + x0(it.ind, localmesh->yend - 2);
+      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+      // Set the value for the rhs of the boundary condition to zero
+      val = 0.0;
+      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+    }
+    if (localmesh->hasBndryUpperY()) {
+      if (localmesh->firstX()) {
+        int ind = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = 3. * x0(localmesh->xstart - 1, localmesh->yend)
+                          - 3. * x0(localmesh->xstart - 1, localmesh->yend - 1)
+                          + x0(localmesh->xstart - 1, localmesh->yend - 2);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+      if (localmesh->lastX()) {
+        int ind = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
+
+        // For the boundary value of the initial guess, use the value that would be set by
+        // applying the boundary condition to the initial guess
+        PetscScalar val = 3. * x0(localmesh->xend + 1, localmesh->yend)
+                          - 3. * x0(localmesh->xend + 1, localmesh->yend - 1)
+                          + x0(localmesh->xend + 1, localmesh->yend - 2);
+        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
+
+        // Set the value for the rhs of the boundary condition to zero
+        val = 0.0;
+        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
+      }
+    }
+  } else {
+    throw BoutException("Unsupported option for y_bndry");
+  }
+}
+
+/*! Preconditioner
+ * NOTE: For generality, this routine does use globalIndex() in the inner loop, although
+ * this may be slightly less efficient than incrementing an integer for the global index,
+ * the finite-volume and finite-difference implementations have slightly different
+ * indexing patterns, so incrementing an integer would be tricky.
+ */
+int LaplaceXYpetsc::precon(Vec input, Vec result) {
+
+  for (auto itdwn = localmesh->iterateBndryLowerY(); !itdwn.isDone(); itdwn++) {
+    // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+    if (itdwn.ind < localmesh->xstart or itdwn.ind > localmesh->xend) {
+      continue;
+    }
+    const int ind = globalIndex(itdwn.ind, localmesh->ystart - 1);
+    PetscScalar val;
+    VecGetValues(input, 1, &ind, &val);
+    VecSetValues(result, 1, &ind, &val, INSERT_VALUES);
+  }
+  for (auto itup = localmesh->iterateBndryUpperY(); !itup.isDone(); itup++) {
+    // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+    if (itup.ind < localmesh->xstart or itup.ind > localmesh->xend) {
+      continue;
+    }
+    const int ind = globalIndex(itup.ind, localmesh->yend + 1);
+    PetscScalar val;
+    VecGetValues(input, 1, &ind, &val);
+    VecSetValues(result, 1, &ind, &val, INSERT_VALUES);
+  }
+
+  // Load vector x into bvals array
+  for (int x = xstart; x <= xend; x++) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int ind = globalIndex(x, y);
+      PetscScalar val;
+      VecGetValues(input, 1, &ind, &val);
+      bvals(y - localmesh->ystart, x - xstart) = val;
+    }
+  }
+
+  // Solve tridiagonal systems using CR solver
+  cr->solve(bvals, xvals);
+
+  // Save result xvals into y array
+  for (int x = xstart; x <= xend; x++) {
+    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
+      const int ind = globalIndex(x, y);
+      PetscScalar val = xvals(y - localmesh->ystart, x - xstart);
+      VecSetValues(result, 1, &ind, &val, INSERT_VALUES);
+    }
+  }
+  VecAssemblyBegin(result);
+  VecAssemblyEnd(result);
+  return 0;
+}
+
+///////////////////////////////////////////////////////////////
+
+int LaplaceXYpetsc::localSize() {
+
+  // Bulk of points
+  const int nx = localmesh->xend - localmesh->xstart + 1;
+  const int ny = localmesh->yend - localmesh->ystart + 1;
+
+  int n = nx * ny;
+
+  // X boundaries
+  if (localmesh->firstX()) {
+    n += ny;
+  }
+  if (localmesh->lastX()) {
+    n += ny;
+  }
+
+  // Y boundaries
+  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
+    // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+      continue;
+    }
+    n++;
+  }
+  if ((not finite_volume) and localmesh->hasBndryLowerY()) {
+    if (localmesh->firstX()) {
+      n++;
+    }
+    if (localmesh->lastX()) {
+      n++;
+    }
+  }
+  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
+    // Should not go into corner cells, LaplaceXYpetsc stencil does not include them
+    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
+      continue;
+    }
+    n++;
+  }
+  if ((not finite_volume) and localmesh->hasBndryUpperY()) {
+    if (localmesh->firstX()) {
+      n++;
+    }
+    if (localmesh->lastX()) {
+      n++;
+    }
+  }
+
+  return n;
+}
+
+int LaplaceXYpetsc::globalIndex(int x, int y) {
+  if ((x < 0) || (x >= localmesh->LocalNx) || (y < 0) || (y >= localmesh->LocalNy)) {
+    return -1; // Out of range
+  }
+
+  // Get the index from a Field2D, round to integer
+  return static_cast<int>(std::round(indexXY(x, y)));
+}
+
+void LaplaceXYpetsc::savePerformance(Solver& solver, const std::string& name) {
+  // set flag so that performance monitoring values are calculated
+  save_performance = true;
+
+  // add values to be saved to the output
+  if (not name.empty()) {
+    default_prefix = name;
+  }
+
+  // add monitor to reset counters/averages for new output timestep
+  // monitor added to back of queue, so that values are reset after being saved
+  solver.addMonitor(&monitor, Solver::BACK);
+}
+
+int LaplaceXYpetsc::LaplaceXYMonitor::call(Solver* /*solver*/, BoutReal /*time*/,
+                                           int /*iter*/, int /*nout*/) {
+  laplacexy->output_average_iterations = laplacexy->average_iterations;
+
+  laplacexy->n_calls = 0;
+  laplacexy->average_iterations = 0.;
+
+  return 0;
+}
+
+void LaplaceXYpetsc::LaplaceXYMonitor::outputVars(Options& output_options,
+                                                  const std::string& time_dimension) {
+  output_options[fmt::format("{}_average_iterations", laplacexy->default_prefix)]
+      .assignRepeat(laplacexy->output_average_iterations, time_dimension);
+}
+
+#endif // BOUT_HAS_PETSC
diff --git a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx
new file mode 100644
index 0000000000..1db812a19d
--- /dev/null
+++ b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx
@@ -0,0 +1,204 @@
+/**************************************************************************
+ * Laplacian solver in 2D (X-Y)
+ *
+ * Equation solved is: 
+ *
+ * Div( A * Grad_perp(x) ) + B*x = b
+ *
+ * Intended for use in solving n = 0 component of potential
+ * from inversion of vorticity equation
+ * 
+ **************************************************************************
+ * Copyright 2015 B.Dudson
+ *
+ * Contact: Ben Dudson, bd512@york.ac.uk
+ * 
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#ifndef BOUT_LAPLACE_XY_PETSC_H
+#define BOUT_LAPLACE_XY_PETSC_H
+
+#include "bout/build_defines.hxx"
+#include "bout/invert/laplacexy.hxx"
+
+#if !BOUT_HAS_PETSC
+
+namespace {
+RegisterUnavailableLaplaceXY
+    registerlaplacexypetsc("petsc", "BOUT++ was not configured with PETSc");
+}
+
+#else // BOUT_HAS_PETSC
+
+#include "bout/solver.hxx"
+#include "bout/utils.hxx"
+#include <bout/cyclic_reduction.hxx>
+#include <bout/mesh.hxx>
+#include <bout/petsclib.hxx>
+
+class Options;
+class Solver;
+
+class LaplaceXYpetsc : public LaplaceXY {
+public:
+  LaplaceXYpetsc(Mesh* m = nullptr, Options* opt = nullptr, CELL_LOC loc = CELL_CENTRE);
+  LaplaceXYpetsc(const LaplaceXYpetsc&) = delete;
+  LaplaceXYpetsc(LaplaceXYpetsc&&) = delete;
+  LaplaceXYpetsc& operator=(const LaplaceXYpetsc&) = delete;
+  LaplaceXYpetsc& operator=(LaplaceXYpetsc&&) = delete;
+  ~LaplaceXYpetsc() override;
+
+  /*!
+   * Set coefficients (A, B) in equation:
+   * Div( A * Grad_perp(x) ) + B*x = b
+   */
+  void setCoefs(const Field2D& A, const Field2D& B) override;
+
+  /*!
+   * Solve Laplacian in X-Y
+   * 
+   * Inputs
+   * ======
+   *
+   * rhs  - The field to be inverted. This must be allocated
+   *        and contain valid data.
+   * x0   - Initial guess at the solution. If this is unallocated
+   *        then an initial guess of zero will be used.
+   * 
+   * Returns
+   * =======
+   * 
+   * The solution as a Field2D. On failure an exception will be raised
+   * 
+   */
+  Field2D solve(const Field2D& rhs, const Field2D& x0) override;
+
+  /*!
+   * Preconditioner function
+   * This is called by PETSc via a static function.
+   * and should not be called by external users
+   */
+  int precon(Vec x, Vec y);
+
+  /*!
+   * If this method is called, save some performance monitoring information
+   */
+  void savePerformance(Solver& solver, const std::string& name = "");
+
+private:
+  PetscLib lib;       ///< Requires PETSc library
+  Mat MatA = nullptr; ///< Matrix to be inverted
+  Vec xs = nullptr;   ///< Solution vector
+  Vec bs = nullptr;   ///< RHS vectors
+  KSP ksp = nullptr;  ///< Krylov Subspace solver
+  PC pc = nullptr;    ///< Preconditioner
+
+  Mesh* localmesh; ///< The mesh this operates on, provides metrics and communication
+
+  /// default prefix for writing performance logging variables
+  std::string default_prefix;
+
+  // Preconditioner
+  int xstart, xend;
+  int nloc, nsys;
+  Matrix<BoutReal> acoef, bcoef, ccoef, xvals, bvals;
+  std::unique_ptr<CyclicReduce<BoutReal>> cr; ///< Tridiagonal solver
+
+  // Use finite volume or finite difference discretization
+  bool finite_volume{true};
+
+  // Y derivatives
+  bool include_y_derivs; // Include Y derivative terms?
+
+  // Boundary conditions
+  bool x_inner_dirichlet;         // Dirichlet on inner X boundary?
+  bool x_outer_dirichlet{false};  // Dirichlet on outer X boundary?
+  std::string y_bndry{"neumann"}; // Boundary condition for y-boundary
+
+  // Location of the rhs and solution
+  CELL_LOC location;
+
+  /*!
+   * Number of grid points on this processor
+   */
+  int localSize();
+
+  /*!
+   * Return the communicator for XY
+   */
+  MPI_Comm communicator();
+
+  /*!
+   * Return the global index of a local (x,y) coordinate
+   * including guard cells.
+   * Boundary cells have a global index of -1
+   *
+   * To do this, a Field2D (indexXY) is used to store
+   * the index as a floating point number which is then rounded
+   * to an integer. Guard cells are filled by communication
+   * so no additional logic is needed in Mesh.
+   */
+  int globalIndex(int x, int y);
+  Field2D indexXY; ///< Global index (integer stored as BoutReal)
+
+  // Save performance information?
+  bool save_performance = false;
+
+  // Running average of number of iterations taken for solve in each output timestep
+  BoutReal average_iterations = 0.;
+
+  // Variable to store the final result of average_iterations, since output is
+  // written after all other monitors have been called, and average_iterations
+  // must be reset in the monitor
+  BoutReal output_average_iterations = 0.;
+
+  // Running total of number of calls to the solver in each output timestep
+  int n_calls = 0;
+
+  // Utility methods
+  void setPreallocationFiniteVolume(PetscInt* d_nnz, PetscInt* o_nnz);
+  void setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nnz);
+  void setMatrixElementsFiniteVolume(const Field2D& A, const Field2D& B);
+  void setMatrixElementsFiniteDifference(const Field2D& A, const Field2D& B);
+  void solveFiniteVolume(const Field2D& x0);
+  void solveFiniteDifference(const Field2D& x0);
+
+  // Monitor class used to reset performance-monitoring variables for a new
+  // output timestep
+  friend class LaplaceXYMonitor;
+  class LaplaceXYMonitor : public Monitor {
+  public:
+    LaplaceXYMonitor(LaplaceXYpetsc& owner) : laplacexy(&owner) {}
+
+    int call(Solver* /*solver*/, BoutReal /*time*/, int /*iter*/, int /*nout*/) override;
+    void outputVars(Options& output_options, const std::string& time_dimension) override;
+
+  private:
+    // LaplaceXY object that this monitor belongs to
+    LaplaceXYpetsc* laplacexy;
+  };
+
+  LaplaceXYMonitor monitor;
+};
+
+namespace {
+const inline RegisterLaplaceXY<LaplaceXYpetsc> registerlaplacexypetsc{"petsc"};
+}
+
+#endif // BOUT_HAS_PETSC
+#endif // BOUT_LAPLACE_XY_PETSC_H
diff --git a/src/invert/laplacexy2/laplacexy2.cxx b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
similarity index 94%
rename from src/invert/laplacexy2/laplacexy2.cxx
rename to src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
index 713fd8e68f..ae2cc8313a 100644
--- a/src/invert/laplacexy2/laplacexy2.cxx
+++ b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
@@ -2,26 +2,25 @@
 
 #if BOUT_HAS_PETSC and not BOUT_USE_METRIC_3D
 
+#include "laplacexy-petsc2.hxx"
+
 #include <bout/assert.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/globals.hxx>
-#include <bout/invert/laplacexy2.hxx>
 #include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 
 #include <petscksp.h>
 
-#include <cmath>
-
 namespace {
 Ind2D index2d(Mesh* mesh, int x, int y) {
   int ny = mesh->LocalNy;
-  return Ind2D(x * ny + y, ny, 1);
+  return Ind2D((x * ny) + y, ny, 1);
 }
 } // namespace
 
-LaplaceXY2::LaplaceXY2(Mesh* m, Options* opt, const CELL_LOC loc)
+LaplaceXYpetsc2::LaplaceXYpetsc2(Mesh* m, Options* opt, const CELL_LOC loc)
     : localmesh(m == nullptr ? bout::globals::mesh : m),
       indexConverter(std::make_shared<GlobalIndexer<Field2D>>(
           localmesh, squareStencil<Field2D::ind_type>(localmesh))),
@@ -100,12 +99,12 @@ LaplaceXY2::LaplaceXY2(Mesh* m, Options* opt, const CELL_LOC loc)
   // Decide boundary condititions
   if (localmesh->periodicY(localmesh->xstart)) {
     // Periodic in Y, so in the core
-    opt->get("core_bndry_dirichlet", x_inner_dirichlet, false);
+    x_inner_dirichlet = (*opt)["core_bndry_dirichlet"].withDefault(false);
   } else {
     // Non-periodic, so in the PF region
-    opt->get("pf_bndry_dirichlet", x_inner_dirichlet, true);
+    x_inner_dirichlet = (*opt)["pf_bndry_dirichlet"].withDefault(true);
   }
-  opt->get("y_bndry_dirichlet", y_bndry_dirichlet, false);
+  y_bndry_dirichlet = (*opt)["y_bndry_dirichlet"].withDefault(false);
 
   ///////////////////////////////////////////////////
   // Including Y derivatives?
@@ -123,7 +122,7 @@ LaplaceXY2::LaplaceXY2(Mesh* m, Options* opt, const CELL_LOC loc)
   setCoefs(one, zero);
 }
 
-void LaplaceXY2::setCoefs(const Field2D& A, const Field2D& B) {
+void LaplaceXYpetsc2::setCoefs(const Field2D& A, const Field2D& B) {
   Timer timer("invert");
 
   ASSERT1(A.getMesh() == localmesh);
@@ -290,7 +289,7 @@ void LaplaceXY2::setCoefs(const Field2D& A, const Field2D& B) {
 #endif
 }
 
-LaplaceXY2::~LaplaceXY2() {
+LaplaceXYpetsc2::~LaplaceXYpetsc2() {
   PetscBool is_finalised;
   PetscFinalized(&is_finalised);
 
@@ -300,7 +299,7 @@ LaplaceXY2::~LaplaceXY2() {
   }
 }
 
-Field2D LaplaceXY2::solve(const Field2D& rhs, const Field2D& x0) {
+Field2D LaplaceXYpetsc2::solve(const Field2D& rhs, const Field2D& x0) {
   Timer timer("invert");
 
   ASSERT1(rhs.getMesh() == localmesh);
@@ -310,7 +309,8 @@ Field2D LaplaceXY2::solve(const Field2D& rhs, const Field2D& x0) {
 
   // Load initial guess x0 into xs and rhs into bs
 
-  PetscVector<Field2D> xs(x0, indexConverter), bs(rhs, indexConverter);
+  PetscVector<Field2D> xs(x0, indexConverter);
+  PetscVector<Field2D> bs(rhs, indexConverter);
 
   if (localmesh->firstX()) {
     if (x_inner_dirichlet) {
@@ -381,11 +381,11 @@ Field2D LaplaceXY2::solve(const Field2D& rhs, const Field2D& x0) {
   // Solve the system
   KSPSolve(ksp, *bs.get(), *xs.get());
 
-  KSPConvergedReason reason;
+  KSPConvergedReason reason = KSP_CONVERGED_ITERATING;
   KSPGetConvergedReason(ksp, &reason);
 
   if (reason <= 0) {
-    throw BoutException("LaplaceXY2 failed to converge. Reason {} ({:d})",
+    throw BoutException("LaplaceXYpetsc2 failed to converge. Reason {} ({:d})",
                         KSPConvergedReasons[reason], static_cast<int>(reason));
   }
 
diff --git a/include/bout/invert/laplacexy2.hxx b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx
similarity index 64%
rename from include/bout/invert/laplacexy2.hxx
rename to src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx
index 51f75f467d..1480f366fe 100644
--- a/include/bout/invert/laplacexy2.hxx
+++ b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx
@@ -30,63 +30,45 @@
  *
  **************************************************************************/
 
-#ifndef BOUT_LAPLACE_XY2_H
-#define BOUT_LAPLACE_XY2_H
+#ifndef BOUT_LAPLACE_XY_PETSC2_H
+#define BOUT_LAPLACE_XY_PETSC2_H
 
 #include "bout/build_defines.hxx"
+#include "bout/invert/laplacexy.hxx"
 
-#if (not BOUT_HAS_PETSC) or BOUT_USE_METRIC_3D
-// If no PETSc or 3D metrics
+#if !BOUT_HAS_PETSC
+namespace {
+RegisterUnavailableLaplaceXY
+    registerlaplacexypetsc2("petsc2", "BOUT++ was not configured with PETSc");
+}
 
-#warning LaplaceXY2 requires PETSc and 2D metrics. No LaplaceXY2 available
+#elif BOUT_USE_METRIC_3D
+namespace {
+RegisterUnavailableLaplaceXY
+    registerlaplacexypetsc2("petsc2", "BOUT++ was configured with 3D metrics");
+}
 
-#include <bout/boutexception.hxx>
-#include <bout/mesh.hxx>
-#include <bout/options.hxx>
-
-/*!
- * Create a dummy class so that code will compile
- * without PETSc, but will throw an exception if
- * LaplaceXY is used.
- */
-class LaplaceXY2 {
-public:
-  LaplaceXY2(Mesh* UNUSED(m) = nullptr, Options* UNUSED(opt) = nullptr,
-             const CELL_LOC UNUSED(loc) = CELL_CENTRE) {
-    throw BoutException(
-        "LaplaceXY2 requires PETSc and 2D metrics. No LaplaceXY2 available");
-  }
-  void setCoefs(const Field2D& UNUSED(A), const Field2D& UNUSED(B)) {}
-  Field2D solve(const Field2D& UNUSED(rhs), const Field2D& UNUSED(x0)) {
-    throw BoutException(
-        "LaplaceXY2 requires PETSc and 2D metrics. No LaplaceXY2 available");
-  }
-};
+#else // BOUT_HAS_PETSC
 
-#else // BOUT_HAS_PETSC and 2D metrics
-
-#include "bout/utils.hxx"
 #include <bout/cyclic_reduction.hxx>
 #include <bout/mesh.hxx>
 #include <bout/petsc_interface.hxx>
 #include <bout/petsclib.hxx>
 
-class LaplaceXY2 {
+class LaplaceXYpetsc2 : public LaplaceXY {
 public:
-  /*!
-   * Constructor
-   */
-  LaplaceXY2(Mesh* m = nullptr, Options* opt = nullptr, const CELL_LOC loc = CELL_CENTRE);
-  /*!
-   * Destructor
-   */
-  ~LaplaceXY2();
+  LaplaceXYpetsc2(Mesh* m = nullptr, Options* opt = nullptr, CELL_LOC loc = CELL_CENTRE);
+  LaplaceXYpetsc2(const LaplaceXYpetsc2&) = default;
+  LaplaceXYpetsc2(LaplaceXYpetsc2&&) = delete;
+  LaplaceXYpetsc2& operator=(const LaplaceXYpetsc2&) = default;
+  LaplaceXYpetsc2& operator=(LaplaceXYpetsc2&&) = delete;
+  ~LaplaceXYpetsc2() override;
 
   /*!
    * Set coefficients (A, B) in equation:
    * Div( A * Grad_perp(x) ) + B*x = b
    */
-  void setCoefs(const Field2D& A, const Field2D& B);
+  void setCoefs(const Field2D& A, const Field2D& B) override;
 
   /*!
    * Solve Laplacian in X-Y
@@ -105,7 +87,7 @@ public:
    * The solution as a Field2D. On failure an exception will be raised
    *
    */
-  Field2D solve(const Field2D& rhs, const Field2D& x0);
+  Field2D solve(const Field2D& rhs, const Field2D& x0) override;
 
   /*!
    * Preconditioner function
@@ -121,8 +103,8 @@ private:
 
   IndexerPtr<Field2D> indexConverter;
   PetscMatrix<Field2D> matrix; ///< Matrix to be inverted
-  KSP ksp;                     ///< Krylov Subspace solver
-  PC pc;                       ///< Preconditioner
+  KSP ksp = nullptr;           ///< Krylov Subspace solver
+  PC pc = nullptr;             ///< Preconditioner
 
   // Y derivatives
   bool include_y_derivs; // Include Y derivative terms?
@@ -140,5 +122,9 @@ private:
   MPI_Comm communicator();
 };
 
+namespace {
+const inline RegisterLaplaceXY<LaplaceXYpetsc2> registerlaplacexypetsc2{"petsc2"};
+}
+
 #endif // BOUT_HAS_PETSC
-#endif // BOUT_LAPLACE_XY2_H
+#endif // BOUT_LAPLACE_XY_PETSC2_H
diff --git a/src/invert/laplacexy/laplacexy.cxx b/src/invert/laplacexy/laplacexy.cxx
index bdd22e29bd..3bac2d9d2b 100644
--- a/src/invert/laplacexy/laplacexy.cxx
+++ b/src/invert/laplacexy/laplacexy.cxx
@@ -1,1889 +1,10 @@
-#include "bout/build_defines.hxx"
-
-#if BOUT_HAS_PETSC
+// NOLINTBEGIN(misc-include-cleaner, unused-includes)
+#include "impls/hypre/laplacexy-hypre.hxx"
+#include "impls/petsc/laplacexy-petsc.hxx"
+#include "impls/petsc2/laplacexy-petsc2.hxx"
+// NOLINTEND(misc-include-cleaner, unused-includes)
 
 #include <bout/invert/laplacexy.hxx>
 
-#include <bout/assert.hxx>
-#include <bout/boutcomm.hxx>
-#include <bout/derivs.hxx>
-#include <bout/globals.hxx>
-#include <bout/output.hxx>
-#include <bout/sys/timer.hxx>
-#include <bout/utils.hxx>
-
-#include <petscksp.h>
-
-#include <cmath>
-
-static PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) {
-  int ierr;
-
-  // Get the context
-  LaplaceXY* s;
-  ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&s));
-  CHKERRQ(ierr);
-
-  PetscFunctionReturn(s->precon(x, y));
-}
-
-LaplaceXY::LaplaceXY(Mesh* m, Options* opt, const CELL_LOC loc)
-    : lib(opt == nullptr ? &(Options::root()["laplacexy"]) : opt),
-      localmesh(m == nullptr ? bout::globals::mesh : m), location(loc), monitor(*this) {
-  Timer timer("invert");
-
-  if (opt == nullptr) {
-    // If no options supplied, use default
-    opt = &(Options::root()["laplacexy"]);
-  }
-
-  finite_volume =
-      (*opt)["finite_volume"]
-          .doc("Use finite volume rather than finite difference discretisation.")
-          .withDefault(true);
-
-  ///////////////////////////////////////////////////
-  // Boundary condititions options
-  if (localmesh->periodicY(localmesh->xstart)) {
-    // Periodic in Y, so in the core
-    x_inner_dirichlet = (*opt)["core_bndry_dirichlet"].withDefault(false);
-  } else {
-    // Non-periodic, so in the PF region
-    x_inner_dirichlet = (*opt)["pf_bndry_dirichlet"].withDefault(true);
-  }
-  if ((*opt)["y_bndry_dirichlet"].isSet()) {
-    throw BoutException("y_bndry_dirichlet has been deprecated. Use y_bndry=dirichlet "
-                        "instead.");
-  } else {
-    y_bndry = (*opt)["y_bndry"].withDefault("neumann");
-  }
-
-  // Check value of y_bndry is a supported option
-  if (not(y_bndry == "dirichlet" or y_bndry == "neumann" or y_bndry == "free_o3")) {
-
-    throw BoutException("Unrecognized option '{}' for laplacexy:ybndry", y_bndry);
-  }
-
-  if (not finite_volume) {
-    // Check we can use corner cells
-    if (not localmesh->include_corner_cells) {
-      throw BoutException(
-          "Finite difference form of LaplaceXY allows non-orthogonal x- and "
-          "y-directions, so requires mesh:include_corner_cells=true.");
-    }
-  }
-
-  // Use name of options section as the default prefix for performance logging variables
-  default_prefix = opt->name();
-
-  // Get MPI communicator
-  auto comm = BoutComm::get();
-
-  // Local size
-  const int localN = localSize();
-
-  // Create Vectors
-  VecCreate(comm, &xs);
-  VecSetSizes(xs, localN, PETSC_DETERMINE);
-  VecSetFromOptions(xs);
-  VecDuplicate(xs, &bs);
-
-  // Set size of Matrix on each processor to localN x localN
-  MatCreate(comm, &MatA);
-  MatSetSizes(MatA, localN, localN, PETSC_DETERMINE, PETSC_DETERMINE);
-  MatSetFromOptions(MatA);
-
-  //////////////////////////////////////////////////
-  // Specify local indices. This creates a mapping
-  // from local indices to index, using a Field2D object
-
-  indexXY = -1; // Set all points to -1, indicating out of domain
-
-  int ind = 0;
-
-  // Y boundaries
-  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-    // Should not go into corner cells, LaplaceXY stencil does not include them
-    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-      continue;
-    }
-    indexXY(it.ind, localmesh->ystart - 1) = ind++;
-  }
-  if ((not finite_volume) and localmesh->hasBndryLowerY()) {
-    // Corner boundary cells
-    if (localmesh->firstX()) {
-      indexXY(localmesh->xstart - 1, localmesh->ystart - 1) = ind++;
-    }
-    if (localmesh->lastX()) {
-      indexXY(localmesh->xend + 1, localmesh->ystart - 1) = ind++;
-    }
-  }
-  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-    // Should not go into corner cells, LaplaceXY stencil does not include them
-    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-      continue;
-    }
-    indexXY(it.ind, localmesh->yend + 1) = ind++;
-  }
-  if ((not finite_volume) and localmesh->hasBndryUpperY()) {
-    // Corner boundary cells
-    if (localmesh->firstX()) {
-      indexXY(localmesh->xstart - 1, localmesh->yend + 1) = ind++;
-    }
-    if (localmesh->lastX()) {
-      indexXY(localmesh->xend + 1, localmesh->yend + 1) = ind++;
-    }
-  }
-
-  xstart = localmesh->xstart;
-  if (localmesh->firstX()) {
-    xstart -= 1; // Include X guard cells
-  }
-  xend = localmesh->xend;
-  if (localmesh->lastX()) {
-    xend += 1;
-  }
-  for (int x = xstart; x <= xend; x++) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      indexXY(x, y) = ind++;
-    }
-  }
-
-  ASSERT1(ind == localN); // Reached end of range
-
-  //////////////////////////////////////////////////
-  // Allocate storage for preconditioner
-
-  nloc = xend - xstart + 1;                       // Number of X points on this processor
-  nsys = localmesh->yend - localmesh->ystart + 1; // Number of separate Y slices
-
-  acoef.reallocate(nsys, nloc);
-  bcoef.reallocate(nsys, nloc);
-  ccoef.reallocate(nsys, nloc);
-  xvals.reallocate(nsys, nloc);
-  bvals.reallocate(nsys, nloc);
-
-  // Create a cyclic reduction object
-  cr = bout::utils::make_unique<CyclicReduce<BoutReal>>(localmesh->getXcomm(), nloc);
-
-  //////////////////////////////////////////////////
-  // Pre-allocate PETSc storage
-
-  PetscInt *d_nnz, *o_nnz;
-  PetscMalloc((localN) * sizeof(PetscInt), &d_nnz);
-  PetscMalloc((localN) * sizeof(PetscInt), &o_nnz);
-
-  if (finite_volume) {
-    setPreallocationFiniteVolume(d_nnz, o_nnz);
-  } else {
-    setPreallocationFiniteDifference(d_nnz, o_nnz);
-  }
-  // Pre-allocate
-  MatMPIAIJSetPreallocation(MatA, 0, d_nnz, 0, o_nnz);
-  MatSetUp(MatA);
-
-  PetscFree(d_nnz);
-  PetscFree(o_nnz);
-
-  // Determine which row/columns of the matrix are locally owned
-  int Istart, Iend;
-  MatGetOwnershipRange(MatA, &Istart, &Iend);
-
-  // Convert indexXY from local index to global index
-  indexXY += Istart;
-
-  // Now communicate to fill guard cells
-  // Note, this includes corner cells if necessary
-  localmesh->communicate(indexXY);
-
-  //////////////////////////////////////////////////
-  // Set up KSP
-
-  // Declare KSP Context
-  KSPCreate(comm, &ksp);
-
-  // Configure Linear Solver
-
-  const bool direct = (*opt)["direct"].doc("Use a direct LU solver").withDefault(false);
-
-  if (direct) {
-    KSPGetPC(ksp, &pc);
-    PCSetType(pc, PCLU);
-#if PETSC_VERSION_GE(3, 9, 0)
-    PCFactorSetMatSolverType(pc, "mumps");
-#else
-    PCFactorSetMatSolverPackage(pc, "mumps");
-#endif
-  } else {
-
-    // Convergence Parameters. Solution is considered converged if |r_k| < max( rtol * |b| , atol )
-    // where r_k = b - Ax_k. The solution is considered diverged if |r_k| > dtol * |b|.
-
-    const BoutReal rtol = (*opt)["rtol"].doc("Relative tolerance").withDefault(1e-5);
-    const BoutReal atol =
-        (*opt)["atol"]
-            .doc("Absolute tolerance. The solution is considered converged if |Ax-b| "
-                 "< max( rtol * |b| , atol )")
-            .withDefault(1e-10);
-    const BoutReal dtol =
-        (*opt)["dtol"]
-            .doc("The solution is considered diverged if |Ax-b| > dtol * |b|")
-            .withDefault(1e3);
-    const int maxits = (*opt)["maxits"].doc("Maximum iterations").withDefault(100000);
-
-    // Get KSP Solver Type
-    const std::string ksptype =
-        (*opt)["ksptype"].doc("KSP solver type").withDefault("gmres");
-
-    // Get PC type
-    const std::string pctype =
-        (*opt)["pctype"].doc("Preconditioner type").withDefault("none");
-
-    KSPSetType(ksp, ksptype.c_str());
-    KSPSetTolerances(ksp, rtol, atol, dtol, maxits);
-
-    KSPSetInitialGuessNonzero(ksp, static_cast<PetscBool>(true));
-
-    KSPGetPC(ksp, &pc);
-    PCSetType(pc, pctype.c_str());
-
-    if (pctype == "shell") {
-      // Using tridiagonal solver as preconditioner
-      PCShellSetApply(pc, laplacePCapply);
-      PCShellSetContext(pc, this);
-
-      const bool rightprec =
-          (*opt)["rightprec"].doc("Use right preconditioning?").withDefault(true);
-      if (rightprec) {
-        KSPSetPCSide(ksp, PC_RIGHT); // Right preconditioning
-      } else {
-        KSPSetPCSide(ksp, PC_LEFT); // Left preconditioning
-      }
-    }
-  }
-
-  lib.setOptionsFromInputFile(ksp);
-
-  ///////////////////////////////////////////////////
-  // Including Y derivatives?
-
-  include_y_derivs = (*opt)["include_y_derivs"]
-                         .doc("Include Y derivatives in operator to invert?")
-                         .withDefault(true);
-
-  ///////////////////////////////////////////////////
-  // Set the default coefficients
-  Field2D one(1., localmesh);
-  Field2D zero(0., localmesh);
-  one.setLocation(location);
-  zero.setLocation(location);
-  setCoefs(one, zero);
-}
-
-void LaplaceXY::setPreallocationFiniteVolume(PetscInt* d_nnz, PetscInt* o_nnz) {
-  const int localN = localSize();
-
-  // This discretisation uses a 5-point stencil
-  for (int i = 0; i < localN; i++) {
-    // Non-zero elements on this processor
-    d_nnz[i] = 5; // Star pattern in 2D
-    // Non-zero elements on neighboring processor
-    o_nnz[i] = 0;
-  }
-
-  // X boundaries
-  if (localmesh->firstX()) {
-    // Lower X boundary
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int localIndex = globalIndex(localmesh->xstart - 1, y);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-
-      d_nnz[localIndex] = 2; // Diagonal sub-matrix
-      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
-    }
-  } else {
-    // On another processor
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int localIndex = globalIndex(localmesh->xstart, y);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] -= 1;
-      o_nnz[localIndex] += 1;
-    }
-  }
-  if (localmesh->lastX()) {
-    // Upper X boundary
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int localIndex = globalIndex(localmesh->xend + 1, y);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] = 2; // Diagonal sub-matrix
-      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
-    }
-  } else {
-    // On another processor
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int localIndex = globalIndex(localmesh->xend, y);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] -= 1;
-      o_nnz[localIndex] += 1;
-    }
-  }
-  // Y boundaries
-
-  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    // Default to no boundary
-    // NOTE: This assumes that communications in Y are to other
-    //   processors. If Y is communicated with this processor (e.g. NYPE=1)
-    //   then this will result in PETSc warnings about out of range allocations
-    {
-      const int localIndex = globalIndex(x, localmesh->ystart);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      // d_nnz[localIndex] -= 1;  // Note: Slightly inefficient
-      o_nnz[localIndex] += 1;
-    }
-    {
-      const int localIndex = globalIndex(x, localmesh->yend);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      // d_nnz[localIndex] -= 1; // Note: Slightly inefficient
-      o_nnz[localIndex] += 1;
-    }
-  }
-
-  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-    // Should not go into corner cells, LaplaceXY stencil does not include them
-    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-      continue;
-    }
-    {
-      const int localIndex = globalIndex(it.ind, localmesh->ystart - 1);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] = 2; // Diagonal sub-matrix
-      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
-    }
-    {
-      const int localIndex = globalIndex(it.ind, localmesh->ystart);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] += 1;
-      o_nnz[localIndex] -= 1;
-    }
-  }
-  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-    // Should not go into corner cells, LaplaceXY stencil does not include them
-    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-      continue;
-    }
-    {
-      const int localIndex = globalIndex(it.ind, localmesh->yend + 1);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] = 2; // Diagonal sub-matrix
-      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
-    }
-    {
-      const int localIndex = globalIndex(it.ind, localmesh->yend);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] += 1;
-      o_nnz[localIndex] -= 1;
-    }
-  }
-}
-
-void LaplaceXY::setPreallocationFiniteDifference(PetscInt* d_nnz, PetscInt* o_nnz) {
-  const int localN = localSize();
-
-  // This discretisation uses a 9-point stencil
-  for (int i = 0; i < localN; i++) {
-    // Non-zero elements on this processor
-    d_nnz[i] = 9; // Square pattern in 2D
-    // Non-zero elements on neighboring processor
-    o_nnz[i] = 0;
-  }
-
-  // X boundaries
-  if (localmesh->firstX()) {
-    // Lower X boundary
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int localIndex = globalIndex(localmesh->xstart - 1, y);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-
-      d_nnz[localIndex] = 2; // Diagonal sub-matrix
-      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
-    }
-  } else {
-    // On another processor
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int localIndex = globalIndex(localmesh->xstart, y);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] -= 3;
-      o_nnz[localIndex] += 3;
-    }
-  }
-  if (localmesh->lastX()) {
-    // Upper X boundary
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int localIndex = globalIndex(localmesh->xend + 1, y);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] = 2; // Diagonal sub-matrix
-      o_nnz[localIndex] = 0; // Off-diagonal sub-matrix
-    }
-  } else {
-    // On another processor
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int localIndex = globalIndex(localmesh->xend, y);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] -= 3;
-      o_nnz[localIndex] += 3;
-    }
-  }
-  // Y boundaries
-  const int y_bndry_stencil_size = (y_bndry == "free_o3") ? 4 : 2;
-
-  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    // Default to no boundary
-    // NOTE: This assumes that communications in Y are to other
-    //   processors. If Y is communicated with this processor (e.g. NYPE=1)
-    //   then this will result in PETSc warnings about out of range allocations
-    {
-      const int localIndex = globalIndex(x, localmesh->ystart);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      // d_nnz[localIndex] -= 3;  // Note: Slightly inefficient
-      o_nnz[localIndex] += 3;
-    }
-    {
-      const int localIndex = globalIndex(x, localmesh->yend);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      // d_nnz[localIndex] -= 3; // Note: Slightly inefficient
-      o_nnz[localIndex] += 3;
-    }
-  }
-
-  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-    // Should not go into corner cells, they are handled specially below
-    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-      continue;
-    }
-    {
-      const int localIndex = globalIndex(it.ind, localmesh->ystart - 1);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] = y_bndry_stencil_size; // Diagonal sub-matrix
-      o_nnz[localIndex] = 0;                    // Off-diagonal sub-matrix
-    }
-    {
-      const int localIndex = globalIndex(it.ind, localmesh->ystart);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      //d_nnz[localIndex] += 3;
-      o_nnz[localIndex] -= 3;
-    }
-  }
-  if (localmesh->hasBndryLowerY()) {
-    if (y_bndry == "dirichlet") {
-      // special handling for the corners, since we use a free_o3 y-boundary
-      // condition just in the corners when y_bndry=="dirichlet"
-      if (localmesh->firstX()) {
-        const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
-        ASSERT1((localIndex >= 0) && (localIndex < localN));
-        d_nnz[localIndex] = 4;
-      }
-      if (localmesh->lastX()) {
-        const int localIndex = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
-        ASSERT1((localIndex >= 0) && (localIndex < localN));
-        d_nnz[localIndex] = 4;
-      }
-    } else {
-      if (localmesh->firstX()) {
-        const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
-        ASSERT1((localIndex >= 0) && (localIndex < localN));
-        d_nnz[localIndex] = y_bndry_stencil_size;
-      }
-      if (localmesh->lastX()) {
-        const int localIndex = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
-        ASSERT1((localIndex >= 0) && (localIndex < localN));
-        d_nnz[localIndex] = y_bndry_stencil_size;
-      }
-    }
-  }
-  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-    // Should not go into corner cells, they are handled specially below
-    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-      continue;
-    }
-    {
-      const int localIndex = globalIndex(it.ind, localmesh->yend + 1);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      d_nnz[localIndex] = y_bndry_stencil_size; // Diagonal sub-matrix
-      o_nnz[localIndex] = 0;                    // Off-diagonal sub-matrix
-    }
-    {
-      const int localIndex = globalIndex(it.ind, localmesh->yend);
-      ASSERT1((localIndex >= 0) && (localIndex < localN));
-      //d_nnz[localIndex] += 3;
-      o_nnz[localIndex] -= 3;
-    }
-  }
-  if (localmesh->hasBndryUpperY()) {
-    if (y_bndry == "dirichlet") {
-      // special handling for the corners, since we use a free_o3 y-boundary
-      // condition just in the corners when y_bndry=="dirichlet"
-      if (localmesh->firstX()) {
-        const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
-        ASSERT1((localIndex >= 0) && (localIndex < localN));
-        d_nnz[localIndex] = 4;
-      }
-      if (localmesh->lastX()) {
-        const int localIndex = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
-        ASSERT1((localIndex >= 0) && (localIndex < localN));
-        d_nnz[localIndex] = 4;
-      }
-    } else {
-      if (localmesh->firstX()) {
-        const int localIndex = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
-        ASSERT1((localIndex >= 0) && (localIndex < localN));
-        d_nnz[localIndex] = y_bndry_stencil_size;
-      }
-      if (localmesh->lastX()) {
-        const int localIndex = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
-        ASSERT1((localIndex >= 0) && (localIndex < localN));
-        d_nnz[localIndex] = y_bndry_stencil_size;
-      }
-    }
-  }
-}
-
-void LaplaceXY::setCoefs(const Field2D& A, const Field2D& B) {
-  Timer timer("invert");
-
-  ASSERT1(A.getMesh() == localmesh);
-  ASSERT1(B.getMesh() == localmesh);
-  ASSERT1(A.getLocation() == location);
-  ASSERT1(B.getLocation() == location);
-
-  if (finite_volume) {
-    setMatrixElementsFiniteVolume(A, B);
-  } else {
-    setMatrixElementsFiniteDifference(A, B);
-  }
-
-  // X boundaries
-  if (localmesh->firstX()) {
-    if (x_inner_dirichlet) {
-
-      // Dirichlet on inner X boundary
-      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-        int row = globalIndex(localmesh->xstart - 1, y);
-        PetscScalar val = 0.5;
-        MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-        int col = globalIndex(localmesh->xstart, y);
-        MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-        // Preconditioner
-        bcoef(y - localmesh->ystart, 0) = 0.5;
-        ccoef(y - localmesh->ystart, 0) = 0.5;
-      }
-
-    } else {
-
-      // Neumann on inner X boundary
-      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-        int row = globalIndex(localmesh->xstart - 1, y);
-        PetscScalar val = 1.0;
-        MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-        int col = globalIndex(localmesh->xstart, y);
-        val = -1.0;
-        MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-        // Preconditioner
-        bcoef(y - localmesh->ystart, 0) = 1.0;
-        ccoef(y - localmesh->ystart, 0) = -1.0;
-      }
-    }
-  }
-  if (localmesh->lastX()) {
-    // Dirichlet on outer X boundary
-
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      int row = globalIndex(localmesh->xend + 1, y);
-      PetscScalar val = 0.5;
-      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-      int col = globalIndex(localmesh->xend, y);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-      // Preconditioner
-      acoef(y - localmesh->ystart, localmesh->xend + 1 - xstart) = 0.5;
-      bcoef(y - localmesh->ystart, localmesh->xend + 1 - xstart) = 0.5;
-    }
-  }
-
-  if (y_bndry == "dirichlet") {
-    // Dirichlet on Y boundaries
-    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int row = globalIndex(it.ind, localmesh->ystart - 1);
-      PetscScalar val = 0.5;
-      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-      int col = globalIndex(it.ind, localmesh->ystart);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-    }
-
-    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int row = globalIndex(it.ind, localmesh->yend + 1);
-      PetscScalar val = 0.5;
-      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-      int col = globalIndex(it.ind, localmesh->yend);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-    }
-  } else if (y_bndry == "neumann") {
-    // Neumann on Y boundaries
-    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int row = globalIndex(it.ind, localmesh->ystart - 1);
-      PetscScalar val = 1.0;
-      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-      val = -1.0;
-      int col = globalIndex(it.ind, localmesh->ystart);
-
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-    }
-
-    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int row = globalIndex(it.ind, localmesh->yend + 1);
-      PetscScalar val = 1.0;
-      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-      val = -1.0;
-      int col = globalIndex(it.ind, localmesh->yend);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-    }
-  } else if (y_bndry == "free_o3") {
-    // 'free_o3' extrapolating boundary condition on Y boundaries
-    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int row = globalIndex(it.ind, localmesh->ystart - 1);
-      PetscScalar val = 1.0;
-      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-      val = -3.0;
-      int col = globalIndex(it.ind, localmesh->ystart);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-      val = 3.0;
-      col = globalIndex(it.ind, localmesh->ystart + 1);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-      val = -1.0;
-      col = globalIndex(it.ind, localmesh->ystart + 2);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-    }
-
-    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int row = globalIndex(it.ind, localmesh->yend + 1);
-      PetscScalar val = 1.0;
-      MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-      val = -3.0;
-      int col = globalIndex(it.ind, localmesh->yend);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-      val = 3.0;
-      col = globalIndex(it.ind, localmesh->yend - 1);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-      val = -1.0;
-      col = globalIndex(it.ind, localmesh->yend - 2);
-      MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-    }
-  } else {
-    throw BoutException("Unsupported option for y_bndry");
-  }
-
-  if (not finite_volume) {
-    // Handle corner boundary cells in case we need to include D2DXDY
-    // Apply the y-boundary-condition to the cells in the x-boundary - this is an
-    // arbitrary choice, cf. connections around the X-point
-
-    if (localmesh->hasBndryLowerY()) {
-      if (localmesh->firstX()) {
-        if (y_bndry == "neumann") {
-          // Neumann y-bc
-          // f(xs-1,ys-1) = f(xs-1,ys)
-          PetscScalar val = 1.0;
-          int row = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
-          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-          val = -1.0;
-          int col = globalIndex(localmesh->xstart - 1, localmesh->ystart);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-        } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") {
-          // 'free_o3' extrapolating boundary condition on Y boundaries
-          // f(xs-1,ys-1) = 3*f(xs-1,ys) - 3*f(xs-1,ys+1) + f(xs-1,ys+2)
-          //
-          // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know
-          // what value to pass for the corner
-          PetscScalar val = 1.0;
-          int row = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
-          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-          val = -3.0;
-          int col = globalIndex(localmesh->xstart - 1, localmesh->ystart);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-          val = 3.0;
-          col = globalIndex(localmesh->xstart - 1, localmesh->ystart + 1);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-          val = -1.0;
-          col = globalIndex(localmesh->xstart - 1, localmesh->ystart + 2);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-        } else {
-          throw BoutException("Unsupported option for y_bndry");
-        }
-      }
-      if (localmesh->lastX()) {
-        if (y_bndry == "neumann") {
-          // Neumann y-bc
-          // f(xe+1,ys-1) = f(xe+1,ys)
-          PetscScalar val = 1.0;
-          int row = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
-          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-          val = -1.0;
-          int col = globalIndex(localmesh->xend + 1, localmesh->ystart);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-        } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") {
-          // 'free_o3' extrapolating boundary condition on Y boundaries
-          // f(xe+1,ys-1) = 3*f(xe+1,ys) - 3*f(xe+1,ys+1) + f(xe+1,ys+2)
-          //
-          // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know
-          // what value to pass for the corner
-          PetscScalar val = 1.0;
-          int row = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
-          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-          val = -3.0;
-          int col = globalIndex(localmesh->xend + 1, localmesh->ystart);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-          val = 3.0;
-          col = globalIndex(localmesh->xend + 1, localmesh->ystart + 1);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-          val = -1.0;
-          col = globalIndex(localmesh->xend + 1, localmesh->ystart + 2);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-        } else {
-          throw BoutException("Unsupported option for y_bndry");
-        }
-      }
-    }
-    if (localmesh->hasBndryUpperY()) {
-      if (localmesh->firstX()) {
-        if (y_bndry == "neumann") {
-          // Neumann y-bc
-          // f(xs-1,ys-1) = f(xs-1,ys)
-          PetscScalar val = 1.0;
-          int row = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
-          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-          val = -1.0;
-          int col = globalIndex(localmesh->xstart - 1, localmesh->yend);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-        } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") {
-          // 'free_o3' extrapolating boundary condition on Y boundaries
-          // f(xs-1,ys-1) = 3*f(xs-1,ys) - 3*f(xs-1,ys+1) + f(xs-1,ys+2)
-          //
-          // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know
-          // what value to pass for the corner
-          PetscScalar val = 1.0;
-          int row = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
-          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-          val = -3.0;
-          int col = globalIndex(localmesh->xstart - 1, localmesh->yend);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-          val = 3.0;
-          col = globalIndex(localmesh->xstart - 1, localmesh->yend - 1);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-          val = -1.0;
-          col = globalIndex(localmesh->xstart - 1, localmesh->yend - 2);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-        } else {
-          throw BoutException("Unsupported option for y_bndry");
-        }
-      }
-      if (localmesh->lastX()) {
-        if (y_bndry == "neumann") {
-          // Neumann y-bc
-          // f(xe+1,ys-1) = f(xe+1,ys)
-          PetscScalar val = 1.0;
-          int row = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
-          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-          val = -1.0;
-          int col = globalIndex(localmesh->xend + 1, localmesh->yend);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-        } else if (y_bndry == "free_o3" or y_bndry == "dirichlet") {
-          // 'free_o3' extrapolating boundary condition on Y boundaries
-          // f(xe+1,ys-1) = 3*f(xe+1,ys) - 3*f(xe+1,ys+1) + f(xe+1,ys+2)
-          //
-          // Use free_o3 at the corners for Dirichlet y-boundaries because we don't know
-          // what value to pass for the corner
-          PetscScalar val = 1.0;
-          int row = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
-          MatSetValues(MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
-
-          val = -3.0;
-          int col = globalIndex(localmesh->xend + 1, localmesh->yend);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-          val = 3.0;
-          col = globalIndex(localmesh->xend + 1, localmesh->yend - 1);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-          val = -1.0;
-          col = globalIndex(localmesh->xend + 1, localmesh->yend - 2);
-          MatSetValues(MatA, 1, &row, 1, &col, &val, INSERT_VALUES);
-        } else {
-          throw BoutException("Unsupported option for y_bndry");
-        }
-      }
-    }
-  }
-
-  // Assemble Matrix
-  MatAssemblyBegin(MatA, MAT_FINAL_ASSEMBLY);
-  MatAssemblyEnd(MatA, MAT_FINAL_ASSEMBLY);
-
-  // Set the operator
-#if PETSC_VERSION_GE(3, 5, 0)
-  KSPSetOperators(ksp, MatA, MatA);
-#else
-  KSPSetOperators(ksp, MatA, MatA, DIFFERENT_NONZERO_PATTERN);
-#endif
-
-  // Set coefficients for preconditioner
-  cr->setCoefs(acoef, bcoef, ccoef);
-}
-
-void LaplaceXY::setMatrixElementsFiniteVolume(const Field2D& A, const Field2D& B) {
-  //////////////////////////////////////////////////
-  // Set Matrix elements
-  //
-  // (1/J) d/dx ( J * g11 d/dx ) + (1/J) d/dy ( J * g22 d/dy )
-
-  auto coords = localmesh->getCoordinates(location);
-  const Field2D J_DC = DC(coords->J);
-  const Field2D g11_DC = DC(coords->g11);
-  const Field2D dx_DC = DC(coords->dx);
-  const Field2D dy_DC = DC(coords->dy);
-  const Field2D g_22_DC = DC(coords->g_22);
-  const Field2D g_23_DC = DC(coords->g_23);
-  const Field2D g23_DC = DC(coords->g23);
-
-  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      // stencil entries
-      PetscScalar c, xm, xp, ym, yp;
-
-      // XX component
-
-      // Metrics on x+1/2 boundary
-      BoutReal J = 0.5 * (J_DC(x, y) + J_DC(x + 1, y));
-      BoutReal g11 = 0.5 * (g11_DC(x, y) + g11_DC(x + 1, y));
-      BoutReal dx = 0.5 * (dx_DC(x, y) + dx_DC(x + 1, y));
-      BoutReal Acoef = 0.5 * (A(x, y) + A(x + 1, y));
-
-      BoutReal val = Acoef * J * g11 / (J_DC(x, y) * dx * dx_DC(x, y));
-      xp = val;
-      c = -val;
-
-      // Metrics on x-1/2 boundary
-      J = 0.5 * (J_DC(x, y) + J_DC(x - 1, y));
-      g11 = 0.5 * (g11_DC(x, y) + g11_DC(x - 1, y));
-      dx = 0.5 * (dx_DC(x, y) + dx_DC(x - 1, y));
-      Acoef = 0.5 * (A(x, y) + A(x - 1, y));
-
-      val = Acoef * J * g11 / (J_DC(x, y) * dx * dx_DC(x, y));
-      xm = val;
-      c -= val;
-
-      c += B(x, y);
-
-      // Put values into the preconditioner, X derivatives only
-      acoef(y - localmesh->ystart, x - xstart) = xm;
-      bcoef(y - localmesh->ystart, x - xstart) = c;
-      ccoef(y - localmesh->ystart, x - xstart) = xp;
-
-      if (include_y_derivs) {
-        // YY component
-        // Metrics at y+1/2
-        J = 0.5 * (J_DC(x, y) + J_DC(x, y + 1));
-        BoutReal g_22 = 0.5 * (g_22_DC(x, y) + g_22_DC(x, y + 1));
-        BoutReal g23 = 0.5 * (g23_DC(x, y) + g23_DC(x, y + 1));
-        BoutReal g_23 = 0.5 * (g_23_DC(x, y) + g_23_DC(x, y + 1));
-        BoutReal dy = 0.5 * (dy_DC(x, y) + dy_DC(x, y + 1));
-        Acoef = 0.5 * (A(x, y + 1) + A(x, y));
-
-        val = -Acoef * J * g23 * g_23 / (g_22 * J_DC(x, y) * dy * dy_DC(x, y));
-        yp = val;
-        c -= val;
-
-        // Metrics at y-1/2
-        J = 0.5 * (J_DC(x, y) + J_DC(x, y - 1));
-        g_22 = 0.5 * (g_22_DC(x, y) + g_22_DC(x, y - 1));
-        g23 = 0.5 * (g23_DC(x, y) + g23_DC(x, y - 1));
-        g_23 = 0.5 * (g_23_DC(x, y) + g_23_DC(x, y - 1));
-        dy = 0.5 * (dy_DC(x, y) + dy_DC(x, y - 1));
-        Acoef = 0.5 * (A(x, y - 1) + A(x, y));
-
-        val = -Acoef * J * g23 * g_23 / (g_22 * J_DC(x, y) * dy * dy_DC(x, y));
-        ym = val;
-        c -= val;
-      }
-
-      /////////////////////////////////////////////////
-      // Now have a 5-point stencil for the Laplacian
-
-      int row = globalIndex(x, y);
-
-      // Set the centre (diagonal)
-      MatSetValues(MatA, 1, &row, 1, &row, &c, INSERT_VALUES);
-
-      // X + 1
-      int col = globalIndex(x + 1, y);
-      MatSetValues(MatA, 1, &row, 1, &col, &xp, INSERT_VALUES);
-
-      // X - 1
-      col = globalIndex(x - 1, y);
-      MatSetValues(MatA, 1, &row, 1, &col, &xm, INSERT_VALUES);
-
-      if (include_y_derivs) {
-        // Y + 1
-        col = globalIndex(x, y + 1);
-        MatSetValues(MatA, 1, &row, 1, &col, &yp, INSERT_VALUES);
-
-        // Y - 1
-        col = globalIndex(x, y - 1);
-        MatSetValues(MatA, 1, &row, 1, &col, &ym, INSERT_VALUES);
-      }
-    }
-  }
-}
-
-void LaplaceXY::setMatrixElementsFiniteDifference(const Field2D& A, const Field2D& B) {
-  //////////////////////////////////////////////////
-  // Set Matrix elements
-  //
-  // Div(A Grad(f)) + B f
-  // = A Laplace_perp(f) + Grad_perp(A).Grad_perp(f) + B f
-  // = A*(G1*dfdx + (G2-1/J*d/dy(J/g_22))*dfdy
-  //      + g11*d2fdx2 + (g22-1/g_22)*d2fdy2 + 2*g12*d2fdxdy)
-  //   + g11*dAdx*dfdx + (g22-1/g_22)*dAdy*dfdy + g12*(dAdx*dfdy + dAdy*dfdx)
-  //   + B*f
-
-  auto coords = localmesh->getCoordinates(location);
-  const Field2D G1_2D = DC(coords->G1);
-  const Field2D G2_2D = DC(coords->G2);
-  const Field2D J_2D = DC(coords->J);
-  const Field2D g11_2D = DC(coords->g11);
-  const Field2D g_22_2D = DC(coords->g_22);
-  const Field2D g22_2D = DC(coords->g22);
-  const Field2D g12_2D = DC(coords->g12);
-  const Field2D d1_dx_2D = DC(coords->d1_dx);
-  const Field2D d1_dy_2D = DC(coords->d1_dy);
-  const Field2D dx_2D = DC(coords->dx);
-  const Field2D dy_2D = DC(coords->dy);
-
-  const Field2D coef_dfdy = G2_2D - DC(DDY(J_2D / g_22_2D) / J_2D);
-
-  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      // stencil entries
-      PetscScalar c, xm, xp, ym, yp, xpyp, xpym, xmyp, xmym;
-
-      BoutReal dx = dx_2D(x, y);
-
-      // A*G1*dfdx
-      BoutReal val = A(x, y) * G1_2D(x, y) / (2. * dx);
-      xp = val;
-      xm = -val;
-
-      // A*g11*d2fdx2
-      val = A(x, y) * g11_2D(x, y) / SQ(dx);
-      xp += val;
-      c = -2. * val;
-      xm += val;
-      // Non-uniform grid correction
-      val = A(x, y) * g11_2D(x, y) * d1_dx_2D(x, y) / (2. * dx);
-      xp += val;
-      xm -= val;
-
-      // g11*dAdx*dfdx
-      val = g11_2D(x, y) * (A(x + 1, y) - A(x - 1, y)) / (4. * SQ(dx));
-      xp += val;
-      xm -= val;
-
-      // B*f
-      c += B(x, y);
-
-      // Put values into the preconditioner, X derivatives only
-      acoef(y - localmesh->ystart, x - xstart) = xm;
-      bcoef(y - localmesh->ystart, x - xstart) = c;
-      ccoef(y - localmesh->ystart, x - xstart) = xp;
-
-      if (include_y_derivs) {
-        BoutReal dy = dy_2D(x, y);
-        BoutReal dAdx = (A(x + 1, y) - A(x - 1, y)) / (2. * dx);
-        BoutReal dAdy = (A(x, y + 1) - A(x, y - 1)) / (2. * dy);
-
-        // A*(G2-1/J*d/dy(J/g_22))*dfdy
-        val = A(x, y) * coef_dfdy(x, y) / (2. * dy);
-        yp = val;
-        ym = -val;
-
-        // A*(g22-1/g_22)*d2fdy2
-        val = A(x, y) * (g22_2D(x, y) - 1. / g_22_2D(x, y)) / SQ(dy);
-        yp += val;
-        c -= 2. * val;
-        ym += val;
-        // Non-uniform mesh correction
-        val = A(x, y) * (g22_2D(x, y) - 1. / g_22_2D(x, y)) * d1_dy_2D(x, y) / (2. * dy);
-        yp += val;
-        ym -= val;
-
-        // 2*A*g12*d2dfdxdy
-        val = A(x, y) * g12_2D(x, y) / (2. * dx * dy);
-        xpyp = val;
-        xpym = -val;
-        xmyp = -val;
-        xmym = val;
-
-        // g22*dAdy*dfdy
-        val = (g22_2D(x, y) - 1. / g_22_2D(x, y)) * dAdy / (2. * dy);
-        yp += val;
-        ym -= val;
-
-        // g12*(dAdx*dfdy + dAdy*dfdx)
-        val = g12_2D(x, y) * dAdx / (2. * dy);
-        yp += val;
-        ym -= val;
-        val = g12_2D(x, y) * dAdy / (2. * dx);
-        xp += val;
-        xm -= val;
-      }
-
-      /////////////////////////////////////////////////
-      // Now have a 9-point stencil for the Laplacian
-
-      int row = globalIndex(x, y);
-
-      // Set the centre (diagonal)
-      MatSetValues(MatA, 1, &row, 1, &row, &c, INSERT_VALUES);
-
-      // X + 1
-      int col = globalIndex(x + 1, y);
-      MatSetValues(MatA, 1, &row, 1, &col, &xp, INSERT_VALUES);
-
-      // X - 1
-      col = globalIndex(x - 1, y);
-      MatSetValues(MatA, 1, &row, 1, &col, &xm, INSERT_VALUES);
-
-      if (include_y_derivs) {
-        // Y + 1
-        col = globalIndex(x, y + 1);
-        MatSetValues(MatA, 1, &row, 1, &col, &yp, INSERT_VALUES);
-
-        // Y - 1
-        col = globalIndex(x, y - 1);
-        MatSetValues(MatA, 1, &row, 1, &col, &ym, INSERT_VALUES);
-
-        // X + 1, Y + 1
-        col = globalIndex(x + 1, y + 1);
-        MatSetValues(MatA, 1, &row, 1, &col, &xpyp, INSERT_VALUES);
-
-        // X + 1, Y - 1
-        col = globalIndex(x + 1, y - 1);
-        MatSetValues(MatA, 1, &row, 1, &col, &xpym, INSERT_VALUES);
-
-        // X - 1, Y + 1
-        col = globalIndex(x - 1, y + 1);
-        MatSetValues(MatA, 1, &row, 1, &col, &xmyp, INSERT_VALUES);
-
-        // X - 1, Y - 1
-        col = globalIndex(x - 1, y - 1);
-        MatSetValues(MatA, 1, &row, 1, &col, &xmym, INSERT_VALUES);
-      }
-    }
-  }
-}
-
-LaplaceXY::~LaplaceXY() {
-  PetscBool is_finalised;
-  PetscFinalized(&is_finalised);
-
-  if (!is_finalised) {
-    // PetscFinalize may already have destroyed this object
-    KSPDestroy(&ksp);
-  }
-
-  VecDestroy(&xs);
-  VecDestroy(&bs);
-  MatDestroy(&MatA);
-}
-
-const Field2D LaplaceXY::solve(const Field2D& rhs, const Field2D& x0) {
-  Timer timer("invert");
-
-  ASSERT1(rhs.getMesh() == localmesh);
-  ASSERT1(x0.getMesh() == localmesh);
-  ASSERT1(rhs.getLocation() == location);
-  ASSERT1(x0.getLocation() == location);
-
-  // Load initial guess x0 into xs and rhs into bs
-
-  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      int ind = globalIndex(x, y);
-
-      PetscScalar val = x0(x, y);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      val = rhs(x, y);
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-  }
-
-  if (finite_volume) {
-    solveFiniteVolume(x0);
-  } else {
-    solveFiniteDifference(x0);
-  }
-
-  // Assemble RHS Vector
-  VecAssemblyBegin(bs);
-  VecAssemblyEnd(bs);
-
-  // Assemble Trial Solution Vector
-  VecAssemblyBegin(xs);
-  VecAssemblyEnd(xs);
-
-  // Solve the system
-  KSPSolve(ksp, bs, xs);
-
-  KSPConvergedReason reason;
-  KSPGetConvergedReason(ksp, &reason);
-
-  if (reason <= 0) {
-    throw BoutException("LaplaceXY failed to converge. Reason {} ({:d})",
-                        KSPConvergedReasons[reason], static_cast<int>(reason));
-  }
-
-  if (save_performance) {
-    // Update performance monitoring information
-    n_calls++;
-
-    int iterations = 0;
-    KSPGetIterationNumber(ksp, &iterations);
-
-    average_iterations = BoutReal(n_calls - 1) / BoutReal(n_calls) * average_iterations
-                         + BoutReal(iterations) / BoutReal(n_calls);
-  }
-
-  //////////////////////////
-  // Copy data into result
-
-  Field2D result;
-  result.allocate();
-  result.setLocation(location);
-
-  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      int ind = globalIndex(x, y);
-
-      PetscScalar val;
-      VecGetValues(xs, 1, &ind, &val);
-      result(x, y) = val;
-    }
-  }
-
-  // Inner X boundary
-  if (localmesh->firstX()) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      int ind = globalIndex(localmesh->xstart - 1, y);
-      PetscScalar val;
-      VecGetValues(xs, 1, &ind, &val);
-      for (int x = localmesh->xstart - 1; x >= 0; x--) {
-        result(x, y) = val;
-      }
-    }
-  }
-
-  // Outer X boundary
-  if (localmesh->lastX()) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      int ind = globalIndex(localmesh->xend + 1, y);
-      PetscScalar val;
-      VecGetValues(xs, 1, &ind, &val);
-      for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
-        result(x, y) = val;
-      }
-    }
-  }
-
-  // Lower Y boundary
-  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-    if (
-        // Should not go into corner cells, finite-volume LaplaceXY stencil does not include
-        // them
-        (finite_volume and (it.ind < localmesh->xstart or it.ind > localmesh->xend))
-
-        // Only go into first corner cell for finite-difference
-        or (it.ind < localmesh->xstart - 1 or it.ind > localmesh->xend + 1)) {
-      continue;
-    }
-    int ind = globalIndex(it.ind, localmesh->ystart - 1);
-    PetscScalar val;
-    VecGetValues(xs, 1, &ind, &val);
-    for (int y = localmesh->ystart - 1; y >= 0; y--) {
-      result(it.ind, y) = val;
-    }
-  }
-
-  // Upper Y boundary
-  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-    if (
-        // Should not go into corner cells, finite-volume LaplaceXY stencil does not include
-        // them
-        (finite_volume and (it.ind < localmesh->xstart or it.ind > localmesh->xend))
-
-        // Only go into first corner cell for finite-difference
-        or (it.ind < localmesh->xstart - 1 or it.ind > localmesh->xend + 1)) {
-      continue;
-    }
-    int ind = globalIndex(it.ind, localmesh->yend + 1);
-    PetscScalar val;
-    VecGetValues(xs, 1, &ind, &val);
-    for (int y = localmesh->yend + 1; y < localmesh->LocalNy; y++) {
-      result(it.ind, y) = val;
-    }
-  }
-
-  return result;
-}
-
-void LaplaceXY::solveFiniteVolume(const Field2D& x0) {
-  // Use original LaplaceXY implementation of passing boundary values for backward
-  // compatibility
-  if (localmesh->firstX()) {
-    if (x_inner_dirichlet) {
-      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-        int ind = globalIndex(localmesh->xstart - 1, y);
-
-        PetscScalar val = x0(localmesh->xstart - 1, y);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        val = 0.5 * (x0(localmesh->xstart - 1, y) + x0(localmesh->xstart, y));
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    } else {
-      // Inner X boundary (Neumann)
-      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-        int ind = globalIndex(localmesh->xstart - 1, y);
-
-        PetscScalar val = x0(localmesh->xstart - 1, y);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        val = 0.0; // x0(localmesh->xstart-1,y) - x0(localmesh->xstart,y);
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    }
-  }
-
-  // Outer X boundary (Dirichlet)
-  if (localmesh->lastX()) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      int ind = globalIndex(localmesh->xend + 1, y);
-
-      PetscScalar val = x0(localmesh->xend + 1, y);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      val = 0.5 * (x0(localmesh->xend, y) + x0(localmesh->xend + 1, y));
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-  }
-
-  if (y_bndry == "dirichlet") {
-    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->ystart - 1);
-
-      PetscScalar val = x0(it.ind, localmesh->ystart - 1);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      val = 0.5 * (x0(it.ind, localmesh->ystart - 1) + x0(it.ind, localmesh->ystart));
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-
-    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->yend + 1);
-
-      PetscScalar val = x0(it.ind, localmesh->yend + 1);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      val = 0.5 * (x0(it.ind, localmesh->yend + 1) + x0(it.ind, localmesh->yend));
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-  } else if (y_bndry == "neumann" or y_bndry == "free_o3") {
-    // Y boundaries Neumann
-    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->ystart - 1);
-
-      PetscScalar val = x0(it.ind, localmesh->ystart - 1);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      val = 0.0;
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-
-    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-      // Should not go into corner cells, LaplaceXY stencil does not include them
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->yend + 1);
-
-      PetscScalar val = x0(it.ind, localmesh->yend + 1);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      val = 0.0;
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-  } else {
-    throw BoutException("Unsupported option for y_bndry");
-  }
-}
-
-void LaplaceXY::solveFiniteDifference(const Field2D& x0) {
-  // For finite-difference implementation pass boundary values in the same way as for
-  // the 'Laplacian' solvers - the value to use (for Dirichlet boundary conditions) on
-  // the boundary (which is half way between grid cell and boundary cell) is passed as
-  // the value in the first boundary cell.
-  if (localmesh->firstX()) {
-    if (x_inner_dirichlet) {
-      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-        int ind = globalIndex(localmesh->xstart - 1, y);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = 2. * x0(localmesh->xstart - 1, y) - x0(localmesh->xstart, y);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Pass the value from boundary cell of x0 as the boundary condition to the rhs
-        val = x0(localmesh->xstart - 1, y);
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    } else {
-      // Inner X boundary (Neumann)
-      for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-        int ind = globalIndex(localmesh->xstart - 1, y);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = x0(localmesh->xstart, y);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    }
-  }
-
-  // Outer X boundary (Dirichlet)
-  if (localmesh->lastX()) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      int ind = globalIndex(localmesh->xend + 1, y);
-
-      // For the boundary value of the initial guess, use the value that would be set by
-      // applying the boundary condition to the initial guess
-      PetscScalar val = 2. * x0(localmesh->xend + 1, y) - x0(localmesh->xend, y);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      // Pass the value from boundary cell of x0 as the boundary condition to the rhs
-      val = x0(localmesh->xend + 1, y);
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-  }
-
-  if (y_bndry == "dirichlet") {
-    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-      // Should not go into corner cells, they are treated specially below
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->ystart - 1);
-
-      // For the boundary value of the initial guess, use the value that would be set by
-      // applying the boundary condition to the initial guess
-      PetscScalar val =
-          2. * x0(it.ind, localmesh->ystart - 1) - x0(it.ind, localmesh->ystart);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      // Pass the value from boundary cell of x0 as the boundary condition to the rhs
-      val = x0(it.ind, localmesh->ystart - 1);
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-
-    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-      // Should not go into corner cells, they are treated specially below
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->yend + 1);
-
-      // For the boundary value of the initial guess, use the value that would be set by
-      // applying the boundary condition to the initial guess
-      PetscScalar val =
-          2. * x0(it.ind, localmesh->yend + 1) - x0(it.ind, localmesh->yend);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      // Pass the value from boundary cell of x0 as the boundary condition to the rhs
-      val = x0(it.ind, localmesh->yend + 1);
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-
-    // Use free_o3 for the corner boundary cells
-    if (localmesh->hasBndryLowerY()) {
-      if (localmesh->firstX()) {
-        int ind = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = 3. * x0(localmesh->xstart - 1, localmesh->ystart)
-                          - 3. * x0(localmesh->xstart - 1, localmesh->ystart + 1)
-                          + x0(localmesh->xstart - 1, localmesh->ystart + 2);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-      if (localmesh->lastX()) {
-        int ind = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = 3. * x0(localmesh->xend + 1, localmesh->ystart)
-                          - 3. * x0(localmesh->xend + 1, localmesh->ystart + 1)
-                          + x0(localmesh->xend + 1, localmesh->ystart + 2);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    }
-    if (localmesh->hasBndryUpperY()) {
-      if (localmesh->firstX()) {
-        int ind = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = 3. * x0(localmesh->xstart - 1, localmesh->yend)
-                          - 3. * x0(localmesh->xstart - 1, localmesh->yend - 1)
-                          + x0(localmesh->xstart - 1, localmesh->yend - 2);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-      if (localmesh->lastX()) {
-        int ind = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = 3. * x0(localmesh->xend + 1, localmesh->yend)
-                          - 3. * x0(localmesh->xend + 1, localmesh->yend - 1)
-                          + x0(localmesh->xend + 1, localmesh->yend - 2);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    }
-  } else if (y_bndry == "neumann") {
-    // Y boundaries Neumann
-    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-      // Should not go into corner cells, they are treated specially below
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->ystart - 1);
-
-      // For the boundary value of the initial guess, use the value that would be set by
-      // applying the boundary condition to the initial guess
-      PetscScalar val = x0(it.ind, localmesh->ystart);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      // Set the value for the rhs of the boundary condition to zero
-      val = 0.0;
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-    if (localmesh->hasBndryLowerY()) {
-      if (localmesh->firstX()) {
-        int ind = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = x0(localmesh->xstart - 1, localmesh->ystart);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-      if (localmesh->lastX()) {
-        int ind = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = x0(localmesh->xend + 1, localmesh->ystart);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    }
-
-    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-      // Should not go into corner cells, they are treated specially below
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->yend + 1);
-
-      // For the boundary value of the initial guess, use the value that would be set by
-      // applying the boundary condition to the initial guess
-      PetscScalar val = x0(it.ind, localmesh->yend);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      // Set the value for the rhs of the boundary condition to zero
-      val = 0.0;
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-    if (localmesh->hasBndryUpperY()) {
-      if (localmesh->firstX()) {
-        int ind = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = x0(localmesh->xstart - 1, localmesh->yend);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-      if (localmesh->lastX()) {
-        int ind = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = x0(localmesh->xend + 1, localmesh->yend);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    }
-  } else if (y_bndry == "free_o3") {
-    // Y boundaries free_o3
-    for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-      // Should not go into corner cells, they are treated specially below
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->ystart - 1);
-
-      // For the boundary value of the initial guess, use the value that would be set by
-      // applying the boundary condition to the initial guess
-      PetscScalar val = 3. * x0(it.ind, localmesh->ystart)
-                        - 3. * x0(it.ind, localmesh->ystart + 1)
-                        + x0(it.ind, localmesh->ystart + 2);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      // Set the value for the rhs of the boundary condition to zero
-      val = 0.0;
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-    if (localmesh->hasBndryLowerY()) {
-      if (localmesh->firstX()) {
-        int ind = globalIndex(localmesh->xstart - 1, localmesh->ystart - 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = 3. * x0(localmesh->xstart - 1, localmesh->ystart)
-                          - 3. * x0(localmesh->xstart - 1, localmesh->ystart + 1)
-                          + x0(localmesh->xstart - 1, localmesh->ystart + 2);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-      if (localmesh->lastX()) {
-        int ind = globalIndex(localmesh->xend + 1, localmesh->ystart - 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = 3. * x0(localmesh->xend + 1, localmesh->ystart)
-                          - 3. * x0(localmesh->xend + 1, localmesh->ystart + 1)
-                          + x0(localmesh->xend + 1, localmesh->ystart + 2);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    }
-
-    for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-      // Should not go into corner cells, they are treated specially below
-      if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-        continue;
-      }
-      int ind = globalIndex(it.ind, localmesh->yend + 1);
-
-      // For the boundary value of the initial guess, use the value that would be set by
-      // applying the boundary condition to the initial guess
-      PetscScalar val = 3. * x0(it.ind, localmesh->yend)
-                        - 3. * x0(it.ind, localmesh->yend - 1)
-                        + x0(it.ind, localmesh->yend - 2);
-      VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-      // Set the value for the rhs of the boundary condition to zero
-      val = 0.0;
-      VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-    }
-    if (localmesh->hasBndryUpperY()) {
-      if (localmesh->firstX()) {
-        int ind = globalIndex(localmesh->xstart - 1, localmesh->yend + 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = 3. * x0(localmesh->xstart - 1, localmesh->yend)
-                          - 3. * x0(localmesh->xstart - 1, localmesh->yend - 1)
-                          + x0(localmesh->xstart - 1, localmesh->yend - 2);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-      if (localmesh->lastX()) {
-        int ind = globalIndex(localmesh->xend + 1, localmesh->yend + 1);
-
-        // For the boundary value of the initial guess, use the value that would be set by
-        // applying the boundary condition to the initial guess
-        PetscScalar val = 3. * x0(localmesh->xend + 1, localmesh->yend)
-                          - 3. * x0(localmesh->xend + 1, localmesh->yend - 1)
-                          + x0(localmesh->xend + 1, localmesh->yend - 2);
-        VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
-
-        // Set the value for the rhs of the boundary condition to zero
-        val = 0.0;
-        VecSetValues(bs, 1, &ind, &val, INSERT_VALUES);
-      }
-    }
-  } else {
-    throw BoutException("Unsupported option for y_bndry");
-  }
-}
-
-/*! Preconditioner
- * NOTE: For generality, this routine does use globalIndex() in the inner loop, although
- * this may be slightly less efficient than incrementing an integer for the global index,
- * the finite-volume and finite-difference implementations have slightly different
- * indexing patterns, so incrementing an integer would be tricky.
- */
-int LaplaceXY::precon(Vec input, Vec result) {
-
-  for (auto itdwn = localmesh->iterateBndryLowerY(); !itdwn.isDone(); itdwn++) {
-    // Should not go into corner cells, LaplaceXY stencil does not include them
-    if (itdwn.ind < localmesh->xstart or itdwn.ind > localmesh->xend) {
-      continue;
-    }
-    const int ind = globalIndex(itdwn.ind, localmesh->ystart - 1);
-    PetscScalar val;
-    VecGetValues(input, 1, &ind, &val);
-    VecSetValues(result, 1, &ind, &val, INSERT_VALUES);
-  }
-  for (auto itup = localmesh->iterateBndryUpperY(); !itup.isDone(); itup++) {
-    // Should not go into corner cells, LaplaceXY stencil does not include them
-    if (itup.ind < localmesh->xstart or itup.ind > localmesh->xend) {
-      continue;
-    }
-    const int ind = globalIndex(itup.ind, localmesh->yend + 1);
-    PetscScalar val;
-    VecGetValues(input, 1, &ind, &val);
-    VecSetValues(result, 1, &ind, &val, INSERT_VALUES);
-  }
-
-  // Load vector x into bvals array
-  for (int x = xstart; x <= xend; x++) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int ind = globalIndex(x, y);
-      PetscScalar val;
-      VecGetValues(input, 1, &ind, &val);
-      bvals(y - localmesh->ystart, x - xstart) = val;
-    }
-  }
-
-  // Solve tridiagonal systems using CR solver
-  cr->solve(bvals, xvals);
-
-  // Save result xvals into y array
-  for (int x = xstart; x <= xend; x++) {
-    for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
-      const int ind = globalIndex(x, y);
-      PetscScalar val = xvals(y - localmesh->ystart, x - xstart);
-      VecSetValues(result, 1, &ind, &val, INSERT_VALUES);
-    }
-  }
-  VecAssemblyBegin(result);
-  VecAssemblyEnd(result);
-  return 0;
-}
-
-///////////////////////////////////////////////////////////////
-
-int LaplaceXY::localSize() {
-
-  // Bulk of points
-  const int nx = localmesh->xend - localmesh->xstart + 1;
-  const int ny = localmesh->yend - localmesh->ystart + 1;
-
-  int n = nx * ny;
-
-  // X boundaries
-  if (localmesh->firstX()) {
-    n += ny;
-  }
-  if (localmesh->lastX()) {
-    n += ny;
-  }
-
-  // Y boundaries
-  for (RangeIterator it = localmesh->iterateBndryLowerY(); !it.isDone(); it++) {
-    // Should not go into corner cells, LaplaceXY stencil does not include them
-    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-      continue;
-    }
-    n++;
-  }
-  if ((not finite_volume) and localmesh->hasBndryLowerY()) {
-    if (localmesh->firstX()) {
-      n++;
-    }
-    if (localmesh->lastX()) {
-      n++;
-    }
-  }
-  for (RangeIterator it = localmesh->iterateBndryUpperY(); !it.isDone(); it++) {
-    // Should not go into corner cells, LaplaceXY stencil does not include them
-    if (it.ind < localmesh->xstart or it.ind > localmesh->xend) {
-      continue;
-    }
-    n++;
-  }
-  if ((not finite_volume) and localmesh->hasBndryUpperY()) {
-    if (localmesh->firstX()) {
-      n++;
-    }
-    if (localmesh->lastX()) {
-      n++;
-    }
-  }
-
-  return n;
-}
-
-int LaplaceXY::globalIndex(int x, int y) {
-  if ((x < 0) || (x >= localmesh->LocalNx) || (y < 0) || (y >= localmesh->LocalNy)) {
-    return -1; // Out of range
-  }
-
-  // Get the index from a Field2D, round to integer
-  return static_cast<int>(std::round(indexXY(x, y)));
-}
-
-void LaplaceXY::savePerformance(Solver& solver, const std::string& name) {
-  // set flag so that performance monitoring values are calculated
-  save_performance = true;
-
-  // add values to be saved to the output
-  if (not name.empty()) {
-    default_prefix = name;
-  }
-
-  // add monitor to reset counters/averages for new output timestep
-  // monitor added to back of queue, so that values are reset after being saved
-  solver.addMonitor(&monitor, Solver::BACK);
-}
-
-int LaplaceXY::LaplaceXYMonitor::call(Solver* /*solver*/, BoutReal /*time*/, int /*iter*/,
-                                      int /*nout*/) {
-  laplacexy.output_average_iterations = laplacexy.average_iterations;
-
-  laplacexy.n_calls = 0;
-  laplacexy.average_iterations = 0.;
-
-  return 0;
-}
-
-void LaplaceXY::LaplaceXYMonitor::outputVars(Options& output_options,
-                                             const std::string& time_dimension) {
-  output_options[fmt::format("{}_average_iterations", laplacexy.default_prefix)]
-      .assignRepeat(laplacexy.output_average_iterations, time_dimension);
-}
-
-#endif // BOUT_HAS_PETSC
+// DO NOT REMOVE: ensures linker keeps all symbols in this TU
+void LaplaceXYFactory::ensureRegistered() {}
diff --git a/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx b/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx
index 8408f08c00..55c4a383b3 100644
--- a/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx
@@ -34,7 +34,7 @@ int main(int argc, char** argv) {
 
   BoutInitialise(argc, argv);
 
-  LaplaceXY laplacexy;
+  auto laplacexy = LaplaceXY::create();
 
   // Solving equations of the form
   // Div(A Grad_perp(f)) + B*f = rhs
@@ -57,9 +57,9 @@ int main(int argc, char** argv) {
   Field2D rhs, rhs_check;
   rhs = Laplace_perpXY(a, f) + b * f;
 
-  laplacexy.setCoefs(a, b);
+  laplacexy->setCoefs(a, b);
 
-  sol = laplacexy.solve(rhs, 0.);
+  sol = laplacexy->solve(rhs, 0.);
   error = (f - sol) / f;
   absolute_error = f - sol;
   max_error = max(abs(absolute_error), true);
diff --git a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx
index 3486760810..fa67079861 100644
--- a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx
@@ -35,20 +35,20 @@ int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
   using bout::globals::mesh;
-  auto coords = mesh->getCoordinates();
+  auto* coords = mesh->getCoordinates();
 
   auto& opt = Options::root();
 
-  LaplaceXY laplacexy;
+  auto laplacexy = LaplaceXY::create();
 
   bool include_y_derivs = opt["laplacexy"]["include_y_derivs"];
 
   // Solving equations of the form
   // Div(A Grad_perp(f)) + B*f = rhs
   // A*Laplace_perp(f) + Grad_perp(A).Grad_perp(f) + B*f = rhs
-  Field2D f, a, b, sol;
-  Field2D error, absolute_error; //Absolute value of relative error: abs((f - sol)/f)
-  BoutReal max_error;            //Output of test
+  Field2D f;
+  Field2D a;
+  Field2D b;
 
   initial_profile("f", f);
   initial_profile("a", a);
@@ -61,7 +61,8 @@ int main(int argc, char** argv) {
 
   ////////////////////////////////////////////////////////////////////////////////////////
 
-  Field2D rhs, rhs_check;
+  Field2D rhs;
+  Field2D rhs_check;
   if (include_y_derivs) {
     rhs = a * DC(Laplace_perp(f)) + DC(Grad_perp(a) * Grad_perp(f)) + b * f;
   } else {
@@ -69,14 +70,14 @@ int main(int argc, char** argv) {
         a * DC(Delp2(f, CELL_DEFAULT, false)) + DC(coords->g11 * DDX(a) * DDX(f)) + b * f;
   }
 
-  laplacexy.setCoefs(a, b);
+  laplacexy->setCoefs(a, b);
 
-  sol = laplacexy.solve(rhs, 0.);
-  error = (f - sol) / f;
-  absolute_error = f - sol;
-  max_error = max(abs(absolute_error), true);
+  auto sol = laplacexy->solve(rhs, 0.);
+  const auto error = (f - sol) / f;
+  const auto absolute_error = f - sol;
+  const auto max_error = max(abs(absolute_error), true);
 
-  output << "Magnitude of maximum absolute error is " << max_error << endl;
+  output.write("Magnitude of maximum absolute error is {}\n", max_error);
 
   mesh->communicate(sol);
   if (include_y_derivs) {
diff --git a/tests/integrated/test-laplacexy/test-laplacexy.cxx b/tests/integrated/test-laplacexy/test-laplacexy.cxx
index 3142d359b1..d7b0a55ec8 100644
--- a/tests/integrated/test-laplacexy/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy/test-laplacexy.cxx
@@ -64,10 +64,10 @@ int main(int argc, char** argv) {
     rhs = a * Delp2(f, CELL_DEFAULT, false) + coords->g11 * DDX(a) * DDX(f) + b * f;
   }
 
-  LaplaceXY laplacexy;
-  laplacexy.setCoefs(a, b);
+  auto laplacexy = LaplaceXY::create();
+  laplacexy->setCoefs(a, b);
 
-  Field2D solution = laplacexy.solve(rhs, 0.);
+  Field2D solution = laplacexy->solve(rhs, 0.);
   Field2D relative_error = (f - solution) / f;
   Field2D absolute_error = f - solution;
   BoutReal max_error = max(abs(absolute_error), true);
diff --git a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx
index 2fb8a10777..7b7ac97517 100644
--- a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx
@@ -27,14 +27,14 @@
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
 #include <bout/initialprofiles.hxx>
-#include <bout/invert/laplacexy2_hypre.hxx>
+#include <bout/invert/laplacexy.hxx>
 #include <bout/options.hxx>
 
 int main(int argc, char** argv) {
 
   BoutInitialise(argc, argv);
 
-  LaplaceXY2Hypre laplacexy;
+  auto laplacexy = LaplaceXYFactory::getInstance().create("hypre", nullptr);
 
   // Solving equations of the form
   // Div(A Grad_perp(f)) + B*f = rhs
@@ -54,10 +54,10 @@ int main(int argc, char** argv) {
 
   Field2D rhs = Laplace_perpXY(a, f) + b * f;
 
-  laplacexy.setCoefs(a, b);
+  laplacexy->setCoefs(a, b);
 
   Field2D guess = 0.0;
-  Field2D sol = laplacexy.solve(rhs, guess);
+  Field2D sol = laplacexy->solve(rhs, guess);
   Field2D error = (f - sol) / f;
   // Absolute value of relative error: abs((f - sol)/f)
   Field2D absolute_error = abs(f - sol);

From 96c86b85cd4f50bc640bfe5c14f6f026bae62e90 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Thu, 23 Oct 2025 17:22:49 +0000
Subject: [PATCH 0277/1827] Apply clang-format changes

---
 src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
index 950fcc4f8e..163b5049ee 100644
--- a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
@@ -12,10 +12,8 @@
 #include "bout/sys/timer.hxx"
 
 #if BOUT_HAS_CUDA && defined(__CUDACC__)
-#define gpuErrchk(ans)                    \
-  {                                       \
-    gpuAssert((ans), __FILE__, __LINE__); \
-  }
+#define gpuErrchk(ans) \
+  { gpuAssert((ans), __FILE__, __LINE__); }
 inline void gpuAssert(cudaError_t code, const char* file, int line, bool abort = true) {
   if (code != cudaSuccess) {
     fprintf(stderr, "GPUassert: %s %s %d\n", cudaGetErrorString(code), file, line);

From cab2e9535f8592bd8e1dc96276918070305ff2df Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 24 Oct 2025 09:57:11 +0200
Subject: [PATCH 0278/1827] set more env vars for container

---
 .docker/fedora/Dockerfile | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.docker/fedora/Dockerfile b/.docker/fedora/Dockerfile
index 56445f8cea..e4a10a263c 100644
--- a/.docker/fedora/Dockerfile
+++ b/.docker/fedora/Dockerfile
@@ -22,7 +22,7 @@ RUN git clone $URL \
  && git checkout $COMMIT \
  && git submodule update --init --recursive
 
-
+ENV HOME=/home/boutuser
 WORKDIR /home/boutuser/BOUT-dev
 
 RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/opt/bout++/ \
@@ -36,4 +36,11 @@ RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/opt/bout++/ \
 RUN make -C build -j 2
 RUN sudo make -C build install
 
+ENV PATH=/opt/bout++/bin:$PATH \
+    LD_LIBRARY_PATH=/opt/bout++/lib:/opt/petsc/lib/:$LD_LIBRARY_PATH \
+    PYTHONPATH=/opt/bout++/lib/python3.13/site-packages/:$PYTHONPATH
+
+# Debug
 RUN find /opt/bout++
+# smoke test
+RUN python3 -c 'import boutpp'

From 6d856001e0c34ee19cfd2451ff0afd1e7c294dae Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 24 Oct 2025 09:57:37 +0200
Subject: [PATCH 0279/1827] CI: Build container for test branch

---
 .github/workflows/docker.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 1380d0ea8e..39c9891338 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -6,7 +6,7 @@ on:
       - master
       - next
       # Add your branch here if you want containers for it
-      - db-WIP
+      - fix3121
       - docker-ci
 
 env:

From 802f8a09b8cb9cc7c6dfacc0688e72eb26b87489 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 24 Oct 2025 10:08:32 +0200
Subject: [PATCH 0280/1827] Build in one step

---
 .docker/fedora/Dockerfile | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/.docker/fedora/Dockerfile b/.docker/fedora/Dockerfile
index e4a10a263c..e152103255 100644
--- a/.docker/fedora/Dockerfile
+++ b/.docker/fedora/Dockerfile
@@ -25,22 +25,19 @@ RUN git clone $URL \
 ENV HOME=/home/boutuser
 WORKDIR /home/boutuser/BOUT-dev
 
-RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/opt/bout++/ \
+RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local/ \
           -DBOUT_GENERATE_FIELDOPS=OFF \
-          -DBOUT_USE_PETSC=ON -DPETSc_ROOT=/opt/petsc \
+          -DBOUT_USE_PETSC=ON -DPETSc_ROOT=/usr/local \
           -DBOUT_ENABLE_PYTHON=ON \
           -DBOUT_USE_SUNDIALS=ON -DSUNDIALS_ROOT=/usr/lib64/$MPI/ -DSUNDIALS_INCLUDE_DIR=/usr/include/$MPI-x86_64/sundials/ \
-	  $CMAKE_OPTIONS || (cat /home/boutuser/BOUT-dev/build/CMakeFiles/CMake{Output,Error}.log  ; exit 1)
+	  $CMAKE_OPTIONS || (cat /home/boutuser/BOUT-dev/build/CMakeFiles/CMake{Output,Error}.log  ; exit 1) \
+    make -C build -j 2 \
+    sudo make -C build install \
+    rm -rf build
 
+ENV PATH=/usr/local/bin:$PATH \
+    LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH \
+    PYTHONPATH=/usr/local/lib/python3.13/site-packages/:$PYTHONPATH
 
-RUN make -C build -j 2
-RUN sudo make -C build install
-
-ENV PATH=/opt/bout++/bin:$PATH \
-    LD_LIBRARY_PATH=/opt/bout++/lib:/opt/petsc/lib/:$LD_LIBRARY_PATH \
-    PYTHONPATH=/opt/bout++/lib/python3.13/site-packages/:$PYTHONPATH
-
-# Debug
-RUN find /opt/bout++
 # smoke test
 RUN python3 -c 'import boutpp'

From 9542428ddd0ba6130262a145e01337f95598b339 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 24 Oct 2025 10:13:01 +0200
Subject: [PATCH 0281/1827] Fixup: add ; at end of line

---
 .docker/fedora/Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.docker/fedora/Dockerfile b/.docker/fedora/Dockerfile
index e152103255..2b6800ce21 100644
--- a/.docker/fedora/Dockerfile
+++ b/.docker/fedora/Dockerfile
@@ -30,9 +30,9 @@ RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local/ \
           -DBOUT_USE_PETSC=ON -DPETSc_ROOT=/usr/local \
           -DBOUT_ENABLE_PYTHON=ON \
           -DBOUT_USE_SUNDIALS=ON -DSUNDIALS_ROOT=/usr/lib64/$MPI/ -DSUNDIALS_INCLUDE_DIR=/usr/include/$MPI-x86_64/sundials/ \
-	  $CMAKE_OPTIONS || (cat /home/boutuser/BOUT-dev/build/CMakeFiles/CMake{Output,Error}.log  ; exit 1) \
-    make -C build -j 2 \
-    sudo make -C build install \
+	  $CMAKE_OPTIONS || (cat /home/boutuser/BOUT-dev/build/CMakeFiles/CMake{Output,Error}.log  ; exit 1); \
+    make -C build -j 2; \
+    sudo make -C build install; \
     rm -rf build
 
 ENV PATH=/usr/local/bin:$PATH \

From 84a684b1887ddb3237e7cc841b66647a690a2a20 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 24 Oct 2025 09:22:17 +0100
Subject: [PATCH 0282/1827] Fix typo in define

---
 src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
index 3950725a89..32e9c05ab1 100644
--- a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
@@ -36,14 +36,14 @@
 #include "bout/build_defines.hxx"
 #include "bout/invert/laplacexy.hxx"
 
-#if !BOUT_HAS_PETSC
+#if !BOUT_HAS_HYPRE
 
 namespace {
 RegisterUnavailableLaplaceXY
     registerlaplacexyhypre("hypre", "BOUT++ was not configured with HYPRE");
 }
 
-#else // BOUT_HAS_PETSC
+#else // BOUT_HAS_HYPRE
 
 class Mesh;
 

From 8f18967b9b22b7eadffb63c70a027ab9f9557c06 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 24 Oct 2025 10:49:09 +0200
Subject: [PATCH 0283/1827] Bump soname

abidiff reports various symbols have been deleted since the v5.1 release
---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5c49e434e4..294cd75c47 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -463,7 +463,7 @@ set(BOUT_LIB_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib")
 set_target_properties(bout++ PROPERTIES
   LIBRARY_OUTPUT_DIRECTORY "${BOUT_LIB_PATH}"
   ARCHIVE_OUTPUT_DIRECTORY "${BOUT_LIB_PATH}"
-  SOVERSION 5.1.0)
+  SOVERSION 5.2.0)
 
 # Set some variables for the bout-config script
 set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -L\$BOUT_LIB_PATH -lbout++")

From b75103dcaf716636987e711dd78defa78a544ddb Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 24 Oct 2025 03:43:11 -0700
Subject: [PATCH 0284/1827] Add FFT GPU shiftZ

---
 include/bout/twiddle.hxx            | 2046 +++++++++++++++++++++++++++
 src/mesh/parallel/shiftedmetric.cxx |  325 ++++-
 2 files changed, 2367 insertions(+), 4 deletions(-)
 create mode 100644 include/bout/twiddle.hxx

diff --git a/include/bout/twiddle.hxx b/include/bout/twiddle.hxx
new file mode 100644
index 0000000000..ae4f729b48
--- /dev/null
+++ b/include/bout/twiddle.hxx
@@ -0,0 +1,2046 @@
+__constant__ double2 c_twiddle_fwd_16[16] = {
+    {1.0000000000000000, -0.0000000000000000},  // k=0
+    {0.9238795325112867, -0.3826834323650898},  // k=1
+    {0.7071067811865476, -0.7071067811865475},  // k=2
+    {0.3826834323650898, -0.9238795325112867},  // k=3
+    {0.0000000000000001, -1.0000000000000000},  // k=4
+    {-0.3826834323650897, -0.9238795325112867}, // k=5
+    {-0.7071067811865475, -0.7071067811865476}, // k=6
+    {-0.9238795325112867, -0.3826834323650899}, // k=7
+    {-1.0000000000000000, -0.0000000000000001}, // k=8
+    {-0.9238795325112868, 0.3826834323650897},  // k=9
+    {-0.7071067811865477, 0.7071067811865475},  // k=10
+    {-0.3826834323650903, 0.9238795325112865},  // k=11
+    {-0.0000000000000002, 1.0000000000000000},  // k=12
+    {0.3826834323650900, 0.9238795325112866},   // k=13
+    {0.7071067811865474, 0.7071067811865477},   // k=14
+    {0.9238795325112865, 0.3826834323650904},   // k=15
+};
+
+__constant__ double2 c_twiddle_inv_16[16] = {
+    {1.0000000000000000, 0.0000000000000000},   // k=0
+    {0.9238795325112867, 0.3826834323650898},   // k=1
+    {0.7071067811865476, 0.7071067811865475},   // k=2
+    {0.3826834323650898, 0.9238795325112867},   // k=3
+    {0.0000000000000001, 1.0000000000000000},   // k=4
+    {-0.3826834323650897, 0.9238795325112867},  // k=5
+    {-0.7071067811865475, 0.7071067811865476},  // k=6
+    {-0.9238795325112867, 0.3826834323650899},  // k=7
+    {-1.0000000000000000, 0.0000000000000001},  // k=8
+    {-0.9238795325112868, -0.3826834323650897}, // k=9
+    {-0.7071067811865477, -0.7071067811865475}, // k=10
+    {-0.3826834323650903, -0.9238795325112865}, // k=11
+    {-0.0000000000000002, -1.0000000000000000}, // k=12
+    {0.3826834323650900, -0.9238795325112866},  // k=13
+    {0.7071067811865474, -0.7071067811865477},  // k=14
+    {0.9238795325112865, -0.3826834323650904},  // k=15
+};
+__constant__ double2 c_twiddle_fwd_32[32] = {
+    {1.0000000000000000, -0.0000000000000000},  // k=0
+    {0.9807852804032304, -0.1950903220161282},  // k=1
+    {0.9238795325112867, -0.3826834323650898},  // k=2
+    {0.8314696123025452, -0.5555702330196022},  // k=3
+    {0.7071067811865476, -0.7071067811865475},  // k=4
+    {0.5555702330196023, -0.8314696123025452},  // k=5
+    {0.3826834323650898, -0.9238795325112867},  // k=6
+    {0.1950903220161283, -0.9807852804032304},  // k=7
+    {0.0000000000000001, -1.0000000000000000},  // k=8
+    {-0.1950903220161282, -0.9807852804032304}, // k=9
+    {-0.3826834323650897, -0.9238795325112867}, // k=10
+    {-0.5555702330196020, -0.8314696123025455}, // k=11
+    {-0.7071067811865475, -0.7071067811865476}, // k=12
+    {-0.8314696123025453, -0.5555702330196022}, // k=13
+    {-0.9238795325112867, -0.3826834323650899}, // k=14
+    {-0.9807852804032304, -0.1950903220161286}, // k=15
+    {-1.0000000000000000, -0.0000000000000001}, // k=16
+    {-0.9807852804032304, 0.1950903220161284},  // k=17
+    {-0.9238795325112868, 0.3826834323650897},  // k=18
+    {-0.8314696123025455, 0.5555702330196020},  // k=19
+    {-0.7071067811865477, 0.7071067811865475},  // k=20
+    {-0.5555702330196022, 0.8314696123025452},  // k=21
+    {-0.3826834323650903, 0.9238795325112865},  // k=22
+    {-0.1950903220161287, 0.9807852804032303},  // k=23
+    {-0.0000000000000002, 1.0000000000000000},  // k=24
+    {0.1950903220161283, 0.9807852804032304},   // k=25
+    {0.3826834323650900, 0.9238795325112866},   // k=26
+    {0.5555702330196018, 0.8314696123025455},   // k=27
+    {0.7071067811865474, 0.7071067811865477},   // k=28
+    {0.8314696123025452, 0.5555702330196022},   // k=29
+    {0.9238795325112865, 0.3826834323650904},   // k=30
+    {0.9807852804032303, 0.1950903220161287},   // k=31
+};
+
+__constant__ double2 c_twiddle_inv_32[32] = {
+    {1.0000000000000000, 0.0000000000000000},   // k=0
+    {0.9807852804032304, 0.1950903220161282},   // k=1
+    {0.9238795325112867, 0.3826834323650898},   // k=2
+    {0.8314696123025452, 0.5555702330196022},   // k=3
+    {0.7071067811865476, 0.7071067811865475},   // k=4
+    {0.5555702330196023, 0.8314696123025452},   // k=5
+    {0.3826834323650898, 0.9238795325112867},   // k=6
+    {0.1950903220161283, 0.9807852804032304},   // k=7
+    {0.0000000000000001, 1.0000000000000000},   // k=8
+    {-0.1950903220161282, 0.9807852804032304},  // k=9
+    {-0.3826834323650897, 0.9238795325112867},  // k=10
+    {-0.5555702330196020, 0.8314696123025455},  // k=11
+    {-0.7071067811865475, 0.7071067811865476},  // k=12
+    {-0.8314696123025453, 0.5555702330196022},  // k=13
+    {-0.9238795325112867, 0.3826834323650899},  // k=14
+    {-0.9807852804032304, 0.1950903220161286},  // k=15
+    {-1.0000000000000000, 0.0000000000000001},  // k=16
+    {-0.9807852804032304, -0.1950903220161284}, // k=17
+    {-0.9238795325112868, -0.3826834323650897}, // k=18
+    {-0.8314696123025455, -0.5555702330196020}, // k=19
+    {-0.7071067811865477, -0.7071067811865475}, // k=20
+    {-0.5555702330196022, -0.8314696123025452}, // k=21
+    {-0.3826834323650903, -0.9238795325112865}, // k=22
+    {-0.1950903220161287, -0.9807852804032303}, // k=23
+    {-0.0000000000000002, -1.0000000000000000}, // k=24
+    {0.1950903220161283, -0.9807852804032304},  // k=25
+    {0.3826834323650900, -0.9238795325112866},  // k=26
+    {0.5555702330196018, -0.8314696123025455},  // k=27
+    {0.7071067811865474, -0.7071067811865477},  // k=28
+    {0.8314696123025452, -0.5555702330196022},  // k=29
+    {0.9238795325112865, -0.3826834323650904},  // k=30
+    {0.9807852804032303, -0.1950903220161287},  // k=31
+};
+__constant__ double2 c_twiddle_fwd_64[64] = {
+    {1.0000000000000000, -0.0000000000000000},  // k=0
+    {0.9951847266721969, -0.0980171403295606},  // k=1
+    {0.9807852804032304, -0.1950903220161282},  // k=2
+    {0.9569403357322088, -0.2902846772544623},  // k=3
+    {0.9238795325112867, -0.3826834323650898},  // k=4
+    {0.8819212643483550, -0.4713967368259976},  // k=5
+    {0.8314696123025452, -0.5555702330196022},  // k=6
+    {0.7730104533627370, -0.6343932841636455},  // k=7
+    {0.7071067811865476, -0.7071067811865475},  // k=8
+    {0.6343932841636455, -0.7730104533627370},  // k=9
+    {0.5555702330196023, -0.8314696123025452},  // k=10
+    {0.4713967368259978, -0.8819212643483549},  // k=11
+    {0.3826834323650898, -0.9238795325112867},  // k=12
+    {0.2902846772544623, -0.9569403357322089},  // k=13
+    {0.1950903220161283, -0.9807852804032304},  // k=14
+    {0.0980171403295608, -0.9951847266721968},  // k=15
+    {0.0000000000000001, -1.0000000000000000},  // k=16
+    {-0.0980171403295606, -0.9951847266721969}, // k=17
+    {-0.1950903220161282, -0.9807852804032304}, // k=18
+    {-0.2902846772544622, -0.9569403357322089}, // k=19
+    {-0.3826834323650897, -0.9238795325112867}, // k=20
+    {-0.4713967368259977, -0.8819212643483550}, // k=21
+    {-0.5555702330196020, -0.8314696123025455}, // k=22
+    {-0.6343932841636454, -0.7730104533627371}, // k=23
+    {-0.7071067811865475, -0.7071067811865476}, // k=24
+    {-0.7730104533627370, -0.6343932841636455}, // k=25
+    {-0.8314696123025453, -0.5555702330196022}, // k=26
+    {-0.8819212643483549, -0.4713967368259979}, // k=27
+    {-0.9238795325112867, -0.3826834323650899}, // k=28
+    {-0.9569403357322088, -0.2902846772544624}, // k=29
+    {-0.9807852804032304, -0.1950903220161286}, // k=30
+    {-0.9951847266721968, -0.0980171403295608}, // k=31
+    {-1.0000000000000000, -0.0000000000000001}, // k=32
+    {-0.9951847266721969, 0.0980171403295606},  // k=33
+    {-0.9807852804032304, 0.1950903220161284},  // k=34
+    {-0.9569403357322089, 0.2902846772544621},  // k=35
+    {-0.9238795325112868, 0.3826834323650897},  // k=36
+    {-0.8819212643483550, 0.4713967368259976},  // k=37
+    {-0.8314696123025455, 0.5555702330196020},  // k=38
+    {-0.7730104533627371, 0.6343932841636453},  // k=39
+    {-0.7071067811865477, 0.7071067811865475},  // k=40
+    {-0.6343932841636459, 0.7730104533627367},  // k=41
+    {-0.5555702330196022, 0.8314696123025452},  // k=42
+    {-0.4713967368259979, 0.8819212643483549},  // k=43
+    {-0.3826834323650903, 0.9238795325112865},  // k=44
+    {-0.2902846772544624, 0.9569403357322088},  // k=45
+    {-0.1950903220161287, 0.9807852804032303},  // k=46
+    {-0.0980171403295605, 0.9951847266721969},  // k=47
+    {-0.0000000000000002, 1.0000000000000000},  // k=48
+    {0.0980171403295601, 0.9951847266721969},   // k=49
+    {0.1950903220161283, 0.9807852804032304},   // k=50
+    {0.2902846772544621, 0.9569403357322089},   // k=51
+    {0.3826834323650900, 0.9238795325112866},   // k=52
+    {0.4713967368259976, 0.8819212643483550},   // k=53
+    {0.5555702330196018, 0.8314696123025455},   // k=54
+    {0.6343932841636456, 0.7730104533627369},   // k=55
+    {0.7071067811865474, 0.7071067811865477},   // k=56
+    {0.7730104533627367, 0.6343932841636459},   // k=57
+    {0.8314696123025452, 0.5555702330196022},   // k=58
+    {0.8819212643483548, 0.4713967368259979},   // k=59
+    {0.9238795325112865, 0.3826834323650904},   // k=60
+    {0.9569403357322088, 0.2902846772544625},   // k=61
+    {0.9807852804032303, 0.1950903220161287},   // k=62
+    {0.9951847266721969, 0.0980171403295605},   // k=63
+};
+
+__constant__ double2 c_twiddle_inv_64[64] = {
+    {1.0000000000000000, 0.0000000000000000},   // k=0
+    {0.9951847266721969, 0.0980171403295606},   // k=1
+    {0.9807852804032304, 0.1950903220161282},   // k=2
+    {0.9569403357322088, 0.2902846772544623},   // k=3
+    {0.9238795325112867, 0.3826834323650898},   // k=4
+    {0.8819212643483550, 0.4713967368259976},   // k=5
+    {0.8314696123025452, 0.5555702330196022},   // k=6
+    {0.7730104533627370, 0.6343932841636455},   // k=7
+    {0.7071067811865476, 0.7071067811865475},   // k=8
+    {0.6343932841636455, 0.7730104533627370},   // k=9
+    {0.5555702330196023, 0.8314696123025452},   // k=10
+    {0.4713967368259978, 0.8819212643483549},   // k=11
+    {0.3826834323650898, 0.9238795325112867},   // k=12
+    {0.2902846772544623, 0.9569403357322089},   // k=13
+    {0.1950903220161283, 0.9807852804032304},   // k=14
+    {0.0980171403295608, 0.9951847266721968},   // k=15
+    {0.0000000000000001, 1.0000000000000000},   // k=16
+    {-0.0980171403295606, 0.9951847266721969},  // k=17
+    {-0.1950903220161282, 0.9807852804032304},  // k=18
+    {-0.2902846772544622, 0.9569403357322089},  // k=19
+    {-0.3826834323650897, 0.9238795325112867},  // k=20
+    {-0.4713967368259977, 0.8819212643483550},  // k=21
+    {-0.5555702330196020, 0.8314696123025455},  // k=22
+    {-0.6343932841636454, 0.7730104533627371},  // k=23
+    {-0.7071067811865475, 0.7071067811865476},  // k=24
+    {-0.7730104533627370, 0.6343932841636455},  // k=25
+    {-0.8314696123025453, 0.5555702330196022},  // k=26
+    {-0.8819212643483549, 0.4713967368259979},  // k=27
+    {-0.9238795325112867, 0.3826834323650899},  // k=28
+    {-0.9569403357322088, 0.2902846772544624},  // k=29
+    {-0.9807852804032304, 0.1950903220161286},  // k=30
+    {-0.9951847266721968, 0.0980171403295608},  // k=31
+    {-1.0000000000000000, 0.0000000000000001},  // k=32
+    {-0.9951847266721969, -0.0980171403295606}, // k=33
+    {-0.9807852804032304, -0.1950903220161284}, // k=34
+    {-0.9569403357322089, -0.2902846772544621}, // k=35
+    {-0.9238795325112868, -0.3826834323650897}, // k=36
+    {-0.8819212643483550, -0.4713967368259976}, // k=37
+    {-0.8314696123025455, -0.5555702330196020}, // k=38
+    {-0.7730104533627371, -0.6343932841636453}, // k=39
+    {-0.7071067811865477, -0.7071067811865475}, // k=40
+    {-0.6343932841636459, -0.7730104533627367}, // k=41
+    {-0.5555702330196022, -0.8314696123025452}, // k=42
+    {-0.4713967368259979, -0.8819212643483549}, // k=43
+    {-0.3826834323650903, -0.9238795325112865}, // k=44
+    {-0.2902846772544624, -0.9569403357322088}, // k=45
+    {-0.1950903220161287, -0.9807852804032303}, // k=46
+    {-0.0980171403295605, -0.9951847266721969}, // k=47
+    {-0.0000000000000002, -1.0000000000000000}, // k=48
+    {0.0980171403295601, -0.9951847266721969},  // k=49
+    {0.1950903220161283, -0.9807852804032304},  // k=50
+    {0.2902846772544621, -0.9569403357322089},  // k=51
+    {0.3826834323650900, -0.9238795325112866},  // k=52
+    {0.4713967368259976, -0.8819212643483550},  // k=53
+    {0.5555702330196018, -0.8314696123025455},  // k=54
+    {0.6343932841636456, -0.7730104533627369},  // k=55
+    {0.7071067811865474, -0.7071067811865477},  // k=56
+    {0.7730104533627367, -0.6343932841636459},  // k=57
+    {0.8314696123025452, -0.5555702330196022},  // k=58
+    {0.8819212643483548, -0.4713967368259979},  // k=59
+    {0.9238795325112865, -0.3826834323650904},  // k=60
+    {0.9569403357322088, -0.2902846772544625},  // k=61
+    {0.9807852804032303, -0.1950903220161287},  // k=62
+    {0.9951847266721969, -0.0980171403295605},  // k=63
+};
+__constant__ double2 c_twiddle_fwd_128[128] = {
+    {1.0000000000000000, -0.0000000000000000},  // k=0
+    {0.9987954562051724, -0.0490676743274180},  // k=1
+    {0.9951847266721969, -0.0980171403295606},  // k=2
+    {0.9891765099647810, -0.1467304744553617},  // k=3
+    {0.9807852804032304, -0.1950903220161282},  // k=4
+    {0.9700312531945440, -0.2429801799032639},  // k=5
+    {0.9569403357322088, -0.2902846772544623},  // k=6
+    {0.9415440651830208, -0.3368898533922201},  // k=7
+    {0.9238795325112867, -0.3826834323650898},  // k=8
+    {0.9039892931234433, -0.4275550934302821},  // k=9
+    {0.8819212643483550, -0.4713967368259976},  // k=10
+    {0.8577286100002721, -0.5141027441932217},  // k=11
+    {0.8314696123025452, -0.5555702330196022},  // k=12
+    {0.8032075314806449, -0.5956993044924334},  // k=13
+    {0.7730104533627370, -0.6343932841636455},  // k=14
+    {0.7409511253549591, -0.6715589548470183},  // k=15
+    {0.7071067811865476, -0.7071067811865475},  // k=16
+    {0.6715589548470183, -0.7409511253549591},  // k=17
+    {0.6343932841636455, -0.7730104533627370},  // k=18
+    {0.5956993044924335, -0.8032075314806448},  // k=19
+    {0.5555702330196023, -0.8314696123025452},  // k=20
+    {0.5141027441932217, -0.8577286100002721},  // k=21
+    {0.4713967368259978, -0.8819212643483549},  // k=22
+    {0.4275550934302822, -0.9039892931234433},  // k=23
+    {0.3826834323650898, -0.9238795325112867},  // k=24
+    {0.3368898533922201, -0.9415440651830208},  // k=25
+    {0.2902846772544623, -0.9569403357322089},  // k=26
+    {0.2429801799032640, -0.9700312531945440},  // k=27
+    {0.1950903220161283, -0.9807852804032304},  // k=28
+    {0.1467304744553617, -0.9891765099647810},  // k=29
+    {0.0980171403295608, -0.9951847266721968},  // k=30
+    {0.0490676743274181, -0.9987954562051724},  // k=31
+    {0.0000000000000001, -1.0000000000000000},  // k=32
+    {-0.0490676743274180, -0.9987954562051724}, // k=33
+    {-0.0980171403295606, -0.9951847266721969}, // k=34
+    {-0.1467304744553616, -0.9891765099647810}, // k=35
+    {-0.1950903220161282, -0.9807852804032304}, // k=36
+    {-0.2429801799032639, -0.9700312531945440}, // k=37
+    {-0.2902846772544622, -0.9569403357322089}, // k=38
+    {-0.3368898533922199, -0.9415440651830208}, // k=39
+    {-0.3826834323650897, -0.9238795325112867}, // k=40
+    {-0.4275550934302819, -0.9039892931234434}, // k=41
+    {-0.4713967368259977, -0.8819212643483550}, // k=42
+    {-0.5141027441932217, -0.8577286100002721}, // k=43
+    {-0.5555702330196020, -0.8314696123025455}, // k=44
+    {-0.5956993044924334, -0.8032075314806449}, // k=45
+    {-0.6343932841636454, -0.7730104533627371}, // k=46
+    {-0.6715589548470184, -0.7409511253549590}, // k=47
+    {-0.7071067811865475, -0.7071067811865476}, // k=48
+    {-0.7409511253549589, -0.6715589548470186}, // k=49
+    {-0.7730104533627370, -0.6343932841636455}, // k=50
+    {-0.8032075314806448, -0.5956993044924335}, // k=51
+    {-0.8314696123025453, -0.5555702330196022}, // k=52
+    {-0.8577286100002720, -0.5141027441932218}, // k=53
+    {-0.8819212643483549, -0.4713967368259979}, // k=54
+    {-0.9039892931234433, -0.4275550934302820}, // k=55
+    {-0.9238795325112867, -0.3826834323650899}, // k=56
+    {-0.9415440651830207, -0.3368898533922203}, // k=57
+    {-0.9569403357322088, -0.2902846772544624}, // k=58
+    {-0.9700312531945440, -0.2429801799032641}, // k=59
+    {-0.9807852804032304, -0.1950903220161286}, // k=60
+    {-0.9891765099647810, -0.1467304744553618}, // k=61
+    {-0.9951847266721968, -0.0980171403295608}, // k=62
+    {-0.9987954562051724, -0.0490676743274180}, // k=63
+    {-1.0000000000000000, -0.0000000000000001}, // k=64
+    {-0.9987954562051724, 0.0490676743274177},  // k=65
+    {-0.9951847266721969, 0.0980171403295606},  // k=66
+    {-0.9891765099647810, 0.1467304744553616},  // k=67
+    {-0.9807852804032304, 0.1950903220161284},  // k=68
+    {-0.9700312531945440, 0.2429801799032638},  // k=69
+    {-0.9569403357322089, 0.2902846772544621},  // k=70
+    {-0.9415440651830208, 0.3368898533922201},  // k=71
+    {-0.9238795325112868, 0.3826834323650897},  // k=72
+    {-0.9039892931234434, 0.4275550934302818},  // k=73
+    {-0.8819212643483550, 0.4713967368259976},  // k=74
+    {-0.8577286100002721, 0.5141027441932216},  // k=75
+    {-0.8314696123025455, 0.5555702330196020},  // k=76
+    {-0.8032075314806449, 0.5956993044924332},  // k=77
+    {-0.7730104533627371, 0.6343932841636453},  // k=78
+    {-0.7409511253549591, 0.6715589548470184},  // k=79
+    {-0.7071067811865477, 0.7071067811865475},  // k=80
+    {-0.6715589548470187, 0.7409511253549589},  // k=81
+    {-0.6343932841636459, 0.7730104533627367},  // k=82
+    {-0.5956993044924331, 0.8032075314806451},  // k=83
+    {-0.5555702330196022, 0.8314696123025452},  // k=84
+    {-0.5141027441932218, 0.8577286100002720},  // k=85
+    {-0.4713967368259979, 0.8819212643483549},  // k=86
+    {-0.4275550934302825, 0.9039892931234431},  // k=87
+    {-0.3826834323650903, 0.9238795325112865},  // k=88
+    {-0.3368898533922199, 0.9415440651830208},  // k=89
+    {-0.2902846772544624, 0.9569403357322088},  // k=90
+    {-0.2429801799032641, 0.9700312531945440},  // k=91
+    {-0.1950903220161287, 0.9807852804032303},  // k=92
+    {-0.1467304744553623, 0.9891765099647809},  // k=93
+    {-0.0980171403295605, 0.9951847266721969},  // k=94
+    {-0.0490676743274180, 0.9987954562051724},  // k=95
+    {-0.0000000000000002, 1.0000000000000000},  // k=96
+    {0.0490676743274177, 0.9987954562051724},   // k=97
+    {0.0980171403295601, 0.9951847266721969},   // k=98
+    {0.1467304744553619, 0.9891765099647809},   // k=99
+    {0.1950903220161283, 0.9807852804032304},   // k=100
+    {0.2429801799032638, 0.9700312531945440},   // k=101
+    {0.2902846772544621, 0.9569403357322089},   // k=102
+    {0.3368898533922196, 0.9415440651830209},   // k=103
+    {0.3826834323650900, 0.9238795325112866},   // k=104
+    {0.4275550934302821, 0.9039892931234433},   // k=105
+    {0.4713967368259976, 0.8819212643483550},   // k=106
+    {0.5141027441932216, 0.8577286100002722},   // k=107
+    {0.5555702330196018, 0.8314696123025455},   // k=108
+    {0.5956993044924329, 0.8032075314806453},   // k=109
+    {0.6343932841636456, 0.7730104533627369},   // k=110
+    {0.6715589548470183, 0.7409511253549591},   // k=111
+    {0.7071067811865474, 0.7071067811865477},   // k=112
+    {0.7409511253549589, 0.6715589548470187},   // k=113
+    {0.7730104533627367, 0.6343932841636459},   // k=114
+    {0.8032075314806451, 0.5956993044924332},   // k=115
+    {0.8314696123025452, 0.5555702330196022},   // k=116
+    {0.8577286100002720, 0.5141027441932219},   // k=117
+    {0.8819212643483548, 0.4713967368259979},   // k=118
+    {0.9039892931234431, 0.4275550934302825},   // k=119
+    {0.9238795325112865, 0.3826834323650904},   // k=120
+    {0.9415440651830208, 0.3368898533922200},   // k=121
+    {0.9569403357322088, 0.2902846772544625},   // k=122
+    {0.9700312531945440, 0.2429801799032642},   // k=123
+    {0.9807852804032303, 0.1950903220161287},   // k=124
+    {0.9891765099647809, 0.1467304744553624},   // k=125
+    {0.9951847266721969, 0.0980171403295605},   // k=126
+    {0.9987954562051724, 0.0490676743274181},   // k=127
+};
+
+__constant__ double2 c_twiddle_inv_128[128] = {
+    {1.0000000000000000, 0.0000000000000000},   // k=0
+    {0.9987954562051724, 0.0490676743274180},   // k=1
+    {0.9951847266721969, 0.0980171403295606},   // k=2
+    {0.9891765099647810, 0.1467304744553617},   // k=3
+    {0.9807852804032304, 0.1950903220161282},   // k=4
+    {0.9700312531945440, 0.2429801799032639},   // k=5
+    {0.9569403357322088, 0.2902846772544623},   // k=6
+    {0.9415440651830208, 0.3368898533922201},   // k=7
+    {0.9238795325112867, 0.3826834323650898},   // k=8
+    {0.9039892931234433, 0.4275550934302821},   // k=9
+    {0.8819212643483550, 0.4713967368259976},   // k=10
+    {0.8577286100002721, 0.5141027441932217},   // k=11
+    {0.8314696123025452, 0.5555702330196022},   // k=12
+    {0.8032075314806449, 0.5956993044924334},   // k=13
+    {0.7730104533627370, 0.6343932841636455},   // k=14
+    {0.7409511253549591, 0.6715589548470183},   // k=15
+    {0.7071067811865476, 0.7071067811865475},   // k=16
+    {0.6715589548470183, 0.7409511253549591},   // k=17
+    {0.6343932841636455, 0.7730104533627370},   // k=18
+    {0.5956993044924335, 0.8032075314806448},   // k=19
+    {0.5555702330196023, 0.8314696123025452},   // k=20
+    {0.5141027441932217, 0.8577286100002721},   // k=21
+    {0.4713967368259978, 0.8819212643483549},   // k=22
+    {0.4275550934302822, 0.9039892931234433},   // k=23
+    {0.3826834323650898, 0.9238795325112867},   // k=24
+    {0.3368898533922201, 0.9415440651830208},   // k=25
+    {0.2902846772544623, 0.9569403357322089},   // k=26
+    {0.2429801799032640, 0.9700312531945440},   // k=27
+    {0.1950903220161283, 0.9807852804032304},   // k=28
+    {0.1467304744553617, 0.9891765099647810},   // k=29
+    {0.0980171403295608, 0.9951847266721968},   // k=30
+    {0.0490676743274181, 0.9987954562051724},   // k=31
+    {0.0000000000000001, 1.0000000000000000},   // k=32
+    {-0.0490676743274180, 0.9987954562051724},  // k=33
+    {-0.0980171403295606, 0.9951847266721969},  // k=34
+    {-0.1467304744553616, 0.9891765099647810},  // k=35
+    {-0.1950903220161282, 0.9807852804032304},  // k=36
+    {-0.2429801799032639, 0.9700312531945440},  // k=37
+    {-0.2902846772544622, 0.9569403357322089},  // k=38
+    {-0.3368898533922199, 0.9415440651830208},  // k=39
+    {-0.3826834323650897, 0.9238795325112867},  // k=40
+    {-0.4275550934302819, 0.9039892931234434},  // k=41
+    {-0.4713967368259977, 0.8819212643483550},  // k=42
+    {-0.5141027441932217, 0.8577286100002721},  // k=43
+    {-0.5555702330196020, 0.8314696123025455},  // k=44
+    {-0.5956993044924334, 0.8032075314806449},  // k=45
+    {-0.6343932841636454, 0.7730104533627371},  // k=46
+    {-0.6715589548470184, 0.7409511253549590},  // k=47
+    {-0.7071067811865475, 0.7071067811865476},  // k=48
+    {-0.7409511253549589, 0.6715589548470186},  // k=49
+    {-0.7730104533627370, 0.6343932841636455},  // k=50
+    {-0.8032075314806448, 0.5956993044924335},  // k=51
+    {-0.8314696123025453, 0.5555702330196022},  // k=52
+    {-0.8577286100002720, 0.5141027441932218},  // k=53
+    {-0.8819212643483549, 0.4713967368259979},  // k=54
+    {-0.9039892931234433, 0.4275550934302820},  // k=55
+    {-0.9238795325112867, 0.3826834323650899},  // k=56
+    {-0.9415440651830207, 0.3368898533922203},  // k=57
+    {-0.9569403357322088, 0.2902846772544624},  // k=58
+    {-0.9700312531945440, 0.2429801799032641},  // k=59
+    {-0.9807852804032304, 0.1950903220161286},  // k=60
+    {-0.9891765099647810, 0.1467304744553618},  // k=61
+    {-0.9951847266721968, 0.0980171403295608},  // k=62
+    {-0.9987954562051724, 0.0490676743274180},  // k=63
+    {-1.0000000000000000, 0.0000000000000001},  // k=64
+    {-0.9987954562051724, -0.0490676743274177}, // k=65
+    {-0.9951847266721969, -0.0980171403295606}, // k=66
+    {-0.9891765099647810, -0.1467304744553616}, // k=67
+    {-0.9807852804032304, -0.1950903220161284}, // k=68
+    {-0.9700312531945440, -0.2429801799032638}, // k=69
+    {-0.9569403357322089, -0.2902846772544621}, // k=70
+    {-0.9415440651830208, -0.3368898533922201}, // k=71
+    {-0.9238795325112868, -0.3826834323650897}, // k=72
+    {-0.9039892931234434, -0.4275550934302818}, // k=73
+    {-0.8819212643483550, -0.4713967368259976}, // k=74
+    {-0.8577286100002721, -0.5141027441932216}, // k=75
+    {-0.8314696123025455, -0.5555702330196020}, // k=76
+    {-0.8032075314806449, -0.5956993044924332}, // k=77
+    {-0.7730104533627371, -0.6343932841636453}, // k=78
+    {-0.7409511253549591, -0.6715589548470184}, // k=79
+    {-0.7071067811865477, -0.7071067811865475}, // k=80
+    {-0.6715589548470187, -0.7409511253549589}, // k=81
+    {-0.6343932841636459, -0.7730104533627367}, // k=82
+    {-0.5956993044924331, -0.8032075314806451}, // k=83
+    {-0.5555702330196022, -0.8314696123025452}, // k=84
+    {-0.5141027441932218, -0.8577286100002720}, // k=85
+    {-0.4713967368259979, -0.8819212643483549}, // k=86
+    {-0.4275550934302825, -0.9039892931234431}, // k=87
+    {-0.3826834323650903, -0.9238795325112865}, // k=88
+    {-0.3368898533922199, -0.9415440651830208}, // k=89
+    {-0.2902846772544624, -0.9569403357322088}, // k=90
+    {-0.2429801799032641, -0.9700312531945440}, // k=91
+    {-0.1950903220161287, -0.9807852804032303}, // k=92
+    {-0.1467304744553623, -0.9891765099647809}, // k=93
+    {-0.0980171403295605, -0.9951847266721969}, // k=94
+    {-0.0490676743274180, -0.9987954562051724}, // k=95
+    {-0.0000000000000002, -1.0000000000000000}, // k=96
+    {0.0490676743274177, -0.9987954562051724},  // k=97
+    {0.0980171403295601, -0.9951847266721969},  // k=98
+    {0.1467304744553619, -0.9891765099647809},  // k=99
+    {0.1950903220161283, -0.9807852804032304},  // k=100
+    {0.2429801799032638, -0.9700312531945440},  // k=101
+    {0.2902846772544621, -0.9569403357322089},  // k=102
+    {0.3368898533922196, -0.9415440651830209},  // k=103
+    {0.3826834323650900, -0.9238795325112866},  // k=104
+    {0.4275550934302821, -0.9039892931234433},  // k=105
+    {0.4713967368259976, -0.8819212643483550},  // k=106
+    {0.5141027441932216, -0.8577286100002722},  // k=107
+    {0.5555702330196018, -0.8314696123025455},  // k=108
+    {0.5956993044924329, -0.8032075314806453},  // k=109
+    {0.6343932841636456, -0.7730104533627369},  // k=110
+    {0.6715589548470183, -0.7409511253549591},  // k=111
+    {0.7071067811865474, -0.7071067811865477},  // k=112
+    {0.7409511253549589, -0.6715589548470187},  // k=113
+    {0.7730104533627367, -0.6343932841636459},  // k=114
+    {0.8032075314806451, -0.5956993044924332},  // k=115
+    {0.8314696123025452, -0.5555702330196022},  // k=116
+    {0.8577286100002720, -0.5141027441932219},  // k=117
+    {0.8819212643483548, -0.4713967368259979},  // k=118
+    {0.9039892931234431, -0.4275550934302825},  // k=119
+    {0.9238795325112865, -0.3826834323650904},  // k=120
+    {0.9415440651830208, -0.3368898533922200},  // k=121
+    {0.9569403357322088, -0.2902846772544625},  // k=122
+    {0.9700312531945440, -0.2429801799032642},  // k=123
+    {0.9807852804032303, -0.1950903220161287},  // k=124
+    {0.9891765099647809, -0.1467304744553624},  // k=125
+    {0.9951847266721969, -0.0980171403295605},  // k=126
+    {0.9987954562051724, -0.0490676743274181},  // k=127
+};
+__constant__ double2 c_twiddle_fwd_256[256] = {
+    {1.0000000000000000, -0.0000000000000000},  // k=0
+    {0.9996988186962042, -0.0245412285229123},  // k=1
+    {0.9987954562051724, -0.0490676743274180},  // k=2
+    {0.9972904566786902, -0.0735645635996674},  // k=3
+    {0.9951847266721969, -0.0980171403295606},  // k=4
+    {0.9924795345987100, -0.1224106751992162},  // k=5
+    {0.9891765099647810, -0.1467304744553617},  // k=6
+    {0.9852776423889412, -0.1709618887603012},  // k=7
+    {0.9807852804032304, -0.1950903220161282},  // k=8
+    {0.9757021300385286, -0.2191012401568698},  // k=9
+    {0.9700312531945440, -0.2429801799032639},  // k=10
+    {0.9637760657954398, -0.2667127574748984},  // k=11
+    {0.9569403357322088, -0.2902846772544623},  // k=12
+    {0.9495281805930367, -0.3136817403988915},  // k=13
+    {0.9415440651830208, -0.3368898533922201},  // k=14
+    {0.9329927988347390, -0.3598950365349881},  // k=15
+    {0.9238795325112867, -0.3826834323650898},  // k=16
+    {0.9142097557035307, -0.4052413140049899},  // k=17
+    {0.9039892931234433, -0.4275550934302821},  // k=18
+    {0.8932243011955153, -0.4496113296546065},  // k=19
+    {0.8819212643483550, -0.4713967368259976},  // k=20
+    {0.8700869911087115, -0.4928981922297840},  // k=21
+    {0.8577286100002721, -0.5141027441932217},  // k=22
+    {0.8448535652497071, -0.5349976198870972},  // k=23
+    {0.8314696123025452, -0.5555702330196022},  // k=24
+    {0.8175848131515837, -0.5758081914178453},  // k=25
+    {0.8032075314806449, -0.5956993044924334},  // k=26
+    {0.7883464276266063, -0.6152315905806268},  // k=27
+    {0.7730104533627370, -0.6343932841636455},  // k=28
+    {0.7572088465064846, -0.6531728429537768},  // k=29
+    {0.7409511253549591, -0.6715589548470183},  // k=30
+    {0.7242470829514670, -0.6895405447370668},  // k=31
+    {0.7071067811865476, -0.7071067811865475},  // k=32
+    {0.6895405447370669, -0.7242470829514669},  // k=33
+    {0.6715589548470183, -0.7409511253549591},  // k=34
+    {0.6531728429537768, -0.7572088465064845},  // k=35
+    {0.6343932841636455, -0.7730104533627370},  // k=36
+    {0.6152315905806268, -0.7883464276266062},  // k=37
+    {0.5956993044924335, -0.8032075314806448},  // k=38
+    {0.5758081914178453, -0.8175848131515837},  // k=39
+    {0.5555702330196023, -0.8314696123025452},  // k=40
+    {0.5349976198870973, -0.8448535652497070},  // k=41
+    {0.5141027441932217, -0.8577286100002721},  // k=42
+    {0.4928981922297841, -0.8700869911087113},  // k=43
+    {0.4713967368259978, -0.8819212643483549},  // k=44
+    {0.4496113296546066, -0.8932243011955153},  // k=45
+    {0.4275550934302822, -0.9039892931234433},  // k=46
+    {0.4052413140049899, -0.9142097557035307},  // k=47
+    {0.3826834323650898, -0.9238795325112867},  // k=48
+    {0.3598950365349883, -0.9329927988347388},  // k=49
+    {0.3368898533922201, -0.9415440651830208},  // k=50
+    {0.3136817403988916, -0.9495281805930367},  // k=51
+    {0.2902846772544623, -0.9569403357322089},  // k=52
+    {0.2667127574748984, -0.9637760657954398},  // k=53
+    {0.2429801799032640, -0.9700312531945440},  // k=54
+    {0.2191012401568698, -0.9757021300385286},  // k=55
+    {0.1950903220161283, -0.9807852804032304},  // k=56
+    {0.1709618887603014, -0.9852776423889412},  // k=57
+    {0.1467304744553617, -0.9891765099647810},  // k=58
+    {0.1224106751992163, -0.9924795345987100},  // k=59
+    {0.0980171403295608, -0.9951847266721968},  // k=60
+    {0.0735645635996675, -0.9972904566786902},  // k=61
+    {0.0490676743274181, -0.9987954562051724},  // k=62
+    {0.0245412285229123, -0.9996988186962042},  // k=63
+    {0.0000000000000001, -1.0000000000000000},  // k=64
+    {-0.0245412285229121, -0.9996988186962042}, // k=65
+    {-0.0490676743274180, -0.9987954562051724}, // k=66
+    {-0.0735645635996673, -0.9972904566786902}, // k=67
+    {-0.0980171403295606, -0.9951847266721969}, // k=68
+    {-0.1224106751992162, -0.9924795345987100}, // k=69
+    {-0.1467304744553616, -0.9891765099647810}, // k=70
+    {-0.1709618887603012, -0.9852776423889412}, // k=71
+    {-0.1950903220161282, -0.9807852804032304}, // k=72
+    {-0.2191012401568697, -0.9757021300385286}, // k=73
+    {-0.2429801799032639, -0.9700312531945440}, // k=74
+    {-0.2667127574748983, -0.9637760657954398}, // k=75
+    {-0.2902846772544622, -0.9569403357322089}, // k=76
+    {-0.3136817403988914, -0.9495281805930367}, // k=77
+    {-0.3368898533922199, -0.9415440651830208}, // k=78
+    {-0.3598950365349882, -0.9329927988347388}, // k=79
+    {-0.3826834323650897, -0.9238795325112867}, // k=80
+    {-0.4052413140049897, -0.9142097557035307}, // k=81
+    {-0.4275550934302819, -0.9039892931234434}, // k=82
+    {-0.4496113296546067, -0.8932243011955152}, // k=83
+    {-0.4713967368259977, -0.8819212643483550}, // k=84
+    {-0.4928981922297840, -0.8700869911087115}, // k=85
+    {-0.5141027441932217, -0.8577286100002721}, // k=86
+    {-0.5349976198870970, -0.8448535652497072}, // k=87
+    {-0.5555702330196020, -0.8314696123025455}, // k=88
+    {-0.5758081914178453, -0.8175848131515837}, // k=89
+    {-0.5956993044924334, -0.8032075314806449}, // k=90
+    {-0.6152315905806267, -0.7883464276266063}, // k=91
+    {-0.6343932841636454, -0.7730104533627371}, // k=92
+    {-0.6531728429537765, -0.7572088465064847}, // k=93
+    {-0.6715589548470184, -0.7409511253549590}, // k=94
+    {-0.6895405447370669, -0.7242470829514669}, // k=95
+    {-0.7071067811865475, -0.7071067811865476}, // k=96
+    {-0.7242470829514668, -0.6895405447370671}, // k=97
+    {-0.7409511253549589, -0.6715589548470186}, // k=98
+    {-0.7572088465064846, -0.6531728429537766}, // k=99
+    {-0.7730104533627370, -0.6343932841636455}, // k=100
+    {-0.7883464276266062, -0.6152315905806269}, // k=101
+    {-0.8032075314806448, -0.5956993044924335}, // k=102
+    {-0.8175848131515836, -0.5758081914178454}, // k=103
+    {-0.8314696123025453, -0.5555702330196022}, // k=104
+    {-0.8448535652497071, -0.5349976198870972}, // k=105
+    {-0.8577286100002720, -0.5141027441932218}, // k=106
+    {-0.8700869911087113, -0.4928981922297841}, // k=107
+    {-0.8819212643483549, -0.4713967368259979}, // k=108
+    {-0.8932243011955152, -0.4496113296546069}, // k=109
+    {-0.9039892931234433, -0.4275550934302820}, // k=110
+    {-0.9142097557035307, -0.4052413140049899}, // k=111
+    {-0.9238795325112867, -0.3826834323650899}, // k=112
+    {-0.9329927988347388, -0.3598950365349883}, // k=113
+    {-0.9415440651830207, -0.3368898533922203}, // k=114
+    {-0.9495281805930367, -0.3136817403988914}, // k=115
+    {-0.9569403357322088, -0.2902846772544624}, // k=116
+    {-0.9637760657954398, -0.2667127574748985}, // k=117
+    {-0.9700312531945440, -0.2429801799032641}, // k=118
+    {-0.9757021300385285, -0.2191012401568700}, // k=119
+    {-0.9807852804032304, -0.1950903220161286}, // k=120
+    {-0.9852776423889412, -0.1709618887603012}, // k=121
+    {-0.9891765099647810, -0.1467304744553618}, // k=122
+    {-0.9924795345987100, -0.1224106751992163}, // k=123
+    {-0.9951847266721968, -0.0980171403295608}, // k=124
+    {-0.9972904566786902, -0.0735645635996677}, // k=125
+    {-0.9987954562051724, -0.0490676743274180}, // k=126
+    {-0.9996988186962042, -0.0245412285229123}, // k=127
+    {-1.0000000000000000, -0.0000000000000001}, // k=128
+    {-0.9996988186962042, 0.0245412285229121},  // k=129
+    {-0.9987954562051724, 0.0490676743274177},  // k=130
+    {-0.9972904566786902, 0.0735645635996675},  // k=131
+    {-0.9951847266721969, 0.0980171403295606},  // k=132
+    {-0.9924795345987100, 0.1224106751992161},  // k=133
+    {-0.9891765099647810, 0.1467304744553616},  // k=134
+    {-0.9852776423889413, 0.1709618887603010},  // k=135
+    {-0.9807852804032304, 0.1950903220161284},  // k=136
+    {-0.9757021300385286, 0.2191012401568698},  // k=137
+    {-0.9700312531945440, 0.2429801799032638},  // k=138
+    {-0.9637760657954400, 0.2667127574748983},  // k=139
+    {-0.9569403357322089, 0.2902846772544621},  // k=140
+    {-0.9495281805930368, 0.3136817403988912},  // k=141
+    {-0.9415440651830208, 0.3368898533922201},  // k=142
+    {-0.9329927988347390, 0.3598950365349881},  // k=143
+    {-0.9238795325112868, 0.3826834323650897},  // k=144
+    {-0.9142097557035307, 0.4052413140049897},  // k=145
+    {-0.9039892931234434, 0.4275550934302818},  // k=146
+    {-0.8932243011955153, 0.4496113296546067},  // k=147
+    {-0.8819212643483550, 0.4713967368259976},  // k=148
+    {-0.8700869911087115, 0.4928981922297839},  // k=149
+    {-0.8577286100002721, 0.5141027441932216},  // k=150
+    {-0.8448535652497072, 0.5349976198870969},  // k=151
+    {-0.8314696123025455, 0.5555702330196020},  // k=152
+    {-0.8175848131515837, 0.5758081914178453},  // k=153
+    {-0.8032075314806449, 0.5956993044924332},  // k=154
+    {-0.7883464276266063, 0.6152315905806267},  // k=155
+    {-0.7730104533627371, 0.6343932841636453},  // k=156
+    {-0.7572088465064848, 0.6531728429537765},  // k=157
+    {-0.7409511253549591, 0.6715589548470184},  // k=158
+    {-0.7242470829514670, 0.6895405447370668},  // k=159
+    {-0.7071067811865477, 0.7071067811865475},  // k=160
+    {-0.6895405447370671, 0.7242470829514668},  // k=161
+    {-0.6715589548470187, 0.7409511253549589},  // k=162
+    {-0.6531728429537771, 0.7572088465064842},  // k=163
+    {-0.6343932841636459, 0.7730104533627367},  // k=164
+    {-0.6152315905806273, 0.7883464276266059},  // k=165
+    {-0.5956993044924331, 0.8032075314806451},  // k=166
+    {-0.5758081914178452, 0.8175848131515838},  // k=167
+    {-0.5555702330196022, 0.8314696123025452},  // k=168
+    {-0.5349976198870973, 0.8448535652497070},  // k=169
+    {-0.5141027441932218, 0.8577286100002720},  // k=170
+    {-0.4928981922297842, 0.8700869911087113},  // k=171
+    {-0.4713967368259979, 0.8819212643483549},  // k=172
+    {-0.4496113296546069, 0.8932243011955152},  // k=173
+    {-0.4275550934302825, 0.9039892931234431},  // k=174
+    {-0.4052413140049904, 0.9142097557035305},  // k=175
+    {-0.3826834323650903, 0.9238795325112865},  // k=176
+    {-0.3598950365349879, 0.9329927988347390},  // k=177
+    {-0.3368898533922199, 0.9415440651830208},  // k=178
+    {-0.3136817403988915, 0.9495281805930367},  // k=179
+    {-0.2902846772544624, 0.9569403357322088},  // k=180
+    {-0.2667127574748985, 0.9637760657954398},  // k=181
+    {-0.2429801799032641, 0.9700312531945440},  // k=182
+    {-0.2191012401568701, 0.9757021300385285},  // k=183
+    {-0.1950903220161287, 0.9807852804032303},  // k=184
+    {-0.1709618887603017, 0.9852776423889411},  // k=185
+    {-0.1467304744553623, 0.9891765099647809},  // k=186
+    {-0.1224106751992160, 0.9924795345987101},  // k=187
+    {-0.0980171403295605, 0.9951847266721969},  // k=188
+    {-0.0735645635996674, 0.9972904566786902},  // k=189
+    {-0.0490676743274180, 0.9987954562051724},  // k=190
+    {-0.0245412285229124, 0.9996988186962042},  // k=191
+    {-0.0000000000000002, 1.0000000000000000},  // k=192
+    {0.0245412285229120, 0.9996988186962042},   // k=193
+    {0.0490676743274177, 0.9987954562051724},   // k=194
+    {0.0735645635996670, 0.9972904566786902},   // k=195
+    {0.0980171403295601, 0.9951847266721969},   // k=196
+    {0.1224106751992156, 0.9924795345987101},   // k=197
+    {0.1467304744553619, 0.9891765099647809},   // k=198
+    {0.1709618887603013, 0.9852776423889412},   // k=199
+    {0.1950903220161283, 0.9807852804032304},   // k=200
+    {0.2191012401568697, 0.9757021300385286},   // k=201
+    {0.2429801799032638, 0.9700312531945440},   // k=202
+    {0.2667127574748982, 0.9637760657954400},   // k=203
+    {0.2902846772544621, 0.9569403357322089},   // k=204
+    {0.3136817403988911, 0.9495281805930368},   // k=205
+    {0.3368898533922196, 0.9415440651830209},   // k=206
+    {0.3598950365349876, 0.9329927988347391},   // k=207
+    {0.3826834323650900, 0.9238795325112866},   // k=208
+    {0.4052413140049900, 0.9142097557035306},   // k=209
+    {0.4275550934302821, 0.9039892931234433},   // k=210
+    {0.4496113296546066, 0.8932243011955153},   // k=211
+    {0.4713967368259976, 0.8819212643483550},   // k=212
+    {0.4928981922297839, 0.8700869911087115},   // k=213
+    {0.5141027441932216, 0.8577286100002722},   // k=214
+    {0.5349976198870969, 0.8448535652497072},   // k=215
+    {0.5555702330196018, 0.8314696123025455},   // k=216
+    {0.5758081914178449, 0.8175848131515840},   // k=217
+    {0.5956993044924329, 0.8032075314806453},   // k=218
+    {0.6152315905806270, 0.7883464276266061},   // k=219
+    {0.6343932841636456, 0.7730104533627369},   // k=220
+    {0.6531728429537768, 0.7572088465064846},   // k=221
+    {0.6715589548470183, 0.7409511253549591},   // k=222
+    {0.6895405447370668, 0.7242470829514670},   // k=223
+    {0.7071067811865474, 0.7071067811865477},   // k=224
+    {0.7242470829514667, 0.6895405447370672},   // k=225
+    {0.7409511253549589, 0.6715589548470187},   // k=226
+    {0.7572088465064842, 0.6531728429537771},   // k=227
+    {0.7730104533627367, 0.6343932841636459},   // k=228
+    {0.7883464276266059, 0.6152315905806274},   // k=229
+    {0.8032075314806451, 0.5956993044924332},   // k=230
+    {0.8175848131515837, 0.5758081914178452},   // k=231
+    {0.8314696123025452, 0.5555702330196022},   // k=232
+    {0.8448535652497070, 0.5349976198870973},   // k=233
+    {0.8577286100002720, 0.5141027441932219},   // k=234
+    {0.8700869911087113, 0.4928981922297843},   // k=235
+    {0.8819212643483548, 0.4713967368259979},   // k=236
+    {0.8932243011955151, 0.4496113296546070},   // k=237
+    {0.9039892931234431, 0.4275550934302825},   // k=238
+    {0.9142097557035305, 0.4052413140049904},   // k=239
+    {0.9238795325112865, 0.3826834323650904},   // k=240
+    {0.9329927988347390, 0.3598950365349880},   // k=241
+    {0.9415440651830208, 0.3368898533922200},   // k=242
+    {0.9495281805930367, 0.3136817403988915},   // k=243
+    {0.9569403357322088, 0.2902846772544625},   // k=244
+    {0.9637760657954398, 0.2667127574748986},   // k=245
+    {0.9700312531945440, 0.2429801799032642},   // k=246
+    {0.9757021300385285, 0.2191012401568702},   // k=247
+    {0.9807852804032303, 0.1950903220161287},   // k=248
+    {0.9852776423889411, 0.1709618887603018},   // k=249
+    {0.9891765099647809, 0.1467304744553624},   // k=250
+    {0.9924795345987100, 0.1224106751992160},   // k=251
+    {0.9951847266721969, 0.0980171403295605},   // k=252
+    {0.9972904566786902, 0.0735645635996674},   // k=253
+    {0.9987954562051724, 0.0490676743274181},   // k=254
+    {0.9996988186962042, 0.0245412285229124},   // k=255
+};
+
+__constant__ double2 c_twiddle_inv_256[256] = {
+    {1.0000000000000000, 0.0000000000000000},   // k=0
+    {0.9996988186962042, 0.0245412285229123},   // k=1
+    {0.9987954562051724, 0.0490676743274180},   // k=2
+    {0.9972904566786902, 0.0735645635996674},   // k=3
+    {0.9951847266721969, 0.0980171403295606},   // k=4
+    {0.9924795345987100, 0.1224106751992162},   // k=5
+    {0.9891765099647810, 0.1467304744553617},   // k=6
+    {0.9852776423889412, 0.1709618887603012},   // k=7
+    {0.9807852804032304, 0.1950903220161282},   // k=8
+    {0.9757021300385286, 0.2191012401568698},   // k=9
+    {0.9700312531945440, 0.2429801799032639},   // k=10
+    {0.9637760657954398, 0.2667127574748984},   // k=11
+    {0.9569403357322088, 0.2902846772544623},   // k=12
+    {0.9495281805930367, 0.3136817403988915},   // k=13
+    {0.9415440651830208, 0.3368898533922201},   // k=14
+    {0.9329927988347390, 0.3598950365349881},   // k=15
+    {0.9238795325112867, 0.3826834323650898},   // k=16
+    {0.9142097557035307, 0.4052413140049899},   // k=17
+    {0.9039892931234433, 0.4275550934302821},   // k=18
+    {0.8932243011955153, 0.4496113296546065},   // k=19
+    {0.8819212643483550, 0.4713967368259976},   // k=20
+    {0.8700869911087115, 0.4928981922297840},   // k=21
+    {0.8577286100002721, 0.5141027441932217},   // k=22
+    {0.8448535652497071, 0.5349976198870972},   // k=23
+    {0.8314696123025452, 0.5555702330196022},   // k=24
+    {0.8175848131515837, 0.5758081914178453},   // k=25
+    {0.8032075314806449, 0.5956993044924334},   // k=26
+    {0.7883464276266063, 0.6152315905806268},   // k=27
+    {0.7730104533627370, 0.6343932841636455},   // k=28
+    {0.7572088465064846, 0.6531728429537768},   // k=29
+    {0.7409511253549591, 0.6715589548470183},   // k=30
+    {0.7242470829514670, 0.6895405447370668},   // k=31
+    {0.7071067811865476, 0.7071067811865475},   // k=32
+    {0.6895405447370669, 0.7242470829514669},   // k=33
+    {0.6715589548470183, 0.7409511253549591},   // k=34
+    {0.6531728429537768, 0.7572088465064845},   // k=35
+    {0.6343932841636455, 0.7730104533627370},   // k=36
+    {0.6152315905806268, 0.7883464276266062},   // k=37
+    {0.5956993044924335, 0.8032075314806448},   // k=38
+    {0.5758081914178453, 0.8175848131515837},   // k=39
+    {0.5555702330196023, 0.8314696123025452},   // k=40
+    {0.5349976198870973, 0.8448535652497070},   // k=41
+    {0.5141027441932217, 0.8577286100002721},   // k=42
+    {0.4928981922297841, 0.8700869911087113},   // k=43
+    {0.4713967368259978, 0.8819212643483549},   // k=44
+    {0.4496113296546066, 0.8932243011955153},   // k=45
+    {0.4275550934302822, 0.9039892931234433},   // k=46
+    {0.4052413140049899, 0.9142097557035307},   // k=47
+    {0.3826834323650898, 0.9238795325112867},   // k=48
+    {0.3598950365349883, 0.9329927988347388},   // k=49
+    {0.3368898533922201, 0.9415440651830208},   // k=50
+    {0.3136817403988916, 0.9495281805930367},   // k=51
+    {0.2902846772544623, 0.9569403357322089},   // k=52
+    {0.2667127574748984, 0.9637760657954398},   // k=53
+    {0.2429801799032640, 0.9700312531945440},   // k=54
+    {0.2191012401568698, 0.9757021300385286},   // k=55
+    {0.1950903220161283, 0.9807852804032304},   // k=56
+    {0.1709618887603014, 0.9852776423889412},   // k=57
+    {0.1467304744553617, 0.9891765099647810},   // k=58
+    {0.1224106751992163, 0.9924795345987100},   // k=59
+    {0.0980171403295608, 0.9951847266721968},   // k=60
+    {0.0735645635996675, 0.9972904566786902},   // k=61
+    {0.0490676743274181, 0.9987954562051724},   // k=62
+    {0.0245412285229123, 0.9996988186962042},   // k=63
+    {0.0000000000000001, 1.0000000000000000},   // k=64
+    {-0.0245412285229121, 0.9996988186962042},  // k=65
+    {-0.0490676743274180, 0.9987954562051724},  // k=66
+    {-0.0735645635996673, 0.9972904566786902},  // k=67
+    {-0.0980171403295606, 0.9951847266721969},  // k=68
+    {-0.1224106751992162, 0.9924795345987100},  // k=69
+    {-0.1467304744553616, 0.9891765099647810},  // k=70
+    {-0.1709618887603012, 0.9852776423889412},  // k=71
+    {-0.1950903220161282, 0.9807852804032304},  // k=72
+    {-0.2191012401568697, 0.9757021300385286},  // k=73
+    {-0.2429801799032639, 0.9700312531945440},  // k=74
+    {-0.2667127574748983, 0.9637760657954398},  // k=75
+    {-0.2902846772544622, 0.9569403357322089},  // k=76
+    {-0.3136817403988914, 0.9495281805930367},  // k=77
+    {-0.3368898533922199, 0.9415440651830208},  // k=78
+    {-0.3598950365349882, 0.9329927988347388},  // k=79
+    {-0.3826834323650897, 0.9238795325112867},  // k=80
+    {-0.4052413140049897, 0.9142097557035307},  // k=81
+    {-0.4275550934302819, 0.9039892931234434},  // k=82
+    {-0.4496113296546067, 0.8932243011955152},  // k=83
+    {-0.4713967368259977, 0.8819212643483550},  // k=84
+    {-0.4928981922297840, 0.8700869911087115},  // k=85
+    {-0.5141027441932217, 0.8577286100002721},  // k=86
+    {-0.5349976198870970, 0.8448535652497072},  // k=87
+    {-0.5555702330196020, 0.8314696123025455},  // k=88
+    {-0.5758081914178453, 0.8175848131515837},  // k=89
+    {-0.5956993044924334, 0.8032075314806449},  // k=90
+    {-0.6152315905806267, 0.7883464276266063},  // k=91
+    {-0.6343932841636454, 0.7730104533627371},  // k=92
+    {-0.6531728429537765, 0.7572088465064847},  // k=93
+    {-0.6715589548470184, 0.7409511253549590},  // k=94
+    {-0.6895405447370669, 0.7242470829514669},  // k=95
+    {-0.7071067811865475, 0.7071067811865476},  // k=96
+    {-0.7242470829514668, 0.6895405447370671},  // k=97
+    {-0.7409511253549589, 0.6715589548470186},  // k=98
+    {-0.7572088465064846, 0.6531728429537766},  // k=99
+    {-0.7730104533627370, 0.6343932841636455},  // k=100
+    {-0.7883464276266062, 0.6152315905806269},  // k=101
+    {-0.8032075314806448, 0.5956993044924335},  // k=102
+    {-0.8175848131515836, 0.5758081914178454},  // k=103
+    {-0.8314696123025453, 0.5555702330196022},  // k=104
+    {-0.8448535652497071, 0.5349976198870972},  // k=105
+    {-0.8577286100002720, 0.5141027441932218},  // k=106
+    {-0.8700869911087113, 0.4928981922297841},  // k=107
+    {-0.8819212643483549, 0.4713967368259979},  // k=108
+    {-0.8932243011955152, 0.4496113296546069},  // k=109
+    {-0.9039892931234433, 0.4275550934302820},  // k=110
+    {-0.9142097557035307, 0.4052413140049899},  // k=111
+    {-0.9238795325112867, 0.3826834323650899},  // k=112
+    {-0.9329927988347388, 0.3598950365349883},  // k=113
+    {-0.9415440651830207, 0.3368898533922203},  // k=114
+    {-0.9495281805930367, 0.3136817403988914},  // k=115
+    {-0.9569403357322088, 0.2902846772544624},  // k=116
+    {-0.9637760657954398, 0.2667127574748985},  // k=117
+    {-0.9700312531945440, 0.2429801799032641},  // k=118
+    {-0.9757021300385285, 0.2191012401568700},  // k=119
+    {-0.9807852804032304, 0.1950903220161286},  // k=120
+    {-0.9852776423889412, 0.1709618887603012},  // k=121
+    {-0.9891765099647810, 0.1467304744553618},  // k=122
+    {-0.9924795345987100, 0.1224106751992163},  // k=123
+    {-0.9951847266721968, 0.0980171403295608},  // k=124
+    {-0.9972904566786902, 0.0735645635996677},  // k=125
+    {-0.9987954562051724, 0.0490676743274180},  // k=126
+    {-0.9996988186962042, 0.0245412285229123},  // k=127
+    {-1.0000000000000000, 0.0000000000000001},  // k=128
+    {-0.9996988186962042, -0.0245412285229121}, // k=129
+    {-0.9987954562051724, -0.0490676743274177}, // k=130
+    {-0.9972904566786902, -0.0735645635996675}, // k=131
+    {-0.9951847266721969, -0.0980171403295606}, // k=132
+    {-0.9924795345987100, -0.1224106751992161}, // k=133
+    {-0.9891765099647810, -0.1467304744553616}, // k=134
+    {-0.9852776423889413, -0.1709618887603010}, // k=135
+    {-0.9807852804032304, -0.1950903220161284}, // k=136
+    {-0.9757021300385286, -0.2191012401568698}, // k=137
+    {-0.9700312531945440, -0.2429801799032638}, // k=138
+    {-0.9637760657954400, -0.2667127574748983}, // k=139
+    {-0.9569403357322089, -0.2902846772544621}, // k=140
+    {-0.9495281805930368, -0.3136817403988912}, // k=141
+    {-0.9415440651830208, -0.3368898533922201}, // k=142
+    {-0.9329927988347390, -0.3598950365349881}, // k=143
+    {-0.9238795325112868, -0.3826834323650897}, // k=144
+    {-0.9142097557035307, -0.4052413140049897}, // k=145
+    {-0.9039892931234434, -0.4275550934302818}, // k=146
+    {-0.8932243011955153, -0.4496113296546067}, // k=147
+    {-0.8819212643483550, -0.4713967368259976}, // k=148
+    {-0.8700869911087115, -0.4928981922297839}, // k=149
+    {-0.8577286100002721, -0.5141027441932216}, // k=150
+    {-0.8448535652497072, -0.5349976198870969}, // k=151
+    {-0.8314696123025455, -0.5555702330196020}, // k=152
+    {-0.8175848131515837, -0.5758081914178453}, // k=153
+    {-0.8032075314806449, -0.5956993044924332}, // k=154
+    {-0.7883464276266063, -0.6152315905806267}, // k=155
+    {-0.7730104533627371, -0.6343932841636453}, // k=156
+    {-0.7572088465064848, -0.6531728429537765}, // k=157
+    {-0.7409511253549591, -0.6715589548470184}, // k=158
+    {-0.7242470829514670, -0.6895405447370668}, // k=159
+    {-0.7071067811865477, -0.7071067811865475}, // k=160
+    {-0.6895405447370671, -0.7242470829514668}, // k=161
+    {-0.6715589548470187, -0.7409511253549589}, // k=162
+    {-0.6531728429537771, -0.7572088465064842}, // k=163
+    {-0.6343932841636459, -0.7730104533627367}, // k=164
+    {-0.6152315905806273, -0.7883464276266059}, // k=165
+    {-0.5956993044924331, -0.8032075314806451}, // k=166
+    {-0.5758081914178452, -0.8175848131515838}, // k=167
+    {-0.5555702330196022, -0.8314696123025452}, // k=168
+    {-0.5349976198870973, -0.8448535652497070}, // k=169
+    {-0.5141027441932218, -0.8577286100002720}, // k=170
+    {-0.4928981922297842, -0.8700869911087113}, // k=171
+    {-0.4713967368259979, -0.8819212643483549}, // k=172
+    {-0.4496113296546069, -0.8932243011955152}, // k=173
+    {-0.4275550934302825, -0.9039892931234431}, // k=174
+    {-0.4052413140049904, -0.9142097557035305}, // k=175
+    {-0.3826834323650903, -0.9238795325112865}, // k=176
+    {-0.3598950365349879, -0.9329927988347390}, // k=177
+    {-0.3368898533922199, -0.9415440651830208}, // k=178
+    {-0.3136817403988915, -0.9495281805930367}, // k=179
+    {-0.2902846772544624, -0.9569403357322088}, // k=180
+    {-0.2667127574748985, -0.9637760657954398}, // k=181
+    {-0.2429801799032641, -0.9700312531945440}, // k=182
+    {-0.2191012401568701, -0.9757021300385285}, // k=183
+    {-0.1950903220161287, -0.9807852804032303}, // k=184
+    {-0.1709618887603017, -0.9852776423889411}, // k=185
+    {-0.1467304744553623, -0.9891765099647809}, // k=186
+    {-0.1224106751992160, -0.9924795345987101}, // k=187
+    {-0.0980171403295605, -0.9951847266721969}, // k=188
+    {-0.0735645635996674, -0.9972904566786902}, // k=189
+    {-0.0490676743274180, -0.9987954562051724}, // k=190
+    {-0.0245412285229124, -0.9996988186962042}, // k=191
+    {-0.0000000000000002, -1.0000000000000000}, // k=192
+    {0.0245412285229120, -0.9996988186962042},  // k=193
+    {0.0490676743274177, -0.9987954562051724},  // k=194
+    {0.0735645635996670, -0.9972904566786902},  // k=195
+    {0.0980171403295601, -0.9951847266721969},  // k=196
+    {0.1224106751992156, -0.9924795345987101},  // k=197
+    {0.1467304744553619, -0.9891765099647809},  // k=198
+    {0.1709618887603013, -0.9852776423889412},  // k=199
+    {0.1950903220161283, -0.9807852804032304},  // k=200
+    {0.2191012401568697, -0.9757021300385286},  // k=201
+    {0.2429801799032638, -0.9700312531945440},  // k=202
+    {0.2667127574748982, -0.9637760657954400},  // k=203
+    {0.2902846772544621, -0.9569403357322089},  // k=204
+    {0.3136817403988911, -0.9495281805930368},  // k=205
+    {0.3368898533922196, -0.9415440651830209},  // k=206
+    {0.3598950365349876, -0.9329927988347391},  // k=207
+    {0.3826834323650900, -0.9238795325112866},  // k=208
+    {0.4052413140049900, -0.9142097557035306},  // k=209
+    {0.4275550934302821, -0.9039892931234433},  // k=210
+    {0.4496113296546066, -0.8932243011955153},  // k=211
+    {0.4713967368259976, -0.8819212643483550},  // k=212
+    {0.4928981922297839, -0.8700869911087115},  // k=213
+    {0.5141027441932216, -0.8577286100002722},  // k=214
+    {0.5349976198870969, -0.8448535652497072},  // k=215
+    {0.5555702330196018, -0.8314696123025455},  // k=216
+    {0.5758081914178449, -0.8175848131515840},  // k=217
+    {0.5956993044924329, -0.8032075314806453},  // k=218
+    {0.6152315905806270, -0.7883464276266061},  // k=219
+    {0.6343932841636456, -0.7730104533627369},  // k=220
+    {0.6531728429537768, -0.7572088465064846},  // k=221
+    {0.6715589548470183, -0.7409511253549591},  // k=222
+    {0.6895405447370668, -0.7242470829514670},  // k=223
+    {0.7071067811865474, -0.7071067811865477},  // k=224
+    {0.7242470829514667, -0.6895405447370672},  // k=225
+    {0.7409511253549589, -0.6715589548470187},  // k=226
+    {0.7572088465064842, -0.6531728429537771},  // k=227
+    {0.7730104533627367, -0.6343932841636459},  // k=228
+    {0.7883464276266059, -0.6152315905806274},  // k=229
+    {0.8032075314806451, -0.5956993044924332},  // k=230
+    {0.8175848131515837, -0.5758081914178452},  // k=231
+    {0.8314696123025452, -0.5555702330196022},  // k=232
+    {0.8448535652497070, -0.5349976198870973},  // k=233
+    {0.8577286100002720, -0.5141027441932219},  // k=234
+    {0.8700869911087113, -0.4928981922297843},  // k=235
+    {0.8819212643483548, -0.4713967368259979},  // k=236
+    {0.8932243011955151, -0.4496113296546070},  // k=237
+    {0.9039892931234431, -0.4275550934302825},  // k=238
+    {0.9142097557035305, -0.4052413140049904},  // k=239
+    {0.9238795325112865, -0.3826834323650904},  // k=240
+    {0.9329927988347390, -0.3598950365349880},  // k=241
+    {0.9415440651830208, -0.3368898533922200},  // k=242
+    {0.9495281805930367, -0.3136817403988915},  // k=243
+    {0.9569403357322088, -0.2902846772544625},  // k=244
+    {0.9637760657954398, -0.2667127574748986},  // k=245
+    {0.9700312531945440, -0.2429801799032642},  // k=246
+    {0.9757021300385285, -0.2191012401568702},  // k=247
+    {0.9807852804032303, -0.1950903220161287},  // k=248
+    {0.9852776423889411, -0.1709618887603018},  // k=249
+    {0.9891765099647809, -0.1467304744553624},  // k=250
+    {0.9924795345987100, -0.1224106751992160},  // k=251
+    {0.9951847266721969, -0.0980171403295605},  // k=252
+    {0.9972904566786902, -0.0735645635996674},  // k=253
+    {0.9987954562051724, -0.0490676743274181},  // k=254
+    {0.9996988186962042, -0.0245412285229124},  // k=255
+};
+__constant__ double2 c_twiddle_fwd_512[512] = {
+    {1.0000000000000000, -0.0000000000000000},  // k=0
+    {0.9999247018391445, -0.0122715382857199},  // k=1
+    {0.9996988186962042, -0.0245412285229123},  // k=2
+    {0.9993223845883495, -0.0368072229413588},  // k=3
+    {0.9987954562051724, -0.0490676743274180},  // k=4
+    {0.9981181129001492, -0.0613207363022086},  // k=5
+    {0.9972904566786902, -0.0735645635996674},  // k=6
+    {0.9963126121827780, -0.0857973123444399},  // k=7
+    {0.9951847266721969, -0.0980171403295606},  // k=8
+    {0.9939069700023561, -0.1102222072938831},  // k=9
+    {0.9924795345987100, -0.1224106751992162},  // k=10
+    {0.9909026354277800, -0.1345807085071262},  // k=11
+    {0.9891765099647810, -0.1467304744553617},  // k=12
+    {0.9873014181578584, -0.1588581433338614},  // k=13
+    {0.9852776423889412, -0.1709618887603012},  // k=14
+    {0.9831054874312163, -0.1830398879551410},  // k=15
+    {0.9807852804032304, -0.1950903220161282},  // k=16
+    {0.9783173707196277, -0.2071113761922186},  // k=17
+    {0.9757021300385286, -0.2191012401568698},  // k=18
+    {0.9729399522055602, -0.2310581082806711},  // k=19
+    {0.9700312531945440, -0.2429801799032639},  // k=20
+    {0.9669764710448521, -0.2548656596045146},  // k=21
+    {0.9637760657954398, -0.2667127574748984},  // k=22
+    {0.9604305194155658, -0.2785196893850531},  // k=23
+    {0.9569403357322088, -0.2902846772544623},  // k=24
+    {0.9533060403541939, -0.3020059493192281},  // k=25
+    {0.9495281805930367, -0.3136817403988915},  // k=26
+    {0.9456073253805213, -0.3253102921622629},  // k=27
+    {0.9415440651830208, -0.3368898533922201},  // k=28
+    {0.9373390119125750, -0.3484186802494346},  // k=29
+    {0.9329927988347390, -0.3598950365349881},  // k=30
+    {0.9285060804732156, -0.3713171939518375},  // k=31
+    {0.9238795325112867, -0.3826834323650898},  // k=32
+    {0.9191138516900578, -0.3939920400610481},  // k=33
+    {0.9142097557035307, -0.4052413140049899},  // k=34
+    {0.9091679830905224, -0.4164295600976372},  // k=35
+    {0.9039892931234433, -0.4275550934302821},  // k=36
+    {0.8986744656939538, -0.4386162385385277},  // k=37
+    {0.8932243011955153, -0.4496113296546065},  // k=38
+    {0.8876396204028539, -0.4605387109582400},  // k=39
+    {0.8819212643483550, -0.4713967368259976},  // k=40
+    {0.8760700941954066, -0.4821837720791227},  // k=41
+    {0.8700869911087115, -0.4928981922297840},  // k=42
+    {0.8639728561215868, -0.5035383837257176},  // k=43
+    {0.8577286100002721, -0.5141027441932217},  // k=44
+    {0.8513551931052652, -0.5245896826784689},  // k=45
+    {0.8448535652497071, -0.5349976198870972},  // k=46
+    {0.8382247055548381, -0.5453249884220465},  // k=47
+    {0.8314696123025452, -0.5555702330196022},  // k=48
+    {0.8245893027850253, -0.5657318107836131},  // k=49
+    {0.8175848131515837, -0.5758081914178453},  // k=50
+    {0.8104571982525948, -0.5857978574564389},  // k=51
+    {0.8032075314806449, -0.5956993044924334},  // k=52
+    {0.7958369046088836, -0.6055110414043255},  // k=53
+    {0.7883464276266063, -0.6152315905806268},  // k=54
+    {0.7807372285720945, -0.6248594881423863},  // k=55
+    {0.7730104533627370, -0.6343932841636455},  // k=56
+    {0.7651672656224590, -0.6438315428897914},  // k=57
+    {0.7572088465064846, -0.6531728429537768},  // k=58
+    {0.7491363945234594, -0.6624157775901718},  // k=59
+    {0.7409511253549591, -0.6715589548470183},  // k=60
+    {0.7326542716724128, -0.6806009977954530},  // k=61
+    {0.7242470829514670, -0.6895405447370668},  // k=62
+    {0.7157308252838186, -0.6983762494089729},  // k=63
+    {0.7071067811865476, -0.7071067811865475},  // k=64
+    {0.6983762494089729, -0.7157308252838186},  // k=65
+    {0.6895405447370669, -0.7242470829514669},  // k=66
+    {0.6806009977954531, -0.7326542716724128},  // k=67
+    {0.6715589548470183, -0.7409511253549591},  // k=68
+    {0.6624157775901718, -0.7491363945234593},  // k=69
+    {0.6531728429537768, -0.7572088465064845},  // k=70
+    {0.6438315428897915, -0.7651672656224590},  // k=71
+    {0.6343932841636455, -0.7730104533627370},  // k=72
+    {0.6248594881423865, -0.7807372285720944},  // k=73
+    {0.6152315905806268, -0.7883464276266062},  // k=74
+    {0.6055110414043255, -0.7958369046088835},  // k=75
+    {0.5956993044924335, -0.8032075314806448},  // k=76
+    {0.5857978574564389, -0.8104571982525948},  // k=77
+    {0.5758081914178453, -0.8175848131515837},  // k=78
+    {0.5657318107836132, -0.8245893027850253},  // k=79
+    {0.5555702330196023, -0.8314696123025452},  // k=80
+    {0.5453249884220465, -0.8382247055548380},  // k=81
+    {0.5349976198870973, -0.8448535652497070},  // k=82
+    {0.5245896826784688, -0.8513551931052652},  // k=83
+    {0.5141027441932217, -0.8577286100002721},  // k=84
+    {0.5035383837257176, -0.8639728561215867},  // k=85
+    {0.4928981922297841, -0.8700869911087113},  // k=86
+    {0.4821837720791228, -0.8760700941954066},  // k=87
+    {0.4713967368259978, -0.8819212643483549},  // k=88
+    {0.4605387109582400, -0.8876396204028539},  // k=89
+    {0.4496113296546066, -0.8932243011955153},  // k=90
+    {0.4386162385385277, -0.8986744656939538},  // k=91
+    {0.4275550934302822, -0.9039892931234433},  // k=92
+    {0.4164295600976373, -0.9091679830905223},  // k=93
+    {0.4052413140049899, -0.9142097557035307},  // k=94
+    {0.3939920400610481, -0.9191138516900578},  // k=95
+    {0.3826834323650898, -0.9238795325112867},  // k=96
+    {0.3713171939518376, -0.9285060804732155},  // k=97
+    {0.3598950365349883, -0.9329927988347388},  // k=98
+    {0.3484186802494345, -0.9373390119125750},  // k=99
+    {0.3368898533922201, -0.9415440651830208},  // k=100
+    {0.3253102921622630, -0.9456073253805213},  // k=101
+    {0.3136817403988916, -0.9495281805930367},  // k=102
+    {0.3020059493192282, -0.9533060403541938},  // k=103
+    {0.2902846772544623, -0.9569403357322089},  // k=104
+    {0.2785196893850531, -0.9604305194155658},  // k=105
+    {0.2667127574748984, -0.9637760657954398},  // k=106
+    {0.2548656596045146, -0.9669764710448521},  // k=107
+    {0.2429801799032640, -0.9700312531945440},  // k=108
+    {0.2310581082806713, -0.9729399522055601},  // k=109
+    {0.2191012401568698, -0.9757021300385286},  // k=110
+    {0.2071113761922186, -0.9783173707196277},  // k=111
+    {0.1950903220161283, -0.9807852804032304},  // k=112
+    {0.1830398879551411, -0.9831054874312163},  // k=113
+    {0.1709618887603014, -0.9852776423889412},  // k=114
+    {0.1588581433338614, -0.9873014181578584},  // k=115
+    {0.1467304744553617, -0.9891765099647810},  // k=116
+    {0.1345807085071262, -0.9909026354277800},  // k=117
+    {0.1224106751992163, -0.9924795345987100},  // k=118
+    {0.1102222072938832, -0.9939069700023561},  // k=119
+    {0.0980171403295608, -0.9951847266721968},  // k=120
+    {0.0857973123444399, -0.9963126121827780},  // k=121
+    {0.0735645635996675, -0.9972904566786902},  // k=122
+    {0.0613207363022086, -0.9981181129001492},  // k=123
+    {0.0490676743274181, -0.9987954562051724},  // k=124
+    {0.0368072229413590, -0.9993223845883495},  // k=125
+    {0.0245412285229123, -0.9996988186962042},  // k=126
+    {0.0122715382857199, -0.9999247018391445},  // k=127
+    {0.0000000000000001, -1.0000000000000000},  // k=128
+    {-0.0122715382857198, -0.9999247018391445}, // k=129
+    {-0.0245412285229121, -0.9996988186962042}, // k=130
+    {-0.0368072229413589, -0.9993223845883495}, // k=131
+    {-0.0490676743274180, -0.9987954562051724}, // k=132
+    {-0.0613207363022085, -0.9981181129001492}, // k=133
+    {-0.0735645635996673, -0.9972904566786902}, // k=134
+    {-0.0857973123444398, -0.9963126121827780}, // k=135
+    {-0.0980171403295606, -0.9951847266721969}, // k=136
+    {-0.1102222072938831, -0.9939069700023561}, // k=137
+    {-0.1224106751992162, -0.9924795345987100}, // k=138
+    {-0.1345807085071261, -0.9909026354277800}, // k=139
+    {-0.1467304744553616, -0.9891765099647810}, // k=140
+    {-0.1588581433338613, -0.9873014181578584}, // k=141
+    {-0.1709618887603012, -0.9852776423889412}, // k=142
+    {-0.1830398879551409, -0.9831054874312163}, // k=143
+    {-0.1950903220161282, -0.9807852804032304}, // k=144
+    {-0.2071113761922184, -0.9783173707196277}, // k=145
+    {-0.2191012401568697, -0.9757021300385286}, // k=146
+    {-0.2310581082806711, -0.9729399522055602}, // k=147
+    {-0.2429801799032639, -0.9700312531945440}, // k=148
+    {-0.2548656596045145, -0.9669764710448521}, // k=149
+    {-0.2667127574748983, -0.9637760657954398}, // k=150
+    {-0.2785196893850529, -0.9604305194155659}, // k=151
+    {-0.2902846772544622, -0.9569403357322089}, // k=152
+    {-0.3020059493192281, -0.9533060403541939}, // k=153
+    {-0.3136817403988914, -0.9495281805930367}, // k=154
+    {-0.3253102921622629, -0.9456073253805214}, // k=155
+    {-0.3368898533922199, -0.9415440651830208}, // k=156
+    {-0.3484186802494344, -0.9373390119125750}, // k=157
+    {-0.3598950365349882, -0.9329927988347388}, // k=158
+    {-0.3713171939518375, -0.9285060804732156}, // k=159
+    {-0.3826834323650897, -0.9238795325112867}, // k=160
+    {-0.3939920400610480, -0.9191138516900578}, // k=161
+    {-0.4052413140049897, -0.9142097557035307}, // k=162
+    {-0.4164295600976370, -0.9091679830905225}, // k=163
+    {-0.4275550934302819, -0.9039892931234434}, // k=164
+    {-0.4386162385385274, -0.8986744656939539}, // k=165
+    {-0.4496113296546067, -0.8932243011955152}, // k=166
+    {-0.4605387109582401, -0.8876396204028539}, // k=167
+    {-0.4713967368259977, -0.8819212643483550}, // k=168
+    {-0.4821837720791227, -0.8760700941954066}, // k=169
+    {-0.4928981922297840, -0.8700869911087115}, // k=170
+    {-0.5035383837257175, -0.8639728561215868}, // k=171
+    {-0.5141027441932217, -0.8577286100002721}, // k=172
+    {-0.5245896826784687, -0.8513551931052652}, // k=173
+    {-0.5349976198870970, -0.8448535652497072}, // k=174
+    {-0.5453249884220462, -0.8382247055548382}, // k=175
+    {-0.5555702330196020, -0.8314696123025455}, // k=176
+    {-0.5657318107836132, -0.8245893027850252}, // k=177
+    {-0.5758081914178453, -0.8175848131515837}, // k=178
+    {-0.5857978574564389, -0.8104571982525948}, // k=179
+    {-0.5956993044924334, -0.8032075314806449}, // k=180
+    {-0.6055110414043254, -0.7958369046088836}, // k=181
+    {-0.6152315905806267, -0.7883464276266063}, // k=182
+    {-0.6248594881423862, -0.7807372285720946}, // k=183
+    {-0.6343932841636454, -0.7730104533627371}, // k=184
+    {-0.6438315428897913, -0.7651672656224591}, // k=185
+    {-0.6531728429537765, -0.7572088465064847}, // k=186
+    {-0.6624157775901719, -0.7491363945234593}, // k=187
+    {-0.6715589548470184, -0.7409511253549590}, // k=188
+    {-0.6806009977954530, -0.7326542716724128}, // k=189
+    {-0.6895405447370669, -0.7242470829514669}, // k=190
+    {-0.6983762494089728, -0.7157308252838187}, // k=191
+    {-0.7071067811865475, -0.7071067811865476}, // k=192
+    {-0.7157308252838186, -0.6983762494089729}, // k=193
+    {-0.7242470829514668, -0.6895405447370671}, // k=194
+    {-0.7326542716724127, -0.6806009977954532}, // k=195
+    {-0.7409511253549589, -0.6715589548470186}, // k=196
+    {-0.7491363945234591, -0.6624157775901720}, // k=197
+    {-0.7572088465064846, -0.6531728429537766}, // k=198
+    {-0.7651672656224590, -0.6438315428897914}, // k=199
+    {-0.7730104533627370, -0.6343932841636455}, // k=200
+    {-0.7807372285720945, -0.6248594881423863}, // k=201
+    {-0.7883464276266062, -0.6152315905806269}, // k=202
+    {-0.7958369046088835, -0.6055110414043257}, // k=203
+    {-0.8032075314806448, -0.5956993044924335}, // k=204
+    {-0.8104571982525947, -0.5857978574564390}, // k=205
+    {-0.8175848131515836, -0.5758081914178454}, // k=206
+    {-0.8245893027850251, -0.5657318107836135}, // k=207
+    {-0.8314696123025453, -0.5555702330196022}, // k=208
+    {-0.8382247055548381, -0.5453249884220464}, // k=209
+    {-0.8448535652497071, -0.5349976198870972}, // k=210
+    {-0.8513551931052652, -0.5245896826784689}, // k=211
+    {-0.8577286100002720, -0.5141027441932218}, // k=212
+    {-0.8639728561215867, -0.5035383837257177}, // k=213
+    {-0.8700869911087113, -0.4928981922297841}, // k=214
+    {-0.8760700941954065, -0.4821837720791229}, // k=215
+    {-0.8819212643483549, -0.4713967368259979}, // k=216
+    {-0.8876396204028538, -0.4605387109582402}, // k=217
+    {-0.8932243011955152, -0.4496113296546069}, // k=218
+    {-0.8986744656939539, -0.4386162385385275}, // k=219
+    {-0.9039892931234433, -0.4275550934302820}, // k=220
+    {-0.9091679830905224, -0.4164295600976372}, // k=221
+    {-0.9142097557035307, -0.4052413140049899}, // k=222
+    {-0.9191138516900578, -0.3939920400610482}, // k=223
+    {-0.9238795325112867, -0.3826834323650899}, // k=224
+    {-0.9285060804732155, -0.3713171939518377}, // k=225
+    {-0.9329927988347388, -0.3598950365349883}, // k=226
+    {-0.9373390119125748, -0.3484186802494348}, // k=227
+    {-0.9415440651830207, -0.3368898533922203}, // k=228
+    {-0.9456073253805212, -0.3253102921622633}, // k=229
+    {-0.9495281805930367, -0.3136817403988914}, // k=230
+    {-0.9533060403541939, -0.3020059493192280}, // k=231
+    {-0.9569403357322088, -0.2902846772544624}, // k=232
+    {-0.9604305194155658, -0.2785196893850532}, // k=233
+    {-0.9637760657954398, -0.2667127574748985}, // k=234
+    {-0.9669764710448521, -0.2548656596045147}, // k=235
+    {-0.9700312531945440, -0.2429801799032641}, // k=236
+    {-0.9729399522055601, -0.2310581082806713}, // k=237
+    {-0.9757021300385285, -0.2191012401568700}, // k=238
+    {-0.9783173707196275, -0.2071113761922188}, // k=239
+    {-0.9807852804032304, -0.1950903220161286}, // k=240
+    {-0.9831054874312163, -0.1830398879551409}, // k=241
+    {-0.9852776423889412, -0.1709618887603012}, // k=242
+    {-0.9873014181578584, -0.1588581433338615}, // k=243
+    {-0.9891765099647810, -0.1467304744553618}, // k=244
+    {-0.9909026354277800, -0.1345807085071263}, // k=245
+    {-0.9924795345987100, -0.1224106751992163}, // k=246
+    {-0.9939069700023561, -0.1102222072938832}, // k=247
+    {-0.9951847266721968, -0.0980171403295608}, // k=248
+    {-0.9963126121827780, -0.0857973123444402}, // k=249
+    {-0.9972904566786902, -0.0735645635996677}, // k=250
+    {-0.9981181129001492, -0.0613207363022085}, // k=251
+    {-0.9987954562051724, -0.0490676743274180}, // k=252
+    {-0.9993223845883495, -0.0368072229413588}, // k=253
+    {-0.9996988186962042, -0.0245412285229123}, // k=254
+    {-0.9999247018391445, -0.0122715382857200}, // k=255
+    {-1.0000000000000000, -0.0000000000000001}, // k=256
+    {-0.9999247018391445, 0.0122715382857198},  // k=257
+    {-0.9996988186962042, 0.0245412285229121},  // k=258
+    {-0.9993223845883495, 0.0368072229413586},  // k=259
+    {-0.9987954562051724, 0.0490676743274177},  // k=260
+    {-0.9981181129001492, 0.0613207363022082},  // k=261
+    {-0.9972904566786902, 0.0735645635996675},  // k=262
+    {-0.9963126121827780, 0.0857973123444399},  // k=263
+    {-0.9951847266721969, 0.0980171403295606},  // k=264
+    {-0.9939069700023561, 0.1102222072938830},  // k=265
+    {-0.9924795345987100, 0.1224106751992161},  // k=266
+    {-0.9909026354277800, 0.1345807085071261},  // k=267
+    {-0.9891765099647810, 0.1467304744553616},  // k=268
+    {-0.9873014181578584, 0.1588581433338612},  // k=269
+    {-0.9852776423889413, 0.1709618887603010},  // k=270
+    {-0.9831054874312164, 0.1830398879551406},  // k=271
+    {-0.9807852804032304, 0.1950903220161284},  // k=272
+    {-0.9783173707196277, 0.2071113761922186},  // k=273
+    {-0.9757021300385286, 0.2191012401568698},  // k=274
+    {-0.9729399522055602, 0.2310581082806711},  // k=275
+    {-0.9700312531945440, 0.2429801799032638},  // k=276
+    {-0.9669764710448522, 0.2548656596045145},  // k=277
+    {-0.9637760657954400, 0.2667127574748983},  // k=278
+    {-0.9604305194155659, 0.2785196893850529},  // k=279
+    {-0.9569403357322089, 0.2902846772544621},  // k=280
+    {-0.9533060403541940, 0.3020059493192278},  // k=281
+    {-0.9495281805930368, 0.3136817403988912},  // k=282
+    {-0.9456073253805213, 0.3253102921622630},  // k=283
+    {-0.9415440651830208, 0.3368898533922201},  // k=284
+    {-0.9373390119125750, 0.3484186802494346},  // k=285
+    {-0.9329927988347390, 0.3598950365349881},  // k=286
+    {-0.9285060804732156, 0.3713171939518374},  // k=287
+    {-0.9238795325112868, 0.3826834323650897},  // k=288
+    {-0.9191138516900578, 0.3939920400610479},  // k=289
+    {-0.9142097557035307, 0.4052413140049897},  // k=290
+    {-0.9091679830905225, 0.4164295600976369},  // k=291
+    {-0.9039892931234434, 0.4275550934302818},  // k=292
+    {-0.8986744656939540, 0.4386162385385273},  // k=293
+    {-0.8932243011955153, 0.4496113296546067},  // k=294
+    {-0.8876396204028539, 0.4605387109582401},  // k=295
+    {-0.8819212643483550, 0.4713967368259976},  // k=296
+    {-0.8760700941954066, 0.4821837720791227},  // k=297
+    {-0.8700869911087115, 0.4928981922297839},  // k=298
+    {-0.8639728561215868, 0.5035383837257175},  // k=299
+    {-0.8577286100002721, 0.5141027441932216},  // k=300
+    {-0.8513551931052653, 0.5245896826784687},  // k=301
+    {-0.8448535652497072, 0.5349976198870969},  // k=302
+    {-0.8382247055548382, 0.5453249884220461},  // k=303
+    {-0.8314696123025455, 0.5555702330196020},  // k=304
+    {-0.8245893027850253, 0.5657318107836132},  // k=305
+    {-0.8175848131515837, 0.5758081914178453},  // k=306
+    {-0.8104571982525948, 0.5857978574564389},  // k=307
+    {-0.8032075314806449, 0.5956993044924332},  // k=308
+    {-0.7958369046088836, 0.6055110414043254},  // k=309
+    {-0.7883464276266063, 0.6152315905806267},  // k=310
+    {-0.7807372285720946, 0.6248594881423862},  // k=311
+    {-0.7730104533627371, 0.6343932841636453},  // k=312
+    {-0.7651672656224591, 0.6438315428897913},  // k=313
+    {-0.7572088465064848, 0.6531728429537765},  // k=314
+    {-0.7491363945234593, 0.6624157775901718},  // k=315
+    {-0.7409511253549591, 0.6715589548470184},  // k=316
+    {-0.7326542716724128, 0.6806009977954530},  // k=317
+    {-0.7242470829514670, 0.6895405447370668},  // k=318
+    {-0.7157308252838187, 0.6983762494089728},  // k=319
+    {-0.7071067811865477, 0.7071067811865475},  // k=320
+    {-0.6983762494089730, 0.7157308252838185},  // k=321
+    {-0.6895405447370671, 0.7242470829514668},  // k=322
+    {-0.6806009977954532, 0.7326542716724126},  // k=323
+    {-0.6715589548470187, 0.7409511253549589},  // k=324
+    {-0.6624157775901720, 0.7491363945234590},  // k=325
+    {-0.6531728429537771, 0.7572088465064842},  // k=326
+    {-0.6438315428897915, 0.7651672656224590},  // k=327
+    {-0.6343932841636459, 0.7730104533627367},  // k=328
+    {-0.6248594881423865, 0.7807372285720944},  // k=329
+    {-0.6152315905806273, 0.7883464276266059},  // k=330
+    {-0.6055110414043257, 0.7958369046088835},  // k=331
+    {-0.5956993044924331, 0.8032075314806451},  // k=332
+    {-0.5857978574564391, 0.8104571982525947},  // k=333
+    {-0.5758081914178452, 0.8175848131515838},  // k=334
+    {-0.5657318107836135, 0.8245893027850251},  // k=335
+    {-0.5555702330196022, 0.8314696123025452},  // k=336
+    {-0.5453249884220468, 0.8382247055548379},  // k=337
+    {-0.5349976198870973, 0.8448535652497070},  // k=338
+    {-0.5245896826784694, 0.8513551931052649},  // k=339
+    {-0.5141027441932218, 0.8577286100002720},  // k=340
+    {-0.5035383837257180, 0.8639728561215865},  // k=341
+    {-0.4928981922297842, 0.8700869911087113},  // k=342
+    {-0.4821837720791226, 0.8760700941954067},  // k=343
+    {-0.4713967368259979, 0.8819212643483549},  // k=344
+    {-0.4605387109582399, 0.8876396204028540},  // k=345
+    {-0.4496113296546069, 0.8932243011955152},  // k=346
+    {-0.4386162385385276, 0.8986744656939538},  // k=347
+    {-0.4275550934302825, 0.9039892931234431},  // k=348
+    {-0.4164295600976372, 0.9091679830905224},  // k=349
+    {-0.4052413140049904, 0.9142097557035305},  // k=350
+    {-0.3939920400610482, 0.9191138516900577},  // k=351
+    {-0.3826834323650903, 0.9238795325112865},  // k=352
+    {-0.3713171939518378, 0.9285060804732155},  // k=353
+    {-0.3598950365349879, 0.9329927988347390},  // k=354
+    {-0.3484186802494348, 0.9373390119125748},  // k=355
+    {-0.3368898533922199, 0.9415440651830208},  // k=356
+    {-0.3253102921622633, 0.9456073253805212},  // k=357
+    {-0.3136817403988915, 0.9495281805930367},  // k=358
+    {-0.3020059493192285, 0.9533060403541938},  // k=359
+    {-0.2902846772544624, 0.9569403357322088},  // k=360
+    {-0.2785196893850536, 0.9604305194155657},  // k=361
+    {-0.2667127574748985, 0.9637760657954398},  // k=362
+    {-0.2548656596045143, 0.9669764710448522},  // k=363
+    {-0.2429801799032641, 0.9700312531945440},  // k=364
+    {-0.2310581082806709, 0.9729399522055602},  // k=365
+    {-0.2191012401568701, 0.9757021300385285},  // k=366
+    {-0.2071113761922185, 0.9783173707196277},  // k=367
+    {-0.1950903220161287, 0.9807852804032303},  // k=368
+    {-0.1830398879551410, 0.9831054874312163},  // k=369
+    {-0.1709618887603017, 0.9852776423889411},  // k=370
+    {-0.1588581433338615, 0.9873014181578583},  // k=371
+    {-0.1467304744553623, 0.9891765099647809},  // k=372
+    {-0.1345807085071264, 0.9909026354277800},  // k=373
+    {-0.1224106751992160, 0.9924795345987101},  // k=374
+    {-0.1102222072938833, 0.9939069700023561},  // k=375
+    {-0.0980171403295605, 0.9951847266721969},  // k=376
+    {-0.0857973123444402, 0.9963126121827780},  // k=377
+    {-0.0735645635996674, 0.9972904566786902},  // k=378
+    {-0.0613207363022090, 0.9981181129001492},  // k=379
+    {-0.0490676743274180, 0.9987954562051724},  // k=380
+    {-0.0368072229413593, 0.9993223845883494},  // k=381
+    {-0.0245412285229124, 0.9996988186962042},  // k=382
+    {-0.0122715382857205, 0.9999247018391445},  // k=383
+    {-0.0000000000000002, 1.0000000000000000},  // k=384
+    {0.0122715382857201, 0.9999247018391445},   // k=385
+    {0.0245412285229120, 0.9996988186962042},   // k=386
+    {0.0368072229413590, 0.9993223845883495},   // k=387
+    {0.0490676743274177, 0.9987954562051724},   // k=388
+    {0.0613207363022086, 0.9981181129001492},   // k=389
+    {0.0735645635996670, 0.9972904566786902},   // k=390
+    {0.0857973123444399, 0.9963126121827780},   // k=391
+    {0.0980171403295601, 0.9951847266721969},   // k=392
+    {0.1102222072938829, 0.9939069700023561},   // k=393
+    {0.1224106751992156, 0.9924795345987101},   // k=394
+    {0.1345807085071260, 0.9909026354277800},   // k=395
+    {0.1467304744553619, 0.9891765099647809},   // k=396
+    {0.1588581433338612, 0.9873014181578584},   // k=397
+    {0.1709618887603013, 0.9852776423889412},   // k=398
+    {0.1830398879551406, 0.9831054874312164},   // k=399
+    {0.1950903220161283, 0.9807852804032304},   // k=400
+    {0.2071113761922181, 0.9783173707196278},   // k=401
+    {0.2191012401568697, 0.9757021300385286},   // k=402
+    {0.2310581082806706, 0.9729399522055603},   // k=403
+    {0.2429801799032638, 0.9700312531945440},   // k=404
+    {0.2548656596045140, 0.9669764710448523},   // k=405
+    {0.2667127574748982, 0.9637760657954400},   // k=406
+    {0.2785196893850533, 0.9604305194155658},   // k=407
+    {0.2902846772544621, 0.9569403357322089},   // k=408
+    {0.3020059493192281, 0.9533060403541939},   // k=409
+    {0.3136817403988911, 0.9495281805930368},   // k=410
+    {0.3253102921622629, 0.9456073253805213},   // k=411
+    {0.3368898533922196, 0.9415440651830209},   // k=412
+    {0.3484186802494345, 0.9373390119125750},   // k=413
+    {0.3598950365349876, 0.9329927988347391},   // k=414
+    {0.3713171939518374, 0.9285060804732156},   // k=415
+    {0.3826834323650900, 0.9238795325112866},   // k=416
+    {0.3939920400610479, 0.9191138516900579},   // k=417
+    {0.4052413140049900, 0.9142097557035306},   // k=418
+    {0.4164295600976369, 0.9091679830905225},   // k=419
+    {0.4275550934302821, 0.9039892931234433},   // k=420
+    {0.4386162385385273, 0.8986744656939540},   // k=421
+    {0.4496113296546066, 0.8932243011955153},   // k=422
+    {0.4605387109582396, 0.8876396204028542},   // k=423
+    {0.4713967368259976, 0.8819212643483550},   // k=424
+    {0.4821837720791222, 0.8760700941954069},   // k=425
+    {0.4928981922297839, 0.8700869911087115},   // k=426
+    {0.5035383837257178, 0.8639728561215866},   // k=427
+    {0.5141027441932216, 0.8577286100002722},   // k=428
+    {0.5245896826784691, 0.8513551931052651},   // k=429
+    {0.5349976198870969, 0.8448535652497072},   // k=430
+    {0.5453249884220465, 0.8382247055548380},   // k=431
+    {0.5555702330196018, 0.8314696123025455},   // k=432
+    {0.5657318107836131, 0.8245893027850253},   // k=433
+    {0.5758081914178449, 0.8175848131515840},   // k=434
+    {0.5857978574564388, 0.8104571982525949},   // k=435
+    {0.5956993044924329, 0.8032075314806453},   // k=436
+    {0.6055110414043253, 0.7958369046088837},   // k=437
+    {0.6152315905806270, 0.7883464276266061},   // k=438
+    {0.6248594881423861, 0.7807372285720946},   // k=439
+    {0.6343932841636456, 0.7730104533627369},   // k=440
+    {0.6438315428897912, 0.7651672656224592},   // k=441
+    {0.6531728429537768, 0.7572088465064846},   // k=442
+    {0.6624157775901715, 0.7491363945234596},   // k=443
+    {0.6715589548470183, 0.7409511253549591},   // k=444
+    {0.6806009977954527, 0.7326542716724131},   // k=445
+    {0.6895405447370668, 0.7242470829514670},   // k=446
+    {0.6983762494089724, 0.7157308252838190},   // k=447
+    {0.7071067811865474, 0.7071067811865477},   // k=448
+    {0.7157308252838188, 0.6983762494089727},   // k=449
+    {0.7242470829514667, 0.6895405447370672},   // k=450
+    {0.7326542716724129, 0.6806009977954530},   // k=451
+    {0.7409511253549589, 0.6715589548470187},   // k=452
+    {0.7491363945234594, 0.6624157775901718},   // k=453
+    {0.7572088465064842, 0.6531728429537771},   // k=454
+    {0.7651672656224588, 0.6438315428897915},   // k=455
+    {0.7730104533627367, 0.6343932841636459},   // k=456
+    {0.7807372285720944, 0.6248594881423865},   // k=457
+    {0.7883464276266059, 0.6152315905806274},   // k=458
+    {0.7958369046088833, 0.6055110414043257},   // k=459
+    {0.8032075314806451, 0.5956993044924332},   // k=460
+    {0.8104571982525947, 0.5857978574564391},   // k=461
+    {0.8175848131515837, 0.5758081914178452},   // k=462
+    {0.8245893027850251, 0.5657318107836136},   // k=463
+    {0.8314696123025452, 0.5555702330196022},   // k=464
+    {0.8382247055548377, 0.5453249884220468},   // k=465
+    {0.8448535652497070, 0.5349976198870973},   // k=466
+    {0.8513551931052649, 0.5245896826784694},   // k=467
+    {0.8577286100002720, 0.5141027441932219},   // k=468
+    {0.8639728561215864, 0.5035383837257181},   // k=469
+    {0.8700869911087113, 0.4928981922297843},   // k=470
+    {0.8760700941954067, 0.4821837720791226},   // k=471
+    {0.8819212643483548, 0.4713967368259979},   // k=472
+    {0.8876396204028539, 0.4605387109582399},   // k=473
+    {0.8932243011955151, 0.4496113296546070},   // k=474
+    {0.8986744656939538, 0.4386162385385277},   // k=475
+    {0.9039892931234431, 0.4275550934302825},   // k=476
+    {0.9091679830905224, 0.4164295600976373},   // k=477
+    {0.9142097557035305, 0.4052413140049904},   // k=478
+    {0.9191138516900577, 0.3939920400610483},   // k=479
+    {0.9238795325112865, 0.3826834323650904},   // k=480
+    {0.9285060804732155, 0.3713171939518378},   // k=481
+    {0.9329927988347390, 0.3598950365349880},   // k=482
+    {0.9373390119125748, 0.3484186802494349},   // k=483
+    {0.9415440651830208, 0.3368898533922200},   // k=484
+    {0.9456073253805212, 0.3253102921622634},   // k=485
+    {0.9495281805930367, 0.3136817403988915},   // k=486
+    {0.9533060403541936, 0.3020059493192286},   // k=487
+    {0.9569403357322088, 0.2902846772544625},   // k=488
+    {0.9604305194155657, 0.2785196893850537},   // k=489
+    {0.9637760657954398, 0.2667127574748986},   // k=490
+    {0.9669764710448522, 0.2548656596045144},   // k=491
+    {0.9700312531945440, 0.2429801799032642},   // k=492
+    {0.9729399522055602, 0.2310581082806710},   // k=493
+    {0.9757021300385285, 0.2191012401568702},   // k=494
+    {0.9783173707196277, 0.2071113761922185},   // k=495
+    {0.9807852804032303, 0.1950903220161287},   // k=496
+    {0.9831054874312163, 0.1830398879551410},   // k=497
+    {0.9852776423889411, 0.1709618887603018},   // k=498
+    {0.9873014181578583, 0.1588581433338616},   // k=499
+    {0.9891765099647809, 0.1467304744553624},   // k=500
+    {0.9909026354277800, 0.1345807085071264},   // k=501
+    {0.9924795345987100, 0.1224106751992160},   // k=502
+    {0.9939069700023561, 0.1102222072938834},   // k=503
+    {0.9951847266721969, 0.0980171403295605},   // k=504
+    {0.9963126121827780, 0.0857973123444403},   // k=505
+    {0.9972904566786902, 0.0735645635996674},   // k=506
+    {0.9981181129001492, 0.0613207363022091},   // k=507
+    {0.9987954562051724, 0.0490676743274181},   // k=508
+    {0.9993223845883494, 0.0368072229413594},   // k=509
+    {0.9996988186962042, 0.0245412285229124},   // k=510
+    {0.9999247018391445, 0.0122715382857206},   // k=511
+};
+
+__constant__ double2 c_twiddle_inv_512[512] = {
+    {1.0000000000000000, 0.0000000000000000},   // k=0
+    {0.9999247018391445, 0.0122715382857199},   // k=1
+    {0.9996988186962042, 0.0245412285229123},   // k=2
+    {0.9993223845883495, 0.0368072229413588},   // k=3
+    {0.9987954562051724, 0.0490676743274180},   // k=4
+    {0.9981181129001492, 0.0613207363022086},   // k=5
+    {0.9972904566786902, 0.0735645635996674},   // k=6
+    {0.9963126121827780, 0.0857973123444399},   // k=7
+    {0.9951847266721969, 0.0980171403295606},   // k=8
+    {0.9939069700023561, 0.1102222072938831},   // k=9
+    {0.9924795345987100, 0.1224106751992162},   // k=10
+    {0.9909026354277800, 0.1345807085071262},   // k=11
+    {0.9891765099647810, 0.1467304744553617},   // k=12
+    {0.9873014181578584, 0.1588581433338614},   // k=13
+    {0.9852776423889412, 0.1709618887603012},   // k=14
+    {0.9831054874312163, 0.1830398879551410},   // k=15
+    {0.9807852804032304, 0.1950903220161282},   // k=16
+    {0.9783173707196277, 0.2071113761922186},   // k=17
+    {0.9757021300385286, 0.2191012401568698},   // k=18
+    {0.9729399522055602, 0.2310581082806711},   // k=19
+    {0.9700312531945440, 0.2429801799032639},   // k=20
+    {0.9669764710448521, 0.2548656596045146},   // k=21
+    {0.9637760657954398, 0.2667127574748984},   // k=22
+    {0.9604305194155658, 0.2785196893850531},   // k=23
+    {0.9569403357322088, 0.2902846772544623},   // k=24
+    {0.9533060403541939, 0.3020059493192281},   // k=25
+    {0.9495281805930367, 0.3136817403988915},   // k=26
+    {0.9456073253805213, 0.3253102921622629},   // k=27
+    {0.9415440651830208, 0.3368898533922201},   // k=28
+    {0.9373390119125750, 0.3484186802494346},   // k=29
+    {0.9329927988347390, 0.3598950365349881},   // k=30
+    {0.9285060804732156, 0.3713171939518375},   // k=31
+    {0.9238795325112867, 0.3826834323650898},   // k=32
+    {0.9191138516900578, 0.3939920400610481},   // k=33
+    {0.9142097557035307, 0.4052413140049899},   // k=34
+    {0.9091679830905224, 0.4164295600976372},   // k=35
+    {0.9039892931234433, 0.4275550934302821},   // k=36
+    {0.8986744656939538, 0.4386162385385277},   // k=37
+    {0.8932243011955153, 0.4496113296546065},   // k=38
+    {0.8876396204028539, 0.4605387109582400},   // k=39
+    {0.8819212643483550, 0.4713967368259976},   // k=40
+    {0.8760700941954066, 0.4821837720791227},   // k=41
+    {0.8700869911087115, 0.4928981922297840},   // k=42
+    {0.8639728561215868, 0.5035383837257176},   // k=43
+    {0.8577286100002721, 0.5141027441932217},   // k=44
+    {0.8513551931052652, 0.5245896826784689},   // k=45
+    {0.8448535652497071, 0.5349976198870972},   // k=46
+    {0.8382247055548381, 0.5453249884220465},   // k=47
+    {0.8314696123025452, 0.5555702330196022},   // k=48
+    {0.8245893027850253, 0.5657318107836131},   // k=49
+    {0.8175848131515837, 0.5758081914178453},   // k=50
+    {0.8104571982525948, 0.5857978574564389},   // k=51
+    {0.8032075314806449, 0.5956993044924334},   // k=52
+    {0.7958369046088836, 0.6055110414043255},   // k=53
+    {0.7883464276266063, 0.6152315905806268},   // k=54
+    {0.7807372285720945, 0.6248594881423863},   // k=55
+    {0.7730104533627370, 0.6343932841636455},   // k=56
+    {0.7651672656224590, 0.6438315428897914},   // k=57
+    {0.7572088465064846, 0.6531728429537768},   // k=58
+    {0.7491363945234594, 0.6624157775901718},   // k=59
+    {0.7409511253549591, 0.6715589548470183},   // k=60
+    {0.7326542716724128, 0.6806009977954530},   // k=61
+    {0.7242470829514670, 0.6895405447370668},   // k=62
+    {0.7157308252838186, 0.6983762494089729},   // k=63
+    {0.7071067811865476, 0.7071067811865475},   // k=64
+    {0.6983762494089729, 0.7157308252838186},   // k=65
+    {0.6895405447370669, 0.7242470829514669},   // k=66
+    {0.6806009977954531, 0.7326542716724128},   // k=67
+    {0.6715589548470183, 0.7409511253549591},   // k=68
+    {0.6624157775901718, 0.7491363945234593},   // k=69
+    {0.6531728429537768, 0.7572088465064845},   // k=70
+    {0.6438315428897915, 0.7651672656224590},   // k=71
+    {0.6343932841636455, 0.7730104533627370},   // k=72
+    {0.6248594881423865, 0.7807372285720944},   // k=73
+    {0.6152315905806268, 0.7883464276266062},   // k=74
+    {0.6055110414043255, 0.7958369046088835},   // k=75
+    {0.5956993044924335, 0.8032075314806448},   // k=76
+    {0.5857978574564389, 0.8104571982525948},   // k=77
+    {0.5758081914178453, 0.8175848131515837},   // k=78
+    {0.5657318107836132, 0.8245893027850253},   // k=79
+    {0.5555702330196023, 0.8314696123025452},   // k=80
+    {0.5453249884220465, 0.8382247055548380},   // k=81
+    {0.5349976198870973, 0.8448535652497070},   // k=82
+    {0.5245896826784688, 0.8513551931052652},   // k=83
+    {0.5141027441932217, 0.8577286100002721},   // k=84
+    {0.5035383837257176, 0.8639728561215867},   // k=85
+    {0.4928981922297841, 0.8700869911087113},   // k=86
+    {0.4821837720791228, 0.8760700941954066},   // k=87
+    {0.4713967368259978, 0.8819212643483549},   // k=88
+    {0.4605387109582400, 0.8876396204028539},   // k=89
+    {0.4496113296546066, 0.8932243011955153},   // k=90
+    {0.4386162385385277, 0.8986744656939538},   // k=91
+    {0.4275550934302822, 0.9039892931234433},   // k=92
+    {0.4164295600976373, 0.9091679830905223},   // k=93
+    {0.4052413140049899, 0.9142097557035307},   // k=94
+    {0.3939920400610481, 0.9191138516900578},   // k=95
+    {0.3826834323650898, 0.9238795325112867},   // k=96
+    {0.3713171939518376, 0.9285060804732155},   // k=97
+    {0.3598950365349883, 0.9329927988347388},   // k=98
+    {0.3484186802494345, 0.9373390119125750},   // k=99
+    {0.3368898533922201, 0.9415440651830208},   // k=100
+    {0.3253102921622630, 0.9456073253805213},   // k=101
+    {0.3136817403988916, 0.9495281805930367},   // k=102
+    {0.3020059493192282, 0.9533060403541938},   // k=103
+    {0.2902846772544623, 0.9569403357322089},   // k=104
+    {0.2785196893850531, 0.9604305194155658},   // k=105
+    {0.2667127574748984, 0.9637760657954398},   // k=106
+    {0.2548656596045146, 0.9669764710448521},   // k=107
+    {0.2429801799032640, 0.9700312531945440},   // k=108
+    {0.2310581082806713, 0.9729399522055601},   // k=109
+    {0.2191012401568698, 0.9757021300385286},   // k=110
+    {0.2071113761922186, 0.9783173707196277},   // k=111
+    {0.1950903220161283, 0.9807852804032304},   // k=112
+    {0.1830398879551411, 0.9831054874312163},   // k=113
+    {0.1709618887603014, 0.9852776423889412},   // k=114
+    {0.1588581433338614, 0.9873014181578584},   // k=115
+    {0.1467304744553617, 0.9891765099647810},   // k=116
+    {0.1345807085071262, 0.9909026354277800},   // k=117
+    {0.1224106751992163, 0.9924795345987100},   // k=118
+    {0.1102222072938832, 0.9939069700023561},   // k=119
+    {0.0980171403295608, 0.9951847266721968},   // k=120
+    {0.0857973123444399, 0.9963126121827780},   // k=121
+    {0.0735645635996675, 0.9972904566786902},   // k=122
+    {0.0613207363022086, 0.9981181129001492},   // k=123
+    {0.0490676743274181, 0.9987954562051724},   // k=124
+    {0.0368072229413590, 0.9993223845883495},   // k=125
+    {0.0245412285229123, 0.9996988186962042},   // k=126
+    {0.0122715382857199, 0.9999247018391445},   // k=127
+    {0.0000000000000001, 1.0000000000000000},   // k=128
+    {-0.0122715382857198, 0.9999247018391445},  // k=129
+    {-0.0245412285229121, 0.9996988186962042},  // k=130
+    {-0.0368072229413589, 0.9993223845883495},  // k=131
+    {-0.0490676743274180, 0.9987954562051724},  // k=132
+    {-0.0613207363022085, 0.9981181129001492},  // k=133
+    {-0.0735645635996673, 0.9972904566786902},  // k=134
+    {-0.0857973123444398, 0.9963126121827780},  // k=135
+    {-0.0980171403295606, 0.9951847266721969},  // k=136
+    {-0.1102222072938831, 0.9939069700023561},  // k=137
+    {-0.1224106751992162, 0.9924795345987100},  // k=138
+    {-0.1345807085071261, 0.9909026354277800},  // k=139
+    {-0.1467304744553616, 0.9891765099647810},  // k=140
+    {-0.1588581433338613, 0.9873014181578584},  // k=141
+    {-0.1709618887603012, 0.9852776423889412},  // k=142
+    {-0.1830398879551409, 0.9831054874312163},  // k=143
+    {-0.1950903220161282, 0.9807852804032304},  // k=144
+    {-0.2071113761922184, 0.9783173707196277},  // k=145
+    {-0.2191012401568697, 0.9757021300385286},  // k=146
+    {-0.2310581082806711, 0.9729399522055602},  // k=147
+    {-0.2429801799032639, 0.9700312531945440},  // k=148
+    {-0.2548656596045145, 0.9669764710448521},  // k=149
+    {-0.2667127574748983, 0.9637760657954398},  // k=150
+    {-0.2785196893850529, 0.9604305194155659},  // k=151
+    {-0.2902846772544622, 0.9569403357322089},  // k=152
+    {-0.3020059493192281, 0.9533060403541939},  // k=153
+    {-0.3136817403988914, 0.9495281805930367},  // k=154
+    {-0.3253102921622629, 0.9456073253805214},  // k=155
+    {-0.3368898533922199, 0.9415440651830208},  // k=156
+    {-0.3484186802494344, 0.9373390119125750},  // k=157
+    {-0.3598950365349882, 0.9329927988347388},  // k=158
+    {-0.3713171939518375, 0.9285060804732156},  // k=159
+    {-0.3826834323650897, 0.9238795325112867},  // k=160
+    {-0.3939920400610480, 0.9191138516900578},  // k=161
+    {-0.4052413140049897, 0.9142097557035307},  // k=162
+    {-0.4164295600976370, 0.9091679830905225},  // k=163
+    {-0.4275550934302819, 0.9039892931234434},  // k=164
+    {-0.4386162385385274, 0.8986744656939539},  // k=165
+    {-0.4496113296546067, 0.8932243011955152},  // k=166
+    {-0.4605387109582401, 0.8876396204028539},  // k=167
+    {-0.4713967368259977, 0.8819212643483550},  // k=168
+    {-0.4821837720791227, 0.8760700941954066},  // k=169
+    {-0.4928981922297840, 0.8700869911087115},  // k=170
+    {-0.5035383837257175, 0.8639728561215868},  // k=171
+    {-0.5141027441932217, 0.8577286100002721},  // k=172
+    {-0.5245896826784687, 0.8513551931052652},  // k=173
+    {-0.5349976198870970, 0.8448535652497072},  // k=174
+    {-0.5453249884220462, 0.8382247055548382},  // k=175
+    {-0.5555702330196020, 0.8314696123025455},  // k=176
+    {-0.5657318107836132, 0.8245893027850252},  // k=177
+    {-0.5758081914178453, 0.8175848131515837},  // k=178
+    {-0.5857978574564389, 0.8104571982525948},  // k=179
+    {-0.5956993044924334, 0.8032075314806449},  // k=180
+    {-0.6055110414043254, 0.7958369046088836},  // k=181
+    {-0.6152315905806267, 0.7883464276266063},  // k=182
+    {-0.6248594881423862, 0.7807372285720946},  // k=183
+    {-0.6343932841636454, 0.7730104533627371},  // k=184
+    {-0.6438315428897913, 0.7651672656224591},  // k=185
+    {-0.6531728429537765, 0.7572088465064847},  // k=186
+    {-0.6624157775901719, 0.7491363945234593},  // k=187
+    {-0.6715589548470184, 0.7409511253549590},  // k=188
+    {-0.6806009977954530, 0.7326542716724128},  // k=189
+    {-0.6895405447370669, 0.7242470829514669},  // k=190
+    {-0.6983762494089728, 0.7157308252838187},  // k=191
+    {-0.7071067811865475, 0.7071067811865476},  // k=192
+    {-0.7157308252838186, 0.6983762494089729},  // k=193
+    {-0.7242470829514668, 0.6895405447370671},  // k=194
+    {-0.7326542716724127, 0.6806009977954532},  // k=195
+    {-0.7409511253549589, 0.6715589548470186},  // k=196
+    {-0.7491363945234591, 0.6624157775901720},  // k=197
+    {-0.7572088465064846, 0.6531728429537766},  // k=198
+    {-0.7651672656224590, 0.6438315428897914},  // k=199
+    {-0.7730104533627370, 0.6343932841636455},  // k=200
+    {-0.7807372285720945, 0.6248594881423863},  // k=201
+    {-0.7883464276266062, 0.6152315905806269},  // k=202
+    {-0.7958369046088835, 0.6055110414043257},  // k=203
+    {-0.8032075314806448, 0.5956993044924335},  // k=204
+    {-0.8104571982525947, 0.5857978574564390},  // k=205
+    {-0.8175848131515836, 0.5758081914178454},  // k=206
+    {-0.8245893027850251, 0.5657318107836135},  // k=207
+    {-0.8314696123025453, 0.5555702330196022},  // k=208
+    {-0.8382247055548381, 0.5453249884220464},  // k=209
+    {-0.8448535652497071, 0.5349976198870972},  // k=210
+    {-0.8513551931052652, 0.5245896826784689},  // k=211
+    {-0.8577286100002720, 0.5141027441932218},  // k=212
+    {-0.8639728561215867, 0.5035383837257177},  // k=213
+    {-0.8700869911087113, 0.4928981922297841},  // k=214
+    {-0.8760700941954065, 0.4821837720791229},  // k=215
+    {-0.8819212643483549, 0.4713967368259979},  // k=216
+    {-0.8876396204028538, 0.4605387109582402},  // k=217
+    {-0.8932243011955152, 0.4496113296546069},  // k=218
+    {-0.8986744656939539, 0.4386162385385275},  // k=219
+    {-0.9039892931234433, 0.4275550934302820},  // k=220
+    {-0.9091679830905224, 0.4164295600976372},  // k=221
+    {-0.9142097557035307, 0.4052413140049899},  // k=222
+    {-0.9191138516900578, 0.3939920400610482},  // k=223
+    {-0.9238795325112867, 0.3826834323650899},  // k=224
+    {-0.9285060804732155, 0.3713171939518377},  // k=225
+    {-0.9329927988347388, 0.3598950365349883},  // k=226
+    {-0.9373390119125748, 0.3484186802494348},  // k=227
+    {-0.9415440651830207, 0.3368898533922203},  // k=228
+    {-0.9456073253805212, 0.3253102921622633},  // k=229
+    {-0.9495281805930367, 0.3136817403988914},  // k=230
+    {-0.9533060403541939, 0.3020059493192280},  // k=231
+    {-0.9569403357322088, 0.2902846772544624},  // k=232
+    {-0.9604305194155658, 0.2785196893850532},  // k=233
+    {-0.9637760657954398, 0.2667127574748985},  // k=234
+    {-0.9669764710448521, 0.2548656596045147},  // k=235
+    {-0.9700312531945440, 0.2429801799032641},  // k=236
+    {-0.9729399522055601, 0.2310581082806713},  // k=237
+    {-0.9757021300385285, 0.2191012401568700},  // k=238
+    {-0.9783173707196275, 0.2071113761922188},  // k=239
+    {-0.9807852804032304, 0.1950903220161286},  // k=240
+    {-0.9831054874312163, 0.1830398879551409},  // k=241
+    {-0.9852776423889412, 0.1709618887603012},  // k=242
+    {-0.9873014181578584, 0.1588581433338615},  // k=243
+    {-0.9891765099647810, 0.1467304744553618},  // k=244
+    {-0.9909026354277800, 0.1345807085071263},  // k=245
+    {-0.9924795345987100, 0.1224106751992163},  // k=246
+    {-0.9939069700023561, 0.1102222072938832},  // k=247
+    {-0.9951847266721968, 0.0980171403295608},  // k=248
+    {-0.9963126121827780, 0.0857973123444402},  // k=249
+    {-0.9972904566786902, 0.0735645635996677},  // k=250
+    {-0.9981181129001492, 0.0613207363022085},  // k=251
+    {-0.9987954562051724, 0.0490676743274180},  // k=252
+    {-0.9993223845883495, 0.0368072229413588},  // k=253
+    {-0.9996988186962042, 0.0245412285229123},  // k=254
+    {-0.9999247018391445, 0.0122715382857200},  // k=255
+    {-1.0000000000000000, 0.0000000000000001},  // k=256
+    {-0.9999247018391445, -0.0122715382857198}, // k=257
+    {-0.9996988186962042, -0.0245412285229121}, // k=258
+    {-0.9993223845883495, -0.0368072229413586}, // k=259
+    {-0.9987954562051724, -0.0490676743274177}, // k=260
+    {-0.9981181129001492, -0.0613207363022082}, // k=261
+    {-0.9972904566786902, -0.0735645635996675}, // k=262
+    {-0.9963126121827780, -0.0857973123444399}, // k=263
+    {-0.9951847266721969, -0.0980171403295606}, // k=264
+    {-0.9939069700023561, -0.1102222072938830}, // k=265
+    {-0.9924795345987100, -0.1224106751992161}, // k=266
+    {-0.9909026354277800, -0.1345807085071261}, // k=267
+    {-0.9891765099647810, -0.1467304744553616}, // k=268
+    {-0.9873014181578584, -0.1588581433338612}, // k=269
+    {-0.9852776423889413, -0.1709618887603010}, // k=270
+    {-0.9831054874312164, -0.1830398879551406}, // k=271
+    {-0.9807852804032304, -0.1950903220161284}, // k=272
+    {-0.9783173707196277, -0.2071113761922186}, // k=273
+    {-0.9757021300385286, -0.2191012401568698}, // k=274
+    {-0.9729399522055602, -0.2310581082806711}, // k=275
+    {-0.9700312531945440, -0.2429801799032638}, // k=276
+    {-0.9669764710448522, -0.2548656596045145}, // k=277
+    {-0.9637760657954400, -0.2667127574748983}, // k=278
+    {-0.9604305194155659, -0.2785196893850529}, // k=279
+    {-0.9569403357322089, -0.2902846772544621}, // k=280
+    {-0.9533060403541940, -0.3020059493192278}, // k=281
+    {-0.9495281805930368, -0.3136817403988912}, // k=282
+    {-0.9456073253805213, -0.3253102921622630}, // k=283
+    {-0.9415440651830208, -0.3368898533922201}, // k=284
+    {-0.9373390119125750, -0.3484186802494346}, // k=285
+    {-0.9329927988347390, -0.3598950365349881}, // k=286
+    {-0.9285060804732156, -0.3713171939518374}, // k=287
+    {-0.9238795325112868, -0.3826834323650897}, // k=288
+    {-0.9191138516900578, -0.3939920400610479}, // k=289
+    {-0.9142097557035307, -0.4052413140049897}, // k=290
+    {-0.9091679830905225, -0.4164295600976369}, // k=291
+    {-0.9039892931234434, -0.4275550934302818}, // k=292
+    {-0.8986744656939540, -0.4386162385385273}, // k=293
+    {-0.8932243011955153, -0.4496113296546067}, // k=294
+    {-0.8876396204028539, -0.4605387109582401}, // k=295
+    {-0.8819212643483550, -0.4713967368259976}, // k=296
+    {-0.8760700941954066, -0.4821837720791227}, // k=297
+    {-0.8700869911087115, -0.4928981922297839}, // k=298
+    {-0.8639728561215868, -0.5035383837257175}, // k=299
+    {-0.8577286100002721, -0.5141027441932216}, // k=300
+    {-0.8513551931052653, -0.5245896826784687}, // k=301
+    {-0.8448535652497072, -0.5349976198870969}, // k=302
+    {-0.8382247055548382, -0.5453249884220461}, // k=303
+    {-0.8314696123025455, -0.5555702330196020}, // k=304
+    {-0.8245893027850253, -0.5657318107836132}, // k=305
+    {-0.8175848131515837, -0.5758081914178453}, // k=306
+    {-0.8104571982525948, -0.5857978574564389}, // k=307
+    {-0.8032075314806449, -0.5956993044924332}, // k=308
+    {-0.7958369046088836, -0.6055110414043254}, // k=309
+    {-0.7883464276266063, -0.6152315905806267}, // k=310
+    {-0.7807372285720946, -0.6248594881423862}, // k=311
+    {-0.7730104533627371, -0.6343932841636453}, // k=312
+    {-0.7651672656224591, -0.6438315428897913}, // k=313
+    {-0.7572088465064848, -0.6531728429537765}, // k=314
+    {-0.7491363945234593, -0.6624157775901718}, // k=315
+    {-0.7409511253549591, -0.6715589548470184}, // k=316
+    {-0.7326542716724128, -0.6806009977954530}, // k=317
+    {-0.7242470829514670, -0.6895405447370668}, // k=318
+    {-0.7157308252838187, -0.6983762494089728}, // k=319
+    {-0.7071067811865477, -0.7071067811865475}, // k=320
+    {-0.6983762494089730, -0.7157308252838185}, // k=321
+    {-0.6895405447370671, -0.7242470829514668}, // k=322
+    {-0.6806009977954532, -0.7326542716724126}, // k=323
+    {-0.6715589548470187, -0.7409511253549589}, // k=324
+    {-0.6624157775901720, -0.7491363945234590}, // k=325
+    {-0.6531728429537771, -0.7572088465064842}, // k=326
+    {-0.6438315428897915, -0.7651672656224590}, // k=327
+    {-0.6343932841636459, -0.7730104533627367}, // k=328
+    {-0.6248594881423865, -0.7807372285720944}, // k=329
+    {-0.6152315905806273, -0.7883464276266059}, // k=330
+    {-0.6055110414043257, -0.7958369046088835}, // k=331
+    {-0.5956993044924331, -0.8032075314806451}, // k=332
+    {-0.5857978574564391, -0.8104571982525947}, // k=333
+    {-0.5758081914178452, -0.8175848131515838}, // k=334
+    {-0.5657318107836135, -0.8245893027850251}, // k=335
+    {-0.5555702330196022, -0.8314696123025452}, // k=336
+    {-0.5453249884220468, -0.8382247055548379}, // k=337
+    {-0.5349976198870973, -0.8448535652497070}, // k=338
+    {-0.5245896826784694, -0.8513551931052649}, // k=339
+    {-0.5141027441932218, -0.8577286100002720}, // k=340
+    {-0.5035383837257180, -0.8639728561215865}, // k=341
+    {-0.4928981922297842, -0.8700869911087113}, // k=342
+    {-0.4821837720791226, -0.8760700941954067}, // k=343
+    {-0.4713967368259979, -0.8819212643483549}, // k=344
+    {-0.4605387109582399, -0.8876396204028540}, // k=345
+    {-0.4496113296546069, -0.8932243011955152}, // k=346
+    {-0.4386162385385276, -0.8986744656939538}, // k=347
+    {-0.4275550934302825, -0.9039892931234431}, // k=348
+    {-0.4164295600976372, -0.9091679830905224}, // k=349
+    {-0.4052413140049904, -0.9142097557035305}, // k=350
+    {-0.3939920400610482, -0.9191138516900577}, // k=351
+    {-0.3826834323650903, -0.9238795325112865}, // k=352
+    {-0.3713171939518378, -0.9285060804732155}, // k=353
+    {-0.3598950365349879, -0.9329927988347390}, // k=354
+    {-0.3484186802494348, -0.9373390119125748}, // k=355
+    {-0.3368898533922199, -0.9415440651830208}, // k=356
+    {-0.3253102921622633, -0.9456073253805212}, // k=357
+    {-0.3136817403988915, -0.9495281805930367}, // k=358
+    {-0.3020059493192285, -0.9533060403541938}, // k=359
+    {-0.2902846772544624, -0.9569403357322088}, // k=360
+    {-0.2785196893850536, -0.9604305194155657}, // k=361
+    {-0.2667127574748985, -0.9637760657954398}, // k=362
+    {-0.2548656596045143, -0.9669764710448522}, // k=363
+    {-0.2429801799032641, -0.9700312531945440}, // k=364
+    {-0.2310581082806709, -0.9729399522055602}, // k=365
+    {-0.2191012401568701, -0.9757021300385285}, // k=366
+    {-0.2071113761922185, -0.9783173707196277}, // k=367
+    {-0.1950903220161287, -0.9807852804032303}, // k=368
+    {-0.1830398879551410, -0.9831054874312163}, // k=369
+    {-0.1709618887603017, -0.9852776423889411}, // k=370
+    {-0.1588581433338615, -0.9873014181578583}, // k=371
+    {-0.1467304744553623, -0.9891765099647809}, // k=372
+    {-0.1345807085071264, -0.9909026354277800}, // k=373
+    {-0.1224106751992160, -0.9924795345987101}, // k=374
+    {-0.1102222072938833, -0.9939069700023561}, // k=375
+    {-0.0980171403295605, -0.9951847266721969}, // k=376
+    {-0.0857973123444402, -0.9963126121827780}, // k=377
+    {-0.0735645635996674, -0.9972904566786902}, // k=378
+    {-0.0613207363022090, -0.9981181129001492}, // k=379
+    {-0.0490676743274180, -0.9987954562051724}, // k=380
+    {-0.0368072229413593, -0.9993223845883494}, // k=381
+    {-0.0245412285229124, -0.9996988186962042}, // k=382
+    {-0.0122715382857205, -0.9999247018391445}, // k=383
+    {-0.0000000000000002, -1.0000000000000000}, // k=384
+    {0.0122715382857201, -0.9999247018391445},  // k=385
+    {0.0245412285229120, -0.9996988186962042},  // k=386
+    {0.0368072229413590, -0.9993223845883495},  // k=387
+    {0.0490676743274177, -0.9987954562051724},  // k=388
+    {0.0613207363022086, -0.9981181129001492},  // k=389
+    {0.0735645635996670, -0.9972904566786902},  // k=390
+    {0.0857973123444399, -0.9963126121827780},  // k=391
+    {0.0980171403295601, -0.9951847266721969},  // k=392
+    {0.1102222072938829, -0.9939069700023561},  // k=393
+    {0.1224106751992156, -0.9924795345987101},  // k=394
+    {0.1345807085071260, -0.9909026354277800},  // k=395
+    {0.1467304744553619, -0.9891765099647809},  // k=396
+    {0.1588581433338612, -0.9873014181578584},  // k=397
+    {0.1709618887603013, -0.9852776423889412},  // k=398
+    {0.1830398879551406, -0.9831054874312164},  // k=399
+    {0.1950903220161283, -0.9807852804032304},  // k=400
+    {0.2071113761922181, -0.9783173707196278},  // k=401
+    {0.2191012401568697, -0.9757021300385286},  // k=402
+    {0.2310581082806706, -0.9729399522055603},  // k=403
+    {0.2429801799032638, -0.9700312531945440},  // k=404
+    {0.2548656596045140, -0.9669764710448523},  // k=405
+    {0.2667127574748982, -0.9637760657954400},  // k=406
+    {0.2785196893850533, -0.9604305194155658},  // k=407
+    {0.2902846772544621, -0.9569403357322089},  // k=408
+    {0.3020059493192281, -0.9533060403541939},  // k=409
+    {0.3136817403988911, -0.9495281805930368},  // k=410
+    {0.3253102921622629, -0.9456073253805213},  // k=411
+    {0.3368898533922196, -0.9415440651830209},  // k=412
+    {0.3484186802494345, -0.9373390119125750},  // k=413
+    {0.3598950365349876, -0.9329927988347391},  // k=414
+    {0.3713171939518374, -0.9285060804732156},  // k=415
+    {0.3826834323650900, -0.9238795325112866},  // k=416
+    {0.3939920400610479, -0.9191138516900579},  // k=417
+    {0.4052413140049900, -0.9142097557035306},  // k=418
+    {0.4164295600976369, -0.9091679830905225},  // k=419
+    {0.4275550934302821, -0.9039892931234433},  // k=420
+    {0.4386162385385273, -0.8986744656939540},  // k=421
+    {0.4496113296546066, -0.8932243011955153},  // k=422
+    {0.4605387109582396, -0.8876396204028542},  // k=423
+    {0.4713967368259976, -0.8819212643483550},  // k=424
+    {0.4821837720791222, -0.8760700941954069},  // k=425
+    {0.4928981922297839, -0.8700869911087115},  // k=426
+    {0.5035383837257178, -0.8639728561215866},  // k=427
+    {0.5141027441932216, -0.8577286100002722},  // k=428
+    {0.5245896826784691, -0.8513551931052651},  // k=429
+    {0.5349976198870969, -0.8448535652497072},  // k=430
+    {0.5453249884220465, -0.8382247055548380},  // k=431
+    {0.5555702330196018, -0.8314696123025455},  // k=432
+    {0.5657318107836131, -0.8245893027850253},  // k=433
+    {0.5758081914178449, -0.8175848131515840},  // k=434
+    {0.5857978574564388, -0.8104571982525949},  // k=435
+    {0.5956993044924329, -0.8032075314806453},  // k=436
+    {0.6055110414043253, -0.7958369046088837},  // k=437
+    {0.6152315905806270, -0.7883464276266061},  // k=438
+    {0.6248594881423861, -0.7807372285720946},  // k=439
+    {0.6343932841636456, -0.7730104533627369},  // k=440
+    {0.6438315428897912, -0.7651672656224592},  // k=441
+    {0.6531728429537768, -0.7572088465064846},  // k=442
+    {0.6624157775901715, -0.7491363945234596},  // k=443
+    {0.6715589548470183, -0.7409511253549591},  // k=444
+    {0.6806009977954527, -0.7326542716724131},  // k=445
+    {0.6895405447370668, -0.7242470829514670},  // k=446
+    {0.6983762494089724, -0.7157308252838190},  // k=447
+    {0.7071067811865474, -0.7071067811865477},  // k=448
+    {0.7157308252838188, -0.6983762494089727},  // k=449
+    {0.7242470829514667, -0.6895405447370672},  // k=450
+    {0.7326542716724129, -0.6806009977954530},  // k=451
+    {0.7409511253549589, -0.6715589548470187},  // k=452
+    {0.7491363945234594, -0.6624157775901718},  // k=453
+    {0.7572088465064842, -0.6531728429537771},  // k=454
+    {0.7651672656224588, -0.6438315428897915},  // k=455
+    {0.7730104533627367, -0.6343932841636459},  // k=456
+    {0.7807372285720944, -0.6248594881423865},  // k=457
+    {0.7883464276266059, -0.6152315905806274},  // k=458
+    {0.7958369046088833, -0.6055110414043257},  // k=459
+    {0.8032075314806451, -0.5956993044924332},  // k=460
+    {0.8104571982525947, -0.5857978574564391},  // k=461
+    {0.8175848131515837, -0.5758081914178452},  // k=462
+    {0.8245893027850251, -0.5657318107836136},  // k=463
+    {0.8314696123025452, -0.5555702330196022},  // k=464
+    {0.8382247055548377, -0.5453249884220468},  // k=465
+    {0.8448535652497070, -0.5349976198870973},  // k=466
+    {0.8513551931052649, -0.5245896826784694},  // k=467
+    {0.8577286100002720, -0.5141027441932219},  // k=468
+    {0.8639728561215864, -0.5035383837257181},  // k=469
+    {0.8700869911087113, -0.4928981922297843},  // k=470
+    {0.8760700941954067, -0.4821837720791226},  // k=471
+    {0.8819212643483548, -0.4713967368259979},  // k=472
+    {0.8876396204028539, -0.4605387109582399},  // k=473
+    {0.8932243011955151, -0.4496113296546070},  // k=474
+    {0.8986744656939538, -0.4386162385385277},  // k=475
+    {0.9039892931234431, -0.4275550934302825},  // k=476
+    {0.9091679830905224, -0.4164295600976373},  // k=477
+    {0.9142097557035305, -0.4052413140049904},  // k=478
+    {0.9191138516900577, -0.3939920400610483},  // k=479
+    {0.9238795325112865, -0.3826834323650904},  // k=480
+    {0.9285060804732155, -0.3713171939518378},  // k=481
+    {0.9329927988347390, -0.3598950365349880},  // k=482
+    {0.9373390119125748, -0.3484186802494349},  // k=483
+    {0.9415440651830208, -0.3368898533922200},  // k=484
+    {0.9456073253805212, -0.3253102921622634},  // k=485
+    {0.9495281805930367, -0.3136817403988915},  // k=486
+    {0.9533060403541936, -0.3020059493192286},  // k=487
+    {0.9569403357322088, -0.2902846772544625},  // k=488
+    {0.9604305194155657, -0.2785196893850537},  // k=489
+    {0.9637760657954398, -0.2667127574748986},  // k=490
+    {0.9669764710448522, -0.2548656596045144},  // k=491
+    {0.9700312531945440, -0.2429801799032642},  // k=492
+    {0.9729399522055602, -0.2310581082806710},  // k=493
+    {0.9757021300385285, -0.2191012401568702},  // k=494
+    {0.9783173707196277, -0.2071113761922185},  // k=495
+    {0.9807852804032303, -0.1950903220161287},  // k=496
+    {0.9831054874312163, -0.1830398879551410},  // k=497
+    {0.9852776423889411, -0.1709618887603018},  // k=498
+    {0.9873014181578583, -0.1588581433338616},  // k=499
+    {0.9891765099647809, -0.1467304744553624},  // k=500
+    {0.9909026354277800, -0.1345807085071264},  // k=501
+    {0.9924795345987100, -0.1224106751992160},  // k=502
+    {0.9939069700023561, -0.1102222072938834},  // k=503
+    {0.9951847266721969, -0.0980171403295605},  // k=504
+    {0.9963126121827780, -0.0857973123444403},  // k=505
+    {0.9972904566786902, -0.0735645635996674},  // k=506
+    {0.9981181129001492, -0.0613207363022091},  // k=507
+    {0.9987954562051724, -0.0490676743274181},  // k=508
+    {0.9993223845883494, -0.0368072229413594},  // k=509
+    {0.9996988186962042, -0.0245412285229124},  // k=510
+    {0.9999247018391445, -0.0122715382857206},  // k=511
+};
diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 382052047d..759c5aaa0a 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -17,6 +17,11 @@
 
 #include <cmath>
 
+#if BOUT_HAS_CUDA
+#include <bout/twiddle.hxx>
+#include <cuda_runtime.h>
+#endif
+
 ShiftedMetric::ShiftedMetric(Mesh& m, CELL_LOC location_in, Field2D zShift_,
                              BoutReal zlength_in, Options* opt)
     : ParallelTransform(m, opt), location(location_in), zShift(std::move(zShift_)),
@@ -38,8 +43,8 @@ void ShiftedMetric::checkInputGrid() {
                             "Should be 'shiftedmetric'.");
     }
   } // else: parallel_transform variable not found in grid input, indicates older input
-    //       file or grid from options so must rely on the user having ensured the type is
-    //       correct
+  //       file or grid from options so must rely on the user having ensured the type is
+  //       correct
 }
 
 void ShiftedMetric::outputVars(Options& output_options) {
@@ -67,6 +72,7 @@ void ShiftedMetric::cachePhases() {
   toAlignedPhs = Tensor<dcomplex>(mesh.LocalNx, mesh.LocalNy, nmodes);
 
   // To/From field aligned phases
+  // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
   BOUT_FOR(i, mesh.getRegion2D("RGN_ALL")) {
     int ix = i.x();
     int iy = i.y();
@@ -105,6 +111,7 @@ void ShiftedMetric::cachePhases() {
 
   // Parallel slice phases -- note we don't shift in the boundaries/guards
   for (auto& slice : parallel_slice_phases) {
+    // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
     BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) {
 
       int ix = i.x();
@@ -166,6 +173,7 @@ Field3D ShiftedMetric::shiftZ(const Field3D& f, const Tensor<dcomplex>& phs,
 
   Field3D result{emptyFrom(f).setDirectionY(y_direction_out)};
 
+  // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
   BOUT_FOR(i, mesh.getRegion2D(toString(region))) {
     shiftZ(&f(i, 0), &phs(i.x(), i.y(), 0), &result(i, 0));
   }
@@ -196,7 +204,8 @@ FieldPerp ShiftedMetric::shiftZ(const FieldPerp& f, const Tensor<dcomplex>& phs,
   return result;
 }
 
-void ShiftedMetric::shiftZ(const BoutReal* in, const dcomplex* phs, BoutReal* out) const {
+void ShiftedMetric::shiftZ(const BoutReal* in, const dcomplex* phs, BoutReal* out,
+                           int num_batches) const {
 #if BOUT_HAS_UMPIRE
   // TODO: This static keyword is a hotfix and should be removed in
   //      future iterations. It is here because otherwise many allocations
@@ -208,7 +217,7 @@ void ShiftedMetric::shiftZ(const BoutReal* in, const dcomplex* phs, BoutReal* ou
 #endif
 
   // Take forward FFT
-  rfft(in, mesh.LocalNz, &cmplx[0]);
+  rfft(in, mesh.LocalNz * num_batches, &cmplx[0]);
 
   // Following is an algorithm approach to write a = a*b where a and b are
   // vectors of dcomplex.
@@ -222,6 +231,267 @@ void ShiftedMetric::shiftZ(const BoutReal* in, const dcomplex* phs, BoutReal* ou
   irfft(&cmplx[0], mesh.LocalNz, out); // Reverse FFT
 }
 
+/* NEW CODE */
+// Bit-reversal
+__device__ inline unsigned int bit_reverse(unsigned int x, unsigned int log2n) {
+  unsigned int result = 0;
+#pragma unroll
+  for (unsigned int i = 0; i < log2n; i++) {
+    result = (result << 1) | (x & 1);
+    x >>= 1;
+  }
+  return result;
+}
+
+// Block-level cooperative FFT
+// Multiple threads cooperate on each FFT using shared memory
+template <int NZ, int FFTS_PER_BLOCK = 4>
+__global__ void
+fft_block_cooperative(const BoutReal** __restrict__ in, BoutReal** __restrict__ out,
+                      const double2** __restrict__ blocks_phs, const int Nz_runtime,
+                      const int nmodes, const int batches, const int nblocks) {
+
+  constexpr int LOG2_NZ = __builtin_ctz(NZ);
+  constexpr double INV_NZ = 1.0 / (double)NZ;
+
+  // Shared memory for FFTS_PER_BLOCK FFTs
+  // Each FFT needs NZ complex values
+  __shared__ double2 shared_fft[FFTS_PER_BLOCK][NZ];
+
+  // Select twiddles based on size
+  const double2* twiddles;
+  if constexpr (NZ == 16) {
+    twiddles = c_twiddle_fwd_16;
+  } else if constexpr (NZ == 64) {
+    twiddles = c_twiddle_fwd_64;
+  } else if constexpr (NZ == 128) {
+    twiddles = c_twiddle_fwd_128;
+  } else if constexpr (NZ == 256) {
+    twiddles = c_twiddle_fwd_256;
+  } else if constexpr (NZ == 512) {
+    twiddles = c_twiddle_fwd_512;
+  } else {
+    static_assert(NZ == 16 || NZ == 64 || NZ == 128 || NZ == 256 || NZ == 512,
+                  "Unsupported NZ");
+  }
+
+  // Each block processes FFTS_PER_BLOCK FFTs
+  const int fft_id_in_block =
+      threadIdx.y; // Which FFT this thread works on (0 to FFTS_PER_BLOCK-1)
+  const int global_fft_id = blockIdx.x * FFTS_PER_BLOCK + fft_id_in_block;
+
+  if (global_fft_id >= nblocks * batches)
+    return;
+
+  const int block = global_fft_id / batches;
+  const int batch = global_fft_id % batches;
+
+  const double* __restrict__ in_line = in[block] + batch * NZ;
+  double* __restrict__ out_line = out[block] + batch * NZ;
+  const double2* __restrict__ phs = blocks_phs[block];
+
+  // Thread ID within the FFT computation
+  const int tid = threadIdx.x;
+  const int threads_per_fft = blockDim.x; // All threads in x-dimension work on same FFT
+
+  // ===== LOAD INPUT WITH BIT-REVERSAL =====
+  // Each thread loads some elements (strided)
+  for (int i = tid; i < NZ; i += threads_per_fft) {
+    const unsigned int rev_i = bit_reverse(i, LOG2_NZ);
+    shared_fft[fft_id_in_block][rev_i].x = in_line[i];
+    shared_fft[fft_id_in_block][rev_i].y = 0.0;
+  }
+  __syncthreads();
+
+  // ===== FORWARD FFT: Cooley-Tukey DIT in Shared Memory =====
+  for (int stage = 0; stage < LOG2_NZ; ++stage) {
+    const int m = 1 << (stage + 1);
+    const int m_half = m >> 1;
+
+    // Each thread processes multiple butterflies
+    for (int k = tid; k < NZ / 2; k += threads_per_fft) {
+      const int butterfly_group = k / m_half;
+      const int j = k % m_half;
+      const int idx_top = butterfly_group * m + j;
+      const int idx_bot = idx_top + m_half;
+
+      // Twiddle factor
+      const int twiddle_k = (j * NZ) / m;
+      const double wr = twiddles[twiddle_k].x;
+      const double wi = twiddles[twiddle_k].y;
+
+      // Load from shared memory
+      const double top_r = shared_fft[fft_id_in_block][idx_top].x;
+      const double top_i = shared_fft[fft_id_in_block][idx_top].y;
+      const double bot_r = shared_fft[fft_id_in_block][idx_bot].x;
+      const double bot_i = shared_fft[fft_id_in_block][idx_bot].y;
+
+      // Butterfly: t = W * bottom
+      const double t_r = wr * bot_r - wi * bot_i;
+      const double t_i = wr * bot_i + wi * bot_r;
+
+      // Write back
+      shared_fft[fft_id_in_block][idx_top].x = top_r + t_r;
+      shared_fft[fft_id_in_block][idx_top].y = top_i + t_i;
+      shared_fft[fft_id_in_block][idx_bot].x = top_r - t_r;
+      shared_fft[fft_id_in_block][idx_bot].y = top_i - t_i;
+    }
+    __syncthreads();
+  }
+
+  // ===== APPLY PHASE SHIFT =====
+  for (int k = tid; k < nmodes; k += threads_per_fft) {
+    const double2 ph = phs[batch * nmodes + k];
+    const double real = shared_fft[fft_id_in_block][k].x;
+    const double imag = shared_fft[fft_id_in_block][k].y;
+    shared_fft[fft_id_in_block][k].x = real * ph.x - imag * ph.y;
+    shared_fft[fft_id_in_block][k].y = real * ph.y + imag * ph.x;
+  }
+
+  for (int k = tid + nmodes; k < NZ; k += threads_per_fft) {
+    if (k >= nmodes) {
+      const int kk = NZ - k;
+      const double2 tmp = phs[batch * nmodes + kk];
+      const double real = shared_fft[fft_id_in_block][k].x;
+      const double imag = shared_fft[fft_id_in_block][k].y;
+      shared_fft[fft_id_in_block][k].x = real * tmp.x + imag * tmp.y;
+      shared_fft[fft_id_in_block][k].y = -real * tmp.y + imag * tmp.x;
+    }
+  }
+  __syncthreads();
+
+  // ===== INVERSE FFT: Conjugate, FFT, Conjugate =====
+  // Conjugate input
+  for (int i = tid; i < NZ; i += threads_per_fft) {
+    shared_fft[fft_id_in_block][i].y = -shared_fft[fft_id_in_block][i].y;
+  }
+  __syncthreads();
+
+  // Bit-reverse for inverse
+  __shared__ double2 temp_fft[FFTS_PER_BLOCK][NZ];
+  for (int i = tid; i < NZ; i += threads_per_fft) {
+    const unsigned int rev_i = bit_reverse(i, LOG2_NZ);
+    temp_fft[fft_id_in_block][rev_i] = shared_fft[fft_id_in_block][i];
+  }
+  __syncthreads();
+
+  for (int i = tid; i < NZ; i += threads_per_fft) {
+    shared_fft[fft_id_in_block][i] = temp_fft[fft_id_in_block][i];
+  }
+  __syncthreads();
+
+  // Forward FFT again (for inverse)
+  for (int stage = 0; stage < LOG2_NZ; ++stage) {
+    const int m = 1 << (stage + 1);
+    const int m_half = m >> 1;
+
+    for (int k = tid; k < NZ / 2; k += threads_per_fft) {
+      const int butterfly_group = k / m_half;
+      const int j = k % m_half;
+      const int idx_top = butterfly_group * m + j;
+      const int idx_bot = idx_top + m_half;
+
+      const int twiddle_k = (j * NZ) / m;
+      const double wr = twiddles[twiddle_k].x;
+      const double wi = twiddles[twiddle_k].y;
+
+      const double top_r = shared_fft[fft_id_in_block][idx_top].x;
+      const double top_i = shared_fft[fft_id_in_block][idx_top].y;
+      const double bot_r = shared_fft[fft_id_in_block][idx_bot].x;
+      const double bot_i = shared_fft[fft_id_in_block][idx_bot].y;
+
+      const double t_r = wr * bot_r - wi * bot_i;
+      const double t_i = wr * bot_i + wi * bot_r;
+
+      shared_fft[fft_id_in_block][idx_top].x = top_r + t_r;
+      shared_fft[fft_id_in_block][idx_top].y = top_i + t_i;
+      shared_fft[fft_id_in_block][idx_bot].x = top_r - t_r;
+      shared_fft[fft_id_in_block][idx_bot].y = top_i - t_i;
+    }
+    __syncthreads();
+  }
+
+  // Store output (conjugate and normalize)
+  for (int i = tid; i < NZ; i += threads_per_fft) {
+    out_line[i] = shared_fft[fft_id_in_block][i].x * INV_NZ;
+  }
+}
+
+// Launcher for block-level cooperative FFT
+static void shiftZ_block_fft(Mesh& mesh, const BoutReal** in, BoutReal** out,
+                             const double2** phs, int nblocks, int batches,
+                             cudaStream_t stream = 0) {
+  int Nz = mesh.LocalNz;
+  int nmodes = Nz / 2 + 1;
+
+  if ((Nz & (Nz - 1)) != 0) {
+    fprintf(stderr, "Error: Nz=%d must be power of 2\n", Nz);
+    return;
+  }
+
+  const int total_ffts = nblocks * batches;
+
+  if (Nz == 16) {
+    constexpr int FFTS_PER_BLOCK = 16;
+    constexpr int THREADS_PER_FFT = 16; // Use 64 threads per FFT
+
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 16 x 16 = 256 threads
+    dim3 grid((total_ffts + FFTS_PER_BLOCK - 1) / FFTS_PER_BLOCK);
+
+    fft_block_cooperative<16, FFTS_PER_BLOCK>
+        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+  } else if (Nz == 64) {
+    constexpr int FFTS_PER_BLOCK = 4;
+    constexpr int THREADS_PER_FFT = 64; // Use 64 threads per FFT
+
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 64 x 4 = 256 threads
+    dim3 grid((total_ffts + FFTS_PER_BLOCK - 1) / FFTS_PER_BLOCK);
+
+    fft_block_cooperative<64, FFTS_PER_BLOCK>
+        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+
+  } else if (Nz == 128) {
+    constexpr int FFTS_PER_BLOCK = 2;
+    constexpr int THREADS_PER_FFT = 128;
+
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 128 x 2 = 256 threads
+    dim3 grid((total_ffts + FFTS_PER_BLOCK - 1) / FFTS_PER_BLOCK);
+
+    fft_block_cooperative<128, FFTS_PER_BLOCK>
+        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+
+  } else if (Nz == 256) {
+    constexpr int FFTS_PER_BLOCK = 1;
+    constexpr int THREADS_PER_FFT = 256;
+
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 256 x 1 = 256 threads
+    dim3 grid(total_ffts);
+
+    fft_block_cooperative<256, FFTS_PER_BLOCK>
+        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+
+  } else if (Nz == 512) {
+    constexpr int FFTS_PER_BLOCK = 1;
+    constexpr int THREADS_PER_FFT = 512; // 512 threads per FFT
+
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 512 x 1 = 512 threads
+    dim3 grid(total_ffts);
+
+    fft_block_cooperative<512, FFTS_PER_BLOCK>
+        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+  } else {
+    fprintf(stderr, "Unsupported Nz=%d for block FFT\n", Nz);
+    throw std::runtime_error("Unsupported Nz for block FFT");
+  }
+
+  cudaError_t err = cudaGetLastError();
+  if (err != cudaSuccess) {
+    throw std::runtime_error(std::string("Block FFT failed: ") + cudaGetErrorString(err));
+  }
+}
+
+/* END NEWER CODE */
+
 void ShiftedMetric::calcParallelSlices(Field3D& f) {
   if (f.getDirectionY() == YDirectionType::Aligned) {
     // Cannot calculate parallel slices for field-aligned fields, so return without
@@ -231,9 +501,51 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
 
   f.splitParallelSlices();
 
+  auto& region = mesh.getRegion2D("RGN_NOY");
+
+  static size_t nblocks = region.getBlocks().size();
+  if (nblocks != region.getBlocks().size()) {
+    throw BoutException("Number of blocks changed in ShiftedMetric::calcParallelSlices");
+  }
+  static Array<const BoutReal*> blocks_in(nblocks);
+  static Array<BoutReal*> blocks_out(nblocks);
+  static Array<const double2*> phs_in(nblocks);
+
   for (const auto& phase : parallel_slice_phases) {
     auto& f_slice = f.ynext(phase.y_offset);
     f_slice.allocate();
+
+#if BOUT_HAS_CUDA
+    size_t block_idx = 0;
+    int num_batches =
+        region.getBlocks().cbegin()->second.ind - region.getBlocks().cbegin()->first.ind;
+
+    for (auto block = region.getBlocks().cbegin(), end = region.getBlocks().cend();
+         block < end; ++block) {
+      auto idx_s = block->first;
+      auto idx_e = block->second;
+      int inner_batches = idx_e.ind - idx_s.ind;
+      if (inner_batches != num_batches) {
+        throw BoutException(
+            "Non-uniform number of batches in ShiftedMetric::calcParallelSlices");
+      }
+      const int ix = idx_s.x();
+      const int iy = idx_s.y();
+      const int iy_offset = iy + phase.y_offset;
+
+      blocks_in[block_idx] = &f(ix, iy_offset, 0);
+      blocks_out[block_idx] = &f_slice(ix, iy_offset, 0);
+      phs_in[block_idx] = reinterpret_cast<const double2*>(&phase.phase_shift(ix, iy, 0));
+
+      block_idx++;
+    }
+
+    shiftZ_block_fft(mesh, &blocks_in[0], &blocks_out[0], &phs_in[0], nblocks,
+                     num_batches, 0);
+
+    cudaDeviceSynchronize();
+#else
+    // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
     BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) {
       const int ix = i.x();
       const int iy = i.y();
@@ -241,6 +553,9 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
       shiftZ(&(f(ix, iy_offset, 0)), &(phase.phase_shift(ix, iy, 0)),
              &(f_slice(ix, iy_offset, 0)));
     }
+    //std::cout << "ShiftedMetric::shiftZ " << __FILE__ << " :" << __LINE__
+    //          << " count = " << count << " each size " << mesh.LocalNz << "\n";
+#endif
   }
 }
 
@@ -257,6 +572,7 @@ ShiftedMetric::shiftZ(const Field3D& f,
   Matrix<Array<dcomplex>> f_fft(mesh.LocalNx, mesh.LocalNy);
   f_fft = Array<dcomplex>(nmodes);
 
+  // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
   BOUT_FOR(i, mesh.getRegion2D("RGN_ALL")) {
     int ix = i.x();
     int iy = i.y();
@@ -271,6 +587,7 @@ ShiftedMetric::shiftZ(const Field3D& f,
     current_result.allocate();
     current_result.setLocation(f.getLocation());
 
+    // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
     BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) {
       // Deep copy the FFT'd field
       int ix = i.x();

From 84d540662d08343c522f0eb06d3fd2c55f633b2d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 24 Oct 2025 13:35:04 +0100
Subject: [PATCH 0285/1827] Remove private variables from base class

---
 include/bout/invert/laplacexy.hxx | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/include/bout/invert/laplacexy.hxx b/include/bout/invert/laplacexy.hxx
index 7ec6901cee..0cdd5e751a 100644
--- a/include/bout/invert/laplacexy.hxx
+++ b/include/bout/invert/laplacexy.hxx
@@ -67,9 +67,7 @@ using RegisterUnavailableLaplaceXY = LaplaceXYFactory::RegisterUnavailableInFact
 
 class LaplaceXY {
 public:
-  LaplaceXY(Mesh* m = nullptr, [[maybe_unused]] Options* options = nullptr,
-            const CELL_LOC loc = CELL_CENTRE)
-      : localmesh(m == nullptr ? bout::globals::mesh : m), location(loc) {}
+  LaplaceXY() = default;
   LaplaceXY(const LaplaceXY&) = default;
   LaplaceXY(LaplaceXY&&) = delete;
   LaplaceXY& operator=(const LaplaceXY&) = default;
@@ -90,9 +88,6 @@ protected:
   static const int INVERT_AC_GRAD = 2; // Use zero neumann (NOTE: AC is a misnomer)
   static const int INVERT_SET = 16;    // Set boundary to x0 value
   static const int INVERT_RHS = 32;    // Set boundary to b value
-private:
-  Mesh* localmesh; ///< The mesh this operates on, provides metrics and communication
-  CELL_LOC location;
 };
 
 #endif // BOUT_LAPLACEXY_H

From 40974a9d98859690646e43f9a8e4391a5d1e585e Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 24 Oct 2025 08:33:29 -0700
Subject: [PATCH 0286/1827] Fixup: add twiddle header in cmake

---
 CMakeLists.txt | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f0a657fe94..b5beb75898 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -177,6 +177,7 @@ set(BOUT_SOURCES
   ./include/bout/sys/range.hxx
   ./include/bout/sys/timer.hxx
   ./include/bout/sys/type_name.hxx
+  ./include/bout/twiddle.hxx
   ./include/bout/sys/uncopyable.hxx
   ./include/bout/sys/uuid.h
   ./include/bout/sys/variant.hxx
@@ -239,7 +240,7 @@ set(BOUT_SOURCES
   ./include/bout/invert/laplacexy2.hxx
   ./src/invert/laplacexy2/laplacexy2.cxx
   ./include/bout/invert/laplacexy2_hypre.hxx
-  ./src/invert/laplacexy2/laplacexy2_hypre.cxx 
+  ./src/invert/laplacexy2/laplacexy2_hypre.cxx
   ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
   ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx
   ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
@@ -525,7 +526,7 @@ if (BOUT_ENABLE_WARNINGS)
     $<$<OR:$<CXX_COMPILER_ID:GNU>,$<CXX_COMPILER_ID:Clang>,$<CXX_COMPILER_ID:AppleClang>>:
       -Wall -Wextra > >
     $<$<CXX_COMPILER_ID:MSVC>:
-      /W4 >  
+      /W4 >
     $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=-Wall -Xcompiler=-Wextra >
    )
 

From ba5eabf34242f8ade482cd7b8486248a44e1f73d Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 24 Oct 2025 08:33:55 -0700
Subject: [PATCH 0287/1827] Default to pinned memory for performance

---
 include/bout/array.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/array.hxx b/include/bout/array.hxx
index 2c42f15aad..4965aee880 100644
--- a/include/bout/array.hxx
+++ b/include/bout/array.hxx
@@ -67,6 +67,7 @@ struct ArrayData {
     auto& rm = umpire::ResourceManager::getInstance();
 #if BOUT_HAS_CUDA
     auto allocator = rm.getAllocator(umpire::resource::Pinned);
+    //auto allocator = rm.getAllocator(umpire::resource::Unified);
 #else
     auto allocator = rm.getAllocator("HOST");
 #endif

From c079bb6f508efa85b8b73dcf0f5ee9ac5ce3b231 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 24 Oct 2025 09:40:56 -0700
Subject: [PATCH 0288/1827] Fixup: remove unused twiddles

---
 include/bout/twiddle.hxx | 1033 +-------------------------------------
 1 file changed, 6 insertions(+), 1027 deletions(-)

diff --git a/include/bout/twiddle.hxx b/include/bout/twiddle.hxx
index ae4f729b48..6da72dd8ff 100644
--- a/include/bout/twiddle.hxx
+++ b/include/bout/twiddle.hxx
@@ -1,4 +1,4 @@
-__constant__ double2 c_twiddle_fwd_16[16] = {
+__constant__ double2 c_twiddle_16[16] = {
     {1.0000000000000000, -0.0000000000000000},  // k=0
     {0.9238795325112867, -0.3826834323650898},  // k=1
     {0.7071067811865476, -0.7071067811865475},  // k=2
@@ -17,25 +17,7 @@ __constant__ double2 c_twiddle_fwd_16[16] = {
     {0.9238795325112865, 0.3826834323650904},   // k=15
 };
 
-__constant__ double2 c_twiddle_inv_16[16] = {
-    {1.0000000000000000, 0.0000000000000000},   // k=0
-    {0.9238795325112867, 0.3826834323650898},   // k=1
-    {0.7071067811865476, 0.7071067811865475},   // k=2
-    {0.3826834323650898, 0.9238795325112867},   // k=3
-    {0.0000000000000001, 1.0000000000000000},   // k=4
-    {-0.3826834323650897, 0.9238795325112867},  // k=5
-    {-0.7071067811865475, 0.7071067811865476},  // k=6
-    {-0.9238795325112867, 0.3826834323650899},  // k=7
-    {-1.0000000000000000, 0.0000000000000001},  // k=8
-    {-0.9238795325112868, -0.3826834323650897}, // k=9
-    {-0.7071067811865477, -0.7071067811865475}, // k=10
-    {-0.3826834323650903, -0.9238795325112865}, // k=11
-    {-0.0000000000000002, -1.0000000000000000}, // k=12
-    {0.3826834323650900, -0.9238795325112866},  // k=13
-    {0.7071067811865474, -0.7071067811865477},  // k=14
-    {0.9238795325112865, -0.3826834323650904},  // k=15
-};
-__constant__ double2 c_twiddle_fwd_32[32] = {
+__constant__ double2 c_twiddle_32[32] = {
     {1.0000000000000000, -0.0000000000000000},  // k=0
     {0.9807852804032304, -0.1950903220161282},  // k=1
     {0.9238795325112867, -0.3826834323650898},  // k=2
@@ -70,41 +52,7 @@ __constant__ double2 c_twiddle_fwd_32[32] = {
     {0.9807852804032303, 0.1950903220161287},   // k=31
 };
 
-__constant__ double2 c_twiddle_inv_32[32] = {
-    {1.0000000000000000, 0.0000000000000000},   // k=0
-    {0.9807852804032304, 0.1950903220161282},   // k=1
-    {0.9238795325112867, 0.3826834323650898},   // k=2
-    {0.8314696123025452, 0.5555702330196022},   // k=3
-    {0.7071067811865476, 0.7071067811865475},   // k=4
-    {0.5555702330196023, 0.8314696123025452},   // k=5
-    {0.3826834323650898, 0.9238795325112867},   // k=6
-    {0.1950903220161283, 0.9807852804032304},   // k=7
-    {0.0000000000000001, 1.0000000000000000},   // k=8
-    {-0.1950903220161282, 0.9807852804032304},  // k=9
-    {-0.3826834323650897, 0.9238795325112867},  // k=10
-    {-0.5555702330196020, 0.8314696123025455},  // k=11
-    {-0.7071067811865475, 0.7071067811865476},  // k=12
-    {-0.8314696123025453, 0.5555702330196022},  // k=13
-    {-0.9238795325112867, 0.3826834323650899},  // k=14
-    {-0.9807852804032304, 0.1950903220161286},  // k=15
-    {-1.0000000000000000, 0.0000000000000001},  // k=16
-    {-0.9807852804032304, -0.1950903220161284}, // k=17
-    {-0.9238795325112868, -0.3826834323650897}, // k=18
-    {-0.8314696123025455, -0.5555702330196020}, // k=19
-    {-0.7071067811865477, -0.7071067811865475}, // k=20
-    {-0.5555702330196022, -0.8314696123025452}, // k=21
-    {-0.3826834323650903, -0.9238795325112865}, // k=22
-    {-0.1950903220161287, -0.9807852804032303}, // k=23
-    {-0.0000000000000002, -1.0000000000000000}, // k=24
-    {0.1950903220161283, -0.9807852804032304},  // k=25
-    {0.3826834323650900, -0.9238795325112866},  // k=26
-    {0.5555702330196018, -0.8314696123025455},  // k=27
-    {0.7071067811865474, -0.7071067811865477},  // k=28
-    {0.8314696123025452, -0.5555702330196022},  // k=29
-    {0.9238795325112865, -0.3826834323650904},  // k=30
-    {0.9807852804032303, -0.1950903220161287},  // k=31
-};
-__constant__ double2 c_twiddle_fwd_64[64] = {
+__constant__ double2 c_twiddle_64[64] = {
     {1.0000000000000000, -0.0000000000000000},  // k=0
     {0.9951847266721969, -0.0980171403295606},  // k=1
     {0.9807852804032304, -0.1950903220161282},  // k=2
@@ -171,73 +119,7 @@ __constant__ double2 c_twiddle_fwd_64[64] = {
     {0.9951847266721969, 0.0980171403295605},   // k=63
 };
 
-__constant__ double2 c_twiddle_inv_64[64] = {
-    {1.0000000000000000, 0.0000000000000000},   // k=0
-    {0.9951847266721969, 0.0980171403295606},   // k=1
-    {0.9807852804032304, 0.1950903220161282},   // k=2
-    {0.9569403357322088, 0.2902846772544623},   // k=3
-    {0.9238795325112867, 0.3826834323650898},   // k=4
-    {0.8819212643483550, 0.4713967368259976},   // k=5
-    {0.8314696123025452, 0.5555702330196022},   // k=6
-    {0.7730104533627370, 0.6343932841636455},   // k=7
-    {0.7071067811865476, 0.7071067811865475},   // k=8
-    {0.6343932841636455, 0.7730104533627370},   // k=9
-    {0.5555702330196023, 0.8314696123025452},   // k=10
-    {0.4713967368259978, 0.8819212643483549},   // k=11
-    {0.3826834323650898, 0.9238795325112867},   // k=12
-    {0.2902846772544623, 0.9569403357322089},   // k=13
-    {0.1950903220161283, 0.9807852804032304},   // k=14
-    {0.0980171403295608, 0.9951847266721968},   // k=15
-    {0.0000000000000001, 1.0000000000000000},   // k=16
-    {-0.0980171403295606, 0.9951847266721969},  // k=17
-    {-0.1950903220161282, 0.9807852804032304},  // k=18
-    {-0.2902846772544622, 0.9569403357322089},  // k=19
-    {-0.3826834323650897, 0.9238795325112867},  // k=20
-    {-0.4713967368259977, 0.8819212643483550},  // k=21
-    {-0.5555702330196020, 0.8314696123025455},  // k=22
-    {-0.6343932841636454, 0.7730104533627371},  // k=23
-    {-0.7071067811865475, 0.7071067811865476},  // k=24
-    {-0.7730104533627370, 0.6343932841636455},  // k=25
-    {-0.8314696123025453, 0.5555702330196022},  // k=26
-    {-0.8819212643483549, 0.4713967368259979},  // k=27
-    {-0.9238795325112867, 0.3826834323650899},  // k=28
-    {-0.9569403357322088, 0.2902846772544624},  // k=29
-    {-0.9807852804032304, 0.1950903220161286},  // k=30
-    {-0.9951847266721968, 0.0980171403295608},  // k=31
-    {-1.0000000000000000, 0.0000000000000001},  // k=32
-    {-0.9951847266721969, -0.0980171403295606}, // k=33
-    {-0.9807852804032304, -0.1950903220161284}, // k=34
-    {-0.9569403357322089, -0.2902846772544621}, // k=35
-    {-0.9238795325112868, -0.3826834323650897}, // k=36
-    {-0.8819212643483550, -0.4713967368259976}, // k=37
-    {-0.8314696123025455, -0.5555702330196020}, // k=38
-    {-0.7730104533627371, -0.6343932841636453}, // k=39
-    {-0.7071067811865477, -0.7071067811865475}, // k=40
-    {-0.6343932841636459, -0.7730104533627367}, // k=41
-    {-0.5555702330196022, -0.8314696123025452}, // k=42
-    {-0.4713967368259979, -0.8819212643483549}, // k=43
-    {-0.3826834323650903, -0.9238795325112865}, // k=44
-    {-0.2902846772544624, -0.9569403357322088}, // k=45
-    {-0.1950903220161287, -0.9807852804032303}, // k=46
-    {-0.0980171403295605, -0.9951847266721969}, // k=47
-    {-0.0000000000000002, -1.0000000000000000}, // k=48
-    {0.0980171403295601, -0.9951847266721969},  // k=49
-    {0.1950903220161283, -0.9807852804032304},  // k=50
-    {0.2902846772544621, -0.9569403357322089},  // k=51
-    {0.3826834323650900, -0.9238795325112866},  // k=52
-    {0.4713967368259976, -0.8819212643483550},  // k=53
-    {0.5555702330196018, -0.8314696123025455},  // k=54
-    {0.6343932841636456, -0.7730104533627369},  // k=55
-    {0.7071067811865474, -0.7071067811865477},  // k=56
-    {0.7730104533627367, -0.6343932841636459},  // k=57
-    {0.8314696123025452, -0.5555702330196022},  // k=58
-    {0.8819212643483548, -0.4713967368259979},  // k=59
-    {0.9238795325112865, -0.3826834323650904},  // k=60
-    {0.9569403357322088, -0.2902846772544625},  // k=61
-    {0.9807852804032303, -0.1950903220161287},  // k=62
-    {0.9951847266721969, -0.0980171403295605},  // k=63
-};
-__constant__ double2 c_twiddle_fwd_128[128] = {
+__constant__ double2 c_twiddle_128[128] = {
     {1.0000000000000000, -0.0000000000000000},  // k=0
     {0.9987954562051724, -0.0490676743274180},  // k=1
     {0.9951847266721969, -0.0980171403295606},  // k=2
@@ -368,137 +250,7 @@ __constant__ double2 c_twiddle_fwd_128[128] = {
     {0.9987954562051724, 0.0490676743274181},   // k=127
 };
 
-__constant__ double2 c_twiddle_inv_128[128] = {
-    {1.0000000000000000, 0.0000000000000000},   // k=0
-    {0.9987954562051724, 0.0490676743274180},   // k=1
-    {0.9951847266721969, 0.0980171403295606},   // k=2
-    {0.9891765099647810, 0.1467304744553617},   // k=3
-    {0.9807852804032304, 0.1950903220161282},   // k=4
-    {0.9700312531945440, 0.2429801799032639},   // k=5
-    {0.9569403357322088, 0.2902846772544623},   // k=6
-    {0.9415440651830208, 0.3368898533922201},   // k=7
-    {0.9238795325112867, 0.3826834323650898},   // k=8
-    {0.9039892931234433, 0.4275550934302821},   // k=9
-    {0.8819212643483550, 0.4713967368259976},   // k=10
-    {0.8577286100002721, 0.5141027441932217},   // k=11
-    {0.8314696123025452, 0.5555702330196022},   // k=12
-    {0.8032075314806449, 0.5956993044924334},   // k=13
-    {0.7730104533627370, 0.6343932841636455},   // k=14
-    {0.7409511253549591, 0.6715589548470183},   // k=15
-    {0.7071067811865476, 0.7071067811865475},   // k=16
-    {0.6715589548470183, 0.7409511253549591},   // k=17
-    {0.6343932841636455, 0.7730104533627370},   // k=18
-    {0.5956993044924335, 0.8032075314806448},   // k=19
-    {0.5555702330196023, 0.8314696123025452},   // k=20
-    {0.5141027441932217, 0.8577286100002721},   // k=21
-    {0.4713967368259978, 0.8819212643483549},   // k=22
-    {0.4275550934302822, 0.9039892931234433},   // k=23
-    {0.3826834323650898, 0.9238795325112867},   // k=24
-    {0.3368898533922201, 0.9415440651830208},   // k=25
-    {0.2902846772544623, 0.9569403357322089},   // k=26
-    {0.2429801799032640, 0.9700312531945440},   // k=27
-    {0.1950903220161283, 0.9807852804032304},   // k=28
-    {0.1467304744553617, 0.9891765099647810},   // k=29
-    {0.0980171403295608, 0.9951847266721968},   // k=30
-    {0.0490676743274181, 0.9987954562051724},   // k=31
-    {0.0000000000000001, 1.0000000000000000},   // k=32
-    {-0.0490676743274180, 0.9987954562051724},  // k=33
-    {-0.0980171403295606, 0.9951847266721969},  // k=34
-    {-0.1467304744553616, 0.9891765099647810},  // k=35
-    {-0.1950903220161282, 0.9807852804032304},  // k=36
-    {-0.2429801799032639, 0.9700312531945440},  // k=37
-    {-0.2902846772544622, 0.9569403357322089},  // k=38
-    {-0.3368898533922199, 0.9415440651830208},  // k=39
-    {-0.3826834323650897, 0.9238795325112867},  // k=40
-    {-0.4275550934302819, 0.9039892931234434},  // k=41
-    {-0.4713967368259977, 0.8819212643483550},  // k=42
-    {-0.5141027441932217, 0.8577286100002721},  // k=43
-    {-0.5555702330196020, 0.8314696123025455},  // k=44
-    {-0.5956993044924334, 0.8032075314806449},  // k=45
-    {-0.6343932841636454, 0.7730104533627371},  // k=46
-    {-0.6715589548470184, 0.7409511253549590},  // k=47
-    {-0.7071067811865475, 0.7071067811865476},  // k=48
-    {-0.7409511253549589, 0.6715589548470186},  // k=49
-    {-0.7730104533627370, 0.6343932841636455},  // k=50
-    {-0.8032075314806448, 0.5956993044924335},  // k=51
-    {-0.8314696123025453, 0.5555702330196022},  // k=52
-    {-0.8577286100002720, 0.5141027441932218},  // k=53
-    {-0.8819212643483549, 0.4713967368259979},  // k=54
-    {-0.9039892931234433, 0.4275550934302820},  // k=55
-    {-0.9238795325112867, 0.3826834323650899},  // k=56
-    {-0.9415440651830207, 0.3368898533922203},  // k=57
-    {-0.9569403357322088, 0.2902846772544624},  // k=58
-    {-0.9700312531945440, 0.2429801799032641},  // k=59
-    {-0.9807852804032304, 0.1950903220161286},  // k=60
-    {-0.9891765099647810, 0.1467304744553618},  // k=61
-    {-0.9951847266721968, 0.0980171403295608},  // k=62
-    {-0.9987954562051724, 0.0490676743274180},  // k=63
-    {-1.0000000000000000, 0.0000000000000001},  // k=64
-    {-0.9987954562051724, -0.0490676743274177}, // k=65
-    {-0.9951847266721969, -0.0980171403295606}, // k=66
-    {-0.9891765099647810, -0.1467304744553616}, // k=67
-    {-0.9807852804032304, -0.1950903220161284}, // k=68
-    {-0.9700312531945440, -0.2429801799032638}, // k=69
-    {-0.9569403357322089, -0.2902846772544621}, // k=70
-    {-0.9415440651830208, -0.3368898533922201}, // k=71
-    {-0.9238795325112868, -0.3826834323650897}, // k=72
-    {-0.9039892931234434, -0.4275550934302818}, // k=73
-    {-0.8819212643483550, -0.4713967368259976}, // k=74
-    {-0.8577286100002721, -0.5141027441932216}, // k=75
-    {-0.8314696123025455, -0.5555702330196020}, // k=76
-    {-0.8032075314806449, -0.5956993044924332}, // k=77
-    {-0.7730104533627371, -0.6343932841636453}, // k=78
-    {-0.7409511253549591, -0.6715589548470184}, // k=79
-    {-0.7071067811865477, -0.7071067811865475}, // k=80
-    {-0.6715589548470187, -0.7409511253549589}, // k=81
-    {-0.6343932841636459, -0.7730104533627367}, // k=82
-    {-0.5956993044924331, -0.8032075314806451}, // k=83
-    {-0.5555702330196022, -0.8314696123025452}, // k=84
-    {-0.5141027441932218, -0.8577286100002720}, // k=85
-    {-0.4713967368259979, -0.8819212643483549}, // k=86
-    {-0.4275550934302825, -0.9039892931234431}, // k=87
-    {-0.3826834323650903, -0.9238795325112865}, // k=88
-    {-0.3368898533922199, -0.9415440651830208}, // k=89
-    {-0.2902846772544624, -0.9569403357322088}, // k=90
-    {-0.2429801799032641, -0.9700312531945440}, // k=91
-    {-0.1950903220161287, -0.9807852804032303}, // k=92
-    {-0.1467304744553623, -0.9891765099647809}, // k=93
-    {-0.0980171403295605, -0.9951847266721969}, // k=94
-    {-0.0490676743274180, -0.9987954562051724}, // k=95
-    {-0.0000000000000002, -1.0000000000000000}, // k=96
-    {0.0490676743274177, -0.9987954562051724},  // k=97
-    {0.0980171403295601, -0.9951847266721969},  // k=98
-    {0.1467304744553619, -0.9891765099647809},  // k=99
-    {0.1950903220161283, -0.9807852804032304},  // k=100
-    {0.2429801799032638, -0.9700312531945440},  // k=101
-    {0.2902846772544621, -0.9569403357322089},  // k=102
-    {0.3368898533922196, -0.9415440651830209},  // k=103
-    {0.3826834323650900, -0.9238795325112866},  // k=104
-    {0.4275550934302821, -0.9039892931234433},  // k=105
-    {0.4713967368259976, -0.8819212643483550},  // k=106
-    {0.5141027441932216, -0.8577286100002722},  // k=107
-    {0.5555702330196018, -0.8314696123025455},  // k=108
-    {0.5956993044924329, -0.8032075314806453},  // k=109
-    {0.6343932841636456, -0.7730104533627369},  // k=110
-    {0.6715589548470183, -0.7409511253549591},  // k=111
-    {0.7071067811865474, -0.7071067811865477},  // k=112
-    {0.7409511253549589, -0.6715589548470187},  // k=113
-    {0.7730104533627367, -0.6343932841636459},  // k=114
-    {0.8032075314806451, -0.5956993044924332},  // k=115
-    {0.8314696123025452, -0.5555702330196022},  // k=116
-    {0.8577286100002720, -0.5141027441932219},  // k=117
-    {0.8819212643483548, -0.4713967368259979},  // k=118
-    {0.9039892931234431, -0.4275550934302825},  // k=119
-    {0.9238795325112865, -0.3826834323650904},  // k=120
-    {0.9415440651830208, -0.3368898533922200},  // k=121
-    {0.9569403357322088, -0.2902846772544625},  // k=122
-    {0.9700312531945440, -0.2429801799032642},  // k=123
-    {0.9807852804032303, -0.1950903220161287},  // k=124
-    {0.9891765099647809, -0.1467304744553624},  // k=125
-    {0.9951847266721969, -0.0980171403295605},  // k=126
-    {0.9987954562051724, -0.0490676743274181},  // k=127
-};
-__constant__ double2 c_twiddle_fwd_256[256] = {
+__constant__ double2 c_twiddle_256[256] = {
     {1.0000000000000000, -0.0000000000000000},  // k=0
     {0.9996988186962042, -0.0245412285229123},  // k=1
     {0.9987954562051724, -0.0490676743274180},  // k=2
@@ -757,265 +509,7 @@ __constant__ double2 c_twiddle_fwd_256[256] = {
     {0.9996988186962042, 0.0245412285229124},   // k=255
 };
 
-__constant__ double2 c_twiddle_inv_256[256] = {
-    {1.0000000000000000, 0.0000000000000000},   // k=0
-    {0.9996988186962042, 0.0245412285229123},   // k=1
-    {0.9987954562051724, 0.0490676743274180},   // k=2
-    {0.9972904566786902, 0.0735645635996674},   // k=3
-    {0.9951847266721969, 0.0980171403295606},   // k=4
-    {0.9924795345987100, 0.1224106751992162},   // k=5
-    {0.9891765099647810, 0.1467304744553617},   // k=6
-    {0.9852776423889412, 0.1709618887603012},   // k=7
-    {0.9807852804032304, 0.1950903220161282},   // k=8
-    {0.9757021300385286, 0.2191012401568698},   // k=9
-    {0.9700312531945440, 0.2429801799032639},   // k=10
-    {0.9637760657954398, 0.2667127574748984},   // k=11
-    {0.9569403357322088, 0.2902846772544623},   // k=12
-    {0.9495281805930367, 0.3136817403988915},   // k=13
-    {0.9415440651830208, 0.3368898533922201},   // k=14
-    {0.9329927988347390, 0.3598950365349881},   // k=15
-    {0.9238795325112867, 0.3826834323650898},   // k=16
-    {0.9142097557035307, 0.4052413140049899},   // k=17
-    {0.9039892931234433, 0.4275550934302821},   // k=18
-    {0.8932243011955153, 0.4496113296546065},   // k=19
-    {0.8819212643483550, 0.4713967368259976},   // k=20
-    {0.8700869911087115, 0.4928981922297840},   // k=21
-    {0.8577286100002721, 0.5141027441932217},   // k=22
-    {0.8448535652497071, 0.5349976198870972},   // k=23
-    {0.8314696123025452, 0.5555702330196022},   // k=24
-    {0.8175848131515837, 0.5758081914178453},   // k=25
-    {0.8032075314806449, 0.5956993044924334},   // k=26
-    {0.7883464276266063, 0.6152315905806268},   // k=27
-    {0.7730104533627370, 0.6343932841636455},   // k=28
-    {0.7572088465064846, 0.6531728429537768},   // k=29
-    {0.7409511253549591, 0.6715589548470183},   // k=30
-    {0.7242470829514670, 0.6895405447370668},   // k=31
-    {0.7071067811865476, 0.7071067811865475},   // k=32
-    {0.6895405447370669, 0.7242470829514669},   // k=33
-    {0.6715589548470183, 0.7409511253549591},   // k=34
-    {0.6531728429537768, 0.7572088465064845},   // k=35
-    {0.6343932841636455, 0.7730104533627370},   // k=36
-    {0.6152315905806268, 0.7883464276266062},   // k=37
-    {0.5956993044924335, 0.8032075314806448},   // k=38
-    {0.5758081914178453, 0.8175848131515837},   // k=39
-    {0.5555702330196023, 0.8314696123025452},   // k=40
-    {0.5349976198870973, 0.8448535652497070},   // k=41
-    {0.5141027441932217, 0.8577286100002721},   // k=42
-    {0.4928981922297841, 0.8700869911087113},   // k=43
-    {0.4713967368259978, 0.8819212643483549},   // k=44
-    {0.4496113296546066, 0.8932243011955153},   // k=45
-    {0.4275550934302822, 0.9039892931234433},   // k=46
-    {0.4052413140049899, 0.9142097557035307},   // k=47
-    {0.3826834323650898, 0.9238795325112867},   // k=48
-    {0.3598950365349883, 0.9329927988347388},   // k=49
-    {0.3368898533922201, 0.9415440651830208},   // k=50
-    {0.3136817403988916, 0.9495281805930367},   // k=51
-    {0.2902846772544623, 0.9569403357322089},   // k=52
-    {0.2667127574748984, 0.9637760657954398},   // k=53
-    {0.2429801799032640, 0.9700312531945440},   // k=54
-    {0.2191012401568698, 0.9757021300385286},   // k=55
-    {0.1950903220161283, 0.9807852804032304},   // k=56
-    {0.1709618887603014, 0.9852776423889412},   // k=57
-    {0.1467304744553617, 0.9891765099647810},   // k=58
-    {0.1224106751992163, 0.9924795345987100},   // k=59
-    {0.0980171403295608, 0.9951847266721968},   // k=60
-    {0.0735645635996675, 0.9972904566786902},   // k=61
-    {0.0490676743274181, 0.9987954562051724},   // k=62
-    {0.0245412285229123, 0.9996988186962042},   // k=63
-    {0.0000000000000001, 1.0000000000000000},   // k=64
-    {-0.0245412285229121, 0.9996988186962042},  // k=65
-    {-0.0490676743274180, 0.9987954562051724},  // k=66
-    {-0.0735645635996673, 0.9972904566786902},  // k=67
-    {-0.0980171403295606, 0.9951847266721969},  // k=68
-    {-0.1224106751992162, 0.9924795345987100},  // k=69
-    {-0.1467304744553616, 0.9891765099647810},  // k=70
-    {-0.1709618887603012, 0.9852776423889412},  // k=71
-    {-0.1950903220161282, 0.9807852804032304},  // k=72
-    {-0.2191012401568697, 0.9757021300385286},  // k=73
-    {-0.2429801799032639, 0.9700312531945440},  // k=74
-    {-0.2667127574748983, 0.9637760657954398},  // k=75
-    {-0.2902846772544622, 0.9569403357322089},  // k=76
-    {-0.3136817403988914, 0.9495281805930367},  // k=77
-    {-0.3368898533922199, 0.9415440651830208},  // k=78
-    {-0.3598950365349882, 0.9329927988347388},  // k=79
-    {-0.3826834323650897, 0.9238795325112867},  // k=80
-    {-0.4052413140049897, 0.9142097557035307},  // k=81
-    {-0.4275550934302819, 0.9039892931234434},  // k=82
-    {-0.4496113296546067, 0.8932243011955152},  // k=83
-    {-0.4713967368259977, 0.8819212643483550},  // k=84
-    {-0.4928981922297840, 0.8700869911087115},  // k=85
-    {-0.5141027441932217, 0.8577286100002721},  // k=86
-    {-0.5349976198870970, 0.8448535652497072},  // k=87
-    {-0.5555702330196020, 0.8314696123025455},  // k=88
-    {-0.5758081914178453, 0.8175848131515837},  // k=89
-    {-0.5956993044924334, 0.8032075314806449},  // k=90
-    {-0.6152315905806267, 0.7883464276266063},  // k=91
-    {-0.6343932841636454, 0.7730104533627371},  // k=92
-    {-0.6531728429537765, 0.7572088465064847},  // k=93
-    {-0.6715589548470184, 0.7409511253549590},  // k=94
-    {-0.6895405447370669, 0.7242470829514669},  // k=95
-    {-0.7071067811865475, 0.7071067811865476},  // k=96
-    {-0.7242470829514668, 0.6895405447370671},  // k=97
-    {-0.7409511253549589, 0.6715589548470186},  // k=98
-    {-0.7572088465064846, 0.6531728429537766},  // k=99
-    {-0.7730104533627370, 0.6343932841636455},  // k=100
-    {-0.7883464276266062, 0.6152315905806269},  // k=101
-    {-0.8032075314806448, 0.5956993044924335},  // k=102
-    {-0.8175848131515836, 0.5758081914178454},  // k=103
-    {-0.8314696123025453, 0.5555702330196022},  // k=104
-    {-0.8448535652497071, 0.5349976198870972},  // k=105
-    {-0.8577286100002720, 0.5141027441932218},  // k=106
-    {-0.8700869911087113, 0.4928981922297841},  // k=107
-    {-0.8819212643483549, 0.4713967368259979},  // k=108
-    {-0.8932243011955152, 0.4496113296546069},  // k=109
-    {-0.9039892931234433, 0.4275550934302820},  // k=110
-    {-0.9142097557035307, 0.4052413140049899},  // k=111
-    {-0.9238795325112867, 0.3826834323650899},  // k=112
-    {-0.9329927988347388, 0.3598950365349883},  // k=113
-    {-0.9415440651830207, 0.3368898533922203},  // k=114
-    {-0.9495281805930367, 0.3136817403988914},  // k=115
-    {-0.9569403357322088, 0.2902846772544624},  // k=116
-    {-0.9637760657954398, 0.2667127574748985},  // k=117
-    {-0.9700312531945440, 0.2429801799032641},  // k=118
-    {-0.9757021300385285, 0.2191012401568700},  // k=119
-    {-0.9807852804032304, 0.1950903220161286},  // k=120
-    {-0.9852776423889412, 0.1709618887603012},  // k=121
-    {-0.9891765099647810, 0.1467304744553618},  // k=122
-    {-0.9924795345987100, 0.1224106751992163},  // k=123
-    {-0.9951847266721968, 0.0980171403295608},  // k=124
-    {-0.9972904566786902, 0.0735645635996677},  // k=125
-    {-0.9987954562051724, 0.0490676743274180},  // k=126
-    {-0.9996988186962042, 0.0245412285229123},  // k=127
-    {-1.0000000000000000, 0.0000000000000001},  // k=128
-    {-0.9996988186962042, -0.0245412285229121}, // k=129
-    {-0.9987954562051724, -0.0490676743274177}, // k=130
-    {-0.9972904566786902, -0.0735645635996675}, // k=131
-    {-0.9951847266721969, -0.0980171403295606}, // k=132
-    {-0.9924795345987100, -0.1224106751992161}, // k=133
-    {-0.9891765099647810, -0.1467304744553616}, // k=134
-    {-0.9852776423889413, -0.1709618887603010}, // k=135
-    {-0.9807852804032304, -0.1950903220161284}, // k=136
-    {-0.9757021300385286, -0.2191012401568698}, // k=137
-    {-0.9700312531945440, -0.2429801799032638}, // k=138
-    {-0.9637760657954400, -0.2667127574748983}, // k=139
-    {-0.9569403357322089, -0.2902846772544621}, // k=140
-    {-0.9495281805930368, -0.3136817403988912}, // k=141
-    {-0.9415440651830208, -0.3368898533922201}, // k=142
-    {-0.9329927988347390, -0.3598950365349881}, // k=143
-    {-0.9238795325112868, -0.3826834323650897}, // k=144
-    {-0.9142097557035307, -0.4052413140049897}, // k=145
-    {-0.9039892931234434, -0.4275550934302818}, // k=146
-    {-0.8932243011955153, -0.4496113296546067}, // k=147
-    {-0.8819212643483550, -0.4713967368259976}, // k=148
-    {-0.8700869911087115, -0.4928981922297839}, // k=149
-    {-0.8577286100002721, -0.5141027441932216}, // k=150
-    {-0.8448535652497072, -0.5349976198870969}, // k=151
-    {-0.8314696123025455, -0.5555702330196020}, // k=152
-    {-0.8175848131515837, -0.5758081914178453}, // k=153
-    {-0.8032075314806449, -0.5956993044924332}, // k=154
-    {-0.7883464276266063, -0.6152315905806267}, // k=155
-    {-0.7730104533627371, -0.6343932841636453}, // k=156
-    {-0.7572088465064848, -0.6531728429537765}, // k=157
-    {-0.7409511253549591, -0.6715589548470184}, // k=158
-    {-0.7242470829514670, -0.6895405447370668}, // k=159
-    {-0.7071067811865477, -0.7071067811865475}, // k=160
-    {-0.6895405447370671, -0.7242470829514668}, // k=161
-    {-0.6715589548470187, -0.7409511253549589}, // k=162
-    {-0.6531728429537771, -0.7572088465064842}, // k=163
-    {-0.6343932841636459, -0.7730104533627367}, // k=164
-    {-0.6152315905806273, -0.7883464276266059}, // k=165
-    {-0.5956993044924331, -0.8032075314806451}, // k=166
-    {-0.5758081914178452, -0.8175848131515838}, // k=167
-    {-0.5555702330196022, -0.8314696123025452}, // k=168
-    {-0.5349976198870973, -0.8448535652497070}, // k=169
-    {-0.5141027441932218, -0.8577286100002720}, // k=170
-    {-0.4928981922297842, -0.8700869911087113}, // k=171
-    {-0.4713967368259979, -0.8819212643483549}, // k=172
-    {-0.4496113296546069, -0.8932243011955152}, // k=173
-    {-0.4275550934302825, -0.9039892931234431}, // k=174
-    {-0.4052413140049904, -0.9142097557035305}, // k=175
-    {-0.3826834323650903, -0.9238795325112865}, // k=176
-    {-0.3598950365349879, -0.9329927988347390}, // k=177
-    {-0.3368898533922199, -0.9415440651830208}, // k=178
-    {-0.3136817403988915, -0.9495281805930367}, // k=179
-    {-0.2902846772544624, -0.9569403357322088}, // k=180
-    {-0.2667127574748985, -0.9637760657954398}, // k=181
-    {-0.2429801799032641, -0.9700312531945440}, // k=182
-    {-0.2191012401568701, -0.9757021300385285}, // k=183
-    {-0.1950903220161287, -0.9807852804032303}, // k=184
-    {-0.1709618887603017, -0.9852776423889411}, // k=185
-    {-0.1467304744553623, -0.9891765099647809}, // k=186
-    {-0.1224106751992160, -0.9924795345987101}, // k=187
-    {-0.0980171403295605, -0.9951847266721969}, // k=188
-    {-0.0735645635996674, -0.9972904566786902}, // k=189
-    {-0.0490676743274180, -0.9987954562051724}, // k=190
-    {-0.0245412285229124, -0.9996988186962042}, // k=191
-    {-0.0000000000000002, -1.0000000000000000}, // k=192
-    {0.0245412285229120, -0.9996988186962042},  // k=193
-    {0.0490676743274177, -0.9987954562051724},  // k=194
-    {0.0735645635996670, -0.9972904566786902},  // k=195
-    {0.0980171403295601, -0.9951847266721969},  // k=196
-    {0.1224106751992156, -0.9924795345987101},  // k=197
-    {0.1467304744553619, -0.9891765099647809},  // k=198
-    {0.1709618887603013, -0.9852776423889412},  // k=199
-    {0.1950903220161283, -0.9807852804032304},  // k=200
-    {0.2191012401568697, -0.9757021300385286},  // k=201
-    {0.2429801799032638, -0.9700312531945440},  // k=202
-    {0.2667127574748982, -0.9637760657954400},  // k=203
-    {0.2902846772544621, -0.9569403357322089},  // k=204
-    {0.3136817403988911, -0.9495281805930368},  // k=205
-    {0.3368898533922196, -0.9415440651830209},  // k=206
-    {0.3598950365349876, -0.9329927988347391},  // k=207
-    {0.3826834323650900, -0.9238795325112866},  // k=208
-    {0.4052413140049900, -0.9142097557035306},  // k=209
-    {0.4275550934302821, -0.9039892931234433},  // k=210
-    {0.4496113296546066, -0.8932243011955153},  // k=211
-    {0.4713967368259976, -0.8819212643483550},  // k=212
-    {0.4928981922297839, -0.8700869911087115},  // k=213
-    {0.5141027441932216, -0.8577286100002722},  // k=214
-    {0.5349976198870969, -0.8448535652497072},  // k=215
-    {0.5555702330196018, -0.8314696123025455},  // k=216
-    {0.5758081914178449, -0.8175848131515840},  // k=217
-    {0.5956993044924329, -0.8032075314806453},  // k=218
-    {0.6152315905806270, -0.7883464276266061},  // k=219
-    {0.6343932841636456, -0.7730104533627369},  // k=220
-    {0.6531728429537768, -0.7572088465064846},  // k=221
-    {0.6715589548470183, -0.7409511253549591},  // k=222
-    {0.6895405447370668, -0.7242470829514670},  // k=223
-    {0.7071067811865474, -0.7071067811865477},  // k=224
-    {0.7242470829514667, -0.6895405447370672},  // k=225
-    {0.7409511253549589, -0.6715589548470187},  // k=226
-    {0.7572088465064842, -0.6531728429537771},  // k=227
-    {0.7730104533627367, -0.6343932841636459},  // k=228
-    {0.7883464276266059, -0.6152315905806274},  // k=229
-    {0.8032075314806451, -0.5956993044924332},  // k=230
-    {0.8175848131515837, -0.5758081914178452},  // k=231
-    {0.8314696123025452, -0.5555702330196022},  // k=232
-    {0.8448535652497070, -0.5349976198870973},  // k=233
-    {0.8577286100002720, -0.5141027441932219},  // k=234
-    {0.8700869911087113, -0.4928981922297843},  // k=235
-    {0.8819212643483548, -0.4713967368259979},  // k=236
-    {0.8932243011955151, -0.4496113296546070},  // k=237
-    {0.9039892931234431, -0.4275550934302825},  // k=238
-    {0.9142097557035305, -0.4052413140049904},  // k=239
-    {0.9238795325112865, -0.3826834323650904},  // k=240
-    {0.9329927988347390, -0.3598950365349880},  // k=241
-    {0.9415440651830208, -0.3368898533922200},  // k=242
-    {0.9495281805930367, -0.3136817403988915},  // k=243
-    {0.9569403357322088, -0.2902846772544625},  // k=244
-    {0.9637760657954398, -0.2667127574748986},  // k=245
-    {0.9700312531945440, -0.2429801799032642},  // k=246
-    {0.9757021300385285, -0.2191012401568702},  // k=247
-    {0.9807852804032303, -0.1950903220161287},  // k=248
-    {0.9852776423889411, -0.1709618887603018},  // k=249
-    {0.9891765099647809, -0.1467304744553624},  // k=250
-    {0.9924795345987100, -0.1224106751992160},  // k=251
-    {0.9951847266721969, -0.0980171403295605},  // k=252
-    {0.9972904566786902, -0.0735645635996674},  // k=253
-    {0.9987954562051724, -0.0490676743274181},  // k=254
-    {0.9996988186962042, -0.0245412285229124},  // k=255
-};
-__constant__ double2 c_twiddle_fwd_512[512] = {
+__constant__ double2 c_twiddle_512[512] = {
     {1.0000000000000000, -0.0000000000000000},  // k=0
     {0.9999247018391445, -0.0122715382857199},  // k=1
     {0.9996988186962042, -0.0245412285229123},  // k=2
@@ -1529,518 +1023,3 @@ __constant__ double2 c_twiddle_fwd_512[512] = {
     {0.9996988186962042, 0.0245412285229124},   // k=510
     {0.9999247018391445, 0.0122715382857206},   // k=511
 };
-
-__constant__ double2 c_twiddle_inv_512[512] = {
-    {1.0000000000000000, 0.0000000000000000},   // k=0
-    {0.9999247018391445, 0.0122715382857199},   // k=1
-    {0.9996988186962042, 0.0245412285229123},   // k=2
-    {0.9993223845883495, 0.0368072229413588},   // k=3
-    {0.9987954562051724, 0.0490676743274180},   // k=4
-    {0.9981181129001492, 0.0613207363022086},   // k=5
-    {0.9972904566786902, 0.0735645635996674},   // k=6
-    {0.9963126121827780, 0.0857973123444399},   // k=7
-    {0.9951847266721969, 0.0980171403295606},   // k=8
-    {0.9939069700023561, 0.1102222072938831},   // k=9
-    {0.9924795345987100, 0.1224106751992162},   // k=10
-    {0.9909026354277800, 0.1345807085071262},   // k=11
-    {0.9891765099647810, 0.1467304744553617},   // k=12
-    {0.9873014181578584, 0.1588581433338614},   // k=13
-    {0.9852776423889412, 0.1709618887603012},   // k=14
-    {0.9831054874312163, 0.1830398879551410},   // k=15
-    {0.9807852804032304, 0.1950903220161282},   // k=16
-    {0.9783173707196277, 0.2071113761922186},   // k=17
-    {0.9757021300385286, 0.2191012401568698},   // k=18
-    {0.9729399522055602, 0.2310581082806711},   // k=19
-    {0.9700312531945440, 0.2429801799032639},   // k=20
-    {0.9669764710448521, 0.2548656596045146},   // k=21
-    {0.9637760657954398, 0.2667127574748984},   // k=22
-    {0.9604305194155658, 0.2785196893850531},   // k=23
-    {0.9569403357322088, 0.2902846772544623},   // k=24
-    {0.9533060403541939, 0.3020059493192281},   // k=25
-    {0.9495281805930367, 0.3136817403988915},   // k=26
-    {0.9456073253805213, 0.3253102921622629},   // k=27
-    {0.9415440651830208, 0.3368898533922201},   // k=28
-    {0.9373390119125750, 0.3484186802494346},   // k=29
-    {0.9329927988347390, 0.3598950365349881},   // k=30
-    {0.9285060804732156, 0.3713171939518375},   // k=31
-    {0.9238795325112867, 0.3826834323650898},   // k=32
-    {0.9191138516900578, 0.3939920400610481},   // k=33
-    {0.9142097557035307, 0.4052413140049899},   // k=34
-    {0.9091679830905224, 0.4164295600976372},   // k=35
-    {0.9039892931234433, 0.4275550934302821},   // k=36
-    {0.8986744656939538, 0.4386162385385277},   // k=37
-    {0.8932243011955153, 0.4496113296546065},   // k=38
-    {0.8876396204028539, 0.4605387109582400},   // k=39
-    {0.8819212643483550, 0.4713967368259976},   // k=40
-    {0.8760700941954066, 0.4821837720791227},   // k=41
-    {0.8700869911087115, 0.4928981922297840},   // k=42
-    {0.8639728561215868, 0.5035383837257176},   // k=43
-    {0.8577286100002721, 0.5141027441932217},   // k=44
-    {0.8513551931052652, 0.5245896826784689},   // k=45
-    {0.8448535652497071, 0.5349976198870972},   // k=46
-    {0.8382247055548381, 0.5453249884220465},   // k=47
-    {0.8314696123025452, 0.5555702330196022},   // k=48
-    {0.8245893027850253, 0.5657318107836131},   // k=49
-    {0.8175848131515837, 0.5758081914178453},   // k=50
-    {0.8104571982525948, 0.5857978574564389},   // k=51
-    {0.8032075314806449, 0.5956993044924334},   // k=52
-    {0.7958369046088836, 0.6055110414043255},   // k=53
-    {0.7883464276266063, 0.6152315905806268},   // k=54
-    {0.7807372285720945, 0.6248594881423863},   // k=55
-    {0.7730104533627370, 0.6343932841636455},   // k=56
-    {0.7651672656224590, 0.6438315428897914},   // k=57
-    {0.7572088465064846, 0.6531728429537768},   // k=58
-    {0.7491363945234594, 0.6624157775901718},   // k=59
-    {0.7409511253549591, 0.6715589548470183},   // k=60
-    {0.7326542716724128, 0.6806009977954530},   // k=61
-    {0.7242470829514670, 0.6895405447370668},   // k=62
-    {0.7157308252838186, 0.6983762494089729},   // k=63
-    {0.7071067811865476, 0.7071067811865475},   // k=64
-    {0.6983762494089729, 0.7157308252838186},   // k=65
-    {0.6895405447370669, 0.7242470829514669},   // k=66
-    {0.6806009977954531, 0.7326542716724128},   // k=67
-    {0.6715589548470183, 0.7409511253549591},   // k=68
-    {0.6624157775901718, 0.7491363945234593},   // k=69
-    {0.6531728429537768, 0.7572088465064845},   // k=70
-    {0.6438315428897915, 0.7651672656224590},   // k=71
-    {0.6343932841636455, 0.7730104533627370},   // k=72
-    {0.6248594881423865, 0.7807372285720944},   // k=73
-    {0.6152315905806268, 0.7883464276266062},   // k=74
-    {0.6055110414043255, 0.7958369046088835},   // k=75
-    {0.5956993044924335, 0.8032075314806448},   // k=76
-    {0.5857978574564389, 0.8104571982525948},   // k=77
-    {0.5758081914178453, 0.8175848131515837},   // k=78
-    {0.5657318107836132, 0.8245893027850253},   // k=79
-    {0.5555702330196023, 0.8314696123025452},   // k=80
-    {0.5453249884220465, 0.8382247055548380},   // k=81
-    {0.5349976198870973, 0.8448535652497070},   // k=82
-    {0.5245896826784688, 0.8513551931052652},   // k=83
-    {0.5141027441932217, 0.8577286100002721},   // k=84
-    {0.5035383837257176, 0.8639728561215867},   // k=85
-    {0.4928981922297841, 0.8700869911087113},   // k=86
-    {0.4821837720791228, 0.8760700941954066},   // k=87
-    {0.4713967368259978, 0.8819212643483549},   // k=88
-    {0.4605387109582400, 0.8876396204028539},   // k=89
-    {0.4496113296546066, 0.8932243011955153},   // k=90
-    {0.4386162385385277, 0.8986744656939538},   // k=91
-    {0.4275550934302822, 0.9039892931234433},   // k=92
-    {0.4164295600976373, 0.9091679830905223},   // k=93
-    {0.4052413140049899, 0.9142097557035307},   // k=94
-    {0.3939920400610481, 0.9191138516900578},   // k=95
-    {0.3826834323650898, 0.9238795325112867},   // k=96
-    {0.3713171939518376, 0.9285060804732155},   // k=97
-    {0.3598950365349883, 0.9329927988347388},   // k=98
-    {0.3484186802494345, 0.9373390119125750},   // k=99
-    {0.3368898533922201, 0.9415440651830208},   // k=100
-    {0.3253102921622630, 0.9456073253805213},   // k=101
-    {0.3136817403988916, 0.9495281805930367},   // k=102
-    {0.3020059493192282, 0.9533060403541938},   // k=103
-    {0.2902846772544623, 0.9569403357322089},   // k=104
-    {0.2785196893850531, 0.9604305194155658},   // k=105
-    {0.2667127574748984, 0.9637760657954398},   // k=106
-    {0.2548656596045146, 0.9669764710448521},   // k=107
-    {0.2429801799032640, 0.9700312531945440},   // k=108
-    {0.2310581082806713, 0.9729399522055601},   // k=109
-    {0.2191012401568698, 0.9757021300385286},   // k=110
-    {0.2071113761922186, 0.9783173707196277},   // k=111
-    {0.1950903220161283, 0.9807852804032304},   // k=112
-    {0.1830398879551411, 0.9831054874312163},   // k=113
-    {0.1709618887603014, 0.9852776423889412},   // k=114
-    {0.1588581433338614, 0.9873014181578584},   // k=115
-    {0.1467304744553617, 0.9891765099647810},   // k=116
-    {0.1345807085071262, 0.9909026354277800},   // k=117
-    {0.1224106751992163, 0.9924795345987100},   // k=118
-    {0.1102222072938832, 0.9939069700023561},   // k=119
-    {0.0980171403295608, 0.9951847266721968},   // k=120
-    {0.0857973123444399, 0.9963126121827780},   // k=121
-    {0.0735645635996675, 0.9972904566786902},   // k=122
-    {0.0613207363022086, 0.9981181129001492},   // k=123
-    {0.0490676743274181, 0.9987954562051724},   // k=124
-    {0.0368072229413590, 0.9993223845883495},   // k=125
-    {0.0245412285229123, 0.9996988186962042},   // k=126
-    {0.0122715382857199, 0.9999247018391445},   // k=127
-    {0.0000000000000001, 1.0000000000000000},   // k=128
-    {-0.0122715382857198, 0.9999247018391445},  // k=129
-    {-0.0245412285229121, 0.9996988186962042},  // k=130
-    {-0.0368072229413589, 0.9993223845883495},  // k=131
-    {-0.0490676743274180, 0.9987954562051724},  // k=132
-    {-0.0613207363022085, 0.9981181129001492},  // k=133
-    {-0.0735645635996673, 0.9972904566786902},  // k=134
-    {-0.0857973123444398, 0.9963126121827780},  // k=135
-    {-0.0980171403295606, 0.9951847266721969},  // k=136
-    {-0.1102222072938831, 0.9939069700023561},  // k=137
-    {-0.1224106751992162, 0.9924795345987100},  // k=138
-    {-0.1345807085071261, 0.9909026354277800},  // k=139
-    {-0.1467304744553616, 0.9891765099647810},  // k=140
-    {-0.1588581433338613, 0.9873014181578584},  // k=141
-    {-0.1709618887603012, 0.9852776423889412},  // k=142
-    {-0.1830398879551409, 0.9831054874312163},  // k=143
-    {-0.1950903220161282, 0.9807852804032304},  // k=144
-    {-0.2071113761922184, 0.9783173707196277},  // k=145
-    {-0.2191012401568697, 0.9757021300385286},  // k=146
-    {-0.2310581082806711, 0.9729399522055602},  // k=147
-    {-0.2429801799032639, 0.9700312531945440},  // k=148
-    {-0.2548656596045145, 0.9669764710448521},  // k=149
-    {-0.2667127574748983, 0.9637760657954398},  // k=150
-    {-0.2785196893850529, 0.9604305194155659},  // k=151
-    {-0.2902846772544622, 0.9569403357322089},  // k=152
-    {-0.3020059493192281, 0.9533060403541939},  // k=153
-    {-0.3136817403988914, 0.9495281805930367},  // k=154
-    {-0.3253102921622629, 0.9456073253805214},  // k=155
-    {-0.3368898533922199, 0.9415440651830208},  // k=156
-    {-0.3484186802494344, 0.9373390119125750},  // k=157
-    {-0.3598950365349882, 0.9329927988347388},  // k=158
-    {-0.3713171939518375, 0.9285060804732156},  // k=159
-    {-0.3826834323650897, 0.9238795325112867},  // k=160
-    {-0.3939920400610480, 0.9191138516900578},  // k=161
-    {-0.4052413140049897, 0.9142097557035307},  // k=162
-    {-0.4164295600976370, 0.9091679830905225},  // k=163
-    {-0.4275550934302819, 0.9039892931234434},  // k=164
-    {-0.4386162385385274, 0.8986744656939539},  // k=165
-    {-0.4496113296546067, 0.8932243011955152},  // k=166
-    {-0.4605387109582401, 0.8876396204028539},  // k=167
-    {-0.4713967368259977, 0.8819212643483550},  // k=168
-    {-0.4821837720791227, 0.8760700941954066},  // k=169
-    {-0.4928981922297840, 0.8700869911087115},  // k=170
-    {-0.5035383837257175, 0.8639728561215868},  // k=171
-    {-0.5141027441932217, 0.8577286100002721},  // k=172
-    {-0.5245896826784687, 0.8513551931052652},  // k=173
-    {-0.5349976198870970, 0.8448535652497072},  // k=174
-    {-0.5453249884220462, 0.8382247055548382},  // k=175
-    {-0.5555702330196020, 0.8314696123025455},  // k=176
-    {-0.5657318107836132, 0.8245893027850252},  // k=177
-    {-0.5758081914178453, 0.8175848131515837},  // k=178
-    {-0.5857978574564389, 0.8104571982525948},  // k=179
-    {-0.5956993044924334, 0.8032075314806449},  // k=180
-    {-0.6055110414043254, 0.7958369046088836},  // k=181
-    {-0.6152315905806267, 0.7883464276266063},  // k=182
-    {-0.6248594881423862, 0.7807372285720946},  // k=183
-    {-0.6343932841636454, 0.7730104533627371},  // k=184
-    {-0.6438315428897913, 0.7651672656224591},  // k=185
-    {-0.6531728429537765, 0.7572088465064847},  // k=186
-    {-0.6624157775901719, 0.7491363945234593},  // k=187
-    {-0.6715589548470184, 0.7409511253549590},  // k=188
-    {-0.6806009977954530, 0.7326542716724128},  // k=189
-    {-0.6895405447370669, 0.7242470829514669},  // k=190
-    {-0.6983762494089728, 0.7157308252838187},  // k=191
-    {-0.7071067811865475, 0.7071067811865476},  // k=192
-    {-0.7157308252838186, 0.6983762494089729},  // k=193
-    {-0.7242470829514668, 0.6895405447370671},  // k=194
-    {-0.7326542716724127, 0.6806009977954532},  // k=195
-    {-0.7409511253549589, 0.6715589548470186},  // k=196
-    {-0.7491363945234591, 0.6624157775901720},  // k=197
-    {-0.7572088465064846, 0.6531728429537766},  // k=198
-    {-0.7651672656224590, 0.6438315428897914},  // k=199
-    {-0.7730104533627370, 0.6343932841636455},  // k=200
-    {-0.7807372285720945, 0.6248594881423863},  // k=201
-    {-0.7883464276266062, 0.6152315905806269},  // k=202
-    {-0.7958369046088835, 0.6055110414043257},  // k=203
-    {-0.8032075314806448, 0.5956993044924335},  // k=204
-    {-0.8104571982525947, 0.5857978574564390},  // k=205
-    {-0.8175848131515836, 0.5758081914178454},  // k=206
-    {-0.8245893027850251, 0.5657318107836135},  // k=207
-    {-0.8314696123025453, 0.5555702330196022},  // k=208
-    {-0.8382247055548381, 0.5453249884220464},  // k=209
-    {-0.8448535652497071, 0.5349976198870972},  // k=210
-    {-0.8513551931052652, 0.5245896826784689},  // k=211
-    {-0.8577286100002720, 0.5141027441932218},  // k=212
-    {-0.8639728561215867, 0.5035383837257177},  // k=213
-    {-0.8700869911087113, 0.4928981922297841},  // k=214
-    {-0.8760700941954065, 0.4821837720791229},  // k=215
-    {-0.8819212643483549, 0.4713967368259979},  // k=216
-    {-0.8876396204028538, 0.4605387109582402},  // k=217
-    {-0.8932243011955152, 0.4496113296546069},  // k=218
-    {-0.8986744656939539, 0.4386162385385275},  // k=219
-    {-0.9039892931234433, 0.4275550934302820},  // k=220
-    {-0.9091679830905224, 0.4164295600976372},  // k=221
-    {-0.9142097557035307, 0.4052413140049899},  // k=222
-    {-0.9191138516900578, 0.3939920400610482},  // k=223
-    {-0.9238795325112867, 0.3826834323650899},  // k=224
-    {-0.9285060804732155, 0.3713171939518377},  // k=225
-    {-0.9329927988347388, 0.3598950365349883},  // k=226
-    {-0.9373390119125748, 0.3484186802494348},  // k=227
-    {-0.9415440651830207, 0.3368898533922203},  // k=228
-    {-0.9456073253805212, 0.3253102921622633},  // k=229
-    {-0.9495281805930367, 0.3136817403988914},  // k=230
-    {-0.9533060403541939, 0.3020059493192280},  // k=231
-    {-0.9569403357322088, 0.2902846772544624},  // k=232
-    {-0.9604305194155658, 0.2785196893850532},  // k=233
-    {-0.9637760657954398, 0.2667127574748985},  // k=234
-    {-0.9669764710448521, 0.2548656596045147},  // k=235
-    {-0.9700312531945440, 0.2429801799032641},  // k=236
-    {-0.9729399522055601, 0.2310581082806713},  // k=237
-    {-0.9757021300385285, 0.2191012401568700},  // k=238
-    {-0.9783173707196275, 0.2071113761922188},  // k=239
-    {-0.9807852804032304, 0.1950903220161286},  // k=240
-    {-0.9831054874312163, 0.1830398879551409},  // k=241
-    {-0.9852776423889412, 0.1709618887603012},  // k=242
-    {-0.9873014181578584, 0.1588581433338615},  // k=243
-    {-0.9891765099647810, 0.1467304744553618},  // k=244
-    {-0.9909026354277800, 0.1345807085071263},  // k=245
-    {-0.9924795345987100, 0.1224106751992163},  // k=246
-    {-0.9939069700023561, 0.1102222072938832},  // k=247
-    {-0.9951847266721968, 0.0980171403295608},  // k=248
-    {-0.9963126121827780, 0.0857973123444402},  // k=249
-    {-0.9972904566786902, 0.0735645635996677},  // k=250
-    {-0.9981181129001492, 0.0613207363022085},  // k=251
-    {-0.9987954562051724, 0.0490676743274180},  // k=252
-    {-0.9993223845883495, 0.0368072229413588},  // k=253
-    {-0.9996988186962042, 0.0245412285229123},  // k=254
-    {-0.9999247018391445, 0.0122715382857200},  // k=255
-    {-1.0000000000000000, 0.0000000000000001},  // k=256
-    {-0.9999247018391445, -0.0122715382857198}, // k=257
-    {-0.9996988186962042, -0.0245412285229121}, // k=258
-    {-0.9993223845883495, -0.0368072229413586}, // k=259
-    {-0.9987954562051724, -0.0490676743274177}, // k=260
-    {-0.9981181129001492, -0.0613207363022082}, // k=261
-    {-0.9972904566786902, -0.0735645635996675}, // k=262
-    {-0.9963126121827780, -0.0857973123444399}, // k=263
-    {-0.9951847266721969, -0.0980171403295606}, // k=264
-    {-0.9939069700023561, -0.1102222072938830}, // k=265
-    {-0.9924795345987100, -0.1224106751992161}, // k=266
-    {-0.9909026354277800, -0.1345807085071261}, // k=267
-    {-0.9891765099647810, -0.1467304744553616}, // k=268
-    {-0.9873014181578584, -0.1588581433338612}, // k=269
-    {-0.9852776423889413, -0.1709618887603010}, // k=270
-    {-0.9831054874312164, -0.1830398879551406}, // k=271
-    {-0.9807852804032304, -0.1950903220161284}, // k=272
-    {-0.9783173707196277, -0.2071113761922186}, // k=273
-    {-0.9757021300385286, -0.2191012401568698}, // k=274
-    {-0.9729399522055602, -0.2310581082806711}, // k=275
-    {-0.9700312531945440, -0.2429801799032638}, // k=276
-    {-0.9669764710448522, -0.2548656596045145}, // k=277
-    {-0.9637760657954400, -0.2667127574748983}, // k=278
-    {-0.9604305194155659, -0.2785196893850529}, // k=279
-    {-0.9569403357322089, -0.2902846772544621}, // k=280
-    {-0.9533060403541940, -0.3020059493192278}, // k=281
-    {-0.9495281805930368, -0.3136817403988912}, // k=282
-    {-0.9456073253805213, -0.3253102921622630}, // k=283
-    {-0.9415440651830208, -0.3368898533922201}, // k=284
-    {-0.9373390119125750, -0.3484186802494346}, // k=285
-    {-0.9329927988347390, -0.3598950365349881}, // k=286
-    {-0.9285060804732156, -0.3713171939518374}, // k=287
-    {-0.9238795325112868, -0.3826834323650897}, // k=288
-    {-0.9191138516900578, -0.3939920400610479}, // k=289
-    {-0.9142097557035307, -0.4052413140049897}, // k=290
-    {-0.9091679830905225, -0.4164295600976369}, // k=291
-    {-0.9039892931234434, -0.4275550934302818}, // k=292
-    {-0.8986744656939540, -0.4386162385385273}, // k=293
-    {-0.8932243011955153, -0.4496113296546067}, // k=294
-    {-0.8876396204028539, -0.4605387109582401}, // k=295
-    {-0.8819212643483550, -0.4713967368259976}, // k=296
-    {-0.8760700941954066, -0.4821837720791227}, // k=297
-    {-0.8700869911087115, -0.4928981922297839}, // k=298
-    {-0.8639728561215868, -0.5035383837257175}, // k=299
-    {-0.8577286100002721, -0.5141027441932216}, // k=300
-    {-0.8513551931052653, -0.5245896826784687}, // k=301
-    {-0.8448535652497072, -0.5349976198870969}, // k=302
-    {-0.8382247055548382, -0.5453249884220461}, // k=303
-    {-0.8314696123025455, -0.5555702330196020}, // k=304
-    {-0.8245893027850253, -0.5657318107836132}, // k=305
-    {-0.8175848131515837, -0.5758081914178453}, // k=306
-    {-0.8104571982525948, -0.5857978574564389}, // k=307
-    {-0.8032075314806449, -0.5956993044924332}, // k=308
-    {-0.7958369046088836, -0.6055110414043254}, // k=309
-    {-0.7883464276266063, -0.6152315905806267}, // k=310
-    {-0.7807372285720946, -0.6248594881423862}, // k=311
-    {-0.7730104533627371, -0.6343932841636453}, // k=312
-    {-0.7651672656224591, -0.6438315428897913}, // k=313
-    {-0.7572088465064848, -0.6531728429537765}, // k=314
-    {-0.7491363945234593, -0.6624157775901718}, // k=315
-    {-0.7409511253549591, -0.6715589548470184}, // k=316
-    {-0.7326542716724128, -0.6806009977954530}, // k=317
-    {-0.7242470829514670, -0.6895405447370668}, // k=318
-    {-0.7157308252838187, -0.6983762494089728}, // k=319
-    {-0.7071067811865477, -0.7071067811865475}, // k=320
-    {-0.6983762494089730, -0.7157308252838185}, // k=321
-    {-0.6895405447370671, -0.7242470829514668}, // k=322
-    {-0.6806009977954532, -0.7326542716724126}, // k=323
-    {-0.6715589548470187, -0.7409511253549589}, // k=324
-    {-0.6624157775901720, -0.7491363945234590}, // k=325
-    {-0.6531728429537771, -0.7572088465064842}, // k=326
-    {-0.6438315428897915, -0.7651672656224590}, // k=327
-    {-0.6343932841636459, -0.7730104533627367}, // k=328
-    {-0.6248594881423865, -0.7807372285720944}, // k=329
-    {-0.6152315905806273, -0.7883464276266059}, // k=330
-    {-0.6055110414043257, -0.7958369046088835}, // k=331
-    {-0.5956993044924331, -0.8032075314806451}, // k=332
-    {-0.5857978574564391, -0.8104571982525947}, // k=333
-    {-0.5758081914178452, -0.8175848131515838}, // k=334
-    {-0.5657318107836135, -0.8245893027850251}, // k=335
-    {-0.5555702330196022, -0.8314696123025452}, // k=336
-    {-0.5453249884220468, -0.8382247055548379}, // k=337
-    {-0.5349976198870973, -0.8448535652497070}, // k=338
-    {-0.5245896826784694, -0.8513551931052649}, // k=339
-    {-0.5141027441932218, -0.8577286100002720}, // k=340
-    {-0.5035383837257180, -0.8639728561215865}, // k=341
-    {-0.4928981922297842, -0.8700869911087113}, // k=342
-    {-0.4821837720791226, -0.8760700941954067}, // k=343
-    {-0.4713967368259979, -0.8819212643483549}, // k=344
-    {-0.4605387109582399, -0.8876396204028540}, // k=345
-    {-0.4496113296546069, -0.8932243011955152}, // k=346
-    {-0.4386162385385276, -0.8986744656939538}, // k=347
-    {-0.4275550934302825, -0.9039892931234431}, // k=348
-    {-0.4164295600976372, -0.9091679830905224}, // k=349
-    {-0.4052413140049904, -0.9142097557035305}, // k=350
-    {-0.3939920400610482, -0.9191138516900577}, // k=351
-    {-0.3826834323650903, -0.9238795325112865}, // k=352
-    {-0.3713171939518378, -0.9285060804732155}, // k=353
-    {-0.3598950365349879, -0.9329927988347390}, // k=354
-    {-0.3484186802494348, -0.9373390119125748}, // k=355
-    {-0.3368898533922199, -0.9415440651830208}, // k=356
-    {-0.3253102921622633, -0.9456073253805212}, // k=357
-    {-0.3136817403988915, -0.9495281805930367}, // k=358
-    {-0.3020059493192285, -0.9533060403541938}, // k=359
-    {-0.2902846772544624, -0.9569403357322088}, // k=360
-    {-0.2785196893850536, -0.9604305194155657}, // k=361
-    {-0.2667127574748985, -0.9637760657954398}, // k=362
-    {-0.2548656596045143, -0.9669764710448522}, // k=363
-    {-0.2429801799032641, -0.9700312531945440}, // k=364
-    {-0.2310581082806709, -0.9729399522055602}, // k=365
-    {-0.2191012401568701, -0.9757021300385285}, // k=366
-    {-0.2071113761922185, -0.9783173707196277}, // k=367
-    {-0.1950903220161287, -0.9807852804032303}, // k=368
-    {-0.1830398879551410, -0.9831054874312163}, // k=369
-    {-0.1709618887603017, -0.9852776423889411}, // k=370
-    {-0.1588581433338615, -0.9873014181578583}, // k=371
-    {-0.1467304744553623, -0.9891765099647809}, // k=372
-    {-0.1345807085071264, -0.9909026354277800}, // k=373
-    {-0.1224106751992160, -0.9924795345987101}, // k=374
-    {-0.1102222072938833, -0.9939069700023561}, // k=375
-    {-0.0980171403295605, -0.9951847266721969}, // k=376
-    {-0.0857973123444402, -0.9963126121827780}, // k=377
-    {-0.0735645635996674, -0.9972904566786902}, // k=378
-    {-0.0613207363022090, -0.9981181129001492}, // k=379
-    {-0.0490676743274180, -0.9987954562051724}, // k=380
-    {-0.0368072229413593, -0.9993223845883494}, // k=381
-    {-0.0245412285229124, -0.9996988186962042}, // k=382
-    {-0.0122715382857205, -0.9999247018391445}, // k=383
-    {-0.0000000000000002, -1.0000000000000000}, // k=384
-    {0.0122715382857201, -0.9999247018391445},  // k=385
-    {0.0245412285229120, -0.9996988186962042},  // k=386
-    {0.0368072229413590, -0.9993223845883495},  // k=387
-    {0.0490676743274177, -0.9987954562051724},  // k=388
-    {0.0613207363022086, -0.9981181129001492},  // k=389
-    {0.0735645635996670, -0.9972904566786902},  // k=390
-    {0.0857973123444399, -0.9963126121827780},  // k=391
-    {0.0980171403295601, -0.9951847266721969},  // k=392
-    {0.1102222072938829, -0.9939069700023561},  // k=393
-    {0.1224106751992156, -0.9924795345987101},  // k=394
-    {0.1345807085071260, -0.9909026354277800},  // k=395
-    {0.1467304744553619, -0.9891765099647809},  // k=396
-    {0.1588581433338612, -0.9873014181578584},  // k=397
-    {0.1709618887603013, -0.9852776423889412},  // k=398
-    {0.1830398879551406, -0.9831054874312164},  // k=399
-    {0.1950903220161283, -0.9807852804032304},  // k=400
-    {0.2071113761922181, -0.9783173707196278},  // k=401
-    {0.2191012401568697, -0.9757021300385286},  // k=402
-    {0.2310581082806706, -0.9729399522055603},  // k=403
-    {0.2429801799032638, -0.9700312531945440},  // k=404
-    {0.2548656596045140, -0.9669764710448523},  // k=405
-    {0.2667127574748982, -0.9637760657954400},  // k=406
-    {0.2785196893850533, -0.9604305194155658},  // k=407
-    {0.2902846772544621, -0.9569403357322089},  // k=408
-    {0.3020059493192281, -0.9533060403541939},  // k=409
-    {0.3136817403988911, -0.9495281805930368},  // k=410
-    {0.3253102921622629, -0.9456073253805213},  // k=411
-    {0.3368898533922196, -0.9415440651830209},  // k=412
-    {0.3484186802494345, -0.9373390119125750},  // k=413
-    {0.3598950365349876, -0.9329927988347391},  // k=414
-    {0.3713171939518374, -0.9285060804732156},  // k=415
-    {0.3826834323650900, -0.9238795325112866},  // k=416
-    {0.3939920400610479, -0.9191138516900579},  // k=417
-    {0.4052413140049900, -0.9142097557035306},  // k=418
-    {0.4164295600976369, -0.9091679830905225},  // k=419
-    {0.4275550934302821, -0.9039892931234433},  // k=420
-    {0.4386162385385273, -0.8986744656939540},  // k=421
-    {0.4496113296546066, -0.8932243011955153},  // k=422
-    {0.4605387109582396, -0.8876396204028542},  // k=423
-    {0.4713967368259976, -0.8819212643483550},  // k=424
-    {0.4821837720791222, -0.8760700941954069},  // k=425
-    {0.4928981922297839, -0.8700869911087115},  // k=426
-    {0.5035383837257178, -0.8639728561215866},  // k=427
-    {0.5141027441932216, -0.8577286100002722},  // k=428
-    {0.5245896826784691, -0.8513551931052651},  // k=429
-    {0.5349976198870969, -0.8448535652497072},  // k=430
-    {0.5453249884220465, -0.8382247055548380},  // k=431
-    {0.5555702330196018, -0.8314696123025455},  // k=432
-    {0.5657318107836131, -0.8245893027850253},  // k=433
-    {0.5758081914178449, -0.8175848131515840},  // k=434
-    {0.5857978574564388, -0.8104571982525949},  // k=435
-    {0.5956993044924329, -0.8032075314806453},  // k=436
-    {0.6055110414043253, -0.7958369046088837},  // k=437
-    {0.6152315905806270, -0.7883464276266061},  // k=438
-    {0.6248594881423861, -0.7807372285720946},  // k=439
-    {0.6343932841636456, -0.7730104533627369},  // k=440
-    {0.6438315428897912, -0.7651672656224592},  // k=441
-    {0.6531728429537768, -0.7572088465064846},  // k=442
-    {0.6624157775901715, -0.7491363945234596},  // k=443
-    {0.6715589548470183, -0.7409511253549591},  // k=444
-    {0.6806009977954527, -0.7326542716724131},  // k=445
-    {0.6895405447370668, -0.7242470829514670},  // k=446
-    {0.6983762494089724, -0.7157308252838190},  // k=447
-    {0.7071067811865474, -0.7071067811865477},  // k=448
-    {0.7157308252838188, -0.6983762494089727},  // k=449
-    {0.7242470829514667, -0.6895405447370672},  // k=450
-    {0.7326542716724129, -0.6806009977954530},  // k=451
-    {0.7409511253549589, -0.6715589548470187},  // k=452
-    {0.7491363945234594, -0.6624157775901718},  // k=453
-    {0.7572088465064842, -0.6531728429537771},  // k=454
-    {0.7651672656224588, -0.6438315428897915},  // k=455
-    {0.7730104533627367, -0.6343932841636459},  // k=456
-    {0.7807372285720944, -0.6248594881423865},  // k=457
-    {0.7883464276266059, -0.6152315905806274},  // k=458
-    {0.7958369046088833, -0.6055110414043257},  // k=459
-    {0.8032075314806451, -0.5956993044924332},  // k=460
-    {0.8104571982525947, -0.5857978574564391},  // k=461
-    {0.8175848131515837, -0.5758081914178452},  // k=462
-    {0.8245893027850251, -0.5657318107836136},  // k=463
-    {0.8314696123025452, -0.5555702330196022},  // k=464
-    {0.8382247055548377, -0.5453249884220468},  // k=465
-    {0.8448535652497070, -0.5349976198870973},  // k=466
-    {0.8513551931052649, -0.5245896826784694},  // k=467
-    {0.8577286100002720, -0.5141027441932219},  // k=468
-    {0.8639728561215864, -0.5035383837257181},  // k=469
-    {0.8700869911087113, -0.4928981922297843},  // k=470
-    {0.8760700941954067, -0.4821837720791226},  // k=471
-    {0.8819212643483548, -0.4713967368259979},  // k=472
-    {0.8876396204028539, -0.4605387109582399},  // k=473
-    {0.8932243011955151, -0.4496113296546070},  // k=474
-    {0.8986744656939538, -0.4386162385385277},  // k=475
-    {0.9039892931234431, -0.4275550934302825},  // k=476
-    {0.9091679830905224, -0.4164295600976373},  // k=477
-    {0.9142097557035305, -0.4052413140049904},  // k=478
-    {0.9191138516900577, -0.3939920400610483},  // k=479
-    {0.9238795325112865, -0.3826834323650904},  // k=480
-    {0.9285060804732155, -0.3713171939518378},  // k=481
-    {0.9329927988347390, -0.3598950365349880},  // k=482
-    {0.9373390119125748, -0.3484186802494349},  // k=483
-    {0.9415440651830208, -0.3368898533922200},  // k=484
-    {0.9456073253805212, -0.3253102921622634},  // k=485
-    {0.9495281805930367, -0.3136817403988915},  // k=486
-    {0.9533060403541936, -0.3020059493192286},  // k=487
-    {0.9569403357322088, -0.2902846772544625},  // k=488
-    {0.9604305194155657, -0.2785196893850537},  // k=489
-    {0.9637760657954398, -0.2667127574748986},  // k=490
-    {0.9669764710448522, -0.2548656596045144},  // k=491
-    {0.9700312531945440, -0.2429801799032642},  // k=492
-    {0.9729399522055602, -0.2310581082806710},  // k=493
-    {0.9757021300385285, -0.2191012401568702},  // k=494
-    {0.9783173707196277, -0.2071113761922185},  // k=495
-    {0.9807852804032303, -0.1950903220161287},  // k=496
-    {0.9831054874312163, -0.1830398879551410},  // k=497
-    {0.9852776423889411, -0.1709618887603018},  // k=498
-    {0.9873014181578583, -0.1588581433338616},  // k=499
-    {0.9891765099647809, -0.1467304744553624},  // k=500
-    {0.9909026354277800, -0.1345807085071264},  // k=501
-    {0.9924795345987100, -0.1224106751992160},  // k=502
-    {0.9939069700023561, -0.1102222072938834},  // k=503
-    {0.9951847266721969, -0.0980171403295605},  // k=504
-    {0.9963126121827780, -0.0857973123444403},  // k=505
-    {0.9972904566786902, -0.0735645635996674},  // k=506
-    {0.9981181129001492, -0.0613207363022091},  // k=507
-    {0.9987954562051724, -0.0490676743274181},  // k=508
-    {0.9993223845883494, -0.0368072229413594},  // k=509
-    {0.9996988186962042, -0.0245412285229124},  // k=510
-    {0.9999247018391445, -0.0122715382857206},  // k=511
-};

From 932f156bfc045f80f28b2dcf72b086b45656e386 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 24 Oct 2025 09:41:22 -0700
Subject: [PATCH 0289/1827] Fixup: cleanup and run GPU fft on its own stream

---
 src/mesh/parallel/shiftedmetric.cxx | 90 +++++++++++++++--------------
 1 file changed, 46 insertions(+), 44 deletions(-)

diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 759c5aaa0a..1b92313117 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -72,7 +72,6 @@ void ShiftedMetric::cachePhases() {
   toAlignedPhs = Tensor<dcomplex>(mesh.LocalNx, mesh.LocalNy, nmodes);
 
   // To/From field aligned phases
-  // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
   BOUT_FOR(i, mesh.getRegion2D("RGN_ALL")) {
     int ix = i.x();
     int iy = i.y();
@@ -111,7 +110,6 @@ void ShiftedMetric::cachePhases() {
 
   // Parallel slice phases -- note we don't shift in the boundaries/guards
   for (auto& slice : parallel_slice_phases) {
-    // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
     BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) {
 
       int ix = i.x();
@@ -173,7 +171,6 @@ Field3D ShiftedMetric::shiftZ(const Field3D& f, const Tensor<dcomplex>& phs,
 
   Field3D result{emptyFrom(f).setDirectionY(y_direction_out)};
 
-  // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
   BOUT_FOR(i, mesh.getRegion2D(toString(region))) {
     shiftZ(&f(i, 0), &phs(i.x(), i.y(), 0), &result(i, 0));
   }
@@ -204,8 +201,7 @@ FieldPerp ShiftedMetric::shiftZ(const FieldPerp& f, const Tensor<dcomplex>& phs,
   return result;
 }
 
-void ShiftedMetric::shiftZ(const BoutReal* in, const dcomplex* phs, BoutReal* out,
-                           int num_batches) const {
+void ShiftedMetric::shiftZ(const BoutReal* in, const dcomplex* phs, BoutReal* out) const {
 #if BOUT_HAS_UMPIRE
   // TODO: This static keyword is a hotfix and should be removed in
   //      future iterations. It is here because otherwise many allocations
@@ -217,7 +213,7 @@ void ShiftedMetric::shiftZ(const BoutReal* in, const dcomplex* phs, BoutReal* ou
 #endif
 
   // Take forward FFT
-  rfft(in, mesh.LocalNz * num_batches, &cmplx[0]);
+  rfft(in, mesh.LocalNz, &cmplx[0]);
 
   // Following is an algorithm approach to write a = a*b where a and b are
   // vectors of dcomplex.
@@ -246,13 +242,14 @@ __device__ inline unsigned int bit_reverse(unsigned int x, unsigned int log2n) {
 // Block-level cooperative FFT
 // Multiple threads cooperate on each FFT using shared memory
 template <int NZ, int FFTS_PER_BLOCK = 4>
-__global__ void
-fft_block_cooperative(const BoutReal** __restrict__ in, BoutReal** __restrict__ out,
-                      const double2** __restrict__ blocks_phs, const int Nz_runtime,
-                      const int nmodes, const int batches, const int nblocks) {
+__global__ void fft_block_cooperative(const BoutReal** __restrict__ in,
+                                      BoutReal** __restrict__ out,
+                                      const double2** __restrict__ blocks_phs,
+                                      const int batches, const int nblocks) {
 
   constexpr int LOG2_NZ = __builtin_ctz(NZ);
   constexpr double INV_NZ = 1.0 / (double)NZ;
+  constexpr int NMODES = (NZ / 2) + 1;
 
   // Shared memory for FFTS_PER_BLOCK FFTs
   // Each FFT needs NZ complex values
@@ -261,15 +258,15 @@ fft_block_cooperative(const BoutReal** __restrict__ in, BoutReal** __restrict__
   // Select twiddles based on size
   const double2* twiddles;
   if constexpr (NZ == 16) {
-    twiddles = c_twiddle_fwd_16;
+    twiddles = c_twiddle_16;
   } else if constexpr (NZ == 64) {
-    twiddles = c_twiddle_fwd_64;
+    twiddles = c_twiddle_64;
   } else if constexpr (NZ == 128) {
-    twiddles = c_twiddle_fwd_128;
+    twiddles = c_twiddle_128;
   } else if constexpr (NZ == 256) {
-    twiddles = c_twiddle_fwd_256;
+    twiddles = c_twiddle_256;
   } else if constexpr (NZ == 512) {
-    twiddles = c_twiddle_fwd_512;
+    twiddles = c_twiddle_512;
   } else {
     static_assert(NZ == 16 || NZ == 64 || NZ == 128 || NZ == 256 || NZ == 512,
                   "Unsupported NZ");
@@ -340,18 +337,18 @@ fft_block_cooperative(const BoutReal** __restrict__ in, BoutReal** __restrict__
   }
 
   // ===== APPLY PHASE SHIFT =====
-  for (int k = tid; k < nmodes; k += threads_per_fft) {
-    const double2 ph = phs[batch * nmodes + k];
+  for (int k = tid; k < NMODES; k += threads_per_fft) {
+    const double2 ph = phs[batch * NMODES + k];
     const double real = shared_fft[fft_id_in_block][k].x;
     const double imag = shared_fft[fft_id_in_block][k].y;
     shared_fft[fft_id_in_block][k].x = real * ph.x - imag * ph.y;
     shared_fft[fft_id_in_block][k].y = real * ph.y + imag * ph.x;
   }
 
-  for (int k = tid + nmodes; k < NZ; k += threads_per_fft) {
-    if (k >= nmodes) {
+  for (int k = tid + NMODES; k < NZ; k += threads_per_fft) {
+    if (k >= NMODES) {
       const int kk = NZ - k;
-      const double2 tmp = phs[batch * nmodes + kk];
+      const double2 tmp = phs[batch * NMODES + kk];
       const double real = shared_fft[fft_id_in_block][k].x;
       const double imag = shared_fft[fft_id_in_block][k].y;
       shared_fft[fft_id_in_block][k].x = real * tmp.x + imag * tmp.y;
@@ -418,18 +415,15 @@ fft_block_cooperative(const BoutReal** __restrict__ in, BoutReal** __restrict__
 }
 
 // Launcher for block-level cooperative FFT
-static void shiftZ_block_fft(Mesh& mesh, const BoutReal** in, BoutReal** out,
-                             const double2** phs, int nblocks, int batches,
+static void shiftZ_block_fft(const int Nz, const BoutReal** in, BoutReal** out,
+                             const double2** phs, int nblocks, int nbatches,
                              cudaStream_t stream = 0) {
-  int Nz = mesh.LocalNz;
-  int nmodes = Nz / 2 + 1;
-
   if ((Nz & (Nz - 1)) != 0) {
     fprintf(stderr, "Error: Nz=%d must be power of 2\n", Nz);
     return;
   }
 
-  const int total_ffts = nblocks * batches;
+  const int total_ffts = nblocks * nbatches;
 
   if (Nz == 16) {
     constexpr int FFTS_PER_BLOCK = 16;
@@ -439,7 +433,7 @@ static void shiftZ_block_fft(Mesh& mesh, const BoutReal** in, BoutReal** out,
     dim3 grid((total_ffts + FFTS_PER_BLOCK - 1) / FFTS_PER_BLOCK);
 
     fft_block_cooperative<16, FFTS_PER_BLOCK>
-        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+        <<<grid, block, 0, stream>>>(in, out, phs, nbatches, nblocks);
   } else if (Nz == 64) {
     constexpr int FFTS_PER_BLOCK = 4;
     constexpr int THREADS_PER_FFT = 64; // Use 64 threads per FFT
@@ -448,7 +442,7 @@ static void shiftZ_block_fft(Mesh& mesh, const BoutReal** in, BoutReal** out,
     dim3 grid((total_ffts + FFTS_PER_BLOCK - 1) / FFTS_PER_BLOCK);
 
     fft_block_cooperative<64, FFTS_PER_BLOCK>
-        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+        <<<grid, block, 0, stream>>>(in, out, phs, nbatches, nblocks);
 
   } else if (Nz == 128) {
     constexpr int FFTS_PER_BLOCK = 2;
@@ -458,7 +452,7 @@ static void shiftZ_block_fft(Mesh& mesh, const BoutReal** in, BoutReal** out,
     dim3 grid((total_ffts + FFTS_PER_BLOCK - 1) / FFTS_PER_BLOCK);
 
     fft_block_cooperative<128, FFTS_PER_BLOCK>
-        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+        <<<grid, block, 0, stream>>>(in, out, phs, nbatches, nblocks);
 
   } else if (Nz == 256) {
     constexpr int FFTS_PER_BLOCK = 1;
@@ -468,7 +462,7 @@ static void shiftZ_block_fft(Mesh& mesh, const BoutReal** in, BoutReal** out,
     dim3 grid(total_ffts);
 
     fft_block_cooperative<256, FFTS_PER_BLOCK>
-        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+        <<<grid, block, 0, stream>>>(in, out, phs, nbatches, nblocks);
 
   } else if (Nz == 512) {
     constexpr int FFTS_PER_BLOCK = 1;
@@ -478,10 +472,9 @@ static void shiftZ_block_fft(Mesh& mesh, const BoutReal** in, BoutReal** out,
     dim3 grid(total_ffts);
 
     fft_block_cooperative<512, FFTS_PER_BLOCK>
-        <<<grid, block, 0, stream>>>(in, out, phs, Nz, nmodes, batches, nblocks);
+        <<<grid, block, 0, stream>>>(in, out, phs, nbatches, nblocks);
   } else {
-    fprintf(stderr, "Unsupported Nz=%d for block FFT\n", Nz);
-    throw std::runtime_error("Unsupported Nz for block FFT");
+    throw std::runtime_error("Unsupported Nz " + std::to_string(Nz) + " for block FFT");
   }
 
   cudaError_t err = cudaGetLastError();
@@ -516,16 +509,30 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
     f_slice.allocate();
 
 #if BOUT_HAS_CUDA
+    static struct StreamRAII {
+      cudaStream_t stream = 0;
+      StreamRAII() {
+        if (cudaStreamCreate(&stream) != cudaSuccess) {
+          throw BoutException("Failed to create CUDA stream");
+        }
+      }
+
+      cudaStream_t get() const { return stream; }
+
+      void synchronize() const { cudaStreamSynchronize(stream); }
+
+      ~StreamRAII() { cudaStreamDestroy(stream); }
+    } stream;
     size_t block_idx = 0;
-    int num_batches =
+    int nbatches =
         region.getBlocks().cbegin()->second.ind - region.getBlocks().cbegin()->first.ind;
 
     for (auto block = region.getBlocks().cbegin(), end = region.getBlocks().cend();
          block < end; ++block) {
       auto idx_s = block->first;
       auto idx_e = block->second;
-      int inner_batches = idx_e.ind - idx_s.ind;
-      if (inner_batches != num_batches) {
+      int inner_nbatches = idx_e.ind - idx_s.ind;
+      if (inner_nbatches != nbatches) {
         throw BoutException(
             "Non-uniform number of batches in ShiftedMetric::calcParallelSlices");
       }
@@ -540,12 +547,11 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
       block_idx++;
     }
 
-    shiftZ_block_fft(mesh, &blocks_in[0], &blocks_out[0], &phs_in[0], nblocks,
-                     num_batches, 0);
+    shiftZ_block_fft(mesh.LocalNz, &blocks_in[0], &blocks_out[0], &phs_in[0], nblocks,
+                     nbatches, stream.get());
 
-    cudaDeviceSynchronize();
+    stream.synchronize();
 #else
-    // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
     BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) {
       const int ix = i.x();
       const int iy = i.y();
@@ -553,8 +559,6 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
       shiftZ(&(f(ix, iy_offset, 0)), &(phase.phase_shift(ix, iy, 0)),
              &(f_slice(ix, iy_offset, 0)));
     }
-    //std::cout << "ShiftedMetric::shiftZ " << __FILE__ << " :" << __LINE__
-    //          << " count = " << count << " each size " << mesh.LocalNz << "\n";
 #endif
   }
 }
@@ -572,7 +576,6 @@ ShiftedMetric::shiftZ(const Field3D& f,
   Matrix<Array<dcomplex>> f_fft(mesh.LocalNx, mesh.LocalNy);
   f_fft = Array<dcomplex>(nmodes);
 
-  // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
   BOUT_FOR(i, mesh.getRegion2D("RGN_ALL")) {
     int ix = i.x();
     int iy = i.y();
@@ -587,7 +590,6 @@ ShiftedMetric::shiftZ(const Field3D& f,
     current_result.allocate();
     current_result.setLocation(f.getLocation());
 
-    // std::cout << "[TRACE] BOUT_FOR " << __FILE__ << ":" << __LINE__ << "\n";
     BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) {
       // Deep copy the FFT'd field
       int ix = i.x();

From 7c7acad3522122b01f8eaa605350c72b07eae587 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 24 Oct 2025 16:46:02 +0100
Subject: [PATCH 0290/1827] Try to appease clang-tidy `misc-include-cleaner`

---
 include/bout/invert/laplacexy.hxx             |  5 +++-
 .../laplacexy/impls/hypre/laplacexy-hypre.cxx | 11 +++++++++
 .../laplacexy/impls/hypre/laplacexy-hypre.hxx |  5 +++-
 .../laplacexy/impls/petsc/laplacexy-petsc.cxx | 24 ++++++++++++-------
 .../laplacexy/impls/petsc/laplacexy-petsc.hxx | 13 ++++++----
 .../impls/petsc2/laplacexy-petsc2.cxx         | 21 +++++++++++-----
 .../impls/petsc2/laplacexy-petsc2.hxx         | 10 ++++----
 .../test-laplacexy-fv/test-laplacexy.cxx      | 17 ++++++++-----
 .../test-laplacexy-short/test-laplacexy.cxx   | 10 +++++++-
 .../test-laplacexy/test-laplacexy.cxx         | 10 +++++++-
 .../test-laplacexy2-hypre/test-laplacexy.cxx  |  9 +++++--
 11 files changed, 101 insertions(+), 34 deletions(-)

diff --git a/include/bout/invert/laplacexy.hxx b/include/bout/invert/laplacexy.hxx
index 0cdd5e751a..51605b9db5 100644
--- a/include/bout/invert/laplacexy.hxx
+++ b/include/bout/invert/laplacexy.hxx
@@ -33,12 +33,15 @@
 #ifndef BOUT_LAPLACEXY_H
 #define BOUT_LAPLACEXY_H
 
+#include <bout/bout_types.hxx>
 #include <bout/field2d.hxx>
 #include <bout/generic_factory.hxx>
 #include <bout/mesh.hxx>
-#include <bout/options.hxx>
+
+#include <string>
 
 class LaplaceXY;
+class Options;
 class Solver;
 
 class LaplaceXYFactory
diff --git a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
index 163b5049ee..9323513f21 100644
--- a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
@@ -5,12 +5,23 @@
 #include "laplacexy-hypre.hxx"
 
 #include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/field2d.hxx"
+#include "bout/globalindexer.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
+#include "bout/operatorstencil.hxx"
+#include "bout/options.hxx"
 #include "bout/output.hxx"
+#include "bout/region.hxx"
+#include "bout/sys/range.hxx"
 #include "bout/sys/timer.hxx"
 
+#include <chrono>
+#include <memory>
+
 #if BOUT_HAS_CUDA && defined(__CUDACC__)
 #define gpuErrchk(ans) \
   { gpuAssert((ans), __FILE__, __LINE__); }
diff --git a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
index 32e9c05ab1..f415f9ebf4 100644
--- a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
@@ -47,7 +47,10 @@ RegisterUnavailableLaplaceXY
 
 class Mesh;
 
-#include <bout/hypre_interface.hxx>
+#include "bout/bout_types.hxx"
+#include "bout/field2d.hxx"
+#include "bout/globalindexer.hxx"
+#include "bout/hypre_interface.hxx"
 
 class LaplaceXY2Hypre : public LaplaceXY {
 public:
diff --git a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
index e80a2ca640..3d7f707678 100644
--- a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
+++ b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
@@ -4,14 +4,22 @@
 
 #include "laplacexy-petsc.hxx"
 
-#include <bout/assert.hxx>
-#include <bout/boutcomm.hxx>
-#include <bout/derivs.hxx>
-#include <bout/globals.hxx>
-#include <bout/output.hxx>
-#include <bout/sys/timer.hxx>
-#include <bout/utils.hxx>
-
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutcomm.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/cyclic_reduction.hxx"
+#include "bout/derivs.hxx"
+#include "bout/field2d.hxx"
+#include "bout/globals.hxx"
+#include "bout/options.hxx"
+#include "bout/petsclib.hxx"
+#include "bout/sys/range.hxx"
+#include "bout/solver.hxx"
+#include "bout/sys/timer.hxx"
+#include "bout/utils.hxx"
+
+#include <fmt/format.h>
 #include <petscksp.h>
 
 #include <cmath>
diff --git a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx
index 1db812a19d..27d25cf9a7 100644
--- a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx
+++ b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx
@@ -45,11 +45,16 @@ RegisterUnavailableLaplaceXY
 
 #else // BOUT_HAS_PETSC
 
-#include "bout/solver.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/cyclic_reduction.hxx"
+#include "bout/field2d.hxx"
+#include "bout/mesh.hxx"
+#include "bout/monitor.hxx"
+#include "bout/petsclib.hxx"
 #include "bout/utils.hxx"
-#include <bout/cyclic_reduction.hxx>
-#include <bout/mesh.hxx>
-#include <bout/petsclib.hxx>
+
+#include <memory>
+#include <string>
 
 class Options;
 class Solver;
diff --git a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
index ae2cc8313a..63fc8d6f91 100644
--- a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
+++ b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
@@ -4,12 +4,21 @@
 
 #include "laplacexy-petsc2.hxx"
 
-#include <bout/assert.hxx>
-#include <bout/boutcomm.hxx>
-#include <bout/globals.hxx>
-#include <bout/output.hxx>
-#include <bout/sys/timer.hxx>
-#include <bout/utils.hxx>
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutcomm.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/field2d.hxx"
+#include "bout/globalindexer.hxx"
+#include "bout/globals.hxx"
+#include "bout/operatorstencil.hxx"
+#include "bout/options.hxx"
+#include "bout/petsc_interface.hxx"
+#include "bout/region.hxx"
+#include "bout/sys/range.hxx"
+#include "bout/sys/timer.hxx"
+
+#include <memory>
 
 #include <petscksp.h>
 
diff --git a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx
index 1480f366fe..eb1be636f2 100644
--- a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx
+++ b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx
@@ -50,10 +50,12 @@ RegisterUnavailableLaplaceXY
 
 #else // BOUT_HAS_PETSC
 
-#include <bout/cyclic_reduction.hxx>
-#include <bout/mesh.hxx>
-#include <bout/petsc_interface.hxx>
-#include <bout/petsclib.hxx>
+#include "bout/bout_types.hxx"
+#include "bout/field2d.hxx"
+#include "bout/globalindexer.hxx"
+#include "bout/mesh.hxx"
+#include "bout/petsc_interface.hxx"
+#include "bout/petsclib.hxx"
 
 class LaplaceXYpetsc2 : public LaplaceXY {
 public:
diff --git a/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx b/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx
index 55c4a383b3..be2f993b31 100644
--- a/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy-fv/test-laplacexy.cxx
@@ -23,12 +23,17 @@
  *
  **************************************************************************/
 
-#include <bout/bout.hxx>
-#include <bout/constants.hxx>
-#include <bout/derivs.hxx>
-#include <bout/initialprofiles.hxx>
-#include <bout/invert/laplacexy.hxx>
-#include <bout/options.hxx>
+#include "bout/bout.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/difops.hxx"
+#include "bout/field2d.hxx"
+#include "bout/initialprofiles.hxx"
+#include "bout/invert/laplacexy.hxx"
+#include "bout/options.hxx"
+#include "bout/options_io.hxx"
+#include "bout/output.hxx"
+
+#include <cstdlib>
 
 int main(int argc, char** argv) {
 
diff --git a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx
index fa67079861..7c284290b3 100644
--- a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx
@@ -24,11 +24,19 @@
  **************************************************************************/
 
 #include <bout/bout.hxx>
-#include <bout/constants.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/derivs.hxx>
+#include <bout/difops.hxx>
+#include <bout/field2d.hxx>
+#include <bout/globals.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/options.hxx>
+#include <bout/options_io.hxx>
+#include <bout/output.hxx>
+#include <bout/vecops.hxx>
+
+#include <cstdlib>
 
 int main(int argc, char** argv) {
 
diff --git a/tests/integrated/test-laplacexy/test-laplacexy.cxx b/tests/integrated/test-laplacexy/test-laplacexy.cxx
index d7b0a55ec8..543274d37d 100644
--- a/tests/integrated/test-laplacexy/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy/test-laplacexy.cxx
@@ -24,11 +24,19 @@
  **************************************************************************/
 
 #include <bout/bout.hxx>
-#include <bout/constants.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/derivs.hxx>
+#include <bout/difops.hxx>
+#include <bout/field2d.hxx>
+#include <bout/globals.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/options.hxx>
+#include <bout/options_io.hxx>
+#include <bout/output.hxx>
+#include <bout/vecops.hxx>
+
+#include <cstdlib>
 
 using bout::globals::mesh;
 
diff --git a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx
index 7b7ac97517..cede14b1f8 100644
--- a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx
@@ -23,13 +23,18 @@
  *
  **************************************************************************/
 
+#include <bout/bout_types.hxx>
+#include <bout/difops.hxx>
+#include <bout/field2d.hxx>
+#include <bout/options_io.hxx>
+#include <bout/output.hxx>
 #include <bout/bout.hxx>
-#include <bout/constants.hxx>
-#include <bout/derivs.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/options.hxx>
 
+#include <cstdlib>
+
 int main(int argc, char** argv) {
 
   BoutInitialise(argc, argv);

From 8fa9f2c054af40c63228f706e9078a55030b6198 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 24 Oct 2025 17:21:22 +0100
Subject: [PATCH 0291/1827] CI: Don't warn about including PETSc or MPI symbols
 directly

---
 .clang-tidy | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.clang-tidy b/.clang-tidy
index 556b8738f8..4caf530aee 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -9,6 +9,9 @@ CheckOptions:
   # otherwise this breaks `ASSERT` macros!
   - key:             readability-simplify-boolean-expr.IgnoreMacros
     value:           'true'
+
+  - key: misc-include-cleaner.IgnoreHeaders
+    value: 'petsc.*\.h;mpi\.h'
 ---
 
 Disabled checks and reasons:

From 2cb22807dc4ffc9e9bfada5a31777335ce44591d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 24 Oct 2025 17:21:42 +0100
Subject: [PATCH 0292/1827] Fix call to virtual function in ctor

---
 src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
index 63fc8d6f91..01019466a8 100644
--- a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
+++ b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
@@ -128,7 +128,7 @@ LaplaceXYpetsc2::LaplaceXYpetsc2(Mesh* m, Options* opt, const CELL_LOC loc)
   Field2D zero(0., localmesh);
   one.setLocation(location);
   zero.setLocation(location);
-  setCoefs(one, zero);
+  LaplaceXYpetsc2::setCoefs(one, zero);
 }
 
 void LaplaceXYpetsc2::setCoefs(const Field2D& A, const Field2D& B) {

From b497f8969ca1f1eb6bdd95a22e346b6c756be6c9 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 24 Oct 2025 17:56:43 +0100
Subject: [PATCH 0293/1827] Update examples for LaplaceXY factory

---
 examples/CMakeLists.txt                       |  1 -
 examples/dalf3/dalf3.cxx                      |  2 +-
 .../elm-pb-outerloop/elm_pb_outerloop.cxx     | 39 ++++++++-----------
 examples/elm-pb/elm_pb.cxx                    | 19 +++------
 examples/laplacexy/alfven-wave/alfven.cxx     |  7 ++--
 examples/laplacexy/laplace_perp/test.cxx      |  4 +-
 examples/laplacexy/simple-hypre/.gitignore    |  1 -
 .../laplacexy/simple-hypre/CMakeLists.txt     | 15 -------
 examples/laplacexy/simple-hypre/data/BOUT.inp | 37 ------------------
 .../simple-hypre/test-laplacexy-hypre.cxx     | 30 --------------
 examples/laplacexy/simple/CMakeLists.txt      |  5 ++-
 examples/laplacexy/simple/README.md           |  7 +++-
 examples/laplacexy/simple/hypre/BOUT.inp      | 23 +++++++++++
 examples/laplacexy/simple/test-laplacexy.cxx  |  8 ++--
 14 files changed, 65 insertions(+), 133 deletions(-)
 delete mode 100644 examples/laplacexy/simple-hypre/.gitignore
 delete mode 100644 examples/laplacexy/simple-hypre/CMakeLists.txt
 delete mode 100644 examples/laplacexy/simple-hypre/data/BOUT.inp
 delete mode 100644 examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx
 create mode 100644 examples/laplacexy/simple/hypre/BOUT.inp

diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index 849f10e85f..f2444e6bf6 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -30,7 +30,6 @@ add_subdirectory(invertable_operator)
 add_subdirectory(laplacexy/alfven-wave)
 add_subdirectory(laplacexy/laplace_perp)
 add_subdirectory(laplacexy/simple)
-add_subdirectory(laplacexy/simple-hypre)
 add_subdirectory(monitor-newapi)
 add_subdirectory(orszag-tang)
 add_subdirectory(preconditioning/wave)
diff --git a/examples/dalf3/dalf3.cxx b/examples/dalf3/dalf3.cxx
index 493e8f5e45..46a9a4286d 100644
--- a/examples/dalf3/dalf3.cxx
+++ b/examples/dalf3/dalf3.cxx
@@ -300,7 +300,7 @@ class DALF3 : public PhysicsModel {
     // LaplaceXY for n=0 solve
     if (split_n0) {
       // Create an XY solver for n=0 component
-      laplacexy = std::make_unique<LaplaceXY>(mesh);
+      laplacexy = LaplaceXY::create(mesh);
       phi2D = 0.0; // Starting guess
     }
 
diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index 8e84901806..e48a1020ca 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -28,33 +28,28 @@
 
 /*******************************************************************************/
 
+#include "bout/build_defines.hxx"
+#include "bout/options.hxx"
 #include <bout/bout.hxx>
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
+#include <bout/derivs.hxx>
+#include <bout/field_factory.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/invert_laplace.hxx>
+#include <bout/invert_laplace.hxx>
 #include <bout/invert_parderiv.hxx>
 #include <bout/msg_stack.hxx>
-#include <bout/sourcex.hxx>
-#include <bout/utils.hxx>
-
-#include <math.h>
-
-#include <bout/derivs.hxx>
-#include <bout/invert_laplace.hxx>
 #include <bout/physicsmodel.hxx>
+#include <bout/rajalib.hxx> // Defines BOUT_FOR_RAJA
 #include <bout/single_index_ops.hxx>
 #include <bout/smoothing.hxx>
+#include <bout/sourcex.hxx>
+#include <bout/utils.hxx>
 
-#include <bout/rajalib.hxx> // Defines BOUT_FOR_RAJA
-
-#if BOUT_HAS_HYPRE
-#include <bout/invert/laplacexy2_hypre.hxx>
-#endif
-
-#include <bout/field_factory.hxx>
+#include <math.h>
 
 CELL_LOC loc = CELL_CENTRE;
 
@@ -91,6 +86,10 @@ BOUT_OVERRIDE_DEFAULT_OPTION("phi:bndry_target", "neumann");
 BOUT_OVERRIDE_DEFAULT_OPTION("phi:bndry_xin", "none");
 BOUT_OVERRIDE_DEFAULT_OPTION("phi:bndry_xout", "none");
 
+#if BOUT_HAS_HYPRE
+BOUT_OVERRIDE_DEFAULT_OPTION("laplacexy:type", "hypre");
+#endif
+
 /// 3-field ELM simulation
 class ELMpb : public PhysicsModel {
 private:
@@ -242,11 +241,7 @@ class ELMpb : public PhysicsModel {
 
   bool split_n0; // Solve the n=0 component of potential
 
-#if BOUT_HAS_HYPRE
-  std::unique_ptr<LaplaceXY2Hypre> laplacexy{nullptr}; // Laplacian solver in X-Y (n=0)
-#else
   std::unique_ptr<LaplaceXY> laplacexy{nullptr}; // Laplacian solver in X-Y (n=0)
-#endif
 
   Field2D phi2D; // Axisymmetric phi
 
@@ -567,13 +562,11 @@ class ELMpb : public PhysicsModel {
     split_n0 = options["split_n0"]
                    .doc("Solve zonal (n=0) component of potential using LaplaceXY?")
                    .withDefault(false);
+
     if (split_n0) {
       // Create an XY solver for n=0 component
-#if BOUT_HAS_HYPRE
-      laplacexy = bout::utils::make_unique<LaplaceXY2Hypre>(mesh);
-#else
-      laplacexy = bout::utils::make_unique<LaplaceXY>(mesh);
-#endif
+      laplacexy = LaplaceXY::create(mesh);
+
       // Set coefficients for Boussinesq solve
       laplacexy->setCoefs(1.0, 0.0);
       phi2D = 0.0; // Starting guess
diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx
index d981796200..fe18a756ae 100644
--- a/examples/elm-pb/elm_pb.cxx
+++ b/examples/elm-pb/elm_pb.cxx
@@ -22,10 +22,6 @@
 
 #include <math.h>
 
-#if BOUT_HAS_HYPRE
-#include <bout/invert/laplacexy2_hypre.hxx>
-#endif
-
 #include <bout/field_factory.hxx>
 
 CELL_LOC loc = CELL_CENTRE;
@@ -36,6 +32,10 @@ BOUT_OVERRIDE_DEFAULT_OPTION("phi:bndry_target", "neumann");
 BOUT_OVERRIDE_DEFAULT_OPTION("phi:bndry_xin", "none");
 BOUT_OVERRIDE_DEFAULT_OPTION("phi:bndry_xout", "none");
 
+#if BOUT_HAS_HYPRE
+BOUT_OVERRIDE_DEFAULT_OPTION("laplacexy:type", "hypre");
+#endif
+
 /// 3-field ELM simulation
 class ELMpb : public PhysicsModel {
 private:
@@ -188,11 +188,7 @@ class ELMpb : public PhysicsModel {
 
   bool split_n0; // Solve the n=0 component of potential
 
-#if BOUT_HAS_HYPRE
-  std::unique_ptr<LaplaceXY2Hypre> laplacexy{nullptr}; // Laplacian solver in X-Y (n=0)
-#else
   std::unique_ptr<LaplaceXY> laplacexy{nullptr}; // Laplacian solver in X-Y (n=0)
-#endif
 
   Field2D phi2D; // Axisymmetric phi
 
@@ -525,11 +521,8 @@ class ELMpb : public PhysicsModel {
                    .withDefault(false);
     if (split_n0) {
       // Create an XY solver for n=0 component
-#if BOUT_HAS_HYPRE
-      laplacexy = bout::utils::make_unique<LaplaceXY2Hypre>(mesh);
-#else
-      laplacexy = bout::utils::make_unique<LaplaceXY>(mesh);
-#endif
+      laplacexy = LaplaceXY::create(mesh);
+
       // Set coefficients for Boussinesq solve
       laplacexy->setCoefs(1.0, 0.0);
       phi2D = 0.0; // Starting guess
diff --git a/examples/laplacexy/alfven-wave/alfven.cxx b/examples/laplacexy/alfven-wave/alfven.cxx
index a4248afcf7..031931c1c4 100644
--- a/examples/laplacexy/alfven-wave/alfven.cxx
+++ b/examples/laplacexy/alfven-wave/alfven.cxx
@@ -1,10 +1,11 @@
-
 #include <bout/field_factory.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/invert/laplacexz.hxx>
 #include <bout/invert_laplace.hxx>
 #include <bout/physicsmodel.hxx>
 
+#include <memory>
+
 /// Fundamental constants
 const BoutReal PI = 3.14159265;
 const BoutReal e0 = 8.854e-12;      // Permittivity of free space
@@ -32,7 +33,7 @@ class Alfven : public PhysicsModel {
 
   bool laplace_perp;    // Use Laplace_perp or Delp2?
   bool split_n0;        // Split solve into n=0 and n~=0?
-  LaplaceXY* laplacexy; // Laplacian solver in X-Y (n=0)
+  std::unique_ptr<LaplaceXY> laplacexy{nullptr}; // Laplacian solver in X-Y (n=0)
 
   bool newXZsolver;
   std::unique_ptr<Laplacian> phiSolver;          // Old Laplacian in X-Z
@@ -80,7 +81,7 @@ class Alfven : public PhysicsModel {
 
     if (split_n0) {
       // Create an XY solver for n=0 component
-      laplacexy = new LaplaceXY(mesh);
+      laplacexy = LaplaceXY::create(mesh);
       phi2D = 0.0; // Starting guess
     }
 
diff --git a/examples/laplacexy/laplace_perp/test.cxx b/examples/laplacexy/laplace_perp/test.cxx
index 75577bb8b7..e3d9528d45 100644
--- a/examples/laplacexy/laplace_perp/test.cxx
+++ b/examples/laplacexy/laplace_perp/test.cxx
@@ -56,10 +56,10 @@ int main(int argc, char** argv) {
       FieldFactory::get()->create2D("input_field", Options::getRoot(), mesh);
 
   // Create a LaplaceXY solver
-  LaplaceXY laplacexy{mesh};
+  auto laplacexy = LaplaceXY::create(mesh);
 
   // Solve, using 0.0 as starting guess
-  Field2D solved = laplacexy.solve(input, 0.0);
+  Field2D solved = laplacexy->solve(input, 0.0);
 
   // Need to communicate guard cells
   mesh->communicate(solved);
diff --git a/examples/laplacexy/simple-hypre/.gitignore b/examples/laplacexy/simple-hypre/.gitignore
deleted file mode 100644
index eeede075f9..0000000000
--- a/examples/laplacexy/simple-hypre/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-test-laplacexy
diff --git a/examples/laplacexy/simple-hypre/CMakeLists.txt b/examples/laplacexy/simple-hypre/CMakeLists.txt
deleted file mode 100644
index 788ebb1776..0000000000
--- a/examples/laplacexy/simple-hypre/CMakeLists.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-cmake_minimum_required(VERSION 3.13)
-
-project(test_laplacexy_hypre LANGUAGES CXX C)
-
-if (NOT TARGET bout++::bout++)
-  find_package(bout++ REQUIRED)
-endif()
-
-bout_add_example(test_laplacexy_hypre
-  SOURCES test-laplacexy-hypre.cxx
-  REQUIRES BOUT_HAS_HYPRE)
-
-if(BOUT_HAS_CUDA)
-  set_source_files_properties(test-laplacexy-hypre.cxx PROPERTIES LANGUAGE CUDA )
-endif()
diff --git a/examples/laplacexy/simple-hypre/data/BOUT.inp b/examples/laplacexy/simple-hypre/data/BOUT.inp
deleted file mode 100644
index 5da492168d..0000000000
--- a/examples/laplacexy/simple-hypre/data/BOUT.inp
+++ /dev/null
@@ -1,37 +0,0 @@
-#
-# Simple test of the LaplaceXY solver.
-#
-# Inverts a given function (rhs), writing "rhs" and solution "x" to file
-#
-
-[mesh]
-
-# Mesh sizes
-nx = 20
-ny = 32
-nz = 1
-
-# mesh spacing
-dx = 1.0
-dy = 1.0
-dz = 1.0
-
-[laplacexy]
-
-ksptype = gmres   # Iterative solver type  - not used with Hypre interface
-pctype = jacobi  # Preconditioner. "jacobi", "bjacobi" and "sor" usually good
-# On one processor"lu" uses direct solver
-
-atol = 1e-12		# type: BoutReal, doc: Relative tolerance for Hypre solver
-core_bndry_dirichlet = false		# type: bool
-hypre_print_level = 3		# type: int, doc: Verbosity for Hypre solver. Integer from 0 (silent) to 4 (most verbose).
-#hypre_solver_type = gmres		# type: HYPRE_SOLVER_TYPE, doc: Type of solver to use when solving Hypre system. Possible values are: gmres, bicgstab
-hypre_solver_type = bicgstab		# type: HYPRE_SOLVER_TYPE, doc: Type of solver to use when solving Hypre system. Possible values are: gmres, bicgstab
-include_y_derivs = true		# type: bool, doc: Include Y derivatives in operator to invert?
-maxits = 2000	# type: int, doc: Maximum iterations for Hypre solver
-print_timing = true		# type: bool, doc: Print extra timing information for LaplaceXY2Hypre
-rtol = 1e-07		# type: BoutReal, doc: Relative tolerance for Hypre solver
-y_bndry_dirichlet = false		# type: bool
-
-# Function to be inverted
-rhs = sin(2*pi*x)*sin(y)
diff --git a/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx b/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx
deleted file mode 100644
index af2367e1a0..0000000000
--- a/examples/laplacexy/simple-hypre/test-laplacexy-hypre.cxx
+++ /dev/null
@@ -1,30 +0,0 @@
-#include <bout/bout.hxx>
-#include <bout/field_factory.hxx>
-#include <bout/invert/laplacexy2_hypre.hxx>
-
-int main(int argc, char** argv) {
-  BoutInitialise(argc, argv);
-  {
-    /// Create a LaplaceXY object
-    LaplaceXY2Hypre laplacexy(bout::globals::mesh);
-
-    /// Generate rhs function
-    Field2D rhs = FieldFactory::get()->create2D("laplacexy:rhs", Options::getRoot(),
-                                                bout::globals::mesh);
-
-    /// Solution
-    Field2D solution = 0.0;
-
-    solution = laplacexy.solve(rhs, solution);
-
-    Options dump;
-    dump["rhs"] = rhs;
-    dump["x"] = solution;
-    bout::writeDefaultOutputFile(dump);
-  }
-  BoutFinalise();
-#if BOUT_HAS_CUDA
-  cudaDeviceReset();
-#endif
-  return 0;
-}
diff --git a/examples/laplacexy/simple/CMakeLists.txt b/examples/laplacexy/simple/CMakeLists.txt
index ec5e7d2492..7859a08259 100644
--- a/examples/laplacexy/simple/CMakeLists.txt
+++ b/examples/laplacexy/simple/CMakeLists.txt
@@ -6,4 +6,7 @@ if (NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(laplacexy-simple SOURCES test-laplacexy.cxx)
+bout_add_example(laplacexy-simple
+  SOURCES test-laplacexy.cxx
+  DATA_DIRS data hypre
+)
diff --git a/examples/laplacexy/simple/README.md b/examples/laplacexy/simple/README.md
index ce7cbebf00..491d00d4b3 100644
--- a/examples/laplacexy/simple/README.md
+++ b/examples/laplacexy/simple/README.md
@@ -8,7 +8,7 @@ and preconditioners. See the "ksptype" and "pctype" settings in BOUT.inp
 
 Run with
 
-    $ ./test-laplacexy -ksp_monitor
+    $ ./test-laplacexy -laplacexy:petsc:ksp_monitor
 
 which should print the KSP norms from PETSc:
 
@@ -31,3 +31,8 @@ which should print the KSP norms from PETSc:
     16 KSP Residual norm 4.309526296050e-01
     17 KSP Residual norm 1.115269396077e-01
     18 KSP Residual norm 4.334487475743e-13
+
+HYPRE
+-----
+
+Use the `hypre` directory to use the HYPRE preconditioner instead of PETSc.
diff --git a/examples/laplacexy/simple/hypre/BOUT.inp b/examples/laplacexy/simple/hypre/BOUT.inp
new file mode 100644
index 0000000000..338e902d4e
--- /dev/null
+++ b/examples/laplacexy/simple/hypre/BOUT.inp
@@ -0,0 +1,23 @@
+#
+# Simple test of the LaplaceXY solver using HYPRE
+#
+# Inverts a given function (rhs), writing "rhs" and solution "x" to file
+#
+
+[mesh]
+
+# Mesh sizes
+nx = 20
+ny = 32
+nz = 1
+
+# mesh spacing
+dx = 1.0
+dy = 1.0
+dz = 1.0
+
+[laplacexy]
+type = hypre
+
+# Function to be inverted
+rhs = sin(2*pi*x)*sin(y)
diff --git a/examples/laplacexy/simple/test-laplacexy.cxx b/examples/laplacexy/simple/test-laplacexy.cxx
index c033eb68e3..49a93aafdb 100644
--- a/examples/laplacexy/simple/test-laplacexy.cxx
+++ b/examples/laplacexy/simple/test-laplacexy.cxx
@@ -7,20 +7,18 @@ int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
   /// Create a LaplaceXY object
-  LaplaceXY laplacexy(bout::globals::mesh);
+  auto laplacexy = LaplaceXY::create(bout::globals::mesh);
 
   /// Generate rhs function
   Field2D rhs = FieldFactory::get()->create2D("laplacexy:rhs", Options::getRoot(),
                                               bout::globals::mesh);
 
   /// Solution
-  Field2D x = 0.0;
-
-  x = laplacexy.solve(rhs, x);
+  Field2D result = laplacexy->solve(rhs, 0.0);
 
   Options dump;
   dump["rhs"] = rhs;
-  dump["x"] = x;
+  dump["result"] = result;
   bout::writeDefaultOutputFile(dump);
 
   BoutFinalise();

From fbe8a7f909a2c33578e1b84520be66688d148d48 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 24 Oct 2025 18:07:06 +0100
Subject: [PATCH 0294/1827] Add `has_hypre` to python `boutconfig`

---
 tools/pylib/boutconfig/__init__.py.cin | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/pylib/boutconfig/__init__.py.cin b/tools/pylib/boutconfig/__init__.py.cin
index d031d599b5..b65b25a75a 100644
--- a/tools/pylib/boutconfig/__init__.py.cin
+++ b/tools/pylib/boutconfig/__init__.py.cin
@@ -31,6 +31,7 @@ config = {
     "has_fftw": "@BOUT_HAS_FFTW@",
     "petsc_has_sundials": "@PETSC_HAS_SUNDIALS@",
     "metric_type": "@BOUT_METRIC_TYPE@",
+    "has_hypre": "@BOUT_HAS_HYPRE@",
 }
 
 for k, v in config.items():

From d1ae6b74e791e092ad27328a7e029103d579b793 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Fri, 24 Oct 2025 17:12:46 +0000
Subject: [PATCH 0295/1827] Apply clang-format changes

---
 examples/elm-pb-outerloop/elm_pb_outerloop.cxx            | 2 --
 src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx      | 2 +-
 tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx | 6 +++---
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index e48a1020ca..4ff8e90dcb 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -33,13 +33,11 @@
 #include <bout/bout.hxx>
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
-#include <bout/derivs.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/invert_laplace.hxx>
-#include <bout/invert_laplace.hxx>
 #include <bout/invert_parderiv.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/physicsmodel.hxx>
diff --git a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
index 3d7f707678..a116d78475 100644
--- a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
+++ b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
@@ -14,8 +14,8 @@
 #include "bout/globals.hxx"
 #include "bout/options.hxx"
 #include "bout/petsclib.hxx"
-#include "bout/sys/range.hxx"
 #include "bout/solver.hxx"
+#include "bout/sys/range.hxx"
 #include "bout/sys/timer.hxx"
 #include "bout/utils.hxx"
 
diff --git a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx
index cede14b1f8..e04de9c675 100644
--- a/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy2-hypre/test-laplacexy.cxx
@@ -23,15 +23,15 @@
  *
  **************************************************************************/
 
+#include <bout/bout.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/difops.hxx>
 #include <bout/field2d.hxx>
-#include <bout/options_io.hxx>
-#include <bout/output.hxx>
-#include <bout/bout.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/options.hxx>
+#include <bout/options_io.hxx>
+#include <bout/output.hxx>
 
 #include <cstdlib>
 

From b6c738c449f9ff32d853687c89169a995bc3a4a2 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 24 Oct 2025 10:25:31 -0700
Subject: [PATCH 0296/1827] Fixup: remove comments, avoid temp for inverse

---
 src/mesh/parallel/shiftedmetric.cxx | 36 +++++++++++++----------------
 1 file changed, 16 insertions(+), 20 deletions(-)

diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 1b92313117..8a71e082d6 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -227,7 +227,6 @@ void ShiftedMetric::shiftZ(const BoutReal* in, const dcomplex* phs, BoutReal* ou
   irfft(&cmplx[0], mesh.LocalNz, out); // Reverse FFT
 }
 
-/* NEW CODE */
 // Bit-reversal
 __device__ inline unsigned int bit_reverse(unsigned int x, unsigned int log2n) {
   unsigned int result = 0;
@@ -364,16 +363,15 @@ __global__ void fft_block_cooperative(const BoutReal** __restrict__ in,
   }
   __syncthreads();
 
-  // Bit-reverse for inverse
-  __shared__ double2 temp_fft[FFTS_PER_BLOCK][NZ];
-  for (int i = tid; i < NZ; i += threads_per_fft) {
+  // Bit-reverse with standard swap to avoid temp array
+  // This is tricky but saves memory
+  for (int i = tid; i < NZ / 2; i += threads_per_fft) {
     const unsigned int rev_i = bit_reverse(i, LOG2_NZ);
-    temp_fft[fft_id_in_block][rev_i] = shared_fft[fft_id_in_block][i];
-  }
-  __syncthreads();
-
-  for (int i = tid; i < NZ; i += threads_per_fft) {
-    shared_fft[fft_id_in_block][i] = temp_fft[fft_id_in_block][i];
+    if (i < rev_i) { // Only swap once per pair
+      double2 temp = shared_fft[fft_id_in_block][i];
+      shared_fft[fft_id_in_block][i] = shared_fft[fft_id_in_block][rev_i];
+      shared_fft[fft_id_in_block][rev_i] = temp;
+    }
   }
   __syncthreads();
 
@@ -427,18 +425,18 @@ static void shiftZ_block_fft(const int Nz, const BoutReal** in, BoutReal** out,
 
   if (Nz == 16) {
     constexpr int FFTS_PER_BLOCK = 16;
-    constexpr int THREADS_PER_FFT = 16; // Use 64 threads per FFT
+    constexpr int THREADS_PER_FFT = 16;
 
-    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 16 x 16 = 256 threads
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK);
     dim3 grid((total_ffts + FFTS_PER_BLOCK - 1) / FFTS_PER_BLOCK);
 
     fft_block_cooperative<16, FFTS_PER_BLOCK>
         <<<grid, block, 0, stream>>>(in, out, phs, nbatches, nblocks);
   } else if (Nz == 64) {
     constexpr int FFTS_PER_BLOCK = 4;
-    constexpr int THREADS_PER_FFT = 64; // Use 64 threads per FFT
+    constexpr int THREADS_PER_FFT = 64;
 
-    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 64 x 4 = 256 threads
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK);
     dim3 grid((total_ffts + FFTS_PER_BLOCK - 1) / FFTS_PER_BLOCK);
 
     fft_block_cooperative<64, FFTS_PER_BLOCK>
@@ -448,7 +446,7 @@ static void shiftZ_block_fft(const int Nz, const BoutReal** in, BoutReal** out,
     constexpr int FFTS_PER_BLOCK = 2;
     constexpr int THREADS_PER_FFT = 128;
 
-    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 128 x 2 = 256 threads
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK);
     dim3 grid((total_ffts + FFTS_PER_BLOCK - 1) / FFTS_PER_BLOCK);
 
     fft_block_cooperative<128, FFTS_PER_BLOCK>
@@ -458,7 +456,7 @@ static void shiftZ_block_fft(const int Nz, const BoutReal** in, BoutReal** out,
     constexpr int FFTS_PER_BLOCK = 1;
     constexpr int THREADS_PER_FFT = 256;
 
-    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 256 x 1 = 256 threads
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK);
     dim3 grid(total_ffts);
 
     fft_block_cooperative<256, FFTS_PER_BLOCK>
@@ -466,9 +464,9 @@ static void shiftZ_block_fft(const int Nz, const BoutReal** in, BoutReal** out,
 
   } else if (Nz == 512) {
     constexpr int FFTS_PER_BLOCK = 1;
-    constexpr int THREADS_PER_FFT = 512; // 512 threads per FFT
+    constexpr int THREADS_PER_FFT = 512;
 
-    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK); // 512 x 1 = 512 threads
+    dim3 block(THREADS_PER_FFT, FFTS_PER_BLOCK);
     dim3 grid(total_ffts);
 
     fft_block_cooperative<512, FFTS_PER_BLOCK>
@@ -483,8 +481,6 @@ static void shiftZ_block_fft(const int Nz, const BoutReal** in, BoutReal** out,
   }
 }
 
-/* END NEWER CODE */
-
 void ShiftedMetric::calcParallelSlices(Field3D& f) {
   if (f.getDirectionY() == YDirectionType::Aligned) {
     // Cannot calculate parallel slices for field-aligned fields, so return without

From 11ebfcd4e9874c7b181f2406e37227dbf4038fd2 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 24 Oct 2025 10:43:12 -0700
Subject: [PATCH 0297/1827] Fixup: preprocessor guards, better variable naming

---
 src/mesh/parallel/shiftedmetric.cxx | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 8a71e082d6..c05550e348 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -227,6 +227,7 @@ void ShiftedMetric::shiftZ(const BoutReal* in, const dcomplex* phs, BoutReal* ou
   irfft(&cmplx[0], mesh.LocalNz, out); // Reverse FFT
 }
 
+#if BOUT_HAS_CUDA
 // Bit-reversal
 __device__ inline unsigned int bit_reverse(unsigned int x, unsigned int log2n) {
   unsigned int result = 0;
@@ -244,7 +245,7 @@ template <int NZ, int FFTS_PER_BLOCK = 4>
 __global__ void fft_block_cooperative(const BoutReal** __restrict__ in,
                                       BoutReal** __restrict__ out,
                                       const double2** __restrict__ blocks_phs,
-                                      const int batches, const int nblocks) {
+                                      const int nbatches, const int nblocks) {
 
   constexpr int LOG2_NZ = __builtin_ctz(NZ);
   constexpr double INV_NZ = 1.0 / (double)NZ;
@@ -276,11 +277,11 @@ __global__ void fft_block_cooperative(const BoutReal** __restrict__ in,
       threadIdx.y; // Which FFT this thread works on (0 to FFTS_PER_BLOCK-1)
   const int global_fft_id = blockIdx.x * FFTS_PER_BLOCK + fft_id_in_block;
 
-  if (global_fft_id >= nblocks * batches)
+  if (global_fft_id >= nblocks * nbatches)
     return;
 
-  const int block = global_fft_id / batches;
-  const int batch = global_fft_id % batches;
+  const int block = global_fft_id / nbatches;
+  const int batch = global_fft_id % nbatches;
 
   const double* __restrict__ in_line = in[block] + batch * NZ;
   double* __restrict__ out_line = out[block] + batch * NZ;
@@ -480,6 +481,7 @@ static void shiftZ_block_fft(const int Nz, const BoutReal** in, BoutReal** out,
     throw std::runtime_error(std::string("Block FFT failed: ") + cudaGetErrorString(err));
   }
 }
+#endif
 
 void ShiftedMetric::calcParallelSlices(Field3D& f) {
   if (f.getDirectionY() == YDirectionType::Aligned) {
@@ -490,8 +492,8 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
 
   f.splitParallelSlices();
 
+#if BOUT_HAS_CUDA
   auto& region = mesh.getRegion2D("RGN_NOY");
-
   static size_t nblocks = region.getBlocks().size();
   if (nblocks != region.getBlocks().size()) {
     throw BoutException("Number of blocks changed in ShiftedMetric::calcParallelSlices");
@@ -499,6 +501,7 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
   static Array<const BoutReal*> blocks_in(nblocks);
   static Array<BoutReal*> blocks_out(nblocks);
   static Array<const double2*> phs_in(nblocks);
+#endif
 
   for (const auto& phase : parallel_slice_phases) {
     auto& f_slice = f.ynext(phase.y_offset);

From cf5a88291036bc20a5922a5fb1563dc8221623f5 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 24 Oct 2025 11:15:49 -0700
Subject: [PATCH 0298/1827] Fixup: saner split with BOUT_HAS_CUDA

---
 src/mesh/parallel/shiftedmetric.cxx | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index c05550e348..981034c1ee 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -501,13 +501,11 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
   static Array<const BoutReal*> blocks_in(nblocks);
   static Array<BoutReal*> blocks_out(nblocks);
   static Array<const double2*> phs_in(nblocks);
-#endif
 
   for (const auto& phase : parallel_slice_phases) {
     auto& f_slice = f.ynext(phase.y_offset);
     f_slice.allocate();
 
-#if BOUT_HAS_CUDA
     static struct StreamRAII {
       cudaStream_t stream = 0;
       StreamRAII() {
@@ -550,7 +548,12 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
                      nbatches, stream.get());
 
     stream.synchronize();
+  }
 #else
+  for (const auto& phase : parallel_slice_phases) {
+    auto& f_slice = f.ynext(phase.y_offset);
+    f_slice.allocate();
+
     BOUT_FOR(i, mesh.getRegion2D("RGN_NOY")) {
       const int ix = i.x();
       const int iy = i.y();
@@ -558,8 +561,8 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
       shiftZ(&(f(ix, iy_offset, 0)), &(phase.phase_shift(ix, iy, 0)),
              &(f_slice(ix, iy_offset, 0)));
     }
-#endif
   }
+#endif
 }
 
 std::vector<Field3D>

From 9f42dcbf7ffadecde2ab51c1dc308549910d1b61 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Fri, 24 Oct 2025 18:28:25 -0700
Subject: [PATCH 0299/1827] Fixup: remove redundant conditional

---
 src/mesh/parallel/shiftedmetric.cxx | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 981034c1ee..45f2988561 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -346,14 +346,12 @@ __global__ void fft_block_cooperative(const BoutReal** __restrict__ in,
   }
 
   for (int k = tid + NMODES; k < NZ; k += threads_per_fft) {
-    if (k >= NMODES) {
-      const int kk = NZ - k;
-      const double2 tmp = phs[batch * NMODES + kk];
-      const double real = shared_fft[fft_id_in_block][k].x;
-      const double imag = shared_fft[fft_id_in_block][k].y;
-      shared_fft[fft_id_in_block][k].x = real * tmp.x + imag * tmp.y;
-      shared_fft[fft_id_in_block][k].y = -real * tmp.y + imag * tmp.x;
-    }
+    const int kk = NZ - k;
+    const double2 tmp = phs[batch * NMODES + kk];
+    const double real = shared_fft[fft_id_in_block][k].x;
+    const double imag = shared_fft[fft_id_in_block][k].y;
+    shared_fft[fft_id_in_block][k].x = real * tmp.x + imag * tmp.y;
+    shared_fft[fft_id_in_block][k].y = -real * tmp.y + imag * tmp.x;
   }
   __syncthreads();
 

From bde263a93b5994dc07bb128c72a9feccd3f4ebf5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Oct 2025 11:39:22 +0100
Subject: [PATCH 0300/1827] CI: Fedora container is already fully setup

---
 .ci_fedora.sh               | 27 +++------------------------
 .github/workflows/tests.yml |  2 +-
 2 files changed, 4 insertions(+), 25 deletions(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 5f0a36efea..e1dc563c6c 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -21,11 +21,10 @@ then
 	cmd="sudo docker"
     fi
     test . != ".$2" && mpi="$2" || mpi=openmpi
-    test . != ".$3" && version="$3" || version=rawhide
-    time $cmd pull registry.fedoraproject.org/fedora:$version
+    time $cmd pull ghcr.io/dschwoerer/bout-container-base:ci-fedora
     time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
 	 --shm-size 256M \
-         --name mobydick registry.fedoraproject.org/fedora:$version \
+         --name mobydick ghcr.io/dschwoerer/bout-container-base:ci-fedora \
 	     /tmp/BOUT-dev/.ci_fedora.sh $mpi
     time $cmd cp ${TRAVIS_BUILD_DIR:-$(pwd)} mobydick:/tmp/BOUT-dev
     time $cmd start -a mobydick
@@ -34,27 +33,8 @@ fi
 
 test . != ".$1" && mpi="$1" || mpi=openmpi
 
-## If we are called as root, setup everything
-if [ $UID -eq 0 ]
-then
-    cat /etc/os-release
-    # Ignore weak depencies
-    echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
-    echo "minrate=10M" >> /etc/dnf/dnf.conf
-    export FORCE_COLUMNS=200
-    time dnf -y install dnf5
-    time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort python3-boututils
-    # Allow to override packages - see #2073
-    time dnf5 copr enable -y davidsch/fixes4bout || :
-    time dnf5 -y upgrade
-    time dnf5 -y builddep bout++
-    useradd test
-    cp -a /tmp/BOUT-dev /home/test/
-    chown -R test /home/test
-    chmod u+rwX /home/test -R
-    su - test -c "${0/\/tmp/\/home\/test} $mpi"
 ## If we are called as normal user, run test
-else
+    cp -a /tmp/BOUT-dev /home/test/
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
     export OMPI_MCA_rmaps_base_oversubscribe=yes
@@ -76,4 +56,3 @@ else
 
     time make -C build build-check -j 2
     time make -C build check
-fi
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 049a03664d..314ee196ae 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -209,7 +209,7 @@ jobs:
         with:
           submodules: true
       - name: Build Fedora
-        run: ./.ci_fedora.sh setup openmpi latest
+        run: ./.ci_fedora.sh setup openmpi
         shell: bash
         env:
           TRAVIS_BUILD_DIR: ${{ github.workspace }}

From 9d63267793d31a12677d34f5d9384801734a17c6 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 31 Oct 2025 23:48:34 -0700
Subject: [PATCH 0301/1827] snes: Add max_snes_failures option

Abort if too many consecutive failures. Prevents getting stuck
in an infinite loop.
---
 src/solver/impls/snes/snes.cxx | 32 ++++++++++++++++++++++++--------
 src/solver/impls/snes/snes.hxx |  2 ++
 2 files changed, 26 insertions(+), 8 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 6a06bf21f5..b8bf8c3e58 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -508,6 +508,9 @@ SNESSolver::SNESSolver(Options* opts)
       upper_its((*options)["upper_its"]
                     .doc("Iterations above which the next timestep is reduced")
                     .withDefault(static_cast<int>(maxits * 0.8))),
+      max_snes_failures((*options)["max_snes_failures"]
+                            .doc("Abort after this number of consecutive failures")
+                            .withDefault(10)),
       timestep_factor_on_failure((*options)["timestep_factor_on_failure"]
                                      .doc("Multiply timestep on convergence failure")
                                      .withDefault(0.5)),
@@ -990,7 +993,10 @@ int SNESSolver::run() {
 
         recent_failure_rate += inv_failure_window;
 
-        if (diagnose_failures) {
+        ++snes_failures;
+        steps_since_snes_failure = 0;
+
+        if (diagnose_failures or (snes_failures == max_snes_failures)) {
           // Print diagnostics to help identify source of the problem
 
           output.write("\n======== SNES failed =========\n");
@@ -1009,15 +1015,25 @@ int SNESSolver::run() {
           }
         }
 
-        ++snes_failures;
-        steps_since_snes_failure = 0;
+        if (snes_failures == max_snes_failures) {
+          output.write("Too many SNES failures ({}). Aborting.");
+          return 1;
+        }
 
         if (equation_form == BoutSnesEquationForm::pseudo_transient) {
-          // Global scaling of timesteps
-          // Note: A better strategy might be to reduce timesteps
-          //       in problematic cells.
-          PetscCall(VecScale(dt_vec, timestep_factor_on_failure));
-
+          if (snes_failures == max_snes_failures - 1) {
+            // Last chance. Set to uniform smallest timestep
+            PetscCall(VecSet(dt_vec, dt_min_reset));
+
+          } else if (snes_failures == 5) {
+            // Set uniform timestep
+            PetscCall(VecSet(dt_vec, timestep));
+          } else {
+            // Global scaling of timesteps
+            // Note: A better strategy might be to reduce timesteps
+            //       in problematic cells.
+            PetscCall(VecScale(dt_vec, timestep_factor_on_failure));
+          }
         } else {
           // Try a smaller timestep
           timestep *= timestep_factor_on_failure;
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 7039954418..5d007f8ad7 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -129,6 +129,8 @@ private:
   int maxits;               ///< Maximum nonlinear iterations
   int lower_its, upper_its; ///< Limits on iterations for timestep adjustment
 
+  int max_snes_failures; ///< Maximum number of consecutive SNES failures before abort.
+
   BoutReal timestep_factor_on_failure;
   BoutReal timestep_factor_on_upper_its;
   BoutReal timestep_factor_on_lower_its;

From 2699cafcfdcf2ee546fca1891086e96022a5f206 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 3 Nov 2025 10:26:59 +0000
Subject: [PATCH 0302/1827] Delete v5 header shims

---
 include/boundary_factory.hxx         | 4 ----
 include/boundary_op.hxx              | 4 ----
 include/boundary_region.hxx          | 4 ----
 include/boundary_standard.hxx        | 4 ----
 include/bout.hxx                     | 4 ----
 include/bout_types.hxx               | 4 ----
 include/boutcomm.hxx                 | 4 ----
 include/boutexception.hxx            | 4 ----
 include/cyclic_reduction.hxx         | 4 ----
 include/dcomplex.hxx                 | 4 ----
 include/derivs.hxx                   | 4 ----
 include/difops.hxx                   | 4 ----
 include/fft.hxx                      | 4 ----
 include/field.hxx                    | 4 ----
 include/field2d.hxx                  | 4 ----
 include/field3d.hxx                  | 4 ----
 include/field_data.hxx               | 4 ----
 include/field_factory.hxx            | 4 ----
 include/fieldperp.hxx                | 4 ----
 include/globals.hxx                  | 4 ----
 include/gyro_average.hxx             | 4 ----
 include/initialprofiles.hxx          | 4 ----
 include/interpolation.hxx            | 4 ----
 include/interpolation_xz.hxx         | 4 ----
 include/interpolation_z.hxx          | 4 ----
 include/invert_laplace.hxx           | 4 ----
 include/invert_parderiv.hxx          | 4 ----
 include/lapack_routines.hxx          | 4 ----
 include/mask.hxx                     | 4 ----
 include/msg_stack.hxx                | 4 ----
 include/multiostream.hxx             | 4 ----
 include/options.hxx                  | 4 ----
 include/optionsreader.hxx            | 4 ----
 include/output.hxx                   | 4 ----
 include/parallel_boundary_op.hxx     | 4 ----
 include/parallel_boundary_region.hxx | 4 ----
 include/smoothing.hxx                | 4 ----
 include/sourcex.hxx                  | 4 ----
 include/stencils.hxx                 | 4 ----
 include/unused.hxx                   | 4 ----
 include/utils.hxx                    | 4 ----
 include/vecops.hxx                   | 4 ----
 include/vector2d.hxx                 | 4 ----
 include/vector3d.hxx                 | 4 ----
 include/where.hxx                    | 4 ----
 45 files changed, 180 deletions(-)
 delete mode 100644 include/boundary_factory.hxx
 delete mode 100644 include/boundary_op.hxx
 delete mode 100644 include/boundary_region.hxx
 delete mode 100644 include/boundary_standard.hxx
 delete mode 100644 include/bout.hxx
 delete mode 100644 include/bout_types.hxx
 delete mode 100644 include/boutcomm.hxx
 delete mode 100644 include/boutexception.hxx
 delete mode 100644 include/cyclic_reduction.hxx
 delete mode 100644 include/dcomplex.hxx
 delete mode 100644 include/derivs.hxx
 delete mode 100644 include/difops.hxx
 delete mode 100644 include/fft.hxx
 delete mode 100644 include/field.hxx
 delete mode 100644 include/field2d.hxx
 delete mode 100644 include/field3d.hxx
 delete mode 100644 include/field_data.hxx
 delete mode 100644 include/field_factory.hxx
 delete mode 100644 include/fieldperp.hxx
 delete mode 100644 include/globals.hxx
 delete mode 100644 include/gyro_average.hxx
 delete mode 100644 include/initialprofiles.hxx
 delete mode 100644 include/interpolation.hxx
 delete mode 100644 include/interpolation_xz.hxx
 delete mode 100644 include/interpolation_z.hxx
 delete mode 100644 include/invert_laplace.hxx
 delete mode 100644 include/invert_parderiv.hxx
 delete mode 100644 include/lapack_routines.hxx
 delete mode 100644 include/mask.hxx
 delete mode 100644 include/msg_stack.hxx
 delete mode 100644 include/multiostream.hxx
 delete mode 100644 include/options.hxx
 delete mode 100644 include/optionsreader.hxx
 delete mode 100644 include/output.hxx
 delete mode 100644 include/parallel_boundary_op.hxx
 delete mode 100644 include/parallel_boundary_region.hxx
 delete mode 100644 include/smoothing.hxx
 delete mode 100644 include/sourcex.hxx
 delete mode 100644 include/stencils.hxx
 delete mode 100644 include/unused.hxx
 delete mode 100644 include/utils.hxx
 delete mode 100644 include/vecops.hxx
 delete mode 100644 include/vector2d.hxx
 delete mode 100644 include/vector3d.hxx
 delete mode 100644 include/where.hxx

diff --git a/include/boundary_factory.hxx b/include/boundary_factory.hxx
deleted file mode 100644
index abbead8fc4..0000000000
--- a/include/boundary_factory.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boundary_factory.hxx" has moved to "bout/boundary_factory.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boundary_factory.hxx"
diff --git a/include/boundary_op.hxx b/include/boundary_op.hxx
deleted file mode 100644
index c96310f2d4..0000000000
--- a/include/boundary_op.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boundary_op.hxx" has moved to "bout/boundary_op.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boundary_op.hxx"
diff --git a/include/boundary_region.hxx b/include/boundary_region.hxx
deleted file mode 100644
index f487e88aeb..0000000000
--- a/include/boundary_region.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boundary_region.hxx" has moved to "bout/boundary_region.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boundary_region.hxx"
diff --git a/include/boundary_standard.hxx b/include/boundary_standard.hxx
deleted file mode 100644
index b7f17cf363..0000000000
--- a/include/boundary_standard.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boundary_standard.hxx" has moved to "bout/boundary_standard.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boundary_standard.hxx"
diff --git a/include/bout.hxx b/include/bout.hxx
deleted file mode 100644
index 926f035d2f..0000000000
--- a/include/bout.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "bout.hxx" has moved to "bout/bout.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/bout.hxx"
diff --git a/include/bout_types.hxx b/include/bout_types.hxx
deleted file mode 100644
index e6048eb885..0000000000
--- a/include/bout_types.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "bout_types.hxx" has moved to "bout/bout_types.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/bout_types.hxx"
diff --git a/include/boutcomm.hxx b/include/boutcomm.hxx
deleted file mode 100644
index 256df49c4f..0000000000
--- a/include/boutcomm.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boutcomm.hxx" has moved to "bout/boutcomm.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boutcomm.hxx"
diff --git a/include/boutexception.hxx b/include/boutexception.hxx
deleted file mode 100644
index 9189babfb3..0000000000
--- a/include/boutexception.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boutexception.hxx" has moved to "bout/boutexception.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boutexception.hxx"
diff --git a/include/cyclic_reduction.hxx b/include/cyclic_reduction.hxx
deleted file mode 100644
index 3ff098b062..0000000000
--- a/include/cyclic_reduction.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "cyclic_reduction.hxx" has moved to "bout/cyclic_reduction.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/cyclic_reduction.hxx"
diff --git a/include/dcomplex.hxx b/include/dcomplex.hxx
deleted file mode 100644
index a91c5485bf..0000000000
--- a/include/dcomplex.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "dcomplex.hxx" has moved to "bout/dcomplex.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/dcomplex.hxx"
diff --git a/include/derivs.hxx b/include/derivs.hxx
deleted file mode 100644
index d0a6eb5831..0000000000
--- a/include/derivs.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "derivs.hxx" has moved to "bout/derivs.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/derivs.hxx"
diff --git a/include/difops.hxx b/include/difops.hxx
deleted file mode 100644
index a61d9712a9..0000000000
--- a/include/difops.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "difops.hxx" has moved to "bout/difops.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/difops.hxx"
diff --git a/include/fft.hxx b/include/fft.hxx
deleted file mode 100644
index d67b257388..0000000000
--- a/include/fft.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "fft.hxx" has moved to "bout/fft.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/fft.hxx"
diff --git a/include/field.hxx b/include/field.hxx
deleted file mode 100644
index a2fcb2464e..0000000000
--- a/include/field.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field.hxx" has moved to "bout/field.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field.hxx"
diff --git a/include/field2d.hxx b/include/field2d.hxx
deleted file mode 100644
index 3b148b3a50..0000000000
--- a/include/field2d.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field2d.hxx" has moved to "bout/field2d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field2d.hxx"
diff --git a/include/field3d.hxx b/include/field3d.hxx
deleted file mode 100644
index 300cec057b..0000000000
--- a/include/field3d.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field3d.hxx" has moved to "bout/field3d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field3d.hxx"
diff --git a/include/field_data.hxx b/include/field_data.hxx
deleted file mode 100644
index 90f5c96c40..0000000000
--- a/include/field_data.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field_data.hxx" has moved to "bout/field_data.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field_data.hxx"
diff --git a/include/field_factory.hxx b/include/field_factory.hxx
deleted file mode 100644
index c6302ee298..0000000000
--- a/include/field_factory.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field_factory.hxx" has moved to "bout/field_factory.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field_factory.hxx"
diff --git a/include/fieldperp.hxx b/include/fieldperp.hxx
deleted file mode 100644
index 1994e53060..0000000000
--- a/include/fieldperp.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "fieldperp.hxx" has moved to "bout/fieldperp.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/fieldperp.hxx"
diff --git a/include/globals.hxx b/include/globals.hxx
deleted file mode 100644
index f07488c10c..0000000000
--- a/include/globals.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "globals.hxx" has moved to "bout/globals.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/globals.hxx"
diff --git a/include/gyro_average.hxx b/include/gyro_average.hxx
deleted file mode 100644
index c0d454eb50..0000000000
--- a/include/gyro_average.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "gyro_average.hxx" has moved to "bout/gyro_average.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/gyro_average.hxx"
diff --git a/include/initialprofiles.hxx b/include/initialprofiles.hxx
deleted file mode 100644
index 7bc1595261..0000000000
--- a/include/initialprofiles.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "initialprofiles.hxx" has moved to "bout/initialprofiles.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/initialprofiles.hxx"
diff --git a/include/interpolation.hxx b/include/interpolation.hxx
deleted file mode 100644
index 80ad60b4e4..0000000000
--- a/include/interpolation.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "interpolation.hxx" has moved to "bout/interpolation.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/interpolation.hxx"
diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx
deleted file mode 100644
index 8845e34b80..0000000000
--- a/include/interpolation_xz.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "interpolation_xz.hxx" has moved to "bout/interpolation_xz.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/interpolation_xz.hxx"
diff --git a/include/interpolation_z.hxx b/include/interpolation_z.hxx
deleted file mode 100644
index a88b486026..0000000000
--- a/include/interpolation_z.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "interpolation_z.hxx" has moved to "bout/interpolation_z.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/interpolation_z.hxx"
diff --git a/include/invert_laplace.hxx b/include/invert_laplace.hxx
deleted file mode 100644
index fbb04acaf1..0000000000
--- a/include/invert_laplace.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "invert_laplace.hxx" has moved to "bout/invert_laplace.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/invert_laplace.hxx"
diff --git a/include/invert_parderiv.hxx b/include/invert_parderiv.hxx
deleted file mode 100644
index 81a8ca4f49..0000000000
--- a/include/invert_parderiv.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "invert_parderiv.hxx" has moved to "bout/invert_parderiv.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/invert_parderiv.hxx"
diff --git a/include/lapack_routines.hxx b/include/lapack_routines.hxx
deleted file mode 100644
index 97fa2c6be9..0000000000
--- a/include/lapack_routines.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "lapack_routines.hxx" has moved to "bout/lapack_routines.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/lapack_routines.hxx"
diff --git a/include/mask.hxx b/include/mask.hxx
deleted file mode 100644
index cbeab65d85..0000000000
--- a/include/mask.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "mask.hxx" has moved to "bout/mask.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/mask.hxx"
diff --git a/include/msg_stack.hxx b/include/msg_stack.hxx
deleted file mode 100644
index 2503961748..0000000000
--- a/include/msg_stack.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "msg_stack.hxx" has moved to "bout/msg_stack.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/msg_stack.hxx"
diff --git a/include/multiostream.hxx b/include/multiostream.hxx
deleted file mode 100644
index 7e7101aad0..0000000000
--- a/include/multiostream.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "multiostream.hxx" has moved to "bout/multiostream.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/multiostream.hxx"
diff --git a/include/options.hxx b/include/options.hxx
deleted file mode 100644
index 4693422c13..0000000000
--- a/include/options.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "options.hxx" has moved to "bout/options.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/options.hxx"
diff --git a/include/optionsreader.hxx b/include/optionsreader.hxx
deleted file mode 100644
index 2c0f8344bf..0000000000
--- a/include/optionsreader.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "optionsreader.hxx" has moved to "bout/optionsreader.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/optionsreader.hxx"
diff --git a/include/output.hxx b/include/output.hxx
deleted file mode 100644
index 7eebcad478..0000000000
--- a/include/output.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "output.hxx" has moved to "bout/output.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/output.hxx"
diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx
deleted file mode 100644
index e82a88d98f..0000000000
--- a/include/parallel_boundary_op.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "parallel_boundary_op.hxx" has moved to "bout/parallel_boundary_op.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/parallel_boundary_op.hxx"
diff --git a/include/parallel_boundary_region.hxx b/include/parallel_boundary_region.hxx
deleted file mode 100644
index dee2277007..0000000000
--- a/include/parallel_boundary_region.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "parallel_boundary_region.hxx" has moved to "bout/parallel_boundary_region.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/parallel_boundary_region.hxx"
diff --git a/include/smoothing.hxx b/include/smoothing.hxx
deleted file mode 100644
index b1a36adfb2..0000000000
--- a/include/smoothing.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "smoothing.hxx" has moved to "bout/smoothing.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/smoothing.hxx"
diff --git a/include/sourcex.hxx b/include/sourcex.hxx
deleted file mode 100644
index e09f3e89e4..0000000000
--- a/include/sourcex.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "sourcex.hxx" has moved to "bout/sourcex.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/sourcex.hxx"
diff --git a/include/stencils.hxx b/include/stencils.hxx
deleted file mode 100644
index fc877f3e1c..0000000000
--- a/include/stencils.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "stencils.hxx" has moved to "bout/stencils.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/stencils.hxx"
diff --git a/include/unused.hxx b/include/unused.hxx
deleted file mode 100644
index fa5ea7b6d1..0000000000
--- a/include/unused.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "unused.hxx" has moved to "bout/unused.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/unused.hxx"
diff --git a/include/utils.hxx b/include/utils.hxx
deleted file mode 100644
index d1a095e491..0000000000
--- a/include/utils.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "utils.hxx" has moved to "bout/utils.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/utils.hxx"
diff --git a/include/vecops.hxx b/include/vecops.hxx
deleted file mode 100644
index 1773418077..0000000000
--- a/include/vecops.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "vecops.hxx" has moved to "bout/vecops.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/vecops.hxx"
diff --git a/include/vector2d.hxx b/include/vector2d.hxx
deleted file mode 100644
index 6746d3f163..0000000000
--- a/include/vector2d.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "vector2d.hxx" has moved to "bout/vector2d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/vector2d.hxx"
diff --git a/include/vector3d.hxx b/include/vector3d.hxx
deleted file mode 100644
index 747b6a75dd..0000000000
--- a/include/vector3d.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "vector3d.hxx" has moved to "bout/vector3d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/vector3d.hxx"
diff --git a/include/where.hxx b/include/where.hxx
deleted file mode 100644
index e5b2bd9d30..0000000000
--- a/include/where.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "where.hxx" has moved to "bout/where.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/where.hxx"

From afc4a3a25c8333cd397cc0bdaa00ec8a6e18c097 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 3 Nov 2025 13:47:09 +0000
Subject: [PATCH 0303/1827] Bump bundled fmt

---
 externalpackages/fmt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/fmt b/externalpackages/fmt
index 486e7ba579..407c905e45 160000
--- a/externalpackages/fmt
+++ b/externalpackages/fmt
@@ -1 +1 @@
-Subproject commit 486e7ba579a2c677772d004ecd0311142ba481be
+Subproject commit 407c905e45ad75fc29bf0f9bb7c5c2fd3475976f

From 1cce8e649d27cd217e48e632e2128f396b9b6ba0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 4 Nov 2025 11:10:29 +0100
Subject: [PATCH 0304/1827] BoutComm::get() might return int

---
 src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
index a116d78475..04abecfe05 100644
--- a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
+++ b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
@@ -84,7 +84,7 @@ LaplaceXYpetsc::LaplaceXYpetsc(Mesh* m, Options* opt, const CELL_LOC loc)
   default_prefix = opt->name();
 
   // Get MPI communicator
-  auto* comm = BoutComm::get();
+  auto comm = BoutComm::get();
 
   // Local size
   const int localN = localSize();

From c2b5e0e283e286d59aeb0e501306ffd3f650e669 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 4 Nov 2025 12:30:46 +0100
Subject: [PATCH 0305/1827] Avoid mpi-compatibility issues

MPI_Comm can be a pointer or an int (or anything else)

Co-authored-by: Peter Hill <peter.hill@york.ac.uk>
---
 .clang-tidy | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.clang-tidy b/.clang-tidy
index 4caf530aee..a142355fc4 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -12,6 +12,12 @@ CheckOptions:
 
   - key: misc-include-cleaner.IgnoreHeaders
     value: 'petsc.*\.h;mpi\.h'
+
+  - key: readability-qualified-auto.IgnoreAliasing
+    value: 'false'
+
+  - key: readability-qualified-auto.AllowedTypes
+    value: 'MPI_Comm'
 ---
 
 Disabled checks and reasons:

From 00b970e118dfeb8abf204f6b9511b3d7938da0c3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 4 Nov 2025 12:36:54 +0100
Subject: [PATCH 0306/1827] Remove configure left overs

---
 build-aux/config.guess | 1568 -------
 build-aux/config.rpath |    0
 build-aux/config.sub   | 1788 --------
 build-aux/install-sh   |  527 ---
 build-aux/ltmain.sh    | 9655 ----------------------------------------
 build-aux/missing      |  215 -
 6 files changed, 13753 deletions(-)
 delete mode 100755 build-aux/config.guess
 delete mode 100644 build-aux/config.rpath
 delete mode 100755 build-aux/config.sub
 delete mode 100755 build-aux/install-sh
 delete mode 100644 build-aux/ltmain.sh
 delete mode 100755 build-aux/missing

diff --git a/build-aux/config.guess b/build-aux/config.guess
deleted file mode 100755
index c6fad2f5e5..0000000000
--- a/build-aux/config.guess
+++ /dev/null
@@ -1,1568 +0,0 @@
-#! /bin/sh
-# Attempt to guess a canonical system name.
-#   Copyright 1992-2013 Free Software Foundation, Inc.
-
-timestamp='2013-06-10'
-
-# This file is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>.
-#
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that
-# program.  This Exception is an additional permission under section 7
-# of the GNU General Public License, version 3 ("GPLv3").
-#
-# Originally written by Per Bothner.
-#
-# You can get the latest version of this script from:
-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
-#
-# Please send patches with a ChangeLog entry to config-patches@gnu.org.
-
-
-me=`echo "$0" | sed -e 's,.*/,,'`
-
-usage="\
-Usage: $0 [OPTION]
-
-Output the configuration name of the system \`$me' is run on.
-
-Operation modes:
-  -h, --help         print this help, then exit
-  -t, --time-stamp   print date of last modification, then exit
-  -v, --version      print version number, then exit
-
-Report bugs and patches to <config-patches@gnu.org>."
-
-version="\
-GNU config.guess ($timestamp)
-
-Originally written by Per Bothner.
-Copyright 1992-2013 Free Software Foundation, Inc.
-
-This is free software; see the source for copying conditions.  There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
-
-help="
-Try \`$me --help' for more information."
-
-# Parse command line
-while test $# -gt 0 ; do
-  case $1 in
-    --time-stamp | --time* | -t )
-       echo "$timestamp" ; exit ;;
-    --version | -v )
-       echo "$version" ; exit ;;
-    --help | --h* | -h )
-       echo "$usage"; exit ;;
-    -- )     # Stop option processing
-       shift; break ;;
-    - )	# Use stdin as input.
-       break ;;
-    -* )
-       echo "$me: invalid option $1$help" >&2
-       exit 1 ;;
-    * )
-       break ;;
-  esac
-done
-
-if test $# != 0; then
-  echo "$me: too many arguments$help" >&2
-  exit 1
-fi
-
-trap 'exit 1' 1 2 15
-
-# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
-# compiler to aid in system detection is discouraged as it requires
-# temporary files to be created and, as you can see below, it is a
-# headache to deal with in a portable fashion.
-
-# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
-# use `HOST_CC' if defined, but it is deprecated.
-
-# Portable tmp directory creation inspired by the Autoconf team.
-
-set_cc_for_build='
-trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
-trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
-: ${TMPDIR=/tmp} ;
- { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
- { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
- { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
- { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
-dummy=$tmp/dummy ;
-tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
-case $CC_FOR_BUILD,$HOST_CC,$CC in
- ,,)    echo "int x;" > $dummy.c ;
-	for c in cc gcc c89 c99 ; do
-	  if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
-	     CC_FOR_BUILD="$c"; break ;
-	  fi ;
-	done ;
-	if test x"$CC_FOR_BUILD" = x ; then
-	  CC_FOR_BUILD=no_compiler_found ;
-	fi
-	;;
- ,,*)   CC_FOR_BUILD=$CC ;;
- ,*,*)  CC_FOR_BUILD=$HOST_CC ;;
-esac ; set_cc_for_build= ;'
-
-# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
-# (ghazi@noc.rutgers.edu 1994-08-24)
-if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
-	PATH=$PATH:/.attbin ; export PATH
-fi
-
-UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
-UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
-UNAME_SYSTEM=`(uname -s) 2>/dev/null`  || UNAME_SYSTEM=unknown
-UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
-
-case "${UNAME_SYSTEM}" in
-Linux|GNU|GNU/*)
-	# If the system lacks a compiler, then just pick glibc.
-	# We could probably try harder.
-	LIBC=gnu
-
-	eval $set_cc_for_build
-	cat <<-EOF > $dummy.c
-	#include <features.h>
-	#if defined(__UCLIBC__)
-	LIBC=uclibc
-	#elif defined(__dietlibc__)
-	LIBC=dietlibc
-	#else
-	LIBC=gnu
-	#endif
-	EOF
-	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
-	;;
-esac
-
-case "${UNAME_MACHINE}" in
-  i?86)
-     test -z "$VENDOR" && VENDOR=pc
-     ;;
-  *)
-     test -z "$VENDOR" && VENDOR=unknown
-     ;;
-esac
-test -f /etc/SuSE-release -o -f /.buildenv && VENDOR=suse
-
-# Note: order is significant - the case branches are not exclusive.
-
-case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
-    *:NetBSD:*:*)
-	# NetBSD (nbsd) targets should (where applicable) match one or
-	# more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*,
-	# *-*-netbsdecoff* and *-*-netbsd*.  For targets that recently
-	# switched to ELF, *-*-netbsd* would select the old
-	# object file format.  This provides both forward
-	# compatibility and a consistent mechanism for selecting the
-	# object file format.
-	#
-	# Note: NetBSD doesn't particularly care about the vendor
-	# portion of the name.  We always set it to "unknown".
-	sysctl="sysctl -n hw.machine_arch"
-	UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
-	    /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
-	case "${UNAME_MACHINE_ARCH}" in
-	    armeb) machine=armeb-unknown ;;
-	    arm*) machine=arm-unknown ;;
-	    sh3el) machine=shl-unknown ;;
-	    sh3eb) machine=sh-unknown ;;
-	    sh5el) machine=sh5le-unknown ;;
-	    *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
-	esac
-	# The Operating System including object format, if it has switched
-	# to ELF recently, or will in the future.
-	case "${UNAME_MACHINE_ARCH}" in
-	    arm*|i386|m68k|ns32k|sh3*|sparc|vax)
-		eval $set_cc_for_build
-		if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
-			| grep -q __ELF__
-		then
-		    # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
-		    # Return netbsd for either.  FIX?
-		    os=netbsd
-		else
-		    os=netbsdelf
-		fi
-		;;
-	    *)
-		os=netbsd
-		;;
-	esac
-	# The OS release
-	# Debian GNU/NetBSD machines have a different userland, and
-	# thus, need a distinct triplet. However, they do not need
-	# kernel version information, so it can be replaced with a
-	# suitable tag, in the style of linux-gnu.
-	case "${UNAME_VERSION}" in
-	    Debian*)
-		release='-gnu'
-		;;
-	    *)
-		release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
-		;;
-	esac
-	# Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
-	# contains redundant information, the shorter form:
-	# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
-	echo "${machine}-${os}${release}"
-	exit ;;
-    *:Bitrig:*:*)
-	UNAME_MACHINE_ARCH=`arch | sed 's/Bitrig.//'`
-	echo ${UNAME_MACHINE_ARCH}-${VENDOR}-bitrig${UNAME_RELEASE}
-	exit ;;
-    *:OpenBSD:*:*)
-	UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
-	echo ${UNAME_MACHINE_ARCH}-${VENDOR}-openbsd${UNAME_RELEASE}
-	exit ;;
-    *:ekkoBSD:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-ekkobsd${UNAME_RELEASE}
-	exit ;;
-    *:SolidBSD:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-solidbsd${UNAME_RELEASE}
-	exit ;;
-    macppc:MirBSD:*:*)
-	echo powerpc-${VENDOR}-mirbsd${UNAME_RELEASE}
-	exit ;;
-    *:MirBSD:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-mirbsd${UNAME_RELEASE}
-	exit ;;
-    alpha:OSF1:*:*)
-	case $UNAME_RELEASE in
-	*4.0)
-		UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
-		;;
-	*5.*)
-		UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
-		;;
-	esac
-	# According to Compaq, /usr/sbin/psrinfo has been available on
-	# OSF/1 and Tru64 systems produced since 1995.  I hope that
-	# covers most systems running today.  This code pipes the CPU
-	# types through head -n 1, so we only detect the type of CPU 0.
-	ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^  The alpha \(.*\) processor.*$/\1/p' | head -n 1`
-	case "$ALPHA_CPU_TYPE" in
-	    "EV4 (21064)")
-		UNAME_MACHINE="alpha" ;;
-	    "EV4.5 (21064)")
-		UNAME_MACHINE="alpha" ;;
-	    "LCA4 (21066/21068)")
-		UNAME_MACHINE="alpha" ;;
-	    "EV5 (21164)")
-		UNAME_MACHINE="alphaev5" ;;
-	    "EV5.6 (21164A)")
-		UNAME_MACHINE="alphaev56" ;;
-	    "EV5.6 (21164PC)")
-		UNAME_MACHINE="alphapca56" ;;
-	    "EV5.7 (21164PC)")
-		UNAME_MACHINE="alphapca57" ;;
-	    "EV6 (21264)")
-		UNAME_MACHINE="alphaev6" ;;
-	    "EV6.7 (21264A)")
-		UNAME_MACHINE="alphaev67" ;;
-	    "EV6.8CB (21264C)")
-		UNAME_MACHINE="alphaev68" ;;
-	    "EV6.8AL (21264B)")
-		UNAME_MACHINE="alphaev68" ;;
-	    "EV6.8CX (21264D)")
-		UNAME_MACHINE="alphaev68" ;;
-	    "EV6.9A (21264/EV69A)")
-		UNAME_MACHINE="alphaev69" ;;
-	    "EV7 (21364)")
-		UNAME_MACHINE="alphaev7" ;;
-	    "EV7.9 (21364A)")
-		UNAME_MACHINE="alphaev79" ;;
-	esac
-	# A Pn.n version is a patched version.
-	# A Vn.n version is a released version.
-	# A Tn.n version is a released field test version.
-	# A Xn.n version is an unreleased experimental baselevel.
-	# 1.2 uses "1.2" for uname -r.
-	echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
-	# Reset EXIT trap before exiting to avoid spurious non-zero exit code.
-	exitcode=$?
-	trap '' 0
-	exit $exitcode ;;
-    Alpha\ *:Windows_NT*:*)
-	# How do we know it's Interix rather than the generic POSIX subsystem?
-	# Should we change UNAME_MACHINE based on the output of uname instead
-	# of the specific Alpha model?
-	echo alpha-pc-interix
-	exit ;;
-    21064:Windows_NT:50:3)
-	echo alpha-dec-winnt3.5
-	exit ;;
-    Amiga*:UNIX_System_V:4.0:*)
-	echo m68k-${VENDOR}-sysv4
-	exit ;;
-    *:[Aa]miga[Oo][Ss]:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-amigaos
-	exit ;;
-    *:[Mm]orph[Oo][Ss]:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-morphos
-	exit ;;
-    *:OS/390:*:*)
-	echo i370-ibm-openedition
-	exit ;;
-    *:z/VM:*:*)
-	echo s390-ibm-zvmoe
-	exit ;;
-    *:OS400:*:*)
-	echo powerpc-ibm-os400
-	exit ;;
-    arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
-	echo arm-acorn-riscix${UNAME_RELEASE}
-	exit ;;
-    arm*:riscos:*:*|arm*:RISCOS:*:*)
-	echo arm-${VENDOR}-riscos
-	exit ;;
-    SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
-	echo hppa1.1-hitachi-hiuxmpp
-	exit ;;
-    Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
-	# akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
-	if test "`(/bin/universe) 2>/dev/null`" = att ; then
-		echo pyramid-pyramid-sysv3
-	else
-		echo pyramid-pyramid-bsd
-	fi
-	exit ;;
-    NILE*:*:*:dcosx)
-	echo pyramid-pyramid-svr4
-	exit ;;
-    DRS?6000:unix:4.0:6*)
-	echo sparc-icl-nx6
-	exit ;;
-    DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
-	case `/usr/bin/uname -p` in
-	    sparc) echo sparc-icl-nx7; exit ;;
-	esac ;;
-    s390x:SunOS:*:*)
-	echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    sun4H:SunOS:5.*:*)
-	echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
-	echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
-	echo i386-pc-auroraux${UNAME_RELEASE}
-	exit ;;
-    i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
-	eval $set_cc_for_build
-	SUN_ARCH="i386"
-	# If there is a compiler, see if it is configured for 64-bit objects.
-	# Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
-	# This test works for both compilers.
-	if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
-	    if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
-		(CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
-		grep IS_64BIT_ARCH >/dev/null
-	    then
-		SUN_ARCH="x86_64"
-	    fi
-	fi
-	echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    sun4*:SunOS:6*:*)
-	# According to config.sub, this is the proper way to canonicalize
-	# SunOS6.  Hard to guess exactly what SunOS6 will be like, but
-	# it's likely to be more like Solaris than SunOS4.
-	echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    sun4*:SunOS:*:*)
-	case "`/usr/bin/arch -k`" in
-	    Series*|S4*)
-		UNAME_RELEASE=`uname -v`
-		;;
-	esac
-	# Japanese Language versions have a version number like `4.1.3-JL'.
-	echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
-	exit ;;
-    sun3*:SunOS:*:*)
-	echo m68k-sun-sunos${UNAME_RELEASE}
-	exit ;;
-    sun*:*:4.2BSD:*)
-	UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
-	test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
-	case "`/bin/arch`" in
-	    sun3)
-		echo m68k-sun-sunos${UNAME_RELEASE}
-		;;
-	    sun4)
-		echo sparc-sun-sunos${UNAME_RELEASE}
-		;;
-	esac
-	exit ;;
-    aushp:SunOS:*:*)
-	echo sparc-auspex-sunos${UNAME_RELEASE}
-	exit ;;
-    # The situation for MiNT is a little confusing.  The machine name
-    # can be virtually everything (everything which is not
-    # "atarist" or "atariste" at least should have a processor
-    # > m68000).  The system name ranges from "MiNT" over "FreeMiNT"
-    # to the lowercase version "mint" (or "freemint").  Finally
-    # the system name "TOS" denotes a system which is actually not
-    # MiNT.  But MiNT is downward compatible to TOS, so this should
-    # be no problem.
-    atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
-	echo m68k-atari-mint${UNAME_RELEASE}
-	exit ;;
-    atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
-	echo m68k-atari-mint${UNAME_RELEASE}
-	exit ;;
-    *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
-	echo m68k-atari-mint${UNAME_RELEASE}
-	exit ;;
-    milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
-	echo m68k-milan-mint${UNAME_RELEASE}
-	exit ;;
-    hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
-	echo m68k-hades-mint${UNAME_RELEASE}
-	exit ;;
-    *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
-	echo m68k-${VENDOR}-mint${UNAME_RELEASE}
-	exit ;;
-    m68k:machten:*:*)
-	echo m68k-apple-machten${UNAME_RELEASE}
-	exit ;;
-    powerpc:machten:*:*)
-	echo powerpc-apple-machten${UNAME_RELEASE}
-	exit ;;
-    RISC*:Mach:*:*)
-	echo mips-dec-mach_bsd4.3
-	exit ;;
-    RISC*:ULTRIX:*:*)
-	echo mips-dec-ultrix${UNAME_RELEASE}
-	exit ;;
-    VAX*:ULTRIX*:*:*)
-	echo vax-dec-ultrix${UNAME_RELEASE}
-	exit ;;
-    2020:CLIX:*:* | 2430:CLIX:*:*)
-	echo clipper-intergraph-clix${UNAME_RELEASE}
-	exit ;;
-    mips:*:*:UMIPS | mips:*:*:RISCos)
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-#ifdef __cplusplus
-#include <stdio.h>  /* for printf() prototype */
-	int main (int argc, char *argv[]) {
-#else
-	int main (argc, argv) int argc; char *argv[]; {
-#endif
-	#if defined (host_mips) && defined (MIPSEB)
-	#if defined (SYSTYPE_SYSV)
-	  printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
-	#endif
-	#if defined (SYSTYPE_SVR4)
-	  printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
-	#endif
-	#if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
-	  printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
-	#endif
-	#endif
-	  exit (-1);
-	}
-EOF
-	$CC_FOR_BUILD -o $dummy $dummy.c &&
-	  dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
-	  SYSTEM_NAME=`$dummy $dummyarg` &&
-	    { echo "$SYSTEM_NAME"; exit; }
-	echo mips-mips-riscos${UNAME_RELEASE}
-	exit ;;
-    Motorola:PowerMAX_OS:*:*)
-	echo powerpc-motorola-powermax
-	exit ;;
-    Motorola:*:4.3:PL8-*)
-	echo powerpc-harris-powermax
-	exit ;;
-    Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
-	echo powerpc-harris-powermax
-	exit ;;
-    Night_Hawk:Power_UNIX:*:*)
-	echo powerpc-harris-powerunix
-	exit ;;
-    m88k:CX/UX:7*:*)
-	echo m88k-harris-cxux7
-	exit ;;
-    m88k:*:4*:R4*)
-	echo m88k-motorola-sysv4
-	exit ;;
-    m88k:*:3*:R3*)
-	echo m88k-motorola-sysv3
-	exit ;;
-    AViiON:dgux:*:*)
-	# DG/UX returns AViiON for all architectures
-	UNAME_PROCESSOR=`/usr/bin/uname -p`
-	if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
-	then
-	    if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
-	       [ ${TARGET_BINARY_INTERFACE}x = x ]
-	    then
-		echo m88k-dg-dgux${UNAME_RELEASE}
-	    else
-		echo m88k-dg-dguxbcs${UNAME_RELEASE}
-	    fi
-	else
-	    echo i586-dg-dgux${UNAME_RELEASE}
-	fi
-	exit ;;
-    M88*:DolphinOS:*:*)	# DolphinOS (SVR3)
-	echo m88k-dolphin-sysv3
-	exit ;;
-    M88*:*:R3*:*)
-	# Delta 88k system running SVR3
-	echo m88k-motorola-sysv3
-	exit ;;
-    XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
-	echo m88k-tektronix-sysv3
-	exit ;;
-    Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
-	echo m68k-tektronix-bsd
-	exit ;;
-    *:IRIX*:*:*)
-	echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
-	exit ;;
-    ????????:AIX?:[12].1:2)   # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
-	echo romp-ibm-aix     # uname -m gives an 8 hex-code CPU id
-	exit ;;               # Note that: echo "'`uname -s`'" gives 'AIX '
-    i*86:AIX:*:*)
-	echo i386-ibm-aix
-	exit ;;
-    ia64:AIX:*:*)
-	if [ -x /usr/bin/oslevel ] ; then
-		IBM_REV=`/usr/bin/oslevel`
-	else
-		IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
-	fi
-	echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
-	exit ;;
-    *:AIX:2:3)
-	if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
-		eval $set_cc_for_build
-		sed 's/^		//' << EOF >$dummy.c
-		#include <sys/systemcfg.h>
-
-		main()
-			{
-			if (!__power_pc())
-				exit(1);
-			puts("powerpc-ibm-aix3.2.5");
-			exit(0);
-			}
-EOF
-		if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
-		then
-			echo "$SYSTEM_NAME"
-		else
-			echo rs6000-ibm-aix3.2.5
-		fi
-	elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
-		echo rs6000-ibm-aix3.2.4
-	else
-		echo rs6000-ibm-aix3.2
-	fi
-	exit ;;
-    *:AIX:*:[4567])
-	IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
-	if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
-		IBM_ARCH=rs6000
-	else
-		IBM_ARCH=powerpc
-	fi
-	if [ -x /usr/bin/oslevel ] ; then
-		IBM_REV=`/usr/bin/oslevel`
-	else
-		IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
-	fi
-	echo ${IBM_ARCH}-ibm-aix${IBM_REV}
-	exit ;;
-    *:AIX:*:*)
-	echo rs6000-ibm-aix
-	exit ;;
-    ibmrt:4.4BSD:*|romp-ibm:BSD:*)
-	echo romp-ibm-bsd4.4
-	exit ;;
-    ibmrt:*BSD:*|romp-ibm:BSD:*)            # covers RT/PC BSD and
-	echo romp-ibm-bsd${UNAME_RELEASE}   # 4.3 with uname added to
-	exit ;;                             # report: romp-ibm BSD 4.3
-    *:BOSX:*:*)
-	echo rs6000-bull-bosx
-	exit ;;
-    DPX/2?00:B.O.S.:*:*)
-	echo m68k-bull-sysv3
-	exit ;;
-    9000/[34]??:4.3bsd:1.*:*)
-	echo m68k-hp-bsd
-	exit ;;
-    hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
-	echo m68k-hp-bsd4.4
-	exit ;;
-    9000/[34678]??:HP-UX:*:*)
-	HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
-	case "${UNAME_MACHINE}" in
-	    9000/31? )            HP_ARCH=m68000 ;;
-	    9000/[34]?? )         HP_ARCH=m68k ;;
-	    9000/[678][0-9][0-9])
-		if [ -x /usr/bin/getconf ]; then
-		    sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
-		    sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
-		    case "${sc_cpu_version}" in
-		      523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
-		      528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
-		      532)                      # CPU_PA_RISC2_0
-			case "${sc_kernel_bits}" in
-			  32) HP_ARCH="hppa2.0n" ;;
-			  64) HP_ARCH="hppa2.0w" ;;
-			  '') HP_ARCH="hppa2.0" ;;   # HP-UX 10.20
-			esac ;;
-		    esac
-		fi
-		if [ "${HP_ARCH}" = "" ]; then
-		    eval $set_cc_for_build
-		    sed 's/^		//' << EOF >$dummy.c
-
-		#define _HPUX_SOURCE
-		#include <stdlib.h>
-		#include <unistd.h>
-
-		int main ()
-		{
-		#if defined(_SC_KERNEL_BITS)
-		    long bits = sysconf(_SC_KERNEL_BITS);
-		#endif
-		    long cpu  = sysconf (_SC_CPU_VERSION);
-
-		    switch (cpu)
-			{
-			case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
-			case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
-			case CPU_PA_RISC2_0:
-		#if defined(_SC_KERNEL_BITS)
-			    switch (bits)
-				{
-				case 64: puts ("hppa2.0w"); break;
-				case 32: puts ("hppa2.0n"); break;
-				default: puts ("hppa2.0"); break;
-				} break;
-		#else  /* !defined(_SC_KERNEL_BITS) */
-			    puts ("hppa2.0"); break;
-		#endif
-			default: puts ("hppa1.0"); break;
-			}
-		    exit (0);
-		}
-EOF
-		    (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
-		    test -z "$HP_ARCH" && HP_ARCH=hppa
-		fi ;;
-	esac
-	if [ ${HP_ARCH} = "hppa2.0w" ]
-	then
-	    eval $set_cc_for_build
-
-	    # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
-	    # 32-bit code.  hppa64-hp-hpux* has the same kernel and a compiler
-	    # generating 64-bit code.  GNU and HP use different nomenclature:
-	    #
-	    # $ CC_FOR_BUILD=cc ./config.guess
-	    # => hppa2.0w-hp-hpux11.23
-	    # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
-	    # => hppa64-hp-hpux11.23
-
-	    if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
-		grep -q __LP64__
-	    then
-		HP_ARCH="hppa2.0w"
-	    else
-		HP_ARCH="hppa64"
-	    fi
-	fi
-	echo ${HP_ARCH}-hp-hpux${HPUX_REV}
-	exit ;;
-    ia64:HP-UX:*:*)
-	HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
-	echo ia64-hp-hpux${HPUX_REV}
-	exit ;;
-    3050*:HI-UX:*:*)
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-	#include <unistd.h>
-	int
-	main ()
-	{
-	  long cpu = sysconf (_SC_CPU_VERSION);
-	  /* The order matters, because CPU_IS_HP_MC68K erroneously returns
-	     true for CPU_PA_RISC1_0.  CPU_IS_PA_RISC returns correct
-	     results, however.  */
-	  if (CPU_IS_PA_RISC (cpu))
-	    {
-	      switch (cpu)
-		{
-		  case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
-		  case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
-		  case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
-		  default: puts ("hppa-hitachi-hiuxwe2"); break;
-		}
-	    }
-	  else if (CPU_IS_HP_MC68K (cpu))
-	    puts ("m68k-hitachi-hiuxwe2");
-	  else puts ("unknown-hitachi-hiuxwe2");
-	  exit (0);
-	}
-EOF
-	$CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
-		{ echo "$SYSTEM_NAME"; exit; }
-	echo unknown-hitachi-hiuxwe2
-	exit ;;
-    9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
-	echo hppa1.1-hp-bsd
-	exit ;;
-    9000/8??:4.3bsd:*:*)
-	echo hppa1.0-hp-bsd
-	exit ;;
-    *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
-	echo hppa1.0-hp-mpeix
-	exit ;;
-    hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
-	echo hppa1.1-hp-osf
-	exit ;;
-    hp8??:OSF1:*:*)
-	echo hppa1.0-hp-osf
-	exit ;;
-    i*86:OSF1:*:*)
-	if [ -x /usr/sbin/sysversion ] ; then
-	    echo ${UNAME_MACHINE}-${VENDOR}-osf1mk
-	else
-	    echo ${UNAME_MACHINE}-${VENDOR}-osf1
-	fi
-	exit ;;
-    parisc*:Lites*:*:*)
-	echo hppa1.1-hp-lites
-	exit ;;
-    C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
-	echo c1-convex-bsd
-	exit ;;
-    C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
-	if getsysinfo -f scalar_acc
-	then echo c32-convex-bsd
-	else echo c2-convex-bsd
-	fi
-	exit ;;
-    C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
-	echo c34-convex-bsd
-	exit ;;
-    C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
-	echo c38-convex-bsd
-	exit ;;
-    C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
-	echo c4-convex-bsd
-	exit ;;
-    CRAY*Y-MP:*:*:*)
-	echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    CRAY*[A-Z]90:*:*:*)
-	echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
-	| sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
-	      -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
-	      -e 's/\.[^.]*$/.X/'
-	exit ;;
-    CRAY*TS:*:*:*)
-	echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    CRAY*T3E:*:*:*)
-	echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    CRAY*SV1:*:*:*)
-	echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    *:UNICOS/mp:*:*)
-	echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
-	FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
-	FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
-	FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
-	echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
-	exit ;;
-    5000:UNIX_System_V:4.*:*)
-	FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
-	FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
-	echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
-	exit ;;
-    i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
-	echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
-	exit ;;
-    sparc*:BSD/OS:*:*)
-	echo sparc-${VENDOR}-bsdi${UNAME_RELEASE}
-	exit ;;
-    *:BSD/OS:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-bsdi${UNAME_RELEASE}
-	exit ;;
-    *:FreeBSD:*:*)
-	UNAME_PROCESSOR=`/usr/bin/uname -p`
-	case ${UNAME_PROCESSOR} in
-	    amd64)
-		echo x86_64-${VENDOR}-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
-	    *)
-		echo ${UNAME_PROCESSOR}-${VENDOR}-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
-	esac
-	exit ;;
-    i*:CYGWIN*:*)
-	echo ${UNAME_MACHINE}-pc-cygwin
-	exit ;;
-    *:MINGW64*:*)
-	echo ${UNAME_MACHINE}-pc-mingw64
-	exit ;;
-    *:MINGW*:*)
-	echo ${UNAME_MACHINE}-pc-mingw32
-	exit ;;
-    i*:MSYS*:*)
-	echo ${UNAME_MACHINE}-pc-msys
-	exit ;;
-    i*:windows32*:*)
-	# uname -m includes "-pc" on this system.
-	echo ${UNAME_MACHINE}-mingw32
-	exit ;;
-    i*:PW*:*)
-	echo ${UNAME_MACHINE}-pc-pw32
-	exit ;;
-    *:Interix*:*)
-	case ${UNAME_MACHINE} in
-	    x86)
-		echo i586-pc-interix${UNAME_RELEASE}
-		exit ;;
-	    authenticamd | genuineintel | EM64T)
-		echo x86_64-${VENDOR}-interix${UNAME_RELEASE}
-		exit ;;
-	    IA64)
-		echo ia64-${VENDOR}-interix${UNAME_RELEASE}
-		exit ;;
-	esac ;;
-    [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
-	echo i${UNAME_MACHINE}-pc-mks
-	exit ;;
-    8664:Windows_NT:*)
-	echo x86_64-pc-mks
-	exit ;;
-    i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
-	# How do we know it's Interix rather than the generic POSIX subsystem?
-	# It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
-	# UNAME_MACHINE based on the output of uname instead of i386?
-	echo i586-pc-interix
-	exit ;;
-    i*:UWIN*:*)
-	echo ${UNAME_MACHINE}-pc-uwin
-	exit ;;
-    amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
-	echo x86_64-${VENDOR}-cygwin
-	exit ;;
-    p*:CYGWIN*:*)
-	echo powerpcle-${VENDOR}-cygwin
-	exit ;;
-    prep*:SunOS:5.*:*)
-	echo powerpcle-${VENDOR}-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    *:GNU:*:*)
-	# the GNU system
-	echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-${VENDOR}-${LIBC}`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
-	exit ;;
-    *:GNU/*:*:*)
-	# other systems with GNU libc and userland
-	echo ${UNAME_MACHINE}-${VENDOR}-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-${LIBC}
-	exit ;;
-    i*86:Minix:*:*)
-	echo ${UNAME_MACHINE}-pc-minix
-	exit ;;
-    aarch64:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    aarch64_be:Linux:*:*)
-	UNAME_MACHINE=aarch64_be
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    alpha:Linux:*:*)
-	case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
-	  EV5)   UNAME_MACHINE=alphaev5 ;;
-	  EV56)  UNAME_MACHINE=alphaev56 ;;
-	  PCA56) UNAME_MACHINE=alphapca56 ;;
-	  PCA57) UNAME_MACHINE=alphapca56 ;;
-	  EV6)   UNAME_MACHINE=alphaev6 ;;
-	  EV67)  UNAME_MACHINE=alphaev67 ;;
-	  EV68*) UNAME_MACHINE=alphaev68 ;;
-	esac
-	objdump --private-headers /bin/sh | grep -q ld.so.1
-	if test "$?" = 0 ; then LIBC="gnulibc1" ; fi
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    arc:Linux:*:* | arceb:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    arm*:Linux:*:*)
-	eval $set_cc_for_build
-	if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
-	    | grep -q __ARM_EABI__
-	then
-	    echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	else
-	    if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
-		| grep -q __ARM_PCS_VFP
-	    then
-		echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}eabi
-	    else
-		echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}eabihf
-	    fi
-	fi
-	exit ;;
-    avr32*:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    cris:Linux:*:*)
-	echo ${UNAME_MACHINE}-axis-linux-${LIBC}
-	exit ;;
-    crisv32:Linux:*:*)
-	echo ${UNAME_MACHINE}-axis-linux-${LIBC}
-	exit ;;
-    frv:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    hexagon:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    i*86:Linux:*:*)
-	echo ${UNAME_MACHINE}-pc-linux-${LIBC}
-	exit ;;
-    ia64:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    m32r*:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    m68*:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    mips:Linux:*:* | mips64:Linux:*:*)
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-	#undef CPU
-	#undef ${UNAME_MACHINE}
-	#undef ${UNAME_MACHINE}el
-	#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
-	CPU=${UNAME_MACHINE}el
-	#else
-	#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
-	CPU=${UNAME_MACHINE}
-	#else
-	CPU=
-	#endif
-	#endif
-EOF
-	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
-	test x"${CPU}" != x && { echo "${CPU}-${VENDOR}-linux-${LIBC}"; exit; }
-	;;
-    or1k:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    or32:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    padre:Linux:*:*)
-	echo sparc-${VENDOR}-linux-${LIBC}
-	exit ;;
-    parisc64:Linux:*:* | hppa64:Linux:*:*)
-	echo hppa64-${VENDOR}-linux-${LIBC}
-	exit ;;
-    parisc:Linux:*:* | hppa:Linux:*:*)
-	# Look for CPU level
-	case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
-	  PA7*) echo hppa1.1-${VENDOR}-linux-${LIBC} ;;
-	  PA8*) echo hppa2.0-${VENDOR}-linux-${LIBC} ;;
-	  *)    echo hppa-${VENDOR}-linux-${LIBC} ;;
-	esac
-	exit ;;
-    ppc64:Linux:*:*)
-	echo powerpc64-${VENDOR}-linux-${LIBC}
-	exit ;;
-    ppc:Linux:*:*)
-	echo powerpc-${VENDOR}-linux-${LIBC}
-	exit ;;
-    ppc64le:Linux:*:*)
-	echo powerpc64le-${VENDOR}-linux-${LIBC}
-	exit ;;
-    ppcle:Linux:*:*)
-	echo powerpcle-${VENDOR}-linux-${LIBC}
-	exit ;;
-    s390:Linux:*:* | s390x:Linux:*:*)
-	echo ${UNAME_MACHINE}-ibm-linux-${LIBC}
-	exit ;;
-    sh64*:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    sh*:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    sparc:Linux:*:* | sparc64:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    tile*:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    vax:Linux:*:*)
-	echo ${UNAME_MACHINE}-dec-linux-${LIBC}
-	exit ;;
-    x86_64:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    xtensa*:Linux:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
-	exit ;;
-    i*86:DYNIX/ptx:4*:*)
-	# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
-	# earlier versions are messed up and put the nodename in both
-	# sysname and nodename.
-	echo i386-sequent-sysv4
-	exit ;;
-    i*86:UNIX_SV:4.2MP:2.*)
-	# Unixware is an offshoot of SVR4, but it has its own version
-	# number series starting with 2...
-	# I am not positive that other SVR4 systems won't match this,
-	# I just have to hope.  -- rms.
-	# Use sysv4.2uw... so that sysv4* matches it.
-	echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
-	exit ;;
-    i*86:OS/2:*:*)
-	# If we were able to find `uname', then EMX Unix compatibility
-	# is probably installed.
-	echo ${UNAME_MACHINE}-pc-os2-emx
-	exit ;;
-    i*86:XTS-300:*:STOP)
-	echo ${UNAME_MACHINE}-${VENDOR}-stop
-	exit ;;
-    i*86:atheos:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-atheos
-	exit ;;
-    i*86:syllable:*:*)
-	echo ${UNAME_MACHINE}-pc-syllable
-	exit ;;
-    i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
-	echo i386-${VENODR}-lynxos${UNAME_RELEASE}
-	exit ;;
-    i*86:*DOS:*:*)
-	echo ${UNAME_MACHINE}-pc-msdosdjgpp
-	exit ;;
-    i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
-	UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
-	if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
-		echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
-	else
-		echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
-	fi
-	exit ;;
-    i*86:*:5:[678]*)
-	# UnixWare 7.x, OpenUNIX and OpenServer 6.
-	case `/bin/uname -X | grep "^Machine"` in
-	    *486*)	     UNAME_MACHINE=i486 ;;
-	    *Pentium)	     UNAME_MACHINE=i586 ;;
-	    *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
-	esac
-	echo ${UNAME_MACHINE}-${VENDOR}-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
-	exit ;;
-    i*86:*:3.2:*)
-	if test -f /usr/options/cb.name; then
-		UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
-		echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
-	elif /bin/uname -X 2>/dev/null >/dev/null ; then
-		UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
-		(/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
-		(/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
-			&& UNAME_MACHINE=i586
-		(/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
-			&& UNAME_MACHINE=i686
-		(/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
-			&& UNAME_MACHINE=i686
-		echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
-	else
-		echo ${UNAME_MACHINE}-pc-sysv32
-	fi
-	exit ;;
-    pc:*:*:*)
-	# Left here for compatibility:
-	# uname -m prints for DJGPP always 'pc', but it prints nothing about
-	# the processor, so we play safe by assuming i586.
-	# Note: whatever this is, it MUST be the same as what config.sub
-	# prints for the "djgpp" host, or else GDB configury will decide that
-	# this is a cross-build.
-	echo i586-pc-msdosdjgpp
-	exit ;;
-    Intel:Mach:3*:*)
-	echo i386-pc-mach3
-	exit ;;
-    paragon:*:*:*)
-	echo i860-intel-osf1
-	exit ;;
-    i860:*:4.*:*) # i860-SVR4
-	if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
-	  echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
-	else # Add other i860-SVR4 vendors below as they are discovered.
-	  echo i860-${VENODR}-sysv${UNAME_RELEASE}  # Unknown i860-SVR4
-	fi
-	exit ;;
-    mini*:CTIX:SYS*5:*)
-	# "miniframe"
-	echo m68010-convergent-sysv
-	exit ;;
-    mc68k:UNIX:SYSTEM5:3.51m)
-	echo m68k-convergent-sysv
-	exit ;;
-    M680?0:D-NIX:5.3:*)
-	echo m68k-diab-dnix
-	exit ;;
-    M68*:*:R3V[5678]*:*)
-	test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
-    3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
-	OS_REL=''
-	test -r /etc/.relid \
-	&& OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
-	/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
-	  && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
-	/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
-	  && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
-    3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
-	/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
-	  && { echo i486-ncr-sysv4; exit; } ;;
-    NCR*:*:4.2:* | MPRAS*:*:4.2:*)
-	OS_REL='.3'
-	test -r /etc/.relid \
-	    && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
-	/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
-	    && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
-	/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
-	    && { echo i586-ncr-sysv4.3${OS_REL}; exit; }
-	/bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
-	    && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
-    m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
-	echo m68k-${VENDOR}-lynxos${UNAME_RELEASE}
-	exit ;;
-    mc68030:UNIX_System_V:4.*:*)
-	echo m68k-atari-sysv4
-	exit ;;
-    TSUNAMI:LynxOS:2.*:*)
-	echo sparc-${VENDOR}-lynxos${UNAME_RELEASE}
-	exit ;;
-    rs6000:LynxOS:2.*:*)
-	echo rs6000-${VENDOR}-lynxos${UNAME_RELEASE}
-	exit ;;
-    PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
-	echo powerpc-${VENDOR}-lynxos${UNAME_RELEASE}
-	exit ;;
-    SM[BE]S:UNIX_SV:*:*)
-	echo mips-dde-sysv${UNAME_RELEASE}
-	exit ;;
-    RM*:ReliantUNIX-*:*:*)
-	echo mips-sni-sysv4
-	exit ;;
-    RM*:SINIX-*:*:*)
-	echo mips-sni-sysv4
-	exit ;;
-    *:SINIX-*:*:*)
-	if uname -p 2>/dev/null >/dev/null ; then
-		UNAME_MACHINE=`(uname -p) 2>/dev/null`
-		echo ${UNAME_MACHINE}-sni-sysv4
-	else
-		echo ns32k-sni-sysv
-	fi
-	exit ;;
-    PENTIUM:*:4.0*:*)	# Unisys `ClearPath HMP IX 4000' SVR4/MP effort
-			# says <Richard.M.Bartel@ccMail.Census.GOV>
-	echo i586-unisys-sysv4
-	exit ;;
-    *:UNIX_System_V:4*:FTX*)
-	# From Gerald Hewes <hewes@openmarket.com>.
-	# How about differentiating between stratus architectures? -djm
-	echo hppa1.1-stratus-sysv4
-	exit ;;
-    *:*:*:FTX*)
-	# From seanf@swdc.stratus.com.
-	echo i860-stratus-sysv4
-	exit ;;
-    i*86:VOS:*:*)
-	# From Paul.Green@stratus.com.
-	echo ${UNAME_MACHINE}-stratus-vos
-	exit ;;
-    *:VOS:*:*)
-	# From Paul.Green@stratus.com.
-	echo hppa1.1-stratus-vos
-	exit ;;
-    mc68*:A/UX:*:*)
-	echo m68k-apple-aux${UNAME_RELEASE}
-	exit ;;
-    news*:NEWS-OS:6*:*)
-	echo mips-sony-newsos6
-	exit ;;
-    R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
-	if [ -d /usr/nec ]; then
-		echo mips-nec-sysv${UNAME_RELEASE}
-	else
-		echo mips-${VENDOR}-sysv${UNAME_RELEASE}
-	fi
-	exit ;;
-    BeBox:BeOS:*:*)	# BeOS running on hardware made by Be, PPC only.
-	echo powerpc-be-beos
-	exit ;;
-    BeMac:BeOS:*:*)	# BeOS running on Mac or Mac clone, PPC only.
-	echo powerpc-apple-beos
-	exit ;;
-    BePC:BeOS:*:*)	# BeOS running on Intel PC compatible.
-	echo i586-pc-beos
-	exit ;;
-    BePC:Haiku:*:*)	# Haiku running on Intel PC compatible.
-	echo i586-pc-haiku
-	exit ;;
-    x86_64:Haiku:*:*)
-	echo x86_64-${VENDOR}-haiku
-	exit ;;
-    SX-4:SUPER-UX:*:*)
-	echo sx4-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-5:SUPER-UX:*:*)
-	echo sx5-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-6:SUPER-UX:*:*)
-	echo sx6-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-7:SUPER-UX:*:*)
-	echo sx7-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-8:SUPER-UX:*:*)
-	echo sx8-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-8R:SUPER-UX:*:*)
-	echo sx8r-nec-superux${UNAME_RELEASE}
-	exit ;;
-    Power*:Rhapsody:*:*)
-	echo powerpc-apple-rhapsody${UNAME_RELEASE}
-	exit ;;
-    *:Rhapsody:*:*)
-	echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
-	exit ;;
-    *:Darwin:*:*)
-	UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
-	eval $set_cc_for_build
-	if test "$UNAME_PROCESSOR" = unknown ; then
-	    UNAME_PROCESSOR=powerpc
-	fi
-	if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
-	    if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
-		(CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
-		grep IS_64BIT_ARCH >/dev/null
-	    then
-		case $UNAME_PROCESSOR in
-		    i386) UNAME_PROCESSOR=x86_64 ;;
-		    powerpc) UNAME_PROCESSOR=powerpc64 ;;
-		esac
-	    fi
-	fi
-	echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
-	exit ;;
-    *:procnto*:*:* | *:QNX:[0123456789]*:*)
-	UNAME_PROCESSOR=`uname -p`
-	if test "$UNAME_PROCESSOR" = "x86"; then
-		UNAME_PROCESSOR=i386
-		UNAME_MACHINE=pc
-	fi
-	echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
-	exit ;;
-    *:QNX:*:4*)
-	echo i386-pc-qnx
-	exit ;;
-    NEO-?:NONSTOP_KERNEL:*:*)
-	echo neo-tandem-nsk${UNAME_RELEASE}
-	exit ;;
-    NSE-*:NONSTOP_KERNEL:*:*)
-	echo nse-tandem-nsk${UNAME_RELEASE}
-	exit ;;
-    NSR-?:NONSTOP_KERNEL:*:*)
-	echo nsr-tandem-nsk${UNAME_RELEASE}
-	exit ;;
-    *:NonStop-UX:*:*)
-	echo mips-compaq-nonstopux
-	exit ;;
-    BS2000:POSIX*:*:*)
-	echo bs2000-siemens-sysv
-	exit ;;
-    DS/*:UNIX_System_V:*:*)
-	echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
-	exit ;;
-    *:Plan9:*:*)
-	# "uname -m" is not consistent, so use $cputype instead. 386
-	# is converted to i386 for consistency with other x86
-	# operating systems.
-	if test "$cputype" = "386"; then
-	    UNAME_MACHINE=i386
-	else
-	    UNAME_MACHINE="$cputype"
-	fi
-	echo ${UNAME_MACHINE}-${VENDOR}-plan9
-	exit ;;
-    *:TOPS-10:*:*)
-	echo pdp10-${VENDOR}-tops10
-	exit ;;
-    *:TENEX:*:*)
-	echo pdp10-${VENDOR}-tenex
-	exit ;;
-    KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
-	echo pdp10-dec-tops20
-	exit ;;
-    XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
-	echo pdp10-xkl-tops20
-	exit ;;
-    *:TOPS-20:*:*)
-	echo pdp10-${VENDOR}-tops20
-	exit ;;
-    *:ITS:*:*)
-	echo pdp10-${VENDOR}-its
-	exit ;;
-    SEI:*:*:SEIUX)
-	echo mips-sei-seiux${UNAME_RELEASE}
-	exit ;;
-    *:DragonFly:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
-	exit ;;
-    *:*VMS:*:*)
-	UNAME_MACHINE=`(uname -p) 2>/dev/null`
-	case "${UNAME_MACHINE}" in
-	    A*) echo alpha-dec-vms ; exit ;;
-	    I*) echo ia64-dec-vms ; exit ;;
-	    V*) echo vax-dec-vms ; exit ;;
-	esac ;;
-    *:XENIX:*:SysV)
-	echo i386-pc-xenix
-	exit ;;
-    i*86:skyos:*:*)
-	echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
-	exit ;;
-    i*86:rdos:*:*)
-	echo ${UNAME_MACHINE}-pc-rdos
-	exit ;;
-    i*86:AROS:*:*)
-	echo ${UNAME_MACHINE}-pc-aros
-	exit ;;
-    x86_64:VMkernel:*:*)
-	echo ${UNAME_MACHINE}-${VENDOR}-esx
-	exit ;;
-esac
-
-eval $set_cc_for_build
-cat >$dummy.c <<EOF
-#ifdef _SEQUENT_
-# include <sys/types.h>
-# include <sys/utsname.h>
-#endif
-main ()
-{
-#if defined (sony)
-#if defined (MIPSEB)
-  /* BFD wants "bsd" instead of "newsos".  Perhaps BFD should be changed,
-     I don't know....  */
-  printf ("mips-sony-bsd\n"); exit (0);
-#else
-#include <sys/param.h>
-  printf ("m68k-sony-newsos%s\n",
-#ifdef NEWSOS4
-	"4"
-#else
-	""
-#endif
-	); exit (0);
-#endif
-#endif
-
-#if defined (__arm) && defined (__acorn) && defined (__unix)
-  printf ("arm-acorn-riscix\n"); exit (0);
-#endif
-
-#if defined (hp300) && !defined (hpux)
-  printf ("m68k-hp-bsd\n"); exit (0);
-#endif
-
-#if defined (NeXT)
-#if !defined (__ARCHITECTURE__)
-#define __ARCHITECTURE__ "m68k"
-#endif
-  int version;
-  version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
-  if (version < 4)
-    printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
-  else
-    printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
-  exit (0);
-#endif
-
-#if defined (MULTIMAX) || defined (n16)
-#if defined (UMAXV)
-  printf ("ns32k-encore-sysv\n"); exit (0);
-#else
-#if defined (CMU)
-  printf ("ns32k-encore-mach\n"); exit (0);
-#else
-  printf ("ns32k-encore-bsd\n"); exit (0);
-#endif
-#endif
-#endif
-
-#if defined (__386BSD__)
-  printf ("i386-pc-bsd\n"); exit (0);
-#endif
-
-#if defined (sequent)
-#if defined (i386)
-  printf ("i386-sequent-dynix\n"); exit (0);
-#endif
-#if defined (ns32000)
-  printf ("ns32k-sequent-dynix\n"); exit (0);
-#endif
-#endif
-
-#if defined (_SEQUENT_)
-    struct utsname un;
-
-    uname(&un);
-
-    if (strncmp(un.version, "V2", 2) == 0) {
-	printf ("i386-sequent-ptx2\n"); exit (0);
-    }
-    if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
-	printf ("i386-sequent-ptx1\n"); exit (0);
-    }
-    printf ("i386-sequent-ptx\n"); exit (0);
-
-#endif
-
-#if defined (vax)
-# if !defined (ultrix)
-#  include <sys/param.h>
-#  if defined (BSD)
-#   if BSD == 43
-      printf ("vax-dec-bsd4.3\n"); exit (0);
-#   else
-#    if BSD == 199006
-      printf ("vax-dec-bsd4.3reno\n"); exit (0);
-#    else
-      printf ("vax-dec-bsd\n"); exit (0);
-#    endif
-#   endif
-#  else
-    printf ("vax-dec-bsd\n"); exit (0);
-#  endif
-# else
-    printf ("vax-dec-ultrix\n"); exit (0);
-# endif
-#endif
-
-#if defined (alliant) && defined (i860)
-  printf ("i860-alliant-bsd\n"); exit (0);
-#endif
-
-  exit (1);
-}
-EOF
-
-$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
-	{ echo "$SYSTEM_NAME"; exit; }
-
-# Apollos put the system type in the environment.
-
-test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
-
-# Convex versions that predate uname can use getsysinfo(1)
-
-if [ -x /usr/convex/getsysinfo ]
-then
-    case `getsysinfo -f cpu_type` in
-    c1*)
-	echo c1-convex-bsd
-	exit ;;
-    c2*)
-	if getsysinfo -f scalar_acc
-	then echo c32-convex-bsd
-	else echo c2-convex-bsd
-	fi
-	exit ;;
-    c34*)
-	echo c34-convex-bsd
-	exit ;;
-    c38*)
-	echo c38-convex-bsd
-	exit ;;
-    c4*)
-	echo c4-convex-bsd
-	exit ;;
-    esac
-fi
-
-cat >&2 <<EOF
-$0: unable to guess system type
-
-This script, last modified $timestamp, has failed to recognize
-the operating system you are using. It is advised that you
-download the most up to date version of the config scripts from
-
-  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
-and
-  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
-
-If the version you run ($0) is already up to date, please
-send the following data and any information you think might be
-pertinent to <config-patches@gnu.org> in order to provide the needed
-information to handle your system.
-
-config.guess timestamp = $timestamp
-
-uname -m = `(uname -m) 2>/dev/null || echo unknown`
-uname -r = `(uname -r) 2>/dev/null || echo unknown`
-uname -s = `(uname -s) 2>/dev/null || echo unknown`
-uname -v = `(uname -v) 2>/dev/null || echo unknown`
-
-/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
-/bin/uname -X     = `(/bin/uname -X) 2>/dev/null`
-
-hostinfo               = `(hostinfo) 2>/dev/null`
-/bin/universe          = `(/bin/universe) 2>/dev/null`
-/usr/bin/arch -k       = `(/usr/bin/arch -k) 2>/dev/null`
-/bin/arch              = `(/bin/arch) 2>/dev/null`
-/usr/bin/oslevel       = `(/usr/bin/oslevel) 2>/dev/null`
-/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
-
-UNAME_MACHINE = ${UNAME_MACHINE}
-UNAME_RELEASE = ${UNAME_RELEASE}
-UNAME_SYSTEM  = ${UNAME_SYSTEM}
-UNAME_VERSION = ${UNAME_VERSION}
-EOF
-
-exit 1
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "timestamp='"
-# time-stamp-format: "%:y-%02m-%02d"
-# time-stamp-end: "'"
-# End:
diff --git a/build-aux/config.rpath b/build-aux/config.rpath
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/build-aux/config.sub b/build-aux/config.sub
deleted file mode 100755
index 8b612ab89d..0000000000
--- a/build-aux/config.sub
+++ /dev/null
@@ -1,1788 +0,0 @@
-#! /bin/sh
-# Configuration validation subroutine script.
-#   Copyright 1992-2013 Free Software Foundation, Inc.
-
-timestamp='2013-04-24'
-
-# This file is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>.
-#
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that
-# program.  This Exception is an additional permission under section 7
-# of the GNU General Public License, version 3 ("GPLv3").
-
-
-# Please send patches with a ChangeLog entry to config-patches@gnu.org.
-#
-# Configuration subroutine to validate and canonicalize a configuration type.
-# Supply the specified configuration type as an argument.
-# If it is invalid, we print an error message on stderr and exit with code 1.
-# Otherwise, we print the canonical config type on stdout and succeed.
-
-# You can get the latest version of this script from:
-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
-
-# This file is supposed to be the same for all GNU packages
-# and recognize all the CPU types, system types and aliases
-# that are meaningful with *any* GNU software.
-# Each package is responsible for reporting which valid configurations
-# it does not support.  The user should be able to distinguish
-# a failure to support a valid configuration from a meaningless
-# configuration.
-
-# The goal of this file is to map all the various variations of a given
-# machine specification into a single specification in the form:
-#	CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
-# or in some cases, the newer four-part form:
-#	CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
-# It is wrong to echo any other type of specification.
-
-me=`echo "$0" | sed -e 's,.*/,,'`
-
-usage="\
-Usage: $0 [OPTION] CPU-MFR-OPSYS
-       $0 [OPTION] ALIAS
-
-Canonicalize a configuration name.
-
-Operation modes:
-  -h, --help         print this help, then exit
-  -t, --time-stamp   print date of last modification, then exit
-  -v, --version      print version number, then exit
-
-Report bugs and patches to <config-patches@gnu.org>."
-
-version="\
-GNU config.sub ($timestamp)
-
-Copyright 1992-2013 Free Software Foundation, Inc.
-
-This is free software; see the source for copying conditions.  There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
-
-help="
-Try \`$me --help' for more information."
-
-# Parse command line
-while test $# -gt 0 ; do
-  case $1 in
-    --time-stamp | --time* | -t )
-       echo "$timestamp" ; exit ;;
-    --version | -v )
-       echo "$version" ; exit ;;
-    --help | --h* | -h )
-       echo "$usage"; exit ;;
-    -- )     # Stop option processing
-       shift; break ;;
-    - )	# Use stdin as input.
-       break ;;
-    -* )
-       echo "$me: invalid option $1$help"
-       exit 1 ;;
-
-    *local*)
-       # First pass through any local machine types.
-       echo $1
-       exit ;;
-
-    * )
-       break ;;
-  esac
-done
-
-case $# in
- 0) echo "$me: missing argument$help" >&2
-    exit 1;;
- 1) ;;
- *) echo "$me: too many arguments$help" >&2
-    exit 1;;
-esac
-
-# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
-# Here we must recognize all the valid KERNEL-OS combinations.
-maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
-case $maybe_os in
-  nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \
-  linux-musl* | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \
-  knetbsd*-gnu* | netbsd*-gnu* | \
-  kopensolaris*-gnu* | \
-  storm-chaos* | os2-emx* | rtmk-nova*)
-    os=-$maybe_os
-    basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
-    ;;
-  android-linux)
-    os=-linux-android
-    basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
-    ;;
-  *)
-    basic_machine=`echo $1 | sed 's/-[^-]*$//'`
-    if [ $basic_machine != $1 ]
-    then os=`echo $1 | sed 's/.*-/-/'`
-    else os=; fi
-    ;;
-esac
-
-### Let's recognize common machines as not being operating systems so
-### that things like config.sub decstation-3100 work.  We also
-### recognize some manufacturers as not being operating systems, so we
-### can provide default operating systems below.
-case $os in
-	-sun*os*)
-		# Prevent following clause from handling this invalid input.
-		;;
-	-dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
-	-att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
-	-unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
-	-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
-	-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
-	-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
-	-apple | -axis | -knuth | -cray | -microblaze*)
-		os=
-		basic_machine=$1
-		;;
-	-bluegene*)
-		os=-cnk
-		;;
-	-sim | -cisco | -oki | -wec | -winbond)
-		os=
-		basic_machine=$1
-		;;
-	-scout)
-		;;
-	-wrs)
-		os=-vxworks
-		basic_machine=$1
-		;;
-	-chorusos*)
-		os=-chorusos
-		basic_machine=$1
-		;;
-	-chorusrdb)
-		os=-chorusrdb
-		basic_machine=$1
-		;;
-	-hiux*)
-		os=-hiuxwe2
-		;;
-	-sco6)
-		os=-sco5v6
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco5)
-		os=-sco3.2v5
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco4)
-		os=-sco3.2v4
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco3.2.[4-9]*)
-		os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco3.2v[4-9]*)
-		# Don't forget version if it is 3.2v4 or newer.
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco5v6*)
-		# Don't forget version if it is 3.2v4 or newer.
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco*)
-		os=-sco3.2v2
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-udk*)
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-isc)
-		os=-isc2.2
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-clix*)
-		basic_machine=clipper-intergraph
-		;;
-	-isc*)
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-lynx*178)
-		os=-lynxos178
-		;;
-	-lynx*5)
-		os=-lynxos5
-		;;
-	-lynx*)
-		os=-lynxos
-		;;
-	-ptx*)
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
-		;;
-	-windowsnt*)
-		os=`echo $os | sed -e 's/windowsnt/winnt/'`
-		;;
-	-psos*)
-		os=-psos
-		;;
-	-mint | -mint[0-9]*)
-		basic_machine=m68k-atari
-		os=-mint
-		;;
-esac
-
-# Decode aliases for certain CPU-COMPANY combinations.
-case $basic_machine in
-	# Recognize the basic CPU types without company name.
-	# Some are omitted here because they have special meanings below.
-	1750a | 580 \
-	| a29k \
-	| aarch64 | aarch64_be \
-	| alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
-	| alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
-	| am33_2.0 \
-	| arc | arceb \
-	| arm | arm[bl]e | arme[lb] | armv[2-8] | armv[3-8][lb] | armv7[arm] \
-	| avr | avr32 \
-	| be32 | be64 \
-	| bfin \
-	| c4x | clipper \
-	| d10v | d30v | dlx | dsp16xx \
-	| epiphany \
-	| fido | fr30 | frv \
-	| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
-	| hexagon \
-	| i370 | i860 | i960 | ia64 \
-	| ip2k | iq2000 \
-	| le32 | le64 \
-	| lm32 \
-	| m32c | m32r | m32rle | m68000 | m68k | m88k \
-	| maxq | mb | microblaze | microblazeel | mcore | mep | metag \
-	| mips | mipsbe | mipseb | mipsel | mipsle \
-	| mips16 \
-	| mips64 | mips64el \
-	| mips64octeon | mips64octeonel \
-	| mips64orion | mips64orionel \
-	| mips64r5900 | mips64r5900el \
-	| mips64vr | mips64vrel \
-	| mips64vr4100 | mips64vr4100el \
-	| mips64vr4300 | mips64vr4300el \
-	| mips64vr5000 | mips64vr5000el \
-	| mips64vr5900 | mips64vr5900el \
-	| mipsisa32 | mipsisa32el \
-	| mipsisa32r2 | mipsisa32r2el \
-	| mipsisa64 | mipsisa64el \
-	| mipsisa64r2 | mipsisa64r2el \
-	| mipsisa64sb1 | mipsisa64sb1el \
-	| mipsisa64sr71k | mipsisa64sr71kel \
-	| mipsr5900 | mipsr5900el \
-	| mipstx39 | mipstx39el \
-	| mn10200 | mn10300 \
-	| moxie \
-	| mt \
-	| msp430 \
-	| nds32 | nds32le | nds32be \
-	| nios | nios2 | nios2eb | nios2el \
-	| ns16k | ns32k \
-	| open8 \
-	| or1k | or32 \
-	| pdp10 | pdp11 | pj | pjl \
-	| powerpc | powerpc64 | powerpc64le | powerpcle \
-	| pyramid \
-	| rl78 | rx \
-	| score \
-	| sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
-	| sh64 | sh64le \
-	| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
-	| sparcv8 | sparcv9 | sparcv9b | sparcv9v \
-	| spu \
-	| tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \
-	| ubicom32 \
-	| v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \
-	| we32k \
-	| x86 | xc16x | xstormy16 | xtensa \
-	| z8k | z80)
-		basic_machine=$basic_machine-unknown
-		;;
-	c54x)
-		basic_machine=tic54x-unknown
-		;;
-	c55x)
-		basic_machine=tic55x-unknown
-		;;
-	c6x)
-		basic_machine=tic6x-unknown
-		;;
-	m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | picochip)
-		basic_machine=$basic_machine-unknown
-		os=-none
-		;;
-	m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
-		;;
-	ms1)
-		basic_machine=mt-unknown
-		;;
-
-	strongarm | thumb | xscale)
-		basic_machine=arm-unknown
-		;;
-	xgate)
-		basic_machine=$basic_machine-unknown
-		os=-none
-		;;
-	xscaleeb)
-		basic_machine=armeb-unknown
-		;;
-
-	xscaleel)
-		basic_machine=armel-unknown
-		;;
-
-	# We use `pc' rather than `unknown'
-	# because (1) that's what they normally are, and
-	# (2) the word "unknown" tends to confuse beginning users.
-	i*86 | x86_64)
-	  basic_machine=$basic_machine-pc
-	  ;;
-	# Object if more than one company name word.
-	*-*-*)
-		echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
-		exit 1
-		;;
-	# Recognize the basic CPU types with company name.
-	580-* \
-	| a29k-* \
-	| aarch64-* | aarch64_be-* \
-	| alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
-	| alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
-	| alphapca5[67]-* | alpha64pca5[67]-* | arc-* | arceb-* \
-	| arm-*  | armbe-* | armle-* | armeb-* | armv*-* \
-	| avr-* | avr32-* \
-	| be32-* | be64-* \
-	| bfin-* | bs2000-* \
-	| c[123]* | c30-* | [cjt]90-* | c4x-* \
-	| clipper-* | craynv-* | cydra-* \
-	| d10v-* | d30v-* | dlx-* \
-	| elxsi-* \
-	| f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
-	| h8300-* | h8500-* \
-	| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
-	| hexagon-* \
-	| i*86-* | i860-* | i960-* | ia64-* \
-	| ip2k-* | iq2000-* \
-	| le32-* | le64-* \
-	| lm32-* \
-	| m32c-* | m32r-* | m32rle-* \
-	| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
-	| m88110-* | m88k-* | maxq-* | mcore-* | metag-* \
-	| microblaze-* | microblazeel-* \
-	| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
-	| mips16-* \
-	| mips64-* | mips64el-* \
-	| mips64octeon-* | mips64octeonel-* \
-	| mips64orion-* | mips64orionel-* \
-	| mips64r5900-* | mips64r5900el-* \
-	| mips64vr-* | mips64vrel-* \
-	| mips64vr4100-* | mips64vr4100el-* \
-	| mips64vr4300-* | mips64vr4300el-* \
-	| mips64vr5000-* | mips64vr5000el-* \
-	| mips64vr5900-* | mips64vr5900el-* \
-	| mipsisa32-* | mipsisa32el-* \
-	| mipsisa32r2-* | mipsisa32r2el-* \
-	| mipsisa64-* | mipsisa64el-* \
-	| mipsisa64r2-* | mipsisa64r2el-* \
-	| mipsisa64sb1-* | mipsisa64sb1el-* \
-	| mipsisa64sr71k-* | mipsisa64sr71kel-* \
-	| mipsr5900-* | mipsr5900el-* \
-	| mipstx39-* | mipstx39el-* \
-	| mmix-* \
-	| mt-* \
-	| msp430-* \
-	| nds32-* | nds32le-* | nds32be-* \
-	| nios-* | nios2-* | nios2eb-* | nios2el-* \
-	| none-* | np1-* | ns16k-* | ns32k-* \
-	| open8-* \
-	| orion-* \
-	| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
-	| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
-	| pyramid-* \
-	| rl78-* | romp-* | rs6000-* | rx-* \
-	| sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
-	| shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
-	| sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
-	| sparclite-* \
-	| sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx?-* \
-	| tahoe-* \
-	| tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
-	| tile*-* \
-	| tron-* \
-	| ubicom32-* \
-	| v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \
-	| vax-* \
-	| we32k-* \
-	| x86-* | x86_64-* | xc16x-* | xps100-* \
-	| xstormy16-* | xtensa*-* \
-	| ymp-* \
-	| z8k-* | z80-*)
-		;;
-	# Recognize the basic CPU types without company name, with glob match.
-	xtensa*)
-		basic_machine=$basic_machine-unknown
-		;;
-	# Recognize the various machine names and aliases which stand
-	# for a CPU type and a company and sometimes even an OS.
-	386bsd)
-		basic_machine=i386-unknown
-		os=-bsd
-		;;
-	3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
-		basic_machine=m68000-att
-		;;
-	3b*)
-		basic_machine=we32k-att
-		;;
-	a29khif)
-		basic_machine=a29k-amd
-		os=-udi
-		;;
-	abacus)
-		basic_machine=abacus-unknown
-		;;
-	adobe68k)
-		basic_machine=m68010-adobe
-		os=-scout
-		;;
-	alliant | fx80)
-		basic_machine=fx80-alliant
-		;;
-	altos | altos3068)
-		basic_machine=m68k-altos
-		;;
-	am29k)
-		basic_machine=a29k-none
-		os=-bsd
-		;;
-	amd64)
-		basic_machine=x86_64-pc
-		;;
-	amd64-*)
-		basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	amdahl)
-		basic_machine=580-amdahl
-		os=-sysv
-		;;
-	amiga | amiga-*)
-		basic_machine=m68k-unknown
-		;;
-	amigaos | amigados)
-		basic_machine=m68k-unknown
-		os=-amigaos
-		;;
-	amigaunix | amix)
-		basic_machine=m68k-unknown
-		os=-sysv4
-		;;
-	apollo68)
-		basic_machine=m68k-apollo
-		os=-sysv
-		;;
-	apollo68bsd)
-		basic_machine=m68k-apollo
-		os=-bsd
-		;;
-	aros)
-		basic_machine=i386-pc
-		os=-aros
-		;;
-	aux)
-		basic_machine=m68k-apple
-		os=-aux
-		;;
-	balance)
-		basic_machine=ns32k-sequent
-		os=-dynix
-		;;
-	blackfin)
-		basic_machine=bfin-unknown
-		os=-linux
-		;;
-	blackfin-*)
-		basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
-		os=-linux
-		;;
-	bluegene*)
-		basic_machine=powerpc-ibm
-		os=-cnk
-		;;
-	c54x-*)
-		basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	c55x-*)
-		basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	c6x-*)
-		basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	c90)
-		basic_machine=c90-cray
-		os=-unicos
-		;;
-	cegcc)
-		basic_machine=arm-unknown
-		os=-cegcc
-		;;
-	convex-c1)
-		basic_machine=c1-convex
-		os=-bsd
-		;;
-	convex-c2)
-		basic_machine=c2-convex
-		os=-bsd
-		;;
-	convex-c32)
-		basic_machine=c32-convex
-		os=-bsd
-		;;
-	convex-c34)
-		basic_machine=c34-convex
-		os=-bsd
-		;;
-	convex-c38)
-		basic_machine=c38-convex
-		os=-bsd
-		;;
-	cray | j90)
-		basic_machine=j90-cray
-		os=-unicos
-		;;
-	craynv)
-		basic_machine=craynv-cray
-		os=-unicosmp
-		;;
-	cr16 | cr16-*)
-		basic_machine=cr16-unknown
-		os=-elf
-		;;
-	crds | unos)
-		basic_machine=m68k-crds
-		;;
-	crisv32 | crisv32-* | etraxfs*)
-		basic_machine=crisv32-axis
-		;;
-	cris | cris-* | etrax*)
-		basic_machine=cris-axis
-		;;
-	crx)
-		basic_machine=crx-unknown
-		os=-elf
-		;;
-	da30 | da30-*)
-		basic_machine=m68k-da30
-		;;
-	decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
-		basic_machine=mips-dec
-		;;
-	decsystem10* | dec10*)
-		basic_machine=pdp10-dec
-		os=-tops10
-		;;
-	decsystem20* | dec20*)
-		basic_machine=pdp10-dec
-		os=-tops20
-		;;
-	delta | 3300 | motorola-3300 | motorola-delta \
-	      | 3300-motorola | delta-motorola)
-		basic_machine=m68k-motorola
-		;;
-	delta88)
-		basic_machine=m88k-motorola
-		os=-sysv3
-		;;
-	dicos)
-		basic_machine=i686-pc
-		os=-dicos
-		;;
-	djgpp)
-		basic_machine=i586-pc
-		os=-msdosdjgpp
-		;;
-	dpx20 | dpx20-*)
-		basic_machine=rs6000-bull
-		os=-bosx
-		;;
-	dpx2* | dpx2*-bull)
-		basic_machine=m68k-bull
-		os=-sysv3
-		;;
-	ebmon29k)
-		basic_machine=a29k-amd
-		os=-ebmon
-		;;
-	elxsi)
-		basic_machine=elxsi-elxsi
-		os=-bsd
-		;;
-	encore | umax | mmax)
-		basic_machine=ns32k-encore
-		;;
-	es1800 | OSE68k | ose68k | ose | OSE)
-		basic_machine=m68k-ericsson
-		os=-ose
-		;;
-	fx2800)
-		basic_machine=i860-alliant
-		;;
-	genix)
-		basic_machine=ns32k-ns
-		;;
-	gmicro)
-		basic_machine=tron-gmicro
-		os=-sysv
-		;;
-	go32)
-		basic_machine=i386-pc
-		os=-go32
-		;;
-	h3050r* | hiux*)
-		basic_machine=hppa1.1-hitachi
-		os=-hiuxwe2
-		;;
-	h8300hms)
-		basic_machine=h8300-hitachi
-		os=-hms
-		;;
-	h8300xray)
-		basic_machine=h8300-hitachi
-		os=-xray
-		;;
-	h8500hms)
-		basic_machine=h8500-hitachi
-		os=-hms
-		;;
-	harris)
-		basic_machine=m88k-harris
-		os=-sysv3
-		;;
-	hp300-*)
-		basic_machine=m68k-hp
-		;;
-	hp300bsd)
-		basic_machine=m68k-hp
-		os=-bsd
-		;;
-	hp300hpux)
-		basic_machine=m68k-hp
-		os=-hpux
-		;;
-	hp3k9[0-9][0-9] | hp9[0-9][0-9])
-		basic_machine=hppa1.0-hp
-		;;
-	hp9k2[0-9][0-9] | hp9k31[0-9])
-		basic_machine=m68000-hp
-		;;
-	hp9k3[2-9][0-9])
-		basic_machine=m68k-hp
-		;;
-	hp9k6[0-9][0-9] | hp6[0-9][0-9])
-		basic_machine=hppa1.0-hp
-		;;
-	hp9k7[0-79][0-9] | hp7[0-79][0-9])
-		basic_machine=hppa1.1-hp
-		;;
-	hp9k78[0-9] | hp78[0-9])
-		# FIXME: really hppa2.0-hp
-		basic_machine=hppa1.1-hp
-		;;
-	hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
-		# FIXME: really hppa2.0-hp
-		basic_machine=hppa1.1-hp
-		;;
-	hp9k8[0-9][13679] | hp8[0-9][13679])
-		basic_machine=hppa1.1-hp
-		;;
-	hp9k8[0-9][0-9] | hp8[0-9][0-9])
-		basic_machine=hppa1.0-hp
-		;;
-	hppa-next)
-		os=-nextstep3
-		;;
-	hppaosf)
-		basic_machine=hppa1.1-hp
-		os=-osf
-		;;
-	hppro)
-		basic_machine=hppa1.1-hp
-		os=-proelf
-		;;
-	i370-ibm* | ibm*)
-		basic_machine=i370-ibm
-		;;
-	i*86v32)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
-		os=-sysv32
-		;;
-	i*86v4*)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
-		os=-sysv4
-		;;
-	i*86v)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
-		os=-sysv
-		;;
-	i*86sol2)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
-		os=-solaris2
-		;;
-	i386mach)
-		basic_machine=i386-mach
-		os=-mach
-		;;
-	i386-vsta | vsta)
-		basic_machine=i386-unknown
-		os=-vsta
-		;;
-	iris | iris4d)
-		basic_machine=mips-sgi
-		case $os in
-		    -irix*)
-			;;
-		    *)
-			os=-irix4
-			;;
-		esac
-		;;
-	isi68 | isi)
-		basic_machine=m68k-isi
-		os=-sysv
-		;;
-	m68knommu)
-		basic_machine=m68k-unknown
-		os=-linux
-		;;
-	m68knommu-*)
-		basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'`
-		os=-linux
-		;;
-	m88k-omron*)
-		basic_machine=m88k-omron
-		;;
-	magnum | m3230)
-		basic_machine=mips-mips
-		os=-sysv
-		;;
-	merlin)
-		basic_machine=ns32k-utek
-		os=-sysv
-		;;
-	microblaze*)
-		basic_machine=microblaze-xilinx
-		;;
-	mingw64)
-		basic_machine=x86_64-pc
-		os=-mingw64
-		;;
-	mingw32)
-		basic_machine=i386-pc
-		os=-mingw32
-		;;
-	mingw32ce)
-		basic_machine=arm-unknown
-		os=-mingw32ce
-		;;
-	miniframe)
-		basic_machine=m68000-convergent
-		;;
-	*mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
-		basic_machine=m68k-atari
-		os=-mint
-		;;
-	mips3*-*)
-		basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
-		;;
-	mips3*)
-		basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
-		;;
-	monitor)
-		basic_machine=m68k-rom68k
-		os=-coff
-		;;
-	morphos)
-		basic_machine=powerpc-unknown
-		os=-morphos
-		;;
-	msdos)
-		basic_machine=i386-pc
-		os=-msdos
-		;;
-	ms1-*)
-		basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
-		;;
-	msys)
-		basic_machine=i386-pc
-		os=-msys
-		;;
-	mvs)
-		basic_machine=i370-ibm
-		os=-mvs
-		;;
-	nacl)
-		basic_machine=le32-unknown
-		os=-nacl
-		;;
-	ncr3000)
-		basic_machine=i486-ncr
-		os=-sysv4
-		;;
-	netbsd386)
-		basic_machine=i386-unknown
-		os=-netbsd
-		;;
-	netwinder)
-		basic_machine=armv4l-rebel
-		os=-linux
-		;;
-	news | news700 | news800 | news900)
-		basic_machine=m68k-sony
-		os=-newsos
-		;;
-	news1000)
-		basic_machine=m68030-sony
-		os=-newsos
-		;;
-	news-3600 | risc-news)
-		basic_machine=mips-sony
-		os=-newsos
-		;;
-	necv70)
-		basic_machine=v70-nec
-		os=-sysv
-		;;
-	next | m*-next )
-		basic_machine=m68k-next
-		case $os in
-		    -nextstep* )
-			;;
-		    -ns2*)
-		      os=-nextstep2
-			;;
-		    *)
-		      os=-nextstep3
-			;;
-		esac
-		;;
-	nh3000)
-		basic_machine=m68k-harris
-		os=-cxux
-		;;
-	nh[45]000)
-		basic_machine=m88k-harris
-		os=-cxux
-		;;
-	nindy960)
-		basic_machine=i960-intel
-		os=-nindy
-		;;
-	mon960)
-		basic_machine=i960-intel
-		os=-mon960
-		;;
-	nonstopux)
-		basic_machine=mips-compaq
-		os=-nonstopux
-		;;
-	np1)
-		basic_machine=np1-gould
-		;;
-	neo-tandem)
-		basic_machine=neo-tandem
-		;;
-	nse-tandem)
-		basic_machine=nse-tandem
-		;;
-	nsr-tandem)
-		basic_machine=nsr-tandem
-		;;
-	op50n-* | op60c-*)
-		basic_machine=hppa1.1-oki
-		os=-proelf
-		;;
-	openrisc | openrisc-*)
-		basic_machine=or32-unknown
-		;;
-	os400)
-		basic_machine=powerpc-ibm
-		os=-os400
-		;;
-	OSE68000 | ose68000)
-		basic_machine=m68000-ericsson
-		os=-ose
-		;;
-	os68k)
-		basic_machine=m68k-none
-		os=-os68k
-		;;
-	pa-hitachi)
-		basic_machine=hppa1.1-hitachi
-		os=-hiuxwe2
-		;;
-	paragon)
-		basic_machine=i860-intel
-		os=-osf
-		;;
-	parisc)
-		basic_machine=hppa-unknown
-		os=-linux
-		;;
-	parisc-*)
-		basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'`
-		os=-linux
-		;;
-	pbd)
-		basic_machine=sparc-tti
-		;;
-	pbb)
-		basic_machine=m68k-tti
-		;;
-	pc532 | pc532-*)
-		basic_machine=ns32k-pc532
-		;;
-	pc98)
-		basic_machine=i386-pc
-		;;
-	pc98-*)
-		basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pentium | p5 | k5 | k6 | nexgen | viac3)
-		basic_machine=i586-pc
-		;;
-	pentiumpro | p6 | 6x86 | athlon | athlon_*)
-		basic_machine=i686-pc
-		;;
-	pentiumii | pentium2 | pentiumiii | pentium3)
-		basic_machine=i686-pc
-		;;
-	pentium4)
-		basic_machine=i786-pc
-		;;
-	pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
-		basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pentiumpro-* | p6-* | 6x86-* | athlon-*)
-		basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
-		basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pentium4-*)
-		basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pn)
-		basic_machine=pn-gould
-		;;
-	power)	basic_machine=power-ibm
-		;;
-	ppc | ppcbe)	basic_machine=powerpc-unknown
-		;;
-	ppc-* | ppcbe-*)
-		basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	ppcle | powerpclittle | ppc-le | powerpc-little)
-		basic_machine=powerpcle-unknown
-		;;
-	ppcle-* | powerpclittle-*)
-		basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	ppc64)	basic_machine=powerpc64-unknown
-		;;
-	ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	ppc64le | powerpc64little | ppc64-le | powerpc64-little)
-		basic_machine=powerpc64le-unknown
-		;;
-	ppc64le-* | powerpc64little-*)
-		basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	ps2)
-		basic_machine=i386-ibm
-		;;
-	pw32)
-		basic_machine=i586-unknown
-		os=-pw32
-		;;
-	rdos | rdos64)
-		basic_machine=x86_64-pc
-		os=-rdos
-		;;
-	rdos32)
-		basic_machine=i386-pc
-		os=-rdos
-		;;
-	rom68k)
-		basic_machine=m68k-rom68k
-		os=-coff
-		;;
-	rm[46]00)
-		basic_machine=mips-siemens
-		;;
-	rtpc | rtpc-*)
-		basic_machine=romp-ibm
-		;;
-	s390 | s390-*)
-		basic_machine=s390-ibm
-		;;
-	s390x | s390x-*)
-		basic_machine=s390x-ibm
-		;;
-	sa29200)
-		basic_machine=a29k-amd
-		os=-udi
-		;;
-	sb1)
-		basic_machine=mipsisa64sb1-unknown
-		;;
-	sb1el)
-		basic_machine=mipsisa64sb1el-unknown
-		;;
-	sde)
-		basic_machine=mipsisa32-sde
-		os=-elf
-		;;
-	sei)
-		basic_machine=mips-sei
-		os=-seiux
-		;;
-	sequent)
-		basic_machine=i386-sequent
-		;;
-	sh)
-		basic_machine=sh-hitachi
-		os=-hms
-		;;
-	sh5el)
-		basic_machine=sh5le-unknown
-		;;
-	sh64)
-		basic_machine=sh64-unknown
-		;;
-	sparclite-wrs | simso-wrs)
-		basic_machine=sparclite-wrs
-		os=-vxworks
-		;;
-	sps7)
-		basic_machine=m68k-bull
-		os=-sysv2
-		;;
-	spur)
-		basic_machine=spur-unknown
-		;;
-	st2000)
-		basic_machine=m68k-tandem
-		;;
-	stratus)
-		basic_machine=i860-stratus
-		os=-sysv4
-		;;
-	strongarm-* | thumb-*)
-		basic_machine=arm-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	sun2)
-		basic_machine=m68000-sun
-		;;
-	sun2os3)
-		basic_machine=m68000-sun
-		os=-sunos3
-		;;
-	sun2os4)
-		basic_machine=m68000-sun
-		os=-sunos4
-		;;
-	sun3os3)
-		basic_machine=m68k-sun
-		os=-sunos3
-		;;
-	sun3os4)
-		basic_machine=m68k-sun
-		os=-sunos4
-		;;
-	sun4os3)
-		basic_machine=sparc-sun
-		os=-sunos3
-		;;
-	sun4os4)
-		basic_machine=sparc-sun
-		os=-sunos4
-		;;
-	sun4sol2)
-		basic_machine=sparc-sun
-		os=-solaris2
-		;;
-	sun3 | sun3-*)
-		basic_machine=m68k-sun
-		;;
-	sun4)
-		basic_machine=sparc-sun
-		;;
-	sun386 | sun386i | roadrunner)
-		basic_machine=i386-sun
-		;;
-	sv1)
-		basic_machine=sv1-cray
-		os=-unicos
-		;;
-	symmetry)
-		basic_machine=i386-sequent
-		os=-dynix
-		;;
-	t3e)
-		basic_machine=alphaev5-cray
-		os=-unicos
-		;;
-	t90)
-		basic_machine=t90-cray
-		os=-unicos
-		;;
-	tile*)
-		basic_machine=$basic_machine-unknown
-		os=-linux-gnu
-		;;
-	tx39)
-		basic_machine=mipstx39-unknown
-		;;
-	tx39el)
-		basic_machine=mipstx39el-unknown
-		;;
-	toad1)
-		basic_machine=pdp10-xkl
-		os=-tops20
-		;;
-	tower | tower-32)
-		basic_machine=m68k-ncr
-		;;
-	tpf)
-		basic_machine=s390x-ibm
-		os=-tpf
-		;;
-	udi29k)
-		basic_machine=a29k-amd
-		os=-udi
-		;;
-	ultra3)
-		basic_machine=a29k-nyu
-		os=-sym1
-		;;
-	v810 | necv810)
-		basic_machine=v810-nec
-		os=-none
-		;;
-	vaxv)
-		basic_machine=vax-dec
-		os=-sysv
-		;;
-	vms)
-		basic_machine=vax-dec
-		os=-vms
-		;;
-	vpp*|vx|vx-*)
-		basic_machine=f301-fujitsu
-		;;
-	vxworks960)
-		basic_machine=i960-wrs
-		os=-vxworks
-		;;
-	vxworks68)
-		basic_machine=m68k-wrs
-		os=-vxworks
-		;;
-	vxworks29k)
-		basic_machine=a29k-wrs
-		os=-vxworks
-		;;
-	w65*)
-		basic_machine=w65-wdc
-		os=-none
-		;;
-	w89k-*)
-		basic_machine=hppa1.1-winbond
-		os=-proelf
-		;;
-	xbox)
-		basic_machine=i686-pc
-		os=-mingw32
-		;;
-	xps | xps100)
-		basic_machine=xps100-honeywell
-		;;
-	xscale-* | xscalee[bl]-*)
-		basic_machine=`echo $basic_machine | sed 's/^xscale/arm/'`
-		;;
-	ymp)
-		basic_machine=ymp-cray
-		os=-unicos
-		;;
-	z8k-*-coff)
-		basic_machine=z8k-unknown
-		os=-sim
-		;;
-	z80-*-coff)
-		basic_machine=z80-unknown
-		os=-sim
-		;;
-	none)
-		basic_machine=none-none
-		os=-none
-		;;
-
-# Here we handle the default manufacturer of certain CPU types.  It is in
-# some cases the only manufacturer, in others, it is the most popular.
-	w89k)
-		basic_machine=hppa1.1-winbond
-		;;
-	op50n)
-		basic_machine=hppa1.1-oki
-		;;
-	op60c)
-		basic_machine=hppa1.1-oki
-		;;
-	romp)
-		basic_machine=romp-ibm
-		;;
-	mmix)
-		basic_machine=mmix-knuth
-		;;
-	rs6000)
-		basic_machine=rs6000-ibm
-		;;
-	vax)
-		basic_machine=vax-dec
-		;;
-	pdp10)
-		# there are many clones, so DEC is not a safe bet
-		basic_machine=pdp10-unknown
-		;;
-	pdp11)
-		basic_machine=pdp11-dec
-		;;
-	we32k)
-		basic_machine=we32k-att
-		;;
-	sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele)
-		basic_machine=sh-unknown
-		;;
-	sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
-		basic_machine=sparc-sun
-		;;
-	cydra)
-		basic_machine=cydra-cydrome
-		;;
-	orion)
-		basic_machine=orion-highlevel
-		;;
-	orion105)
-		basic_machine=clipper-highlevel
-		;;
-	mac | mpw | mac-mpw)
-		basic_machine=m68k-apple
-		;;
-	pmac | pmac-mpw)
-		basic_machine=powerpc-apple
-		;;
-	*-unknown)
-		# Make sure to match an already-canonicalized machine name.
-		;;
-	*)
-		echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
-		exit 1
-		;;
-esac
-
-# Here we canonicalize certain aliases for manufacturers.
-case $basic_machine in
-	*-digital*)
-		basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
-		;;
-	*-commodore*)
-		basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
-		;;
-	*)
-		;;
-esac
-
-# Decode manufacturer-specific aliases for certain operating systems.
-
-if [ x"$os" != x"" ]
-then
-case $os in
-	# First match some system type aliases
-	# that might get confused with valid system types.
-	# -solaris* is a basic system type, with this one exception.
-	-auroraux)
-		os=-auroraux
-		;;
-	-solaris1 | -solaris1.*)
-		os=`echo $os | sed -e 's|solaris1|sunos4|'`
-		;;
-	-solaris)
-		os=-solaris2
-		;;
-	-svr4*)
-		os=-sysv4
-		;;
-	-unixware*)
-		os=-sysv4.2uw
-		;;
-	-gnu/linux*)
-		os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
-		;;
-	# First accept the basic system types.
-	# The portable systems comes first.
-	# Each alternative MUST END IN A *, to match a version number.
-	# -sysv* is not here because it comes later, after sysvr4.
-	-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
-	      | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
-	      | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
-	      | -sym* | -kopensolaris* | -plan9* \
-	      | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
-	      | -aos* | -aros* \
-	      | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
-	      | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
-	      | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
-	      | -bitrig* | -openbsd* | -solidbsd* \
-	      | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
-	      | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
-	      | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
-	      | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
-	      | -chorusos* | -chorusrdb* | -cegcc* \
-	      | -cygwin* | -msys* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
-	      | -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \
-	      | -linux-newlib* | -linux-musl* | -linux-uclibc* \
-	      | -uxpv* | -beos* | -mpeix* | -udk* \
-	      | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
-	      | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
-	      | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
-	      | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
-	      | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
-	      | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
-	      | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*)
-	# Remember, each alternative MUST END IN *, to match a version number.
-		;;
-	-qnx*)
-		case $basic_machine in
-		    x86-* | i*86-*)
-			;;
-		    *)
-			os=-nto$os
-			;;
-		esac
-		;;
-	-nto-qnx*)
-		;;
-	-nto*)
-		os=`echo $os | sed -e 's|nto|nto-qnx|'`
-		;;
-	-sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
-	      | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
-	      | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
-		;;
-	-mac*)
-		os=`echo $os | sed -e 's|mac|macos|'`
-		;;
-	-linux-dietlibc)
-		os=-linux-dietlibc
-		;;
-	-linux*)
-		os=`echo $os | sed -e 's|linux|linux-gnu|'`
-		;;
-	-sunos5*)
-		os=`echo $os | sed -e 's|sunos5|solaris2|'`
-		;;
-	-sunos6*)
-		os=`echo $os | sed -e 's|sunos6|solaris3|'`
-		;;
-	-opened*)
-		os=-openedition
-		;;
-	-os400*)
-		os=-os400
-		;;
-	-wince*)
-		os=-wince
-		;;
-	-osfrose*)
-		os=-osfrose
-		;;
-	-osf*)
-		os=-osf
-		;;
-	-utek*)
-		os=-bsd
-		;;
-	-dynix*)
-		os=-bsd
-		;;
-	-acis*)
-		os=-aos
-		;;
-	-atheos*)
-		os=-atheos
-		;;
-	-syllable*)
-		os=-syllable
-		;;
-	-386bsd)
-		os=-bsd
-		;;
-	-ctix* | -uts*)
-		os=-sysv
-		;;
-	-nova*)
-		os=-rtmk-nova
-		;;
-	-ns2 )
-		os=-nextstep2
-		;;
-	-nsk*)
-		os=-nsk
-		;;
-	# Preserve the version number of sinix5.
-	-sinix5.*)
-		os=`echo $os | sed -e 's|sinix|sysv|'`
-		;;
-	-sinix*)
-		os=-sysv4
-		;;
-	-tpf*)
-		os=-tpf
-		;;
-	-triton*)
-		os=-sysv3
-		;;
-	-oss*)
-		os=-sysv3
-		;;
-	-svr4)
-		os=-sysv4
-		;;
-	-svr3)
-		os=-sysv3
-		;;
-	-sysvr4)
-		os=-sysv4
-		;;
-	# This must come after -sysvr4.
-	-sysv*)
-		;;
-	-ose*)
-		os=-ose
-		;;
-	-es1800*)
-		os=-ose
-		;;
-	-xenix)
-		os=-xenix
-		;;
-	-*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
-		os=-mint
-		;;
-	-aros*)
-		os=-aros
-		;;
-	-zvmoe)
-		os=-zvmoe
-		;;
-	-dicos*)
-		os=-dicos
-		;;
-	-nacl*)
-		;;
-	-none)
-		;;
-	*)
-		# Get rid of the `-' at the beginning of $os.
-		os=`echo $os | sed 's/[^-]*-//'`
-		echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
-		exit 1
-		;;
-esac
-else
-
-# Here we handle the default operating systems that come with various machines.
-# The value should be what the vendor currently ships out the door with their
-# machine or put another way, the most popular os provided with the machine.
-
-# Note that if you're going to try to match "-MANUFACTURER" here (say,
-# "-sun"), then you have to tell the case statement up towards the top
-# that MANUFACTURER isn't an operating system.  Otherwise, code above
-# will signal an error saying that MANUFACTURER isn't an operating
-# system, and we'll never get to this point.
-
-case $basic_machine in
-	score-*)
-		os=-elf
-		;;
-	spu-*)
-		os=-elf
-		;;
-	*-acorn)
-		os=-riscix1.2
-		;;
-	arm*-rebel)
-		os=-linux
-		;;
-	arm*-semi)
-		os=-aout
-		;;
-	c4x-* | tic4x-*)
-		os=-coff
-		;;
-	hexagon-*)
-		os=-elf
-		;;
-	tic54x-*)
-		os=-coff
-		;;
-	tic55x-*)
-		os=-coff
-		;;
-	tic6x-*)
-		os=-coff
-		;;
-	# This must come before the *-dec entry.
-	pdp10-*)
-		os=-tops20
-		;;
-	pdp11-*)
-		os=-none
-		;;
-	*-dec | vax-*)
-		os=-ultrix4.2
-		;;
-	m68*-apollo)
-		os=-domain
-		;;
-	i386-sun)
-		os=-sunos4.0.2
-		;;
-	m68000-sun)
-		os=-sunos3
-		;;
-	m68*-cisco)
-		os=-aout
-		;;
-	mep-*)
-		os=-elf
-		;;
-	mips*-cisco)
-		os=-elf
-		;;
-	mips*-*)
-		os=-elf
-		;;
-	or1k-*)
-		os=-elf
-		;;
-	or32-*)
-		os=-coff
-		;;
-	*-tti)	# must be before sparc entry or we get the wrong os.
-		os=-sysv3
-		;;
-	sparc-* | *-sun)
-		os=-sunos4.1.1
-		;;
-	*-be)
-		os=-beos
-		;;
-	*-haiku)
-		os=-haiku
-		;;
-	*-ibm)
-		os=-aix
-		;;
-	*-knuth)
-		os=-mmixware
-		;;
-	*-wec)
-		os=-proelf
-		;;
-	*-winbond)
-		os=-proelf
-		;;
-	*-oki)
-		os=-proelf
-		;;
-	*-hp)
-		os=-hpux
-		;;
-	*-hitachi)
-		os=-hiux
-		;;
-	i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
-		os=-sysv
-		;;
-	*-cbm)
-		os=-amigaos
-		;;
-	*-dg)
-		os=-dgux
-		;;
-	*-dolphin)
-		os=-sysv3
-		;;
-	m68k-ccur)
-		os=-rtu
-		;;
-	m88k-omron*)
-		os=-luna
-		;;
-	*-next )
-		os=-nextstep
-		;;
-	*-sequent)
-		os=-ptx
-		;;
-	*-crds)
-		os=-unos
-		;;
-	*-ns)
-		os=-genix
-		;;
-	i370-*)
-		os=-mvs
-		;;
-	*-next)
-		os=-nextstep3
-		;;
-	*-gould)
-		os=-sysv
-		;;
-	*-highlevel)
-		os=-bsd
-		;;
-	*-encore)
-		os=-bsd
-		;;
-	*-sgi)
-		os=-irix
-		;;
-	*-siemens)
-		os=-sysv4
-		;;
-	*-masscomp)
-		os=-rtu
-		;;
-	f30[01]-fujitsu | f700-fujitsu)
-		os=-uxpv
-		;;
-	*-rom68k)
-		os=-coff
-		;;
-	*-*bug)
-		os=-coff
-		;;
-	*-apple)
-		os=-macos
-		;;
-	*-atari*)
-		os=-mint
-		;;
-	*)
-		os=-none
-		;;
-esac
-fi
-
-# Here we handle the case where we know the os, and the CPU type, but not the
-# manufacturer.  We pick the logical manufacturer.
-vendor=unknown
-case $basic_machine in
-	*-unknown)
-		case $os in
-			-riscix*)
-				vendor=acorn
-				;;
-			-sunos*)
-				vendor=sun
-				;;
-			-cnk*|-aix*)
-				vendor=ibm
-				;;
-			-beos*)
-				vendor=be
-				;;
-			-hpux*)
-				vendor=hp
-				;;
-			-mpeix*)
-				vendor=hp
-				;;
-			-hiux*)
-				vendor=hitachi
-				;;
-			-unos*)
-				vendor=crds
-				;;
-			-dgux*)
-				vendor=dg
-				;;
-			-luna*)
-				vendor=omron
-				;;
-			-genix*)
-				vendor=ns
-				;;
-			-mvs* | -opened*)
-				vendor=ibm
-				;;
-			-os400*)
-				vendor=ibm
-				;;
-			-ptx*)
-				vendor=sequent
-				;;
-			-tpf*)
-				vendor=ibm
-				;;
-			-vxsim* | -vxworks* | -windiss*)
-				vendor=wrs
-				;;
-			-aux*)
-				vendor=apple
-				;;
-			-hms*)
-				vendor=hitachi
-				;;
-			-mpw* | -macos*)
-				vendor=apple
-				;;
-			-*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
-				vendor=atari
-				;;
-			-vos*)
-				vendor=stratus
-				;;
-		esac
-		basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
-		;;
-esac
-
-echo $basic_machine$os
-exit
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "timestamp='"
-# time-stamp-format: "%:y-%02m-%02d"
-# time-stamp-end: "'"
-# End:
diff --git a/build-aux/install-sh b/build-aux/install-sh
deleted file mode 100755
index 377bb8687f..0000000000
--- a/build-aux/install-sh
+++ /dev/null
@@ -1,527 +0,0 @@
-#!/bin/sh
-# install - install a program, script, or datafile
-
-scriptversion=2011-11-20.07; # UTC
-
-# This originates from X11R5 (mit/util/scripts/install.sh), which was
-# later released in X11R6 (xc/config/util/install.sh) with the
-# following copyright and license.
-#
-# Copyright (C) 1994 X Consortium
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to
-# deal in the Software without restriction, including without limitation the
-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-# sell copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
-# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
-# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
-# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-#
-# Except as contained in this notice, the name of the X Consortium shall not
-# be used in advertising or otherwise to promote the sale, use or other deal-
-# ings in this Software without prior written authorization from the X Consor-
-# tium.
-#
-#
-# FSF changes to this file are in the public domain.
-#
-# Calling this script install-sh is preferred over install.sh, to prevent
-# 'make' implicit rules from creating a file called install from it
-# when there is no Makefile.
-#
-# This script is compatible with the BSD install script, but was written
-# from scratch.
-
-nl='
-'
-IFS=" ""	$nl"
-
-# set DOITPROG to echo to test this script
-
-# Don't use :- since 4.3BSD and earlier shells don't like it.
-doit=${DOITPROG-}
-if test -z "$doit"; then
-  doit_exec=exec
-else
-  doit_exec=$doit
-fi
-
-# Put in absolute file names if you don't have them in your path;
-# or use environment vars.
-
-chgrpprog=${CHGRPPROG-chgrp}
-chmodprog=${CHMODPROG-chmod}
-chownprog=${CHOWNPROG-chown}
-cmpprog=${CMPPROG-cmp}
-cpprog=${CPPROG-cp}
-mkdirprog=${MKDIRPROG-mkdir}
-mvprog=${MVPROG-mv}
-rmprog=${RMPROG-rm}
-stripprog=${STRIPPROG-strip}
-
-posix_glob='?'
-initialize_posix_glob='
-  test "$posix_glob" != "?" || {
-    if (set -f) 2>/dev/null; then
-      posix_glob=
-    else
-      posix_glob=:
-    fi
-  }
-'
-
-posix_mkdir=
-
-# Desired mode of installed file.
-mode=0755
-
-chgrpcmd=
-chmodcmd=$chmodprog
-chowncmd=
-mvcmd=$mvprog
-rmcmd="$rmprog -f"
-stripcmd=
-
-src=
-dst=
-dir_arg=
-dst_arg=
-
-copy_on_change=false
-no_target_directory=
-
-usage="\
-Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
-   or: $0 [OPTION]... SRCFILES... DIRECTORY
-   or: $0 [OPTION]... -t DIRECTORY SRCFILES...
-   or: $0 [OPTION]... -d DIRECTORIES...
-
-In the 1st form, copy SRCFILE to DSTFILE.
-In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
-In the 4th, create DIRECTORIES.
-
-Options:
-     --help     display this help and exit.
-     --version  display version info and exit.
-
-  -c            (ignored)
-  -C            install only if different (preserve the last data modification time)
-  -d            create directories instead of installing files.
-  -g GROUP      $chgrpprog installed files to GROUP.
-  -m MODE       $chmodprog installed files to MODE.
-  -o USER       $chownprog installed files to USER.
-  -s            $stripprog installed files.
-  -t DIRECTORY  install into DIRECTORY.
-  -T            report an error if DSTFILE is a directory.
-
-Environment variables override the default commands:
-  CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
-  RMPROG STRIPPROG
-"
-
-while test $# -ne 0; do
-  case $1 in
-    -c) ;;
-
-    -C) copy_on_change=true;;
-
-    -d) dir_arg=true;;
-
-    -g) chgrpcmd="$chgrpprog $2"
-	shift;;
-
-    --help) echo "$usage"; exit $?;;
-
-    -m) mode=$2
-	case $mode in
-	  *' '* | *'	'* | *'
-'*	  | *'*'* | *'?'* | *'['*)
-	    echo "$0: invalid mode: $mode" >&2
-	    exit 1;;
-	esac
-	shift;;
-
-    -o) chowncmd="$chownprog $2"
-	shift;;
-
-    -s) stripcmd=$stripprog;;
-
-    -t) dst_arg=$2
-	# Protect names problematic for 'test' and other utilities.
-	case $dst_arg in
-	  -* | [=\(\)!]) dst_arg=./$dst_arg;;
-	esac
-	shift;;
-
-    -T) no_target_directory=true;;
-
-    --version) echo "$0 $scriptversion"; exit $?;;
-
-    --)	shift
-	break;;
-
-    -*)	echo "$0: invalid option: $1" >&2
-	exit 1;;
-
-    *)  break;;
-  esac
-  shift
-done
-
-if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
-  # When -d is used, all remaining arguments are directories to create.
-  # When -t is used, the destination is already specified.
-  # Otherwise, the last argument is the destination.  Remove it from $@.
-  for arg
-  do
-    if test -n "$dst_arg"; then
-      # $@ is not empty: it contains at least $arg.
-      set fnord "$@" "$dst_arg"
-      shift # fnord
-    fi
-    shift # arg
-    dst_arg=$arg
-    # Protect names problematic for 'test' and other utilities.
-    case $dst_arg in
-      -* | [=\(\)!]) dst_arg=./$dst_arg;;
-    esac
-  done
-fi
-
-if test $# -eq 0; then
-  if test -z "$dir_arg"; then
-    echo "$0: no input file specified." >&2
-    exit 1
-  fi
-  # It's OK to call 'install-sh -d' without argument.
-  # This can happen when creating conditional directories.
-  exit 0
-fi
-
-if test -z "$dir_arg"; then
-  do_exit='(exit $ret); exit $ret'
-  trap "ret=129; $do_exit" 1
-  trap "ret=130; $do_exit" 2
-  trap "ret=141; $do_exit" 13
-  trap "ret=143; $do_exit" 15
-
-  # Set umask so as not to create temps with too-generous modes.
-  # However, 'strip' requires both read and write access to temps.
-  case $mode in
-    # Optimize common cases.
-    *644) cp_umask=133;;
-    *755) cp_umask=22;;
-
-    *[0-7])
-      if test -z "$stripcmd"; then
-	u_plus_rw=
-      else
-	u_plus_rw='% 200'
-      fi
-      cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
-    *)
-      if test -z "$stripcmd"; then
-	u_plus_rw=
-      else
-	u_plus_rw=,u+rw
-      fi
-      cp_umask=$mode$u_plus_rw;;
-  esac
-fi
-
-for src
-do
-  # Protect names problematic for 'test' and other utilities.
-  case $src in
-    -* | [=\(\)!]) src=./$src;;
-  esac
-
-  if test -n "$dir_arg"; then
-    dst=$src
-    dstdir=$dst
-    test -d "$dstdir"
-    dstdir_status=$?
-  else
-
-    # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
-    # might cause directories to be created, which would be especially bad
-    # if $src (and thus $dsttmp) contains '*'.
-    if test ! -f "$src" && test ! -d "$src"; then
-      echo "$0: $src does not exist." >&2
-      exit 1
-    fi
-
-    if test -z "$dst_arg"; then
-      echo "$0: no destination specified." >&2
-      exit 1
-    fi
-    dst=$dst_arg
-
-    # If destination is a directory, append the input filename; won't work
-    # if double slashes aren't ignored.
-    if test -d "$dst"; then
-      if test -n "$no_target_directory"; then
-	echo "$0: $dst_arg: Is a directory" >&2
-	exit 1
-      fi
-      dstdir=$dst
-      dst=$dstdir/`basename "$src"`
-      dstdir_status=0
-    else
-      # Prefer dirname, but fall back on a substitute if dirname fails.
-      dstdir=`
-	(dirname "$dst") 2>/dev/null ||
-	expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-	     X"$dst" : 'X\(//\)[^/]' \| \
-	     X"$dst" : 'X\(//\)$' \| \
-	     X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
-	echo X"$dst" |
-	    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-		   s//\1/
-		   q
-		 }
-		 /^X\(\/\/\)[^/].*/{
-		   s//\1/
-		   q
-		 }
-		 /^X\(\/\/\)$/{
-		   s//\1/
-		   q
-		 }
-		 /^X\(\/\).*/{
-		   s//\1/
-		   q
-		 }
-		 s/.*/./; q'
-      `
-
-      test -d "$dstdir"
-      dstdir_status=$?
-    fi
-  fi
-
-  obsolete_mkdir_used=false
-
-  if test $dstdir_status != 0; then
-    case $posix_mkdir in
-      '')
-	# Create intermediate dirs using mode 755 as modified by the umask.
-	# This is like FreeBSD 'install' as of 1997-10-28.
-	umask=`umask`
-	case $stripcmd.$umask in
-	  # Optimize common cases.
-	  *[2367][2367]) mkdir_umask=$umask;;
-	  .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
-
-	  *[0-7])
-	    mkdir_umask=`expr $umask + 22 \
-	      - $umask % 100 % 40 + $umask % 20 \
-	      - $umask % 10 % 4 + $umask % 2
-	    `;;
-	  *) mkdir_umask=$umask,go-w;;
-	esac
-
-	# With -d, create the new directory with the user-specified mode.
-	# Otherwise, rely on $mkdir_umask.
-	if test -n "$dir_arg"; then
-	  mkdir_mode=-m$mode
-	else
-	  mkdir_mode=
-	fi
-
-	posix_mkdir=false
-	case $umask in
-	  *[123567][0-7][0-7])
-	    # POSIX mkdir -p sets u+wx bits regardless of umask, which
-	    # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
-	    ;;
-	  *)
-	    tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
-	    trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
-
-	    if (umask $mkdir_umask &&
-		exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
-	    then
-	      if test -z "$dir_arg" || {
-		   # Check for POSIX incompatibilities with -m.
-		   # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
-		   # other-writable bit of parent directory when it shouldn't.
-		   # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
-		   ls_ld_tmpdir=`ls -ld "$tmpdir"`
-		   case $ls_ld_tmpdir in
-		     d????-?r-*) different_mode=700;;
-		     d????-?--*) different_mode=755;;
-		     *) false;;
-		   esac &&
-		   $mkdirprog -m$different_mode -p -- "$tmpdir" && {
-		     ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
-		     test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
-		   }
-		 }
-	      then posix_mkdir=:
-	      fi
-	      rmdir "$tmpdir/d" "$tmpdir"
-	    else
-	      # Remove any dirs left behind by ancient mkdir implementations.
-	      rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
-	    fi
-	    trap '' 0;;
-	esac;;
-    esac
-
-    if
-      $posix_mkdir && (
-	umask $mkdir_umask &&
-	$doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
-      )
-    then :
-    else
-
-      # The umask is ridiculous, or mkdir does not conform to POSIX,
-      # or it failed possibly due to a race condition.  Create the
-      # directory the slow way, step by step, checking for races as we go.
-
-      case $dstdir in
-	/*) prefix='/';;
-	[-=\(\)!]*) prefix='./';;
-	*)  prefix='';;
-      esac
-
-      eval "$initialize_posix_glob"
-
-      oIFS=$IFS
-      IFS=/
-      $posix_glob set -f
-      set fnord $dstdir
-      shift
-      $posix_glob set +f
-      IFS=$oIFS
-
-      prefixes=
-
-      for d
-      do
-	test X"$d" = X && continue
-
-	prefix=$prefix$d
-	if test -d "$prefix"; then
-	  prefixes=
-	else
-	  if $posix_mkdir; then
-	    (umask=$mkdir_umask &&
-	     $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
-	    # Don't fail if two instances are running concurrently.
-	    test -d "$prefix" || exit 1
-	  else
-	    case $prefix in
-	      *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
-	      *) qprefix=$prefix;;
-	    esac
-	    prefixes="$prefixes '$qprefix'"
-	  fi
-	fi
-	prefix=$prefix/
-      done
-
-      if test -n "$prefixes"; then
-	# Don't fail if two instances are running concurrently.
-	(umask $mkdir_umask &&
-	 eval "\$doit_exec \$mkdirprog $prefixes") ||
-	  test -d "$dstdir" || exit 1
-	obsolete_mkdir_used=true
-      fi
-    fi
-  fi
-
-  if test -n "$dir_arg"; then
-    { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
-    { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
-    { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
-      test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
-  else
-
-    # Make a couple of temp file names in the proper directory.
-    dsttmp=$dstdir/_inst.$$_
-    rmtmp=$dstdir/_rm.$$_
-
-    # Trap to clean up those temp files at exit.
-    trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
-
-    # Copy the file name to the temp name.
-    (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
-
-    # and set any options; do chmod last to preserve setuid bits.
-    #
-    # If any of these fail, we abort the whole thing.  If we want to
-    # ignore errors from any of these, just make sure not to ignore
-    # errors from the above "$doit $cpprog $src $dsttmp" command.
-    #
-    { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
-    { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
-    { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
-    { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
-
-    # If -C, don't bother to copy if it wouldn't change the file.
-    if $copy_on_change &&
-       old=`LC_ALL=C ls -dlL "$dst"	2>/dev/null` &&
-       new=`LC_ALL=C ls -dlL "$dsttmp"	2>/dev/null` &&
-
-       eval "$initialize_posix_glob" &&
-       $posix_glob set -f &&
-       set X $old && old=:$2:$4:$5:$6 &&
-       set X $new && new=:$2:$4:$5:$6 &&
-       $posix_glob set +f &&
-
-       test "$old" = "$new" &&
-       $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
-    then
-      rm -f "$dsttmp"
-    else
-      # Rename the file to the real destination.
-      $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
-
-      # The rename failed, perhaps because mv can't rename something else
-      # to itself, or perhaps because mv is so ancient that it does not
-      # support -f.
-      {
-	# Now remove or move aside any old file at destination location.
-	# We try this two ways since rm can't unlink itself on some
-	# systems and the destination file might be busy for other
-	# reasons.  In this case, the final cleanup might fail but the new
-	# file should still install successfully.
-	{
-	  test ! -f "$dst" ||
-	  $doit $rmcmd -f "$dst" 2>/dev/null ||
-	  { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
-	    { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
-	  } ||
-	  { echo "$0: cannot unlink or rename $dst" >&2
-	    (exit 1); exit 1
-	  }
-	} &&
-
-	# Now rename the file to the real destination.
-	$doit $mvcmd "$dsttmp" "$dst"
-      }
-    fi || exit 1
-
-    trap '' 0
-  fi
-done
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:
diff --git a/build-aux/ltmain.sh b/build-aux/ltmain.sh
deleted file mode 100644
index 63ae69dc6f..0000000000
--- a/build-aux/ltmain.sh
+++ /dev/null
@@ -1,9655 +0,0 @@
-
-# libtool (GNU libtool) 2.4.2
-# Written by Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996
-
-# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006,
-# 2007, 2008, 2009, 2010, 2011 Free Software Foundation, Inc.
-# This is free software; see the source for copying conditions.  There is NO
-# warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
-# GNU Libtool is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-#
-# As a special exception to the GNU General Public License,
-# if you distribute this file as part of a program or library that
-# is built using GNU Libtool, you may include this file under the
-# same distribution terms that you use for the rest of that program.
-#
-# GNU Libtool is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with GNU Libtool; see the file COPYING.  If not, a copy
-# can be downloaded from http://www.gnu.org/licenses/gpl.html,
-# or obtained by writing to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# Usage: $progname [OPTION]... [MODE-ARG]...
-#
-# Provide generalized library-building support services.
-#
-#       --config             show all configuration variables
-#       --debug              enable verbose shell tracing
-#   -n, --dry-run            display commands without modifying any files
-#       --features           display basic configuration information and exit
-#       --mode=MODE          use operation mode MODE
-#       --preserve-dup-deps  don't remove duplicate dependency libraries
-#       --quiet, --silent    don't print informational messages
-#       --no-quiet, --no-silent
-#                            print informational messages (default)
-#       --no-warn            don't display warning messages
-#       --tag=TAG            use configuration variables from tag TAG
-#   -v, --verbose            print more informational messages than default
-#       --no-verbose         don't print the extra informational messages
-#       --version            print version information
-#   -h, --help, --help-all   print short, long, or detailed help message
-#
-# MODE must be one of the following:
-#
-#         clean              remove files from the build directory
-#         compile            compile a source file into a libtool object
-#         execute            automatically set library path, then run a program
-#         finish             complete the installation of libtool libraries
-#         install            install libraries or executables
-#         link               create a library or an executable
-#         uninstall          remove libraries from an installed directory
-#
-# MODE-ARGS vary depending on the MODE.  When passed as first option,
-# `--mode=MODE' may be abbreviated as `MODE' or a unique abbreviation of that.
-# Try `$progname --help --mode=MODE' for a more detailed description of MODE.
-#
-# When reporting a bug, please describe a test case to reproduce it and
-# include the following information:
-#
-#         host-triplet:	$host
-#         shell:		$SHELL
-#         compiler:		$LTCC
-#         compiler flags:		$LTCFLAGS
-#         linker:		$LD (gnu? $with_gnu_ld)
-#         $progname:	(GNU libtool) 2.4.2
-#         automake:	$automake_version
-#         autoconf:	$autoconf_version
-#
-# Report bugs to <bug-libtool@gnu.org>.
-# GNU libtool home page: <http://www.gnu.org/software/libtool/>.
-# General help using GNU software: <http://www.gnu.org/gethelp/>.
-
-PROGRAM=libtool
-PACKAGE=libtool
-VERSION=2.4.2
-TIMESTAMP=""
-package_revision=1.3337
-
-# Be Bourne compatible
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
-  emulate sh
-  NULLCMD=:
-  # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
-  # is contrary to our usage.  Disable this feature.
-  alias -g '${1+"$@"}'='"$@"'
-  setopt NO_GLOB_SUBST
-else
-  case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
-fi
-BIN_SH=xpg4; export BIN_SH # for Tru64
-DUALCASE=1; export DUALCASE # for MKS sh
-
-# A function that is used when there is no print builtin or printf.
-func_fallback_echo ()
-{
-  eval 'cat <<_LTECHO_EOF
-$1
-_LTECHO_EOF'
-}
-
-# NLS nuisances: We save the old values to restore during execute mode.
-lt_user_locale=
-lt_safe_locale=
-for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
-do
-  eval "if test \"\${$lt_var+set}\" = set; then
-          save_$lt_var=\$$lt_var
-          $lt_var=C
-	  export $lt_var
-	  lt_user_locale=\"$lt_var=\\\$save_\$lt_var; \$lt_user_locale\"
-	  lt_safe_locale=\"$lt_var=C; \$lt_safe_locale\"
-	fi"
-done
-LC_ALL=C
-LANGUAGE=C
-export LANGUAGE LC_ALL
-
-$lt_unset CDPATH
-
-
-# Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh
-# is ksh but when the shell is invoked as "sh" and the current value of
-# the _XPG environment variable is not equal to 1 (one), the special
-# positional parameter $0, within a function call, is the name of the
-# function.
-progpath="$0"
-
-
-
-: ${CP="cp -f"}
-test "${ECHO+set}" = set || ECHO=${as_echo-'printf %s\n'}
-: ${MAKE="make"}
-: ${MKDIR="mkdir"}
-: ${MV="mv -f"}
-: ${RM="rm -f"}
-: ${SHELL="${CONFIG_SHELL-/bin/sh}"}
-: ${Xsed="$SED -e 1s/^X//"}
-
-# Global variables:
-EXIT_SUCCESS=0
-EXIT_FAILURE=1
-EXIT_MISMATCH=63  # $? = 63 is used to indicate version mismatch to missing.
-EXIT_SKIP=77	  # $? = 77 is used to indicate a skipped test to automake.
-
-exit_status=$EXIT_SUCCESS
-
-# Make sure IFS has a sensible default
-lt_nl='
-'
-IFS=" 	$lt_nl"
-
-dirname="s,/[^/]*$,,"
-basename="s,^.*/,,"
-
-# func_dirname file append nondir_replacement
-# Compute the dirname of FILE.  If nonempty, add APPEND to the result,
-# otherwise set result to NONDIR_REPLACEMENT.
-func_dirname ()
-{
-    func_dirname_result=`$ECHO "${1}" | $SED "$dirname"`
-    if test "X$func_dirname_result" = "X${1}"; then
-      func_dirname_result="${3}"
-    else
-      func_dirname_result="$func_dirname_result${2}"
-    fi
-} # func_dirname may be replaced by extended shell implementation
-
-
-# func_basename file
-func_basename ()
-{
-    func_basename_result=`$ECHO "${1}" | $SED "$basename"`
-} # func_basename may be replaced by extended shell implementation
-
-
-# func_dirname_and_basename file append nondir_replacement
-# perform func_basename and func_dirname in a single function
-# call:
-#   dirname:  Compute the dirname of FILE.  If nonempty,
-#             add APPEND to the result, otherwise set result
-#             to NONDIR_REPLACEMENT.
-#             value returned in "$func_dirname_result"
-#   basename: Compute filename of FILE.
-#             value retuned in "$func_basename_result"
-# Implementation must be kept synchronized with func_dirname
-# and func_basename. For efficiency, we do not delegate to
-# those functions but instead duplicate the functionality here.
-func_dirname_and_basename ()
-{
-    # Extract subdirectory from the argument.
-    func_dirname_result=`$ECHO "${1}" | $SED -e "$dirname"`
-    if test "X$func_dirname_result" = "X${1}"; then
-      func_dirname_result="${3}"
-    else
-      func_dirname_result="$func_dirname_result${2}"
-    fi
-    func_basename_result=`$ECHO "${1}" | $SED -e "$basename"`
-} # func_dirname_and_basename may be replaced by extended shell implementation
-
-
-# func_stripname prefix suffix name
-# strip PREFIX and SUFFIX off of NAME.
-# PREFIX and SUFFIX must not contain globbing or regex special
-# characters, hashes, percent signs, but SUFFIX may contain a leading
-# dot (in which case that matches only a dot).
-# func_strip_suffix prefix name
-func_stripname ()
-{
-    case ${2} in
-      .*) func_stripname_result=`$ECHO "${3}" | $SED "s%^${1}%%; s%\\\\${2}\$%%"`;;
-      *)  func_stripname_result=`$ECHO "${3}" | $SED "s%^${1}%%; s%${2}\$%%"`;;
-    esac
-} # func_stripname may be replaced by extended shell implementation
-
-
-# These SED scripts presuppose an absolute path with a trailing slash.
-pathcar='s,^/\([^/]*\).*$,\1,'
-pathcdr='s,^/[^/]*,,'
-removedotparts=':dotsl
-		s@/\./@/@g
-		t dotsl
-		s,/\.$,/,'
-collapseslashes='s@/\{1,\}@/@g'
-finalslash='s,/*$,/,'
-
-# func_normal_abspath PATH
-# Remove doubled-up and trailing slashes, "." path components,
-# and cancel out any ".." path components in PATH after making
-# it an absolute path.
-#             value returned in "$func_normal_abspath_result"
-func_normal_abspath ()
-{
-  # Start from root dir and reassemble the path.
-  func_normal_abspath_result=
-  func_normal_abspath_tpath=$1
-  func_normal_abspath_altnamespace=
-  case $func_normal_abspath_tpath in
-    "")
-      # Empty path, that just means $cwd.
-      func_stripname '' '/' "`pwd`"
-      func_normal_abspath_result=$func_stripname_result
-      return
-    ;;
-    # The next three entries are used to spot a run of precisely
-    # two leading slashes without using negated character classes;
-    # we take advantage of case's first-match behaviour.
-    ///*)
-      # Unusual form of absolute path, do nothing.
-    ;;
-    //*)
-      # Not necessarily an ordinary path; POSIX reserves leading '//'
-      # and for example Cygwin uses it to access remote file shares
-      # over CIFS/SMB, so we conserve a leading double slash if found.
-      func_normal_abspath_altnamespace=/
-    ;;
-    /*)
-      # Absolute path, do nothing.
-    ;;
-    *)
-      # Relative path, prepend $cwd.
-      func_normal_abspath_tpath=`pwd`/$func_normal_abspath_tpath
-    ;;
-  esac
-  # Cancel out all the simple stuff to save iterations.  We also want
-  # the path to end with a slash for ease of parsing, so make sure
-  # there is one (and only one) here.
-  func_normal_abspath_tpath=`$ECHO "$func_normal_abspath_tpath" | $SED \
-        -e "$removedotparts" -e "$collapseslashes" -e "$finalslash"`
-  while :; do
-    # Processed it all yet?
-    if test "$func_normal_abspath_tpath" = / ; then
-      # If we ascended to the root using ".." the result may be empty now.
-      if test -z "$func_normal_abspath_result" ; then
-        func_normal_abspath_result=/
-      fi
-      break
-    fi
-    func_normal_abspath_tcomponent=`$ECHO "$func_normal_abspath_tpath" | $SED \
-        -e "$pathcar"`
-    func_normal_abspath_tpath=`$ECHO "$func_normal_abspath_tpath" | $SED \
-        -e "$pathcdr"`
-    # Figure out what to do with it
-    case $func_normal_abspath_tcomponent in
-      "")
-        # Trailing empty path component, ignore it.
-      ;;
-      ..)
-        # Parent dir; strip last assembled component from result.
-        func_dirname "$func_normal_abspath_result"
-        func_normal_abspath_result=$func_dirname_result
-      ;;
-      *)
-        # Actual path component, append it.
-        func_normal_abspath_result=$func_normal_abspath_result/$func_normal_abspath_tcomponent
-      ;;
-    esac
-  done
-  # Restore leading double-slash if one was found on entry.
-  func_normal_abspath_result=$func_normal_abspath_altnamespace$func_normal_abspath_result
-}
-
-# func_relative_path SRCDIR DSTDIR
-# generates a relative path from SRCDIR to DSTDIR, with a trailing
-# slash if non-empty, suitable for immediately appending a filename
-# without needing to append a separator.
-#             value returned in "$func_relative_path_result"
-func_relative_path ()
-{
-  func_relative_path_result=
-  func_normal_abspath "$1"
-  func_relative_path_tlibdir=$func_normal_abspath_result
-  func_normal_abspath "$2"
-  func_relative_path_tbindir=$func_normal_abspath_result
-
-  # Ascend the tree starting from libdir
-  while :; do
-    # check if we have found a prefix of bindir
-    case $func_relative_path_tbindir in
-      $func_relative_path_tlibdir)
-        # found an exact match
-        func_relative_path_tcancelled=
-        break
-        ;;
-      $func_relative_path_tlibdir*)
-        # found a matching prefix
-        func_stripname "$func_relative_path_tlibdir" '' "$func_relative_path_tbindir"
-        func_relative_path_tcancelled=$func_stripname_result
-        if test -z "$func_relative_path_result"; then
-          func_relative_path_result=.
-        fi
-        break
-        ;;
-      *)
-        func_dirname $func_relative_path_tlibdir
-        func_relative_path_tlibdir=${func_dirname_result}
-        if test "x$func_relative_path_tlibdir" = x ; then
-          # Have to descend all the way to the root!
-          func_relative_path_result=../$func_relative_path_result
-          func_relative_path_tcancelled=$func_relative_path_tbindir
-          break
-        fi
-        func_relative_path_result=../$func_relative_path_result
-        ;;
-    esac
-  done
-
-  # Now calculate path; take care to avoid doubling-up slashes.
-  func_stripname '' '/' "$func_relative_path_result"
-  func_relative_path_result=$func_stripname_result
-  func_stripname '/' '/' "$func_relative_path_tcancelled"
-  if test "x$func_stripname_result" != x ; then
-    func_relative_path_result=${func_relative_path_result}/${func_stripname_result}
-  fi
-
-  # Normalisation. If bindir is libdir, return empty string,
-  # else relative path ending with a slash; either way, target
-  # file name can be directly appended.
-  if test ! -z "$func_relative_path_result"; then
-    func_stripname './' '' "$func_relative_path_result/"
-    func_relative_path_result=$func_stripname_result
-  fi
-}
-
-# The name of this program:
-func_dirname_and_basename "$progpath"
-progname=$func_basename_result
-
-# Make sure we have an absolute path for reexecution:
-case $progpath in
-  [\\/]*|[A-Za-z]:\\*) ;;
-  *[\\/]*)
-     progdir=$func_dirname_result
-     progdir=`cd "$progdir" && pwd`
-     progpath="$progdir/$progname"
-     ;;
-  *)
-     save_IFS="$IFS"
-     IFS=${PATH_SEPARATOR-:}
-     for progdir in $PATH; do
-       IFS="$save_IFS"
-       test -x "$progdir/$progname" && break
-     done
-     IFS="$save_IFS"
-     test -n "$progdir" || progdir=`pwd`
-     progpath="$progdir/$progname"
-     ;;
-esac
-
-# Sed substitution that helps us do robust quoting.  It backslashifies
-# metacharacters that are still active within double-quoted strings.
-Xsed="${SED}"' -e 1s/^X//'
-sed_quote_subst='s/\([`"$\\]\)/\\\1/g'
-
-# Same as above, but do not quote variable references.
-double_quote_subst='s/\(["`\\]\)/\\\1/g'
-
-# Sed substitution that turns a string into a regex matching for the
-# string literally.
-sed_make_literal_regex='s,[].[^$\\*\/],\\&,g'
-
-# Sed substitution that converts a w32 file name or path
-# which contains forward slashes, into one that contains
-# (escaped) backslashes.  A very naive implementation.
-lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g'
-
-# Re-`\' parameter expansions in output of double_quote_subst that were
-# `\'-ed in input to the same.  If an odd number of `\' preceded a '$'
-# in input to double_quote_subst, that '$' was protected from expansion.
-# Since each input `\' is now two `\'s, look for any number of runs of
-# four `\'s followed by two `\'s and then a '$'.  `\' that '$'.
-bs='\\'
-bs2='\\\\'
-bs4='\\\\\\\\'
-dollar='\$'
-sed_double_backslash="\
-  s/$bs4/&\\
-/g
-  s/^$bs2$dollar/$bs&/
-  s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g
-  s/\n//g"
-
-# Standard options:
-opt_dry_run=false
-opt_help=false
-opt_quiet=false
-opt_verbose=false
-opt_warning=:
-
-# func_echo arg...
-# Echo program name prefixed message, along with the current mode
-# name if it has been set yet.
-func_echo ()
-{
-    $ECHO "$progname: ${opt_mode+$opt_mode: }$*"
-}
-
-# func_verbose arg...
-# Echo program name prefixed message in verbose mode only.
-func_verbose ()
-{
-    $opt_verbose && func_echo ${1+"$@"}
-
-    # A bug in bash halts the script if the last line of a function
-    # fails when set -e is in force, so we need another command to
-    # work around that:
-    :
-}
-
-# func_echo_all arg...
-# Invoke $ECHO with all args, space-separated.
-func_echo_all ()
-{
-    $ECHO "$*"
-}
-
-# func_error arg...
-# Echo program name prefixed message to standard error.
-func_error ()
-{
-    $ECHO "$progname: ${opt_mode+$opt_mode: }"${1+"$@"} 1>&2
-}
-
-# func_warning arg...
-# Echo program name prefixed warning message to standard error.
-func_warning ()
-{
-    $opt_warning && $ECHO "$progname: ${opt_mode+$opt_mode: }warning: "${1+"$@"} 1>&2
-
-    # bash bug again:
-    :
-}
-
-# func_fatal_error arg...
-# Echo program name prefixed message to standard error, and exit.
-func_fatal_error ()
-{
-    func_error ${1+"$@"}
-    exit $EXIT_FAILURE
-}
-
-# func_fatal_help arg...
-# Echo program name prefixed message to standard error, followed by
-# a help hint, and exit.
-func_fatal_help ()
-{
-    func_error ${1+"$@"}
-    func_fatal_error "$help"
-}
-help="Try \`$progname --help' for more information."  ## default
-
-
-# func_grep expression filename
-# Check whether EXPRESSION matches any line of FILENAME, without output.
-func_grep ()
-{
-    $GREP "$1" "$2" >/dev/null 2>&1
-}
-
-
-# func_mkdir_p directory-path
-# Make sure the entire path to DIRECTORY-PATH is available.
-func_mkdir_p ()
-{
-    my_directory_path="$1"
-    my_dir_list=
-
-    if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then
-
-      # Protect directory names starting with `-'
-      case $my_directory_path in
-        -*) my_directory_path="./$my_directory_path" ;;
-      esac
-
-      # While some portion of DIR does not yet exist...
-      while test ! -d "$my_directory_path"; do
-        # ...make a list in topmost first order.  Use a colon delimited
-	# list incase some portion of path contains whitespace.
-        my_dir_list="$my_directory_path:$my_dir_list"
-
-        # If the last portion added has no slash in it, the list is done
-        case $my_directory_path in */*) ;; *) break ;; esac
-
-        # ...otherwise throw away the child directory and loop
-        my_directory_path=`$ECHO "$my_directory_path" | $SED -e "$dirname"`
-      done
-      my_dir_list=`$ECHO "$my_dir_list" | $SED 's,:*$,,'`
-
-      save_mkdir_p_IFS="$IFS"; IFS=':'
-      for my_dir in $my_dir_list; do
-	IFS="$save_mkdir_p_IFS"
-        # mkdir can fail with a `File exist' error if two processes
-        # try to create one of the directories concurrently.  Don't
-        # stop in that case!
-        $MKDIR "$my_dir" 2>/dev/null || :
-      done
-      IFS="$save_mkdir_p_IFS"
-
-      # Bail out if we (or some other process) failed to create a directory.
-      test -d "$my_directory_path" || \
-        func_fatal_error "Failed to create \`$1'"
-    fi
-}
-
-
-# func_mktempdir [string]
-# Make a temporary directory that won't clash with other running
-# libtool processes, and avoids race conditions if possible.  If
-# given, STRING is the basename for that directory.
-func_mktempdir ()
-{
-    my_template="${TMPDIR-/tmp}/${1-$progname}"
-
-    if test "$opt_dry_run" = ":"; then
-      # Return a directory name, but don't create it in dry-run mode
-      my_tmpdir="${my_template}-$$"
-    else
-
-      # If mktemp works, use that first and foremost
-      my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null`
-
-      if test ! -d "$my_tmpdir"; then
-        # Failing that, at least try and use $RANDOM to avoid a race
-        my_tmpdir="${my_template}-${RANDOM-0}$$"
-
-        save_mktempdir_umask=`umask`
-        umask 0077
-        $MKDIR "$my_tmpdir"
-        umask $save_mktempdir_umask
-      fi
-
-      # If we're not in dry-run mode, bomb out on failure
-      test -d "$my_tmpdir" || \
-        func_fatal_error "cannot create temporary directory \`$my_tmpdir'"
-    fi
-
-    $ECHO "$my_tmpdir"
-}
-
-
-# func_quote_for_eval arg
-# Aesthetically quote ARG to be evaled later.
-# This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT
-# is double-quoted, suitable for a subsequent eval, whereas
-# FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters
-# which are still active within double quotes backslashified.
-func_quote_for_eval ()
-{
-    case $1 in
-      *[\\\`\"\$]*)
-	func_quote_for_eval_unquoted_result=`$ECHO "$1" | $SED "$sed_quote_subst"` ;;
-      *)
-        func_quote_for_eval_unquoted_result="$1" ;;
-    esac
-
-    case $func_quote_for_eval_unquoted_result in
-      # Double-quote args containing shell metacharacters to delay
-      # word splitting, command substitution and and variable
-      # expansion for a subsequent eval.
-      # Many Bourne shells cannot handle close brackets correctly
-      # in scan sets, so we specify it separately.
-      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
-        func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\""
-        ;;
-      *)
-        func_quote_for_eval_result="$func_quote_for_eval_unquoted_result"
-    esac
-}
-
-
-# func_quote_for_expand arg
-# Aesthetically quote ARG to be evaled later; same as above,
-# but do not quote variable references.
-func_quote_for_expand ()
-{
-    case $1 in
-      *[\\\`\"]*)
-	my_arg=`$ECHO "$1" | $SED \
-	    -e "$double_quote_subst" -e "$sed_double_backslash"` ;;
-      *)
-        my_arg="$1" ;;
-    esac
-
-    case $my_arg in
-      # Double-quote args containing shell metacharacters to delay
-      # word splitting and command substitution for a subsequent eval.
-      # Many Bourne shells cannot handle close brackets correctly
-      # in scan sets, so we specify it separately.
-      *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \	]*|*]*|"")
-        my_arg="\"$my_arg\""
-        ;;
-    esac
-
-    func_quote_for_expand_result="$my_arg"
-}
-
-
-# func_show_eval cmd [fail_exp]
-# Unless opt_silent is true, then output CMD.  Then, if opt_dryrun is
-# not true, evaluate CMD.  If the evaluation of CMD fails, and FAIL_EXP
-# is given, then evaluate it.
-func_show_eval ()
-{
-    my_cmd="$1"
-    my_fail_exp="${2-:}"
-
-    ${opt_silent-false} || {
-      func_quote_for_expand "$my_cmd"
-      eval "func_echo $func_quote_for_expand_result"
-    }
-
-    if ${opt_dry_run-false}; then :; else
-      eval "$my_cmd"
-      my_status=$?
-      if test "$my_status" -eq 0; then :; else
-	eval "(exit $my_status); $my_fail_exp"
-      fi
-    fi
-}
-
-
-# func_show_eval_locale cmd [fail_exp]
-# Unless opt_silent is true, then output CMD.  Then, if opt_dryrun is
-# not true, evaluate CMD.  If the evaluation of CMD fails, and FAIL_EXP
-# is given, then evaluate it.  Use the saved locale for evaluation.
-func_show_eval_locale ()
-{
-    my_cmd="$1"
-    my_fail_exp="${2-:}"
-
-    ${opt_silent-false} || {
-      func_quote_for_expand "$my_cmd"
-      eval "func_echo $func_quote_for_expand_result"
-    }
-
-    if ${opt_dry_run-false}; then :; else
-      eval "$lt_user_locale
-	    $my_cmd"
-      my_status=$?
-      eval "$lt_safe_locale"
-      if test "$my_status" -eq 0; then :; else
-	eval "(exit $my_status); $my_fail_exp"
-      fi
-    fi
-}
-
-# func_tr_sh
-# Turn $1 into a string suitable for a shell variable name.
-# Result is stored in $func_tr_sh_result.  All characters
-# not in the set a-zA-Z0-9_ are replaced with '_'. Further,
-# if $1 begins with a digit, a '_' is prepended as well.
-func_tr_sh ()
-{
-  case $1 in
-  [0-9]* | *[!a-zA-Z0-9_]*)
-    func_tr_sh_result=`$ECHO "$1" | $SED 's/^\([0-9]\)/_\1/; s/[^a-zA-Z0-9_]/_/g'`
-    ;;
-  * )
-    func_tr_sh_result=$1
-    ;;
-  esac
-}
-
-
-# func_version
-# Echo version message to standard output and exit.
-func_version ()
-{
-    $opt_debug
-
-    $SED -n '/(C)/!b go
-	:more
-	/\./!{
-	  N
-	  s/\n# / /
-	  b more
-	}
-	:go
-	/^# '$PROGRAM' (GNU /,/# warranty; / {
-        s/^# //
-	s/^# *$//
-        s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/
-        p
-     }' < "$progpath"
-     exit $?
-}
-
-# func_usage
-# Echo short help message to standard output and exit.
-func_usage ()
-{
-    $opt_debug
-
-    $SED -n '/^# Usage:/,/^#  *.*--help/ {
-        s/^# //
-	s/^# *$//
-	s/\$progname/'$progname'/
-	p
-    }' < "$progpath"
-    echo
-    $ECHO "run \`$progname --help | more' for full usage"
-    exit $?
-}
-
-# func_help [NOEXIT]
-# Echo long help message to standard output and exit,
-# unless 'noexit' is passed as argument.
-func_help ()
-{
-    $opt_debug
-
-    $SED -n '/^# Usage:/,/# Report bugs to/ {
-	:print
-        s/^# //
-	s/^# *$//
-	s*\$progname*'$progname'*
-	s*\$host*'"$host"'*
-	s*\$SHELL*'"$SHELL"'*
-	s*\$LTCC*'"$LTCC"'*
-	s*\$LTCFLAGS*'"$LTCFLAGS"'*
-	s*\$LD*'"$LD"'*
-	s/\$with_gnu_ld/'"$with_gnu_ld"'/
-	s/\$automake_version/'"`(${AUTOMAKE-automake} --version) 2>/dev/null |$SED 1q`"'/
-	s/\$autoconf_version/'"`(${AUTOCONF-autoconf} --version) 2>/dev/null |$SED 1q`"'/
-	p
-	d
-     }
-     /^# .* home page:/b print
-     /^# General help using/b print
-     ' < "$progpath"
-    ret=$?
-    if test -z "$1"; then
-      exit $ret
-    fi
-}
-
-# func_missing_arg argname
-# Echo program name prefixed message to standard error and set global
-# exit_cmd.
-func_missing_arg ()
-{
-    $opt_debug
-
-    func_error "missing argument for $1."
-    exit_cmd=exit
-}
-
-
-# func_split_short_opt shortopt
-# Set func_split_short_opt_name and func_split_short_opt_arg shell
-# variables after splitting SHORTOPT after the 2nd character.
-func_split_short_opt ()
-{
-    my_sed_short_opt='1s/^\(..\).*$/\1/;q'
-    my_sed_short_rest='1s/^..\(.*\)$/\1/;q'
-
-    func_split_short_opt_name=`$ECHO "$1" | $SED "$my_sed_short_opt"`
-    func_split_short_opt_arg=`$ECHO "$1" | $SED "$my_sed_short_rest"`
-} # func_split_short_opt may be replaced by extended shell implementation
-
-
-# func_split_long_opt longopt
-# Set func_split_long_opt_name and func_split_long_opt_arg shell
-# variables after splitting LONGOPT at the `=' sign.
-func_split_long_opt ()
-{
-    my_sed_long_opt='1s/^\(--[^=]*\)=.*/\1/;q'
-    my_sed_long_arg='1s/^--[^=]*=//'
-
-    func_split_long_opt_name=`$ECHO "$1" | $SED "$my_sed_long_opt"`
-    func_split_long_opt_arg=`$ECHO "$1" | $SED "$my_sed_long_arg"`
-} # func_split_long_opt may be replaced by extended shell implementation
-
-exit_cmd=:
-
-
-
-
-
-magic="%%%MAGIC variable%%%"
-magic_exe="%%%MAGIC EXE variable%%%"
-
-# Global variables.
-nonopt=
-preserve_args=
-lo2o="s/\\.lo\$/.${objext}/"
-o2lo="s/\\.${objext}\$/.lo/"
-extracted_archives=
-extracted_serial=0
-
-# If this variable is set in any of the actions, the command in it
-# will be execed at the end.  This prevents here-documents from being
-# left over by shells.
-exec_cmd=
-
-# func_append var value
-# Append VALUE to the end of shell variable VAR.
-func_append ()
-{
-    eval "${1}=\$${1}\${2}"
-} # func_append may be replaced by extended shell implementation
-
-# func_append_quoted var value
-# Quote VALUE and append to the end of shell variable VAR, separated
-# by a space.
-func_append_quoted ()
-{
-    func_quote_for_eval "${2}"
-    eval "${1}=\$${1}\\ \$func_quote_for_eval_result"
-} # func_append_quoted may be replaced by extended shell implementation
-
-
-# func_arith arithmetic-term...
-func_arith ()
-{
-    func_arith_result=`expr "${@}"`
-} # func_arith may be replaced by extended shell implementation
-
-
-# func_len string
-# STRING may not start with a hyphen.
-func_len ()
-{
-    func_len_result=`expr "${1}" : ".*" 2>/dev/null || echo $max_cmd_len`
-} # func_len may be replaced by extended shell implementation
-
-
-# func_lo2o object
-func_lo2o ()
-{
-    func_lo2o_result=`$ECHO "${1}" | $SED "$lo2o"`
-} # func_lo2o may be replaced by extended shell implementation
-
-
-# func_xform libobj-or-source
-func_xform ()
-{
-    func_xform_result=`$ECHO "${1}" | $SED 's/\.[^.]*$/.lo/'`
-} # func_xform may be replaced by extended shell implementation
-
-
-# func_fatal_configuration arg...
-# Echo program name prefixed message to standard error, followed by
-# a configuration failure hint, and exit.
-func_fatal_configuration ()
-{
-    func_error ${1+"$@"}
-    func_error "See the $PACKAGE documentation for more information."
-    func_fatal_error "Fatal configuration error."
-}
-
-
-# func_config
-# Display the configuration for all the tags in this script.
-func_config ()
-{
-    re_begincf='^# ### BEGIN LIBTOOL'
-    re_endcf='^# ### END LIBTOOL'
-
-    # Default configuration.
-    $SED "1,/$re_begincf CONFIG/d;/$re_endcf CONFIG/,\$d" < "$progpath"
-
-    # Now print the configurations for the tags.
-    for tagname in $taglist; do
-      $SED -n "/$re_begincf TAG CONFIG: $tagname\$/,/$re_endcf TAG CONFIG: $tagname\$/p" < "$progpath"
-    done
-
-    exit $?
-}
-
-# func_features
-# Display the features supported by this script.
-func_features ()
-{
-    echo "host: $host"
-    if test "$build_libtool_libs" = yes; then
-      echo "enable shared libraries"
-    else
-      echo "disable shared libraries"
-    fi
-    if test "$build_old_libs" = yes; then
-      echo "enable static libraries"
-    else
-      echo "disable static libraries"
-    fi
-
-    exit $?
-}
-
-# func_enable_tag tagname
-# Verify that TAGNAME is valid, and either flag an error and exit, or
-# enable the TAGNAME tag.  We also add TAGNAME to the global $taglist
-# variable here.
-func_enable_tag ()
-{
-  # Global variable:
-  tagname="$1"
-
-  re_begincf="^# ### BEGIN LIBTOOL TAG CONFIG: $tagname\$"
-  re_endcf="^# ### END LIBTOOL TAG CONFIG: $tagname\$"
-  sed_extractcf="/$re_begincf/,/$re_endcf/p"
-
-  # Validate tagname.
-  case $tagname in
-    *[!-_A-Za-z0-9,/]*)
-      func_fatal_error "invalid tag name: $tagname"
-      ;;
-  esac
-
-  # Don't test for the "default" C tag, as we know it's
-  # there but not specially marked.
-  case $tagname in
-    CC) ;;
-    *)
-      if $GREP "$re_begincf" "$progpath" >/dev/null 2>&1; then
-	taglist="$taglist $tagname"
-
-	# Evaluate the configuration.  Be careful to quote the path
-	# and the sed script, to avoid splitting on whitespace, but
-	# also don't use non-portable quotes within backquotes within
-	# quotes we have to do it in 2 steps:
-	extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"`
-	eval "$extractedcf"
-      else
-	func_error "ignoring unknown tag $tagname"
-      fi
-      ;;
-  esac
-}
-
-# func_check_version_match
-# Ensure that we are using m4 macros, and libtool script from the same
-# release of libtool.
-func_check_version_match ()
-{
-  if test "$package_revision" != "$macro_revision"; then
-    if test "$VERSION" != "$macro_version"; then
-      if test -z "$macro_version"; then
-        cat >&2 <<_LT_EOF
-$progname: Version mismatch error.  This is $PACKAGE $VERSION, but the
-$progname: definition of this LT_INIT comes from an older release.
-$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
-$progname: and run autoconf again.
-_LT_EOF
-      else
-        cat >&2 <<_LT_EOF
-$progname: Version mismatch error.  This is $PACKAGE $VERSION, but the
-$progname: definition of this LT_INIT comes from $PACKAGE $macro_version.
-$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
-$progname: and run autoconf again.
-_LT_EOF
-      fi
-    else
-      cat >&2 <<_LT_EOF
-$progname: Version mismatch error.  This is $PACKAGE $VERSION, revision $package_revision,
-$progname: but the definition of this LT_INIT comes from revision $macro_revision.
-$progname: You should recreate aclocal.m4 with macros from revision $package_revision
-$progname: of $PACKAGE $VERSION and run autoconf again.
-_LT_EOF
-    fi
-
-    exit $EXIT_MISMATCH
-  fi
-}
-
-
-# Shorthand for --mode=foo, only valid as the first argument
-case $1 in
-clean|clea|cle|cl)
-  shift; set dummy --mode clean ${1+"$@"}; shift
-  ;;
-compile|compil|compi|comp|com|co|c)
-  shift; set dummy --mode compile ${1+"$@"}; shift
-  ;;
-execute|execut|execu|exec|exe|ex|e)
-  shift; set dummy --mode execute ${1+"$@"}; shift
-  ;;
-finish|finis|fini|fin|fi|f)
-  shift; set dummy --mode finish ${1+"$@"}; shift
-  ;;
-install|instal|insta|inst|ins|in|i)
-  shift; set dummy --mode install ${1+"$@"}; shift
-  ;;
-link|lin|li|l)
-  shift; set dummy --mode link ${1+"$@"}; shift
-  ;;
-uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u)
-  shift; set dummy --mode uninstall ${1+"$@"}; shift
-  ;;
-esac
-
-
-
-# Option defaults:
-opt_debug=:
-opt_dry_run=false
-opt_config=false
-opt_preserve_dup_deps=false
-opt_features=false
-opt_finish=false
-opt_help=false
-opt_help_all=false
-opt_silent=:
-opt_warning=:
-opt_verbose=:
-opt_silent=false
-opt_verbose=false
-
-
-# Parse options once, thoroughly.  This comes as soon as possible in the
-# script to make things like `--version' happen as quickly as we can.
-{
-  # this just eases exit handling
-  while test $# -gt 0; do
-    opt="$1"
-    shift
-    case $opt in
-      --debug|-x)	opt_debug='set -x'
-			func_echo "enabling shell trace mode"
-			$opt_debug
-			;;
-      --dry-run|--dryrun|-n)
-			opt_dry_run=:
-			;;
-      --config)
-			opt_config=:
-func_config
-			;;
-      --dlopen|-dlopen)
-			optarg="$1"
-			opt_dlopen="${opt_dlopen+$opt_dlopen
-}$optarg"
-			shift
-			;;
-      --preserve-dup-deps)
-			opt_preserve_dup_deps=:
-			;;
-      --features)
-			opt_features=:
-func_features
-			;;
-      --finish)
-			opt_finish=:
-set dummy --mode finish ${1+"$@"}; shift
-			;;
-      --help)
-			opt_help=:
-			;;
-      --help-all)
-			opt_help_all=:
-opt_help=': help-all'
-			;;
-      --mode)
-			test $# = 0 && func_missing_arg $opt && break
-			optarg="$1"
-			opt_mode="$optarg"
-case $optarg in
-  # Valid mode arguments:
-  clean|compile|execute|finish|install|link|relink|uninstall) ;;
-
-  # Catch anything else as an error
-  *) func_error "invalid argument for $opt"
-     exit_cmd=exit
-     break
-     ;;
-esac
-			shift
-			;;
-      --no-silent|--no-quiet)
-			opt_silent=false
-func_append preserve_args " $opt"
-			;;
-      --no-warning|--no-warn)
-			opt_warning=false
-func_append preserve_args " $opt"
-			;;
-      --no-verbose)
-			opt_verbose=false
-func_append preserve_args " $opt"
-			;;
-      --silent|--quiet)
-			opt_silent=:
-func_append preserve_args " $opt"
-        opt_verbose=false
-			;;
-      --verbose|-v)
-			opt_verbose=:
-func_append preserve_args " $opt"
-opt_silent=false
-			;;
-      --tag)
-			test $# = 0 && func_missing_arg $opt && break
-			optarg="$1"
-			opt_tag="$optarg"
-func_append preserve_args " $opt $optarg"
-func_enable_tag "$optarg"
-			shift
-			;;
-
-      -\?|-h)		func_usage				;;
-      --help)		func_help				;;
-      --version)	func_version				;;
-
-      # Separate optargs to long options:
-      --*=*)
-			func_split_long_opt "$opt"
-			set dummy "$func_split_long_opt_name" "$func_split_long_opt_arg" ${1+"$@"}
-			shift
-			;;
-
-      # Separate non-argument short options:
-      -\?*|-h*|-n*|-v*)
-			func_split_short_opt "$opt"
-			set dummy "$func_split_short_opt_name" "-$func_split_short_opt_arg" ${1+"$@"}
-			shift
-			;;
-
-      --)		break					;;
-      -*)		func_fatal_help "unrecognized option \`$opt'" ;;
-      *)		set dummy "$opt" ${1+"$@"};	shift; break  ;;
-    esac
-  done
-
-  # Validate options:
-
-  # save first non-option argument
-  if test "$#" -gt 0; then
-    nonopt="$opt"
-    shift
-  fi
-
-  # preserve --debug
-  test "$opt_debug" = : || func_append preserve_args " --debug"
-
-  case $host in
-    *cygwin* | *mingw* | *pw32* | *cegcc*)
-      # don't eliminate duplications in $postdeps and $predeps
-      opt_duplicate_compiler_generated_deps=:
-      ;;
-    *)
-      opt_duplicate_compiler_generated_deps=$opt_preserve_dup_deps
-      ;;
-  esac
-
-  $opt_help || {
-    # Sanity checks first:
-    func_check_version_match
-
-    if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then
-      func_fatal_configuration "not configured to build any kind of library"
-    fi
-
-    # Darwin sucks
-    eval std_shrext=\"$shrext_cmds\"
-
-    # Only execute mode is allowed to have -dlopen flags.
-    if test -n "$opt_dlopen" && test "$opt_mode" != execute; then
-      func_error "unrecognized option \`-dlopen'"
-      $ECHO "$help" 1>&2
-      exit $EXIT_FAILURE
-    fi
-
-    # Change the help message to a mode-specific one.
-    generic_help="$help"
-    help="Try \`$progname --help --mode=$opt_mode' for more information."
-  }
-
-
-  # Bail if the options were screwed
-  $exit_cmd $EXIT_FAILURE
-}
-
-
-
-
-## ----------- ##
-##    Main.    ##
-## ----------- ##
-
-# func_lalib_p file
-# True iff FILE is a libtool `.la' library or `.lo' object file.
-# This function is only a basic sanity check; it will hardly flush out
-# determined imposters.
-func_lalib_p ()
-{
-    test -f "$1" &&
-      $SED -e 4q "$1" 2>/dev/null \
-        | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1
-}
-
-# func_lalib_unsafe_p file
-# True iff FILE is a libtool `.la' library or `.lo' object file.
-# This function implements the same check as func_lalib_p without
-# resorting to external programs.  To this end, it redirects stdin and
-# closes it afterwards, without saving the original file descriptor.
-# As a safety measure, use it only where a negative result would be
-# fatal anyway.  Works if `file' does not exist.
-func_lalib_unsafe_p ()
-{
-    lalib_p=no
-    if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then
-	for lalib_p_l in 1 2 3 4
-	do
-	    read lalib_p_line
-	    case "$lalib_p_line" in
-		\#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;;
-	    esac
-	done
-	exec 0<&5 5<&-
-    fi
-    test "$lalib_p" = yes
-}
-
-# func_ltwrapper_script_p file
-# True iff FILE is a libtool wrapper script
-# This function is only a basic sanity check; it will hardly flush out
-# determined imposters.
-func_ltwrapper_script_p ()
-{
-    func_lalib_p "$1"
-}
-
-# func_ltwrapper_executable_p file
-# True iff FILE is a libtool wrapper executable
-# This function is only a basic sanity check; it will hardly flush out
-# determined imposters.
-func_ltwrapper_executable_p ()
-{
-    func_ltwrapper_exec_suffix=
-    case $1 in
-    *.exe) ;;
-    *) func_ltwrapper_exec_suffix=.exe ;;
-    esac
-    $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1
-}
-
-# func_ltwrapper_scriptname file
-# Assumes file is an ltwrapper_executable
-# uses $file to determine the appropriate filename for a
-# temporary ltwrapper_script.
-func_ltwrapper_scriptname ()
-{
-    func_dirname_and_basename "$1" "" "."
-    func_stripname '' '.exe' "$func_basename_result"
-    func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper"
-}
-
-# func_ltwrapper_p file
-# True iff FILE is a libtool wrapper script or wrapper executable
-# This function is only a basic sanity check; it will hardly flush out
-# determined imposters.
-func_ltwrapper_p ()
-{
-    func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1"
-}
-
-
-# func_execute_cmds commands fail_cmd
-# Execute tilde-delimited COMMANDS.
-# If FAIL_CMD is given, eval that upon failure.
-# FAIL_CMD may read-access the current command in variable CMD!
-func_execute_cmds ()
-{
-    $opt_debug
-    save_ifs=$IFS; IFS='~'
-    for cmd in $1; do
-      IFS=$save_ifs
-      eval cmd=\"$cmd\"
-      func_show_eval "$cmd" "${2-:}"
-    done
-    IFS=$save_ifs
-}
-
-
-# func_source file
-# Source FILE, adding directory component if necessary.
-# Note that it is not necessary on cygwin/mingw to append a dot to
-# FILE even if both FILE and FILE.exe exist: automatic-append-.exe
-# behavior happens only for exec(3), not for open(2)!  Also, sourcing
-# `FILE.' does not work on cygwin managed mounts.
-func_source ()
-{
-    $opt_debug
-    case $1 in
-    */* | *\\*)	. "$1" ;;
-    *)		. "./$1" ;;
-    esac
-}
-
-
-# func_resolve_sysroot PATH
-# Replace a leading = in PATH with a sysroot.  Store the result into
-# func_resolve_sysroot_result
-func_resolve_sysroot ()
-{
-  func_resolve_sysroot_result=$1
-  case $func_resolve_sysroot_result in
-  =*)
-    func_stripname '=' '' "$func_resolve_sysroot_result"
-    func_resolve_sysroot_result=$lt_sysroot$func_stripname_result
-    ;;
-  esac
-}
-
-# func_replace_sysroot PATH
-# If PATH begins with the sysroot, replace it with = and
-# store the result into func_replace_sysroot_result.
-func_replace_sysroot ()
-{
-  case "$lt_sysroot:$1" in
-  ?*:"$lt_sysroot"*)
-    func_stripname "$lt_sysroot" '' "$1"
-    func_replace_sysroot_result="=$func_stripname_result"
-    ;;
-  *)
-    # Including no sysroot.
-    func_replace_sysroot_result=$1
-    ;;
-  esac
-}
-
-# func_infer_tag arg
-# Infer tagged configuration to use if any are available and
-# if one wasn't chosen via the "--tag" command line option.
-# Only attempt this if the compiler in the base compile
-# command doesn't match the default compiler.
-# arg is usually of the form 'gcc ...'
-func_infer_tag ()
-{
-    $opt_debug
-    if test -n "$available_tags" && test -z "$tagname"; then
-      CC_quoted=
-      for arg in $CC; do
-	func_append_quoted CC_quoted "$arg"
-      done
-      CC_expanded=`func_echo_all $CC`
-      CC_quoted_expanded=`func_echo_all $CC_quoted`
-      case $@ in
-      # Blanks in the command may have been stripped by the calling shell,
-      # but not from the CC environment variable when configure was run.
-      " $CC "* | "$CC "* | " $CC_expanded "* | "$CC_expanded "* | \
-      " $CC_quoted"* | "$CC_quoted "* | " $CC_quoted_expanded "* | "$CC_quoted_expanded "*) ;;
-      # Blanks at the start of $base_compile will cause this to fail
-      # if we don't check for them as well.
-      *)
-	for z in $available_tags; do
-	  if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then
-	    # Evaluate the configuration.
-	    eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`"
-	    CC_quoted=
-	    for arg in $CC; do
-	      # Double-quote args containing other shell metacharacters.
-	      func_append_quoted CC_quoted "$arg"
-	    done
-	    CC_expanded=`func_echo_all $CC`
-	    CC_quoted_expanded=`func_echo_all $CC_quoted`
-	    case "$@ " in
-	    " $CC "* | "$CC "* | " $CC_expanded "* | "$CC_expanded "* | \
-	    " $CC_quoted"* | "$CC_quoted "* | " $CC_quoted_expanded "* | "$CC_quoted_expanded "*)
-	      # The compiler in the base compile command matches
-	      # the one in the tagged configuration.
-	      # Assume this is the tagged configuration we want.
-	      tagname=$z
-	      break
-	      ;;
-	    esac
-	  fi
-	done
-	# If $tagname still isn't set, then no tagged configuration
-	# was found and let the user know that the "--tag" command
-	# line option must be used.
-	if test -z "$tagname"; then
-	  func_echo "unable to infer tagged configuration"
-	  func_fatal_error "specify a tag with \`--tag'"
-#	else
-#	  func_verbose "using $tagname tagged configuration"
-	fi
-	;;
-      esac
-    fi
-}
-
-
-
-# func_write_libtool_object output_name pic_name nonpic_name
-# Create a libtool object file (analogous to a ".la" file),
-# but don't create it if we're doing a dry run.
-func_write_libtool_object ()
-{
-    write_libobj=${1}
-    if test "$build_libtool_libs" = yes; then
-      write_lobj=\'${2}\'
-    else
-      write_lobj=none
-    fi
-
-    if test "$build_old_libs" = yes; then
-      write_oldobj=\'${3}\'
-    else
-      write_oldobj=none
-    fi
-
-    $opt_dry_run || {
-      cat >${write_libobj}T <<EOF
-# $write_libobj - a libtool object file
-# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
-#
-# Please DO NOT delete this file!
-# It is necessary for linking the library.
-
-# Name of the PIC object.
-pic_object=$write_lobj
-
-# Name of the non-PIC object
-non_pic_object=$write_oldobj
-
-EOF
-      $MV "${write_libobj}T" "${write_libobj}"
-    }
-}
-
-
-##################################################
-# FILE NAME AND PATH CONVERSION HELPER FUNCTIONS #
-##################################################
-
-# func_convert_core_file_wine_to_w32 ARG
-# Helper function used by file name conversion functions when $build is *nix,
-# and $host is mingw, cygwin, or some other w32 environment. Relies on a
-# correctly configured wine environment available, with the winepath program
-# in $build's $PATH.
-#
-# ARG is the $build file name to be converted to w32 format.
-# Result is available in $func_convert_core_file_wine_to_w32_result, and will
-# be empty on error (or when ARG is empty)
-func_convert_core_file_wine_to_w32 ()
-{
-  $opt_debug
-  func_convert_core_file_wine_to_w32_result="$1"
-  if test -n "$1"; then
-    # Unfortunately, winepath does not exit with a non-zero error code, so we
-    # are forced to check the contents of stdout. On the other hand, if the
-    # command is not found, the shell will set an exit code of 127 and print
-    # *an error message* to stdout. So we must check for both error code of
-    # zero AND non-empty stdout, which explains the odd construction:
-    func_convert_core_file_wine_to_w32_tmp=`winepath -w "$1" 2>/dev/null`
-    if test "$?" -eq 0 && test -n "${func_convert_core_file_wine_to_w32_tmp}"; then
-      func_convert_core_file_wine_to_w32_result=`$ECHO "$func_convert_core_file_wine_to_w32_tmp" |
-        $SED -e "$lt_sed_naive_backslashify"`
-    else
-      func_convert_core_file_wine_to_w32_result=
-    fi
-  fi
-}
-# end: func_convert_core_file_wine_to_w32
-
-
-# func_convert_core_path_wine_to_w32 ARG
-# Helper function used by path conversion functions when $build is *nix, and
-# $host is mingw, cygwin, or some other w32 environment. Relies on a correctly
-# configured wine environment available, with the winepath program in $build's
-# $PATH. Assumes ARG has no leading or trailing path separator characters.
-#
-# ARG is path to be converted from $build format to win32.
-# Result is available in $func_convert_core_path_wine_to_w32_result.
-# Unconvertible file (directory) names in ARG are skipped; if no directory names
-# are convertible, then the result may be empty.
-func_convert_core_path_wine_to_w32 ()
-{
-  $opt_debug
-  # unfortunately, winepath doesn't convert paths, only file names
-  func_convert_core_path_wine_to_w32_result=""
-  if test -n "$1"; then
-    oldIFS=$IFS
-    IFS=:
-    for func_convert_core_path_wine_to_w32_f in $1; do
-      IFS=$oldIFS
-      func_convert_core_file_wine_to_w32 "$func_convert_core_path_wine_to_w32_f"
-      if test -n "$func_convert_core_file_wine_to_w32_result" ; then
-        if test -z "$func_convert_core_path_wine_to_w32_result"; then
-          func_convert_core_path_wine_to_w32_result="$func_convert_core_file_wine_to_w32_result"
-        else
-          func_append func_convert_core_path_wine_to_w32_result ";$func_convert_core_file_wine_to_w32_result"
-        fi
-      fi
-    done
-    IFS=$oldIFS
-  fi
-}
-# end: func_convert_core_path_wine_to_w32
-
-
-# func_cygpath ARGS...
-# Wrapper around calling the cygpath program via LT_CYGPATH. This is used when
-# when (1) $build is *nix and Cygwin is hosted via a wine environment; or (2)
-# $build is MSYS and $host is Cygwin, or (3) $build is Cygwin. In case (1) or
-# (2), returns the Cygwin file name or path in func_cygpath_result (input
-# file name or path is assumed to be in w32 format, as previously converted
-# from $build's *nix or MSYS format). In case (3), returns the w32 file name
-# or path in func_cygpath_result (input file name or path is assumed to be in
-# Cygwin format). Returns an empty string on error.
-#
-# ARGS are passed to cygpath, with the last one being the file name or path to
-# be converted.
-#
-# Specify the absolute *nix (or w32) name to cygpath in the LT_CYGPATH
-# environment variable; do not put it in $PATH.
-func_cygpath ()
-{
-  $opt_debug
-  if test -n "$LT_CYGPATH" && test -f "$LT_CYGPATH"; then
-    func_cygpath_result=`$LT_CYGPATH "$@" 2>/dev/null`
-    if test "$?" -ne 0; then
-      # on failure, ensure result is empty
-      func_cygpath_result=
-    fi
-  else
-    func_cygpath_result=
-    func_error "LT_CYGPATH is empty or specifies non-existent file: \`$LT_CYGPATH'"
-  fi
-}
-#end: func_cygpath
-
-
-# func_convert_core_msys_to_w32 ARG
-# Convert file name or path ARG from MSYS format to w32 format.  Return
-# result in func_convert_core_msys_to_w32_result.
-func_convert_core_msys_to_w32 ()
-{
-  $opt_debug
-  # awkward: cmd appends spaces to result
-  func_convert_core_msys_to_w32_result=`( cmd //c echo "$1" ) 2>/dev/null |
-    $SED -e 's/[ ]*$//' -e "$lt_sed_naive_backslashify"`
-}
-#end: func_convert_core_msys_to_w32
-
-
-# func_convert_file_check ARG1 ARG2
-# Verify that ARG1 (a file name in $build format) was converted to $host
-# format in ARG2. Otherwise, emit an error message, but continue (resetting
-# func_to_host_file_result to ARG1).
-func_convert_file_check ()
-{
-  $opt_debug
-  if test -z "$2" && test -n "$1" ; then
-    func_error "Could not determine host file name corresponding to"
-    func_error "  \`$1'"
-    func_error "Continuing, but uninstalled executables may not work."
-    # Fallback:
-    func_to_host_file_result="$1"
-  fi
-}
-# end func_convert_file_check
-
-
-# func_convert_path_check FROM_PATHSEP TO_PATHSEP FROM_PATH TO_PATH
-# Verify that FROM_PATH (a path in $build format) was converted to $host
-# format in TO_PATH. Otherwise, emit an error message, but continue, resetting
-# func_to_host_file_result to a simplistic fallback value (see below).
-func_convert_path_check ()
-{
-  $opt_debug
-  if test -z "$4" && test -n "$3"; then
-    func_error "Could not determine the host path corresponding to"
-    func_error "  \`$3'"
-    func_error "Continuing, but uninstalled executables may not work."
-    # Fallback.  This is a deliberately simplistic "conversion" and
-    # should not be "improved".  See libtool.info.
-    if test "x$1" != "x$2"; then
-      lt_replace_pathsep_chars="s|$1|$2|g"
-      func_to_host_path_result=`echo "$3" |
-        $SED -e "$lt_replace_pathsep_chars"`
-    else
-      func_to_host_path_result="$3"
-    fi
-  fi
-}
-# end func_convert_path_check
-
-
-# func_convert_path_front_back_pathsep FRONTPAT BACKPAT REPL ORIG
-# Modifies func_to_host_path_result by prepending REPL if ORIG matches FRONTPAT
-# and appending REPL if ORIG matches BACKPAT.
-func_convert_path_front_back_pathsep ()
-{
-  $opt_debug
-  case $4 in
-  $1 ) func_to_host_path_result="$3$func_to_host_path_result"
-    ;;
-  esac
-  case $4 in
-  $2 ) func_append func_to_host_path_result "$3"
-    ;;
-  esac
-}
-# end func_convert_path_front_back_pathsep
-
-
-##################################################
-# $build to $host FILE NAME CONVERSION FUNCTIONS #
-##################################################
-# invoked via `$to_host_file_cmd ARG'
-#
-# In each case, ARG is the path to be converted from $build to $host format.
-# Result will be available in $func_to_host_file_result.
-
-
-# func_to_host_file ARG
-# Converts the file name ARG from $build format to $host format. Return result
-# in func_to_host_file_result.
-func_to_host_file ()
-{
-  $opt_debug
-  $to_host_file_cmd "$1"
-}
-# end func_to_host_file
-
-
-# func_to_tool_file ARG LAZY
-# converts the file name ARG from $build format to toolchain format. Return
-# result in func_to_tool_file_result.  If the conversion in use is listed
-# in (the comma separated) LAZY, no conversion takes place.
-func_to_tool_file ()
-{
-  $opt_debug
-  case ,$2, in
-    *,"$to_tool_file_cmd",*)
-      func_to_tool_file_result=$1
-      ;;
-    *)
-      $to_tool_file_cmd "$1"
-      func_to_tool_file_result=$func_to_host_file_result
-      ;;
-  esac
-}
-# end func_to_tool_file
-
-
-# func_convert_file_noop ARG
-# Copy ARG to func_to_host_file_result.
-func_convert_file_noop ()
-{
-  func_to_host_file_result="$1"
-}
-# end func_convert_file_noop
-
-
-# func_convert_file_msys_to_w32 ARG
-# Convert file name ARG from (mingw) MSYS to (mingw) w32 format; automatic
-# conversion to w32 is not available inside the cwrapper.  Returns result in
-# func_to_host_file_result.
-func_convert_file_msys_to_w32 ()
-{
-  $opt_debug
-  func_to_host_file_result="$1"
-  if test -n "$1"; then
-    func_convert_core_msys_to_w32 "$1"
-    func_to_host_file_result="$func_convert_core_msys_to_w32_result"
-  fi
-  func_convert_file_check "$1" "$func_to_host_file_result"
-}
-# end func_convert_file_msys_to_w32
-
-
-# func_convert_file_cygwin_to_w32 ARG
-# Convert file name ARG from Cygwin to w32 format.  Returns result in
-# func_to_host_file_result.
-func_convert_file_cygwin_to_w32 ()
-{
-  $opt_debug
-  func_to_host_file_result="$1"
-  if test -n "$1"; then
-    # because $build is cygwin, we call "the" cygpath in $PATH; no need to use
-    # LT_CYGPATH in this case.
-    func_to_host_file_result=`cygpath -m "$1"`
-  fi
-  func_convert_file_check "$1" "$func_to_host_file_result"
-}
-# end func_convert_file_cygwin_to_w32
-
-
-# func_convert_file_nix_to_w32 ARG
-# Convert file name ARG from *nix to w32 format.  Requires a wine environment
-# and a working winepath. Returns result in func_to_host_file_result.
-func_convert_file_nix_to_w32 ()
-{
-  $opt_debug
-  func_to_host_file_result="$1"
-  if test -n "$1"; then
-    func_convert_core_file_wine_to_w32 "$1"
-    func_to_host_file_result="$func_convert_core_file_wine_to_w32_result"
-  fi
-  func_convert_file_check "$1" "$func_to_host_file_result"
-}
-# end func_convert_file_nix_to_w32
-
-
-# func_convert_file_msys_to_cygwin ARG
-# Convert file name ARG from MSYS to Cygwin format.  Requires LT_CYGPATH set.
-# Returns result in func_to_host_file_result.
-func_convert_file_msys_to_cygwin ()
-{
-  $opt_debug
-  func_to_host_file_result="$1"
-  if test -n "$1"; then
-    func_convert_core_msys_to_w32 "$1"
-    func_cygpath -u "$func_convert_core_msys_to_w32_result"
-    func_to_host_file_result="$func_cygpath_result"
-  fi
-  func_convert_file_check "$1" "$func_to_host_file_result"
-}
-# end func_convert_file_msys_to_cygwin
-
-
-# func_convert_file_nix_to_cygwin ARG
-# Convert file name ARG from *nix to Cygwin format.  Requires Cygwin installed
-# in a wine environment, working winepath, and LT_CYGPATH set.  Returns result
-# in func_to_host_file_result.
-func_convert_file_nix_to_cygwin ()
-{
-  $opt_debug
-  func_to_host_file_result="$1"
-  if test -n "$1"; then
-    # convert from *nix to w32, then use cygpath to convert from w32 to cygwin.
-    func_convert_core_file_wine_to_w32 "$1"
-    func_cygpath -u "$func_convert_core_file_wine_to_w32_result"
-    func_to_host_file_result="$func_cygpath_result"
-  fi
-  func_convert_file_check "$1" "$func_to_host_file_result"
-}
-# end func_convert_file_nix_to_cygwin
-
-
-#############################################
-# $build to $host PATH CONVERSION FUNCTIONS #
-#############################################
-# invoked via `$to_host_path_cmd ARG'
-#
-# In each case, ARG is the path to be converted from $build to $host format.
-# The result will be available in $func_to_host_path_result.
-#
-# Path separators are also converted from $build format to $host format.  If
-# ARG begins or ends with a path separator character, it is preserved (but
-# converted to $host format) on output.
-#
-# All path conversion functions are named using the following convention:
-#   file name conversion function    : func_convert_file_X_to_Y ()
-#   path conversion function         : func_convert_path_X_to_Y ()
-# where, for any given $build/$host combination the 'X_to_Y' value is the
-# same.  If conversion functions are added for new $build/$host combinations,
-# the two new functions must follow this pattern, or func_init_to_host_path_cmd
-# will break.
-
-
-# func_init_to_host_path_cmd
-# Ensures that function "pointer" variable $to_host_path_cmd is set to the
-# appropriate value, based on the value of $to_host_file_cmd.
-to_host_path_cmd=
-func_init_to_host_path_cmd ()
-{
-  $opt_debug
-  if test -z "$to_host_path_cmd"; then
-    func_stripname 'func_convert_file_' '' "$to_host_file_cmd"
-    to_host_path_cmd="func_convert_path_${func_stripname_result}"
-  fi
-}
-
-
-# func_to_host_path ARG
-# Converts the path ARG from $build format to $host format. Return result
-# in func_to_host_path_result.
-func_to_host_path ()
-{
-  $opt_debug
-  func_init_to_host_path_cmd
-  $to_host_path_cmd "$1"
-}
-# end func_to_host_path
-
-
-# func_convert_path_noop ARG
-# Copy ARG to func_to_host_path_result.
-func_convert_path_noop ()
-{
-  func_to_host_path_result="$1"
-}
-# end func_convert_path_noop
-
-
-# func_convert_path_msys_to_w32 ARG
-# Convert path ARG from (mingw) MSYS to (mingw) w32 format; automatic
-# conversion to w32 is not available inside the cwrapper.  Returns result in
-# func_to_host_path_result.
-func_convert_path_msys_to_w32 ()
-{
-  $opt_debug
-  func_to_host_path_result="$1"
-  if test -n "$1"; then
-    # Remove leading and trailing path separator characters from ARG.  MSYS
-    # behavior is inconsistent here; cygpath turns them into '.;' and ';.';
-    # and winepath ignores them completely.
-    func_stripname : : "$1"
-    func_to_host_path_tmp1=$func_stripname_result
-    func_convert_core_msys_to_w32 "$func_to_host_path_tmp1"
-    func_to_host_path_result="$func_convert_core_msys_to_w32_result"
-    func_convert_path_check : ";" \
-      "$func_to_host_path_tmp1" "$func_to_host_path_result"
-    func_convert_path_front_back_pathsep ":*" "*:" ";" "$1"
-  fi
-}
-# end func_convert_path_msys_to_w32
-
-
-# func_convert_path_cygwin_to_w32 ARG
-# Convert path ARG from Cygwin to w32 format.  Returns result in
-# func_to_host_file_result.
-func_convert_path_cygwin_to_w32 ()
-{
-  $opt_debug
-  func_to_host_path_result="$1"
-  if test -n "$1"; then
-    # See func_convert_path_msys_to_w32:
-    func_stripname : : "$1"
-    func_to_host_path_tmp1=$func_stripname_result
-    func_to_host_path_result=`cygpath -m -p "$func_to_host_path_tmp1"`
-    func_convert_path_check : ";" \
-      "$func_to_host_path_tmp1" "$func_to_host_path_result"
-    func_convert_path_front_back_pathsep ":*" "*:" ";" "$1"
-  fi
-}
-# end func_convert_path_cygwin_to_w32
-
-
-# func_convert_path_nix_to_w32 ARG
-# Convert path ARG from *nix to w32 format.  Requires a wine environment and
-# a working winepath.  Returns result in func_to_host_file_result.
-func_convert_path_nix_to_w32 ()
-{
-  $opt_debug
-  func_to_host_path_result="$1"
-  if test -n "$1"; then
-    # See func_convert_path_msys_to_w32:
-    func_stripname : : "$1"
-    func_to_host_path_tmp1=$func_stripname_result
-    func_convert_core_path_wine_to_w32 "$func_to_host_path_tmp1"
-    func_to_host_path_result="$func_convert_core_path_wine_to_w32_result"
-    func_convert_path_check : ";" \
-      "$func_to_host_path_tmp1" "$func_to_host_path_result"
-    func_convert_path_front_back_pathsep ":*" "*:" ";" "$1"
-  fi
-}
-# end func_convert_path_nix_to_w32
-
-
-# func_convert_path_msys_to_cygwin ARG
-# Convert path ARG from MSYS to Cygwin format.  Requires LT_CYGPATH set.
-# Returns result in func_to_host_file_result.
-func_convert_path_msys_to_cygwin ()
-{
-  $opt_debug
-  func_to_host_path_result="$1"
-  if test -n "$1"; then
-    # See func_convert_path_msys_to_w32:
-    func_stripname : : "$1"
-    func_to_host_path_tmp1=$func_stripname_result
-    func_convert_core_msys_to_w32 "$func_to_host_path_tmp1"
-    func_cygpath -u -p "$func_convert_core_msys_to_w32_result"
-    func_to_host_path_result="$func_cygpath_result"
-    func_convert_path_check : : \
-      "$func_to_host_path_tmp1" "$func_to_host_path_result"
-    func_convert_path_front_back_pathsep ":*" "*:" : "$1"
-  fi
-}
-# end func_convert_path_msys_to_cygwin
-
-
-# func_convert_path_nix_to_cygwin ARG
-# Convert path ARG from *nix to Cygwin format.  Requires Cygwin installed in a
-# a wine environment, working winepath, and LT_CYGPATH set.  Returns result in
-# func_to_host_file_result.
-func_convert_path_nix_to_cygwin ()
-{
-  $opt_debug
-  func_to_host_path_result="$1"
-  if test -n "$1"; then
-    # Remove leading and trailing path separator characters from
-    # ARG. msys behavior is inconsistent here, cygpath turns them
-    # into '.;' and ';.', and winepath ignores them completely.
-    func_stripname : : "$1"
-    func_to_host_path_tmp1=$func_stripname_result
-    func_convert_core_path_wine_to_w32 "$func_to_host_path_tmp1"
-    func_cygpath -u -p "$func_convert_core_path_wine_to_w32_result"
-    func_to_host_path_result="$func_cygpath_result"
-    func_convert_path_check : : \
-      "$func_to_host_path_tmp1" "$func_to_host_path_result"
-    func_convert_path_front_back_pathsep ":*" "*:" : "$1"
-  fi
-}
-# end func_convert_path_nix_to_cygwin
-
-
-# func_mode_compile arg...
-func_mode_compile ()
-{
-    $opt_debug
-    # Get the compilation command and the source file.
-    base_compile=
-    srcfile="$nonopt"  #  always keep a non-empty value in "srcfile"
-    suppress_opt=yes
-    suppress_output=
-    arg_mode=normal
-    libobj=
-    later=
-    pie_flag=
-
-    for arg
-    do
-      case $arg_mode in
-      arg  )
-	# do not "continue".  Instead, add this to base_compile
-	lastarg="$arg"
-	arg_mode=normal
-	;;
-
-      target )
-	libobj="$arg"
-	arg_mode=normal
-	continue
-	;;
-
-      normal )
-	# Accept any command-line options.
-	case $arg in
-	-o)
-	  test -n "$libobj" && \
-	    func_fatal_error "you cannot specify \`-o' more than once"
-	  arg_mode=target
-	  continue
-	  ;;
-
-	-pie | -fpie | -fPIE)
-          func_append pie_flag " $arg"
-	  continue
-	  ;;
-
-	-shared | -static | -prefer-pic | -prefer-non-pic)
-	  func_append later " $arg"
-	  continue
-	  ;;
-
-	-no-suppress)
-	  suppress_opt=no
-	  continue
-	  ;;
-
-	-Xcompiler)
-	  arg_mode=arg  #  the next one goes into the "base_compile" arg list
-	  continue      #  The current "srcfile" will either be retained or
-	  ;;            #  replaced later.  I would guess that would be a bug.
-
-	-Wc,*)
-	  func_stripname '-Wc,' '' "$arg"
-	  args=$func_stripname_result
-	  lastarg=
-	  save_ifs="$IFS"; IFS=','
-	  for arg in $args; do
-	    IFS="$save_ifs"
-	    func_append_quoted lastarg "$arg"
-	  done
-	  IFS="$save_ifs"
-	  func_stripname ' ' '' "$lastarg"
-	  lastarg=$func_stripname_result
-
-	  # Add the arguments to base_compile.
-	  func_append base_compile " $lastarg"
-	  continue
-	  ;;
-
-	*)
-	  # Accept the current argument as the source file.
-	  # The previous "srcfile" becomes the current argument.
-	  #
-	  lastarg="$srcfile"
-	  srcfile="$arg"
-	  ;;
-	esac  #  case $arg
-	;;
-      esac    #  case $arg_mode
-
-      # Aesthetically quote the previous argument.
-      func_append_quoted base_compile "$lastarg"
-    done # for arg
-
-    case $arg_mode in
-    arg)
-      func_fatal_error "you must specify an argument for -Xcompile"
-      ;;
-    target)
-      func_fatal_error "you must specify a target with \`-o'"
-      ;;
-    *)
-      # Get the name of the library object.
-      test -z "$libobj" && {
-	func_basename "$srcfile"
-	libobj="$func_basename_result"
-      }
-      ;;
-    esac
-
-    # Recognize several different file suffixes.
-    # If the user specifies -o file.o, it is replaced with file.lo
-    case $libobj in
-    *.[cCFSifmso] | \
-    *.ada | *.adb | *.ads | *.asm | \
-    *.c++ | *.cc | *.ii | *.class | *.cpp | *.cxx | \
-    *.[fF][09]? | *.for | *.java | *.go | *.obj | *.sx | *.cu | *.cup)
-      func_xform "$libobj"
-      libobj=$func_xform_result
-      ;;
-    esac
-
-    case $libobj in
-    *.lo) func_lo2o "$libobj"; obj=$func_lo2o_result ;;
-    *)
-      func_fatal_error "cannot determine name of library object from \`$libobj'"
-      ;;
-    esac
-
-    func_infer_tag $base_compile
-
-    for arg in $later; do
-      case $arg in
-      -shared)
-	test "$build_libtool_libs" != yes && \
-	  func_fatal_configuration "can not build a shared library"
-	build_old_libs=no
-	continue
-	;;
-
-      -static)
-	build_libtool_libs=no
-	build_old_libs=yes
-	continue
-	;;
-
-      -prefer-pic)
-	pic_mode=yes
-	continue
-	;;
-
-      -prefer-non-pic)
-	pic_mode=no
-	continue
-	;;
-      esac
-    done
-
-    func_quote_for_eval "$libobj"
-    test "X$libobj" != "X$func_quote_for_eval_result" \
-      && $ECHO "X$libobj" | $GREP '[]~#^*{};<>?"'"'"'	 &()|`$[]' \
-      && func_warning "libobj name \`$libobj' may not contain shell special characters."
-    func_dirname_and_basename "$obj" "/" ""
-    objname="$func_basename_result"
-    xdir="$func_dirname_result"
-    lobj=${xdir}$objdir/$objname
-
-    test -z "$base_compile" && \
-      func_fatal_help "you must specify a compilation command"
-
-    # Delete any leftover library objects.
-    if test "$build_old_libs" = yes; then
-      removelist="$obj $lobj $libobj ${libobj}T"
-    else
-      removelist="$lobj $libobj ${libobj}T"
-    fi
-
-    # On Cygwin there's no "real" PIC flag so we must build both object types
-    case $host_os in
-    cygwin* | mingw* | pw32* | os2* | cegcc*)
-      pic_mode=default
-      ;;
-    esac
-    if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then
-      # non-PIC code in shared libraries is not supported
-      pic_mode=default
-    fi
-
-    # Calculate the filename of the output object if compiler does
-    # not support -o with -c
-    if test "$compiler_c_o" = no; then
-      output_obj=`$ECHO "$srcfile" | $SED 's%^.*/%%; s%\.[^.]*$%%'`.${objext}
-      lockfile="$output_obj.lock"
-    else
-      output_obj=
-      need_locks=no
-      lockfile=
-    fi
-
-    # Lock this critical section if it is needed
-    # We use this script file to make the link, it avoids creating a new file
-    if test "$need_locks" = yes; then
-      until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do
-	func_echo "Waiting for $lockfile to be removed"
-	sleep 2
-      done
-    elif test "$need_locks" = warn; then
-      if test -f "$lockfile"; then
-	$ECHO "\
-*** ERROR, $lockfile exists and contains:
-`cat $lockfile 2>/dev/null`
-
-This indicates that another process is trying to use the same
-temporary object file, and libtool could not work around it because
-your compiler does not support \`-c' and \`-o' together.  If you
-repeat this compilation, it may succeed, by chance, but you had better
-avoid parallel builds (make -j) in this platform, or get a better
-compiler."
-
-	$opt_dry_run || $RM $removelist
-	exit $EXIT_FAILURE
-      fi
-      func_append removelist " $output_obj"
-      $ECHO "$srcfile" > "$lockfile"
-    fi
-
-    $opt_dry_run || $RM $removelist
-    func_append removelist " $lockfile"
-    trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15
-
-    func_to_tool_file "$srcfile" func_convert_file_msys_to_w32
-    srcfile=$func_to_tool_file_result
-    func_quote_for_eval "$srcfile"
-    qsrcfile=$func_quote_for_eval_result
-
-    # Only build a PIC object if we are building libtool libraries.
-    if test "$build_libtool_libs" = yes; then
-      # Without this assignment, base_compile gets emptied.
-      fbsd_hideous_sh_bug=$base_compile
-
-      if test "$pic_mode" != no; then
-	command="$base_compile $qsrcfile $pic_flag"
-      else
-	# Don't build PIC code
-	command="$base_compile $qsrcfile"
-      fi
-
-      func_mkdir_p "$xdir$objdir"
-
-      if test -z "$output_obj"; then
-	# Place PIC objects in $objdir
-	func_append command " -o $lobj"
-      fi
-
-      func_show_eval_locale "$command"	\
-          'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE'
-
-      if test "$need_locks" = warn &&
-	 test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
-	$ECHO "\
-*** ERROR, $lockfile contains:
-`cat $lockfile 2>/dev/null`
-
-but it should contain:
-$srcfile
-
-This indicates that another process is trying to use the same
-temporary object file, and libtool could not work around it because
-your compiler does not support \`-c' and \`-o' together.  If you
-repeat this compilation, it may succeed, by chance, but you had better
-avoid parallel builds (make -j) in this platform, or get a better
-compiler."
-
-	$opt_dry_run || $RM $removelist
-	exit $EXIT_FAILURE
-      fi
-
-      # Just move the object if needed, then go on to compile the next one
-      if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then
-	func_show_eval '$MV "$output_obj" "$lobj"' \
-	  'error=$?; $opt_dry_run || $RM $removelist; exit $error'
-      fi
-
-      # Allow error messages only from the first compilation.
-      if test "$suppress_opt" = yes; then
-	suppress_output=' >/dev/null 2>&1'
-      fi
-    fi
-
-    # Only build a position-dependent object if we build old libraries.
-    if test "$build_old_libs" = yes; then
-      if test "$pic_mode" != yes; then
-	# Don't build PIC code
-	command="$base_compile $qsrcfile$pie_flag"
-      else
-	command="$base_compile $qsrcfile $pic_flag"
-      fi
-      if test "$compiler_c_o" = yes; then
-	func_append command " -o $obj"
-      fi
-
-      # Suppress compiler output if we already did a PIC compilation.
-      func_append command "$suppress_output"
-      func_show_eval_locale "$command" \
-        '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE'
-
-      if test "$need_locks" = warn &&
-	 test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
-	$ECHO "\
-*** ERROR, $lockfile contains:
-`cat $lockfile 2>/dev/null`
-
-but it should contain:
-$srcfile
-
-This indicates that another process is trying to use the same
-temporary object file, and libtool could not work around it because
-your compiler does not support \`-c' and \`-o' together.  If you
-repeat this compilation, it may succeed, by chance, but you had better
-avoid parallel builds (make -j) in this platform, or get a better
-compiler."
-
-	$opt_dry_run || $RM $removelist
-	exit $EXIT_FAILURE
-      fi
-
-      # Just move the object if needed
-      if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then
-	func_show_eval '$MV "$output_obj" "$obj"' \
-	  'error=$?; $opt_dry_run || $RM $removelist; exit $error'
-      fi
-    fi
-
-    $opt_dry_run || {
-      func_write_libtool_object "$libobj" "$objdir/$objname" "$objname"
-
-      # Unlock the critical section if it was locked
-      if test "$need_locks" != no; then
-	removelist=$lockfile
-        $RM "$lockfile"
-      fi
-    }
-
-    exit $EXIT_SUCCESS
-}
-
-$opt_help || {
-  test "$opt_mode" = compile && func_mode_compile ${1+"$@"}
-}
-
-func_mode_help ()
-{
-    # We need to display help for each of the modes.
-    case $opt_mode in
-      "")
-        # Generic help is extracted from the usage comments
-        # at the start of this file.
-        func_help
-        ;;
-
-      clean)
-        $ECHO \
-"Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE...
-
-Remove files from the build directory.
-
-RM is the name of the program to use to delete files associated with each FILE
-(typically \`/bin/rm').  RM-OPTIONS are options (such as \`-f') to be passed
-to RM.
-
-If FILE is a libtool library, object or program, all the files associated
-with it are deleted. Otherwise, only FILE itself is deleted using RM."
-        ;;
-
-      compile)
-      $ECHO \
-"Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE
-
-Compile a source file into a libtool library object.
-
-This mode accepts the following additional options:
-
-  -o OUTPUT-FILE    set the output file name to OUTPUT-FILE
-  -no-suppress      do not suppress compiler output for multiple passes
-  -prefer-pic       try to build PIC objects only
-  -prefer-non-pic   try to build non-PIC objects only
-  -shared           do not build a \`.o' file suitable for static linking
-  -static           only build a \`.o' file suitable for static linking
-  -Wc,FLAG          pass FLAG directly to the compiler
-
-COMPILE-COMMAND is a command to be used in creating a \`standard' object file
-from the given SOURCEFILE.
-
-The output file name is determined by removing the directory component from
-SOURCEFILE, then substituting the C source code suffix \`.c' with the
-library object suffix, \`.lo'."
-        ;;
-
-      execute)
-        $ECHO \
-"Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]...
-
-Automatically set library path, then run a program.
-
-This mode accepts the following additional options:
-
-  -dlopen FILE      add the directory containing FILE to the library path
-
-This mode sets the library path environment variable according to \`-dlopen'
-flags.
-
-If any of the ARGS are libtool executable wrappers, then they are translated
-into their corresponding uninstalled binary, and any of their required library
-directories are added to the library path.
-
-Then, COMMAND is executed, with ARGS as arguments."
-        ;;
-
-      finish)
-        $ECHO \
-"Usage: $progname [OPTION]... --mode=finish [LIBDIR]...
-
-Complete the installation of libtool libraries.
-
-Each LIBDIR is a directory that contains libtool libraries.
-
-The commands that this mode executes may require superuser privileges.  Use
-the \`--dry-run' option if you just want to see what would be executed."
-        ;;
-
-      install)
-        $ECHO \
-"Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND...
-
-Install executables or libraries.
-
-INSTALL-COMMAND is the installation command.  The first component should be
-either the \`install' or \`cp' program.
-
-The following components of INSTALL-COMMAND are treated specially:
-
-  -inst-prefix-dir PREFIX-DIR  Use PREFIX-DIR as a staging area for installation
-
-The rest of the components are interpreted as arguments to that command (only
-BSD-compatible install options are recognized)."
-        ;;
-
-      link)
-        $ECHO \
-"Usage: $progname [OPTION]... --mode=link LINK-COMMAND...
-
-Link object files or libraries together to form another library, or to
-create an executable program.
-
-LINK-COMMAND is a command using the C compiler that you would use to create
-a program from several object files.
-
-The following components of LINK-COMMAND are treated specially:
-
-  -all-static       do not do any dynamic linking at all
-  -avoid-version    do not add a version suffix if possible
-  -bindir BINDIR    specify path to binaries directory (for systems where
-                    libraries must be found in the PATH setting at runtime)
-  -dlopen FILE      \`-dlpreopen' FILE if it cannot be dlopened at runtime
-  -dlpreopen FILE   link in FILE and add its symbols to lt_preloaded_symbols
-  -export-dynamic   allow symbols from OUTPUT-FILE to be resolved with dlsym(3)
-  -export-symbols SYMFILE
-                    try to export only the symbols listed in SYMFILE
-  -export-symbols-regex REGEX
-                    try to export only the symbols matching REGEX
-  -LLIBDIR          search LIBDIR for required installed libraries
-  -lNAME            OUTPUT-FILE requires the installed library libNAME
-  -module           build a library that can dlopened
-  -no-fast-install  disable the fast-install mode
-  -no-install       link a not-installable executable
-  -no-undefined     declare that a library does not refer to external symbols
-  -o OUTPUT-FILE    create OUTPUT-FILE from the specified objects
-  -objectlist FILE  Use a list of object files found in FILE to specify objects
-  -precious-files-regex REGEX
-                    don't remove output files matching REGEX
-  -release RELEASE  specify package release information
-  -rpath LIBDIR     the created library will eventually be installed in LIBDIR
-  -R[ ]LIBDIR       add LIBDIR to the runtime path of programs and libraries
-  -shared           only do dynamic linking of libtool libraries
-  -shrext SUFFIX    override the standard shared library file extension
-  -static           do not do any dynamic linking of uninstalled libtool libraries
-  -static-libtool-libs
-                    do not do any dynamic linking of libtool libraries
-  -version-info CURRENT[:REVISION[:AGE]]
-                    specify library version info [each variable defaults to 0]
-  -weak LIBNAME     declare that the target provides the LIBNAME interface
-  -Wc,FLAG
-  -Xcompiler FLAG   pass linker-specific FLAG directly to the compiler
-  -Wl,FLAG
-  -Xlinker FLAG     pass linker-specific FLAG directly to the linker
-  -XCClinker FLAG   pass link-specific FLAG to the compiler driver (CC)
-
-All other options (arguments beginning with \`-') are ignored.
-
-Every other argument is treated as a filename.  Files ending in \`.la' are
-treated as uninstalled libtool libraries, other files are standard or library
-object files.
-
-If the OUTPUT-FILE ends in \`.la', then a libtool library is created,
-only library objects (\`.lo' files) may be specified, and \`-rpath' is
-required, except when creating a convenience library.
-
-If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created
-using \`ar' and \`ranlib', or on Windows using \`lib'.
-
-If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file
-is created, otherwise an executable program is created."
-        ;;
-
-      uninstall)
-        $ECHO \
-"Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE...
-
-Remove libraries from an installation directory.
-
-RM is the name of the program to use to delete files associated with each FILE
-(typically \`/bin/rm').  RM-OPTIONS are options (such as \`-f') to be passed
-to RM.
-
-If FILE is a libtool library, all the files associated with it are deleted.
-Otherwise, only FILE itself is deleted using RM."
-        ;;
-
-      *)
-        func_fatal_help "invalid operation mode \`$opt_mode'"
-        ;;
-    esac
-
-    echo
-    $ECHO "Try \`$progname --help' for more information about other modes."
-}
-
-# Now that we've collected a possible --mode arg, show help if necessary
-if $opt_help; then
-  if test "$opt_help" = :; then
-    func_mode_help
-  else
-    {
-      func_help noexit
-      for opt_mode in compile link execute install finish uninstall clean; do
-	func_mode_help
-      done
-    } | sed -n '1p; 2,$s/^Usage:/  or: /p'
-    {
-      func_help noexit
-      for opt_mode in compile link execute install finish uninstall clean; do
-	echo
-	func_mode_help
-      done
-    } |
-    sed '1d
-      /^When reporting/,/^Report/{
-	H
-	d
-      }
-      $x
-      /information about other modes/d
-      /more detailed .*MODE/d
-      s/^Usage:.*--mode=\([^ ]*\) .*/Description of \1 mode:/'
-  fi
-  exit $?
-fi
-
-
-# func_mode_execute arg...
-func_mode_execute ()
-{
-    $opt_debug
-    # The first argument is the command name.
-    cmd="$nonopt"
-    test -z "$cmd" && \
-      func_fatal_help "you must specify a COMMAND"
-
-    # Handle -dlopen flags immediately.
-    for file in $opt_dlopen; do
-      test -f "$file" \
-	|| func_fatal_help "\`$file' is not a file"
-
-      dir=
-      case $file in
-      *.la)
-	func_resolve_sysroot "$file"
-	file=$func_resolve_sysroot_result
-
-	# Check to see that this really is a libtool archive.
-	func_lalib_unsafe_p "$file" \
-	  || func_fatal_help "\`$lib' is not a valid libtool archive"
-
-	# Read the libtool library.
-	dlname=
-	library_names=
-	func_source "$file"
-
-	# Skip this library if it cannot be dlopened.
-	if test -z "$dlname"; then
-	  # Warn if it was a shared library.
-	  test -n "$library_names" && \
-	    func_warning "\`$file' was not linked with \`-export-dynamic'"
-	  continue
-	fi
-
-	func_dirname "$file" "" "."
-	dir="$func_dirname_result"
-
-	if test -f "$dir/$objdir/$dlname"; then
-	  func_append dir "/$objdir"
-	else
-	  if test ! -f "$dir/$dlname"; then
-	    func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'"
-	  fi
-	fi
-	;;
-
-      *.lo)
-	# Just add the directory containing the .lo file.
-	func_dirname "$file" "" "."
-	dir="$func_dirname_result"
-	;;
-
-      *)
-	func_warning "\`-dlopen' is ignored for non-libtool libraries and objects"
-	continue
-	;;
-      esac
-
-      # Get the absolute pathname.
-      absdir=`cd "$dir" && pwd`
-      test -n "$absdir" && dir="$absdir"
-
-      # Now add the directory to shlibpath_var.
-      if eval "test -z \"\$$shlibpath_var\""; then
-	eval "$shlibpath_var=\"\$dir\""
-      else
-	eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\""
-      fi
-    done
-
-    # This variable tells wrapper scripts just to set shlibpath_var
-    # rather than running their programs.
-    libtool_execute_magic="$magic"
-
-    # Check if any of the arguments is a wrapper script.
-    args=
-    for file
-    do
-      case $file in
-      -* | *.la | *.lo ) ;;
-      *)
-	# Do a test to see if this is really a libtool program.
-	if func_ltwrapper_script_p "$file"; then
-	  func_source "$file"
-	  # Transform arg to wrapped name.
-	  file="$progdir/$program"
-	elif func_ltwrapper_executable_p "$file"; then
-	  func_ltwrapper_scriptname "$file"
-	  func_source "$func_ltwrapper_scriptname_result"
-	  # Transform arg to wrapped name.
-	  file="$progdir/$program"
-	fi
-	;;
-      esac
-      # Quote arguments (to preserve shell metacharacters).
-      func_append_quoted args "$file"
-    done
-
-    if test "X$opt_dry_run" = Xfalse; then
-      if test -n "$shlibpath_var"; then
-	# Export the shlibpath_var.
-	eval "export $shlibpath_var"
-      fi
-
-      # Restore saved environment variables
-      for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
-      do
-	eval "if test \"\${save_$lt_var+set}\" = set; then
-                $lt_var=\$save_$lt_var; export $lt_var
-	      else
-		$lt_unset $lt_var
-	      fi"
-      done
-
-      # Now prepare to actually exec the command.
-      exec_cmd="\$cmd$args"
-    else
-      # Display what would be done.
-      if test -n "$shlibpath_var"; then
-	eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\""
-	echo "export $shlibpath_var"
-      fi
-      $ECHO "$cmd$args"
-      exit $EXIT_SUCCESS
-    fi
-}
-
-test "$opt_mode" = execute && func_mode_execute ${1+"$@"}
-
-
-# func_mode_finish arg...
-func_mode_finish ()
-{
-    $opt_debug
-    libs=
-    libdirs=
-    admincmds=
-
-    for opt in "$nonopt" ${1+"$@"}
-    do
-      if test -d "$opt"; then
-	func_append libdirs " $opt"
-
-      elif test -f "$opt"; then
-	if func_lalib_unsafe_p "$opt"; then
-	  func_append libs " $opt"
-	else
-	  func_warning "\`$opt' is not a valid libtool archive"
-	fi
-
-      else
-	func_fatal_error "invalid argument \`$opt'"
-      fi
-    done
-
-    if test -n "$libs"; then
-      if test -n "$lt_sysroot"; then
-        sysroot_regex=`$ECHO "$lt_sysroot" | $SED "$sed_make_literal_regex"`
-        sysroot_cmd="s/\([ ']\)$sysroot_regex/\1/g;"
-      else
-        sysroot_cmd=
-      fi
-
-      # Remove sysroot references
-      if $opt_dry_run; then
-        for lib in $libs; do
-          echo "removing references to $lt_sysroot and \`=' prefixes from $lib"
-        done
-      else
-        tmpdir=`func_mktempdir`
-        for lib in $libs; do
-	  sed -e "${sysroot_cmd} s/\([ ']-[LR]\)=/\1/g; s/\([ ']\)=/\1/g" $lib \
-	    > $tmpdir/tmp-la
-	  mv -f $tmpdir/tmp-la $lib
-	done
-        ${RM}r "$tmpdir"
-      fi
-    fi
-
-    if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then
-      for libdir in $libdirs; do
-	if test -n "$finish_cmds"; then
-	  # Do each command in the finish commands.
-	  func_execute_cmds "$finish_cmds" 'admincmds="$admincmds
-'"$cmd"'"'
-	fi
-	if test -n "$finish_eval"; then
-	  # Do the single finish_eval.
-	  eval cmds=\"$finish_eval\"
-	  $opt_dry_run || eval "$cmds" || func_append admincmds "
-       $cmds"
-	fi
-      done
-    fi
-
-    # Exit here if they wanted silent mode.
-    $opt_silent && exit $EXIT_SUCCESS
-
-    if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then
-      echo "----------------------------------------------------------------------"
-      echo "Libraries have been installed in:"
-      for libdir in $libdirs; do
-	$ECHO "   $libdir"
-      done
-      echo
-      echo "If you ever happen to want to link against installed libraries"
-      echo "in a given directory, LIBDIR, you must either use libtool, and"
-      echo "specify the full pathname of the library, or use the \`-LLIBDIR'"
-      echo "flag during linking and do at least one of the following:"
-      if test -n "$shlibpath_var"; then
-	echo "   - add LIBDIR to the \`$shlibpath_var' environment variable"
-	echo "     during execution"
-      fi
-      if test -n "$runpath_var"; then
-	echo "   - add LIBDIR to the \`$runpath_var' environment variable"
-	echo "     during linking"
-      fi
-      if test -n "$hardcode_libdir_flag_spec"; then
-	libdir=LIBDIR
-	eval flag=\"$hardcode_libdir_flag_spec\"
-
-	$ECHO "   - use the \`$flag' linker flag"
-      fi
-      if test -n "$admincmds"; then
-	$ECHO "   - have your system administrator run these commands:$admincmds"
-      fi
-      if test -f /etc/ld.so.conf; then
-	echo "   - have your system administrator add LIBDIR to \`/etc/ld.so.conf'"
-      fi
-      echo
-
-      echo "See any operating system documentation about shared libraries for"
-      case $host in
-	solaris2.[6789]|solaris2.1[0-9])
-	  echo "more information, such as the ld(1), crle(1) and ld.so(8) manual"
-	  echo "pages."
-	  ;;
-	*)
-	  echo "more information, such as the ld(1) and ld.so(8) manual pages."
-	  ;;
-      esac
-      echo "----------------------------------------------------------------------"
-    fi
-    exit $EXIT_SUCCESS
-}
-
-test "$opt_mode" = finish && func_mode_finish ${1+"$@"}
-
-
-# func_mode_install arg...
-func_mode_install ()
-{
-    $opt_debug
-    # There may be an optional sh(1) argument at the beginning of
-    # install_prog (especially on Windows NT).
-    if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh ||
-       # Allow the use of GNU shtool's install command.
-       case $nonopt in *shtool*) :;; *) false;; esac; then
-      # Aesthetically quote it.
-      func_quote_for_eval "$nonopt"
-      install_prog="$func_quote_for_eval_result "
-      arg=$1
-      shift
-    else
-      install_prog=
-      arg=$nonopt
-    fi
-
-    # The real first argument should be the name of the installation program.
-    # Aesthetically quote it.
-    func_quote_for_eval "$arg"
-    func_append install_prog "$func_quote_for_eval_result"
-    install_shared_prog=$install_prog
-    case " $install_prog " in
-      *[\\\ /]cp\ *) install_cp=: ;;
-      *) install_cp=false ;;
-    esac
-
-    # We need to accept at least all the BSD install flags.
-    dest=
-    files=
-    opts=
-    prev=
-    install_type=
-    isdir=no
-    stripme=
-    no_mode=:
-    for arg
-    do
-      arg2=
-      if test -n "$dest"; then
-	func_append files " $dest"
-	dest=$arg
-	continue
-      fi
-
-      case $arg in
-      -d) isdir=yes ;;
-      -f)
-	if $install_cp; then :; else
-	  prev=$arg
-	fi
-	;;
-      -g | -m | -o)
-	prev=$arg
-	;;
-      -s)
-	stripme=" -s"
-	continue
-	;;
-      -*)
-	;;
-      *)
-	# If the previous option needed an argument, then skip it.
-	if test -n "$prev"; then
-	  if test "x$prev" = x-m && test -n "$install_override_mode"; then
-	    arg2=$install_override_mode
-	    no_mode=false
-	  fi
-	  prev=
-	else
-	  dest=$arg
-	  continue
-	fi
-	;;
-      esac
-
-      # Aesthetically quote the argument.
-      func_quote_for_eval "$arg"
-      func_append install_prog " $func_quote_for_eval_result"
-      if test -n "$arg2"; then
-	func_quote_for_eval "$arg2"
-      fi
-      func_append install_shared_prog " $func_quote_for_eval_result"
-    done
-
-    test -z "$install_prog" && \
-      func_fatal_help "you must specify an install program"
-
-    test -n "$prev" && \
-      func_fatal_help "the \`$prev' option requires an argument"
-
-    if test -n "$install_override_mode" && $no_mode; then
-      if $install_cp; then :; else
-	func_quote_for_eval "$install_override_mode"
-	func_append install_shared_prog " -m $func_quote_for_eval_result"
-      fi
-    fi
-
-    if test -z "$files"; then
-      if test -z "$dest"; then
-	func_fatal_help "no file or destination specified"
-      else
-	func_fatal_help "you must specify a destination"
-      fi
-    fi
-
-    # Strip any trailing slash from the destination.
-    func_stripname '' '/' "$dest"
-    dest=$func_stripname_result
-
-    # Check to see that the destination is a directory.
-    test -d "$dest" && isdir=yes
-    if test "$isdir" = yes; then
-      destdir="$dest"
-      destname=
-    else
-      func_dirname_and_basename "$dest" "" "."
-      destdir="$func_dirname_result"
-      destname="$func_basename_result"
-
-      # Not a directory, so check to see that there is only one file specified.
-      set dummy $files; shift
-      test "$#" -gt 1 && \
-	func_fatal_help "\`$dest' is not a directory"
-    fi
-    case $destdir in
-    [\\/]* | [A-Za-z]:[\\/]*) ;;
-    *)
-      for file in $files; do
-	case $file in
-	*.lo) ;;
-	*)
-	  func_fatal_help "\`$destdir' must be an absolute directory name"
-	  ;;
-	esac
-      done
-      ;;
-    esac
-
-    # This variable tells wrapper scripts just to set variables rather
-    # than running their programs.
-    libtool_install_magic="$magic"
-
-    staticlibs=
-    future_libdirs=
-    current_libdirs=
-    for file in $files; do
-
-      # Do each installation.
-      case $file in
-      *.$libext)
-	# Do the static libraries later.
-	func_append staticlibs " $file"
-	;;
-
-      *.la)
-	func_resolve_sysroot "$file"
-	file=$func_resolve_sysroot_result
-
-	# Check to see that this really is a libtool archive.
-	func_lalib_unsafe_p "$file" \
-	  || func_fatal_help "\`$file' is not a valid libtool archive"
-
-	library_names=
-	old_library=
-	relink_command=
-	func_source "$file"
-
-	# Add the libdir to current_libdirs if it is the destination.
-	if test "X$destdir" = "X$libdir"; then
-	  case "$current_libdirs " in
-	  *" $libdir "*) ;;
-	  *) func_append current_libdirs " $libdir" ;;
-	  esac
-	else
-	  # Note the libdir as a future libdir.
-	  case "$future_libdirs " in
-	  *" $libdir "*) ;;
-	  *) func_append future_libdirs " $libdir" ;;
-	  esac
-	fi
-
-	func_dirname "$file" "/" ""
-	dir="$func_dirname_result"
-	func_append dir "$objdir"
-
-	if test -n "$relink_command"; then
-	  # Determine the prefix the user has applied to our future dir.
-	  inst_prefix_dir=`$ECHO "$destdir" | $SED -e "s%$libdir\$%%"`
-
-	  # Don't allow the user to place us outside of our expected
-	  # location b/c this prevents finding dependent libraries that
-	  # are installed to the same prefix.
-	  # At present, this check doesn't affect windows .dll's that
-	  # are installed into $libdir/../bin (currently, that works fine)
-	  # but it's something to keep an eye on.
-	  test "$inst_prefix_dir" = "$destdir" && \
-	    func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir"
-
-	  if test -n "$inst_prefix_dir"; then
-	    # Stick the inst_prefix_dir data into the link command.
-	    relink_command=`$ECHO "$relink_command" | $SED "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"`
-	  else
-	    relink_command=`$ECHO "$relink_command" | $SED "s%@inst_prefix_dir@%%"`
-	  fi
-
-	  func_warning "relinking \`$file'"
-	  func_show_eval "$relink_command" \
-	    'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"'
-	fi
-
-	# See the names of the shared library.
-	set dummy $library_names; shift
-	if test -n "$1"; then
-	  realname="$1"
-	  shift
-
-	  srcname="$realname"
-	  test -n "$relink_command" && srcname="$realname"T
-
-	  # Install the shared library and build the symlinks.
-	  func_show_eval "$install_shared_prog $dir/$srcname $destdir/$realname" \
-	      'exit $?'
-	  tstripme="$stripme"
-	  case $host_os in
-	  cygwin* | mingw* | pw32* | cegcc*)
-	    case $realname in
-	    *.dll.a)
-	      tstripme=""
-	      ;;
-	    esac
-	    ;;
-	  esac
-	  if test -n "$tstripme" && test -n "$striplib"; then
-	    func_show_eval "$striplib $destdir/$realname" 'exit $?'
-	  fi
-
-	  if test "$#" -gt 0; then
-	    # Delete the old symlinks, and create new ones.
-	    # Try `ln -sf' first, because the `ln' binary might depend on
-	    # the symlink we replace!  Solaris /bin/ln does not understand -f,
-	    # so we also need to try rm && ln -s.
-	    for linkname
-	    do
-	      test "$linkname" != "$realname" \
-		&& func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })"
-	    done
-	  fi
-
-	  # Do each command in the postinstall commands.
-	  lib="$destdir/$realname"
-	  func_execute_cmds "$postinstall_cmds" 'exit $?'
-	fi
-
-	# Install the pseudo-library for information purposes.
-	func_basename "$file"
-	name="$func_basename_result"
-	instname="$dir/$name"i
-	func_show_eval "$install_prog $instname $destdir/$name" 'exit $?'
-
-	# Maybe install the static library, too.
-	test -n "$old_library" && func_append staticlibs " $dir/$old_library"
-	;;
-
-      *.lo)
-	# Install (i.e. copy) a libtool object.
-
-	# Figure out destination file name, if it wasn't already specified.
-	if test -n "$destname"; then
-	  destfile="$destdir/$destname"
-	else
-	  func_basename "$file"
-	  destfile="$func_basename_result"
-	  destfile="$destdir/$destfile"
-	fi
-
-	# Deduce the name of the destination old-style object file.
-	case $destfile in
-	*.lo)
-	  func_lo2o "$destfile"
-	  staticdest=$func_lo2o_result
-	  ;;
-	*.$objext)
-	  staticdest="$destfile"
-	  destfile=
-	  ;;
-	*)
-	  func_fatal_help "cannot copy a libtool object to \`$destfile'"
-	  ;;
-	esac
-
-	# Install the libtool object if requested.
-	test -n "$destfile" && \
-	  func_show_eval "$install_prog $file $destfile" 'exit $?'
-
-	# Install the old object if enabled.
-	if test "$build_old_libs" = yes; then
-	  # Deduce the name of the old-style object file.
-	  func_lo2o "$file"
-	  staticobj=$func_lo2o_result
-	  func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?'
-	fi
-	exit $EXIT_SUCCESS
-	;;
-
-      *)
-	# Figure out destination file name, if it wasn't already specified.
-	if test -n "$destname"; then
-	  destfile="$destdir/$destname"
-	else
-	  func_basename "$file"
-	  destfile="$func_basename_result"
-	  destfile="$destdir/$destfile"
-	fi
-
-	# If the file is missing, and there is a .exe on the end, strip it
-	# because it is most likely a libtool script we actually want to
-	# install
-	stripped_ext=""
-	case $file in
-	  *.exe)
-	    if test ! -f "$file"; then
-	      func_stripname '' '.exe' "$file"
-	      file=$func_stripname_result
-	      stripped_ext=".exe"
-	    fi
-	    ;;
-	esac
-
-	# Do a test to see if this is really a libtool program.
-	case $host in
-	*cygwin* | *mingw*)
-	    if func_ltwrapper_executable_p "$file"; then
-	      func_ltwrapper_scriptname "$file"
-	      wrapper=$func_ltwrapper_scriptname_result
-	    else
-	      func_stripname '' '.exe' "$file"
-	      wrapper=$func_stripname_result
-	    fi
-	    ;;
-	*)
-	    wrapper=$file
-	    ;;
-	esac
-	if func_ltwrapper_script_p "$wrapper"; then
-	  notinst_deplibs=
-	  relink_command=
-
-	  func_source "$wrapper"
-
-	  # Check the variables that should have been set.
-	  test -z "$generated_by_libtool_version" && \
-	    func_fatal_error "invalid libtool wrapper script \`$wrapper'"
-
-	  finalize=yes
-	  for lib in $notinst_deplibs; do
-	    # Check to see that each library is installed.
-	    libdir=
-	    if test -f "$lib"; then
-	      func_source "$lib"
-	    fi
-	    libfile="$libdir/"`$ECHO "$lib" | $SED 's%^.*/%%g'` ### testsuite: skip nested quoting test
-	    if test -n "$libdir" && test ! -f "$libfile"; then
-	      func_warning "\`$lib' has not been installed in \`$libdir'"
-	      finalize=no
-	    fi
-	  done
-
-	  relink_command=
-	  func_source "$wrapper"
-
-	  outputname=
-	  if test "$fast_install" = no && test -n "$relink_command"; then
-	    $opt_dry_run || {
-	      if test "$finalize" = yes; then
-	        tmpdir=`func_mktempdir`
-		func_basename "$file$stripped_ext"
-		file="$func_basename_result"
-	        outputname="$tmpdir/$file"
-	        # Replace the output file specification.
-	        relink_command=`$ECHO "$relink_command" | $SED 's%@OUTPUT@%'"$outputname"'%g'`
-
-	        $opt_silent || {
-	          func_quote_for_expand "$relink_command"
-		  eval "func_echo $func_quote_for_expand_result"
-	        }
-	        if eval "$relink_command"; then :
-	          else
-		  func_error "error: relink \`$file' with the above command before installing it"
-		  $opt_dry_run || ${RM}r "$tmpdir"
-		  continue
-	        fi
-	        file="$outputname"
-	      else
-	        func_warning "cannot relink \`$file'"
-	      fi
-	    }
-	  else
-	    # Install the binary that we compiled earlier.
-	    file=`$ECHO "$file$stripped_ext" | $SED "s%\([^/]*\)$%$objdir/\1%"`
-	  fi
-	fi
-
-	# remove .exe since cygwin /usr/bin/install will append another
-	# one anyway
-	case $install_prog,$host in
-	*/usr/bin/install*,*cygwin*)
-	  case $file:$destfile in
-	  *.exe:*.exe)
-	    # this is ok
-	    ;;
-	  *.exe:*)
-	    destfile=$destfile.exe
-	    ;;
-	  *:*.exe)
-	    func_stripname '' '.exe' "$destfile"
-	    destfile=$func_stripname_result
-	    ;;
-	  esac
-	  ;;
-	esac
-	func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?'
-	$opt_dry_run || if test -n "$outputname"; then
-	  ${RM}r "$tmpdir"
-	fi
-	;;
-      esac
-    done
-
-    for file in $staticlibs; do
-      func_basename "$file"
-      name="$func_basename_result"
-
-      # Set up the ranlib parameters.
-      oldlib="$destdir/$name"
-      func_to_tool_file "$oldlib" func_convert_file_msys_to_w32
-      tool_oldlib=$func_to_tool_file_result
-
-      func_show_eval "$install_prog \$file \$oldlib" 'exit $?'
-
-      if test -n "$stripme" && test -n "$old_striplib"; then
-	func_show_eval "$old_striplib $tool_oldlib" 'exit $?'
-      fi
-
-      # Do each command in the postinstall commands.
-      func_execute_cmds "$old_postinstall_cmds" 'exit $?'
-    done
-
-    test -n "$future_libdirs" && \
-      func_warning "remember to run \`$progname --finish$future_libdirs'"
-
-    if test -n "$current_libdirs"; then
-      # Maybe just do a dry run.
-      $opt_dry_run && current_libdirs=" -n$current_libdirs"
-      exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs'
-    else
-      exit $EXIT_SUCCESS
-    fi
-}
-
-test "$opt_mode" = install && func_mode_install ${1+"$@"}
-
-
-# func_generate_dlsyms outputname originator pic_p
-# Extract symbols from dlprefiles and create ${outputname}S.o with
-# a dlpreopen symbol table.
-func_generate_dlsyms ()
-{
-    $opt_debug
-    my_outputname="$1"
-    my_originator="$2"
-    my_pic_p="${3-no}"
-    my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'`
-    my_dlsyms=
-
-    if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
-      if test -n "$NM" && test -n "$global_symbol_pipe"; then
-	my_dlsyms="${my_outputname}S.c"
-      else
-	func_error "not configured to extract global symbols from dlpreopened files"
-      fi
-    fi
-
-    if test -n "$my_dlsyms"; then
-      case $my_dlsyms in
-      "") ;;
-      *.c)
-	# Discover the nlist of each of the dlfiles.
-	nlist="$output_objdir/${my_outputname}.nm"
-
-	func_show_eval "$RM $nlist ${nlist}S ${nlist}T"
-
-	# Parse the name list into a source file.
-	func_verbose "creating $output_objdir/$my_dlsyms"
-
-	$opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\
-/* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */
-/* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */
-
-#ifdef __cplusplus
-extern \"C\" {
-#endif
-
-#if defined(__GNUC__) && (((__GNUC__ == 4) && (__GNUC_MINOR__ >= 4)) || (__GNUC__ > 4))
-#pragma GCC diagnostic ignored \"-Wstrict-prototypes\"
-#endif
-
-/* Keep this code in sync between libtool.m4, ltmain, lt_system.h, and tests.  */
-#if defined(_WIN32) || defined(__CYGWIN__) || defined(_WIN32_WCE)
-/* DATA imports from DLLs on WIN32 con't be const, because runtime
-   relocations are performed -- see ld's documentation on pseudo-relocs.  */
-# define LT_DLSYM_CONST
-#elif defined(__osf__)
-/* This system does not cope well with relocations in const data.  */
-# define LT_DLSYM_CONST
-#else
-# define LT_DLSYM_CONST const
-#endif
-
-/* External symbol declarations for the compiler. */\
-"
-
-	if test "$dlself" = yes; then
-	  func_verbose "generating symbol list for \`$output'"
-
-	  $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist"
-
-	  # Add our own program objects to the symbol list.
-	  progfiles=`$ECHO "$objs$old_deplibs" | $SP2NL | $SED "$lo2o" | $NL2SP`
-	  for progfile in $progfiles; do
-	    func_to_tool_file "$progfile" func_convert_file_msys_to_w32
-	    func_verbose "extracting global C symbols from \`$func_to_tool_file_result'"
-	    $opt_dry_run || eval "$NM $func_to_tool_file_result | $global_symbol_pipe >> '$nlist'"
-	  done
-
-	  if test -n "$exclude_expsyms"; then
-	    $opt_dry_run || {
-	      eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T'
-	      eval '$MV "$nlist"T "$nlist"'
-	    }
-	  fi
-
-	  if test -n "$export_symbols_regex"; then
-	    $opt_dry_run || {
-	      eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T'
-	      eval '$MV "$nlist"T "$nlist"'
-	    }
-	  fi
-
-	  # Prepare the list of exported symbols
-	  if test -z "$export_symbols"; then
-	    export_symbols="$output_objdir/$outputname.exp"
-	    $opt_dry_run || {
-	      $RM $export_symbols
-	      eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"'
-	      case $host in
-	      *cygwin* | *mingw* | *cegcc* )
-                eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
-                eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"'
-	        ;;
-	      esac
-	    }
-	  else
-	    $opt_dry_run || {
-	      eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"'
-	      eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T'
-	      eval '$MV "$nlist"T "$nlist"'
-	      case $host in
-	        *cygwin* | *mingw* | *cegcc* )
-	          eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
-	          eval 'cat "$nlist" >> "$output_objdir/$outputname.def"'
-	          ;;
-	      esac
-	    }
-	  fi
-	fi
-
-	for dlprefile in $dlprefiles; do
-	  func_verbose "extracting global C symbols from \`$dlprefile'"
-	  func_basename "$dlprefile"
-	  name="$func_basename_result"
-          case $host in
-	    *cygwin* | *mingw* | *cegcc* )
-	      # if an import library, we need to obtain dlname
-	      if func_win32_import_lib_p "$dlprefile"; then
-	        func_tr_sh "$dlprefile"
-	        eval "curr_lafile=\$libfile_$func_tr_sh_result"
-	        dlprefile_dlbasename=""
-	        if test -n "$curr_lafile" && func_lalib_p "$curr_lafile"; then
-	          # Use subshell, to avoid clobbering current variable values
-	          dlprefile_dlname=`source "$curr_lafile" && echo "$dlname"`
-	          if test -n "$dlprefile_dlname" ; then
-	            func_basename "$dlprefile_dlname"
-	            dlprefile_dlbasename="$func_basename_result"
-	          else
-	            # no lafile. user explicitly requested -dlpreopen <import library>.
-	            $sharedlib_from_linklib_cmd "$dlprefile"
-	            dlprefile_dlbasename=$sharedlib_from_linklib_result
-	          fi
-	        fi
-	        $opt_dry_run || {
-	          if test -n "$dlprefile_dlbasename" ; then
-	            eval '$ECHO ": $dlprefile_dlbasename" >> "$nlist"'
-	          else
-	            func_warning "Could not compute DLL name from $name"
-	            eval '$ECHO ": $name " >> "$nlist"'
-	          fi
-	          func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32
-	          eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe |
-	            $SED -e '/I __imp/d' -e 's/I __nm_/D /;s/_nm__//' >> '$nlist'"
-	        }
-	      else # not an import lib
-	        $opt_dry_run || {
-	          eval '$ECHO ": $name " >> "$nlist"'
-	          func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32
-	          eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe >> '$nlist'"
-	        }
-	      fi
-	    ;;
-	    *)
-	      $opt_dry_run || {
-	        eval '$ECHO ": $name " >> "$nlist"'
-	        func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32
-	        eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe >> '$nlist'"
-	      }
-	    ;;
-          esac
-	done
-
-	$opt_dry_run || {
-	  # Make sure we have at least an empty file.
-	  test -f "$nlist" || : > "$nlist"
-
-	  if test -n "$exclude_expsyms"; then
-	    $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T
-	    $MV "$nlist"T "$nlist"
-	  fi
-
-	  # Try sorting and uniquifying the output.
-	  if $GREP -v "^: " < "$nlist" |
-	      if sort -k 3 </dev/null >/dev/null 2>&1; then
-		sort -k 3
-	      else
-		sort +2
-	      fi |
-	      uniq > "$nlist"S; then
-	    :
-	  else
-	    $GREP -v "^: " < "$nlist" > "$nlist"S
-	  fi
-
-	  if test -f "$nlist"S; then
-	    eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"'
-	  else
-	    echo '/* NONE */' >> "$output_objdir/$my_dlsyms"
-	  fi
-
-	  echo >> "$output_objdir/$my_dlsyms" "\
-
-/* The mapping between symbol names and symbols.  */
-typedef struct {
-  const char *name;
-  void *address;
-} lt_dlsymlist;
-extern LT_DLSYM_CONST lt_dlsymlist
-lt_${my_prefix}_LTX_preloaded_symbols[];
-LT_DLSYM_CONST lt_dlsymlist
-lt_${my_prefix}_LTX_preloaded_symbols[] =
-{\
-  { \"$my_originator\", (void *) 0 },"
-
-	  case $need_lib_prefix in
-	  no)
-	    eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms"
-	    ;;
-	  *)
-	    eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms"
-	    ;;
-	  esac
-	  echo >> "$output_objdir/$my_dlsyms" "\
-  {0, (void *) 0}
-};
-
-/* This works around a problem in FreeBSD linker */
-#ifdef FREEBSD_WORKAROUND
-static const void *lt_preloaded_setup() {
-  return lt_${my_prefix}_LTX_preloaded_symbols;
-}
-#endif
-
-#ifdef __cplusplus
-}
-#endif\
-"
-	} # !$opt_dry_run
-
-	pic_flag_for_symtable=
-	case "$compile_command " in
-	*" -static "*) ;;
-	*)
-	  case $host in
-	  # compiling the symbol table file with pic_flag works around
-	  # a FreeBSD bug that causes programs to crash when -lm is
-	  # linked before any other PIC object.  But we must not use
-	  # pic_flag when linking with -static.  The problem exists in
-	  # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1.
-	  *-*-freebsd2.*|*-*-freebsd3.0*|*-*-freebsdelf3.0*)
-	    pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;;
-	  *-*-hpux*)
-	    pic_flag_for_symtable=" $pic_flag"  ;;
-	  *)
-	    if test "X$my_pic_p" != Xno; then
-	      pic_flag_for_symtable=" $pic_flag"
-	    fi
-	    ;;
-	  esac
-	  ;;
-	esac
-	symtab_cflags=
-	for arg in $LTCFLAGS; do
-	  case $arg in
-	  -pie | -fpie | -fPIE) ;;
-	  *) func_append symtab_cflags " $arg" ;;
-	  esac
-	done
-
-	# Now compile the dynamic symbol file.
-	func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?'
-
-	# Clean up the generated files.
-	func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"'
-
-	# Transform the symbol file into the correct name.
-	symfileobj="$output_objdir/${my_outputname}S.$objext"
-	case $host in
-	*cygwin* | *mingw* | *cegcc* )
-	  if test -f "$output_objdir/$my_outputname.def"; then
-	    compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
-	    finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
-	  else
-	    compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$symfileobj%"`
-	    finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$symfileobj%"`
-	  fi
-	  ;;
-	*)
-	  compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$symfileobj%"`
-	  finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$symfileobj%"`
-	  ;;
-	esac
-	;;
-      *)
-	func_fatal_error "unknown suffix for \`$my_dlsyms'"
-	;;
-      esac
-    else
-      # We keep going just in case the user didn't refer to
-      # lt_preloaded_symbols.  The linker will fail if global_symbol_pipe
-      # really was required.
-
-      # Nullify the symbol file.
-      compile_command=`$ECHO "$compile_command" | $SED "s% @SYMFILE@%%"`
-      finalize_command=`$ECHO "$finalize_command" | $SED "s% @SYMFILE@%%"`
-    fi
-}
-
-# func_win32_libid arg
-# return the library type of file 'arg'
-#
-# Need a lot of goo to handle *both* DLLs and import libs
-# Has to be a shell function in order to 'eat' the argument
-# that is supplied when $file_magic_command is called.
-# Despite the name, also deal with 64 bit binaries.
-func_win32_libid ()
-{
-  $opt_debug
-  win32_libid_type="unknown"
-  win32_fileres=`file -L $1 2>/dev/null`
-  case $win32_fileres in
-  *ar\ archive\ import\ library*) # definitely import
-    win32_libid_type="x86 archive import"
-    ;;
-  *ar\ archive*) # could be an import, or static
-    # Keep the egrep pattern in sync with the one in _LT_CHECK_MAGIC_METHOD.
-    if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null |
-       $EGREP 'file format (pei*-i386(.*architecture: i386)?|pe-arm-wince|pe-x86-64)' >/dev/null; then
-      func_to_tool_file "$1" func_convert_file_msys_to_w32
-      win32_nmres=`eval $NM -f posix -A \"$func_to_tool_file_result\" |
-	$SED -n -e '
-	    1,100{
-		/ I /{
-		    s,.*,import,
-		    p
-		    q
-		}
-	    }'`
-      case $win32_nmres in
-      import*)  win32_libid_type="x86 archive import";;
-      *)        win32_libid_type="x86 archive static";;
-      esac
-    fi
-    ;;
-  *DLL*)
-    win32_libid_type="x86 DLL"
-    ;;
-  *executable*) # but shell scripts are "executable" too...
-    case $win32_fileres in
-    *MS\ Windows\ PE\ Intel*)
-      win32_libid_type="x86 DLL"
-      ;;
-    esac
-    ;;
-  esac
-  $ECHO "$win32_libid_type"
-}
-
-# func_cygming_dll_for_implib ARG
-#
-# Platform-specific function to extract the
-# name of the DLL associated with the specified
-# import library ARG.
-# Invoked by eval'ing the libtool variable
-#    $sharedlib_from_linklib_cmd
-# Result is available in the variable
-#    $sharedlib_from_linklib_result
-func_cygming_dll_for_implib ()
-{
-  $opt_debug
-  sharedlib_from_linklib_result=`$DLLTOOL --identify-strict --identify "$1"`
-}
-
-# func_cygming_dll_for_implib_fallback_core SECTION_NAME LIBNAMEs
-#
-# The is the core of a fallback implementation of a
-# platform-specific function to extract the name of the
-# DLL associated with the specified import library LIBNAME.
-#
-# SECTION_NAME is either .idata$6 or .idata$7, depending
-# on the platform and compiler that created the implib.
-#
-# Echos the name of the DLL associated with the
-# specified import library.
-func_cygming_dll_for_implib_fallback_core ()
-{
-  $opt_debug
-  match_literal=`$ECHO "$1" | $SED "$sed_make_literal_regex"`
-  $OBJDUMP -s --section "$1" "$2" 2>/dev/null |
-    $SED '/^Contents of section '"$match_literal"':/{
-      # Place marker at beginning of archive member dllname section
-      s/.*/====MARK====/
-      p
-      d
-    }
-    # These lines can sometimes be longer than 43 characters, but
-    # are always uninteresting
-    /:[	 ]*file format pe[i]\{,1\}-/d
-    /^In archive [^:]*:/d
-    # Ensure marker is printed
-    /^====MARK====/p
-    # Remove all lines with less than 43 characters
-    /^.\{43\}/!d
-    # From remaining lines, remove first 43 characters
-    s/^.\{43\}//' |
-    $SED -n '
-      # Join marker and all lines until next marker into a single line
-      /^====MARK====/ b para
-      H
-      $ b para
-      b
-      :para
-      x
-      s/\n//g
-      # Remove the marker
-      s/^====MARK====//
-      # Remove trailing dots and whitespace
-      s/[\. \t]*$//
-      # Print
-      /./p' |
-    # we now have a list, one entry per line, of the stringified
-    # contents of the appropriate section of all members of the
-    # archive which possess that section. Heuristic: eliminate
-    # all those which have a first or second character that is
-    # a '.' (that is, objdump's representation of an unprintable
-    # character.) This should work for all archives with less than
-    # 0x302f exports -- but will fail for DLLs whose name actually
-    # begins with a literal '.' or a single character followed by
-    # a '.'.
-    #
-    # Of those that remain, print the first one.
-    $SED -e '/^\./d;/^.\./d;q'
-}
-
-# func_cygming_gnu_implib_p ARG
-# This predicate returns with zero status (TRUE) if
-# ARG is a GNU/binutils-style import library. Returns
-# with nonzero status (FALSE) otherwise.
-func_cygming_gnu_implib_p ()
-{
-  $opt_debug
-  func_to_tool_file "$1" func_convert_file_msys_to_w32
-  func_cygming_gnu_implib_tmp=`$NM "$func_to_tool_file_result" | eval "$global_symbol_pipe" | $EGREP ' (_head_[A-Za-z0-9_]+_[ad]l*|[A-Za-z0-9_]+_[ad]l*_iname)$'`
-  test -n "$func_cygming_gnu_implib_tmp"
-}
-
-# func_cygming_ms_implib_p ARG
-# This predicate returns with zero status (TRUE) if
-# ARG is an MS-style import library. Returns
-# with nonzero status (FALSE) otherwise.
-func_cygming_ms_implib_p ()
-{
-  $opt_debug
-  func_to_tool_file "$1" func_convert_file_msys_to_w32
-  func_cygming_ms_implib_tmp=`$NM "$func_to_tool_file_result" | eval "$global_symbol_pipe" | $GREP '_NULL_IMPORT_DESCRIPTOR'`
-  test -n "$func_cygming_ms_implib_tmp"
-}
-
-# func_cygming_dll_for_implib_fallback ARG
-# Platform-specific function to extract the
-# name of the DLL associated with the specified
-# import library ARG.
-#
-# This fallback implementation is for use when $DLLTOOL
-# does not support the --identify-strict option.
-# Invoked by eval'ing the libtool variable
-#    $sharedlib_from_linklib_cmd
-# Result is available in the variable
-#    $sharedlib_from_linklib_result
-func_cygming_dll_for_implib_fallback ()
-{
-  $opt_debug
-  if func_cygming_gnu_implib_p "$1" ; then
-    # binutils import library
-    sharedlib_from_linklib_result=`func_cygming_dll_for_implib_fallback_core '.idata$7' "$1"`
-  elif func_cygming_ms_implib_p "$1" ; then
-    # ms-generated import library
-    sharedlib_from_linklib_result=`func_cygming_dll_for_implib_fallback_core '.idata$6' "$1"`
-  else
-    # unknown
-    sharedlib_from_linklib_result=""
-  fi
-}
-
-
-# func_extract_an_archive dir oldlib
-func_extract_an_archive ()
-{
-    $opt_debug
-    f_ex_an_ar_dir="$1"; shift
-    f_ex_an_ar_oldlib="$1"
-    if test "$lock_old_archive_extraction" = yes; then
-      lockfile=$f_ex_an_ar_oldlib.lock
-      until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do
-	func_echo "Waiting for $lockfile to be removed"
-	sleep 2
-      done
-    fi
-    func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" \
-		   'stat=$?; rm -f "$lockfile"; exit $stat'
-    if test "$lock_old_archive_extraction" = yes; then
-      $opt_dry_run || rm -f "$lockfile"
-    fi
-    if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then
-     :
-    else
-      func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib"
-    fi
-}
-
-
-# func_extract_archives gentop oldlib ...
-func_extract_archives ()
-{
-    $opt_debug
-    my_gentop="$1"; shift
-    my_oldlibs=${1+"$@"}
-    my_oldobjs=""
-    my_xlib=""
-    my_xabs=""
-    my_xdir=""
-
-    for my_xlib in $my_oldlibs; do
-      # Extract the objects.
-      case $my_xlib in
-	[\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;;
-	*) my_xabs=`pwd`"/$my_xlib" ;;
-      esac
-      func_basename "$my_xlib"
-      my_xlib="$func_basename_result"
-      my_xlib_u=$my_xlib
-      while :; do
-        case " $extracted_archives " in
-	*" $my_xlib_u "*)
-	  func_arith $extracted_serial + 1
-	  extracted_serial=$func_arith_result
-	  my_xlib_u=lt$extracted_serial-$my_xlib ;;
-	*) break ;;
-	esac
-      done
-      extracted_archives="$extracted_archives $my_xlib_u"
-      my_xdir="$my_gentop/$my_xlib_u"
-
-      func_mkdir_p "$my_xdir"
-
-      case $host in
-      *-darwin*)
-	func_verbose "Extracting $my_xabs"
-	# Do not bother doing anything if just a dry run
-	$opt_dry_run || {
-	  darwin_orig_dir=`pwd`
-	  cd $my_xdir || exit $?
-	  darwin_archive=$my_xabs
-	  darwin_curdir=`pwd`
-	  darwin_base_archive=`basename "$darwin_archive"`
-	  darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true`
-	  if test -n "$darwin_arches"; then
-	    darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'`
-	    darwin_arch=
-	    func_verbose "$darwin_base_archive has multiple architectures $darwin_arches"
-	    for darwin_arch in  $darwin_arches ; do
-	      func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}"
-	      $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}"
-	      cd "unfat-$$/${darwin_base_archive}-${darwin_arch}"
-	      func_extract_an_archive "`pwd`" "${darwin_base_archive}"
-	      cd "$darwin_curdir"
-	      $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}"
-	    done # $darwin_arches
-            ## Okay now we've a bunch of thin objects, gotta fatten them up :)
-	    darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u`
-	    darwin_file=
-	    darwin_files=
-	    for darwin_file in $darwin_filelist; do
-	      darwin_files=`find unfat-$$ -name $darwin_file -print | sort | $NL2SP`
-	      $LIPO -create -output "$darwin_file" $darwin_files
-	    done # $darwin_filelist
-	    $RM -rf unfat-$$
-	    cd "$darwin_orig_dir"
-	  else
-	    cd $darwin_orig_dir
-	    func_extract_an_archive "$my_xdir" "$my_xabs"
-	  fi # $darwin_arches
-	} # !$opt_dry_run
-	;;
-      *)
-        func_extract_an_archive "$my_xdir" "$my_xabs"
-	;;
-      esac
-      my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | sort | $NL2SP`
-    done
-
-    func_extract_archives_result="$my_oldobjs"
-}
-
-
-# func_emit_wrapper [arg=no]
-#
-# Emit a libtool wrapper script on stdout.
-# Don't directly open a file because we may want to
-# incorporate the script contents within a cygwin/mingw
-# wrapper executable.  Must ONLY be called from within
-# func_mode_link because it depends on a number of variables
-# set therein.
-#
-# ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR
-# variable will take.  If 'yes', then the emitted script
-# will assume that the directory in which it is stored is
-# the $objdir directory.  This is a cygwin/mingw-specific
-# behavior.
-func_emit_wrapper ()
-{
-	func_emit_wrapper_arg1=${1-no}
-
-	$ECHO "\
-#! $SHELL
-
-# $output - temporary wrapper script for $objdir/$outputname
-# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
-#
-# The $output program cannot be directly executed until all the libtool
-# libraries that it depends on are installed.
-#
-# This wrapper script should never be moved out of the build directory.
-# If it is, it will not operate correctly.
-
-# Sed substitution that helps us do robust quoting.  It backslashifies
-# metacharacters that are still active within double-quoted strings.
-sed_quote_subst='$sed_quote_subst'
-
-# Be Bourne compatible
-if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then
-  emulate sh
-  NULLCMD=:
-  # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which
-  # is contrary to our usage.  Disable this feature.
-  alias -g '\${1+\"\$@\"}'='\"\$@\"'
-  setopt NO_GLOB_SUBST
-else
-  case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac
-fi
-BIN_SH=xpg4; export BIN_SH # for Tru64
-DUALCASE=1; export DUALCASE # for MKS sh
-
-# The HP-UX ksh and POSIX shell print the target directory to stdout
-# if CDPATH is set.
-(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-
-relink_command=\"$relink_command\"
-
-# This environment variable determines our operation mode.
-if test \"\$libtool_install_magic\" = \"$magic\"; then
-  # install mode needs the following variables:
-  generated_by_libtool_version='$macro_version'
-  notinst_deplibs='$notinst_deplibs'
-else
-  # When we are sourced in execute mode, \$file and \$ECHO are already set.
-  if test \"\$libtool_execute_magic\" != \"$magic\"; then
-    file=\"\$0\""
-
-    qECHO=`$ECHO "$ECHO" | $SED "$sed_quote_subst"`
-    $ECHO "\
-
-# A function that is used when there is no print builtin or printf.
-func_fallback_echo ()
-{
-  eval 'cat <<_LTECHO_EOF
-\$1
-_LTECHO_EOF'
-}
-    ECHO=\"$qECHO\"
-  fi
-
-# Very basic option parsing. These options are (a) specific to
-# the libtool wrapper, (b) are identical between the wrapper
-# /script/ and the wrapper /executable/ which is used only on
-# windows platforms, and (c) all begin with the string "--lt-"
-# (application programs are unlikely to have options which match
-# this pattern).
-#
-# There are only two supported options: --lt-debug and
-# --lt-dump-script. There is, deliberately, no --lt-help.
-#
-# The first argument to this parsing function should be the
-# script's $0 value, followed by "$@".
-lt_option_debug=
-func_parse_lt_options ()
-{
-  lt_script_arg0=\$0
-  shift
-  for lt_opt
-  do
-    case \"\$lt_opt\" in
-    --lt-debug) lt_option_debug=1 ;;
-    --lt-dump-script)
-        lt_dump_D=\`\$ECHO \"X\$lt_script_arg0\" | $SED -e 's/^X//' -e 's%/[^/]*$%%'\`
-        test \"X\$lt_dump_D\" = \"X\$lt_script_arg0\" && lt_dump_D=.
-        lt_dump_F=\`\$ECHO \"X\$lt_script_arg0\" | $SED -e 's/^X//' -e 's%^.*/%%'\`
-        cat \"\$lt_dump_D/\$lt_dump_F\"
-        exit 0
-      ;;
-    --lt-*)
-        \$ECHO \"Unrecognized --lt- option: '\$lt_opt'\" 1>&2
-        exit 1
-      ;;
-    esac
-  done
-
-  # Print the debug banner immediately:
-  if test -n \"\$lt_option_debug\"; then
-    echo \"${outputname}:${output}:\${LINENO}: libtool wrapper (GNU $PACKAGE$TIMESTAMP) $VERSION\" 1>&2
-  fi
-}
-
-# Used when --lt-debug. Prints its arguments to stdout
-# (redirection is the responsibility of the caller)
-func_lt_dump_args ()
-{
-  lt_dump_args_N=1;
-  for lt_arg
-  do
-    \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[\$lt_dump_args_N]: \$lt_arg\"
-    lt_dump_args_N=\`expr \$lt_dump_args_N + 1\`
-  done
-}
-
-# Core function for launching the target application
-func_exec_program_core ()
-{
-"
-  case $host in
-  # Backslashes separate directories on plain windows
-  *-*-mingw | *-*-os2* | *-cegcc*)
-    $ECHO "\
-      if test -n \"\$lt_option_debug\"; then
-        \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[0]: \$progdir\\\\\$program\" 1>&2
-        func_lt_dump_args \${1+\"\$@\"} 1>&2
-      fi
-      exec \"\$progdir\\\\\$program\" \${1+\"\$@\"}
-"
-    ;;
-
-  *)
-    $ECHO "\
-      if test -n \"\$lt_option_debug\"; then
-        \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[0]: \$progdir/\$program\" 1>&2
-        func_lt_dump_args \${1+\"\$@\"} 1>&2
-      fi
-      exec \"\$progdir/\$program\" \${1+\"\$@\"}
-"
-    ;;
-  esac
-  $ECHO "\
-      \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2
-      exit 1
-}
-
-# A function to encapsulate launching the target application
-# Strips options in the --lt-* namespace from \$@ and
-# launches target application with the remaining arguments.
-func_exec_program ()
-{
-  case \" \$* \" in
-  *\\ --lt-*)
-    for lt_wr_arg
-    do
-      case \$lt_wr_arg in
-      --lt-*) ;;
-      *) set x \"\$@\" \"\$lt_wr_arg\"; shift;;
-      esac
-      shift
-    done ;;
-  esac
-  func_exec_program_core \${1+\"\$@\"}
-}
-
-  # Parse options
-  func_parse_lt_options \"\$0\" \${1+\"\$@\"}
-
-  # Find the directory that this script lives in.
-  thisdir=\`\$ECHO \"\$file\" | $SED 's%/[^/]*$%%'\`
-  test \"x\$thisdir\" = \"x\$file\" && thisdir=.
-
-  # Follow symbolic links until we get to the real thisdir.
-  file=\`ls -ld \"\$file\" | $SED -n 's/.*-> //p'\`
-  while test -n \"\$file\"; do
-    destdir=\`\$ECHO \"\$file\" | $SED 's%/[^/]*\$%%'\`
-
-    # If there was a directory component, then change thisdir.
-    if test \"x\$destdir\" != \"x\$file\"; then
-      case \"\$destdir\" in
-      [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;;
-      *) thisdir=\"\$thisdir/\$destdir\" ;;
-      esac
-    fi
-
-    file=\`\$ECHO \"\$file\" | $SED 's%^.*/%%'\`
-    file=\`ls -ld \"\$thisdir/\$file\" | $SED -n 's/.*-> //p'\`
-  done
-
-  # Usually 'no', except on cygwin/mingw when embedded into
-  # the cwrapper.
-  WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_arg1
-  if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then
-    # special case for '.'
-    if test \"\$thisdir\" = \".\"; then
-      thisdir=\`pwd\`
-    fi
-    # remove .libs from thisdir
-    case \"\$thisdir\" in
-    *[\\\\/]$objdir ) thisdir=\`\$ECHO \"\$thisdir\" | $SED 's%[\\\\/][^\\\\/]*$%%'\` ;;
-    $objdir )   thisdir=. ;;
-    esac
-  fi
-
-  # Try to get the absolute directory name.
-  absdir=\`cd \"\$thisdir\" && pwd\`
-  test -n \"\$absdir\" && thisdir=\"\$absdir\"
-"
-
-	if test "$fast_install" = yes; then
-	  $ECHO "\
-  program=lt-'$outputname'$exeext
-  progdir=\"\$thisdir/$objdir\"
-
-  if test ! -f \"\$progdir/\$program\" ||
-     { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\
-       test \"X\$file\" != \"X\$progdir/\$program\"; }; then
-
-    file=\"\$\$-\$program\"
-
-    if test ! -d \"\$progdir\"; then
-      $MKDIR \"\$progdir\"
-    else
-      $RM \"\$progdir/\$file\"
-    fi"
-
-	  $ECHO "\
-
-    # relink executable if necessary
-    if test -n \"\$relink_command\"; then
-      if relink_command_output=\`eval \$relink_command 2>&1\`; then :
-      else
-	$ECHO \"\$relink_command_output\" >&2
-	$RM \"\$progdir/\$file\"
-	exit 1
-      fi
-    fi
-
-    $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null ||
-    { $RM \"\$progdir/\$program\";
-      $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; }
-    $RM \"\$progdir/\$file\"
-  fi"
-	else
-	  $ECHO "\
-  program='$outputname'
-  progdir=\"\$thisdir/$objdir\"
-"
-	fi
-
-	$ECHO "\
-
-  if test -f \"\$progdir/\$program\"; then"
-
-	# fixup the dll searchpath if we need to.
-	#
-	# Fix the DLL searchpath if we need to.  Do this before prepending
-	# to shlibpath, because on Windows, both are PATH and uninstalled
-	# libraries must come first.
-	if test -n "$dllsearchpath"; then
-	  $ECHO "\
-    # Add the dll search path components to the executable PATH
-    PATH=$dllsearchpath:\$PATH
-"
-	fi
-
-	# Export our shlibpath_var if we have one.
-	if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
-	  $ECHO "\
-    # Add our own library path to $shlibpath_var
-    $shlibpath_var=\"$temp_rpath\$$shlibpath_var\"
-
-    # Some systems cannot cope with colon-terminated $shlibpath_var
-    # The second colon is a workaround for a bug in BeOS R4 sed
-    $shlibpath_var=\`\$ECHO \"\$$shlibpath_var\" | $SED 's/::*\$//'\`
-
-    export $shlibpath_var
-"
-	fi
-
-	$ECHO "\
-    if test \"\$libtool_execute_magic\" != \"$magic\"; then
-      # Run the actual program with our arguments.
-      func_exec_program \${1+\"\$@\"}
-    fi
-  else
-    # The program doesn't exist.
-    \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2
-    \$ECHO \"This script is just a wrapper for \$program.\" 1>&2
-    \$ECHO \"See the $PACKAGE documentation for more information.\" 1>&2
-    exit 1
-  fi
-fi\
-"
-}
-
-
-# func_emit_cwrapperexe_src
-# emit the source code for a wrapper executable on stdout
-# Must ONLY be called from within func_mode_link because
-# it depends on a number of variable set therein.
-func_emit_cwrapperexe_src ()
-{
-	cat <<EOF
-
-/* $cwrappersource - temporary wrapper executable for $objdir/$outputname
-   Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
-
-   The $output program cannot be directly executed until all the libtool
-   libraries that it depends on are installed.
-
-   This wrapper executable should never be moved out of the build directory.
-   If it is, it will not operate correctly.
-*/
-EOF
-	    cat <<"EOF"
-#ifdef _MSC_VER
-# define _CRT_SECURE_NO_DEPRECATE 1
-#endif
-#include <stdio.h>
-#include <stdlib.h>
-#ifdef _MSC_VER
-# include <direct.h>
-# include <process.h>
-# include <io.h>
-#else
-# include <unistd.h>
-# include <stdint.h>
-# ifdef __CYGWIN__
-#  include <io.h>
-# endif
-#endif
-#include <malloc.h>
-#include <stdarg.h>
-#include <assert.h>
-#include <string.h>
-#include <ctype.h>
-#include <errno.h>
-#include <fcntl.h>
-#include <sys/stat.h>
-
-/* declarations of non-ANSI functions */
-#if defined(__MINGW32__)
-# ifdef __STRICT_ANSI__
-int _putenv (const char *);
-# endif
-#elif defined(__CYGWIN__)
-# ifdef __STRICT_ANSI__
-char *realpath (const char *, char *);
-int putenv (char *);
-int setenv (const char *, const char *, int);
-# endif
-/* #elif defined (other platforms) ... */
-#endif
-
-/* portability defines, excluding path handling macros */
-#if defined(_MSC_VER)
-# define setmode _setmode
-# define stat    _stat
-# define chmod   _chmod
-# define getcwd  _getcwd
-# define putenv  _putenv
-# define S_IXUSR _S_IEXEC
-# ifndef _INTPTR_T_DEFINED
-#  define _INTPTR_T_DEFINED
-#  define intptr_t int
-# endif
-#elif defined(__MINGW32__)
-# define setmode _setmode
-# define stat    _stat
-# define chmod   _chmod
-# define getcwd  _getcwd
-# define putenv  _putenv
-#elif defined(__CYGWIN__)
-# define HAVE_SETENV
-# define FOPEN_WB "wb"
-/* #elif defined (other platforms) ... */
-#endif
-
-#if defined(PATH_MAX)
-# define LT_PATHMAX PATH_MAX
-#elif defined(MAXPATHLEN)
-# define LT_PATHMAX MAXPATHLEN
-#else
-# define LT_PATHMAX 1024
-#endif
-
-#ifndef S_IXOTH
-# define S_IXOTH 0
-#endif
-#ifndef S_IXGRP
-# define S_IXGRP 0
-#endif
-
-/* path handling portability macros */
-#ifndef DIR_SEPARATOR
-# define DIR_SEPARATOR '/'
-# define PATH_SEPARATOR ':'
-#endif
-
-#if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \
-  defined (__OS2__)
-# define HAVE_DOS_BASED_FILE_SYSTEM
-# define FOPEN_WB "wb"
-# ifndef DIR_SEPARATOR_2
-#  define DIR_SEPARATOR_2 '\\'
-# endif
-# ifndef PATH_SEPARATOR_2
-#  define PATH_SEPARATOR_2 ';'
-# endif
-#endif
-
-#ifndef DIR_SEPARATOR_2
-# define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR)
-#else /* DIR_SEPARATOR_2 */
-# define IS_DIR_SEPARATOR(ch) \
-	(((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2))
-#endif /* DIR_SEPARATOR_2 */
-
-#ifndef PATH_SEPARATOR_2
-# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR)
-#else /* PATH_SEPARATOR_2 */
-# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2)
-#endif /* PATH_SEPARATOR_2 */
-
-#ifndef FOPEN_WB
-# define FOPEN_WB "w"
-#endif
-#ifndef _O_BINARY
-# define _O_BINARY 0
-#endif
-
-#define XMALLOC(type, num)      ((type *) xmalloc ((num) * sizeof(type)))
-#define XFREE(stale) do { \
-  if (stale) { free ((void *) stale); stale = 0; } \
-} while (0)
-
-#if defined(LT_DEBUGWRAPPER)
-static int lt_debug = 1;
-#else
-static int lt_debug = 0;
-#endif
-
-const char *program_name = "libtool-wrapper"; /* in case xstrdup fails */
-
-void *xmalloc (size_t num);
-char *xstrdup (const char *string);
-const char *base_name (const char *name);
-char *find_executable (const char *wrapper);
-char *chase_symlinks (const char *pathspec);
-int make_executable (const char *path);
-int check_executable (const char *path);
-char *strendzap (char *str, const char *pat);
-void lt_debugprintf (const char *file, int line, const char *fmt, ...);
-void lt_fatal (const char *file, int line, const char *message, ...);
-static const char *nonnull (const char *s);
-static const char *nonempty (const char *s);
-void lt_setenv (const char *name, const char *value);
-char *lt_extend_str (const char *orig_value, const char *add, int to_end);
-void lt_update_exe_path (const char *name, const char *value);
-void lt_update_lib_path (const char *name, const char *value);
-char **prepare_spawn (char **argv);
-void lt_dump_script (FILE *f);
-EOF
-
-	    cat <<EOF
-volatile const char * MAGIC_EXE = "$magic_exe";
-const char * LIB_PATH_VARNAME = "$shlibpath_var";
-EOF
-
-	    if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
-              func_to_host_path "$temp_rpath"
-	      cat <<EOF
-const char * LIB_PATH_VALUE   = "$func_to_host_path_result";
-EOF
-	    else
-	      cat <<"EOF"
-const char * LIB_PATH_VALUE   = "";
-EOF
-	    fi
-
-	    if test -n "$dllsearchpath"; then
-              func_to_host_path "$dllsearchpath:"
-	      cat <<EOF
-const char * EXE_PATH_VARNAME = "PATH";
-const char * EXE_PATH_VALUE   = "$func_to_host_path_result";
-EOF
-	    else
-	      cat <<"EOF"
-const char * EXE_PATH_VARNAME = "";
-const char * EXE_PATH_VALUE   = "";
-EOF
-	    fi
-
-	    if test "$fast_install" = yes; then
-	      cat <<EOF
-const char * TARGET_PROGRAM_NAME = "lt-$outputname"; /* hopefully, no .exe */
-EOF
-	    else
-	      cat <<EOF
-const char * TARGET_PROGRAM_NAME = "$outputname"; /* hopefully, no .exe */
-EOF
-	    fi
-
-
-	    cat <<"EOF"
-
-#define LTWRAPPER_OPTION_PREFIX         "--lt-"
-
-static const char *ltwrapper_option_prefix = LTWRAPPER_OPTION_PREFIX;
-static const char *dumpscript_opt       = LTWRAPPER_OPTION_PREFIX "dump-script";
-static const char *debug_opt            = LTWRAPPER_OPTION_PREFIX "debug";
-
-int
-main (int argc, char *argv[])
-{
-  char **newargz;
-  int  newargc;
-  char *tmp_pathspec;
-  char *actual_cwrapper_path;
-  char *actual_cwrapper_name;
-  char *target_name;
-  char *lt_argv_zero;
-  intptr_t rval = 127;
-
-  int i;
-
-  program_name = (char *) xstrdup (base_name (argv[0]));
-  newargz = XMALLOC (char *, argc + 1);
-
-  /* very simple arg parsing; don't want to rely on getopt
-   * also, copy all non cwrapper options to newargz, except
-   * argz[0], which is handled differently
-   */
-  newargc=0;
-  for (i = 1; i < argc; i++)
-    {
-      if (strcmp (argv[i], dumpscript_opt) == 0)
-	{
-EOF
-	    case "$host" in
-	      *mingw* | *cygwin* )
-		# make stdout use "unix" line endings
-		echo "          setmode(1,_O_BINARY);"
-		;;
-	      esac
-
-	    cat <<"EOF"
-	  lt_dump_script (stdout);
-	  return 0;
-	}
-      if (strcmp (argv[i], debug_opt) == 0)
-	{
-          lt_debug = 1;
-          continue;
-	}
-      if (strcmp (argv[i], ltwrapper_option_prefix) == 0)
-        {
-          /* however, if there is an option in the LTWRAPPER_OPTION_PREFIX
-             namespace, but it is not one of the ones we know about and
-             have already dealt with, above (inluding dump-script), then
-             report an error. Otherwise, targets might begin to believe
-             they are allowed to use options in the LTWRAPPER_OPTION_PREFIX
-             namespace. The first time any user complains about this, we'll
-             need to make LTWRAPPER_OPTION_PREFIX a configure-time option
-             or a configure.ac-settable value.
-           */
-          lt_fatal (__FILE__, __LINE__,
-		    "unrecognized %s option: '%s'",
-                    ltwrapper_option_prefix, argv[i]);
-        }
-      /* otherwise ... */
-      newargz[++newargc] = xstrdup (argv[i]);
-    }
-  newargz[++newargc] = NULL;
-
-EOF
-	    cat <<EOF
-  /* The GNU banner must be the first non-error debug message */
-  lt_debugprintf (__FILE__, __LINE__, "libtool wrapper (GNU $PACKAGE$TIMESTAMP) $VERSION\n");
-EOF
-	    cat <<"EOF"
-  lt_debugprintf (__FILE__, __LINE__, "(main) argv[0]: %s\n", argv[0]);
-  lt_debugprintf (__FILE__, __LINE__, "(main) program_name: %s\n", program_name);
-
-  tmp_pathspec = find_executable (argv[0]);
-  if (tmp_pathspec == NULL)
-    lt_fatal (__FILE__, __LINE__, "couldn't find %s", argv[0]);
-  lt_debugprintf (__FILE__, __LINE__,
-                  "(main) found exe (before symlink chase) at: %s\n",
-		  tmp_pathspec);
-
-  actual_cwrapper_path = chase_symlinks (tmp_pathspec);
-  lt_debugprintf (__FILE__, __LINE__,
-                  "(main) found exe (after symlink chase) at: %s\n",
-		  actual_cwrapper_path);
-  XFREE (tmp_pathspec);
-
-  actual_cwrapper_name = xstrdup (base_name (actual_cwrapper_path));
-  strendzap (actual_cwrapper_path, actual_cwrapper_name);
-
-  /* wrapper name transforms */
-  strendzap (actual_cwrapper_name, ".exe");
-  tmp_pathspec = lt_extend_str (actual_cwrapper_name, ".exe", 1);
-  XFREE (actual_cwrapper_name);
-  actual_cwrapper_name = tmp_pathspec;
-  tmp_pathspec = 0;
-
-  /* target_name transforms -- use actual target program name; might have lt- prefix */
-  target_name = xstrdup (base_name (TARGET_PROGRAM_NAME));
-  strendzap (target_name, ".exe");
-  tmp_pathspec = lt_extend_str (target_name, ".exe", 1);
-  XFREE (target_name);
-  target_name = tmp_pathspec;
-  tmp_pathspec = 0;
-
-  lt_debugprintf (__FILE__, __LINE__,
-		  "(main) libtool target name: %s\n",
-		  target_name);
-EOF
-
-	    cat <<EOF
-  newargz[0] =
-    XMALLOC (char, (strlen (actual_cwrapper_path) +
-		    strlen ("$objdir") + 1 + strlen (actual_cwrapper_name) + 1));
-  strcpy (newargz[0], actual_cwrapper_path);
-  strcat (newargz[0], "$objdir");
-  strcat (newargz[0], "/");
-EOF
-
-	    cat <<"EOF"
-  /* stop here, and copy so we don't have to do this twice */
-  tmp_pathspec = xstrdup (newargz[0]);
-
-  /* do NOT want the lt- prefix here, so use actual_cwrapper_name */
-  strcat (newargz[0], actual_cwrapper_name);
-
-  /* DO want the lt- prefix here if it exists, so use target_name */
-  lt_argv_zero = lt_extend_str (tmp_pathspec, target_name, 1);
-  XFREE (tmp_pathspec);
-  tmp_pathspec = NULL;
-EOF
-
-	    case $host_os in
-	      mingw*)
-	    cat <<"EOF"
-  {
-    char* p;
-    while ((p = strchr (newargz[0], '\\')) != NULL)
-      {
-	*p = '/';
-      }
-    while ((p = strchr (lt_argv_zero, '\\')) != NULL)
-      {
-	*p = '/';
-      }
-  }
-EOF
-	    ;;
-	    esac
-
-	    cat <<"EOF"
-  XFREE (target_name);
-  XFREE (actual_cwrapper_path);
-  XFREE (actual_cwrapper_name);
-
-  lt_setenv ("BIN_SH", "xpg4"); /* for Tru64 */
-  lt_setenv ("DUALCASE", "1");  /* for MSK sh */
-  /* Update the DLL searchpath.  EXE_PATH_VALUE ($dllsearchpath) must
-     be prepended before (that is, appear after) LIB_PATH_VALUE ($temp_rpath)
-     because on Windows, both *_VARNAMEs are PATH but uninstalled
-     libraries must come first. */
-  lt_update_exe_path (EXE_PATH_VARNAME, EXE_PATH_VALUE);
-  lt_update_lib_path (LIB_PATH_VARNAME, LIB_PATH_VALUE);
-
-  lt_debugprintf (__FILE__, __LINE__, "(main) lt_argv_zero: %s\n",
-		  nonnull (lt_argv_zero));
-  for (i = 0; i < newargc; i++)
-    {
-      lt_debugprintf (__FILE__, __LINE__, "(main) newargz[%d]: %s\n",
-		      i, nonnull (newargz[i]));
-    }
-
-EOF
-
-	    case $host_os in
-	      mingw*)
-		cat <<"EOF"
-  /* execv doesn't actually work on mingw as expected on unix */
-  newargz = prepare_spawn (newargz);
-  rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz);
-  if (rval == -1)
-    {
-      /* failed to start process */
-      lt_debugprintf (__FILE__, __LINE__,
-		      "(main) failed to launch target \"%s\": %s\n",
-		      lt_argv_zero, nonnull (strerror (errno)));
-      return 127;
-    }
-  return rval;
-EOF
-		;;
-	      *)
-		cat <<"EOF"
-  execv (lt_argv_zero, newargz);
-  return rval; /* =127, but avoids unused variable warning */
-EOF
-		;;
-	    esac
-
-	    cat <<"EOF"
-}
-
-void *
-xmalloc (size_t num)
-{
-  void *p = (void *) malloc (num);
-  if (!p)
-    lt_fatal (__FILE__, __LINE__, "memory exhausted");
-
-  return p;
-}
-
-char *
-xstrdup (const char *string)
-{
-  return string ? strcpy ((char *) xmalloc (strlen (string) + 1),
-			  string) : NULL;
-}
-
-const char *
-base_name (const char *name)
-{
-  const char *base;
-
-#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
-  /* Skip over the disk name in MSDOS pathnames. */
-  if (isalpha ((unsigned char) name[0]) && name[1] == ':')
-    name += 2;
-#endif
-
-  for (base = name; *name; name++)
-    if (IS_DIR_SEPARATOR (*name))
-      base = name + 1;
-  return base;
-}
-
-int
-check_executable (const char *path)
-{
-  struct stat st;
-
-  lt_debugprintf (__FILE__, __LINE__, "(check_executable): %s\n",
-                  nonempty (path));
-  if ((!path) || (!*path))
-    return 0;
-
-  if ((stat (path, &st) >= 0)
-      && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH)))
-    return 1;
-  else
-    return 0;
-}
-
-int
-make_executable (const char *path)
-{
-  int rval = 0;
-  struct stat st;
-
-  lt_debugprintf (__FILE__, __LINE__, "(make_executable): %s\n",
-                  nonempty (path));
-  if ((!path) || (!*path))
-    return 0;
-
-  if (stat (path, &st) >= 0)
-    {
-      rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR);
-    }
-  return rval;
-}
-
-/* Searches for the full path of the wrapper.  Returns
-   newly allocated full path name if found, NULL otherwise
-   Does not chase symlinks, even on platforms that support them.
-*/
-char *
-find_executable (const char *wrapper)
-{
-  int has_slash = 0;
-  const char *p;
-  const char *p_next;
-  /* static buffer for getcwd */
-  char tmp[LT_PATHMAX + 1];
-  int tmp_len;
-  char *concat_name;
-
-  lt_debugprintf (__FILE__, __LINE__, "(find_executable): %s\n",
-                  nonempty (wrapper));
-
-  if ((wrapper == NULL) || (*wrapper == '\0'))
-    return NULL;
-
-  /* Absolute path? */
-#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
-  if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':')
-    {
-      concat_name = xstrdup (wrapper);
-      if (check_executable (concat_name))
-	return concat_name;
-      XFREE (concat_name);
-    }
-  else
-    {
-#endif
-      if (IS_DIR_SEPARATOR (wrapper[0]))
-	{
-	  concat_name = xstrdup (wrapper);
-	  if (check_executable (concat_name))
-	    return concat_name;
-	  XFREE (concat_name);
-	}
-#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
-    }
-#endif
-
-  for (p = wrapper; *p; p++)
-    if (*p == '/')
-      {
-	has_slash = 1;
-	break;
-      }
-  if (!has_slash)
-    {
-      /* no slashes; search PATH */
-      const char *path = getenv ("PATH");
-      if (path != NULL)
-	{
-	  for (p = path; *p; p = p_next)
-	    {
-	      const char *q;
-	      size_t p_len;
-	      for (q = p; *q; q++)
-		if (IS_PATH_SEPARATOR (*q))
-		  break;
-	      p_len = q - p;
-	      p_next = (*q == '\0' ? q : q + 1);
-	      if (p_len == 0)
-		{
-		  /* empty path: current directory */
-		  if (getcwd (tmp, LT_PATHMAX) == NULL)
-		    lt_fatal (__FILE__, __LINE__, "getcwd failed: %s",
-                              nonnull (strerror (errno)));
-		  tmp_len = strlen (tmp);
-		  concat_name =
-		    XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
-		  memcpy (concat_name, tmp, tmp_len);
-		  concat_name[tmp_len] = '/';
-		  strcpy (concat_name + tmp_len + 1, wrapper);
-		}
-	      else
-		{
-		  concat_name =
-		    XMALLOC (char, p_len + 1 + strlen (wrapper) + 1);
-		  memcpy (concat_name, p, p_len);
-		  concat_name[p_len] = '/';
-		  strcpy (concat_name + p_len + 1, wrapper);
-		}
-	      if (check_executable (concat_name))
-		return concat_name;
-	      XFREE (concat_name);
-	    }
-	}
-      /* not found in PATH; assume curdir */
-    }
-  /* Relative path | not found in path: prepend cwd */
-  if (getcwd (tmp, LT_PATHMAX) == NULL)
-    lt_fatal (__FILE__, __LINE__, "getcwd failed: %s",
-              nonnull (strerror (errno)));
-  tmp_len = strlen (tmp);
-  concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
-  memcpy (concat_name, tmp, tmp_len);
-  concat_name[tmp_len] = '/';
-  strcpy (concat_name + tmp_len + 1, wrapper);
-
-  if (check_executable (concat_name))
-    return concat_name;
-  XFREE (concat_name);
-  return NULL;
-}
-
-char *
-chase_symlinks (const char *pathspec)
-{
-#ifndef S_ISLNK
-  return xstrdup (pathspec);
-#else
-  char buf[LT_PATHMAX];
-  struct stat s;
-  char *tmp_pathspec = xstrdup (pathspec);
-  char *p;
-  int has_symlinks = 0;
-  while (strlen (tmp_pathspec) && !has_symlinks)
-    {
-      lt_debugprintf (__FILE__, __LINE__,
-		      "checking path component for symlinks: %s\n",
-		      tmp_pathspec);
-      if (lstat (tmp_pathspec, &s) == 0)
-	{
-	  if (S_ISLNK (s.st_mode) != 0)
-	    {
-	      has_symlinks = 1;
-	      break;
-	    }
-
-	  /* search backwards for last DIR_SEPARATOR */
-	  p = tmp_pathspec + strlen (tmp_pathspec) - 1;
-	  while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
-	    p--;
-	  if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
-	    {
-	      /* no more DIR_SEPARATORS left */
-	      break;
-	    }
-	  *p = '\0';
-	}
-      else
-	{
-	  lt_fatal (__FILE__, __LINE__,
-		    "error accessing file \"%s\": %s",
-		    tmp_pathspec, nonnull (strerror (errno)));
-	}
-    }
-  XFREE (tmp_pathspec);
-
-  if (!has_symlinks)
-    {
-      return xstrdup (pathspec);
-    }
-
-  tmp_pathspec = realpath (pathspec, buf);
-  if (tmp_pathspec == 0)
-    {
-      lt_fatal (__FILE__, __LINE__,
-		"could not follow symlinks for %s", pathspec);
-    }
-  return xstrdup (tmp_pathspec);
-#endif
-}
-
-char *
-strendzap (char *str, const char *pat)
-{
-  size_t len, patlen;
-
-  assert (str != NULL);
-  assert (pat != NULL);
-
-  len = strlen (str);
-  patlen = strlen (pat);
-
-  if (patlen <= len)
-    {
-      str += len - patlen;
-      if (strcmp (str, pat) == 0)
-	*str = '\0';
-    }
-  return str;
-}
-
-void
-lt_debugprintf (const char *file, int line, const char *fmt, ...)
-{
-  va_list args;
-  if (lt_debug)
-    {
-      (void) fprintf (stderr, "%s:%s:%d: ", program_name, file, line);
-      va_start (args, fmt);
-      (void) vfprintf (stderr, fmt, args);
-      va_end (args);
-    }
-}
-
-static void
-lt_error_core (int exit_status, const char *file,
-	       int line, const char *mode,
-	       const char *message, va_list ap)
-{
-  fprintf (stderr, "%s:%s:%d: %s: ", program_name, file, line, mode);
-  vfprintf (stderr, message, ap);
-  fprintf (stderr, ".\n");
-
-  if (exit_status >= 0)
-    exit (exit_status);
-}
-
-void
-lt_fatal (const char *file, int line, const char *message, ...)
-{
-  va_list ap;
-  va_start (ap, message);
-  lt_error_core (EXIT_FAILURE, file, line, "FATAL", message, ap);
-  va_end (ap);
-}
-
-static const char *
-nonnull (const char *s)
-{
-  return s ? s : "(null)";
-}
-
-static const char *
-nonempty (const char *s)
-{
-  return (s && !*s) ? "(empty)" : nonnull (s);
-}
-
-void
-lt_setenv (const char *name, const char *value)
-{
-  lt_debugprintf (__FILE__, __LINE__,
-		  "(lt_setenv) setting '%s' to '%s'\n",
-                  nonnull (name), nonnull (value));
-  {
-#ifdef HAVE_SETENV
-    /* always make a copy, for consistency with !HAVE_SETENV */
-    char *str = xstrdup (value);
-    setenv (name, str, 1);
-#else
-    int len = strlen (name) + 1 + strlen (value) + 1;
-    char *str = XMALLOC (char, len);
-    sprintf (str, "%s=%s", name, value);
-    if (putenv (str) != EXIT_SUCCESS)
-      {
-        XFREE (str);
-      }
-#endif
-  }
-}
-
-char *
-lt_extend_str (const char *orig_value, const char *add, int to_end)
-{
-  char *new_value;
-  if (orig_value && *orig_value)
-    {
-      int orig_value_len = strlen (orig_value);
-      int add_len = strlen (add);
-      new_value = XMALLOC (char, add_len + orig_value_len + 1);
-      if (to_end)
-        {
-          strcpy (new_value, orig_value);
-          strcpy (new_value + orig_value_len, add);
-        }
-      else
-        {
-          strcpy (new_value, add);
-          strcpy (new_value + add_len, orig_value);
-        }
-    }
-  else
-    {
-      new_value = xstrdup (add);
-    }
-  return new_value;
-}
-
-void
-lt_update_exe_path (const char *name, const char *value)
-{
-  lt_debugprintf (__FILE__, __LINE__,
-		  "(lt_update_exe_path) modifying '%s' by prepending '%s'\n",
-                  nonnull (name), nonnull (value));
-
-  if (name && *name && value && *value)
-    {
-      char *new_value = lt_extend_str (getenv (name), value, 0);
-      /* some systems can't cope with a ':'-terminated path #' */
-      int len = strlen (new_value);
-      while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1]))
-        {
-          new_value[len-1] = '\0';
-        }
-      lt_setenv (name, new_value);
-      XFREE (new_value);
-    }
-}
-
-void
-lt_update_lib_path (const char *name, const char *value)
-{
-  lt_debugprintf (__FILE__, __LINE__,
-		  "(lt_update_lib_path) modifying '%s' by prepending '%s'\n",
-                  nonnull (name), nonnull (value));
-
-  if (name && *name && value && *value)
-    {
-      char *new_value = lt_extend_str (getenv (name), value, 0);
-      lt_setenv (name, new_value);
-      XFREE (new_value);
-    }
-}
-
-EOF
-	    case $host_os in
-	      mingw*)
-		cat <<"EOF"
-
-/* Prepares an argument vector before calling spawn().
-   Note that spawn() does not by itself call the command interpreter
-     (getenv ("COMSPEC") != NULL ? getenv ("COMSPEC") :
-      ({ OSVERSIONINFO v; v.dwOSVersionInfoSize = sizeof(OSVERSIONINFO);
-         GetVersionEx(&v);
-         v.dwPlatformId == VER_PLATFORM_WIN32_NT;
-      }) ? "cmd.exe" : "command.com").
-   Instead it simply concatenates the arguments, separated by ' ', and calls
-   CreateProcess().  We must quote the arguments since Win32 CreateProcess()
-   interprets characters like ' ', '\t', '\\', '"' (but not '<' and '>') in a
-   special way:
-   - Space and tab are interpreted as delimiters. They are not treated as
-     delimiters if they are surrounded by double quotes: "...".
-   - Unescaped double quotes are removed from the input. Their only effect is
-     that within double quotes, space and tab are treated like normal
-     characters.
-   - Backslashes not followed by double quotes are not special.
-   - But 2*n+1 backslashes followed by a double quote become
-     n backslashes followed by a double quote (n >= 0):
-       \" -> "
-       \\\" -> \"
-       \\\\\" -> \\"
- */
-#define SHELL_SPECIAL_CHARS "\"\\ \001\002\003\004\005\006\007\010\011\012\013\014\015\016\017\020\021\022\023\024\025\026\027\030\031\032\033\034\035\036\037"
-#define SHELL_SPACE_CHARS " \001\002\003\004\005\006\007\010\011\012\013\014\015\016\017\020\021\022\023\024\025\026\027\030\031\032\033\034\035\036\037"
-char **
-prepare_spawn (char **argv)
-{
-  size_t argc;
-  char **new_argv;
-  size_t i;
-
-  /* Count number of arguments.  */
-  for (argc = 0; argv[argc] != NULL; argc++)
-    ;
-
-  /* Allocate new argument vector.  */
-  new_argv = XMALLOC (char *, argc + 1);
-
-  /* Put quoted arguments into the new argument vector.  */
-  for (i = 0; i < argc; i++)
-    {
-      const char *string = argv[i];
-
-      if (string[0] == '\0')
-	new_argv[i] = xstrdup ("\"\"");
-      else if (strpbrk (string, SHELL_SPECIAL_CHARS) != NULL)
-	{
-	  int quote_around = (strpbrk (string, SHELL_SPACE_CHARS) != NULL);
-	  size_t length;
-	  unsigned int backslashes;
-	  const char *s;
-	  char *quoted_string;
-	  char *p;
-
-	  length = 0;
-	  backslashes = 0;
-	  if (quote_around)
-	    length++;
-	  for (s = string; *s != '\0'; s++)
-	    {
-	      char c = *s;
-	      if (c == '"')
-		length += backslashes + 1;
-	      length++;
-	      if (c == '\\')
-		backslashes++;
-	      else
-		backslashes = 0;
-	    }
-	  if (quote_around)
-	    length += backslashes + 1;
-
-	  quoted_string = XMALLOC (char, length + 1);
-
-	  p = quoted_string;
-	  backslashes = 0;
-	  if (quote_around)
-	    *p++ = '"';
-	  for (s = string; *s != '\0'; s++)
-	    {
-	      char c = *s;
-	      if (c == '"')
-		{
-		  unsigned int j;
-		  for (j = backslashes + 1; j > 0; j--)
-		    *p++ = '\\';
-		}
-	      *p++ = c;
-	      if (c == '\\')
-		backslashes++;
-	      else
-		backslashes = 0;
-	    }
-	  if (quote_around)
-	    {
-	      unsigned int j;
-	      for (j = backslashes; j > 0; j--)
-		*p++ = '\\';
-	      *p++ = '"';
-	    }
-	  *p = '\0';
-
-	  new_argv[i] = quoted_string;
-	}
-      else
-	new_argv[i] = (char *) string;
-    }
-  new_argv[argc] = NULL;
-
-  return new_argv;
-}
-EOF
-		;;
-	    esac
-
-            cat <<"EOF"
-void lt_dump_script (FILE* f)
-{
-EOF
-	    func_emit_wrapper yes |
-	      $SED -n -e '
-s/^\(.\{79\}\)\(..*\)/\1\
-\2/
-h
-s/\([\\"]\)/\\\1/g
-s/$/\\n/
-s/\([^\n]*\).*/  fputs ("\1", f);/p
-g
-D'
-            cat <<"EOF"
-}
-EOF
-}
-# end: func_emit_cwrapperexe_src
-
-# func_win32_import_lib_p ARG
-# True if ARG is an import lib, as indicated by $file_magic_cmd
-func_win32_import_lib_p ()
-{
-    $opt_debug
-    case `eval $file_magic_cmd \"\$1\" 2>/dev/null | $SED -e 10q` in
-    *import*) : ;;
-    *) false ;;
-    esac
-}
-
-# func_mode_link arg...
-func_mode_link ()
-{
-    $opt_debug
-    case $host in
-    *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
-      # It is impossible to link a dll without this setting, and
-      # we shouldn't force the makefile maintainer to figure out
-      # which system we are compiling for in order to pass an extra
-      # flag for every libtool invocation.
-      # allow_undefined=no
-
-      # FIXME: Unfortunately, there are problems with the above when trying
-      # to make a dll which has undefined symbols, in which case not
-      # even a static library is built.  For now, we need to specify
-      # -no-undefined on the libtool link line when we can be certain
-      # that all symbols are satisfied, otherwise we get a static library.
-      allow_undefined=yes
-      ;;
-    *)
-      allow_undefined=yes
-      ;;
-    esac
-    libtool_args=$nonopt
-    base_compile="$nonopt $@"
-    compile_command=$nonopt
-    finalize_command=$nonopt
-
-    compile_rpath=
-    finalize_rpath=
-    compile_shlibpath=
-    finalize_shlibpath=
-    convenience=
-    old_convenience=
-    deplibs=
-    old_deplibs=
-    compiler_flags=
-    linker_flags=
-    dllsearchpath=
-    lib_search_path=`pwd`
-    inst_prefix_dir=
-    new_inherited_linker_flags=
-
-    avoid_version=no
-    bindir=
-    dlfiles=
-    dlprefiles=
-    dlself=no
-    export_dynamic=no
-    export_symbols=
-    export_symbols_regex=
-    generated=
-    libobjs=
-    ltlibs=
-    module=no
-    no_install=no
-    objs=
-    non_pic_objects=
-    precious_files_regex=
-    prefer_static_libs=no
-    preload=no
-    prev=
-    prevarg=
-    release=
-    rpath=
-    xrpath=
-    perm_rpath=
-    temp_rpath=
-    thread_safe=no
-    vinfo=
-    vinfo_number=no
-    weak_libs=
-    single_module="${wl}-single_module"
-    func_infer_tag $base_compile
-
-    # We need to know -static, to get the right output filenames.
-    for arg
-    do
-      case $arg in
-      -shared)
-	test "$build_libtool_libs" != yes && \
-	  func_fatal_configuration "can not build a shared library"
-	build_old_libs=no
-	break
-	;;
-      -all-static | -static | -static-libtool-libs)
-	case $arg in
-	-all-static)
-	  if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then
-	    func_warning "complete static linking is impossible in this configuration"
-	  fi
-	  if test -n "$link_static_flag"; then
-	    dlopen_self=$dlopen_self_static
-	  fi
-	  prefer_static_libs=yes
-	  ;;
-	-static)
-	  if test -z "$pic_flag" && test -n "$link_static_flag"; then
-	    dlopen_self=$dlopen_self_static
-	  fi
-	  prefer_static_libs=built
-	  ;;
-	-static-libtool-libs)
-	  if test -z "$pic_flag" && test -n "$link_static_flag"; then
-	    dlopen_self=$dlopen_self_static
-	  fi
-	  prefer_static_libs=yes
-	  ;;
-	esac
-	build_libtool_libs=no
-	build_old_libs=yes
-	break
-	;;
-      esac
-    done
-
-    # See if our shared archives depend on static archives.
-    test -n "$old_archive_from_new_cmds" && build_old_libs=yes
-
-    # Go through the arguments, transforming them on the way.
-    while test "$#" -gt 0; do
-      arg="$1"
-      shift
-      func_quote_for_eval "$arg"
-      qarg=$func_quote_for_eval_unquoted_result
-      func_append libtool_args " $func_quote_for_eval_result"
-
-      # If the previous option needs an argument, assign it.
-      if test -n "$prev"; then
-	case $prev in
-	output)
-	  func_append compile_command " @OUTPUT@"
-	  func_append finalize_command " @OUTPUT@"
-	  ;;
-	esac
-
-	case $prev in
-	bindir)
-	  bindir="$arg"
-	  prev=
-	  continue
-	  ;;
-	dlfiles|dlprefiles)
-	  if test "$preload" = no; then
-	    # Add the symbol object into the linking commands.
-	    func_append compile_command " @SYMFILE@"
-	    func_append finalize_command " @SYMFILE@"
-	    preload=yes
-	  fi
-	  case $arg in
-	  *.la | *.lo) ;;  # We handle these cases below.
-	  force)
-	    if test "$dlself" = no; then
-	      dlself=needless
-	      export_dynamic=yes
-	    fi
-	    prev=
-	    continue
-	    ;;
-	  self)
-	    if test "$prev" = dlprefiles; then
-	      dlself=yes
-	    elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then
-	      dlself=yes
-	    else
-	      dlself=needless
-	      export_dynamic=yes
-	    fi
-	    prev=
-	    continue
-	    ;;
-	  *)
-	    if test "$prev" = dlfiles; then
-	      func_append dlfiles " $arg"
-	    else
-	      func_append dlprefiles " $arg"
-	    fi
-	    prev=
-	    continue
-	    ;;
-	  esac
-	  ;;
-	expsyms)
-	  export_symbols="$arg"
-	  test -f "$arg" \
-	    || func_fatal_error "symbol file \`$arg' does not exist"
-	  prev=
-	  continue
-	  ;;
-	expsyms_regex)
-	  export_symbols_regex="$arg"
-	  prev=
-	  continue
-	  ;;
-	framework)
-	  case $host in
-	    *-*-darwin*)
-	      case "$deplibs " in
-		*" $qarg.ltframework "*) ;;
-		*) func_append deplibs " $qarg.ltframework" # this is fixed later
-		   ;;
-	      esac
-	      ;;
-	  esac
-	  prev=
-	  continue
-	  ;;
-	inst_prefix)
-	  inst_prefix_dir="$arg"
-	  prev=
-	  continue
-	  ;;
-	objectlist)
-	  if test -f "$arg"; then
-	    save_arg=$arg
-	    moreargs=
-	    for fil in `cat "$save_arg"`
-	    do
-#	      func_append moreargs " $fil"
-	      arg=$fil
-	      # A libtool-controlled object.
-
-	      # Check to see that this really is a libtool object.
-	      if func_lalib_unsafe_p "$arg"; then
-		pic_object=
-		non_pic_object=
-
-		# Read the .lo file
-		func_source "$arg"
-
-		if test -z "$pic_object" ||
-		   test -z "$non_pic_object" ||
-		   test "$pic_object" = none &&
-		   test "$non_pic_object" = none; then
-		  func_fatal_error "cannot find name of object for \`$arg'"
-		fi
-
-		# Extract subdirectory from the argument.
-		func_dirname "$arg" "/" ""
-		xdir="$func_dirname_result"
-
-		if test "$pic_object" != none; then
-		  # Prepend the subdirectory the object is found in.
-		  pic_object="$xdir$pic_object"
-
-		  if test "$prev" = dlfiles; then
-		    if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
-		      func_append dlfiles " $pic_object"
-		      prev=
-		      continue
-		    else
-		      # If libtool objects are unsupported, then we need to preload.
-		      prev=dlprefiles
-		    fi
-		  fi
-
-		  # CHECK ME:  I think I busted this.  -Ossama
-		  if test "$prev" = dlprefiles; then
-		    # Preload the old-style object.
-		    func_append dlprefiles " $pic_object"
-		    prev=
-		  fi
-
-		  # A PIC object.
-		  func_append libobjs " $pic_object"
-		  arg="$pic_object"
-		fi
-
-		# Non-PIC object.
-		if test "$non_pic_object" != none; then
-		  # Prepend the subdirectory the object is found in.
-		  non_pic_object="$xdir$non_pic_object"
-
-		  # A standard non-PIC object
-		  func_append non_pic_objects " $non_pic_object"
-		  if test -z "$pic_object" || test "$pic_object" = none ; then
-		    arg="$non_pic_object"
-		  fi
-		else
-		  # If the PIC object exists, use it instead.
-		  # $xdir was prepended to $pic_object above.
-		  non_pic_object="$pic_object"
-		  func_append non_pic_objects " $non_pic_object"
-		fi
-	      else
-		# Only an error if not doing a dry-run.
-		if $opt_dry_run; then
-		  # Extract subdirectory from the argument.
-		  func_dirname "$arg" "/" ""
-		  xdir="$func_dirname_result"
-
-		  func_lo2o "$arg"
-		  pic_object=$xdir$objdir/$func_lo2o_result
-		  non_pic_object=$xdir$func_lo2o_result
-		  func_append libobjs " $pic_object"
-		  func_append non_pic_objects " $non_pic_object"
-	        else
-		  func_fatal_error "\`$arg' is not a valid libtool object"
-		fi
-	      fi
-	    done
-	  else
-	    func_fatal_error "link input file \`$arg' does not exist"
-	  fi
-	  arg=$save_arg
-	  prev=
-	  continue
-	  ;;
-	precious_regex)
-	  precious_files_regex="$arg"
-	  prev=
-	  continue
-	  ;;
-	release)
-	  release="-$arg"
-	  prev=
-	  continue
-	  ;;
-	rpath | xrpath)
-	  # We need an absolute path.
-	  case $arg in
-	  [\\/]* | [A-Za-z]:[\\/]*) ;;
-	  *)
-	    func_fatal_error "only absolute run-paths are allowed"
-	    ;;
-	  esac
-	  if test "$prev" = rpath; then
-	    case "$rpath " in
-	    *" $arg "*) ;;
-	    *) func_append rpath " $arg" ;;
-	    esac
-	  else
-	    case "$xrpath " in
-	    *" $arg "*) ;;
-	    *) func_append xrpath " $arg" ;;
-	    esac
-	  fi
-	  prev=
-	  continue
-	  ;;
-	shrext)
-	  shrext_cmds="$arg"
-	  prev=
-	  continue
-	  ;;
-	weak)
-	  func_append weak_libs " $arg"
-	  prev=
-	  continue
-	  ;;
-	xcclinker)
-	  func_append linker_flags " $qarg"
-	  func_append compiler_flags " $qarg"
-	  prev=
-	  func_append compile_command " $qarg"
-	  func_append finalize_command " $qarg"
-	  continue
-	  ;;
-	xcompiler)
-	  func_append compiler_flags " $qarg"
-	  prev=
-	  func_append compile_command " $qarg"
-	  func_append finalize_command " $qarg"
-	  continue
-	  ;;
-	xlinker)
-	  func_append linker_flags " $qarg"
-	  func_append compiler_flags " $wl$qarg"
-	  prev=
-	  func_append compile_command " $wl$qarg"
-	  func_append finalize_command " $wl$qarg"
-	  continue
-	  ;;
-	*)
-	  eval "$prev=\"\$arg\""
-	  prev=
-	  continue
-	  ;;
-	esac
-      fi # test -n "$prev"
-
-      prevarg="$arg"
-
-      case $arg in
-      -all-static)
-	if test -n "$link_static_flag"; then
-	  # See comment for -static flag below, for more details.
-	  func_append compile_command " $link_static_flag"
-	  func_append finalize_command " $link_static_flag"
-	fi
-	continue
-	;;
-
-      -allow-undefined)
-	# FIXME: remove this flag sometime in the future.
-	func_fatal_error "\`-allow-undefined' must not be used because it is the default"
-	;;
-
-      -avoid-version)
-	avoid_version=yes
-	continue
-	;;
-
-      -bindir)
-	prev=bindir
-	continue
-	;;
-
-      -dlopen)
-	prev=dlfiles
-	continue
-	;;
-
-      -dlpreopen)
-	prev=dlprefiles
-	continue
-	;;
-
-      -export-dynamic)
-	export_dynamic=yes
-	continue
-	;;
-
-      -export-symbols | -export-symbols-regex)
-	if test -n "$export_symbols" || test -n "$export_symbols_regex"; then
-	  func_fatal_error "more than one -exported-symbols argument is not allowed"
-	fi
-	if test "X$arg" = "X-export-symbols"; then
-	  prev=expsyms
-	else
-	  prev=expsyms_regex
-	fi
-	continue
-	;;
-
-      -framework)
-	prev=framework
-	continue
-	;;
-
-      -inst-prefix-dir)
-	prev=inst_prefix
-	continue
-	;;
-
-      # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:*
-      # so, if we see these flags be careful not to treat them like -L
-      -L[A-Z][A-Z]*:*)
-	case $with_gcc/$host in
-	no/*-*-irix* | /*-*-irix*)
-	  func_append compile_command " $arg"
-	  func_append finalize_command " $arg"
-	  ;;
-	esac
-	continue
-	;;
-
-      -L*)
-	func_stripname "-L" '' "$arg"
-	if test -z "$func_stripname_result"; then
-	  if test "$#" -gt 0; then
-	    func_fatal_error "require no space between \`-L' and \`$1'"
-	  else
-	    func_fatal_error "need path for \`-L' option"
-	  fi
-	fi
-	func_resolve_sysroot "$func_stripname_result"
-	dir=$func_resolve_sysroot_result
-	# We need an absolute path.
-	case $dir in
-	[\\/]* | [A-Za-z]:[\\/]*) ;;
-	*)
-	  absdir=`cd "$dir" && pwd`
-	  test -z "$absdir" && \
-	    func_fatal_error "cannot determine absolute directory name of \`$dir'"
-	  dir="$absdir"
-	  ;;
-	esac
-	case "$deplibs " in
-	*" -L$dir "* | *" $arg "*)
-	  # Will only happen for absolute or sysroot arguments
-	  ;;
-	*)
-	  # Preserve sysroot, but never include relative directories
-	  case $dir in
-	    [\\/]* | [A-Za-z]:[\\/]* | =*) func_append deplibs " $arg" ;;
-	    *) func_append deplibs " -L$dir" ;;
-	  esac
-	  func_append lib_search_path " $dir"
-	  ;;
-	esac
-	case $host in
-	*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
-	  testbindir=`$ECHO "$dir" | $SED 's*/lib$*/bin*'`
-	  case :$dllsearchpath: in
-	  *":$dir:"*) ;;
-	  ::) dllsearchpath=$dir;;
-	  *) func_append dllsearchpath ":$dir";;
-	  esac
-	  case :$dllsearchpath: in
-	  *":$testbindir:"*) ;;
-	  ::) dllsearchpath=$testbindir;;
-	  *) func_append dllsearchpath ":$testbindir";;
-	  esac
-	  ;;
-	esac
-	continue
-	;;
-
-      -l*)
-	if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then
-	  case $host in
-	  *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc* | *-*-haiku*)
-	    # These systems don't actually have a C or math library (as such)
-	    continue
-	    ;;
-	  *-*-os2*)
-	    # These systems don't actually have a C library (as such)
-	    test "X$arg" = "X-lc" && continue
-	    ;;
-	  *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
-	    # Do not include libc due to us having libc/libc_r.
-	    test "X$arg" = "X-lc" && continue
-	    ;;
-	  *-*-rhapsody* | *-*-darwin1.[012])
-	    # Rhapsody C and math libraries are in the System framework
-	    func_append deplibs " System.ltframework"
-	    continue
-	    ;;
-	  *-*-sco3.2v5* | *-*-sco5v6*)
-	    # Causes problems with __ctype
-	    test "X$arg" = "X-lc" && continue
-	    ;;
-	  *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
-	    # Compiler inserts libc in the correct place for threads to work
-	    test "X$arg" = "X-lc" && continue
-	    ;;
-	  esac
-	elif test "X$arg" = "X-lc_r"; then
-	 case $host in
-	 *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
-	   # Do not include libc_r directly, use -pthread flag.
-	   continue
-	   ;;
-	 esac
-	fi
-	func_append deplibs " $arg"
-	continue
-	;;
-
-      -module)
-	module=yes
-	continue
-	;;
-
-      # Tru64 UNIX uses -model [arg] to determine the layout of C++
-      # classes, name mangling, and exception handling.
-      # Darwin uses the -arch flag to determine output architecture.
-      -model|-arch|-isysroot|--sysroot)
-	func_append compiler_flags " $arg"
-	func_append compile_command " $arg"
-	func_append finalize_command " $arg"
-	prev=xcompiler
-	continue
-	;;
-
-      -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe \
-      |-threads|-fopenmp|-openmp|-mp|-xopenmp|-omp|-qsmp=*)
-	func_append compiler_flags " $arg"
-	func_append compile_command " $arg"
-	func_append finalize_command " $arg"
-	case "$new_inherited_linker_flags " in
-	    *" $arg "*) ;;
-	    * ) func_append new_inherited_linker_flags " $arg" ;;
-	esac
-	continue
-	;;
-
-      -multi_module)
-	single_module="${wl}-multi_module"
-	continue
-	;;
-
-      -no-fast-install)
-	fast_install=no
-	continue
-	;;
-
-      -no-install)
-	case $host in
-	*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*)
-	  # The PATH hackery in wrapper scripts is required on Windows
-	  # and Darwin in order for the loader to find any dlls it needs.
-	  func_warning "\`-no-install' is ignored for $host"
-	  func_warning "assuming \`-no-fast-install' instead"
-	  fast_install=no
-	  ;;
-	*) no_install=yes ;;
-	esac
-	continue
-	;;
-
-      -no-undefined)
-	allow_undefined=no
-	continue
-	;;
-
-      -objectlist)
-	prev=objectlist
-	continue
-	;;
-
-      -o) prev=output ;;
-
-      -precious-files-regex)
-	prev=precious_regex
-	continue
-	;;
-
-      -release)
-	prev=release
-	continue
-	;;
-
-      -rpath)
-	prev=rpath
-	continue
-	;;
-
-      -R)
-	prev=xrpath
-	continue
-	;;
-
-      -R*)
-	func_stripname '-R' '' "$arg"
-	dir=$func_stripname_result
-	# We need an absolute path.
-	case $dir in
-	[\\/]* | [A-Za-z]:[\\/]*) ;;
-	=*)
-	  func_stripname '=' '' "$dir"
-	  dir=$lt_sysroot$func_stripname_result
-	  ;;
-	*)
-	  func_fatal_error "only absolute run-paths are allowed"
-	  ;;
-	esac
-	case "$xrpath " in
-	*" $dir "*) ;;
-	*) func_append xrpath " $dir" ;;
-	esac
-	continue
-	;;
-
-      -shared)
-	# The effects of -shared are defined in a previous loop.
-	continue
-	;;
-
-      -shrext)
-	prev=shrext
-	continue
-	;;
-
-      -static | -static-libtool-libs)
-	# The effects of -static are defined in a previous loop.
-	# We used to do the same as -all-static on platforms that
-	# didn't have a PIC flag, but the assumption that the effects
-	# would be equivalent was wrong.  It would break on at least
-	# Digital Unix and AIX.
-	continue
-	;;
-
-      -thread-safe)
-	thread_safe=yes
-	continue
-	;;
-
-      -version-info)
-	prev=vinfo
-	continue
-	;;
-
-      -version-number)
-	prev=vinfo
-	vinfo_number=yes
-	continue
-	;;
-
-      -weak)
-        prev=weak
-	continue
-	;;
-
-      -Wc,*)
-	func_stripname '-Wc,' '' "$arg"
-	args=$func_stripname_result
-	arg=
-	save_ifs="$IFS"; IFS=','
-	for flag in $args; do
-	  IFS="$save_ifs"
-          func_quote_for_eval "$flag"
-	  func_append arg " $func_quote_for_eval_result"
-	  func_append compiler_flags " $func_quote_for_eval_result"
-	done
-	IFS="$save_ifs"
-	func_stripname ' ' '' "$arg"
-	arg=$func_stripname_result
-	;;
-
-      -Wl,*)
-	func_stripname '-Wl,' '' "$arg"
-	args=$func_stripname_result
-	arg=
-	save_ifs="$IFS"; IFS=','
-	for flag in $args; do
-	  IFS="$save_ifs"
-          func_quote_for_eval "$flag"
-	  func_append arg " $wl$func_quote_for_eval_result"
-	  func_append compiler_flags " $wl$func_quote_for_eval_result"
-	  func_append linker_flags " $func_quote_for_eval_result"
-	done
-	IFS="$save_ifs"
-	func_stripname ' ' '' "$arg"
-	arg=$func_stripname_result
-	;;
-
-      -Xcompiler)
-	prev=xcompiler
-	continue
-	;;
-
-      -Xlinker)
-	prev=xlinker
-	continue
-	;;
-
-      -XCClinker)
-	prev=xcclinker
-	continue
-	;;
-
-      # -msg_* for osf cc
-      -msg_*)
-	func_quote_for_eval "$arg"
-	arg="$func_quote_for_eval_result"
-	;;
-
-      # Flags to be passed through unchanged, with rationale:
-      # -64, -mips[0-9]      enable 64-bit mode for the SGI compiler
-      # -r[0-9][0-9]*        specify processor for the SGI compiler
-      # -xarch=*, -xtarget=* enable 64-bit mode for the Sun compiler
-      # +DA*, +DD*           enable 64-bit mode for the HP compiler
-      # -q*                  compiler args for the IBM compiler
-      # -m*, -t[45]*, -txscale* architecture-specific flags for GCC
-      # -F/path              path to uninstalled frameworks, gcc on darwin
-      # -p, -pg, --coverage, -fprofile-*  profiling flags for GCC
-      # @file                GCC response files
-      # -tp=*                Portland pgcc target processor selection
-      # --sysroot=*          for sysroot support
-      # -O*, -flto*, -fwhopr*, -fuse-linker-plugin GCC link-time optimization
-      -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \
-      -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*|-tp=*|--sysroot=*| \
-      -O*|-flto*|-fwhopr*|-fuse-linker-plugin)
-        func_quote_for_eval "$arg"
-	arg="$func_quote_for_eval_result"
-        func_append compile_command " $arg"
-        func_append finalize_command " $arg"
-        func_append compiler_flags " $arg"
-        continue
-        ;;
-
-      # Some other compiler flag.
-      -* | +*)
-        func_quote_for_eval "$arg"
-	arg="$func_quote_for_eval_result"
-	;;
-
-      *.$objext)
-	# A standard object.
-	func_append objs " $arg"
-	;;
-
-      *.lo)
-	# A libtool-controlled object.
-
-	# Check to see that this really is a libtool object.
-	if func_lalib_unsafe_p "$arg"; then
-	  pic_object=
-	  non_pic_object=
-
-	  # Read the .lo file
-	  func_source "$arg"
-
-	  if test -z "$pic_object" ||
-	     test -z "$non_pic_object" ||
-	     test "$pic_object" = none &&
-	     test "$non_pic_object" = none; then
-	    func_fatal_error "cannot find name of object for \`$arg'"
-	  fi
-
-	  # Extract subdirectory from the argument.
-	  func_dirname "$arg" "/" ""
-	  xdir="$func_dirname_result"
-
-	  if test "$pic_object" != none; then
-	    # Prepend the subdirectory the object is found in.
-	    pic_object="$xdir$pic_object"
-
-	    if test "$prev" = dlfiles; then
-	      if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
-		func_append dlfiles " $pic_object"
-		prev=
-		continue
-	      else
-		# If libtool objects are unsupported, then we need to preload.
-		prev=dlprefiles
-	      fi
-	    fi
-
-	    # CHECK ME:  I think I busted this.  -Ossama
-	    if test "$prev" = dlprefiles; then
-	      # Preload the old-style object.
-	      func_append dlprefiles " $pic_object"
-	      prev=
-	    fi
-
-	    # A PIC object.
-	    func_append libobjs " $pic_object"
-	    arg="$pic_object"
-	  fi
-
-	  # Non-PIC object.
-	  if test "$non_pic_object" != none; then
-	    # Prepend the subdirectory the object is found in.
-	    non_pic_object="$xdir$non_pic_object"
-
-	    # A standard non-PIC object
-	    func_append non_pic_objects " $non_pic_object"
-	    if test -z "$pic_object" || test "$pic_object" = none ; then
-	      arg="$non_pic_object"
-	    fi
-	  else
-	    # If the PIC object exists, use it instead.
-	    # $xdir was prepended to $pic_object above.
-	    non_pic_object="$pic_object"
-	    func_append non_pic_objects " $non_pic_object"
-	  fi
-	else
-	  # Only an error if not doing a dry-run.
-	  if $opt_dry_run; then
-	    # Extract subdirectory from the argument.
-	    func_dirname "$arg" "/" ""
-	    xdir="$func_dirname_result"
-
-	    func_lo2o "$arg"
-	    pic_object=$xdir$objdir/$func_lo2o_result
-	    non_pic_object=$xdir$func_lo2o_result
-	    func_append libobjs " $pic_object"
-	    func_append non_pic_objects " $non_pic_object"
-	  else
-	    func_fatal_error "\`$arg' is not a valid libtool object"
-	  fi
-	fi
-	;;
-
-      *.$libext)
-	# An archive.
-	func_append deplibs " $arg"
-	func_append old_deplibs " $arg"
-	continue
-	;;
-
-      *.la)
-	# A libtool-controlled library.
-
-	func_resolve_sysroot "$arg"
-	if test "$prev" = dlfiles; then
-	  # This library was specified with -dlopen.
-	  func_append dlfiles " $func_resolve_sysroot_result"
-	  prev=
-	elif test "$prev" = dlprefiles; then
-	  # The library was specified with -dlpreopen.
-	  func_append dlprefiles " $func_resolve_sysroot_result"
-	  prev=
-	else
-	  func_append deplibs " $func_resolve_sysroot_result"
-	fi
-	continue
-	;;
-
-      # Some other compiler argument.
-      *)
-	# Unknown arguments in both finalize_command and compile_command need
-	# to be aesthetically quoted because they are evaled later.
-	func_quote_for_eval "$arg"
-	arg="$func_quote_for_eval_result"
-	;;
-      esac # arg
-
-      # Now actually substitute the argument into the commands.
-      if test -n "$arg"; then
-	func_append compile_command " $arg"
-	func_append finalize_command " $arg"
-      fi
-    done # argument parsing loop
-
-    test -n "$prev" && \
-      func_fatal_help "the \`$prevarg' option requires an argument"
-
-    if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then
-      eval arg=\"$export_dynamic_flag_spec\"
-      func_append compile_command " $arg"
-      func_append finalize_command " $arg"
-    fi
-
-    oldlibs=
-    # calculate the name of the file, without its directory
-    func_basename "$output"
-    outputname="$func_basename_result"
-    libobjs_save="$libobjs"
-
-    if test -n "$shlibpath_var"; then
-      # get the directories listed in $shlibpath_var
-      eval shlib_search_path=\`\$ECHO \"\${$shlibpath_var}\" \| \$SED \'s/:/ /g\'\`
-    else
-      shlib_search_path=
-    fi
-    eval sys_lib_search_path=\"$sys_lib_search_path_spec\"
-    eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\"
-
-    func_dirname "$output" "/" ""
-    output_objdir="$func_dirname_result$objdir"
-    func_to_tool_file "$output_objdir/"
-    tool_output_objdir=$func_to_tool_file_result
-    # Create the object directory.
-    func_mkdir_p "$output_objdir"
-
-    # Determine the type of output
-    case $output in
-    "")
-      func_fatal_help "you must specify an output file"
-      ;;
-    *.$libext) linkmode=oldlib ;;
-    *.lo | *.$objext) linkmode=obj ;;
-    *.la) linkmode=lib ;;
-    *) linkmode=prog ;; # Anything else should be a program.
-    esac
-
-    specialdeplibs=
-
-    libs=
-    # Find all interdependent deplibs by searching for libraries
-    # that are linked more than once (e.g. -la -lb -la)
-    for deplib in $deplibs; do
-      if $opt_preserve_dup_deps ; then
-	case "$libs " in
-	*" $deplib "*) func_append specialdeplibs " $deplib" ;;
-	esac
-      fi
-      func_append libs " $deplib"
-    done
-
-    if test "$linkmode" = lib; then
-      libs="$predeps $libs $compiler_lib_search_path $postdeps"
-
-      # Compute libraries that are listed more than once in $predeps
-      # $postdeps and mark them as special (i.e., whose duplicates are
-      # not to be eliminated).
-      pre_post_deps=
-      if $opt_duplicate_compiler_generated_deps; then
-	for pre_post_dep in $predeps $postdeps; do
-	  case "$pre_post_deps " in
-	  *" $pre_post_dep "*) func_append specialdeplibs " $pre_post_deps" ;;
-	  esac
-	  func_append pre_post_deps " $pre_post_dep"
-	done
-      fi
-      pre_post_deps=
-    fi
-
-    deplibs=
-    newdependency_libs=
-    newlib_search_path=
-    need_relink=no # whether we're linking any uninstalled libtool libraries
-    notinst_deplibs= # not-installed libtool libraries
-    notinst_path= # paths that contain not-installed libtool libraries
-
-    case $linkmode in
-    lib)
-	passes="conv dlpreopen link"
-	for file in $dlfiles $dlprefiles; do
-	  case $file in
-	  *.la) ;;
-	  *)
-	    func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file"
-	    ;;
-	  esac
-	done
-	;;
-    prog)
-	compile_deplibs=
-	finalize_deplibs=
-	alldeplibs=no
-	newdlfiles=
-	newdlprefiles=
-	passes="conv scan dlopen dlpreopen link"
-	;;
-    *)  passes="conv"
-	;;
-    esac
-
-    for pass in $passes; do
-      # The preopen pass in lib mode reverses $deplibs; put it back here
-      # so that -L comes before libs that need it for instance...
-      if test "$linkmode,$pass" = "lib,link"; then
-	## FIXME: Find the place where the list is rebuilt in the wrong
-	##        order, and fix it there properly
-        tmp_deplibs=
-	for deplib in $deplibs; do
-	  tmp_deplibs="$deplib $tmp_deplibs"
-	done
-	deplibs="$tmp_deplibs"
-      fi
-
-      if test "$linkmode,$pass" = "lib,link" ||
-	 test "$linkmode,$pass" = "prog,scan"; then
-	libs="$deplibs"
-	deplibs=
-      fi
-      if test "$linkmode" = prog; then
-	case $pass in
-	dlopen) libs="$dlfiles" ;;
-	dlpreopen) libs="$dlprefiles" ;;
-	link) libs="$deplibs %DEPLIBS% $dependency_libs" ;;
-	esac
-      fi
-      if test "$linkmode,$pass" = "lib,dlpreopen"; then
-	# Collect and forward deplibs of preopened libtool libs
-	for lib in $dlprefiles; do
-	  # Ignore non-libtool-libs
-	  dependency_libs=
-	  func_resolve_sysroot "$lib"
-	  case $lib in
-	  *.la)	func_source "$func_resolve_sysroot_result" ;;
-	  esac
-
-	  # Collect preopened libtool deplibs, except any this library
-	  # has declared as weak libs
-	  for deplib in $dependency_libs; do
-	    func_basename "$deplib"
-            deplib_base=$func_basename_result
-	    case " $weak_libs " in
-	    *" $deplib_base "*) ;;
-	    *) func_append deplibs " $deplib" ;;
-	    esac
-	  done
-	done
-	libs="$dlprefiles"
-      fi
-      if test "$pass" = dlopen; then
-	# Collect dlpreopened libraries
-	save_deplibs="$deplibs"
-	deplibs=
-      fi
-
-      for deplib in $libs; do
-	lib=
-	found=no
-	case $deplib in
-	-mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe \
-        |-threads|-fopenmp|-openmp|-mp|-xopenmp|-omp|-qsmp=*)
-	  if test "$linkmode,$pass" = "prog,link"; then
-	    compile_deplibs="$deplib $compile_deplibs"
-	    finalize_deplibs="$deplib $finalize_deplibs"
-	  else
-	    func_append compiler_flags " $deplib"
-	    if test "$linkmode" = lib ; then
-		case "$new_inherited_linker_flags " in
-		    *" $deplib "*) ;;
-		    * ) func_append new_inherited_linker_flags " $deplib" ;;
-		esac
-	    fi
-	  fi
-	  continue
-	  ;;
-	-l*)
-	  if test "$linkmode" != lib && test "$linkmode" != prog; then
-	    func_warning "\`-l' is ignored for archives/objects"
-	    continue
-	  fi
-	  func_stripname '-l' '' "$deplib"
-	  name=$func_stripname_result
-	  if test "$linkmode" = lib; then
-	    searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path"
-	  else
-	    searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path"
-	  fi
-	  for searchdir in $searchdirs; do
-	    for search_ext in .la $std_shrext .so .a; do
-	      # Search the libtool library
-	      lib="$searchdir/lib${name}${search_ext}"
-	      if test -f "$lib"; then
-		if test "$search_ext" = ".la"; then
-		  found=yes
-		else
-		  found=no
-		fi
-		break 2
-	      fi
-	    done
-	  done
-	  if test "$found" != yes; then
-	    # deplib doesn't seem to be a libtool library
-	    if test "$linkmode,$pass" = "prog,link"; then
-	      compile_deplibs="$deplib $compile_deplibs"
-	      finalize_deplibs="$deplib $finalize_deplibs"
-	    else
-	      deplibs="$deplib $deplibs"
-	      test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
-	    fi
-	    continue
-	  else # deplib is a libtool library
-	    # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib,
-	    # We need to do some special things here, and not later.
-	    if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
-	      case " $predeps $postdeps " in
-	      *" $deplib "*)
-		if func_lalib_p "$lib"; then
-		  library_names=
-		  old_library=
-		  func_source "$lib"
-		  for l in $old_library $library_names; do
-		    ll="$l"
-		  done
-		  if test "X$ll" = "X$old_library" ; then # only static version available
-		    found=no
-		    func_dirname "$lib" "" "."
-		    ladir="$func_dirname_result"
-		    lib=$ladir/$old_library
-		    if test "$linkmode,$pass" = "prog,link"; then
-		      compile_deplibs="$deplib $compile_deplibs"
-		      finalize_deplibs="$deplib $finalize_deplibs"
-		    else
-		      deplibs="$deplib $deplibs"
-		      test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
-		    fi
-		    continue
-		  fi
-		fi
-		;;
-	      *) ;;
-	      esac
-	    fi
-	  fi
-	  ;; # -l
-	*.ltframework)
-	  if test "$linkmode,$pass" = "prog,link"; then
-	    compile_deplibs="$deplib $compile_deplibs"
-	    finalize_deplibs="$deplib $finalize_deplibs"
-	  else
-	    deplibs="$deplib $deplibs"
-	    if test "$linkmode" = lib ; then
-		case "$new_inherited_linker_flags " in
-		    *" $deplib "*) ;;
-		    * ) func_append new_inherited_linker_flags " $deplib" ;;
-		esac
-	    fi
-	  fi
-	  continue
-	  ;;
-	-L*)
-	  case $linkmode in
-	  lib)
-	    deplibs="$deplib $deplibs"
-	    test "$pass" = conv && continue
-	    newdependency_libs="$deplib $newdependency_libs"
-	    func_stripname '-L' '' "$deplib"
-	    func_resolve_sysroot "$func_stripname_result"
-	    func_append newlib_search_path " $func_resolve_sysroot_result"
-	    ;;
-	  prog)
-	    if test "$pass" = conv; then
-	      deplibs="$deplib $deplibs"
-	      continue
-	    fi
-	    if test "$pass" = scan; then
-	      deplibs="$deplib $deplibs"
-	    else
-	      compile_deplibs="$deplib $compile_deplibs"
-	      finalize_deplibs="$deplib $finalize_deplibs"
-	    fi
-	    func_stripname '-L' '' "$deplib"
-	    func_resolve_sysroot "$func_stripname_result"
-	    func_append newlib_search_path " $func_resolve_sysroot_result"
-	    ;;
-	  *)
-	    func_warning "\`-L' is ignored for archives/objects"
-	    ;;
-	  esac # linkmode
-	  continue
-	  ;; # -L
-	-R*)
-	  if test "$pass" = link; then
-	    func_stripname '-R' '' "$deplib"
-	    func_resolve_sysroot "$func_stripname_result"
-	    dir=$func_resolve_sysroot_result
-	    # Make sure the xrpath contains only unique directories.
-	    case "$xrpath " in
-	    *" $dir "*) ;;
-	    *) func_append xrpath " $dir" ;;
-	    esac
-	  fi
-	  deplibs="$deplib $deplibs"
-	  continue
-	  ;;
-	*.la)
-	  func_resolve_sysroot "$deplib"
-	  lib=$func_resolve_sysroot_result
-	  ;;
-	*.$libext)
-	  if test "$pass" = conv; then
-	    deplibs="$deplib $deplibs"
-	    continue
-	  fi
-	  case $linkmode in
-	  lib)
-	    # Linking convenience modules into shared libraries is allowed,
-	    # but linking other static libraries is non-portable.
-	    case " $dlpreconveniencelibs " in
-	    *" $deplib "*) ;;
-	    *)
-	      valid_a_lib=no
-	      case $deplibs_check_method in
-		match_pattern*)
-		  set dummy $deplibs_check_method; shift
-		  match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
-		  if eval "\$ECHO \"$deplib\"" 2>/dev/null | $SED 10q \
-		    | $EGREP "$match_pattern_regex" > /dev/null; then
-		    valid_a_lib=yes
-		  fi
-		;;
-		pass_all)
-		  valid_a_lib=yes
-		;;
-	      esac
-	      if test "$valid_a_lib" != yes; then
-		echo
-		$ECHO "*** Warning: Trying to link with static lib archive $deplib."
-		echo "*** I have the capability to make that library automatically link in when"
-		echo "*** you link to this library.  But I can only do this if you have a"
-		echo "*** shared version of the library, which you do not appear to have"
-		echo "*** because the file extensions .$libext of this argument makes me believe"
-		echo "*** that it is just a static archive that I should not use here."
-	      else
-		echo
-		$ECHO "*** Warning: Linking the shared library $output against the"
-		$ECHO "*** static library $deplib is not portable!"
-		deplibs="$deplib $deplibs"
-	      fi
-	      ;;
-	    esac
-	    continue
-	    ;;
-	  prog)
-	    if test "$pass" != link; then
-	      deplibs="$deplib $deplibs"
-	    else
-	      compile_deplibs="$deplib $compile_deplibs"
-	      finalize_deplibs="$deplib $finalize_deplibs"
-	    fi
-	    continue
-	    ;;
-	  esac # linkmode
-	  ;; # *.$libext
-	*.lo | *.$objext)
-	  if test "$pass" = conv; then
-	    deplibs="$deplib $deplibs"
-	  elif test "$linkmode" = prog; then
-	    if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then
-	      # If there is no dlopen support or we're linking statically,
-	      # we need to preload.
-	      func_append newdlprefiles " $deplib"
-	      compile_deplibs="$deplib $compile_deplibs"
-	      finalize_deplibs="$deplib $finalize_deplibs"
-	    else
-	      func_append newdlfiles " $deplib"
-	    fi
-	  fi
-	  continue
-	  ;;
-	%DEPLIBS%)
-	  alldeplibs=yes
-	  continue
-	  ;;
-	esac # case $deplib
-
-	if test "$found" = yes || test -f "$lib"; then :
-	else
-	  func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'"
-	fi
-
-	# Check to see that this really is a libtool archive.
-	func_lalib_unsafe_p "$lib" \
-	  || func_fatal_error "\`$lib' is not a valid libtool archive"
-
-	func_dirname "$lib" "" "."
-	ladir="$func_dirname_result"
-
-	dlname=
-	dlopen=
-	dlpreopen=
-	libdir=
-	library_names=
-	old_library=
-	inherited_linker_flags=
-	# If the library was installed with an old release of libtool,
-	# it will not redefine variables installed, or shouldnotlink
-	installed=yes
-	shouldnotlink=no
-	avoidtemprpath=
-
-
-	# Read the .la file
-	func_source "$lib"
-
-	# Convert "-framework foo" to "foo.ltframework"
-	if test -n "$inherited_linker_flags"; then
-	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
-	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
-	    case " $new_inherited_linker_flags " in
-	      *" $tmp_inherited_linker_flag "*) ;;
-	      *) func_append new_inherited_linker_flags " $tmp_inherited_linker_flag";;
-	    esac
-	  done
-	fi
-	dependency_libs=`$ECHO " $dependency_libs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'`
-	if test "$linkmode,$pass" = "lib,link" ||
-	   test "$linkmode,$pass" = "prog,scan" ||
-	   { test "$linkmode" != prog && test "$linkmode" != lib; }; then
-	  test -n "$dlopen" && func_append dlfiles " $dlopen"
-	  test -n "$dlpreopen" && func_append dlprefiles " $dlpreopen"
-	fi
-
-	if test "$pass" = conv; then
-	  # Only check for convenience libraries
-	  deplibs="$lib $deplibs"
-	  if test -z "$libdir"; then
-	    if test -z "$old_library"; then
-	      func_fatal_error "cannot find name of link library for \`$lib'"
-	    fi
-	    # It is a libtool convenience library, so add in its objects.
-	    func_append convenience " $ladir/$objdir/$old_library"
-	    func_append old_convenience " $ladir/$objdir/$old_library"
-	  elif test "$linkmode" != prog && test "$linkmode" != lib; then
-	    func_fatal_error "\`$lib' is not a convenience library"
-	  fi
-	  tmp_libs=
-	  for deplib in $dependency_libs; do
-	    deplibs="$deplib $deplibs"
-	    if $opt_preserve_dup_deps ; then
-	      case "$tmp_libs " in
-	      *" $deplib "*) func_append specialdeplibs " $deplib" ;;
-	      esac
-	    fi
-	    func_append tmp_libs " $deplib"
-	  done
-	  continue
-	fi # $pass = conv
-
-
-	# Get the name of the library we link against.
-	linklib=
-	if test -n "$old_library" &&
-	   { test "$prefer_static_libs" = yes ||
-	     test "$prefer_static_libs,$installed" = "built,no"; }; then
-	  linklib=$old_library
-	else
-	  for l in $old_library $library_names; do
-	    linklib="$l"
-	  done
-	fi
-	if test -z "$linklib"; then
-	  func_fatal_error "cannot find name of link library for \`$lib'"
-	fi
-
-	# This library was specified with -dlopen.
-	if test "$pass" = dlopen; then
-	  if test -z "$libdir"; then
-	    func_fatal_error "cannot -dlopen a convenience library: \`$lib'"
-	  fi
-	  if test -z "$dlname" ||
-	     test "$dlopen_support" != yes ||
-	     test "$build_libtool_libs" = no; then
-	    # If there is no dlname, no dlopen support or we're linking
-	    # statically, we need to preload.  We also need to preload any
-	    # dependent libraries so libltdl's deplib preloader doesn't
-	    # bomb out in the load deplibs phase.
-	    func_append dlprefiles " $lib $dependency_libs"
-	  else
-	    func_append newdlfiles " $lib"
-	  fi
-	  continue
-	fi # $pass = dlopen
-
-	# We need an absolute path.
-	case $ladir in
-	[\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;;
-	*)
-	  abs_ladir=`cd "$ladir" && pwd`
-	  if test -z "$abs_ladir"; then
-	    func_warning "cannot determine absolute directory name of \`$ladir'"
-	    func_warning "passing it literally to the linker, although it might fail"
-	    abs_ladir="$ladir"
-	  fi
-	  ;;
-	esac
-	func_basename "$lib"
-	laname="$func_basename_result"
-
-	# Find the relevant object directory and library name.
-	if test "X$installed" = Xyes; then
-	  if test ! -f "$lt_sysroot$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then
-	    func_warning "library \`$lib' was moved."
-	    dir="$ladir"
-	    absdir="$abs_ladir"
-	    libdir="$abs_ladir"
-	  else
-	    dir="$lt_sysroot$libdir"
-	    absdir="$lt_sysroot$libdir"
-	  fi
-	  test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes
-	else
-	  if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then
-	    dir="$ladir"
-	    absdir="$abs_ladir"
-	    # Remove this search path later
-	    func_append notinst_path " $abs_ladir"
-	  else
-	    dir="$ladir/$objdir"
-	    absdir="$abs_ladir/$objdir"
-	    # Remove this search path later
-	    func_append notinst_path " $abs_ladir"
-	  fi
-	fi # $installed = yes
-	func_stripname 'lib' '.la' "$laname"
-	name=$func_stripname_result
-
-	# This library was specified with -dlpreopen.
-	if test "$pass" = dlpreopen; then
-	  if test -z "$libdir" && test "$linkmode" = prog; then
-	    func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'"
-	  fi
-	  case "$host" in
-	    # special handling for platforms with PE-DLLs.
-	    *cygwin* | *mingw* | *cegcc* )
-	      # Linker will automatically link against shared library if both
-	      # static and shared are present.  Therefore, ensure we extract
-	      # symbols from the import library if a shared library is present
-	      # (otherwise, the dlopen module name will be incorrect).  We do
-	      # this by putting the import library name into $newdlprefiles.
-	      # We recover the dlopen module name by 'saving' the la file
-	      # name in a special purpose variable, and (later) extracting the
-	      # dlname from the la file.
-	      if test -n "$dlname"; then
-	        func_tr_sh "$dir/$linklib"
-	        eval "libfile_$func_tr_sh_result=\$abs_ladir/\$laname"
-	        func_append newdlprefiles " $dir/$linklib"
-	      else
-	        func_append newdlprefiles " $dir/$old_library"
-	        # Keep a list of preopened convenience libraries to check
-	        # that they are being used correctly in the link pass.
-	        test -z "$libdir" && \
-	          func_append dlpreconveniencelibs " $dir/$old_library"
-	      fi
-	    ;;
-	    * )
-	      # Prefer using a static library (so that no silly _DYNAMIC symbols
-	      # are required to link).
-	      if test -n "$old_library"; then
-	        func_append newdlprefiles " $dir/$old_library"
-	        # Keep a list of preopened convenience libraries to check
-	        # that they are being used correctly in the link pass.
-	        test -z "$libdir" && \
-	          func_append dlpreconveniencelibs " $dir/$old_library"
-	      # Otherwise, use the dlname, so that lt_dlopen finds it.
-	      elif test -n "$dlname"; then
-	        func_append newdlprefiles " $dir/$dlname"
-	      else
-	        func_append newdlprefiles " $dir/$linklib"
-	      fi
-	    ;;
-	  esac
-	fi # $pass = dlpreopen
-
-	if test -z "$libdir"; then
-	  # Link the convenience library
-	  if test "$linkmode" = lib; then
-	    deplibs="$dir/$old_library $deplibs"
-	  elif test "$linkmode,$pass" = "prog,link"; then
-	    compile_deplibs="$dir/$old_library $compile_deplibs"
-	    finalize_deplibs="$dir/$old_library $finalize_deplibs"
-	  else
-	    deplibs="$lib $deplibs" # used for prog,scan pass
-	  fi
-	  continue
-	fi
-
-
-	if test "$linkmode" = prog && test "$pass" != link; then
-	  func_append newlib_search_path " $ladir"
-	  deplibs="$lib $deplibs"
-
-	  linkalldeplibs=no
-	  if test "$link_all_deplibs" != no || test -z "$library_names" ||
-	     test "$build_libtool_libs" = no; then
-	    linkalldeplibs=yes
-	  fi
-
-	  tmp_libs=
-	  for deplib in $dependency_libs; do
-	    case $deplib in
-	    -L*) func_stripname '-L' '' "$deplib"
-	         func_resolve_sysroot "$func_stripname_result"
-	         func_append newlib_search_path " $func_resolve_sysroot_result"
-		 ;;
-	    esac
-	    # Need to link against all dependency_libs?
-	    if test "$linkalldeplibs" = yes; then
-	      deplibs="$deplib $deplibs"
-	    else
-	      # Need to hardcode shared library paths
-	      # or/and link against static libraries
-	      newdependency_libs="$deplib $newdependency_libs"
-	    fi
-	    if $opt_preserve_dup_deps ; then
-	      case "$tmp_libs " in
-	      *" $deplib "*) func_append specialdeplibs " $deplib" ;;
-	      esac
-	    fi
-	    func_append tmp_libs " $deplib"
-	  done # for deplib
-	  continue
-	fi # $linkmode = prog...
-
-	if test "$linkmode,$pass" = "prog,link"; then
-	  if test -n "$library_names" &&
-	     { { test "$prefer_static_libs" = no ||
-	         test "$prefer_static_libs,$installed" = "built,yes"; } ||
-	       test -z "$old_library"; }; then
-	    # We need to hardcode the library path
-	    if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then
-	      # Make sure the rpath contains only unique directories.
-	      case "$temp_rpath:" in
-	      *"$absdir:"*) ;;
-	      *) func_append temp_rpath "$absdir:" ;;
-	      esac
-	    fi
-
-	    # Hardcode the library path.
-	    # Skip directories that are in the system default run-time
-	    # search path.
-	    case " $sys_lib_dlsearch_path " in
-	    *" $absdir "*) ;;
-	    *)
-	      case "$compile_rpath " in
-	      *" $absdir "*) ;;
-	      *) func_append compile_rpath " $absdir" ;;
-	      esac
-	      ;;
-	    esac
-	    case " $sys_lib_dlsearch_path " in
-	    *" $libdir "*) ;;
-	    *)
-	      case "$finalize_rpath " in
-	      *" $libdir "*) ;;
-	      *) func_append finalize_rpath " $libdir" ;;
-	      esac
-	      ;;
-	    esac
-	  fi # $linkmode,$pass = prog,link...
-
-	  if test "$alldeplibs" = yes &&
-	     { test "$deplibs_check_method" = pass_all ||
-	       { test "$build_libtool_libs" = yes &&
-		 test -n "$library_names"; }; }; then
-	    # We only need to search for static libraries
-	    continue
-	  fi
-	fi
-
-	link_static=no # Whether the deplib will be linked statically
-	use_static_libs=$prefer_static_libs
-	if test "$use_static_libs" = built && test "$installed" = yes; then
-	  use_static_libs=no
-	fi
-	if test -n "$library_names" &&
-	   { test "$use_static_libs" = no || test -z "$old_library"; }; then
-	  case $host in
-	  *cygwin* | *mingw* | *cegcc*)
-	      # No point in relinking DLLs because paths are not encoded
-	      func_append notinst_deplibs " $lib"
-	      need_relink=no
-	    ;;
-	  *)
-	    if test "$installed" = no; then
-	      func_append notinst_deplibs " $lib"
-	      need_relink=yes
-	    fi
-	    ;;
-	  esac
-	  # This is a shared library
-
-	  # Warn about portability, can't link against -module's on some
-	  # systems (darwin).  Don't bleat about dlopened modules though!
-	  dlopenmodule=""
-	  for dlpremoduletest in $dlprefiles; do
-	    if test "X$dlpremoduletest" = "X$lib"; then
-	      dlopenmodule="$dlpremoduletest"
-	      break
-	    fi
-	  done
-	  if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then
-	    echo
-	    if test "$linkmode" = prog; then
-	      $ECHO "*** Warning: Linking the executable $output against the loadable module"
-	    else
-	      $ECHO "*** Warning: Linking the shared library $output against the loadable module"
-	    fi
-	    $ECHO "*** $linklib is not portable!"
-	  fi
-	  if test "$linkmode" = lib &&
-	     test "$hardcode_into_libs" = yes; then
-	    # Hardcode the library path.
-	    # Skip directories that are in the system default run-time
-	    # search path.
-	    case " $sys_lib_dlsearch_path " in
-	    *" $absdir "*) ;;
-	    *)
-	      case "$compile_rpath " in
-	      *" $absdir "*) ;;
-	      *) func_append compile_rpath " $absdir" ;;
-	      esac
-	      ;;
-	    esac
-	    case " $sys_lib_dlsearch_path " in
-	    *" $libdir "*) ;;
-	    *)
-	      case "$finalize_rpath " in
-	      *" $libdir "*) ;;
-	      *) func_append finalize_rpath " $libdir" ;;
-	      esac
-	      ;;
-	    esac
-	  fi
-
-	  if test -n "$old_archive_from_expsyms_cmds"; then
-	    # figure out the soname
-	    set dummy $library_names
-	    shift
-	    realname="$1"
-	    shift
-	    libname=`eval "\\$ECHO \"$libname_spec\""`
-	    # use dlname if we got it. it's perfectly good, no?
-	    if test -n "$dlname"; then
-	      soname="$dlname"
-	    elif test -n "$soname_spec"; then
-	      # bleh windows
-	      case $host in
-	      *cygwin* | mingw* | *cegcc*)
-	        func_arith $current - $age
-		major=$func_arith_result
-		versuffix="-$major"
-		;;
-	      esac
-	      eval soname=\"$soname_spec\"
-	    else
-	      soname="$realname"
-	    fi
-
-	    # Make a new name for the extract_expsyms_cmds to use
-	    soroot="$soname"
-	    func_basename "$soroot"
-	    soname="$func_basename_result"
-	    func_stripname 'lib' '.dll' "$soname"
-	    newlib=libimp-$func_stripname_result.a
-
-	    # If the library has no export list, then create one now
-	    if test -f "$output_objdir/$soname-def"; then :
-	    else
-	      func_verbose "extracting exported symbol list from \`$soname'"
-	      func_execute_cmds "$extract_expsyms_cmds" 'exit $?'
-	    fi
-
-	    # Create $newlib
-	    if test -f "$output_objdir/$newlib"; then :; else
-	      func_verbose "generating import library for \`$soname'"
-	      func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?'
-	    fi
-	    # make sure the library variables are pointing to the new library
-	    dir=$output_objdir
-	    linklib=$newlib
-	  fi # test -n "$old_archive_from_expsyms_cmds"
-
-	  if test "$linkmode" = prog || test "$opt_mode" != relink; then
-	    add_shlibpath=
-	    add_dir=
-	    add=
-	    lib_linked=yes
-	    case $hardcode_action in
-	    immediate | unsupported)
-	      if test "$hardcode_direct" = no; then
-		add="$dir/$linklib"
-		case $host in
-		  *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;;
-		  *-*-sysv4*uw2*) add_dir="-L$dir" ;;
-		  *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \
-		    *-*-unixware7*) add_dir="-L$dir" ;;
-		  *-*-darwin* )
-		    # if the lib is a (non-dlopened) module then we can not
-		    # link against it, someone is ignoring the earlier warnings
-		    if /usr/bin/file -L $add 2> /dev/null |
-			 $GREP ": [^:]* bundle" >/dev/null ; then
-		      if test "X$dlopenmodule" != "X$lib"; then
-			$ECHO "*** Warning: lib $linklib is a module, not a shared library"
-			if test -z "$old_library" ; then
-			  echo
-			  echo "*** And there doesn't seem to be a static archive available"
-			  echo "*** The link will probably fail, sorry"
-			else
-			  add="$dir/$old_library"
-			fi
-		      elif test -n "$old_library"; then
-			add="$dir/$old_library"
-		      fi
-		    fi
-		esac
-	      elif test "$hardcode_minus_L" = no; then
-		case $host in
-		*-*-sunos*) add_shlibpath="$dir" ;;
-		esac
-		add_dir="-L$dir"
-		add="-l$name"
-	      elif test "$hardcode_shlibpath_var" = no; then
-		add_shlibpath="$dir"
-		add="-l$name"
-	      else
-		lib_linked=no
-	      fi
-	      ;;
-	    relink)
-	      if test "$hardcode_direct" = yes &&
-	         test "$hardcode_direct_absolute" = no; then
-		add="$dir/$linklib"
-	      elif test "$hardcode_minus_L" = yes; then
-		add_dir="-L$absdir"
-		# Try looking first in the location we're being installed to.
-		if test -n "$inst_prefix_dir"; then
-		  case $libdir in
-		    [\\/]*)
-		      func_append add_dir " -L$inst_prefix_dir$libdir"
-		      ;;
-		  esac
-		fi
-		add="-l$name"
-	      elif test "$hardcode_shlibpath_var" = yes; then
-		add_shlibpath="$dir"
-		add="-l$name"
-	      else
-		lib_linked=no
-	      fi
-	      ;;
-	    *) lib_linked=no ;;
-	    esac
-
-	    if test "$lib_linked" != yes; then
-	      func_fatal_configuration "unsupported hardcode properties"
-	    fi
-
-	    if test -n "$add_shlibpath"; then
-	      case :$compile_shlibpath: in
-	      *":$add_shlibpath:"*) ;;
-	      *) func_append compile_shlibpath "$add_shlibpath:" ;;
-	      esac
-	    fi
-	    if test "$linkmode" = prog; then
-	      test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs"
-	      test -n "$add" && compile_deplibs="$add $compile_deplibs"
-	    else
-	      test -n "$add_dir" && deplibs="$add_dir $deplibs"
-	      test -n "$add" && deplibs="$add $deplibs"
-	      if test "$hardcode_direct" != yes &&
-		 test "$hardcode_minus_L" != yes &&
-		 test "$hardcode_shlibpath_var" = yes; then
-		case :$finalize_shlibpath: in
-		*":$libdir:"*) ;;
-		*) func_append finalize_shlibpath "$libdir:" ;;
-		esac
-	      fi
-	    fi
-	  fi
-
-	  if test "$linkmode" = prog || test "$opt_mode" = relink; then
-	    add_shlibpath=
-	    add_dir=
-	    add=
-	    # Finalize command for both is simple: just hardcode it.
-	    if test "$hardcode_direct" = yes &&
-	       test "$hardcode_direct_absolute" = no; then
-	      add="$libdir/$linklib"
-	    elif test "$hardcode_minus_L" = yes; then
-	      add_dir="-L$libdir"
-	      add="-l$name"
-	    elif test "$hardcode_shlibpath_var" = yes; then
-	      case :$finalize_shlibpath: in
-	      *":$libdir:"*) ;;
-	      *) func_append finalize_shlibpath "$libdir:" ;;
-	      esac
-	      add="-l$name"
-	    elif test "$hardcode_automatic" = yes; then
-	      if test -n "$inst_prefix_dir" &&
-		 test -f "$inst_prefix_dir$libdir/$linklib" ; then
-		add="$inst_prefix_dir$libdir/$linklib"
-	      else
-		add="$libdir/$linklib"
-	      fi
-	    else
-	      # We cannot seem to hardcode it, guess we'll fake it.
-	      add_dir="-L$libdir"
-	      # Try looking first in the location we're being installed to.
-	      if test -n "$inst_prefix_dir"; then
-		case $libdir in
-		  [\\/]*)
-		    func_append add_dir " -L$inst_prefix_dir$libdir"
-		    ;;
-		esac
-	      fi
-	      add="-l$name"
-	    fi
-
-	    if test "$linkmode" = prog; then
-	      test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs"
-	      test -n "$add" && finalize_deplibs="$add $finalize_deplibs"
-	    else
-	      test -n "$add_dir" && deplibs="$add_dir $deplibs"
-	      test -n "$add" && deplibs="$add $deplibs"
-	    fi
-	  fi
-	elif test "$linkmode" = prog; then
-	  # Here we assume that one of hardcode_direct or hardcode_minus_L
-	  # is not unsupported.  This is valid on all known static and
-	  # shared platforms.
-	  if test "$hardcode_direct" != unsupported; then
-	    test -n "$old_library" && linklib="$old_library"
-	    compile_deplibs="$dir/$linklib $compile_deplibs"
-	    finalize_deplibs="$dir/$linklib $finalize_deplibs"
-	  else
-	    compile_deplibs="-l$name -L$dir $compile_deplibs"
-	    finalize_deplibs="-l$name -L$dir $finalize_deplibs"
-	  fi
-	elif test "$build_libtool_libs" = yes; then
-	  # Not a shared library
-	  if test "$deplibs_check_method" != pass_all; then
-	    # We're trying link a shared library against a static one
-	    # but the system doesn't support it.
-
-	    # Just print a warning and add the library to dependency_libs so
-	    # that the program can be linked against the static library.
-	    echo
-	    $ECHO "*** Warning: This system can not link to static lib archive $lib."
-	    echo "*** I have the capability to make that library automatically link in when"
-	    echo "*** you link to this library.  But I can only do this if you have a"
-	    echo "*** shared version of the library, which you do not appear to have."
-	    if test "$module" = yes; then
-	      echo "*** But as you try to build a module library, libtool will still create "
-	      echo "*** a static module, that should work as long as the dlopening application"
-	      echo "*** is linked with the -dlopen flag to resolve symbols at runtime."
-	      if test -z "$global_symbol_pipe"; then
-		echo
-		echo "*** However, this would only work if libtool was able to extract symbol"
-		echo "*** lists from a program, using \`nm' or equivalent, but libtool could"
-		echo "*** not find such a program.  So, this module is probably useless."
-		echo "*** \`nm' from GNU binutils and a full rebuild may help."
-	      fi
-	      if test "$build_old_libs" = no; then
-		build_libtool_libs=module
-		build_old_libs=yes
-	      else
-		build_libtool_libs=no
-	      fi
-	    fi
-	  else
-	    deplibs="$dir/$old_library $deplibs"
-	    link_static=yes
-	  fi
-	fi # link shared/static library?
-
-	if test "$linkmode" = lib; then
-	  if test -n "$dependency_libs" &&
-	     { test "$hardcode_into_libs" != yes ||
-	       test "$build_old_libs" = yes ||
-	       test "$link_static" = yes; }; then
-	    # Extract -R from dependency_libs
-	    temp_deplibs=
-	    for libdir in $dependency_libs; do
-	      case $libdir in
-	      -R*) func_stripname '-R' '' "$libdir"
-	           temp_xrpath=$func_stripname_result
-		   case " $xrpath " in
-		   *" $temp_xrpath "*) ;;
-		   *) func_append xrpath " $temp_xrpath";;
-		   esac;;
-	      *) func_append temp_deplibs " $libdir";;
-	      esac
-	    done
-	    dependency_libs="$temp_deplibs"
-	  fi
-
-	  func_append newlib_search_path " $absdir"
-	  # Link against this library
-	  test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs"
-	  # ... and its dependency_libs
-	  tmp_libs=
-	  for deplib in $dependency_libs; do
-	    newdependency_libs="$deplib $newdependency_libs"
-	    case $deplib in
-              -L*) func_stripname '-L' '' "$deplib"
-                   func_resolve_sysroot "$func_stripname_result";;
-              *) func_resolve_sysroot "$deplib" ;;
-            esac
-	    if $opt_preserve_dup_deps ; then
-	      case "$tmp_libs " in
-	      *" $func_resolve_sysroot_result "*)
-                func_append specialdeplibs " $func_resolve_sysroot_result" ;;
-	      esac
-	    fi
-	    func_append tmp_libs " $func_resolve_sysroot_result"
-	  done
-
-	  if test "$link_all_deplibs" != no; then
-	    # Add the search paths of all dependency libraries
-	    for deplib in $dependency_libs; do
-	      path=
-	      case $deplib in
-	      -L*) path="$deplib" ;;
-	      *.la)
-	        func_resolve_sysroot "$deplib"
-	        deplib=$func_resolve_sysroot_result
-	        func_dirname "$deplib" "" "."
-		dir=$func_dirname_result
-		# We need an absolute path.
-		case $dir in
-		[\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;;
-		*)
-		  absdir=`cd "$dir" && pwd`
-		  if test -z "$absdir"; then
-		    func_warning "cannot determine absolute directory name of \`$dir'"
-		    absdir="$dir"
-		  fi
-		  ;;
-		esac
-		if $GREP "^installed=no" $deplib > /dev/null; then
-		case $host in
-		*-*-darwin*)
-		  depdepl=
-		  eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib`
-		  if test -n "$deplibrary_names" ; then
-		    for tmp in $deplibrary_names ; do
-		      depdepl=$tmp
-		    done
-		    if test -f "$absdir/$objdir/$depdepl" ; then
-		      depdepl="$absdir/$objdir/$depdepl"
-		      darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'`
-                      if test -z "$darwin_install_name"; then
-                          darwin_install_name=`${OTOOL64} -L $depdepl  | awk '{if (NR == 2) {print $1;exit}}'`
-                      fi
-		      func_append compiler_flags " ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}"
-		      func_append linker_flags " -dylib_file ${darwin_install_name}:${depdepl}"
-		      path=
-		    fi
-		  fi
-		  ;;
-		*)
-		  path="-L$absdir/$objdir"
-		  ;;
-		esac
-		else
-		  eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
-		  test -z "$libdir" && \
-		    func_fatal_error "\`$deplib' is not a valid libtool archive"
-		  test "$absdir" != "$libdir" && \
-		    func_warning "\`$deplib' seems to be moved"
-
-		  path="-L$absdir"
-		fi
-		;;
-	      esac
-	      case " $deplibs " in
-	      *" $path "*) ;;
-	      *) deplibs="$path $deplibs" ;;
-	      esac
-	    done
-	  fi # link_all_deplibs != no
-	fi # linkmode = lib
-      done # for deplib in $libs
-      if test "$pass" = link; then
-	if test "$linkmode" = "prog"; then
-	  compile_deplibs="$new_inherited_linker_flags $compile_deplibs"
-	  finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs"
-	else
-	  compiler_flags="$compiler_flags "`$ECHO " $new_inherited_linker_flags" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'`
-	fi
-      fi
-      dependency_libs="$newdependency_libs"
-      if test "$pass" = dlpreopen; then
-	# Link the dlpreopened libraries before other libraries
-	for deplib in $save_deplibs; do
-	  deplibs="$deplib $deplibs"
-	done
-      fi
-      if test "$pass" != dlopen; then
-	if test "$pass" != conv; then
-	  # Make sure lib_search_path contains only unique directories.
-	  lib_search_path=
-	  for dir in $newlib_search_path; do
-	    case "$lib_search_path " in
-	    *" $dir "*) ;;
-	    *) func_append lib_search_path " $dir" ;;
-	    esac
-	  done
-	  newlib_search_path=
-	fi
-
-	if test "$linkmode,$pass" != "prog,link"; then
-	  vars="deplibs"
-	else
-	  vars="compile_deplibs finalize_deplibs"
-	fi
-	for var in $vars dependency_libs; do
-	  # Add libraries to $var in reverse order
-	  eval tmp_libs=\"\$$var\"
-	  new_libs=
-	  for deplib in $tmp_libs; do
-	    # FIXME: Pedantically, this is the right thing to do, so
-	    #        that some nasty dependency loop isn't accidentally
-	    #        broken:
-	    #new_libs="$deplib $new_libs"
-	    # Pragmatically, this seems to cause very few problems in
-	    # practice:
-	    case $deplib in
-	    -L*) new_libs="$deplib $new_libs" ;;
-	    -R*) ;;
-	    *)
-	      # And here is the reason: when a library appears more
-	      # than once as an explicit dependence of a library, or
-	      # is implicitly linked in more than once by the
-	      # compiler, it is considered special, and multiple
-	      # occurrences thereof are not removed.  Compare this
-	      # with having the same library being listed as a
-	      # dependency of multiple other libraries: in this case,
-	      # we know (pedantically, we assume) the library does not
-	      # need to be listed more than once, so we keep only the
-	      # last copy.  This is not always right, but it is rare
-	      # enough that we require users that really mean to play
-	      # such unportable linking tricks to link the library
-	      # using -Wl,-lname, so that libtool does not consider it
-	      # for duplicate removal.
-	      case " $specialdeplibs " in
-	      *" $deplib "*) new_libs="$deplib $new_libs" ;;
-	      *)
-		case " $new_libs " in
-		*" $deplib "*) ;;
-		*) new_libs="$deplib $new_libs" ;;
-		esac
-		;;
-	      esac
-	      ;;
-	    esac
-	  done
-	  tmp_libs=
-	  for deplib in $new_libs; do
-	    case $deplib in
-	    -L*)
-	      case " $tmp_libs " in
-	      *" $deplib "*) ;;
-	      *) func_append tmp_libs " $deplib" ;;
-	      esac
-	      ;;
-	    *) func_append tmp_libs " $deplib" ;;
-	    esac
-	  done
-	  eval $var=\"$tmp_libs\"
-	done # for var
-      fi
-      # Last step: remove runtime libs from dependency_libs
-      # (they stay in deplibs)
-      tmp_libs=
-      for i in $dependency_libs ; do
-	case " $predeps $postdeps $compiler_lib_search_path " in
-	*" $i "*)
-	  i=""
-	  ;;
-	esac
-	if test -n "$i" ; then
-	  func_append tmp_libs " $i"
-	fi
-      done
-      dependency_libs=$tmp_libs
-    done # for pass
-    if test "$linkmode" = prog; then
-      dlfiles="$newdlfiles"
-    fi
-    if test "$linkmode" = prog || test "$linkmode" = lib; then
-      dlprefiles="$newdlprefiles"
-    fi
-
-    case $linkmode in
-    oldlib)
-      if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
-	func_warning "\`-dlopen' is ignored for archives"
-      fi
-
-      case " $deplibs" in
-      *\ -l* | *\ -L*)
-	func_warning "\`-l' and \`-L' are ignored for archives" ;;
-      esac
-
-      test -n "$rpath" && \
-	func_warning "\`-rpath' is ignored for archives"
-
-      test -n "$xrpath" && \
-	func_warning "\`-R' is ignored for archives"
-
-      test -n "$vinfo" && \
-	func_warning "\`-version-info/-version-number' is ignored for archives"
-
-      test -n "$release" && \
-	func_warning "\`-release' is ignored for archives"
-
-      test -n "$export_symbols$export_symbols_regex" && \
-	func_warning "\`-export-symbols' is ignored for archives"
-
-      # Now set the variables for building old libraries.
-      build_libtool_libs=no
-      oldlibs="$output"
-      func_append objs "$old_deplibs"
-      ;;
-
-    lib)
-      # Make sure we only generate libraries of the form `libNAME.la'.
-      case $outputname in
-      lib*)
-	func_stripname 'lib' '.la' "$outputname"
-	name=$func_stripname_result
-	eval shared_ext=\"$shrext_cmds\"
-	eval libname=\"$libname_spec\"
-	;;
-      *)
-	test "$module" = no && \
-	  func_fatal_help "libtool library \`$output' must begin with \`lib'"
-
-	if test "$need_lib_prefix" != no; then
-	  # Add the "lib" prefix for modules if required
-	  func_stripname '' '.la' "$outputname"
-	  name=$func_stripname_result
-	  eval shared_ext=\"$shrext_cmds\"
-	  eval libname=\"$libname_spec\"
-	else
-	  func_stripname '' '.la' "$outputname"
-	  libname=$func_stripname_result
-	fi
-	;;
-      esac
-
-      if test -n "$objs"; then
-	if test "$deplibs_check_method" != pass_all; then
-	  func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs"
-	else
-	  echo
-	  $ECHO "*** Warning: Linking the shared library $output against the non-libtool"
-	  $ECHO "*** objects $objs is not portable!"
-	  func_append libobjs " $objs"
-	fi
-      fi
-
-      test "$dlself" != no && \
-	func_warning "\`-dlopen self' is ignored for libtool libraries"
-
-      set dummy $rpath
-      shift
-      test "$#" -gt 1 && \
-	func_warning "ignoring multiple \`-rpath's for a libtool library"
-
-      install_libdir="$1"
-
-      oldlibs=
-      if test -z "$rpath"; then
-	if test "$build_libtool_libs" = yes; then
-	  # Building a libtool convenience library.
-	  # Some compilers have problems with a `.al' extension so
-	  # convenience libraries should have the same extension an
-	  # archive normally would.
-	  oldlibs="$output_objdir/$libname.$libext $oldlibs"
-	  build_libtool_libs=convenience
-	  build_old_libs=yes
-	fi
-
-	test -n "$vinfo" && \
-	  func_warning "\`-version-info/-version-number' is ignored for convenience libraries"
-
-	test -n "$release" && \
-	  func_warning "\`-release' is ignored for convenience libraries"
-      else
-
-	# Parse the version information argument.
-	save_ifs="$IFS"; IFS=':'
-	set dummy $vinfo 0 0 0
-	shift
-	IFS="$save_ifs"
-
-	test -n "$7" && \
-	  func_fatal_help "too many parameters to \`-version-info'"
-
-	# convert absolute version numbers to libtool ages
-	# this retains compatibility with .la files and attempts
-	# to make the code below a bit more comprehensible
-
-	case $vinfo_number in
-	yes)
-	  number_major="$1"
-	  number_minor="$2"
-	  number_revision="$3"
-	  #
-	  # There are really only two kinds -- those that
-	  # use the current revision as the major version
-	  # and those that subtract age and use age as
-	  # a minor version.  But, then there is irix
-	  # which has an extra 1 added just for fun
-	  #
-	  case $version_type in
-	  # correct linux to gnu/linux during the next big refactor
-	  darwin|linux|osf|windows|none)
-	    func_arith $number_major + $number_minor
-	    current=$func_arith_result
-	    age="$number_minor"
-	    revision="$number_revision"
-	    ;;
-	  freebsd-aout|freebsd-elf|qnx|sunos)
-	    current="$number_major"
-	    revision="$number_minor"
-	    age="0"
-	    ;;
-	  irix|nonstopux)
-	    func_arith $number_major + $number_minor
-	    current=$func_arith_result
-	    age="$number_minor"
-	    revision="$number_minor"
-	    lt_irix_increment=no
-	    ;;
-	  esac
-	  ;;
-	no)
-	  current="$1"
-	  revision="$2"
-	  age="$3"
-	  ;;
-	esac
-
-	# Check that each of the things are valid numbers.
-	case $current in
-	0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
-	*)
-	  func_error "CURRENT \`$current' must be a nonnegative integer"
-	  func_fatal_error "\`$vinfo' is not valid version information"
-	  ;;
-	esac
-
-	case $revision in
-	0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
-	*)
-	  func_error "REVISION \`$revision' must be a nonnegative integer"
-	  func_fatal_error "\`$vinfo' is not valid version information"
-	  ;;
-	esac
-
-	case $age in
-	0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
-	*)
-	  func_error "AGE \`$age' must be a nonnegative integer"
-	  func_fatal_error "\`$vinfo' is not valid version information"
-	  ;;
-	esac
-
-	if test "$age" -gt "$current"; then
-	  func_error "AGE \`$age' is greater than the current interface number \`$current'"
-	  func_fatal_error "\`$vinfo' is not valid version information"
-	fi
-
-	# Calculate the version variables.
-	major=
-	versuffix=
-	verstring=
-	case $version_type in
-	none) ;;
-
-	darwin)
-	  # Like Linux, but with the current version available in
-	  # verstring for coding it into the library header
-	  func_arith $current - $age
-	  major=.$func_arith_result
-	  versuffix="$major.$age.$revision"
-	  # Darwin ld doesn't like 0 for these options...
-	  func_arith $current + 1
-	  minor_current=$func_arith_result
-	  xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision"
-	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
-	  ;;
-
-	freebsd-aout)
-	  major=".$current"
-	  versuffix=".$current.$revision";
-	  ;;
-
-	freebsd-elf)
-	  major=".$current"
-	  versuffix=".$current"
-	  ;;
-
-	irix | nonstopux)
-	  if test "X$lt_irix_increment" = "Xno"; then
-	    func_arith $current - $age
-	  else
-	    func_arith $current - $age + 1
-	  fi
-	  major=$func_arith_result
-
-	  case $version_type in
-	    nonstopux) verstring_prefix=nonstopux ;;
-	    *)         verstring_prefix=sgi ;;
-	  esac
-	  verstring="$verstring_prefix$major.$revision"
-
-	  # Add in all the interfaces that we are compatible with.
-	  loop=$revision
-	  while test "$loop" -ne 0; do
-	    func_arith $revision - $loop
-	    iface=$func_arith_result
-	    func_arith $loop - 1
-	    loop=$func_arith_result
-	    verstring="$verstring_prefix$major.$iface:$verstring"
-	  done
-
-	  # Before this point, $major must not contain `.'.
-	  major=.$major
-	  versuffix="$major.$revision"
-	  ;;
-
-	linux) # correct to gnu/linux during the next big refactor
-	  func_arith $current - $age
-	  major=.$func_arith_result
-	  versuffix="$major.$age.$revision"
-	  ;;
-
-	osf)
-	  func_arith $current - $age
-	  major=.$func_arith_result
-	  versuffix=".$current.$age.$revision"
-	  verstring="$current.$age.$revision"
-
-	  # Add in all the interfaces that we are compatible with.
-	  loop=$age
-	  while test "$loop" -ne 0; do
-	    func_arith $current - $loop
-	    iface=$func_arith_result
-	    func_arith $loop - 1
-	    loop=$func_arith_result
-	    verstring="$verstring:${iface}.0"
-	  done
-
-	  # Make executables depend on our current version.
-	  func_append verstring ":${current}.0"
-	  ;;
-
-	qnx)
-	  major=".$current"
-	  versuffix=".$current"
-	  ;;
-
-	sunos)
-	  major=".$current"
-	  versuffix=".$current.$revision"
-	  ;;
-
-	windows)
-	  # Use '-' rather than '.', since we only want one
-	  # extension on DOS 8.3 filesystems.
-	  func_arith $current - $age
-	  major=$func_arith_result
-	  versuffix="-$major"
-	  ;;
-
-	*)
-	  func_fatal_configuration "unknown library version type \`$version_type'"
-	  ;;
-	esac
-
-	# Clear the version info if we defaulted, and they specified a release.
-	if test -z "$vinfo" && test -n "$release"; then
-	  major=
-	  case $version_type in
-	  darwin)
-	    # we can't check for "0.0" in archive_cmds due to quoting
-	    # problems, so we reset it completely
-	    verstring=
-	    ;;
-	  *)
-	    verstring="0.0"
-	    ;;
-	  esac
-	  if test "$need_version" = no; then
-	    versuffix=
-	  else
-	    versuffix=".0.0"
-	  fi
-	fi
-
-	# Remove version info from name if versioning should be avoided
-	if test "$avoid_version" = yes && test "$need_version" = no; then
-	  major=
-	  versuffix=
-	  verstring=""
-	fi
-
-	# Check to see if the archive will have undefined symbols.
-	if test "$allow_undefined" = yes; then
-	  if test "$allow_undefined_flag" = unsupported; then
-	    func_warning "undefined symbols not allowed in $host shared libraries"
-	    build_libtool_libs=no
-	    build_old_libs=yes
-	  fi
-	else
-	  # Don't allow undefined symbols.
-	  allow_undefined_flag="$no_undefined_flag"
-	fi
-
-      fi
-
-      func_generate_dlsyms "$libname" "$libname" "yes"
-      func_append libobjs " $symfileobj"
-      test "X$libobjs" = "X " && libobjs=
-
-      if test "$opt_mode" != relink; then
-	# Remove our outputs, but don't remove object files since they
-	# may have been created when compiling PIC objects.
-	removelist=
-	tempremovelist=`$ECHO "$output_objdir/*"`
-	for p in $tempremovelist; do
-	  case $p in
-	    *.$objext | *.gcno)
-	       ;;
-	    $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*)
-	       if test "X$precious_files_regex" != "X"; then
-		 if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1
-		 then
-		   continue
-		 fi
-	       fi
-	       func_append removelist " $p"
-	       ;;
-	    *) ;;
-	  esac
-	done
-	test -n "$removelist" && \
-	  func_show_eval "${RM}r \$removelist"
-      fi
-
-      # Now set the variables for building old libraries.
-      if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then
-	func_append oldlibs " $output_objdir/$libname.$libext"
-
-	# Transform .lo files to .o files.
-	oldobjs="$objs "`$ECHO "$libobjs" | $SP2NL | $SED "/\.${libext}$/d; $lo2o" | $NL2SP`
-      fi
-
-      # Eliminate all temporary directories.
-      #for path in $notinst_path; do
-      #	lib_search_path=`$ECHO "$lib_search_path " | $SED "s% $path % %g"`
-      #	deplibs=`$ECHO "$deplibs " | $SED "s% -L$path % %g"`
-      #	dependency_libs=`$ECHO "$dependency_libs " | $SED "s% -L$path % %g"`
-      #done
-
-      if test -n "$xrpath"; then
-	# If the user specified any rpath flags, then add them.
-	temp_xrpath=
-	for libdir in $xrpath; do
-	  func_replace_sysroot "$libdir"
-	  func_append temp_xrpath " -R$func_replace_sysroot_result"
-	  case "$finalize_rpath " in
-	  *" $libdir "*) ;;
-	  *) func_append finalize_rpath " $libdir" ;;
-	  esac
-	done
-	if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then
-	  dependency_libs="$temp_xrpath $dependency_libs"
-	fi
-      fi
-
-      # Make sure dlfiles contains only unique files that won't be dlpreopened
-      old_dlfiles="$dlfiles"
-      dlfiles=
-      for lib in $old_dlfiles; do
-	case " $dlprefiles $dlfiles " in
-	*" $lib "*) ;;
-	*) func_append dlfiles " $lib" ;;
-	esac
-      done
-
-      # Make sure dlprefiles contains only unique files
-      old_dlprefiles="$dlprefiles"
-      dlprefiles=
-      for lib in $old_dlprefiles; do
-	case "$dlprefiles " in
-	*" $lib "*) ;;
-	*) func_append dlprefiles " $lib" ;;
-	esac
-      done
-
-      if test "$build_libtool_libs" = yes; then
-	if test -n "$rpath"; then
-	  case $host in
-	  *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc* | *-*-haiku*)
-	    # these systems don't actually have a c library (as such)!
-	    ;;
-	  *-*-rhapsody* | *-*-darwin1.[012])
-	    # Rhapsody C library is in the System framework
-	    func_append deplibs " System.ltframework"
-	    ;;
-	  *-*-netbsd*)
-	    # Don't link with libc until the a.out ld.so is fixed.
-	    ;;
-	  *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
-	    # Do not include libc due to us having libc/libc_r.
-	    ;;
-	  *-*-sco3.2v5* | *-*-sco5v6*)
-	    # Causes problems with __ctype
-	    ;;
-	  *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
-	    # Compiler inserts libc in the correct place for threads to work
-	    ;;
-	  *)
-	    # Add libc to deplibs on all other systems if necessary.
-	    if test "$build_libtool_need_lc" = "yes"; then
-	      func_append deplibs " -lc"
-	    fi
-	    ;;
-	  esac
-	fi
-
-	# Transform deplibs into only deplibs that can be linked in shared.
-	name_save=$name
-	libname_save=$libname
-	release_save=$release
-	versuffix_save=$versuffix
-	major_save=$major
-	# I'm not sure if I'm treating the release correctly.  I think
-	# release should show up in the -l (ie -lgmp5) so we don't want to
-	# add it in twice.  Is that correct?
-	release=""
-	versuffix=""
-	major=""
-	newdeplibs=
-	droppeddeps=no
-	case $deplibs_check_method in
-	pass_all)
-	  # Don't check for shared/static.  Everything works.
-	  # This might be a little naive.  We might want to check
-	  # whether the library exists or not.  But this is on
-	  # osf3 & osf4 and I'm not really sure... Just
-	  # implementing what was already the behavior.
-	  newdeplibs=$deplibs
-	  ;;
-	test_compile)
-	  # This code stresses the "libraries are programs" paradigm to its
-	  # limits. Maybe even breaks it.  We compile a program, linking it
-	  # against the deplibs as a proxy for the library.  Then we can check
-	  # whether they linked in statically or dynamically with ldd.
-	  $opt_dry_run || $RM conftest.c
-	  cat > conftest.c <<EOF
-	  int main() { return 0; }
-EOF
-	  $opt_dry_run || $RM conftest
-	  if $LTCC $LTCFLAGS -o conftest conftest.c $deplibs; then
-	    ldd_output=`ldd conftest`
-	    for i in $deplibs; do
-	      case $i in
-	      -l*)
-		func_stripname -l '' "$i"
-		name=$func_stripname_result
-		if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
-		  case " $predeps $postdeps " in
-		  *" $i "*)
-		    func_append newdeplibs " $i"
-		    i=""
-		    ;;
-		  esac
-		fi
-		if test -n "$i" ; then
-		  libname=`eval "\\$ECHO \"$libname_spec\""`
-		  deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
-		  set dummy $deplib_matches; shift
-		  deplib_match=$1
-		  if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
-		    func_append newdeplibs " $i"
-		  else
-		    droppeddeps=yes
-		    echo
-		    $ECHO "*** Warning: dynamic linker does not accept needed library $i."
-		    echo "*** I have the capability to make that library automatically link in when"
-		    echo "*** you link to this library.  But I can only do this if you have a"
-		    echo "*** shared version of the library, which I believe you do not have"
-		    echo "*** because a test_compile did reveal that the linker did not use it for"
-		    echo "*** its dynamic dependency list that programs get resolved with at runtime."
-		  fi
-		fi
-		;;
-	      *)
-		func_append newdeplibs " $i"
-		;;
-	      esac
-	    done
-	  else
-	    # Error occurred in the first compile.  Let's try to salvage
-	    # the situation: Compile a separate program for each library.
-	    for i in $deplibs; do
-	      case $i in
-	      -l*)
-		func_stripname -l '' "$i"
-		name=$func_stripname_result
-		$opt_dry_run || $RM conftest
-		if $LTCC $LTCFLAGS -o conftest conftest.c $i; then
-		  ldd_output=`ldd conftest`
-		  if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
-		    case " $predeps $postdeps " in
-		    *" $i "*)
-		      func_append newdeplibs " $i"
-		      i=""
-		      ;;
-		    esac
-		  fi
-		  if test -n "$i" ; then
-		    libname=`eval "\\$ECHO \"$libname_spec\""`
-		    deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
-		    set dummy $deplib_matches; shift
-		    deplib_match=$1
-		    if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
-		      func_append newdeplibs " $i"
-		    else
-		      droppeddeps=yes
-		      echo
-		      $ECHO "*** Warning: dynamic linker does not accept needed library $i."
-		      echo "*** I have the capability to make that library automatically link in when"
-		      echo "*** you link to this library.  But I can only do this if you have a"
-		      echo "*** shared version of the library, which you do not appear to have"
-		      echo "*** because a test_compile did reveal that the linker did not use this one"
-		      echo "*** as a dynamic dependency that programs can get resolved with at runtime."
-		    fi
-		  fi
-		else
-		  droppeddeps=yes
-		  echo
-		  $ECHO "*** Warning!  Library $i is needed by this library but I was not able to"
-		  echo "*** make it link in!  You will probably need to install it or some"
-		  echo "*** library that it depends on before this library will be fully"
-		  echo "*** functional.  Installing it before continuing would be even better."
-		fi
-		;;
-	      *)
-		func_append newdeplibs " $i"
-		;;
-	      esac
-	    done
-	  fi
-	  ;;
-	file_magic*)
-	  set dummy $deplibs_check_method; shift
-	  file_magic_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
-	  for a_deplib in $deplibs; do
-	    case $a_deplib in
-	    -l*)
-	      func_stripname -l '' "$a_deplib"
-	      name=$func_stripname_result
-	      if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
-		case " $predeps $postdeps " in
-		*" $a_deplib "*)
-		  func_append newdeplibs " $a_deplib"
-		  a_deplib=""
-		  ;;
-		esac
-	      fi
-	      if test -n "$a_deplib" ; then
-		libname=`eval "\\$ECHO \"$libname_spec\""`
-		if test -n "$file_magic_glob"; then
-		  libnameglob=`func_echo_all "$libname" | $SED -e $file_magic_glob`
-		else
-		  libnameglob=$libname
-		fi
-		test "$want_nocaseglob" = yes && nocaseglob=`shopt -p nocaseglob`
-		for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
-		  if test "$want_nocaseglob" = yes; then
-		    shopt -s nocaseglob
-		    potential_libs=`ls $i/$libnameglob[.-]* 2>/dev/null`
-		    $nocaseglob
-		  else
-		    potential_libs=`ls $i/$libnameglob[.-]* 2>/dev/null`
-		  fi
-		  for potent_lib in $potential_libs; do
-		      # Follow soft links.
-		      if ls -lLd "$potent_lib" 2>/dev/null |
-			 $GREP " -> " >/dev/null; then
-			continue
-		      fi
-		      # The statement above tries to avoid entering an
-		      # endless loop below, in case of cyclic links.
-		      # We might still enter an endless loop, since a link
-		      # loop can be closed while we follow links,
-		      # but so what?
-		      potlib="$potent_lib"
-		      while test -h "$potlib" 2>/dev/null; do
-			potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'`
-			case $potliblink in
-			[\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";;
-			*) potlib=`$ECHO "$potlib" | $SED 's,[^/]*$,,'`"$potliblink";;
-			esac
-		      done
-		      if eval $file_magic_cmd \"\$potlib\" 2>/dev/null |
-			 $SED -e 10q |
-			 $EGREP "$file_magic_regex" > /dev/null; then
-			func_append newdeplibs " $a_deplib"
-			a_deplib=""
-			break 2
-		      fi
-		  done
-		done
-	      fi
-	      if test -n "$a_deplib" ; then
-		droppeddeps=yes
-		echo
-		$ECHO "*** Warning: linker path does not have real file for library $a_deplib."
-		echo "*** I have the capability to make that library automatically link in when"
-		echo "*** you link to this library.  But I can only do this if you have a"
-		echo "*** shared version of the library, which you do not appear to have"
-		echo "*** because I did check the linker path looking for a file starting"
-		if test -z "$potlib" ; then
-		  $ECHO "*** with $libname but no candidates were found. (...for file magic test)"
-		else
-		  $ECHO "*** with $libname and none of the candidates passed a file format test"
-		  $ECHO "*** using a file magic. Last file checked: $potlib"
-		fi
-	      fi
-	      ;;
-	    *)
-	      # Add a -L argument.
-	      func_append newdeplibs " $a_deplib"
-	      ;;
-	    esac
-	  done # Gone through all deplibs.
-	  ;;
-	match_pattern*)
-	  set dummy $deplibs_check_method; shift
-	  match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
-	  for a_deplib in $deplibs; do
-	    case $a_deplib in
-	    -l*)
-	      func_stripname -l '' "$a_deplib"
-	      name=$func_stripname_result
-	      if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
-		case " $predeps $postdeps " in
-		*" $a_deplib "*)
-		  func_append newdeplibs " $a_deplib"
-		  a_deplib=""
-		  ;;
-		esac
-	      fi
-	      if test -n "$a_deplib" ; then
-		libname=`eval "\\$ECHO \"$libname_spec\""`
-		for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
-		  potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
-		  for potent_lib in $potential_libs; do
-		    potlib="$potent_lib" # see symlink-check above in file_magic test
-		    if eval "\$ECHO \"$potent_lib\"" 2>/dev/null | $SED 10q | \
-		       $EGREP "$match_pattern_regex" > /dev/null; then
-		      func_append newdeplibs " $a_deplib"
-		      a_deplib=""
-		      break 2
-		    fi
-		  done
-		done
-	      fi
-	      if test -n "$a_deplib" ; then
-		droppeddeps=yes
-		echo
-		$ECHO "*** Warning: linker path does not have real file for library $a_deplib."
-		echo "*** I have the capability to make that library automatically link in when"
-		echo "*** you link to this library.  But I can only do this if you have a"
-		echo "*** shared version of the library, which you do not appear to have"
-		echo "*** because I did check the linker path looking for a file starting"
-		if test -z "$potlib" ; then
-		  $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)"
-		else
-		  $ECHO "*** with $libname and none of the candidates passed a file format test"
-		  $ECHO "*** using a regex pattern. Last file checked: $potlib"
-		fi
-	      fi
-	      ;;
-	    *)
-	      # Add a -L argument.
-	      func_append newdeplibs " $a_deplib"
-	      ;;
-	    esac
-	  done # Gone through all deplibs.
-	  ;;
-	none | unknown | *)
-	  newdeplibs=""
-	  tmp_deplibs=`$ECHO " $deplibs" | $SED 's/ -lc$//; s/ -[LR][^ ]*//g'`
-	  if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
-	    for i in $predeps $postdeps ; do
-	      # can't use Xsed below, because $i might contain '/'
-	      tmp_deplibs=`$ECHO " $tmp_deplibs" | $SED "s,$i,,"`
-	    done
-	  fi
-	  case $tmp_deplibs in
-	  *[!\	\ ]*)
-	    echo
-	    if test "X$deplibs_check_method" = "Xnone"; then
-	      echo "*** Warning: inter-library dependencies are not supported in this platform."
-	    else
-	      echo "*** Warning: inter-library dependencies are not known to be supported."
-	    fi
-	    echo "*** All declared inter-library dependencies are being dropped."
-	    droppeddeps=yes
-	    ;;
-	  esac
-	  ;;
-	esac
-	versuffix=$versuffix_save
-	major=$major_save
-	release=$release_save
-	libname=$libname_save
-	name=$name_save
-
-	case $host in
-	*-*-rhapsody* | *-*-darwin1.[012])
-	  # On Rhapsody replace the C library with the System framework
-	  newdeplibs=`$ECHO " $newdeplibs" | $SED 's/ -lc / System.ltframework /'`
-	  ;;
-	esac
-
-	if test "$droppeddeps" = yes; then
-	  if test "$module" = yes; then
-	    echo
-	    echo "*** Warning: libtool could not satisfy all declared inter-library"
-	    $ECHO "*** dependencies of module $libname.  Therefore, libtool will create"
-	    echo "*** a static module, that should work as long as the dlopening"
-	    echo "*** application is linked with the -dlopen flag."
-	    if test -z "$global_symbol_pipe"; then
-	      echo
-	      echo "*** However, this would only work if libtool was able to extract symbol"
-	      echo "*** lists from a program, using \`nm' or equivalent, but libtool could"
-	      echo "*** not find such a program.  So, this module is probably useless."
-	      echo "*** \`nm' from GNU binutils and a full rebuild may help."
-	    fi
-	    if test "$build_old_libs" = no; then
-	      oldlibs="$output_objdir/$libname.$libext"
-	      build_libtool_libs=module
-	      build_old_libs=yes
-	    else
-	      build_libtool_libs=no
-	    fi
-	  else
-	    echo "*** The inter-library dependencies that have been dropped here will be"
-	    echo "*** automatically added whenever a program is linked with this library"
-	    echo "*** or is declared to -dlopen it."
-
-	    if test "$allow_undefined" = no; then
-	      echo
-	      echo "*** Since this library must not contain undefined symbols,"
-	      echo "*** because either the platform does not support them or"
-	      echo "*** it was explicitly requested with -no-undefined,"
-	      echo "*** libtool will only create a static version of it."
-	      if test "$build_old_libs" = no; then
-		oldlibs="$output_objdir/$libname.$libext"
-		build_libtool_libs=module
-		build_old_libs=yes
-	      else
-		build_libtool_libs=no
-	      fi
-	    fi
-	  fi
-	fi
-	# Done checking deplibs!
-	deplibs=$newdeplibs
-      fi
-      # Time to change all our "foo.ltframework" stuff back to "-framework foo"
-      case $host in
-	*-*-darwin*)
-	  newdeplibs=`$ECHO " $newdeplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'`
-	  new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'`
-	  deplibs=`$ECHO " $deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'`
-	  ;;
-      esac
-
-      # move library search paths that coincide with paths to not yet
-      # installed libraries to the beginning of the library search list
-      new_libs=
-      for path in $notinst_path; do
-	case " $new_libs " in
-	*" -L$path/$objdir "*) ;;
-	*)
-	  case " $deplibs " in
-	  *" -L$path/$objdir "*)
-	    func_append new_libs " -L$path/$objdir" ;;
-	  esac
-	  ;;
-	esac
-      done
-      for deplib in $deplibs; do
-	case $deplib in
-	-L*)
-	  case " $new_libs " in
-	  *" $deplib "*) ;;
-	  *) func_append new_libs " $deplib" ;;
-	  esac
-	  ;;
-	*) func_append new_libs " $deplib" ;;
-	esac
-      done
-      deplibs="$new_libs"
-
-      # All the library-specific variables (install_libdir is set above).
-      library_names=
-      old_library=
-      dlname=
-
-      # Test again, we may have decided not to build it any more
-      if test "$build_libtool_libs" = yes; then
-	# Remove ${wl} instances when linking with ld.
-	# FIXME: should test the right _cmds variable.
-	case $archive_cmds in
-	  *\$LD\ *) wl= ;;
-        esac
-	if test "$hardcode_into_libs" = yes; then
-	  # Hardcode the library paths
-	  hardcode_libdirs=
-	  dep_rpath=
-	  rpath="$finalize_rpath"
-	  test "$opt_mode" != relink && rpath="$compile_rpath$rpath"
-	  for libdir in $rpath; do
-	    if test -n "$hardcode_libdir_flag_spec"; then
-	      if test -n "$hardcode_libdir_separator"; then
-		func_replace_sysroot "$libdir"
-		libdir=$func_replace_sysroot_result
-		if test -z "$hardcode_libdirs"; then
-		  hardcode_libdirs="$libdir"
-		else
-		  # Just accumulate the unique libdirs.
-		  case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
-		  *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
-		    ;;
-		  *)
-		    func_append hardcode_libdirs "$hardcode_libdir_separator$libdir"
-		    ;;
-		  esac
-		fi
-	      else
-		eval flag=\"$hardcode_libdir_flag_spec\"
-		func_append dep_rpath " $flag"
-	      fi
-	    elif test -n "$runpath_var"; then
-	      case "$perm_rpath " in
-	      *" $libdir "*) ;;
-	      *) func_append perm_rpath " $libdir" ;;
-	      esac
-	    fi
-	  done
-	  # Substitute the hardcoded libdirs into the rpath.
-	  if test -n "$hardcode_libdir_separator" &&
-	     test -n "$hardcode_libdirs"; then
-	    libdir="$hardcode_libdirs"
-	    eval "dep_rpath=\"$hardcode_libdir_flag_spec\""
-	  fi
-	  if test -n "$runpath_var" && test -n "$perm_rpath"; then
-	    # We should set the runpath_var.
-	    rpath=
-	    for dir in $perm_rpath; do
-	      func_append rpath "$dir:"
-	    done
-	    eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var"
-	  fi
-	  test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs"
-	fi
-
-	shlibpath="$finalize_shlibpath"
-	test "$opt_mode" != relink && shlibpath="$compile_shlibpath$shlibpath"
-	if test -n "$shlibpath"; then
-	  eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var"
-	fi
-
-	# Get the real and link names of the library.
-	eval shared_ext=\"$shrext_cmds\"
-	eval library_names=\"$library_names_spec\"
-	set dummy $library_names
-	shift
-	realname="$1"
-	shift
-
-	if test -n "$soname_spec"; then
-	  eval soname=\"$soname_spec\"
-	else
-	  soname="$realname"
-	fi
-	if test -z "$dlname"; then
-	  dlname=$soname
-	fi
-
-	lib="$output_objdir/$realname"
-	linknames=
-	for link
-	do
-	  func_append linknames " $link"
-	done
-
-	# Use standard objects if they are pic
-	test -z "$pic_flag" && libobjs=`$ECHO "$libobjs" | $SP2NL | $SED "$lo2o" | $NL2SP`
-	test "X$libobjs" = "X " && libobjs=
-
-	delfiles=
-	if test -n "$export_symbols" && test -n "$include_expsyms"; then
-	  $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp"
-	  export_symbols="$output_objdir/$libname.uexp"
-	  func_append delfiles " $export_symbols"
-	fi
-
-	orig_export_symbols=
-	case $host_os in
-	cygwin* | mingw* | cegcc*)
-	  if test -n "$export_symbols" && test -z "$export_symbols_regex"; then
-	    # exporting using user supplied symfile
-	    if test "x`$SED 1q $export_symbols`" != xEXPORTS; then
-	      # and it's NOT already a .def file. Must figure out
-	      # which of the given symbols are data symbols and tag
-	      # them as such. So, trigger use of export_symbols_cmds.
-	      # export_symbols gets reassigned inside the "prepare
-	      # the list of exported symbols" if statement, so the
-	      # include_expsyms logic still works.
-	      orig_export_symbols="$export_symbols"
-	      export_symbols=
-	      always_export_symbols=yes
-	    fi
-	  fi
-	  ;;
-	esac
-
-	# Prepare the list of exported symbols
-	if test -z "$export_symbols"; then
-	  if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then
-	    func_verbose "generating symbol list for \`$libname.la'"
-	    export_symbols="$output_objdir/$libname.exp"
-	    $opt_dry_run || $RM $export_symbols
-	    cmds=$export_symbols_cmds
-	    save_ifs="$IFS"; IFS='~'
-	    for cmd1 in $cmds; do
-	      IFS="$save_ifs"
-	      # Take the normal branch if the nm_file_list_spec branch
-	      # doesn't work or if tool conversion is not needed.
-	      case $nm_file_list_spec~$to_tool_file_cmd in
-		*~func_convert_file_noop | *~func_convert_file_msys_to_w32 | ~*)
-		  try_normal_branch=yes
-		  eval cmd=\"$cmd1\"
-		  func_len " $cmd"
-		  len=$func_len_result
-		  ;;
-		*)
-		  try_normal_branch=no
-		  ;;
-	      esac
-	      if test "$try_normal_branch" = yes \
-		 && { test "$len" -lt "$max_cmd_len" \
-		      || test "$max_cmd_len" -le -1; }
-	      then
-		func_show_eval "$cmd" 'exit $?'
-		skipped_export=false
-	      elif test -n "$nm_file_list_spec"; then
-		func_basename "$output"
-		output_la=$func_basename_result
-		save_libobjs=$libobjs
-		save_output=$output
-		output=${output_objdir}/${output_la}.nm
-		func_to_tool_file "$output"
-		libobjs=$nm_file_list_spec$func_to_tool_file_result
-		func_append delfiles " $output"
-		func_verbose "creating $NM input file list: $output"
-		for obj in $save_libobjs; do
-		  func_to_tool_file "$obj"
-		  $ECHO "$func_to_tool_file_result"
-		done > "$output"
-		eval cmd=\"$cmd1\"
-		func_show_eval "$cmd" 'exit $?'
-		output=$save_output
-		libobjs=$save_libobjs
-		skipped_export=false
-	      else
-		# The command line is too long to execute in one step.
-		func_verbose "using reloadable object file for export list..."
-		skipped_export=:
-		# Break out early, otherwise skipped_export may be
-		# set to false by a later but shorter cmd.
-		break
-	      fi
-	    done
-	    IFS="$save_ifs"
-	    if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then
-	      func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
-	      func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
-	    fi
-	  fi
-	fi
-
-	if test -n "$export_symbols" && test -n "$include_expsyms"; then
-	  tmp_export_symbols="$export_symbols"
-	  test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
-	  $opt_dry_run || eval '$ECHO "$include_expsyms" | $SP2NL >> "$tmp_export_symbols"'
-	fi
-
-	if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then
-	  # The given exports_symbols file has to be filtered, so filter it.
-	  func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
-	  # FIXME: $output_objdir/$libname.filter potentially contains lots of
-	  # 's' commands which not all seds can handle. GNU sed should be fine
-	  # though. Also, the filter scales superlinearly with the number of
-	  # global variables. join(1) would be nice here, but unfortunately
-	  # isn't a blessed tool.
-	  $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
-	  func_append delfiles " $export_symbols $output_objdir/$libname.filter"
-	  export_symbols=$output_objdir/$libname.def
-	  $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
-	fi
-
-	tmp_deplibs=
-	for test_deplib in $deplibs; do
-	  case " $convenience " in
-	  *" $test_deplib "*) ;;
-	  *)
-	    func_append tmp_deplibs " $test_deplib"
-	    ;;
-	  esac
-	done
-	deplibs="$tmp_deplibs"
-
-	if test -n "$convenience"; then
-	  if test -n "$whole_archive_flag_spec" &&
-	    test "$compiler_needs_object" = yes &&
-	    test -z "$libobjs"; then
-	    # extract the archives, so we have objects to list.
-	    # TODO: could optimize this to just extract one archive.
-	    whole_archive_flag_spec=
-	  fi
-	  if test -n "$whole_archive_flag_spec"; then
-	    save_libobjs=$libobjs
-	    eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
-	    test "X$libobjs" = "X " && libobjs=
-	  else
-	    gentop="$output_objdir/${outputname}x"
-	    func_append generated " $gentop"
-
-	    func_extract_archives $gentop $convenience
-	    func_append libobjs " $func_extract_archives_result"
-	    test "X$libobjs" = "X " && libobjs=
-	  fi
-	fi
-
-	if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then
-	  eval flag=\"$thread_safe_flag_spec\"
-	  func_append linker_flags " $flag"
-	fi
-
-	# Make a backup of the uninstalled library when relinking
-	if test "$opt_mode" = relink; then
-	  $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $?
-	fi
-
-	# Do each of the archive commands.
-	if test "$module" = yes && test -n "$module_cmds" ; then
-	  if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
-	    eval test_cmds=\"$module_expsym_cmds\"
-	    cmds=$module_expsym_cmds
-	  else
-	    eval test_cmds=\"$module_cmds\"
-	    cmds=$module_cmds
-	  fi
-	else
-	  if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
-	    eval test_cmds=\"$archive_expsym_cmds\"
-	    cmds=$archive_expsym_cmds
-	  else
-	    eval test_cmds=\"$archive_cmds\"
-	    cmds=$archive_cmds
-	  fi
-	fi
-
-	if test "X$skipped_export" != "X:" &&
-	   func_len " $test_cmds" &&
-	   len=$func_len_result &&
-	   test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
-	  :
-	else
-	  # The command line is too long to link in one step, link piecewise
-	  # or, if using GNU ld and skipped_export is not :, use a linker
-	  # script.
-
-	  # Save the value of $output and $libobjs because we want to
-	  # use them later.  If we have whole_archive_flag_spec, we
-	  # want to use save_libobjs as it was before
-	  # whole_archive_flag_spec was expanded, because we can't
-	  # assume the linker understands whole_archive_flag_spec.
-	  # This may have to be revisited, in case too many
-	  # convenience libraries get linked in and end up exceeding
-	  # the spec.
-	  if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then
-	    save_libobjs=$libobjs
-	  fi
-	  save_output=$output
-	  func_basename "$output"
-	  output_la=$func_basename_result
-
-	  # Clear the reloadable object creation command queue and
-	  # initialize k to one.
-	  test_cmds=
-	  concat_cmds=
-	  objlist=
-	  last_robj=
-	  k=1
-
-	  if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then
-	    output=${output_objdir}/${output_la}.lnkscript
-	    func_verbose "creating GNU ld script: $output"
-	    echo 'INPUT (' > $output
-	    for obj in $save_libobjs
-	    do
-	      func_to_tool_file "$obj"
-	      $ECHO "$func_to_tool_file_result" >> $output
-	    done
-	    echo ')' >> $output
-	    func_append delfiles " $output"
-	    func_to_tool_file "$output"
-	    output=$func_to_tool_file_result
-	  elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then
-	    output=${output_objdir}/${output_la}.lnk
-	    func_verbose "creating linker input file list: $output"
-	    : > $output
-	    set x $save_libobjs
-	    shift
-	    firstobj=
-	    if test "$compiler_needs_object" = yes; then
-	      firstobj="$1 "
-	      shift
-	    fi
-	    for obj
-	    do
-	      func_to_tool_file "$obj"
-	      $ECHO "$func_to_tool_file_result" >> $output
-	    done
-	    func_append delfiles " $output"
-	    func_to_tool_file "$output"
-	    output=$firstobj\"$file_list_spec$func_to_tool_file_result\"
-	  else
-	    if test -n "$save_libobjs"; then
-	      func_verbose "creating reloadable object files..."
-	      output=$output_objdir/$output_la-${k}.$objext
-	      eval test_cmds=\"$reload_cmds\"
-	      func_len " $test_cmds"
-	      len0=$func_len_result
-	      len=$len0
-
-	      # Loop over the list of objects to be linked.
-	      for obj in $save_libobjs
-	      do
-		func_len " $obj"
-		func_arith $len + $func_len_result
-		len=$func_arith_result
-		if test "X$objlist" = X ||
-		   test "$len" -lt "$max_cmd_len"; then
-		  func_append objlist " $obj"
-		else
-		  # The command $test_cmds is almost too long, add a
-		  # command to the queue.
-		  if test "$k" -eq 1 ; then
-		    # The first file doesn't have a previous command to add.
-		    reload_objs=$objlist
-		    eval concat_cmds=\"$reload_cmds\"
-		  else
-		    # All subsequent reloadable object files will link in
-		    # the last one created.
-		    reload_objs="$objlist $last_robj"
-		    eval concat_cmds=\"\$concat_cmds~$reload_cmds~\$RM $last_robj\"
-		  fi
-		  last_robj=$output_objdir/$output_la-${k}.$objext
-		  func_arith $k + 1
-		  k=$func_arith_result
-		  output=$output_objdir/$output_la-${k}.$objext
-		  objlist=" $obj"
-		  func_len " $last_robj"
-		  func_arith $len0 + $func_len_result
-		  len=$func_arith_result
-		fi
-	      done
-	      # Handle the remaining objects by creating one last
-	      # reloadable object file.  All subsequent reloadable object
-	      # files will link in the last one created.
-	      test -z "$concat_cmds" || concat_cmds=$concat_cmds~
-	      reload_objs="$objlist $last_robj"
-	      eval concat_cmds=\"\${concat_cmds}$reload_cmds\"
-	      if test -n "$last_robj"; then
-	        eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\"
-	      fi
-	      func_append delfiles " $output"
-
-	    else
-	      output=
-	    fi
-
-	    if ${skipped_export-false}; then
-	      func_verbose "generating symbol list for \`$libname.la'"
-	      export_symbols="$output_objdir/$libname.exp"
-	      $opt_dry_run || $RM $export_symbols
-	      libobjs=$output
-	      # Append the command to create the export file.
-	      test -z "$concat_cmds" || concat_cmds=$concat_cmds~
-	      eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\"
-	      if test -n "$last_robj"; then
-		eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\"
-	      fi
-	    fi
-
-	    test -n "$save_libobjs" &&
-	      func_verbose "creating a temporary reloadable object file: $output"
-
-	    # Loop through the commands generated above and execute them.
-	    save_ifs="$IFS"; IFS='~'
-	    for cmd in $concat_cmds; do
-	      IFS="$save_ifs"
-	      $opt_silent || {
-		  func_quote_for_expand "$cmd"
-		  eval "func_echo $func_quote_for_expand_result"
-	      }
-	      $opt_dry_run || eval "$cmd" || {
-		lt_exit=$?
-
-		# Restore the uninstalled library and exit
-		if test "$opt_mode" = relink; then
-		  ( cd "$output_objdir" && \
-		    $RM "${realname}T" && \
-		    $MV "${realname}U" "$realname" )
-		fi
-
-		exit $lt_exit
-	      }
-	    done
-	    IFS="$save_ifs"
-
-	    if test -n "$export_symbols_regex" && ${skipped_export-false}; then
-	      func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
-	      func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
-	    fi
-	  fi
-
-          if ${skipped_export-false}; then
-	    if test -n "$export_symbols" && test -n "$include_expsyms"; then
-	      tmp_export_symbols="$export_symbols"
-	      test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
-	      $opt_dry_run || eval '$ECHO "$include_expsyms" | $SP2NL >> "$tmp_export_symbols"'
-	    fi
-
-	    if test -n "$orig_export_symbols"; then
-	      # The given exports_symbols file has to be filtered, so filter it.
-	      func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
-	      # FIXME: $output_objdir/$libname.filter potentially contains lots of
-	      # 's' commands which not all seds can handle. GNU sed should be fine
-	      # though. Also, the filter scales superlinearly with the number of
-	      # global variables. join(1) would be nice here, but unfortunately
-	      # isn't a blessed tool.
-	      $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
-	      func_append delfiles " $export_symbols $output_objdir/$libname.filter"
-	      export_symbols=$output_objdir/$libname.def
-	      $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
-	    fi
-	  fi
-
-	  libobjs=$output
-	  # Restore the value of output.
-	  output=$save_output
-
-	  if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then
-	    eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
-	    test "X$libobjs" = "X " && libobjs=
-	  fi
-	  # Expand the library linking commands again to reset the
-	  # value of $libobjs for piecewise linking.
-
-	  # Do each of the archive commands.
-	  if test "$module" = yes && test -n "$module_cmds" ; then
-	    if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
-	      cmds=$module_expsym_cmds
-	    else
-	      cmds=$module_cmds
-	    fi
-	  else
-	    if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
-	      cmds=$archive_expsym_cmds
-	    else
-	      cmds=$archive_cmds
-	    fi
-	  fi
-	fi
-
-	if test -n "$delfiles"; then
-	  # Append the command to remove temporary files to $cmds.
-	  eval cmds=\"\$cmds~\$RM $delfiles\"
-	fi
-
-	# Add any objects from preloaded convenience libraries
-	if test -n "$dlprefiles"; then
-	  gentop="$output_objdir/${outputname}x"
-	  func_append generated " $gentop"
-
-	  func_extract_archives $gentop $dlprefiles
-	  func_append libobjs " $func_extract_archives_result"
-	  test "X$libobjs" = "X " && libobjs=
-	fi
-
-	save_ifs="$IFS"; IFS='~'
-	for cmd in $cmds; do
-	  IFS="$save_ifs"
-	  eval cmd=\"$cmd\"
-	  $opt_silent || {
-	    func_quote_for_expand "$cmd"
-	    eval "func_echo $func_quote_for_expand_result"
-	  }
-	  $opt_dry_run || eval "$cmd" || {
-	    lt_exit=$?
-
-	    # Restore the uninstalled library and exit
-	    if test "$opt_mode" = relink; then
-	      ( cd "$output_objdir" && \
-	        $RM "${realname}T" && \
-		$MV "${realname}U" "$realname" )
-	    fi
-
-	    exit $lt_exit
-	  }
-	done
-	IFS="$save_ifs"
-
-	# Restore the uninstalled library and exit
-	if test "$opt_mode" = relink; then
-	  $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $?
-
-	  if test -n "$convenience"; then
-	    if test -z "$whole_archive_flag_spec"; then
-	      func_show_eval '${RM}r "$gentop"'
-	    fi
-	  fi
-
-	  exit $EXIT_SUCCESS
-	fi
-
-	# Create links to the real library.
-	for linkname in $linknames; do
-	  if test "$realname" != "$linkname"; then
-	    func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?'
-	  fi
-	done
-
-	# If -module or -export-dynamic was specified, set the dlname.
-	if test "$module" = yes || test "$export_dynamic" = yes; then
-	  # On all known operating systems, these are identical.
-	  dlname="$soname"
-	fi
-      fi
-      ;;
-
-    obj)
-      if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
-	func_warning "\`-dlopen' is ignored for objects"
-      fi
-
-      case " $deplibs" in
-      *\ -l* | *\ -L*)
-	func_warning "\`-l' and \`-L' are ignored for objects" ;;
-      esac
-
-      test -n "$rpath" && \
-	func_warning "\`-rpath' is ignored for objects"
-
-      test -n "$xrpath" && \
-	func_warning "\`-R' is ignored for objects"
-
-      test -n "$vinfo" && \
-	func_warning "\`-version-info' is ignored for objects"
-
-      test -n "$release" && \
-	func_warning "\`-release' is ignored for objects"
-
-      case $output in
-      *.lo)
-	test -n "$objs$old_deplibs" && \
-	  func_fatal_error "cannot build library object \`$output' from non-libtool objects"
-
-	libobj=$output
-	func_lo2o "$libobj"
-	obj=$func_lo2o_result
-	;;
-      *)
-	libobj=
-	obj="$output"
-	;;
-      esac
-
-      # Delete the old objects.
-      $opt_dry_run || $RM $obj $libobj
-
-      # Objects from convenience libraries.  This assumes
-      # single-version convenience libraries.  Whenever we create
-      # different ones for PIC/non-PIC, this we'll have to duplicate
-      # the extraction.
-      reload_conv_objs=
-      gentop=
-      # reload_cmds runs $LD directly, so let us get rid of
-      # -Wl from whole_archive_flag_spec and hope we can get by with
-      # turning comma into space..
-      wl=
-
-      if test -n "$convenience"; then
-	if test -n "$whole_archive_flag_spec"; then
-	  eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\"
-	  reload_conv_objs=$reload_objs\ `$ECHO "$tmp_whole_archive_flags" | $SED 's|,| |g'`
-	else
-	  gentop="$output_objdir/${obj}x"
-	  func_append generated " $gentop"
-
-	  func_extract_archives $gentop $convenience
-	  reload_conv_objs="$reload_objs $func_extract_archives_result"
-	fi
-      fi
-
-      # If we're not building shared, we need to use non_pic_objs
-      test "$build_libtool_libs" != yes && libobjs="$non_pic_objects"
-
-      # Create the old-style object.
-      reload_objs="$objs$old_deplibs "`$ECHO "$libobjs" | $SP2NL | $SED "/\.${libext}$/d; /\.lib$/d; $lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test
-
-      output="$obj"
-      func_execute_cmds "$reload_cmds" 'exit $?'
-
-      # Exit if we aren't doing a library object file.
-      if test -z "$libobj"; then
-	if test -n "$gentop"; then
-	  func_show_eval '${RM}r "$gentop"'
-	fi
-
-	exit $EXIT_SUCCESS
-      fi
-
-      if test "$build_libtool_libs" != yes; then
-	if test -n "$gentop"; then
-	  func_show_eval '${RM}r "$gentop"'
-	fi
-
-	# Create an invalid libtool object if no PIC, so that we don't
-	# accidentally link it into a program.
-	# $show "echo timestamp > $libobj"
-	# $opt_dry_run || eval "echo timestamp > $libobj" || exit $?
-	exit $EXIT_SUCCESS
-      fi
-
-      if test -n "$pic_flag" || test "$pic_mode" != default; then
-	# Only do commands if we really have different PIC objects.
-	reload_objs="$libobjs $reload_conv_objs"
-	output="$libobj"
-	func_execute_cmds "$reload_cmds" 'exit $?'
-      fi
-
-      if test -n "$gentop"; then
-	func_show_eval '${RM}r "$gentop"'
-      fi
-
-      exit $EXIT_SUCCESS
-      ;;
-
-    prog)
-      case $host in
-	*cygwin*) func_stripname '' '.exe' "$output"
-	          output=$func_stripname_result.exe;;
-      esac
-      test -n "$vinfo" && \
-	func_warning "\`-version-info' is ignored for programs"
-
-      test -n "$release" && \
-	func_warning "\`-release' is ignored for programs"
-
-      test "$preload" = yes \
-        && test "$dlopen_support" = unknown \
-	&& test "$dlopen_self" = unknown \
-	&& test "$dlopen_self_static" = unknown && \
-	  func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support."
-
-      case $host in
-      *-*-rhapsody* | *-*-darwin1.[012])
-	# On Rhapsody replace the C library is the System framework
-	compile_deplibs=`$ECHO " $compile_deplibs" | $SED 's/ -lc / System.ltframework /'`
-	finalize_deplibs=`$ECHO " $finalize_deplibs" | $SED 's/ -lc / System.ltframework /'`
-	;;
-      esac
-
-      case $host in
-      *-*-darwin*)
-	# Don't allow lazy linking, it breaks C++ global constructors
-	# But is supposedly fixed on 10.4 or later (yay!).
-	if test "$tagname" = CXX ; then
-	  case ${MACOSX_DEPLOYMENT_TARGET-10.0} in
-	    10.[0123])
-	      func_append compile_command " ${wl}-bind_at_load"
-	      func_append finalize_command " ${wl}-bind_at_load"
-	    ;;
-	  esac
-	fi
-	# Time to change all our "foo.ltframework" stuff back to "-framework foo"
-	compile_deplibs=`$ECHO " $compile_deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'`
-	finalize_deplibs=`$ECHO " $finalize_deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'`
-	;;
-      esac
-
-
-      # move library search paths that coincide with paths to not yet
-      # installed libraries to the beginning of the library search list
-      new_libs=
-      for path in $notinst_path; do
-	case " $new_libs " in
-	*" -L$path/$objdir "*) ;;
-	*)
-	  case " $compile_deplibs " in
-	  *" -L$path/$objdir "*)
-	    func_append new_libs " -L$path/$objdir" ;;
-	  esac
-	  ;;
-	esac
-      done
-      for deplib in $compile_deplibs; do
-	case $deplib in
-	-L*)
-	  case " $new_libs " in
-	  *" $deplib "*) ;;
-	  *) func_append new_libs " $deplib" ;;
-	  esac
-	  ;;
-	*) func_append new_libs " $deplib" ;;
-	esac
-      done
-      compile_deplibs="$new_libs"
-
-
-      func_append compile_command " $compile_deplibs"
-      func_append finalize_command " $finalize_deplibs"
-
-      if test -n "$rpath$xrpath"; then
-	# If the user specified any rpath flags, then add them.
-	for libdir in $rpath $xrpath; do
-	  # This is the magic to use -rpath.
-	  case "$finalize_rpath " in
-	  *" $libdir "*) ;;
-	  *) func_append finalize_rpath " $libdir" ;;
-	  esac
-	done
-      fi
-
-      # Now hardcode the library paths
-      rpath=
-      hardcode_libdirs=
-      for libdir in $compile_rpath $finalize_rpath; do
-	if test -n "$hardcode_libdir_flag_spec"; then
-	  if test -n "$hardcode_libdir_separator"; then
-	    if test -z "$hardcode_libdirs"; then
-	      hardcode_libdirs="$libdir"
-	    else
-	      # Just accumulate the unique libdirs.
-	      case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
-	      *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
-		;;
-	      *)
-		func_append hardcode_libdirs "$hardcode_libdir_separator$libdir"
-		;;
-	      esac
-	    fi
-	  else
-	    eval flag=\"$hardcode_libdir_flag_spec\"
-	    func_append rpath " $flag"
-	  fi
-	elif test -n "$runpath_var"; then
-	  case "$perm_rpath " in
-	  *" $libdir "*) ;;
-	  *) func_append perm_rpath " $libdir" ;;
-	  esac
-	fi
-	case $host in
-	*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
-	  testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'`
-	  case :$dllsearchpath: in
-	  *":$libdir:"*) ;;
-	  ::) dllsearchpath=$libdir;;
-	  *) func_append dllsearchpath ":$libdir";;
-	  esac
-	  case :$dllsearchpath: in
-	  *":$testbindir:"*) ;;
-	  ::) dllsearchpath=$testbindir;;
-	  *) func_append dllsearchpath ":$testbindir";;
-	  esac
-	  ;;
-	esac
-      done
-      # Substitute the hardcoded libdirs into the rpath.
-      if test -n "$hardcode_libdir_separator" &&
-	 test -n "$hardcode_libdirs"; then
-	libdir="$hardcode_libdirs"
-	eval rpath=\" $hardcode_libdir_flag_spec\"
-      fi
-      compile_rpath="$rpath"
-
-      rpath=
-      hardcode_libdirs=
-      for libdir in $finalize_rpath; do
-	if test -n "$hardcode_libdir_flag_spec"; then
-	  if test -n "$hardcode_libdir_separator"; then
-	    if test -z "$hardcode_libdirs"; then
-	      hardcode_libdirs="$libdir"
-	    else
-	      # Just accumulate the unique libdirs.
-	      case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
-	      *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
-		;;
-	      *)
-		func_append hardcode_libdirs "$hardcode_libdir_separator$libdir"
-		;;
-	      esac
-	    fi
-	  else
-	    eval flag=\"$hardcode_libdir_flag_spec\"
-	    func_append rpath " $flag"
-	  fi
-	elif test -n "$runpath_var"; then
-	  case "$finalize_perm_rpath " in
-	  *" $libdir "*) ;;
-	  *) func_append finalize_perm_rpath " $libdir" ;;
-	  esac
-	fi
-      done
-      # Substitute the hardcoded libdirs into the rpath.
-      if test -n "$hardcode_libdir_separator" &&
-	 test -n "$hardcode_libdirs"; then
-	libdir="$hardcode_libdirs"
-	eval rpath=\" $hardcode_libdir_flag_spec\"
-      fi
-      finalize_rpath="$rpath"
-
-      if test -n "$libobjs" && test "$build_old_libs" = yes; then
-	# Transform all the library objects into standard objects.
-	compile_command=`$ECHO "$compile_command" | $SP2NL | $SED "$lo2o" | $NL2SP`
-	finalize_command=`$ECHO "$finalize_command" | $SP2NL | $SED "$lo2o" | $NL2SP`
-      fi
-
-      func_generate_dlsyms "$outputname" "@PROGRAM@" "no"
-
-      # template prelinking step
-      if test -n "$prelink_cmds"; then
-	func_execute_cmds "$prelink_cmds" 'exit $?'
-      fi
-
-      wrappers_required=yes
-      case $host in
-      *cegcc* | *mingw32ce*)
-        # Disable wrappers for cegcc and mingw32ce hosts, we are cross compiling anyway.
-        wrappers_required=no
-        ;;
-      *cygwin* | *mingw* )
-        if test "$build_libtool_libs" != yes; then
-          wrappers_required=no
-        fi
-        ;;
-      *)
-        if test "$need_relink" = no || test "$build_libtool_libs" != yes; then
-          wrappers_required=no
-        fi
-        ;;
-      esac
-      if test "$wrappers_required" = no; then
-	# Replace the output file specification.
-	compile_command=`$ECHO "$compile_command" | $SED 's%@OUTPUT@%'"$output"'%g'`
-	link_command="$compile_command$compile_rpath"
-
-	# We have no uninstalled library dependencies, so finalize right now.
-	exit_status=0
-	func_show_eval "$link_command" 'exit_status=$?'
-
-	if test -n "$postlink_cmds"; then
-	  func_to_tool_file "$output"
-	  postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'`
-	  func_execute_cmds "$postlink_cmds" 'exit $?'
-	fi
-
-	# Delete the generated files.
-	if test -f "$output_objdir/${outputname}S.${objext}"; then
-	  func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"'
-	fi
-
-	exit $exit_status
-      fi
-
-      if test -n "$compile_shlibpath$finalize_shlibpath"; then
-	compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command"
-      fi
-      if test -n "$finalize_shlibpath"; then
-	finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command"
-      fi
-
-      compile_var=
-      finalize_var=
-      if test -n "$runpath_var"; then
-	if test -n "$perm_rpath"; then
-	  # We should set the runpath_var.
-	  rpath=
-	  for dir in $perm_rpath; do
-	    func_append rpath "$dir:"
-	  done
-	  compile_var="$runpath_var=\"$rpath\$$runpath_var\" "
-	fi
-	if test -n "$finalize_perm_rpath"; then
-	  # We should set the runpath_var.
-	  rpath=
-	  for dir in $finalize_perm_rpath; do
-	    func_append rpath "$dir:"
-	  done
-	  finalize_var="$runpath_var=\"$rpath\$$runpath_var\" "
-	fi
-      fi
-
-      if test "$no_install" = yes; then
-	# We don't need to create a wrapper script.
-	link_command="$compile_var$compile_command$compile_rpath"
-	# Replace the output file specification.
-	link_command=`$ECHO "$link_command" | $SED 's%@OUTPUT@%'"$output"'%g'`
-	# Delete the old output file.
-	$opt_dry_run || $RM $output
-	# Link the executable and exit
-	func_show_eval "$link_command" 'exit $?'
-
-	if test -n "$postlink_cmds"; then
-	  func_to_tool_file "$output"
-	  postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'`
-	  func_execute_cmds "$postlink_cmds" 'exit $?'
-	fi
-
-	exit $EXIT_SUCCESS
-      fi
-
-      if test "$hardcode_action" = relink; then
-	# Fast installation is not supported
-	link_command="$compile_var$compile_command$compile_rpath"
-	relink_command="$finalize_var$finalize_command$finalize_rpath"
-
-	func_warning "this platform does not like uninstalled shared libraries"
-	func_warning "\`$output' will be relinked during installation"
-      else
-	if test "$fast_install" != no; then
-	  link_command="$finalize_var$compile_command$finalize_rpath"
-	  if test "$fast_install" = yes; then
-	    relink_command=`$ECHO "$compile_var$compile_command$compile_rpath" | $SED 's%@OUTPUT@%\$progdir/\$file%g'`
-	  else
-	    # fast_install is set to needless
-	    relink_command=
-	  fi
-	else
-	  link_command="$compile_var$compile_command$compile_rpath"
-	  relink_command="$finalize_var$finalize_command$finalize_rpath"
-	fi
-      fi
-
-      # Replace the output file specification.
-      link_command=`$ECHO "$link_command" | $SED 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'`
-
-      # Delete the old output files.
-      $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname
-
-      func_show_eval "$link_command" 'exit $?'
-
-      if test -n "$postlink_cmds"; then
-	func_to_tool_file "$output_objdir/$outputname"
-	postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'`
-	func_execute_cmds "$postlink_cmds" 'exit $?'
-      fi
-
-      # Now create the wrapper script.
-      func_verbose "creating $output"
-
-      # Quote the relink command for shipping.
-      if test -n "$relink_command"; then
-	# Preserve any variables that may affect compiler behavior
-	for var in $variables_saved_for_relink; do
-	  if eval test -z \"\${$var+set}\"; then
-	    relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
-	  elif eval var_value=\$$var; test -z "$var_value"; then
-	    relink_command="$var=; export $var; $relink_command"
-	  else
-	    func_quote_for_eval "$var_value"
-	    relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
-	  fi
-	done
-	relink_command="(cd `pwd`; $relink_command)"
-	relink_command=`$ECHO "$relink_command" | $SED "$sed_quote_subst"`
-      fi
-
-      # Only actually do things if not in dry run mode.
-      $opt_dry_run || {
-	# win32 will think the script is a binary if it has
-	# a .exe suffix, so we strip it off here.
-	case $output in
-	  *.exe) func_stripname '' '.exe' "$output"
-	         output=$func_stripname_result ;;
-	esac
-	# test for cygwin because mv fails w/o .exe extensions
-	case $host in
-	  *cygwin*)
-	    exeext=.exe
-	    func_stripname '' '.exe' "$outputname"
-	    outputname=$func_stripname_result ;;
-	  *) exeext= ;;
-	esac
-	case $host in
-	  *cygwin* | *mingw* )
-	    func_dirname_and_basename "$output" "" "."
-	    output_name=$func_basename_result
-	    output_path=$func_dirname_result
-	    cwrappersource="$output_path/$objdir/lt-$output_name.c"
-	    cwrapper="$output_path/$output_name.exe"
-	    $RM $cwrappersource $cwrapper
-	    trap "$RM $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15
-
-	    func_emit_cwrapperexe_src > $cwrappersource
-
-	    # The wrapper executable is built using the $host compiler,
-	    # because it contains $host paths and files. If cross-
-	    # compiling, it, like the target executable, must be
-	    # executed on the $host or under an emulation environment.
-	    $opt_dry_run || {
-	      $LTCC $LTCFLAGS -o $cwrapper $cwrappersource
-	      $STRIP $cwrapper
-	    }
-
-	    # Now, create the wrapper script for func_source use:
-	    func_ltwrapper_scriptname $cwrapper
-	    $RM $func_ltwrapper_scriptname_result
-	    trap "$RM $func_ltwrapper_scriptname_result; exit $EXIT_FAILURE" 1 2 15
-	    $opt_dry_run || {
-	      # note: this script will not be executed, so do not chmod.
-	      if test "x$build" = "x$host" ; then
-		$cwrapper --lt-dump-script > $func_ltwrapper_scriptname_result
-	      else
-		func_emit_wrapper no > $func_ltwrapper_scriptname_result
-	      fi
-	    }
-	  ;;
-	  * )
-	    $RM $output
-	    trap "$RM $output; exit $EXIT_FAILURE" 1 2 15
-
-	    func_emit_wrapper no > $output
-	    chmod +x $output
-	  ;;
-	esac
-      }
-      exit $EXIT_SUCCESS
-      ;;
-    esac
-
-    # See if we need to build an old-fashioned archive.
-    for oldlib in $oldlibs; do
-
-      if test "$build_libtool_libs" = convenience; then
-	oldobjs="$libobjs_save $symfileobj"
-	addlibs="$convenience"
-	build_libtool_libs=no
-      else
-	if test "$build_libtool_libs" = module; then
-	  oldobjs="$libobjs_save"
-	  build_libtool_libs=no
-	else
-	  oldobjs="$old_deplibs $non_pic_objects"
-	  if test "$preload" = yes && test -f "$symfileobj"; then
-	    func_append oldobjs " $symfileobj"
-	  fi
-	fi
-	addlibs="$old_convenience"
-      fi
-
-      if test -n "$addlibs"; then
-	gentop="$output_objdir/${outputname}x"
-	func_append generated " $gentop"
-
-	func_extract_archives $gentop $addlibs
-	func_append oldobjs " $func_extract_archives_result"
-      fi
-
-      # Do each command in the archive commands.
-      if test -n "$old_archive_from_new_cmds" && test "$build_libtool_libs" = yes; then
-	cmds=$old_archive_from_new_cmds
-      else
-
-	# Add any objects from preloaded convenience libraries
-	if test -n "$dlprefiles"; then
-	  gentop="$output_objdir/${outputname}x"
-	  func_append generated " $gentop"
-
-	  func_extract_archives $gentop $dlprefiles
-	  func_append oldobjs " $func_extract_archives_result"
-	fi
-
-	# POSIX demands no paths to be encoded in archives.  We have
-	# to avoid creating archives with duplicate basenames if we
-	# might have to extract them afterwards, e.g., when creating a
-	# static archive out of a convenience library, or when linking
-	# the entirety of a libtool archive into another (currently
-	# not supported by libtool).
-	if (for obj in $oldobjs
-	    do
-	      func_basename "$obj"
-	      $ECHO "$func_basename_result"
-	    done | sort | sort -uc >/dev/null 2>&1); then
-	  :
-	else
-	  echo "copying selected object files to avoid basename conflicts..."
-	  gentop="$output_objdir/${outputname}x"
-	  func_append generated " $gentop"
-	  func_mkdir_p "$gentop"
-	  save_oldobjs=$oldobjs
-	  oldobjs=
-	  counter=1
-	  for obj in $save_oldobjs
-	  do
-	    func_basename "$obj"
-	    objbase="$func_basename_result"
-	    case " $oldobjs " in
-	    " ") oldobjs=$obj ;;
-	    *[\ /]"$objbase "*)
-	      while :; do
-		# Make sure we don't pick an alternate name that also
-		# overlaps.
-		newobj=lt$counter-$objbase
-		func_arith $counter + 1
-		counter=$func_arith_result
-		case " $oldobjs " in
-		*[\ /]"$newobj "*) ;;
-		*) if test ! -f "$gentop/$newobj"; then break; fi ;;
-		esac
-	      done
-	      func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj"
-	      func_append oldobjs " $gentop/$newobj"
-	      ;;
-	    *) func_append oldobjs " $obj" ;;
-	    esac
-	  done
-	fi
-	func_to_tool_file "$oldlib" func_convert_file_msys_to_w32
-	tool_oldlib=$func_to_tool_file_result
-	eval cmds=\"$old_archive_cmds\"
-
-	func_len " $cmds"
-	len=$func_len_result
-	if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
-	  cmds=$old_archive_cmds
-	elif test -n "$archiver_list_spec"; then
-	  func_verbose "using command file archive linking..."
-	  for obj in $oldobjs
-	  do
-	    func_to_tool_file "$obj"
-	    $ECHO "$func_to_tool_file_result"
-	  done > $output_objdir/$libname.libcmd
-	  func_to_tool_file "$output_objdir/$libname.libcmd"
-	  oldobjs=" $archiver_list_spec$func_to_tool_file_result"
-	  cmds=$old_archive_cmds
-	else
-	  # the command line is too long to link in one step, link in parts
-	  func_verbose "using piecewise archive linking..."
-	  save_RANLIB=$RANLIB
-	  RANLIB=:
-	  objlist=
-	  concat_cmds=
-	  save_oldobjs=$oldobjs
-	  oldobjs=
-	  # Is there a better way of finding the last object in the list?
-	  for obj in $save_oldobjs
-	  do
-	    last_oldobj=$obj
-	  done
-	  eval test_cmds=\"$old_archive_cmds\"
-	  func_len " $test_cmds"
-	  len0=$func_len_result
-	  len=$len0
-	  for obj in $save_oldobjs
-	  do
-	    func_len " $obj"
-	    func_arith $len + $func_len_result
-	    len=$func_arith_result
-	    func_append objlist " $obj"
-	    if test "$len" -lt "$max_cmd_len"; then
-	      :
-	    else
-	      # the above command should be used before it gets too long
-	      oldobjs=$objlist
-	      if test "$obj" = "$last_oldobj" ; then
-		RANLIB=$save_RANLIB
-	      fi
-	      test -z "$concat_cmds" || concat_cmds=$concat_cmds~
-	      eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\"
-	      objlist=
-	      len=$len0
-	    fi
-	  done
-	  RANLIB=$save_RANLIB
-	  oldobjs=$objlist
-	  if test "X$oldobjs" = "X" ; then
-	    eval cmds=\"\$concat_cmds\"
-	  else
-	    eval cmds=\"\$concat_cmds~\$old_archive_cmds\"
-	  fi
-	fi
-      fi
-      func_execute_cmds "$cmds" 'exit $?'
-    done
-
-    test -n "$generated" && \
-      func_show_eval "${RM}r$generated"
-
-    # Now create the libtool archive.
-    case $output in
-    *.la)
-      old_library=
-      test "$build_old_libs" = yes && old_library="$libname.$libext"
-      func_verbose "creating $output"
-
-      # Preserve any variables that may affect compiler behavior
-      for var in $variables_saved_for_relink; do
-	if eval test -z \"\${$var+set}\"; then
-	  relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
-	elif eval var_value=\$$var; test -z "$var_value"; then
-	  relink_command="$var=; export $var; $relink_command"
-	else
-	  func_quote_for_eval "$var_value"
-	  relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
-	fi
-      done
-      # Quote the link command for shipping.
-      relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)"
-      relink_command=`$ECHO "$relink_command" | $SED "$sed_quote_subst"`
-      if test "$hardcode_automatic" = yes ; then
-	relink_command=
-      fi
-
-      # Only create the output if not a dry run.
-      $opt_dry_run || {
-	for installed in no yes; do
-	  if test "$installed" = yes; then
-	    if test -z "$install_libdir"; then
-	      break
-	    fi
-	    output="$output_objdir/$outputname"i
-	    # Replace all uninstalled libtool libraries with the installed ones
-	    newdependency_libs=
-	    for deplib in $dependency_libs; do
-	      case $deplib in
-	      *.la)
-		func_basename "$deplib"
-		name="$func_basename_result"
-		func_resolve_sysroot "$deplib"
-		eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $func_resolve_sysroot_result`
-		test -z "$libdir" && \
-		  func_fatal_error "\`$deplib' is not a valid libtool archive"
-		func_append newdependency_libs " ${lt_sysroot:+=}$libdir/$name"
-		;;
-	      -L*)
-		func_stripname -L '' "$deplib"
-		func_replace_sysroot "$func_stripname_result"
-		func_append newdependency_libs " -L$func_replace_sysroot_result"
-		;;
-	      -R*)
-		func_stripname -R '' "$deplib"
-		func_replace_sysroot "$func_stripname_result"
-		func_append newdependency_libs " -R$func_replace_sysroot_result"
-		;;
-	      *) func_append newdependency_libs " $deplib" ;;
-	      esac
-	    done
-	    dependency_libs="$newdependency_libs"
-	    newdlfiles=
-
-	    for lib in $dlfiles; do
-	      case $lib in
-	      *.la)
-	        func_basename "$lib"
-		name="$func_basename_result"
-		eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
-		test -z "$libdir" && \
-		  func_fatal_error "\`$lib' is not a valid libtool archive"
-		func_append newdlfiles " ${lt_sysroot:+=}$libdir/$name"
-		;;
-	      *) func_append newdlfiles " $lib" ;;
-	      esac
-	    done
-	    dlfiles="$newdlfiles"
-	    newdlprefiles=
-	    for lib in $dlprefiles; do
-	      case $lib in
-	      *.la)
-		# Only pass preopened files to the pseudo-archive (for
-		# eventual linking with the app. that links it) if we
-		# didn't already link the preopened objects directly into
-		# the library:
-		func_basename "$lib"
-		name="$func_basename_result"
-		eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
-		test -z "$libdir" && \
-		  func_fatal_error "\`$lib' is not a valid libtool archive"
-		func_append newdlprefiles " ${lt_sysroot:+=}$libdir/$name"
-		;;
-	      esac
-	    done
-	    dlprefiles="$newdlprefiles"
-	  else
-	    newdlfiles=
-	    for lib in $dlfiles; do
-	      case $lib in
-		[\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
-		*) abs=`pwd`"/$lib" ;;
-	      esac
-	      func_append newdlfiles " $abs"
-	    done
-	    dlfiles="$newdlfiles"
-	    newdlprefiles=
-	    for lib in $dlprefiles; do
-	      case $lib in
-		[\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
-		*) abs=`pwd`"/$lib" ;;
-	      esac
-	      func_append newdlprefiles " $abs"
-	    done
-	    dlprefiles="$newdlprefiles"
-	  fi
-	  $RM $output
-	  # place dlname in correct position for cygwin
-	  # In fact, it would be nice if we could use this code for all target
-	  # systems that can't hard-code library paths into their executables
-	  # and that have no shared library path variable independent of PATH,
-	  # but it turns out we can't easily determine that from inspecting
-	  # libtool variables, so we have to hard-code the OSs to which it
-	  # applies here; at the moment, that means platforms that use the PE
-	  # object format with DLL files.  See the long comment at the top of
-	  # tests/bindir.at for full details.
-	  tdlname=$dlname
-	  case $host,$output,$installed,$module,$dlname in
-	    *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll)
-	      # If a -bindir argument was supplied, place the dll there.
-	      if test "x$bindir" != x ;
-	      then
-		func_relative_path "$install_libdir" "$bindir"
-		tdlname=$func_relative_path_result$dlname
-	      else
-		# Otherwise fall back on heuristic.
-		tdlname=../bin/$dlname
-	      fi
-	      ;;
-	  esac
-	  $ECHO > $output "\
-# $outputname - a libtool library file
-# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
-#
-# Please DO NOT delete this file!
-# It is necessary for linking the library.
-
-# The name that we can dlopen(3).
-dlname='$tdlname'
-
-# Names of this library.
-library_names='$library_names'
-
-# The name of the static archive.
-old_library='$old_library'
-
-# Linker flags that can not go in dependency_libs.
-inherited_linker_flags='$new_inherited_linker_flags'
-
-# Libraries that this one depends upon.
-dependency_libs='$dependency_libs'
-
-# Names of additional weak libraries provided by this library
-weak_library_names='$weak_libs'
-
-# Version information for $libname.
-current=$current
-age=$age
-revision=$revision
-
-# Is this an already installed library?
-installed=$installed
-
-# Should we warn about portability when linking against -modules?
-shouldnotlink=$module
-
-# Files to dlopen/dlpreopen
-dlopen='$dlfiles'
-dlpreopen='$dlprefiles'
-
-# Directory that this library needs to be installed in:
-libdir='$install_libdir'"
-	  if test "$installed" = no && test "$need_relink" = yes; then
-	    $ECHO >> $output "\
-relink_command=\"$relink_command\""
-	  fi
-	done
-      }
-
-      # Do a symbolic link so that the libtool archive can be found in
-      # LD_LIBRARY_PATH before the program is installed.
-      func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?'
-      ;;
-    esac
-    exit $EXIT_SUCCESS
-}
-
-{ test "$opt_mode" = link || test "$opt_mode" = relink; } &&
-    func_mode_link ${1+"$@"}
-
-
-# func_mode_uninstall arg...
-func_mode_uninstall ()
-{
-    $opt_debug
-    RM="$nonopt"
-    files=
-    rmforce=
-    exit_status=0
-
-    # This variable tells wrapper scripts just to set variables rather
-    # than running their programs.
-    libtool_install_magic="$magic"
-
-    for arg
-    do
-      case $arg in
-      -f) func_append RM " $arg"; rmforce=yes ;;
-      -*) func_append RM " $arg" ;;
-      *) func_append files " $arg" ;;
-      esac
-    done
-
-    test -z "$RM" && \
-      func_fatal_help "you must specify an RM program"
-
-    rmdirs=
-
-    for file in $files; do
-      func_dirname "$file" "" "."
-      dir="$func_dirname_result"
-      if test "X$dir" = X.; then
-	odir="$objdir"
-      else
-	odir="$dir/$objdir"
-      fi
-      func_basename "$file"
-      name="$func_basename_result"
-      test "$opt_mode" = uninstall && odir="$dir"
-
-      # Remember odir for removal later, being careful to avoid duplicates
-      if test "$opt_mode" = clean; then
-	case " $rmdirs " in
-	  *" $odir "*) ;;
-	  *) func_append rmdirs " $odir" ;;
-	esac
-      fi
-
-      # Don't error if the file doesn't exist and rm -f was used.
-      if { test -L "$file"; } >/dev/null 2>&1 ||
-	 { test -h "$file"; } >/dev/null 2>&1 ||
-	 test -f "$file"; then
-	:
-      elif test -d "$file"; then
-	exit_status=1
-	continue
-      elif test "$rmforce" = yes; then
-	continue
-      fi
-
-      rmfiles="$file"
-
-      case $name in
-      *.la)
-	# Possibly a libtool archive, so verify it.
-	if func_lalib_p "$file"; then
-	  func_source $dir/$name
-
-	  # Delete the libtool libraries and symlinks.
-	  for n in $library_names; do
-	    func_append rmfiles " $odir/$n"
-	  done
-	  test -n "$old_library" && func_append rmfiles " $odir/$old_library"
-
-	  case "$opt_mode" in
-	  clean)
-	    case " $library_names " in
-	    *" $dlname "*) ;;
-	    *) test -n "$dlname" && func_append rmfiles " $odir/$dlname" ;;
-	    esac
-	    test -n "$libdir" && func_append rmfiles " $odir/$name $odir/${name}i"
-	    ;;
-	  uninstall)
-	    if test -n "$library_names"; then
-	      # Do each command in the postuninstall commands.
-	      func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
-	    fi
-
-	    if test -n "$old_library"; then
-	      # Do each command in the old_postuninstall commands.
-	      func_execute_cmds "$old_postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
-	    fi
-	    # FIXME: should reinstall the best remaining shared library.
-	    ;;
-	  esac
-	fi
-	;;
-
-      *.lo)
-	# Possibly a libtool object, so verify it.
-	if func_lalib_p "$file"; then
-
-	  # Read the .lo file
-	  func_source $dir/$name
-
-	  # Add PIC object to the list of files to remove.
-	  if test -n "$pic_object" &&
-	     test "$pic_object" != none; then
-	    func_append rmfiles " $dir/$pic_object"
-	  fi
-
-	  # Add non-PIC object to the list of files to remove.
-	  if test -n "$non_pic_object" &&
-	     test "$non_pic_object" != none; then
-	    func_append rmfiles " $dir/$non_pic_object"
-	  fi
-	fi
-	;;
-
-      *)
-	if test "$opt_mode" = clean ; then
-	  noexename=$name
-	  case $file in
-	  *.exe)
-	    func_stripname '' '.exe' "$file"
-	    file=$func_stripname_result
-	    func_stripname '' '.exe' "$name"
-	    noexename=$func_stripname_result
-	    # $file with .exe has already been added to rmfiles,
-	    # add $file without .exe
-	    func_append rmfiles " $file"
-	    ;;
-	  esac
-	  # Do a test to see if this is a libtool program.
-	  if func_ltwrapper_p "$file"; then
-	    if func_ltwrapper_executable_p "$file"; then
-	      func_ltwrapper_scriptname "$file"
-	      relink_command=
-	      func_source $func_ltwrapper_scriptname_result
-	      func_append rmfiles " $func_ltwrapper_scriptname_result"
-	    else
-	      relink_command=
-	      func_source $dir/$noexename
-	    fi
-
-	    # note $name still contains .exe if it was in $file originally
-	    # as does the version of $file that was added into $rmfiles
-	    func_append rmfiles " $odir/$name $odir/${name}S.${objext}"
-	    if test "$fast_install" = yes && test -n "$relink_command"; then
-	      func_append rmfiles " $odir/lt-$name"
-	    fi
-	    if test "X$noexename" != "X$name" ; then
-	      func_append rmfiles " $odir/lt-${noexename}.c"
-	    fi
-	  fi
-	fi
-	;;
-      esac
-      func_show_eval "$RM $rmfiles" 'exit_status=1'
-    done
-
-    # Try to remove the ${objdir}s in the directories where we deleted files
-    for dir in $rmdirs; do
-      if test -d "$dir"; then
-	func_show_eval "rmdir $dir >/dev/null 2>&1"
-      fi
-    done
-
-    exit $exit_status
-}
-
-{ test "$opt_mode" = uninstall || test "$opt_mode" = clean; } &&
-    func_mode_uninstall ${1+"$@"}
-
-test -z "$opt_mode" && {
-  help="$generic_help"
-  func_fatal_help "you must specify a MODE"
-}
-
-test -z "$exec_cmd" && \
-  func_fatal_help "invalid operation mode \`$opt_mode'"
-
-if test -n "$exec_cmd"; then
-  eval exec "$exec_cmd"
-  exit $EXIT_FAILURE
-fi
-
-exit $exit_status
-
-
-# The TAGs below are defined such that we never get into a situation
-# in which we disable both kinds of libraries.  Given conflicting
-# choices, we go for a static library, that is the most portable,
-# since we can't tell whether shared libraries were disabled because
-# the user asked for that or because the platform doesn't support
-# them.  This is particularly important on AIX, because we don't
-# support having both static and shared libraries enabled at the same
-# time on that platform, so we default to a shared-only configuration.
-# If a disable-shared tag is given, we'll fallback to a static-only
-# configuration.  But we'll never go from static-only to shared-only.
-
-# ### BEGIN LIBTOOL TAG CONFIG: disable-shared
-build_libtool_libs=no
-build_old_libs=yes
-# ### END LIBTOOL TAG CONFIG: disable-shared
-
-# ### BEGIN LIBTOOL TAG CONFIG: disable-static
-build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac`
-# ### END LIBTOOL TAG CONFIG: disable-static
-
-# Local Variables:
-# mode:shell-script
-# sh-indentation:2
-# End:
-# vi:sw=2
-
diff --git a/build-aux/missing b/build-aux/missing
deleted file mode 100755
index cdea514931..0000000000
--- a/build-aux/missing
+++ /dev/null
@@ -1,215 +0,0 @@
-#! /bin/sh
-# Common wrapper for a few potentially missing GNU programs.
-
-scriptversion=2012-06-26.16; # UTC
-
-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
-# Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-if test $# -eq 0; then
-  echo 1>&2 "Try '$0 --help' for more information"
-  exit 1
-fi
-
-case $1 in
-
-  --is-lightweight)
-    # Used by our autoconf macros to check whether the available missing
-    # script is modern enough.
-    exit 0
-    ;;
-
-  --run)
-    # Back-compat with the calling convention used by older automake.
-    shift
-    ;;
-
-  -h|--h|--he|--hel|--help)
-    echo "\
-$0 [OPTION]... PROGRAM [ARGUMENT]...
-
-Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
-to PROGRAM being missing or too old.
-
-Options:
-  -h, --help      display this help and exit
-  -v, --version   output version information and exit
-
-Supported PROGRAM values:
-  aclocal   autoconf  autoheader   autom4te  automake  makeinfo
-  bison     yacc      flex         lex       help2man
-
-Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and
-'g' are ignored when checking the name.
-
-Send bug reports to <bug-automake@gnu.org>."
-    exit $?
-    ;;
-
-  -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
-    echo "missing $scriptversion (GNU Automake)"
-    exit $?
-    ;;
-
-  -*)
-    echo 1>&2 "$0: unknown '$1' option"
-    echo 1>&2 "Try '$0 --help' for more information"
-    exit 1
-    ;;
-
-esac
-
-# Run the given program, remember its exit status.
-"$@"; st=$?
-
-# If it succeeded, we are done.
-test $st -eq 0 && exit 0
-
-# Also exit now if we it failed (or wasn't found), and '--version' was
-# passed; such an option is passed most likely to detect whether the
-# program is present and works.
-case $2 in --version|--help) exit $st;; esac
-
-# Exit code 63 means version mismatch.  This often happens when the user
-# tries to use an ancient version of a tool on a file that requires a
-# minimum version.
-if test $st -eq 63; then
-  msg="probably too old"
-elif test $st -eq 127; then
-  # Program was missing.
-  msg="missing on your system"
-else
-  # Program was found and executed, but failed.  Give up.
-  exit $st
-fi
-
-perl_URL=http://www.perl.org/
-flex_URL=http://flex.sourceforge.net/
-gnu_software_URL=http://www.gnu.org/software
-
-program_details ()
-{
-  case $1 in
-    aclocal|automake)
-      echo "The '$1' program is part of the GNU Automake package:"
-      echo "<$gnu_software_URL/automake>"
-      echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
-      echo "<$gnu_software_URL/autoconf>"
-      echo "<$gnu_software_URL/m4/>"
-      echo "<$perl_URL>"
-      ;;
-    autoconf|autom4te|autoheader)
-      echo "The '$1' program is part of the GNU Autoconf package:"
-      echo "<$gnu_software_URL/autoconf/>"
-      echo "It also requires GNU m4 and Perl in order to run:"
-      echo "<$gnu_software_URL/m4/>"
-      echo "<$perl_URL>"
-      ;;
-  esac
-}
-
-give_advice ()
-{
-  # Normalize program name to check for.
-  normalized_program=`echo "$1" | sed '
-    s/^gnu-//; t
-    s/^gnu//; t
-    s/^g//; t'`
-
-  printf '%s\n' "'$1' is $msg."
-
-  configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
-  case $normalized_program in
-    autoconf*)
-      echo "You should only need it if you modified 'configure.ac',"
-      echo "or m4 files included by it."
-      program_details 'autoconf'
-      ;;
-    autoheader*)
-      echo "You should only need it if you modified 'acconfig.h' or"
-      echo "$configure_deps."
-      program_details 'autoheader'
-      ;;
-    automake*)
-      echo "You should only need it if you modified 'Makefile.am' or"
-      echo "$configure_deps."
-      program_details 'automake'
-      ;;
-    aclocal*)
-      echo "You should only need it if you modified 'acinclude.m4' or"
-      echo "$configure_deps."
-      program_details 'aclocal'
-      ;;
-   autom4te*)
-      echo "You might have modified some maintainer files that require"
-      echo "the 'automa4te' program to be rebuilt."
-      program_details 'autom4te'
-      ;;
-    bison*|yacc*)
-      echo "You should only need it if you modified a '.y' file."
-      echo "You may want to install the GNU Bison package:"
-      echo "<$gnu_software_URL/bison/>"
-      ;;
-    lex*|flex*)
-      echo "You should only need it if you modified a '.l' file."
-      echo "You may want to install the Fast Lexical Analyzer package:"
-      echo "<$flex_URL>"
-      ;;
-    help2man*)
-      echo "You should only need it if you modified a dependency" \
-           "of a man page."
-      echo "You may want to install the GNU Help2man package:"
-      echo "<$gnu_software_URL/help2man/>"
-    ;;
-    makeinfo*)
-      echo "You should only need it if you modified a '.texi' file, or"
-      echo "any other file indirectly affecting the aspect of the manual."
-      echo "You might want to install the Texinfo package:"
-      echo "<$gnu_software_URL/texinfo/>"
-      echo "The spurious makeinfo call might also be the consequence of"
-      echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
-      echo "want to install GNU make:"
-      echo "<$gnu_software_URL/make/>"
-      ;;
-    *)
-      echo "You might have modified some files without having the proper"
-      echo "tools for further handling them.  Check the 'README' file, it"
-      echo "often tells you about the needed prerequisites for installing"
-      echo "this package.  You may also peek at any GNU archive site, in"
-      echo "case some other package contains this missing '$1' program."
-      ;;
-  esac
-}
-
-give_advice "$1" | sed -e '1s/^/WARNING: /' \
-                       -e '2,$s/^/         /' >&2
-
-# Propagate the correct exit status (expected to be 127 for a program
-# not found, 63 for a program that failed due to version mismatch).
-exit $st
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:

From 5587f5bded46e94d639b7de8475b8b2829592be2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 4 Nov 2025 12:42:01 +0100
Subject: [PATCH 0307/1827] Remove makefiles

They are not needed anymore with cmake
---
 externalpackages/PVODE/makefile               |  16 ---
 output.make                                   |  22 ----
 tests/MMS/GBS/makefile                        |   6 -
 tests/MMS/advection/makefile                  |   6 -
 tests/MMS/diffusion/makefile                  |   8 --
 tests/MMS/diffusion2/makefile                 |   8 --
 tests/MMS/elm-pb/makefile                     |   6 -
 tests/MMS/elm-pb/makegrids.py                 |  65 ----------
 tests/MMS/fieldalign/doc/makefile             |  12 --
 tests/MMS/fieldalign/makefile                 |   7 --
 tests/MMS/hw/makefile                         |   6 -
 tests/MMS/laplace/makefile                    |   6 -
 tests/MMS/makefile                            |   1 -
 tests/MMS/spatial/advection/makefile          |   6 -
 tests/MMS/spatial/d2dx2/makefile              |   6 -
 tests/MMS/spatial/d2dz2/makefile              |   6 -
 tests/MMS/spatial/diffusion/makefile          |   8 --
 tests/MMS/spatial/fci/makefile                |   6 -
 tests/MMS/test_suite_make                     |   1 -
 tests/MMS/time/makefile                       |   6 -
 tests/MMS/tokamak/makefile                    |   6 -
 tests/MMS/wave-1d-y/makefile                  |   8 --
 tests/MMS/wave-1d/makefile                    |   8 --
 tests/integrated/makefile                     |  33 -----
 tests/integrated/test-backtrace/makefile      |   6 -
 tests/integrated/test-beuler/makefile         |   5 -
 .../makefile                                  |   6 -
 tests/integrated/test-collect/makefile        |   6 -
 tests/integrated/test-command-args/makefile   |   6 -
 tests/integrated/test-communications/makefile |   6 -
 .../test-coordinates-initialization/makefile  |   6 -
 tests/integrated/test-cyclic/makefile         |   6 -
 tests/integrated/test-datafilefacade/makefile |   5 -
 tests/integrated/test-dataformat/makefile     |   6 -
 tests/integrated/test-delp2/makefile          |   6 -
 .../test-drift-instability-staggered/makefile |   1 -
 .../test-drift-instability/make_d.pro         |  23 ----
 .../test-drift-instability/makefile           |   5 -
 tests/integrated/test-fieldgroupComm/makefile |   3 -
 tests/integrated/test-globalfield/makefile    |   6 -
 .../test-griddata-yboundary-guards/makefile   |   6 -
 tests/integrated/test-griddata/makefile       |   6 -
 tests/integrated/test-gyro/makefile           |   6 -
 tests/integrated/test-include/makefile        |   4 -
 tests/integrated/test-initial/makefile        |   6 -
 tests/integrated/test-integrate/makefile      |   6 -
 .../test-interchange-instability/makefile     |   5 -
 tests/integrated/test-interpolate-z/makefile  |   6 -
 tests/integrated/test-interpolate/makefile    |   6 -
 .../test-invertable-operator/makefile         |   5 -
 tests/integrated/test-invpar/makefile         |   6 -
 .../integrated/test-laplace-hypre3d/makefile  |   5 -
 .../integrated/test-laplace-petsc3d/makefile  |   5 -
 tests/integrated/test-laplace/makefile        |   6 -
 tests/integrated/test-laplace2/makefile       |   6 -
 tests/integrated/test-laplacexy-fv/makefile   |   5 -
 .../integrated/test-laplacexy-short/makefile  |   5 -
 tests/integrated/test-laplacexy/makefile      |   5 -
 .../integrated/test-laplacexy2-hypre/makefile |   5 -
 tests/integrated/test-laplacexz/makefile      |   6 -
 .../test-multigrid_laplace/makefile           |   5 -
 tests/integrated/test-naulin-laplace/makefile |   5 -
 tests/integrated/test-nonuniform/makefile     |   6 -
 tests/integrated/test-options-adios/makefile  |   6 -
 tests/integrated/test-options-netcdf/makefile |   6 -
 tests/integrated/test-petsc_laplace/makefile  |   9 --
 .../test-petsc_laplace_MAST-grid/makefile     |   9 --
 .../integrated/test-region-iterator/makefile  |   6 -
 tests/integrated/test-restart-io/makefile     |   5 -
 tests/integrated/test-restarting/makefile     |   6 -
 tests/integrated/test-slepc-solver/makefile   |   5 -
 tests/integrated/test-smooth/makefile         |   6 -
 tests/integrated/test-snb/makefile            |   6 -
 tests/integrated/test-solver/makefile         |   5 -
 tests/integrated/test-squash/makefile         |   6 -
 tests/integrated/test-stopCheck-file/makefile |   6 -
 tests/integrated/test-stopCheck/makefile      |   6 -
 tests/integrated/test-subdir/bar/makefile     |   6 -
 tests/integrated/test-subdir/fuu/makefile     |   6 -
 tests/integrated/test-subdir/makefile         |  10 --
 .../test-twistshift-staggered/makefile        |   5 -
 tests/integrated/test-twistshift/makefile     |   5 -
 tests/integrated/test-vec/makefile            |   6 -
 .../integrated/test-yupdown-weights/makefile  |   6 -
 tests/integrated/test-yupdown/makefile        |   6 -
 tests/integrated/test_suite_make              |   3 -
 tests/unit/makefile                           | 114 ------------------
 tools/pdb2idl/make.config.in                  |  19 ---
 88 files changed, 764 deletions(-)
 delete mode 100644 externalpackages/PVODE/makefile
 delete mode 100644 output.make
 delete mode 100644 tests/MMS/GBS/makefile
 delete mode 100644 tests/MMS/advection/makefile
 delete mode 100644 tests/MMS/diffusion/makefile
 delete mode 100644 tests/MMS/diffusion2/makefile
 delete mode 100644 tests/MMS/elm-pb/makefile
 delete mode 100644 tests/MMS/elm-pb/makegrids.py
 delete mode 100644 tests/MMS/fieldalign/doc/makefile
 delete mode 100644 tests/MMS/fieldalign/makefile
 delete mode 100644 tests/MMS/hw/makefile
 delete mode 100644 tests/MMS/laplace/makefile
 delete mode 120000 tests/MMS/makefile
 delete mode 100644 tests/MMS/spatial/advection/makefile
 delete mode 100644 tests/MMS/spatial/d2dx2/makefile
 delete mode 100644 tests/MMS/spatial/d2dz2/makefile
 delete mode 100644 tests/MMS/spatial/diffusion/makefile
 delete mode 100644 tests/MMS/spatial/fci/makefile
 delete mode 120000 tests/MMS/test_suite_make
 delete mode 100644 tests/MMS/time/makefile
 delete mode 100644 tests/MMS/tokamak/makefile
 delete mode 100644 tests/MMS/wave-1d-y/makefile
 delete mode 100644 tests/MMS/wave-1d/makefile
 delete mode 100644 tests/integrated/makefile
 delete mode 100644 tests/integrated/test-backtrace/makefile
 delete mode 100644 tests/integrated/test-beuler/makefile
 delete mode 100644 tests/integrated/test-bout-override-default-option/makefile
 delete mode 100644 tests/integrated/test-collect/makefile
 delete mode 100644 tests/integrated/test-command-args/makefile
 delete mode 100644 tests/integrated/test-communications/makefile
 delete mode 100644 tests/integrated/test-coordinates-initialization/makefile
 delete mode 100644 tests/integrated/test-cyclic/makefile
 delete mode 100644 tests/integrated/test-datafilefacade/makefile
 delete mode 100644 tests/integrated/test-dataformat/makefile
 delete mode 100644 tests/integrated/test-delp2/makefile
 delete mode 120000 tests/integrated/test-drift-instability-staggered/makefile
 delete mode 100644 tests/integrated/test-drift-instability/make_d.pro
 delete mode 100644 tests/integrated/test-drift-instability/makefile
 delete mode 100644 tests/integrated/test-fieldgroupComm/makefile
 delete mode 100644 tests/integrated/test-globalfield/makefile
 delete mode 100644 tests/integrated/test-griddata-yboundary-guards/makefile
 delete mode 100644 tests/integrated/test-griddata/makefile
 delete mode 100644 tests/integrated/test-gyro/makefile
 delete mode 100644 tests/integrated/test-include/makefile
 delete mode 100644 tests/integrated/test-initial/makefile
 delete mode 100644 tests/integrated/test-integrate/makefile
 delete mode 100644 tests/integrated/test-interchange-instability/makefile
 delete mode 100644 tests/integrated/test-interpolate-z/makefile
 delete mode 100644 tests/integrated/test-interpolate/makefile
 delete mode 100644 tests/integrated/test-invertable-operator/makefile
 delete mode 100644 tests/integrated/test-invpar/makefile
 delete mode 100644 tests/integrated/test-laplace-hypre3d/makefile
 delete mode 100644 tests/integrated/test-laplace-petsc3d/makefile
 delete mode 100644 tests/integrated/test-laplace/makefile
 delete mode 100644 tests/integrated/test-laplace2/makefile
 delete mode 100644 tests/integrated/test-laplacexy-fv/makefile
 delete mode 100644 tests/integrated/test-laplacexy-short/makefile
 delete mode 100644 tests/integrated/test-laplacexy/makefile
 delete mode 100644 tests/integrated/test-laplacexy2-hypre/makefile
 delete mode 100644 tests/integrated/test-laplacexz/makefile
 delete mode 100644 tests/integrated/test-multigrid_laplace/makefile
 delete mode 100644 tests/integrated/test-naulin-laplace/makefile
 delete mode 100644 tests/integrated/test-nonuniform/makefile
 delete mode 100644 tests/integrated/test-options-adios/makefile
 delete mode 100644 tests/integrated/test-options-netcdf/makefile
 delete mode 100644 tests/integrated/test-petsc_laplace/makefile
 delete mode 100644 tests/integrated/test-petsc_laplace_MAST-grid/makefile
 delete mode 100644 tests/integrated/test-region-iterator/makefile
 delete mode 100644 tests/integrated/test-restart-io/makefile
 delete mode 100644 tests/integrated/test-restarting/makefile
 delete mode 100644 tests/integrated/test-slepc-solver/makefile
 delete mode 100644 tests/integrated/test-smooth/makefile
 delete mode 100644 tests/integrated/test-snb/makefile
 delete mode 100644 tests/integrated/test-solver/makefile
 delete mode 100644 tests/integrated/test-squash/makefile
 delete mode 100644 tests/integrated/test-stopCheck-file/makefile
 delete mode 100644 tests/integrated/test-stopCheck/makefile
 delete mode 100644 tests/integrated/test-subdir/bar/makefile
 delete mode 100644 tests/integrated/test-subdir/fuu/makefile
 delete mode 100644 tests/integrated/test-subdir/makefile
 delete mode 100644 tests/integrated/test-twistshift-staggered/makefile
 delete mode 100644 tests/integrated/test-twistshift/makefile
 delete mode 100644 tests/integrated/test-vec/makefile
 delete mode 100644 tests/integrated/test-yupdown-weights/makefile
 delete mode 100644 tests/integrated/test-yupdown/makefile
 delete mode 100755 tests/integrated/test_suite_make
 delete mode 100644 tests/unit/makefile
 delete mode 100644 tools/pdb2idl/make.config.in

diff --git a/externalpackages/PVODE/makefile b/externalpackages/PVODE/makefile
deleted file mode 100644
index 410470a320..0000000000
--- a/externalpackages/PVODE/makefile
+++ /dev/null
@@ -1,16 +0,0 @@
-# Makefile for example codes
-# Works in the same way as the root Makefile
-
-TARGET?=all
-
-DIRS		= source precon
-
-all: $(DIRS)
-
-.PHONY: $(DIRS)
-
-$(DIRS):
-	@$(MAKE) -s --no-print-directory TARGET=$(TARGET) -C $@ $(TARGET)
-
-clean::
-	@for pp in $(DIRS); do echo "  " $$pp cleaned; $(MAKE) --no-print-directory -C $$pp clean; done
diff --git a/output.make b/output.make
deleted file mode 100644
index eae6b1be64..0000000000
--- a/output.make
+++ /dev/null
@@ -1,22 +0,0 @@
-BOUT_TOP ?= .
-
-include make.config
-
-# These expand to literals of the same name, which are then
-# set in the bout.config script. This enables
-# the final paths to the include and lib files to be set
-# in the make/make install targets
-
-BOUT_INCLUDE_PATH="\$$BOUT_INCLUDE_PATH"
-BOUT_LIB_PATH="\$$BOUT_LIB_PATH"
-MPARK_VARIANT_INCLUDE_PATH="\$$MPARK_VARIANT_INCLUDE_PATH"
-FMT_INCLUDE_PATH="\$$FMT_INCLUDE_PATH"
-
-.PHONY: cflags
-cflags:
-	@echo $(BOUT_INCLUDE) $(BOUT_FLAGS)
-
-.PHONY: ldflags
-ldflags:
-	@echo $(LDFLAGS) $(BOUT_LIBS)
-
diff --git a/tests/MMS/GBS/makefile b/tests/MMS/GBS/makefile
deleted file mode 100644
index 7dbf15255f..0000000000
--- a/tests/MMS/GBS/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= gbs.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/advection/makefile b/tests/MMS/advection/makefile
deleted file mode 100644
index 305cd9bebe..0000000000
--- a/tests/MMS/advection/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../../
-
-SOURCEC		= advection.cxx  
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/diffusion/makefile b/tests/MMS/diffusion/makefile
deleted file mode 100644
index 4b4c30ff62..0000000000
--- a/tests/MMS/diffusion/makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-
-BOUT_TOP	= ../../../
-
-SOURCEC		= diffusion.cxx  
-SOURCEH 	= mathematica.h
-TARGET 		= cyto
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/diffusion2/makefile b/tests/MMS/diffusion2/makefile
deleted file mode 100644
index 4b4c30ff62..0000000000
--- a/tests/MMS/diffusion2/makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-
-BOUT_TOP	= ../../../
-
-SOURCEC		= diffusion.cxx  
-SOURCEH 	= mathematica.h
-TARGET 		= cyto
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/elm-pb/makefile b/tests/MMS/elm-pb/makefile
deleted file mode 100644
index 815a018b94..0000000000
--- a/tests/MMS/elm-pb/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= elm_pb.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/elm-pb/makegrids.py b/tests/MMS/elm-pb/makegrids.py
deleted file mode 100644
index b627977469..0000000000
--- a/tests/MMS/elm-pb/makegrids.py
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/usr/bin/env python3
-#
-# Creates the grid files and input options for
-# a set of simulations. These can then be submitted
-# to a batch queue and then processed with runtest
-# (setting "running = False")
-#
-
-from __future__ import print_function
-from __future__ import division
-
-nxlist = [4, 8, 16, 32, 64, 128]
-
-from boututils.datafile import DataFile
-from boututils.run_wrapper import shell
-
-from os.path import isfile
-
-from boutdata.mms import SimpleTokamak, x, y
-from sympy import sin, cos
-
-from math import pi
-
-shape = SimpleTokamak()
-
-## Add equilibrium profiles
-MU0 = 4.0e-7 * pi
-
-J0 = 1 - x - sin(x * pi) ** 2 * cos(y)  # Parallel current
-P0 = 2 + cos(x * pi)  # Pressure pedestal
-bxcvz = -((1.0 / shape.Rxy) ** 2) * cos(y)  # Curvature
-
-# Normalisation
-Lbar = 1.0
-Bbar = 1.0
-J0 = -J0 * shape.Bxy / (MU0 * Lbar)  # Turn into A/m^2
-P0 = P0 * Bbar**2 / (2.0 * MU0)  # Pascals
-
-shape.add(P0, "pressure")
-shape.add(J0, "Jpar0")
-shape.add(bxcvz, "bxcvz")
-
-for nx in nxlist:
-    # Generate a new mesh file
-
-    filename = "grid%d.nc" % nx
-
-    if isfile(filename):
-        print("Grid file '%s' already exists" % filename)
-    else:
-        print("Creating grid file '%s'" % filename)
-        f = DataFile(filename, create=True)
-        shape.write(nx, nx, f)
-        f.close()
-
-    # Generate BOUT.inp file
-
-    directory = "grid%d" % nx
-    shell("mkdir " + directory)
-    shell("cp data/BOUT.inp " + directory)
-    shell("sed -i 's/MZ = 17/MZ = %d/g' %s/BOUT.inp" % (nx, directory))
-    shell(
-        'sed -i \'s/grid = "grid16.nc"/grid = "%s"/g\' %s/BOUT.inp'
-        % (filename, directory)
-    )
diff --git a/tests/MMS/fieldalign/doc/makefile b/tests/MMS/fieldalign/doc/makefile
deleted file mode 100644
index 70bb3220d0..0000000000
--- a/tests/MMS/fieldalign/doc/makefile
+++ /dev/null
@@ -1,12 +0,0 @@
-
-DOCS = fieldalign.pdf
-
-.PHONY: all
-
-all: $(DOCS)
-
-%.pdf: %.tex 
-	latexmk -pdf $< -interaction=batchmode
-
-clean:
-	latexmk -C
diff --git a/tests/MMS/fieldalign/makefile b/tests/MMS/fieldalign/makefile
deleted file mode 100644
index 30f47ccf0a..0000000000
--- a/tests/MMS/fieldalign/makefile
+++ /dev/null
@@ -1,7 +0,0 @@
-
-BOUT_TOP	= ../../../
-
-SOURCEC		= fieldalign.cxx  
-SOURCEH 	= mathematica.h
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/hw/makefile b/tests/MMS/hw/makefile
deleted file mode 100644
index 0a68a26d50..0000000000
--- a/tests/MMS/hw/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= hw.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/laplace/makefile b/tests/MMS/laplace/makefile
deleted file mode 100644
index fa561d91da..0000000000
--- a/tests/MMS/laplace/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= laplace.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/makefile b/tests/MMS/makefile
deleted file mode 120000
index 065bc377f3..0000000000
--- a/tests/MMS/makefile
+++ /dev/null
@@ -1 +0,0 @@
-../integrated/makefile
\ No newline at end of file
diff --git a/tests/MMS/spatial/advection/makefile b/tests/MMS/spatial/advection/makefile
deleted file mode 100644
index fdb2043641..0000000000
--- a/tests/MMS/spatial/advection/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../../..
-
-SOURCEC		= advection.cxx  
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/spatial/d2dx2/makefile b/tests/MMS/spatial/d2dx2/makefile
deleted file mode 100644
index 8975c2c713..0000000000
--- a/tests/MMS/spatial/d2dx2/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../../../
-
-SOURCEC		= test_d2dx2.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/spatial/d2dz2/makefile b/tests/MMS/spatial/d2dz2/makefile
deleted file mode 100644
index 043b0567dd..0000000000
--- a/tests/MMS/spatial/d2dz2/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../../../
-
-SOURCEC		= test_d2dz2.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/spatial/diffusion/makefile b/tests/MMS/spatial/diffusion/makefile
deleted file mode 100644
index 47a79d0916..0000000000
--- a/tests/MMS/spatial/diffusion/makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-
-BOUT_TOP	= ../../../..
-
-SOURCEC		= diffusion.cxx  
-SOURCEH 	= mathematica.h
-TARGET 		= diffusion
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/spatial/fci/makefile b/tests/MMS/spatial/fci/makefile
deleted file mode 100644
index 88ba6c77e7..0000000000
--- a/tests/MMS/spatial/fci/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../../..
-
-SOURCEC		= fci_mms.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/test_suite_make b/tests/MMS/test_suite_make
deleted file mode 120000
index 97f7df4edb..0000000000
--- a/tests/MMS/test_suite_make
+++ /dev/null
@@ -1 +0,0 @@
-../integrated/test_suite_make
\ No newline at end of file
diff --git a/tests/MMS/time/makefile b/tests/MMS/time/makefile
deleted file mode 100644
index a45b4a3888..0000000000
--- a/tests/MMS/time/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../../
-
-SOURCEC		= time.cxx  
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/tokamak/makefile b/tests/MMS/tokamak/makefile
deleted file mode 100644
index f94969cccf..0000000000
--- a/tests/MMS/tokamak/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../../
-
-SOURCEC		= tokamak.cxx  
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/wave-1d-y/makefile b/tests/MMS/wave-1d-y/makefile
deleted file mode 100644
index fb4dd1430a..0000000000
--- a/tests/MMS/wave-1d-y/makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-
-BOUT_TOP	= ../../../
-
-SOURCEC		= wave.cxx  
-SOURCEH 	= mathematica.h
-TARGET 		= wave
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/wave-1d/makefile b/tests/MMS/wave-1d/makefile
deleted file mode 100644
index fb4dd1430a..0000000000
--- a/tests/MMS/wave-1d/makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-
-BOUT_TOP	= ../../../
-
-SOURCEC		= wave.cxx  
-SOURCEH 	= mathematica.h
-TARGET 		= wave
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/makefile b/tests/integrated/makefile
deleted file mode 100644
index 29215a7185..0000000000
--- a/tests/integrated/makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-# Makefile for example codes
-# Works in the same way as the root Makefile
-
-BOUT_TOP = ../..
-
-BUILD = $(shell PYTHONPATH=../../tools/pylib:$$PYTHONPATH ./test_suite_make --get-list)
-BUILD_ALL = $(shell PYTHONPATH=../../tools/pylib:$$PYTHONPATH ./test_suite_make --get-list --all)
-
-CHECKING = $(shell PYTHONPATH=../../tools/pylib:$$PYTHONPATH ./test_suite --get-list)
-CHECKING_ALL = $(shell PYTHONPATH=../../tools/pylib:$$PYTHONPATH ./test_suite --get-list --all)
-
-include $(BOUT_TOP)/make.config
-
-CHECKING_ = $(CHECKING:%=%_checking)
-CHECKING_ALL_ = $(CHECKING_ALL:%=%_checking)
-
-DIRS_CLEAN = $(BUILD)
-
-.PHONY: $(BUILD_ALL) $(CHECKING_ALL) check
-
-all: $(BUILD)
-
-all-all: $(BUILD_ALL)
-
-buildncheck: all check
-
-$(BUILDALL):
-	@$(MAKE) --no-print-directory -C $@
-
-check: $(CHECKING_)
-
-$(CHECKING_ALL_):
-	@$(MAKE) --no-print-directory -C $(@:%_checking=%) runtest
diff --git a/tests/integrated/test-backtrace/makefile b/tests/integrated/test-backtrace/makefile
deleted file mode 100644
index 27a1ecaf3a..0000000000
--- a/tests/integrated/test-backtrace/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	?= ../../..
-
-SOURCEC = boutexcept.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-beuler/makefile b/tests/integrated/test-beuler/makefile
deleted file mode 100644
index 4eb9387e29..0000000000
--- a/tests/integrated/test-beuler/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_beuler.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-bout-override-default-option/makefile b/tests/integrated/test-bout-override-default-option/makefile
deleted file mode 100644
index 72fb7693e9..0000000000
--- a/tests/integrated/test-bout-override-default-option/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-bout-override-default-option.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-collect/makefile b/tests/integrated/test-collect/makefile
deleted file mode 100644
index d599972ccb..0000000000
--- a/tests/integrated/test-collect/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-collect.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-command-args/makefile b/tests/integrated/test-command-args/makefile
deleted file mode 100644
index 395ef9b6fa..0000000000
--- a/tests/integrated/test-command-args/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= command-args.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-communications/makefile b/tests/integrated/test-communications/makefile
deleted file mode 100644
index 62bfa7e1ca..0000000000
--- a/tests/integrated/test-communications/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-communications.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-coordinates-initialization/makefile b/tests/integrated/test-coordinates-initialization/makefile
deleted file mode 100644
index 805ac0e1da..0000000000
--- a/tests/integrated/test-coordinates-initialization/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-coordinates-initialization.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-cyclic/makefile b/tests/integrated/test-cyclic/makefile
deleted file mode 100644
index 9d67f1fce2..0000000000
--- a/tests/integrated/test-cyclic/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_cyclic.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-datafilefacade/makefile b/tests/integrated/test-datafilefacade/makefile
deleted file mode 100644
index 26b62c9998..0000000000
--- a/tests/integrated/test-datafilefacade/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-datafile-facade.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-dataformat/makefile b/tests/integrated/test-dataformat/makefile
deleted file mode 100644
index ccf812ed6f..0000000000
--- a/tests/integrated/test-dataformat/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_dataformat.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-delp2/makefile b/tests/integrated/test-delp2/makefile
deleted file mode 100644
index 0c6ba8b3a9..0000000000
--- a/tests/integrated/test-delp2/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_delp2.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-drift-instability-staggered/makefile b/tests/integrated/test-drift-instability-staggered/makefile
deleted file mode 120000
index 4970135770..0000000000
--- a/tests/integrated/test-drift-instability-staggered/makefile
+++ /dev/null
@@ -1 +0,0 @@
-../test-drift-instability/makefile
\ No newline at end of file
diff --git a/tests/integrated/test-drift-instability/make_d.pro b/tests/integrated/test-drift-instability/make_d.pro
deleted file mode 100644
index 861f846307..0000000000
--- a/tests/integrated/test-drift-instability/make_d.pro
+++ /dev/null
@@ -1,23 +0,0 @@
-function make_d, path=path
- 
-if not keyword_set(PATH) then path='' 
-
-ni=collect(path=path, var="Ni") 
-phi=collect(path=path, var="phi")
-ni=ni[2,*,*,*] 
-phi=phi[2,*,*,*] 
-
-du=file_import("uedge.grd_std.cdl")
-
-new_zmax = collect(path=path, var="ZMAX") ;-fraction of 2PI
-rho_s    = collect(path=path, var="rho_s")
-wci      = collect(path=path, var="wci")
-t_array  = collect(path=path, var="t_array")
-
-old_zmax=new_zmax/(rho_s/du.hthe0)
-print, 'new_zmax=', new_zmax, "; old_zmax=", old_zmax
-
-d={ni_xyzt:ni, phi_xyzt:phi, rho_s:rho_s, zmax:old_zmax, Zeff:0., AA:0.0, t_array:t_array, wci:wci}
-
-return,d
-end
diff --git a/tests/integrated/test-drift-instability/makefile b/tests/integrated/test-drift-instability/makefile
deleted file mode 100644
index 419aa3c503..0000000000
--- a/tests/integrated/test-drift-instability/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP	?= ../../..
-
-SOURCEC		= 2fluid.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-fieldgroupComm/makefile b/tests/integrated/test-fieldgroupComm/makefile
deleted file mode 100644
index f3215eccde..0000000000
--- a/tests/integrated/test-fieldgroupComm/makefile
+++ /dev/null
@@ -1,3 +0,0 @@
-BOUT_TOP	= ../../../
-SOURCEC		= test_fieldgroupcomm.cxx
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-globalfield/makefile b/tests/integrated/test-globalfield/makefile
deleted file mode 100644
index fddd978535..0000000000
--- a/tests/integrated/test-globalfield/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_globalfield.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-griddata-yboundary-guards/makefile b/tests/integrated/test-griddata-yboundary-guards/makefile
deleted file mode 100644
index f2ff47b18b..0000000000
--- a/tests/integrated/test-griddata-yboundary-guards/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_griddata.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-griddata/makefile b/tests/integrated/test-griddata/makefile
deleted file mode 100644
index f2ff47b18b..0000000000
--- a/tests/integrated/test-griddata/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_griddata.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-gyro/makefile b/tests/integrated/test-gyro/makefile
deleted file mode 100644
index 72dcff3424..0000000000
--- a/tests/integrated/test-gyro/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_gyro.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-include/makefile b/tests/integrated/test-include/makefile
deleted file mode 100644
index 6b94f31f99..0000000000
--- a/tests/integrated/test-include/makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-initial/makefile b/tests/integrated/test-initial/makefile
deleted file mode 100644
index b314e92006..0000000000
--- a/tests/integrated/test-initial/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_initial.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-integrate/makefile b/tests/integrated/test-integrate/makefile
deleted file mode 100644
index 2c1dc520b6..0000000000
--- a/tests/integrated/test-integrate/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_integrate.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-interchange-instability/makefile b/tests/integrated/test-interchange-instability/makefile
deleted file mode 100644
index 23554affba..0000000000
--- a/tests/integrated/test-interchange-instability/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP	= ../../..
-
-SOURCEC		= 2fluid.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-interpolate-z/makefile b/tests/integrated/test-interpolate-z/makefile
deleted file mode 100644
index 5b925e1a97..0000000000
--- a/tests/integrated/test-interpolate-z/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_interpolate.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-interpolate/makefile b/tests/integrated/test-interpolate/makefile
deleted file mode 100644
index 5b925e1a97..0000000000
--- a/tests/integrated/test-interpolate/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_interpolate.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-invertable-operator/makefile b/tests/integrated/test-invertable-operator/makefile
deleted file mode 100644
index e0b6d92849..0000000000
--- a/tests/integrated/test-invertable-operator/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP	= ../../..
-
-SOURCEC		= invertable_operator.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-invpar/makefile b/tests/integrated/test-invpar/makefile
deleted file mode 100644
index fc4b99517a..0000000000
--- a/tests/integrated/test-invpar/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_invpar.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-laplace-hypre3d/makefile b/tests/integrated/test-laplace-hypre3d/makefile
deleted file mode 100644
index 88af7fb5e1..0000000000
--- a/tests/integrated/test-laplace-hypre3d/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP = ../../..
-
-SOURCEC = test-laplace3d.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-laplace-petsc3d/makefile b/tests/integrated/test-laplace-petsc3d/makefile
deleted file mode 100644
index 88af7fb5e1..0000000000
--- a/tests/integrated/test-laplace-petsc3d/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP = ../../..
-
-SOURCEC = test-laplace3d.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-laplace/makefile b/tests/integrated/test-laplace/makefile
deleted file mode 100644
index a8a63959d3..0000000000
--- a/tests/integrated/test-laplace/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_laplace.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-laplace2/makefile b/tests/integrated/test-laplace2/makefile
deleted file mode 100644
index a8a63959d3..0000000000
--- a/tests/integrated/test-laplace2/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_laplace.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-laplacexy-fv/makefile b/tests/integrated/test-laplacexy-fv/makefile
deleted file mode 100644
index e7789b2203..0000000000
--- a/tests/integrated/test-laplacexy-fv/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP        = ../../..
-
-SOURCEC         = test-laplacexy.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-laplacexy-short/makefile b/tests/integrated/test-laplacexy-short/makefile
deleted file mode 100644
index e7789b2203..0000000000
--- a/tests/integrated/test-laplacexy-short/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP        = ../../..
-
-SOURCEC         = test-laplacexy.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-laplacexy/makefile b/tests/integrated/test-laplacexy/makefile
deleted file mode 100644
index e7789b2203..0000000000
--- a/tests/integrated/test-laplacexy/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP        = ../../..
-
-SOURCEC         = test-laplacexy.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-laplacexy2-hypre/makefile b/tests/integrated/test-laplacexy2-hypre/makefile
deleted file mode 100644
index e7789b2203..0000000000
--- a/tests/integrated/test-laplacexy2-hypre/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP        = ../../..
-
-SOURCEC         = test-laplacexy.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-laplacexz/makefile b/tests/integrated/test-laplacexz/makefile
deleted file mode 100644
index 49ac5e5baf..0000000000
--- a/tests/integrated/test-laplacexz/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-laplacexz.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-multigrid_laplace/makefile b/tests/integrated/test-multigrid_laplace/makefile
deleted file mode 100644
index 6eddb8b84d..0000000000
--- a/tests/integrated/test-multigrid_laplace/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP = ../../..
-
-SOURCEC = test_multigrid_laplace.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-naulin-laplace/makefile b/tests/integrated/test-naulin-laplace/makefile
deleted file mode 100644
index fb89ff2e71..0000000000
--- a/tests/integrated/test-naulin-laplace/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP = ../../..
-
-SOURCEC = test_naulin_laplace.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-nonuniform/makefile b/tests/integrated/test-nonuniform/makefile
deleted file mode 100644
index 0c6ba8b3a9..0000000000
--- a/tests/integrated/test-nonuniform/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_delp2.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-options-adios/makefile b/tests/integrated/test-options-adios/makefile
deleted file mode 100644
index 7dbbce8736..0000000000
--- a/tests/integrated/test-options-adios/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-options-adios.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-options-netcdf/makefile b/tests/integrated/test-options-netcdf/makefile
deleted file mode 100644
index f9197480fb..0000000000
--- a/tests/integrated/test-options-netcdf/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-options-netcdf.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-petsc_laplace/makefile b/tests/integrated/test-petsc_laplace/makefile
deleted file mode 100644
index 58633ec996..0000000000
--- a/tests/integrated/test-petsc_laplace/makefile
+++ /dev/null
@@ -1,9 +0,0 @@
-BOUT_TOP        = ../../..
-
-SOURCEC         = test_petsc_laplace.cxx
-TARGET          = test_petsc_laplace
-
-CXXFLAGS        +=-g
-
-include $(BOUT_TOP)/make.config
-
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/makefile b/tests/integrated/test-petsc_laplace_MAST-grid/makefile
deleted file mode 100644
index 8a5ff1b27a..0000000000
--- a/tests/integrated/test-petsc_laplace_MAST-grid/makefile
+++ /dev/null
@@ -1,9 +0,0 @@
-BOUT_TOP        = ../../..
-
-SOURCEC         = test_petsc_laplace_MAST_grid.cxx
-TARGET          = test_petsc_laplace_MAST_grid
-
-CXXFLAGS        +=-g
-
-include $(BOUT_TOP)/make.config
-
diff --git a/tests/integrated/test-region-iterator/makefile b/tests/integrated/test-region-iterator/makefile
deleted file mode 100644
index fae70dbfa0..0000000000
--- a/tests/integrated/test-region-iterator/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_region_iterator.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-restart-io/makefile b/tests/integrated/test-restart-io/makefile
deleted file mode 100644
index 4be85e426e..0000000000
--- a/tests/integrated/test-restart-io/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-restart-io.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-restarting/makefile b/tests/integrated/test-restarting/makefile
deleted file mode 100644
index c1a416dcf9..0000000000
--- a/tests/integrated/test-restarting/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_restarting.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-slepc-solver/makefile b/tests/integrated/test-slepc-solver/makefile
deleted file mode 100644
index 8fc1b74cf5..0000000000
--- a/tests/integrated/test-slepc-solver/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP	= ../../..
-
-SOURCEC		= test-slepc-solver.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-smooth/makefile b/tests/integrated/test-smooth/makefile
deleted file mode 100644
index 141a214a50..0000000000
--- a/tests/integrated/test-smooth/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_smooth.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-snb/makefile b/tests/integrated/test-snb/makefile
deleted file mode 100644
index 526313b1cf..0000000000
--- a/tests/integrated/test-snb/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_snb.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-solver/makefile b/tests/integrated/test-solver/makefile
deleted file mode 100644
index 8d16dfc55c..0000000000
--- a/tests/integrated/test-solver/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_solver.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-squash/makefile b/tests/integrated/test-squash/makefile
deleted file mode 100644
index cecff798ec..0000000000
--- a/tests/integrated/test-squash/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= squash.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-stopCheck-file/makefile b/tests/integrated/test-stopCheck-file/makefile
deleted file mode 100644
index 2d2e644a9e..0000000000
--- a/tests/integrated/test-stopCheck-file/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_stopCheck.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-stopCheck/makefile b/tests/integrated/test-stopCheck/makefile
deleted file mode 100644
index 2d2e644a9e..0000000000
--- a/tests/integrated/test-stopCheck/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_stopCheck.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-subdir/bar/makefile b/tests/integrated/test-subdir/bar/makefile
deleted file mode 100644
index ffa825d218..0000000000
--- a/tests/integrated/test-subdir/bar/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-BOUT_TOP = ../../../..
-
-SOURCEC		= bar.cxx
-SOURCEH		= $(SOURCEC:%.cxx=%.hxx)
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-subdir/fuu/makefile b/tests/integrated/test-subdir/fuu/makefile
deleted file mode 100644
index 2c8332ee44..0000000000
--- a/tests/integrated/test-subdir/fuu/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-BOUT_TOP = ../../../..
-
-SOURCEC		= fuu.cxx
-SOURCEH		= $(SOURCEC:%.cxx=%.hxx)
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-subdir/makefile b/tests/integrated/test-subdir/makefile
deleted file mode 100644
index ed52b47451..0000000000
--- a/tests/integrated/test-subdir/makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-BOUT_TOP	= ../../..
-SOURCEH =
-SOURCEC = subdirs.cxx
-
-# make sure we extract the folder
-# DIRS = fuu bar would work as well, but we want to make sure
-# ../otherproject/fuu and /some/long/path/bar works as well ...
-DIRS = fuu/ ././bar/
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-twistshift-staggered/makefile b/tests/integrated/test-twistshift-staggered/makefile
deleted file mode 100644
index 0018135bce..0000000000
--- a/tests/integrated/test-twistshift-staggered/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP = ../../..
-
-SOURCEC = test-twistshift.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-twistshift/makefile b/tests/integrated/test-twistshift/makefile
deleted file mode 100644
index 0018135bce..0000000000
--- a/tests/integrated/test-twistshift/makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-BOUT_TOP = ../../..
-
-SOURCEC = test-twistshift.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-vec/makefile b/tests/integrated/test-vec/makefile
deleted file mode 100644
index 75385e5460..0000000000
--- a/tests/integrated/test-vec/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= testVec.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-yupdown-weights/makefile b/tests/integrated/test-yupdown-weights/makefile
deleted file mode 100644
index 4e3a173b0e..0000000000
--- a/tests/integrated/test-yupdown-weights/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_yupdown_weights.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-yupdown/makefile b/tests/integrated/test-yupdown/makefile
deleted file mode 100644
index 26728c595f..0000000000
--- a/tests/integrated/test-yupdown/makefile
+++ /dev/null
@@ -1,6 +0,0 @@
-
-BOUT_TOP	= ../../..
-
-SOURCEC		= test_yupdown.cxx
-
-include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test_suite_make b/tests/integrated/test_suite_make
deleted file mode 100755
index 36fe54225a..0000000000
--- a/tests/integrated/test_suite_make
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/env sh
-
-./test_suite --make "$@"
diff --git a/tests/unit/makefile b/tests/unit/makefile
deleted file mode 100644
index 1264705559..0000000000
--- a/tests/unit/makefile
+++ /dev/null
@@ -1,114 +0,0 @@
-####################################################################
-# Tests
-####################################################################
-
-BOUT_TOP = ../..
-
-BOUT_TEST_DIR = .
-
-GTEST_BASE = $(BOUT_TOP)/externalpackages/googletest
-GTEST_DIR = $(GTEST_BASE)/googletest
-GMOCK_DIR = $(GTEST_BASE)/googlemock
-
-GTEST_SOURCES = $(GTEST_DIR)/src/gtest-all.cc
-
-# Flags passed to the preprocessor.
-# Set Google Test's header directory as a system directory, such that
-# the compiler doesn't generate warnings in Google Test headers.
-CXXFLAGS += -isystem ${GTEST_DIR}/include -I${GTEST_DIR} -I${BOUT_TEST_DIR}
-CXXFLAGS += -isystem ${GMOCK_DIR}/include -I${GMOCK_DIR}
-
-# Flags passed to the C++ compiler.
-CXXFLAGS += -g -Wall -Wextra -pthread
-
-
-# All Google Test headers.  Usually you shouldn't change this
-# definition.
-GTEST_HEADERS = $(GTEST_DIR)/include/gtest/*.h \
-                $(GTEST_DIR)/include/gtest/internal/*.h
-
-all:  serial_tests
-include $(BOUT_TOP)/make.config
-
-LDFLAGS += -pthread
-
-# Existence of this file indicates that GTEST has been downloaded
-GTEST_SENTINEL = $(GTEST_BASE)/README.md
-
-# House-keeping build targets.
-
-clean ::
-	@$(RM) -f gtest.a bout_test_main.a *.o $(TEST_OBJECTS)
-
-# Builds gtest.a and bout_test_main.a.
-
-# Download Google Test
-$(GTEST_SENTINEL) :
-	@echo "Downloading Google Test"
-	git submodule update --init --recursive
-
-# For simplicity and to avoid depending on Google Test's
-# implementation details, the dependencies specified below are
-# conservative and not optimized.  This is fine as Google Test
-# compiles fast and for ordinary users its source rarely changes.
-#
-# Note: If the GoogleTest submodule has not been checked out when
-# this makefile is run, then the list of .cc and .h files is not
-# correctly captured. Since we will probably not be modifying googletest
-# this rule just depends on the sentinel file.
-gtest-all.o : $(GTEST_SENTINEL)
-	@echo "  Compiling" $@
-	@$(CXX) $(CPPFLAGS) -I$(GTEST_DIR) $(BOUT_FLAGS) -c \
-            $(GTEST_DIR)/src/gtest-all.cc
-
-gmock-all.o : $(GTEST_SENTINEL)
-	@echo "  Compiling" $@
-	@$(CXX) $(CPPFLAGS) -I$(GTEST_DIR) $(BOUT_FLAGS) -c \
-	    $(GMOCK_DIR)/src/gmock-all.cc
-
-bout_test_main.o : $(GTEST_SENTINEL) $(BOUT_TEST_DIR)/bout_test_main.cxx
-	@echo "  Compiling" $@
-	@$(CXX) $(CPPFLAGS) -I$(GTEST_DIR) $(BOUT_INCLUDE) $(BOUT_FLAGS) -c $(@:.o=.cxx)
-
-gtest.a : gtest-all.o
-	@echo "  Linking" $@
-	@$(AR) $(ARFLAGS) $@ $^
-
-gmock.a : gmock-all.o
-	@echo "  Linking" $@
-	@$(AR) $(ARFLAGS) $@ $^
-
-bout_test_main.a : gtest-all.o gmock-all.o bout_test_main.o
-	@echo "  Linking" $@
-	@$(AR) $(ARFLAGS) $@ $^
-
-$(TARGET): makefile $(BOUT_TOP)/make.config $(OBJ) $(SUB_LIBS) bout_test_main.a
-	@echo "  Linking" $(TARGET)
-	@$(LD) $(LDFLAGS) -o $(TARGET) $(OBJ) $(BOUT_LIBS) $(SUB_LIBS) bout_test_main.a
-
-TEST_SOURCES = $(shell find $(BOUT_TEST_DIR) -type f -name "test_*.cxx" 2> /dev/null)
-TEST_OBJECTS = $(TEST_SOURCES:%.cxx=%.o)
-
-$(TEST_OBJECTS): | $(GTEST_SENTINEL)
-
-serial_tests: makefile $(BOUT_TOP)/make.config $(OBJ) $(LIB) \
-              $(SUB_LIBS) $(TEST_OBJECTS) bout_test_main.a
-	@echo "  Linking tests"
-	@$(LD) -o $@ $(TEST_OBJECTS) bout_test_main.a $(LDFLAGS) $(BOUT_LIBS) $(SUB_LIBS)
-
-# Override this on the command line to print full output from the unit tests
-QUIET ?= --gtest_brief=1
-
-# Note: This depends on GTEST_SENTINEL, which checks out Google Test if not present
-#       The correct behaviour relies on the dependencies being checked in left-to-right order
-#       The GTEST_SENTINEL dependency cannot be added to the %.o target, since this results in the %.o
-#       target in make.config being used instead.
-check: $(GTEST_SENTINEL) serial_tests
-	@echo "Running unit test"
-	@./serial_tests $(QUIET) $(GTEST_ARGS)
-
-# This is the same target as a make rule in make.config. Adding unmet dependencies here
-# results in makefile reverting to the make.config version.
-%.o: $(BOUT_TOP)/make.config %.cxx
-	@echo "  Compiling " $(@:.o=.cxx)
-	@$(CXX) $(BOUT_INCLUDE) $(BOUT_FLAGS) -c $(@:.o=.cxx) -o $(@)
diff --git a/tools/pdb2idl/make.config.in b/tools/pdb2idl/make.config.in
deleted file mode 100644
index 36c97e7789..0000000000
--- a/tools/pdb2idl/make.config.in
+++ /dev/null
@@ -1,19 +0,0 @@
-# configuration file for PDB2IDL
-
-CFLAGS = @CFLAGS@
-LDFLAGS = @LDFLAGS@
-
-CC = @CC@
-LD = @LD@
-
-# Set the location of the PACT installation
-PACT = @PACT@
-
-# IDL external library
-IDLPATH = @IDLPATH@
-
-####################################
-# Do not need to alter this section
-
-INCLUDE = -I$(PACT)/include -I$(IDLPATH)
-LIB = -L$(PACT)/lib -lpdb -lpml -lscore

From 83cf45131efd234f6ffe080f53c4e0350f0ff39e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 4 Nov 2025 12:47:24 +0100
Subject: [PATCH 0308/1827] Remove vagrant config

It was very outdated
---
 tools/vagrant/README.md    | 12 ------------
 tools/vagrant/Vagrantfile  |  9 ---------
 tools/vagrant/bootstrap.sh | 31 -------------------------------
 3 files changed, 52 deletions(-)
 delete mode 100644 tools/vagrant/README.md
 delete mode 100644 tools/vagrant/Vagrantfile
 delete mode 100644 tools/vagrant/bootstrap.sh

diff --git a/tools/vagrant/README.md b/tools/vagrant/README.md
deleted file mode 100644
index 0adb67fa67..0000000000
--- a/tools/vagrant/README.md
+++ /dev/null
@@ -1,12 +0,0 @@
-This is a basic vagrant config which you can use to compile and run BOUT++ on your local machine. For more info on vagrant see https://www.vagrantup.com/.
-
-To use it, cd into this directory and run: 
-
-	vagrant up                    # this creates the VM, installs BOUT including dependencies and runs all the tests. 
-	vagrant ssh                   # logs in to the VM.
-
-At this point you should be able to run one of the examples: 
-
-	cd BOUT/examples/conduction   # find a simple example.
-	make                          # compile the example.
-	mpirun -np 2 ./conduction     # run the example.
diff --git a/tools/vagrant/Vagrantfile b/tools/vagrant/Vagrantfile
deleted file mode 100644
index 0b0b3bc49c..0000000000
--- a/tools/vagrant/Vagrantfile
+++ /dev/null
@@ -1,9 +0,0 @@
-# -*- mode: ruby -*-
-# vi: set ft=ruby :
-
-VAGRANTFILE_API_VERSION = "2"
-
-Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
-  config.vm.box = "ubuntu/trusty64"
-  config.vm.provision :shell, path: "bootstrap.sh"
-end
diff --git a/tools/vagrant/bootstrap.sh b/tools/vagrant/bootstrap.sh
deleted file mode 100644
index 6737eac53c..0000000000
--- a/tools/vagrant/bootstrap.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env bash
-
-# install dependencies
-apt-get update
-apt-get install -y mpich2 libmpich2-dev 
-apt-get install -y libfftw3-dev libnetcdf-dev
-apt-get install -y g++ make
-apt-get install -y python-scipy
-
-# get the bout++ code
-apt-get install -y git
-rm -rf BOUT
-git clone https://github.com/bendudson/BOUT.git
-
-# environment variables for both this session and the vagrant user
-echo "export IDL_PATH=$(pwd)/BOUT/tools/idllib" >> $(pwd)/.bashrc
-echo "export PYTHONPATH=$(pwd)/BOUT/tools/pylib/:$PYTHONPATH" >> $(pwd)/.bashrc
-source $(pwd)/.bashrc
-export IDL_PATH=$(pwd)/BOUT/tools/idllib
-export PYTHONPATH=$(pwd)/BOUT/tools/pylib/:$PYTHONPATH
-
-# configure bout++
-cd BOUT
-./configure
-make
-cd examples
-./test_suite
-
-# set owner to vagrant user so compilation works
-cd ../..
-chown -R vagrant:vagrant BOUT

From bb08c43619cdd81f022e78a28a4cd3ed1b22b057 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 17 Nov 2025 19:14:11 +0000
Subject: [PATCH 0309/1827] Bump externalpackages/googletest from `244cec8` to
 `1b96fa1`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `244cec8` to `1b96fa1`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/244cec869d12e53378fa0efb610cd4c32a454ec8...1b96fa13f549387b7549cc89e1a785cf143a1a50)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: 1b96fa13f549387b7549cc89e1a785cf143a1a50
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 244cec869d..1b96fa13f5 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 244cec869d12e53378fa0efb610cd4c32a454ec8
+Subproject commit 1b96fa13f549387b7549cc89e1a785cf143a1a50

From 2f8384c5fade4c8de65497e5cef22ea7d20e29ba Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 17 Nov 2025 12:54:30 +0100
Subject: [PATCH 0310/1827] applyParallelBoundary can be a no-op for non-fci

---
 src/field/field3d.cxx | 35 ++++++++++++++++++++++++++++++-----
 1 file changed, 30 insertions(+), 5 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 0d2bc0694e..4c5ffa9748 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -478,7 +478,12 @@ void Field3D::applyParallelBoundary() {
   TRACE("Field3D::applyParallelBoundary()");
 
   checkData(*this);
-  ASSERT1(hasParallelSlices());
+  if (isFci()) {
+    ASSERT1(hasParallelSlices());
+  }
+  if (!hasParallelSlices()) {
+    return;
+  }
 
   // Apply boundary to this field
   for (const auto& bndry : getBoundaryOpPars()) {
@@ -491,7 +496,12 @@ void Field3D::applyParallelBoundary(BoutReal t) {
   TRACE("Field3D::applyParallelBoundary(t)");
 
   checkData(*this);
-  ASSERT1(hasParallelSlices());
+  if (isFci()) {
+    ASSERT1(hasParallelSlices());
+  }
+  if (!hasParallelSlices()) {
+    return;
+  }
 
   // Apply boundary to this field
   for (const auto& bndry : getBoundaryOpPars()) {
@@ -504,7 +514,12 @@ void Field3D::applyParallelBoundary(const std::string& condition) {
   TRACE("Field3D::applyParallelBoundary(condition)");
 
   checkData(*this);
-  ASSERT1(hasParallelSlices());
+  if (isFci()) {
+    ASSERT1(hasParallelSlices());
+  }
+  if (!hasParallelSlices()) {
+    return;
+  }
 
   /// Get the boundary factory (singleton)
   BoundaryFactory* bfact = BoundaryFactory::getInstance();
@@ -523,7 +538,12 @@ void Field3D::applyParallelBoundary(const std::string& region,
   TRACE("Field3D::applyParallelBoundary(region, condition)");
 
   checkData(*this);
-  ASSERT1(hasParallelSlices());
+  if (isFci()) {
+    ASSERT1(hasParallelSlices());
+  }
+  if (!hasParallelSlices()) {
+    return;
+  }
 
   /// Get the boundary factory (singleton)
   BoundaryFactory* bfact = BoundaryFactory::getInstance();
@@ -545,7 +565,12 @@ void Field3D::applyParallelBoundary(const std::string& region,
   TRACE("Field3D::applyParallelBoundary(region, condition, f)");
 
   checkData(*this);
-  ASSERT1(hasParallelSlices());
+  if (isFci()) {
+    ASSERT1(hasParallelSlices());
+  }
+  if (!hasParallelSlices()) {
+    return;
+  }
 
   /// Get the boundary factory (singleton)
   BoundaryFactory* bfact = BoundaryFactory::getInstance();

From f3882d3f02b984631326427cf82be19be5bdaf13 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Feb 2023 12:42:27 +0100
Subject: [PATCH 0311/1827] Add some asserts for non parallelised XZ
 interpolation

---
 src/mesh/interpolation/bilinear_xz.cxx       | 4 ++++
 src/mesh/interpolation/hermite_spline_xz.cxx | 4 ++--
 src/mesh/interpolation/lagrange_4pt_xz.cxx   | 4 ++++
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/mesh/interpolation/bilinear_xz.cxx b/src/mesh/interpolation/bilinear_xz.cxx
index 8445764a8f..4facdac34c 100644
--- a/src/mesh/interpolation/bilinear_xz.cxx
+++ b/src/mesh/interpolation/bilinear_xz.cxx
@@ -31,6 +31,10 @@ XZBilinear::XZBilinear(int y_offset, Mesh* mesh)
     : XZInterpolation(y_offset, mesh), w0(localmesh), w1(localmesh), w2(localmesh),
       w3(localmesh) {
 
+  if (localmesh->getNXPE() > 1) {
+    throw BoutException("Do not support MPI splitting in X");
+  }
+
   // Index arrays contain guard cells in order to get subscripts right
   i_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
   k_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index c0040d096e..165d387d66 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -101,8 +101,8 @@ class IndConverter {
   }
 };
 
-XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* mesh)
-    : XZInterpolation(y_offset, mesh), h00_x(localmesh), h01_x(localmesh),
+XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* meshin)
+    : XZInterpolation(y_offset, meshin), h00_x(localmesh), h01_x(localmesh),
       h10_x(localmesh), h11_x(localmesh), h00_z(localmesh), h01_z(localmesh),
       h10_z(localmesh), h11_z(localmesh) {
 
diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx
index 92c14ecfd5..8fa201ba72 100644
--- a/src/mesh/interpolation/lagrange_4pt_xz.cxx
+++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx
@@ -29,6 +29,10 @@
 XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh* mesh)
     : XZInterpolation(y_offset, mesh), t_x(localmesh), t_z(localmesh) {
 
+  if (localmesh->getNXPE() > 1) {
+    throw BoutException("Do not support MPI splitting in X");
+  }
+
   // Index arrays contain guard cells in order to get subscripts right
   i_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
   k_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);

From d1c137f01f0f53cdefcdbb9789c43ef384da30ab Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Jul 2024 15:38:01 +0200
Subject: [PATCH 0312/1827] Add option to disable tracking

---
 include/bout/field3d.hxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 8866f17b49..ac2baf56ba 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -302,6 +302,13 @@ public:
     return *this;
   }
 
+  /// Disable tracking
+  Field3D& disableTracking() {
+    tracking = nullptr;
+    tracking_state = 0;
+    return *this;
+  }
+
   /////////////////////////////////////////////////////////
   // Data access
 

From ee8a9d6b5ac711a78507c292757f14e57c69b0ef Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Tue, 18 Nov 2025 15:01:45 +0000
Subject: [PATCH 0313/1827] Apply clang-format changes

---
 include/bout/invertable_operator.hxx |  4 ++--
 src/bout++.cxx                       |  2 +-
 src/field/field3d.cxx                |  4 ++--
 src/solver/impls/arkode/arkode.cxx   |  6 ++----
 src/solver/impls/snes/snes.hxx       | 14 +++++++-------
 5 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx
index fe139986be..99f7d9b675 100644
--- a/include/bout/invertable_operator.hxx
+++ b/include/bout/invertable_operator.hxx
@@ -575,7 +575,7 @@ public:
 };
 
 #endif // PETSC
-};     // namespace inversion
-};     // namespace bout
+}; // namespace inversion
+}; // namespace bout
 
 #endif // HEADER GUARD
diff --git a/src/bout++.cxx b/src/bout++.cxx
index 7f23cf5f91..4e9e37fe8d 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -84,7 +84,7 @@ const char DEFAULT_DIR[] = "data";
 // Define S_ISDIR if not defined by system headers (that is, MSVC)
 // Taken from https://github.com/curl/curl/blob/e59540139a398dc70fde6aec487b19c5085105af/lib/curl_setup.h#L748-L751
 #if !defined(S_ISDIR) && defined(S_IFMT) && defined(S_IFDIR)
-#define S_ISDIR(m) (((m)&S_IFMT) == S_IFDIR)
+#define S_ISDIR(m) (((m) & S_IFMT) == S_IFDIR)
 #endif
 
 #ifdef _MSC_VER
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 1eeb0dd344..17571ea4c1 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -869,9 +869,9 @@ void Field3D::_track(const T& change, std::string operation) {
   const std::string changename = change.name;
 #endif
   (*locked)[outname].setAttributes({
-    {"operation", operation},
+      {"operation", operation},
 #if BOUT_USE_TRACK
-        {"rhs.name", changename},
+      {"rhs.name", changename},
 #endif
   });
 }
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 23883cc043..02f2cb7b81 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -229,8 +229,7 @@ int ArkodeSolver::init() {
     throw BoutException("ARKodeSetUserData failed\n");
   }
 
-  if (ARKodeSetLinear(arkode_mem, static_cast<int>(set_linear))
-      != ARK_SUCCESS) {
+  if (ARKodeSetLinear(arkode_mem, static_cast<int>(set_linear)) != ARK_SUCCESS) {
     throw BoutException("ARKodeSetLinear failed\n");
   }
 
@@ -415,8 +414,7 @@ int ArkodeSolver::init() {
         if (hasPreconditioner()) {
           output.write("\tUsing user-supplied preconditioner\n");
 
-          if (ARKodeSetPreconditioner(arkode_mem, nullptr, arkode_pre)
-              != ARKLS_SUCCESS) {
+          if (ARKodeSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARKLS_SUCCESS) {
             throw BoutException("ARKodeSetPreconditioner failed\n");
           }
         } else {
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 17050ad775..f695ba3718 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -121,9 +121,9 @@ private:
   Vec x1;               ///< Previous solution
   BoutReal time1{-1.0}; ///< Time of previous solution
 
-  SNES snes;                ///< SNES context
-  Mat Jmf;                  ///< Matrix Free Jacobian
-  Mat Jfd;                  ///< Finite Difference Jacobian
+  SNES snes;                         ///< SNES context
+  Mat Jmf;                           ///< Matrix Free Jacobian
+  Mat Jfd;                           ///< Finite Difference Jacobian
   MatFDColoring fdcoloring{nullptr}; ///< Matrix coloring context
                                      ///< Jacobian evaluation
 
@@ -135,10 +135,10 @@ private:
   std::string pc_hypre_type;      ///< Hypre preconditioner type
   std::string line_search_type;   ///< Line search type
 
-  bool matrix_free;               ///< Use matrix free Jacobian
-  bool matrix_free_operator;      ///< Use matrix free Jacobian in the operator?
-  int lag_jacobian;               ///< Re-use Jacobian
-  bool use_coloring;              ///< Use matrix coloring
+  bool matrix_free;          ///< Use matrix free Jacobian
+  bool matrix_free_operator; ///< Use matrix free Jacobian in the operator?
+  int lag_jacobian;          ///< Re-use Jacobian
+  bool use_coloring;         ///< Use matrix coloring
 
   bool jacobian_recalculated; ///< Flag set when Jacobian is recalculated
   bool prune_jacobian;        ///< Remove small elements in the Jacobian?

From cfe4d40085f21348367b99ab13f674342964c74b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 11:56:57 +0200
Subject: [PATCH 0314/1827] Always set region for hermite_spline_xz

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 165d387d66..69df6d8906 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -346,6 +346,8 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
 
+  const auto region2 = fmt::format("RGN_YPAR_{:+d}", y_offset);
+
 #if USE_NEW_WEIGHTS
 #ifdef HS_USE_PETSC
   BoutReal* ptr;
@@ -355,7 +357,6 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   VecRestoreArray(rhs, &ptr);
   MatMult(petscWeights, rhs, result);
   VecGetArrayRead(result, &cptr);
-  const auto region2 = y_offset == 0 ? region : fmt::format("RGN_YPAR_{:+d}", y_offset);
   BOUT_FOR(i, f.getRegion(region2)) {
     f_interp[i] = cptr[int(i)];
     ASSERT2(std::isfinite(cptr[int(i)]));
@@ -375,11 +376,10 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
     }
   }
 #endif
-  return f_interp;
 #else
   // Derivatives are used for tension and need to be on dimensionless
   // coordinates
-  const auto region2 = fmt::format("RGN_YPAR_{:+d}", y_offset);
+
   // f has been communcated, and thus we can assume that the x-boundaries are
   // also valid in the y-boundary.  Thus the differentiated field needs no
   // extra comms.
@@ -418,8 +418,10 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
     ASSERT2(std::isfinite(f_interp[iyp]) || i.x() < localmesh->xstart
             || i.x() > localmesh->xend);
   }
-  return f_interp;
 #endif
+  f_interp.setRegion(region2);
+  ASSERT2(f_interp.getRegionID());
+  return f_interp;
 }
 
 Field3D XZHermiteSpline::interpolate(const Field3D& f, const Field3D& delta_x,

From cdaa62623ac60676e4fefefc94bbf67d3b5e8ea6 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 18 Nov 2025 13:39:46 +0000
Subject: [PATCH 0315/1827] Add helper function for `Options::as` for
 `Array/Matrix/Tensor`

---
 include/bout/sys/type_name.hxx |  19 +++++
 src/sys/options.cxx            | 139 +++++++++------------------------
 src/sys/type_name.cxx          |  26 ++++++
 3 files changed, 80 insertions(+), 104 deletions(-)

diff --git a/include/bout/sys/type_name.hxx b/include/bout/sys/type_name.hxx
index be4d096b4d..ff2ccfc8fd 100644
--- a/include/bout/sys/type_name.hxx
+++ b/include/bout/sys/type_name.hxx
@@ -4,13 +4,19 @@
 #ifndef TYPE_NAME_HXX
 #define TYPE_NAME_HXX
 
+#include "bout/array.hxx"
 #include "bout/bout_types.hxx"
+
 #include <string>
 #include <typeinfo>
 
 class Field2D;
 class Field3D;
 class FieldPerp;
+template<class T>
+class Matrix;
+template<class T>
+class Tensor;
 
 namespace bout {
 namespace utils {
@@ -41,6 +47,19 @@ std::string typeName<Field3D>();
 
 template <>
 std::string typeName<FieldPerp>();
+
+template <>
+std::string typeName<Array<int>>();
+template <>
+std::string typeName<Array<BoutReal>>();
+template <>
+std::string typeName<Matrix<int>>();
+template <>
+std::string typeName<Matrix<BoutReal>>();
+template <>
+std::string typeName<Tensor<int>>();
+template <>
+std::string typeName<Tensor<BoutReal>>();
 } // namespace utils
 } // namespace bout
 
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 387a851f3b..077b2a6d85 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -754,138 +754,69 @@ struct ConvertContainer {
 };
 } // namespace
 
-template <>
-Array<BoutReal> Options::as<Array<BoutReal>>(const Array<BoutReal>& similar_to) const {
-  if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
+namespace {
+// `Options::as` helper for `Array`, `Matrix`, `Tensor` (amt)
+template <class T>
+T as_amt(const Options& self, const T& similar_to) {
+  if (self.isSection()) {
+    throw BoutException(_("Option {:s} has no value"), self.str());
   }
 
-  Array<BoutReal> result = bout::utils::visit(
-      ConvertContainer<Array<BoutReal>>{
-          fmt::format(
-              _("Value for option {:s} cannot be converted to an Array<BoutReal>"),
-              full_name),
+  const T result = bout::utils::visit(
+      ConvertContainer<T>{
+          fmt::format(_("Value for option {:s} cannot be converted to an {}"), self.str(),
+                      bout::utils::typeName<T>()),
           similar_to},
-      value);
+      self.value);
 
-  // Mark this option as used
-  value_used = true;
+  printNameValueSourceLine(self, bout::utils::typeName<T>());
 
-  printNameValueSourceLine(*this, "Array<BoutReal>");
+  output_info.write("{} {} = {}", _("\tOption "), self.str(), bout::utils::typeName<T>());
+  if (self.hasAttribute("source")) {
+    // Specify the source of the setting
+    output_info.write(" ({})",
+                      bout::utils::variantToString(self.attributes.at("source")));
+  }
+  output_info.write("\n");
 
   return result;
 }
+} // namespace
 
 template <>
-Array<int> Options::as<Array<int>>(const Array<int>& similar_to) const {
-  if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
-  }
-
-  Array<int> result = bout::utils::visit(
-      ConvertContainer<Array<int>>{
-          fmt::format(_("Value for option {:s} cannot be converted to an Array<int>"),
-                      full_name),
-          similar_to},
-      value);
-
-  // Mark this option as used
+auto Options::as(const Array<BoutReal>& similar_to) const -> Array<BoutReal> {
   value_used = true;
-
-  output_info << _("\tOption ") << full_name << " = Array<int>";
-  if (hasAttribute("source")) {
-    // Specify the source of the setting
-    output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
-  }
-  output_info << endl;
-
-  return result;
+  return as_amt(*this, similar_to);
 }
 
 template <>
-Matrix<BoutReal> Options::as<Matrix<BoutReal>>(const Matrix<BoutReal>& similar_to) const {
-  if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
-  }
-
-  auto result = bout::utils::visit(
-      ConvertContainer<Matrix<BoutReal>>{
-          fmt::format(
-              _("Value for option {:s} cannot be converted to an Matrix<BoutReal>"),
-              full_name),
-          similar_to},
-      value);
-
-  // Mark this option as used
+auto Options::as(const Array<int>& similar_to) const -> Array<int> {
   value_used = true;
-
-  printNameValueSourceLine(*this, "Matrix<BoutReal>");
-
-  return result;
+  return as_amt(*this, similar_to);
 }
 
 template <>
-Matrix<int> Options::as<Matrix<int>>(const Matrix<int>& similar_to) const {
-  if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
-  }
-
-  auto result = bout::utils::visit(
-      ConvertContainer<Matrix<int>>{
-          fmt::format(_("Value for option {:s} cannot be converted to an Matrix<int>"),
-                      full_name),
-          similar_to},
-      value);
-
-  // Mark this option as used
+auto Options::as(const Matrix<BoutReal>& similar_to) const -> Matrix<BoutReal> {
   value_used = true;
-
-  printNameValueSourceLine(*this, "Matrix<int>");
-
-  return result;
+  return as_amt(*this, similar_to);
 }
 
 template <>
-Tensor<BoutReal> Options::as<Tensor<BoutReal>>(const Tensor<BoutReal>& similar_to) const {
-  if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
-  }
-
-  auto result = bout::utils::visit(
-      ConvertContainer<Tensor<BoutReal>>{
-          fmt::format(
-              _("Value for option {:s} cannot be converted to an Tensor<BoutReal>"),
-              full_name),
-          similar_to},
-      value);
-
-  // Mark this option as used
+auto Options::as(const Matrix<int>& similar_to) const -> Matrix<int> {
   value_used = true;
-
-  printNameValueSourceLine(*this, "Tensor<BoutReal>");
-
-  return result;
+  return as_amt(*this, similar_to);
 }
 
 template <>
-Tensor<int> Options::as<Tensor<int>>(const Tensor<int>& similar_to) const {
-  if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
-  }
-
-  auto result = bout::utils::visit(
-      ConvertContainer<Tensor<int>>{
-          fmt::format(_("Value for option {:s} cannot be converted to an Tensor<int>"),
-                      full_name),
-          similar_to},
-      value);
-
-  // Mark this option as used
+auto Options::as(const Tensor<BoutReal>& similar_to) const -> Tensor<BoutReal> {
   value_used = true;
+  return as_amt(*this, similar_to);
+}
 
-  printNameValueSourceLine(*this, "Tensor<int>");
-
-  return result;
+template <>
+auto Options::as(const Tensor<int>& similar_to) const -> Tensor<int> {
+  value_used = true;
+  return as_amt(*this, similar_to);
 }
 
 // Note: This is defined here rather than in the header
diff --git a/src/sys/type_name.cxx b/src/sys/type_name.cxx
index c1082c499a..68272bd473 100644
--- a/src/sys/type_name.cxx
+++ b/src/sys/type_name.cxx
@@ -41,5 +41,31 @@ template <>
 std::string typeName<FieldPerp>() {
   return "FieldPerp";
 }
+
+template <>
+std::string typeName<Array<int>>() {
+  return "Array<int>";
+}
+template <>
+std::string typeName<Array<BoutReal>>() {
+  return "Array<BoutReal>";
+}
+template <>
+std::string typeName<Matrix<int>>() {
+  return "Matrix<int>";
+}
+template <>
+std::string typeName<Matrix<BoutReal>>() {
+  return "Matrix<BoutReal>";
+}
+template <>
+std::string typeName<Tensor<int>>() {
+  return "Tensor<int>";
+}
+template <>
+std::string typeName<Tensor<BoutReal>>() {
+  return "Tensor<BoutReal>";
+}
+
 } // namespace utils
 } // namespace bout

From da418b17fa00464cf21c8635f86412eaa14b347e Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 18 Nov 2025 13:40:30 +0000
Subject: [PATCH 0316/1827] Remove unnecessary template argument from
 specialisations

---
 include/bout/options.hxx | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index f53faeea7c..7bad26d990 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -982,31 +982,31 @@ inline bool Options::similar<BoutReal>(BoutReal lhs, BoutReal rhs) const {
 
 /// Specialised as routines
 template <>
-std::string Options::as<std::string>(const std::string& similar_to) const;
+auto Options::as(const std::string& similar_to) const -> std::string;
 template <>
-int Options::as<int>(const int& similar_to) const;
+auto Options::as(const int& similar_to) const -> int;
 template <>
-BoutReal Options::as<BoutReal>(const BoutReal& similar_to) const;
+auto Options::as(const BoutReal& similar_to) const -> BoutReal;
 template <>
-bool Options::as<bool>(const bool& similar_to) const;
+auto Options::as(const bool& similar_to) const -> bool;
 template <>
-Field2D Options::as<Field2D>(const Field2D& similar_to) const;
+auto Options::as(const Field2D& similar_to) const -> Field2D;
 template <>
-Field3D Options::as<Field3D>(const Field3D& similar_to) const;
+auto Options::as(const Field3D& similar_to) const -> Field3D;
 template <>
-FieldPerp Options::as<FieldPerp>(const FieldPerp& similar_to) const;
+auto Options::as(const FieldPerp& similar_to) const -> FieldPerp;
 template <>
-Array<BoutReal> Options::as<Array<BoutReal>>(const Array<BoutReal>& similar_to) const;
+auto Options::as(const Array<BoutReal>& similar_to) const -> Array<BoutReal>;
 template <>
-Array<int> Options::as<Array<int>>(const Array<int>& similar_to) const;
+auto Options::as(const Array<int>& similar_to) const -> Array<int>;
 template <>
-Matrix<BoutReal> Options::as<Matrix<BoutReal>>(const Matrix<BoutReal>& similar_to) const;
+auto Options::as(const Matrix<BoutReal>& similar_to) const -> Matrix<BoutReal>;
 template <>
-Matrix<int> Options::as<Matrix<int>>(const Matrix<int>& similar_to) const;
+auto Options::as(const Matrix<int>& similar_to) const -> Matrix<int>;
 template <>
-Tensor<BoutReal> Options::as<Tensor<BoutReal>>(const Tensor<BoutReal>& similar_to) const;
+auto Options::as(const Tensor<BoutReal>& similar_to) const -> Tensor<BoutReal>;
 template <>
-Tensor<int> Options::as<Tensor<int>>(const Tensor<int>& similar_to) const;
+auto Options::as(const Tensor<int>& similar_to) const -> Tensor<int>;
 
 /// Convert \p value to string
 std::string toString(const Options& value);

From 1adfb2f6061837c2c03792932b668e69613299e9 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 18 Nov 2025 15:28:13 +0000
Subject: [PATCH 0317/1827] Reduce duplication in `ADIOSPutVarVisitor` for
 `Array/Matrix/Tensor`

---
 include/bout/adios_object.hxx     |   6 +-
 include/bout/array.hxx            |   4 +
 src/sys/options/options_adios.cxx | 133 ++++++++++++------------------
 3 files changed, 59 insertions(+), 84 deletions(-)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 12da8ce4c7..07482a0dcb 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -57,9 +57,9 @@ public:
   }
 
   template <class T>
-  adios2::Variable<T> GetArrayVariable(const std::string& varname, adios2::Dims& shape,
-                                       const std::vector<std::string>& dimNames,
-                                       int rank) {
+  adios2::Variable<T>
+  GetArrayVariable(const std::string& varname, const adios2::Dims& shape,
+                   const std::vector<std::string>& dimNames, int rank) {
     adios2::Variable<T> v = io.InquireVariable<T>(varname);
     if (!v) {
       adios2::Dims start(shape.size());
diff --git a/include/bout/array.hxx b/include/bout/array.hxx
index 2c42f15aad..2305fe3b22 100644
--- a/include/bout/array.hxx
+++ b/include/bout/array.hxx
@@ -29,6 +29,7 @@
 #include <algorithm>
 #include <map>
 #include <memory>
+#include <tuple>
 #include <vector>
 
 #if BOUT_USE_OPENMP
@@ -283,6 +284,9 @@ public:
     return ptr->size();
   }
 
+  /// Return shape of the array (the `size()` in a length-1 tuple)
+  std::tuple<size_type> shape() const { return std::make_tuple(size()); };
+
   /*!
    * Returns true if the data is unique to this Array.
    *
diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 06353a1de8..9be064ec19 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -12,8 +12,11 @@
 #include "bout/sys/timer.hxx"
 
 #include "adios2.h"
+
+#include <cstddef>
 #include <exception>
-#include <iostream>
+#include <tuple>
+#include <utility>
 #include <vector>
 
 namespace bout {
@@ -313,6 +316,38 @@ const std::vector<std::string> DIMS_XY = {"x", "y"};
 const std::vector<std::string> DIMS_XZ = {"x", "z"};
 const std::vector<std::string> DIMS_XYZ = {"x", "y", "z"};
 
+namespace {
+template <typename T>
+using tuple_index_sequence = std::make_index_sequence<std::tuple_size_v<T>>;
+
+template <class Tuple, std::size_t... I>
+auto make_shape_impl(std::size_t first, Tuple&& t,
+                     std::index_sequence<I...> /* index */) {
+  return adios2::Dims{first,
+                      static_cast<std::size_t>(std::get<I>(std::forward<Tuple>(t)))...};
+}
+// Return an `adios2::Dims` with value ``{first, value.shape()[0]...}``
+template <class T>
+auto make_shape(std::size_t first, const T& value) {
+  const auto shape = value.shape();
+  return make_shape_impl(first, shape, tuple_index_sequence<decltype(shape)>{});
+}
+
+template <class Tuple, std::size_t... I>
+auto make_start_impl(Tuple&& t, std::index_sequence<I...> /* index */) {
+  // Hey look, a legitimate use of the comma operator to get a bunch
+  // of zeros the length of the index_sequence!
+  return adios2::Dims{static_cast<std::size_t>(BoutComm::rank()),
+                      (std::get<I>(std::forward<Tuple>(t)), std::size_t{0})...};
+}
+// Return an `adios2::Dims` with value ``{rank, 0...}``, with as many zeros as the dimension of ``T``
+template <class T>
+auto make_start(const T& value) {
+  const auto shape = value.shape();
+  return make_start_impl(shape, tuple_index_sequence<decltype(shape)>{});
+}
+} // namespace
+
 /// Visit a variant type, and put the data into a NcVar
 struct ADIOSPutVarVisitor {
   ADIOSPutVarVisitor(const std::string& name, ADIOSStream& stream)
@@ -323,9 +358,25 @@ struct ADIOSPutVarVisitor {
     stream.engine.Put(var, value);
   }
 
+  void operator()(const Array<int>& value) { put_helper(value); }
+  void operator()(const Array<BoutReal>& value) { put_helper(value); }
+  void operator()(const Matrix<int>& value) { put_helper(value); }
+  void operator()(const Matrix<BoutReal>& value) { put_helper(value); }
+  void operator()(const Tensor<int>& value) { put_helper(value); }
+  void operator()(const Tensor<BoutReal>& value) { put_helper(value); }
+
 private:
   const std::string& varname;
   ADIOSStream& stream;
+
+  // helper for `Array`, `Matrix`, `Tensor`
+  template <template <class> class T, class U>
+  void put_helper(const T<U>& value) {
+    const auto shape = make_shape(static_cast<std::size_t>(BoutComm::size()), value);
+    auto var = stream.GetArrayVariable<U>(varname, shape, DIMS_NONE, BoutComm::rank());
+    var.SetSelection({make_start(value), make_shape(1, value)});
+    stream.engine.Put<U>(var, value.begin());
+  }
 };
 
 template <>
@@ -472,86 +523,6 @@ void ADIOSPutVarVisitor::operator()<FieldPerp>(const FieldPerp& value) {
   stream.engine.Put<BoutReal>(var, &value(0, 0));
 }
 
-template <>
-void ADIOSPutVarVisitor::operator()<Array<int>>(const Array<int>& value) {
-  // Pointer to data. Assumed to be contiguous array
-  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.size()};
-  adios2::Dims start = {(size_t)BoutComm::rank(), 0};
-  adios2::Dims count = {1, shape[1]};
-  adios2::Variable<int> var =
-      stream.GetArrayVariable<int>(varname, shape, DIMS_NONE, BoutComm::rank());
-  var.SetSelection({start, count});
-  stream.engine.Put<int>(var, value.begin());
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<Array<BoutReal>>(const Array<BoutReal>& value) {
-  // Pointer to data. Assumed to be contiguous array
-  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)value.size()};
-  adios2::Dims start = {(size_t)BoutComm::rank(), 0};
-  adios2::Dims count = {1, shape[1]};
-  adios2::Variable<BoutReal> var =
-      stream.GetArrayVariable<BoutReal>(varname, shape, DIMS_NONE, BoutComm::rank());
-  var.SetSelection({start, count});
-  stream.engine.Put<BoutReal>(var, value.begin());
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<Matrix<int>>(const Matrix<int>& value) {
-  // Pointer to data. Assumed to be contiguous array
-  auto s = value.shape();
-  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s),
-                        (size_t)std::get<1>(s)};
-  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0};
-  adios2::Dims count = {1, shape[1], shape[2]};
-  adios2::Variable<int> var =
-      stream.GetArrayVariable<int>(varname, shape, DIMS_NONE, BoutComm::rank());
-  var.SetSelection({start, count});
-  stream.engine.Put<int>(var, value.begin());
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<Matrix<BoutReal>>(const Matrix<BoutReal>& value) {
-  // Pointer to data. Assumed to be contiguous array
-  auto s = value.shape();
-  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s),
-                        (size_t)std::get<1>(s)};
-  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0};
-  adios2::Dims count = {1, shape[1], shape[2]};
-  adios2::Variable<BoutReal> var =
-      stream.GetArrayVariable<BoutReal>(varname, shape, DIMS_NONE, BoutComm::rank());
-  var.SetSelection({start, count});
-  stream.engine.Put<BoutReal>(var, value.begin());
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<Tensor<int>>(const Tensor<int>& value) {
-  // Pointer to data. Assumed to be contiguous array
-  auto s = value.shape();
-  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s),
-                        (size_t)std::get<1>(s), (size_t)std::get<2>(s)};
-  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0};
-  adios2::Dims count = {1, shape[1], shape[2], shape[3]};
-  adios2::Variable<int> var =
-      stream.GetArrayVariable<int>(varname, shape, DIMS_NONE, BoutComm::rank());
-  var.SetSelection({start, count});
-  stream.engine.Put<int>(var, value.begin());
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<Tensor<BoutReal>>(const Tensor<BoutReal>& value) {
-  // Pointer to data. Assumed to be contiguous array
-  auto s = value.shape();
-  adios2::Dims shape = {(size_t)BoutComm::size(), (size_t)std::get<0>(s),
-                        (size_t)std::get<1>(s), (size_t)std::get<2>(s)};
-  adios2::Dims start = {(size_t)BoutComm::rank(), 0, 0, 0};
-  adios2::Dims count = {1, shape[1], shape[2], shape[3]};
-  adios2::Variable<BoutReal> var =
-      stream.GetArrayVariable<BoutReal>(varname, shape, DIMS_NONE, BoutComm::rank());
-  var.SetSelection({start, count});
-  stream.engine.Put<BoutReal>(var, value.begin());
-}
-
 /// Visit a variant type, and put the data into a NcVar
 struct ADIOSPutAttVisitor {
   ADIOSPutAttVisitor(const std::string& varname, const std::string& attrname,

From f09c14cb1c5a1dac4baacb870558604111aa48ee Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 18 Nov 2025 17:32:06 +0000
Subject: [PATCH 0318/1827] Support `Array/Matrix/Tensor<int>` in
 `OptionsNetCDF`

---
 include/bout/sys/type_name.hxx                |  4 +-
 include/bout/traits.hxx                       |  5 ++
 src/sys/options/options_adios.cxx             |  4 +-
 src/sys/options/options_netcdf.cxx            | 87 +++++++++++++++----
 .../test-options-adios/test-options-adios.cxx | 32 +++++--
 tests/unit/sys/test_options.cxx               | 18 ++++
 tests/unit/sys/test_options_netcdf.cxx        | 24 +++++
 7 files changed, 146 insertions(+), 28 deletions(-)

diff --git a/include/bout/sys/type_name.hxx b/include/bout/sys/type_name.hxx
index ff2ccfc8fd..fcd251bf7a 100644
--- a/include/bout/sys/type_name.hxx
+++ b/include/bout/sys/type_name.hxx
@@ -13,9 +13,9 @@
 class Field2D;
 class Field3D;
 class FieldPerp;
-template<class T>
+template <class T>
 class Matrix;
-template<class T>
+template <class T>
 class Tensor;
 
 namespace bout {
diff --git a/include/bout/traits.hxx b/include/bout/traits.hxx
index 4e03d6b526..5796c65879 100644
--- a/include/bout/traits.hxx
+++ b/include/bout/traits.hxx
@@ -1,6 +1,7 @@
 #ifndef BOUT_TRAITS_H
 #define BOUT_TRAITS_H
 
+#include <tuple>
 #include <type_traits>
 
 class Field;
@@ -112,6 +113,10 @@ using EnableIfFieldPerp =
 /// Enable a function if T is a subclass of Options
 template <class T>
 using EnableIfOptions = std::enable_if_t<std::is_base_of_v<Options, T>>;
+
+/// Create a `std::index_sequence` with the length of a tuple ``T``
+template <typename T>
+using tuple_index_sequence = std::make_index_sequence<std::tuple_size_v<T>>;
 } // namespace utils
 } // namespace bout
 
diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 9be064ec19..4a41a014eb 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -1,4 +1,5 @@
 #include "bout/build_defines.hxx"
+#include "bout/traits.hxx"
 
 #if BOUT_HAS_ADIOS2
 
@@ -317,8 +318,7 @@ const std::vector<std::string> DIMS_XZ = {"x", "z"};
 const std::vector<std::string> DIMS_XYZ = {"x", "y", "z"};
 
 namespace {
-template <typename T>
-using tuple_index_sequence = std::make_index_sequence<std::tuple_size_v<T>>;
+using bout::utils::tuple_index_sequence;
 
 template <class Tuple, std::size_t... I>
 auto make_shape_impl(std::size_t first, Tuple&& t,
diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx
index 12be01a25b..f6edb26dbc 100644
--- a/src/sys/options/options_netcdf.cxx
+++ b/src/sys/options/options_netcdf.cxx
@@ -5,13 +5,15 @@
 #include "options_netcdf.hxx"
 
 #include "bout/bout.hxx"
-#include "bout/globals.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/mesh.hxx"
 #include "bout/sys/timer.hxx"
+#include "bout/traits.hxx"
+
+#include <fmt/format.h>
 
 #include <climits>
 #include <exception>
-#include <iostream>
 #include <netcdf>
 #include <vector>
 
@@ -108,6 +110,11 @@ void readGroup(const std::string& filename, const NcGroup& group, Options& resul
                              static_cast<int>(dims[1].getSize()));
         var.getVar(value.begin());
         result[var_name] = value;
+      } else if (var_type == ncInt) {
+        Matrix<int> value(static_cast<int>(dims[0].getSize()),
+                          static_cast<int>(dims[1].getSize()));
+        var.getVar(value.begin());
+        result[var_name] = value;
       }
       break;
     }
@@ -217,6 +224,13 @@ struct NcTypeVisitor {
   NcType operator()(const T& UNUSED(t)) {
     return {}; // Null object by default
   }
+
+  NcType operator()([[maybe_unused]] const Array<int>& t) { return ncInt; }
+  NcType operator()([[maybe_unused]] const Array<BoutReal>& t) { return ncDouble; }
+  NcType operator()([[maybe_unused]] const Matrix<int>& t) { return ncInt; }
+  NcType operator()([[maybe_unused]] const Matrix<BoutReal>& t) { return ncDouble; }
+  NcType operator()([[maybe_unused]] const Tensor<int>& t) { return ncInt; }
+  NcType operator()([[maybe_unused]] const Tensor<BoutReal>& t) { return ncDouble; }
 };
 
 template <>
@@ -259,20 +273,9 @@ NcType NcTypeVisitor::operator()<FieldPerp>(const FieldPerp& UNUSED(t)) {
   return operator()<BoutReal>(0.0);
 }
 
-/// Visit a variant type, returning dimensions
-struct NcDimVisitor {
-  NcDimVisitor(NcGroup& group) : group(group) {}
-  template <typename T>
-  std::vector<NcDim> operator()(const T& UNUSED(value)) {
-    return {};
-  }
-
-private:
-  NcGroup& group;
-};
-
+namespace {
+// Find dimension with name and size in group, creating it if it doesn't exist
 NcDim findDimension(NcGroup& group, const std::string& name, unsigned int size) {
-  // Get the dimension
   try {
     auto dim = group.getDim(name, NcGroup::ParentsAndCurrent);
     if (dim.isNull()) {
@@ -297,6 +300,40 @@ NcDim findDimension(NcGroup& group, const std::string& name, unsigned int size)
   }
 }
 
+using bout::utils::tuple_index_sequence;
+
+template <class Tuple, std::size_t... I>
+auto make_dims_impl(NcGroup& group, Tuple&& t, std::index_sequence<I...> /* index */) {
+  return std::vector{findDimension(group, fmt::format("dim_{}", I),
+                                   std::get<I>(std::forward<Tuple>(t)))...};
+}
+// Help get the dimensions for `Array`, `Matrix`, `Tensor` (amt)
+template <class T>
+auto make_amt_dims(NcGroup& group, const T& value) {
+  const auto shape = value.shape();
+  return make_dims_impl(group, shape, tuple_index_sequence<decltype(shape)>{});
+}
+} // namespace
+
+/// Visit a variant type, returning dimensions
+struct NcDimVisitor {
+  NcDimVisitor(NcGroup& group) : group(group) {}
+  template <typename T>
+  std::vector<NcDim> operator()(const T& UNUSED(value)) {
+    return {};
+  }
+
+  auto operator()(const Array<int>& value) { return make_amt_dims(group, value); }
+  auto operator()(const Array<BoutReal>& value) { return make_amt_dims(group, value); }
+  auto operator()(const Matrix<int>& value) { return make_amt_dims(group, value); }
+  auto operator()(const Matrix<BoutReal>& value) { return make_amt_dims(group, value); }
+  auto operator()(const Tensor<int>& value) { return make_amt_dims(group, value); }
+  auto operator()(const Tensor<BoutReal>& value) { return make_amt_dims(group, value); }
+
+private:
+  NcGroup& group;
+};
+
 template <>
 std::vector<NcDim> NcDimVisitor::operator()<Field2D>(const Field2D& value) {
   auto xdim = findDimension(group, "x", value.getNx());
@@ -341,6 +378,13 @@ struct NcPutVarVisitor {
     var.putVar(&value);
   }
 
+  void operator()(const Array<int>& value) { var.putVar(value.begin()); }
+  void operator()(const Array<BoutReal>& value) { var.putVar(value.begin()); }
+  void operator()(const Matrix<int>& value) { var.putVar(value.begin()); }
+  void operator()(const Matrix<BoutReal>& value) { var.putVar(value.begin()); }
+  void operator()(const Tensor<int>& value) { var.putVar(value.begin()); }
+  void operator()(const Tensor<BoutReal>& value) { var.putVar(value.begin()); }
+
 private:
   NcVar& var;
 };
@@ -387,6 +431,19 @@ struct NcPutVarCountVisitor {
     var.putVar(start, &value);
   }
 
+  void operator()(const Array<int>& value) { var.putVar(start, count, value.begin()); }
+  void operator()(const Array<BoutReal>& value) {
+    var.putVar(start, count, value.begin());
+  }
+  void operator()(const Matrix<int>& value) { var.putVar(start, count, value.begin()); }
+  void operator()(const Matrix<BoutReal>& value) {
+    var.putVar(start, count, value.begin());
+  }
+  void operator()(const Tensor<int>& value) { var.putVar(start, count, value.begin()); }
+  void operator()(const Tensor<BoutReal>& value) {
+    var.putVar(start, count, value.begin());
+  }
+
 private:
   NcVar& var;
   const std::vector<size_t>& start; ///< Starting (corner) index
diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx
index 60604e1aa3..ba0bbe3898 100644
--- a/tests/integrated/test-options-adios/test-options-adios.cxx
+++ b/tests/integrated/test-options-adios/test-options-adios.cxx
@@ -3,6 +3,7 @@
 
 #include "bout/options_io.hxx"
 #include "bout/optionsreader.hxx"
+#include "bout/utils.hxx"
 
 using bout::OptionsIO;
 
@@ -45,18 +46,31 @@ int main(int argc, char** argv) {
   ///////////////////////////
   // Write fields
 
-  Options fields;
-  fields["f2d"] = Field2D(1.0);
-  fields["f3d"] = Field3D(2.0);
-  fields["fperp"] = FieldPerp(3.0);
-  auto f = OptionsIO::create({{"file", "fields.bp"}, {"type", "adios"}});
-  /*
+  {
+    constexpr int nx = 2;
+    constexpr int ny = 3;
+    Matrix<int> matrix_in(nx, ny);
+    int count = 0;
+
+    for (int i = 0; i < nx; ++i) {
+      for (int j = 0; j < ny; ++j) {
+        matrix_in(i, j) = ++count;
+      }
+    }
+
+    Options fields{{"f2d", Field2D(1.0)},
+                   {"f3d", Field3D(2.0)},
+                   {"fperp", FieldPerp(3.0)},
+                   {"matrix", matrix_in}};
+    auto f = OptionsIO::create({{"file", "fields.bp"}, {"type", "adios"}});
+    /*
      write() for adios only buffers data but does not guarantee writing to disk
      unless singleWriteFile is set to true 
      */
-  f->write(fields);
-  // indicate completion of step, required to get data on disk
-  f->verifyTimesteps();
+    f->write(fields);
+    // indicate completion of step, required to get data on disk
+    f->verifyTimesteps();
+  }
 
   ///////////////////////////
   // Read fields
diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx
index 67e405953d..b74cfdcb9f 100644
--- a/tests/unit/sys/test_options.cxx
+++ b/tests/unit/sys/test_options.cxx
@@ -1450,3 +1450,21 @@ TEST_F(OptionsTest, Iterate) {
   ASSERT_EQ(option["value1"], 2);
   ASSERT_EQ(option["value2"], 3);
 }
+
+TEST_F(OptionsTest, MatrixInt) {
+  constexpr int nx = 2;
+  constexpr int ny = 3;
+  Matrix<int> matrix_in(nx, ny);
+  int count = 0;
+
+  for (int i = 0; i < nx; ++i) {
+    for (int j = 0; j < ny; ++j) {
+      matrix_in(i, j) = ++count;
+    }
+  }
+
+  Options options{{"int_matrix", matrix_in}};
+
+  const auto matrix_out = options["int_matrix"].as<Matrix<int>>();
+  ASSERT_EQ(matrix_out(nx - 1, ny - 1), matrix_in(nx - 1, ny - 1));
+}
diff --git a/tests/unit/sys/test_options_netcdf.cxx b/tests/unit/sys/test_options_netcdf.cxx
index 127874b2ad..b16d838b54 100644
--- a/tests/unit/sys/test_options_netcdf.cxx
+++ b/tests/unit/sys/test_options_netcdf.cxx
@@ -1,6 +1,7 @@
 // Test reading and writing to NetCDF
 
 #include "bout/build_defines.hxx"
+#include "bout/utils.hxx"
 
 #if BOUT_HAS_NETCDF && !BOUT_HAS_LEGACY_NETCDF
 
@@ -93,6 +94,29 @@ TEST_F(OptionsNetCDFTest, ReadWriteField3D) {
   EXPECT_DOUBLE_EQ(value(1, 1, 1), 2.4);
 }
 
+TEST_F(OptionsNetCDFTest, ReadWriteMatrixInt) {
+  constexpr int nx = 2;
+  constexpr int ny = 3;
+  Matrix<int> matrix_in(nx, ny);
+  int count = 0;
+
+  for (int i = 0; i < nx; ++i) {
+    for (int j = 0; j < ny; ++j) {
+      matrix_in(i, j) = ++count;
+    }
+  }
+
+  {
+    Options options{{"int_matrix", matrix_in}};
+    OptionsIO::create(filename)->write(options);
+  }
+
+  Options data = OptionsIO::create(filename)->read();
+
+  const auto matrix_out = data["int_matrix"].as<Matrix<int>>();
+  ASSERT_EQ(matrix_out(nx - 1, ny - 1), matrix_in(nx - 1, ny - 1));
+}
+
 TEST_F(OptionsNetCDFTest, Groups) {
   {
     Options options;

From 134eb2bd37e9d282a5e80300a3d0308b422f4498 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 18 Nov 2025 17:54:51 +0000
Subject: [PATCH 0319/1827] Fix a bunch of clang-tidy warnings

---
 include/bout/options.hxx         | 1 +
 src/mesh/data/gridfromfile.cxx   | 4 ++++
 src/mesh/impls/bout/boutmesh.cxx | 4 +++-
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 7bad26d990..1c552cd4f9 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -39,6 +39,7 @@ class Options;
 #ifndef OPTIONS_H
 #define OPTIONS_H
 
+#include "bout/array.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 3cfadde9a9..5078882136 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -2,6 +2,7 @@
 #include "bout/traits.hxx"
 #include <bout/griddata.hxx>
 
+#include <bout/array.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
@@ -11,6 +12,9 @@
 #include <bout/sys/timer.hxx>
 #include <bout/unused.hxx>
 #include <bout/utils.hxx>
+
+#include <algorithm>
+#include <iterator>
 #include <utility>
 
 GridFile::GridFile(std::string gridfilename)
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index fe928f377d..9f366d9456 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -2146,15 +2146,17 @@ void BoutMesh::topology() {
   int limiter_count = 0;
   Mesh::get(limiter_count, "limiter_count", 0);
   if (limiter_count > 0) {
-    std::vector<int> limiter_yinds, limiter_xstarts, limiter_xends;
+    std::vector<int> limiter_yinds;
     if (!source->get(this, limiter_yinds, "limiter_yinds", limiter_count)) {
       throw BoutException("Couldn't read limiter_yinds vector of length {} from mesh",
                           limiter_count);
     }
+    std::vector<int> limiter_xstarts;
     if (!source->get(this, limiter_xstarts, "limiter_xstarts", limiter_count)) {
       throw BoutException("Couldn't read limiter_xstarts vector of length {} from mesh",
                           limiter_count);
     }
+    std::vector<int> limiter_xends;
     if (!source->get(this, limiter_xends, "limiter_xends", limiter_count)) {
       throw BoutException("Couldn't read limiter_xend vector of length {} from mesh",
                           limiter_count);

From 26130f4de8fdc5c9933afb23aaf2604a99773793 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 19 Nov 2025 17:34:52 +0000
Subject: [PATCH 0320/1827] Fix bug in reading `FieldPerp` with adios

---
 src/sys/options/options_adios.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 4a41a014eb..4342ab5104 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -129,7 +129,7 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
       return Options(value);
     }
     if ((static_cast<int>(dims[0]) == mesh->GlobalNx)
-        and (static_cast<int>(dims[2]) == mesh->GlobalNz)) {
+        and (static_cast<int>(dims[1]) == mesh->GlobalNz)) {
       // Probably a FieldPerp
 
       // Read just the local piece of the array

From e684304083bc5594f85bea2fed5a03ab42987a53 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 20 Nov 2025 14:19:39 +0100
Subject: [PATCH 0321/1827] Forward f to avoid copy

---
 include/bout/field.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index fb74dcb93d..9e576f938f 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -690,7 +690,7 @@ inline T setName(T&& f, const std::string& name, Types... args) {
 #if BOUT_USE_TRACK
   f.name = fmt::format(name, args...);
 #endif
-  return f;
+  return std::forward<T>(f);
 }
 
 #endif /* FIELD_H */

From 56287eb9fd4780b5a831d59bd2a7d0542195c738 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 19 Nov 2025 17:03:15 +0000
Subject: [PATCH 0322/1827] Add unit tests for `OptionsADIOS2`

- Replaces half-implemented integrated tests
- Ensure `engine` is always created before use
- Ensure `io` is always created before use
---
 include/bout/adios_object.hxx                 |  57 +++-
 src/sys/adios_object.cxx                      |  14 +-
 src/sys/options/options_adios.cxx             |  86 ++---
 src/sys/options/options_adios.hxx             |  13 +-
 tests/integrated/CMakeLists.txt               |   1 -
 .../test-options-adios/CMakeLists.txt         |   6 -
 .../test-options-adios/data/BOUT.inp          |   6 -
 tests/integrated/test-options-adios/runtest   |  74 ----
 .../test-options-adios/test-options-adios.cxx | 125 -------
 tests/unit/CMakeLists.txt                     |   1 +
 tests/unit/fake_mesh.hxx                      |  11 +
 tests/unit/sys/test_options_adios2.cxx        | 322 ++++++++++++++++++
 tests/unit/test_tmpfiles.hxx                  |   2 +-
 13 files changed, 431 insertions(+), 287 deletions(-)
 delete mode 100644 tests/integrated/test-options-adios/CMakeLists.txt
 delete mode 100644 tests/integrated/test-options-adios/data/BOUT.inp
 delete mode 100755 tests/integrated/test-options-adios/runtest
 delete mode 100644 tests/integrated/test-options-adios/test-options-adios.cxx
 create mode 100644 tests/unit/sys/test_options_adios2.cxx

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 07482a0dcb..cab27d1a0b 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -16,6 +16,8 @@
 
 #if BOUT_HAS_ADIOS2
 
+#include "bout/boutexception.hxx"
+
 #include <adios2.h>
 #include <memory>
 #include <mpi.h>
@@ -36,14 +38,12 @@ IOPtr GetIOPtr(const std::string IOName);
 class ADIOSStream {
 public:
   adios2::IO io;
-  adios2::Engine engine;
   adios2::Variable<double> vTime;
   adios2::Variable<int> vStep;
   int adiosStep = 0;
-  bool isInStep = false; // true if BeginStep was called and EndStep was not yet called
 
   /** create or return the ADIOSStream based on the target file name */
-  static ADIOSStream& ADIOSGetStream(const std::string& fname);
+  static ADIOSStream& ADIOSGetStream(const std::string& fname, adios2::Mode mode);
 
   ~ADIOSStream();
 
@@ -74,9 +74,58 @@ public:
     return v;
   }
 
+  auto engine() -> adios2::Engine& {
+    if (not engine_) {
+      engine_ = io.Open(fname, file_mode);
+      if (not engine_) {
+        throw BoutException("Could not open ADIOS file '{:s}' for writing", fname);
+      }
+    }
+    return engine_;
+  }
+
+  void beginStep() {
+    if (not isInStep) {
+      engine().BeginStep();
+      isInStep = true;
+      adiosStep = static_cast<int>(engine().CurrentStep());
+    }
+  }
+
+  void endStep() {
+    if (isInStep) {
+      engine().EndStep();
+      isInStep = false;
+    }
+  }
+
+  void finish() {
+    if (engine_) {
+      engine().EndStep();
+      engine().Close();
+    }
+  }
+
 private:
-  ADIOSStream(const std::string fname) : fname(fname){};
+  ADIOSStream(const std::string& fname, adios2::Mode mode)
+      : fname(fname), file_mode(mode) {
+
+    ADIOSPtr adiosp = GetADIOSPtr();
+    std::string ioname = "write_" + fname;
+    try {
+      io = adiosp->AtIO(ioname);
+    } catch (const std::invalid_argument& e) {
+      io = adiosp->DeclareIO(ioname);
+      io.SetEngine("BP5");
+    }
+  };
+
   std::string fname;
+  adios2::Mode file_mode;
+  adios2::Engine engine_;
+
+  /// true if BeginStep was called and EndStep was not yet called
+  bool isInStep = false;
 };
 
 /** Set user parameters for an IO group */
diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx
index 53d8ccaa84..e2220386ec 100644
--- a/src/sys/adios_object.cxx
+++ b/src/sys/adios_object.cxx
@@ -5,8 +5,8 @@
 #include "bout/adios_object.hxx"
 #include "bout/boutexception.hxx"
 
-#include <exception>
-#include <iostream>
+#include <adios2.h>
+
 #include <unordered_map>
 
 namespace bout {
@@ -48,19 +48,19 @@ IOPtr GetIOPtr(const std::string IOName) {
 }
 
 ADIOSStream::~ADIOSStream() {
-  if (engine) {
+  if (engine_) {
     if (isInStep) {
-      engine.EndStep();
+      engine_.EndStep();
       isInStep = false;
     }
-    engine.Close();
+    engine_.Close();
   }
 }
 
-ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname) {
+ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname, adios2::Mode mode) {
   auto it = adiosStreams.find(fname);
   if (it == adiosStreams.end()) {
-    it = adiosStreams.emplace(fname, ADIOSStream(fname)).first;
+    it = adiosStreams.emplace(fname, ADIOSStream(fname, mode)).first;
   }
   return it->second;
 }
diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 4342ab5104..e17ef948e2 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -4,15 +4,15 @@
 #if BOUT_HAS_ADIOS2
 
 #include "options_adios.hxx"
-#include "bout/adios_object.hxx"
 
-#include "bout/bout.hxx"
+#include "bout/adios_object.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
+#include "bout/options.hxx"
 #include "bout/sys/timer.hxx"
 
-#include "adios2.h"
+#include <adios2.h>
 
 #include <cstddef>
 #include <exception>
@@ -34,8 +34,8 @@ OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) {
   }
 
   file_mode = (options["append"].doc("Append to existing file?").withDefault<bool>(false))
-                  ? FileMode::append
-                  : FileMode::replace;
+                  ? adios2::Mode::Append
+                  : adios2::Mode::Write;
 
   singleWriteFile = options["singleWriteFile"].withDefault<bool>(false);
 }
@@ -305,10 +305,16 @@ Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
 }
 
 void OptionsADIOS::verifyTimesteps() const {
-  ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename);
-  stream.engine.EndStep();
-  stream.isInStep = false;
-  return;
+  // This doesn't _verify_ the timesteps, but does flush to disk.
+  // Maybe this is fine, because ADIOS2 doesn't require every variable
+  // to be in sync?
+  if (singleWriteFile) {
+    return;
+  }
+
+  ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename, file_mode);
+
+  stream.endStep();
 }
 
 const std::vector<std::string> DIMS_NONE;
@@ -355,7 +361,7 @@ struct ADIOSPutVarVisitor {
   template <typename T>
   void operator()(const T& value) {
     adios2::Variable<T> var = stream.GetValueVariable<T>(varname);
-    stream.engine.Put(var, value);
+    stream.engine().Put(var, value);
   }
 
   void operator()(const Array<int>& value) { put_helper(value); }
@@ -375,7 +381,7 @@ struct ADIOSPutVarVisitor {
     const auto shape = make_shape(static_cast<std::size_t>(BoutComm::size()), value);
     auto var = stream.GetArrayVariable<U>(varname, shape, DIMS_NONE, BoutComm::rank());
     var.SetSelection({make_start(value), make_shape(1, value)});
-    stream.engine.Put<U>(var, value.begin());
+    stream.engine().Put<U>(var, value.begin());
   }
 };
 
@@ -386,7 +392,7 @@ void ADIOSPutVarVisitor::operator()<bool>(const bool& value) {
     return;
   }
   adios2::Variable<int> var = stream.GetValueVariable<int>(varname);
-  stream.engine.Put<int>(var, static_cast<int>(value));
+  stream.engine().Put<int>(var, static_cast<int>(value));
 }
 
 template <>
@@ -396,7 +402,7 @@ void ADIOSPutVarVisitor::operator()<int>(const int& value) {
     return;
   }
   adios2::Variable<int> var = stream.GetValueVariable<int>(varname);
-  stream.engine.Put<int>(var, value);
+  stream.engine().Put<int>(var, value);
 }
 
 template <>
@@ -406,7 +412,7 @@ void ADIOSPutVarVisitor::operator()<BoutReal>(const BoutReal& value) {
     return;
   }
   adios2::Variable<BoutReal> var = stream.GetValueVariable<BoutReal>(varname);
-  stream.engine.Put<BoutReal>(var, value);
+  stream.engine().Put<BoutReal>(var, value);
 }
 
 template <>
@@ -416,7 +422,7 @@ void ADIOSPutVarVisitor::operator()<std::string>(const std::string& value) {
     return;
   }
   adios2::Variable<std::string> var = stream.GetValueVariable<std::string>(varname);
-  stream.engine.Put<std::string>(var, value, adios2::Mode::Sync);
+  stream.engine().Put<std::string>(var, value, adios2::Mode::Sync);
 }
 
 template <>
@@ -449,7 +455,7 @@ void ADIOSPutVarVisitor::operator()<Field2D>(const Field2D& value) {
       stream.GetArrayVariable<BoutReal>(varname, shape, DIMS_XY, BoutComm::rank());
   var.SetSelection({start, count});
   var.SetMemorySelection({memStart, memCount});
-  stream.engine.Put<BoutReal>(var, &value(0, 0));
+  stream.engine().Put<BoutReal>(var, &value(0, 0));
 }
 
 template <>
@@ -487,7 +493,7 @@ void ADIOSPutVarVisitor::operator()<Field3D>(const Field3D& value) {
       stream.GetArrayVariable<BoutReal>(varname, shape, DIMS_XYZ, BoutComm::rank());
   var.SetSelection({start, count});
   var.SetMemorySelection({memStart, memCount});
-  stream.engine.Put<BoutReal>(var, &value(0, 0, 0));
+  stream.engine().Put<BoutReal>(var, &value(0, 0, 0));
 }
 
 template <>
@@ -520,7 +526,7 @@ void ADIOSPutVarVisitor::operator()<FieldPerp>(const FieldPerp& value) {
       stream.GetArrayVariable<BoutReal>(varname, shape, DIMS_XZ, BoutComm::rank());
   var.SetSelection({start, count});
   var.SetMemorySelection({memStart, memCount});
-  stream.engine.Put<BoutReal>(var, &value(0, 0));
+  stream.engine().Put<BoutReal>(var, &value(0, 0));
 }
 
 /// Visit a variant type, and put the data into a NcVar
@@ -604,48 +610,18 @@ void OptionsADIOS::write(const Options& options, const std::string& time_dim) {
   Timer timer("io");
 
   // ADIOSStream is just a BOUT++ object, it does not create anything inside ADIOS
-  ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename);
-
-  // Need to have an adios2::IO object first, which can only be created once.
-  if (!stream.io) {
-    ADIOSPtr adiosp = GetADIOSPtr();
-    std::string ioname = "write_" + filename;
-    try {
-      stream.io = adiosp->AtIO(ioname);
-    } catch (const std::invalid_argument& e) {
-      stream.io = adiosp->DeclareIO(ioname);
-      stream.io.SetEngine("BP5");
-    }
-  }
-
-  /* Open file once and keep it open, close in stream desctructor
-     or close after writing if singleWriteFile == true
-    */
-  if (!stream.engine) {
-    adios2::Mode amode =
-        (file_mode == FileMode::append ? adios2::Mode::Append : adios2::Mode::Write);
-    stream.engine = stream.io.Open(filename, amode);
-    if (!stream.engine) {
-      throw BoutException("Could not open ADIOS file '{:s}' for writing", filename);
-    }
-  }
+  ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename, file_mode);
 
-  /* Multiple write() calls allowed in a single adios step to output multiple
-     Options objects in the same step. verifyTimesteps() will indicate the 
-     completion of the step (and adios will publish the step).
-  */
-  if (!stream.isInStep) {
-    stream.engine.BeginStep();
-    stream.isInStep = true;
-    stream.adiosStep = stream.engine.CurrentStep();
-  }
+  // Multiple write() calls allowed in a single adios step to output multiple
+  // Options objects in the same step. verifyTimesteps() will indicate the
+  // completion of the step (and adios will publish the step).
+  stream.beginStep();
 
   writeGroup(options, stream, "", time_dim);
 
-  /* In singleWriteFile mode, we complete the step and close the file */
+  // In singleWriteFile mode, we complete the step and close the file
   if (singleWriteFile) {
-    stream.engine.EndStep();
-    stream.engine.Close();
+    stream.finish();
   }
 }
 
diff --git a/src/sys/options/options_adios.hxx b/src/sys/options/options_adios.hxx
index 6e81508ca3..f5b397188d 100644
--- a/src/sys/options/options_adios.hxx
+++ b/src/sys/options/options_adios.hxx
@@ -5,7 +5,6 @@
 #define OPTIONS_ADIOS_H
 
 #include "bout/build_defines.hxx"
-#include "bout/options.hxx"
 #include "bout/options_io.hxx"
 
 #if !BOUT_HAS_ADIOS2
@@ -17,7 +16,10 @@ bout::RegisterUnavailableOptionsIO
 
 #else
 
-#include <memory>
+#include "bout/options.hxx"
+
+#include <adios2.h>
+
 #include <string>
 
 namespace bout {
@@ -61,15 +63,10 @@ public:
   void verifyTimesteps() const override;
 
 private:
-  enum class FileMode {
-    replace, ///< Overwrite file when writing
-    append   ///< Append to file when writing
-  };
-
   /// Name of the file on disk
   std::string filename;
   /// How to open the file for writing
-  FileMode file_mode{FileMode::replace};
+  adios2::Mode file_mode{adios2::Mode::Write};
   bool singleWriteFile = false;
 };
 
diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt
index e11403efb9..3696ef0372 100644
--- a/tests/integrated/CMakeLists.txt
+++ b/tests/integrated/CMakeLists.txt
@@ -32,7 +32,6 @@ add_subdirectory(test-laplacexz)
 add_subdirectory(test-multigrid_laplace)
 add_subdirectory(test-naulin-laplace)
 add_subdirectory(test-options-netcdf)
-add_subdirectory(test-options-adios)
 add_subdirectory(test-petsc_laplace)
 add_subdirectory(test-petsc_laplace_MAST-grid)
 add_subdirectory(test-restart-io)
diff --git a/tests/integrated/test-options-adios/CMakeLists.txt b/tests/integrated/test-options-adios/CMakeLists.txt
deleted file mode 100644
index cc61fabe57..0000000000
--- a/tests/integrated/test-options-adios/CMakeLists.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-bout_add_integrated_test(test-options-adios
-  SOURCES test-options-adios.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  REQUIRES BOUT_HAS_ADIOS2
-  )
diff --git a/tests/integrated/test-options-adios/data/BOUT.inp b/tests/integrated/test-options-adios/data/BOUT.inp
deleted file mode 100644
index fa0f6d3681..0000000000
--- a/tests/integrated/test-options-adios/data/BOUT.inp
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
-[mesh]
-nx = 5
-ny = 2
-nz = 2
diff --git a/tests/integrated/test-options-adios/runtest b/tests/integrated/test-options-adios/runtest
deleted file mode 100755
index 03a83fc0ba..0000000000
--- a/tests/integrated/test-options-adios/runtest
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/usr/bin/env python3
-
-# Note: This test requires NCDF4, whereas on Travis NCDF is used
-# requires: netcdf
-# requires: adios
-# requires: not legacy_netcdf
-
-from boututils.datafile import DataFile
-from boututils.run_wrapper import build_and_log, shell, launch
-from boutdata.data import BoutOptionsFile
-
-import math
-import numpy as np
-
-build_and_log("options-netcdf test")
-shell("rm -f test-out.ini")
-shell("rm -f test-out.nc")
-
-# Create a NetCDF input file
-with DataFile("test.nc", create=True, format="NETCDF4") as f:
-    f.write("int", 42)
-    f.write("real", 3.1415)
-    f.write("string", "hello")
-
-# run BOUT++
-launch("./test-options-adios", nproc=1, mthread=1)
-
-# Check the output INI file
-result = BoutOptionsFile("test-out.ini")
-
-print(result)
-
-assert result["int"] == 42
-assert math.isclose(result["real"], 3.1415)
-assert result["string"] == "hello"
-
-print("Checking saved ADIOS2 test-out file -- Not implemented")
-
-# Check the output NetCDF file
-# with DataFile("test-out.nc") as f:
-#    assert f["int"] == 42
-#    assert math.isclose(f["real"], 3.1415)
-#    assert result["string"] == "hello"
-
-print("Checking saved settings.ini")
-
-# Check the settings.ini file, coming from BOUT.inp
-# which is converted to NetCDF, read in, then written again
-settings = BoutOptionsFile("settings.ini")
-
-assert settings["mesh"]["nx"] == 5
-assert settings["mesh"]["ny"] == 2
-
-print("Checking saved fields.bp -- Not implemented")
-
-# with DataFile("fields.nc") as f:
-#    assert f["f2d"].shape == (5, 6)  # Field2D
-#    assert f["f3d"].shape == (5, 6, 2)  # Field3D
-#    assert f["fperp"].shape == (5, 2)  # FieldPerp
-#    assert np.allclose(f["f2d"], 1.0)
-#    assert np.allclose(f["f3d"], 2.0)
-#    assert np.allclose(f["fperp"], 3.0)
-
-print("Checking saved fields2.bp -- Not implemented")
-
-# with DataFile("fields2.nc") as f:
-#    assert f["f2d"].shape == (5, 6)  # Field2D
-#    assert f["f3d"].shape == (5, 6, 2)  # Field3D
-#    assert f["fperp"].shape == (5, 2)  # FieldPerp
-#    assert np.allclose(f["f2d"], 1.0)
-#    assert np.allclose(f["f3d"], 2.0)
-#    assert np.allclose(f["fperp"], 3.0)
-
-print(" => Passed")
diff --git a/tests/integrated/test-options-adios/test-options-adios.cxx b/tests/integrated/test-options-adios/test-options-adios.cxx
deleted file mode 100644
index ba0bbe3898..0000000000
--- a/tests/integrated/test-options-adios/test-options-adios.cxx
+++ /dev/null
@@ -1,125 +0,0 @@
-
-#include "bout/bout.hxx"
-
-#include "bout/options_io.hxx"
-#include "bout/optionsreader.hxx"
-#include "bout/utils.hxx"
-
-using bout::OptionsIO;
-
-int main(int argc, char** argv) {
-  BoutInitialise(argc, argv);
-
-  // Read values from a NetCDF file
-  auto file = bout::OptionsIO::create("test.nc");
-
-  auto values = file->read();
-
-  values.printUnused();
-
-  // Write to an INI text file
-  OptionsReader* reader = OptionsReader::getInstance();
-  reader->write(&values, "test-out.ini");
-
-  // Write to ADIOS file, by setting file type "adios"
-  OptionsIO::create({{"file", "test-out.bp"},
-                     {"type", "adios"},
-                     {"append", false},
-                     {"singleWriteFile", true}})
-      ->write(values);
-
-  ///////////////////////////
-
-  // Write the BOUT.inp settings to ADIOS file
-  OptionsIO::create({{"file", "settings.bp"},
-                     {"type", "adios"},
-                     {"append", false},
-                     {"singleWriteFile", true}})
-      ->write(Options::root());
-
-  // Read back in
-  auto settings = OptionsIO::create({{"file", "settings.bp"}, {"type", "adios"}})->read();
-
-  // Write to INI file
-  reader->write(&settings, "settings.ini");
-
-  ///////////////////////////
-  // Write fields
-
-  {
-    constexpr int nx = 2;
-    constexpr int ny = 3;
-    Matrix<int> matrix_in(nx, ny);
-    int count = 0;
-
-    for (int i = 0; i < nx; ++i) {
-      for (int j = 0; j < ny; ++j) {
-        matrix_in(i, j) = ++count;
-      }
-    }
-
-    Options fields{{"f2d", Field2D(1.0)},
-                   {"f3d", Field3D(2.0)},
-                   {"fperp", FieldPerp(3.0)},
-                   {"matrix", matrix_in}};
-    auto f = OptionsIO::create({{"file", "fields.bp"}, {"type", "adios"}});
-    /*
-     write() for adios only buffers data but does not guarantee writing to disk
-     unless singleWriteFile is set to true 
-     */
-    f->write(fields);
-    // indicate completion of step, required to get data on disk
-    f->verifyTimesteps();
-  }
-
-  ///////////////////////////
-  // Read fields
-
-  Options fields_in =
-      OptionsIO::create({{"file", "fields.bp"}, {"type", "adios"}})->read();
-
-  auto f2d = fields_in["f2d"].as<Field2D>(bout::globals::mesh);
-  auto f3d = fields_in["f3d"].as<Field3D>(bout::globals::mesh);
-  auto fperp = fields_in["fperp"].as<FieldPerp>(bout::globals::mesh);
-
-  Options fields2;
-  fields2["f2d"] = f2d;
-  fields2["f3d"] = f3d;
-  fields2["fperp"] = fperp;
-
-  // Write out again
-  auto f2 = OptionsIO::create({{"file", "fields2.bp"},
-                               {"type", "adios"},
-                               {"append", false},
-                               {"singleWriteFile", true}});
-  f2->write(fields2);
-
-  ///////////////////////////
-  // Time dependent values
-
-  Options data;
-  data["scalar"] = 1.0;
-  data["scalar"].attributes["time_dimension"] = "t";
-
-  data["field"] = Field3D(2.0);
-  data["field"].attributes["time_dimension"] = "t";
-
-  OptionsIO::create({{"file", "time.bp"},
-                     {"type", "adios"},
-                     {"append", false},
-                     {"singleWriteFile", true}})
-      ->write(data);
-
-  // Update time-dependent values
-  data["scalar"] = 2.0;
-  data["field"] = Field3D(3.0);
-
-  // Append data to file
-  OptionsIO::create({{"file", "time.bp"},
-                     {"type", "adios"},
-                     {"append", true},
-                     {"singleWriteFile", true}})
-      ->write(data);
-
-  BoutFinalise();
-};
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 47253c508f..40aa207dea 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -80,6 +80,7 @@ set(serial_tests_source
   ./sys/test_expressionparser.cxx
   ./sys/test_msg_stack.cxx
   ./sys/test_options.cxx
+  ./sys/test_options_adios2.cxx
   ./sys/test_options_fields.cxx
   ./sys/test_options_netcdf.cxx
   ./sys/test_optionsreader.cxx
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index e6f78f8767..b945b46524 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -50,6 +50,17 @@ public:
     OffsetY = 0;
     OffsetZ = 0;
 
+    // These bits only for ADIOS2, also boring due to single process
+    MapCountX = nx - 2;
+    MapCountY = ny - 2;
+    MapCountZ = nz;
+    MapGlobalX = nx;
+    MapGlobalY = ny;
+    MapGlobalZ = nz;
+    MapLocalX = nx - 2;
+    MapLocalY = ny - 2;
+    MapLocalZ = nz;
+
     // Small "inner" region
     xstart = 1;
     xend = nx - 2;
diff --git a/tests/unit/sys/test_options_adios2.cxx b/tests/unit/sys/test_options_adios2.cxx
new file mode 100644
index 0000000000..d5bb4653a6
--- /dev/null
+++ b/tests/unit/sys/test_options_adios2.cxx
@@ -0,0 +1,322 @@
+// Test reading and writing to ADIOS2
+
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_ADIOS2
+
+#include "gtest/gtest.h"
+
+#include "test_extras.hxx"
+#include "test_tmpfiles.hxx"
+#include "bout/adios_object.hxx"
+#include "bout/field3d.hxx"
+#include "bout/mesh.hxx"
+#include "bout/options_io.hxx"
+#include "bout/utils.hxx"
+
+using bout::OptionsIO;
+
+#include <string>
+
+#include "fake_mesh_fixture.hxx"
+
+// Reuse the "standard" fixture for FakeMesh
+class OptionsAdios2Test : public FakeMeshFixture {
+public:
+  static void SetUpTestSuite() { bout::ADIOSInit(BoutComm::get()); }
+  static void TearDownTestSuite() { bout::ADIOSFinalize(); }
+
+  ~OptionsAdios2Test() override {
+    bout::ADIOSStream::ADIOSGetStream(filename, adios2::Mode::Deferred).engine().Close();
+  }
+
+  // A temporary filename
+  bout::testing::TempFile filename;
+  WithQuietOutput quiet{output_info};
+  Options file_options{
+      {"file", filename.string()},
+      {"type", "adios"},
+      {"singleWriteFile", true},
+  };
+  Options no_write_options{
+      {"file", filename.string()},
+      {"type", "adios"},
+      {"singleWriteFile", false},
+  };
+};
+
+TEST_F(OptionsAdios2Test, ReadWriteInt) {
+  {
+    Options options;
+    options["test"] = 42;
+
+    // Write the file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read again
+  Options data = OptionsIO::create(file_options)->read();
+
+  EXPECT_EQ(data["test"], 42);
+}
+
+TEST_F(OptionsAdios2Test, ReadWriteString) {
+  {
+    Options options;
+    options["test"] = std::string{"hello"};
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+
+  EXPECT_EQ(data["test"], std::string("hello"));
+}
+
+TEST_F(OptionsAdios2Test, ReadWriteField2D) {
+  {
+    Options options;
+    options["test"] = Field2D(1.0);
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+
+  Field2D value = data["test"].as<Field2D>(bout::globals::mesh);
+
+  EXPECT_DOUBLE_EQ(value(0, 1), 1.0);
+  EXPECT_DOUBLE_EQ(value(1, 0), 1.0);
+}
+
+TEST_F(OptionsAdios2Test, ReadWriteField3D) {
+  {
+    Options options;
+    options["test"] = Field3D(2.4);
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+
+  Field3D value = data["test"].as<Field3D>(bout::globals::mesh);
+
+  EXPECT_DOUBLE_EQ(value(0, 1, 0), 2.4);
+  EXPECT_DOUBLE_EQ(value(1, 0, 1), 2.4);
+  EXPECT_DOUBLE_EQ(value(1, 1, 1), 2.4);
+}
+
+TEST_F(OptionsAdios2Test, Groups) {
+  {
+    Options options;
+    options["test"]["key"] = 42;
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+  EXPECT_EQ(data["test"]["key"], 42);
+}
+
+TEST_F(OptionsAdios2Test, AttributeInt) {
+  {
+    Options options;
+    options["test"] = 3;
+    options["test"].attributes["thing"] = 4;
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+  EXPECT_EQ(data["test"].attributes["thing"].as<int>(), 4);
+}
+
+TEST_F(OptionsAdios2Test, AttributeBoutReal) {
+  {
+    Options options;
+    options["test"] = 3;
+    options["test"].attributes["thing"] = 3.14;
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+  EXPECT_DOUBLE_EQ(data["test"].attributes["thing"].as<BoutReal>(), 3.14);
+}
+
+TEST_F(OptionsAdios2Test, AttributeString) {
+  {
+    Options options;
+    options["test"] = 3;
+    options["test"].attributes["thing"] = "hello";
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+  EXPECT_EQ(data["test"].attributes["thing"].as<std::string>(), "hello");
+}
+
+TEST_F(OptionsAdios2Test, Field2DWriteCellCentre) {
+  {
+    Options options;
+    options["f2d"] = Field2D(2.0);
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+
+  EXPECT_EQ(data["f2d"].attributes["cell_location"].as<std::string>(),
+            toString(CELL_CENTRE));
+}
+
+TEST_F(OptionsAdios2Test, Field2DWriteCellYLow) {
+  {
+    Options options;
+    options["f2d"] = Field2D(2.0, mesh_staggered).setLocation(CELL_YLOW);
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+
+  EXPECT_EQ(data["f2d"].attributes["cell_location"].as<std::string>(),
+            toString(CELL_YLOW));
+}
+
+TEST_F(OptionsAdios2Test, Field3DWriteCellCentre) {
+  {
+    Options options;
+    options["f3d"] = Field3D(2.0);
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+
+  EXPECT_EQ(data["f3d"].attributes["cell_location"].as<std::string>(),
+            toString(CELL_CENTRE));
+}
+
+TEST_F(OptionsAdios2Test, Field3DWriteCellYLow) {
+  {
+    Options options;
+    options["f3d"] = Field3D(2.0, mesh_staggered).setLocation(CELL_YLOW);
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+
+  EXPECT_EQ(data["f3d"].attributes["cell_location"].as<std::string>(),
+            toString(CELL_YLOW));
+}
+
+TEST_F(OptionsAdios2Test, FieldPerpWriteCellCentre) {
+  {
+    Options options;
+    FieldPerp fperp(3.0);
+    fperp.setIndex(2);
+    options["fperp"] = fperp;
+
+    // Ensure MPI is initialised, otherwise we end up creating threads while
+    // the file is open, and the lock is not removed on closing.
+    fperp.getMesh()->getXcomm();
+
+    // Write file
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  // Read file
+  Options data = OptionsIO::create(file_options)->read();
+
+  EXPECT_EQ(data["fperp"].attributes["cell_location"].as<std::string>(),
+            toString(CELL_CENTRE));
+  EXPECT_EQ(data["fperp"].attributes["yindex_global"].as<int>(), 2);
+}
+
+TEST_F(OptionsAdios2Test, VerifyTimesteps) {
+  {
+    Options options;
+    options["thing1"] = 1.0;
+    options["thing1"].attributes["time_dimension"] = "t";
+
+    auto f = OptionsIO::create(no_write_options);
+    f->write(options);
+    EXPECT_NO_THROW(f->verifyTimesteps());
+  }
+
+  {
+    Options options;
+    options["thing1"] = 2.0;
+    options["thing1"].attributes["time_dimension"] = "t";
+
+    options["thing2"] = 3.0;
+    options["thing2"].attributes["time_dimension"] = "t";
+
+    OptionsIO::create({{"type", "adios"}, {"file", filename.string()}, {"append", true}})
+        ->write(options);
+  }
+
+  // Doesn't throw, but it's less of a problem for ADIOS2 than netCDF?
+  // EXPECT_THROW(OptionsIO::create(no_write_options)->verifyTimesteps(), BoutException);
+}
+
+TEST_F(OptionsAdios2Test, WriteTimeDimension) {
+  {
+    Options options;
+    options["thing1"].assignRepeat(1.0);       // default time dim
+    options["thing2"].assignRepeat(2.0, "t2"); // non-default
+
+    // Only write non-default time dim
+    OptionsIO::create(file_options)->write(options, "t2");
+  }
+
+  Options data = OptionsIO::create(file_options)->read();
+
+  EXPECT_FALSE(data.isSet("thing1"));
+  EXPECT_TRUE(data.isSet("thing2"));
+}
+
+TEST_F(OptionsAdios2Test, WriteMultipleTimeDimensions) {
+  {
+    Options options;
+    options["thing1_t1"].assignRepeat(1.0); // default time dim
+    options["thing2_t1"].assignRepeat(1.0); // default time dim
+
+    options["thing3_t2"].assignRepeat(2.0, "t2"); // non-default
+    options["thing4_t2"].assignRepeat(2.0, "t2"); // non-default
+
+    // Write the non-default time dim twice
+    OptionsIO::create(no_write_options)->write(options, "t2");
+    OptionsIO::create(no_write_options)->write(options, "t2");
+    OptionsIO::create(no_write_options)->write(options, "t");
+  }
+
+  EXPECT_NO_THROW(OptionsIO::create(no_write_options)->verifyTimesteps());
+}
+
+#endif // Bout_Has_ADIOS2
diff --git a/tests/unit/test_tmpfiles.hxx b/tests/unit/test_tmpfiles.hxx
index 35d7579df2..6c37e7c792 100644
--- a/tests/unit/test_tmpfiles.hxx
+++ b/tests/unit/test_tmpfiles.hxx
@@ -30,7 +30,7 @@ public:
   TempFile& operator=(const TempFile&) = delete;
   TempFile& operator=(TempFile&&) = delete;
 
-  ~TempFile() { std::filesystem::remove(filename); }
+  ~TempFile() { std::filesystem::remove_all(filename); }
 
   // Enable conversions to std::string / const char*
   operator std::string() const { return filename.string(); }

From 8f2c0d1185c380d8d02445a208a9fcd36aa2a5d1 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 19 Nov 2025 17:35:27 +0000
Subject: [PATCH 0323/1827] Fix some clang-tidy warnings

---
 include/bout/adios_object.hxx     | 4 ++--
 src/sys/adios_object.cxx          | 6 +++---
 src/sys/options/options_adios.hxx | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index cab27d1a0b..fcade4f55c 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -129,8 +129,8 @@ private:
 };
 
 /** Set user parameters for an IO group */
-void ADIOSSetParameters(const std::string& input, const char delimKeyValue,
-                        const char delimItem, adios2::IO& io);
+void ADIOSSetParameters(const std::string& input, char delimKeyValue, char delimItem,
+                        adios2::IO& io);
 
 } // namespace bout
 
diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx
index e2220386ec..83bdf45f27 100644
--- a/src/sys/adios_object.cxx
+++ b/src/sys/adios_object.cxx
@@ -65,8 +65,8 @@ ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname, adios2::Mode
   return it->second;
 }
 
-void ADIOSSetParameters(const std::string& input, const char delimKeyValue,
-                        const char delimItem, adios2::IO& io) {
+void ADIOSSetParameters(const std::string& input, char delimKeyValue,
+                        char delimItem, adios2::IO& io) {
   auto lf_Trim = [](std::string& input) {
     input.erase(0, input.find_first_not_of(" \n\r\t")); // prefixing spaces
     input.erase(input.find_last_not_of(" \n\r\t") + 1); // suffixing spaces
@@ -76,7 +76,7 @@ void ADIOSSetParameters(const std::string& input, const char delimKeyValue,
   std::string parameter;
   while (std::getline(inputSS, parameter, delimItem)) {
     const size_t position = parameter.find(delimKeyValue);
-    if (position == parameter.npos) {
+    if (position == std::string::npos) {
       throw BoutException("ADIOSSetParameters(): wrong format for IO parameter "
                           + parameter + ", format must be key" + delimKeyValue
                           + "value for each entry");
diff --git a/src/sys/options/options_adios.hxx b/src/sys/options/options_adios.hxx
index f5b397188d..534c3e1707 100644
--- a/src/sys/options/options_adios.hxx
+++ b/src/sys/options/options_adios.hxx
@@ -46,7 +46,7 @@ public:
 
   OptionsADIOS(const OptionsADIOS&) = delete;
   OptionsADIOS(OptionsADIOS&&) noexcept = default;
-  ~OptionsADIOS() = default;
+  ~OptionsADIOS() override = default;
 
   OptionsADIOS& operator=(const OptionsADIOS&) = delete;
   OptionsADIOS& operator=(OptionsADIOS&&) noexcept = default;

From 602de3d622deb12b3aa7dbca3e7eca883b1904f3 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 20 Nov 2025 09:43:46 +0000
Subject: [PATCH 0324/1827] Remove unused constant

---
 src/sys/options/options_adios.cxx | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index e17ef948e2..24e92544c4 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -21,9 +21,6 @@
 #include <vector>
 
 namespace bout {
-/// Name of the attribute used to track individual variable's time indices
-constexpr auto current_time_index_name = "current_time_index";
-
 OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) {
   if (options["file"].doc("File name. Defaults to <path>/<prefix>.pb").isSet()) {
     filename = options["file"].as<std::string>();

From 80cf88d16a19ef9441a60c7d5f02d99061db71ba Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 20 Nov 2025 09:47:41 +0000
Subject: [PATCH 0325/1827] Switch to `BoutException`

---
 src/sys/options/options_adios.cxx | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 24e92544c4..28eba431d3 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -52,30 +52,30 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
   }
 
   if (variable.ShapeID() == adios2::ShapeID::LocalArray) {
-    throw std::invalid_argument(
-        "ADIOS reader did not implement reading local arrays like " + type + " " + name
-        + " in file " + reader.Name());
+    throw BoutException(
+        "ADIOS reader did not implement reading local arrays like `{}` '{}' in file '{}'",
+        type, name, reader.Name());
   }
 
   if (type != "double" && type != "float") {
-    throw std::invalid_argument(
-        "ADIOS reader did not implement reading arrays that are not double/float type. "
-        "Found "
-        + type + " " + name + " in file " + reader.Name());
+    throw BoutException("ADIOS reader did not implement reading arrays that are not "
+                        "`double`/`float` type. "
+                        "Found `{}` '{}' in file '{}'",
+                        type, name, reader.Name());
   }
 
   if (type == "double" && sizeof(BoutReal) != sizeof(double)) {
-    throw std::invalid_argument(
+    throw BoutException(
         "ADIOS does not allow for implicit type conversions. BoutReal type is "
-        "float but found "
-        + type + " " + name + " in file " + reader.Name());
+        "float but found `{}` '{}' in file '{}'",
+        type, name, reader.Name());
   }
 
   if (type == "float" && sizeof(BoutReal) != sizeof(float)) {
-    throw std::invalid_argument(
+    throw BoutException(
         "ADIOS reader does not allow for implicit type conversions. BoutReal type is "
-        "double but found "
-        + type + " " + name + " in file " + reader.Name());
+        "double but found `{}` '{}' in file '{}'",
+        type, name, reader.Name());
   }
 
   auto dims = variable.Shape();

From 4dba6a97f8a468350d80ef50217fa8e720c854e6 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 20 Nov 2025 13:45:44 +0000
Subject: [PATCH 0326/1827] Add some helper variables for options_adios

---
 src/sys/options/options_adios.cxx | 41 ++++++++++++++++++++-----------
 1 file changed, 26 insertions(+), 15 deletions(-)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 28eba431d3..a1ddc71326 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -1,5 +1,4 @@
 #include "bout/build_defines.hxx"
-#include "bout/traits.hxx"
 
 #if BOUT_HAS_ADIOS2
 
@@ -11,15 +10,27 @@
 #include "bout/mesh.hxx"
 #include "bout/options.hxx"
 #include "bout/sys/timer.hxx"
+#include "bout/traits.hxx"
 
 #include <adios2.h>
 
+#include <algorithm>
 #include <cstddef>
 #include <exception>
-#include <tuple>
+#include <iterator>
 #include <utility>
 #include <vector>
 
+namespace {
+auto to_int_dims(const adios2::Dims& dims) {
+  std::vector<int> int_dims;
+  int_dims.reserve(dims.size());
+  std::transform(dims.begin(), dims.end(), std::back_inserter(int_dims),
+                 [](auto dim) { return static_cast<int>(dim); });
+  return int_dims;
+}
+} // namespace
+
 namespace bout {
 OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) {
   if (options["file"].doc("File name. Defaults to <path>/<prefix>.pb").isSet()) {
@@ -78,13 +89,18 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
         type, name, reader.Name());
   }
 
-  auto dims = variable.Shape();
-  auto ndims = dims.size();
+  const auto dims = to_int_dims(variable.Shape());
+  const auto ndims = dims.size();
   adios2::Variable<BoutReal> variableD = io.InquireVariable<BoutReal>(name);
 
+  const bool dim0_is_x = ndims > 0 ? (dims[0] == mesh->GlobalNx) : false;
+  const bool dim1_is_y = ndims > 1 ? (dims[1] == mesh->GlobalNy) : false;
+  const bool dim1_is_z = ndims > 1 ? (dims[1] == mesh->GlobalNz) : false;
+  const bool dim2_is_z = ndims > 2 ? (dims[2] == mesh->GlobalNz) : false;
+
   switch (ndims) {
   case 1: {
-    Array<BoutReal> value(static_cast<int>(dims[0]));
+    Array<BoutReal> value(dims[0]);
     BoutReal* data = value.begin();
     reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
     return Options(value);
@@ -97,8 +113,7 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
     // - Add an attribute to specify field type or dimension labels
     // - Load all the data, and select a region when converting to a Field in Options
     // - Add a lazy loading type to Options, and load data when needed
-    if ((static_cast<int>(dims[0]) == mesh->GlobalNx)
-        and (static_cast<int>(dims[1]) == mesh->GlobalNy)) {
+    if (dim0_is_x and dim1_is_y) {
       // Probably a Field2D
 
       // Read just the local piece of the array
@@ -125,8 +140,7 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
       reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
       return Options(value);
     }
-    if ((static_cast<int>(dims[0]) == mesh->GlobalNx)
-        and (static_cast<int>(dims[1]) == mesh->GlobalNz)) {
+    if (dim0_is_x and dim1_is_z) {
       // Probably a FieldPerp
 
       // Read just the local piece of the array
@@ -153,15 +167,13 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
       reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
       return Options(value);
     }
-    Matrix<BoutReal> value(static_cast<int>(dims[0]), static_cast<int>(dims[1]));
+    Matrix<BoutReal> value(dims[0], dims[1]);
     BoutReal* data = value.begin();
     reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
     return Options(value);
   }
   case 3: {
-    if ((static_cast<int>(dims[0]) == mesh->GlobalNx)
-        and (static_cast<int>(dims[1]) == mesh->GlobalNy)
-        and (static_cast<int>(dims[2]) == mesh->GlobalNz)) {
+    if (dim0_is_x and dim1_is_y and dim2_is_z) {
       // Global array. Read just this processor's part of it
 
       Tensor<BoutReal> value(mesh->LocalNx, mesh->LocalNy, mesh->LocalNz);
@@ -194,8 +206,7 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
     }
     // Doesn't match global array size.
     // Read the entire array, in case it can be handled later
-    Tensor<BoutReal> value(static_cast<int>(dims[0]), static_cast<int>(dims[1]),
-                           static_cast<int>(dims[2]));
+    Tensor<BoutReal> value(dims[0], dims[1], dims[2]);
     BoutReal* data = value.begin();
     reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
     return Options(value);

From 5645907a04fe194363375ddb582475f773a2038d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 20 Nov 2025 17:44:53 +0000
Subject: [PATCH 0327/1827] Support reading `Array/Matrix/Tensor<int>` in
 `OptionsAdios2`

---
 src/sys/options/options_adios.cxx      | 290 +++++++++++++++----------
 tests/unit/sys/test_options_adios2.cxx |  24 ++
 2 files changed, 195 insertions(+), 119 deletions(-)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index a1ddc71326..10cc4ddf6a 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -5,6 +5,7 @@
 #include "options_adios.hxx"
 
 #include "bout/adios_object.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
@@ -13,11 +14,14 @@
 #include "bout/traits.hxx"
 
 #include <adios2.h>
+#include <fmt/format.h>
+#include <fmt/ranges.h>
 
 #include <algorithm>
 #include <cstddef>
 #include <exception>
 #include <iterator>
+#include <string>
 #include <utility>
 #include <vector>
 
@@ -29,6 +33,119 @@ auto to_int_dims(const adios2::Dims& dims) {
                  [](auto dim) { return static_cast<int>(dim); });
   return int_dims;
 }
+
+struct Selection {
+  // Offset of this processor's data into the global array
+  adios2::Dims start;
+  // The size of the mapped region
+  adios2::Dims count;
+  // Where the actual data starts in data pointer (to exclude ghost cells)
+  adios2::Dims mem_start;
+  // The actual size of data pointer in memory (including ghost cells)
+  adios2::Dims mem_count;
+  // Shape of the local variable to read into
+  std::vector<int> dims;
+
+  // Distributed Field/Array/Matrix/Tensor
+  bool should_set_selection{false};
+
+  Selection(const std::vector<std::string>& dim_names, const std::vector<int>& dim_sizes,
+            const Mesh& mesh) {
+    const auto ndims = dim_names.size();
+    const bool dim0_is_rank = ndims > 0 ? (dim_names[0] == "rank") : false;
+    const bool dim0_is_x = ndims > 0 ? (dim_names[0] == "x") : false;
+    const bool dim1_is_y = ndims > 1 ? (dim_names[1] == "y") : false;
+    const bool dim1_is_z = ndims > 1 ? (dim_names[1] == "z") : false;
+    const bool dim2_is_z = ndims > 2 ? (dim_names[2] == "z") : false;
+
+    should_set_selection = dim0_is_rank or (ndims == 2 and dim0_is_x and dim1_is_y)
+                           or (ndims == 2 and dim0_is_x and dim1_is_z)
+                           or (ndims == 3 and dim0_is_x and dim1_is_y and dim2_is_z);
+
+    if (dim0_is_rank) {
+      const auto ndim_sizes = dim_sizes.size();
+      ASSERT3(ndim_sizes > 1);
+
+      // This is a distributed array, so the local variable is going
+      // to be shape (dim_sizes[1]...) (that is, drop the rank)
+      dims.push_back(dim_sizes[1]);
+      // but we tell adios to read our rank's bit with the full ndims
+      start = {static_cast<std::size_t>(BoutComm::rank()), 0};
+      count = {std::size_t{1}, static_cast<std::size_t>(dim_sizes[0])};
+
+      if (ndim_sizes > 2) {
+        dims.push_back(dim_sizes[2]);
+        start.push_back(0);
+        count.push_back(dim_sizes[1]);
+      }
+      if (ndim_sizes > 3) {
+        dims.push_back(dim_sizes[3]);
+        start.push_back(0);
+        count.push_back(dim_sizes[2]);
+      }
+      mem_count = count;
+      mem_start = start;
+      return;
+    }
+
+    if (ndims > 0) {
+      dims.push_back(dim0_is_x ? mesh.LocalNx : dim_sizes[0]);
+    }
+    if (ndims > 1) {
+      if (dim1_is_y) {
+        dims.push_back(mesh.LocalNy);
+      } else if (dim1_is_z) {
+        dims.push_back(mesh.LocalNz);
+      } else {
+        dims.push_back(dim_sizes[1]);
+      }
+    }
+    if (ndims > 2) {
+      dims.push_back(dim2_is_z ? mesh.LocalNz : dim_sizes[2]);
+    }
+
+    start.push_back(static_cast<std::size_t>(mesh.MapGlobalX));
+    count.push_back(static_cast<std::size_t>(mesh.MapCountX));
+    mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalX));
+    mem_count.push_back(static_cast<std::size_t>(mesh.LocalNx));
+
+    if (dim1_is_y) {
+      start.push_back(static_cast<std::size_t>(mesh.MapGlobalY));
+      count.push_back(static_cast<std::size_t>(mesh.MapCountY));
+      mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalY));
+      mem_count.push_back(static_cast<std::size_t>(mesh.LocalNy));
+    } else if (dim1_is_z) {
+      start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
+      count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
+      mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));
+      mem_count.push_back(static_cast<std::size_t>(mesh.LocalNz));
+    }
+
+    if (dim2_is_z) {
+      start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
+      count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
+      mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));
+      mem_count.push_back(static_cast<std::size_t>(mesh.LocalNz));
+    }
+  }
+
+  auto selection() const { return adios2::Box<adios2::Dims>{start, count}; }
+  auto memorySelection() const { return adios2::Box<adios2::Dims>{mem_start, mem_count}; }
+};
+
+template <template <class> class T, class U>
+auto read_variable(adios2::IO& io, adios2::Engine& reader, const std::string& name,
+                   const Selection& selection, T<U>& value) {
+  auto variable = io.InquireVariable<U>(name);
+
+  if (selection.should_set_selection) {
+    variable.SetSelection(selection.selection());
+    variable.SetMemorySelection(selection.memorySelection());
+  }
+
+  reader.Get<U>(variable, value.begin(), adios2::Mode::Sync);
+  return Options(value);
+}
 } // namespace
 
 namespace bout {
@@ -51,8 +168,7 @@ OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) {
 template <class T>
 Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name,
                      const std::string& type) {
-  std::vector<T> data;
-  adios2::Variable<T> variable = io.InquireVariable<T>(name);
+  auto variable = io.InquireVariable<T>(name);
 
   using bout::globals::mesh;
 
@@ -68,9 +184,9 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
         type, name, reader.Name());
   }
 
-  if (type != "double" && type != "float") {
+  if (type != "double" && type != "float" && type != "int32_t") {
     throw BoutException("ADIOS reader did not implement reading arrays that are not "
-                        "`double`/`float` type. "
+                        "`double`/`float`/`int32_t` type. "
                         "Found `{}` '{}' in file '{}'",
                         type, name, reader.Name());
   }
@@ -90,130 +206,54 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
   }
 
   const auto dims = to_int_dims(variable.Shape());
-  const auto ndims = dims.size();
-  adios2::Variable<BoutReal> variableD = io.InquireVariable<BoutReal>(name);
+  auto dims_attr =
+      io.InquireAttribute<std::string>(fmt::format("{}/__xarray_dimensions__", name))
+          .Data();
 
-  const bool dim0_is_x = ndims > 0 ? (dims[0] == mesh->GlobalNx) : false;
-  const bool dim1_is_y = ndims > 1 ? (dims[1] == mesh->GlobalNy) : false;
-  const bool dim1_is_z = ndims > 1 ? (dims[1] == mesh->GlobalNz) : false;
-  const bool dim2_is_z = ndims > 2 ? (dims[2] == mesh->GlobalNz) : false;
+  const auto selection = Selection(dims_attr, dims, *mesh);
+  const auto ndims = selection.dims.size();
 
   switch (ndims) {
   case 1: {
-    Array<BoutReal> value(dims[0]);
-    BoutReal* data = value.begin();
-    reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
-    return Options(value);
+    if (type == "float" or type == "double") {
+      Array<BoutReal> value(dims[0]);
+      return read_variable(io, reader, name, selection, value);
+    }
+    if (type == "int32_t") {
+      Array<int> value(dims[0]);
+      return read_variable(io, reader, name, selection, value);
+    }
+    break;
   }
   case 2: {
-    // This could be a Field2D (XY) or FieldPerp (XZ)
-    // Here we look for array sizes, but if Y and Z dimensions are the same size
-    // then it's ambiguous. This method also depends on the global Mesh object.
-    // Some possibilities:
-    // - Add an attribute to specify field type or dimension labels
-    // - Load all the data, and select a region when converting to a Field in Options
-    // - Add a lazy loading type to Options, and load data when needed
-    if (dim0_is_x and dim1_is_y) {
-      // Probably a Field2D
-
-      // Read just the local piece of the array
-      Matrix<BoutReal> value(mesh->LocalNx, mesh->LocalNy);
-
-      // Offset of this processor's data into the global array
-      adios2::Dims start = {static_cast<size_t>(mesh->MapGlobalX),
-                            static_cast<size_t>(mesh->MapGlobalY)};
-
-      // The size of the mapped region
-      adios2::Dims count = {static_cast<size_t>(mesh->MapCountX),
-                            static_cast<size_t>(mesh->MapCountY)};
-
-      // Where the actual data starts in data pointer (to exclude ghost cells)
-      adios2::Dims memStart = {static_cast<size_t>(mesh->MapLocalX),
-                               static_cast<size_t>(mesh->MapLocalY)};
-
-      // The actual size of data pointer in memory (including ghost cells)
-      adios2::Dims memCount = {static_cast<size_t>(mesh->LocalNx),
-                               static_cast<size_t>(mesh->LocalNy)};
-      variableD.SetSelection({start, count});
-      variableD.SetMemorySelection({memStart, memCount});
-      BoutReal* data = value.begin();
-      reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
-      return Options(value);
+    if (type == "float" or type == "double") {
+      Matrix<BoutReal> value(selection.dims[0], selection.dims[1]);
+      return read_variable(io, reader, name, selection, value);
     }
-    if (dim0_is_x and dim1_is_z) {
-      // Probably a FieldPerp
-
-      // Read just the local piece of the array
-      Matrix<BoutReal> value(mesh->LocalNx, mesh->LocalNz);
-
-      // Offset of this processor's data into the global array
-      adios2::Dims start = {static_cast<size_t>(mesh->MapGlobalX),
-                            static_cast<size_t>(mesh->MapGlobalZ)};
-
-      // The size of the mapped region
-      adios2::Dims count = {static_cast<size_t>(mesh->MapCountX),
-                            static_cast<size_t>(mesh->MapCountZ)};
-
-      // Where the actual data starts in data pointer (to exclude ghost cells)
-      adios2::Dims memStart = {static_cast<size_t>(mesh->MapLocalX),
-                               static_cast<size_t>(mesh->MapLocalZ)};
-
-      // The actual size of data pointer in memory (including ghost cells)
-      adios2::Dims memCount = {static_cast<size_t>(mesh->LocalNx),
-                               static_cast<size_t>(mesh->LocalNz)};
-      variableD.SetSelection({start, count});
-      variableD.SetMemorySelection({memStart, memCount});
-      BoutReal* data = value.begin();
-      reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
-      return Options(value);
+    if (type == "int32_t") {
+      Matrix<int> value(selection.dims[0], selection.dims[1]);
+      return read_variable(io, reader, name, selection, value);
     }
-    Matrix<BoutReal> value(dims[0], dims[1]);
-    BoutReal* data = value.begin();
-    reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
-    return Options(value);
+    break;
   }
   case 3: {
-    if (dim0_is_x and dim1_is_y and dim2_is_z) {
-      // Global array. Read just this processor's part of it
-
-      Tensor<BoutReal> value(mesh->LocalNx, mesh->LocalNy, mesh->LocalNz);
-
-      // Offset of this processor's data into the global array
-      adios2::Dims start = {static_cast<size_t>(mesh->MapGlobalX),
-                            static_cast<size_t>(mesh->MapGlobalY),
-                            static_cast<size_t>(mesh->MapGlobalZ)};
-
-      // The size of the mapped region
-      adios2::Dims count = {static_cast<size_t>(mesh->MapCountX),
-                            static_cast<size_t>(mesh->MapCountY),
-                            static_cast<size_t>(mesh->MapCountZ)};
-
-      // Where the actual data starts in data pointer (to exclude ghost cells)
-      adios2::Dims memStart = {static_cast<size_t>(mesh->MapLocalX),
-                               static_cast<size_t>(mesh->MapLocalY),
-                               static_cast<size_t>(mesh->MapLocalZ)};
-
-      // The actual size of data pointer in memory (including ghost cells)
-      adios2::Dims memCount = {static_cast<size_t>(mesh->LocalNx),
-                               static_cast<size_t>(mesh->LocalNy),
-                               static_cast<size_t>(mesh->LocalNz)};
-
-      variableD.SetSelection({start, count});
-      variableD.SetMemorySelection({memStart, memCount});
-      BoutReal* data = value.begin();
-      reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
-      return Options(value);
+    if (type == "float" or type == "double") {
+      Tensor<BoutReal> value(selection.dims[0], selection.dims[1], selection.dims[2]);
+      return read_variable(io, reader, name, selection, value);
     }
-    // Doesn't match global array size.
-    // Read the entire array, in case it can be handled later
-    Tensor<BoutReal> value(dims[0], dims[1], dims[2]);
-    BoutReal* data = value.begin();
-    reader.Get<BoutReal>(variableD, data, adios2::Mode::Sync);
-    return Options(value);
+    if (type == "int32_t") {
+      Tensor<int> value(selection.dims[0], selection.dims[1], selection.dims[2]);
+      return read_variable(io, reader, name, selection, value);
+    }
+    break;
   }
+  // Throw below
+  default: break;
   }
-  throw BoutException("ADIOS reader failed to read '{}' of dimension {} in file '{}'",
-                      name, ndims, reader.Name());
+  auto dims_str = fmt::format("[{}]", fmt::join(dims, ", "));
+  throw BoutException(
+      "ADIOS reader failed to read '{}' (shape: {}, type: '{}') in file '{}'", name,
+      dims_str, type, reader.Name());
 }
 
 Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name,
@@ -325,7 +365,6 @@ void OptionsADIOS::verifyTimesteps() const {
   stream.endStep();
 }
 
-const std::vector<std::string> DIMS_NONE;
 const std::vector<std::string> DIMS_X = {"x"};
 const std::vector<std::string> DIMS_XY = {"x", "y"};
 const std::vector<std::string> DIMS_XZ = {"x", "z"};
@@ -360,6 +399,17 @@ auto make_start(const T& value) {
   const auto shape = value.shape();
   return make_start_impl(shape, tuple_index_sequence<decltype(shape)>{});
 }
+
+template <std::size_t... I>
+auto make_dims_impl(std::index_sequence<I...> /*index*/) {
+  using namespace std::string_literals;
+  return std::vector{"rank"s, (fmt::format("dim_{}", I))...};
+}
+// Return vector of dimension names: `{"rank", "dim_0", ...}`
+template <class T>
+auto make_dims(const T& value) {
+  return make_dims_impl(tuple_index_sequence<decltype(value.shape())>{});
+}
 } // namespace
 
 /// Visit a variant type, and put the data into a NcVar
@@ -387,7 +437,8 @@ struct ADIOSPutVarVisitor {
   template <template <class> class T, class U>
   void put_helper(const T<U>& value) {
     const auto shape = make_shape(static_cast<std::size_t>(BoutComm::size()), value);
-    auto var = stream.GetArrayVariable<U>(varname, shape, DIMS_NONE, BoutComm::rank());
+    auto var =
+        stream.GetArrayVariable<U>(varname, shape, make_dims(value), BoutComm::rank());
     var.SetSelection({make_start(value), make_shape(1, value)});
     stream.engine().Put<U>(var, value.begin());
   }
@@ -593,11 +644,12 @@ void writeGroup(const Options& options, ADIOSStream& stream, const std::string&
 
         // Write the variable
         // Note: ADIOS2 uses '/' to as a group separator; BOUT++ uses ':'
-        std::string varname = groupname.empty() ? name : groupname + "/" + name;
+        std::string varname =
+            groupname.empty() ? name : fmt::format("{}/{}", groupname, name);
         bout::utils::visit(ADIOSPutVarVisitor(varname, stream), child.value);
 
         // Write attributes
-        if (!BoutComm::rank()) {
+        if (BoutComm::rank() == 0) {
           for (const auto& attribute : child.attributes) {
             const std::string& att_name = attribute.first;
             const auto& att = attribute.second;
diff --git a/tests/unit/sys/test_options_adios2.cxx b/tests/unit/sys/test_options_adios2.cxx
index d5bb4653a6..8d221b6bea 100644
--- a/tests/unit/sys/test_options_adios2.cxx
+++ b/tests/unit/sys/test_options_adios2.cxx
@@ -112,6 +112,30 @@ TEST_F(OptionsAdios2Test, ReadWriteField3D) {
   EXPECT_DOUBLE_EQ(value(1, 1, 1), 2.4);
 }
 
+
+TEST_F(OptionsAdios2Test, ReadWriteMatrixInt) {
+  constexpr int nx = 2;
+  constexpr int ny = 3;
+  Matrix<int> matrix_in(nx, ny);
+  int count = 0;
+
+  for (int i = 0; i < nx; ++i) {
+    for (int j = 0; j < ny; ++j) {
+      matrix_in(i, j) = ++count;
+    }
+  }
+
+  {
+    Options options{{"int_matrix", matrix_in}};
+    OptionsIO::create(file_options)->write(options);
+  }
+
+  Options data = OptionsIO::create(file_options)->read();
+
+  const auto matrix_out = data["int_matrix"].as<Matrix<int>>();
+  ASSERT_EQ(matrix_out(nx - 1, ny - 1), matrix_in(nx - 1, ny - 1));
+}
+
 TEST_F(OptionsAdios2Test, Groups) {
   {
     Options options;

From 41157f88ecb4f0f73636c71c33f004c8f846adfd Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Nov 2025 10:39:00 +0000
Subject: [PATCH 0328/1827] Move some local functions/structs to anonymous
 namespace

---
 src/sys/options/options_adios.cxx | 53 ++++++++++++++++---------------
 1 file changed, 28 insertions(+), 25 deletions(-)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 10cc4ddf6a..6255a7d44c 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -146,24 +146,6 @@ auto read_variable(adios2::IO& io, adios2::Engine& reader, const std::string& na
   reader.Get<U>(variable, value.begin(), adios2::Mode::Sync);
   return Options(value);
 }
-} // namespace
-
-namespace bout {
-OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) {
-  if (options["file"].doc("File name. Defaults to <path>/<prefix>.pb").isSet()) {
-    filename = options["file"].as<std::string>();
-  } else {
-    // Both path and prefix must be set
-    filename = fmt::format("{}/{}.bp", options["path"].as<std::string>(),
-                           options["prefix"].as<std::string>());
-  }
-
-  file_mode = (options["append"].doc("Append to existing file?").withDefault<bool>(false))
-                  ? adios2::Mode::Append
-                  : adios2::Mode::Write;
-
-  singleWriteFile = options["singleWriteFile"].withDefault<bool>(false);
-}
 
 template <class T>
 Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name,
@@ -248,7 +230,8 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
     break;
   }
   // Throw below
-  default: break;
+  default:
+    break;
   }
   auto dims_str = fmt::format("[{}]", fmt::join(dims, ", "));
   throw BoutException(
@@ -296,6 +279,24 @@ bool readAttribute(adios2::IO& io, const std::string& name, const std::string& t
                             type, name);
   return false;
 }
+} // namespace
+
+namespace bout {
+OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) {
+  if (options["file"].doc("File name. Defaults to <path>/<prefix>.pb").isSet()) {
+    filename = options["file"].as<std::string>();
+  } else {
+    // Both path and prefix must be set
+    filename = fmt::format("{}/{}.bp", options["path"].as<std::string>(),
+                           options["prefix"].as<std::string>());
+  }
+
+  file_mode = (options["append"].doc("Append to existing file?").withDefault<bool>(false))
+                  ? adios2::Mode::Append
+                  : adios2::Mode::Write;
+
+  singleWriteFile = options["singleWriteFile"].withDefault<bool>(false);
+}
 
 Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
   Timer timer("io");
@@ -364,6 +365,7 @@ void OptionsADIOS::verifyTimesteps() const {
 
   stream.endStep();
 }
+}
 
 const std::vector<std::string> DIMS_X = {"x"};
 const std::vector<std::string> DIMS_XY = {"x", "y"};
@@ -410,11 +412,10 @@ template <class T>
 auto make_dims(const T& value) {
   return make_dims_impl(tuple_index_sequence<decltype(value.shape())>{});
 }
-} // namespace
 
 /// Visit a variant type, and put the data into a NcVar
 struct ADIOSPutVarVisitor {
-  ADIOSPutVarVisitor(const std::string& name, ADIOSStream& stream)
+  ADIOSPutVarVisitor(const std::string& name, bout::ADIOSStream& stream)
       : varname(name), stream(stream) {}
   template <typename T>
   void operator()(const T& value) {
@@ -431,7 +432,7 @@ struct ADIOSPutVarVisitor {
 
 private:
   const std::string& varname;
-  ADIOSStream& stream;
+  bout::ADIOSStream& stream;
 
   // helper for `Array`, `Matrix`, `Tensor`
   template <template <class> class T, class U>
@@ -591,7 +592,7 @@ void ADIOSPutVarVisitor::operator()<FieldPerp>(const FieldPerp& value) {
 /// Visit a variant type, and put the data into a NcVar
 struct ADIOSPutAttVisitor {
   ADIOSPutAttVisitor(const std::string& varname, const std::string& attrname,
-                     ADIOSStream& stream)
+                     bout::ADIOSStream& stream)
       : varname(varname), attrname(attrname), stream(stream) {}
   template <typename T>
   void operator()(const T& value) {
@@ -601,7 +602,7 @@ struct ADIOSPutAttVisitor {
 private:
   const std::string& varname;
   const std::string& attrname;
-  ADIOSStream& stream;
+  bout::ADIOSStream& stream;
 };
 
 template <>
@@ -609,7 +610,7 @@ void ADIOSPutAttVisitor::operator()<bool>(const bool& value) {
   stream.io.DefineAttribute<int>(attrname, (int)value, varname, "/", false);
 }
 
-void writeGroup(const Options& options, ADIOSStream& stream, const std::string& groupname,
+void writeGroup(const Options& options, bout::ADIOSStream& stream, const std::string& groupname,
                 const std::string& time_dimension) {
 
   for (const auto& childpair : options.getChildren()) {
@@ -664,7 +665,9 @@ void writeGroup(const Options& options, ADIOSStream& stream, const std::string&
     }
   }
 }
+} // namespace
 
+namespace bout {
 /// Write options to file
 void OptionsADIOS::write(const Options& options, const std::string& time_dim) {
   Timer timer("io");

From 7cde30e9a262603f3b92af37f1bafcd7f47061ae Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Nov 2025 10:45:59 +0000
Subject: [PATCH 0329/1827] Remove macros from `OptionsAdios`

---
 src/sys/options/options_adios.cxx | 89 +++++++++++++++++++++----------
 1 file changed, 61 insertions(+), 28 deletions(-)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 6255a7d44c..12d96b9939 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -241,42 +241,75 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
 
 Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name,
                      const std::string& type) {
-#define declare_template_instantiation(T)           \
-  if (type == adios2::GetType<T>()) {               \
-    return readVariable<T>(reader, io, name, type); \
-  }
-  ADIOS2_FOREACH_ATTRIBUTE_PRIMITIVE_STDTYPE_1ARG(declare_template_instantiation)
-  declare_template_instantiation(std::string)
-#undef declare_template_instantiation
-      output_warn.write("ADIOS readVariable can't read type '{}' (variable '{}')", type,
-                        name);
+  if (type == adios2::GetType<std::string>()) {
+    return readVariable<std::string>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<char>()) {
+    return readVariable<char>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<int8_t>()) {
+    return readVariable<int8_t>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<int16_t>()) {
+    return readVariable<int16_t>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<int32_t>()) {
+    return readVariable<int32_t>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<int64_t>()) {
+    return readVariable<int64_t>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<uint8_t>()) {
+    return readVariable<uint8_t>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<uint16_t>()) {
+    return readVariable<uint16_t>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<uint32_t>()) {
+    return readVariable<uint32_t>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<uint64_t>()) {
+    return readVariable<uint64_t>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<float>()) {
+    return readVariable<float>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<double>()) {
+    return readVariable<double>(reader, io, name, type);
+  }
+  if (type == adios2::GetType<long double>()) {
+    return readVariable<long double>(reader, io, name, type);
+  }
+
+  output_warn.write("ADIOS readVariable can't read type '{}' (variable '{}')", type,
+                    name);
   return Options{};
 }
 
 bool readAttribute(adios2::IO& io, const std::string& name, const std::string& type,
                    Options& result) {
   // Attribute is the part of 'name' after the last '/' separator
-  std::string attrname;
+  std::string attrname = name;
   auto pos = name.find_last_of('/');
-  if (pos == std::string::npos) {
-    attrname = name;
-  } else {
+  if (pos != std::string::npos) {
     attrname = name.substr(pos + 1);
   }
 
-#define declare_template_instantiation(T)                  \
-  if (type == adios2::GetType<T>()) {                      \
-    adios2::Attribute<T> a = io.InquireAttribute<T>(name); \
-    result.attributes[attrname] = *a.Data().data();        \
-    return true;                                           \
+  if (type == adios2::GetType<int>()) {
+    result.attributes[attrname] = *io.InquireAttribute<int>(name).Data().data();
+    return true;
   }
-  // Only some types of attributes are supported
-  //declare_template_instantiation(bool)
-  declare_template_instantiation(int) declare_template_instantiation(BoutReal)
-      declare_template_instantiation(std::string)
-#undef declare_template_instantiation
-          output_warn.write("ADIOS readAttribute can't read type '{}' (variable '{}')",
-                            type, name);
+  if (type == adios2::GetType<BoutReal>()) {
+    result.attributes[attrname] = *io.InquireAttribute<BoutReal>(name).Data().data();
+    return true;
+  }
+  if (type == adios2::GetType<std::string>()) {
+    result.attributes[attrname] = *io.InquireAttribute<std::string>(name).Data().data();
+    return true;
+  }
+
+  output_warn.write("ADIOS readAttribute can't read type '{}' (variable '{}')", type,
+                    name);
   return false;
 }
 } // namespace
@@ -365,7 +398,7 @@ void OptionsADIOS::verifyTimesteps() const {
 
   stream.endStep();
 }
-}
+} // namespace bout
 
 const std::vector<std::string> DIMS_X = {"x"};
 const std::vector<std::string> DIMS_XY = {"x", "y"};
@@ -610,8 +643,8 @@ void ADIOSPutAttVisitor::operator()<bool>(const bool& value) {
   stream.io.DefineAttribute<int>(attrname, (int)value, varname, "/", false);
 }
 
-void writeGroup(const Options& options, bout::ADIOSStream& stream, const std::string& groupname,
-                const std::string& time_dimension) {
+void writeGroup(const Options& options, bout::ADIOSStream& stream,
+                const std::string& groupname, const std::string& time_dimension) {
 
   for (const auto& childpair : options.getChildren()) {
     const auto& name = childpair.first;

From bb407a4079fa5faa8d7f9f1a8f275255731dca9e Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Nov 2025 11:15:11 +0000
Subject: [PATCH 0330/1827] Reduce duplication in `OptionsAdios` visitors

---
 src/sys/options/options_adios.cxx | 231 ++++++++++--------------------
 1 file changed, 75 insertions(+), 156 deletions(-)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 12d96b9939..d0726a58df 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -43,6 +43,8 @@ struct Selection {
   adios2::Dims mem_start;
   // The actual size of data pointer in memory (including ghost cells)
   adios2::Dims mem_count;
+  // Global shape, including boundaries but not guard cells
+  adios2::Dims shape;
   // Shape of the local variable to read into
   std::vector<int> dims;
 
@@ -104,17 +106,20 @@ struct Selection {
       dims.push_back(dim2_is_z ? mesh.LocalNz : dim_sizes[2]);
     }
 
+    shape.push_back(static_cast<std::size_t>(mesh.GlobalNx));
     start.push_back(static_cast<std::size_t>(mesh.MapGlobalX));
     count.push_back(static_cast<std::size_t>(mesh.MapCountX));
     mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalX));
     mem_count.push_back(static_cast<std::size_t>(mesh.LocalNx));
 
     if (dim1_is_y) {
+      shape.push_back(static_cast<std::size_t>(mesh.GlobalNy));
       start.push_back(static_cast<std::size_t>(mesh.MapGlobalY));
       count.push_back(static_cast<std::size_t>(mesh.MapCountY));
       mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalY));
       mem_count.push_back(static_cast<std::size_t>(mesh.LocalNy));
     } else if (dim1_is_z) {
+      shape.push_back(static_cast<std::size_t>(mesh.GlobalNz));
       start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
       count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
       mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));
@@ -122,6 +127,7 @@ struct Selection {
     }
 
     if (dim2_is_z) {
+      shape.push_back(static_cast<std::size_t>(mesh.GlobalNz));
       start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
       count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
       mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));
@@ -456,12 +462,69 @@ struct ADIOSPutVarVisitor {
     stream.engine().Put(var, value);
   }
 
-  void operator()(const Array<int>& value) { put_helper(value); }
-  void operator()(const Array<BoutReal>& value) { put_helper(value); }
-  void operator()(const Matrix<int>& value) { put_helper(value); }
-  void operator()(const Matrix<BoutReal>& value) { put_helper(value); }
-  void operator()(const Tensor<int>& value) { put_helper(value); }
-  void operator()(const Tensor<BoutReal>& value) { put_helper(value); }
+  void operator()(const Array<int>& value) { amt_put_helper(value); }
+  void operator()(const Array<BoutReal>& value) { amt_put_helper(value); }
+  void operator()(const Matrix<int>& value) { amt_put_helper(value); }
+  void operator()(const Matrix<BoutReal>& value) { amt_put_helper(value); }
+  void operator()(const Tensor<int>& value) { amt_put_helper(value); }
+  void operator()(const Tensor<BoutReal>& value) { amt_put_helper(value); }
+  void operator()(bool value) {
+    // Scalars are only written from processor 0
+    if (BoutComm::rank() != 0) {
+      return;
+    }
+    stream.engine().Put(stream.GetValueVariable<int>(varname), static_cast<int>(value));
+  }
+  void operator()(int value) {
+    // Scalars are only written from processor 0
+    if (BoutComm::rank() != 0) {
+      return;
+    }
+    stream.engine().Put(stream.GetValueVariable<int>(varname), value);
+  }
+  void operator()(BoutReal value) {
+    // Scalars are only written from processor 0
+    if (BoutComm::rank() != 0) {
+      return;
+    }
+    stream.engine().Put(stream.GetValueVariable<BoutReal>(varname), value);
+  }
+
+  void operator()(const std::string& value) {
+    // Scalars are only written from processor 0
+    if (BoutComm::rank() != 0) {
+      return;
+    }
+    stream.engine().Put<std::string>(stream.GetValueVariable<std::string>(varname), value,
+                                     adios2::Mode::Sync);
+  }
+
+  void operator()(const Field2D& value) {
+    auto selection = Selection(DIMS_XY, {}, *value.getMesh());
+    auto var = stream.GetArrayVariable<BoutReal>(varname, selection.shape, DIMS_XY,
+                                                 BoutComm::rank());
+    var.SetSelection(selection.selection());
+    var.SetMemorySelection(selection.memorySelection());
+    stream.engine().Put(var, &value(0, 0));
+  }
+
+  void operator()(const Field3D& value) {
+    auto selection = Selection(DIMS_XYZ, {}, *value.getMesh());
+    auto var = stream.GetArrayVariable<BoutReal>(varname, selection.shape, DIMS_XYZ,
+                                                 BoutComm::rank());
+    var.SetSelection(selection.selection());
+    var.SetMemorySelection(selection.memorySelection());
+    stream.engine().Put(var, &value(0, 0, 0));
+  }
+
+  void operator()(const FieldPerp& value) {
+    auto selection = Selection(DIMS_XZ, {}, *value.getMesh());
+    auto var = stream.GetArrayVariable<BoutReal>(varname, selection.shape, DIMS_XZ,
+                                                 BoutComm::rank());
+    var.SetSelection(selection.selection());
+    var.SetMemorySelection(selection.memorySelection());
+    stream.engine().Put<BoutReal>(var, &value(0, 0));
+  }
 
 private:
   const std::string& varname;
@@ -469,7 +532,7 @@ struct ADIOSPutVarVisitor {
 
   // helper for `Array`, `Matrix`, `Tensor`
   template <template <class> class T, class U>
-  void put_helper(const T<U>& value) {
+  void amt_put_helper(const T<U>& value) {
     const auto shape = make_shape(static_cast<std::size_t>(BoutComm::size()), value);
     auto var =
         stream.GetArrayVariable<U>(varname, shape, make_dims(value), BoutComm::rank());
@@ -478,150 +541,6 @@ struct ADIOSPutVarVisitor {
   }
 };
 
-template <>
-void ADIOSPutVarVisitor::operator()<bool>(const bool& value) {
-  // Scalars are only written from processor 0
-  if (BoutComm::rank() != 0) {
-    return;
-  }
-  adios2::Variable<int> var = stream.GetValueVariable<int>(varname);
-  stream.engine().Put<int>(var, static_cast<int>(value));
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<int>(const int& value) {
-  // Scalars are only written from processor 0
-  if (BoutComm::rank() != 0) {
-    return;
-  }
-  adios2::Variable<int> var = stream.GetValueVariable<int>(varname);
-  stream.engine().Put<int>(var, value);
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<BoutReal>(const BoutReal& value) {
-  // Scalars are only written from processor 0
-  if (BoutComm::rank() != 0) {
-    return;
-  }
-  adios2::Variable<BoutReal> var = stream.GetValueVariable<BoutReal>(varname);
-  stream.engine().Put<BoutReal>(var, value);
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<std::string>(const std::string& value) {
-  // Scalars are only written from processor 0
-  if (BoutComm::rank() != 0) {
-    return;
-  }
-  adios2::Variable<std::string> var = stream.GetValueVariable<std::string>(varname);
-  stream.engine().Put<std::string>(var, value, adios2::Mode::Sync);
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<Field2D>(const Field2D& value) {
-  // Get the mesh that describes how local data relates to global arrays
-  auto mesh = value.getMesh();
-
-  // The global size of this array includes boundary cells but not communication guard cells.
-  // In general this array will be sparse because it may have gaps.
-  adios2::Dims shape = {static_cast<size_t>(mesh->GlobalNx),
-                        static_cast<size_t>(mesh->GlobalNy)};
-
-  // Offset of this processor's data into the global array
-  adios2::Dims start = {static_cast<size_t>(mesh->MapGlobalX),
-                        static_cast<size_t>(mesh->MapGlobalY)};
-
-  // The size of the mapped region
-  adios2::Dims count = {static_cast<size_t>(mesh->MapCountX),
-                        static_cast<size_t>(mesh->MapCountY)};
-
-  // Where the actual data starts in data pointer (to exclude ghost cells)
-  adios2::Dims memStart = {static_cast<size_t>(mesh->MapLocalX),
-                           static_cast<size_t>(mesh->MapLocalY)};
-
-  // The actual size of data pointer in memory (including ghost cells)
-  adios2::Dims memCount = {static_cast<size_t>(value.getNx()),
-                           static_cast<size_t>(value.getNy())};
-
-  adios2::Variable<BoutReal> var =
-      stream.GetArrayVariable<BoutReal>(varname, shape, DIMS_XY, BoutComm::rank());
-  var.SetSelection({start, count});
-  var.SetMemorySelection({memStart, memCount});
-  stream.engine().Put<BoutReal>(var, &value(0, 0));
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<Field3D>(const Field3D& value) {
-  // Get the mesh that describes how local data relates to global arrays
-  auto mesh = value.getMesh();
-
-  // The global size of this array includes boundary cells but not communication guard cells.
-  // In general this array will be sparse because it may have gaps.
-  adios2::Dims shape = {static_cast<size_t>(mesh->GlobalNx),
-                        static_cast<size_t>(mesh->GlobalNy),
-                        static_cast<size_t>(mesh->GlobalNz)};
-
-  // Offset of this processor's data into the global array
-  adios2::Dims start = {static_cast<size_t>(mesh->MapGlobalX),
-                        static_cast<size_t>(mesh->MapGlobalY),
-                        static_cast<size_t>(mesh->MapGlobalZ)};
-
-  // The size of the mapped region
-  adios2::Dims count = {static_cast<size_t>(mesh->MapCountX),
-                        static_cast<size_t>(mesh->MapCountY),
-                        static_cast<size_t>(mesh->MapCountZ)};
-
-  // Where the actual data starts in data pointer (to exclude ghost cells)
-  adios2::Dims memStart = {static_cast<size_t>(mesh->MapLocalX),
-                           static_cast<size_t>(mesh->MapLocalY),
-                           static_cast<size_t>(mesh->MapLocalZ)};
-
-  // The actual size of data pointer in memory (including ghost cells)
-  adios2::Dims memCount = {static_cast<size_t>(value.getNx()),
-                           static_cast<size_t>(value.getNy()),
-                           static_cast<size_t>(value.getNz())};
-
-  adios2::Variable<BoutReal> var =
-      stream.GetArrayVariable<BoutReal>(varname, shape, DIMS_XYZ, BoutComm::rank());
-  var.SetSelection({start, count});
-  var.SetMemorySelection({memStart, memCount});
-  stream.engine().Put<BoutReal>(var, &value(0, 0, 0));
-}
-
-template <>
-void ADIOSPutVarVisitor::operator()<FieldPerp>(const FieldPerp& value) {
-  // Get the mesh that describes how local data relates to global arrays
-  auto mesh = value.getMesh();
-
-  // The global size of this array includes boundary cells but not communication guard cells.
-  // In general this array will be sparse because it may have gaps.
-  adios2::Dims shape = {static_cast<size_t>(mesh->GlobalNx),
-                        static_cast<size_t>(mesh->GlobalNz)};
-
-  // Offset of this processor's data into the global array
-  adios2::Dims start = {static_cast<size_t>(mesh->MapGlobalX),
-                        static_cast<size_t>(mesh->MapGlobalZ)};
-
-  // The size of the mapped region
-  adios2::Dims count = {static_cast<size_t>(mesh->MapCountX),
-                        static_cast<size_t>(mesh->MapCountZ)};
-
-  // Where the actual data starts in data pointer (to exclude ghost cells)
-  adios2::Dims memStart = {static_cast<size_t>(mesh->MapLocalX),
-                           static_cast<size_t>(mesh->MapLocalZ)};
-
-  // The actual size of data pointer in memory (including ghost cells)
-  adios2::Dims memCount = {static_cast<size_t>(value.getNx()),
-                           static_cast<size_t>(value.getNz())};
-
-  adios2::Variable<BoutReal> var =
-      stream.GetArrayVariable<BoutReal>(varname, shape, DIMS_XZ, BoutComm::rank());
-  var.SetSelection({start, count});
-  var.SetMemorySelection({memStart, memCount});
-  stream.engine().Put<BoutReal>(var, &value(0, 0));
-}
-
 /// Visit a variant type, and put the data into a NcVar
 struct ADIOSPutAttVisitor {
   ADIOSPutAttVisitor(const std::string& varname, const std::string& attrname,
@@ -632,17 +551,17 @@ struct ADIOSPutAttVisitor {
     stream.io.DefineAttribute<T>(attrname, value, varname, "/", false);
   }
 
+  void operator()(bool value) {
+    stream.io.DefineAttribute<int>(attrname, static_cast<int>(value), varname, "/",
+                                   false);
+  }
+
 private:
   const std::string& varname;
   const std::string& attrname;
   bout::ADIOSStream& stream;
 };
 
-template <>
-void ADIOSPutAttVisitor::operator()<bool>(const bool& value) {
-  stream.io.DefineAttribute<int>(attrname, (int)value, varname, "/", false);
-}
-
 void writeGroup(const Options& options, bout::ADIOSStream& stream,
                 const std::string& groupname, const std::string& time_dimension) {
 

From 126e586762aa62fb425617ac01b09e9a368b83b2 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Nov 2025 11:18:00 +0000
Subject: [PATCH 0331/1827] Silence some clang-tidy warnings

---
 src/sys/options/options_adios.cxx | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index d0726a58df..b1bc08a433 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -527,8 +527,9 @@ struct ADIOSPutVarVisitor {
   }
 
 private:
-  const std::string& varname;
-  bout::ADIOSStream& stream;
+  // Ok to keep const/refs here as visitor is only a temporary
+  const std::string& varname; // NOLINT(*-avoid-const-or-ref-data-members)
+  bout::ADIOSStream& stream;  // NOLINT(*-avoid-const-or-ref-data-members)
 
   // helper for `Array`, `Matrix`, `Tensor`
   template <template <class> class T, class U>
@@ -557,9 +558,10 @@ struct ADIOSPutAttVisitor {
   }
 
 private:
-  const std::string& varname;
-  const std::string& attrname;
-  bout::ADIOSStream& stream;
+  // Ok to keep const/refs here as visitor is only a temporary
+  const std::string& varname;  // NOLINT(*-avoid-const-or-ref-data-members)
+  const std::string& attrname; // NOLINT(*-avoid-const-or-ref-data-members)
+  bout::ADIOSStream& stream;   // NOLINT(*-avoid-const-or-ref-data-members)
 };
 
 void writeGroup(const Options& options, bout::ADIOSStream& stream,

From 672f5fe82e88325c2121c237fe9be2b1419782f8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Nov 2025 11:39:32 +0000
Subject: [PATCH 0332/1827] Fix a bunch of clang-tidy warnings

---
 .clang-tidy                       |  3 +++
 src/sys/options/options_adios.cxx | 34 +++++++++++++++++++++----------
 src/sys/options/options_adios.hxx |  6 +++---
 3 files changed, 29 insertions(+), 14 deletions(-)

diff --git a/.clang-tidy b/.clang-tidy
index a142355fc4..23167e93d0 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -18,6 +18,9 @@ CheckOptions:
 
   - key: readability-qualified-auto.AllowedTypes
     value: 'MPI_Comm'
+
+  - key: misc-include-cleaner.IgnoreHeaders
+    value: 'adios2/.*;bits/.*'
 ---
 
 Disabled checks and reasons:
diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index b1bc08a433..2e64423824 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -5,22 +5,31 @@
 #include "options_adios.hxx"
 
 #include "bout/adios_object.hxx"
+#include "bout/array.hxx"
+#include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/field2d.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
 #include "bout/options.hxx"
+#include "bout/options_io.hxx"
+#include "bout/output.hxx"
 #include "bout/sys/timer.hxx"
+#include "bout/sys/variant.hxx"
 #include "bout/traits.hxx"
+#include "bout/utils.hxx"
 
-#include <adios2.h>
+#include <adios2.h> // IWYU pragma: keep
 #include <fmt/format.h>
 #include <fmt/ranges.h>
 
 #include <algorithm>
 #include <cstddef>
+#include <cstdint>
 #include <exception>
 #include <iterator>
+#include <stdexcept>
 #include <string>
 #include <utility>
 #include <vector>
@@ -34,6 +43,7 @@ auto to_int_dims(const adios2::Dims& dims) {
   return int_dims;
 }
 
+// Helper class to construct Adios hyperslices
 struct Selection {
   // Offset of this processor's data into the global array
   adios2::Dims start;
@@ -338,12 +348,12 @@ OptionsADIOS::OptionsADIOS(Options& options) : OptionsIO(options) {
 }
 
 Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
-  Timer timer("io");
+  const Timer timer("io");
 
   // Open file
-  ADIOSPtr adiosp = GetADIOSPtr();
+  ADIOSPtr const adiosp = GetADIOSPtr();
   adios2::IO io;
-  std::string ioname = "read_" + filename;
+  const std::string ioname = "read_" + filename;
   try {
     io = adiosp->AtIO(ioname);
   } catch (const std::invalid_argument& e) {
@@ -415,10 +425,9 @@ namespace {
 using bout::utils::tuple_index_sequence;
 
 template <class Tuple, std::size_t... I>
-auto make_shape_impl(std::size_t first, Tuple&& t,
+auto make_shape_impl(std::size_t first, const Tuple& t,
                      std::index_sequence<I...> /* index */) {
-  return adios2::Dims{first,
-                      static_cast<std::size_t>(std::get<I>(std::forward<Tuple>(t)))...};
+  return adios2::Dims{first, static_cast<std::size_t>(std::get<I>(t))...};
 }
 // Return an `adios2::Dims` with value ``{first, value.shape()[0]...}``
 template <class T>
@@ -428,11 +437,11 @@ auto make_shape(std::size_t first, const T& value) {
 }
 
 template <class Tuple, std::size_t... I>
-auto make_start_impl(Tuple&& t, std::index_sequence<I...> /* index */) {
+auto make_start_impl(const Tuple& t, std::index_sequence<I...> /* index */) {
   // Hey look, a legitimate use of the comma operator to get a bunch
   // of zeros the length of the index_sequence!
   return adios2::Dims{static_cast<std::size_t>(BoutComm::rank()),
-                      (std::get<I>(std::forward<Tuple>(t)), std::size_t{0})...};
+                      (std::get<I>(t), std::size_t{0})...};
 }
 // Return an `adios2::Dims` with value ``{rank, 0...}``, with as many zeros as the dimension of ``T``
 template <class T>
@@ -500,6 +509,7 @@ struct ADIOSPutVarVisitor {
   }
 
   void operator()(const Field2D& value) {
+    // Empty dim_sizes is fine because we provide full list of dim_names
     auto selection = Selection(DIMS_XY, {}, *value.getMesh());
     auto var = stream.GetArrayVariable<BoutReal>(varname, selection.shape, DIMS_XY,
                                                  BoutComm::rank());
@@ -509,6 +519,7 @@ struct ADIOSPutVarVisitor {
   }
 
   void operator()(const Field3D& value) {
+    // Empty dim_sizes is fine because we provide full list of dim_names
     auto selection = Selection(DIMS_XYZ, {}, *value.getMesh());
     auto var = stream.GetArrayVariable<BoutReal>(varname, selection.shape, DIMS_XYZ,
                                                  BoutComm::rank());
@@ -518,6 +529,7 @@ struct ADIOSPutVarVisitor {
   }
 
   void operator()(const FieldPerp& value) {
+    // Empty dim_sizes is fine because we provide full list of dim_names
     auto selection = Selection(DIMS_XZ, {}, *value.getMesh());
     auto var = stream.GetArrayVariable<BoutReal>(varname, selection.shape, DIMS_XZ,
                                                  BoutComm::rank());
@@ -599,7 +611,7 @@ void writeGroup(const Options& options, bout::ADIOSStream& stream,
 
         // Write the variable
         // Note: ADIOS2 uses '/' to as a group separator; BOUT++ uses ':'
-        std::string varname =
+        const std::string varname =
             groupname.empty() ? name : fmt::format("{}/{}", groupname, name);
         bout::utils::visit(ADIOSPutVarVisitor(varname, stream), child.value);
 
@@ -624,7 +636,7 @@ void writeGroup(const Options& options, bout::ADIOSStream& stream,
 namespace bout {
 /// Write options to file
 void OptionsADIOS::write(const Options& options, const std::string& time_dim) {
-  Timer timer("io");
+  const Timer timer("io");
 
   // ADIOSStream is just a BOUT++ object, it does not create anything inside ADIOS
   ADIOSStream& stream = ADIOSStream::ADIOSGetStream(filename, file_mode);
diff --git a/src/sys/options/options_adios.hxx b/src/sys/options/options_adios.hxx
index 534c3e1707..d3066378ce 100644
--- a/src/sys/options/options_adios.hxx
+++ b/src/sys/options/options_adios.hxx
@@ -10,7 +10,7 @@
 #if !BOUT_HAS_ADIOS2
 
 namespace {
-bout::RegisterUnavailableOptionsIO
+const bout::RegisterUnavailableOptionsIO
     registerunavailableoptionsadios("adios", "BOUT++ was not configured with ADIOS2");
 }
 
@@ -18,7 +18,7 @@ bout::RegisterUnavailableOptionsIO
 
 #include "bout/options.hxx"
 
-#include <adios2.h>
+#include <adios2.h> // IWYU pragma: keep
 
 #include <string>
 
@@ -71,7 +71,7 @@ private:
 };
 
 namespace {
-RegisterOptionsIO<OptionsADIOS> registeroptionsadios("adios");
+const RegisterOptionsIO<OptionsADIOS> registeroptionsadios("adios");
 }
 
 } // namespace bout

From 0543d24f1df3e73042b92eee996ded65b0afe103 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Nov 2025 11:39:55 +0000
Subject: [PATCH 0333/1827] Apply clang-format

---
 src/sys/adios_object.cxx               | 4 ++--
 tests/unit/sys/test_options_adios2.cxx | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx
index 83bdf45f27..1b3e0a12e2 100644
--- a/src/sys/adios_object.cxx
+++ b/src/sys/adios_object.cxx
@@ -65,8 +65,8 @@ ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname, adios2::Mode
   return it->second;
 }
 
-void ADIOSSetParameters(const std::string& input, char delimKeyValue,
-                        char delimItem, adios2::IO& io) {
+void ADIOSSetParameters(const std::string& input, char delimKeyValue, char delimItem,
+                        adios2::IO& io) {
   auto lf_Trim = [](std::string& input) {
     input.erase(0, input.find_first_not_of(" \n\r\t")); // prefixing spaces
     input.erase(input.find_last_not_of(" \n\r\t") + 1); // suffixing spaces
diff --git a/tests/unit/sys/test_options_adios2.cxx b/tests/unit/sys/test_options_adios2.cxx
index 8d221b6bea..13bbe3db54 100644
--- a/tests/unit/sys/test_options_adios2.cxx
+++ b/tests/unit/sys/test_options_adios2.cxx
@@ -112,7 +112,6 @@ TEST_F(OptionsAdios2Test, ReadWriteField3D) {
   EXPECT_DOUBLE_EQ(value(1, 1, 1), 2.4);
 }
 
-
 TEST_F(OptionsAdios2Test, ReadWriteMatrixInt) {
   constexpr int nx = 2;
   constexpr int ny = 3;

From d0600ba1678a006d5f08c46f85a39780a882a264 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Nov 2025 17:54:58 +0000
Subject: [PATCH 0334/1827] Remove `static` local variables from
 `Mesh::hasBndry*Y`

Fixes #3160

Didn't strictly need to make these virtual, but given they need to be calculated
after `load`, this was probably the easiest way of achieving this
---
 include/bout/mesh.hxx            |  4 ++--
 src/mesh/impls/bout/boutmesh.cxx | 14 ++++++++++++++
 src/mesh/impls/bout/boutmesh.hxx |  5 +++++
 src/mesh/mesh.cxx                | 28 ----------------------------
 tests/unit/fake_mesh.hxx         |  2 ++
 5 files changed, 23 insertions(+), 30 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 02e2a23905..4c8cb35a05 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -464,11 +464,11 @@ public:
 
   /// Is there a boundary on the lower guard cells in Y
   /// on any processor along the X direction?
-  bool hasBndryLowerY();
+  virtual bool hasBndryLowerY() const = 0;
 
   /// Is there a boundary on the upper guard cells in Y
   /// on any processor along the X direction?
-  bool hasBndryUpperY();
+  virtual bool hasBndryUpperY() const = 0;
   // Boundary regions
 
   /// Return a vector containing all the boundary regions on this processor
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 9f366d9456..8917fa3753 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -607,6 +607,20 @@ int BoutMesh::load() {
   // Add boundary regions
   addBoundaryRegions();
 
+  // Set cached values
+  {
+    int mybndry = static_cast<int>(!(iterateBndryLowerY().isDone()));
+    int allbndry = 0;
+    mpi->MPI_Allreduce(&mybndry, &allbndry, 1, MPI_INT, MPI_BOR, getXcomm(yend));
+    has_boundary_lower_y = static_cast<bool>(allbndry);
+  }
+  {
+    int mybndry = static_cast<int>(!(iterateBndryUpperY().isDone()));
+    int allbndry = 0;
+    mpi->MPI_Allreduce(&mybndry, &allbndry, 1, MPI_INT, MPI_BOR, getXcomm(ystart));
+    has_boundary_upper_y = static_cast<bool>(allbndry);
+  }
+
   // Initialize default coordinates
   getCoordinates();
 
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index cc674d401a..a22e0e4473 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -156,6 +156,9 @@ public:
   RangeIterator iterateBndryUpperInnerY() const override;
   RangeIterator iterateBndryUpperOuterY() const override;
 
+  bool hasBndryLowerY() const override { return has_boundary_lower_y; }
+  bool hasBndryUpperY() const override { return has_boundary_upper_y; }
+
   // Boundary regions
   std::vector<BoundaryRegion*> getBoundaries() override;
   std::vector<std::shared_ptr<BoundaryRegionPar>>
@@ -400,6 +403,8 @@ private:
              static_cast<int>(BoundaryParType::SIZE)>
       par_boundary; // Vector of parallel boundary regions
 
+  bool has_boundary_lower_y{false};
+  bool has_boundary_upper_y{false};
   //////////////////////////////////////////////////
   // Communications
 
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index cb6cb8410c..1d3f3b0dbe 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -408,34 +408,6 @@ int Mesh::ySize(int jx) const {
   return all;
 }
 
-bool Mesh::hasBndryLowerY() {
-  static bool calc = false, answer;
-  if (calc) {
-    return answer; // Already calculated
-  }
-
-  int mybndry = static_cast<int>(!(iterateBndryLowerY().isDone()));
-  int allbndry;
-  mpi->MPI_Allreduce(&mybndry, &allbndry, 1, MPI_INT, MPI_BOR, getXcomm(yend));
-  answer = static_cast<bool>(allbndry);
-  calc = true;
-  return answer;
-}
-
-bool Mesh::hasBndryUpperY() {
-  static bool calc = false, answer;
-  if (calc) {
-    return answer; // Already calculated
-  }
-
-  int mybndry = static_cast<int>(!(iterateBndryUpperY().isDone()));
-  int allbndry;
-  mpi->MPI_Allreduce(&mybndry, &allbndry, 1, MPI_INT, MPI_BOR, getXcomm(ystart));
-  answer = static_cast<bool>(allbndry);
-  calc = true;
-  return answer;
-}
-
 int Mesh::localSize3D() {
   if (localNumCells3D < 0) {
     const int xs = firstX() ? xstart - 1 : xstart;
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index e6f78f8767..dc43b647ec 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -143,6 +143,8 @@ public:
   RangeIterator iterateBndryLowerInnerY() const override { return RangeIterator(); }
   RangeIterator iterateBndryUpperOuterY() const override { return RangeIterator(); }
   RangeIterator iterateBndryUpperInnerY() const override { return RangeIterator(); }
+  bool hasBndryLowerY() const override { return false; }
+  bool hasBndryUpperY() const override { return false; }
   void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); }
   std::vector<BoundaryRegion*> getBoundaries() override { return boundaries; }
   std::vector<std::shared_ptr<BoundaryRegionPar>>

From 1b5084eac8c49e5bfabb37424bc51d2b4213f4b5 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Nov 2025 18:19:11 +0000
Subject: [PATCH 0335/1827] Add `Mesh::communicate_no_slices`

We need to communicate fields without calculating the parallel slices in a
couple of places, this is a convenience function for doing just that
---
 include/bout/mesh.hxx                         | 12 +++++
 src/mesh/coordinates.cxx                      | 53 ++++++++-----------
 .../monotonic_hermite_spline_xz.cxx           | 20 +------
 tests/unit/fake_parallel_mesh.hxx             |  1 -
 4 files changed, 35 insertions(+), 51 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 02e2a23905..aeca3bdb5f 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -262,6 +262,16 @@ public:
     communicate(g);
   }
 
+  /// Communicate Fields without calculating the parallel slices
+  template <typename... Ts>
+  void communicate_no_slices(Ts&... ts) {
+    FieldGroup g(ts...);
+    const bool old = calcParallelSlices_on_communicate;
+    calcParallelSlices_on_communicate = false;
+    communicate(g);
+    calcParallelSlices_on_communicate = old;
+  }
+
   template <typename... Ts>
   void communicateXZ(Ts&... ts) {
     FieldGroup g(ts...);
@@ -795,9 +805,11 @@ protected:
   /// Mesh options section
   Options* options{nullptr};
 
+private:
   /// Set whether to call calcParallelSlices on all communicated fields (true) or not (false)
   bool calcParallelSlices_on_communicate{true};
 
+protected:
   /// Read a 1D array of integers
   const std::vector<int> readInts(const std::string& name, int n);
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 34c524d1e7..3dfee6a553 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -23,19 +23,7 @@
 #include "parallel/fci.hxx"
 #include "parallel/shiftedmetricinterp.hxx"
 
-// use anonymous namespace so this utility function is not available outside this file
 namespace {
-template <typename T, typename... Ts>
-// Use sendY()/sendX() and wait() instead of Mesh::communicate() to ensure we
-// don't try to calculate parallel slices as Coordinates are not constructed yet
-void communicate(T& t, Ts&... ts) {
-  FieldGroup g(t, ts...);
-  auto h = t.getMesh()->sendY(g);
-  t.getMesh()->wait(h);
-  h = t.getMesh()->sendX(g);
-  t.getMesh()->wait(h);
-}
-
 /// Interpolate a Field2D to a new CELL_LOC with interp_to.
 /// Communicates to set internal guard cells.
 /// Boundary guard cells are set by extrapolating from the grid, like
@@ -55,7 +43,7 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr
   // communicate f. We will sort out result's boundary guard cells below, but
   // not f's so we don't want to change f.
   result.allocate();
-  communicate(result);
+  localmesh->communicate_no_slices(result);
 
   // Extrapolate into boundaries (if requested) so that differential geometry
   // terms can be interpolated if necessary
@@ -204,7 +192,7 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
   // communicate f. We will sort out result's boundary guard cells below, but
   // not f's so we don't want to change f.
   result.allocate();
-  communicate(result);
+  localmesh->communicate_no_slices(result);
 
   // Extrapolate into boundaries (if requested) so that differential geometry
   // terms can be interpolated if necessary
@@ -444,7 +432,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
                                  transform.get());
 
   if (mesh->periodicX) {
-    communicate(dx);
+    mesh->communicate_no_slices(dx);
   }
 
   dy = interpolateAndExtrapolate(dy, location, extrapolate_x, extrapolate_y, false,
@@ -553,7 +541,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
     // Compare calculated and loaded values
     output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(J - Jcalc)));
 
-    communicate(J);
+    mesh->communicate_no_slices(J);
 
     // Re-evaluate Bxy using new J
     Bxy = sqrt(g_22) / J;
@@ -660,7 +648,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
                           extrapolate_y, false, transform.get());
 
     if (mesh->periodicX) {
-      communicate(dx);
+      mesh->communicate_no_slices(dx);
     }
 
     getAtLocAndFillGuards(mesh, dy, "dy", suffix, location, 1.0, extrapolate_x,
@@ -944,8 +932,8 @@ const Field2D& Coordinates::zlength() const {
 int Coordinates::geometry(bool recalculate_staggered,
                           bool force_interpolate_from_centre) {
   TRACE("Coordinates::geometry");
-  communicate(dx, dy, dz, g11, g22, g33, g12, g13, g23, g_11, g_22, g_33, g_12, g_13,
-              g_23, J, Bxy);
+  localmesh->communicate_no_slices(dx, dy, dz, g11, g22, g33, g12, g13, g23, g_11, g_22,
+                                   g_33, g_12, g_13, g_23, J, Bxy);
 
   output_progress.write("Calculating differential geometry terms\n");
 
@@ -1028,20 +1016,21 @@ int Coordinates::geometry(bool recalculate_staggered,
           + 0.5 * g33 * DDY(g_33);
 
   auto tmp = J * g12;
-  communicate(tmp);
+  localmesh->communicate_no_slices(tmp);
   G1 = (DDX(J * g11) + DDY(tmp) + DDZ(J * g13)) / J;
   tmp = J * g22;
-  communicate(tmp);
+  localmesh->communicate_no_slices(tmp);
   G2 = (DDX(J * g12) + DDY(tmp) + DDZ(J * g23)) / J;
   tmp = J * g23;
-  communicate(tmp);
+  localmesh->communicate_no_slices(tmp);
   G3 = (DDX(J * g13) + DDY(tmp) + DDZ(J * g33)) / J;
 
   // Communicate christoffel symbol terms
   output_progress.write("\tCommunicating connection terms\n");
 
-  communicate(G1_11, G1_22, G1_33, G1_12, G1_13, G1_23, G2_11, G2_22, G2_33, G2_12, G2_13,
-              G2_23, G3_11, G3_22, G3_33, G3_12, G3_13, G3_23, G1, G2, G3);
+  localmesh->communicate_no_slices(G1_11, G1_22, G1_33, G1_12, G1_13, G1_23, G2_11, G2_22,
+                                   G2_33, G2_12, G2_13, G2_23, G3_11, G3_22, G3_33, G3_12,
+                                   G3_13, G3_23, G1, G2, G3);
 
   // Set boundary guard cells of Christoffel symbol terms
   // Ideally, when location is staggered, we would set the upper/outer boundary point
@@ -1098,7 +1087,7 @@ int Coordinates::geometry(bool recalculate_staggered,
           "\tWARNING: differencing quantity 'd2x' not found. Calculating from dx\n");
       d1_dx = bout::derivatives::index::DDX(1. / dx); // d/di(1/dx)
 
-      communicate(d1_dx);
+      localmesh->communicate_no_slices(d1_dx);
       d1_dx =
           interpolateAndExtrapolate(d1_dx, location, true, true, true, transform.get());
     } else {
@@ -1115,7 +1104,7 @@ int Coordinates::geometry(bool recalculate_staggered,
           "\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
       d1_dy = DDY(1. / dy); // d/di(1/dy)
 
-      communicate(d1_dy);
+      localmesh->communicate_no_slices(d1_dy);
       d1_dy =
           interpolateAndExtrapolate(d1_dy, location, true, true, true, transform.get());
     } else {
@@ -1132,7 +1121,7 @@ int Coordinates::geometry(bool recalculate_staggered,
       output_warn.write(
           "\tWARNING: differencing quantity 'd2z' not found. Calculating from dz\n");
       d1_dz = bout::derivatives::index::DDZ(1. / dz);
-      communicate(d1_dz);
+      localmesh->communicate_no_slices(d1_dz);
       d1_dz =
           interpolateAndExtrapolate(d1_dz, location, true, true, true, transform.get());
     } else {
@@ -1152,7 +1141,7 @@ int Coordinates::geometry(bool recalculate_staggered,
           "\tWARNING: differencing quantity 'd2x' not found. Calculating from dx\n");
       d1_dx = bout::derivatives::index::DDX(1. / dx); // d/di(1/dx)
 
-      communicate(d1_dx);
+      localmesh->communicate_no_slices(d1_dx);
       d1_dx =
           interpolateAndExtrapolate(d1_dx, location, true, true, true, transform.get());
     } else {
@@ -1167,7 +1156,7 @@ int Coordinates::geometry(bool recalculate_staggered,
           "\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
       d1_dy = DDY(1. / dy); // d/di(1/dy)
 
-      communicate(d1_dy);
+      localmesh->communicate_no_slices(d1_dy);
       d1_dy =
           interpolateAndExtrapolate(d1_dy, location, true, true, true, transform.get());
     } else {
@@ -1183,7 +1172,7 @@ int Coordinates::geometry(bool recalculate_staggered,
           "\tWARNING: differencing quantity 'd2z' not found. Calculating from dz\n");
       d1_dz = bout::derivatives::index::DDZ(1. / dz);
 
-      communicate(d1_dz);
+      localmesh->communicate_no_slices(d1_dz);
       d1_dz =
           interpolateAndExtrapolate(d1_dz, location, true, true, true, transform.get());
     } else {
@@ -1196,7 +1185,7 @@ int Coordinates::geometry(bool recalculate_staggered,
     d1_dz = 0;
 #endif
   }
-  communicate(d1_dx, d1_dy, d1_dz);
+  localmesh->communicate_no_slices(d1_dx, d1_dy, d1_dz);
 
   if (location == CELL_CENTRE && recalculate_staggered) {
     // Re-calculate interpolated Coordinates at staggered locations
@@ -1366,7 +1355,7 @@ void fixZShiftGuards(Field2D& zShift) {
                                      not localmesh->sourceHasYBoundaryGuards(), false);
 
   // make sure zShift has been communicated
-  communicate(zShift);
+  localmesh->communicate_no_slices(zShift);
 
   // Correct guard cells for discontinuity of zShift at poloidal branch cut
   for (int x = 0; x < localmesh->LocalNx; x++) {
diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
index 4b84bcd265..f23bfd499e 100644
--- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
@@ -36,26 +36,10 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
   // Derivatives are used for tension and need to be on dimensionless
   // coordinates
   Field3D fx = bout::derivatives::index::DDX(f, CELL_DEFAULT, "DEFAULT");
-  localmesh->communicateXZ(fx);
-  // communicate in y, but do not calculate parallel slices
-  {
-    auto h = localmesh->sendY(fx);
-    localmesh->wait(h);
-  }
   Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", "RGN_ALL");
-  localmesh->communicateXZ(fz);
-  // communicate in y, but do not calculate parallel slices
-  {
-    auto h = localmesh->sendY(fz);
-    localmesh->wait(h);
-  }
+  localmesh->communicate_no_slices(fx, fz);
   Field3D fxz = bout::derivatives::index::DDX(fz, CELL_DEFAULT, "DEFAULT");
-  localmesh->communicateXZ(fxz);
-  // communicate in y, but do not calculate parallel slices
-  {
-    auto h = localmesh->sendY(fxz);
-    localmesh->wait(h);
-  }
+  localmesh->communicate_no_slices(fxz);
 
   const auto curregion{getRegion(region)};
   BOUT_FOR(i, curregion) {
diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx
index 805dcb2a0a..80406fb676 100644
--- a/tests/unit/fake_parallel_mesh.hxx
+++ b/tests/unit/fake_parallel_mesh.hxx
@@ -53,7 +53,6 @@ public:
     StaggerGrids = false;
     periodicX = false;
     IncIntShear = false;
-    calcParallelSlices_on_communicate = true;
     options = Options::getRoot();
     mpi = mpiSmart.get();
   }

From 11d0c17abd9579301a4bb455122acf4474ea8457 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Nov 2025 10:35:19 +0100
Subject: [PATCH 0336/1827] Ensure we only use special name for offsetted
 regions

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 69df6d8906..a5ef9f871d 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -346,7 +346,7 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
 
-  const auto region2 = fmt::format("RGN_YPAR_{:+d}", y_offset);
+  const auto region2 = y_offset == 0 ? "RGN_NOY" : fmt::format("RGN_YPAR_{:+d}", y_offset);
 
 #if USE_NEW_WEIGHTS
 #ifdef HS_USE_PETSC

From 81fd46189abdd05adfa99631985c84b800824cc4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Nov 2025 10:36:14 +0100
Subject: [PATCH 0337/1827] Clarify message

---
 src/mesh/interpolation/bilinear_xz.cxx     | 2 +-
 src/mesh/interpolation/lagrange_4pt_xz.cxx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/interpolation/bilinear_xz.cxx b/src/mesh/interpolation/bilinear_xz.cxx
index 4facdac34c..1ed18a7303 100644
--- a/src/mesh/interpolation/bilinear_xz.cxx
+++ b/src/mesh/interpolation/bilinear_xz.cxx
@@ -32,7 +32,7 @@ XZBilinear::XZBilinear(int y_offset, Mesh* mesh)
       w3(localmesh) {
 
   if (localmesh->getNXPE() > 1) {
-    throw BoutException("Do not support MPI splitting in X");
+    throw BoutException("XZBilinear interpolation does not support MPI splitting in X");
   }
 
   // Index arrays contain guard cells in order to get subscripts right
diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx
index 8fa201ba72..1f6543b019 100644
--- a/src/mesh/interpolation/lagrange_4pt_xz.cxx
+++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx
@@ -30,7 +30,7 @@ XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh* mesh)
     : XZInterpolation(y_offset, mesh), t_x(localmesh), t_z(localmesh) {
 
   if (localmesh->getNXPE() > 1) {
-    throw BoutException("Do not support MPI splitting in X");
+    throw BoutException("XZLagrange4pt interpolation does not support MPI splitting in X");
   }
 
   // Index arrays contain guard cells in order to get subscripts right

From 34b4f3b82d0957126f90a5365660a7d32317f483 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Mon, 24 Nov 2025 09:39:00 +0000
Subject: [PATCH 0338/1827] Apply clang-format changes

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 3 ++-
 src/mesh/interpolation/lagrange_4pt_xz.cxx   | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index a5ef9f871d..06d5b393a2 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -346,7 +346,8 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
 
-  const auto region2 = y_offset == 0 ? "RGN_NOY" : fmt::format("RGN_YPAR_{:+d}", y_offset);
+  const auto region2 =
+      y_offset == 0 ? "RGN_NOY" : fmt::format("RGN_YPAR_{:+d}", y_offset);
 
 #if USE_NEW_WEIGHTS
 #ifdef HS_USE_PETSC
diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx
index 1f6543b019..e16b2699d1 100644
--- a/src/mesh/interpolation/lagrange_4pt_xz.cxx
+++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx
@@ -30,7 +30,8 @@ XZLagrange4pt::XZLagrange4pt(int y_offset, Mesh* mesh)
     : XZInterpolation(y_offset, mesh), t_x(localmesh), t_z(localmesh) {
 
   if (localmesh->getNXPE() > 1) {
-    throw BoutException("XZLagrange4pt interpolation does not support MPI splitting in X");
+    throw BoutException(
+        "XZLagrange4pt interpolation does not support MPI splitting in X");
   }
 
   // Index arrays contain guard cells in order to get subscripts right

From b75d020bc10ca6b6dc86418118a575a8d70a2b5f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Nov 2025 10:58:50 +0100
Subject: [PATCH 0339/1827] Add missing header from clang-tidy

---
 include/bout/field.hxx           |  1 +
 include/bout/field3d.hxx         |  4 ++++
 src/field/field3d.cxx            |  4 ++++
 src/field/gen_fieldops.py        | 15 +++++++++------
 src/field/generated_fieldops.cxx | 15 +++++++++------
 src/mesh/coordinates.cxx         |  1 +
 src/solver/impls/euler/euler.cxx |  6 ++++++
 src/solver/impls/pvode/pvode.cxx |  5 +++++
 8 files changed, 39 insertions(+), 12 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 9e576f938f..2d813bb275 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -36,6 +36,7 @@ class Field;
 #include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/field_data.hxx"
 #include "bout/msg_stack.hxx"
 #include "bout/region.hxx"
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 039c085cfd..4dff626d7b 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -33,11 +33,15 @@ class Field3D;
 #include "bout/field2d.hxx"
 #include "bout/fieldperp.hxx"
 #include "bout/region.hxx"
+#include "bout/traits.hxx"
 
+#include <memory>
 #include <optional>
+#include <string>
 #include <vector>
 
 class Mesh;
+class Options;
 
 /// Class for 3D X-Y-Z scalar fields
 /*!
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index cf7c339e39..3b4765e063 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -31,6 +31,8 @@
 #include <bout/globals.hxx>
 
 #include <cmath>
+#include <memory>
+#include <utility>
 
 #include "bout/parallel_boundary_op.hxx"
 #include "bout/parallel_boundary_region.hxx"
@@ -47,6 +49,8 @@
 #include <bout/output.hxx>
 #include <bout/utils.hxx>
 
+#include "fmt/format.h"
+
 /// Constructor
 Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in)
     : Field(localmesh, location_in, directions_in) {
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 29631ff7aa..b6f99549d2 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -65,12 +65,15 @@ def smart_open(filename, mode="r"):
 )
 
 header = """// This file is autogenerated - see gen_fieldops.py
-#include <bout/field2d.hxx>
-#include <bout/field3d.hxx>
-#include <bout/globals.hxx>
-#include <bout/interpolation.hxx>
-#include <bout/mesh.hxx>
-#include <bout/region.hxx>
+#include "bout/build_defines.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/globals.hxx"
+#include "bout/interpolation.hxx"
+#include "bout/mesh.hxx"
+#include "bout/region.hxx"
+
+#include "fmt/format.h"
 """
 
 
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 3495d87dbc..f37a870c74 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -1,10 +1,13 @@
 // This file is autogenerated - see gen_fieldops.py
-#include <bout/field2d.hxx>
-#include <bout/field3d.hxx>
-#include <bout/globals.hxx>
-#include <bout/interpolation.hxx>
-#include <bout/mesh.hxx>
-#include <bout/region.hxx>
+#include "bout/build_defines.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/globals.hxx"
+#include "bout/interpolation.hxx"
+#include "bout/mesh.hxx"
+#include "bout/region.hxx"
+
+#include "fmt/format.h"
 
 // Provide the C++ wrapper for multiplication of Field3D and Field3D
 Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 3f67a5dc72..e805df00f2 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -7,6 +7,7 @@
 #include <bout/assert.hxx>
 #include <bout/constants.hxx>
 #include <bout/coordinates.hxx>
+#include <bout/field.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 110331eeb1..7d81b979a2 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -4,11 +4,17 @@
 #include "bout/version.hxx"
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
+#include "bout/field.hxx"
+#include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/openmpwrap.hxx>
+#include <bout/options.hxx>
 #include <bout/utils.hxx>
 
+#include <fmt/format.h>
+
 #include <cmath>
+#include <memory>
 
 #include <bout/output.hxx>
 
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 4815f0153b..339508c385 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -31,6 +31,7 @@
 
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/field.hxx>
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
@@ -42,7 +43,11 @@
 #include <pvode/iterativ.h> // contains the enum for types of preconditioning
 #include <pvode/pvbbdpre.h> // band preconditioner function prototypes
 
+#include "fmt/format.h"
+
 #include <string>
+#include <memory>
+#include <bits/basic_string.h>
 
 using namespace pvode;
 

From b824cfc15e4312d2eb10edee56144b0492e6b45f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Nov 2025 10:59:47 +0100
Subject: [PATCH 0340/1827] Apply more clang-tidy suggestions

---
 include/bout/field3d.hxx         | 2 +-
 src/field/field3d.cxx            | 2 +-
 src/solver/impls/pvode/pvode.cxx | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 4dff626d7b..537613eda8 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -540,7 +540,7 @@ private:
   // non-changing copy that is used for the variable names in the dump files
   std::string selfname;
   template <typename T>
-  inline void track(const T& change, const std::string& operation) {
+  void track(const T& change, const std::string& operation) {
     if (tracking_state != 0) {
       _track(change, operation);
     }
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 3b4765e063..7ece06a454 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -875,7 +875,7 @@ void Field3D::setRegion(const std::string& region_name) {
 
 Field3D& Field3D::enableTracking(const std::string& name,
                                  std::weak_ptr<Options> _tracking) {
-  tracking = _tracking;
+  tracking = std::move(_tracking);
   tracking_state = 1;
   selfname = name;
   return *this;
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 339508c385..a7b5f2e242 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -364,7 +364,7 @@ BoutReal PvodeSolver::run(BoutReal tout) {
   if (flag != SUCCESS) {
     output_error.write("ERROR CVODE step failed, flag = {:d}\n", flag);
     if (debug_on_failure) {
-      CVodeMemRec* cv_mem = (CVodeMem)cvode_mem;
+      CVodeMemRec* cv_mem = static_cast<CVodeMem>(cvode_mem);
       if (!(f2d.empty() and v2d.empty() and v3d.empty())) {
         output_warn.write("debug_on_failure is currently only supported for Field3Ds");
         return -1.0;

From 90815fa149704ae97124880df0f1b15e840619c6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Nov 2025 11:04:14 +0100
Subject: [PATCH 0341/1827] Add more headers explicitly

---
 src/solver/impls/pvode/pvode.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index a7b5f2e242..601cfc2448 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -32,6 +32,7 @@
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/field.hxx>
+#include <bout/field3d.hxx>
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
@@ -39,6 +40,7 @@
 #include <bout/unused.hxx>
 #include <bout/version.hxx>
 
+#include <pvode/cvode.h>
 #include <pvode/cvspgmr.h>  // use CVSPGMR linear solver each internal step
 #include <pvode/iterativ.h> // contains the enum for types of preconditioning
 #include <pvode/pvbbdpre.h> // band preconditioner function prototypes
@@ -47,6 +49,7 @@
 
 #include <string>
 #include <memory>
+#include <vector>
 #include <bits/basic_string.h>
 
 using namespace pvode;

From 69457b855d00aadec2463b77853cc8f42eef17a6 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Mon, 24 Nov 2025 10:08:34 +0000
Subject: [PATCH 0342/1827] Apply clang-format changes

---
 src/solver/impls/euler/euler.cxx | 2 +-
 src/solver/impls/pvode/pvode.cxx | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 7d81b979a2..a4804590dc 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -1,10 +1,10 @@
 
 #include "euler.hxx"
 
+#include "bout/field.hxx"
 #include "bout/version.hxx"
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
-#include "bout/field.hxx"
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/openmpwrap.hxx>
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 601cfc2448..f25c5bd9f2 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -47,10 +47,10 @@
 
 #include "fmt/format.h"
 
-#include <string>
+#include <bits/basic_string.h>
 #include <memory>
+#include <string>
 #include <vector>
-#include <bits/basic_string.h>
 
 using namespace pvode;
 

From b265c907dcae25dd0f326e82fcd805328328674e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Nov 2025 11:12:30 +0100
Subject: [PATCH 0343/1827] Remove duplicate definition

---
 include/bout/field3d.hxx | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 537613eda8..fad4815b92 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -306,13 +306,6 @@ public:
     return *this;
   }
 
-  /// Disable tracking
-  Field3D& disableTracking() {
-    tracking = nullptr;
-    tracking_state = 0;
-    return *this;
-  }
-
   /////////////////////////////////////////////////////////
   // Data access
 

From 9c47bb8ae02c23d7027c210979cbb16ed3ae76a5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Nov 2025 11:16:24 +0100
Subject: [PATCH 0344/1827] Add more headers explicitly

---
 src/solver/impls/pvode/pvode.cxx | 1 +
 src/sys/options.cxx              | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index f25c5bd9f2..6bd218e86b 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -36,6 +36,7 @@
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
+#include <bout/options.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/unused.hxx>
 #include <bout/version.hxx>
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index b3238bf758..ada63bd526 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -22,6 +22,7 @@
 
 #include <algorithm>
 #include <cmath>
+#include <cstddef>
 #include <iterator>
 #include <map>
 #include <set>

From 02cc7d17e806a0617069987c426f9bbdc2f4f9fd Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Mon, 24 Nov 2025 10:17:09 +0000
Subject: [PATCH 0345/1827] Apply clang-format changes

---
 src/solver/impls/pvode/pvode.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 6bd218e86b..2b83d4f155 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -35,8 +35,8 @@
 #include <bout/field3d.hxx>
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
-#include <bout/output.hxx>
 #include <bout/options.hxx>
+#include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/unused.hxx>
 #include <bout/version.hxx>

From 49028fe22d59f7b13c215631e82f1b6b183eaf1c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Nov 2025 12:08:04 +0100
Subject: [PATCH 0346/1827] Add doc strings

---
 include/bout/interpolation_xz.hxx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index def8a60a3e..6c7419f7e4 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -238,6 +238,9 @@ public:
                       const std::string& region = "RGN_NOBNDRY") const override;
 };
 
+/// XZLagrange4pt interpolation class
+///
+/// Does not support MPI splitting in X
 class XZLagrange4pt : public XZInterpolation {
   Tensor<int> i_corner; // x-index of bottom-left grid point
   Tensor<int> k_corner; // z-index of bottom-left grid point
@@ -271,6 +274,9 @@ public:
   BoutReal lagrange_4pt(const BoutReal v[], BoutReal offset) const;
 };
 
+/// XZBilinear interpolation calss
+///
+/// Does not support MPI splitting in X.
 class XZBilinear : public XZInterpolation {
   Tensor<int> i_corner; // x-index of bottom-left grid point
   Tensor<int> k_corner; // z-index of bottom-left grid point

From de2316741425c60fb0eefea1137a636ffe80410e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 24 Nov 2025 19:28:45 +0000
Subject: [PATCH 0347/1827] Bump ZedThree/clang-tidy-review from 0.21.0 to
 0.22.2

Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.21.0 to 0.22.2.
- [Release notes](https://github.com/zedthree/clang-tidy-review/releases)
- [Changelog](https://github.com/ZedThree/clang-tidy-review/blob/master/CHANGELOG.md)
- [Commits](https://github.com/zedthree/clang-tidy-review/compare/v0.21.0...v0.22.2)

---
updated-dependencies:
- dependency-name: ZedThree/clang-tidy-review
  dependency-version: 0.22.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/clang-tidy-review.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 3f20db608f..3661be9627 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -21,7 +21,7 @@ jobs:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.21.0
+        uses: ZedThree/clang-tidy-review@v0.22.2
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.21.0
+        uses: ZedThree/clang-tidy-review/upload@v0.22.2

From 85a0367eef674eb8492d8b7ac52e5ac255ebee95 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 24 Nov 2025 19:28:52 +0000
Subject: [PATCH 0348/1827] Bump actions/checkout from 5 to 6

Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/black-fix.yml         | 2 +-
 .github/workflows/clang-format.yml      | 2 +-
 .github/workflows/clang-tidy-review.yml | 2 +-
 .github/workflows/docker.yml            | 2 +-
 .github/workflows/python-package.yml    | 6 +++---
 .github/workflows/tests.yml             | 6 +++---
 6 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/black-fix.yml b/.github/workflows/black-fix.yml
index 5cddbbfac6..4306ee8b43 100644
--- a/.github/workflows/black-fix.yml
+++ b/.github/workflows/black-fix.yml
@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         ref: ${{ github.head_ref }}
 
diff --git a/.github/workflows/clang-format.yml b/.github/workflows/clang-format.yml
index 4c1307d7c9..678960ba3e 100644
--- a/.github/workflows/clang-format.yml
+++ b/.github/workflows/clang-format.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0
diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 3f20db608f..f0f3c73dac 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -16,7 +16,7 @@ jobs:
     if: ${{ !endsWith(github.head_ref, '-rc') }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
 
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 1380d0ea8e..0b510c48e8 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -52,7 +52,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Log in to the Container registry
         uses: docker/login-action@master
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index fc5e84662c..915265e850 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -17,7 +17,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: true
@@ -57,7 +57,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: true
@@ -106,7 +106,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: true
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 314ee196ae..f2c3618fab 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -168,7 +168,7 @@ jobs:
                  libparpack2-dev
                  libhypre-dev
 
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
 
@@ -205,7 +205,7 @@ jobs:
     timeout-minutes: 120
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
       - name: Build Fedora
@@ -219,7 +219,7 @@ jobs:
     container: ghcr.io/ggeorgakoudis/boutdev-cuda:latest
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
       - name: Build minimal CUDA 12.2 @ GCC9.4.0 @ Ubuntu 20.04

From 35e6f423859c4f6b5554f005e31576f18cc23c56 Mon Sep 17 00:00:00 2001
From: Giorgis Georgakoudis <georgakoudis1@llnl.gov>
Date: Mon, 24 Nov 2025 12:31:35 -0800
Subject: [PATCH 0349/1827] Use streams to reduce synchronization overhead

---
 include/bout/bout_types.hxx         |  7 ++--
 include/bout/field2d.hxx            |  6 +--
 include/bout/field3d.hxx            | 40 ++++++++++----------
 include/bout/fieldops.hxx           | 57 +++++++++++++++++++++++++----
 include/bout/rajalib.hxx            | 14 -------
 src/mesh/parallel/shiftedmetric.cxx | 46 +++++++++++++----------
 6 files changed, 103 insertions(+), 67 deletions(-)

diff --git a/include/bout/bout_types.hxx b/include/bout/bout_types.hxx
index c725c281d3..03bc4dcee4 100644
--- a/include/bout/bout_types.hxx
+++ b/include/bout/bout_types.hxx
@@ -2,7 +2,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -145,8 +145,9 @@ struct Constant {
   T val;
   struct View {
     T v;
-   View(T v) : v(v) {}
-   __host__ __device__ T operator()(int) const { return v; }
+    cudaStream_t stream = 0;
+    View(T v) : v(v) {}
+    __host__ __device__ T operator()(int) const { return v; }
   };
   operator View() const { return {val}; }
 };
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index da8de551ad..b452df7fd6 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -273,10 +273,10 @@ public:
 #define FIELD2D_OP_EQUALS(OP_SYM)                                           \
   template <typename R>                                                     \
   std::enable_if_t<is_expr_field2d_v<R> || is_expr_constant_v<R>, Field2D&> \
-  operator OP_SYM##=(R rhs) {                                               \
+  operator OP_SYM## = (R rhs) {                                             \
     if (data.unique()) {                                                    \
-      auto BE = (*this)OP_SYM rhs;                                          \
-      BE.evaluate(&data[0]);                                                \
+      auto expr = (*this)OP_SYM rhs;                                        \
+      expr.evaluate(&data[0]);                                              \
     } else {                                                                \
       (*this) = (*this)OP_SYM rhs;                                          \
     }                                                                       \
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 62b299bc48..9dc064d6e6 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -2,7 +2,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -355,7 +355,7 @@ public:
    * Direct access to the underlying data array
    *
    * If CHECK > 2 then bounds checking is performed
-   * 
+   *
    * If CHECK <= 2 then no checks are performed, to
    * allow inlining and optimisation of inner loops
    */
@@ -473,19 +473,19 @@ public:
 
   ///@}
 
-#define FIELD3D_OP_EQUALS(OP_SYM)                                \
-  template <typename R>                                          \
-  std::enable_if_t<is_expr_field3d_v<R> || is_expr_field2d_v<R>  \
-                       || is_expr_constant_v<R>,                 \
-                   Field3D&> operator OP_SYM##=(const R & rhs) { \
-    if (data.unique()) {                                         \
-      clearParallelSlices();                                     \
-      auto Expr = (*this)OP_SYM rhs;                             \
-      Expr.evaluate(&data[0]);                                   \
-    } else {                                                     \
-      (*this) = (*this)OP_SYM rhs;                               \
-    }                                                            \
-    return *this;                                                \
+#define FIELD3D_OP_EQUALS(OP_SYM)                                                      \
+  template <typename R>                                                                \
+  std::enable_if_t<                                                                    \
+      is_expr_field3d_v<R> || is_expr_field2d_v<R> || is_expr_constant_v<R>, Field3D&> \
+  operator OP_SYM## = (const R& rhs) {                                                 \
+    if (data.unique()) {                                                               \
+      clearParallelSlices();                                                           \
+      auto expr = (*this)OP_SYM rhs;                                                   \
+      expr.evaluate(&data[0]);                                                         \
+    } else {                                                                           \
+      (*this) = (*this)OP_SYM rhs;                                                     \
+    }                                                                                  \
+    return *this;                                                                      \
   }
 
   FIELD3D_OP_EQUALS(+)
@@ -565,8 +565,8 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
 #define FIELD3D_FIELD3D_FIELD3D_OP(OP_SYM, OP_TYPE)                                    \
   template <typename L, typename R,                                                    \
             typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>> \
-  BinaryExpr<Field3D, L, R, bout::op::OP_TYPE> operator OP_SYM(const L & lhs,          \
-                                                               const R & rhs) {        \
+  BinaryExpr<Field3D, L, R, bout::op::OP_TYPE> operator OP_SYM(const L& lhs,           \
+                                                               const R& rhs) {         \
     auto regionID =                                                                    \
         lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());          \
     return BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>{                               \
@@ -590,7 +590,7 @@ FIELD3D_FIELD3D_FIELD3D_OP(/, Div)
   template <typename L, typename R>                              \
   std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>, \
                    BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>> \
-  operator OP_SYM(const L & lhs, const R & rhs) {                \
+  operator OP_SYM(const L& lhs, const R& rhs) {                  \
     auto regionID = lhs.getRegionID();                           \
     int mesh_nz = lhs.getMesh()->LocalNz;                        \
     return BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>{         \
@@ -613,7 +613,7 @@ FIELD3D_FIELD3D_FIELD2D_OP(/, Div)
   template <typename L, typename R>                                        \
   std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>,          \
                    BinaryExpr<Field3D, L, Constant<R>, bout::op::OP_TYPE>> \
-  operator OP_SYM(const L & lhs, R rhs) {                                  \
+  operator OP_SYM(const L& lhs, R rhs) {                                   \
     auto regionID = lhs.getRegionID();                                     \
     return BinaryExpr<Field3D, L, Constant<R>, bout::op::OP_TYPE>{         \
         static_cast<typename L::View>(lhs),                                \
@@ -635,7 +635,7 @@ FIELD3D_FIELD3D_BOUTREAL_OP(/, Div)
   template <typename L, typename R>                                        \
   std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,          \
                    BinaryExpr<Field3D, Constant<L>, R, bout::op::OP_TYPE>> \
-  operator OP_SYM(const L & lhs, const R & rhs) {                          \
+  operator OP_SYM(const L& lhs, const R& rhs) {                            \
     auto regionID = rhs.getRegionID();                                     \
     return BinaryExpr<Field3D, Constant<L>, R, bout::op::OP_TYPE>{         \
         static_cast<typename Constant<L>::View>(lhs),                      \
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 48d104e3ea..114793ebc8 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -130,6 +130,40 @@ __global__ void __launch_bounds__(THREADS) evaluatorExpr(BoutReal* out, const Ex
 
 inline std::unordered_map<void*, Array<int>> regionIndicesCache;
 
+struct StreamsRAII {
+  std::vector<cudaStream_t> streams;
+
+  cudaStream_t get() {
+    cudaStream_t stream = 0;
+
+    if (streams.empty()) {
+      if (cudaStreamCreate(&stream) != cudaSuccess) {
+        throw BoutException("Failed to create CUDA stream");
+      }
+    } else {
+      stream = streams.back();
+      streams.pop_back();
+    }
+
+    return stream;
+  }
+
+  void put(cudaStream_t stream) { streams.push_back(stream); }
+
+  ~StreamsRAII() {
+    for (auto& stream : streams) {
+      cudaStreamDestroy(stream);
+    }
+  }
+
+  StreamsRAII() = default;
+  StreamsRAII(const StreamsRAII&) = delete;
+  StreamsRAII(StreamsRAII&&) = delete;
+  StreamsRAII& operator=(const StreamsRAII&) = delete;
+  StreamsRAII& operator=(StreamsRAII&&) = delete;
+};
+inline struct StreamsRAII streams;
+
 template <typename ResT, typename L, typename R, typename Func>
 struct BinaryExpr {
   typename L::View lhs;
@@ -220,16 +254,23 @@ struct BinaryExpr {
   operator View() const { return View{lhs, rhs, &indices[0], indices.size(), f}; }
 
   void evaluate(BoutReal* data) const {
+#if 1
+    cudaStream_t stream = streams.get();
     int blocks = (size() + THREADS - 1) / THREADS;
-    evaluatorExpr<<<blocks, THREADS>>>(&data[0], static_cast<View>(*this));
-    cudaDeviceSynchronize();
+    evaluatorExpr<<<blocks, THREADS, 0, stream>>>(&data[0], static_cast<View>(*this));
+    cudaStreamSynchronize(stream);
+    streams.put(stream);
+#endif
+
+#if 0
     // OpenMP impl.
-    //int e = size();
+    int e = size();
     //#pragma omp parallel for
-    //for (int i = 0; i < e; ++i) {
-    //  int idx = regionIdx(i);
-    //  data[idx] = operator()(idx); // single‐pass fusion
-    //}
+    for (int i = 0; i < e; ++i) {
+      int idx = regionIdx(i);
+      data[idx] = operator()(idx); // single‐pass fusion
+    }
+#endif
   }
 
   Mesh* getMesh() const { return mesh; }
@@ -238,4 +279,4 @@ struct BinaryExpr {
   std::optional<size_t> getRegionID() const { return regionID; };
 };
 
-#endif // BOUT_EXPRESSION_HX
\ No newline at end of file
+#endif // BOUT_FIELDSOPS_HXX
diff --git a/include/bout/rajalib.hxx b/include/bout/rajalib.hxx
index d61a58e0d8..20929304b5 100644
--- a/include/bout/rajalib.hxx
+++ b/include/bout/rajalib.hxx
@@ -139,20 +139,6 @@ private:
 #define BOUT_FOR_RAJA(index, region, ...) \
 RajaForAll(region) << [ =, ##__VA_ARGS__ ] RAJA_DEVICE(int index) mutable
 
-// NEW STUFF
-
-template <typename Expr>
-__global__ void evaluator(BoutReal *out, Expr &expr) {
-  int tid = threadIdx.x + blockIdx.x * blockDim.x;
-  int stride = blockDim.x * gridDim.x;
-  for (int i = tid; i < expr.size(); i += stride) {
-    out[expr.regionIdx(i)] = expr(expr.regionIdx(i)); // single‐pass fusion
-  }
-}
-
-// END OF NEW STUFF
-
-
 #else // BOUT_HAS_RAJA
 
 #warning RAJA not enabled. BOUT_FOR_RAJA falling back to BOUT_FOR.
diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 45f2988561..40085eaf92 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -496,32 +496,39 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
   if (nblocks != region.getBlocks().size()) {
     throw BoutException("Number of blocks changed in ShiftedMetric::calcParallelSlices");
   }
-  static Array<const BoutReal*> blocks_in(nblocks);
-  static Array<BoutReal*> blocks_out(nblocks);
-  static Array<const double2*> phs_in(nblocks);
 
-  for (const auto& phase : parallel_slice_phases) {
-    auto& f_slice = f.ynext(phase.y_offset);
-    f_slice.allocate();
-
-    static struct StreamRAII {
-      cudaStream_t stream = 0;
-      StreamRAII() {
-        if (cudaStreamCreate(&stream) != cudaSuccess) {
-          throw BoutException("Failed to create CUDA stream");
-        }
+  static struct StreamRAII {
+    cudaStream_t stream = 0;
+    StreamRAII() {
+      if (cudaStreamCreate(&stream) != cudaSuccess) {
+        throw BoutException("Failed to create CUDA stream");
       }
+    }
+
+    cudaStream_t get() const { return stream; }
+
+    void synchronize() const { cudaStreamSynchronize(stream); }
 
-      cudaStream_t get() const { return stream; }
+    ~StreamRAII() { cudaStreamDestroy(stream); }
+  } stream;
 
-      void synchronize() const { cudaStreamSynchronize(stream); }
+  // Vector of Arrays for each phase.
+  std::vector<Array<const BoutReal*>> blocks_in_phase;
+  std::vector<Array<BoutReal*>> blocks_out_phase;
+  std::vector<Array<const double2*>> phs_in_phase;
+
+  for (const auto& phase : parallel_slice_phases) {
+    auto& f_slice = f.ynext(phase.y_offset);
+    f_slice.allocate();
 
-      ~StreamRAII() { cudaStreamDestroy(stream); }
-    } stream;
     size_t block_idx = 0;
     int nbatches =
         region.getBlocks().cbegin()->second.ind - region.getBlocks().cbegin()->first.ind;
 
+    Array<const BoutReal*>& blocks_in = blocks_in_phase.emplace_back(nblocks);
+    Array<BoutReal*>& blocks_out = blocks_out_phase.emplace_back(nblocks);
+    Array<const double2*>& phs_in = phs_in_phase.emplace_back(nblocks);
+
     for (auto block = region.getBlocks().cbegin(), end = region.getBlocks().cend();
          block < end; ++block) {
       auto idx_s = block->first;
@@ -544,9 +551,10 @@ void ShiftedMetric::calcParallelSlices(Field3D& f) {
 
     shiftZ_block_fft(mesh.LocalNz, &blocks_in[0], &blocks_out[0], &phs_in[0], nblocks,
                      nbatches, stream.get());
-
-    stream.synchronize();
   }
+
+  // Synchronize to ensure all shifts are complete.
+  stream.synchronize();
 #else
   for (const auto& phase : parallel_slice_phases) {
     auto& f_slice = f.ynext(phase.y_offset);

From ab58ba5a077981f2e5c92ab569adadd9c7f69c01 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 1 Dec 2025 10:45:40 +0000
Subject: [PATCH 0350/1827] Remove deprecated `FieldGenerator::generate`

---
 include/bout/sys/expressionparser.hxx |  8 +--
 src/mesh/boundary_standard.cxx        | 79 ++++++++++++++-------------
 src/sys/expressionparser.cxx          |  6 --
 3 files changed, 42 insertions(+), 51 deletions(-)

diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx
index 660ad20ab3..b312ce2fb1 100644
--- a/include/bout/sys/expressionparser.hxx
+++ b/include/bout/sys/expressionparser.hxx
@@ -64,12 +64,6 @@ public:
     return nullptr;
   }
 
-  [[deprecated("This will be removed in a future version. Implementations should "
-               "override the Context version of this function.")]] virtual double
-  generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) {
-    return generate(bout::generator::Context().set("x", x, "y", y, "z", z, "t", t));
-  }
-
   /// Generate a value at the given coordinates (x,y,z,t)
   /// This should be deterministic, always returning the same value given the same inputs
   ///
@@ -78,7 +72,7 @@ public:
   /// them or an infinite recursion results.  This is for backward
   /// compatibility for users and implementors.  In a future version
   /// this function will be made pure virtual.
-  virtual double generate(const bout::generator::Context& ctx);
+  virtual double generate(const bout::generator::Context& ctx) = 0;
 
   /// Create a string representation of the generator, for debugging output
   virtual std::string str() const { return std::string("?"); }
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index c12901e53a..8f2c7df5ec 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -8,6 +8,7 @@
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
+#include <bout/sys/generator_context.hxx>
 #include <bout/utils.hxx>
 
 using bout::generator::Context;
@@ -460,18 +461,18 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
 
       for (; !bndry->isDone(); bndry->next1d()) {
         // Calculate the X and Y normalised values half-way between the guard cell and grid cell
-        BoutReal xnorm = 0.5
-                         * (mesh->GlobalX(bndry->x)                 // In the guard cell
-                            + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell
+        const BoutReal xnorm = 0.5
+                               * (mesh->GlobalX(bndry->x) // In the guard cell
+                                  + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell
 
-        BoutReal ynorm = 0.5
-                         * (mesh->GlobalY(bndry->y)                 // In the guard cell
-                            + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
+        const BoutReal ynorm = TWOPI * 0.5
+                               * (mesh->GlobalY(bndry->y) // In the guard cell
+                                  + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
 
         for (int zk = 0; zk < mesh->LocalNz; zk++) {
           if (fg) {
-            val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz),
-                               t);
+            val = fg->generate(
+                Context(bndry, zk, loc, t, mesh).set("x", xnorm, "y", ynorm));
           }
           f(bndry->x, bndry->y, zk) =
               2 * val - f(bndry->x - bndry->bx, bndry->y - bndry->by, zk);
@@ -508,14 +509,14 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
         // can help with the stability of higher order methods.
         for (int i = 1; i < bndry->width; i++) {
           // Set any other guard cells using the values on the cells
-          int xi = bndry->x + i * bndry->bx;
-          int yi = bndry->y + i * bndry->by;
-          xnorm = mesh->GlobalX(xi);
-          ynorm = mesh->GlobalY(yi);
+          const int xi = bndry->x + (i * bndry->bx);
+          const int yi = bndry->y + (i * bndry->by);
+          const auto xnorm = mesh->GlobalX(xi);
+          const auto ynorm = mesh->GlobalY(yi) * TWOPI;
           for (int zk = 0; zk < mesh->LocalNz; zk++) {
             if (fg) {
-              val = fg->generate(xnorm, TWOPI * ynorm,
-                                 TWOPI * (zk - 0.5) / (mesh->LocalNz), t);
+              val = fg->generate(
+                  Context(bndry, zk, loc, t, mesh).set("x", xnorm, "y", ynorm));
             }
             f(xi, yi, zk) = val;
           }
@@ -965,18 +966,18 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
 
       for (; !bndry->isDone(); bndry->next1d()) {
         // Calculate the X and Y normalised values half-way between the guard cell and grid cell
-        BoutReal xnorm = 0.5
-                         * (mesh->GlobalX(bndry->x)                 // In the guard cell
-                            + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell
+        const BoutReal xnorm = 0.5
+                               * (mesh->GlobalX(bndry->x) // In the guard cell
+                                  + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell
 
-        BoutReal ynorm = 0.5
-                         * (mesh->GlobalY(bndry->y)                 // In the guard cell
-                            + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
+        const BoutReal ynorm = TWOPI * 0.5
+                               * (mesh->GlobalY(bndry->y) // In the guard cell
+                                  + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
 
         for (int zk = 0; zk < mesh->LocalNz; zk++) {
           if (fg) {
-            val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz),
-                               t);
+            val = fg->generate(
+                Context(bndry, zk, loc, t, mesh).set("x", xnorm, "y", ynorm));
           }
 
           f(bndry->x, bndry->y, zk) =
@@ -1431,18 +1432,18 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
       // Shifted in Z
       for (; !bndry->isDone(); bndry->next1d()) {
         // Calculate the X and Y normalised values half-way between the guard cell and grid cell
-        BoutReal xnorm = 0.5
-                         * (mesh->GlobalX(bndry->x)                 // In the guard cell
-                            + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell
+        const BoutReal xnorm = 0.5
+                               * (mesh->GlobalX(bndry->x) // In the guard cell
+                                  + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell
 
-        BoutReal ynorm = 0.5
-                         * (mesh->GlobalY(bndry->y)                 // In the guard cell
-                            + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
+        const BoutReal ynorm = TWOPI * 0.5
+                               * (mesh->GlobalY(bndry->y) // In the guard cell
+                                  + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
 
         for (int zk = 0; zk < mesh->LocalNz; zk++) {
           if (fg) {
-            val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz),
-                               t);
+            val = fg->generate(
+                Context(bndry, zk, loc, t, mesh).set("x", xnorm, "y", ynorm));
           }
 
           f(bndry->x, bndry->y, zk) =
@@ -2137,20 +2138,22 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         for (; !bndry->isDone(); bndry->next1d()) {
           // Calculate the X and Y normalised values half-way between the guard cell and
           // grid cell
-          BoutReal xnorm = 0.5
-                           * (mesh->GlobalX(bndry->x)                 // In the guard cell
-                              + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell
+          const BoutReal xnorm =
+              0.5
+              * (mesh->GlobalX(bndry->x)                 // In the guard cell
+                 + mesh->GlobalX(bndry->x - bndry->bx)); // the grid cell
 
-          BoutReal ynorm = 0.5
-                           * (mesh->GlobalY(bndry->y)                 // In the guard cell
-                              + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
+          const BoutReal ynorm =
+              TWOPI * 0.5
+              * (mesh->GlobalY(bndry->y)                 // In the guard cell
+                 + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
 
           for (int zk = 0; zk < mesh->LocalNz; zk++) {
             BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                              + bndry->by * metric->dy(bndry->x, bndry->y, zk);
             if (fg) {
-              val = fg->generate(xnorm, TWOPI * ynorm,
-                                 TWOPI * (zk - 0.5) / (mesh->LocalNz), t);
+              val = fg->generate(
+                  Context(bndry, zk, loc, t, mesh).set("x", xnorm, "y", ynorm));
             }
             f(bndry->x, bndry->y, zk) =
                 f(bndry->x - bndry->bx, bndry->y - bndry->by, zk) + delta * val;
diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx
index 8290a4cae0..804f371bbe 100644
--- a/src/sys/expressionparser.cxx
+++ b/src/sys/expressionparser.cxx
@@ -37,12 +37,6 @@ using namespace std::string_literals;
 
 using bout::generator::Context;
 
-// Note: Here rather than in header to avoid many deprecated warnings
-// Remove in future and make this function pure virtual
-double FieldGenerator::generate(const Context& ctx) {
-  return generate(ctx.x(), ctx.y(), ctx.z(), ctx.t());
-}
-
 /////////////////////////////////////////////
 namespace { // These classes only visible in this file
 

From 6703d0ee10aa820cb0bd2f77c18557596033d282 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 1 Dec 2025 14:21:42 +0000
Subject: [PATCH 0351/1827] Remove explicit use of `MPI_COMM_WORLD`

Fixes #3215
---
 src/invert/laplace/impls/cyclic/cyclic_laplace.cxx | 14 ++++++++------
 src/invert/laplace/impls/pcr/pcr.cxx               |  8 ++++----
 src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx |  8 ++++----
 src/mesh/interpolation/hermite_spline_xz.cxx       | 10 ++--------
 4 files changed, 18 insertions(+), 22 deletions(-)

diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
index 5ce4e540b7..837ac3755f 100644
--- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
+++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
@@ -38,8 +38,10 @@
 #if not BOUT_USE_METRIC_3D
 
 #include "cyclic_laplace.hxx"
-#include "bout/assert.hxx"
-#include "bout/bout_types.hxx"
+
+#include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
+#include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
@@ -591,21 +593,21 @@ void LaplaceCyclic ::verify_solution(const Matrix<dcomplex>& a_ver,
   }
 
   if (xproc > 0) {
-    MPI_Irecv(&rbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 901, MPI_COMM_WORLD,
+    MPI_Irecv(&rbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 901, BoutComm::get(),
               &request[1]);
     for (int kz = 0; kz < nsys; kz++) {
       sbufdown[kz] = x_ver(kz, 1);
     }
-    MPI_Isend(&sbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 900, MPI_COMM_WORLD,
+    MPI_Isend(&sbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 900, BoutComm::get(),
               &request[0]);
   }
   if (xproc < nprocs - 1) {
-    MPI_Irecv(&rbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 900, MPI_COMM_WORLD,
+    MPI_Irecv(&rbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 900, BoutComm::get(),
               &request[3]);
     for (int kz = 0; kz < nsys; kz++) {
       sbufup[kz] = x_ver(kz, nx);
     }
-    MPI_Isend(&sbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 901, MPI_COMM_WORLD,
+    MPI_Isend(&sbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 901, BoutComm::get(),
               &request[2]);
   }
 
diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx
index 48bbdbac4b..b619d80100 100644
--- a/src/invert/laplace/impls/pcr/pcr.cxx
+++ b/src/invert/laplace/impls/pcr/pcr.cxx
@@ -1041,21 +1041,21 @@ void LaplacePCR ::verify_solution(const Matrix<dcomplex>& a_ver,
   }
 
   if (xproc > 0) {
-    MPI_Irecv(&rbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 901, MPI_COMM_WORLD,
+    MPI_Irecv(&rbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 901, BoutComm::get(),
               &request[1]);
     for (int kz = 0; kz < nsys; kz++) {
       sbufdown[kz] = x_ver(kz, 1);
     }
-    MPI_Isend(&sbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 900, MPI_COMM_WORLD,
+    MPI_Isend(&sbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 900, BoutComm::get(),
               &request[0]);
   }
   if (xproc < nprocs - 1) {
-    MPI_Irecv(&rbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 900, MPI_COMM_WORLD,
+    MPI_Irecv(&rbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 900, BoutComm::get(),
               &request[3]);
     for (int kz = 0; kz < nsys; kz++) {
       sbufup[kz] = x_ver(kz, nx);
     }
-    MPI_Isend(&sbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 901, MPI_COMM_WORLD,
+    MPI_Isend(&sbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 901, BoutComm::get(),
               &request[2]);
   }
 
diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
index 61c8f58694..b48b20f246 100644
--- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
+++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
@@ -1140,21 +1140,21 @@ void LaplacePCR_THOMAS ::verify_solution(const Matrix<dcomplex>& a_ver,
   }
 
   if (xproc > 0) {
-    MPI_Irecv(&rbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 901, MPI_COMM_WORLD,
+    MPI_Irecv(&rbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 901, BoutComm::get(),
               &request[1]);
     for (int kz = 0; kz < nsys; kz++) {
       sbufdown[kz] = x_ver(kz, 1);
     }
-    MPI_Isend(&sbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 900, MPI_COMM_WORLD,
+    MPI_Isend(&sbufdown[0], nsys, MPI_DOUBLE_COMPLEX, myrank - 1, 900, BoutComm::get(),
               &request[0]);
   }
   if (xproc < nprocs - 1) {
-    MPI_Irecv(&rbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 900, MPI_COMM_WORLD,
+    MPI_Irecv(&rbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 900, BoutComm::get(),
               &request[3]);
     for (int kz = 0; kz < nsys; kz++) {
       sbufup[kz] = x_ver(kz, nx);
     }
-    MPI_Isend(&sbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 901, MPI_COMM_WORLD,
+    MPI_Isend(&sbufup[0], nsys, MPI_DOUBLE_COMPLEX, myrank + 1, 901, BoutComm::get(),
               &request[2]);
   }
 
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index c0040d096e..5064c7d4a1 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -21,6 +21,7 @@
  **************************************************************************/
 
 #include "../impls/bout/boutmesh.hxx"
+#include "bout/bout.hxx"
 #include "bout/globals.hxx"
 #include "bout/index_derivs_interface.hxx"
 #include "bout/interpolation_xz.hxx"
@@ -133,16 +134,9 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* mesh)
 #ifdef HS_USE_PETSC
   petsclib = new PetscLib(
       &Options::root()["mesh:paralleltransform:xzinterpolation:hermitespline"]);
-  // MatCreate(MPI_Comm comm,Mat *A)
-  // MatCreate(MPI_COMM_WORLD, &petscWeights);
-  //  MatSetSizes(petscWeights, m, m, M, M);
-  // PetscErrorCode MatCreateAIJ(MPI_Comm comm, PetscInt m, PetscInt n, PetscInt M,
-  // PetscInt N, 			      PetscInt d_nz, const PetscInt d_nnz[],
-  // PetscInt o_nz, const PetscInt o_nnz[], Mat *A)
-  //  MatSetSizes(Mat A,PetscInt m,PetscInt n,PetscInt M,PetscInt N)
   const int m = localmesh->LocalNx * localmesh->LocalNy * localmesh->LocalNz;
   const int M = m * localmesh->getNXPE() * localmesh->getNYPE();
-  MatCreateAIJ(MPI_COMM_WORLD, m, m, M, M, 16, nullptr, 16, nullptr, &petscWeights);
+  MatCreateAIJ(BoutComm::get(), m, m, M, M, 16, nullptr, 16, nullptr, &petscWeights);
 #endif
 #endif
 #ifndef HS_USE_PETSC

From e5f91f10cf19ec941199be2421b514b8bae9a346 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 1 Dec 2025 16:46:31 +0000
Subject: [PATCH 0352/1827] Silence all output in `BoutMesh` unit tests

---
 tests/unit/mesh/test_boutmesh.cxx | 255 ++++++++----------------------
 1 file changed, 66 insertions(+), 189 deletions(-)

diff --git a/tests/unit/mesh/test_boutmesh.cxx b/tests/unit/mesh/test_boutmesh.cxx
index fd2ba50d28..8a446a742b 100644
--- a/tests/unit/mesh/test_boutmesh.cxx
+++ b/tests/unit/mesh/test_boutmesh.cxx
@@ -242,21 +242,20 @@ BoutMeshParameters createDisconnectedDoubleNull(const BoutMeshGridInfo& grid) {
 ////////////////////////////////////////////////////////////
 // Start of tests
 
-TEST(BoutMeshTest, NullOptionsCheck) {
+struct BoutMeshTest : public ::testing::Test {
+  WithQuietOutput debug{output_debug};
   WithQuietOutput info{output_info};
   WithQuietOutput warn{output_warn};
+  WithQuietOutput progress{output_progress};
+};
 
+TEST_F(BoutMeshTest, NullOptionsCheck) {
   EXPECT_NO_THROW(BoutMesh mesh(new FakeGridDataSource, nullptr));
 }
 
 // Not a great test as it's not specific to the thing we want to test,
 // and can also take a whopping ~300ms!
-TEST(BoutMeshTest, SingleCoreDecomposition) {
-  WithQuietOutput debug{output_debug};
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-  WithQuietOutput progress{output_progress};
-
+TEST_F(BoutMeshTest, SingleCoreDecomposition) {
   Options options{};
   options["ny"] = 1;
   options["nx"] = 4;
@@ -327,8 +326,7 @@ TEST_P(BoutMeshSetYDecompositionTest, BasicTest) {
   EXPECT_EQ(mesh.numberOfXPoints, params.number_of_X_points);
 }
 
-TEST(BoutMeshTest, SetYDecompositionIndicesJyseps22LowInconsistent) {
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, SetYDecompositionIndicesJyseps22LowInconsistent) {
   BoutMeshExposer mesh(1, 24, 1, 1, 1);
 
   EXPECT_THROW(mesh.setYDecompositionIndices({3, 7, 32, 8, 12}), BoutException);
@@ -466,8 +464,7 @@ TEST_P(BadBoutMeshDecompositionTest, BadSingleCoreYDecomposition) {
   EXPECT_THAT(result.reason, HasSubstr(params.expected_message));
 }
 
-TEST(BoutMeshTest, ChooseProcessorSplitBadNXPE) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPE) {
   Options options{{"NXPE", 3}};
 
   BoutMeshExposer mesh(1, 24, 1, 1, 1, 8);
@@ -475,8 +472,7 @@ TEST(BoutMeshTest, ChooseProcessorSplitBadNXPE) {
   EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
 }
 
-TEST(BoutMeshTest, ChooseProcessorSplitBadNYPE) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPE) {
   Options options{{"NYPE", 7}};
 
   BoutMeshExposer mesh(1, 24, 1, 1, 1, 8);
@@ -484,8 +480,7 @@ TEST(BoutMeshTest, ChooseProcessorSplitBadNYPE) {
   EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
 }
 
-TEST(BoutMeshTest, ChooseProcessorSplitNXPE) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, ChooseProcessorSplitNXPE) {
   Options options{{"NXPE", 4}};
 
   BoutMeshExposer mesh(1, 24, 1, 1, 1, 8);
@@ -496,8 +491,7 @@ TEST(BoutMeshTest, ChooseProcessorSplitNXPE) {
   EXPECT_EQ(mesh.getNYPE(), 2);
 }
 
-TEST(BoutMeshTest, ChooseProcessorSplitBadNXPENotEnoughGuards) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPENotEnoughGuards) {
   Options options{{"NXPE", 4}};
 
   BoutMeshExposer mesh(1, 24, 1, 1, 13, 8);
@@ -505,8 +499,7 @@ TEST(BoutMeshTest, ChooseProcessorSplitBadNXPENotEnoughGuards) {
   EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
 }
 
-TEST(BoutMeshTest, ChooseProcessorSplitNYPE) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, ChooseProcessorSplitNYPE) {
   Options options{{"NYPE", 4}};
 
   BoutMeshExposer mesh(1, 24, 1, 1, 1, 8);
@@ -698,9 +691,7 @@ TEST_P(BoutMeshProcNumTest, ProcNum) {
   EXPECT_EQ(result, params.expected_result);
 }
 
-TEST(BoutMeshTest, YProc) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, YProc) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
   BoutMeshExposer mesh(5, 3, 1, 2, 2, 0, 0);
 
@@ -716,9 +707,7 @@ TEST(BoutMeshTest, YProc) {
   EXPECT_EQ(mesh.YPROC(7), -1);
 }
 
-TEST(BoutMeshTest, XProc) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, XProc) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
   BoutMeshExposer mesh(5, 3, 1, 2, 2, 0, 0);
 
@@ -735,9 +724,7 @@ TEST(BoutMeshTest, XProc) {
   // one example, so probably fine
 }
 
-TEST(BoutMeshTest, GetGlobalXIndex) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetGlobalXIndex) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Boundaries are included in the global index
@@ -781,9 +768,7 @@ TEST(BoutMeshTest, GetGlobalXIndex) {
   EXPECT_EQ(mesh11.getGlobalXIndex(4), 7);
 }
 
-TEST(BoutMeshTest, GetGlobalXIndexNoBoundaries) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetGlobalXIndexNoBoundaries) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Global indices start counting from the first non-boundary point
@@ -827,10 +812,7 @@ TEST(BoutMeshTest, GetGlobalXIndexNoBoundaries) {
   EXPECT_EQ(mesh11.getGlobalXIndexNoBoundaries(4), 6);
 }
 
-TEST(BoutMeshTest, GlobalXIntSymmetricX) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GlobalXIntSymmetricX) {
   BoutMeshExposer mesh01(4, 3, 1, 2, 2, 0, 1);
   EXPECT_EQ(mesh01.GlobalX(0), -0.125);
   EXPECT_EQ(mesh01.GlobalX(1), 0.125);
@@ -839,10 +821,7 @@ TEST(BoutMeshTest, GlobalXIntSymmetricX) {
   EXPECT_EQ(mesh01.GlobalX(4), 0.875);
 }
 
-TEST(BoutMeshTest, GlobalXIntAsymmetricX) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GlobalXIntAsymmetricX) {
   BoutMeshExposer mesh01(4, 3, 1, 2, 2, 0, 1, false, false);
   EXPECT_EQ(mesh01.GlobalX(0), 0.);
   EXPECT_EQ(mesh01.GlobalX(1), 0.25);
@@ -851,10 +830,7 @@ TEST(BoutMeshTest, GlobalXIntAsymmetricX) {
   EXPECT_EQ(mesh01.GlobalX(4), 1.0);
 }
 
-TEST(BoutMeshTest, GlobalXRealSymmetricX) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GlobalXRealSymmetricX) {
   BoutMeshExposer mesh01(4, 3, 1, 2, 2, 0, 1);
   EXPECT_EQ(mesh01.GlobalX(0.5), 0.);
   EXPECT_EQ(mesh01.GlobalX(1.5), 0.25);
@@ -863,10 +839,7 @@ TEST(BoutMeshTest, GlobalXRealSymmetricX) {
   EXPECT_EQ(mesh01.GlobalX(4.5), 1.0);
 }
 
-TEST(BoutMeshTest, GlobalXRealAsymmetricX) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GlobalXRealAsymmetricX) {
   BoutMeshExposer mesh01(4, 3, 1, 2, 2, 0, 1, false, false);
   EXPECT_EQ(mesh01.GlobalX(0.5), 0.125);
   EXPECT_EQ(mesh01.GlobalX(1.5), 0.375);
@@ -875,9 +848,7 @@ TEST(BoutMeshTest, GlobalXRealAsymmetricX) {
   EXPECT_EQ(mesh01.GlobalX(4.5), 1.125);
 }
 
-TEST(BoutMeshTest, GetLocalXIndex) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetLocalXIndex) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Boundaries are included in the local index
@@ -921,9 +892,7 @@ TEST(BoutMeshTest, GetLocalXIndex) {
   EXPECT_EQ(mesh11.getLocalXIndex(7), 4);
 }
 
-TEST(BoutMeshTest, GetLocalXIndexNoBoundaries) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetLocalXIndexNoBoundaries) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Local indices start counting from the first non-boundary point
@@ -967,9 +936,7 @@ TEST(BoutMeshTest, GetLocalXIndexNoBoundaries) {
   EXPECT_EQ(mesh11.getLocalXIndexNoBoundaries(6), 4);
 }
 
-TEST(BoutMeshTest, GetGlobalYIndexSingleNull) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetGlobalYIndexSingleNull) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Boundaries are included in the global index
@@ -1013,9 +980,7 @@ TEST(BoutMeshTest, GetGlobalYIndexSingleNull) {
   EXPECT_EQ(mesh11.getGlobalYIndex(4), 7);
 }
 
-TEST(BoutMeshTest, GetGlobalYIndexDoubleNull) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetGlobalYIndexDoubleNull) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Boundaries are included in the global index
@@ -1064,9 +1029,7 @@ TEST(BoutMeshTest, GetGlobalYIndexDoubleNull) {
   EXPECT_EQ(mesh11.getGlobalYIndex(4), 9);
 }
 
-TEST(BoutMeshTest, GetGlobalYIndexNoBoundaries) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetGlobalYIndexNoBoundaries) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Global indices start counting from the first non-boundary point
@@ -1110,9 +1073,7 @@ TEST(BoutMeshTest, GetGlobalYIndexNoBoundaries) {
   EXPECT_EQ(mesh11.getGlobalYIndexNoBoundaries(4), 6);
 }
 
-TEST(BoutMeshTest, GetLocalYIndexSingleNull) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetLocalYIndexSingleNull) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Boundaries are included in the local index
@@ -1156,9 +1117,7 @@ TEST(BoutMeshTest, GetLocalYIndexSingleNull) {
   EXPECT_EQ(mesh11.getLocalYIndex(7), 4);
 }
 
-TEST(BoutMeshTest, GetLocalYIndexDoubleNull) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetLocalYIndexDoubleNull) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Boundaries are included in the global index
@@ -1207,9 +1166,7 @@ TEST(BoutMeshTest, GetLocalYIndexDoubleNull) {
   EXPECT_EQ(mesh11.getLocalYIndex(9), 4);
 }
 
-TEST(BoutMeshTest, GetLocalYIndexNoBoundaries) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetLocalYIndexNoBoundaries) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Local indices start counting from the first non-boundary point
@@ -1253,10 +1210,7 @@ TEST(BoutMeshTest, GetLocalYIndexNoBoundaries) {
   EXPECT_EQ(mesh11.getLocalYIndexNoBoundaries(6), 4);
 }
 
-TEST(BoutMeshTest, GlobalYIntSymmetricY) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GlobalYIntSymmetricY) {
   BoutMeshExposer mesh_inner_pf(createDisconnectedDoubleNull({12, 4, 1, 1, 1, 6, 0, 0}));
   EXPECT_EQ(mesh_inner_pf.GlobalY(0), -0.5625);
   EXPECT_EQ(mesh_inner_pf.GlobalY(1), -0.4375);
@@ -1284,10 +1238,7 @@ TEST(BoutMeshTest, GlobalYIntSymmetricY) {
   EXPECT_EQ(mesh_outer_pf.GlobalY(3), 1.3125);
 }
 
-TEST(BoutMeshTest, GlobalYIntAsymmetricY) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GlobalYIntAsymmetricY) {
   auto grid_inner_pf = createDisconnectedDoubleNull({12, 4, 1, 1, 1, 6, 0, 0});
   grid_inner_pf.grid.symmetric_Y = false;
   BoutMeshExposer mesh_inner_pf(grid_inner_pf);
@@ -1321,10 +1272,7 @@ TEST(BoutMeshTest, GlobalYIntAsymmetricY) {
   EXPECT_EQ(mesh_outer_pf.GlobalY(3), 1);
 }
 
-TEST(BoutMeshTest, GlobalYRealSymmetricY) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GlobalYRealSymmetricY) {
   BoutMeshExposer mesh_inner_pf(createDisconnectedDoubleNull({12, 4, 1, 1, 1, 6, 0, 0}));
   EXPECT_EQ(mesh_inner_pf.GlobalY(0.5), -0.5);
   EXPECT_EQ(mesh_inner_pf.GlobalY(1.5), -0.375);
@@ -1352,10 +1300,7 @@ TEST(BoutMeshTest, GlobalYRealSymmetricY) {
   EXPECT_EQ(mesh_outer_pf.GlobalY(3.5), 1.375);
 }
 
-TEST(BoutMeshTest, GlobalYRealAsymmetricY) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GlobalYRealAsymmetricY) {
   auto grid_inner_pf = createDisconnectedDoubleNull({12, 4, 1, 1, 1, 6, 0, 0});
   grid_inner_pf.grid.symmetric_Y = false;
   BoutMeshExposer mesh_inner_pf(grid_inner_pf);
@@ -1389,9 +1334,7 @@ TEST(BoutMeshTest, GlobalYRealAsymmetricY) {
   EXPECT_EQ(mesh_outer_pf.GlobalY(3.5), 1);
 }
 
-TEST(BoutMeshTest, GetGlobalZIndex) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetGlobalZIndex) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Boundaries are included in the global index
@@ -1427,9 +1370,7 @@ TEST(BoutMeshTest, GetGlobalZIndex) {
   EXPECT_EQ(mesh11.getGlobalZIndex(4), 4);
 }
 
-TEST(BoutMeshTest, GetGlobalZIndexNoBoundaries) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetGlobalZIndexNoBoundaries) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   BoutMeshExposer mesh00(5, 3, 4, 2, 2, 0, 0);
@@ -1461,9 +1402,7 @@ TEST(BoutMeshTest, GetGlobalZIndexNoBoundaries) {
   EXPECT_EQ(mesh11.getGlobalZIndexNoBoundaries(4), 4);
 }
 
-TEST(BoutMeshTest, GetLocalZIndex) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetLocalZIndex) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Boundaries are included in the local index
@@ -1507,9 +1446,7 @@ TEST(BoutMeshTest, GetLocalZIndex) {
   EXPECT_EQ(mesh11.getLocalZIndex(4), 4);
 }
 
-TEST(BoutMeshTest, GetLocalZIndexNoBoundaries) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
+TEST_F(BoutMeshTest, GetLocalZIndexNoBoundaries) {
   // 2x2 processors, 3x3x1 (not including guards) on each processor
 
   // Local indices start counting from the first non-boundary point
@@ -1553,10 +1490,7 @@ TEST(BoutMeshTest, GetLocalZIndexNoBoundaries) {
   EXPECT_EQ(mesh11.getLocalZIndexNoBoundaries(4), 4);
 }
 
-TEST(BoutMeshTest, FirstX) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, FirstX) {
   BoutMeshExposer mesh00(5, 3, 4, 3, 3, 0, 0);
   EXPECT_TRUE(mesh00.firstX());
   BoutMeshExposer mesh10(5, 3, 4, 3, 3, 1, 0);
@@ -1577,10 +1511,7 @@ TEST(BoutMeshTest, FirstX) {
   EXPECT_FALSE(mesh22.firstX());
 }
 
-TEST(BoutMeshTest, LastX) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, LastX) {
   BoutMeshExposer mesh00(5, 3, 4, 3, 3, 0, 0);
   EXPECT_FALSE(mesh00.lastX());
   BoutMeshExposer mesh10(5, 3, 4, 3, 3, 1, 0);
@@ -1601,10 +1532,7 @@ TEST(BoutMeshTest, LastX) {
   EXPECT_TRUE(mesh22.lastX());
 }
 
-TEST(BoutMeshTest, FirstY) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, FirstY) {
   BoutMeshExposer mesh00(5, 3, 4, 3, 3, 0, 0);
   EXPECT_TRUE(mesh00.firstY());
   BoutMeshExposer mesh10(5, 3, 4, 3, 3, 1, 0);
@@ -1625,10 +1553,7 @@ TEST(BoutMeshTest, FirstY) {
   EXPECT_FALSE(mesh22.firstY());
 }
 
-TEST(BoutMeshTest, LastY) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, LastY) {
   BoutMeshExposer mesh00(5, 3, 4, 3, 3, 0, 0);
   EXPECT_FALSE(mesh00.lastY());
   BoutMeshExposer mesh10(5, 3, 4, 3, 3, 1, 0);
@@ -1666,8 +1591,7 @@ void checkRegionSizes(const BoutMeshExposer& mesh, std::array<int, 3> rgn_lower_
 // These next few tests check both default_connections and the Region
 // creation, as these are quite tightly linked.
 
-TEST(BoutMeshTest, DefaultConnectionsCore1x1) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, DefaultConnectionsCore1x1) {
   // 5x3x1 grid on 1 processor, 1 boundary point. Boundaries should be
   // simple 1D rectangles, with 4 boundaries on this processor
   BoutMeshExposer mesh00(5, 3, 1, 1, 1, 0, 0, false);
@@ -1685,9 +1609,7 @@ TEST(BoutMeshTest, DefaultConnectionsCore1x1) {
   checkRegionSizes(mesh00, {5, 0, 5}, {0, 5, 5}, {3, 3});
 }
 
-TEST(BoutMeshTest, TopologySOL2x2) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, TopologySOL2x2) {
   {
     SCOPED_TRACE("TopologySOL2x2, mesh00");
     BoutMeshExposer mesh00(createSOL({3, 3, 1, 1, 2, 2, 0, 0}));
@@ -1725,9 +1647,7 @@ TEST(BoutMeshTest, TopologySOL2x2) {
   }
 }
 
-TEST(BoutMeshTest, TopologySOLPeriodicX2x2) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, TopologySOLPeriodicX2x2) {
   {
     SCOPED_TRACE("TopologySOLPeriodicX2x2, mesh00");
 
@@ -1766,9 +1686,7 @@ TEST(BoutMeshTest, TopologySOLPeriodicX2x2) {
   }
 }
 
-TEST(BoutMeshTest, TopologySingleNull2x3) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, TopologySingleNull2x3) {
   {
     SCOPED_TRACE("TopologySingleNull2x3, mesh00");
     BoutMeshExposer mesh00(createSingleNull({3, 3, 1, 1, 2, 3, 0, 0}));
@@ -1824,9 +1742,7 @@ TEST(BoutMeshTest, TopologySingleNull2x3) {
   }
 }
 
-TEST(BoutMeshTest, TopologyDisconnectedDoubleNull1x6) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, TopologyDisconnectedDoubleNull1x6) {
   {
     SCOPED_TRACE("TopologyDisconnectedDoubleNull1x6, mesh00"); // Inner lower leg
     BoutMeshExposer mesh00(createDisconnectedDoubleNull({12, 3, 1, 1, 1, 6, 0, 0}));
@@ -1882,8 +1798,7 @@ TEST(BoutMeshTest, TopologyDisconnectedDoubleNull1x6) {
   }
 }
 
-TEST(BoutMeshTest, SetDerivedGridSizes) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, SetDerivedGridSizes) {
   BoutMeshGridInfo grid{12, 3, 1, 2, 3, 6, 2, 2};
   BoutMeshExposer mesh(createDisconnectedDoubleNull(grid));
 
@@ -1911,8 +1826,7 @@ TEST(BoutMeshTest, SetDerivedGridSizes) {
   EXPECT_EQ(mesh.zend, 0);
 }
 
-TEST(BoutMeshTest, CreateXBoundariesPeriodicX) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, CreateXBoundariesPeriodicX) {
   // Periodic in X, so no boundaries
   BoutMeshExposer mesh(createDisconnectedDoubleNull({12, 3, 1, 1, 3, 6, 1, 0}));
   mesh.periodicX = true;
@@ -1922,8 +1836,7 @@ TEST(BoutMeshTest, CreateXBoundariesPeriodicX) {
   EXPECT_TRUE(boundaries.empty());
 }
 
-TEST(BoutMeshTest, CreateXBoundariesNoGuards) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, CreateXBoundariesNoGuards) {
   // No guards in X, so no boundaries
   BoutMeshExposer mesh(createDisconnectedDoubleNull({12, 3, 0, 1, 3, 6, 1, 0}));
   mesh.createXBoundaries();
@@ -1932,8 +1845,7 @@ TEST(BoutMeshTest, CreateXBoundariesNoGuards) {
   EXPECT_TRUE(boundaries.empty());
 }
 
-TEST(BoutMeshTest, CreateXBoundariesDoubleNullInsidePF) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, CreateXBoundariesDoubleNullInsidePF) {
   // Three cores in X, inside core, one boundary
   BoutMeshExposer mesh_inside(createDisconnectedDoubleNull({12, 3, 1, 1, 3, 6, 0, 0}));
   mesh_inside.createXBoundaries();
@@ -1943,8 +1855,7 @@ TEST(BoutMeshTest, CreateXBoundariesDoubleNullInsidePF) {
   EXPECT_EQ(boundaries_inside[0]->label, "pf");
 }
 
-TEST(BoutMeshTest, CreateXBoundariesDoubleNullMiddlePF) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, CreateXBoundariesDoubleNullMiddlePF) {
   // Three cores in X, middle core, so no boundaries
   BoutMeshExposer mesh_middle(createDisconnectedDoubleNull({12, 3, 1, 1, 3, 6, 1, 0}));
   mesh_middle.createXBoundaries();
@@ -1953,8 +1864,7 @@ TEST(BoutMeshTest, CreateXBoundariesDoubleNullMiddlePF) {
   EXPECT_TRUE(boundaries_middle.empty());
 }
 
-TEST(BoutMeshTest, CreateXBoundariesDoubleNullOutsidePF) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, CreateXBoundariesDoubleNullOutsidePF) {
   // Three cores in X, outside core, one boundary
   BoutMeshExposer mesh_inside(createDisconnectedDoubleNull({12, 3, 1, 1, 3, 6, 0, 0}));
   mesh_inside.createXBoundaries();
@@ -1964,8 +1874,7 @@ TEST(BoutMeshTest, CreateXBoundariesDoubleNullOutsidePF) {
   EXPECT_EQ(boundaries_inside[0]->label, "pf");
 }
 
-TEST(BoutMeshTest, CreateXBoundariesDoubleNullInsideOutsideCore) {
-  WithQuietOutput info{output_info};
+TEST_F(BoutMeshTest, CreateXBoundariesDoubleNullInsideOutsideCore) {
   // One core in X, so we expect two boundaries
   BoutMeshExposer mesh(createDisconnectedDoubleNull({12, 3, 1, 1, 1, 6, 0, 1}));
   mesh.createXBoundaries();
@@ -1976,9 +1885,7 @@ TEST(BoutMeshTest, CreateXBoundariesDoubleNullInsideOutsideCore) {
   EXPECT_EQ(boundaries[1]->label, "sol");
 }
 
-TEST(BoutMeshTest, CreateYBoundariesNoGuards) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, CreateYBoundariesNoGuards) {
   BoutMeshExposer mesh(createDisconnectedDoubleNull({12, 3, 1, 0, 1, 6, 0, 0}));
   mesh.createYBoundaries();
 
@@ -1986,10 +1893,7 @@ TEST(BoutMeshTest, CreateYBoundariesNoGuards) {
   EXPECT_TRUE(boundaries.empty());
 }
 
-TEST(BoutMeshTest, CreateYBoundariesClosedFieldLines) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, CreateYBoundariesClosedFieldLines) {
   BoutMeshExposer mesh(createCore({4, 4, 2, 2, 4, 4}));
   mesh.createYBoundaries();
 
@@ -1997,9 +1901,7 @@ TEST(BoutMeshTest, CreateYBoundariesClosedFieldLines) {
   EXPECT_TRUE(boundaries.empty());
 }
 
-TEST(BoutMeshTest, CreateYBoundariesInnerLower) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, CreateYBoundariesInnerLower) {
   BoutMeshExposer mesh(createDisconnectedDoubleNull({12, 3, 1, 1, 1, 6, 0, 0}));
   mesh.createYBoundaries();
 
@@ -2008,9 +1910,7 @@ TEST(BoutMeshTest, CreateYBoundariesInnerLower) {
   EXPECT_EQ(boundaries[0]->label, "lower_target");
 }
 
-TEST(BoutMeshTest, CreateYBoundariesInnerUpper) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, CreateYBoundariesInnerUpper) {
   BoutMeshExposer mesh(createDisconnectedDoubleNull({12, 3, 1, 1, 1, 6, 0, 2}));
   mesh.createYBoundaries();
 
@@ -2019,9 +1919,7 @@ TEST(BoutMeshTest, CreateYBoundariesInnerUpper) {
   EXPECT_EQ(boundaries[0]->label, "upper_target");
 }
 
-TEST(BoutMeshTest, CreateYBoundariesOuterUpper) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, CreateYBoundariesOuterUpper) {
   BoutMeshExposer mesh(createDisconnectedDoubleNull({12, 3, 1, 1, 1, 6, 0, 5}));
   mesh.createYBoundaries();
 
@@ -2030,9 +1928,7 @@ TEST(BoutMeshTest, CreateYBoundariesOuterUpper) {
   EXPECT_EQ(boundaries[0]->label, "upper_target");
 }
 
-TEST(BoutMeshTest, CreateYBoundariesOuterLower) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, CreateYBoundariesOuterLower) {
   BoutMeshExposer mesh(createDisconnectedDoubleNull({12, 3, 1, 1, 1, 6, 0, 3}));
   mesh.createYBoundaries();
 
@@ -2041,9 +1937,7 @@ TEST(BoutMeshTest, CreateYBoundariesOuterLower) {
   EXPECT_EQ(boundaries[0]->label, "lower_target");
 }
 
-TEST(BoutMestTest, PeriodicY) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, PeriodicY) {
   BoutMeshExposer mesh00(createDisconnectedDoubleNull({12, 3, 1, 1, 1, 6, 0, 0}));
   EXPECT_FALSE(mesh00.periodicY(2));
   EXPECT_FALSE(mesh00.periodicY(10));
@@ -2053,9 +1947,7 @@ TEST(BoutMestTest, PeriodicY) {
   EXPECT_FALSE(mesh01.periodicY(10));
 }
 
-TEST(BoutMestTest, PeriodicYWithShiftAngle) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, PeriodicYWithShiftAngle) {
   const std::vector<BoutReal> shift_angle = {-1., 11., 10., 9., 8., 7., 6.,
                                              5.,  4.,  3.,  2., 1., 0., -1.};
 
@@ -2076,9 +1968,7 @@ TEST(BoutMestTest, PeriodicYWithShiftAngle) {
   EXPECT_EQ(twist_shift01, 0.);
 }
 
-TEST(BoutMeshTest, NumberOfYBoundaries) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, NumberOfYBoundaries) {
   BoutMeshExposer mesh_SOL(createSOL({3, 3, 1, 1, 2, 2, 1, 1}));
   EXPECT_EQ(mesh_SOL.numberOfYBoundaries(), 1);
 
@@ -2086,9 +1976,7 @@ TEST(BoutMeshTest, NumberOfYBoundaries) {
   EXPECT_EQ(mesh_DND.numberOfYBoundaries(), 2);
 }
 
-TEST(BoutMeshTest, HasBranchCutLower) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, HasBranchCutLower) {
   BoutMeshExposer mesh_SOL(createSOL({3, 3, 1, 1, 2, 2, 1, 1}));
   EXPECT_EQ(mesh_SOL.hasBranchCutLower(2), std::make_pair(false, 0.));
 
@@ -2103,9 +1991,7 @@ TEST(BoutMeshTest, HasBranchCutLower) {
   EXPECT_EQ(mesh_DND04.hasBranchCutLower(2), std::make_pair(false, 0.));
 }
 
-TEST(BoutMeshTest, HasBranchCutUpper) {
-  WithQuietOutput info{output_info};
-
+TEST_F(BoutMeshTest, HasBranchCutUpper) {
   BoutMeshExposer mesh_SOL(createSOL({3, 3, 1, 1, 2, 2, 1, 1}));
   EXPECT_EQ(mesh_SOL.hasBranchCutUpper(2), std::make_pair(false, 0.));
 
@@ -2120,10 +2006,7 @@ TEST(BoutMeshTest, HasBranchCutUpper) {
   EXPECT_EQ(mesh_DND04.hasBranchCutUpper(2), std::make_pair(true, 10.));
 }
 
-TEST(BoutMeshTest, GetPossibleBoundariesCore) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GetPossibleBoundariesCore) {
   BoutMeshExposer mesh_core_1x1(createCore({12, 3, 1, 1, 1, 1, 0, 0}));
   BoutMeshExposer mesh_core_32x64(createCore({12, 3, 1, 1, 32, 64, 7, 4}));
 
@@ -2133,10 +2016,7 @@ TEST(BoutMeshTest, GetPossibleBoundariesCore) {
   EXPECT_EQ(mesh_core_32x64.getPossibleBoundaries(), boundaries);
 }
 
-TEST(BoutMeshTest, GetPossibleBoundariesCorePeriodicX) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GetPossibleBoundariesCorePeriodicX) {
   BoutMeshExposer mesh_core_1x1(createCore({12, 3, 1, 1, 1, 1, 0, 0}), true);
   BoutMeshExposer mesh_core_32x64(createCore({12, 3, 1, 1, 32, 64, 7, 4}), true);
 
@@ -2144,10 +2024,7 @@ TEST(BoutMeshTest, GetPossibleBoundariesCorePeriodicX) {
   EXPECT_TRUE(mesh_core_32x64.getPossibleBoundaries().empty());
 }
 
-TEST(BoutMeshTest, GetPossibleBoundariesDND) {
-  WithQuietOutput info{output_info};
-  WithQuietOutput warn{output_warn};
-
+TEST_F(BoutMeshTest, GetPossibleBoundariesDND) {
   BoutMeshExposer mesh_DND_1x6(createDisconnectedDoubleNull({12, 3, 1, 1, 1, 6, 0, 1}));
   BoutMeshExposer mesh_DND_32x64(
       createDisconnectedDoubleNull({12, 3, 1, 1, 32, 64, 0, 4}));

From 80b01691599609dd4db2cc63c919cbdbc63bccb3 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 1 Dec 2025 16:51:32 +0000
Subject: [PATCH 0353/1827] Silence all output in `Coordinates` unit tests

---
 tests/unit/mesh/test_coordinates.cxx | 32 +++-------------------------
 1 file changed, 3 insertions(+), 29 deletions(-)

diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx
index c5091b6599..fb400e593e 100644
--- a/tests/unit/mesh/test_coordinates.cxx
+++ b/tests/unit/mesh/test_coordinates.cxx
@@ -14,7 +14,9 @@ using bout::globals::mesh;
 class CoordinatesTest : public FakeMeshFixture {
 public:
   using FieldMetric = Coordinates::FieldMetric;
-  CoordinatesTest() : FakeMeshFixture() {}
+  WithQuietOutput info{output_info};
+  WithQuietOutput warn{output_warn};
+  WithQuietOutput progress{output_progress};
 };
 
 constexpr BoutReal default_dz{TWOPI / CoordinatesTest::nz};
@@ -133,9 +135,7 @@ TEST_F(CoordinatesTest, CalcContravariant) {
                      FieldMetric{0.0}}; // IntShiftTorsion
   // No call to Coordinates::geometry() needed here
 
-  output_info.disable();
   coords.calcCovariant();
-  output_info.enable();
 
   EXPECT_TRUE(IsFieldEqual(coords.g_11, 1.0));
   EXPECT_TRUE(IsFieldEqual(coords.g_22, 1.0));
@@ -168,9 +168,7 @@ TEST_F(CoordinatesTest, CalcCovariant) {
                      FieldMetric{0.0}}; // IntShiftTorsion
   // No call to Coordinates::geometry() needed here
 
-  output_info.disable();
   coords.calcContravariant();
-  output_info.enable();
 
   EXPECT_TRUE(IsFieldEqual(coords.g11, 1.0));
   EXPECT_TRUE(IsFieldEqual(coords.g22, 1.0));
@@ -182,11 +180,7 @@ TEST_F(CoordinatesTest, CalcCovariant) {
 // #endif
 
 TEST_F(CoordinatesTest, DefaultConstructor) {
-  output_info.disable();
-  output_warn.disable();
   Coordinates coords(mesh);
-  output_warn.enable();
-  output_info.enable();
 
   EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
   EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
@@ -208,11 +202,7 @@ TEST_F(CoordinatesTest, ConstructWithMeshSpacing) {
   static_cast<FakeMesh*>(bout::globals::mesh)
       ->setGridDataSource(new FakeGridDataSource({{"dx", 2.0}, {"dy", 3.2}, {"dz", 42}}));
 
-  output_info.disable();
-  output_warn.disable();
   Coordinates coords(mesh);
-  output_warn.enable();
-  output_info.enable();
 
   EXPECT_TRUE(IsFieldEqual(coords.dx, 2.0));
   EXPECT_TRUE(IsFieldEqual(coords.dy, 3.2));
@@ -233,12 +223,8 @@ TEST_F(CoordinatesTest, SmallMeshSpacing) {
   static_cast<FakeMesh*>(bout::globals::mesh)
       ->setGridDataSource(new FakeGridDataSource({{"dx", 1e-9}}));
 
-  output_info.disable();
-  output_warn.disable();
   Coordinates coords(mesh);
   EXPECT_THROW(coords.geometry(), BoutException);
-  output_warn.enable();
-  output_info.enable();
 }
 
 TEST_F(CoordinatesTest, ConstructWithDiagonalContravariantMetric) {
@@ -247,11 +233,7 @@ TEST_F(CoordinatesTest, ConstructWithDiagonalContravariantMetric) {
       ->setGridDataSource(
           new FakeGridDataSource({{"g11", 2.0}, {"g22", 3.2}, {"g33", 42}}));
 
-  output_info.disable();
-  output_warn.disable();
   Coordinates coords(mesh);
-  output_warn.enable();
-  output_info.enable();
 
   // Didn't specify grid spacing, so default to 1
   EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
@@ -280,20 +262,12 @@ TEST_F(CoordinatesTest, NegativeJacobian) {
   static_cast<FakeMesh*>(bout::globals::mesh)
       ->setGridDataSource(new FakeGridDataSource({{"J", -1.0}}));
 
-  output_info.disable();
-  output_warn.disable();
   EXPECT_THROW(Coordinates coords(mesh), BoutException);
-  output_warn.enable();
-  output_info.enable();
 }
 
 TEST_F(CoordinatesTest, NegativeB) {
   static_cast<FakeMesh*>(bout::globals::mesh)
       ->setGridDataSource(new FakeGridDataSource({{"Bxy", -1.0}}));
 
-  output_info.disable();
-  output_warn.disable();
   EXPECT_THROW(Coordinates coords(mesh), BoutException);
-  output_warn.enable();
-  output_info.enable();
 }

From 77420d139ea4f20578f409e69fa7dbf2df5fcf76 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 1 Dec 2025 16:59:44 +0000
Subject: [PATCH 0354/1827] Silence all output in `Timer` unit tests

---
 tests/unit/sys/test_timer.cxx | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/tests/unit/sys/test_timer.cxx b/tests/unit/sys/test_timer.cxx
index 7641c5f8cf..ed749c14f3 100644
--- a/tests/unit/sys/test_timer.cxx
+++ b/tests/unit/sys/test_timer.cxx
@@ -227,7 +227,6 @@ TEST(TimerTest, Cleanup) {
 
 // Don't currently know why this test fails, and also causes segfault when unwinding the
 // tests
-#if 1
 TEST(TimerTest, ListAllInfo) {
   Timer::cleanup();
 
@@ -245,33 +244,17 @@ TEST(TimerTest, ListAllInfo) {
     Timer time_long{"18 characters long"};
   }
 
-  printf("Timer::resetTime\n");
   Timer::resetTime("two");
-#if 0
   std::streambuf* old_cout_rdbuf(std::cout.rdbuf());
   std::stringstream cout_capture;
-  cout_capture.str("");
-  cout_capture.clear();
   std::cout.rdbuf(cout_capture.rdbuf());
 
-  printf("Timer printTimeReport\n");
   Timer::printTimeReport();
 
-  printf("Timer printTimeReport done\n");
   std::cout.rdbuf(old_cout_rdbuf);
-#else
-
-  std::stringstream cout_capture;
-  std::streambuf* oldbuf = std::cout.rdbuf(cout_capture.rdbuf());
-  Timer::printTimeReport();
-  std::cout.rdbuf(oldbuf);
-
-#endif
-  std::cerr << cout_capture.str();
 
   using namespace ::testing;
   EXPECT_THAT(cout_capture.str(), HasSubstr("Timer name         |"));
   EXPECT_THAT(cout_capture.str(), ContainsRegex("one *| 0\\.[0-9]+ | 1    | 0\\.[0-9]+"));
   EXPECT_THAT(cout_capture.str(), ContainsRegex("two *| 0 * | 2    | 0\\.[0-9]+"));
 }
-#endif

From 305e1773088daa8e5954db18a176ebc3b3a0c537 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Dec 2025 14:05:54 +0100
Subject: [PATCH 0355/1827] Add unversioned python path

---
 .docker/fedora/Dockerfile | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.docker/fedora/Dockerfile b/.docker/fedora/Dockerfile
index 2b6800ce21..5d74886b50 100644
--- a/.docker/fedora/Dockerfile
+++ b/.docker/fedora/Dockerfile
@@ -35,9 +35,12 @@ RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local/ \
     sudo make -C build install; \
     rm -rf build
 
+# Add unversioned path for python
+RUN sudo ln -s /usr/local/lib/python3.* /usr/local/lib/python3.x/
+
 ENV PATH=/usr/local/bin:$PATH \
     LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH \
-    PYTHONPATH=/usr/local/lib/python3.13/site-packages/:$PYTHONPATH
+    PYTHONPATH=/usr/local/lib/python3.x/site-packages/:$PYTHONPATH
 
 # smoke test
 RUN python3 -c 'import boutpp'

From 938ca44bc62aa91f0d655652f9548521c36174c1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Dec 2025 14:52:51 +0100
Subject: [PATCH 0356/1827] Fix ln command

---
 .docker/fedora/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.docker/fedora/Dockerfile b/.docker/fedora/Dockerfile
index 5d74886b50..da4d2d9fac 100644
--- a/.docker/fedora/Dockerfile
+++ b/.docker/fedora/Dockerfile
@@ -36,7 +36,7 @@ RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local/ \
     rm -rf build
 
 # Add unversioned path for python
-RUN sudo ln -s /usr/local/lib/python3.* /usr/local/lib/python3.x/
+RUN sudo ln -s /usr/local/lib/python3.* /usr/local/lib/python3.x
 
 ENV PATH=/usr/local/bin:$PATH \
     LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH \

From 74b736d0b630637805217a2b678b6cc508647099 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 7 Oct 2025 09:56:07 +0100
Subject: [PATCH 0357/1827] tests: Ruff fixes for FCI runtest

---
 tests/MMS/spatial/fci/runtest | 238 +++++++++++++++-------------------
 1 file changed, 105 insertions(+), 133 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 7a9d6e655e..1f0b297ebc 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -6,19 +6,28 @@
 # Cores: 2
 # requires: zoidberg
 
-from boututils.run_wrapper import build_and_log, launch_safe
-from boutdata.collect import collect
+import pathlib
+import pickle
+import sys
+
 import boutconfig as conf
+import zoidberg as zb
+from boutdata.collect import collect
+from boututils.run_wrapper import build_and_log, launch_safe
+from numpy import arange, array, linspace, log, polyfit
+from scipy.interpolate import RectBivariateSpline as RBS
 
-from numpy import array, log, polyfit, linspace, arange
 
-import pickle
+def myRBS(a, b, c):
+    mx, _ = c.shape
+    kx = max(mx - 1, 1)
+    kx = min(kx, 3)
+    return RBS(a, b, c, kx=kx)
 
-from sys import stdout
 
-import zoidberg as zb
+zb.poloidal_grid.RectBivariateSpline = myRBS
 
-nx = 4  # Not changed for these tests
+nx = 3  # Not changed for these tests
 
 # Resolution in y and z
 nlist = [8, 16, 32, 64, 128]
@@ -31,7 +40,6 @@ directory = "data"
 nproc = 2
 mthread = 2
 
-
 success = True
 
 error_2 = {}
@@ -46,115 +54,88 @@ failures = []
 build_and_log("FCI MMS test")
 
 for nslice in nslices:
-    for method in [
-        "hermitespline",
-        "lagrange4pt",
-        "bilinear",
-        # "monotonichermitespline",
-    ]:
-        error_2[nslice] = []
-        error_inf[nslice] = []
-
-        # Which central difference scheme to use and its expected order
-        order = nslice * 2
-        method_orders[nslice] = {"name": "C{}".format(order), "order": order}
-
-        for n in nlist:
-            # Define the magnetic field using new poloidal gridding method
-            # Note that the Bz and Bzprime parameters here must be the same as in mms.py
-            field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
-            # Create rectangular poloidal grids
-            poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(
-                nx, n, 0.1, 1.0, MXG=1
-            )
-            # Set the ylength and y locations
-            ylength = 10.0
-
-            if yperiodic:
-                ycoords = linspace(0.0, ylength, n, endpoint=False)
-            else:
-                # Doesn't include the end points
-                ycoords = (arange(n) + 0.5) * ylength / float(n)
-
-            # Create the grid
-            grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
-            # Make and write maps
-            maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
-            zb.write_maps(
-                grid,
-                field,
-                maps,
-                new_names=False,
-                metric2d=conf.isMetric2D(),
-                quiet=True,
-            )
-
-            args = " MZ={} MYG={} mesh:paralleltransform:y_periodic={} mesh:ddy:first={} NXPE={}".format(
-                n,
-                nslice,
-                yperiodic,
-                method_orders[nslice]["name"],
-                2 if conf.has["petsc"] and method == "hermitespline" else 1,
-            )
-            args += f" mesh:paralleltransform:xzinterpolation:type={method}"
-
-            # Command to run
-            cmd = "./fci_mms " + args
-
-            print("Running command: " + cmd)
-
-            # Launch using MPI
-            s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-
-            # Save output to log file
-            with open("run.log." + str(n), "w") as f:
-                f.write(out)
-
-            if s:
-                print("Run failed!\nOutput was:\n")
-                print(out)
-                exit(s)
-
-            # Collect data
-            l_2 = collect(
-                "l_2",
-                tind=[1, 1],
-                info=False,
-                path=directory,
-                xguards=False,
-                yguards=False,
-            )
-            l_inf = collect(
-                "l_inf",
-                tind=[1, 1],
-                info=False,
-                path=directory,
-                xguards=False,
-                yguards=False,
-            )
-
-            error_2[nslice].append(l_2)
-            error_inf[nslice].append(l_inf)
-
-            print("Errors : l-2 {:f} l-inf {:f}".format(l_2, l_inf))
-
-        dx = 1.0 / array(nlist)
-
-        # Calculate convergence order
-        fit = polyfit(log(dx), log(error_2[nslice]), 1)
-        order = fit[0]
-        stdout.write("Convergence order = {:f} (fit)".format(order))
-
-        order = log(error_2[nslice][-2] / error_2[nslice][-1]) / log(dx[-2] / dx[-1])
-        stdout.write(", {:f} (small spacing)".format(order))
-
-        # Should be close to the expected order
-        if order > method_orders[nslice]["order"] * 0.95:
-            print("............ PASS\n")
+    error_2[nslice] = []
+    error_inf[nslice] = []
+
+    # Which central difference scheme to use and its expected order
+    order = nslice * 2
+    name = f"C{order}"
+    method_orders[nslice] = {"name": name, "order": order}
+
+    for n in nlist:
+        # Define the magnetic field using new poloidal gridding method
+        # Note that the Bz and Bzprime parameters here must be the same as in mms.py
+        field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
+        # Create rectangular poloidal grids
+        poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(nx, n, 0.1, 1.0, MXG=1)
+        # Set the ylength and y locations
+        ylength = 10.0
+
+        if yperiodic:
+            ycoords = linspace(0.0, ylength, n, endpoint=False)
         else:
-            print("............ FAIL\n")
-            success = False
-            failures.append(method_orders[nslice]["name"])
+            # Doesn't include the end points
+            ycoords = (arange(n) + 0.5) * ylength / float(n)
+
+        # Create the grid
+        grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
+        # Make and write maps
+        maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
+        zb.write_maps(
+            grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True
+        )
+
+        # Command to run
+        args = f" MZ={n} MYG={nslice} mesh:paralleltransform:y_periodic={yperiodic} mesh:ddy:first={name}"
+        cmd = f"./fci_mms {args}"
+
+        print(f"Running command: {cmd}")
+
+        # Launch using MPI
+        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
+
+        # Save output to log file
+        pathlib.Path(f"run.log.{n}").write_text(out)
+
+        if s:
+            print(f"Run failed!\nOutput was:\n{out}")
+            sys.exit(s)
+
+        # Collect data
+        l_2 = collect(
+            "l_2", tind=[1, 1], info=False, path=directory, xguards=False, yguards=False
+        )
+        l_inf = collect(
+            "l_inf",
+            tind=[1, 1],
+            info=False,
+            path=directory,
+            xguards=False,
+            yguards=False,
+        )
+
+        error_2[nslice].append(l_2)
+        error_inf[nslice].append(l_inf)
+
+        print(f"Errors : l-2 {l_2:f} l-inf {l_inf:f}")
+
+    dx = 1.0 / array(nlist)
+
+    # Calculate convergence order
+    fit = polyfit(log(dx), log(error_2[nslice]), 1)
+    order = fit[0]
+    print(f"Convergence order = {order:f} (fit)", end="")
+
+    order = log(error_2[nslice][-2] / error_2[nslice][-1]) / log(dx[-2] / dx[-1])
+    print(f", {order:f} (small spacing)")
+
+    # Should be close to the expected order
+    if order > order * 0.95:
+        print("............ PASS\n")
+    else:
+        print("............ FAIL\n")
+        success = False
+        failures.append(name)
 
 
 with open("fci_mms.pkl", "wb") as output:
@@ -164,7 +145,7 @@ with open("fci_mms.pkl", "wb") as output:
         pickle.dump(error_inf[nslice], output)
 
 # Do we want to show the plot as well as save it to file.
-showPlot = True
+show_plot = True
 
 if False:
     try:
@@ -174,18 +155,9 @@ if False:
         fig, ax = plt.subplots(1, 1)
 
         for nslice in nslices:
-            ax.plot(
-                dx,
-                error_2[nslice],
-                "-",
-                label="{} $l_2$".format(method_orders[nslice]["name"]),
-            )
-            ax.plot(
-                dx,
-                error_inf[nslice],
-                "--",
-                label="{} $l_\\inf$".format(method_orders[nslice]["name"]),
-            )
+            name = method_orders[nslice]["name"]
+            ax.plot(dx, error_2[nslice], "-", label=f"{name} $l_2$")
+            ax.plot(dx, error_inf[nslice], "--", label=f"{name} $l_\\inf$")
         ax.legend(loc="upper left")
         ax.grid()
         ax.set_yscale("log")
@@ -198,7 +170,7 @@ if False:
 
         print("Plot saved to fci_mms.pdf")
 
-        if showPlot:
+        if show_plot:
             plt.show()
         plt.close()
     except ImportError:
@@ -206,9 +178,9 @@ if False:
 
 if success:
     print("All tests passed")
-    exit(0)
+    sys.exit(0)
 else:
     print("Some tests failed:")
     for failure in failures:
-        print("\t" + failure)
-    exit(1)
+        print(f"\t{failure}")
+    sys.exit(1)

From eb589e16948c795bc4137e85e72d77cd452c3142 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 7 Oct 2025 12:05:01 +0100
Subject: [PATCH 0358/1827] tests: Expand FCI MMS test to `Grad2_par2`

---
 CMakeLists.txt                      |  1 +
 tests/MMS/spatial/fci/data/BOUT.inp |  5 +-
 tests/MMS/spatial/fci/fci_mms.cxx   | 48 ++++++++++-----
 tests/MMS/spatial/fci/mms.py        |  5 +-
 tests/MMS/spatial/fci/runtest       | 96 +++++++++++++++--------------
 5 files changed, 90 insertions(+), 65 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 44d100e444..eabfc055ee 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -376,6 +376,7 @@ if (zoidberg_FOUND EQUAL 0)
 else()
   set(zoidberg_FOUND OFF)
 endif()
+message(STATUS "Found Zoidberg for FCI tests: ${zoidberg_FOUND}")
 
 option(BOUT_GENERATE_FIELDOPS "Automatically re-generate the Field arithmetic operators from the Python templates. \
 Requires Python3, clang-format, and Jinja2. Turn this OFF to skip generating them if, for example, \
diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index 5f2001a906..f065989524 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -1,7 +1,6 @@
-
 input_field = sin(y - 2*z) + sin(y - z)
-
-solution = (6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0)
+grad_par_solution = (6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0)
+grad2_par2_solution = (6.28318530717959*(0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0))/sqrt((0.01*x + 0.045)^2 + 1.0)
 
 MXG = 1
 MYG = 1
diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index 18405a7f88..48b18f04ef 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -1,5 +1,4 @@
 #include "bout/bout.hxx"
-#include "bout/derivs.hxx"
 #include "bout/field_factory.hxx"
 
 int main(int argc, char** argv) {
@@ -8,29 +7,50 @@ int main(int argc, char** argv) {
   using bout::globals::mesh;
 
   Field3D input{FieldFactory::get()->create3D("input_field", Options::getRoot(), mesh)};
-  Field3D solution{FieldFactory::get()->create3D("solution", Options::getRoot(), mesh)};
 
   // Communicate to calculate parallel transform
   mesh->communicate(input);
 
-  Field3D result{Grad_par(input)};
-  Field3D error{result - solution};
-
   Options dump;
   // Add mesh geometry variables
   mesh->outputVars(dump);
 
-  dump["l_2"] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
-  dump["l_inf"] = max(abs(error), true, "RGN_NOBNDRY");
+  auto* factory = FieldFactory::get();
+  {
+    Field3D solution{factory->create3D("grad_par_solution", Options::getRoot(), mesh)};
+    Field3D result{Grad_par(input)};
+    Field3D error{result - solution};
+
+    dump["grad_par_l_2"] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
+    dump["grad_par_l_inf"] = max(abs(error), true, "RGN_NOBNDRY");
 
-  dump["result"] = result;
-  dump["error"] = error;
-  dump["input"] = input;
-  dump["solution"] = solution;
+    dump["grad_par_result"] = result;
+    dump["grad_par_error"] = error;
+    dump["grad_par_input"] = input;
+    dump["grad_par_solution"] = solution;
 
-  for (int slice = 1; slice < mesh->ystart; ++slice) {
-    dump[fmt::format("input.ynext(-{})", slice)] = input.ynext(-slice);
-    dump[fmt::format("input.ynext({})", slice)] = input.ynext(slice);
+    for (int slice = 1; slice < mesh->ystart; ++slice) {
+      dump[fmt::format("grad_par_input.ynext(-{})", slice)] = input.ynext(-slice);
+      dump[fmt::format("grad_par_input.ynext({})", slice)] = input.ynext(slice);
+    }
+  }
+  {
+    Field3D solution{factory->create3D("grad2_par2_solution", Options::getRoot(), mesh)};
+    Field3D result{Grad2_par2(input)};
+    Field3D error{result - solution};
+
+    dump["grad2_par2_l_2"] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
+    dump["grad2_par2_l_inf"] = max(abs(error), true, "RGN_NOBNDRY");
+
+    dump["grad2_par2_result"] = result;
+    dump["grad2_par2_error"] = error;
+    dump["grad2_par2_input"] = input;
+    dump["grad2_par2_solution"] = solution;
+
+    for (int slice = 1; slice < mesh->ystart; ++slice) {
+      dump[fmt::format("grad2_par2_input.ynext(-{})", slice)] = input.ynext(-slice);
+      dump[fmt::format("grad2_par2_input.ynext({})", slice)] = input.ynext(slice);
+    }
   }
 
   bout::writeDefaultOutputFile(dump);
diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index 1e71135c90..ae48ef8f06 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -30,5 +30,6 @@ def FCI_ddy(f):
 ############################################
 # Equations solved
 
-print("input = " + exprToStr(f))
-print("solution = " + exprToStr(FCI_ddy(f)))
+print(f"input_field = {exprToStr(f)}")
+print(f"grad_par_solution = {exprToStr(FCI_ddy(f))}")
+print(f"grad2_par2_solution = {exprToStr(FCI_ddy(FCI_ddy(f)))}")
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 1f0b297ebc..27b18baafd 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -9,6 +9,7 @@
 import pathlib
 import pickle
 import sys
+from collections import defaultdict
 
 import boutconfig as conf
 import zoidberg as zb
@@ -19,6 +20,7 @@ from scipy.interpolate import RectBivariateSpline as RBS
 
 
 def myRBS(a, b, c):
+    """RectBivariateSpline, but automatically tune spline degree for small arrays"""
     mx, _ = c.shape
     kx = max(mx - 1, 1)
     kx = min(kx, 3)
@@ -27,6 +29,13 @@ def myRBS(a, b, c):
 
 zb.poloidal_grid.RectBivariateSpline = myRBS
 
+
+def quiet_collect(name: str):
+    return collect(
+        name, tind=[1, 1], info=False, path=directory, xguards=False, yguards=False,
+    )
+
+
 nx = 3  # Not changed for these tests
 
 # Resolution in y and z
@@ -50,12 +59,29 @@ method_orders = {}
 yperiodic = True
 
 failures = []
+operators = ("grad_par", "grad2_par2")
 
 build_and_log("FCI MMS test")
 
+
+def assert_convergence(error, dx, name, order) -> bool:
+    fit = polyfit(log(dx), log(error), 1)
+    order = fit[0]
+    print(f"{name} convergence order = {order:f} (fit)", end="")
+
+    order = log(error[-2] / error[-1]) / log(dx[-2] / dx[-1])
+    print(f", {order:f} (small spacing)", end="")
+
+    # Should be close to the expected order
+    success = order > order * 0.95
+    print(f" ............ {'PASS' if success else 'FAIL'}")
+
+    return success
+
+
 for nslice in nslices:
-    error_2[nslice] = []
-    error_inf[nslice] = []
+    error_2[nslice] = defaultdict(list)
+    error_inf[nslice] = defaultdict(list)
 
     # Which central difference scheme to use and its expected order
     order = nslice * 2
@@ -79,70 +105,48 @@ for nslice in nslices:
 
         # Create the grid
         grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
-        # Make and write maps
         maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
         zb.write_maps(
-            grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True
+            grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True,
         )
 
         # Command to run
         args = f" MZ={n} MYG={nslice} mesh:paralleltransform:y_periodic={yperiodic} mesh:ddy:first={name}"
         cmd = f"./fci_mms {args}"
-
         print(f"Running command: {cmd}")
 
         # Launch using MPI
-        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
+        status, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
 
         # Save output to log file
         pathlib.Path(f"run.log.{n}").write_text(out)
 
-        if s:
+        if status:
             print(f"Run failed!\nOutput was:\n{out}")
-            sys.exit(s)
+            sys.exit(status)
 
         # Collect data
-        l_2 = collect(
-            "l_2", tind=[1, 1], info=False, path=directory, xguards=False, yguards=False
-        )
-        l_inf = collect(
-            "l_inf",
-            tind=[1, 1],
-            info=False,
-            path=directory,
-            xguards=False,
-            yguards=False,
-        )
+        for operator in operators:
+            l_2 = quiet_collect(f"{operator}_l_2")
+            l_inf = quiet_collect(f"{operator}_l_inf")
 
-        error_2[nslice].append(l_2)
-        error_inf[nslice].append(l_inf)
+            error_2[nslice][operator].append(l_2)
+            error_inf[nslice][operator].append(l_inf)
 
-        print(f"Errors : l-2 {l_2:f} l-inf {l_inf:f}")
+            print(f"{operator} errors: l-2 {l_2:f} l-inf {l_inf:f}")
 
     dx = 1.0 / array(nlist)
+    for operator in operators:
+        test_name = f"{operator} {name}"
+        success &= assert_convergence(error_2[nslice][operator], dx, test_name, order)
+        if not success:
+            failures.append(test_name)
 
-    # Calculate convergence order
-    fit = polyfit(log(dx), log(error_2[nslice]), 1)
-    order = fit[0]
-    print(f"Convergence order = {order:f} (fit)", end="")
-
-    order = log(error_2[nslice][-2] / error_2[nslice][-1]) / log(dx[-2] / dx[-1])
-    print(f", {order:f} (small spacing)")
-
-    # Should be close to the expected order
-    if order > order * 0.95:
-        print("............ PASS\n")
-    else:
-        print("............ FAIL\n")
-        success = False
-        failures.append(name)
 
-
-with open("fci_mms.pkl", "wb") as output:
+with pathlib.Path("fci_mms.pkl").open("wb") as output:
     pickle.dump(nlist, output)
-    for nslice in nslices:
-        pickle.dump(error_2[nslice], output)
-        pickle.dump(error_inf[nslice], output)
+    pickle.dump(error_2, output)
+    pickle.dump(error_inf, output)
 
 # Do we want to show the plot as well as save it to file.
 show_plot = True
@@ -177,10 +181,10 @@ if False:
         print("No matplotlib")
 
 if success:
-    print("All tests passed")
-    sys.exit(0)
+    print("\nAll tests passed")
 else:
-    print("Some tests failed:")
+    print("\nSome tests failed:")
     for failure in failures:
         print(f"\t{failure}")
-    sys.exit(1)
+
+sys.exit(0 if success else 1)

From c0cc84b78ffe127fea61414db92d92c23743906b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 7 Oct 2025 15:10:32 +0100
Subject: [PATCH 0359/1827] tests: Generalise FCI MMS test to allow for more
 cases

---
 tests/MMS/spatial/fci/runtest | 302 +++++++++++++++++++++-------------
 1 file changed, 188 insertions(+), 114 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 27b18baafd..c575f1afbc 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -6,10 +6,12 @@
 # Cores: 2
 # requires: zoidberg
 
+import argparse
+import json
 import pathlib
-import pickle
 import sys
-from collections import defaultdict
+from time import time
+from typing import Any
 
 import boutconfig as conf
 import zoidberg as zb
@@ -18,6 +20,16 @@ from boututils.run_wrapper import build_and_log, launch_safe
 from numpy import arange, array, linspace, log, polyfit
 from scipy.interpolate import RectBivariateSpline as RBS
 
+# Global parameters
+DIRECTORY = "data"
+NPROC = 2
+MTHREAD = 2
+OPERATORS = ("grad_par", "grad2_par2")
+NX = 3
+# Resolution in y and z
+NLIST = [8, 16, 32, 64, 128]
+dx = 1.0 / array(NLIST)
+
 
 def myRBS(a, b, c):
     """RectBivariateSpline, but automatically tune spline degree for small arrays"""
@@ -30,38 +42,16 @@ def myRBS(a, b, c):
 zb.poloidal_grid.RectBivariateSpline = myRBS
 
 
-def quiet_collect(name: str):
+def quiet_collect(name: str) -> float:
+    # Index to return a plain (numpy) float rather than `BoutArray`
     return collect(
-        name, tind=[1, 1], info=False, path=directory, xguards=False, yguards=False,
-    )
-
-
-nx = 3  # Not changed for these tests
-
-# Resolution in y and z
-nlist = [8, 16, 32, 64, 128]
-
-# Number of parallel slices (in each direction)
-nslices = [1]
-
-directory = "data"
-
-nproc = 2
-mthread = 2
-
-success = True
-
-error_2 = {}
-error_inf = {}
-method_orders = {}
-
-# Run with periodic Y?
-yperiodic = True
-
-failures = []
-operators = ("grad_par", "grad2_par2")
-
-build_and_log("FCI MMS test")
+        name,
+        tind=[1, 1],
+        info=False,
+        path=DIRECTORY,
+        xguards=False,
+        yguards=False,
+    )[()]
 
 
 def assert_convergence(error, dx, name, order) -> bool:
@@ -74,117 +64,201 @@ def assert_convergence(error, dx, name, order) -> bool:
 
     # Should be close to the expected order
     success = order > order * 0.95
-    print(f" ............ {'PASS' if success else 'FAIL'}")
+    print(f"\t............ {'PASS' if success else 'FAIL'}")
 
     return success
 
 
-for nslice in nslices:
-    error_2[nslice] = defaultdict(list)
-    error_inf[nslice] = defaultdict(list)
+def run_fci_operators(
+    nslice: int, nz: int, yperiodic: bool, name: str
+) -> dict[str, float]:
+    # Define the magnetic field using new poloidal gridding method
+    # Note that the Bz and Bzprime parameters here must be the same as in mms.py
+    field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
+    # Create rectangular poloidal grids
+    poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(NX, nz, 0.1, 1.0, MXG=1)
+    # Set the ylength and y locations
+    ylength = 10.0
+
+    if yperiodic:
+        ycoords = linspace(0.0, ylength, nz, endpoint=False)
+    else:
+        # Doesn't include the end points
+        ycoords = (arange(nz) + 0.5) * ylength / float(nz)
+
+    # Create the grid
+    grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
+    maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
+    zb.write_maps(
+        grid,
+        field,
+        maps,
+        new_names=False,
+        metric2d=conf.isMetric2D(),
+        quiet=True,
+    )
 
-    # Which central difference scheme to use and its expected order
-    order = nslice * 2
-    name = f"C{order}"
-    method_orders[nslice] = {"name": name, "order": order}
-
-    for n in nlist:
-        # Define the magnetic field using new poloidal gridding method
-        # Note that the Bz and Bzprime parameters here must be the same as in mms.py
-        field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
-        # Create rectangular poloidal grids
-        poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(nx, n, 0.1, 1.0, MXG=1)
-        # Set the ylength and y locations
-        ylength = 10.0
-
-        if yperiodic:
-            ycoords = linspace(0.0, ylength, n, endpoint=False)
-        else:
-            # Doesn't include the end points
-            ycoords = (arange(n) + 0.5) * ylength / float(n)
-
-        # Create the grid
-        grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
-        maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
-        zb.write_maps(
-            grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True,
-        )
+    # Command to run
+    args = f"MZ={nz} MYG={nslice} mesh:paralleltransform:y_periodic={yperiodic} mesh:ddy:first={name}"
+    cmd = f"./fci_mms {args}"
+    print(f"Running command: {cmd}", end="")
+
+    # Launch using MPI
+    start = time()
+    status, out = launch_safe(cmd, nproc=NPROC, mthread=MTHREAD, pipe=True)
+    print(f" ... done in {time() - start:.3}s")
+
+    # Save output to log file
+    pathlib.Path(f"run.log.{nz}").write_text(out)
+
+    if status:
+        print(f"Run failed!\nOutput was:\n{out}")
+        sys.exit(status)
+
+    return {
+        operator: {
+            "l_2": quiet_collect(f"{operator}_l_2"),
+            "l_inf": quiet_collect(f"{operator}_l_inf"),
+        }
+        for operator in OPERATORS
+    }
 
-        # Command to run
-        args = f" MZ={n} MYG={nslice} mesh:paralleltransform:y_periodic={yperiodic} mesh:ddy:first={name}"
-        cmd = f"./fci_mms {args}"
-        print(f"Running command: {cmd}")
 
-        # Launch using MPI
-        status, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
+def transpose(
+    errors: list[dict[str, dict[str, float]]],
+) -> dict[str, dict[str, list[float]]]:
+    """Turn a list of {operator: error} into a dict of {operator: [errors]}"""
 
-        # Save output to log file
-        pathlib.Path(f"run.log.{n}").write_text(out)
+    kinds = ("l_2", "l_inf")
+    result = {operator: {kind: [] for kind in kinds} for operator in OPERATORS}
+    for error in errors:
+        for k, v in error.items():
+            for kind in kinds:
+                result[k][kind].append(v[kind])
+    return result
 
-        if status:
-            print(f"Run failed!\nOutput was:\n{out}")
-            sys.exit(status)
 
-        # Collect data
-        for operator in operators:
-            l_2 = quiet_collect(f"{operator}_l_2")
-            l_inf = quiet_collect(f"{operator}_l_inf")
+def check_fci_operators(case: dict) -> bool:
+    failures = []
 
-            error_2[nslice][operator].append(l_2)
-            error_inf[nslice][operator].append(l_inf)
+    nslice = case["nslice"]
+    yperiodic = case["yperiodic"]
+    name = case["name"]
+    order = case["order"]
+
+    all_errors = []
+
+    for n in NLIST:
+        errors = run_fci_operators(nslice, n, yperiodic, name)
+        all_errors.append(errors)
+
+        for operator in OPERATORS:
+            l_2 = errors[operator]["l_2"]
+            l_inf = errors[operator]["l_inf"]
 
             print(f"{operator} errors: l-2 {l_2:f} l-inf {l_inf:f}")
 
-    dx = 1.0 / array(nlist)
-    for operator in operators:
+    final_errors = transpose(all_errors)
+    for operator in OPERATORS:
         test_name = f"{operator} {name}"
-        success &= assert_convergence(error_2[nslice][operator], dx, test_name, order)
+        success = assert_convergence(
+            final_errors[operator]["l_2"], dx, test_name, order
+        )
         if not success:
             failures.append(test_name)
 
+    return final_errors, failures
 
-with pathlib.Path("fci_mms.pkl").open("wb") as output:
-    pickle.dump(nlist, output)
-    pickle.dump(error_2, output)
-    pickle.dump(error_inf, output)
-
-# Do we want to show the plot as well as save it to file.
-show_plot = True
 
-if False:
+def make_plots(cases):
     try:
-        # Plot using matplotlib if available
         import matplotlib.pyplot as plt
+    except ImportError:
+        print("No matplotlib")
+        return
 
-        fig, ax = plt.subplots(1, 1)
+    fig, axes = plt.subplots(1, len(OPERATORS), figsize=(9, 4))
 
-        for nslice in nslices:
-            name = method_orders[nslice]["name"]
-            ax.plot(dx, error_2[nslice], "-", label=f"{name} $l_2$")
-            ax.plot(dx, error_inf[nslice], "--", label=f"{name} $l_\\inf$")
+    for ax, operator in zip(axes, OPERATORS):
+        for name, case in cases.items():
+            ax.loglog(dx, case[operator]["l_2"], "-", label=f"{name} $l_2$")
+            ax.loglog(dx, case[operator]["l_inf"], "--", label=f"{name} $l_\\inf$")
         ax.legend(loc="upper left")
         ax.grid()
-        ax.set_yscale("log")
-        ax.set_xscale("log")
-        ax.set_title("error scaling")
+        ax.set_title(f"Error scaling for {operator}")
         ax.set_xlabel(r"Mesh spacing $\delta x$")
         ax.set_ylabel("Error norm")
 
-        plt.savefig("fci_mms.pdf")
+    fig.tight_layout()
+    fig.savefig("fci_mms.pdf")
+    print("Plot saved to fci_mms.pdf")
 
-        print("Plot saved to fci_mms.pdf")
+    if args.show_plots:
+        plt.show()
+    plt.close()
 
-        if show_plot:
-            plt.show()
-        plt.close()
-    except ImportError:
-        print("No matplotlib")
 
-if success:
-    print("\nAll tests passed")
-else:
-    print("\nSome tests failed:")
-    for failure in failures:
-        print(f"\t{failure}")
+def make_case(nslice: int, yperiodic: bool) -> dict[str, Any]:
+    """
+    nslice:
+        Number of parallel slices (in each direction)
+    yperiodic:
+        Run with periodic Y
+    """
+    order = nslice * 2
+    return {
+        "nslice": nslice,
+        # Which central difference scheme to use and its expected order
+        "order": order,
+        "name": f"C{order}",
+        "yperiodic": yperiodic,
+    }
+
+
+if __name__ == "__main__":
+    build_and_log("FCI MMS test")
+
+    parser = argparse.ArgumentParser("Error scaling test for FCI operators")
+    parser.add_argument(
+        "--make-plots", action="store_true", help="Create plots of error scaling"
+    )
+    parser.add_argument(
+        "--show-plots",
+        action="store_true",
+        help="Stop and show plots, implies --make-plots",
+    )
+    parser.add_argument(
+        "--dump-errors",
+        type=str,
+        help="Output file to dump errors as JSON",
+        default="fci_operator_errors.json",
+    )
+
+    args = parser.parse_args()
+
+    success = True
+    failures = []
+    cases = {
+        "nslice=1": make_case(nslice=1, yperiodic=True),
+    }
+
+    for case in cases.values():
+        error2, failures_ = check_fci_operators(case)
+        case.update(error2)
+        failures.extend(failures_)
+        success &= len(failures) == 0
+
+    if args.dump_errors:
+        pathlib.Path(args.dump_errors).write_text(json.dumps(cases))
+
+    if args.make_plots or args.show_plots:
+        make_plots(cases)
+
+    if success:
+        print("\nAll tests passed")
+    else:
+        print("\nSome tests failed:")
+        for failure in failures:
+            print(f"\t{failure}")
 
-sys.exit(0 if success else 1)
+    sys.exit(0 if success else 1)

From 2eda48cf04bb41abaa8fce6d61336fc5b5dddf2d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 7 Oct 2025 15:30:58 +0100
Subject: [PATCH 0360/1827] tests: Add test for FCI `Div_par`

---
 tests/MMS/spatial/fci/data/BOUT.inp |  1 +
 tests/MMS/spatial/fci/fci_mms.cxx   | 67 +++++++++++++----------------
 tests/MMS/spatial/fci/mms.py        |  4 ++
 tests/MMS/spatial/fci/runtest       |  2 +-
 4 files changed, 36 insertions(+), 38 deletions(-)

diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index f065989524..3103b37e2d 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -1,6 +1,7 @@
 input_field = sin(y - 2*z) + sin(y - z)
 grad_par_solution = (6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0)
 grad2_par2_solution = (6.28318530717959*(0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0))/sqrt((0.01*x + 0.045)^2 + 1.0)
+div_par_solution = (0.01*x + 0.045)*(-12.5663706143592*cos(y - 2*z) - 6.28318530717959*cos(y - z) + 0.628318530717959*(cos(y - 2*z) + cos(y - z))/(0.01*x + 0.045))/sqrt((0.01*x + 0.045)^2 + 1.0)
 
 MXG = 1
 MYG = 1
diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index 48b18f04ef..bc995424c6 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -1,6 +1,33 @@
 #include "bout/bout.hxx"
+#include "bout/difops.hxx"
+#include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
 
+#include <string>
+
+namespace {
+auto fci_op_test(const std::string& name, Options& dump, const Field3D& input,
+                 const Field3D& result) {
+  auto* mesh = input.getMesh();
+  Field3D solution{FieldFactory::get()->create3D(fmt::format("{}_solution", name),
+                                                 Options::getRoot(), mesh)};
+  Field3D error{result - solution};
+
+  dump[fmt::format("{}_l_2", name)] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
+  dump[fmt::format("{}_l_inf", name)] = max(abs(error), true, "RGN_NOBNDRY");
+
+  dump[fmt::format("{}_result", name)] = result;
+  dump[fmt::format("{}_error", name)] = error;
+  dump[fmt::format("{}_input", name)] = input;
+  dump[fmt::format("{}_solution", name)] = solution;
+
+  for (int slice = 1; slice < mesh->ystart; ++slice) {
+    dump[fmt::format("{}_input.ynext(-{})", name, slice)] = input.ynext(-slice);
+    dump[fmt::format("{}_input.ynext({})", name, slice)] = input.ynext(slice);
+  }
+}
+} // namespace
+
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
@@ -15,43 +42,9 @@ int main(int argc, char** argv) {
   // Add mesh geometry variables
   mesh->outputVars(dump);
 
-  auto* factory = FieldFactory::get();
-  {
-    Field3D solution{factory->create3D("grad_par_solution", Options::getRoot(), mesh)};
-    Field3D result{Grad_par(input)};
-    Field3D error{result - solution};
-
-    dump["grad_par_l_2"] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
-    dump["grad_par_l_inf"] = max(abs(error), true, "RGN_NOBNDRY");
-
-    dump["grad_par_result"] = result;
-    dump["grad_par_error"] = error;
-    dump["grad_par_input"] = input;
-    dump["grad_par_solution"] = solution;
-
-    for (int slice = 1; slice < mesh->ystart; ++slice) {
-      dump[fmt::format("grad_par_input.ynext(-{})", slice)] = input.ynext(-slice);
-      dump[fmt::format("grad_par_input.ynext({})", slice)] = input.ynext(slice);
-    }
-  }
-  {
-    Field3D solution{factory->create3D("grad2_par2_solution", Options::getRoot(), mesh)};
-    Field3D result{Grad2_par2(input)};
-    Field3D error{result - solution};
-
-    dump["grad2_par2_l_2"] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
-    dump["grad2_par2_l_inf"] = max(abs(error), true, "RGN_NOBNDRY");
-
-    dump["grad2_par2_result"] = result;
-    dump["grad2_par2_error"] = error;
-    dump["grad2_par2_input"] = input;
-    dump["grad2_par2_solution"] = solution;
-
-    for (int slice = 1; slice < mesh->ystart; ++slice) {
-      dump[fmt::format("grad2_par2_input.ynext(-{})", slice)] = input.ynext(-slice);
-      dump[fmt::format("grad2_par2_input.ynext({})", slice)] = input.ynext(slice);
-    }
-  }
+  fci_op_test("grad_par", dump, input, Grad_par(input));
+  fci_op_test("grad2_par2", dump, input, Grad2_par2(input));
+  fci_op_test("div_par", dump, input, Div_par(input));
 
   bout::writeDefaultOutputFile(dump);
 
diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index ae48ef8f06..5f5d48bee2 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -26,6 +26,9 @@
 def FCI_ddy(f):
     return (Bt * diff(f, y) * 2.0 * pi / Ly + Bpx * diff(f, z) * 2.0 * pi / Lz) / B
 
+def FCI_div_par(f):
+    return Bpx * FCI_ddy(f / Bpx)
+
 
 ############################################
 # Equations solved
@@ -33,3 +36,4 @@ def FCI_ddy(f):
 print(f"input_field = {exprToStr(f)}")
 print(f"grad_par_solution = {exprToStr(FCI_ddy(f))}")
 print(f"grad2_par2_solution = {exprToStr(FCI_ddy(FCI_ddy(f)))}")
+print(f"div_par_solution = {exprToStr(FCI_div_par(f))}")
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index c575f1afbc..c98d924e7b 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -24,7 +24,7 @@ from scipy.interpolate import RectBivariateSpline as RBS
 DIRECTORY = "data"
 NPROC = 2
 MTHREAD = 2
-OPERATORS = ("grad_par", "grad2_par2")
+OPERATORS = ("grad_par", "grad2_par2", "div_par")
 NX = 3
 # Resolution in y and z
 NLIST = [8, 16, 32, 64, 128]

From 636bf288f616f67e2d84552e569a24d64d8f5485 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 7 Oct 2025 15:47:01 +0100
Subject: [PATCH 0361/1827] tests: Make MMS script update input in-place

---
 tests/MMS/spatial/fci/data/BOUT.inp |  7 +++---
 tests/MMS/spatial/fci/mms.py        | 36 +++++++++++++++++++++--------
 2 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index 3103b37e2d..f44773667c 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -3,13 +3,12 @@ grad_par_solution = (6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y
 grad2_par2_solution = (6.28318530717959*(0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0))/sqrt((0.01*x + 0.045)^2 + 1.0)
 div_par_solution = (0.01*x + 0.045)*(-12.5663706143592*cos(y - 2*z) - 6.28318530717959*cos(y - z) + 0.628318530717959*(cos(y - 2*z) + cos(y - z))/(0.01*x + 0.045))/sqrt((0.01*x + 0.045)^2 + 1.0)
 
-MXG = 1
-MYG = 1
-NXPE = 1
-
 [mesh]
 symmetricglobalx = true
 file = fci.grid.nc
+MXG = 1
+MYG = 1
+NXPE = 1
 
 [mesh:ddy]
 first = C2
diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index 5f5d48bee2..e434ea3ecf 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -3,11 +3,15 @@
 # Generate manufactured solution and sources for FCI test
 #
 
-from boutdata.mms import *
+from math import pi
+import warnings
 
-from sympy import sin, cos, sqrt
+from boututils.boutwarnings import AlwaysWarning
+from boutdata.data import BoutOptionsFile
+from boutdata.mms import diff, exprToStr, x, y, z
+from sympy import sin, sqrt, Expr
 
-from math import pi
+warnings.simplefilter("ignore", AlwaysWarning)
 
 f = sin(y - z) + sin(y - 2 * z)
 
@@ -23,17 +27,31 @@
 B = sqrt(Bpx**2 + Bt**2)
 
 
-def FCI_ddy(f):
+def FCI_ddy(f: Expr) -> Expr:
     return (Bt * diff(f, y) * 2.0 * pi / Ly + Bpx * diff(f, z) * 2.0 * pi / Lz) / B
 
-def FCI_div_par(f):
+
+def FCI_div_par(f: Expr) -> Expr:
     return Bpx * FCI_ddy(f / Bpx)
 
 
 ############################################
 # Equations solved
 
-print(f"input_field = {exprToStr(f)}")
-print(f"grad_par_solution = {exprToStr(FCI_ddy(f))}")
-print(f"grad2_par2_solution = {exprToStr(FCI_ddy(FCI_ddy(f)))}")
-print(f"div_par_solution = {exprToStr(FCI_div_par(f))}")
+input_field = exprToStr(f)
+grad_par_solution = exprToStr(FCI_ddy(f))
+grad2_par2_solution = exprToStr(FCI_ddy(FCI_ddy(f)))
+div_par_solution = exprToStr(FCI_div_par(f))
+
+print(f"input_field = {input_field}")
+print(f"grad_par_solution = {grad_par_solution}")
+print(f"grad2_par2_solution = {grad2_par2_solution}")
+print(f"div_par_solution = {div_par_solution}")
+print(f"div_par_K_grad_par_solution = {div_par_K_grad_par_solution}")
+
+options = BoutOptionsFile("data/BOUT.inp")
+options["input_field"] = input_field
+options["grad_par_solution"] = grad_par_solution
+options["grad2_par2_solution"] = grad2_par2_solution
+options["div_par_solution"] = div_par_solution
+options.write("data/BOUT.inp", overwrite=True)

From 16318eccf35685ca4caf7fe9263a06c4d884abe4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 7 Oct 2025 16:34:44 +0100
Subject: [PATCH 0362/1827] tests: Add test for FCI `Div_par_K_Grad_par`

---
 tests/MMS/spatial/fci/data/BOUT.inp |  2 ++
 tests/MMS/spatial/fci/fci_mms.cxx   |  5 ++++-
 tests/MMS/spatial/fci/mms.py        | 23 ++++++++++++++++++-----
 tests/MMS/spatial/fci/runtest       |  5 +++--
 4 files changed, 27 insertions(+), 8 deletions(-)

diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index f44773667c..e31d84cb35 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -2,6 +2,8 @@ input_field = sin(y - 2*z) + sin(y - z)
 grad_par_solution = (6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0)
 grad2_par2_solution = (6.28318530717959*(0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0))/sqrt((0.01*x + 0.045)^2 + 1.0)
 div_par_solution = (0.01*x + 0.045)*(-12.5663706143592*cos(y - 2*z) - 6.28318530717959*cos(y - z) + 0.628318530717959*(cos(y - 2*z) + cos(y - z))/(0.01*x + 0.045))/sqrt((0.01*x + 0.045)^2 + 1.0)
+div_par_K_grad_par_solution = (0.01*x + 0.045)*(6.28318530717959*sin(y - z) - 0.628318530717959*sin(y - z)/(0.01*x + 0.045))*(6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/((0.01*x + 0.045)^2 + 1.0) + (6.28318530717959*(0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0))*cos(y - z)/sqrt((0.01*x + 0.045)^2 + 1.0)
+K = cos(y - z)
 
 [mesh]
 symmetricglobalx = true
diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index bc995424c6..a0b70e9da6 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -2,6 +2,7 @@
 #include "bout/difops.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
+#include "bout/options.hxx"
 
 #include <string>
 
@@ -34,9 +35,10 @@ int main(int argc, char** argv) {
   using bout::globals::mesh;
 
   Field3D input{FieldFactory::get()->create3D("input_field", Options::getRoot(), mesh)};
+  Field3D K{FieldFactory::get()->create3D("K", Options::getRoot(), mesh)};
 
   // Communicate to calculate parallel transform
-  mesh->communicate(input);
+  mesh->communicate(input, K);
 
   Options dump;
   // Add mesh geometry variables
@@ -45,6 +47,7 @@ int main(int argc, char** argv) {
   fci_op_test("grad_par", dump, input, Grad_par(input));
   fci_op_test("grad2_par2", dump, input, Grad2_par2(input));
   fci_op_test("div_par", dump, input, Div_par(input));
+  fci_op_test("div_par_K_grad_par", dump, input, Div_par_K_Grad_par(K, input));
 
   bout::writeDefaultOutputFile(dump);
 
diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index e434ea3ecf..79ec661507 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -9,11 +9,12 @@
 from boututils.boutwarnings import AlwaysWarning
 from boutdata.data import BoutOptionsFile
 from boutdata.mms import diff, exprToStr, x, y, z
-from sympy import sin, sqrt, Expr
+from sympy import sin, cos, sqrt, Expr
 
 warnings.simplefilter("ignore", AlwaysWarning)
 
 f = sin(y - z) + sin(y - 2 * z)
+K = cos(z - y)
 
 Lx = 0.1
 Ly = 10.0
@@ -27,23 +28,33 @@
 B = sqrt(Bpx**2 + Bt**2)
 
 
-def FCI_ddy(f: Expr) -> Expr:
+def FCI_grad_par(f: Expr) -> Expr:
     return (Bt * diff(f, y) * 2.0 * pi / Ly + Bpx * diff(f, z) * 2.0 * pi / Lz) / B
 
 
+def FCI_grad2_par2(f: Expr) -> Expr:
+    return FCI_grad_par(FCI_grad_par(f))
+
+
 def FCI_div_par(f: Expr) -> Expr:
-    return Bpx * FCI_ddy(f / Bpx)
+    return Bpx * FCI_grad_par(f / Bpx)
+
+
+def FCI_div_par_K_grad_par(f: Expr, K: Expr) -> Expr:
+    return (K * FCI_grad2_par2(f)) + (FCI_div_par(K) * FCI_grad_par(f))
 
 
 ############################################
 # Equations solved
 
 input_field = exprToStr(f)
-grad_par_solution = exprToStr(FCI_ddy(f))
-grad2_par2_solution = exprToStr(FCI_ddy(FCI_ddy(f)))
+grad_par_solution = exprToStr(FCI_grad_par(f))
+grad2_par2_solution = exprToStr(FCI_grad2_par2(f))
 div_par_solution = exprToStr(FCI_div_par(f))
+div_par_K_grad_par_solution = exprToStr(FCI_div_par_K_grad_par(f, K))
 
 print(f"input_field = {input_field}")
+print(f"K = {K}")
 print(f"grad_par_solution = {grad_par_solution}")
 print(f"grad2_par2_solution = {grad2_par2_solution}")
 print(f"div_par_solution = {div_par_solution}")
@@ -51,7 +62,9 @@ def FCI_div_par(f: Expr) -> Expr:
 
 options = BoutOptionsFile("data/BOUT.inp")
 options["input_field"] = input_field
+options["K"] = K
 options["grad_par_solution"] = grad_par_solution
 options["grad2_par2_solution"] = grad2_par2_solution
 options["div_par_solution"] = div_par_solution
+options["div_par_K_grad_par_solution"] = div_par_K_grad_par_solution
 options.write("data/BOUT.inp", overwrite=True)
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index c98d924e7b..5a19877a45 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -24,7 +24,7 @@ from scipy.interpolate import RectBivariateSpline as RBS
 DIRECTORY = "data"
 NPROC = 2
 MTHREAD = 2
-OPERATORS = ("grad_par", "grad2_par2", "div_par")
+OPERATORS = ("grad_par", "grad2_par2", "div_par", "div_par_K_grad_par")
 NX = 3
 # Resolution in y and z
 NLIST = [8, 16, 32, 64, 128]
@@ -177,7 +177,8 @@ def make_plots(cases):
         print("No matplotlib")
         return
 
-    fig, axes = plt.subplots(1, len(OPERATORS), figsize=(9, 4))
+    num_operators = len(OPERATORS)
+    fig, axes = plt.subplots(1, num_operators, figsize=(num_operators * 4, 4))
 
     for ax, operator in zip(axes, OPERATORS):
         for name, case in cases.items():

From 14b4b11a097320b6c936a27fe81b24161cc924ff Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 7 Oct 2025 17:30:48 +0100
Subject: [PATCH 0363/1827] Many small fixes for FCI

- Include all relevant headers, remove unused ones, add some forward
  declarations
- Make data `private` instead of `protected`
- Add getter instead of `const` member
- Change member reference to pointer
- Move ctor to .cxx file
- Use `std::array` instead of C array
- Bunch of other small clang-tidy fixes
---
 src/mesh/parallel/fci.cxx | 178 ++++++++++++++++++++++++++------------
 src/mesh/parallel/fci.hxx |  83 ++++++------------
 2 files changed, 150 insertions(+), 111 deletions(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index e8d3af1cdb..e44a74966e 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -37,79 +37,99 @@
  **************************************************************************/
 
 #include "fci.hxx"
+
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/field_data.hxx"
+#include "bout/mesh.hxx"
+#include "bout/msg_stack.hxx"
+#include "bout/options.hxx"
 #include "bout/parallel_boundary_op.hxx"
 #include "bout/parallel_boundary_region.hxx"
-#include <bout/bout_types.hxx>
-#include <bout/constants.hxx>
-#include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
-#include <bout/utils.hxx>
+#include "bout/paralleltransform.hxx"
+#include "bout/region.hxx"
+
+#include <fmt/format.h>
 
+#include <array>
+#include <cmath>
+#include <cstddef>
+#include <cstdlib>
+#include <memory>
 #include <string>
+#include <string_view>
+
+using namespace std::string_view_literals;
 
-FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& UNUSED(dy), Options& options,
-               int offset_, const std::shared_ptr<BoundaryRegionPar>& inner_boundary,
+FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
+               Options& options, int offset,
+               const std::shared_ptr<BoundaryRegionPar>& inner_boundary,
                const std::shared_ptr<BoundaryRegionPar>& outer_boundary, bool zperiodic)
-    : map_mesh(mesh), offset(offset_),
-      region_no_boundary(map_mesh.getRegion("RGN_NOBNDRY")),
+    : map_mesh(&mesh), offset_(offset),
+      region_no_boundary(map_mesh->getRegion("RGN_NOBNDRY")),
       corner_boundary_mask(map_mesh) {
 
-  TRACE("Creating FCIMAP for direction {:d}", offset);
+  TRACE("Creating FCIMAP for direction {:d}", offset_);
 
-  if (offset == 0) {
+  if (offset_ == 0) {
     throw BoutException(
         "FCIMap called with offset = 0; You probably didn't mean to do that");
   }
 
   auto& interpolation_options = options["xzinterpolation"];
-  interp =
-      XZInterpolationFactory::getInstance().create(&interpolation_options, &map_mesh);
-  interp->setYOffset(offset);
+  interp = XZInterpolationFactory::getInstance().create(&interpolation_options, map_mesh);
+  interp->setYOffset(offset_);
 
   interp_corner =
-      XZInterpolationFactory::getInstance().create(&interpolation_options, &map_mesh);
-  interp_corner->setYOffset(offset);
+      XZInterpolationFactory::getInstance().create(&interpolation_options, map_mesh);
+  interp_corner->setYOffset(offset_);
 
   // Index-space coordinates of forward/backward points
-  Field3D xt_prime{&map_mesh}, zt_prime{&map_mesh};
+  Field3D xt_prime{map_mesh};
+  Field3D zt_prime{map_mesh};
 
   // Real-space coordinates of grid points
-  Field3D R{&map_mesh}, Z{&map_mesh};
+  Field3D R{map_mesh};
+  Field3D Z{map_mesh};
 
   // Real-space coordinates of forward/backward points
-  Field3D R_prime{&map_mesh}, Z_prime{&map_mesh};
+  Field3D R_prime{map_mesh};
+  Field3D Z_prime{map_mesh};
 
-  map_mesh.get(R, "R", 0.0, false);
-  map_mesh.get(Z, "Z", 0.0, false);
+  map_mesh->get(R, "R", 0.0, false);
+  map_mesh->get(Z, "Z", 0.0, false);
 
   // Get a unique name for a field based on the sign/magnitude of the offset
-  const auto parallel_slice_field_name = [&](std::string field) -> std::string {
-    const std::string direction = (offset > 0) ? "forward" : "backward";
+  const auto parallel_slice_field_name = [&](std::string_view field) -> std::string {
+    const auto direction = (offset_ > 0) ? "forward"sv : "backward"sv;
     // We only have a suffix for parallel slices beyond the first
     // This is for backwards compatibility
-    const std::string slice_suffix =
-        (std::abs(offset) > 1) ? "_" + std::to_string(std::abs(offset)) : "";
-    return direction + "_" + field + slice_suffix;
+    const auto slice_suffix =
+        (std::abs(offset_) > 1) ? fmt::format("_{}", std::abs(offset_)) : "";
+    return fmt::format("{}_{}{}", direction, field, slice_suffix);
   };
 
   // If we can't read in any of these fields, things will silently not
   // work, so best throw
-  if (map_mesh.get(xt_prime, parallel_slice_field_name("xt_prime"), 0.0, false) != 0) {
+  if (map_mesh->get(xt_prime, parallel_slice_field_name("xt_prime"), 0.0, false) != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
                         parallel_slice_field_name("xt_prime"));
   }
-  if (map_mesh.get(zt_prime, parallel_slice_field_name("zt_prime"), 0.0, false) != 0) {
+  if (map_mesh->get(zt_prime, parallel_slice_field_name("zt_prime"), 0.0, false) != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
                         parallel_slice_field_name("zt_prime"));
   }
-  if (map_mesh.get(R_prime, parallel_slice_field_name("R"), 0.0, false) != 0) {
+  if (map_mesh->get(R_prime, parallel_slice_field_name("R"), 0.0, false) != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
                         parallel_slice_field_name("R"));
   }
-  if (map_mesh.get(Z_prime, parallel_slice_field_name("Z"), 0.0, false) != 0) {
+  if (map_mesh->get(Z_prime, parallel_slice_field_name("Z"), 0.0, false) != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
                         parallel_slice_field_name("Z"));
@@ -157,7 +177,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& UNUSED(dy), Options&
     interp->calcWeights(xt_prime, zt_prime);
   }
 
-  const int ncz = map_mesh.LocalNz;
+  const int ncz = map_mesh->LocalNz;
 
   BoutMask to_remove(map_mesh);
   const int xend =
@@ -167,15 +187,16 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& UNUSED(dy), Options&
   BOUT_FOR_SERIAL(i, xt_prime.getRegion("RGN_NOBNDRY")) {
     // z is periodic, so make sure the z-index wraps around
     if (zperiodic) {
-      zt_prime[i] = zt_prime[i]
-                    - ncz * (static_cast<int>(zt_prime[i] / static_cast<BoutReal>(ncz)));
+      zt_prime[i] =
+          zt_prime[i]
+          - (ncz * (static_cast<int>(zt_prime[i] / static_cast<BoutReal>(ncz))));
 
       if (zt_prime[i] < 0.0) {
         zt_prime[i] += ncz;
       }
     }
 
-    if ((xt_prime[i] >= map_mesh.xstart) and (xt_prime[i] <= xend)) {
+    if ((xt_prime[i] >= map_mesh->xstart) and (xt_prime[i] <= xend)) {
       // Not a boundary
       continue;
     }
@@ -215,7 +236,7 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& UNUSED(dy), Options&
     const BoutReal dR_dz = 0.5 * (R[i_zp] - R[i_zm]);
     const BoutReal dZ_dz = 0.5 * (Z[i_zp] - Z[i_zm]);
 
-    const BoutReal det = dR_dx * dZ_dz - dR_dz * dZ_dx; // Determinant of 2x2 matrix
+    const BoutReal det = (dR_dx * dZ_dz) - (dR_dz * dZ_dx); // Determinant of 2x2 matrix
 
     const BoutReal dR = R_prime[i] - R[i];
     const BoutReal dZ = Z_prime[i] - Z[i];
@@ -228,9 +249,9 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& UNUSED(dy), Options&
     // outer boundary. However, if any of the surrounding points are negative,
     // that also means inner. So to differentiate between inner and outer we
     // need at least 2 points in the domain.
-    ASSERT2(map_mesh.xend - map_mesh.xstart >= 2);
-    auto boundary = (xt_prime[i] < map_mesh.xstart) ? inner_boundary : outer_boundary;
-    boundary->add_point(x, y, z, x + dx, y + 0.5 * offset,
+    ASSERT2(map_mesh->xend - map_mesh->xstart >= 2);
+    auto boundary = (xt_prime[i] < map_mesh->xstart) ? inner_boundary : outer_boundary;
+    boundary->add_point(x, y, z, x + dx, y + (0.5 * offset_),
                         z + dz, // Intersection point in local index space
                         0.5,    // Distance to intersection
                         1       // Default to that there is a point in the other direction
@@ -240,13 +261,14 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& UNUSED(dy), Options&
 
   interp->setRegion(region_no_boundary);
 
-  const auto region = fmt::format("RGN_YPAR_{:+d}", offset);
-  if (not map_mesh.hasRegion3D(region)) {
+  const auto region = fmt::format("RGN_YPAR_{:+d}", offset_);
+  if (not map_mesh->hasRegion3D(region)) {
     // The valid region for this slice
-    map_mesh.addRegion3D(
-        region, Region<Ind3D>(map_mesh.xstart, map_mesh.xend, map_mesh.ystart + offset,
-                              map_mesh.yend + offset, 0, map_mesh.LocalNz - 1,
-                              map_mesh.LocalNy, map_mesh.LocalNz));
+    map_mesh->addRegion3D(region, Region<Ind3D>(map_mesh->xstart, map_mesh->xend,
+                                                map_mesh->ystart + offset_,
+                                                map_mesh->yend + offset_, 0,
+                                                map_mesh->LocalNz - 1, map_mesh->LocalNy,
+                                                map_mesh->LocalNz));
   }
 }
 
@@ -254,7 +276,7 @@ Field3D FCIMap::integrate(Field3D& f) const {
   TRACE("FCIMap::integrate");
 
   ASSERT1(f.getDirectionY() == YDirectionType::Standard);
-  ASSERT1(&map_mesh == f.getMesh());
+  ASSERT1(map_mesh == f.getMesh());
 
   // Cell centre values
   Field3D centre = interp->interpolate(f);
@@ -269,7 +291,7 @@ Field3D FCIMap::integrate(Field3D& f) const {
 #endif
 
   BOUT_FOR(i, region_no_boundary) {
-    const auto inext = i.yp(offset);
+    const auto inext = i.yp(offset_);
     const BoutReal f_c = centre[inext];
     const auto izm = i.zm();
     const int x = i.x();
@@ -278,7 +300,7 @@ Field3D FCIMap::integrate(Field3D& f) const {
     const int zm = izm.z();
     if (corner_boundary_mask(x, y, z) || corner_boundary_mask(x - 1, y, z)
         || corner_boundary_mask(x, y, zm) || corner_boundary_mask(x - 1, y, zm)
-        || (x == map_mesh.xstart)) {
+        || (x == map_mesh->xstart)) {
       // One of the corners leaves the domain.
       // Use the cell centre value, since boundary conditions are not
       // currently applied to corners.
@@ -299,10 +321,60 @@ Field3D FCIMap::integrate(Field3D& f) const {
   return result;
 }
 
+FCITransform::FCITransform(Mesh& mesh, const Coordinates::FieldMetric& dy, bool zperiodic,
+                           Options* opt)
+    : ParallelTransform(mesh, opt), R{&mesh}, Z{&mesh} {
+
+  // check the coordinate system used for the grid data source
+  FCITransform::checkInputGrid();
+
+  // Real-space coordinates of grid cells
+  mesh.get(R, "R", 0.0, false);
+  mesh.get(Z, "Z", 0.0, false);
+
+  auto forward_boundary_xin =
+      std::make_shared<BoundaryRegionPar>("FCI_forward", BNDRY_PAR_FWD_XIN, +1, &mesh);
+  auto backward_boundary_xin =
+      std::make_shared<BoundaryRegionPar>("FCI_backward", BNDRY_PAR_BKWD_XIN, -1, &mesh);
+  auto forward_boundary_xout =
+      std::make_shared<BoundaryRegionPar>("FCI_forward", BNDRY_PAR_FWD_XOUT, +1, &mesh);
+  auto backward_boundary_xout =
+      std::make_shared<BoundaryRegionPar>("FCI_backward", BNDRY_PAR_BKWD_XOUT, -1, &mesh);
+
+  // Add the boundary region to the mesh's vector of parallel boundaries
+  mesh.addBoundaryPar(forward_boundary_xin, BoundaryParType::xin_fwd);
+  mesh.addBoundaryPar(backward_boundary_xin, BoundaryParType::xin_bwd);
+  mesh.addBoundaryPar(forward_boundary_xout, BoundaryParType::xout_fwd);
+  mesh.addBoundaryPar(backward_boundary_xout, BoundaryParType::xout_bwd);
+
+  field_line_maps.reserve(static_cast<std::size_t>(mesh.ystart) * 2);
+  for (int offset = 1; offset < mesh.ystart + 1; ++offset) {
+    field_line_maps.emplace_back(mesh, dy, options, offset, forward_boundary_xin,
+                                 forward_boundary_xout, zperiodic);
+    field_line_maps.emplace_back(mesh, dy, options, -offset, backward_boundary_xin,
+                                 backward_boundary_xout, zperiodic);
+  }
+  ASSERT0(mesh.ystart == 1);
+  const std::array bndries = {forward_boundary_xin, forward_boundary_xout,
+                              backward_boundary_xin, backward_boundary_xout};
+  for (const auto& bndry : bndries) {
+    for (const auto& bndry2 : bndries) {
+      if (bndry->dir == bndry2->dir) {
+        continue;
+      }
+      for (bndry->first(); !bndry->isDone(); bndry->next()) {
+        if (bndry2->contains(*bndry)) {
+          bndry->setValid(0);
+        }
+      }
+    }
+  }
+}
+
 void FCITransform::checkInputGrid() {
   std::string parallel_transform;
   if (mesh.isDataSourceGridFile()
-      && !mesh.get(parallel_transform, "parallel_transform")) {
+      && (mesh.get(parallel_transform, "parallel_transform") == 0)) {
     if (parallel_transform != "fci") {
       throw BoutException(
           "Incorrect parallel transform type '" + parallel_transform
@@ -310,8 +382,8 @@ void FCITransform::checkInputGrid() {
             "to generate metric components for FCITransform. Should be 'fci'.");
     }
   } // else: parallel_transform variable not found in grid input, indicates older input
-    //       file or grid from options so must rely on the user having ensured the type is
-    //       correct
+  //       file or grid from options so must rely on the user having ensured the type is
+  //       correct
 }
 
 void FCITransform::calcParallelSlices(Field3D& f) {
@@ -327,8 +399,8 @@ void FCITransform::calcParallelSlices(Field3D& f) {
 
   // Interpolate f onto yup and ydown fields
   for (const auto& map : field_line_maps) {
-    f.ynext(map.offset) = map.interpolate(f);
-    f.ynext(map.offset).setRegion(fmt::format("RGN_YPAR_{:+d}", map.offset));
+    f.ynext(map.offset()) = map.interpolate(f);
+    f.ynext(map.offset()).setRegion(fmt::format("RGN_YPAR_{:+d}", map.offset()));
   }
 }
 
@@ -345,7 +417,7 @@ void FCITransform::integrateParallelSlices(Field3D& f) {
 
   // Integrate f onto yup and ydown fields
   for (const auto& map : field_line_maps) {
-    f.ynext(map.offset) = map.integrate(f);
+    f.ynext(map.offset()) = map.integrate(f);
   }
 }
 
diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx
index 1a02f558e1..65529a4c4e 100644
--- a/src/mesh/parallel/fci.hxx
+++ b/src/mesh/parallel/fci.hxx
@@ -26,6 +26,11 @@
 #ifndef BOUT_FCITRANSFORM_H
 #define BOUT_FCITRANSFORM_H
 
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/region.hxx"
 #include <bout/interpolation_xz.hxx>
 #include <bout/mask.hxx>
 #include <bout/parallel_boundary_region.hxx>
@@ -33,25 +38,26 @@
 #include <bout/unused.hxx>
 
 #include <memory>
+#include <string>
 #include <vector>
 
+class BoundaryRegionPar;
+class FieldPerp;
+class Field2D;
+class Field3D;
+class Options;
+
 /// Field line map - contains the coefficients for interpolation
 class FCIMap {
   /// Interpolation objects
   std::unique_ptr<XZInterpolation> interp;        // Cell centre
   std::unique_ptr<XZInterpolation> interp_corner; // Cell corner at (x+1, z+1)
 
-public:
-  FCIMap() = delete;
-  FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, int offset,
-         const std::shared_ptr<BoundaryRegionPar>& inner_boundary,
-         const std::shared_ptr<BoundaryRegionPar>& outer_boundary, bool zperiodic);
-
   // The mesh this map was created on
-  Mesh& map_mesh;
+  Mesh* map_mesh;
 
   /// Direction of map
-  const int offset;
+  int offset_;
 
   /// region containing all points where the field line has not left the
   /// domain
@@ -59,8 +65,17 @@ public:
   /// If any of the integration area has left the domain
   BoutMask corner_boundary_mask;
 
+public:
+  FCIMap() = delete;
+  FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, int offset,
+         const std::shared_ptr<BoundaryRegionPar>& inner_boundary,
+         const std::shared_ptr<BoundaryRegionPar>& outer_boundary, bool zperiodic);
+
+  /// Direction of map
+  int offset() const { return offset_; }
+
   Field3D interpolate(Field3D& f) const {
-    ASSERT1(&map_mesh == f.getMesh());
+    ASSERT1(map_mesh == f.getMesh());
     return interp->interpolate(f);
   }
 
@@ -72,55 +87,7 @@ class FCITransform : public ParallelTransform {
 public:
   FCITransform() = delete;
   FCITransform(Mesh& mesh, const Coordinates::FieldMetric& dy, bool zperiodic = true,
-               Options* opt = nullptr)
-    : ParallelTransform(mesh, opt), R{&mesh}, Z{&mesh} {
-
-    // check the coordinate system used for the grid data source
-    FCITransform::checkInputGrid();
-
-    // Real-space coordinates of grid cells
-    mesh.get(R, "R", 0.0, false);
-    mesh.get(Z, "Z", 0.0, false);
-
-    auto forward_boundary_xin =
-        std::make_shared<BoundaryRegionPar>("FCI_forward", BNDRY_PAR_FWD_XIN, +1, &mesh);
-    auto backward_boundary_xin = std::make_shared<BoundaryRegionPar>(
-        "FCI_backward", BNDRY_PAR_BKWD_XIN, -1, &mesh);
-    auto forward_boundary_xout =
-        std::make_shared<BoundaryRegionPar>("FCI_forward", BNDRY_PAR_FWD_XOUT, +1, &mesh);
-    auto backward_boundary_xout = std::make_shared<BoundaryRegionPar>(
-        "FCI_backward", BNDRY_PAR_BKWD_XOUT, -1, &mesh);
-
-    // Add the boundary region to the mesh's vector of parallel boundaries
-    mesh.addBoundaryPar(forward_boundary_xin, BoundaryParType::xin_fwd);
-    mesh.addBoundaryPar(backward_boundary_xin, BoundaryParType::xin_bwd);
-    mesh.addBoundaryPar(forward_boundary_xout, BoundaryParType::xout_fwd);
-    mesh.addBoundaryPar(backward_boundary_xout, BoundaryParType::xout_bwd);
-
-    field_line_maps.reserve(mesh.ystart * 2);
-    for (int offset = 1; offset < mesh.ystart + 1; ++offset) {
-      field_line_maps.emplace_back(mesh, dy, options, offset, forward_boundary_xin,
-                                   forward_boundary_xout, zperiodic);
-      field_line_maps.emplace_back(mesh, dy, options, -offset, backward_boundary_xin,
-                                   backward_boundary_xout, zperiodic);
-    }
-    ASSERT0(mesh.ystart == 1);
-    std::shared_ptr<BoundaryRegionPar> bndries[]{
-        forward_boundary_xin, forward_boundary_xout, backward_boundary_xin,
-        backward_boundary_xout};
-    for (auto& bndry : bndries) {
-      for (const auto& bndry2 : bndries) {
-        if (bndry->dir == bndry2->dir) {
-          continue;
-        }
-        for (bndry->first(); !bndry->isDone(); bndry->next()) {
-          if (bndry2->contains(*bndry)) {
-            bndry->setValid(0);
-          }
-        }
-      }
-    }
-  }
+               Options* opt = nullptr);
 
   void calcParallelSlices(Field3D& f) override;
 

From da0d4c4a8df2d98f924c87d7f2ac4af290bfb284 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 8 Oct 2025 10:11:22 +0100
Subject: [PATCH 0364/1827] tests: Fix for 3D metric in FCI test

The Div_par operators use parallel slices of B -- with 2D metrics,
these are just the field itself, in 3D we need the actual
slices. While `Coordinates::geometry` does communicate the fields, it
puts off calculating the parallel slices because that needs the fully
constructed `Coordinates`.

Upcoming changes should fix this and remove the need to explicitly
communicate `Coordinates` members.
---
 src/mesh/coordinates.cxx          | 2 +-
 tests/MMS/spatial/fci/fci_mms.cxx | 9 ++++++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 3dfee6a553..12e465ffb6 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1577,7 +1577,7 @@ Field3D Coordinates::Div_par(const Field3D& f, CELL_LOC outloc,
 
   // Need Bxy at location of f, which might be different from location of this
   // Coordinates object
-  auto Bxy_floc = f.getCoordinates()->Bxy;
+  const auto& Bxy_floc = f.getCoordinates()->Bxy;
 
   if (!f.hasParallelSlices()) {
     // No yup/ydown fields. The Grad_par operator will
diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index a0b70e9da6..b30ec05e9a 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -1,4 +1,5 @@
 #include "bout/bout.hxx"
+#include "bout/build_config.hxx"
 #include "bout/difops.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
@@ -37,7 +38,13 @@ int main(int argc, char** argv) {
   Field3D input{FieldFactory::get()->create3D("input_field", Options::getRoot(), mesh)};
   Field3D K{FieldFactory::get()->create3D("K", Options::getRoot(), mesh)};
 
-  // Communicate to calculate parallel transform
+  // Communicate to calculate parallel transform.
+  if constexpr (bout::build::use_metric_3d) {
+    // Div_par operators require B parallel slices:
+    // Coordinates::geometry doesn't ensure this (yet)
+    auto& Bxy = mesh->getCoordinates()->Bxy;
+    mesh->communicate(Bxy);
+  }
   mesh->communicate(input, K);
 
   Options dump;

From 2f83692721c64579910175148517b63b9cff7677 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 8 Oct 2025 11:18:59 +0100
Subject: [PATCH 0365/1827] tests: Add test for FCI `Laplace_par`

---
 tests/MMS/spatial/fci/data/BOUT.inp | 1 +
 tests/MMS/spatial/fci/fci_mms.cxx   | 1 +
 tests/MMS/spatial/fci/mms.py        | 7 +++++++
 tests/MMS/spatial/fci/runtest       | 2 +-
 4 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index e31d84cb35..93e2101473 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -4,6 +4,7 @@ grad2_par2_solution = (6.28318530717959*(0.01*x + 0.045)*(6.28318530717959*(0.01
 div_par_solution = (0.01*x + 0.045)*(-12.5663706143592*cos(y - 2*z) - 6.28318530717959*cos(y - z) + 0.628318530717959*(cos(y - 2*z) + cos(y - z))/(0.01*x + 0.045))/sqrt((0.01*x + 0.045)^2 + 1.0)
 div_par_K_grad_par_solution = (0.01*x + 0.045)*(6.28318530717959*sin(y - z) - 0.628318530717959*sin(y - z)/(0.01*x + 0.045))*(6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/((0.01*x + 0.045)^2 + 1.0) + (6.28318530717959*(0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0))*cos(y - z)/sqrt((0.01*x + 0.045)^2 + 1.0)
 K = cos(y - z)
+laplace_par_solution = (0.01*x + 0.045)*(6.28318530717959*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/((0.01*x + 0.045)*sqrt((0.01*x + 0.045)^2 + 1.0)))/sqrt((0.01*x + 0.045)^2 + 1.0)
 
 [mesh]
 symmetricglobalx = true
diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index b30ec05e9a..b9d335a3c4 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -55,6 +55,7 @@ int main(int argc, char** argv) {
   fci_op_test("grad2_par2", dump, input, Grad2_par2(input));
   fci_op_test("div_par", dump, input, Div_par(input));
   fci_op_test("div_par_K_grad_par", dump, input, Div_par_K_Grad_par(K, input));
+  fci_op_test("laplace_par", dump, input, Laplace_par(input));
 
   bout::writeDefaultOutputFile(dump);
 
diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index 79ec661507..178c158572 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -44,6 +44,10 @@ def FCI_div_par_K_grad_par(f: Expr, K: Expr) -> Expr:
     return (K * FCI_grad2_par2(f)) + (FCI_div_par(K) * FCI_grad_par(f))
 
 
+def FCI_Laplace_par(f: Expr) -> Expr:
+    return FCI_div_par(FCI_grad_par(f))
+
+
 ############################################
 # Equations solved
 
@@ -52,6 +56,7 @@ def FCI_div_par_K_grad_par(f: Expr, K: Expr) -> Expr:
 grad2_par2_solution = exprToStr(FCI_grad2_par2(f))
 div_par_solution = exprToStr(FCI_div_par(f))
 div_par_K_grad_par_solution = exprToStr(FCI_div_par_K_grad_par(f, K))
+Laplace_par_solution = exprToStr(FCI_Laplace_par(f))
 
 print(f"input_field = {input_field}")
 print(f"K = {K}")
@@ -59,6 +64,7 @@ def FCI_div_par_K_grad_par(f: Expr, K: Expr) -> Expr:
 print(f"grad2_par2_solution = {grad2_par2_solution}")
 print(f"div_par_solution = {div_par_solution}")
 print(f"div_par_K_grad_par_solution = {div_par_K_grad_par_solution}")
+print(f"laplace_par_solution = {Laplace_par_solution}")
 
 options = BoutOptionsFile("data/BOUT.inp")
 options["input_field"] = input_field
@@ -67,4 +73,5 @@ def FCI_div_par_K_grad_par(f: Expr, K: Expr) -> Expr:
 options["grad2_par2_solution"] = grad2_par2_solution
 options["div_par_solution"] = div_par_solution
 options["div_par_K_grad_par_solution"] = div_par_K_grad_par_solution
+options["laplace_par_solution"] = Laplace_par_solution
 options.write("data/BOUT.inp", overwrite=True)
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 5a19877a45..612486bdf4 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -24,7 +24,7 @@ from scipy.interpolate import RectBivariateSpline as RBS
 DIRECTORY = "data"
 NPROC = 2
 MTHREAD = 2
-OPERATORS = ("grad_par", "grad2_par2", "div_par", "div_par_K_grad_par")
+OPERATORS = ("grad_par", "grad2_par2", "div_par", "div_par_K_grad_par", "laplace_par")
 NX = 3
 # Resolution in y and z
 NLIST = [8, 16, 32, 64, 128]

From 0cde140be713e61b3ab0636aaa3fb5fccc1218e7 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 8 Oct 2025 11:22:57 +0100
Subject: [PATCH 0366/1827] Reduce duplication in FCI mms script

---
 tests/MMS/spatial/fci/mms.py | 36 ++++++++++++++----------------------
 1 file changed, 14 insertions(+), 22 deletions(-)

diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index 178c158572..b28e337ac0 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -51,27 +51,19 @@ def FCI_Laplace_par(f: Expr) -> Expr:
 ############################################
 # Equations solved
 
-input_field = exprToStr(f)
-grad_par_solution = exprToStr(FCI_grad_par(f))
-grad2_par2_solution = exprToStr(FCI_grad2_par2(f))
-div_par_solution = exprToStr(FCI_div_par(f))
-div_par_K_grad_par_solution = exprToStr(FCI_div_par_K_grad_par(f, K))
-Laplace_par_solution = exprToStr(FCI_Laplace_par(f))
-
-print(f"input_field = {input_field}")
-print(f"K = {K}")
-print(f"grad_par_solution = {grad_par_solution}")
-print(f"grad2_par2_solution = {grad2_par2_solution}")
-print(f"div_par_solution = {div_par_solution}")
-print(f"div_par_K_grad_par_solution = {div_par_K_grad_par_solution}")
-print(f"laplace_par_solution = {Laplace_par_solution}")
-
 options = BoutOptionsFile("data/BOUT.inp")
-options["input_field"] = input_field
-options["K"] = K
-options["grad_par_solution"] = grad_par_solution
-options["grad2_par2_solution"] = grad2_par2_solution
-options["div_par_solution"] = div_par_solution
-options["div_par_K_grad_par_solution"] = div_par_K_grad_par_solution
-options["laplace_par_solution"] = Laplace_par_solution
+
+for name, expr in (
+    ("input_field", f),
+    ("K", K),
+    ("grad_par_solution", FCI_grad_par(f)),
+    ("grad2_par2_solution", FCI_grad2_par2(f)),
+    ("div_par_solution", FCI_div_par(f)),
+    ("div_par_K_grad_par_solution", FCI_div_par_K_grad_par(f, K)),
+    ("laplace_par_solution", FCI_Laplace_par(f)),
+):
+    expr_str = exprToStr(expr)
+    print(f"{name} = {expr_str}")
+    options[name] = expr_str
+
 options.write("data/BOUT.inp", overwrite=True)

From 37dc27341019c5bf962269e4f015a777014535c4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 8 Oct 2025 11:25:56 +0100
Subject: [PATCH 0367/1827] Remove circular include

---
 include/bout/difops.hxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 71053d454a..c2fdac195d 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -40,7 +40,9 @@
 #include "bout/field3d.hxx"
 
 #include "bout/bout_types.hxx"
-#include "bout/solver.hxx"
+#include "bout/coordinates.hxx"
+
+class Solver;
 
 /*!
  * Parallel derivative (central differencing) in Y

From 9ac46e845b65adb16da3f6e2240bc6cb177636c4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 8 Oct 2025 16:48:20 +0100
Subject: [PATCH 0368/1827] tests: Add cases for FCI interpolation methods

---
 tests/MMS/spatial/fci/runtest | 44 +++++++++++++++--------------------
 1 file changed, 19 insertions(+), 25 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 612486bdf4..6ac0b0bca8 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -99,7 +99,7 @@ def run_fci_operators(
     )
 
     # Command to run
-    args = f"MZ={nz} MYG={nslice} mesh:paralleltransform:y_periodic={yperiodic} mesh:ddy:first={name}"
+    args = f"MZ={nz} MYG={nslice} mesh:paralleltransform:y_periodic={yperiodic} {name}"
     cmd = f"./fci_mms {args}"
     print(f"Running command: {cmd}", end="")
 
@@ -138,18 +138,18 @@ def transpose(
     return result
 
 
-def check_fci_operators(case: dict) -> bool:
+def check_fci_operators(name: str, case: dict) -> bool:
     failures = []
 
     nslice = case["nslice"]
     yperiodic = case["yperiodic"]
-    name = case["name"]
     order = case["order"]
+    args = case["args"]
 
     all_errors = []
 
     for n in NLIST:
-        errors = run_fci_operators(nslice, n, yperiodic, name)
+        errors = run_fci_operators(nslice, n, yperiodic, args)
         all_errors.append(errors)
 
         for operator in OPERATORS:
@@ -170,7 +170,7 @@ def check_fci_operators(case: dict) -> bool:
     return final_errors, failures
 
 
-def make_plots(cases):
+def make_plots(cases: dict[str, dict]):
     try:
         import matplotlib.pyplot as plt
     except ImportError:
@@ -199,23 +199,6 @@ def make_plots(cases):
     plt.close()
 
 
-def make_case(nslice: int, yperiodic: bool) -> dict[str, Any]:
-    """
-    nslice:
-        Number of parallel slices (in each direction)
-    yperiodic:
-        Run with periodic Y
-    """
-    order = nslice * 2
-    return {
-        "nslice": nslice,
-        # Which central difference scheme to use and its expected order
-        "order": order,
-        "name": f"C{order}",
-        "yperiodic": yperiodic,
-    }
-
-
 if __name__ == "__main__":
     build_and_log("FCI MMS test")
 
@@ -240,11 +223,22 @@ if __name__ == "__main__":
     success = True
     failures = []
     cases = {
-        "nslice=1": make_case(nslice=1, yperiodic=True),
+        "nslice=1 hermitespline": {
+            "nslice": 1,
+            "order": 2,
+            "yperiodic": True,
+            "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=hermitespline",
+        },
+        "nslice=1 lagrange4pt": {
+            "nslice": 1,
+            "order": 2,
+            "yperiodic": True,
+            "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=lagrange4pt",
+        },
     }
 
-    for case in cases.values():
-        error2, failures_ = check_fci_operators(case)
+    for name, case in cases.items():
+        error2, failures_ = check_fci_operators(name, case)
         case.update(error2)
         failures.extend(failures_)
         success &= len(failures) == 0

From 5974a6e89d457a8e6cbcdad177837aeda924ad50 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 9 Oct 2025 17:23:45 +0100
Subject: [PATCH 0369/1827] tests: Increase nx for hermitespline interpolation
 boundary problem

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 14 +++++++++++++-
 tests/MMS/spatial/fci/runtest                |  4 +++-
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 5020a5b9a3..27a4f1d614 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -171,7 +171,19 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     BoutReal t_x = delta_x(x, y, z) - static_cast<BoutReal>(i_corn);
     BoutReal t_z = delta_z(x, y, z) - static_cast<BoutReal>(k_corner(x, y, z));
 
-    // NOTE: A (small) hack to avoid one-sided differences
+    // NOTE: A (small) hack to avoid one-sided differences. We need at
+    // least 2 interior points due to an awkwardness with the
+    // boundaries. The splines need derivatives in x, but we don't
+    // know the value in the boundaries, so _any_ interpolation in the
+    // last interior cell can't be done. Instead, we fudge the
+    // interpolation in the last cell to be at the extreme right-hand
+    // edge of the previous cell (that is, exactly on the last
+    // interior point). However, this doesn't work with only one
+    // interior point, because we have to do something similar to the
+    // _first_ cell, and these two fudges cancel out and we end up
+    // indexing into the boundary anyway.
+    // TODO(peter): Can we remove this if we apply (dirichlet?) BCs to
+    // the X derivatives? Note that we need at least _2_
     if (i_corn >= xend) {
       i_corn = xend - 1;
       t_x = 1.0;
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 6ac0b0bca8..5393437ff7 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -25,7 +25,9 @@ DIRECTORY = "data"
 NPROC = 2
 MTHREAD = 2
 OPERATORS = ("grad_par", "grad2_par2", "div_par", "div_par_K_grad_par", "laplace_par")
-NX = 3
+# Note that we need at least _2_ interior points for hermite spline
+# interpolation due to an awkwardness with the boundaries
+NX = 4
 # Resolution in y and z
 NLIST = [8, 16, 32, 64, 128]
 dx = 1.0 / array(NLIST)

From 6ab945e6783b754acf6e84d4fbefcfcd16d94c6f Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 9 Oct 2025 17:24:28 +0100
Subject: [PATCH 0370/1827] tests: Add monotonichermitespline, decrease
 resolution scan

---
 tests/MMS/spatial/fci/runtest | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 5393437ff7..e3d10d989b 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -11,7 +11,6 @@ import json
 import pathlib
 import sys
 from time import time
-from typing import Any
 
 import boutconfig as conf
 import zoidberg as zb
@@ -29,7 +28,7 @@ OPERATORS = ("grad_par", "grad2_par2", "div_par", "div_par_K_grad_par", "laplace
 # interpolation due to an awkwardness with the boundaries
 NX = 4
 # Resolution in y and z
-NLIST = [8, 16, 32, 64, 128]
+NLIST = [8, 16, 32, 64]
 dx = 1.0 / array(NLIST)
 
 
@@ -237,6 +236,12 @@ if __name__ == "__main__":
             "yperiodic": True,
             "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=lagrange4pt",
         },
+        "nslice=1 monotonichermitespline": {
+            "nslice": 1,
+            "order": 2,
+            "yperiodic": True,
+            "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=monotonichermitespline",
+        },
     }
 
     for name, case in cases.items():

From 16c3718187378e28c37c5c8304e2d9a5e326d794 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 3 Nov 2025 15:52:25 +0000
Subject: [PATCH 0371/1827] tests: Small refactor of FCI tests

---
 .../test-fci-boundary/get_par_bndry.cxx       |  22 ++--
 tests/integrated/test-fci-boundary/runtest    |  36 ++----
 tests/integrated/test-fci-mpi/fci_mpi.cxx     |  59 +++++-----
 tests/integrated/test-fci-mpi/runtest         | 107 +++++++++++-------
 4 files changed, 116 insertions(+), 108 deletions(-)

diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index ac0f5de2a6..ba282d8988 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -1,5 +1,5 @@
 #include "bout/bout.hxx"
-#include "bout/derivs.hxx"
+#include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
 #include "bout/parallel_boundary_region.hxx"
 
@@ -8,24 +8,24 @@ int main(int argc, char** argv) {
 
   using bout::globals::mesh;
 
-  std::vector<Field3D> fields;
-  fields.resize(static_cast<int>(BoundaryParType::SIZE));
+  std::vector<Field3D> fields (static_cast<int>(BoundaryParType::SIZE), Field3D{0.0});
+
   Options dump;
   for (int i = 0; i < fields.size(); i++) {
-    fields[i] = Field3D{0.0};
+    fields[i].allocate();
+    const auto boundary = static_cast<BoundaryParType>(i);
+    const auto boundary_name = toString(boundary);
     mesh->communicate(fields[i]);
-    for (const auto& bndry_par :
-         mesh->getBoundariesPar(static_cast<BoundaryParType>(i))) {
-      output.write("{:s} region\n", toString(static_cast<BoundaryParType>(i)));
+    for (const auto& bndry_par : mesh->getBoundariesPar(boundary)) {
+      output.write("{:s} region\n", boundary_name);
       for (bndry_par->first(); !bndry_par->isDone(); bndry_par->next()) {
         fields[i][bndry_par->ind()] += 1;
-        output.write("{:s} increment\n", toString(static_cast<BoundaryParType>(i)));
+        output.write("{:s} increment\n", boundary_name);
       }
     }
-    output.write("{:s} done\n", toString(static_cast<BoundaryParType>(i)));
+    output.write("{:s} done\n", boundary_name);
 
-    dump[fmt::format("field_{:s}", toString(static_cast<BoundaryParType>(i)))] =
-        fields[i];
+    dump[fmt::format("field_{:s}", boundary_name)] = fields[i];
   }
 
   bout::writeDefaultOutputFile(dump);
diff --git a/tests/integrated/test-fci-boundary/runtest b/tests/integrated/test-fci-boundary/runtest
index 1b1460da53..e749055185 100755
--- a/tests/integrated/test-fci-boundary/runtest
+++ b/tests/integrated/test-fci-boundary/runtest
@@ -1,29 +1,15 @@
 #!/usr/bin/env python3
 #
 # Python script to run and analyse MMS test
-#
 
-# Cores: 2
-# only working with cmake
-# requires: False
 from boututils.run_wrapper import launch_safe
 from boututils.datafile import DataFile
-from boutdata.collect import collect as _collect
+from boutdata.collect import collect
 
 import numpy as np
 
 
-def collect(var):
-    return _collect(
-        var,
-        info=False,
-        path=directory,
-        xguards=False,
-        yguards=False,
-    )
-
-
-nprocs = [1]  # , 2, 4]
+nprocs = [1]
 mthread = 2
 
 directory = "data"
@@ -43,11 +29,6 @@ regions = {
 }
 regions = {k: v.astype(int) for k, v in regions.items()}
 
-# for x in "xout", "xin":
-#     regions[x] = np.logical_or(regions[f"{x}_fwd"], regions[f"{x}_bwd"])
-# for x in "fwd", "bwd":
-#     regions[x] = np.logical_or(regions[f"xin_{x}"], regions[f"xout_{x}"])
-# regions["all"] = np.logical_or(regions["xin"], regions["xout"])
 for x in "xout", "xin":
     regions[x] = regions[f"{x}_fwd"] + regions[f"{x}_bwd"]
 for x in "fwd", "bwd":
@@ -56,15 +37,18 @@ regions["all"] = regions["xin"] + regions["xout"]
 
 for nproc in nprocs:
     cmd = "./get_par_bndry"
-
-    # Launch using MPI
     _, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
 
     for k, v in regions.items():
-        # Collect data
-        data = collect(f"field_{k}")
+        data = collect(
+            f"field_{k}",
+            info=False,
+            path=directory,
+            xguards=False,
+            yguards=False,
+        )
         assert np.allclose(data, v), (
-            k + " does not match",
+            f"{k} does not match",
             np.sum(data),
             np.sum(v),
             np.max(data),
diff --git a/tests/integrated/test-fci-mpi/fci_mpi.cxx b/tests/integrated/test-fci-mpi/fci_mpi.cxx
index 94520dd4a6..cc4fba8ffe 100644
--- a/tests/integrated/test-fci-mpi/fci_mpi.cxx
+++ b/tests/integrated/test-fci-mpi/fci_mpi.cxx
@@ -1,38 +1,37 @@
+#include "fmt/format.h"
 #include "bout/bout.hxx"
-#include "bout/derivs.hxx"
 #include "bout/field_factory.hxx"
 
+namespace {
+auto fci_mpi_test(int num, Options& dump) {
+  using bout::globals::mesh;
+  Field3D input{FieldFactory::get()->create3D(fmt::format("input_{:d}:function", num),
+                                              Options::getRoot(), mesh)};
+  mesh->communicate(input);
+
+  input.applyParallelBoundary("parallel_neumann_o2");
+
+  for (int slice = -mesh->ystart; slice <= mesh->ystart; ++slice) {
+    if (slice == 0) {
+      continue;
+    }
+    Field3D tmp{0.};
+    BOUT_FOR(i, tmp.getRegion("RGN_NOBNDRY")) {
+      tmp[i] = input.ynext(slice)[i.yp(slice)];
+    }
+    dump[fmt::format("output_{:d}_{:+d}", num, slice)] = tmp;
+  }
+}
+} // namespace
+
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
-  {
-    using bout::globals::mesh;
-    Options* options = Options::getRoot();
-    int i = 0;
-    const std::string default_str{"not_set"};
-    Options dump;
-    while (true) {
-      std::string temp_str;
-      options->get(fmt::format("input_{:d}:function", i), temp_str, default_str);
-      if (temp_str == default_str) {
-        break;
-      }
-      Field3D input{FieldFactory::get()->create3D(fmt::format("input_{:d}:function", i),
-                                                  Options::getRoot(), mesh)};
-      // options->get(fmt::format("input_{:d}:boundary_perp", i), temp_str, s"free_o3");
-      mesh->communicate(input);
-      input.applyParallelBoundary("parallel_neumann_o2");
-      for (int slice = -mesh->ystart; slice <= mesh->ystart; ++slice) {
-        if (slice != 0) {
-          Field3D tmp{0.};
-          BOUT_FOR(i, tmp.getRegion("RGN_NOBNDRY")) {
-            tmp[i] = input.ynext(slice)[i.yp(slice)];
-          }
-          dump[fmt::format("output_{:d}_{:+d}", i, slice)] = tmp;
-        }
-      }
-      ++i;
-    }
-    bout::writeDefaultOutputFile(dump);
+  Options dump;
+
+  for (auto num : {0, 1, 2, 3}) {
+    fci_mpi_test(num, dump);
   }
+
+  bout::writeDefaultOutputFile(dump);
   BoutFinalise();
 }
diff --git a/tests/integrated/test-fci-mpi/runtest b/tests/integrated/test-fci-mpi/runtest
index 6676f8f7a5..828d8d4a50 100755
--- a/tests/integrated/test-fci-mpi/runtest
+++ b/tests/integrated/test-fci-mpi/runtest
@@ -1,57 +1,82 @@
 #!/usr/bin/env python3
 #
 # Python script to run and analyse MMS test
-#
-
-# Cores: 8
-# requires: metric_3d
 
-from boututils.run_wrapper import build_and_log, launch_safe, shell_safe
+from boututils.run_wrapper import build_and_log, launch_safe
 from boutdata.collect import collect
-import boutconfig as conf
 import itertools
+import sys
 
-import numpy as np
+import numpy.testing as npt
 
 # Resolution in x and y
-nlist = [1, 2, 4]
+NLIST = [1, 2, 4]
+MAXCORES = 8
+NSLICES = [1]
 
-maxcores = 8
+build_and_log("FCI MMS test")
 
-nslices = [1]
+COLLECT_KW = dict(info=False, xguards=False, yguards=False, path="data")
 
-success = True
 
-build_and_log("FCI MMS test")
+def run_case(nxpe: int, nype: int, mthread: int):
+    cmd = f"./fci_mpi NXPE={nxpe} NYPE={nype}"
+    print(f"Running command: {cmd}")
+
+    _, out = launch_safe(cmd, nproc=nxpe * nype, mthread=mthread, pipe=True)
+
+    # Save output to log file
+    with open(f"run.log.{nxpe}.{nype}.{nslice}.log", "w") as f:
+        f.write(out)
+
+
+def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
+    run_case(nxpe, nype, mthread)
+
+    failures = []
+
+    for name, val in ref.items():
+        try:
+            npt.assert_allclose(val, collect(name, **COLLECT_KW))
+        except AssertionError as e:
+            failures.append((nxpe, nype, name, e))
 
-for nslice in nslices:
-    for NXPE, NYPE in itertools.product(nlist, nlist):
-        if NXPE * NYPE > maxcores:
+    return failures
+
+
+failures = []
+
+for nslice in NSLICES:
+    # reference data!
+    run_case(1, 1, MAXCORES)
+
+    ref = {}
+    for i in range(4):
+        for yp in range(1, nslice + 1):
+            for y in [-yp, yp]:
+                name = f"output_{i}_{y:+d}"
+                ref[name] = collect(name, **COLLECT_KW)
+
+    for nxpe, nype in itertools.product(NLIST, NLIST):
+        if (nxpe, nype) == (1, 1):
+            # reference case, done above
             continue
 
-        args = f"NXPE={NXPE} NYPE={NYPE}"
-        # Command to run
-        cmd = f"./fci_mpi {args}"
-
-        print(f"Running command: {cmd}")
-
-        mthread = maxcores // (NXPE * NYPE)
-        # Launch using MPI
-        _, out = launch_safe(cmd, nproc=NXPE * NYPE, mthread=mthread, pipe=True)
-
-        # Save output to log file
-        with open(f"run.log.{NXPE}.{NYPE}.{nslice}.log", "w") as f:
-            f.write(out)
-
-        collect_kw = dict(info=False, xguards=False, yguards=False, path="data")
-        if NXPE == NYPE == 1:
-            # reference data!
-            ref = {}
-            for i in range(4):
-                for yp in range(1, nslice + 1):
-                    for y in [-yp, yp]:
-                        name = f"output_{i}_{y:+d}"
-                        ref[name] = collect(name, **collect_kw)
-        else:
-            for name, val in ref.items():
-                assert np.allclose(val, collect(name, **collect_kw))
+        if nxpe * nype > MAXCORES:
+            continue
+
+        mthread = MAXCORES // (nxpe * nype)
+        failures_ = test_case(nxpe, nype, mthread, ref)
+        failures.extend(failures_)
+
+
+success = len(failures) == 0
+if success:
+    print("\nAll tests passed")
+else:
+    print("\nSome tests failed:")
+    for (nxpe, nype, name, error) in failures:
+        print("----------")
+        print(f"case {nxpe=} {nype=} {name=}\n{error}")
+
+sys.exit(0 if success else 1)

From 3d3ff654b60308e249ae8410a849bfec728f26f1 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Mon, 3 Nov 2025 17:05:43 +0000
Subject: [PATCH 0372/1827] Apply black changes

---
 tests/integrated/test-fci-mpi/runtest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-fci-mpi/runtest b/tests/integrated/test-fci-mpi/runtest
index 828d8d4a50..c18ab0391d 100755
--- a/tests/integrated/test-fci-mpi/runtest
+++ b/tests/integrated/test-fci-mpi/runtest
@@ -75,7 +75,7 @@ if success:
     print("\nAll tests passed")
 else:
     print("\nSome tests failed:")
-    for (nxpe, nype, name, error) in failures:
+    for nxpe, nype, name, error in failures:
         print("----------")
         print(f"case {nxpe=} {nype=} {name=}\n{error}")
 

From 79f9d0fe70c00bc578404351e8379f1fa79a3dc0 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Tue, 4 Nov 2025 11:58:36 +0000
Subject: [PATCH 0373/1827] Apply clang-format changes

---
 src/mesh/parallel/fci.cxx                            | 4 ++--
 tests/integrated/test-fci-boundary/get_par_bndry.cxx | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index e44a74966e..7c7ade1c8d 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -180,8 +180,8 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
   const int ncz = map_mesh->LocalNz;
 
   BoutMask to_remove(map_mesh);
-  const int xend =
-      map_mesh.xstart + (map_mesh.xend - map_mesh.xstart + 1) * map_mesh.getNXPE() - 1;
+  const int xend = map_mesh->xstart
+                   + ((map_mesh->xend - map_mesh->xstart + 1) * map_mesh->getNXPE()) - 1;
   // Serial loop because call to BoundaryRegionPar::addPoint
   // (probably?) can't be done in parallel
   BOUT_FOR_SERIAL(i, xt_prime.getRegion("RGN_NOBNDRY")) {
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index ba282d8988..8183d989d1 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -8,7 +8,7 @@ int main(int argc, char** argv) {
 
   using bout::globals::mesh;
 
-  std::vector<Field3D> fields (static_cast<int>(BoundaryParType::SIZE), Field3D{0.0});
+  std::vector<Field3D> fields(static_cast<int>(BoundaryParType::SIZE), Field3D{0.0});
 
   Options dump;
   for (int i = 0; i < fields.size(); i++) {

From cee3e445cb7da3d7ce24cbae32cd5ccf53a9509c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 4 Nov 2025 16:13:29 +0000
Subject: [PATCH 0374/1827] Apply clang-tidy fixes to FCI tests

---
 tests/MMS/spatial/fci/fci_mms.cxx                   | 13 ++++++++++---
 .../integrated/test-fci-boundary/get_par_bndry.cxx  |  8 ++++++++
 tests/integrated/test-fci-mpi/fci_mpi.cxx           |  6 +++++-
 3 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index b9d335a3c4..7967452f3d 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -1,19 +1,26 @@
 #include "bout/bout.hxx"
 #include "bout/build_config.hxx"
 #include "bout/difops.hxx"
+#include "bout/field.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
+#include "bout/globals.hxx"
 #include "bout/options.hxx"
+#include "bout/options_io.hxx"
+#include "bout/utils.hxx"
 
+#include <fmt/format.h>
+
+#include <cmath>
 #include <string>
 
 namespace {
 auto fci_op_test(const std::string& name, Options& dump, const Field3D& input,
                  const Field3D& result) {
   auto* mesh = input.getMesh();
-  Field3D solution{FieldFactory::get()->create3D(fmt::format("{}_solution", name),
-                                                 Options::getRoot(), mesh)};
-  Field3D error{result - solution};
+  const Field3D solution{FieldFactory::get()->create3D(fmt::format("{}_solution", name),
+                                                       Options::getRoot(), mesh)};
+  const Field3D error{result - solution};
 
   dump[fmt::format("{}_l_2", name)] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
   dump[fmt::format("{}_l_inf", name)] = max(abs(error), true, "RGN_NOBNDRY");
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 8183d989d1..8e3cfac2f7 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -1,8 +1,16 @@
 #include "bout/bout.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
+#include "bout/globals.hxx"
+#include "bout/options.hxx"
+#include "bout/options_io.hxx"
+#include "bout/output.hxx"
 #include "bout/parallel_boundary_region.hxx"
 
+#include <fmt/format.h>
+
+#include <vector>
+
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
diff --git a/tests/integrated/test-fci-mpi/fci_mpi.cxx b/tests/integrated/test-fci-mpi/fci_mpi.cxx
index cc4fba8ffe..94e8e878ef 100644
--- a/tests/integrated/test-fci-mpi/fci_mpi.cxx
+++ b/tests/integrated/test-fci-mpi/fci_mpi.cxx
@@ -1,6 +1,11 @@
 #include "fmt/format.h"
 #include "bout/bout.hxx"
+#include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
+#include "bout/globals.hxx"
+#include "bout/options.hxx"
+#include "bout/options_io.hxx"
+#include "bout/region.hxx"
 
 namespace {
 auto fci_mpi_test(int num, Options& dump) {
@@ -8,7 +13,6 @@ auto fci_mpi_test(int num, Options& dump) {
   Field3D input{FieldFactory::get()->create3D(fmt::format("input_{:d}:function", num),
                                               Options::getRoot(), mesh)};
   mesh->communicate(input);
-
   input.applyParallelBoundary("parallel_neumann_o2");
 
   for (int slice = -mesh->ystart; slice <= mesh->ystart; ++slice) {

From 88d8db852528f91dffe9d16e93cc3f107baadebb Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 4 Nov 2025 16:14:55 +0000
Subject: [PATCH 0375/1827] Fix comment formatting

---
 src/mesh/parallel/fci.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 7c7ade1c8d..055e239725 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -381,7 +381,8 @@ void FCITransform::checkInputGrid() {
           + "' used "
             "to generate metric components for FCITransform. Should be 'fci'.");
     }
-  } // else: parallel_transform variable not found in grid input, indicates older input
+  }
+  // else: parallel_transform variable not found in grid input, indicates older input
   //       file or grid from options so must rely on the user having ensured the type is
   //       correct
 }

From 9d9922c522a1fbe377377e9498ea839b9f7ce82d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 6 Nov 2025 14:27:05 +0000
Subject: [PATCH 0376/1827] Apply suggestion from @dschwoerer

Co-authored-by: David Bold <dschwoerer@users.noreply.github.com>
---
 src/mesh/parallel/fci.cxx | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 055e239725..6243bbb67a 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -107,9 +107,10 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
     const auto direction = (offset_ > 0) ? "forward"sv : "backward"sv;
     // We only have a suffix for parallel slices beyond the first
     // This is for backwards compatibility
-    const auto slice_suffix =
-        (std::abs(offset_) > 1) ? fmt::format("_{}", std::abs(offset_)) : "";
-    return fmt::format("{}_{}{}", direction, field, slice_suffix);
+    if (std::abs(offset_) == 1) {
+      return fmt::format("{}_{}", direction, field);
+    }
+    return fmt::format("{}_{}_{}", direction, field, std::abs(offset_));
   };
 
   // If we can't read in any of these fields, things will silently not

From e961e75696aa7fcaf194c6994732725df9bc900c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 6 Nov 2025 17:13:18 +0000
Subject: [PATCH 0377/1827] tests: Fix typo that made tests always pass

---
 tests/MMS/spatial/fci/runtest | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index e3d10d989b..b1321c0c5d 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -55,7 +55,7 @@ def quiet_collect(name: str) -> float:
     )[()]
 
 
-def assert_convergence(error, dx, name, order) -> bool:
+def assert_convergence(error, dx, name, expected) -> bool:
     fit = polyfit(log(dx), log(error), 1)
     order = fit[0]
     print(f"{name} convergence order = {order:f} (fit)", end="")
@@ -64,7 +64,7 @@ def assert_convergence(error, dx, name, order) -> bool:
     print(f", {order:f} (small spacing)", end="")
 
     # Should be close to the expected order
-    success = order > order * 0.95
+    success = order > expected * 0.95
     print(f"\t............ {'PASS' if success else 'FAIL'}")
 
     return success

From 2674a58d4e77fda0db5bc213164b245c2854dc8b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 6 Nov 2025 17:28:58 +0000
Subject: [PATCH 0378/1827] tests: Remove monotonichermitespline FCI case

---
 tests/MMS/spatial/fci/runtest             | 6 ------
 tests/integrated/test-interpolate/runtest | 1 +
 2 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index b1321c0c5d..2bfde26f51 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -236,12 +236,6 @@ if __name__ == "__main__":
             "yperiodic": True,
             "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=lagrange4pt",
         },
-        "nslice=1 monotonichermitespline": {
-            "nslice": 1,
-            "order": 2,
-            "yperiodic": True,
-            "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=monotonichermitespline",
-        },
     }
 
     for name, case in cases.items():
diff --git a/tests/integrated/test-interpolate/runtest b/tests/integrated/test-interpolate/runtest
index f5460aff2a..da10472610 100755
--- a/tests/integrated/test-interpolate/runtest
+++ b/tests/integrated/test-interpolate/runtest
@@ -25,6 +25,7 @@ methods = {
     "hermitespline": 3,
     "lagrange4pt": 3,
     "bilinear": 2,
+    "monotonichermitespline": 2,
 }
 
 

From f00db393cf180eba7a44136ada78483e30f965eb Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Nov 2025 15:23:30 +0000
Subject: [PATCH 0379/1827] Add `rtol`, `atol` to `MonotonicHermiteSpline`

This allows the user to control the clipping, allowing some overshoot

Also restore the FCI MMS test with this interpolator
---
 include/bout/interpolation_xz.hxx             | 40 +++++++++++++++----
 .../monotonic_hermite_spline_xz.cxx           | 13 +++---
 tests/MMS/spatial/fci/runtest                 | 11 +++++
 tests/integrated/test-interpolate/runtest     |  1 -
 4 files changed, 48 insertions(+), 17 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 6c7419f7e4..d12eecc3d3 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -24,6 +24,7 @@
 #ifndef BOUT_INTERP_XZ_H
 #define BOUT_INTERP_XZ_H
 
+#include "bout/bout_types.hxx"
 #include "bout/mask.hxx"
 
 #define USE_NEW_WEIGHTS 1
@@ -166,7 +167,8 @@ protected:
 #endif
 
 public:
-  XZHermiteSpline(Mesh* mesh = nullptr) : XZHermiteSpline(0, mesh) {}
+  XZHermiteSpline(Mesh* mesh = nullptr, [[maybe_unused]] Options* options = nullptr)
+      : XZHermiteSpline(0, mesh) {}
   XZHermiteSpline(int y_offset = 0, Mesh* mesh = nullptr);
   XZHermiteSpline(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr)
       : XZHermiteSpline(y_offset, mesh) {
@@ -210,9 +212,29 @@ public:
 /// but also degrades accuracy near maxima and minima.
 /// Perhaps should only impose near boundaries, since that is where
 /// problems most obviously occur.
+///
+/// You can control how tight the clipping to the range of the neighbouring cell
+/// values through ``rtol`` and ``atol``:
+///
+///     diff = (max_of_neighours - min_of_neighours) * rtol + atol
+///
+/// and the interpolated value is instead clipped to the range
+/// ``[min_of_neighours - diff, max_of_neighours + diff]``
 class XZMonotonicHermiteSpline : public XZHermiteSpline {
+  /// Absolute tolerance for clipping
+  BoutReal atol = 0.0;
+  /// Relative tolerance for clipping
+  BoutReal rtol = 1.0;
+
 public:
-  XZMonotonicHermiteSpline(Mesh* mesh = nullptr) : XZHermiteSpline(0, mesh) {
+  XZMonotonicHermiteSpline(Mesh* mesh = nullptr, Options* options = nullptr)
+      : XZHermiteSpline(0, mesh),
+        atol{(*options)["atol"]
+                 .doc("Absolute tolerance for clipping overshoot")
+                 .withDefault(0.0)},
+        rtol{(*options)["rtol"]
+                 .doc("Relative tolerance for clipping overshoot")
+                 .withDefault(1.0)} {
     if (localmesh->getNXPE() > 1) {
       throw BoutException("Do not support MPI splitting in X");
     }
@@ -248,7 +270,8 @@ class XZLagrange4pt : public XZInterpolation {
   Field3D t_x, t_z;
 
 public:
-  XZLagrange4pt(Mesh* mesh = nullptr) : XZLagrange4pt(0, mesh) {}
+  XZLagrange4pt(Mesh* mesh = nullptr, [[maybe_unused]] Options* options = nullptr)
+      : XZLagrange4pt(0, mesh) {}
   XZLagrange4pt(int y_offset = 0, Mesh* mesh = nullptr);
   XZLagrange4pt(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr)
       : XZLagrange4pt(y_offset, mesh) {
@@ -284,7 +307,8 @@ class XZBilinear : public XZInterpolation {
   Field3D w0, w1, w2, w3;
 
 public:
-  XZBilinear(Mesh* mesh = nullptr) : XZBilinear(0, mesh) {}
+  XZBilinear(Mesh* mesh = nullptr, [[maybe_unused]] Options* options = nullptr)
+      : XZBilinear(0, mesh) {}
   XZBilinear(int y_offset = 0, Mesh* mesh = nullptr);
   XZBilinear(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr)
       : XZBilinear(y_offset, mesh) {
@@ -308,7 +332,7 @@ public:
 };
 
 class XZInterpolationFactory
-    : public Factory<XZInterpolation, XZInterpolationFactory, Mesh*> {
+    : public Factory<XZInterpolation, XZInterpolationFactory, Mesh*, Options*> {
 public:
   static constexpr auto type_name = "XZInterpolation";
   static constexpr auto section_name = "xzinterpolation";
@@ -316,10 +340,10 @@ public:
   static constexpr auto default_type = "hermitespline";
 
   ReturnType create(Options* options = nullptr, Mesh* mesh = nullptr) const {
-    return Factory::create(getType(options), mesh);
+    return Factory::create(getType(options), mesh, options);
   }
-  ReturnType create(const std::string& type, [[maybe_unused]] Options* options) const {
-    return Factory::create(type, nullptr);
+  ReturnType create(const std::string& type, Options* options) const {
+    return Factory::create(type, nullptr, options);
   }
 
   static void ensureRegistered();
diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
index f23bfd499e..f206ed1e0f 100644
--- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
@@ -25,7 +25,7 @@
 #include "bout/interpolation_xz.hxx"
 #include "bout/mesh.hxx"
 
-#include <vector>
+#include <algorithm>
 
 Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
                                               const std::string& region) const {
@@ -80,7 +80,6 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
     // Perhaps should only impose near boundaries, since that is where
     // problems most obviously occur.
     const BoutReal localmax = BOUTMAX(f[ic], f[icxp], f[iczp], f[icxpzp]);
-
     const BoutReal localmin = BOUTMIN(f[ic], f[icxp], f[iczp], f[icxpzp]);
 
     ASSERT2(std::isfinite(localmax) || i.x() < localmesh->xstart
@@ -88,12 +87,10 @@ Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
     ASSERT2(std::isfinite(localmin) || i.x() < localmesh->xstart
             || i.x() > localmesh->xend);
 
-    if (result > localmax) {
-      result = localmax;
-    }
-    if (result < localmin) {
-      result = localmin;
-    }
+    const auto diff = ((localmax - localmin) * rtol) + atol;
+
+    result = std::min(result, localmax + diff);
+    result = std::max(result, localmin - diff);
 
     f_interp[iyp] = result;
   }
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 2bfde26f51..34340e53f4 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -236,6 +236,17 @@ if __name__ == "__main__":
             "yperiodic": True,
             "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=lagrange4pt",
         },
+        "nslice=1 monotonichermitespline": {
+            "nslice": 1,
+            "order": 2,
+            "yperiodic": True,
+            "args": (
+                "mesh:ddy:first=C2 "
+                "mesh:paralleltransform:xzinterpolation:type=monotonichermitespline "
+                "mesh:paralleltransform:xzinterpolation:rtol=1e-3 "
+                "mesh:paralleltransform:xzinterpolation:atol=5e-3"
+            ),
+        },
     }
 
     for name, case in cases.items():
diff --git a/tests/integrated/test-interpolate/runtest b/tests/integrated/test-interpolate/runtest
index da10472610..f5460aff2a 100755
--- a/tests/integrated/test-interpolate/runtest
+++ b/tests/integrated/test-interpolate/runtest
@@ -25,7 +25,6 @@ methods = {
     "hermitespline": 3,
     "lagrange4pt": 3,
     "bilinear": 2,
-    "monotonichermitespline": 2,
 }
 
 

From 0efe4e3d68486f8a7282ce3d6d695876867ca3c9 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 3 Dec 2025 14:34:36 +0000
Subject: [PATCH 0380/1827] Add missing header

---
 include/bout/interpolation_xz.hxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index d12eecc3d3..4dd24259fd 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -24,8 +24,9 @@
 #ifndef BOUT_INTERP_XZ_H
 #define BOUT_INTERP_XZ_H
 
-#include "bout/bout_types.hxx"
-#include "bout/mask.hxx"
+#include <bout/bout_types.hxx>
+#include <bout/generic_factory.hxx>
+#include <bout/mask.hxx>
 
 #define USE_NEW_WEIGHTS 1
 #if BOUT_HAS_PETSC

From af3cbd1e6108aea30fdee462ea64c0521ca0ad12 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 4 Dec 2025 16:28:01 +0000
Subject: [PATCH 0381/1827] Forward arguments to `BoutException` and
 `Output::write`

This enables passing views like `fmt::join` which otherwise fail with:

```
error: static assertion failed: passing views as lvalues is disallowed
```
---
 include/bout/boutexception.hxx        | 15 ++++++----
 include/bout/output.hxx               | 43 ++++++++++++++-------------
 tests/unit/sys/test_boutexception.cxx | 12 +++++++-
 tests/unit/sys/test_output.cxx        | 11 +++++++
 4 files changed, 54 insertions(+), 27 deletions(-)

diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx
index 238c88654c..9c47eed86c 100644
--- a/include/bout/boutexception.hxx
+++ b/include/bout/boutexception.hxx
@@ -19,8 +19,9 @@ public:
   BoutException(std::string msg);
 
   template <class S, class... Args>
-  BoutException(const S& format, const Args&... args)
-      : BoutException(fmt::format(format, args...)) {}
+  BoutException(S&& format, Args&&... args)
+      : BoutException(fmt::format(std::forward<S>(format),
+                                  std::forward<decltype(args)>(args)...)) {}
 
   ~BoutException() override;
 
@@ -46,16 +47,18 @@ class BoutRhsFail : public BoutException {
 public:
   BoutRhsFail(std::string message) : BoutException(std::move(message)) {}
   template <class S, class... Args>
-  BoutRhsFail(const S& format, const Args&... args)
-      : BoutRhsFail(fmt::format(format, args...)) {}
+  BoutRhsFail(S&& format, Args&&... args)
+      : BoutRhsFail(fmt::format(std::forward<S>(format),
+                                std::forward<decltype(args)>(args)...)) {}
 };
 
 class BoutIterationFail : public BoutException {
 public:
   BoutIterationFail(std::string message) : BoutException(std::move(message)) {}
   template <class S, class... Args>
-  BoutIterationFail(const S& format, const Args&... args)
-      : BoutIterationFail(fmt::format(format, args...)) {}
+  BoutIterationFail(S&& format, Args&&... args)
+      : BoutIterationFail(fmt::format(std::forward<S>(format),
+                                      std::forward<decltype(args)>(args)...)) {}
 };
 
 #endif
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index 2862899067..124f170aea 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -42,6 +42,8 @@ class Output;
 
 #include "fmt/core.h"
 
+#include <utility>
+
 using std::endl;
 
 /// Class for text output to stdout and/or log file
@@ -76,7 +78,8 @@ public:
   }
 
   template <class S, class... Args>
-  Output(const S& format, const Args&... args) : Output(fmt::format(format, args...)) {}
+  Output(const S& format, Args&&... args)
+      : Output(fmt::format(format, std::forward<decltype(args)>(args)...)) {}
 
   ~Output() override { close(); }
 
@@ -87,8 +90,8 @@ public:
   int open(const std::string& filename);
 
   template <class S, class... Args>
-  int open(const S& format, const Args&... args) {
-    return open(fmt::format(format, args...));
+  int open(const S& format, Args&&... args) {
+    return open(fmt::format(format, std::forward<decltype(args)>(args)...));
   }
 
   /// Close the log file
@@ -98,15 +101,15 @@ public:
   virtual void write(const std::string& message);
 
   template <class S, class... Args>
-  void write(const S& format, const Args&... args) {
-    write(fmt::format(format, args...));
+  void write(const S& format, Args&&... args) {
+    write(fmt::format(format, std::forward<decltype(args)>(args)...));
   }
   /// Same as write, but only to screen
   virtual void print(const std::string& message);
 
   template <class S, class... Args>
-  void print(const S& format, const Args&... args) {
-    print(fmt::format(format, args...));
+  void print(const S& format, Args&&... args) {
+    print(fmt::format(format, std::forward<decltype(args)>(args)...));
   }
 
   /// Add an output stream. All output will be sent to all streams
@@ -136,14 +139,14 @@ private:
 class DummyOutput : public Output {
 public:
   template <class S, class... Args>
-  void write([[maybe_unused]] const S& format, [[maybe_unused]] const Args&... args){};
+  void write([[maybe_unused]] const S& format, [[maybe_unused]] Args&&... args) {};
   template <class S, class... Args>
-  void print([[maybe_unused]] const S& format, [[maybe_unused]] const Args&... args){};
-  void write([[maybe_unused]] const std::string& message) override{};
-  void print([[maybe_unused]] const std::string& message) override{};
-  void enable() override{};
-  void disable() override{};
-  void enable([[maybe_unused]] bool enable){};
+  void print([[maybe_unused]] const S& format, [[maybe_unused]] Args&&... args) {};
+  void write([[maybe_unused]] const std::string& message) override {};
+  void print([[maybe_unused]] const std::string& message) override {};
+  void enable() override {};
+  void disable() override {};
+  void enable([[maybe_unused]] bool enable) {};
   bool isEnabled() override { return false; }
 };
 
@@ -156,13 +159,13 @@ class ConditionalOutput : public Output {
 public:
   /// @param[in] base    The Output object which will be written to if enabled
   /// @param[in] enabled Should this be enabled by default?
-  ConditionalOutput(Output* base, bool enabled = true) : base(base), enabled(enabled){};
+  ConditionalOutput(Output* base, bool enabled = true) : base(base), enabled(enabled) {};
 
   /// Constuctor taking ConditionalOutput. This allows several layers of conditions
   ///
   /// @param[in] base    A ConditionalOutput which will be written to if enabled
   ///
-  ConditionalOutput(ConditionalOutput* base) : base(base), enabled(base->enabled){};
+  ConditionalOutput(ConditionalOutput* base) : base(base), enabled(base->enabled) {};
 
   /// If enabled, writes a string using fmt formatting
   /// by calling base->write
@@ -170,10 +173,10 @@ public:
   void write(const std::string& message) override;
 
   template <class S, class... Args>
-  void write(const S& format, const Args&... args) {
+  void write(const S& format, Args&&... args) {
     if (enabled) {
       ASSERT1(base != nullptr);
-      base->write(fmt::format(format, args...));
+      base->write(fmt::format(format, std::forward<decltype(args)>(args)...));
     }
   }
 
@@ -182,10 +185,10 @@ public:
   void print(const std::string& message) override;
 
   template <class S, class... Args>
-  void print(const S& format, const Args&... args) {
+  void print(const S& format, Args&&... args) {
     if (enabled) {
       ASSERT1(base != nullptr);
-      base->print(fmt::format(format, args...));
+      base->print(fmt::format(format, std::forward<decltype(args)>(args)...));
     }
   }
 
diff --git a/tests/unit/sys/test_boutexception.cxx b/tests/unit/sys/test_boutexception.cxx
index 39f8ee2145..322c7d6e42 100644
--- a/tests/unit/sys/test_boutexception.cxx
+++ b/tests/unit/sys/test_boutexception.cxx
@@ -4,8 +4,11 @@
 #include "bout/boutexception.hxx"
 #include "gtest/gtest.h"
 
-#include <iostream>
+#include <fmt/ranges.h>
+
 #include <string>
+#include <string_view>
+#include <vector>
 
 TEST(BoutExceptionTest, ThrowCorrect) {
   EXPECT_THROW(throw BoutException("test"), BoutException);
@@ -45,6 +48,13 @@ TEST(BoutExceptionTest, GetBacktrace) {
   }
 }
 
+TEST(BoutExceptionTest, FmtJoin) {
+  const std::vector things = {1, 2, 3, 4};
+  constexpr std::string_view expected = "list: 1, 2, 3, 4";
+  const BoutException exception{"list: {}", fmt::join(things, ", ")};
+  EXPECT_EQ(exception.what(), expected);
+}
+
 TEST(BoutRhsFailTest, ThrowCorrect) {
   EXPECT_THROW(throw BoutRhsFail("RHS Fail test"), BoutRhsFail);
 }
diff --git a/tests/unit/sys/test_output.cxx b/tests/unit/sys/test_output.cxx
index 1338d9ce13..959823ede3 100644
--- a/tests/unit/sys/test_output.cxx
+++ b/tests/unit/sys/test_output.cxx
@@ -4,7 +4,10 @@
 #include "bout/output_bout_types.hxx"
 #include "gtest/gtest.h"
 
+#include <fmt/ranges.h>
+
 #include <string>
+#include <vector>
 
 // stdout redirection code from https://stackoverflow.com/a/4043813/2043465
 class OutputTest : public ::testing::Test {
@@ -385,3 +388,11 @@ TEST_F(OutputTest, FormatIndPerpi) {
 
   EXPECT_EQ(buffer.str(), "(15)");
 }
+
+TEST_F(OutputTest, FmtJoin) {
+  const std::vector things = {1, 2, 3, 4};
+  Output local_output;
+  local_output.write("list: {}", fmt::join(things, ", "));
+
+  EXPECT_EQ(buffer.str(), "list: 1, 2, 3, 4");
+}

From e3f07907e06d555106fbe10d49fb9aa887ae2fc0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 4 Dec 2025 18:08:45 +0000
Subject: [PATCH 0382/1827] Clang-tidy fixes

---
 include/bout/boutexception.hxx |  6 +++--
 include/bout/output.hxx        | 41 ++++++++++++++++++---------------
 src/sys/boutexception.cxx      | 42 +++++++++++++++++++---------------
 src/sys/output.cxx             | 14 ++++++++----
 4 files changed, 59 insertions(+), 44 deletions(-)

diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx
index 9c47eed86c..ffd4a03a6c 100644
--- a/include/bout/boutexception.hxx
+++ b/include/bout/boutexception.hxx
@@ -16,6 +16,10 @@ void BoutParallelThrowRhsFail(int status, const char* message);
 
 class BoutException : public std::exception {
 public:
+  BoutException(const BoutException&) = default;
+  BoutException(BoutException&&) = delete;
+  BoutException& operator=(const BoutException&) = default;
+  BoutException& operator=(BoutException&&) = delete;
   BoutException(std::string msg);
 
   template <class S, class... Args>
@@ -39,8 +43,6 @@ private:
   int trace_size;
   char** messages;
 #endif
-
-  void makeBacktrace();
 };
 
 class BoutRhsFail : public BoutException {
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index 124f170aea..205ca3a874 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -31,13 +31,11 @@ class Output;
 
 #include "bout/multiostream.hxx"
 #include <fstream>
-#include <functional>
 #include <iostream>
 #include <string>
 
 #include "bout/assert.hxx"
-#include "bout/boutexception.hxx"
-#include "bout/sys/gettext.hxx" // for gettext _() macro
+#include "bout/sys/gettext.hxx" // IWYU pragma: keep for gettext _() macro
 #include "bout/unused.hxx"
 
 #include "fmt/core.h"
@@ -63,14 +61,19 @@ using std::endl;
 class Output : private multioutbuf_init<char, std::char_traits<char>>,
                public std::basic_ostream<char, std::char_traits<char>> {
 
-  using _Tr = std::char_traits<char>;
-  using multioutbuf_init = ::multioutbuf_init<char, _Tr>;
+  using Tr = std::char_traits<char>;
+  using multioutbuf_init = ::multioutbuf_init<char, Tr>;
 
 public:
-  Output() : multioutbuf_init(), std::basic_ostream<char, _Tr>(multioutbuf_init::buf()) {
+  Output() : multioutbuf_init(), std::basic_ostream<char, Tr>(multioutbuf_init::buf()) {
     Output::enable();
   }
 
+  Output(const Output&) = delete;
+  Output(Output&&) = delete;
+  Output& operator=(const Output&) = delete;
+  Output& operator=(Output&&) = delete;
+
   /// Specify a log file to open
   Output(const std::string& filename) {
     Output::enable();
@@ -113,12 +116,10 @@ public:
   }
 
   /// Add an output stream. All output will be sent to all streams
-  void add(std::basic_ostream<char, _Tr>& str) { multioutbuf_init::buf()->add(str); }
+  void add(std::basic_ostream<char, Tr>& str) { multioutbuf_init::buf()->add(str); }
 
   /// Remove an output stream
-  void remove(std::basic_ostream<char, _Tr>& str) {
-    multioutbuf_init::buf()->remove(str);
-  }
+  void remove(std::basic_ostream<char, Tr>& str) { multioutbuf_init::buf()->remove(str); }
 
   static Output* getInstance(); ///< Return pointer to instance
 
@@ -129,7 +130,7 @@ protected:
 
 private:
   std::ofstream file; ///< Log file stream
-  bool enabled;       ///< Whether output to stdout is enabled
+  bool enabled{};     ///< Whether output to stdout is enabled
 };
 
 /// Class which behaves like Output, but has no effect.
@@ -219,8 +220,6 @@ private:
   /// The lower-level Output to send output to
   Output* base;
 
-protected:
-  friend class WithQuietOutput;
   /// Does this instance output anything?
   bool enabled;
 };
@@ -279,18 +278,23 @@ ConditionalOutput& operator<<(ConditionalOutput& out, const T* t) {
 ///     // output now enabled
 class WithQuietOutput {
 public:
-  explicit WithQuietOutput(ConditionalOutput& output_in) : output(output_in) {
-    state = output.enabled;
-    output.disable();
+  WithQuietOutput(const WithQuietOutput&) = delete;
+  WithQuietOutput(WithQuietOutput&&) = delete;
+  WithQuietOutput& operator=(const WithQuietOutput&) = delete;
+  WithQuietOutput& operator=(WithQuietOutput&&) = delete;
+  explicit WithQuietOutput(ConditionalOutput& output_in)
+      : output(&output_in), state(output->isEnabled()) {
+    output->disable();
   }
 
-  ~WithQuietOutput() { output.enable(state); }
+  ~WithQuietOutput() { output->enable(state); }
 
 private:
-  ConditionalOutput& output;
+  ConditionalOutput* output;
   bool state;
 };
 
+// NOLINTBEGIN(cppcoreguidelines-avoid-non-const-global-variables)
 /// To allow statements like "output.write(...)" or "output << ..."
 /// Output for debugging
 #ifdef BOUT_USE_OUTPUT_DEBUG
@@ -306,5 +310,6 @@ extern ConditionalOutput output_verbose;  ///< less interesting messages
 
 /// Generic output, given the same level as output_progress
 extern ConditionalOutput output;
+// NOLINTEND(cppcoreguidelines-avoid-non-const-global-variables)
 
 #endif // BOUT_OUTPUT_H
diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index 825fb37e28..e81e395bf8 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -4,16 +4,19 @@
 #include <bout/boutexception.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/utils.hxx>
+
 #include <mpi.h>
 
 #if BOUT_USE_BACKTRACE
 #include <dlfcn.h>
 #include <execinfo.h>
+#include <stdio.h>
 #endif
 
 #include <array>
 #include <cstdlib>
 #include <string>
+#include <utility>
 
 #include <fmt/format.h>
 
@@ -22,18 +25,24 @@ const std::string header{"====== Exception thrown ======\n"};
 }
 
 void BoutParallelThrowRhsFail(int status, const char* message) {
-  int allstatus;
+  int allstatus = 0;
   MPI_Allreduce(&status, &allstatus, 1, MPI_INT, MPI_LOR, BoutComm::get());
 
-  if (allstatus) {
+  if (allstatus != 0) {
     throw BoutRhsFail(message);
   }
 }
 
-BoutException::BoutException(std::string msg) : message(std::move(msg)) {
-  makeBacktrace();
+BoutException::BoutException(std::string msg)
+    : message(std::move(msg))
+#if BOUT_USE_BACKTRACE
+      ,
+      trace_size(backtrace(trace.data(), TRACE_MAX)),
+      messages(backtrace_symbols(trace.data(), trace_size))
+#endif
+{
   if (std::getenv("BOUT_SHOW_BACKTRACE") != nullptr) {
-    message = getBacktrace() + "\n" + message;
+    message = fmt::format("{}\n{}", getBacktrace(), message);
   }
 }
 
@@ -54,7 +63,8 @@ std::string BoutException::getBacktrace() const {
   backtrace_message = "====== Exception path ======\n";
   // skip first stack frame (points here)
   for (int i = trace_size - 1; i > 1; --i) {
-    backtrace_message += fmt::format(FMT_STRING("[bt] #{:d} {:s}\n"), i - 1, messages[i]);
+    backtrace_message = fmt::format(FMT_STRING("{}[bt] #{:d} {:s}\n"), backtrace_message,
+                                    i - 1, messages[i]);
     // find first occurence of '(' or ' ' in message[i] and assume
     // everything before that is the file name. (Don't go beyond 0 though
     // (string terminator)
@@ -65,11 +75,11 @@ std::string BoutException::getBacktrace() const {
 
     // If we are compiled as PIE, need to get base pointer of .so and substract
     Dl_info info;
-    void* ptr = trace[i];
-    if (dladdr(trace[i], &info)) {
+    const void* ptr = trace[i];
+    if (dladdr(ptr, &info) != 0) {
       // Additionally, check whether this is the default offset for an executable
       if (info.dli_fbase != reinterpret_cast<void*>(0x400000)) {
-        ptr = reinterpret_cast<void*>(reinterpret_cast<size_t>(trace[i])
+        ptr = reinterpret_cast<void*>(reinterpret_cast<size_t>(ptr)
                                       - reinterpret_cast<size_t>(info.dli_fbase));
       }
     }
@@ -82,14 +92,14 @@ std::string BoutException::getBacktrace() const {
     FILE* file = popen(syscom.c_str(), "r");
     if (file != nullptr) {
       std::array<char, 1024> out{};
-      char* retstr = nullptr;
+      const char* retstr = nullptr;
       std::string buf;
       while ((retstr = fgets(out.data(), out.size() - 1, file)) != nullptr) {
         buf += retstr;
       }
       int const status = pclose(file);
       if (status == 0) {
-        backtrace_message += buf;
+        backtrace_message = fmt::format("{}{}", backtrace_message, buf);
       }
     }
   }
@@ -97,12 +107,6 @@ std::string BoutException::getBacktrace() const {
   backtrace_message = "Stacktrace not enabled.\n";
 #endif
 
-  return backtrace_message + msg_stack.getDump() + "\n" + header + message + "\n";
-}
-
-void BoutException::makeBacktrace() {
-#if BOUT_USE_BACKTRACE
-  trace_size = backtrace(trace.data(), TRACE_MAX);
-  messages = backtrace_symbols(trace.data(), trace_size);
-#endif
+  return fmt::format("{}{}\n{}{}\n", backtrace_message, msg_stack.getDump(), header,
+                     message);
 }
diff --git a/src/sys/output.cxx b/src/sys/output.cxx
index c07cd53474..2c5e06bb7c 100644
--- a/src/sys/output.cxx
+++ b/src/sys/output.cxx
@@ -23,11 +23,13 @@
  *
  **************************************************************************/
 
+#include <bout/assert.hxx>
 #include <bout/output.hxx>
-#include <bout/utils.hxx>
-#include <cstdarg>
-#include <cstdio>
-#include <cstring>
+
+#include <fmt/base.h>
+
+#include <iostream>
+#include <string>
 
 void Output::enable() {
   add(std::cout);
@@ -68,7 +70,7 @@ void Output::close() {
 }
 
 void Output::write(const std::string& message) {
-  multioutbuf_init::buf()->sputn(message.c_str(), message.length());
+  multioutbuf_init::buf()->sputn(message.c_str(), static_cast<long>(message.length()));
 }
 
 void Output::print(const std::string& message) {
@@ -98,6 +100,7 @@ void ConditionalOutput::print(const std::string& message) {
   }
 }
 
+// NOLINTBEGIN(cppcoreguidelines-avoid-non-const-global-variables)
 #ifdef BOUT_USE_OUTPUT_DEBUG
 ConditionalOutput output_debug(Output::getInstance());
 #else
@@ -109,3 +112,4 @@ ConditionalOutput output_progress(Output::getInstance());
 ConditionalOutput output_error(Output::getInstance());
 ConditionalOutput output_verbose(Output::getInstance(), false);
 ConditionalOutput output(Output::getInstance());
+// NOLINTEND(cppcoreguidelines-avoid-non-const-global-variables)

From ab61b9e3c65f974ec5d0ac09ef7c6dd53f15b516 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Thu, 4 Dec 2025 18:12:08 +0000
Subject: [PATCH 0383/1827] Apply clang-format changes

---
 include/bout/output.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index 205ca3a874..823e359753 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -160,13 +160,13 @@ class ConditionalOutput : public Output {
 public:
   /// @param[in] base    The Output object which will be written to if enabled
   /// @param[in] enabled Should this be enabled by default?
-  ConditionalOutput(Output* base, bool enabled = true) : base(base), enabled(enabled) {};
+  ConditionalOutput(Output* base, bool enabled = true) : base(base), enabled(enabled){};
 
   /// Constuctor taking ConditionalOutput. This allows several layers of conditions
   ///
   /// @param[in] base    A ConditionalOutput which will be written to if enabled
   ///
-  ConditionalOutput(ConditionalOutput* base) : base(base), enabled(base->enabled) {};
+  ConditionalOutput(ConditionalOutput* base) : base(base), enabled(base->enabled){};
 
   /// If enabled, writes a string using fmt formatting
   /// by calling base->write

From 4323aa527f03af553a6232a582c636cfb2c6d093 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 5 Dec 2025 10:35:33 -0800
Subject: [PATCH 0384/1827] petsc solver: Catch exceptions from run_rhs

If run_rhs throws an exception then it should be caught, and SNES
notified that an error occurred.
---
 src/solver/impls/petsc/petsc.cxx | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index ed48d87312..98e58d7afa 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -903,8 +903,19 @@ PetscErrorCode PetscSolver::rhs(BoutReal t, Vec udata, Vec dudata, bool linear)
   load_vars(const_cast<BoutReal*>(udata_array));
   VecRestoreArrayRead(udata, &udata_array);
 
-  // Call RHS function
-  run_rhs(t, linear);
+  try {
+    // Call RHS function
+    run_rhs(t, linear);
+  } catch (BoutException& e) {
+    // Simulation might fail, e.g. negative densities
+    // if timestep too large
+    output_warn.write("WARNING: BoutException thrown: {}\n", e.what());
+
+    // Tell SNES that the input was out of domain
+    SNESSetFunctionDomainError(snes);
+    // Note: Returning non-zero error here leaves vectors in locked state
+    return 0;
+  }
 
   // Save derivatives to PETSc
   BoutReal* dudata_array;

From 210ce59f09a782a58cc95d4797b451bc4558bb3a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 5 Dec 2025 12:18:12 -0800
Subject: [PATCH 0385/1827] petsc solver: Add diagnostics compatible with snes
 solver

If solver:diagnose is set then a line will be printed for
each internal (TS) step. The format is the same as the `snes`
solver, so the same post-processing scripts can be used.
---
 src/solver/impls/petsc/petsc.cxx | 33 ++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 98e58d7afa..e7e0296677 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -165,6 +165,39 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
   PetscFunctionBegin;
 
   auto* s = static_cast<PetscSolver*>(ctx);
+
+  if (s->diagnose) {
+    // Print diagnostic information.
+    // Using the same format at the SNES solver
+
+    SNESConvergedReason reason;
+    SNESGetConvergedReason(s->snes, &reason);
+
+    PetscReal timestep;
+    TSGetTimeStep(s->ts, &timestep);
+
+    // SNES failure counter is only reset when TSSolve is called
+    static PetscInt prev_snes_failures = 0;
+    PetscInt snes_failures;
+    TSGetSNESFailures(s->ts, &snes_failures);
+    snes_failures -= prev_snes_failures;
+    prev_snes_failures += snes_failures;
+
+    // Get number of iterations
+    int nl_its;
+    SNESGetIterationNumber(s->snes, &nl_its);
+    int lin_its;
+    SNESGetLinearSolveIterations(s->snes, &lin_its);
+
+    output.print("\r"); // Carriage return for printing to screen
+    output.write("Time: {}, timestep: {}, nl iter: {}, lin iter: {}, reason: {}",
+                     t, timestep, nl_its, lin_its, static_cast<int>(reason));
+    if (snes_failures > 0) {
+      output.write(", SNES failures: {}", snes_failures);
+    }
+    output.write("\n");
+  }
+
   if (t < s->next_output) {
     // Not reached output time yet => return
     PetscFunctionReturn(0);

From 1ddf5b8cff07e67ea47ffc30f83570190aafd390 Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Fri, 5 Dec 2025 20:24:44 +0000
Subject: [PATCH 0386/1827] Apply clang-format changes

---
 src/solver/impls/petsc/petsc.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index e7e0296677..d0535f069d 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -190,8 +190,8 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
     SNESGetLinearSolveIterations(s->snes, &lin_its);
 
     output.print("\r"); // Carriage return for printing to screen
-    output.write("Time: {}, timestep: {}, nl iter: {}, lin iter: {}, reason: {}",
-                     t, timestep, nl_its, lin_its, static_cast<int>(reason));
+    output.write("Time: {}, timestep: {}, nl iter: {}, lin iter: {}, reason: {}", t,
+                 timestep, nl_its, lin_its, static_cast<int>(reason));
     if (snes_failures > 0) {
       output.write(", SNES failures: {}", snes_failures);
     }

From 666d0e6d68ade7b09a0ee5a594eb6b62b6c40ccf Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 15 Dec 2025 19:06:24 +0000
Subject: [PATCH 0387/1827] Bump actions/cache from 4 to 5

Bumps [actions/cache](https://github.com/actions/cache) from 4 to 5.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](https://github.com/actions/cache/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index f2c3618fab..82f3d6aea0 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -182,7 +182,7 @@ jobs:
           python -m pip install -r requirements.txt
 
       - name: Cache SUNDIALS build
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: /home/runner/local
           key: bout-sundials-${{ matrix.config.os }}${{ matrix.config.build_petsc }}

From 50764ef185a55314f3a8adc7e6a3f7196c55e684 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Dec 2025 08:43:13 -0800
Subject: [PATCH 0388/1827] snes solver: Wrap all run_rhs calls in try...catch

Calls to run_rhs may throw an exception if given out of domain
values. Catch and return error code if this happens.
---
 src/solver/impls/snes/snes.cxx | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index c10095af53..23b82982f4 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -993,7 +993,13 @@ int SNESSolver::run() {
           ierr = VecRestoreArrayRead(snes_x, &xdata);
           CHKERRQ(ierr);
         }
-        run_rhs(simtime);
+
+        try {
+          run_rhs(simtime);
+        } catch (BoutException& e) {
+          output_error.write("ERROR: BoutException thrown: {}\n", e.what());
+          return 1;
+        }
 
         // Copy derivatives back
         {
@@ -1168,7 +1174,12 @@ int SNESSolver::run() {
       ierr = VecRestoreArrayRead(output_x, &xdata);
       CHKERRQ(ierr);
     }
-    run_rhs(target); // Run RHS to calculate auxilliary variables
+
+    try {
+      run_rhs(target); // Run RHS to calculate auxilliary variables
+    } catch (BoutException& e) {
+      output_error.write("ERROR: BoutException thrown: {}\n", e.what());
+    }
 
     if (call_monitors(target, s, getNumberOutputSteps()) != 0) {
       break; // User signalled to quit

From 4b86f92296de57149cab592114be901bec751755 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 22 Dec 2025 19:04:47 +0000
Subject: [PATCH 0389/1827] Bump externalpackages/googletest from `1b96fa1` to
 `9156d4c`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `1b96fa1` to `9156d4c`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/1b96fa13f549387b7549cc89e1a785cf143a1a50...9156d4caac880b513264ecbe0aa4746a3fead3d7)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: 9156d4caac880b513264ecbe0aa4746a3fead3d7
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 1b96fa13f5..9156d4caac 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 1b96fa13f549387b7549cc89e1a785cf143a1a50
+Subproject commit 9156d4caac880b513264ecbe0aa4746a3fead3d7

From cbea5c5c0327f7e76151d4682291c89a5dc6996b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 22 Dec 2025 19:04:52 +0000
Subject: [PATCH 0390/1827] Bump ZedThree/clang-tidy-review from 0.22.2 to
 0.22.3

Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.22.2 to 0.22.3.
- [Release notes](https://github.com/zedthree/clang-tidy-review/releases)
- [Changelog](https://github.com/ZedThree/clang-tidy-review/blob/master/CHANGELOG.md)
- [Commits](https://github.com/zedthree/clang-tidy-review/compare/v0.22.2...v0.22.3)

---
updated-dependencies:
- dependency-name: ZedThree/clang-tidy-review
  dependency-version: 0.22.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/clang-tidy-review.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 06c2f88b03..4e3cef8fe6 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -21,7 +21,7 @@ jobs:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.22.2
+        uses: ZedThree/clang-tidy-review@v0.22.3
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.22.2
+        uses: ZedThree/clang-tidy-review/upload@v0.22.3

From f84f7116a3cfde8f16f805a86c6440aedf2b7701 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 29 Dec 2025 10:27:39 -0800
Subject: [PATCH 0391/1827] Rename is_periodic_y

Calls mesh->periodicY internally
---
 src/field/field_factory.cxx   | 2 +-
 src/field/fieldgenerators.cxx | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index 08a7f14fa3..b93a39eeda 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -178,7 +178,7 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
   addGenerator("where", std::make_shared<FieldWhere>(nullptr, nullptr, nullptr));
 
   // Periodic in the Y direction?
-  addGenerator("periodicY", std::make_shared<FieldPeriodicY>());
+  addGenerator("is_periodic_y", std::make_shared<FieldPeriodicY>());
 }
 
 Field2D FieldFactory::create2D(const std::string& value, const Options* opt,
diff --git a/src/field/fieldgenerators.cxx b/src/field/fieldgenerators.cxx
index 1f21f5c262..7e728664f8 100644
--- a/src/field/fieldgenerators.cxx
+++ b/src/field/fieldgenerators.cxx
@@ -1,6 +1,8 @@
 
 #include "fieldgenerators.hxx"
 
+#include <memory>
+
 #include <bout/constants.hxx>
 #include <bout/utils.hxx>
 

From 7b30663b262012f600be382735246d3afb74b487 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 29 Dec 2025 14:29:12 -0800
Subject: [PATCH 0392/1827] Unit test is_periodic_y

Extends FakeMesh to mock periodicY methods.
---
 tests/unit/fake_mesh.hxx                |  8 +++-
 tests/unit/field/test_field_factory.cxx | 54 +++++++++++++++++++++++++
 2 files changed, 60 insertions(+), 2 deletions(-)

diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index e6f78f8767..99c8d04546 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -120,8 +120,12 @@ public:
   }
   MPI_Comm getXcomm(int UNUSED(jy)) const override { return BoutComm::get(); }
   MPI_Comm getYcomm(int UNUSED(jx)) const override { return BoutComm::get(); }
-  bool periodicY(int UNUSED(jx)) const override { return true; }
-  bool periodicY(int UNUSED(jx), BoutReal& UNUSED(ts)) const override { return true; }
+
+  // Periodic Y
+  int ix_separatrix {1000000}; // separatrix index
+
+  bool periodicY(int jx) const override { return jx < ix_separatrix; }
+  bool periodicY(int jx, BoutReal& UNUSED(ts)) const override { return jx < ix_separatrix; }
   int numberOfYBoundaries() const override { return 1; }
   std::pair<bool, BoutReal> hasBranchCutLower(int UNUSED(jx)) const override {
     return std::make_pair(false, 0.);
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index 964788b25a..2c47ae90a6 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -969,3 +969,57 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create3DCantTransform) {
 
   EXPECT_TRUE(IsFieldEqual(output, expected));
 }
+
+TYPED_TEST(FieldFactoryCreationTest, CreatePeriodicY) {
+  auto output = this->create("is_periodic_y");
+
+  auto expected = makeField<TypeParam>(
+                                     [](typename TypeParam::ind_type& index) -> BoutReal { return mesh->periodicY(index.x()); }, mesh);
+
+  EXPECT_TRUE(IsFieldEqual(output, expected));
+}
+
+TYPED_TEST(FieldFactoryCreationTest, CreatePeriodicYoutsideCore) {
+  FakeMesh localmesh{5, 1, 1};
+  localmesh.createDefaultRegions();
+  localmesh.setCoordinates(std::make_shared<Coordinates>(
+      &localmesh, Field2D{1.0}, Field2D{1.0}, BoutReal{1.0}, Field2D{1.0}, Field2D{0.0},
+      Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0},
+      Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0},
+      Field2D{0.0}, Field2D{0.0}));
+  // No call to Coordinates::geometry() needed here
+
+  localmesh.getCoordinates()->setParallelTransform(
+      bout::utils::make_unique<ParallelTransformIdentity>(localmesh));
+
+  localmesh.ix_separatrix = 0; // All points outside core
+
+  auto output = this->create("is_periodic_y", nullptr, &localmesh);
+
+  auto expected = makeField<TypeParam>(
+                                     [](typename TypeParam::ind_type& index) -> BoutReal { return 0.0; }, &localmesh);
+
+  EXPECT_TRUE(IsFieldEqual(output, expected));
+}
+
+TYPED_TEST(FieldFactoryCreationTest, CreatePeriodicYacrossSeparatrix) {
+  FakeMesh localmesh{5, 1, 1};
+  localmesh.createDefaultRegions();
+  localmesh.ix_separatrix = 2; // All points in core
+  localmesh.setCoordinates(std::make_shared<Coordinates>(
+      &localmesh, Field2D{1.0}, Field2D{1.0}, BoutReal{1.0}, Field2D{1.0}, Field2D{0.0},
+      Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0},
+      Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0},
+      Field2D{0.0}, Field2D{0.0}));
+  // No call to Coordinates::geometry() needed here
+
+  localmesh.getCoordinates()->setParallelTransform(
+      bout::utils::make_unique<ParallelTransformIdentity>(localmesh));
+
+  auto output = this->create("is_periodic_y", nullptr, &localmesh);
+
+  auto expected = makeField<TypeParam>(
+                                       [&](typename TypeParam::ind_type& index) -> BoutReal { return index.x() < localmesh.ix_separatrix; }, &localmesh);
+
+  EXPECT_TRUE(IsFieldEqual(output, expected));
+}

From 1f264d0914e29a352238e7d413b1d3dcacbb9693 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 29 Dec 2025 14:29:57 -0800
Subject: [PATCH 0393/1827] Add is_periodic_y to manual page

Include in table of values available to expressions.
---
 manual/sphinx/user_docs/variable_init.rst | 24 ++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/manual/sphinx/user_docs/variable_init.rst b/manual/sphinx/user_docs/variable_init.rst
index 4ac13e0ead..1baaba5e84 100644
--- a/manual/sphinx/user_docs/variable_init.rst
+++ b/manual/sphinx/user_docs/variable_init.rst
@@ -81,17 +81,19 @@ following values are also already defined:
 .. _tab-initexprvals:
 .. table:: Initialisation expression values
 
-   +--------+------------------------------------------------------------------------------------+
-   | Name   | Description                                                                        |
-   +========+====================================================================================+
-   | x      | :math:`x` position between :math:`0` and :math:`1`                                 |
-   +--------+------------------------------------------------------------------------------------+
-   | y      | :math:`y` angle-like position, definition depends on topology of grid              |
-   +--------+------------------------------------------------------------------------------------+
-   | z      | :math:`z` position between :math:`0` and :math:`2\pi` (excluding the last point)   |
-   +--------+------------------------------------------------------------------------------------+
-   | pi  π  | :math:`3.1415\ldots`                                                               |
-   +--------+------------------------------------------------------------------------------------+
+   +----------------+------------------------------------------------------------------------------------+
+   | Name           | Description                                                                        |
+   +================+====================================================================================+
+   | x              | :math:`x` position between :math:`0` and :math:`1`                                 |
+   +----------------+------------------------------------------------------------------------------------+
+   | y              | :math:`y` angle-like position, definition depends on topology of grid              |
+   +----------------+------------------------------------------------------------------------------------+
+   | z              | :math:`z` position between :math:`0` and :math:`2\pi` (excluding the last point)   |
+   +----------------+------------------------------------------------------------------------------------+
+   | pi  π          | :math:`3.1415\ldots`                                                               |
+   +----------------+------------------------------------------------------------------------------------+
+   | is_periodic_y  | :math:`1` in core region where Y is periodic. :math:`0` otherwise                  |
+   +----------------+------------------------------------------------------------------------------------+
 
 
 By default, :math:`x` is defined as ``(i+0.5) / (nx - 2*MXG)``, where ``MXG``

From 67bddf3e9c76440141f5d5c32a5d57c96215145e Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Mon, 29 Dec 2025 22:31:09 +0000
Subject: [PATCH 0394/1827] Apply clang-format changes

---
 include/bout/invertable_operator.hxx    |  4 ++--
 include/bout/output.hxx                 | 14 +++++++-------
 src/solver/impls/arkode/arkode.cxx      |  3 +--
 tests/unit/fake_mesh.hxx                |  6 ++++--
 tests/unit/field/test_field_factory.cxx | 12 +++++++++---
 5 files changed, 23 insertions(+), 16 deletions(-)

diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx
index fe139986be..99f7d9b675 100644
--- a/include/bout/invertable_operator.hxx
+++ b/include/bout/invertable_operator.hxx
@@ -575,7 +575,7 @@ public:
 };
 
 #endif // PETSC
-};     // namespace inversion
-};     // namespace bout
+}; // namespace inversion
+}; // namespace bout
 
 #endif // HEADER GUARD
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index 2862899067..8f50f9029b 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -136,14 +136,14 @@ private:
 class DummyOutput : public Output {
 public:
   template <class S, class... Args>
-  void write([[maybe_unused]] const S& format, [[maybe_unused]] const Args&... args){};
+  void write([[maybe_unused]] const S& format, [[maybe_unused]] const Args&... args) {};
   template <class S, class... Args>
-  void print([[maybe_unused]] const S& format, [[maybe_unused]] const Args&... args){};
-  void write([[maybe_unused]] const std::string& message) override{};
-  void print([[maybe_unused]] const std::string& message) override{};
-  void enable() override{};
-  void disable() override{};
-  void enable([[maybe_unused]] bool enable){};
+  void print([[maybe_unused]] const S& format, [[maybe_unused]] const Args&... args) {};
+  void write([[maybe_unused]] const std::string& message) override {};
+  void print([[maybe_unused]] const std::string& message) override {};
+  void enable() override {};
+  void disable() override {};
+  void enable([[maybe_unused]] bool enable) {};
   bool isEnabled() override { return false; }
 };
 
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 6f20ce11a6..e5c70ae9ba 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -417,8 +417,7 @@ int ArkodeSolver::init() {
         if (hasPreconditioner()) {
           output.write("\tUsing user-supplied preconditioner\n");
 
-          if (ARKodeSetPreconditioner(arkode_mem, nullptr, arkode_pre)
-              != ARKLS_SUCCESS) {
+          if (ARKodeSetPreconditioner(arkode_mem, nullptr, arkode_pre) != ARKLS_SUCCESS) {
             throw BoutException("ARKodeSetPreconditioner failed\n");
           }
         } else {
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 99c8d04546..e8ba4f3e93 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -122,10 +122,12 @@ public:
   MPI_Comm getYcomm(int UNUSED(jx)) const override { return BoutComm::get(); }
 
   // Periodic Y
-  int ix_separatrix {1000000}; // separatrix index
+  int ix_separatrix{1000000}; // separatrix index
 
   bool periodicY(int jx) const override { return jx < ix_separatrix; }
-  bool periodicY(int jx, BoutReal& UNUSED(ts)) const override { return jx < ix_separatrix; }
+  bool periodicY(int jx, BoutReal& UNUSED(ts)) const override {
+    return jx < ix_separatrix;
+  }
   int numberOfYBoundaries() const override { return 1; }
   std::pair<bool, BoutReal> hasBranchCutLower(int UNUSED(jx)) const override {
     return std::make_pair(false, 0.);
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index 2c47ae90a6..26dc1e2990 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -974,7 +974,10 @@ TYPED_TEST(FieldFactoryCreationTest, CreatePeriodicY) {
   auto output = this->create("is_periodic_y");
 
   auto expected = makeField<TypeParam>(
-                                     [](typename TypeParam::ind_type& index) -> BoutReal { return mesh->periodicY(index.x()); }, mesh);
+      [](typename TypeParam::ind_type& index) -> BoutReal {
+        return mesh->periodicY(index.x());
+      },
+      mesh);
 
   EXPECT_TRUE(IsFieldEqual(output, expected));
 }
@@ -997,7 +1000,7 @@ TYPED_TEST(FieldFactoryCreationTest, CreatePeriodicYoutsideCore) {
   auto output = this->create("is_periodic_y", nullptr, &localmesh);
 
   auto expected = makeField<TypeParam>(
-                                     [](typename TypeParam::ind_type& index) -> BoutReal { return 0.0; }, &localmesh);
+      [](typename TypeParam::ind_type& index) -> BoutReal { return 0.0; }, &localmesh);
 
   EXPECT_TRUE(IsFieldEqual(output, expected));
 }
@@ -1019,7 +1022,10 @@ TYPED_TEST(FieldFactoryCreationTest, CreatePeriodicYacrossSeparatrix) {
   auto output = this->create("is_periodic_y", nullptr, &localmesh);
 
   auto expected = makeField<TypeParam>(
-                                       [&](typename TypeParam::ind_type& index) -> BoutReal { return index.x() < localmesh.ix_separatrix; }, &localmesh);
+      [&](typename TypeParam::ind_type& index) -> BoutReal {
+        return index.x() < localmesh.ix_separatrix;
+      },
+      &localmesh);
 
   EXPECT_TRUE(IsFieldEqual(output, expected));
 }

From 236437b46622f1b045d35ed1105580fc5e8431eb Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 31 Dec 2025 19:01:25 +0000
Subject: [PATCH 0395/1827] Update ruamel-yaml requirement from ~=0.18 to
 ~=0.19

Updates the requirements on ruamel-yaml to permit the latest version.

---
updated-dependencies:
- dependency-name: ruamel-yaml
  dependency-version: 0.19.0
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements_maint.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements_maint.txt b/requirements_maint.txt
index b1d9db5ff8..05375dd39e 100644
--- a/requirements_maint.txt
+++ b/requirements_maint.txt
@@ -1,3 +1,3 @@
 pygithub~=2.8
-ruamel-yaml~=0.18
+ruamel-yaml~=0.19
 Unidecode~=1.3

From c430a2659c882e8de5c0d8e3b64df7a62046de09 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 5 Jan 2026 19:05:08 +0000
Subject: [PATCH 0396/1827] Bump ZedThree/clang-tidy-review from 0.22.3 to
 0.23.0

Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.22.3 to 0.23.0.
- [Release notes](https://github.com/zedthree/clang-tidy-review/releases)
- [Changelog](https://github.com/ZedThree/clang-tidy-review/blob/master/CHANGELOG.md)
- [Commits](https://github.com/zedthree/clang-tidy-review/compare/v0.22.3...v0.23.0)

---
updated-dependencies:
- dependency-name: ZedThree/clang-tidy-review
  dependency-version: 0.23.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/clang-tidy-review.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 4e3cef8fe6..087c910987 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -21,7 +21,7 @@ jobs:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.22.3
+        uses: ZedThree/clang-tidy-review@v0.23.0
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.22.3
+        uses: ZedThree/clang-tidy-review/upload@v0.23.0

From bc2dad1d8e4c0d5e7de8f12351b67d7fc73adb33 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 6 Jan 2026 14:56:42 +0000
Subject: [PATCH 0397/1827] cmake: Set `_ROOT` variable from corresponding
 `_DIR`

Using the build directory directly for some dependencies (sometimes?) doesn't
set the `_ROOT` variable, causing issues with our `bout++Config.cmake` file.
---
 cmake/SetupBOUTThirdParty.cmake | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 53ceb4351c..1256fbbeba 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -186,6 +186,12 @@ if (BOUT_USE_NETCDF)
       set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${NETCDF_LDFLAGS_STRING}")
     endif()
   endif()
+  if (netCDF_DIR)
+    set(netCDF_ROOT "${netCDF_DIR}")
+  endif()
+  if (netCDFCxx_DIR)
+    set(netCDFCxx_ROOT "${netCDFCxx_DIR}")
+  endif()
 endif()
 message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}")
 set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})
@@ -299,6 +305,9 @@ if (BOUT_USE_SUNDIALS)
       message(FATAL_ERROR "SUNDIALS_VERSION 4.0.0 or newer is required. Found version ${SUNDIALS_VERSION}.")
     endif()
   endif()
+  if (SUNDIALS_DIR)
+    set(SUNDIALS_ROOT "${SUNDIALS_DIR}")
+  endif()
   target_link_libraries(bout++ PUBLIC SUNDIALS::nvecparallel)
   target_link_libraries(bout++ PUBLIC SUNDIALS::cvode)
   target_link_libraries(bout++ PUBLIC SUNDIALS::ida)

From 1034ba5cfeb7910daba034160e97f7ff34122236 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 6 Jan 2026 14:27:02 +0000
Subject: [PATCH 0398/1827] Switch use of `fmt` header

Technically `base.h` is sufficient, but this causes backwards compatibility
issues, and the compilation penalty is minor.
---
 src/sys/output.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sys/output.cxx b/src/sys/output.cxx
index 2c5e06bb7c..0a9bb5f4c4 100644
--- a/src/sys/output.cxx
+++ b/src/sys/output.cxx
@@ -26,7 +26,7 @@
 #include <bout/assert.hxx>
 #include <bout/output.hxx>
 
-#include <fmt/base.h>
+#include <fmt/format.h>         // NOLINT(misc-include-cleaner)
 
 #include <iostream>
 #include <string>

From 489cde624f9ae93e31fffd6ab99de9a39735ce50 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Tue, 6 Jan 2026 17:19:07 +0000
Subject: [PATCH 0399/1827] Apply clang-format changes

---
 src/sys/output.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sys/output.cxx b/src/sys/output.cxx
index 0a9bb5f4c4..97b58edec7 100644
--- a/src/sys/output.cxx
+++ b/src/sys/output.cxx
@@ -26,7 +26,7 @@
 #include <bout/assert.hxx>
 #include <bout/output.hxx>
 
-#include <fmt/format.h>         // NOLINT(misc-include-cleaner)
+#include <fmt/format.h> // NOLINT(misc-include-cleaner)
 
 #include <iostream>
 #include <string>

From d9e789cd3f67d0e883ab849a476360be367627a2 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 5 Dec 2025 13:30:23 +0000
Subject: [PATCH 0400/1827] Switch to `cpptrace` for stack traces in exceptions

---
 .clang-tidy                                   |  2 +-
 CMakeLists.txt                                | 13 ---
 bout++Config.cmake.in                         |  7 +-
 cmake/SetupBOUTThirdParty.cmake               | 16 ++++
 cmake_build_defines.hxx.in                    |  4 +-
 include/bout/boutexception.hxx                |  9 --
 include/bout/physicsmodel.hxx                 |  3 +-
 manual/doxygen/Doxyfile                       |  1 -
 manual/doxygen/Doxyfile_readthedocs           |  1 -
 src/sys/boutexception.cxx                     | 92 +++++--------------
 .../integrated/test-backtrace/CMakeLists.txt  |  4 +-
 tests/integrated/test-backtrace/runtest       |  4 +-
 tests/unit/sys/test_boutexception.cxx         | 25 ++---
 13 files changed, 61 insertions(+), 120 deletions(-)

diff --git a/.clang-tidy b/.clang-tidy
index 23167e93d0..cf29b759cd 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -20,7 +20,7 @@ CheckOptions:
     value: 'MPI_Comm'
 
   - key: misc-include-cleaner.IgnoreHeaders
-    value: 'adios2/.*;bits/.*'
+    value: 'adios2/.*;bits/.*;cpptrace/.*'
 ---
 
 Disabled checks and reasons:
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 44d100e444..7864705519 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -574,18 +574,6 @@ option(BOUT_ENABLE_SIGFPE "Signalling floating point exceptions" OFF)
 message(STATUS "Signalling floating point exceptions: BOUT_USE_SIGFPE=${BOUT_ENABLE_SIGFPE}")
 set(BOUT_USE_SIGFPE ${BOUT_ENABLE_SIGFPE})
 
-option(BOUT_ENABLE_BACKTRACE "Enable backtrace" ON)
-if (BOUT_ENABLE_BACKTRACE)
-  find_program(ADDR2LINE_FOUND addr2line)
-  if (NOT ADDR2LINE_FOUND)
-    message(FATAL_ERROR "addr2line not found. Disable backtrace by setting BOUT_ENABLE_BACKTRACE=Off")
-  endif()
-  target_link_libraries(bout++ PUBLIC ${CMAKE_DL_LIBS})
-  set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -l${CMAKE_DL_LIBS}")
-endif()
-message(STATUS "Enable backtrace: BOUT_USE_BACKTRACE=${BOUT_ENABLE_BACKTRACE}")
-set(BOUT_USE_BACKTRACE ${BOUT_ENABLE_BACKTRACE})
-
 option(BOUT_ENABLE_METRIC_3D "Enable 3D metric support" OFF)
 if(BOUT_ENABLE_METRIC_3D)
   set(BOUT_METRIC_TYPE "3D")
@@ -958,7 +946,6 @@ message("
    Output coloring          : ${BOUT_USE_COLOR}
    Field name tracking      : ${BOUT_USE_TRACK}
    Floating point exceptions: ${BOUT_USE_SIGFPE}
-   Backtrace enabled        : ${BOUT_USE_BACKTRACE}
    RAJA enabled             : ${BOUT_HAS_RAJA}
    Umpire enabled           : ${BOUT_HAS_UMPIRE}
    Caliper enabled          : ${BOUT_HAS_CALIPER}
diff --git a/bout++Config.cmake.in b/bout++Config.cmake.in
index d461e58e4b..a82479f41c 100644
--- a/bout++Config.cmake.in
+++ b/bout++Config.cmake.in
@@ -6,7 +6,6 @@ set(BOUT_USE_SIGNAL @BOUT_USE_SIGNAL@)
 set(BOUT_USE_COLOR @BOUT_USE_COLOR@)
 set(BOUT_USE_TRACK @BOUT_USE_TRACK@)
 set(BOUT_USE_SIGFPE @BOUT_USE_SIGFPE@)
-set(BOUT_USE_BACKTRACE @BOUT_USE_BACKTRACE@)
 set(BOUT_USE_OPENMP @BOUT_USE_OPENMP@)
 set(BOUT_HAS_CUDA @BOUT_HAS_CUDA@)
 set(BOUT_HAS_OUTPUT_DEBUG @BOUT_HAS_OUTPUT_DEBUG@)
@@ -109,6 +108,11 @@ elseif(EXISTS "@ADIOS2_BINARY_DIR@")
   # If we downloaded ADIOS2, then we need to add its build directory to our search paths
   list(APPEND CMAKE_PREFIX_PATH "@ADIOS2_BINARY_DIR@")
 endif()
+if(EXISTS "@cpptrace_ROOT@")
+  set(cpptrace_ROOT "@cpptrace_ROOT@")
+elseif(EXISTS "@cpptrace_BINARY_DIR@")
+  list(APPEND CMAKE_PREFIX_PATH "@cpptrace_BINARY_DIR@")
+endif()
 
 if(@BOUT_USE_SYSTEM_MPARK_VARIANT@)
   set(mpark_variant_ROOT "@mpark_variant_ROOT@")
@@ -160,6 +164,7 @@ if (BOUT_HAS_GETTEXT)
 endif()
 find_dependency(mpark_variant @mpark_variant_VERSION@)
 find_dependency(fmt @fmt_VERSION@)
+find_dependency(cpptrace @cpptrace_VERSION@)
 if (BOUT_HAS_SLEPC)
   find_dependency(SLEPc @SLEPC_VERSION@)
 endif()
diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 1256fbbeba..2249fb3468 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -369,3 +369,19 @@ if (BOUT_USE_UUID_SYSTEM_GENERATOR)
 endif()
 message(STATUS "UUID_SYSTEM_GENERATOR: ${BOUT_USE_UUID_SYSTEM_GENERATOR}")
 set(BOUT_HAS_UUID_SYSTEM_GENERATOR ${BOUT_USE_UUID_SYSTEM_GENERATOR})
+
+option(BOUT_DOWNLOAD_CPPTRACE "Download cpptrace for backtrace support" ON)
+if (BOUT_DOWNLOAD_CPPTRACE)
+  include(FetchContent)
+  set(CPPTRACE_LIBDWARF_REPO "https://github.com/ZedThree/libdwarf-lite.git" CACHE STRING "" FORCE)
+  set(CPPTRACE_LIBDWARF_TAG "5f15f145d96278a64440f3c700f475233b4fd0e7" CACHE STRING "" FORCE)
+  FetchContent_Declare(
+    cpptrace
+    GIT_REPOSITORY https://github.com/jeremy-rifkin/cpptrace.git
+    GIT_TAG        v1.0.4
+  )
+  FetchContent_MakeAvailable(cpptrace)
+else()
+  find_package(cpptrace REQUIRED)
+endif()
+target_link_libraries(bout++ PUBLIC cpptrace::cpptrace)
diff --git a/cmake_build_defines.hxx.in b/cmake_build_defines.hxx.in
index 4d63a01b7d..9c73679f29 100644
--- a/cmake_build_defines.hxx.in
+++ b/cmake_build_defines.hxx.in
@@ -21,7 +21,6 @@
 #cmakedefine01 BOUT_HAS_SLEPC
 #cmakedefine01 BOUT_HAS_SUNDIALS
 #cmakedefine01 BOUT_HAS_UUID_SYSTEM_GENERATOR
-#cmakedefine01 BOUT_USE_BACKTRACE
 #cmakedefine01 BOUT_USE_COLOR
 #cmakedefine01 BOUT_USE_OPENMP
 #cmakedefine01 BOUT_USE_OUTPUT_DEBUG
@@ -39,4 +38,7 @@
 // CMake build does not support legacy interface
 #define BOUT_HAS_LEGACY_NETCDF 0
 
+// We now always turn this on
+#define BOUT_USE_BACKTRACE 1
+
 #endif // BOUT_BUILD_CONFIG_HXX
diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx
index ffd4a03a6c..3d8a9cd71d 100644
--- a/include/bout/boutexception.hxx
+++ b/include/bout/boutexception.hxx
@@ -1,9 +1,6 @@
 #ifndef BOUT_EXCEPTION_H
 #define BOUT_EXCEPTION_H
 
-#include "bout/build_defines.hxx"
-
-#include <array>
 #include <exception>
 #include <string>
 #include <utility>
@@ -37,12 +34,6 @@ public:
 
 private:
   std::string message;
-#if BOUT_USE_BACKTRACE
-  static constexpr unsigned int TRACE_MAX = 128;
-  std::array<void*, TRACE_MAX> trace{};
-  int trace_size;
-  char** messages;
-#endif
 };
 
 class BoutRhsFail : public BoutException {
diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index 9fa25d8b0f..baa284c862 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -433,8 +433,7 @@ private:
       solver->addMonitor(bout_monitor.get(), Solver::BACK);        \
       solver->solve();                                             \
     } catch (const BoutException& e) {                             \
-      output << "Error encountered: " << e.what();                 \
-      output << e.getBacktrace() << endl;                          \
+      output.write("Error encountered: {}\n", e.what());           \
       MPI_Abort(BoutComm::get(), 1);                               \
     }                                                              \
     BoutFinalise();                                                \
diff --git a/manual/doxygen/Doxyfile b/manual/doxygen/Doxyfile
index e7998854b0..e2fef90a8c 100644
--- a/manual/doxygen/Doxyfile
+++ b/manual/doxygen/Doxyfile
@@ -2065,7 +2065,6 @@ PREDEFINED             = BACKTRACE \
                          BOUT_HAS_SLEPC \
                          BOUT_HAS_SUNDIALS \
                          BOUT_HAS_UUID_SYSTEM_GENERATOR \
-                         BOUT_USE_BACKTRACE \
                          BOUT_USE_COLOR \
                          BOUT_USE_OPENMP \
                          BOUT_USE_OUTPUT_DEBUG \
diff --git a/manual/doxygen/Doxyfile_readthedocs b/manual/doxygen/Doxyfile_readthedocs
index 73060bb6b4..94113490d9 100644
--- a/manual/doxygen/Doxyfile_readthedocs
+++ b/manual/doxygen/Doxyfile_readthedocs
@@ -1025,7 +1025,6 @@ PREDEFINED             = BACKTRACE \
                          BOUT_HAS_SLEPC \
                          BOUT_HAS_SUNDIALS \
                          BOUT_HAS_UUID_SYSTEM_GENERATOR \
-                         BOUT_USE_BACKTRACE \
                          BOUT_USE_COLOR \
                          BOUT_USE_OPENMP \
                          BOUT_USE_OUTPUT_DEBUG \
diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index e81e395bf8..edf7509077 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -1,5 +1,3 @@
-#include "bout/build_defines.hxx"
-
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/msg_stack.hxx>
@@ -7,13 +5,10 @@
 
 #include <mpi.h>
 
-#if BOUT_USE_BACKTRACE
-#include <dlfcn.h>
-#include <execinfo.h>
-#include <stdio.h>
-#endif
+#include <cpptrace/cpptrace.hpp> // IWYU pragma: keep
+#include <cpptrace/formatting.hpp>
+#include <cpptrace/utils.hpp>
 
-#include <array>
 #include <cstdlib>
 #include <string>
 #include <utility>
@@ -33,16 +28,10 @@ void BoutParallelThrowRhsFail(int status, const char* message) {
   }
 }
 
-BoutException::BoutException(std::string msg)
-    : message(std::move(msg))
-#if BOUT_USE_BACKTRACE
-      ,
-      trace_size(backtrace(trace.data(), TRACE_MAX)),
-      messages(backtrace_symbols(trace.data(), trace_size))
-#endif
-{
-  if (std::getenv("BOUT_SHOW_BACKTRACE") != nullptr) {
-    message = fmt::format("{}\n{}", getBacktrace(), message);
+BoutException::BoutException(std::string msg) : message(std::move(msg)) {
+  const char* show_backtrace = std::getenv("BOUT_SHOW_BACKTRACE");
+  if (show_backtrace == nullptr or std::string{show_backtrace} != "0") {
+    message = getBacktrace();
   }
 }
 
@@ -51,62 +40,27 @@ BoutException::~BoutException() {
   // up the msg_stack. We also won't know how many messages to pop, so
   // just clear everything
   msg_stack.clear();
-#if BOUT_USE_BACKTRACE
-  // Call required for memory allocated by `backtrace_symbols`
-  free(messages); // NOLINT
-#endif
 }
 
 std::string BoutException::getBacktrace() const {
-  std::string backtrace_message;
-#if BOUT_USE_BACKTRACE
-  backtrace_message = "====== Exception path ======\n";
-  // skip first stack frame (points here)
-  for (int i = trace_size - 1; i > 1; --i) {
-    backtrace_message = fmt::format(FMT_STRING("{}[bt] #{:d} {:s}\n"), backtrace_message,
-                                    i - 1, messages[i]);
-    // find first occurence of '(' or ' ' in message[i] and assume
-    // everything before that is the file name. (Don't go beyond 0 though
-    // (string terminator)
-    int p = 0; // snprintf %.*s expects int
-    while (messages[i][p] != '(' && messages[i][p] != ' ' && messages[i][p] != 0) {
-      ++p;
-    }
+  using namespace cpptrace;
 
-    // If we are compiled as PIE, need to get base pointer of .so and substract
-    Dl_info info;
-    const void* ptr = trace[i];
-    if (dladdr(ptr, &info) != 0) {
-      // Additionally, check whether this is the default offset for an executable
-      if (info.dli_fbase != reinterpret_cast<void*>(0x400000)) {
-        ptr = reinterpret_cast<void*>(reinterpret_cast<size_t>(ptr)
-                                      - reinterpret_cast<size_t>(info.dli_fbase));
-      }
-    }
+  const auto colours = isatty(stdout_fileno) || isatty(stderr_fileno)
+                           ? formatter::color_mode::always
+                           : formatter ::color_mode::none;
 
-    // Pipe stderr to /dev/null to avoid cluttering output
-    // when addr2line fails or is not installed
-    const auto syscom = fmt::format(
-        FMT_STRING("addr2line {:p} -Cfpie {:.{}s} 2> /dev/null"), ptr, messages[i], p);
-    // last parameter is the file name of the symbol
-    FILE* file = popen(syscom.c_str(), "r");
-    if (file != nullptr) {
-      std::array<char, 1024> out{};
-      const char* retstr = nullptr;
-      std::string buf;
-      while ((retstr = fgets(out.data(), out.size() - 1, file)) != nullptr) {
-        buf += retstr;
-      }
-      int const status = pclose(file);
-      if (status == 0) {
-        backtrace_message = fmt::format("{}{}", backtrace_message, buf);
-      }
-    }
-  }
-#else
-  backtrace_message = "Stacktrace not enabled.\n";
-#endif
+  auto formatter = cpptrace::formatter{}
+                       .addresses(formatter::address_mode::none)
+                       .break_before_filename(true)
+                       .colors(colours)
+                       .snippets(true)
+                       .filter([](const stacktrace_frame& frame) {
+                         return frame.symbol.find("BoutException::") == std::string::npos;
+                       })
+                       .filtered_frame_placeholders(false);
+
+  const std::string backtrace_message = formatter.format(generate_trace());
 
-  return fmt::format("{}{}\n{}{}\n", backtrace_message, msg_stack.getDump(), header,
+  return fmt::format("{}\n{}\n{}{}\n", backtrace_message, msg_stack.getDump(), header,
                      message);
 }
diff --git a/tests/integrated/test-backtrace/CMakeLists.txt b/tests/integrated/test-backtrace/CMakeLists.txt
index b20262f1b1..579f4863ac 100644
--- a/tests/integrated/test-backtrace/CMakeLists.txt
+++ b/tests/integrated/test-backtrace/CMakeLists.txt
@@ -1,6 +1,4 @@
 bout_add_integrated_test(test-backtrace
   SOURCES boutexcept.cxx
-  REQUIRES BOUT_USE_BACKTRACE
-  CONFLICTS CMAKE_SYSTEM_NAME MATCHES "FreeBSD"
   USE_RUNTEST
-  )
+)
diff --git a/tests/integrated/test-backtrace/runtest b/tests/integrated/test-backtrace/runtest
index b41506175e..4010873b56 100755
--- a/tests/integrated/test-backtrace/runtest
+++ b/tests/integrated/test-backtrace/runtest
@@ -17,13 +17,13 @@ except KeyError:
 success = True
 errors = []
 
-_, output = shell("./boutexcept", pipe=True)
+_, output = shell("BOUT_SHOW_BACKTRACE=0 ./boutexcept", pipe=True)
 
 if "troublemaker" in output:
     success = False
     print("Fail: detected offending function name in output when not expected")
 
-_, output = shell("BOUT_SHOW_BACKTRACE=yes ./boutexcept", pipe=True)
+_, output = shell("./boutexcept", pipe=True)
 
 if "troublemaker" not in output:
     success = False
diff --git a/tests/unit/sys/test_boutexception.cxx b/tests/unit/sys/test_boutexception.cxx
index 322c7d6e42..5eb2c4d719 100644
--- a/tests/unit/sys/test_boutexception.cxx
+++ b/tests/unit/sys/test_boutexception.cxx
@@ -1,5 +1,3 @@
-#include "bout/build_defines.hxx"
-
 #include "test_extras.hxx"
 #include "bout/boutexception.hxx"
 #include "gtest/gtest.h"
@@ -7,7 +5,6 @@
 #include <fmt/ranges.h>
 
 #include <string>
-#include <string_view>
 #include <vector>
 
 TEST(BoutExceptionTest, ThrowCorrect) {
@@ -19,13 +16,13 @@ TEST(BoutExceptionTest, What) {
   try {
     throw BoutException(test_message);
   } catch (const BoutException& e) {
-    EXPECT_EQ(e.what(), test_message);
+    EXPECT_TRUE(IsSubString(e.what(), test_message));
   }
   try {
     throw BoutException("this is {}", "second");
   } catch (const BoutException& e) {
     std::string message(e.what());
-    EXPECT_EQ(message, "this is second");
+    EXPECT_TRUE(IsSubString(message, "this is second"));
   }
 }
 
@@ -34,25 +31,19 @@ TEST(BoutExceptionTest, GetBacktrace) {
   try {
     throw BoutException(test_message);
   } catch (const BoutException& e) {
-    std::string expected_1{"[bt] #1"};
-    std::string expected_2{"serial_tests"};
-#if BOUT_USE_BACKTRACE
+    std::string expected_1{"#2"};
+    std::string expected_2{"bout_test_main"};
     // Should be able to find something about backtrace
-    EXPECT_TRUE(IsSubString(e.getBacktrace(), expected_1));
-    EXPECT_TRUE(IsSubString(e.getBacktrace(), expected_2));
-#else
-    // Should *not* be able to find something about backtrace
-    EXPECT_FALSE(IsSubString(e.getBacktrace(), expected_1));
-    EXPECT_FALSE(IsSubString(e.getBacktrace(), expected_2));
-#endif
+    EXPECT_TRUE(IsSubString(e.what(), expected_1));
+    EXPECT_TRUE(IsSubString(e.what(), expected_2));
   }
 }
 
 TEST(BoutExceptionTest, FmtJoin) {
   const std::vector things = {1, 2, 3, 4};
-  constexpr std::string_view expected = "list: 1, 2, 3, 4";
+  const std::string expected = "list: 1, 2, 3, 4";
   const BoutException exception{"list: {}", fmt::join(things, ", ")};
-  EXPECT_EQ(exception.what(), expected);
+  EXPECT_TRUE(IsSubString(std::string{exception.what()}, expected));
 }
 
 TEST(BoutRhsFailTest, ThrowCorrect) {

From 199ba5ae60a58c63722a81b8e0a51bdf0abdfbbd Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 5 Dec 2025 14:35:13 +0000
Subject: [PATCH 0401/1827] Add some control over `BoutException` backtraces

Always generating the backtraces can slow the unit tests down by a factor x2-3

An alternative might be to store the `cpptrace:stacktrace` and only convert to
string in `BoutException::what()`
---
 include/bout/boutexception.hxx        |  5 +++++
 src/sys/boutexception.cxx             | 11 +++++++++--
 tests/unit/bout_test_main.cxx         |  5 +++++
 tests/unit/sys/test_boutexception.cxx | 14 ++++++++++----
 tests/unit/test_extras.cxx            |  3 ++-
 5 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx
index 3d8a9cd71d..565eb6b46d 100644
--- a/include/bout/boutexception.hxx
+++ b/include/bout/boutexception.hxx
@@ -32,8 +32,13 @@ public:
   /// backtrace (if available)
   std::string getBacktrace() const;
 
+  static void enableBacktrace() { show_backtrace = true; }
+  static void disableBacktrace() { show_backtrace = false; }
+
 private:
   std::string message;
+
+  static bool show_backtrace;
 };
 
 class BoutRhsFail : public BoutException {
diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index edf7509077..f08679de83 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -19,6 +19,8 @@ namespace {
 const std::string header{"====== Exception thrown ======\n"};
 }
 
+bool BoutException::show_backtrace = true;
+
 void BoutParallelThrowRhsFail(int status, const char* message) {
   int allstatus = 0;
   MPI_Allreduce(&status, &allstatus, 1, MPI_INT, MPI_LOR, BoutComm::get());
@@ -29,8 +31,13 @@ void BoutParallelThrowRhsFail(int status, const char* message) {
 }
 
 BoutException::BoutException(std::string msg) : message(std::move(msg)) {
-  const char* show_backtrace = std::getenv("BOUT_SHOW_BACKTRACE");
-  if (show_backtrace == nullptr or std::string{show_backtrace} != "0") {
+  const char* show_backtrace_env_var = std::getenv("BOUT_SHOW_BACKTRACE");
+  const auto should_show_backtrace =
+      show_backtrace
+      and ((show_backtrace_env_var == nullptr)
+           or (show_backtrace_env_var != nullptr
+               and std::string{show_backtrace_env_var} != "0"));
+  if (should_show_backtrace) {
     message = getBacktrace();
   }
 }
diff --git a/tests/unit/bout_test_main.cxx b/tests/unit/bout_test_main.cxx
index 999b5b0dc3..09aeeed0ea 100644
--- a/tests/unit/bout_test_main.cxx
+++ b/tests/unit/bout_test_main.cxx
@@ -1,6 +1,7 @@
 #include <cstdio>
 
 #include "bout/array.hxx"
+#include "bout/boutexception.hxx"
 #include "bout/fft.hxx"
 #include "bout/globalindexer.hxx"
 #include "bout/output.hxx"
@@ -22,6 +23,10 @@ GTEST_API_ int main(int argc, char** argv) {
   printf("Running main() from bout_test_main.cxx\n");
   testing::InitGoogleTest(&argc, argv);
 
+  // We throw and catch a bunch of exceptions as part of running the tests, and
+  // the backtrace generation can _significantly_ slow them down
+  BoutException::disableBacktrace();
+
   // Explicitly setup and teardown PETSc to avoid reentry problems
   // with certain MPI implementations (see #1916 for details)
   output.disable();
diff --git a/tests/unit/sys/test_boutexception.cxx b/tests/unit/sys/test_boutexception.cxx
index 5eb2c4d719..1ba12ef943 100644
--- a/tests/unit/sys/test_boutexception.cxx
+++ b/tests/unit/sys/test_boutexception.cxx
@@ -7,11 +7,17 @@
 #include <string>
 #include <vector>
 
-TEST(BoutExceptionTest, ThrowCorrect) {
+// NOLINTNEXTLINE(cppcoreguidelines-special-member-functions)
+struct BoutExceptionTest : public ::testing::Test {
+  BoutExceptionTest() { BoutException::enableBacktrace(); }
+  ~BoutExceptionTest() override { BoutException::disableBacktrace(); }
+};
+
+TEST_F(BoutExceptionTest, ThrowCorrect) {
   EXPECT_THROW(throw BoutException("test"), BoutException);
 }
 
-TEST(BoutExceptionTest, What) {
+TEST_F(BoutExceptionTest, What) {
   std::string test_message{"Test message"};
   try {
     throw BoutException(test_message);
@@ -26,7 +32,7 @@ TEST(BoutExceptionTest, What) {
   }
 }
 
-TEST(BoutExceptionTest, GetBacktrace) {
+TEST_F(BoutExceptionTest, GetBacktrace) {
   std::string test_message{"Test message"};
   try {
     throw BoutException(test_message);
@@ -39,7 +45,7 @@ TEST(BoutExceptionTest, GetBacktrace) {
   }
 }
 
-TEST(BoutExceptionTest, FmtJoin) {
+TEST_F(BoutExceptionTest, FmtJoin) {
   const std::vector things = {1, 2, 3, 4};
   const std::string expected = "list: 1, 2, 3, 4";
   const BoutException exception{"list: {}", fmt::join(things, ", ")};
diff --git a/tests/unit/test_extras.cxx b/tests/unit/test_extras.cxx
index 332a53089b..b1caf038d3 100644
--- a/tests/unit/test_extras.cxx
+++ b/tests/unit/test_extras.cxx
@@ -14,7 +14,8 @@ ::testing::AssertionResult IsSubString(const std::string& str,
   if (str.find(substring) != std::string::npos) {
     return ::testing::AssertionSuccess();
   } else {
-    return ::testing::AssertionFailure() << '"' << substring << "\" not found in " << str;
+    return ::testing::AssertionFailure()
+           << '"' << substring << "\" not found in \"" << str << '"';
   }
 }
 

From dc865d338a9b62f2406375410426723dc009147c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 5 Dec 2025 15:01:05 +0000
Subject: [PATCH 0402/1827] Try to ensure `build_defines` is included where
 it's used

---
 include/bout/coordinates.hxx                      | 9 +++++----
 include/bout/fv_ops.hxx                           | 4 ++--
 include/bout/interpolation_xz.hxx                 | 1 +
 include/bout/output.hxx                           | 3 ++-
 src/invert/laplace/invert_laplace.cxx             | 1 +
 src/mesh/boundary_standard.cxx                    | 1 +
 src/mesh/coordinates.cxx                          | 1 +
 src/mesh/coordinates_accessor.cxx                 | 1 +
 src/sys/derivs.cxx                                | 1 +
 tests/unit/field/test_vector2d.cxx                | 6 ++++--
 tests/unit/include/bout/test_single_index_ops.cxx | 1 +
 tests/unit/mesh/data/test_gridfromoptions.cxx     | 2 +-
 tests/unit/solver/test_solver.cxx                 | 1 +
 tests/unit/sys/test_output.cxx                    | 4 ++--
 14 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index d7c80ed8bc..e7ead42ee5 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -33,10 +33,11 @@
 #ifndef BOUT_COORDINATES_H
 #define BOUT_COORDINATES_H
 
-#include "bout/bout_types.hxx"
-#include "bout/field2d.hxx"
-#include "bout/field3d.hxx"
-#include "bout/paralleltransform.hxx"
+#include <bout/bout_types.hxx>
+#include <bout/build_defines.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/paralleltransform.hxx>
 
 class Mesh;
 
diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 94007a57a2..ce98e03008 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -5,11 +5,11 @@
 #ifndef BOUT_FV_OPS_H
 #define BOUT_FV_OPS_H
 
+#include "bout/build_defines.hxx"
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
-#include "bout/vector2d.hxx"
-
 #include "bout/utils.hxx"
+#include "bout/vector2d.hxx"
 #include <bout/mesh.hxx>
 
 namespace FV {
diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 6c7419f7e4..79e959b3af 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -24,6 +24,7 @@
 #ifndef BOUT_INTERP_XZ_H
 #define BOUT_INTERP_XZ_H
 
+#include "bout/build_defines.hxx"
 #include "bout/mask.hxx"
 
 #define USE_NEW_WEIGHTS 1
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index 823e359753..34b4f19376 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -29,12 +29,13 @@ class Output;
 #ifndef BOUT_OUTPUT_H
 #define BOUT_OUTPUT_H
 
-#include "bout/multiostream.hxx"
 #include <fstream>
 #include <iostream>
 #include <string>
 
 #include "bout/assert.hxx"
+#include "bout/build_defines.hxx"
+#include "bout/multiostream.hxx"
 #include "bout/sys/gettext.hxx" // IWYU pragma: keep for gettext _() macro
 #include "bout/unused.hxx"
 
diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx
index 4032499781..7a8af20fbd 100644
--- a/src/invert/laplace/invert_laplace.cxx
+++ b/src/invert/laplace/invert_laplace.cxx
@@ -33,6 +33,7 @@
 
 #include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
 #include <bout/globals.hxx>
 #include <bout/invert_laplace.hxx>
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 8f2c7df5ec..5508f8db71 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -1,5 +1,6 @@
 #include <bout/boundary_standard.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 3dfee6a553..58d54f826e 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -5,6 +5,7 @@
  **************************************************************************/
 
 #include <bout/assert.hxx>
+#include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
 #include <bout/coordinates.hxx>
 #include <bout/msg_stack.hxx>
diff --git a/src/mesh/coordinates_accessor.cxx b/src/mesh/coordinates_accessor.cxx
index aff546c2b0..0ce4b664b5 100644
--- a/src/mesh/coordinates_accessor.cxx
+++ b/src/mesh/coordinates_accessor.cxx
@@ -1,4 +1,5 @@
 #include "bout/coordinates_accessor.hxx"
+#include <bout/build_defines.hxx>
 
 #include "bout/mesh.hxx"
 
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index ee9bcbcc2c..ed036fffd4 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -38,6 +38,7 @@
  *
  **************************************************************************/
 
+#include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
diff --git a/tests/unit/field/test_vector2d.cxx b/tests/unit/field/test_vector2d.cxx
index df438c3dbf..de662c7df8 100644
--- a/tests/unit/field/test_vector2d.cxx
+++ b/tests/unit/field/test_vector2d.cxx
@@ -1,8 +1,8 @@
-#include "gtest/gtest.h"
+#include <bout/build_defines.hxx>
 
-#include "bout/boutexception.hxx"
 #if not(BOUT_USE_METRIC_3D)
 #include "test_extras.hxx"
+#include "bout/boutexception.hxx"
 #include "bout/mesh.hxx"
 #include "bout/mpi_wrapper.hxx"
 #include "bout/output.hxx"
@@ -11,6 +11,8 @@
 
 #include "fake_mesh.hxx"
 
+#include "gtest/gtest.h"
+
 // The unit tests use the global mesh
 using namespace bout::globals;
 
diff --git a/tests/unit/include/bout/test_single_index_ops.cxx b/tests/unit/include/bout/test_single_index_ops.cxx
index 4359d1d282..a809ae3683 100644
--- a/tests/unit/include/bout/test_single_index_ops.cxx
+++ b/tests/unit/include/bout/test_single_index_ops.cxx
@@ -2,6 +2,7 @@
 
 #include "test_extras.hxx"
 
+#include "bout/build_defines.hxx"
 #include "bout/derivs.hxx"
 #include "bout/difops.hxx"
 #include "bout/single_index_ops.hxx"
diff --git a/tests/unit/mesh/data/test_gridfromoptions.cxx b/tests/unit/mesh/data/test_gridfromoptions.cxx
index 8d3dbfebdf..b821d2e225 100644
--- a/tests/unit/mesh/data/test_gridfromoptions.cxx
+++ b/tests/unit/mesh/data/test_gridfromoptions.cxx
@@ -1,13 +1,13 @@
 #include "gtest/gtest.h"
 
 #include "test_extras.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/constants.hxx"
 #include "bout/griddata.hxx"
 #include "bout/mesh.hxx"
 #include "bout/options.hxx"
 #include "bout/output.hxx"
 
-#include <numeric>
 #include <string>
 #include <vector>
 
diff --git a/tests/unit/solver/test_solver.cxx b/tests/unit/solver/test_solver.cxx
index 2e29fd90bc..e9a612103c 100644
--- a/tests/unit/solver/test_solver.cxx
+++ b/tests/unit/solver/test_solver.cxx
@@ -4,6 +4,7 @@
 #include "test_extras.hxx"
 #include "test_fakesolver.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/physicsmodel.hxx"
diff --git a/tests/unit/sys/test_output.cxx b/tests/unit/sys/test_output.cxx
index 959823ede3..2f13df9cb7 100644
--- a/tests/unit/sys/test_output.cxx
+++ b/tests/unit/sys/test_output.cxx
@@ -1,7 +1,7 @@
 #include "test_tmpfiles.hxx"
-#include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/output.hxx"
-#include "bout/output_bout_types.hxx"
+#include "bout/output_bout_types.hxx" // IWYU pragma: keep
 #include "gtest/gtest.h"
 
 #include <fmt/ranges.h>

From e0710f8b88ad3ed4cdfadb731e446cd4dcaac75d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 16 Dec 2025 15:43:49 +0000
Subject: [PATCH 0403/1827] Try to make backtrace unit test more portable

---
 tests/unit/sys/test_boutexception.cxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/unit/sys/test_boutexception.cxx b/tests/unit/sys/test_boutexception.cxx
index 1ba12ef943..7cde2f57a1 100644
--- a/tests/unit/sys/test_boutexception.cxx
+++ b/tests/unit/sys/test_boutexception.cxx
@@ -37,11 +37,11 @@ TEST_F(BoutExceptionTest, GetBacktrace) {
   try {
     throw BoutException(test_message);
   } catch (const BoutException& e) {
-    std::string expected_1{"#2"};
-    std::string expected_2{"bout_test_main"};
     // Should be able to find something about backtrace
-    EXPECT_TRUE(IsSubString(e.what(), expected_1));
-    EXPECT_TRUE(IsSubString(e.what(), expected_2));
+    EXPECT_TRUE(IsSubString(e.what(), "#2"));
+    // We should be able to see either the main source file or the executable name
+    EXPECT_TRUE(IsSubString(e.what(), "bout_test_main")
+                || IsSubString(e.what(), "serial_tests"));
   }
 }
 

From 9dd86c53443c8a6253cebab4fbff65bbf03ecebd Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 11:52:10 +0000
Subject: [PATCH 0404/1827] cmake: Fix some issues with building with cpptrace

- Add paths to `FetchContent` dirs in config file
- Switch to custom versions of cpptrace/libdward-lite
  - Includes some cmake fixes in both projects
---
 bout++Config.cmake.in           | 3 +++
 cmake/SetupBOUTThirdParty.cmake | 6 +++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/bout++Config.cmake.in b/bout++Config.cmake.in
index a82479f41c..a8cf041901 100644
--- a/bout++Config.cmake.in
+++ b/bout++Config.cmake.in
@@ -112,6 +112,9 @@ if(EXISTS "@cpptrace_ROOT@")
   set(cpptrace_ROOT "@cpptrace_ROOT@")
 elseif(EXISTS "@cpptrace_BINARY_DIR@")
   list(APPEND CMAKE_PREFIX_PATH "@cpptrace_BINARY_DIR@")
+  list(APPEND CMAKE_PREFIX_PATH "@cpptrace_BINARY_DIR@/cmake")
+  list(APPEND CMAKE_PREFIX_PATH "@libdwarf_BINARY_DIR@/src/lib/libdwarf")
+  list(APPEND CMAKE_PREFIX_PATH "@zstd_BINARY_DIR@")
 endif()
 
 if(@BOUT_USE_SYSTEM_MPARK_VARIANT@)
diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 2249fb3468..2c5b9a1cfb 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -374,11 +374,11 @@ option(BOUT_DOWNLOAD_CPPTRACE "Download cpptrace for backtrace support" ON)
 if (BOUT_DOWNLOAD_CPPTRACE)
   include(FetchContent)
   set(CPPTRACE_LIBDWARF_REPO "https://github.com/ZedThree/libdwarf-lite.git" CACHE STRING "" FORCE)
-  set(CPPTRACE_LIBDWARF_TAG "5f15f145d96278a64440f3c700f475233b4fd0e7" CACHE STRING "" FORCE)
+  set(CPPTRACE_LIBDWARF_TAG "ebe10a39afd56b8247de633bfe17666ad50ab95e" CACHE STRING "" FORCE)
   FetchContent_Declare(
     cpptrace
-    GIT_REPOSITORY https://github.com/jeremy-rifkin/cpptrace.git
-    GIT_TAG        v1.0.4
+    GIT_REPOSITORY https://github.com/ZedThree/cpptrace.git
+    GIT_TAG        "027f9aee2d34dbe1c98f26224e1fbe1654cb4aae"
   )
   FetchContent_MakeAvailable(cpptrace)
 else()

From 00995ea544670a409f584015ab4e07485683b86b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 12:03:50 +0000
Subject: [PATCH 0405/1827] Prettify symbols in cpptrace output

---
 src/sys/boutexception.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index f08679de83..5bcec420f3 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -54,13 +54,14 @@ std::string BoutException::getBacktrace() const {
 
   const auto colours = isatty(stdout_fileno) || isatty(stderr_fileno)
                            ? formatter::color_mode::always
-                           : formatter ::color_mode::none;
+                           : formatter::color_mode::none;
 
   auto formatter = cpptrace::formatter{}
                        .addresses(formatter::address_mode::none)
                        .break_before_filename(true)
                        .colors(colours)
                        .snippets(true)
+                       .symbols(formatter::symbol_mode::pretty)
                        .filter([](const stacktrace_frame& frame) {
                          return frame.symbol.find("BoutException::") == std::string::npos;
                        })

From 3fc530d5c45e719546c929a831d1f6daf8eabbce Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 12:11:03 +0000
Subject: [PATCH 0406/1827] Filter out pre-main functions from stacktrace

---
 src/sys/boutexception.cxx | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index 5bcec420f3..c91bb186bf 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -63,7 +63,12 @@ std::string BoutException::getBacktrace() const {
                        .snippets(true)
                        .symbols(formatter::symbol_mode::pretty)
                        .filter([](const stacktrace_frame& frame) {
-                         return frame.symbol.find("BoutException::") == std::string::npos;
+                         return (
+                             // Don't include our exception machinery
+                             (frame.symbol.find("BoutException::") == std::string::npos)
+                             // Don't include pre-main functions
+                             and (frame.symbol.find("__libc_start") == std::string::npos)
+                             and (frame.symbol != "_start"));
                        })
                        .filtered_frame_placeholders(false);
 

From 5f77485d249c17f76b453ee7fe4cb08aea423cdb Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 12:12:48 +0000
Subject: [PATCH 0407/1827] Include filtered placeholders

---
 src/sys/boutexception.cxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index c91bb186bf..8509dc40ba 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -69,8 +69,7 @@ std::string BoutException::getBacktrace() const {
                              // Don't include pre-main functions
                              and (frame.symbol.find("__libc_start") == std::string::npos)
                              and (frame.symbol != "_start"));
-                       })
-                       .filtered_frame_placeholders(false);
+                       });
 
   const std::string backtrace_message = formatter.format(generate_trace());
 

From cbc4cf20bb3effb66a1656a9fea9424a5e228350 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 15:53:29 +0000
Subject: [PATCH 0408/1827] Remove `AUTO_TRACE` macro

---
 include/bout/bout_enum_class.hxx              |  4 +-
 include/bout/deriv_store.hxx                  | 39 +++++++------------
 include/bout/field.hxx                        | 11 +-----
 include/bout/hypre_interface.hxx              |  6 +--
 include/bout/index_derivs.hxx                 |  6 +--
 include/bout/index_derivs_interface.hxx       | 31 +++++++--------
 include/bout/interpolation.hxx                |  2 +-
 include/bout/invertable_operator.hxx          | 13 +++----
 include/bout/mesh.hxx                         |  6 +--
 include/bout/msg_stack.hxx                    | 31 ---------------
 include/bout/petsc_interface.hxx              |  6 +--
 include/bout/scorepwrapper.hxx                | 13 ++++++-
 include/bout/sys/timer.hxx                    |  1 -
 manual/doxygen/Doxyfile                       |  1 -
 manual/doxygen/Doxyfile_readthedocs           |  1 -
 manual/sphinx/developer_docs/debugging.rst    | 14 ++-----
 src/bout++.cxx                                |  3 --
 src/field/field_data.cxx                      |  7 +---
 src/field/field_factory.cxx                   |  3 --
 src/field/initialprofiles.cxx                 |  4 --
 src/field/vecops.cxx                          |  4 +-
 .../laplace/impls/petsc3damg/petsc3damg.cxx   |  1 -
 src/mesh/data/gridfromfile.cxx                |  1 -
 src/mesh/index_derivs.cxx                     | 12 +++---
 src/mesh/parallel/shiftedmetricinterp.cxx     |  1 -
 src/physics/smoothing.cxx                     |  2 +-
 .../impls/adams_bashforth/adams_bashforth.cxx | 31 +++++++--------
 src/solver/impls/split-rk/split-rk.cxx        |  2 -
 src/solver/solver.cxx                         |  4 +-
 src/sys/bout_types.cxx                        | 26 ++++++-------
 src/sys/msg_stack.cxx                         |  2 +-
 .../integrated/test-backtrace/boutexcept.cxx  | 15 ++-----
 32 files changed, 107 insertions(+), 196 deletions(-)

diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index 585e5b020e..07140220a4 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -70,7 +70,7 @@
   enum class enumname { __VA_ARGS__ };                                         \
                                                                                \
   inline std::string toString(enumname e) {                                    \
-    AUTO_TRACE();                                                              \
+                                                                               \
     const static std::map<enumname, std::string> toString_map = {              \
         BOUT_ENUM_CLASS_MAP_ARGS(BOUT_ENUM_CLASS_STR, enumname, __VA_ARGS__)}; \
     auto found = toString_map.find(e);                                         \
@@ -81,7 +81,7 @@
   }                                                                            \
                                                                                \
   inline enumname BOUT_MAKE_FROMSTRING_NAME(enumname)(const std::string& s) {  \
-    AUTO_TRACE();                                                              \
+                                                                               \
     const static std::map<std::string, enumname> fromString_map = {            \
         BOUT_ENUM_CLASS_MAP_ARGS(BOUT_STR_ENUM_CLASS, enumname, __VA_ARGS__)}; \
     auto found = fromString_map.find(s);                                       \
diff --git a/include/bout/deriv_store.hxx b/include/bout/deriv_store.hxx
index 6dc44c76ad..866ac558e5 100644
--- a/include/bout/deriv_store.hxx
+++ b/include/bout/deriv_store.hxx
@@ -75,21 +75,14 @@ struct DerivativeStore {
   }
 
   /// Report if store has any registered methods
-  bool isEmpty() const {
-    AUTO_TRACE();
-    return registeredMethods.empty();
-  };
+  bool isEmpty() const { return registeredMethods.empty(); };
 
   /// Report if store has any registered methods for specific type determined by key
-  bool isEmpty(std::size_t key) const {
-    AUTO_TRACE();
-    return registeredMethods.count(key) == 0;
-  }
+  bool isEmpty(std::size_t key) const { return registeredMethods.count(key) == 0; }
 
   /// Report if store has any registered methods for specific type
   bool isEmpty(DERIV derivType, DIRECTION direction,
                STAGGER stagger = STAGGER::None) const {
-    AUTO_TRACE();
 
     // Get the key
     auto key = getKey(direction, stagger, toString(derivType));
@@ -100,7 +93,6 @@ struct DerivativeStore {
   /// specified derivative type, direction and stagger.
   std::set<std::string> getAvailableMethods(DERIV derivType, DIRECTION direction,
                                             STAGGER stagger = STAGGER::None) const {
-    AUTO_TRACE();
 
     // Get the key
     auto key = getKey(direction, stagger, toString(derivType));
@@ -115,7 +107,6 @@ struct DerivativeStore {
   /// specified derivative type, direction and stagger.
   void listAvailableMethods(DERIV derivType, DIRECTION direction,
                             STAGGER stagger = STAGGER::None) const {
-    AUTO_TRACE();
 
     // Introductory information
     output_info << "Available methods for derivative type '";
@@ -134,7 +125,7 @@ struct DerivativeStore {
   /// depends on the derivType input.
   void registerDerivative(standardFunc func, DERIV derivType, DIRECTION direction,
                           STAGGER stagger, std::string methodName) {
-    AUTO_TRACE();
+
     const auto key = getKey(direction, stagger, methodName);
 
     switch (derivType) {
@@ -176,7 +167,7 @@ struct DerivativeStore {
   /// depends on the derivType input.
   void registerDerivative(upwindFunc func, DERIV derivType, DIRECTION direction,
                           STAGGER stagger, std::string methodName) {
-    AUTO_TRACE();
+
     const auto key = getKey(direction, stagger, methodName);
 
     switch (derivType) {
@@ -210,14 +201,14 @@ struct DerivativeStore {
   template <typename Direction, typename Stagger, typename Method>
   void registerDerivative(standardFunc func, Direction direction, Stagger stagger,
                           Method method) {
-    AUTO_TRACE();
+
     registerDerivative(func, method.meta.derivType, direction.lookup(), stagger.lookup(),
                        method.meta.key);
   }
   template <typename Direction, typename Stagger, typename Method>
   void registerDerivative(upwindFunc func, Direction direction, Stagger stagger,
                           Method method) {
-    AUTO_TRACE();
+
     registerDerivative(func, method.meta.derivType, direction.lookup(), stagger.lookup(),
                        method.meta.key);
   }
@@ -231,7 +222,6 @@ struct DerivativeStore {
                                      STAGGER stagger = STAGGER::None,
                                      DERIV derivType = DERIV::Standard) const {
 
-    AUTO_TRACE();
     const auto realName = nameLookup(
         name, defaultMethods.at(getKey(direction, stagger, toString(derivType))));
     const auto key = getKey(direction, stagger, realName);
@@ -262,20 +252,20 @@ struct DerivativeStore {
 
   standardFunc getStandard2ndDerivative(std::string name, DIRECTION direction,
                                         STAGGER stagger = STAGGER::None) const {
-    AUTO_TRACE();
+
     return getStandardDerivative(name, direction, stagger, DERIV::StandardSecond);
   };
 
   standardFunc getStandard4thDerivative(std::string name, DIRECTION direction,
                                         STAGGER stagger = STAGGER::None) const {
-    AUTO_TRACE();
+
     return getStandardDerivative(name, direction, stagger, DERIV::StandardFourth);
   };
 
   flowFunc getFlowDerivative(std::string name, DIRECTION direction,
                              STAGGER stagger = STAGGER::None,
                              DERIV derivType = DERIV::Upwind) const {
-    AUTO_TRACE();
+
     const auto realName = nameLookup(
         name, defaultMethods.at(getKey(direction, stagger, toString(derivType))));
     const auto key = getKey(direction, stagger, realName);
@@ -305,18 +295,17 @@ struct DerivativeStore {
 
   upwindFunc getUpwindDerivative(std::string name, DIRECTION direction,
                                  STAGGER stagger = STAGGER::None) const {
-    AUTO_TRACE();
+
     return getFlowDerivative(name, direction, stagger, DERIV::Upwind);
   };
 
   fluxFunc getFluxDerivative(std::string name, DIRECTION direction,
                              STAGGER stagger = STAGGER::None) const {
-    AUTO_TRACE();
+
     return getFlowDerivative(name, direction, stagger, DERIV::Flux);
   };
 
   void initialise(Options* options) {
-    AUTO_TRACE();
 
     // To replicate the existing behaviour we first search for a section called
     //"dd?" and if the option isn't in there we search a section called "diff"
@@ -490,7 +479,7 @@ private:
 
   std::string getMethodName(std::string name, DIRECTION direction,
                             STAGGER stagger = STAGGER::None) const {
-    AUTO_TRACE();
+
     return name + " (" + toString(direction) + ", " + toString(stagger) + ")";
   };
 
@@ -506,7 +495,7 @@ private:
   /// methods with the same function interface in the same map, which
   /// might be nice.
   std::size_t getKey(DIRECTION direction, STAGGER stagger, std::string key) const {
-    AUTO_TRACE();
+
     // Note this key is indepedent of the field type (and hence the
     // key is the same for 3D/2D fields) as we have to use different
     // maps to store the different field types as the signature is
@@ -524,7 +513,7 @@ private:
   /// that can be used to account for run-time choices
   template <typename Direction, typename Stagger, typename Method>
   std::size_t getKey() const {
-    AUTO_TRACE();
+
     // Note this key is indepedent of the field type (and hence the
     // key is the same for 3D/2D fields) as we have to use different
     // maps to store the different field types as the signature is
diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 61edff6723..35ce42716d 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -239,7 +239,6 @@ namespace bout {
 template <typename T>
 inline void checkFinite(const T& f, const std::string& name = "field",
                         const std::string& rgn = "RGN_ALL") {
-  AUTO_TRACE();
 
   if (!f.isAllocated()) {
     throw BoutException("{:s} is not allocated", name);
@@ -263,7 +262,6 @@ inline void checkFinite(const T& f, const std::string& name = "field",
 template <typename T>
 inline void checkPositive(const T& f, const std::string& name = "field",
                           const std::string& rgn = "RGN_ALL") {
-  AUTO_TRACE();
 
   if (!f.isAllocated()) {
     throw BoutException("{:s} is not allocated", name);
@@ -307,7 +305,6 @@ inline T fromFieldAligned(const T& f, const std::string& region = "RGN_ALL") {
 template <typename T, typename = bout::utils::EnableIfField<T>>
 inline BoutReal min(const T& f, bool allpe = false,
                     const std::string& rgn = "RGN_NOBNDRY") {
-  AUTO_TRACE();
 
   checkData(f);
 
@@ -392,7 +389,6 @@ inline BoutReal getUniform(const T& f, [[maybe_unused]] bool allpe = false,
 template <typename T, typename = bout::utils::EnableIfField<T>>
 inline BoutReal max(const T& f, bool allpe = false,
                     const std::string& rgn = "RGN_NOBNDRY") {
-  AUTO_TRACE();
 
   checkData(f);
 
@@ -426,7 +422,6 @@ inline BoutReal max(const T& f, bool allpe = false,
 template <typename T, typename = bout::utils::EnableIfField<T>>
 inline BoutReal mean(const T& f, bool allpe = false,
                      const std::string& rgn = "RGN_NOBNDRY") {
-  AUTO_TRACE();
 
   checkData(f);
 
@@ -457,7 +452,6 @@ inline BoutReal mean(const T& f, bool allpe = false,
 /// If CHECK >= 3 then the result will be checked for non-finite numbers
 template <typename T, typename = bout::utils::EnableIfField<T>>
 T pow(const T& lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
-  AUTO_TRACE();
 
   ASSERT1(areFieldsCompatible(lhs, rhs));
 
@@ -471,7 +465,6 @@ T pow(const T& lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
 
 template <typename T, typename = bout::utils::EnableIfField<T>>
 T pow(const T& lhs, BoutReal rhs, const std::string& rgn = "RGN_ALL") {
-  AUTO_TRACE();
 
   // Check if the inputs are allocated
   checkData(lhs);
@@ -487,7 +480,6 @@ T pow(const T& lhs, BoutReal rhs, const std::string& rgn = "RGN_ALL") {
 
 template <typename T, typename = bout::utils::EnableIfField<T>>
 T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
-  AUTO_TRACE();
 
   // Check if the inputs are allocated
   checkData(lhs);
@@ -524,7 +516,7 @@ T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
 #define FIELD_FUNC(name, func)                                     \
   template <typename T, typename = bout::utils::EnableIfField<T>>  \
   inline T name(const T& f, const std::string& rgn = "RGN_ALL") {  \
-    AUTO_TRACE();                                                  \
+                                                                   \
     /* Check if the input is allocated */                          \
     checkData(f);                                                  \
     /* Define and allocate the output result */                    \
@@ -632,7 +624,6 @@ FIELD_FUNC(tanh, ::tanh)
 /// default (can be changed using the \p rgn argument
 template <typename T, typename = bout::utils::EnableIfField<T>>
 inline bool finite(const T& f, const std::string& rgn = "RGN_ALL") {
-  AUTO_TRACE();
 
   if (!f.isAllocated()) {
     return false;
diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index ae392de4f3..65d8875a9a 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -444,19 +444,19 @@ public:
       value = matrix->getVal(row, column);
     }
     Element& operator=(const Element& other) {
-      AUTO_TRACE();
+
       ASSERT3(finite(static_cast<BoutReal>(other)));
       return *this = static_cast<BoutReal>(other);
     }
     Element& operator=(BoutReal value_) {
-      AUTO_TRACE();
+
       ASSERT3(finite(value_));
       value = value_;
       setValues(value);
       return *this;
     }
     Element& operator+=(BoutReal value_) {
-      AUTO_TRACE();
+
       ASSERT3(finite(value_));
       auto column_position = std::find(cbegin(positions), cend(positions), column);
       if (column_position != cend(positions)) {
diff --git a/include/bout/index_derivs.hxx b/include/bout/index_derivs.hxx
index 456f98f8c2..7c2be52ded 100644
--- a/include/bout/index_derivs.hxx
+++ b/include/bout/index_derivs.hxx
@@ -84,7 +84,7 @@ class DerivativeType {
 public:
   template <DIRECTION direction, STAGGER stagger, int nGuards, typename T>
   void standard(const T& var, T& result, const std::string& region) const {
-    AUTO_TRACE();
+
     ASSERT2(meta.derivType == DERIV::Standard || meta.derivType == DERIV::StandardSecond
             || meta.derivType == DERIV::StandardFourth)
     ASSERT2(var.getMesh()->getNguard(direction) >= nGuards);
@@ -98,7 +98,7 @@ public:
   template <DIRECTION direction, STAGGER stagger, int nGuards, typename T>
   void upwindOrFlux(const T& vel, const T& var, T& result,
                     const std::string& region) const {
-    AUTO_TRACE();
+
     ASSERT2(meta.derivType == DERIV::Upwind || meta.derivType == DERIV::Flux)
     ASSERT2(var.getMesh()->getNguard(direction) >= nGuards);
 
@@ -133,7 +133,7 @@ struct registerMethod {
   template <typename Direction, typename Stagger, typename FieldTypeContainer,
             typename Method>
   void operator()(Direction, Stagger, FieldTypeContainer, Method) {
-    AUTO_TRACE();
+
     using namespace std::placeholders;
 
     // Now we want to get the actual field type out of the TypeContainer
diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx
index 8f7e41a68e..242492c3f8 100644
--- a/include/bout/index_derivs_interface.hxx
+++ b/include/bout/index_derivs_interface.hxx
@@ -45,7 +45,6 @@ namespace index {
 template <typename T, DIRECTION direction, DERIV derivType>
 T flowDerivative(const T& vel, const T& f, CELL_LOC outloc, const std::string& method,
                  const std::string& region) {
-  AUTO_TRACE();
 
   // Checks
   static_assert(bout::utils::is_Field2D_v<T> || bout::utils::is_Field3D_v<T>,
@@ -110,7 +109,6 @@ T flowDerivative(const T& vel, const T& f, CELL_LOC outloc, const std::string& m
 template <typename T, DIRECTION direction, DERIV derivType>
 T standardDerivative(const T& f, CELL_LOC outloc, const std::string& method,
                      const std::string& region) {
-  AUTO_TRACE();
 
   // Checks
   static_assert(bout::utils::is_Field2D_v<T> || bout::utils::is_Field3D_v<T>,
@@ -174,14 +172,14 @@ T standardDerivative(const T& f, CELL_LOC outloc, const std::string& method,
 template <typename T>
 T DDX(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
       const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return standardDerivative<T, DIRECTION::X, DERIV::Standard>(f, outloc, method, region);
 }
 
 template <typename T>
 T D2DX2(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
         const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return standardDerivative<T, DIRECTION::X, DERIV::StandardSecond>(f, outloc, method,
                                                                     region);
 }
@@ -189,7 +187,7 @@ T D2DX2(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method =
 template <typename T>
 T D4DX4(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
         const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return standardDerivative<T, DIRECTION::X, DERIV::StandardFourth>(f, outloc, method,
                                                                     region);
 }
@@ -199,7 +197,7 @@ T D4DX4(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method =
 template <typename T>
 T DDY(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
       const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   if (f.hasParallelSlices()) {
     ASSERT1(f.getDirectionY() == YDirectionType::Standard);
     return standardDerivative<T, DIRECTION::YOrthogonal, DERIV::Standard>(f, outloc,
@@ -216,7 +214,7 @@ T DDY(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "D
 template <typename T>
 T D2DY2(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
         const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   if (f.hasParallelSlices()) {
     ASSERT1(f.getDirectionY() == YDirectionType::Standard);
     return standardDerivative<T, DIRECTION::YOrthogonal, DERIV::StandardSecond>(
@@ -233,7 +231,7 @@ T D2DY2(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method =
 template <typename T>
 T D4DY4(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
         const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   if (f.hasParallelSlices()) {
     ASSERT1(f.getDirectionY() == YDirectionType::Standard);
     return standardDerivative<T, DIRECTION::YOrthogonal, DERIV::StandardFourth>(
@@ -251,14 +249,14 @@ T D4DY4(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method =
 template <typename T>
 T DDZ(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
       const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return standardDerivative<T, DIRECTION::Z, DERIV::Standard>(f, outloc, method, region);
 }
 
 template <typename T>
 T D2DZ2(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
         const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return standardDerivative<T, DIRECTION::Z, DERIV::StandardSecond>(f, outloc, method,
                                                                     region);
 }
@@ -266,7 +264,7 @@ T D2DZ2(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method =
 template <typename T>
 T D4DZ4(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
         const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return standardDerivative<T, DIRECTION::Z, DERIV::StandardFourth>(f, outloc, method,
                                                                     region);
 }
@@ -291,14 +289,14 @@ T D4DZ4(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method =
 template <typename T>
 T VDDX(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
        const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return flowDerivative<T, DIRECTION::X, DERIV::Upwind>(vel, f, outloc, method, region);
 }
 
 template <typename T>
 T FDDX(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
        const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return flowDerivative<T, DIRECTION::X, DERIV::Flux>(vel, f, outloc, method, region);
 }
 
@@ -307,7 +305,6 @@ T FDDX(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
 template <typename T>
 T VDDY(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
        const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
 
   // Note the following chunk is copy+pasted from flowDerivative
   // above. Not pulled out as a separate function due the number of
@@ -363,7 +360,7 @@ T VDDY(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
 template <typename T>
 T FDDY(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
        const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   const bool fHasParallelSlices = (f.hasParallelSlices());
   const bool velHasParallelSlices = (vel.hasParallelSlices());
   if (fHasParallelSlices && velHasParallelSlices) {
@@ -389,14 +386,14 @@ T FDDY(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
 template <typename T>
 T VDDZ(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
        const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return flowDerivative<T, DIRECTION::Z, DERIV::Upwind>(vel, f, outloc, method, region);
 }
 
 template <typename T>
 T FDDZ(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
        const std::string& method = "DEFAULT", const std::string& region = "RGN_NOBNDRY") {
-  AUTO_TRACE();
+
   return flowDerivative<T, DIRECTION::Z, DERIV::Flux>(vel, f, outloc, method, region);
 }
 
diff --git a/include/bout/interpolation.hxx b/include/bout/interpolation.hxx
index 2c7df4472d..1753dfe0c0 100644
--- a/include/bout/interpolation.hxx
+++ b/include/bout/interpolation.hxx
@@ -56,7 +56,7 @@ inline BoutReal interp(const stencil& s) {
 */
 template <typename T>
 const T interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_ALL") {
-  AUTO_TRACE();
+
   static_assert(bout::utils::is_Field2D_v<T> || bout::utils::is_Field3D_v<T>,
                 "interp_to must be templated with one of Field2D or Field3D.");
   ASSERT1(loc != CELL_DEFAULT); // doesn't make sense to interplote to CELL_DEFAULT
diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx
index 9b9dbba41a..ffc0910dce 100644
--- a/include/bout/invertable_operator.hxx
+++ b/include/bout/invertable_operator.hxx
@@ -61,7 +61,7 @@ namespace inversion {
 /// No-op function to use as a default -- may wish to remove once testing phase complete
 template <typename T>
 T identity(const T& in) {
-  AUTO_TRACE();
+
   return in;
 };
 
@@ -137,8 +137,8 @@ public:
         opt(optIn == nullptr ? Options::getRoot()->getSection("invertableOperator")
                              : optIn),
         localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), lib(opt) {
-    AUTO_TRACE();
-  };
+
+        };
 
   /// Destructor just has to cleanup the PETSc owned objects.
   ~InvertableOperator() {
@@ -177,10 +177,7 @@ public:
   }
 
   /// Provide a synonym for applying the operator to a Field
-  T apply(const T& input) {
-    AUTO_TRACE();
-    return operator()(input);
-  }
+  T apply(const T& input) { return operator()(input); }
 
   /// Sets up the PETSc objects required for inverting the operator
   /// Currently also takes the functor that applies the operator this class
@@ -386,7 +383,7 @@ public:
   // but suspect it's not as there are KSPGuess objects
   // to deal with.
   T invert(const T& rhsField, const T& guess) {
-    AUTO_TRACE();
+
     auto ierr = fieldToPetscVec(guess, lhs);
     CHKERRQ(ierr);
     return invert(rhsField);
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 2e27bed777..0d9471d1d2 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -652,7 +652,7 @@ public:
   /// Returns the non-CELL_CENTRE location
   /// allowed as a staggered location
   static CELL_LOC getAllowedStaggerLoc(DIRECTION direction) {
-    AUTO_TRACE();
+
     switch (direction) {
     case (DIRECTION::X):
       return CELL_XLOW;
@@ -670,7 +670,7 @@ public:
   /// Returns the number of grid points in the
   /// particular direction
   int getNpoints(DIRECTION direction) const {
-    AUTO_TRACE();
+
     switch (direction) {
     case (DIRECTION::X):
       return LocalNx;
@@ -688,7 +688,7 @@ public:
   /// Returns the number of guard points in the
   /// particular direction
   int getNguard(DIRECTION direction) const {
-    AUTO_TRACE();
+
     switch (direction) {
     case (DIRECTION::X):
       return xstart;
diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx
index 6d19469e25..765a3120cf 100644
--- a/include/bout/msg_stack.hxx
+++ b/include/bout/msg_stack.hxx
@@ -40,18 +40,6 @@ class MsgStack;
 #include <string>
 #include <vector>
 
-/// The __PRETTY_FUNCTION__ variable is defined by GCC (and some other families) but is
-/// not a part of the standard. The __func__ variable *is* a part of the c++11 standard so
-/// we'd like to fall back to this if possible. However as these are variables/constants
-/// and not macros we can't just check if __PRETTY_FUNCITON__ is defined or not. Instead
-/// we need to say if we support this or not by defining BOUT_HAS_PRETTY_FUNCTION (to be
-/// implemented in configure)
-#if BOUT_HAS_PRETTY_FUNCTION
-#define __thefunc__ __PRETTY_FUNCTION__
-#else
-#define __thefunc__ __func__
-#endif
-
 /*!
  * Message stack
  *
@@ -193,23 +181,4 @@ private:
 #define TRACE(...)
 #endif
 
-/*!
- * The AUTO_TRACE macro provides a convenient way to put messages onto the msg_stack
- * It pushes a message onto the stack, and pops it when the scope ends
- * The message is automatically derived from the function signature
- * as identified by the compiler. This will be PRETTY_FUNCTION if available
- * else it will be the mangled form.
- *
- * This is implemented as a use of the TRACE macro with specific arguments.
- *
- * Example
- * -------
- *
- * {
- *   AUTO_TRACE();
- *
- * } // Scope ends, message popped
- */
-#define AUTO_TRACE() TRACE(__thefunc__) // NOLINT
-
 #endif // BOUT_MSG_STACK_H
diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 3ae02f41a6..5edd42a441 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -363,7 +363,7 @@ public:
       }
     }
     Element& operator=(const Element& other) {
-      AUTO_TRACE();
+
       if (this == &other) {
         return *this;
       }
@@ -372,14 +372,14 @@ public:
       return *this;
     }
     Element& operator=(BoutReal val) {
-      AUTO_TRACE();
+
       ASSERT3(finite(val));
       value = val;
       setValues(val, INSERT_VALUES);
       return *this;
     }
     Element& operator+=(BoutReal val) {
-      AUTO_TRACE();
+
       ASSERT3(finite(val));
       auto columnPosition = std::find(positions.begin(), positions.end(), petscCol);
       if (columnPosition != positions.end()) {
diff --git a/include/bout/scorepwrapper.hxx b/include/bout/scorepwrapper.hxx
index 81761530f0..40c2232040 100644
--- a/include/bout/scorepwrapper.hxx
+++ b/include/bout/scorepwrapper.hxx
@@ -3,7 +3,6 @@
 
 #include "bout/build_defines.hxx"
 
-#include "bout/msg_stack.hxx"
 #include <bout/bout_types.hxx>
 
 #if BOUT_HAS_SCOREP
@@ -14,6 +13,18 @@
 #define SCOREPLVL 0
 #endif
 
+/// The __PRETTY_FUNCTION__ variable is defined by GCC (and some other families) but is
+/// not a part of the standard. The __func__ variable *is* a part of the c++11 standard so
+/// we'd like to fall back to this if possible. However as these are variables/constants
+/// and not macros we can't just check if __PRETTY_FUNCITON__ is defined or not. Instead
+/// we need to say if we support this or not by defining BOUT_HAS_PRETTY_FUNCTION (to be
+/// implemented in configure)
+#if BOUT_HAS_PRETTY_FUNCTION
+#define __thefunc__ __PRETTY_FUNCTION__
+#else
+#define __thefunc__ __func__
+#endif
+
 /// Instrument a function with scorep
 ///
 /// The scorep call is identical for all levels, so just define it here.
diff --git a/include/bout/sys/timer.hxx b/include/bout/sys/timer.hxx
index f3beba27b1..90fd632f62 100644
--- a/include/bout/sys/timer.hxx
+++ b/include/bout/sys/timer.hxx
@@ -133,5 +133,4 @@ public:
   static void printTimeReport();
 };
 
-#define AUTO_TIME() Timer CONCATENATE(time_, __LINE__)(__thefunc__)
 #endif // BOUT_TIMER_H
diff --git a/manual/doxygen/Doxyfile b/manual/doxygen/Doxyfile
index e2fef90a8c..82cfa5a8a4 100644
--- a/manual/doxygen/Doxyfile
+++ b/manual/doxygen/Doxyfile
@@ -2059,7 +2059,6 @@ PREDEFINED             = BACKTRACE \
                          BOUT_HAS_LAPACK \
                          BOUT_HAS_NETCDF \
                          BOUT_HAS_PETSC \
-                         BOUT_HAS_PRETTY_FUNCTION \
                          BOUT_HAS_PVODE \
                          BOUT_HAS_SCOREP \
                          BOUT_HAS_SLEPC \
diff --git a/manual/doxygen/Doxyfile_readthedocs b/manual/doxygen/Doxyfile_readthedocs
index 94113490d9..0ddca11de0 100644
--- a/manual/doxygen/Doxyfile_readthedocs
+++ b/manual/doxygen/Doxyfile_readthedocs
@@ -1019,7 +1019,6 @@ PREDEFINED             = BACKTRACE \
                          BOUT_HAS_LAPACK \
                          BOUT_HAS_NETCDF \
                          BOUT_HAS_PETSC \
-                         BOUT_HAS_PRETTY_FUNCTION \
                          BOUT_HAS_PVODE \
                          BOUT_HAS_SCOREP \
                          BOUT_HAS_SLEPC \
diff --git a/manual/sphinx/developer_docs/debugging.rst b/manual/sphinx/developer_docs/debugging.rst
index 805cb5409a..fc8d80d9fc 100644
--- a/manual/sphinx/developer_docs/debugging.rst
+++ b/manual/sphinx/developer_docs/debugging.rst
@@ -37,11 +37,10 @@ add a ``-v -v`` flag to see ``output_debug`` messages.
 Message Stack
 =============
 
-The second utility BOUT++ has to help debugging is the message stack
-using the `TRACE` (and related `AUTO_TRACE`) macro. These are very
-useful for when a bug only occurs after a long time of running, and/or
-only occasionally. The ``TRACE`` macro can simply be dropped in
-anywhere in the code::
+The second utility BOUT++ has to help debugging is the message stack using the
+`TRACE` macro. This is very useful for when a bug only occurs after a long time
+of running, and/or only occasionally. The ``TRACE`` macro can simply be dropped
+in anywhere in the code::
 
     {
       TRACE("Some message here"); // message pushed
@@ -95,11 +94,6 @@ the ``fmt`` syntax also used by the loggers::
 
     TRACE("Value of i={}, some arbitrary {}", i, "string");
 
-There is also an ``AUTO_TRACE`` macro that automatically captures the
-name of the function it's used in. This is used throughout the main
-library, especially in functions where numerical issues are likely to
-arise.
-
 Backtrace
 =========
 
diff --git a/src/bout++.cxx b/src/bout++.cxx
index 48ab96298b..9c859aaaa7 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -566,8 +566,6 @@ void printCompileTimeOptions() {
   output_info.write(_("\tNetCDF support {}{}\n"), is_enabled(has_netcdf), netcdf_flavour);
   output_info.write(_("\tADIOS2 support {}\n"), is_enabled(has_adios2));
   output_info.write(_("\tPETSc support {}\n"), is_enabled(has_petsc));
-  output_info.write(_("\tPretty function name support {}\n"),
-                    is_enabled(has_pretty_function));
   output_info.write(_("\tPVODE support {}\n"), is_enabled(has_pvode));
   output_info.write(_("\tScore-P support {}\n"), is_enabled(has_scorep));
   output_info.write(_("\tSLEPc support {}\n"), is_enabled(has_slepc));
@@ -696,7 +694,6 @@ void addBuildFlagsToOptions(Options& options) {
   options["has_umpire"].force(bout::build::has_umpire);
   options["has_caliper"].force(bout::build::has_caliper);
   options["has_raja"].force(bout::build::has_raja);
-  options["has_pretty_function"].force(bout::build::has_pretty_function);
   options["has_pvode"].force(bout::build::has_pvode);
   options["has_scorep"].force(bout::build::has_scorep);
   options["has_slepc"].force(bout::build::has_slepc);
diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx
index b95c0462d9..b925cb1426 100644
--- a/src/field/field_data.cxx
+++ b/src/field/field_data.cxx
@@ -15,7 +15,6 @@ namespace bout {
 /// Throws if checks are enabled and trying to use a staggered
 /// location on a non-staggered mesh
 CELL_LOC normaliseLocation(CELL_LOC location, Mesh* mesh) {
-  AUTO_TRACE();
 
   // CELL_DEFAULT always means CELL_CENTRE
   if (location == CELL_DEFAULT) {
@@ -216,7 +215,6 @@ Mesh* FieldData::getMesh() const {
 }
 
 FieldData& FieldData::setLocation(CELL_LOC new_location) {
-  AUTO_TRACE();
 
   location = bout::normaliseLocation(new_location, getMesh());
 
@@ -228,10 +226,7 @@ FieldData& FieldData::setLocation(CELL_LOC new_location) {
   return *this;
 }
 
-CELL_LOC FieldData::getLocation() const {
-  AUTO_TRACE();
-  return location;
-}
+CELL_LOC FieldData::getLocation() const { return location; }
 
 Coordinates* FieldData::getCoordinates() const {
   auto fieldCoordinates_shared = fieldCoordinates.lock();
diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index b93a39eeda..188a64cf0c 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -188,7 +188,6 @@ Field2D FieldFactory::create2D(const std::string& value, const Options* opt,
 
 Field2D FieldFactory::create2D(FieldGeneratorPtr gen, Mesh* localmesh, CELL_LOC loc,
                                BoutReal t) const {
-  AUTO_TRACE();
 
   if (localmesh == nullptr) {
     if (fieldmesh == nullptr) {
@@ -220,7 +219,6 @@ Field3D FieldFactory::create3D(const std::string& value, const Options* opt,
 
 Field3D FieldFactory::create3D(FieldGeneratorPtr gen, Mesh* localmesh, CELL_LOC loc,
                                BoutReal t) const {
-  AUTO_TRACE();
 
   if (localmesh == nullptr) {
     if (fieldmesh == nullptr) {
@@ -271,7 +269,6 @@ FieldPerp FieldFactory::createPerp(const std::string& value, const Options* opt,
 
 FieldPerp FieldFactory::createPerp(FieldGeneratorPtr gen, Mesh* localmesh, CELL_LOC loc,
                                    BoutReal t) const {
-  AUTO_TRACE();
 
   if (localmesh == nullptr) {
     if (fieldmesh == nullptr) {
diff --git a/src/field/initialprofiles.cxx b/src/field/initialprofiles.cxx
index ded5aa9882..5e96d6005a 100644
--- a/src/field/initialprofiles.cxx
+++ b/src/field/initialprofiles.cxx
@@ -45,7 +45,6 @@
 #include <bout/msg_stack.hxx>
 
 void initial_profile(const std::string& name, Field3D& var) {
-  AUTO_TRACE();
 
   Mesh* localmesh = var.getMesh();
 
@@ -65,7 +64,6 @@ void initial_profile(const std::string& name, Field3D& var) {
 }
 
 void initial_profile(const std::string& name, Field2D& var) {
-  AUTO_TRACE();
 
   Mesh* localmesh = var.getMesh();
 
@@ -85,7 +83,6 @@ void initial_profile(const std::string& name, Field2D& var) {
 }
 
 void initial_profile(const std::string& name, Vector2D& var) {
-  AUTO_TRACE();
 
   if (var.covariant) {
     initial_profile(name + "_x", var.x);
@@ -99,7 +96,6 @@ void initial_profile(const std::string& name, Vector2D& var) {
 }
 
 void initial_profile(const std::string& name, Vector3D& var) {
-  AUTO_TRACE();
 
   if (var.covariant) {
     initial_profile(name + "_x", var.x);
diff --git a/src/field/vecops.cxx b/src/field/vecops.cxx
index 5f34e2af02..4d62d1a1d7 100644
--- a/src/field/vecops.cxx
+++ b/src/field/vecops.cxx
@@ -119,7 +119,7 @@ Vector3D Grad_perp(const Field3D& f, CELL_LOC outloc, const std::string& method)
 }
 
 Vector2D Grad_perp(const Field2D& f, CELL_LOC outloc, const std::string& method) {
-  AUTO_TRACE();
+
   SCOREP0();
   ASSERT1(outloc == CELL_DEFAULT || outloc == f.getLocation());
 
@@ -370,7 +370,7 @@ Field3D V_dot_Grad(const Vector3D& v, const Field3D& f) {
 // operation (addition) between the two input types.
 template <typename T, typename F, typename R = decltype(T{} + F{})>
 R V_dot_Grad(const T& v, const F& a) {
-  AUTO_TRACE();
+
   SCOREP0();
   ASSERT1(v.getLocation() == a.getLocation());
   ASSERT1(v.getLocation() != CELL_VSHIFT);
diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
index efca1d70be..3be5e43e63 100644
--- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
+++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
@@ -174,7 +174,6 @@ void setBC(PetscVector<Field3D>& rhs, const Field3D& b_in,
 }
 
 Field3D LaplacePetsc3dAmg::solve(const Field3D& b_in, const Field3D& x0) {
-  AUTO_TRACE();
 
   // Timing reported in the log files. Includes any matrix construction.
   // The timing for just the solve phase can be retrieved from the "petscsolve"
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 5078882136..fba64eaa59 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -143,7 +143,6 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def,
       "templated GridFile::getField only works for Field2D, Field3D or FieldPerp");
 
   Timer timer("io");
-  AUTO_TRACE();
 
   if (not data.isSet(name)) {
     // Variable not found
diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx
index add67a77c8..595081e3ae 100644
--- a/src/mesh/index_derivs.cxx
+++ b/src/mesh/index_derivs.cxx
@@ -423,7 +423,7 @@ class FFTDerivativeType {
 public:
   template <DIRECTION direction, STAGGER stagger, int nGuards, typename T>
   void standard(const T& var, T& result, const std::string& region) const {
-    AUTO_TRACE();
+
     ASSERT2(meta.derivType == DERIV::Standard)
     ASSERT2(var.getMesh()->getNguard(direction) >= nGuards);
     ASSERT2(direction == DIRECTION::Z);    // Only in Z for now
@@ -479,7 +479,7 @@ class FFTDerivativeType {
   template <DIRECTION direction, STAGGER stagger, int nGuards, typename T>
   void upwindOrFlux(const T& UNUSED(vel), const T& UNUSED(var), T& UNUSED(result),
                     const std::string& UNUSED(region)) const {
-    AUTO_TRACE();
+
     throw BoutException("The FFT METHOD isn't available in upwind/Flux");
   }
   static constexpr metaData meta{"FFT", 0, DERIV::Standard};
@@ -489,7 +489,7 @@ class FFT2ndDerivativeType {
 public:
   template <DIRECTION direction, STAGGER stagger, int nGuards, typename T>
   void standard(const T& var, T& result, const std::string& region) const {
-    AUTO_TRACE();
+
     ASSERT2(meta.derivType == DERIV::StandardSecond);
     ASSERT2(var.getMesh()->getNguard(direction) >= nGuards);
     ASSERT2(direction == DIRECTION::Z);    // Only in Z for now
@@ -536,7 +536,7 @@ class FFT2ndDerivativeType {
   template <DIRECTION direction, STAGGER stagger, int nGuards, typename T>
   void upwindOrFlux(const T& UNUSED(vel), const T& UNUSED(var), T& UNUSED(result),
                     const std::string& UNUSED(region)) const {
-    AUTO_TRACE();
+
     throw BoutException("The FFT METHOD isn't available in upwind/Flux");
   }
   static constexpr metaData meta{"FFT", 0, DERIV::StandardSecond};
@@ -552,14 +552,14 @@ class SplitFluxDerivativeType {
 public:
   template <DIRECTION direction, STAGGER stagger, int nGuards, typename T>
   void standard(const T&, T&, const std::string) const {
-    AUTO_TRACE();
+
     throw BoutException("The SPLIT method isn't available for standard");
   }
 
   template <DIRECTION direction, STAGGER stagger, int nGuards, typename T>
   void upwindOrFlux(const T& vel, const T& var, T& result,
                     const std::string region) const {
-    AUTO_TRACE();
+
     // Split into an upwind and a central differencing part
     // d/dx(v*f) = v*d/dx(f) + f*d/dx(v)
     result = bout::derivatives::index::flowDerivative<T, direction, DERIV::Upwind>(
diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx
index 7f3637e79c..4543c4c3fb 100644
--- a/src/mesh/parallel/shiftedmetricinterp.cxx
+++ b/src/mesh/parallel/shiftedmetricinterp.cxx
@@ -211,7 +211,6 @@ void ShiftedMetricInterp::checkInputGrid() {
  * Calculate the Y up and down fields
  */
 void ShiftedMetricInterp::calcParallelSlices(Field3D& f) {
-  AUTO_TRACE();
 
   // Ensure that yup and ydown are different fields
   f.splitParallelSlices();
diff --git a/src/physics/smoothing.cxx b/src/physics/smoothing.cxx
index 0a1391907f..d8f7fb8b6b 100644
--- a/src/physics/smoothing.cxx
+++ b/src/physics/smoothing.cxx
@@ -352,7 +352,7 @@ BoutReal Average_XY(const Field2D& var) {
 
 BoutReal Vol_Integral(const Field2D& var) {
 #if BOUT_USE_METRIC_3D
-  AUTO_TRACE();
+
   throw BoutException("Vol_Intregral currently incompatible with 3D metrics");
 #else
   Mesh* mesh = var.getMesh();
diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
index 79161fcdbf..bb81e3d53f 100644
--- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx
+++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
@@ -14,7 +14,6 @@
 namespace {
 BoutReal lagrange_at_position_denominator(const std::deque<BoutReal>& grid,
                                           const int position, const int order) {
-  AUTO_TRACE();
 
   const auto xj = grid[position];
 
@@ -28,7 +27,7 @@ BoutReal lagrange_at_position_denominator(const std::deque<BoutReal>& grid,
 BoutReal lagrange_at_position_numerator(const BoutReal varX,
                                         const std::deque<BoutReal>& grid,
                                         const int position, const int order) {
-  AUTO_TRACE();
+
   BoutReal result = 1.0;
   for (int i = 0; i < order; i++) {
     result *= (i != position) ? (varX - grid[i]) : 1.0;
@@ -55,7 +54,7 @@ BoutReal lagrange_interpolate(BoutReal start, BoutReal end,
 BoutReal integrate_lagrange_curve_nc9(const BoutReal start, const BoutReal end,
                                       const std::deque<BoutReal>& points,
                                       const int position) {
-  AUTO_TRACE();
+
   constexpr std::size_t size = 9;
   constexpr BoutReal fac = 4.0 / 14175.0;
   constexpr std::array<BoutReal, size> facs{989.0 * fac,   5888.0 * fac,  -928.0 * fac,
@@ -68,7 +67,7 @@ BoutReal integrate_lagrange_curve_nc9(const BoutReal start, const BoutReal end,
 BoutReal integrate_lagrange_curve_nc8(const BoutReal start, const BoutReal end,
                                       const std::deque<BoutReal>& points,
                                       const int position) {
-  AUTO_TRACE();
+
   constexpr std::size_t size = 8;
   constexpr BoutReal fac = 7.0 / 17280.0;
   constexpr std::array<BoutReal, size> facs{751.0 * fac,  3577.0 * fac, 1323.0 * fac,
@@ -81,7 +80,7 @@ BoutReal integrate_lagrange_curve_nc8(const BoutReal start, const BoutReal end,
 BoutReal integrate_lagrange_curve_nc7(const BoutReal start, const BoutReal end,
                                       const std::deque<BoutReal>& points,
                                       const int position) {
-  AUTO_TRACE();
+
   constexpr std::size_t size = 7;
   constexpr BoutReal fac = 1.0 / 140.0;
   constexpr std::array<BoutReal, size> facs{41.0 * fac,  216.0 * fac, 27.0 * fac,
@@ -94,7 +93,7 @@ BoutReal integrate_lagrange_curve_nc7(const BoutReal start, const BoutReal end,
 BoutReal integrate_lagrange_curve_nc6(const BoutReal start, const BoutReal end,
                                       const std::deque<BoutReal>& points,
                                       const int position) {
-  AUTO_TRACE();
+
   constexpr std::size_t size = 6;
   constexpr BoutReal fac = 5.0 / 288.0;
   constexpr std::array<BoutReal, size> facs{19.0 * fac, 75.0 * fac, 50.0 * fac,
@@ -106,7 +105,7 @@ BoutReal integrate_lagrange_curve_nc6(const BoutReal start, const BoutReal end,
 BoutReal integrate_lagrange_curve_nc5(const BoutReal start, const BoutReal end,
                                       const std::deque<BoutReal>& points,
                                       const int position) {
-  AUTO_TRACE();
+
   constexpr std::size_t size = 5;
   constexpr BoutReal fac = 2.0 / 45.0;
   constexpr std::array<BoutReal, size> facs{7.0 * fac, 32.0 * fac, 12.0 * fac, 32.0 * fac,
@@ -118,7 +117,7 @@ BoutReal integrate_lagrange_curve_nc5(const BoutReal start, const BoutReal end,
 BoutReal integrate_lagrange_curve_nc4(const BoutReal start, const BoutReal end,
                                       const std::deque<BoutReal>& points,
                                       const int position) {
-  AUTO_TRACE();
+
   constexpr std::size_t size = 4;
   constexpr BoutReal fac = 3.0 / 8.0;
   constexpr std::array<BoutReal, size> facs{1.0 * fac, 3.0 * fac, 3.0 * fac, 1.0 * fac};
@@ -129,7 +128,7 @@ BoutReal integrate_lagrange_curve_nc4(const BoutReal start, const BoutReal end,
 BoutReal integrate_lagrange_curve_nc3(const BoutReal start, const BoutReal end,
                                       const std::deque<BoutReal>& points,
                                       const int position) {
-  AUTO_TRACE();
+
   constexpr std::size_t size = 3;
   constexpr BoutReal fac = 1.0 / 3.0;
   constexpr std::array<BoutReal, size> facs{1.0 * fac, 4.0 * fac, 1.0 * fac};
@@ -140,7 +139,7 @@ BoutReal integrate_lagrange_curve_nc3(const BoutReal start, const BoutReal end,
 BoutReal integrate_lagrange_curve_nc2(const BoutReal start, const BoutReal end,
                                       const std::deque<BoutReal>& points,
                                       const int position) {
-  AUTO_TRACE();
+
   constexpr std::size_t size = 2;
   constexpr BoutReal fac = 1.0 / 2.0;
   constexpr std::array<BoutReal, size> facs{1.0 * fac, 1.0 * fac};
@@ -151,7 +150,6 @@ BoutReal integrate_lagrange_curve_nc2(const BoutReal start, const BoutReal end,
 BoutReal integrate_lagrange_curve(const BoutReal start, const BoutReal end,
                                   const std::deque<BoutReal>& points, const int position,
                                   const int order) {
-  AUTO_TRACE();
 
   switch (order) {
   case 1:
@@ -179,7 +177,7 @@ BoutReal integrate_lagrange_curve(const BoutReal start, const BoutReal end,
 std::vector<BoutReal> get_adams_bashforth_coefficients(const BoutReal nextPoint,
                                                        const std::deque<BoutReal>& points,
                                                        const int order) {
-  AUTO_TRACE();
+
   ASSERT2(static_cast<std::size_t>(order) <= points.size());
 
   std::vector<BoutReal> result;
@@ -235,7 +233,7 @@ BoutReal get_timestep_limit(const BoutReal error, const BoutReal tolerance,
 /// over all processors.
 BoutReal get_error(const Array<BoutReal>& stateApprox,
                    const Array<BoutReal>& stateAccurate) {
-  AUTO_TRACE();
+
   BoutReal local_result = 0.0;
   BoutReal err = 0.0;
 
@@ -287,12 +285,12 @@ AdamsBashforthSolver::AdamsBashforthSolver(Options* options)
                        .withDefault(getOutputTimestep())),
       timestep(
           (*options)["timestep"].doc("Starting timestep").withDefault(max_timestep)) {
-  AUTO_TRACE();
+
   canReset = true;
 }
 
 void AdamsBashforthSolver::setMaxTimestep(BoutReal dt) {
-  AUTO_TRACE();
+
   if (dt > timestep) {
     return; // Already less than this
   }
@@ -345,7 +343,6 @@ int AdamsBashforthSolver::init() {
 }
 
 void AdamsBashforthSolver::resetInternalFields() {
-  AUTO_TRACE();
 
   // History and times
   history.clear();
@@ -360,7 +357,6 @@ void AdamsBashforthSolver::resetInternalFields() {
 }
 
 int AdamsBashforthSolver::run() {
-  AUTO_TRACE();
 
   // Just for developer diagnostics
   int nwasted = 0;
@@ -563,7 +559,6 @@ int AdamsBashforthSolver::run() {
 BoutReal AdamsBashforthSolver::take_step(const BoutReal timeIn, const BoutReal dt,
                                          const int order, Array<BoutReal>& current,
                                          Array<BoutReal>& result) {
-  AUTO_TRACE();
 
   Array<BoutReal> full_update = AB_integrate(nlocal, timeIn + dt, times, history, order);
 
diff --git a/src/solver/impls/split-rk/split-rk.cxx b/src/solver/impls/split-rk/split-rk.cxx
index cd6bd1718c..fd9a99a6c5 100644
--- a/src/solver/impls/split-rk/split-rk.cxx
+++ b/src/solver/impls/split-rk/split-rk.cxx
@@ -35,7 +35,6 @@ SplitRK::SplitRK(Options* opts)
 }
 
 int SplitRK::init() {
-  AUTO_TRACE();
 
   Solver::init();
   output.write(_("\n\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"));
@@ -79,7 +78,6 @@ int SplitRK::init() {
 }
 
 int SplitRK::run() {
-  AUTO_TRACE();
 
   for (int step = 0; step < getNumberOutputSteps(); step++) {
     // Take an output step
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index a3f6a874f6..ea7866051b 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -636,7 +636,7 @@ std::string Solver::createRunID() const {
 }
 
 std::string Solver::getRunID() const {
-  AUTO_TRACE();
+
   if (run_id == default_run_id) {
     throw BoutException("run_id not set!");
   }
@@ -644,7 +644,7 @@ std::string Solver::getRunID() const {
 }
 
 std::string Solver::getRunRestartFrom() const {
-  AUTO_TRACE();
+
   // Check against run_id, because this might not be a restarted run
   if (run_id == default_run_id) {
     throw BoutException("run_restart_from not set!");
diff --git a/src/sys/bout_types.cxx b/src/sys/bout_types.cxx
index 35d37f11be..f5e971af78 100644
--- a/src/sys/bout_types.cxx
+++ b/src/sys/bout_types.cxx
@@ -6,7 +6,7 @@
 namespace {
 template <typename T>
 const std::string& safeAt(const std::map<T, std::string>& mymap, T t) {
-  AUTO_TRACE();
+
   auto found = mymap.find(t);
   if (found == mymap.end()) {
     throw BoutException("Did not find enum {:d}", static_cast<int>(t));
@@ -16,7 +16,7 @@ const std::string& safeAt(const std::map<T, std::string>& mymap, T t) {
 
 template <typename T>
 const T& safeAt(const std::map<std::string, T>& mymap, const std::string& s) {
-  AUTO_TRACE();
+
   auto found = mymap.find(s);
   if (found == mymap.end()) {
     throw BoutException("Did not find enum {:s}", s);
@@ -26,7 +26,7 @@ const T& safeAt(const std::map<std::string, T>& mymap, const std::string& s) {
 } // namespace
 
 std::string toString(CELL_LOC location) {
-  AUTO_TRACE();
+
   const static std::map<CELL_LOC, std::string> CELL_LOCtoString = {
       ENUMSTR(CELL_DEFAULT), ENUMSTR(CELL_CENTRE), ENUMSTR(CELL_XLOW),
       ENUMSTR(CELL_YLOW),    ENUMSTR(CELL_ZLOW),   ENUMSTR(CELL_VSHIFT)};
@@ -35,7 +35,7 @@ std::string toString(CELL_LOC location) {
 }
 
 CELL_LOC CELL_LOCFromString(const std::string& location_string) {
-  AUTO_TRACE();
+
   const static std::map<std::string, CELL_LOC> stringtoCELL_LOC = {
       STRENUM(CELL_DEFAULT), STRENUM(CELL_CENTRE), STRENUM(CELL_XLOW),
       STRENUM(CELL_YLOW),    STRENUM(CELL_ZLOW),   STRENUM(CELL_VSHIFT)};
@@ -44,7 +44,7 @@ CELL_LOC CELL_LOCFromString(const std::string& location_string) {
 }
 
 std::string toString(DIFF_METHOD location) {
-  AUTO_TRACE();
+
   const static std::map<DIFF_METHOD, std::string> DIFF_METHODtoString = {
       {DIFF_DEFAULT, "DEFAULT"}, {DIFF_U1, "U1"},   {DIFF_U2, "U2"},      {DIFF_U3, "U3"},
       {DIFF_C2, "C2"},           {DIFF_C4, "C4"},   {DIFF_S2, "S2"},      {DIFF_W2, "W2"},
@@ -54,7 +54,7 @@ std::string toString(DIFF_METHOD location) {
 }
 
 std::string toString(REGION region) {
-  AUTO_TRACE();
+
   const static std::map<REGION, std::string> REGIONtoString = {
       ENUMSTR(RGN_ALL), ENUMSTR(RGN_NOBNDRY), ENUMSTR(RGN_NOX), ENUMSTR(RGN_NOY),
       ENUMSTR(RGN_NOZ)};
@@ -62,7 +62,7 @@ std::string toString(REGION region) {
 }
 
 std::string toString(DIRECTION direction) {
-  AUTO_TRACE();
+
   const static std::map<DIRECTION, std::string> DIRECTIONtoString = {
       {DIRECTION::X, "X"},
       {DIRECTION::Y, "Y"},
@@ -116,7 +116,7 @@ bool areDirectionsCompatible(const DirectionTypes& d1, const DirectionTypes& d2)
 }
 
 std::string toString(STAGGER stagger) {
-  AUTO_TRACE();
+
   const static std::map<STAGGER, std::string> STAGGERtoString = {
       {STAGGER::None, "No staggering"},
       {STAGGER::C2L, "Centre to Low"},
@@ -126,7 +126,7 @@ std::string toString(STAGGER stagger) {
 }
 
 std::string toString(DERIV deriv) {
-  AUTO_TRACE();
+
   const static std::map<DERIV, std::string> DERIVtoString = {
       {DERIV::Standard, "Standard"},
       {DERIV::StandardSecond, "Standard -- second order"},
@@ -138,7 +138,7 @@ std::string toString(DERIV deriv) {
 }
 
 std::string toString(YDirectionType d) {
-  AUTO_TRACE();
+
   const static std::map<YDirectionType, std::string> YDirectionTypeToString = {
       {YDirectionType::Standard, "Standard"}, {YDirectionType::Aligned, "Aligned"}};
 
@@ -146,7 +146,7 @@ std::string toString(YDirectionType d) {
 }
 
 YDirectionType YDirectionTypeFromString(const std::string& y_direction_string) {
-  AUTO_TRACE();
+
   const static std::map<std::string, YDirectionType> stringToYDirectionType = {
       {"Standard", YDirectionType::Standard}, {"Aligned", YDirectionType::Aligned}};
 
@@ -154,7 +154,7 @@ YDirectionType YDirectionTypeFromString(const std::string& y_direction_string) {
 }
 
 std::string toString(ZDirectionType d) {
-  AUTO_TRACE();
+
   const static std::map<ZDirectionType, std::string> ZDirectionTypeToString = {
       {ZDirectionType::Standard, "Standard"}, {ZDirectionType::Average, "Average"}};
 
@@ -162,7 +162,7 @@ std::string toString(ZDirectionType d) {
 }
 
 ZDirectionType ZDirectionTypeFromString(const std::string& z_direction_string) {
-  AUTO_TRACE();
+
   const static std::map<std::string, ZDirectionType> stringToZDirectionType = {
       {"Standard", ZDirectionType::Standard}, {"Average", ZDirectionType::Average}};
 
diff --git a/src/sys/msg_stack.cxx b/src/sys/msg_stack.cxx
index 502836324c..81eb6c4b0f 100644
--- a/src/sys/msg_stack.cxx
+++ b/src/sys/msg_stack.cxx
@@ -27,7 +27,7 @@
 #include "bout/openmpwrap.hxx"
 #include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
-#include <cstdarg>
+
 #include <string>
 
 #if BOUT_USE_OPENMP
diff --git a/tests/integrated/test-backtrace/boutexcept.cxx b/tests/integrated/test-backtrace/boutexcept.cxx
index bd965a9c2b..ed33a4c018 100644
--- a/tests/integrated/test-backtrace/boutexcept.cxx
+++ b/tests/integrated/test-backtrace/boutexcept.cxx
@@ -1,18 +1,9 @@
 #include "bout/boutexception.hxx"
 #include "bout/msg_stack.hxx"
 
-void troublemaker() {
-  AUTO_TRACE();
-  throw BoutException("test");
-}
-void f() {
-  AUTO_TRACE();
-  troublemaker();
-}
-void e() {
-  AUTO_TRACE();
-  f();
-}
+void troublemaker() { throw BoutException("test"); }
+void f() { troublemaker(); }
+void e() { f(); }
 
 int main() {
   e();

From 505d5adde26e2f70a129582b676bd99fcb85fafd Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 15:11:05 +0000
Subject: [PATCH 0409/1827] Remove uses of `TRACE` which are just the function
 name

---
 examples/6field-simple/elm_6f.cxx             |  4 --
 .../invertable_operator.cxx                   |  5 +--
 include/bout/cyclic_reduction.hxx             |  4 +-
 include/bout/invertable_operator.hxx          | 25 ++++-------
 .../sphinx/user_docs/invertable_operator.rst  |  2 -
 src/field/field2d.cxx                         | 36 ++++------------
 src/field/field3d.cxx                         | 43 ++-----------------
 src/field/fieldperp.cxx                       |  3 --
 src/field/vecops.cxx                          | 26 +++++------
 src/field/vector2d.cxx                        |  2 +-
 src/field/vector3d.cxx                        |  2 +-
 .../laplace/impls/cyclic/cyclic_laplace.cxx   |  1 -
 .../iterative_parallel_tri.cxx                |  1 -
 .../impls/multigrid/multigrid_laplace.cxx     |  5 ---
 src/invert/laplace/impls/pcr/pcr.cxx          |  1 -
 .../laplace/impls/pcr_thomas/pcr_thomas.cxx   |  1 -
 .../laplace/impls/petsc/petsc_laplace.cxx     |  1 -
 src/invert/laplace/invert_laplace.cxx         |  2 -
 .../impls/cyclic/laplacexz-cyclic.cxx         |  2 +-
 .../laplacexz/impls/petsc/laplacexz-petsc.cxx |  8 ----
 src/invert/parderiv/impls/cyclic/cyclic.cxx   |  2 +-
 .../pardiv/impls/cyclic/pardiv_cyclic.cxx     |  2 +-
 src/mesh/boundary_standard.cxx                |  5 ---
 src/mesh/coordinates.cxx                      | 28 ++++++------
 src/mesh/data/gridfromfile.cxx                |  9 ++--
 src/mesh/difops.cxx                           | 11 -----
 src/mesh/fv_ops.cxx                           |  1 -
 src/mesh/impls/bout/boutmesh.cxx              |  2 -
 src/mesh/index_derivs.cxx                     |  4 --
 src/mesh/interpolation_xz.cxx                 |  4 --
 src/mesh/invert3x3.hxx                        |  1 -
 src/mesh/mesh.cxx                             |  3 --
 src/mesh/parallel/fci.cxx                     |  3 --
 src/physics/physicsmodel.cxx                  |  1 -
 src/physics/smoothing.cxx                     | 14 +-----
 src/physics/sourcex.cxx                       |  4 --
 .../impls/adams_bashforth/adams_bashforth.cxx |  2 -
 src/solver/impls/arkode/arkode.cxx            |  3 --
 src/solver/impls/cvode/cvode.cxx              |  5 +--
 src/solver/impls/euler/euler.cxx              |  2 -
 src/solver/impls/ida/ida.cxx                  |  3 --
 src/solver/impls/imex-bdf2/imex-bdf2.cxx      |  3 --
 src/solver/impls/petsc/petsc.cxx              |  3 --
 src/solver/impls/power/power.cxx              |  2 -
 src/solver/impls/pvode/pvode.cxx              |  2 -
 src/solver/impls/rk3-ssp/rk3-ssp.cxx          |  2 -
 src/solver/impls/rk4/rk4.cxx                  |  4 --
 src/solver/impls/rkgeneric/rkgeneric.cxx      |  4 --
 src/solver/impls/slepc/slepc.cxx              |  2 -
 src/solver/impls/snes/snes.cxx                |  5 ---
 src/solver/solver.cxx                         |  3 --
 src/sys/options.cxx                           |  4 --
 src/sys/options/options_ini.cxx               |  6 +--
 src/sys/optionsreader.cxx                     |  3 --
 .../invertable_operator.cxx                   |  3 +-
 tests/integrated/test-vec/testVec.cxx         |  2 -
 56 files changed, 60 insertions(+), 271 deletions(-)

diff --git a/examples/6field-simple/elm_6f.cxx b/examples/6field-simple/elm_6f.cxx
index 40e4f7b3b3..24256333df 100644
--- a/examples/6field-simple/elm_6f.cxx
+++ b/examples/6field-simple/elm_6f.cxx
@@ -273,8 +273,6 @@ class Elm_6f : public PhysicsModel {
      * This function implements d2/dy2 where y is the poloidal coordinate theta
      */
 
-    TRACE("Grad2_par2new( Field3D )");
-
     Field3D result = D2DY2(f);
 
 #if BOUT_USE_TRACK
@@ -342,8 +340,6 @@ class Elm_6f : public PhysicsModel {
 
   // Parallel gradient along perturbed field-line
   Field3D Grad_parP(const Field3D& f, CELL_LOC loc = CELL_DEFAULT) {
-    TRACE("Grad_parP");
-
     Field3D result;
 
     if (parallel_lagrange || parallel_project) {
diff --git a/examples/invertable_operator/invertable_operator.cxx b/examples/invertable_operator/invertable_operator.cxx
index 57f9e24b08..99db7f7a1e 100644
--- a/examples/invertable_operator/invertable_operator.cxx
+++ b/examples/invertable_operator/invertable_operator.cxx
@@ -1,5 +1,4 @@
 #include <bout/invert_laplace.hxx>
-#include <bout/msg_stack.hxx>
 
 #include <bout/derivs.hxx>
 #include <bout/invertable_operator.hxx>
@@ -26,7 +25,7 @@ class HW : public PhysicsModel {
 
     // Drop C term for now
     Field3D operator()(const Field3D& input) {
-      TRACE("myLaplacian::operator()");
+
       Timer timer("invertable_operator_operate");
       Field3D result = A * input + D * Delp2(input);
 
@@ -43,7 +42,7 @@ class HW : public PhysicsModel {
 
     // Drop C term for now
     Field3D operator()(const Field3D& input) {
-      TRACE("myLaplacian::operator()");
+
       Timer timer("invertable_operator_operate");
       Field3D result = A * input + B * Laplace_perp(input);
       if (withDiv) {
diff --git a/include/bout/cyclic_reduction.hxx b/include/bout/cyclic_reduction.hxx
index d4c0920910..cf54b63059 100644
--- a/include/bout/cyclic_reduction.hxx
+++ b/include/bout/cyclic_reduction.hxx
@@ -47,7 +47,6 @@
 //#define DIAGNOSE 1
 
 #include "mpi.h"
-#include "bout/msg_stack.hxx"
 #include "bout/utils.hxx"
 #include <bout/lapack_routines.hxx>
 
@@ -118,7 +117,6 @@ public:
   /// @param[in] b   Diagonal values. Should have size [nsys][N]
   /// @param[in] c   Right diagonal. Should have size [nsys][N]
   void setCoefs(const Matrix<T>& a, const Matrix<T>& b, const Matrix<T>& c) {
-    TRACE("CyclicReduce::setCoefs");
 
     int nsys = std::get<0>(a.shape());
 
@@ -169,7 +167,7 @@ public:
   /// @param[in] rhs Matrix storing Values of the rhs for each system
   /// @param[out] x  Matrix storing the result for each system
   void solve(const Matrix<T>& rhs, Matrix<T>& x) {
-    TRACE("CyclicReduce::solve");
+
     ASSERT2(static_cast<int>(std::get<0>(rhs.shape())) == Nsys);
     ASSERT2(static_cast<int>(std::get<0>(x.shape())) == Nsys);
     ASSERT2(static_cast<int>(std::get<1>(rhs.shape())) == N);
diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx
index ffc0910dce..6dcd92897a 100644
--- a/include/bout/invertable_operator.hxx
+++ b/include/bout/invertable_operator.hxx
@@ -42,7 +42,6 @@ class InvertableOperator;
 #include <bout/boutexception.hxx>
 #include <bout/globals.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/options.hxx>
 #include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
@@ -68,7 +67,7 @@ T identity(const T& in) {
 /// Pack a PetscVec from a Field<T>
 template <typename T>
 PetscErrorCode fieldToPetscVec(const T& in, Vec out) {
-  TRACE("fieldToPetscVec<T>");
+
   Timer timer("invertable_operator_packing");
 
   PetscScalar* vecData;
@@ -93,7 +92,7 @@ PetscErrorCode fieldToPetscVec(const T& in, Vec out) {
 /// Pack a Field<T> from a PetscVec
 template <typename T>
 PetscErrorCode petscVecToField(Vec in, T& out) {
-  TRACE("petscVecToField<T>");
+
   Timer timer("invertable_operator_packing");
 
   const PetscScalar* vecData;
@@ -142,7 +141,6 @@ public:
 
   /// Destructor just has to cleanup the PETSc owned objects.
   ~InvertableOperator() {
-    TRACE("InvertableOperator<T>::destructor");
 
     KSPDestroy(&ksp);
     MatDestroy(&matOperator);
@@ -157,7 +155,7 @@ public:
   /// do this they can set alsoSetPreconditioner to false.
   void setOperatorFunction(const function_signature& func,
                            bool alsoSetPreconditioner = true) {
-    TRACE("InvertableOperator<T>::setOperatorFunction");
+
     operatorFunction = func;
     if (alsoSetPreconditioner) {
       preconditionerFunction = func;
@@ -166,15 +164,12 @@ public:
 
   /// Allow the user to override the existing preconditioner function
   void setPreconditionerFunction(const function_signature& func) {
-    TRACE("InvertableOperator<T>::setPreconditionerFunction");
+
     preconditionerFunction = func;
   }
 
   /// Provide a way to apply the operator to a Field
-  T operator()(const T& input) {
-    TRACE("InvertableOperator<T>::operator()");
-    return operatorFunction(input);
-  }
+  T operator()(const T& input) { return operatorFunction(input); }
 
   /// Provide a synonym for applying the operator to a Field
   T apply(const T& input) { return operator()(input); }
@@ -184,7 +179,6 @@ public:
   /// represents. Not actually required by any of the setup so this should
   /// probably be moved to a separate place (maybe the constructor).
   PetscErrorCode setup() {
-    TRACE("InvertableOperator<T>::setup");
 
     Timer timer("invertable_operator_setup");
     if (doneSetup) {
@@ -394,7 +388,7 @@ public:
   /// of the operator we represent. Should probably provide an overload or similar as a
   /// way of setting the initial guess.
   T invert(const T& rhsField) {
-    TRACE("InvertableOperator<T>::invert");
+
     Timer timer("invertable_operator_invert");
 
     if (!doneSetup) {
@@ -441,7 +435,6 @@ public:
   /// applying the registered function on the calculated inverse gives
   /// back the initial values.
   bool verify(const T& rhsIn, BoutReal tol = 1.0e-5) {
-    TRACE("InvertableOperator<T>::verify");
 
     T result = invert(rhsIn);
     localmesh->communicate(result);
@@ -460,7 +453,7 @@ public:
   /// that as the Timer "labels" are not unique to an instance the time
   /// reported is summed across all different instances.
   static void reportTime() {
-    TRACE("InvertableOperator<T>::reportTime");
+
     BoutReal time_setup = Timer::resetTime("invertable_operator_setup");
     BoutReal time_invert = Timer::resetTime("invertable_operator_invert");
     BoutReal time_packing = Timer::resetTime("invertable_operator_packing");
@@ -500,7 +493,7 @@ private:
   /// Copies data from v1 into a field of type T, calls the function on this and then
   /// copies the result into the v2 argument.
   static PetscErrorCode functionWrapper(Mat m, Vec v1, Vec v2) {
-    TRACE("InvertableOperator<T>::functionWrapper");
+
     InvertableOperator<T>* ctx;
     auto ierr = MatShellGetContext(m, &ctx);
     T tmpField(ctx->localmesh);
@@ -531,7 +524,7 @@ private:
   /// Copies data from v1 into a field of type T, calls the function on this and then
   /// copies the result into the v2 argument.
   static PetscErrorCode preconditionerWrapper(Mat m, Vec v1, Vec v2) {
-    TRACE("InvertableOperator<T>::functionWrapper");
+
     InvertableOperator<T>* ctx;
     auto ierr = MatShellGetContext(m, &ctx);
     T tmpField(ctx->localmesh);
diff --git a/manual/sphinx/user_docs/invertable_operator.rst b/manual/sphinx/user_docs/invertable_operator.rst
index 92b7efd288..8f92796c9c 100644
--- a/manual/sphinx/user_docs/invertable_operator.rst
+++ b/manual/sphinx/user_docs/invertable_operator.rst
@@ -48,7 +48,6 @@ the ``operator()`` call::
 
     // Drop C term for now
     Field3D operator()(const Field3D &input) {
-      TRACE("myLaplacian::operator()");
       Timer timer("invertable_operator_operate");
       Field3D result = A * input + D * Delp2(input);
 
@@ -68,7 +67,6 @@ A more complete example is ::
 
     // Drop C term for now
     Field3D operator()(const Field3D &input) {
-      TRACE("myLaplacian::operator()");
       Timer timer("invertable_operator_operate");
       Field3D result = A * input + D * Delp2(input);
 
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index c8b9ebb689..01f2d8c4a6 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -25,28 +25,21 @@
  *
  **************************************************************************/
 
-#include "bout/build_config.hxx"
-
-#include <bout/boutcomm.hxx>
-#include <bout/rvec.hxx>
-
-#include <bout/globals.hxx> // for mesh
-
-#include <bout/field2d.hxx>
-
-#include <bout/utils.hxx>
+#include "bout/build_defines.hxx"
 
+#include <bout/assert.hxx>
 #include <bout/boundary_factory.hxx>
 #include <bout/boundary_op.hxx>
-
+#include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/field2d.hxx>
+#include <bout/globals.hxx> // for mesh
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
-
 #include <bout/output.hxx>
-#include <cmath>
+#include <bout/rvec.hxx>
+#include <bout/utils.hxx>
 
-#include <bout/assert.hxx>
+#include <cmath>
 
 Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in)
     : Field(localmesh, location_in, directions_in) {
@@ -62,7 +55,6 @@ Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes direction
 }
 
 Field2D::Field2D(const Field2D& f) : Field(f), data(f.data) {
-  TRACE("Field2D(Field2D&)");
 
 #if BOUT_USE_TRACK
   name = f.name;
@@ -145,8 +137,6 @@ Field2D& Field2D::operator=(const Field2D& rhs) {
     return (*this); // skip this assignment
   }
 
-  TRACE("Field2D: Assignment from Field2D");
-
   Field::operator=(rhs);
 
   // Copy the data and data sizes
@@ -165,8 +155,6 @@ Field2D& Field2D::operator=(Field2D&& rhs) noexcept {
     return (*this); // skip this assignment
   }
 
-  TRACE("Field2D: Move assignment from Field2D");
-
   // Move the data and data sizes
   nx = rhs.nx;
   ny = rhs.ny;
@@ -185,7 +173,6 @@ Field2D& Field2D::operator=(const BoutReal rhs) {
   name = "<r2D>";
 #endif
 
-  TRACE("Field2D = BoutReal");
   allocate();
 
   BOUT_FOR(i, getRegion("RGN_ALL")) { (*this)[i] = rhs; }
@@ -196,7 +183,6 @@ Field2D& Field2D::operator=(const BoutReal rhs) {
 ///////////////////// BOUNDARY CONDITIONS //////////////////
 
 void Field2D::applyBoundary(bool init) {
-  TRACE("Field2D::applyBoundary()");
 
 #if CHECK > 0
   if (init) {
@@ -218,7 +204,6 @@ void Field2D::applyBoundary(bool init) {
 }
 
 void Field2D::applyBoundary(BoutReal time) {
-  TRACE("Field2D::applyBoundary(time)");
 
 #if CHECK > 0
   if (not isBoundarySet()) {
@@ -234,7 +219,6 @@ void Field2D::applyBoundary(BoutReal time) {
 }
 
 void Field2D::applyBoundary(const std::string& condition) {
-  TRACE("Field2D::applyBoundary(condition)");
 
   checkData(*this);
 
@@ -268,7 +252,7 @@ void Field2D::applyBoundary(const std::string& condition) {
 }
 
 void Field2D::applyBoundary(const std::string& region, const std::string& condition) {
-  TRACE("Field2D::applyBoundary(string, string)");
+
   checkData(*this);
 
   /// Get the boundary factory (singleton)
@@ -310,7 +294,6 @@ void Field2D::applyBoundary(const std::string& region, const std::string& condit
 }
 
 void Field2D::applyTDerivBoundary() {
-  TRACE("Field2D::applyTDerivBoundary()");
 
   checkData(*this);
   ASSERT1(deriv != nullptr);
@@ -322,7 +305,6 @@ void Field2D::applyTDerivBoundary() {
 }
 
 void Field2D::setBoundaryTo(const Field2D& f2d) {
-  TRACE("Field2D::setBoundary(const Field2D&)");
 
   checkData(f2d);
 
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 4c5ffa9748..9821c638f7 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -25,7 +25,7 @@
  *
  **************************************************************************/
 
-#include "bout/build_config.hxx"
+#include "bout/build_defines.hxx"
 
 #include <bout/boutcomm.hxx>
 #include <bout/globals.hxx>
@@ -43,7 +43,6 @@
 #include <bout/fft.hxx>
 #include <bout/field3d.hxx>
 #include <bout/interpolation.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 #include <bout/utils.hxx>
 
@@ -67,8 +66,6 @@ Field3D::Field3D(const Field3D& f)
     : Field(f), data(f.data), yup_fields(f.yup_fields), ydown_fields(f.ydown_fields),
       regionID(f.regionID) {
 
-  TRACE("Field3D(Field3D&)");
-
   if (fieldmesh) {
     nx = fieldmesh->LocalNx;
     ny = fieldmesh->LocalNy;
@@ -78,8 +75,6 @@ Field3D::Field3D(const Field3D& f)
 
 Field3D::Field3D(const Field2D& f) : Field(f) {
 
-  TRACE("Field3D: Copy constructor from Field2D");
-
   nx = fieldmesh->LocalNx;
   ny = fieldmesh->LocalNy;
   nz = fieldmesh->LocalNz;
@@ -89,15 +84,12 @@ Field3D::Field3D(const Field2D& f) : Field(f) {
 
 Field3D::Field3D(const BoutReal val, Mesh* localmesh) : Field3D(localmesh) {
 
-  TRACE("Field3D: Copy constructor from value");
-
   *this = val;
 }
 
 Field3D::Field3D(Array<BoutReal> data_in, Mesh* localmesh, CELL_LOC datalocation,
                  DirectionTypes directions_in)
     : Field(localmesh, datalocation, directions_in), data(std::move(data_in)) {
-  TRACE("Field3D: Copy constructor from Array and Mesh");
 
   nx = fieldmesh->LocalNx;
   ny = fieldmesh->LocalNy;
@@ -137,7 +129,6 @@ Field3D* Field3D::timeDeriv() {
 }
 
 void Field3D::splitParallelSlices() {
-  TRACE("Field3D::splitParallelSlices");
 
   if (hasParallelSlices()) {
     return;
@@ -152,7 +143,6 @@ void Field3D::splitParallelSlices() {
 }
 
 void Field3D::clearParallelSlices() {
-  TRACE("Field3D::clearParallelSlices");
 
   if (!hasParallelSlices()) {
     return;
@@ -245,8 +235,6 @@ Field3D& Field3D::operator=(const Field3D& rhs) {
     return (*this); // skip this assignment
   }
 
-  TRACE("Field3D: Assignment from Field3D");
-
   // Copy base slice
   Field::operator=(rhs);
 
@@ -266,7 +254,6 @@ Field3D& Field3D::operator=(const Field3D& rhs) {
 }
 
 Field3D& Field3D::operator=(Field3D&& rhs) {
-  TRACE("Field3D: Assignment from Field3D");
 
   // Move parallel slices or delete existing ones.
   yup_fields = std::move(rhs.yup_fields);
@@ -287,7 +274,6 @@ Field3D& Field3D::operator=(Field3D&& rhs) {
 }
 
 Field3D& Field3D::operator=(const Field2D& rhs) {
-  TRACE("Field3D = Field2D");
 
   /// Check that the data is allocated
   ASSERT1(rhs.isAllocated());
@@ -314,7 +300,6 @@ Field3D& Field3D::operator=(const Field2D& rhs) {
 }
 
 void Field3D::operator=(const FieldPerp& rhs) {
-  TRACE("Field3D = FieldPerp");
 
   ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
   /// Check that the data is allocated
@@ -333,7 +318,6 @@ void Field3D::operator=(const FieldPerp& rhs) {
 }
 
 Field3D& Field3D::operator=(const BoutReal val) {
-  TRACE("Field3D = BoutReal");
 
   // Delete existing parallel slices. We don't copy parallel slices, so any
   // that currently exist will be incorrect.
@@ -355,7 +339,6 @@ Field3D& Field3D::calcParallelSlices() {
 ///////////////////// BOUNDARY CONDITIONS //////////////////
 
 void Field3D::applyBoundary(bool init) {
-  TRACE("Field3D::applyBoundary()");
 
 #if CHECK > 0
   if (init) {
@@ -378,7 +361,6 @@ void Field3D::applyBoundary(bool init) {
 }
 
 void Field3D::applyBoundary(BoutReal t) {
-  TRACE("Field3D::applyBoundary()");
 
 #if CHECK > 0
   if (not isBoundarySet()) {
@@ -395,7 +377,6 @@ void Field3D::applyBoundary(BoutReal t) {
 }
 
 void Field3D::applyBoundary(const std::string& condition) {
-  TRACE("Field3D::applyBoundary(condition)");
 
   checkData(*this);
 
@@ -413,7 +394,7 @@ void Field3D::applyBoundary(const std::string& condition) {
 }
 
 void Field3D::applyBoundary(const std::string& region, const std::string& condition) {
-  TRACE("Field3D::applyBoundary(string, string)");
+
   checkData(*this);
 
   /// Get the boundary factory (singleton)
@@ -439,7 +420,6 @@ void Field3D::applyBoundary(const std::string& region, const std::string& condit
 }
 
 void Field3D::applyTDerivBoundary() {
-  TRACE("Field3D::applyTDerivBoundary()");
 
   checkData(*this);
   ASSERT1(deriv != nullptr);
@@ -451,7 +431,6 @@ void Field3D::applyTDerivBoundary() {
 }
 
 void Field3D::setBoundaryTo(const Field3D& f3d) {
-  TRACE("Field3D::setBoundary(const Field3D&)");
 
   checkData(f3d);
 
@@ -475,8 +454,6 @@ void Field3D::setBoundaryTo(const Field3D& f3d) {
 
 void Field3D::applyParallelBoundary() {
 
-  TRACE("Field3D::applyParallelBoundary()");
-
   checkData(*this);
   if (isFci()) {
     ASSERT1(hasParallelSlices());
@@ -493,8 +470,6 @@ void Field3D::applyParallelBoundary() {
 
 void Field3D::applyParallelBoundary(BoutReal t) {
 
-  TRACE("Field3D::applyParallelBoundary(t)");
-
   checkData(*this);
   if (isFci()) {
     ASSERT1(hasParallelSlices());
@@ -511,8 +486,6 @@ void Field3D::applyParallelBoundary(BoutReal t) {
 
 void Field3D::applyParallelBoundary(const std::string& condition) {
 
-  TRACE("Field3D::applyParallelBoundary(condition)");
-
   checkData(*this);
   if (isFci()) {
     ASSERT1(hasParallelSlices());
@@ -535,8 +508,6 @@ void Field3D::applyParallelBoundary(const std::string& condition) {
 void Field3D::applyParallelBoundary(const std::string& region,
                                     const std::string& condition) {
 
-  TRACE("Field3D::applyParallelBoundary(region, condition)");
-
   checkData(*this);
   if (isFci()) {
     ASSERT1(hasParallelSlices());
@@ -562,8 +533,6 @@ void Field3D::applyParallelBoundary(const std::string& region,
 void Field3D::applyParallelBoundary(const std::string& region,
                                     const std::string& condition, Field3D* f) {
 
-  TRACE("Field3D::applyParallelBoundary(region, condition, f)");
-
   checkData(*this);
   if (isFci()) {
     ASSERT1(hasParallelSlices());
@@ -599,7 +568,7 @@ Field3D operator-(const Field3D& f) { return -1.0 * f; }
 //////////////// NON-MEMBER FUNCTIONS //////////////////
 
 Field3D pow(const Field3D& lhs, const Field2D& rhs, const std::string& rgn) {
-  TRACE("pow(Field3D, Field2D)");
+
   // Check if the inputs are allocated
   checkData(lhs);
   checkData(rhs);
@@ -615,7 +584,6 @@ Field3D pow(const Field3D& lhs, const Field2D& rhs, const std::string& rgn) {
 }
 
 FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs, const std::string& rgn) {
-  TRACE("pow(Field3D, FieldPerp)");
 
   checkData(lhs);
   checkData(rhs);
@@ -635,7 +603,6 @@ FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs, const std::string& rgn)
 // Friend functions
 
 Field3D filter(const Field3D& var, int N0, const std::string& rgn) {
-  TRACE("filter(Field3D, int)");
 
   checkData(var);
 
@@ -681,7 +648,6 @@ Field3D filter(const Field3D& var, int N0, const std::string& rgn) {
 
 // Fourier filter in z with zmin
 Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string& rgn) {
-  TRACE("lowPass(Field3D, {}, {})", zmax, keep_zonal);
 
   checkData(var);
   int ncz = var.getNz();
@@ -731,7 +697,7 @@ Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string
  * Use FFT to shift by an angle in the Z direction
  */
 void shiftZ(Field3D& var, int jx, int jy, double zangle) {
-  TRACE("shiftZ");
+
   checkData(var);
   var.allocate(); // Ensure that var is unique
   Mesh* localmesh = var.getMesh();
@@ -800,7 +766,6 @@ void checkData(const Field3D& f, const std::string& region) {
 #endif
 
 Field2D DC(const Field3D& f, const std::string& rgn) {
-  TRACE("DC(Field3D)");
 
   checkData(f);
 
diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index ca9bdc0397..d74a986473 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -31,7 +31,6 @@
 #include <bout/boutexception.hxx>
 #include <bout/fieldperp.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/utils.hxx>
 
 FieldPerp::FieldPerp(Mesh* localmesh, CELL_LOC location_in, int yindex_in,
@@ -51,7 +50,6 @@ FieldPerp::FieldPerp(Array<BoutReal> data_in, Mesh* localmesh, CELL_LOC location
                      int yindex_in, DirectionTypes directions)
     : Field(localmesh, location_in, directions), yindex(yindex_in),
       nx(fieldmesh->LocalNx), nz(fieldmesh->LocalNz), data(std::move(data_in)) {
-  TRACE("FieldPerp: Copy constructor from Array and Mesh");
 
   ASSERT1(data.size() == nx * nz);
 }
@@ -97,7 +95,6 @@ FieldPerp& FieldPerp::operator=(const FieldPerp& rhs) {
 }
 
 FieldPerp& FieldPerp::operator=(const BoutReal rhs) {
-  TRACE("FieldPerp = BoutReal");
 
   allocate();
 
diff --git a/src/field/vecops.cxx b/src/field/vecops.cxx
index 4d62d1a1d7..1677187fcd 100644
--- a/src/field/vecops.cxx
+++ b/src/field/vecops.cxx
@@ -29,7 +29,6 @@
 
 #include <bout/derivs.hxx>
 #include <bout/globals.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/unused.hxx>
 #include <bout/utils.hxx>
 #include <bout/vecops.hxx>
@@ -39,7 +38,7 @@
  **************************************************************************/
 
 Vector2D Grad(const Field2D& f, CELL_LOC outloc, const std::string& method) {
-  TRACE("Grad( Field2D )");
+
   SCOREP0();
   CELL_LOC outloc_x, outloc_y, outloc_z;
   if (outloc == CELL_VSHIFT) {
@@ -68,7 +67,7 @@ Vector2D Grad(const Field2D& f, CELL_LOC outloc, const std::string& method) {
 }
 
 Vector3D Grad(const Field3D& f, CELL_LOC outloc, const std::string& method) {
-  TRACE("Grad( Field3D )");
+
   SCOREP0();
   CELL_LOC outloc_x, outloc_y, outloc_z;
   if (outloc == CELL_VSHIFT) {
@@ -97,7 +96,7 @@ Vector3D Grad(const Field3D& f, CELL_LOC outloc, const std::string& method) {
 }
 
 Vector3D Grad_perp(const Field3D& f, CELL_LOC outloc, const std::string& method) {
-  TRACE("Grad_perp( Field3D )");
+
   SCOREP0();
   ASSERT1(outloc == CELL_DEFAULT || outloc == f.getLocation());
 
@@ -145,7 +144,7 @@ Vector2D Grad_perp(const Field2D& f, CELL_LOC outloc, const std::string& method)
 
 Coordinates::FieldMetric Div(const Vector2D& v, CELL_LOC outloc,
                              const std::string& method) {
-  TRACE("Div( Vector2D )");
+
   SCOREP0();
   if (outloc == CELL_DEFAULT) {
     outloc = v.getLocation();
@@ -170,7 +169,7 @@ Coordinates::FieldMetric Div(const Vector2D& v, CELL_LOC outloc,
 }
 
 Field3D Div(const Vector3D& v, CELL_LOC outloc, const std::string& method) {
-  TRACE("Div( Vector3D )");
+
   SCOREP0();
   if (outloc == CELL_DEFAULT) {
     outloc = v.getLocation();
@@ -209,7 +208,7 @@ Field3D Div(const Vector3D& v, CELL_LOC outloc, const std::string& method) {
 
 Coordinates::FieldMetric Div(const Vector2D& v, const Field2D& f, CELL_LOC outloc,
                              const std::string& method) {
-  TRACE("Div( Vector2D, Field2D )");
+
   SCOREP0();
   if (outloc == CELL_DEFAULT) {
     outloc = v.getLocation();
@@ -236,7 +235,6 @@ Coordinates::FieldMetric Div(const Vector2D& v, const Field2D& f, CELL_LOC outlo
 
 Field3D Div(const Vector3D& v, const Field3D& f, CELL_LOC outloc,
             const std::string& method) {
-  TRACE("Div( Vector3D, Field3D )");
 
   if (outloc == CELL_DEFAULT) {
     outloc = v.getLocation();
@@ -265,8 +263,6 @@ Field3D Div(const Vector3D& v, const Field3D& f, CELL_LOC outloc,
 
 Vector2D Curl(const Vector2D& v) {
 
-  TRACE("Curl( Vector2D )");
-
   ASSERT1(v.getLocation() != CELL_VSHIFT);
   Mesh* localmesh = v.getMesh();
   auto metric = v.x.getCoordinates();
@@ -292,7 +288,7 @@ Vector2D Curl(const Vector2D& v) {
 }
 
 Vector3D Curl(const Vector3D& v) {
-  TRACE("Curl( Vector3D )");
+
   SCOREP0();
   ASSERT1(v.getLocation() != CELL_VSHIFT);
 
@@ -323,7 +319,7 @@ Vector3D Curl(const Vector3D& v) {
  * Upwinding operators
  **************************************************************************/
 Coordinates::FieldMetric V_dot_Grad(const Vector2D& v, const Field2D& f) {
-  TRACE("V_dot_Grad( Vector2D , Field2D )");
+
   SCOREP0();
 
   // Get contravariant components of v
@@ -334,7 +330,7 @@ Coordinates::FieldMetric V_dot_Grad(const Vector2D& v, const Field2D& f) {
 }
 
 Field3D V_dot_Grad(const Vector2D& v, const Field3D& f) {
-  TRACE("V_dot_Grad( Vector2D , Field3D )");
+
   SCOREP0();
 
   // Get contravariant components of v
@@ -345,7 +341,7 @@ Field3D V_dot_Grad(const Vector2D& v, const Field3D& f) {
 }
 
 Field3D V_dot_Grad(const Vector3D& v, const Field2D& f) {
-  TRACE("V_dot_Grad( Vector3D , Field2D )");
+
   SCOREP0();
 
   // Get contravariant components of v
@@ -356,7 +352,7 @@ Field3D V_dot_Grad(const Vector3D& v, const Field2D& f) {
 }
 
 Field3D V_dot_Grad(const Vector3D& v, const Field3D& f) {
-  TRACE("V_dot_Grad( Vector3D , Field3D )");
+
   SCOREP0();
 
   // Get contravariant components of v
diff --git a/src/field/vector2d.cxx b/src/field/vector2d.cxx
index 74d3a88a22..ab2d993549 100644
--- a/src/field/vector2d.cxx
+++ b/src/field/vector2d.cxx
@@ -429,7 +429,7 @@ CELL_LOC Vector2D::getLocation() const {
 
 Vector2D& Vector2D::setLocation(CELL_LOC loc) {
   SCOREP0();
-  TRACE("Vector2D::setLocation");
+
   if (loc == CELL_DEFAULT) {
     loc = CELL_CENTRE;
   }
diff --git a/src/field/vector3d.cxx b/src/field/vector3d.cxx
index 56124595b3..7fb4a88918 100644
--- a/src/field/vector3d.cxx
+++ b/src/field/vector3d.cxx
@@ -551,7 +551,7 @@ CELL_LOC Vector3D::getLocation() const {
 
 Vector3D& Vector3D::setLocation(CELL_LOC loc) {
   SCOREP0();
-  TRACE("Vector3D::setLocation");
+
   if (loc == CELL_DEFAULT) {
     loc = CELL_CENTRE;
   }
diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
index 837ac3755f..99aacea4f8 100644
--- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
+++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
@@ -304,7 +304,6 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) {
 }
 
 Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) {
-  TRACE("LaplaceCyclic::solve(Field3D, Field3D)");
 
   ASSERT1(rhs.getLocation() == location);
   ASSERT1(x0.getLocation() == location);
diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
index 5255ea939d..926facd9e6 100644
--- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
+++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
@@ -234,7 +234,6 @@ FieldPerp LaplaceIPT::solve(const FieldPerp& b, const FieldPerp& x0) {
   ASSERT1(localmesh == b.getMesh() && localmesh == x0.getMesh());
   ASSERT1(b.getLocation() == location);
   ASSERT1(x0.getLocation() == location);
-  TRACE("LaplaceIPT::solve(const, const)");
 
   FieldPerp x{emptyFrom(b)};
 
diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
index 04c8c7e0c9..48137a13bf 100644
--- a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
+++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
@@ -46,8 +46,6 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_
                                    Solver* UNUSED(solver))
     : Laplacian(opt, loc, mesh_in), A(0.0), C1(1.0), C2(1.0), D(1.0) {
 
-  TRACE("LaplaceMultigrid::LaplaceMultigrid(Options *opt)");
-
   // periodic x-direction not handled: see MultigridAlg::communications
   ASSERT1(!localmesh->periodicX);
 
@@ -223,8 +221,6 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_
 
 FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) {
 
-  TRACE("LaplaceMultigrid::solve(const FieldPerp, const FieldPerp)");
-
   ASSERT1(localmesh == b_in.getMesh() && localmesh == x0.getMesh());
   ASSERT1(b_in.getLocation() == location);
   ASSERT1(x0.getLocation() == location);
@@ -578,7 +574,6 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) {
 }
 
 void LaplaceMultigrid::generateMatrixF(int level) {
-  TRACE("LaplaceMultigrid::generateMatrixF(int)");
 
   // Set (fine-level) matrix entries
 
diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx
index b619d80100..60169c6eb4 100644
--- a/src/invert/laplace/impls/pcr/pcr.cxx
+++ b/src/invert/laplace/impls/pcr/pcr.cxx
@@ -308,7 +308,6 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) {
 }
 
 Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) {
-  TRACE("LaplacePCR::solve(Field3D, Field3D)");
 
   ASSERT1(rhs.getLocation() == location);
   ASSERT1(x0.getLocation() == location);
diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
index b48b20f246..600166aa6b 100644
--- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
+++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
@@ -304,7 +304,6 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) {
 }
 
 Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) {
-  TRACE("LaplacePCR_THOMAS::solve(Field3D, Field3D)");
 
   ASSERT1(rhs.getLocation() == location);
   ASSERT1(x0.getLocation() == location);
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 5f417d4faa..65c80ec48c 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -336,7 +336,6 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b) { return solve(b, b); }
  * \returns sol     The solution x of the problem Ax=b.
  */
 FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
-  TRACE("LaplacePetsc::solve");
 
   ASSERT1(localmesh == b.getMesh() && localmesh == x0.getMesh());
   ASSERT1(b.getLocation() == location);
diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx
index 7a8af20fbd..b8650d1d68 100644
--- a/src/invert/laplace/invert_laplace.cxx
+++ b/src/invert/laplace/invert_laplace.cxx
@@ -156,7 +156,6 @@ void Laplacian::cleanup() { instance.reset(); }
  **********************************************************************************/
 
 Field3D Laplacian::solve(const Field3D& b) {
-  TRACE("Laplacian::solve(Field3D)");
 
   ASSERT1(b.getLocation() == location);
   ASSERT1(localmesh == b.getMesh());
@@ -217,7 +216,6 @@ Field2D Laplacian::solve(const Field2D& b) {
  * \returns x All the y-slices of x_slice in the equation A*x_slice = b_slice
  */
 Field3D Laplacian::solve(const Field3D& b, const Field3D& x0) {
-  TRACE("Laplacian::solve(Field3D, Field3D)");
 
   ASSERT1(b.getLocation() == location);
   ASSERT1(x0.getLocation() == location);
diff --git a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
index a242bf3432..1de9d58b26 100644
--- a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
+++ b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
@@ -61,7 +61,7 @@ LaplaceXZcyclic::LaplaceXZcyclic(Mesh* m, Options* options, const CELL_LOC loc)
 }
 
 void LaplaceXZcyclic::setCoefs(const Field2D& A2D, const Field2D& B2D) {
-  TRACE("LaplaceXZcyclic::setCoefs");
+
   Timer timer("invert");
 
   ASSERT1(A2D.getMesh() == localmesh);
diff --git a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
index 769e797352..d81446d522 100644
--- a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
+++ b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
@@ -97,8 +97,6 @@ LaplaceXZpetsc::LaplaceXZpetsc(Mesh* m, Options* opt, const CELL_LOC loc)
    *                  given by b
    */
 
-  TRACE("LaplaceXZpetsc::LaplaceXZpetsc");
-
   if (opt == nullptr) {
     // If no options supplied, use default
     opt = &(Options::root())["laplacexz"];
@@ -260,8 +258,6 @@ LaplaceXZpetsc::LaplaceXZpetsc(Mesh* m, Options* opt, const CELL_LOC loc)
 
 LaplaceXZpetsc::~LaplaceXZpetsc() {
 
-  TRACE("LaplaceXZpetsc::~LaplaceXZpetsc");
-
   PetscBool petsc_is_finalised;
   PetscFinalized(&petsc_is_finalised);
 
@@ -293,8 +289,6 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
    * Bin       - The B coefficient in div(A grad_perp(B)) + Bf = b
    */
 
-  TRACE("LaplaceXZpetsc::setCoefs");
-
   ASSERT1(Ain.getMesh() == localmesh);
   ASSERT1(Bin.getMesh() == localmesh);
   ASSERT1(Ain.getLocation() == location);
@@ -767,8 +761,6 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
    * result    - The solved x (returned as a Field3D) in the matrix problem Ax=b
    */
 
-  TRACE("LaplaceXZpetsc::solve");
-
   ASSERT1(bin.getMesh() == localmesh);
   ASSERT1(x0in.getMesh() == localmesh);
   ASSERT1(bin.getLocation() == location);
diff --git a/src/invert/parderiv/impls/cyclic/cyclic.cxx b/src/invert/parderiv/impls/cyclic/cyclic.cxx
index 5a798ca1d5..692d5f2660 100644
--- a/src/invert/parderiv/impls/cyclic/cyclic.cxx
+++ b/src/invert/parderiv/impls/cyclic/cyclic.cxx
@@ -63,7 +63,7 @@ InvertParCR::InvertParCR(Options* opt, CELL_LOC location, Mesh* mesh_in)
 }
 
 const Field3D InvertParCR::solve(const Field3D& f) {
-  TRACE("InvertParCR::solve(Field3D)");
+
   ASSERT1(localmesh == f.getMesh());
   ASSERT1(location == f.getLocation());
 
diff --git a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
index be65d5ab0b..bd644dc625 100644
--- a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
+++ b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
@@ -59,7 +59,7 @@ InvertParDivCR::InvertParDivCR(Options* opt, CELL_LOC location, Mesh* mesh_in)
 }
 
 Field3D InvertParDivCR::solve(const Field3D& f) {
-  TRACE("InvertParDivCR::solve(Field3D)");
+
   ASSERT1(localmesh == f.getMesh());
   ASSERT1(location == f.getLocation());
 
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 5508f8db71..4019fc4eea 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -7,7 +7,6 @@
 #include <bout/globals.hxx>
 #include <bout/invert_laplace.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 #include <bout/sys/generator_context.hxx>
 #include <bout/utils.hxx>
@@ -30,8 +29,6 @@ using bout::generator::Context;
  */
 #if CHECK > 0
 void verifyNumPoints(BoundaryRegion* region, int ptsRequired) {
-  TRACE("Verifying number of points available for BC");
-
   int ptsAvailGlobal, ptsAvailLocal, ptsAvail;
   std::string side, gridType;
   Mesh* mesh = region->localmesh;
@@ -3606,7 +3603,6 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
   }
 
   void BoundaryRelax::apply_ddt(Field2D & f) {
-    TRACE("BoundaryRelax::apply_ddt(Field2D)");
 
     // Make a copy of f
     Field2D g = f;
@@ -3622,7 +3618,6 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
   }
 
   void BoundaryRelax::apply_ddt(Field3D & f) {
-    TRACE("BoundaryRelax::apply_ddt(Field3D)");
 
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 58d54f826e..b275f0c8de 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -932,7 +932,7 @@ const Field2D& Coordinates::zlength() const {
 
 int Coordinates::geometry(bool recalculate_staggered,
                           bool force_interpolate_from_centre) {
-  TRACE("Coordinates::geometry");
+
   localmesh->communicate_no_slices(dx, dy, dz, g11, g22, g33, g12, g13, g23, g_11, g_22,
                                    g_33, g_12, g_13, g_23, J, Bxy);
 
@@ -1202,7 +1202,6 @@ int Coordinates::geometry(bool recalculate_staggered,
 }
 
 int Coordinates::calcCovariant(const std::string& region) {
-  TRACE("Coordinates::calcCovariant");
 
   // Make sure metric elements are allocated
   g_11.allocate();
@@ -1265,7 +1264,6 @@ int Coordinates::calcCovariant(const std::string& region) {
 }
 
 int Coordinates::calcContravariant(const std::string& region) {
-  TRACE("Coordinates::calcContravariant");
 
   // Make sure metric elements are allocated
   g11.allocate();
@@ -1320,7 +1318,7 @@ int Coordinates::calcContravariant(const std::string& region) {
 }
 
 int Coordinates::jacobian() {
-  TRACE("Coordinates::jacobian");
+
   // calculate Jacobian using g^-1 = det[g^ij], J = sqrt(g)
 
   const bool extrapolate_x = not localmesh->sourceHasXBoundaryGuards();
@@ -1522,7 +1520,7 @@ Field3D Coordinates::DDZ(const Field3D& f, CELL_LOC outloc, const std::string& m
 Coordinates::FieldMetric Coordinates::Grad_par(const Field2D& var,
                                                [[maybe_unused]] CELL_LOC outloc,
                                                const std::string& UNUSED(method)) {
-  TRACE("Coordinates::Grad_par( Field2D )");
+
   ASSERT1(location == outloc
           || (outloc == CELL_DEFAULT && location == var.getLocation()));
 
@@ -1531,7 +1529,7 @@ Coordinates::FieldMetric Coordinates::Grad_par(const Field2D& var,
 
 Field3D Coordinates::Grad_par(const Field3D& var, CELL_LOC outloc,
                               const std::string& method) {
-  TRACE("Coordinates::Grad_par( Field3D )");
+
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
   return ::DDY(var, outloc, method) * invSg();
@@ -1561,7 +1559,7 @@ Field3D Coordinates::Vpar_Grad_par(const Field3D& v, const Field3D& f, CELL_LOC
 
 Coordinates::FieldMetric Coordinates::Div_par(const Field2D& f, CELL_LOC outloc,
                                               const std::string& method) {
-  TRACE("Coordinates::Div_par( Field2D )");
+
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
   // Need Bxy at location of f, which might be different from location of this
@@ -1573,7 +1571,7 @@ Coordinates::FieldMetric Coordinates::Div_par(const Field2D& f, CELL_LOC outloc,
 
 Field3D Coordinates::Div_par(const Field3D& f, CELL_LOC outloc,
                              const std::string& method) {
-  TRACE("Coordinates::Div_par( Field3D )");
+
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
   // Need Bxy at location of f, which might be different from location of this
@@ -1602,7 +1600,7 @@ Field3D Coordinates::Div_par(const Field3D& f, CELL_LOC outloc,
 
 Coordinates::FieldMetric Coordinates::Grad2_par2(const Field2D& f, CELL_LOC outloc,
                                                  const std::string& method) {
-  TRACE("Coordinates::Grad2_par2( Field2D )");
+
   ASSERT1(location == outloc || (outloc == CELL_DEFAULT && location == f.getLocation()));
 
   auto result = Grad2_par2_DDY_invSg(outloc, method) * DDY(f, outloc, method)
@@ -1613,7 +1611,7 @@ Coordinates::FieldMetric Coordinates::Grad2_par2(const Field2D& f, CELL_LOC outl
 
 Field3D Coordinates::Grad2_par2(const Field3D& f, CELL_LOC outloc,
                                 const std::string& method) {
-  TRACE("Coordinates::Grad2_par2( Field3D )");
+
   if (outloc == CELL_DEFAULT) {
     outloc = f.getLocation();
   }
@@ -1637,7 +1635,7 @@ Field3D Coordinates::Grad2_par2(const Field3D& f, CELL_LOC outloc,
 
 Coordinates::FieldMetric Coordinates::Delp2(const Field2D& f, CELL_LOC outloc,
                                             bool UNUSED(useFFT)) {
-  TRACE("Coordinates::Delp2( Field2D )");
+
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
   auto result = G1 * DDX(f, outloc) + g11 * D2DX2(f, outloc);
@@ -1646,7 +1644,6 @@ Coordinates::FieldMetric Coordinates::Delp2(const Field2D& f, CELL_LOC outloc,
 }
 
 Field3D Coordinates::Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
-  TRACE("Coordinates::Delp2( Field3D )");
 
   if (outloc == CELL_DEFAULT) {
     outloc = f.getLocation();
@@ -1712,7 +1709,6 @@ Field3D Coordinates::Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
 }
 
 FieldPerp Coordinates::Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
-  TRACE("Coordinates::Delp2( FieldPerp )");
 
   if (outloc == CELL_DEFAULT) {
     outloc = f.getLocation();
@@ -1789,7 +1785,7 @@ Field3D Coordinates::Laplace_par(const Field3D& f, CELL_LOC outloc) {
 Coordinates::FieldMetric Coordinates::Laplace(const Field2D& f, CELL_LOC outloc,
                                               const std::string& dfdy_boundary_conditions,
                                               const std::string& dfdy_dy_region) {
-  TRACE("Coordinates::Laplace( Field2D )");
+
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
   auto result = G1 * DDX(f, outloc) + G2 * DDY(f, outloc) + g11 * D2DX2(f, outloc)
@@ -1804,7 +1800,7 @@ Coordinates::FieldMetric Coordinates::Laplace(const Field2D& f, CELL_LOC outloc,
 Field3D Coordinates::Laplace(const Field3D& f, CELL_LOC outloc,
                              const std::string& dfdy_boundary_conditions,
                              const std::string& dfdy_dy_region) {
-  TRACE("Coordinates::Laplace( Field3D )");
+
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
   Field3D result = G1 * ::DDX(f, outloc) + G2 * ::DDY(f, outloc) + G3 * ::DDZ(f, outloc)
@@ -1823,7 +1819,7 @@ Field3D Coordinates::Laplace(const Field3D& f, CELL_LOC outloc,
 // solver
 Field2D Coordinates::Laplace_perpXY([[maybe_unused]] const Field2D& A,
                                     [[maybe_unused]] const Field2D& f) {
-  TRACE("Coordinates::Laplace_perpXY( Field2D )");
+
 #if not(BOUT_USE_METRIC_3D)
   Field2D result;
   result.allocate();
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index fba64eaa59..952ea22243 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -20,7 +20,6 @@
 GridFile::GridFile(std::string gridfilename)
     : GridDataSource(true), data(bout::OptionsIO::create(gridfilename)->read()),
       filename(std::move(gridfilename)) {
-  TRACE("GridFile constructor");
 
   // Get number of y-boundary guard cells saved in the grid file
   grid_yguards = data["y_boundary_guards"].withDefault<int>(0);
@@ -60,7 +59,7 @@ bool GridFile::hasVar(const std::string& name) { return data.isSet(name); }
 bool GridFile::get(Mesh* UNUSED(m), std::string& sval, const std::string& name,
                    const std::string& def) {
   Timer timer("io");
-  TRACE("GridFile::get(std::string)");
+
   const bool success = data.isSet(name);
   if (not success) {
     // Override any previously set defaults
@@ -93,7 +92,7 @@ bool GridFile::get(Mesh* UNUSED(m), std::string& sval, const std::string& name,
  */
 bool GridFile::get(Mesh* UNUSED(m), int& ival, const std::string& name, int def) {
   Timer timer("io");
-  TRACE("GridFile::get(int)");
+
   const bool success = data.isSet(name);
   if (not success) {
     // Override any previously set defaults
@@ -110,7 +109,7 @@ bool GridFile::get(Mesh* UNUSED(m), int& ival, const std::string& name, int def)
 bool GridFile::get(Mesh* UNUSED(m), BoutReal& rval, const std::string& name,
                    BoutReal def) {
   Timer timer("io");
-  TRACE("GridFile::get(BoutReal)");
+
   const bool success = data.isSet(name);
   if (not success) {
     // Override any previously set defaults
@@ -472,7 +471,6 @@ bool GridFile::get([[maybe_unused]] Mesh* m, [[maybe_unused]] std::vector<int>&
                    [[maybe_unused]] const std::string& name, [[maybe_unused]] int len,
                    [[maybe_unused]] int offset,
                    [[maybe_unused]] GridDataSource::Direction dir) {
-  TRACE("GridFile::get(vector<int>)");
 
   if (not data.isSet(name)) {
     return false;
@@ -498,7 +496,6 @@ bool GridFile::get([[maybe_unused]] Mesh* m, [[maybe_unused]] std::vector<int>&
 
 bool GridFile::get(Mesh* UNUSED(m), std::vector<BoutReal>& var, const std::string& name,
                    int len, int offset, GridDataSource::Direction UNUSED(dir)) {
-  TRACE("GridFile::get(vector<BoutReal>)");
 
   if (not data.isSet(name)) {
     return false;
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 42fa4d6ca5..9084f90465 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -30,7 +30,6 @@
 #include <bout/difops.hxx>
 #include <bout/fft.hxx>
 #include <bout/globals.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/solver.hxx>
 #include <bout/utils.hxx>
 #include <bout/vecops.hxx>
@@ -458,8 +457,6 @@ Field2D Laplace_perpXY(const Field2D& A, const Field2D& f) {
 Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
                                           CELL_LOC outloc) {
 
-  TRACE("b0xGrad_dot_Grad( Field2D , Field2D )");
-
   if (outloc == CELL_DEFAULT) {
     outloc = A.getLocation();
   }
@@ -489,7 +486,6 @@ Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
 }
 
 Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc) {
-  TRACE("b0xGrad_dot_Grad( Field2D , Field3D )");
 
   if (outloc == CELL_DEFAULT) {
     outloc = A.getLocation();
@@ -531,7 +527,6 @@ Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc)
 }
 
 Field3D b0xGrad_dot_Grad(const Field3D& p, const Field2D& A, CELL_LOC outloc) {
-  TRACE("b0xGrad_dot_Grad( Field3D , Field2D )");
 
   if (outloc == CELL_DEFAULT) {
     outloc = A.getLocation();
@@ -566,7 +561,6 @@ Field3D b0xGrad_dot_Grad(const Field3D& p, const Field2D& A, CELL_LOC outloc) {
 }
 
 Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A, CELL_LOC outloc) {
-  TRACE("b0xGrad_dot_Grad( Field3D , Field3D )");
 
   if (outloc == CELL_DEFAULT) {
     outloc = A.getLocation();
@@ -614,7 +608,6 @@ Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A, CELL_LOC outloc)
 Coordinates::FieldMetric bracket(const Field2D& f, const Field2D& g,
                                  BRACKET_METHOD method, CELL_LOC outloc,
                                  Solver* UNUSED(solver)) {
-  TRACE("bracket(Field2D, Field2D)");
 
   ASSERT1_FIELDS_COMPATIBLE(f, g);
   if (outloc == CELL_DEFAULT) {
@@ -637,7 +630,6 @@ Coordinates::FieldMetric bracket(const Field2D& f, const Field2D& g,
 
 Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
                 CELL_LOC outloc, Solver* solver) {
-  TRACE("bracket(Field3D, Field2D)");
 
   ASSERT1_FIELDS_COMPATIBLE(f, g);
   if (outloc == CELL_DEFAULT) {
@@ -826,7 +818,6 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
 
 Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method,
                 CELL_LOC outloc, Solver* solver) {
-  TRACE("bracket(Field2D, Field3D)");
 
   ASSERT1_FIELDS_COMPATIBLE(f, g);
   if (outloc == CELL_DEFAULT) {
@@ -863,8 +854,6 @@ Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method,
 
 Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
                 CELL_LOC outloc, [[maybe_unused]] Solver* solver) {
-  TRACE("Field3D, Field3D");
-
   ASSERT1_FIELDS_COMPATIBLE(f, g);
   if (outloc == CELL_DEFAULT) {
     outloc = g.getLocation();
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index fe5422b4d1..2f3398b2c0 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -181,7 +181,6 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
 
 const Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin,
                                  bool bndry_flux) {
-  TRACE("FV::Div_par_K_Grad_par");
 
   ASSERT2(Kin.getLocation() == fin.getLocation());
 
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 8917fa3753..8eb09f84ec 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -431,7 +431,6 @@ void BoutMesh::setDerivedGridSizes() {
 }
 
 int BoutMesh::load() {
-  TRACE("BoutMesh::load()");
 
   output_progress << _("Loading mesh") << endl;
 
@@ -1363,7 +1362,6 @@ comm_handle BoutMesh::sendY(FieldGroup& g, comm_handle handle) {
 }
 
 int BoutMesh::wait(comm_handle handle) {
-  TRACE("BoutMesh::wait(comm_handle)");
 
   if (handle == nullptr) {
     return 1;
diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx
index 595081e3ae..48284c3536 100644
--- a/src/mesh/index_derivs.cxx
+++ b/src/mesh/index_derivs.cxx
@@ -25,7 +25,6 @@
 #include "bout/traits.hxx"
 #include <bout/index_derivs.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/unused.hxx>
 
 /*******************************************************************************
@@ -34,7 +33,6 @@
 
 /// Initialise the derivative methods. Must be called before any derivatives are used
 void Mesh::derivs_init(Options* options) {
-  TRACE("Initialising derivatives");
   // For each direction need to set what the default method is for each type
   // of derivative.
   DerivativeStore<Field3D>::getInstance().initialise(options);
@@ -45,7 +43,6 @@ void Mesh::derivs_init(Options* options) {
 
 STAGGER Mesh::getStagger(const CELL_LOC inloc, const CELL_LOC outloc,
                          const CELL_LOC allowedStaggerLoc) const {
-  TRACE("Mesh::getStagger -- three arguments");
   ASSERT1(outloc == inloc || (outloc == CELL_CENTRE && inloc == allowedStaggerLoc)
           || (outloc == allowedStaggerLoc && inloc == CELL_CENTRE));
 
@@ -61,7 +58,6 @@ STAGGER Mesh::getStagger(const CELL_LOC inloc, const CELL_LOC outloc,
 
 STAGGER Mesh::getStagger(const CELL_LOC vloc, [[maybe_unused]] const CELL_LOC inloc,
                          const CELL_LOC outloc, const CELL_LOC allowedStaggerLoc) const {
-  TRACE("Mesh::getStagger -- four arguments");
   ASSERT1(inloc == outloc);
   ASSERT1(vloc == inloc || (vloc == CELL_CENTRE && inloc == allowedStaggerLoc)
           || (vloc == allowedStaggerLoc && inloc == CELL_CENTRE));
diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx
index f7f0b457f2..a58554dc82 100644
--- a/src/mesh/interpolation_xz.cxx
+++ b/src/mesh/interpolation_xz.cxx
@@ -25,7 +25,6 @@
 
 #include <bout/globals.hxx>
 #include <bout/interpolation_xz.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 #include <bout/unused.hxx>
 
@@ -36,7 +35,6 @@ const char* strLocation(CELL_LOC loc) { return toString(loc).c_str(); }
 
 const Field3D interpolate(const Field3D& f, const Field3D& delta_x,
                           const Field3D& delta_z) {
-  TRACE("Interpolating 3D field");
   XZLagrange4pt interpolateMethod{f.getMesh()};
   return interpolateMethod.interpolate(f, delta_x, delta_z);
 }
@@ -47,8 +45,6 @@ const Field3D interpolate(const Field2D& f, const Field3D& delta_x,
 }
 
 const Field3D interpolate(const Field2D& f, const Field3D& delta_x) {
-  TRACE("interpolate(Field2D, Field3D)");
-
   Mesh* mesh = f.getMesh();
   ASSERT1(mesh == delta_x.getMesh());
   Field3D result{emptyFrom(delta_x)};
diff --git a/src/mesh/invert3x3.hxx b/src/mesh/invert3x3.hxx
index c011f55bf7..746765d913 100644
--- a/src/mesh/invert3x3.hxx
+++ b/src/mesh/invert3x3.hxx
@@ -37,7 +37,6 @@
 /// return. Otherwise, an empty `std::optional` is return
 namespace bout {
 inline std::optional<BoutReal> invert3x3(Matrix<BoutReal>& a) {
-  TRACE("invert3x3");
 
   // Calculate the first co-factors
   const BoutReal A = a(1, 1) * a(2, 2) - a(1, 2) * a(2, 1);
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 1d3f3b0dbe..8964a6b797 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -298,7 +298,6 @@ bool Mesh::sourceHasYBoundaryGuards() { return source->hasYBoundaryGuards(); }
  **************************************************************************/
 
 void Mesh::communicateXZ(FieldGroup& g) {
-  TRACE("Mesh::communicate(FieldGroup&)");
 
   // Send data
   comm_handle h = sendX(g);
@@ -308,7 +307,6 @@ void Mesh::communicateXZ(FieldGroup& g) {
 }
 
 void Mesh::communicateYZ(FieldGroup& g) {
-  TRACE("Mesh::communicate(FieldGroup&)");
 
   // Send data
   comm_handle h = sendY(g);
@@ -325,7 +323,6 @@ void Mesh::communicateYZ(FieldGroup& g) {
 }
 
 void Mesh::communicate(FieldGroup& g) {
-  TRACE("Mesh::communicate(FieldGroup&)");
 
   if (include_corner_cells) {
     // Send data in y-direction
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index e8d3af1cdb..08e56584e1 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -251,7 +251,6 @@ FCIMap::FCIMap(Mesh& mesh, const Coordinates::FieldMetric& UNUSED(dy), Options&
 }
 
 Field3D FCIMap::integrate(Field3D& f) const {
-  TRACE("FCIMap::integrate");
 
   ASSERT1(f.getDirectionY() == YDirectionType::Standard);
   ASSERT1(&map_mesh == f.getMesh());
@@ -315,7 +314,6 @@ void FCITransform::checkInputGrid() {
 }
 
 void FCITransform::calcParallelSlices(Field3D& f) {
-  TRACE("FCITransform::calcParallelSlices");
 
   ASSERT1(f.getDirectionY() == YDirectionType::Standard);
   // Only have forward_map/backward_map for CELL_CENTRE, so can only deal with
@@ -333,7 +331,6 @@ void FCITransform::calcParallelSlices(Field3D& f) {
 }
 
 void FCITransform::integrateParallelSlices(Field3D& f) {
-  TRACE("FCITransform::integrateParallelSlices");
 
   ASSERT1(f.getDirectionY() == YDirectionType::Standard);
   // Only have forward_map/backward_map for CELL_CENTRE, so can only deal with
diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx
index f4be3bde2a..a1bde18248 100644
--- a/src/physics/physicsmodel.cxx
+++ b/src/physics/physicsmodel.cxx
@@ -164,7 +164,6 @@ void PhysicsModel::bout_solve(Vector3D& var, const char* name,
 }
 
 int PhysicsModel::postInit(bool restarting) {
-  TRACE("PhysicsModel::postInit");
 
   if (restarting) {
     solver->readEvolvingVariablesFromOptions(restart_options);
diff --git a/src/physics/smoothing.cxx b/src/physics/smoothing.cxx
index d8f7fb8b6b..309fff1542 100644
--- a/src/physics/smoothing.cxx
+++ b/src/physics/smoothing.cxx
@@ -37,7 +37,6 @@
 #include <bout/bout_types.hxx>
 #include <bout/globals.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/smoothing.hxx>
 
 #include <bout/constants.hxx>
@@ -46,7 +45,6 @@
 
 // Smooth using simple 1-2-1 filter
 const Field3D smooth_x(const Field3D& f) {
-  TRACE("smooth_x");
   Mesh* mesh = f.getMesh();
   Field3D result{emptyFrom(f)};
 
@@ -76,7 +74,6 @@ const Field3D smooth_x(const Field3D& f) {
 }
 
 const Field3D smooth_y(const Field3D& f) {
-  TRACE("smooth_y");
   Mesh* mesh = f.getMesh();
   Field3D result{emptyFrom(f)};
 
@@ -117,7 +114,6 @@ const Field3D smooth_y(const Field3D& f) {
   so no processor/branch cuts in X
  */
 const Field2D averageX(const Field2D& f) {
-  TRACE("averageX(Field2D)");
   Mesh* mesh = f.getMesh();
 
   int ngx = mesh->LocalNx;
@@ -176,8 +172,6 @@ const Field2D averageX(const Field2D& f) {
   
  */
 const Field3D averageX(const Field3D& f) {
-  TRACE("averageX(Field3D)");
-
   Mesh* mesh = f.getMesh();
 
   int ngx = mesh->LocalNx;
@@ -230,8 +224,6 @@ const Field3D averageX(const Field3D& f) {
 }
 
 const Field2D averageY(const Field2D& f) {
-  TRACE("averageY(Field2D)");
-
   Mesh* mesh = f.getMesh();
   int ngx = mesh->LocalNx;
   int ngy = mesh->LocalNy;
@@ -275,8 +267,6 @@ const Field2D averageY(const Field2D& f) {
 }
 
 const Field3D averageY(const Field3D& f) {
-  TRACE("averageY(Field3D)");
-
   Mesh* mesh = f.getMesh();
 
   int ngx = mesh->LocalNx;
@@ -431,7 +421,7 @@ void nl_filter(rvec& f, BoutReal w) {
 }
 
 const Field3D nl_filter_x(const Field3D& f, BoutReal w) {
-  TRACE("nl_filter_x( Field3D )");
+
   Mesh* mesh = f.getMesh();
 
   Field3D result{emptyFrom(f)};
@@ -453,7 +443,6 @@ const Field3D nl_filter_x(const Field3D& f, BoutReal w) {
 }
 
 const Field3D nl_filter_y(const Field3D& f, BoutReal w) {
-  TRACE("nl_filter_x( Field3D )");
 
   Mesh* mesh = f.getMesh();
 
@@ -481,7 +470,6 @@ const Field3D nl_filter_y(const Field3D& f, BoutReal w) {
 }
 
 const Field3D nl_filter_z(const Field3D& fs, BoutReal w) {
-  TRACE("nl_filter_z( Field3D )");
 
   Mesh* mesh = fs.getMesh();
   Field3D result{emptyFrom(fs)};
diff --git a/src/physics/sourcex.cxx b/src/physics/sourcex.cxx
index 1cfc2fdc6e..b3244a4109 100644
--- a/src/physics/sourcex.cxx
+++ b/src/physics/sourcex.cxx
@@ -77,7 +77,6 @@ const Field3D sink_tanhx(const Field2D& UNUSED(f0), const Field3D& f, BoutReal s
 
 // create radial buffer zones to set jpar zero near radial boundaries
 const Field3D mask_x(const Field3D& f, bool UNUSED(BoutRealspace)) {
-  TRACE("mask_x");
 
   Mesh* localmesh = f.getMesh();
 
@@ -101,7 +100,6 @@ const Field3D mask_x(const Field3D& f, bool UNUSED(BoutRealspace)) {
 // create radial buffer zones to set jpar zero near radial boundaries
 const Field3D sink_tanhxl(const Field2D& UNUSED(f0), const Field3D& f, BoutReal swidth,
                           BoutReal slength, bool UNUSED(BoutRealspace)) {
-  TRACE("sink_tanhx");
 
   Mesh* localmesh = f.getMesh();
 
@@ -123,7 +121,6 @@ const Field3D sink_tanhxl(const Field2D& UNUSED(f0), const Field3D& f, BoutReal
 // create radial buffer zones to set jpar zero near radial boundaries
 const Field3D sink_tanhxr(const Field2D& UNUSED(f0), const Field3D& f, BoutReal swidth,
                           BoutReal slength, bool UNUSED(BoutRealspace)) {
-  TRACE("sink_tanhxr");
 
   Mesh* localmesh = f.getMesh();
 
@@ -144,7 +141,6 @@ const Field3D sink_tanhxr(const Field2D& UNUSED(f0), const Field3D& f, BoutReal
 
 // create radial buffer zones to damp Psi to zero near radial boundaries
 const Field3D buff_x(const Field3D& f, bool UNUSED(BoutRealspace)) {
-  TRACE("buff_x");
 
   Mesh* localmesh = f.getMesh();
 
diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
index bb81e3d53f..f911e0045a 100644
--- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx
+++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
@@ -304,8 +304,6 @@ void AdamsBashforthSolver::setMaxTimestep(BoutReal dt) {
 
 int AdamsBashforthSolver::init() {
 
-  TRACE("Initialising AdamsBashforth solver");
-
   Solver::init();
   output << "\n\tAdams-Bashforth (explicit) multistep solver\n";
 
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 0151f90167..804e67a803 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -188,7 +188,6 @@ ArkodeSolver::~ArkodeSolver() {
  **************************************************************************/
 
 int ArkodeSolver::init() {
-  TRACE("Initialising ARKODE solver");
 
   Solver::init();
 
@@ -507,8 +506,6 @@ int ArkodeSolver::init() {
  **************************************************************************/
 
 int ArkodeSolver::run() {
-  TRACE("ArkodeSolver::run()");
-
   if (!initialised) {
     throw BoutException("ArkodeSolver not initialised\n");
   }
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 8b81a66f6d..4f72e65933 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -177,7 +177,6 @@ CvodeSolver::~CvodeSolver() {
  **************************************************************************/
 
 int CvodeSolver::init() {
-  TRACE("Initialising CVODE solver");
 
   Solver::init();
 
@@ -346,7 +345,6 @@ int CvodeSolver::init() {
     }
   } else {
     output_info.write("\tUsing Newton iteration\n");
-    TRACE("Setting preconditioner");
 
     const auto prectype =
         use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE;
@@ -486,7 +484,6 @@ CvodeSolver::create_constraints(const std::vector<VarStr<FieldType>>& fields) {
  **************************************************************************/
 
 int CvodeSolver::run() {
-  TRACE("CvodeSolver::run()");
 
   if (!cvode_initialised) {
     throw BoutException("CvodeSolver not initialised\n");
@@ -814,7 +811,7 @@ void CvodeSolver::loop_vector_option_values_op(Ind2D UNUSED(i2d), BoutReal* opti
 }
 
 void CvodeSolver::resetInternalFields() {
-  TRACE("CvodeSolver::resetInternalFields");
+
   save_vars(N_VGetArrayPointer(uvec));
 
   if (CVodeReInit(cvode_mem, simtime, uvec) != CV_SUCCESS) {
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 3976f4402c..7e31576a3f 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -33,7 +33,6 @@ void EulerSolver::setMaxTimestep(BoutReal dt) {
 }
 
 int EulerSolver::init() {
-  TRACE("Initialising Euler solver");
 
   Solver::init();
 
@@ -63,7 +62,6 @@ int EulerSolver::init() {
 }
 
 int EulerSolver::run() {
-  TRACE("EulerSolver::run()");
 
   for (int s = 0; s < getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx
index e0354e8b57..84a0bd4abd 100644
--- a/src/solver/impls/ida/ida.cxx
+++ b/src/solver/impls/ida/ida.cxx
@@ -100,8 +100,6 @@ IdaSolver::~IdaSolver() {
 
 int IdaSolver::init() {
 
-  TRACE("Initialising IDA solver");
-
   Solver::init();
 
   output.write("Initialising IDA solver\n");
@@ -233,7 +231,6 @@ int IdaSolver::init() {
  **************************************************************************/
 
 int IdaSolver::run() {
-  TRACE("IDA IdaSolver::run()");
 
   if (!initialised) {
     throw BoutException("IdaSolver not initialised\n");
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
index 07188110ab..f18550ed80 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
@@ -136,8 +136,6 @@ static PetscErrorCode imexbdf2PCapply(PC pc, Vec x, Vec y) {
  */
 int IMEXBDF2::init() {
 
-  TRACE("Initialising IMEX-BDF2 solver");
-
   Solver::init();
   output << "\n\tIMEX-BDF2 time-integration solver\n";
 
@@ -741,7 +739,6 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
 }
 
 int IMEXBDF2::run() {
-  TRACE("IMEXBDF2::run()");
 
   // Multi-step scheme, so first steps are different
   int order = 1;
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index d0535f069d..41e43c31ed 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -325,8 +325,6 @@ PetscSolver::~PetscSolver() {
 
 int PetscSolver::init() {
 
-  TRACE("Initialising PETSc-dev solver");
-
   Solver::init();
 
   int nlocal = getLocalN(); // Number of evolving variables on this processor
@@ -970,7 +968,6 @@ PetscErrorCode PetscSolver::formFunction(Vec U, Vec F) {
 
 // Matrix-free preconditioner function
 PetscErrorCode PetscSolver::pre(Vec x, Vec y) {
-  TRACE("PetscSolver::pre()");
 
   BoutReal* data;
 
diff --git a/src/solver/impls/power/power.cxx b/src/solver/impls/power/power.cxx
index 888338b94c..486129562d 100644
--- a/src/solver/impls/power/power.cxx
+++ b/src/solver/impls/power/power.cxx
@@ -15,7 +15,6 @@ PowerSolver::PowerSolver(Options* opts)
       curtime((*options)["curtime"].doc("Simulation time (fixed)").withDefault(0.0)) {}
 
 int PowerSolver::init() {
-  TRACE("Initialising Power solver");
 
   Solver::init();
   output << "\n\tPower eigenvalue solver\n";
@@ -44,7 +43,6 @@ int PowerSolver::init() {
 }
 
 int PowerSolver::run() {
-  TRACE("PowerSolver::run()");
 
   // Make sure that f0 has a norm of 1
   divide(f0, norm(f0));
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 63d3c11753..cb6e81d80a 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -90,7 +90,6 @@ PvodeSolver::~PvodeSolver() {
  **************************************************************************/
 
 int PvodeSolver::init() {
-  TRACE("Initialising PVODE solver");
 
   int mudq, mldq, mukeep, mlkeep;
   boole optIn;
@@ -218,7 +217,6 @@ int PvodeSolver::init() {
  **************************************************************************/
 
 int PvodeSolver::run() {
-  TRACE("PvodeSolver::run()");
 
   if (!pvode_initialised) {
     throw BoutException("PvodeSolver not initialised\n");
diff --git a/src/solver/impls/rk3-ssp/rk3-ssp.cxx b/src/solver/impls/rk3-ssp/rk3-ssp.cxx
index e13d996c00..14a3c3b0f9 100644
--- a/src/solver/impls/rk3-ssp/rk3-ssp.cxx
+++ b/src/solver/impls/rk3-ssp/rk3-ssp.cxx
@@ -28,7 +28,6 @@ void RK3SSP::setMaxTimestep(BoutReal dt) {
 }
 
 int RK3SSP::init() {
-  TRACE("Initialising RK3 SSP solver");
 
   Solver::init();
   output << "\n\tRunge-Kutta 3rd-order SSP solver\n";
@@ -63,7 +62,6 @@ int RK3SSP::init() {
 }
 
 int RK3SSP::run() {
-  TRACE("RK3SSP::run()");
 
   for (int s = 0; s < getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
diff --git a/src/solver/impls/rk4/rk4.cxx b/src/solver/impls/rk4/rk4.cxx
index 0e7a942a45..ca77f3fc77 100644
--- a/src/solver/impls/rk4/rk4.cxx
+++ b/src/solver/impls/rk4/rk4.cxx
@@ -39,8 +39,6 @@ void RK4Solver::setMaxTimestep(BoutReal dt) {
 
 int RK4Solver::init() {
 
-  TRACE("Initialising RK4 solver");
-
   Solver::init();
   output << "\n\tRunge-Kutta 4th-order solver\n";
 
@@ -77,8 +75,6 @@ int RK4Solver::init() {
 }
 
 int RK4Solver::run() {
-  TRACE("RK4Solver::run()");
-
   for (int s = 0; s < getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
 
diff --git a/src/solver/impls/rkgeneric/rkgeneric.cxx b/src/solver/impls/rkgeneric/rkgeneric.cxx
index 1c332d26de..c5d4ea35e7 100644
--- a/src/solver/impls/rkgeneric/rkgeneric.cxx
+++ b/src/solver/impls/rkgeneric/rkgeneric.cxx
@@ -40,8 +40,6 @@ void RKGenericSolver::setMaxTimestep(BoutReal dt) {
 
 int RKGenericSolver::init() {
 
-  TRACE("Initialising RKGeneric solver");
-
   Solver::init();
   output << "\n\tRunge-Kutta generic solver with scheme type " << scheme->getType()
          << "\n";
@@ -86,8 +84,6 @@ void RKGenericSolver::resetInternalFields() {
 }
 
 int RKGenericSolver::run() {
-  TRACE("RKGenericSolver::run()");
-
   for (int s = 0; s < getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
 
diff --git a/src/solver/impls/slepc/slepc.cxx b/src/solver/impls/slepc/slepc.cxx
index 13657a4553..d2eef6d59f 100644
--- a/src/solver/impls/slepc/slepc.cxx
+++ b/src/solver/impls/slepc/slepc.cxx
@@ -241,8 +241,6 @@ SlepcSolver::~SlepcSolver() {
 
 int SlepcSolver::init() {
 
-  TRACE("Initialising SLEPc solver");
-
   // Report initialisation
   output.write("Initialising SLEPc solver\n");
   if (selfSolve) {
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 311bc371fe..05c3cbdc5c 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -607,9 +607,6 @@ SNESSolver::SNESSolver(Options* opts)
                      .withDefault<bool>(false)) {}
 
 int SNESSolver::init() {
-
-  TRACE("Initialising SNES solver");
-
   Solver::init();
   output << "\n\tSNES steady state solver\n";
 
@@ -829,8 +826,6 @@ int SNESSolver::init() {
 }
 
 int SNESSolver::run() {
-  TRACE("SNESSolver::run()");
-
   // Set initial guess at the solution from variables
   {
     BoutReal* xdata = nullptr;
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index ea7866051b..ac3d632419 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -664,9 +664,6 @@ void Solver::writeToModelOutputFile(const Options& options) {
  **************************************************************************/
 
 int Solver::init() {
-
-  TRACE("Solver::init()");
-
   if (initialised) {
     throw BoutException(_("ERROR: Solver is already initialised\n"));
   }
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 077b2a6d85..bb4c920b90 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -106,8 +106,6 @@ Options::Options(InitializerList values, Options* parent_instance,
 }
 
 Options& Options::operator[](const std::string& name) {
-  TRACE("Options::operator[]");
-
   if (isValue()) {
     throw BoutException(_("Trying to index Option '{0}' with '{1}', but '{0}' is a "
                           "value, not a section.\n"
@@ -145,8 +143,6 @@ Options& Options::operator[](const std::string& name) {
 }
 
 const Options& Options::operator[](const std::string& name) const {
-  TRACE("Options::operator[] const");
-
   if (isValue()) {
     throw BoutException(_("Trying to index Option '{0}' with '{1}', but '{0}' is a "
                           "value, not a section.\n"
diff --git a/src/sys/options/options_ini.cxx b/src/sys/options/options_ini.cxx
index d1889f993b..939e100f1b 100644
--- a/src/sys/options/options_ini.cxx
+++ b/src/sys/options/options_ini.cxx
@@ -50,12 +50,10 @@
  **************************************************************************/
 
 #include "options_ini.hxx"
+
 #include <bout/boutexception.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/utils.hxx>
 
-#include <algorithm>
-
 using namespace std;
 
 /**************************************************************************
@@ -151,8 +149,6 @@ void OptionINI::read(Options* options, const string& filename) {
 }
 
 void OptionINI::write(Options* options, const std::string& filename) {
-  TRACE("OptionsINI::write");
-
   std::ofstream fout;
   fout.open(filename, ios::out | ios::trunc);
 
diff --git a/src/sys/optionsreader.cxx b/src/sys/optionsreader.cxx
index 8624f646df..e16df31c97 100644
--- a/src/sys/optionsreader.cxx
+++ b/src/sys/optionsreader.cxx
@@ -1,6 +1,5 @@
 #include <bout/assert.hxx>
 #include <bout/boutexception.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/optionsreader.hxx>
 #include <bout/utils.hxx>
 
@@ -23,7 +22,6 @@ OptionsReader* OptionsReader::getInstance() {
 }
 
 void OptionsReader::read(Options* options, const std::string& filename) {
-  TRACE("OptionsReader::read");
   if (filename.empty()) {
     throw BoutException("OptionsReader::read passed empty filename\n");
   }
@@ -34,7 +32,6 @@ void OptionsReader::read(Options* options, const std::string& filename) {
 }
 
 void OptionsReader::write(Options* options, const std::string& filename) {
-  TRACE("OptionsReader::write");
   if (filename.empty()) {
     throw BoutException("OptionsReader::write passed empty filename\n");
   }
diff --git a/tests/integrated/test-invertable-operator/invertable_operator.cxx b/tests/integrated/test-invertable-operator/invertable_operator.cxx
index 3c99c3dbbd..9f00fad304 100644
--- a/tests/integrated/test-invertable-operator/invertable_operator.cxx
+++ b/tests/integrated/test-invertable-operator/invertable_operator.cxx
@@ -1,5 +1,4 @@
 #include <bout/invert_laplace.hxx>
-#include <bout/msg_stack.hxx>
 
 #include <bout/invertable_operator.hxx>
 #include <bout/physicsmodel.hxx>
@@ -16,7 +15,7 @@ class InvertableOperatorTest : public PhysicsModel {
 
     // Drop C term for now
     Field3D operator()(const Field3D& input) {
-      TRACE("myLaplacian::operator()");
+
       Field3D result = A * input + D * Delp2(input);
 
       // Ensure boundary points are set appropriately as given by the input field.
diff --git a/tests/integrated/test-vec/testVec.cxx b/tests/integrated/test-vec/testVec.cxx
index bd0e5f2b80..905ffac01a 100644
--- a/tests/integrated/test-vec/testVec.cxx
+++ b/tests/integrated/test-vec/testVec.cxx
@@ -14,13 +14,11 @@ class VecTest : public PhysicsModel {
 };
 
 int VecTest::init(bool UNUSED(restarting)) {
-  TRACE("Halt in VecTest::init");
   SOLVE_FOR(n);
   return 0;
 }
 
 int VecTest::rhs(BoutReal UNUSED(t)) {
-  TRACE("Halt in VecTest::rhs");
   mesh->communicate(n);
   gradPerpN = Grad_perp(n);
   mesh->communicate(gradPerpN);

From 63e78ae3738fa89ee2b4ac9f309805c296ff906c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 15:56:59 +0000
Subject: [PATCH 0410/1827] Fix unnecessary includes of `msg_stack.hxx`

---
 examples/elm-pb-outerloop/elm_pb_outerloop.cxx           | 1 -
 examples/elm-pb/elm_pb.cxx                               | 1 -
 include/bout/bout_enum_class.hxx                         | 9 ++++-----
 include/bout/deriv_store.hxx                             | 1 -
 include/bout/field.hxx                                   | 2 --
 include/bout/index_derivs.hxx                            | 1 -
 include/bout/mask.hxx                                    | 1 -
 include/bout/sys/timer.hxx                               | 1 -
 include/bout/utils.hxx                                   | 1 -
 src/field/field.cxx                                      | 1 -
 src/field/initialprofiles.cxx                            | 1 -
 src/invert/laplace/impls/multigrid/multigrid_laplace.cxx | 1 -
 src/invert/laplace/invert_laplace.cxx                    | 1 -
 src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx   | 1 -
 src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx     | 4 +---
 src/invert/parderiv/impls/cyclic/cyclic.cxx              | 4 +---
 src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx         | 1 -
 src/mesh/coordinates.cxx                                 | 1 -
 src/mesh/data/gridfromfile.cxx                           | 1 -
 src/mesh/fv_ops.cxx                                      | 1 -
 src/physics/sourcex.cxx                                  | 8 +++-----
 src/solver/impls/adams_bashforth/adams_bashforth.cxx     | 4 +---
 src/solver/impls/euler/euler.cxx                         | 6 +-----
 src/solver/impls/imex-bdf2/imex-bdf2.cxx                 | 1 -
 src/solver/impls/power/power.cxx                         | 4 +---
 src/solver/impls/rk3-ssp/rk3-ssp.cxx                     | 2 --
 src/solver/impls/rk4/rk4.cxx                             | 4 +---
 src/solver/impls/rkgeneric/rkgeneric.cxx                 | 6 +-----
 src/solver/impls/slepc/slepc.cxx                         | 1 -
 src/solver/impls/snes/snes.cxx                           | 6 ++----
 src/sys/bout_types.cxx                                   | 2 +-
 src/sys/derivs.cxx                                       | 8 ++------
 src/sys/timer.cxx                                        | 2 ++
 tests/integrated/test-backtrace/boutexcept.cxx           | 1 -
 34 files changed, 21 insertions(+), 69 deletions(-)

diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index 4ff8e90dcb..3cc5227b30 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -39,7 +39,6 @@
 #include <bout/invert/laplacexy.hxx>
 #include <bout/invert_laplace.hxx>
 #include <bout/invert_parderiv.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/physicsmodel.hxx>
 #include <bout/rajalib.hxx> // Defines BOUT_FOR_RAJA
 #include <bout/single_index_ops.hxx>
diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx
index fe18a756ae..643f36f5bb 100644
--- a/examples/elm-pb/elm_pb.cxx
+++ b/examples/elm-pb/elm_pb.cxx
@@ -13,7 +13,6 @@
 #include <bout/invert/laplacexy.hxx>
 #include <bout/invert_laplace.hxx>
 #include <bout/invert_parderiv.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/sourcex.hxx>
 #include <bout/utils.hxx>
 
diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index 07140220a4..fa4abc8090 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -22,13 +22,12 @@
 #ifndef BOUT_ENUM_CLASS_H
 #define BOUT_ENUM_CLASS_H
 
-#include "bout/boutexception.hxx"
+#include "bout/boutexception.hxx" // IWYU pragma: keep
 #include "bout/macro_for_each.hxx"
-#include "bout/msg_stack.hxx"
-#include "bout/options.hxx"
+#include "bout/options.hxx" // IWYU pragma: keep
 
-#include <map>
-#include <string>
+#include <map>    // IWYU pragma: keep
+#include <string> // IWYU pragma: keep
 
 /// Create some macro magic similar to bout/macro_for_each.hxx, but allowing for the enum
 /// class name to be passed through to each _call
diff --git a/include/bout/deriv_store.hxx b/include/bout/deriv_store.hxx
index 866ac558e5..0e03d6a32e 100644
--- a/include/bout/deriv_store.hxx
+++ b/include/bout/deriv_store.hxx
@@ -38,7 +38,6 @@
 
 #include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/options.hxx>
 
 /// Here we have a templated singleton that is used to store DerivativeFunctions
diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 35ce42716d..4e41aa3632 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -30,14 +30,12 @@ class Field;
 #define FIELD_H
 
 #include <cmath>
-#include <cstdio>
 #include <string>
 
 #include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field_data.hxx"
-#include "bout/msg_stack.hxx"
 #include "bout/region.hxx"
 #include "bout/traits.hxx"
 #include "bout/utils.hxx"
diff --git a/include/bout/index_derivs.hxx b/include/bout/index_derivs.hxx
index 7c2be52ded..ccce9a7f5e 100644
--- a/include/bout/index_derivs.hxx
+++ b/include/bout/index_derivs.hxx
@@ -43,7 +43,6 @@
 #include <bout/bout_types.hxx>
 #include <bout/fft.hxx>
 #include <bout/interpolation.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/stencils.hxx>
 #include <bout/unused.hxx>
 
diff --git a/include/bout/mask.hxx b/include/bout/mask.hxx
index fd90ae7345..fc5f814676 100644
--- a/include/bout/mask.hxx
+++ b/include/bout/mask.hxx
@@ -26,7 +26,6 @@
 
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
-#include "bout/msg_stack.hxx"
 
 /**
  * 3D array of bools to mask Field3Ds
diff --git a/include/bout/sys/timer.hxx b/include/bout/sys/timer.hxx
index 90fd632f62..c6a0c9020a 100644
--- a/include/bout/sys/timer.hxx
+++ b/include/bout/sys/timer.hxx
@@ -7,7 +7,6 @@
 #include <type_traits>
 
 #include "bout/msg_stack.hxx"
-#include "bout/output.hxx"
 
 /*!
  * Timing class for performance benchmarking and diagnosis
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index f8d6f08856..04aa0b281d 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -35,7 +35,6 @@
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
-#include "bout/msg_stack.hxx"
 #include "bout/region.hxx"
 #include "bout/unused.hxx"
 
diff --git a/src/field/field.cxx b/src/field/field.cxx
index 797df6c405..e9b01f0bcb 100644
--- a/src/field/field.cxx
+++ b/src/field/field.cxx
@@ -27,7 +27,6 @@
 #include <bout/coordinates.hxx>
 #include <bout/field.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 #include <bout/utils.hxx>
 
diff --git a/src/field/initialprofiles.cxx b/src/field/initialprofiles.cxx
index 5e96d6005a..2c34caa6e1 100644
--- a/src/field/initialprofiles.cxx
+++ b/src/field/initialprofiles.cxx
@@ -42,7 +42,6 @@
 #include <bout/globals.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 
 void initial_profile(const std::string& name, Field3D& var) {
 
diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
index 48137a13bf..4be5bfbad3 100644
--- a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
+++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
@@ -33,7 +33,6 @@
 #if not BOUT_USE_METRIC_3D
 
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/openmpwrap.hxx>
 
 #if BOUT_USE_OPENMP
diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx
index b8650d1d68..e96248ef7e 100644
--- a/src/invert/laplace/invert_laplace.cxx
+++ b/src/invert/laplace/invert_laplace.cxx
@@ -38,7 +38,6 @@
 #include <bout/globals.hxx>
 #include <bout/invert_laplace.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/openmpwrap.hxx>
 #include <bout/options.hxx>
 #include <bout/output.hxx>
diff --git a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
index 1de9d58b26..dc987edc75 100644
--- a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
+++ b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
@@ -5,7 +5,6 @@
 
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 
diff --git a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
index d81446d522..be23d8d014 100644
--- a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
+++ b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
@@ -15,10 +15,8 @@
 #if BOUT_HAS_PETSC // Requires PETSc
 
 #include <bout/assert.hxx>
-#include <bout/sys/timer.hxx>
-
-#include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
+#include <bout/sys/timer.hxx>
 
 LaplaceXZpetsc::LaplaceXZpetsc(Mesh* m, Options* opt, const CELL_LOC loc)
     : LaplaceXZ(m, opt, loc), lib(opt == nullptr ? &(Options::root()["laplacexz"]) : opt),
diff --git a/src/invert/parderiv/impls/cyclic/cyclic.cxx b/src/invert/parderiv/impls/cyclic/cyclic.cxx
index 692d5f2660..61d23be823 100644
--- a/src/invert/parderiv/impls/cyclic/cyclic.cxx
+++ b/src/invert/parderiv/impls/cyclic/cyclic.cxx
@@ -46,10 +46,8 @@
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
 #include <bout/globals.hxx>
-#include <bout/msg_stack.hxx>
-#include <bout/utils.hxx>
-
 #include <bout/surfaceiter.hxx>
+#include <bout/utils.hxx>
 
 #include <cmath>
 
diff --git a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
index bd644dc625..d4e773f017 100644
--- a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
+++ b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
@@ -46,7 +46,6 @@
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
 #include <bout/globals.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/surfaceiter.hxx>
 #include <bout/utils.hxx>
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index b275f0c8de..8453a5205f 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -8,7 +8,6 @@
 #include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
 #include <bout/coordinates.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 952ea22243..10f6f6926e 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -6,7 +6,6 @@
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/options_io.hxx>
 #include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index 2f3398b2c0..a0a6e1d3c1 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -1,6 +1,5 @@
 #include <bout/fv_ops.hxx>
 #include <bout/globals.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 #include <bout/utils.hxx>
 
diff --git a/src/physics/sourcex.cxx b/src/physics/sourcex.cxx
index b3244a4109..659abbf409 100644
--- a/src/physics/sourcex.cxx
+++ b/src/physics/sourcex.cxx
@@ -2,15 +2,13 @@
  * radial source and mask operators
  **************************************************************/
 
-#include <bout/globals.hxx>
-#include <cmath>
-
 #include <bout/field2d.hxx>
+#include <bout/globals.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/sourcex.hxx>
+#include <bout/unused.hxx>
 
-#include "bout/unused.hxx"
+#include <cmath>
 
 BoutReal TanH(BoutReal a) {
   BoutReal temp = exp(a);
diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
index f911e0045a..72748fd52e 100644
--- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx
+++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
@@ -4,10 +4,8 @@
 
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
-#include <bout/msg_stack.hxx>
-#include <bout/utils.hxx>
-
 #include <bout/output.hxx>
+#include <bout/utils.hxx>
 
 #include <array>
 
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 7e31576a3f..2a9e5813f2 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -3,13 +3,9 @@
 
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/openmpwrap.hxx>
-#include <bout/utils.hxx>
-
-#include <cmath>
-
 #include <bout/output.hxx>
+#include <bout/utils.hxx>
 
 EulerSolver::EulerSolver(Options* options)
     : Solver(options), mxstep((*options)["mxstep"]
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
index f18550ed80..062979b59a 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
@@ -8,7 +8,6 @@
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/mesh.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/petsc_interface.hxx>
 #include <bout/utils.hxx>
 
diff --git a/src/solver/impls/power/power.cxx b/src/solver/impls/power/power.cxx
index 486129562d..5dfccfedda 100644
--- a/src/solver/impls/power/power.cxx
+++ b/src/solver/impls/power/power.cxx
@@ -3,13 +3,11 @@
 #include "power.hxx"
 
 #include <bout/boutcomm.hxx>
-#include <bout/msg_stack.hxx>
+#include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
 
 #include <cmath>
 
-#include <bout/output.hxx>
-
 PowerSolver::PowerSolver(Options* opts)
     : Solver(opts),
       curtime((*options)["curtime"].doc("Simulation time (fixed)").withDefault(0.0)) {}
diff --git a/src/solver/impls/rk3-ssp/rk3-ssp.cxx b/src/solver/impls/rk3-ssp/rk3-ssp.cxx
index 14a3c3b0f9..7c00d44b34 100644
--- a/src/solver/impls/rk3-ssp/rk3-ssp.cxx
+++ b/src/solver/impls/rk3-ssp/rk3-ssp.cxx
@@ -3,10 +3,8 @@
 
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/openmpwrap.hxx>
 #include <bout/utils.hxx>
-#include <cmath>
 
 #include <bout/output.hxx>
 
diff --git a/src/solver/impls/rk4/rk4.cxx b/src/solver/impls/rk4/rk4.cxx
index ca77f3fc77..35b3cc2268 100644
--- a/src/solver/impls/rk4/rk4.cxx
+++ b/src/solver/impls/rk4/rk4.cxx
@@ -3,14 +3,12 @@
 
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/openmpwrap.hxx>
+#include <bout/output.hxx>
 #include <bout/utils.hxx>
 
 #include <cmath>
 
-#include <bout/output.hxx>
-
 RK4Solver::RK4Solver(Options* opts)
     : Solver(opts), atol((*options)["atol"].doc("Absolute tolerance").withDefault(1.e-5)),
       rtol((*options)["rtol"].doc("Relative tolerance").withDefault(1.e-3)),
diff --git a/src/solver/impls/rkgeneric/rkgeneric.cxx b/src/solver/impls/rkgeneric/rkgeneric.cxx
index c5d4ea35e7..edf8ed50e3 100644
--- a/src/solver/impls/rkgeneric/rkgeneric.cxx
+++ b/src/solver/impls/rkgeneric/rkgeneric.cxx
@@ -4,12 +4,8 @@
 
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
-#include <bout/msg_stack.hxx>
-#include <bout/utils.hxx>
-
-#include <cmath>
-
 #include <bout/output.hxx>
+#include <bout/utils.hxx>
 
 RKGenericSolver::RKGenericSolver(Options* opts)
     : Solver(opts), atol((*options)["atol"].doc("Absolute tolerance").withDefault(1.e-5)),
diff --git a/src/solver/impls/slepc/slepc.cxx b/src/solver/impls/slepc/slepc.cxx
index d2eef6d59f..2c52cb3b38 100644
--- a/src/solver/impls/slepc/slepc.cxx
+++ b/src/solver/impls/slepc/slepc.cxx
@@ -31,7 +31,6 @@
 #include <bout/boutcomm.hxx>
 #include <bout/globals.hxx>
 #include <bout/interpolation.hxx>
-#include <bout/msg_stack.hxx>
 #include <bout/output.hxx>
 
 #include <cstdlib>
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 05c3cbdc5c..e1ef477105 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -1,4 +1,4 @@
-#include "bout/build_config.hxx"
+#include "bout/build_defines.hxx"
 
 #if BOUT_HAS_PETSC
 
@@ -7,7 +7,7 @@
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/globals.hxx>
-#include <bout/msg_stack.hxx>
+#include <bout/output.hxx>
 #include <bout/output_bout_types.hxx>
 #include <bout/petsc_interface.hxx>
 #include <bout/utils.hxx>
@@ -18,8 +18,6 @@
 #include <set>
 #include <vector>
 
-#include <bout/output.hxx>
-
 #include "petscerror.h"
 #include "petscmat.h"
 #include "petscpc.h"
diff --git a/src/sys/bout_types.cxx b/src/sys/bout_types.cxx
index f5e971af78..b27fab7ae7 100644
--- a/src/sys/bout_types.cxx
+++ b/src/sys/bout_types.cxx
@@ -1,6 +1,6 @@
 #include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
-#include <bout/msg_stack.hxx>
+
 #include <map>
 
 namespace {
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index ed036fffd4..13be388e97 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -44,14 +44,10 @@
 #include <bout/fft.hxx>
 #include <bout/globals.hxx>
 #include <bout/interpolation.hxx>
-#include <bout/msg_stack.hxx>
-#include <bout/stencils.hxx>
-#include <bout/utils.hxx>
-
-#include <cmath>
-
 #include <bout/output.hxx>
+#include <bout/stencils.hxx>
 #include <bout/unused.hxx>
+#include <bout/utils.hxx>
 
 /*******************************************************************************
  * First central derivatives
diff --git a/src/sys/timer.cxx b/src/sys/timer.cxx
index 314d599905..410cffad94 100644
--- a/src/sys/timer.cxx
+++ b/src/sys/timer.cxx
@@ -1,5 +1,7 @@
 #include "bout/sys/timer.hxx"
 
+#include <bout/output.hxx>
+
 #include <fmt/core.h>
 
 #include <algorithm>
diff --git a/tests/integrated/test-backtrace/boutexcept.cxx b/tests/integrated/test-backtrace/boutexcept.cxx
index ed33a4c018..70bf480862 100644
--- a/tests/integrated/test-backtrace/boutexcept.cxx
+++ b/tests/integrated/test-backtrace/boutexcept.cxx
@@ -1,5 +1,4 @@
 #include "bout/boutexception.hxx"
-#include "bout/msg_stack.hxx"
 
 void troublemaker() { throw BoutException("test"); }
 void f() { troublemaker(); }

From c42afa3bd3de747bd1daf3a63dede907112e5fa8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 16:37:07 +0000
Subject: [PATCH 0411/1827] Don't duplicate exception message when thrown from
 `BoutInitialise`

---
 include/bout/physicsmodel.hxx |  27 ++++-----
 src/bout++.cxx                | 106 ++++++++++++++++------------------
 2 files changed, 62 insertions(+), 71 deletions(-)

diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index baa284c862..d952c45efb 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -418,26 +418,26 @@ private:
  */
 #define BOUTMAIN(ModelClass)                                       \
   int main(int argc, char** argv) {                                \
-    int init_err = BoutInitialise(argc, argv);                     \
-    if (init_err < 0) {                                            \
-      return 0;                                                    \
-    }                                                              \
-    if (init_err > 0) {                                            \
-      return init_err;                                             \
-    }                                                              \
     try {                                                          \
+      int init_err = BoutInitialise(argc, argv);                   \
+      if (init_err < 0) {                                          \
+        return 0;                                                  \
+      }                                                            \
+      if (init_err > 0) {                                          \
+        return init_err;                                           \
+      }                                                            \
       auto model = bout::utils::make_unique<ModelClass>();         \
       auto solver = Solver::create();                              \
       solver->setModel(model.get());                               \
       auto bout_monitor = bout::utils::make_unique<BoutMonitor>(); \
       solver->addMonitor(bout_monitor.get(), Solver::BACK);        \
       solver->solve();                                             \
+      BoutFinalise();                                              \
+      return 0;                                                    \
     } catch (const BoutException& e) {                             \
       output.write("Error encountered: {}\n", e.what());           \
       MPI_Abort(BoutComm::get(), 1);                               \
     }                                                              \
-    BoutFinalise();                                                \
-    return 0;                                                      \
   }
 
 /// Macro to replace solver->add, passing variable name
@@ -480,8 +480,7 @@ private:
 
 /// Add fields to the solver.
 /// This should accept up to ten arguments
-#define SOLVE_FOR(...) \
-  { MACRO_FOR_EACH(SOLVE_FOR1, __VA_ARGS__) }
+#define SOLVE_FOR(...) {MACRO_FOR_EACH(SOLVE_FOR1, __VA_ARGS__)}
 
 /// Write this variable once to the grid file
 #define SAVE_ONCE1(var) dump.addOnce(var, #var);
@@ -521,8 +520,7 @@ private:
     dump.addOnce(var6, #var6);                         \
   }
 
-#define SAVE_ONCE(...) \
-  { MACRO_FOR_EACH(SAVE_ONCE1, __VA_ARGS__) }
+#define SAVE_ONCE(...) {MACRO_FOR_EACH(SAVE_ONCE1, __VA_ARGS__)}
 
 /// Write this variable every timestep
 #define SAVE_REPEAT1(var) dump.addRepeat(var, #var);
@@ -562,7 +560,6 @@ private:
     dump.addRepeat(var6, #var6);                         \
   }
 
-#define SAVE_REPEAT(...) \
-  { MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__) }
+#define SAVE_REPEAT(...) {MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__)}
 
 #endif // BOUT_PHYSICS_MODEL_H
diff --git a/src/bout++.cxx b/src/bout++.cxx
index 9c859aaaa7..ba49a208be 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -141,74 +141,68 @@ int BoutInitialise(int& argc, char**& argv) {
     return 1;
   }
 
-  try {
-    checkDataDirectoryIsAccessible(args.data_dir);
+  checkDataDirectoryIsAccessible(args.data_dir);
 
-    // Set the command-line arguments
-    SlepcLib::setArgs(argc, argv); // SLEPc initialisation
-    PetscLib::setArgs(argc, argv); // PETSc initialisation
-    Solver::setArgs(argc, argv);   // Solver initialisation
-    BoutComm::setArgs(argc, argv); // MPI initialisation
+  // Set the command-line arguments
+  SlepcLib::setArgs(argc, argv); // SLEPc initialisation
+  PetscLib::setArgs(argc, argv); // PETSc initialisation
+  Solver::setArgs(argc, argv);   // Solver initialisation
+  BoutComm::setArgs(argc, argv); // MPI initialisation
 
-    const int MYPE = BoutComm::rank();
+  const int MYPE = BoutComm::rank();
 
-    setupBoutLogColor(args.color_output, MYPE);
+  setupBoutLogColor(args.color_output, MYPE);
 
-    setupOutput(args.data_dir, args.log_file, args.verbosity, MYPE);
+  setupOutput(args.data_dir, args.log_file, args.verbosity, MYPE);
 
-    savePIDtoFile(args.data_dir, MYPE);
+  savePIDtoFile(args.data_dir, MYPE);
 
 #if BOUT_HAS_ADIOS2
-    bout::ADIOSInit(BoutComm::get());
+  bout::ADIOSInit(BoutComm::get());
 #endif
 
-    // Print the different parts of the startup info
-    printStartupHeader(MYPE, BoutComm::size());
-    printCompileTimeOptions();
-    printCommandLineArguments(args.original_argv);
-
-    // Load settings file
-    OptionsReader* reader = OptionsReader::getInstance();
-    // Ideally we'd use the long options for `datadir` and
-    // `optionfile` here, but we'd need to call parseCommandLine
-    // _first_ in order to do that and set the source, etc., but we
-    // need to call that _second_ in order to override the input file
-    reader->read(Options::getRoot(), "{}", (args.data_dir / args.opt_file).string());
-
-    // Get options override from command-line
-    reader->parseCommandLine(Options::getRoot(), args.argv);
-
-    // Get the variables back out so they count as having been used
-    // when checking for unused options. They normally _do_ get used,
-    // but it's possible that only happens in BoutFinalise, which is
-    // too late for that check.
-    const auto datadir = Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
-    [[maybe_unused]] const auto optionfile =
-        Options::root()["optionfile"].withDefault<std::string>(args.opt_file);
-    const auto settingsfile =
-        Options::root()["settingsfile"].withDefault<std::string>(args.set_file);
-
-    setRunStartInfo(Options::root());
-
-    if (MYPE == 0) {
-      writeSettingsFile(Options::root(), datadir, settingsfile);
-    }
-
-    bout::globals::mpi = new MpiWrapper();
+  // Print the different parts of the startup info
+  printStartupHeader(MYPE, BoutComm::size());
+  printCompileTimeOptions();
+  printCommandLineArguments(args.original_argv);
+
+  // Load settings file
+  OptionsReader* reader = OptionsReader::getInstance();
+  // Ideally we'd use the long options for `datadir` and
+  // `optionfile` here, but we'd need to call parseCommandLine
+  // _first_ in order to do that and set the source, etc., but we
+  // need to call that _second_ in order to override the input file
+  reader->read(Options::getRoot(), "{}", (args.data_dir / args.opt_file).string());
+
+  // Get options override from command-line
+  reader->parseCommandLine(Options::getRoot(), args.argv);
+
+  // Get the variables back out so they count as having been used
+  // when checking for unused options. They normally _do_ get used,
+  // but it's possible that only happens in BoutFinalise, which is
+  // too late for that check.
+  const auto datadir = Options::root()["datadir"].withDefault<std::string>(DEFAULT_DIR);
+  [[maybe_unused]] const auto optionfile =
+      Options::root()["optionfile"].withDefault<std::string>(args.opt_file);
+  const auto settingsfile =
+      Options::root()["settingsfile"].withDefault<std::string>(args.set_file);
+
+  setRunStartInfo(Options::root());
+
+  if (MYPE == 0) {
+    writeSettingsFile(Options::root(), datadir, settingsfile);
+  }
 
-    // Create the mesh
-    bout::globals::mesh = Mesh::create();
-    // Load from sources. Required for Field initialisation
-    bout::globals::mesh->load();
+  bout::globals::mpi = new MpiWrapper();
 
-    // time_report options are used in BoutFinalise, i.e. after we
-    // check for unused options
-    Options::root()["time_report"].setConditionallyUsed();
+  // Create the mesh
+  bout::globals::mesh = Mesh::create();
+  // Load from sources. Required for Field initialisation
+  bout::globals::mesh->load();
 
-  } catch (const BoutException& e) {
-    output_error.write(_("Error encountered during initialisation: {:s}\n"), e.what());
-    throw;
-  }
+  // time_report options are used in BoutFinalise, i.e. after we
+  // check for unused options
+  Options::root()["time_report"].setConditionallyUsed();
 
   return 0;
 }

From 6d89b6fd6543482d8b5bda02c1d276682eb2423e Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 16:38:11 +0000
Subject: [PATCH 0412/1827] Don't print `MsgStack` dump if it's empty

---
 include/bout/msg_stack.hxx |  3 +++
 src/sys/boutexception.cxx  | 15 ++++++++-------
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx
index 765a3120cf..9e218e9efb 100644
--- a/include/bout/msg_stack.hxx
+++ b/include/bout/msg_stack.hxx
@@ -89,6 +89,9 @@ public:
   std::string getDump() { return ""; }
 #endif
 
+  /// Current stack size
+  std::size_t size() const { return position; }
+
 private:
   std::vector<std::string> stack;                  ///< Message stack;
   std::vector<std::string>::size_type position{0}; ///< Position in stack
diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index 8509dc40ba..931720d537 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -15,10 +15,6 @@
 
 #include <fmt/format.h>
 
-namespace {
-const std::string header{"====== Exception thrown ======\n"};
-}
-
 bool BoutException::show_backtrace = true;
 
 void BoutParallelThrowRhsFail(int status, const char* message) {
@@ -71,8 +67,13 @@ std::string BoutException::getBacktrace() const {
                              and (frame.symbol != "_start"));
                        });
 
-  const std::string backtrace_message = formatter.format(generate_trace());
+  std::string backtrace_message =
+      fmt::format("{}\n\n====== Exception thrown ======\n{}",
+                  formatter.format(generate_trace()), message);
 
-  return fmt::format("{}\n{}\n{}{}\n", backtrace_message, msg_stack.getDump(), header,
-                     message);
+  if (msg_stack.size() > 0) {
+    return fmt::format("{}\n\nAdditional information:\n{}", backtrace_message,
+                       msg_stack.getDump());
+  }
+  return backtrace_message;
 }

From 8896f6eb05674772d7fe00e08d35471eae8319d1 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Mon, 5 Jan 2026 16:43:08 +0000
Subject: [PATCH 0413/1827] Apply clang-format changes

---
 include/bout/bout_enum_class.hxx     | 5 +++--
 include/bout/invertable_operator.hxx | 4 ++--
 include/bout/physicsmodel.hxx        | 9 ++++++---
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index fa4abc8090..6f632747ed 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -85,11 +85,12 @@
         BOUT_ENUM_CLASS_MAP_ARGS(BOUT_STR_ENUM_CLASS, enumname, __VA_ARGS__)}; \
     auto found = fromString_map.find(s);                                       \
     if (found == fromString_map.end()) {                                       \
-      std::string valid_values {};                                             \
+      std::string valid_values{};                                              \
       for (auto const& entry : fromString_map) {                               \
         valid_values += std::string(" ") + entry.first;                        \
       }                                                                        \
-      throw BoutException("Did not find enum {:s}. Valid values: {:s}", s, valid_values); \
+      throw BoutException("Did not find enum {:s}. Valid values: {:s}", s,     \
+                          valid_values);                                       \
     }                                                                          \
     return found->second;                                                      \
   }                                                                            \
diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx
index 6dcd92897a..d61c258654 100644
--- a/include/bout/invertable_operator.hxx
+++ b/include/bout/invertable_operator.hxx
@@ -135,9 +135,9 @@ public:
       : operatorFunction(func), preconditionerFunction(func),
         opt(optIn == nullptr ? Options::getRoot()->getSection("invertableOperator")
                              : optIn),
-        localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), lib(opt) {
+        localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), lib(opt){
 
-        };
+                                                                               };
 
   /// Destructor just has to cleanup the PETSc owned objects.
   ~InvertableOperator() {
diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index d952c45efb..81f17a39f0 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -480,7 +480,8 @@ private:
 
 /// Add fields to the solver.
 /// This should accept up to ten arguments
-#define SOLVE_FOR(...) {MACRO_FOR_EACH(SOLVE_FOR1, __VA_ARGS__)}
+#define SOLVE_FOR(...) \
+  { MACRO_FOR_EACH(SOLVE_FOR1, __VA_ARGS__) }
 
 /// Write this variable once to the grid file
 #define SAVE_ONCE1(var) dump.addOnce(var, #var);
@@ -520,7 +521,8 @@ private:
     dump.addOnce(var6, #var6);                         \
   }
 
-#define SAVE_ONCE(...) {MACRO_FOR_EACH(SAVE_ONCE1, __VA_ARGS__)}
+#define SAVE_ONCE(...) \
+  { MACRO_FOR_EACH(SAVE_ONCE1, __VA_ARGS__) }
 
 /// Write this variable every timestep
 #define SAVE_REPEAT1(var) dump.addRepeat(var, #var);
@@ -560,6 +562,7 @@ private:
     dump.addRepeat(var6, #var6);                         \
   }
 
-#define SAVE_REPEAT(...) {MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__)}
+#define SAVE_REPEAT(...) \
+  { MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__) }
 
 #endif // BOUT_PHYSICS_MODEL_H

From e497fcd3a0f9811538cd374369b97bb9631f9abf Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 16:59:29 +0000
Subject: [PATCH 0414/1827] docs: Use build directory for building library

Required because cpptrace prevents in-source builds

Also switch to using `subprocess.run` so we can better see errors
---
 manual/sphinx/conf.py | 29 ++++++++++++++---------------
 1 file changed, 14 insertions(+), 15 deletions(-)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 3aa6e94dc3..6b997ec111 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -82,22 +82,21 @@ def __getattr__(cls, name):
     pwd = "/".join(os.getcwd().split("/")[:-2])
     os.system("git submodule update --init --recursive ../../externalpackages/fmt")
     cmake = (
-        "cmake  . -DBOUT_USE_FFTW=ON"
-        + " -DBOUT_USE_LAPACK=OFF"
-        + " -DBOUT_ENABLE_PYTHON=ON"
-        + " -DBOUT_UPDATE_GIT_SUBMODULE=OFF"
-        + " -DBOUT_TESTS=OFF"
-        + " -DBOUT_ALLOW_INSOURCE_BUILD=ON"
-        + f" -DPython3_ROOT_DIR={pydir}"
-        + f" -Dmpark_variant_DIR={pwd}/externalpackages/mpark.variant/"
-        + f" -Dfmt_DIR={pwd}/externalpackages/fmt/"
+        "cmake  . "
+        " -B build"
+        " -DBOUT_USE_FFTW=ON"
+        " -DBOUT_USE_LAPACK=OFF"
+        " -DBOUT_ENABLE_PYTHON=ON"
+        " -DBOUT_UPDATE_GIT_SUBMODULE=OFF"
+        " -DBOUT_TESTS=OFF"
+        " -DBOUT_ALLOW_INSOURCE_BUILD=ON"
+        f" -DPython3_ROOT_DIR={pydir}"
+        f" -Dmpark_variant_DIR={pwd}/externalpackages/mpark.variant/"
+        f" -Dfmt_DIR={pwd}/externalpackages/fmt/"
     )
-    # os.system("mkdir ../../build")
-    os.system("echo " + cmake)
-    x = os.system("cd ../.. ;" + cmake)
-    assert x == 0
-    x = os.system("cd ../.. ; make -j 2 -f Makefile")
-    assert x == 0
+    subprocess.run(f"echo {cmake}", shell=True)
+    subprocess.run(f"cd ../../; {cmake}", shell=True, check=True)
+    subprocess.run("cd ../.. ; cmake --build build -j 2", shell=True, check=True)
 
 
 # readthedocs currently runs out of memory if we actually dare to try to do this

From 6ccdca8fd2877dee1bbc04bd09b682f92fee9739 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 5 Jan 2026 17:23:41 +0000
Subject: [PATCH 0415/1827] Partial revert of d0cd5f0aee

Seems to cause MPI problems?
---
 include/bout/physicsmodel.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index 81f17a39f0..e6d34daef9 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -432,12 +432,12 @@ private:
       auto bout_monitor = bout::utils::make_unique<BoutMonitor>(); \
       solver->addMonitor(bout_monitor.get(), Solver::BACK);        \
       solver->solve();                                             \
-      BoutFinalise();                                              \
-      return 0;                                                    \
     } catch (const BoutException& e) {                             \
       output.write("Error encountered: {}\n", e.what());           \
       MPI_Abort(BoutComm::get(), 1);                               \
     }                                                              \
+    BoutFinalise();                                                \
+    return 0;                                                      \
   }
 
 /// Macro to replace solver->add, passing variable name

From d8b360fee146fd8837330943a3fa20523b8f4974 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 6 Jan 2026 14:19:22 +0000
Subject: [PATCH 0416/1827] Remove some more unused headers

---
 include/bout/deriv_store.hxx                         | 1 +
 include/bout/msg_stack.hxx                           | 6 ++----
 src/field/field2d.cxx                                | 2 --
 src/solver/impls/adams_bashforth/adams_bashforth.cxx | 3 ---
 src/solver/impls/euler/euler.cxx                     | 1 -
 src/sys/derivs.cxx                                   | 1 -
 6 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/include/bout/deriv_store.hxx b/include/bout/deriv_store.hxx
index 0e03d6a32e..b2b7928c2e 100644
--- a/include/bout/deriv_store.hxx
+++ b/include/bout/deriv_store.hxx
@@ -29,6 +29,7 @@
 #ifndef __DERIV_STORE_HXX__
 #define __DERIV_STORE_HXX__
 
+#include <cstddef>
 #include <functional>
 #include <map>
 #include <set>
diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx
index 9e218e9efb..1abb26d2c7 100644
--- a/include/bout/msg_stack.hxx
+++ b/include/bout/msg_stack.hxx
@@ -31,11 +31,9 @@ class MsgStack;
 
 #include "bout/build_defines.hxx"
 
-#include "bout/unused.hxx"
-
 #include "fmt/core.h"
 
-#include <cstdarg>
+#include <cstddef>
 #include <exception>
 #include <string>
 #include <vector>
@@ -82,7 +80,7 @@ public:
   }
 
   void pop() {}
-  void pop(int UNUSED(id)) {}
+  void pop(int [[maybe_unused]] id) {}
   void clear() {}
 
   void dump() {}
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index 01f2d8c4a6..a046078585 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -36,8 +36,6 @@
 #include <bout/globals.hxx> // for mesh
 #include <bout/mesh.hxx>
 #include <bout/output.hxx>
-#include <bout/rvec.hxx>
-#include <bout/utils.hxx>
 
 #include <cmath>
 
diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
index 72748fd52e..51fff4fe6a 100644
--- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx
+++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
@@ -5,9 +5,6 @@
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/output.hxx>
-#include <bout/utils.hxx>
-
-#include <array>
 
 namespace {
 BoutReal lagrange_at_position_denominator(const std::deque<BoutReal>& grid,
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 2a9e5813f2..a3911e78d6 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -5,7 +5,6 @@
 #include <bout/boutexception.hxx>
 #include <bout/openmpwrap.hxx>
 #include <bout/output.hxx>
-#include <bout/utils.hxx>
 
 EulerSolver::EulerSolver(Options* options)
     : Solver(options), mxstep((*options)["mxstep"]
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index 13be388e97..aab75b8f19 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -45,7 +45,6 @@
 #include <bout/globals.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/output.hxx>
-#include <bout/stencils.hxx>
 #include <bout/unused.hxx>
 #include <bout/utils.hxx>
 

From 5306125a4a9bb834888e1949ddf8f1cbfd7d6bdf Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 6 Jan 2026 14:19:34 +0000
Subject: [PATCH 0417/1827] tests: Add functions to anon namespace

---
 tests/integrated/test-backtrace/boutexcept.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/integrated/test-backtrace/boutexcept.cxx b/tests/integrated/test-backtrace/boutexcept.cxx
index 70bf480862..6017ecd8f9 100644
--- a/tests/integrated/test-backtrace/boutexcept.cxx
+++ b/tests/integrated/test-backtrace/boutexcept.cxx
@@ -1,8 +1,10 @@
 #include "bout/boutexception.hxx"
 
+namespace {
 void troublemaker() { throw BoutException("test"); }
 void f() { troublemaker(); }
 void e() { f(); }
+}
 
 int main() {
   e();

From 68fab1b2e338c0631e15372b2f1255642d693807 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 6 Jan 2026 14:19:45 +0000
Subject: [PATCH 0418/1827] Don't use `char[]` for constant

---
 src/bout++.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/bout++.cxx b/src/bout++.cxx
index ba49a208be..d6888874c6 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -27,7 +27,7 @@
 
 #include "bout/build_config.hxx"
 
-const char DEFAULT_DIR[] = "data";
+static constexpr auto DEFAULT_DIR = "data";
 
 #define GLOBALORIGIN
 

From 563ab24f4a30ba18b85f9a25d28ab4f3a78f637d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 6 Jan 2026 14:22:59 +0000
Subject: [PATCH 0419/1827] Fix use of reserved identifier

---
 include/bout/scorepwrapper.hxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/scorepwrapper.hxx b/include/bout/scorepwrapper.hxx
index 40c2232040..8b37b2ff61 100644
--- a/include/bout/scorepwrapper.hxx
+++ b/include/bout/scorepwrapper.hxx
@@ -20,9 +20,9 @@
 /// we need to say if we support this or not by defining BOUT_HAS_PRETTY_FUNCTION (to be
 /// implemented in configure)
 #if BOUT_HAS_PRETTY_FUNCTION
-#define __thefunc__ __PRETTY_FUNCTION__
+#define _thefunc_ __PRETTY_FUNCTION__
 #else
-#define __thefunc__ __func__
+#define _thefunc_ __func__
 #endif
 
 /// Instrument a function with scorep
@@ -31,7 +31,7 @@
 /// If we don't have scorep support then just define a null function
 #if BOUT_HAS_SCOREP
 #define SCOREP_BASE_CALL(...) \
-  SCOREP_USER_REGION(__thefunc__, SCOREP_USER_REGION_TYPE_FUNCTION)
+  SCOREP_USER_REGION(_thefunc_, SCOREP_USER_REGION_TYPE_FUNCTION)
 #else
 #define SCOREP_BASE_CALL(...)
 #endif

From 1a9210cbc6a846caaef63bc2cb562a65bff349e5 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 6 Jan 2026 14:45:16 +0000
Subject: [PATCH 0420/1827] docs: Update example backtrace

---
 manual/sphinx/developer_docs/debugging.rst | 97 +++++++++++++---------
 src/sys/boutexception.cxx                  |  2 +-
 src/sys/msg_stack.cxx                      |  2 +-
 3 files changed, 58 insertions(+), 43 deletions(-)

diff --git a/manual/sphinx/developer_docs/debugging.rst b/manual/sphinx/developer_docs/debugging.rst
index fc8d80d9fc..4e8bd0feab 100644
--- a/manual/sphinx/developer_docs/debugging.rst
+++ b/manual/sphinx/developer_docs/debugging.rst
@@ -69,14 +69,15 @@ help find where an error occurred. For example, given this snippet::
 we would see something like the following output:
 
 .. code:: text
-       
-    ====== Back trace ======
+
+    ====== Exception thrown ======
+    Something went wrong
+
+    === Additional information ===
     -> 4. Inner-most scope on line 58 of '/path/to/model.cxx'
     -> 2. Middle scope on line 53 of '/path/to/model.cxx'
     -> 1. Outer-most scope on line 51 of '/path/to/model.cxx'
 
-    ====== Exception thrown ======
-    Something went wrong
 
 The third ``TRACE`` message doesn't appear in the output because we've
 left its scope and it's no longer relevant.
@@ -97,44 +98,58 @@ the ``fmt`` syntax also used by the loggers::
 Backtrace
 =========
 
-Lastly, BOUT++ can also automatically print a backtrace in the event
-of a crash. This is a compile-time option in the BOUT++ library
-(``-DBOUT_ENABLE_BACKTRACE=ON``, the default, requires the
-``addr2line`` program to be installed), and debug symbols to be turned
-on (``-DCMAKE_BUILD_TYPE=Debug`` or ``=RelWithDebInfo``) in BOUT++
-_and_ the physics model. If debug symbols are only present in part, the
-backtrace will be missing names for the other part.
-
-The output looks something like this:
+Lastly, BOUT++ can also automatically print a backtrace in the event of a
+crash. This is very useful to include if you ever need to report a bug to the
+developers! The output looks something like this:
 
 .. code:: text
 
     ...
-    Error encountered
-    ====== Exception path ======
-    [bt] #10 ./backtrace() [0x40a27e]
-    _start at /home/abuild/rpmbuild/BUILD/glibc-2.33/csu/../sysdeps/x86_64/start.S:122
-    [bt] #9 /lib64/libc.so.6(__libc_start_main+0xd5) [0x7fecbfa28b25]
-    __libc_start_main at /usr/src/debug/glibc-2.33-4.1.x86_64/csu/../csu/libc-start.c:332
-    [bt] #8 ./backtrace() [0x40a467]
-    main at /path/to/BOUT-dev/build/../examples/backtrace/backtrace.cxx:32 (discriminator 9)
-    [bt] #7 /path/to/BOUT-dev/build/libbout++.so(_ZN6Solver8setModelEP12PhysicsModel+0xb5) [0x7fecc0ca2e93]
-    Solver::setModel(PhysicsModel*) at /path/to/BOUT-dev/build/../src/solver/solver.cxx:94
-    [bt] #6 /path/to/BOUT-dev/build/libbout++.so(_ZN12PhysicsModel10initialiseEP6Solver+0xc0) [0x7fecc0cad594]
-    PhysicsModel::initialise(Solver*) at /path/to/BOUT-dev/build/../include/bout/physicsmodel.hxx:93 (discriminator 5)
-    [bt] #5 ./backtrace() [0x40a986]
-    Backtrace::init(bool) at /path/to/BOUT-dev/build/../examples/backtrace/backtrace.cxx:27
-    [bt] #4 ./backtrace() [0x40a3cf]
-    f3() at /path/to/BOUT-dev/build/../examples/backtrace/backtrace.cxx:19
-    [bt] #3 ./backtrace() [0x40a3be]
-    f2(int) at /path/to/BOUT-dev/build/../examples/backtrace/backtrace.cxx:15
-    [bt] #2 ./backtrace() [0x40a386]
-    f1() at /path/to/BOUT-dev/build/../examples/backtrace/backtrace.cxx:13 (discriminator 2)
-    [bt] #1 ./backtrace(_ZN13BoutExceptionC1IA19_cJEEERKT_DpRKT0_+0xba) [0x40ae16]
-    BoutException::BoutException<char [19]>(char const (&) [19]) at /path/to/BOUT-dev/build/../include/bout/../boutexception.hxx:28 (discriminator 2)
-              
-
-This output tends to be much harder to read than the message stack
-from ``TRACE`` macros, but the advantage is that it doesn't require
-any modifications to the code to use, and can give you more precise
-location information.
+    Error encountered: Stack trace (most recent call first):
+    #0 (filtered)
+    #1 (filtered)
+    #2 (filtered)
+    #3 in BoutMesh::createCommunicators()
+       at BOUT-dev/src/mesh/impls/bout/boutmesh.cxx:709:64
+         707:       }
+         708:       // Unconditional exception for demo purposes
+       > 709:       throw BoutException("Single null outer SOL not correct\n");
+                                                                             ^
+         710:       MPI_Group_free(&group);
+         711:     }
+    #4 in BoutMesh::load()
+       at BOUT-dev/src/mesh/impls/bout/boutmesh.cxx:575:22
+         573:   /// Communicator
+         574:
+       > 575:   createCommunicators();
+                                   ^
+         576:   output_debug << "Got communicators" << endl;
+    #5 in BoutInitialise(int&, char**&)
+       at BOUT-dev/src/bout++.cxx:201:28
+         199:   bout::globals::mesh = Mesh::create();
+         200:   // Load from sources. Required for Field initialisation
+       > 201:   bout::globals::mesh->load();
+                                         ^
+         202:
+         203:   // time_report options are used in BoutFinalise, i.e. after we
+    #6 in main
+       at BOUT-dev/examples/elm-pb/elm_pb.cxx:2161:1
+        2159: };
+        2160:
+      > 2161: BOUTMAIN(ELMpb);
+              ^
+    #7 (filtered)
+    #8 (filtered)
+    #9 (filtered)
+
+    ====== Exception thrown ======
+    Single null outer SOL not correct
+
+
+Debug symbols are required to get the filename/line number and code snippets. If
+they are missing in either BOUT++ or the physics model, only the function name
+and signature will be included for that part.
+
+Including debug symbols is a configure time ``CMake`` option, set either:
+``-DCMAKE_BUILD_TYPE=Debug`` or ``-DCMAKE_BUILD_TYPE=RelWithDebInfo`` (the
+default).
diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index 931720d537..02b6ef3391 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -72,7 +72,7 @@ std::string BoutException::getBacktrace() const {
                   formatter.format(generate_trace()), message);
 
   if (msg_stack.size() > 0) {
-    return fmt::format("{}\n\nAdditional information:\n{}", backtrace_message,
+    return fmt::format("{}\n\n{}", backtrace_message,
                        msg_stack.getDump());
   }
   return backtrace_message;
diff --git a/src/sys/msg_stack.cxx b/src/sys/msg_stack.cxx
index 81eb6c4b0f..3dbd7c2797 100644
--- a/src/sys/msg_stack.cxx
+++ b/src/sys/msg_stack.cxx
@@ -91,7 +91,7 @@ void MsgStack::dump() {
 }
 
 std::string MsgStack::getDump() {
-  std::string res = "====== Back trace ======\n";
+  std::string res = "=== Additional information ===\n";
   for (int i = position - 1; i >= 0; i--) {
     if (stack[i] != "") {
       res += " -> ";

From 0285b949d124d9896f47c5e6b7ed570c084a9144 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 7 Jan 2026 16:38:45 +0000
Subject: [PATCH 0421/1827] Remove `Mesh::smoothSeparatrix`

Closes #3239
---
 examples/dalf3/dalf3.cxx         |  8 -------
 include/bout/mesh.hxx            |  3 ---
 src/mesh/impls/bout/boutmesh.cxx | 41 --------------------------------
 src/mesh/impls/bout/boutmesh.hxx |  2 --
 4 files changed, 54 deletions(-)

diff --git a/examples/dalf3/dalf3.cxx b/examples/dalf3/dalf3.cxx
index 46a9a4286d..b27ae97113 100644
--- a/examples/dalf3/dalf3.cxx
+++ b/examples/dalf3/dalf3.cxx
@@ -71,8 +71,6 @@ class DALF3 : public PhysicsModel {
 
   BoutReal viscosity, hyper_viscosity;
 
-  bool smooth_separatrix;
-
   FieldGroup comms;
 
   std::unique_ptr<Laplacian> phiSolver{nullptr};  // Laplacian solver in X-Z
@@ -132,7 +130,6 @@ class DALF3 : public PhysicsModel {
     viscosity = options["viscosity"].withDefault(-1.0);
     hyper_viscosity = options["hyper_viscosity"].withDefault(-1.0);
     viscosity_par = options["viscosity_par"].withDefault(-1.0);
-    smooth_separatrix = options["smooth_separatrix"].withDefault(false);
 
     filter_z = options["filter_z"].withDefault(false);
 
@@ -466,11 +463,6 @@ class DALF3 : public PhysicsModel {
     ddt(Pe) = -bracket(phi, Pet, bm)
               + Pet * (Kappa(phi - Pe) + B0 * Grad_parP(jpar - Vpar) / B0);
 
-    if (smooth_separatrix) {
-      // Experimental smoothing across separatrix
-      ddt(Vort) += mesh->smoothSeparatrix(Vort);
-    }
-
     if (filter_z) {
       ddt(Pe) = filter(ddt(Pe), 1);
     }
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 2e27bed777..da8ac51127 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -505,9 +505,6 @@ public:
   virtual void addBoundaryPar(std::shared_ptr<BoundaryRegionPar> UNUSED(bndry),
                               BoundaryParType UNUSED(type)) {}
 
-  /// Branch-cut special handling (experimental)
-  virtual Field3D smoothSeparatrix(const Field3D& f) { return f; }
-
   virtual BoutReal GlobalX(int jx) const = 0;      ///< Continuous X index between 0 and 1
   virtual BoutReal GlobalY(int jy) const = 0;      ///< Continuous Y index (0 -> 1)
   virtual BoutReal GlobalX(BoutReal jx) const = 0; ///< Continuous X index between 0 and 1
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 8917fa3753..11ea2f5c89 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -3115,47 +3115,6 @@ void BoutMesh::addBoundaryPar(std::shared_ptr<BoundaryRegionPar> bndry,
   par_boundary[static_cast<int>(BoundaryParType::all)].push_back(bndry);
 }
 
-Field3D BoutMesh::smoothSeparatrix(const Field3D& f) {
-  Field3D result{emptyFrom(f)};
-  if ((ixseps_inner > 0) && (ixseps_inner < nx - 1)) {
-    if (XPROC(ixseps_inner) == PE_XIND) {
-      int x = getLocalXIndex(ixseps_inner);
-      for (int y = 0; y < LocalNy; y++) {
-        for (int z = 0; z < LocalNz; z++) {
-          result(x, y, z) = 0.5 * (f(x, y, z) + f(x - 1, y, z));
-        }
-      }
-    }
-    if (XPROC(ixseps_inner - 1) == PE_XIND) {
-      int x = getLocalXIndex(ixseps_inner - 1);
-      for (int y = 0; y < LocalNy; y++) {
-        for (int z = 0; z < LocalNz; z++) {
-          result(x, y, z) = 0.5 * (f(x, y, z) + f(x + 1, y, z));
-        }
-      }
-    }
-  }
-  if ((ixseps_outer > 0) && (ixseps_outer < nx - 1) && (ixseps_outer != ixseps_inner)) {
-    if (XPROC(ixseps_outer) == PE_XIND) {
-      int x = getLocalXIndex(ixseps_outer);
-      for (int y = 0; y < LocalNy; y++) {
-        for (int z = 0; z < LocalNz; z++) {
-          result(x, y, z) = 0.5 * (f(x, y, z) + f(x - 1, y, z));
-        }
-      }
-    }
-    if (XPROC(ixseps_outer - 1) == PE_XIND) {
-      int x = getLocalXIndex(ixseps_outer - 1);
-      for (int y = 0; y < LocalNy; y++) {
-        for (int z = 0; z < LocalNz; z++) {
-          result(x, y, z) = 0.5 * (f(x, y, z) + f(x + 1, y, z));
-        }
-      }
-    }
-  }
-  return result;
-}
-
 BoutReal BoutMesh::GlobalX(int jx) const {
   if (symmetricGlobalX) {
     // With this definition the boundary sits dx/2 away form the first/last inner points
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index a22e0e4473..876edab1da 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -167,8 +167,6 @@ public:
                       BoundaryParType type) override;
   std::set<std::string> getPossibleBoundaries() const override;
 
-  Field3D smoothSeparatrix(const Field3D& f) override;
-
   int getNx() const { return nx; }
   int getNy() const { return ny; }
 

From 0386f676712594aea5c4df308804b39139a5a884 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 7 Jan 2026 17:09:12 +0000
Subject: [PATCH 0422/1827] Use `zstart/zend` in more loops

---
 examples/elm-pb/elm_pb.cxx                    |  18 +--
 .../iterator-offsets/iterator-offsets.cxx     |   4 +-
 examples/performance/iterator/iterator.cxx    |   4 +-
 include/bout/fv_ops.hxx                       |   2 +-
 manual/sphinx/developer_docs/data_types.rst   |   6 +-
 manual/sphinx/user_docs/boundary_options.rst  |   2 +-
 .../laplace/impls/naulin/naulin_laplace.cxx   |   4 +-
 .../laplace/impls/petsc/petsc_laplace.cxx     |  40 +++---
 src/invert/laplace/impls/spt/spt.cxx          |  12 +-
 .../laplacexz/impls/petsc/laplacexz-petsc.cxx |  50 +++----
 src/mesh/boundary_standard.cxx                | 136 +++++++++---------
 src/mesh/coordinates.cxx                      |   6 +-
 src/mesh/difops.cxx                           |   4 +-
 src/mesh/fv_ops.cxx                           |  16 +--
 src/solver/impls/imex-bdf2/imex-bdf2.cxx      |  20 +--
 src/solver/impls/petsc/petsc.cxx              |   6 +-
 src/solver/impls/snes/snes.cxx                |  10 +-
 tests/integrated/test-invpar/test_invpar.cxx  |   2 +-
 .../test_multigrid_laplace.cxx                |  10 +-
 .../test_naulin_laplace.cxx                   |  10 +-
 .../test-petsc_laplace/test_petsc_laplace.cxx |  54 +++----
 .../test_petsc_laplace_MAST_grid.cxx          |  66 ++++-----
 22 files changed, 241 insertions(+), 241 deletions(-)

diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx
index fe18a756ae..57f0ec0778 100644
--- a/examples/elm-pb/elm_pb.cxx
+++ b/examples/elm-pb/elm_pb.cxx
@@ -1366,7 +1366,7 @@ class ELMpb : public PhysicsModel {
               // Calculate a single phi boundary value for all Y slices
               BoutReal philocal = 0.0;
               for (int j = mesh->ystart; j <= mesh->yend; j++) {
-                for (int k = 0; k < mesh->LocalNz; k++) {
+                for (int k = mesh->zstart; k <= mesh->zend; k++) {
                   philocal += phi(mesh->xstart, j, k);
                 }
               }
@@ -1379,7 +1379,7 @@ class ELMpb : public PhysicsModel {
             for (int j = mesh->ystart; j <= mesh->yend; j++) {
               if (!phi_core_averagey) {
                 phivalue = 0.0; // Calculate phi boundary for each Y index separately
-                for (int k = 0; k < mesh->LocalNz; k++) {
+                for (int k = mesh->zstart; k <= mesh->zend; k++) {
                   phivalue += phi(mesh->xstart, j, k);
                 }
                 phivalue /= mesh->LocalNz; // Average in Z of point next to boundary
@@ -1393,7 +1393,7 @@ class ELMpb : public PhysicsModel {
               BoutReal const newvalue = weight * oldvalue + (1. - weight) * phivalue;
 
               // Set phi at the boundary to this value
-              for (int k = 0; k < mesh->LocalNz; k++) {
+              for (int k = mesh->zstart; k <= mesh->zend; k++) {
                 phi(mesh->xstart - 1, j, k) = 2. * newvalue - phi(mesh->xstart, j, k);
                 phi(mesh->xstart - 2, j, k) = phi(mesh->xstart - 1, j, k);
               }
@@ -1403,7 +1403,7 @@ class ELMpb : public PhysicsModel {
           if (mesh->lastX()) {
             for (int j = mesh->ystart; j <= mesh->yend; j++) {
               BoutReal phivalue = 0.0;
-              for (int k = 0; k < mesh->LocalNz; k++) {
+              for (int k = mesh->zstart; k <= mesh->zend; k++) {
                 phivalue += phi(mesh->xend, j, k);
               }
               phivalue /= mesh->LocalNz; // Average in Z of point next to boundary
@@ -1416,7 +1416,7 @@ class ELMpb : public PhysicsModel {
               BoutReal const newvalue = weight * oldvalue + (1. - weight) * phivalue;
 
               // Set phi at the boundary to this value
-              for (int k = 0; k < mesh->LocalNz; k++) {
+              for (int k = mesh->zstart; k <= mesh->zend; k++) {
                 phi(mesh->xend + 1, j, k) = 2. * newvalue - phi(mesh->xend, j, k);
                 phi(mesh->xend + 2, j, k) = phi(mesh->xend + 1, j, k);
               }
@@ -1441,7 +1441,7 @@ class ELMpb : public PhysicsModel {
 
       if (mesh->firstX()) {
         for (int j = mesh->ystart; j <= mesh->yend; j++) {
-          for (int k = 0; k < mesh->LocalNz; k++) {
+          for (int k = mesh->zstart; k <= mesh->zend; k++) {
             // Average phi + Pi at the boundary, and set the boundary cell
             // to this value. The phi solver will then put the value back
             // onto the cell mid-point
@@ -1453,7 +1453,7 @@ class ELMpb : public PhysicsModel {
 
       if (mesh->lastX()) {
         for (int j = mesh->ystart; j <= mesh->yend; j++) {
-          for (int k = 0; k < mesh->LocalNz; k++) {
+          for (int k = mesh->zstart; k <= mesh->zend; k++) {
             phi_shift(mesh->xend + 1, j, k) =
                 0.5 * (phi_shift(mesh->xend + 1, j, k) + phi_shift(mesh->xend, j, k));
           }
@@ -1513,7 +1513,7 @@ class ELMpb : public PhysicsModel {
     if (mesh->firstX()) {
       for (int i = mesh->xstart - 2; i >= 0; --i) {
         for (int j = mesh->ystart; j <= mesh->yend; ++j) {
-          for (int k = 0; k < mesh->LocalNz; ++k) {
+          for (int k = mesh->zstart; k <= mesh->zend; ++k) {
             phi(i, j, k) = phi(i + 1, j, k);
           }
         }
@@ -1523,7 +1523,7 @@ class ELMpb : public PhysicsModel {
     if (mesh->lastX()) {
       for (int i = mesh->xend + 2; i < mesh->LocalNx; ++i) {
         for (int j = mesh->ystart; j <= mesh->yend; ++j) {
-          for (int k = 0; k < mesh->LocalNz; ++k) {
+          for (int k = mesh->zstart; k <= mesh->zend; ++k) {
             phi(i, j, k) = phi(i - 1, j, k);
           }
         }
diff --git a/examples/performance/iterator-offsets/iterator-offsets.cxx b/examples/performance/iterator-offsets/iterator-offsets.cxx
index 455df38ea5..48012f1793 100644
--- a/examples/performance/iterator-offsets/iterator-offsets.cxx
+++ b/examples/performance/iterator-offsets/iterator-offsets.cxx
@@ -65,7 +65,7 @@ int main(int argc, char** argv) {
   ITERATOR_TEST_BLOCK(
       "Nested loop", for (int i = 0; i < mesh->LocalNx; ++i) {
         for (int j = mesh->ystart; j < mesh->yend; ++j) {
-          for (int k = 0; k < mesh->LocalNz; ++k) {
+          for (int k = mesh->zstart; k <= mesh->zend; ++k) {
             result(i, j, k) = (a(i, j + 1, k) - a(i, j - 1, k));
           }
         }
@@ -76,7 +76,7 @@ int main(int argc, char** argv) {
     BOUT_OMP_PERF(parallel for)
     for(int i=0;i<mesh->LocalNx;++i) {
     for (int j = mesh->ystart; j < mesh->yend; ++j) {
-      for (int k = 0; k < mesh->LocalNz; ++k) {
+      for (int k = mesh->zstart; k <= mesh->zend; ++k) {
         result(i, j, k) = (a(i, j + 1, k) - a(i, j - 1, k));
       }
     }
diff --git a/examples/performance/iterator/iterator.cxx b/examples/performance/iterator/iterator.cxx
index 7a29b00298..e1fc59d067 100644
--- a/examples/performance/iterator/iterator.cxx
+++ b/examples/performance/iterator/iterator.cxx
@@ -77,7 +77,7 @@ int main(int argc, char** argv) {
   ITERATOR_TEST_BLOCK(
       "Nested loop", for (int i = 0; i < mesh->LocalNx; ++i) {
         for (int j = 0; j < mesh->LocalNy; ++j) {
-          for (int k = 0; k < mesh->LocalNz; ++k) {
+          for (int k = mesh->zstart; k <= mesh->zend; ++k) {
             result(i, j, k) = a(i, j, k) + b(i, j, k);
           }
         }
@@ -88,7 +88,7 @@ int main(int argc, char** argv) {
 		      BOUT_OMP_PERF(parallel for)
 		      for(int i=0;i<mesh->LocalNx;++i) {
     for (int j = 0; j < mesh->LocalNy; ++j) {
-      for (int k = 0; k < mesh->LocalNz; ++k) {
+      for (int k = mesh->zstart; k <= mesh->zend; ++k) {
         result(i, j, k) = a(i, j, k) + b(i, j, k);
       }
     }
diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 94007a57a2..df61c6aa24 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -258,7 +258,7 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
       BoutReal flux_factor_lm =
           common_factor / (coord->dy(i, j - 1) * coord->J(i, j - 1));
 #endif
-      for (int k = 0; k < mesh->LocalNz; k++) {
+      for (int k = mesh->zstart; k <= mesh->zend; k++) {
 #if BOUT_USE_METRIC_3D
         // For right cell boundaries
         BoutReal common_factor =
diff --git a/manual/sphinx/developer_docs/data_types.rst b/manual/sphinx/developer_docs/data_types.rst
index fa8e9e6ea6..f9411dcb39 100644
--- a/manual/sphinx/developer_docs/data_types.rst
+++ b/manual/sphinx/developer_docs/data_types.rst
@@ -255,9 +255,9 @@ parallelise and vectorise. Some tuning of this is possible, see below
 for details. It replaces the C-style triple-nested loop::
 
    Field3D f(0.0);
-   for (int i = mesh->xstart; i < mesh->xend; ++i) {
-     for (int j = mesh->ystart; j < mesh->yend; ++j) {
-       for (int k = 0; k < mesh->LocalNz; ++k) {
+   for (int i = mesh->xstart; i <= mesh->xend; ++i) {
+     for (int j = mesh->ystart; j <= mesh->yend; ++j) {
+       for (int k = mesh->zstart; k <= mesh->zend; ++k) {
          f(i,j,k) = a(i,j,k) + b(i,j,k)
        }
      }
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index a3cdf0078b..8493049516 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -575,7 +575,7 @@ and implemented in ``boundary_standard.cxx``
 
     void BoundaryNeumann::apply(Field3D &f) {
       for(bndry->first(); !bndry->isDone(); bndry->next())
-        for(int z=0;z<mesh->LocalNz;z++)
+        for(int z= mesh->zstart; z <= mesh->zend;z++)
           f[bndry->x][bndry->y][z] = f[bndry->x - bndry->bx][bndry->y -
     bndry->by][z];
     }
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index e6f68d850d..f61dc93908 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -402,7 +402,7 @@ void LaplaceNaulin::copy_x_boundaries(Field3D& x, const Field3D& x0, Mesh* local
   if (localmesh->firstX()) {
     for (int i = localmesh->xstart - 1; i >= 0; --i) {
       for (int j = localmesh->ystart; j <= localmesh->yend; ++j) {
-        for (int k = 0; k < localmesh->LocalNz; ++k) {
+        for (int k = localmesh->zstart; k <= localmesh->zend; ++k) {
           x(i, j, k) = x0(i, j, k);
         }
       }
@@ -411,7 +411,7 @@ void LaplaceNaulin::copy_x_boundaries(Field3D& x, const Field3D& x0, Mesh* local
   if (localmesh->lastX()) {
     for (int i = localmesh->xend + 1; i < localmesh->LocalNx; ++i) {
       for (int j = localmesh->ystart; j <= localmesh->yend; ++j) {
-        for (int k = 0; k < localmesh->LocalNz; ++k) {
+        for (int k = localmesh->zstart; k <= localmesh->zend; ++k) {
           x(i, j, k) = x0(i, j, k);
         }
       }
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 5f417d4faa..4170c88e80 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -145,7 +145,7 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   if (fourth_order) {
     // first and last 2*localmesh-LocalNz entries are the edge x-values that (may) have 'off-diagonal' components (i.e. on another processor)
     if (localmesh->firstX() && localmesh->lastX()) {
-      for (int i = 0; i < localmesh->LocalNz; i++) {
+      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
         d_nnz[i] = 15;
         d_nnz[localN - 1 - i] = 15;
         o_nnz[i] = 0;
@@ -158,7 +158,7 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
         o_nnz[localN - 1 - i] = 0;
       }
     } else if (localmesh->firstX()) {
-      for (int i = 0; i < localmesh->LocalNz; i++) {
+      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
         d_nnz[i] = 15;
         d_nnz[localN - 1 - i] = 15;
         o_nnz[i] = 0;
@@ -171,7 +171,7 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
         o_nnz[localN - 1 - i] = 5;
       }
     } else if (localmesh->lastX()) {
-      for (int i = 0; i < localmesh->LocalNz; i++) {
+      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
         d_nnz[i] = 15;
         d_nnz[localN - 1 - i] = 15;
         o_nnz[i] = 10;
@@ -184,7 +184,7 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
         o_nnz[localN - 1 - i] = 0;
       }
     } else {
-      for (int i = 0; i < localmesh->LocalNz; i++) {
+      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
         d_nnz[i] = 15;
         d_nnz[localN - 1 - i] = 15;
         o_nnz[i] = 10;
@@ -215,28 +215,28 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   } else {
     // first and last localmesh->LocalNz entries are the edge x-values that (may) have 'off-diagonal' components (i.e. on another processor)
     if (localmesh->firstX() && localmesh->lastX()) {
-      for (int i = 0; i < localmesh->LocalNz; i++) {
+      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
         d_nnz[i] = 6;
         d_nnz[localN - 1 - i] = 6;
         o_nnz[i] = 0;
         o_nnz[localN - 1 - i] = 0;
       }
     } else if (localmesh->firstX()) {
-      for (int i = 0; i < localmesh->LocalNz; i++) {
+      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
         d_nnz[i] = 6;
         d_nnz[localN - 1 - i] = 6;
         o_nnz[i] = 0;
         o_nnz[localN - 1 - i] = 3;
       }
     } else if (localmesh->lastX()) {
-      for (int i = 0; i < localmesh->LocalNz; i++) {
+      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
         d_nnz[i] = 6;
         d_nnz[localN - 1 - i] = 6;
         o_nnz[i] = 3;
         o_nnz[localN - 1 - i] = 0;
       }
     } else {
-      for (int i = 0; i < localmesh->LocalNz; i++) {
+      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
         d_nnz[i] = 6;
         d_nnz[localN - 1 - i] = 6;
         o_nnz[i] = 3;
@@ -377,7 +377,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
     // Set the values for the inner boundary region
     if (localmesh->firstX()) {
       for (int x = 0; x < localmesh->xstart; x++) {
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           PetscScalar val; // Value of element to be set in the matrix
           // If Neumann Boundary Conditions are set.
           if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) {
@@ -461,7 +461,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
 
     // Set the values for the main domain
     for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         // NOTE: Only A0 is the A from setCoefA ()
         BoutReal A0, A1, A2, A3, A4, A5;
         A0 = A(x, y, z);
@@ -639,7 +639,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
     // Set the values for the outer boundary region
     if (localmesh->lastX()) {
       for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           // Set Diagonal Values to 1
           PetscScalar val = 1;
           Element(i, x, z, 0, 0, val, MatA);
@@ -829,7 +829,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
   // Set the inner boundary values
   if (localmesh->firstX()) {
     for (int x = 0; x < localmesh->xstart; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val = 0;
         VecGetValues(xs, 1, &i, &val);
         sol[x][z] = val;
@@ -840,7 +840,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
 
   // Set the main domain values
   for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int z = 0; z < localmesh->LocalNz; z++) {
+    for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
       PetscScalar val = 0;
       VecGetValues(xs, 1, &i, &val);
       sol[x][z] = val;
@@ -851,7 +851,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
   // Set the outer boundary values
   if (localmesh->lastX()) {
     for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val = 0;
         VecGetValues(xs, 1, &i, &val);
         sol[x][z] = val;
@@ -1076,7 +1076,7 @@ void LaplacePetsc::vecToField(Vec xs, FieldPerp& f) {
   int i = Istart;
   if (localmesh->firstX()) {
     for (int x = 0; x < localmesh->xstart; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val;
         VecGetValues(xs, 1, &i, &val);
         f[x][z] = val;
@@ -1086,7 +1086,7 @@ void LaplacePetsc::vecToField(Vec xs, FieldPerp& f) {
   }
 
   for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int z = 0; z < localmesh->LocalNz; z++) {
+    for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
       PetscScalar val;
       VecGetValues(xs, 1, &i, &val);
       f[x][z] = val;
@@ -1096,7 +1096,7 @@ void LaplacePetsc::vecToField(Vec xs, FieldPerp& f) {
 
   if (localmesh->lastX()) {
     for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val;
         VecGetValues(xs, 1, &i, &val);
         f[x][z] = val;
@@ -1113,7 +1113,7 @@ void LaplacePetsc::fieldToVec(const FieldPerp& f, Vec bs) {
   int i = Istart;
   if (localmesh->firstX()) {
     for (int x = 0; x < localmesh->xstart; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val = f[x][z];
         VecSetValues(bs, 1, &i, &val, INSERT_VALUES);
         i++; // Increment row in Petsc matrix
@@ -1122,7 +1122,7 @@ void LaplacePetsc::fieldToVec(const FieldPerp& f, Vec bs) {
   }
 
   for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int z = 0; z < localmesh->LocalNz; z++) {
+    for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
       PetscScalar val = f[x][z];
       VecSetValues(bs, 1, &i, &val, INSERT_VALUES);
       i++; // Increment row in Petsc matrix
@@ -1131,7 +1131,7 @@ void LaplacePetsc::fieldToVec(const FieldPerp& f, Vec bs) {
 
   if (localmesh->lastX()) {
     for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val = f[x][z];
         VecSetValues(bs, 1, &i, &val, INSERT_VALUES);
         i++; // Increment row in Petsc matrix
diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx
index 2e4c844c94..e39ca7e89f 100644
--- a/src/invert/laplace/impls/spt/spt.cxx
+++ b/src/invert/laplace/impls/spt/spt.cxx
@@ -95,7 +95,7 @@ FieldPerp LaplaceSPT::solve(const FieldPerp& b, const FieldPerp& x0) {
     if (isInnerBoundaryFlagSetOnFirstX(INVERT_SET)) {
       // Copy x0 inner boundary into bs
       for (int ix = 0; ix < xbndry; ix++) {
-        for (int iz = 0; iz < localmesh->LocalNz; iz++) {
+        for (int iz = localmesh->zstart; iz <= localmesh->zend; iz++) {
           bs[ix][iz] = x0[ix][iz];
         }
       }
@@ -103,7 +103,7 @@ FieldPerp LaplaceSPT::solve(const FieldPerp& b, const FieldPerp& x0) {
     if (isOuterBoundaryFlagSetOnLastX(INVERT_SET)) {
       // Copy x0 outer boundary into bs
       for (int ix = localmesh->LocalNx - 1; ix >= localmesh->LocalNx - xbndry; ix--) {
-        for (int iz = 0; iz < localmesh->LocalNz; iz++) {
+        for (int iz = localmesh->zstart; iz <= localmesh->zend; iz++) {
           bs[ix][iz] = x0[ix][iz];
         }
       }
@@ -181,7 +181,7 @@ Field3D LaplaceSPT::solve(const Field3D& b, const Field3D& x0) {
       // Copy x0 inner boundary into bs
       for (int ix = 0; ix < xbndry; ix++) {
         for (int iy = 0; iy < localmesh->LocalNy; iy++) {
-          for (int iz = 0; iz < localmesh->LocalNz; iz++) {
+          for (int iz = localmesh->zstart; iz <= localmesh->zend; iz++) {
             bs(ix, iy, iz) = x0(ix, iy, iz);
           }
         }
@@ -191,7 +191,7 @@ Field3D LaplaceSPT::solve(const Field3D& b, const Field3D& x0) {
       // Copy x0 outer boundary into bs
       for (int ix = localmesh->LocalNx - 1; ix >= localmesh->LocalNx - xbndry; ix--) {
         for (int iy = 0; iy < localmesh->LocalNy; iy++) {
-          for (int iz = 0; iz < localmesh->LocalNz; iz++) {
+          for (int iz = localmesh->zstart; iz <= localmesh->zend; iz++) {
             bs(ix, iy, iz) = x0(ix, iy, iz);
           }
         }
@@ -519,7 +519,7 @@ void LaplaceSPT::finish(SPT_data& data, FieldPerp& x) {
   if (!localmesh->firstX()) {
     // Set left boundary to zero (Prevent unassigned values in corners)
     for (int ix = 0; ix < localmesh->xstart; ix++) {
-      for (int kz = 0; kz < localmesh->LocalNz; kz++) {
+      for (int kz = localmesh->zstart; kz <= localmesh->zend; kz++) {
         x(ix, kz) = 0.0;
       }
     }
@@ -527,7 +527,7 @@ void LaplaceSPT::finish(SPT_data& data, FieldPerp& x) {
   if (!localmesh->lastX()) {
     // Same for right boundary
     for (int ix = localmesh->xend + 1; ix < localmesh->LocalNx; ix++) {
-      for (int kz = 0; kz < localmesh->LocalNz; kz++) {
+      for (int kz = localmesh->zstart; kz <= localmesh->zend; kz++) {
         x(ix, kz) = 0.0;
       }
     }
diff --git a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
index 769e797352..c61db141b8 100644
--- a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
+++ b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
@@ -202,25 +202,25 @@ LaplaceXZpetsc::LaplaceXZpetsc(Mesh* m, Options* opt, const CELL_LOC loc)
 
     // X boundaries
     if (localmesh->firstX()) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         d_nnz[z] = 2;
       }
     } else {
       // One point on another processor
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         d_nnz[z] -= 1;
         o_nnz[z] += 1;
       }
     }
 
     if (localmesh->lastX()) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         int ind = localN - (localmesh->LocalNz) + z;
         d_nnz[ind] = 2;
       }
     } else {
       // One point on another processor
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         int ind = localN - (localmesh->LocalNz) + z;
         d_nnz[ind] -= 1;
         o_nnz[ind] += 1;
@@ -335,7 +335,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
         /* NOTE: Sign of the elements are opposite of what one might expect,
          *       see note about BC in LaplaceXZ constructor for more details
          */
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           PetscScalar val = 1.0;
           MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
 
@@ -347,7 +347,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
         }
       } else if (inner_boundary_flags & INVERT_SET) {
         // Setting BC from x0
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           PetscScalar val = 1.0;
           MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
 
@@ -359,7 +359,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
         }
       } else if (inner_boundary_flags & INVERT_RHS) {
         // Setting BC from b
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           PetscScalar val = 1.0;
           MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
 
@@ -374,7 +374,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
         /* NOTE: Sign of the elements are opposite of what one might expect,
          *       see note about BC in LaplaceXZ constructor for more details
          */
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           PetscScalar val = 0.5;
           MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
 
@@ -393,7 +393,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
     Coordinates* coords = localmesh->getCoordinates(location);
 
     for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         // stencil entries
         PetscScalar c, xm, xp, zm, zp;
         // Diagonal entries
@@ -655,7 +655,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
     if (localmesh->lastX()) {
       if (outer_boundary_flags & INVERT_AC_GRAD) {
         // Neumann 0
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           PetscScalar val = 1.0;
           MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
 
@@ -667,7 +667,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
         }
       } else if (outer_boundary_flags & INVERT_SET) {
         // Setting BC from x0
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           PetscScalar val = 1.0;
           MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
 
@@ -679,7 +679,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
         }
       } else if (outer_boundary_flags & INVERT_RHS) {
         // Setting BC from b
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           PetscScalar val = 1.0;
           MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
 
@@ -693,7 +693,7 @@ void LaplaceXZpetsc::setCoefs(const Field3D& Ain, const Field3D& Bin) {
         //Default: Dirichlet on outer X boundary
         PetscScalar val = 0.5;
 
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           MatSetValues(it.MatA, 1, &row, 1, &row, &val, INSERT_VALUES);
 
           int col = row - (localmesh->LocalNz); // -1 in X
@@ -804,7 +804,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
     if (localmesh->firstX()) {
       if (inner_boundary_flags & INVERT_AC_GRAD) {
         // Neumann 0
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           // Setting the initial guess x0
           PetscScalar val = x0(localmesh->xstart - 1, y, z);
           VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
@@ -816,7 +816,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
         }
       } else if (inner_boundary_flags & INVERT_SET) {
         // Setting BC from x0
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           // Setting the initial guess x0
           PetscScalar val = x0(localmesh->xstart - 1, y, z);
           VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
@@ -828,7 +828,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
         }
       } else if (inner_boundary_flags & INVERT_RHS) {
         // Setting BC from b
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           // Setting the initial guess x0
           PetscScalar val = x0(localmesh->xstart - 1, y, z);
           VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
@@ -840,7 +840,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
         }
       } else {
         // Default: Neumann on inner x boundary
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           // Setting the initial guess x0
           PetscScalar val = x0(localmesh->xstart - 1, y, z);
           VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
@@ -855,7 +855,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
 
     // Set the inner points
     for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val = x0(x, y, z);
         VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
 
@@ -869,7 +869,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
     if (localmesh->lastX()) {
       if (outer_boundary_flags & INVERT_AC_GRAD) {
         // Neumann 0
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           // Setting the initial guess x0
           PetscScalar val = x0(localmesh->xend + 1, y, z);
           VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
@@ -882,7 +882,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
         }
       } else if (outer_boundary_flags & INVERT_SET) {
         // Setting BC from x0
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           // Setting the initial guess x0
           PetscScalar val = x0(localmesh->xend + 1, y, z);
           VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
@@ -895,7 +895,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
         }
       } else if (outer_boundary_flags & INVERT_RHS) {
         // Setting BC from b
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           // Setting the initial guess x0
           PetscScalar val = x0(localmesh->xend + 1, y, z);
           VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
@@ -908,7 +908,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
         }
       } else {
         //Default: Dirichlet on outer X boundary
-        for (int z = 0; z < localmesh->LocalNz; z++) {
+        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
           // Setting the initial guess x0
           PetscScalar val = x0(localmesh->xend + 1, y, z);
           VecSetValues(xs, 1, &ind, &val, INSERT_VALUES);
@@ -952,7 +952,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
     ind = Istart;
     // Inner X boundary
     if (localmesh->firstX()) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val;
         VecGetValues(xs, 1, &ind, &val);
         for (int x = localmesh->xstart - 1; x >= 0; --x) {
@@ -963,7 +963,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
     }
 
     for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val;
         VecGetValues(xs, 1, &ind, &val);
         result(x, y, z) = val;
@@ -973,7 +973,7 @@ Field3D LaplaceXZpetsc::solve(const Field3D& bin, const Field3D& x0in) {
 
     // Outer X boundary
     if (localmesh->lastX()) {
-      for (int z = 0; z < localmesh->LocalNz; z++) {
+      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
         PetscScalar val;
         VecGetValues(xs, 1, &ind, &val);
         for (int x = localmesh->xend + 1; x < localmesh->LocalNx; ++x) {
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 8f2c7df5ec..c3fd5f8f2e 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -325,7 +325,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
         // Outer x boundary
 
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -346,7 +346,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
       if (bndry->bx < 0) {
         // Inner x boundary. Set one point inwards
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -368,7 +368,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
       if (bndry->by != 0) {
         // y boundaries
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -394,7 +394,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
         // Upper y boundary boundary
 
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -415,7 +415,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
       if (bndry->by < 0) {
         // Lower y boundary. Set one point inwards
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -436,7 +436,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
       if (bndry->bx != 0) {
         // x boundaries
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -469,7 +469,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
                                * (mesh->GlobalY(bndry->y) // In the guard cell
                                   + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
 
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           if (fg) {
             val = fg->generate(
                 Context(bndry, zk, loc, t, mesh).set("x", xnorm, "y", ynorm));
@@ -513,7 +513,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
           const int yi = bndry->y + (i * bndry->by);
           const auto xnorm = mesh->GlobalX(xi);
           const auto ynorm = mesh->GlobalY(yi) * TWOPI;
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(
                   Context(bndry, zk, loc, t, mesh).set("x", xnorm, "y", ynorm));
@@ -528,7 +528,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
   } else {
     // Standard (non-staggered) case
     for (; !bndry->isDone(); bndry->next1d()) {
-      for (int zk = 0; zk < mesh->LocalNz; zk++) {
+      for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
         if (fg) {
           val = fg->generate(Context(bndry, zk, loc, t, mesh));
         }
@@ -572,7 +572,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
         // Set any other guard cells using the values on the cells
         int xi = bndry->x + i * bndry->bx;
         int yi = bndry->y + i * bndry->by;
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           if (fg) {
             val = fg->generate(Context(bndry, zk, loc, t, mesh));
           }
@@ -596,7 +596,7 @@ void BoundaryDirichlet::apply_ddt(Field3D& f) {
   Field3D* dt = f.timeDeriv();
 
   for (bndry->first(); !bndry->isDone(); bndry->next()) {
-    for (int z = 0; z < mesh->LocalNz; z++) {
+    for (int z = mesh->zstart; z <= mesh->zend; z++) {
       (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
     }
   }
@@ -827,7 +827,7 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
         // Outer x boundary
 
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -848,7 +848,7 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
       if (bndry->bx < 0) {
         // Inner x boundary. Set one point inwards
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -870,7 +870,7 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
         // y boundaries
 
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -898,7 +898,7 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
         // Upper y boundary
 
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -919,7 +919,7 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
       if (bndry->by < 0) {
         // Lower y boundary. Set one point inwards
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -940,7 +940,7 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
       if (bndry->bx != 0) {
         // x boundaries
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -974,7 +974,7 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
                                * (mesh->GlobalY(bndry->y) // In the guard cell
                                   + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
 
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           if (fg) {
             val = fg->generate(
                 Context(bndry, zk, loc, t, mesh).set("x", xnorm, "y", ynorm));
@@ -1000,7 +1000,7 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
   } else {
     // Standard (non-staggered) case
     for (; !bndry->isDone(); bndry->next1d()) {
-      for (int zk = 0; zk < mesh->LocalNz; zk++) {
+      for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
         if (fg) {
           val = fg->generate(Context(bndry, zk, loc, t, mesh));
         }
@@ -1038,7 +1038,7 @@ void BoundaryDirichlet_O3::apply_ddt(Field3D& f) {
 
   bndry->first();
   for (bndry->first(); !bndry->isDone(); bndry->next()) {
-    for (int z = 0; z < mesh->LocalNz; z++) {
+    for (int z = mesh->zstart; z <= mesh->zend; z++) {
       (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
     }
   }
@@ -1284,7 +1284,7 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
         // Outer x boundary
 
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -1306,7 +1306,7 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
       if (bndry->bx < 0) {
         // Inner x boundary. Set one point inwards
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -1329,7 +1329,7 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
         // y boundaries
 
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -1358,7 +1358,7 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
         // Outer y boundary
 
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -1381,7 +1381,7 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
       if (bndry->by < 0) {
         // Inner y boundary. Set one point inwards
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -1405,7 +1405,7 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
         // x boundaries
 
         for (; !bndry->isDone(); bndry->next1d()) {
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             if (fg) {
               val = fg->generate(Context(bndry, zk, loc, t, mesh));
             }
@@ -1440,7 +1440,7 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
                                * (mesh->GlobalY(bndry->y) // In the guard cell
                                   + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
 
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           if (fg) {
             val = fg->generate(
                 Context(bndry, zk, loc, t, mesh).set("x", xnorm, "y", ynorm));
@@ -1468,7 +1468,7 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
   } else {
     // Standard (non-staggered) case
     for (; !bndry->isDone(); bndry->next1d()) {
-      for (int zk = 0; zk < mesh->LocalNz; zk++) {
+      for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
         if (fg) {
           val = fg->generate(Context(bndry, zk, loc, t, mesh));
         }
@@ -1505,7 +1505,7 @@ void BoundaryDirichlet_O4::apply_ddt(Field3D& f) {
   ASSERT1(mesh == f.getMesh());
   Field3D* dt = f.timeDeriv();
   for (bndry->first(); !bndry->isDone(); bndry->next()) {
-    for (int z = 0; z < mesh->LocalNz; z++) {
+    for (int z = mesh->zstart; z <= mesh->zend; z++) {
       (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
     }
   }
@@ -1547,7 +1547,7 @@ void BoundaryDirichlet_4thOrder::apply(Field3D& f) {
   // Set (at 4th order) the value at the mid-point between the guard cell and the grid
   // cell to be val
   for (bndry->first(); !bndry->isDone(); bndry->next1d()) {
-    for (int z = 0; z < mesh->LocalNz; z++) {
+    for (int z = mesh->zstart; z <= mesh->zend; z++) {
       f(bndry->x, bndry->y, z) =
           128. / 35. * val - 4. * f(bndry->x - bndry->bx, bndry->y - bndry->by, z)
           + 2. * f(bndry->x - 2 * bndry->bx, bndry->y - 2 * bndry->by, z)
@@ -1574,7 +1574,7 @@ void BoundaryDirichlet_4thOrder::apply_ddt(Field3D& f) {
   ASSERT1(mesh == f.getMesh());
   Field3D* dt = f.timeDeriv();
   for (bndry->first(); !bndry->isDone(); bndry->next()) {
-    for (int z = 0; z < mesh->LocalNz; z++) {
+    for (int z = mesh->zstart; z <= mesh->zend; z++) {
       (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
     }
   }
@@ -1661,7 +1661,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
   // Loop over all elements and set equal to the next point in
   for (bndry->first(); !bndry->isDone(); bndry->next1d()) {
 #if BOUT_USE_METRIC_3D
-    for (int z = 0; z < mesh->LocalNz; z++) {
+    for (int z = mesh->zstart; z <= mesh->zend; z++) {
 #else
     int z = 0;
 #endif
@@ -1680,7 +1680,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       //   because derivative values don't exist in boundary region
       // NOTE: should be fixed to interpolate to boundary line
 #if not(BOUT_USE_METRIC_3D)
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
 #endif
         BoutReal xshift = g12shift * dfdy(bndry->x - bndry->bx, bndry->y, z)
                           + g13shift * dfdz(bndry->x - bndry->bx, bndry->y, z);
@@ -1968,7 +1968,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         if (bndry->bx > 0) {
           // Outer x boundary
           for (; !bndry->isDone(); bndry->next1d()) {
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               if (fg) {
                 val = fg->generate(Context(bndry, zk, loc, t, mesh))
                       * metric->dx(bndry->x, bndry->y, zk);
@@ -1997,7 +1997,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         if (bndry->bx < 0) {
           // Inner x boundary
           for (; !bndry->isDone(); bndry->next1d()) {
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               if (fg) {
                 val = fg->generate(Context(bndry, zk, loc, t, mesh))
                       * metric->dx(bndry->x - bndry->bx, bndry->y, zk);
@@ -2029,7 +2029,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
             BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
                              + bndry->by * metric->dy(bndry->x, bndry->y);
 #endif
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
 #if BOUT_USE_METRIC_3D
               BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                                + bndry->by * metric->dy(bndry->x, bndry->y, zk);
@@ -2053,7 +2053,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         if (bndry->by > 0) {
           // Outer y boundary
           for (; !bndry->isDone(); bndry->next1d()) {
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               if (fg) {
                 val = fg->generate(Context(bndry, zk, loc, t, mesh))
                       * metric->dy(bndry->x, bndry->y, zk);
@@ -2081,7 +2081,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         if (bndry->by < 0) {
           // Inner y boundary. Set one point inwards
           for (; !bndry->isDone(); bndry->next1d()) {
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               if (fg) {
                 val = fg->generate(Context(bndry, zk, loc, t, mesh))
                       * metric->dy(bndry->x, bndry->y - bndry->by, zk);
@@ -2115,7 +2115,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
             BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                              + bndry->by * metric->dy(bndry->x, bndry->y, zk);
 #endif
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
 #if BOUT_USE_METRIC_3D
               BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                                + bndry->by * metric->dy(bndry->x, bndry->y, zk);
@@ -2148,7 +2148,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
               * (mesh->GlobalY(bndry->y)                 // In the guard cell
                  + mesh->GlobalY(bndry->y - bndry->by)); // the grid cell
 
-          for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
             BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                              + bndry->by * metric->dy(bndry->x, bndry->y, zk);
             if (fg) {
@@ -2170,13 +2170,13 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     } else {
       for (; !bndry->isDone(); bndry->next1d()) {
 #if BOUT_USE_METRIC_3D
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                            + bndry->by * metric->dy(bndry->x, bndry->y, zk);
 #else
       BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
                        + bndry->by * metric->dy(bndry->x, bndry->y);
-      for (int zk = 0; zk < mesh->LocalNz; zk++) {
+      for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
 #endif
           if (fg) {
             val = fg->generate(Context(bndry, zk, loc, t, mesh));
@@ -2205,7 +2205,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     ASSERT1(mesh == f.getMesh());
     Field3D* dt = f.timeDeriv();
     for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
       }
     }
@@ -2303,7 +2303,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     } else {
       Coordinates* coords = f.getCoordinates();
       for (; !bndry->isDone(); bndry->next1d()) {
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           BoutReal delta = bndry->bx * coords->dx(bndry->x, bndry->y, zk)
                            + bndry->by * coords->dy(bndry->x, bndry->y, zk);
           if (fg) {
@@ -2339,7 +2339,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     ASSERT1(mesh == f.getMesh());
     Field3D* dt = f.timeDeriv();
     for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
       }
     }
@@ -2398,7 +2398,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     // grid cell to be val This sets the value of the co-ordinate derivative, i.e. DDX/DDY
     // not Grad_par/Grad_perp.x
     for (bndry->first(); !bndry->isDone(); bndry->next1d()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         BoutReal delta = -(bndry->bx * metric->dx(bndry->x, bndry->y, z)
                            + bndry->by * metric->dy(bndry->x, bndry->y, z));
         f(bndry->x, bndry->y, z) =
@@ -2431,7 +2431,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     ASSERT1(mesh == f.getMesh());
     Field3D* dt = f.timeDeriv();
     for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
       }
     }
@@ -2469,7 +2469,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     ASSERT1(mesh == f.getMesh());
     Coordinates* metric = f.getCoordinates();
     for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         f(bndry->x, bndry->y, z) =
             f(bndry->x - bndry->bx, bndry->y - bndry->by, z)
             * sqrt(metric->g_22(bndry->x, bndry->y, z)
@@ -2536,7 +2536,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     ASSERT1(mesh == f.getMesh());
     if (fabs(bval) < 1.e-12) {
       for (bndry->first(); !bndry->isDone(); bndry->next()) {
-        for (int z = 0; z < mesh->LocalNz; z++) {
+        for (int z = mesh->zstart; z <= mesh->zend; z++) {
           f(bndry->x, bndry->y, z) = gval / aval;
         }
       }
@@ -2546,7 +2546,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         sign = -1.;
       }
       for (bndry->first(); !bndry->isDone(); bndry->next()) {
-        for (int z = 0; z < mesh->LocalNz; z++) {
+        for (int z = mesh->zstart; z <= mesh->zend; z++) {
           f(bndry->x, bndry->y, z) =
               f(bndry->x - bndry->bx, bndry->y - bndry->by, z)
               + sign * (gval - aval * f(bndry->x - bndry->bx, bndry->y - bndry->by, z))
@@ -2570,7 +2570,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
     for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         f(bndry->x, bndry->y, z) =
             2. * f(bndry->x - bndry->bx, bndry->y - bndry->by, z)
             - f(bndry->x - 2 * bndry->bx, bndry->y - 2 * bndry->by, z);
@@ -3191,7 +3191,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = 0; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3205,7 +3205,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           // Inner x boundary. Set one point inwards
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = -1; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3220,7 +3220,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = 0; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3236,7 +3236,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         if (bndry->by > 0) {
           // Upper y boundary
           for (; !bndry->isDone(); bndry->next1d()) {
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = 0; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3250,7 +3250,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           // Lower y boundary. Set one point inwards
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = -1; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3264,7 +3264,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           // x boundaries
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = 0; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3279,7 +3279,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       // Standard (non-staggered) case
       for (; !bndry->isDone(); bndry->next1d()) {
 
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           for (int i = 0; i < bndry->width; i++) {
             int xi = bndry->x + i * bndry->bx;
             int yi = bndry->y + i * bndry->by;
@@ -3303,7 +3303,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     ASSERT1(mesh == f.getMesh());
     Field3D* dt = f.timeDeriv();
     for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
       }
     }
@@ -3453,7 +3453,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = 0; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3468,7 +3468,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           // Inner x boundary. Set one point inwards
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = -1; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3484,7 +3484,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = 0; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3501,7 +3501,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         if (bndry->by > 0) {
           // Upper y boundary
           for (; !bndry->isDone(); bndry->next1d()) {
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = 0; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3516,7 +3516,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           // Lower y boundary. Set one point inwards
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = -1; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3531,7 +3531,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           // x boundaries
           for (; !bndry->isDone(); bndry->next1d()) {
 
-            for (int zk = 0; zk < mesh->LocalNz; zk++) {
+            for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
               for (int i = 0; i < bndry->width; i++) {
                 int xi = bndry->x + i * bndry->bx;
                 int yi = bndry->y + i * bndry->by;
@@ -3547,7 +3547,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       // Standard (non-staggered) case
       for (; !bndry->isDone(); bndry->next1d()) {
 
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           for (int i = 0; i < bndry->width; i++) {
             int xi = bndry->x + i * bndry->bx;
             int yi = bndry->y + i * bndry->by;
@@ -3572,7 +3572,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     ASSERT1(mesh == f.getMesh());
     Field3D* dt = f.timeDeriv();
     for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
       }
     }
@@ -3632,7 +3632,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     op->apply(g);
     // Set time-derivatives
     for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         ddt(f)(bndry->x, bndry->y, z) =
             r * (g(bndry->x, bndry->y, z) - f(bndry->x, bndry->y, z));
       }
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 3dfee6a553..986707a79e 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -225,7 +225,7 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
           ASSERT1(bndry->bx == 0 or localmesh->xstart > 1);
           ASSERT1(bndry->by == 0 or localmesh->ystart > 1);
           // note that either bx or by is >0 here
-          for (int zi = 0; zi < localmesh->LocalNz; ++zi) {
+          for (int zi = localmesh->zstart; zi <= localmesh->zend; ++zi) {
             result(bndry->x, bndry->y, zi) =
                 (9.
                      * (f(bndry->x - bndry->bx, bndry->y - bndry->by, zi)
@@ -256,7 +256,7 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
           for (int i = extrap_start; i < bndry->width; i++) {
             int xi = bndry->x + i * bndry->bx;
             int yi = bndry->y + i * bndry->by;
-            for (int zi = 0; zi < localmesh->LocalNz; ++zi) {
+            for (int zi = localmesh->zstart; zi <= localmesh->zend; ++zi) {
               result(xi, yi, zi) =
                   3.0 * result(xi - bndry->bx, yi - bndry->by, zi)
                   - 3.0 * result(xi - 2 * bndry->bx, yi - 2 * bndry->by, zi)
@@ -266,7 +266,7 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
         } else {
           // not enough grid points to extrapolate, set equal to last grid point
           for (int i = extrap_start; i < bndry->width; i++) {
-            for (int zi = 0; zi < localmesh->LocalNz; ++zi) {
+            for (int zi = localmesh->zstart; zi <= localmesh->zend; ++zi) {
               result(bndry->x + i * bndry->bx, bndry->y + i * bndry->by, zi) =
                   result(bndry->x - bndry->bx, bndry->y - bndry->by, zi);
             }
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 42fa4d6ca5..64b072e5ec 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -779,7 +779,7 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
       for (int jy = mesh->ystart; jy <= mesh->yend; jy++) {
         const BoutReal partialFactor = 1.0 / (12 * metric->dz(jx, jy));
         const BoutReal spacingFactor = partialFactor / metric->dx(jx, jy);
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
           const int jzp = jz + 1 < ncz ? jz + 1 : 0;
           // Above is alternative to const int jzp = (jz + 1) % ncz;
           const int jzm = jz - 1 >= 0 ? jz - 1 : ncz - 1;
@@ -904,7 +904,7 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
     int ncz = mesh->LocalNz;
     for (int y = mesh->ystart; y <= mesh->yend; y++) {
       for (int x = 1; x <= mesh->LocalNx - 2; x++) {
-        for (int z = 0; z < mesh->LocalNz; z++) {
+        for (int z = mesh->zstart; z <= mesh->zend; z++) {
           int zm = (z - 1 + ncz) % ncz;
           int zp = (z + 1) % ncz;
 
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index fe5422b4d1..723e1d45da 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -48,7 +48,7 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
 
   for (int i = xs; i <= xe; i++) {
     for (int j = mesh->ystart; j <= mesh->yend; j++) {
-      for (int k = 0; k < mesh->LocalNz; k++) {
+      for (int k = mesh->zstart; k <= mesh->zend; k++) {
         // Calculate flux from i to i+1
 
         BoutReal fout = 0.5 * (a(i, j, k) + a(i + 1, j, k))
@@ -282,7 +282,7 @@ const Field3D D4DY4(const Field3D& d_in, const Field3D& f_in) {
                          mesh->yend;
 
     for (int j = ystart; j <= yend; j++) {
-      for (int k = 0; k < mesh->LocalNz; k++) {
+      for (int k = mesh->zstart; k <= mesh->zend; k++) {
         BoutReal dy3 = SQ(coord->dy(i, j, k)) * coord->dy(i, j, k);
         // 3rd derivative at upper boundary
 
@@ -329,7 +329,7 @@ const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
 
         if (j != mesh->yend || !has_upper_boundary) {
 
-          for (int k = 0; k < mesh->LocalNz; k++) {
+          for (int k = mesh->zstart; k <= mesh->zend; k++) {
             // Right boundary common factors
             const BoutReal common_factor = 0.25
                                            * (coord->dy(i, j, k) + coord->dy(i, j + 1, k))
@@ -353,7 +353,7 @@ const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
           // At a domain boundary
           // Use a one-sided difference formula
 
-          for (int k = 0; k < mesh->LocalNz; k++) {
+          for (int k = mesh->zstart; k <= mesh->zend; k++) {
             // Right boundary common factors
             const BoutReal common_factor = 0.25
                                            * (coord->dy(i, j, k) + coord->dy(i, j + 1, k))
@@ -383,7 +383,7 @@ const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
         // Calculate the fluxes
 
         if (j != mesh->ystart || !has_lower_boundary) {
-          for (int k = 0; k < mesh->LocalNz; k++) {
+          for (int k = mesh->zstart; k <= mesh->zend; k++) {
             const BoutReal common_factor = 0.25
                                            * (coord->dy(i, j, k) + coord->dy(i, j + 1, k))
                                            * (coord->J(i, j, k) + coord->J(i, j - 1, k));
@@ -402,7 +402,7 @@ const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
           }
         } else {
           // On a domain (Y) boundary
-          for (int k = 0; k < mesh->LocalNz; k++) {
+          for (int k = mesh->zstart; k <= mesh->zend; k++) {
             const BoutReal common_factor = 0.25
                                            * (coord->dy(i, j, k) + coord->dy(i, j + 1, k))
                                            * (coord->J(i, j, k) + coord->J(i, j - 1, k));
@@ -463,7 +463,7 @@ void communicateFluxes(Field3D& f) {
     mesh->wait(xin);
     // Add to cells
     for (int y = mesh->ystart; y <= mesh->yend; y++) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         f(2, y, z) += f(0, y, z);
       }
     }
@@ -472,7 +472,7 @@ void communicateFluxes(Field3D& f) {
     mesh->wait(xout);
     // Add to cells
     for (int y = mesh->ystart; y <= mesh->yend; y++) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         f(mesh->LocalNx - 3, y, z) += f(mesh->LocalNx - 1, y, z);
       }
     }
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
index 07188110ab..5ad70a9b8b 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
@@ -331,7 +331,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
       if (mesh->firstX()) {
         // Lower X boundary
         for (int y = mesh->ystart; y <= mesh->yend; y++) {
-          for (int z = 0; z < mesh->LocalNz; z++) {
+          for (int z = mesh->zstart; z <= mesh->zend; z++) {
             int localIndex = ROUND(index(mesh->xstart, y, z));
             ASSERT2((localIndex >= 0) && (localIndex < localN));
             if (z == 0) {
@@ -350,7 +350,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
       } else {
         // On another processor
         for (int y = mesh->ystart; y <= mesh->yend; y++) {
-          for (int z = 0; z < mesh->LocalNz; z++) {
+          for (int z = mesh->zstart; z <= mesh->zend; z++) {
             int localIndex = ROUND(index(mesh->xstart, y, z));
             ASSERT2((localIndex >= 0) && (localIndex < localN));
             if (z == 0) {
@@ -373,7 +373,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
       if (mesh->lastX()) {
         // Upper X boundary
         for (int y = mesh->ystart; y <= mesh->yend; y++) {
-          for (int z = 0; z < mesh->LocalNz; z++) {
+          for (int z = mesh->zstart; z <= mesh->zend; z++) {
             int localIndex = ROUND(index(mesh->xend, y, z));
             ASSERT2((localIndex >= 0) && (localIndex < localN));
             if (z == 0) {
@@ -392,7 +392,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
       } else {
         // On another processor
         for (int y = mesh->ystart; y <= mesh->yend; y++) {
-          for (int z = 0; z < mesh->LocalNz; z++) {
+          for (int z = mesh->zstart; z <= mesh->zend; z++) {
             int localIndex = ROUND(index(mesh->xend, y, z));
             ASSERT2((localIndex >= 0) && (localIndex < localN));
             if (z == 0) {
@@ -559,7 +559,7 @@ void IMEXBDF2::constructSNES(SNES* snesIn) {
           }
 
           // 3D fields
-          for (int z = 0; z < mesh->LocalNz; z++) {
+          for (int z = mesh->zstart; z <= mesh->zend; z++) {
 
             int ind = ROUND(index(x, y, z));
 
@@ -1420,7 +1420,7 @@ void IMEXBDF2::loopVars(BoutReal* u) {
       if (mesh->firstX() && !mesh->periodicX) {
         for (int jx = 0; jx < mesh->xstart; ++jx) {
           for (int jy = mesh->ystart; jy <= mesh->yend; ++jy) {
-            for (int jz = 0; jz < mesh->LocalNz; ++jz) {
+            for (int jz = mesh->zstart; jz <= mesh->zend; ++jz) {
               op.run(jx, jy, jz, u);
               ++u;
             }
@@ -1432,7 +1432,7 @@ void IMEXBDF2::loopVars(BoutReal* u) {
       if (mesh->lastX() && !mesh->periodicX) {
         for (int jx = mesh->xend + 1; jx < mesh->LocalNx; ++jx) {
           for (int jy = mesh->ystart; jy <= mesh->yend; ++jy) {
-            for (int jz = 0; jz < mesh->LocalNz; ++jz) {
+            for (int jz = mesh->zstart; jz <= mesh->zend; ++jz) {
               op.run(jx, jy, jz, u);
               ++u;
             }
@@ -1442,7 +1442,7 @@ void IMEXBDF2::loopVars(BoutReal* u) {
       // Lower Y
       for (RangeIterator xi = mesh->iterateBndryLowerY(); !xi.isDone(); ++xi) {
         for (int jy = 0; jy < mesh->ystart; ++jy) {
-          for (int jz = 0; jz < mesh->LocalNz; ++jz) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; ++jz) {
             op.run(*xi, jy, jz, u);
             ++u;
           }
@@ -1452,7 +1452,7 @@ void IMEXBDF2::loopVars(BoutReal* u) {
       // Upper Y
       for (RangeIterator xi = mesh->iterateBndryUpperY(); !xi.isDone(); ++xi) {
         for (int jy = mesh->yend + 1; jy < mesh->LocalNy; ++jy) {
-          for (int jz = 0; jz < mesh->LocalNz; ++jz) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; ++jz) {
             op.run(*xi, jy, jz, u);
             ++u;
           }
@@ -1463,7 +1463,7 @@ void IMEXBDF2::loopVars(BoutReal* u) {
     // Bulk of points
     for (int jx = mesh->xstart; jx <= mesh->xend; ++jx) {
       for (int jy = mesh->ystart; jy <= mesh->yend; ++jy) {
-        for (int jz = 0; jz < mesh->LocalNz; ++jz) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; ++jz) {
           op.run(jx, jy, jz, u);
           ++u;
         }
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index d0535f069d..81f1cc7951 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -660,7 +660,7 @@ int PetscSolver::init() {
               }
             }
             // 3D fields
-            for (int z = 0; z < mesh->LocalNz; z++) {
+            for (int z = mesh->zstart; z <= mesh->zend; z++) {
               const int ind = ROUND(index(x, y, z)) - Istart;
 
               for (int i = 0; i < n3d; i++) {
@@ -768,7 +768,7 @@ int PetscSolver::init() {
             }
           }
           // 3D fields
-          for (int z = 0; z < mesh->LocalNz; z++) {
+          for (int z = mesh->zstart; z <= mesh->zend; z++) {
             int const ind = ROUND(index(x, y, z));
 
             for (int i = 0; i < n3d; i++) {
@@ -792,7 +792,7 @@ int PetscSolver::init() {
                     || (yi >= mesh->LocalNy)) {
                   continue;
                 }
-                for (int zi = 0; zi < mesh->LocalNz; ++zi) {
+                for (int zi = mesh->zstart; zi <= mesh->zend; ++zi) {
                   int ind2 = ROUND(index(xi, yi, zi));
                   if (ind2 < 0) {
                     continue; // Boundary point
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 311bc371fe..446903dd4f 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -200,7 +200,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
             }
           }
           // 3D fields
-          for (int z = 0; z < mesh->LocalNz; z++) {
+          for (int z = mesh->zstart; z <= mesh->zend; z++) {
             const int ind = ROUND(index(x, y, z)) - Istart;
 
             for (int i = 0; i < n3d; i++) {
@@ -305,7 +305,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
           }
         }
         // 3D fields
-        for (int z = 0; z < mesh->LocalNz; z++) {
+        for (int z = mesh->zstart; z <= mesh->zend; z++) {
           int ind = ROUND(index(x, y, z));
 
           for (int i = 0; i < n3d; i++) {
@@ -329,7 +329,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
                   || (yi >= mesh->LocalNy)) {
                 continue;
               }
-              for (int zi = 0; zi < mesh->LocalNz; ++zi) {
+              for (int zi = mesh->zstart; zi <= mesh->zend; ++zi) {
                 int ind2 = ROUND(index(xi, yi, zi));
                 if (ind2 < 0) {
                   continue; // Boundary point
@@ -1331,7 +1331,7 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
     }
 
     // Field3D quantities evolved together within a cell
-    for (int jz = 0; jz < mesh->LocalNz; jz++) {
+    for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
       count = 0;
       residual = 0.0;
       for (const auto& f : f3d) {
@@ -1380,7 +1380,7 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
 
     // Field3D quantities evolved together within a cell
     if (!f3d.empty()) {
-      for (int jz = 0; jz < mesh->LocalNz; jz++) {
+      for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
         auto i3d = mesh->ind2Dto3D(i2d, jz);
 
         BoutReal residual = 0.0;
diff --git a/tests/integrated/test-invpar/test_invpar.cxx b/tests/integrated/test-invpar/test_invpar.cxx
index 350437d66b..99b4e99c5c 100644
--- a/tests/integrated/test-invpar/test_invpar.cxx
+++ b/tests/integrated/test-invpar/test_invpar.cxx
@@ -47,7 +47,7 @@ int test(const std::string& acoef, const std::string& bcoef, const std::string&
     local_ystart = mesh->ystart + 1;
   }
   for (int y = local_ystart; y < mesh->yend; y++) {
-    for (int z = 0; z < mesh->LocalNz; z++) {
+    for (int z = mesh->zstart; z <= mesh->zend; z++) {
       output.write("result: [{:d},{:d}] : {:e}, {:e}, {:e}\n", y, z,
                    input(mesh->xstart, y, z), result(mesh->xstart, y, z),
                    deriv(mesh->xstart, y, z));
diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx
index 2b03f78049..a3e128bfdc 100644
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx
@@ -173,14 +173,14 @@ int main(int argc, char** argv) {
   // make field to pass in boundary conditions
   Field3D x0 = 0.;
   if (mesh->firstX()) {
-    for (int k = 0; k < mesh->LocalNz; k++) {
+    for (int k = mesh->zstart; k <= mesh->zend; k++) {
       x0(mesh->xstart - 1, mesh->ystart, k) =
           0.5
           * (f3(mesh->xstart - 1, mesh->ystart, k) + f3(mesh->xstart, mesh->ystart, k));
     }
   }
   if (mesh->lastX()) {
-    for (int k = 0; k < mesh->LocalNz; k++) {
+    for (int k = mesh->zstart; k <= mesh->zend; k++) {
       x0(mesh->xend + 1, mesh->ystart, k) =
           0.5 * (f3(mesh->xend + 1, mesh->ystart, k) + f3(mesh->xend, mesh->ystart, k));
     }
@@ -238,7 +238,7 @@ int main(int argc, char** argv) {
   // make field to pass in boundary conditions
   x0 = 0.;
   if (mesh->firstX()) {
-    for (int k = 0; k < mesh->LocalNz; k++) {
+    for (int k = mesh->zstart; k <= mesh->zend; k++) {
       x0(mesh->xstart - 1, mesh->ystart, k) =
           (f4(mesh->xstart, mesh->ystart, k) - f4(mesh->xstart - 1, mesh->ystart, k))
           / mesh->getCoordinates()->dx(mesh->xstart, mesh->ystart, k)
@@ -246,7 +246,7 @@ int main(int argc, char** argv) {
     }
   }
   if (mesh->lastX()) {
-    for (int k = 0; k < mesh->LocalNz; k++) {
+    for (int k = mesh->zstart; k <= mesh->zend; k++) {
       x0(mesh->xend + 1, mesh->ystart, k) =
           (f4(mesh->xend + 1, mesh->ystart, k) - f4(mesh->xend, mesh->ystart, k))
           / mesh->getCoordinates()->dx(mesh->xend, mesh->ystart, k)
@@ -311,7 +311,7 @@ BoutReal max_error_at_ystart(const Field3D& error) {
   BoutReal local_max_error = error(mesh->xstart, mesh->ystart, 0);
 
   for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
-    for (int jz = 0; jz < mesh->LocalNz; jz++) {
+    for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
       if (local_max_error < error(jx, mesh->ystart, jz)) {
         local_max_error = error(jx, mesh->ystart, jz);
       }
diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx b/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx
index 07a403e2e2..e9af4e5b36 100644
--- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx
+++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx
@@ -175,14 +175,14 @@ int main(int argc, char** argv) {
   // make field to pass in boundary conditions
   Field3D x0 = 0.;
   if (mesh->firstX()) {
-    for (int k = 0; k < mesh->LocalNz; k++) {
+    for (int k = mesh->zstart; k <= mesh->zend; k++) {
       x0(mesh->xstart - 1, mesh->ystart, k) =
           0.5
           * (f3(mesh->xstart - 1, mesh->ystart, k) + f3(mesh->xstart, mesh->ystart, k));
     }
   }
   if (mesh->lastX()) {
-    for (int k = 0; k < mesh->LocalNz; k++) {
+    for (int k = mesh->zstart; k <= mesh->zend; k++) {
       x0(mesh->xend + 1, mesh->ystart, k) =
           0.5 * (f3(mesh->xend + 1, mesh->ystart, k) + f3(mesh->xend, mesh->ystart, k));
     }
@@ -242,7 +242,7 @@ int main(int argc, char** argv) {
   // make field to pass in boundary conditions
   x0 = 0.;
   if (mesh->firstX()) {
-    for (int k = 0; k < mesh->LocalNz; k++) {
+    for (int k = mesh->zstart; k <= mesh->zend; k++) {
       x0(mesh->xstart - 1, mesh->ystart, k) =
           (f4(mesh->xstart, mesh->ystart, k) - f4(mesh->xstart - 1, mesh->ystart, k))
           / mesh->getCoordinates()->dx(mesh->xstart, mesh->ystart, k)
@@ -250,7 +250,7 @@ int main(int argc, char** argv) {
     }
   }
   if (mesh->lastX()) {
-    for (int k = 0; k < mesh->LocalNz; k++) {
+    for (int k = mesh->zstart; k <= mesh->zend; k++) {
       x0(mesh->xend + 1, mesh->ystart, k) =
           (f4(mesh->xend + 1, mesh->ystart, k) - f4(mesh->xend, mesh->ystart, k))
           / mesh->getCoordinates()->dx(mesh->xend, mesh->ystart, k)
@@ -315,7 +315,7 @@ BoutReal max_error_at_ystart(const Field3D& error) {
   BoutReal local_max_error = error(mesh->xstart, mesh->ystart, 0);
 
   for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
-    for (int jz = 0; jz < mesh->LocalNz; jz++) {
+    for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
       if (local_max_error < error(jx, mesh->ystart, jz)) {
         local_max_error = error(jx, mesh->ystart, jz);
       }
diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
index 1e3cdde310..c42c55d8d6 100644
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
@@ -222,7 +222,7 @@ BoutReal max_error_at_ystart(const Field3D& error) {
   BoutReal local_max_error = error(mesh->xstart, mesh->ystart, 0);
 
   for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
-    for (int jz = 0; jz < mesh->LocalNz; jz++) {
+    for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
       if (local_max_error < error(jx, mesh->ystart, jz)) {
         local_max_error = error(jx, mesh->ystart, jz);
       }
@@ -241,7 +241,7 @@ void apply_flat_boundary(Field3D& bcoef) {
   if (mesh.firstX()) {
     for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           bcoef(jx, jy, jz) = bcoef(jx + 1, jy, jz);
         }
       }
@@ -250,7 +250,7 @@ void apply_flat_boundary(Field3D& bcoef) {
   if (mesh.lastX()) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           bcoef(jx, jy, jz) = bcoef(jx - 1, jy, jz);
         }
       }
@@ -270,7 +270,7 @@ Field3D generate_f1(const Mesh& mesh) {
   for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
     const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
     for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = 0; jz < mesh.LocalNz; jz++) {
+      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
         const BoutReal z = BoutReal(jz) / nz;
         //make the gradients zero at both x-boundaries
         result(jx, jy, jz) = 0.
@@ -289,7 +289,7 @@ Field3D generate_f1(const Mesh& mesh) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
 
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           //make the gradients zero at both x-boundaries
           result(jx, jy, jz) = 0.
@@ -308,7 +308,7 @@ Field3D generate_f1(const Mesh& mesh) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           //make the gradients zero at both x-boundaries
           result(jx, jy, jz) = 0.
@@ -340,7 +340,7 @@ Field3D generate_d1(const Mesh& mesh) {
   for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
     const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
     for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = 0; jz < mesh.LocalNz; jz++) {
+      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
         const BoutReal z = BoutReal(jz) / nz;
         result(jx, jy, jz) =
             1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.);
@@ -351,7 +351,7 @@ Field3D generate_d1(const Mesh& mesh) {
     for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.);
@@ -363,7 +363,7 @@ Field3D generate_d1(const Mesh& mesh) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.);
@@ -386,7 +386,7 @@ Field3D generate_c1(const Mesh& mesh) {
   for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
     const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
     for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = 0; jz < mesh.LocalNz; jz++) {
+      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
         const BoutReal z = BoutReal(jz) / nz;
         result(jx, jy, jz) =
             1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.);
@@ -397,7 +397,7 @@ Field3D generate_c1(const Mesh& mesh) {
     for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.);
@@ -409,7 +409,7 @@ Field3D generate_c1(const Mesh& mesh) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.);
@@ -433,7 +433,7 @@ Field3D generate_a1(const Mesh& mesh) {
   for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
     const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
     for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = 0; jz < mesh.LocalNz; jz++) {
+      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
         const BoutReal z = BoutReal(jz) / nz;
         result(jx, jy, jz) =
             -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.);
@@ -444,7 +444,7 @@ Field3D generate_a1(const Mesh& mesh) {
     for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.);
@@ -456,7 +456,7 @@ Field3D generate_a1(const Mesh& mesh) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.);
@@ -479,7 +479,7 @@ Field3D generate_f5(const Mesh& mesh) {
   for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
     const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
     for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = 0; jz < mesh.LocalNz; jz++) {
+      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
         const BoutReal z = BoutReal(jz) / nz;
         //make the gradients zero at both x-boundaries
         result(jx, jy, jz) =
@@ -496,7 +496,7 @@ Field3D generate_f5(const Mesh& mesh) {
     for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           //make the gradients zero at both x-boundaries
           result(jx, jy, jz) = 0.
@@ -515,7 +515,7 @@ Field3D generate_f5(const Mesh& mesh) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           //make the gradients zero at both x-boundaries
           result(jx, jy, jz) = 0.
@@ -545,7 +545,7 @@ Field3D generate_d5(const Mesh& mesh) {
   for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
     const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
     for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = 0; jz < mesh.LocalNz; jz++) {
+      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
         const BoutReal z = BoutReal(jz) / nz;
         result(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.);
       }
@@ -555,7 +555,7 @@ Field3D generate_d5(const Mesh& mesh) {
     for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.);
         }
@@ -566,7 +566,7 @@ Field3D generate_d5(const Mesh& mesh) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.);
         }
@@ -589,7 +589,7 @@ Field3D generate_c5(const Mesh& mesh) {
   for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
     const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
     for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = 0; jz < mesh.LocalNz; jz++) {
+      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
         const BoutReal z = BoutReal(jz) / nz;
         result(jx, jy, jz) = 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.);
       }
@@ -599,7 +599,7 @@ Field3D generate_c5(const Mesh& mesh) {
     for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.);
@@ -611,7 +611,7 @@ Field3D generate_c5(const Mesh& mesh) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.);
@@ -633,7 +633,7 @@ Field3D generate_a5(const Mesh& mesh) {
   for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
     const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
     for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = 0; jz < mesh.LocalNz; jz++) {
+      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
         const BoutReal z = BoutReal(jz) / nz;
         result(jx, jy, jz) =
             -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.);
@@ -644,7 +644,7 @@ Field3D generate_a5(const Mesh& mesh) {
     for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.);
@@ -656,7 +656,7 @@ Field3D generate_a5(const Mesh& mesh) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
       const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = 0; jz < mesh.LocalNz; jz++) {
+        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
           const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
               -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.);
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx
index 7646b915a7..945d5c6443 100644
--- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx
@@ -63,7 +63,7 @@ int main(int argc, char** argv) {
     f1.allocate();
     for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
       for (int jy = 0; jy < mesh->LocalNy; jy++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
           BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
           BoutReal z = BoutReal(jz) / nz;
           f1(jx, jy, jz) =
@@ -84,7 +84,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             f1(jx, jy, jz) =
@@ -106,7 +106,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             f1(jx, jy, jz) =
@@ -131,7 +131,7 @@ int main(int argc, char** argv) {
     d1.allocate();
     for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
       for (int jy = 0; jy < mesh->LocalNy; jy++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
           BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
           BoutReal z = BoutReal(jz) / nz;
           d1(jx, jy, jz) =
@@ -143,7 +143,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             d1(jx, jy, jz) =
@@ -157,7 +157,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             d1(jx, jy, jz) =
@@ -174,7 +174,7 @@ int main(int argc, char** argv) {
     c1.allocate();
     for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
       for (int jy = 0; jy < mesh->LocalNy; jy++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
           BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
           BoutReal z = BoutReal(jz) / nz;
           c1(jx, jy, jz) = 1.
@@ -186,7 +186,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             c1(jx, jy, jz) = 1.
@@ -199,7 +199,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             c1(jx, jy, jz) = 1.
@@ -215,7 +215,7 @@ int main(int argc, char** argv) {
     a1.allocate();
     for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
       for (int jy = 0; jy < mesh->LocalNy; jy++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
           BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
           BoutReal z = BoutReal(jz) / nz;
           a1(jx, jy, jz) =
@@ -226,7 +226,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             a1(jx, jy, jz) =
@@ -238,7 +238,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             a1(jx, jy, jz) =
@@ -256,7 +256,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             b1(jx, jy, jz) = b1(jx + 1, jy, jz);
           }
         }
@@ -265,7 +265,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             b1(jx, jy, jz) = b1(jx - 1, jy, jz);
           }
         }
@@ -371,7 +371,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             b3(jx, jy, jz) = b3(jx + 1, jy, jz);
           }
         }
@@ -380,7 +380,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             b3(jx, jy, jz) = b3(jx - 1, jy, jz);
           }
         }
@@ -468,7 +468,7 @@ int main(int argc, char** argv) {
     f5.allocate();
     for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
       for (int jy = 0; jy < mesh->LocalNy; jy++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
           BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
           BoutReal z = BoutReal(jz) / nz;
           f5(jx, jy, jz) =
@@ -489,7 +489,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             f5(jx, jy, jz) =
@@ -511,7 +511,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             f5(jx, jy, jz) =
@@ -536,7 +536,7 @@ int main(int argc, char** argv) {
     d5.allocate();
     for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
       for (int jy = 0; jy < mesh->LocalNy; jy++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
           BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
           BoutReal z = BoutReal(jz) / nz;
           d5(jx, jy, jz) =
@@ -547,7 +547,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             d5(jx, jy, jz) =
@@ -559,7 +559,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             d5(jx, jy, jz) =
@@ -574,7 +574,7 @@ int main(int argc, char** argv) {
     c5.allocate();
     for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
       for (int jy = 0; jy < mesh->LocalNy; jy++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
           BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
           BoutReal z = BoutReal(jz) / nz;
           c5(jx, jy, jz) =
@@ -585,7 +585,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             c5(jx, jy, jz) =
@@ -597,7 +597,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             c5(jx, jy, jz) =
@@ -612,7 +612,7 @@ int main(int argc, char** argv) {
     a5.allocate();
     for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
       for (int jy = 0; jy < mesh->LocalNy; jy++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
           BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
           BoutReal z = BoutReal(jz) / nz;
           a5(jx, jy, jz) = -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.);
@@ -622,7 +622,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             a5(jx, jy, jz) =
@@ -634,7 +634,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             BoutReal x = BoutReal(mesh->getGlobalXIndex(jx) - mesh->xstart) / nx;
             BoutReal z = BoutReal(jz) / nz;
             a5(jx, jy, jz) =
@@ -650,7 +650,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             b5(jx, jy, jz) = b5(jx + 1, jy, jz);
           }
         }
@@ -659,7 +659,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             b5(jx, jy, jz) = b5(jx - 1, jy, jz);
           }
         }
@@ -762,7 +762,7 @@ int main(int argc, char** argv) {
     if (mesh->firstX()) {
       for (int jx = mesh->xstart - 1; jx >= 0; jx--) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             b7(jx, jy, jz) = b7(jx + 1, jy, jz);
           }
         }
@@ -771,7 +771,7 @@ int main(int argc, char** argv) {
     if (mesh->lastX()) {
       for (int jx = mesh->xend + 1; jx < mesh->LocalNx; jx++) {
         for (int jy = 0; jy < mesh->LocalNy; jy++) {
-          for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
             b7(jx, jy, jz) = b7(jx - 1, jy, jz);
           }
         }
@@ -864,7 +864,7 @@ BoutReal max_error_at_ystart(const Field3D& error) {
   BoutReal local_max_error = error(mesh->xstart, mesh->ystart, 0);
 
   for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
-    for (int jz = 0; jz < mesh->LocalNz; jz++) {
+    for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
       if (local_max_error < error(jx, mesh->ystart, jz)) {
         local_max_error = error(jx, mesh->ystart, jz);
       }

From 2dba4b436b518a2f9e32dc0fc749984b7ea01093 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 7 Jan 2026 17:22:53 +0000
Subject: [PATCH 0423/1827] Remove `BRACKET_ARAKAWA_OLD`

---
 examples/performance/bracket/bracket.cxx  | 12 ---
 include/bout/difops.hxx                   |  2 -
 manual/sphinx/user_docs/python_boutpp.rst |  2 +-
 src/mesh/difops.cxx                       | 97 -----------------------
 tests/MMS/spatial/advection/runtest       |  1 -
 tools/pylib/_boutpp_build/other_enums.hxx |  2 +-
 tools/pylib/_boutpp_build/scan_enums.py   |  2 -
 7 files changed, 2 insertions(+), 116 deletions(-)

diff --git a/examples/performance/bracket/bracket.cxx b/examples/performance/bracket/bracket.cxx
index 50012510ff..0ef9e241fb 100644
--- a/examples/performance/bracket/bracket.cxx
+++ b/examples/performance/bracket/bracket.cxx
@@ -68,9 +68,6 @@ int main(int argc, char** argv) {
     ITERATOR_TEST_BLOCK("Bracket [2D,3D] ARAKAWA",
                         result = bracket(a, c, BRACKET_ARAKAWA););
 
-    ITERATOR_TEST_BLOCK("Bracket [2D,3D] ARAKAWA_OLD",
-                        result = bracket(a, c, BRACKET_ARAKAWA_OLD););
-
     ITERATOR_TEST_BLOCK("Bracket [2D,3D] SIMPLE",
                         result = bracket(a, c, BRACKET_SIMPLE););
 
@@ -81,21 +78,12 @@ int main(int argc, char** argv) {
     ITERATOR_TEST_BLOCK("Bracket [3D,3D] ARAKAWA",
                         result = bracket(a, b, BRACKET_ARAKAWA););
 
-    ITERATOR_TEST_BLOCK("Bracket [3D,3D] ARAKAWA_OLD",
-                        result = bracket(a, b, BRACKET_ARAKAWA_OLD););
-
     ITERATOR_TEST_BLOCK("Bracket [3D,3D] SIMPLE",
                         result = bracket(a, b, BRACKET_SIMPLE););
 
     ITERATOR_TEST_BLOCK("Bracket [3D,3D] DEFAULT", result = bracket(a, b, BRACKET_STD););
   }
 
-  // Uncomment below for a "correctness" check
-  // Field3D resNew = bracket(a, b, BRACKET_ARAKAWA); mesh->communicate(resNew);
-  // Field3D resOld = bracket(a, b, BRACKET_ARAKAWA_OLD); mesh->communicate(resOld);
-  // time_output << "Max abs diff is
-  // "<<max(abs(resNew-resOld),true)/max(abs(resOld),true)<<std::endl;
-
   if (profileMode) {
     int nthreads = 0;
 #if BOUT_USE_OPENMP
diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 71053d454a..a11975d89b 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -276,13 +276,11 @@ enum class BRACKET_METHOD {
   arakawa,    ///< Arakawa method in X-Z (optimised)
   ctu,        ///< Corner Transport Upwind (CTU) method. Explicit method only, needs the
               ///  timestep from the solver
-  arakawa_old ///< Older version, for regression testing of optimised version.
 };
 constexpr BRACKET_METHOD BRACKET_STD = BRACKET_METHOD::standard;
 constexpr BRACKET_METHOD BRACKET_SIMPLE = BRACKET_METHOD::simple;
 constexpr BRACKET_METHOD BRACKET_ARAKAWA = BRACKET_METHOD::arakawa;
 constexpr BRACKET_METHOD BRACKET_CTU = BRACKET_METHOD::ctu;
-constexpr BRACKET_METHOD BRACKET_ARAKAWA_OLD = BRACKET_METHOD::arakawa_old;
 
 /*!
  * Compute advection operator terms, which can be cast as
diff --git a/manual/sphinx/user_docs/python_boutpp.rst b/manual/sphinx/user_docs/python_boutpp.rst
index 939a817ffe..e79facbf55 100644
--- a/manual/sphinx/user_docs/python_boutpp.rst
+++ b/manual/sphinx/user_docs/python_boutpp.rst
@@ -160,7 +160,7 @@ A real example - check derivative contributions:
               phi[-1,:,z]=phi_arr
       with open(path+"/equilibrium/phi_eq.dat","rb") as inf:
           phi_arr=np.fromfile(inf,dtype=np.double)
-          bm="BRACKET_ARAKAWA_OLD"
+          bm="BRACKET_ARAKAWA"
 
           for tind in range(len(times)):
               vort     = Field3D.fromCollect("vort"     ,path=path,tind=tind,info=False)
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 42fa4d6ca5..53ba6f5ad3 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -771,46 +771,6 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
 
     break;
   }
-  case BRACKET_ARAKAWA_OLD: {
-#if not(BOUT_USE_METRIC_3D)
-    const int ncz = mesh->LocalNz;
-    BOUT_OMP_PERF(parallel for)
-    for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
-      for (int jy = mesh->ystart; jy <= mesh->yend; jy++) {
-        const BoutReal partialFactor = 1.0 / (12 * metric->dz(jx, jy));
-        const BoutReal spacingFactor = partialFactor / metric->dx(jx, jy);
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
-          const int jzp = jz + 1 < ncz ? jz + 1 : 0;
-          // Above is alternative to const int jzp = (jz + 1) % ncz;
-          const int jzm = jz - 1 >= 0 ? jz - 1 : ncz - 1;
-          // Above is alternative to const int jzmTmp = (jz - 1 + ncz) % ncz;
-
-          // J++ = DDZ(f)*DDX(g) - DDX(f)*DDZ(g)
-          BoutReal Jpp =
-              ((f(jx, jy, jzp) - f(jx, jy, jzm)) * (g(jx + 1, jy) - g(jx - 1, jy))
-               - (f(jx + 1, jy, jz) - f(jx - 1, jy, jz)) * (g(jx, jy) - g(jx, jy)));
-
-          // J+x
-          BoutReal Jpx = (g(jx + 1, jy) * (f(jx + 1, jy, jzp) - f(jx + 1, jy, jzm))
-                          - g(jx - 1, jy) * (f(jx - 1, jy, jzp) - f(jx - 1, jy, jzm))
-                          - g(jx, jy) * (f(jx + 1, jy, jzp) - f(jx - 1, jy, jzp))
-                          + g(jx, jy) * (f(jx + 1, jy, jzm) - f(jx - 1, jy, jzm)));
-
-          // Jx+
-          BoutReal Jxp = (g(jx + 1, jy) * (f(jx, jy, jzp) - f(jx + 1, jy, jz))
-                          - g(jx - 1, jy) * (f(jx - 1, jy, jz) - f(jx, jy, jzm))
-                          - g(jx - 1, jy) * (f(jx, jy, jzp) - f(jx - 1, jy, jz))
-                          + g(jx + 1, jy) * (f(jx + 1, jy, jz) - f(jx, jy, jzm)));
-
-          result(jx, jy, jz) = (Jpp + Jpx + Jxp) * spacingFactor;
-        }
-      }
-    }
-#else
-    throw BoutException("BRACKET_ARAKAWA_OLD not valid with 3D metrics yet.");
-#endif
-    break;
-  }
   case BRACKET_SIMPLE: {
     // Use a subset of terms for comparison to BOUT-06
     result = VDDX(DDZ(f, outloc), g, outloc);
@@ -1090,63 +1050,6 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
     }
     break;
   }
-  case BRACKET_ARAKAWA_OLD: {
-    // Arakawa scheme for perpendicular flow
-
-    const int ncz = mesh->LocalNz;
-
-    // We need to discard const qualifier in order to manipulate
-    // storage array directly
-    Field3D f_temp = f;
-    Field3D g_temp = g;
-
-    BOUT_OMP_PERF(parallel for)
-    for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
-      for (int jy = mesh->ystart; jy <= mesh->yend; jy++) {
-#if not(BOUT_USE_METRIC_3D)
-        const BoutReal spacingFactor =
-            1.0 / (12 * metric->dz(jx, jy) * metric->dx(jx, jy));
-#endif
-        const BoutReal* Fxm = f_temp(jx - 1, jy);
-        const BoutReal* Fx = f_temp(jx, jy);
-        const BoutReal* Fxp = f_temp(jx + 1, jy);
-        const BoutReal* Gxm = g_temp(jx - 1, jy);
-        const BoutReal* Gx = g_temp(jx, jy);
-        const BoutReal* Gxp = g_temp(jx + 1, jy);
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
-#if BOUT_USE_METRIC_3D
-          const BoutReal spacingFactor =
-              1.0 / (12 * metric->dz(jx, jy, jz) * metric->dx(jx, jy, jz));
-#endif
-          const int jzp = jz + 1 < ncz ? jz + 1 : 0;
-          // Above is alternative to const int jzp = (jz + 1) % ncz;
-          const int jzm = jz - 1 >= 0 ? jz - 1 : ncz - 1;
-          // Above is alternative to const int jzm = (jz - 1 + ncz) % ncz;
-
-          // J++ = DDZ(f)*DDX(g) - DDX(f)*DDZ(g)
-          // NOLINTNEXTLINE
-          BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz])
-                          - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm]));
-
-          // J+x
-          // NOLINTNEXTLINE
-          BoutReal Jpx =
-              (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm])
-               - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm]));
-
-          // Jx+
-          // NOLINTNEXTLINE
-          BoutReal Jxp =
-              (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm])
-               - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm]));
-
-          result(jx, jy, jz) = (Jpp + Jpx + Jxp) * spacingFactor;
-        }
-      }
-    }
-
-    break;
-  }
   case BRACKET_SIMPLE: {
     // Use a subset of terms for comparison to BOUT-06
     result = VDDX(DDZ(f, outloc), g, outloc) + VDDZ(-DDX(f, outloc), g, outloc);
diff --git a/tests/MMS/spatial/advection/runtest b/tests/MMS/spatial/advection/runtest
index 9114664b47..fa06c478ee 100755
--- a/tests/MMS/spatial/advection/runtest
+++ b/tests/MMS/spatial/advection/runtest
@@ -43,7 +43,6 @@ build_and_log("MMS steady-state advection test")
 # List of options to be passed for each test
 options = [
     ("method=2", "Arakawa", "-^", 2),
-    ("method=4", "Arakawa-old", "-.", 2),
     (
         "method=1 mesh:ddx:upwind=u1 mesh:ddz:upwind=u1",
         "SIMPLE: 1st order upwind",
diff --git a/tools/pylib/_boutpp_build/other_enums.hxx b/tools/pylib/_boutpp_build/other_enums.hxx
index 30480a1007..a1da5ded7e 100644
--- a/tools/pylib/_boutpp_build/other_enums.hxx
+++ b/tools/pylib/_boutpp_build/other_enums.hxx
@@ -1,4 +1,4 @@
 #ifdef YOU_SHOULDNT_READ_THIS
 #error YOU_SHOULDNT_BE_HERE
-enum class BRACKET_METHOD { standard, simple, arakawa, ctu, arakawa_old };
+enum class BRACKET_METHOD { standard, simple, arakawa, ctu };
 #endif
diff --git a/tools/pylib/_boutpp_build/scan_enums.py b/tools/pylib/_boutpp_build/scan_enums.py
index 837380c828..a403a92625 100644
--- a/tools/pylib/_boutpp_build/scan_enums.py
+++ b/tools/pylib/_boutpp_build/scan_enums.py
@@ -78,8 +78,6 @@ def __str__(self):
     "ARAKAWA": "arakawa",
     "BRACKET_CTU": "ctu",
     "CTU": "ctu",
-    "BRACKET_ARAKAWA_OLD": "arakawa_old",
-    "ARAKAWA_OLD": "arakawa_old",
 }
 enums["CELL_LOC"].extra = {
     "CELL_DEFAULT": "deflt",

From f9c066a59e71dbc63e439bd0ecb4b86536921032 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Wed, 7 Jan 2026 17:30:04 +0000
Subject: [PATCH 0424/1827] Apply clang-format changes

---
 include/bout/difops.hxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index a11975d89b..169403a945 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -271,11 +271,11 @@ Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A,
  * Poisson bracket methods
  */
 enum class BRACKET_METHOD {
-  standard,   ///< Use b0xGrad_dot_Grad
-  simple,     ///< Keep only terms in X-Z
-  arakawa,    ///< Arakawa method in X-Z (optimised)
-  ctu,        ///< Corner Transport Upwind (CTU) method. Explicit method only, needs the
-              ///  timestep from the solver
+  standard, ///< Use b0xGrad_dot_Grad
+  simple,   ///< Keep only terms in X-Z
+  arakawa,  ///< Arakawa method in X-Z (optimised)
+  ctu,      ///< Corner Transport Upwind (CTU) method. Explicit method only, needs the
+            ///  timestep from the solver
 };
 constexpr BRACKET_METHOD BRACKET_STD = BRACKET_METHOD::standard;
 constexpr BRACKET_METHOD BRACKET_SIMPLE = BRACKET_METHOD::simple;

From 0b48cc8852b88e7aeacee03ef57d5ef494f75b4d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 8 Jan 2026 09:54:34 +0000
Subject: [PATCH 0425/1827] Fix outdated comment on `arakawa` enum

Co-authored-by: David Bold <dschwoerer@users.noreply.github.com>
---
 include/bout/difops.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 169403a945..8b502002f2 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -273,7 +273,7 @@ Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A,
 enum class BRACKET_METHOD {
   standard, ///< Use b0xGrad_dot_Grad
   simple,   ///< Keep only terms in X-Z
-  arakawa,  ///< Arakawa method in X-Z (optimised)
+  arakawa,  ///< Arakawa method in X-Z
   ctu,      ///< Corner Transport Upwind (CTU) method. Explicit method only, needs the
             ///  timestep from the solver
 };

From 4ac87c13a12b4fda73c9b5bcf6a5606138656fe0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 8 Jan 2026 15:17:57 +0000
Subject: [PATCH 0426/1827] docs: Expand on using `cpptrace` and the backtrace

---
 manual/sphinx/developer_docs/debugging.rst | 125 +++++++++++----------
 manual/sphinx/user_docs/installing.rst     |  13 ++-
 2 files changed, 74 insertions(+), 64 deletions(-)

diff --git a/manual/sphinx/developer_docs/debugging.rst b/manual/sphinx/developer_docs/debugging.rst
index 4e8bd0feab..f16d0b6a3b 100644
--- a/manual/sphinx/developer_docs/debugging.rst
+++ b/manual/sphinx/developer_docs/debugging.rst
@@ -34,10 +34,74 @@ To enable the ``output_debug`` messages, configure BOUT++ with a
 configure BOUT++ with ``-DENABLE_OUTPUT_DEBUG``. When running BOUT++
 add a ``-v -v`` flag to see ``output_debug`` messages.
 
+Backtrace
+=========
+
+BOUT++ can also automatically print a backtrace in the event of a crash. This is
+very useful to include if you ever need to report a bug to the developers! The
+output looks something like this:
+
+.. code:: text
+
+    ...
+    Error encountered: Stack trace (most recent call first):
+    #0 (filtered)
+    #1 (filtered)
+    #2 (filtered)
+    #3 in BoutMesh::createCommunicators()
+       at BOUT-dev/src/mesh/impls/bout/boutmesh.cxx:709:64
+         707:       }
+         708:       // Unconditional exception for demo purposes
+       > 709:       throw BoutException("Single null outer SOL not correct\n");
+                                                                             ^
+         710:       MPI_Group_free(&group);
+         711:     }
+    #4 in BoutMesh::load()
+       at BOUT-dev/src/mesh/impls/bout/boutmesh.cxx:575:22
+         573:   /// Communicator
+         574:
+       > 575:   createCommunicators();
+                                   ^
+         576:   output_debug << "Got communicators" << endl;
+    #5 in BoutInitialise(int&, char**&)
+       at BOUT-dev/src/bout++.cxx:201:28
+         199:   bout::globals::mesh = Mesh::create();
+         200:   // Load from sources. Required for Field initialisation
+       > 201:   bout::globals::mesh->load();
+                                         ^
+         202:
+         203:   // time_report options are used in BoutFinalise, i.e. after we
+    #6 in main
+       at BOUT-dev/examples/elm-pb/elm_pb.cxx:2161:1
+        2159: };
+        2160:
+      > 2161: BOUTMAIN(ELMpb);
+              ^
+    #7 (filtered)
+    #8 (filtered)
+    #9 (filtered)
+
+    ====== Exception thrown ======
+    Single null outer SOL not correct
+
+
+Debug symbols are required to get the filename/line number and code snippets. If
+they are missing in either BOUT++ or the physics model, only the function name
+and signature will be included for that part.
+
+Including debug symbols is a configure time ``CMake`` option, set either:
+``-DCMAKE_BUILD_TYPE=Debug`` or ``-DCMAKE_BUILD_TYPE=RelWithDebInfo`` (the
+default).
+
+The formatting of this backtrace is controlled in
+`BoutException::getBacktrace()` using the `cpptrace
+<https://github.com/jeremy-rifkin/cpptrace>`_ library.
+
+
 Message Stack
 =============
 
-The second utility BOUT++ has to help debugging is the message stack using the
+Another utility BOUT++ has to help debugging is the message stack using the
 `TRACE` macro. This is very useful for when a bug only occurs after a long time
 of running, and/or only occasionally. The ``TRACE`` macro can simply be dropped
 in anywhere in the code::
@@ -94,62 +158,3 @@ If you need to capture runtime information in the message, you can use
 the ``fmt`` syntax also used by the loggers::
 
     TRACE("Value of i={}, some arbitrary {}", i, "string");
-
-Backtrace
-=========
-
-Lastly, BOUT++ can also automatically print a backtrace in the event of a
-crash. This is very useful to include if you ever need to report a bug to the
-developers! The output looks something like this:
-
-.. code:: text
-
-    ...
-    Error encountered: Stack trace (most recent call first):
-    #0 (filtered)
-    #1 (filtered)
-    #2 (filtered)
-    #3 in BoutMesh::createCommunicators()
-       at BOUT-dev/src/mesh/impls/bout/boutmesh.cxx:709:64
-         707:       }
-         708:       // Unconditional exception for demo purposes
-       > 709:       throw BoutException("Single null outer SOL not correct\n");
-                                                                             ^
-         710:       MPI_Group_free(&group);
-         711:     }
-    #4 in BoutMesh::load()
-       at BOUT-dev/src/mesh/impls/bout/boutmesh.cxx:575:22
-         573:   /// Communicator
-         574:
-       > 575:   createCommunicators();
-                                   ^
-         576:   output_debug << "Got communicators" << endl;
-    #5 in BoutInitialise(int&, char**&)
-       at BOUT-dev/src/bout++.cxx:201:28
-         199:   bout::globals::mesh = Mesh::create();
-         200:   // Load from sources. Required for Field initialisation
-       > 201:   bout::globals::mesh->load();
-                                         ^
-         202:
-         203:   // time_report options are used in BoutFinalise, i.e. after we
-    #6 in main
-       at BOUT-dev/examples/elm-pb/elm_pb.cxx:2161:1
-        2159: };
-        2160:
-      > 2161: BOUTMAIN(ELMpb);
-              ^
-    #7 (filtered)
-    #8 (filtered)
-    #9 (filtered)
-
-    ====== Exception thrown ======
-    Single null outer SOL not correct
-
-
-Debug symbols are required to get the filename/line number and code snippets. If
-they are missing in either BOUT++ or the physics model, only the function name
-and signature will be included for that part.
-
-Including debug symbols is a configure time ``CMake`` option, set either:
-``-DCMAKE_BUILD_TYPE=Debug`` or ``-DCMAKE_BUILD_TYPE=RelWithDebInfo`` (the
-default).
diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst
index 10f5d9b9f1..2c4b8e847d 100644
--- a/manual/sphinx/user_docs/installing.rst
+++ b/manual/sphinx/user_docs/installing.rst
@@ -332,10 +332,13 @@ The default build configuration options try to be sensible for new
 users and developers, but there are a few you probably want to set
 manually for production runs or for debugging:
 
-* ``CMAKE_BUILD_TYPE``: The default is ``RelWithDebInfo``, which
-  builds an optimised executable with debug symbols included. Change
-  this to ``Release`` to remove the debug symbols, or ``Debug`` for an
-  unoptimised build, but better debug experience
+* ``CMAKE_BUILD_TYPE``: The default is ``RelWithDebInfo``, which builds an
+  optimised executable with debug symbols included. This is generally the most
+  useful, except for developers, who may wish to use ``Debug`` for an
+  unoptimised build, but better debug experience. There are a couple of other
+  choices (``Release`` and ``MinSizeRel``) which also produce optimised
+  executables, but without debug symbols, which is only really useful for
+  producing smaller binaries.
 
 * ``CHECK``: This sets the level of internal runtime checking done in
   the BOUT++ library, and ranges from 0 to 4 (inclusive). By default,
@@ -377,6 +380,8 @@ For ADIOS2, use ``-DBOUT_DOWNLOAD_ADIOS2=ON``. This will download and
 configure `ADIOS2 <https://adios2.readthedocs.io/>`_, enabling BOUT++
 to read and write this high-performance parallel file format.
 
+For cpptrace, use ``-DBOUT_DOWNLOAD_CPPTRACE=on`` (the default).
+
 Bundled Dependencies
 ~~~~~~~~~~~~~~~~~~~~
 

From 73e585768078fb32364d8801c30c36e46f6807f8 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Thu, 8 Jan 2026 15:18:45 +0000
Subject: [PATCH 0427/1827] Apply clang-format changes

---
 src/sys/boutexception.cxx                      | 3 +--
 tests/integrated/test-backtrace/boutexcept.cxx | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index 02b6ef3391..b5ea01d231 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -72,8 +72,7 @@ std::string BoutException::getBacktrace() const {
                   formatter.format(generate_trace()), message);
 
   if (msg_stack.size() > 0) {
-    return fmt::format("{}\n\n{}", backtrace_message,
-                       msg_stack.getDump());
+    return fmt::format("{}\n\n{}", backtrace_message, msg_stack.getDump());
   }
   return backtrace_message;
 }
diff --git a/tests/integrated/test-backtrace/boutexcept.cxx b/tests/integrated/test-backtrace/boutexcept.cxx
index 6017ecd8f9..6ebe2d05c4 100644
--- a/tests/integrated/test-backtrace/boutexcept.cxx
+++ b/tests/integrated/test-backtrace/boutexcept.cxx
@@ -4,7 +4,7 @@ namespace {
 void troublemaker() { throw BoutException("test"); }
 void f() { troublemaker(); }
 void e() { f(); }
-}
+} // namespace
 
 int main() {
   e();

From 8edb351b1f75382ae014f770676c239ee92e74be Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 8 Jan 2026 16:01:24 +0000
Subject: [PATCH 0428/1827] tests: Fix exception test inlining functions

---
 tests/integrated/test-backtrace/boutexcept.cxx | 6 ++++--
 tests/integrated/test-backtrace/runtest        | 4 ++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/tests/integrated/test-backtrace/boutexcept.cxx b/tests/integrated/test-backtrace/boutexcept.cxx
index 6ebe2d05c4..3019c690a9 100644
--- a/tests/integrated/test-backtrace/boutexcept.cxx
+++ b/tests/integrated/test-backtrace/boutexcept.cxx
@@ -1,10 +1,12 @@
 #include "bout/boutexception.hxx"
 
-namespace {
+// Can't use anonymous namespace, or the compiler will inline everything,
+// defeating the point of this test.
+// NOLINTBEGIN(misc-use-internal-linkage)
 void troublemaker() { throw BoutException("test"); }
 void f() { troublemaker(); }
 void e() { f(); }
-} // namespace
+// NOLINTEND(misc-use-internal-linkage)
 
 int main() {
   e();
diff --git a/tests/integrated/test-backtrace/runtest b/tests/integrated/test-backtrace/runtest
index 4010873b56..06497ec65a 100755
--- a/tests/integrated/test-backtrace/runtest
+++ b/tests/integrated/test-backtrace/runtest
@@ -21,13 +21,13 @@ _, output = shell("BOUT_SHOW_BACKTRACE=0 ./boutexcept", pipe=True)
 
 if "troublemaker" in output:
     success = False
-    print("Fail: detected offending function name in output when not expected")
+    print(f"Fail: detected offending function name in output when not expected:\n{output}")
 
 _, output = shell("./boutexcept", pipe=True)
 
 if "troublemaker" not in output:
     success = False
-    print("Fail: did not detect offending function name in output when expected")
+    print(f"Fail: did not detect offending function name in output when expected:\n{output}")
 
 if success:
     print("=> All BoutException backtrace tests passed")

From 6b03b6c1c214f476cf2280ddcfe69a336b324df4 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Thu, 8 Jan 2026 16:02:30 +0000
Subject: [PATCH 0429/1827] Apply black changes

---
 tests/integrated/test-backtrace/runtest | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-backtrace/runtest b/tests/integrated/test-backtrace/runtest
index 06497ec65a..c4020e6d99 100755
--- a/tests/integrated/test-backtrace/runtest
+++ b/tests/integrated/test-backtrace/runtest
@@ -21,13 +21,17 @@ _, output = shell("BOUT_SHOW_BACKTRACE=0 ./boutexcept", pipe=True)
 
 if "troublemaker" in output:
     success = False
-    print(f"Fail: detected offending function name in output when not expected:\n{output}")
+    print(
+        f"Fail: detected offending function name in output when not expected:\n{output}"
+    )
 
 _, output = shell("./boutexcept", pipe=True)
 
 if "troublemaker" not in output:
     success = False
-    print(f"Fail: did not detect offending function name in output when expected:\n{output}")
+    print(
+        f"Fail: did not detect offending function name in output when expected:\n{output}"
+    )
 
 if success:
     print("=> All BoutException backtrace tests passed")

From 86e3c1c576a2bd3cd7a513db976fbffce7de7e3a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 8 Jan 2026 16:24:17 +0000
Subject: [PATCH 0430/1827] docs: Fix typo in use of `OptionsIO`

Closes #3227
---
 manual/sphinx/user_docs/bout_options.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst
index 85a8a17d59..926c201c16 100644
--- a/manual/sphinx/user_docs/bout_options.rst
+++ b/manual/sphinx/user_docs/bout_options.rst
@@ -950,7 +950,7 @@ automatically set the ``"time_dimension"`` attribute::
   data["field"] = Field3D(3.0);
   
   // Append data to file
-  bout::OptionsIO({{"file", "time.nc"}, {"append", true}})->write(data);
+  bout::OptionsIO::create({{"file", "time.nc"}, {"append", true}})->write(data);
 
 .. note:: By default, `bout::OptionsIO::write` will only write variables
           with a ``"time_dimension"`` of ``"t"``. You can write

From 9855b5f21cb8e4b19d5c430033e57d0aa239bbe8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 9 Jan 2026 13:50:02 +0000
Subject: [PATCH 0431/1827] Add `cpptrace` as git submodule

---
 .gitmodules                            |  3 ++
 cmake/SetupBOUTThirdParty.cmake        | 28 +++++++++++--------
 externalpackages/cpptrace              |  1 +
 manual/sphinx/user_docs/installing.rst | 38 ++++++++++++++++++--------
 4 files changed, 47 insertions(+), 23 deletions(-)
 create mode 160000 externalpackages/cpptrace

diff --git a/.gitmodules b/.gitmodules
index 4b33b3b615..2bdbd2a57b 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -13,3 +13,6 @@
 [submodule "externalpackages/boutdata"]
 	path = externalpackages/boutdata
 	url = https://github.com/boutproject/boutdata.git
+[submodule "externalpackages/cpptrace"]
+	path = externalpackages/cpptrace
+	url = https://github.com/ZedThree/cpptrace.git
diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 2c5b9a1cfb..52b7468012 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -370,18 +370,24 @@ endif()
 message(STATUS "UUID_SYSTEM_GENERATOR: ${BOUT_USE_UUID_SYSTEM_GENERATOR}")
 set(BOUT_HAS_UUID_SYSTEM_GENERATOR ${BOUT_USE_UUID_SYSTEM_GENERATOR})
 
-option(BOUT_DOWNLOAD_CPPTRACE "Download cpptrace for backtrace support" ON)
-if (BOUT_DOWNLOAD_CPPTRACE)
-  include(FetchContent)
+cmake_dependent_option(BOUT_USE_SYSTEM_CPPTRACE "Use external installation of cpptrace" OFF
+  "BOUT_UPDATE_GIT_SUBMODULE OR EXISTS ${PROJECT_SOURCE_DIR}/externalpackages/cpptrace/CMakeLists.txt" ON)
+
+if(BOUT_USE_SYSTEM_CPPTRACE)
+  message(STATUS "Using external cpptrace")
+  find_package(cpptrace REQUIRED)
+  get_target_property(CPPTRACE_INCLUDE_PATH cpptrace::cpptrace INTERFACE_INCLUDE_DIRECTORIES)
+else()
+  message(STATUS "Using cpptrace submodule")
+  bout_update_submodules()
+  # Need a fork with some fixes for CMake
   set(CPPTRACE_LIBDWARF_REPO "https://github.com/ZedThree/libdwarf-lite.git" CACHE STRING "" FORCE)
   set(CPPTRACE_LIBDWARF_TAG "ebe10a39afd56b8247de633bfe17666ad50ab95e" CACHE STRING "" FORCE)
-  FetchContent_Declare(
-    cpptrace
-    GIT_REPOSITORY https://github.com/ZedThree/cpptrace.git
-    GIT_TAG        "027f9aee2d34dbe1c98f26224e1fbe1654cb4aae"
-  )
-  FetchContent_MakeAvailable(cpptrace)
-else()
-  find_package(cpptrace REQUIRED)
+  add_subdirectory(externalpackages/cpptrace)
+  if(NOT TARGET cpptrace::cpptrace)
+    message(FATAL_ERROR "cpptrace not found! Have you disabled the git submodules (BOUT_UPDATE_GIT_SUBMODULE)?")
+  endif()
+  set(CPPTRACE_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/externalpackages/cpptrace/include")
 endif()
+set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${CPPTRACE_INCLUDE_PATH}")
 target_link_libraries(bout++ PUBLIC cpptrace::cpptrace)
diff --git a/externalpackages/cpptrace b/externalpackages/cpptrace
new file mode 160000
index 0000000000..027f9aee2d
--- /dev/null
+++ b/externalpackages/cpptrace
@@ -0,0 +1 @@
+Subproject commit 027f9aee2d34dbe1c98f26224e1fbe1654cb4aae
diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst
index 2c4b8e847d..a493f932c4 100644
--- a/manual/sphinx/user_docs/installing.rst
+++ b/manual/sphinx/user_docs/installing.rst
@@ -380,21 +380,35 @@ For ADIOS2, use ``-DBOUT_DOWNLOAD_ADIOS2=ON``. This will download and
 configure `ADIOS2 <https://adios2.readthedocs.io/>`_, enabling BOUT++
 to read and write this high-performance parallel file format.
 
-For cpptrace, use ``-DBOUT_DOWNLOAD_CPPTRACE=on`` (the default).
-
 Bundled Dependencies
 ~~~~~~~~~~~~~~~~~~~~
 
-BOUT++ bundles some dependencies, currently `mpark.variant
-<https://github.com/mpark/variant>`_, `fmt <https://fmt.dev>`_ and
-`googletest <https://github.com/google/googletest>`_. If you wish to
-use an existing installation of ``mpark.variant``, you can set
-``-DBOUT_USE_SYSTEM_MPARK_VARIANT=ON``, and supply the installation
-path using ``mpark_variant_ROOT`` via the command line or environment
-variable if it is installed in a non standard loction. Similarly for
-``fmt``, using ``-DBOUT_USE_SYSTEM_FMT=ON`` and ``fmt_ROOT``
-respectively. To turn off both, you can set
-``-DBOUT_USE_GIT_SUBMODULE=OFF``.
+BOUT++ bundles some dependencies, currently:
+
+- `mpark.variant <https://github.com/mpark/variant>`_
+- `fmt <https://fmt.dev>`_
+- `cpptrace <https://github.com/jeremy-rifkin/cpptrace>`_
+- ``googletest <https://github.com/google/googletest>`_ (for unit tests)
+
+Aside from ``googletest``, the others are required dependencies and can either
+be built as part of the BOUT++ build, or provided externally. If you wish to use
+existing installations of some of these, set the following flags:
+
++--------------------+-----------------------------------+------------------------+
+| Name               | Flag for external installation    | Library path           |
++====================+===================================+========================+
+| ``mpark.variant``  | ``BOUT_USE_SYSTEM_MPARK_VARIANT`` | ``mpark_variant_ROOT`` |
++--------------------+-----------------------------------+------------------------+
+| ``fmt``            | ``BOUT_USE_SYSTEM_FMT``           | ``fmt_ROOT``           |
++--------------------+-----------------------------------+------------------------+
+| ``cpptrace``       | ``BOUT_USE_SYSTEM_CPPTRACE``      | ``cpptrace_ROOT``      |
++--------------------+-----------------------------------+------------------------+
+
+You can also set ``-DBOUT_USE_GIT_SUBMODULE=OFF`` to not use any of the bundled
+versions.
+
+If the libraries are in non-standard locations, you may also need to supply the
+relevant library path flags.
 
 The recommended way to use ``googletest`` is to compile it at the same
 time as your project, therefore there is no option to use an external

From 7fa1c5f3ff790f4a641c0f54d443d924e93ae48f Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 9 Jan 2026 17:12:06 +0000
Subject: [PATCH 0432/1827] boutpp: Add `cpptrace` to sdist

---
 tools/pylib/_boutpp_build/backend.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 31a4694d10..6455c203ad 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -176,7 +176,7 @@ def build_sdist(sdist_directory, config_settings=None):
     print(config_settings, sdist_directory)
     enable_gz = True
     enable_xz = False
-    external = {"fmt", "mpark.variant"}
+    external = {"fmt", "mpark.variant", "cpptrace"}
     if config_settings is not None:
         global useLocalVersion, pkgname
         for k, v in config_settings.items():

From 68904f93c08637dd2394f93bcfb42d62c2bc3848 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 9 Jan 2026 17:12:26 +0000
Subject: [PATCH 0433/1827] docs: Init all submodules

---
 manual/sphinx/conf.py | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 6b997ec111..5c6b7ef1d5 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -76,11 +76,7 @@ def __getattr__(cls, name):
     pydir = "/".join(python.split("/")[:-2])
     os.system("which clang-format")
     os.system("which clang-format-6.0")
-    os.system(
-        "git submodule update --init --recursive ../../externalpackages/mpark.variant"
-    )
-    pwd = "/".join(os.getcwd().split("/")[:-2])
-    os.system("git submodule update --init --recursive ../../externalpackages/fmt")
+    subprocess.run("git submodule update --init --recursive", shell=True)
     cmake = (
         "cmake  . "
         " -B build"
@@ -91,8 +87,6 @@ def __getattr__(cls, name):
         " -DBOUT_TESTS=OFF"
         " -DBOUT_ALLOW_INSOURCE_BUILD=ON"
         f" -DPython3_ROOT_DIR={pydir}"
-        f" -Dmpark_variant_DIR={pwd}/externalpackages/mpark.variant/"
-        f" -Dfmt_DIR={pwd}/externalpackages/fmt/"
     )
     subprocess.run(f"echo {cmake}", shell=True)
     subprocess.run(f"cd ../../; {cmake}", shell=True, check=True)

From 4a09719018050984656ed31309a3910b7ca73ca8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 9 Jan 2026 17:31:07 +0000
Subject: [PATCH 0434/1827] cmake: Update cpptrace include dir for install

---
 CMakeLists.txt | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7864705519..a5ca6e8717 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -818,6 +818,9 @@ endif()
 if (NOT BOUT_USE_SYSTEM_FMT)
   set(FMT_INCLUDE_PATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
 endif()
+if (NOT BOUT_USE_SYSTEM_CPPTRACE)
+  set(CPPTRACE_INCLUDE_PATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
+endif()
 set(BOUT_INCLUDE_PATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
 # We don't need the build include path any more
 string(REPLACE "-I${CMAKE_CURRENT_BINARY_DIR}/include" "" CONFIG_CFLAGS "${CONFIG_CFLAGS}")

From 5374e241a50e569964e9869006ffe9981f2c39e4 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 13 Jan 2026 00:12:37 +0000
Subject: [PATCH 0435/1827] Bump externalpackages/boutdata from `7164a89` to
 `962d5a5`

Bumps [externalpackages/boutdata](https://github.com/boutproject/boutdata) from `7164a89` to `962d5a5`.
- [Release notes](https://github.com/boutproject/boutdata/releases)
- [Commits](https://github.com/boutproject/boutdata/compare/7164a89c16dba1049d42e1715506b988c0af5926...962d5a58b8e6133a2977c3e44f1d4751a11d2b1c)

---
updated-dependencies:
- dependency-name: externalpackages/boutdata
  dependency-version: 962d5a58b8e6133a2977c3e44f1d4751a11d2b1c
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/boutdata | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/boutdata b/externalpackages/boutdata
index 7164a89c16..962d5a58b8 160000
--- a/externalpackages/boutdata
+++ b/externalpackages/boutdata
@@ -1 +1 @@
-Subproject commit 7164a89c16dba1049d42e1715506b988c0af5926
+Subproject commit 962d5a58b8e6133a2977c3e44f1d4751a11d2b1c

From 74acd738baae630c9ce05b425cbf1862965db072 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 15 Jan 2026 15:54:46 -0800
Subject: [PATCH 0436/1827] snes and petsc solvers: MPI_Abort on exceptions

Catch exceptions and call MPI_Abort rather than trying to continue.

There is no way to recover and synchronise processors unless all
processors threw an exception at the same point. If only one processor
throws an exception then the others will wait indefinitely on the
next MPI communication or collective operation.
---
 include/bout/boutcomm.hxx        |  6 ++++--
 src/solver/impls/petsc/petsc.cxx | 12 +++++-------
 src/solver/impls/snes/snes.cxx   | 12 ++++++++++--
 src/sys/boutcomm.cxx             |  4 ++++
 4 files changed, 23 insertions(+), 11 deletions(-)

diff --git a/include/bout/boutcomm.hxx b/include/bout/boutcomm.hxx
index 68c7559fee..29bff53087 100644
--- a/include/bout/boutcomm.hxx
+++ b/include/bout/boutcomm.hxx
@@ -4,9 +4,9 @@
 * 
 *
 **************************************************************************
-* Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+* Copyright 2010 - 2026 BOUT++ contributors
 *
-* Contact: Ben Dudson, bd512@york.ac.uk
+* Contact: Ben Dudson, dudson2@llnl.gov
 * 
 * This file is part of BOUT++.
 *
@@ -49,6 +49,8 @@ public:
   static int rank(); ///< Rank: my processor number
   static int size(); ///< Size: number of processors
 
+  static void abort(int errorcode); ///< MPI abort
+
   // Setting options
   void setComm(MPI_Comm c);
 
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 81f1cc7951..834a60ba19 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -2,7 +2,7 @@
  * Interface to PETSc solver
  *
  **************************************************************************
- * Copyright 2010 - 2025 BOUT++ contributors
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -942,12 +942,10 @@ PetscErrorCode PetscSolver::rhs(BoutReal t, Vec udata, Vec dudata, bool linear)
   } catch (BoutException& e) {
     // Simulation might fail, e.g. negative densities
     // if timestep too large
-    output_warn.write("WARNING: BoutException thrown: {}\n", e.what());
-
-    // Tell SNES that the input was out of domain
-    SNESSetFunctionDomainError(snes);
-    // Note: Returning non-zero error here leaves vectors in locked state
-    return 0;
+    output_error.write("BoutException thrown: {}\n", e.what());
+    // There is no way to recover and synchronise MPI ranks
+    // unless they all threw an exception at the same point.
+    BoutComm::abort(1);
   }
 
   // Save derivatives to PETSc
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 446903dd4f..564ff6f33b 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -1108,7 +1108,10 @@ int SNESSolver::run() {
           run_rhs(simtime);
         } catch (BoutException& e) {
           output_error.write("ERROR: BoutException thrown: {}\n", e.what());
-          return 1;
+          // Abort simulation. There is no way to recover and
+          // synchronise unless all processors throw exceptions
+          // together
+          BoutComm::abort(1);
         }
 
         // Copy derivatives back
@@ -1262,6 +1265,9 @@ int SNESSolver::run() {
       run_rhs(target); // Run RHS to calculate auxilliary variables
     } catch (BoutException& e) {
       output_error.write("ERROR: BoutException thrown: {}\n", e.what());
+      // Abort simulation. There is no way to recover unless
+      // all processors throw an exception at the same point.
+      BoutComm::abort(1);
     }
 
     if (call_monitors(target, s, getNumberOutputSteps()) != 0) {
@@ -1538,7 +1544,9 @@ PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
     // Simulation might fail, e.g. negative densities
     // if timestep too large
     output_warn.write("WARNING: BoutException thrown: {}\n", e.what());
-    return 2;
+    // Abort simulation. Unless all processors threw an exception
+    // at the same point, there is no way to synchronise again.
+    BoutComm::abort(2);
   }
 
   // Copy derivatives back
diff --git a/src/sys/boutcomm.cxx b/src/sys/boutcomm.cxx
index 2d78a24076..d85a64501e 100644
--- a/src/sys/boutcomm.cxx
+++ b/src/sys/boutcomm.cxx
@@ -58,6 +58,10 @@ int BoutComm::size() {
   return NPES;
 }
 
+void BoutComm::abort(int errorcode) {
+  MPI_Abort(get(), errorcode);
+}
+
 BoutComm* BoutComm::getInstance() {
   if (instance == nullptr) {
     // Create the singleton object

From 5f0645294ca49db6a934871103e0586de00c3fdf Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Fri, 16 Jan 2026 00:01:54 +0000
Subject: [PATCH 0437/1827] Apply clang-format changes

---
 src/sys/boutcomm.cxx | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/sys/boutcomm.cxx b/src/sys/boutcomm.cxx
index d85a64501e..358f2346f9 100644
--- a/src/sys/boutcomm.cxx
+++ b/src/sys/boutcomm.cxx
@@ -58,9 +58,7 @@ int BoutComm::size() {
   return NPES;
 }
 
-void BoutComm::abort(int errorcode) {
-  MPI_Abort(get(), errorcode);
-}
+void BoutComm::abort(int errorcode) { MPI_Abort(get(), errorcode); }
 
 BoutComm* BoutComm::getInstance() {
   if (instance == nullptr) {

From 52299eaf8a6e76a88bbe5329aae67af9b2382634 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 10:25:41 +0000
Subject: [PATCH 0438/1827] docs: Fix building `boutpp` docs on readthedocs

---
 manual/sphinx/conf.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 5c6b7ef1d5..6f2e12f349 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -78,8 +78,8 @@ def __getattr__(cls, name):
     os.system("which clang-format-6.0")
     subprocess.run("git submodule update --init --recursive", shell=True)
     cmake = (
-        "cmake  . "
-        " -B build"
+        "cmake -S ../.. "
+        " -B bout_build"
         " -DBOUT_USE_FFTW=ON"
         " -DBOUT_USE_LAPACK=OFF"
         " -DBOUT_ENABLE_PYTHON=ON"
@@ -89,8 +89,12 @@ def __getattr__(cls, name):
         f" -DPython3_ROOT_DIR={pydir}"
     )
     subprocess.run(f"echo {cmake}", shell=True)
-    subprocess.run(f"cd ../../; {cmake}", shell=True, check=True)
-    subprocess.run("cd ../.. ; cmake --build build -j 2", shell=True, check=True)
+    subprocess.run(f"{cmake}", shell=True, check=True)
+    subprocess.run("cmake --build bout_build", shell=True, check=True)
+
+    # Add the build directory to sys.path so that sphinx picks up the built
+    # Python modules
+    sys.path.append("bout_build/tools/pylib")
 
 
 # readthedocs currently runs out of memory if we actually dare to try to do this

From 60546f61ecd25c825862e08a4f18c568c56b89e4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 10:26:16 +0000
Subject: [PATCH 0439/1827] docs: Exclude CMake-built dependencies from docs

---
 manual/doxygen/Doxyfile             | 3 ++-
 manual/doxygen/Doxyfile_readthedocs | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/manual/doxygen/Doxyfile b/manual/doxygen/Doxyfile
index 82cfa5a8a4..973c5fce58 100644
--- a/manual/doxygen/Doxyfile
+++ b/manual/doxygen/Doxyfile
@@ -840,7 +840,8 @@ EXCLUDE                = ../../examples \
                          ../../manual/ \
                          ../../bin/ \
                          ../../externalpackages/googletest/ \
-                         ../../tests/
+                         ../../tests/ \
+                         ../../build/_deps/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
diff --git a/manual/doxygen/Doxyfile_readthedocs b/manual/doxygen/Doxyfile_readthedocs
index 0ddca11de0..08de92fc79 100644
--- a/manual/doxygen/Doxyfile_readthedocs
+++ b/manual/doxygen/Doxyfile_readthedocs
@@ -790,7 +790,8 @@ EXCLUDE                = ../../examples \
                          ../../manual/ \
                          ../../bin/ \
                          ../../externalpackages/googletest/ \
-                         ../../tests/
+                         ../../tests/ \
+                         ../sphinx/bout_build/_deps/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

From f9cb4d8a4c9b31ced214ed7a19d1a7fd9db948c9 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 10:26:37 +0000
Subject: [PATCH 0440/1827] docs: Use builtin path to Python to set location
 for CMake

---
 manual/sphinx/conf.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 6f2e12f349..98b0f60d06 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -72,8 +72,6 @@ def __getattr__(cls, name):
     sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
     print(os.environ)
     print(sys.argv)
-    python = sys.argv[0]
-    pydir = "/".join(python.split("/")[:-2])
     os.system("which clang-format")
     os.system("which clang-format-6.0")
     subprocess.run("git submodule update --init --recursive", shell=True)
@@ -86,7 +84,7 @@ def __getattr__(cls, name):
         " -DBOUT_UPDATE_GIT_SUBMODULE=OFF"
         " -DBOUT_TESTS=OFF"
         " -DBOUT_ALLOW_INSOURCE_BUILD=ON"
-        f" -DPython3_ROOT_DIR={pydir}"
+        f" -DPython3_ROOT_DIR={sys.exec_prefix}"
     )
     subprocess.run(f"echo {cmake}", shell=True)
     subprocess.run(f"{cmake}", shell=True, check=True)

From 3252e41690bc0b97b27feb3193220b8ca4e24638 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 10:27:36 +0000
Subject: [PATCH 0441/1827] docs: Remove outdated comment

---
 manual/sphinx/conf.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 98b0f60d06..6046173aef 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -95,7 +95,6 @@ def __getattr__(cls, name):
     sys.path.append("bout_build/tools/pylib")
 
 
-# readthedocs currently runs out of memory if we actually dare to try to do this
 if has_breathe:
     # Run doxygen to generate the XML sources
     if on_readthedocs:

From 876fe2c0e77788eae2f58082a80ba7fe42228605 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Mon, 19 Jan 2026 10:28:55 +0000
Subject: [PATCH 0442/1827] Apply black changes

---
 bin/bout-add-mod-path                         | 12 +++----
 bin/bout-pylib-cmd-to-bin                     | 31 ++++++-------------
 bin/bout-v5-factory-upgrader.py               | 21 +++----------
 bin/bout-v5-format-upgrader.py                |  1 -
 bin/bout-v5-header-upgrader.py                |  7 ++---
 bin/bout-v5-input-file-upgrader.py            |  6 ++--
 bin/bout-v5-macro-upgrader.py                 |  6 ++--
 bin/bout-v5-physics-model-upgrader.py         | 13 +++-----
 bin/bout-v5-xzinterpolation-upgrader.py       | 12 ++-----
 bin/update_version_number_in_files.py         |  6 ++--
 src/field/gen_fieldops.py                     |  1 -
 tests/MMS/GBS/runtest-slab2d                  |  1 -
 tests/MMS/GBS/runtest-slab3d                  |  1 -
 tests/MMS/advection/runtest                   |  1 -
 tests/MMS/diffusion/runtest                   |  1 -
 tests/MMS/diffusion2/Z/plot_error.py          |  1 +
 tests/MMS/diffusion2/runtest                  |  1 -
 tests/MMS/fieldalign/runtest.broken           |  1 -
 tests/MMS/hw/runtest                          |  1 -
 tests/MMS/laplace/runtest                     |  1 -
 tests/MMS/spatial/diffusion/runtest           |  1 -
 tests/MMS/wave-1d-y/runtest                   |  1 -
 tests/MMS/wave-1d/runtest                     |  1 -
 tests/integrated/test-command-args/runtest    |  1 -
 tests/integrated/test-cyclic/runtest          |  1 -
 tests/integrated/test-griddata/runtest        |  1 -
 tests/integrated/test-gyro/runtest            |  1 -
 tests/integrated/test-invpar/runtest          |  1 -
 tests/integrated/test-laplace/runtest         |  1 -
 .../integrated/test-multigrid_laplace/runtest |  1 -
 .../runtest_multiple_grids                    |  1 -
 .../test-multigrid_laplace/runtest_unsheared  |  1 -
 tests/integrated/test-naulin-laplace/runtest  |  1 -
 .../runtest_multiple_grids                    |  1 -
 .../test-naulin-laplace/runtest_unsheared     |  1 -
 tests/integrated/test-petsc_laplace/runtest   |  1 -
 .../test-petsc_laplace_MAST-grid/runtest      |  1 -
 tests/integrated/test-region-iterator/runtest |  1 -
 tests/integrated/test-restarting/runtest      |  1 -
 tests/integrated/test-smooth/runtest          |  1 -
 tests/integrated/test-squash/runtest          |  1 -
 tests/integrated/test-yupdown/runtest         |  1 -
 tools/pylib/_boutpp_build/backend.py          | 18 ++++-------
 43 files changed, 41 insertions(+), 124 deletions(-)

diff --git a/bin/bout-add-mod-path b/bin/bout-add-mod-path
index 9faf1be3de..ee7ea66d25 100755
--- a/bin/bout-add-mod-path
+++ b/bin/bout-add-mod-path
@@ -104,8 +104,7 @@ def create_mod(modulepath, name, top, build):
     else:
         prereq = ""
     with open(filename, "w") as f:
-        f.write(
-            f"""#%Module 1.0
+        f.write(f"""#%Module 1.0
 #
 #  BOUT++ module for use with 'environment-modules' package
 #  Created by bout-add-mod-path v0.9
@@ -119,17 +118,14 @@ setenv        BOUT_TOP         {top}
 prepend-path  PATH             {top}/bin
 prepend-path  PYTHONPATH       {top}/tools/pylib
 prepend-path  IDL_PATH        +{top}/tools/idllib:'<IDL_DEFAULT>'
-"""
-        )
+""")
         if build != top:
-            f.write(
-                f"""#%Module 1.0
+            f.write(f"""#%Module 1.0
 setenv        BOUT_BUILD       {build}
 prepend-path  PATH             {build}/bin
 prepend-path  LD_LIBRARY_PATH  {build}/lib
 prepend-path  PYTHONPATH       {build}/tools/pylib
-"""
-            )
+""")
     print(f"created `{filename}`")
 
 
diff --git a/bin/bout-pylib-cmd-to-bin b/bin/bout-pylib-cmd-to-bin
index 8f88a5dbf4..8d6dbed7ae 100755
--- a/bin/bout-pylib-cmd-to-bin
+++ b/bin/bout-pylib-cmd-to-bin
@@ -126,8 +126,7 @@ def createwrapper(mod, func_name, func, name):
             out += end
             f.write(out)
 
-        fprint(
-            """#!/usr/bin/env python3
+        fprint("""#!/usr/bin/env python3
 # PYTHON_ARGCOMPLETE_OK
 
 import argparse
@@ -136,8 +135,7 @@ try:
 except ImportError:
     argcomplete=None
 
-"""
-        )
+""")
         doc = True
         para = False
         ret = False
@@ -183,19 +181,16 @@ except ImportError:
                         arg_help[curarg].append(esc(blas))
         # Print functions that are needed
         if "str_to_slice" in arg_type.values():
-            fprint(
-                """
+            fprint("""
 def str_to_slice(sstr):
     args=[]
     for s in sstr.split(','):
         args.append(int(s))
     print(args)
     return slice(*args)
-"""
-            )
+""")
         if "str_to_bool" in arg_type.values():
-            fprint(
-                """
+            fprint("""
 def str_to_bool(sstr):
     low=sstr.lower()
     # no or false
@@ -206,8 +201,7 @@ def str_to_bool(sstr):
         return True
     else:
         raise ArgumentTypeError("Cannot parse %s to bool type"%sstr)
-"""
-            )
+""")
         # Create the parser
         fprint("parser = argparse.ArgumentParser(%s)" % (esc(docs)))
         spec = inspect.signature(func)
@@ -247,24 +241,19 @@ def str_to_bool(sstr):
                     pre = "\n    "
             fprint(")")
 
-        fprint(
-            """
+        fprint("""
 if argcomplete:
     argcomplete.autocomplete(parser)
 
-# late import for faster auto-complete"""
-        )
+# late import for faster auto-complete""")
         fprint("from %s import %s" % (mod, func_name))
-        fprint(
-            """
+        fprint("""
 args = parser.parse_args()
 
 # Call the function %s, using command line arguments
 %s(**args.__dict__)
 
-"""
-            % (func_name, func_name)
-        )
+""" % (func_name, func_name))
     # alternative, but I think 0o755 is easier to read
     # import stat
     # os.chmod(filename,stat.S_IRWXU|stat.S_IRGRP|stat.S_IXGRP|stat.S_IROTH|stat.S_IXOTH)
diff --git a/bin/bout-v5-factory-upgrader.py b/bin/bout-v5-factory-upgrader.py
index 29fc07db30..ee24572a94 100755
--- a/bin/bout-v5-factory-upgrader.py
+++ b/bin/bout-v5-factory-upgrader.py
@@ -5,7 +5,6 @@
 import difflib
 import re
 
-
 # Dictionary of factory methods that may need updating
 factories = {
     "Interpolation": {
@@ -62,9 +61,7 @@ def find_factory_calls(factory, source):
         \s*=\s*
         {factory_name}::
         .*{create_method}.*
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -75,9 +72,7 @@ def find_type_pointers(factory, source):
         r"""
         \b{type_name}\s*\*\s*   # Type name and pointer
         ([\w_]+)\s*;            # Variable name
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -107,9 +102,7 @@ def fix_declarations(factory, variables, source):
             (.*?)(class\s*)?         # optional "class" keyword
             \b({type_name})\s*\*\s*  # Type-pointer
             ({variable_name})\s*;    # Variable
-            """.format(
-                type_name=factory["type_name"], variable_name=variable
-            ),
+            """.format(type_name=factory["type_name"], variable_name=variable),
             r"\1std::unique_ptr<\3> \4{nullptr};",
             source,
             flags=re.VERBOSE,
@@ -123,9 +116,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment from factory
             ({factory_name}::.*{create_method}.*);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1auto \4 = \5;",
             source,
             flags=re.VERBOSE,
@@ -139,9 +130,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment
             (0|nullptr|NULL);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1std::unique_ptr<\2> \3{nullptr};",
             source,
             flags=re.VERBOSE,
diff --git a/bin/bout-v5-format-upgrader.py b/bin/bout-v5-format-upgrader.py
index 7c7d13ac7f..a534ca240a 100755
--- a/bin/bout-v5-format-upgrader.py
+++ b/bin/bout-v5-format-upgrader.py
@@ -5,7 +5,6 @@
 import difflib
 import re
 
-
 format_replacements = {
     "c": "c",
     "d": "d",
diff --git a/bin/bout-v5-header-upgrader.py b/bin/bout-v5-header-upgrader.py
index 49a8fbcbe4..77794ab920 100755
--- a/bin/bout-v5-header-upgrader.py
+++ b/bin/bout-v5-header-upgrader.py
@@ -9,7 +9,6 @@
 from typing import List
 from subprocess import run
 
-
 header_shim_sentinel = "// BOUT++ header shim"
 
 header_warning = f"""\
@@ -122,8 +121,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Fix deprecated header locations for BOUT++ v4 -> v5
 
             All BOUT++ headers are now under ``include/bout`` and
@@ -142,8 +140,7 @@ def create_patch(filename, original, modified):
             If you have staged changes, this tool will not work, so to
             avoid committing undesired or unrelated changes.
 
-            """
-        ),
+            """),
     )
 
     parser.add_argument(
diff --git a/bin/bout-v5-input-file-upgrader.py b/bin/bout-v5-input-file-upgrader.py
index e2940ff58a..ea979005d5 100755
--- a/bin/bout-v5-input-file-upgrader.py
+++ b/bin/bout-v5-input-file-upgrader.py
@@ -271,8 +271,7 @@ def possibly_apply_patch(patch, options_file, quiet=False, force=False):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Fix input files for BOUT++ v5+
 
             Please note that this will only fix input options in sections with
@@ -300,8 +299,7 @@ def possibly_apply_patch(patch, options_file, quiet=False, force=False):
 
             Files that change in this way will have the "canonicalisation" patch
             presented first. If you choose not to apply this patch, the "upgrade
-            fixer" patch will still include it."""
-        ),
+            fixer" patch will still include it."""),
     )
 
     parser.add_argument("files", action="store", nargs="+", help="Input files")
diff --git a/bin/bout-v5-macro-upgrader.py b/bin/bout-v5-macro-upgrader.py
index 11b4926255..d644fed9e8 100755
--- a/bin/bout-v5-macro-upgrader.py
+++ b/bin/bout-v5-macro-upgrader.py
@@ -342,8 +342,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Fix macro defines for BOUT++ v4 -> v5
 
             Please note that this is only slightly better than dumb text replacement. It
@@ -359,8 +358,7 @@ def create_patch(filename, original, modified):
             still replace them in strings or comments.
 
             Please check the diff output carefully!
-            """
-        ),
+            """),
     )
 
     parser.add_argument("files", action="store", nargs="+", help="Input files")
diff --git a/bin/bout-v5-physics-model-upgrader.py b/bin/bout-v5-physics-model-upgrader.py
index 26fb8ef6e0..260d1d59ee 100755
--- a/bin/bout-v5-physics-model-upgrader.py
+++ b/bin/bout-v5-physics-model-upgrader.py
@@ -8,7 +8,6 @@
 import textwrap
 import warnings
 
-
 PHYSICS_MODEL_INCLUDE = '#include "bout/physicsmodel.hxx"'
 
 PHYSICS_MODEL_SKELETON = """
@@ -213,13 +212,11 @@ def fix_bout_constrain(source, error_on_warning):
             "\n  ".join(["{}:{}".format(i, source_lines[i]) for i in line_range])
         )
 
-    message = textwrap.dedent(
-        """\
+    message = textwrap.dedent("""\
         Some uses of `bout_constrain` remain, but we could not automatically
         convert them to use `Solver::constraint`. Please fix them before
         continuing:
-        """
-    )
+        """)
     message += "  " + "\n  ".join(lines_context)
 
     if error_on_warning:
@@ -389,8 +386,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Upgrade legacy physics models to use the PhysicsModel class
 
             This will do the bare minimum required to compile, and
@@ -403,8 +399,7 @@ def create_patch(filename, original, modified):
             By default, this will use the file name stripped of file
             extensions as the name of the new class. Use '--name=<new
             name>' to give a different name.
-            """
-        ),
+            """),
     )
 
     parser.add_argument("files", action="store", nargs="+", help="Files to fix")
diff --git a/bin/bout-v5-xzinterpolation-upgrader.py b/bin/bout-v5-xzinterpolation-upgrader.py
index 37c79e0de8..e70c3c54ae 100755
--- a/bin/bout-v5-xzinterpolation-upgrader.py
+++ b/bin/bout-v5-xzinterpolation-upgrader.py
@@ -54,9 +54,7 @@ def fix_header_includes(old_header, new_header, source):
         (<|")
         ({header})              # Header name
         (>|")
-        """.format(
-            header=old_header
-        ),
+        """.format(header=old_header),
         r"\1\2{header}\4".format(header=new_header),
         source,
         flags=re.VERBOSE,
@@ -67,9 +65,7 @@ def fix_interpolations(old_interpolation, new_interpolation, source):
     return re.sub(
         r"""
         \b{}\b
-        """.format(
-            old_interpolation
-        ),
+        """.format(old_interpolation),
         r"{}".format(new_interpolation),
         source,
         flags=re.VERBOSE,
@@ -120,9 +116,7 @@ def fix_factories(old_factory, new_factory, source):
     return re.sub(
         r"""
         \b{}\b
-        """.format(
-            old_factory
-        ),
+        """.format(old_factory),
         r"{}".format(new_factory),
         source,
         flags=re.VERBOSE,
diff --git a/bin/update_version_number_in_files.py b/bin/update_version_number_in_files.py
index ec9a31bc32..3e9758a8c1 100755
--- a/bin/update_version_number_in_files.py
+++ b/bin/update_version_number_in_files.py
@@ -158,8 +158,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Update the software version number to the specified version, 
             to be given in the form major.minor.patch, 
             e.g. 5.10.3
@@ -172,8 +171,7 @@ def create_patch(filename, original, modified):
             the 'minor' version number of the provided version will be incremented by 1, 
             e.g. 5.10.3 -> 5.11.3
             
-            """
-        ),
+            """),
     )
 
     parser.add_argument(
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 29631ff7aa..3e07d6fec4 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -11,7 +11,6 @@
 
 """
 
-
 from __future__ import print_function
 
 from builtins import object
diff --git a/tests/MMS/GBS/runtest-slab2d b/tests/MMS/GBS/runtest-slab2d
index 97c7e11459..221c34e815 100755
--- a/tests/MMS/GBS/runtest-slab2d
+++ b/tests/MMS/GBS/runtest-slab2d
@@ -11,7 +11,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate
 
-
 build_and_log("MMS test")
 
 
diff --git a/tests/MMS/GBS/runtest-slab3d b/tests/MMS/GBS/runtest-slab3d
index f193583e47..45acd53af7 100755
--- a/tests/MMS/GBS/runtest-slab3d
+++ b/tests/MMS/GBS/runtest-slab3d
@@ -14,7 +14,6 @@ from numpy import sqrt, max, abs, mean, array, log, concatenate
 
 import pickle
 
-
 build_and_log("MMS test")
 
 # List of NX values to use
diff --git a/tests/MMS/advection/runtest b/tests/MMS/advection/runtest
index 1290a4c247..9a0a691287 100755
--- a/tests/MMS/advection/runtest
+++ b/tests/MMS/advection/runtest
@@ -20,7 +20,6 @@ import pickle
 
 import time
 
-
 if __name__ == "__main__":
     build_and_log("MMS advection")
 
diff --git a/tests/MMS/diffusion/runtest b/tests/MMS/diffusion/runtest
index a25b3519a6..ef6b335f70 100755
--- a/tests/MMS/diffusion/runtest
+++ b/tests/MMS/diffusion/runtest
@@ -15,7 +15,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log
 
-
 build_and_log("MMS diffusion test")
 
 # List of NX values to use
diff --git a/tests/MMS/diffusion2/Z/plot_error.py b/tests/MMS/diffusion2/Z/plot_error.py
index 5c4e1164c1..4b4b666758 100644
--- a/tests/MMS/diffusion2/Z/plot_error.py
+++ b/tests/MMS/diffusion2/Z/plot_error.py
@@ -4,6 +4,7 @@
 
 @author: yolen
 """
+
 import boutdata
 import matplotlib.pyplot as plt
 
diff --git a/tests/MMS/diffusion2/runtest b/tests/MMS/diffusion2/runtest
index 546be3b2c1..d1b8072fc8 100755
--- a/tests/MMS/diffusion2/runtest
+++ b/tests/MMS/diffusion2/runtest
@@ -20,7 +20,6 @@ from numpy import sqrt, max, abs, mean, array, log
 
 from os.path import join
 
-
 build_and_log("MMS diffusion test")
 
 # List of input directories
diff --git a/tests/MMS/fieldalign/runtest.broken b/tests/MMS/fieldalign/runtest.broken
index e09fbeccd5..bfb2023c1d 100755
--- a/tests/MMS/fieldalign/runtest.broken
+++ b/tests/MMS/fieldalign/runtest.broken
@@ -18,7 +18,6 @@ from os.path import join
 
 import time
 
-
 build_and_log("MMS test")
 
 # nxlist = [256, 128, 64, 32, 16, 8] # do in reverse order to save disk space
diff --git a/tests/MMS/hw/runtest b/tests/MMS/hw/runtest
index b6abadc3b9..62740fcbbd 100755
--- a/tests/MMS/hw/runtest
+++ b/tests/MMS/hw/runtest
@@ -15,7 +15,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate
 
-
 build_and_log("MMS test")
 
 # List of NX values to use
diff --git a/tests/MMS/laplace/runtest b/tests/MMS/laplace/runtest
index 98eb62da87..80c8bf08af 100755
--- a/tests/MMS/laplace/runtest
+++ b/tests/MMS/laplace/runtest
@@ -14,7 +14,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate
 
-
 build_and_log("MMS test")
 
 # List of NX values to use
diff --git a/tests/MMS/spatial/diffusion/runtest b/tests/MMS/spatial/diffusion/runtest
index 000cf8f09b..8d4e759d59 100755
--- a/tests/MMS/spatial/diffusion/runtest
+++ b/tests/MMS/spatial/diffusion/runtest
@@ -22,7 +22,6 @@ from os.path import join
 
 import matplotlib.pyplot as plt
 
-
 build_and_log("MMS diffusion test")
 
 # List of input directories
diff --git a/tests/MMS/wave-1d-y/runtest b/tests/MMS/wave-1d-y/runtest
index 9a4de5a3bb..332d6864b0 100755
--- a/tests/MMS/wave-1d-y/runtest
+++ b/tests/MMS/wave-1d-y/runtest
@@ -20,7 +20,6 @@ from sys import stdout
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate, pi
 
-
 build_and_log("Making MMS wave test")
 
 # List of NX values to use
diff --git a/tests/MMS/wave-1d/runtest b/tests/MMS/wave-1d/runtest
index f13fb7bd11..1adb7c7d6d 100755
--- a/tests/MMS/wave-1d/runtest
+++ b/tests/MMS/wave-1d/runtest
@@ -15,7 +15,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate
 
-
 build_and_log("Making MMS wave test")
 
 # List of NX values to use
diff --git a/tests/integrated/test-command-args/runtest b/tests/integrated/test-command-args/runtest
index 39939bb105..a8dc3f020c 100755
--- a/tests/integrated/test-command-args/runtest
+++ b/tests/integrated/test-command-args/runtest
@@ -7,7 +7,6 @@ import shutil
 import unittest
 import platform
 
-
 OUTPUT_FILE = "stdout.log" if platform.system() == "FreeBSD" else "stderr.log"
 
 
diff --git a/tests/integrated/test-cyclic/runtest b/tests/integrated/test-cyclic/runtest
index 5e31da6239..c68f9b033e 100755
--- a/tests/integrated/test-cyclic/runtest
+++ b/tests/integrated/test-cyclic/runtest
@@ -17,7 +17,6 @@ from boututils.run_wrapper import build_and_log, shell, launch
 from boutdata.collect import collect
 from sys import stdout, exit
 
-
 build_and_log("Cyclic Reduction test")
 
 flags = ["", "nsys=2", "nsys=5 periodic", "nsys=7 n=10"]
diff --git a/tests/integrated/test-griddata/runtest b/tests/integrated/test-griddata/runtest
index 1c57bf5be7..6aef955023 100755
--- a/tests/integrated/test-griddata/runtest
+++ b/tests/integrated/test-griddata/runtest
@@ -13,7 +13,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("griddata test")
 
 for nproc in [1]:
diff --git a/tests/integrated/test-gyro/runtest b/tests/integrated/test-gyro/runtest
index 52ab0de4ab..7a0209fa57 100755
--- a/tests/integrated/test-gyro/runtest
+++ b/tests/integrated/test-gyro/runtest
@@ -25,7 +25,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("Gyro-average inversion test")
 
 # Read benchmark values
diff --git a/tests/integrated/test-invpar/runtest b/tests/integrated/test-invpar/runtest
index de7f028528..53f6015fe9 100755
--- a/tests/integrated/test-invpar/runtest
+++ b/tests/integrated/test-invpar/runtest
@@ -12,7 +12,6 @@ from boututils.run_wrapper import build_and_log, shell, launch
 from boutdata.collect import collect
 from sys import stdout, exit
 
-
 build_and_log("parallel inversion test")
 
 flags_src = [
diff --git a/tests/integrated/test-laplace/runtest b/tests/integrated/test-laplace/runtest
index e54e46d0d8..d1e9c3d1c9 100755
--- a/tests/integrated/test-laplace/runtest
+++ b/tests/integrated/test-laplace/runtest
@@ -41,7 +41,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("Laplacian inversion test")
 
 # Read benchmark values
diff --git a/tests/integrated/test-multigrid_laplace/runtest b/tests/integrated/test-multigrid_laplace/runtest
index 4a7455f80b..f325185c46 100755
--- a/tests/integrated/test-multigrid_laplace/runtest
+++ b/tests/integrated/test-multigrid_laplace/runtest
@@ -22,7 +22,6 @@ from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("multigrid Laplacian inversion test")
 
 print("Running multigrid Laplacian inversion test")
diff --git a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
index 6817120b13..739d15f7d4 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
+++ b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
@@ -18,7 +18,6 @@ from boututils.run_wrapper import shell, build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("Multigrid Laplacian inversion test")
 
 print("Running multigrid Laplacian inversion test")
diff --git a/tests/integrated/test-multigrid_laplace/runtest_unsheared b/tests/integrated/test-multigrid_laplace/runtest_unsheared
index cda68f2167..d0dca3a808 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_unsheared
+++ b/tests/integrated/test-multigrid_laplace/runtest_unsheared
@@ -18,7 +18,6 @@ from boututils.run_wrapper import shell, build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("Making multigrid Laplacian inversion test")
 
 print("Running multigrid Laplacian inversion test")
diff --git a/tests/integrated/test-naulin-laplace/runtest b/tests/integrated/test-naulin-laplace/runtest
index f972eab6cc..145257c23b 100755
--- a/tests/integrated/test-naulin-laplace/runtest
+++ b/tests/integrated/test-naulin-laplace/runtest
@@ -22,7 +22,6 @@ from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("LaplaceNaulin inversion test")
 
 print("Running LaplaceNaulin inversion test")
diff --git a/tests/integrated/test-naulin-laplace/runtest_multiple_grids b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
index c0281c3a4e..f56a80677e 100755
--- a/tests/integrated/test-naulin-laplace/runtest_multiple_grids
+++ b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
@@ -18,7 +18,6 @@ from boututils.run_wrapper import shell, build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("Making LaplaceNaulin inversion test")
 
 print("Running LaplaceNaulin inversion test")
diff --git a/tests/integrated/test-naulin-laplace/runtest_unsheared b/tests/integrated/test-naulin-laplace/runtest_unsheared
index 8f47f33026..a845a9d92f 100755
--- a/tests/integrated/test-naulin-laplace/runtest_unsheared
+++ b/tests/integrated/test-naulin-laplace/runtest_unsheared
@@ -18,7 +18,6 @@ from boututils.run_wrapper import shell, build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("LaplaceNaulin inversion test")
 
 print("Running LaplaceNaulin inversion test")
diff --git a/tests/integrated/test-petsc_laplace/runtest b/tests/integrated/test-petsc_laplace/runtest
index ac248c4ce7..83e1006338 100755
--- a/tests/integrated/test-petsc_laplace/runtest
+++ b/tests/integrated/test-petsc_laplace/runtest
@@ -30,7 +30,6 @@ from boutdata.collect import collect
 # import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("PETSc Laplacian inversion test")
 
 print("Running PETSc Laplacian inversion test")
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/runtest b/tests/integrated/test-petsc_laplace_MAST-grid/runtest
index 5a4cbf875a..3be39949c3 100755
--- a/tests/integrated/test-petsc_laplace_MAST-grid/runtest
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/runtest
@@ -28,7 +28,6 @@ from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 from sys import stdout, exit
 
-
 build_and_log(
     "PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)"
 )
diff --git a/tests/integrated/test-region-iterator/runtest b/tests/integrated/test-region-iterator/runtest
index e5825285de..2277ef15e9 100755
--- a/tests/integrated/test-region-iterator/runtest
+++ b/tests/integrated/test-region-iterator/runtest
@@ -17,7 +17,6 @@ from boututils.run_wrapper import build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("Region Iterator test")
 
 flags = [""]
diff --git a/tests/integrated/test-restarting/runtest b/tests/integrated/test-restarting/runtest
index 262aa818b6..daf19ebac6 100755
--- a/tests/integrated/test-restarting/runtest
+++ b/tests/integrated/test-restarting/runtest
@@ -5,7 +5,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("restart test")
 
 # Run once for 10 timesteps
diff --git a/tests/integrated/test-smooth/runtest b/tests/integrated/test-smooth/runtest
index bd7296341a..91ae793164 100755
--- a/tests/integrated/test-smooth/runtest
+++ b/tests/integrated/test-smooth/runtest
@@ -16,7 +16,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("smoothing operator test")
 
 # Read benchmark values
diff --git a/tests/integrated/test-squash/runtest b/tests/integrated/test-squash/runtest
index 2f35e00589..8bf358ee8e 100755
--- a/tests/integrated/test-squash/runtest
+++ b/tests/integrated/test-squash/runtest
@@ -9,7 +9,6 @@ import argparse
 import re
 import os.path
 
-
 # requires: all_tests
 # requires: netcdf
 # cores: 4
diff --git a/tests/integrated/test-yupdown/runtest b/tests/integrated/test-yupdown/runtest
index 34fcd36496..13d7365b53 100755
--- a/tests/integrated/test-yupdown/runtest
+++ b/tests/integrated/test-yupdown/runtest
@@ -6,7 +6,6 @@ from sys import exit
 
 from numpy import max, abs
 
-
 build_and_log("parallel slices test")
 
 failed = False
diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 6455c203ad..9e305b3048 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -212,12 +212,10 @@ def build_sdist(sdist_directory, config_settings=None):
         run(f"rm {tmp}")
 
     with open(tmp, "w") as f:
-        f.write(
-            f"""Metadata-Version: 2.1
+        f.write(f"""Metadata-Version: 2.1
 Name: {pkgname}
 Version: {getversion()}
-"""
-        )
+""")
         with open("LICENSE") as src:
             pre = "License: "
             for l in src:
@@ -269,23 +267,19 @@ def prepare_metadata_for_build_wheel(
     distinfo = f"{metadata_directory}/{thisdir}"
     mkdir_p(distinfo)
     with open(f"{distinfo}/METADATA", "w") as f:
-        f.write(
-            f"""Metadata-Version: 2.1
+        f.write(f"""Metadata-Version: 2.1
 Name: {pkgname}
 Version: {getversion()}
 License-File: COPYING
-"""
-        )
+""")
     run(f"cp LICENSE {distinfo}/COPYING")
     run(f"cp LICENSE.GPL {distinfo}/COPYING.GPL")
     with open(f"{distinfo}/WHEEL", "w") as f:
-        f.write(
-            f"""Wheel-Version: 1.0
+        f.write(f"""Wheel-Version: 1.0
 Generator: boutpp_custom_build_wheel ({getversion()})
 Root-Is-Purelib: false
 Tag: {gettag()}
-"""
-        )
+""")
 
     if record:
         with open(f"{distinfo}/RECORD", "w") as f:

From 79d6ed0375f7d5d5cdf21f9b019503ef75e2a6f1 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 10:32:57 +0000
Subject: [PATCH 0443/1827] cmake: Bump netcdf-cxx4 `FetchContent` version

---
 cmake/SetupBOUTThirdParty.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 1256fbbeba..704b3b6a5f 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -164,8 +164,8 @@ if (BOUT_USE_NETCDF)
     include(FetchContent)
     FetchContent_Declare(
       netcdf-cxx4
-      GIT_REPOSITORY https://github.com/ZedThree/netcdf-cxx4
-      GIT_TAG        "ad3e50953190615cb69dcc8a4652f9a88a8499cf"
+      GIT_REPOSITORY https://github.com/Unidata/netcdf-cxx4
+      GIT_TAG        "a43d6d4d415d407712c246faca553bd951730dc1"
       )
     # Don't build the netcdf tests, they have lots of warnings
     set(NCXX_ENABLE_TESTS OFF CACHE BOOL "" FORCE)

From e2f03beb97e0b3adc3694c2c111f24b4d0aa2d88 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Mon, 19 Jan 2026 10:34:26 +0000
Subject: [PATCH 0444/1827] Apply black changes

---
 bin/bout-add-mod-path                         | 12 +++----
 bin/bout-pylib-cmd-to-bin                     | 31 ++++++-------------
 bin/bout-v5-factory-upgrader.py               | 21 +++----------
 bin/bout-v5-format-upgrader.py                |  1 -
 bin/bout-v5-header-upgrader.py                |  7 ++---
 bin/bout-v5-input-file-upgrader.py            |  6 ++--
 bin/bout-v5-macro-upgrader.py                 |  6 ++--
 bin/bout-v5-physics-model-upgrader.py         | 13 +++-----
 bin/bout-v5-xzinterpolation-upgrader.py       | 12 ++-----
 bin/update_version_number_in_files.py         |  6 ++--
 src/field/gen_fieldops.py                     |  1 -
 tests/MMS/GBS/runtest-slab2d                  |  1 -
 tests/MMS/GBS/runtest-slab3d                  |  1 -
 tests/MMS/advection/runtest                   |  1 -
 tests/MMS/diffusion/runtest                   |  1 -
 tests/MMS/diffusion2/Z/plot_error.py          |  1 +
 tests/MMS/diffusion2/runtest                  |  1 -
 tests/MMS/fieldalign/runtest.broken           |  1 -
 tests/MMS/hw/runtest                          |  1 -
 tests/MMS/laplace/runtest                     |  1 -
 tests/MMS/spatial/diffusion/runtest           |  1 -
 tests/MMS/wave-1d-y/runtest                   |  1 -
 tests/MMS/wave-1d/runtest                     |  1 -
 tests/integrated/test-command-args/runtest    |  1 -
 tests/integrated/test-cyclic/runtest          |  1 -
 tests/integrated/test-griddata/runtest        |  1 -
 tests/integrated/test-gyro/runtest            |  1 -
 tests/integrated/test-invpar/runtest          |  1 -
 tests/integrated/test-laplace/runtest         |  1 -
 .../integrated/test-multigrid_laplace/runtest |  1 -
 .../runtest_multiple_grids                    |  1 -
 .../test-multigrid_laplace/runtest_unsheared  |  1 -
 tests/integrated/test-naulin-laplace/runtest  |  1 -
 .../runtest_multiple_grids                    |  1 -
 .../test-naulin-laplace/runtest_unsheared     |  1 -
 tests/integrated/test-petsc_laplace/runtest   |  1 -
 .../test-petsc_laplace_MAST-grid/runtest      |  1 -
 tests/integrated/test-region-iterator/runtest |  1 -
 tests/integrated/test-restarting/runtest      |  1 -
 tests/integrated/test-smooth/runtest          |  1 -
 tests/integrated/test-squash/runtest          |  1 -
 tests/integrated/test-yupdown/runtest         |  1 -
 tools/pylib/_boutpp_build/backend.py          | 18 ++++-------
 43 files changed, 41 insertions(+), 124 deletions(-)

diff --git a/bin/bout-add-mod-path b/bin/bout-add-mod-path
index 9faf1be3de..ee7ea66d25 100755
--- a/bin/bout-add-mod-path
+++ b/bin/bout-add-mod-path
@@ -104,8 +104,7 @@ def create_mod(modulepath, name, top, build):
     else:
         prereq = ""
     with open(filename, "w") as f:
-        f.write(
-            f"""#%Module 1.0
+        f.write(f"""#%Module 1.0
 #
 #  BOUT++ module for use with 'environment-modules' package
 #  Created by bout-add-mod-path v0.9
@@ -119,17 +118,14 @@ setenv        BOUT_TOP         {top}
 prepend-path  PATH             {top}/bin
 prepend-path  PYTHONPATH       {top}/tools/pylib
 prepend-path  IDL_PATH        +{top}/tools/idllib:'<IDL_DEFAULT>'
-"""
-        )
+""")
         if build != top:
-            f.write(
-                f"""#%Module 1.0
+            f.write(f"""#%Module 1.0
 setenv        BOUT_BUILD       {build}
 prepend-path  PATH             {build}/bin
 prepend-path  LD_LIBRARY_PATH  {build}/lib
 prepend-path  PYTHONPATH       {build}/tools/pylib
-"""
-            )
+""")
     print(f"created `{filename}`")
 
 
diff --git a/bin/bout-pylib-cmd-to-bin b/bin/bout-pylib-cmd-to-bin
index 8f88a5dbf4..8d6dbed7ae 100755
--- a/bin/bout-pylib-cmd-to-bin
+++ b/bin/bout-pylib-cmd-to-bin
@@ -126,8 +126,7 @@ def createwrapper(mod, func_name, func, name):
             out += end
             f.write(out)
 
-        fprint(
-            """#!/usr/bin/env python3
+        fprint("""#!/usr/bin/env python3
 # PYTHON_ARGCOMPLETE_OK
 
 import argparse
@@ -136,8 +135,7 @@ try:
 except ImportError:
     argcomplete=None
 
-"""
-        )
+""")
         doc = True
         para = False
         ret = False
@@ -183,19 +181,16 @@ except ImportError:
                         arg_help[curarg].append(esc(blas))
         # Print functions that are needed
         if "str_to_slice" in arg_type.values():
-            fprint(
-                """
+            fprint("""
 def str_to_slice(sstr):
     args=[]
     for s in sstr.split(','):
         args.append(int(s))
     print(args)
     return slice(*args)
-"""
-            )
+""")
         if "str_to_bool" in arg_type.values():
-            fprint(
-                """
+            fprint("""
 def str_to_bool(sstr):
     low=sstr.lower()
     # no or false
@@ -206,8 +201,7 @@ def str_to_bool(sstr):
         return True
     else:
         raise ArgumentTypeError("Cannot parse %s to bool type"%sstr)
-"""
-            )
+""")
         # Create the parser
         fprint("parser = argparse.ArgumentParser(%s)" % (esc(docs)))
         spec = inspect.signature(func)
@@ -247,24 +241,19 @@ def str_to_bool(sstr):
                     pre = "\n    "
             fprint(")")
 
-        fprint(
-            """
+        fprint("""
 if argcomplete:
     argcomplete.autocomplete(parser)
 
-# late import for faster auto-complete"""
-        )
+# late import for faster auto-complete""")
         fprint("from %s import %s" % (mod, func_name))
-        fprint(
-            """
+        fprint("""
 args = parser.parse_args()
 
 # Call the function %s, using command line arguments
 %s(**args.__dict__)
 
-"""
-            % (func_name, func_name)
-        )
+""" % (func_name, func_name))
     # alternative, but I think 0o755 is easier to read
     # import stat
     # os.chmod(filename,stat.S_IRWXU|stat.S_IRGRP|stat.S_IXGRP|stat.S_IROTH|stat.S_IXOTH)
diff --git a/bin/bout-v5-factory-upgrader.py b/bin/bout-v5-factory-upgrader.py
index 29fc07db30..ee24572a94 100755
--- a/bin/bout-v5-factory-upgrader.py
+++ b/bin/bout-v5-factory-upgrader.py
@@ -5,7 +5,6 @@
 import difflib
 import re
 
-
 # Dictionary of factory methods that may need updating
 factories = {
     "Interpolation": {
@@ -62,9 +61,7 @@ def find_factory_calls(factory, source):
         \s*=\s*
         {factory_name}::
         .*{create_method}.*
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -75,9 +72,7 @@ def find_type_pointers(factory, source):
         r"""
         \b{type_name}\s*\*\s*   # Type name and pointer
         ([\w_]+)\s*;            # Variable name
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -107,9 +102,7 @@ def fix_declarations(factory, variables, source):
             (.*?)(class\s*)?         # optional "class" keyword
             \b({type_name})\s*\*\s*  # Type-pointer
             ({variable_name})\s*;    # Variable
-            """.format(
-                type_name=factory["type_name"], variable_name=variable
-            ),
+            """.format(type_name=factory["type_name"], variable_name=variable),
             r"\1std::unique_ptr<\3> \4{nullptr};",
             source,
             flags=re.VERBOSE,
@@ -123,9 +116,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment from factory
             ({factory_name}::.*{create_method}.*);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1auto \4 = \5;",
             source,
             flags=re.VERBOSE,
@@ -139,9 +130,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment
             (0|nullptr|NULL);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1std::unique_ptr<\2> \3{nullptr};",
             source,
             flags=re.VERBOSE,
diff --git a/bin/bout-v5-format-upgrader.py b/bin/bout-v5-format-upgrader.py
index 7c7d13ac7f..a534ca240a 100755
--- a/bin/bout-v5-format-upgrader.py
+++ b/bin/bout-v5-format-upgrader.py
@@ -5,7 +5,6 @@
 import difflib
 import re
 
-
 format_replacements = {
     "c": "c",
     "d": "d",
diff --git a/bin/bout-v5-header-upgrader.py b/bin/bout-v5-header-upgrader.py
index 49a8fbcbe4..77794ab920 100755
--- a/bin/bout-v5-header-upgrader.py
+++ b/bin/bout-v5-header-upgrader.py
@@ -9,7 +9,6 @@
 from typing import List
 from subprocess import run
 
-
 header_shim_sentinel = "// BOUT++ header shim"
 
 header_warning = f"""\
@@ -122,8 +121,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Fix deprecated header locations for BOUT++ v4 -> v5
 
             All BOUT++ headers are now under ``include/bout`` and
@@ -142,8 +140,7 @@ def create_patch(filename, original, modified):
             If you have staged changes, this tool will not work, so to
             avoid committing undesired or unrelated changes.
 
-            """
-        ),
+            """),
     )
 
     parser.add_argument(
diff --git a/bin/bout-v5-input-file-upgrader.py b/bin/bout-v5-input-file-upgrader.py
index e2940ff58a..ea979005d5 100755
--- a/bin/bout-v5-input-file-upgrader.py
+++ b/bin/bout-v5-input-file-upgrader.py
@@ -271,8 +271,7 @@ def possibly_apply_patch(patch, options_file, quiet=False, force=False):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Fix input files for BOUT++ v5+
 
             Please note that this will only fix input options in sections with
@@ -300,8 +299,7 @@ def possibly_apply_patch(patch, options_file, quiet=False, force=False):
 
             Files that change in this way will have the "canonicalisation" patch
             presented first. If you choose not to apply this patch, the "upgrade
-            fixer" patch will still include it."""
-        ),
+            fixer" patch will still include it."""),
     )
 
     parser.add_argument("files", action="store", nargs="+", help="Input files")
diff --git a/bin/bout-v5-macro-upgrader.py b/bin/bout-v5-macro-upgrader.py
index 11b4926255..d644fed9e8 100755
--- a/bin/bout-v5-macro-upgrader.py
+++ b/bin/bout-v5-macro-upgrader.py
@@ -342,8 +342,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Fix macro defines for BOUT++ v4 -> v5
 
             Please note that this is only slightly better than dumb text replacement. It
@@ -359,8 +358,7 @@ def create_patch(filename, original, modified):
             still replace them in strings or comments.
 
             Please check the diff output carefully!
-            """
-        ),
+            """),
     )
 
     parser.add_argument("files", action="store", nargs="+", help="Input files")
diff --git a/bin/bout-v5-physics-model-upgrader.py b/bin/bout-v5-physics-model-upgrader.py
index 26fb8ef6e0..260d1d59ee 100755
--- a/bin/bout-v5-physics-model-upgrader.py
+++ b/bin/bout-v5-physics-model-upgrader.py
@@ -8,7 +8,6 @@
 import textwrap
 import warnings
 
-
 PHYSICS_MODEL_INCLUDE = '#include "bout/physicsmodel.hxx"'
 
 PHYSICS_MODEL_SKELETON = """
@@ -213,13 +212,11 @@ def fix_bout_constrain(source, error_on_warning):
             "\n  ".join(["{}:{}".format(i, source_lines[i]) for i in line_range])
         )
 
-    message = textwrap.dedent(
-        """\
+    message = textwrap.dedent("""\
         Some uses of `bout_constrain` remain, but we could not automatically
         convert them to use `Solver::constraint`. Please fix them before
         continuing:
-        """
-    )
+        """)
     message += "  " + "\n  ".join(lines_context)
 
     if error_on_warning:
@@ -389,8 +386,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Upgrade legacy physics models to use the PhysicsModel class
 
             This will do the bare minimum required to compile, and
@@ -403,8 +399,7 @@ def create_patch(filename, original, modified):
             By default, this will use the file name stripped of file
             extensions as the name of the new class. Use '--name=<new
             name>' to give a different name.
-            """
-        ),
+            """),
     )
 
     parser.add_argument("files", action="store", nargs="+", help="Files to fix")
diff --git a/bin/bout-v5-xzinterpolation-upgrader.py b/bin/bout-v5-xzinterpolation-upgrader.py
index 37c79e0de8..e70c3c54ae 100755
--- a/bin/bout-v5-xzinterpolation-upgrader.py
+++ b/bin/bout-v5-xzinterpolation-upgrader.py
@@ -54,9 +54,7 @@ def fix_header_includes(old_header, new_header, source):
         (<|")
         ({header})              # Header name
         (>|")
-        """.format(
-            header=old_header
-        ),
+        """.format(header=old_header),
         r"\1\2{header}\4".format(header=new_header),
         source,
         flags=re.VERBOSE,
@@ -67,9 +65,7 @@ def fix_interpolations(old_interpolation, new_interpolation, source):
     return re.sub(
         r"""
         \b{}\b
-        """.format(
-            old_interpolation
-        ),
+        """.format(old_interpolation),
         r"{}".format(new_interpolation),
         source,
         flags=re.VERBOSE,
@@ -120,9 +116,7 @@ def fix_factories(old_factory, new_factory, source):
     return re.sub(
         r"""
         \b{}\b
-        """.format(
-            old_factory
-        ),
+        """.format(old_factory),
         r"{}".format(new_factory),
         source,
         flags=re.VERBOSE,
diff --git a/bin/update_version_number_in_files.py b/bin/update_version_number_in_files.py
index ec9a31bc32..3e9758a8c1 100755
--- a/bin/update_version_number_in_files.py
+++ b/bin/update_version_number_in_files.py
@@ -158,8 +158,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Update the software version number to the specified version, 
             to be given in the form major.minor.patch, 
             e.g. 5.10.3
@@ -172,8 +171,7 @@ def create_patch(filename, original, modified):
             the 'minor' version number of the provided version will be incremented by 1, 
             e.g. 5.10.3 -> 5.11.3
             
-            """
-        ),
+            """),
     )
 
     parser.add_argument(
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 29631ff7aa..3e07d6fec4 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -11,7 +11,6 @@
 
 """
 
-
 from __future__ import print_function
 
 from builtins import object
diff --git a/tests/MMS/GBS/runtest-slab2d b/tests/MMS/GBS/runtest-slab2d
index 97c7e11459..221c34e815 100755
--- a/tests/MMS/GBS/runtest-slab2d
+++ b/tests/MMS/GBS/runtest-slab2d
@@ -11,7 +11,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate
 
-
 build_and_log("MMS test")
 
 
diff --git a/tests/MMS/GBS/runtest-slab3d b/tests/MMS/GBS/runtest-slab3d
index f193583e47..45acd53af7 100755
--- a/tests/MMS/GBS/runtest-slab3d
+++ b/tests/MMS/GBS/runtest-slab3d
@@ -14,7 +14,6 @@ from numpy import sqrt, max, abs, mean, array, log, concatenate
 
 import pickle
 
-
 build_and_log("MMS test")
 
 # List of NX values to use
diff --git a/tests/MMS/advection/runtest b/tests/MMS/advection/runtest
index 1290a4c247..9a0a691287 100755
--- a/tests/MMS/advection/runtest
+++ b/tests/MMS/advection/runtest
@@ -20,7 +20,6 @@ import pickle
 
 import time
 
-
 if __name__ == "__main__":
     build_and_log("MMS advection")
 
diff --git a/tests/MMS/diffusion/runtest b/tests/MMS/diffusion/runtest
index a25b3519a6..ef6b335f70 100755
--- a/tests/MMS/diffusion/runtest
+++ b/tests/MMS/diffusion/runtest
@@ -15,7 +15,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log
 
-
 build_and_log("MMS diffusion test")
 
 # List of NX values to use
diff --git a/tests/MMS/diffusion2/Z/plot_error.py b/tests/MMS/diffusion2/Z/plot_error.py
index 5c4e1164c1..4b4b666758 100644
--- a/tests/MMS/diffusion2/Z/plot_error.py
+++ b/tests/MMS/diffusion2/Z/plot_error.py
@@ -4,6 +4,7 @@
 
 @author: yolen
 """
+
 import boutdata
 import matplotlib.pyplot as plt
 
diff --git a/tests/MMS/diffusion2/runtest b/tests/MMS/diffusion2/runtest
index 546be3b2c1..d1b8072fc8 100755
--- a/tests/MMS/diffusion2/runtest
+++ b/tests/MMS/diffusion2/runtest
@@ -20,7 +20,6 @@ from numpy import sqrt, max, abs, mean, array, log
 
 from os.path import join
 
-
 build_and_log("MMS diffusion test")
 
 # List of input directories
diff --git a/tests/MMS/fieldalign/runtest.broken b/tests/MMS/fieldalign/runtest.broken
index e09fbeccd5..bfb2023c1d 100755
--- a/tests/MMS/fieldalign/runtest.broken
+++ b/tests/MMS/fieldalign/runtest.broken
@@ -18,7 +18,6 @@ from os.path import join
 
 import time
 
-
 build_and_log("MMS test")
 
 # nxlist = [256, 128, 64, 32, 16, 8] # do in reverse order to save disk space
diff --git a/tests/MMS/hw/runtest b/tests/MMS/hw/runtest
index b6abadc3b9..62740fcbbd 100755
--- a/tests/MMS/hw/runtest
+++ b/tests/MMS/hw/runtest
@@ -15,7 +15,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate
 
-
 build_and_log("MMS test")
 
 # List of NX values to use
diff --git a/tests/MMS/laplace/runtest b/tests/MMS/laplace/runtest
index 98eb62da87..80c8bf08af 100755
--- a/tests/MMS/laplace/runtest
+++ b/tests/MMS/laplace/runtest
@@ -14,7 +14,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate
 
-
 build_and_log("MMS test")
 
 # List of NX values to use
diff --git a/tests/MMS/spatial/diffusion/runtest b/tests/MMS/spatial/diffusion/runtest
index 000cf8f09b..8d4e759d59 100755
--- a/tests/MMS/spatial/diffusion/runtest
+++ b/tests/MMS/spatial/diffusion/runtest
@@ -22,7 +22,6 @@ from os.path import join
 
 import matplotlib.pyplot as plt
 
-
 build_and_log("MMS diffusion test")
 
 # List of input directories
diff --git a/tests/MMS/wave-1d-y/runtest b/tests/MMS/wave-1d-y/runtest
index 9a4de5a3bb..332d6864b0 100755
--- a/tests/MMS/wave-1d-y/runtest
+++ b/tests/MMS/wave-1d-y/runtest
@@ -20,7 +20,6 @@ from sys import stdout
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate, pi
 
-
 build_and_log("Making MMS wave test")
 
 # List of NX values to use
diff --git a/tests/MMS/wave-1d/runtest b/tests/MMS/wave-1d/runtest
index f13fb7bd11..1adb7c7d6d 100755
--- a/tests/MMS/wave-1d/runtest
+++ b/tests/MMS/wave-1d/runtest
@@ -15,7 +15,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate
 
-
 build_and_log("Making MMS wave test")
 
 # List of NX values to use
diff --git a/tests/integrated/test-command-args/runtest b/tests/integrated/test-command-args/runtest
index 39939bb105..a8dc3f020c 100755
--- a/tests/integrated/test-command-args/runtest
+++ b/tests/integrated/test-command-args/runtest
@@ -7,7 +7,6 @@ import shutil
 import unittest
 import platform
 
-
 OUTPUT_FILE = "stdout.log" if platform.system() == "FreeBSD" else "stderr.log"
 
 
diff --git a/tests/integrated/test-cyclic/runtest b/tests/integrated/test-cyclic/runtest
index 5e31da6239..c68f9b033e 100755
--- a/tests/integrated/test-cyclic/runtest
+++ b/tests/integrated/test-cyclic/runtest
@@ -17,7 +17,6 @@ from boututils.run_wrapper import build_and_log, shell, launch
 from boutdata.collect import collect
 from sys import stdout, exit
 
-
 build_and_log("Cyclic Reduction test")
 
 flags = ["", "nsys=2", "nsys=5 periodic", "nsys=7 n=10"]
diff --git a/tests/integrated/test-griddata/runtest b/tests/integrated/test-griddata/runtest
index 1c57bf5be7..6aef955023 100755
--- a/tests/integrated/test-griddata/runtest
+++ b/tests/integrated/test-griddata/runtest
@@ -13,7 +13,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("griddata test")
 
 for nproc in [1]:
diff --git a/tests/integrated/test-gyro/runtest b/tests/integrated/test-gyro/runtest
index 52ab0de4ab..7a0209fa57 100755
--- a/tests/integrated/test-gyro/runtest
+++ b/tests/integrated/test-gyro/runtest
@@ -25,7 +25,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("Gyro-average inversion test")
 
 # Read benchmark values
diff --git a/tests/integrated/test-invpar/runtest b/tests/integrated/test-invpar/runtest
index de7f028528..53f6015fe9 100755
--- a/tests/integrated/test-invpar/runtest
+++ b/tests/integrated/test-invpar/runtest
@@ -12,7 +12,6 @@ from boututils.run_wrapper import build_and_log, shell, launch
 from boutdata.collect import collect
 from sys import stdout, exit
 
-
 build_and_log("parallel inversion test")
 
 flags_src = [
diff --git a/tests/integrated/test-laplace/runtest b/tests/integrated/test-laplace/runtest
index e54e46d0d8..d1e9c3d1c9 100755
--- a/tests/integrated/test-laplace/runtest
+++ b/tests/integrated/test-laplace/runtest
@@ -41,7 +41,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("Laplacian inversion test")
 
 # Read benchmark values
diff --git a/tests/integrated/test-multigrid_laplace/runtest b/tests/integrated/test-multigrid_laplace/runtest
index 4a7455f80b..f325185c46 100755
--- a/tests/integrated/test-multigrid_laplace/runtest
+++ b/tests/integrated/test-multigrid_laplace/runtest
@@ -22,7 +22,6 @@ from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("multigrid Laplacian inversion test")
 
 print("Running multigrid Laplacian inversion test")
diff --git a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
index 6817120b13..739d15f7d4 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
+++ b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
@@ -18,7 +18,6 @@ from boututils.run_wrapper import shell, build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("Multigrid Laplacian inversion test")
 
 print("Running multigrid Laplacian inversion test")
diff --git a/tests/integrated/test-multigrid_laplace/runtest_unsheared b/tests/integrated/test-multigrid_laplace/runtest_unsheared
index cda68f2167..d0dca3a808 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_unsheared
+++ b/tests/integrated/test-multigrid_laplace/runtest_unsheared
@@ -18,7 +18,6 @@ from boututils.run_wrapper import shell, build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("Making multigrid Laplacian inversion test")
 
 print("Running multigrid Laplacian inversion test")
diff --git a/tests/integrated/test-naulin-laplace/runtest b/tests/integrated/test-naulin-laplace/runtest
index f972eab6cc..145257c23b 100755
--- a/tests/integrated/test-naulin-laplace/runtest
+++ b/tests/integrated/test-naulin-laplace/runtest
@@ -22,7 +22,6 @@ from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("LaplaceNaulin inversion test")
 
 print("Running LaplaceNaulin inversion test")
diff --git a/tests/integrated/test-naulin-laplace/runtest_multiple_grids b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
index c0281c3a4e..f56a80677e 100755
--- a/tests/integrated/test-naulin-laplace/runtest_multiple_grids
+++ b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
@@ -18,7 +18,6 @@ from boututils.run_wrapper import shell, build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("Making LaplaceNaulin inversion test")
 
 print("Running LaplaceNaulin inversion test")
diff --git a/tests/integrated/test-naulin-laplace/runtest_unsheared b/tests/integrated/test-naulin-laplace/runtest_unsheared
index 8f47f33026..a845a9d92f 100755
--- a/tests/integrated/test-naulin-laplace/runtest_unsheared
+++ b/tests/integrated/test-naulin-laplace/runtest_unsheared
@@ -18,7 +18,6 @@ from boututils.run_wrapper import shell, build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("LaplaceNaulin inversion test")
 
 print("Running LaplaceNaulin inversion test")
diff --git a/tests/integrated/test-petsc_laplace/runtest b/tests/integrated/test-petsc_laplace/runtest
index ac248c4ce7..83e1006338 100755
--- a/tests/integrated/test-petsc_laplace/runtest
+++ b/tests/integrated/test-petsc_laplace/runtest
@@ -30,7 +30,6 @@ from boutdata.collect import collect
 # import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("PETSc Laplacian inversion test")
 
 print("Running PETSc Laplacian inversion test")
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/runtest b/tests/integrated/test-petsc_laplace_MAST-grid/runtest
index 5a4cbf875a..3be39949c3 100755
--- a/tests/integrated/test-petsc_laplace_MAST-grid/runtest
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/runtest
@@ -28,7 +28,6 @@ from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 from sys import stdout, exit
 
-
 build_and_log(
     "PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)"
 )
diff --git a/tests/integrated/test-region-iterator/runtest b/tests/integrated/test-region-iterator/runtest
index e5825285de..2277ef15e9 100755
--- a/tests/integrated/test-region-iterator/runtest
+++ b/tests/integrated/test-region-iterator/runtest
@@ -17,7 +17,6 @@ from boututils.run_wrapper import build_and_log, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-
 build_and_log("Region Iterator test")
 
 flags = [""]
diff --git a/tests/integrated/test-restarting/runtest b/tests/integrated/test-restarting/runtest
index 262aa818b6..daf19ebac6 100755
--- a/tests/integrated/test-restarting/runtest
+++ b/tests/integrated/test-restarting/runtest
@@ -5,7 +5,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("restart test")
 
 # Run once for 10 timesteps
diff --git a/tests/integrated/test-smooth/runtest b/tests/integrated/test-smooth/runtest
index bd7296341a..91ae793164 100755
--- a/tests/integrated/test-smooth/runtest
+++ b/tests/integrated/test-smooth/runtest
@@ -16,7 +16,6 @@ from boutdata.collect import collect
 import numpy as np
 from sys import stdout, exit
 
-
 build_and_log("smoothing operator test")
 
 # Read benchmark values
diff --git a/tests/integrated/test-squash/runtest b/tests/integrated/test-squash/runtest
index 2f35e00589..8bf358ee8e 100755
--- a/tests/integrated/test-squash/runtest
+++ b/tests/integrated/test-squash/runtest
@@ -9,7 +9,6 @@ import argparse
 import re
 import os.path
 
-
 # requires: all_tests
 # requires: netcdf
 # cores: 4
diff --git a/tests/integrated/test-yupdown/runtest b/tests/integrated/test-yupdown/runtest
index 34fcd36496..13d7365b53 100755
--- a/tests/integrated/test-yupdown/runtest
+++ b/tests/integrated/test-yupdown/runtest
@@ -6,7 +6,6 @@ from sys import exit
 
 from numpy import max, abs
 
-
 build_and_log("parallel slices test")
 
 failed = False
diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 31a4694d10..61bb826016 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -212,12 +212,10 @@ def build_sdist(sdist_directory, config_settings=None):
         run(f"rm {tmp}")
 
     with open(tmp, "w") as f:
-        f.write(
-            f"""Metadata-Version: 2.1
+        f.write(f"""Metadata-Version: 2.1
 Name: {pkgname}
 Version: {getversion()}
-"""
-        )
+""")
         with open("LICENSE") as src:
             pre = "License: "
             for l in src:
@@ -269,23 +267,19 @@ def prepare_metadata_for_build_wheel(
     distinfo = f"{metadata_directory}/{thisdir}"
     mkdir_p(distinfo)
     with open(f"{distinfo}/METADATA", "w") as f:
-        f.write(
-            f"""Metadata-Version: 2.1
+        f.write(f"""Metadata-Version: 2.1
 Name: {pkgname}
 Version: {getversion()}
 License-File: COPYING
-"""
-        )
+""")
     run(f"cp LICENSE {distinfo}/COPYING")
     run(f"cp LICENSE.GPL {distinfo}/COPYING.GPL")
     with open(f"{distinfo}/WHEEL", "w") as f:
-        f.write(
-            f"""Wheel-Version: 1.0
+        f.write(f"""Wheel-Version: 1.0
 Generator: boutpp_custom_build_wheel ({getversion()})
 Root-Is-Purelib: false
 Tag: {gettag()}
-"""
-        )
+""")
 
     if record:
         with open(f"{distinfo}/RECORD", "w") as f:

From 47e30d5e5667f0a6cc533d43a7ebde0cc190b6b0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 11:54:11 +0000
Subject: [PATCH 0445/1827] ci: Cache Zenodo data, and retry on http 502, 503
 errors

Also:
- reduce max number of tries to avoid hammering Zenodo
- update moved URL
---
 .github/workflows/tests.yml                  | 23 ++++++++++++++++++++
 tests/integrated/test-fci-mpi/CMakeLists.txt |  2 +-
 2 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 314ee196ae..3124a11762 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -181,6 +181,29 @@ jobs:
           python -m pip install --upgrade pip setuptools
           python -m pip install -r requirements.txt
 
+      - name: Cache Zenodo test data
+        uses: actions/cache@v4
+        with:
+          path: ./zenodo_data
+          # Data doesn't depend on matrix job, so this should cache between all jobs
+          key: zenodo-data
+
+      - name: Download Zenodo test data
+        run: |
+          if [[ ! -e zenodo_data/grid.fci.nc ]]; then
+            echo "Downloading Zenodo data"
+            mkdir -p zenodo_data
+            wget \
+              https://zenodo.org/records/7614499/files/W7X-conf4-36x8x128.fci.nc?download=1 \
+              --output-document=zenodo_data/grid.fci.nc \
+              --retry-on-http-error=502,503,504 \
+              --tries 3
+          else
+            echo "Using cached Zenodo data"
+          fi
+          mkdir -pv build/tests/integrated/test-fci-mpi
+          cp -v zenodo_data/grid.fci.nc build/tests/integrated/test-fci-mpi
+
       - name: Cache SUNDIALS build
         uses: actions/cache@v4
         with:
diff --git a/tests/integrated/test-fci-mpi/CMakeLists.txt b/tests/integrated/test-fci-mpi/CMakeLists.txt
index 0dd38487a3..aea0421c0a 100644
--- a/tests/integrated/test-fci-mpi/CMakeLists.txt
+++ b/tests/integrated/test-fci-mpi/CMakeLists.txt
@@ -3,7 +3,7 @@ bout_add_mms_test(test-fci-mpi
   USE_RUNTEST
   USE_DATA_BOUT_INP
   PROCESSORS 6
-  DOWNLOAD https://zenodo.org/record/7614499/files/W7X-conf4-36x8x128.fci.nc?download=1
+  DOWNLOAD https://zenodo.org/records/7614499/files/W7X-conf4-36x8x128.fci.nc?download=1
   DOWNLOAD_NAME grid.fci.nc
   REQUIRES BOUT_HAS_PETSC
 )

From 51d2ceb79105055d84ac4f60d1636b0fe073f53d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 13:37:47 +0000
Subject: [PATCH 0446/1827] ci: Use wget flags from env var

This avoids duplicating the download in all jobs
---
 .github/workflows/tests.yml | 44 ++++++++++++++++++++-----------------
 cmake/BOUT++functions.cmake |  2 +-
 2 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 3124a11762..e50154e615 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -30,6 +30,7 @@ jobs:
       OMPI_MCA_rmaps_base_oversubscribe: yes
       PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe"
       MPIRUN: mpiexec -np
+      BOUT_TEST_DOWNLOAD_FLAGS: --retry-on-http-error=502,503,504 --tries 3
     strategy:
       fail-fast: true
       matrix:
@@ -184,25 +185,9 @@ jobs:
       - name: Cache Zenodo test data
         uses: actions/cache@v4
         with:
-          path: ./zenodo_data
-          # Data doesn't depend on matrix job, so this should cache between all jobs
-          key: zenodo-data
-
-      - name: Download Zenodo test data
-        run: |
-          if [[ ! -e zenodo_data/grid.fci.nc ]]; then
-            echo "Downloading Zenodo data"
-            mkdir -p zenodo_data
-            wget \
-              https://zenodo.org/records/7614499/files/W7X-conf4-36x8x128.fci.nc?download=1 \
-              --output-document=zenodo_data/grid.fci.nc \
-              --retry-on-http-error=502,503,504 \
-              --tries 3
-          else
-            echo "Using cached Zenodo data"
-          fi
-          mkdir -pv build/tests/integrated/test-fci-mpi
-          cp -v zenodo_data/grid.fci.nc build/tests/integrated/test-fci-mpi
+          path: build/tests/integrated/test-fci-mpi/grid.fci.nc
+          # If we update the test, invalidate the cache
+          key: zenodo-data-${{ hashFiles('tests/integrated/test-fci-mpi/CMakeLists.txt') }}
 
       - name: Cache SUNDIALS build
         uses: actions/cache@v4
@@ -227,10 +212,20 @@ jobs:
     # standard_tests
     timeout-minutes: 120
     runs-on: ubuntu-latest
+    env:
+      BOUT_TEST_DOWNLOAD_FLAGS: --retry-on-http-error=502,503,504 --tries 3
     steps:
       - uses: actions/checkout@v5
         with:
           submodules: true
+
+      - name: Cache Zenodo test data
+        uses: actions/cache@v4
+        with:
+          path: build/tests/integrated/test-fci-mpi/grid.fci.nc
+          # If we update the test, invalidate the cache
+          key: zenodo-data-${{ hashFiles('tests/integrated/test-fci-mpi/CMakeLists.txt') }}
+
       - name: Build Fedora
         run: ./.ci_fedora.sh setup openmpi
         shell: bash
@@ -240,11 +235,20 @@ jobs:
     timeout-minutes: 60
     runs-on: ubuntu-latest
     container: ghcr.io/ggeorgakoudis/boutdev-cuda:latest
-
+    env:
+      BOUT_TEST_DOWNLOAD_FLAGS: --retry-on-http-error=502,503,504 --tries 3
     steps:
       - uses: actions/checkout@v5
         with:
           submodules: true
+
+      - name: Cache Zenodo test data
+        uses: actions/cache@v4
+        with:
+          path: build/tests/integrated/test-fci-mpi/grid.fci.nc
+          # If we update the test, invalidate the cache
+          key: zenodo-data-${{ hashFiles('tests/integrated/test-fci-mpi/CMakeLists.txt') }}
+
       - name: Build minimal CUDA 12.2 @ GCC9.4.0 @ Ubuntu 20.04
         run: |
           . /spack/share/spack/setup-env.sh
diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 77279dfd4b..074d803fb6 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -208,7 +208,7 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
     endif()
     set(output )
     add_custom_command(OUTPUT ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
-      COMMAND wget ${BOUT_TEST_OPTIONS_DOWNLOAD} -O ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
+      COMMAND wget ${BOUT_TEST_OPTIONS_DOWNLOAD} -O ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME} $ENV{BOUT_TEST_DOWNLOAD_FLAGS}
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
       COMMENT "Downloading ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}"
       )

From bbaeeaf05ea80488d295313eca12ed3dbd22a51f Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 13:39:44 +0000
Subject: [PATCH 0447/1827] ci: Cache Python packages

---
 .github/workflows/tests.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index e50154e615..47c053744f 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -176,6 +176,7 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: '3.x'
+          cache: 'pip'
 
       - name: Install pip packages
         run: |

From cb0d3f12061424e81c199272ff6e9f8589be35f0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 21 Jan 2026 12:12:12 +0100
Subject: [PATCH 0448/1827] Add backtrace to tracked operations

This avoids mostly the need for annotations using BOUT_USE_TRACK.
setName could thus be dropped.
---
 src/field/field3d.cxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index a2ca5aad5e..00cdd8982f 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -33,6 +33,7 @@
 #include <cmath>
 #include <memory>
 #include <utility>
+#include <cpptrace/cpptrace.hpp>
 
 #include "bout/parallel_boundary_op.hxx"
 #include "bout/parallel_boundary_region.hxx"
@@ -859,6 +860,9 @@ void Field3D::_track(const T& change, std::string operation) {
   const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
 
   locked->set(outname, change, "tracking");
+
+  const std::string trace = cpptrace::generate_trace().to_string();
+
   // Workaround for bug in gcc9.4
 #if BOUT_USE_TRACK
   const std::string changename = change.name;
@@ -868,6 +872,7 @@ void Field3D::_track(const T& change, std::string operation) {
 #if BOUT_USE_TRACK
       {"rhs.name", changename},
 #endif
+      {"trace", trace},
   });
 }
 
@@ -885,10 +890,12 @@ void Field3D::_track(const BoutReal& change, std::string operation) {
   if (locked == nullptr) {
     return;
   }
+  const std::string trace = cpptrace::generate_trace().to_string();
   const std::string outname{fmt::format("track_{:s}_{:d}", selfname, tracking_state++)};
   locked->set(outname, change, "tracking");
   (*locked)[outname].setAttributes({
       {"operation", operation},
       {"rhs.name", "BoutReal"},
+      {"trace", trace},
   });
 }

From f2ed814db206d92c729980d4ad9d317ff3ebcf59 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Thu, 29 Jan 2026 09:07:41 +0000
Subject: [PATCH 0449/1827] Apply clang-format changes

---
 src/field/field3d.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 00cdd8982f..c669516399 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -31,9 +31,9 @@
 #include <bout/globals.hxx>
 
 #include <cmath>
+#include <cpptrace/cpptrace.hpp>
 #include <memory>
 #include <utility>
-#include <cpptrace/cpptrace.hpp>
 
 #include "bout/parallel_boundary_op.hxx"
 #include "bout/parallel_boundary_region.hxx"

From e3f8923b4692a4d969127147cf4b57b00ea72aab Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 29 Jan 2026 10:25:08 +0100
Subject: [PATCH 0450/1827] Apply clang-format suggestions

---
 src/solver/impls/euler/euler.cxx | 4 +++-
 src/solver/impls/pvode/pvode.cxx | 4 ++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index f33d07f9d3..4b7a1bc029 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -1,6 +1,8 @@
-
 #include "euler.hxx"
 
+#include <cstdlib>
+#include <memory>
+
 #include "bout/field.hxx"
 #include "bout/version.hxx"
 #include <bout/boutcomm.hxx>
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index a0a0efa377..59f7b3867f 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -64,7 +64,7 @@ namespace {
 void pvode_load_data_f3d(const std::vector<bool>& evolve_bndrys,
                          std::vector<Field3D>& ffs, const BoutReal* udata) {
   int p = 0;
-  Mesh* mesh = ffs[0].getMesh();
+  const Mesh* mesh = ffs[0].getMesh();
   const int nz = mesh->LocalNz;
   for (const auto& bndry : {true, false}) {
     for (const auto& i2d : mesh->getRegion2D(bndry ? "RGN_BNDRY" : "RGN_NOBNDRY")) {
@@ -366,7 +366,7 @@ BoutReal PvodeSolver::run(BoutReal tout) {
   if (flag != SUCCESS) {
     output_error.write("ERROR CVODE step failed, flag = {:d}\n", flag);
     if (debug_on_failure) {
-      CVodeMemRec* cv_mem = static_cast<CVodeMem>(cvode_mem);
+      const CVodeMemRec* cv_mem = static_cast<CVodeMem>(cvode_mem);
       if (!(f2d.empty() and v2d.empty() and v3d.empty())) {
         output_warn.write("debug_on_failure is currently only supported for Field3Ds");
         return -1.0;

From 873c94f89117d1af0aa35a7781bdec4f26293ff5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 29 Jan 2026 10:33:14 +0100
Subject: [PATCH 0451/1827] Apply clang-format suggestions

---
 src/solver/impls/euler/euler.cxx | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 4b7a1bc029..a430f0a585 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -1,15 +1,16 @@
 #include "euler.hxx"
 
-#include <cstdlib>
-#include <memory>
-
-#include "bout/field.hxx"
-#include "bout/version.hxx"
+#include <bout/field.hxx>
+#include <bout/version.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/openmpwrap.hxx>
 #include <bout/output.hxx>
 
+#include <cstdlib>
+#include <memory>
+#include <fmt/format.h>
+
 EulerSolver::EulerSolver(Options* options)
     : Solver(options), mxstep((*options)["mxstep"]
                                   .doc("Maximum number of steps between outputs")

From 7e5c3112667544350007225f58998a1782214561 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Thu, 29 Jan 2026 09:39:23 +0000
Subject: [PATCH 0452/1827] Apply clang-format changes

---
 src/solver/impls/euler/euler.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index a430f0a585..78721d2e8f 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -1,15 +1,15 @@
 #include "euler.hxx"
 
-#include <bout/field.hxx>
-#include <bout/version.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/field.hxx>
 #include <bout/openmpwrap.hxx>
 #include <bout/output.hxx>
+#include <bout/version.hxx>
 
 #include <cstdlib>
-#include <memory>
 #include <fmt/format.h>
+#include <memory>
 
 EulerSolver::EulerSolver(Options* options)
     : Solver(options), mxstep((*options)["mxstep"]

From 227d5438dfecf5414e4a5064dbbd82f909ce8130 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 29 Jan 2026 11:04:02 +0100
Subject: [PATCH 0453/1827] CI: Rework formatting workflows

All formatting is done in one task. So there will be no more different commits
for clang-format and ruff/black.
Also adds clang-format to the pipeline.

In addition it adds an additional commit, with the hash from the formatting
commit added to `.git-blame-ignore-revs`. This tells GitHub (and local git, if
you have it configured) to ignore that commit in blames.
---
 .github/workflows/auto-formatting.yml | 62 +++++++++++++++++++++++++++
 .github/workflows/black-fix.yml       | 46 --------------------
 .github/workflows/clang-format.yml    | 33 --------------
 3 files changed, 62 insertions(+), 79 deletions(-)
 create mode 100644 .github/workflows/auto-formatting.yml
 delete mode 100644 .github/workflows/black-fix.yml
 delete mode 100644 .github/workflows/clang-format.yml

diff --git a/.github/workflows/auto-formatting.yml b/.github/workflows/auto-formatting.yml
new file mode 100644
index 0000000000..61a537403f
--- /dev/null
+++ b/.github/workflows/auto-formatting.yml
@@ -0,0 +1,62 @@
+name: format-command
+
+on:
+  pull_request:
+
+jobs:
+  clang-format:
+    # Release candidate branches tend to have big PRs which causes all sorts of problems
+    if: ${{ !endsWith(github.head_ref, '-rc') }}
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the pull request branch, also include all history
+      - uses: actions/checkout@v5
+        with:
+          ref: ${{ github.head_ref }}
+          fetch-depth: 0
+
+      # This also installs git-clang-format
+      - name: Install formatters
+        run: |
+          sudo apt install clang-format python3-pip python3-setuptools python3-wheel
+          pip3 install ruff cmake-format
+
+      - name: Version
+        run: |
+          python3 --version
+          $HOME/.local/bin/ruff --version
+          clang-format --version
+          $HOME/.local/bin/cmake-format --version
+
+      - name: Run clang-format
+        id: format
+        run:
+          while ! git clang-format origin/${{ github.base_ref }} ; do git add . ; done
+
+      - name: Run ruff
+        run: |
+          pwd
+          ls
+          $HOME/.local/bin/ruff format .
+          
+      - name: Run cmake-format
+        run: |
+          pwd
+          ls
+          $HOME/.local/bin/cmake-format $(find -name CMakeLists.txt) cmake/*.cmake
+
+      - name: Commit formatting
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "[bot] Apply format changes"
+          skip_push: true
+
+      - name: Ignore formatting
+        run: |
+          msg=$(git rev-list --format=%s --max-count=1 HEAD|tail -n -1)
+          test "$msg" == "Apply format changes" && git rev-parse HEAD > .git-blame-ignore-revs
+
+      - name: Commit formatting
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "[bot] Add last format changes commit to ignore file"
diff --git a/.github/workflows/black-fix.yml b/.github/workflows/black-fix.yml
deleted file mode 100644
index 4306ee8b43..0000000000
--- a/.github/workflows/black-fix.yml
+++ /dev/null
@@ -1,46 +0,0 @@
-name: black
-
-on:
-  push:
-    paths:
-      - '**.py'
-      - 'bin/**'
-      - '**/runtest'
-      - '**/run'
-      - 'tests/integrated/test_suite'
-      - 'tests/requirements/*'
-      - 'tools/tokamak_grids/**'
-
-defaults:
-  run:
-    shell: bash
-
-jobs:
-  black:
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v6
-      with:
-        ref: ${{ github.head_ref }}
-
-    - name: Install black
-      run: |
-        sudo apt update -y
-        sudo apt -y install python3-pip python3-setuptools python3-wheel
-        pip3 install black
-
-    - name: Version
-      run: |
-        python3 --version
-        $HOME/.local/bin/black --version
-
-    - name: Run black
-      run: |
-        pwd
-        ls
-        $HOME/.local/bin/black tests/ tools/ $(grep -EIlr '^#!.*python.*$' bin/ tests/ tools/ src/ | grep -v _boutpp_build)
-
-    - uses: stefanzweifel/git-auto-commit-action@v7
-      with:
-        commit_message: "Apply black changes"
diff --git a/.github/workflows/clang-format.yml b/.github/workflows/clang-format.yml
deleted file mode 100644
index 678960ba3e..0000000000
--- a/.github/workflows/clang-format.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: clang-format-command
-
-on:
-  pull_request:
-    paths:
-      - '**.cxx'
-      - '**.hxx'
-
-jobs:
-  clang-format:
-    # Release candidate branches tend to have big PRs which causes all sorts of problems
-    if: ${{ !endsWith(github.head_ref, '-rc') }}
-    runs-on: ubuntu-latest
-    steps:
-      # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v6
-        with:
-          ref: ${{ github.head_ref }}
-          fetch-depth: 0
-
-      # This also installs git-clang-format
-      - name: Install clang-format
-        run: sudo apt install clang-format
-
-      - name: Run clang-format
-        id: format
-        run:
-          while ! git clang-format origin/${{ github.base_ref }} ; do git add . ; done
-
-      - name: Commit to the PR branch
-        uses: stefanzweifel/git-auto-commit-action@v7
-        with:
-          commit_message: "Apply clang-format changes"

From 9d509cb3a1ff301ad5c7f1571b0684064a0d26c6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 29 Jan 2026 11:37:24 +0100
Subject: [PATCH 0454/1827] Do not format matlab files

---
 .clang-format-ignore | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 .clang-format-ignore

diff --git a/.clang-format-ignore b/.clang-format-ignore
new file mode 100644
index 0000000000..58566f02b1
--- /dev/null
+++ b/.clang-format-ignore
@@ -0,0 +1,2 @@
+# ignore matlab files
+**/*.m

From f1f22c89ed96c3bf8b7d2ab57a469f9802eeee1f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 29 Jan 2026 11:42:26 +0100
Subject: [PATCH 0455/1827] CI: Fix pipeline

---
 .github/workflows/auto-formatting.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/auto-formatting.yml b/.github/workflows/auto-formatting.yml
index 61a537403f..38c6e8189f 100644
--- a/.github/workflows/auto-formatting.yml
+++ b/.github/workflows/auto-formatting.yml
@@ -46,7 +46,7 @@ jobs:
           $HOME/.local/bin/cmake-format $(find -name CMakeLists.txt) cmake/*.cmake
 
       - name: Commit formatting
-        uses: stefanzweifel/git-auto-commit-action@v5
+        uses: stefanzweifel/git-auto-commit-action@v7
         with:
           commit_message: "[bot] Apply format changes"
           skip_push: true
@@ -54,9 +54,9 @@ jobs:
       - name: Ignore formatting
         run: |
           msg=$(git rev-list --format=%s --max-count=1 HEAD|tail -n -1)
-          test "$msg" == "Apply format changes" && git rev-parse HEAD > .git-blame-ignore-revs
+          test "$msg" = "[bot] Apply format changes" && git rev-parse HEAD > .git-blame-ignore-revs || :
 
       - name: Commit formatting
-        uses: stefanzweifel/git-auto-commit-action@v5
+        uses: stefanzweifel/git-auto-commit-action@v7
         with:
           commit_message: "[bot] Add last format changes commit to ignore file"

From 3e444b2a1adbf10c79457ccc2eabeb436bb771d3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 29 Jan 2026 11:44:22 +0100
Subject: [PATCH 0456/1827] CI: Ammend to ignore file

---
 .git-blame-ignore-revs                | 1 +
 .github/workflows/auto-formatting.yml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 4990f2586e..ead5bc3729 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -1,3 +1,4 @@
 # Clang-format whole repo
 d8f14fdddb5ca0fbb32d8e2bf5ac2960d6ac5ce6
 ed2117e6d6826a98b6988e2f18c0c34e408563b6
+# Added by the bot
diff --git a/.github/workflows/auto-formatting.yml b/.github/workflows/auto-formatting.yml
index 38c6e8189f..b3512f02cf 100644
--- a/.github/workflows/auto-formatting.yml
+++ b/.github/workflows/auto-formatting.yml
@@ -54,7 +54,7 @@ jobs:
       - name: Ignore formatting
         run: |
           msg=$(git rev-list --format=%s --max-count=1 HEAD|tail -n -1)
-          test "$msg" = "[bot] Apply format changes" && git rev-parse HEAD > .git-blame-ignore-revs || :
+          test "$msg" = "[bot] Apply format changes" && git rev-parse HEAD >> .git-blame-ignore-revs || :
 
       - name: Commit formatting
         uses: stefanzweifel/git-auto-commit-action@v7

From 4b010b7634aee1045743be80c268d4644522cd29 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Thu, 29 Jan 2026 10:45:02 +0000
Subject: [PATCH 0457/1827] [bot] Apply format changes

---
 examples/blob2d/blob_velocity.py              | 154 ++++++------
 examples/boutpp/simulation.py                 |   5 +-
 examples/conduction-snb/fit_temperature.py    |  24 +-
 examples/conduction-snb/sinusoid.py           |  30 ++-
 examples/conduction-snb/step.py               |  31 ++-
 examples/conduction/generate.py               |   4 +-
 examples/eigen-box/eigenvals.py               |  35 +--
 examples/elm-pb/Python/2dprofile.py           |  91 ++++---
 examples/elm-pb/Python/analysis.py            |  16 +-
 examples/elm-pb/Python/elm_size.py            | 179 +++++++------
 examples/elm-pb/Python/fftall.py              |   9 +-
 examples/elm-pb/Python/fftall2.py             |  10 +-
 examples/elm-pb/Python/grate.py               |   9 +-
 examples/elm-pb/Python/grate2.py              |  45 ++--
 examples/elm-pb/Python/plotcollapse.py        |  47 ++--
 examples/elm-pb/Python/plotmode.py            |  93 ++++---
 examples/elm-pb/Python/plotmode2.py           |  94 ++++---
 examples/elm-pb/Python/plotphase.py           |  45 ++--
 examples/elm-pb/Python/polslice.py            |  26 +-
 examples/elm-pb/Python/post.py                | 142 +++++++----
 examples/elm-pb/Python/read_elmsize.py        |  46 ++--
 examples/elm-pb/Python/showpolslice.py        |  36 +--
 examples/elm-pb/Python/sprofiles.py           |  41 +--
 examples/elm-pb/runexample.py                 |  28 ++-
 examples/fci-wave/compare-density.py          |  45 ++--
 examples/finite-volume/diffusion/mms.py       |  14 +-
 examples/finite-volume/fluid/mms.py           |  20 +-
 examples/laplace-petsc3d/plotcheck.py         |  16 +-
 examples/orszag-tang/generate.py              | 116 +++++----
 .../performance/bracket/scaling_parser.py     |   5 +-
 .../performance/ddx/new_scaling_parser.py     |  32 +--
 .../performance/ddy/new_scaling_parser.py     |  32 +--
 .../performance/ddz/new_scaling_parser.py     |  32 +--
 .../performance/iterator/scaling_parser.py    |   5 +-
 examples/staggered_grid/generate.py           |   6 +-
 examples/subsampling/show.py                  |  10 +-
 examples/wave-slab/generate.py                |   2 +-
 .../figure_creators/LaplacianMatrices.ipynb   | 236 ++++++++++--------
 .../bout_runners_folder_structure.py          |  97 +++----
 tests/MMS/advection/runtest                   |   2 +-
 40 files changed, 1039 insertions(+), 871 deletions(-)

diff --git a/examples/blob2d/blob_velocity.py b/examples/blob2d/blob_velocity.py
index d044946320..6de0937d0f 100644
--- a/examples/blob2d/blob_velocity.py
+++ b/examples/blob2d/blob_velocity.py
@@ -3,96 +3,100 @@
 import pickle
 
 try:
-        from past.utils import old_div
+    from past.utils import old_div
 except ImportError:
-        def old_div(a,b):
-                return a/b
 
-
-def blob_velocity(n,**kwargs):
-
-        from boututils import calculus as Calc
-        # Calculate blob velocity in normalized time and normalized grid spacing
-        #
-        # Input: Blob density as a 3D vector in the form  n[t,x,z] where t is time and x,z are the perpendicular spatial coordinates
-        #
-        # Keywords:
-        #
-        #           type='peak' -> Calculate velocity of the peak density
-        #           type='COM' -> Calculate centre of mass velocity
-        #           Index=True -> return indices used to create velocity
-        #
-        # Default: Peak velocity with no index returning
-
-        size = n.shape
-
-        try:
-                v_type = kwargs['type']
-        except:
-                v_type = 'peak'         #Default to peak velocity calculation
-        try:
-                return_index = kwargs['Index']
-        except:
-                return_index = False    #Default to no index returning
-
-
-        if v_type == 'peak':
-                x = np.zeros(size[0])
-                z = np.zeros(size[0])
-                for i in np.arange(size[0]):
-                        nmax,nmin = np.amax((n[i,:,:])),np.amin((n[i,:,:]))
-                        xpos,zpos = np.where(n[i,:,:]==nmax)
-                        x[i] = xpos[0]
-                        z[i] = zpos[0]
-
-        if v_type == 'COM':
-                x = np.zeros(size[0])
-                z = np.zeros(size[0])
-                for i in np.arange(size[0]):
-                        data = n[i,:,:] - n[0,0,0]   #use corner cell rather than nmin
-                        ntot = np.sum(data[:,:])
-
-                        z[i] = old_div(np.sum(np.sum(data[:,:],axis=0)*(np.arange(size[2]))),ntot)
-                        x[i] = old_div(np.sum(np.sum(data[:,:],axis=1)*(np.arange(size[1]))),ntot)
-
-        vx = Calc.deriv(x)
-        vz = Calc.deriv(z)
-
-        if return_index:
-                return vx,vz,x,z
-        else:
-                return vx,vz
-
-
-
-data='data'
+    def old_div(a, b):
+        return a / b
+
+
+def blob_velocity(n, **kwargs):
+    from boututils import calculus as Calc
+    # Calculate blob velocity in normalized time and normalized grid spacing
+    #
+    # Input: Blob density as a 3D vector in the form  n[t,x,z] where t is time and x,z are the perpendicular spatial coordinates
+    #
+    # Keywords:
+    #
+    #           type='peak' -> Calculate velocity of the peak density
+    #           type='COM' -> Calculate centre of mass velocity
+    #           Index=True -> return indices used to create velocity
+    #
+    # Default: Peak velocity with no index returning
+
+    size = n.shape
+
+    try:
+        v_type = kwargs["type"]
+    except:
+        v_type = "peak"  # Default to peak velocity calculation
+    try:
+        return_index = kwargs["Index"]
+    except:
+        return_index = False  # Default to no index returning
+
+    if v_type == "peak":
+        x = np.zeros(size[0])
+        z = np.zeros(size[0])
+        for i in np.arange(size[0]):
+            nmax, nmin = np.amax((n[i, :, :])), np.amin((n[i, :, :]))
+            xpos, zpos = np.where(n[i, :, :] == nmax)
+            x[i] = xpos[0]
+            z[i] = zpos[0]
+
+    if v_type == "COM":
+        x = np.zeros(size[0])
+        z = np.zeros(size[0])
+        for i in np.arange(size[0]):
+            data = n[i, :, :] - n[0, 0, 0]  # use corner cell rather than nmin
+            ntot = np.sum(data[:, :])
+
+            z[i] = old_div(
+                np.sum(np.sum(data[:, :], axis=0) * (np.arange(size[2]))), ntot
+            )
+            x[i] = old_div(
+                np.sum(np.sum(data[:, :], axis=1) * (np.arange(size[1]))), ntot
+            )
+
+    vx = Calc.deriv(x)
+    vz = Calc.deriv(z)
+
+    if return_index:
+        return vx, vz, x, z
+    else:
+        return vx, vz
+
+
+data = "data"
 
 if True:
-        import sys
-        if len(sys.argv) > 1:
-                data=sys.argv[1]
+    import sys
+
+    if len(sys.argv) > 1:
+        data = sys.argv[1]
 
-n = collect('n', path=data, info=False)
+n = collect("n", path=data, info=False)
 
 
-vx,vy,xx,yy = blob_velocity(n[:,:,0,:],type='COM',Index=True)
+vx, vy, xx, yy = blob_velocity(n[:, :, 0, :], type="COM", Index=True)
 
-f = open('Velocity.dat','wb')
-pickle.dump(vx,f)
+f = open("Velocity.dat", "wb")
+pickle.dump(vx, f)
 f.close()
 
-f = open('Position.dat','wb')
-pickle.dump(xx,f)
+f = open("Position.dat", "wb")
+pickle.dump(xx, f)
 f.close()
 
 
-f = open('Velocity.dat','rb')
+f = open("Velocity.dat", "rb")
 vx = pickle.load(f)
 f.close()
 
 try:
-        import matplotlib.pyplot as plt
-        plt.plot(vx)
-        plt.show()
+    import matplotlib.pyplot as plt
+
+    plt.plot(vx)
+    plt.show()
 except ImportError:
-        pass
+    pass
diff --git a/examples/boutpp/simulation.py b/examples/boutpp/simulation.py
index 1b57ff8b33..9948bd9b03 100755
--- a/examples/boutpp/simulation.py
+++ b/examples/boutpp/simulation.py
@@ -3,12 +3,13 @@
 
 bc.init("mesh:n=48")
 
+
 class Model(bc.PhysicsModel):
-    def init(self,restart):
+    def init(self, restart):
         self.dens = bc.create3D("sin(x)")
         self.solve_for(n=self.dens)
 
-    def rhs(self,time):
+    def rhs(self, time):
         self.dens.ddt(bc.DDX(self.dens))
 
 
diff --git a/examples/conduction-snb/fit_temperature.py b/examples/conduction-snb/fit_temperature.py
index 1e7f3ddf94..81faa9cf93 100644
--- a/examples/conduction-snb/fit_temperature.py
+++ b/examples/conduction-snb/fit_temperature.py
@@ -3,23 +3,31 @@
 import matplotlib.pyplot as plt
 
 Te_ref = np.loadtxt("temperature.csv", delimiter=",")
-Te_ref[:,0] *= 1e-4 # Convert X axis to m
+Te_ref[:, 0] *= 1e-4  # Convert X axis to m
+
 
 def te_function(ypos, mid, wwid, w0, w1, w2, Tmax, Tmin, clip=False):
-    width = w0 + ((ypos - mid)*w1 + (ypos - mid)**2 * w2) * np.exp(-((ypos - mid)/wwid)**2)
+    width = w0 + ((ypos - mid) * w1 + (ypos - mid) ** 2 * w2) * np.exp(
+        -(((ypos - mid) / wwid) ** 2)
+    )
 
     if clip:
         width = np.clip(width, 1e-10, None)
 
-    return Tmax - 0.5 * (1 + np.tanh((ypos - mid)/width)) * (Tmax - Tmin)
+    return Tmax - 0.5 * (1 + np.tanh((ypos - mid) / width)) * (Tmax - Tmin)
+
 
-popt, pcov = optimize.curve_fit(te_function, Te_ref[:,0], Te_ref[:,1],
-                                p0 = [2.2e-4, 1e-4, 1e-4, 0.0, 0.0, 0.960, 0.190])
+popt, pcov = optimize.curve_fit(
+    te_function,
+    Te_ref[:, 0],
+    Te_ref[:, 1],
+    p0=[2.2e-4, 1e-4, 1e-4, 0.0, 0.0, 0.960, 0.190],
+)
 
 print(popt)
 
-xfit = np.linspace(Te_ref[0,0], Te_ref[-1,0], 100)
+xfit = np.linspace(Te_ref[0, 0], Te_ref[-1, 0], 100)
 
-plt.plot(xfit, te_function(xfit, *popt, clip=True), '-k')
-plt.plot(Te_ref[:,0], Te_ref[:,1], 'or')
+plt.plot(xfit, te_function(xfit, *popt, clip=True), "-k")
+plt.plot(Te_ref[:, 0], Te_ref[:, 1], "or")
 plt.show()
diff --git a/examples/conduction-snb/sinusoid.py b/examples/conduction-snb/sinusoid.py
index 10c81923a3..439530383e 100644
--- a/examples/conduction-snb/sinusoid.py
+++ b/examples/conduction-snb/sinusoid.py
@@ -11,7 +11,7 @@
 build_and_log("Sinusoidal SNB")
 
 # Electron temperature in eV
-Telist = 10 ** np.linspace(0,3,20)
+Telist = 10 ** np.linspace(0, 3, 20)
 
 # Electron density in m^-3
 Ne = 1e20
@@ -19,29 +19,30 @@
 # Length of the domain in m
 length = 1.0
 
-c   = 299792458
-mu0 = 4.e-7*np.pi
-e0  = 1/(c*c*mu0)
+c = 299792458
+mu0 = 4.0e-7 * np.pi
+e0 = 1 / (c * c * mu0)
 qe = 1.602176634e-19
 me = 9.10938356e-31
 
-thermal_speed = np.sqrt(2.*qe  * Telist / me)
-Y = (qe**2 / (e0 * me))**2 / (4 * np.pi)
+thermal_speed = np.sqrt(2.0 * qe * Telist / me)
+Y = (qe**2 / (e0 * me)) ** 2 / (4 * np.pi)
 coulomb_log = 6.6 - 0.5 * np.log(Ne * 1e-20) + 1.5 * np.log(Telist)
-lambda_ee_T = thermal_speed**4 / (Y * Ne  * coulomb_log)
+lambda_ee_T = thermal_speed**4 / (Y * Ne * coulomb_log)
 
 beta_max_list = [5, 10, 20, 40]
-colors = ['k','b','g','r']
+colors = ["k", "b", "g", "r"]
 
 ngroups_list = [20, 40, 80]
-syms = ['x', 'o', 'D']
+syms = ["x", "o", "D"]
 
 for beta_max, color in zip(beta_max_list, colors):
     for ngroups, sym in zip(ngroups_list, syms):
-
         flux_ratio = []
         for Te in Telist:
-            cmd = "./conduction-snb \"Te={0}+0.01*sin(y)\" Ne={1} mesh:length={2} snb:beta_max={3} snb:ngroups={4}".format(Te, Ne, length, beta_max, ngroups)
+            cmd = './conduction-snb "Te={0}+0.01*sin(y)" Ne={1} mesh:length={2} snb:beta_max={3} snb:ngroups={4}'.format(
+                Te, Ne, length, beta_max, ngroups
+            )
 
             # Run the case
             s, out = launch_safe(cmd, nproc=1, mthread=1, pipe=True)
@@ -54,7 +55,12 @@
 
             flux_ratio.append(div_q[ind] / div_q_SH[ind])
 
-        plt.plot(lambda_ee_T / length, flux_ratio, '-'+sym+color, label=r"$\beta_{{max}}={0}, N_g={1}$".format(beta_max,ngroups))
+        plt.plot(
+            lambda_ee_T / length,
+            flux_ratio,
+            "-" + sym + color,
+            label=r"$\beta_{{max}}={0}, N_g={1}$".format(beta_max, ngroups),
+        )
 
 plt.legend()
 plt.xlabel(r"$\lambda_{ee,T} / L$")
diff --git a/examples/conduction-snb/step.py b/examples/conduction-snb/step.py
index 1f8933e66b..63a13149f4 100644
--- a/examples/conduction-snb/step.py
+++ b/examples/conduction-snb/step.py
@@ -3,7 +3,7 @@
 #
 # Uses a step in the temperature, intended for comparison to VFP results
 
-length = 6e-4 # Domain length in m
+length = 6e-4  # Domain length in m
 
 qe = 1.602176634e-19
 
@@ -40,37 +40,37 @@
 
 # Read reference values
 Te_ref = np.loadtxt("temperature.csv", delimiter=",")
-Te_ref[:,0] *= 1e-4 # Convert X axis to m
+Te_ref[:, 0] *= 1e-4  # Convert X axis to m
 
 SH_ref = np.loadtxt("spitzer-harm.csv", delimiter=",")
-SH_ref[:,0] *= 1e-4
+SH_ref[:, 0] *= 1e-4
 
 SNB_ref = np.loadtxt("snb.csv", delimiter=",")
-SNB_ref[:,0] *= 1e-4
+SNB_ref[:, 0] *= 1e-4
 
 VFP_ref = np.loadtxt("vfp.csv", delimiter=",")
-VFP_ref[:,0] *= 1e-4
+VFP_ref[:, 0] *= 1e-4
 
 #########################################
 
 fig, ax1 = plt.subplots()
 
-color='tab:red'
+color = "tab:red"
 ax1.plot(position, Te * 1e-3, color=color, label="Te")
-ax1.plot(Te_ref[:,0], Te_ref[:,1], color=color, marker="o", label="Reference Te")
+ax1.plot(Te_ref[:, 0], Te_ref[:, 1], color=color, marker="o", label="Reference Te")
 ax1.set_xlabel("position [m]")
 ax1.set_ylabel("Electron temperature [keV]", color=color)
-ax1.set_ylim(0,1)
-ax1.tick_params(axis='y', colors=color)
+ax1.set_ylim(0, 1)
+ax1.tick_params(axis="y", colors=color)
 
 ax2 = ax1.twinx()
-ax2.plot(position, q_SH * 1e-4, '-k', label="Spitzer-Harm")
-ax2.plot(SH_ref[:,0], SH_ref[:,1], '--k', label="Reference SH")
+ax2.plot(position, q_SH * 1e-4, "-k", label="Spitzer-Harm")
+ax2.plot(SH_ref[:, 0], SH_ref[:, 1], "--k", label="Reference SH")
 
-ax2.plot(position, q * 1e-4, '-b', label="SNB")
-ax2.plot(SNB_ref[:,0], SNB_ref[:,1], '--b', label="Reference SNB")
+ax2.plot(position, q * 1e-4, "-b", label="SNB")
+ax2.plot(SNB_ref[:, 0], SNB_ref[:, 1], "--b", label="Reference SNB")
 
-ax2.plot(VFP_ref[:,0], VFP_ref[:,1], '--g', label="Reference VFP")
+ax2.plot(VFP_ref[:, 0], VFP_ref[:, 1], "--g", label="Reference VFP")
 
 ax2.set_ylabel("Heat flux W/cm^2")
 ax2.set_ylim(bottom=0.0)
@@ -78,8 +78,7 @@
 plt.legend()
 fig.tight_layout()
 
-plt.xlim(0,3.5e-4)
+plt.xlim(0, 3.5e-4)
 
 plt.savefig("snb-step.png")
 plt.show()
-
diff --git a/examples/conduction/generate.py b/examples/conduction/generate.py
index 7138026898..4a2a2acfc0 100755
--- a/examples/conduction/generate.py
+++ b/examples/conduction/generate.py
@@ -4,9 +4,9 @@
 # Generate an input mesh
 #
 
-from boututils.datafile import DataFile # Wrapper around NetCDF4 libraries
+from boututils.datafile import DataFile  # Wrapper around NetCDF4 libraries
 
-nx = 5   # Minimum is 5: 2 boundary, one evolved
+nx = 5  # Minimum is 5: 2 boundary, one evolved
 ny = 64  # Minimum 5. Should be divisible by number of processors (so powers of 2 nice)
 
 f = DataFile()
diff --git a/examples/eigen-box/eigenvals.py b/examples/eigen-box/eigenvals.py
index 7b52fc60f2..5a71aabfc6 100755
--- a/examples/eigen-box/eigenvals.py
+++ b/examples/eigen-box/eigenvals.py
@@ -27,7 +27,8 @@ def plot_eigenvals(eigenvalues, eigenvectors=None):
             raise ValueError("Expecting eigenvectors to be 2D")
         if eigenvectors.shape[0] != len(eigenvalues):
             raise ValueError(
-                "First dimension of eigenvectors must match length of eigenvalues")
+                "First dimension of eigenvectors must match length of eigenvalues"
+            )
 
     # If no eigenvectors supplied, only plot eigenvalues, otherwise
     # eigenvalues and eigenvectors
@@ -44,18 +45,18 @@ def plot_eigenvals(eigenvalues, eigenvectors=None):
     range_r = amax(eigs_r) - amin(eigs_r)
     range_i = amax(eigs_i) - amin(eigs_i)
 
-    ax[0].plot(eigs_r, eigs_i, 'x')
+    ax[0].plot(eigs_r, eigs_i, "x")
     ax[0].set_xlabel("Real component")
     ax[0].set_ylabel("Imaginary component")
     ax[0].set_title("Eigenvalue")
 
-    overplot, = ax[0].plot([], [], 'ok')
+    (overplot,) = ax[0].plot([], [], "ok")
 
     if eigenvectors is not None:
         # Add a eigenvectors plot
-        vector_r, = ax[1].plot([], [], '-k', label="Real")
-        vector_i, = ax[1].plot([], [], '-r', label="Imag")
-        ax[1].legend(loc='upper right')
+        (vector_r,) = ax[1].plot([], [], "-k", label="Real")
+        (vector_i,) = ax[1].plot([], [], "-r", label="Imag")
+        ax[1].legend(loc="upper right")
         ax[1].set_xlabel("X")
         ax[1].set_ylabel("Amplitude")
         ax[1].set_title("Eigenvector")
@@ -68,33 +69,33 @@ def onclick(event):
 
         # Find closest eigenvectors point, but stretch axes so
         # real and imaginary components are weighted equally
-        if(range_r == 0):
-            dist = ((eigs_i - event.ydata)/range_i)**2
-        elif(range_i == 0):
-            dist = ((eigs_r - event.xdata)/range_r)**2
+        if range_r == 0:
+            dist = ((eigs_i - event.ydata) / range_i) ** 2
+        elif range_i == 0:
+            dist = ((eigs_r - event.xdata) / range_r) ** 2
         else:
-            dist = ((eigs_r - event.xdata)/range_r)**2 + \
-                ((eigs_i - event.ydata)/range_i)**2
+            dist = ((eigs_r - event.xdata) / range_r) ** 2 + (
+                (eigs_i - event.ydata) / range_i
+            ) ** 2
 
         ind = argmin(dist)
 
         # Update the highlight plot
         overplot.set_data([eigs_r[ind]], [eigs_i[ind]])
 
-        print("Eigenvalue number: %d (%e,%e)" %
-              (ind, eigs_r[ind], eigs_i[ind]))
+        print("Eigenvalue number: %d (%e,%e)" % (ind, eigs_r[ind], eigs_i[ind]))
 
         if eigenvectors is not None:
             # Update plots
             nx = eigenvectors.shape[1]
-            vector_r.set_data(arange(nx), eigenvectors[2*ind, :])
-            vector_i.set_data(arange(nx), eigenvectors[2*ind+1, :])
+            vector_r.set_data(arange(nx), eigenvectors[2 * ind, :])
+            vector_i.set_data(arange(nx), eigenvectors[2 * ind + 1, :])
             ax[1].relim()
             ax[1].autoscale_view()
 
         fig.canvas.draw()
 
-    fig.canvas.mpl_connect('button_press_event', onclick)
+    fig.canvas.mpl_connect("button_press_event", onclick)
     plt.show()
 
 
diff --git a/examples/elm-pb/Python/2dprofile.py b/examples/elm-pb/Python/2dprofile.py
index 5bb01972f9..e95709ab5b 100644
--- a/examples/elm-pb/Python/2dprofile.py
+++ b/examples/elm-pb/Python/2dprofile.py
@@ -4,81 +4,92 @@
 import numpy as np
 import matplotlib.pyplot as plt
 from boututils.datafile import DataFile
-from matplotlib.ticker import FixedFormatter, FormatStrFormatter, AutoLocator, AutoMinorLocator
+from matplotlib.ticker import (
+    FixedFormatter,
+    FormatStrFormatter,
+    AutoLocator,
+    AutoMinorLocator,
+)
 
 with DataFile("./cbm18_dens8.grid_nx68ny64.nc") as f:
     g = {v: f.read(v) for v in f.keys()}
 
-majorLocator   = AutoLocator()
-majorFormatter = FormatStrFormatter('%3.0e')
-minorLocator   = AutoMinorLocator()
-Fm = FixedFormatter(['0','$1 \\times 10^4$','$2 \\times  10^4$','$3 \\times 10^4$','$4 \\times 10^4$'])
-Fm2 = FixedFormatter(['0','$2 \\times 10^5$','$4 \\times  10^5$','$6 \\times 10^5$'])
-
-bxy=g.get('Bxy')
-p=g.get('pressure')
-jpar0=g.get('Jpar0')
-psixy=g.get('psixy')
-btxy=g.get('Btxy')
-shiftangle=g.get('ShiftAngle')
-
-nx=g.get('nx')
-ny=g.get('ny')
+majorLocator = AutoLocator()
+majorFormatter = FormatStrFormatter("%3.0e")
+minorLocator = AutoMinorLocator()
+Fm = FixedFormatter(
+    [
+        "0",
+        "$1 \\times 10^4$",
+        "$2 \\times  10^4$",
+        "$3 \\times 10^4$",
+        "$4 \\times 10^4$",
+    ]
+)
+Fm2 = FixedFormatter(["0", "$2 \\times 10^5$", "$4 \\times  10^5$", "$6 \\times 10^5$"])
+
+bxy = g.get("Bxy")
+p = g.get("pressure")
+jpar0 = g.get("Jpar0")
+psixy = g.get("psixy")
+btxy = g.get("Btxy")
+shiftangle = g.get("ShiftAngle")
+
+nx = g.get("nx")
+ny = g.get("ny")
 
 q = np.zeros((nx, ny))
 for i in range(ny):
-    q[:,i] = old_div(- shiftangle, (2 * np.pi))
-
-
+    q[:, i] = old_div(-shiftangle, (2 * np.pi))
 
 
-xarr = psixy[:,0]
+xarr = psixy[:, 0]
 xarr = old_div((xarr + 0.854856), (0.854856 + 0.0760856))
 
 
-fig=plt.figure()
-plt.plot(xarr,q[:,32])
-plt.xlabel('normalized $\psi$', fontsize=25)
-plt.ylabel('$q$',rotation='horizontal',fontsize=25)
+fig = plt.figure()
+plt.plot(xarr, q[:, 32])
+plt.xlabel("normalized $\psi$", fontsize=25)
+plt.ylabel("$q$", rotation="horizontal", fontsize=25)
 
 fig.set_tight_layout(True)
 
 fig, ax1 = plt.subplots()
 
-ax1.plot(xarr, p[:,32], 'r-', markevery=1, linewidth=3)
-ax1.set_xlabel('normalized $\psi$',fontsize=25)
+ax1.plot(xarr, p[:, 32], "r-", markevery=1, linewidth=3)
+ax1.set_xlabel("normalized $\psi$", fontsize=25)
 # Make the y-axis label and tick labels match the line color.
-ax1.set_ylabel('Pressure [Pa]', color='k',fontsize=25)
+ax1.set_ylabel("Pressure [Pa]", color="k", fontsize=25)
 
-#set y limit
-ax1.set_ylim(0,40000,10000)
+# set y limit
+ax1.set_ylim(0, 40000, 10000)
 
-#define ticks#
+# define ticks#
 ax1.yaxis.set_ticks(np.arange(0, 40000, 10000))
-#ax1.yaxis.set_major_locator(majorLocator)
-#ax1.yaxis.set_major_formatter(majorFormatter)
+# ax1.yaxis.set_major_locator(majorLocator)
+# ax1.yaxis.set_major_formatter(majorFormatter)
 ax1.yaxis.set_major_formatter(Fm)
 
-#for the minor ticks, use no labels; default NullFormatter
+# for the minor ticks, use no labels; default NullFormatter
 ax1.xaxis.set_minor_locator(AutoMinorLocator())
 ax1.yaxis.set_minor_locator(AutoMinorLocator(10))
 
-#format tick labels
+# format tick labels
 for tl in ax1.get_yticklabels():
-    tl.set_color('k')
+    tl.set_color("k")
 
 
 ax2 = ax1.twinx()
 
 s2 = -jpar0
 
-ax2.plot(xarr, s2[:,32], 'r-',markevery=1,linewidth=3)
-ax2.set_ylabel('$J_\parallel  [A/m^2]$', color='k',fontsize=25)
-ax2.set_ylim(0,600000)
+ax2.plot(xarr, s2[:, 32], "r-", markevery=1, linewidth=3)
+ax2.set_ylabel("$J_\parallel  [A/m^2]$", color="k", fontsize=25)
+ax2.set_ylim(0, 600000)
 ax2.yaxis.set_ticks(np.arange(0, 600000, 200000))
 ax2.yaxis.set_major_formatter(Fm2)
 for tl in ax2.get_yticklabels():
-    tl.set_color('k')
+    tl.set_color("k")
 
 
 fig.set_tight_layout(True)
@@ -86,4 +97,4 @@
 plt.show()
 
 
-#plt.savefig('2d.png', transparent=True)
+# plt.savefig('2d.png', transparent=True)
diff --git a/examples/elm-pb/Python/analysis.py b/examples/elm-pb/Python/analysis.py
index 4faf85f8ce..0e4a3acfdd 100644
--- a/examples/elm-pb/Python/analysis.py
+++ b/examples/elm-pb/Python/analysis.py
@@ -6,24 +6,24 @@
 import pylab as plt
 from boutdata.collect import collect
 
-path='./data/'
-var=collect('P', path=path)
+path = "./data/"
+var = collect("P", path=path)
 
-dcvar=np.mean(var, axis=3)
-rmsvar=np.sqrt(np.mean(var**2,axis=3)-dcvar**2)
+dcvar = np.mean(var, axis=3)
+rmsvar = np.sqrt(np.mean(var**2, axis=3) - dcvar**2)
 
 plt.figure()
-plt.plot(rmsvar[:,34,32])
+plt.plot(rmsvar[:, 34, 32])
 plt.show(block=False)
-fvar=np.fft.rfft(var,axis=3)
+fvar = np.fft.rfft(var, axis=3)
 
 plt.figure()
-plt.plot(abs(fvar[:,34,32,1:10]))
+plt.plot(abs(fvar[:, 34, 32, 1:10]))
 plt.show(block=False)
 
 
 plt.figure()
-plt.semilogy(abs(fvar[:,34,32,1:7]))
+plt.semilogy(abs(fvar[:, 34, 32, 1:7]))
 plt.show(block=False)
 
 plt.show()
diff --git a/examples/elm-pb/Python/elm_size.py b/examples/elm-pb/Python/elm_size.py
index 0d5c105870..6ad2ed6a0d 100644
--- a/examples/elm-pb/Python/elm_size.py
+++ b/examples/elm-pb/Python/elm_size.py
@@ -4,87 +4,126 @@
 from past.utils import old_div
 import numpy as np
 
-def elm_size(dcp,p0,uedge,xmin=None,xmax=None,yind=None,Bbar=None):
-  
-    lis=[dcp,p0,uedge]
-    if np.size(lis) != 3 :
+
+def elm_size(dcp, p0, uedge, xmin=None, xmax=None, yind=None, Bbar=None):
+    lis = [dcp, p0, uedge]
+    if np.size(lis) != 3:
         print("lack of parameters")
         return 0
-    
 
-    if xmin == None : xmin=0
-    if xmax == None : xmax=327 
-    if yind == None : yind=63 # choose the poloidal location for 1D size
-    if Bbar == None : Bbar=1.992782  # the normalized magnetic field 
+    if xmin == None:
+        xmin = 0
+    if xmax == None:
+        xmax = 327
+    if yind == None:
+        yind = 63  # choose the poloidal location for 1D size
+    if Bbar == None:
+        Bbar = 1.992782  # the normalized magnetic field
 
-    mydcp=dcp
-    myp0=p0
-    g=uedge
+    mydcp = dcp
+    myp0 = p0
+    g = uedge
 
     PI = 3.1415926
-    MU0 = 4.0e-7*PI
+    MU0 = 4.0e-7 * PI
 
-    s=np.shape(mydcp)
+    s = np.shape(mydcp)
 
-    if np.ndim(mydcp) != 3 :
+    if np.ndim(mydcp) != 3:
         print("dcp should be 3D(t,x,y)")
- 
-
-    nt=s[0]
-    nx=s[1]
-    ny=s[2]
-
-    Dtheta=g['dy']     #using correct poloidal angle
-    psixy=g['psixy']
-    R=g['Rxy']
-    Bp=g['Bpxy']
-    hthe=g['hthe']
-
-    Dpsi=np.zeros((nx,ny))
-    Dpsi[0,:]=psixy[1,:]-psixy[0,:]
-    Dpsi[nx-1,:]=psixy[nx-1,:]-psixy[nx-2,:]
-    for i in range(1,nx-2):
-        Dpsi[i,:]=old_div((psixy[i+1,:]-psixy[i-1,:]),2)
-     
-
-    Ddcp1=np.zeros(nt)
-    Ddcp2=np.zeros(nt)
-    Ddcp3=np.zeros(nt)
-    Tp01=0.
-    Tp02=0.
-    Tp03=0.
-
-    for t in range(nt) :
-        Ddcp3[t]=2.0*PI*np.sum(mydcp[t,xmin:xmax,:]*hthe[xmin:xmax,:]*Dtheta[xmin:xmax,:]*Dpsi[xmin:xmax,:]/Bp[xmin:xmax,:])
-        Ddcp2[t]=np.sum(mydcp[t,xmin:xmax,:]*hthe[xmin:xmax,:]*Dtheta[xmin:xmax,:]*Dpsi[xmin:xmax,:]/(R[xmin:xmax,:]*Bp[xmin:xmax,:]))
-        Ddcp1[t]=np.sum(mydcp[t,xmin:xmax,yind]*Dpsi[xmin:xmax,yind]/(R[xmin:xmax,yind]*Bp[xmin:xmax,yind])) 
-    
-
-    Tp03=2.0*PI*np.sum(myp0[xmin:xmax,:]*hthe[xmin:xmax,:]*Dtheta[xmin:xmax,:]*Dpsi[xmin:xmax,:]/Bp[xmin:xmax,:])
-    Tp02=np.sum(myp0[xmin:xmax,:]*hthe[xmin:xmax,:]*Dtheta[xmin:xmax,:]*Dpsi[xmin:xmax,:]/(R[xmin:xmax,:]*Bp[xmin:xmax,:]))
-    Tp01=np.sum(myp0[xmin:xmax,yind]*Dpsi[xmin:xmax,yind]/(R[xmin:xmax,yind]*Bp[xmin:xmax,yind]))
-
-    s1=np.zeros(nt)
-    s2=np.zeros(nt)
-    s3=np.zeros(nt)
-    E_loss=np.zeros(nt)
-
-    s1=old_div(-Ddcp1,Tp01)   #1D elm size
-    s2=old_div(-Ddcp2,Tp02)   #2D elm size
-    s3=old_div(-Ddcp3,Tp03)   #3D elm size
-
-    E_loss=-Ddcp3*(0.5*Bbar*Bbar/MU0)    #energy loss, unit J
-    E_total=Tp03*(0.5*Bbar*Bbar/MU0)     #total energy, unit J
+
+    nt = s[0]
+    nx = s[1]
+    ny = s[2]
+
+    Dtheta = g["dy"]  # using correct poloidal angle
+    psixy = g["psixy"]
+    R = g["Rxy"]
+    Bp = g["Bpxy"]
+    hthe = g["hthe"]
+
+    Dpsi = np.zeros((nx, ny))
+    Dpsi[0, :] = psixy[1, :] - psixy[0, :]
+    Dpsi[nx - 1, :] = psixy[nx - 1, :] - psixy[nx - 2, :]
+    for i in range(1, nx - 2):
+        Dpsi[i, :] = old_div((psixy[i + 1, :] - psixy[i - 1, :]), 2)
+
+    Ddcp1 = np.zeros(nt)
+    Ddcp2 = np.zeros(nt)
+    Ddcp3 = np.zeros(nt)
+    Tp01 = 0.0
+    Tp02 = 0.0
+    Tp03 = 0.0
+
+    for t in range(nt):
+        Ddcp3[t] = (
+            2.0
+            * PI
+            * np.sum(
+                mydcp[t, xmin:xmax, :]
+                * hthe[xmin:xmax, :]
+                * Dtheta[xmin:xmax, :]
+                * Dpsi[xmin:xmax, :]
+                / Bp[xmin:xmax, :]
+            )
+        )
+        Ddcp2[t] = np.sum(
+            mydcp[t, xmin:xmax, :]
+            * hthe[xmin:xmax, :]
+            * Dtheta[xmin:xmax, :]
+            * Dpsi[xmin:xmax, :]
+            / (R[xmin:xmax, :] * Bp[xmin:xmax, :])
+        )
+        Ddcp1[t] = np.sum(
+            mydcp[t, xmin:xmax, yind]
+            * Dpsi[xmin:xmax, yind]
+            / (R[xmin:xmax, yind] * Bp[xmin:xmax, yind])
+        )
+
+    Tp03 = (
+        2.0
+        * PI
+        * np.sum(
+            myp0[xmin:xmax, :]
+            * hthe[xmin:xmax, :]
+            * Dtheta[xmin:xmax, :]
+            * Dpsi[xmin:xmax, :]
+            / Bp[xmin:xmax, :]
+        )
+    )
+    Tp02 = np.sum(
+        myp0[xmin:xmax, :]
+        * hthe[xmin:xmax, :]
+        * Dtheta[xmin:xmax, :]
+        * Dpsi[xmin:xmax, :]
+        / (R[xmin:xmax, :] * Bp[xmin:xmax, :])
+    )
+    Tp01 = np.sum(
+        myp0[xmin:xmax, yind]
+        * Dpsi[xmin:xmax, yind]
+        / (R[xmin:xmax, yind] * Bp[xmin:xmax, yind])
+    )
+
+    s1 = np.zeros(nt)
+    s2 = np.zeros(nt)
+    s3 = np.zeros(nt)
+    E_loss = np.zeros(nt)
+
+    s1 = old_div(-Ddcp1, Tp01)  # 1D elm size
+    s2 = old_div(-Ddcp2, Tp02)  # 2D elm size
+    s3 = old_div(-Ddcp3, Tp03)  # 3D elm size
+
+    E_loss = -Ddcp3 * (0.5 * Bbar * Bbar / MU0)  # energy loss, unit J
+    E_total = Tp03 * (0.5 * Bbar * Bbar / MU0)  # total energy, unit J
 
     class ELM:
         pass
-    elmsize=ELM()
-    elmsize.s1=s1
-    elmsize.s2=s2
-    elmsize.s3=s3
-    elmsize.E_loss=E_loss
-    elmsize.E_total=E_total
+
+    elmsize = ELM()
+    elmsize.s1 = s1
+    elmsize.s2 = s2
+    elmsize.s3 = s3
+    elmsize.E_loss = E_loss
+    elmsize.E_total = E_total
 
     return elmsize
-  
-    
diff --git a/examples/elm-pb/Python/fftall.py b/examples/elm-pb/Python/fftall.py
index e0a4385764..c6d5b87ded 100644
--- a/examples/elm-pb/Python/fftall.py
+++ b/examples/elm-pb/Python/fftall.py
@@ -2,8 +2,7 @@
 from numpy import *
 from scipy.io import readsav
 
-print('Calculating P..')
-a=transpose(readsav('phi.idl.dat')['phi'])
-fa=fft.fft(a,axis=2)
-save('fp',fa)
-
+print("Calculating P..")
+a = transpose(readsav("phi.idl.dat")["phi"])
+fa = fft.fft(a, axis=2)
+save("fp", fa)
diff --git a/examples/elm-pb/Python/fftall2.py b/examples/elm-pb/Python/fftall2.py
index d864f356d0..64b08c437a 100644
--- a/examples/elm-pb/Python/fftall2.py
+++ b/examples/elm-pb/Python/fftall2.py
@@ -2,9 +2,9 @@
 from numpy import *
 from boutdata.collect import collect
 
-path='./data/'
-data=collect('P',path=path)
+path = "./data/"
+data = collect("P", path=path)
 
-print('Saving P..')
-fa=fft.fft(data,axis=3)
-save('fp',rollaxis(fa,0,4))
+print("Saving P..")
+fa = fft.fft(data, axis=3)
+save("fp", rollaxis(fa, 0, 4))
diff --git a/examples/elm-pb/Python/grate.py b/examples/elm-pb/Python/grate.py
index 003f38ff8e..65d6da6449 100644
--- a/examples/elm-pb/Python/grate.py
+++ b/examples/elm-pb/Python/grate.py
@@ -8,12 +8,11 @@
 from boututils.moment_xyzt import moment_xyzt
 
 
+path = "./data/"
 
-path='./data/'
 
+p = collect("P", path=path)
+rmsp_f = moment_xyzt(p[:, 34:35, 32:33, :], "RMS").rms
 
-p=collect('P',path=path)
-rmsp_f=moment_xyzt(p[:,34:35,32:33,:], 'RMS').rms
 
-
-print(np.gradient(np.log(rmsp_f[:,0,0]))[-1])
+print(np.gradient(np.log(rmsp_f[:, 0, 0]))[-1])
diff --git a/examples/elm-pb/Python/grate2.py b/examples/elm-pb/Python/grate2.py
index f8172bcf08..af0768803a 100644
--- a/examples/elm-pb/Python/grate2.py
+++ b/examples/elm-pb/Python/grate2.py
@@ -2,6 +2,7 @@
 from __future__ import division
 from builtins import range
 from past.utils import old_div
+
 ###
 # computes average growth rate for all points at the final timestep
 # computes average growth rate for points in the mead plane at the final timestep
@@ -10,40 +11,44 @@
 from boutdata.collect import collect
 from boututils.moment_xyzt import moment_xyzt
 
-path='./data/'
+path = "./data/"
+
+p = collect("P", path=path)
 
-p=collect('P',path=path)
+nmpy = old_div(p.shape[2], 2)  # define mead plane
 
-nmpy=old_div(p.shape[2],2)  # define mead plane
+ik = 50  # disregard the first ik timesteps
 
-ik = 50 # disregard the first ik timesteps
 
 def gr(p):
-        rmsp_f=moment_xyzt(p, 'RMS').rms
+    rmsp_f = moment_xyzt(p, "RMS").rms
 
-        ni=np.shape(rmsp_f)[1]
-        nj=np.shape(rmsp_f)[2]
+    ni = np.shape(rmsp_f)[1]
+    nj = np.shape(rmsp_f)[2]
 
-        growth=np.zeros((ni,nj))
+    growth = np.zeros((ni, nj))
 
-        for i in range(ni):
-                for j in range(nj):
-                         growth[i,j]=np.gradient(np.log(rmsp_f[ik::,i,j]))[-1]
+    for i in range(ni):
+        for j in range(nj):
+            growth[i, j] = np.gradient(np.log(rmsp_f[ik::, i, j]))[-1]
 
-        return growth
+    return growth
 
 
-growth=gr(p)
+growth = gr(p)
 
-d=np.ma.masked_array(growth,np.isnan(growth))
+d = np.ma.masked_array(growth, np.isnan(growth))
 
 # masked arrays
 # http://stackoverflow.com/questions/5480694/numpy-calculate-averages-with-nans-removed
 
-print('Total mean value = ', np.mean(np.ma.masked_array(d,np.isinf(d))))
-mm=np.ma.masked_array(growth[:,nmpy],np.isnan(growth[:,nmpy]))
-if np.isinf(np.mean(mm)) :
-    print('There is an Inf value in the mead plane')
-    print('Mean value of floating numbers in mead plane is = ', np.mean(np.ma.masked_array(mm,np.isinf(mm))))
+print("Total mean value = ", np.mean(np.ma.masked_array(d, np.isinf(d))))
+mm = np.ma.masked_array(growth[:, nmpy], np.isnan(growth[:, nmpy]))
+if np.isinf(np.mean(mm)):
+    print("There is an Inf value in the mead plane")
+    print(
+        "Mean value of floating numbers in mead plane is = ",
+        np.mean(np.ma.masked_array(mm, np.isinf(mm))),
+    )
 else:
-    print('Mean value in mead plane= ', np.mean(mm))
+    print("Mean value in mead plane= ", np.mean(mm))
diff --git a/examples/elm-pb/Python/plotcollapse.py b/examples/elm-pb/Python/plotcollapse.py
index ee64ca381f..f68e7b06aa 100755
--- a/examples/elm-pb/Python/plotcollapse.py
+++ b/examples/elm-pb/Python/plotcollapse.py
@@ -10,49 +10,52 @@
 import os
 from pathlib import Path
 
-#Dynamic matplotlib settings
+# Dynamic matplotlib settings
 from matplotlib import rcParams
-rcParams['font.size'] = 20.
-rcParams['legend.fontsize'] = 'small'
-rcParams['lines.linewidth'] = 2
 
-if not os.path.exists('image'):
-   os.makedirs('image')
+rcParams["font.size"] = 20.0
+rcParams["legend.fontsize"] = "small"
+rcParams["lines.linewidth"] = 2
+
+if not os.path.exists("image"):
+    os.makedirs("image")
 filename = Path(__file__).with_name("cbm18_dens8.grid_nx68ny64.nc")
 with DataFile(str(filename)) as f:
     g = {v: f.read(v) for v in f.keys()}
 
-psi = old_div((g['psixy'][:, 32] - g['psi_axis']), (g['psi_bndry'] - g['psi_axis']))
+psi = old_div((g["psixy"][:, 32] - g["psi_axis"]), (g["psi_bndry"] - g["psi_axis"]))
 
-path = './data'
+path = "./data"
 
 plt.figure()
 
-p0=collect('P0', path=path)
+p0 = collect("P0", path=path)
 
-p=collect('P', path=path)
-res = moment_xyzt(p,'RMS','DC')
+p = collect("P", path=path)
+res = moment_xyzt(p, "RMS", "DC")
 rmsp = res.rms
 dcp = res.dc
 nt = dcp.shape[0]
 
-plt.plot(psi, p0[:, 32], 'k--', label='t=0')
-plt.plot(psi, p0[:, 32] + dcp[nt//4, :, 32], 'r-', label='t='+np.str(nt//4))
-plt.plot(psi, p0[:, 32] + dcp[nt//2, :, 32], 'g-', label='t='+np.str(nt//2))
-plt.plot(psi, p0[:, 32] + dcp[3*nt//4, :, 32], 'b-', label='t='+np.str(3*nt//4))
-plt.plot(psi, p0[:, 32] + dcp[-1, :, 32], 'c-', label='t='+np.str(nt))
+plt.plot(psi, p0[:, 32], "k--", label="t=0")
+plt.plot(psi, p0[:, 32] + dcp[nt // 4, :, 32], "r-", label="t=" + np.str(nt // 4))
+plt.plot(psi, p0[:, 32] + dcp[nt // 2, :, 32], "g-", label="t=" + np.str(nt // 2))
+plt.plot(
+    psi, p0[:, 32] + dcp[3 * nt // 4, :, 32], "b-", label="t=" + np.str(3 * nt // 4)
+)
+plt.plot(psi, p0[:, 32] + dcp[-1, :, 32], "c-", label="t=" + np.str(nt))
 
 plt.legend()
-#plt.xlim(0.6, 1.0)
-plt.xlabel(r'Normalized poloidal flux ($\psi$)')
-plt.ylabel(r'$\langle p\rangle_\xi$')
-plt.title(r'Pressure')
+# plt.xlim(0.6, 1.0)
+plt.xlabel(r"Normalized poloidal flux ($\psi$)")
+plt.ylabel(r"$\langle p\rangle_\xi$")
+plt.title(r"Pressure")
 xmin, xmax = plt.xlim()
 ymin, ymax = plt.ylim()
 
 
-#plt.savefig('image/plotcollapse.png', bbox_inches='tight')
-#plt.savefig('image/plotcollapse.eps', bbox_inches='tight')
+# plt.savefig('image/plotcollapse.png', bbox_inches='tight')
+# plt.savefig('image/plotcollapse.eps', bbox_inches='tight')
 
 
 plt.tight_layout()
diff --git a/examples/elm-pb/Python/plotmode.py b/examples/elm-pb/Python/plotmode.py
index d89fdaf940..9325ee8764 100644
--- a/examples/elm-pb/Python/plotmode.py
+++ b/examples/elm-pb/Python/plotmode.py
@@ -4,60 +4,57 @@
 from builtins import range
 from past.utils import old_div
 
-from numpy import *;
-#from scipy.io import readsav;
-import matplotlib.pyplot as plt;
+from numpy import *
+
+# from scipy.io import readsav;
+import matplotlib.pyplot as plt
 
 # Dynamic matplotlib settings
-from matplotlib import rcParams;
-rcParams['font.size'] = 20;
-rcParams['legend.fontsize'] = 'small';
-rcParams['legend.labelspacing'] = 0.1;
-rcParams['lines.linewidth'] = 2;
-rcParams['savefig.bbox'] = 'tight';
+from matplotlib import rcParams
 
+rcParams["font.size"] = 20
+rcParams["legend.fontsize"] = "small"
+rcParams["legend.labelspacing"] = 0.1
+rcParams["lines.linewidth"] = 2
+rcParams["savefig.bbox"] = "tight"
 # Create image directory if not exists
-import os;
-if not os.path.exists('image'):
-   os.makedirs('image');
-
-#fphi = transpose(readsav('fphi.idl.dat')['fphi'])[:,:,:,];
-fphi = load('fp.npy')
-
-plt.figure();
-for i in range(1, 9):
-   print("Growth rate for mode number", i)
-   print(gradient(log(abs(fphi[34, 32, i, :]))))
-   plt.semilogy(((abs(fphi[34, 32, i, :]))), label = 'n=' + str(i * 5));
+import os
 
-plt.legend(loc=2);
-plt.xlabel('Time');
-plt.savefig('image/plotmode.png');
-plt.savefig('image/plotmode.eps');
+if not os.path.exists("image"):
+    os.makedirs("image")
 
+# fphi = transpose(readsav('fphi.idl.dat')['fphi'])[:,:,:,];
+fphi = load("fp.npy")
 
-plt.show(block=False);
-plt.figure();
+plt.figure()
 for i in range(1, 9):
-   plt.plot(abs(fphi[:, 32, i, -1]), label = 'n=' + str(i * 5));
-
-plt.legend();
-plt.xlabel('X index');
-
-plt.savefig('image/plotmodeamp.png');
-plt.savefig('image/plotmodeamp.eps');
-
-plt.show(block=False);
-
-plt.figure();
+    print("Growth rate for mode number", i)
+    print(gradient(log(abs(fphi[34, 32, i, :]))))
+    plt.semilogy((abs(fphi[34, 32, i, :])), label="n=" + str(i * 5))
+
+plt.legend(loc=2)
+plt.xlabel("Time")
+plt.savefig("image/plotmode.png")
+plt.savefig("image/plotmode.eps")
+plt.show(block=False)
+plt.figure()
 for i in range(1, 9):
-   plt.plot(old_div(abs(fphi[:, 32, i, -1]),abs(fphi[:, 32, i, -1]).max()), label = 'n=' + str(i * 5));
-
-plt.legend();
-plt.xlabel('X index');
-
-plt.savefig('image/plotmodenorm.png');
-plt.savefig('image/plotmodenorm.eps');
-
-plt.show();
-
+    plt.plot(abs(fphi[:, 32, i, -1]), label="n=" + str(i * 5))
+
+plt.legend()
+plt.xlabel("X index")
+plt.savefig("image/plotmodeamp.png")
+plt.savefig("image/plotmodeamp.eps")
+plt.show(block=False)
+plt.figure()
+for i in range(1, 9):
+    plt.plot(
+        old_div(abs(fphi[:, 32, i, -1]), abs(fphi[:, 32, i, -1]).max()),
+        label="n=" + str(i * 5),
+    )
+
+plt.legend()
+plt.xlabel("X index")
+plt.savefig("image/plotmodenorm.png")
+plt.savefig("image/plotmodenorm.eps")
+plt.show()
diff --git a/examples/elm-pb/Python/plotmode2.py b/examples/elm-pb/Python/plotmode2.py
index d0c63f32d9..c298a3a5ef 100644
--- a/examples/elm-pb/Python/plotmode2.py
+++ b/examples/elm-pb/Python/plotmode2.py
@@ -4,63 +4,61 @@
 from builtins import range
 from past.utils import old_div
 
-from numpy import *;
-#from scipy.io import readsav;
-import matplotlib.pyplot as plt;
+from numpy import *
+
+# from scipy.io import readsav;
+import matplotlib.pyplot as plt
 from boutdata.collect import collect
 
 # Dynamic matplotlib settings
-from matplotlib import rcParams;
-rcParams['font.size'] = 20;
-rcParams['legend.fontsize'] = 'small';
-rcParams['legend.labelspacing'] = 0.1;
-rcParams['lines.linewidth'] = 2;
-rcParams['savefig.bbox'] = 'tight';
+from matplotlib import rcParams
 
+rcParams["font.size"] = 20
+rcParams["legend.fontsize"] = "small"
+rcParams["legend.labelspacing"] = 0.1
+rcParams["lines.linewidth"] = 2
+rcParams["savefig.bbox"] = "tight"
 # Create image directory if not exists
-import os;
-if not os.path.exists('image'):
-   os.makedirs('image');
+import os
+
+if not os.path.exists("image"):
+    os.makedirs("image")
 
-path='./data/'
-data=collect('P',path=path)
+path = "./data/"
+data = collect("P", path=path)
 
-#fphi = transpose(readsav('fphi.idl.dat')['fphi'])[:,:,:,];
+# fphi = transpose(readsav('fphi.idl.dat')['fphi'])[:,:,:,];
 fphi = fft.fft(data, axis=3)
 
-plt.figure();
+plt.figure()
 for i in range(1, 9):
-   print("Growth rate for mode number", i)
-   print(gradient(log(abs(fphi[:,34, 32, i]))))
-   plt.semilogy(((abs(fphi[:,34, 32, i]))), label = 'n=' + str(i * 5));
-
-plt.legend(loc=2);
-plt.xlabel('Time');
-plt.savefig('image/plotmode.png');
-plt.savefig('image/plotmode.eps');
-
-
-plt.show(block=False);
-plt.figure();
+    print("Growth rate for mode number", i)
+    print(gradient(log(abs(fphi[:, 34, 32, i]))))
+    plt.semilogy((abs(fphi[:, 34, 32, i])), label="n=" + str(i * 5))
+
+plt.legend(loc=2)
+plt.xlabel("Time")
+plt.savefig("image/plotmode.png")
+plt.savefig("image/plotmode.eps")
+plt.show(block=False)
+plt.figure()
 for i in range(1, 9):
-   plt.plot(abs(fphi[-1, :, 32, i]), label = 'n=' + str(i * 5));
-
-plt.legend();
-plt.xlabel('X index');
-
-plt.savefig('image/plotmodeamp.png');
-plt.savefig('image/plotmodeamp.eps');
-
-plt.show(block=False);
-
-plt.figure();
+    plt.plot(abs(fphi[-1, :, 32, i]), label="n=" + str(i * 5))
+
+plt.legend()
+plt.xlabel("X index")
+plt.savefig("image/plotmodeamp.png")
+plt.savefig("image/plotmodeamp.eps")
+plt.show(block=False)
+plt.figure()
 for i in range(1, 9):
-   plt.plot(old_div(abs(fphi[-1, :, 32, i]),abs(fphi[-1, :, 32, i]).max()), label = 'n=' + str(i * 5));
-
-plt.legend();
-plt.xlabel('X index');
-
-plt.savefig('image/plotmodenorm.png');
-plt.savefig('image/plotmodenorm.eps');
-
-plt.show();
+    plt.plot(
+        old_div(abs(fphi[-1, :, 32, i]), abs(fphi[-1, :, 32, i]).max()),
+        label="n=" + str(i * 5),
+    )
+
+plt.legend()
+plt.xlabel("X index")
+plt.savefig("image/plotmodenorm.png")
+plt.savefig("image/plotmodenorm.eps")
+plt.show()
diff --git a/examples/elm-pb/Python/plotphase.py b/examples/elm-pb/Python/plotphase.py
index 9225e498ae..10f4279cf4 100755
--- a/examples/elm-pb/Python/plotphase.py
+++ b/examples/elm-pb/Python/plotphase.py
@@ -4,34 +4,33 @@
 from numpy import save, load, angle
 import matplotlib.pyplot as plt
 
-fphi = load('fphi.npy')
+fphi = load("fphi.npy")
 
-fte = load('fte.npy')
-phase_te = angle(old_div(fphi,fte))
-save('phase_te', phase_te)
+fte = load("fte.npy")
+phase_te = angle(old_div(fphi, fte))
+save("phase_te", phase_te)
 plt.figure()
-plt.plot(mean(mean(phase_te[:,:,3,:],axis=1),axis=1))
-plt.title('Te')
-plt.savefig('image/phase_te.png')
-plt.savefig('image/phase_te.eps')
+plt.plot(mean(mean(phase_te[:, :, 3, :], axis=1), axis=1))
+plt.title("Te")
+plt.savefig("image/phase_te.png")
+plt.savefig("image/phase_te.eps")
 
-fti = load('fti.npy')
-phase_ti = angle(old_div(fphi,fti))
-save('phase_ti', phase_ti)
+fti = load("fti.npy")
+phase_ti = angle(old_div(fphi, fti))
+save("phase_ti", phase_ti)
 plt.figure()
-plt.plot(mean(mean(phase_ti[:,:,3,:],axis=1),axis=1))
-plt.title('ti')
-plt.savefig('image/phase_ti.png')
-plt.savefig('image/phase_ti.eps')
+plt.plot(mean(mean(phase_ti[:, :, 3, :], axis=1), axis=1))
+plt.title("ti")
+plt.savefig("image/phase_ti.png")
+plt.savefig("image/phase_ti.eps")
 
-fni = load('fni.npy')
-phase_ni = angle(old_div(fphi,fni))
-save('phase_ni', phase_ni)
+fni = load("fni.npy")
+phase_ni = angle(old_div(fphi, fni))
+save("phase_ni", phase_ni)
 plt.figure()
-plt.plot(mean(mean(phase_ni[:,:,3,:],axis=1),axis=1))
-plt.title('ni')
-plt.savefig('image/phase_ni.png')
-plt.savefig('image/phase_ni.eps')
+plt.plot(mean(mean(phase_ni[:, :, 3, :], axis=1), axis=1))
+plt.title("ni")
+plt.savefig("image/phase_ni.png")
+plt.savefig("image/phase_ni.eps")
 
 plt.show()
-
diff --git a/examples/elm-pb/Python/polslice.py b/examples/elm-pb/Python/polslice.py
index fe78495b5a..6a1179b2ae 100644
--- a/examples/elm-pb/Python/polslice.py
+++ b/examples/elm-pb/Python/polslice.py
@@ -11,31 +11,33 @@
 # Specify parameters
 
 
-path='./data/'
+path = "./data/"
 
-variable="P"
+variable = "P"
 
 p = collect(variable, path=path)
 
-period=15
+period = 15
 
-grid='../cbm18_dens8.grid_nx68ny64.nc'
+grid = "../cbm18_dens8.grid_nx68ny64.nc"
 
 ########################################################
 # Call plotpolslice once to get extended poloidal grid
 
-r,z,fun=plotpolslice(p[0,:,:,:],grid,period=period,rz=1)
+r, z, fun = plotpolslice(p[0, :, :, :], grid, period=period, rz=1)
 
-nx=r.shape[0] # number of points in r
-ny=r.shape[1] # number of points in z
-nt=p.shape[0] # time intervals
+nx = r.shape[0]  # number of points in r
+ny = r.shape[1]  # number of points in z
+nt = p.shape[0]  # time intervals
 
 
-fm=np.zeros((nt,nx,ny)) # array to store the time sequence of the poloidal cross section
+fm = np.zeros(
+    (nt, nx, ny)
+)  # array to store the time sequence of the poloidal cross section
 
-#Compute all time frames
+# Compute all time frames
 
 for k in range(nt):
-    fm[k,:,:]=plotpolslice(p[k,:,:,:],grid,period=period,rz=0)
+    fm[k, :, :] = plotpolslice(p[k, :, :, :], grid, period=period, rz=0)
 
-np.savez('pslice',fm=fm, z=z, r=r)
+np.savez("pslice", fm=fm, z=z, r=r)
diff --git a/examples/elm-pb/Python/post.py b/examples/elm-pb/Python/post.py
index 9bb67347f0..cdaefa98cf 100644
--- a/examples/elm-pb/Python/post.py
+++ b/examples/elm-pb/Python/post.py
@@ -15,12 +15,12 @@
 from mayavi import mlab
 
 
-path0="./data0/"
-path1="./data/"
+path0 = "./data0/"
+path1 = "./data/"
 
-period=15
+period = 15
 
-gfile='./cbm18_dens8.grid_nx68ny64.nc'
+gfile = "./cbm18_dens8.grid_nx68ny64.nc"
 
 
 with DataFile(gfile) as f:
@@ -28,71 +28,115 @@
 
 
 Dphi0 = collect("Dphi0", path=path0)
-phi0 = collect("phi0", path=path1) # needs diamagnetic effects
+phi0 = collect("phi0", path=path1)  # needs diamagnetic effects
 #
-psixy=g.get('psixy')
-PSI_AXIS=g.get('psi_axis')
-PSI_BNDRY=g.get('psi_bndry')
+psixy = g.get("psixy")
+PSI_AXIS = g.get("psi_axis")
+PSI_BNDRY = g.get("psi_bndry")
 #
-psix=old_div((psixy[:,32]-PSI_AXIS),(PSI_BNDRY-PSI_AXIS))
-Epsi=-deriv(phi0[:,32],psix)
+psix = old_div((psixy[:, 32] - PSI_AXIS), (PSI_BNDRY - PSI_AXIS))
+Epsi = -deriv(phi0[:, 32], psix)
 #
 #
-fig=figure()
-plot(psix,-Dphi0[:,32], 'r', linewidth=5)
-plot(psix,Epsi,'k',linewidth=5)
-annotate('w/o flow', xy=(.3, .7),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', size=30)
-annotate('w/ flow', xy=(.7, .4),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', color='r', size=30)
-xlabel('Radial $\psi$',fontsize=25)
-ylabel('$\Omega(\psi)/\omega_A$',fontsize=25)
-ylim([-.05,0])
-xlim([0.4,1.2])
+fig = figure()
+plot(psix, -Dphi0[:, 32], "r", linewidth=5)
+plot(psix, Epsi, "k", linewidth=5)
+annotate(
+    "w/o flow",
+    xy=(0.3, 0.7),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    size=30,
+)
+annotate(
+    "w/ flow",
+    xy=(0.7, 0.4),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    color="r",
+    size=30,
+)
+xlabel("Radial $\psi$", fontsize=25)
+ylabel("$\Omega(\psi)/\omega_A$", fontsize=25)
+ylim([-0.05, 0])
+xlim([0.4, 1.2])
 fig.set_tight_layout(True)
 show(block=False)
 
 p_f0 = collect("P", path=path0)
 p_f = collect("P", path=path1)
 #
-rmsp_f0=moment_xyzt(p_f0, 'RMS').rms
-rmsp_f=moment_xyzt(p_f, 'RMS').rms
+rmsp_f0 = moment_xyzt(p_f0, "RMS").rms
+rmsp_f = moment_xyzt(p_f, "RMS").rms
 #
 
-fig=figure(figsize=(10, 8))
-plot(np.gradient(np.log(rmsp_f0[:,34,32])), color='k',linewidth=3)
-plot(np.gradient(np.log(rmsp_f[:,34,32])),color='red',linewidth=3)
-
-ylabel('$\gamma / \omega_A$',fontsize=25)
-xlabel('Time$(\\tau_A)$',fontsize=25)
-annotate('w/o flow', xy=(.5, .7),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', size=30)
-annotate('w/ flow', xy=(.5, .4),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', color='r', size=30)
-ylim([0,0.5])
-xlim([0,100])
+fig = figure(figsize=(10, 8))
+plot(np.gradient(np.log(rmsp_f0[:, 34, 32])), color="k", linewidth=3)
+plot(np.gradient(np.log(rmsp_f[:, 34, 32])), color="red", linewidth=3)
+
+ylabel("$\gamma / \omega_A$", fontsize=25)
+xlabel("Time$(\\tau_A)$", fontsize=25)
+annotate(
+    "w/o flow",
+    xy=(0.5, 0.7),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    size=30,
+)
+annotate(
+    "w/ flow",
+    xy=(0.5, 0.4),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    color="r",
+    size=30,
+)
+ylim([0, 0.5])
+xlim([0, 100])
 fig.set_tight_layout(True)
 show(block=False)
 
 
-
-plotpolslice(p_f0[50,:,:,:],gfile,period=period, fig=1)
-mlab.text(.01,.99,"w/o flow")
-
-plotpolslice(p_f[50,:,:,:],gfile,period=period, fig=1)
-mlab.text(.01,.99,"w/ flow")
-
-fig=figure()
-mode_structure(p_f0[50,:,:,:], g, period=period)
-plot([40,40],[0,.014],'k--',linewidth=5)
-annotate('w/o flow', xy=(.3, .7),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', size=30)
-ylim([0,0.014])
-xlim([0,80])
+plotpolslice(p_f0[50, :, :, :], gfile, period=period, fig=1)
+mlab.text(0.01, 0.99, "w/o flow")
+
+plotpolslice(p_f[50, :, :, :], gfile, period=period, fig=1)
+mlab.text(0.01, 0.99, "w/ flow")
+
+fig = figure()
+mode_structure(p_f0[50, :, :, :], g, period=period)
+plot([40, 40], [0, 0.014], "k--", linewidth=5)
+annotate(
+    "w/o flow",
+    xy=(0.3, 0.7),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    size=30,
+)
+ylim([0, 0.014])
+xlim([0, 80])
 fig.set_tight_layout(True)
 show(block=False)
 
 
 figure()
-mode_structure(p_f[50,:,:,:], g, period=period)
-plot([40,40],[0,.014],'k--',linewidth=5)
-annotate('w/ flow', xy=(.3, .7),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', color='k', size=30)
-ylim([0,0.0001])
-xlim([0,80])
+mode_structure(p_f[50, :, :, :], g, period=period)
+plot([40, 40], [0, 0.014], "k--", linewidth=5)
+annotate(
+    "w/ flow",
+    xy=(0.3, 0.7),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    color="k",
+    size=30,
+)
+ylim([0, 0.0001])
+xlim([0, 80])
 show(block=False)
 show()
diff --git a/examples/elm-pb/Python/read_elmsize.py b/examples/elm-pb/Python/read_elmsize.py
index fcd3d24e53..340f57ce7b 100644
--- a/examples/elm-pb/Python/read_elmsize.py
+++ b/examples/elm-pb/Python/read_elmsize.py
@@ -4,12 +4,12 @@
 from pylab import save, figure, plot, title, xlabel, ylabel, show, tight_layout
 from elm_size import elm_size
 
-path='./data'
+path = "./data"
 
-t_array=collect('t_array', path=path)
-save('t_array.dat', t_array)
-p0=collect('P0', path=path)
-save('p0.dat', p0)
+t_array = collect("t_array", path=path)
+save("t_array.dat", t_array)
+p0 = collect("P0", path=path)
+save("p0.dat", p0)
 
 
 # n0=collect('n0', path=path)
@@ -22,27 +22,27 @@
 with DataFile("./cbm18_dens8.grid_nx68ny64.nc") as f:
     gfile = {v: f.read(v) for v in f.keys()}
 
-p=collect('P', path=path)
-save('p.dat', p)
-res=moment_xyzt(p,'RMS','DC')
-rmsp=res.rms
-dcp=res.dc
-save('rmsp.dat', rmsp)
-save('dcp.dat',  dcp)
-elmsp=elm_size(dcp,p0,gfile,yind=32,Bbar=gfile['bmag'])
-save('elmsp.dat',  elmsp)
+p = collect("P", path=path)
+save("p.dat", p)
+res = moment_xyzt(p, "RMS", "DC")
+rmsp = res.rms
+dcp = res.dc
+save("rmsp.dat", rmsp)
+save("dcp.dat", dcp)
+elmsp = elm_size(dcp, p0, gfile, yind=32, Bbar=gfile["bmag"])
+save("elmsp.dat", elmsp)
 
 figure(0)
-plot(t_array,elmsp.s2, 'k-')
-xlabel('t/Ta')
-ylabel('Elm size')
-title('Elm size, P')
+plot(t_array, elmsp.s2, "k-")
+xlabel("t/Ta")
+ylabel("Elm size")
+title("Elm size, P")
 tight_layout()
 show()
 
 
-phi=collect('phi', path=path )
-save('phi.dat', phi)
-res=moment_xyzt( phi, 'DC', 'RMS')
-save('dcphi.dat',res.dc)
-save('rmsphi.dat', res.rms)
+phi = collect("phi", path=path)
+save("phi.dat", phi)
+res = moment_xyzt(phi, "DC", "RMS")
+save("dcphi.dat", res.dc)
+save("rmsphi.dat", res.rms)
diff --git a/examples/elm-pb/Python/showpolslice.py b/examples/elm-pb/Python/showpolslice.py
index d292575e35..072c53dcd6 100644
--- a/examples/elm-pb/Python/showpolslice.py
+++ b/examples/elm-pb/Python/showpolslice.py
@@ -6,10 +6,12 @@
 import numpy as np
 
 from tvtk.tools import visual
+
 try:
     from enthought.mayavi import mlab
 except ImportError:
-    try: from mayavi import mlab
+    try:
+        from mayavi import mlab
     except ImportError:
         print("No mlab available")
 
@@ -17,40 +19,42 @@
 ###########################
 # Read polslice array
 
-npzfile=np.load('pslice.npz')
-r=npzfile['r']
-z=npzfile['z']
-fm=npzfile['fm']
+npzfile = np.load("pslice.npz")
+r = npzfile["r"]
+z = npzfile["z"]
+fm = npzfile["fm"]
 
 ########################################################
 # Set up the window
 
-f = mlab.figure(size=(800,600))
+f = mlab.figure(size=(800, 600))
 # Tell visual to use this as the viewer.
 visual.set_viewer(f)
 
 ########################################################
 # Do the appropriate graph
 
-#s = mlab.contour_surf(r,z,fun, contours=30, line_width=.5, transparent=True)
-#s=mlab.surf(r,z,fun, colormap='Spectral')
-s = mlab.mesh(r,z,fm[0,:,:], scalars=fm[0,:,:], colormap='PuOr')#, wrap_scale='true')#, representation='wireframe')
-s.enable_contours=True
-s.contour.filled_contours=True
+# s = mlab.contour_surf(r,z,fun, contours=30, line_width=.5, transparent=True)
+# s=mlab.surf(r,z,fun, colormap='Spectral')
+s = mlab.mesh(
+    r, z, fm[0, :, :], scalars=fm[0, :, :], colormap="PuOr"
+)  # , wrap_scale='true')#, representation='wireframe')
+s.enable_contours = True
+s.contour.filled_contours = True
 
 # Define perspective and optional attributes. You can also implement from the window afterwards
 
-mlab.view(0,0)
-#mlab.view(-94.159958841373324,
+mlab.view(0, 0)
+# mlab.view(-94.159958841373324,
 # 53.777002382688906,
 # 8.2311808018087582)
 mlab.draw(f)
 mlab.colorbar(orientation="vertical")
-#mlab.axes()
-#mlab.outline()
+# mlab.axes()
+# mlab.outline()
 
 
 ########################################################
 # mlab animation
 
-anim(s,fm, save=True)
+anim(s, fm, save=True)
diff --git a/examples/elm-pb/Python/sprofiles.py b/examples/elm-pb/Python/sprofiles.py
index 9d8eea48de..244599f8af 100644
--- a/examples/elm-pb/Python/sprofiles.py
+++ b/examples/elm-pb/Python/sprofiles.py
@@ -16,45 +16,46 @@
 with DataFile(gfile) as f:
     g = {v: f.read(v) for v in f.keys()}
 
-var=collect("P", path=path)
+var = collect("P", path=path)
 
-sol=surface_average(var, g)
-#sol=np.mean(var,axis=3)
+sol = surface_average(var, g)
+# sol=np.mean(var,axis=3)
 
-p0av=collect("P0", path=path)
+p0av = collect("P0", path=path)
 
-q=np.zeros(sol.shape)
+q = np.zeros(sol.shape)
 
 for i in range(sol.shape[1]):
-    q[:,i]=sol[:,i]+p0av[:,0]
+    q[:, i] = sol[:, i] + p0av[:, 0]
 
 
-psixy=g.get('psixy')
-psi0=g.get('psi_axis')
-psix=g.get('psi_bndry')
+psixy = g.get("psixy")
+psi0 = g.get("psi_axis")
+psix = g.get("psi_bndry")
 
-xarr = psixy[:,0]
-xarr = old_div((xarr - psi0), (-psi0 + psix)) #for this grid
+xarr = psixy[:, 0]
+xarr = old_div((xarr - psi0), (-psi0 + psix))  # for this grid
 
 
-fig=figure()
+fig = figure()
 
-nt=q.shape[1]
+nt = q.shape[1]
 
-plot(xarr, p0av,'k',label='t=0')
-plot(xarr,q[:,nt/4],'r',label='t='+np.str(nt/4))
-plot(xarr,q[:,nt/2],'b',label='t='+np.str(nt/2))
-plot(xarr,q[:,3*nt/4],'g',label='t='+np.str(3*nt/4))
-plot(xarr, q[:,-1],'k',label='t='+np.str(nt))
+plot(xarr, p0av, "k", label="t=0")
+plot(xarr, q[:, nt / 4], "r", label="t=" + np.str(nt / 4))
+plot(xarr, q[:, nt / 2], "b", label="t=" + np.str(nt / 2))
+plot(xarr, q[:, 3 * nt / 4], "g", label="t=" + np.str(3 * nt / 4))
+plot(xarr, q[:, -1], "k", label="t=" + np.str(nt))
 
 from collections import OrderedDict
+
 handles, labels = gca().get_legend_handles_labels()
 by_label = OrderedDict(list(zip(labels, handles)))
 legend(list(by_label.values()), list(by_label.keys()))
 
 
-xlabel(r"$\psi$",fontsize=25)
-ylabel(r"$2 \mu_0 <P^2> / B^2$",fontsize=25)
+xlabel(r"$\psi$", fontsize=25)
+ylabel(r"$2 \mu_0 <P^2> / B^2$", fontsize=25)
 
 fig.set_tight_layout(True)
 
diff --git a/examples/elm-pb/runexample.py b/examples/elm-pb/runexample.py
index f7ebc01028..b49902d29c 100755
--- a/examples/elm-pb/runexample.py
+++ b/examples/elm-pb/runexample.py
@@ -28,18 +28,22 @@
 # Calculate RMS in toroidal direction
 prms = np.sqrt(np.mean(p**2, axis=3))
 
-growth = np.gradient(np.log(prms[:,42,32]))
+growth = np.gradient(np.log(prms[:, 42, 32]))
 
 # Final growth-rate
 gamma = growth[-2]
 
 import matplotlib.pyplot as plt
 
-plt.plot(tarr, prms[:,42,32], label='Outboard midplane')
-plt.plot( [tarr[0], tarr[-1]],
-	  [prms[-1,42,32]*np.exp(gamma*(tarr[0] - tarr[-1])), prms[-1,42,32]], '--', label=r'$\gamma =$'+str(gamma))
+plt.plot(tarr, prms[:, 42, 32], label="Outboard midplane")
+plt.plot(
+    [tarr[0], tarr[-1]],
+    [prms[-1, 42, 32] * np.exp(gamma * (tarr[0] - tarr[-1])), prms[-1, 42, 32]],
+    "--",
+    label=r"$\gamma =$" + str(gamma),
+)
 
-plt.yscale('log')
+plt.yscale("log")
 plt.grid()
 
 plt.xlabel(r"Time [$1/\tau_A$]")
@@ -57,19 +61,21 @@
 
 # Take a poloidal slice at fixed toroidal angle
 from boutdata.pol_slice import pol_slice
-p2d = pol_slice(p[-1,:,:,:], 'cbm18_dens8.grid_nx68ny64.nc', n=15, zangle=0.0)
+
+p2d = pol_slice(p[-1, :, :, :], "cbm18_dens8.grid_nx68ny64.nc", n=15, zangle=0.0)
 
 # Read grid file to get coordinates
 from boututils.datafile import DataFile
-g = DataFile('cbm18_dens8.grid_nx68ny64.nc')
 
-Rxy = g.read("Rxy") # Major radius [m]
-Zxy = g.read("Zxy") # Height [m]
+g = DataFile("cbm18_dens8.grid_nx68ny64.nc")
+
+Rxy = g.read("Rxy")  # Major radius [m]
+Zxy = g.read("Zxy")  # Height [m]
 
 plt.contourf(Rxy, Zxy, p2d, 30)
-plt.axis('equal')  # Maintain aspect ratio
+plt.axis("equal")  # Maintain aspect ratio
 
-plt.colorbar()   # Plot a bar down the side with a color scale
+plt.colorbar()  # Plot a bar down the side with a color scale
 
 plt.savefig("poloidal_slice.pdf")
 
diff --git a/examples/fci-wave/compare-density.py b/examples/fci-wave/compare-density.py
index c039c250b6..16e620a08f 100644
--- a/examples/fci-wave/compare-density.py
+++ b/examples/fci-wave/compare-density.py
@@ -1,4 +1,3 @@
-
 import matplotlib.pyplot as plt
 from boutdata import collect
 import numpy as np
@@ -9,60 +8,61 @@
 # Note: Data from fci-wave-logn examples commented out.
 
 data_noboundary = [
-    ("div", "Model 1 (density, point interpolation)")
-    ,("div-integrate", "Model 2 (density, area integration)")
-    ,("logn", "Model 3 (log density, area integration)")
-    #,("../fci-wave-logn/div-integrate", "Model 5 (velocity, log density, area integration)")
+    ("div", "Model 1 (density, point interpolation)"),
+    ("div-integrate", "Model 2 (density, area integration)"),
+    ("logn", "Model 3 (log density, area integration)"),
+    # ,("../fci-wave-logn/div-integrate", "Model 5 (velocity, log density, area integration)")
 ]
 
 data_boundary = [
-    ("boundary", "Model 2 (density, momentum)")
-    ,("boundary-logn", "Model 3 (log density, momentum)")
-    #,("../fci-wave-logn/boundary", "Model 5 (log density, velocity)")
-    ]
+    ("boundary", "Model 2 (density, momentum)"),
+    ("boundary-logn", "Model 3 (log density, momentum)"),
+    # ,("../fci-wave-logn/boundary", "Model 5 (log density, velocity)")
+]
 
 # Change this to select no boundary or boundary cases
 data = data_noboundary
 
 if run:
     from boututils.run_wrapper import shell_safe, launch_safe
+
     shell_safe("make > make.log")
 
-    for path,label in data:
-        launch_safe("./fci-wave -d "+path, nproc=nproc, pipe=False)
+    for path, label in data:
+        launch_safe("./fci-wave -d " + path, nproc=nproc, pipe=False)
 
-# Collect the results into a dictionary 
+# Collect the results into a dictionary
 sum_n_B = {}
 
-for path,label in data:
+for path, label in data:
     n = collect("n", path=path)
     Bxyz = collect("Bxyz", path=path)
 
     time = collect("t_array", path=path)
-    
+
     nt, nx, ny, nz = n.shape
-    
+
     n_B = np.ndarray(nt)
     for t in range(nt):
-        n_B[t] = np.sum(n[t,:,:,:] / Bxyz)
+        n_B[t] = np.sum(n[t, :, :, :] / Bxyz)
 
     sum_n_B[path] = (time, n_B)
 
     # Plot the density at the final time
-    
+
     plt.figure()
-    plt.contourf(n[-1,:,0,:].T, 100)
+    plt.contourf(n[-1, :, 0, :].T, 100)
     plt.colorbar()
     plt.xlabel("Major radius")
     plt.ylabel("Height")
-    plt.title("Density n, "+label)
-    plt.savefig(path+".pdf")
+    plt.title("Density n, " + label)
+    plt.savefig(path + ".pdf")
     plt.show()
 
 # Make a plot comparing total sum density / B
-    
+
 plt.figure()
-for path,label in data:
+for path, label in data:
     time, n_B = sum_n_B[path]
     plt.plot(time, n_B, label=label)
 plt.legend()
@@ -71,4 +71,3 @@
 plt.savefig("compare-density.pdf")
 
 plt.show()
-
diff --git a/examples/finite-volume/diffusion/mms.py b/examples/finite-volume/diffusion/mms.py
index 2c609ca82e..31b7714727 100644
--- a/examples/finite-volume/diffusion/mms.py
+++ b/examples/finite-volume/diffusion/mms.py
@@ -5,26 +5,26 @@
 from math import pi
 
 # Length of the y domain
-Ly = 10.
+Ly = 10.0
 
 # metric tensor
 metric = Metric()  # Identity
 
 # Define solution in terms of input x,y,z
 
-f = 1 + 0.1*sin(2*y - t)
-k = 1 + 0.1*sin(y)
+f = 1 + 0.1 * sin(2 * y - t)
+k = 1 + 0.1 * sin(y)
 
 # Turn solution into real x and z coordinates
-replace = [ (y, metric.y*2*pi/Ly) ]
+replace = [(y, metric.y * 2 * pi / Ly)]
 
 f = f.subs(replace)
-k = k.subs(replace) 
+k = k.subs(replace)
 
 ##############################
 # Calculate time derivatives
 
-dfdt = Div_par( k * Grad_par(f) )
+dfdt = Div_par(k * Grad_par(f))
 
 #############################
 # Calculate sources
@@ -32,7 +32,7 @@
 Sf = diff(f, t) - dfdt
 
 # Substitute back to get input y coordinates
-replace = [ (metric.y, y*Ly/(2*pi) ) ]
+replace = [(metric.y, y * Ly / (2 * pi))]
 
 k = k.subs(replace)
 f = f.subs(replace)
diff --git a/examples/finite-volume/fluid/mms.py b/examples/finite-volume/fluid/mms.py
index 8ed8fba517..a31782e2c7 100644
--- a/examples/finite-volume/fluid/mms.py
+++ b/examples/finite-volume/fluid/mms.py
@@ -5,19 +5,19 @@
 from math import pi
 
 # Length of the y domain
-Ly = 10.
+Ly = 10.0
 
 # metric tensor
 metric = Metric()  # Identity
 
 # Define solution in terms of input x,y,z
 
-n = 1 + 0.1*sin(2*y - t)
-p = 1 + 0.1*cos(3*y + t)
-nv = 0.1*sin(y + 2*t)
+n = 1 + 0.1 * sin(2 * y - t)
+p = 1 + 0.1 * cos(3 * y + t)
+nv = 0.1 * sin(y + 2 * t)
 
 # Turn solution into real x and z coordinates
-replace = [ (y, metric.y*2*pi/Ly) ]
+replace = [(y, metric.y * 2 * pi / Ly)]
 
 n = n.subs(replace)
 p = p.subs(replace)
@@ -27,16 +27,16 @@
 # Calculate time derivatives
 
 v = nv / n
-gamma = 5./3
+gamma = 5.0 / 3
 
 # Density equation
-dndt = - Div_par(nv)
+dndt = -Div_par(nv)
 
 # Pressure equation
-dpdt = - Div_par(p*v) - (gamma-1.0)*p*Div_par(v)
+dpdt = -Div_par(p * v) - (gamma - 1.0) * p * Div_par(v)
 
 # Momentum equation
-dnvdt = - Div_par(nv*v) - Grad_par(p)
+dnvdt = -Div_par(nv * v) - Grad_par(p)
 
 #############################
 # Calculate sources
@@ -46,7 +46,7 @@
 Snv = diff(nv, t) - dnvdt
 
 # Substitute back to get input y coordinates
-replace = [ (metric.y, y*Ly/(2*pi) ) ]
+replace = [(metric.y, y * Ly / (2 * pi))]
 
 n = n.subs(replace)
 p = p.subs(replace)
diff --git a/examples/laplace-petsc3d/plotcheck.py b/examples/laplace-petsc3d/plotcheck.py
index 707e5db1ee..7f2758dd81 100755
--- a/examples/laplace-petsc3d/plotcheck.py
+++ b/examples/laplace-petsc3d/plotcheck.py
@@ -10,27 +10,27 @@
 
 xg = 2
 
-f = collect('f', path=datadir)[xg:-xg, :, :]
-rhs = collect('rhs', path=datadir)[xg:-xg, :, :]
-rhs_check = collect('rhs_check', path=datadir)[xg:-xg, :, :]
-error = collect('error', path=datadir)[xg:-xg, :, :]
+f = collect("f", path=datadir)[xg:-xg, :, :]
+rhs = collect("rhs", path=datadir)[xg:-xg, :, :]
+rhs_check = collect("rhs_check", path=datadir)[xg:-xg, :, :]
+error = collect("error", path=datadir)[xg:-xg, :, :]
 
 pyplot.subplot(221)
 pyplot.pcolormesh(f[:, yind, :])
 pyplot.colorbar()
-pyplot.title('f')
+pyplot.title("f")
 pyplot.subplot(222)
 pyplot.pcolormesh(rhs[:, yind, :])
 pyplot.colorbar()
-pyplot.title('rhs')
+pyplot.title("rhs")
 pyplot.subplot(223)
 pyplot.pcolormesh(rhs_check[:, yind, :])
 pyplot.colorbar()
-pyplot.title('rhs_check')
+pyplot.title("rhs_check")
 pyplot.subplot(224)
 pyplot.pcolormesh(error[:, yind, :])
 pyplot.colorbar()
-pyplot.title('error')
+pyplot.title("error")
 
 pyplot.show()
 
diff --git a/examples/orszag-tang/generate.py b/examples/orszag-tang/generate.py
index 3ba6dbbea9..acce7497c3 100644
--- a/examples/orszag-tang/generate.py
+++ b/examples/orszag-tang/generate.py
@@ -2,14 +2,16 @@
 from __future__ import division
 from builtins import range
 from past.utils import old_div
+
 # the Scientific Python netCDF 3 interface
 # http://dirac.cnrs-orleans.fr/ScientificPython/
-#from Scientific.IO.NetCDF import NetCDFFile as Dataset
+# from Scientific.IO.NetCDF import NetCDFFile as Dataset
 # the 'classic' version of the netCDF4 python interface
 # http://code.google.com/p/netcdf4-python/
 import numpy as np
 from netCDF4 import Dataset
-from numpy import dtype # array module from http://numpy.scipy.org
+from numpy import dtype  # array module from http://numpy.scipy.org
+
 """
 This example writes some surface pressure and temperatures
 The companion program sfc_pres_temp_rd.py shows how to read the netCDF
@@ -30,44 +32,45 @@
 #
 
 # the output array to write will be nx x ny
-ny = 100; nx = ny + 4
+ny = 100
+nx = ny + 4
 
 # dy of grid
 dy = old_div(1.0, np.float(ny))
 dx = dy
 # create grid
-dxarr=np.zeros((nx,ny),dtype='float32')+dx
-dyarr=np.zeros((nx,ny),dtype='float32')+dy
+dxarr = np.zeros((nx, ny), dtype="float32") + dx
+dyarr = np.zeros((nx, ny), dtype="float32") + dy
 
-xarr=np.arange(0.,np.float(nx),1.,dtype='float32')*dx
-yarr=np.arange(0.,np.float(ny),1.,dtype='float32')*dy
+xarr = np.arange(0.0, np.float(nx), 1.0, dtype="float32") * dx
+yarr = np.arange(0.0, np.float(ny), 1.0, dtype="float32") * dy
 
 # compute initial variables
 
-rho=np.zeros((nx,ny),dtype='float32')+old_div(25.,(36.*np.pi))
-p=np.zeros((nx,ny),dtype='float32')+old_div(5.,(12.*np.pi))
+rho = np.zeros((nx, ny), dtype="float32") + old_div(25.0, (36.0 * np.pi))
+p = np.zeros((nx, ny), dtype="float32") + old_div(5.0, (12.0 * np.pi))
 
-rho=1.
-p=old_div(rho,3.)
+rho = 1.0
+p = old_div(rho, 3.0)
 
-v_x=np.zeros((nx,ny),dtype='float32')
-Bx=np.zeros((nx,ny),dtype='float32')
+v_x = np.zeros((nx, ny), dtype="float32")
+Bx = np.zeros((nx, ny), dtype="float32")
 
 for y in range(ny):
-    v_x[:,y]=-np.sin(2.*np.pi*yarr[y])
-    Bx[:,y]=-np.sin(2.*np.pi*yarr[y])
- 
-#Bx=Bx/np.sqrt(4.*np.pi)
+    v_x[:, y] = -np.sin(2.0 * np.pi * yarr[y])
+    Bx[:, y] = -np.sin(2.0 * np.pi * yarr[y])
 
+# Bx=Bx/np.sqrt(4.*np.pi)
 
-v_y=np.zeros((nx,ny),dtype='float32')
-By=np.zeros((nx,ny),dtype='float32')
+
+v_y = np.zeros((nx, ny), dtype="float32")
+By = np.zeros((nx, ny), dtype="float32")
 
 for x in range(nx):
-    v_y[x,:]=np.sin(2.*np.pi*xarr[x])
-    By[x,:]=np.sin(4.*np.pi*xarr[x])
-    
-#By=By/np.sqrt(4.*np.pi)
+    v_y[x, :] = np.sin(2.0 * np.pi * xarr[x])
+    By[x, :] = np.sin(4.0 * np.pi * xarr[x])
+
+# By=By/np.sqrt(4.*np.pi)
 
 
 # Domain inside core (periodic)
@@ -76,55 +79,62 @@
 ixseps2 = nx
 
 # open a new netCDF file for writing.
-ncfile = Dataset('otv.grd.128.nc','w', format='NETCDF3_CLASSIC') 
+ncfile = Dataset("otv.grd.128.nc", "w", format="NETCDF3_CLASSIC")
 
 # output data.
 
 # create the nx and ny dimensions.
-ncfile.createDimension('x',nx)
-ncfile.createDimension('y',ny)
-ncfile.createDimension('single',1)
+ncfile.createDimension("x", nx)
+ncfile.createDimension("y", ny)
+ncfile.createDimension("single", 1)
 
 # create and write nx,ny variables
-nxx=ncfile.createVariable('nx','i4',('single'))
-nyy=ncfile.createVariable('ny','i4',('single'))
+nxx = ncfile.createVariable("nx", "i4", ("single"))
+nyy = ncfile.createVariable("ny", "i4", ("single"))
 
-nxx[:]=nx
-nyy[:]=ny
+nxx[:] = nx
+nyy[:] = ny
 
 # Define the coordinate variables. They will hold the coordinate
 # information, that is, xarr,yarr
-dx = ncfile.createVariable('dx',dtype('float32').char,('x','y'))
-dy = ncfile.createVariable('dy',dtype('float32').char,('x','y',))
+dx = ncfile.createVariable("dx", dtype("float32").char, ("x", "y"))
+dy = ncfile.createVariable(
+    "dy",
+    dtype("float32").char,
+    (
+        "x",
+        "y",
+    ),
+)
 
 # write data to coordinate vars.
-dx[:,:] = dxarr
-dy[:,:] = dyarr
+dx[:, :] = dxarr
+dy[:, :] = dyarr
 
 # create and write ixseps* dimensions.
-ix1=ncfile.createVariable('ixseps1','i4',('single'))
-ix2=ncfile.createVariable('ixseps2','i4',('single'))
+ix1 = ncfile.createVariable("ixseps1", "i4", ("single"))
+ix2 = ncfile.createVariable("ixseps2", "i4", ("single"))
 
-ix1[:]=ixseps1
-ix2[:]=ixseps2
+ix1[:] = ixseps1
+ix2[:] = ixseps2
 
-# create the corresponding variables 
-rho0 = ncfile.createVariable('rho0',dtype('float32').char,('x','y'))
-p0 = ncfile.createVariable('p0',dtype('float32').char,('x','y'))
-v0_x = ncfile.createVariable('v0_x',dtype('float32').char,('x','y'))
-v0_y = ncfile.createVariable('v0_y',dtype('float32').char,('x','y'))
-B0x = ncfile.createVariable('B0x',dtype('float32').char,('x','y'))
-B0y = ncfile.createVariable('B0y',dtype('float32').char,('x','y'))
+# create the corresponding variables
+rho0 = ncfile.createVariable("rho0", dtype("float32").char, ("x", "y"))
+p0 = ncfile.createVariable("p0", dtype("float32").char, ("x", "y"))
+v0_x = ncfile.createVariable("v0_x", dtype("float32").char, ("x", "y"))
+v0_y = ncfile.createVariable("v0_y", dtype("float32").char, ("x", "y"))
+B0x = ncfile.createVariable("B0x", dtype("float32").char, ("x", "y"))
+B0y = ncfile.createVariable("B0y", dtype("float32").char, ("x", "y"))
 
 # write data to variables.
 
-rho0[:,:]=rho
-p0[:,:]=p
-v0_x[:,:]=v_x
-v0_y[:,:]=v_y
-B0x[:,:]=Bx
-B0y[:,:]=By
+rho0[:, :] = rho
+p0[:, :] = p
+v0_x[:, :] = v_x
+v0_y[:, :] = v_y
+B0x[:, :] = Bx
+B0y[:, :] = By
 
 
 ncfile.close()
-print('*** SUCCESS writing file otv.grd.py.nc!')
+print("*** SUCCESS writing file otv.grd.py.nc!")
diff --git a/examples/performance/bracket/scaling_parser.py b/examples/performance/bracket/scaling_parser.py
index d7a23842d4..15f0ea8780 100644
--- a/examples/performance/bracket/scaling_parser.py
+++ b/examples/performance/bracket/scaling_parser.py
@@ -2,8 +2,7 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
@@ -13,7 +12,7 @@ def read_file(filename):
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
diff --git a/examples/performance/ddx/new_scaling_parser.py b/examples/performance/ddx/new_scaling_parser.py
index d2a5fee191..5c0c92ff5e 100644
--- a/examples/performance/ddx/new_scaling_parser.py
+++ b/examples/performance/ddx/new_scaling_parser.py
@@ -2,19 +2,19 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
         continue
 
     from collections import OrderedDict
-    case_lines = OrderedDict() #{}
+
+    case_lines = OrderedDict()  # {}
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
@@ -25,12 +25,13 @@ def read_file(filename):
         for title, col in zip(titles, line[:-1]):
             cases_weak[title].append(float(col))
 
-    axis = cases_weak['Local grid']
+    axis = cases_weak["Local grid"]
     data = [cases_weak[x] for x in case_lines]
     labels = [case_lines[x] for x in case_lines]
-    return {'axis':axis, 'data':data, 'labels':labels}
+    return {"axis": axis, "data": data, "labels": labels}
+
 
-def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
+def getScan(baseName="timing_{n}.txt", nthreads=(1, 2, 4, 8, 16, 32)):
     from numpy import zeros
 
     dataS = []
@@ -38,17 +39,16 @@ def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
         f = baseName.format(n=n)
         dataS.append(read_file(f))
 
-
     nnt = len(dataS)
-    nlines = len(dataS[0]['data'])
-    nval = len(dataS[0]['data'][0])
-    rawDat = zeros([nnt,nval,nlines])
+    nlines = len(dataS[0]["data"])
+    nval = len(dataS[0]["data"][0])
+    rawDat = zeros([nnt, nval, nlines])
 
     for i, dat in enumerate(dataS):
-        print(len(dat['data']))
-        
-        rawDat[i,:,:] = dat['data']
+        print(len(dat["data"]))
+
+        rawDat[i, :, :] = dat["data"]
 
-    axes = [nthreads, dataS[0]['axis']]
+    axes = [nthreads, dataS[0]["axis"]]
 
-    return axes, rawDat, dataS[0]['labels']
+    return axes, rawDat, dataS[0]["labels"]
diff --git a/examples/performance/ddy/new_scaling_parser.py b/examples/performance/ddy/new_scaling_parser.py
index d2a5fee191..5c0c92ff5e 100644
--- a/examples/performance/ddy/new_scaling_parser.py
+++ b/examples/performance/ddy/new_scaling_parser.py
@@ -2,19 +2,19 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
         continue
 
     from collections import OrderedDict
-    case_lines = OrderedDict() #{}
+
+    case_lines = OrderedDict()  # {}
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
@@ -25,12 +25,13 @@ def read_file(filename):
         for title, col in zip(titles, line[:-1]):
             cases_weak[title].append(float(col))
 
-    axis = cases_weak['Local grid']
+    axis = cases_weak["Local grid"]
     data = [cases_weak[x] for x in case_lines]
     labels = [case_lines[x] for x in case_lines]
-    return {'axis':axis, 'data':data, 'labels':labels}
+    return {"axis": axis, "data": data, "labels": labels}
+
 
-def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
+def getScan(baseName="timing_{n}.txt", nthreads=(1, 2, 4, 8, 16, 32)):
     from numpy import zeros
 
     dataS = []
@@ -38,17 +39,16 @@ def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
         f = baseName.format(n=n)
         dataS.append(read_file(f))
 
-
     nnt = len(dataS)
-    nlines = len(dataS[0]['data'])
-    nval = len(dataS[0]['data'][0])
-    rawDat = zeros([nnt,nval,nlines])
+    nlines = len(dataS[0]["data"])
+    nval = len(dataS[0]["data"][0])
+    rawDat = zeros([nnt, nval, nlines])
 
     for i, dat in enumerate(dataS):
-        print(len(dat['data']))
-        
-        rawDat[i,:,:] = dat['data']
+        print(len(dat["data"]))
+
+        rawDat[i, :, :] = dat["data"]
 
-    axes = [nthreads, dataS[0]['axis']]
+    axes = [nthreads, dataS[0]["axis"]]
 
-    return axes, rawDat, dataS[0]['labels']
+    return axes, rawDat, dataS[0]["labels"]
diff --git a/examples/performance/ddz/new_scaling_parser.py b/examples/performance/ddz/new_scaling_parser.py
index d2a5fee191..5c0c92ff5e 100644
--- a/examples/performance/ddz/new_scaling_parser.py
+++ b/examples/performance/ddz/new_scaling_parser.py
@@ -2,19 +2,19 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
         continue
 
     from collections import OrderedDict
-    case_lines = OrderedDict() #{}
+
+    case_lines = OrderedDict()  # {}
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
@@ -25,12 +25,13 @@ def read_file(filename):
         for title, col in zip(titles, line[:-1]):
             cases_weak[title].append(float(col))
 
-    axis = cases_weak['Local grid']
+    axis = cases_weak["Local grid"]
     data = [cases_weak[x] for x in case_lines]
     labels = [case_lines[x] for x in case_lines]
-    return {'axis':axis, 'data':data, 'labels':labels}
+    return {"axis": axis, "data": data, "labels": labels}
+
 
-def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
+def getScan(baseName="timing_{n}.txt", nthreads=(1, 2, 4, 8, 16, 32)):
     from numpy import zeros
 
     dataS = []
@@ -38,17 +39,16 @@ def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
         f = baseName.format(n=n)
         dataS.append(read_file(f))
 
-
     nnt = len(dataS)
-    nlines = len(dataS[0]['data'])
-    nval = len(dataS[0]['data'][0])
-    rawDat = zeros([nnt,nval,nlines])
+    nlines = len(dataS[0]["data"])
+    nval = len(dataS[0]["data"][0])
+    rawDat = zeros([nnt, nval, nlines])
 
     for i, dat in enumerate(dataS):
-        print(len(dat['data']))
-        
-        rawDat[i,:,:] = dat['data']
+        print(len(dat["data"]))
+
+        rawDat[i, :, :] = dat["data"]
 
-    axes = [nthreads, dataS[0]['axis']]
+    axes = [nthreads, dataS[0]["axis"]]
 
-    return axes, rawDat, dataS[0]['labels']
+    return axes, rawDat, dataS[0]["labels"]
diff --git a/examples/performance/iterator/scaling_parser.py b/examples/performance/iterator/scaling_parser.py
index d7a23842d4..15f0ea8780 100644
--- a/examples/performance/iterator/scaling_parser.py
+++ b/examples/performance/iterator/scaling_parser.py
@@ -2,8 +2,7 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
@@ -13,7 +12,7 @@ def read_file(filename):
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
diff --git a/examples/staggered_grid/generate.py b/examples/staggered_grid/generate.py
index da84e9c2e6..a5a0120612 100755
--- a/examples/staggered_grid/generate.py
+++ b/examples/staggered_grid/generate.py
@@ -4,11 +4,11 @@
 # Generate an input mesh
 #
 
-from boututils.datafile import DataFile # Wrapper around NetCDF4 libraries
+from boututils.datafile import DataFile  # Wrapper around NetCDF4 libraries
 
-nx = 5   # Minimum is 5: 2 boundary, one evolved
+nx = 5  # Minimum is 5: 2 boundary, one evolved
 ny = 32  # Minimum 5. Should be divisible by number of processors (so powers of 2 nice)
-dy = 1. # distance between points in y, in m/g22/lengthunit
+dy = 1.0  # distance between points in y, in m/g22/lengthunit
 ixseps1 = -1
 ixseps2 = -1
 
diff --git a/examples/subsampling/show.py b/examples/subsampling/show.py
index 34c6ee3084..b79c5e2964 100755
--- a/examples/subsampling/show.py
+++ b/examples/subsampling/show.py
@@ -11,14 +11,14 @@
 
 for pack in monitors:
     filename, data_name = pack
-    t = DataFile(path+'/'+filename+'.dmp.0.nc').read('t_array')
-    data = DataFile(path+'/'+filename+'.dmp.0.nc').read(data_name).flatten()
+    t = DataFile(path + "/" + filename + ".dmp.0.nc").read("t_array")
+    data = DataFile(path + "/" + filename + ".dmp.0.nc").read(data_name).flatten()
     plt.plot(t, data, label="{} {}".format(filename, data_name))
 
-time = DataFile(path+'/BOUT.dmp.0.nc').read('t_array')
-data = DataFile(path+'/BOUT.dmp.0.nc').read("T")[:, 2, 2, 0]
+time = DataFile(path + "/BOUT.dmp.0.nc").read("t_array")
+data = DataFile(path + "/BOUT.dmp.0.nc").read("T")[:, 2, 2, 0]
 
-plt.plot(time, data, marker='+', label="BOUT++ T")
+plt.plot(time, data, marker="+", label="BOUT++ T")
 
 plt.xlabel("Time")
 plt.legend()
diff --git a/examples/wave-slab/generate.py b/examples/wave-slab/generate.py
index 0a2e8f3049..12698d1e24 100755
--- a/examples/wave-slab/generate.py
+++ b/examples/wave-slab/generate.py
@@ -51,7 +51,7 @@
 for x in range(nx):
     Bpxy[x, :] = Bpx[x]
 
-Bxy = sqrt(Bpxy ** 2 + Bt ** 2)
+Bxy = sqrt(Bpxy**2 + Bt**2)
 
 # Calculate change in poloidal flux
 dr = Lx / nx  # Constant mesh spacing in radius
diff --git a/manual/sphinx/figs/figure_creators/LaplacianMatrices.ipynb b/manual/sphinx/figs/figure_creators/LaplacianMatrices.ipynb
index c3c39a3c12..4e940b998f 100644
--- a/manual/sphinx/figs/figure_creators/LaplacianMatrices.ipynb
+++ b/manual/sphinx/figs/figure_creators/LaplacianMatrices.ipynb
@@ -40,10 +40,10 @@
    "outputs": [],
    "source": [
     "# Note, these can be max 9 due to the current index convention\n",
-    "nx = 3 # Not including ghost points\n",
+    "nx = 3  # Not including ghost points\n",
     "nz = 3\n",
     "\n",
-    "startXIndex = 10 # The x indices are the slowest growing indices\n",
+    "startXIndex = 10  # The x indices are the slowest growing indices\n",
     "startZIndex = 1  # The z indices are the fastest growing indices"
    ]
   },
@@ -85,13 +85,13 @@
     "for z in range(nz):\n",
     "    f.append([])\n",
     "    xStart = startZIndex\n",
-    "    xEnd   = startXIndex*(nx+1)  # +1 due to ghost point\n",
+    "    xEnd = startXIndex * (nx + 1)  # +1 due to ghost point\n",
     "    # +startXIndex in the range as the range does not include endpoint\n",
-    "    for xInd in range(xStart, xEnd+startXIndex, 10):\n",
-    "        ind = str(xInd+z)\n",
-    "        if (xInd+z) < startXIndex:\n",
-    "            ind = '0'+str(xInd+z)\n",
-    "        f[z].append(symbols('f_' + ind))\n",
+    "    for xInd in range(xStart, xEnd + startXIndex, 10):\n",
+    "        ind = str(xInd + z)\n",
+    "        if (xInd + z) < startXIndex:\n",
+    "            ind = \"0\" + str(xInd + z)\n",
+    "        f[z].append(symbols(\"f_\" + ind))\n",
     "\n",
     "mesh = Matrix(f[::-1])\n",
     "display(mesh)"
@@ -195,21 +195,21 @@
     }
    ],
    "source": [
-    "xVec=[]\n",
-    "bVec=[]\n",
+    "xVec = []\n",
+    "bVec = []\n",
     "# Do the inner loop, so start ranges at 1\n",
     "# (nx+1) to include outer ghost point, +1 in the range as the range does not include endpoint\n",
-    "for x in range(1, (nx+1)+1):\n",
-    "    for z in range(1,nz+1):\n",
-    "        xVec.append(symbols('x_'+str(x)+'_'+str(z)))\n",
-    "        bVec.append(symbols('b_'+str(x)+'_'+str(z)))\n",
+    "for x in range(1, (nx + 1) + 1):\n",
+    "    for z in range(1, nz + 1):\n",
+    "        xVec.append(symbols(\"x_\" + str(x) + \"_\" + str(z)))\n",
+    "        bVec.append(symbols(\"b_\" + str(x) + \"_\" + str(z)))\n",
     "\n",
     "# Do the inner ghost points\n",
     "# Must count backwards since we are inserting in the front\n",
-    "for ind in range(nz,0,-1):\n",
-    "    xVec.insert(0, symbols('x_0_'+str(ind)))\n",
-    "    bVec.insert(0, symbols('b_0_'+str(ind)))\n",
-    "    \n",
+    "for ind in range(nz, 0, -1):\n",
+    "    xVec.insert(0, symbols(\"x_0_\" + str(ind)))\n",
+    "    bVec.insert(0, symbols(\"b_0_\" + str(ind)))\n",
+    "\n",
     "display(Matrix(xVec))\n",
     "display(Matrix(bVec))"
    ]
@@ -274,7 +274,7 @@
     "globInd = []\n",
     "for rows in range(len(xVec)):\n",
     "    cols = []\n",
-    "    for col in range(rows*len(xVec), (rows+1)*len(xVec)):\n",
+    "    for col in range(rows * len(xVec), (rows + 1) * len(xVec)):\n",
     "        cols.append(col)\n",
     "    globInd.append(cols)\n",
     "\n",
@@ -305,10 +305,14 @@
    "source": [
     "c = []\n",
     "for x in range(nx):\n",
-    "    indexStart = (startXIndex+1)+(startXIndex*x)     # Multiply by 10 due to index system\n",
-    "    indexEnd   = (startXIndex+nz+1)+(startXIndex*x)  # Multiply by 10 due to index system\n",
+    "    indexStart = (startXIndex + 1) + (\n",
+    "        startXIndex * x\n",
+    "    )  # Multiply by 10 due to index system\n",
+    "    indexEnd = (startXIndex + nz + 1) + (\n",
+    "        startXIndex * x\n",
+    "    )  # Multiply by 10 due to index system\n",
     "    for ind in range(indexStart, indexEnd):\n",
-    "        c.append(symbols('c_'+str(ind)))"
+    "        c.append(symbols(\"c_\" + str(ind)))"
    ]
   },
   {
@@ -328,11 +332,11 @@
    "source": [
     "# The inner ghost\n",
     "innerGhostStart = startZIndex\n",
-    "innerGhostEnd   = nz\n",
+    "innerGhostEnd = nz\n",
     "ig = []\n",
     "# +1 in the range as last point is not included\n",
-    "for z in range(innerGhostStart, innerGhostEnd+1):\n",
-    "    ig.append(symbols('ig_0_'+str(z)))"
+    "for z in range(innerGhostStart, innerGhostEnd + 1):\n",
+    "    ig.append(symbols(\"ig_0_\" + str(z)))"
    ]
   },
   {
@@ -345,12 +349,12 @@
    "source": [
     "# The outer ghost\n",
     "# nx+1 as we want to go past the last inner x grid point\n",
-    "outerGhostStart = startXIndex*(nx+1) + startZIndex\n",
-    "outerGhostEnd   = startXIndex*(nx+1) + nz\n",
+    "outerGhostStart = startXIndex * (nx + 1) + startZIndex\n",
+    "outerGhostEnd = startXIndex * (nx + 1) + nz\n",
     "og = []\n",
     "# +1 in the range as last point is not included\n",
-    "for z in range(outerGhostStart, outerGhostEnd+1):\n",
-    "    og.append(symbols('og_'+str(z)))"
+    "for z in range(outerGhostStart, outerGhostEnd + 1):\n",
+    "    og.append(symbols(\"og_\" + str(z)))"
    ]
   },
   {
@@ -396,21 +400,27 @@
     "for x in range(nx):\n",
     "    # The indices referring to the matrix index\n",
     "    # The last -1 is there as the matrix indices count from 0\n",
-    "    startRow = (nz+1)+(x*nz)-1  # Starting at row+1 after inner ghost point sub-matrix\n",
-    "    endRow   = (nz+1)+(x*nz)+(nz-1)-1 # Ending row-1 before the last z-index (last z will be wrapped around)\n",
+    "    startRow = (\n",
+    "        (nz + 1) + (x * nz) - 1\n",
+    "    )  # Starting at row+1 after inner ghost point sub-matrix\n",
+    "    endRow = (\n",
+    "        (nz + 1) + (x * nz) + (nz - 1) - 1\n",
+    "    )  # Ending row-1 before the last z-index (last z will be wrapped around)\n",
     "    # +1 in range as last point is not included\n",
-    "    rows     = range(startRow,   endRow+1)\n",
-    "    cols     = range(startRow+1, endRow+1) # Column is shifted +1 from the diagonal\n",
-    "    \n",
+    "    rows = range(startRow, endRow + 1)\n",
+    "    cols = range(startRow + 1, endRow + 1)  # Column is shifted +1 from the diagonal\n",
+    "\n",
     "    # The indices referring to the spatial point in the grid\n",
     "    # The last \"+1\" is fue to the fact that the column is shifted +1 from the diagonal\n",
-    "    startInd = (startXIndex+startZIndex) + (startXIndex*x) + 1\n",
-    "    endInd   = (startXIndex+startZIndex) + (nz-1) + (startXIndex*x) + 1 # Wrap around last point\n",
+    "    startInd = (startXIndex + startZIndex) + (startXIndex * x) + 1\n",
+    "    endInd = (\n",
+    "        (startXIndex + startZIndex) + (nz - 1) + (startXIndex * x) + 1\n",
+    "    )  # Wrap around last point\n",
     "    # +1 in range as last point is not included\n",
-    "    inds     = range(startInd, endInd+1)\n",
-    "    \n",
+    "    inds = range(startInd, endInd + 1)\n",
+    "\n",
     "    for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "        InvM[rInd, cInd] = symbols('zp_'+str(ind))"
+    "        InvM[rInd, cInd] = symbols(\"zp_\" + str(ind))"
    ]
   },
   {
@@ -423,15 +433,17 @@
    "source": [
     "# The wrap around\n",
     "# The index referring to the spatial point in the grid\n",
-    "startInd = startXIndex+startZIndex\n",
+    "startInd = startXIndex + startZIndex\n",
     "# The indices referring to the matrix index\n",
-    "# Last -1 as the matrix indices are counted from 0 \n",
-    "startRow = (nz+1) + (nz-1) - 1 # nz+1 below from the ghost sub matrix, nz-1 below after that\n",
-    "startCol = (nz+1)-1            # nz+1 left of the ghost sub matrix\n",
+    "# Last -1 as the matrix indices are counted from 0\n",
+    "startRow = (\n",
+    "    (nz + 1) + (nz - 1) - 1\n",
+    ")  # nz+1 below from the ghost sub matrix, nz-1 below after that\n",
+    "startCol = (nz + 1) - 1  # nz+1 left of the ghost sub matrix\n",
     "for wrap in range(nx):\n",
-    "    row = startRow+wrap*nz\n",
-    "    col = startCol+wrap*nz\n",
-    "    InvM[row, col] = symbols('zp_'+str(startInd+startXIndex*wrap))"
+    "    row = startRow + wrap * nz\n",
+    "    col = startCol + wrap * nz\n",
+    "    InvM[row, col] = symbols(\"zp_\" + str(startInd + startXIndex * wrap))"
    ]
   },
   {
@@ -452,20 +464,26 @@
     "for x in range(nx):\n",
     "    # The indices referring to the matrix index\n",
     "    # The last -1 is there as the matrix indices count from 0\n",
-    "    startRow = (nz+1)+(x*nz)-1  # Starting at row+1 after inner ghost point sub-matrix\n",
-    "    endRow   = (nz+1)+(x*nz)+(nz-1)-1 # Ending row-1 before the last z-index (last z will be wrapped around)\n",
+    "    startRow = (\n",
+    "        (nz + 1) + (x * nz) - 1\n",
+    "    )  # Starting at row+1 after inner ghost point sub-matrix\n",
+    "    endRow = (\n",
+    "        (nz + 1) + (x * nz) + (nz - 1) - 1\n",
+    "    )  # Ending row-1 before the last z-index (last z will be wrapped around)\n",
     "    # +1 in range as last point is not included\n",
-    "    rows     = range(startRow+1, endRow+1) # Row is shifted +1 from the diagonal\n",
-    "    cols     = range(startRow,   endRow+1)\n",
-    "    \n",
+    "    rows = range(startRow + 1, endRow + 1)  # Row is shifted +1 from the diagonal\n",
+    "    cols = range(startRow, endRow + 1)\n",
+    "\n",
     "    # The indices referring to the spatial point in the grid\n",
-    "    startInd = (startXIndex+startZIndex) + (startXIndex*x)\n",
-    "    endInd   = (startXIndex+startZIndex) + (nz-1) + (startXIndex*x) # Wrap around last point\n",
+    "    startInd = (startXIndex + startZIndex) + (startXIndex * x)\n",
+    "    endInd = (\n",
+    "        (startXIndex + startZIndex) + (nz - 1) + (startXIndex * x)\n",
+    "    )  # Wrap around last point\n",
     "    # +1 in range as last point is not included\n",
-    "    inds     = range(startInd, endInd+1)\n",
-    "    \n",
+    "    inds = range(startInd, endInd + 1)\n",
+    "\n",
     "    for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "        InvM[rInd, cInd] = symbols('zm_'+str(ind))"
+    "        InvM[rInd, cInd] = symbols(\"zm_\" + str(ind))"
    ]
   },
   {
@@ -478,15 +496,19 @@
    "source": [
     "# The wrap around\n",
     "# The index referring to the spatial point in the grid\n",
-    "startInd = startXIndex+startZIndex+(nz-1) # +(nz-1) as this will be the last z point for the current x\n",
+    "startInd = (\n",
+    "    startXIndex + startZIndex + (nz - 1)\n",
+    ")  # +(nz-1) as this will be the last z point for the current x\n",
     "# The indices referring to the matrix index\n",
-    "# Last -1 as the matrix indices are counted from 0 \n",
-    "startRow = (nz+1)-1            # nz+1 below the ghost sub matrix\n",
-    "startCol = (nz+1) + (nz-1) - 1 # nz+1 left from the ghost sub matrix, nz-1 left after that\n",
+    "# Last -1 as the matrix indices are counted from 0\n",
+    "startRow = (nz + 1) - 1  # nz+1 below the ghost sub matrix\n",
+    "startCol = (\n",
+    "    (nz + 1) + (nz - 1) - 1\n",
+    ")  # nz+1 left from the ghost sub matrix, nz-1 left after that\n",
     "for wrap in range(nx):\n",
-    "    row = startRow+wrap*nz\n",
-    "    col = startCol+wrap*nz\n",
-    "    InvM[row, col] = symbols('zm_'+str(startInd+startXIndex*wrap))"
+    "    row = startRow + wrap * nz\n",
+    "    col = startCol + wrap * nz\n",
+    "    InvM[row, col] = symbols(\"zm_\" + str(startInd + startXIndex * wrap))"
    ]
   },
   {
@@ -505,23 +527,29 @@
    "outputs": [],
    "source": [
     "# Indices referring to the spatial points in the grid\n",
-    "startInd = startXIndex*2 + startZIndex # *2 as we start at the second inner x-index\n",
-    "endInd   = startInd + (startZIndex*nz) # *nz as this is the last z-index in the current x-index\n",
+    "startInd = startXIndex * 2 + startZIndex  # *2 as we start at the second inner x-index\n",
+    "endInd = startInd + (\n",
+    "    startZIndex * nz\n",
+    ")  # *nz as this is the last z-index in the current x-index\n",
     "\n",
     "for x in range(nx):\n",
     "    # The indices referring to the matrix index\n",
     "    # The last -1 as the matrix indices counts from 0\n",
-    "    startRow = (nz+1)+(x*nz)-1      # Starting at row+1 after inner ghost point sub-matrix\n",
-    "    endRow   = (nz+1)+(x*nz)+(nz)-1 # Ending at the row referring to the last z-index\n",
+    "    startRow = (\n",
+    "        (nz + 1) + (x * nz) - 1\n",
+    "    )  # Starting at row+1 after inner ghost point sub-matrix\n",
+    "    endRow = (\n",
+    "        (nz + 1) + (x * nz) + (nz) - 1\n",
+    "    )  # Ending at the row referring to the last z-index\n",
     "    # Not +1 in range as we do not want to include last point\n",
-    "    rows     = range(startRow,    endRow)\n",
-    "    cols     = range(startRow+nz, endRow+nz)           # Start at first index after last z-index\n",
-    "    \n",
+    "    rows = range(startRow, endRow)\n",
+    "    cols = range(startRow + nz, endRow + nz)  # Start at first index after last z-index\n",
+    "\n",
     "    # Indices referring to the spatial points in the grid\n",
-    "    inds     = range(startInd+startXIndex*x, endInd+startXIndex*x)\n",
-    "    \n",
+    "    inds = range(startInd + startXIndex * x, endInd + startXIndex * x)\n",
+    "\n",
     "    for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "        InvM[rInd, cInd] = symbols('xp_'+str(ind))"
+    "        InvM[rInd, cInd] = symbols(\"xp_\" + str(ind))"
    ]
   },
   {
@@ -534,22 +562,22 @@
    "source": [
     "# x+1 for inner ghost point\n",
     "# Indices referring to the spatial points in the grid\n",
-    "startInd = startXIndex + startZIndex   # First inner point for first z\n",
-    "endInd   = startInd + (startZIndex*nz) # First inner point for last z\n",
+    "startInd = startXIndex + startZIndex  # First inner point for first z\n",
+    "endInd = startInd + (startZIndex * nz)  # First inner point for last z\n",
     "\n",
     "# The indices referring to the matrix index\n",
     "# The last -1 as the matrix indices counts from 0\n",
-    "startRow = startZIndex-1    # Starting at first row\n",
-    "endRow   = startZIndex+nz-1 # Ending at the row referring to the last z-index\n",
+    "startRow = startZIndex - 1  # Starting at first row\n",
+    "endRow = startZIndex + nz - 1  # Ending at the row referring to the last z-index\n",
     "# Not +1 in range as we do not want to include last point\n",
-    "rows     = range(startRow,    endRow)\n",
-    "cols     = range(startRow+nz, endRow+nz)           # Start at first index after last z-index\n",
-    "    \n",
+    "rows = range(startRow, endRow)\n",
+    "cols = range(startRow + nz, endRow + nz)  # Start at first index after last z-index\n",
+    "\n",
     "# Indices referring to the spatial points in the grid\n",
-    "inds     = range(startInd, endInd)\n",
-    "    \n",
+    "inds = range(startInd, endInd)\n",
+    "\n",
     "for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "    InvM[rInd, cInd] = symbols('igxp_'+str(ind))"
+    "    InvM[rInd, cInd] = symbols(\"igxp_\" + str(ind))"
    ]
   },
   {
@@ -569,25 +597,25 @@
    "source": [
     "# Indices referring to the spatial points in the grid\n",
     "startInd = startZIndex\n",
-    "endInd   = startInd + nz\n",
+    "endInd = startInd + nz\n",
     "\n",
     "for x in range(nx):\n",
     "    # The indices referring to the matrix index\n",
     "    # Note that x starts counting from zero, so we must add 1 to x in the rows\n",
-    "    startRow = ((x+1)*nz)      # Starting at row+1 after inner ghost point sub-matrix\n",
-    "    endRow   = ((x+1)*nz)+(nz) # Ending at the row referring to the last z-index\n",
+    "    startRow = (x + 1) * nz  # Starting at row+1 after inner ghost point sub-matrix\n",
+    "    endRow = ((x + 1) * nz) + (nz)  # Ending at the row referring to the last z-index\n",
     "    # Not +1 in range as we do not want to include last point\n",
-    "    rows = range(startRow,    endRow)\n",
-    "    cols = range(startRow-nz, endRow-nz)           # Start at first index after last z-index\n",
-    "    \n",
+    "    rows = range(startRow, endRow)\n",
+    "    cols = range(startRow - nz, endRow - nz)  # Start at first index after last z-index\n",
+    "\n",
     "    # Indices referring to the spatial points in the grid\n",
-    "    inds = range(startInd+startXIndex*x, endInd+startXIndex*x)\n",
-    "    \n",
+    "    inds = range(startInd + startXIndex * x, endInd + startXIndex * x)\n",
+    "\n",
     "    for rInd, cInd, ind in zip(rows, cols, inds):\n",
     "        if (ind) < startXIndex:\n",
-    "            ind = '0'+str(ind)\n",
+    "            ind = \"0\" + str(ind)\n",
     "\n",
-    "        InvM[rInd, cInd] = symbols('xm_'+str(ind))"
+    "        InvM[rInd, cInd] = symbols(\"xm_\" + str(ind))"
    ]
   },
   {
@@ -600,22 +628,24 @@
    "source": [
     "# x-1 for inner ghost point\n",
     "# Indices referring to the spatial points in the grid\n",
-    "startInd = startXIndex*nx + startZIndex   # Last inner point for first z\n",
-    "endInd   = startInd + (startZIndex*nz)    # Last inner point for last z\n",
+    "startInd = startXIndex * nx + startZIndex  # Last inner point for first z\n",
+    "endInd = startInd + (startZIndex * nz)  # Last inner point for last z\n",
     "\n",
     "# The indices referring to the matrix index\n",
     "# The last -1 as the matrix indices counts from 0\n",
-    "startRow = len(xVec)-nz-1    # Starting at last inner point row\n",
-    "endRow   = len(xVec)-1       # Ending at the last row\n",
+    "startRow = len(xVec) - nz - 1  # Starting at last inner point row\n",
+    "endRow = len(xVec) - 1  # Ending at the last row\n",
     "# +1 in range as last point is not included\n",
-    "rows     = range(startRow+1,    endRow+1)\n",
-    "cols     = range(startRow-nz+1, endRow-nz+1) # Start at first index after last z-index\n",
-    "    \n",
+    "rows = range(startRow + 1, endRow + 1)\n",
+    "cols = range(\n",
+    "    startRow - nz + 1, endRow - nz + 1\n",
+    ")  # Start at first index after last z-index\n",
+    "\n",
     "# Indices referring to the spatial points in the grid\n",
-    "inds     = range(startInd, endInd)\n",
-    "    \n",
+    "inds = range(startInd, endInd)\n",
+    "\n",
     "for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "    InvM[rInd, cInd] = symbols('ogxm_'+str(ind))"
+    "    InvM[rInd, cInd] = symbols(\"ogxm_\" + str(ind))"
    ]
   },
   {
diff --git a/manual/sphinx/figs/figure_creators/bout_runners_folder_structure.py b/manual/sphinx/figs/figure_creators/bout_runners_folder_structure.py
index 8a95a13436..5a4a2a0843 100644
--- a/manual/sphinx/figs/figure_creators/bout_runners_folder_structure.py
+++ b/manual/sphinx/figs/figure_creators/bout_runners_folder_structure.py
@@ -10,10 +10,10 @@
 mmag@fysik.dtu.dk
 """
 
-__authors__ = 'Michael Loeiten'
-__email__   = 'mmag@fysik.dtu.dk'
-__version__ = '1.0'
-__date__    = '21.01.2016'
+__authors__ = "Michael Loeiten"
+__email__ = "mmag@fysik.dtu.dk"
+__version__ = "1.0"
+__date__ = "21.01.2016"
 
 import pygraphviz as pgv
 
@@ -21,113 +21,118 @@
 tree = pgv.AGraph()
 
 # Appendable lists
-files     = []
+files = []
 dead_ends = []
 
 # Default node attributes
-tree.node_attr['shape']='box'
-tree.node_attr['style']='bold'
+tree.node_attr["shape"] = "box"
+tree.node_attr["style"] = "bold"
 
 # Adding nodes and edges
-l0 = 'project'
-l1 = ['data', 'source\nfiles', 'driver.py']
+l0 = "project"
+l1 = ["data", "source\nfiles", "driver.py"]
 # Append the files
 files.append(l1[1])
 files.append(l1[2])
 # Add the boxes to the mother node
 for box in l1:
-    tree.add_edge(l0,box)
+    tree.add_edge(l0, box)
 
-l2 = ['solver1', 'solver2',\
-      'BOUT.inp', 'run_log.txt']
+l2 = ["solver1", "solver2", "BOUT.inp", "run_log.txt"]
 # Append the files
 files.append(l2[2])
 files.append(l2[3])
 # Add the boxes to the mother node
 for box in l2:
-    tree.add_edge('data', box)
-tree.add_edge('solver2', 'solver2/...')
+    tree.add_edge("data", box)
+tree.add_edge("solver2", "solver2/...")
 # Append the dead_end
-de = l2[1] + '/...'
+de = l2[1] + "/..."
 dead_ends.append(de)
 
-l3 = ['method1', 'method2', 'solver1/...']
+l3 = ["method1", "method2", "solver1/..."]
 for box in l3:
-    tree.add_edge('solver1', box)
-tree.add_edge('method2', 'method2/...')
+    tree.add_edge("solver1", box)
+tree.add_edge("method2", "method2/...")
 # Append the dead_end
 de = l3[2]
 dead_ends.append(de)
-de = l3[1] + '/...'
+de = l3[1] + "/..."
 dead_ends.append(de)
 
-l4 = ['nout\ntimestep1', 'nout\ntimestep2', 'method1/...']
+l4 = ["nout\ntimestep1", "nout\ntimestep2", "method1/..."]
 for box in l4:
-    tree.add_edge('method1', box)
-tree.add_edge('nout\ntimestep2', 'nout\ntimestep2/...')
+    tree.add_edge("method1", box)
+tree.add_edge("nout\ntimestep2", "nout\ntimestep2/...")
 # Append the dead_end
 de = l4[2]
 dead_ends.append(de)
-de = l4[1] + '/...'
+de = l4[1] + "/..."
 dead_ends.append(de)
 
-l5 = ['mesh1', 'mesh2', 'nout\ntimestep1/...']
+l5 = ["mesh1", "mesh2", "nout\ntimestep1/..."]
 for box in l5:
-    tree.add_edge('nout\ntimestep1', box)
-tree.add_edge('mesh2', 'mesh2/...')
+    tree.add_edge("nout\ntimestep1", box)
+tree.add_edge("mesh2", "mesh2/...")
 # Append the dead_end
 de = l5[2]
 dead_ends.append(de)
-de = l5[1] + '/...'
+de = l5[1] + "/..."
 dead_ends.append(de)
 
-l6 = ['additional1', 'additional2', 'mesh1/...']
+l6 = ["additional1", "additional2", "mesh1/..."]
 for box in l6:
-    tree.add_edge('mesh1', box)
-tree.add_edge('additional2', 'additional2/...')
+    tree.add_edge("mesh1", box)
+tree.add_edge("additional2", "additional2/...")
 # Append the dead_end
 de = l6[2]
 dead_ends.append(de)
-de = l6[1] + '/...'
+de = l6[1] + "/..."
 dead_ends.append(de)
 
-l7 = ['grid_file1', 'grid_file2', 'additional1/...']
+l7 = ["grid_file1", "grid_file2", "additional1/..."]
 for box in l7:
-    tree.add_edge('additional1', box)
-tree.add_edge('grid_file2', 'grid_file2/...')
+    tree.add_edge("additional1", box)
+tree.add_edge("grid_file2", "grid_file2/...")
 # Append the dead_end
 de = l7[2]
 dead_ends.append(de)
-de = l7[1] + '/...'
+de = l7[1] + "/..."
 dead_ends.append(de)
 
-l8 = ['BOUT.inp\n(copy)', 'BOUT.log', 'BOUT.dmp',\
-      'BOUT.restart', '(source_files\n(copy))', '(grid_file\n(copy))']
+l8 = [
+    "BOUT.inp\n(copy)",
+    "BOUT.log",
+    "BOUT.dmp",
+    "BOUT.restart",
+    "(source_files\n(copy))",
+    "(grid_file\n(copy))",
+]
 # Add l8 to the files list
 for cur_file in l8:
     files.append(cur_file)
 # Append them to the mother node
 for box in l8:
-    tree.add_edge('grid_file1', box)
+    tree.add_edge("grid_file1", box)
 
 
 # Change colors for the files
 for the_file in files:
-    member=tree.get_node(the_file)
-#    member.attr['fontcolor'] = 'limegreen'
-    member.attr['color'] = 'limegreen'
+    member = tree.get_node(the_file)
+    #    member.attr['fontcolor'] = 'limegreen'
+    member.attr["color"] = "limegreen"
 
 # Change colors for the dead_ends
 for dead_end in dead_ends:
-    member=tree.get_node(dead_end)
-#    member.attr['fontcolor'] = 'darksalmon'
-    member.attr['color'] = 'darksalmon'
+    member = tree.get_node(dead_end)
+    #    member.attr['fontcolor'] = 'darksalmon'
+    member.attr["color"] = "darksalmon"
 
 
 # Print the graph
 print(tree.string())
 
 # Set layout
-tree.layout('dot')
+tree.layout("dot")
 # Write to file
-tree.draw('folder_tree.svg')
+tree.draw("folder_tree.svg")
diff --git a/tests/MMS/advection/runtest b/tests/MMS/advection/runtest
index 9a0a691287..5109c47815 100755
--- a/tests/MMS/advection/runtest
+++ b/tests/MMS/advection/runtest
@@ -50,7 +50,7 @@ def run_mms(options, exit=True):
 
             dx = 2.0 * pi / (nx)
 
-            args = f"{opts} mesh:nx={nx+4} mesh:dx={dx} MZ={nx}"
+            args = f"{opts} mesh:nx={nx + 4} mesh:dx={dx} MZ={nx}"
 
             print("  Running with " + args)
 

From 96b86a4c785f326c79f7604f05832fce6a099a10 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Thu, 29 Jan 2026 10:45:03 +0000
Subject: [PATCH 0458/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index ead5bc3729..5e90d36c14 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -2,3 +2,4 @@
 d8f14fdddb5ca0fbb32d8e2bf5ac2960d6ac5ce6
 ed2117e6d6826a98b6988e2f18c0c34e408563b6
 # Added by the bot
+4b010b7634aee1045743be80c268d4644522cd29

From 6305598f8b3578205fe4327314b61e443f95c56b Mon Sep 17 00:00:00 2001
From: David Dickinson <d7919@users.noreply.github.com>
Date: Fri, 14 Dec 2018 10:09:28 +0000
Subject: [PATCH 0459/1827] Provide `GlobalZ` and related routines on mesh

Tests are updated because `FakeMesh` has `GlobalZ(z) == z`. This is completely
arbitrary, we could have a `GlobalZ` definition that matches `BoutMesh` (`z / nz`)
then we wouldn't need to change the tests, but this way is a bit clearer what
we're testing.
---
 include/bout/mesh.hxx                         |  2 +
 src/mesh/data/gridfromoptions.cxx             |  3 +-
 src/mesh/impls/bout/boutmesh.cxx              | 40 ++++++++++++++++---
 src/mesh/impls/bout/boutmesh.hxx              | 13 ++++--
 src/sys/generator_context.cxx                 | 16 ++++----
 .../test-interpolate-z/test_interpolate.cxx   |  3 +-
 .../test-interpolate/test_interpolate.cxx     |  3 +-
 tests/unit/fake_mesh.hxx                      | 10 +++--
 tests/unit/field/test_field_factory.cxx       |  6 +--
 tests/unit/mesh/data/test_gridfromoptions.cxx | 27 ++++++-------
 10 files changed, 76 insertions(+), 47 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 2b24a0e24a..c22d6e969b 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -507,8 +507,10 @@ public:
 
   virtual BoutReal GlobalX(int jx) const = 0;      ///< Continuous X index between 0 and 1
   virtual BoutReal GlobalY(int jy) const = 0;      ///< Continuous Y index (0 -> 1)
+  virtual BoutReal GlobalZ(int jz) const = 0;      ///< Continuous Z index (0 -> 1)
   virtual BoutReal GlobalX(BoutReal jx) const = 0; ///< Continuous X index between 0 and 1
   virtual BoutReal GlobalY(BoutReal jy) const = 0; ///< Continuous Y index (0 -> 1)
+  virtual BoutReal GlobalZ(BoutReal jz) const = 0; ///< Continuous Z index (0 -> 1)
 
   //////////////////////////////////////////////////////////
 
diff --git a/src/mesh/data/gridfromoptions.cxx b/src/mesh/data/gridfromoptions.cxx
index 379e279de0..662329c526 100644
--- a/src/mesh/data/gridfromoptions.cxx
+++ b/src/mesh/data/gridfromoptions.cxx
@@ -146,8 +146,7 @@ bool GridFromOptions::get(Mesh* m, std::vector<BoutReal>& var, const std::string
   }
   case GridDataSource::Z: {
     for (int z = 0; z < len; z++) {
-      pos.set("z",
-              (TWOPI * (z - m->OffsetZ + offset)) / static_cast<BoutReal>(m->LocalNz));
+      pos.set("z", TWOPI * m->GlobalZ(z - m->OffsetZ + offset));
       var[z] = gen->generate(pos);
     }
     break;
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 4be01d4637..507e3b9495 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -57,6 +57,8 @@ If you want the old setting, you have to specify mesh:symmetricGlobalY=false in
                 << optionfile << "\n";
   }
   OPTION(options, symmetricGlobalY, true);
+  OPTION(options, symmetricGlobalZ, false); // The default should be updated to true but
+                                            // this breaks backwards compatibility
 
   comm_x = MPI_COMM_NULL;
   comm_inner = MPI_COMM_NULL;
@@ -516,9 +518,10 @@ int BoutMesh::load() {
     findProcessorSplit();
   }
 
-  // Get X and Y processor indices
+  // Get X, Y, Z processor indices
   PE_YIND = MYPE / NXPE;
   PE_XIND = MYPE % NXPE;
+  PE_ZIND = 0;
 
   // Set the other grid sizes from nx, ny, nz
   setDerivedGridSizes();
@@ -1741,16 +1744,22 @@ int BoutMesh::getLocalYIndexNoBoundaries(int yglobal) const {
   return yglobal - PE_YIND * MYSUB + MYG;
 }
 
-int BoutMesh::YGLOBAL(int yloc, int yproc) const { return yloc + yproc * MYSUB - MYG; }
+int BoutMesh::YGLOBAL(int yloc, int yproc) const { return yloc + (yproc * MYSUB) - MYG; }
 
-int BoutMesh::YLOCAL(int yglo, int yproc) const { return yglo - yproc * MYSUB + MYG; }
+int BoutMesh::YLOCAL(int yglo, int yproc) const { return yglo - (yproc * MYSUB) + MYG; }
 
-int BoutMesh::getGlobalZIndex(int zlocal) const { return zlocal; }
+int BoutMesh::getGlobalZIndex(int zlocal) const { return zlocal + (PE_ZIND * MZSUB); }
 
-int BoutMesh::getGlobalZIndexNoBoundaries(int zlocal) const { return zlocal; }
+int BoutMesh::getGlobalZIndexNoBoundaries(int zlocal) const { return zlocal + (PE_ZIND * MZSUB) - MZG; }
 
 int BoutMesh::getLocalZIndex(int zglobal) const { return zglobal; }
 
+/// Returns the global Z index given a local index
+int BoutMesh::ZGLOBAL(BoutReal zloc, BoutReal& zglo) const {
+  zglo = zloc + (PE_ZIND * MZSUB);
+  return static_cast<int>(zglo);
+}
+
 int BoutMesh::getLocalZIndexNoBoundaries(int zglobal) const { return zglobal; }
 
 int BoutMesh::YPROC(int yind) const {
@@ -3222,6 +3231,27 @@ BoutReal BoutMesh::GlobalY(BoutReal jy) const {
   return yglo / static_cast<BoutReal>(nycore);
 }
 
+BoutReal BoutMesh::GlobalZ(int jz) const {
+  if (symmetricGlobalZ) {
+    // With this definition the boundary sits dz/2 away form the first/last inner points
+    return (0.5 + getGlobalZIndex(jz) - (nz - MZ) * 0.5) / static_cast<BoutReal>(MZ);
+  }
+  return static_cast<BoutReal>(getGlobalZIndex(jz)) / static_cast<BoutReal>(MZ);
+}
+
+BoutReal BoutMesh::GlobalZ(BoutReal jz) const {
+
+  // Get global Z index as a BoutReal
+  BoutReal zglo;
+  ZGLOBAL(jz, zglo);
+
+  if (symmetricGlobalZ) {
+    // With this definition the boundary sits dx/2 away form the first/last inner points
+    return (0.5 + zglo - (nz - MZ) * 0.5) / static_cast<BoutReal>(MZ);
+  }
+  return zglo / static_cast<BoutReal>(MZ);
+}
+
 void BoutMesh::outputVars(Options& output_options) {
   Timer time("io");
   output_options["zperiod"].force(zperiod, "BoutMesh");
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index 876edab1da..f39856867c 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -172,8 +172,10 @@ public:
 
   BoutReal GlobalX(int jx) const override;
   BoutReal GlobalY(int jy) const override;
+  BoutReal GlobalZ(int jz) const override;
   BoutReal GlobalX(BoutReal jx) const override;
   BoutReal GlobalY(BoutReal jy) const override;
+  BoutReal GlobalZ(BoutReal jz) const override;
 
   BoutReal getIxseps1() const { return ixseps1; }
   BoutReal getIxseps2() const { return ixseps2; }
@@ -296,15 +298,17 @@ private:
   int MYPE; ///< Rank of this processor
 
   int PE_YIND; ///< Y index of this processor
-  int NYPE;    // Number of processors in the Y direction
+  int NYPE;    ///< Number of processors in the Y direction
 
-  int NZPE;
+  int PE_ZIND{0}; ///< Z index of this processor
+  int NZPE{1};    ///< Number of processors in the Z direction
 
   /// Is this processor in the core region?
   bool MYPE_IN_CORE{false};
 
   int XGLOBAL(BoutReal xloc, BoutReal& xglo) const;
   int YGLOBAL(BoutReal yloc, BoutReal& yglo) const;
+  int ZGLOBAL(BoutReal zloc, BoutReal& zglo) const;
 
   // Topology
   int ixseps1, ixseps2, jyseps1_1, jyseps2_1, jyseps1_2, jyseps2_2;
@@ -355,8 +359,9 @@ private:
   // Settings
   bool TwistShift; // Use a twist-shift condition in core?
 
-  bool symmetricGlobalX; ///< Use a symmetric definition in GlobalX() function
-  bool symmetricGlobalY;
+  bool symmetricGlobalX;        ///< Use a symmetric definition in `GlobalX()` function
+  bool symmetricGlobalY;        ///< Use a symmetric definition in `GlobalY()` function
+  bool symmetricGlobalZ{false}; ///< Use a symmetric definition in `GlobalZ()` function
 
   int zperiod;
   BoutReal ZMIN, ZMAX; // Range of the Z domain (in fractions of 2pi)
diff --git a/src/sys/generator_context.cxx b/src/sys/generator_context.cxx
index 25274e8107..03b52ad24b 100644
--- a/src/sys/generator_context.cxx
+++ b/src/sys/generator_context.cxx
@@ -15,9 +15,8 @@ Context::Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t)
   parameters["y"] = (loc == CELL_YLOW) ? PI * (msh->GlobalY(iy) + msh->GlobalY(iy - 1))
                                        : TWOPI * msh->GlobalY(iy);
 
-  parameters["z"] = (loc == CELL_ZLOW)
-                        ? TWOPI * (iz - 0.5) / static_cast<BoutReal>(msh->LocalNz)
-                        : TWOPI * iz / static_cast<BoutReal>(msh->LocalNz);
+  parameters["z"] = (loc == CELL_ZLOW) ? PI * (msh->GlobalZ(iz) + msh->GlobalZ(iz - 1))
+                                       : TWOPI * msh->GlobalZ(iz);
 
   parameters["t"] = t;
 }
@@ -26,21 +25,20 @@ Context::Context(const BoundaryRegion* bndry, int iz, CELL_LOC loc, BoutReal t,
     : localmesh(msh) {
 
   // Add one to X index if boundary is in -x direction, so that XLOW is on the boundary
-  int ix = (bndry->bx < 0) ? bndry->x + 1 : bndry->x;
+  const int ix = (bndry->bx < 0) ? bndry->x + 1 : bndry->x;
 
   parameters["x"] = ((loc == CELL_XLOW) || (bndry->bx != 0))
                         ? 0.5 * (msh->GlobalX(ix) + msh->GlobalX(ix - 1))
                         : msh->GlobalX(ix);
 
-  int iy = (bndry->by < 0) ? bndry->y + 1 : bndry->y;
+  const int iy = (bndry->by < 0) ? bndry->y + 1 : bndry->y;
 
-  parameters["y"] = ((loc == CELL_YLOW) || bndry->by)
+  parameters["y"] = ((loc == CELL_YLOW) || (bndry->by != 0))
                         ? PI * (msh->GlobalY(iy) + msh->GlobalY(iy - 1))
                         : TWOPI * msh->GlobalY(iy);
 
-  parameters["z"] = (loc == CELL_ZLOW)
-                        ? TWOPI * (iz - 0.5) / static_cast<BoutReal>(msh->LocalNz)
-                        : TWOPI * iz / static_cast<BoutReal>(msh->LocalNz);
+  parameters["z"] = (loc == CELL_ZLOW) ? PI * (msh->GlobalZ(iz) + msh->GlobalZ(iz - 1))
+                                       : TWOPI * msh->GlobalZ(iz);
 
   parameters["t"] = t;
 }
diff --git a/tests/integrated/test-interpolate-z/test_interpolate.cxx b/tests/integrated/test-interpolate-z/test_interpolate.cxx
index 3ef6e50425..8ee96d2897 100644
--- a/tests/integrated/test-interpolate-z/test_interpolate.cxx
+++ b/tests/integrated/test-interpolate-z/test_interpolate.cxx
@@ -71,8 +71,7 @@ int main(int argc, char** argv) {
     deltaz[index] = dz;
     // Get the global indices
     bout::generator::Context pos{index, CELL_CENTRE, deltaz.getMesh(), 0.0};
-    pos.set("x", mesh->GlobalX(index.x()), "z",
-            TWOPI * static_cast<BoutReal>(dz) / static_cast<BoutReal>(mesh->LocalNz));
+    pos.set("x", mesh->GlobalX(index.x()), "z", TWOPI * mesh->GlobalZ(dz));
     // Generate the analytic solution at the displacements
     a_solution[index] = a_gen->generate(pos);
     b_solution[index] = b_gen->generate(pos);
diff --git a/tests/integrated/test-interpolate/test_interpolate.cxx b/tests/integrated/test-interpolate/test_interpolate.cxx
index 33963dbb9e..98ecd68bc5 100644
--- a/tests/integrated/test-interpolate/test_interpolate.cxx
+++ b/tests/integrated/test-interpolate/test_interpolate.cxx
@@ -79,8 +79,7 @@ int main(int argc, char** argv) {
       deltaz[index] = dz;
       // Get the global indices
       bout::generator::Context pos{index, CELL_CENTRE, deltax.getMesh(), 0.0};
-      pos.set("x", mesh->GlobalX(dx), "z",
-              TWOPI * static_cast<BoutReal>(dz) / static_cast<BoutReal>(mesh->LocalNz));
+      pos.set("x", mesh->GlobalX(dx), "z", TWOPI * mesh->GlobalZ(dz));
       // Generate the analytic solution at the displacements
       a_solution[index] = a_gen->generate(pos);
       b_solution[index] = b_gen->generate(pos);
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 2feb43826d..b93cddf9ca 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -170,20 +170,22 @@ public:
   }
   BoutReal GlobalX(int jx) const override { return jx; }
   BoutReal GlobalY(int jy) const override { return jy; }
+  BoutReal GlobalZ(int jz) const override { return jz; }
   BoutReal GlobalX(BoutReal jx) const override { return jx; }
   BoutReal GlobalY(BoutReal jy) const override { return jy; }
+  BoutReal GlobalZ(BoutReal jz) const override { return jz; }
   int getGlobalXIndex(int) const override { return 0; }
   int getGlobalXIndexNoBoundaries(int) const override { return 0; }
   int getGlobalYIndex(int y) const override { return y; }
   int getGlobalYIndexNoBoundaries(int y) const override { return y; }
-  int getGlobalZIndex(int) const override { return 0; }
-  int getGlobalZIndexNoBoundaries(int) const override { return 0; }
+  int getGlobalZIndex(int z) const override { return z; }
+  int getGlobalZIndexNoBoundaries(int z) const override { return z; }
   int getLocalXIndex(int) const override { return 0; }
   int getLocalXIndexNoBoundaries(int) const override { return 0; }
   int getLocalYIndex(int y) const override { return y; }
   int getLocalYIndexNoBoundaries(int y) const override { return y; }
-  int getLocalZIndex(int) const override { return 0; }
-  int getLocalZIndexNoBoundaries(int) const override { return 0; }
+  int getLocalZIndex(int z) const override { return z; }
+  int getLocalZIndexNoBoundaries(int z) const override { return z; }
 
   void initDerivs(Options* opt) {
     StaggerGrids = true;
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index 26dc1e2990..b45206b979 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -161,9 +161,7 @@ TYPED_TEST(FieldFactoryCreationTest, CreateZ) {
   auto output = this->create("z");
 
   auto expected = makeField<TypeParam>(
-      [](typename TypeParam::ind_type& index) -> BoutReal {
-        return TWOPI * index.z() / FieldFactoryCreationTest<TypeParam>::nz;
-      },
+      [](typename TypeParam::ind_type& index) -> BoutReal { return TWOPI * index.z(); },
       mesh);
 
   EXPECT_TRUE(IsFieldEqual(output, expected));
@@ -209,7 +207,7 @@ TYPED_TEST(FieldFactoryCreationTest, CreateZStaggered) {
           offset = 0.5;
         }
 
-        return TWOPI * (index.z() - offset) / FieldFactoryCreationTest<TypeParam>::nz;
+        return TWOPI * (index.z() - offset);
       },
       mesh);
 
diff --git a/tests/unit/mesh/data/test_gridfromoptions.cxx b/tests/unit/mesh/data/test_gridfromoptions.cxx
index b821d2e225..41dd40fcc3 100644
--- a/tests/unit/mesh/data/test_gridfromoptions.cxx
+++ b/tests/unit/mesh/data/test_gridfromoptions.cxx
@@ -57,13 +57,13 @@ class GridFromOptionsTest : public ::testing::Test {
 
     expected_2d = makeField<Field2D>(
         [](Field2D::ind_type& index) {
-          return index.x() + (TWOPI * index.y()) + (TWOPI * index.z() / nz) + 3;
+          return index.x() + (TWOPI * index.y()) + (TWOPI * index.z()) + 3;
         },
         &mesh_from_options);
 
     expected_3d = makeField<Field3D>(
         [](Field3D::ind_type& index) {
-          return index.x() + (TWOPI * index.y()) + (TWOPI * index.z() / nz) + 3;
+          return index.x() + (TWOPI * index.y()) + (TWOPI * index.z()) + 3;
         },
         &mesh_from_options);
     expected_metric =
@@ -316,8 +316,8 @@ TEST_F(GridFromOptionsTest, GetVectorBoutRealYNone) {
 
 TEST_F(GridFromOptionsTest, GetVectorBoutRealZ) {
   std::vector<BoutReal> result{};
-  std::vector<BoutReal> expected{3., 3. + (1. * TWOPI / nz), 3. + (2. * TWOPI / nz),
-                                 3. + (3. * TWOPI / nz), 3. + (4. * TWOPI / nz)};
+  std::vector<BoutReal> expected{3., 3. + (1. * TWOPI), 3. + (2. * TWOPI),
+                                 3. + (3. * TWOPI), 3. + (4. * TWOPI)};
 
   EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nz, 0,
                             GridDataSource::Direction::Z));
@@ -326,9 +326,8 @@ TEST_F(GridFromOptionsTest, GetVectorBoutRealZ) {
 
 TEST_F(GridFromOptionsTest, GetVectorBoutRealZOffset) {
   std::vector<BoutReal> result{};
-  std::vector<BoutReal> expected{3. + (1. * TWOPI / nz), 3. + (2. * TWOPI / nz),
-                                 3. + (3. * TWOPI / nz), 3. + (4. * TWOPI / nz),
-                                 3. + (5. * TWOPI / nz)};
+  std::vector<BoutReal> expected{3. + (1. * TWOPI), 3. + (2. * TWOPI), 3. + (3. * TWOPI),
+                                 3. + (4. * TWOPI), 3. + (5. * TWOPI)};
 
   EXPECT_TRUE(griddata->get(&mesh_from_options, result, "f", nz, 1,
                             GridDataSource::Direction::Z));
@@ -337,8 +336,8 @@ TEST_F(GridFromOptionsTest, GetVectorBoutRealZOffset) {
 
 TEST_F(GridFromOptionsTest, GetVectorBoutRealZMeshOffset) {
   std::vector<BoutReal> result{};
-  std::vector<BoutReal> expected{3. + (-1. * TWOPI / nz), 3., 3. + (1. * TWOPI / nz),
-                                 3. + (2. * TWOPI / nz), 3. + (3. * TWOPI / nz)};
+  std::vector<BoutReal> expected{3. + (-1. * TWOPI), 3., 3. + (1. * TWOPI),
+                                 3. + (2. * TWOPI), 3. + (3. * TWOPI)};
 
   mesh_from_options.OffsetX = 100;
   mesh_from_options.OffsetY = 100;
@@ -397,7 +396,7 @@ TEST_F(GridFromOptionsTest, CoordinatesXlowInterp) {
 
   Coordinates::FieldMetric expected_xlow = makeField<Coordinates::FieldMetric>(
       [](Coordinates::FieldMetric::ind_type& index) {
-        return index.x() - 0.5 + (TWOPI * index.y()) + (TWOPI * index.z() / nz) + 3;
+        return index.x() - 0.5 + (TWOPI * index.y()) + (TWOPI * index.z()) + 3;
       },
       &mesh_from_options);
 
@@ -438,8 +437,7 @@ TEST_F(GridFromOptionsTest, CoordinatesXlowRead) {
 
   Field2D expected_xlow = makeField<Field2D>(
       [](Field2D::ind_type& index) {
-        return (nx - index.x() + 0.5) + (TWOPI * index.y()) + (TWOPI * index.z() / nz)
-               + 3;
+        return (nx - index.x() + 0.5) + (TWOPI * index.y()) + (TWOPI * index.z()) + 3;
       },
       &mesh_from_options);
 
@@ -471,7 +469,7 @@ TEST_F(GridFromOptionsTest, CoordinatesYlowInterp) {
 
   Field2D expected_ylow = makeField<Field2D>(
       [](Field2D::ind_type& index) {
-        return index.x() + (TWOPI * (index.y() - 0.5)) + (TWOPI * index.z() / nz) + 3;
+        return index.x() + (TWOPI * (index.y() - 0.5)) + (TWOPI * index.z()) + 3;
       },
       &mesh_from_options);
 
@@ -521,8 +519,7 @@ TEST_F(GridFromOptionsTest, CoordinatesYlowRead) {
 
   Field2D expected_ylow = makeField<Field2D>(
       [](Field2D::ind_type& index) {
-        return index.x() + (TWOPI * (ny - index.y() + 0.5)) + (TWOPI * index.z() / nz)
-               + 3;
+        return index.x() + (TWOPI * (ny - index.y() + 0.5)) + (TWOPI * index.z()) + 3;
       },
       &mesh_from_options);
 

From 6c6872505dd013e7bee3d5be48e2dba90b05572a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 8 Jan 2026 17:13:58 +0000
Subject: [PATCH 0460/1827] Move `NXPE`/`PE_XIND` out of `Mesh`

---
 include/bout/mesh.hxx                                |  2 --
 .../iterative_parallel_tri.cxx                       |  2 +-
 src/invert/laplace/impls/spt/spt.cxx                 | 12 ++++++------
 src/mesh/impls/bout/boutmesh.cxx                     | 11 +++++------
 src/mesh/impls/bout/boutmesh.hxx                     |  6 ++++--
 tests/unit/fake_mesh.hxx                             |  2 --
 6 files changed, 16 insertions(+), 19 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index c22d6e969b..83066b860f 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -368,8 +368,6 @@ public:
   /// Domain is periodic in X?
   bool periodicX{false};
 
-  int NXPE, PE_XIND; ///< Number of processors in X, and X processor index
-
   /// Send a buffer of data to processor at X index +1
   ///
   /// @param[in] buffer  The data to send. Must be at least length \p size
diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
index 926facd9e6..7535ffb3c7 100644
--- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
+++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
@@ -72,7 +72,7 @@ LaplaceIPT::LaplaceIPT(Options* opt, CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED
   D.setLocation(location);
 
   // Number of procs must be a factor of 2
-  const int n = localmesh->NXPE;
+  const int n = localmesh->getNXPE();
   if (!is_pow2(n)) {
     throw BoutException("LaplaceIPT error: NXPE must be a power of 2");
   }
diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx
index e39ca7e89f..e4eab810af 100644
--- a/src/invert/laplace/impls/spt/spt.cxx
+++ b/src/invert/laplace/impls/spt/spt.cxx
@@ -341,14 +341,14 @@ int LaplaceSPT::start(const FieldPerp& b, SPT_data& data) {
     // Send data
     localmesh->sendXOut(std::begin(data.buffer), 4 * (maxmode + 1), data.comm_tag);
 
-  } else if (localmesh->PE_XIND == 1) {
+  } else if (localmesh->getXProcIndex() == 1) {
     // Post a receive
     data.recv_handle =
         localmesh->irecvXIn(std::begin(data.buffer), 4 * (maxmode + 1), data.comm_tag);
   }
 
   data.proc++; // Now moved onto the next processor
-  if (localmesh->NXPE == 2) {
+  if (localmesh->getNXPE() == 2) {
     data.dir = -1; // Special case. Otherwise reversal handled in spt_continue
   }
 
@@ -366,7 +366,7 @@ int LaplaceSPT::next(SPT_data& data) {
     return 1;
   }
 
-  if (localmesh->PE_XIND == data.proc) {
+  if (localmesh->getXProcIndex() == data.proc) {
     /// This processor's turn to do inversion
 
     // Wait for data to arrive
@@ -450,7 +450,7 @@ int LaplaceSPT::next(SPT_data& data) {
       }
     }
 
-    if (localmesh->PE_XIND != 0) { // If not finished yet
+    if (localmesh->getXProcIndex() != 0) { // If not finished yet
       /// Send data
 
       if (data.dir > 0) {
@@ -460,7 +460,7 @@ int LaplaceSPT::next(SPT_data& data) {
       }
     }
 
-  } else if (localmesh->PE_XIND == data.proc + data.dir) {
+  } else if (localmesh->getXProcIndex() == data.proc + data.dir) {
     // This processor is next, post receive
 
     if (data.dir > 0) {
@@ -474,7 +474,7 @@ int LaplaceSPT::next(SPT_data& data) {
 
   data.proc += data.dir;
 
-  if (data.proc == localmesh->NXPE - 1) {
+  if (data.proc == localmesh->getNXPE() - 1) {
     data.dir = -1; // Reverses direction at the end
   }
 
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 507e3b9495..74c06dfce4 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -1827,16 +1827,15 @@ BoutMesh::BoutMesh(int input_nx, int input_ny, int input_nz, int mxg, int myg, i
 
 BoutMesh::BoutMesh(int input_nx, int input_ny, int input_nz, int mxg, int myg, int nxpe,
                    int nype, int pe_xind, int pe_yind, bool symmetric_X, bool symmetric_Y,
-                   bool periodicX_, int ixseps1_, int ixseps2_, int jyseps1_1_,
+                   bool periodic_X_, int ixseps1_, int ixseps2_, int jyseps1_1_,
                    int jyseps2_1_, int jyseps1_2_, int jyseps2_2_, int ny_inner_,
                    bool create_regions)
     : nx(input_nx), ny(input_ny), nz(input_nz), NPES(nxpe * nype),
-      MYPE(nxpe * pe_yind + pe_xind), PE_YIND(pe_yind), NYPE(nype), NZPE(1),
-      ixseps1(ixseps1_), ixseps2(ixseps2_), symmetricGlobalX(symmetric_X),
+      MYPE((nxpe * pe_yind) + pe_xind), PE_XIND(pe_xind), NXPE(nxpe), PE_YIND(pe_yind),
+      NYPE(nype), ixseps1(ixseps1_), ixseps2(ixseps2_), symmetricGlobalX(symmetric_X),
       symmetricGlobalY(symmetric_Y), MXG(mxg), MYG(myg), MZG(0) {
-  NXPE = nxpe;
-  PE_XIND = pe_xind;
-  periodicX = periodicX_;
+
+  periodicX = periodic_X_;
   setYDecompositionIndices(jyseps1_1_, jyseps2_1_, jyseps1_2_, jyseps2_2_, ny_inner_);
   setDerivedGridSizes();
   topology();
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index f39856867c..09d0015890 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -7,7 +7,6 @@
 #include "bout/unused.hxx"
 #include <bout/mesh.hxx>
 
-#include <cmath>
 #include <list>
 #include <set>
 #include <string>
@@ -208,7 +207,7 @@ protected:
   /// `getPossibleBoundaries`. \p create_regions controls whether or
   /// not the various `Region`s are created on the new mesh
   BoutMesh(int input_nx, int input_ny, int input_nz, int mxg, int myg, int nxpe, int nype,
-           int pe_xind, int pe_yind, bool symmetric_X, bool symmetric_Y, bool periodic_X,
+           int pe_xind, int pe_yind, bool symmetric_X, bool symmetric_Y, bool periodic_X_,
            int ixseps1_, int ixseps2_, int jyseps1_1_, int jyseps2_1_, int jyseps1_2_,
            int jyseps2_2_, int ny_inner_, bool create_regions = true);
 
@@ -297,6 +296,9 @@ private:
   int NPES; ///< Number of processors
   int MYPE; ///< Rank of this processor
 
+  int PE_XIND; ///< X index of this processor
+  int NXPE;    ///< Number of processors in the X direction
+
   int PE_YIND; ///< Y index of this processor
   int NYPE;    ///< Number of processors in the Y direction
 
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index b93cddf9ca..255e13ae36 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -73,8 +73,6 @@ public:
 
     // Unused variables
     periodicX = false;
-    NXPE = 1;
-    PE_XIND = 0;
     IncIntShear = false;
     maxregionblocksize = MAXREGIONBLOCKSIZE;
 

From eaf4c57665da8d66d5e14bf0b53ec7a644a36f24 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 8 Jan 2026 17:27:56 +0000
Subject: [PATCH 0461/1827] Add `Mesh::getNZPE()/getZProcIndex`

Also make related methods all `const`
---
 include/bout/mesh.hxx            | 10 ++++++----
 src/mesh/impls/bout/boutmesh.cxx | 12 ++++++++----
 src/mesh/impls/bout/boutmesh.hxx | 10 ++++++----
 tests/unit/fake_mesh.hxx         | 10 ++++++----
 4 files changed, 26 insertions(+), 16 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 83066b860f..502b0c5668 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -354,10 +354,12 @@ public:
 
   // non-local communications
 
-  virtual int getNXPE() = 0;       ///< The number of processors in the X direction
-  virtual int getNYPE() = 0;       ///< The number of processors in the Y direction
-  virtual int getXProcIndex() = 0; ///< This processor's index in X direction
-  virtual int getYProcIndex() = 0; ///< This processor's index in Y direction
+  virtual int getNXPE() const = 0;       ///< The number of processors in the X direction
+  virtual int getNYPE() const = 0;       ///< The number of processors in the Y direction
+  virtual int getNZPE() const = 0;       ///< The number of processors in the Z direction
+  virtual int getXProcIndex() const = 0; ///< This processor's index in X direction
+  virtual int getYProcIndex() const = 0; ///< This processor's index in Y direction
+  virtual int getZProcIndex() const = 0; ///< This processor's index in Z direction
 
   // X communications
   virtual bool firstX()
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 74c06dfce4..6ce6f8783e 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -1522,13 +1522,17 @@ int BoutMesh::wait(comm_handle handle) {
  *             Non-Local Communications
  ***************************************************************/
 
-int BoutMesh::getNXPE() { return NXPE; }
+int BoutMesh::getNXPE() const { return NXPE; }
 
-int BoutMesh::getNYPE() { return NYPE; }
+int BoutMesh::getNYPE() const { return NYPE; }
 
-int BoutMesh::getXProcIndex() { return PE_XIND; }
+int BoutMesh::getNZPE() const { return NZPE; }
 
-int BoutMesh::getYProcIndex() { return PE_YIND; }
+int BoutMesh::getXProcIndex() const { return PE_XIND; }
+
+int BoutMesh::getYProcIndex() const { return PE_YIND; }
+
+int BoutMesh::getZProcIndex() const { return PE_ZIND; }
 
 /****************************************************************
  *                 X COMMUNICATIONS
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index 09d0015890..fea3583c4b 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -57,10 +57,12 @@ public:
   /////////////////////////////////////////////
   // non-local communications
 
-  int getNXPE() override;       ///< The number of processors in the X direction
-  int getNYPE() override;       ///< The number of processors in the Y direction
-  int getXProcIndex() override; ///< This processor's index in X direction
-  int getYProcIndex() override; ///< This processor's index in Y direction
+  int getNXPE() const override;       ///< The number of processors in the X direction
+  int getNYPE() const override;       ///< The number of processors in the Y direction
+  int getNZPE() const override;       ///< The number of processors in the Z direction
+  int getXProcIndex() const override; ///< This processor's index in X direction
+  int getYProcIndex() const override; ///< This processor's index in Y direction
+  int getZProcIndex() const override; ///< This processor's index in Z direction
 
   /////////////////////////////////////////////
   // X communications
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 255e13ae36..5e37406f5d 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -107,10 +107,12 @@ public:
     return nullptr;
   }
   int wait(comm_handle UNUSED(handle)) override { return 0; }
-  int getNXPE() override { return 1; }
-  int getNYPE() override { return 1; }
-  int getXProcIndex() override { return 1; }
-  int getYProcIndex() override { return 1; }
+  int getNXPE() const override { return 1; }
+  int getNYPE() const override { return 1; }
+  int getNZPE() const override { return 1; }
+  int getXProcIndex() const override { return 1; }
+  int getYProcIndex() const override { return 1; }
+  int getZProcIndex() const override { return 1; }
   bool firstX() const override { return true; }
   bool lastX() const override { return true; }
   int sendXOut(BoutReal* UNUSED(buffer), int UNUSED(size), int UNUSED(tag)) override {

From ca3507674ac5130c15a669a5740b0fb1bf567acf Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 9 Jan 2026 09:50:22 +0000
Subject: [PATCH 0462/1827] Add guards for FFT routines against parallel-in-z
 runs

---
 include/bout/fft.hxx                           | 16 +++++++++++++++-
 src/field/field3d.cxx                          |  4 +++-
 src/invert/fft_fftw.cxx                        | 18 +++++++++++++++++-
 .../laplace/impls/cyclic/cyclic_laplace.cxx    |  2 ++
 .../iterative_parallel_tri.cxx                 |  2 ++
 src/invert/laplace/impls/pcr/pcr.cxx           |  2 ++
 .../laplace/impls/pcr_thomas/pcr_thomas.cxx    |  2 ++
 .../laplace/impls/serial_band/serial_band.cxx  |  3 +++
 .../laplace/impls/serial_tri/serial_tri.cxx    |  7 ++++---
 src/invert/laplace/impls/spt/spt.cxx           |  3 +++
 .../impls/cyclic/laplacexz-cyclic.cxx          |  1 +
 src/invert/parderiv/impls/cyclic/cyclic.cxx    |  2 ++
 .../pardiv/impls/cyclic/pardiv_cyclic.cxx      |  1 +
 src/mesh/boundary_standard.cxx                 |  4 ++++
 src/mesh/coordinates.cxx                       |  4 ++--
 src/mesh/index_derivs.cxx                      |  2 ++
 src/mesh/parallel/shiftedmetric.cxx            |  1 +
 17 files changed, 66 insertions(+), 8 deletions(-)

diff --git a/include/bout/fft.hxx b/include/bout/fft.hxx
index fdec8b7bec..649b3bb5db 100644
--- a/include/bout/fft.hxx
+++ b/include/bout/fft.hxx
@@ -28,9 +28,13 @@
 #ifndef BOUT_FFT_H
 #define BOUT_FFT_H
 
-#include "bout/dcomplex.hxx"
+#include "bout/build_defines.hxx"
+
 #include <bout/array.hxx>
 #include <bout/bout_enum_class.hxx>
+#include <bout/dcomplex.hxx>
+
+#include <string_view>
 
 class Options;
 
@@ -111,6 +115,16 @@ Array<dcomplex> rfft(const Array<BoutReal>& in);
 /// Expects that `in.size() == (length / 2) + 1`
 Array<BoutReal> irfft(const Array<dcomplex>& in, int length);
 
+/// Check simulation is using 1 processor in Z, throw exception if not
+///
+/// Generally, FFTs must be done over the full Z domain. Currently, most
+/// methods using FFTs don't handle parallelising in Z
+#if BOUT_CHECK_LEVEL > 0
+void checkZSerial(const Mesh& mesh, std::string_view name);
+#else
+inline void checkZSerial([[maybe_unused]] const Mesh& mesh,
+                         [[maybe_unused]] std::string_view name) {}
+#endif
 } // namespace fft
 } // namespace bout
 
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 9821c638f7..c0209947b6 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -604,6 +604,7 @@ FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs, const std::string& rgn)
 
 Field3D filter(const Field3D& var, int N0, const std::string& rgn) {
 
+  bout::fft::checkZSerial(*var.getMesh(), "`filter`");
   checkData(var);
 
   int ncz = var.getNz();
@@ -649,6 +650,7 @@ Field3D filter(const Field3D& var, int N0, const std::string& rgn) {
 // Fourier filter in z with zmin
 Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string& rgn) {
 
+  bout::fft::checkZSerial(*var.getMesh(), "`lowPass`");
   checkData(var);
   int ncz = var.getNz();
 
@@ -697,7 +699,7 @@ Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string
  * Use FFT to shift by an angle in the Z direction
  */
 void shiftZ(Field3D& var, int jx, int jy, double zangle) {
-
+  bout::fft::checkZSerial(*var.getMesh(), "`shiftZ`");
   checkData(var);
   var.allocate(); // Ensure that var is unique
   Mesh* localmesh = var.getMesh();
diff --git a/src/invert/fft_fftw.cxx b/src/invert/fft_fftw.cxx
index 05977e5f3f..94dd528b27 100644
--- a/src/invert/fft_fftw.cxx
+++ b/src/invert/fft_fftw.cxx
@@ -27,8 +27,10 @@
 
 #include "bout/build_defines.hxx"
 
+#include <bout/coordinates.hxx>
 #include <bout/fft.hxx>
 #include <bout/globals.hxx>
+#include <bout/mesh.hxx>
 #include <bout/options.hxx>
 #include <bout/unused.hxx>
 
@@ -36,7 +38,6 @@
 #include <bout/constants.hxx>
 #include <bout/openmpwrap.hxx>
 
-#include <cmath>
 #include <fftw3.h>
 
 #if BOUT_USE_OPENMP
@@ -46,6 +47,12 @@
 #include <bout/boutexception.hxx>
 #endif // BOUT_HAS_FFTW
 
+#if BOUT_CHECK_LEVEL > 0
+#include <bout/boutexception.hxx>
+
+#include <string_view>
+#endif
+
 namespace bout {
 namespace fft {
 
@@ -527,5 +534,14 @@ Array<BoutReal> irfft(const Array<dcomplex>& in, int length) {
   return out;
 }
 
+#if BOUT_CHECK_LEVEL > 0
+void checkZSerial(const Mesh& mesh, std::string_view name) {
+  if (mesh.getNZPE() != 1) {
+    throw BoutException("{} uses FFTs which are currently incompatible with multiple "
+                        "processors in Z (using {})",
+                        name, mesh.getNZPE());
+  }
+}
+#endif
 } // namespace fft
 } // namespace bout
diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
index 99aacea4f8..adb30def83 100644
--- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
+++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
@@ -57,6 +57,8 @@ LaplaceCyclic::LaplaceCyclic(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
                              Solver* UNUSED(solver))
     : Laplacian(opt, loc, mesh_in), Acoef(0.0), C1coef(1.0), C2coef(1.0), Dcoef(1.0) {
 
+  bout::fft::checkZSerial(*localmesh, "`cyclic` inversion");
+
   Acoef.setLocation(location);
   C1coef.setLocation(location);
   C2coef.setLocation(location);
diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
index 7535ffb3c7..8743d59db2 100644
--- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
+++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
@@ -67,6 +67,8 @@ LaplaceIPT::LaplaceIPT(Options* opt, CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED
       au(ny, nmode), bu(ny, nmode), rl(nmode), ru(nmode), r1(ny, nmode), r2(ny, nmode),
       first_call(ny), x0saved(ny, 4, nmode), converged(nmode), fine_error(4, nmode) {
 
+  bout::fft::checkZSerial(*localmesh, "`ipt` inversion");
+
   A.setLocation(location);
   C.setLocation(location);
   D.setLocation(location);
diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx
index 60169c6eb4..29f007118c 100644
--- a/src/invert/laplace/impls/pcr/pcr.cxx
+++ b/src/invert/laplace/impls/pcr/pcr.cxx
@@ -67,6 +67,8 @@ LaplacePCR::LaplacePCR(Options* opt, CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED
       ncx(localmesh->LocalNx), ny(localmesh->LocalNy), avec(ny, nmode, ncx),
       bvec(ny, nmode, ncx), cvec(ny, nmode, ncx) {
 
+  bout::fft::checkZSerial(*localmesh, "`pcr` inversion");
+
   Acoef.setLocation(location);
   C1coef.setLocation(location);
   C2coef.setLocation(location);
diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
index 600166aa6b..73b7d6ec5c 100644
--- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
+++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
@@ -65,6 +65,8 @@ LaplacePCR_THOMAS::LaplacePCR_THOMAS(Options* opt, CELL_LOC loc, Mesh* mesh_in,
       ncx(localmesh->LocalNx), ny(localmesh->LocalNy), avec(ny, nmode, ncx),
       bvec(ny, nmode, ncx), cvec(ny, nmode, ncx) {
 
+  bout::fft::checkZSerial(*localmesh, "`pcr_thomas` inversion");
+
   Acoef.setLocation(location);
   C1coef.setLocation(location);
   C2coef.setLocation(location);
diff --git a/src/invert/laplace/impls/serial_band/serial_band.cxx b/src/invert/laplace/impls/serial_band/serial_band.cxx
index d7b4ac5d3b..921f2af24d 100644
--- a/src/invert/laplace/impls/serial_band/serial_band.cxx
+++ b/src/invert/laplace/impls/serial_band/serial_band.cxx
@@ -45,6 +45,9 @@
 LaplaceSerialBand::LaplaceSerialBand(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
                                      Solver* UNUSED(solver))
     : Laplacian(opt, loc, mesh_in), Acoef(0.0), Ccoef(1.0), Dcoef(1.0) {
+
+  bout::fft::checkZSerial(*localmesh, "`band` inversion");
+
   Acoef.setLocation(location);
   Ccoef.setLocation(location);
   Dcoef.setLocation(location);
diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.cxx b/src/invert/laplace/impls/serial_tri/serial_tri.cxx
index 0fb9294d76..1a64984a3e 100644
--- a/src/invert/laplace/impls/serial_tri/serial_tri.cxx
+++ b/src/invert/laplace/impls/serial_tri/serial_tri.cxx
@@ -33,14 +33,15 @@
 #include <bout/lapack_routines.hxx>
 #include <bout/mesh.hxx>
 #include <bout/openmpwrap.hxx>
-#include <bout/utils.hxx>
-#include <cmath>
-
 #include <bout/output.hxx>
+#include <bout/utils.hxx>
 
 LaplaceSerialTri::LaplaceSerialTri(Options* opt, CELL_LOC loc, Mesh* mesh_in,
                                    Solver* UNUSED(solver))
     : Laplacian(opt, loc, mesh_in), A(0.0), C(1.0), D(1.0) {
+
+  bout::fft::checkZSerial(*localmesh, "`tri` inversion");
+
   A.setLocation(location);
   C.setLocation(location);
   D.setLocation(location);
diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx
index e4eab810af..1a5cb5f23c 100644
--- a/src/invert/laplace/impls/spt/spt.cxx
+++ b/src/invert/laplace/impls/spt/spt.cxx
@@ -45,6 +45,9 @@
 LaplaceSPT::LaplaceSPT(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
                        Solver* UNUSED(solver))
     : Laplacian(opt, loc, mesh_in), Acoef(0.0), Ccoef(1.0), Dcoef(1.0) {
+
+  bout::fft::checkZSerial(*localmesh, "`spt` inversion");
+
   Acoef.setLocation(location);
   Ccoef.setLocation(location);
   Dcoef.setLocation(location);
diff --git a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
index dc987edc75..56780eaf5c 100644
--- a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
+++ b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
@@ -13,6 +13,7 @@
 LaplaceXZcyclic::LaplaceXZcyclic(Mesh* m, Options* options, const CELL_LOC loc)
     : LaplaceXZ(m, options, loc) {
   // Note: `m` may be nullptr, but localmesh is set in LaplaceXZ base constructor
+  bout::fft::checkZSerial(*localmesh, "`cyclic` X-Z inversion");
 
   // Number of Z Fourier modes, including DC
   nmode = (localmesh->LocalNz) / 2 + 1;
diff --git a/src/invert/parderiv/impls/cyclic/cyclic.cxx b/src/invert/parderiv/impls/cyclic/cyclic.cxx
index 61d23be823..d20537a0f3 100644
--- a/src/invert/parderiv/impls/cyclic/cyclic.cxx
+++ b/src/invert/parderiv/impls/cyclic/cyclic.cxx
@@ -53,6 +53,8 @@
 
 InvertParCR::InvertParCR(Options* opt, CELL_LOC location, Mesh* mesh_in)
     : InvertPar(opt, location, mesh_in), A(1.0), B(0.0), C(0.0), D(0.0), E(0.0) {
+
+  bout::fft::checkZSerial(*localmesh, "InvertParCR");
   // Number of k equations to solve for each x location
   nsys = 1 + (localmesh->LocalNz) / 2;
 
diff --git a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
index d4e773f017..67ddef9d6f 100644
--- a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
+++ b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
@@ -53,6 +53,7 @@
 
 InvertParDivCR::InvertParDivCR(Options* opt, CELL_LOC location, Mesh* mesh_in)
     : InvertParDiv(opt, location, mesh_in) {
+  bout::fft::checkZSerial(*localmesh, "InvertParDivCR");
   // Number of k equations to solve for each x location
   nsys = 1 + (localmesh->LocalNz) / 2;
 }
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 6fd659b375..ae92e6165d 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -2631,6 +2631,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 #if not(BOUT_USE_METRIC_3D)
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
+    bout::fft::checkZSerial(*mesh, "Zero Laplace on Field3D");
     int ncz = mesh->LocalNz;
 
     Coordinates* metric = f.getCoordinates();
@@ -2734,6 +2735,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 #if not(BOUT_USE_METRIC_3D)
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
+    bout::fft::checkZSerial(*mesh, "Zero Laplace on Field3D");
     const int ncz = mesh->LocalNz;
 
     ASSERT0(ncz % 2 == 0); // Allocation assumes even number
@@ -2843,6 +2845,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
+    bout::fft::checkZSerial(*mesh, "Zero Laplace on Field3D");
+
     Coordinates* metric = f.getCoordinates();
 
     int ncz = mesh->LocalNz;
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 086fa2e23e..91bbddfd56 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1659,7 +1659,7 @@ Field3D Coordinates::Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
 
   Field3D result{emptyFrom(f).setLocation(outloc)};
 
-  if (useFFT and not bout::build::use_metric_3d) {
+  if (useFFT and not bout::build::use_metric_3d and localmesh->getNZPE() == 1) {
     int ncz = localmesh->LocalNz;
 
     // Allocate memory
@@ -1727,7 +1727,7 @@ FieldPerp Coordinates::Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
   int jy = f.getIndex();
   result.setIndex(jy);
 
-  if (useFFT) {
+  if (useFFT and localmesh->getNZPE() == 1) {
     int ncz = localmesh->LocalNz;
 
     // Allocate memory
diff --git a/src/mesh/index_derivs.cxx b/src/mesh/index_derivs.cxx
index 48284c3536..70fc47b538 100644
--- a/src/mesh/index_derivs.cxx
+++ b/src/mesh/index_derivs.cxx
@@ -427,6 +427,7 @@ class FFTDerivativeType {
     ASSERT2(bout::utils::is_Field3D_v<T>); // Should never need to call this with Field2D
 
     auto* theMesh = var.getMesh();
+    ASSERT2(theMesh->getNZPE() == 1); // Only works if serial in Z for FFTs
 
     // Calculate how many Z wavenumbers will be removed
     const int ncz = theMesh->getNpoints(direction);
@@ -493,6 +494,7 @@ class FFT2ndDerivativeType {
     ASSERT2(bout::utils::is_Field3D_v<T>); // Should never need to call this with Field2D
 
     auto* theMesh = var.getMesh();
+    ASSERT2(theMesh->getNZPE() == 1); // Only works if serial in Z for FFTs
 
     // Calculate how many Z wavenumbers will be removed
     const int ncz = theMesh->getNpoints(direction);
diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 382052047d..121c52fe3c 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -24,6 +24,7 @@ ShiftedMetric::ShiftedMetric(Mesh& m, CELL_LOC location_in, Field2D zShift_,
   ASSERT1(zShift.getLocation() == location);
   // check the coordinate system used for the grid data source
   ShiftedMetric::checkInputGrid();
+  bout::fft::checkZSerial(m, "ShiftedMetric");
 
   cachePhases();
 }

From 3b0510f539d128cb0ec4d5abcad1f24f7dbba96b Mon Sep 17 00:00:00 2001
From: David Dickinson <d7919@users.noreply.github.com>
Date: Fri, 14 Dec 2018 15:27:31 +0000
Subject: [PATCH 0463/1827] Update unit tests for z-guards

---
 tests/unit/fake_mesh.hxx                |  2 +-
 tests/unit/include/bout/test_region.cxx | 16 ++++++++--------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 5e37406f5d..7d7326c149 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -66,7 +66,7 @@ public:
     xend = nx - 2;
     ystart = 1;
     yend = ny - 2;
-    zstart = 0;
+    zstart = 0; // no guards
     zend = nz - 1;
 
     StaggerGrids = false;
diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx
index 3b21700412..00137c1ce7 100644
--- a/tests/unit/include/bout/test_region.cxx
+++ b/tests/unit/include/bout/test_region.cxx
@@ -211,8 +211,8 @@ TEST_F(RegionTest, regionLoopNoBndry) {
   BOUT_FOR(i, region) { a[i] = 1.0; }
 
   const int nmesh = RegionTest::nx * RegionTest::ny * RegionTest::nz;
-  const int ninner =
-      (mesh->LocalNz * (1 + mesh->xend - mesh->xstart) * (1 + mesh->yend - mesh->ystart));
+  const int ninner = ((1 + mesh->zend - mesh->zstart) * (1 + mesh->xend - mesh->xstart)
+                      * (1 + mesh->yend - mesh->ystart));
   int numExpectNotMatching = nmesh - ninner;
 
   int numNotMatching = 0;
@@ -249,8 +249,8 @@ TEST_F(RegionTest, regionLoopNoBndrySerial) {
   int count = 0;
   BOUT_FOR_SERIAL(i, region) { ++count; }
 
-  const int ninner =
-      (mesh->LocalNz * (1 + mesh->xend - mesh->xstart) * (1 + mesh->yend - mesh->ystart));
+  const int ninner = ((1 + mesh->zend - mesh->zstart) * (1 + mesh->xend - mesh->xstart)
+                      * (1 + mesh->yend - mesh->ystart));
 
   EXPECT_EQ(count, ninner);
 }
@@ -300,8 +300,8 @@ TEST_F(RegionTest, regionLoopNoBndrySection) {
     }
   }
 
-  const int ninner =
-      (mesh->LocalNz * (1 + mesh->xend - mesh->xstart) * (1 + mesh->yend - mesh->ystart));
+  const int ninner = ((1 + mesh->zend - mesh->zstart) * (1 + mesh->xend - mesh->xstart)
+                      * (1 + mesh->yend - mesh->ystart));
 
   EXPECT_EQ(count, ninner);
 }
@@ -334,8 +334,8 @@ TEST_F(RegionTest, regionLoopNoBndryInner) {
   }
 
   const int nmesh = RegionTest::nx * RegionTest::ny * RegionTest::nz;
-  const int ninner =
-      (mesh->LocalNz * (1 + mesh->xend - mesh->xstart) * (1 + mesh->yend - mesh->ystart));
+  const int ninner = ((1 + mesh->zend - mesh->zstart) * (1 + mesh->xend - mesh->xstart)
+                      * (1 + mesh->yend - mesh->ystart));
   int numExpectNotMatching = nmesh - ninner;
 
   int numNotMatching = 0;

From f75b6a628942c481f68b2d76bfaff19197e49e9a Mon Sep 17 00:00:00 2001
From: David Dickinson <d7919@users.noreply.github.com>
Date: Fri, 14 Dec 2018 15:25:31 +0000
Subject: [PATCH 0464/1827] Update mms tests for z-guards

---
 tests/MMS/laplace/laplace.cxx | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/MMS/laplace/laplace.cxx b/tests/MMS/laplace/laplace.cxx
index fbcdee355c..214c022cd5 100644
--- a/tests/MMS/laplace/laplace.cxx
+++ b/tests/MMS/laplace/laplace.cxx
@@ -26,9 +26,8 @@ int main(int argc, char** argv) {
   meshoptions->get("Lx", Lx, 1.0);
 
   /*this assumes equidistant grid*/
-  int nguard = mesh->xstart;
-  mesh->getCoordinates()->dx = Lx / (mesh->GlobalNx - 2 * nguard);
-  mesh->getCoordinates()->dz = TWOPI * Lx / (mesh->LocalNz);
+  mesh->getCoordinates()->dx = Lx / (mesh->GlobalNx - 2 * mesh->xstart);
+  mesh->getCoordinates()->dz = TWOPI * Lx / (mesh->GlobalNz - 2 * mesh->zstart);
   /////
 
   // Create a Laplacian inversion solver

From 5c7bf58b5d64bd843d64b2424c6e21be5b5686fa Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 9 Jan 2026 11:40:05 +0000
Subject: [PATCH 0465/1827] Use `Mesh::GlobalZ` in `shiftedmetricinterp`

---
 src/mesh/parallel/shiftedmetricinterp.cxx | 32 +++++++++++------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx
index 4543c4c3fb..f55081410d 100644
--- a/src/mesh/parallel/shiftedmetricinterp.cxx
+++ b/src/mesh/parallel/shiftedmetricinterp.cxx
@@ -128,10 +128,10 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
     for (int z = mesh.zstart; z <= mesh.zend; z++) {
       forward_boundary_xin->add_point(
           it.ind, mesh.yend, z,
-          mesh.GlobalX(it.ind),                           // x
-          2. * PI * mesh.GlobalY(mesh.yend + 0.5),        // y
-          zlength * BoutReal(z) / BoutReal(mesh.GlobalNz) // z
-              + 0.5 * (zShift(it.ind, mesh.yend + 1) - zShift(it.ind, mesh.yend)),
+          mesh.GlobalX(it.ind),                    // x
+          2. * PI * mesh.GlobalY(mesh.yend + 0.5), // y
+          (zlength * mesh.GlobalZ(z))              // z
+              + (0.5 * (zShift(it.ind, mesh.yend + 1) - zShift(it.ind, mesh.yend))),
           0.25
               * (1                                                     // dy/2
                  + dy(it.ind, mesh.yend + 1) / dy(it.ind, mesh.yend)), // length
@@ -144,10 +144,10 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
     for (int z = mesh.zstart; z <= mesh.zend; z++) {
       backward_boundary_xin->add_point(
           it.ind, mesh.ystart, z,
-          mesh.GlobalX(it.ind),                           // x
-          2. * PI * mesh.GlobalY(mesh.ystart - 0.5),      // y
-          zlength * BoutReal(z) / BoutReal(mesh.GlobalNz) // z
-              + 0.5 * (zShift(it.ind, mesh.ystart) - zShift(it.ind, mesh.ystart - 1)),
+          mesh.GlobalX(it.ind),                      // x
+          2. * PI * mesh.GlobalY(mesh.ystart - 0.5), // y
+          (zlength * mesh.GlobalZ(z))                // z
+              + (0.5 * (zShift(it.ind, mesh.ystart) - zShift(it.ind, mesh.ystart - 1))),
           0.25
               * (1 // dy/2
                  + dy(it.ind, mesh.ystart - 1) / dy(it.ind, mesh.ystart)),
@@ -161,10 +161,10 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
     for (int z = mesh.zstart; z <= mesh.zend; z++) {
       forward_boundary_xout->add_point(
           it.ind, mesh.yend, z,
-          mesh.GlobalX(it.ind),                           // x
-          2. * PI * mesh.GlobalY(mesh.yend + 0.5),        // y
-          zlength * BoutReal(z) / BoutReal(mesh.GlobalNz) // z
-              + 0.5 * (zShift(it.ind, mesh.yend + 1) - zShift(it.ind, mesh.yend)),
+          mesh.GlobalX(it.ind),                    // x
+          2. * PI * mesh.GlobalY(mesh.yend + 0.5), // y
+          (zlength * mesh.GlobalZ(z))              // z
+              + (0.5 * (zShift(it.ind, mesh.yend + 1) - zShift(it.ind, mesh.yend))),
           0.25
               * (1 // dy/2
                  + dy(it.ind, mesh.yend + 1) / dy(it.ind, mesh.yend)),
@@ -177,10 +177,10 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
     for (int z = mesh.zstart; z <= mesh.zend; z++) {
       backward_boundary_xout->add_point(
           it.ind, mesh.ystart, z,
-          mesh.GlobalX(it.ind),                           // x
-          2. * PI * mesh.GlobalY(mesh.ystart - 0.5),      // y
-          zlength * BoutReal(z) / BoutReal(mesh.GlobalNz) // z
-              + 0.5 * (zShift(it.ind, mesh.ystart) - zShift(it.ind, mesh.ystart - 1)),
+          mesh.GlobalX(it.ind),                      // x
+          2. * PI * mesh.GlobalY(mesh.ystart - 0.5), // y
+          (zlength * mesh.GlobalZ(z))                // z
+              + (0.5 * (zShift(it.ind, mesh.ystart) - zShift(it.ind, mesh.ystart - 1))),
           0.25
               * (dy(it.ind, mesh.ystart - 1) / dy(it.ind, mesh.ystart) // dy/2
                  + 1),

From 97d245b3ce26f6dacab4701c0b784e41e6b05da4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 9 Jan 2026 11:47:14 +0000
Subject: [PATCH 0466/1827] Fix incorrect type of local variable

---
 src/mesh/parallel/shiftedmetricinterp.cxx | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx
index f55081410d..91a889af0f 100644
--- a/src/mesh/parallel/shiftedmetricinterp.cxx
+++ b/src/mesh/parallel/shiftedmetricinterp.cxx
@@ -27,6 +27,8 @@
  *
  **************************************************************************/
 
+#include <algorithm>
+
 #include "shiftedmetricinterp.hxx"
 #include "bout/constants.hxx"
 #include "bout/parallel_boundary_region.hxx"
@@ -114,11 +116,10 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
 
   interp_from_aligned->calcWeights(zt_prime_from);
 
-  int yvalid = mesh.LocalNy - 2 * mesh.ystart;
   // avoid overflow - no stencil need more than 5 points
-  if (yvalid > 20) {
-    yvalid = 20;
-  }
+  const auto yvalid =
+      static_cast<signed char>(std::min(mesh.LocalNy - (2 * mesh.ystart), 20));
+
   // Create regions for parallel boundary conditions
   Field2D dy;
   mesh.get(dy, "dy", 1.);

From daff6a135f2e26878ffb679d9d99669ff621935e Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 9 Jan 2026 14:07:04 +0000
Subject: [PATCH 0467/1827] Fix some clang-tidy warnings about includes

---
 include/bout/fft.hxx          | 1 +
 src/sys/generator_context.cxx | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/include/bout/fft.hxx b/include/bout/fft.hxx
index 649b3bb5db..afc7bb8f36 100644
--- a/include/bout/fft.hxx
+++ b/include/bout/fft.hxx
@@ -36,6 +36,7 @@
 
 #include <string_view>
 
+class Mesh;
 class Options;
 
 BOUT_ENUM_CLASS(FFT_MEASUREMENT_FLAG, estimate, measure, exhaustive);
diff --git a/src/sys/generator_context.cxx b/src/sys/generator_context.cxx
index 03b52ad24b..31a5662378 100644
--- a/src/sys/generator_context.cxx
+++ b/src/sys/generator_context.cxx
@@ -1,5 +1,7 @@
 #include "bout/sys/generator_context.hxx"
+
 #include "bout/boundary_region.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/constants.hxx"
 #include "bout/mesh.hxx"
 

From 9cf05c26277e6b4d60357f3f188615b775a0a700 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 9 Jan 2026 14:47:04 +0000
Subject: [PATCH 0468/1827] Rename private `BoutMesh::{X,Y,Z}GLOBAL` methods
 for consistency

These are just the `BoutReal` overloads of the equivalent `getGlobal?Index` methods
---
 src/mesh/impls/bout/boutmesh.cxx | 52 ++++++++++++++------------------
 src/mesh/impls/bout/boutmesh.hxx |  9 ++++--
 2 files changed, 29 insertions(+), 32 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 6ce6f8783e..4e6e88bd20 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -1696,35 +1696,32 @@ int BoutMesh::PROC_NUM(int xind, int yind) const {
     return -1;
   }
 
-  return yind * NXPE + xind;
+  return (yind * NXPE) + xind;
 }
 
-/// Returns the global X index given a local index
-int BoutMesh::XGLOBAL(BoutReal xloc, BoutReal& xglo) const {
-  xglo = xloc + PE_XIND * MXSUB;
-  return static_cast<int>(xglo);
+BoutReal BoutMesh::getGlobalXIndex(BoutReal xloc) const {
+  return xloc + (PE_XIND * MXSUB);
 }
 
-int BoutMesh::getGlobalXIndex(int xlocal) const { return xlocal + PE_XIND * MXSUB; }
+int BoutMesh::getGlobalXIndex(int xlocal) const { return xlocal + (PE_XIND * MXSUB); }
 
 int BoutMesh::getGlobalXIndexNoBoundaries(int xlocal) const {
-  return xlocal + PE_XIND * MXSUB - MXG;
+  return xlocal + (PE_XIND * MXSUB) - MXG;
 }
 
-int BoutMesh::getLocalXIndex(int xglobal) const { return xglobal - PE_XIND * MXSUB; }
+int BoutMesh::getLocalXIndex(int xglobal) const { return xglobal - (PE_XIND * MXSUB); }
 
 int BoutMesh::getLocalXIndexNoBoundaries(int xglobal) const {
-  return xglobal - PE_XIND * MXSUB + MXG;
+  return xglobal - (PE_XIND * MXSUB) + MXG;
 }
 
-int BoutMesh::YGLOBAL(BoutReal yloc, BoutReal& yglo) const {
-  yglo = yloc + PE_YIND * MYSUB - MYG;
-  return static_cast<int>(yglo);
+BoutReal BoutMesh::getGlobalYIndex(BoutReal yloc) const {
+  return yloc + (PE_YIND * MYSUB) - MYG;
 }
 
 int BoutMesh::getGlobalYIndex(int ylocal) const {
-  int yglobal = ylocal + PE_YIND * MYSUB;
-  if (jyseps1_2 > jyseps2_1 and PE_YIND * MYSUB + 2 * MYG + 1 > ny_inner) {
+  int yglobal = ylocal + (PE_YIND * MYSUB);
+  if (jyseps1_2 > jyseps2_1 and (PE_YIND * MYSUB) + (2 * MYG) + 1 > ny_inner) {
     // Double null, and we are past the upper target
     yglobal += 2 * MYG;
   }
@@ -1732,12 +1729,12 @@ int BoutMesh::getGlobalYIndex(int ylocal) const {
 }
 
 int BoutMesh::getGlobalYIndexNoBoundaries(int ylocal) const {
-  return ylocal + PE_YIND * MYSUB - MYG;
+  return ylocal + (PE_YIND * MYSUB) - MYG;
 }
 
 int BoutMesh::getLocalYIndex(int yglobal) const {
-  int ylocal = yglobal - PE_YIND * MYSUB;
-  if (jyseps1_2 > jyseps2_1 and PE_YIND * MYSUB + 2 * MYG + 1 > ny_inner) {
+  int ylocal = yglobal - (PE_YIND * MYSUB);
+  if (jyseps1_2 > jyseps2_1 and (PE_YIND * MYSUB) + (2 * MYG) + 1 > ny_inner) {
     // Double null, and we are past the upper target
     ylocal -= 2 * MYG;
   }
@@ -1745,7 +1742,7 @@ int BoutMesh::getLocalYIndex(int yglobal) const {
 }
 
 int BoutMesh::getLocalYIndexNoBoundaries(int yglobal) const {
-  return yglobal - PE_YIND * MYSUB + MYG;
+  return yglobal - (PE_YIND * MYSUB) + MYG;
 }
 
 int BoutMesh::YGLOBAL(int yloc, int yproc) const { return yloc + (yproc * MYSUB) - MYG; }
@@ -1754,14 +1751,14 @@ int BoutMesh::YLOCAL(int yglo, int yproc) const { return yglo - (yproc * MYSUB)
 
 int BoutMesh::getGlobalZIndex(int zlocal) const { return zlocal + (PE_ZIND * MZSUB); }
 
-int BoutMesh::getGlobalZIndexNoBoundaries(int zlocal) const { return zlocal + (PE_ZIND * MZSUB) - MZG; }
+int BoutMesh::getGlobalZIndexNoBoundaries(int zlocal) const {
+  return zlocal + (PE_ZIND * MZSUB) - MZG;
+}
 
 int BoutMesh::getLocalZIndex(int zglobal) const { return zglobal; }
 
-/// Returns the global Z index given a local index
-int BoutMesh::ZGLOBAL(BoutReal zloc, BoutReal& zglo) const {
-  zglo = zloc + (PE_ZIND * MZSUB);
-  return static_cast<int>(zglo);
+BoutReal BoutMesh::getGlobalZIndex(BoutReal zloc) const {
+  return zloc + (PE_ZIND * MZSUB);
 }
 
 int BoutMesh::getLocalZIndexNoBoundaries(int zglobal) const { return zglobal; }
@@ -3136,8 +3133,7 @@ BoutReal BoutMesh::GlobalX(int jx) const {
 BoutReal BoutMesh::GlobalX(BoutReal jx) const {
 
   // Get global X index as a BoutReal
-  BoutReal xglo;
-  XGLOBAL(jx, xglo);
+  const BoutReal xglo = getGlobalXIndex(jx);
 
   if (symmetricGlobalX) {
     // With this definition the boundary sits dx/2 away form the first/last inner points
@@ -3191,8 +3187,7 @@ BoutReal BoutMesh::GlobalY(int jy) const {
 BoutReal BoutMesh::GlobalY(BoutReal jy) const {
 
   // Get global Y index as a BoutReal
-  BoutReal yglo;
-  YGLOBAL(jy, yglo);
+  BoutReal yglo = getGlobalYIndex(jy);
 
   if (symmetricGlobalY) {
     BoutReal yi = yglo;
@@ -3245,8 +3240,7 @@ BoutReal BoutMesh::GlobalZ(int jz) const {
 BoutReal BoutMesh::GlobalZ(BoutReal jz) const {
 
   // Get global Z index as a BoutReal
-  BoutReal zglo;
-  ZGLOBAL(jz, zglo);
+  const BoutReal zglo = getGlobalZIndex(jz);
 
   if (symmetricGlobalZ) {
     // With this definition the boundary sits dx/2 away form the first/last inner points
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index fea3583c4b..3923c34511 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -310,9 +310,12 @@ private:
   /// Is this processor in the core region?
   bool MYPE_IN_CORE{false};
 
-  int XGLOBAL(BoutReal xloc, BoutReal& xglo) const;
-  int YGLOBAL(BoutReal yloc, BoutReal& yglo) const;
-  int ZGLOBAL(BoutReal zloc, BoutReal& zglo) const;
+  /// Returns the global X index given a local index
+  BoutReal getGlobalXIndex(BoutReal xloc) const;
+  /// Returns the global Y index given a local index
+  BoutReal getGlobalYIndex(BoutReal yloc) const;
+  /// Returns the global Z index given a local index
+  BoutReal getGlobalZIndex(BoutReal zloc) const;
 
   // Topology
   int ixseps1, ixseps2, jyseps1_1, jyseps2_1, jyseps1_2, jyseps2_2;

From 22a848f6f524d29f050717ea515faa0db3128e60 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 14:00:43 +0000
Subject: [PATCH 0469/1827] Fix a couple of typos in comments

[skip ci]

Co-authored-by: David Bold <dschwoerer@users.noreply.github.com>
---
 src/mesh/impls/bout/boutmesh.cxx          | 2 +-
 src/mesh/parallel/shiftedmetricinterp.cxx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 4e6e88bd20..0310b2e5bd 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -3243,7 +3243,7 @@ BoutReal BoutMesh::GlobalZ(BoutReal jz) const {
   const BoutReal zglo = getGlobalZIndex(jz);
 
   if (symmetricGlobalZ) {
-    // With this definition the boundary sits dx/2 away form the first/last inner points
+    // With this definition the boundary sits dz/2 away form the first/last inner points
     return (0.5 + zglo - (nz - MZ) * 0.5) / static_cast<BoutReal>(MZ);
   }
   return zglo / static_cast<BoutReal>(MZ);
diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx
index 91a889af0f..fa94416da1 100644
--- a/src/mesh/parallel/shiftedmetricinterp.cxx
+++ b/src/mesh/parallel/shiftedmetricinterp.cxx
@@ -116,7 +116,7 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
 
   interp_from_aligned->calcWeights(zt_prime_from);
 
-  // avoid overflow - no stencil need more than 5 points
+  // avoid overflow - no stencil needs more than 5 points
   const auto yvalid =
       static_cast<signed char>(std::min(mesh.LocalNy - (2 * mesh.ystart), 20));
 

From b1ffc21666a88e14a140275b75dedf3fb1274c70 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 19 Jan 2026 14:02:20 +0000
Subject: [PATCH 0470/1827] Rename Z-serial assert function

---
 include/bout/fft.hxx                                        | 6 +++---
 src/field/field3d.cxx                                       | 6 +++---
 src/invert/fft_fftw.cxx                                     | 2 +-
 src/invert/laplace/impls/cyclic/cyclic_laplace.cxx          | 2 +-
 .../impls/iterative_parallel_tri/iterative_parallel_tri.cxx | 2 +-
 src/invert/laplace/impls/pcr/pcr.cxx                        | 2 +-
 src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx          | 2 +-
 src/invert/laplace/impls/serial_band/serial_band.cxx        | 2 +-
 src/invert/laplace/impls/serial_tri/serial_tri.cxx          | 2 +-
 src/invert/laplace/impls/spt/spt.cxx                        | 2 +-
 src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx      | 2 +-
 src/invert/parderiv/impls/cyclic/cyclic.cxx                 | 2 +-
 src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx            | 2 +-
 src/mesh/boundary_standard.cxx                              | 6 +++---
 src/mesh/parallel/shiftedmetric.cxx                         | 2 +-
 15 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/include/bout/fft.hxx b/include/bout/fft.hxx
index afc7bb8f36..b7d36d2166 100644
--- a/include/bout/fft.hxx
+++ b/include/bout/fft.hxx
@@ -121,10 +121,10 @@ Array<BoutReal> irfft(const Array<dcomplex>& in, int length);
 /// Generally, FFTs must be done over the full Z domain. Currently, most
 /// methods using FFTs don't handle parallelising in Z
 #if BOUT_CHECK_LEVEL > 0
-void checkZSerial(const Mesh& mesh, std::string_view name);
+void assertZSerial(const Mesh& mesh, std::string_view name);
 #else
-inline void checkZSerial([[maybe_unused]] const Mesh& mesh,
-                         [[maybe_unused]] std::string_view name) {}
+inline void assertZSerial([[maybe_unused]] const Mesh& mesh,
+                          [[maybe_unused]] std::string_view name) {}
 #endif
 } // namespace fft
 } // namespace bout
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index c0209947b6..b3448238f5 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -604,7 +604,7 @@ FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs, const std::string& rgn)
 
 Field3D filter(const Field3D& var, int N0, const std::string& rgn) {
 
-  bout::fft::checkZSerial(*var.getMesh(), "`filter`");
+  bout::fft::assertZSerial(*var.getMesh(), "`filter`");
   checkData(var);
 
   int ncz = var.getNz();
@@ -650,7 +650,7 @@ Field3D filter(const Field3D& var, int N0, const std::string& rgn) {
 // Fourier filter in z with zmin
 Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string& rgn) {
 
-  bout::fft::checkZSerial(*var.getMesh(), "`lowPass`");
+  bout::fft::assertZSerial(*var.getMesh(), "`lowPass`");
   checkData(var);
   int ncz = var.getNz();
 
@@ -699,7 +699,7 @@ Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string
  * Use FFT to shift by an angle in the Z direction
  */
 void shiftZ(Field3D& var, int jx, int jy, double zangle) {
-  bout::fft::checkZSerial(*var.getMesh(), "`shiftZ`");
+  bout::fft::assertZSerial(*var.getMesh(), "`shiftZ`");
   checkData(var);
   var.allocate(); // Ensure that var is unique
   Mesh* localmesh = var.getMesh();
diff --git a/src/invert/fft_fftw.cxx b/src/invert/fft_fftw.cxx
index 94dd528b27..2c633da6d5 100644
--- a/src/invert/fft_fftw.cxx
+++ b/src/invert/fft_fftw.cxx
@@ -535,7 +535,7 @@ Array<BoutReal> irfft(const Array<dcomplex>& in, int length) {
 }
 
 #if BOUT_CHECK_LEVEL > 0
-void checkZSerial(const Mesh& mesh, std::string_view name) {
+void assertZSerial(const Mesh& mesh, std::string_view name) {
   if (mesh.getNZPE() != 1) {
     throw BoutException("{} uses FFTs which are currently incompatible with multiple "
                         "processors in Z (using {})",
diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
index adb30def83..80b22e73f7 100644
--- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
+++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
@@ -57,7 +57,7 @@ LaplaceCyclic::LaplaceCyclic(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
                              Solver* UNUSED(solver))
     : Laplacian(opt, loc, mesh_in), Acoef(0.0), C1coef(1.0), C2coef(1.0), Dcoef(1.0) {
 
-  bout::fft::checkZSerial(*localmesh, "`cyclic` inversion");
+  bout::fft::assertZSerial(*localmesh, "`cyclic` inversion");
 
   Acoef.setLocation(location);
   C1coef.setLocation(location);
diff --git a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
index 8743d59db2..e9219091e2 100644
--- a/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
+++ b/src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
@@ -67,7 +67,7 @@ LaplaceIPT::LaplaceIPT(Options* opt, CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED
       au(ny, nmode), bu(ny, nmode), rl(nmode), ru(nmode), r1(ny, nmode), r2(ny, nmode),
       first_call(ny), x0saved(ny, 4, nmode), converged(nmode), fine_error(4, nmode) {
 
-  bout::fft::checkZSerial(*localmesh, "`ipt` inversion");
+  bout::fft::assertZSerial(*localmesh, "`ipt` inversion");
 
   A.setLocation(location);
   C.setLocation(location);
diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx
index 29f007118c..a33bd7eef2 100644
--- a/src/invert/laplace/impls/pcr/pcr.cxx
+++ b/src/invert/laplace/impls/pcr/pcr.cxx
@@ -67,7 +67,7 @@ LaplacePCR::LaplacePCR(Options* opt, CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED
       ncx(localmesh->LocalNx), ny(localmesh->LocalNy), avec(ny, nmode, ncx),
       bvec(ny, nmode, ncx), cvec(ny, nmode, ncx) {
 
-  bout::fft::checkZSerial(*localmesh, "`pcr` inversion");
+  bout::fft::assertZSerial(*localmesh, "`pcr` inversion");
 
   Acoef.setLocation(location);
   C1coef.setLocation(location);
diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
index 73b7d6ec5c..d471775990 100644
--- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
+++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
@@ -65,7 +65,7 @@ LaplacePCR_THOMAS::LaplacePCR_THOMAS(Options* opt, CELL_LOC loc, Mesh* mesh_in,
       ncx(localmesh->LocalNx), ny(localmesh->LocalNy), avec(ny, nmode, ncx),
       bvec(ny, nmode, ncx), cvec(ny, nmode, ncx) {
 
-  bout::fft::checkZSerial(*localmesh, "`pcr_thomas` inversion");
+  bout::fft::assertZSerial(*localmesh, "`pcr_thomas` inversion");
 
   Acoef.setLocation(location);
   C1coef.setLocation(location);
diff --git a/src/invert/laplace/impls/serial_band/serial_band.cxx b/src/invert/laplace/impls/serial_band/serial_band.cxx
index 921f2af24d..0cf8d7259d 100644
--- a/src/invert/laplace/impls/serial_band/serial_band.cxx
+++ b/src/invert/laplace/impls/serial_band/serial_band.cxx
@@ -46,7 +46,7 @@ LaplaceSerialBand::LaplaceSerialBand(Options* opt, const CELL_LOC loc, Mesh* mes
                                      Solver* UNUSED(solver))
     : Laplacian(opt, loc, mesh_in), Acoef(0.0), Ccoef(1.0), Dcoef(1.0) {
 
-  bout::fft::checkZSerial(*localmesh, "`band` inversion");
+  bout::fft::assertZSerial(*localmesh, "`band` inversion");
 
   Acoef.setLocation(location);
   Ccoef.setLocation(location);
diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.cxx b/src/invert/laplace/impls/serial_tri/serial_tri.cxx
index 1a64984a3e..a14e0e4a26 100644
--- a/src/invert/laplace/impls/serial_tri/serial_tri.cxx
+++ b/src/invert/laplace/impls/serial_tri/serial_tri.cxx
@@ -40,7 +40,7 @@ LaplaceSerialTri::LaplaceSerialTri(Options* opt, CELL_LOC loc, Mesh* mesh_in,
                                    Solver* UNUSED(solver))
     : Laplacian(opt, loc, mesh_in), A(0.0), C(1.0), D(1.0) {
 
-  bout::fft::checkZSerial(*localmesh, "`tri` inversion");
+  bout::fft::assertZSerial(*localmesh, "`tri` inversion");
 
   A.setLocation(location);
   C.setLocation(location);
diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx
index 1a5cb5f23c..cd24ee1acf 100644
--- a/src/invert/laplace/impls/spt/spt.cxx
+++ b/src/invert/laplace/impls/spt/spt.cxx
@@ -46,7 +46,7 @@ LaplaceSPT::LaplaceSPT(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
                        Solver* UNUSED(solver))
     : Laplacian(opt, loc, mesh_in), Acoef(0.0), Ccoef(1.0), Dcoef(1.0) {
 
-  bout::fft::checkZSerial(*localmesh, "`spt` inversion");
+  bout::fft::assertZSerial(*localmesh, "`spt` inversion");
 
   Acoef.setLocation(location);
   Ccoef.setLocation(location);
diff --git a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
index 56780eaf5c..b3e619df0c 100644
--- a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
+++ b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
@@ -13,7 +13,7 @@
 LaplaceXZcyclic::LaplaceXZcyclic(Mesh* m, Options* options, const CELL_LOC loc)
     : LaplaceXZ(m, options, loc) {
   // Note: `m` may be nullptr, but localmesh is set in LaplaceXZ base constructor
-  bout::fft::checkZSerial(*localmesh, "`cyclic` X-Z inversion");
+  bout::fft::assertZSerial(*localmesh, "`cyclic` X-Z inversion");
 
   // Number of Z Fourier modes, including DC
   nmode = (localmesh->LocalNz) / 2 + 1;
diff --git a/src/invert/parderiv/impls/cyclic/cyclic.cxx b/src/invert/parderiv/impls/cyclic/cyclic.cxx
index d20537a0f3..c32c3d4b2d 100644
--- a/src/invert/parderiv/impls/cyclic/cyclic.cxx
+++ b/src/invert/parderiv/impls/cyclic/cyclic.cxx
@@ -54,7 +54,7 @@
 InvertParCR::InvertParCR(Options* opt, CELL_LOC location, Mesh* mesh_in)
     : InvertPar(opt, location, mesh_in), A(1.0), B(0.0), C(0.0), D(0.0), E(0.0) {
 
-  bout::fft::checkZSerial(*localmesh, "InvertParCR");
+  bout::fft::assertZSerial(*localmesh, "InvertParCR");
   // Number of k equations to solve for each x location
   nsys = 1 + (localmesh->LocalNz) / 2;
 
diff --git a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
index 67ddef9d6f..aad01c5f2f 100644
--- a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
+++ b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
@@ -53,7 +53,7 @@
 
 InvertParDivCR::InvertParDivCR(Options* opt, CELL_LOC location, Mesh* mesh_in)
     : InvertParDiv(opt, location, mesh_in) {
-  bout::fft::checkZSerial(*localmesh, "InvertParDivCR");
+  bout::fft::assertZSerial(*localmesh, "InvertParDivCR");
   // Number of k equations to solve for each x location
   nsys = 1 + (localmesh->LocalNz) / 2;
 }
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index ae92e6165d..39a1ea3641 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -2631,7 +2631,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 #if not(BOUT_USE_METRIC_3D)
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
-    bout::fft::checkZSerial(*mesh, "Zero Laplace on Field3D");
+    bout::fft::assertZSerial(*mesh, "Zero Laplace on Field3D");
     int ncz = mesh->LocalNz;
 
     Coordinates* metric = f.getCoordinates();
@@ -2735,7 +2735,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 #if not(BOUT_USE_METRIC_3D)
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
-    bout::fft::checkZSerial(*mesh, "Zero Laplace on Field3D");
+    bout::fft::assertZSerial(*mesh, "Zero Laplace on Field3D");
     const int ncz = mesh->LocalNz;
 
     ASSERT0(ncz % 2 == 0); // Allocation assumes even number
@@ -2845,7 +2845,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
-    bout::fft::checkZSerial(*mesh, "Zero Laplace on Field3D");
+    bout::fft::assertZSerial(*mesh, "Zero Laplace on Field3D");
 
     Coordinates* metric = f.getCoordinates();
 
diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 121c52fe3c..64c6d9a2ce 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -24,7 +24,7 @@ ShiftedMetric::ShiftedMetric(Mesh& m, CELL_LOC location_in, Field2D zShift_,
   ASSERT1(zShift.getLocation() == location);
   // check the coordinate system used for the grid data source
   ShiftedMetric::checkInputGrid();
-  bout::fft::checkZSerial(m, "ShiftedMetric");
+  bout::fft::assertZSerial(m, "ShiftedMetric");
 
   cachePhases();
 }

From a058da43591c666ae4108977358a1ae5d3674959 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 30 Jan 2026 13:10:06 +0000
Subject: [PATCH 0471/1827] Don't include boundaries in `GlobalZ`

---
 src/mesh/impls/bout/boutmesh.cxx | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 0310b2e5bd..4aaa760c04 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -3232,9 +3232,11 @@ BoutReal BoutMesh::GlobalY(BoutReal jy) const {
 BoutReal BoutMesh::GlobalZ(int jz) const {
   if (symmetricGlobalZ) {
     // With this definition the boundary sits dz/2 away form the first/last inner points
-    return (0.5 + getGlobalZIndex(jz) - (nz - MZ) * 0.5) / static_cast<BoutReal>(MZ);
+    return (0.5 + getGlobalZIndexNoBoundaries(jz) - (nz - MZ) * 0.5)
+           / static_cast<BoutReal>(MZ);
   }
-  return static_cast<BoutReal>(getGlobalZIndex(jz)) / static_cast<BoutReal>(MZ);
+  return static_cast<BoutReal>(getGlobalZIndexNoBoundaries(jz))
+         / static_cast<BoutReal>(MZ);
 }
 
 BoutReal BoutMesh::GlobalZ(BoutReal jz) const {

From f03eabd8cfd1d9dc71622fd90e395f904b281ebb Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 30 Jan 2026 13:10:38 +0000
Subject: [PATCH 0472/1827] Use global Z index functions in test-communications

---
 .../test-communications.cxx                   | 32 ++++++++++---------
 1 file changed, 17 insertions(+), 15 deletions(-)

diff --git a/tests/integrated/test-communications/test-communications.cxx b/tests/integrated/test-communications/test-communications.cxx
index 54c266ece2..5acbe3ee1a 100644
--- a/tests/integrated/test-communications/test-communications.cxx
+++ b/tests/integrated/test-communications/test-communications.cxx
@@ -11,10 +11,10 @@ int main(int argc, char** argv) {
 
   // interior cells
   BOUT_FOR(i, f.getRegion("RGN_NOBNDRY")) {
-    f[i] = mesh->GlobalNzNoBoundaries
-               * (mesh->GlobalNyNoBoundaries * mesh->getGlobalXIndexNoBoundaries(i.x())
-                  + mesh->getGlobalYIndexNoBoundaries(i.y()))
-           + i.z();
+    f[i] = (mesh->GlobalNzNoBoundaries
+            * (mesh->GlobalNyNoBoundaries * mesh->getGlobalXIndexNoBoundaries(i.x())
+               + mesh->getGlobalYIndexNoBoundaries(i.y())))
+           + mesh->getGlobalZIndexNoBoundaries(i.z());
   }
 
   // lower x-boundary cells
@@ -25,10 +25,10 @@ int main(int argc, char** argv) {
       for (int y = mesh->ystart; y <= mesh->yend; y++) {
         for (int z = mesh->zstart; z <= mesh->zend; z++) {
           f(x, y, z) = startind
-                       + mesh->GlobalNzNoBoundaries
-                             * (mesh->GlobalNyNoBoundaries * x
-                                + mesh->getGlobalYIndexNoBoundaries(y))
-                       + z;
+                       + (mesh->GlobalNzNoBoundaries
+                          * (mesh->GlobalNyNoBoundaries * x
+                             + mesh->getGlobalYIndexNoBoundaries(y)))
+                       + mesh->getGlobalZIndexNoBoundaries(z);
         }
       }
     }
@@ -41,10 +41,10 @@ int main(int argc, char** argv) {
       for (int y = mesh->ystart; y <= mesh->yend; y++) {
         for (int z = mesh->zstart; z <= mesh->zend; z++) {
           f(mesh->xend + 1 + x, y, z) = startind
-                                        + mesh->GlobalNzNoBoundaries
-                                              * (mesh->GlobalNyNoBoundaries * x
-                                                 + mesh->getGlobalYIndexNoBoundaries(y))
-                                        + z;
+                                        + (mesh->GlobalNzNoBoundaries
+                                           * (mesh->GlobalNyNoBoundaries * x
+                                              + mesh->getGlobalYIndexNoBoundaries(y)))
+                                        + mesh->getGlobalZIndexNoBoundaries(z);
         }
       }
     }
@@ -56,8 +56,9 @@ int main(int argc, char** argv) {
     int x = it.ind;
     for (int y = 0; y < mesh->ystart; y++) {
       for (int z = mesh->zstart; z <= mesh->zend; z++) {
-        f(x, y, z) =
-            startind + mesh->GlobalNzNoBoundaries * (mesh->getGlobalXIndex(x) + y) + z;
+        f(x, y, z) = startind
+                     + (mesh->GlobalNzNoBoundaries * (mesh->getGlobalXIndex(x) + y))
+                     + mesh->getGlobalZIndexNoBoundaries(z);
       }
     }
   }
@@ -69,7 +70,8 @@ int main(int argc, char** argv) {
     for (int y = 0; y < mesh->ystart; y++) {
       for (int z = mesh->zstart; z <= mesh->zend; z++) {
         f(x, mesh->yend + 1 + y, z) =
-            startind + mesh->GlobalNzNoBoundaries * (mesh->getGlobalXIndex(x) + y) + z;
+            startind + (mesh->GlobalNzNoBoundaries * (mesh->getGlobalXIndex(x) + y))
+            + mesh->getGlobalZIndexNoBoundaries(z);
       }
     }
   }

From 30c0efd74c1abfb5f32254debad3db5d2d960344 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 30 Jan 2026 13:12:49 +0000
Subject: [PATCH 0473/1827] Use global Z index functions in
 `ShiftedMetricInterp`

---
 src/mesh/parallel/shiftedmetricinterp.cxx | 34 +++++++++++++++--------
 1 file changed, 22 insertions(+), 12 deletions(-)

diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx
index fa94416da1..c71618ab19 100644
--- a/src/mesh/parallel/shiftedmetricinterp.cxx
+++ b/src/mesh/parallel/shiftedmetricinterp.cxx
@@ -30,7 +30,10 @@
 #include <algorithm>
 
 #include "shiftedmetricinterp.hxx"
+
+#include "bout/boutexception.hxx"
 #include "bout/constants.hxx"
+#include "bout/field3d.hxx"
 #include "bout/parallel_boundary_region.hxx"
 
 ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
@@ -38,12 +41,19 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
                                          Options* opt)
     : ParallelTransform(mesh, opt), location(location_in), zShift(std::move(zShift_in)),
       zlength(zlength_in), ydown_index(mesh.ystart) {
+
+  if (mesh.getNZPE() > 1) {
+    throw BoutException("ShiftedMetricInterp only works with 1 processor in Z");
+  }
+
   // check the coordinate system used for the grid data source
   ShiftedMetricInterp::checkInputGrid();
 
   // Allocate space for interpolator cache: y-guard cells in each direction
   parallel_slice_interpolators.resize(mesh.ystart * 2);
 
+  const BoutReal z_factor = static_cast<BoutReal>(mesh.GlobalNzNoBoundaries) / zlength;
+
   // Create the Interpolation objects and set whether they go up or down the
   // magnetic field
   auto& interp_options = options["zinterpolation"];
@@ -62,16 +72,16 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
 
     // Find the index positions where the magnetic field line intersects the x-z plane
     // y_offset points up
-    Field3D zt_prime_up(&mesh), zt_prime_down(&mesh);
+    Field3D zt_prime_up(&mesh);
+    Field3D zt_prime_down(&mesh);
     zt_prime_up.allocate();
     zt_prime_down.allocate();
 
     for (const auto& i : zt_prime_up.getRegion(RGN_NOY)) {
       // Field line moves in z by an angle zShift(i,j+1)-zShift(i,j) when going
       // from j to j+1, but we want the shift in index-space
-      zt_prime_up[i] = static_cast<BoutReal>(i.z())
-                       + (zShift[i.yp(y_offset + 1)] - zShift[i])
-                             * static_cast<BoutReal>(mesh.GlobalNz) / zlength;
+      zt_prime_up[i] = static_cast<BoutReal>(mesh.getGlobalZIndexNoBoundaries(i.z()))
+                       + ((zShift[i.yp(y_offset + 1)] - zShift[i]) * z_factor);
     }
 
     parallel_slice_interpolators[yup_index + y_offset]->calcWeights(zt_prime_up);
@@ -79,9 +89,8 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
     for (const auto& i : zt_prime_down.getRegion(RGN_NOY)) {
       // Field line moves in z by an angle -(zShift(i,j)-zShift(i,j-1)) when going
       // from j to j-1, but we want the shift in index-space
-      zt_prime_down[i] = static_cast<BoutReal>(i.z())
-                         - (zShift[i] - zShift[i.ym(y_offset + 1)])
-                               * static_cast<BoutReal>(mesh.GlobalNz) / zlength;
+      zt_prime_down[i] = static_cast<BoutReal>(mesh.getGlobalZIndexNoBoundaries(i.z()))
+                         - ((zShift[i] - zShift[i.ym(y_offset + 1)]) * z_factor);
     }
 
     parallel_slice_interpolators[ydown_index + y_offset]->calcWeights(zt_prime_down);
@@ -93,15 +102,16 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
   interp_from_aligned =
       ZInterpolationFactory::getInstance().create(&interp_options, 0, &mesh);
 
-  Field3D zt_prime_to(&mesh), zt_prime_from(&mesh);
+  Field3D zt_prime_to(&mesh);
+  Field3D zt_prime_from(&mesh);
   zt_prime_to.allocate();
   zt_prime_from.allocate();
 
   for (const auto& i : zt_prime_to) {
     // Field line moves in z by an angle zShift(i,j) when going
     // from y0 to y(j), but we want the shift in index-space
-    zt_prime_to[i] = static_cast<BoutReal>(i.z())
-                     + zShift[i] * static_cast<BoutReal>(mesh.GlobalNz) / zlength;
+    zt_prime_to[i] = static_cast<BoutReal>(mesh.getGlobalZIndexNoBoundaries(i.z()))
+                     + (zShift[i] * z_factor);
   }
 
   interp_to_aligned->calcWeights(zt_prime_to);
@@ -110,8 +120,8 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
     // Field line moves in z by an angle zShift(i,j) when going
     // from y0 to y(j), but we want the shift in index-space.
     // Here we reverse the shift, so subtract zShift
-    zt_prime_from[i] = static_cast<BoutReal>(i.z())
-                       - zShift[i] * static_cast<BoutReal>(mesh.GlobalNz) / zlength;
+    zt_prime_from[i] = static_cast<BoutReal>(mesh.getGlobalZIndexNoBoundaries(i.z()))
+                       - (zShift[i] * z_factor);
   }
 
   interp_from_aligned->calcWeights(zt_prime_from);

From ef95de8ed745f466cc6d355b38bcfac52f6b8ab8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 30 Jan 2026 16:55:39 +0000
Subject: [PATCH 0474/1827] Add unit tests for `ShiftedMetricInterp`

---
 .../unit/mesh/parallel/test_shiftedmetric.cxx | 109 +++++++++++-------
 1 file changed, 68 insertions(+), 41 deletions(-)

diff --git a/tests/unit/mesh/parallel/test_shiftedmetric.cxx b/tests/unit/mesh/parallel/test_shiftedmetric.cxx
index 7e111e9c4e..ecbce620c3 100644
--- a/tests/unit/mesh/parallel/test_shiftedmetric.cxx
+++ b/tests/unit/mesh/parallel/test_shiftedmetric.cxx
@@ -1,9 +1,14 @@
 #include "bout/build_defines.hxx"
 
 #include "gtest/gtest.h"
+#include <type_traits>
 
+#include "../../src/mesh/parallel/shiftedmetricinterp.hxx"
 #include "test_extras.hxx"
 #include "bout/fft.hxx"
+#include "bout/options_io.hxx"
+#include "bout/output.hxx"
+#include "bout/paralleltransform.hxx"
 
 #if BOUT_HAS_FFTW
 #include "fake_mesh.hxx"
@@ -11,6 +16,7 @@
 // The unit tests use the global mesh
 using namespace bout::globals;
 
+template <class Transform>
 class ShiftedMetricTest : public ::testing::Test {
 public:
   ShiftedMetricTest() {
@@ -41,7 +47,7 @@ class ShiftedMetricTest : public ::testing::Test {
     // No call to Coordinates::geometry() needed here
 
     auto coords = mesh->getCoordinates();
-    coords->setParallelTransform(bout::utils::make_unique<ShiftedMetric>(
+    coords->setParallelTransform(bout::utils::make_unique<Transform>(
         *mesh, CELL_CENTRE, zShift, coords->zlength()(0, 0)));
 
     Field3D input_temp{mesh};
@@ -90,7 +96,10 @@ class ShiftedMetricTest : public ::testing::Test {
   Field3D input;
 };
 
-TEST_F(ShiftedMetricTest, ToFieldAligned) {
+using ShiftedMetricTypes = ::testing::Types<ShiftedMetric, ShiftedMetricInterp>;
+TYPED_TEST_SUITE(ShiftedMetricTest, ShiftedMetricTypes);
+
+TYPED_TEST(ShiftedMetricTest, ToFieldAligned) {
   Field3D expected{mesh};
   expected.setDirectionY(YDirectionType::Aligned);
 
@@ -118,18 +127,18 @@ TEST_F(ShiftedMetricTest, ToFieldAligned) {
                         {4., 5., 1., 3., 2.},
                         {2., 4., 3., 5., 1.}}});
 
-  Field3D result = toFieldAligned(input);
+  Field3D result = toFieldAligned(this->input);
 
   EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_ALL", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(fromFieldAligned(result), input));
+  EXPECT_TRUE(IsFieldEqual(fromFieldAligned(result), this->input));
   EXPECT_TRUE(areFieldsCompatible(result, expected));
-  EXPECT_FALSE(areFieldsCompatible(result, input));
+  EXPECT_FALSE(areFieldsCompatible(result, this->input));
 }
 
-TEST_F(ShiftedMetricTest, FromFieldAligned) {
+TYPED_TEST(ShiftedMetricTest, FromFieldAligned) {
   // reset input.yDirectionType so that fromFieldAligned is not a null
   // operation
-  input.setDirectionY(YDirectionType::Aligned);
+  this->input.setDirectionY(YDirectionType::Aligned);
 
   Field3D expected{mesh, CELL_CENTRE};
   expected.setDirectionY(YDirectionType::Standard);
@@ -158,28 +167,33 @@ TEST_F(ShiftedMetricTest, FromFieldAligned) {
                         {2., 4., 5., 1., 3.},
                         {5., 1., 2., 4., 3.}}});
 
-  Field3D result = fromFieldAligned(input);
+  Field3D result = fromFieldAligned(this->input);
+
 
   // Loosen tolerance a bit due to FFTs
   EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_ALL", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(toFieldAligned(result), input, "RGN_ALL", FFTTolerance));
+  EXPECT_TRUE(IsFieldEqual(toFieldAligned(result), this->input, "RGN_ALL", FFTTolerance));
   EXPECT_TRUE(areFieldsCompatible(result, expected));
-  EXPECT_FALSE(areFieldsCompatible(result, input));
+  EXPECT_FALSE(areFieldsCompatible(result, this->input));
 }
 
-TEST_F(ShiftedMetricTest, FromToFieldAligned) {
-  EXPECT_TRUE(IsFieldEqual(fromFieldAligned(toFieldAligned(input)), input, "RGN_ALL",
+TYPED_TEST(ShiftedMetricTest, FromToFieldAligned) {
+  EXPECT_TRUE(IsFieldEqual(fromFieldAligned(toFieldAligned(this->input)), this->input, "RGN_ALL",
                            FFTTolerance));
 }
 
-TEST_F(ShiftedMetricTest, ToFromFieldAligned) {
-  input.setDirectionY(YDirectionType::Aligned);
+TYPED_TEST(ShiftedMetricTest, ToFromFieldAligned) {
+  this->input.setDirectionY(YDirectionType::Aligned);
 
-  EXPECT_TRUE(IsFieldEqual(toFieldAligned(fromFieldAligned(input)), input, "RGN_ALL",
+  EXPECT_TRUE(IsFieldEqual(toFieldAligned(fromFieldAligned(this->input)), this->input, "RGN_ALL",
                            FFTTolerance));
 }
 
-TEST_F(ShiftedMetricTest, ToFieldAlignedFieldPerp) {
+TYPED_TEST(ShiftedMetricTest, ToFieldAlignedFieldPerp) {
+  if constexpr (std::is_same_v<TypeParam, ShiftedMetricInterp>) {
+    GTEST_SKIP_("Not implemented yet");
+  }
+
   Field3D expected{mesh};
   expected.setDirectionY(YDirectionType::Aligned);
 
@@ -207,22 +221,26 @@ TEST_F(ShiftedMetricTest, ToFieldAlignedFieldPerp) {
                         {4., 5., 1., 3., 2.},
                         {2., 4., 3., 5., 1.}}});
 
-  FieldPerp result = toFieldAligned(sliceXZ(input, 3), "RGN_NOX");
+  FieldPerp result = toFieldAligned(sliceXZ(this->input, 3), "RGN_NOX");
 
   // Note that the region argument does not do anything for FieldPerp, as
   // FieldPerp does not have a getRegion2D() method. Values are never set in
   // the x-guard or x-boundary cells
   EXPECT_TRUE(IsFieldEqual(result, sliceXZ(expected, 3), "RGN_NOBNDRY", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(fromFieldAligned(result, "RGN_NOX"), sliceXZ(input, 3),
+  EXPECT_TRUE(IsFieldEqual(fromFieldAligned(result, "RGN_NOX"), sliceXZ(this->input, 3),
                            "RGN_NOBNDRY", FFTTolerance));
   EXPECT_TRUE(areFieldsCompatible(result, sliceXZ(expected, 3)));
-  EXPECT_FALSE(areFieldsCompatible(result, sliceXZ(input, 3)));
+  EXPECT_FALSE(areFieldsCompatible(result, sliceXZ(this->input, 3)));
 }
 
-TEST_F(ShiftedMetricTest, FromFieldAlignedFieldPerp) {
-  // reset input.yDirectionType so that fromFieldAligned is not a null
+TYPED_TEST(ShiftedMetricTest, FromFieldAlignedFieldPerp) {
+  if constexpr (std::is_same_v<TypeParam, ShiftedMetricInterp>) {
+    GTEST_SKIP_("Not implemented yet");
+  }
+
+  // reset this->input.yDirectionType so that fromFieldAligned is not a null
   // operation
-  input.setDirectionY(YDirectionType::Aligned);
+  this->input.setDirectionY(YDirectionType::Aligned);
 
   Field3D expected{mesh, CELL_CENTRE};
   expected.setDirectionY(YDirectionType::Standard);
@@ -251,43 +269,52 @@ TEST_F(ShiftedMetricTest, FromFieldAlignedFieldPerp) {
                         {2., 4., 5., 1., 3.},
                         {5., 1., 2., 4., 3.}}});
 
-  FieldPerp result = fromFieldAligned(sliceXZ(input, 4), "RGN_NOX");
+  FieldPerp result = fromFieldAligned(sliceXZ(this->input, 4), "RGN_NOX");
 
   // Note that the region argument does not do anything for FieldPerp, as
   // FieldPerp does not have a getRegion2D() method. Values are never set in
   // the x-guard or x-boundary cells
   EXPECT_TRUE(IsFieldEqual(result, sliceXZ(expected, 4), "RGN_NOBNDRY", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(toFieldAligned(result, "RGN_NOX"), sliceXZ(input, 4),
+  EXPECT_TRUE(IsFieldEqual(toFieldAligned(result, "RGN_NOX"), sliceXZ(this->input, 4),
                            "RGN_NOBNDRY", FFTTolerance));
   EXPECT_TRUE(areFieldsCompatible(result, sliceXZ(expected, 4)));
-  EXPECT_FALSE(areFieldsCompatible(result, sliceXZ(input, 4)));
+  EXPECT_FALSE(areFieldsCompatible(result, sliceXZ(this->input, 4)));
 }
 
-TEST_F(ShiftedMetricTest, FromToFieldAlignedFieldPerp) {
+TYPED_TEST(ShiftedMetricTest, FromToFieldAlignedFieldPerp) {
+  if constexpr (std::is_same_v<TypeParam, ShiftedMetricInterp>) {
+    GTEST_SKIP_("Not implemented yet");
+  }
+
   // Note that the region argument does not do anything for FieldPerp, as
   // FieldPerp does not have a getRegion2D() method. Values are never set in
   // the x-guard or x-boundary cells
   EXPECT_TRUE(IsFieldEqual(
-      fromFieldAligned(toFieldAligned(sliceXZ(input, 2), "RGN_NOX"), "RGN_NOX"),
-      sliceXZ(input, 2), "RGN_NOBNDRY", FFTTolerance));
+      fromFieldAligned(toFieldAligned(sliceXZ(this->input, 2), "RGN_NOX"), "RGN_NOX"),
+      sliceXZ(this->input, 2), "RGN_NOBNDRY", FFTTolerance));
 }
 
-TEST_F(ShiftedMetricTest, ToFromFieldAlignedFieldPerp) {
+TYPED_TEST(ShiftedMetricTest, ToFromFieldAlignedFieldPerp) {
+  if constexpr (std::is_same_v<TypeParam, ShiftedMetricInterp>) {
+    GTEST_SKIP_("Not implemented yet");
+  }
+
   // Note that the region argument does not do anything for FieldPerp, as
   // FieldPerp does not have a getRegion2D() method. Values are never set in
   // the x-guard or x-boundary cells
-  input.setDirectionY(YDirectionType::Aligned);
+  this->input.setDirectionY(YDirectionType::Aligned);
 
   EXPECT_TRUE(IsFieldEqual(
-      toFieldAligned(fromFieldAligned(sliceXZ(input, 6), "RGN_NOX"), "RGN_NOX"),
-      sliceXZ(input, 6), "RGN_NOBNDRY", FFTTolerance));
+      toFieldAligned(fromFieldAligned(sliceXZ(this->input, 6), "RGN_NOX"), "RGN_NOX"),
+      sliceXZ(this->input, 6), "RGN_NOBNDRY", FFTTolerance));
 }
 
-TEST_F(ShiftedMetricTest, CalcParallelSlices) {
+TYPED_TEST(ShiftedMetricTest, CalcParallelSlices) {
+  WithQuietOutput quiet_info{output_info};
+
   // We don't shift in the guard cells, and the parallel slices are
   // stored offset in y, therefore we need to make new regions that we
   // can compare the expected and actual outputs over
-  output_info.disable();
   mesh->addRegion3D("RGN_YUP",
                     Region<Ind3D>(0, mesh->LocalNx - 1, mesh->ystart + 1, mesh->yend + 1,
                                   0, mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz));
@@ -304,7 +331,7 @@ TEST_F(ShiftedMetricTest, CalcParallelSlices) {
   output_info.enable();
 
   // Actual interesting bit here!
-  input.getCoordinates()->getParallelTransform().calcParallelSlices(input);
+  this->input.getCoordinates()->getParallelTransform().calcParallelSlices(this->input);
   // Expected output values
 
   Field3D expected_up_1{mesh};
@@ -386,9 +413,9 @@ TEST_F(ShiftedMetricTest, CalcParallelSlices) {
                                {0., 0., 0., 0., 0.},
                                {0., 0., 0., 0., 0.}}});
 
-  Field3D expected_down2{mesh};
+  Field3D expected_down_2{mesh};
 
-  fillField(expected_down2, {{{4., 5., 1., 2., 3.},
+  fillField(expected_down_2, {{{4., 5., 1., 2., 3.},
                               {4., 5., 2., 1., 3.},
                               {4., 5., 1., 3., 2.},
                               {0., 0., 0., 0., 0.},
@@ -412,9 +439,9 @@ TEST_F(ShiftedMetricTest, CalcParallelSlices) {
                               {0., 0., 0., 0., 0.},
                               {0., 0., 0., 0., 0.}}});
 
-  EXPECT_TRUE(IsFieldEqual(input.ynext(1), expected_up_1, "RGN_YUP", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(input.ynext(2), expected_up_2, "RGN_YUP2", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(input.ynext(-1), expected_down_1, "RGN_YDOWN", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(input.ynext(-2), expected_down2, "RGN_YDOWN2", FFTTolerance));
+  EXPECT_TRUE(IsFieldEqual(this->input.ynext(1), expected_up_1, "RGN_YUP", FFTTolerance));
+  EXPECT_TRUE(IsFieldEqual(this->input.ynext(2), expected_up_2, "RGN_YUP2", FFTTolerance));
+  EXPECT_TRUE(IsFieldEqual(this->input.ynext(-1), expected_down_1, "RGN_YDOWN", FFTTolerance));
+  EXPECT_TRUE(IsFieldEqual(this->input.ynext(-2), expected_down_2, "RGN_YDOWN2", FFTTolerance));
 }
 #endif

From 81817bbce9c77c0b506e2e5f873ee262724cd0dc Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 30 Jan 2026 17:59:08 +0000
Subject: [PATCH 0475/1827] Don't check `ShiftedMetricInterp` results in any
 guard cells

---
 .../unit/mesh/parallel/test_shiftedmetric.cxx | 32 ++++++++++++++-----
 1 file changed, 24 insertions(+), 8 deletions(-)

diff --git a/tests/unit/mesh/parallel/test_shiftedmetric.cxx b/tests/unit/mesh/parallel/test_shiftedmetric.cxx
index ecbce620c3..3e6f90104b 100644
--- a/tests/unit/mesh/parallel/test_shiftedmetric.cxx
+++ b/tests/unit/mesh/parallel/test_shiftedmetric.cxx
@@ -315,19 +315,35 @@ TYPED_TEST(ShiftedMetricTest, CalcParallelSlices) {
   // We don't shift in the guard cells, and the parallel slices are
   // stored offset in y, therefore we need to make new regions that we
   // can compare the expected and actual outputs over
+
+  constexpr bool is_shifted_interp = std::is_same_v<TypeParam, ShiftedMetricInterp>;
+
+  // ShiftedMetricInterp doesn't seem to store interpolated values in _any_ of the
+  // guards, so we can only check the interior X point
+  const int xstart = is_shifted_interp ? mesh->xstart : 0;
+  const int xend = is_shifted_interp ? mesh->xend : mesh->LocalNx - 1;
+
+  // It also means we can't check in the _y_ guards either.
+  // TODO(peter): Is this a bug?
+  const int yup_1_end = is_shifted_interp ? mesh->yend : mesh->yend + 1;
+  const int yup_2_end = is_shifted_interp ? mesh->yend : mesh->yend + 2;
+
+  const int ydown_1_start = is_shifted_interp ? mesh->ystart : mesh->ystart - 1;
+  const int ydown_2_start = is_shifted_interp ? mesh->ystart : mesh->ystart - 2;
+
   mesh->addRegion3D("RGN_YUP",
-                    Region<Ind3D>(0, mesh->LocalNx - 1, mesh->ystart + 1, mesh->yend + 1,
-                                  0, mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz));
+                    Region<Ind3D>(xstart, xend, mesh->ystart + 1, yup_1_end, 0,
+                                  mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz));
   mesh->addRegion3D("RGN_YUP2",
-                    Region<Ind3D>(0, mesh->LocalNx - 1, mesh->ystart + 2, mesh->yend + 2,
-                                  0, mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz));
+                    Region<Ind3D>(xstart, xend, mesh->ystart + 2, yup_2_end, 0,
+                                  mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz));
 
   mesh->addRegion3D("RGN_YDOWN",
-                    Region<Ind3D>(0, mesh->LocalNx - 1, mesh->ystart - 1, mesh->yend - 1,
-                                  0, mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz));
+                    Region<Ind3D>(xstart, xend, ydown_1_start, mesh->yend - 1, 0,
+                                  mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz));
   mesh->addRegion3D("RGN_YDOWN2",
-                    Region<Ind3D>(0, mesh->LocalNx - 1, mesh->ystart - 2, mesh->yend - 2,
-                                  0, mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz));
+                    Region<Ind3D>(xstart, xend, ydown_2_start, mesh->yend - 2, 0,
+                                  mesh->LocalNz - 1, mesh->LocalNy, mesh->LocalNz));
   output_info.enable();
 
   // Actual interesting bit here!

From a71cad2dd6ace5741a754e2ca7daacd4bb094e0e Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Fri, 30 Jan 2026 18:20:30 +0000
Subject: [PATCH 0476/1827] [bot] Apply format changes

---
 .../unit/mesh/parallel/test_shiftedmetric.cxx | 62 ++++++++++---------
 1 file changed, 32 insertions(+), 30 deletions(-)

diff --git a/tests/unit/mesh/parallel/test_shiftedmetric.cxx b/tests/unit/mesh/parallel/test_shiftedmetric.cxx
index 3e6f90104b..579e6fdd7b 100644
--- a/tests/unit/mesh/parallel/test_shiftedmetric.cxx
+++ b/tests/unit/mesh/parallel/test_shiftedmetric.cxx
@@ -169,7 +169,6 @@ TYPED_TEST(ShiftedMetricTest, FromFieldAligned) {
 
   Field3D result = fromFieldAligned(this->input);
 
-
   // Loosen tolerance a bit due to FFTs
   EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_ALL", FFTTolerance));
   EXPECT_TRUE(IsFieldEqual(toFieldAligned(result), this->input, "RGN_ALL", FFTTolerance));
@@ -178,15 +177,15 @@ TYPED_TEST(ShiftedMetricTest, FromFieldAligned) {
 }
 
 TYPED_TEST(ShiftedMetricTest, FromToFieldAligned) {
-  EXPECT_TRUE(IsFieldEqual(fromFieldAligned(toFieldAligned(this->input)), this->input, "RGN_ALL",
-                           FFTTolerance));
+  EXPECT_TRUE(IsFieldEqual(fromFieldAligned(toFieldAligned(this->input)), this->input,
+                           "RGN_ALL", FFTTolerance));
 }
 
 TYPED_TEST(ShiftedMetricTest, ToFromFieldAligned) {
   this->input.setDirectionY(YDirectionType::Aligned);
 
-  EXPECT_TRUE(IsFieldEqual(toFieldAligned(fromFieldAligned(this->input)), this->input, "RGN_ALL",
-                           FFTTolerance));
+  EXPECT_TRUE(IsFieldEqual(toFieldAligned(fromFieldAligned(this->input)), this->input,
+                           "RGN_ALL", FFTTolerance));
 }
 
 TYPED_TEST(ShiftedMetricTest, ToFieldAlignedFieldPerp) {
@@ -432,32 +431,35 @@ TYPED_TEST(ShiftedMetricTest, CalcParallelSlices) {
   Field3D expected_down_2{mesh};
 
   fillField(expected_down_2, {{{4., 5., 1., 2., 3.},
-                              {4., 5., 2., 1., 3.},
-                              {4., 5., 1., 3., 2.},
-                              {0., 0., 0., 0., 0.},
-                              {0., 0., 0., 0., 0.},
-                              {0., 0., 0., 0., 0.},
-                              {0., 0., 0., 0., 0.}},
-
-                             {{1., 3., 4., 5., 2.},
-                              {3., 2., 4., 5., 1.},
-                              {2., 4., 3., 5., 1.},
-                              {0., 0., 0., 0., 0.},
-                              {0., 0., 0., 0., 0.},
-                              {0., 0., 0., 0., 0.},
-                              {0., 0., 0., 0., 0.}},
-
-                             {{5., 1., 3., 2., 4.},
-                              {5., 1., 2., 4., 3.},
-                              {4., 1., 2., 3., 5.},
-                              {0., 0., 0., 0., 0.},
-                              {0., 0., 0., 0., 0.},
-                              {0., 0., 0., 0., 0.},
-                              {0., 0., 0., 0., 0.}}});
+                               {4., 5., 2., 1., 3.},
+                               {4., 5., 1., 3., 2.},
+                               {0., 0., 0., 0., 0.},
+                               {0., 0., 0., 0., 0.},
+                               {0., 0., 0., 0., 0.},
+                               {0., 0., 0., 0., 0.}},
+
+                              {{1., 3., 4., 5., 2.},
+                               {3., 2., 4., 5., 1.},
+                               {2., 4., 3., 5., 1.},
+                               {0., 0., 0., 0., 0.},
+                               {0., 0., 0., 0., 0.},
+                               {0., 0., 0., 0., 0.},
+                               {0., 0., 0., 0., 0.}},
+
+                              {{5., 1., 3., 2., 4.},
+                               {5., 1., 2., 4., 3.},
+                               {4., 1., 2., 3., 5.},
+                               {0., 0., 0., 0., 0.},
+                               {0., 0., 0., 0., 0.},
+                               {0., 0., 0., 0., 0.},
+                               {0., 0., 0., 0., 0.}}});
 
   EXPECT_TRUE(IsFieldEqual(this->input.ynext(1), expected_up_1, "RGN_YUP", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(this->input.ynext(2), expected_up_2, "RGN_YUP2", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(this->input.ynext(-1), expected_down_1, "RGN_YDOWN", FFTTolerance));
-  EXPECT_TRUE(IsFieldEqual(this->input.ynext(-2), expected_down_2, "RGN_YDOWN2", FFTTolerance));
+  EXPECT_TRUE(
+      IsFieldEqual(this->input.ynext(2), expected_up_2, "RGN_YUP2", FFTTolerance));
+  EXPECT_TRUE(
+      IsFieldEqual(this->input.ynext(-1), expected_down_1, "RGN_YDOWN", FFTTolerance));
+  EXPECT_TRUE(
+      IsFieldEqual(this->input.ynext(-2), expected_down_2, "RGN_YDOWN2", FFTTolerance));
 }
 #endif

From ae9bb9caead818448456ad117da4b839fd7f2cd4 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Fri, 30 Jan 2026 18:20:31 +0000
Subject: [PATCH 0477/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 5e90d36c14..a8bd688f08 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -3,3 +3,4 @@ d8f14fdddb5ca0fbb32d8e2bf5ac2960d6ac5ce6
 ed2117e6d6826a98b6988e2f18c0c34e408563b6
 # Added by the bot
 4b010b7634aee1045743be80c268d4644522cd29
+a71cad2dd6ace5741a754e2ca7daacd4bb094e0e

From e5f2d373ff594776d6f878f598647fc5905551ba Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 2 Feb 2026 11:49:51 +0100
Subject: [PATCH 0478/1827] do not TRACK names

---
 src/field/gen_fieldops.jinja |  7 -------
 src/field/gen_fieldops.py    | 15 ++++++---------
 2 files changed, 6 insertions(+), 16 deletions(-)

diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index 58b1ae28ba..5476242d50 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -61,10 +61,6 @@
 	}
   {% endif %}
 
-#if BOUT_USE_TRACK
-  {{out.name}}.name = fmt::format("{:s} {{operator}} {:s}", {{'"BR"' if lhs == "BoutReal" else lhs.name + ".name"}}
-  		      				     	  , {{'"BR"' if rhs == "BoutReal" else rhs.name + ".name"}});
-#endif
   checkData({{out.name}});
   return {{out.name}};
 }
@@ -136,9 +132,6 @@
   {% if lhs == "Field3D" %}
     track(rhs, "operator{{operator}}=");
   {% endif %}
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} {{operator}}= {:s}", this->name, {{'"BR"' if rhs == "BoutReal" else rhs.name + ".name"}});
-#endif
 
     checkData(*this);
 
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 30c8101e97..3e07d6fec4 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -64,15 +64,12 @@ def smart_open(filename, mode="r"):
 )
 
 header = """// This file is autogenerated - see gen_fieldops.py
-#include "bout/build_defines.hxx"
-#include "bout/field2d.hxx"
-#include "bout/field3d.hxx"
-#include "bout/globals.hxx"
-#include "bout/interpolation.hxx"
-#include "bout/mesh.hxx"
-#include "bout/region.hxx"
-
-#include "fmt/format.h"
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/globals.hxx>
+#include <bout/interpolation.hxx>
+#include <bout/mesh.hxx>
+#include <bout/region.hxx>
 """
 
 

From 751abc463ec6f9dd53eb3cc334b15cbf16ba7bc1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 2 Feb 2026 11:50:05 +0100
Subject: [PATCH 0479/1827] Remove setName again

---
 include/bout/field.hxx           | 16 ----------------
 src/mesh/coordinates.cxx         |  4 ++--
 src/solver/impls/euler/euler.cxx |  1 -
 src/solver/impls/pvode/pvode.cxx |  1 -
 4 files changed, 2 insertions(+), 20 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index c188a0d8eb..4e41aa3632 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -35,7 +35,6 @@ class Field;
 #include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
-#include "bout/build_defines.hxx"
 #include "bout/field_data.hxx"
 #include "bout/region.hxx"
 #include "bout/traits.hxx"
@@ -668,19 +667,4 @@ inline T floor(const T& var, BoutReal f, const std::string& rgn = "RGN_ALL") {
 
 #undef FIELD_FUNC
 
-template <typename T, typename = bout::utils::EnableIfField<T>, class... Types>
-inline void setName(T& f, const std::string& name, Types... args) {
-#if BOUT_USE_TRACK
-  f.name = fmt::format(name, args...);
-#endif
-}
-
-template <typename T, typename = bout::utils::EnableIfField<T>, class... Types>
-inline T setName(T&& f, const std::string& name, Types... args) {
-#if BOUT_USE_TRACK
-  f.name = fmt::format(name, args...);
-#endif
-  return std::forward<T>(f);
-}
-
 #endif /* FIELD_H */
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index ade7ac158a..b8b0f9ea55 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1531,7 +1531,7 @@ Field3D Coordinates::Grad_par(const Field3D& var, CELL_LOC outloc,
 
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
-  return setName(::DDY(var, outloc, method) * invSg(), "Grad_par({:s})", var.name);
+  return ::DDY(var, outloc, method) * invSg();
 }
 
 /////////////////////////////////////////////////////////
@@ -1590,7 +1590,7 @@ Field3D Coordinates::Div_par(const Field3D& f, CELL_LOC outloc,
     f_B.yup(i) = f.yup(i) / Bxy_floc.yup(i);
     f_B.ydown(i) = f.ydown(i) / Bxy_floc.ydown(i);
   }
-  return setName(Bxy * Grad_par(f_B, outloc, method), "C:Div_par({:s})", f.name);
+  return xy * Grad_par(f_B, outloc, method);
 }
 
 /////////////////////////////////////////////////////////
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 78721d2e8f..6bdceab516 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -150,7 +150,6 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
     Options& debug = *debug_ptr;
     for (auto& f : f3d) {
       f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug_ptr);
-      setName(*f.var, f.name);
       debug[fmt::format("pre_{:s}", f.name)] = *f.var;
       f.var->allocate();
     }
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 59f7b3867f..4cc90af8fd 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -393,7 +393,6 @@ BoutReal PvodeSolver::run(BoutReal tout) {
 
       for (auto& f : f3d) {
         f.F_var->enableTracking(fmt::format("ddt_{:s}", f.name), debug_ptr);
-        setName(*f.var, f.name);
       }
       run_rhs(simtime);
 

From 3cc061bb7181cd2cd42f74f39fe864c08d4f3a90 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 2 Feb 2026 11:51:42 +0100
Subject: [PATCH 0480/1827] Update generated source code

---
 src/field/generated_fieldops.cxx | 327 +------------------------------
 1 file changed, 6 insertions(+), 321 deletions(-)

diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index f37a870c74..24bfde425c 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -1,13 +1,10 @@
 // This file is autogenerated - see gen_fieldops.py
-#include "bout/build_defines.hxx"
-#include "bout/field2d.hxx"
-#include "bout/field3d.hxx"
-#include "bout/globals.hxx"
-#include "bout/interpolation.hxx"
-#include "bout/mesh.hxx"
-#include "bout/region.hxx"
-
-#include "fmt/format.h"
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/globals.hxx>
+#include <bout/interpolation.hxx>
+#include <bout/mesh.hxx>
+#include <bout/region.hxx>
 
 // Provide the C++ wrapper for multiplication of Field3D and Field3D
 Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
@@ -23,9 +20,6 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] * rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -49,9 +43,6 @@ Field3D& Field3D::operator*=(const Field3D& rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
 
     track(rhs, "operator*=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
-#endif
 
     checkData(*this);
 
@@ -76,9 +67,6 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] / rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -102,9 +90,6 @@ Field3D& Field3D::operator/=(const Field3D& rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
 
     track(rhs, "operator/=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
-#endif
 
     checkData(*this);
 
@@ -129,9 +114,6 @@ Field3D operator+(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] + rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -155,9 +137,6 @@ Field3D& Field3D::operator+=(const Field3D& rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
 
     track(rhs, "operator+=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
-#endif
 
     checkData(*this);
 
@@ -182,9 +161,6 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
     result[index] = lhs[index] - rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -208,9 +184,6 @@ Field3D& Field3D::operator-=(const Field3D& rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
 
     track(rhs, "operator-=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
-#endif
 
     checkData(*this);
 
@@ -240,9 +213,6 @@ Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
     }
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -269,9 +239,6 @@ Field3D& Field3D::operator*=(const Field2D& rhs) {
     }
 
     track(rhs, "operator*=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
-#endif
 
     checkData(*this);
 
@@ -302,9 +269,6 @@ Field3D operator/(const Field3D& lhs, const Field2D& rhs) {
     }
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -332,9 +296,6 @@ Field3D& Field3D::operator/=(const Field2D& rhs) {
     }
 
     track(rhs, "operator/=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
-#endif
 
     checkData(*this);
 
@@ -364,9 +325,6 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
     }
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -393,9 +351,6 @@ Field3D& Field3D::operator+=(const Field2D& rhs) {
     }
 
     track(rhs, "operator+=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
-#endif
 
     checkData(*this);
 
@@ -425,9 +380,6 @@ Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
     }
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -454,9 +406,6 @@ Field3D& Field3D::operator-=(const Field2D& rhs) {
     }
 
     track(rhs, "operator-=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
-#endif
 
     checkData(*this);
 
@@ -483,9 +432,6 @@ FieldPerp operator*(const Field3D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] * rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -506,9 +452,6 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] / rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -529,9 +472,6 @@ FieldPerp operator+(const Field3D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] + rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -552,9 +492,6 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] - rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -572,9 +509,6 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -595,9 +529,6 @@ Field3D& Field3D::operator*=(const BoutReal rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
 
     track(rhs, "operator*=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, "BR");
-#endif
 
     checkData(*this);
 
@@ -622,9 +553,6 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * tmp;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -646,9 +574,6 @@ Field3D& Field3D::operator/=(const BoutReal rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; }
 
     track(rhs, "operator/=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, "BR");
-#endif
 
     checkData(*this);
 
@@ -672,9 +597,6 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] + rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -695,9 +617,6 @@ Field3D& Field3D::operator+=(const BoutReal rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
 
     track(rhs, "operator+=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, "BR");
-#endif
 
     checkData(*this);
 
@@ -721,9 +640,6 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] - rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -744,9 +660,6 @@ Field3D& Field3D::operator-=(const BoutReal rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
 
     track(rhs, "operator-=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, "BR");
-#endif
 
     checkData(*this);
 
@@ -776,9 +689,6 @@ Field3D operator*(const Field2D& lhs, const Field3D& rhs) {
     }
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -802,9 +712,6 @@ Field3D operator/(const Field2D& lhs, const Field3D& rhs) {
     }
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -828,9 +735,6 @@ Field3D operator+(const Field2D& lhs, const Field3D& rhs) {
     }
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -854,9 +758,6 @@ Field3D operator-(const Field2D& lhs, const Field3D& rhs) {
     }
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -873,9 +774,6 @@ Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
     result[index] = lhs[index] * rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -892,10 +790,6 @@ Field2D& Field2D::operator*=(const Field2D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -916,9 +810,6 @@ Field2D operator/(const Field2D& lhs, const Field2D& rhs) {
     result[index] = lhs[index] / rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -935,10 +826,6 @@ Field2D& Field2D::operator/=(const Field2D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -959,9 +846,6 @@ Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
     result[index] = lhs[index] + rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -978,10 +862,6 @@ Field2D& Field2D::operator+=(const Field2D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1002,9 +882,6 @@ Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
     result[index] = lhs[index] - rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1021,10 +898,6 @@ Field2D& Field2D::operator-=(const Field2D& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1049,9 +922,6 @@ FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] * rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1072,9 +942,6 @@ FieldPerp operator/(const Field2D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] / rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1095,9 +962,6 @@ FieldPerp operator+(const Field2D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] + rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1118,9 +982,6 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) {
     result[index] = lhs[base_ind] - rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1136,9 +997,6 @@ Field2D operator*(const Field2D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -1154,10 +1012,6 @@ Field2D& Field2D::operator*=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, "BR");
-#endif
-
     checkData(*this);
 
   } else {
@@ -1178,9 +1032,6 @@ Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * tmp;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -1197,10 +1048,6 @@ Field2D& Field2D::operator/=(const BoutReal rhs) {
     const auto tmp = 1.0 / rhs;
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, "BR");
-#endif
-
     checkData(*this);
 
   } else {
@@ -1220,9 +1067,6 @@ Field2D operator+(const Field2D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] + rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -1238,10 +1082,6 @@ Field2D& Field2D::operator+=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, "BR");
-#endif
-
     checkData(*this);
 
   } else {
@@ -1261,9 +1101,6 @@ Field2D operator-(const Field2D& lhs, const BoutReal rhs) {
     result[index] = lhs[index] - rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -1279,10 +1116,6 @@ Field2D& Field2D::operator-=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, "BR");
-#endif
-
     checkData(*this);
 
   } else {
@@ -1307,9 +1140,6 @@ FieldPerp operator*(const FieldPerp& lhs, const Field3D& rhs) {
     result[index] = lhs[index] * rhs[base_ind];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1332,10 +1162,6 @@ FieldPerp& FieldPerp::operator*=(const Field3D& rhs) {
       (*this)[index] *= rhs[base_ind];
     }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1360,9 +1186,6 @@ FieldPerp operator/(const FieldPerp& lhs, const Field3D& rhs) {
     result[index] = lhs[index] / rhs[base_ind];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1385,10 +1208,6 @@ FieldPerp& FieldPerp::operator/=(const Field3D& rhs) {
       (*this)[index] /= rhs[base_ind];
     }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1413,9 +1232,6 @@ FieldPerp operator+(const FieldPerp& lhs, const Field3D& rhs) {
     result[index] = lhs[index] + rhs[base_ind];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1438,10 +1254,6 @@ FieldPerp& FieldPerp::operator+=(const Field3D& rhs) {
       (*this)[index] += rhs[base_ind];
     }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1466,9 +1278,6 @@ FieldPerp operator-(const FieldPerp& lhs, const Field3D& rhs) {
     result[index] = lhs[index] - rhs[base_ind];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1491,10 +1300,6 @@ FieldPerp& FieldPerp::operator-=(const Field3D& rhs) {
       (*this)[index] -= rhs[base_ind];
     }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1519,9 +1324,6 @@ FieldPerp operator*(const FieldPerp& lhs, const Field2D& rhs) {
     result[index] = lhs[index] * rhs[base_ind];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1544,10 +1346,6 @@ FieldPerp& FieldPerp::operator*=(const Field2D& rhs) {
       (*this)[index] *= rhs[base_ind];
     }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1572,9 +1370,6 @@ FieldPerp operator/(const FieldPerp& lhs, const Field2D& rhs) {
     result[index] = lhs[index] / rhs[base_ind];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1597,10 +1392,6 @@ FieldPerp& FieldPerp::operator/=(const Field2D& rhs) {
       (*this)[index] /= rhs[base_ind];
     }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1625,9 +1416,6 @@ FieldPerp operator+(const FieldPerp& lhs, const Field2D& rhs) {
     result[index] = lhs[index] + rhs[base_ind];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1650,10 +1438,6 @@ FieldPerp& FieldPerp::operator+=(const Field2D& rhs) {
       (*this)[index] += rhs[base_ind];
     }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1678,9 +1462,6 @@ FieldPerp operator-(const FieldPerp& lhs, const Field2D& rhs) {
     result[index] = lhs[index] - rhs[base_ind];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1703,10 +1484,6 @@ FieldPerp& FieldPerp::operator-=(const Field2D& rhs) {
       (*this)[index] -= rhs[base_ind];
     }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1727,9 +1504,6 @@ FieldPerp operator*(const FieldPerp& lhs, const FieldPerp& rhs) {
     result[index] = lhs[index] * rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1746,10 +1520,6 @@ FieldPerp& FieldPerp::operator*=(const FieldPerp& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1770,9 +1540,6 @@ FieldPerp operator/(const FieldPerp& lhs, const FieldPerp& rhs) {
     result[index] = lhs[index] / rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1789,10 +1556,6 @@ FieldPerp& FieldPerp::operator/=(const FieldPerp& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1813,9 +1576,6 @@ FieldPerp operator+(const FieldPerp& lhs, const FieldPerp& rhs) {
     result[index] = lhs[index] + rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1832,10 +1592,6 @@ FieldPerp& FieldPerp::operator+=(const FieldPerp& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1856,9 +1612,6 @@ FieldPerp operator-(const FieldPerp& lhs, const FieldPerp& rhs) {
     result[index] = lhs[index] - rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -1875,10 +1628,6 @@ FieldPerp& FieldPerp::operator-=(const FieldPerp& rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
-#endif
-
     checkData(*this);
 
   } else {
@@ -1898,9 +1647,6 @@ FieldPerp operator*(const FieldPerp& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -1916,10 +1662,6 @@ FieldPerp& FieldPerp::operator*=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, "BR");
-#endif
-
     checkData(*this);
 
   } else {
@@ -1940,9 +1682,6 @@ FieldPerp operator/(const FieldPerp& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * tmp;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -1958,10 +1697,6 @@ FieldPerp& FieldPerp::operator/=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, "BR");
-#endif
-
     checkData(*this);
 
   } else {
@@ -1981,9 +1716,6 @@ FieldPerp operator+(const FieldPerp& lhs, const BoutReal rhs) {
     result[index] = lhs[index] + rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -1999,10 +1731,6 @@ FieldPerp& FieldPerp::operator+=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, "BR");
-#endif
-
     checkData(*this);
 
   } else {
@@ -2022,9 +1750,6 @@ FieldPerp operator-(const FieldPerp& lhs, const BoutReal rhs) {
     result[index] = lhs[index] - rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -2040,10 +1765,6 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) {
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
 
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, "BR");
-#endif
-
     checkData(*this);
 
   } else {
@@ -2065,9 +1786,6 @@ Field3D operator*(const BoutReal lhs, const Field3D& rhs) {
     result[index] = lhs * rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2085,9 +1803,6 @@ Field3D operator/(const BoutReal lhs, const Field3D& rhs) {
     result[index] = lhs / rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2105,9 +1820,6 @@ Field3D operator+(const BoutReal lhs, const Field3D& rhs) {
     result[index] = lhs + rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2125,9 +1837,6 @@ Field3D operator-(const BoutReal lhs, const Field3D& rhs) {
     result[index] = lhs - rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2143,9 +1852,6 @@ Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
     result[index] = lhs * rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2161,9 +1867,6 @@ Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
     result[index] = lhs / rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2179,9 +1882,6 @@ Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
     result[index] = lhs + rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2197,9 +1897,6 @@ Field2D operator-(const BoutReal lhs, const Field2D& rhs) {
     result[index] = lhs - rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2215,9 +1912,6 @@ FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {
     result[index] = lhs * rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2233,9 +1927,6 @@ FieldPerp operator/(const BoutReal lhs, const FieldPerp& rhs) {
     result[index] = lhs / rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2251,9 +1942,6 @@ FieldPerp operator+(const BoutReal lhs, const FieldPerp& rhs) {
     result[index] = lhs + rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }
@@ -2269,9 +1957,6 @@ FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) {
     result[index] = lhs - rhs[index];
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", "BR", rhs.name);
-#endif
   checkData(result);
   return result;
 }

From 52301380586fdbf890f620c04f689b08d89a6c34 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Mon, 2 Feb 2026 10:52:25 +0000
Subject: [PATCH 0481/1827] [bot] Apply format changes

---
 examples/blob2d/blob_velocity.py              | 154 ++++++------
 examples/boutpp/simulation.py                 |   5 +-
 examples/conduction-snb/fit_temperature.py    |  24 +-
 examples/conduction-snb/sinusoid.py           |  30 ++-
 examples/conduction-snb/step.py               |  31 ++-
 examples/conduction/generate.py               |   4 +-
 examples/eigen-box/eigenvals.py               |  35 +--
 examples/elm-pb/Python/2dprofile.py           |  91 ++++---
 examples/elm-pb/Python/analysis.py            |  16 +-
 examples/elm-pb/Python/elm_size.py            | 179 +++++++------
 examples/elm-pb/Python/fftall.py              |   9 +-
 examples/elm-pb/Python/fftall2.py             |  10 +-
 examples/elm-pb/Python/grate.py               |   9 +-
 examples/elm-pb/Python/grate2.py              |  45 ++--
 examples/elm-pb/Python/plotcollapse.py        |  47 ++--
 examples/elm-pb/Python/plotmode.py            |  93 ++++---
 examples/elm-pb/Python/plotmode2.py           |  94 ++++---
 examples/elm-pb/Python/plotphase.py           |  45 ++--
 examples/elm-pb/Python/polslice.py            |  26 +-
 examples/elm-pb/Python/post.py                | 142 +++++++----
 examples/elm-pb/Python/read_elmsize.py        |  46 ++--
 examples/elm-pb/Python/showpolslice.py        |  36 +--
 examples/elm-pb/Python/sprofiles.py           |  41 +--
 examples/elm-pb/runexample.py                 |  28 ++-
 examples/fci-wave/compare-density.py          |  45 ++--
 examples/finite-volume/diffusion/mms.py       |  14 +-
 examples/finite-volume/fluid/mms.py           |  20 +-
 examples/laplace-petsc3d/plotcheck.py         |  16 +-
 examples/orszag-tang/generate.py              | 116 +++++----
 .../performance/bracket/scaling_parser.py     |   5 +-
 .../performance/ddx/new_scaling_parser.py     |  32 +--
 .../performance/ddy/new_scaling_parser.py     |  32 +--
 .../performance/ddz/new_scaling_parser.py     |  32 +--
 .../performance/iterator/scaling_parser.py    |   5 +-
 examples/staggered_grid/generate.py           |   6 +-
 examples/subsampling/show.py                  |  10 +-
 examples/wave-slab/generate.py                |   2 +-
 .../figure_creators/LaplacianMatrices.ipynb   | 236 ++++++++++--------
 .../bout_runners_folder_structure.py          |  97 +++----
 tests/MMS/advection/runtest                   |   2 +-
 40 files changed, 1039 insertions(+), 871 deletions(-)

diff --git a/examples/blob2d/blob_velocity.py b/examples/blob2d/blob_velocity.py
index d044946320..6de0937d0f 100644
--- a/examples/blob2d/blob_velocity.py
+++ b/examples/blob2d/blob_velocity.py
@@ -3,96 +3,100 @@
 import pickle
 
 try:
-        from past.utils import old_div
+    from past.utils import old_div
 except ImportError:
-        def old_div(a,b):
-                return a/b
 
-
-def blob_velocity(n,**kwargs):
-
-        from boututils import calculus as Calc
-        # Calculate blob velocity in normalized time and normalized grid spacing
-        #
-        # Input: Blob density as a 3D vector in the form  n[t,x,z] where t is time and x,z are the perpendicular spatial coordinates
-        #
-        # Keywords:
-        #
-        #           type='peak' -> Calculate velocity of the peak density
-        #           type='COM' -> Calculate centre of mass velocity
-        #           Index=True -> return indices used to create velocity
-        #
-        # Default: Peak velocity with no index returning
-
-        size = n.shape
-
-        try:
-                v_type = kwargs['type']
-        except:
-                v_type = 'peak'         #Default to peak velocity calculation
-        try:
-                return_index = kwargs['Index']
-        except:
-                return_index = False    #Default to no index returning
-
-
-        if v_type == 'peak':
-                x = np.zeros(size[0])
-                z = np.zeros(size[0])
-                for i in np.arange(size[0]):
-                        nmax,nmin = np.amax((n[i,:,:])),np.amin((n[i,:,:]))
-                        xpos,zpos = np.where(n[i,:,:]==nmax)
-                        x[i] = xpos[0]
-                        z[i] = zpos[0]
-
-        if v_type == 'COM':
-                x = np.zeros(size[0])
-                z = np.zeros(size[0])
-                for i in np.arange(size[0]):
-                        data = n[i,:,:] - n[0,0,0]   #use corner cell rather than nmin
-                        ntot = np.sum(data[:,:])
-
-                        z[i] = old_div(np.sum(np.sum(data[:,:],axis=0)*(np.arange(size[2]))),ntot)
-                        x[i] = old_div(np.sum(np.sum(data[:,:],axis=1)*(np.arange(size[1]))),ntot)
-
-        vx = Calc.deriv(x)
-        vz = Calc.deriv(z)
-
-        if return_index:
-                return vx,vz,x,z
-        else:
-                return vx,vz
-
-
-
-data='data'
+    def old_div(a, b):
+        return a / b
+
+
+def blob_velocity(n, **kwargs):
+    from boututils import calculus as Calc
+    # Calculate blob velocity in normalized time and normalized grid spacing
+    #
+    # Input: Blob density as a 3D vector in the form  n[t,x,z] where t is time and x,z are the perpendicular spatial coordinates
+    #
+    # Keywords:
+    #
+    #           type='peak' -> Calculate velocity of the peak density
+    #           type='COM' -> Calculate centre of mass velocity
+    #           Index=True -> return indices used to create velocity
+    #
+    # Default: Peak velocity with no index returning
+
+    size = n.shape
+
+    try:
+        v_type = kwargs["type"]
+    except:
+        v_type = "peak"  # Default to peak velocity calculation
+    try:
+        return_index = kwargs["Index"]
+    except:
+        return_index = False  # Default to no index returning
+
+    if v_type == "peak":
+        x = np.zeros(size[0])
+        z = np.zeros(size[0])
+        for i in np.arange(size[0]):
+            nmax, nmin = np.amax((n[i, :, :])), np.amin((n[i, :, :]))
+            xpos, zpos = np.where(n[i, :, :] == nmax)
+            x[i] = xpos[0]
+            z[i] = zpos[0]
+
+    if v_type == "COM":
+        x = np.zeros(size[0])
+        z = np.zeros(size[0])
+        for i in np.arange(size[0]):
+            data = n[i, :, :] - n[0, 0, 0]  # use corner cell rather than nmin
+            ntot = np.sum(data[:, :])
+
+            z[i] = old_div(
+                np.sum(np.sum(data[:, :], axis=0) * (np.arange(size[2]))), ntot
+            )
+            x[i] = old_div(
+                np.sum(np.sum(data[:, :], axis=1) * (np.arange(size[1]))), ntot
+            )
+
+    vx = Calc.deriv(x)
+    vz = Calc.deriv(z)
+
+    if return_index:
+        return vx, vz, x, z
+    else:
+        return vx, vz
+
+
+data = "data"
 
 if True:
-        import sys
-        if len(sys.argv) > 1:
-                data=sys.argv[1]
+    import sys
+
+    if len(sys.argv) > 1:
+        data = sys.argv[1]
 
-n = collect('n', path=data, info=False)
+n = collect("n", path=data, info=False)
 
 
-vx,vy,xx,yy = blob_velocity(n[:,:,0,:],type='COM',Index=True)
+vx, vy, xx, yy = blob_velocity(n[:, :, 0, :], type="COM", Index=True)
 
-f = open('Velocity.dat','wb')
-pickle.dump(vx,f)
+f = open("Velocity.dat", "wb")
+pickle.dump(vx, f)
 f.close()
 
-f = open('Position.dat','wb')
-pickle.dump(xx,f)
+f = open("Position.dat", "wb")
+pickle.dump(xx, f)
 f.close()
 
 
-f = open('Velocity.dat','rb')
+f = open("Velocity.dat", "rb")
 vx = pickle.load(f)
 f.close()
 
 try:
-        import matplotlib.pyplot as plt
-        plt.plot(vx)
-        plt.show()
+    import matplotlib.pyplot as plt
+
+    plt.plot(vx)
+    plt.show()
 except ImportError:
-        pass
+    pass
diff --git a/examples/boutpp/simulation.py b/examples/boutpp/simulation.py
index 1b57ff8b33..9948bd9b03 100755
--- a/examples/boutpp/simulation.py
+++ b/examples/boutpp/simulation.py
@@ -3,12 +3,13 @@
 
 bc.init("mesh:n=48")
 
+
 class Model(bc.PhysicsModel):
-    def init(self,restart):
+    def init(self, restart):
         self.dens = bc.create3D("sin(x)")
         self.solve_for(n=self.dens)
 
-    def rhs(self,time):
+    def rhs(self, time):
         self.dens.ddt(bc.DDX(self.dens))
 
 
diff --git a/examples/conduction-snb/fit_temperature.py b/examples/conduction-snb/fit_temperature.py
index 1e7f3ddf94..81faa9cf93 100644
--- a/examples/conduction-snb/fit_temperature.py
+++ b/examples/conduction-snb/fit_temperature.py
@@ -3,23 +3,31 @@
 import matplotlib.pyplot as plt
 
 Te_ref = np.loadtxt("temperature.csv", delimiter=",")
-Te_ref[:,0] *= 1e-4 # Convert X axis to m
+Te_ref[:, 0] *= 1e-4  # Convert X axis to m
+
 
 def te_function(ypos, mid, wwid, w0, w1, w2, Tmax, Tmin, clip=False):
-    width = w0 + ((ypos - mid)*w1 + (ypos - mid)**2 * w2) * np.exp(-((ypos - mid)/wwid)**2)
+    width = w0 + ((ypos - mid) * w1 + (ypos - mid) ** 2 * w2) * np.exp(
+        -(((ypos - mid) / wwid) ** 2)
+    )
 
     if clip:
         width = np.clip(width, 1e-10, None)
 
-    return Tmax - 0.5 * (1 + np.tanh((ypos - mid)/width)) * (Tmax - Tmin)
+    return Tmax - 0.5 * (1 + np.tanh((ypos - mid) / width)) * (Tmax - Tmin)
+
 
-popt, pcov = optimize.curve_fit(te_function, Te_ref[:,0], Te_ref[:,1],
-                                p0 = [2.2e-4, 1e-4, 1e-4, 0.0, 0.0, 0.960, 0.190])
+popt, pcov = optimize.curve_fit(
+    te_function,
+    Te_ref[:, 0],
+    Te_ref[:, 1],
+    p0=[2.2e-4, 1e-4, 1e-4, 0.0, 0.0, 0.960, 0.190],
+)
 
 print(popt)
 
-xfit = np.linspace(Te_ref[0,0], Te_ref[-1,0], 100)
+xfit = np.linspace(Te_ref[0, 0], Te_ref[-1, 0], 100)
 
-plt.plot(xfit, te_function(xfit, *popt, clip=True), '-k')
-plt.plot(Te_ref[:,0], Te_ref[:,1], 'or')
+plt.plot(xfit, te_function(xfit, *popt, clip=True), "-k")
+plt.plot(Te_ref[:, 0], Te_ref[:, 1], "or")
 plt.show()
diff --git a/examples/conduction-snb/sinusoid.py b/examples/conduction-snb/sinusoid.py
index 10c81923a3..439530383e 100644
--- a/examples/conduction-snb/sinusoid.py
+++ b/examples/conduction-snb/sinusoid.py
@@ -11,7 +11,7 @@
 build_and_log("Sinusoidal SNB")
 
 # Electron temperature in eV
-Telist = 10 ** np.linspace(0,3,20)
+Telist = 10 ** np.linspace(0, 3, 20)
 
 # Electron density in m^-3
 Ne = 1e20
@@ -19,29 +19,30 @@
 # Length of the domain in m
 length = 1.0
 
-c   = 299792458
-mu0 = 4.e-7*np.pi
-e0  = 1/(c*c*mu0)
+c = 299792458
+mu0 = 4.0e-7 * np.pi
+e0 = 1 / (c * c * mu0)
 qe = 1.602176634e-19
 me = 9.10938356e-31
 
-thermal_speed = np.sqrt(2.*qe  * Telist / me)
-Y = (qe**2 / (e0 * me))**2 / (4 * np.pi)
+thermal_speed = np.sqrt(2.0 * qe * Telist / me)
+Y = (qe**2 / (e0 * me)) ** 2 / (4 * np.pi)
 coulomb_log = 6.6 - 0.5 * np.log(Ne * 1e-20) + 1.5 * np.log(Telist)
-lambda_ee_T = thermal_speed**4 / (Y * Ne  * coulomb_log)
+lambda_ee_T = thermal_speed**4 / (Y * Ne * coulomb_log)
 
 beta_max_list = [5, 10, 20, 40]
-colors = ['k','b','g','r']
+colors = ["k", "b", "g", "r"]
 
 ngroups_list = [20, 40, 80]
-syms = ['x', 'o', 'D']
+syms = ["x", "o", "D"]
 
 for beta_max, color in zip(beta_max_list, colors):
     for ngroups, sym in zip(ngroups_list, syms):
-
         flux_ratio = []
         for Te in Telist:
-            cmd = "./conduction-snb \"Te={0}+0.01*sin(y)\" Ne={1} mesh:length={2} snb:beta_max={3} snb:ngroups={4}".format(Te, Ne, length, beta_max, ngroups)
+            cmd = './conduction-snb "Te={0}+0.01*sin(y)" Ne={1} mesh:length={2} snb:beta_max={3} snb:ngroups={4}'.format(
+                Te, Ne, length, beta_max, ngroups
+            )
 
             # Run the case
             s, out = launch_safe(cmd, nproc=1, mthread=1, pipe=True)
@@ -54,7 +55,12 @@
 
             flux_ratio.append(div_q[ind] / div_q_SH[ind])
 
-        plt.plot(lambda_ee_T / length, flux_ratio, '-'+sym+color, label=r"$\beta_{{max}}={0}, N_g={1}$".format(beta_max,ngroups))
+        plt.plot(
+            lambda_ee_T / length,
+            flux_ratio,
+            "-" + sym + color,
+            label=r"$\beta_{{max}}={0}, N_g={1}$".format(beta_max, ngroups),
+        )
 
 plt.legend()
 plt.xlabel(r"$\lambda_{ee,T} / L$")
diff --git a/examples/conduction-snb/step.py b/examples/conduction-snb/step.py
index 1f8933e66b..63a13149f4 100644
--- a/examples/conduction-snb/step.py
+++ b/examples/conduction-snb/step.py
@@ -3,7 +3,7 @@
 #
 # Uses a step in the temperature, intended for comparison to VFP results
 
-length = 6e-4 # Domain length in m
+length = 6e-4  # Domain length in m
 
 qe = 1.602176634e-19
 
@@ -40,37 +40,37 @@
 
 # Read reference values
 Te_ref = np.loadtxt("temperature.csv", delimiter=",")
-Te_ref[:,0] *= 1e-4 # Convert X axis to m
+Te_ref[:, 0] *= 1e-4  # Convert X axis to m
 
 SH_ref = np.loadtxt("spitzer-harm.csv", delimiter=",")
-SH_ref[:,0] *= 1e-4
+SH_ref[:, 0] *= 1e-4
 
 SNB_ref = np.loadtxt("snb.csv", delimiter=",")
-SNB_ref[:,0] *= 1e-4
+SNB_ref[:, 0] *= 1e-4
 
 VFP_ref = np.loadtxt("vfp.csv", delimiter=",")
-VFP_ref[:,0] *= 1e-4
+VFP_ref[:, 0] *= 1e-4
 
 #########################################
 
 fig, ax1 = plt.subplots()
 
-color='tab:red'
+color = "tab:red"
 ax1.plot(position, Te * 1e-3, color=color, label="Te")
-ax1.plot(Te_ref[:,0], Te_ref[:,1], color=color, marker="o", label="Reference Te")
+ax1.plot(Te_ref[:, 0], Te_ref[:, 1], color=color, marker="o", label="Reference Te")
 ax1.set_xlabel("position [m]")
 ax1.set_ylabel("Electron temperature [keV]", color=color)
-ax1.set_ylim(0,1)
-ax1.tick_params(axis='y', colors=color)
+ax1.set_ylim(0, 1)
+ax1.tick_params(axis="y", colors=color)
 
 ax2 = ax1.twinx()
-ax2.plot(position, q_SH * 1e-4, '-k', label="Spitzer-Harm")
-ax2.plot(SH_ref[:,0], SH_ref[:,1], '--k', label="Reference SH")
+ax2.plot(position, q_SH * 1e-4, "-k", label="Spitzer-Harm")
+ax2.plot(SH_ref[:, 0], SH_ref[:, 1], "--k", label="Reference SH")
 
-ax2.plot(position, q * 1e-4, '-b', label="SNB")
-ax2.plot(SNB_ref[:,0], SNB_ref[:,1], '--b', label="Reference SNB")
+ax2.plot(position, q * 1e-4, "-b", label="SNB")
+ax2.plot(SNB_ref[:, 0], SNB_ref[:, 1], "--b", label="Reference SNB")
 
-ax2.plot(VFP_ref[:,0], VFP_ref[:,1], '--g', label="Reference VFP")
+ax2.plot(VFP_ref[:, 0], VFP_ref[:, 1], "--g", label="Reference VFP")
 
 ax2.set_ylabel("Heat flux W/cm^2")
 ax2.set_ylim(bottom=0.0)
@@ -78,8 +78,7 @@
 plt.legend()
 fig.tight_layout()
 
-plt.xlim(0,3.5e-4)
+plt.xlim(0, 3.5e-4)
 
 plt.savefig("snb-step.png")
 plt.show()
-
diff --git a/examples/conduction/generate.py b/examples/conduction/generate.py
index 7138026898..4a2a2acfc0 100755
--- a/examples/conduction/generate.py
+++ b/examples/conduction/generate.py
@@ -4,9 +4,9 @@
 # Generate an input mesh
 #
 
-from boututils.datafile import DataFile # Wrapper around NetCDF4 libraries
+from boututils.datafile import DataFile  # Wrapper around NetCDF4 libraries
 
-nx = 5   # Minimum is 5: 2 boundary, one evolved
+nx = 5  # Minimum is 5: 2 boundary, one evolved
 ny = 64  # Minimum 5. Should be divisible by number of processors (so powers of 2 nice)
 
 f = DataFile()
diff --git a/examples/eigen-box/eigenvals.py b/examples/eigen-box/eigenvals.py
index 7b52fc60f2..5a71aabfc6 100755
--- a/examples/eigen-box/eigenvals.py
+++ b/examples/eigen-box/eigenvals.py
@@ -27,7 +27,8 @@ def plot_eigenvals(eigenvalues, eigenvectors=None):
             raise ValueError("Expecting eigenvectors to be 2D")
         if eigenvectors.shape[0] != len(eigenvalues):
             raise ValueError(
-                "First dimension of eigenvectors must match length of eigenvalues")
+                "First dimension of eigenvectors must match length of eigenvalues"
+            )
 
     # If no eigenvectors supplied, only plot eigenvalues, otherwise
     # eigenvalues and eigenvectors
@@ -44,18 +45,18 @@ def plot_eigenvals(eigenvalues, eigenvectors=None):
     range_r = amax(eigs_r) - amin(eigs_r)
     range_i = amax(eigs_i) - amin(eigs_i)
 
-    ax[0].plot(eigs_r, eigs_i, 'x')
+    ax[0].plot(eigs_r, eigs_i, "x")
     ax[0].set_xlabel("Real component")
     ax[0].set_ylabel("Imaginary component")
     ax[0].set_title("Eigenvalue")
 
-    overplot, = ax[0].plot([], [], 'ok')
+    (overplot,) = ax[0].plot([], [], "ok")
 
     if eigenvectors is not None:
         # Add a eigenvectors plot
-        vector_r, = ax[1].plot([], [], '-k', label="Real")
-        vector_i, = ax[1].plot([], [], '-r', label="Imag")
-        ax[1].legend(loc='upper right')
+        (vector_r,) = ax[1].plot([], [], "-k", label="Real")
+        (vector_i,) = ax[1].plot([], [], "-r", label="Imag")
+        ax[1].legend(loc="upper right")
         ax[1].set_xlabel("X")
         ax[1].set_ylabel("Amplitude")
         ax[1].set_title("Eigenvector")
@@ -68,33 +69,33 @@ def onclick(event):
 
         # Find closest eigenvectors point, but stretch axes so
         # real and imaginary components are weighted equally
-        if(range_r == 0):
-            dist = ((eigs_i - event.ydata)/range_i)**2
-        elif(range_i == 0):
-            dist = ((eigs_r - event.xdata)/range_r)**2
+        if range_r == 0:
+            dist = ((eigs_i - event.ydata) / range_i) ** 2
+        elif range_i == 0:
+            dist = ((eigs_r - event.xdata) / range_r) ** 2
         else:
-            dist = ((eigs_r - event.xdata)/range_r)**2 + \
-                ((eigs_i - event.ydata)/range_i)**2
+            dist = ((eigs_r - event.xdata) / range_r) ** 2 + (
+                (eigs_i - event.ydata) / range_i
+            ) ** 2
 
         ind = argmin(dist)
 
         # Update the highlight plot
         overplot.set_data([eigs_r[ind]], [eigs_i[ind]])
 
-        print("Eigenvalue number: %d (%e,%e)" %
-              (ind, eigs_r[ind], eigs_i[ind]))
+        print("Eigenvalue number: %d (%e,%e)" % (ind, eigs_r[ind], eigs_i[ind]))
 
         if eigenvectors is not None:
             # Update plots
             nx = eigenvectors.shape[1]
-            vector_r.set_data(arange(nx), eigenvectors[2*ind, :])
-            vector_i.set_data(arange(nx), eigenvectors[2*ind+1, :])
+            vector_r.set_data(arange(nx), eigenvectors[2 * ind, :])
+            vector_i.set_data(arange(nx), eigenvectors[2 * ind + 1, :])
             ax[1].relim()
             ax[1].autoscale_view()
 
         fig.canvas.draw()
 
-    fig.canvas.mpl_connect('button_press_event', onclick)
+    fig.canvas.mpl_connect("button_press_event", onclick)
     plt.show()
 
 
diff --git a/examples/elm-pb/Python/2dprofile.py b/examples/elm-pb/Python/2dprofile.py
index 5bb01972f9..e95709ab5b 100644
--- a/examples/elm-pb/Python/2dprofile.py
+++ b/examples/elm-pb/Python/2dprofile.py
@@ -4,81 +4,92 @@
 import numpy as np
 import matplotlib.pyplot as plt
 from boututils.datafile import DataFile
-from matplotlib.ticker import FixedFormatter, FormatStrFormatter, AutoLocator, AutoMinorLocator
+from matplotlib.ticker import (
+    FixedFormatter,
+    FormatStrFormatter,
+    AutoLocator,
+    AutoMinorLocator,
+)
 
 with DataFile("./cbm18_dens8.grid_nx68ny64.nc") as f:
     g = {v: f.read(v) for v in f.keys()}
 
-majorLocator   = AutoLocator()
-majorFormatter = FormatStrFormatter('%3.0e')
-minorLocator   = AutoMinorLocator()
-Fm = FixedFormatter(['0','$1 \\times 10^4$','$2 \\times  10^4$','$3 \\times 10^4$','$4 \\times 10^4$'])
-Fm2 = FixedFormatter(['0','$2 \\times 10^5$','$4 \\times  10^5$','$6 \\times 10^5$'])
-
-bxy=g.get('Bxy')
-p=g.get('pressure')
-jpar0=g.get('Jpar0')
-psixy=g.get('psixy')
-btxy=g.get('Btxy')
-shiftangle=g.get('ShiftAngle')
-
-nx=g.get('nx')
-ny=g.get('ny')
+majorLocator = AutoLocator()
+majorFormatter = FormatStrFormatter("%3.0e")
+minorLocator = AutoMinorLocator()
+Fm = FixedFormatter(
+    [
+        "0",
+        "$1 \\times 10^4$",
+        "$2 \\times  10^4$",
+        "$3 \\times 10^4$",
+        "$4 \\times 10^4$",
+    ]
+)
+Fm2 = FixedFormatter(["0", "$2 \\times 10^5$", "$4 \\times  10^5$", "$6 \\times 10^5$"])
+
+bxy = g.get("Bxy")
+p = g.get("pressure")
+jpar0 = g.get("Jpar0")
+psixy = g.get("psixy")
+btxy = g.get("Btxy")
+shiftangle = g.get("ShiftAngle")
+
+nx = g.get("nx")
+ny = g.get("ny")
 
 q = np.zeros((nx, ny))
 for i in range(ny):
-    q[:,i] = old_div(- shiftangle, (2 * np.pi))
-
-
+    q[:, i] = old_div(-shiftangle, (2 * np.pi))
 
 
-xarr = psixy[:,0]
+xarr = psixy[:, 0]
 xarr = old_div((xarr + 0.854856), (0.854856 + 0.0760856))
 
 
-fig=plt.figure()
-plt.plot(xarr,q[:,32])
-plt.xlabel('normalized $\psi$', fontsize=25)
-plt.ylabel('$q$',rotation='horizontal',fontsize=25)
+fig = plt.figure()
+plt.plot(xarr, q[:, 32])
+plt.xlabel("normalized $\psi$", fontsize=25)
+plt.ylabel("$q$", rotation="horizontal", fontsize=25)
 
 fig.set_tight_layout(True)
 
 fig, ax1 = plt.subplots()
 
-ax1.plot(xarr, p[:,32], 'r-', markevery=1, linewidth=3)
-ax1.set_xlabel('normalized $\psi$',fontsize=25)
+ax1.plot(xarr, p[:, 32], "r-", markevery=1, linewidth=3)
+ax1.set_xlabel("normalized $\psi$", fontsize=25)
 # Make the y-axis label and tick labels match the line color.
-ax1.set_ylabel('Pressure [Pa]', color='k',fontsize=25)
+ax1.set_ylabel("Pressure [Pa]", color="k", fontsize=25)
 
-#set y limit
-ax1.set_ylim(0,40000,10000)
+# set y limit
+ax1.set_ylim(0, 40000, 10000)
 
-#define ticks#
+# define ticks#
 ax1.yaxis.set_ticks(np.arange(0, 40000, 10000))
-#ax1.yaxis.set_major_locator(majorLocator)
-#ax1.yaxis.set_major_formatter(majorFormatter)
+# ax1.yaxis.set_major_locator(majorLocator)
+# ax1.yaxis.set_major_formatter(majorFormatter)
 ax1.yaxis.set_major_formatter(Fm)
 
-#for the minor ticks, use no labels; default NullFormatter
+# for the minor ticks, use no labels; default NullFormatter
 ax1.xaxis.set_minor_locator(AutoMinorLocator())
 ax1.yaxis.set_minor_locator(AutoMinorLocator(10))
 
-#format tick labels
+# format tick labels
 for tl in ax1.get_yticklabels():
-    tl.set_color('k')
+    tl.set_color("k")
 
 
 ax2 = ax1.twinx()
 
 s2 = -jpar0
 
-ax2.plot(xarr, s2[:,32], 'r-',markevery=1,linewidth=3)
-ax2.set_ylabel('$J_\parallel  [A/m^2]$', color='k',fontsize=25)
-ax2.set_ylim(0,600000)
+ax2.plot(xarr, s2[:, 32], "r-", markevery=1, linewidth=3)
+ax2.set_ylabel("$J_\parallel  [A/m^2]$", color="k", fontsize=25)
+ax2.set_ylim(0, 600000)
 ax2.yaxis.set_ticks(np.arange(0, 600000, 200000))
 ax2.yaxis.set_major_formatter(Fm2)
 for tl in ax2.get_yticklabels():
-    tl.set_color('k')
+    tl.set_color("k")
 
 
 fig.set_tight_layout(True)
@@ -86,4 +97,4 @@
 plt.show()
 
 
-#plt.savefig('2d.png', transparent=True)
+# plt.savefig('2d.png', transparent=True)
diff --git a/examples/elm-pb/Python/analysis.py b/examples/elm-pb/Python/analysis.py
index 4faf85f8ce..0e4a3acfdd 100644
--- a/examples/elm-pb/Python/analysis.py
+++ b/examples/elm-pb/Python/analysis.py
@@ -6,24 +6,24 @@
 import pylab as plt
 from boutdata.collect import collect
 
-path='./data/'
-var=collect('P', path=path)
+path = "./data/"
+var = collect("P", path=path)
 
-dcvar=np.mean(var, axis=3)
-rmsvar=np.sqrt(np.mean(var**2,axis=3)-dcvar**2)
+dcvar = np.mean(var, axis=3)
+rmsvar = np.sqrt(np.mean(var**2, axis=3) - dcvar**2)
 
 plt.figure()
-plt.plot(rmsvar[:,34,32])
+plt.plot(rmsvar[:, 34, 32])
 plt.show(block=False)
-fvar=np.fft.rfft(var,axis=3)
+fvar = np.fft.rfft(var, axis=3)
 
 plt.figure()
-plt.plot(abs(fvar[:,34,32,1:10]))
+plt.plot(abs(fvar[:, 34, 32, 1:10]))
 plt.show(block=False)
 
 
 plt.figure()
-plt.semilogy(abs(fvar[:,34,32,1:7]))
+plt.semilogy(abs(fvar[:, 34, 32, 1:7]))
 plt.show(block=False)
 
 plt.show()
diff --git a/examples/elm-pb/Python/elm_size.py b/examples/elm-pb/Python/elm_size.py
index 0d5c105870..6ad2ed6a0d 100644
--- a/examples/elm-pb/Python/elm_size.py
+++ b/examples/elm-pb/Python/elm_size.py
@@ -4,87 +4,126 @@
 from past.utils import old_div
 import numpy as np
 
-def elm_size(dcp,p0,uedge,xmin=None,xmax=None,yind=None,Bbar=None):
-  
-    lis=[dcp,p0,uedge]
-    if np.size(lis) != 3 :
+
+def elm_size(dcp, p0, uedge, xmin=None, xmax=None, yind=None, Bbar=None):
+    lis = [dcp, p0, uedge]
+    if np.size(lis) != 3:
         print("lack of parameters")
         return 0
-    
 
-    if xmin == None : xmin=0
-    if xmax == None : xmax=327 
-    if yind == None : yind=63 # choose the poloidal location for 1D size
-    if Bbar == None : Bbar=1.992782  # the normalized magnetic field 
+    if xmin == None:
+        xmin = 0
+    if xmax == None:
+        xmax = 327
+    if yind == None:
+        yind = 63  # choose the poloidal location for 1D size
+    if Bbar == None:
+        Bbar = 1.992782  # the normalized magnetic field
 
-    mydcp=dcp
-    myp0=p0
-    g=uedge
+    mydcp = dcp
+    myp0 = p0
+    g = uedge
 
     PI = 3.1415926
-    MU0 = 4.0e-7*PI
+    MU0 = 4.0e-7 * PI
 
-    s=np.shape(mydcp)
+    s = np.shape(mydcp)
 
-    if np.ndim(mydcp) != 3 :
+    if np.ndim(mydcp) != 3:
         print("dcp should be 3D(t,x,y)")
- 
-
-    nt=s[0]
-    nx=s[1]
-    ny=s[2]
-
-    Dtheta=g['dy']     #using correct poloidal angle
-    psixy=g['psixy']
-    R=g['Rxy']
-    Bp=g['Bpxy']
-    hthe=g['hthe']
-
-    Dpsi=np.zeros((nx,ny))
-    Dpsi[0,:]=psixy[1,:]-psixy[0,:]
-    Dpsi[nx-1,:]=psixy[nx-1,:]-psixy[nx-2,:]
-    for i in range(1,nx-2):
-        Dpsi[i,:]=old_div((psixy[i+1,:]-psixy[i-1,:]),2)
-     
-
-    Ddcp1=np.zeros(nt)
-    Ddcp2=np.zeros(nt)
-    Ddcp3=np.zeros(nt)
-    Tp01=0.
-    Tp02=0.
-    Tp03=0.
-
-    for t in range(nt) :
-        Ddcp3[t]=2.0*PI*np.sum(mydcp[t,xmin:xmax,:]*hthe[xmin:xmax,:]*Dtheta[xmin:xmax,:]*Dpsi[xmin:xmax,:]/Bp[xmin:xmax,:])
-        Ddcp2[t]=np.sum(mydcp[t,xmin:xmax,:]*hthe[xmin:xmax,:]*Dtheta[xmin:xmax,:]*Dpsi[xmin:xmax,:]/(R[xmin:xmax,:]*Bp[xmin:xmax,:]))
-        Ddcp1[t]=np.sum(mydcp[t,xmin:xmax,yind]*Dpsi[xmin:xmax,yind]/(R[xmin:xmax,yind]*Bp[xmin:xmax,yind])) 
-    
-
-    Tp03=2.0*PI*np.sum(myp0[xmin:xmax,:]*hthe[xmin:xmax,:]*Dtheta[xmin:xmax,:]*Dpsi[xmin:xmax,:]/Bp[xmin:xmax,:])
-    Tp02=np.sum(myp0[xmin:xmax,:]*hthe[xmin:xmax,:]*Dtheta[xmin:xmax,:]*Dpsi[xmin:xmax,:]/(R[xmin:xmax,:]*Bp[xmin:xmax,:]))
-    Tp01=np.sum(myp0[xmin:xmax,yind]*Dpsi[xmin:xmax,yind]/(R[xmin:xmax,yind]*Bp[xmin:xmax,yind]))
-
-    s1=np.zeros(nt)
-    s2=np.zeros(nt)
-    s3=np.zeros(nt)
-    E_loss=np.zeros(nt)
-
-    s1=old_div(-Ddcp1,Tp01)   #1D elm size
-    s2=old_div(-Ddcp2,Tp02)   #2D elm size
-    s3=old_div(-Ddcp3,Tp03)   #3D elm size
-
-    E_loss=-Ddcp3*(0.5*Bbar*Bbar/MU0)    #energy loss, unit J
-    E_total=Tp03*(0.5*Bbar*Bbar/MU0)     #total energy, unit J
+
+    nt = s[0]
+    nx = s[1]
+    ny = s[2]
+
+    Dtheta = g["dy"]  # using correct poloidal angle
+    psixy = g["psixy"]
+    R = g["Rxy"]
+    Bp = g["Bpxy"]
+    hthe = g["hthe"]
+
+    Dpsi = np.zeros((nx, ny))
+    Dpsi[0, :] = psixy[1, :] - psixy[0, :]
+    Dpsi[nx - 1, :] = psixy[nx - 1, :] - psixy[nx - 2, :]
+    for i in range(1, nx - 2):
+        Dpsi[i, :] = old_div((psixy[i + 1, :] - psixy[i - 1, :]), 2)
+
+    Ddcp1 = np.zeros(nt)
+    Ddcp2 = np.zeros(nt)
+    Ddcp3 = np.zeros(nt)
+    Tp01 = 0.0
+    Tp02 = 0.0
+    Tp03 = 0.0
+
+    for t in range(nt):
+        Ddcp3[t] = (
+            2.0
+            * PI
+            * np.sum(
+                mydcp[t, xmin:xmax, :]
+                * hthe[xmin:xmax, :]
+                * Dtheta[xmin:xmax, :]
+                * Dpsi[xmin:xmax, :]
+                / Bp[xmin:xmax, :]
+            )
+        )
+        Ddcp2[t] = np.sum(
+            mydcp[t, xmin:xmax, :]
+            * hthe[xmin:xmax, :]
+            * Dtheta[xmin:xmax, :]
+            * Dpsi[xmin:xmax, :]
+            / (R[xmin:xmax, :] * Bp[xmin:xmax, :])
+        )
+        Ddcp1[t] = np.sum(
+            mydcp[t, xmin:xmax, yind]
+            * Dpsi[xmin:xmax, yind]
+            / (R[xmin:xmax, yind] * Bp[xmin:xmax, yind])
+        )
+
+    Tp03 = (
+        2.0
+        * PI
+        * np.sum(
+            myp0[xmin:xmax, :]
+            * hthe[xmin:xmax, :]
+            * Dtheta[xmin:xmax, :]
+            * Dpsi[xmin:xmax, :]
+            / Bp[xmin:xmax, :]
+        )
+    )
+    Tp02 = np.sum(
+        myp0[xmin:xmax, :]
+        * hthe[xmin:xmax, :]
+        * Dtheta[xmin:xmax, :]
+        * Dpsi[xmin:xmax, :]
+        / (R[xmin:xmax, :] * Bp[xmin:xmax, :])
+    )
+    Tp01 = np.sum(
+        myp0[xmin:xmax, yind]
+        * Dpsi[xmin:xmax, yind]
+        / (R[xmin:xmax, yind] * Bp[xmin:xmax, yind])
+    )
+
+    s1 = np.zeros(nt)
+    s2 = np.zeros(nt)
+    s3 = np.zeros(nt)
+    E_loss = np.zeros(nt)
+
+    s1 = old_div(-Ddcp1, Tp01)  # 1D elm size
+    s2 = old_div(-Ddcp2, Tp02)  # 2D elm size
+    s3 = old_div(-Ddcp3, Tp03)  # 3D elm size
+
+    E_loss = -Ddcp3 * (0.5 * Bbar * Bbar / MU0)  # energy loss, unit J
+    E_total = Tp03 * (0.5 * Bbar * Bbar / MU0)  # total energy, unit J
 
     class ELM:
         pass
-    elmsize=ELM()
-    elmsize.s1=s1
-    elmsize.s2=s2
-    elmsize.s3=s3
-    elmsize.E_loss=E_loss
-    elmsize.E_total=E_total
+
+    elmsize = ELM()
+    elmsize.s1 = s1
+    elmsize.s2 = s2
+    elmsize.s3 = s3
+    elmsize.E_loss = E_loss
+    elmsize.E_total = E_total
 
     return elmsize
-  
-    
diff --git a/examples/elm-pb/Python/fftall.py b/examples/elm-pb/Python/fftall.py
index e0a4385764..c6d5b87ded 100644
--- a/examples/elm-pb/Python/fftall.py
+++ b/examples/elm-pb/Python/fftall.py
@@ -2,8 +2,7 @@
 from numpy import *
 from scipy.io import readsav
 
-print('Calculating P..')
-a=transpose(readsav('phi.idl.dat')['phi'])
-fa=fft.fft(a,axis=2)
-save('fp',fa)
-
+print("Calculating P..")
+a = transpose(readsav("phi.idl.dat")["phi"])
+fa = fft.fft(a, axis=2)
+save("fp", fa)
diff --git a/examples/elm-pb/Python/fftall2.py b/examples/elm-pb/Python/fftall2.py
index d864f356d0..64b08c437a 100644
--- a/examples/elm-pb/Python/fftall2.py
+++ b/examples/elm-pb/Python/fftall2.py
@@ -2,9 +2,9 @@
 from numpy import *
 from boutdata.collect import collect
 
-path='./data/'
-data=collect('P',path=path)
+path = "./data/"
+data = collect("P", path=path)
 
-print('Saving P..')
-fa=fft.fft(data,axis=3)
-save('fp',rollaxis(fa,0,4))
+print("Saving P..")
+fa = fft.fft(data, axis=3)
+save("fp", rollaxis(fa, 0, 4))
diff --git a/examples/elm-pb/Python/grate.py b/examples/elm-pb/Python/grate.py
index 003f38ff8e..65d6da6449 100644
--- a/examples/elm-pb/Python/grate.py
+++ b/examples/elm-pb/Python/grate.py
@@ -8,12 +8,11 @@
 from boututils.moment_xyzt import moment_xyzt
 
 
+path = "./data/"
 
-path='./data/'
 
+p = collect("P", path=path)
+rmsp_f = moment_xyzt(p[:, 34:35, 32:33, :], "RMS").rms
 
-p=collect('P',path=path)
-rmsp_f=moment_xyzt(p[:,34:35,32:33,:], 'RMS').rms
 
-
-print(np.gradient(np.log(rmsp_f[:,0,0]))[-1])
+print(np.gradient(np.log(rmsp_f[:, 0, 0]))[-1])
diff --git a/examples/elm-pb/Python/grate2.py b/examples/elm-pb/Python/grate2.py
index f8172bcf08..af0768803a 100644
--- a/examples/elm-pb/Python/grate2.py
+++ b/examples/elm-pb/Python/grate2.py
@@ -2,6 +2,7 @@
 from __future__ import division
 from builtins import range
 from past.utils import old_div
+
 ###
 # computes average growth rate for all points at the final timestep
 # computes average growth rate for points in the mead plane at the final timestep
@@ -10,40 +11,44 @@
 from boutdata.collect import collect
 from boututils.moment_xyzt import moment_xyzt
 
-path='./data/'
+path = "./data/"
+
+p = collect("P", path=path)
 
-p=collect('P',path=path)
+nmpy = old_div(p.shape[2], 2)  # define mead plane
 
-nmpy=old_div(p.shape[2],2)  # define mead plane
+ik = 50  # disregard the first ik timesteps
 
-ik = 50 # disregard the first ik timesteps
 
 def gr(p):
-        rmsp_f=moment_xyzt(p, 'RMS').rms
+    rmsp_f = moment_xyzt(p, "RMS").rms
 
-        ni=np.shape(rmsp_f)[1]
-        nj=np.shape(rmsp_f)[2]
+    ni = np.shape(rmsp_f)[1]
+    nj = np.shape(rmsp_f)[2]
 
-        growth=np.zeros((ni,nj))
+    growth = np.zeros((ni, nj))
 
-        for i in range(ni):
-                for j in range(nj):
-                         growth[i,j]=np.gradient(np.log(rmsp_f[ik::,i,j]))[-1]
+    for i in range(ni):
+        for j in range(nj):
+            growth[i, j] = np.gradient(np.log(rmsp_f[ik::, i, j]))[-1]
 
-        return growth
+    return growth
 
 
-growth=gr(p)
+growth = gr(p)
 
-d=np.ma.masked_array(growth,np.isnan(growth))
+d = np.ma.masked_array(growth, np.isnan(growth))
 
 # masked arrays
 # http://stackoverflow.com/questions/5480694/numpy-calculate-averages-with-nans-removed
 
-print('Total mean value = ', np.mean(np.ma.masked_array(d,np.isinf(d))))
-mm=np.ma.masked_array(growth[:,nmpy],np.isnan(growth[:,nmpy]))
-if np.isinf(np.mean(mm)) :
-    print('There is an Inf value in the mead plane')
-    print('Mean value of floating numbers in mead plane is = ', np.mean(np.ma.masked_array(mm,np.isinf(mm))))
+print("Total mean value = ", np.mean(np.ma.masked_array(d, np.isinf(d))))
+mm = np.ma.masked_array(growth[:, nmpy], np.isnan(growth[:, nmpy]))
+if np.isinf(np.mean(mm)):
+    print("There is an Inf value in the mead plane")
+    print(
+        "Mean value of floating numbers in mead plane is = ",
+        np.mean(np.ma.masked_array(mm, np.isinf(mm))),
+    )
 else:
-    print('Mean value in mead plane= ', np.mean(mm))
+    print("Mean value in mead plane= ", np.mean(mm))
diff --git a/examples/elm-pb/Python/plotcollapse.py b/examples/elm-pb/Python/plotcollapse.py
index ee64ca381f..f68e7b06aa 100755
--- a/examples/elm-pb/Python/plotcollapse.py
+++ b/examples/elm-pb/Python/plotcollapse.py
@@ -10,49 +10,52 @@
 import os
 from pathlib import Path
 
-#Dynamic matplotlib settings
+# Dynamic matplotlib settings
 from matplotlib import rcParams
-rcParams['font.size'] = 20.
-rcParams['legend.fontsize'] = 'small'
-rcParams['lines.linewidth'] = 2
 
-if not os.path.exists('image'):
-   os.makedirs('image')
+rcParams["font.size"] = 20.0
+rcParams["legend.fontsize"] = "small"
+rcParams["lines.linewidth"] = 2
+
+if not os.path.exists("image"):
+    os.makedirs("image")
 filename = Path(__file__).with_name("cbm18_dens8.grid_nx68ny64.nc")
 with DataFile(str(filename)) as f:
     g = {v: f.read(v) for v in f.keys()}
 
-psi = old_div((g['psixy'][:, 32] - g['psi_axis']), (g['psi_bndry'] - g['psi_axis']))
+psi = old_div((g["psixy"][:, 32] - g["psi_axis"]), (g["psi_bndry"] - g["psi_axis"]))
 
-path = './data'
+path = "./data"
 
 plt.figure()
 
-p0=collect('P0', path=path)
+p0 = collect("P0", path=path)
 
-p=collect('P', path=path)
-res = moment_xyzt(p,'RMS','DC')
+p = collect("P", path=path)
+res = moment_xyzt(p, "RMS", "DC")
 rmsp = res.rms
 dcp = res.dc
 nt = dcp.shape[0]
 
-plt.plot(psi, p0[:, 32], 'k--', label='t=0')
-plt.plot(psi, p0[:, 32] + dcp[nt//4, :, 32], 'r-', label='t='+np.str(nt//4))
-plt.plot(psi, p0[:, 32] + dcp[nt//2, :, 32], 'g-', label='t='+np.str(nt//2))
-plt.plot(psi, p0[:, 32] + dcp[3*nt//4, :, 32], 'b-', label='t='+np.str(3*nt//4))
-plt.plot(psi, p0[:, 32] + dcp[-1, :, 32], 'c-', label='t='+np.str(nt))
+plt.plot(psi, p0[:, 32], "k--", label="t=0")
+plt.plot(psi, p0[:, 32] + dcp[nt // 4, :, 32], "r-", label="t=" + np.str(nt // 4))
+plt.plot(psi, p0[:, 32] + dcp[nt // 2, :, 32], "g-", label="t=" + np.str(nt // 2))
+plt.plot(
+    psi, p0[:, 32] + dcp[3 * nt // 4, :, 32], "b-", label="t=" + np.str(3 * nt // 4)
+)
+plt.plot(psi, p0[:, 32] + dcp[-1, :, 32], "c-", label="t=" + np.str(nt))
 
 plt.legend()
-#plt.xlim(0.6, 1.0)
-plt.xlabel(r'Normalized poloidal flux ($\psi$)')
-plt.ylabel(r'$\langle p\rangle_\xi$')
-plt.title(r'Pressure')
+# plt.xlim(0.6, 1.0)
+plt.xlabel(r"Normalized poloidal flux ($\psi$)")
+plt.ylabel(r"$\langle p\rangle_\xi$")
+plt.title(r"Pressure")
 xmin, xmax = plt.xlim()
 ymin, ymax = plt.ylim()
 
 
-#plt.savefig('image/plotcollapse.png', bbox_inches='tight')
-#plt.savefig('image/plotcollapse.eps', bbox_inches='tight')
+# plt.savefig('image/plotcollapse.png', bbox_inches='tight')
+# plt.savefig('image/plotcollapse.eps', bbox_inches='tight')
 
 
 plt.tight_layout()
diff --git a/examples/elm-pb/Python/plotmode.py b/examples/elm-pb/Python/plotmode.py
index d89fdaf940..9325ee8764 100644
--- a/examples/elm-pb/Python/plotmode.py
+++ b/examples/elm-pb/Python/plotmode.py
@@ -4,60 +4,57 @@
 from builtins import range
 from past.utils import old_div
 
-from numpy import *;
-#from scipy.io import readsav;
-import matplotlib.pyplot as plt;
+from numpy import *
+
+# from scipy.io import readsav;
+import matplotlib.pyplot as plt
 
 # Dynamic matplotlib settings
-from matplotlib import rcParams;
-rcParams['font.size'] = 20;
-rcParams['legend.fontsize'] = 'small';
-rcParams['legend.labelspacing'] = 0.1;
-rcParams['lines.linewidth'] = 2;
-rcParams['savefig.bbox'] = 'tight';
+from matplotlib import rcParams
 
+rcParams["font.size"] = 20
+rcParams["legend.fontsize"] = "small"
+rcParams["legend.labelspacing"] = 0.1
+rcParams["lines.linewidth"] = 2
+rcParams["savefig.bbox"] = "tight"
 # Create image directory if not exists
-import os;
-if not os.path.exists('image'):
-   os.makedirs('image');
-
-#fphi = transpose(readsav('fphi.idl.dat')['fphi'])[:,:,:,];
-fphi = load('fp.npy')
-
-plt.figure();
-for i in range(1, 9):
-   print("Growth rate for mode number", i)
-   print(gradient(log(abs(fphi[34, 32, i, :]))))
-   plt.semilogy(((abs(fphi[34, 32, i, :]))), label = 'n=' + str(i * 5));
+import os
 
-plt.legend(loc=2);
-plt.xlabel('Time');
-plt.savefig('image/plotmode.png');
-plt.savefig('image/plotmode.eps');
+if not os.path.exists("image"):
+    os.makedirs("image")
 
+# fphi = transpose(readsav('fphi.idl.dat')['fphi'])[:,:,:,];
+fphi = load("fp.npy")
 
-plt.show(block=False);
-plt.figure();
+plt.figure()
 for i in range(1, 9):
-   plt.plot(abs(fphi[:, 32, i, -1]), label = 'n=' + str(i * 5));
-
-plt.legend();
-plt.xlabel('X index');
-
-plt.savefig('image/plotmodeamp.png');
-plt.savefig('image/plotmodeamp.eps');
-
-plt.show(block=False);
-
-plt.figure();
+    print("Growth rate for mode number", i)
+    print(gradient(log(abs(fphi[34, 32, i, :]))))
+    plt.semilogy((abs(fphi[34, 32, i, :])), label="n=" + str(i * 5))
+
+plt.legend(loc=2)
+plt.xlabel("Time")
+plt.savefig("image/plotmode.png")
+plt.savefig("image/plotmode.eps")
+plt.show(block=False)
+plt.figure()
 for i in range(1, 9):
-   plt.plot(old_div(abs(fphi[:, 32, i, -1]),abs(fphi[:, 32, i, -1]).max()), label = 'n=' + str(i * 5));
-
-plt.legend();
-plt.xlabel('X index');
-
-plt.savefig('image/plotmodenorm.png');
-plt.savefig('image/plotmodenorm.eps');
-
-plt.show();
-
+    plt.plot(abs(fphi[:, 32, i, -1]), label="n=" + str(i * 5))
+
+plt.legend()
+plt.xlabel("X index")
+plt.savefig("image/plotmodeamp.png")
+plt.savefig("image/plotmodeamp.eps")
+plt.show(block=False)
+plt.figure()
+for i in range(1, 9):
+    plt.plot(
+        old_div(abs(fphi[:, 32, i, -1]), abs(fphi[:, 32, i, -1]).max()),
+        label="n=" + str(i * 5),
+    )
+
+plt.legend()
+plt.xlabel("X index")
+plt.savefig("image/plotmodenorm.png")
+plt.savefig("image/plotmodenorm.eps")
+plt.show()
diff --git a/examples/elm-pb/Python/plotmode2.py b/examples/elm-pb/Python/plotmode2.py
index d0c63f32d9..c298a3a5ef 100644
--- a/examples/elm-pb/Python/plotmode2.py
+++ b/examples/elm-pb/Python/plotmode2.py
@@ -4,63 +4,61 @@
 from builtins import range
 from past.utils import old_div
 
-from numpy import *;
-#from scipy.io import readsav;
-import matplotlib.pyplot as plt;
+from numpy import *
+
+# from scipy.io import readsav;
+import matplotlib.pyplot as plt
 from boutdata.collect import collect
 
 # Dynamic matplotlib settings
-from matplotlib import rcParams;
-rcParams['font.size'] = 20;
-rcParams['legend.fontsize'] = 'small';
-rcParams['legend.labelspacing'] = 0.1;
-rcParams['lines.linewidth'] = 2;
-rcParams['savefig.bbox'] = 'tight';
+from matplotlib import rcParams
 
+rcParams["font.size"] = 20
+rcParams["legend.fontsize"] = "small"
+rcParams["legend.labelspacing"] = 0.1
+rcParams["lines.linewidth"] = 2
+rcParams["savefig.bbox"] = "tight"
 # Create image directory if not exists
-import os;
-if not os.path.exists('image'):
-   os.makedirs('image');
+import os
+
+if not os.path.exists("image"):
+    os.makedirs("image")
 
-path='./data/'
-data=collect('P',path=path)
+path = "./data/"
+data = collect("P", path=path)
 
-#fphi = transpose(readsav('fphi.idl.dat')['fphi'])[:,:,:,];
+# fphi = transpose(readsav('fphi.idl.dat')['fphi'])[:,:,:,];
 fphi = fft.fft(data, axis=3)
 
-plt.figure();
+plt.figure()
 for i in range(1, 9):
-   print("Growth rate for mode number", i)
-   print(gradient(log(abs(fphi[:,34, 32, i]))))
-   plt.semilogy(((abs(fphi[:,34, 32, i]))), label = 'n=' + str(i * 5));
-
-plt.legend(loc=2);
-plt.xlabel('Time');
-plt.savefig('image/plotmode.png');
-plt.savefig('image/plotmode.eps');
-
-
-plt.show(block=False);
-plt.figure();
+    print("Growth rate for mode number", i)
+    print(gradient(log(abs(fphi[:, 34, 32, i]))))
+    plt.semilogy((abs(fphi[:, 34, 32, i])), label="n=" + str(i * 5))
+
+plt.legend(loc=2)
+plt.xlabel("Time")
+plt.savefig("image/plotmode.png")
+plt.savefig("image/plotmode.eps")
+plt.show(block=False)
+plt.figure()
 for i in range(1, 9):
-   plt.plot(abs(fphi[-1, :, 32, i]), label = 'n=' + str(i * 5));
-
-plt.legend();
-plt.xlabel('X index');
-
-plt.savefig('image/plotmodeamp.png');
-plt.savefig('image/plotmodeamp.eps');
-
-plt.show(block=False);
-
-plt.figure();
+    plt.plot(abs(fphi[-1, :, 32, i]), label="n=" + str(i * 5))
+
+plt.legend()
+plt.xlabel("X index")
+plt.savefig("image/plotmodeamp.png")
+plt.savefig("image/plotmodeamp.eps")
+plt.show(block=False)
+plt.figure()
 for i in range(1, 9):
-   plt.plot(old_div(abs(fphi[-1, :, 32, i]),abs(fphi[-1, :, 32, i]).max()), label = 'n=' + str(i * 5));
-
-plt.legend();
-plt.xlabel('X index');
-
-plt.savefig('image/plotmodenorm.png');
-plt.savefig('image/plotmodenorm.eps');
-
-plt.show();
+    plt.plot(
+        old_div(abs(fphi[-1, :, 32, i]), abs(fphi[-1, :, 32, i]).max()),
+        label="n=" + str(i * 5),
+    )
+
+plt.legend()
+plt.xlabel("X index")
+plt.savefig("image/plotmodenorm.png")
+plt.savefig("image/plotmodenorm.eps")
+plt.show()
diff --git a/examples/elm-pb/Python/plotphase.py b/examples/elm-pb/Python/plotphase.py
index 9225e498ae..10f4279cf4 100755
--- a/examples/elm-pb/Python/plotphase.py
+++ b/examples/elm-pb/Python/plotphase.py
@@ -4,34 +4,33 @@
 from numpy import save, load, angle
 import matplotlib.pyplot as plt
 
-fphi = load('fphi.npy')
+fphi = load("fphi.npy")
 
-fte = load('fte.npy')
-phase_te = angle(old_div(fphi,fte))
-save('phase_te', phase_te)
+fte = load("fte.npy")
+phase_te = angle(old_div(fphi, fte))
+save("phase_te", phase_te)
 plt.figure()
-plt.plot(mean(mean(phase_te[:,:,3,:],axis=1),axis=1))
-plt.title('Te')
-plt.savefig('image/phase_te.png')
-plt.savefig('image/phase_te.eps')
+plt.plot(mean(mean(phase_te[:, :, 3, :], axis=1), axis=1))
+plt.title("Te")
+plt.savefig("image/phase_te.png")
+plt.savefig("image/phase_te.eps")
 
-fti = load('fti.npy')
-phase_ti = angle(old_div(fphi,fti))
-save('phase_ti', phase_ti)
+fti = load("fti.npy")
+phase_ti = angle(old_div(fphi, fti))
+save("phase_ti", phase_ti)
 plt.figure()
-plt.plot(mean(mean(phase_ti[:,:,3,:],axis=1),axis=1))
-plt.title('ti')
-plt.savefig('image/phase_ti.png')
-plt.savefig('image/phase_ti.eps')
+plt.plot(mean(mean(phase_ti[:, :, 3, :], axis=1), axis=1))
+plt.title("ti")
+plt.savefig("image/phase_ti.png")
+plt.savefig("image/phase_ti.eps")
 
-fni = load('fni.npy')
-phase_ni = angle(old_div(fphi,fni))
-save('phase_ni', phase_ni)
+fni = load("fni.npy")
+phase_ni = angle(old_div(fphi, fni))
+save("phase_ni", phase_ni)
 plt.figure()
-plt.plot(mean(mean(phase_ni[:,:,3,:],axis=1),axis=1))
-plt.title('ni')
-plt.savefig('image/phase_ni.png')
-plt.savefig('image/phase_ni.eps')
+plt.plot(mean(mean(phase_ni[:, :, 3, :], axis=1), axis=1))
+plt.title("ni")
+plt.savefig("image/phase_ni.png")
+plt.savefig("image/phase_ni.eps")
 
 plt.show()
-
diff --git a/examples/elm-pb/Python/polslice.py b/examples/elm-pb/Python/polslice.py
index fe78495b5a..6a1179b2ae 100644
--- a/examples/elm-pb/Python/polslice.py
+++ b/examples/elm-pb/Python/polslice.py
@@ -11,31 +11,33 @@
 # Specify parameters
 
 
-path='./data/'
+path = "./data/"
 
-variable="P"
+variable = "P"
 
 p = collect(variable, path=path)
 
-period=15
+period = 15
 
-grid='../cbm18_dens8.grid_nx68ny64.nc'
+grid = "../cbm18_dens8.grid_nx68ny64.nc"
 
 ########################################################
 # Call plotpolslice once to get extended poloidal grid
 
-r,z,fun=plotpolslice(p[0,:,:,:],grid,period=period,rz=1)
+r, z, fun = plotpolslice(p[0, :, :, :], grid, period=period, rz=1)
 
-nx=r.shape[0] # number of points in r
-ny=r.shape[1] # number of points in z
-nt=p.shape[0] # time intervals
+nx = r.shape[0]  # number of points in r
+ny = r.shape[1]  # number of points in z
+nt = p.shape[0]  # time intervals
 
 
-fm=np.zeros((nt,nx,ny)) # array to store the time sequence of the poloidal cross section
+fm = np.zeros(
+    (nt, nx, ny)
+)  # array to store the time sequence of the poloidal cross section
 
-#Compute all time frames
+# Compute all time frames
 
 for k in range(nt):
-    fm[k,:,:]=plotpolslice(p[k,:,:,:],grid,period=period,rz=0)
+    fm[k, :, :] = plotpolslice(p[k, :, :, :], grid, period=period, rz=0)
 
-np.savez('pslice',fm=fm, z=z, r=r)
+np.savez("pslice", fm=fm, z=z, r=r)
diff --git a/examples/elm-pb/Python/post.py b/examples/elm-pb/Python/post.py
index 9bb67347f0..cdaefa98cf 100644
--- a/examples/elm-pb/Python/post.py
+++ b/examples/elm-pb/Python/post.py
@@ -15,12 +15,12 @@
 from mayavi import mlab
 
 
-path0="./data0/"
-path1="./data/"
+path0 = "./data0/"
+path1 = "./data/"
 
-period=15
+period = 15
 
-gfile='./cbm18_dens8.grid_nx68ny64.nc'
+gfile = "./cbm18_dens8.grid_nx68ny64.nc"
 
 
 with DataFile(gfile) as f:
@@ -28,71 +28,115 @@
 
 
 Dphi0 = collect("Dphi0", path=path0)
-phi0 = collect("phi0", path=path1) # needs diamagnetic effects
+phi0 = collect("phi0", path=path1)  # needs diamagnetic effects
 #
-psixy=g.get('psixy')
-PSI_AXIS=g.get('psi_axis')
-PSI_BNDRY=g.get('psi_bndry')
+psixy = g.get("psixy")
+PSI_AXIS = g.get("psi_axis")
+PSI_BNDRY = g.get("psi_bndry")
 #
-psix=old_div((psixy[:,32]-PSI_AXIS),(PSI_BNDRY-PSI_AXIS))
-Epsi=-deriv(phi0[:,32],psix)
+psix = old_div((psixy[:, 32] - PSI_AXIS), (PSI_BNDRY - PSI_AXIS))
+Epsi = -deriv(phi0[:, 32], psix)
 #
 #
-fig=figure()
-plot(psix,-Dphi0[:,32], 'r', linewidth=5)
-plot(psix,Epsi,'k',linewidth=5)
-annotate('w/o flow', xy=(.3, .7),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', size=30)
-annotate('w/ flow', xy=(.7, .4),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', color='r', size=30)
-xlabel('Radial $\psi$',fontsize=25)
-ylabel('$\Omega(\psi)/\omega_A$',fontsize=25)
-ylim([-.05,0])
-xlim([0.4,1.2])
+fig = figure()
+plot(psix, -Dphi0[:, 32], "r", linewidth=5)
+plot(psix, Epsi, "k", linewidth=5)
+annotate(
+    "w/o flow",
+    xy=(0.3, 0.7),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    size=30,
+)
+annotate(
+    "w/ flow",
+    xy=(0.7, 0.4),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    color="r",
+    size=30,
+)
+xlabel("Radial $\psi$", fontsize=25)
+ylabel("$\Omega(\psi)/\omega_A$", fontsize=25)
+ylim([-0.05, 0])
+xlim([0.4, 1.2])
 fig.set_tight_layout(True)
 show(block=False)
 
 p_f0 = collect("P", path=path0)
 p_f = collect("P", path=path1)
 #
-rmsp_f0=moment_xyzt(p_f0, 'RMS').rms
-rmsp_f=moment_xyzt(p_f, 'RMS').rms
+rmsp_f0 = moment_xyzt(p_f0, "RMS").rms
+rmsp_f = moment_xyzt(p_f, "RMS").rms
 #
 
-fig=figure(figsize=(10, 8))
-plot(np.gradient(np.log(rmsp_f0[:,34,32])), color='k',linewidth=3)
-plot(np.gradient(np.log(rmsp_f[:,34,32])),color='red',linewidth=3)
-
-ylabel('$\gamma / \omega_A$',fontsize=25)
-xlabel('Time$(\\tau_A)$',fontsize=25)
-annotate('w/o flow', xy=(.5, .7),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', size=30)
-annotate('w/ flow', xy=(.5, .4),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', color='r', size=30)
-ylim([0,0.5])
-xlim([0,100])
+fig = figure(figsize=(10, 8))
+plot(np.gradient(np.log(rmsp_f0[:, 34, 32])), color="k", linewidth=3)
+plot(np.gradient(np.log(rmsp_f[:, 34, 32])), color="red", linewidth=3)
+
+ylabel("$\gamma / \omega_A$", fontsize=25)
+xlabel("Time$(\\tau_A)$", fontsize=25)
+annotate(
+    "w/o flow",
+    xy=(0.5, 0.7),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    size=30,
+)
+annotate(
+    "w/ flow",
+    xy=(0.5, 0.4),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    color="r",
+    size=30,
+)
+ylim([0, 0.5])
+xlim([0, 100])
 fig.set_tight_layout(True)
 show(block=False)
 
 
-
-plotpolslice(p_f0[50,:,:,:],gfile,period=period, fig=1)
-mlab.text(.01,.99,"w/o flow")
-
-plotpolslice(p_f[50,:,:,:],gfile,period=period, fig=1)
-mlab.text(.01,.99,"w/ flow")
-
-fig=figure()
-mode_structure(p_f0[50,:,:,:], g, period=period)
-plot([40,40],[0,.014],'k--',linewidth=5)
-annotate('w/o flow', xy=(.3, .7),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', size=30)
-ylim([0,0.014])
-xlim([0,80])
+plotpolslice(p_f0[50, :, :, :], gfile, period=period, fig=1)
+mlab.text(0.01, 0.99, "w/o flow")
+
+plotpolslice(p_f[50, :, :, :], gfile, period=period, fig=1)
+mlab.text(0.01, 0.99, "w/ flow")
+
+fig = figure()
+mode_structure(p_f0[50, :, :, :], g, period=period)
+plot([40, 40], [0, 0.014], "k--", linewidth=5)
+annotate(
+    "w/o flow",
+    xy=(0.3, 0.7),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    size=30,
+)
+ylim([0, 0.014])
+xlim([0, 80])
 fig.set_tight_layout(True)
 show(block=False)
 
 
 figure()
-mode_structure(p_f[50,:,:,:], g, period=period)
-plot([40,40],[0,.014],'k--',linewidth=5)
-annotate('w/ flow', xy=(.3, .7),  xycoords='axes fraction',horizontalalignment='center', verticalalignment='center', color='k', size=30)
-ylim([0,0.0001])
-xlim([0,80])
+mode_structure(p_f[50, :, :, :], g, period=period)
+plot([40, 40], [0, 0.014], "k--", linewidth=5)
+annotate(
+    "w/ flow",
+    xy=(0.3, 0.7),
+    xycoords="axes fraction",
+    horizontalalignment="center",
+    verticalalignment="center",
+    color="k",
+    size=30,
+)
+ylim([0, 0.0001])
+xlim([0, 80])
 show(block=False)
 show()
diff --git a/examples/elm-pb/Python/read_elmsize.py b/examples/elm-pb/Python/read_elmsize.py
index fcd3d24e53..340f57ce7b 100644
--- a/examples/elm-pb/Python/read_elmsize.py
+++ b/examples/elm-pb/Python/read_elmsize.py
@@ -4,12 +4,12 @@
 from pylab import save, figure, plot, title, xlabel, ylabel, show, tight_layout
 from elm_size import elm_size
 
-path='./data'
+path = "./data"
 
-t_array=collect('t_array', path=path)
-save('t_array.dat', t_array)
-p0=collect('P0', path=path)
-save('p0.dat', p0)
+t_array = collect("t_array", path=path)
+save("t_array.dat", t_array)
+p0 = collect("P0", path=path)
+save("p0.dat", p0)
 
 
 # n0=collect('n0', path=path)
@@ -22,27 +22,27 @@
 with DataFile("./cbm18_dens8.grid_nx68ny64.nc") as f:
     gfile = {v: f.read(v) for v in f.keys()}
 
-p=collect('P', path=path)
-save('p.dat', p)
-res=moment_xyzt(p,'RMS','DC')
-rmsp=res.rms
-dcp=res.dc
-save('rmsp.dat', rmsp)
-save('dcp.dat',  dcp)
-elmsp=elm_size(dcp,p0,gfile,yind=32,Bbar=gfile['bmag'])
-save('elmsp.dat',  elmsp)
+p = collect("P", path=path)
+save("p.dat", p)
+res = moment_xyzt(p, "RMS", "DC")
+rmsp = res.rms
+dcp = res.dc
+save("rmsp.dat", rmsp)
+save("dcp.dat", dcp)
+elmsp = elm_size(dcp, p0, gfile, yind=32, Bbar=gfile["bmag"])
+save("elmsp.dat", elmsp)
 
 figure(0)
-plot(t_array,elmsp.s2, 'k-')
-xlabel('t/Ta')
-ylabel('Elm size')
-title('Elm size, P')
+plot(t_array, elmsp.s2, "k-")
+xlabel("t/Ta")
+ylabel("Elm size")
+title("Elm size, P")
 tight_layout()
 show()
 
 
-phi=collect('phi', path=path )
-save('phi.dat', phi)
-res=moment_xyzt( phi, 'DC', 'RMS')
-save('dcphi.dat',res.dc)
-save('rmsphi.dat', res.rms)
+phi = collect("phi", path=path)
+save("phi.dat", phi)
+res = moment_xyzt(phi, "DC", "RMS")
+save("dcphi.dat", res.dc)
+save("rmsphi.dat", res.rms)
diff --git a/examples/elm-pb/Python/showpolslice.py b/examples/elm-pb/Python/showpolslice.py
index d292575e35..072c53dcd6 100644
--- a/examples/elm-pb/Python/showpolslice.py
+++ b/examples/elm-pb/Python/showpolslice.py
@@ -6,10 +6,12 @@
 import numpy as np
 
 from tvtk.tools import visual
+
 try:
     from enthought.mayavi import mlab
 except ImportError:
-    try: from mayavi import mlab
+    try:
+        from mayavi import mlab
     except ImportError:
         print("No mlab available")
 
@@ -17,40 +19,42 @@
 ###########################
 # Read polslice array
 
-npzfile=np.load('pslice.npz')
-r=npzfile['r']
-z=npzfile['z']
-fm=npzfile['fm']
+npzfile = np.load("pslice.npz")
+r = npzfile["r"]
+z = npzfile["z"]
+fm = npzfile["fm"]
 
 ########################################################
 # Set up the window
 
-f = mlab.figure(size=(800,600))
+f = mlab.figure(size=(800, 600))
 # Tell visual to use this as the viewer.
 visual.set_viewer(f)
 
 ########################################################
 # Do the appropriate graph
 
-#s = mlab.contour_surf(r,z,fun, contours=30, line_width=.5, transparent=True)
-#s=mlab.surf(r,z,fun, colormap='Spectral')
-s = mlab.mesh(r,z,fm[0,:,:], scalars=fm[0,:,:], colormap='PuOr')#, wrap_scale='true')#, representation='wireframe')
-s.enable_contours=True
-s.contour.filled_contours=True
+# s = mlab.contour_surf(r,z,fun, contours=30, line_width=.5, transparent=True)
+# s=mlab.surf(r,z,fun, colormap='Spectral')
+s = mlab.mesh(
+    r, z, fm[0, :, :], scalars=fm[0, :, :], colormap="PuOr"
+)  # , wrap_scale='true')#, representation='wireframe')
+s.enable_contours = True
+s.contour.filled_contours = True
 
 # Define perspective and optional attributes. You can also implement from the window afterwards
 
-mlab.view(0,0)
-#mlab.view(-94.159958841373324,
+mlab.view(0, 0)
+# mlab.view(-94.159958841373324,
 # 53.777002382688906,
 # 8.2311808018087582)
 mlab.draw(f)
 mlab.colorbar(orientation="vertical")
-#mlab.axes()
-#mlab.outline()
+# mlab.axes()
+# mlab.outline()
 
 
 ########################################################
 # mlab animation
 
-anim(s,fm, save=True)
+anim(s, fm, save=True)
diff --git a/examples/elm-pb/Python/sprofiles.py b/examples/elm-pb/Python/sprofiles.py
index 9d8eea48de..244599f8af 100644
--- a/examples/elm-pb/Python/sprofiles.py
+++ b/examples/elm-pb/Python/sprofiles.py
@@ -16,45 +16,46 @@
 with DataFile(gfile) as f:
     g = {v: f.read(v) for v in f.keys()}
 
-var=collect("P", path=path)
+var = collect("P", path=path)
 
-sol=surface_average(var, g)
-#sol=np.mean(var,axis=3)
+sol = surface_average(var, g)
+# sol=np.mean(var,axis=3)
 
-p0av=collect("P0", path=path)
+p0av = collect("P0", path=path)
 
-q=np.zeros(sol.shape)
+q = np.zeros(sol.shape)
 
 for i in range(sol.shape[1]):
-    q[:,i]=sol[:,i]+p0av[:,0]
+    q[:, i] = sol[:, i] + p0av[:, 0]
 
 
-psixy=g.get('psixy')
-psi0=g.get('psi_axis')
-psix=g.get('psi_bndry')
+psixy = g.get("psixy")
+psi0 = g.get("psi_axis")
+psix = g.get("psi_bndry")
 
-xarr = psixy[:,0]
-xarr = old_div((xarr - psi0), (-psi0 + psix)) #for this grid
+xarr = psixy[:, 0]
+xarr = old_div((xarr - psi0), (-psi0 + psix))  # for this grid
 
 
-fig=figure()
+fig = figure()
 
-nt=q.shape[1]
+nt = q.shape[1]
 
-plot(xarr, p0av,'k',label='t=0')
-plot(xarr,q[:,nt/4],'r',label='t='+np.str(nt/4))
-plot(xarr,q[:,nt/2],'b',label='t='+np.str(nt/2))
-plot(xarr,q[:,3*nt/4],'g',label='t='+np.str(3*nt/4))
-plot(xarr, q[:,-1],'k',label='t='+np.str(nt))
+plot(xarr, p0av, "k", label="t=0")
+plot(xarr, q[:, nt / 4], "r", label="t=" + np.str(nt / 4))
+plot(xarr, q[:, nt / 2], "b", label="t=" + np.str(nt / 2))
+plot(xarr, q[:, 3 * nt / 4], "g", label="t=" + np.str(3 * nt / 4))
+plot(xarr, q[:, -1], "k", label="t=" + np.str(nt))
 
 from collections import OrderedDict
+
 handles, labels = gca().get_legend_handles_labels()
 by_label = OrderedDict(list(zip(labels, handles)))
 legend(list(by_label.values()), list(by_label.keys()))
 
 
-xlabel(r"$\psi$",fontsize=25)
-ylabel(r"$2 \mu_0 <P^2> / B^2$",fontsize=25)
+xlabel(r"$\psi$", fontsize=25)
+ylabel(r"$2 \mu_0 <P^2> / B^2$", fontsize=25)
 
 fig.set_tight_layout(True)
 
diff --git a/examples/elm-pb/runexample.py b/examples/elm-pb/runexample.py
index f7ebc01028..b49902d29c 100755
--- a/examples/elm-pb/runexample.py
+++ b/examples/elm-pb/runexample.py
@@ -28,18 +28,22 @@
 # Calculate RMS in toroidal direction
 prms = np.sqrt(np.mean(p**2, axis=3))
 
-growth = np.gradient(np.log(prms[:,42,32]))
+growth = np.gradient(np.log(prms[:, 42, 32]))
 
 # Final growth-rate
 gamma = growth[-2]
 
 import matplotlib.pyplot as plt
 
-plt.plot(tarr, prms[:,42,32], label='Outboard midplane')
-plt.plot( [tarr[0], tarr[-1]],
-	  [prms[-1,42,32]*np.exp(gamma*(tarr[0] - tarr[-1])), prms[-1,42,32]], '--', label=r'$\gamma =$'+str(gamma))
+plt.plot(tarr, prms[:, 42, 32], label="Outboard midplane")
+plt.plot(
+    [tarr[0], tarr[-1]],
+    [prms[-1, 42, 32] * np.exp(gamma * (tarr[0] - tarr[-1])), prms[-1, 42, 32]],
+    "--",
+    label=r"$\gamma =$" + str(gamma),
+)
 
-plt.yscale('log')
+plt.yscale("log")
 plt.grid()
 
 plt.xlabel(r"Time [$1/\tau_A$]")
@@ -57,19 +61,21 @@
 
 # Take a poloidal slice at fixed toroidal angle
 from boutdata.pol_slice import pol_slice
-p2d = pol_slice(p[-1,:,:,:], 'cbm18_dens8.grid_nx68ny64.nc', n=15, zangle=0.0)
+
+p2d = pol_slice(p[-1, :, :, :], "cbm18_dens8.grid_nx68ny64.nc", n=15, zangle=0.0)
 
 # Read grid file to get coordinates
 from boututils.datafile import DataFile
-g = DataFile('cbm18_dens8.grid_nx68ny64.nc')
 
-Rxy = g.read("Rxy") # Major radius [m]
-Zxy = g.read("Zxy") # Height [m]
+g = DataFile("cbm18_dens8.grid_nx68ny64.nc")
+
+Rxy = g.read("Rxy")  # Major radius [m]
+Zxy = g.read("Zxy")  # Height [m]
 
 plt.contourf(Rxy, Zxy, p2d, 30)
-plt.axis('equal')  # Maintain aspect ratio
+plt.axis("equal")  # Maintain aspect ratio
 
-plt.colorbar()   # Plot a bar down the side with a color scale
+plt.colorbar()  # Plot a bar down the side with a color scale
 
 plt.savefig("poloidal_slice.pdf")
 
diff --git a/examples/fci-wave/compare-density.py b/examples/fci-wave/compare-density.py
index c039c250b6..16e620a08f 100644
--- a/examples/fci-wave/compare-density.py
+++ b/examples/fci-wave/compare-density.py
@@ -1,4 +1,3 @@
-
 import matplotlib.pyplot as plt
 from boutdata import collect
 import numpy as np
@@ -9,60 +8,61 @@
 # Note: Data from fci-wave-logn examples commented out.
 
 data_noboundary = [
-    ("div", "Model 1 (density, point interpolation)")
-    ,("div-integrate", "Model 2 (density, area integration)")
-    ,("logn", "Model 3 (log density, area integration)")
-    #,("../fci-wave-logn/div-integrate", "Model 5 (velocity, log density, area integration)")
+    ("div", "Model 1 (density, point interpolation)"),
+    ("div-integrate", "Model 2 (density, area integration)"),
+    ("logn", "Model 3 (log density, area integration)"),
+    # ,("../fci-wave-logn/div-integrate", "Model 5 (velocity, log density, area integration)")
 ]
 
 data_boundary = [
-    ("boundary", "Model 2 (density, momentum)")
-    ,("boundary-logn", "Model 3 (log density, momentum)")
-    #,("../fci-wave-logn/boundary", "Model 5 (log density, velocity)")
-    ]
+    ("boundary", "Model 2 (density, momentum)"),
+    ("boundary-logn", "Model 3 (log density, momentum)"),
+    # ,("../fci-wave-logn/boundary", "Model 5 (log density, velocity)")
+]
 
 # Change this to select no boundary or boundary cases
 data = data_noboundary
 
 if run:
     from boututils.run_wrapper import shell_safe, launch_safe
+
     shell_safe("make > make.log")
 
-    for path,label in data:
-        launch_safe("./fci-wave -d "+path, nproc=nproc, pipe=False)
+    for path, label in data:
+        launch_safe("./fci-wave -d " + path, nproc=nproc, pipe=False)
 
-# Collect the results into a dictionary 
+# Collect the results into a dictionary
 sum_n_B = {}
 
-for path,label in data:
+for path, label in data:
     n = collect("n", path=path)
     Bxyz = collect("Bxyz", path=path)
 
     time = collect("t_array", path=path)
-    
+
     nt, nx, ny, nz = n.shape
-    
+
     n_B = np.ndarray(nt)
     for t in range(nt):
-        n_B[t] = np.sum(n[t,:,:,:] / Bxyz)
+        n_B[t] = np.sum(n[t, :, :, :] / Bxyz)
 
     sum_n_B[path] = (time, n_B)
 
     # Plot the density at the final time
-    
+
     plt.figure()
-    plt.contourf(n[-1,:,0,:].T, 100)
+    plt.contourf(n[-1, :, 0, :].T, 100)
     plt.colorbar()
     plt.xlabel("Major radius")
     plt.ylabel("Height")
-    plt.title("Density n, "+label)
-    plt.savefig(path+".pdf")
+    plt.title("Density n, " + label)
+    plt.savefig(path + ".pdf")
     plt.show()
 
 # Make a plot comparing total sum density / B
-    
+
 plt.figure()
-for path,label in data:
+for path, label in data:
     time, n_B = sum_n_B[path]
     plt.plot(time, n_B, label=label)
 plt.legend()
@@ -71,4 +71,3 @@
 plt.savefig("compare-density.pdf")
 
 plt.show()
-
diff --git a/examples/finite-volume/diffusion/mms.py b/examples/finite-volume/diffusion/mms.py
index 2c609ca82e..31b7714727 100644
--- a/examples/finite-volume/diffusion/mms.py
+++ b/examples/finite-volume/diffusion/mms.py
@@ -5,26 +5,26 @@
 from math import pi
 
 # Length of the y domain
-Ly = 10.
+Ly = 10.0
 
 # metric tensor
 metric = Metric()  # Identity
 
 # Define solution in terms of input x,y,z
 
-f = 1 + 0.1*sin(2*y - t)
-k = 1 + 0.1*sin(y)
+f = 1 + 0.1 * sin(2 * y - t)
+k = 1 + 0.1 * sin(y)
 
 # Turn solution into real x and z coordinates
-replace = [ (y, metric.y*2*pi/Ly) ]
+replace = [(y, metric.y * 2 * pi / Ly)]
 
 f = f.subs(replace)
-k = k.subs(replace) 
+k = k.subs(replace)
 
 ##############################
 # Calculate time derivatives
 
-dfdt = Div_par( k * Grad_par(f) )
+dfdt = Div_par(k * Grad_par(f))
 
 #############################
 # Calculate sources
@@ -32,7 +32,7 @@
 Sf = diff(f, t) - dfdt
 
 # Substitute back to get input y coordinates
-replace = [ (metric.y, y*Ly/(2*pi) ) ]
+replace = [(metric.y, y * Ly / (2 * pi))]
 
 k = k.subs(replace)
 f = f.subs(replace)
diff --git a/examples/finite-volume/fluid/mms.py b/examples/finite-volume/fluid/mms.py
index 8ed8fba517..a31782e2c7 100644
--- a/examples/finite-volume/fluid/mms.py
+++ b/examples/finite-volume/fluid/mms.py
@@ -5,19 +5,19 @@
 from math import pi
 
 # Length of the y domain
-Ly = 10.
+Ly = 10.0
 
 # metric tensor
 metric = Metric()  # Identity
 
 # Define solution in terms of input x,y,z
 
-n = 1 + 0.1*sin(2*y - t)
-p = 1 + 0.1*cos(3*y + t)
-nv = 0.1*sin(y + 2*t)
+n = 1 + 0.1 * sin(2 * y - t)
+p = 1 + 0.1 * cos(3 * y + t)
+nv = 0.1 * sin(y + 2 * t)
 
 # Turn solution into real x and z coordinates
-replace = [ (y, metric.y*2*pi/Ly) ]
+replace = [(y, metric.y * 2 * pi / Ly)]
 
 n = n.subs(replace)
 p = p.subs(replace)
@@ -27,16 +27,16 @@
 # Calculate time derivatives
 
 v = nv / n
-gamma = 5./3
+gamma = 5.0 / 3
 
 # Density equation
-dndt = - Div_par(nv)
+dndt = -Div_par(nv)
 
 # Pressure equation
-dpdt = - Div_par(p*v) - (gamma-1.0)*p*Div_par(v)
+dpdt = -Div_par(p * v) - (gamma - 1.0) * p * Div_par(v)
 
 # Momentum equation
-dnvdt = - Div_par(nv*v) - Grad_par(p)
+dnvdt = -Div_par(nv * v) - Grad_par(p)
 
 #############################
 # Calculate sources
@@ -46,7 +46,7 @@
 Snv = diff(nv, t) - dnvdt
 
 # Substitute back to get input y coordinates
-replace = [ (metric.y, y*Ly/(2*pi) ) ]
+replace = [(metric.y, y * Ly / (2 * pi))]
 
 n = n.subs(replace)
 p = p.subs(replace)
diff --git a/examples/laplace-petsc3d/plotcheck.py b/examples/laplace-petsc3d/plotcheck.py
index 707e5db1ee..7f2758dd81 100755
--- a/examples/laplace-petsc3d/plotcheck.py
+++ b/examples/laplace-petsc3d/plotcheck.py
@@ -10,27 +10,27 @@
 
 xg = 2
 
-f = collect('f', path=datadir)[xg:-xg, :, :]
-rhs = collect('rhs', path=datadir)[xg:-xg, :, :]
-rhs_check = collect('rhs_check', path=datadir)[xg:-xg, :, :]
-error = collect('error', path=datadir)[xg:-xg, :, :]
+f = collect("f", path=datadir)[xg:-xg, :, :]
+rhs = collect("rhs", path=datadir)[xg:-xg, :, :]
+rhs_check = collect("rhs_check", path=datadir)[xg:-xg, :, :]
+error = collect("error", path=datadir)[xg:-xg, :, :]
 
 pyplot.subplot(221)
 pyplot.pcolormesh(f[:, yind, :])
 pyplot.colorbar()
-pyplot.title('f')
+pyplot.title("f")
 pyplot.subplot(222)
 pyplot.pcolormesh(rhs[:, yind, :])
 pyplot.colorbar()
-pyplot.title('rhs')
+pyplot.title("rhs")
 pyplot.subplot(223)
 pyplot.pcolormesh(rhs_check[:, yind, :])
 pyplot.colorbar()
-pyplot.title('rhs_check')
+pyplot.title("rhs_check")
 pyplot.subplot(224)
 pyplot.pcolormesh(error[:, yind, :])
 pyplot.colorbar()
-pyplot.title('error')
+pyplot.title("error")
 
 pyplot.show()
 
diff --git a/examples/orszag-tang/generate.py b/examples/orszag-tang/generate.py
index 3ba6dbbea9..acce7497c3 100644
--- a/examples/orszag-tang/generate.py
+++ b/examples/orszag-tang/generate.py
@@ -2,14 +2,16 @@
 from __future__ import division
 from builtins import range
 from past.utils import old_div
+
 # the Scientific Python netCDF 3 interface
 # http://dirac.cnrs-orleans.fr/ScientificPython/
-#from Scientific.IO.NetCDF import NetCDFFile as Dataset
+# from Scientific.IO.NetCDF import NetCDFFile as Dataset
 # the 'classic' version of the netCDF4 python interface
 # http://code.google.com/p/netcdf4-python/
 import numpy as np
 from netCDF4 import Dataset
-from numpy import dtype # array module from http://numpy.scipy.org
+from numpy import dtype  # array module from http://numpy.scipy.org
+
 """
 This example writes some surface pressure and temperatures
 The companion program sfc_pres_temp_rd.py shows how to read the netCDF
@@ -30,44 +32,45 @@
 #
 
 # the output array to write will be nx x ny
-ny = 100; nx = ny + 4
+ny = 100
+nx = ny + 4
 
 # dy of grid
 dy = old_div(1.0, np.float(ny))
 dx = dy
 # create grid
-dxarr=np.zeros((nx,ny),dtype='float32')+dx
-dyarr=np.zeros((nx,ny),dtype='float32')+dy
+dxarr = np.zeros((nx, ny), dtype="float32") + dx
+dyarr = np.zeros((nx, ny), dtype="float32") + dy
 
-xarr=np.arange(0.,np.float(nx),1.,dtype='float32')*dx
-yarr=np.arange(0.,np.float(ny),1.,dtype='float32')*dy
+xarr = np.arange(0.0, np.float(nx), 1.0, dtype="float32") * dx
+yarr = np.arange(0.0, np.float(ny), 1.0, dtype="float32") * dy
 
 # compute initial variables
 
-rho=np.zeros((nx,ny),dtype='float32')+old_div(25.,(36.*np.pi))
-p=np.zeros((nx,ny),dtype='float32')+old_div(5.,(12.*np.pi))
+rho = np.zeros((nx, ny), dtype="float32") + old_div(25.0, (36.0 * np.pi))
+p = np.zeros((nx, ny), dtype="float32") + old_div(5.0, (12.0 * np.pi))
 
-rho=1.
-p=old_div(rho,3.)
+rho = 1.0
+p = old_div(rho, 3.0)
 
-v_x=np.zeros((nx,ny),dtype='float32')
-Bx=np.zeros((nx,ny),dtype='float32')
+v_x = np.zeros((nx, ny), dtype="float32")
+Bx = np.zeros((nx, ny), dtype="float32")
 
 for y in range(ny):
-    v_x[:,y]=-np.sin(2.*np.pi*yarr[y])
-    Bx[:,y]=-np.sin(2.*np.pi*yarr[y])
- 
-#Bx=Bx/np.sqrt(4.*np.pi)
+    v_x[:, y] = -np.sin(2.0 * np.pi * yarr[y])
+    Bx[:, y] = -np.sin(2.0 * np.pi * yarr[y])
 
+# Bx=Bx/np.sqrt(4.*np.pi)
 
-v_y=np.zeros((nx,ny),dtype='float32')
-By=np.zeros((nx,ny),dtype='float32')
+
+v_y = np.zeros((nx, ny), dtype="float32")
+By = np.zeros((nx, ny), dtype="float32")
 
 for x in range(nx):
-    v_y[x,:]=np.sin(2.*np.pi*xarr[x])
-    By[x,:]=np.sin(4.*np.pi*xarr[x])
-    
-#By=By/np.sqrt(4.*np.pi)
+    v_y[x, :] = np.sin(2.0 * np.pi * xarr[x])
+    By[x, :] = np.sin(4.0 * np.pi * xarr[x])
+
+# By=By/np.sqrt(4.*np.pi)
 
 
 # Domain inside core (periodic)
@@ -76,55 +79,62 @@
 ixseps2 = nx
 
 # open a new netCDF file for writing.
-ncfile = Dataset('otv.grd.128.nc','w', format='NETCDF3_CLASSIC') 
+ncfile = Dataset("otv.grd.128.nc", "w", format="NETCDF3_CLASSIC")
 
 # output data.
 
 # create the nx and ny dimensions.
-ncfile.createDimension('x',nx)
-ncfile.createDimension('y',ny)
-ncfile.createDimension('single',1)
+ncfile.createDimension("x", nx)
+ncfile.createDimension("y", ny)
+ncfile.createDimension("single", 1)
 
 # create and write nx,ny variables
-nxx=ncfile.createVariable('nx','i4',('single'))
-nyy=ncfile.createVariable('ny','i4',('single'))
+nxx = ncfile.createVariable("nx", "i4", ("single"))
+nyy = ncfile.createVariable("ny", "i4", ("single"))
 
-nxx[:]=nx
-nyy[:]=ny
+nxx[:] = nx
+nyy[:] = ny
 
 # Define the coordinate variables. They will hold the coordinate
 # information, that is, xarr,yarr
-dx = ncfile.createVariable('dx',dtype('float32').char,('x','y'))
-dy = ncfile.createVariable('dy',dtype('float32').char,('x','y',))
+dx = ncfile.createVariable("dx", dtype("float32").char, ("x", "y"))
+dy = ncfile.createVariable(
+    "dy",
+    dtype("float32").char,
+    (
+        "x",
+        "y",
+    ),
+)
 
 # write data to coordinate vars.
-dx[:,:] = dxarr
-dy[:,:] = dyarr
+dx[:, :] = dxarr
+dy[:, :] = dyarr
 
 # create and write ixseps* dimensions.
-ix1=ncfile.createVariable('ixseps1','i4',('single'))
-ix2=ncfile.createVariable('ixseps2','i4',('single'))
+ix1 = ncfile.createVariable("ixseps1", "i4", ("single"))
+ix2 = ncfile.createVariable("ixseps2", "i4", ("single"))
 
-ix1[:]=ixseps1
-ix2[:]=ixseps2
+ix1[:] = ixseps1
+ix2[:] = ixseps2
 
-# create the corresponding variables 
-rho0 = ncfile.createVariable('rho0',dtype('float32').char,('x','y'))
-p0 = ncfile.createVariable('p0',dtype('float32').char,('x','y'))
-v0_x = ncfile.createVariable('v0_x',dtype('float32').char,('x','y'))
-v0_y = ncfile.createVariable('v0_y',dtype('float32').char,('x','y'))
-B0x = ncfile.createVariable('B0x',dtype('float32').char,('x','y'))
-B0y = ncfile.createVariable('B0y',dtype('float32').char,('x','y'))
+# create the corresponding variables
+rho0 = ncfile.createVariable("rho0", dtype("float32").char, ("x", "y"))
+p0 = ncfile.createVariable("p0", dtype("float32").char, ("x", "y"))
+v0_x = ncfile.createVariable("v0_x", dtype("float32").char, ("x", "y"))
+v0_y = ncfile.createVariable("v0_y", dtype("float32").char, ("x", "y"))
+B0x = ncfile.createVariable("B0x", dtype("float32").char, ("x", "y"))
+B0y = ncfile.createVariable("B0y", dtype("float32").char, ("x", "y"))
 
 # write data to variables.
 
-rho0[:,:]=rho
-p0[:,:]=p
-v0_x[:,:]=v_x
-v0_y[:,:]=v_y
-B0x[:,:]=Bx
-B0y[:,:]=By
+rho0[:, :] = rho
+p0[:, :] = p
+v0_x[:, :] = v_x
+v0_y[:, :] = v_y
+B0x[:, :] = Bx
+B0y[:, :] = By
 
 
 ncfile.close()
-print('*** SUCCESS writing file otv.grd.py.nc!')
+print("*** SUCCESS writing file otv.grd.py.nc!")
diff --git a/examples/performance/bracket/scaling_parser.py b/examples/performance/bracket/scaling_parser.py
index d7a23842d4..15f0ea8780 100644
--- a/examples/performance/bracket/scaling_parser.py
+++ b/examples/performance/bracket/scaling_parser.py
@@ -2,8 +2,7 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
@@ -13,7 +12,7 @@ def read_file(filename):
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
diff --git a/examples/performance/ddx/new_scaling_parser.py b/examples/performance/ddx/new_scaling_parser.py
index d2a5fee191..5c0c92ff5e 100644
--- a/examples/performance/ddx/new_scaling_parser.py
+++ b/examples/performance/ddx/new_scaling_parser.py
@@ -2,19 +2,19 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
         continue
 
     from collections import OrderedDict
-    case_lines = OrderedDict() #{}
+
+    case_lines = OrderedDict()  # {}
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
@@ -25,12 +25,13 @@ def read_file(filename):
         for title, col in zip(titles, line[:-1]):
             cases_weak[title].append(float(col))
 
-    axis = cases_weak['Local grid']
+    axis = cases_weak["Local grid"]
     data = [cases_weak[x] for x in case_lines]
     labels = [case_lines[x] for x in case_lines]
-    return {'axis':axis, 'data':data, 'labels':labels}
+    return {"axis": axis, "data": data, "labels": labels}
+
 
-def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
+def getScan(baseName="timing_{n}.txt", nthreads=(1, 2, 4, 8, 16, 32)):
     from numpy import zeros
 
     dataS = []
@@ -38,17 +39,16 @@ def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
         f = baseName.format(n=n)
         dataS.append(read_file(f))
 
-
     nnt = len(dataS)
-    nlines = len(dataS[0]['data'])
-    nval = len(dataS[0]['data'][0])
-    rawDat = zeros([nnt,nval,nlines])
+    nlines = len(dataS[0]["data"])
+    nval = len(dataS[0]["data"][0])
+    rawDat = zeros([nnt, nval, nlines])
 
     for i, dat in enumerate(dataS):
-        print(len(dat['data']))
-        
-        rawDat[i,:,:] = dat['data']
+        print(len(dat["data"]))
+
+        rawDat[i, :, :] = dat["data"]
 
-    axes = [nthreads, dataS[0]['axis']]
+    axes = [nthreads, dataS[0]["axis"]]
 
-    return axes, rawDat, dataS[0]['labels']
+    return axes, rawDat, dataS[0]["labels"]
diff --git a/examples/performance/ddy/new_scaling_parser.py b/examples/performance/ddy/new_scaling_parser.py
index d2a5fee191..5c0c92ff5e 100644
--- a/examples/performance/ddy/new_scaling_parser.py
+++ b/examples/performance/ddy/new_scaling_parser.py
@@ -2,19 +2,19 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
         continue
 
     from collections import OrderedDict
-    case_lines = OrderedDict() #{}
+
+    case_lines = OrderedDict()  # {}
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
@@ -25,12 +25,13 @@ def read_file(filename):
         for title, col in zip(titles, line[:-1]):
             cases_weak[title].append(float(col))
 
-    axis = cases_weak['Local grid']
+    axis = cases_weak["Local grid"]
     data = [cases_weak[x] for x in case_lines]
     labels = [case_lines[x] for x in case_lines]
-    return {'axis':axis, 'data':data, 'labels':labels}
+    return {"axis": axis, "data": data, "labels": labels}
+
 
-def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
+def getScan(baseName="timing_{n}.txt", nthreads=(1, 2, 4, 8, 16, 32)):
     from numpy import zeros
 
     dataS = []
@@ -38,17 +39,16 @@ def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
         f = baseName.format(n=n)
         dataS.append(read_file(f))
 
-
     nnt = len(dataS)
-    nlines = len(dataS[0]['data'])
-    nval = len(dataS[0]['data'][0])
-    rawDat = zeros([nnt,nval,nlines])
+    nlines = len(dataS[0]["data"])
+    nval = len(dataS[0]["data"][0])
+    rawDat = zeros([nnt, nval, nlines])
 
     for i, dat in enumerate(dataS):
-        print(len(dat['data']))
-        
-        rawDat[i,:,:] = dat['data']
+        print(len(dat["data"]))
+
+        rawDat[i, :, :] = dat["data"]
 
-    axes = [nthreads, dataS[0]['axis']]
+    axes = [nthreads, dataS[0]["axis"]]
 
-    return axes, rawDat, dataS[0]['labels']
+    return axes, rawDat, dataS[0]["labels"]
diff --git a/examples/performance/ddz/new_scaling_parser.py b/examples/performance/ddz/new_scaling_parser.py
index d2a5fee191..5c0c92ff5e 100644
--- a/examples/performance/ddz/new_scaling_parser.py
+++ b/examples/performance/ddz/new_scaling_parser.py
@@ -2,19 +2,19 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
         continue
 
     from collections import OrderedDict
-    case_lines = OrderedDict() #{}
+
+    case_lines = OrderedDict()  # {}
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
@@ -25,12 +25,13 @@ def read_file(filename):
         for title, col in zip(titles, line[:-1]):
             cases_weak[title].append(float(col))
 
-    axis = cases_weak['Local grid']
+    axis = cases_weak["Local grid"]
     data = [cases_weak[x] for x in case_lines]
     labels = [case_lines[x] for x in case_lines]
-    return {'axis':axis, 'data':data, 'labels':labels}
+    return {"axis": axis, "data": data, "labels": labels}
+
 
-def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
+def getScan(baseName="timing_{n}.txt", nthreads=(1, 2, 4, 8, 16, 32)):
     from numpy import zeros
 
     dataS = []
@@ -38,17 +39,16 @@ def getScan(baseName = "timing_{n}.txt", nthreads = (1,2,4,8,16,32)):
         f = baseName.format(n=n)
         dataS.append(read_file(f))
 
-
     nnt = len(dataS)
-    nlines = len(dataS[0]['data'])
-    nval = len(dataS[0]['data'][0])
-    rawDat = zeros([nnt,nval,nlines])
+    nlines = len(dataS[0]["data"])
+    nval = len(dataS[0]["data"][0])
+    rawDat = zeros([nnt, nval, nlines])
 
     for i, dat in enumerate(dataS):
-        print(len(dat['data']))
-        
-        rawDat[i,:,:] = dat['data']
+        print(len(dat["data"]))
+
+        rawDat[i, :, :] = dat["data"]
 
-    axes = [nthreads, dataS[0]['axis']]
+    axes = [nthreads, dataS[0]["axis"]]
 
-    return axes, rawDat, dataS[0]['labels']
+    return axes, rawDat, dataS[0]["labels"]
diff --git a/examples/performance/iterator/scaling_parser.py b/examples/performance/iterator/scaling_parser.py
index d7a23842d4..15f0ea8780 100644
--- a/examples/performance/iterator/scaling_parser.py
+++ b/examples/performance/iterator/scaling_parser.py
@@ -2,8 +2,7 @@
 
 
 def read_file(filename):
-    reader = csv.reader(open(filename, 'r'), delimiter='\t',
-                        skipinitialspace=True)
+    reader = csv.reader(open(filename, "r"), delimiter="\t", skipinitialspace=True)
 
     # Skip header
     for _, _ in zip(range(4), reader):
@@ -13,7 +12,7 @@ def read_file(filename):
     for line in reader:
         if line == []:
             break
-        case_lines[line[0].rstrip('.')] = line[1]
+        case_lines[line[0].rstrip(".")] = line[1]
 
     titles = next(reader)
     cases_weak = {col.strip(): [] for col in titles[:-1]}
diff --git a/examples/staggered_grid/generate.py b/examples/staggered_grid/generate.py
index da84e9c2e6..a5a0120612 100755
--- a/examples/staggered_grid/generate.py
+++ b/examples/staggered_grid/generate.py
@@ -4,11 +4,11 @@
 # Generate an input mesh
 #
 
-from boututils.datafile import DataFile # Wrapper around NetCDF4 libraries
+from boututils.datafile import DataFile  # Wrapper around NetCDF4 libraries
 
-nx = 5   # Minimum is 5: 2 boundary, one evolved
+nx = 5  # Minimum is 5: 2 boundary, one evolved
 ny = 32  # Minimum 5. Should be divisible by number of processors (so powers of 2 nice)
-dy = 1. # distance between points in y, in m/g22/lengthunit
+dy = 1.0  # distance between points in y, in m/g22/lengthunit
 ixseps1 = -1
 ixseps2 = -1
 
diff --git a/examples/subsampling/show.py b/examples/subsampling/show.py
index 34c6ee3084..b79c5e2964 100755
--- a/examples/subsampling/show.py
+++ b/examples/subsampling/show.py
@@ -11,14 +11,14 @@
 
 for pack in monitors:
     filename, data_name = pack
-    t = DataFile(path+'/'+filename+'.dmp.0.nc').read('t_array')
-    data = DataFile(path+'/'+filename+'.dmp.0.nc').read(data_name).flatten()
+    t = DataFile(path + "/" + filename + ".dmp.0.nc").read("t_array")
+    data = DataFile(path + "/" + filename + ".dmp.0.nc").read(data_name).flatten()
     plt.plot(t, data, label="{} {}".format(filename, data_name))
 
-time = DataFile(path+'/BOUT.dmp.0.nc').read('t_array')
-data = DataFile(path+'/BOUT.dmp.0.nc').read("T")[:, 2, 2, 0]
+time = DataFile(path + "/BOUT.dmp.0.nc").read("t_array")
+data = DataFile(path + "/BOUT.dmp.0.nc").read("T")[:, 2, 2, 0]
 
-plt.plot(time, data, marker='+', label="BOUT++ T")
+plt.plot(time, data, marker="+", label="BOUT++ T")
 
 plt.xlabel("Time")
 plt.legend()
diff --git a/examples/wave-slab/generate.py b/examples/wave-slab/generate.py
index 0a2e8f3049..12698d1e24 100755
--- a/examples/wave-slab/generate.py
+++ b/examples/wave-slab/generate.py
@@ -51,7 +51,7 @@
 for x in range(nx):
     Bpxy[x, :] = Bpx[x]
 
-Bxy = sqrt(Bpxy ** 2 + Bt ** 2)
+Bxy = sqrt(Bpxy**2 + Bt**2)
 
 # Calculate change in poloidal flux
 dr = Lx / nx  # Constant mesh spacing in radius
diff --git a/manual/sphinx/figs/figure_creators/LaplacianMatrices.ipynb b/manual/sphinx/figs/figure_creators/LaplacianMatrices.ipynb
index c3c39a3c12..4e940b998f 100644
--- a/manual/sphinx/figs/figure_creators/LaplacianMatrices.ipynb
+++ b/manual/sphinx/figs/figure_creators/LaplacianMatrices.ipynb
@@ -40,10 +40,10 @@
    "outputs": [],
    "source": [
     "# Note, these can be max 9 due to the current index convention\n",
-    "nx = 3 # Not including ghost points\n",
+    "nx = 3  # Not including ghost points\n",
     "nz = 3\n",
     "\n",
-    "startXIndex = 10 # The x indices are the slowest growing indices\n",
+    "startXIndex = 10  # The x indices are the slowest growing indices\n",
     "startZIndex = 1  # The z indices are the fastest growing indices"
    ]
   },
@@ -85,13 +85,13 @@
     "for z in range(nz):\n",
     "    f.append([])\n",
     "    xStart = startZIndex\n",
-    "    xEnd   = startXIndex*(nx+1)  # +1 due to ghost point\n",
+    "    xEnd = startXIndex * (nx + 1)  # +1 due to ghost point\n",
     "    # +startXIndex in the range as the range does not include endpoint\n",
-    "    for xInd in range(xStart, xEnd+startXIndex, 10):\n",
-    "        ind = str(xInd+z)\n",
-    "        if (xInd+z) < startXIndex:\n",
-    "            ind = '0'+str(xInd+z)\n",
-    "        f[z].append(symbols('f_' + ind))\n",
+    "    for xInd in range(xStart, xEnd + startXIndex, 10):\n",
+    "        ind = str(xInd + z)\n",
+    "        if (xInd + z) < startXIndex:\n",
+    "            ind = \"0\" + str(xInd + z)\n",
+    "        f[z].append(symbols(\"f_\" + ind))\n",
     "\n",
     "mesh = Matrix(f[::-1])\n",
     "display(mesh)"
@@ -195,21 +195,21 @@
     }
    ],
    "source": [
-    "xVec=[]\n",
-    "bVec=[]\n",
+    "xVec = []\n",
+    "bVec = []\n",
     "# Do the inner loop, so start ranges at 1\n",
     "# (nx+1) to include outer ghost point, +1 in the range as the range does not include endpoint\n",
-    "for x in range(1, (nx+1)+1):\n",
-    "    for z in range(1,nz+1):\n",
-    "        xVec.append(symbols('x_'+str(x)+'_'+str(z)))\n",
-    "        bVec.append(symbols('b_'+str(x)+'_'+str(z)))\n",
+    "for x in range(1, (nx + 1) + 1):\n",
+    "    for z in range(1, nz + 1):\n",
+    "        xVec.append(symbols(\"x_\" + str(x) + \"_\" + str(z)))\n",
+    "        bVec.append(symbols(\"b_\" + str(x) + \"_\" + str(z)))\n",
     "\n",
     "# Do the inner ghost points\n",
     "# Must count backwards since we are inserting in the front\n",
-    "for ind in range(nz,0,-1):\n",
-    "    xVec.insert(0, symbols('x_0_'+str(ind)))\n",
-    "    bVec.insert(0, symbols('b_0_'+str(ind)))\n",
-    "    \n",
+    "for ind in range(nz, 0, -1):\n",
+    "    xVec.insert(0, symbols(\"x_0_\" + str(ind)))\n",
+    "    bVec.insert(0, symbols(\"b_0_\" + str(ind)))\n",
+    "\n",
     "display(Matrix(xVec))\n",
     "display(Matrix(bVec))"
    ]
@@ -274,7 +274,7 @@
     "globInd = []\n",
     "for rows in range(len(xVec)):\n",
     "    cols = []\n",
-    "    for col in range(rows*len(xVec), (rows+1)*len(xVec)):\n",
+    "    for col in range(rows * len(xVec), (rows + 1) * len(xVec)):\n",
     "        cols.append(col)\n",
     "    globInd.append(cols)\n",
     "\n",
@@ -305,10 +305,14 @@
    "source": [
     "c = []\n",
     "for x in range(nx):\n",
-    "    indexStart = (startXIndex+1)+(startXIndex*x)     # Multiply by 10 due to index system\n",
-    "    indexEnd   = (startXIndex+nz+1)+(startXIndex*x)  # Multiply by 10 due to index system\n",
+    "    indexStart = (startXIndex + 1) + (\n",
+    "        startXIndex * x\n",
+    "    )  # Multiply by 10 due to index system\n",
+    "    indexEnd = (startXIndex + nz + 1) + (\n",
+    "        startXIndex * x\n",
+    "    )  # Multiply by 10 due to index system\n",
     "    for ind in range(indexStart, indexEnd):\n",
-    "        c.append(symbols('c_'+str(ind)))"
+    "        c.append(symbols(\"c_\" + str(ind)))"
    ]
   },
   {
@@ -328,11 +332,11 @@
    "source": [
     "# The inner ghost\n",
     "innerGhostStart = startZIndex\n",
-    "innerGhostEnd   = nz\n",
+    "innerGhostEnd = nz\n",
     "ig = []\n",
     "# +1 in the range as last point is not included\n",
-    "for z in range(innerGhostStart, innerGhostEnd+1):\n",
-    "    ig.append(symbols('ig_0_'+str(z)))"
+    "for z in range(innerGhostStart, innerGhostEnd + 1):\n",
+    "    ig.append(symbols(\"ig_0_\" + str(z)))"
    ]
   },
   {
@@ -345,12 +349,12 @@
    "source": [
     "# The outer ghost\n",
     "# nx+1 as we want to go past the last inner x grid point\n",
-    "outerGhostStart = startXIndex*(nx+1) + startZIndex\n",
-    "outerGhostEnd   = startXIndex*(nx+1) + nz\n",
+    "outerGhostStart = startXIndex * (nx + 1) + startZIndex\n",
+    "outerGhostEnd = startXIndex * (nx + 1) + nz\n",
     "og = []\n",
     "# +1 in the range as last point is not included\n",
-    "for z in range(outerGhostStart, outerGhostEnd+1):\n",
-    "    og.append(symbols('og_'+str(z)))"
+    "for z in range(outerGhostStart, outerGhostEnd + 1):\n",
+    "    og.append(symbols(\"og_\" + str(z)))"
    ]
   },
   {
@@ -396,21 +400,27 @@
     "for x in range(nx):\n",
     "    # The indices referring to the matrix index\n",
     "    # The last -1 is there as the matrix indices count from 0\n",
-    "    startRow = (nz+1)+(x*nz)-1  # Starting at row+1 after inner ghost point sub-matrix\n",
-    "    endRow   = (nz+1)+(x*nz)+(nz-1)-1 # Ending row-1 before the last z-index (last z will be wrapped around)\n",
+    "    startRow = (\n",
+    "        (nz + 1) + (x * nz) - 1\n",
+    "    )  # Starting at row+1 after inner ghost point sub-matrix\n",
+    "    endRow = (\n",
+    "        (nz + 1) + (x * nz) + (nz - 1) - 1\n",
+    "    )  # Ending row-1 before the last z-index (last z will be wrapped around)\n",
     "    # +1 in range as last point is not included\n",
-    "    rows     = range(startRow,   endRow+1)\n",
-    "    cols     = range(startRow+1, endRow+1) # Column is shifted +1 from the diagonal\n",
-    "    \n",
+    "    rows = range(startRow, endRow + 1)\n",
+    "    cols = range(startRow + 1, endRow + 1)  # Column is shifted +1 from the diagonal\n",
+    "\n",
     "    # The indices referring to the spatial point in the grid\n",
     "    # The last \"+1\" is fue to the fact that the column is shifted +1 from the diagonal\n",
-    "    startInd = (startXIndex+startZIndex) + (startXIndex*x) + 1\n",
-    "    endInd   = (startXIndex+startZIndex) + (nz-1) + (startXIndex*x) + 1 # Wrap around last point\n",
+    "    startInd = (startXIndex + startZIndex) + (startXIndex * x) + 1\n",
+    "    endInd = (\n",
+    "        (startXIndex + startZIndex) + (nz - 1) + (startXIndex * x) + 1\n",
+    "    )  # Wrap around last point\n",
     "    # +1 in range as last point is not included\n",
-    "    inds     = range(startInd, endInd+1)\n",
-    "    \n",
+    "    inds = range(startInd, endInd + 1)\n",
+    "\n",
     "    for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "        InvM[rInd, cInd] = symbols('zp_'+str(ind))"
+    "        InvM[rInd, cInd] = symbols(\"zp_\" + str(ind))"
    ]
   },
   {
@@ -423,15 +433,17 @@
    "source": [
     "# The wrap around\n",
     "# The index referring to the spatial point in the grid\n",
-    "startInd = startXIndex+startZIndex\n",
+    "startInd = startXIndex + startZIndex\n",
     "# The indices referring to the matrix index\n",
-    "# Last -1 as the matrix indices are counted from 0 \n",
-    "startRow = (nz+1) + (nz-1) - 1 # nz+1 below from the ghost sub matrix, nz-1 below after that\n",
-    "startCol = (nz+1)-1            # nz+1 left of the ghost sub matrix\n",
+    "# Last -1 as the matrix indices are counted from 0\n",
+    "startRow = (\n",
+    "    (nz + 1) + (nz - 1) - 1\n",
+    ")  # nz+1 below from the ghost sub matrix, nz-1 below after that\n",
+    "startCol = (nz + 1) - 1  # nz+1 left of the ghost sub matrix\n",
     "for wrap in range(nx):\n",
-    "    row = startRow+wrap*nz\n",
-    "    col = startCol+wrap*nz\n",
-    "    InvM[row, col] = symbols('zp_'+str(startInd+startXIndex*wrap))"
+    "    row = startRow + wrap * nz\n",
+    "    col = startCol + wrap * nz\n",
+    "    InvM[row, col] = symbols(\"zp_\" + str(startInd + startXIndex * wrap))"
    ]
   },
   {
@@ -452,20 +464,26 @@
     "for x in range(nx):\n",
     "    # The indices referring to the matrix index\n",
     "    # The last -1 is there as the matrix indices count from 0\n",
-    "    startRow = (nz+1)+(x*nz)-1  # Starting at row+1 after inner ghost point sub-matrix\n",
-    "    endRow   = (nz+1)+(x*nz)+(nz-1)-1 # Ending row-1 before the last z-index (last z will be wrapped around)\n",
+    "    startRow = (\n",
+    "        (nz + 1) + (x * nz) - 1\n",
+    "    )  # Starting at row+1 after inner ghost point sub-matrix\n",
+    "    endRow = (\n",
+    "        (nz + 1) + (x * nz) + (nz - 1) - 1\n",
+    "    )  # Ending row-1 before the last z-index (last z will be wrapped around)\n",
     "    # +1 in range as last point is not included\n",
-    "    rows     = range(startRow+1, endRow+1) # Row is shifted +1 from the diagonal\n",
-    "    cols     = range(startRow,   endRow+1)\n",
-    "    \n",
+    "    rows = range(startRow + 1, endRow + 1)  # Row is shifted +1 from the diagonal\n",
+    "    cols = range(startRow, endRow + 1)\n",
+    "\n",
     "    # The indices referring to the spatial point in the grid\n",
-    "    startInd = (startXIndex+startZIndex) + (startXIndex*x)\n",
-    "    endInd   = (startXIndex+startZIndex) + (nz-1) + (startXIndex*x) # Wrap around last point\n",
+    "    startInd = (startXIndex + startZIndex) + (startXIndex * x)\n",
+    "    endInd = (\n",
+    "        (startXIndex + startZIndex) + (nz - 1) + (startXIndex * x)\n",
+    "    )  # Wrap around last point\n",
     "    # +1 in range as last point is not included\n",
-    "    inds     = range(startInd, endInd+1)\n",
-    "    \n",
+    "    inds = range(startInd, endInd + 1)\n",
+    "\n",
     "    for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "        InvM[rInd, cInd] = symbols('zm_'+str(ind))"
+    "        InvM[rInd, cInd] = symbols(\"zm_\" + str(ind))"
    ]
   },
   {
@@ -478,15 +496,19 @@
    "source": [
     "# The wrap around\n",
     "# The index referring to the spatial point in the grid\n",
-    "startInd = startXIndex+startZIndex+(nz-1) # +(nz-1) as this will be the last z point for the current x\n",
+    "startInd = (\n",
+    "    startXIndex + startZIndex + (nz - 1)\n",
+    ")  # +(nz-1) as this will be the last z point for the current x\n",
     "# The indices referring to the matrix index\n",
-    "# Last -1 as the matrix indices are counted from 0 \n",
-    "startRow = (nz+1)-1            # nz+1 below the ghost sub matrix\n",
-    "startCol = (nz+1) + (nz-1) - 1 # nz+1 left from the ghost sub matrix, nz-1 left after that\n",
+    "# Last -1 as the matrix indices are counted from 0\n",
+    "startRow = (nz + 1) - 1  # nz+1 below the ghost sub matrix\n",
+    "startCol = (\n",
+    "    (nz + 1) + (nz - 1) - 1\n",
+    ")  # nz+1 left from the ghost sub matrix, nz-1 left after that\n",
     "for wrap in range(nx):\n",
-    "    row = startRow+wrap*nz\n",
-    "    col = startCol+wrap*nz\n",
-    "    InvM[row, col] = symbols('zm_'+str(startInd+startXIndex*wrap))"
+    "    row = startRow + wrap * nz\n",
+    "    col = startCol + wrap * nz\n",
+    "    InvM[row, col] = symbols(\"zm_\" + str(startInd + startXIndex * wrap))"
    ]
   },
   {
@@ -505,23 +527,29 @@
    "outputs": [],
    "source": [
     "# Indices referring to the spatial points in the grid\n",
-    "startInd = startXIndex*2 + startZIndex # *2 as we start at the second inner x-index\n",
-    "endInd   = startInd + (startZIndex*nz) # *nz as this is the last z-index in the current x-index\n",
+    "startInd = startXIndex * 2 + startZIndex  # *2 as we start at the second inner x-index\n",
+    "endInd = startInd + (\n",
+    "    startZIndex * nz\n",
+    ")  # *nz as this is the last z-index in the current x-index\n",
     "\n",
     "for x in range(nx):\n",
     "    # The indices referring to the matrix index\n",
     "    # The last -1 as the matrix indices counts from 0\n",
-    "    startRow = (nz+1)+(x*nz)-1      # Starting at row+1 after inner ghost point sub-matrix\n",
-    "    endRow   = (nz+1)+(x*nz)+(nz)-1 # Ending at the row referring to the last z-index\n",
+    "    startRow = (\n",
+    "        (nz + 1) + (x * nz) - 1\n",
+    "    )  # Starting at row+1 after inner ghost point sub-matrix\n",
+    "    endRow = (\n",
+    "        (nz + 1) + (x * nz) + (nz) - 1\n",
+    "    )  # Ending at the row referring to the last z-index\n",
     "    # Not +1 in range as we do not want to include last point\n",
-    "    rows     = range(startRow,    endRow)\n",
-    "    cols     = range(startRow+nz, endRow+nz)           # Start at first index after last z-index\n",
-    "    \n",
+    "    rows = range(startRow, endRow)\n",
+    "    cols = range(startRow + nz, endRow + nz)  # Start at first index after last z-index\n",
+    "\n",
     "    # Indices referring to the spatial points in the grid\n",
-    "    inds     = range(startInd+startXIndex*x, endInd+startXIndex*x)\n",
-    "    \n",
+    "    inds = range(startInd + startXIndex * x, endInd + startXIndex * x)\n",
+    "\n",
     "    for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "        InvM[rInd, cInd] = symbols('xp_'+str(ind))"
+    "        InvM[rInd, cInd] = symbols(\"xp_\" + str(ind))"
    ]
   },
   {
@@ -534,22 +562,22 @@
    "source": [
     "# x+1 for inner ghost point\n",
     "# Indices referring to the spatial points in the grid\n",
-    "startInd = startXIndex + startZIndex   # First inner point for first z\n",
-    "endInd   = startInd + (startZIndex*nz) # First inner point for last z\n",
+    "startInd = startXIndex + startZIndex  # First inner point for first z\n",
+    "endInd = startInd + (startZIndex * nz)  # First inner point for last z\n",
     "\n",
     "# The indices referring to the matrix index\n",
     "# The last -1 as the matrix indices counts from 0\n",
-    "startRow = startZIndex-1    # Starting at first row\n",
-    "endRow   = startZIndex+nz-1 # Ending at the row referring to the last z-index\n",
+    "startRow = startZIndex - 1  # Starting at first row\n",
+    "endRow = startZIndex + nz - 1  # Ending at the row referring to the last z-index\n",
     "# Not +1 in range as we do not want to include last point\n",
-    "rows     = range(startRow,    endRow)\n",
-    "cols     = range(startRow+nz, endRow+nz)           # Start at first index after last z-index\n",
-    "    \n",
+    "rows = range(startRow, endRow)\n",
+    "cols = range(startRow + nz, endRow + nz)  # Start at first index after last z-index\n",
+    "\n",
     "# Indices referring to the spatial points in the grid\n",
-    "inds     = range(startInd, endInd)\n",
-    "    \n",
+    "inds = range(startInd, endInd)\n",
+    "\n",
     "for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "    InvM[rInd, cInd] = symbols('igxp_'+str(ind))"
+    "    InvM[rInd, cInd] = symbols(\"igxp_\" + str(ind))"
    ]
   },
   {
@@ -569,25 +597,25 @@
    "source": [
     "# Indices referring to the spatial points in the grid\n",
     "startInd = startZIndex\n",
-    "endInd   = startInd + nz\n",
+    "endInd = startInd + nz\n",
     "\n",
     "for x in range(nx):\n",
     "    # The indices referring to the matrix index\n",
     "    # Note that x starts counting from zero, so we must add 1 to x in the rows\n",
-    "    startRow = ((x+1)*nz)      # Starting at row+1 after inner ghost point sub-matrix\n",
-    "    endRow   = ((x+1)*nz)+(nz) # Ending at the row referring to the last z-index\n",
+    "    startRow = (x + 1) * nz  # Starting at row+1 after inner ghost point sub-matrix\n",
+    "    endRow = ((x + 1) * nz) + (nz)  # Ending at the row referring to the last z-index\n",
     "    # Not +1 in range as we do not want to include last point\n",
-    "    rows = range(startRow,    endRow)\n",
-    "    cols = range(startRow-nz, endRow-nz)           # Start at first index after last z-index\n",
-    "    \n",
+    "    rows = range(startRow, endRow)\n",
+    "    cols = range(startRow - nz, endRow - nz)  # Start at first index after last z-index\n",
+    "\n",
     "    # Indices referring to the spatial points in the grid\n",
-    "    inds = range(startInd+startXIndex*x, endInd+startXIndex*x)\n",
-    "    \n",
+    "    inds = range(startInd + startXIndex * x, endInd + startXIndex * x)\n",
+    "\n",
     "    for rInd, cInd, ind in zip(rows, cols, inds):\n",
     "        if (ind) < startXIndex:\n",
-    "            ind = '0'+str(ind)\n",
+    "            ind = \"0\" + str(ind)\n",
     "\n",
-    "        InvM[rInd, cInd] = symbols('xm_'+str(ind))"
+    "        InvM[rInd, cInd] = symbols(\"xm_\" + str(ind))"
    ]
   },
   {
@@ -600,22 +628,24 @@
    "source": [
     "# x-1 for inner ghost point\n",
     "# Indices referring to the spatial points in the grid\n",
-    "startInd = startXIndex*nx + startZIndex   # Last inner point for first z\n",
-    "endInd   = startInd + (startZIndex*nz)    # Last inner point for last z\n",
+    "startInd = startXIndex * nx + startZIndex  # Last inner point for first z\n",
+    "endInd = startInd + (startZIndex * nz)  # Last inner point for last z\n",
     "\n",
     "# The indices referring to the matrix index\n",
     "# The last -1 as the matrix indices counts from 0\n",
-    "startRow = len(xVec)-nz-1    # Starting at last inner point row\n",
-    "endRow   = len(xVec)-1       # Ending at the last row\n",
+    "startRow = len(xVec) - nz - 1  # Starting at last inner point row\n",
+    "endRow = len(xVec) - 1  # Ending at the last row\n",
     "# +1 in range as last point is not included\n",
-    "rows     = range(startRow+1,    endRow+1)\n",
-    "cols     = range(startRow-nz+1, endRow-nz+1) # Start at first index after last z-index\n",
-    "    \n",
+    "rows = range(startRow + 1, endRow + 1)\n",
+    "cols = range(\n",
+    "    startRow - nz + 1, endRow - nz + 1\n",
+    ")  # Start at first index after last z-index\n",
+    "\n",
     "# Indices referring to the spatial points in the grid\n",
-    "inds     = range(startInd, endInd)\n",
-    "    \n",
+    "inds = range(startInd, endInd)\n",
+    "\n",
     "for rInd, cInd, ind in zip(rows, cols, inds):\n",
-    "    InvM[rInd, cInd] = symbols('ogxm_'+str(ind))"
+    "    InvM[rInd, cInd] = symbols(\"ogxm_\" + str(ind))"
    ]
   },
   {
diff --git a/manual/sphinx/figs/figure_creators/bout_runners_folder_structure.py b/manual/sphinx/figs/figure_creators/bout_runners_folder_structure.py
index 8a95a13436..5a4a2a0843 100644
--- a/manual/sphinx/figs/figure_creators/bout_runners_folder_structure.py
+++ b/manual/sphinx/figs/figure_creators/bout_runners_folder_structure.py
@@ -10,10 +10,10 @@
 mmag@fysik.dtu.dk
 """
 
-__authors__ = 'Michael Loeiten'
-__email__   = 'mmag@fysik.dtu.dk'
-__version__ = '1.0'
-__date__    = '21.01.2016'
+__authors__ = "Michael Loeiten"
+__email__ = "mmag@fysik.dtu.dk"
+__version__ = "1.0"
+__date__ = "21.01.2016"
 
 import pygraphviz as pgv
 
@@ -21,113 +21,118 @@
 tree = pgv.AGraph()
 
 # Appendable lists
-files     = []
+files = []
 dead_ends = []
 
 # Default node attributes
-tree.node_attr['shape']='box'
-tree.node_attr['style']='bold'
+tree.node_attr["shape"] = "box"
+tree.node_attr["style"] = "bold"
 
 # Adding nodes and edges
-l0 = 'project'
-l1 = ['data', 'source\nfiles', 'driver.py']
+l0 = "project"
+l1 = ["data", "source\nfiles", "driver.py"]
 # Append the files
 files.append(l1[1])
 files.append(l1[2])
 # Add the boxes to the mother node
 for box in l1:
-    tree.add_edge(l0,box)
+    tree.add_edge(l0, box)
 
-l2 = ['solver1', 'solver2',\
-      'BOUT.inp', 'run_log.txt']
+l2 = ["solver1", "solver2", "BOUT.inp", "run_log.txt"]
 # Append the files
 files.append(l2[2])
 files.append(l2[3])
 # Add the boxes to the mother node
 for box in l2:
-    tree.add_edge('data', box)
-tree.add_edge('solver2', 'solver2/...')
+    tree.add_edge("data", box)
+tree.add_edge("solver2", "solver2/...")
 # Append the dead_end
-de = l2[1] + '/...'
+de = l2[1] + "/..."
 dead_ends.append(de)
 
-l3 = ['method1', 'method2', 'solver1/...']
+l3 = ["method1", "method2", "solver1/..."]
 for box in l3:
-    tree.add_edge('solver1', box)
-tree.add_edge('method2', 'method2/...')
+    tree.add_edge("solver1", box)
+tree.add_edge("method2", "method2/...")
 # Append the dead_end
 de = l3[2]
 dead_ends.append(de)
-de = l3[1] + '/...'
+de = l3[1] + "/..."
 dead_ends.append(de)
 
-l4 = ['nout\ntimestep1', 'nout\ntimestep2', 'method1/...']
+l4 = ["nout\ntimestep1", "nout\ntimestep2", "method1/..."]
 for box in l4:
-    tree.add_edge('method1', box)
-tree.add_edge('nout\ntimestep2', 'nout\ntimestep2/...')
+    tree.add_edge("method1", box)
+tree.add_edge("nout\ntimestep2", "nout\ntimestep2/...")
 # Append the dead_end
 de = l4[2]
 dead_ends.append(de)
-de = l4[1] + '/...'
+de = l4[1] + "/..."
 dead_ends.append(de)
 
-l5 = ['mesh1', 'mesh2', 'nout\ntimestep1/...']
+l5 = ["mesh1", "mesh2", "nout\ntimestep1/..."]
 for box in l5:
-    tree.add_edge('nout\ntimestep1', box)
-tree.add_edge('mesh2', 'mesh2/...')
+    tree.add_edge("nout\ntimestep1", box)
+tree.add_edge("mesh2", "mesh2/...")
 # Append the dead_end
 de = l5[2]
 dead_ends.append(de)
-de = l5[1] + '/...'
+de = l5[1] + "/..."
 dead_ends.append(de)
 
-l6 = ['additional1', 'additional2', 'mesh1/...']
+l6 = ["additional1", "additional2", "mesh1/..."]
 for box in l6:
-    tree.add_edge('mesh1', box)
-tree.add_edge('additional2', 'additional2/...')
+    tree.add_edge("mesh1", box)
+tree.add_edge("additional2", "additional2/...")
 # Append the dead_end
 de = l6[2]
 dead_ends.append(de)
-de = l6[1] + '/...'
+de = l6[1] + "/..."
 dead_ends.append(de)
 
-l7 = ['grid_file1', 'grid_file2', 'additional1/...']
+l7 = ["grid_file1", "grid_file2", "additional1/..."]
 for box in l7:
-    tree.add_edge('additional1', box)
-tree.add_edge('grid_file2', 'grid_file2/...')
+    tree.add_edge("additional1", box)
+tree.add_edge("grid_file2", "grid_file2/...")
 # Append the dead_end
 de = l7[2]
 dead_ends.append(de)
-de = l7[1] + '/...'
+de = l7[1] + "/..."
 dead_ends.append(de)
 
-l8 = ['BOUT.inp\n(copy)', 'BOUT.log', 'BOUT.dmp',\
-      'BOUT.restart', '(source_files\n(copy))', '(grid_file\n(copy))']
+l8 = [
+    "BOUT.inp\n(copy)",
+    "BOUT.log",
+    "BOUT.dmp",
+    "BOUT.restart",
+    "(source_files\n(copy))",
+    "(grid_file\n(copy))",
+]
 # Add l8 to the files list
 for cur_file in l8:
     files.append(cur_file)
 # Append them to the mother node
 for box in l8:
-    tree.add_edge('grid_file1', box)
+    tree.add_edge("grid_file1", box)
 
 
 # Change colors for the files
 for the_file in files:
-    member=tree.get_node(the_file)
-#    member.attr['fontcolor'] = 'limegreen'
-    member.attr['color'] = 'limegreen'
+    member = tree.get_node(the_file)
+    #    member.attr['fontcolor'] = 'limegreen'
+    member.attr["color"] = "limegreen"
 
 # Change colors for the dead_ends
 for dead_end in dead_ends:
-    member=tree.get_node(dead_end)
-#    member.attr['fontcolor'] = 'darksalmon'
-    member.attr['color'] = 'darksalmon'
+    member = tree.get_node(dead_end)
+    #    member.attr['fontcolor'] = 'darksalmon'
+    member.attr["color"] = "darksalmon"
 
 
 # Print the graph
 print(tree.string())
 
 # Set layout
-tree.layout('dot')
+tree.layout("dot")
 # Write to file
-tree.draw('folder_tree.svg')
+tree.draw("folder_tree.svg")
diff --git a/tests/MMS/advection/runtest b/tests/MMS/advection/runtest
index 9a0a691287..5109c47815 100755
--- a/tests/MMS/advection/runtest
+++ b/tests/MMS/advection/runtest
@@ -50,7 +50,7 @@ def run_mms(options, exit=True):
 
             dx = 2.0 * pi / (nx)
 
-            args = f"{opts} mesh:nx={nx+4} mesh:dx={dx} MZ={nx}"
+            args = f"{opts} mesh:nx={nx + 4} mesh:dx={dx} MZ={nx}"
 
             print("  Running with " + args)
 

From 03283f45a50a4f883ca0f1a95c906474b7f4e4d5 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Mon, 2 Feb 2026 10:52:26 +0000
Subject: [PATCH 0482/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 4990f2586e..a6948a0684 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -1,3 +1,4 @@
 # Clang-format whole repo
 d8f14fdddb5ca0fbb32d8e2bf5ac2960d6ac5ce6
 ed2117e6d6826a98b6988e2f18c0c34e408563b6
+52301380586fdbf890f620c04f689b08d89a6c34

From 26651cc10565d47b381febf3b863f3ee79dca597 Mon Sep 17 00:00:00 2001
From: David Bold <dschwoerer@users.noreply.github.com>
Date: Mon, 2 Feb 2026 12:15:45 +0100
Subject: [PATCH 0483/1827] Revert accidential typo

---
 src/mesh/coordinates.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index b8b0f9ea55..086fa2e23e 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1590,7 +1590,7 @@ Field3D Coordinates::Div_par(const Field3D& f, CELL_LOC outloc,
     f_B.yup(i) = f.yup(i) / Bxy_floc.yup(i);
     f_B.ydown(i) = f.ydown(i) / Bxy_floc.ydown(i);
   }
-  return xy * Grad_par(f_B, outloc, method);
+  return Bxy * Grad_par(f_B, outloc, method);
 }
 
 /////////////////////////////////////////////////////////

From f319c61b58ecb145e1607846e10e6748713fd519 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:04:49 +0100
Subject: [PATCH 0484/1827] Fix comment

---
 include/bout/options_io.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index 509305aad0..3892ccbc1f 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -14,7 +14,7 @@
 ///
 /// 2. Restart files:
 ///
-///       auto restart = OptionsIOFactory::getInstance().createOutput();
+///       auto restart = OptionsIOFactory::getInstance().createRestart();
 ///       restart->write(data);
 ///
 ///    where data is an Options tree. By default restart files are configured

From 1519bf29232c90be0933153d7a6ae027f7887e29 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:11:06 +0100
Subject: [PATCH 0485/1827] Add simple method to write data in parallel

---
 include/bout/options_io.hxx    | 28 ++++++++++++++++++++--------
 src/sys/options/options_io.cxx |  9 +++++++++
 2 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index 3892ccbc1f..f35aab6716 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -5,8 +5,8 @@
 ///
 /// 1. Dump files, containing time history:
 ///
-///       auto dump = OptionsIOFactory::getInstance().createOutput();
-///       dump->write(data);
+///        auto dump = OptionsIOFactory::getInstance().createOutput();
+///        dump->write(data);
 ///
 ///    where data is an Options tree. By default dump files are configured
 ///    with the root `output` section, or an Option tree can be passed to
@@ -14,20 +14,27 @@
 ///
 /// 2. Restart files:
 ///
-///       auto restart = OptionsIOFactory::getInstance().createRestart();
-///       restart->write(data);
+///        auto restart = OptionsIOFactory::getInstance().createRestart();
+///        restart->write(data);
 ///
 ///    where data is an Options tree. By default restart files are configured
 ///    with the root `restart_files` section, or an Option tree can be passed to
 ///    `createRestart`.
 ///
 /// 3. Ad-hoc single files
-///   Note: The caller should consider how multiple processors interact with the file.
+///    Note: The caller should consider how multiple processors interact with the file.
 ///
-///       auto file = OptionsIOFactory::getInstance().createFile("some_file.nc");
-///   or
-///       auto file = OptionsIO::create("some_file.nc");
+///        auto file = OptionsIOFactory::getInstance().createFile("some_file.nc");
+///    or
+///        auto file = OptionsIO::create("some_file.nc");
 ///
+/// 4. Ad-hoc parallel files
+///    This adds also metric information, such that the file can be read with
+///    boutdata or xBOUT
+///
+///        OptionIO::write("some_file", data, mesh);
+///
+///    if mesh is omitted, no grid information is added.
 ///
 
 #pragma once
@@ -77,6 +84,11 @@ public:
   /// This uses the default file type and default options.
   static std::unique_ptr<OptionsIO> create(const std::string& file);
 
+  /// Write some data to a file with a given name prefix
+  /// This will be done in parallel. If Mesh is given, also mesh data will be
+  /// added, which is needed for xBOUT or boutdata to read the files.
+  static void write(const std::string& prefix, Options data, Mesh* mesh = nullptr);
+
   /// Create an OptionsIO for I/O to the given file.
   /// The file will be configured using the given `config` options:
   ///  - "type" : string   The file type e.g. "netcdf" or "adios"
diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx
index 6717b6b07d..9ac5b69cc8 100644
--- a/src/sys/options/options_io.cxx
+++ b/src/sys/options/options_io.cxx
@@ -2,6 +2,7 @@
 #include "bout/bout.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
+#include "bout/version.hxx"
 
 #include "options_adios.hxx"
 #include "options_netcdf.hxx"
@@ -55,4 +56,12 @@ void writeDefaultOutputFile(Options& data) {
   OptionsIOFactory::getInstance().createOutput()->write(data);
 }
 
+void OptionsIO::write(const std::string& prefix, Options data, Mesh* mesh) {
+  Options file_options = {{"prefix", prefix}};
+  data["BOUT_VERSION"].force(bout::version::as_double);
+  if (mesh != nullptr) {
+    mesh->outputVars(data);
+  }
+  OptionsIOFactory::getInstance().createOutput(&file_options)->write(data);
+}
 } // namespace bout

From b61f8158906fa877a806523a93de181465d82988 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:11:26 +0100
Subject: [PATCH 0486/1827] Use new interface to write data

Allows to use other backends then netcdf
---
 src/solver/impls/euler/euler.cxx | 13 ++-----------
 src/solver/impls/pvode/pvode.cxx | 12 +-----------
 2 files changed, 3 insertions(+), 22 deletions(-)

diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 6bdceab516..ed8621a874 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -164,19 +164,10 @@ void EulerSolver::take_step(BoutReal curtime, BoutReal dt, Array<BoutReal>& star
       mesh = f.var->getMesh();
     }
 
-    if (mesh != nullptr) {
-      mesh->outputVars(debug);
-      debug["BOUT_VERSION"].force(bout::version::as_double);
-    }
-
     const std::string outnumber =
         dump_at_time < -3 ? fmt::format(".{}", debug_counter++) : "";
-    const std::string outname =
-        fmt::format("{}/BOUT.debug{}.{}.nc",
-                    Options::root()["datadir"].withDefault<std::string>("data"),
-                    outnumber, BoutComm::rank());
-
-    bout::OptionsIO::create(outname)->write(debug);
+    const std::string outname = fmt::format("BOUT.debug{}", outnumber);
+    bout::OptionsIO::write(outname, debug, mesh);
     MPI_Barrier(BoutComm::get());
     for (auto& f : f3d) {
       f.F_var->disableTracking();
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 4cc90af8fd..5fbabe5bd2 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -399,17 +399,7 @@ BoutReal PvodeSolver::run(BoutReal tout) {
       for (auto& f : f3d) {
         saveParallel(debug, f.name, *f.var);
       }
-
-      if (mesh != nullptr) {
-        mesh->outputVars(debug);
-        debug["BOUT_VERSION"].force(bout::version::as_double);
-      }
-
-      const std::string outname = fmt::format(
-          "{}/BOUT.debug.{}.nc",
-          Options::root()["datadir"].withDefault<std::string>("data"), BoutComm::rank());
-
-      bout::OptionsIO::create(outname)->write(debug);
+      bout::OptionsIO::write("BOUT.debug", debug, mesh);
       MPI_Barrier(BoutComm::get());
     }
     return -1.0;

From eab6b0356545c84114ffdd7b6d351f77671d17d9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:30:10 +0100
Subject: [PATCH 0487/1827] Add docs on using solver-dumping

---
 manual/sphinx/developer_docs/debugging.rst | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/manual/sphinx/developer_docs/debugging.rst b/manual/sphinx/developer_docs/debugging.rst
index f16d0b6a3b..63c4f4e389 100644
--- a/manual/sphinx/developer_docs/debugging.rst
+++ b/manual/sphinx/developer_docs/debugging.rst
@@ -158,3 +158,23 @@ If you need to capture runtime information in the message, you can use
 the ``fmt`` syntax also used by the loggers::
 
     TRACE("Value of i={}, some arbitrary {}", i, "string");
+
+
+Time evolution
+==============
+
+It can be convinient to know what happend when the simulation failed.
+The pvode solver can dump the state of the simulation, at the time where the
+solver failed. This information does include the single terms in the
+derivative. This allows to identify which term is causing the issue.
+In addition the residuum is dump. This not only tells which term, but also
+where the solver is struggeling.
+This can be enabled with::
+
+     solver:type=pvode solver:debug_on_failure=true
+
+It is also possible to dump at a specific time using the euler solver.
+This can be handy to track down what is causing differences between two
+different versions. It can be used with::
+
+      solver:type=euler solver:dump_at_time=0 input:error_on_unused_options=false

From 508dcdae51d09b49f12b1303d834275b0229a03a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:39:14 +0100
Subject: [PATCH 0488/1827] Improve docs

---
 manual/sphinx/developer_docs/debugging.rst | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/manual/sphinx/developer_docs/debugging.rst b/manual/sphinx/developer_docs/debugging.rst
index 63c4f4e389..b23d882a42 100644
--- a/manual/sphinx/developer_docs/debugging.rst
+++ b/manual/sphinx/developer_docs/debugging.rst
@@ -163,18 +163,18 @@ the ``fmt`` syntax also used by the loggers::
 Time evolution
 ==============
 
-It can be convinient to know what happend when the simulation failed.
-The pvode solver can dump the state of the simulation, at the time where the
-solver failed. This information does include the single terms in the
-derivative. This allows to identify which term is causing the issue.
-In addition the residuum is dump. This not only tells which term, but also
-where the solver is struggeling.
-This can be enabled with::
+It can be useful to know what happened when the simulation failed.  The pvode
+solver can dump the state of the simulation, at the time the solver
+failed. This information includes the individual terms in the derivative. This
+allows to identify which term is causing the issue.  Additionally, the
+residuum is dumped. This identifies not only which term is causing the issue,
+but also where in the domain the solver is struggling.  This can be enabled
+with::
 
      solver:type=pvode solver:debug_on_failure=true
 
 It is also possible to dump at a specific time using the euler solver.
-This can be handy to track down what is causing differences between two
+This can be useful for tracking down what is causing differences between two
 different versions. It can be used with::
 
       solver:type=euler solver:dump_at_time=0 input:error_on_unused_options=false

From c9732b7fa2802b07dd2c329b04df647fafb63ad4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 14:48:31 +0100
Subject: [PATCH 0489/1827] Add more docs

---
 manual/sphinx/developer_docs/debugging.rst | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/manual/sphinx/developer_docs/debugging.rst b/manual/sphinx/developer_docs/debugging.rst
index b23d882a42..4f47cd63e3 100644
--- a/manual/sphinx/developer_docs/debugging.rst
+++ b/manual/sphinx/developer_docs/debugging.rst
@@ -171,10 +171,17 @@ residuum is dumped. This identifies not only which term is causing the issue,
 but also where in the domain the solver is struggling.  This can be enabled
 with::
 
-     solver:type=pvode solver:debug_on_failure=true
+    solver:type=pvode solver:debug_on_failure=true
+
+It can be also useful for understanding why the solver is slow. Forcing a
+higher min_timestep, the solver will fail to evolve the system as it
+encounters the situation, and provides information where it is happening.
+This can be done with::
+
+    solver:type=pvode solver:debug_on_failure=true solver:min_timestep=1e2
 
 It is also possible to dump at a specific time using the euler solver.
 This can be useful for tracking down what is causing differences between two
 different versions. It can be used with::
 
-      solver:type=euler solver:dump_at_time=0 input:error_on_unused_options=false
+    solver:type=euler solver:dump_at_time=0 input:error_on_unused_options=false

From 9b96dad5490af5515fad8464f830a22335a831be Mon Sep 17 00:00:00 2001
From: David Bold <dschwoerer@users.noreply.github.com>
Date: Tue, 3 Feb 2026 14:50:05 +0100
Subject: [PATCH 0490/1827] simplify to_load creation

Co-authored-by: Peter Hill <peter.hill@york.ac.uk>
---
 src/solver/impls/pvode/pvode.cxx | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 5fbabe5bd2..d8e2ab2438 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -380,9 +380,7 @@ BoutReal PvodeSolver::run(BoutReal tout) {
         std::vector<bool> evolve_bndrys{};
         for (const auto& f : f3d) {
           mesh = f.var->getMesh();
-          Field3D to_load{0., mesh};
-          to_load.allocate();
-          to_load.setLocation(f.location);
+          Field3D to_load{0., mesh}.setLocation(f.location);
           debug[fmt::format("{:s}{:s}", prefix, f.name)] = to_load;
           list_of_fields.push_back(to_load);
           evolve_bndrys.push_back(f.evolve_bndry);

From 94f9ea601d153f3f8020efa7fb38b4448aaf5e61 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 15:13:46 +0100
Subject: [PATCH 0491/1827] Fixup to_load

---
 src/solver/impls/pvode/pvode.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index d8e2ab2438..95adecaec1 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -380,7 +380,8 @@ BoutReal PvodeSolver::run(BoutReal tout) {
         std::vector<bool> evolve_bndrys{};
         for (const auto& f : f3d) {
           mesh = f.var->getMesh();
-          Field3D to_load{0., mesh}.setLocation(f.location);
+          Field3D to_load{0., mesh};
+          to_load.setLocation(f.location);
           debug[fmt::format("{:s}{:s}", prefix, f.name)] = to_load;
           list_of_fields.push_back(to_load);
           evolve_bndrys.push_back(f.evolve_bndry);

From 6ec39173f20de8a3aab59cf24f23e5793623fee6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 15:35:18 +0100
Subject: [PATCH 0492/1827] Take reference to avoid copy

---
 include/bout/options_io.hxx    | 2 +-
 src/sys/options/options_io.cxx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index f35aab6716..4fab70aea8 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -87,7 +87,7 @@ public:
   /// Write some data to a file with a given name prefix
   /// This will be done in parallel. If Mesh is given, also mesh data will be
   /// added, which is needed for xBOUT or boutdata to read the files.
-  static void write(const std::string& prefix, Options data, Mesh* mesh = nullptr);
+  static void write(const std::string& prefix, Options& data, Mesh* mesh = nullptr);
 
   /// Create an OptionsIO for I/O to the given file.
   /// The file will be configured using the given `config` options:
diff --git a/src/sys/options/options_io.cxx b/src/sys/options/options_io.cxx
index 9ac5b69cc8..256ec56b28 100644
--- a/src/sys/options/options_io.cxx
+++ b/src/sys/options/options_io.cxx
@@ -56,7 +56,7 @@ void writeDefaultOutputFile(Options& data) {
   OptionsIOFactory::getInstance().createOutput()->write(data);
 }
 
-void OptionsIO::write(const std::string& prefix, Options data, Mesh* mesh) {
+void OptionsIO::write(const std::string& prefix, Options& data, Mesh* mesh) {
   Options file_options = {{"prefix", prefix}};
   data["BOUT_VERSION"].force(bout::version::as_double);
   if (mesh != nullptr) {

From bc59d075f251660a476c241465be6f5bcee35e4c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Feb 2026 10:59:38 +0100
Subject: [PATCH 0493/1827] Fix manual build

---
 manual/CMakeLists.txt | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/manual/CMakeLists.txt b/manual/CMakeLists.txt
index b5224440bf..af4c528446 100644
--- a/manual/CMakeLists.txt
+++ b/manual/CMakeLists.txt
@@ -7,21 +7,18 @@ set(BOUT_SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/sphinx)
 set(BOUT_SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR}/docs)
 
 set(env_command
-    ${CMAKE_COMMAND} -E env
-    PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
+    ${CMAKE_COMMAND} -E env PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
 )
 
 add_custom_target(sphinx-html
-  COMMAND ${env_command}
-  COMMAND ${SPHINX_EXECUTABLE} -b html ${BOUT_SPHINX_SOURCE} ${BOUT_SPHINX_BUILD}
+  COMMAND ${env_command} ${SPHINX_EXECUTABLE} -b html ${BOUT_SPHINX_SOURCE} ${BOUT_SPHINX_BUILD}
   COMMAND ${CMAKE_COMMAND} -E echo "Generated HTML docs in file://${BOUT_SPHINX_BUILD}/index.html"
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   COMMENT "Generating HTML documentation with Sphinx in ${BOUT_SPHINX_BUILD}"
 )
 
 add_custom_target(sphinx-pdf
-  COMMAND ${env_command}
-  COMMAND ${SPHINX_EXECUTABLE} -M latexpdf ${BOUT_SPHINX_SOURCE} ${BOUT_SPHINX_BUILD}
+  COMMAND ${env_command} ${SPHINX_EXECUTABLE} -M latexpdf ${BOUT_SPHINX_SOURCE} ${BOUT_SPHINX_BUILD}
   COMMAND ${CMAKE_COMMAND} -E echo "Generated PDF docs in file://${BOUT_SPHINX_BUILD}"
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   COMMENT "Generating PDF documentation with Sphinx in ${BOUT_SPHINX_BUILD}"

From 5053c8f753e6cd9d98ea34e4161f82f1716e1b15 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 6 Feb 2026 09:16:44 -0800
Subject: [PATCH 0494/1827] initial_profiles: Use FieldFactory singleton

Rather than creating a new FieldFactory, use the singleton object.
This allows users to register new generators and use them to
intialise variables.
---
 src/field/initialprofiles.cxx | 25 ++++---------------------
 1 file changed, 4 insertions(+), 21 deletions(-)

diff --git a/src/field/initialprofiles.cxx b/src/field/initialprofiles.cxx
index 2c34caa6e1..6a437dbe02 100644
--- a/src/field/initialprofiles.cxx
+++ b/src/field/initialprofiles.cxx
@@ -1,23 +1,10 @@
 /**************************************************************************
  * Sets initial profiles
  *
- * ChangeLog
- * =========
- *
- * 2011-02-12 Ben Dudson <bd512@york.ac.uk>
- *    * Changed to use new options system. For now the structure of the
- *      options is the same, but this could be modified more easily in future
- *
- * 2010-05-12 Ben Dudson <bd512@york.ac.uk>
- *
- *    * Changed random numbers to use a hash of the parameters
- *      so that the phase doesn't vary with number of processors or grid size
- *      User can vary phase to give a different random sequence
- *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -49,12 +36,10 @@ void initial_profile(const std::string& name, Field3D& var) {
 
   Options* varOpts = Options::getRoot()->getSection(name);
 
-  FieldFactory f(localmesh);
-
   std::string function;
   VAROPTION(varOpts, function, "0.0");
 
-  var = f.create3D(function, varOpts, nullptr, var.getLocation());
+  var = FieldFactory::get()->create3D(function, varOpts, localmesh, var.getLocation());
 
   // Optionally scale the variable
   BoutReal scale;
@@ -68,12 +53,10 @@ void initial_profile(const std::string& name, Field2D& var) {
 
   Options* varOpts = Options::getRoot()->getSection(name);
 
-  FieldFactory f(localmesh);
-
   std::string function;
   VAROPTION(varOpts, function, "0.0");
 
-  var = f.create2D(function, varOpts, nullptr, var.getLocation());
+  var = FieldFactory::get()->create2D(function, varOpts, localmesh, var.getLocation());
 
   // Optionally scale the variable
   BoutReal scale;

From 8c351e45204e5ec1a1e5760d60a6e749707ee8f5 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Feb 2026 10:49:18 -0800
Subject: [PATCH 0495/1827] snes: Change target_its to BoutReal

Allows the target to be set to push timestep rather than
stall once reaching a set number of iterations.
---
 src/solver/impls/snes/snes.hxx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 5d007f8ad7..15f97c42a7 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -162,8 +162,11 @@ private:
 
   ///< PID controller parameters
   bool pid_controller; ///< Use PID controller?
-  int target_its;      ///< Target number of nonlinear iterations for the PID controller.
-  ///< Use with caution! Not tested values.
+
+  /// Target number of nonlinear iterations for the PID controller.
+  /// This can be non-integer to push timestep more aggressively
+  BoutReal target_its;
+
   BoutReal kP; ///< (0.6 - 0.8) Proportional parameter (main response to current step)
   BoutReal kI; ///< (0.2 - 0.4) Integral parameter (smooths history of changes)
   BoutReal kD; ///< (0.1 - 0.3) Derivative (dampens oscillation - optional)

From 20613a4ad6419218da21e785addf01a88159aa8b Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Feb 2026 10:53:55 -0800
Subject: [PATCH 0496/1827] snes: last_failure_weight input for tuning
 recent_failure_rate

Calculates a moving average of recent SNES failures.
Enables timestep controllers to be more cautious when SNES
is repeatedly failing.
---
 src/solver/impls/snes/snes.cxx | 7 +++++--
 src/solver/impls/snes/snes.hxx | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index da66092e84..7684c79a86 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -545,6 +545,9 @@ SNESSolver::SNESSolver(Options* opts)
           (*options)["pid_consider_failures"]
               .doc("Reduce timestep increases if recent solves have failed")
               .withDefault<bool>(false)),
+      last_failure_weight((*options)["last_failure_weight"]
+                              .doc("Weighting of last timestep in recent failure rate")
+                              .withDefault(0.1)),
       diagnose(
           (*options)["diagnose"].doc("Print additional diagnostics").withDefault(false)),
       diagnose_failures((*options)["diagnose_failures"]
@@ -979,12 +982,12 @@ int SNESSolver::run() {
       SNESGetLinearSolveIterations(snes, &lin_its);
 
       // Rolling average of recent failures
-      recent_failure_rate *= 1. - inv_failure_window;
+      recent_failure_rate *= 1. - last_failure_weight;
 
       if ((ierr != PETSC_SUCCESS) or (reason < 0)) {
         // Diverged or SNES failed
 
-        recent_failure_rate += inv_failure_window;
+        recent_failure_rate += last_failure_weight;
 
         ++snes_failures;
         steps_since_snes_failure = 0;
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 15f97c42a7..0cf9eef4b0 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -172,7 +172,7 @@ private:
   BoutReal kD; ///< (0.1 - 0.3) Derivative (dampens oscillation - optional)
   bool pid_consider_failures; ///< Reduce timestep increases if recent solves have failed
   BoutReal recent_failure_rate;            ///< Rolling average of recent failure rate
-  const BoutReal inv_failure_window = 0.1; ///< 1 / number of recent solves
+  BoutReal last_failure_weight;            ///< 1 / number of recent solves
 
   int nl_its_prev;
   int nl_its_prev2;

From a4c48fb4db25d7957f580db68b2ea76ac3510bf9 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Feb 2026 10:57:09 -0800
Subject: [PATCH 0497/1827] snes: updateGlobalTimestep for global timestep
 control

Separate out the global timestep control into a function
---
 src/solver/impls/snes/snes.cxx | 89 +++++++++++++---------------------
 src/solver/impls/snes/snes.hxx |  4 ++
 2 files changed, 39 insertions(+), 54 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 7684c79a86..32a9902543 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -851,7 +851,6 @@ int SNESSolver::run() {
 
     bool looping = true;
     int snes_failures = 0; // Count SNES convergence failures
-    int steps_since_snes_failure = 0;
     int saved_jacobian_lag = 0;
     int loop_count = 0;
     recent_failure_rate = 0.0;
@@ -990,7 +989,6 @@ int SNESSolver::run() {
         recent_failure_rate += last_failure_weight;
 
         ++snes_failures;
-        steps_since_snes_failure = 0;
 
         if (diagnose_failures or (snes_failures == max_snes_failures)) {
           // Print diagnostics to help identify source of the problem
@@ -1123,7 +1121,6 @@ int SNESSolver::run() {
       }
 
       simtime += dt;
-      ++steps_since_snes_failure;
 
       if (diagnose) {
         // Gather and print diagnostic information
@@ -1145,67 +1142,25 @@ int SNESSolver::run() {
       }
 
       if (equation_form == BoutSnesEquationForm::pseudo_transient) {
-        if (pid_controller) {
-          // Adjust pseudo_alpha based on nonlinear iterations
-          pseudo_alpha = pid(pseudo_alpha, nl_its, max_timestep * atol * 100);
-        }
+        // Adjust pseudo_alpha to globally scale timesteps
+        pseudo_alpha = updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate, max_timestep * atol * 100);
 
         // Adjust local timesteps
         PetscCall(updatePseudoTimestepping(snes_x));
 
-      } else if (pid_controller) {
-        // Changing the timestep using a PID controller.
-        // Note: The preconditioner depends on the timestep,
-        // so we recalculate the jacobian and the preconditioner
-        //  every time the timestep changes
-
-        timestep = pid(timestep, nl_its, max_timestep);
+      } else {
+        // Adjust timestep
+        timestep = updateGlobalTimestep(timestep, nl_its, recent_failure_rate, max_timestep);
+      }
 
-        // NOTE(malamast): Do we really need this?
-        // Recompute Jacobian (for now)
+      if (static_cast<BoutReal>(lin_its) / nl_its > 0.5 * maxl) {
+        // Recompute Jacobian if number of linear iterations is too high
         if (saved_jacobian_lag == 0) {
           SNESGetLagJacobian(snes, &saved_jacobian_lag);
           SNESSetLagJacobian(snes, 1);
         }
-
-      } else {
-        // Consider changing the timestep.
-        // Note: The preconditioner depends on the timestep,
-        // so if it is not recalculated the it will be less
-        // effective.
-        if ((nl_its <= lower_its) && (timestep < max_timestep)
-            && (steps_since_snes_failure > 2)) {
-          // Increase timestep slightly
-          timestep *= timestep_factor_on_lower_its;
-
-          timestep = std::min(timestep, max_timestep);
-
-          // Note: Setting the SNESJacobianFn to NULL retains
-          // previously set evaluation function.
-          //
-          // The SNES Jacobian is a combination of the RHS Jacobian
-          // and a factor involving the timestep.
-          // Depends on equation_form
-          // -> Probably call SNESSetJacobian(snes, Jfd, Jfd, NULL, fdcoloring);
-          if (static_cast<BoutReal>(lin_its) / nl_its > 4) {
-            // Recompute Jacobian (for now)
-            if (saved_jacobian_lag == 0) {
-              SNESGetLagJacobian(snes, &saved_jacobian_lag);
-              SNESSetLagJacobian(snes, 1);
-            }
-          }
-
-        } else if (nl_its >= upper_its) {
-          // Reduce timestep slightly
-          timestep *= timestep_factor_on_upper_its;
-
-          // Recompute Jacobian
-          if (saved_jacobian_lag == 0) {
-            SNESGetLagJacobian(snes, &saved_jacobian_lag);
-            SNESSetLagJacobian(snes, 1);
-          }
-        }
       }
+
       snes_failures = 0;
     } while (looping);
 
@@ -1274,6 +1229,32 @@ int SNESSolver::run() {
   return 0;
 }
 
+BoutReal SNESSolver::updateGlobalTimestep(BoutReal timestep, int nl_its,
+                                          BoutReal recent_failure_rate, BoutReal max_dt) {
+  // Note: The preconditioner depends on the timestep,
+  // so if it is not recalculated the it will be less
+  // effective.
+
+  if (pid_controller) {
+    // Changing the timestep using a PID controller.
+    return pid(timestep, nl_its, max_dt);
+  }
+
+  // Consider changing the timestep.
+  if ((nl_its <= lower_its) && (timestep < max_timestep) && (recent_failure_rate < 0.5)) {
+    // Increase timestep slightly
+    timestep *= timestep_factor_on_lower_its;
+
+    return std::min(timestep, max_timestep);
+  }
+
+  if (nl_its >= upper_its) {
+    // Reduce timestep slightly
+    return timestep * timestep_factor_on_upper_its;
+  }
+  return timestep; // No change
+}
+
 PetscErrorCode SNESSolver::initPseudoTimestepping() {
   // Storage for per-variable timestep
   PetscCall(VecDuplicate(snes_x, &dt_vec));
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 0cf9eef4b0..5b8ed14f7c 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -144,6 +144,10 @@ private:
   BoutReal pseudo_max_ratio;        ///< Maximum timestep ratio between neighboring cells
   Vec dt_vec;                       ///< Each quantity can have its own timestep
 
+  /// Adjust the global timestep
+  BoutReal updateGlobalTimestep(BoutReal timestep, int nl_its,
+                                BoutReal recent_failure_rate, BoutReal max_dt);
+
   /// Initialize the Pseudo-Transient Continuation method
   PetscErrorCode initPseudoTimestepping();
   /// Update dt_vec based on new solution x

From 39b259594ebbe92c719716a79be6d4ff7a04f0ba Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Feb 2026 12:39:18 -0800
Subject: [PATCH 0498/1827] snes: Split residual and pseudo-timestep
 calculation

Now always calculates local and global residuals.
If pseudo timestepping is used then another loop over variables
is used to update per-cell timesteps and set `dt_vec`.

When `diagnose=true`, the local residual will be saved as
`snes_local_residual`, and the global residual will be printed
after each internal timestep.
---
 src/solver/impls/snes/snes.cxx | 168 +++++++++++++++++++++++----------
 src/solver/impls/snes/snes.hxx |  17 +++-
 2 files changed, 133 insertions(+), 52 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 32a9902543..4513cb5aeb 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -670,6 +670,10 @@ int SNESSolver::init() {
   if (equation_form == BoutSnesEquationForm::pseudo_transient) {
     PetscCall(initPseudoTimestepping());
   }
+  // Per-cell residuals
+  local_residual = 0.0;
+  local_residual_2d = 0.0;
+  global_residual = 0.0;
 
   // Nonlinear solver interface (SNES)
   output_info.write("Create SNES\n");
@@ -845,6 +849,15 @@ int SNESSolver::run() {
     PetscCall(VecRestoreArray(snes_x, &xdata));
   }
 
+  // Initialise residuals
+  local_residual = 0.0;
+  local_residual_2d = 0.0;
+  global_residual = 0.0;
+  PetscCall(updateResiduals(snes_x));
+  if (diagnose) {
+    output.write("\n    Residual: {}\n", global_residual);
+  }
+
   BoutReal target = simtime;
   for (int s = 0; s < getNumberOutputSteps(); s++) {
     target += getOutputTimestep();
@@ -1122,6 +1135,9 @@ int SNESSolver::run() {
 
       simtime += dt;
 
+      // Update local and global residuals
+      PetscCall(updateResiduals(snes_x));
+
       if (diagnose) {
         // Gather and print diagnostic information
 
@@ -1132,6 +1148,8 @@ int SNESSolver::run() {
           output.write(", SNES failures: {}", snes_failures);
         }
         output.write("\n");
+        // Print residual on separate line, so post-processing isn't affected
+        output.write("    Residual: {}\n", global_residual);
       }
 
       // MatFilter and MatEliminateZeros(Mat, bool) require PETSc >= 3.20
@@ -1146,7 +1164,7 @@ int SNESSolver::run() {
         pseudo_alpha = updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate, max_timestep * atol * 100);
 
         // Adjust local timesteps
-        PetscCall(updatePseudoTimestepping(snes_x));
+        PetscCall(updatePseudoTimestepping());
 
       } else {
         // Adjust timestep
@@ -1255,6 +1273,95 @@ BoutReal SNESSolver::updateGlobalTimestep(BoutReal timestep, int nl_its,
   return timestep; // No change
 }
 
+PetscErrorCode SNESSolver::updateResiduals(Vec x) {
+  // Push residuals to previous residuals
+  // Copying so that data is not shared
+  local_residual_prev = copy(local_residual);
+  local_residual_2d_prev = copy(local_residual_2d);
+  global_residual_prev = global_residual;
+
+  // Call RHS function to get time derivatives
+  PetscCall(rhs_function(x, snes_f, false));
+
+  // Reading the residual vectors
+  const BoutReal* current_residual = nullptr;
+  PetscCall(VecGetArrayRead(snes_f, &current_residual));
+
+  // Note: The ordering of quantities in the PETSc vectors
+  // depends on the Solver::loop_vars function
+  Mesh* mesh = bout::globals::mesh;
+  int idx = 0; // Index into PETSc Vecs
+
+  // Boundary cells
+  for (const auto& i2d : mesh->getRegion2D("RGN_BNDRY")) {
+    // Field2D quantities evolved together
+    BoutReal residual = 0.0;
+    int count = 0;
+
+    for (const auto& f : f2d) {
+      if (!f.evolve_bndry) {
+        continue; // Not evolving boundary => Skip
+      }
+      residual += SQ(current_residual[idx++]);
+      ++count;
+    }
+    if (count > 0) {
+      local_residual_2d[i2d] = sqrt(residual / count);
+    }
+
+    // Field3D quantities evolved together within a cell
+    for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
+      count = 0;
+      residual = 0.0;
+      for (const auto& f : f3d) {
+        if (!f.evolve_bndry) {
+          continue; // Not evolving boundary => Skip
+        }
+        residual += SQ(current_residual[idx++]);
+        ++count;
+      }
+      if (count > 0) {
+        auto i3d = mesh->ind2Dto3D(i2d, jz);
+        local_residual[i3d] = sqrt(residual / count);
+      }
+    }
+  }
+
+  // Bulk of domain.
+  // These loops don't check the boundary flags
+  for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) {
+    // Field2D quantities evolved together
+    if (!f2d.empty()) {
+      BoutReal residual = 0.0;
+      for (std::size_t i = 0; i != f2d.size(); ++i) {
+        residual += SQ(current_residual[idx++]);
+      }
+      local_residual_2d[i2d] = sqrt(residual / static_cast<BoutReal>(f2d.size()));
+    }
+
+    // Field3D quantities evolved together within a cell
+    if (!f3d.empty()) {
+      for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
+        auto i3d = mesh->ind2Dto3D(i2d, jz);
+
+        BoutReal residual = 0.0;
+        for (std::size_t i = 0; i != f3d.size(); ++i) {
+          residual += SQ(current_residual[idx++]);
+        }
+        local_residual[i3d] = sqrt(residual / static_cast<BoutReal>(f3d.size()));
+      }
+    }
+  }
+
+  // Restore Vec data arrays
+  PetscCall(VecRestoreArrayRead(snes_f, &current_residual));
+
+  // Global residual metric (RMS)
+  global_residual = std::sqrt(mean(SQ(local_residual), true));
+
+  return PETSC_SUCCESS;
+}
+
 PetscErrorCode SNESSolver::initPseudoTimestepping() {
   // Storage for per-variable timestep
   PetscCall(VecDuplicate(snes_x, &dt_vec));
@@ -1263,22 +1370,14 @@ PetscErrorCode SNESSolver::initPseudoTimestepping() {
 
   // Diagnostic outputs
   pseudo_timestep = timestep;
-  pseudo_residual = 0.0;
-  pseudo_residual_2d = 0.0;
 
   return PETSC_SUCCESS;
 }
 
-PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
-  // Call RHS function to get time derivatives
-  PetscCall(rhs_function(x, snes_f, false));
-
+PetscErrorCode SNESSolver::updatePseudoTimestepping() {
   // Use a per-cell timestep so that e.g density and pressure
   // evolve in a way consistent with the equation of state.
 
-  // Reading the residual vectors
-  const BoutReal* current_residual = nullptr;
-  PetscCall(VecGetArrayRead(snes_f, &current_residual));
   // Modifying the dt_vec values
   BoutReal* dt_data = nullptr;
   PetscCall(VecGetArray(dt_vec, &dt_data));
@@ -1292,47 +1391,34 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
   for (const auto& i2d : mesh->getRegion2D("RGN_BNDRY")) {
     // Field2D quantities evolved together
     int count = 0;
-    BoutReal residual = 0.0;
-
     for (const auto& f : f2d) {
       if (!f.evolve_bndry) {
         continue; // Not evolving boundary => Skip
       }
-      residual += SQ(current_residual[idx + count]);
       ++count;
     }
     if (count > 0) {
-      residual = sqrt(residual / count);
-
       // Adjust timestep for these quantities
-      BoutReal new_timestep =
-          updatePseudoTimestep(dt_data[idx], pseudo_residual_2d[i2d], residual);
+      BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], local_residual_2d_prev[i2d],
+                                                   local_residual_2d[i2d]);
       for (int i = 0; i != count; ++i) {
         dt_data[idx++] = new_timestep;
       }
-      pseudo_residual_2d[i2d] = residual;
     }
 
     // Field3D quantities evolved together within a cell
     for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
       count = 0;
-      residual = 0.0;
       for (const auto& f : f3d) {
         if (!f.evolve_bndry) {
           continue; // Not evolving boundary => Skip
         }
-        residual += SQ(current_residual[idx + count]);
         ++count;
       }
       if (count > 0) {
-        residual = sqrt(residual / count);
-
         auto i3d = mesh->ind2Dto3D(i2d, jz);
-        const BoutReal new_timestep =
-            updatePseudoTimestep(dt_data[idx], pseudo_residual[i3d], residual);
-
-        pseudo_residual[i3d] = residual;
-        pseudo_timestep[i3d] = new_timestep;
+        const BoutReal new_timestep = updatePseudoTimestep(
+            dt_data[idx], local_residual_prev[i3d], local_residual[i3d]);
 
         for (int i = 0; i != count; ++i) {
           dt_data[idx++] = new_timestep;
@@ -1346,19 +1432,12 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
   for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) {
     // Field2D quantities evolved together
     if (!f2d.empty()) {
-      BoutReal residual = 0.0;
-      for (std::size_t i = 0; i != f2d.size(); ++i) {
-        residual += SQ(current_residual[idx + i]);
-      }
-      residual = sqrt(residual / f2d.size());
-
       // Adjust timestep for these quantities
-      const BoutReal new_timestep =
-          updatePseudoTimestep(dt_data[idx], pseudo_residual_2d[i2d], residual);
+      const BoutReal new_timestep = updatePseudoTimestep(
+          dt_data[idx], local_residual_2d_prev[i2d], local_residual_2d[i2d]);
       for (std::size_t i = 0; i != f2d.size(); ++i) {
         dt_data[idx++] = new_timestep;
       }
-      pseudo_residual_2d[i2d] = residual;
     }
 
     // Field3D quantities evolved together within a cell
@@ -1366,15 +1445,8 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
       for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
         auto i3d = mesh->ind2Dto3D(i2d, jz);
 
-        BoutReal residual = 0.0;
-        for (std::size_t i = 0; i != f3d.size(); ++i) {
-          residual += SQ(current_residual[idx + i]);
-        }
-        residual = sqrt(residual / f3d.size());
-        BoutReal new_timestep =
-            updatePseudoTimestep(dt_data[idx], pseudo_residual[i3d], residual);
-
-        pseudo_residual[i3d] = residual;
+        BoutReal new_timestep = updatePseudoTimestep(
+            dt_data[idx], local_residual_prev[i3d], local_residual[i3d]);
 
         // Compare to neighbors
         BoutReal min_neighboring_dt = max_timestep;
@@ -1404,7 +1476,6 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping(Vec x) {
   }
 
   // Restore Vec data arrays
-  PetscCall(VecRestoreArrayRead(snes_f, &current_residual));
   PetscCall(VecRestoreArray(dt_vec, &dt_data));
 
   // Need timesteps on neighboring processors
@@ -1801,11 +1872,12 @@ void SNESSolver::outputVars(Options& output_options, bool save_repeat) {
     return; // Don't save diagnostics to restart files
   }
 
+  output_options["snes_local_residual"].assignRepeat(local_residual, "t", save_repeat,
+                                                     "SNESSolver");
+
   if (equation_form == BoutSnesEquationForm::pseudo_transient) {
     output_options["snes_pseudo_alpha"].assignRepeat(pseudo_alpha, "t", save_repeat,
                                                      "SNESSolver");
-    output_options["snes_pseudo_residual"].assignRepeat(pseudo_residual, "t", save_repeat,
-                                                        "SNESSolver");
     output_options["snes_pseudo_timestep"].assignRepeat(pseudo_timestep, "t", save_repeat,
                                                         "SNESSolver");
   }
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 5b8ed14f7c..b36212ade2 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -148,10 +148,20 @@ private:
   BoutReal updateGlobalTimestep(BoutReal timestep, int nl_its,
                                 BoutReal recent_failure_rate, BoutReal max_dt);
 
+  /// Calculate per-cell and global residuals
+  /// given an input system state `x`
+  PetscErrorCode updateResiduals(Vec x);
+  Field3D local_residual;         ///< Residual of Field3D quantities in each cell
+  Field2D local_residual_2d;      ///< Residual of Field2D quantities in each cell
+  BoutReal global_residual;       ///< Global residual measure
+  Field3D local_residual_prev;    ///< Previous Field3D local residuals
+  Field2D local_residual_2d_prev; ///< Previous Field2D local residuals
+  BoutReal global_residual_prev;  ///< Previous global residual
+
   /// Initialize the Pseudo-Transient Continuation method
   PetscErrorCode initPseudoTimestepping();
-  /// Update dt_vec based on new solution x
-  PetscErrorCode updatePseudoTimestepping(Vec x);
+  /// Update dt_vec based on residuals
+  PetscErrorCode updatePseudoTimestepping();
   /// Decide the next pseudo-timestep. Called by updatePseudoTimestepping
   BoutReal updatePseudoTimestep(BoutReal previous_timestep, BoutReal previous_residual,
                                 BoutReal current_residual);
@@ -160,8 +170,7 @@ private:
   BoutReal updatePseudoTimestep_history_based(BoutReal previous_timestep,
                                               BoutReal previous_residual,
                                               BoutReal current_residual);
-  Field3D pseudo_residual; ///< Diagnostic output
-  Field2D pseudo_residual_2d;
+
   Field3D pseudo_timestep;
 
   ///< PID controller parameters

From b2102d058a9a9cbe89c69abc05b30f4744c71715 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Feb 2026 15:04:12 -0800
Subject: [PATCH 0499/1827] snes: output_trigger option

Selects the trigger for writing an output.
The default is `fixed_time_interval` that outputs at regular time
intervals. Other choice is `residual_ratio` that outputs when the
global residual falls by a factor `output_residual_ratio`.
---
 src/solver/impls/snes/snes.cxx | 93 +++++++++++++++++++++-------------
 src/solver/impls/snes/snes.hxx | 27 ++++++++--
 2 files changed, 80 insertions(+), 40 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 4513cb5aeb..1766c94186 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -474,6 +474,14 @@ PetscErrorCode SNESSolver::FDJrestoreFromPruning() {
 
 SNESSolver::SNESSolver(Options* opts)
     : Solver(opts),
+      output_trigger(
+          (*options)["output_trigger"]
+              .doc("Decides when to save outputs. fixed_time_interval, residual_ratio")
+              .withDefault(BoutSnesOutput::fixed_time_interval)),
+      output_residual_ratio(
+          (*options)["output_residual_ratio"]
+              .doc("Trigger an output when residual falls by this ratio")
+              .withDefault(0.5)),
       timestep(
           (*options)["timestep"].doc("Initial backward Euler timestep").withDefault(1.0)),
       dt_min_reset((*options)["dt_min_reset"]
@@ -535,8 +543,13 @@ SNESSolver::SNESSolver(Options* opts)
       pseudo_max_ratio((*options)["pseudo_max_ratio"]
                            .doc("PTC maximum timestep ratio between neighbors")
                            .withDefault(2.)),
-      pid_controller(
-          (*options)["pid_controller"].doc("Use PID controller?").withDefault(false)),
+      timestep_control((*options)["timestep_control"]
+                           .doc("Timestep control method")
+                           .withDefault(BoutSnesTimestep::pid_nonlinear_its)),
+      timestep_factor((*options)["timestep_factor"]
+                          .doc("When timestep_control=residual_ratio, multiply timestep "
+                               "by this factor each step")
+                          .withDefault(1.1)),
       target_its((*options)["target_its"].doc("Target snes iterations").withDefault(7)),
       kP((*options)["kP"].doc("Proportional PID parameter").withDefault(0.7)),
       kI((*options)["kI"].doc("Integral PID parameter").withDefault(0.3)),
@@ -733,16 +746,10 @@ int SNESSolver::init() {
     // Note: If the 'Amat' Jacobian is matrix free, SNESComputeJacobian
     //       always updates its reference 'u' vector every nonlinear iteration
     SNESSetLagJacobian(snes, lag_jacobian);
-    if (pid_controller) {
-      nl_its_prev = target_its;
-      nl_its_prev2 = target_its;
-      SNESSetLagJacobianPersists(snes, PETSC_FALSE);
-      SNESSetLagPreconditionerPersists(snes, PETSC_FALSE);
-    } else {
-      // Set Jacobian and preconditioner to persist across time steps
-      SNESSetLagJacobianPersists(snes, PETSC_TRUE);
-      SNESSetLagPreconditionerPersists(snes, PETSC_TRUE);
-    }
+    nl_its_prev = target_its;
+    nl_its_prev2 = target_its;
+    SNESSetLagJacobianPersists(snes, PETSC_FALSE);
+    SNESSetLagPreconditionerPersists(snes, PETSC_FALSE);
     SNESSetLagPreconditioner(snes, 1); // Rebuild when Jacobian is rebuilt
   }
 
@@ -859,6 +866,7 @@ int SNESSolver::run() {
   }
 
   BoutReal target = simtime;
+  recent_failure_rate = 0.0;
   for (int s = 0; s < getNumberOutputSteps(); s++) {
     target += getOutputTimestep();
 
@@ -866,10 +874,14 @@ int SNESSolver::run() {
     int snes_failures = 0; // Count SNES convergence failures
     int saved_jacobian_lag = 0;
     int loop_count = 0;
-    recent_failure_rate = 0.0;
+
+    BoutReal start_global_residual = global_residual;
     do {
-      if (simtime >= target)
+      if ((output_trigger == BoutSnesOutput::fixed_time_interval && (simtime >= target))
+          || (output_trigger == BoutSnesOutput::residual_ratio
+              && (global_residual <= start_global_residual * output_residual_ratio)))
         break; // Could happen if step over multiple outputs
+
       if (scale_vars) {
         // Individual variable scaling
         // Note: If variables are rescaled then the Jacobian columns
@@ -930,8 +942,7 @@ int SNESSolver::run() {
         PetscCall(VecMin(dt_vec, nullptr, &timestep));
         dt = timestep;
 
-        looping = true;
-        if (simtime + timestep >= target) {
+        if (output_trigger == BoutSnesOutput::fixed_time_interval && simtime + timestep >= target) {
           looping = false;
         }
       } else {
@@ -954,8 +965,7 @@ int SNESSolver::run() {
 
         // Set the timestep
         dt = timestep;
-        looping = true;
-        if (simtime + dt >= target) {
+        if (output_trigger == BoutSnesOutput::fixed_time_interval && simtime + dt >= target) {
           // Note: When the timestep is changed the preconditioner needs to be updated
           // => Step over the output time and interpolate if not matrix free
 
@@ -975,9 +985,7 @@ int SNESSolver::run() {
           VecAXPBY(snes_x, -beta, (1. + beta), x1);
         }
 
-        if (pid_controller) {
-          SNESSetLagJacobian(snes, lag_jacobian);
-        }
+        SNESSetLagJacobian(snes, lag_jacobian);
       }
 
       // Run the solver
@@ -1182,7 +1190,8 @@ int SNESSolver::run() {
       snes_failures = 0;
     } while (looping);
 
-    if (!matrix_free) {
+    BoutReal output_time = simtime;
+    if (output_trigger == BoutSnesOutput::fixed_time_interval && !matrix_free) {
       ASSERT2(simtime >= target);
       ASSERT2(simtime - dt <= target);
       // Stepped over output timestep => Interpolate
@@ -1197,6 +1206,7 @@ int SNESSolver::run() {
 
       // output_x <- alpha * x0 + (1 - alpha) * output_x
       VecAXPBY(output_x, alpha, 1. - alpha, x0);
+      output_time = target;
 
     } else {
       // Timestep was adjusted to hit target output time
@@ -1231,7 +1241,7 @@ int SNESSolver::run() {
     PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
 
     try {
-      run_rhs(target); // Run RHS to calculate auxilliary variables
+      run_rhs(output_time); // Run RHS to calculate auxilliary variables
     } catch (BoutException& e) {
       output_error.write("ERROR: BoutException thrown: {}\n", e.what());
       // Abort simulation. There is no way to recover unless
@@ -1239,7 +1249,7 @@ int SNESSolver::run() {
       BoutComm::abort(1);
     }
 
-    if (call_monitors(target, s, getNumberOutputSteps()) != 0) {
+    if (call_monitors(output_time, s, getNumberOutputSteps()) != 0) {
       break; // User signalled to quit
     }
   }
@@ -1253,22 +1263,35 @@ BoutReal SNESSolver::updateGlobalTimestep(BoutReal timestep, int nl_its,
   // so if it is not recalculated the it will be less
   // effective.
 
-  if (pid_controller) {
+  switch (timestep_control) {
+  case BoutSnesTimestep::pid_nonlinear_its:
     // Changing the timestep using a PID controller.
     return pid(timestep, nl_its, max_dt);
-  }
 
-  // Consider changing the timestep.
-  if ((nl_its <= lower_its) && (timestep < max_timestep) && (recent_failure_rate < 0.5)) {
-    // Increase timestep slightly
-    timestep *= timestep_factor_on_lower_its;
+  case BoutSnesTimestep::threshold_nonlinear_its:
+    // Consider changing the timestep, based on thresholds in NL iterations
+    if ((nl_its <= lower_its) && (timestep < max_timestep) && (recent_failure_rate < 0.5)) {
+      // Increase timestep slightly
+      timestep *= timestep_factor_on_lower_its;
+      return std::min(timestep, max_timestep);
+    }
 
-    return std::min(timestep, max_timestep);
-  }
+    if (nl_its >= upper_its) {
+      // Reduce timestep slightly
+      return timestep * timestep_factor_on_upper_its;
+    }
+    return timestep; // No change
 
-  if (nl_its >= upper_its) {
-    // Reduce timestep slightly
-    return timestep * timestep_factor_on_upper_its;
+  case BoutSnesTimestep::residual_ratio:
+    // Use ratio of previous and current global residual
+    // Intended to be the same as https://petsc.org/release/manualpages/TS/TSPSEUDO/
+    // (Note the PETSc manual has the expression for dt_n upside down)
+
+    return std::min({timestep_factor * timestep * global_residual_prev / global_residual,
+                     max_timestep});
+
+  case BoutSnesTimestep::fixed:
+    break;
   }
   return timestep; // No change
 }
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index b36212ade2..768ba33520 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -4,7 +4,7 @@
  * using PETSc for the SNES interface
  *
  **************************************************************************
- * Copyright 2015-2025 BOUT++ contributors
+ * Copyright 2015-2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -59,6 +59,16 @@ BOUT_ENUM_CLASS(BoutPTCStrategy,
                 history_based,    ///< Grow/shrink dt based on residual decrease/increase
                 hybrid); ///< Combine inverse_residual and history_based strategies
 
+BOUT_ENUM_CLASS(BoutSnesTimestep,
+                pid_nonlinear_its,       ///< PID controller on nonlinear iterations
+                threshold_nonlinear_its, ///< Use thresholds on nonlinear iterations
+                residual_ratio,          ///< Use ratio of previous and current residual
+                fixed);                  ///< Fixed timestep (no adaptation)
+
+BOUT_ENUM_CLASS(BoutSnesOutput,
+                fixed_time_interval, ///< Output at fixed time intervals
+                residual_ratio);     ///< When the residual is reduced by a given ratio
+
 /// Uses PETSc's SNES interface to find a steady state solution to a
 /// nonlinear ODE by integrating in time with Backward Euler
 class SNESSolver : public Solver {
@@ -112,6 +122,10 @@ private:
   /// @param[in] linear  Specifies that the SNES solver is in a linear (KSP) inner loop
   PetscErrorCode rhs_function(Vec x, Vec f, bool linear);
 
+  BoutSnesOutput output_trigger; ///< Sets when outputs are written
+
+  BoutReal output_residual_ratio; ///< Trigger an output when residual falls by this ratio
+
   BoutReal timestep;     ///< Internal timestep
   BoutReal dt;           ///< Current timestep used in snes_function.
   BoutReal dt_min_reset; ///< If dt falls below this, reset solve
@@ -173,8 +187,11 @@ private:
 
   Field3D pseudo_timestep;
 
-  ///< PID controller parameters
-  bool pid_controller; ///< Use PID controller?
+  /// Timestep controller method
+  BoutSnesTimestep timestep_control;
+
+  /// When using BoutSnesTimestep::residual_ratio
+  BoutReal timestep_factor; ///< Multiply timestep by this each step
 
   /// Target number of nonlinear iterations for the PID controller.
   /// This can be non-integer to push timestep more aggressively
@@ -187,8 +204,8 @@ private:
   BoutReal recent_failure_rate;            ///< Rolling average of recent failure rate
   BoutReal last_failure_weight;            ///< 1 / number of recent solves
 
-  int nl_its_prev;
-  int nl_its_prev2;
+  BoutReal nl_its_prev;
+  BoutReal nl_its_prev2;
 
   BoutReal pid(BoutReal timestep, int nl_its, BoutReal max_dt); ///< Updates the timestep
 

From 4e134e9ab0080cf859802f31f893a7cb51ded0e2 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Feb 2026 15:33:23 -0800
Subject: [PATCH 0500/1827] snes: Update manual

Describe new settings `timestep_control` and `output_trigger` that
select different strategies to adjust global timesteps and
output simulation state.
---
 manual/sphinx/user_docs/time_integration.rst | 70 ++++++++++++++++----
 1 file changed, 57 insertions(+), 13 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 7658602bc8..70b9c3df92 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -444,29 +444,73 @@ on nonlinear iteration count.
    dt_min_reset = 1e-6                    # Reset the solver when timestep < this
 
    # Timestep adaptation
+   timestep_control = pid_nonlinear_its
+   target_its = 7        # Target number of nonlinear iterations
+   kP = 0.7              # Proportional gain
+   kI = 0.3              # Integral gain
+   kD = 0.2              # Derivative gain
+
+This uses a PID controller that adjusts the timestep to maintain approximately ``target_its``
+nonlinear iterations per solve.
+
+Residual Ratio
+^^^^^^^^^^^^^^
+
+This adjusts the timestep using the ratio of global residuals and a timestep factor:
+
+.. math::
+
+   dt_n = r dt_{n-1} \frac{||F(X_{n-1})||}{||F(X_{n})||
+
+so that as the residual falls the timestep :math:`dt` is increased.
+The :math:`r` parameter is input option ``timestep_factor`` that has
+default value 1.1.
+
+.. code-block:: ini
+
+   [solver]
+   timestep_control = residual_ratio  # Use global residual
+   timestep_factor = 1.1              # Constant timestep factor
+
+Threshold Controller
+^^^^^^^^^^^^^^^^^^^^
+
+An alternative adaptive strategy uses thresholds in nonlinear iterations
+to adjust the timestep:
+
+.. code-block:: ini
+
+   [solver]
+   timestep_control = threshold_nonlinear_its
    lower_its = 3                          # Increase dt if iterations < this
    upper_its = 10                         # Decrease dt if iterations > this
    timestep_factor_on_lower_its = 1.4     # Growth factor
    timestep_factor_on_upper_its = 0.9     # Reduction factor
    timestep_factor_on_failure = 0.5       # Reduction on convergence failure
 
-PID Controller
-^^^^^^^^^^^^^^
+The adjustments are less smooth than the default PID method, but the
+timestep is changed less frequently. This may enable the Jacobian and
+preconditioner to be used for more iterations.
 
-An alternative adaptive strategy using a PID controller:
+Output trigger
+~~~~~~~~~~~~~~
+
+The default behavior is to save outputs at a regular time interval, as
+BOUT++ solvers do. This is desirable when performing time-dependent
+simulations, but for simulations that are trying to get to steady
+state a better measure of progress is reduction of the global residual
+(norm of the time-derivatives of the system).
 
 .. code-block:: ini
 
    [solver]
-   pid_controller = true
-   target_its = 7        # Target number of nonlinear iterations
-   kP = 0.7              # Proportional gain
-   kI = 0.3              # Integral gain
-   kD = 0.2              # Derivative gain
+   output_trigger = residual_ratio  # Trigger an output based on the ratio of residuals
+   output_residual_ratio = 0.5     # Output when global residual is multiplied by this
 
-The PID controller adjusts the timestep to maintain approximately ``target_its``
-nonlinear iterations per solve, providing smoother adaptation than threshold-based
-methods.
+With this choice, each output has a global residual that is less than
+or equal to `output_residual_ratio` times the last output global
+residual. This provides a way of measuring progress to steady state
+that is independent of time integration accuracy.
 
 Pseudo-Transient Continuation and Switched Evolution Relaxation
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -518,7 +562,7 @@ state.
    timestep = 1.0                # Initial timestep
 
    # SER parameters
-   pid_controller = true          # Scale timesteps based on iterations
+   timestep_control = pid_controller  # Scale timesteps based on iterations
    pseudo_max_ratio = 2.0         # Limit neighbor timestep ratio
 
    # Tolerances
@@ -588,7 +632,7 @@ adjust ``pseudo_alpha`` depending on the nonlinearity of the system:
 .. code-block:: ini
 
    [solver]
-   pid_controller = true
+   timestep_control = pid_controller   # Scale global timestep using PID controller
    target_its = 7        # Target number of nonlinear iterations
    kP = 0.7              # Proportional gain
    kI = 0.3              # Integral gain

From e5bb430240546531d2180e6bbad01543bd0809da Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Feb 2026 15:39:06 -0800
Subject: [PATCH 0501/1827] snes: Add snes_global_residual scalar to dmp files

Save the global residual diagnostic
---
 src/solver/impls/snes/snes.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 1766c94186..75798bfca5 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -1897,6 +1897,8 @@ void SNESSolver::outputVars(Options& output_options, bool save_repeat) {
 
   output_options["snes_local_residual"].assignRepeat(local_residual, "t", save_repeat,
                                                      "SNESSolver");
+  output_options["snes_global_residual"].assignRepeat(global_residual, "t", save_repeat,
+                                                      "SNESSolver");
 
   if (equation_form == BoutSnesEquationForm::pseudo_transient) {
     output_options["snes_pseudo_alpha"].assignRepeat(pseudo_alpha, "t", save_repeat,

From b9b038b0243d3a54e8f89448fb0eb6664f7821d9 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Feb 2026 16:11:01 -0800
Subject: [PATCH 0502/1827] snes: Fix manual

Uses setting `pid_controller` rather than `pid_nonlinear_its`.
---
 manual/sphinx/user_docs/time_integration.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 70b9c3df92..37bf9a6abf 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -562,7 +562,7 @@ state.
    timestep = 1.0                # Initial timestep
 
    # SER parameters
-   timestep_control = pid_controller  # Scale timesteps based on iterations
+   timestep_control = pid_nonlinear_its  # Scale timesteps based on iterations
    pseudo_max_ratio = 2.0         # Limit neighbor timestep ratio
 
    # Tolerances
@@ -632,7 +632,7 @@ adjust ``pseudo_alpha`` depending on the nonlinearity of the system:
 .. code-block:: ini
 
    [solver]
-   timestep_control = pid_controller   # Scale global timestep using PID controller
+   timestep_control = pid_nonlinear_its   # Scale global timestep using PID controller
    target_its = 7        # Target number of nonlinear iterations
    kP = 0.7              # Proportional gain
    kI = 0.3              # Integral gain

From 2c2402ed59c91164eaff46dee0f79386b7347e9e Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Thu, 12 Feb 2026 00:14:36 +0000
Subject: [PATCH 0503/1827] [bot] Apply format changes

---
 src/solver/impls/snes/snes.cxx | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 75798bfca5..420adaf046 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -942,7 +942,8 @@ int SNESSolver::run() {
         PetscCall(VecMin(dt_vec, nullptr, &timestep));
         dt = timestep;
 
-        if (output_trigger == BoutSnesOutput::fixed_time_interval && simtime + timestep >= target) {
+        if (output_trigger == BoutSnesOutput::fixed_time_interval
+            && simtime + timestep >= target) {
           looping = false;
         }
       } else {
@@ -965,7 +966,8 @@ int SNESSolver::run() {
 
         // Set the timestep
         dt = timestep;
-        if (output_trigger == BoutSnesOutput::fixed_time_interval && simtime + dt >= target) {
+        if (output_trigger == BoutSnesOutput::fixed_time_interval
+            && simtime + dt >= target) {
           // Note: When the timestep is changed the preconditioner needs to be updated
           // => Step over the output time and interpolate if not matrix free
 
@@ -1169,14 +1171,16 @@ int SNESSolver::run() {
 
       if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Adjust pseudo_alpha to globally scale timesteps
-        pseudo_alpha = updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate, max_timestep * atol * 100);
+        pseudo_alpha = updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate,
+                                            max_timestep * atol * 100);
 
         // Adjust local timesteps
         PetscCall(updatePseudoTimestepping());
 
       } else {
         // Adjust timestep
-        timestep = updateGlobalTimestep(timestep, nl_its, recent_failure_rate, max_timestep);
+        timestep =
+            updateGlobalTimestep(timestep, nl_its, recent_failure_rate, max_timestep);
       }
 
       if (static_cast<BoutReal>(lin_its) / nl_its > 0.5 * maxl) {
@@ -1270,7 +1274,8 @@ BoutReal SNESSolver::updateGlobalTimestep(BoutReal timestep, int nl_its,
 
   case BoutSnesTimestep::threshold_nonlinear_its:
     // Consider changing the timestep, based on thresholds in NL iterations
-    if ((nl_its <= lower_its) && (timestep < max_timestep) && (recent_failure_rate < 0.5)) {
+    if ((nl_its <= lower_its) && (timestep < max_timestep)
+        && (recent_failure_rate < 0.5)) {
       // Increase timestep slightly
       timestep *= timestep_factor_on_lower_its;
       return std::min(timestep, max_timestep);
@@ -1422,8 +1427,8 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping() {
     }
     if (count > 0) {
       // Adjust timestep for these quantities
-      BoutReal new_timestep = updatePseudoTimestep(dt_data[idx], local_residual_2d_prev[i2d],
-                                                   local_residual_2d[i2d]);
+      BoutReal new_timestep = updatePseudoTimestep(
+          dt_data[idx], local_residual_2d_prev[i2d], local_residual_2d[i2d]);
       for (int i = 0; i != count; ++i) {
         dt_data[idx++] = new_timestep;
       }

From d5ad38cb0506762b72ae513ea26341afcc51a61b Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Thu, 12 Feb 2026 00:14:37 +0000
Subject: [PATCH 0504/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index a8bd688f08..3c401e4195 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -4,3 +4,4 @@ ed2117e6d6826a98b6988e2f18c0c34e408563b6
 # Added by the bot
 4b010b7634aee1045743be80c268d4644522cd29
 a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
+2c2402ed59c91164eaff46dee0f79386b7347e9e

From 74ce9aad802cf355ce7fdabab55e7c90cd0f5c9b Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 12 Feb 2026 10:59:13 -0800
Subject: [PATCH 0505/1827] snes: jacobian_persists option

False by default. If true, re-uses the Jacobian and preconditioner
across SNES calls.
---
 src/solver/impls/snes/snes.cxx | 31 ++++++++++++++++++++-----------
 src/solver/impls/snes/snes.hxx |  1 +
 2 files changed, 21 insertions(+), 11 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 420adaf046..a05a19b02c 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -256,8 +256,10 @@ PetscErrorCode SNESSolver::FDJinitialise() {
 
       for (int i = 0; i < nlocal; ++i) {
         // Assume all elements in the z direction are potentially coupled
-        d_nnz.emplace_back(d_nnz_map3d[i].size() * mesh->LocalNz + d_nnz_map2d[i].size());
-        o_nnz.emplace_back(o_nnz_map3d[i].size() * mesh->LocalNz + o_nnz_map2d[i].size());
+        d_nnz.emplace_back((d_nnz_map3d[i].size() * mesh->LocalNz)
+                           + d_nnz_map2d[i].size());
+        o_nnz.emplace_back((o_nnz_map3d[i].size() * mesh->LocalNz)
+                           + o_nnz_map2d[i].size());
       }
     }
 
@@ -369,7 +371,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
       // Values are 0 or 1 so tolerance (1e-5) shouldn't matter
       PetscBool symmetric;
       PetscCall(MatIsSymmetric(Jfd, 1e-5, &symmetric));
-      if (!symmetric) {
+      if (!static_cast<bool>(symmetric)) {
         output_warn.write("Jacobian pattern is not symmetric\n");
       }
     }
@@ -597,6 +599,10 @@ SNESSolver::SNESSolver(Options* opts)
       lag_jacobian((*options)["lag_jacobian"]
                        .doc("Re-use the Jacobian this number of SNES iterations")
                        .withDefault(50)),
+      jacobian_persists(
+          (*options)["jacobian_persists"]
+              .doc("Re-use Jacobian and preconditioner across nonlinear solves")
+              .withDefault<bool>(false)),
       use_coloring((*options)["use_coloring"]
                        .doc("Use matrix coloring to calculate Jacobian?")
                        .withDefault<bool>(true)),
@@ -630,7 +636,7 @@ int SNESSolver::init() {
   // Get total problem size
   int ntmp;
   if (bout::globals::mpi->MPI_Allreduce(&nlocal, &ntmp, 1, MPI_INT, MPI_SUM,
-                                        BoutComm::get())) {
+                                        BoutComm::get()) != 0) {
     throw BoutException("MPI_Allreduce failed!");
   }
   neq = ntmp;
@@ -748,9 +754,11 @@ int SNESSolver::init() {
     SNESSetLagJacobian(snes, lag_jacobian);
     nl_its_prev = target_its;
     nl_its_prev2 = target_its;
-    SNESSetLagJacobianPersists(snes, PETSC_FALSE);
-    SNESSetLagPreconditionerPersists(snes, PETSC_FALSE);
-    SNESSetLagPreconditioner(snes, 1); // Rebuild when Jacobian is rebuilt
+    PetscCall(
+        SNESSetLagJacobianPersists(snes, static_cast<PetscBool>(jacobian_persists)));
+    PetscCall(SNESSetLagPreconditionerPersists(
+        snes, static_cast<PetscBool>(jacobian_persists)));
+    PetscCall(SNESSetLagPreconditioner(snes, 1)); // Rebuild when Jacobian is rebuilt
   }
 
   // Set tolerances
@@ -826,10 +834,10 @@ int SNESSolver::init() {
     SNESType snestype;
     SNESGetType(snes, &snestype);
     output_info.write("SNES Type : {}\n", snestype);
-    if (ksptype) {
+    if (ksptype != nullptr) {
       output_info.write("KSP Type  : {}\n", ksptype);
     }
-    if (pctype) {
+    if (pctype != nullptr) {
       output_info.write("PC Type   : {}\n", pctype);
     }
   }
@@ -879,8 +887,9 @@ int SNESSolver::run() {
     do {
       if ((output_trigger == BoutSnesOutput::fixed_time_interval && (simtime >= target))
           || (output_trigger == BoutSnesOutput::residual_ratio
-              && (global_residual <= start_global_residual * output_residual_ratio)))
+              && (global_residual <= start_global_residual * output_residual_ratio))) {
         break; // Could happen if step over multiple outputs
+      }
 
       if (scale_vars) {
         // Individual variable scaling
@@ -1033,7 +1042,7 @@ int SNESSolver::run() {
         }
 
         if (snes_failures == max_snes_failures) {
-          output.write("Too many SNES failures ({}). Aborting.");
+          output.write("Too many SNES failures ({}). Aborting.", snes_failures);
           return 1;
         }
 
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 768ba33520..ca0ca50d36 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -243,6 +243,7 @@ private:
   bool matrix_free;          ///< Use matrix free Jacobian
   bool matrix_free_operator; ///< Use matrix free Jacobian in the operator?
   int lag_jacobian;          ///< Re-use Jacobian
+  bool jacobian_persists;    ///< Re-use Jacobian and preconditioner across nonlinear solves
   bool use_coloring;         ///< Use matrix coloring
 
   bool jacobian_recalculated; ///< Flag set when Jacobian is recalculated

From 05b7c571544c3bcb153fce67d12b9ac48947fc2d Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Thu, 12 Feb 2026 19:02:18 +0000
Subject: [PATCH 0506/1827] [bot] Apply format changes

---
 src/solver/impls/snes/snes.cxx | 3 ++-
 src/solver/impls/snes/snes.hxx | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index a05a19b02c..2e4744eb44 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -636,7 +636,8 @@ int SNESSolver::init() {
   // Get total problem size
   int ntmp;
   if (bout::globals::mpi->MPI_Allreduce(&nlocal, &ntmp, 1, MPI_INT, MPI_SUM,
-                                        BoutComm::get()) != 0) {
+                                        BoutComm::get())
+      != 0) {
     throw BoutException("MPI_Allreduce failed!");
   }
   neq = ntmp;
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index ca0ca50d36..40412f83b7 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -243,7 +243,7 @@ private:
   bool matrix_free;          ///< Use matrix free Jacobian
   bool matrix_free_operator; ///< Use matrix free Jacobian in the operator?
   int lag_jacobian;          ///< Re-use Jacobian
-  bool jacobian_persists;    ///< Re-use Jacobian and preconditioner across nonlinear solves
+  bool jacobian_persists; ///< Re-use Jacobian and preconditioner across nonlinear solves
   bool use_coloring;         ///< Use matrix coloring
 
   bool jacobian_recalculated; ///< Flag set when Jacobian is recalculated

From 2d51378948980d1bdce739d9dd7112a77f1c137f Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Thu, 12 Feb 2026 19:02:20 +0000
Subject: [PATCH 0507/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 3c401e4195..93c768a148 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -5,3 +5,4 @@ ed2117e6d6826a98b6988e2f18c0c34e408563b6
 4b010b7634aee1045743be80c268d4644522cd29
 a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
 2c2402ed59c91164eaff46dee0f79386b7347e9e
+05b7c571544c3bcb153fce67d12b9ac48947fc2d

From 6f19419c56a3fee47b9cb90855eaaac7fcc0b0fa Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Feb 2026 14:05:18 +0100
Subject: [PATCH 0508/1827] Cleanup included headers

---
 include/bout/options_io.hxx      | 1 +
 src/solver/impls/euler/euler.cxx | 2 +-
 src/solver/impls/pvode/pvode.cxx | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index 4fab70aea8..81addc1521 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -45,6 +45,7 @@
 #include "bout/build_defines.hxx"
 #include "bout/generic_factory.hxx"
 #include "bout/options.hxx"
+#include "bout/mesh.hxx"
 
 #include <memory>
 #include <string>
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index ed8621a874..19dc9d7015 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -5,7 +5,7 @@
 #include <bout/field.hxx>
 #include <bout/openmpwrap.hxx>
 #include <bout/output.hxx>
-#include <bout/version.hxx>
+#include <bout/options_io.hxx>
 
 #include <cstdlib>
 #include <fmt/format.h>
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 95adecaec1..115ffb2056 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -37,9 +37,9 @@
 #include <bout/msg_stack.hxx>
 #include <bout/options.hxx>
 #include <bout/output.hxx>
+#include <bout/options_io.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/unused.hxx>
-#include <bout/version.hxx>
 
 #include <pvode/cvode.h>
 #include <pvode/cvspgmr.h>  // use CVSPGMR linear solver each internal step

From b04a24232eeeeee29ff5e5951f2b9011f863c3d7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Feb 2026 14:05:32 +0100
Subject: [PATCH 0509/1827] Switch to [[maybe_unused]]

---
 src/solver/impls/pvode/pvode.cxx | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 115ffb2056..aadb4a87c6 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -39,7 +39,6 @@
 #include <bout/output.hxx>
 #include <bout/options_io.hxx>
 #include <bout/sys/timer.hxx>
-#include <bout/unused.hxx>
 
 #include <pvode/cvode.h>
 #include <pvode/cvspgmr.h>  // use CVSPGMR linear solver each internal step
@@ -411,7 +410,7 @@ BoutReal PvodeSolver::run(BoutReal tout) {
  * RHS function
  **************************************************************************/
 
-void PvodeSolver::rhs(int UNUSED(N), BoutReal t, BoutReal* udata, BoutReal* dudata) {
+void PvodeSolver::rhs([[maybe_unused]] int N, BoutReal t, BoutReal* udata, BoutReal* dudata) {
   TRACE("Running RHS: PvodeSolver::rhs({})", t);
 
   // Get current timestep
@@ -427,7 +426,7 @@ void PvodeSolver::rhs(int UNUSED(N), BoutReal t, BoutReal* udata, BoutReal* duda
   save_derivs(dudata);
 }
 
-void PvodeSolver::gloc(int UNUSED(N), BoutReal t, BoutReal* udata, BoutReal* dudata) {
+void PvodeSolver::gloc([[maybe_unused]] int N, BoutReal t, BoutReal* udata, BoutReal* dudata) {
   TRACE("Running RHS: PvodeSolver::gloc({})", t);
 
   Timer timer("rhs");
@@ -468,8 +467,8 @@ void solver_gloc(integer N, BoutReal t, BoutReal* u, BoutReal* udot, void* f_dat
 }
 
 // Preconditioner communication function
-void solver_cfn(integer UNUSED(N), BoutReal UNUSED(t), N_Vector UNUSED(u),
-                void* UNUSED(f_data)) {
+void solver_cfn([[maybe_unused]] integer N, [[maybe_unused]] BoutReal t, [[maybe_unused]] N_Vector u,
+                [[maybe_unused]] void* f_data) {
   // doesn't do anything at the moment
 }
 

From 83cf77923a4c72e44303354923021acf932b4fd2 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Fri, 13 Feb 2026 13:07:08 +0000
Subject: [PATCH 0510/1827] [bot] Apply format changes

---
 include/bout/options_io.hxx      |  2 +-
 src/solver/impls/euler/euler.cxx |  2 +-
 src/solver/impls/pvode/pvode.cxx | 12 +++++++-----
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index 81addc1521..00dd0c4cf3 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -44,8 +44,8 @@
 
 #include "bout/build_defines.hxx"
 #include "bout/generic_factory.hxx"
-#include "bout/options.hxx"
 #include "bout/mesh.hxx"
+#include "bout/options.hxx"
 
 #include <memory>
 #include <string>
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 19dc9d7015..9754a68826 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -4,8 +4,8 @@
 #include <bout/boutexception.hxx>
 #include <bout/field.hxx>
 #include <bout/openmpwrap.hxx>
-#include <bout/output.hxx>
 #include <bout/options_io.hxx>
+#include <bout/output.hxx>
 
 #include <cstdlib>
 #include <fmt/format.h>
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index aadb4a87c6..8ccd5f134a 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -36,8 +36,8 @@
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/options.hxx>
-#include <bout/output.hxx>
 #include <bout/options_io.hxx>
+#include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
 
 #include <pvode/cvode.h>
@@ -410,7 +410,8 @@ BoutReal PvodeSolver::run(BoutReal tout) {
  * RHS function
  **************************************************************************/
 
-void PvodeSolver::rhs([[maybe_unused]] int N, BoutReal t, BoutReal* udata, BoutReal* dudata) {
+void PvodeSolver::rhs([[maybe_unused]] int N, BoutReal t, BoutReal* udata,
+                      BoutReal* dudata) {
   TRACE("Running RHS: PvodeSolver::rhs({})", t);
 
   // Get current timestep
@@ -426,7 +427,8 @@ void PvodeSolver::rhs([[maybe_unused]] int N, BoutReal t, BoutReal* udata, BoutR
   save_derivs(dudata);
 }
 
-void PvodeSolver::gloc([[maybe_unused]] int N, BoutReal t, BoutReal* udata, BoutReal* dudata) {
+void PvodeSolver::gloc([[maybe_unused]] int N, BoutReal t, BoutReal* udata,
+                       BoutReal* dudata) {
   TRACE("Running RHS: PvodeSolver::gloc({})", t);
 
   Timer timer("rhs");
@@ -467,8 +469,8 @@ void solver_gloc(integer N, BoutReal t, BoutReal* u, BoutReal* udot, void* f_dat
 }
 
 // Preconditioner communication function
-void solver_cfn([[maybe_unused]] integer N, [[maybe_unused]] BoutReal t, [[maybe_unused]] N_Vector u,
-                [[maybe_unused]] void* f_data) {
+void solver_cfn([[maybe_unused]] integer N, [[maybe_unused]] BoutReal t,
+                [[maybe_unused]] N_Vector u, [[maybe_unused]] void* f_data) {
   // doesn't do anything at the moment
 }
 

From bc86a19972d60c640c60268e880de9883870dd2d Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Fri, 13 Feb 2026 13:07:10 +0000
Subject: [PATCH 0511/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 31b33eb76b..99f926614e 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -5,3 +5,4 @@ ed2117e6d6826a98b6988e2f18c0c34e408563b6
 4b010b7634aee1045743be80c268d4644522cd29
 52301380586fdbf890f620c04f689b08d89a6c34
 a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
+83cf77923a4c72e44303354923021acf932b4fd2

From 603e7d669272e71eb27c5b7b23398e5fa173e6a5 Mon Sep 17 00:00:00 2001
From: Owen Parry <owen.parry@ukaea.uk>
Date: Wed, 18 Feb 2026 10:53:30 +0000
Subject: [PATCH 0512/1827] Fix CI CMake formatting.

---
 .github/workflows/auto-formatting.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/auto-formatting.yml b/.github/workflows/auto-formatting.yml
index b3512f02cf..f54b012298 100644
--- a/.github/workflows/auto-formatting.yml
+++ b/.github/workflows/auto-formatting.yml
@@ -43,7 +43,7 @@ jobs:
         run: |
           pwd
           ls
-          $HOME/.local/bin/cmake-format $(find -name CMakeLists.txt) cmake/*.cmake
+          $HOME/.local/bin/cmake-format -i $(find -name CMakeLists.txt) cmake/*.cmake
 
       - name: Commit formatting
         uses: stefanzweifel/git-auto-commit-action@v7

From 0ba969553ac13c20370546cf52d1f30a972954b7 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 17 Feb 2026 15:28:08 +0000
Subject: [PATCH 0513/1827] tests: Set missing `mesh` members in `FakeMesh`

---
 tests/unit/fake_mesh.hxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 7d7326c149..4656ee0282 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -43,6 +43,9 @@ public:
     GlobalNx = nx;
     GlobalNy = ny;
     GlobalNz = nz;
+    GlobalNxNoBoundaries = nx - 2;
+    GlobalNyNoBoundaries = ny - 2;
+    GlobalNzNoBoundaries = nz;
     LocalNx = nx;
     LocalNy = ny;
     LocalNz = nz;

From 598b1d9c4cf311d40755ba166708cfe550f049b6 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 18 Feb 2026 09:31:58 +0000
Subject: [PATCH 0514/1827] Fix missing headers

---
 src/mesh/interpolation/interpolation_z.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mesh/interpolation/interpolation_z.cxx b/src/mesh/interpolation/interpolation_z.cxx
index 8d39e6baa8..e743ec8555 100644
--- a/src/mesh/interpolation/interpolation_z.cxx
+++ b/src/mesh/interpolation/interpolation_z.cxx
@@ -20,8 +20,10 @@
  *
  **************************************************************************/
 
+#include <bout/globals.hxx>
 #include <bout/interpolation_z.hxx>
 #include <bout/mesh.hxx>
+#include <bout/region.hxx>
 
 ZInterpolation::ZInterpolation(int y_offset, Mesh* mesh, Region<Ind3D> region_in)
     : localmesh(mesh == nullptr ? bout::globals::mesh : mesh), region(region_in),

From c66dbb6a8f11cfd250824980478b4b19f334bbab Mon Sep 17 00:00:00 2001
From: Owen Parry <owen.parry@ukaea.uk>
Date: Fri, 20 Feb 2026 11:44:27 +0000
Subject: [PATCH 0515/1827] Add cmake-format config. Dangle parentheses and
 format bout_add_example, bout_add_integrated_test, bout_add_mms_test,
 bout_handle_requires_conflicts more nicely.

---
 cmake-format.yaml | 48 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 cmake-format.yaml

diff --git a/cmake-format.yaml b/cmake-format.yaml
new file mode 100644
index 0000000000..082e7b5ef1
--- /dev/null
+++ b/cmake-format.yaml
@@ -0,0 +1,48 @@
+parse:
+  additional_commands:
+    bout_add_example:
+      pargs: 1
+      kwargs:
+        CONFLICTS: '*'
+        DATA_DIRS: '*'
+        EXTRA_FILES: '*'
+        REQUIRES: '*'
+        SOURCES: '*'
+    bout_add_integrated_test:
+      pargs: 1
+      flags: [USE_DATA_BOUT_INP, USE_RUNTEST]
+      kwargs:
+        CONFLICTS: '*'
+        DOWNLOAD: 1
+        DOWNLOAD_NAME: 1
+        EXECUTABLE_NAME: 1
+        EXTRA_DEPENDS: '*'
+        EXTRA_FILES: '*'
+        PROCESSORS: 1
+        REQUIRES: '*'
+        SOURCES: '*'
+        TESTARGS: '*'
+    bout_add_mms_test:
+      pargs: 1
+      flags: [USE_DATA_BOUT_INP, USE_RUNTEST]
+      kwargs:
+        CONFLICTS: '*'
+        DOWNLOAD: 1
+        DOWNLOAD_NAME: 1
+        EXECUTABLE_NAME: 1
+        EXTRA_DEPENDS: '*'
+        EXTRA_FILES: '*'
+        PROCESSORS: 1
+        REQUIRES: '*'
+        SOURCES: '*'
+        TESTARGS: '*'
+    bout_handle_requires_conflicts:
+      pargs: 2
+      kwargs:
+        CONFLICTS: '*'
+        REQUIRES: '*'
+format:
+  dangle_parens: true
+markup:
+  # markup messes up comments - disable it
+  enable_markup: false
\ No newline at end of file

From 17ac13c28aa3b34a0e46dbe87bb3874f6b25e706 Mon Sep 17 00:00:00 2001
From: Owen Parry <owen.parry@ukaea.uk>
Date: Fri, 20 Feb 2026 12:02:38 +0000
Subject: [PATCH 0516/1827] Apply CMake formatting.

---
 CMakeLists.txt                                | 1055 +++++++++--------
 cmake/BOUT++functions.cmake                   |  167 ++-
 cmake/BuildType.cmake                         |   17 +-
 cmake/CorrectWindowsPaths.cmake               |   14 +-
 cmake/EnableCXXWarningIfSupport.cmake         |   22 +-
 cmake/FindBash.cmake                          |   21 +-
 cmake/FindClangFormat.cmake                   |   24 +-
 cmake/FindCython.cmake                        |   12 +-
 cmake/FindFFTW.cmake                          |   72 +-
 cmake/FindHYPRE.cmake                         |   58 +-
 cmake/FindLibuuid.cmake                       |   31 +-
 cmake/FindNumpy.cmake                         |   45 +-
 cmake/FindPETSc.cmake                         |  699 +++++++----
 cmake/FindPackageMultipass.cmake              |  163 +--
 cmake/FindSLEPc.cmake                         |  156 ++-
 cmake/FindSUNDIALS.cmake                      |  131 +-
 cmake/FindScoreP.cmake                        |  100 +-
 cmake/FindSphinx.cmake                        |   14 +-
 cmake/FindnetCDF.cmake                        |  130 +-
 cmake/FindnetCDFCxx.cmake                     |  109 +-
 cmake/GenerateDateTimeFile.cmake              |    7 +-
 cmake/GetGitRevisionDescription.cmake         |  235 ++--
 cmake/ResolveCompilerPaths.cmake              |  121 +-
 cmake/Sanitizers.cmake                        |   96 +-
 cmake/SetupBOUTThirdParty.cmake               |  325 +++--
 cmake/SetupCompilers.cmake                    |   64 +-
 examples/6field-simple/CMakeLists.txt         |    8 +-
 .../IMEX/advection-diffusion/CMakeLists.txt   |    2 +-
 .../IMEX/advection-reaction/CMakeLists.txt    |    8 +-
 examples/IMEX/diffusion-nl/CMakeLists.txt     |    2 +-
 .../IMEX/drift-wave-constraint/CMakeLists.txt |    2 +-
 examples/IMEX/drift-wave/CMakeLists.txt       |    2 +-
 examples/blob2d-laplacexz/CMakeLists.txt      |    2 +-
 examples/blob2d-outerloop/CMakeLists.txt      |    2 +-
 examples/blob2d/CMakeLists.txt                |    8 +-
 .../advection/CMakeLists.txt                  |   11 +-
 examples/boutpp/CMakeLists.txt                |    2 +-
 examples/conducting-wall-mode/CMakeLists.txt  |    8 +-
 examples/conduction-snb/CMakeLists.txt        |   17 +-
 examples/conduction/CMakeLists.txt            |    8 +-
 .../constraints/alfven-wave/CMakeLists.txt    |    9 +-
 .../constraints/laplace-dae/CMakeLists.txt    |    8 +-
 examples/dalf3/CMakeLists.txt                 |    9 +-
 examples/eigen-box/CMakeLists.txt             |    8 +-
 examples/elm-pb-outerloop/CMakeLists.txt      |    8 +-
 examples/elm-pb/CMakeLists.txt                |   13 +-
 examples/fci-wave/CMakeLists.txt              |    8 +-
 .../finite-volume/diffusion/CMakeLists.txt    |    8 +-
 examples/finite-volume/fluid/CMakeLists.txt   |    8 +-
 examples/finite-volume/test/CMakeLists.txt    |    2 +-
 examples/gas-compress/CMakeLists.txt          |    8 +-
 examples/gyro-gem/CMakeLists.txt              |    8 +-
 examples/hasegawa-wakatani-3d/CMakeLists.txt  |    2 +-
 examples/hasegawa-wakatani/CMakeLists.txt     |    3 +-
 examples/invertable_operator/CMakeLists.txt   |    8 +-
 examples/laplacexy/alfven-wave/CMakeLists.txt |    8 +-
 .../laplacexy/laplace_perp/CMakeLists.txt     |   10 +-
 examples/laplacexy/simple/CMakeLists.txt      |    5 +-
 examples/monitor-newapi/CMakeLists.txt        |    2 +-
 examples/orszag-tang/CMakeLists.txt           |    8 +-
 examples/preconditioning/wave/CMakeLists.txt  |    2 +-
 examples/staggered_grid/CMakeLists.txt        |    8 +-
 examples/subsampling/CMakeLists.txt           |    9 +-
 examples/wave-slab/CMakeLists.txt             |    8 +-
 externalpackages/PVODE/CMakeLists.txt         |   73 +-
 manual/CMakeLists.txt                         |   25 +-
 tests/MMS/CMakeLists.txt                      |    2 +-
 tests/MMS/advection/arakawa/CMakeLists.txt    |    6 +-
 tests/MMS/advection/central/CMakeLists.txt    |    6 +-
 tests/MMS/advection/upwind/CMakeLists.txt     |    6 +-
 tests/MMS/advection/weno3/CMakeLists.txt      |    6 +-
 tests/MMS/bracket/CMakeLists.txt              |    6 +-
 tests/MMS/derivatives3/CMakeLists.txt         |    6 +-
 tests/MMS/diffusion/CMakeLists.txt            |    8 +-
 tests/MMS/diffusion2/CMakeLists.txt           |   10 +-
 tests/MMS/hw/CMakeLists.txt                   |    6 +-
 tests/MMS/laplace/CMakeLists.txt              |    8 +-
 tests/MMS/shiftedmetricinterp/CMakeLists.txt  |    6 +-
 tests/MMS/spatial/advection/CMakeLists.txt    |    6 +-
 tests/MMS/spatial/d2dx2/CMakeLists.txt        |    6 +-
 tests/MMS/spatial/d2dz2/CMakeLists.txt        |    6 +-
 tests/MMS/spatial/diffusion/CMakeLists.txt    |    3 +-
 tests/MMS/spatial/fci/CMakeLists.txt          |    6 +-
 tests/MMS/time-petsc/CMakeLists.txt           |    7 +-
 tests/MMS/time/CMakeLists.txt                 |    6 +-
 tests/MMS/upwinding3/CMakeLists.txt           |    6 +-
 tests/MMS/wave-1d-y/CMakeLists.txt            |    6 +-
 tests/MMS/wave-1d/CMakeLists.txt              |    6 +-
 .../integrated/test-backtrace/CMakeLists.txt  |    3 +-
 tests/integrated/test-beuler/CMakeLists.txt   |    7 +-
 .../CMakeLists.txt                            |    5 +-
 tests/integrated/test-boutpp/CMakeLists.txt   |    2 +-
 .../collect-staggered/CMakeLists.txt          |    6 +-
 .../test-boutpp/collect/CMakeLists.txt        |    3 +-
 .../test-boutpp/legacy-model/CMakeLists.txt   |    6 +-
 .../test-boutpp/mms-ddz/CMakeLists.txt        |    6 +-
 .../test-boutpp/print/CMakeLists.txt          |    3 +-
 .../test-boutpp/simple-model/CMakeLists.txt   |    3 +-
 .../test-boutpp/slicing/CMakeLists.txt        |    3 +-
 tests/integrated/test-collect/CMakeLists.txt  |    8 +-
 .../test-command-args/CMakeLists.txt          |    5 +-
 .../test-communications/CMakeLists.txt        |   11 +-
 .../CMakeLists.txt                            |    8 +-
 tests/integrated/test-cyclic/CMakeLists.txt   |    8 +-
 .../test-datafilefacade/CMakeLists.txt        |    8 +-
 tests/integrated/test-delp2/CMakeLists.txt    |    8 +-
 .../CMakeLists.txt                            |    8 +-
 .../test-drift-instability/CMakeLists.txt     |    8 +-
 .../test-fci-boundary/CMakeLists.txt          |   25 +-
 tests/integrated/test-fci-mpi/CMakeLists.txt  |    9 +-
 .../test-fieldgroupComm/CMakeLists.txt        |    8 +-
 .../CMakeLists.txt                            |   14 +-
 tests/integrated/test-griddata/CMakeLists.txt |    5 +-
 tests/integrated/test-gyro/CMakeLists.txt     |    8 +-
 tests/integrated/test-initial/CMakeLists.txt  |    8 +-
 .../CMakeLists.txt                            |    5 +-
 .../test-interpolate-z/CMakeLists.txt         |    8 +-
 .../test-interpolate/CMakeLists.txt           |    8 +-
 .../test-invertable-operator/CMakeLists.txt   |    8 +-
 tests/integrated/test-invpar/CMakeLists.txt   |    8 +-
 .../test-laplace-hypre3d/CMakeLists.txt       |   12 +-
 .../test-laplace-petsc3d/CMakeLists.txt       |   12 +-
 tests/integrated/test-laplace/CMakeLists.txt  |    8 +-
 .../test-laplacexy-fv/CMakeLists.txt          |   11 +-
 .../test-laplacexy-short/CMakeLists.txt       |   11 +-
 .../integrated/test-laplacexy/CMakeLists.txt  |    8 +-
 .../test-laplacexy2-hypre/CMakeLists.txt      |    8 +-
 .../integrated/test-laplacexz/CMakeLists.txt  |    8 +-
 .../test-multigrid_laplace/CMakeLists.txt     |    8 +-
 .../test-naulin-laplace/CMakeLists.txt        |    8 +-
 .../test-options-netcdf/CMakeLists.txt        |    8 +-
 .../test-petsc_laplace/CMakeLists.txt         |   11 +-
 .../CMakeLists.txt                            |   14 +-
 .../integrated/test-restart-io/CMakeLists.txt |    8 +-
 .../integrated/test-restarting/CMakeLists.txt |    8 +-
 .../test-slepc-solver/CMakeLists.txt          |    8 +-
 tests/integrated/test-smooth/CMakeLists.txt   |    8 +-
 tests/integrated/test-snb/CMakeLists.txt      |    5 +-
 tests/integrated/test-solver/CMakeLists.txt   |    4 +-
 tests/integrated/test-squash/CMakeLists.txt   |    8 +-
 .../test-stopCheck-file/CMakeLists.txt        |   13 +-
 .../integrated/test-stopCheck/CMakeLists.txt  |    8 +-
 .../test-twistshift-staggered/CMakeLists.txt  |    8 +-
 .../integrated/test-twistshift/CMakeLists.txt |    8 +-
 tests/integrated/test-vec/CMakeLists.txt      |    8 +-
 .../test-yupdown-weights/CMakeLists.txt       |    8 +-
 tests/integrated/test-yupdown/CMakeLists.txt  |    8 +-
 tests/unit/CMakeLists.txt                     |  210 ++--
 tools/pylib/_boutpp_build/CMakeLists.txt      |  108 +-
 149 files changed, 2979 insertions(+), 2181 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 479b13b668..c05bad29db 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -15,10 +15,15 @@ if(${CMAKE_VERSION} VERSION_GREATER_EQUAL 3.22)
   cmake_policy(SET CMP0127 NEW)
 endif()
 
-if ("${CMAKE_CURRENT_BINARY_DIR}" STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}")
-  option(BOUT_ALLOW_INSOURCE_BUILD "Whether BOUT++ should really allow to build in source." OFF)
-  if (NOT ${BOUT_ALLOW_INSOURCE_BUILD})
-    message(FATAL_ERROR "BOUT++ does not recommend in source builds. Try building out of source, e.g. with `cmake -S . -B build` or set -DBOUT_ALLOW_INSOURCE_BUILD=ON - but things may break!")
+if("${CMAKE_CURRENT_BINARY_DIR}" STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}")
+  option(BOUT_ALLOW_INSOURCE_BUILD
+         "Whether BOUT++ should really allow to build in source." OFF
+  )
+  if(NOT ${BOUT_ALLOW_INSOURCE_BUILD})
+    message(
+      FATAL_ERROR
+        "BOUT++ does not recommend in source builds. Try building out of source, e.g. with `cmake -S . -B build` or set -DBOUT_ALLOW_INSOURCE_BUILD=ON - but things may break!"
+    )
   endif()
 endif()
 
@@ -29,41 +34,53 @@ set(_bout_previous_version "5.2.0")
 set(_bout_next_version "5.2.1")
 execute_process(
   COMMAND "git" describe --tags --match=v${_bout_previous_version}
-  COMMAND sed -e s/${_bout_previous_version}-/${_bout_next_version}.dev/ -e s/-/+/
-  RESULTS_VARIABLE error_codes
+  COMMAND sed -e s/${_bout_previous_version}-/${_bout_next_version}.dev/ -e
+          s/-/+/ RESULTS_VARIABLE error_codes
   OUTPUT_VARIABLE BOUT_FULL_VERSION
   OUTPUT_STRIP_TRAILING_WHITESPACE
-  )
+)
 
 foreach(error_code ${error_codes})
-  if (NOT ${error_code} STREQUAL 0)
+  if(NOT ${error_code} STREQUAL 0)
     set(BOUT_FULL_VERSION ${_bout_next_version})
   endif()
 endforeach()
 # Remove leading "v"
 string(REGEX REPLACE "^v(.*)" "\\1" BOUT_FULL_VERSION ${BOUT_FULL_VERSION})
 # Remove trailing tag
-string(REGEX REPLACE "^([0-9]+\.[0-9]+\.[0-9]+)\..*" "\\1" BOUT_CMAKE_ACCEPTABLE_VERSION ${BOUT_FULL_VERSION})
+string(REGEX REPLACE "^([0-9]+\.[0-9]+\.[0-9]+)\..*" "\\1"
+                     BOUT_CMAKE_ACCEPTABLE_VERSION ${BOUT_FULL_VERSION}
+)
 # Get the trailing tag
-string(REGEX REPLACE "^[0-9]+\.[0-9]+\.[0-9]+\.(.*)" "\\1" BOUT_VERSION_TAG ${BOUT_FULL_VERSION})
+string(REGEX REPLACE "^[0-9]+\.[0-9]+\.[0-9]+\.(.*)" "\\1" BOUT_VERSION_TAG
+                     ${BOUT_FULL_VERSION}
+)
 
 message(STATUS "Configuring BOUT++ version ${BOUT_FULL_VERSION}")
-project(BOUT++
+project(
+  BOUT++
   DESCRIPTION "Fluid PDE solver framework"
   VERSION ${BOUT_CMAKE_ACCEPTABLE_VERSION}
-  LANGUAGES CXX)
+  LANGUAGES CXX
+)
 
 include(CMakeDependentOption)
 
 option(BUILD_SHARED_LIBS "Build shared libs" ON)
 
 # Override default
-option(INSTALL_GTEST "Enable installation of googletest. (Projects embedding googletest may want to turn this OFF.)" OFF)
+option(
+  INSTALL_GTEST
+  "Enable installation of googletest. (Projects embedding googletest may want to turn this OFF.)"
+  OFF
+)
 
 set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 include(BOUT++functions)
 
-option(BOUT_UPDATE_GIT_SUBMODULE "Check submodules are up-to-date during build" ON)
+option(BOUT_UPDATE_GIT_SUBMODULE "Check submodules are up-to-date during build"
+       ON
+)
 # Adapted from https://cliutils.gitlab.io/modern-cmake/chapters/projects/submodule.html
 # Update submodules as needed
 function(bout_update_submodules)
@@ -73,337 +90,363 @@ function(bout_update_submodules)
   find_package(Git QUIET)
   if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
     message(STATUS "Submodule update")
-    execute_process(COMMAND ${GIT_EXECUTABLE} -c submodule.recurse=false submodule update --init --recursive
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} -c submodule.recurse=false submodule update
+              --init --recursive
       WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
-      RESULT_VARIABLE GIT_SUBMOD_RESULT)
+      RESULT_VARIABLE GIT_SUBMOD_RESULT
+    )
     if(NOT GIT_SUBMOD_RESULT EQUAL "0")
-      message(FATAL_ERROR "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
+      message(
+        FATAL_ERROR
+          "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules"
+      )
     endif()
   endif()
 endfunction()
 
 set(BOUT_SOURCES
-  ./include/bout/adios_object.hxx
-  ./include/bout/array.hxx
-  ./include/bout/assert.hxx
-  ./include/bout/boundary_factory.hxx
-  ./include/bout/boundary_op.hxx
-  ./include/bout/boundary_region.hxx
-  ./include/bout/boundary_standard.hxx
-  ./include/bout/bout.hxx
-  ./include/bout/bout_enum_class.hxx
-  ./include/bout/bout_types.hxx
-  ./include/bout/build_config.hxx
-  ./include/bout/boutcomm.hxx
-  ./include/bout/boutexception.hxx
-  ./include/bout/caliper_wrapper.hxx
-  ./include/bout/constants.hxx
-  ./include/bout/coordinates.hxx
-  ./include/bout/coordinates_accessor.hxx
-  ./include/bout/cyclic_reduction.hxx
-  ./include/bout/dcomplex.hxx
-  ./include/bout/deriv_store.hxx
-  ./include/bout/derivs.hxx
-  ./include/bout/difops.hxx
-  ./include/bout/expr.hxx
-  ./include/bout/fft.hxx
-  ./include/bout/field.hxx
-  ./include/bout/field2d.hxx
-  ./include/bout/field3d.hxx
-  ./include/bout/field_accessor.hxx
-  ./include/bout/field_data.hxx
-  ./include/bout/field_factory.hxx
-  ./include/bout/fieldgroup.hxx
-  ./include/bout/fieldperp.hxx
-  ./include/bout/fv_ops.hxx
-  ./include/bout/generic_factory.hxx
-  ./include/bout/globalfield.hxx
-  ./include/bout/globalindexer.hxx
-  ./include/bout/globals.hxx
-  ./include/bout/griddata.hxx
-  ./include/bout/gyro_average.hxx
-  ./include/bout/hypre_interface.hxx
-  ./include/bout/index_derivs.hxx
-  ./include/bout/index_derivs_interface.hxx
-  ./include/bout/initialprofiles.hxx
-  ./include/bout/interpolation.hxx
-  ./include/bout/interpolation_xz.hxx
-  ./include/bout/interpolation_z.hxx
-  ./include/bout/invert/laplacexy.hxx
-  ./include/bout/invert/laplacexz.hxx
-  ./include/bout/invert_laplace.hxx
-  ./include/bout/invert_parderiv.hxx
-  ./include/bout/invert_pardiv.hxx
-  ./include/bout/invertable_operator.hxx
-  ./include/bout/lapack_routines.hxx
-  ./include/bout/macro_for_each.hxx
-  ./include/bout/mask.hxx
-  ./include/bout/mesh.hxx
-  ./include/bout/monitor.hxx
-  ./include/bout/mpi_wrapper.hxx
-  ./include/bout/msg_stack.hxx
-  ./include/bout/multiostream.hxx
-  ./include/bout/openmpwrap.hxx
-  ./include/bout/operatorstencil.hxx
-  ./include/bout/options.hxx
-  ./include/bout/options_io.hxx
-  ./include/bout/optionsreader.hxx
-  ./include/bout/output.hxx
-  ./include/bout/output_bout_types.hxx
-  ./include/bout/parallel_boundary_op.hxx
-  ./include/bout/parallel_boundary_region.hxx
-  ./include/bout/paralleltransform.hxx
-  ./include/bout/petsc_interface.hxx
-  ./include/bout/petsclib.hxx
-  ./include/bout/physicsmodel.hxx
-  ./include/bout/rajalib.hxx
-  ./include/bout/region.hxx
-  ./include/bout/rkscheme.hxx
-  ./include/bout/rvec.hxx
-  ./include/bout/scorepwrapper.hxx
-  ./include/bout/single_index_ops.hxx
-  ./include/bout/slepclib.hxx
-  ./include/bout/smoothing.hxx
-  ./include/bout/snb.hxx
-  ./include/bout/solver.hxx
-  ./include/bout/solverfactory.hxx
-  ./include/bout/sourcex.hxx
-  ./include/bout/stencils.hxx
-  ./include/bout/sundials_backports.hxx
-  ./include/bout/surfaceiter.hxx
-  ./include/bout/sys/expressionparser.hxx
-  ./include/bout/sys/generator_context.hxx
-  ./include/bout/sys/gettext.hxx
-  ./include/bout/sys/range.hxx
-  ./include/bout/sys/timer.hxx
-  ./include/bout/sys/type_name.hxx
-  ./include/bout/sys/uncopyable.hxx
-  ./include/bout/sys/uuid.h
-  ./include/bout/sys/variant.hxx
-  ./include/bout/template_combinations.hxx
-  ./include/bout/traits.hxx
-  ./include/bout/unused.hxx
-  ./include/bout/utils.hxx
-  ./include/bout/vecops.hxx
-  ./include/bout/vector2d.hxx
-  ./include/bout/vector3d.hxx
-  ./include/bout/where.hxx
-  ./src/bout++.cxx
-  ./src/bout++-time.hxx
-  ./src/field/field.cxx
-  ./src/field/field2d.cxx
-  ./src/field/field3d.cxx
-  ./src/field/field_data.cxx
-  ./src/field/field_factory.cxx
-  ./src/field/fieldgenerators.cxx
-  ./src/field/fieldgenerators.hxx
-  ./src/field/fieldgroup.cxx
-  ./src/field/fieldperp.cxx
-  ./src/field/generated_fieldops.cxx
-  ./src/field/globalfield.cxx
-  ./src/field/initialprofiles.cxx
-  ./src/field/vecops.cxx
-  ./src/field/vector2d.cxx
-  ./src/field/vector3d.cxx
-  ./src/field/where.cxx
-  ./src/invert/fft_fftw.cxx
-  ./src/invert/lapack_routines.cxx
-  ./src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
-  ./src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
-  ./src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
-  ./src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx
-  ./src/invert/laplace/impls/multigrid/multigrid_alg.cxx
-  ./src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
-  ./src/invert/laplace/impls/multigrid/multigrid_laplace.hxx
-  ./src/invert/laplace/impls/multigrid/multigrid_solver.cxx
-  ./src/invert/laplace/impls/naulin/naulin_laplace.cxx
-  ./src/invert/laplace/impls/naulin/naulin_laplace.hxx
-  ./src/invert/laplace/impls/pcr/pcr.cxx
-  ./src/invert/laplace/impls/pcr/pcr.hxx
-  ./src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
-  ./src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx
-  ./src/invert/laplace/impls/petsc/petsc_laplace.cxx
-  ./src/invert/laplace/impls/petsc/petsc_laplace.hxx
-  ./src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
-  ./src/invert/laplace/impls/petsc3damg/petsc3damg.hxx
-  ./src/invert/laplace/impls/serial_band/serial_band.cxx
-  ./src/invert/laplace/impls/serial_band/serial_band.hxx
-  ./src/invert/laplace/impls/serial_tri/serial_tri.cxx
-  ./src/invert/laplace/impls/serial_tri/serial_tri.hxx
-  ./src/invert/laplace/impls/spt/spt.cxx
-  ./src/invert/laplace/impls/spt/spt.hxx
-  ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
-  ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx
-  ./src/invert/laplace/invert_laplace.cxx
-  ./src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
-  ./src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
-  ./src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
-  ./src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx
-  ./src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
-  ./src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx
-  ./src/invert/laplacexy/laplacexy.cxx
-  ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
-  ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx
-  ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
-  ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx
-  ./src/invert/laplacexz/laplacexz.cxx
-  ./src/invert/parderiv/impls/cyclic/cyclic.cxx
-  ./src/invert/parderiv/impls/cyclic/cyclic.hxx
-  ./src/invert/parderiv/invert_parderiv.cxx
-  ./src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
-  ./src/invert/pardiv/impls/cyclic/pardiv_cyclic.hxx
-  ./src/invert/pardiv/invert_pardiv.cxx
-  ./src/mesh/boundary_factory.cxx
-  ./src/mesh/boundary_region.cxx
-  ./src/mesh/boundary_standard.cxx
-  ./src/mesh/coordinates.cxx
-  ./src/mesh/coordinates_accessor.cxx
-  ./src/mesh/data/gridfromfile.cxx
-  ./src/mesh/data/gridfromoptions.cxx
-  ./src/mesh/difops.cxx
-  ./src/mesh/fv_ops.cxx
-  ./src/mesh/impls/bout/boutmesh.cxx
-  ./src/mesh/impls/bout/boutmesh.hxx
-  ./src/mesh/index_derivs.cxx
-  ./src/mesh/interpolation_xz.cxx
-  ./src/mesh/interpolation/bilinear_xz.cxx
-  ./src/mesh/interpolation/hermite_spline_xz.cxx
-  ./src/mesh/interpolation/hermite_spline_z.cxx
-  ./src/mesh/interpolation/interpolation_z.cxx
-  ./src/mesh/interpolation/lagrange_4pt_xz.cxx
-  ./src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
-  ./src/mesh/invert3x3.hxx
-  ./src/mesh/mesh.cxx
-  ./src/mesh/parallel/fci.cxx
-  ./src/mesh/parallel/fci.hxx
-  ./src/mesh/parallel/identity.cxx
-  ./src/mesh/parallel/shiftedmetric.cxx
-  ./src/mesh/parallel/shiftedmetricinterp.cxx
-  ./src/mesh/parallel/shiftedmetricinterp.hxx
-  ./src/mesh/parallel_boundary_op.cxx
-  ./src/mesh/parallel_boundary_region.cxx
-  ./src/mesh/surfaceiter.cxx
-  ./src/physics/gyro_average.cxx
-  ./src/physics/physicsmodel.cxx
-  ./src/physics/smoothing.cxx
-  ./src/physics/snb.cxx
-  ./src/physics/sourcex.cxx
-  ./src/solver/impls/adams_bashforth/adams_bashforth.cxx
-  ./src/solver/impls/adams_bashforth/adams_bashforth.hxx
-  ./src/solver/impls/arkode/arkode.cxx
-  ./src/solver/impls/arkode/arkode.hxx
-  ./src/solver/impls/cvode/cvode.cxx
-  ./src/solver/impls/cvode/cvode.hxx
-  ./src/solver/impls/euler/euler.cxx
-  ./src/solver/impls/euler/euler.hxx
-  ./src/solver/impls/ida/ida.cxx
-  ./src/solver/impls/ida/ida.hxx
-  ./src/solver/impls/imex-bdf2/imex-bdf2.cxx
-  ./src/solver/impls/imex-bdf2/imex-bdf2.hxx
-  ./src/solver/impls/petsc/petsc.cxx
-  ./src/solver/impls/petsc/petsc.hxx
-  ./src/solver/impls/power/power.cxx
-  ./src/solver/impls/power/power.hxx
-  ./src/solver/impls/pvode/pvode.cxx
-  ./src/solver/impls/pvode/pvode.hxx
-  ./src/solver/impls/rk3-ssp/rk3-ssp.cxx
-  ./src/solver/impls/rk3-ssp/rk3-ssp.hxx
-  ./src/solver/impls/rk4/rk4.cxx
-  ./src/solver/impls/rk4/rk4.hxx
-  ./src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.cxx
-  ./src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.hxx
-  ./src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.cxx
-  ./src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.hxx
-  ./src/solver/impls/rkgeneric/impls/rkf34/rkf34.cxx
-  ./src/solver/impls/rkgeneric/impls/rkf34/rkf34.hxx
-  ./src/solver/impls/rkgeneric/impls/rkf45/rkf45.cxx
-  ./src/solver/impls/rkgeneric/impls/rkf45/rkf45.hxx
-  ./src/solver/impls/rkgeneric/rkgeneric.cxx
-  ./src/solver/impls/rkgeneric/rkgeneric.hxx
-  ./src/solver/impls/rkgeneric/rkscheme.cxx
-  ./src/solver/impls/slepc/slepc.cxx
-  ./src/solver/impls/slepc/slepc.hxx
-  ./src/solver/impls/snes/snes.cxx
-  ./src/solver/impls/snes/snes.hxx
-  ./src/solver/impls/split-rk/split-rk.cxx
-  ./src/solver/impls/split-rk/split-rk.hxx
-  ./src/solver/solver.cxx
-  ./src/sys/adios_object.cxx
-  ./src/sys/bout_types.cxx
-  ./src/sys/boutcomm.cxx
-  ./src/sys/boutexception.cxx
-  ./src/sys/derivs.cxx
-  ./src/sys/expressionparser.cxx
-  ./src/sys/generator_context.cxx
-  ./include/bout/hyprelib.hxx
-  ./src/sys/hyprelib.cxx
-  ./src/sys/msg_stack.cxx
-  ./src/sys/options.cxx
-  ./src/sys/options/optionparser.hxx
-  ./src/sys/options/options_ini.cxx
-  ./src/sys/options/options_ini.hxx
-  ./src/sys/options/options_io.cxx
-  ./src/sys/options/options_netcdf.cxx
-  ./src/sys/options/options_netcdf.hxx
-  ./src/sys/options/options_adios.cxx
-  ./src/sys/options/options_adios.hxx
-  ./src/sys/optionsreader.cxx
-  ./src/sys/output.cxx
-  ./src/sys/petsclib.cxx
-  ./src/sys/range.cxx
-  ./src/sys/slepclib.cxx
-  ./src/sys/timer.cxx
-  ./src/sys/type_name.cxx
-  ./src/sys/utils.cxx
-  ${CMAKE_CURRENT_BINARY_DIR}/include/bout/revision.hxx
-  ${CMAKE_CURRENT_BINARY_DIR}/include/bout/version.hxx
-  )
-
+    ./include/bout/adios_object.hxx
+    ./include/bout/array.hxx
+    ./include/bout/assert.hxx
+    ./include/bout/boundary_factory.hxx
+    ./include/bout/boundary_op.hxx
+    ./include/bout/boundary_region.hxx
+    ./include/bout/boundary_standard.hxx
+    ./include/bout/bout.hxx
+    ./include/bout/bout_enum_class.hxx
+    ./include/bout/bout_types.hxx
+    ./include/bout/build_config.hxx
+    ./include/bout/boutcomm.hxx
+    ./include/bout/boutexception.hxx
+    ./include/bout/caliper_wrapper.hxx
+    ./include/bout/constants.hxx
+    ./include/bout/coordinates.hxx
+    ./include/bout/coordinates_accessor.hxx
+    ./include/bout/cyclic_reduction.hxx
+    ./include/bout/dcomplex.hxx
+    ./include/bout/deriv_store.hxx
+    ./include/bout/derivs.hxx
+    ./include/bout/difops.hxx
+    ./include/bout/expr.hxx
+    ./include/bout/fft.hxx
+    ./include/bout/field.hxx
+    ./include/bout/field2d.hxx
+    ./include/bout/field3d.hxx
+    ./include/bout/field_accessor.hxx
+    ./include/bout/field_data.hxx
+    ./include/bout/field_factory.hxx
+    ./include/bout/fieldgroup.hxx
+    ./include/bout/fieldperp.hxx
+    ./include/bout/fv_ops.hxx
+    ./include/bout/generic_factory.hxx
+    ./include/bout/globalfield.hxx
+    ./include/bout/globalindexer.hxx
+    ./include/bout/globals.hxx
+    ./include/bout/griddata.hxx
+    ./include/bout/gyro_average.hxx
+    ./include/bout/hypre_interface.hxx
+    ./include/bout/index_derivs.hxx
+    ./include/bout/index_derivs_interface.hxx
+    ./include/bout/initialprofiles.hxx
+    ./include/bout/interpolation.hxx
+    ./include/bout/interpolation_xz.hxx
+    ./include/bout/interpolation_z.hxx
+    ./include/bout/invert/laplacexy.hxx
+    ./include/bout/invert/laplacexz.hxx
+    ./include/bout/invert_laplace.hxx
+    ./include/bout/invert_parderiv.hxx
+    ./include/bout/invert_pardiv.hxx
+    ./include/bout/invertable_operator.hxx
+    ./include/bout/lapack_routines.hxx
+    ./include/bout/macro_for_each.hxx
+    ./include/bout/mask.hxx
+    ./include/bout/mesh.hxx
+    ./include/bout/monitor.hxx
+    ./include/bout/mpi_wrapper.hxx
+    ./include/bout/msg_stack.hxx
+    ./include/bout/multiostream.hxx
+    ./include/bout/openmpwrap.hxx
+    ./include/bout/operatorstencil.hxx
+    ./include/bout/options.hxx
+    ./include/bout/options_io.hxx
+    ./include/bout/optionsreader.hxx
+    ./include/bout/output.hxx
+    ./include/bout/output_bout_types.hxx
+    ./include/bout/parallel_boundary_op.hxx
+    ./include/bout/parallel_boundary_region.hxx
+    ./include/bout/paralleltransform.hxx
+    ./include/bout/petsc_interface.hxx
+    ./include/bout/petsclib.hxx
+    ./include/bout/physicsmodel.hxx
+    ./include/bout/rajalib.hxx
+    ./include/bout/region.hxx
+    ./include/bout/rkscheme.hxx
+    ./include/bout/rvec.hxx
+    ./include/bout/scorepwrapper.hxx
+    ./include/bout/single_index_ops.hxx
+    ./include/bout/slepclib.hxx
+    ./include/bout/smoothing.hxx
+    ./include/bout/snb.hxx
+    ./include/bout/solver.hxx
+    ./include/bout/solverfactory.hxx
+    ./include/bout/sourcex.hxx
+    ./include/bout/stencils.hxx
+    ./include/bout/sundials_backports.hxx
+    ./include/bout/surfaceiter.hxx
+    ./include/bout/sys/expressionparser.hxx
+    ./include/bout/sys/generator_context.hxx
+    ./include/bout/sys/gettext.hxx
+    ./include/bout/sys/range.hxx
+    ./include/bout/sys/timer.hxx
+    ./include/bout/sys/type_name.hxx
+    ./include/bout/sys/uncopyable.hxx
+    ./include/bout/sys/uuid.h
+    ./include/bout/sys/variant.hxx
+    ./include/bout/template_combinations.hxx
+    ./include/bout/traits.hxx
+    ./include/bout/unused.hxx
+    ./include/bout/utils.hxx
+    ./include/bout/vecops.hxx
+    ./include/bout/vector2d.hxx
+    ./include/bout/vector3d.hxx
+    ./include/bout/where.hxx
+    ./src/bout++.cxx
+    ./src/bout++-time.hxx
+    ./src/field/field.cxx
+    ./src/field/field2d.cxx
+    ./src/field/field3d.cxx
+    ./src/field/field_data.cxx
+    ./src/field/field_factory.cxx
+    ./src/field/fieldgenerators.cxx
+    ./src/field/fieldgenerators.hxx
+    ./src/field/fieldgroup.cxx
+    ./src/field/fieldperp.cxx
+    ./src/field/generated_fieldops.cxx
+    ./src/field/globalfield.cxx
+    ./src/field/initialprofiles.cxx
+    ./src/field/vecops.cxx
+    ./src/field/vector2d.cxx
+    ./src/field/vector3d.cxx
+    ./src/field/where.cxx
+    ./src/invert/fft_fftw.cxx
+    ./src/invert/lapack_routines.cxx
+    ./src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
+    ./src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
+    ./src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
+    ./src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx
+    ./src/invert/laplace/impls/multigrid/multigrid_alg.cxx
+    ./src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
+    ./src/invert/laplace/impls/multigrid/multigrid_laplace.hxx
+    ./src/invert/laplace/impls/multigrid/multigrid_solver.cxx
+    ./src/invert/laplace/impls/naulin/naulin_laplace.cxx
+    ./src/invert/laplace/impls/naulin/naulin_laplace.hxx
+    ./src/invert/laplace/impls/pcr/pcr.cxx
+    ./src/invert/laplace/impls/pcr/pcr.hxx
+    ./src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
+    ./src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx
+    ./src/invert/laplace/impls/petsc/petsc_laplace.cxx
+    ./src/invert/laplace/impls/petsc/petsc_laplace.hxx
+    ./src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
+    ./src/invert/laplace/impls/petsc3damg/petsc3damg.hxx
+    ./src/invert/laplace/impls/serial_band/serial_band.cxx
+    ./src/invert/laplace/impls/serial_band/serial_band.hxx
+    ./src/invert/laplace/impls/serial_tri/serial_tri.cxx
+    ./src/invert/laplace/impls/serial_tri/serial_tri.hxx
+    ./src/invert/laplace/impls/spt/spt.cxx
+    ./src/invert/laplace/impls/spt/spt.hxx
+    ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
+    ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx
+    ./src/invert/laplace/invert_laplace.cxx
+    ./src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
+    ./src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
+    ./src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
+    ./src/invert/laplacexy/impls/petsc/laplacexy-petsc.hxx
+    ./src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
+    ./src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.hxx
+    ./src/invert/laplacexy/laplacexy.cxx
+    ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
+    ./src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.hxx
+    ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
+    ./src/invert/laplacexz/impls/petsc/laplacexz-petsc.hxx
+    ./src/invert/laplacexz/laplacexz.cxx
+    ./src/invert/parderiv/impls/cyclic/cyclic.cxx
+    ./src/invert/parderiv/impls/cyclic/cyclic.hxx
+    ./src/invert/parderiv/invert_parderiv.cxx
+    ./src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
+    ./src/invert/pardiv/impls/cyclic/pardiv_cyclic.hxx
+    ./src/invert/pardiv/invert_pardiv.cxx
+    ./src/mesh/boundary_factory.cxx
+    ./src/mesh/boundary_region.cxx
+    ./src/mesh/boundary_standard.cxx
+    ./src/mesh/coordinates.cxx
+    ./src/mesh/coordinates_accessor.cxx
+    ./src/mesh/data/gridfromfile.cxx
+    ./src/mesh/data/gridfromoptions.cxx
+    ./src/mesh/difops.cxx
+    ./src/mesh/fv_ops.cxx
+    ./src/mesh/impls/bout/boutmesh.cxx
+    ./src/mesh/impls/bout/boutmesh.hxx
+    ./src/mesh/index_derivs.cxx
+    ./src/mesh/interpolation_xz.cxx
+    ./src/mesh/interpolation/bilinear_xz.cxx
+    ./src/mesh/interpolation/hermite_spline_xz.cxx
+    ./src/mesh/interpolation/hermite_spline_z.cxx
+    ./src/mesh/interpolation/interpolation_z.cxx
+    ./src/mesh/interpolation/lagrange_4pt_xz.cxx
+    ./src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
+    ./src/mesh/invert3x3.hxx
+    ./src/mesh/mesh.cxx
+    ./src/mesh/parallel/fci.cxx
+    ./src/mesh/parallel/fci.hxx
+    ./src/mesh/parallel/identity.cxx
+    ./src/mesh/parallel/shiftedmetric.cxx
+    ./src/mesh/parallel/shiftedmetricinterp.cxx
+    ./src/mesh/parallel/shiftedmetricinterp.hxx
+    ./src/mesh/parallel_boundary_op.cxx
+    ./src/mesh/parallel_boundary_region.cxx
+    ./src/mesh/surfaceiter.cxx
+    ./src/physics/gyro_average.cxx
+    ./src/physics/physicsmodel.cxx
+    ./src/physics/smoothing.cxx
+    ./src/physics/snb.cxx
+    ./src/physics/sourcex.cxx
+    ./src/solver/impls/adams_bashforth/adams_bashforth.cxx
+    ./src/solver/impls/adams_bashforth/adams_bashforth.hxx
+    ./src/solver/impls/arkode/arkode.cxx
+    ./src/solver/impls/arkode/arkode.hxx
+    ./src/solver/impls/cvode/cvode.cxx
+    ./src/solver/impls/cvode/cvode.hxx
+    ./src/solver/impls/euler/euler.cxx
+    ./src/solver/impls/euler/euler.hxx
+    ./src/solver/impls/ida/ida.cxx
+    ./src/solver/impls/ida/ida.hxx
+    ./src/solver/impls/imex-bdf2/imex-bdf2.cxx
+    ./src/solver/impls/imex-bdf2/imex-bdf2.hxx
+    ./src/solver/impls/petsc/petsc.cxx
+    ./src/solver/impls/petsc/petsc.hxx
+    ./src/solver/impls/power/power.cxx
+    ./src/solver/impls/power/power.hxx
+    ./src/solver/impls/pvode/pvode.cxx
+    ./src/solver/impls/pvode/pvode.hxx
+    ./src/solver/impls/rk3-ssp/rk3-ssp.cxx
+    ./src/solver/impls/rk3-ssp/rk3-ssp.hxx
+    ./src/solver/impls/rk4/rk4.cxx
+    ./src/solver/impls/rk4/rk4.hxx
+    ./src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.cxx
+    ./src/solver/impls/rkgeneric/impls/cashkarp/cashkarp.hxx
+    ./src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.cxx
+    ./src/solver/impls/rkgeneric/impls/rk4simple/rk4simple.hxx
+    ./src/solver/impls/rkgeneric/impls/rkf34/rkf34.cxx
+    ./src/solver/impls/rkgeneric/impls/rkf34/rkf34.hxx
+    ./src/solver/impls/rkgeneric/impls/rkf45/rkf45.cxx
+    ./src/solver/impls/rkgeneric/impls/rkf45/rkf45.hxx
+    ./src/solver/impls/rkgeneric/rkgeneric.cxx
+    ./src/solver/impls/rkgeneric/rkgeneric.hxx
+    ./src/solver/impls/rkgeneric/rkscheme.cxx
+    ./src/solver/impls/slepc/slepc.cxx
+    ./src/solver/impls/slepc/slepc.hxx
+    ./src/solver/impls/snes/snes.cxx
+    ./src/solver/impls/snes/snes.hxx
+    ./src/solver/impls/split-rk/split-rk.cxx
+    ./src/solver/impls/split-rk/split-rk.hxx
+    ./src/solver/solver.cxx
+    ./src/sys/adios_object.cxx
+    ./src/sys/bout_types.cxx
+    ./src/sys/boutcomm.cxx
+    ./src/sys/boutexception.cxx
+    ./src/sys/derivs.cxx
+    ./src/sys/expressionparser.cxx
+    ./src/sys/generator_context.cxx
+    ./include/bout/hyprelib.hxx
+    ./src/sys/hyprelib.cxx
+    ./src/sys/msg_stack.cxx
+    ./src/sys/options.cxx
+    ./src/sys/options/optionparser.hxx
+    ./src/sys/options/options_ini.cxx
+    ./src/sys/options/options_ini.hxx
+    ./src/sys/options/options_io.cxx
+    ./src/sys/options/options_netcdf.cxx
+    ./src/sys/options/options_netcdf.hxx
+    ./src/sys/options/options_adios.cxx
+    ./src/sys/options/options_adios.hxx
+    ./src/sys/optionsreader.cxx
+    ./src/sys/output.cxx
+    ./src/sys/petsclib.cxx
+    ./src/sys/range.cxx
+    ./src/sys/slepclib.cxx
+    ./src/sys/timer.cxx
+    ./src/sys/type_name.cxx
+    ./src/sys/utils.cxx
+    ${CMAKE_CURRENT_BINARY_DIR}/include/bout/revision.hxx
+    ${CMAKE_CURRENT_BINARY_DIR}/include/bout/version.hxx
+)
 
 find_package(Python3)
 find_package(ClangFormat)
 
-if (Python3_FOUND AND ClangFormat_FOUND)
+if(Python3_FOUND AND ClangFormat_FOUND)
   set(BOUT_GENERATE_FIELDOPS_DEFAULT ON)
 else()
   set(BOUT_GENERATE_FIELDOPS_DEFAULT OFF)
 endif()
 
-execute_process(COMMAND ${Python3_EXECUTABLE} -c "import importlib.util ; import sys; sys.exit(importlib.util.find_spec(\"zoidberg\") is None)"
-  RESULT_VARIABLE zoidberg_FOUND)
-if (zoidberg_FOUND EQUAL 0)
+execute_process(
+  COMMAND
+    ${Python3_EXECUTABLE} -c
+    "import importlib.util ; import sys; sys.exit(importlib.util.find_spec(\"zoidberg\") is None)"
+  RESULT_VARIABLE zoidberg_FOUND
+)
+if(zoidberg_FOUND EQUAL 0)
   set(zoidberg_FOUND ON)
 else()
   set(zoidberg_FOUND OFF)
 endif()
 
-option(BOUT_GENERATE_FIELDOPS "Automatically re-generate the Field arithmetic operators from the Python templates. \
+option(
+  BOUT_GENERATE_FIELDOPS
+  "Automatically re-generate the Field arithmetic operators from the Python templates. \
 Requires Python3, clang-format, and Jinja2. Turn this OFF to skip generating them if, for example, \
-you are unable to install the Jinja2 Python module. This is only important for BOUT++ developers." ${BOUT_GENERATE_FIELDOPS_DEFAULT})
+you are unable to install the Jinja2 Python module. This is only important for BOUT++ developers."
+  ${BOUT_GENERATE_FIELDOPS_DEFAULT}
+)
 
-if (BOUT_GENERATE_FIELDOPS)
-  if (NOT Python3_FOUND)
-    message(FATAL_ERROR "python not found, but you have requested to generate code!")
+if(BOUT_GENERATE_FIELDOPS)
+  if(NOT Python3_FOUND)
+    message(
+      FATAL_ERROR "python not found, but you have requested to generate code!"
+    )
   endif()
-  if (NOT ClangFormat_FOUND)
-    message(FATAL_ERROR "clang-format not found, but you have requested to generate code!")
+  if(NOT ClangFormat_FOUND)
+    message(
+      FATAL_ERROR
+        "clang-format not found, but you have requested to generate code!"
+    )
   endif()
-  add_custom_command( OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/src/field/generated_fieldops.cxx
-    COMMAND ${Python3_EXECUTABLE} gen_fieldops.py --filename generated_fieldops.cxx.tmp
+  add_custom_command(
+    OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/src/field/generated_fieldops.cxx
+    COMMAND ${Python3_EXECUTABLE} gen_fieldops.py --filename
+            generated_fieldops.cxx.tmp
     COMMAND ${ClangFormat_BIN} generated_fieldops.cxx.tmp -i
-    COMMAND ${CMAKE_COMMAND} -E rename generated_fieldops.cxx.tmp generated_fieldops.cxx
-    DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/src/field/gen_fieldops.jinja  ${CMAKE_CURRENT_SOURCE_DIR}/src/field/gen_fieldops.py
+    COMMAND ${CMAKE_COMMAND} -E rename generated_fieldops.cxx.tmp
+            generated_fieldops.cxx
+    DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/src/field/gen_fieldops.jinja
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/field/gen_fieldops.py
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/src/field/
-    COMMENT "Generating source code" )
+    COMMENT "Generating source code"
+  )
 else()
-  message(AUTHOR_WARNING "'src/field/generated_fieldops.cxx' will not be \
+  message(
+    AUTHOR_WARNING
+      "'src/field/generated_fieldops.cxx' will not be \
 regenerated when you make changes to either \
 'src/field/gen_fieldops.py' or 'src/field/gen_fieldops.jinja'. \
 This is because either Python3 or clang-format is missing \
 (see above messages for more information) \
 or BOUT_GENERATE_FIELDOPS is OFF (current value: ${BOUT_GENERATE_FIELDOPS}). \
 This warning is only important for BOUT++ developers and can otherwise be \
-safely ignored.")
+safely ignored."
+  )
 endif()
 
 include(GNUInstallDirs)
@@ -420,21 +463,29 @@ set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
 # which point to directories outside the build tree to the install RPATH
 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
-
-execute_process(COMMAND ${Python3_EXECUTABLE} -c "import site ; print('/'.join(site.getusersitepackages().split('/')[-2:]))"
+execute_process(
+  COMMAND
+    ${Python3_EXECUTABLE} -c
+    "import site ; print('/'.join(site.getusersitepackages().split('/')[-2:]))"
   RESULT_VARIABLE PYTHON_WORKING
   OUTPUT_VARIABLE PYTHON_SITEPATH_SUFFIX
   OUTPUT_STRIP_TRAILING_WHITESPACE
 )
-set(CMAKE_INSTALL_PYTHON_SITEARCH lib/${PYTHON_SITEPATH_SUFFIX} CACHE STRING "Location to install python arch-specific modules")
+set(CMAKE_INSTALL_PYTHON_SITEARCH
+    lib/${PYTHON_SITEPATH_SUFFIX}
+    CACHE STRING "Location to install python arch-specific modules"
+)
 
 set(ON_OFF_AUTO ON OFF AUTO)
-set(BOUT_ENABLE_PYTHON AUTO CACHE STRING "Build the Python interface")
+set(BOUT_ENABLE_PYTHON
+    AUTO
+    CACHE STRING "Build the Python interface"
+)
 set_property(CACHE BOUT_ENABLE_PYTHON PROPERTY STRINGS ${ON_OFF_AUTO})
-if (NOT BOUT_ENABLE_PYTHON IN_LIST ON_OFF_AUTO)
+if(NOT BOUT_ENABLE_PYTHON IN_LIST ON_OFF_AUTO)
   message(FATAL_ERROR "BOUT_ENABLE_PYTHON must be one of ${ON_OFF_AUTO}")
 endif()
-if (BOUT_ENABLE_PYTHON OR BOUT_ENABLE_PYTHON STREQUAL "AUTO")
+if(BOUT_ENABLE_PYTHON OR BOUT_ENABLE_PYTHON STREQUAL "AUTO")
   add_subdirectory(tools/pylib/_boutpp_build)
 else()
   set(BOUT_ENABLE_PYTHON OFF)
@@ -444,33 +495,35 @@ set(BOUT_USE_PYTHON ${BOUT_ENABLE_PYTHON})
 # Ensure that the compile date/time is up-to-date when any of the sources change
 add_custom_command(
   OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx
-  COMMAND ${CMAKE_COMMAND} -P "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateDateTimeFile.cmake"
+  COMMAND ${CMAKE_COMMAND} -P
+          "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateDateTimeFile.cmake"
   DEPENDS ${BOUT_SOURCES}
   MAIN_DEPENDENCY "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateDateTimeFile.cmake"
-  )
-
+)
 
-add_library(bout++
-  ${BOUT_SOURCES}
-  ${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx
-  )
+add_library(bout++ ${BOUT_SOURCES} ${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx)
 add_library(bout++::bout++ ALIAS bout++)
 target_link_libraries(bout++ PUBLIC MPI::MPI_CXX)
-target_include_directories(bout++ PUBLIC
-  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
-  $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
-  $<INSTALL_INTERFACE:include>
-  )
+target_include_directories(
+  bout++
+  PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+         $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
+         $<INSTALL_INTERFACE:include>
+)
 set(BOUT_LIB_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib")
-set_target_properties(bout++ PROPERTIES
-  LIBRARY_OUTPUT_DIRECTORY "${BOUT_LIB_PATH}"
-  ARCHIVE_OUTPUT_DIRECTORY "${BOUT_LIB_PATH}"
-  SOVERSION 5.2.0)
+set_target_properties(
+  bout++
+  PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${BOUT_LIB_PATH}"
+             ARCHIVE_OUTPUT_DIRECTORY "${BOUT_LIB_PATH}"
+             SOVERSION 5.2.0
+)
 
 # Set some variables for the bout-config script
 set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -L\$BOUT_LIB_PATH -lbout++")
 set(BOUT_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/include")
-set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS} -std=c++17")
+set(CONFIG_CFLAGS
+    "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS} -std=c++17"
+)
 
 target_compile_features(bout++ PUBLIC cxx_std_17)
 set_target_properties(bout++ PROPERTIES CXX_EXTENSIONS OFF)
@@ -504,58 +557,77 @@ message(STATUS "Git revision: ${BOUT_REVISION}")
 # Build the file containing the version information
 configure_file(
   "${PROJECT_SOURCE_DIR}/include/bout/version.hxx.in"
-  "${PROJECT_BINARY_DIR}/include/bout/version.hxx")
+  "${PROJECT_BINARY_DIR}/include/bout/version.hxx"
+)
 # Build the file containing just the commit hash
 # This will be rebuilt on every commit!
 configure_file(
   "${PROJECT_SOURCE_DIR}/include/bout/revision.hxx.in"
-  "${PROJECT_BINARY_DIR}/include/bout/revision.hxx")
+  "${PROJECT_BINARY_DIR}/include/bout/revision.hxx"
+)
 
 ##################################################
 
 option(BOUT_ENABLE_WARNINGS "Enable compiler warnings" ON)
-if (BOUT_ENABLE_WARNINGS)
-  target_compile_options(bout++ PRIVATE
-    $<$<NOT:$<COMPILE_LANGUAGE:CUDA>>:
-    $<$<OR:$<CXX_COMPILER_ID:GNU>,$<CXX_COMPILER_ID:Clang>,$<CXX_COMPILER_ID:AppleClang>>:
-      -Wall -Wextra > >
-    $<$<CXX_COMPILER_ID:MSVC>:
-      /W4 >  
-    $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=-Wall -Xcompiler=-Wextra >
-   )
-
- include(EnableCXXWarningIfSupport)
- # Note we explicitly turn off -Wcast-function-type as PETSc *requires*
- # we cast a function to the wrong type in MatFDColoringSetFunction
- target_enable_cxx_warning_if_supported(bout++
-   FLAGS -Wnull-dereference -Wno-cast-function-type
-   )
+if(BOUT_ENABLE_WARNINGS)
+  target_compile_options(
+    bout++
+    PRIVATE
+      $<$<NOT:$<COMPILE_LANGUAGE:CUDA>>:
+      $<$<OR:$<CXX_COMPILER_ID:GNU>,$<CXX_COMPILER_ID:Clang>,$<CXX_COMPILER_ID:AppleClang>>:
+      -Wall
+      -Wextra
+      >
+      >
+      $<$<CXX_COMPILER_ID:MSVC>:
+      /W4
+      >
+      $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=-Wall
+      -Xcompiler=-Wextra
+      >
+  )
+
+  include(EnableCXXWarningIfSupport)
+  # Note we explicitly turn off -Wcast-function-type as PETSc *requires*
+  # we cast a function to the wrong type in MatFDColoringSetFunction
+  target_enable_cxx_warning_if_supported(
+    bout++ FLAGS -Wnull-dereference -Wno-cast-function-type
+  )
 endif()
 
 # Compile time features
 
 set(CHECK_LEVELS 0 1 2 3 4)
-set(CHECK 2 CACHE STRING "Set run-time checking level")
+set(CHECK
+    2
+    CACHE STRING "Set run-time checking level"
+)
 set_property(CACHE CHECK PROPERTY STRINGS ${CHECK_LEVELS})
-if (NOT CHECK IN_LIST CHECK_LEVELS)
+if(NOT CHECK IN_LIST CHECK_LEVELS)
   message(FATAL_ERROR "CHECK must be one of ${CHECK_LEVELS}")
 endif()
 message(STATUS "Runtime checking level: CHECK=${CHECK}")
 target_compile_definitions(bout++ PUBLIC "CHECK=${CHECK}")
 set(BOUT_CHECK_LEVEL ${CHECK})
 
-if (CHECK GREATER 1)
+if(CHECK GREATER 1)
   set(bout_use_msgstack_default ON)
 else()
   set(bout_use_msgstack_default OFF)
 endif()
-set(BOUT_ENABLE_MSGSTACK ${bout_use_msgstack_default} CACHE BOOL "Enable debug message stack")
+set(BOUT_ENABLE_MSGSTACK
+    ${bout_use_msgstack_default}
+    CACHE BOOL "Enable debug message stack"
+)
 message(STATUS "Message stack: BOUT_USE_MSGSTACK=${BOUT_ENABLE_MSGSTACK}")
 set(BOUT_USE_MSGSTACK ${BOUT_ENABLE_MSGSTACK})
 
-cmake_dependent_option(BOUT_ENABLE_OUTPUT_DEBUG "Enable extra debug output" OFF
-  "CHECK LESS 3" ON)
-message(STATUS "Extra debug output: BOUT_USE_OUTPUT_DEBUG=${BOUT_ENABLE_OUTPUT_DEBUG}")
+cmake_dependent_option(
+  BOUT_ENABLE_OUTPUT_DEBUG "Enable extra debug output" OFF "CHECK LESS 3" ON
+)
+message(
+  STATUS "Extra debug output: BOUT_USE_OUTPUT_DEBUG=${BOUT_ENABLE_OUTPUT_DEBUG}"
+)
 set(BOUT_USE_OUTPUT_DEBUG ${BOUT_ENABLE_OUTPUT_DEBUG})
 
 option(BOUT_ENABLE_SIGNAL "SegFault handling" ON)
@@ -571,7 +643,10 @@ message(STATUS "Field name tracking: BOUT_USE_TRACK=${BOUT_ENABLE_TRACK}")
 set(BOUT_USE_TRACK ${BOUT_ENABLE_TRACK})
 
 option(BOUT_ENABLE_SIGFPE "Signalling floating point exceptions" OFF)
-message(STATUS "Signalling floating point exceptions: BOUT_USE_SIGFPE=${BOUT_ENABLE_SIGFPE}")
+message(
+  STATUS
+    "Signalling floating point exceptions: BOUT_USE_SIGFPE=${BOUT_ENABLE_SIGFPE}"
+)
 set(BOUT_USE_SIGFPE ${BOUT_ENABLE_SIGFPE})
 
 option(BOUT_ENABLE_METRIC_3D "Enable 3D metric support" OFF)
@@ -583,12 +658,15 @@ endif()
 set(BOUT_USE_METRIC_3D ${BOUT_ENABLE_METRIC_3D})
 
 include(CheckCXXSourceCompiles)
-check_cxx_source_compiles("int main() { const char* name = __PRETTY_FUNCTION__; }"
-  HAS_PRETTY_FUNCTION)
+check_cxx_source_compiles(
+  "int main() { const char* name = __PRETTY_FUNCTION__; }" HAS_PRETTY_FUNCTION
+)
 set(BOUT_HAS_PRETTY_FUNCTION ${HAS_PRETTY_FUNCTION})
 
 # Locations of the various Python modules, including the generated boutconfig module
-set(BOUT_PYTHONPATH "${CMAKE_CURRENT_BINARY_DIR}/tools/pylib:${CMAKE_CURRENT_SOURCE_DIR}/tools/pylib")
+set(BOUT_PYTHONPATH
+    "${CMAKE_CURRENT_BINARY_DIR}/tools/pylib:${CMAKE_CURRENT_SOURCE_DIR}/tools/pylib"
+)
 # Variables for boutconfig module -- note that these will contain
 # generator expressions and CMake targets, and not generally be very
 # useful
@@ -601,18 +679,22 @@ get_target_property(BOUT_CFLAGS bout++ INTERFACE_INCLUDE_DIRECTORIES)
 # 1. Get the macro definitions. They come as a ;-separated list and
 #    without the -D. We also need to also stick a -D on the front of
 #    the first item
-get_property(BOUT_COMPILE_DEFINITIONS
+get_property(
+  BOUT_COMPILE_DEFINITIONS
   TARGET bout++
-  PROPERTY COMPILE_DEFINITIONS)
+  PROPERTY COMPILE_DEFINITIONS
+)
 string(REPLACE ";" " -D" BOUT_COMPILE_DEFINITIONS "${BOUT_COMPILE_DEFINITIONS}")
 string(CONCAT BOUT_COMPILE_DEFINITIONS " -D" "${BOUT_COMPILE_DEFINITIONS}")
 
 # 2. Get the compiler options. Again, they come as a ;-separated
 #    list. Note that they don't include optimisation or debug flags:
 #    they're in the CMAKE_CXX_FLAGS* variables
-get_property(BOUT_COMPILE_OPTIONS
+get_property(
+  BOUT_COMPILE_OPTIONS
   TARGET bout++
-  PROPERTY COMPILE_OPTIONS)
+  PROPERTY COMPILE_OPTIONS
+)
 string(REPLACE ";" " " BOUT_COMPILE_OPTIONS "${BOUT_COMPILE_OPTIONS}")
 
 # 3. The optimisation and/or debug flags are in the CMAKE_CXX_FLAGS*
@@ -624,31 +706,33 @@ string(REPLACE ";" " " BOUT_COMPILE_OPTIONS "${BOUT_COMPILE_OPTIONS}")
 include(BuildType)
 # Here CMAKE_BUILD_TYPE is always set
 string(TOUPPER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_UPPER)
-string(CONCAT BOUT_COMPILE_BUILD_FLAGS
-  " "
-  "${CMAKE_CXX_FLAGS}"
-  "${CMAKE_CXX_FLAGS_${CMAKE_BUILD_TYPE_UPPER}}")
+string(CONCAT BOUT_COMPILE_BUILD_FLAGS " " "${CMAKE_CXX_FLAGS}"
+              "${CMAKE_CXX_FLAGS_${CMAKE_BUILD_TYPE_UPPER}}"
+)
 
 # 4. Now we join all the flags from the first three steps together
-string(CONCAT BOUT_FLAGS_STRING
-  "${BOUT_COMPILE_OPTIONS}"
-  "${BOUT_COMPILE_DEFINITIONS}"
-  "${BOUT_COMPILE_BUILD_FLAGS}")
+string(CONCAT BOUT_FLAGS_STRING "${BOUT_COMPILE_OPTIONS}"
+              "${BOUT_COMPILE_DEFINITIONS}" "${BOUT_COMPILE_BUILD_FLAGS}"
+)
 
 # 5. Finally actually add the flags as a define
-target_compile_definitions(bout++
-  PRIVATE BOUT_FLAGS_STRING=${BOUT_FLAGS_STRING})
+target_compile_definitions(
+  bout++ PRIVATE BOUT_FLAGS_STRING=${BOUT_FLAGS_STRING}
+)
 
 ##################################################
 # Tests
 
 # Are we building BOUT++ directly, or as part of another project
-string(COMPARE EQUAL
-  "${PROJECT_NAME}" "${CMAKE_PROJECT_NAME}"
-  PROJECT_IS_TOP_LEVEL
+string(COMPARE EQUAL "${PROJECT_NAME}" "${CMAKE_PROJECT_NAME}"
+               PROJECT_IS_TOP_LEVEL
 )
 option(BOUT_TESTS "Build the tests" ${PROJECT_IS_TOP_LEVEL})
-option(BOUT_ENABLE_ALL_TESTS "Enable running all of the tests, rather then the standard selection of fast tests" OFF)
+option(
+  BOUT_ENABLE_ALL_TESTS
+  "Enable running all of the tests, rather then the standard selection of fast tests"
+  OFF
+)
 if(BOUT_TESTS)
   enable_testing()
   # Targets for just building the tests
@@ -659,31 +743,35 @@ if(BOUT_TESTS)
 
   # Build all the tests
   add_custom_target(build-check)
-  add_dependencies(build-check build-check-unit-tests build-check-integrated-tests build-check-mms-tests)
+  add_dependencies(
+    build-check build-check-unit-tests build-check-integrated-tests
+    build-check-mms-tests
+  )
 
   add_subdirectory(tests/unit EXCLUDE_FROM_ALL)
   add_subdirectory(tests/integrated EXCLUDE_FROM_ALL)
   add_subdirectory(tests/MMS EXCLUDE_FROM_ALL)
 
   # Targets for running the tests
-  if (BOUT_ENABLE_UNIT_TESTS)
-    add_custom_target(check-unit-tests
-      COMMAND ctest -R serial_tests --output-on-failure)
+  if(BOUT_ENABLE_UNIT_TESTS)
+    add_custom_target(
+      check-unit-tests COMMAND ctest -R serial_tests --output-on-failure
+    )
     add_dependencies(check-unit-tests build-check-unit-tests)
   endif()
 
-  add_custom_target(check-integrated-tests
-    COMMAND ctest -R "test-" --output-on-failure)
+  add_custom_target(
+    check-integrated-tests COMMAND ctest -R "test-" --output-on-failure
+  )
   add_dependencies(check-integrated-tests build-check-integrated-tests)
 
-  add_custom_target(check-mms-tests
-    COMMAND ctest -R "MMS-" --output-on-failure)
+  add_custom_target(check-mms-tests COMMAND ctest -R "MMS-" --output-on-failure)
   add_dependencies(check-mms-tests build-check-mms-tests)
 
   # Run all the tests
   add_custom_target(check)
   add_dependencies(check check-integrated-tests check-mms-tests)
-  if (BOUT_ENABLE_UNIT_TESTS)
+  if(BOUT_ENABLE_UNIT_TESTS)
     add_dependencies(check check-unit-tests)
   endif()
 
@@ -695,21 +783,22 @@ if(BOUT_BUILD_EXAMPLES)
   add_subdirectory(examples EXCLUDE_FROM_ALL)
 endif()
 
-
 ##################################################
 # L10N: localisation - include translations
 
 find_package(Gettext)
 
-if (GETTEXT_FOUND)
+if(GETTEXT_FOUND)
   #add_custom_target(mofiles ALL)
   set(bout_langs es de fr zh_CN zh_TW)
 
   foreach(_lang IN LISTS bout_langs)
     set(_gmoFile ${CMAKE_CURRENT_BINARY_DIR}/locale/${_lang}/libbout.gmo)
     set(_poFile ${CMAKE_CURRENT_SOURCE_DIR}/locale/${_lang}/libbout.po)
-    add_custom_command(OUTPUT ${_gmoFile} _mo_file_${_lang}
-      COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_CURRENT_BINARY_DIR}/locale/${_lang}/
+    add_custom_command(
+      OUTPUT ${_gmoFile} _mo_file_${_lang}
+      COMMAND ${CMAKE_COMMAND} -E make_directory
+              ${CMAKE_CURRENT_BINARY_DIR}/locale/${_lang}/
       COMMAND ${GETTEXT_MSGFMT_EXECUTABLE} -o ${_gmoFile} ${_poFile}
       WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
       DEPENDS ${_poFile}
@@ -717,41 +806,46 @@ if (GETTEXT_FOUND)
 
     list(APPEND _gmoFiles ${_gmoFile})
 
-    install(FILES ${_gmoFile} DESTINATION ${CMAKE_INSTALL_LOCALEDIR}/${_lang}/LC_MESSAGES/ RENAME libbout.mo)
+    install(
+      FILES ${_gmoFile}
+      DESTINATION ${CMAKE_INSTALL_LOCALEDIR}/${_lang}/LC_MESSAGES/
+      RENAME libbout.mo
+    )
   endforeach()
-  add_custom_target(mofiles ALL
-    DEPENDS ${_gmoFiles})
+  add_custom_target(mofiles ALL DEPENDS ${_gmoFiles})
 endif()
 
-
 ##################################################
 # Documentation
 
 option(BOUT_BUILD_DOCS "Build the documentation" OFF)
-if (BOUT_BUILD_DOCS)
+if(BOUT_BUILD_DOCS)
   add_subdirectory(manual)
 endif()
 
-
-add_custom_target(dist
-  COMMAND ${Python3_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/pylib/_boutpp_build/backend.py dist
+add_custom_target(
+  dist
+  COMMAND ${Python3_EXECUTABLE}
+          ${CMAKE_SOURCE_DIR}/tools/pylib/_boutpp_build/backend.py dist
   # there is no cmake equivalent to `mv` - so only works on systems that are not inentionally non-POSIX complient
   COMMAND mv BOUT++-v${BOUT_FULL_VERSION}.tar.gz ${CMAKE_CURRENT_BINARY_DIR}/
   WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-  )
+)
 ##################################################
 # Generate the build config header
 
-if (EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/include/bout/build_defines.hxx")
+if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/include/bout/build_defines.hxx")
   # If we do in source builds, this is fine
-  if (NOT ${CMAKE_CURRENT_SOURCE_DIR} STREQUAL ${CMAKE_CURRENT_BINARY_DIR})
-    message(FATAL_ERROR "Generated build_defines.hxx header already exists; please remove '${CMAKE_CURRENT_SOURCE_DIR}/include/bout/build_defines.hxx' before continuing")
+  if(NOT ${CMAKE_CURRENT_SOURCE_DIR} STREQUAL ${CMAKE_CURRENT_BINARY_DIR})
+    message(
+      FATAL_ERROR
+        "Generated build_defines.hxx header already exists; please remove '${CMAKE_CURRENT_SOURCE_DIR}/include/bout/build_defines.hxx' before continuing"
+    )
   endif()
 endif()
 
 configure_file(cmake_build_defines.hxx.in include/bout/build_defines.hxx)
 
-
 ##################################################
 # Generate the bout-config script
 
@@ -763,9 +857,11 @@ set(BOUT_HAS_PNETCDF OFF)
 
 # For shared libraries we only need to know how to link against BOUT++,
 # while for static builds we need the dependencies too
-if (BUILD_SHARED_LIBS)
+if(BUILD_SHARED_LIBS)
   # Include rpath linker flag so user doesn't need to set LD_LIBRARY_PATH
-  set(CONFIG_LDFLAGS "${CMAKE_SHARED_LIBRARY_RUNTIME_CXX_FLAG}\$BOUT_LIB_PATH -L\$BOUT_LIB_PATH -lbout++ -lfmt ${CONFIG_LDFLAGS_SHARED}")
+  set(CONFIG_LDFLAGS
+      "${CMAKE_SHARED_LIBRARY_RUNTIME_CXX_FLAG}\$BOUT_LIB_PATH -L\$BOUT_LIB_PATH -lbout++ -lfmt ${CONFIG_LDFLAGS_SHARED}"
+  )
 else()
   set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS}")
 endif()
@@ -774,9 +870,9 @@ set(ISINSTALLED "FALSE")
 
 set(_CONFIG_LDFLAGS)
 string(REPLACE " " ";" CONFIG_LDFLAGS_LIST ${CONFIG_LDFLAGS})
-foreach (flag ${CONFIG_LDFLAGS_LIST})
+foreach(flag ${CONFIG_LDFLAGS_LIST})
   string(REGEX MATCH "^-.*$" isopt "${flag}")
-  if (isopt)
+  if(isopt)
     # message("${flag} is an option")
     set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} ${flag}")
     # All good
@@ -786,73 +882,93 @@ foreach (flag ${CONFIG_LDFLAGS_LIST})
       set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} ${flag}")
     else()
       string(FIND "${flag}" "::" hascolcol)
-      if (${hascolcol} EQUAL -1)
-	message("Fixing ${flag} to -l${flag}")
-	set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag}")
+      if(${hascolcol} EQUAL -1)
+        message("Fixing ${flag} to -l${flag}")
+        set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag}")
       else()
-	string(REGEX MATCH "[^:]*$" flag2 "${flag}")
-	message("Fixing ${flag} to -l${flag2}")
-	set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag2}")
+        string(REGEX MATCH "[^:]*$" flag2 "${flag}")
+        message("Fixing ${flag} to -l${flag2}")
+        set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag2}")
       endif()
     endif()
   endif()
 endforeach()
-set( CONFIG_LDFLAGS ${_CONFIG_LDFLAGS})
+set(CONFIG_LDFLAGS ${_CONFIG_LDFLAGS})
 
 # This version of the file allows the build directory to be used directly
 configure_file(bin/bout-config.in bin/bout-config @ONLY)
-configure_file(tools/pylib/boutconfig/__init__.py.cin tools/pylib/boutconfig/__init__.py @ONLY)
+configure_file(
+  tools/pylib/boutconfig/__init__.py.cin tools/pylib/boutconfig/__init__.py
+  @ONLY
+)
 configure_file(bout++Config.cmake.in bout++Config.cmake @ONLY)
 
 # We need to generate a separate version for installation, with the
 # correct install paths. So first we need to replace the build
 # directory library path with the installation path
-string(REPLACE
-  "${CMAKE_BINARY_DIR}/lib" "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}"
-  CONFIG_LDFLAGS "${CONFIG_LDFLAGS}")
+string(REPLACE "${CMAKE_BINARY_DIR}/lib"
+               "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}" CONFIG_LDFLAGS
+               "${CONFIG_LDFLAGS}"
+)
 set(BOUT_LIB_PATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
 # Update mpark.variant and fmt include paths if we're building them
-if (NOT BOUT_USE_SYSTEM_MPARK_VARIANT)
-  set(MPARK_VARIANT_INCLUDE_PATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
+if(NOT BOUT_USE_SYSTEM_MPARK_VARIANT)
+  set(MPARK_VARIANT_INCLUDE_PATH
+      "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}"
+  )
 endif()
-if (NOT BOUT_USE_SYSTEM_FMT)
+if(NOT BOUT_USE_SYSTEM_FMT)
   set(FMT_INCLUDE_PATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
 endif()
-if (NOT BOUT_USE_SYSTEM_CPPTRACE)
-  set(CPPTRACE_INCLUDE_PATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
+if(NOT BOUT_USE_SYSTEM_CPPTRACE)
+  set(CPPTRACE_INCLUDE_PATH
+      "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}"
+  )
 endif()
 set(BOUT_INCLUDE_PATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
 # We don't need the build include path any more
-string(REPLACE "-I${CMAKE_CURRENT_BINARY_DIR}/include" "" CONFIG_CFLAGS "${CONFIG_CFLAGS}")
+string(REPLACE "-I${CMAKE_CURRENT_BINARY_DIR}/include" "" CONFIG_CFLAGS
+               "${CONFIG_CFLAGS}"
+)
 
 set(PYTHONCONFIGPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_PYTHON_SITEARCH}")
 set(ISINSTALLED "TRUE")
 
 # This version now has the correct paths to use the final installation
 configure_file(bin/bout-config.in bin/bout-config-install @ONLY)
-configure_file(tools/pylib/boutconfig/__init__.py.cin tools/pylib/boutconfig/__init__.py-install @ONLY)
+configure_file(
+  tools/pylib/boutconfig/__init__.py.cin
+  tools/pylib/boutconfig/__init__.py-install @ONLY
+)
 configure_file(bout++Config.cmake.in bout++Config.cmake-install @ONLY)
 
 ##################################################
 # Installation
 
-install(TARGETS bout++
+install(
+  TARGETS bout++
   EXPORT bout++Targets
   LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
   ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
   RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
-  INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
-  )
+  INCLUDES
+  DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+)
 # Repo files
-install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
-  FILES_MATCHING PATTERN "*.hxx")
+install(
+  DIRECTORY include/
+  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+  FILES_MATCHING
+  PATTERN "*.hxx"
+)
 # Generated headers
 install(DIRECTORY "${PROJECT_BINARY_DIR}/include/"
-  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+        DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+)
 
 # The various helper scripts
-install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin/"
-  USE_SOURCE_PERMISSIONS
+install(
+  DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin/" USE_SOURCE_PERMISSIONS
   DESTINATION "${CMAKE_INSTALL_BINDIR}"
   REGEX "bout-squashoutput" EXCLUDE
   REGEX "bout-config\.in" EXCLUDE
@@ -863,69 +979,71 @@ install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin/"
 # it. Note this MUST be done after the installation of bin/, to make
 # sure we clobber any versions of bout-config hanging around from an
 # autotools build
-install(PROGRAMS "${CMAKE_CURRENT_BINARY_DIR}/bin/bout-config-install"
+install(
+  PROGRAMS "${CMAKE_CURRENT_BINARY_DIR}/bin/bout-config-install"
   DESTINATION "${CMAKE_INSTALL_BINDIR}"
   RENAME "bout-config"
-  )
+)
 
 install(
   FILES "${CMAKE_CURRENT_BINARY_DIR}/tools/pylib/boutconfig/__init__.py-install"
   DESTINATION "${CMAKE_INSTALL_PYTHON_SITEARCH}/boutconfig"
   RENAME "__init__.py"
-  )
+)
 
 include(CMakePackageConfigHelpers)
 write_basic_package_version_file(
   bout++ConfigVersion.cmake
   VERSION ${PACKAGE_VERSION}
   COMPATIBILITY SameMajorVersion
-  )
+)
 
-install(EXPORT bout++Targets
+install(
+  EXPORT bout++Targets
   FILE bout++Targets.cmake
   NAMESPACE bout++::
   DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/bout++"
-  )
+)
 
 # CMake configuration files
 install(
-  FILES
-      "${CMAKE_CURRENT_BINARY_DIR}/bout++ConfigVersion.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/BOUT++functions.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/CorrectWindowsPaths.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindClangFormat.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindFFTW.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindHYPRE.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindnetCDF.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindnetCDFCxx.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindPackageMultipass.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindLibuuid.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindPETSc.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindScoreP.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindSLEPc.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindSUNDIALS.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindSphinx.cmake"
-      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/ResolveCompilerPaths.cmake"
+  FILES "${CMAKE_CURRENT_BINARY_DIR}/bout++ConfigVersion.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/BOUT++functions.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/CorrectWindowsPaths.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindClangFormat.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindFFTW.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindHYPRE.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindnetCDF.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindnetCDFCxx.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindPackageMultipass.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindLibuuid.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindPETSc.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindScoreP.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindSLEPc.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindSUNDIALS.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindSphinx.cmake"
+        "${CMAKE_CURRENT_SOURCE_DIR}/cmake/ResolveCompilerPaths.cmake"
   DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/bout++"
-  )
+)
 install(
-  FILES
-      "${CMAKE_CURRENT_BINARY_DIR}/bout++Config.cmake-install"
+  FILES "${CMAKE_CURRENT_BINARY_DIR}/bout++Config.cmake-install"
   DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/bout++"
   RENAME "bout++Config.cmake"
-  )
+)
 
-export(EXPORT bout++Targets
+export(
+  EXPORT bout++Targets
   FILE "${CMAKE_CURRENT_BINARY_DIR}/bout++Targets.cmake"
   NAMESPACE bout++::
-  )
+)
 
 export(PACKAGE bout)
 
 ##################################################
 # Configure summary
 
-message("
+message(
+  "
    --------------------------------
      BOUT++ Configuration Summary
    --------------------------------
@@ -965,4 +1083,5 @@ message("
        export PYTHONPATH=${BOUT_PYTHONPATH}:\$PYTHONPATH
 
 *** Now run `cmake --build ${CMAKE_BINARY_DIR}` to compile BOUT++ ***
-")
+"
+)
diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 074d803fb6..cff7e4b808 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -3,9 +3,9 @@
 # Copy FILENAME from source directory to build directory
 macro(bout_copy_file FILENAME)
   configure_file(
-      ${CMAKE_CURRENT_SOURCE_DIR}/${FILENAME}
-      ${CMAKE_CURRENT_BINARY_DIR}/${FILENAME}
-      COPYONLY)
+    ${CMAKE_CURRENT_SOURCE_DIR}/${FILENAME}
+    ${CMAKE_CURRENT_BINARY_DIR}/${FILENAME} COPYONLY
+  )
 endmacro()
 
 # Handle the REQUIRES and CONFLICTS arguments for models, examples,
@@ -15,16 +15,22 @@ macro(bout_handle_requires_conflicts TYPENAME TYPEVAR)
   set(multiValueArgs REQUIRES CONFLICTS)
   cmake_parse_arguments(BOUT_HANDLE_OPTIONS "" "" "${multiValueArgs}" ${ARGN})
 
-  foreach (REQUIREMENT IN LISTS BOUT_HANDLE_OPTIONS_REQUIRES)
-    if (NOT ${REQUIREMENT})
-      message(STATUS "Not building ${TYPENAME} ${TYPEVAR}, requirement not met: ${REQUIREMENT}")
+  foreach(REQUIREMENT IN LISTS BOUT_HANDLE_OPTIONS_REQUIRES)
+    if(NOT ${REQUIREMENT})
+      message(
+        STATUS
+          "Not building ${TYPENAME} ${TYPEVAR}, requirement not met: ${REQUIREMENT}"
+      )
       return()
     endif()
   endforeach()
 
-  foreach (CONFLICT IN LISTS BOUT_HANDLE_OPTIONS_CONFLICTS)
-    if (${CONFLICT})
-      message(STATUS "Not building ${TYPENAME} ${TYPEVAR}, conflicts with: ${CONFLICT}")
+  foreach(CONFLICT IN LISTS BOUT_HANDLE_OPTIONS_CONFLICTS)
+    if(${CONFLICT})
+      message(
+        STATUS
+          "Not building ${TYPENAME} ${TYPEVAR}, conflicts with: ${CONFLICT}"
+      )
       return()
     endif()
   endforeach()
@@ -46,25 +52,29 @@ function(bout_add_model MODEL)
   set(multiValueArgs SOURCES REQUIRES CONFLICTS)
   cmake_parse_arguments(BOUT_MODEL_OPTIONS "" "" "${multiValueArgs}" ${ARGN})
 
-  bout_handle_requires_conflicts("model" MODEL
+  bout_handle_requires_conflicts(
+    "model" MODEL
     REQUIRES ${BOUT_MODEL_OPTIONS_REQUIRES}
     CONFLICTS ${BOUT_MODEL_OPTIONS_CONFLICTS}
-    )
+  )
 
-  if (NOT BOUT_MODEL_OPTIONS_SOURCES)
-    message(FATAL_ERROR "Required argument SOURCES missing from 'bout_add_model'")
+  if(NOT BOUT_MODEL_OPTIONS_SOURCES)
+    message(
+      FATAL_ERROR "Required argument SOURCES missing from 'bout_add_model'"
+    )
   endif()
 
-  if ("SOURCES" IN_LIST BOUT_MODEL_OPTIONS_KEYWORDS_MISSING_VALUES)
+  if("SOURCES" IN_LIST BOUT_MODEL_OPTIONS_KEYWORDS_MISSING_VALUES)
     message(FATAL_ERROR "SOURCES missing values from 'bout_add_model'")
   endif()
 
   add_executable(${MODEL} ${BOUT_MODEL_OPTIONS_SOURCES})
   target_link_libraries(${MODEL} bout++::bout++)
-  target_include_directories(${MODEL} PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>)
+  target_include_directories(
+    ${MODEL} PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+  )
 endfunction()
 
-
 # Build a BOUT++ example
 #
 # If called from a standalone project, just builds the example as a
@@ -85,37 +95,38 @@ function(bout_add_example EXAMPLENAME)
   set(multiValueArgs SOURCES REQUIRES CONFLICTS DATA_DIRS EXTRA_FILES)
   cmake_parse_arguments(BOUT_EXAMPLE_OPTIONS "" "" "${multiValueArgs}" ${ARGN})
 
-  bout_handle_requires_conflicts("example" ${EXAMPLENAME}
+  bout_handle_requires_conflicts(
+    "example" ${EXAMPLENAME}
     REQUIRES ${BOUT_EXAMPLE_OPTIONS_REQUIRES}
     CONFLICTS ${BOUT_EXAMPLE_OPTIONS_CONFLICTS}
-    )
+  )
 
   bout_add_model(${EXAMPLENAME} SOURCES ${BOUT_EXAMPLE_OPTIONS_SOURCES})
 
   # If this is a standalone project, we can stop here. Otherwise, we
   # need to copy the various input files to the build directory
   get_directory_property(HAS_PARENT PARENT_DIRECTORY)
-  if (NOT HAS_PARENT)
+  if(NOT HAS_PARENT)
     return()
   endif()
 
   # Copy the documentation if it exists
-  if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/README.md)
+  if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/README.md)
     bout_copy_file(README.md)
   endif()
 
   # Copy the input file
-  if (NOT BOUT_EXAMPLE_OPTIONS_DATA_DIRS)
+  if(NOT BOUT_EXAMPLE_OPTIONS_DATA_DIRS)
     bout_copy_file(data/BOUT.inp)
   else()
-    foreach (DATA_DIR IN LISTS BOUT_EXAMPLE_OPTIONS_DATA_DIRS)
+    foreach(DATA_DIR IN LISTS BOUT_EXAMPLE_OPTIONS_DATA_DIRS)
       bout_copy_file(${DATA_DIR}/BOUT.inp)
     endforeach()
   endif()
 
   # Copy any other needed files
-  if (BOUT_EXAMPLE_OPTIONS_EXTRA_FILES)
-    foreach (FILE ${BOUT_EXAMPLE_OPTIONS_EXTRA_FILES})
+  if(BOUT_EXAMPLE_OPTIONS_EXTRA_FILES)
+    foreach(FILE ${BOUT_EXAMPLE_OPTIONS_EXTRA_FILES})
       bout_copy_file("${FILE}")
     endforeach()
   endif()
@@ -125,7 +136,6 @@ function(bout_add_example EXAMPLENAME)
   add_dependencies(build-all-examples ${EXAMPLENAME})
 endfunction()
 
-
 # Add a new integrated or MMS test. By default, the executable is
 # named like the first source, stripped of its file extension. If no
 # sources are given, then you probably at least want to set
@@ -163,37 +173,51 @@ endfunction()
 function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
   set(options USE_RUNTEST USE_DATA_BOUT_INP)
   set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME)
-  set(multiValueArgs SOURCES EXTRA_FILES REQUIRES CONFLICTS TESTARGS EXTRA_DEPENDS)
-  cmake_parse_arguments(BOUT_TEST_OPTIONS "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+  set(multiValueArgs SOURCES EXTRA_FILES REQUIRES CONFLICTS TESTARGS
+                     EXTRA_DEPENDS
+  )
+  cmake_parse_arguments(
+    BOUT_TEST_OPTIONS "${options}" "${oneValueArgs}" "${multiValueArgs}"
+    ${ARGN}
+  )
 
-  bout_handle_requires_conflicts("test" ${TESTNAME}
+  bout_handle_requires_conflicts(
+    "test" ${TESTNAME}
     REQUIRES ${BOUT_TEST_OPTIONS_REQUIRES}
     CONFLICTS ${BOUT_TEST_OPTIONS_CONFLICTS}
-    )
+  )
 
-  if (BOUT_TEST_OPTIONS_SOURCES)
+  if(BOUT_TEST_OPTIONS_SOURCES)
     # We've got some sources, so compile them into an executable and
     # link against BOUT++
     add_executable(${TESTNAME} ${BOUT_TEST_OPTIONS_SOURCES})
     target_link_libraries(${TESTNAME} bout++)
-    target_include_directories(${TESTNAME} PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>)
+    target_include_directories(
+      ${TESTNAME} PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+    )
     set_target_properties(${TESTNAME} PROPERTIES FOLDER tests/integrated)
 
     # Set the name of the executable. We either take it as an option,
     # or use the first source file, stripping the file suffix
-    if (BOUT_TEST_OPTIONS_EXECUTABLE_NAME)
-      set_target_properties(${TESTNAME} PROPERTIES OUTPUT_NAME ${BOUT_TEST_OPTIONS_EXECUTABLE_NAME})
+    if(BOUT_TEST_OPTIONS_EXECUTABLE_NAME)
+      set_target_properties(
+        ${TESTNAME} PROPERTIES OUTPUT_NAME ${BOUT_TEST_OPTIONS_EXECUTABLE_NAME}
+      )
     else()
       # If more than one source file, just get the first one
       list(LENGTH ${BOUT_TEST_OPTIONS_SOURCES} BOUT_SOURCES_LENGTH)
-      if (BOUT_SOURCES_LENGTH GREATER 0)
+      if(BOUT_SOURCES_LENGTH GREATER 0)
         list(GET ${BOUT_TEST_OPTIONS_SOURCES} 0 BOUT_TEST_FIRST_SOURCE)
       else()
         set(BOUT_TEST_FIRST_SOURCE ${BOUT_TEST_OPTIONS_SOURCES})
       endif()
       # Strip the directory and file extension from the source file
-      get_filename_component(BOUT_TEST_EXECUTABLE_NAME ${BOUT_TEST_FIRST_SOURCE} NAME_WE)
-      set_target_properties(${TESTNAME} PROPERTIES OUTPUT_NAME ${BOUT_TEST_EXECUTABLE_NAME})
+      get_filename_component(
+        BOUT_TEST_EXECUTABLE_NAME ${BOUT_TEST_FIRST_SOURCE} NAME_WE
+      )
+      set_target_properties(
+        ${TESTNAME} PROPERTIES OUTPUT_NAME ${BOUT_TEST_EXECUTABLE_NAME}
+      )
     endif()
 
     # Add the test to the build-check-integrated-tests target
@@ -202,54 +226,57 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
     add_custom_target(${TESTNAME})
   endif()
 
-  if (BOUT_TEST_OPTIONS_DOWNLOAD)
-    if (NOT BOUT_TEST_OPTIONS_DOWNLOAD_NAME)
+  if(BOUT_TEST_OPTIONS_DOWNLOAD)
+    if(NOT BOUT_TEST_OPTIONS_DOWNLOAD_NAME)
       message(FATAL_ERROR "We need DOWNLOAD_NAME if we should DOWNLOAD!")
     endif()
-    set(output )
-    add_custom_command(OUTPUT ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
-      COMMAND wget ${BOUT_TEST_OPTIONS_DOWNLOAD} -O ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME} $ENV{BOUT_TEST_DOWNLOAD_FLAGS}
+    set(output)
+    add_custom_command(
+      OUTPUT ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
+      COMMAND wget ${BOUT_TEST_OPTIONS_DOWNLOAD} -O
+              ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME} $ENV{BOUT_TEST_DOWNLOAD_FLAGS}
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
       COMMENT "Downloading ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}"
-      )
-    add_custom_target(download_test_data DEPENDS ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME})
+    )
+    add_custom_target(
+      download_test_data DEPENDS ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
+    )
     add_dependencies(${TESTNAME} download_test_data)
   endif()
 
-  if (BOUT_TEST_OPTIONS_EXTRA_DEPENDS)
+  if(BOUT_TEST_OPTIONS_EXTRA_DEPENDS)
     add_dependencies(${TESTNAME} ${BOUT_TEST_OPTIONS_EXTRA_DEPENDS})
   endif()
 
-  if (NOT BOUT_TEST_OPTIONS_PROCESSORS)
+  if(NOT BOUT_TEST_OPTIONS_PROCESSORS)
     set(BOUT_TEST_OPTIONS_PROCESSORS 1)
   endif()
 
   # Set the actual test command
-  if (BOUT_TEST_OPTIONS_USE_RUNTEST)
-    add_test(NAME ${TESTNAME}
-      COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS}
-      )
-    set_tests_properties(${TESTNAME} PROPERTIES
-      ENVIRONMENT PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
-      )
+  if(BOUT_TEST_OPTIONS_USE_RUNTEST)
+    add_test(NAME ${TESTNAME} COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS})
+    set_tests_properties(
+      ${TESTNAME} PROPERTIES ENVIRONMENT
+                             PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
+    )
     bout_copy_file(runtest)
   else()
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()
 
-  set_tests_properties(${TESTNAME} PROPERTIES
-    PROCESSORS ${BOUT_TEST_OPTIONS_PROCESSORS}
-    PROCESSOR_AFFINITY ON
-    )
+  set_tests_properties(
+    ${TESTNAME} PROPERTIES PROCESSORS ${BOUT_TEST_OPTIONS_PROCESSORS}
+                           PROCESSOR_AFFINITY ON
+  )
 
   # Copy the input file if needed
-  if (BOUT_TEST_OPTIONS_USE_DATA_BOUT_INP)
+  if(BOUT_TEST_OPTIONS_USE_DATA_BOUT_INP)
     bout_copy_file(data/BOUT.inp)
   endif()
 
   # Copy any other needed files
-  if (BOUT_TEST_OPTIONS_EXTRA_FILES)
-    foreach (FILE ${BOUT_TEST_OPTIONS_EXTRA_FILES})
+  if(BOUT_TEST_OPTIONS_EXTRA_FILES)
+    foreach(FILE ${BOUT_TEST_OPTIONS_EXTRA_FILES})
       bout_copy_file("${FILE}")
     endforeach()
   endif()
@@ -257,7 +284,9 @@ endfunction()
 
 # Add a new integrated test. See `bout_add_integrated_or_mms_test` for arguments
 function(bout_add_integrated_test TESTNAME)
-  bout_add_integrated_or_mms_test(build-check-integrated-tests ${TESTNAME} ${ARGV})
+  bout_add_integrated_or_mms_test(
+    build-check-integrated-tests ${TESTNAME} ${ARGV}
+  )
 endfunction()
 
 # Add a new MMS test. See `bout_add_integrated_or_mms_test` for arguments
@@ -270,13 +299,18 @@ endfunction()
 # Taken from https://github.com/conan-io/conan/issues/2125#issuecomment-351176653
 function(bout_add_library_alias dst src)
   add_library(${dst} INTERFACE IMPORTED)
-  foreach(name INTERFACE_LINK_LIBRARIES INTERFACE_INCLUDE_DIRECTORIES INTERFACE_COMPILE_DEFINITIONS INTERFACE_COMPILE_OPTIONS)
-    get_property(value TARGET ${src} PROPERTY ${name} )
+  foreach(name INTERFACE_LINK_LIBRARIES INTERFACE_INCLUDE_DIRECTORIES
+               INTERFACE_COMPILE_DEFINITIONS INTERFACE_COMPILE_OPTIONS
+  )
+    get_property(
+      value
+      TARGET ${src}
+      PROPERTY ${name}
+    )
     set_property(TARGET ${dst} PROPERTY ${name} ${value})
   endforeach()
 endfunction()
 
-
 # Call nx-config with an argument, and append the resulting path to a list
 # Taken from https://github.com/LiamBindle/geos-chem/blob/feature/CMake/CMakeScripts/FindNetCDF.cmake
 function(bout_inspect_netcdf_config VAR NX_CONFIG ARG)
@@ -285,7 +319,10 @@ function(bout_inspect_netcdf_config VAR NX_CONFIG ARG)
     OUTPUT_VARIABLE NX_CONFIG_OUTPUT
     OUTPUT_STRIP_TRAILING_WHITESPACE
   )
-  if (NX_CONFIG_OUTPUT)
-    set(${VAR} ${NX_CONFIG_OUTPUT} PARENT_SCOPE)
+  if(NX_CONFIG_OUTPUT)
+    set(${VAR}
+        ${NX_CONFIG_OUTPUT}
+        PARENT_SCOPE
+    )
   endif()
 endfunction()
diff --git a/cmake/BuildType.cmake b/cmake/BuildType.cmake
index c4dd7ff73d..7aced6d8ad 100644
--- a/cmake/BuildType.cmake
+++ b/cmake/BuildType.cmake
@@ -12,10 +12,17 @@
 set(default_build_type "RelWithDebInfo")
 
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
-  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
-  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
-      STRING "Choose the type of build." FORCE)
+  message(
+    STATUS
+      "Setting build type to '${default_build_type}' as none was specified."
+  )
+  set(CMAKE_BUILD_TYPE
+      "${default_build_type}"
+      CACHE STRING "Choose the type of build." FORCE
+  )
   # Set the possible values of build type for cmake-gui
-  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
-    "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+  set_property(
+    CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel"
+                                    "RelWithDebInfo"
+  )
 endif()
diff --git a/cmake/CorrectWindowsPaths.cmake b/cmake/CorrectWindowsPaths.cmake
index 09bcdd67dc..cd2ac529ca 100644
--- a/cmake/CorrectWindowsPaths.cmake
+++ b/cmake/CorrectWindowsPaths.cmake
@@ -4,11 +4,9 @@
 #  This uses the command cygpath (provided by cygwin) to convert
 #  unix-style paths into paths useable by cmake on windows
 
-macro (CONVERT_CYGWIN_PATH _path)
-  if (WIN32)
-    EXECUTE_PROCESS(COMMAND cygpath.exe -m ${${_path}}
-      OUTPUT_VARIABLE ${_path})
-    string (STRIP ${${_path}} ${_path})
-  endif (WIN32)
-endmacro (CONVERT_CYGWIN_PATH)
-
+macro(CONVERT_CYGWIN_PATH _path)
+  if(WIN32)
+    execute_process(COMMAND cygpath.exe -m ${${_path}} OUTPUT_VARIABLE ${_path})
+    string(STRIP ${${_path}} ${_path})
+  endif(WIN32)
+endmacro(CONVERT_CYGWIN_PATH)
diff --git a/cmake/EnableCXXWarningIfSupport.cmake b/cmake/EnableCXXWarningIfSupport.cmake
index 6d7a64265f..9b9ae52af5 100644
--- a/cmake/EnableCXXWarningIfSupport.cmake
+++ b/cmake/EnableCXXWarningIfSupport.cmake
@@ -5,7 +5,7 @@ function(target_enable_cxx_warning_if_supported TARGET)
   set(multiValueArgs FLAGS)
   cmake_parse_arguments(TARGET_ENABLE_WARNING "" "" "${multiValueArgs}" ${ARGN})
 
-  foreach (WARNING_FLAG IN LISTS TARGET_ENABLE_WARNING_FLAGS)
+  foreach(WARNING_FLAG IN LISTS TARGET_ENABLE_WARNING_FLAGS)
     string(REPLACE "-" "_" WARNING_FLAG_STRIPPED ${WARNING_FLAG})
 
     # Note that gcc ignores unknown flags of the form "-Wno-warning"
@@ -13,31 +13,33 @@ function(target_enable_cxx_warning_if_supported TARGET)
     # positive form as an additional flag which it will choke on (if
     # it doesn't exist). See: https://gcc.gnu.org/wiki/FAQ#wnowarning
     string(FIND ${WARNING_FLAG} "Wno-" NEGATIVE_FLAG_${WARNING_FLAG_STRIPPED})
-    if (NEGATIVE_FLAG_${WARNING_FLAG_STRIPPED} EQUAL -1)
+    if(NEGATIVE_FLAG_${WARNING_FLAG_STRIPPED} EQUAL -1)
       set(IS_NEGATIVE_FLAG_${WARNING_FLAG_STRIPPED} FALSE)
     else()
       set(IS_NEGATIVE_FLAG_${WARNING_FLAG_STRIPPED} TRUE)
     endif()
 
-    if (IS_NEGATIVE_FLAG_${WARNING_FLAG_STRIPPED})
+    if(IS_NEGATIVE_FLAG_${WARNING_FLAG_STRIPPED})
       set(ORIGINAL_FLAG ${WARNING_FLAG})
       string(REPLACE "no-" "" WARNING_FLAG ${WARNING_FLAG})
       message(STATUS "Found negative flag: ${ORIGINAL_FLAG}\n"
-        "   replaced with ${WARNING_FLAG}")
+                     "   replaced with ${WARNING_FLAG}"
+      )
     endif()
 
     check_cxx_compiler_flag(${WARNING_FLAG} HAS_FLAG_${WARNING_FLAG_STRIPPED})
 
-    if (IS_NEGATIVE_FLAG_${WARNING_FLAG_STRIPPED})
+    if(IS_NEGATIVE_FLAG_${WARNING_FLAG_STRIPPED})
       set(WARNING_FLAG ${ORIGINAL_FLAG})
     endif()
 
-    if (HAS_FLAG_${WARNING_FLAG_STRIPPED})
-      message(STATUS "Warning flag is supported by compiler: ${WARNING_FLAG}")      
+    if(HAS_FLAG_${WARNING_FLAG_STRIPPED})
+      message(STATUS "Warning flag is supported by compiler: ${WARNING_FLAG}")
 
-      target_compile_options(${TARGET} PRIVATE 
-        $<$<NOT:$<COMPILE_LANGUAGE:CUDA>>:${WARNING_FLAG} >
-        $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=${WARNING_FLAG} >
+      target_compile_options(
+        ${TARGET}
+        PRIVATE $<$<NOT:$<COMPILE_LANGUAGE:CUDA>>:${WARNING_FLAG} >
+                $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=${WARNING_FLAG} >
       )
     else()
       message(STATUS "Warning flag not supported by compiler: ${WARNING_FLAG}")
diff --git a/cmake/FindBash.cmake b/cmake/FindBash.cmake
index feb195f9f1..faa5303646 100644
--- a/cmake/FindBash.cmake
+++ b/cmake/FindBash.cmake
@@ -11,27 +11,30 @@
 #   Bash_VERSION - Bash version
 #   Bash_EXECUTABLE - Path to bash executable
 
-find_program(Bash_EXECUTABLE
-  bash
-  )
+find_program(Bash_EXECUTABLE bash)
 
 mark_as_advanced(Bash_EXECUTABLE)
 
-if (Bash_EXECUTABLE)
-  execute_process(COMMAND "${Bash_EXECUTABLE}" --version
+if(Bash_EXECUTABLE)
+  execute_process(
+    COMMAND "${Bash_EXECUTABLE}" --version
     RESULT_VARIABLE _bash_runs
     OUTPUT_VARIABLE _bash_stdout
     OUTPUT_STRIP_TRAILING_WHITESPACE
-    )
+  )
   if(_bash_stdout MATCHES "version ([0-9]+\\.[0-9]+\\.[0-9]+)")
     set(Bash_VERSION "${CMAKE_MATCH_1}")
   else()
-    message (WARNING "Failed to determine version of Bash interpreter (${Bash_EXECUTABLE})! Error:\n${_Bash_STDERR}")
+    message(
+      WARNING
+        "Failed to determine version of Bash interpreter (${Bash_EXECUTABLE})! Error:\n${_Bash_STDERR}"
+    )
   endif()
 endif()
 
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(Bash
+find_package_handle_standard_args(
+  Bash
   VERSION_VAR Bash_VERSION
   REQUIRED_VARS Bash_EXECUTABLE
-  )
+)
diff --git a/cmake/FindClangFormat.cmake b/cmake/FindClangFormat.cmake
index c940002c3b..cd5ca5865b 100644
--- a/cmake/FindClangFormat.cmake
+++ b/cmake/FindClangFormat.cmake
@@ -3,27 +3,23 @@
 # Taken from https://github.com/ttroy50/cmake-examples commit 64bd54a
 # This file is under MIT Licence
 
-if (NOT ClangFormat_BIN_NAME)
+if(NOT ClangFormat_BIN_NAME)
   set(ClangFormat_BIN_NAME clang-format)
 endif()
 
 # if custom path check there first
-if (ClangFormat_ROOT_DIR)
-  find_program(ClangFormat_BIN
-    NAMES
-    ${ClangFormat_BIN_NAME}
-    PATHS
-    "${ClangFormat_ROOT_DIR}"
-    NO_DEFAULT_PATH)
+if(ClangFormat_ROOT_DIR)
+  find_program(
+    ClangFormat_BIN
+    NAMES ${ClangFormat_BIN_NAME}
+    PATHS "${ClangFormat_ROOT_DIR}"
+    NO_DEFAULT_PATH
+  )
 endif()
 
 find_program(ClangFormat_BIN NAMES ${ClangFormat_BIN_NAME})
 
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(
-  ClangFormat
-  DEFAULT_MSG
-  ClangFormat_BIN)
+find_package_handle_standard_args(ClangFormat DEFAULT_MSG ClangFormat_BIN)
 
-mark_as_advanced(
-  ClangFormat_BIN)
+mark_as_advanced(ClangFormat_BIN)
diff --git a/cmake/FindCython.cmake b/cmake/FindCython.cmake
index 3b98cde89e..5a58cf4335 100644
--- a/cmake/FindCython.cmake
+++ b/cmake/FindCython.cmake
@@ -10,20 +10,22 @@
 #   CYTHON_FOUND - true if Cython was found
 #   CYTHON_VERSION - Cython version
 
-execute_process(COMMAND ${Python3_EXECUTABLE} -c "import cython ; print(cython.__version__)"
+execute_process(
+  COMMAND ${Python3_EXECUTABLE} -c "import cython ; print(cython.__version__)"
   RESULT_VARIABLE _cython_runs
   OUTPUT_VARIABLE CYTHON_VERSION
   OUTPUT_STRIP_TRAILING_WHITESPACE
-  )
+)
 
-if (${_cython_runs} EQUAL 0)
+if(${_cython_runs} EQUAL 0)
   set(CYTHON_RUNS TRUE)
 else()
   set(CYTHON_RUNS FALSE)
 endif()
 
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(Cython
+find_package_handle_standard_args(
+  Cython
   VERSION_VAR CYTHON_VERSION
   REQUIRED_VARS CYTHON_RUNS
-  )
+)
diff --git a/cmake/FindFFTW.cmake b/cmake/FindFFTW.cmake
index e1940c687d..7ca5518a6f 100644
--- a/cmake/FindFFTW.cmake
+++ b/cmake/FindFFTW.cmake
@@ -24,72 +24,78 @@
 # ``FFTW_DEBUG``
 #   Set to TRUE to get extra debugging output
 
-if (FFTW_INCLUDE_DIRS)
+if(FFTW_INCLUDE_DIRS)
   # Already in cache, be silent
-  set (FFTW_FIND_QUIETLY TRUE)
-endif (FFTW_INCLUDE_DIRS)
+  set(FFTW_FIND_QUIETLY TRUE)
+endif(FFTW_INCLUDE_DIRS)
 
-if (EXISTS ${FFTW_ROOT})
+if(EXISTS ${FFTW_ROOT})
   # Make sure FFTW_ROOT is an absolute path by setting it as a 'FILEPATH'
-  set (FFTW_ROOT "" CACHE FILEPATH "Location of the FFTW library")
+  set(FFTW_ROOT
+      ""
+      CACHE FILEPATH "Location of the FFTW library"
+  )
 endif()
 
-find_program(FFTW_WISDOM "fftw-wisdom"
+find_program(
+  FFTW_WISDOM "fftw-wisdom"
   PATHS "${FFTW_ROOT}"
   PATH_SUFFIXES bin
   NO_DEFAULT_PATH
   DOC "Path to fftw-wisdom executable"
-  )
+)
 
-find_program(FFTW_WISDOM "fftw-wisdom"
-  DOC "Path to fftw-wisdom executable"
-  )
-if (FFTW_DEBUG)
+find_program(FFTW_WISDOM "fftw-wisdom" DOC "Path to fftw-wisdom executable")
+if(FFTW_DEBUG)
   message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " FFTW_WISDOM = ${FFTW_WISDOM}"
-    )
+                 " FFTW_WISDOM = ${FFTW_WISDOM}"
+  )
 endif()
 
 get_filename_component(FFTW_WISDOM_TMP "${FFTW_WISDOM}" DIRECTORY)
 get_filename_component(FFTW_HINT_DIR "${FFTW_WISDOM_TMP}" DIRECTORY)
 
-find_path(FFTW_INCLUDE_DIRS
+find_path(
+  FFTW_INCLUDE_DIRS
   NAMES fftw3.h
   DOC "FFTW include directory"
   HINTS "${FFTW_HINT_DIR}"
   PATH_SUFFIXES "include"
-  )
-if (FFTW_DEBUG)
+)
+if(FFTW_DEBUG)
   message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " FFTW_INCLUDE_DIRS = ${FFTW_INCLUDE_DIRS}"
-    " FFTW_HINT_DIR = ${FFTW_HINT_DIR}"
-    )
+                 " FFTW_INCLUDE_DIRS = ${FFTW_INCLUDE_DIRS}"
+                 " FFTW_HINT_DIR = ${FFTW_HINT_DIR}"
+  )
 endif()
 
-find_library (FFTW_LIBRARIES
+find_library(
+  FFTW_LIBRARIES
   NAMES fftw3
   DOC "FFTW library location"
   HINTS "${FFTW_HINT_DIR}"
   PATH_SUFFIXES "lib" "lib64"
-  )
-if (FFTW_DEBUG)
+)
+if(FFTW_DEBUG)
   message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " FFTW_LIBRARIES = ${FFTW_LIBRARIES}"
-    " FFTW_HINT_DIR = ${FFTW_HINT_DIR}"
-    )
+                 " FFTW_LIBRARIES = ${FFTW_LIBRARIES}"
+                 " FFTW_HINT_DIR = ${FFTW_HINT_DIR}"
+  )
 endif()
 
 # handle the QUIETLY and REQUIRED arguments and set FFTW_FOUND to TRUE if
 # all listed variables are TRUE
-include (FindPackageHandleStandardArgs)
-find_package_handle_standard_args (FFTW DEFAULT_MSG FFTW_LIBRARIES FFTW_INCLUDE_DIRS)
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(
+  FFTW DEFAULT_MSG FFTW_LIBRARIES FFTW_INCLUDE_DIRS
+)
 
-mark_as_advanced (FFTW_LIBRARIES FFTW_INCLUDE_DIRS)
+mark_as_advanced(FFTW_LIBRARIES FFTW_INCLUDE_DIRS)
 
-if (FFTW_FOUND AND NOT TARGET FFTW::FFTW)
+if(FFTW_FOUND AND NOT TARGET FFTW::FFTW)
   add_library(FFTW::FFTW UNKNOWN IMPORTED)
-  set_target_properties(FFTW::FFTW PROPERTIES
-    IMPORTED_LOCATION "${FFTW_LIBRARIES}"
-    INTERFACE_INCLUDE_DIRECTORIES "${FFTW_INCLUDE_DIRS}"
-    )
+  set_target_properties(
+    FFTW::FFTW PROPERTIES IMPORTED_LOCATION "${FFTW_LIBRARIES}"
+                          INTERFACE_INCLUDE_DIRECTORIES "${FFTW_INCLUDE_DIRS}"
+  )
 endif()
diff --git a/cmake/FindHYPRE.cmake b/cmake/FindHYPRE.cmake
index 1b9a5ca6f9..d2a1b4746c 100644
--- a/cmake/FindHYPRE.cmake
+++ b/cmake/FindHYPRE.cmake
@@ -6,54 +6,62 @@
 include(FindPackageHandleStandardArgs)
 
 find_package(HYPRE CONFIG QUIET)
-if (HYPRE_FOUND)
+if(HYPRE_FOUND)
   message(STATUS "Found HYPRE: ${HYPRE_VERSION}")
   return()
 endif()
 
-find_path(HYPRE_INCLUDE_DIR
+find_path(
+  HYPRE_INCLUDE_DIR
   NAMES HYPRE.h
-  DOC "HYPRE include directories"
-  REQUIRED
+  DOC "HYPRE include directories" REQUIRED
   PATH_SUFFIXES include include/hypre
 )
 
-find_library(HYPRE_LIBRARY
+find_library(
+  HYPRE_LIBRARY
   NAMES HYPRE
-  DOC "HYPRE library"
-  REQUIRED
+  DOC "HYPRE library" REQUIRED
   PATH_SUFFIXES lib64 lib
-  )
+)
 
-if (HYPRE_INCLUDE_DIR)
+if(HYPRE_INCLUDE_DIR)
   file(READ "${HYPRE_INCLUDE_DIR}/HYPRE_config.h" HYPRE_CONFIG_FILE)
-  string(REGEX MATCH ".*#define HYPRE_RELEASE_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*"
-    _ "${HYPRE_CONFIG_FILE}")
+  string(
+    REGEX MATCH
+          ".*#define HYPRE_RELEASE_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*"
+          _ "${HYPRE_CONFIG_FILE}"
+  )
   set(HYPRE_VERSION_MAJOR ${CMAKE_MATCH_1})
   set(HYPRE_VERSION_MINOR ${CMAKE_MATCH_2})
   set(HYPRE_VERSION_PATCH ${CMAKE_MATCH_3})
-  set(HYPRE_VERSION "${HYPRE_VERSION_MAJOR}.${HYPRE_VERSION_MINOR}.${HYPRE_VERSION_PATCH}")
+  set(HYPRE_VERSION
+      "${HYPRE_VERSION_MAJOR}.${HYPRE_VERSION_MINOR}.${HYPRE_VERSION_PATCH}"
+  )
 endif()
 
-if (HYPRE_DEBUG)
-  message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ]"
-     " HYPRE_ROOT = ${HYPRE_ROOT}"
-    " HYPRE_INCLUDE_DIR = ${HYPRE_INCLUDE_DIR}"
-    " HYPRE_LIBRARY = ${HYPRE_LIBRARY}"
-    )
+if(HYPRE_DEBUG)
+  message(
+    STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ]"
+           " HYPRE_ROOT = ${HYPRE_ROOT}"
+           " HYPRE_INCLUDE_DIR = ${HYPRE_INCLUDE_DIR}"
+           " HYPRE_LIBRARY = ${HYPRE_LIBRARY}"
+  )
 endif()
 
 mark_as_advanced(HYPRE_INCLUDE_DIR HYPRE_LIBRARY)
 
-find_package_handle_standard_args(HYPRE
+find_package_handle_standard_args(
+  HYPRE
   REQUIRED_VARS HYPRE_LIBRARY HYPRE_INCLUDE_DIR
   VERSION_VAR HYPRE_VERSION
-  )
+)
 
-if (HYPRE_FOUND AND NOT TARGET HYPRE::HYPRE)
+if(HYPRE_FOUND AND NOT TARGET HYPRE::HYPRE)
   add_library(HYPRE::HYPRE UNKNOWN IMPORTED)
-  set_target_properties(HYPRE::HYPRE PROPERTIES
-    IMPORTED_LOCATION "${HYPRE_LIBRARY}"
-    INTERFACE_INCLUDE_DIRECTORIES "${HYPRE_INCLUDE_DIR}"
-    )
+  set_target_properties(
+    HYPRE::HYPRE
+    PROPERTIES IMPORTED_LOCATION "${HYPRE_LIBRARY}"
+               INTERFACE_INCLUDE_DIRECTORIES "${HYPRE_INCLUDE_DIR}"
+  )
 endif()
diff --git a/cmake/FindLibuuid.cmake b/cmake/FindLibuuid.cmake
index 91880487a2..2492388b32 100644
--- a/cmake/FindLibuuid.cmake
+++ b/cmake/FindLibuuid.cmake
@@ -21,38 +21,41 @@
 # ``Libuuid_DEBUG``
 #   Set to TRUE to get extra debugging output
 
-include (FindPackageHandleStandardArgs)
+include(FindPackageHandleStandardArgs)
 
-if (WIN32)
+if(WIN32)
   find_package_handle_standard_args(Libuuid DEFAULT_MSG)
   return()
 endif()
 
-if (APPLE)
+if(APPLE)
   find_library(CFLIB CoreFoundation)
   find_package_handle_standard_args(Libuuid DEFAULT_MSG CFLIB)
   mark_as_advanced(${CFLIB})
 
-  if (Libuuid_FOUND AND NOT TARGET Libuuid::libuuid)
+  if(Libuuid_FOUND AND NOT TARGET Libuuid::libuuid)
     add_library(Libuuid::libuuid UNKNOWN IMPORTED)
-    set_target_properties(Libuuid::libuuid PROPERTIES
-      IMPORTED_LOCATION ${CFLIB}
-      )
+    set_target_properties(
+      Libuuid::libuuid PROPERTIES IMPORTED_LOCATION ${CFLIB}
+    )
   endif()
   return()
-endif ()
+endif()
 
 find_path(Libuuid_INCLUDE_DIRS uuid/uuid.h)
 find_library(Libuuid_LIBRARIES uuid)
 
-find_package_handle_standard_args(Libuuid DEFAULT_MSG Libuuid_LIBRARIES Libuuid_INCLUDE_DIRS)
+find_package_handle_standard_args(
+  Libuuid DEFAULT_MSG Libuuid_LIBRARIES Libuuid_INCLUDE_DIRS
+)
 
 mark_as_advanced(Libuuid_LIBRARIES Libuuid_INCLUDE_DIRS)
 
-if (Libuuid_FOUND AND NOT TARGET Libuuid::libuuid)
+if(Libuuid_FOUND AND NOT TARGET Libuuid::libuuid)
   add_library(Libuuid::libuuid UNKNOWN IMPORTED)
-  set_target_properties(Libuuid::libuuid PROPERTIES
-    IMPORTED_LOCATION "${Libuuid_LIBRARIES}"
-    INTERFACE_INCLUDE_DIRECTORIES "${Libuuid_INCLUDE_DIRS}"
-    )
+  set_target_properties(
+    Libuuid::libuuid
+    PROPERTIES IMPORTED_LOCATION "${Libuuid_LIBRARIES}"
+               INTERFACE_INCLUDE_DIRECTORIES "${Libuuid_INCLUDE_DIRS}"
+  )
 endif()
diff --git a/cmake/FindNumpy.cmake b/cmake/FindNumpy.cmake
index b6de6e3e35..cfdbdcc96c 100644
--- a/cmake/FindNumpy.cmake
+++ b/cmake/FindNumpy.cmake
@@ -11,46 +11,57 @@
 #   Numpy_VERSION
 #   Numpy_INCLUDE_DIR
 
-
 find_package(Python3 3.6 COMPONENTS Interpreter Development)
 
-if (NOT Python3_FOUND)
-  message(STATUS "Could not find numpy as python was not found. Maybe the developement package is missing?")
+if(NOT Python3_FOUND)
+  message(
+    STATUS
+      "Could not find numpy as python was not found. Maybe the developement package is missing?"
+  )
   set(Numpy_FOUND ${Python3_FOUND})
   return()
 endif()
 
-if (NOT Numpy_FOUND)
-  execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.__version__)"
+if(NOT Numpy_FOUND)
+  execute_process(
+    COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.__version__)"
     OUTPUT_STRIP_TRAILING_WHITESPACE
     OUTPUT_VARIABLE Numpy_VERSION
-    )
-  execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.get_include())"
+  )
+  execute_process(
+    COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.get_include())"
     OUTPUT_STRIP_TRAILING_WHITESPACE
     OUTPUT_VARIABLE _numpy_include_dirs
-    )
+  )
 endif()
 
-if (Numpy_DEBUG)
-  message(STATUS "Looking for numpy headers in: ${_numpy_include_dirs} ${Python3_INCLUDE_DIRS}")
+if(Numpy_DEBUG)
+  message(
+    STATUS
+      "Looking for numpy headers in: ${_numpy_include_dirs} ${Python3_INCLUDE_DIRS}"
+  )
 endif()
 
-find_path(Numpy_INCLUDE_DIR
-  numpy/arrayobject.h
+find_path(
+  Numpy_INCLUDE_DIR numpy/arrayobject.h
   PATHS "${_numpy_include_dirs}" "${Python3_INCLUDE_DIRS}"
   PATH_SUFFIXES numpy/core/include
-  )
+)
 
-if (NOT Numpy_INCLUDE_DIR)
-  message(STATUS "Numpy headers not found -- do you need to install the development package?")
+if(NOT Numpy_INCLUDE_DIR)
+  message(
+    STATUS
+      "Numpy headers not found -- do you need to install the development package?"
+  )
 endif()
 
 set(Numpy_INCLUDE_DIRS ${Numpy_INCLUDE_DIR})
 
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(Numpy
+find_package_handle_standard_args(
+  Numpy
   VERSION_VAR Numpy_VERSION
   REQUIRED_VARS Numpy_INCLUDE_DIR
-  )
+)
 
 mark_as_advanced(Numpy_INCLUDE_DIR)
diff --git a/cmake/FindPETSc.cmake b/cmake/FindPETSc.cmake
index c93d464673..f0595a7a68 100644
--- a/cmake/FindPETSc.cmake
+++ b/cmake/FindPETSc.cmake
@@ -25,23 +25,23 @@
 
 find_package(MPI REQUIRED)
 
-set(PETSC_VALID_COMPONENTS
-  C
-  CXX)
+set(PETSC_VALID_COMPONENTS C CXX)
 
 if(NOT PETSc_FIND_COMPONENTS)
-  get_property (_enabled_langs GLOBAL PROPERTY ENABLED_LANGUAGES)
-  if ("C" IN_LIST _enabled_langs)
+  get_property(_enabled_langs GLOBAL PROPERTY ENABLED_LANGUAGES)
+  if("C" IN_LIST _enabled_langs)
     set(PETSC_LANGUAGE_BINDINGS "C")
-  else ()
+  else()
     set(PETSC_LANGUAGE_BINDINGS "CXX")
-  endif ()
+  endif()
 else()
   # Right now, this is designed for compatability with the --with-clanguage option, so
   # only allow one item in the components list.
   list(LENGTH ${PETSc_FIND_COMPONENTS} components_length)
   if(${components_length} GREATER 1)
-    message(FATAL_ERROR "Only one component for PETSc is allowed to be specified")
+    message(
+      FATAL_ERROR "Only one component for PETSc is allowed to be specified"
+    )
   endif()
   # This is a stub for allowing multiple components should that time ever come. Perhaps
   # to also test Fortran bindings?
@@ -61,218 +61,328 @@ if(NOT PETSC_DIR)
   endif()
 endif()
 
-function (petsc_get_version)
-  if (EXISTS "${PETSC_DIR}/include/petscversion.h")
-    file (STRINGS "${PETSC_DIR}/include/petscversion.h" vstrings REGEX "#define PETSC_VERSION_(RELEASE|MAJOR|MINOR|SUBMINOR|PATCH) ")
-    foreach (line ${vstrings})
-      string (REGEX REPLACE " +" ";" fields ${line}) # break line into three fields (the first is always "#define")
-      list (GET fields 1 var)
-      list (GET fields 2 val)
-      set (${var} ${val} PARENT_SCOPE)
-      set (${var} ${val})         # Also in local scope so we have access below
-    endforeach ()
-    if (PETSC_VERSION_RELEASE)
-      if ($(PETSC_VERSION_PATCH) GREATER 0)
-        set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}p${PETSC_VERSION_PATCH}" CACHE INTERNAL "PETSc version")
-      else ()
-        set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}" CACHE INTERNAL "PETSc version")
-      endif ()
-    else ()
+function(petsc_get_version)
+  if(EXISTS "${PETSC_DIR}/include/petscversion.h")
+    file(STRINGS "${PETSC_DIR}/include/petscversion.h" vstrings
+         REGEX "#define PETSC_VERSION_(RELEASE|MAJOR|MINOR|SUBMINOR|PATCH) "
+    )
+    foreach(line ${vstrings})
+      string(REGEX REPLACE " +" ";" fields ${line}
+      )# break line into three fields (the first is always "#define")
+      list(GET fields 1 var)
+      list(GET fields 2 val)
+      set(${var}
+          ${val}
+          PARENT_SCOPE
+      )
+      set(${var} ${val}) # Also in local scope so we have access below
+    endforeach()
+    if(PETSC_VERSION_RELEASE)
+      if($(PETSC_VERSION_PATCH) GREATER 0)
+        set(PETSC_VERSION
+            "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}p${PETSC_VERSION_PATCH}"
+            CACHE INTERNAL "PETSc version"
+        )
+      else()
+        set(PETSC_VERSION
+            "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}"
+            CACHE INTERNAL "PETSc version"
+        )
+      endif()
+    else()
       # make dev version compare higher than any patch level of a released version
-      set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}.99" CACHE INTERNAL "PETSc version")
-    endif ()
-  else ()
-    message (SEND_ERROR "PETSC_DIR can not be used, ${PETSC_DIR}/include/petscversion.h does not exist")
-  endif ()
-endfunction ()
+      set(PETSC_VERSION
+          "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}.99"
+          CACHE INTERNAL "PETSc version"
+      )
+    endif()
+  else()
+    message(
+      SEND_ERROR
+        "PETSC_DIR can not be used, ${PETSC_DIR}/include/petscversion.h does not exist"
+    )
+  endif()
+endfunction()
 
 # Debian uses versioned paths e.g /usr/lib/petscdir/3.5/
-file (GLOB DEB_PATHS "/usr/lib/petscdir/*")
+file(GLOB DEB_PATHS "/usr/lib/petscdir/*")
 
-find_path (PETSC_DIR include/petsc.h
+find_path(
+  PETSC_DIR include/petsc.h
   HINTS ENV PETSC_DIR
-  PATHS
-  /usr/lib/petsc
-  # Debian paths
-  ${DEB_PATHS}
-  # Arch Linux path
-  /opt/petsc/linux-c-opt
-  # MacPorts path
-  /opt/local/lib/petsc
-  $ENV{HOME}/petsc
-  DOC "PETSc Directory")
-
-find_program (MAKE_EXECUTABLE NAMES make gmake)
-
-if (PETSC_DIR AND NOT PETSC_ARCH)
-  set (_petsc_arches
-    $ENV{PETSC_ARCH}                   # If set, use environment variable first
-    linux-gnu-c-debug linux-gnu-c-opt  # Debian defaults
-    x86_64-unknown-linux-gnu i386-unknown-linux-gnu)
-  set (petscconf "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
-  foreach (arch ${_petsc_arches})
-    if (NOT PETSC_ARCH)
-      find_path (petscconf petscconf.h
+  PATHS /usr/lib/petsc
+        # Debian paths
+        ${DEB_PATHS}
+        # Arch Linux path
+        /opt/petsc/linux-c-opt
+        # MacPorts path
+        /opt/local/lib/petsc
+        $ENV{HOME}/petsc
+  DOC "PETSc Directory"
+)
+
+find_program(MAKE_EXECUTABLE NAMES make gmake)
+
+if(PETSC_DIR AND NOT PETSC_ARCH)
+  set(_petsc_arches
+      $ENV{PETSC_ARCH} # If set, use environment variable first
+      linux-gnu-c-debug linux-gnu-c-opt # Debian defaults
+      x86_64-unknown-linux-gnu i386-unknown-linux-gnu
+  )
+  set(petscconf
+      "NOTFOUND"
+      CACHE FILEPATH "Cleared" FORCE
+  )
+  foreach(arch ${_petsc_arches})
+    if(NOT PETSC_ARCH)
+      find_path(
+        petscconf petscconf.h
         HINTS ${PETSC_DIR}
         PATH_SUFFIXES ${arch}/include bmake/${arch}
-        NO_DEFAULT_PATH)
-      if (petscconf)
-        set (PETSC_ARCH "${arch}" CACHE STRING "PETSc build architecture")
-      endif (petscconf)
-    endif (NOT PETSC_ARCH)
-  endforeach (arch)
-  set (petscconf "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
-endif (PETSC_DIR AND NOT PETSC_ARCH)
-
-set (petsc_slaves LIBRARIES_SYS LIBRARIES_VEC LIBRARIES_MAT LIBRARIES_DM LIBRARIES_KSP LIBRARIES_SNES LIBRARIES_TS
-  INCLUDE_DIR INCLUDE_CONF)
-include (FindPackageMultipass)
-find_package_multipass (PETSc petsc_config_current
-  STATES DIR ARCH
-  DEPENDENTS INCLUDES LIBRARIES COMPILER MPIEXEC ${petsc_slaves})
+        NO_DEFAULT_PATH
+      )
+      if(petscconf)
+        set(PETSC_ARCH
+            "${arch}"
+            CACHE STRING "PETSc build architecture"
+        )
+      endif(petscconf)
+    endif(NOT PETSC_ARCH)
+  endforeach(arch)
+  set(petscconf
+      "NOTFOUND"
+      CACHE INTERNAL "Scratch variable" FORCE
+  )
+endif(PETSC_DIR AND NOT PETSC_ARCH)
+
+set(petsc_slaves
+    LIBRARIES_SYS
+    LIBRARIES_VEC
+    LIBRARIES_MAT
+    LIBRARIES_DM
+    LIBRARIES_KSP
+    LIBRARIES_SNES
+    LIBRARIES_TS
+    INCLUDE_DIR
+    INCLUDE_CONF
+)
+include(FindPackageMultipass)
+find_package_multipass(
+  PETSc
+  petsc_config_current
+  STATES
+  DIR
+  ARCH
+  DEPENDENTS
+  INCLUDES
+  LIBRARIES
+  COMPILER
+  MPIEXEC
+  ${petsc_slaves}
+)
 
 # Determine whether the PETSc layout is old-style (through 2.3.3) or
 # new-style (>= 3.0.0)
-if (EXISTS "${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/petscvariables") # > 3.5
-  set (petsc_conf_rules "${PETSC_DIR}/lib/petsc/conf/rules")
-  set (petsc_conf_variables "${PETSC_DIR}/lib/petsc/conf/variables")
-elseif (EXISTS "${PETSC_DIR}/${PETSC_ARCH}/include/petscconf.h")   # > 2.3.3
-  set (petsc_conf_rules "${PETSC_DIR}/conf/rules")
-  set (petsc_conf_variables "${PETSC_DIR}/conf/variables")
-elseif (EXISTS "${PETSC_DIR}/bmake/${PETSC_ARCH}/petscconf.h") # <= 2.3.3
-  set (petsc_conf_rules "${PETSC_DIR}/bmake/common/rules")
-  set (petsc_conf_variables "${PETSC_DIR}/bmake/common/variables")
-elseif (PETSC_DIR)
-  message (SEND_ERROR "The pair PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} do not specify a valid PETSc installation")
-endif ()
-
-if (petsc_conf_rules AND petsc_conf_variables AND NOT petsc_config_current)
+if(EXISTS "${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/petscvariables") # > 3.5
+  set(petsc_conf_rules "${PETSC_DIR}/lib/petsc/conf/rules")
+  set(petsc_conf_variables "${PETSC_DIR}/lib/petsc/conf/variables")
+elseif(EXISTS "${PETSC_DIR}/${PETSC_ARCH}/include/petscconf.h") # > 2.3.3
+  set(petsc_conf_rules "${PETSC_DIR}/conf/rules")
+  set(petsc_conf_variables "${PETSC_DIR}/conf/variables")
+elseif(EXISTS "${PETSC_DIR}/bmake/${PETSC_ARCH}/petscconf.h") # <= 2.3.3
+  set(petsc_conf_rules "${PETSC_DIR}/bmake/common/rules")
+  set(petsc_conf_variables "${PETSC_DIR}/bmake/common/variables")
+elseif(PETSC_DIR)
+  message(
+    SEND_ERROR
+      "The pair PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} do not specify a valid PETSc installation"
+  )
+endif()
+
+if(petsc_conf_rules
+   AND petsc_conf_variables
+   AND NOT petsc_config_current
+)
   petsc_get_version()
 
   # Put variables into environment since they are needed to get
   # configuration (petscvariables) in the PETSc makefile
-  set (ENV{PETSC_DIR} "${PETSC_DIR}")
-  set (ENV{PETSC_ARCH} "${PETSC_ARCH}")
+  set(ENV{PETSC_DIR} "${PETSC_DIR}")
+  set(ENV{PETSC_ARCH} "${PETSC_ARCH}")
 
   # A temporary makefile to probe the PETSc configuration
-  set (petsc_config_makefile "${PROJECT_BINARY_DIR}/Makefile.petsc")
-  file (WRITE "${petsc_config_makefile}"
-"## This file was autogenerated by FindPETSc.cmake
+  set(petsc_config_makefile "${PROJECT_BINARY_DIR}/Makefile.petsc")
+  file(
+    WRITE "${petsc_config_makefile}"
+    "## This file was autogenerated by FindPETSc.cmake
 # PETSC_DIR  = ${PETSC_DIR}
 # PETSC_ARCH = ${PETSC_ARCH}
 include ${petsc_conf_rules}
 include ${petsc_conf_variables}
 show :
 \t-@echo -n \${\${VARIABLE}}
-")
-
-  macro (PETSC_GET_VARIABLE name var)
-    set (${var} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
-    execute_process (COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${petsc_config_makefile} show VARIABLE=${name}
+"
+  )
+
+  macro(PETSC_GET_VARIABLE name var)
+    set(${var}
+        "NOTFOUND"
+        CACHE INTERNAL "Cleared" FORCE
+    )
+    execute_process(
+      COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f
+              ${petsc_config_makefile} show VARIABLE=${name}
       OUTPUT_VARIABLE ${var}
-      RESULT_VARIABLE petsc_return)
-  endmacro (PETSC_GET_VARIABLE)
-  petsc_get_variable (PETSC_LIB_DIR            petsc_lib_dir)
-  petsc_get_variable (PETSC_EXTERNAL_LIB_BASIC petsc_libs_external)
-  petsc_get_variable (PETSC_CCPPFLAGS          petsc_cpp_line)
-  petsc_get_variable (PETSC_INCLUDE            petsc_include)
-  petsc_get_variable (PCC                      petsc_cc)
-  petsc_get_variable (PCC_FLAGS                petsc_cc_flags)
-  petsc_get_variable (MPIEXEC                  petsc_mpiexec)
+      RESULT_VARIABLE petsc_return
+    )
+  endmacro(PETSC_GET_VARIABLE)
+  petsc_get_variable(PETSC_LIB_DIR petsc_lib_dir)
+  petsc_get_variable(PETSC_EXTERNAL_LIB_BASIC petsc_libs_external)
+  petsc_get_variable(PETSC_CCPPFLAGS petsc_cpp_line)
+  petsc_get_variable(PETSC_INCLUDE petsc_include)
+  petsc_get_variable(PCC petsc_cc)
+  petsc_get_variable(PCC_FLAGS petsc_cc_flags)
+  petsc_get_variable(MPIEXEC petsc_mpiexec)
   # We are done with the temporary Makefile, calling PETSC_GET_VARIABLE after this point is invalid!
-  file (REMOVE ${petsc_config_makefile})
+  file(REMOVE ${petsc_config_makefile})
 
-  include (ResolveCompilerPaths)
+  include(ResolveCompilerPaths)
   # Extract include paths and libraries from compile command line
-  resolve_includes (petsc_includes_all "${petsc_cpp_line}")
+  resolve_includes(petsc_includes_all "${petsc_cpp_line}")
 
   #on windows we need to make sure we're linking against the right
   #runtime library
-  if (WIN32)
-    if (petsc_cc_flags MATCHES "-MT")
+  if(WIN32)
+    if(petsc_cc_flags MATCHES "-MT")
       set(using_md False)
-      foreach(flag_var
-          CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-          CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO
-          CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
-          CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO)
+      foreach(
+        flag_var
+        CMAKE_C_FLAGS
+        CMAKE_C_FLAGS_DEBUG
+        CMAKE_C_FLAGS_RELEASE
+        CMAKE_C_FLAGS_MINSIZEREL
+        CMAKE_C_FLAGS_RELWITHDEBINFO
+        CMAKE_CXX_FLAGS
+        CMAKE_CXX_FLAGS_DEBUG
+        CMAKE_CXX_FLAGS_RELEASE
+        CMAKE_CXX_FLAGS_MINSIZEREL
+        CMAKE_CXX_FLAGS_RELWITHDEBINFO
+      )
         if(${flag_var} MATCHES "/MD")
           set(using_md True)
         endif(${flag_var} MATCHES "/MD")
       endforeach(flag_var)
       if(${using_md} MATCHES "True")
-        message(WARNING "PETSc was built with /MT, but /MD is currently set.
- See http://www.cmake.org/Wiki/CMake_FAQ#How_can_I_build_my_MSVC_application_with_a_static_runtime.3F")
+        message(
+          WARNING
+            "PETSc was built with /MT, but /MD is currently set.
+ See http://www.cmake.org/Wiki/CMake_FAQ#How_can_I_build_my_MSVC_application_with_a_static_runtime.3F"
+        )
       endif(${using_md} MATCHES "True")
-    endif (petsc_cc_flags MATCHES "-MT")
-  endif (WIN32)
+    endif(petsc_cc_flags MATCHES "-MT")
+  endif(WIN32)
 
-  include (CorrectWindowsPaths)
+  include(CorrectWindowsPaths)
   convert_cygwin_path(petsc_lib_dir)
-  message (STATUS "petsc_lib_dir ${petsc_lib_dir}")
-
-  macro (PETSC_FIND_LIBRARY suffix name)
-    set (PETSC_LIBRARY_${suffix} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # Clear any stale value, if we got here, we need to find it again
-    if (WIN32)
-      set (libname lib${name}) #windows expects "libfoo", linux expects "foo"
-    else (WIN32)
-      set (libname ${name})
-    endif (WIN32)
-    find_library (PETSC_LIBRARY_${suffix} NAMES ${libname} HINTS ${petsc_lib_dir} NO_DEFAULT_PATH)
-    set (PETSC_LIBRARIES_${suffix} "${PETSC_LIBRARY_${suffix}}")
-    mark_as_advanced (PETSC_LIBRARY_${suffix})
-  endmacro (PETSC_FIND_LIBRARY suffix name)
+  message(STATUS "petsc_lib_dir ${petsc_lib_dir}")
+
+  macro(PETSC_FIND_LIBRARY suffix name)
+    set(PETSC_LIBRARY_${suffix}
+        "NOTFOUND"
+        CACHE INTERNAL "Cleared" FORCE
+    ) # Clear any stale value, if we got here, we need to find it again
+    if(WIN32)
+      set(libname lib${name}) #windows expects "libfoo", linux expects "foo"
+    else(WIN32)
+      set(libname ${name})
+    endif(WIN32)
+    find_library(
+      PETSC_LIBRARY_${suffix}
+      NAMES ${libname}
+      HINTS ${petsc_lib_dir}
+      NO_DEFAULT_PATH
+    )
+    set(PETSC_LIBRARIES_${suffix} "${PETSC_LIBRARY_${suffix}}")
+    mark_as_advanced(PETSC_LIBRARY_${suffix})
+  endmacro(
+    PETSC_FIND_LIBRARY
+    suffix
+    name
+  )
 
   # Look for petscvec first, if it doesn't exist, we must be using single-library
-  petsc_find_library (VEC petscvec)
-  if (PETSC_LIBRARY_VEC)
-    petsc_find_library (SYS  "petscsys;petsc") # libpetscsys is called libpetsc prior to 3.1 (when single-library was introduced)
-    petsc_find_library (MAT  petscmat)
-    petsc_find_library (DM   petscdm)
-    petsc_find_library (KSP  petscksp)
-    petsc_find_library (SNES petscsnes)
-    petsc_find_library (TS   petscts)
-    macro (PETSC_JOIN libs deps)
-      list (APPEND PETSC_LIBRARIES_${libs} ${PETSC_LIBRARIES_${deps}})
-    endmacro (PETSC_JOIN libs deps)
-    petsc_join (VEC  SYS)
-    petsc_join (MAT  VEC)
-    petsc_join (DM   MAT)
-    petsc_join (KSP  DM)
-    petsc_join (SNES KSP)
-    petsc_join (TS   SNES)
-    petsc_join (ALL  TS)
-  else ()
-    set (PETSC_LIBRARY_VEC "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # There is no libpetscvec
-    petsc_find_library (SINGLE petsc)
+  petsc_find_library(VEC petscvec)
+  if(PETSC_LIBRARY_VEC)
+    petsc_find_library(SYS "petscsys;petsc")
+    # libpetscsys is called libpetsc prior to 3.1 (when single-library was introduced)
+    petsc_find_library(MAT petscmat)
+    petsc_find_library(DM petscdm)
+    petsc_find_library(KSP petscksp)
+    petsc_find_library(SNES petscsnes)
+    petsc_find_library(TS petscts)
+    macro(PETSC_JOIN libs deps)
+      list(APPEND PETSC_LIBRARIES_${libs} ${PETSC_LIBRARIES_${deps}})
+    endmacro(
+      PETSC_JOIN
+      libs
+      deps
+    )
+    petsc_join(VEC SYS)
+    petsc_join(MAT VEC)
+    petsc_join(DM MAT)
+    petsc_join(KSP DM)
+    petsc_join(SNES KSP)
+    petsc_join(TS SNES)
+    petsc_join(ALL TS)
+  else()
+    set(PETSC_LIBRARY_VEC
+        "NOTFOUND"
+        CACHE INTERNAL "Cleared" FORCE
+    ) # There is no libpetscvec
+    petsc_find_library(SINGLE petsc)
     # Debian 9/Ubuntu 16.04 uses _real and _complex extensions when using libraries in /usr/lib/petsc.
-    if (NOT PETSC_LIBRARY_SINGLE)
-      petsc_find_library (SINGLE petsc_real)
+    if(NOT PETSC_LIBRARY_SINGLE)
+      petsc_find_library(SINGLE petsc_real)
     endif()
-    if (NOT PETSC_LIBRARY_SINGLE)
-      petsc_find_library (SINGLE petsc_complex)
+    if(NOT PETSC_LIBRARY_SINGLE)
+      petsc_find_library(SINGLE petsc_complex)
     endif()
-    foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
-      set (PETSC_LIBRARIES_${pkg} "${PETSC_LIBRARY_SINGLE}")
-    endforeach ()
-  endif ()
-  if (PETSC_LIBRARY_TS)
-    message (STATUS "Recognized PETSc install with separate libraries for each package")
-  else ()
-    message (STATUS "Recognized PETSc install with single library for all packages")
-  endif ()
+    foreach(
+      pkg
+      SYS
+      VEC
+      MAT
+      DM
+      KSP
+      SNES
+      TS
+      ALL
+    )
+      set(PETSC_LIBRARIES_${pkg} "${PETSC_LIBRARY_SINGLE}")
+    endforeach()
+  endif()
+  if(PETSC_LIBRARY_TS)
+    message(
+      STATUS "Recognized PETSc install with separate libraries for each package"
+    )
+  else()
+    message(
+      STATUS "Recognized PETSc install with single library for all packages"
+    )
+  endif()
 
   include(Check${PETSC_LANGUAGE_BINDINGS}SourceRuns)
 
-  macro (petsc_test_compiles includes libraries runs)
-    message(STATUS "PETSc test with : ${includes} ${libraries}" )
-    if (PETSC_VERSION VERSION_GREATER 3.1)
-      set (_PETSC_TSDestroy "TSDestroy(&ts)")
-    else ()
-      set (_PETSC_TSDestroy "TSDestroy(ts)")
-    endif ()
+  macro(petsc_test_compiles includes libraries runs)
+    message(STATUS "PETSc test with : ${includes} ${libraries}")
+    if(PETSC_VERSION VERSION_GREATER 3.1)
+      set(_PETSC_TSDestroy "TSDestroy(&ts)")
+    else()
+      set(_PETSC_TSDestroy "TSDestroy(ts)")
+    endif()
 
-    set(_PETSC_TEST_SOURCE "
+    set(_PETSC_TEST_SOURCE
+        "
 static const char help[] = \"PETSc test program.\";
 #include <petscts.h>
 int main(int argc,char *argv[]) {
@@ -286,116 +396,197 @@ int main(int argc,char *argv[]) {
   ierr = PetscFinalize();CHKERRQ(ierr);
   return 0;
 }
-")
-    multipass_source_compiles ("${includes}" "${libraries}" "${_PETSC_TEST_SOURCE}" ${runs} "${PETSC_LANGUAGE_BINDINGS}")
-    if (${${runs}})
-      set (PETSC_EXECUTABLE_COMPILES "YES" CACHE BOOL
-        "Can the system successfully run a PETSc executable?  This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build.  If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
-    endif (${${runs}})
-  endmacro ()
-
+"
+    )
+    multipass_source_compiles(
+      "${includes}" "${libraries}" "${_PETSC_TEST_SOURCE}" ${runs}
+      "${PETSC_LANGUAGE_BINDINGS}"
+    )
+    if(${${runs}})
+      set(PETSC_EXECUTABLE_COMPILES
+          "YES"
+          CACHE
+            BOOL
+            "Can the system successfully run a PETSc executable?  This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build.  If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable."
+            FORCE
+      )
+    endif(${${runs}})
+  endmacro()
 
-  find_path (PETSC_INCLUDE_DIR petscts.h
+  find_path(
+    PETSC_INCLUDE_DIR petscts.h
     HINTS "${PETSC_DIR}"
     PATH_SUFFIXES include
-    NO_DEFAULT_PATH)
-  find_path (PETSC_INCLUDE_CONF petscconf.h
+    NO_DEFAULT_PATH
+  )
+  find_path(
+    PETSC_INCLUDE_CONF petscconf.h
     HINTS "${PETSC_DIR}"
     PATH_SUFFIXES "${PETSC_ARCH}/include" "bmake/${PETSC_ARCH}"
-    NO_DEFAULT_PATH)
-  mark_as_advanced (PETSC_INCLUDE_DIR PETSC_INCLUDE_CONF)
-  set (petsc_includes_minimal ${PETSC_INCLUDE_CONF} ${PETSC_INCLUDE_DIR})
-
-  file (STRINGS "${PETSC_INCLUDE_CONF}/petscconf.h" PETSC_HAS_OPENMP REGEX "#define PETSC_HAVE_OPENMP 1")
-  if (PETSC_HAS_OPENMP)
+    NO_DEFAULT_PATH
+  )
+  mark_as_advanced(PETSC_INCLUDE_DIR PETSC_INCLUDE_CONF)
+  set(petsc_includes_minimal ${PETSC_INCLUDE_CONF} ${PETSC_INCLUDE_DIR})
+
+  file(STRINGS "${PETSC_INCLUDE_CONF}/petscconf.h" PETSC_HAS_OPENMP
+       REGEX "#define PETSC_HAVE_OPENMP 1"
+  )
+  if(PETSC_HAS_OPENMP)
     find_package(OpenMP REQUIRED)
-    set (petsc_openmp_library ";OpenMP::OpenMP_${PETSC_LANGUAGE_BINDINGS}")
+    set(petsc_openmp_library ";OpenMP::OpenMP_${PETSC_LANGUAGE_BINDINGS}")
   endif()
-  set (petsc_mpi_include_dirs "${MPI_${PETSC_LANGUAGE_BINDINGS}_INCLUDE_DIRS}")
+  set(petsc_mpi_include_dirs "${MPI_${PETSC_LANGUAGE_BINDINGS}_INCLUDE_DIRS}")
   #set (petsc_additional_libraries "MPI::MPI_${PETSC_LANGUAGE_BINDINGS}${petsc_openmp_library}")
 
-  petsc_test_compiles ("${petsc_includes_minimal};${petsc_mpi_include_dirs}"
-    "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}"
-    petsc_works_minimal)
-  if (petsc_works_minimal)
-    message (STATUS "Minimal PETSc includes and libraries work.  This probably means we are building with shared libs.")
-    set (petsc_includes_needed "${petsc_includes_minimal}")
-  else (petsc_works_minimal)     # Minimal includes fail, see if just adding full includes fixes it
-    petsc_test_compiles ("${petsc_includes_all};${petsc_mpi_include_dirs}"
+  petsc_test_compiles(
+    "${petsc_includes_minimal};${petsc_mpi_include_dirs}"
+    "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}" petsc_works_minimal
+  )
+  if(petsc_works_minimal)
+    message(
+      STATUS
+        "Minimal PETSc includes and libraries work.  This probably means we are building with shared libs."
+    )
+    set(petsc_includes_needed "${petsc_includes_minimal}")
+  else(petsc_works_minimal
+  )# Minimal includes fail, see if just adding full includes fixes it
+    petsc_test_compiles(
+      "${petsc_includes_all};${petsc_mpi_include_dirs}"
       "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}"
-      petsc_works_allincludes)
-    if (petsc_works_allincludes) # It does, we just need all the includes (
-      message (STATUS "PETSc requires extra include paths, but links correctly with only interface libraries.  This is an unexpected configuration (but it seems to work fine).")
-      set (petsc_includes_needed ${petsc_includes_all})
-    else (petsc_works_allincludes) # We are going to need to link the external libs explicitly
-      resolve_libraries (petsc_libraries_external "${petsc_libs_external}")
-      foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
-        list (APPEND PETSC_LIBRARIES_${pkg}  ${petsc_libraries_external})
-      endforeach (pkg)
-      petsc_test_compiles ("${petsc_includes_minimal};${petsc_mpi_include_dirs}"
+      petsc_works_allincludes
+    )
+    if(petsc_works_allincludes) # It does, we just need all the includes (
+      message(
+        STATUS
+          "PETSc requires extra include paths, but links correctly with only interface libraries.  This is an unexpected configuration (but it seems to work fine)."
+      )
+      set(petsc_includes_needed ${petsc_includes_all})
+    else(petsc_works_allincludes
+    )# We are going to need to link the external libs explicitly
+      resolve_libraries(petsc_libraries_external "${petsc_libs_external}")
+      foreach(
+        pkg
+        SYS
+        VEC
+        MAT
+        DM
+        KSP
+        SNES
+        TS
+        ALL
+      )
+        list(APPEND PETSC_LIBRARIES_${pkg} ${petsc_libraries_external})
+      endforeach(pkg)
+      petsc_test_compiles(
+        "${petsc_includes_minimal};${petsc_mpi_include_dirs}"
         "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}"
-        petsc_works_alllibraries)
-      if (petsc_works_alllibraries)
-         message (STATUS "PETSc only need minimal includes, but requires explicit linking to all dependencies.  This is expected when PETSc is built with static libraries.")
-        set (petsc_includes_needed ${petsc_includes_minimal})
-      else (petsc_works_alllibraries)
+        petsc_works_alllibraries
+      )
+      if(petsc_works_alllibraries)
+        message(
+          STATUS
+            "PETSc only need minimal includes, but requires explicit linking to all dependencies.  This is expected when PETSc is built with static libraries."
+        )
+        set(petsc_includes_needed ${petsc_includes_minimal})
+      else(petsc_works_alllibraries)
         # It looks like we really need everything, should have listened to Matt
-        set (petsc_includes_needed ${petsc_includes_all})
-        petsc_test_compiles ("${petsc_includes_all};${petsc_mpi_include_dirs}"
-          "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}"
-          petsc_works_all)
-        if (petsc_works_all) # We fail anyways
-          message (STATUS "PETSc requires extra include paths and explicit linking to all dependencies.  This probably means you have static libraries and something unexpected in PETSc headers.")
-        else (petsc_works_all) # We fail anyways
-          message (STATUS "PETSc could not be used, maybe the install is broken.")
-        endif (petsc_works_all)
-      endif (petsc_works_alllibraries)
-    endif (petsc_works_allincludes)
-  endif (petsc_works_minimal)
+        set(petsc_includes_needed ${petsc_includes_all})
+        petsc_test_compiles(
+          "${petsc_includes_all};${petsc_mpi_include_dirs}"
+          "${PETSC_LIBRARIES_TS};${petsc_additional_libraries}" petsc_works_all
+        )
+        if(petsc_works_all) # We fail anyways
+          message(
+            STATUS
+              "PETSc requires extra include paths and explicit linking to all dependencies.  This probably means you have static libraries and something unexpected in PETSc headers."
+          )
+        else(petsc_works_all) # We fail anyways
+          message(
+            STATUS "PETSc could not be used, maybe the install is broken."
+          )
+        endif(petsc_works_all)
+      endif(petsc_works_alllibraries)
+    endif(petsc_works_allincludes)
+  endif(petsc_works_minimal)
 
   # We do an out-of-source build so __FILE__ will be an absolute path, hence __INSDIR__ is superfluous
-  if (${PETSC_VERSION} VERSION_LESS 3.1)
-    set (PETSC_DEFINITIONS "-D__SDIR__=\"\"" CACHE STRING "PETSc definitions" FORCE)
-  else ()
-    set (PETSC_DEFINITIONS "-D__INSDIR__=" CACHE STRING "PETSc definitions" FORCE)
-  endif ()
+  if(${PETSC_VERSION} VERSION_LESS 3.1)
+    set(PETSC_DEFINITIONS
+        "-D__SDIR__=\"\""
+        CACHE STRING "PETSc definitions" FORCE
+    )
+  else()
+    set(PETSC_DEFINITIONS
+        "-D__INSDIR__="
+        CACHE STRING "PETSc definitions" FORCE
+    )
+  endif()
   # Sometimes this can be used to assist FindMPI.cmake
-  set (PETSC_MPIEXEC ${petsc_mpiexec} CACHE FILEPATH "Executable for running PETSc MPI programs" FORCE)
-  set (PETSC_INCLUDES ${petsc_includes_needed} CACHE STRING "PETSc include path" FORCE)
-  set (PETSC_LIBRARIES ${PETSC_LIBRARIES_ALL} CACHE STRING "PETSc libraries" FORCE)
-  set (PETSC_COMPILER ${petsc_cc} CACHE FILEPATH "PETSc compiler" FORCE)
-endif ()
+  set(PETSC_MPIEXEC
+      ${petsc_mpiexec}
+      CACHE FILEPATH "Executable for running PETSc MPI programs" FORCE
+  )
+  set(PETSC_INCLUDES
+      ${petsc_includes_needed}
+      CACHE STRING "PETSc include path" FORCE
+  )
+  set(PETSC_LIBRARIES
+      ${PETSC_LIBRARIES_ALL}
+      CACHE STRING "PETSc libraries" FORCE
+  )
+  set(PETSC_COMPILER
+      ${petsc_cc}
+      CACHE FILEPATH "PETSc compiler" FORCE
+  )
+endif()
 
-if (NOT PETSC_INCLUDES AND NOT TARGET PETSc::PETSc)
+if(NOT PETSC_INCLUDES AND NOT TARGET PETSc::PETSc)
   find_package(PkgConfig)
-  if (PkgConfig_FOUND)
+  if(PkgConfig_FOUND)
     pkg_search_module(PkgPETSC PETSc>3.4.0 petsc>3.4.0)
-    set (PETSC_LIBRARIES ${PkgPETSC_LINK_LIBRARIES} CACHE STRING "PETSc libraries" FORCE)
-    set (PETSC_INCLUDES ${PkgPETSC_INCLUDE_DIRS} CACHE STRING "PETSc include path" FORCE)
-    set (PETSC_EXECUTABLE_COMPILES "YES" CACHE BOOL
-        "Can the system successfully run a PETSc executable?  This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build.  If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
+    set(PETSC_LIBRARIES
+        ${PkgPETSC_LINK_LIBRARIES}
+        CACHE STRING "PETSc libraries" FORCE
+    )
+    set(PETSC_INCLUDES
+        ${PkgPETSC_INCLUDE_DIRS}
+        CACHE STRING "PETSc include path" FORCE
+    )
+    set(PETSC_EXECUTABLE_COMPILES
+        "YES"
+        CACHE
+          BOOL
+          "Can the system successfully run a PETSc executable?  This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build.  If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable."
+          FORCE
+    )
   endif()
 endif()
 
 # Note that we have forced values for all these choices.  If you
 # change these, you are telling the system to trust you that they
 # work.  It is likely that you will end up with a broken build.
-mark_as_advanced (PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC PETSC_EXECUTABLE_COMPILES)
-
-include (FindPackageHandleStandardArgs)
-find_package_handle_standard_args (PETSc
+mark_as_advanced(
+  PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC
+  PETSC_EXECUTABLE_COMPILES
+)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(
+  PETSc
   REQUIRED_VARS PETSC_INCLUDES PETSC_LIBRARIES
   VERSION_VAR PETSC_VERSION
-  FAIL_MESSAGE "PETSc could not be found.  Be sure to set PETSC_DIR and PETSC_ARCH.")
+  FAIL_MESSAGE
+    "PETSc could not be found.  Be sure to set PETSC_DIR and PETSC_ARCH."
+)
 
-if (PETSC_FOUND)
-  if (NOT TARGET PETSc::PETSc)
+if(PETSC_FOUND)
+  if(NOT TARGET PETSc::PETSc)
     add_library(PETSc::PETSc UNKNOWN IMPORTED)
     list(GET PETSC_LIBRARIES 0 PETSC_LIBRARY)
     target_link_libraries(PETSc::PETSc INTERFACE "${PETSC_LIBRARIES}")
-    set_target_properties(PETSc::PETSc PROPERTIES
-      IMPORTED_LOCATION "${PETSC_LIBRARY}"
-      INTERFACE_INCLUDE_DIRECTORIES "${PETSC_INCLUDES}"
-      )
+    set_target_properties(
+      PETSc::PETSc PROPERTIES IMPORTED_LOCATION "${PETSC_LIBRARY}"
+                              INTERFACE_INCLUDE_DIRECTORIES "${PETSC_INCLUDES}"
+    )
   endif()
 endif()
diff --git a/cmake/FindPackageMultipass.cmake b/cmake/FindPackageMultipass.cmake
index 99bbace448..b2762f5d28 100644
--- a/cmake/FindPackageMultipass.cmake
+++ b/cmake/FindPackageMultipass.cmake
@@ -34,99 +34,124 @@
 
 include(CheckCXXSourceCompiles)
 
-macro (FIND_PACKAGE_MULTIPASS _name _current)
-  string (TOUPPER ${_name} _NAME)
-  set (_args ${ARGV})
-  list (REMOVE_AT _args 0 1)
+macro(FIND_PACKAGE_MULTIPASS _name _current)
+  string(TOUPPER ${_name} _NAME)
+  set(_args ${ARGV})
+  list(REMOVE_AT _args 0 1)
 
-  set (_states_current "YES")
-  list (GET _args 0 _cmd)
-  if (_cmd STREQUAL "STATES")
-    list (REMOVE_AT _args 0)
-    list (GET _args 0 _state)
-    while (_state AND NOT _state STREQUAL "DEPENDENTS")
+  set(_states_current "YES")
+  list(GET _args 0 _cmd)
+  if(_cmd STREQUAL "STATES")
+    list(REMOVE_AT _args 0)
+    list(GET _args 0 _state)
+    while(_state AND NOT _state STREQUAL "DEPENDENTS")
       # The name of the stored value for the given state
-      set (_stored_var PACKAGE_MULTIPASS_${_NAME}_${_state})
-      if (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
-        set (_states_current "NO")
-      endif (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
-      set (${_stored_var} "${${_NAME}_${_state}}" CACHE INTERNAL "Stored state for ${_name}." FORCE)
-      list (REMOVE_AT _args 0)
-      list (GET _args 0 _state)
-    endwhile (_state AND NOT _state STREQUAL "DEPENDENTS")
-  endif (_cmd STREQUAL "STATES")
+      set(_stored_var PACKAGE_MULTIPASS_${_NAME}_${_state})
+      if(NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+        set(_states_current "NO")
+      endif(NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+      set(${_stored_var}
+          "${${_NAME}_${_state}}"
+          CACHE INTERNAL "Stored state for ${_name}." FORCE
+      )
+      list(REMOVE_AT _args 0)
+      list(GET _args 0 _state)
+    endwhile(_state AND NOT _state STREQUAL "DEPENDENTS")
+  endif(_cmd STREQUAL "STATES")
 
-  set (_stored ${_NAME}_CURRENT)
-  if (NOT ${_stored})
-    set (${_stored} "YES" CACHE BOOL "Is the configuration for ${_name} current?  Set to \"NO\" to reconfigure." FORCE)
-    set (_states_current "NO")
-  endif (NOT ${_stored})
+  set(_stored ${_NAME}_CURRENT)
+  if(NOT ${_stored})
+    set(${_stored}
+        "YES"
+        CACHE
+          BOOL
+          "Is the configuration for ${_name} current?  Set to \"NO\" to reconfigure."
+          FORCE
+    )
+    set(_states_current "NO")
+  endif(NOT ${_stored})
 
-  set (${_current} ${_states_current})
-  if (NOT ${_current} AND PACKAGE_MULTIPASS_${_name}_CALLED)
-    message (STATUS "Clearing ${_name} dependent variables")
+  set(${_current} ${_states_current})
+  if(NOT ${_current} AND PACKAGE_MULTIPASS_${_name}_CALLED)
+    message(STATUS "Clearing ${_name} dependent variables")
     # Clear all the dependent variables so that the module can reset them
-    list (GET _args 0 _cmd)
-    if (_cmd STREQUAL "DEPENDENTS")
-      list (REMOVE_AT _args 0)
-      foreach (dep ${_args})
-        set (${_NAME}_${dep} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
-      endforeach (dep)
-    endif (_cmd STREQUAL "DEPENDENTS")
-    set (${_NAME}_FOUND "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
-  endif ()
-  set (PACKAGE_MULTIPASS_${name}_CALLED YES CACHE INTERNAL "Private" FORCE)
-endmacro (FIND_PACKAGE_MULTIPASS)
-
+    list(GET _args 0 _cmd)
+    if(_cmd STREQUAL "DEPENDENTS")
+      list(REMOVE_AT _args 0)
+      foreach(dep ${_args})
+        set(${_NAME}_${dep}
+            "NOTFOUND"
+            CACHE INTERNAL "Cleared" FORCE
+        )
+      endforeach(dep)
+    endif(_cmd STREQUAL "DEPENDENTS")
+    set(${_NAME}_FOUND
+        "NOTFOUND"
+        CACHE INTERNAL "Cleared" FORCE
+    )
+  endif()
+  set(PACKAGE_MULTIPASS_${name}_CALLED
+      YES
+      CACHE INTERNAL "Private" FORCE
+  )
+endmacro(FIND_PACKAGE_MULTIPASS)
 
-macro (MULTIPASS_SOURCE_RUNS includes libraries source runs language)
-  include (Check${language}SourceRuns)
+macro(MULTIPASS_SOURCE_RUNS includes libraries source runs language)
+  include(Check${language}SourceRuns)
   # This is a ridiculous hack.  CHECK_${language}_SOURCE_* thinks that if the
   # *name* of the return variable doesn't change, then the test does
   # not need to be re-run.  We keep an internal count which we
   # increment to guarantee that every test name is unique.  If we've
   # gotten here, then the configuration has changed enough that the
   # test *needs* to be rerun.
-  if (NOT MULTIPASS_TEST_COUNT)
-    set (MULTIPASS_TEST_COUNT 00)
-  endif (NOT MULTIPASS_TEST_COUNT)
-  math (EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1") # Why can't I add to a cache variable?
-  set (MULTIPASS_TEST_COUNT ${_tmp} CACHE INTERNAL "Unique test ID")
-  set (testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
-  set (CMAKE_REQUIRED_INCLUDES ${includes})
-  set (CMAKE_REQUIRED_LIBRARIES ${libraries})
+  if(NOT MULTIPASS_TEST_COUNT)
+    set(MULTIPASS_TEST_COUNT 00)
+  endif(NOT MULTIPASS_TEST_COUNT)
+  math(EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1"
+  )# Why can't I add to a cache variable?
+  set(MULTIPASS_TEST_COUNT
+      ${_tmp}
+      CACHE INTERNAL "Unique test ID"
+  )
+  set(testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
+  set(CMAKE_REQUIRED_INCLUDES ${includes})
+  set(CMAKE_REQUIRED_LIBRARIES ${libraries})
   if(${language} STREQUAL "C")
-    check_c_source_runs ("${source}" ${testname})
+    check_c_source_runs("${source}" ${testname})
   elseif(${language} STREQUAL "CXX")
-    check_cxx_source_runs ("${source}" ${testname})
+    check_cxx_source_runs("${source}" ${testname})
   endif()
-  set (${runs} "${${testname}}")
-endmacro (MULTIPASS_SOURCE_RUNS)
+  set(${runs} "${${testname}}")
+endmacro(MULTIPASS_SOURCE_RUNS)
 
-macro (MULTIPASS_C_SOURCE_RUNS includes libraries source runs)
+macro(MULTIPASS_C_SOURCE_RUNS includes libraries source runs)
   multipass_source_runs("${includes}" "${libraries}" "${source}" ${runs} "C")
-endmacro (MULTIPASS_C_SOURCE_RUNS)
+endmacro(MULTIPASS_C_SOURCE_RUNS)
 
-macro (MULTIPASS_SOURCE_COMPILES includes libraries source runs language)
-  include (Check${language}SourceCompiles)
+macro(MULTIPASS_SOURCE_COMPILES includes libraries source runs language)
+  include(Check${language}SourceCompiles)
   # This is a ridiculous hack.  CHECK_${language}_SOURCE_* thinks that if the
   # *name* of the return variable doesn't change, then the test does
   # not need to be re-run.  We keep an internal count which we
   # increment to guarantee that every test name is unique.  If we've
   # gotten here, then the configuration has changed enough that the
   # test *needs* to be rerun.
-  if (NOT MULTIPASS_TEST_COUNT)
-    set (MULTIPASS_TEST_COUNT 00)
-  endif (NOT MULTIPASS_TEST_COUNT)
-  math (EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1") # Why can't I add to a cache variable?
-  set (MULTIPASS_TEST_COUNT ${_tmp} CACHE INTERNAL "Unique test ID")
-  set (testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
-  set (CMAKE_REQUIRED_INCLUDES ${includes})
-  set (CMAKE_REQUIRED_LIBRARIES ${libraries})
+  if(NOT MULTIPASS_TEST_COUNT)
+    set(MULTIPASS_TEST_COUNT 00)
+  endif(NOT MULTIPASS_TEST_COUNT)
+  math(EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1"
+  )# Why can't I add to a cache variable?
+  set(MULTIPASS_TEST_COUNT
+      ${_tmp}
+      CACHE INTERNAL "Unique test ID"
+  )
+  set(testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
+  set(CMAKE_REQUIRED_INCLUDES ${includes})
+  set(CMAKE_REQUIRED_LIBRARIES ${libraries})
   if(${language} STREQUAL "C")
-    check_c_source_compiles ("${source}" ${testname})
+    check_c_source_compiles("${source}" ${testname})
   elseif(${language} STREQUAL "CXX")
-    check_cxx_source_compiles ("${source}" ${testname})
+    check_cxx_source_compiles("${source}" ${testname})
   endif()
-  set (${runs} "${${testname}}")
-endmacro ()
+  set(${runs} "${${testname}}")
+endmacro()
diff --git a/cmake/FindSLEPc.cmake b/cmake/FindSLEPc.cmake
index 3add8eba8b..4df855569b 100644
--- a/cmake/FindSLEPc.cmake
+++ b/cmake/FindSLEPc.cmake
@@ -48,74 +48,92 @@ find_package(PETSc REQUIRED)
 find_package(MPI REQUIRED)
 
 # Set debian_arches (PETSC_ARCH for Debian-style installations)
-foreach (debian_arches linux kfreebsd)
-  if ("${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
-    set(DEBIAN_FLAVORS ${debian_arches}-gnu-c-debug ${debian_arches}-gnu-c-opt ${DEBIAN_FLAVORS})
+foreach(debian_arches linux kfreebsd)
+  if("${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
+    set(DEBIAN_FLAVORS ${debian_arches}-gnu-c-debug ${debian_arches}-gnu-c-opt
+                       ${DEBIAN_FLAVORS}
+    )
   else()
-    set(DEBIAN_FLAVORS ${debian_arches}-gnu-c-opt ${debian_arches}-gnu-c-debug ${DEBIAN_FLAVORS})
+    set(DEBIAN_FLAVORS ${debian_arches}-gnu-c-opt ${debian_arches}-gnu-c-debug
+                       ${DEBIAN_FLAVORS}
+    )
   endif()
 endforeach()
 
 # List of possible locations for SLEPC_DIR
 set(slepc_dir_locations "")
 list(APPEND slepc_dir_locations "/usr/lib/slepc")
-list(APPEND slepc_dir_locations "/opt/local/lib/petsc")    # Macports
+list(APPEND slepc_dir_locations "/opt/local/lib/petsc") # Macports
 list(APPEND slepc_dir_locations "/usr/local/lib/slepc")
 list(APPEND slepc_dir_locations "$ENV{HOME}/slepc")
 
 # Try to figure out SLEPC_DIR by finding slepc.h
-find_path(SLEPC_DIR include/slepc.h
+find_path(
+  SLEPC_DIR include/slepc.h
   HINTS ${SLEPC_DIR} $ENV{SLEPC_DIR}
   PATHS ${slepc_dir_locations}
-  DOC "SLEPc directory")
+  DOC "SLEPc directory"
+)
 
 # Report result of search for SLEPC_DIR
-if (DEFINED SLEPC_DIR)
+if(DEFINED SLEPC_DIR)
   message(STATUS "SLEPC_DIR is ${SLEPC_DIR}")
 else()
   message(STATUS "SLEPC_DIR is empty")
 endif()
 
 # Get variables from SLEPc configuration
-if (SLEPC_DIR)
+if(SLEPC_DIR)
 
-  find_library(SLEPC_LIBRARY
+  find_library(
+    SLEPC_LIBRARY
     NAMES slepc
-    HINTS
-      ${SLEPC_DIR}/lib
-      $ENV{SLEPC_DIR}/lib
-      ${SLEPC_DIR}/${PETSC_ARCH}/lib
-      $ENV{SLEPC_DIR}/$ENV{PETSC_ARCH}/lib
+    HINTS ${SLEPC_DIR}/lib $ENV{SLEPC_DIR}/lib ${SLEPC_DIR}/${PETSC_ARCH}/lib
+          $ENV{SLEPC_DIR}/$ENV{PETSC_ARCH}/lib
     NO_DEFAULT_PATH
-    DOC "The SLEPc library")
-  find_library(SLEPC_LIBRARY
+    DOC "The SLEPc library"
+  )
+  find_library(
+    SLEPC_LIBRARY
     NAMES slepc
-    DOC "The SLEPc library")
+    DOC "The SLEPc library"
+  )
   mark_as_advanced(SLEPC_LIBRARY)
 
   # Find SLEPc config file
-  find_file(SLEPC_CONFIG_FILE NAMES slepc_common PATHS
-    ${SLEPC_DIR}/lib/slepc/conf
-    ${SLEPC_DIR}/lib/slepc-conf ${SLEPC_DIR}/conf)
+  find_file(
+    SLEPC_CONFIG_FILE
+    NAMES slepc_common
+    PATHS ${SLEPC_DIR}/lib/slepc/conf ${SLEPC_DIR}/lib/slepc-conf
+          ${SLEPC_DIR}/conf
+  )
 
   # Create a temporary Makefile to probe the SLEPc configuration
   set(slepc_config_makefile ${PROJECT_BINARY_DIR}/Makefile.slepc)
-  file(WRITE ${slepc_config_makefile}
-"# This file was autogenerated by FindSLEPc.cmake
+  file(
+    WRITE ${slepc_config_makefile}
+    "# This file was autogenerated by FindSLEPc.cmake
 SLEPC_DIR  = ${SLEPC_DIR}
 PETSC_ARCH = ${PETSC_ARCH}
 PETSC_DIR = ${PETSC_DIR}
 include ${SLEPC_CONFIG_FILE}
 show :
 	-@echo -n \${\${VARIABLE}}
-")
+"
+  )
 
   # Define macro for getting SLEPc variables from Makefile
   macro(SLEPC_GET_VARIABLE var name)
-    set(${var} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
-    execute_process(COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${slepc_config_makefile} show VARIABLE=${name}
+    set(${var}
+        "NOTFOUND"
+        CACHE INTERNAL "Cleared" FORCE
+    )
+    execute_process(
+      COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f
+              ${slepc_config_makefile} show VARIABLE=${name}
       OUTPUT_VARIABLE ${var}
-      RESULT_VARIABLE slepc_return)
+      RESULT_VARIABLE slepc_return
+    )
   endmacro()
 
   # Call macro to get the SLEPc variables
@@ -131,15 +149,21 @@ show :
   resolve_libraries(SLEPC_EXTERNAL_LIBRARIES "${SLEPC_EXTERNAL_LIB}")
 
   # Add variables to CMake cache and mark as advanced
-  set(SLEPC_INCLUDE_DIRS ${SLEPC_INCLUDE_DIRS} CACHE STRING "SLEPc include paths." FORCE)
-  set(SLEPC_LIBRARIES ${SLEPC_LIBRARY} CACHE STRING "SLEPc libraries." FORCE)
+  set(SLEPC_INCLUDE_DIRS
+      ${SLEPC_INCLUDE_DIRS}
+      CACHE STRING "SLEPc include paths." FORCE
+  )
+  set(SLEPC_LIBRARIES
+      ${SLEPC_LIBRARY}
+      CACHE STRING "SLEPc libraries." FORCE
+  )
   mark_as_advanced(SLEPC_INCLUDE_DIRS SLEPC_LIBRARIES)
 endif()
 
-if (SLEPC_SKIP_BUILD_TESTS)
+if(SLEPC_SKIP_BUILD_TESTS)
   set(SLEPC_VERSION "UNKNOWN")
   set(SLEPC_VERSION_OK TRUE)
-elseif (SLEPC_LIBRARIES AND SLEPC_INCLUDE_DIRS)
+elseif(SLEPC_LIBRARIES AND SLEPC_INCLUDE_DIRS)
 
   # Set flags for building test program
   set(CMAKE_REQUIRED_INCLUDES ${SLEPC_INCLUDE_DIRS})
@@ -147,8 +171,11 @@ elseif (SLEPC_LIBRARIES AND SLEPC_INCLUDE_DIRS)
 
   # Check SLEPc version
   set(SLEPC_CONFIG_TEST_VERSION_CPP
-    "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/slepc_config_test_version.cpp")
-  file(WRITE ${SLEPC_CONFIG_TEST_VERSION_CPP} "
+      "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/slepc_config_test_version.cpp"
+  )
+  file(
+    WRITE ${SLEPC_CONFIG_TEST_VERSION_CPP}
+    "
 #include <iostream>
 #include \"slepcversion.h\"
 
@@ -158,56 +185,69 @@ int main() {
         << SLEPC_VERSION_SUBMINOR;
   return 0;
 }
-")
+"
+  )
 
   try_run(
-    SLEPC_CONFIG_TEST_VERSION_EXITCODE
-    SLEPC_CONFIG_TEST_VERSION_COMPILED
-    ${CMAKE_CURRENT_BINARY_DIR}
-    ${SLEPC_CONFIG_TEST_VERSION_CPP}
-    CMAKE_FLAGS
-      "-DINCLUDE_DIRECTORIES:STRING=${CMAKE_REQUIRED_INCLUDES}"
+    SLEPC_CONFIG_TEST_VERSION_EXITCODE SLEPC_CONFIG_TEST_VERSION_COMPILED
+    ${CMAKE_CURRENT_BINARY_DIR} ${SLEPC_CONFIG_TEST_VERSION_CPP}
+    CMAKE_FLAGS "-DINCLUDE_DIRECTORIES:STRING=${CMAKE_REQUIRED_INCLUDES}"
     COMPILE_OUTPUT_VARIABLE COMPILE_OUTPUT
     RUN_OUTPUT_VARIABLE OUTPUT
-    )
+  )
 
-  if (SLEPC_CONFIG_TEST_VERSION_EXITCODE EQUAL 0)
-    set(SLEPC_VERSION "${OUTPUT}" CACHE STRING "SLEPC version number")
+  if(SLEPC_CONFIG_TEST_VERSION_EXITCODE EQUAL 0)
+    set(SLEPC_VERSION
+        "${OUTPUT}"
+        CACHE STRING "SLEPC version number"
+    )
     string(REPLACE "." ";" SLEPC_VERSION_LIST ${SLEPC_VERSION})
     list(GET SLEPC_VERSION_LIST 0 SLEPC_VERSION_MAJOR)
     list(GET SLEPC_VERSION_LIST 1 SLEPC_VERSION_MINOR)
     list(GET SLEPC_VERSION_LIST 2 SLEPC_VERSION_SUBMINOR)
     mark_as_advanced(SLEPC_VERSION)
-    mark_as_advanced(SLEPC_VERSION_MAJOR SLEPC_VERSION_MINOR SLEPC_VERSION_SUBMINOR)
+    mark_as_advanced(
+      SLEPC_VERSION_MAJOR SLEPC_VERSION_MINOR SLEPC_VERSION_SUBMINOR
+    )
   endif()
 
-  if (SLEPc_FIND_VERSION)
+  if(SLEPc_FIND_VERSION)
     # Check if version found is >= required version
-    if (NOT "${SLEPC_VERSION}" VERSION_LESS "${SLEPc_FIND_VERSION}")
-      set(SLEPC_VERSION_OK TRUE CACHE BOOL "")
+    if(NOT "${SLEPC_VERSION}" VERSION_LESS "${SLEPc_FIND_VERSION}")
+      set(SLEPC_VERSION_OK
+          TRUE
+          CACHE BOOL ""
+      )
     endif()
   else()
     # No specific version requested
-    set(SLEPC_VERSION_OK TRUE CACHE BOOL "")
+    set(SLEPC_VERSION_OK
+        TRUE
+        CACHE BOOL ""
+    )
   endif()
   mark_as_advanced(SLEPC_VERSION_OK)
 endif()
 
 # Standard package handling
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(SLEPc
+find_package_handle_standard_args(
+  SLEPc
   FOUND_VAR SLEPC_FOUND
-  FAIL_MESSAGE "SLEPc could not be found. Be sure to set SLEPC_DIR, PETSC_DIR, and PETSC_ARCH."
+  FAIL_MESSAGE
+    "SLEPc could not be found. Be sure to set SLEPC_DIR, PETSC_DIR, and PETSC_ARCH."
   VERSION_VAR SLEPC_VERSION
-  REQUIRED_VARS SLEPC_LIBRARIES SLEPC_DIR SLEPC_INCLUDE_DIRS SLEPC_VERSION_OK)
+  REQUIRED_VARS SLEPC_LIBRARIES SLEPC_DIR SLEPC_INCLUDE_DIRS SLEPC_VERSION_OK
+)
 
-if (SLEPC_FOUND)
-  if (NOT TARGET SLEPc::SLEPc)
+if(SLEPC_FOUND)
+  if(NOT TARGET SLEPc::SLEPc)
     add_library(SLEPc::SLEPc UNKNOWN IMPORTED)
-    set_target_properties(SLEPc::SLEPc PROPERTIES
-      IMPORTED_LOCATION "${SLEPC_LIBRARIES}"
-      INTERFACE_INCLUDE_DIRECTORIES "${SLEPC_INCLUDE_DIRS}"
-      INTERFACE_LINK_LIBRARIES PETSc::PETSc
-      )
+    set_target_properties(
+      SLEPc::SLEPc
+      PROPERTIES IMPORTED_LOCATION "${SLEPC_LIBRARIES}"
+                 INTERFACE_INCLUDE_DIRECTORIES "${SLEPC_INCLUDE_DIRS}"
+                 INTERFACE_LINK_LIBRARIES PETSc::PETSc
+    )
   endif()
 endif()
diff --git a/cmake/FindSUNDIALS.cmake b/cmake/FindSUNDIALS.cmake
index 15b266d06a..e5cec34510 100644
--- a/cmake/FindSUNDIALS.cmake
+++ b/cmake/FindSUNDIALS.cmake
@@ -33,47 +33,48 @@ include(FindPackageHandleStandardArgs)
 
 find_package(SUNDIALS CONFIG QUIET)
 
-if (SUNDIALS_FOUND)
-  if (TARGET SUNDIALS::nvecparallel)
+if(SUNDIALS_FOUND)
+  if(TARGET SUNDIALS::nvecparallel)
     return()
   else()
     message(STATUS "SUNDIALS found but not SUNDIALS::nvecparallel")
   endif()
 endif()
 
-find_path(SUNDIALS_INCLUDE_DIR
-  sundials_config.h
-  HINTS
-    "${SUNDIALS_ROOT}"
-    ENV SUNDIALS_DIR
+find_path(
+  SUNDIALS_INCLUDE_DIR sundials_config.h
+  HINTS "${SUNDIALS_ROOT}" ENV SUNDIALS_DIR
   PATH_SUFFIXES include include/sundials
-  DOC "SUNDIALS Directory")
+  DOC "SUNDIALS Directory"
+)
 
-if (SUNDIALS_DEBUG)
+if(SUNDIALS_DEBUG)
   message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " SUNDIALS_INCLUDE_DIR = ${SUNDIALS_INCLUDE_DIR}"
-    " SUNDIALS_ROOT = ${SUNDIALS_ROOT}")
+                 " SUNDIALS_INCLUDE_DIR = ${SUNDIALS_INCLUDE_DIR}"
+                 " SUNDIALS_ROOT = ${SUNDIALS_ROOT}"
+  )
 endif()
 
 set(SUNDIALS_INCLUDE_DIRS
-  "${SUNDIALS_INCLUDE_DIR}"
-  "${SUNDIALS_INCLUDE_DIR}/.."
-  CACHE STRING "SUNDIALS include directories")
+    "${SUNDIALS_INCLUDE_DIR}" "${SUNDIALS_INCLUDE_DIR}/.."
+    CACHE STRING "SUNDIALS include directories"
+)
 
-find_library(SUNDIALS_nvecparallel_LIBRARY
+find_library(
+  SUNDIALS_nvecparallel_LIBRARY
   NAMES sundials_nvecparallel
-  HINTS
-    "${SUNDIALS_INCLUDE_DIR}/.."
-    "${SUNDIALS_INCLUDE_DIR}/../.."
+  HINTS "${SUNDIALS_INCLUDE_DIR}/.." "${SUNDIALS_INCLUDE_DIR}/../.."
   PATH_SUFFIXES lib lib64
-  )
+)
 
-if (SUNDIALS_DEBUG)
-  message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " SUNDIALS_nvecparallel_LIBRARY = ${SUNDIALS_nvecparallel_LIBRARY}")
+if(SUNDIALS_DEBUG)
+  message(
+    STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
+           " SUNDIALS_nvecparallel_LIBRARY = ${SUNDIALS_nvecparallel_LIBRARY}"
+  )
 endif()
 
-if (NOT SUNDIALS_nvecparallel_LIBRARY)
+if(NOT SUNDIALS_nvecparallel_LIBRARY)
   message(FATAL_ERROR "Sundials requested but SUNDIALS nvecparallel not found.")
 endif()
 list(APPEND SUNDIALS_LIBRARIES "${SUNDIALS_nvecparallel_LIBRARY}")
@@ -81,62 +82,86 @@ mark_as_advanced(SUNDIALS_nvecparallel_LIBRARY)
 
 set(SUNDIALS_COMPONENTS arkode cvode ida)
 
-foreach (LIB ${SUNDIALS_COMPONENTS})
-  find_library(SUNDIALS_${LIB}_LIBRARY
+foreach(LIB ${SUNDIALS_COMPONENTS})
+  find_library(
+    SUNDIALS_${LIB}_LIBRARY
     NAMES sundials_${LIB}
-    HINTS
-      "${SUNDIALS_INCLUDE_DIR}/.."
-      "${SUNDIALS_INCLUDE_DIR}/../.."
+    HINTS "${SUNDIALS_INCLUDE_DIR}/.." "${SUNDIALS_INCLUDE_DIR}/../.."
     PATH_SUFFIXES lib lib64
-    )
+  )
 
-  if (SUNDIALS_DEBUG)
+  if(SUNDIALS_DEBUG)
     message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-      " SUNDIALS_${LIB}_LIBRARY = ${SUNDIALS_${LIB}_LIBRARY}")
+                   " SUNDIALS_${LIB}_LIBRARY = ${SUNDIALS_${LIB}_LIBRARY}"
+    )
   endif()
 
-  if (NOT SUNDIALS_${LIB}_LIBRARY)
+  if(NOT SUNDIALS_${LIB}_LIBRARY)
     message(FATAL_ERROR "Sundials requested but SUNDIALS ${LIB} not found.")
   endif()
   list(APPEND SUNDIALS_LIBRARIES "${SUNDIALS_${LIB}_LIBRARY}")
   mark_as_advanced(SUNDIALS_${LIB}_LIBRARY)
 endforeach()
 
-if (SUNDIALS_INCLUDE_DIR)
+if(SUNDIALS_INCLUDE_DIR)
   file(READ "${SUNDIALS_INCLUDE_DIR}/sundials_config.h" SUNDIALS_CONFIG_FILE)
   set(SUNDIALS_VERSION_REGEX_PATTERN
-    ".*#define SUNDIALS_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*")
-  string(REGEX MATCH ${SUNDIALS_VERSION_REGEX_PATTERN} _ "${SUNDIALS_CONFIG_FILE}")
-  set(SUNDIALS_VERSION_MAJOR ${CMAKE_MATCH_1} CACHE STRING "")
-  set(SUNDIALS_VERSION_MINOR ${CMAKE_MATCH_2} CACHE STRING "")
-  set(SUNDIALS_VERSION_PATCH ${CMAKE_MATCH_3} CACHE STRING "")
-  set(SUNDIALS_VERSION "${SUNDIALS_VERSION_MAJOR}.${SUNDIALS_VERSION_MINOR}.${SUNDIALS_VERSION_PATCH}" CACHE STRING "SUNDIALS version")
+      ".*#define SUNDIALS_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*"
+  )
+  string(REGEX MATCH ${SUNDIALS_VERSION_REGEX_PATTERN} _
+               "${SUNDIALS_CONFIG_FILE}"
+  )
+  set(SUNDIALS_VERSION_MAJOR
+      ${CMAKE_MATCH_1}
+      CACHE STRING ""
+  )
+  set(SUNDIALS_VERSION_MINOR
+      ${CMAKE_MATCH_2}
+      CACHE STRING ""
+  )
+  set(SUNDIALS_VERSION_PATCH
+      ${CMAKE_MATCH_3}
+      CACHE STRING ""
+  )
+  set(SUNDIALS_VERSION
+      "${SUNDIALS_VERSION_MAJOR}.${SUNDIALS_VERSION_MINOR}.${SUNDIALS_VERSION_PATCH}"
+      CACHE STRING "SUNDIALS version"
+  )
 endif()
 
-if (SUNDIALS_DEBUG)
+if(SUNDIALS_DEBUG)
   message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " SUNDIALS_VERSION = ${SUNDIALS_VERSION}")
+                 " SUNDIALS_VERSION = ${SUNDIALS_VERSION}"
+  )
 endif()
 
-find_package_handle_standard_args(SUNDIALS
+find_package_handle_standard_args(
+  SUNDIALS
   REQUIRED_VARS SUNDIALS_LIBRARIES SUNDIALS_INCLUDE_DIR SUNDIALS_INCLUDE_DIRS
   VERSION_VAR SUNDIALS_VERSION
-  )
+)
 
-set(SUNDIALS_LIBRARIES "${SUNDIALS_LIBRARIES}" CACHE STRING "SUNDIALS libraries")
+set(SUNDIALS_LIBRARIES
+    "${SUNDIALS_LIBRARIES}"
+    CACHE STRING "SUNDIALS libraries"
+)
 mark_as_advanced(SUNDIALS_LIBRARIES SUNDIALS_INCLUDE_DIR SUNDIALS_INCLUDE_DIRS)
 
-if (SUNDIALS_FOUND AND NOT TARGET SUNDIALS::SUNDIALS)
+if(SUNDIALS_FOUND AND NOT TARGET SUNDIALS::SUNDIALS)
   add_library(SUNDIALS::nvecparallel UNKNOWN IMPORTED)
-  set_target_properties(SUNDIALS::nvecparallel PROPERTIES
-    IMPORTED_LOCATION "${SUNDIALS_nvecparallel_LIBRARY}"
-    INTERFACE_INCLUDE_DIRECTORIES "${SUNDIALS_INCLUDE_DIRS}")
+  set_target_properties(
+    SUNDIALS::nvecparallel
+    PROPERTIES IMPORTED_LOCATION "${SUNDIALS_nvecparallel_LIBRARY}"
+               INTERFACE_INCLUDE_DIRECTORIES "${SUNDIALS_INCLUDE_DIRS}"
+  )
 
-  foreach (LIB ${SUNDIALS_COMPONENTS})  
+  foreach(LIB ${SUNDIALS_COMPONENTS})
     add_library(SUNDIALS::${LIB} UNKNOWN IMPORTED)
-    set_target_properties(SUNDIALS::${LIB} PROPERTIES
-      IMPORTED_LOCATION "${SUNDIALS_${LIB}_LIBRARY}"
-      INTERFACE_INCLUDE_DIRECTORIES "${SUNDIALS_INCLUDE_DIRS}"
-      INTERFACE_LINK_LIBRARIES SUNDIALS::nvecparallel)
+    set_target_properties(
+      SUNDIALS::${LIB}
+      PROPERTIES IMPORTED_LOCATION "${SUNDIALS_${LIB}_LIBRARY}"
+                 INTERFACE_INCLUDE_DIRECTORIES "${SUNDIALS_INCLUDE_DIRS}"
+                 INTERFACE_LINK_LIBRARIES SUNDIALS::nvecparallel
+    )
   endforeach()
 endif()
diff --git a/cmake/FindScoreP.cmake b/cmake/FindScoreP.cmake
index dd119545e8..80fe102749 100644
--- a/cmake/FindScoreP.cmake
+++ b/cmake/FindScoreP.cmake
@@ -61,76 +61,90 @@
 # IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
 # THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-
 find_program(ScoreP_CONFIG scorep-config)
 mark_as_advanced(ScoreP_CONFIG)
 
 get_filename_component(ScoreP_TMP "${ScoreP_CONFIG}" DIRECTORY)
 get_filename_component(ScoreP_EXEC_LOCATION "${ScoreP_TMP}" DIRECTORY)
 
-if (ScoreP_DEBUG)
+if(ScoreP_DEBUG)
   message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " ScoreP_CONFIG = ${ScoreP_CONFIG}"
-    " ScoreP_EXEC_LOCATION = ${ScoreP_EXEC_LOCATION}")
+                 " ScoreP_CONFIG = ${ScoreP_CONFIG}"
+                 " ScoreP_EXEC_LOCATION = ${ScoreP_EXEC_LOCATION}"
+  )
 endif()
 
 if(ScoreP_CONFIG)
   message(STATUS "SCOREP library found. (using ${ScoreP_CONFIG})")
 
-  execute_process(COMMAND ${ScoreP_CONFIG} "--user" "--nocompiler" "--cppflags"
-    OUTPUT_VARIABLE ScoreP_CONFIG_FLAGS)
+  execute_process(
+    COMMAND ${ScoreP_CONFIG} "--user" "--nocompiler" "--cppflags"
+    OUTPUT_VARIABLE ScoreP_CONFIG_FLAGS
+  )
 
-  string(REGEX MATCHALL "-I[^ ]*" ScoreP_CONFIG_INCLUDES "${ScoreP_CONFIG_FLAGS}")
+  string(REGEX MATCHALL "-I[^ ]*" ScoreP_CONFIG_INCLUDES
+               "${ScoreP_CONFIG_FLAGS}"
+  )
   foreach(inc ${ScoreP_CONFIG_INCLUDES})
     string(SUBSTRING ${inc} 2 -1 inc)
     list(APPEND ScoreP_INCLUDE_DIRS ${inc})
   endforeach()
 
-  if (ScoreP_DEBUG)
+  if(ScoreP_DEBUG)
     message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-      " ScoreP_INCLUDE_DIRS = ${ScoreP_INCLUDE_DIRS}")
+                   " ScoreP_INCLUDE_DIRS = ${ScoreP_INCLUDE_DIRS}"
+    )
   endif()
 
-  string(REGEX MATCHALL "(^| +)-[^I][^ ]*" ScoreP_CONFIG_CXXFLAGS "${ScoreP_CONFIG_FLAGS}")
+  string(REGEX MATCHALL "(^| +)-[^I][^ ]*" ScoreP_CONFIG_CXXFLAGS
+               "${ScoreP_CONFIG_FLAGS}"
+  )
   foreach(flag ${ScoreP_CONFIG_CXXFLAGS})
     string(STRIP ${flag} flag)
     list(APPEND ScoreP_CXX_FLAGS ${flag})
   endforeach()
 
-  if (ScoreP_DEBUG)
+  if(ScoreP_DEBUG)
     message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-      " ScoreP_CXX_FLAGS = ${ScoreP_CXX_FLAGS}")
+                   " ScoreP_CXX_FLAGS = ${ScoreP_CXX_FLAGS}"
+    )
   endif()
 
   unset(ScoreP_CONFIG_FLAGS)
   unset(ScoreP_CONFIG_INCLUDES)
   unset(ScoreP_CONFIG_CXXFLAGS)
 
-  execute_process(COMMAND ${ScoreP_CONFIG} "--user" "--nocompiler" "--ldflags"
-    OUTPUT_VARIABLE _LINK_LD_ARGS)
-  string( REPLACE " " ";" _LINK_LD_ARGS ${_LINK_LD_ARGS} )
-  foreach( _ARG ${_LINK_LD_ARGS} )
+  execute_process(
+    COMMAND ${ScoreP_CONFIG} "--user" "--nocompiler" "--ldflags"
+    OUTPUT_VARIABLE _LINK_LD_ARGS
+  )
+  string(REPLACE " " ";" _LINK_LD_ARGS ${_LINK_LD_ARGS})
+  foreach(_ARG ${_LINK_LD_ARGS})
     if(${_ARG} MATCHES "^-L")
-      STRING(REGEX REPLACE "^-L" "" _ARG ${_ARG})
-      SET(ScoreP_LINK_DIRS ${ScoreP_LINK_DIRS} ${_ARG})
+      string(REGEX REPLACE "^-L" "" _ARG ${_ARG})
+      set(ScoreP_LINK_DIRS ${ScoreP_LINK_DIRS} ${_ARG})
     endif()
   endforeach()
 
-  if (ScoreP_DEBUG)
+  if(ScoreP_DEBUG)
     message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-      " ScoreP_LINK_DIRS = ${ScoreP_LINK_DIRS}")
+                   " ScoreP_LINK_DIRS = ${ScoreP_LINK_DIRS}"
+    )
   endif()
 
-  execute_process(COMMAND ${ScoreP_CONFIG} "--user" "--nocompiler" "--libs"
-    OUTPUT_VARIABLE _LINK_LD_ARGS)
-  string( REPLACE " " ";" _LINK_LD_ARGS ${_LINK_LD_ARGS} )
-  foreach( _ARG ${_LINK_LD_ARGS} )
+  execute_process(
+    COMMAND ${ScoreP_CONFIG} "--user" "--nocompiler" "--libs"
+    OUTPUT_VARIABLE _LINK_LD_ARGS
+  )
+  string(REPLACE " " ";" _LINK_LD_ARGS ${_LINK_LD_ARGS})
+  foreach(_ARG ${_LINK_LD_ARGS})
     if(${_ARG} MATCHES "^-l")
       string(REGEX REPLACE "^-l" "" _ARG ${_ARG})
-      find_library(_SCOREP_LIB_FROM_ARG NAMES ${_ARG}
-        PATHS
-        ${ScoreP_LINK_DIRS}
-        )
+      find_library(
+        _SCOREP_LIB_FROM_ARG
+        NAMES ${_ARG}
+        PATHS ${ScoreP_LINK_DIRS}
+      )
       if(_SCOREP_LIB_FROM_ARG)
         set(ScoreP_LIBRARIES ${ScoreP_LIBRARIES} ${_SCOREP_LIB_FROM_ARG})
       endif()
@@ -138,26 +152,26 @@ if(ScoreP_CONFIG)
     endif()
   endforeach()
 
-  if (ScoreP_DEBUG)
+  if(ScoreP_DEBUG)
     message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-      " ScoreP_LIBRARIES = ${ScoreP_LIBRARIES}")
+                   " ScoreP_LIBRARIES = ${ScoreP_LIBRARIES}"
+    )
   endif()
 
 endif()
 
-include (FindPackageHandleStandardArgs)
-find_package_handle_standard_args(ScoreP DEFAULT_MSG
-    ScoreP_CONFIG
-    ScoreP_LIBRARIES
-    ScoreP_INCLUDE_DIRS
-  )
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(
+  ScoreP DEFAULT_MSG ScoreP_CONFIG ScoreP_LIBRARIES ScoreP_INCLUDE_DIRS
+)
 
-if (ScoreP_FOUND AND NOT TARGET ScoreP::ScoreP)
+if(ScoreP_FOUND AND NOT TARGET ScoreP::ScoreP)
   add_library(ScoreP::ScoreP UNKNOWN IMPORTED)
-  set_target_properties(ScoreP::ScoreP PROPERTIES
-    INTERFACE_INCLUDE_DIRECTORIES "${ScoreP_INCLUDE_DIRS}"
-    IMPORTED_LINK_INTERFACE_LIBRARIES "${ScoreP_LIBRARIES}"
-    INTERFACE_INCLUDE_DEFINITIONS "${ScoreP_CXX_FLAGS}"
-    IMPORTED_LINK_INTERFACE_LANGUAGES "C"
-    )
+  set_target_properties(
+    ScoreP::ScoreP
+    PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${ScoreP_INCLUDE_DIRS}"
+               IMPORTED_LINK_INTERFACE_LIBRARIES "${ScoreP_LIBRARIES}"
+               INTERFACE_INCLUDE_DEFINITIONS "${ScoreP_CXX_FLAGS}"
+               IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+  )
 endif()
diff --git a/cmake/FindSphinx.cmake b/cmake/FindSphinx.cmake
index fd377d0d00..a15ae8d6f9 100644
--- a/cmake/FindSphinx.cmake
+++ b/cmake/FindSphinx.cmake
@@ -14,13 +14,15 @@
 # https://devblogs.microsoft.com/cppblog/clear-functional-c-documentation-with-sphinx-breathe-doxygen-cmake/
 
 #Look for an executable called sphinx-build
-find_program(SPHINX_EXECUTABLE
-             NAMES sphinx-build sphinx-build-3
-             DOC "Path to sphinx-build executable")
+find_program(
+  SPHINX_EXECUTABLE
+  NAMES sphinx-build sphinx-build-3
+  DOC "Path to sphinx-build executable"
+)
 
 include(FindPackageHandleStandardArgs)
 
 #Handle standard arguments to find_package like REQUIRED and QUIET
-find_package_handle_standard_args(Sphinx
-                                  "Failed to find sphinx-build executable"
-                                  SPHINX_EXECUTABLE)
+find_package_handle_standard_args(
+  Sphinx "Failed to find sphinx-build executable" SPHINX_EXECUTABLE
+)
diff --git a/cmake/FindnetCDF.cmake b/cmake/FindnetCDF.cmake
index 361095954e..ca6eff8d75 100644
--- a/cmake/FindnetCDF.cmake
+++ b/cmake/FindnetCDF.cmake
@@ -28,119 +28,129 @@
 include(BOUT++functions)
 include(CMakePrintHelpers)
 
-if (NOT netCDF_ROOT AND EXISTS "${BOUT_USE_NETCDF}")
+if(NOT netCDF_ROOT AND EXISTS "${BOUT_USE_NETCDF}")
   set(netCDF_ROOT "${BOUT_USE_NETCDF}")
 endif()
 
 enable_language(C)
 find_package(netCDF QUIET CONFIG)
 
-if (netCDF_FOUND)
+if(netCDF_FOUND)
   message(STATUS "netCDF CONFIG found")
   set(netCDF_FOUND TRUE)
-  if (NOT TARGET netCDF::netcdf)
+  if(NOT TARGET netCDF::netcdf)
     bout_add_library_alias(netCDF::netcdf netcdf)
   endif()
-  if (netCDF_DEBUG)
-     cmake_print_properties(TARGETS netcdf PROPERTIES LOCATION VERSION)
-  endif (netCDF_DEBUG)
+  if(netCDF_DEBUG)
+    cmake_print_properties(TARGETS netcdf PROPERTIES LOCATION VERSION)
+  endif(netCDF_DEBUG)
   return()
 endif()
 
-find_program(NC_CONFIG "nc-config"
+find_program(
+  NC_CONFIG "nc-config"
   PATHS "${netCDF_ROOT}"
   PATH_SUFFIXES bin
   DOC "Path to netCDF C config helper"
   NO_DEFAULT_PATH
-  )
+)
 
-find_program(NC_CONFIG "nc-config"
-  DOC "Path to netCDF C config helper"
-  )
+find_program(NC_CONFIG "nc-config" DOC "Path to netCDF C config helper")
 
 get_filename_component(NC_CONFIG_TMP "${NC_CONFIG}" DIRECTORY)
 get_filename_component(NC_CONFIG_LOCATION "${NC_CONFIG_TMP}" DIRECTORY)
-if (netCDF_DEBUG)
+if(netCDF_DEBUG)
   message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " NC_CONFIG_LOCATION = ${NC_CONFIG_LOCATION}"
-    " netCDF_ROOT = ${netCDF_ROOT}")
+                 " NC_CONFIG_LOCATION = ${NC_CONFIG_LOCATION}"
+                 " netCDF_ROOT = ${netCDF_ROOT}"
+  )
 endif()
 
 bout_inspect_netcdf_config(NC_HINTS_INCLUDE_DIR "${NC_CONFIG}" "--includedir")
 bout_inspect_netcdf_config(NC_HINTS_PREFIX "${NC_CONFIG}" "--prefix")
 
-find_path(netCDF_C_INCLUDE_DIR
+find_path(
+  netCDF_C_INCLUDE_DIR
   NAMES netcdf.h
   DOC "netCDF C include directories"
-  HINTS
-    "${NC_HINTS_INCLUDE_DIR}"
-    "${NC_HINTS_PREFIX}"
-    "${NC_CONFIG_LOCATION}"
-  PATH_SUFFIXES
-    "include"
+  HINTS "${NC_HINTS_INCLUDE_DIR}" "${NC_HINTS_PREFIX}" "${NC_CONFIG_LOCATION}"
+  PATH_SUFFIXES "include"
+)
+if(netCDF_DEBUG)
+  message(
+    STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
+           " netCDF_C_INCLUDE_DIR = ${netCDF_C_INCLUDE_DIR}"
+           " NC_HINTS_INCLUDE_DIR = ${NC_HINTS_INCLUDE_DIR}"
+           " NC_HINTS_PREFIX = ${NC_HINTS_PREFIX}"
   )
-if (netCDF_DEBUG)
-  message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " netCDF_C_INCLUDE_DIR = ${netCDF_C_INCLUDE_DIR}"
-    " NC_HINTS_INCLUDE_DIR = ${NC_HINTS_INCLUDE_DIR}"
-    " NC_HINTS_PREFIX = ${NC_HINTS_PREFIX}"
-    )
 endif()
 mark_as_advanced(netCDF_C_INCLUDE_DIR)
 
-find_library(netCDF_C_LIBRARY
+find_library(
+  netCDF_C_LIBRARY
   NAMES netcdf
   DOC "netCDF C library"
-  HINTS
-    "${NC_HINTS_INCLUDE_DIR}"
-    "${NC_HINTS_PREFIX}"
-    "${NC_CONFIG_LOCATION}"
-  PATH_SUFFIXES
-    "lib" "lib64"
- )
-if (netCDF_DEBUG)
-  message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " netCDF_C_LIBRARY = ${netCDF_C_LIBRARY}"
-    " NC_HINTS_INCLUDE_DIR = ${NC_HINTS_INCLUDE_DIR}"
-    " NC_HINTS_PREFIX = ${NC_HINTS_PREFIX}"
-    )
+  HINTS "${NC_HINTS_INCLUDE_DIR}" "${NC_HINTS_PREFIX}" "${NC_CONFIG_LOCATION}"
+  PATH_SUFFIXES "lib" "lib64"
+)
+if(netCDF_DEBUG)
+  message(
+    STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
+           " netCDF_C_LIBRARY = ${netCDF_C_LIBRARY}"
+           " NC_HINTS_INCLUDE_DIR = ${NC_HINTS_INCLUDE_DIR}"
+           " NC_HINTS_PREFIX = ${NC_HINTS_PREFIX}"
+  )
 endif()
 mark_as_advanced(netCDF_C_LIBRARY)
 
-if (netCDF_C_INCLUDE_DIR)
+if(netCDF_C_INCLUDE_DIR)
   file(STRINGS "${netCDF_C_INCLUDE_DIR}/netcdf_meta.h" _netcdf_version_lines
-    REGEX "#define[ \t]+NC_VERSION_(MAJOR|MINOR|PATCH|NOTE)")
-  string(REGEX REPLACE ".*NC_VERSION_MAJOR *\([0-9]*\).*" "\\1" _netcdf_version_major "${_netcdf_version_lines}")
-  string(REGEX REPLACE ".*NC_VERSION_MINOR *\([0-9]*\).*" "\\1" _netcdf_version_minor "${_netcdf_version_lines}")
-  string(REGEX REPLACE ".*NC_VERSION_PATCH *\([0-9]*\).*" "\\1" _netcdf_version_patch "${_netcdf_version_lines}")
-  string(REGEX REPLACE ".*NC_VERSION_NOTE *\"\([^\"]*\)\".*" "\\1" _netcdf_version_note "${_netcdf_version_lines}")
-  if (NOT _netcdf_version_note STREQUAL "")
+       REGEX "#define[ \t]+NC_VERSION_(MAJOR|MINOR|PATCH|NOTE)"
+  )
+  string(REGEX REPLACE ".*NC_VERSION_MAJOR *\([0-9]*\).*" "\\1"
+                       _netcdf_version_major "${_netcdf_version_lines}"
+  )
+  string(REGEX REPLACE ".*NC_VERSION_MINOR *\([0-9]*\).*" "\\1"
+                       _netcdf_version_minor "${_netcdf_version_lines}"
+  )
+  string(REGEX REPLACE ".*NC_VERSION_PATCH *\([0-9]*\).*" "\\1"
+                       _netcdf_version_patch "${_netcdf_version_lines}"
+  )
+  string(REGEX REPLACE ".*NC_VERSION_NOTE *\"\([^\"]*\)\".*" "\\1"
+                       _netcdf_version_note "${_netcdf_version_lines}"
+  )
+  if(NOT _netcdf_version_note STREQUAL "")
     # Make development version compare higher than any patch level
     set(_netcdf_version_note ".99")
   endif()
-  set(netCDF_VERSION "${_netcdf_version_major}.${_netcdf_version_minor}.${_netcdf_version_patch}${_netcdf_version_note}")
+  set(netCDF_VERSION
+      "${_netcdf_version_major}.${_netcdf_version_minor}.${_netcdf_version_patch}${_netcdf_version_note}"
+  )
   unset(_netcdf_version_major)
   unset(_netcdf_version_minor)
   unset(_netcdf_version_patch)
   unset(_netcdf_version_note)
   unset(_netcdf_version_lines)
-endif ()
+endif()
 
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(netCDF
+find_package_handle_standard_args(
+  netCDF
   REQUIRED_VARS netCDF_C_LIBRARY netCDF_C_INCLUDE_DIR
-  VERSION_VAR netCDF_VERSION)
+  VERSION_VAR netCDF_VERSION
+)
 
-if (netCDF_FOUND)
+if(netCDF_FOUND)
   set(netCDF_INCLUDE_DIR "${netCDF_C_INCLUDE_DIR}")
   set(netCDF_INCLUDE_DIRS "${netCDF_C_INCLUDE_DIR}")
   set(netCDF_LIBRARIES "${netCDF_C_LIBRARY}")
 
-  if (NOT TARGET netCDF::netcdf)
+  if(NOT TARGET netCDF::netcdf)
     add_library(netCDF::netcdf UNKNOWN IMPORTED)
-    set_target_properties(netCDF::netcdf PROPERTIES
-      IMPORTED_LOCATION "${netCDF_C_LIBRARY}"
-      INTERFACE_INCLUDE_DIRECTORIES "${netCDF_C_INCLUDE_DIR}"
-      )
-  endif ()
-endif ()
+    set_target_properties(
+      netCDF::netcdf
+      PROPERTIES IMPORTED_LOCATION "${netCDF_C_LIBRARY}"
+                 INTERFACE_INCLUDE_DIRECTORIES "${netCDF_C_INCLUDE_DIR}"
+    )
+  endif()
+endif()
diff --git a/cmake/FindnetCDFCxx.cmake b/cmake/FindnetCDFCxx.cmake
index d4155dc760..78bd93851e 100644
--- a/cmake/FindnetCDFCxx.cmake
+++ b/cmake/FindnetCDFCxx.cmake
@@ -27,16 +27,16 @@
 
 include(BOUT++functions)
 
-if (NOT netCDFCxx_ROOT AND EXISTS "${BOUT_USE_NETCDF}")
+if(NOT netCDFCxx_ROOT AND EXISTS "${BOUT_USE_NETCDF}")
   set(netCDFCxx_ROOT "${BOUT_USE_NETCDF}")
 endif()
 
-if (NOT EXISTS ${NCXX4_CONFIG})
+if(NOT EXISTS ${NCXX4_CONFIG})
   # Only search if NCXX4_CONFIG was not set explicitly
   find_package(netCDFCxx QUIET CONFIG)
-  if (netCDFCxx_FOUND)
+  if(netCDFCxx_FOUND)
     set(netCDFCxx_FOUND TRUE)
-    if (NOT TARGET netCDF::netcdf-cxx4)
+    if(NOT TARGET netCDF::netcdf-cxx4)
       bout_add_library_alias(netCDF::netcdf-cxx4 netcdf-cxx4)
     endif()
     return()
@@ -45,73 +45,74 @@ endif()
 
 find_package(netCDF REQUIRED)
 
-find_program(NCXX4_CONFIG "ncxx4-config"
+find_program(
+  NCXX4_CONFIG "ncxx4-config"
   PATHS "${netCDFCxx_ROOT}"
   PATH_SUFFIXES bin
   DOC "Path to netCDF C++ config helper"
   NO_DEFAULT_PATH
-  )
+)
 
-find_program(NCXX4_CONFIG "ncxx4-config"
-  DOC "Path to netCDF C++ config helper"
-  )
+find_program(NCXX4_CONFIG "ncxx4-config" DOC "Path to netCDF C++ config helper")
 
 get_filename_component(NCXX4_CONFIG_TMP "${NCXX4_CONFIG}" DIRECTORY)
 get_filename_component(NCXX4_CONFIG_LOCATION "${NCXX4_CONFIG_TMP}" DIRECTORY)
-if (netCDFCxx_DEBUG)
+if(netCDFCxx_DEBUG)
   message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " NCXX4_CONFIG_LOCATION = ${NCXX4_CONFIG_LOCATION}")
+                 " NCXX4_CONFIG_LOCATION = ${NCXX4_CONFIG_LOCATION}"
+  )
 endif()
 
-bout_inspect_netcdf_config(NCXX4_HINTS_INCLUDE_DIR "${NCXX4_CONFIG}" "--includedir")
+bout_inspect_netcdf_config(
+  NCXX4_HINTS_INCLUDE_DIR "${NCXX4_CONFIG}" "--includedir"
+)
 bout_inspect_netcdf_config(NCXX4_HINTS_PREFIX "${NCXX4_CONFIG}" "--prefix")
 
-find_path(netCDF_CXX_INCLUDE_DIR
+find_path(
+  netCDF_CXX_INCLUDE_DIR
   NAMES netcdf
   DOC "netCDF C++ include directories"
-  HINTS
-    "${netCDF_C_INCLUDE_DIR}"
-    "${NCXX4_HINTS_INCLUDE_DIR}"
-    "${NCXX4_HINTS_PREFIX}"
-    "${NCXX4_CONFIG_LOCATION}"
-  PATH_SUFFIXES
-    "include"
+  HINTS "${netCDF_C_INCLUDE_DIR}" "${NCXX4_HINTS_INCLUDE_DIR}"
+        "${NCXX4_HINTS_PREFIX}" "${NCXX4_CONFIG_LOCATION}"
+  PATH_SUFFIXES "include"
+)
+if(netCDFCxx_DEBUG)
+  message(
+    STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
+           " netCDF_CXX_INCLUDE_DIR = ${netCDF_CXX_INCLUDE_DIR}"
+           " NCXX4_HINTS_INCLUDE_DIR = ${NCXX4_HINTS_INCLUDE_DIR}"
+           " NCXX4_HINTS_PREFIX = ${NCXX4_HINTS_PREFIX}"
   )
-if (netCDFCxx_DEBUG)
-  message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " netCDF_CXX_INCLUDE_DIR = ${netCDF_CXX_INCLUDE_DIR}"
-    " NCXX4_HINTS_INCLUDE_DIR = ${NCXX4_HINTS_INCLUDE_DIR}"
-    " NCXX4_HINTS_PREFIX = ${NCXX4_HINTS_PREFIX}"
-    )
 endif()
 mark_as_advanced(netCDF_CXX_INCLUDE_DIR)
 
-find_library(netCDF_CXX_LIBRARY
+find_library(
+  netCDF_CXX_LIBRARY
   NAMES netcdf_c++4 netcdf-cxx4
   DOC "netCDF C++ library"
-  HINTS
-    "${NCXX4_HINTS_INCLUDE_DIR}"
-    "${NCXX4_HINTS_PREFIX}"
-    "${NCXX4_CONFIG_LOCATION}"
-  PATH_SUFFIXES
-    "lib" "lib64"
+  HINTS "${NCXX4_HINTS_INCLUDE_DIR}" "${NCXX4_HINTS_PREFIX}"
+        "${NCXX4_CONFIG_LOCATION}"
+  PATH_SUFFIXES "lib" "lib64"
+)
+if(netCDFCxx_DEBUG)
+  message(
+    STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
+           " netCDF_CXX_LIBRARY = ${netCDF_CXX_LIBRARY}"
+           " NCXX4_HINTS_INCLUDE_DIR = ${NCXX4_HINTS_INCLUDE_DIR}"
+           " NCXX4_HINTS_PREFIX = ${NCXX4_HINTS_PREFIX}"
   )
-if (netCDFCxx_DEBUG)
-  message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
-    " netCDF_CXX_LIBRARY = ${netCDF_CXX_LIBRARY}"
-    " NCXX4_HINTS_INCLUDE_DIR = ${NCXX4_HINTS_INCLUDE_DIR}"
-    " NCXX4_HINTS_PREFIX = ${NCXX4_HINTS_PREFIX}"
-    )
 endif()
 mark_as_advanced(netCDF_CXX_LIBRARY)
 
 bout_inspect_netcdf_config(_ncxx4_version "${NCXX4_CONFIG}" "--version")
-if (_ncxx4_version)
+if(_ncxx4_version)
   # Change to lower case before matching, to avoid case problems
   string(TOLOWER "${_ncxx4_version}" _ncxx4_version_lower)
-  string(REGEX REPLACE "netcdf-cxx4 \([0-9]+\\.[0-9]+\\.[0-9]+\).*" "\\1" netCDFCxx_VERSION "${_ncxx4_version_lower}")
+  string(REGEX REPLACE "netcdf-cxx4 \([0-9]+\\.[0-9]+\\.[0-9]+\).*" "\\1"
+                       netCDFCxx_VERSION "${_ncxx4_version_lower}"
+  )
   message(STATUS "Found netCDFCxx version ${netCDFCxx_VERSION}")
-else ()
+else()
   message(WARNING "Couldn't get NetCDF version")
 endif()
 
@@ -121,19 +122,23 @@ unset(_netcdf_version_minor)
 unset(_netcdf_version_patch)
 
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(netCDFCxx
+find_package_handle_standard_args(
+  netCDFCxx
   REQUIRED_VARS netCDF_CXX_LIBRARY netCDF_CXX_INCLUDE_DIR
-  VERSION_VAR netCDFCxx_VERSION)
+  VERSION_VAR netCDFCxx_VERSION
+)
 
-if (netCDFCxx_FOUND)
+if(netCDFCxx_FOUND)
   set(netCDFCxx_INCLUDE_DIRS "${netCDF_CXX_INCLUDE_DIR}")
   set(netCDFCxx_LIBRARIES "${netCDF_CXX_LIBRARY}")
 
-  if (NOT TARGET netCDF::netcdf-cxx4)
+  if(NOT TARGET netCDF::netcdf-cxx4)
     add_library(netCDF::netcdf-cxx4 UNKNOWN IMPORTED)
-    set_target_properties(netCDF::netcdf-cxx4 PROPERTIES
-      IMPORTED_LINK_INTERFACE_LIBRARIES netCDF::netcdf
-      IMPORTED_LOCATION "${netCDF_CXX_LIBRARY}"
-      INTERFACE_INCLUDE_DIRECTORIES "${netCDF_CXX_INCLUDE_DIR}")
-  endif ()
-endif ()
+    set_target_properties(
+      netCDF::netcdf-cxx4
+      PROPERTIES IMPORTED_LINK_INTERFACE_LIBRARIES netCDF::netcdf
+                 IMPORTED_LOCATION "${netCDF_CXX_LIBRARY}"
+                 INTERFACE_INCLUDE_DIRECTORIES "${netCDF_CXX_INCLUDE_DIR}"
+    )
+  endif()
+endif()
diff --git a/cmake/GenerateDateTimeFile.cmake b/cmake/GenerateDateTimeFile.cmake
index ef48fc4638..8ed742b31a 100644
--- a/cmake/GenerateDateTimeFile.cmake
+++ b/cmake/GenerateDateTimeFile.cmake
@@ -2,6 +2,9 @@
 # compilation date and time as variables
 
 set(bout_date_time_file
-  "const char* boutcompiledate{__DATE__}; const char* boutcompiletime{__TIME__};")
+    "const char* boutcompiledate{__DATE__}; const char* boutcompiletime{__TIME__};"
+)
 
-file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx" "${bout_date_time_file}")
+file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx"
+     "${bout_date_time_file}"
+)
diff --git a/cmake/GetGitRevisionDescription.cmake b/cmake/GetGitRevisionDescription.cmake
index 8ab03bc5f0..33f95dd589 100644
--- a/cmake/GetGitRevisionDescription.cmake
+++ b/cmake/GetGitRevisionDescription.cmake
@@ -37,7 +37,7 @@
 # http://www.boost.org/LICENSE_1_0.txt)
 
 if(__get_git_revision_description)
-	return()
+  return()
 endif()
 set(__get_git_revision_description YES)
 
@@ -46,123 +46,152 @@ set(__get_git_revision_description YES)
 get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
 
 function(get_git_head_revision _refspecvar _hashvar)
-	set(GIT_PARENT_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
-	set(GIT_DIR "${GIT_PARENT_DIR}/.git")
-	while(NOT EXISTS "${GIT_DIR}")	# .git dir not found, search parent directories
-		set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}")
-		get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH)
-		if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT)
-			# We have reached the root directory, we are not in git
-			set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
-			set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
-			return()
-		endif()
-		set(GIT_DIR "${GIT_PARENT_DIR}/.git")
-	endwhile()
-	# check if this is a submodule
-	if(NOT IS_DIRECTORY ${GIT_DIR})
-		file(READ ${GIT_DIR} submodule)
-		string(REGEX REPLACE "gitdir: (.*)\n$" "\\1" GIT_DIR_RELATIVE ${submodule})
-		get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH)
-		get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE)
-	endif()
-	set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
-	if(NOT EXISTS "${GIT_DATA}")
-		file(MAKE_DIRECTORY "${GIT_DATA}")
-	endif()
+  set(GIT_PARENT_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+  set(GIT_DIR "${GIT_PARENT_DIR}/.git")
+  while(NOT EXISTS "${GIT_DIR}") # .git dir not found, search parent directories
+    set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}")
+    get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH)
+    if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT)
+      # We have reached the root directory, we are not in git
+      set(${_refspecvar}
+          "GITDIR-NOTFOUND"
+          PARENT_SCOPE
+      )
+      set(${_hashvar}
+          "GITDIR-NOTFOUND"
+          PARENT_SCOPE
+      )
+      return()
+    endif()
+    set(GIT_DIR "${GIT_PARENT_DIR}/.git")
+  endwhile()
+  # check if this is a submodule
+  if(NOT IS_DIRECTORY ${GIT_DIR})
+    file(READ ${GIT_DIR} submodule)
+    string(REGEX REPLACE "gitdir: (.*)\n$" "\\1" GIT_DIR_RELATIVE ${submodule})
+    get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH)
+    get_filename_component(
+      GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE
+    )
+  endif()
+  set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
+  if(NOT EXISTS "${GIT_DATA}")
+    file(MAKE_DIRECTORY "${GIT_DATA}")
+  endif()
 
-	if(NOT EXISTS "${GIT_DIR}/HEAD")
-		return()
-	endif()
-	set(HEAD_FILE "${GIT_DATA}/HEAD")
-	configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY)
+  if(NOT EXISTS "${GIT_DIR}/HEAD")
+    return()
+  endif()
+  set(HEAD_FILE "${GIT_DATA}/HEAD")
+  configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY)
 
-	configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
-		"${GIT_DATA}/grabRef.cmake"
-		@ONLY)
-	include("${GIT_DATA}/grabRef.cmake")
+  configure_file(
+    "${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
+    "${GIT_DATA}/grabRef.cmake" @ONLY
+  )
+  include("${GIT_DATA}/grabRef.cmake")
 
-	set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE)
-	set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE)
+  set(${_refspecvar}
+      "${HEAD_REF}"
+      PARENT_SCOPE
+  )
+  set(${_hashvar}
+      "${HEAD_HASH}"
+      PARENT_SCOPE
+  )
 endfunction()
 
 function(git_describe _var)
-	if(NOT GIT_FOUND)
-		find_package(Git QUIET)
-	endif()
-	get_git_head_revision(refspec hash)
-	if(NOT GIT_FOUND)
-		set(${_var} "GIT-NOTFOUND" PARENT_SCOPE)
-		return()
-	endif()
-	if(NOT hash)
-		set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE)
-		return()
-	endif()
+  if(NOT GIT_FOUND)
+    find_package(Git QUIET)
+  endif()
+  get_git_head_revision(refspec hash)
+  if(NOT GIT_FOUND)
+    set(${_var}
+        "GIT-NOTFOUND"
+        PARENT_SCOPE
+    )
+    return()
+  endif()
+  if(NOT hash)
+    set(${_var}
+        "HEAD-HASH-NOTFOUND"
+        PARENT_SCOPE
+    )
+    return()
+  endif()
 
-	# TODO sanitize
-	#if((${ARGN}" MATCHES "&&") OR
-	#	(ARGN MATCHES "||") OR
-	#	(ARGN MATCHES "\\;"))
-	#	message("Please report the following error to the project!")
-	#	message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
-	#endif()
+  # TODO sanitize
+  #if((${ARGN}" MATCHES "&&") OR
+  #	(ARGN MATCHES "||") OR
+  #	(ARGN MATCHES "\\;"))
+  #	message("Please report the following error to the project!")
+  #	message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
+  #endif()
 
-	#message(STATUS "Arguments to execute_process: ${ARGN}")
+  #message(STATUS "Arguments to execute_process: ${ARGN}")
 
-	execute_process(COMMAND
-		"${GIT_EXECUTABLE}"
-		describe
-		${hash}
-		${ARGN}
-		WORKING_DIRECTORY
-		"${CMAKE_CURRENT_SOURCE_DIR}"
-		RESULT_VARIABLE
-		res
-		OUTPUT_VARIABLE
-		out
-		ERROR_QUIET
-		OUTPUT_STRIP_TRAILING_WHITESPACE)
-	if(NOT res EQUAL 0)
-		set(out "${out}-${res}-NOTFOUND")
-	endif()
+  execute_process(
+    COMMAND "${GIT_EXECUTABLE}" describe ${hash} ${ARGN}
+    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+    RESULT_VARIABLE res
+    OUTPUT_VARIABLE out
+    ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+  if(NOT res EQUAL 0)
+    set(out "${out}-${res}-NOTFOUND")
+  endif()
 
-	set(${_var} "${out}" PARENT_SCOPE)
+  set(${_var}
+      "${out}"
+      PARENT_SCOPE
+  )
 endfunction()
 
 function(git_get_exact_tag _var)
-	git_describe(out --exact-match ${ARGN})
-	set(${_var} "${out}" PARENT_SCOPE)
+  git_describe(out --exact-match ${ARGN})
+  set(${_var}
+      "${out}"
+      PARENT_SCOPE
+  )
 endfunction()
 
 function(git_local_changes _var)
-	if(NOT GIT_FOUND)
-		find_package(Git QUIET)
-	endif()
-	get_git_head_revision(refspec hash)
-	if(NOT GIT_FOUND)
-		set(${_var} "GIT-NOTFOUND" PARENT_SCOPE)
-		return()
-	endif()
-	if(NOT hash)
-		set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE)
-		return()
-	endif()
+  if(NOT GIT_FOUND)
+    find_package(Git QUIET)
+  endif()
+  get_git_head_revision(refspec hash)
+  if(NOT GIT_FOUND)
+    set(${_var}
+        "GIT-NOTFOUND"
+        PARENT_SCOPE
+    )
+    return()
+  endif()
+  if(NOT hash)
+    set(${_var}
+        "HEAD-HASH-NOTFOUND"
+        PARENT_SCOPE
+    )
+    return()
+  endif()
 
-	execute_process(COMMAND
-		"${GIT_EXECUTABLE}"
-		diff-index --quiet HEAD --
-		WORKING_DIRECTORY
-		"${CMAKE_CURRENT_SOURCE_DIR}"
-		RESULT_VARIABLE
-		res
-		OUTPUT_VARIABLE
-		out
-		ERROR_QUIET
-		OUTPUT_STRIP_TRAILING_WHITESPACE)
-	if(res EQUAL 0)
-		set(${_var} "CLEAN" PARENT_SCOPE)
-	else()
-		set(${_var} "DIRTY" PARENT_SCOPE)
-	endif()
+  execute_process(
+    COMMAND "${GIT_EXECUTABLE}" diff-index --quiet HEAD --
+    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+    RESULT_VARIABLE res
+    OUTPUT_VARIABLE out
+    ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+  if(res EQUAL 0)
+    set(${_var}
+        "CLEAN"
+        PARENT_SCOPE
+    )
+  else()
+    set(${_var}
+        "DIRTY"
+        PARENT_SCOPE
+    )
+  endif()
 endfunction()
diff --git a/cmake/ResolveCompilerPaths.cmake b/cmake/ResolveCompilerPaths.cmake
index 54787fa38f..d4274496df 100644
--- a/cmake/ResolveCompilerPaths.cmake
+++ b/cmake/ResolveCompilerPaths.cmake
@@ -38,68 +38,77 @@
 #
 #  assuming both directories exist.
 #  Note: as currently implemented, the -I/string will be picked up mistakenly (cry, cry)
-include (CorrectWindowsPaths)
+include(CorrectWindowsPaths)
 
-macro (RESOLVE_LIBRARIES LIBS LINK_LINE)
-  string (REGEX MATCHALL "((-L|-l|-Wl)([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))" _all_tokens "${LINK_LINE}")
-  set (_libs_found "")
-  set (_directory_list "")
-  foreach (token ${_all_tokens})
-    if (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+macro(RESOLVE_LIBRARIES LIBS LINK_LINE)
+  string(REGEX MATCHALL
+               "((-L|-l|-Wl)([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))"
+               _all_tokens "${LINK_LINE}"
+  )
+  set(_libs_found "")
+  set(_directory_list "")
+  foreach(token ${_all_tokens})
+    if(token MATCHES "-L([^\" ]+|\"[^\"]+\")")
       # If it's a library path, add it to the list
-      string (REGEX REPLACE "^-L" "" token ${token})
-      string (REGEX REPLACE "//" "/" token ${token})
+      string(REGEX REPLACE "^-L" "" token ${token})
+      string(REGEX REPLACE "//" "/" token ${token})
       convert_cygwin_path(token)
-      list (APPEND _directory_list ${token})
-    elseif (token MATCHES "^(-l([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))")
+      list(APPEND _directory_list ${token})
+    elseif(token MATCHES "^(-l([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))")
       # It's a library, resolve the path by looking in the list and then (by default) in system directories
-      if (WIN32) #windows expects "libfoo", linux expects "foo"
-        string (REGEX REPLACE "^-l" "lib" token ${token})
-      else (WIN32)
-        string (REGEX REPLACE "^-l" "" token ${token})
-      endif (WIN32)
-      set (_root "")
-      if (token MATCHES "^/")	# We have an absolute path
+      if(WIN32) #windows expects "libfoo", linux expects "foo"
+        string(REGEX REPLACE "^-l" "lib" token ${token})
+      else(WIN32)
+        string(REGEX REPLACE "^-l" "" token ${token})
+      endif(WIN32)
+      set(_root "")
+      if(token MATCHES "^/") # We have an absolute path
         #separate into a path and a library name:
-        string (REGEX MATCH "[^/]*\\.(a|so|dll|lib)$" libname ${token})
-        string (REGEX MATCH ".*[^${libname}$]" libpath ${token})
+        string(REGEX MATCH "[^/]*\\.(a|so|dll|lib)$" libname ${token})
+        string(REGEX MATCH ".*[^${libname}$]" libpath ${token})
         convert_cygwin_path(libpath)
-        set (_directory_list ${_directory_list} ${libpath})
-        set (token ${libname})
-      endif (token MATCHES "^/")
-      set (_lib "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
-      find_library (_lib ${token} HINTS ${_directory_list} ${_root})
-      if (_lib)
-	string (REPLACE "//" "/" _lib ${_lib})
-        list (APPEND _libs_found ${_lib})
-      else (_lib)
-        message (STATUS "Unable to find library ${token}")
-      endif (_lib)
-    endif (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
-  endforeach (token)
-  set (_lib "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+        set(_directory_list ${_directory_list} ${libpath})
+        set(token ${libname})
+      endif(token MATCHES "^/")
+      set(_lib
+          "NOTFOUND"
+          CACHE FILEPATH "Cleared" FORCE
+      )
+      find_library(_lib ${token} HINTS ${_directory_list} ${_root})
+      if(_lib)
+        string(REPLACE "//" "/" _lib ${_lib})
+        list(APPEND _libs_found ${_lib})
+      else(_lib)
+        message(STATUS "Unable to find library ${token}")
+      endif(_lib)
+    endif(token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+  endforeach(token)
+  set(_lib
+      "NOTFOUND"
+      CACHE INTERNAL "Scratch variable" FORCE
+  )
   # only the LAST occurence of each library is required since there should be no circular dependencies
-  if (_libs_found)
-    list (REVERSE _libs_found)
-    list (REMOVE_DUPLICATES _libs_found)
-    list (REVERSE _libs_found)
-  endif (_libs_found)
-  set (${LIBS} "${_libs_found}")
-endmacro (RESOLVE_LIBRARIES)
+  if(_libs_found)
+    list(REVERSE _libs_found)
+    list(REMOVE_DUPLICATES _libs_found)
+    list(REVERSE _libs_found)
+  endif(_libs_found)
+  set(${LIBS} "${_libs_found}")
+endmacro(RESOLVE_LIBRARIES)
 
-macro (RESOLVE_INCLUDES INCS COMPILE_LINE)
-  string (REGEX MATCHALL "-I([^\" ]+|\"[^\"]+\")" _all_tokens "${COMPILE_LINE}")
-  set (_incs_found "")
-  foreach (token ${_all_tokens})
-    string (REGEX REPLACE "^-I" "" token ${token})
-    string (REGEX REPLACE "//" "/" token ${token})
+macro(RESOLVE_INCLUDES INCS COMPILE_LINE)
+  string(REGEX MATCHALL "-I([^\" ]+|\"[^\"]+\")" _all_tokens "${COMPILE_LINE}")
+  set(_incs_found "")
+  foreach(token ${_all_tokens})
+    string(REGEX REPLACE "^-I" "" token ${token})
+    string(REGEX REPLACE "//" "/" token ${token})
     convert_cygwin_path(token)
-    if (EXISTS ${token})
-      list (APPEND _incs_found ${token})
-    else (EXISTS ${token})
-      message (STATUS "Include directory ${token} does not exist")
-    endif (EXISTS ${token})
-  endforeach (token)
-  list (REMOVE_DUPLICATES _incs_found)
-  set (${INCS} "${_incs_found}")
-endmacro (RESOLVE_INCLUDES)
+    if(EXISTS ${token})
+      list(APPEND _incs_found ${token})
+    else(EXISTS ${token})
+      message(STATUS "Include directory ${token} does not exist")
+    endif(EXISTS ${token})
+  endforeach(token)
+  list(REMOVE_DUPLICATES _incs_found)
+  set(${INCS} "${_incs_found}")
+endmacro(RESOLVE_INCLUDES)
diff --git a/cmake/Sanitizers.cmake b/cmake/Sanitizers.cmake
index 715a08ab88..aab58d6f70 100644
--- a/cmake/Sanitizers.cmake
+++ b/cmake/Sanitizers.cmake
@@ -4,7 +4,9 @@
 
 function(enable_sanitizers target_name)
 
-  if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID MATCHES ".*Clang")
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID MATCHES
+                                             ".*Clang"
+  )
     option(ENABLE_COVERAGE "Enable coverage reporting for gcc/clang" FALSE)
     message(STATUS "Enable coverage: ${ENABLE_COVERAGE}")
 
@@ -17,33 +19,40 @@ function(enable_sanitizers target_name)
       find_program(genhtml_FOUND genhtml)
       message(STATUS "Looking for genhtml: ${genhtml_FOUND}")
 
-      if (lcov_FOUND AND genhtml_FOUND)
-        set(COVERAGE_NAME coverage CACHE STRING "Name of coverage output file")
+      if(lcov_FOUND AND genhtml_FOUND)
+        set(COVERAGE_NAME
+            coverage
+            CACHE STRING "Name of coverage output file"
+        )
         set(COVERAGE_FILE "${COVERAGE_NAME}.info")
-        set(COVERAGE_MSG "Open file://${PROJECT_SOURCE_DIR}/${COVERAGE_NAME}/index.html in your browser to view coverage HTML output")
+        set(COVERAGE_MSG
+            "Open file://${PROJECT_SOURCE_DIR}/${COVERAGE_NAME}/index.html in your browser to view coverage HTML output"
+        )
 
-        add_custom_target(code-coverage-capture
+        add_custom_target(
+          code-coverage-capture
           COMMAND
-            lcov -c --directory  "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/bout++.dir/src"
-              --output-file "${COVERAGE_FILE}"
-          COMMAND
-            genhtml --output-directory "${COVERAGE_NAME}" --demangle-cpp --legend --show-details "${COVERAGE_FILE}"
-          COMMAND
-            "${CMAKE_COMMAND}" -E echo ${COVERAGE_MSG}
+            lcov -c --directory
+            "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/bout++.dir/src"
+            --output-file "${COVERAGE_FILE}"
+          COMMAND genhtml --output-directory "${COVERAGE_NAME}" --demangle-cpp
+                  --legend --show-details "${COVERAGE_FILE}"
+          COMMAND "${CMAKE_COMMAND}" -E echo ${COVERAGE_MSG}
           WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
           COMMENT "Capturing coverage information"
-          BYPRODUCTS
-            "${COVERAGE_FILE}"
-            "${COVERAGE_NAME}/index.html"
-          )
+          BYPRODUCTS "${COVERAGE_FILE}" "${COVERAGE_NAME}/index.html"
+        )
 
-        add_custom_target(code-coverage-clean
-          COMMAND
-          lcov --zerocounters
+        add_custom_target(
+          code-coverage-clean
+          COMMAND lcov --zerocounters
           COMMENT "Cleaning coverage information"
-          )
+        )
       else()
-        message(FATAL_ERROR "Coverage enabled, but coverage-capture not available. Please install lcov")
+        message(
+          FATAL_ERROR
+            "Coverage enabled, but coverage-capture not available. Please install lcov"
+        )
       endif()
 
     endif()
@@ -60,7 +69,9 @@ function(enable_sanitizers target_name)
       list(APPEND SANITIZERS "leak")
     endif()
 
-    option(ENABLE_SANITIZER_UNDEFINED_BEHAVIOR "Enable undefined behavior sanitizer" FALSE)
+    option(ENABLE_SANITIZER_UNDEFINED_BEHAVIOR
+           "Enable undefined behavior sanitizer" FALSE
+    )
     if(ENABLE_SANITIZER_UNDEFINED_BEHAVIOR)
       list(APPEND SANITIZERS "undefined")
     endif()
@@ -68,7 +79,10 @@ function(enable_sanitizers target_name)
     option(ENABLE_SANITIZER_THREAD "Enable thread sanitizer" FALSE)
     if(ENABLE_SANITIZER_THREAD)
       if("address" IN_LIST SANITIZERS OR "leak" IN_LIST SANITIZERS)
-        message(WARNING "Thread sanitizer does not work with Address and Leak sanitizer enabled")
+        message(
+          WARNING
+            "Thread sanitizer does not work with Address and Leak sanitizer enabled"
+        )
       else()
         list(APPEND SANITIZERS "thread")
       endif()
@@ -78,32 +92,40 @@ function(enable_sanitizers target_name)
     if(ENABLE_SANITIZER_MEMORY AND CMAKE_CXX_COMPILER_ID MATCHES ".*Clang")
       if("address" IN_LIST SANITIZERS
          OR "thread" IN_LIST SANITIZERS
-         OR "leak" IN_LIST SANITIZERS)
-        message(WARNING "Memory sanitizer does not work with Address, Thread and Leak sanitizer enabled")
+         OR "leak" IN_LIST SANITIZERS
+      )
+        message(
+          WARNING
+            "Memory sanitizer does not work with Address, Thread and Leak sanitizer enabled"
+        )
       else()
         list(APPEND SANITIZERS "memory")
       endif()
     endif()
 
-    list(
-      JOIN
-      SANITIZERS
-      ","
-      LIST_OF_SANITIZERS)
+    list(JOIN SANITIZERS "," LIST_OF_SANITIZERS)
 
   endif()
 
   # Default value gets overridden below
-  set(BOUT_USE_SANITIZERS "None" PARENT_SCOPE)
+  set(BOUT_USE_SANITIZERS
+      "None"
+      PARENT_SCOPE
+  )
 
   if(LIST_OF_SANITIZERS)
-    if(NOT
-       "${LIST_OF_SANITIZERS}"
-       STREQUAL
-       "")
-      set(BOUT_USE_SANITIZERS ${LIST_OF_SANITIZERS} PARENT_SCOPE)
-      target_compile_options(${target_name} PUBLIC -fsanitize=${LIST_OF_SANITIZERS} -fno-omit-frame-pointer)
-      target_link_options(${target_name} PUBLIC -fsanitize=${LIST_OF_SANITIZERS})
+    if(NOT "${LIST_OF_SANITIZERS}" STREQUAL "")
+      set(BOUT_USE_SANITIZERS
+          ${LIST_OF_SANITIZERS}
+          PARENT_SCOPE
+      )
+      target_compile_options(
+        ${target_name} PUBLIC -fsanitize=${LIST_OF_SANITIZERS}
+                              -fno-omit-frame-pointer
+      )
+      target_link_options(
+        ${target_name} PUBLIC -fsanitize=${LIST_OF_SANITIZERS}
+      )
     endif()
   endif()
 
diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 42ba52b948..850809e856 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -1,12 +1,12 @@
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/cmake/")
 
 # determined in SetupCompilers.cmake
-if (BOUT_USE_MPI)
+if(BOUT_USE_MPI)
   target_link_libraries(bout++ PUBLIC MPI::MPI_CXX)
-endif ()
+endif()
 
 # determined in SetupCompilers.cmake
-if (BOUT_USE_OPENMP)
+if(BOUT_USE_OPENMP)
   target_link_libraries(bout++ PUBLIC OpenMP::OpenMP_CXX)
   set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -fopenmp")
   set(CONFIG_LDFLAGS_SHARED "${CONFIG_LDFLAGS_SHARED} -fopenmp")
@@ -14,7 +14,7 @@ if (BOUT_USE_OPENMP)
 endif()
 
 # determined in SetupCompilers.cmake
-if (BOUT_HAS_CUDA)
+if(BOUT_HAS_CUDA)
   enable_language(CUDA)
   message(STATUS "BOUT_HAS_CUDA ${CMAKE_CUDA_COMPILER}")
 
@@ -29,58 +29,65 @@ if (BOUT_HAS_CUDA)
   set_target_properties(bout++ PROPERTIES CUDA_SEPARABLE_COMPILATION ON)
   set_target_properties(bout++ PROPERTIES POSITION_INDEPENDENT_CODE ON)
   set_target_properties(bout++ PROPERTIES LINKER_LANGUAGE CUDA)
-endif ()   
+endif()
 
 # Caliper
 option(BOUT_ENABLE_CALIPER "Enable Caliper" OFF)
-if (BOUT_ENABLE_CALIPER)
+if(BOUT_ENABLE_CALIPER)
   find_package(caliper REQUIRED)
   target_include_directories(bout++ PUBLIC ${caliper_INCLUDE_DIR})
   target_link_libraries(bout++ PUBLIC caliper)
-endif ()
+endif()
 set(BOUT_HAS_CALIPER ${BOUT_ENABLE_CALIPER})
 
 # UMPIRE
 option(BOUT_ENABLE_UMPIRE "Enable UMPIRE memory management" OFF)
-if (BOUT_ENABLE_UMPIRE)
+if(BOUT_ENABLE_UMPIRE)
   find_package(UMPIRE REQUIRED)
   target_include_directories(bout++ PUBLIC ${UMPIRE_INCLUDE_DIRS}/include)
   target_link_libraries(bout++ PUBLIC umpire)
-endif ()
+endif()
 set(BOUT_HAS_UMPIRE ${BOUT_ENABLE_UMPIRE})
 
 # RAJA
 option(BOUT_ENABLE_RAJA "Enable RAJA" OFF)
-if (BOUT_ENABLE_RAJA)
+if(BOUT_ENABLE_RAJA)
   find_package(RAJA REQUIRED)
-  message(STATUS "RAJA_CONFIG:" ${RAJA_CONFIG}) 
+  message(STATUS "RAJA_CONFIG:" ${RAJA_CONFIG})
   string(FIND ${RAJA_CONFIG} "raja" loc)
   math(EXPR value "${loc} + 5" OUTPUT_FORMAT DECIMAL)
-  string(SUBSTRING ${RAJA_CONFIG} 0 ${value}  RAJA_PATH)
+  string(SUBSTRING ${RAJA_CONFIG} 0 ${value} RAJA_PATH)
   message(STATUS "RAJA_PATH" ${RAJA_PATH})
   target_include_directories(bout++ PUBLIC ${RAJA_PATH}/include)
   target_link_libraries(bout++ PUBLIC RAJA)
-endif ()
+endif()
 set(BOUT_HAS_RAJA ${BOUT_ENABLE_RAJA})
 
 # Hypre
 option(BOUT_USE_HYPRE "Enable support for Hypre solvers" OFF)
-if (BOUT_USE_HYPRE)
+if(BOUT_USE_HYPRE)
   enable_language(C)
   find_package(HYPRE REQUIRED)
   target_link_libraries(bout++ PUBLIC HYPRE::HYPRE)
-  if (HYPRE_WITH_CUDA AND BOUT_HAS_CUDA)
-     target_compile_definitions(bout++ PUBLIC "HYPRE_USING_CUDA;HYPRE_USING_UNIFIED_MEMORY")
-     target_link_libraries(bout++ PUBLIC CUDA::cusparse CUDA::curand CUDA::culibos CUDA::cublas CUDA::cublasLt)
-  endif ()
-endif ()
+  if(HYPRE_WITH_CUDA AND BOUT_HAS_CUDA)
+    target_compile_definitions(
+      bout++ PUBLIC "HYPRE_USING_CUDA;HYPRE_USING_UNIFIED_MEMORY"
+    )
+    target_link_libraries(
+      bout++ PUBLIC CUDA::cusparse CUDA::curand CUDA::culibos CUDA::cublas
+                    CUDA::cublasLt
+    )
+  endif()
+endif()
 message(STATUS "HYPRE support: ${BOUT_USE_HYPRE}")
 set(BOUT_HAS_HYPRE ${BOUT_USE_HYPRE})
 
 # PETSc
-option(BOUT_USE_PETSC "Enable support for PETSc time solvers and inversions" OFF)
-if (BOUT_USE_PETSC)
-  if (NOT CMAKE_SYSTEM_NAME STREQUAL "CrayLinuxEnvironment")
+option(BOUT_USE_PETSC "Enable support for PETSc time solvers and inversions"
+       OFF
+)
+if(BOUT_USE_PETSC)
+  if(NOT CMAKE_SYSTEM_NAME STREQUAL "CrayLinuxEnvironment")
     # Cray wrappers sort this out for us
     find_package(PETSc REQUIRED)
     target_link_libraries(bout++ PUBLIC PETSc::PETSc)
@@ -94,28 +101,44 @@ endif()
 message(STATUS "PETSc support: ${BOUT_USE_PETSC}")
 set(BOUT_HAS_PETSC ${BOUT_USE_PETSC})
 
-
-cmake_dependent_option(BOUT_USE_SYSTEM_MPARK_VARIANT "Use external installation of mpark.variant" OFF
-  "BOUT_UPDATE_GIT_SUBMODULE OR EXISTS ${PROJECT_SOURCE_DIR}/externalpackages/mpark.variant/CMakeLists.txt" ON)
+cmake_dependent_option(
+  BOUT_USE_SYSTEM_MPARK_VARIANT
+  "Use external installation of mpark.variant"
+  OFF
+  "BOUT_UPDATE_GIT_SUBMODULE OR EXISTS ${PROJECT_SOURCE_DIR}/externalpackages/mpark.variant/CMakeLists.txt"
+  ON
+)
 
 if(BOUT_USE_SYSTEM_MPARK_VARIANT)
   message(STATUS "Using external mpark.variant")
   find_package(mpark_variant REQUIRED)
-  get_target_property(MPARK_VARIANT_INCLUDE_PATH mpark_variant INTERFACE_INCLUDE_DIRECTORIES)
+  get_target_property(
+    MPARK_VARIANT_INCLUDE_PATH mpark_variant INTERFACE_INCLUDE_DIRECTORIES
+  )
 else()
   message(STATUS "Using mpark.variant submodule")
   bout_update_submodules()
   add_subdirectory(externalpackages/mpark.variant)
   if(NOT TARGET mpark_variant)
-    message(FATAL_ERROR "mpark_variant not found! Have you disabled the git submodules (BOUT_UPDATE_GIT_SUBMODULE)?")
+    message(
+      FATAL_ERROR
+        "mpark_variant not found! Have you disabled the git submodules (BOUT_UPDATE_GIT_SUBMODULE)?"
+    )
   endif()
-  set(MPARK_VARIANT_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/externalpackages/mpark.variant/include")
+  set(MPARK_VARIANT_INCLUDE_PATH
+      "${CMAKE_CURRENT_SOURCE_DIR}/externalpackages/mpark.variant/include"
+  )
   set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${MPARK_VARIANT_INCLUDE_PATH}")
 endif()
 target_link_libraries(bout++ PUBLIC mpark_variant)
 
-cmake_dependent_option(BOUT_USE_SYSTEM_FMT "Use external installation of fmt" OFF
-  "BOUT_UPDATE_GIT_SUBMODULE OR EXISTS ${PROJECT_SOURCE_DIR}/externalpackages/fmt/CMakeLists.txt" ON)
+cmake_dependent_option(
+  BOUT_USE_SYSTEM_FMT
+  "Use external installation of fmt"
+  OFF
+  "BOUT_UPDATE_GIT_SUBMODULE OR EXISTS ${PROJECT_SOURCE_DIR}/externalpackages/fmt/CMakeLists.txt"
+  ON
+)
 
 if(BOUT_USE_SYSTEM_FMT)
   message(STATUS "Using external fmt")
@@ -125,32 +148,46 @@ else()
   message(STATUS "Using fmt submodule")
   bout_update_submodules()
   # Need to install fmt alongside BOUT++
-  set(FMT_INSTALL ON CACHE BOOL "")
-  set(FMT_DEBUG_POSTFIX "" CACHE STRING "")
+  set(FMT_INSTALL
+      ON
+      CACHE BOOL ""
+  )
+  set(FMT_DEBUG_POSTFIX
+      ""
+      CACHE STRING ""
+  )
   add_subdirectory(externalpackages/fmt)
   if(NOT TARGET fmt::fmt)
-    message(FATAL_ERROR "fmt not found! Have you disabled the git submodules (BOUT_UPDATE_GIT_SUBMODULE)?")
+    message(
+      FATAL_ERROR
+        "fmt not found! Have you disabled the git submodules (BOUT_UPDATE_GIT_SUBMODULE)?"
+    )
   endif()
   # Build the library in <build dir>/lib: this makes updating the path
   # for bout-config much easier
-  set_target_properties(fmt PROPERTIES
-    LIBRARY_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib"
-    ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib")
-  set(FMT_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/externalpackages/fmt/include")
+  set_target_properties(
+    fmt PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib"
+                   ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib"
+  )
+  set(FMT_INCLUDE_PATH
+      "${CMAKE_CURRENT_SOURCE_DIR}/externalpackages/fmt/include"
+  )
   set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${FMT_INCLUDE_PATH}")
   set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -lfmt")
 endif()
 target_link_libraries(bout++ PUBLIC fmt::fmt)
 
 option(BOUT_USE_PVODE "Enable support for bundled PVODE" ON)
-if (BOUT_USE_PVODE)
+if(BOUT_USE_PVODE)
   add_subdirectory(externalpackages/PVODE)
   target_link_libraries(bout++ PUBLIC pvode pvpre)
   # Build the libraries in <build dir>/lib: this makes updating the
   # path for bout-config much easier
-  set_target_properties(pvode pvpre PROPERTIES
-    LIBRARY_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib"
-    ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib")
+  set_target_properties(
+    pvode pvpre
+    PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib"
+               ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib"
+  )
   set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -lpvode -lpvpre")
 endif()
 message(STATUS "PVODE support: ${BOUT_USE_PVODE}")
@@ -158,25 +195,30 @@ set(BOUT_HAS_PVODE ${BOUT_USE_PVODE})
 
 option(BOUT_USE_NETCDF "Enable support for NetCDF output" ON)
 option(BOUT_DOWNLOAD_NETCDF_CXX4 "Download and build netCDF-cxx4" OFF)
-if (BOUT_USE_NETCDF)
-  if (BOUT_DOWNLOAD_NETCDF_CXX4)
+if(BOUT_USE_NETCDF)
+  if(BOUT_DOWNLOAD_NETCDF_CXX4)
     message(STATUS "Downloading and configuring NetCDF-cxx4")
     include(FetchContent)
     FetchContent_Declare(
       netcdf-cxx4
       GIT_REPOSITORY https://github.com/Unidata/netcdf-cxx4
-      GIT_TAG        "a43d6d4d415d407712c246faca553bd951730dc1"
-      )
+      GIT_TAG "a43d6d4d415d407712c246faca553bd951730dc1"
+    )
     # Don't build the netcdf tests, they have lots of warnings
-    set(NCXX_ENABLE_TESTS OFF CACHE BOOL "" FORCE)
+    set(NCXX_ENABLE_TESTS
+        OFF
+        CACHE BOOL "" FORCE
+    )
     # Use our own FindnetCDF module which uses nc-config
     find_package(netCDF REQUIRED)
     FetchContent_MakeAvailable(netcdf-cxx4)
     target_link_libraries(bout++ PUBLIC netCDF::netcdf-cxx4)
   else()
     find_package(netCDFCxx)
-    if (netCDFCxx_FOUND)
-      set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${netCDF_CXX_LIBRARY} ${netCDF_LIBRARIES}")
+    if(netCDFCxx_FOUND)
+      set(CONFIG_LDFLAGS
+          "${CONFIG_LDFLAGS} ${netCDF_CXX_LIBRARY} ${netCDF_LIBRARIES}"
+      )
       target_link_libraries(bout++ PUBLIC netCDF::netcdf-cxx4)
     else()
       find_package(PkgConfig REQUIRED)
@@ -186,10 +228,10 @@ if (BOUT_USE_NETCDF)
       set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${NETCDF_LDFLAGS_STRING}")
     endif()
   endif()
-  if (netCDF_DIR)
+  if(netCDF_DIR)
     set(netCDF_ROOT "${netCDF_DIR}")
   endif()
-  if (netCDFCxx_DIR)
+  if(netCDFCxx_DIR)
     set(netCDFCxx_ROOT "${netCDFCxx_DIR}")
   endif()
 endif()
@@ -198,11 +240,11 @@ set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})
 
 option(BOUT_USE_ADIOS2 "Enable support for ADIOS output" OFF)
 option(BOUT_DOWNLOAD_ADIOS2 "Download and build ADIOS2" OFF)
-if (BOUT_USE_ADIOS2)
+if(BOUT_USE_ADIOS2)
   enable_language(C)
   find_package(MPI REQUIRED COMPONENTS C)
 
-  if (BOUT_DOWNLOAD_ADIOS2)
+  if(BOUT_DOWNLOAD_ADIOS2)
     message(STATUS "Downloading and configuring ADIOS2")
     include(FetchContent)
     FetchContent_Declare(
@@ -210,15 +252,33 @@ if (BOUT_USE_ADIOS2)
       GIT_REPOSITORY https://github.com/ornladios/ADIOS2.git
       GIT_TAG origin/master
       GIT_SHALLOW 1
-      )
-    set(ADIOS2_USE_MPI ON CACHE BOOL "" FORCE)
-    set(ADIOS2_USE_Fortran OFF CACHE BOOL "" FORCE)
-    set(ADIOS2_USE_Python OFF CACHE BOOL "" FORCE)
-    set(ADIOS2_BUILD_EXAMPLES OFF CACHE BOOL "" FORCE)
+    )
+    set(ADIOS2_USE_MPI
+        ON
+        CACHE BOOL "" FORCE
+    )
+    set(ADIOS2_USE_Fortran
+        OFF
+        CACHE BOOL "" FORCE
+    )
+    set(ADIOS2_USE_Python
+        OFF
+        CACHE BOOL "" FORCE
+    )
+    set(ADIOS2_BUILD_EXAMPLES
+        OFF
+        CACHE BOOL "" FORCE
+    )
     # Disable testing, or ADIOS will try to find or install GTEST
-    set(BUILD_TESTING OFF CACHE BOOL "" FORCE)
+    set(BUILD_TESTING
+        OFF
+        CACHE BOOL "" FORCE
+    )
     # Note: SST requires <rdma/fabric.h> but doesn't check at configure time
-    set(ADIOS2_USE_SST OFF CACHE BOOL "" FORCE)
+    set(ADIOS2_USE_SST
+        OFF
+        CACHE BOOL "" FORCE
+    )
     FetchContent_MakeAvailable(adios2)
     message(STATUS "ADIOS2 done configuring")
   else()
@@ -229,9 +289,8 @@ endif()
 message(STATUS "ADIOS2 support: ${BOUT_USE_ADIOS2}")
 set(BOUT_HAS_ADIOS2 ${BOUT_USE_ADIOS2})
 
-
 option(BOUT_USE_FFTW "Enable support for FFTW" ON)
-if (BOUT_USE_FFTW)
+if(BOUT_USE_FFTW)
   find_package(FFTW REQUIRED)
   target_link_libraries(bout++ PUBLIC FFTW::FFTW)
   set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${FFTW_LIBRARIES}")
@@ -244,15 +303,15 @@ option(BOUT_USE_LAPACK "Enable support for LAPACK" AUTO)
 set_property(CACHE BOUT_USE_LAPACK PROPERTY STRINGS ${ON_OFF_AUTO})
 
 set(LAPACK_FOUND OFF)
-if (BOUT_USE_LAPACK)
-  if (NOT CMAKE_SYSTEM_NAME STREQUAL "CrayLinuxEnvironment")
+if(BOUT_USE_LAPACK)
+  if(NOT CMAKE_SYSTEM_NAME STREQUAL "CrayLinuxEnvironment")
     # Cray wrappers sort this out for us
-    if (BOUT_USE_LAPACK STREQUAL ON)
+    if(BOUT_USE_LAPACK STREQUAL ON)
       find_package(LAPACK REQUIRED)
     else()
       find_package(LAPACK)
     endif()
-    if (LAPACK_FOUND)
+    if(LAPACK_FOUND)
       target_link_libraries(bout++ PUBLIC "${LAPACK_LIBRARIES}")
       string(JOIN " " CONFIG_LAPACK_LIBRARIES ${LAPACK_LIBRARIES})
       set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${CONFIG_LAPACK_LIBRARIES}")
@@ -264,7 +323,7 @@ message(STATUS "LAPACK support: ${LAPACK_FOUND}")
 set(BOUT_HAS_LAPACK ${LAPACK_FOUND})
 
 option(BOUT_USE_SLEPC "Enable support for SLEPc eigen solver" OFF)
-if (BOUT_USE_SLEPC)
+if(BOUT_USE_SLEPC)
   find_package(SLEPc REQUIRED)
   target_link_libraries(bout++ PUBLIC SLEPc::SLEPc)
   string(JOIN " " CONFIG_SLEPC_LIBRARIES ${SLEPC_LIBRARIES})
@@ -275,44 +334,69 @@ set(BOUT_HAS_SLEPC ${BOUT_USE_SLEPC})
 
 option(BOUT_DOWNLOAD_SUNDIALS "Download and build SUNDIALS" OFF)
 # Force BOUT_USE_SUNDIALS if we're downloading it!
-cmake_dependent_option(BOUT_USE_SUNDIALS "Enable support for SUNDIALS time solvers" OFF
-  "NOT BOUT_DOWNLOAD_SUNDIALS" ON)
-if (BOUT_USE_SUNDIALS)
+cmake_dependent_option(
+  BOUT_USE_SUNDIALS "Enable support for SUNDIALS time solvers" OFF
+  "NOT BOUT_DOWNLOAD_SUNDIALS" ON
+)
+if(BOUT_USE_SUNDIALS)
   enable_language(C)
-  if (BOUT_DOWNLOAD_SUNDIALS)
+  if(BOUT_DOWNLOAD_SUNDIALS)
     message(STATUS "Downloading and configuring SUNDIALS")
     include(FetchContent)
     FetchContent_Declare(
       sundials
       GIT_REPOSITORY https://github.com/LLNL/sundials
-      GIT_TAG        v7.2.1
-      )
+      GIT_TAG v7.2.1
+    )
     # Note: These are settings for building SUNDIALS
-    set(EXAMPLES_ENABLE_C OFF CACHE BOOL "" FORCE)
-    set(EXAMPLES_INSTALL OFF CACHE BOOL "" FORCE)
-    set(ENABLE_MPI ${BOUT_USE_MPI} CACHE BOOL "" FORCE)
-    set(ENABLE_OPENMP OFF CACHE BOOL "" FORCE)
-    if (BUILD_SHARED_LIBS)
-      set(BUILD_STATIC_LIBS OFF CACHE BOOL "" FORCE)
+    set(EXAMPLES_ENABLE_C
+        OFF
+        CACHE BOOL "" FORCE
+    )
+    set(EXAMPLES_INSTALL
+        OFF
+        CACHE BOOL "" FORCE
+    )
+    set(ENABLE_MPI
+        ${BOUT_USE_MPI}
+        CACHE BOOL "" FORCE
+    )
+    set(ENABLE_OPENMP
+        OFF
+        CACHE BOOL "" FORCE
+    )
+    if(BUILD_SHARED_LIBS)
+      set(BUILD_STATIC_LIBS
+          OFF
+          CACHE BOOL "" FORCE
+      )
     else()
-      set(BUILD_STATIC_LIBS ON CACHE BOOL "" FORCE)
+      set(BUILD_STATIC_LIBS
+          ON
+          CACHE BOOL "" FORCE
+      )
     endif()
     FetchContent_MakeAvailable(sundials)
     message(STATUS "SUNDIALS done configuring")
   else()
     find_package(SUNDIALS REQUIRED)
-    if (SUNDIALS_VERSION VERSION_LESS 4.0.0)
-      message(FATAL_ERROR "SUNDIALS_VERSION 4.0.0 or newer is required. Found version ${SUNDIALS_VERSION}.")
+    if(SUNDIALS_VERSION VERSION_LESS 4.0.0)
+      message(
+        FATAL_ERROR
+          "SUNDIALS_VERSION 4.0.0 or newer is required. Found version ${SUNDIALS_VERSION}."
+      )
     endif()
   endif()
-  if (SUNDIALS_DIR)
+  if(SUNDIALS_DIR)
     set(SUNDIALS_ROOT "${SUNDIALS_DIR}")
   endif()
   target_link_libraries(bout++ PUBLIC SUNDIALS::nvecparallel)
   target_link_libraries(bout++ PUBLIC SUNDIALS::cvode)
   target_link_libraries(bout++ PUBLIC SUNDIALS::ida)
   target_link_libraries(bout++ PUBLIC SUNDIALS::arkode)
-  set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${SUNDIALS_cvode_LIBRARY} ${SUNDIALS_ida_LIBRARY} ${SUNDIALS_arkode_LIBRARY} ${SUNDIALS_nvecparallel_LIBRARY}")
+  set(CONFIG_LDFLAGS
+      "${CONFIG_LDFLAGS} ${SUNDIALS_cvode_LIBRARY} ${SUNDIALS_ida_LIBRARY} ${SUNDIALS_arkode_LIBRARY} ${SUNDIALS_nvecparallel_LIBRARY}"
+  )
 endif()
 message(STATUS "SUNDIALS support: ${BOUT_USE_SUNDIALS}")
 set(BOUT_HAS_SUNDIALS ${BOUT_USE_SUNDIALS})
@@ -321,46 +405,51 @@ set(BOUT_HAS_CVODE ${BOUT_USE_SUNDIALS})
 set(BOUT_HAS_IDA ${BOUT_USE_SUNDIALS})
 
 set(ON_OFF_AUTO ON OFF AUTO)
-set(BOUT_USE_NLS AUTO CACHE STRING "Enable Native Language Support")
+set(BOUT_USE_NLS
+    AUTO
+    CACHE STRING "Enable Native Language Support"
+)
 set_property(CACHE BOUT_USE_NLS PROPERTY STRINGS ${ON_OFF_AUTO})
 set(BOUT_HAS_GETTEXT OFF)
-if (BOUT_USE_NLS)
+if(BOUT_USE_NLS)
   find_package(Gettext)
-  if (GETTEXT_FOUND)
+  if(GETTEXT_FOUND)
     find_package(Intl)
-    if (Intl_FOUND)
-      target_link_libraries(bout++
-        PUBLIC ${Intl_LIBRARIES})
-      target_include_directories(bout++
-        PUBLIC ${Intl_INCLUDE_DIRS})
+    if(Intl_FOUND)
+      target_link_libraries(bout++ PUBLIC ${Intl_LIBRARIES})
+      target_include_directories(bout++ PUBLIC ${Intl_INCLUDE_DIRS})
       set(BOUT_HAS_GETTEXT ON)
     else()
-      if (NOT BOUT_USE_NLS STREQUAL "AUTO")
-	message(FATAL_ERROR "Intl not found but requested!")
+      if(NOT BOUT_USE_NLS STREQUAL "AUTO")
+        message(FATAL_ERROR "Intl not found but requested!")
       endif()
     endif()
   else()
-    if (NOT BOUT_USE_NLS STREQUAL "AUTO")
+    if(NOT BOUT_USE_NLS STREQUAL "AUTO")
       message(FATAL_ERROR "GETTEXT not found but requested!")
     endif()
   endif()
 endif()
 
 option(BOUT_USE_SCOREP "Enable support for Score-P based instrumentation" OFF)
-if (BOUT_USE_SCOREP)
-  message(STATUS "Score-P support enabled. Please make sure you are calling CMake like so:
+if(BOUT_USE_SCOREP)
+  message(
+    STATUS
+      "Score-P support enabled. Please make sure you are calling CMake like so:
 
   SCOREP_WRAPPER=off cmake -DCMAKE_C_COMPILER=scorep-mpicc -DCMAKE_CXX_COMPILER=scorep-mpicxx <other CMake options>
-")
+"
+  )
 endif()
 set(BOUT_HAS_SCOREP ${BOUT_USE_SCOREP})
 
-option(BOUT_USE_UUID_SYSTEM_GENERATOR "Enable support for using a system UUID generator" ON)
-if (BOUT_USE_UUID_SYSTEM_GENERATOR)
+option(BOUT_USE_UUID_SYSTEM_GENERATOR
+       "Enable support for using a system UUID generator" ON
+)
+if(BOUT_USE_UUID_SYSTEM_GENERATOR)
   find_package(Libuuid QUIET)
-  if (Libuuid_FOUND)
-    target_link_libraries(bout++
-      PUBLIC Libuuid::libuuid)
+  if(Libuuid_FOUND)
+    target_link_libraries(bout++ PUBLIC Libuuid::libuuid)
     set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${Libuuid_LIBRARIES}")
   else()
     message(STATUS "libuuid not found, using fallback UUID generator")
@@ -370,24 +459,42 @@ endif()
 message(STATUS "UUID_SYSTEM_GENERATOR: ${BOUT_USE_UUID_SYSTEM_GENERATOR}")
 set(BOUT_HAS_UUID_SYSTEM_GENERATOR ${BOUT_USE_UUID_SYSTEM_GENERATOR})
 
-cmake_dependent_option(BOUT_USE_SYSTEM_CPPTRACE "Use external installation of cpptrace" OFF
-  "BOUT_UPDATE_GIT_SUBMODULE OR EXISTS ${PROJECT_SOURCE_DIR}/externalpackages/cpptrace/CMakeLists.txt" ON)
+cmake_dependent_option(
+  BOUT_USE_SYSTEM_CPPTRACE
+  "Use external installation of cpptrace"
+  OFF
+  "BOUT_UPDATE_GIT_SUBMODULE OR EXISTS ${PROJECT_SOURCE_DIR}/externalpackages/cpptrace/CMakeLists.txt"
+  ON
+)
 
 if(BOUT_USE_SYSTEM_CPPTRACE)
   message(STATUS "Using external cpptrace")
   find_package(cpptrace REQUIRED)
-  get_target_property(CPPTRACE_INCLUDE_PATH cpptrace::cpptrace INTERFACE_INCLUDE_DIRECTORIES)
+  get_target_property(
+    CPPTRACE_INCLUDE_PATH cpptrace::cpptrace INTERFACE_INCLUDE_DIRECTORIES
+  )
 else()
   message(STATUS "Using cpptrace submodule")
   bout_update_submodules()
   # Need a fork with some fixes for CMake
-  set(CPPTRACE_LIBDWARF_REPO "https://github.com/ZedThree/libdwarf-lite.git" CACHE STRING "" FORCE)
-  set(CPPTRACE_LIBDWARF_TAG "ebe10a39afd56b8247de633bfe17666ad50ab95e" CACHE STRING "" FORCE)
+  set(CPPTRACE_LIBDWARF_REPO
+      "https://github.com/ZedThree/libdwarf-lite.git"
+      CACHE STRING "" FORCE
+  )
+  set(CPPTRACE_LIBDWARF_TAG
+      "ebe10a39afd56b8247de633bfe17666ad50ab95e"
+      CACHE STRING "" FORCE
+  )
   add_subdirectory(externalpackages/cpptrace)
   if(NOT TARGET cpptrace::cpptrace)
-    message(FATAL_ERROR "cpptrace not found! Have you disabled the git submodules (BOUT_UPDATE_GIT_SUBMODULE)?")
+    message(
+      FATAL_ERROR
+        "cpptrace not found! Have you disabled the git submodules (BOUT_UPDATE_GIT_SUBMODULE)?"
+    )
   endif()
-  set(CPPTRACE_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/externalpackages/cpptrace/include")
+  set(CPPTRACE_INCLUDE_PATH
+      "${CMAKE_CURRENT_SOURCE_DIR}/externalpackages/cpptrace/include"
+  )
 endif()
 set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${CPPTRACE_INCLUDE_PATH}")
 target_link_libraries(bout++ PUBLIC cpptrace::cpptrace)
diff --git a/cmake/SetupCompilers.cmake b/cmake/SetupCompilers.cmake
index 647cb20f75..fbe960b0f0 100644
--- a/cmake/SetupCompilers.cmake
+++ b/cmake/SetupCompilers.cmake
@@ -1,44 +1,58 @@
-
 # Note: Currently BOUT++ always needs MPI. This option just determines
 # whether the find_* routines are used
 option(BOUT_ENABLE_MPI "Enable MPI support" ON)
 if(BOUT_ENABLE_MPI)
-   # This might not be entirely sensible, but helps CMake to find the
-   # correct MPI, workaround for https://gitlab.kitware.com/cmake/cmake/issues/18895
-   find_program(MPIEXEC_EXECUTABLE NAMES mpiexec mpirun)
-   find_package(MPI REQUIRED)
-endif ()
+  # This might not be entirely sensible, but helps CMake to find the
+  # correct MPI, workaround for https://gitlab.kitware.com/cmake/cmake/issues/18895
+  find_program(MPIEXEC_EXECUTABLE NAMES mpiexec mpirun)
+  find_package(MPI REQUIRED)
+endif()
 set(BOUT_USE_MPI ${BOUT_ENABLE_MPI})
 
 option(BOUT_ENABLE_OPENMP "Enable OpenMP support" OFF)
-set(BOUT_OPENMP_SCHEDULE static CACHE STRING "Set OpenMP schedule")
-set_property(CACHE BOUT_OPENMP_SCHEDULE PROPERTY STRINGS static dynamic guided auto)
-if (BOUT_ENABLE_OPENMP)
+set(BOUT_OPENMP_SCHEDULE
+    static
+    CACHE STRING "Set OpenMP schedule"
+)
+set_property(
+  CACHE BOUT_OPENMP_SCHEDULE PROPERTY STRINGS static dynamic guided auto
+)
+if(BOUT_ENABLE_OPENMP)
   find_package(OpenMP REQUIRED)
   set(possible_openmp_schedules static dynamic guided auto)
-  if (NOT BOUT_OPENMP_SCHEDULE IN_LIST possible_openmp_schedules)
-    message(FATAL_ERROR "BOUT_OPENMP_SCHEDULE must be one of ${possible_openmp_schedules}; got ${BOUT_OPENMP_SCHEDULE}")
+  if(NOT BOUT_OPENMP_SCHEDULE IN_LIST possible_openmp_schedules)
+    message(
+      FATAL_ERROR
+        "BOUT_OPENMP_SCHEDULE must be one of ${possible_openmp_schedules}; got ${BOUT_OPENMP_SCHEDULE}"
+    )
   endif()
   message(STATUS "OpenMP schedule: ${BOUT_OPENMP_SCHEDULE}")
-endif ()
+endif()
 set(BOUT_USE_OPENMP ${BOUT_ENABLE_OPENMP})
 message(STATUS "Enable OpenMP: ${BOUT_ENABLE_OPENMP}")
 
 option(BOUT_ENABLE_CUDA "Enable CUDA support" OFF)
-set(CUDA_ARCH "compute_70,code=sm_70" CACHE STRING "CUDA architecture")
+set(CUDA_ARCH
+    "compute_70,code=sm_70"
+    CACHE STRING "CUDA architecture"
+)
 if(BOUT_ENABLE_CUDA)
-   # Set specific options for CUDA if enabled
-   enable_language(CUDA)
-   set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -gencode arch=${CUDA_ARCH} -ccbin ${CMAKE_CXX_COMPILER}")
-   if (BOUT_ENABLE_RAJA)
-      # RAJA uses lambda expressions
-      set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} --expt-extended-lambda --expt-relaxed-constexpr")
-   endif ()
+  # Set specific options for CUDA if enabled
+  enable_language(CUDA)
+  set(CMAKE_CUDA_FLAGS
+      "${CMAKE_CUDA_FLAGS} -gencode arch=${CUDA_ARCH} -ccbin ${CMAKE_CXX_COMPILER}"
+  )
+  if(BOUT_ENABLE_RAJA)
+    # RAJA uses lambda expressions
+    set(CMAKE_CUDA_FLAGS
+        "${CMAKE_CUDA_FLAGS} --expt-extended-lambda --expt-relaxed-constexpr"
+    )
+  endif()
 
-# TODO Ensure openmp flags are not enabled twice!
-   if (BOUT_ENABLE_OPENMP)
-      # CMAKE_CUDA_FLAGS does not pass OpenMP_CXX_FLAGS to the host compiler by default
-      set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Xcompiler ${OpenMP_CXX_FLAGS}")
-   endif ()
+  # TODO Ensure openmp flags are not enabled twice!
+  if(BOUT_ENABLE_OPENMP)
+    # CMAKE_CUDA_FLAGS does not pass OpenMP_CXX_FLAGS to the host compiler by default
+    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Xcompiler ${OpenMP_CXX_FLAGS}")
+  endif()
 endif()
 set(BOUT_HAS_CUDA ${BOUT_ENABLE_CUDA})
diff --git a/examples/6field-simple/CMakeLists.txt b/examples/6field-simple/CMakeLists.txt
index 6a51327cda..b6584c49e4 100644
--- a/examples/6field-simple/CMakeLists.txt
+++ b/examples/6field-simple/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(6field-simple LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(elm_6f
+bout_add_example(
+  elm_6f
   SOURCES elm_6f.cxx
-  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc)
+  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc
+)
diff --git a/examples/IMEX/advection-diffusion/CMakeLists.txt b/examples/IMEX/advection-diffusion/CMakeLists.txt
index 334d48d767..f2008f3479 100644
--- a/examples/IMEX/advection-diffusion/CMakeLists.txt
+++ b/examples/IMEX/advection-diffusion/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(advection-diffusion LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/IMEX/advection-reaction/CMakeLists.txt b/examples/IMEX/advection-reaction/CMakeLists.txt
index 03e8686371..d89ff10a78 100644
--- a/examples/IMEX/advection-reaction/CMakeLists.txt
+++ b/examples/IMEX/advection-reaction/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(advection-reaction LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(split_operator
+bout_add_example(
+  split_operator
   SOURCES split_operator.cxx
-  EXTRA_FILES simple_xz.nc)
+  EXTRA_FILES simple_xz.nc
+)
diff --git a/examples/IMEX/diffusion-nl/CMakeLists.txt b/examples/IMEX/diffusion-nl/CMakeLists.txt
index 664d16e042..73c7250bb5 100644
--- a/examples/IMEX/diffusion-nl/CMakeLists.txt
+++ b/examples/IMEX/diffusion-nl/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(diffusion-nl LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/IMEX/drift-wave-constraint/CMakeLists.txt b/examples/IMEX/drift-wave-constraint/CMakeLists.txt
index 5680b5367e..b72396d2f0 100644
--- a/examples/IMEX/drift-wave-constraint/CMakeLists.txt
+++ b/examples/IMEX/drift-wave-constraint/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(drift-wave-constraint LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/IMEX/drift-wave/CMakeLists.txt b/examples/IMEX/drift-wave/CMakeLists.txt
index e3e2a1b8ee..44fbbd7b0f 100644
--- a/examples/IMEX/drift-wave/CMakeLists.txt
+++ b/examples/IMEX/drift-wave/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(drift-wave LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/blob2d-laplacexz/CMakeLists.txt b/examples/blob2d-laplacexz/CMakeLists.txt
index 17f9ebe97a..855d86af70 100644
--- a/examples/blob2d-laplacexz/CMakeLists.txt
+++ b/examples/blob2d-laplacexz/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(blob2d-laplacexz LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/blob2d-outerloop/CMakeLists.txt b/examples/blob2d-outerloop/CMakeLists.txt
index cd7187ee3f..e991b45d51 100644
--- a/examples/blob2d-outerloop/CMakeLists.txt
+++ b/examples/blob2d-outerloop/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(blob2d-outerloop LANGUAGES CXX C)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/blob2d/CMakeLists.txt b/examples/blob2d/CMakeLists.txt
index a4772874d9..f3f93f0246 100644
--- a/examples/blob2d/CMakeLists.txt
+++ b/examples/blob2d/CMakeLists.txt
@@ -2,11 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(blob2d LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(blob2d
+bout_add_example(
+  blob2d
   SOURCES blob2d.cxx
   DATA_DIRS delta_0.25 delta_1 delta_10 two_blobs data
-  EXTRA_FILES blob_velocity.py)
+  EXTRA_FILES blob_velocity.py
+)
diff --git a/examples/boundary-conditions/advection/CMakeLists.txt b/examples/boundary-conditions/advection/CMakeLists.txt
index a4ab73a24d..edd55d183a 100644
--- a/examples/boundary-conditions/advection/CMakeLists.txt
+++ b/examples/boundary-conditions/advection/CMakeLists.txt
@@ -2,13 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(advection LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(advection
+bout_add_example(
+  advection
   SOURCES advection.cxx
-  DATA_DIRS central-dirichlet 
-            central-free 
-            central-free-o3 
-            upwind)
+  DATA_DIRS central-dirichlet central-free central-free-o3 upwind
+)
diff --git a/examples/boutpp/CMakeLists.txt b/examples/boutpp/CMakeLists.txt
index e46a7ae990..1cc5c9619b 100644
--- a/examples/boutpp/CMakeLists.txt
+++ b/examples/boutpp/CMakeLists.txt
@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.13)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/conducting-wall-mode/CMakeLists.txt b/examples/conducting-wall-mode/CMakeLists.txt
index 857a22038e..0e000c1ba8 100644
--- a/examples/conducting-wall-mode/CMakeLists.txt
+++ b/examples/conducting-wall-mode/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(conducting-wall-mode LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(conducting-wall-mode
+bout_add_example(
+  conducting-wall-mode
   SOURCES cwm.cxx
-  EXTRA_FILES cwm_grid.nc)
+  EXTRA_FILES cwm_grid.nc
+)
diff --git a/examples/conduction-snb/CMakeLists.txt b/examples/conduction-snb/CMakeLists.txt
index 45072dbe59..3de25718d1 100644
--- a/examples/conduction-snb/CMakeLists.txt
+++ b/examples/conduction-snb/CMakeLists.txt
@@ -2,11 +2,20 @@ cmake_minimum_required(VERSION 3.13)
 
 project(conduction-snb LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(conduction-snb
+bout_add_example(
+  conduction-snb
   SOURCES conduction-snb.cxx
-  EXTRA_FILES fit_temperature.py sinusoid.py snb.csv spitzer-harm.csv step.py temperature.csv vfp.csv
-  DATA_DIRS data step)
+  EXTRA_FILES
+    fit_temperature.py
+    sinusoid.py
+    snb.csv
+    spitzer-harm.csv
+    step.py
+    temperature.csv
+    vfp.csv
+  DATA_DIRS data step
+)
diff --git a/examples/conduction/CMakeLists.txt b/examples/conduction/CMakeLists.txt
index f26b838621..b81164f614 100644
--- a/examples/conduction/CMakeLists.txt
+++ b/examples/conduction/CMakeLists.txt
@@ -2,11 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(conduction LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(conduction
+bout_add_example(
+  conduction
   SOURCES conduction.cxx
   DATA_DIRS data fromfile
-  EXTRA_FILES generate.py)
+  EXTRA_FILES generate.py
+)
diff --git a/examples/constraints/alfven-wave/CMakeLists.txt b/examples/constraints/alfven-wave/CMakeLists.txt
index a95ace4086..375415ab3c 100644
--- a/examples/constraints/alfven-wave/CMakeLists.txt
+++ b/examples/constraints/alfven-wave/CMakeLists.txt
@@ -2,12 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(constraints-alfven-wave LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(constraints-alfven-wave
+bout_add_example(
+  constraints-alfven-wave
   SOURCES alfven.cxx
   DATA_DIRS cbm18 data
-  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc d3d_119919.nc)
-
+  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc d3d_119919.nc
+)
diff --git a/examples/constraints/laplace-dae/CMakeLists.txt b/examples/constraints/laplace-dae/CMakeLists.txt
index e487bd6a0a..d515fc3515 100644
--- a/examples/constraints/laplace-dae/CMakeLists.txt
+++ b/examples/constraints/laplace-dae/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(constraints-laplace-dae LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(constraints-laplace-dae
+bout_add_example(
+  constraints-laplace-dae
   SOURCES laplace_dae.cxx
-  EXTRA_FILES simple_xz.nc)
+  EXTRA_FILES simple_xz.nc
+)
diff --git a/examples/dalf3/CMakeLists.txt b/examples/dalf3/CMakeLists.txt
index 5f5b3d701d..0b6f8461f5 100644
--- a/examples/dalf3/CMakeLists.txt
+++ b/examples/dalf3/CMakeLists.txt
@@ -2,11 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(dalf3 LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-
-bout_add_example(dalf3
+bout_add_example(
+  dalf3
   SOURCES dalf3.cxx
-  EXTRA_FILES cbm18_8_y064_x516_090309.nc)
+  EXTRA_FILES cbm18_8_y064_x516_090309.nc
+)
diff --git a/examples/eigen-box/CMakeLists.txt b/examples/eigen-box/CMakeLists.txt
index 76af4fbaa6..305e330652 100644
--- a/examples/eigen-box/CMakeLists.txt
+++ b/examples/eigen-box/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(eigen-box LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(eigen-box
+bout_add_example(
+  eigen-box
   SOURCES eigen-box.cxx
-  EXTRA_FILES eigenvals.py)
+  EXTRA_FILES eigenvals.py
+)
diff --git a/examples/elm-pb-outerloop/CMakeLists.txt b/examples/elm-pb-outerloop/CMakeLists.txt
index 008918a87f..12dc2f7696 100644
--- a/examples/elm-pb-outerloop/CMakeLists.txt
+++ b/examples/elm-pb-outerloop/CMakeLists.txt
@@ -2,16 +2,16 @@ cmake_minimum_required(VERSION 3.13)
 
 project(elm_pb LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(elm_pb_outerloop
+bout_add_example(
+  elm_pb_outerloop
   SOURCES elm_pb_outerloop.cxx
   EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc
 )
 
 if(BOUT_HAS_CUDA)
-  set_source_files_properties(elm_pb_outerloop.cxx PROPERTIES LANGUAGE CUDA )
+  set_source_files_properties(elm_pb_outerloop.cxx PROPERTIES LANGUAGE CUDA)
 endif()
-
diff --git a/examples/elm-pb/CMakeLists.txt b/examples/elm-pb/CMakeLists.txt
index 8c672822cf..6cdd0f9cd9 100644
--- a/examples/elm-pb/CMakeLists.txt
+++ b/examples/elm-pb/CMakeLists.txt
@@ -2,14 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(elm_pb LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(elm_pb
+bout_add_example(
+  elm_pb
   SOURCES elm_pb.cxx
-  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc
-              data/BOUT.inp
-              data-hypre/BOUT.inp
-              data-nonlinear/BOUT.inp)
-
+  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc data/BOUT.inp data-hypre/BOUT.inp
+              data-nonlinear/BOUT.inp
+)
diff --git a/examples/fci-wave/CMakeLists.txt b/examples/fci-wave/CMakeLists.txt
index 2680b1310e..ea299edb5a 100644
--- a/examples/fci-wave/CMakeLists.txt
+++ b/examples/fci-wave/CMakeLists.txt
@@ -2,11 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(fci-wave LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(fci-wave
+bout_add_example(
+  fci-wave
   SOURCES fci-wave.cxx
   DATA_DIRS div div-integrate logn
-  EXTRA_FILES compare-density.py)
+  EXTRA_FILES compare-density.py
+)
diff --git a/examples/finite-volume/diffusion/CMakeLists.txt b/examples/finite-volume/diffusion/CMakeLists.txt
index 0dd7d220f6..ccc3d0f7e0 100644
--- a/examples/finite-volume/diffusion/CMakeLists.txt
+++ b/examples/finite-volume/diffusion/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(finite-volume-diffusion LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(finite-volume-diffusion
+bout_add_example(
+  finite-volume-diffusion
   SOURCES diffusion.cxx
-  EXTRA_FILES mms.py)
+  EXTRA_FILES mms.py
+)
diff --git a/examples/finite-volume/fluid/CMakeLists.txt b/examples/finite-volume/fluid/CMakeLists.txt
index e9028459ec..e798da77fe 100644
--- a/examples/finite-volume/fluid/CMakeLists.txt
+++ b/examples/finite-volume/fluid/CMakeLists.txt
@@ -2,11 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(finite-volume-fluid LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(finite-volume-fluid
+bout_add_example(
+  finite-volume-fluid
   SOURCES fluid.cxx
   DATA_DIRS data mms
-  EXTRA_FILES mms.py)
+  EXTRA_FILES mms.py
+)
diff --git a/examples/finite-volume/test/CMakeLists.txt b/examples/finite-volume/test/CMakeLists.txt
index 73fe99f960..d09567e193 100644
--- a/examples/finite-volume/test/CMakeLists.txt
+++ b/examples/finite-volume/test/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(finite-volume-test LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/gas-compress/CMakeLists.txt b/examples/gas-compress/CMakeLists.txt
index 1b4416d32b..75978ba584 100644
--- a/examples/gas-compress/CMakeLists.txt
+++ b/examples/gas-compress/CMakeLists.txt
@@ -2,11 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(gas-compress LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(gas-compress
+bout_add_example(
+  gas-compress
   SOURCES gas_compress.cxx gas_compress.hxx
   DATA_DIRS rayleigh-taylor sod-shock
-  EXTRA_FILES rt.grd.nc sod.grd.nc)
+  EXTRA_FILES rt.grd.nc sod.grd.nc
+)
diff --git a/examples/gyro-gem/CMakeLists.txt b/examples/gyro-gem/CMakeLists.txt
index 7189bb06b8..5d83848688 100644
--- a/examples/gyro-gem/CMakeLists.txt
+++ b/examples/gyro-gem/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(gyro-gem LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(gyro-gem
+bout_add_example(
+  gyro-gem
   SOURCES gem.cxx
-  EXTRA_FILES cyclone_68x32.nc)
+  EXTRA_FILES cyclone_68x32.nc
+)
diff --git a/examples/hasegawa-wakatani-3d/CMakeLists.txt b/examples/hasegawa-wakatani-3d/CMakeLists.txt
index 0cdb5207f8..c555d6d7f9 100644
--- a/examples/hasegawa-wakatani-3d/CMakeLists.txt
+++ b/examples/hasegawa-wakatani-3d/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(hw3d LANGUAGES CXX C)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/hasegawa-wakatani/CMakeLists.txt b/examples/hasegawa-wakatani/CMakeLists.txt
index c9b9401b3a..53f4e5ed4f 100644
--- a/examples/hasegawa-wakatani/CMakeLists.txt
+++ b/examples/hasegawa-wakatani/CMakeLists.txt
@@ -2,9 +2,8 @@ cmake_minimum_required(VERSION 3.13)
 
 project(hasegawa-wakatani LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
 bout_add_example(hasegawa-wakatani SOURCES hw.cxx)
-
diff --git a/examples/invertable_operator/CMakeLists.txt b/examples/invertable_operator/CMakeLists.txt
index f054466f23..f18a085ec1 100644
--- a/examples/invertable_operator/CMakeLists.txt
+++ b/examples/invertable_operator/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(invertable_operator LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(invertable_operator
+bout_add_example(
+  invertable_operator
   SOURCES invertable_operator.cxx
-  REQUIRES BOUT_HAS_PETSC)
+  REQUIRES BOUT_HAS_PETSC
+)
diff --git a/examples/laplacexy/alfven-wave/CMakeLists.txt b/examples/laplacexy/alfven-wave/CMakeLists.txt
index 2423400519..ebda7703e6 100644
--- a/examples/laplacexy/alfven-wave/CMakeLists.txt
+++ b/examples/laplacexy/alfven-wave/CMakeLists.txt
@@ -2,11 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(laplacexy-alfven-wave LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(laplacexy-alfven-wave
+bout_add_example(
+  laplacexy-alfven-wave
   SOURCES alfven.cxx
   DATA_DIRS cbm18 data
-  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc d3d_119919.nc)
+  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc d3d_119919.nc
+)
diff --git a/examples/laplacexy/laplace_perp/CMakeLists.txt b/examples/laplacexy/laplace_perp/CMakeLists.txt
index 388513b044..d12725c5de 100644
--- a/examples/laplacexy/laplace_perp/CMakeLists.txt
+++ b/examples/laplacexy/laplace_perp/CMakeLists.txt
@@ -2,11 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(laplacexy-laplace_perp LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(laplacexy-laplace_perp
+bout_add_example(
+  laplacexy-laplace_perp
   SOURCES test.cxx
-  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc 
-  DATA_DIRS square torus)
+  EXTRA_FILES cbm18_dens8.grid_nx68ny64.nc
+  DATA_DIRS square torus
+)
diff --git a/examples/laplacexy/simple/CMakeLists.txt b/examples/laplacexy/simple/CMakeLists.txt
index 7859a08259..e999b9cf58 100644
--- a/examples/laplacexy/simple/CMakeLists.txt
+++ b/examples/laplacexy/simple/CMakeLists.txt
@@ -2,11 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(laplacexy-simple LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(laplacexy-simple
+bout_add_example(
+  laplacexy-simple
   SOURCES test-laplacexy.cxx
   DATA_DIRS data hypre
 )
diff --git a/examples/monitor-newapi/CMakeLists.txt b/examples/monitor-newapi/CMakeLists.txt
index 0ee3ee7f85..5c2022b792 100644
--- a/examples/monitor-newapi/CMakeLists.txt
+++ b/examples/monitor-newapi/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(monitor-newapi LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/orszag-tang/CMakeLists.txt b/examples/orszag-tang/CMakeLists.txt
index 9ac8fd8d1c..46eae5d0f2 100644
--- a/examples/orszag-tang/CMakeLists.txt
+++ b/examples/orszag-tang/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(orszag-tang LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(orszag-tang
+bout_add_example(
+  orszag-tang
   SOURCES mhd.cxx
-  EXTRA_FILES data/otv.grd.nc)
+  EXTRA_FILES data/otv.grd.nc
+)
diff --git a/examples/preconditioning/wave/CMakeLists.txt b/examples/preconditioning/wave/CMakeLists.txt
index 437f39fe3a..05d7548832 100644
--- a/examples/preconditioning/wave/CMakeLists.txt
+++ b/examples/preconditioning/wave/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13)
 
 project(preconditioning-wave LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
diff --git a/examples/staggered_grid/CMakeLists.txt b/examples/staggered_grid/CMakeLists.txt
index dd2b3b463e..1950d16c0b 100644
--- a/examples/staggered_grid/CMakeLists.txt
+++ b/examples/staggered_grid/CMakeLists.txt
@@ -2,11 +2,13 @@ cmake_minimum_required(VERSION 3.13)
 
 project(staggered_grid LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(staggered_grid
+bout_add_example(
+  staggered_grid
   SOURCES test_staggered.cxx
   EXTRA_FILES generate.py run test-staggered.nc
-  DATA_DIRS data test)
+  DATA_DIRS data test
+)
diff --git a/examples/subsampling/CMakeLists.txt b/examples/subsampling/CMakeLists.txt
index 86f71d98f5..c6c487e687 100644
--- a/examples/subsampling/CMakeLists.txt
+++ b/examples/subsampling/CMakeLists.txt
@@ -2,11 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(subsampling LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(subsampling
+bout_add_example(
+  subsampling
   SOURCES monitor.cxx
-  EXTRA_FILES show.py)
-
+  EXTRA_FILES show.py
+)
diff --git a/examples/wave-slab/CMakeLists.txt b/examples/wave-slab/CMakeLists.txt
index b1943c4e1c..8de548b71d 100644
--- a/examples/wave-slab/CMakeLists.txt
+++ b/examples/wave-slab/CMakeLists.txt
@@ -2,10 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 
 project(wave-slab LANGUAGES CXX)
 
-if (NOT TARGET bout++::bout++)
+if(NOT TARGET bout++::bout++)
   find_package(bout++ REQUIRED)
 endif()
 
-bout_add_example(wave-slab
+bout_add_example(
+  wave-slab
   SOURCES wave_slab.cxx
-  EXTRA_FILES generate.py)
+  EXTRA_FILES generate.py
+)
diff --git a/externalpackages/PVODE/CMakeLists.txt b/externalpackages/PVODE/CMakeLists.txt
index 5e3f8f2f63..51afe8047c 100644
--- a/externalpackages/PVODE/CMakeLists.txt
+++ b/externalpackages/PVODE/CMakeLists.txt
@@ -6,14 +6,17 @@ else()
   cmake_policy(VERSION 3.12)
 endif()
 
-project(PVODE
+project(
+  PVODE
   DESCRIPTION "ODE Solver"
   VERSION 0.1
-  LANGUAGES CXX)
+  LANGUAGES CXX
+)
 
 find_package(MPI REQUIRED)
 
-add_library(pvode
+add_library(
+  pvode
   source/cvode.cpp
   source/nvector.cpp
   source/llnlmath.cpp
@@ -33,45 +36,43 @@ add_library(pvode
   include/pvode/smalldense.h
   include/pvode/spgmr.h
   include/pvode/vector.h
-  )
-
-target_include_directories(pvode PUBLIC
-  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/pvode>
-  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
-  $<INSTALL_INTERFACE:include>
-  )
+)
+
+target_include_directories(
+  pvode
+  PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/pvode>
+         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+         $<INSTALL_INTERFACE:include>
+)
 target_link_libraries(pvode PUBLIC MPI::MPI_CXX)
 
-add_library(pvpre
-  include/pvode/pvbbdpre.h
-  precon/pvbbdpre.cpp
-  precon/band.cpp
-  precon/band.h
-  )
-
+add_library(
+  pvpre include/pvode/pvbbdpre.h precon/pvbbdpre.cpp precon/band.cpp
+        precon/band.h
+)
 
-set_target_properties(pvode PROPERTIES
-  SOVERSION 1.0.0)
+set_target_properties(pvode PROPERTIES SOVERSION 1.0.0)
 
-target_include_directories(pvpre PUBLIC
-  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/pvode>
-  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
-  $<INSTALL_INTERFACE:include>
-  )
+target_include_directories(
+  pvpre
+  PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/pvode>
+         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+         $<INSTALL_INTERFACE:include>
+)
 target_link_libraries(pvpre PUBLIC pvode MPI::MPI_CXX)
 
-
-set_target_properties(pvpre PROPERTIES
-  SOVERSION 1.0.0)
+set_target_properties(pvpre PROPERTIES SOVERSION 1.0.0)
 
 include(GNUInstallDirs)
-install(TARGETS pvode pvpre
+install(
+  TARGETS pvode pvpre
   EXPORT PVODETargets
   LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
   ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
   RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
-  INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
-  )
+  INCLUDES
+  DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+)
 install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 
 include(CMakePackageConfigHelpers)
@@ -79,17 +80,19 @@ write_basic_package_version_file(
   PVODEConfigVersion.cmake
   VERSION ${PACKAGE_VERSION}
   COMPATIBILITY SameMajorVersion
-  )
+)
 
-install(EXPORT PVODETargets
+install(
+  EXPORT PVODETargets
   FILE PVODEConfig.cmake
   NAMESPACE PVODE::
   DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/PVODE"
-  )
+)
 
-export(EXPORT PVODETargets
+export(
+  EXPORT PVODETargets
   FILE "${CMAKE_CURRENT_BINARY_DIR}/PVODEConfig.cmake"
   NAMESPACE PVODE::
-  )
+)
 
 export(PACKAGE PVODE)
diff --git a/manual/CMakeLists.txt b/manual/CMakeLists.txt
index af4c528446..87f5101e58 100644
--- a/manual/CMakeLists.txt
+++ b/manual/CMakeLists.txt
@@ -6,20 +6,26 @@ find_package(Sphinx REQUIRED)
 set(BOUT_SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/sphinx)
 set(BOUT_SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR}/docs)
 
-set(env_command
-    ${CMAKE_COMMAND} -E env PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
+set(env_command ${CMAKE_COMMAND} -E env
+                PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
 )
 
-add_custom_target(sphinx-html
-  COMMAND ${env_command} ${SPHINX_EXECUTABLE} -b html ${BOUT_SPHINX_SOURCE} ${BOUT_SPHINX_BUILD}
-  COMMAND ${CMAKE_COMMAND} -E echo "Generated HTML docs in file://${BOUT_SPHINX_BUILD}/index.html"
+add_custom_target(
+  sphinx-html
+  COMMAND ${env_command} ${SPHINX_EXECUTABLE} -b html ${BOUT_SPHINX_SOURCE}
+          ${BOUT_SPHINX_BUILD}
+  COMMAND ${CMAKE_COMMAND} -E echo
+          "Generated HTML docs in file://${BOUT_SPHINX_BUILD}/index.html"
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   COMMENT "Generating HTML documentation with Sphinx in ${BOUT_SPHINX_BUILD}"
 )
 
-add_custom_target(sphinx-pdf
-  COMMAND ${env_command} ${SPHINX_EXECUTABLE} -M latexpdf ${BOUT_SPHINX_SOURCE} ${BOUT_SPHINX_BUILD}
-  COMMAND ${CMAKE_COMMAND} -E echo "Generated PDF docs in file://${BOUT_SPHINX_BUILD}"
+add_custom_target(
+  sphinx-pdf
+  COMMAND ${env_command} ${SPHINX_EXECUTABLE} -M latexpdf ${BOUT_SPHINX_SOURCE}
+          ${BOUT_SPHINX_BUILD}
+  COMMAND ${CMAKE_COMMAND} -E echo
+          "Generated PDF docs in file://${BOUT_SPHINX_BUILD}"
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   COMMENT "Generating PDF documentation with Sphinx in ${BOUT_SPHINX_BUILD}"
 )
@@ -27,7 +33,8 @@ add_custom_target(sphinx-pdf
 add_custom_target(docs)
 add_dependencies(docs sphinx-html)
 
-install(DIRECTORY ${BOUT_SPHINX_BUILD}/
+install(
+  DIRECTORY ${BOUT_SPHINX_BUILD}/
   DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/doc/bout++/
   EXCLUDE_FROM_ALL
   COMPONENT docs
diff --git a/tests/MMS/CMakeLists.txt b/tests/MMS/CMakeLists.txt
index 0c42da7074..a6667bcfa5 100644
--- a/tests/MMS/CMakeLists.txt
+++ b/tests/MMS/CMakeLists.txt
@@ -15,7 +15,7 @@ add_subdirectory(wave-1d-y)
 
 ########################################
 # The following require boutpp:
-if (BOUT_ENABLE_PYTHON)
+if(BOUT_ENABLE_PYTHON)
   add_subdirectory(bracket)
   add_subdirectory(derivatives3)
   add_subdirectory(shiftedmetricinterp)
diff --git a/tests/MMS/advection/arakawa/CMakeLists.txt b/tests/MMS/advection/arakawa/CMakeLists.txt
index 267146ed51..6594cab2c2 100644
--- a/tests/MMS/advection/arakawa/CMakeLists.txt
+++ b/tests/MMS/advection/arakawa/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-advection-arakawa
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_mms_test(
+  MMS-advection-arakawa
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES parent.py
   EXTRA_DEPENDS MMS-advection
   REQUIRES BOUT_RUN_ALL_TESTS
diff --git a/tests/MMS/advection/central/CMakeLists.txt b/tests/MMS/advection/central/CMakeLists.txt
index 9b2288856e..a5b5d3795d 100644
--- a/tests/MMS/advection/central/CMakeLists.txt
+++ b/tests/MMS/advection/central/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-advection-central
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_mms_test(
+  MMS-advection-central
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES parent.py
   EXTRA_DEPENDS MMS-advection
   REQUIRES BOUT_RUN_ALL_TESTS
diff --git a/tests/MMS/advection/upwind/CMakeLists.txt b/tests/MMS/advection/upwind/CMakeLists.txt
index 3a9db4630a..baec34914e 100644
--- a/tests/MMS/advection/upwind/CMakeLists.txt
+++ b/tests/MMS/advection/upwind/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-advection-upwind
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_mms_test(
+  MMS-advection-upwind
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES parent.py
   EXTRA_DEPENDS MMS-advection
   REQUIRES BOUT_RUN_ALL_TESTS
diff --git a/tests/MMS/advection/weno3/CMakeLists.txt b/tests/MMS/advection/weno3/CMakeLists.txt
index 293b6b95c9..5d6c1baefa 100644
--- a/tests/MMS/advection/weno3/CMakeLists.txt
+++ b/tests/MMS/advection/weno3/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-advection-weno3
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_mms_test(
+  MMS-advection-weno3
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES parent.py
   EXTRA_DEPENDS MMS-advection
   REQUIRES BOUT_RUN_ALL_TESTS
diff --git a/tests/MMS/bracket/CMakeLists.txt b/tests/MMS/bracket/CMakeLists.txt
index fc8103aab0..e4cb7da9f9 100644
--- a/tests/MMS/bracket/CMakeLists.txt
+++ b/tests/MMS/bracket/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-bracket
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_mms_test(
+  MMS-bracket
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_ENABLE_PYTHON
 )
 
diff --git a/tests/MMS/derivatives3/CMakeLists.txt b/tests/MMS/derivatives3/CMakeLists.txt
index 5615a46a38..476934ba00 100644
--- a/tests/MMS/derivatives3/CMakeLists.txt
+++ b/tests/MMS/derivatives3/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-derivatives3
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_mms_test(
+  MMS-derivatives3
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_ENABLE_PYTHON
 )
 
diff --git a/tests/MMS/diffusion/CMakeLists.txt b/tests/MMS/diffusion/CMakeLists.txt
index b91b6a8327..358fdce403 100644
--- a/tests/MMS/diffusion/CMakeLists.txt
+++ b/tests/MMS/diffusion/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-diffusion
+bout_add_mms_test(
+  MMS-diffusion
   SOURCES diffusion.cxx
   EXECUTABLE_NAME cyto
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  )
+  USE_RUNTEST USE_DATA_BOUT_INP
+)
diff --git a/tests/MMS/diffusion2/CMakeLists.txt b/tests/MMS/diffusion2/CMakeLists.txt
index 910be46481..0d2e0a2903 100644
--- a/tests/MMS/diffusion2/CMakeLists.txt
+++ b/tests/MMS/diffusion2/CMakeLists.txt
@@ -1,11 +1,9 @@
-bout_add_mms_test(MMS-diffusion2
+bout_add_mms_test(
+  MMS-diffusion2
   SOURCES diffusion.cxx
   EXECUTABLE_NAME cyto
   USE_RUNTEST
-  EXTRA_FILES
-    X/BOUT.inp
-    Y/BOUT.inp
-    Z/BOUT.inp
+  EXTRA_FILES X/BOUT.inp Y/BOUT.inp Z/BOUT.inp
   REQUIRES BOUT_RUN_ALL_TESTS
   PROCESSORS 2
-  )
+)
diff --git a/tests/MMS/hw/CMakeLists.txt b/tests/MMS/hw/CMakeLists.txt
index 6fda0448be..e7449dfff3 100644
--- a/tests/MMS/hw/CMakeLists.txt
+++ b/tests/MMS/hw/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_mms_test(MMS-hw
+bout_add_mms_test(
+  MMS-hw
   SOURCES hw.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_RUN_ALL_TESTS
   PROCESSORS 4
 )
diff --git a/tests/MMS/laplace/CMakeLists.txt b/tests/MMS/laplace/CMakeLists.txt
index 4825fc7fd6..4c2e9fee1f 100644
--- a/tests/MMS/laplace/CMakeLists.txt
+++ b/tests/MMS/laplace/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_mms_test(MMS-laplace
+bout_add_mms_test(
+  MMS-laplace
   SOURCES laplace.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_RUN_ALL_TESTS
   PROCESSORS 2
-)  
+)
diff --git a/tests/MMS/shiftedmetricinterp/CMakeLists.txt b/tests/MMS/shiftedmetricinterp/CMakeLists.txt
index 1693428da6..1e61b9e25d 100644
--- a/tests/MMS/shiftedmetricinterp/CMakeLists.txt
+++ b/tests/MMS/shiftedmetricinterp/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-shiftedmetricinterp
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_mms_test(
+  MMS-shiftedmetricinterp
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_ENABLE_PYTHON
 )
 
diff --git a/tests/MMS/spatial/advection/CMakeLists.txt b/tests/MMS/spatial/advection/CMakeLists.txt
index 4adb108612..bdc1c2f615 100644
--- a/tests/MMS/spatial/advection/CMakeLists.txt
+++ b/tests/MMS/spatial/advection/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_mms_test(MMS-spatial-advection
+bout_add_mms_test(
+  MMS-spatial-advection
   SOURCES advection.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_RUN_ALL_TESTS
   PROCESSORS 4
 )
diff --git a/tests/MMS/spatial/d2dx2/CMakeLists.txt b/tests/MMS/spatial/d2dx2/CMakeLists.txt
index 0affa9beee..2b6ede3e4a 100644
--- a/tests/MMS/spatial/d2dx2/CMakeLists.txt
+++ b/tests/MMS/spatial/d2dx2/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-spatial-d2dx2
+bout_add_mms_test(
+  MMS-spatial-d2dx2
   SOURCES test_d2dx2.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_RUN_ALL_TESTS
 )
diff --git a/tests/MMS/spatial/d2dz2/CMakeLists.txt b/tests/MMS/spatial/d2dz2/CMakeLists.txt
index 01b61eaa5d..d60e4028fc 100644
--- a/tests/MMS/spatial/d2dz2/CMakeLists.txt
+++ b/tests/MMS/spatial/d2dz2/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-spatial-d2dz2
+bout_add_mms_test(
+  MMS-spatial-d2dz2
   SOURCES test_d2dz2.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_RUN_ALL_TESTS
 )
diff --git a/tests/MMS/spatial/diffusion/CMakeLists.txt b/tests/MMS/spatial/diffusion/CMakeLists.txt
index 67a27aafa4..0e7b99ab84 100644
--- a/tests/MMS/spatial/diffusion/CMakeLists.txt
+++ b/tests/MMS/spatial/diffusion/CMakeLists.txt
@@ -1,4 +1,5 @@
-bout_add_mms_test(MMS-spatial-diffusion
+bout_add_mms_test(
+  MMS-spatial-diffusion
   SOURCES diffusion.cxx
   USE_RUNTEST
   EXTRA_FILES X/BOUT.inp
diff --git a/tests/MMS/spatial/fci/CMakeLists.txt b/tests/MMS/spatial/fci/CMakeLists.txt
index 94b9682c9c..dcdb183fdd 100644
--- a/tests/MMS/spatial/fci/CMakeLists.txt
+++ b/tests/MMS/spatial/fci/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_mms_test(MMS-spatial-fci
+bout_add_mms_test(
+  MMS-spatial-fci
   SOURCES fci_mms.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES zoidberg_FOUND
   PROCESSORS 2
 )
diff --git a/tests/MMS/time-petsc/CMakeLists.txt b/tests/MMS/time-petsc/CMakeLists.txt
index 3cbbe6f717..554602ccfe 100644
--- a/tests/MMS/time-petsc/CMakeLists.txt
+++ b/tests/MMS/time-petsc/CMakeLists.txt
@@ -1,7 +1,6 @@
-bout_add_mms_test(MMS-time-petsc
+bout_add_mms_test(
+  MMS-time-petsc
   USE_RUNTEST
-  REQUIRES
-    BOUT_HAS_PETSC
-    BOUT_RUN_ALL_TESTS
+  REQUIRES BOUT_HAS_PETSC BOUT_RUN_ALL_TESTS
   EXTRA_DEPENDS MMS-time
 )
diff --git a/tests/MMS/time/CMakeLists.txt b/tests/MMS/time/CMakeLists.txt
index 9c3480629e..5924356122 100644
--- a/tests/MMS/time/CMakeLists.txt
+++ b/tests/MMS/time/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-time
+bout_add_mms_test(
+  MMS-time
   SOURCES time.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_RUN_ALL_TESTS
 )
diff --git a/tests/MMS/upwinding3/CMakeLists.txt b/tests/MMS/upwinding3/CMakeLists.txt
index 5daf58b29b..a1664c03e9 100644
--- a/tests/MMS/upwinding3/CMakeLists.txt
+++ b/tests/MMS/upwinding3/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-upwinding3
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_mms_test(
+  MMS-upwinding3
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_ENABLE_PYTHON
 )
 
diff --git a/tests/MMS/wave-1d-y/CMakeLists.txt b/tests/MMS/wave-1d-y/CMakeLists.txt
index cc5cddfff4..ce7b1b7c0e 100644
--- a/tests/MMS/wave-1d-y/CMakeLists.txt
+++ b/tests/MMS/wave-1d-y/CMakeLists.txt
@@ -1,5 +1,5 @@
-bout_add_mms_test(MMS-wave-1d-y
+bout_add_mms_test(
+  MMS-wave-1d-y
   SOURCES wave.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
 )
diff --git a/tests/MMS/wave-1d/CMakeLists.txt b/tests/MMS/wave-1d/CMakeLists.txt
index a9ae3d748c..568cf11beb 100644
--- a/tests/MMS/wave-1d/CMakeLists.txt
+++ b/tests/MMS/wave-1d/CMakeLists.txt
@@ -1,5 +1,5 @@
-bout_add_mms_test(MMS-wave-1d
+bout_add_mms_test(
+  MMS-wave-1d
   SOURCES wave.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
 )
diff --git a/tests/integrated/test-backtrace/CMakeLists.txt b/tests/integrated/test-backtrace/CMakeLists.txt
index 579f4863ac..420558bc04 100644
--- a/tests/integrated/test-backtrace/CMakeLists.txt
+++ b/tests/integrated/test-backtrace/CMakeLists.txt
@@ -1,4 +1,5 @@
-bout_add_integrated_test(test-backtrace
+bout_add_integrated_test(
+  test-backtrace
   SOURCES boutexcept.cxx
   USE_RUNTEST
 )
diff --git a/tests/integrated/test-beuler/CMakeLists.txt b/tests/integrated/test-beuler/CMakeLists.txt
index c67b2dce44..495cd670d0 100644
--- a/tests/integrated/test-beuler/CMakeLists.txt
+++ b/tests/integrated/test-beuler/CMakeLists.txt
@@ -1,2 +1,5 @@
-bout_add_integrated_test(test_beuler SOURCES test_beuler.cxx
-  REQUIRES BOUT_HAS_PETSC)
+bout_add_integrated_test(
+  test_beuler
+  SOURCES test_beuler.cxx
+  REQUIRES BOUT_HAS_PETSC
+)
diff --git a/tests/integrated/test-bout-override-default-option/CMakeLists.txt b/tests/integrated/test-bout-override-default-option/CMakeLists.txt
index 7c3d6390b0..0c8b643e98 100644
--- a/tests/integrated/test-bout-override-default-option/CMakeLists.txt
+++ b/tests/integrated/test-bout-override-default-option/CMakeLists.txt
@@ -1,3 +1,4 @@
-bout_add_integrated_test(test-bout-override-default-option
+bout_add_integrated_test(
+  test-bout-override-default-option
   SOURCES test-bout-override-default-option.cxx
-  )
+)
diff --git a/tests/integrated/test-boutpp/CMakeLists.txt b/tests/integrated/test-boutpp/CMakeLists.txt
index 0a16bba43e..8aa0d55869 100644
--- a/tests/integrated/test-boutpp/CMakeLists.txt
+++ b/tests/integrated/test-boutpp/CMakeLists.txt
@@ -1,4 +1,4 @@
-if (BOUT_ENABLE_PYTHON)
+if(BOUT_ENABLE_PYTHON)
   add_subdirectory(collect)
   add_subdirectory(collect-staggered)
   add_subdirectory(legacy-model)
diff --git a/tests/integrated/test-boutpp/collect-staggered/CMakeLists.txt b/tests/integrated/test-boutpp/collect-staggered/CMakeLists.txt
index 7a41adc15d..c893384389 100644
--- a/tests/integrated/test-boutpp/collect-staggered/CMakeLists.txt
+++ b/tests/integrated/test-boutpp/collect-staggered/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-boutpp-collect-staggered
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_integrated_test(
+  test-boutpp-collect-staggered
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_ENABLE_PYTHON
 )
 
diff --git a/tests/integrated/test-boutpp/collect/CMakeLists.txt b/tests/integrated/test-boutpp/collect/CMakeLists.txt
index beb78086c6..5a8e7579f1 100644
--- a/tests/integrated/test-boutpp/collect/CMakeLists.txt
+++ b/tests/integrated/test-boutpp/collect/CMakeLists.txt
@@ -1,4 +1,5 @@
-bout_add_integrated_test(test-boutpp-collect
+bout_add_integrated_test(
+  test-boutpp-collect
   USE_RUNTEST
   EXTRA_FILES input/BOUT.inp
   REQUIRES BOUT_ENABLE_PYTHON
diff --git a/tests/integrated/test-boutpp/legacy-model/CMakeLists.txt b/tests/integrated/test-boutpp/legacy-model/CMakeLists.txt
index a32b1f4f4b..eddeae92fc 100644
--- a/tests/integrated/test-boutpp/legacy-model/CMakeLists.txt
+++ b/tests/integrated/test-boutpp/legacy-model/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-boutpp-legacy-model
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_integrated_test(
+  test-boutpp-legacy-model
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_ENABLE_PYTHON
 )
 
diff --git a/tests/integrated/test-boutpp/mms-ddz/CMakeLists.txt b/tests/integrated/test-boutpp/mms-ddz/CMakeLists.txt
index dfac88662a..3cfafb6a6a 100644
--- a/tests/integrated/test-boutpp/mms-ddz/CMakeLists.txt
+++ b/tests/integrated/test-boutpp/mms-ddz/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-boutpp-mms-ddz
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+bout_add_integrated_test(
+  test-boutpp-mms-ddz
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_ENABLE_PYTHON
 )
 
diff --git a/tests/integrated/test-boutpp/print/CMakeLists.txt b/tests/integrated/test-boutpp/print/CMakeLists.txt
index 2e61b29257..84b005df89 100644
--- a/tests/integrated/test-boutpp/print/CMakeLists.txt
+++ b/tests/integrated/test-boutpp/print/CMakeLists.txt
@@ -1,4 +1,5 @@
-bout_add_integrated_test(test-boutpp-print
+bout_add_integrated_test(
+  test-boutpp-print
   USE_RUNTEST
   EXTRA_FILES test/BOUT.inp test.py
   REQUIRES BOUT_ENABLE_PYTHON
diff --git a/tests/integrated/test-boutpp/simple-model/CMakeLists.txt b/tests/integrated/test-boutpp/simple-model/CMakeLists.txt
index 891a2ce018..a17bb6291a 100644
--- a/tests/integrated/test-boutpp/simple-model/CMakeLists.txt
+++ b/tests/integrated/test-boutpp/simple-model/CMakeLists.txt
@@ -1,4 +1,5 @@
-bout_add_integrated_test(test-boutpp-simple-model
+bout_add_integrated_test(
+  test-boutpp-simple-model
   USE_RUNTEST
   EXTRA_FILES mini/BOUT.inp
   REQUIRES BOUT_ENABLE_PYTHON
diff --git a/tests/integrated/test-boutpp/slicing/CMakeLists.txt b/tests/integrated/test-boutpp/slicing/CMakeLists.txt
index 4f314a40cc..57f74aa125 100644
--- a/tests/integrated/test-boutpp/slicing/CMakeLists.txt
+++ b/tests/integrated/test-boutpp/slicing/CMakeLists.txt
@@ -1,4 +1,5 @@
-bout_add_integrated_test(test-boutpp-slicing
+bout_add_integrated_test(
+  test-boutpp-slicing
   USE_RUNTEST
   EXTRA_FILES test/BOUT.inp test.py
   REQUIRES BOUT_ENABLE_PYTHON
diff --git a/tests/integrated/test-collect/CMakeLists.txt b/tests/integrated/test-collect/CMakeLists.txt
index e5fa43dde8..a3487d6443 100644
--- a/tests/integrated/test-collect/CMakeLists.txt
+++ b/tests/integrated/test-collect/CMakeLists.txt
@@ -1,5 +1,5 @@
-bout_add_integrated_test(test-collect
+bout_add_integrated_test(
+  test-collect
   SOURCES test-collect.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  )
+  USE_RUNTEST USE_DATA_BOUT_INP
+)
diff --git a/tests/integrated/test-command-args/CMakeLists.txt b/tests/integrated/test-command-args/CMakeLists.txt
index 1a2cf88a5e..331994ac11 100644
--- a/tests/integrated/test-command-args/CMakeLists.txt
+++ b/tests/integrated/test-command-args/CMakeLists.txt
@@ -1,5 +1,6 @@
-bout_add_integrated_test(test-command-args
+bout_add_integrated_test(
+  test-command-args
   SOURCES command-args.cxx
   USE_RUNTEST
   EXTRA_FILES BOUT.inp
-  )
+)
diff --git a/tests/integrated/test-communications/CMakeLists.txt b/tests/integrated/test-communications/CMakeLists.txt
index de6197ce3b..84c940d2f6 100644
--- a/tests/integrated/test-communications/CMakeLists.txt
+++ b/tests/integrated/test-communications/CMakeLists.txt
@@ -1,9 +1,8 @@
-bout_add_integrated_test(test-communications
+bout_add_integrated_test(
+  test-communications
   SOURCES test-communications.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  EXTRA_FILES
-    data_limiter/BOUT.inp
+  USE_RUNTEST USE_DATA_BOUT_INP
+  EXTRA_FILES data_limiter/BOUT.inp
   REQUIRES BOUT_HAS_NETCDF
   PROCESSORS 18
-  )
+)
diff --git a/tests/integrated/test-coordinates-initialization/CMakeLists.txt b/tests/integrated/test-coordinates-initialization/CMakeLists.txt
index ad47be272c..f3f50ff17a 100644
--- a/tests/integrated/test-coordinates-initialization/CMakeLists.txt
+++ b/tests/integrated/test-coordinates-initialization/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-coordinates-initialization
+bout_add_integrated_test(
+  test-coordinates-initialization
   SOURCES test-coordinates-initialization.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 3
-  )
+)
diff --git a/tests/integrated/test-cyclic/CMakeLists.txt b/tests/integrated/test-cyclic/CMakeLists.txt
index a6296858e2..0a98e29450 100644
--- a/tests/integrated/test-cyclic/CMakeLists.txt
+++ b/tests/integrated/test-cyclic/CMakeLists.txt
@@ -1,8 +1,8 @@
-bout_add_integrated_test(test-cyclic
+bout_add_integrated_test(
+  test-cyclic
   SOURCES test_cyclic.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES test_io.grd.nc
   REQUIRES BOUT_HAS_NETCDF
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-datafilefacade/CMakeLists.txt b/tests/integrated/test-datafilefacade/CMakeLists.txt
index a6d1876e16..3032ece263 100644
--- a/tests/integrated/test-datafilefacade/CMakeLists.txt
+++ b/tests/integrated/test-datafilefacade/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_integrated_test(test-datafile-facade
+bout_add_integrated_test(
+  test-datafile-facade
   SOURCES test-datafile-facade.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_NETCDF
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-delp2/CMakeLists.txt b/tests/integrated/test-delp2/CMakeLists.txt
index c1de3ed940..bab68fbfaf 100644
--- a/tests/integrated/test-delp2/CMakeLists.txt
+++ b/tests/integrated/test-delp2/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_integrated_test(test-delp2
+bout_add_integrated_test(
+  test-delp2
   SOURCES test_delp2.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-drift-instability-staggered/CMakeLists.txt b/tests/integrated/test-drift-instability-staggered/CMakeLists.txt
index 18383286cd..6bebf454a0 100644
--- a/tests/integrated/test-drift-instability-staggered/CMakeLists.txt
+++ b/tests/integrated/test-drift-instability-staggered/CMakeLists.txt
@@ -1,10 +1,10 @@
-bout_add_integrated_test(test-drift-instability-staggered
+bout_add_integrated_test(
+  test-drift-instability-staggered
   SOURCES 2fluid.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES uedge.grd_std.cdl
   REQUIRES BOUT_HAS_NETCDF
   REQUIRES BOUT_HAS_FFTW
   PROCESSORS 2
-  )
+)
diff --git a/tests/integrated/test-drift-instability/CMakeLists.txt b/tests/integrated/test-drift-instability/CMakeLists.txt
index b0b73eca01..55b08726f9 100644
--- a/tests/integrated/test-drift-instability/CMakeLists.txt
+++ b/tests/integrated/test-drift-instability/CMakeLists.txt
@@ -1,10 +1,10 @@
-bout_add_integrated_test(test-drift-instability
+bout_add_integrated_test(
+  test-drift-instability
   SOURCES 2fluid.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES uedge.grd_std.cdl
   REQUIRES BOUT_HAS_NETCDF
   REQUIRES BOUT_HAS_FFTW
   PROCESSORS 2
-  )
+)
diff --git a/tests/integrated/test-fci-boundary/CMakeLists.txt b/tests/integrated/test-fci-boundary/CMakeLists.txt
index bf25cd7c57..b9164ce000 100644
--- a/tests/integrated/test-fci-boundary/CMakeLists.txt
+++ b/tests/integrated/test-fci-boundary/CMakeLists.txt
@@ -1,22 +1,25 @@
-bout_add_mms_test(test-fci-boundary
+bout_add_mms_test(
+  test-fci-boundary
   SOURCES get_par_bndry.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES zoidberg_FOUND
   PROCESSORS 1
-  )
+)
 
-if (zoidberg_FOUND)
+if(zoidberg_FOUND)
   set(gridfile ${CMAKE_CURRENT_BINARY_DIR}/grid.fci.nc)
-  add_custom_command(OUTPUT ${gridfile}
-    COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH} ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/grid.py ${gridfile}
+  add_custom_command(
+    OUTPUT ${gridfile}
+    COMMAND
+      ${CMAKE_COMMAND} -E env PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
+      ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/grid.py ${gridfile}
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-    DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/../../../tools/pylib/boutconfig/__init__.py
+    DEPENDS
+      ${CMAKE_CURRENT_BINARY_DIR}/../../../tools/pylib/boutconfig/__init__.py
     DEPENDS grid.py
-    IMPLICIT_DEPENDS  ${CMAKE_CURRENT_BINARY_DIR}
+    IMPLICIT_DEPENDS ${CMAKE_CURRENT_BINARY_DIR}
     COMMENT "Creating test-fci-boundary grid file"
   )
   add_custom_target(test-fci-boundary-grid DEPENDS ${gridfile})
-  add_dependencies(test-fci-boundary
-    test-fci-boundary-grid)
+  add_dependencies(test-fci-boundary test-fci-boundary-grid)
 endif()
diff --git a/tests/integrated/test-fci-mpi/CMakeLists.txt b/tests/integrated/test-fci-mpi/CMakeLists.txt
index aea0421c0a..0abbbce099 100644
--- a/tests/integrated/test-fci-mpi/CMakeLists.txt
+++ b/tests/integrated/test-fci-mpi/CMakeLists.txt
@@ -1,9 +1,10 @@
-bout_add_mms_test(test-fci-mpi
+bout_add_mms_test(
+  test-fci-mpi
   SOURCES fci_mpi.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 6
-  DOWNLOAD https://zenodo.org/records/7614499/files/W7X-conf4-36x8x128.fci.nc?download=1
+  DOWNLOAD
+    https://zenodo.org/records/7614499/files/W7X-conf4-36x8x128.fci.nc?download=1
   DOWNLOAD_NAME grid.fci.nc
   REQUIRES BOUT_HAS_PETSC
 )
diff --git a/tests/integrated/test-fieldgroupComm/CMakeLists.txt b/tests/integrated/test-fieldgroupComm/CMakeLists.txt
index 17a699c187..d5d59eedf5 100644
--- a/tests/integrated/test-fieldgroupComm/CMakeLists.txt
+++ b/tests/integrated/test-fieldgroupComm/CMakeLists.txt
@@ -1,9 +1,9 @@
-bout_add_integrated_test(test-fieldgroupComm
+bout_add_integrated_test(
+  test-fieldgroupComm
   SOURCES test_fieldgroupcomm.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES cyclone_68x32.nc
   REQUIRES BOUT_HAS_NETCDF
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-griddata-yboundary-guards/CMakeLists.txt b/tests/integrated/test-griddata-yboundary-guards/CMakeLists.txt
index b01afa5f32..4766549cbb 100644
--- a/tests/integrated/test-griddata-yboundary-guards/CMakeLists.txt
+++ b/tests/integrated/test-griddata-yboundary-guards/CMakeLists.txt
@@ -1,13 +1,11 @@
-bout_add_integrated_test(test-griddata-yboundary-guards
+bout_add_integrated_test(
+  test-griddata-yboundary-guards
   SOURCES test_griddata.cxx
   USE_RUNTEST
   EXTRA_FILES
-    data-doublenull-0/BOUT.inp
-    data-doublenull-1/BOUT.inp
-    data-doublenull-2/BOUT.inp
-    data-singlenull-0/BOUT.inp
-    data-singlenull-1/BOUT.inp
-    data-singlenull-2/BOUT.inp
+    data-doublenull-0/BOUT.inp data-doublenull-1/BOUT.inp
+    data-doublenull-2/BOUT.inp data-singlenull-0/BOUT.inp
+    data-singlenull-1/BOUT.inp data-singlenull-2/BOUT.inp
   REQUIRES BOUT_HAS_NETCDF
   PROCESSORS 6
-  )
+)
diff --git a/tests/integrated/test-griddata/CMakeLists.txt b/tests/integrated/test-griddata/CMakeLists.txt
index 8e03b5de0d..3ea14a4d49 100644
--- a/tests/integrated/test-griddata/CMakeLists.txt
+++ b/tests/integrated/test-griddata/CMakeLists.txt
@@ -1,5 +1,6 @@
-bout_add_integrated_test(test-griddata
+bout_add_integrated_test(
+  test-griddata
   SOURCES test_griddata.cxx
   USE_RUNTEST
   EXTRA_FILES screw/BOUT.inp
-  )
+)
diff --git a/tests/integrated/test-gyro/CMakeLists.txt b/tests/integrated/test-gyro/CMakeLists.txt
index 00be4d29a0..339625f048 100644
--- a/tests/integrated/test-gyro/CMakeLists.txt
+++ b/tests/integrated/test-gyro/CMakeLists.txt
@@ -1,10 +1,10 @@
-bout_add_integrated_test(test-gyro
+bout_add_integrated_test(
+  test-gyro
   SOURCES test_gyro.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES cyclone_68x32.nc data/benchmark.0.nc
   REQUIRES BOUT_HAS_NETCDF
   REQUIRES BOUT_HAS_FFTW
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-initial/CMakeLists.txt b/tests/integrated/test-initial/CMakeLists.txt
index 33a03d89ca..0c2ec14c1c 100644
--- a/tests/integrated/test-initial/CMakeLists.txt
+++ b/tests/integrated/test-initial/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-initial
+bout_add_integrated_test(
+  test-initial
   SOURCES test_initial.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-interchange-instability/CMakeLists.txt b/tests/integrated/test-interchange-instability/CMakeLists.txt
index 380c93d029..a4c8108bbb 100644
--- a/tests/integrated/test-interchange-instability/CMakeLists.txt
+++ b/tests/integrated/test-interchange-instability/CMakeLists.txt
@@ -1,4 +1,5 @@
-bout_add_integrated_test(test-interchange-instability
+bout_add_integrated_test(
+  test-interchange-instability
   SOURCES 2fluid.cxx
   CONFLICTS BOUT_USE_METRIC_3D
   USE_RUNTEST
@@ -6,4 +7,4 @@ bout_add_integrated_test(test-interchange-instability
   REQUIRES BOUT_HAS_NETCDF
   REQUIRES BOUT_HAS_FFTW
   PROCESSORS 2
-  )
+)
diff --git a/tests/integrated/test-interpolate-z/CMakeLists.txt b/tests/integrated/test-interpolate-z/CMakeLists.txt
index 399edcd8ff..7328807cd3 100644
--- a/tests/integrated/test-interpolate-z/CMakeLists.txt
+++ b/tests/integrated/test-interpolate-z/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-interpolate-z
+bout_add_integrated_test(
+  test-interpolate-z
   SOURCES test_interpolate.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
-  )
+)
diff --git a/tests/integrated/test-interpolate/CMakeLists.txt b/tests/integrated/test-interpolate/CMakeLists.txt
index de4bd14f8a..3a12855a65 100644
--- a/tests/integrated/test-interpolate/CMakeLists.txt
+++ b/tests/integrated/test-interpolate/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-interpolate
+bout_add_integrated_test(
+  test-interpolate
   SOURCES test_interpolate.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
-  )
+)
diff --git a/tests/integrated/test-invertable-operator/CMakeLists.txt b/tests/integrated/test-invertable-operator/CMakeLists.txt
index de45de14a2..eed109c450 100644
--- a/tests/integrated/test-invertable-operator/CMakeLists.txt
+++ b/tests/integrated/test-invertable-operator/CMakeLists.txt
@@ -1,8 +1,8 @@
-bout_add_integrated_test(test-invertable-operator
+bout_add_integrated_test(
+  test-invertable-operator
   SOURCES invertable_operator.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_PETSC
   PROCESSORS 2
-  )
+)
diff --git a/tests/integrated/test-invpar/CMakeLists.txt b/tests/integrated/test-invpar/CMakeLists.txt
index 8e143a1188..8df5b477ac 100644
--- a/tests/integrated/test-invpar/CMakeLists.txt
+++ b/tests/integrated/test-invpar/CMakeLists.txt
@@ -1,8 +1,8 @@
-bout_add_integrated_test(test-invpar
+bout_add_integrated_test(
+  test-invpar
   SOURCES test_invpar.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-laplace-hypre3d/CMakeLists.txt b/tests/integrated/test-laplace-hypre3d/CMakeLists.txt
index 2645c18c67..df68e9e5af 100644
--- a/tests/integrated/test-laplace-hypre3d/CMakeLists.txt
+++ b/tests/integrated/test-laplace-hypre3d/CMakeLists.txt
@@ -1,10 +1,8 @@
-bout_add_integrated_test(test-laplace-hypre3d
+bout_add_integrated_test(
+  test-laplace-hypre3d
   SOURCES test-laplace3d.cxx
-  EXTRA_FILES
-    data_circular_core/BOUT.inp
-    data_circular_core-sol/BOUT.inp
-    data_slab_core/BOUT.inp
-    data_slab_sol/BOUT.inp
+  EXTRA_FILES data_circular_core/BOUT.inp data_circular_core-sol/BOUT.inp
+              data_slab_core/BOUT.inp data_slab_sol/BOUT.inp
   USE_RUNTEST
   REQUIRES BOUT_HAS_HYPRE
-  )
+)
diff --git a/tests/integrated/test-laplace-petsc3d/CMakeLists.txt b/tests/integrated/test-laplace-petsc3d/CMakeLists.txt
index 93bf4f7efa..0f0e4a2cac 100644
--- a/tests/integrated/test-laplace-petsc3d/CMakeLists.txt
+++ b/tests/integrated/test-laplace-petsc3d/CMakeLists.txt
@@ -1,10 +1,8 @@
-bout_add_integrated_test(test-laplace-petsc3d
+bout_add_integrated_test(
+  test-laplace-petsc3d
   SOURCES test-laplace3d.cxx
-  EXTRA_FILES
-    data_circular_core/BOUT.inp
-    data_circular_core-sol/BOUT.inp
-    data_slab_core/BOUT.inp
-    data_slab_sol/BOUT.inp
+  EXTRA_FILES data_circular_core/BOUT.inp data_circular_core-sol/BOUT.inp
+              data_slab_core/BOUT.inp data_slab_sol/BOUT.inp
   USE_RUNTEST
   REQUIRES BOUT_HAS_PETSC
-  )
+)
diff --git a/tests/integrated/test-laplace/CMakeLists.txt b/tests/integrated/test-laplace/CMakeLists.txt
index f3e95f3fa5..455e9cf769 100644
--- a/tests/integrated/test-laplace/CMakeLists.txt
+++ b/tests/integrated/test-laplace/CMakeLists.txt
@@ -1,10 +1,10 @@
-bout_add_integrated_test(test-laplace
+bout_add_integrated_test(
+  test-laplace
   SOURCES test_laplace.cxx
   CONFLICTS BOUT_USE_METRIC_3D
   EXTRA_FILES test_laplace.grd.nc data/benchmark.0.nc
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_NETCDF
   REQUIRES BOUT_HAS_FFTW
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-laplacexy-fv/CMakeLists.txt b/tests/integrated/test-laplacexy-fv/CMakeLists.txt
index 57e98edd38..14887b6ff6 100644
--- a/tests/integrated/test-laplacexy-fv/CMakeLists.txt
+++ b/tests/integrated/test-laplacexy-fv/CMakeLists.txt
@@ -1,8 +1,9 @@
-bout_add_integrated_test(test-laplacexy-fv
+bout_add_integrated_test(
+  test-laplacexy-fv
   SOURCES test-laplacexy.cxx
   REQUIRES BOUT_HAS_PETSC
-  CONFLICTS BOUT_USE_METRIC_3D # Test requires Laplace_perpXY operator, which is not implemented for 3d metrics
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  CONFLICTS
+    BOUT_USE_METRIC_3D # Test requires Laplace_perpXY operator, which is not implemented for 3d metrics
+  USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 8
-  )
+)
diff --git a/tests/integrated/test-laplacexy-short/CMakeLists.txt b/tests/integrated/test-laplacexy-short/CMakeLists.txt
index c5576b58ac..58b8e49962 100644
--- a/tests/integrated/test-laplacexy-short/CMakeLists.txt
+++ b/tests/integrated/test-laplacexy-short/CMakeLists.txt
@@ -1,8 +1,9 @@
-bout_add_integrated_test(test-laplacexy-short
+bout_add_integrated_test(
+  test-laplacexy-short
   SOURCES test-laplacexy.cxx
   REQUIRES BOUT_HAS_PETSC
-  CONFLICTS BOUT_USE_METRIC_3D # Test uses cyclic Laplace solver as a preconditioner, which is not available with 3d metrics
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  CONFLICTS
+    BOUT_USE_METRIC_3D # Test uses cyclic Laplace solver as a preconditioner, which is not available with 3d metrics
+  USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 8
-  )
+)
diff --git a/tests/integrated/test-laplacexy/CMakeLists.txt b/tests/integrated/test-laplacexy/CMakeLists.txt
index 338bb46763..43c75b1cd8 100644
--- a/tests/integrated/test-laplacexy/CMakeLists.txt
+++ b/tests/integrated/test-laplacexy/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_integrated_test(test-laplacexy
+bout_add_integrated_test(
+  test-laplacexy
   SOURCES test-laplacexy.cxx
   REQUIRES BOUT_HAS_PETSC
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 8
-  )
+)
diff --git a/tests/integrated/test-laplacexy2-hypre/CMakeLists.txt b/tests/integrated/test-laplacexy2-hypre/CMakeLists.txt
index a787752ebc..e56829b243 100644
--- a/tests/integrated/test-laplacexy2-hypre/CMakeLists.txt
+++ b/tests/integrated/test-laplacexy2-hypre/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-laplacexy2-hypre
+bout_add_integrated_test(
+  test-laplacexy2-hypre
   SOURCES test-laplacexy.cxx
   REQUIRES BOUT_HAS_HYPRE
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  )
+  USE_RUNTEST USE_DATA_BOUT_INP
+)
diff --git a/tests/integrated/test-laplacexz/CMakeLists.txt b/tests/integrated/test-laplacexz/CMakeLists.txt
index b19aa986ad..e0569d5ea6 100644
--- a/tests/integrated/test-laplacexz/CMakeLists.txt
+++ b/tests/integrated/test-laplacexz/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_integrated_test(test-laplacexz
+bout_add_integrated_test(
+  test-laplacexz
   SOURCES test-laplacexz.cxx
   REQUIRES BOUT_HAS_PETSC
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  )
+  USE_RUNTEST USE_DATA_BOUT_INP
+)
diff --git a/tests/integrated/test-multigrid_laplace/CMakeLists.txt b/tests/integrated/test-multigrid_laplace/CMakeLists.txt
index 67cf38b510..b6bb16b8a8 100644
--- a/tests/integrated/test-multigrid_laplace/CMakeLists.txt
+++ b/tests/integrated/test-multigrid_laplace/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_integrated_test(test-multigrid-laplace
+bout_add_integrated_test(
+  test-multigrid-laplace
   SOURCES test_multigrid_laplace.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 3
-  )
+)
diff --git a/tests/integrated/test-naulin-laplace/CMakeLists.txt b/tests/integrated/test-naulin-laplace/CMakeLists.txt
index 9e63477a53..8ec20b3875 100644
--- a/tests/integrated/test-naulin-laplace/CMakeLists.txt
+++ b/tests/integrated/test-naulin-laplace/CMakeLists.txt
@@ -1,8 +1,8 @@
-bout_add_integrated_test(test-naulin-laplace
+bout_add_integrated_test(
+  test-naulin-laplace
   SOURCES test_naulin_laplace.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
   PROCESSORS 3
-  )
+)
diff --git a/tests/integrated/test-options-netcdf/CMakeLists.txt b/tests/integrated/test-options-netcdf/CMakeLists.txt
index f2d115d768..e956e9a16f 100644
--- a/tests/integrated/test-options-netcdf/CMakeLists.txt
+++ b/tests/integrated/test-options-netcdf/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_integrated_test(test-options-netcdf
+bout_add_integrated_test(
+  test-options-netcdf
   SOURCES test-options-netcdf.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_NETCDF
   CONFLICTS BOUT_HAS_LEGACY_NETCDF
-  )
+)
diff --git a/tests/integrated/test-petsc_laplace/CMakeLists.txt b/tests/integrated/test-petsc_laplace/CMakeLists.txt
index 9492b9f34f..1d2e7896f0 100644
--- a/tests/integrated/test-petsc_laplace/CMakeLists.txt
+++ b/tests/integrated/test-petsc_laplace/CMakeLists.txt
@@ -1,8 +1,9 @@
-bout_add_integrated_test(test-petsc-laplace
+bout_add_integrated_test(
+  test-petsc-laplace
   SOURCES test_petsc_laplace.cxx
   REQUIRES BOUT_HAS_PETSC
-  CONFLICTS BOUT_USE_METRIC_3D # default preconditioner uses 'cyclic' Laplace solver which is not available with 3d metrics
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  CONFLICTS
+    BOUT_USE_METRIC_3D # default preconditioner uses 'cyclic' Laplace solver which is not available with 3d metrics
+  USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/CMakeLists.txt b/tests/integrated/test-petsc_laplace_MAST-grid/CMakeLists.txt
index 53e4acbedb..34042223a0 100644
--- a/tests/integrated/test-petsc_laplace_MAST-grid/CMakeLists.txt
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/CMakeLists.txt
@@ -1,14 +1,12 @@
-bout_add_integrated_test(test-petsc-laplace-MAST-grid
+bout_add_integrated_test(
+  test-petsc-laplace-MAST-grid
   SOURCES test_petsc_laplace_MAST_grid.cxx
   REQUIRES BOUT_HAS_PETSC
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES
-    grids/grid_MAST_SOL_jyis2.nc
-    grids/grid_MAST_SOL_jyis34.nc
-    grids/grid_MAST_SOL_jyis65.nc
-    grids/grid_MAST_SOL_jyis81.nc
+    grids/grid_MAST_SOL_jyis2.nc grids/grid_MAST_SOL_jyis34.nc
+    grids/grid_MAST_SOL_jyis65.nc grids/grid_MAST_SOL_jyis81.nc
     grids/grid_MAST_SOL_jyis113.nc
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-restart-io/CMakeLists.txt b/tests/integrated/test-restart-io/CMakeLists.txt
index c3de2ad0e1..0a98019248 100644
--- a/tests/integrated/test-restart-io/CMakeLists.txt
+++ b/tests/integrated/test-restart-io/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_integrated_test(test-restart-io
+bout_add_integrated_test(
+  test-restart-io
   SOURCES test-restart-io.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_NETCDF
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-restarting/CMakeLists.txt b/tests/integrated/test-restarting/CMakeLists.txt
index 83cb9c808f..8174743459 100644
--- a/tests/integrated/test-restarting/CMakeLists.txt
+++ b/tests/integrated/test-restarting/CMakeLists.txt
@@ -1,5 +1,5 @@
-bout_add_integrated_test(test-restarting
+bout_add_integrated_test(
+  test-restarting
   SOURCES test_restarting.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  )
+  USE_RUNTEST USE_DATA_BOUT_INP
+)
diff --git a/tests/integrated/test-slepc-solver/CMakeLists.txt b/tests/integrated/test-slepc-solver/CMakeLists.txt
index bc4c178de9..cdfc7018c6 100644
--- a/tests/integrated/test-slepc-solver/CMakeLists.txt
+++ b/tests/integrated/test-slepc-solver/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-slepc-solver
+bout_add_integrated_test(
+  test-slepc-solver
   SOURCES test-slepc-solver.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_SLEPC
-  )
+)
diff --git a/tests/integrated/test-smooth/CMakeLists.txt b/tests/integrated/test-smooth/CMakeLists.txt
index 6b6f0c2001..728ea8e3b4 100644
--- a/tests/integrated/test-smooth/CMakeLists.txt
+++ b/tests/integrated/test-smooth/CMakeLists.txt
@@ -1,8 +1,8 @@
-bout_add_integrated_test(test-smooth
+bout_add_integrated_test(
+  test-smooth
   SOURCES test_smooth.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   EXTRA_FILES test_smooth.nc data/benchmark.0.nc
   REQUIRES BOUT_HAS_NETCDF
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-snb/CMakeLists.txt b/tests/integrated/test-snb/CMakeLists.txt
index 1a81c392a4..5308b63e53 100644
--- a/tests/integrated/test-snb/CMakeLists.txt
+++ b/tests/integrated/test-snb/CMakeLists.txt
@@ -1,6 +1,7 @@
-bout_add_integrated_test(test-snb
+bout_add_integrated_test(
+  test-snb
   SOURCES test_snb.cxx
   CONFLICTS BOUT_USE_METRIC_3D
   USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
-  )
+)
diff --git a/tests/integrated/test-solver/CMakeLists.txt b/tests/integrated/test-solver/CMakeLists.txt
index f20e11f1eb..de3c602621 100644
--- a/tests/integrated/test-solver/CMakeLists.txt
+++ b/tests/integrated/test-solver/CMakeLists.txt
@@ -1,3 +1 @@
-bout_add_integrated_test(test-solver
-  SOURCES test_solver.cxx
-  )
+bout_add_integrated_test(test-solver SOURCES test_solver.cxx)
diff --git a/tests/integrated/test-squash/CMakeLists.txt b/tests/integrated/test-squash/CMakeLists.txt
index 2c7e8d734d..f422331831 100644
--- a/tests/integrated/test-squash/CMakeLists.txt
+++ b/tests/integrated/test-squash/CMakeLists.txt
@@ -1,8 +1,8 @@
-bout_add_integrated_test(test-squash
+bout_add_integrated_test(
+  test-squash
   SOURCES squash.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_NETCDF
   TESTARGS "${CMAKE_CURRENT_LIST_DIR}/../../../bin"
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-stopCheck-file/CMakeLists.txt b/tests/integrated/test-stopCheck-file/CMakeLists.txt
index 60b9b23489..914142d85a 100644
--- a/tests/integrated/test-stopCheck-file/CMakeLists.txt
+++ b/tests/integrated/test-stopCheck-file/CMakeLists.txt
@@ -1,9 +1,6 @@
-bout_add_integrated_test(test-stopCheck-file
+bout_add_integrated_test(
+  test-stopCheck-file
   SOURCES test_stopCheck.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  EXTRA_FILES
-    data/BOUT.stop
-    dataSecond/BOUT.inp
-    dataSecond/otherStop.check
-  )
+  USE_RUNTEST USE_DATA_BOUT_INP
+  EXTRA_FILES data/BOUT.stop dataSecond/BOUT.inp dataSecond/otherStop.check
+)
diff --git a/tests/integrated/test-stopCheck/CMakeLists.txt b/tests/integrated/test-stopCheck/CMakeLists.txt
index 93cf5fb67b..09f4063818 100644
--- a/tests/integrated/test-stopCheck/CMakeLists.txt
+++ b/tests/integrated/test-stopCheck/CMakeLists.txt
@@ -1,5 +1,5 @@
-bout_add_integrated_test(test-stopCheck
+bout_add_integrated_test(
+  test-stopCheck
   SOURCES test_stopCheck.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  )
+  USE_RUNTEST USE_DATA_BOUT_INP
+)
diff --git a/tests/integrated/test-twistshift-staggered/CMakeLists.txt b/tests/integrated/test-twistshift-staggered/CMakeLists.txt
index 747e64dda1..7f741c5173 100644
--- a/tests/integrated/test-twistshift-staggered/CMakeLists.txt
+++ b/tests/integrated/test-twistshift-staggered/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-twistshift-staggered
+bout_add_integrated_test(
+  test-twistshift-staggered
   SOURCES test-twistshift.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
-  )
+)
diff --git a/tests/integrated/test-twistshift/CMakeLists.txt b/tests/integrated/test-twistshift/CMakeLists.txt
index e8712e9844..9e876f0b12 100644
--- a/tests/integrated/test-twistshift/CMakeLists.txt
+++ b/tests/integrated/test-twistshift/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-twistshift
+bout_add_integrated_test(
+  test-twistshift
   SOURCES test-twistshift.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
-  )
+)
diff --git a/tests/integrated/test-vec/CMakeLists.txt b/tests/integrated/test-vec/CMakeLists.txt
index 111840c71a..921650d06a 100644
--- a/tests/integrated/test-vec/CMakeLists.txt
+++ b/tests/integrated/test-vec/CMakeLists.txt
@@ -1,7 +1,7 @@
-bout_add_integrated_test(test-vec
+bout_add_integrated_test(
+  test-vec
   SOURCES testVec.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
   PROCESSORS 4
-  )
+)
diff --git a/tests/integrated/test-yupdown-weights/CMakeLists.txt b/tests/integrated/test-yupdown-weights/CMakeLists.txt
index 5b6d825c87..eb14dcb074 100644
--- a/tests/integrated/test-yupdown-weights/CMakeLists.txt
+++ b/tests/integrated/test-yupdown-weights/CMakeLists.txt
@@ -1,5 +1,5 @@
-bout_add_integrated_test(test-yupdown-weights
+bout_add_integrated_test(
+  test-yupdown-weights
   SOURCES test_yupdown_weights.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  )
+  USE_RUNTEST USE_DATA_BOUT_INP
+)
diff --git a/tests/integrated/test-yupdown/CMakeLists.txt b/tests/integrated/test-yupdown/CMakeLists.txt
index 3c6d500b4e..0e0636e9b2 100644
--- a/tests/integrated/test-yupdown/CMakeLists.txt
+++ b/tests/integrated/test-yupdown/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_integrated_test(test-yupdown
+bout_add_integrated_test(
+  test-yupdown
   SOURCES test_yupdown.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
-  )
+)
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 40aa207dea..7cf0bb0af7 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -1,122 +1,148 @@
 bout_update_submodules()
 
-if (NOT EXISTS "${PROJECT_SOURCE_DIR}/externalpackages/googletest/CMakeLists.txt")
-  set(BOUT_ENABLE_UNIT_TESTS OFF PARENT_SCOPE)
-  message(WARNING "googletest not found! Have you disabled the git submodules (GIT_SUBMODULE)?")
+if(NOT EXISTS
+   "${PROJECT_SOURCE_DIR}/externalpackages/googletest/CMakeLists.txt"
+)
+  set(BOUT_ENABLE_UNIT_TESTS
+      OFF
+      PARENT_SCOPE
+  )
+  message(
+    WARNING
+      "googletest not found! Have you disabled the git submodules (GIT_SUBMODULE)?"
+  )
   return()
 endif()
 
-set(BOUT_ENABLE_UNIT_TESTS ON PARENT_SCOPE)
+set(BOUT_ENABLE_UNIT_TESTS
+    ON
+    PARENT_SCOPE
+)
 
 # disable gtest pthreads for proper execution of Death tests (on some platforms)
 add_definitions(-DGTEST_HAS_PTHREAD=0)
-set(gtest_disable_pthreads ON CACHE BOOL "" FORCE)
+set(gtest_disable_pthreads
+    ON
+    CACHE BOOL "" FORCE
+)
 
-add_subdirectory("${PROJECT_SOURCE_DIR}/externalpackages/googletest"
-  "externalpackages/googletest")
+add_subdirectory(
+  "${PROJECT_SOURCE_DIR}/externalpackages/googletest"
+  "externalpackages/googletest"
+)
 
 if(NOT TARGET gtest)
-  message(FATAL_ERROR "googletest not found! Have you disabled the git submodules (GIT_SUBMODULE)?")
+  message(
+    FATAL_ERROR
+      "googletest not found! Have you disabled the git submodules (GIT_SUBMODULE)?"
+  )
 endif()
 
 # Some unit tests require GMOCK, so make sure we build it
 set(BUILD_GMOCK ON)
 
 mark_as_advanced(
-  BUILD_GMOCK BUILD_GTEST BUILD_SHARED_LIBS
-  gmock_build_tests gtest_build_samples gtest_build_tests
-  gtest_disable_pthreads gtest_force_shared_crt gtest_hide_internal_symbols
-  )
+  BUILD_GMOCK
+  BUILD_GTEST
+  BUILD_SHARED_LIBS
+  gmock_build_tests
+  gtest_build_samples
+  gtest_build_tests
+  gtest_disable_pthreads
+  gtest_force_shared_crt
+  gtest_hide_internal_symbols
+)
 
 set(serial_tests_source
-  ./bout_test_main.cxx
-  ./field/test_field.cxx
-  ./field/test_field2d.cxx
-  ./field/test_field3d.cxx
-  ./field/test_field_factory.cxx
-  ./field/test_fieldgroup.cxx
-  ./field/test_fieldperp.cxx
-  ./field/test_initialprofiles.cxx
-  ./field/test_vector2d.cxx
-  ./field/test_vector3d.cxx
-  ./field/test_where.cxx
-  ./include/bout/test_array.cxx
-  ./include/bout/test_assert.cxx
-  ./include/bout/test_bout_enum_class.cxx
-  ./include/bout/test_deriv_store.cxx
-  ./include/bout/test_generic_factory.cxx
-  ./include/bout/test_macro_for_each.cxx
-  ./include/bout/test_monitor.cxx
-  ./include/bout/test_petsc_indexer.cxx
-  ./include/bout/test_petsc_matrix.cxx
-  ./include/bout/test_petsc_setters.cxx
-  ./include/bout/test_petsc_vector.cxx
-  ./include/bout/test_region.cxx
-  ./include/bout/test_single_index_ops.cxx
-  ./include/bout/test_stencil.cxx
-  ./include/bout/test_template_combinations.cxx
-  ./include/bout/test_traits.cxx
-  ./include/test_cyclic_reduction.cxx
-  ./include/test_derivs.cxx
-  ./include/test_mask.cxx
-  ./invert/test_fft.cxx
-  ./invert/laplace/test_laplace_petsc3damg.cxx
-  ./invert/laplace/test_laplace_cyclic.cxx
-  ./mesh/data/test_gridfromoptions.cxx
-  ./mesh/parallel/test_shiftedmetric.cxx
-  ./mesh/test_boundary_factory.cxx
-  ./mesh/test_boutmesh.cxx
-  ./mesh/test_coordinates.cxx
-  ./mesh/test_coordinates_accessor.cxx
-  ./mesh/test_interpolation.cxx
-  ./mesh/test_invert3x3.cxx
-  ./mesh/test_mesh.cxx
-  ./mesh/test_paralleltransform.cxx
-  ./solver/test_fakesolver.cxx
-  ./solver/test_fakesolver.hxx
-  ./solver/test_solver.cxx
-  ./solver/test_solverfactory.cxx
-  ./sys/test_boutexception.cxx
-  ./sys/test_expressionparser.cxx
-  ./sys/test_msg_stack.cxx
-  ./sys/test_options.cxx
-  ./sys/test_options_adios2.cxx
-  ./sys/test_options_fields.cxx
-  ./sys/test_options_netcdf.cxx
-  ./sys/test_optionsreader.cxx
-  ./sys/test_output.cxx
-  ./sys/test_range.cxx
-  ./sys/test_timer.cxx
-  ./sys/test_type_name.cxx
-  ./sys/test_utils.cxx
-  ./sys/test_variant.cxx
-  ./sys/test_raja.cxx
-  ./test_extras.cxx
-  ./test_extras.hxx
-  ./fake_mesh.hxx
-  ./fake_mesh_fixture.hxx
-  ./src/test_bout++.cxx)
+    ./bout_test_main.cxx
+    ./field/test_field.cxx
+    ./field/test_field2d.cxx
+    ./field/test_field3d.cxx
+    ./field/test_field_factory.cxx
+    ./field/test_fieldgroup.cxx
+    ./field/test_fieldperp.cxx
+    ./field/test_initialprofiles.cxx
+    ./field/test_vector2d.cxx
+    ./field/test_vector3d.cxx
+    ./field/test_where.cxx
+    ./include/bout/test_array.cxx
+    ./include/bout/test_assert.cxx
+    ./include/bout/test_bout_enum_class.cxx
+    ./include/bout/test_deriv_store.cxx
+    ./include/bout/test_generic_factory.cxx
+    ./include/bout/test_macro_for_each.cxx
+    ./include/bout/test_monitor.cxx
+    ./include/bout/test_petsc_indexer.cxx
+    ./include/bout/test_petsc_matrix.cxx
+    ./include/bout/test_petsc_setters.cxx
+    ./include/bout/test_petsc_vector.cxx
+    ./include/bout/test_region.cxx
+    ./include/bout/test_single_index_ops.cxx
+    ./include/bout/test_stencil.cxx
+    ./include/bout/test_template_combinations.cxx
+    ./include/bout/test_traits.cxx
+    ./include/test_cyclic_reduction.cxx
+    ./include/test_derivs.cxx
+    ./include/test_mask.cxx
+    ./invert/test_fft.cxx
+    ./invert/laplace/test_laplace_petsc3damg.cxx
+    ./invert/laplace/test_laplace_cyclic.cxx
+    ./mesh/data/test_gridfromoptions.cxx
+    ./mesh/parallel/test_shiftedmetric.cxx
+    ./mesh/test_boundary_factory.cxx
+    ./mesh/test_boutmesh.cxx
+    ./mesh/test_coordinates.cxx
+    ./mesh/test_coordinates_accessor.cxx
+    ./mesh/test_interpolation.cxx
+    ./mesh/test_invert3x3.cxx
+    ./mesh/test_mesh.cxx
+    ./mesh/test_paralleltransform.cxx
+    ./solver/test_fakesolver.cxx
+    ./solver/test_fakesolver.hxx
+    ./solver/test_solver.cxx
+    ./solver/test_solverfactory.cxx
+    ./sys/test_boutexception.cxx
+    ./sys/test_expressionparser.cxx
+    ./sys/test_msg_stack.cxx
+    ./sys/test_options.cxx
+    ./sys/test_options_adios2.cxx
+    ./sys/test_options_fields.cxx
+    ./sys/test_options_netcdf.cxx
+    ./sys/test_optionsreader.cxx
+    ./sys/test_output.cxx
+    ./sys/test_range.cxx
+    ./sys/test_timer.cxx
+    ./sys/test_type_name.cxx
+    ./sys/test_utils.cxx
+    ./sys/test_variant.cxx
+    ./sys/test_raja.cxx
+    ./test_extras.cxx
+    ./test_extras.hxx
+    ./fake_mesh.hxx
+    ./fake_mesh_fixture.hxx
+    ./src/test_bout++.cxx
+)
 
 if(BOUT_HAS_HYPRE)
-   list(APPEND serial_tests_source ./include/bout/test_hypre_interface.cxx)
-   list(APPEND serial_tests_source ./invert/laplace/test_laplace_hypre3d.cxx)
-endif ()
+  list(APPEND serial_tests_source ./include/bout/test_hypre_interface.cxx)
+  list(APPEND serial_tests_source ./invert/laplace/test_laplace_hypre3d.cxx)
+endif()
 
 add_executable(serial_tests ${serial_tests_source})
 
-target_include_directories(serial_tests PUBLIC bout++
-   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
-   $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/../../include>
-   ${CMAKE_INSTALL_PREFIX}/include
-  )
+target_include_directories(
+  serial_tests
+  PUBLIC bout++ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+         $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/../../include>
+         ${CMAKE_INSTALL_PREFIX}/include
+)
 set_target_properties(serial_tests PROPERTIES LINKER_LANGUAGE CXX)
 target_link_libraries(serial_tests gtest gmock bout++::bout++)
 add_test(NAME serial_tests COMMAND serial_tests --gtest_brief=1)
 set_target_properties(serial_tests PROPERTIES FOLDER tests/unit)
 add_dependencies(build-check-unit-tests serial_tests)
 
-if (BOUT_HAS_CUDA)
-   set_source_files_properties(${serial_tests_source} PROPERTIES LANGUAGE CUDA )
-   set_target_properties(serial_tests PROPERTIES CUDA_STANDARD 14)
-endif ()   
-
+if(BOUT_HAS_CUDA)
+  set_source_files_properties(${serial_tests_source} PROPERTIES LANGUAGE CUDA)
+  set_target_properties(serial_tests PROPERTIES CUDA_STANDARD 14)
+endif()
diff --git a/tools/pylib/_boutpp_build/CMakeLists.txt b/tools/pylib/_boutpp_build/CMakeLists.txt
index 3be2a5d2aa..bf5ba35261 100644
--- a/tools/pylib/_boutpp_build/CMakeLists.txt
+++ b/tools/pylib/_boutpp_build/CMakeLists.txt
@@ -1,19 +1,21 @@
 # Error if Python API was explicitly requested, otherwise just a
 # warning and don't build Python API
 macro(bout_python_maybe_error VAR NAME)
-  if (NOT ${VAR})
+  if(NOT ${VAR})
     set(_error_msg "${NAME} is required for the Python interface")
-    if (NOT "${BOUT_ENABLE_PYTHON}" STREQUAL "AUTO")
+    if(NOT "${BOUT_ENABLE_PYTHON}" STREQUAL "AUTO")
       message(FATAL_ERROR ${_error_msg})
     else()
       message(WARNING ${_error_msg})
-      set(BOUT_ENABLE_PYTHON OFF PARENT_SCOPE)
+      set(BOUT_ENABLE_PYTHON
+          OFF
+          PARENT_SCOPE
+      )
       return()
     endif()
   endif()
 endmacro()
 
-
 bout_python_maybe_error(BUILD_SHARED_LIBS "BOUT++ shared library")
 
 find_package(Numpy)
@@ -25,35 +27,41 @@ bout_python_maybe_error(${Cython_FOUND} Cython)
 find_package(Bash)
 bout_python_maybe_error(${Bash_FOUND} Bash)
 
-execute_process(COMMAND ${Python3_EXECUTABLE} -c "import jinja2"
-  RESULT_VARIABLE jinja2_FOUND)
-if (jinja2_FOUND EQUAL 0)
+execute_process(
+  COMMAND ${Python3_EXECUTABLE} -c "import jinja2" RESULT_VARIABLE jinja2_FOUND
+)
+if(jinja2_FOUND EQUAL 0)
   # We have jinja2 - all good
 else()
   bout_python_maybe_error(OFF jinja2)
 endif()
 
-execute_process(COMMAND ${Python3_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX')[:-3])"
+execute_process(
+  COMMAND ${Python3_EXECUTABLE} -c
+          "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX')[:-3])"
   RESULT_VARIABLE PYTHON_WORKING
   OUTPUT_VARIABLE PYTHON_EXT_SUFFIX
   OUTPUT_STRIP_TRAILING_WHITESPACE
-  )
-if (NOT ${PYTHON_WORKING} EQUAL 0)
+)
+if(NOT ${PYTHON_WORKING} EQUAL 0)
   set(MSG "Failed to get the extension name from python!")
-  if ("${BOUT_ENABLE_PYTHON}" STREQUAL "ON")
+  if("${BOUT_ENABLE_PYTHON}" STREQUAL "ON")
     message(FATAL_ERROR ${MSG})
   else()
     message(WARNING ${MSG})
-    set(BOUT_ENABLE_PYTHON OFF )
+    set(BOUT_ENABLE_PYTHON OFF)
   endif()
 endif()
 
 # No errors? We can build the interface!
-if ("${BOUT_ENABLE_PYTHON}" STREQUAL "AUTO")
-  set(BOUT_ENABLE_PYTHON ON PARENT_SCOPE)
+if("${BOUT_ENABLE_PYTHON}" STREQUAL "AUTO")
+  set(BOUT_ENABLE_PYTHON
+      ON
+      PARENT_SCOPE
+  )
 endif()
 
-if (NOT BOUT_ENABLE_PYTHON)
+if(NOT BOUT_ENABLE_PYTHON)
   message(WARNING "Python interface will not be built, see warnings above")
   return()
 endif()
@@ -71,54 +79,70 @@ foreach(file IN LISTS files)
   set(gen ${tar}/${file})
   list(APPEND generated ${gen})
   #message(FATAL_ERROR "${gen} ${src}/${file}.jinja")
-  add_custom_command(OUTPUT ${gen}
-	COMMAND ${CMAKE_COMMAND} -E make_directory ${tar}
-	COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${tar}/..:\${PYTHONPATH} ${Python3_EXECUTABLE} generate.py ${file}.jinja ${gen}
-	DEPENDS ${src}/${file}.jinja
-	DEPENDS ${src}/helper.py
-	DEPENDS ${src}/resolve_enum_inv.pyx.jinja
-	DEPENDS ${src}/generate.py
-	DEPENDS bout++
-	WORKING_DIRECTORY ${src}/
-	COMMENT "Generating ${file}")
+  add_custom_command(
+    OUTPUT ${gen}
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${tar}
+    COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${tar}/..:\${PYTHONPATH}
+            ${Python3_EXECUTABLE} generate.py ${file}.jinja ${gen}
+    DEPENDS ${src}/${file}.jinja
+    DEPENDS ${src}/helper.py
+    DEPENDS ${src}/resolve_enum_inv.pyx.jinja
+    DEPENDS ${src}/generate.py
+    DEPENDS bout++
+    WORKING_DIRECTORY ${src}/
+    COMMENT "Generating ${file}"
+  )
 endforeach()
 
 set(boutpp_depends ${generated})
 
-set(files "boutexception_helper.hxx" "boutexception_helper.cxx" "boutpp_openmpi_compat.hxx" "bout_options.pxd" "setup.py")
+set(files "boutexception_helper.hxx" "boutexception_helper.cxx"
+          "boutpp_openmpi_compat.hxx" "bout_options.pxd" "setup.py"
+)
 foreach(file IN LISTS files)
   list(APPEND ${boutpp_depends} "${CMAKE_CURRENT_BINARY_DIR}/${file}")
   bout_copy_file("${file}")
 endforeach()
 
-add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libboutpp.cpp
+add_custom_command(
+  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libboutpp.cpp
   COMMAND ${CMAKE_COMMAND} -E copy boutpp.pyx libboutpp.pyx
-  COMMAND ${Python3_EXECUTABLE} -m cython libboutpp.pyx --cplus -3  -X binding=True -X embedsignature=True
+  COMMAND ${Python3_EXECUTABLE} -m cython libboutpp.pyx --cplus -3 -X
+          binding=True -X embedsignature=True
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   DEPENDS ${boutpp_depends}
-  )
+)
 
-add_library(boutpp${PYTHON_EXT_SUFFIX} SHARED
-  ${tar}/libboutpp.cpp
-  ${tar}/helper.cxx
-  ${tar}/boutexception_helper.cxx
-  )
+add_library(
+  boutpp${PYTHON_EXT_SUFFIX} SHARED ${tar}/libboutpp.cpp ${tar}/helper.cxx
+                                    ${tar}/boutexception_helper.cxx
+)
 
-add_custom_target(boutpp ALL
-  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_BINARY_DIR}/libboutpp${PYTHON_EXT_SUFFIX}.so  ${CMAKE_CURRENT_BINARY_DIR}/../boutpp/libboutpp${PYTHON_EXT_SUFFIX}.so
-  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/boutpp.py ${CMAKE_CURRENT_BINARY_DIR}/../boutpp/__init__.py
+add_custom_target(
+  boutpp ALL
+  COMMAND
+    ${CMAKE_COMMAND} -E copy
+    ${CMAKE_CURRENT_BINARY_DIR}/libboutpp${PYTHON_EXT_SUFFIX}.so
+    ${CMAKE_CURRENT_BINARY_DIR}/../boutpp/libboutpp${PYTHON_EXT_SUFFIX}.so
+  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/boutpp.py
+          ${CMAKE_CURRENT_BINARY_DIR}/../boutpp/__init__.py
   DEPENDS boutpp${PYTHON_EXT_SUFFIX}
   COMMENT "Building python interface"
 )
 
-install(TARGETS  boutpp${PYTHON_EXT_SUFFIX}
-  DESTINATION ${CMAKE_INSTALL_PYTHON_SITEARCH}/boutpp/
+install(TARGETS boutpp${PYTHON_EXT_SUFFIX}
+        DESTINATION ${CMAKE_INSTALL_PYTHON_SITEARCH}/boutpp/
 )
 
-install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/boutpp.py
+install(
+  FILES ${CMAKE_CURRENT_SOURCE_DIR}/boutpp.py
   DESTINATION ${CMAKE_INSTALL_PYTHON_SITEARCH}/boutpp/
   RENAME __init__.py
-  )
+)
 
 target_link_libraries(boutpp${PYTHON_EXT_SUFFIX} bout++)
-target_include_directories(boutpp${PYTHON_EXT_SUFFIX} PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}> ${Numpy_INCLUDE_DIRS} ${Python3_INCLUDE_DIRS})
+target_include_directories(
+  boutpp${PYTHON_EXT_SUFFIX}
+  PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}> ${Numpy_INCLUDE_DIRS}
+          ${Python3_INCLUDE_DIRS}
+)

From 523ee8a9e0cea2469e503cefa8ad1bf8f73cac8a Mon Sep 17 00:00:00 2001
From: Owen Parry <owen.parry@ukaea.uk>
Date: Fri, 20 Feb 2026 12:03:38 +0000
Subject: [PATCH 0517/1827] Ignore initial CMake formatting commit.

---
 .git-blame-ignore-revs | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 93c768a148..010100588c 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -1,6 +1,8 @@
 # Clang-format whole repo
 d8f14fdddb5ca0fbb32d8e2bf5ac2960d6ac5ce6
 ed2117e6d6826a98b6988e2f18c0c34e408563b6
+# CMake formatting
+17ac13c28aa3b34a0e46dbe87bb3874f6b25e706
 # Added by the bot
 4b010b7634aee1045743be80c268d4644522cd29
 a71cad2dd6ace5741a754e2ca7daacd4bb094e0e

From 7dbac074f0f6d0a7b2155faedef1f71259be2590 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 20 Feb 2026 15:44:19 +0000
Subject: [PATCH 0518/1827] Add some very basic FieldPerp Laplacian solver
 tests

Also fix PCR and PCRThomas which were always using the global `nsys` array size,
instead of the local array size
---
 src/invert/laplace/impls/pcr/pcr.cxx          | 25 +++++---
 .../laplace/impls/pcr_thomas/pcr_thomas.cxx   | 20 ++++++-
 tests/integrated/test-laplace/runtest         | 59 +++++++++++--------
 .../integrated/test-laplace/test_laplace.cxx  |  8 ++-
 4 files changed, 77 insertions(+), 35 deletions(-)

diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx
index a33bd7eef2..61e493d3ed 100644
--- a/src/invert/laplace/impls/pcr/pcr.cxx
+++ b/src/invert/laplace/impls/pcr/pcr.cxx
@@ -37,22 +37,21 @@
  **************************************************************************/
 
 #include "pcr.hxx"
-#include "bout/globals.hxx"
 
+#include <bout/array.hxx>
+#include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
+#include <bout/dcomplex.hxx>
 #include <bout/fft.hxx>
+#include <bout/globals.hxx>
 #include <bout/lapack_routines.hxx>
 #include <bout/mesh.hxx>
 #include <bout/openmpwrap.hxx>
-#include <bout/sys/timer.hxx>
-#include <bout/utils.hxx>
-#include <cmath>
-
-#include "bout/boutcomm.hxx"
 #include <bout/output.hxx>
-
 #include <bout/scorepwrapper.hxx>
+#include <bout/sys/timer.hxx>
+#include <bout/utils.hxx>
 
 #include <algorithm>
 #include <cmath>
@@ -556,6 +555,8 @@ void LaplacePCR ::cr_pcr_solver(Matrix<dcomplex>& a_mpi, Matrix<dcomplex>& b_mpi
   const int xend = localmesh->xend;
   const int nx = xend - xstart + 1; // number of interior points
 
+  const int nsys = std::get<0>(a_mpi.shape());
+
   // Handle boundary points so that the PCR algorithm works with arrays of
   // the same size on each rank.
   // Note that this modifies the coefficients of b and r in the first and last
@@ -622,6 +623,8 @@ void LaplacePCR ::cr_pcr_solver(Matrix<dcomplex>& a_mpi, Matrix<dcomplex>& b_mpi
 void LaplacePCR ::eliminate_boundary_rows(Matrix<dcomplex>& a, Matrix<dcomplex>& b,
                                           Matrix<dcomplex>& c, Matrix<dcomplex>& r) {
 
+  const int nsys = std::get<0>(a.shape());
+
   if (localmesh->firstX()) {
     for (int kz = 0; kz < nsys; kz++) {
       // Do forward elimination on *all* boundary rows up to xstart
@@ -657,6 +660,8 @@ void LaplacePCR ::apply_boundary_conditions(const Matrix<dcomplex>& a,
                                             const Matrix<dcomplex>& r,
                                             Matrix<dcomplex>& x) {
 
+  const int nsys = std::get<0>(a.shape());
+
   if (localmesh->firstX()) {
     for (int kz = 0; kz < nsys; kz++) {
       for (int ix = localmesh->xstart - 1; ix >= 0; ix--) {
@@ -682,6 +687,8 @@ void LaplacePCR ::apply_boundary_conditions(const Matrix<dcomplex>& a,
 void LaplacePCR ::cr_forward_multiple_row(Matrix<dcomplex>& a, Matrix<dcomplex>& b,
                                           Matrix<dcomplex>& c,
                                           Matrix<dcomplex>& r) const {
+  const int nsys = std::get<0>(a.shape());
+
   MPI_Comm comm = BoutComm::get();
   Array<dcomplex> alpha(nsys);
   Array<dcomplex> gamma(nsys);
@@ -755,6 +762,8 @@ void LaplacePCR ::cr_forward_multiple_row(Matrix<dcomplex>& a, Matrix<dcomplex>&
 void LaplacePCR ::cr_backward_multiple_row(Matrix<dcomplex>& a, Matrix<dcomplex>& b,
                                            Matrix<dcomplex>& c, Matrix<dcomplex>& r,
                                            Matrix<dcomplex>& x) const {
+  const int nsys = std::get<0>(a.shape());
+
   MPI_Comm comm = BoutComm::get();
 
   MPI_Status status;
@@ -806,6 +815,8 @@ void LaplacePCR ::pcr_forward_single_row(Matrix<dcomplex>& a, Matrix<dcomplex>&
                                          Matrix<dcomplex>& c, Matrix<dcomplex>& r,
                                          Matrix<dcomplex>& x) const {
 
+  const int nsys = std::get<0>(a.shape());
+
   Array<dcomplex> alpha(nsys);
   Array<dcomplex> gamma(nsys);
   Array<dcomplex> sbuf(4 * nsys);
diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
index d471775990..604a630feb 100644
--- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
+++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
@@ -37,9 +37,11 @@
  **************************************************************************/
 
 #include "pcr_thomas.hxx"
-#include "bout/globals.hxx"
 
+#include "bout/array.hxx"
 #include "bout/boutcomm.hxx"
+#include "bout/dcomplex.hxx"
+#include "bout/globals.hxx"
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
@@ -556,6 +558,8 @@ void LaplacePCR_THOMAS ::pcr_thomas_solver(Matrix<dcomplex>& a_mpi,
   const int xend = localmesh->xend;
   const int nx = xend - xstart + 1; // number of interior points
 
+  const int nsys = std::get<0>(a_mpi.shape());
+
   // Handle boundary points so that the PCR algorithm works with arrays of
   // the same size on each rank.
   // Note that this modifies the coefficients of b and r in the first and last
@@ -622,6 +626,8 @@ void LaplacePCR_THOMAS ::eliminate_boundary_rows(const Matrix<dcomplex>& a,
                                                  const Matrix<dcomplex>& c,
                                                  Matrix<dcomplex>& r) {
 
+  const int nsys = std::get<0>(a.shape());
+
   if (localmesh->firstX()) {
     // x index is first interior row
     const int xstart = localmesh->xstart;
@@ -656,6 +662,8 @@ void LaplacePCR_THOMAS ::apply_boundary_conditions(const Matrix<dcomplex>& a,
                                                    const Matrix<dcomplex>& r,
                                                    Matrix<dcomplex>& x) {
 
+  const int nsys = std::get<0>(a.shape());
+
   if (localmesh->firstX()) {
     for (int kz = 0; kz < nsys; kz++) {
       for (int ix = localmesh->xstart - 1; ix >= 0; ix--) {
@@ -681,6 +689,8 @@ void LaplacePCR_THOMAS ::apply_boundary_conditions(const Matrix<dcomplex>& a,
 void LaplacePCR_THOMAS ::cr_forward_multiple_row(Matrix<dcomplex>& a, Matrix<dcomplex>& b,
                                                  Matrix<dcomplex>& c,
                                                  Matrix<dcomplex>& r) const {
+  const int nsys = std::get<0>(a.shape());
+
   MPI_Comm comm = BoutComm::get();
   Array<dcomplex> alpha(nsys);
   Array<dcomplex> gamma(nsys);
@@ -756,6 +766,8 @@ void LaplacePCR_THOMAS ::cr_backward_multiple_row(Matrix<dcomplex>& a,
                                                   Matrix<dcomplex>& c,
                                                   Matrix<dcomplex>& r,
                                                   Matrix<dcomplex>& x) const {
+  const int nsys = std::get<0>(a.shape());
+
   MPI_Comm comm = BoutComm::get();
 
   MPI_Status status;
@@ -807,6 +819,8 @@ void LaplacePCR_THOMAS ::pcr_forward_single_row(Matrix<dcomplex>& a, Matrix<dcom
                                                 Matrix<dcomplex>& c, Matrix<dcomplex>& r,
                                                 Matrix<dcomplex>& x) const {
 
+  const int nsys = std::get<0>(a.shape());
+
   Array<dcomplex> alpha(nsys);
   Array<dcomplex> gamma(nsys);
   Array<dcomplex> sbuf(4 * nsys);
@@ -984,6 +998,8 @@ void LaplacePCR_THOMAS ::pThomas_forward_multiple_row(Matrix<dcomplex>& a,
                                                       Matrix<dcomplex>& b,
                                                       Matrix<dcomplex>& c,
                                                       Matrix<dcomplex>& r) const {
+  const int nsys = std::get<0>(a.shape());
+
   for (int kz = 0; kz < nsys; kz++) {
     for (int i = 3; i <= n_mpi; i++) {
       const dcomplex alpha = -a(kz, i) / b(kz, i - 1);
@@ -1015,6 +1031,8 @@ void LaplacePCR_THOMAS ::pcr_double_row_substitution(Matrix<dcomplex>& a,
                                                      Matrix<dcomplex>& c,
                                                      Matrix<dcomplex>& r,
                                                      Matrix<dcomplex>& x) {
+  const int nsys = std::get<0>(a.shape());
+
   Array<dcomplex> alpha(nsys);
   Array<dcomplex> gamma(nsys);
   Array<dcomplex> sbuf(4 * nsys);
diff --git a/tests/integrated/test-laplace/runtest b/tests/integrated/test-laplace/runtest
index d1e9c3d1c9..8704447d66 100755
--- a/tests/integrated/test-laplace/runtest
+++ b/tests/integrated/test-laplace/runtest
@@ -8,12 +8,11 @@
 # Requires: netcdf
 # Cores: 4
 
-from __future__ import print_function
+from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boutdata.collect import collect, create_cache
+import numpy.testing as npt
+from sys import exit
 
-try:
-    from builtins import str
-except:
-    pass
 
 # Variables to compare
 vars = [
@@ -36,18 +35,11 @@ vars = [
 ]
 tol = 1e-6  # Absolute tolerance
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
-from boutdata.collect import collect
-import numpy as np
-from sys import stdout, exit
-
 build_and_log("Laplacian inversion test")
 
 # Read benchmark values
 print("Reading benchmark data")
-bmk = {}
-for v in vars:
-    bmk[v] = collect(v, path="data", prefix="benchmark", info=False)
+bmk = {v: collect(v, path="data", prefix="benchmark", info=False) for v in vars}
 
 print("Running Laplacian inversion test")
 success = True
@@ -58,29 +50,44 @@ for solver in ["cyclic", "pcr", "pcr_thomas"]:
         if nproc > 2:
             nxpe = 2
 
-        cmd = "./test_laplace NXPE=" + str(nxpe) + " laplace:type=" + solver
+        cmd = f"./test_laplace NXPE={nxpe} laplace:type={solver}"
 
         shell("rm data/BOUT.dmp.*.nc")
 
-        print("   %s solver with %d processors (nxpe = %d)...." % (solver, nproc, nxpe))
+        print(f"   {solver} solver with {nproc} processors ({nxpe=})....")
         s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True)
-        with open("run.log." + str(nproc), "w") as f:
+        with open(f"run.log.{nproc}", "w") as f:
             f.write(out)
 
+        cache = create_cache(path="data", prefix="BOUT.dmp")
+
         # Collect output data
         for v in vars:
-            stdout.write("      Checking variable " + v + " ... ")
-            result = collect(v, path="data", info=False)
+            print(f"      Checking variable {v} ...", end="")
+            result = collect(v, path="data", info=False, datafile_cache=cache)
             # Compare benchmark and output
-            if np.shape(bmk[v]) != np.shape(result):
-                print("Fail, wrong shape")
-                success = False
-            diff = np.max(np.abs(bmk[v] - result))
-            if diff > tol:
-                print("Fail, maximum difference = " + str(diff))
-                success = False
-            else:
+            try:
+                npt.assert_allclose(result, bmk[v], atol=tol, rtol=tol)
                 print("Pass")
+            except AssertionError as e:
+                print(f"Fail: {e}")
+                success = False
+
+        # Only check FieldPerps on one processor because reading them in is
+        # quite annoying on mutliple cores due to mismatched global y indices
+        if nproc == 1:
+            for v in ["flag0_perp", "flag3_perp"]:
+                print(f"      Checking variable {v} ...", end="")
+                result = collect(v, path="data", info=False, datafile_cache=cache)
+                # Compare benchmark and output
+                try:
+                    npt.assert_allclose(
+                        result, bmk[v.replace("_perp", "")][:, 0, :], atol=tol, rtol=tol
+                    )
+                    print("Pass")
+                except AssertionError as e:
+                    print(f"Fail: {e}")
+                    success = False
 
 if success:
     print(" => All Laplacian inversion tests passed")
diff --git a/tests/integrated/test-laplace/test_laplace.cxx b/tests/integrated/test-laplace/test_laplace.cxx
index 94887c718e..abdf796dc6 100644
--- a/tests/integrated/test-laplace/test_laplace.cxx
+++ b/tests/integrated/test-laplace/test_laplace.cxx
@@ -3,6 +3,8 @@
  *
  */
 
+#include "bout/field2d.hxx"
+#include "bout/globals.hxx"
 #include <bout/bout.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/invert_laplace.hxx>
@@ -12,6 +14,8 @@ int main(int argc, char** argv) {
   // Initialise BOUT++, setting up mesh
   BoutInitialise(argc, argv);
 
+  using bout::globals::mesh;
+
   FieldFactory f{bout::globals::mesh};
   Options dump;
 
@@ -24,14 +28,16 @@ int main(int argc, char** argv) {
   dump["c"] = c;
   dump["d"] = d;
 
-  auto lap = std::unique_ptr<Laplacian>{Laplacian::create()};
+  auto lap = Laplacian::create();
 
   lap->setCoefA(0.0);
   lap->setCoefC(1.0);
   lap->setCoefD(1.0);
   dump["flag0"] = lap->solve(input);
+  dump["flag0_perp"] = lap->solve(sliceXZ(input, mesh->ystart));
   lap->setInnerBoundaryFlags(INVERT_DC_GRAD + INVERT_AC_GRAD);
   dump["flag3"] = lap->solve(input);
+  dump["flag3_perp"] = lap->solve(sliceXZ(input, mesh->ystart));
 
   lap->setCoefA(a);
   lap->setInnerBoundaryFlags(0);

From 83d6660357a767a214c8af344d9403df28367c69 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 30 Jan 2026 13:32:15 +0000
Subject: [PATCH 0519/1827] Pull out common classes for FFT/DST transforms in
 some Laplacians

The Laplacian inversion solvers `LaplaceCyclic`, `LaplacePCR`,
`LaplacePCR_THOMAS` all use identical code for transforming using
FFTs/DSTs. This commit pulls out that common code to make it easier to maintain.

Also, make the transforms parallel-Z-ready by using the Z guard cells as offsets
---
 CMakeLists.txt                                |   2 +
 include/bout/invert_laplace.hxx               |  18 +-
 src/invert/laplace/common_transform.cxx       | 381 +++++++++++++++
 src/invert/laplace/common_transform.hxx       | 132 ++++++
 .../laplace/impls/cyclic/cyclic_laplace.cxx   | 435 ++++--------------
 src/invert/laplace/impls/pcr/pcr.cxx          | 342 ++------------
 .../laplace/impls/pcr_thomas/pcr_thomas.cxx   | 349 ++------------
 src/invert/laplace/invert_laplace.cxx         |  27 +-
 8 files changed, 689 insertions(+), 997 deletions(-)
 create mode 100644 src/invert/laplace/common_transform.cxx
 create mode 100644 src/invert/laplace/common_transform.hxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c05bad29db..871079763e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -231,6 +231,8 @@ set(BOUT_SOURCES
     ./src/field/where.cxx
     ./src/invert/fft_fftw.cxx
     ./src/invert/lapack_routines.cxx
+    ./src/invert/laplace/common_transform.cxx
+    ./src/invert/laplace/common_transform.hxx
     ./src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
     ./src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
     ./src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx
index 187056d115..258b4d2e80 100644
--- a/include/bout/invert_laplace.hxx
+++ b/include/bout/invert_laplace.hxx
@@ -40,6 +40,7 @@ class Laplacian;
 #define PVEC_REAL_MPI_TYPE MPI_DOUBLE
 #endif
 
+#include "bout/bout_types.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/fieldperp.hxx"
@@ -50,6 +51,8 @@ class Laplacian;
 
 #include "bout/dcomplex.hxx"
 
+class DSTTransform;
+class FFTTransform;
 class Solver;
 
 constexpr auto LAPLACE_SPT = "spt";
@@ -258,7 +261,7 @@ public:
   /// Coefficients in tridiagonal inversion
   void tridagCoefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dcomplex& c,
                    const Field2D* ccoef = nullptr, const Field2D* d = nullptr,
-                   CELL_LOC loc = CELL_DEFAULT);
+                   CELL_LOC loc = CELL_DEFAULT) const;
 
   /*!
    * Create a new Laplacian solver
@@ -301,6 +304,10 @@ public:
   void savePerformance(Solver& solver, const std::string& name);
 
 protected:
+  // Give access for tridagMatrix
+  friend class DSTTransform;
+  friend class FFTTransform;
+
   bool async_send; ///< If true, use asyncronous send in parallel algorithms
 
   int maxmode; ///< The maximum Z mode to solve for
@@ -332,23 +339,24 @@ protected:
 
   void tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex& a, dcomplex& b, dcomplex& c,
                    const Field2D* ccoef = nullptr, const Field2D* d = nullptr,
-                   CELL_LOC loc = CELL_DEFAULT) {
+                   CELL_LOC loc = CELL_DEFAULT) const {
     tridagCoefs(jx, jy, kwave, a, b, c, ccoef, ccoef, d, loc);
   }
   void tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex& a, dcomplex& b, dcomplex& c,
                    const Field2D* c1coef, const Field2D* c2coef, const Field2D* d,
-                   CELL_LOC loc = CELL_DEFAULT);
+                   CELL_LOC loc = CELL_DEFAULT) const;
 
   void tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dcomplex* bk, int jy,
                     int kz, BoutReal kwave, const Field2D* a, const Field2D* ccoef,
-                    const Field2D* d, bool includeguards = true, bool zperiodic = true) {
+                    const Field2D* d, bool includeguards = true,
+                    bool zperiodic = true) const {
     tridagMatrix(avec, bvec, cvec, bk, jy, kz, kwave, a, ccoef, ccoef, d, includeguards,
                  zperiodic);
   }
   void tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dcomplex* bk, int jy,
                     int kz, BoutReal kwave, const Field2D* a, const Field2D* c1coef,
                     const Field2D* c2coef, const Field2D* d, bool includeguards = true,
-                    bool zperiodic = true);
+                    bool zperiodic = true) const;
   CELL_LOC location;   ///< staggered grid location of this solver
   Mesh* localmesh;     ///< Mesh object for this solver
   Coordinates* coords; ///< Coordinates object, so we only have to call
diff --git a/src/invert/laplace/common_transform.cxx b/src/invert/laplace/common_transform.cxx
new file mode 100644
index 0000000000..98571624a1
--- /dev/null
+++ b/src/invert/laplace/common_transform.cxx
@@ -0,0 +1,381 @@
+#include "common_transform.hxx"
+
+#include "bout/array.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/constants.hxx"
+#include "bout/dcomplex.hxx"
+#include "bout/fft.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/fieldperp.hxx"
+#include "bout/invert_laplace.hxx"
+#include "bout/mesh.hxx"
+#include "bout/openmpwrap.hxx"
+#include "bout/utils.hxx"
+
+#include <iterator>
+
+FFTTransform::FFTTransform(const Mesh& mesh, int nmode, int xs, int xe, int ys, int ye,
+                           int zs, int ze, int inbndry, int outbndry,
+                           bool inner_boundary_set_on_first_x,
+                           bool outer_boundary_set_on_last_x, bool zero_DC)
+    : zlength(getUniform(mesh.getCoordinatesConst()->zlength())), nmode(nmode), xs(xs),
+      xe(xe), ys(ys), ye(ye), zs(zs), ze(ze), nx(xe - xs + 1), ny(ye - ys + 1),
+      nz(ze - zs + 1), nxny(nx * ny), nsys(nmode * ny), inbndry(inbndry),
+      outbndry(outbndry), inner_boundary_set_on_first_x(inner_boundary_set_on_first_x),
+      outer_boundary_set_on_last_x(outer_boundary_set_on_last_x), zero_DC(zero_DC),
+      localmesh(&mesh) {}
+
+auto FFTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
+                           const Field3D& x0, const Field2D& Acoef, const Field2D& C1coef,
+                           const Field2D& C2coef, const Field2D& Dcoef) const
+    -> Matrices {
+
+  Matrices result(nsys, nx);
+
+  BOUT_OMP_PERF(parallel)
+  {
+    /// Create a local thread-scope working array
+    // ZFFT routine expects input of this length
+    auto k1d = Array<dcomplex>((nz / 2) + 1);
+
+    // Loop over X and Y indices, including boundaries but not guard cells
+    // (unless periodic in x)
+    BOUT_OMP_PERF(for)
+    for (int ind = 0; ind < nxny; ++ind) {
+      const int ix = xs + (ind / ny);
+      const int iy = ys + (ind % ny);
+
+      // Take FFT in Z direction, apply shift, and put result in k1d
+
+      if (((ix < inbndry) and inner_boundary_set_on_first_x)
+          || ((localmesh->LocalNx - ix - 1 < outbndry)
+              and outer_boundary_set_on_last_x)) {
+        // Use the values in x0 in the boundary
+        rfft(&(x0(ix, iy, zs)), nz, std::begin(k1d));
+      } else {
+        rfft(&(rhs(ix, iy, zs)), nz, std::begin(k1d));
+      }
+
+      // Copy into array, transposing so kz is first index
+      for (int kz = 0; kz < nmode; kz++) {
+        result.bcmplx(((iy - ys) * nmode) + kz, ix - xs) = k1d[kz];
+      }
+    }
+
+    // Get elements of the tridiagonal matrix
+    // including boundary conditions
+    BOUT_OMP_PERF(for nowait)
+    for (int ind = 0; ind < nsys; ind++) {
+      const int iy = ys + (ind / nmode);
+      const int kz = ind % nmode;
+
+      const BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad]
+      laplacian.tridagMatrix(&result.a(ind, 0), &result.b(ind, 0), &result.c(ind, 0),
+                             &result.bcmplx(ind, 0), iy, kz, kwave, &Acoef, &C1coef,
+                             &C2coef, &Dcoef, false);
+    }
+  }
+  return result;
+}
+
+auto FFTTransform::backward(const Field3D& rhs, const Matrix<dcomplex>& xcmplx3D) const
+    -> Field3D {
+  Field3D x{emptyFrom(rhs)};
+
+  // FFT back to real space
+  BOUT_OMP_PERF(parallel)
+  {
+    /// Create a local thread-scope working array
+    // ZFFT routine expects input of this length
+    auto k1d = Array<dcomplex>((nz / 2) + 1);
+
+    BOUT_OMP_PERF(for nowait)
+    for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y
+      const int ix = xs + (ind / ny);
+      const int iy = ys + (ind % ny);
+
+      if (zero_DC) {
+        k1d[0] = 0.;
+      }
+
+      for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
+        k1d[kz] = xcmplx3D(((iy - ys) * nmode) + kz, ix - xs);
+      }
+
+      for (int kz = nmode; kz < (nz / 2) + 1; kz++) {
+        k1d[kz] = 0.0; // Filtering out all higher harmonics
+      }
+
+      irfft(std::begin(k1d), nz, &(x(ix, iy, zs)));
+    }
+  }
+
+  return x;
+}
+
+auto FFTTransform::forward(const Laplacian& laplacian, const FieldPerp& rhs,
+                           const FieldPerp& x0, const Field2D& Acoef,
+                           const Field2D& C1coef, const Field2D& C2coef,
+                           const Field2D& Dcoef) const -> Matrices {
+
+  Matrices result(nmode, nx);
+  const int jy = rhs.getIndex();
+
+  BOUT_OMP_PERF(parallel)
+  {
+    /// Create a local thread-scope working array
+    // ZFFT routine expects input of this length
+    auto k1d = Array<dcomplex>((nz / 2) + 1);
+
+    // Loop over X indices, including boundaries but not guard
+    // cells (unless periodic in x)
+    BOUT_OMP_PERF(for)
+    for (int ix = xs; ix <= xe; ix++) {
+      // Take FFT in Z direction, apply shift, and put result in k1d
+
+      if (((ix < inbndry) and inner_boundary_set_on_first_x)
+          || ((localmesh->LocalNx - ix - 1 < outbndry)
+              and outer_boundary_set_on_last_x)) {
+        // Use the values in x0 in the boundary
+        rfft(&(x0(ix, zs)), nz, std::begin(k1d));
+      } else {
+        rfft(&(rhs(ix, zs)), nz, std::begin(k1d));
+      }
+
+      // Copy into array, transposing so kz is first index
+      for (int kz = 0; kz < nmode; kz++) {
+        result.bcmplx(kz, ix - xs) = k1d[kz];
+      }
+    }
+
+    // Get elements of the tridiagonal matrix
+    // including boundary conditions
+    BOUT_OMP_PERF(for nowait)
+    for (int kz = 0; kz < nmode; kz++) {
+      const BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad]
+      laplacian.tridagMatrix(&result.a(kz, 0), &result.b(kz, 0), &result.c(kz, 0),
+                             &result.bcmplx(kz, 0), jy, kz, kwave, &Acoef, &C1coef,
+                             &C2coef, &Dcoef, false);
+    }
+  }
+  return result;
+}
+
+auto FFTTransform::backward(const FieldPerp& rhs, const Matrix<dcomplex>& xcmplx) const
+    -> FieldPerp {
+  FieldPerp x{emptyFrom(rhs)};
+
+  // FFT back to real space
+  BOUT_OMP_PERF(parallel)
+  {
+    /// Create a local thread-scope working array
+    // ZFFT routine expects input of this length
+    auto k1d = Array<dcomplex>((nz / 2) + 1);
+
+    BOUT_OMP_PERF(for nowait)
+    for (int ix = xs; ix <= xe; ++ix) {
+      if (zero_DC) {
+        k1d[0] = 0.;
+      }
+
+      for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
+        k1d[kz] = xcmplx(kz, ix - xs);
+      }
+
+      for (int kz = nmode; kz < (nz / 2) + 1; kz++) {
+        k1d[kz] = 0.0; // Filtering out all higher harmonics
+      }
+
+      irfft(std::begin(k1d), nz, &(x(ix, zs)));
+    }
+  }
+
+  checkData(x);
+
+  return x;
+}
+
+DSTTransform::DSTTransform(const Mesh& mesh, int nmode, int xs, int xe, int ys, int ye,
+                           int zs, int ze, int inbndry, int outbndry,
+                           bool inner_boundary_set_on_first_x,
+                           bool outer_boundary_set_on_last_x, bool zero_DC)
+    : zlength(getUniform(mesh.getCoordinatesConst()->zlength())), nmode(nmode), xs(xs),
+      xe(xe), ys(ys), ye(ye), zs(zs), ze(ze), nx(xe - xs + 1), ny(ye - ys + 1),
+      nz(ze - zs + 1), nxny(nx * ny), nsys(nmode * ny), inbndry(inbndry),
+      outbndry(outbndry), inner_boundary_set_on_first_x(inner_boundary_set_on_first_x),
+      outer_boundary_set_on_last_x(outer_boundary_set_on_last_x), zero_DC(zero_DC),
+      localmesh(&mesh) {}
+
+auto DSTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
+                           const Field3D& x0, const Field2D& Acoef, const Field2D& C1coef,
+                           const Field2D& C2coef, const Field2D& Dcoef) const
+    -> Matrices {
+
+  Matrices result(nsys, nx);
+
+  BOUT_OMP_PERF(parallel)
+  {
+    /// Create a local thread-scope working array
+    // ZDST routine expects input of this length
+    auto k1d = Array<dcomplex>(nz);
+
+    // Loop over X and Y indices, including boundaries but not guard cells
+    // (unless periodic in x)
+    BOUT_OMP_PERF(for)
+    for (int ind = 0; ind < nxny; ++ind) {
+      const int ix = xs + (ind / ny);
+      const int iy = ys + (ind % ny);
+
+      // Take DST in Z direction, apply shift, and put result in k1d
+
+      if (((ix < inbndry) and inner_boundary_set_on_first_x)
+          || ((localmesh->LocalNx - ix - 1 < outbndry)
+              and outer_boundary_set_on_last_x)) {
+        // Use the values in x0 in the boundary
+        bout::fft::DST(&(x0(ix, iy, zs + 1)), nz - 2, std::begin(k1d));
+      } else {
+        bout::fft::DST(&(rhs(ix, iy, zs + 1)), nz - 2, std::begin(k1d));
+      }
+
+      // Copy into array, transposing so kz is first index
+      for (int kz = 0; kz < nmode; kz++) {
+        result.bcmplx(((iy - ys) * nmode) + kz, ix - xs) = k1d[kz];
+      }
+    }
+
+    // Get elements of the tridiagonal matrix
+    // including boundary conditions
+    BOUT_OMP_PERF(for nowait)
+    for (int ind = 0; ind < nsys; ind++) {
+      const int iy = ys + (ind / nmode);
+      const int kz = ind % nmode;
+
+      const BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad]
+      laplacian.tridagMatrix(&result.a(ind, 0), &result.b(ind, 0), &result.c(ind, 0),
+                             &result.bcmplx(ind, 0), iy, kz, kwave, &Acoef, &C1coef,
+                             &C2coef, &Dcoef, false);
+    }
+  }
+  return result;
+}
+
+auto DSTTransform::backward(const Field3D& rhs, const Matrix<dcomplex>& xcmplx3D) const
+    -> Field3D {
+  Field3D x{emptyFrom(rhs)};
+
+  // DST back to real space
+  BOUT_OMP_PERF(parallel)
+  {
+    /// Create a local thread-scope working array
+    // ZDST routine expects input of this length
+    auto k1d = Array<dcomplex>((nz / 2) + 1);
+
+    BOUT_OMP_PERF(for nowait)
+    for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y
+      const int ix = xs + (ind / ny);
+      const int iy = ys + (ind % ny);
+
+      if (zero_DC) {
+        k1d[0] = 0.;
+      }
+
+      for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
+        k1d[kz] = xcmplx3D(((iy - ys) * nmode) + kz, ix - xs);
+      }
+
+      for (int kz = nmode; kz < (nz / 2) + 1; kz++) {
+        k1d[kz] = 0.0; // Filtering out all higher harmonics
+      }
+
+      bout::fft::DST_rev(std::begin(k1d), nz - 2, &(x(ix, iy, zs + 1)));
+
+      x(ix, iy, zs) = -x(ix, iy, zs + 2);
+      x(ix, iy, ze) = -x(ix, iy, ze - 2);
+    }
+  }
+
+  return x;
+}
+
+auto DSTTransform::forward(const Laplacian& laplacian, const FieldPerp& rhs,
+                           const FieldPerp& x0, const Field2D& Acoef,
+                           const Field2D& C1coef, const Field2D& C2coef,
+                           const Field2D& Dcoef) const -> Matrices {
+
+  Matrices result(nmode, nx);
+  const int jy = rhs.getIndex();
+
+  BOUT_OMP_PERF(parallel)
+  {
+    /// Create a local thread-scope working array
+    // ZDST routine expects input of this length
+    auto k1d = Array<dcomplex>((nz / 2) + 1);
+
+    // Loop over X indices, including boundaries but not guard
+    // cells (unless periodic in x)
+    BOUT_OMP_PERF(for)
+    for (int ix = xs; ix <= xe; ix++) {
+      // Take DST in Z direction, apply shift, and put result in k1d
+
+      if (((ix < inbndry) and inner_boundary_set_on_first_x)
+          || ((localmesh->LocalNx - ix - 1 < outbndry)
+              and outer_boundary_set_on_last_x)) {
+        // Use the values in x0 in the boundary
+        rfft(&(x0(ix, zs)), nz, std::begin(k1d));
+      } else {
+        rfft(&(rhs(ix, zs)), nz, std::begin(k1d));
+      }
+
+      // Copy into array, transposing so kz is first index
+      for (int kz = 0; kz < nmode; kz++) {
+        result.bcmplx(kz, ix - xs) = k1d[kz];
+      }
+    }
+
+    // Get elements of the tridiagonal matrix
+    // including boundary conditions
+    BOUT_OMP_PERF(for nowait)
+    for (int kz = 0; kz < nmode; kz++) {
+      const BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad]
+      laplacian.tridagMatrix(&result.a(kz, 0), &result.b(kz, 0), &result.c(kz, 0),
+                             &result.bcmplx(kz, 0), jy, kz, kwave, &Acoef, &C1coef,
+                             &C2coef, &Dcoef, false);
+    }
+  }
+  return result;
+}
+
+auto DSTTransform::backward(const FieldPerp& rhs, const Matrix<dcomplex>& xcmplx) const
+    -> FieldPerp {
+  FieldPerp x{emptyFrom(rhs)};
+
+  // DST back to real space
+  BOUT_OMP_PERF(parallel)
+  {
+    /// Create a local thread-scope working array
+    // ZDST routine expects input of this length
+    auto k1d = Array<dcomplex>((nz / 2) + 1);
+
+    BOUT_OMP_PERF(for nowait)
+    for (int ix = xs; ix < xe; ++ix) {
+      if (zero_DC) {
+        k1d[0] = 0.;
+      }
+
+      for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
+        k1d[kz] = xcmplx(kz, ix - xs);
+      }
+
+      for (int kz = nmode; kz < (nz / 2) + 1; kz++) {
+        k1d[kz] = 0.0; // Filtering out all higher harmonics
+      }
+
+      irfft(std::begin(k1d), nz, &(x(ix, zs)));
+    }
+  }
+
+  checkData(x);
+
+  return x;
+}
diff --git a/src/invert/laplace/common_transform.hxx b/src/invert/laplace/common_transform.hxx
new file mode 100644
index 0000000000..a05ca2feb3
--- /dev/null
+++ b/src/invert/laplace/common_transform.hxx
@@ -0,0 +1,132 @@
+#pragma once
+
+#include "bout/bout_types.hxx"
+#include "bout/dcomplex.hxx"
+#include "bout/utils.hxx"
+
+class Laplacian;
+class Field2D;
+class Field3D;
+class FieldPerp;
+class Mesh;
+
+/// Helper class to do FFTs for `LaplaceCyclic`, `LaplacePCR`, `LaplacePCR_THOMAS`
+class FFTTransform {
+  /// Physical length of the Z domain
+  BoutReal zlength;
+  /// Number of unfiltered Fourier modes
+  int nmode;
+
+  int xs;
+  int xe;
+  int ys;
+  int ye;
+  int zs;
+  int ze;
+
+  int nx;
+  int ny;
+  /// Number of (interior) points in Z
+  int nz;
+  int nxny;
+  /// Number of systems to solve = number of unfiltered Fourier modes times number of y
+  /// points
+  int nsys;
+  /// Number of inner boundary cells
+  int inbndry;
+  /// Number of outer boundary cells
+  int outbndry;
+
+  bool inner_boundary_set_on_first_x;
+  bool outer_boundary_set_on_last_x;
+
+  bool zero_DC;
+
+  const Mesh* localmesh;
+
+public:
+  FFTTransform(const Mesh& mesh, int nmode, int xs, int xe, int ys, int ye, int zs,
+               int ze, int inbndry, int outbndry, bool inner_boundary_set_on_first_x,
+               bool outer_boundary_set_on_last_x, bool zero_DC);
+
+  struct Matrices {
+    Matrix<dcomplex> a;
+    Matrix<dcomplex> b;
+    Matrix<dcomplex> c;
+    Matrix<dcomplex> bcmplx;
+
+    Matrices(int nsys, int nx)
+        : a(nsys, nx), b(nsys, nx), c(nsys, nx), bcmplx(nsys, nx) {}
+  };
+
+  auto forward(const Laplacian& laplacian, const Field3D& rhs, const Field3D& x0,
+               const Field2D& Acoef, const Field2D& C1coef, const Field2D& C2coef,
+               const Field2D& Dcoef) const -> Matrices;
+  auto backward(const Field3D& rhs, const Matrix<dcomplex>& xcmplx3D) const -> Field3D;
+
+  auto forward(const Laplacian& laplacian, const FieldPerp& rhs, const FieldPerp& x0,
+               const Field2D& Acoef, const Field2D& C1coef, const Field2D& C2coef,
+               const Field2D& Dcoef) const -> Matrices;
+  auto backward(const FieldPerp& rhs, const Matrix<dcomplex>& xcmplx) const -> FieldPerp;
+};
+
+/// Helper class to do discrete sin transforms (DSTs) for `LaplaceCyclic`,
+/// `LaplacePCR`, `LaplacePCR_THOMAS`
+class DSTTransform {
+  /// Physical length of the Z domain
+  BoutReal zlength;
+  /// Number of unfiltered Fourier modes
+  int nmode;
+
+  int xs;
+  int xe;
+  int ys;
+  int ye;
+  int zs;
+  int ze;
+
+  int nx;
+  int ny;
+  /// Number of (interior) points in Z
+  int nz;
+  int nxny;
+  /// Number of systems to solve = number of unfiltered Fourier modes times number of y
+  /// points
+  int nsys;
+  /// Number of inner boundary cells
+  int inbndry;
+  /// Number of outer boundary cells
+  int outbndry;
+
+  bool inner_boundary_set_on_first_x;
+  bool outer_boundary_set_on_last_x;
+
+  bool zero_DC;
+
+  const Mesh* localmesh;
+
+public:
+  DSTTransform(const Mesh& mesh, int nmode, int xs, int xe, int ys, int ye, int zs,
+               int ze, int inbndry, int outbndry, bool inner_boundary_set_on_first_x,
+               bool outer_boundary_set_on_last_x, bool zero_DC);
+
+  struct Matrices {
+    Matrix<dcomplex> a;
+    Matrix<dcomplex> b;
+    Matrix<dcomplex> c;
+    Matrix<dcomplex> bcmplx;
+
+    Matrices(int nsys, int nx)
+        : a(nsys, nx), b(nsys, nx), c(nsys, nx), bcmplx(nsys, nx) {}
+  };
+
+  auto forward(const Laplacian& laplacian, const Field3D& rhs, const Field3D& x0,
+               const Field2D& Acoef, const Field2D& C1coef, const Field2D& C2coef,
+               const Field2D& Dcoef) const -> Matrices;
+  auto backward(const Field3D& rhs, const Matrix<dcomplex>& xcmplx3D) const -> Field3D;
+
+  auto forward(const Laplacian& laplacian, const FieldPerp& rhs, const FieldPerp& x0,
+               const Field2D& Acoef, const Field2D& C1coef, const Field2D& C2coef,
+               const Field2D& Dcoef) const -> Matrices;
+  auto backward(const FieldPerp& rhs, const Matrix<dcomplex>& xcmplx) const -> FieldPerp;
+};
diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
index 80b22e73f7..0ee6fbe0cd 100644
--- a/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
+++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
@@ -39,6 +39,10 @@
 
 #include "cyclic_laplace.hxx"
 
+#include "../../common_transform.hxx"
+
+#include "bout/array.hxx"
+#include "bout/dcomplex.hxx"
 #include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
@@ -51,6 +55,7 @@
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 
+#include <array>
 #include <vector>
 
 LaplaceCyclic::LaplaceCyclic(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
@@ -117,15 +122,11 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) {
   ASSERT1(rhs.getLocation() == location);
   ASSERT1(x0.getLocation() == location);
 
-  FieldPerp x{emptyFrom(rhs)}; // Result
-
-  int jy = rhs.getIndex(); // Get the Y index
-  x.setIndex(jy);
-
   // Get the width of the boundary
 
   // If the flags to assign that only one guard cell should be used is set
-  int inbndry = localmesh->xstart, outbndry = localmesh->xstart;
+  int inbndry = localmesh->xstart;
+  int outbndry = localmesh->xstart;
   if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) {
     inbndry = outbndry = 1;
   }
@@ -137,172 +138,50 @@ FieldPerp LaplaceCyclic::solve(const FieldPerp& rhs, const FieldPerp& x0) {
   }
 
   if (dst) {
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(
-          localmesh->LocalNz); // ZFFT routine expects input of this length
-
-      // Loop over X indices, including boundaries but not guard cells. (unless periodic
-      // in x)
-      BOUT_OMP_PERF(for)
-      for (int ix = xs; ix <= xe; ix++) {
-        // Take DST in Z direction and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          DST(x0[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        } else {
-          DST(rhs[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx(kz, ix - xs) = k1d[kz];
-        }
-      }
+    const DSTTransform transform(
+        *localmesh, nmode, xs, xe, 0, 0, localmesh->zstart, localmesh->zend, inbndry,
+        outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+        isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3);
-      BOUT_OMP_PERF(for nowait)
-      for (int kz = 0; kz < nmode; kz++) {
-        // wave number is 1/[rad]; DST has extra 2.
-        BoutReal kwave = kz * 2.0 * PI / (2. * zlen);
-
-        tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy,
-                     kz,    // wave number index
-                     kwave, // kwave (inverse wave length)
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false,  // Don't include guard cells in arrays
-                     false); // Z domain not periodic
-      }
-    }
+    auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
     // Solve tridiagonal systems
     cr->setCoefs(a, b, c);
     cr->solve(bcmplx, xcmplx);
 
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-
-      // ZFFT routine expects input of this length
-      auto k1d = Array<dcomplex>(localmesh->LocalNz);
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ix = xs; ix <= xe; ix++) {
-        for (int kz = 0; kz < nmode; kz++) {
-          k1d[kz] = xcmplx(kz, ix - xs);
-        }
-
-        for (int kz = nmode; kz < (localmesh->LocalNz); kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
-
-        DST_rev(std::begin(k1d), localmesh->LocalNz - 2, x[ix] + 1);
-
-        x(ix, 0) = -x(ix, 2);
-        x(ix, localmesh->LocalNz - 1) = -x(ix, localmesh->LocalNz - 3);
-      }
-    }
-  } else {
-    const BoutReal zlength = getUniform(coords->zlength());
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      // ZFFT routine expects input of this length
-      auto k1d = Array<dcomplex>((localmesh->LocalNz) / 2 + 1);
-
-      // Loop over X indices, including boundaries but not guard
-      // cells (unless periodic in x)
-      BOUT_OMP_PERF(for)
-      for (int ix = xs; ix <= xe; ix++) {
-        // Take FFT in Z direction, apply shift, and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          rfft(x0[ix], localmesh->LocalNz, std::begin(k1d));
-        } else {
-          rfft(rhs[ix], localmesh->LocalNz, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx(kz, ix - xs) = k1d[kz];
-        }
-      }
-
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int kz = 0; kz < nmode; kz++) {
-        BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad]
-        tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy,
-                     kz,    // True for the component constant (DC) in Z
-                     kwave, // Z wave number
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    }
-
-    // Solve tridiagonal systems
-    cr->setCoefs(a, b, c);
-    cr->solve(bcmplx, xcmplx);
+    return transform.backward(rhs, xcmplx);
+  }
 
-    if (localmesh->periodicX) {
-      // Subtract X average of kz=0 mode
-      BoutReal local[2] = {
-          0.0,                               // index 0 = sum of coefficients
-          static_cast<BoutReal>(xe - xs + 1) // number of grid cells
-      };
-      for (int ix = xs; ix <= xe; ix++) {
-        local[0] += xcmplx(0, ix - xs).real();
-      }
-      BoutReal global[2];
-      MPI_Allreduce(local, global, 2, MPI_DOUBLE, MPI_SUM, localmesh->getXcomm());
-      BoutReal avg = global[0] / global[1];
-      for (int ix = xs; ix <= xe; ix++) {
-        xcmplx(0, ix - xs) -= avg;
-      }
+  const FFTTransform transform(
+      *localmesh, nmode, xs, xe, 0, 0, localmesh->zstart, localmesh->zend, inbndry,
+      outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+      isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
+
+  auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
+
+  // Solve tridiagonal systems
+  cr->setCoefs(matrices.a, matrices.b, matrices.c);
+  cr->solve(matrices.bcmplx, xcmplx);
+
+  if (localmesh->periodicX) {
+    // Subtract X average of kz=0 mode
+    std::array<BoutReal, 2> local = {
+        0.0,                               // index 0 = sum of coefficients
+        static_cast<BoutReal>(xe - xs + 1) // number of grid cells
+    };
+    for (int ix = xs; ix <= xe; ix++) {
+      local[0] += xcmplx(0, ix - xs).real();
     }
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      // ZFFT routine expects input of this length
-      auto k1d = Array<dcomplex>((localmesh->LocalNz) / 2 + 1);
-
-      const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC);
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ix = xs; ix <= xe; ix++) {
-        if (zero_DC) {
-          k1d[0] = 0.;
-        }
-
-        for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
-          k1d[kz] = xcmplx(kz, ix - xs);
-        }
-
-        for (int kz = nmode; kz < (localmesh->LocalNz) / 2 + 1; kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
-
-        irfft(std::begin(k1d), localmesh->LocalNz, x[ix]);
-      }
+    std::array<BoutReal, 2> global{};
+    MPI_Allreduce(local.data(), global.data(), 2, MPI_DOUBLE, MPI_SUM,
+                  localmesh->getXcomm());
+    const BoutReal avg = global[0] / global[1];
+    for (int ix = xs; ix <= xe; ix++) {
+      xcmplx(0, ix - xs) -= avg;
     }
   }
 
-  checkData(x);
-
-  return x;
+  return transform.backward(rhs, xcmplx);
 }
 
 Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) {
@@ -318,7 +197,8 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) {
   // Get the width of the boundary
 
   // If the flags to assign that only one guard cell should be used is set
-  int inbndry = localmesh->xstart, outbndry = localmesh->xstart;
+  int inbndry = localmesh->xstart;
+  int outbndry = localmesh->xstart;
   if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) {
     inbndry = outbndry = 1;
   }
@@ -332,7 +212,8 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) {
   int nx = xe - xs + 1; // Number of X points on this processor
 
   // Get range of Y indices
-  int ys = localmesh->ystart, ye = localmesh->yend;
+  int ys = localmesh->ystart;
+  int ye = localmesh->yend;
 
   if (localmesh->hasBndryLowerY()) {
     if (include_yguards) {
@@ -351,215 +232,61 @@ Field3D LaplaceCyclic::solve(const Field3D& rhs, const Field3D& x0) {
 
   const int ny = (ye - ys + 1); // Number of Y points
   const int nsys = nmode * ny;  // Number of systems of equations to solve
-  const int nxny = nx * ny;     // Number of points in X-Y
 
   // This is just to silence static analysis
   ASSERT0(ny > 0);
 
-  auto a3D = Matrix<dcomplex>(nsys, nx);
-  auto b3D = Matrix<dcomplex>(nsys, nx);
-  auto c3D = Matrix<dcomplex>(nsys, nx);
-
   auto xcmplx3D = Matrix<dcomplex>(nsys, nx);
-  auto bcmplx3D = Matrix<dcomplex>(nsys, nx);
 
   if (dst) {
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      // ZFFT routine expects input of this length
-      auto k1d = Array<dcomplex>(localmesh->LocalNz);
-
-      // Loop over X and Y indices, including boundaries but not guard cells.
-      // (unless periodic in x)
-      BOUT_OMP_PERF(for)
-      for (int ind = 0; ind < nxny; ++ind) {
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        // Take DST in Z direction and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          DST(x0(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        } else {
-          DST(rhs(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx3D((iy - ys) * nmode + kz, ix - xs) = k1d[kz];
-        }
-      }
-
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      const BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3);
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nsys; ind++) {
-        // ind = (iy - ys) * nmode + kz
-        int iy = ys + ind / nmode;
-        int kz = ind % nmode;
-
-        // wave number is 1/[rad]; DST has extra 2.
-        BoutReal kwave = kz * 2.0 * PI / (2. * zlen);
-
-        tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy,
-                     kz,    // wave number index
-                     kwave, // kwave (inverse wave length)
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false,  // Don't include guard cells in arrays
-                     false); // Z domain not periodic
-      }
-    }
-
-    // Solve tridiagonal systems
-    cr->setCoefs(a3D, b3D, c3D);
-    cr->solve(bcmplx3D, xcmplx3D);
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      // ZFFT routine expects input of length LocalNz
-      auto k1d = Array<dcomplex>(localmesh->LocalNz);
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        for (int kz = 0; kz < nmode; kz++) {
-          k1d[kz] = xcmplx3D((iy - ys) * nmode + kz, ix - xs);
-        }
-
-        for (int kz = nmode; kz < localmesh->LocalNz; kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
-
-        DST_rev(std::begin(k1d), localmesh->LocalNz - 2, &x(ix, iy, 1));
-
-        x(ix, iy, 0) = -x(ix, iy, 2);
-        x(ix, iy, localmesh->LocalNz - 1) = -x(ix, iy, localmesh->LocalNz - 3);
-      }
-    }
-  } else {
-    const BoutReal zlength = getUniform(coords->zlength());
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      // ZFFT routine expects input of this length
-      auto k1d = Array<dcomplex>(localmesh->LocalNz / 2 + 1);
-
-      // Loop over X and Y indices, including boundaries but not guard cells
-      // (unless periodic in x)
-
-      BOUT_OMP_PERF(for)
-      for (int ind = 0; ind < nxny; ++ind) {
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        // Take FFT in Z direction, apply shift, and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          rfft(x0(ix, iy), localmesh->LocalNz, std::begin(k1d));
-        } else {
-          rfft(rhs(ix, iy), localmesh->LocalNz, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx3D((iy - ys) * nmode + kz, ix - xs) = k1d[kz];
-        }
-      }
+    const DSTTransform transform(
+        *localmesh, nmode, xs, xe, ys, ye, localmesh->zstart, localmesh->zend, inbndry,
+        outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+        isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nsys; ind++) {
-        // ind = (iy - ys) * nmode + kz
-        int iy = ys + ind / nmode;
-        int kz = ind % nmode;
-
-        BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad]
-        tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy,
-                     kz,    // True for the component constant (DC) in Z
-                     kwave, // Z wave number
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    }
+    auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
     // Solve tridiagonal systems
-    cr->setCoefs(a3D, b3D, c3D);
-    cr->solve(bcmplx3D, xcmplx3D);
-
-    if (localmesh->periodicX) {
-      // Subtract X average of kz=0 mode
-      std::vector<BoutReal> local(ny + 1, 0.0);
-      for (int y = 0; y < ny; y++) {
-        for (int ix = xs; ix <= xe; ix++) {
-          local[y] += xcmplx3D(y * nmode, ix - xs).real();
-        }
-      }
-      local[ny] = static_cast<BoutReal>(xe - xs + 1);
-
-      // Global reduce
-      std::vector<BoutReal> global(ny + 1, 0.0);
-      MPI_Allreduce(local.data(), global.data(), ny + 1, MPI_DOUBLE, MPI_SUM,
-                    localmesh->getXcomm());
-      // Subtract average from kz=0 modes
-      for (int y = 0; y < ny; y++) {
-        BoutReal avg = global[y] / global[ny];
-        for (int ix = xs; ix <= xe; ix++) {
-          xcmplx3D(y * nmode, ix - xs) -= avg;
-        }
-      }
-    }
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>((localmesh->LocalNz) / 2
-                                 + 1); // ZFFT routine expects input of this length
+    cr->setCoefs(matrices.a, matrices.b, matrices.c);
+    cr->solve(matrices.bcmplx, xcmplx3D);
 
-      const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC);
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        if (zero_DC) {
-          k1d[0] = 0.;
-        }
+    return transform.backward(rhs, xcmplx3D);
+  }
+  const FFTTransform transform(
+      *localmesh, nmode, xs, xe, ys, ye, localmesh->zstart, localmesh->zend, inbndry,
+      outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+      isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-        for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
-          k1d[kz] = xcmplx3D((iy - ys) * nmode + kz, ix - xs);
-        }
+  auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
-        for (int kz = nmode; kz < localmesh->LocalNz / 2 + 1; kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
+  // Solve tridiagonal systems
+  cr->setCoefs(matrices.a, matrices.b, matrices.c);
+  cr->solve(matrices.bcmplx, xcmplx3D);
 
-        irfft(std::begin(k1d), localmesh->LocalNz, x(ix, iy));
+  if (localmesh->periodicX) {
+    // Subtract X average of kz=0 mode
+    std::vector<BoutReal> local(ny + 1, 0.0);
+    for (int y = 0; y < ny; y++) {
+      for (int ix = xs; ix <= xe; ix++) {
+        local[y] += xcmplx3D(y * nmode, ix - xs).real();
+      }
+    }
+    local[ny] = static_cast<BoutReal>(xe - xs + 1);
+
+    // Global reduce
+    std::vector<BoutReal> global(ny + 1, 0.0);
+    MPI_Allreduce(local.data(), global.data(), ny + 1, MPI_DOUBLE, MPI_SUM,
+                  localmesh->getXcomm());
+    // Subtract average from kz=0 modes
+    for (int y = 0; y < ny; y++) {
+      BoutReal avg = global[y] / global[ny];
+      for (int ix = xs; ix <= xe; ix++) {
+        xcmplx3D(y * nmode, ix - xs) -= avg;
       }
     }
   }
 
-  checkData(x);
-
-  return x;
+  return transform.backward(rhs, xcmplx3D);
 }
 
 void LaplaceCyclic ::verify_solution(const Matrix<dcomplex>& a_ver,
diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx
index 61e493d3ed..db9aaf814a 100644
--- a/src/invert/laplace/impls/pcr/pcr.cxx
+++ b/src/invert/laplace/impls/pcr/pcr.cxx
@@ -38,6 +38,8 @@
 
 #include "pcr.hxx"
 
+#include "../../common_transform.hxx"
+
 #include <bout/array.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
@@ -161,151 +163,29 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) {
   }
 
   if (dst) {
-    const BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3);
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(
-          localmesh->LocalNz); // ZFFT routine expects input of this length
-
-      // Loop over X indices, including boundaries but not guard cells. (unless periodic
-      // in x)
-      BOUT_OMP_PERF(for)
-      for (int ix = xs; ix <= xe; ix++) {
-        // Take DST in Z direction and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          DST(x0[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        } else {
-          DST(rhs[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx(kz, ix - xs) = k1d[kz];
-        }
-      }
-
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int kz = 0; kz < nmode; kz++) {
-        BoutReal kwave =
-            kz * 2.0 * PI / (2. * zlen); // wave number is 1/[rad]; DST has extra 2.
-
-        tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy,
-                     kz,    // wave number index
-                     kwave, // kwave (inverse wave length)
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    } // BOUT_OMP_PERF(parallel)
-
-    // Solve tridiagonal systems
-    cr_pcr_solver(a, b, c, bcmplx, xcmplx);
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(
-          localmesh->LocalNz); // ZFFT routine expects input of this length
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ix = xs; ix <= xe; ix++) {
-        for (int kz = 0; kz < nmode; kz++) {
-          k1d[kz] = xcmplx(kz, ix - xs);
-        }
-
-        for (int kz = nmode; kz < (localmesh->LocalNz); kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
-
-        DST_rev(std::begin(k1d), localmesh->LocalNz - 2, x[ix] + 1);
-
-        x(ix, 0) = -x(ix, 2);
-        x(ix, localmesh->LocalNz - 1) = -x(ix, localmesh->LocalNz - 3);
-      }
-    }
-  } else {
-    const BoutReal zlength = getUniform(coords->zlength());
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>((localmesh->LocalNz) / 2
-                                 + 1); // ZFFT routine expects input of this length
-
-      // Loop over X indices, including boundaries but not guard cells (unless periodic in
-      // x)
-      BOUT_OMP_PERF(for)
-      for (int ix = xs; ix <= xe; ix++) {
-        // Take FFT in Z direction, apply shift, and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          rfft(x0[ix], localmesh->LocalNz, std::begin(k1d));
-        } else {
-          rfft(rhs[ix], localmesh->LocalNz, std::begin(k1d));
-        }
+    const DSTTransform transform(
+        *localmesh, nmode, xs, xe, 0, 0, localmesh->zstart, localmesh->zend, inbndry,
+        outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+        isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx(kz, ix - xs) = k1d[kz];
-        }
-      }
-
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int kz = 0; kz < nmode; kz++) {
-        BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad]
-        tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy,
-                     kz,    // True for the component constant (DC) in Z
-                     kwave, // Z wave number
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    } // BOUT_OMP_PERF(parallel)
+    auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
     // Solve tridiagonal systems
-    cr_pcr_solver(a, b, c, bcmplx, xcmplx);
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>((localmesh->LocalNz) / 2
-                                 + 1); // ZFFT routine expects input of this length
-
-      const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC);
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ix = xs; ix <= xe; ix++) {
-        if (zero_DC) {
-          k1d[0] = 0.;
-        }
+    cr_pcr_solver(matrices.a, matrices.b, matrices.c, matrices.bcmplx, xcmplx);
 
-        for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
-          k1d[kz] = xcmplx(kz, ix - xs);
-        }
-
-        for (int kz = nmode; kz < (localmesh->LocalNz) / 2 + 1; kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
-
-        irfft(std::begin(k1d), localmesh->LocalNz, x[ix]);
-      }
-    }
+    return transform.backward(rhs, xcmplx);
   }
+  const FFTTransform transform(
+      *localmesh, nmode, xs, xe, 0, 0, localmesh->zstart, localmesh->zend, inbndry,
+      outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+      isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-  checkData(x);
+  auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
-  return x;
+  // Solve tridiagonal systems
+  cr_pcr_solver(matrices.a, matrices.b, matrices.c, matrices.bcmplx, xcmplx);
+
+  return transform.backward(rhs, xcmplx);
 }
 
 Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) {
@@ -316,8 +196,6 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) {
 
   Timer timer("invert");
 
-  Field3D x{emptyFrom(rhs)}; // Result
-
   // Get the width of the boundary
 
   // If the flags to assign that only one guard cell should be used is set
@@ -356,185 +234,33 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) {
 
   const int ny = (ye - ys + 1); // Number of Y points
   nsys = nmode * ny;            // Number of systems of equations to solve
-  const int nxny = nx * ny;     // Number of points in X-Y
-
-  auto a3D = Matrix<dcomplex>(nsys, nx);
-  auto b3D = Matrix<dcomplex>(nsys, nx);
-  auto c3D = Matrix<dcomplex>(nsys, nx);
 
   auto xcmplx3D = Matrix<dcomplex>(nsys, nx);
-  auto bcmplx3D = Matrix<dcomplex>(nsys, nx);
 
   if (dst) {
-    const BoutReal zlen = getUniform(coords->dz) * (localmesh->LocalNz - 3);
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(
-          localmesh->LocalNz); // ZFFT routine expects input of this length
-
-      // Loop over X and Y indices, including boundaries but not guard cells.
-      // (unless periodic in x)
-      BOUT_OMP_PERF(for)
-      for (int ind = 0; ind < nxny; ++ind) {
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        // Take DST in Z direction and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          DST(x0(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        } else {
-          DST(rhs(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx3D((iy - ys) * nmode + kz, ix - xs) = k1d[kz];
-        }
-      }
-
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nsys; ind++) {
-        // ind = (iy - ys) * nmode + kz
-        int iy = ys + ind / nmode;
-        int kz = ind % nmode;
-
-        BoutReal kwave =
-            kz * 2.0 * PI / (2. * zlen); // wave number is 1/[rad]; DST has extra 2.
-
-        tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy,
-                     kz,    // wave number index
-                     kwave, // kwave (inverse wave length)
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    } // BOUT_OMP_PERF(parallel)
-
-    // Solve tridiagonal systems
-    cr_pcr_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D);
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(
-          localmesh->LocalNz); // ZFFT routine expects input of this length
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        for (int kz = 0; kz < nmode; kz++) {
-          k1d[kz] = xcmplx3D((iy - ys) * nmode + kz, ix - xs);
-        }
-
-        for (int kz = nmode; kz < localmesh->LocalNz; kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
-
-        DST_rev(std::begin(k1d), localmesh->LocalNz - 2, &x(ix, iy, 1));
-
-        x(ix, iy, 0) = -x(ix, iy, 2);
-        x(ix, iy, localmesh->LocalNz - 1) = -x(ix, iy, localmesh->LocalNz - 3);
-      }
-    }
-  } else {
-    const BoutReal zlength = getUniform(coords->zlength());
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(localmesh->LocalNz / 2
-                                 + 1); // ZFFT routine expects input of this length
-
-      // Loop over X and Y indices, including boundaries but not guard cells
-      // (unless periodic in x)
-
-      BOUT_OMP_PERF(for)
-      for (int ind = 0; ind < nxny; ++ind) {
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        // Take FFT in Z direction, apply shift, and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          rfft(x0(ix, iy), localmesh->LocalNz, std::begin(k1d));
-        } else {
-          rfft(rhs(ix, iy), localmesh->LocalNz, std::begin(k1d));
-        }
+    const DSTTransform transform(
+        *localmesh, nmode, xs, xe, ys, ye, localmesh->zstart, localmesh->zend, inbndry,
+        outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+        isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx3D((iy - ys) * nmode + kz, ix - xs) = k1d[kz];
-        }
-      }
-
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nsys; ind++) {
-        // ind = (iy - ys) * nmode + kz
-        int iy = ys + ind / nmode;
-        int kz = ind % nmode;
-
-        BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad]
-        tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy,
-                     kz,    // True for the component constant (DC) in Z
-                     kwave, // Z wave number
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    } // BOUT_OMP_PERF(parallel)
+    auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
     // Solve tridiagonal systems
-    cr_pcr_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D);
+    cr_pcr_solver(matrices.a, matrices.b, matrices.c, matrices.bcmplx, xcmplx3D);
 
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>((localmesh->LocalNz) / 2
-                                 + 1); // ZFFT routine expects input of this length
-
-      const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC);
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        if (zero_DC) {
-          k1d[0] = 0.;
-        }
-
-        for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
-          k1d[kz] = xcmplx3D((iy - ys) * nmode + kz, ix - xs);
-        }
-
-        for (int kz = nmode; kz < localmesh->LocalNz / 2 + 1; kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
-
-        irfft(std::begin(k1d), localmesh->LocalNz, x(ix, iy));
-      }
-    }
+    return transform.backward(rhs, xcmplx3D);
   }
+  const FFTTransform transform(
+      *localmesh, nmode, xs, xe, ys, ye, localmesh->zstart, localmesh->zend, inbndry,
+      outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+      isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
+
+  auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
-  checkData(x);
+  // Solve tridiagonal systems
+  cr_pcr_solver(matrices.a, matrices.b, matrices.c, matrices.bcmplx, xcmplx3D);
 
-  return x;
+  return transform.backward(rhs, xcmplx3D);
 }
 
 /**
diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
index 604a630feb..99d1a4e30a 100644
--- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
+++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
@@ -38,6 +38,8 @@
 
 #include "pcr_thomas.hxx"
 
+#include "../../common_transform.hxx"
+
 #include "bout/array.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/dcomplex.hxx"
@@ -139,11 +141,6 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) {
   ASSERT1(rhs.getLocation() == location);
   ASSERT1(x0.getLocation() == location);
 
-  FieldPerp x{emptyFrom(rhs)}; // Result
-
-  int jy = rhs.getIndex(); // Get the Y index
-  x.setIndex(jy);
-
   // Get the width of the boundary
 
   // If the flags to assign that only one guard cell should be used is set
@@ -160,151 +157,30 @@ FieldPerp LaplacePCR_THOMAS::solve(const FieldPerp& rhs, const FieldPerp& x0) {
   }
 
   if (dst) {
-    const BoutReal zlength = getUniform(coords->dz) * (localmesh->LocalNz - 3);
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(
-          localmesh->LocalNz); // ZFFT routine expects input of this length
-
-      // Loop over X indices, including boundaries but not guard cells. (unless periodic
-      // in x)
-      BOUT_OMP_PERF(for)
-      for (int ix = xs; ix <= xe; ix++) {
-        // Take DST in Z direction and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          DST(x0[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        } else {
-          DST(rhs[ix] + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx(kz, ix - xs) = k1d[kz];
-        }
-      }
-
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int kz = 0; kz < nmode; kz++) {
-        // wave number is 1/[rad]; DST has extra 2.
-        const BoutReal kwave = kz * 2.0 * PI / (2. * zlength);
-
-        tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy,
-                     kz,    // wave number index
-                     kwave, // kwave (inverse wave length)
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    }
-
-    // Solve tridiagonal systems
-    pcr_thomas_solver(a, b, c, bcmplx, xcmplx);
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(
-          localmesh->LocalNz); // ZFFT routine expects input of this length
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ix = xs; ix <= xe; ix++) {
-        for (int kz = 0; kz < nmode; kz++) {
-          k1d[kz] = xcmplx(kz, ix - xs);
-        }
-
-        for (int kz = nmode; kz < (localmesh->LocalNz); kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
-
-        DST_rev(std::begin(k1d), localmesh->LocalNz - 2, x[ix] + 1);
-
-        x(ix, 0) = -x(ix, 2);
-        x(ix, localmesh->LocalNz - 1) = -x(ix, localmesh->LocalNz - 3);
-      }
-    }
-  } else {
-    const BoutReal zlength = getUniform(coords->zlength());
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>((localmesh->LocalNz) / 2
-                                 + 1); // ZFFT routine expects input of this length
-
-      // Loop over X indices, including boundaries but not guard cells (unless periodic in
-      // x)
-      BOUT_OMP_PERF(for)
-      for (int ix = xs; ix <= xe; ix++) {
-        // Take FFT in Z direction, apply shift, and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          rfft(x0[ix], localmesh->LocalNz, std::begin(k1d));
-        } else {
-          rfft(rhs[ix], localmesh->LocalNz, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx(kz, ix - xs) = k1d[kz];
-        }
-      }
+    const DSTTransform transform(
+        *localmesh, nmode, xs, xe, 0, 0, localmesh->zstart, localmesh->zend, inbndry,
+        outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+        isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int kz = 0; kz < nmode; kz++) {
-        const BoutReal kwave = kz * 2.0 * PI / zlength; // wave number is 1/[rad]
-        tridagMatrix(&a(kz, 0), &b(kz, 0), &c(kz, 0), &bcmplx(kz, 0), jy,
-                     kz,    // True for the component constant (DC) in Z
-                     kwave, // Z wave number
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    }
+    auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
     // Solve tridiagonal systems
-    pcr_thomas_solver(a, b, c, bcmplx, xcmplx);
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>((localmesh->LocalNz) / 2
-                                 + 1); // ZFFT routine expects input of this length
+    pcr_thomas_solver(matrices.a, matrices.b, matrices.c, matrices.bcmplx, xcmplx);
 
-      const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC);
+    return transform.backward(rhs, xcmplx);
+  }
 
-      BOUT_OMP_PERF(for nowait)
-      for (int ix = xs; ix <= xe; ix++) {
-        if (zero_DC) {
-          k1d[0] = 0.;
-        }
+  const FFTTransform transform(
+      *localmesh, nmode, xs, xe, 0, 0, localmesh->zstart, localmesh->zend, inbndry,
+      outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+      isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-        for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
-          k1d[kz] = xcmplx(kz, ix - xs);
-        }
+  auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
-        for (int kz = nmode; kz < (localmesh->LocalNz) / 2 + 1; kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
+  // Solve tridiagonal systems
+  pcr_thomas_solver(matrices.a, matrices.b, matrices.c, matrices.bcmplx, xcmplx);
 
-        irfft(std::begin(k1d), localmesh->LocalNz, x[ix]);
-      }
-    }
-  }
-
-  checkData(x);
-
-  return x;
+  return transform.backward(rhs, xcmplx);
 }
 
 Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) {
@@ -315,8 +191,6 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) {
 
   Timer timer("invert");
 
-  Field3D x{emptyFrom(rhs)}; // Result
-
   // Get the width of the boundary
 
   // If the flags to assign that only one guard cell should be used is set
@@ -332,7 +206,7 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) {
     outbndry = 1;
   }
 
-  int nx = xe - xs + 1; // Number of X points on this processor
+  const int nx = xe - xs + 1; // Number of X points on this processor
 
   // Get range of Y indices
   int ys = localmesh->ystart;
@@ -355,186 +229,33 @@ Field3D LaplacePCR_THOMAS::solve(const Field3D& rhs, const Field3D& x0) {
 
   const int ny = (ye - ys + 1); // Number of Y points
   nsys = nmode * ny;            // Number of systems of equations to solve
-  const int nxny = nx * ny;     // Number of points in X-Y
-
-  auto a3D = Matrix<dcomplex>(nsys, nx);
-  auto b3D = Matrix<dcomplex>(nsys, nx);
-  auto c3D = Matrix<dcomplex>(nsys, nx);
-
   auto xcmplx3D = Matrix<dcomplex>(nsys, nx);
-  auto bcmplx3D = Matrix<dcomplex>(nsys, nx);
 
   if (dst) {
-    const BoutReal zlength = getUniform(coords->dz) * (localmesh->LocalNz - 3);
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(
-          localmesh->LocalNz); // ZFFT routine expects input of this length
-
-      // Loop over X and Y indices, including boundaries but not guard cells.
-      // (unless periodic in x)
-      BOUT_OMP_PERF(for)
-      for (int ind = 0; ind < nxny; ++ind) {
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        // Take DST in Z direction and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          DST(x0(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        } else {
-          DST(rhs(ix, iy) + 1, localmesh->LocalNz - 2, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx3D((iy - ys) * nmode + kz, ix - xs) = k1d[kz];
-        }
-      }
-
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nsys; ind++) {
-        // ind = (iy - ys) * nmode + kz
-        int iy = ys + ind / nmode;
-        int kz = ind % nmode;
-
-        // wave number is 1/[rad]; DST has extra 2.
-        BoutReal kwave = kz * 2.0 * PI / (2. * zlength);
-
-        tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy,
-                     kz,    // wave number index
-                     kwave, // kwave (inverse wave length)
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    }
-
-    // Solve tridiagonal systems
-    pcr_thomas_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D);
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(
-          localmesh->LocalNz); // ZFFT routine expects input of this length
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        for (int kz = 0; kz < nmode; kz++) {
-          k1d[kz] = xcmplx3D((iy - ys) * nmode + kz, ix - xs);
-        }
-
-        for (int kz = nmode; kz < localmesh->LocalNz; kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
-
-        DST_rev(std::begin(k1d), localmesh->LocalNz - 2, &x(ix, iy, 1));
-
-        x(ix, iy, 0) = -x(ix, iy, 2);
-        x(ix, iy, localmesh->LocalNz - 1) = -x(ix, iy, localmesh->LocalNz - 3);
-      }
-    }
-  } else {
-    const BoutReal zlength = getUniform(coords->zlength());
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>(localmesh->LocalNz / 2
-                                 + 1); // ZFFT routine expects input of this length
-
-      // Loop over X and Y indices, including boundaries but not guard cells
-      // (unless periodic in x)
-
-      BOUT_OMP_PERF(for)
-      for (int ind = 0; ind < nxny; ++ind) {
-        // ind = (ix - xs)*(ye - ys + 1) + (iy - ys)
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        // Take FFT in Z direction, apply shift, and put result in k1d
-
-        if (((ix < inbndry) && isInnerBoundaryFlagSetOnFirstX(INVERT_SET))
-            || ((localmesh->LocalNx - ix - 1 < outbndry)
-                && isOuterBoundaryFlagSetOnLastX(INVERT_SET))) {
-          // Use the values in x0 in the boundary
-          rfft(x0(ix, iy), localmesh->LocalNz, std::begin(k1d));
-        } else {
-          rfft(rhs(ix, iy), localmesh->LocalNz, std::begin(k1d));
-        }
-
-        // Copy into array, transposing so kz is first index
-        for (int kz = 0; kz < nmode; kz++) {
-          bcmplx3D((iy - ys) * nmode + kz, ix - xs) = k1d[kz];
-        }
-      }
+    const DSTTransform transform(
+        *localmesh, nmode, xs, xe, ys, ye, localmesh->zstart, localmesh->zend, inbndry,
+        outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+        isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-      // Get elements of the tridiagonal matrix
-      // including boundary conditions
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nsys; ind++) {
-        // ind = (iy - ys) * nmode + kz
-        int iy = ys + ind / nmode;
-        int kz = ind % nmode;
-
-        // wave number is 1/[rad]
-        BoutReal kwave = kz * 2.0 * PI / zlength;
-        tridagMatrix(&a3D(ind, 0), &b3D(ind, 0), &c3D(ind, 0), &bcmplx3D(ind, 0), iy,
-                     kz,    // True for the component constant (DC) in Z
-                     kwave, // Z wave number
-                     &Acoef, &C1coef, &C2coef, &Dcoef,
-                     false); // Don't include guard cells in arrays
-      }
-    }
+    auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
     // Solve tridiagonal systems
-    pcr_thomas_solver(a3D, b3D, c3D, bcmplx3D, xcmplx3D);
-
-    // FFT back to real space
-    BOUT_OMP_PERF(parallel)
-    {
-      /// Create a local thread-scope working array
-      auto k1d = Array<dcomplex>((localmesh->LocalNz) / 2
-                                 + 1); // ZFFT routine expects input of this length
+    pcr_thomas_solver(matrices.a, matrices.b, matrices.c, matrices.bcmplx, xcmplx3D);
 
-      const bool zero_DC = isGlobalFlagSet(INVERT_ZERO_DC);
-
-      BOUT_OMP_PERF(for nowait)
-      for (int ind = 0; ind < nxny; ++ind) { // Loop over X and Y
-        int ix = xs + ind / ny;
-        int iy = ys + ind % ny;
-
-        if (zero_DC) {
-          k1d[0] = 0.;
-        }
-
-        for (int kz = static_cast<int>(zero_DC); kz < nmode; kz++) {
-          k1d[kz] = xcmplx3D((iy - ys) * nmode + kz, ix - xs);
-        }
+    return transform.backward(rhs, xcmplx3D);
+  }
 
-        for (int kz = nmode; kz < localmesh->LocalNz / 2 + 1; kz++) {
-          k1d[kz] = 0.0; // Filtering out all higher harmonics
-        }
+  const FFTTransform transform(
+      *localmesh, nmode, xs, xe, ys, ye, localmesh->zstart, localmesh->zend, inbndry,
+      outbndry, isInnerBoundaryFlagSetOnFirstX(INVERT_SET),
+      isOuterBoundaryFlagSetOnLastX(INVERT_SET), isGlobalFlagSet(INVERT_ZERO_DC));
 
-        irfft(std::begin(k1d), localmesh->LocalNz, x(ix, iy));
-      }
-    }
-  }
+  auto matrices = transform.forward(*this, rhs, x0, Acoef, C1coef, C2coef, Dcoef);
 
-  checkData(x);
+  // Solve tridiagonal systems
+  pcr_thomas_solver(matrices.a, matrices.b, matrices.c, matrices.bcmplx, xcmplx3D);
 
-  return x;
+  return transform.backward(rhs, xcmplx3D);
 }
 
 /**
diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx
index e96248ef7e..e9182042de 100644
--- a/src/invert/laplace/invert_laplace.cxx
+++ b/src/invert/laplace/invert_laplace.cxx
@@ -44,6 +44,7 @@
 #include <bout/solver.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
+#include <algorithm>
 #include <cmath>
 
 // Implementations:
@@ -90,19 +91,12 @@ Laplacian::Laplacian(Options* options, const CELL_LOC loc, Mesh* mesh_in,
   const BoutReal filter = (*options)["filter"]
                               .doc("Fraction of Z modes to filter out. Between 0 and 1")
                               .withDefault(0.0);
-  const int ncz = localmesh->LocalNz;
+  const int ncz = localmesh->zend - localmesh->zstart + 1;
   // convert filtering into an integer number of modes
   maxmode = (*options)["maxmode"]
                 .doc("The maximum Z mode to solve for")
-                .withDefault(ROUND((1.0 - filter) * static_cast<BoutReal>(ncz / 2)));
-
-  // Clamp maxmode between 0 and nz/2
-  if (maxmode < 0) {
-    maxmode = 0;
-  }
-  if (maxmode > ncz / 2) {
-    maxmode = ncz / 2;
-  }
+                .withDefault(ROUND((1.0 - filter) * static_cast<BoutReal>(ncz) / 2.0));
+  maxmode = std::clamp(maxmode, 0, ncz / 2);
 
   low_mem = (*options)["low_mem"]
                 .doc("If true, reduce the amount of memory used")
@@ -259,7 +253,7 @@ Field2D Laplacian::solve(const Field2D& b, const Field2D& x0) {
  **********************************************************************************/
 
 void Laplacian::tridagCoefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dcomplex& c,
-                            const Field2D* ccoef, const Field2D* d, CELL_LOC loc) {
+                            const Field2D* ccoef, const Field2D* d, CELL_LOC loc) const {
 
   if (loc == CELL_DEFAULT) {
     loc = location;
@@ -276,13 +270,13 @@ void Laplacian::tridagCoefs(int jx, int jy, int jz, dcomplex& a, dcomplex& b, dc
 void Laplacian::tridagCoefs(int /* jx */, int /* jy */, BoutReal /* kwave */,
                             dcomplex& /* a */, dcomplex& /* b */, dcomplex& /* c */,
                             const Field2D* /* c1coef */, const Field2D* /* c2coef */,
-                            const Field2D* /* d */, CELL_LOC /* loc */) {
+                            const Field2D* /* d */, CELL_LOC /* loc */) const {
   throw BoutException("Laplacian::tridagCoefs() does not support 3d metrics.");
 }
 #else
 void Laplacian::tridagCoefs(int jx, int jy, BoutReal kwave, dcomplex& a, dcomplex& b,
                             dcomplex& c, const Field2D* c1coef, const Field2D* c2coef,
-                            const Field2D* d, CELL_LOC loc) {
+                            const Field2D* d, CELL_LOC loc) const {
   /* Function: Laplacian::tridagCoef
    * Purpose:  - Set the matrix components of A in Ax=b, solving
    *
@@ -424,14 +418,14 @@ void Laplacian::tridagMatrix(dcomplex* /*avec*/, dcomplex* /*bvec*/, dcomplex* /
                              dcomplex* /*bk*/, int /*jy*/, int /*kz*/, BoutReal /*kwave*/,
                              const Field2D* /*a*/, const Field2D* /*c1coef*/,
                              const Field2D* /*c2coef*/, const Field2D* /*d*/,
-                             bool /*includeguards*/, bool /*zperiodic*/) {
+                             bool /*includeguards*/, bool /*zperiodic*/) const {
   throw BoutException("Error: tridagMatrix does not yet work with 3D metric.");
 }
 #else
 void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dcomplex* bk,
                              int jy, int kz, BoutReal kwave, const Field2D* a,
                              const Field2D* c1coef, const Field2D* c2coef,
-                             const Field2D* d, bool includeguards, bool zperiodic) {
+                             const Field2D* d, bool includeguards, bool zperiodic) const {
   ASSERT1(a->getLocation() == location);
   ASSERT1(c1coef->getLocation() == location);
   ASSERT1(c2coef->getLocation() == location);
@@ -460,7 +454,8 @@ void Laplacian::tridagMatrix(dcomplex* avec, dcomplex* bvec, dcomplex* cvec, dco
 
   // Setting the width of the boundary.
   // NOTE: The default is a width of (localmesh->xstart) guard cells
-  int inbndry = localmesh->xstart, outbndry = localmesh->xstart;
+  int inbndry = localmesh->xstart;
+  int outbndry = localmesh->xstart;
 
   // If the flags to assign that only one guard cell should be used is set
   if (isGlobalFlagSet(INVERT_BOTH_BNDRY_ONE) || (localmesh->xstart < 2)) {

From c8f38049359170a34c915e209276238ea66b9a1e Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Fri, 20 Feb 2026 17:31:44 +0000
Subject: [PATCH 0520/1827] [bot] Apply format changes

---
 src/invert/laplace/common_transform.cxx | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/invert/laplace/common_transform.cxx b/src/invert/laplace/common_transform.cxx
index 98571624a1..847add4fea 100644
--- a/src/invert/laplace/common_transform.cxx
+++ b/src/invert/laplace/common_transform.cxx
@@ -28,8 +28,8 @@ FFTTransform::FFTTransform(const Mesh& mesh, int nmode, int xs, int xe, int ys,
 
 auto FFTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
                            const Field3D& x0, const Field2D& Acoef, const Field2D& C1coef,
-                           const Field2D& C2coef, const Field2D& Dcoef) const
-    -> Matrices {
+                           const Field2D& C2coef,
+                           const Field2D& Dcoef) const -> Matrices {
 
   Matrices result(nsys, nx);
 
@@ -79,8 +79,8 @@ auto FFTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
   return result;
 }
 
-auto FFTTransform::backward(const Field3D& rhs, const Matrix<dcomplex>& xcmplx3D) const
-    -> Field3D {
+auto FFTTransform::backward(const Field3D& rhs,
+                            const Matrix<dcomplex>& xcmplx3D) const -> Field3D {
   Field3D x{emptyFrom(rhs)};
 
   // FFT back to real space
@@ -162,8 +162,8 @@ auto FFTTransform::forward(const Laplacian& laplacian, const FieldPerp& rhs,
   return result;
 }
 
-auto FFTTransform::backward(const FieldPerp& rhs, const Matrix<dcomplex>& xcmplx) const
-    -> FieldPerp {
+auto FFTTransform::backward(const FieldPerp& rhs,
+                            const Matrix<dcomplex>& xcmplx) const -> FieldPerp {
   FieldPerp x{emptyFrom(rhs)};
 
   // FFT back to real space
@@ -209,8 +209,8 @@ DSTTransform::DSTTransform(const Mesh& mesh, int nmode, int xs, int xe, int ys,
 
 auto DSTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
                            const Field3D& x0, const Field2D& Acoef, const Field2D& C1coef,
-                           const Field2D& C2coef, const Field2D& Dcoef) const
-    -> Matrices {
+                           const Field2D& C2coef,
+                           const Field2D& Dcoef) const -> Matrices {
 
   Matrices result(nsys, nx);
 
@@ -260,8 +260,8 @@ auto DSTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
   return result;
 }
 
-auto DSTTransform::backward(const Field3D& rhs, const Matrix<dcomplex>& xcmplx3D) const
-    -> Field3D {
+auto DSTTransform::backward(const Field3D& rhs,
+                            const Matrix<dcomplex>& xcmplx3D) const -> Field3D {
   Field3D x{emptyFrom(rhs)};
 
   // DST back to real space
@@ -346,8 +346,8 @@ auto DSTTransform::forward(const Laplacian& laplacian, const FieldPerp& rhs,
   return result;
 }
 
-auto DSTTransform::backward(const FieldPerp& rhs, const Matrix<dcomplex>& xcmplx) const
-    -> FieldPerp {
+auto DSTTransform::backward(const FieldPerp& rhs,
+                            const Matrix<dcomplex>& xcmplx) const -> FieldPerp {
   FieldPerp x{emptyFrom(rhs)};
 
   // DST back to real space

From fee25979c8bfd9c8d427df262b3be91b75f49b5c Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Fri, 20 Feb 2026 17:31:45 +0000
Subject: [PATCH 0521/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 010100588c..d04b9f1259 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -8,3 +8,4 @@ ed2117e6d6826a98b6988e2f18c0c34e408563b6
 a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
 2c2402ed59c91164eaff46dee0f79386b7347e9e
 05b7c571544c3bcb153fce67d12b9ac48947fc2d
+c8f38049359170a34c915e209276238ea66b9a1e

From 353e709d6f9958faeda4e381efe6d52097bcb571 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 23 Feb 2026 17:22:15 +0000
Subject: [PATCH 0522/1827] Disable LaplaceXYHypre and test if using 3D metrics

---
 src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx  | 2 +-
 src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx  | 6 ++++++
 tests/integrated/test-laplacexy2-hypre/CMakeLists.txt | 1 +
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
index 9323513f21..439d07a4e5 100644
--- a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
@@ -1,6 +1,6 @@
 #include "bout/build_defines.hxx"
 
-#if BOUT_HAS_HYPRE
+#if BOUT_HAS_HYPRE and not BOUT_USE_METRIC_3D
 
 #include "laplacexy-hypre.hxx"
 
diff --git a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
index f415f9ebf4..f9b1d90fb3 100644
--- a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
@@ -43,6 +43,12 @@ RegisterUnavailableLaplaceXY
     registerlaplacexyhypre("hypre", "BOUT++ was not configured with HYPRE");
 }
 
+#elif BOUT_USE_METRIC_3D
+namespace {
+RegisterUnavailableLaplaceXY
+    registerlaplacexyhypre("hypre", "BOUT++ was configured with 3D metrics");
+}
+
 #else // BOUT_HAS_HYPRE
 
 class Mesh;
diff --git a/tests/integrated/test-laplacexy2-hypre/CMakeLists.txt b/tests/integrated/test-laplacexy2-hypre/CMakeLists.txt
index e56829b243..4f16f78713 100644
--- a/tests/integrated/test-laplacexy2-hypre/CMakeLists.txt
+++ b/tests/integrated/test-laplacexy2-hypre/CMakeLists.txt
@@ -2,5 +2,6 @@ bout_add_integrated_test(
   test-laplacexy2-hypre
   SOURCES test-laplacexy.cxx
   REQUIRES BOUT_HAS_HYPRE
+  CONFLICTS BOUT_USE_METRIC_3D
   USE_RUNTEST USE_DATA_BOUT_INP
 )

From f887aed94e50bcef5b7cf9bc4568f62435b581c0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 23 Feb 2026 17:24:51 +0000
Subject: [PATCH 0523/1827] CI: remove (mostly) redundant test

This test has significant overlap with other tests, it doesn't really give us
any useful information
---
 .github/workflows/tests.yml | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index f44ebb87ec..0abc01ef5f 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -121,22 +121,6 @@ jobs:
             omp_num_threads: 2
             on_cron: false
 
-          - name: "CMake, new PETSc"
-            os: ubuntu-latest
-            cmake_options: "-DBUILD_SHARED_LIBS=ON
-                            -DBOUT_ENABLE_METRIC_3D=ON
-                            -DBOUT_ENABLE_OPENMP=ON
-                            -DBOUT_USE_PETSC=ON
-                            -DBOUT_USE_SLEPC=ON
-                            -DBOUT_USE_SUNDIALS=ON
-                            -DBOUT_USE_HYPRE=OFF
-                            -DBOUT_ENABLE_PYTHON=ON
-                            -DSUNDIALS_ROOT=/home/runner/local
-                            -DPETSC_DIR=/home/runner/local/petsc
-                            -DSLEPC_DIR=/home/runner/local/slepc"
-            build_petsc: -petsc
-            on_cron: false
-
         exclude:
           - is_cron: true
             config:

From 4c96e9b9639e236def795f1efd17289c63e52828 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 23 Feb 2026 17:25:41 +0000
Subject: [PATCH 0524/1827] CI: rename build to be more accurate

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 0abc01ef5f..e45e082232 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -40,7 +40,7 @@ jobs:
         is_cron:
           - ${{ github.event_name == 'cron' }}
         config:
-          - name: "CMake, PETSc unreleased, ADIOS2"
+          - name: "PETSc unreleased, ADIOS2, 3D metrics"
             os: ubuntu-24.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON

From 18ed91d855ebd7ac7d230b59c5ad44aeb818d426 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 23 Feb 2026 18:45:05 +0000
Subject: [PATCH 0525/1827] Mark unavailable Laplacian solvers that don't work
 with 3D metrics

---
 .../laplace/impls/naulin/naulin_laplace.cxx     |  6 ++++++
 .../laplace/impls/naulin/naulin_laplace.hxx     | 15 ++++++++++++++-
 src/invert/laplace/impls/pcr/pcr.cxx            |  6 ++++++
 src/invert/laplace/impls/pcr/pcr.hxx            | 17 +++++++++++++++--
 .../laplace/impls/pcr_thomas/pcr_thomas.cxx     |  6 ++++++
 .../laplace/impls/pcr_thomas/pcr_thomas.hxx     | 15 ++++++++++++++-
 .../laplace/impls/serial_tri/serial_tri.cxx     |  6 ++++++
 .../laplace/impls/serial_tri/serial_tri.hxx     | 15 ++++++++++++++-
 src/invert/laplace/impls/spt/spt.cxx            |  6 ++++++
 src/invert/laplace/impls/spt/spt.hxx            | 16 ++++++++++++++--
 10 files changed, 101 insertions(+), 7 deletions(-)

diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index f61dc93908..1c90976ce6 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -138,6 +138,10 @@
  */
 // clang-format on
 
+#include "bout/build_defines.hxx"
+
+#if not BOUT_USE_METRIC_3D
+
 #include <bout/boutexception.hxx>
 #include <bout/coordinates.hxx>
 #include <bout/derivs.hxx>
@@ -426,3 +430,5 @@ void LaplaceNaulin::outputVars(Options& output_options,
   output_options[fmt::format("{}_mean_underrelax_counts", getPerformanceName())]
       .assignRepeat(naulinsolver_mean_underrelax_counts, time_dimension);
 }
+
+#endif
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.hxx b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
index 1998a046d7..c4e7d41d9e 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.hxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
@@ -28,11 +28,22 @@ class LaplaceNaulin;
 #ifndef BOUT_LAP_NAULIN_H
 #define BOUT_LAP_NAULIN_H
 
+#include <bout/build_defines.hxx>
 #include <bout/invert_laplace.hxx>
+
+#if BOUT_USE_METRIC_3D
+
+namespace {
+const RegisterUnavailableLaplace
+    registerlaplacenaulin(LAPLACE_NAULIN, "BOUT++ was configured with 3D metrics");
+}
+
+#else
+
 #include <bout/options.hxx>
 
 namespace {
-RegisterLaplace<LaplaceNaulin> registerlaplacenaulin(LAPLACE_NAULIN);
+const RegisterLaplace<LaplaceNaulin> registerlaplacenaulin(LAPLACE_NAULIN);
 }
 
 /// Solves the 2D Laplacian equation
@@ -198,4 +209,6 @@ private:
   void copy_x_boundaries(Field3D& x, const Field3D& x0, Mesh* mesh);
 };
 
+#endif // BOUT_USE_METRIC_3D
+
 #endif // BOUT_LAP_NAULIN_H
diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx
index a33bd7eef2..591edb5080 100644
--- a/src/invert/laplace/impls/pcr/pcr.cxx
+++ b/src/invert/laplace/impls/pcr/pcr.cxx
@@ -36,6 +36,10 @@
  *
  **************************************************************************/
 
+#include "bout/build_defines.hxx"
+
+#if not BOUT_USE_METRIC_3D
+
 #include "pcr.hxx"
 #include "bout/globals.hxx"
 
@@ -1108,3 +1112,5 @@ void LaplacePCR ::verify_solution(const Matrix<dcomplex>& a_ver,
   output.write("max abs error {}\n", max_error);
   output.write("max abs error location {} {}\n", max_loc_x, max_loc_z);
 }
+
+#endif // BOUT_USE_METRIC_3D
diff --git a/src/invert/laplace/impls/pcr/pcr.hxx b/src/invert/laplace/impls/pcr/pcr.hxx
index ec4637f56c..2b90e17466 100644
--- a/src/invert/laplace/impls/pcr/pcr.hxx
+++ b/src/invert/laplace/impls/pcr/pcr.hxx
@@ -29,13 +29,24 @@ class LaplacePCR;
 #ifndef BOUT_PCR_H
 #define BOUT_PCR_H
 
-#include <bout/dcomplex.hxx>
+#include <bout/build_defines.hxx>
 #include <bout/invert_laplace.hxx>
+
+#if BOUT_USE_METRIC_3D
+
+namespace {
+const RegisterUnavailableLaplace
+    registerlaplacepcr(LAPLACE_PCR, "BOUT++ was configured with 3D metrics");
+}
+
+#else
+
+#include <bout/dcomplex.hxx>
 #include <bout/options.hxx>
 #include <bout/utils.hxx>
 
 namespace {
-RegisterLaplace<LaplacePCR> registerlaplacepcr(LAPLACE_PCR);
+const RegisterLaplace<LaplacePCR> registerlaplacepcr(LAPLACE_PCR);
 }
 
 class LaplacePCR : public Laplacian {
@@ -175,4 +186,6 @@ private:
   bool dst{false};
 };
 
+#endif // BOUT_USE_METRIC_3D
+
 #endif // BOUT_PCR_H
diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
index d471775990..1b8c66dfdf 100644
--- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
+++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.cxx
@@ -36,6 +36,10 @@
  *
  **************************************************************************/
 
+#include "bout/build_defines.hxx"
+
+#if not BOUT_USE_METRIC_3D
+
 #include "pcr_thomas.hxx"
 #include "bout/globals.hxx"
 
@@ -1190,3 +1194,5 @@ void LaplacePCR_THOMAS ::verify_solution(const Matrix<dcomplex>& a_ver,
   }
   output.write("max abs error {}\n", max_error);
 }
+
+#endif // BOUT_USE_METRIC_3D
diff --git a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx
index e12a647789..1b5c6b97b9 100644
--- a/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx
+++ b/src/invert/laplace/impls/pcr_thomas/pcr_thomas.hxx
@@ -29,8 +29,19 @@ class LaplacePCR_THOMAS;
 #ifndef BOUT_PCR_THOMAS_H
 #define BOUT_PCR_THOMAS_H
 
+#include "bout/build_defines.hxx"
+#include "bout/invert_laplace.hxx"
+
+#if BOUT_USE_METRIC_3D
+
+namespace {
+const RegisterUnavailableLaplace
+    registerlaplacepcrthomas(LAPLACE_PCR_THOMAS, "BOUT++ was configured with 3D metrics");
+}
+
+#else
+
 #include <bout/dcomplex.hxx>
-#include <bout/invert_laplace.hxx>
 #include <bout/options.hxx>
 #include <bout/utils.hxx>
 
@@ -178,4 +189,6 @@ private:
   bool dst{false};
 };
 
+#endif // BOUT_USE_METRIC_3D
+
 #endif // BOUT_PCR_THOMAS_H
diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.cxx b/src/invert/laplace/impls/serial_tri/serial_tri.cxx
index a14e0e4a26..d051ce0c1e 100644
--- a/src/invert/laplace/impls/serial_tri/serial_tri.cxx
+++ b/src/invert/laplace/impls/serial_tri/serial_tri.cxx
@@ -24,6 +24,10 @@
  *
  **************************************************************************/
 
+#include "bout/build_defines.hxx"
+
+#if not BOUT_USE_METRIC_3D
+
 #include "serial_tri.hxx"
 #include "bout/globals.hxx"
 
@@ -247,3 +251,5 @@ FieldPerp LaplaceSerialTri::solve(const FieldPerp& b, const FieldPerp& x0) {
 
   return x; // Result of the inversion
 }
+
+#endif // BOUT_USE_METRIC_3D
diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.hxx b/src/invert/laplace/impls/serial_tri/serial_tri.hxx
index 5b0419fa27..4aed777b7c 100644
--- a/src/invert/laplace/impls/serial_tri/serial_tri.hxx
+++ b/src/invert/laplace/impls/serial_tri/serial_tri.hxx
@@ -29,8 +29,19 @@ class LaplaceSerialTri;
 #ifndef BOUT_SERIAL_TRI_H
 #define BOUT_SERIAL_TRI_H
 
+#include "bout/build_defines.hxx"
+#include "bout/invert_laplace.hxx"
+
+#if BOUT_USE_METRIC_3D
+
+namespace {
+const RegisterUnavailableLaplace
+    registerlaplacetri(LAPLACE_TRI, "BOUT++ was configured with 3D metrics");
+}
+
+#else
+
 #include <bout/dcomplex.hxx>
-#include <bout/invert_laplace.hxx>
 #include <bout/options.hxx>
 
 namespace {
@@ -80,4 +91,6 @@ private:
   Field2D A, C, D;
 };
 
+#endif // BOUT_USE_METRIC_3D
+
 #endif // BOUT_SERIAL_TRI_H
diff --git a/src/invert/laplace/impls/spt/spt.cxx b/src/invert/laplace/impls/spt/spt.cxx
index cd24ee1acf..34a1a64cae 100644
--- a/src/invert/laplace/impls/spt/spt.cxx
+++ b/src/invert/laplace/impls/spt/spt.cxx
@@ -31,6 +31,10 @@
  *
  */
 
+#include "bout/build_defines.hxx"
+
+#if not BOUT_USE_METRIC_3D
+
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
@@ -553,3 +557,5 @@ void LaplaceSPT::SPT_data::allocate(int mm, int nx) {
 
   buffer.reallocate(4 * mm);
 }
+
+#endif // BOUT_USE_METRIC_3D
diff --git a/src/invert/laplace/impls/spt/spt.hxx b/src/invert/laplace/impls/spt/spt.hxx
index a9d5b2583f..a3b1acb7c3 100644
--- a/src/invert/laplace/impls/spt/spt.hxx
+++ b/src/invert/laplace/impls/spt/spt.hxx
@@ -39,10 +39,20 @@
 class LaplaceSPT;
 
 #ifndef BOUT_SPT_H
+#include "bout/build_defines.hxx"
+#include "bout/invert_laplace.hxx"
+
+#if BOUT_USE_METRIC_3D
+
+namespace {
+const RegisterUnavailableLaplace
+    registerlaplacespt(LAPLACE_SPT, "BOUT++ was configured with 3D metrics");
+}
+
+#else
 #define BOUT_SPT_H
 
 #include <bout/dcomplex.hxx>
-#include <bout/invert_laplace.hxx>
 #include <bout/mesh.hxx>
 #include <bout/options.hxx>
 #include <bout/utils.hxx>
@@ -153,7 +163,9 @@ private:
 namespace {
 // Note: After class definition so compiler knows that
 //       registered class is derived from Laplacian
-RegisterLaplace<LaplaceSPT> registerlaplacespt(LAPLACE_SPT);
+const RegisterLaplace<LaplaceSPT> registerlaplacespt(LAPLACE_SPT);
 } // namespace
 
+#endif // BOUT_USE_METRIC_3D
+
 #endif // BOUT_SPT_H

From daf63738b55d315bb221bf20bc4d8e28b7a7c10c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 23 Feb 2026 18:48:08 +0000
Subject: [PATCH 0526/1827] Get PETSc Laplacian test working with 3D metrics

- Remove comparison to default solver
  - The default is cyclic which doesn't work with 3D metrics
  - Also we don't actually do any comparison, so it doesn't help us test
    anything
- Use one of PETSc's preconditioners instead of one of our solvers
  - Prefer MUMPS but fall back to LU, which should always be available
---
 .../test-petsc_laplace/CMakeLists.txt         |  2 -
 .../test-petsc_laplace/data/BOUT.inp          |  9 ---
 tests/integrated/test-petsc_laplace/runtest   |  2 -
 .../test-petsc_laplace/test_petsc_laplace.cxx | 80 +++++++++++--------
 4 files changed, 46 insertions(+), 47 deletions(-)

diff --git a/tests/integrated/test-petsc_laplace/CMakeLists.txt b/tests/integrated/test-petsc_laplace/CMakeLists.txt
index 1d2e7896f0..977b33afe2 100644
--- a/tests/integrated/test-petsc_laplace/CMakeLists.txt
+++ b/tests/integrated/test-petsc_laplace/CMakeLists.txt
@@ -2,8 +2,6 @@ bout_add_integrated_test(
   test-petsc-laplace
   SOURCES test_petsc_laplace.cxx
   REQUIRES BOUT_HAS_PETSC
-  CONFLICTS
-    BOUT_USE_METRIC_3D # default preconditioner uses 'cyclic' Laplace solver which is not available with 3d metrics
   USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 4
 )
diff --git a/tests/integrated/test-petsc_laplace/data/BOUT.inp b/tests/integrated/test-petsc_laplace/data/BOUT.inp
index e7c285b54c..15e54ff753 100644
--- a/tests/integrated/test-petsc_laplace/data/BOUT.inp
+++ b/tests/integrated/test-petsc_laplace/data/BOUT.inp
@@ -67,15 +67,6 @@ outer_boundary_flags = 32 # Identity in boundary
 
 #############################################
 
-[SPT]
-#type=spt
-all_terms = true
-nonuniform = true
-#flags=15
-include_yguards = false
-
-#maxits=10000
-
 [laplace]
 all_terms = true
 nonuniform = true
diff --git a/tests/integrated/test-petsc_laplace/runtest b/tests/integrated/test-petsc_laplace/runtest
index 83e1006338..5496987128 100755
--- a/tests/integrated/test-petsc_laplace/runtest
+++ b/tests/integrated/test-petsc_laplace/runtest
@@ -16,11 +16,9 @@ vars = [
     ("max_error1", 2.0e-4),
     ("max_error2", 2.0e-4),
     ("max_error3", 2.0e-4),
-    ("max_error4", 1.0e-5),
     ("max_error5", 2.0e-4),
     ("max_error6", 2.0e-5),
     ("max_error7", 2.0e-4),
-    ("max_error8", 2.0e-5),
 ]
 # tol = 1e-4                  # Absolute (?) tolerance
 
diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
index c42c55d8d6..e869cd1b1d 100644
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
@@ -26,6 +26,7 @@
 #include "bout/bout.hxx" // NOLINT
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_config.hxx"
 #include "bout/constants.hxx"
 #include "bout/difops.hxx"
 #include "bout/field2d.hxx"
@@ -39,6 +40,7 @@
 #include "fmt/core.h"
 #include <mpi.h>
 
+#include <algorithm>
 #include <cmath>
 #include <string_view>
 
@@ -112,10 +114,37 @@ int main(int argc, char** argv) {
 
   BoutInitialise(argc, argv);
   {
-    Options* options = Options::getRoot()->getSection("petsc2nd");
-    auto invert = Laplacian::create(options);
-    options = Options::getRoot()->getSection("petsc4th");
-    auto invert_4th = Laplacian::create(options);
+    // Not be used for 3D metrics
+    Options::root()["laplace"].setConditionallyUsed();
+
+    // For 3D metrics, we need to use one of PETSc's preconditioners
+    // and mumps seems to be the best? Or at least HYPRE doesn't work
+    // on this test with more than one processor.
+#ifdef PETSC_HAVE_MUMPS
+    constexpr auto petsc_has_mumps = true;
+#else
+    constexpr auto petsc_has_mumps = false;
+#endif
+
+    // Preconditioner to use for 3D metrics
+    constexpr auto petsc_pc = petsc_has_mumps ? "mumps" : "lu";
+
+    auto& options_2nd = Options::root()["petsc2nd"];
+    if constexpr (bout::build::use_metric_3d) {
+      options_2nd["pctype"] = petsc_pc;
+      options_2nd["rightprec"].setConditionallyUsed();
+      options_2nd["precon"].setConditionallyUsed();
+    }
+
+    auto invert = Laplacian::create(&options_2nd);
+
+    auto& options_4th = Options::root()["petsc4th"];
+    if constexpr (bout::build::use_metric_3d) {
+      options_4th["pctype"] = petsc_pc;
+      options_4th["rightprec"].setConditionallyUsed();
+      options_4th["precon"].setConditionallyUsed();
+    }
+    auto invert_4th = Laplacian::create(&options_4th);
 
     Options dump;
 
@@ -136,35 +165,27 @@ int main(int argc, char** argv) {
 
     const Field3D b_1 = forward_laplace(f_1, a_1, c_1, d_1);
 
-    int test_num = 0;
-    check_laplace(++test_num, "PETSc 2nd order", *invert, INVERT_AC_GRAD, INVERT_AC_GRAD,
-                  a_1, c_1, d_1, b_1, f_1, mesh->ystart, dump);
+    check_laplace(1, "PETSc 2nd order", *invert, INVERT_AC_GRAD, INVERT_AC_GRAD, a_1, c_1,
+                  d_1, b_1, f_1, mesh->ystart, dump);
 
     /////////////////////////////////////////////////
     // Test 2: Gaussian x-profiles, 4th order Krylov
 
-    check_laplace(++test_num, "PETSc 4th order", *invert_4th, INVERT_AC_GRAD,
-                  INVERT_AC_GRAD, a_1, c_1, d_1, b_1, f_1, mesh->ystart, dump);
+    check_laplace(2, "PETSc 4th order", *invert_4th, INVERT_AC_GRAD, INVERT_AC_GRAD, a_1,
+                  c_1, d_1, b_1, f_1, mesh->ystart, dump);
 
     ////////////////////////////////////////////////////////////////////////////////////////
-    // Test 3+4: Gaussian x-profiles, z-independent coefficients and compare with SPT method
+    // Test 3+4: Gaussian x-profiles, z-independent coefficients
 
     const Field2D a_3 = DC(a_1);
     const Field2D c_3 = DC(c_1);
     const Field2D d_3 = DC(d_1);
     const Field3D b_3 = forward_laplace(f_1, a_3, c_3, d_3);
 
-    check_laplace(++test_num, "with coefficients constant in z, PETSc 2nd order", *invert,
+    check_laplace(3, "with coefficients constant in z, PETSc 2nd order", *invert,
                   INVERT_AC_GRAD, INVERT_AC_GRAD, a_3, c_3, d_3, b_3, f_1, mesh->ystart,
                   dump);
 
-    Options* SPT_options = Options::getRoot()->getSection("SPT");
-    auto invert_SPT = Laplacian::create(SPT_options);
-
-    check_laplace(++test_num, "with coefficients constant in z, default solver",
-                  *invert_SPT, INVERT_AC_GRAD, INVERT_AC_GRAD | INVERT_DC_GRAD, a_3, c_3,
-                  d_3, b_3, f_1, mesh->ystart, dump);
-
     //////////////////////////////////////////////
     // Test 5: Cosine x-profiles, 2nd order Krylov
     Field3D f_5 = generate_f5(*mesh);
@@ -176,16 +197,14 @@ int main(int argc, char** argv) {
 
     const Field3D b_5 = forward_laplace(f_5, a_5, c_5, d_5);
 
-    check_laplace(++test_num, "different profiles, PETSc 2nd order", *invert,
-                  INVERT_AC_GRAD, INVERT_AC_GRAD, a_5, c_5, d_5, b_5, f_5, mesh->ystart,
-                  dump);
+    check_laplace(5, "different profiles, PETSc 2nd order", *invert, INVERT_AC_GRAD,
+                  INVERT_AC_GRAD, a_5, c_5, d_5, b_5, f_5, mesh->ystart, dump);
 
     //////////////////////////////////////////////
     // Test 6: Cosine x-profiles, 4th order Krylov
 
-    check_laplace(++test_num, "different profiles, PETSc 4th order", *invert_4th,
-                  INVERT_AC_GRAD, INVERT_AC_GRAD, a_5, c_5, d_5, b_5, f_5, mesh->ystart,
-                  dump);
+    check_laplace(6, "different profiles, PETSc 4th order", *invert_4th, INVERT_AC_GRAD,
+                  INVERT_AC_GRAD, a_5, c_5, d_5, b_5, f_5, mesh->ystart, dump);
 
     //////////////////////////////////////////////////////////////////////////////////////
     // Test 7+8: Cosine x-profiles, z-independent coefficients and compare with SPT method
@@ -195,16 +214,11 @@ int main(int argc, char** argv) {
     const Field2D d_7 = DC(d_5);
     const Field3D b_7 = forward_laplace(f_5, a_7, c_7, d_7);
 
-    check_laplace(++test_num,
+    check_laplace(7,
                   "different profiles, with coefficients constant in z, PETSc 2nd order",
                   *invert, INVERT_AC_GRAD, INVERT_AC_GRAD, a_7, c_7, d_7, b_7, f_5,
                   mesh->ystart, dump);
 
-    check_laplace(++test_num,
-                  "different profiles, with coefficients constant in z, default solver",
-                  *invert_SPT, INVERT_AC_GRAD, INVERT_AC_GRAD | INVERT_DC_GRAD, a_7, c_7,
-                  d_7, b_7, f_5, mesh->ystart, dump);
-
     // Write and close the output file
     bout::writeDefaultOutputFile(dump);
 
@@ -219,13 +233,11 @@ int main(int argc, char** argv) {
 
 BoutReal max_error_at_ystart(const Field3D& error) {
   const auto* mesh = error.getMesh();
-  BoutReal local_max_error = error(mesh->xstart, mesh->ystart, 0);
+  BoutReal local_max_error = 0.0;
 
   for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
     for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
-      if (local_max_error < error(jx, mesh->ystart, jz)) {
-        local_max_error = error(jx, mesh->ystart, jz);
-      }
+      local_max_error = std::max(local_max_error, error(jx, mesh->ystart, jz));
     }
   }
 

From ec6a97f8ebd6a0909939091b663825c97d396380 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 12:07:38 +0000
Subject: [PATCH 0527/1827] tests: Refactor petsc-laplace test

- use field factory, rather than explicit loops
---
 tests/integrated/test-petsc_laplace/runtest   |  52 +-
 .../test-petsc_laplace/test_petsc_laplace.cxx | 490 ++++--------------
 2 files changed, 135 insertions(+), 407 deletions(-)

diff --git a/tests/integrated/test-petsc_laplace/runtest b/tests/integrated/test-petsc_laplace/runtest
index 5496987128..b4379f7754 100755
--- a/tests/integrated/test-petsc_laplace/runtest
+++ b/tests/integrated/test-petsc_laplace/runtest
@@ -8,25 +8,21 @@
 # requires: all_tests
 # cores: 4
 
-# Variables to compare
-from __future__ import print_function
-from builtins import str
-
-vars = [
-    ("max_error1", 2.0e-4),
-    ("max_error2", 2.0e-4),
-    ("max_error3", 2.0e-4),
-    ("max_error5", 2.0e-4),
-    ("max_error6", 2.0e-5),
-    ("max_error7", 2.0e-4),
-]
-# tol = 1e-4                  # Absolute (?) tolerance
-
 from boututils.run_wrapper import build_and_log, shell, launch_safe
-from boutdata.collect import collect
-
-# import numpy as np
-from sys import stdout, exit
+from boutdata.collect import collect, create_cache
+
+import pathlib
+from sys import exit
+
+errors = [
+    "max_error1",
+    "max_error2",
+    "max_error3",
+    "max_error5",
+    "max_error6",
+    "max_error7",
+]
+tol = 2e-4  # Absolute (?) tolerance
 
 build_and_log("PETSc Laplacian inversion test")
 
@@ -34,29 +30,25 @@ print("Running PETSc Laplacian inversion test")
 success = True
 
 for nproc in [1, 2, 4]:
-    #  nxpe = 1
-    #  if nproc > 2:
-    #    nxpe = 2
-
     cmd = "./test_petsc_laplace"
 
     shell("rm data/BOUT.dmp.*.nc")
 
-    print("   %d processors...." % nproc)
+    print(f"   {nproc} processors....")
     s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
-    f = open("run.log." + str(nproc), "w")
-    f.write(out)
-    f.close()
+
+    pathlib.Path(f"run.log.{nproc}").write_text(out)
+    cache = create_cache(path="data", prefix="BOUT.dmp")
 
     # Collect output data
-    for varname, tol in vars:
-        stdout.write("      Checking " + varname + " ... ")
-        error = collect(varname, path="data", info=False)
+    for varname in errors:
+        print(f"      Checking {varname} ... ", end="")
+        error = collect(varname, path="data", info=False, datafile_cache=cache)
         if error <= 0:
             print("Convergence error")
             success = False
         elif error > tol:
-            print("Fail, maximum error is = " + str(error))
+            print(f"Fail, maximum error is = {error:e}")
             success = False
         else:
             print("Pass")
diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
index e869cd1b1d..96e7994637 100644
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
@@ -31,19 +31,22 @@
 #include "bout/difops.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
+#include "bout/field_factory.hxx"
 #include "bout/invert_laplace.hxx"
 #include "bout/options.hxx"
 #include "bout/options_io.hxx"
 #include "bout/output.hxx"
 #include "bout/traits.hxx"
+#include "bout/vecops.hxx"
 
-#include "fmt/core.h"
+#include "fmt/format.h"
 #include <mpi.h>
 
 #include <algorithm>
 #include <cmath>
 #include <string_view>
 
+namespace {
 BoutReal max_error_at_ystart(const Field3D& error);
 void apply_flat_boundary(Field3D& bcoef);
 
@@ -101,14 +104,69 @@ Field3D forward_laplace(const Field3D& field, const T& acoef, const T& ccoef,
 }
 
 Field3D generate_f1(const Mesh& mesh);
-Field3D generate_a1(const Mesh& mesh);
-Field3D generate_c1(const Mesh& mesh);
-Field3D generate_d1(const Mesh& mesh);
 
-Field3D generate_f5(const Mesh& mesh);
-Field3D generate_a5(const Mesh& mesh);
-Field3D generate_c5(const Mesh& mesh);
-Field3D generate_d5(const Mesh& mesh);
+Field3D generate_d1(Mesh& mesh) {
+  Options options{{"p_d1", 0.512547}, {"q_d1", 0.30908712}};
+
+  return FieldFactory::get()->create3D(
+      "1. + (0.2 * exp(-50. * (x - p_d1)^2 / 4.) * sin((z - 2. * pi * q_d1) * 3.))",
+      &options, &mesh);
+}
+
+Field3D generate_c1(Mesh& mesh) {
+  Options options{{"p_c1", 0.18439023}, {"q_c1", 0.401089473}};
+
+  return FieldFactory::get()->create3D(
+      "1. + (0.15 * exp(-50. * (x - p_c1)^2 * 2.) * sin((z - 2. * pi * q_c1) * 2.))",
+      &options, &mesh);
+}
+
+Field3D generate_a1(Mesh& mesh) {
+  Options options{{"p_a1", 0.612547}, {"q_a1", 0.30908712}};
+
+  return FieldFactory::get()->create3D(
+      "-1. + (0.1 * exp(-50. * (x - p_a1)^2 * 2.5) * sin((z - 2. * pi * q_a1) * 7.))",
+      &options, &mesh);
+}
+
+Field3D generate_f5(Mesh& mesh) {
+  Options options{{"p_f5", 0.623901}, {"q_f5", 0.01209489}};
+
+  auto result = FieldFactory::get()->create3D(
+      "exp(-((50. * (x - p_f5)^2) + 1. - cos((z - 2. * pi * q_f5))))"
+      "- 50 * (2. * p_f5 * exp(-50. * (-p_f5)^2) * x"
+      "         + (-p_f5 * exp(-50. * (-p_f5)^2) - (1 - p_f5) * exp(-50. * (1 - "
+      "p_f5)^2)) * x^2)"
+      "     * exp(-(1. - cos(z - 2. * pi * q_f5)))",
+      &options, &mesh);
+  result.applyBoundary("neumann");
+  checkData(result);
+  return result;
+}
+
+Field3D generate_d5(Mesh& mesh) {
+  Options options{{"p_d5", 0.63298589}, {"q_d5", 0.889237890}};
+
+  return FieldFactory::get()->create3D(
+      "1. + (p_d5 * cos(2. * pi * x) * sin((z - 2 * pi * q_d5) * 3.))", &options, &mesh);
+}
+
+Field3D generate_c5(Mesh& mesh) {
+  Options options{{"p_c5", 0.160983834}, {"q_c5", 0.73050121087}};
+
+  return FieldFactory::get()->create3D(
+      "1. + (p_c5 * cos(2. * pi * x * 5) * sin((z - 2 * pi * q_c5) * 2.))", &options,
+      &mesh);
+}
+
+Field3D generate_a5(Mesh& mesh) {
+  Options options{{"p_a5", 0.5378950}, {"q_a5", 0.2805870}};
+
+  return FieldFactory::get()->create3D(
+      "-1. + (p_a5 * cos(2. * pi * x * 2.) * sin((z - 2. * pi * q_a5) * 7.))", &options,
+      &mesh);
+}
+} // namespace
 
 int main(int argc, char** argv) {
 
@@ -151,6 +209,25 @@ int main(int argc, char** argv) {
     // Solving equations of the form d*Delp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various f, a, c, d
     using bout::globals::mesh;
 
+    Field3D loop_x;
+    Field3D loop_z;
+    loop_x.allocate();
+    loop_z.allocate();
+    for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
+      const BoutReal x = mesh->GlobalX(jx);
+      for (int jy = 0; jy < mesh->LocalNy; jy++) {
+        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
+          const BoutReal z = mesh->GlobalZ(jz);
+          loop_x(jx, jy, jz) = x;
+          loop_z(jx, jy, jz) = z;
+        }
+      }
+    }
+    dump["loop_x"] = loop_x;
+    dump["loop_z"] = loop_z;
+    dump["exp_x"] = FieldFactory::get()->create3D("x");
+    dump["exp_z"] = FieldFactory::get()->create3D("z");
+
     // Only Neumann x-boundary conditions are implemented so far, so test functions should be Neumann in x and periodic in z.
     // Use Field3D's, but solver only works on FieldPerp slices, so only use 1 y-point
 
@@ -231,6 +308,7 @@ int main(int argc, char** argv) {
   return 0;
 }
 
+namespace {
 BoutReal max_error_at_ystart(const Field3D& error) {
   const auto* mesh = error.getMesh();
   BoutReal local_max_error = 0.0;
@@ -271,234 +349,23 @@ void apply_flat_boundary(Field3D& bcoef) {
 }
 
 Field3D generate_f1(const Mesh& mesh) {
-  const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1;
-  const BoutReal nz = mesh.GlobalNz;
-
   constexpr BoutReal p = 0.39503274; // NOLINT
   constexpr BoutReal q = 0.20974396; // NOLINT
 
   Field3D result;
   result.allocate();
   for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
-    const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-    for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-        const BoutReal z = BoutReal(jz) / nz;
-        //make the gradients zero at both x-boundaries
-        result(jx, jy, jz) = 0.
-                             + exp(-(100. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q))))
-                             - 50.
-                                   * (2. * p * exp(-100. * pow(-p, 2)) * x
-                                      + (-p * exp(-100. * pow(-p, 2))
-                                         - (1 - p) * exp(-100. * pow(1 - p, 2)))
-                                            * pow(x, 2))
-                                   * exp(-(1. - cos(2. * PI * (z - q))));
-      }
-    }
-  }
-  if (mesh.firstX()) {
-    for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          //make the gradients zero at both x-boundaries
-          result(jx, jy, jz) = 0.
-                               + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q))))
-                               - 50.
-                                     * (2. * p * exp(-60. * pow(-p, 2)) * x
-                                        + (-p * exp(-60. * pow(-p, 2))
-                                           - (1 - p) * exp(-60. * pow(1 - p, 2)))
-                                              * pow(x, 2))
-                                     * exp(-(1. - cos(2. * PI * (z - q))));
-        }
-      }
-    }
-  }
-  if (mesh.lastX()) {
-    for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          //make the gradients zero at both x-boundaries
-          result(jx, jy, jz) = 0.
-                               + exp(-(60. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q))))
-                               - 50.
-                                     * (2. * p * exp(-60. * pow(-p, 2)) * x
-                                        + (-p * exp(-60. * pow(-p, 2))
-                                           - (1 - p) * exp(-60. * pow(1 - p, 2)))
-                                              * pow(x, 2))
-                                     * exp(-(1. - cos(2. * PI * (z - q))));
-        }
-      }
-    }
-  }
-
-  checkData(result);
-  result.applyBoundary("neumann");
-  return result;
-}
-
-Field3D generate_d1(const Mesh& mesh) {
-  const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1;
-  const BoutReal nz = mesh.GlobalNz;
-
-  constexpr BoutReal p = 0.512547;   // NOLINT
-  constexpr BoutReal q = 0.30908712; // NOLINT
-  Field3D result;
-  result.allocate();
-  for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
-    const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-    for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-        const BoutReal z = BoutReal(jz) / nz;
-        result(jx, jy, jz) =
-            1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.);
-      }
-    }
-  }
-  if (mesh.firstX()) {
-    for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) =
-              1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.);
-        }
-      }
-    }
-  }
-  if (mesh.lastX()) {
-    for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) =
-              1. + 0.2 * exp(-50. * pow(x - p, 2) / 4.) * sin(2. * PI * (z - q) * 3.);
-        }
-      }
-    }
-  }
-  checkData(result);
-  return result;
-}
-
-Field3D generate_c1(const Mesh& mesh) {
-  const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1;
-  const BoutReal nz = mesh.GlobalNz;
-
-  constexpr BoutReal p = 0.18439023;  // NOLINT
-  constexpr BoutReal q = 0.401089473; // NOLINT
-  Field3D result;
-  result.allocate();
-  for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
-    const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-    for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-        const BoutReal z = BoutReal(jz) / nz;
-        result(jx, jy, jz) =
-            1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.);
-      }
-    }
-  }
-  if (mesh.firstX()) {
-    for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) =
-              1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.);
-        }
-      }
-    }
-  }
-  if (mesh.lastX()) {
-    for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) =
-              1. + 0.15 * exp(-50. * pow(x - p, 2) * 2.) * sin(2. * PI * (z - q) * 2.);
-        }
-      }
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-
-Field3D generate_a1(const Mesh& mesh) {
-  const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1;
-  const BoutReal nz = mesh.GlobalNz;
-
-  constexpr BoutReal p = 0.612547;   // NOLINT
-  constexpr BoutReal q = 0.30908712; // NOLINT
-  Field3D result;
-  result.allocate();
-  for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
-    const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
+    const BoutReal x = mesh.GlobalX(jx);
     for (int jy = 0; jy < mesh.LocalNy; jy++) {
       for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-        const BoutReal z = BoutReal(jz) / nz;
-        result(jx, jy, jz) =
-            -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.);
-      }
-    }
-  }
-  if (mesh.firstX()) {
-    for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) =
-              -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.);
-        }
-      }
-    }
-  }
-  if (mesh.lastX()) {
-    for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) =
-              -1. + 0.1 * exp(-50. * pow(x - p, 2) * 2.5) * sin(2. * PI * (z - q) * 7.);
-        }
-      }
-    }
-  }
-
-  checkData(result);
-  return result;
-}
-
-Field3D generate_f5(const Mesh& mesh) {
-  const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1;
-  const BoutReal nz = mesh.GlobalNz;
-  constexpr BoutReal p = 0.623901;   // NOLINT
-  constexpr BoutReal q = 0.01209489; // NOLINT
-  Field3D result;
-  result.allocate();
-  for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
-    const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-    for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-        const BoutReal z = BoutReal(jz) / nz;
+        const BoutReal z = mesh.GlobalZ(jz);
         //make the gradients zero at both x-boundaries
         result(jx, jy, jz) =
-            0. + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q))))
+            0. + exp(-((100. * pow(x - p, 2)) + 1. - cos(2. * PI * (z - q))))
             - 50.
-                  * (2. * p * exp(-50. * pow(-p, 2)) * x
-                     + (-p * exp(-50. * pow(-p, 2)) - (1 - p) * exp(-50. * pow(1 - p, 2)))
+                  * (2. * p * exp(-100. * pow(-p, 2)) * x
+                     + (-p * exp(-100. * pow(-p, 2))
+                        - (1 - p) * exp(-100. * pow(1 - p, 2)))
                            * pow(x, 2))
                   * exp(-(1. - cos(2. * PI * (z - q))));
       }
@@ -506,176 +373,45 @@ Field3D generate_f5(const Mesh& mesh) {
   }
   if (mesh.firstX()) {
     for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          //make the gradients zero at both x-boundaries
-          result(jx, jy, jz) = 0.
-                               + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q))))
-                               - 50.
-                                     * (2. * p * exp(-50. * pow(-p, 2)) * x
-                                        + (-p * exp(-50. * pow(-p, 2))
-                                           - (1 - p) * exp(-50. * pow(1 - p, 2)))
-                                              * pow(x, 2))
-                                     * exp(-(1. - cos(2. * PI * (z - q))));
-        }
-      }
-    }
-  }
-  if (mesh.lastX()) {
-    for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
+      const BoutReal x = mesh.GlobalX(jx);
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
         for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
+          const BoutReal z = mesh.GlobalZ(jz);
           //make the gradients zero at both x-boundaries
-          result(jx, jy, jz) = 0.
-                               + exp(-(50. * pow(x - p, 2) + 1. - cos(2. * PI * (z - q))))
-                               - 50.
-                                     * (2. * p * exp(-50. * pow(-p, 2)) * x
-                                        + (-p * exp(-50. * pow(-p, 2))
-                                           - (1 - p) * exp(-50. * pow(1 - p, 2)))
-                                              * pow(x, 2))
-                                     * exp(-(1. - cos(2. * PI * (z - q))));
-        }
-      }
-    }
-  }
-  result.applyBoundary("neumann");
-  checkData(result);
-  return result;
-}
-
-Field3D generate_d5(const Mesh& mesh) {
-  const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1;
-  const BoutReal nz = mesh.GlobalNz;
-  constexpr BoutReal p = 0.63298589;  // NOLINT
-  constexpr BoutReal q = 0.889237890; // NOLINT
-  Field3D result;
-  result.allocate();
-  for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
-    const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-    for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-        const BoutReal z = BoutReal(jz) / nz;
-        result(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.);
-      }
-    }
-  }
-  if (mesh.firstX()) {
-    for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.);
-        }
-      }
-    }
-  }
-  if (mesh.lastX()) {
-    for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) = 1. + p * cos(2. * PI * x) * sin(2. * PI * (z - q) * 3.);
-        }
-      }
-    }
-  }
-  checkData(result);
-  return result;
-}
-
-Field3D generate_c5(const Mesh& mesh) {
-  const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1;
-  const BoutReal nz = mesh.GlobalNz;
-  constexpr BoutReal p = 0.160983834;   // NOLINT
-  constexpr BoutReal q = 0.73050121087; // NOLINT
-
-  Field3D result;
-
-  result.allocate();
-  for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
-    const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-    for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-        const BoutReal z = BoutReal(jz) / nz;
-        result(jx, jy, jz) = 1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.);
-      }
-    }
-  }
-  if (mesh.firstX()) {
-    for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
           result(jx, jy, jz) =
-              1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.);
+              0. + exp(-((60. * pow(x - p, 2)) + 1. - cos(2. * PI * (z - q))))
+              - 50.
+                    * (2. * p * exp(-60. * pow(-p, 2)) * x
+                       + (-p * exp(-60. * pow(-p, 2))
+                          - (1 - p) * exp(-60. * pow(1 - p, 2)))
+                             * pow(x, 2))
+                    * exp(-(1. - cos(2. * PI * (z - q))));
         }
       }
     }
   }
   if (mesh.lastX()) {
     for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
+      const BoutReal x = mesh.GlobalX(jx);
       for (int jy = 0; jy < mesh.LocalNy; jy++) {
         for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
+          const BoutReal z = mesh.GlobalZ(jz);
+          //make the gradients zero at both x-boundaries
           result(jx, jy, jz) =
-              1. + p * cos(2. * PI * x * 5) * sin(2. * PI * (z - q) * 2.);
+              0. + exp(-((60. * pow(x - p, 2)) + 1. - cos(2. * PI * (z - q))))
+              - 50.
+                    * (2. * p * exp(-60. * pow(-p, 2)) * x
+                       + (-p * exp(-60. * pow(-p, 2))
+                          - (1 - p) * exp(-60. * pow(1 - p, 2)))
+                             * pow(x, 2))
+                    * exp(-(1. - cos(2. * PI * (z - q))));
         }
       }
     }
   }
-  checkData(result);
-  return result;
-}
 
-Field3D generate_a5(const Mesh& mesh) {
-  const BoutReal nx = mesh.GlobalNx - 2 * mesh.xstart - 1;
-  const BoutReal nz = mesh.GlobalNz;
-  constexpr BoutReal p = 0.5378950; // NOLINT
-  constexpr BoutReal q = 0.2805870; // NOLINT
-  Field3D result;
-  result.allocate();
-  for (int jx = mesh.xstart; jx <= mesh.xend; jx++) {
-    const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-    for (int jy = 0; jy < mesh.LocalNy; jy++) {
-      for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-        const BoutReal z = BoutReal(jz) / nz;
-        result(jx, jy, jz) =
-            -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.);
-      }
-    }
-  }
-  if (mesh.firstX()) {
-    for (int jx = mesh.xstart - 1; jx >= 0; jx--) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) =
-              -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.);
-        }
-      }
-    }
-  }
-  if (mesh.lastX()) {
-    for (int jx = mesh.xend + 1; jx < mesh.LocalNx; jx++) {
-      const BoutReal x = BoutReal(mesh.getGlobalXIndex(jx) - mesh.xstart) / nx;
-      for (int jy = 0; jy < mesh.LocalNy; jy++) {
-        for (int jz = mesh.zstart; jz <= mesh.zend; jz++) {
-          const BoutReal z = BoutReal(jz) / nz;
-          result(jx, jy, jz) =
-              -1. + p * cos(2. * PI * x * 2.) * sin(2. * PI * (z - q) * 7.);
-        }
-      }
-    }
-  }
   checkData(result);
+  result.applyBoundary("neumann");
   return result;
 }
+} // namespace

From 6e0ac334eea7efb1568d0cf20e3eddf0cd9f1098 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 13:18:11 +0000
Subject: [PATCH 0528/1827] Reduce some duplicated loops in `LaplacePetsc` ctor

---
 .../laplace/impls/petsc/petsc_laplace.cxx     | 142 ++++++------------
 1 file changed, 43 insertions(+), 99 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index c6a6712f4d..d9076dc6a5 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -132,6 +132,9 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   MatSetSizes(MatA, localN, localN, size, size);
   MatSetFromOptions(MatA);
 
+  const bool first_x = localmesh->firstX();
+  const bool last_x = localmesh->lastX();
+
   /* Pre allocate memory
    * nnz denotes an array containing the number of non-zeros in the various rows
    * for
@@ -139,109 +142,49 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
    * o_nnz - The off-diagonal terms in the matrix (needed when running in
    *         parallel)
    */
-  PetscInt *d_nnz, *o_nnz;
+  PetscInt *d_nnz = nullptr;
+  PetscInt *o_nnz = nullptr;
   PetscMalloc((localN) * sizeof(PetscInt), &d_nnz);
   PetscMalloc((localN) * sizeof(PetscInt), &o_nnz);
   if (fourth_order) {
-    // first and last 2*localmesh-LocalNz entries are the edge x-values that (may) have 'off-diagonal' components (i.e. on another processor)
-    if (localmesh->firstX() && localmesh->lastX()) {
-      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
-        d_nnz[i] = 15;
-        d_nnz[localN - 1 - i] = 15;
-        o_nnz[i] = 0;
-        o_nnz[localN - 1 - i] = 0;
-      }
-      for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) {
-        d_nnz[i] = 20;
-        d_nnz[localN - 1 - i] = 20;
-        o_nnz[i] = 0;
-        o_nnz[localN - 1 - i] = 0;
-      }
-    } else if (localmesh->firstX()) {
-      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
-        d_nnz[i] = 15;
-        d_nnz[localN - 1 - i] = 15;
-        o_nnz[i] = 0;
-        o_nnz[localN - 1 - i] = 10;
-      }
-      for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) {
-        d_nnz[i] = 20;
-        d_nnz[localN - 1 - i] = 20;
-        o_nnz[i] = 0;
-        o_nnz[localN - 1 - i] = 5;
-      }
-    } else if (localmesh->lastX()) {
-      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
-        d_nnz[i] = 15;
-        d_nnz[localN - 1 - i] = 15;
-        o_nnz[i] = 10;
-        o_nnz[localN - 1 - i] = 0;
-      }
-      for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) {
-        d_nnz[i] = 20;
-        d_nnz[localN - 1 - i] = 20;
-        o_nnz[i] = 5;
-        o_nnz[localN - 1 - i] = 0;
-      }
-    } else {
-      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
-        d_nnz[i] = 15;
-        d_nnz[localN - 1 - i] = 15;
-        o_nnz[i] = 10;
-        o_nnz[localN - 1 - i] = 10;
-      }
-      for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) {
-        d_nnz[i] = 20;
-        d_nnz[localN - 1 - i] = 20;
-        o_nnz[i] = 5;
-        o_nnz[localN - 1 - i] = 5;
-      }
+    // first and last 2*localmesh-LocalNz entries are the edge x-values that
+    // (may) have 'off-diagonal' components (i.e. on another processor)
+
+    const int first_first_off = first_x ? 0 : 10;
+    const int first_last_off = last_x ? 0 : 10;
+    const int second_first_off = first_x ? 0 : 5;
+    const int second_last_off = last_x ? 0 : 5;
+
+    for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
+      d_nnz[i] = 15;
+      d_nnz[localN - 1 - i] = 15;
+      o_nnz[i] = first_first_off;
+      o_nnz[localN - 1 - i] = first_last_off;
+    }
+    for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) {
+      d_nnz[i] = 20;
+      d_nnz[localN - 1 - i] = 20;
+      o_nnz[i] = second_first_off;
+      o_nnz[localN - 1 - i] = second_last_off;
     }
 
-    for (int i = 2 * (localmesh->LocalNz); i < localN - 2 * ((localmesh->LocalNz)); i++) {
+    for (int i = 2 * (localmesh->LocalNz); i < localN - (2 * localmesh->LocalNz); i++) {
       d_nnz[i] = 25;
       d_nnz[localN - 1 - i] = 25;
       o_nnz[i] = 0;
       o_nnz[localN - 1 - i] = 0;
     }
-
-    // Use d_nnz and o_nnz for preallocating the matrix
-    if (localmesh->firstX() && localmesh->lastX()) {
-      // Only one processor in X
-      MatSeqAIJSetPreallocation(MatA, 0, d_nnz);
-    } else {
-      MatMPIAIJSetPreallocation(MatA, 0, d_nnz, 0, o_nnz);
-    }
   } else {
-    // first and last localmesh->LocalNz entries are the edge x-values that (may) have 'off-diagonal' components (i.e. on another processor)
-    if (localmesh->firstX() && localmesh->lastX()) {
-      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
-        d_nnz[i] = 6;
-        d_nnz[localN - 1 - i] = 6;
-        o_nnz[i] = 0;
-        o_nnz[localN - 1 - i] = 0;
-      }
-    } else if (localmesh->firstX()) {
-      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
-        d_nnz[i] = 6;
-        d_nnz[localN - 1 - i] = 6;
-        o_nnz[i] = 0;
-        o_nnz[localN - 1 - i] = 3;
-      }
-    } else if (localmesh->lastX()) {
-      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
-        d_nnz[i] = 6;
-        d_nnz[localN - 1 - i] = 6;
-        o_nnz[i] = 3;
-        o_nnz[localN - 1 - i] = 0;
-      }
-    } else {
-      for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
-        d_nnz[i] = 6;
-        d_nnz[localN - 1 - i] = 6;
-        o_nnz[i] = 3;
-        o_nnz[localN - 1 - i] = 3;
-      }
+    // first and last localmesh->LocalNz entries are the edge x-values that
+    // (may) have 'off-diagonal' components (i.e. on another processor)
+    const int first_off = first_x ? 0 : 3;
+    const int last_off = last_x ? 0 : 3;
+
+    for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
+      d_nnz[i] = 6;
+      d_nnz[localN - 1 - i] = 6;
+      o_nnz[i] = first_off;
+      o_nnz[localN - 1 - i] = last_off;
     }
 
     for (int i = localmesh->LocalNz; i < localN - (localmesh->LocalNz); i++) {
@@ -250,14 +193,15 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
       o_nnz[i] = 0;
       o_nnz[localN - 1 - i] = 0;
     }
-
-    // Use d_nnz and o_nnz for preallocating the matrix
-    if (localmesh->firstX() && localmesh->lastX()) {
-      MatSeqAIJSetPreallocation(MatA, 0, d_nnz);
-    } else {
-      MatMPIAIJSetPreallocation(MatA, 0, d_nnz, 0, o_nnz);
-    }
   }
+  // Use d_nnz and o_nnz for preallocating the matrix
+  if (localmesh->firstX() && localmesh->lastX()) {
+    // Only one processor in X
+    MatSeqAIJSetPreallocation(MatA, 0, d_nnz);
+  } else {
+    MatMPIAIJSetPreallocation(MatA, 0, d_nnz, 0, o_nnz);
+  }
+
   // Free the d_nnz and o_nnz arrays, as these are will not be used anymore
   PetscFree(d_nnz);
   PetscFree(o_nnz);

From a5e3f366a79bec2ee1dc3dc8744d818b177c0790 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 13:45:33 +0000
Subject: [PATCH 0529/1827] Use `std::vector` instead of `PetscMalloc`

---
 .../laplace/impls/petsc/petsc_laplace.cxx     | 31 ++++++++-----------
 1 file changed, 13 insertions(+), 18 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index d9076dc6a5..1f422ad19d 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -38,6 +38,8 @@
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 
+#include <vector>
+
 #define KSP_RICHARDSON "richardson"
 #define KSP_CHEBYSHEV "chebyshev"
 #define KSP_CG "cg"
@@ -134,18 +136,14 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
 
   const bool first_x = localmesh->firstX();
   const bool last_x = localmesh->lastX();
+  // Pre allocate memory. See MatMPIAIJSetPreallocation docs for more info
+  // Number of non-zero elements in each row of matrix owned by this processor
+  // ("diagonal submatrices")
+  std::vector<PetscInt> d_nnz(localN, 0);
+  // Number of non-zero elements in each row of matrix owned by other processors
+  // ("offdiagonal submatrices")
+  std::vector<PetscInt> o_nnz(localN, 0);
 
-  /* Pre allocate memory
-   * nnz denotes an array containing the number of non-zeros in the various rows
-   * for
-   * d_nnz - The diagonal terms in the matrix
-   * o_nnz - The off-diagonal terms in the matrix (needed when running in
-   *         parallel)
-   */
-  PetscInt *d_nnz = nullptr;
-  PetscInt *o_nnz = nullptr;
-  PetscMalloc((localN) * sizeof(PetscInt), &d_nnz);
-  PetscMalloc((localN) * sizeof(PetscInt), &o_nnz);
   if (fourth_order) {
     // first and last 2*localmesh-LocalNz entries are the edge x-values that
     // (may) have 'off-diagonal' components (i.e. on another processor)
@@ -194,17 +192,14 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
       o_nnz[localN - 1 - i] = 0;
     }
   }
-  // Use d_nnz and o_nnz for preallocating the matrix
-  if (localmesh->firstX() && localmesh->lastX()) {
+
+  if (first_x and last_x) {
     // Only one processor in X
-    MatSeqAIJSetPreallocation(MatA, 0, d_nnz);
+    MatSeqAIJSetPreallocation(MatA, 0, d_nnz.data());
   } else {
-    MatMPIAIJSetPreallocation(MatA, 0, d_nnz, 0, o_nnz);
+    MatMPIAIJSetPreallocation(MatA, 0, d_nnz.data(), 0, o_nnz.data());
   }
 
-  // Free the d_nnz and o_nnz arrays, as these are will not be used anymore
-  PetscFree(d_nnz);
-  PetscFree(o_nnz);
   // Sets up the internal matrix data structures for the later use.
   MatSetUp(MatA);
 

From 0aa79db9bbe334c1c17f5451260612a0bd6c2612 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 13:51:24 +0000
Subject: [PATCH 0530/1827] Set member variables in `LaplacePetsc` initialiser

---
 .clang-tidy                                   |   2 +-
 .../laplace/impls/petsc/petsc_laplace.cxx     | 102 +++++++-----------
 .../laplace/impls/petsc/petsc_laplace.hxx     |  18 ++--
 3 files changed, 52 insertions(+), 70 deletions(-)

diff --git a/.clang-tidy b/.clang-tidy
index cf29b759cd..121c3f3a60 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -20,7 +20,7 @@ CheckOptions:
     value: 'MPI_Comm'
 
   - key: misc-include-cleaner.IgnoreHeaders
-    value: 'adios2/.*;bits/.*;cpptrace/.*'
+    value: 'adios2/.*;bits/.*;cpptrace/.*;petsc.*\.h'
 ---
 
 Disabled checks and reasons:
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 1f422ad19d..878d18b4f3 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -31,7 +31,10 @@
 #include "petsc_laplace.hxx"
 
 #include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
+#include <bout/boutexception.hxx>
+#include <bout/globals.hxx>
 #include <bout/mesh.hxx>
 #include <bout/output.hxx>
 #include <bout/petsclib.hxx>
@@ -53,21 +56,43 @@
 #define KSP_BICG "bicg"
 #define KSP_PREONLY "preonly"
 
-static PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) {
+namespace {
+PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) {
   PetscFunctionBegin; // NOLINT
 
   LaplacePetsc* laplace = nullptr;
-  const int ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&laplace)); // NOLINT
-  CHKERRQ(ierr);
+  CHKERRQ(PCShellGetContext(pc, reinterpret_cast<void**>(&laplace))); // NOLINT
 
   PetscFunctionReturn(laplace->precon(x, y)); // NOLINT
 }
+} // namespace
 
 LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
-                           Solver* UNUSED(solver))
+                           [[maybe_unused]] Solver* solver)
     : Laplacian(opt, loc, mesh_in), A(0.0), C1(1.0), C2(1.0), D(1.0), Ex(0.0), Ez(0.0),
-      issetD(false), issetC(false), issetE(false),
-      lib(opt == nullptr ? &(Options::root()["laplace"]) : opt) {
+      issetD(false), issetC(false), issetE(false), comm(localmesh->getXcomm()),
+      opts(opt == nullptr ? &(Options::root()["laplace"]) : opt),
+      // WARNING: only a few of these options actually make sense: see the
+      // PETSc documentation to work out which they are (possibly
+      // pbjacobi, sor might be useful choices?)
+      ksptype((*opts)["ksptype"].doc("KSP solver type").withDefault(KSPGMRES)),
+      pctype((*opts)["pctype"]
+                 .doc("Preconditioner type. See the PETSc documentation for options")
+                 .withDefault("none")),
+      richardson_damping_factor((*opts)["richardson_damping_factor"].withDefault(1.0)),
+      chebyshev_max((*opts)["chebyshev_max"].withDefault(100)),
+      chebyshev_min((*opts)["chebyshev_min"].withDefault(0.01)),
+      gmres_max_steps((*opts)["gmres_max_steps"].withDefault(30)),
+      rtol((*opts)["rtol"].doc("Relative tolerance for KSP solver").withDefault(1e-5)),
+      atol((*opts)["atol"].doc("Absolute tolerance for KSP solver").withDefault(1e-50)),
+      dtol((*opts)["dtol"].doc("Divergence tolerance for KSP solver").withDefault(1e5)),
+      maxits(
+          (*opts)["maxits"].doc("Maximum number of KSP iterations").withDefault(100000)),
+      direct((*opts)["direct"].doc("Use direct (LU) solver?").withDefault(false)),
+      fourth_order(
+          (*opts)["fourth_order"].doc("Use fourth order stencil").withDefault(false)),
+      lib(opts) {
+
   A.setLocation(location);
   C1.setLocation(location);
   C2.setLocation(location);
@@ -75,13 +100,6 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   Ex.setLocation(location);
   Ez.setLocation(location);
 
-  // Get Options in Laplace Section
-  if (!opt) {
-    opts = Options::getRoot()->getSection("laplace");
-  } else {
-    opts = opt;
-  }
-
 #if CHECK > 0
   // Checking flags are set to something which is not implemented
   checkFlags();
@@ -93,24 +111,23 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   }
 #endif
 
-  // Get communicator for group of processors in X - all points in z-x plane for fixed y.
-  comm = localmesh->getXcomm();
+  const bool first_x = localmesh->firstX();
+  const bool last_x = localmesh->lastX();
 
   // Need to determine local size to use based on prior parallelisation
   // Coefficient values are stored only on local processors.
   localN = (localmesh->xend - localmesh->xstart + 1) * (localmesh->LocalNz);
-  if (localmesh->firstX()) {
-    localN +=
-        localmesh->xstart
-        * (localmesh->LocalNz); // If on first processor add on width of boundary region
+  if (first_x) {
+    // If on first processor add on width of boundary region
+    localN += localmesh->xstart * (localmesh->LocalNz);
   }
-  if (localmesh->lastX()) {
-    localN +=
-        localmesh->xstart
-        * (localmesh->LocalNz); // If on last processor add on width of boundary region
+  if (last_x) {
+    // If on last processor add on width of boundary region
+    localN += localmesh->xstart * (localmesh->LocalNz);
   }
 
   // Calculate 'size' (the total number of points in physical grid)
+  size = localN;
   if (bout::globals::mpi->MPI_Allreduce(&localN, &size, 1, MPI_INT, MPI_SUM, comm)
       != MPI_SUCCESS) {
     throw BoutException("Error in MPI_Allreduce during LaplacePetsc initialisation");
@@ -126,16 +143,11 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   VecSetFromOptions(xs);
   VecDuplicate(xs, &bs);
 
-  // Get 4th order solver switch
-  opts->get("fourth_order", fourth_order, false);
-
   // Set size of (the PETSc) Matrix on each processor to localN x localN
   MatCreate(comm, &MatA);
   MatSetSizes(MatA, localN, localN, size, size);
   MatSetFromOptions(MatA);
 
-  const bool first_x = localmesh->firstX();
-  const bool last_x = localmesh->lastX();
   // Pre allocate memory. See MatMPIAIJSetPreallocation docs for more info
   // Number of non-zero elements in each row of matrix owned by this processor
   // ("diagonal submatrices")
@@ -206,53 +218,21 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   // Declare KSP Context (abstract PETSc object that manages all Krylov methods)
   KSPCreate(comm, &ksp);
 
-  // Get KSP Solver Type (Generalizes Minimal RESidual is the default)
-  ksptype = (*opts)["ksptype"].doc("KSP solver type").withDefault(KSP_GMRES);
-
-  // Get preconditioner type
-  // WARNING: only a few of these options actually make sense: see the
-  // PETSc documentation to work out which they are (possibly
-  // pbjacobi, sor might be useful choices?)
-  pctype = (*opts)["pctype"]
-               .doc("Preconditioner type. See the PETSc documentation for options")
-               .withDefault("none");
-
   // Let "user" be a synonym for "shell"
   if (pctype == "user") {
     pctype = PCSHELL;
   }
 
-  // Get Options specific to particular solver types
-  opts->get("richardson_damping_factor", richardson_damping_factor, 1.0, true);
-  opts->get("chebyshev_max", chebyshev_max, 100, true);
-  opts->get("chebyshev_min", chebyshev_min, 0.01, true);
-  opts->get("gmres_max_steps", gmres_max_steps, 30, true);
-
-  // Get Tolerances for KSP solver
-  rtol = (*opts)["rtol"].doc("Relative tolerance for KSP solver").withDefault(1e-5);
-  atol = (*opts)["atol"].doc("Absolute tolerance for KSP solver").withDefault(1e-50);
-  dtol = (*opts)["dtol"].doc("Divergence tolerance for KSP solver").withDefault(1e5);
-  maxits = (*opts)["maxits"].doc("Maximum number of KSP iterations").withDefault(100000);
-
-  // Get direct solver switch
-  direct = (*opts)["direct"].doc("Use direct (LU) solver?").withDefault(false);
   if (direct) {
-    output << endl
-           << "Using LU decompostion for direct solution of system" << endl
-           << endl;
+    output.write("\nUsing LU decompostion for direct solution of system\n");
   }
 
   if (pctype == PCSHELL) {
-
     rightprec = (*opts)["rightprec"].doc("Right preconditioning?").withDefault(true);
 
     // Options for preconditioner are in a subsection
     pcsolve = Laplacian::create(opts->getSection("precon"));
   }
-
-  // Ensure that the matrix is constructed first time
-  //   coefchanged = true;
-  //  lastflag = -1;
 }
 
 FieldPerp LaplacePetsc::solve(const FieldPerp& b) { return solve(b, b); }
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.hxx b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
index 1d56abd00b..611bfd6fa1 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.hxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
@@ -220,17 +220,19 @@ private:
 
   FieldPerp sol; // solution Field
 
-  // Istart is the first row of MatA owned by the process, Iend is 1 greater than the last row.
-  int Istart, Iend;
+  /// Istart is the first row of MatA owned by the process, Iend is 1 greater than the last row.
+  int Istart = -1;
+  int Iend = -1;
 
-  int meshx, meshz, size,
-      localN; // Mesh sizes, total size, no of points on this processor
+  /// Mesh sizes, total size, no of points on this processor
+  int meshx, meshz, size, localN;
   MPI_Comm comm;
-  Mat MatA;
-  Vec xs, bs; // Solution and RHS vectors
-  KSP ksp;
+  Mat MatA = nullptr; ///< Stencil matrix
+  Vec xs = nullptr;   ///< Solution vector
+  Vec bs = nullptr;   ///< RHS vector
+  KSP ksp = nullptr;  ///< PETSc solver
 
-  Options* opts;       // Laplace Section Options Object
+  Options* opts;       ///< Laplace Section Options Object
   std::string ksptype; ///< KSP solver type
   std::string pctype;  ///< Preconditioner type
 

From 3d34d0cafc5b296734c863237255afa78bab0617 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 14:02:04 +0000
Subject: [PATCH 0531/1827] Prepare `LaplacePetsc` for Z guards

---
 .../laplace/impls/petsc/petsc_laplace.cxx     | 33 +++++++++++--------
 1 file changed, 19 insertions(+), 14 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 878d18b4f3..673f9c0df5 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -116,14 +116,15 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
 
   // Need to determine local size to use based on prior parallelisation
   // Coefficient values are stored only on local processors.
-  localN = (localmesh->xend - localmesh->xstart + 1) * (localmesh->LocalNz);
+  const auto local_nz = localmesh->zend - localmesh->zstart + 1;
+  localN = (localmesh->xend - localmesh->xstart + 1) * local_nz;
   if (first_x) {
     // If on first processor add on width of boundary region
-    localN += localmesh->xstart * (localmesh->LocalNz);
+    localN += localmesh->xstart * local_nz;
   }
   if (last_x) {
     // If on last processor add on width of boundary region
-    localN += localmesh->xstart * (localmesh->LocalNz);
+    localN += localmesh->xstart * local_nz;
   }
 
   // Calculate 'size' (the total number of points in physical grid)
@@ -134,7 +135,7 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   }
 
   // Calculate total (physical) grid dimensions
-  meshz = localmesh->LocalNz;
+  meshz = local_nz;
   meshx = size / meshz;
 
   // Create PETSc type of vectors for the solution and the RHS vector
@@ -165,39 +166,39 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
     const int second_first_off = first_x ? 0 : 5;
     const int second_last_off = last_x ? 0 : 5;
 
-    for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
+    for (int i = 0; i <= local_nz; i++) {
       d_nnz[i] = 15;
       d_nnz[localN - 1 - i] = 15;
       o_nnz[i] = first_first_off;
       o_nnz[localN - 1 - i] = first_last_off;
     }
-    for (int i = (localmesh->LocalNz); i < 2 * (localmesh->LocalNz); i++) {
+    for (int i = local_nz; i < 2 * local_nz; i++) {
       d_nnz[i] = 20;
       d_nnz[localN - 1 - i] = 20;
       o_nnz[i] = second_first_off;
       o_nnz[localN - 1 - i] = second_last_off;
     }
 
-    for (int i = 2 * (localmesh->LocalNz); i < localN - (2 * localmesh->LocalNz); i++) {
+    for (int i = 2 * local_nz; i < localN - (2 * local_nz); i++) {
       d_nnz[i] = 25;
       d_nnz[localN - 1 - i] = 25;
       o_nnz[i] = 0;
       o_nnz[localN - 1 - i] = 0;
     }
   } else {
-    // first and last localmesh->LocalNz entries are the edge x-values that
+    // first and last local_nz entries are the edge x-values that
     // (may) have 'off-diagonal' components (i.e. on another processor)
     const int first_off = first_x ? 0 : 3;
     const int last_off = last_x ? 0 : 3;
 
-    for (int i = localmesh->zstart; i <= localmesh->zend; i++) {
+    for (int i = 0; i <= local_nz; i++) {
       d_nnz[i] = 6;
       d_nnz[localN - 1 - i] = 6;
       o_nnz[i] = first_off;
       o_nnz[localN - 1 - i] = last_off;
     }
 
-    for (int i = localmesh->LocalNz; i < localN - (localmesh->LocalNz); i++) {
+    for (int i = local_nz; i < localN - local_nz; i++) {
       d_nnz[i] = 9;
       d_nnz[localN - 1 - i] = 9;
       o_nnz[i] = 0;
@@ -639,7 +640,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
     }
 
     if (i != Iend) {
-      throw BoutException("Petsc index sanity check failed");
+      throw BoutException("Petsc index sanity check failed: i={} != Iend={}", i, Iend);
     }
 
     // Assemble Matrix
@@ -809,9 +810,13 @@ void LaplacePetsc::Element(int i, int x, int z, int xshift, int zshift, PetscSca
   // Need to convert LOCAL x to GLOBAL x in order to correctly calculate
   // PETSC Matrix Index.
   int xoffset = Istart / meshz;
-  if (Istart % meshz != 0) {
-    throw BoutException("Petsc index sanity check 3 failed");
+#if CHECK > 2
+  const int rem = Istart % meshz;
+  if (rem != 0) {
+    throw BoutException("Petsc index sanity check 3 failed: Istart={} % meshz={} == {}",
+                        Istart, meshz, rem);
   }
+#endif
 
   // Calculate the row to be set
   int row_new = x + xshift; // should never be out of range.
@@ -820,7 +825,7 @@ void LaplacePetsc::Element(int i, int x, int z, int xshift, int zshift, PetscSca
   }
 
   // Calculate the column to be set
-  int col_new = z + zshift;
+  int col_new = z + zshift - localmesh->zstart;
   if (col_new < 0) {
     col_new += meshz;
   } else if (col_new > meshz - 1) {

From df99cdba5963dd293ff0cfb892630e856db938ea Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 14:53:28 +0000
Subject: [PATCH 0532/1827] Apply clang-tidy fixes

---
 .../test-petsc_laplace/test_petsc_laplace.cxx | 48 +++++++++----------
 1 file changed, 23 insertions(+), 25 deletions(-)

diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
index 96e7994637..902156f4c0 100644
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
@@ -32,6 +32,7 @@
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
+#include "bout/globals.hxx"
 #include "bout/invert_laplace.hxx"
 #include "bout/options.hxx"
 #include "bout/options_io.hxx"
@@ -106,7 +107,7 @@ Field3D forward_laplace(const Field3D& field, const T& acoef, const T& ccoef,
 Field3D generate_f1(const Mesh& mesh);
 
 Field3D generate_d1(Mesh& mesh) {
-  Options options{{"p_d1", 0.512547}, {"q_d1", 0.30908712}};
+  const Options options{{"p_d1", 0.512547}, {"q_d1", 0.30908712}};
 
   return FieldFactory::get()->create3D(
       "1. + (0.2 * exp(-50. * (x - p_d1)^2 / 4.) * sin((z - 2. * pi * q_d1) * 3.))",
@@ -114,7 +115,7 @@ Field3D generate_d1(Mesh& mesh) {
 }
 
 Field3D generate_c1(Mesh& mesh) {
-  Options options{{"p_c1", 0.18439023}, {"q_c1", 0.401089473}};
+  const Options options{{"p_c1", 0.18439023}, {"q_c1", 0.401089473}};
 
   return FieldFactory::get()->create3D(
       "1. + (0.15 * exp(-50. * (x - p_c1)^2 * 2.) * sin((z - 2. * pi * q_c1) * 2.))",
@@ -122,7 +123,7 @@ Field3D generate_c1(Mesh& mesh) {
 }
 
 Field3D generate_a1(Mesh& mesh) {
-  Options options{{"p_a1", 0.612547}, {"q_a1", 0.30908712}};
+  const Options options{{"p_a1", 0.612547}, {"q_a1", 0.30908712}};
 
   return FieldFactory::get()->create3D(
       "-1. + (0.1 * exp(-50. * (x - p_a1)^2 * 2.5) * sin((z - 2. * pi * q_a1) * 7.))",
@@ -130,7 +131,7 @@ Field3D generate_a1(Mesh& mesh) {
 }
 
 Field3D generate_f5(Mesh& mesh) {
-  Options options{{"p_f5", 0.623901}, {"q_f5", 0.01209489}};
+  const Options options{{"p_f5", 0.623901}, {"q_f5", 0.01209489}};
 
   auto result = FieldFactory::get()->create3D(
       "exp(-((50. * (x - p_f5)^2) + 1. - cos((z - 2. * pi * q_f5))))"
@@ -145,14 +146,14 @@ Field3D generate_f5(Mesh& mesh) {
 }
 
 Field3D generate_d5(Mesh& mesh) {
-  Options options{{"p_d5", 0.63298589}, {"q_d5", 0.889237890}};
+  const Options options{{"p_d5", 0.63298589}, {"q_d5", 0.889237890}};
 
   return FieldFactory::get()->create3D(
       "1. + (p_d5 * cos(2. * pi * x) * sin((z - 2 * pi * q_d5) * 3.))", &options, &mesh);
 }
 
 Field3D generate_c5(Mesh& mesh) {
-  Options options{{"p_c5", 0.160983834}, {"q_c5", 0.73050121087}};
+  const Options options{{"p_c5", 0.160983834}, {"q_c5", 0.73050121087}};
 
   return FieldFactory::get()->create3D(
       "1. + (p_c5 * cos(2. * pi * x * 5) * sin((z - 2 * pi * q_c5) * 2.))", &options,
@@ -160,7 +161,7 @@ Field3D generate_c5(Mesh& mesh) {
 }
 
 Field3D generate_a5(Mesh& mesh) {
-  Options options{{"p_a5", 0.5378950}, {"q_a5", 0.2805870}};
+  const Options options{{"p_a5", 0.5378950}, {"q_a5", 0.2805870}};
 
   return FieldFactory::get()->create3D(
       "-1. + (p_a5 * cos(2. * pi * x * 2.) * sin((z - 2. * pi * q_a5) * 7.))", &options,
@@ -362,12 +363,11 @@ Field3D generate_f1(const Mesh& mesh) {
         //make the gradients zero at both x-boundaries
         result(jx, jy, jz) =
             0. + exp(-((100. * pow(x - p, 2)) + 1. - cos(2. * PI * (z - q))))
-            - 50.
-                  * (2. * p * exp(-100. * pow(-p, 2)) * x
-                     + (-p * exp(-100. * pow(-p, 2))
-                        - (1 - p) * exp(-100. * pow(1 - p, 2)))
-                           * pow(x, 2))
-                  * exp(-(1. - cos(2. * PI * (z - q))));
+            - (50.
+               * (2. * p * exp(-100. * pow(-p, 2)) * x
+                  + (-p * exp(-100. * pow(-p, 2)) - (1 - p) * exp(-100. * pow(1 - p, 2)))
+                        * pow(x, 2))
+               * exp(-(1. - cos(2. * PI * (z - q)))));
       }
     }
   }
@@ -380,12 +380,11 @@ Field3D generate_f1(const Mesh& mesh) {
           //make the gradients zero at both x-boundaries
           result(jx, jy, jz) =
               0. + exp(-((60. * pow(x - p, 2)) + 1. - cos(2. * PI * (z - q))))
-              - 50.
-                    * (2. * p * exp(-60. * pow(-p, 2)) * x
-                       + (-p * exp(-60. * pow(-p, 2))
-                          - (1 - p) * exp(-60. * pow(1 - p, 2)))
-                             * pow(x, 2))
-                    * exp(-(1. - cos(2. * PI * (z - q))));
+              - (50.
+                 * (2. * p * exp(-60. * pow(-p, 2)) * x
+                    + (-p * exp(-60. * pow(-p, 2)) - (1 - p) * exp(-60. * pow(1 - p, 2)))
+                          * pow(x, 2))
+                 * exp(-(1. - cos(2. * PI * (z - q)))));
         }
       }
     }
@@ -399,12 +398,11 @@ Field3D generate_f1(const Mesh& mesh) {
           //make the gradients zero at both x-boundaries
           result(jx, jy, jz) =
               0. + exp(-((60. * pow(x - p, 2)) + 1. - cos(2. * PI * (z - q))))
-              - 50.
-                    * (2. * p * exp(-60. * pow(-p, 2)) * x
-                       + (-p * exp(-60. * pow(-p, 2))
-                          - (1 - p) * exp(-60. * pow(1 - p, 2)))
-                             * pow(x, 2))
-                    * exp(-(1. - cos(2. * PI * (z - q))));
+              - (50.
+                 * (2. * p * exp(-60. * pow(-p, 2)) * x
+                    + (-p * exp(-60. * pow(-p, 2)) - (1 - p) * exp(-60. * pow(1 - p, 2)))
+                          * pow(x, 2))
+                 * exp(-(1. - cos(2. * PI * (z - q)))));
         }
       }
     }

From 3ca3e689f2fedb8b4979998849904890258e6405 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 15:01:51 +0000
Subject: [PATCH 0533/1827] Try `sor` preconditioner for 3D metrics in
 test-petsc-laplace

---
 tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
index 902156f4c0..d4f375e1d7 100644
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
@@ -186,7 +186,7 @@ int main(int argc, char** argv) {
 #endif
 
     // Preconditioner to use for 3D metrics
-    constexpr auto petsc_pc = petsc_has_mumps ? "mumps" : "lu";
+    constexpr auto petsc_pc = petsc_has_mumps ? "mumps" : "sor";
 
     auto& options_2nd = Options::root()["petsc2nd"];
     if constexpr (bout::build::use_metric_3d) {

From 63af212ca1d2bec365c11f74f0825770f15823e3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 25 Feb 2026 10:19:57 +0100
Subject: [PATCH 0534/1827] Remove v prefix from version for wheels

---
 tools/pylib/_boutpp_build/backend.py | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 9e305b3048..922ef1c48c 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -33,7 +33,7 @@ def getversion():
         with contextlib.suppress(KeyError):
             # 0. Check whether version is set via environment variable
             version = os.environ["BOUT_PRETEND_VERSION"]
-            return version
+            return version.lstrip("v")
 
         _bout_previous_version = "v5.2.0"
         _bout_next_version = "v5.2.1"
@@ -74,7 +74,7 @@ def getversion():
                 version = _bout_previous_version + ".rc+" + hash
                 with open("_version.txt", "w") as f:
                     f.write(version + "\n")
-    return version
+    return version.lstrip("v")
 
 
 def run(cmd):
@@ -212,10 +212,12 @@ def build_sdist(sdist_directory, config_settings=None):
         run(f"rm {tmp}")
 
     with open(tmp, "w") as f:
-        f.write(f"""Metadata-Version: 2.1
+        f.write(
+            f"""Metadata-Version: 2.1
 Name: {pkgname}
 Version: {getversion()}
-""")
+"""
+        )
         with open("LICENSE") as src:
             pre = "License: "
             for l in src:
@@ -267,19 +269,23 @@ def prepare_metadata_for_build_wheel(
     distinfo = f"{metadata_directory}/{thisdir}"
     mkdir_p(distinfo)
     with open(f"{distinfo}/METADATA", "w") as f:
-        f.write(f"""Metadata-Version: 2.1
+        f.write(
+            f"""Metadata-Version: 2.1
 Name: {pkgname}
 Version: {getversion()}
 License-File: COPYING
-""")
+"""
+        )
     run(f"cp LICENSE {distinfo}/COPYING")
     run(f"cp LICENSE.GPL {distinfo}/COPYING.GPL")
     with open(f"{distinfo}/WHEEL", "w") as f:
-        f.write(f"""Wheel-Version: 1.0
-Generator: boutpp_custom_build_wheel ({getversion()})
+        f.write(
+            f"""Wheel-Version: 1.0
+Generator: boutpp_custom_build_wheel (version {getversion()})
 Root-Is-Purelib: false
 Tag: {gettag()}
-""")
+"""
+        )
 
     if record:
         with open(f"{distinfo}/RECORD", "w") as f:

From 6007eeddc6ab7ae0dcc5325a105a4e3aa54c278b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:00:34 +0100
Subject: [PATCH 0535/1827] Use fmt::runtime

Otherwise fmt tries to do compile-time checks, but fails as it cannot be
checked at compile time.
https://github.com/fmtlib/fmt/issues/4179
---
 include/bout/boutexception.hxx        |  6 +--
 include/bout/msg_stack.hxx            |  6 +--
 include/bout/optionsreader.hxx        |  4 +-
 include/bout/output.hxx               | 15 ++++---
 include/bout/sys/expressionparser.hxx |  2 +-
 src/bout++.cxx                        |  2 +-
 src/mesh/impls/bout/boutmesh.cxx      | 59 +++++++++++++++------------
 src/sys/expressionparser.cxx          | 10 +++--
 src/sys/options.cxx                   | 15 ++++---
 src/sys/options/options_ini.cxx       |  2 +-
 tests/unit/sys/test_options.cxx       | 22 +++++-----
 11 files changed, 81 insertions(+), 62 deletions(-)

diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx
index 565eb6b46d..d525aeb608 100644
--- a/include/bout/boutexception.hxx
+++ b/include/bout/boutexception.hxx
@@ -21,7 +21,7 @@ public:
 
   template <class S, class... Args>
   BoutException(S&& format, Args&&... args)
-      : BoutException(fmt::format(std::forward<S>(format),
+      : BoutException(fmt::format(fmt::runtime(std::forward<S>(format)),
                                   std::forward<decltype(args)>(args)...)) {}
 
   ~BoutException() override;
@@ -46,7 +46,7 @@ public:
   BoutRhsFail(std::string message) : BoutException(std::move(message)) {}
   template <class S, class... Args>
   BoutRhsFail(S&& format, Args&&... args)
-      : BoutRhsFail(fmt::format(std::forward<S>(format),
+      : BoutRhsFail(fmt::format(fmt::runtime(std::forward<S>(format)),
                                 std::forward<decltype(args)>(args)...)) {}
 };
 
@@ -55,7 +55,7 @@ public:
   BoutIterationFail(std::string message) : BoutException(std::move(message)) {}
   template <class S, class... Args>
   BoutIterationFail(S&& format, Args&&... args)
-      : BoutIterationFail(fmt::format(std::forward<S>(format),
+      : BoutIterationFail(fmt::format(fmt::runtime(std::forward<S>(format)),
                                       std::forward<decltype(args)>(args)...)) {}
 };
 
diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx
index 1abb26d2c7..8771aeab42 100644
--- a/include/bout/msg_stack.hxx
+++ b/include/bout/msg_stack.hxx
@@ -62,7 +62,7 @@ public:
 
   template <class S, class... Args>
   int push(const S& format, const Args&... args) {
-    return push(fmt::format(format, args...));
+    return push(fmt::format(fmt::runtime(format), args...));
   }
 
   void pop();       ///< Remove the last message
@@ -134,8 +134,8 @@ public:
 
   template <class S, class... Args>
   MsgStackItem(const std::string& file, int line, const S& msg, const Args&... args)
-      : point(msg_stack.push("{:s} on line {:d} of '{:s}'", fmt::format(msg, args...),
-                             line, file)) {}
+      : point(msg_stack.push("{:s} on line {:d} of '{:s}'",
+                             fmt::format(fmt::runtime(msg), args...), line, file)) {}
   ~MsgStackItem() {
     // If an exception has occurred, don't pop the message
     if (exception_count == std::uncaught_exceptions()) {
diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx
index de3d40514d..0c9c227916 100644
--- a/include/bout/optionsreader.hxx
+++ b/include/bout/optionsreader.hxx
@@ -71,7 +71,7 @@ public:
 
   template <class S, class... Args>
   void read(Options* options, const S& format, const Args&... args) {
-    return read(options, fmt::format(format, args...));
+    return read(options, fmt::format(fmt::runtime(format), args...));
   }
 
   /// Write options to file
@@ -82,7 +82,7 @@ public:
 
   template <class S, class... Args>
   void write(Options* options, const S& format, const Args&... args) {
-    return write(options, fmt::format(format, args...));
+    return write(options, fmt::format(fmt::runtime(format), args...));
   }
 
   /// Parse options from the command line
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index 34b4f19376..4eb1d615ca 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -83,7 +83,8 @@ public:
 
   template <class S, class... Args>
   Output(const S& format, Args&&... args)
-      : Output(fmt::format(format, std::forward<decltype(args)>(args)...)) {}
+      : Output(fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...)) {
+  }
 
   ~Output() override { close(); }
 
@@ -95,7 +96,7 @@ public:
 
   template <class S, class... Args>
   int open(const S& format, Args&&... args) {
-    return open(fmt::format(format, std::forward<decltype(args)>(args)...));
+    return open(fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
   }
 
   /// Close the log file
@@ -106,14 +107,14 @@ public:
 
   template <class S, class... Args>
   void write(const S& format, Args&&... args) {
-    write(fmt::format(format, std::forward<decltype(args)>(args)...));
+    write(fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
   }
   /// Same as write, but only to screen
   virtual void print(const std::string& message);
 
   template <class S, class... Args>
   void print(const S& format, Args&&... args) {
-    print(fmt::format(format, std::forward<decltype(args)>(args)...));
+    print(fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
   }
 
   /// Add an output stream. All output will be sent to all streams
@@ -178,7 +179,8 @@ public:
   void write(const S& format, Args&&... args) {
     if (enabled) {
       ASSERT1(base != nullptr);
-      base->write(fmt::format(format, std::forward<decltype(args)>(args)...));
+      base->write(
+          fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
     }
   }
 
@@ -190,7 +192,8 @@ public:
   void print(const S& format, Args&&... args) {
     if (enabled) {
       ASSERT1(base != nullptr);
-      base->print(fmt::format(format, std::forward<decltype(args)>(args)...));
+      base->print(
+          fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
     }
   }
 
diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx
index b312ce2fb1..78525e5b69 100644
--- a/include/bout/sys/expressionparser.hxx
+++ b/include/bout/sys/expressionparser.hxx
@@ -243,7 +243,7 @@ public:
 
   template <class S, class... Args>
   ParseException(const S& format, const Args&... args)
-      : message(fmt::format(format, args...)) {}
+      : message(fmt::format(fmt::runtime(format), args...)) {}
 
   ~ParseException() override = default;
 
diff --git a/src/bout++.cxx b/src/bout++.cxx
index d6888874c6..4ca4d352ca 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -324,7 +324,7 @@ template <class Factory>
   // type. Note that this does require all the options are used in the
   // constructor, and not in a `init` method or similar
   std::cout << fmt::format("Input options for {} '{}':\n\n", Factory::type_name, type);
-  std::cout << fmt::format("{:id}\n", help_options);
+  std::cout << fmt::format(fmt::runtime("{:id}\n"), help_options);
   std::exit(EXIT_SUCCESS);
 }
 
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 4aaa760c04..2e4aebdd44 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -165,14 +165,16 @@ CheckMeshResult checkBoutMeshYDecomposition(int num_y_processors, int ny,
   // Check size of Y mesh if we've got multiple processors in Y
   if (num_local_y_points < num_y_guards and num_y_processors != 1) {
     return {false,
-            fmt::format(_("\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"), ny,
-                        num_y_processors, num_local_y_points, num_y_guards)};
+            fmt::format(fmt::runtime(_(
+                            "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n")),
+                        ny, num_y_processors, num_local_y_points, num_y_guards)};
   }
   // Check branch cuts
   if ((jyseps1_1 + 1) % num_local_y_points != 0) {
-    return {false, fmt::format(_("\t -> Leg region jyseps1_1+1 ({:d}) must be a "
-                                 "multiple of MYSUB ({:d})\n"),
-                               jyseps1_1 + 1, num_local_y_points)};
+    return {false,
+            fmt::format(fmt::runtime(_("\t -> Leg region jyseps1_1+1 ({:d}) must be a "
+                                       "multiple of MYSUB ({:d})\n")),
+                        jyseps1_1 + 1, num_local_y_points)};
   }
 
   if (jyseps2_1 != jyseps1_2) {
@@ -181,50 +183,57 @@ CheckMeshResult checkBoutMeshYDecomposition(int num_y_processors, int ny,
     if ((jyseps2_1 - jyseps1_1) % num_local_y_points != 0) {
       return {
           false,
-          fmt::format(_("\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must "
-                        "be a multiple of MYSUB ({:d})\n"),
+          fmt::format(fmt::runtime(_(
+                          "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must "
+                          "be a multiple of MYSUB ({:d})\n")),
                       jyseps2_1, jyseps1_1, jyseps2_1 - jyseps1_1, num_local_y_points)};
     }
 
     if ((jyseps2_2 - jyseps1_2) % num_local_y_points != 0) {
       return {
           false,
-          fmt::format(_("\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must "
-                        "be a multiple of MYSUB ({:d})\n"),
+          fmt::format(fmt::runtime(_(
+                          "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must "
+                          "be a multiple of MYSUB ({:d})\n")),
                       jyseps2_2, jyseps1_2, jyseps2_2 - jyseps1_2, num_local_y_points)};
     }
 
     // Check upper legs
     if ((ny_inner - jyseps2_1 - 1) % num_local_y_points != 0) {
-      return {
-          false,
-          fmt::format(_("\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must "
-                        "be a multiple of MYSUB ({:d})\n"),
-                      ny_inner, jyseps2_1, ny_inner - jyseps2_1 - 1, num_local_y_points)};
+      return {false,
+              fmt::format(
+                  fmt::runtime(
+                      _("\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must "
+                        "be a multiple of MYSUB ({:d})\n")),
+                  ny_inner, jyseps2_1, ny_inner - jyseps2_1 - 1, num_local_y_points)};
     }
     if ((jyseps1_2 - ny_inner + 1) % num_local_y_points != 0) {
-      return {
-          false,
-          fmt::format(_("\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must "
-                        "be a multiple of MYSUB ({:d})\n"),
-                      jyseps1_2, ny_inner, jyseps1_2 - ny_inner + 1, num_local_y_points)};
+      return {false,
+              fmt::format(
+                  fmt::runtime(
+                      _("\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must "
+                        "be a multiple of MYSUB ({:d})\n")),
+                  jyseps1_2, ny_inner, jyseps1_2 - ny_inner + 1, num_local_y_points)};
     }
   } else {
     // Single Null
     if ((jyseps2_2 - jyseps1_1) % num_local_y_points != 0) {
       return {
           false,
-          fmt::format(_("\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must "
-                        "be a multiple of MYSUB ({:d})\n"),
+          fmt::format(fmt::runtime(_(
+                          "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must "
+                          "be a multiple of MYSUB ({:d})\n")),
                       jyseps2_2, jyseps1_1, jyseps2_2 - jyseps1_1, num_local_y_points)};
     }
   }
 
   if ((ny - jyseps2_2 - 1) % num_local_y_points != 0) {
-    return {false, fmt::format(
-                       _("\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a "
-                         "multiple of MYSUB ({:d})\n"),
-                       ny, jyseps2_2, ny - jyseps2_2 - 1, num_local_y_points)};
+    return {
+        false,
+        fmt::format(fmt::runtime(_(
+                        "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a "
+                        "multiple of MYSUB ({:d})\n")),
+                    ny, jyseps2_2, ny - jyseps2_2 - 1, num_local_y_points)};
   }
 
   return {true, ""};
diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx
index 804f371bbe..1c381b26df 100644
--- a/src/sys/expressionparser.cxx
+++ b/src/sys/expressionparser.cxx
@@ -327,13 +327,15 @@ may need to change your input file.
 
     // No matches, just point out the error
     if (possible_matches.empty()) {
-      return fmt::format(message_template, name, problem_bit);
+      return fmt::format(fmt::runtime(message_template), name, problem_bit);
     }
 
     // Give the first suggestion as a possible alternative
-    std::string error_message = fmt::format(message_template, name, problem_bit);
-    error_message += fmt::format(_("\n  {1: ^{2}}{0}\n  Did you mean '{0}'?"),
-                                 possible_matches.begin()->name, "", start);
+    std::string error_message =
+        fmt::format(fmt::runtime(message_template), name, problem_bit);
+    error_message +=
+        fmt::format(fmt::runtime(_("\n  {1: ^{2}}{0}\n  Did you mean '{0}'?")),
+                    possible_matches.begin()->name, "", start);
     return error_message;
   };
 
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index bb4c920b90..fb90868081 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -760,8 +760,9 @@ T as_amt(const Options& self, const T& similar_to) {
 
   const T result = bout::utils::visit(
       ConvertContainer<T>{
-          fmt::format(_("Value for option {:s} cannot be converted to an {}"), self.str(),
-                      bout::utils::typeName<T>()),
+          fmt::format(
+              fmt::runtime(_("Value for option {:s} cannot be converted to an {}")),
+              self.str(), bout::utils::typeName<T>()),
           similar_to},
       self.value);
 
@@ -1098,20 +1099,22 @@ bout::details::OptionsFormatterBase::format(const Options& options,
   // Get all the child values first
   for (const auto& child : children) {
     if (child.second.isValue()) {
-      fmt::format_to(ctx.out(), format_string, child.second);
+      fmt::format_to(ctx.out(), fmt::runtime(format_string), child.second);
       fmt::format_to(ctx.out(), "\n");
     }
   }
 
   // Now descend the tree, accumulating subsections
   for (const auto& subsection : options.subsections()) {
-    fmt::format_to(ctx.out(), format_string, *subsection.second);
+    fmt::format_to(ctx.out(), fmt::runtime(format_string), *subsection.second);
   }
 
   return ctx.out();
 }
 
-std::string toString(const Options& value) { return fmt::format("{}", value); }
+std::string toString(const Options& value) {
+  return fmt::format(fmt::runtime("{}"), value);
+}
 
 namespace bout {
 void checkForUnusedOptions() {
@@ -1157,7 +1160,7 @@ void checkForUnusedOptions(const Options& options, const std::string& data_dir,
       }
       possible_misspellings += fmt::format("\nUnused option '{}', did you mean:\n", key);
       for (const auto& match : fuzzy_matches) {
-        possible_misspellings += fmt::format("\t{:idk}\n", match.match);
+        possible_misspellings += fmt::format(fmt::runtime("\t{:idk}\n"), match.match);
       }
     }
 
diff --git a/src/sys/options/options_ini.cxx b/src/sys/options/options_ini.cxx
index 939e100f1b..b51af8fdcf 100644
--- a/src/sys/options/options_ini.cxx
+++ b/src/sys/options/options_ini.cxx
@@ -157,7 +157,7 @@ void OptionINI::write(Options* options, const std::string& filename) {
   }
 
   // Call recursive function to write to file
-  fout << fmt::format("{:uds}", *options);
+  fout << fmt::format(fmt::runtime("{:uds}"), *options);
 
   fout.close();
 }
diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx
index b74cfdcb9f..f0256b6aa7 100644
--- a/tests/unit/sys/test_options.cxx
+++ b/tests/unit/sys/test_options.cxx
@@ -1099,7 +1099,9 @@ value6 = 12
 }
 
 TEST_F(OptionsTest, InvalidFormat) {
-  EXPECT_THROW([[maybe_unused]] auto none = fmt::format("{:nope}", Options{}), fmt::format_error);
+  EXPECT_THROW([[maybe_unused]] auto none =
+                   fmt::format(fmt::runtime("{:nope}"), Options{}),
+               fmt::format_error);
 }
 
 TEST_F(OptionsTest, FormatValue) {
@@ -1110,7 +1112,7 @@ TEST_F(OptionsTest, FormatValue) {
   const std::string expected =
       "value1 = 4		# type: int, doc: This is a value, source: some test";
 
-  EXPECT_EQ(expected, fmt::format("{:ds}", options["value1"]));
+  EXPECT_EQ(expected, fmt::format(fmt::runtime("{:ds}"), options["value1"]));
 }
 
 TEST_F(OptionsTest, FormatDefault) {
@@ -1138,7 +1140,7 @@ value4 = 3.2
 value6 = 12
 )";
 
-  EXPECT_EQ(fmt::format("{}", option), expected);
+  EXPECT_EQ(fmt::format(fmt::runtime("{}"), option), expected);
 }
 
 TEST_F(OptionsTest, FormatDocstrings) {
@@ -1169,7 +1171,7 @@ value4 = 3.2
 value6 = 12
 )";
 
-  EXPECT_EQ(fmt::format("{:d}", option), expected);
+  EXPECT_EQ(fmt::format(fmt::runtime("{:d}"), option), expected);
 }
 
 TEST_F(OptionsTest, FormatDocstringsAndInline) {
@@ -1192,9 +1194,9 @@ section2:subsection1:value4 = 3.2
 section3:subsection2:value6 = 12
 )";
 
-  EXPECT_EQ(fmt::format("{:di}", option), expected);
+  EXPECT_EQ(fmt::format(fmt::runtime("{:di}"), option), expected);
   // Order of format spec shouldn't matter
-  EXPECT_EQ(fmt::format("{:id}", option), expected);
+  EXPECT_EQ(fmt::format(fmt::runtime("{:id}"), option), expected);
 }
 
 TEST_F(OptionsTest, FormatDocstringsAndInlineKeysOnly) {
@@ -1219,16 +1221,16 @@ section2:subsection1:value4
 section3:subsection2:value6		# source: a test
 )";
 
-  EXPECT_EQ(fmt::format("{:ksdi}", option), expected);
+  EXPECT_EQ(fmt::format(fmt::runtime("{:ksdi}"), option), expected);
   // Order of format spec shouldn't matter
-  EXPECT_EQ(fmt::format("{:idsk}", option), expected);
+  EXPECT_EQ(fmt::format(fmt::runtime("{:idsk}"), option), expected);
 }
 
 TEST_F(OptionsTest, FormatUnused) {
   Options option{{"section1", {{"value1", 42}}}};
   std::string expected =
       "section1:value1\t\t# unused value (NOT marked conditionally used)\n";
-  EXPECT_EQ(fmt::format("{:iku}", option), expected);
+  EXPECT_EQ(fmt::format(fmt::runtime("{:iku}"), option), expected);
 }
 
 TEST_F(OptionsTest, FormatConditionallyUsed) {
@@ -1236,7 +1238,7 @@ TEST_F(OptionsTest, FormatConditionallyUsed) {
   option.setConditionallyUsed();
   std::string expected =
       "section1:value1\t\t# unused value (marked conditionally used)\n";
-  EXPECT_EQ(fmt::format("{:iku}", option), expected);
+  EXPECT_EQ(fmt::format(fmt::runtime("{:iku}"), option), expected);
 }
 
 TEST_F(OptionsTest, GetUnused) {

From 7d8418e00286d466c3bac4d69a1fde9172a5e6cf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:00:47 +0100
Subject: [PATCH 0536/1827] Expose erase even with C++20

---
 include/bout/utils.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 04aa0b281d..560f97f954 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -186,6 +186,7 @@ typename std::vector<T, Alloc>::size_type erase_if(std::vector<T, Alloc>& c, Pre
   return r;
 }
 #else
+using std::erase;
 using std::erase_if;
 #endif
 } // namespace utils

From 27d5c932b6cc4ba0eed6b3d379663ca4b9f35ea9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:01:47 +0100
Subject: [PATCH 0537/1827] Do not pass by reference

With C++ std::accumulate uses std::move, which fails with the reference.
---
 tests/unit/fake_mesh.hxx | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 4656ee0282..7c5d0b3637 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -236,18 +236,17 @@ public:
                                  "RGN_OUTER_X"};
 
     // Sum up and get unique points in the boundaries defined above
-    addRegion2D("RGN_BNDRY",
-                std::accumulate(begin(boundary_names), end(boundary_names),
-                                Region<Ind2D>{},
-                                [this](Region<Ind2D>& a, const std::string& b) {
-                                  return a + getRegion2D(b);
-                                })
-                    .unique());
+    addRegion2D("RGN_BNDRY", std::accumulate(begin(boundary_names), end(boundary_names),
+                                             Region<Ind2D>{},
+                                             [&](Region<Ind2D> a, const std::string& b) {
+                                               return a + getRegion2D(b);
+                                             })
+                                 .unique());
 
     addRegion3D("RGN_BNDRY",
                 std::accumulate(begin(boundary_names), end(boundary_names),
                                 Region<Ind3D>{},
-                                [this](Region<Ind3D>& a, const std::string& b) {
+                                [this](Region<Ind3D> a, const std::string& b) {
                                   return a + getRegion3D(b);
                                 })
                     .unique());

From cf1c7f49854acf337f03026ce533ac7516d9bbe6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:03:14 +0100
Subject: [PATCH 0538/1827] Do not include unneeded header

isatty is provided by both cpptrace and unistd.h, so we should only
include one.
---
 src/sys/boutexception.cxx | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/sys/boutexception.cxx b/src/sys/boutexception.cxx
index b5ea01d231..eff2de2e1f 100644
--- a/src/sys/boutexception.cxx
+++ b/src/sys/boutexception.cxx
@@ -1,7 +1,6 @@
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/msg_stack.hxx>
-#include <bout/utils.hxx>
 
 #include <mpi.h>
 
@@ -11,7 +10,6 @@
 
 #include <cstdlib>
 #include <string>
-#include <utility>
 
 #include <fmt/format.h>
 

From caad51bec7b68514bf7455fcc92104ce4f7966bd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Feb 2026 13:04:11 +0100
Subject: [PATCH 0539/1827] Switch to C++20

---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c05bad29db..e52d1753f1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -522,10 +522,10 @@ set_target_properties(
 set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -L\$BOUT_LIB_PATH -lbout++")
 set(BOUT_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/include")
 set(CONFIG_CFLAGS
-    "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS} -std=c++17"
+    "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS} -std=c++20"
 )
 
-target_compile_features(bout++ PUBLIC cxx_std_17)
+target_compile_features(bout++ PUBLIC cxx_std_20)
 set_target_properties(bout++ PROPERTIES CXX_EXTENSIONS OFF)
 
 # Optional compiler features

From bd3175bf09861f52105c844bd3fbb1856727b3b6 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 17 Feb 2026 14:24:19 +0000
Subject: [PATCH 0540/1827] Re-enable compile-time format checks

Mostly involves using `fmt::vformat` with `fmt::make_format_args` in
functions/ctors that act like `fmt::format`.

Note that `fmt::make_format_args` requires lvalues, so although we take `Args&&`
we _must not_ call `std::forward`.

We also have to introduce a new gettext macro `_f` to allow compile-time format
arg checking _and_ runtime i18n substitution.
---
 include/bout/boutexception.hxx              |  25 +--
 include/bout/msg_stack.hxx                  |  21 ++-
 include/bout/options.hxx                    |  46 ++++-
 include/bout/optionsreader.hxx              |  17 +-
 include/bout/output.hxx                     |  48 +++---
 include/bout/sys/expressionparser.hxx       |  14 +-
 include/bout/sys/gettext.hxx                |  36 +++-
 src/bout++.cxx                              | 176 +++++++++++---------
 src/mesh/coordinates.cxx                    |   4 +-
 src/mesh/impls/bout/boutmesh.cxx            | 108 ++++++------
 src/mesh/mesh.cxx                           |  57 +++++--
 src/solver/impls/petsc/petsc.cxx            |   2 +-
 src/solver/impls/snes/snes.cxx              |   2 +-
 src/solver/impls/split-rk/split-rk.cxx      |  18 +-
 src/solver/solver.cxx                       |  45 +++--
 src/sys/expressionparser.cxx                |  49 ++++--
 src/sys/options.cxx                         | 110 ++++--------
 src/sys/options/options_ini.cxx             |  21 ++-
 src/sys/optionsreader.cxx                   |  13 +-
 tests/unit/sys/test_options.cxx             |  18 +-
 tests/unit/sys/test_output.cxx              |   2 +-
 tools/pylib/_boutpp_build/boutcpp.pxd.jinja |   2 +-
 tools/pylib/_boutpp_build/boutpp.pyx.jinja  |   2 +-
 23 files changed, 495 insertions(+), 341 deletions(-)

diff --git a/include/bout/boutexception.hxx b/include/bout/boutexception.hxx
index d525aeb608..735f98c7d6 100644
--- a/include/bout/boutexception.hxx
+++ b/include/bout/boutexception.hxx
@@ -5,6 +5,7 @@
 #include <string>
 #include <utility>
 
+#include "fmt/base.h"
 #include "fmt/core.h"
 
 /// Throw BoutRhsFail with \p message if any one process has non-zero
@@ -19,10 +20,10 @@ public:
   BoutException& operator=(BoutException&&) = delete;
   BoutException(std::string msg);
 
-  template <class S, class... Args>
-  BoutException(S&& format, Args&&... args)
-      : BoutException(fmt::format(fmt::runtime(std::forward<S>(format)),
-                                  std::forward<decltype(args)>(args)...)) {}
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  BoutException(fmt::format_string<Args...> format, Args&&... args)
+      : BoutException(fmt::vformat(format, fmt::make_format_args(args...))) {}
 
   ~BoutException() override;
 
@@ -44,19 +45,19 @@ private:
 class BoutRhsFail : public BoutException {
 public:
   BoutRhsFail(std::string message) : BoutException(std::move(message)) {}
-  template <class S, class... Args>
-  BoutRhsFail(S&& format, Args&&... args)
-      : BoutRhsFail(fmt::format(fmt::runtime(std::forward<S>(format)),
-                                std::forward<decltype(args)>(args)...)) {}
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  BoutRhsFail(fmt::format_string<Args...> format, Args&&... args)
+      : BoutRhsFail(fmt::vformat(format, fmt::make_format_args(args...))) {}
 };
 
 class BoutIterationFail : public BoutException {
 public:
   BoutIterationFail(std::string message) : BoutException(std::move(message)) {}
-  template <class S, class... Args>
-  BoutIterationFail(S&& format, Args&&... args)
-      : BoutIterationFail(fmt::format(fmt::runtime(std::forward<S>(format)),
-                                      std::forward<decltype(args)>(args)...)) {}
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  BoutIterationFail(fmt::format_string<Args...> format, Args&&... args)
+      : BoutIterationFail(fmt::vformat(format, fmt::make_format_args(args...))) {}
 };
 
 #endif
diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx
index 8771aeab42..89b9f2d8d5 100644
--- a/include/bout/msg_stack.hxx
+++ b/include/bout/msg_stack.hxx
@@ -31,6 +31,7 @@ class MsgStack;
 
 #include "bout/build_defines.hxx"
 
+#include "fmt/base.h"
 #include "fmt/core.h"
 
 #include <cstddef>
@@ -60,9 +61,10 @@ public:
   int push(std::string message);
   int push() { return push(""); }
 
-  template <class S, class... Args>
-  int push(const S& format, const Args&... args) {
-    return push(fmt::format(fmt::runtime(format), args...));
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  int push(fmt::format_string<Args...> format, Args&&... args) {
+    return push(fmt::vformat(format, fmt::make_format_args(args...)));
   }
 
   void pop();       ///< Remove the last message
@@ -74,8 +76,8 @@ public:
 #else
   /// Dummy functions which should be optimised out
   int push(const std::string&) { return 0; }
-  template <class S, class... Args>
-  int push(const S&, const Args&...) {
+  template <class... Args>
+  int push(fmt::format_string<Args...> format, const Args&... args) {
     return 0;
   }
 
@@ -132,10 +134,13 @@ public:
   MsgStackItem(const std::string& file, int line, const char* msg)
       : point(msg_stack.push("{:s} on line {:d} of '{:s}'", msg, line, file)) {}
 
-  template <class S, class... Args>
-  MsgStackItem(const std::string& file, int line, const S& msg, const Args&... args)
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  MsgStackItem(const std::string& file, int line, fmt::format_string<Args...> msg,
+               Args&&... args)
       : point(msg_stack.push("{:s} on line {:d} of '{:s}'",
-                             fmt::format(fmt::runtime(msg), args...), line, file)) {}
+                             fmt::vformat(msg, fmt::make_format_args(args...)), line,
+                             file)) {}
   ~MsgStackItem() {
     // If an exception has occurred, don't pop the message
     if (exception_count == std::uncaught_exceptions()) {
diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 1c552cd4f9..775b65ba1c 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -52,6 +52,7 @@ class Options;
 #include "bout/utils.hxx"
 
 #include <fmt/core.h>
+#include <fmt/format.h>
 
 #include <cmath>
 #include <functional>
@@ -626,8 +627,8 @@ public:
       // Option not found. Copy the value from the default.
       this->_set_no_check(def.value, DEFAULT_SOURCE);
 
-      output_info << _("\tOption ") << full_name << " = " << def.full_name << " ("
-                  << DEFAULT_SOURCE << ")\n";
+      output_info.write("{}{} = {}({})\n", _("\tOption "), full_name, def.full_name,
+                        DEFAULT_SOURCE);
     } else {
       // Check if this was previously set as a default option
       if (bout::utils::variantEqualTo(attributes.at("source"), DEFAULT_SOURCE)) {
@@ -911,8 +912,8 @@ private:
                       << ")\n";
         } else {
           throw BoutException(
-              _("Options: Setting a value from same source ({:s}) to new value "
-                "'{:s}' - old value was '{:s}'."),
+              _f("Options: Setting a value from same source ({:s}) to new value "
+                 "'{:s}' - old value was '{:s}'."),
               source, toString(val), bout::utils::variantToString(value));
         }
       }
@@ -1043,7 +1044,40 @@ namespace details {
 /// so that we can put the function definitions in the .cxx file,
 /// avoiding lengthy recompilation if we change it
 struct OptionsFormatterBase {
-  auto parse(fmt::format_parse_context& ctx) -> fmt::format_parse_context::iterator;
+  constexpr auto parse(fmt::format_parse_context& ctx) {
+    const auto* it = ctx.begin();
+    const auto* const end = ctx.end();
+
+    while (it != end and *it != '}') {
+      switch (*it) {
+      case 'd':
+        docstrings = true;
+        ++it;
+        break;
+      case 'i':
+        inline_section_names = true;
+        ++it;
+        break;
+      case 'k':
+        key_only = true;
+        ++it;
+        break;
+      case 's':
+        source = true;
+        ++it;
+        break;
+      case 'u':
+        unused = true;
+        ++it;
+        break;
+      default:
+        throw fmt::format_error("invalid format for 'Options'");
+      }
+    }
+
+    return it;
+  }
+
   auto format(const Options& options, fmt::format_context& ctx) const
       -> fmt::format_context::iterator;
 
@@ -1060,8 +1094,6 @@ private:
   bool key_only{false};
   /// Include the 'source' attribute, if present
   bool source{false};
-  /// Format string to passed down to subsections
-  std::string format_string;
 };
 } // namespace details
 } // namespace bout
diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx
index 0c9c227916..c5cda6ef1f 100644
--- a/include/bout/optionsreader.hxx
+++ b/include/bout/optionsreader.hxx
@@ -36,7 +36,8 @@ class OptionsReader;
 
 #include "bout/options.hxx"
 
-#include "fmt/core.h"
+#include <fmt/base.h>
+#include <fmt/core.h>
 
 #include <string>
 #include <vector>
@@ -69,9 +70,10 @@ public:
   /// @param[in] file  The name of the file. printf style arguments can be used to create the file name.
   void read(Options* options, const std::string& filename);
 
-  template <class S, class... Args>
-  void read(Options* options, const S& format, const Args&... args) {
-    return read(options, fmt::format(fmt::runtime(format), args...));
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  void read(Options* options, fmt::format_string<Args...> format, Args&&... args) {
+    return read(options, fmt::vformat(format, fmt::make_format_args(args...)));
   }
 
   /// Write options to file
@@ -80,9 +82,10 @@ public:
   /// @param[in] file   The name of the file to (over)write
   void write(Options* options, const std::string& filename);
 
-  template <class S, class... Args>
-  void write(Options* options, const S& format, const Args&... args) {
-    return write(options, fmt::format(fmt::runtime(format), args...));
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  void write(Options* options, fmt::format_string<Args...> format, Args&&... args) {
+    return write(options, fmt::vformat(format, fmt::make_format_args(args...)));
   }
 
   /// Parse options from the command line
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index 4eb1d615ca..9416ab411b 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -39,7 +39,8 @@ class Output;
 #include "bout/sys/gettext.hxx" // IWYU pragma: keep for gettext _() macro
 #include "bout/unused.hxx"
 
-#include "fmt/core.h"
+#include <fmt/base.h>
+#include <fmt/core.h>
 
 #include <utility>
 
@@ -81,10 +82,10 @@ public:
     open(filename);
   }
 
-  template <class S, class... Args>
-  Output(const S& format, Args&&... args)
-      : Output(fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...)) {
-  }
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  Output(fmt::format_string<Args...> format, Args&&... args)
+      : Output(fmt::vformat(format, fmt::make_format_args(args...))) {}
 
   ~Output() override { close(); }
 
@@ -94,9 +95,10 @@ public:
   /// Open an output log file
   int open(const std::string& filename);
 
-  template <class S, class... Args>
-  int open(const S& format, Args&&... args) {
-    return open(fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  int open(fmt::format_string<Args...> format, Args&&... args) {
+    return open(fmt::vformat(format, fmt::make_format_args(args...)));
   }
 
   /// Close the log file
@@ -105,16 +107,18 @@ public:
   /// Write a string using fmt format
   virtual void write(const std::string& message);
 
-  template <class S, class... Args>
-  void write(const S& format, Args&&... args) {
-    write(fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  void write(fmt::format_string<Args...> format, Args&&... args) {
+    write(fmt::vformat(format, fmt::make_format_args(args...)));
   }
   /// Same as write, but only to screen
   virtual void print(const std::string& message);
 
-  template <class S, class... Args>
-  void print(const S& format, Args&&... args) {
-    print(fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  void print(fmt::format_string<Args...> format, Args&&... args) {
+    print(fmt::vformat(format, fmt::make_format_args(args...)));
   }
 
   /// Add an output stream. All output will be sent to all streams
@@ -175,12 +179,12 @@ public:
   /// This string is then sent to log file and stdout (on processor 0)
   void write(const std::string& message) override;
 
-  template <class S, class... Args>
-  void write(const S& format, Args&&... args) {
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  void write(fmt::format_string<Args...> format, Args&&... args) {
     if (enabled) {
       ASSERT1(base != nullptr);
-      base->write(
-          fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
+      base->write(fmt::vformat(format, fmt::make_format_args(args...)));
     }
   }
 
@@ -188,12 +192,12 @@ public:
   /// note: unlike write, this is not also sent to log files
   void print(const std::string& message) override;
 
-  template <class S, class... Args>
-  void print(const S& format, Args&&... args) {
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  void print(fmt::format_string<Args...> format, Args&&... args) {
     if (enabled) {
       ASSERT1(base != nullptr);
-      base->print(
-          fmt::format(fmt::runtime(format), std::forward<decltype(args)>(args)...));
+      base->print(fmt::vformat(format, fmt::make_format_args(args...)));
     }
   }
 
diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx
index 78525e5b69..8b2442e843 100644
--- a/include/bout/sys/expressionparser.hxx
+++ b/include/bout/sys/expressionparser.hxx
@@ -29,7 +29,8 @@
 
 #include "bout/unused.hxx"
 
-#include "fmt/core.h"
+#include <fmt/base.h>
+#include <fmt/core.h>
 
 #include <exception>
 #include <list>
@@ -239,11 +240,16 @@ private:
 
 class ParseException : public std::exception {
 public:
+  ParseException(const ParseException&) = default;
+  ParseException(ParseException&&) = delete;
+  ParseException& operator=(const ParseException&) = default;
+  ParseException& operator=(ParseException&&) = delete;
   ParseException(const std::string& message_) : message(message_) {}
 
-  template <class S, class... Args>
-  ParseException(const S& format, const Args&... args)
-      : message(fmt::format(fmt::runtime(format), args...)) {}
+  template <class... Args>
+  // NOLINTNEXTLINE(cppcoreguidelines-missing-std-forward)
+  ParseException(fmt::format_string<Args...> format, Args&&... args)
+      : message(fmt::vformat(format, fmt::make_format_args(args...))) {}
 
   ~ParseException() override = default;
 
diff --git a/include/bout/sys/gettext.hxx b/include/bout/sys/gettext.hxx
index d67becd54d..d62cd66882 100644
--- a/include/bout/sys/gettext.hxx
+++ b/include/bout/sys/gettext.hxx
@@ -7,15 +7,47 @@
 
 #if BOUT_HAS_GETTEXT
 
-#include <clocale>
+#include <clocale> // IWYU pragma: keep
+
 #include <libintl.h>
 
 #define GETTEXT_PACKAGE "libbout"
 
-#define _(string) dgettext(GETTEXT_PACKAGE, string)
+// If we have C++23, we can get fmt to do compile-time checks of our format
+// strings, _and_ have gettext do runtime replacement
+#if __cpp_if_consteval >= 202106L
+constexpr const char* dgettext_wrap(const char* __domainname, const char* __msgid) __THROW
+    __attribute_format_arg__(2);
+
+constexpr const char* dgettext_wrap(const char* __domainname, const char* __msgid) {
+  if consteval {
+    return __msgid;
+  }
+  return dgettext(__domainname, __msgid);
+}
+
+/// Gettext i18n macro for text containing fmt format specifiers
+// NOLINTNEXTLINE(cppcoreguidelines-macro-usage)
+#define _f(string) dgettext_wrap(GETTEXT_PACKAGE, string)
 
 #else
+// We're pre-C++23, so all our i18n text must be fmt runtime formats
+#include "fmt/base.h" // IWYU pragma: keep
+
+/// Gettext i18n macro for text containing fmt format specifiers
+// NOLINTNEXTLINE(cppcoreguidelines-macro-usage)
+#define _f(string) fmt::runtime(dgettext(GETTEXT_PACKAGE, string))
+#endif
+
+/// Gettext i18n macro for plain text that doesn't need formatting
+// NOLINTNEXTLINE(cppcoreguidelines-macro-usage)
+#define _(string) dgettext(GETTEXT_PACKAGE, string)
+
+#else // BOUT_HAS_GETTEXT
 
+// NOLINTNEXTLINE(cppcoreguidelines-macro-usage)
+#define _f(string) string
+// NOLINTNEXTLINE(cppcoreguidelines-macro-usage)
 #define _(string) string
 
 #endif // BOUT_HAS_GETTEXT
diff --git a/src/bout++.cxx b/src/bout++.cxx
index 4ca4d352ca..cad3edf6c3 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -32,16 +32,23 @@ static constexpr auto DEFAULT_DIR = "data";
 #define GLOBALORIGIN
 
 #include "bout++-time.hxx"
+#include "bout/array.hxx"
 #include "bout/boundary_factory.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/coordinates_accessor.hxx"
+#include "bout/dcomplex.hxx"
+#include "bout/globals.hxx"
 #include "bout/hyprelib.hxx"
 #include "bout/interpolation_xz.hxx"
 #include "bout/interpolation_z.hxx"
 #include "bout/invert/laplacexz.hxx"
 #include "bout/invert_laplace.hxx"
 #include "bout/invert_parderiv.hxx"
+#include "bout/mask.hxx"
+#include "bout/monitor.hxx"
 #include "bout/mpi_wrapper.hxx"
 #include "bout/msg_stack.hxx"
 #include "bout/openmpwrap.hxx"
@@ -52,7 +59,9 @@ static constexpr auto DEFAULT_DIR = "data";
 #include "bout/rkscheme.hxx"
 #include "bout/slepclib.hxx"
 #include "bout/solver.hxx"
+#include "bout/sys/gettext.hxx"
 #include "bout/sys/timer.hxx"
+#include "bout/utils.hxx"
 #include "bout/version.hxx"
 
 #define BOUT_NO_USING_NAMESPACE_BOUTGLOBALS
@@ -63,11 +72,22 @@ static constexpr auto DEFAULT_DIR = "data";
 #include "bout/adios_object.hxx"
 #endif
 
+#include <fmt/base.h>
 #include <fmt/format.h>
+#include <fmt/ranges.h>
 
+#include <algorithm>
 #include <csignal>
+#include <cstdio>
+#include <cstdlib>
 #include <ctime>
 #include <filesystem>
+#include <fstream>
+#include <ios>
+#include <iostream>
+#include <iterator>
+#include <ostream>
+#include <sstream>
 #include <string>
 #include <vector>
 
@@ -137,7 +157,7 @@ int BoutInitialise(int& argc, char**& argv) {
   try {
     args = parseCommandLineArgs(argc, argv);
   } catch (const BoutException& e) {
-    output_error << _("Bad command line arguments:\n") << e.what() << std::endl;
+    output_error.write("{:s}{:s}\n", _("Bad command line arguments:\n"), e.what());
     return 1;
   }
 
@@ -323,8 +343,8 @@ template <class Factory>
   // Now we can print all the options used in constructing our
   // type. Note that this does require all the options are used in the
   // constructor, and not in a `init` method or similar
-  std::cout << fmt::format("Input options for {} '{}':\n\n", Factory::type_name, type);
-  std::cout << fmt::format(fmt::runtime("{:id}\n"), help_options);
+  fmt::println("Input options for {:s} '{}':\n", Factory::type_name, type);
+  fmt::println("{:id}", help_options);
   std::exit(EXIT_SUCCESS);
 }
 
@@ -344,7 +364,7 @@ void handleFactoryHelp(const std::string& current_arg, int i, int argc, char** a
 
   if (current_arg == help_arg) {
     if (i + 1 >= argc) {
-      throw BoutException(_("Usage is {} {} <name>\n"), argv[0], help_arg);
+      throw BoutException(_f("Usage is {} {} <name>\n"), argv[0], help_arg);
     }
     printTypeOptions<Factory>(argv[i + 1]);
   }
@@ -358,9 +378,10 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs {
     if (current_arg == "-h" || current_arg == "--help") {
       // Print help message -- note this will be displayed once per processor as we've not
       // started MPI yet.
-      output.write(_("Usage: {:s} [-d <data directory>] [-f <options filename>] [restart "
-                     "[append]] [VAR=VALUE]\n"),
-                   argv[0]);
+      output.write(
+          _f("Usage: {:s} [-d <data directory>] [-f <options filename>] [restart "
+             "[append]] [VAR=VALUE]\n"),
+          argv[0]);
       output.write(
           _("\n"
             "  -d <data directory>\t\tLook in <data directory> for input/output files\n"
@@ -373,33 +394,33 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs {
       output.write(_("  -c, --color\t\t\tColor output using bout-log-color\n"));
 #endif
       output.write(
-          _("  --print-config\t\tPrint the compile-time configuration\n"
-            "  --list-solvers\t\tList the available time solvers\n"
-            "  --help-solver <solver>\tPrint help for the given time solver\n"
-            "  --list-laplacians\t\tList the available Laplacian inversion solvers\n"
-            "  --help-laplacian <laplacian>\tPrint help for the given Laplacian "
-            "inversion solver\n"
-            "  --list-laplacexz\t\tList the available LaplaceXZ inversion solvers\n"
-            "  --help-laplacexz <laplacexz>\tPrint help for the given LaplaceXZ "
-            "inversion solver\n"
-            "  --list-invertpars\t\tList the available InvertPar solvers\n"
-            "  --help-invertpar <invertpar>\tPrint help for the given InvertPar solver\n"
-            "  --list-rkschemes\t\tList the available Runge-Kutta schemes\n"
-            "  --help-rkscheme <rkscheme>\tPrint help for the given Runge-Kutta scheme\n"
-            "  --list-meshes\t\t\tList the available Meshes\n"
-            "  --help-mesh <mesh>\t\tPrint help for the given Mesh\n"
-            "  --list-xzinterpolations\tList the available XZInterpolations\n"
-            "  --help-xzinterpolation <xzinterpolation>\tPrint help for the given "
-            "XZInterpolation\n"
-            "  --list-zinterpolations\tList the available ZInterpolations\n"
-            "  --help-zinterpolation <zinterpolation>\tPrint help for the given "
-            "ZInterpolation\n"
-            "  -h, --help\t\t\tThis message\n"
-            "  restart [append]\t\tRestart the simulation. If append is specified, "
-            "append to the existing output files, otherwise overwrite them\n"
-            "  VAR=VALUE\t\t\tSpecify a VALUE for input parameter VAR\n"
-            "\nFor all possible input parameters, see the user manual and/or the "
-            "physics model source (e.g. {:s}.cxx)\n"),
+          _f("  --print-config\t\tPrint the compile-time configuration\n"
+             "  --list-solvers\t\tList the available time solvers\n"
+             "  --help-solver <solver>\tPrint help for the given time solver\n"
+             "  --list-laplacians\t\tList the available Laplacian inversion solvers\n"
+             "  --help-laplacian <laplacian>\tPrint help for the given Laplacian "
+             "inversion solver\n"
+             "  --list-laplacexz\t\tList the available LaplaceXZ inversion solvers\n"
+             "  --help-laplacexz <laplacexz>\tPrint help for the given LaplaceXZ "
+             "inversion solver\n"
+             "  --list-invertpars\t\tList the available InvertPar solvers\n"
+             "  --help-invertpar <invertpar>\tPrint help for the given InvertPar solver\n"
+             "  --list-rkschemes\t\tList the available Runge-Kutta schemes\n"
+             "  --help-rkscheme <rkscheme>\tPrint help for the given Runge-Kutta scheme\n"
+             "  --list-meshes\t\t\tList the available Meshes\n"
+             "  --help-mesh <mesh>\t\tPrint help for the given Mesh\n"
+             "  --list-xzinterpolations\tList the available XZInterpolations\n"
+             "  --help-xzinterpolation <xzinterpolation>\tPrint help for the given "
+             "XZInterpolation\n"
+             "  --list-zinterpolations\tList the available ZInterpolations\n"
+             "  --help-zinterpolation <zinterpolation>\tPrint help for the given "
+             "ZInterpolation\n"
+             "  -h, --help\t\t\tThis message\n"
+             "  restart [append]\t\tRestart the simulation. If append is specified, "
+             "append to the existing output files, otherwise overwrite them\n"
+             "  VAR=VALUE\t\t\tSpecify a VALUE for input parameter VAR\n"
+             "\nFor all possible input parameters, see the user manual and/or the "
+             "physics model source (e.g. {:s}.cxx)\n"),
           argv[0]);
 
       std::exit(EXIT_SUCCESS);
@@ -430,7 +451,7 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs {
     if (string(argv[i]) == "-d") {
       // Set data directory
       if (i + 1 >= argc) {
-        throw BoutException(_("Usage is {:s} -d <data directory>\n"), argv[0]);
+        throw BoutException(_f("Usage is {:s} -d <data directory>\n"), argv[0]);
       }
 
       args.data_dir = argv[++i];
@@ -439,7 +460,7 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs {
     } else if (string(argv[i]) == "-f") {
       // Set options file
       if (i + 1 >= argc) {
-        throw BoutException(_("Usage is {:s} -f <options filename>\n"), argv[0]);
+        throw BoutException(_f("Usage is {:s} -f <options filename>\n"), argv[0]);
       }
 
       args.opt_file = argv[++i];
@@ -448,7 +469,7 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs {
     } else if (string(argv[i]) == "-o") {
       // Set options file
       if (i + 1 >= argc) {
-        throw BoutException(_("Usage is {:s} -o <settings filename>\n"), argv[0]);
+        throw BoutException(_f("Usage is {:s} -o <settings filename>\n"), argv[0]);
       }
 
       args.set_file = argv[++i];
@@ -457,7 +478,7 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs {
     } else if ((string(argv[i]) == "-l") || (string(argv[i]) == "--log")) {
       // Set log file
       if (i + 1 >= argc) {
-        throw BoutException(_("Usage is {:s} -l <log filename>\n"), argv[0]);
+        throw BoutException(_f("Usage is {:s} -l <log filename>\n"), argv[0]);
       }
 
       args.log_file = argv[++i];
@@ -495,10 +516,10 @@ auto parseCommandLineArgs(int argc, char** argv) -> CommandLineArgs {
 void checkDataDirectoryIsAccessible(const std::string& data_dir) {
   if (std::filesystem::exists(data_dir)) {
     if (!std::filesystem::is_directory(data_dir)) {
-      throw BoutException(_("DataDir \"{:s}\" is not a directory\n"), data_dir);
+      throw BoutException(_f("DataDir \"{:s}\" is not a directory\n"), data_dir);
     }
   } else {
-    throw BoutException(_("DataDir \"{:s}\" does not exist or is not accessible\n"),
+    throw BoutException(_f("DataDir \"{:s}\" does not exist or is not accessible\n"),
                         data_dir);
   }
 }
@@ -510,7 +531,7 @@ void savePIDtoFile(const std::string& data_dir, int MYPE) {
   pid_file.open(filename.str(), std::ios::out | std::ios::trunc);
 
   if (not pid_file.is_open()) {
-    throw BoutException(_("Could not create PID file {:s}"), filename.str());
+    throw BoutException(_f("Could not create PID file {:s}"), filename.str());
   }
 
   pid_file << getpid() << "\n";
@@ -518,17 +539,17 @@ void savePIDtoFile(const std::string& data_dir, int MYPE) {
 }
 
 void printStartupHeader(int MYPE, int NPES) {
-  output_progress.write(_("BOUT++ version {:s}\n"), bout::version::full);
-  output_progress.write(_("Revision: {:s}\n"), bout::version::revision);
+  output_progress.write(_f("BOUT++ version {:s}\n"), bout::version::full);
+  output_progress.write(_f("Revision: {:s}\n"), bout::version::revision);
 #ifdef MD5SUM
   output_progress.write("MD5 checksum: {:s}\n", BUILDFLAG(MD5SUM));
 #endif
-  output_progress.write(_("Code compiled on {:s} at {:s}\n\n"), boutcompiledate,
+  output_progress.write(_f("Code compiled on {:s} at {:s}\n\n"), boutcompiledate,
                         boutcompiletime);
   output_info.write("B.Dudson (University of York), M.Umansky (LLNL) 2007\n");
   output_info.write("Based on BOUT by Xueqiao Xu, 1999\n\n");
 
-  output_info.write(_("Processor number: {:d} of {:d}\n\n"), MYPE, NPES);
+  output_info.write(_f("Processor number: {:d} of {:d}\n\n"), MYPE, NPES);
 
   output_info.write("pid: {:d}\n\n", getpid());
 }
@@ -538,53 +559,51 @@ void printCompileTimeOptions() {
 
   using namespace bout::build;
 
-  output_info.write(_("\tRuntime error checking {}"), is_enabled(check_level > 0));
+  output_info.write(_f("\tRuntime error checking {}"), is_enabled(check_level > 0));
   if (check_level > 0) {
-    output_info.write(_(", level {}"), check_level);
+    output_info.write(_f(", level {}"), check_level);
   }
   output_info.write("\n");
 
 #ifdef PNCDF
-  output_info.write(_("\tParallel NetCDF support enabled\n"));
+  output_info.write(_f("\tParallel NetCDF support enabled\n"));
 #else
-  output_info.write(_("\tParallel NetCDF support disabled\n"));
+  output_info.write(_f("\tParallel NetCDF support disabled\n"));
 #endif
 
-  output_info.write(_("\tMetrics mode is {}\n"), use_metric_3d ? "3D" : "2D");
-  output_info.write(_("\tFFT support {}\n"), is_enabled(has_fftw));
-  output_info.write(_("\tNatural language support {}\n"), is_enabled(has_gettext));
-  output_info.write(_("\tLAPACK support {}\n"), is_enabled(has_lapack));
+  output_info.write(_f("\tMetrics mode is {}\n"), use_metric_3d ? "3D" : "2D");
+  output_info.write(_f("\tFFT support {}\n"), is_enabled(has_fftw));
+  output_info.write(_f("\tNatural language support {}\n"), is_enabled(has_gettext));
+  output_info.write(_f("\tLAPACK support {}\n"), is_enabled(has_lapack));
   // Horrible nested ternary to set this at compile time
   constexpr auto netcdf_flavour =
       has_netcdf ? (has_legacy_netcdf ? " (Legacy)" : " (NetCDF4)") : "";
-  output_info.write(_("\tNetCDF support {}{}\n"), is_enabled(has_netcdf), netcdf_flavour);
-  output_info.write(_("\tADIOS2 support {}\n"), is_enabled(has_adios2));
-  output_info.write(_("\tPETSc support {}\n"), is_enabled(has_petsc));
-  output_info.write(_("\tPVODE support {}\n"), is_enabled(has_pvode));
-  output_info.write(_("\tScore-P support {}\n"), is_enabled(has_scorep));
-  output_info.write(_("\tSLEPc support {}\n"), is_enabled(has_slepc));
-  output_info.write(_("\tSUNDIALS support {}\n"), is_enabled(has_sundials));
-  output_info.write(_("\tBacktrace in exceptions {}\n"), is_enabled(use_backtrace));
-  output_info.write(_("\tColour in logs {}\n"), is_enabled(use_color));
-  output_info.write(_("\tOpenMP parallelisation {}, using {} threads\n"),
+  output_info.write(_f("\tNetCDF support {}{}\n"), is_enabled(has_netcdf),
+                    netcdf_flavour);
+  output_info.write(_f("\tADIOS2 support {}\n"), is_enabled(has_adios2));
+  output_info.write(_f("\tPETSc support {}\n"), is_enabled(has_petsc));
+  output_info.write(_f("\tPVODE support {}\n"), is_enabled(has_pvode));
+  output_info.write(_f("\tScore-P support {}\n"), is_enabled(has_scorep));
+  output_info.write(_f("\tSLEPc support {}\n"), is_enabled(has_slepc));
+  output_info.write(_f("\tSUNDIALS support {}\n"), is_enabled(has_sundials));
+  output_info.write(_f("\tBacktrace in exceptions {}\n"), is_enabled(use_backtrace));
+  output_info.write(_f("\tColour in logs {}\n"), is_enabled(use_color));
+  output_info.write(_f("\tOpenMP parallelisation {}, using {} threads\n"),
                     is_enabled(use_openmp), omp_get_max_threads());
-  output_info.write(_("\tExtra debug output {}\n"), is_enabled(use_output_debug));
-  output_info.write(_("\tFloating-point exceptions {}\n"), is_enabled(use_sigfpe));
-  output_info.write(_("\tSignal handling support {}\n"), is_enabled(use_signal));
-  output_info.write(_("\tField name tracking {}\n"), is_enabled(use_track));
-  output_info.write(_("\tMessage stack {}\n"), is_enabled(use_msgstack));
+  output_info.write(_f("\tExtra debug output {}\n"), is_enabled(use_output_debug));
+  output_info.write(_f("\tFloating-point exceptions {}\n"), is_enabled(use_sigfpe));
+  output_info.write(_f("\tSignal handling support {}\n"), is_enabled(use_signal));
+  output_info.write(_f("\tField name tracking {}\n"), is_enabled(use_track));
+  output_info.write(_f("\tMessage stack {}\n"), is_enabled(use_msgstack));
 
   // The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
   // which could cause problems (e.g. terminate strings).
-  output_info.write(_("\tCompiled with flags : {:s}\n"), STRINGIFY(BOUT_FLAGS_STRING));
+  output_info.write(_f("\tCompiled with flags : {:s}\n"), STRINGIFY(BOUT_FLAGS_STRING));
 }
 
 void printCommandLineArguments(const std::vector<std::string>& original_argv) {
-  output_info.write(_("\tCommand line options for this run : "));
-  for (auto& arg : original_argv) {
-    output_info << arg << " ";
-  }
-  output_info.write("\n");
+  output_info.write("{:s}{}\n", _("\tCommand line options for this run : "),
+                    fmt::join(original_argv, " "));
 }
 
 bool setupBoutLogColor(bool color_output, int MYPE) {
@@ -618,7 +637,8 @@ bool setupBoutLogColor(bool color_output, int MYPE) {
     }
     if (!success) {
       // Failed . Probably not important enough to stop the simulation
-      std::cerr << _("Could not run bout-log-color. Make sure it is in your PATH\n");
+      fmt::print(stderr, "{:s}",
+                 _("Could not run bout-log-color. Make sure it is in your PATH\n"));
     }
     return success;
   }
@@ -638,7 +658,7 @@ void setupOutput(const std::string& data_dir, const std::string& log_file, int v
     /// Open an output file to echo everything to
     /// On processor 0 anything written to output will go to stdout and the file
     if (output.open("{:s}/{:s}.{:d}", data_dir, log_file, MYPE)) {
-      throw BoutException(_("Could not open {:s}/{:s}.{:d} for writing"), data_dir,
+      throw BoutException(_f("Could not open {:s}/{:s}.{:d} for writing"), data_dir,
                           log_file, MYPE);
     }
   }
@@ -731,7 +751,7 @@ int BoutFinalise(bool write_settings) {
         writeSettingsFile(options, data_dir, set_file);
       }
     } catch (const BoutException& e) {
-      output_error << _("Error whilst writing settings") << e.what() << endl;
+      output_error.write("{} {}\n", _("Error whilst writing settings"), e.what());
     }
   }
 
@@ -888,7 +908,7 @@ int BoutMonitor::call(Solver* solver, BoutReal t, [[maybe_unused]] int iter, int
     BoutReal t_remain = mpi_start_time + wall_limit - bout::globals::mpi->MPI_Wtime();
     if (t_remain < run_data.wtime * 2) {
       // Less than 2 time-steps left
-      output_warn.write(_("Only {:e} seconds ({:.2f} steps) left. Quitting\n"), t_remain,
+      output_warn.write(_f("Only {:e} seconds ({:.2f} steps) left. Quitting\n"), t_remain,
                         t_remain / run_data.wtime);
       user_requested_exit = true;
     } else {
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 91bbddfd56..79ed2e1f21 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1232,7 +1232,7 @@ int Coordinates::calcCovariant(const std::string& region) {
     a(0, 2) = a(2, 0) = g13[i];
 
     if (const auto det = bout::invert3x3(a); det.has_value()) {
-      output_error.write("\tERROR: metric tensor is singular at {}, determinant: {:d}\n",
+      output_error.write("\tERROR: metric tensor is singular at {}, determinant: {:e}\n",
                          i, det.value());
       return 1;
     }
@@ -1287,7 +1287,7 @@ int Coordinates::calcContravariant(const std::string& region) {
     a(0, 2) = a(2, 0) = g_13[i];
 
     if (const auto det = bout::invert3x3(a); det.has_value()) {
-      output_error.write("\tERROR: metric tensor is singular at {}, determinant: {:d}\n",
+      output_error.write("\tERROR: metric tensor is singular at {}, determinant: {:e}\n",
                          i, det.value());
       return 1;
     }
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 2e4aebdd44..00314c20f6 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -26,24 +26,44 @@
 
 #include "boutmesh.hxx"
 
+#include <bout/assert.hxx>
 #include <bout/boundary_region.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/dcomplex.hxx>
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/field_data.hxx>
+#include <bout/fieldgroup.hxx>
+#include <bout/globals.hxx>
 #include <bout/griddata.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/options.hxx>
 #include <bout/output.hxx>
 #include <bout/parallel_boundary_region.hxx>
+#include <bout/region.hxx>
+#include <bout/sys/gettext.hxx>
+#include <bout/sys/range.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 
+#include <fmt/format.h>
+
 #include <algorithm>
+#include <cmath>
+#include <cstddef>
 #include <iterator>
+#include <list>
+#include <memory>
+#include <ostream>
 #include <set>
+#include <string>
+#include <utility>
+#include <vector>
 
 /// MPI type of BoutReal for communications
 #define PVEC_REAL_MPI_TYPE MPI_DOUBLE
@@ -165,16 +185,14 @@ CheckMeshResult checkBoutMeshYDecomposition(int num_y_processors, int ny,
   // Check size of Y mesh if we've got multiple processors in Y
   if (num_local_y_points < num_y_guards and num_y_processors != 1) {
     return {false,
-            fmt::format(fmt::runtime(_(
-                            "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n")),
+            fmt::format(_f("\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"),
                         ny, num_y_processors, num_local_y_points, num_y_guards)};
   }
   // Check branch cuts
   if ((jyseps1_1 + 1) % num_local_y_points != 0) {
-    return {false,
-            fmt::format(fmt::runtime(_("\t -> Leg region jyseps1_1+1 ({:d}) must be a "
-                                       "multiple of MYSUB ({:d})\n")),
-                        jyseps1_1 + 1, num_local_y_points)};
+    return {false, fmt::format(_f("\t -> Leg region jyseps1_1+1 ({:d}) must be a "
+                                  "multiple of MYSUB ({:d})\n"),
+                               jyseps1_1 + 1, num_local_y_points)};
   }
 
   if (jyseps2_1 != jyseps1_2) {
@@ -183,18 +201,16 @@ CheckMeshResult checkBoutMeshYDecomposition(int num_y_processors, int ny,
     if ((jyseps2_1 - jyseps1_1) % num_local_y_points != 0) {
       return {
           false,
-          fmt::format(fmt::runtime(_(
-                          "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must "
-                          "be a multiple of MYSUB ({:d})\n")),
+          fmt::format(_f("\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must "
+                         "be a multiple of MYSUB ({:d})\n"),
                       jyseps2_1, jyseps1_1, jyseps2_1 - jyseps1_1, num_local_y_points)};
     }
 
     if ((jyseps2_2 - jyseps1_2) % num_local_y_points != 0) {
       return {
           false,
-          fmt::format(fmt::runtime(_(
-                          "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must "
-                          "be a multiple of MYSUB ({:d})\n")),
+          fmt::format(_f("\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must "
+                         "be a multiple of MYSUB ({:d})\n"),
                       jyseps2_2, jyseps1_2, jyseps2_2 - jyseps1_2, num_local_y_points)};
     }
 
@@ -202,17 +218,15 @@ CheckMeshResult checkBoutMeshYDecomposition(int num_y_processors, int ny,
     if ((ny_inner - jyseps2_1 - 1) % num_local_y_points != 0) {
       return {false,
               fmt::format(
-                  fmt::runtime(
-                      _("\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must "
-                        "be a multiple of MYSUB ({:d})\n")),
+                  _f("\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must "
+                     "be a multiple of MYSUB ({:d})\n"),
                   ny_inner, jyseps2_1, ny_inner - jyseps2_1 - 1, num_local_y_points)};
     }
     if ((jyseps1_2 - ny_inner + 1) % num_local_y_points != 0) {
       return {false,
               fmt::format(
-                  fmt::runtime(
-                      _("\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must "
-                        "be a multiple of MYSUB ({:d})\n")),
+                  _f("\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must "
+                     "be a multiple of MYSUB ({:d})\n"),
                   jyseps1_2, ny_inner, jyseps1_2 - ny_inner + 1, num_local_y_points)};
     }
   } else {
@@ -220,9 +234,8 @@ CheckMeshResult checkBoutMeshYDecomposition(int num_y_processors, int ny,
     if ((jyseps2_2 - jyseps1_1) % num_local_y_points != 0) {
       return {
           false,
-          fmt::format(fmt::runtime(_(
-                          "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must "
-                          "be a multiple of MYSUB ({:d})\n")),
+          fmt::format(_f("\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must "
+                         "be a multiple of MYSUB ({:d})\n"),
                       jyseps2_2, jyseps1_1, jyseps2_2 - jyseps1_1, num_local_y_points)};
     }
   }
@@ -230,9 +243,8 @@ CheckMeshResult checkBoutMeshYDecomposition(int num_y_processors, int ny,
   if ((ny - jyseps2_2 - 1) % num_local_y_points != 0) {
     return {
         false,
-        fmt::format(fmt::runtime(_(
-                        "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a "
-                        "multiple of MYSUB ({:d})\n")),
+        fmt::format(_f("\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a "
+                       "multiple of MYSUB ({:d})\n"),
                     ny, jyseps2_2, ny - jyseps2_2 - 1, num_local_y_points)};
   }
 
@@ -253,7 +265,7 @@ void BoutMesh::chooseProcessorSplit(Options& options) {
                .withDefault(1);
     if ((NPES % NXPE) != 0) {
       throw BoutException(
-          _("Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"),
+          _f("Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"),
           NPES, NXPE);
     }
 
@@ -266,7 +278,7 @@ void BoutMesh::chooseProcessorSplit(Options& options) {
                .withDefault(1);
     if ((NPES % NYPE) != 0) {
       throw BoutException(
-          _("Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"),
+          _f("Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"),
           NPES, NYPE);
     }
 
@@ -289,14 +301,14 @@ void BoutMesh::findProcessorSplit() {
   // Results in square domains
   const BoutReal ideal = sqrt(MX * NPES / static_cast<BoutReal>(ny));
 
-  output_info.write(_("Finding value for NXPE (ideal = {:f})\n"), ideal);
+  output_info.write(_f("Finding value for NXPE (ideal = {:f})\n"), ideal);
 
   for (int i = 1; i <= NPES; i++) { // Loop over all possibilities
     if ((NPES % i == 0) &&          // Processors divide equally
         (MX % i == 0) &&            // Mesh in X divides equally
         (ny % (NPES / i) == 0)) {   // Mesh in Y divides equally
 
-      output_info.write(_("\tCandidate value: {:d}\n"), i);
+      output_info.write(_f("\tCandidate value: {:d}\n"), i);
 
       const int nyp = NPES / i;
 
@@ -323,15 +335,15 @@ void BoutMesh::findProcessorSplit() {
 
   NYPE = NPES / NXPE;
 
-  output_progress.write(_("\tDomain split (NXPE={:d}, NYPE={:d}) into domains "
-                          "(localNx={:d}, localNy={:d})\n"),
+  output_progress.write(_f("\tDomain split (NXPE={:d}, NYPE={:d}) into domains "
+                           "(localNx={:d}, localNy={:d})\n"),
                         NXPE, NYPE, MX / NXPE, ny / NYPE);
 }
 
 void BoutMesh::setDerivedGridSizes() {
   // Check that nx is large enough
   if (nx <= 2 * MXG) {
-    throw BoutException(_("Error: nx must be greater than 2 times MXG (2 * {:d})"), MXG);
+    throw BoutException(_f("Error: nx must be greater than 2 times MXG (2 * {:d})"), MXG);
   }
 
   GlobalNx = nx;
@@ -356,8 +368,8 @@ void BoutMesh::setDerivedGridSizes() {
   MX = nx - 2 * MXG;
   MXSUB = MX / NXPE;
   if ((MX % NXPE) != 0) {
-    throw BoutException(_("Cannot split {:d} X points equally between {:d} processors\n"),
-                        MX, NXPE);
+    throw BoutException(
+        _f("Cannot split {:d} X points equally between {:d} processors\n"), MX, NXPE);
   }
 
   // NOTE: No grid data reserved for Y boundary cells - copy from neighbours
@@ -365,7 +377,7 @@ void BoutMesh::setDerivedGridSizes() {
   MYSUB = MY / NYPE;
   if ((MY % NYPE) != 0) {
     throw BoutException(
-        _("\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"), MY,
+        _f("\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"), MY,
         NYPE);
   }
 
@@ -373,7 +385,7 @@ void BoutMesh::setDerivedGridSizes() {
   MZSUB = MZ / NZPE;
   if ((MZ % NZPE) != 0) {
     throw BoutException(
-        _("\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"), MZ,
+        _f("\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"), MZ,
         NZPE);
   }
 
@@ -474,8 +486,8 @@ int BoutMesh::load() {
     if (!is_pow2(nz)) {
       // Should be a power of 2 for efficient FFTs
       output_warn.write(
-          _("WARNING: Number of toroidal points should be 2^n for efficient "
-            "FFT performance -- consider changing MZ ({:d}) if using FFTs\n"),
+          _f("WARNING: Number of toroidal points should be 2^n for efficient "
+             "FFT performance -- consider changing MZ ({:d}) if using FFTs\n"),
           nz);
     }
   } else {
@@ -1556,7 +1568,7 @@ bool BoutMesh::lastX() const { return PE_XIND == NXPE - 1; }
 int BoutMesh::sendXOut(BoutReal* buffer, int size, int tag) {
   Timer timer("comms");
 
-  int proc {-1};
+  int proc{-1};
   if (PE_XIND == NXPE - 1) {
     if (periodicX) {
       // Wrap around to first processor in X
@@ -1568,8 +1580,7 @@ int BoutMesh::sendXOut(BoutReal* buffer, int size, int tag) {
     proc = PROC_NUM(PE_XIND + 1, PE_YIND);
   }
 
-  mpi->MPI_Send(buffer, size, PVEC_REAL_MPI_TYPE, proc, tag,
-                BoutComm::get());
+  mpi->MPI_Send(buffer, size, PVEC_REAL_MPI_TYPE, proc, tag, BoutComm::get());
 
   return 0;
 }
@@ -1577,7 +1588,7 @@ int BoutMesh::sendXOut(BoutReal* buffer, int size, int tag) {
 int BoutMesh::sendXIn(BoutReal* buffer, int size, int tag) {
   Timer timer("comms");
 
-  int proc {-1};
+  int proc{-1};
   if (PE_XIND == 0) {
     if (periodicX) {
       // Wrap around to last processor in X
@@ -1589,8 +1600,7 @@ int BoutMesh::sendXIn(BoutReal* buffer, int size, int tag) {
     proc = PROC_NUM(PE_XIND - 1, PE_YIND);
   }
 
-  mpi->MPI_Send(buffer, size, PVEC_REAL_MPI_TYPE, proc, tag,
-                BoutComm::get());
+  mpi->MPI_Send(buffer, size, PVEC_REAL_MPI_TYPE, proc, tag, BoutComm::get());
 
   return 0;
 }
@@ -1598,7 +1608,7 @@ int BoutMesh::sendXIn(BoutReal* buffer, int size, int tag) {
 comm_handle BoutMesh::irecvXOut(BoutReal* buffer, int size, int tag) {
   Timer timer("comms");
 
-  int proc {-1};
+  int proc{-1};
   if (PE_XIND == NXPE - 1) {
     if (periodicX) {
       // Wrap around to first processor in X
@@ -1613,8 +1623,8 @@ comm_handle BoutMesh::irecvXOut(BoutReal* buffer, int size, int tag) {
   // Get a communications handle. Not fussy about size of arrays
   CommHandle* ch = get_handle(0, 0);
 
-  mpi->MPI_Irecv(buffer, size, PVEC_REAL_MPI_TYPE, proc, tag,
-                 BoutComm::get(), ch->request);
+  mpi->MPI_Irecv(buffer, size, PVEC_REAL_MPI_TYPE, proc, tag, BoutComm::get(),
+                 ch->request);
 
   ch->in_progress = true;
 
@@ -1624,7 +1634,7 @@ comm_handle BoutMesh::irecvXOut(BoutReal* buffer, int size, int tag) {
 comm_handle BoutMesh::irecvXIn(BoutReal* buffer, int size, int tag) {
   Timer timer("comms");
 
-  int proc {-1};
+  int proc{-1};
   if (PE_XIND == 0) {
     if (periodicX) {
       // Wrap around to last processor in X
@@ -1639,8 +1649,8 @@ comm_handle BoutMesh::irecvXIn(BoutReal* buffer, int size, int tag) {
   // Get a communications handle. Not fussy about size of arrays
   CommHandle* ch = get_handle(0, 0);
 
-  mpi->MPI_Irecv(buffer, size, PVEC_REAL_MPI_TYPE, proc, tag,
-                 BoutComm::get(), ch->request);
+  mpi->MPI_Irecv(buffer, size, PVEC_REAL_MPI_TYPE, proc, tag, BoutComm::get(),
+                 ch->request);
 
   ch->in_progress = true;
 
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 8964a6b797..6278f2741a 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -1,14 +1,38 @@
+#include <bout/array.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
+#include <bout/boutexception.hxx>
+#include <bout/build_defines.hxx>
 #include <bout/coordinates.hxx>
 #include <bout/derivs.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/field_data.hxx>
+#include <bout/fieldgroup.hxx>
+#include <bout/generic_factory.hxx>
 #include <bout/globals.hxx>
 #include <bout/griddata.hxx>
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
+#include <bout/openmpwrap.hxx>
+#include <bout/options.hxx>
 #include <bout/output.hxx>
+#include <bout/region.hxx>
+#include <bout/sys/gettext.hxx>
+#include <bout/sys/range.hxx>
+#include <bout/unused.hxx>
 #include <bout/utils.hxx>
-
-#include <cmath>
+#include <bout/vector2d.hxx>
+#include <bout/vector3d.hxx>
+
+#include <algorithm>
+#include <cstddef>
+#include <iterator>
+#include <memory>
+#include <optional>
+#include <string>
+#include <utility>
+#include <vector>
 
 #include "impls/bout/boutmesh.hxx"
 
@@ -509,11 +533,11 @@ const std::vector<int> Mesh::readInts(const std::string& name, int n) {
   if (source->hasVar(name)) {
     if (!source->get(this, result, name, n, 0)) {
       // Error reading
-      throw BoutException(_("Could not read integer array '{:s}'\n"), name.c_str());
+      throw BoutException(_f("Could not read integer array '{:s}'\n"), name.c_str());
     }
   } else {
     // Not found
-    throw BoutException(_("Missing integer array {:s}\n"), name.c_str());
+    throw BoutException(_f("Missing integer array {:s}\n"), name.c_str());
   }
 
   return result;
@@ -537,7 +561,7 @@ Mesh::createDefaultCoordinates(const CELL_LOC location,
 const Region<>& Mesh::getRegion3D(const std::string& region_name) const {
   const auto found = regionMap3D.find(region_name);
   if (found == end(regionMap3D)) {
-    throw BoutException(_("Couldn't find region {:s} in regionMap3D"), region_name);
+    throw BoutException(_f("Couldn't find region {:s} in regionMap3D"), region_name);
   }
   return region3D[found->second];
 }
@@ -545,7 +569,7 @@ const Region<>& Mesh::getRegion3D(const std::string& region_name) const {
 size_t Mesh::getRegionID(const std::string& region_name) const {
   const auto found = regionMap3D.find(region_name);
   if (found == end(regionMap3D)) {
-    throw BoutException(_("Couldn't find region {:s} in regionMap3D"), region_name);
+    throw BoutException(_f("Couldn't find region {:s} in regionMap3D"), region_name);
   }
   return found->second;
 }
@@ -553,7 +577,7 @@ size_t Mesh::getRegionID(const std::string& region_name) const {
 const Region<Ind2D>& Mesh::getRegion2D(const std::string& region_name) const {
   const auto found = regionMap2D.find(region_name);
   if (found == end(regionMap2D)) {
-    throw BoutException(_("Couldn't find region {:s} in regionMap2D"), region_name);
+    throw BoutException(_f("Couldn't find region {:s} in regionMap2D"), region_name);
   }
   return found->second;
 }
@@ -561,7 +585,7 @@ const Region<Ind2D>& Mesh::getRegion2D(const std::string& region_name) const {
 const Region<IndPerp>& Mesh::getRegionPerp(const std::string& region_name) const {
   const auto found = regionMapPerp.find(region_name);
   if (found == end(regionMapPerp)) {
-    throw BoutException(_("Couldn't find region {:s} in regionMapPerp"), region_name);
+    throw BoutException(_f("Couldn't find region {:s} in regionMapPerp"), region_name);
   }
   return found->second;
 }
@@ -580,8 +604,8 @@ bool Mesh::hasRegionPerp(const std::string& region_name) const {
 
 void Mesh::addRegion3D(const std::string& region_name, const Region<>& region) {
   if (regionMap3D.count(region_name)) {
-    throw BoutException(_("Trying to add an already existing region {:s} to regionMap3D"),
-                        region_name);
+    throw BoutException(
+        _f("Trying to add an already existing region {:s} to regionMap3D"), region_name);
   }
 
   std::optional<size_t> id;
@@ -598,27 +622,28 @@ void Mesh::addRegion3D(const std::string& region_name, const Region<>& region) {
 
   regionMap3D[region_name] = id.value();
 
-  output_verbose.write(_("Registered region 3D {:s}"), region_name);
+  output_verbose.write(_f("Registered region 3D {:s}"), region_name);
   output_verbose << "\n:\t" << region.getStats() << "\n";
 }
 
 void Mesh::addRegion2D(const std::string& region_name, const Region<Ind2D>& region) {
   if (regionMap2D.count(region_name)) {
-    throw BoutException(_("Trying to add an already existing region {:s} to regionMap2D"),
-                        region_name);
+    throw BoutException(
+        _f("Trying to add an already existing region {:s} to regionMap2D"), region_name);
   }
   regionMap2D[region_name] = region;
-  output_verbose.write(_("Registered region 2D {:s}"), region_name);
+  output_verbose.write(_f("Registered region 2D {:s}"), region_name);
   output_verbose << "\n:\t" << region.getStats() << "\n";
 }
 
 void Mesh::addRegionPerp(const std::string& region_name, const Region<IndPerp>& region) {
   if (regionMapPerp.count(region_name)) {
     throw BoutException(
-        _("Trying to add an already existing region {:s} to regionMapPerp"), region_name);
+        _f("Trying to add an already existing region {:s} to regionMapPerp"),
+        region_name);
   }
   regionMapPerp[region_name] = region;
-  output_verbose.write(_("Registered region Perp {:s}"), region_name);
+  output_verbose.write(_f("Registered region Perp {:s}"), region_name);
   output_verbose << "\n:\t" << region.getStats() << "\n";
 }
 
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 13e4876048..1e1e05596b 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -807,7 +807,7 @@ int PetscSolver::init() {
 
                     if (ierr != 0) {
                       output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n",
-                                   row, x, y, xi, yi, ind2, ind2 + n3d - 1);
+                                   row, col, x, y, xi, yi, ind2, ind2 + n3d - 1);
                     }
                     CHKERRQ(ierr);
                   }
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 2e4744eb44..31877f8aac 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -347,7 +347,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
 
                   if (ierr != PETSC_SUCCESS) {
                     output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n", row,
-                                 x, y, xi, yi, ind2, ind2 + n3d - 1);
+                                 col, x, y, xi, yi, ind2, ind2 + n3d - 1);
                   }
                   CHKERRQ(ierr);
                 }
diff --git a/src/solver/impls/split-rk/split-rk.cxx b/src/solver/impls/split-rk/split-rk.cxx
index fd9a99a6c5..ac4d62ebe2 100644
--- a/src/solver/impls/split-rk/split-rk.cxx
+++ b/src/solver/impls/split-rk/split-rk.cxx
@@ -1,5 +1,21 @@
 #include "split-rk.hxx"
 
+#include "bout/array.hxx"
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/field2d.hxx"
+#include "bout/globals.hxx"
+#include "bout/openmpwrap.hxx"
+#include "bout/options.hxx"
+#include "bout/output.hxx"
+#include "bout/solver.hxx"
+#include "bout/sys/gettext.hxx"
+#include "bout/utils.hxx"
+
+#include <cmath>
+#include <iterator>
+
 SplitRK::SplitRK(Options* opts)
     : Solver(opts), nstages((*options)["nstages"]
                                 .doc("Number of stages in RKL step. Must be > 1")
@@ -72,7 +88,7 @@ int SplitRK::init() {
   ASSERT0(ninternal_steps > 0);
 
   timestep = getOutputTimestep() / ninternal_steps;
-  output.write(_("\tUsing a timestep {:e}\n"), timestep);
+  output.write(_f("\tUsing a timestep {:e}\n"), timestep);
 
   return 0;
 }
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index ac3d632419..c6e9b464fe 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -24,23 +24,38 @@
 
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
+#include "bout/globals.hxx"
 #include "bout/initialprofiles.hxx"
 #include "bout/interpolation.hxx"
+#include "bout/monitor.hxx"
 #include "bout/msg_stack.hxx"
+#include "bout/options.hxx"
 #include "bout/output.hxx"
 #include "bout/region.hxx"
 #include "bout/solver.hxx"
+#include "bout/sys/gettext.hxx"
 #include "bout/sys/timer.hxx"
 #include "bout/sys/uuid.h"
+#include "bout/unused.hxx"
+#include "bout/utils.hxx"
+#include "bout/vector2d.hxx"
+#include "bout/vector3d.hxx"
+
+#include <fmt/format.h>
 
 #include <cmath>
-#include <cstring>
 #include <ctime>
+#include <memory>
 #include <numeric>
 #include <set>
+#include <string>
+#include <utility>
 
 // Implementations:
 #include "impls/adams_bashforth/adams_bashforth.hxx"
@@ -507,11 +522,11 @@ int Solver::solve(int nout, BoutReal timestep) {
   finaliseMonitorPeriods(nout, timestep);
 
   output_progress.write(
-      _("Solver running for {:d} outputs with output timestep of {:e}\n"), nout,
+      _f("Solver running for {:d} outputs with output timestep of {:e}\n"), nout,
       timestep);
   if (default_monitor_period > 1) {
     output_progress.write(
-        _("Solver running for {:d} outputs with monitor timestep of {:e}\n"),
+        _f("Solver running for {:d} outputs with monitor timestep of {:e}\n"),
         nout / default_monitor_period, timestep * default_monitor_period);
   }
 
@@ -537,7 +552,7 @@ int Solver::solve(int nout, BoutReal timestep) {
   }
 
   time_t start_time = time(nullptr);
-  output_progress.write(_("\nRun started at  : {:s}\n"), toString(start_time));
+  output_progress.write(_f("\nRun started at  : {:s}\n"), toString(start_time));
 
   Timer timer("run"); // Start timer
 
@@ -583,7 +598,7 @@ int Solver::solve(int nout, BoutReal timestep) {
     status = run();
 
     time_t end_time = time(nullptr);
-    output_progress.write(_("\nRun finished at  : {:s}\n"), toString(end_time));
+    output_progress.write(_f("\nRun finished at  : {:s}\n"), toString(end_time));
     output_progress.write(_("Run time : "));
 
     int dt = end_time - start_time;
@@ -766,7 +781,7 @@ BoutReal Solver::adjustMonitorPeriods(Monitor* new_monitor) {
   }
 
   if (!isMultiple(internal_timestep, new_monitor->timestep)) {
-    throw BoutException(_("Couldn't add Monitor: {:g} is not a multiple of {:g}!"),
+    throw BoutException(_f("Couldn't add Monitor: {:g} is not a multiple of {:g}!"),
                         internal_timestep, new_monitor->timestep);
   }
 
@@ -782,8 +797,8 @@ BoutReal Solver::adjustMonitorPeriods(Monitor* new_monitor) {
 
   if (initialised) {
     throw BoutException(
-        _("Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) "
-          "after init is called!"),
+        _f("Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) "
+           "after init is called!"),
         internal_timestep, new_monitor->timestep);
   }
 
@@ -883,7 +898,7 @@ int Solver::call_monitors(BoutReal simtime, int iter, int NOUT) {
             monitor.monitor->call(this, simtime, iter / monitor.monitor->period,
                                   NOUT / monitor.monitor->period);
         if (ret != 0) {
-          throw BoutException(_("Monitor signalled to quit (return code {})"), ret);
+          throw BoutException(_f("Monitor signalled to quit (return code {})"), ret);
         }
         // Write the monitor's diagnostics to the main output file
         Options monitor_dump;
@@ -905,7 +920,7 @@ int Solver::call_monitors(BoutReal simtime, int iter, int NOUT) {
     for (const auto& monitor : monitors) {
       monitor.monitor->cleanup();
     }
-    output_error.write(_("Monitor signalled to quit (exception {})\n"), e.what());
+    output_error.write(_f("Monitor signalled to quit (exception {})\n"), e.what());
     throw;
   }
 
@@ -1234,13 +1249,13 @@ void Solver::load_derivs(BoutReal* udata) {
 void Solver::save_vars(BoutReal* udata) {
   for (const auto& f : f2d) {
     if (!f.var->isAllocated()) {
-      throw BoutException(_("Variable '{:s}' not initialised"), f.name);
+      throw BoutException(_f("Variable '{:s}' not initialised"), f.name);
     }
   }
 
   for (const auto& f : f3d) {
     if (!f.var->isAllocated()) {
-      throw BoutException(_("Variable '{:s}' not initialised"), f.name);
+      throw BoutException(_f("Variable '{:s}' not initialised"), f.name);
     }
   }
 
@@ -1283,8 +1298,8 @@ void Solver::save_derivs(BoutReal* dudata) {
   // Make sure 3D fields are at the correct cell location
   for (const auto& f : f3d) {
     if (f.var->getLocation() != (f.F_var)->getLocation()) {
-      throw BoutException(_("Time derivative at wrong location - Field is at {:s}, "
-                            "derivative is at {:s} for field '{:s}'\n"),
+      throw BoutException(_f("Time derivative at wrong location - Field is at {:s}, "
+                             "derivative is at {:s} for field '{:s}'\n"),
                           toString(f.var->getLocation()),
                           toString(f.F_var->getLocation()), f.name);
     }
@@ -1488,7 +1503,7 @@ void Solver::post_rhs(BoutReal UNUSED(t)) {
 #if CHECK > 0
   for (const auto& f : f3d) {
     if (!f.F_var->isAllocated()) {
-      throw BoutException(_("Time derivative for variable '{:s}' not set"), f.name);
+      throw BoutException(_f("Time derivative for variable '{:s}' not set"), f.name);
     }
   }
 #endif
diff --git a/src/sys/expressionparser.cxx b/src/sys/expressionparser.cxx
index 1c381b26df..5573846c4f 100644
--- a/src/sys/expressionparser.cxx
+++ b/src/sys/expressionparser.cxx
@@ -22,12 +22,29 @@
  *
  **************************************************************************/
 
-#include <bout/sys/expressionparser.hxx>
-
+#include "bout/sys/expressionparser.hxx"
+
+#include <bout/bout_types.hxx>
+#include <bout/boutexception.hxx>
+#include <bout/sys/generator_context.hxx>
+#include <bout/sys/gettext.hxx>
+#include <bout/unused.hxx>
+#include <bout/utils.hxx>
+
+#include <fmt/format.h>
+
+#include <algorithm>
+#include <cctype>
+#include <cmath>
+#include <cstdio>
+#include <ios>
+#include <list>
+#include <memory>
+#include <set>
+#include <sstream>
+#include <string>
 #include <utility>
-
-#include "bout/sys/gettext.hxx"
-#include "bout/utils.hxx"
+#include <vector>
 
 using std::list;
 using std::string;
@@ -183,7 +200,7 @@ FieldGeneratorPtr FieldBinary::clone(const list<FieldGeneratorPtr> args) {
 bool toBool(BoutReal rval) {
   int ival = ROUND(rval);
   if ((fabs(rval - static_cast<BoutReal>(ival)) > 1e-3) or (ival < 0) or (ival > 1)) {
-    throw BoutException(_("Boolean operator argument {:e} is not a bool"), rval);
+    throw BoutException(_f("Boolean operator argument {:e} is not a bool"), rval);
   }
   return ival == 1;
 }
@@ -302,11 +319,6 @@ ExpressionParser::fuzzyFind(const std::string& name,
 FieldGeneratorPtr ExpressionParser::parseIdentifierExpr(LexInfo& lex) const {
   // Make a nice error message if we couldn't find the identifier
   const auto generatorNotFoundErrorMessage = [&](const std::string& name) -> std::string {
-    const std::string message_template = _(
-        R"(Couldn't find generator '{}'. BOUT++ expressions are now case-sensitive, so you
-may need to change your input file.
-{})");
-
     // Start position of the current identifier: by this point, we've either
     // moved one character past the token, or we're still at the start
     const auto start =
@@ -326,16 +338,19 @@ may need to change your input file.
                           [](const auto& match) -> bool { return match.distance == 0; });
 
     // No matches, just point out the error
+    std::string error_message = fmt::format(
+        _f(
+            R"(Couldn't find generator '{}'. BOUT++ expressions are now case-sensitive, so you
+may need to change your input file.
+{})"),
+        name, problem_bit);
     if (possible_matches.empty()) {
-      return fmt::format(fmt::runtime(message_template), name, problem_bit);
+      return error_message;
     }
 
     // Give the first suggestion as a possible alternative
-    std::string error_message =
-        fmt::format(fmt::runtime(message_template), name, problem_bit);
-    error_message +=
-        fmt::format(fmt::runtime(_("\n  {1: ^{2}}{0}\n  Did you mean '{0}'?")),
-                    possible_matches.begin()->name, "", start);
+    error_message += fmt::format(_f("\n  {1: ^{2}}{0}\n  Did you mean '{0}'?"),
+                                 possible_matches.begin()->name, "", start);
     return error_message;
   };
 
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index fb90868081..d409a2e1b1 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -107,10 +107,10 @@ Options::Options(InitializerList values, Options* parent_instance,
 
 Options& Options::operator[](const std::string& name) {
   if (isValue()) {
-    throw BoutException(_("Trying to index Option '{0}' with '{1}', but '{0}' is a "
-                          "value, not a section.\n"
-                          "This is likely the result of clashing input options, and you "
-                          "may have to rename one of them.\n"),
+    throw BoutException(_f("Trying to index Option '{0}' with '{1}', but '{0}' is a "
+                           "value, not a section.\n"
+                           "This is likely the result of clashing input options, and you "
+                           "may have to rename one of them.\n"),
                         full_name, name);
   }
 
@@ -144,10 +144,10 @@ Options& Options::operator[](const std::string& name) {
 
 const Options& Options::operator[](const std::string& name) const {
   if (isValue()) {
-    throw BoutException(_("Trying to index Option '{0}' with '{1}', but '{0}' is a "
-                          "value, not a section.\n"
-                          "This is likely the result of clashing input options, and you "
-                          "may have to rename one of them.\n"),
+    throw BoutException(_f("Trying to index Option '{0}' with '{1}', but '{0}' is a "
+                           "value, not a section.\n"
+                           "This is likely the result of clashing input options, and you "
+                           "may have to rename one of them.\n"),
                         full_name, name);
   }
 
@@ -165,7 +165,7 @@ const Options& Options::operator[](const std::string& name) const {
   auto child = children.find(name);
   if (child == children.end()) {
     // Doesn't exist
-    throw BoutException(_("Option {:s}:{:s} does not exist"), full_name, name);
+    throw BoutException(_f("Option {:s}:{:s} does not exist"), full_name, name);
   }
 
   return child->second;
@@ -369,7 +369,7 @@ double parseExpression(const Options::ValueType& value, const Options* options,
     return gen->generate({});
   } catch (ParseException& error) {
     // Convert any exceptions to something a bit more useful
-    throw BoutException(_("Couldn't get {} from option {:s} = '{:s}': {}"), type,
+    throw BoutException(_f("Couldn't get {} from option {:s} = '{:s}': {}"), type,
                         full_name, bout::utils::variantToString(value), error.what());
   }
 }
@@ -377,7 +377,7 @@ double parseExpression(const Options::ValueType& value, const Options* options,
 /// Helper function to print `key = value` with optional source
 template <class T>
 void printNameValueSourceLine(const Options& option, const T& value) {
-  output_info.write(_("\tOption {} = {}"), option.str(), value);
+  output_info.write(_f("\tOption {} = {}"), option.str(), value);
   if (option.hasAttribute("source")) {
     // Specify the source of the setting
     output_info.write(" ({})",
@@ -390,7 +390,7 @@ void printNameValueSourceLine(const Options& option, const T& value) {
 template <>
 std::string Options::as<std::string>(const std::string& UNUSED(similar_to)) const {
   if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
+    throw BoutException(_f("Option {:s} has no value"), full_name);
   }
 
   // Mark this option as used
@@ -406,7 +406,7 @@ std::string Options::as<std::string>(const std::string& UNUSED(similar_to)) cons
 template <>
 int Options::as<int>(const int& UNUSED(similar_to)) const {
   if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
+    throw BoutException(_f("Option {:s} has no value"), full_name);
   }
 
   int result = 0;
@@ -426,7 +426,7 @@ int Options::as<int>(const int& UNUSED(similar_to)) const {
 
     } else {
       // Another type which can't be converted
-      throw BoutException(_("Value for option {:s} is not an integer"), full_name);
+      throw BoutException(_f("Value for option {:s} is not an integer"), full_name);
     }
 
     // Convert to int by rounding
@@ -434,7 +434,7 @@ int Options::as<int>(const int& UNUSED(similar_to)) const {
 
     // Check that the value is close to an integer
     if (fabs(rval - static_cast<BoutReal>(result)) > 1e-3) {
-      throw BoutException(_("Value for option {:s} = {:e} is not an integer"), full_name,
+      throw BoutException(_f("Value for option {:s} = {:e} is not an integer"), full_name,
                           rval);
     }
   }
@@ -449,7 +449,7 @@ int Options::as<int>(const int& UNUSED(similar_to)) const {
 template <>
 BoutReal Options::as<BoutReal>(const BoutReal& UNUSED(similar_to)) const {
   if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
+    throw BoutException(_f("Option {:s} has no value"), full_name);
   }
 
   BoutReal result = BoutNaN;
@@ -464,7 +464,7 @@ BoutReal Options::as<BoutReal>(const BoutReal& UNUSED(similar_to)) const {
     result = parseExpression(value, this, "BoutReal", full_name);
 
   } else {
-    throw BoutException(_("Value for option {:s} cannot be converted to a BoutReal"),
+    throw BoutException(_f("Value for option {:s} cannot be converted to a BoutReal"),
                         full_name);
   }
 
@@ -479,7 +479,7 @@ BoutReal Options::as<BoutReal>(const BoutReal& UNUSED(similar_to)) const {
 template <>
 bool Options::as<bool>(const bool& UNUSED(similar_to)) const {
   if (is_section) {
-    throw BoutException(_("Option {:s} has no value"), full_name);
+    throw BoutException(_f("Option {:s} has no value"), full_name);
   }
 
   bool result = false;
@@ -494,12 +494,12 @@ bool Options::as<bool>(const bool& UNUSED(similar_to)) const {
     // Check that the result is either close to 1 (true) or close to 0 (false)
     const int ival = ROUND(rval);
     if ((fabs(rval - static_cast<BoutReal>(ival)) > 1e-3) or (ival < 0) or (ival > 1)) {
-      throw BoutException(_("Value for option {:s} = {:e} is not a bool"), full_name,
+      throw BoutException(_f("Value for option {:s} = {:e} is not a bool"), full_name,
                           rval);
     }
     result = ival == 1;
   } else {
-    throw BoutException(_("Value for option {:s} cannot be converted to a bool"),
+    throw BoutException(_f("Value for option {:s} cannot be converted to a bool"),
                         full_name);
   }
 
@@ -579,7 +579,7 @@ Field3D Options::as<Field3D>(const Field3D& similar_to) const {
                         localmesh->LocalNz);
   }
 
-  throw BoutException(_("Value for option {:s} cannot be converted to a Field3D"),
+  throw BoutException(_f("Value for option {:s} cannot be converted to a Field3D"),
                       full_name);
 }
 
@@ -631,7 +631,7 @@ Field2D Options::as<Field2D>(const Field2D& similar_to) const {
     }
   }
 
-  throw BoutException(_("Value for option {:s} cannot be converted to a Field2D"),
+  throw BoutException(_f("Value for option {:s} cannot be converted to a Field2D"),
                       full_name);
 }
 
@@ -713,7 +713,7 @@ FieldPerp Options::as<FieldPerp>(const FieldPerp& similar_to) const {
     // to select a region from it using Mesh e.g. if this
     // is from the input grid file.
   }
-  throw BoutException(_("Value for option {:s} cannot be converted to a FieldPerp"),
+  throw BoutException(_f("Value for option {:s} cannot be converted to a FieldPerp"),
                       full_name);
 }
 
@@ -755,14 +755,13 @@ namespace {
 template <class T>
 T as_amt(const Options& self, const T& similar_to) {
   if (self.isSection()) {
-    throw BoutException(_("Option {:s} has no value"), self.str());
+    throw BoutException(_f("Option {:s} has no value"), self.str());
   }
 
   const T result = bout::utils::visit(
       ConvertContainer<T>{
-          fmt::format(
-              fmt::runtime(_("Value for option {:s} cannot be converted to an {}")),
-              self.str(), bout::utils::typeName<T>()),
+          fmt::format(_f("Value for option {:s} cannot be converted to an {}"),
+                      self.str(), bout::utils::typeName<T>()),
           similar_to},
       self.value);
 
@@ -984,43 +983,6 @@ std::vector<int> Options::getShape() const {
   return lazy_shape;
 }
 
-fmt::format_parse_context::iterator
-bout::details::OptionsFormatterBase::parse(fmt::format_parse_context& ctx) {
-
-  const auto* closing_brace = std::find(ctx.begin(), ctx.end(), '}');
-  std::for_each(ctx.begin(), closing_brace, [&](auto ctx_opt) {
-    switch (ctx_opt) {
-    case 'd':
-      docstrings = true;
-      break;
-    case 'i':
-      inline_section_names = true;
-      break;
-    case 'k':
-      key_only = true;
-      break;
-    case 's':
-      source = true;
-      break;
-    case 'u':
-      unused = true;
-      break;
-    default:
-      throw fmt::format_error("invalid format for 'Options'");
-    }
-  });
-
-  // Keep a copy of the format string (without the last '}') so we can
-  // pass it down to the subsections.
-  const auto size = std::distance(ctx.begin(), closing_brace);
-  format_string.reserve(size + 3);
-  format_string.assign("{:");
-  format_string.append(ctx.begin(), closing_brace);
-  format_string.push_back('}');
-
-  return closing_brace;
-}
-
 fmt::format_context::iterator
 bout::details::OptionsFormatterBase::format(const Options& options,
                                             fmt::format_context& ctx) const {
@@ -1099,22 +1061,20 @@ bout::details::OptionsFormatterBase::format(const Options& options,
   // Get all the child values first
   for (const auto& child : children) {
     if (child.second.isValue()) {
-      fmt::format_to(ctx.out(), fmt::runtime(format_string), child.second);
+      format(child.second, ctx);
       fmt::format_to(ctx.out(), "\n");
     }
   }
 
   // Now descend the tree, accumulating subsections
   for (const auto& subsection : options.subsections()) {
-    fmt::format_to(ctx.out(), fmt::runtime(format_string), *subsection.second);
+    format(*subsection.second, ctx);
   }
 
   return ctx.out();
 }
 
-std::string toString(const Options& value) {
-  return fmt::format(fmt::runtime("{}"), value);
-}
+std::string toString(const Options& value) { return fmt::format("{}", value); }
 
 namespace bout {
 void checkForUnusedOptions() {
@@ -1160,7 +1120,7 @@ void checkForUnusedOptions(const Options& options, const std::string& data_dir,
       }
       possible_misspellings += fmt::format("\nUnused option '{}', did you mean:\n", key);
       for (const auto& match : fuzzy_matches) {
-        possible_misspellings += fmt::format(fmt::runtime("\t{:idk}\n"), match.match);
+        possible_misspellings += fmt::format("\t{:idk}\n", match.match);
       }
     }
 
@@ -1170,10 +1130,7 @@ void checkForUnusedOptions(const Options& options, const std::string& data_dir,
             ? ""
             : fmt::format("Suggested alternatives:\n{}", possible_misspellings);
 
-    // Raw string to help with the formatting of the message, and a
-    // separate variable so clang-format doesn't barf on the
-    // exception
-    const std::string unused_message = _(R"(
+    throw BoutException(_f(R"(
 There were unused input options:
 -----
 {:i}
@@ -1196,9 +1153,8 @@ turn off this check for unused options. You can always set
 'input:validate=true' to check inputs without running the full
 simulation.
 
-{})");
-
-    throw BoutException(unused_message, unused, data_dir, option_file,
+{})"),
+                        unused, data_dir, option_file,
                         unused.getChildren().begin()->first, additional_info);
   }
 }
diff --git a/src/sys/options/options_ini.cxx b/src/sys/options/options_ini.cxx
index b51af8fdcf..b5f813d168 100644
--- a/src/sys/options/options_ini.cxx
+++ b/src/sys/options/options_ini.cxx
@@ -52,8 +52,17 @@
 #include "options_ini.hxx"
 
 #include <bout/boutexception.hxx>
+#include <bout/options.hxx>
+#include <bout/sys/gettext.hxx>
 #include <bout/utils.hxx>
 
+#include <cstddef>
+#include <fstream>
+#include <ios>
+#include <string>
+
+#include "fmt/format.h"
+
 using namespace std;
 
 /**************************************************************************
@@ -65,7 +74,7 @@ void OptionINI::read(Options* options, const string& filename) {
   fin.open(filename.c_str());
 
   if (!fin.good()) {
-    throw BoutException(_("\tOptions file '{:s}' not found\n"), filename);
+    throw BoutException(_f("\tOptions file '{:s}' not found\n"), filename);
   }
 
   Options* section = options; // Current section
@@ -142,7 +151,7 @@ void OptionINI::read(Options* options, const string& filename) {
         // Add this to the current section
         section->set(key, value, filename);
       } // section test
-    }   // buffer.empty
+    } // buffer.empty
   } while (!fin.eof());
 
   fin.close();
@@ -153,11 +162,11 @@ void OptionINI::write(Options* options, const std::string& filename) {
   fout.open(filename, ios::out | ios::trunc);
 
   if (!fout.good()) {
-    throw BoutException(_("Could not open output file '{:s}'\n"), filename);
+    throw BoutException(_f("Could not open output file '{:s}'\n"), filename);
   }
 
   // Call recursive function to write to file
-  fout << fmt::format(fmt::runtime("{:uds}"), *options);
+  fout << fmt::format("{:uds}", *options);
 
   fout.close();
 }
@@ -193,10 +202,10 @@ void OptionINI::parse(const string& buffer, string& key, string& value) {
   value = trim(buffer.substr(startpos + 1), " \t\r\n\"");
 
   if (key.empty()) {
-    throw BoutException(_("\tEmpty key\n\tLine: {:s}"), buffer);
+    throw BoutException(_f("\tEmpty key\n\tLine: {:s}"), buffer);
   }
 
   if (key.find(':') != std::string::npos) {
-    throw BoutException(_("\tKey must not contain ':' character\n\tLine: {:s}"), buffer);
+    throw BoutException(_f("\tKey must not contain ':' character\n\tLine: {:s}"), buffer);
   }
 }
diff --git a/src/sys/optionsreader.cxx b/src/sys/optionsreader.cxx
index e16df31c97..3ce668a421 100644
--- a/src/sys/optionsreader.cxx
+++ b/src/sys/optionsreader.cxx
@@ -1,6 +1,9 @@
 #include <bout/assert.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/options.hxx>
 #include <bout/optionsreader.hxx>
+#include <bout/output.hxx>
+#include <bout/sys/gettext.hxx>
 #include <bout/utils.hxx>
 
 // Interface for option file parsers
@@ -9,7 +12,9 @@
 // Individual parsers
 #include "options/options_ini.hxx"
 
-#include <bout/output.hxx>
+#include <cstddef>
+#include <string>
+#include <vector>
 
 OptionsReader* OptionsReader::instance = nullptr;
 
@@ -36,7 +41,7 @@ void OptionsReader::write(Options* options, const std::string& filename) {
     throw BoutException("OptionsReader::write passed empty filename\n");
   }
 
-  output_info.write(_("Writing options to file {:s}\n"), filename);
+  output_info.write(_f("Writing options to file {:s}\n"), filename);
 
   OptionINI{}.write(options, filename);
 }
@@ -105,7 +110,7 @@ void OptionsReader::parseCommandLine(Options* options,
       size_t endpos = buffer.find_last_of('=');
 
       if (startpos != endpos) {
-        throw BoutException(_("\tMultiple '=' in command-line argument '{:s}'\n"),
+        throw BoutException(_f("\tMultiple '=' in command-line argument '{:s}'\n"),
                             buffer);
       }
 
@@ -121,7 +126,7 @@ void OptionsReader::parseCommandLine(Options* options,
       }
 
       if (key.empty() || value.empty()) {
-        throw BoutException(_("\tEmpty key or value in command line '{:s}'\n"), buffer);
+        throw BoutException(_f("\tEmpty key or value in command line '{:s}'\n"), buffer);
       }
 
       options->set(key, value, _("Command line"));
diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx
index f0256b6aa7..fb3e6a62c5 100644
--- a/tests/unit/sys/test_options.cxx
+++ b/tests/unit/sys/test_options.cxx
@@ -1112,7 +1112,7 @@ TEST_F(OptionsTest, FormatValue) {
   const std::string expected =
       "value1 = 4		# type: int, doc: This is a value, source: some test";
 
-  EXPECT_EQ(expected, fmt::format(fmt::runtime("{:ds}"), options["value1"]));
+  EXPECT_EQ(expected, fmt::format("{:ds}", options["value1"]));
 }
 
 TEST_F(OptionsTest, FormatDefault) {
@@ -1140,7 +1140,7 @@ value4 = 3.2
 value6 = 12
 )";
 
-  EXPECT_EQ(fmt::format(fmt::runtime("{}"), option), expected);
+  EXPECT_EQ(fmt::format("{}", option), expected);
 }
 
 TEST_F(OptionsTest, FormatDocstrings) {
@@ -1171,7 +1171,7 @@ value4 = 3.2
 value6 = 12
 )";
 
-  EXPECT_EQ(fmt::format(fmt::runtime("{:d}"), option), expected);
+  EXPECT_EQ(fmt::format("{:d}", option), expected);
 }
 
 TEST_F(OptionsTest, FormatDocstringsAndInline) {
@@ -1194,9 +1194,9 @@ section2:subsection1:value4 = 3.2
 section3:subsection2:value6 = 12
 )";
 
-  EXPECT_EQ(fmt::format(fmt::runtime("{:di}"), option), expected);
+  EXPECT_EQ(fmt::format("{:di}", option), expected);
   // Order of format spec shouldn't matter
-  EXPECT_EQ(fmt::format(fmt::runtime("{:id}"), option), expected);
+  EXPECT_EQ(fmt::format("{:id}", option), expected);
 }
 
 TEST_F(OptionsTest, FormatDocstringsAndInlineKeysOnly) {
@@ -1221,16 +1221,16 @@ section2:subsection1:value4
 section3:subsection2:value6		# source: a test
 )";
 
-  EXPECT_EQ(fmt::format(fmt::runtime("{:ksdi}"), option), expected);
+  EXPECT_EQ(fmt::format("{:ksdi}", option), expected);
   // Order of format spec shouldn't matter
-  EXPECT_EQ(fmt::format(fmt::runtime("{:idsk}"), option), expected);
+  EXPECT_EQ(fmt::format("{:idsk}", option), expected);
 }
 
 TEST_F(OptionsTest, FormatUnused) {
   Options option{{"section1", {{"value1", 42}}}};
   std::string expected =
       "section1:value1\t\t# unused value (NOT marked conditionally used)\n";
-  EXPECT_EQ(fmt::format(fmt::runtime("{:iku}"), option), expected);
+  EXPECT_EQ(fmt::format("{:iku}", option), expected);
 }
 
 TEST_F(OptionsTest, FormatConditionallyUsed) {
@@ -1238,7 +1238,7 @@ TEST_F(OptionsTest, FormatConditionallyUsed) {
   option.setConditionallyUsed();
   std::string expected =
       "section1:value1\t\t# unused value (marked conditionally used)\n";
-  EXPECT_EQ(fmt::format(fmt::runtime("{:iku}"), option), expected);
+  EXPECT_EQ(fmt::format("{:iku}", option), expected);
 }
 
 TEST_F(OptionsTest, GetUnused) {
diff --git a/tests/unit/sys/test_output.cxx b/tests/unit/sys/test_output.cxx
index 2f13df9cb7..5beb12c0c2 100644
--- a/tests/unit/sys/test_output.cxx
+++ b/tests/unit/sys/test_output.cxx
@@ -332,7 +332,7 @@ TEST_F(OutputTest, FormatInd3DInvalid) {
   Ind3D ind(11, 2, 3);
 
   Output local_output;
-  EXPECT_THROW(local_output.write("{:b}", ind), fmt::format_error);
+  EXPECT_THROW(local_output.write(fmt::runtime("{:b}"), ind), fmt::format_error);
 }
 
 TEST_F(OutputTest, FormatInd2Ddefault) {
diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
index 8f838b864c..40aecb923e 100644
--- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
+++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
@@ -162,7 +162,7 @@ cdef extern from "helper.h":
 
 cdef extern from "bout/output.hxx":
     cppclass ConditionalOutput:
-        void write(const char * str, const char * str)
+        void write(const char * str)
     ConditionalOutput output_info
 
 cdef extern from "bout/vecops.hxx":
diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index d6f0601f1c..2710c9f21f 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -1709,7 +1709,7 @@ def print(*args, sep=" ", end="\n"):
 
 cdef _print(value):
     cdef c.string str_ = value.encode()
-    c.output_info.write("{:s}", str_.c_str())
+    c.output_info.write(str_.c_str())
 
 {% include "helper.py" %}
 

From 5269a7d59be6af4892062312853386aa2231d71c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 27 Feb 2026 09:44:51 +0000
Subject: [PATCH 0541/1827] Add `operator+(Region&&, const Region&)` to make
 `clang-tidy` happy

---
 include/bout/region.hxx  | 6 ++++++
 tests/unit/fake_mesh.hxx | 5 +++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index bb1cf82bf1..181582c7d6 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -972,6 +972,12 @@ Region<T> operator+(const Region<T>& lhs, const Region<T>& rhs) {
   return Region<T>(indices);
 }
 
+template <typename T>
+Region<T> operator+(Region<T>&& lhs, const Region<T>& rhs) {
+  lhs += rhs;
+  return std::move(lhs);
+}
+
 /// Returns a new region based on input but with indices offset by
 /// a constant
 template <typename T>
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 7c5d0b3637..b79f5b0593 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -19,6 +19,7 @@
 #include <iterator>
 #include <memory>
 #include <numeric>
+#include <string>
 #include <utility>
 #include <vector>
 
@@ -239,7 +240,7 @@ public:
     addRegion2D("RGN_BNDRY", std::accumulate(begin(boundary_names), end(boundary_names),
                                              Region<Ind2D>{},
                                              [&](Region<Ind2D> a, const std::string& b) {
-                                               return a + getRegion2D(b);
+                                               return std::move(a) + getRegion2D(b);
                                              })
                                  .unique());
 
@@ -247,7 +248,7 @@ public:
                 std::accumulate(begin(boundary_names), end(boundary_names),
                                 Region<Ind3D>{},
                                 [this](Region<Ind3D> a, const std::string& b) {
-                                  return a + getRegion3D(b);
+                                  return std::move(a) + getRegion3D(b);
                                 })
                     .unique());
     addRegionPerp("RGN_BNDRY",

From 570a76397481f17495a0735e34f406994638229e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Feb 2026 19:37:22 +0000
Subject: [PATCH 0542/1827] Bump ZedThree/clang-tidy-review from 0.23.0 to
 0.23.1

Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.23.0 to 0.23.1.
- [Release notes](https://github.com/zedthree/clang-tidy-review/releases)
- [Changelog](https://github.com/ZedThree/clang-tidy-review/blob/master/CHANGELOG.md)
- [Commits](https://github.com/zedthree/clang-tidy-review/compare/v0.23.0...v0.23.1)

---
updated-dependencies:
- dependency-name: ZedThree/clang-tidy-review
  dependency-version: 0.23.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/clang-tidy-review.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 087c910987..360a162456 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -21,7 +21,7 @@ jobs:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.23.0
+        uses: ZedThree/clang-tidy-review@v0.23.1
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.23.0
+        uses: ZedThree/clang-tidy-review/upload@v0.23.1

From 53f838c9713c33213cd90031d863d48531a0195e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Feb 2026 19:37:26 +0000
Subject: [PATCH 0543/1827] Bump actions/cache from 4 to 5

Bumps [actions/cache](https://github.com/actions/cache) from 4 to 5.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](https://github.com/actions/cache/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index e45e082232..bd59fede37 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -168,7 +168,7 @@ jobs:
           python -m pip install -r requirements.txt
 
       - name: Cache Zenodo test data
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: build/tests/integrated/test-fci-mpi/grid.fci.nc
           # If we update the test, invalidate the cache
@@ -205,7 +205,7 @@ jobs:
           submodules: true
 
       - name: Cache Zenodo test data
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: build/tests/integrated/test-fci-mpi/grid.fci.nc
           # If we update the test, invalidate the cache
@@ -228,7 +228,7 @@ jobs:
           submodules: true
 
       - name: Cache Zenodo test data
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: build/tests/integrated/test-fci-mpi/grid.fci.nc
           # If we update the test, invalidate the cache

From 518c5a5478fbc8962dacea19df6ef02a42d66b94 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Feb 2026 19:37:30 +0000
Subject: [PATCH 0544/1827] Bump externalpackages/boutdata from `962d5a5` to
 `0e06267`

Bumps [externalpackages/boutdata](https://github.com/boutproject/boutdata) from `962d5a5` to `0e06267`.
- [Release notes](https://github.com/boutproject/boutdata/releases)
- [Commits](https://github.com/boutproject/boutdata/compare/962d5a58b8e6133a2977c3e44f1d4751a11d2b1c...0e0626716f7fec01d318c427a96e596055540efe)

---
updated-dependencies:
- dependency-name: externalpackages/boutdata
  dependency-version: 0e0626716f7fec01d318c427a96e596055540efe
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/boutdata | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/boutdata b/externalpackages/boutdata
index 962d5a58b8..0e0626716f 160000
--- a/externalpackages/boutdata
+++ b/externalpackages/boutdata
@@ -1 +1 @@
-Subproject commit 962d5a58b8e6133a2977c3e44f1d4751a11d2b1c
+Subproject commit 0e0626716f7fec01d318c427a96e596055540efe

From a34c4fa1821fac4076804c6e53cdf807cff8b4d7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Feb 2026 19:37:33 +0000
Subject: [PATCH 0545/1827] Bump externalpackages/googletest from `9156d4c` to
 `73a63ea`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `9156d4c` to `73a63ea`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/9156d4caac880b513264ecbe0aa4746a3fead3d7...73a63ea05dc8ca29ec1d2c1d66481dd0de1950f1)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: 73a63ea05dc8ca29ec1d2c1d66481dd0de1950f1
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 9156d4caac..73a63ea05d 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 9156d4caac880b513264ecbe0aa4746a3fead3d7
+Subproject commit 73a63ea05dc8ca29ec1d2c1d66481dd0de1950f1

From 9f618b80cc39a42f4af190bfcf1be5d297363070 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Feb 2026 19:37:34 +0000
Subject: [PATCH 0546/1827] Bump actions/checkout from 5 to 6

Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/auto-formatting.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/auto-formatting.yml b/.github/workflows/auto-formatting.yml
index f54b012298..b7f1584515 100644
--- a/.github/workflows/auto-formatting.yml
+++ b/.github/workflows/auto-formatting.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0

From 96586162257f922db352a2fbef25b5065cb21f57 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 23 Feb 2023 13:52:03 +0100
Subject: [PATCH 0547/1827] enable openmp for sundials if it is enabled for
 BOUT++

---
 cmake/SetupBOUTThirdParty.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 850809e856..9e6bdc6d2a 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -362,7 +362,7 @@ if(BOUT_USE_SUNDIALS)
         CACHE BOOL "" FORCE
     )
     set(ENABLE_OPENMP
-        OFF
+        ${BOUT_USE_OPENMP}
         CACHE BOOL "" FORCE
     )
     if(BUILD_SHARED_LIBS)

From e96744a44066d45f0a740de343d05c3c09b87aac Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 18 Mar 2024 17:29:18 +0100
Subject: [PATCH 0548/1827] Inherit applyParallelBoundary functions

---
 include/bout/field3d.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index fad4815b92..d1be32dd84 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -496,6 +496,7 @@ public:
   /// Note: does not just copy values in boundary region.
   void setBoundaryTo(const Field3D& f3d);
 
+  using FieldData::applyParallelBoundary;
   void applyParallelBoundary() override;
   void applyParallelBoundary(BoutReal t) override;
   void applyParallelBoundary(const std::string& condition) override;

From ab783f0fe4554db8f541763353bb7528c6777ae6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 6 Nov 2023 16:30:06 +0100
Subject: [PATCH 0549/1827] Make Field2d and Field3D more similar

Useful for templates
---
 include/bout/field2d.hxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 92658f1bbf..3bafe3b116 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -133,8 +133,9 @@ public:
     return *this;
   }
 
-  /// Check if this field has yup and ydown fields
+  /// Dummy functions to increase portability
   bool hasParallelSlices() const { return true; }
+  void calcParallelSlices() const {}
 
   Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) { return *this; }
   const Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) const {

From fc2decea8723e1ac868796fd02c1a381754ac47b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 Mar 2024 13:30:54 +0100
Subject: [PATCH 0550/1827] Add more dummy functions to field2d

Allows to write code for Field3D, that also works for Field2D
---
 include/bout/field2d.hxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 3bafe3b116..6e82526bca 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -136,6 +136,8 @@ public:
   /// Dummy functions to increase portability
   bool hasParallelSlices() const { return true; }
   void calcParallelSlices() const {}
+  void clearParallelSlices() {}
+  int numberParallelSlices() { return 0; }
 
   Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) { return *this; }
   const Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) const {
@@ -275,7 +277,7 @@ public:
 
   friend void swap(Field2D& first, Field2D& second) noexcept;
 
-  int size() const override { return nx * ny; };
+  int size() const override { return nx * ny; }
 
 private:
   /// Internal data array. Handles allocation/freeing of memory

From 4d6873dba47411408f895117cba6d31ed34bb1c9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 27 Sep 2024 11:05:33 +0200
Subject: [PATCH 0551/1827] Add dummy functions for FieldPerp

---
 include/bout/fieldperp.hxx | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 6995308dbe..ad069f0d01 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -157,6 +157,25 @@ public:
     return *this;
   }
 
+  /// Dummy functions to increase portability
+  bool hasParallelSlices() const { return true; }
+  void calcParallelSlices() const {}
+  void clearParallelSlices() {}
+  int numberParallelSlices() { return 0; }
+
+  FieldPerp& yup(std::vector<FieldPerp>::size_type UNUSED(index) = 0) { return *this; }
+  const FieldPerp& yup(std::vector<FieldPerp>::size_type UNUSED(index) = 0) const {
+    return *this;
+  }
+
+  FieldPerp& ydown(std::vector<FieldPerp>::size_type UNUSED(index) = 0) { return *this; }
+  const FieldPerp& ydown(std::vector<FieldPerp>::size_type UNUSED(index) = 0) const {
+    return *this;
+  }
+
+  FieldPerp& ynext(int UNUSED(dir)) { return *this; }
+  const FieldPerp& ynext(int UNUSED(dir)) const { return *this; }
+
   /*!
    * Ensure that data array is allocated and unique
    */

From 3156681fdcd7bee3384a55ec3a3b98e0f2323744 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 16 Oct 2024 10:27:20 +0200
Subject: [PATCH 0552/1827] add setRegion / getRegionID to all fields

---
 include/bout/field.hxx   |  9 +++++++++
 include/bout/field3d.hxx | 12 +++++++-----
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 4e41aa3632..d6af2be3c2 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -30,6 +30,9 @@ class Field;
 #define FIELD_H
 
 #include <cmath>
+#include <cstdio>
+#include <memory>
+#include <optional>
 #include <string>
 
 #include "bout/bout_types.hxx"
@@ -125,6 +128,12 @@ public:
     swap(first.directions, second.directions);
   }
 
+  virtual void setRegion(size_t UNUSED(regionID)) {}
+  virtual void setRegion(std::optional<size_t> UNUSED(regionID)) {}
+  virtual void setRegion(const std::string& UNUSED(region_name)) {}
+  virtual void resetRegion() {}
+  virtual std::optional<size_t> getRegionID() const { return {}; }
+
 private:
   /// Labels for the type of coordinate system this field is defined over
   DirectionTypes directions{YDirectionType::Standard, ZDirectionType::Standard};
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index fad4815b92..607cbb37c4 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -327,11 +327,11 @@ public:
   const Region<Ind3D>& getRegion(const std::string& region_name) const;
   /// Use region provided by the default, and if none is set, use the provided one
   const Region<Ind3D>& getValidRegionWithDefault(const std::string& region_name) const;
-  void setRegion(const std::string& region_name);
-  void resetRegion() { regionID.reset(); };
-  void setRegion(size_t id) { regionID = id; };
-  void setRegion(std::optional<size_t> id) { regionID = id; };
-  std::optional<size_t> getRegionID() const { return regionID; };
+  void setRegion(const std::string& region_name) override;
+  void resetRegion() override { regionID.reset(); };
+  void setRegion(size_t id) override { regionID = id; };
+  void setRegion(std::optional<size_t> id) override { regionID = id; };
+  std::optional<size_t> getRegionID() const override { return regionID; };
 
   /// Return a Region<Ind2D> reference to use to iterate over the x- and
   /// y-indices of this field
@@ -510,6 +510,8 @@ public:
 
   std::weak_ptr<Options> getTracking() { return tracking; };
 
+  bool allowCalcParallelSlices{true};
+
 private:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
   int nx{-1}, ny{-1}, nz{-1};

From 160adb41523556bc93ad00c16975f871e65c7006 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 14 Mar 2025 15:38:24 +0100
Subject: [PATCH 0553/1827] Add Field2D::splitParallelSlices() for writing FCI
 aware code

---
 include/bout/field2d.hxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 6e82526bca..fca0dd3c3f 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -136,8 +136,9 @@ public:
   /// Dummy functions to increase portability
   bool hasParallelSlices() const { return true; }
   void calcParallelSlices() const {}
-  void clearParallelSlices() {}
-  int numberParallelSlices() { return 0; }
+  void splitParallelSlices() const {}
+  void clearParallelSlices() const {}
+  int numberParallelSlices() const { return 0; }
 
   Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) { return *this; }
   const Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) const {

From 5502ce360b975ed9d47a3e49dae88b49bdc033ef Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 27 Sep 2024 11:05:58 +0200
Subject: [PATCH 0554/1827] Allow XZHermiteSpline also without y-offset

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 27a4f1d614..40dad9b7bd 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -352,8 +352,7 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
 
-  const auto region2 =
-      y_offset == 0 ? "RGN_NOY" : fmt::format("RGN_YPAR_{:+d}", y_offset);
+  const auto region2 = y_offset != 0 ? fmt::format("RGN_YPAR_{:+d}", y_offset) : region;
 
 #if USE_NEW_WEIGHTS
 #ifdef HS_USE_PETSC

From c74d33065293652ded5b64f130cb3c1e0891c4e3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Jan 2025 13:20:10 +0100
Subject: [PATCH 0555/1827] Add communication routine for FCI operation

For FCI we need to be able to access "random" data from the adjacent
slices. If they are split in x-direction, this requires some tricky
communication pattern.

It can be used like this:
```
// Create object
GlobalField3DAccess fci_comm(thismesh);
// let it know what data points will be required:
// where IndG3D is an index in the global field, which would be the
// normal Ind3D if there would be only one proc.
fci_comm.get(IndG3D(i, ny, nz));
// If all index have been added, the communication pattern will be
// established. This has to be called by all processors in parallel
fci_comm.setup()
// Once the data for a given field is needed, it needs to be
// communicated:
GlobalField3DAccessInstance global_data = fci_comm.communicate(f3d);
// and can be accessed like this
BoutReal data = global_data[IndG3D(i, ny, nz)];
// ny and nz in the IndG3D are always optional.
```
---
 CMakeLists.txt                 |   2 +
 include/bout/region.hxx        |   3 +-
 src/mesh/parallel/fci_comm.cxx |  34 +++++
 src/mesh/parallel/fci_comm.hxx | 241 +++++++++++++++++++++++++++++++++
 4 files changed, 279 insertions(+), 1 deletion(-)
 create mode 100644 src/mesh/parallel/fci_comm.cxx
 create mode 100644 src/mesh/parallel/fci_comm.hxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e8c4657fb0..615a31d722 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -301,6 +301,8 @@ set(BOUT_SOURCES
     ./src/mesh/mesh.cxx
     ./src/mesh/parallel/fci.cxx
     ./src/mesh/parallel/fci.hxx
+    ./src/mesh/parallel/fci_comm.cxx
+    ./src/mesh/parallel/fci_comm.hxx
     ./src/mesh/parallel/identity.cxx
     ./src/mesh/parallel/shiftedmetric.cxx
     ./src/mesh/parallel/shiftedmetricinterp.cxx
diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index bb1cf82bf1..f441b3edd7 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -139,7 +139,7 @@ class BoutMask;
   BOUT_FOR_OMP(index, (region), for schedule(BOUT_OPENMP_SCHEDULE) nowait)
 // NOLINTEND(cppcoreguidelines-macro-usage,bugprone-macro-parentheses)
 
-enum class IND_TYPE { IND_3D = 0, IND_2D = 1, IND_PERP = 2 };
+enum class IND_TYPE { IND_3D = 0, IND_2D = 1, IND_PERP = 2, IND_GLOBAL_3D };
 
 /// Indices base class for Fields -- Regions are dereferenced into these
 ///
@@ -386,6 +386,7 @@ inline SpecificInd<N> operator-(SpecificInd<N> lhs, const SpecificInd<N>& rhs) {
 using Ind3D = SpecificInd<IND_TYPE::IND_3D>;
 using Ind2D = SpecificInd<IND_TYPE::IND_2D>;
 using IndPerp = SpecificInd<IND_TYPE::IND_PERP>;
+using IndG3D = SpecificInd<IND_TYPE::IND_GLOBAL_3D>;
 
 /// Get string representation of Ind3D
 inline std::string toString(const Ind3D& i) {
diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
new file mode 100644
index 0000000000..c0d51d1eb9
--- /dev/null
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -0,0 +1,34 @@
+/**************************************************************************
+ * Communication for Flux-coordinate Independent interpolation
+ *
+ **************************************************************************
+ * Copyright 2025 BOUT++ contributors
+ *
+ * Contact: Ben Dudson, dudson2@llnl.gov
+ *
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#include "fci_comm.hxx"
+
+#include <vector>
+
+const BoutReal& GlobalField3DAccessInstance::operator[](IndG3D ind) const {
+  auto it = gfa.mapping.find(ind.ind);
+  ASSERT2(it != gfa.mapping.end());
+  return data[it->second];
+}
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
new file mode 100644
index 0000000000..aa3b5ecfb5
--- /dev/null
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -0,0 +1,241 @@
+/**************************************************************************
+ * Communication for Flux-coordinate Independent interpolation
+ *
+ **************************************************************************
+ * Copyright 2025 BOUT++ contributors
+ *
+ * Contact: Ben Dudson, dudson2@llnl.gov
+ *
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#pragma once
+
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutcomm.hxx"
+#include "bout/field3d.hxx"
+#include "bout/mesh.hxx"
+#include "bout/region.hxx"
+#include <algorithm>
+#include <map>
+#include <memory>
+#include <set>
+#include <stddef.h>
+#include <utility>
+#include <vector>
+class GlobalField3DAccess;
+
+namespace fci_comm {
+struct ProcLocal {
+  int proc;
+  int ind;
+};
+struct globalToLocal1D {
+  const int mg;
+  const int npe;
+  const int localwith;
+  const int local;
+  const int global;
+  const int globalwith;
+  globalToLocal1D(int mg, int npe, int localwith)
+      : mg(mg), npe(npe), localwith(localwith), local(localwith - 2 * mg),
+        global(local * npe), globalwith(global + 2 * mg) {};
+  ProcLocal convert(int id) const {
+    int idwo = id - mg;
+    int proc = idwo / local;
+    if (proc >= npe) {
+      proc = npe - 1;
+    }
+    ASSERT2(proc >= 0);
+    int loc = id - local * proc;
+    ASSERT2(0 <= loc);
+    ASSERT2(loc < (local + 2 * mg));
+    return {proc, loc};
+  }
+};
+template <class ind>
+struct XYZ2Ind {
+  const int nx;
+  const int ny;
+  const int nz;
+  ind convert(const int x, const int y, const int z) const {
+    return {z + (y + x * ny) * nz, ny, nz};
+  }
+  ind operator()(const int x, const int y, const int z) const { return convert(x, y, z); }
+  XYZ2Ind(const int nx, const int ny, const int nz) : nx(nx), ny(ny), nz(nz) {}
+};
+} // namespace fci_comm
+
+class GlobalField3DAccessInstance {
+public:
+  const BoutReal& operator[](IndG3D ind) const;
+
+  GlobalField3DAccessInstance(const GlobalField3DAccess* gfa,
+                              const std::vector<BoutReal>&& data)
+      : gfa(*gfa), data(std::move(data)) {};
+
+private:
+  const GlobalField3DAccess& gfa;
+  const std::vector<BoutReal> data;
+};
+
+class GlobalField3DAccess {
+public:
+  friend class GlobalField3DAccessInstance;
+  GlobalField3DAccess(Mesh* mesh)
+      : mesh(mesh), g2lx(mesh->xstart, mesh->getNXPE(), mesh->LocalNx),
+        g2ly(mesh->ystart, mesh->getNYPE(), mesh->LocalNy),
+        g2lz(mesh->zstart, 1, mesh->LocalNz),
+        xyzl(g2lx.localwith, g2ly.localwith, g2lz.localwith),
+        xyzg(g2lx.globalwith, g2ly.globalwith, g2lz.globalwith), comm(BoutComm::get()) {};
+  void get(IndG3D ind) { ids.emplace(ind.ind); }
+  void operator[](IndG3D ind) { return get(ind); }
+  void setup() {
+    ASSERT2(is_setup == false);
+    toGet.resize(g2lx.npe * g2ly.npe * g2lz.npe);
+    for (const auto id : ids) {
+      IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
+      const auto pix = g2lx.convert(gind.x());
+      const auto piy = g2ly.convert(gind.y());
+      const auto piz = g2lz.convert(gind.z());
+      ASSERT3(piz.proc == 0);
+      toGet[piy.proc * g2lx.npe + pix.proc].push_back(
+          xyzl.convert(pix.ind, piy.ind, piz.ind).ind);
+    }
+    for (auto v : toGet) {
+      std::sort(v.begin(), v.end());
+    }
+    commCommLists();
+    {
+      int offset = 0;
+      for (auto get : toGet) {
+        offsets.push_back(offset);
+        offset += get.size();
+      }
+      offsets.push_back(offset);
+    }
+    std::map<int, int> mapping;
+    for (const auto id : ids) {
+      IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
+      const auto pix = g2lx.convert(gind.x());
+      const auto piy = g2ly.convert(gind.y());
+      const auto piz = g2lz.convert(gind.z());
+      ASSERT3(piz.proc == 0);
+      const auto proc = piy.proc * g2lx.npe + pix.proc;
+      const auto& vec = toGet[proc];
+      auto it =
+          std::find(vec.begin(), vec.end(), xyzl.convert(pix.ind, piy.ind, piz.ind).ind);
+      ASSERT3(it != vec.end());
+      mapping[id] = it - vec.begin() + offsets[proc];
+    }
+    is_setup = true;
+  }
+  GlobalField3DAccessInstance communicate(const Field3D& f) {
+    return {this, communicate_data(f)};
+  }
+  std::unique_ptr<GlobalField3DAccessInstance> communicate_asPtr(const Field3D& f) {
+    return std::make_unique<GlobalField3DAccessInstance>(this, communicate_data(f));
+  }
+
+private:
+  void commCommLists() {
+    toSend.resize(toGet.size());
+    std::vector<int> toGetSizes(toGet.size());
+    std::vector<int> toSendSizes(toSend.size());
+    //const int thisproc = mesh->getYProcIndex() * g2lx.npe + mesh->getXProcIndex();
+    std::vector<MPI_Request> reqs(toSend.size());
+    for (size_t proc = 0; proc < toGet.size(); ++proc) {
+      auto ret = MPI_Irecv(static_cast<void*>(&toSendSizes[proc]), 1, MPI_INT, proc,
+                           666 + proc, comm, &reqs[proc]);
+      ASSERT0(ret == MPI_SUCCESS);
+    }
+    for (size_t proc = 0; proc < toGet.size(); ++proc) {
+      toGetSizes[proc] = toGet[proc].size();
+      sendBufferSize += toGetSizes[proc];
+      auto ret = MPI_Send(static_cast<void*>(&toGetSizes[proc]), 1, MPI_INT, proc,
+                          666 + proc, comm);
+      ASSERT0(ret == MPI_SUCCESS);
+    }
+    for ([[maybe_unused]] auto dummy : reqs) {
+      int ind{0};
+      auto ret = MPI_Waitany(reqs.size(), &reqs[0], &ind, MPI_STATUS_IGNORE);
+      ASSERT0(ret == MPI_SUCCESS);
+      ASSERT3(ind != MPI_UNDEFINED);
+      toSend[ind].resize(toSendSizes[ind]);
+      ret = MPI_Irecv(static_cast<void*>(&toSend[ind]), toSend[ind].size(), MPI_INT, ind,
+                      666 * 666 + ind, comm, &reqs[ind]);
+      ASSERT0(ret == MPI_SUCCESS);
+    }
+    for (size_t proc = 0; proc < toGet.size(); ++proc) {
+      const auto ret = MPI_Send(static_cast<void*>(&toGet[proc]), toGet[proc].size(),
+                                MPI_INT, proc, 666 * 666 + proc, comm);
+      ASSERT0(ret == MPI_SUCCESS);
+    }
+    for ([[maybe_unused]] auto dummy : reqs) {
+      int ind{0};
+      const auto ret = MPI_Waitany(reqs.size(), &reqs[0], &ind, MPI_STATUS_IGNORE);
+      ASSERT0(ret == MPI_SUCCESS);
+      ASSERT3(ind != MPI_UNDEFINED);
+    }
+  }
+  Mesh* mesh;
+  std::set<int> ids;
+  std::map<int, int> mapping;
+  bool is_setup{false};
+  const fci_comm::globalToLocal1D g2lx;
+  const fci_comm::globalToLocal1D g2ly;
+  const fci_comm::globalToLocal1D g2lz;
+
+public:
+  const fci_comm::XYZ2Ind<Ind3D> xyzl;
+  const fci_comm::XYZ2Ind<IndG3D> xyzg;
+
+private:
+  std::vector<std::vector<int>> toGet;
+  std::vector<std::vector<int>> toSend;
+  std::vector<int> offsets;
+  int sendBufferSize{0};
+  MPI_Comm comm;
+  std::vector<BoutReal> communicate_data(const Field3D& f) {
+    ASSERT2(f.getMesh() == mesh);
+    std::vector<BoutReal> data(offsets.back());
+    std::vector<BoutReal> sendBuffer(sendBufferSize);
+    std::vector<MPI_Request> reqs(toSend.size());
+    for (size_t proc = 0; proc < toGet.size(); ++proc) {
+      auto ret = MPI_Irecv(static_cast<void*>(&data[proc]), toGet[proc].size(),
+                           MPI_DOUBLE, proc, 666 + proc, comm, &reqs[proc]);
+      ASSERT0(ret == MPI_SUCCESS);
+    }
+    int cnt = 0;
+    for (size_t proc = 0; proc < toGet.size(); ++proc) {
+      void* start = static_cast<void*>(&sendBuffer[cnt]);
+      for (auto i : toSend[proc]) {
+        sendBuffer[cnt++] = f[Ind3D(i)];
+      }
+      auto ret = MPI_Send(start, toSend[proc].size(), MPI_DOUBLE, proc, 666 + proc, comm);
+      ASSERT0(ret == MPI_SUCCESS);
+    }
+    for ([[maybe_unused]] auto dummy : reqs) {
+      int ind{0};
+      auto ret = MPI_Waitany(reqs.size(), &reqs[0], &ind, MPI_STATUS_IGNORE);
+      ASSERT0(ret == MPI_SUCCESS);
+      ASSERT3(ind != MPI_UNDEFINED);
+    }
+    return data;
+  }
+};

From afc68d971bb6c0c6c93fa66873d0a2ff397a211e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Jan 2025 13:26:37 +0100
Subject: [PATCH 0556/1827] Unify XZMonotonicHermiteSpline and
 XZMonotonicHermiteSpline

If they are two instances of the same template, this allows to have an
if in the inner loop that can be optimised out.
---
 CMakeLists.txt                                |  1 -
 include/bout/interpolation_xz.hxx             | 84 +++++-----------
 src/mesh/interpolation/hermite_spline_xz.cxx  | 74 +++++++++++---
 .../monotonic_hermite_spline_xz.cxx           | 98 -------------------
 src/mesh/interpolation_xz.cxx                 |  1 +
 5 files changed, 85 insertions(+), 173 deletions(-)
 delete mode 100644 src/mesh/interpolation/monotonic_hermite_spline_xz.cxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 615a31d722..11ff1df22e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -296,7 +296,6 @@ set(BOUT_SOURCES
     ./src/mesh/interpolation/hermite_spline_z.cxx
     ./src/mesh/interpolation/interpolation_z.cxx
     ./src/mesh/interpolation/lagrange_4pt_xz.cxx
-    ./src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
     ./src/mesh/invert3x3.hxx
     ./src/mesh/mesh.cxx
     ./src/mesh/parallel/fci.cxx
diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 4dd24259fd..2832899e8a 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -38,6 +38,7 @@
 #endif
 
 class Options;
+class GlobalField3DAccess;
 
 /// Interpolate a field onto a perturbed set of points
 const Field3D interpolate(const Field3D& f, const Field3D& delta_x,
@@ -135,7 +136,16 @@ public:
   }
 };
 
-class XZHermiteSpline : public XZInterpolation {
+/// Monotonic Hermite spline interpolator
+///
+/// Similar to XZHermiteSpline, so uses most of the same code.
+/// Forces the interpolated result to be in the range of the
+/// neighbouring cell values. This prevents unphysical overshoots,
+/// but also degrades accuracy near maxima and minima.
+/// Perhaps should only impose near boundaries, since that is where
+/// problems most obviously occur.
+template <bool monotonic>
+class XZHermiteSplineBase : public XZInterpolation {
 protected:
   /// This is protected rather than private so that it can be
   /// extended and used by HermiteSplineMonotonic
@@ -143,6 +153,9 @@ protected:
   Tensor<SpecificInd<IND_TYPE::IND_3D>> i_corner; // index of bottom-left grid point
   Tensor<int> k_corner;                           // z-index of bottom-left grid point
 
+  std::unique_ptr<GlobalField3DAccess> gf3daccess;
+  Tensor<std::array<int, 4>> g3dinds;
+
   // Basis functions for cubic Hermite spline interpolation
   //    see http://en.wikipedia.org/wiki/Cubic_Hermite_spline
   // The h00 and h01 basis functions are applied to the function itself
@@ -168,14 +181,14 @@ protected:
 #endif
 
 public:
-  XZHermiteSpline(Mesh* mesh = nullptr, [[maybe_unused]] Options* options = nullptr)
-      : XZHermiteSpline(0, mesh) {}
-  XZHermiteSpline(int y_offset = 0, Mesh* mesh = nullptr);
-  XZHermiteSpline(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr)
-      : XZHermiteSpline(y_offset, mesh) {
+  XZHermiteSplineBase(Mesh* mesh = nullptr, [[maybe_unused]] Options* options = nullptr)
+      : XZHermiteSplineBase(0, mesh) {}
+  XZHermiteSplineBase(int y_offset = 0, Mesh* mesh = nullptr);
+  XZHermiteSplineBase(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr)
+      : XZHermiteSplineBase(y_offset, mesh) {
     setRegion(regionFromMask(mask, localmesh));
   }
-  ~XZHermiteSpline() {
+  ~XZHermiteSplineBase() {
 #if HS_USE_PETSC
     if (isInit) {
       MatDestroy(&petscWeights);
@@ -205,61 +218,8 @@ public:
   getWeightsForYApproximation(int i, int j, int k, int yoffset) override;
 };
 
-/// Monotonic Hermite spline interpolator
-///
-/// Similar to XZHermiteSpline, so uses most of the same code.
-/// Forces the interpolated result to be in the range of the
-/// neighbouring cell values. This prevents unphysical overshoots,
-/// but also degrades accuracy near maxima and minima.
-/// Perhaps should only impose near boundaries, since that is where
-/// problems most obviously occur.
-///
-/// You can control how tight the clipping to the range of the neighbouring cell
-/// values through ``rtol`` and ``atol``:
-///
-///     diff = (max_of_neighours - min_of_neighours) * rtol + atol
-///
-/// and the interpolated value is instead clipped to the range
-/// ``[min_of_neighours - diff, max_of_neighours + diff]``
-class XZMonotonicHermiteSpline : public XZHermiteSpline {
-  /// Absolute tolerance for clipping
-  BoutReal atol = 0.0;
-  /// Relative tolerance for clipping
-  BoutReal rtol = 1.0;
-
-public:
-  XZMonotonicHermiteSpline(Mesh* mesh = nullptr, Options* options = nullptr)
-      : XZHermiteSpline(0, mesh),
-        atol{(*options)["atol"]
-                 .doc("Absolute tolerance for clipping overshoot")
-                 .withDefault(0.0)},
-        rtol{(*options)["rtol"]
-                 .doc("Relative tolerance for clipping overshoot")
-                 .withDefault(1.0)} {
-    if (localmesh->getNXPE() > 1) {
-      throw BoutException("Do not support MPI splitting in X");
-    }
-  }
-  XZMonotonicHermiteSpline(int y_offset = 0, Mesh* mesh = nullptr)
-      : XZHermiteSpline(y_offset, mesh) {
-    if (localmesh->getNXPE() > 1) {
-      throw BoutException("Do not support MPI splitting in X");
-    }
-  }
-  XZMonotonicHermiteSpline(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr)
-      : XZHermiteSpline(mask, y_offset, mesh) {
-    if (localmesh->getNXPE() > 1) {
-      throw BoutException("Do not support MPI splitting in X");
-    }
-  }
-
-  using XZHermiteSpline::interpolate;
-  /// Interpolate using precalculated weights.
-  /// This function is called by the other interpolate functions
-  /// in the base class XZHermiteSpline.
-  Field3D interpolate(const Field3D& f,
-                      const std::string& region = "RGN_NOBNDRY") const override;
-};
+using XZMonotonicHermiteSpline = XZHermiteSplineBase<true>;
+using XZHermiteSpline = XZHermiteSplineBase<false>;
 
 /// XZLagrange4pt interpolation class
 ///
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 40dad9b7bd..59c2f4724d 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -22,6 +22,7 @@
 
 #include "../impls/bout/boutmesh.hxx"
 #include "bout/bout.hxx"
+#include "../parallel/fci_comm.hxx"
 #include "bout/globals.hxx"
 #include "bout/index_derivs_interface.hxx"
 #include "bout/interpolation_xz.hxx"
@@ -102,7 +103,8 @@ class IndConverter {
   }
 };
 
-XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* meshin)
+template <bool monotonic>
+XZHermiteSplineBase<monotonic>::XZHermiteSplineBase(int y_offset, Mesh* meshin)
     : XZInterpolation(y_offset, meshin), h00_x(localmesh), h01_x(localmesh),
       h10_x(localmesh), h11_x(localmesh), h00_z(localmesh), h01_z(localmesh),
       h10_z(localmesh), h11_z(localmesh) {
@@ -139,6 +141,10 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* meshin)
   MatCreateAIJ(BoutComm::get(), m, m, M, M, 16, nullptr, 16, nullptr, &petscWeights);
 #endif
 #endif
+  if constexpr (monotonic) {
+    gf3daccess = std::make_unique<GlobalField3DAccess>(localmesh);
+    g3dinds.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
+  }
 #ifndef HS_USE_PETSC
   if (localmesh->getNXPE() > 1) {
     throw BoutException("Require PETSc for MPI splitting in X");
@@ -146,8 +152,10 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* meshin)
 #endif
 }
 
-void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
-                                  const std::string& region) {
+template <bool monotonic>
+void XZHermiteSplineBase<monotonic>::calcWeights(const Field3D& delta_x,
+                                                 const Field3D& delta_z,
+                                                 const std::string& region) {
 
   const int ny = localmesh->LocalNy;
   const int nz = localmesh->LocalNz;
@@ -300,6 +308,14 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
     }
 #endif
 #endif
+    if constexpr (monotonic) {
+      const auto gind = gf3daccess->xyzg(i_corn, y + y_offset, k_corner(x, y, z));
+      gf3daccess->get(gind);
+      gf3daccess->get(gind.xp(1));
+      gf3daccess->get(gind.zp(1));
+      gf3daccess->get(gind.xp(1).zp(1));
+      g3dinds[i] = {gind.ind, gind.xp(1).ind, gind.zp(1).ind, gind.xp(1).zp(1).ind};
+    }
   }
 #ifdef HS_USE_PETSC
   MatAssemblyBegin(petscWeights, MAT_FINAL_ASSEMBLY);
@@ -311,8 +327,11 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
 #endif
 }
 
-void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z,
-                                  const BoutMask& mask, const std::string& region) {
+template <bool monotonic>
+void XZHermiteSplineBase<monotonic>::calcWeights(const Field3D& delta_x,
+                                                 const Field3D& delta_z,
+                                                 const BoutMask& mask,
+                                                 const std::string& region) {
   setMask(mask);
   calcWeights(delta_x, delta_z, region);
 }
@@ -333,8 +352,10 @@ void XZHermiteSpline::calcWeights(const Field3D& delta_x, const Field3D& delta_z
  *   (i, j+1, k+1)	h01_z + h10_z / 2
  *   (i, j+1, k+2)	h11_z / 2
  */
+template <bool monotonic>
 std::vector<ParallelTransform::PositionsAndWeights>
-XZHermiteSpline::getWeightsForYApproximation(int i, int j, int k, int yoffset) {
+XZHermiteSplineBase<monotonic>::getWeightsForYApproximation(int i, int j, int k,
+                                                            int yoffset) {
   const int nz = localmesh->LocalNz;
   const int k_mod = k_corner(i, j, k);
   const int k_mod_m1 = (k_mod > 0) ? (k_mod - 1) : (nz - 1);
@@ -347,7 +368,9 @@ XZHermiteSpline::getWeightsForYApproximation(int i, int j, int k, int yoffset) {
           {i, j + yoffset, k_mod_p2, 0.5 * h11_z(i, j, k)}};
 }
 
-Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region) const {
+template <bool monotonic>
+Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
+                                                    const std::string& region) const {
 
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
@@ -393,6 +416,11 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", region2);
   Field3D fxz = bout::derivatives::index::DDZ(fx, CELL_DEFAULT, "DEFAULT", region2);
 
+  std::unique_ptr<GlobalField3DAccessInstance> g3d;
+  if constexpr (monotonic) {
+    gf = gf3daccess.communicate_asPtr(f);
+  }
+
   BOUT_FOR(i, getRegion(region)) {
     const auto iyp = i.yp(y_offset);
 
@@ -421,6 +449,19 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
     f_interp[iyp] =
         +f_z * h00_z[i] + f_zp1 * h01_z[i] + fz_z * h10_z[i] + fz_zp1 * h11_z[i];
 
+    if constexpr (monotonic) {
+      const auto corners = {gf[g3dinds[i][0]], gf[g3dinds[i][1]], gf[g3dinds[i][2]],
+                            gf[g3dinds[i][3]]};
+      const auto minmax = std::minmax(corners);
+      if (f_interp[iyp] < minmax.first) {
+        f_interp[iyp] = minmax.first;
+      } else {
+        if (f_interp[iyp] > minmax.second) {
+          f_interp[iyp] = minmax.second;
+        }
+      }
+    }
+
     ASSERT2(std::isfinite(f_interp[iyp]) || i.x() < localmesh->xstart
             || i.x() > localmesh->xend);
   }
@@ -430,15 +471,24 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
   return f_interp;
 }
 
-Field3D XZHermiteSpline::interpolate(const Field3D& f, const Field3D& delta_x,
-                                     const Field3D& delta_z, const std::string& region) {
+template <bool monotonic>
+Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
+                                                    const Field3D& delta_x,
+                                                    const Field3D& delta_z,
+                                                    const std::string& region) {
   calcWeights(delta_x, delta_z, region);
   return interpolate(f, region);
 }
 
-Field3D XZHermiteSpline::interpolate(const Field3D& f, const Field3D& delta_x,
-                                     const Field3D& delta_z, const BoutMask& mask,
-                                     const std::string& region) {
+template <bool monotonic>
+Field3D
+XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f, const Field3D& delta_x,
+                                            const Field3D& delta_z, const BoutMask& mask,
+                                            const std::string& region) {
   calcWeights(delta_x, delta_z, mask, region);
   return interpolate(f, region);
 }
+
+// ensure they are instantiated
+template class XZHermiteSplineBase<true>;
+template class XZHermiteSplineBase<false>;
diff --git a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx b/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
deleted file mode 100644
index f206ed1e0f..0000000000
--- a/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx
+++ /dev/null
@@ -1,98 +0,0 @@
-/**************************************************************************
- * Copyright 2018 B.D.Dudson, P. Hill
- *
- * Contact: Ben Dudson, bd512@york.ac.uk
- *
- * This file is part of BOUT++.
- *
- * BOUT++ is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * BOUT++ is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
- *
- **************************************************************************/
-
-#include "bout/globals.hxx"
-#include "bout/index_derivs_interface.hxx"
-#include "bout/interpolation_xz.hxx"
-#include "bout/mesh.hxx"
-
-#include <algorithm>
-
-Field3D XZMonotonicHermiteSpline::interpolate(const Field3D& f,
-                                              const std::string& region) const {
-  ASSERT1(f.getMesh() == localmesh);
-  Field3D f_interp(f.getMesh());
-  f_interp.allocate();
-
-  // Derivatives are used for tension and need to be on dimensionless
-  // coordinates
-  Field3D fx = bout::derivatives::index::DDX(f, CELL_DEFAULT, "DEFAULT");
-  Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", "RGN_ALL");
-  localmesh->communicate_no_slices(fx, fz);
-  Field3D fxz = bout::derivatives::index::DDX(fz, CELL_DEFAULT, "DEFAULT");
-  localmesh->communicate_no_slices(fxz);
-
-  const auto curregion{getRegion(region)};
-  BOUT_FOR(i, curregion) {
-    const auto iyp = i.yp(y_offset);
-
-    const auto ic = i_corner[i];
-    const auto iczp = ic.zp();
-    const auto icxp = ic.xp();
-    const auto icxpzp = iczp.xp();
-
-    // Interpolate f in X at Z
-    const BoutReal f_z =
-        f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
-
-    // Interpolate f in X at Z+1
-    const BoutReal f_zp1 = f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] + fx[iczp] * h10_x[i]
-                           + fx[icxpzp] * h11_x[i];
-
-    // Interpolate fz in X at Z
-    const BoutReal fz_z = fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] + fxz[ic] * h10_x[i]
-                          + fxz[icxp] * h11_x[i];
-
-    // Interpolate fz in X at Z+1
-    const BoutReal fz_zp1 = fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i]
-                            + fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
-
-    // Interpolate in Z
-    BoutReal result =
-        +f_z * h00_z[i] + f_zp1 * h01_z[i] + fz_z * h10_z[i] + fz_zp1 * h11_z[i];
-
-    ASSERT2(std::isfinite(result) || i.x() < localmesh->xstart
-            || i.x() > localmesh->xend);
-
-    // Monotonicity
-    // Force the interpolated result to be in the range of the
-    // neighbouring cell values. This prevents unphysical overshoots,
-    // but also degrades accuracy near maxima and minima.
-    // Perhaps should only impose near boundaries, since that is where
-    // problems most obviously occur.
-    const BoutReal localmax = BOUTMAX(f[ic], f[icxp], f[iczp], f[icxpzp]);
-    const BoutReal localmin = BOUTMIN(f[ic], f[icxp], f[iczp], f[icxpzp]);
-
-    ASSERT2(std::isfinite(localmax) || i.x() < localmesh->xstart
-            || i.x() > localmesh->xend);
-    ASSERT2(std::isfinite(localmin) || i.x() < localmesh->xstart
-            || i.x() > localmesh->xend);
-
-    const auto diff = ((localmax - localmin) * rtol) + atol;
-
-    result = std::min(result, localmax + diff);
-    result = std::max(result, localmin - diff);
-
-    f_interp[iyp] = result;
-  }
-  return f_interp;
-}
diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx
index a58554dc82..f80a361bd1 100644
--- a/src/mesh/interpolation_xz.cxx
+++ b/src/mesh/interpolation_xz.cxx
@@ -23,6 +23,7 @@
  *
  **************************************************************************/
 
+#include "parallel/fci_comm.hxx"
 #include <bout/globals.hxx>
 #include <bout/interpolation_xz.hxx>
 #include <bout/output.hxx>

From 84237c8a474ff6b8b4f2cf04dc76beb3aa4dac9d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Jan 2025 13:26:59 +0100
Subject: [PATCH 0557/1827] Use x-splitting for monotonichermitespline test

---
 tests/MMS/spatial/fci/runtest | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 34340e53f4..c76ad27833 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -17,7 +17,6 @@ import zoidberg as zb
 from boutdata.collect import collect
 from boututils.run_wrapper import build_and_log, launch_safe
 from numpy import arange, array, linspace, log, polyfit
-from scipy.interpolate import RectBivariateSpline as RBS
 
 # Global parameters
 DIRECTORY = "data"
@@ -32,15 +31,16 @@ NLIST = [8, 16, 32, 64]
 dx = 1.0 / array(NLIST)
 
 
-def myRBS(a, b, c):
-    """RectBivariateSpline, but automatically tune spline degree for small arrays"""
-    mx, _ = c.shape
-    kx = max(mx - 1, 1)
-    kx = min(kx, 3)
-    return RBS(a, b, c, kx=kx)
+success = True
 
+error_2 = {}
+error_inf = {}
+method_orders = {}
 
-zb.poloidal_grid.RectBivariateSpline = myRBS
+# Run with periodic Y?
+yperiodic = True
+
+build_and_log("FCI MMS test")
 
 
 def quiet_collect(name: str) -> float:

From 06624497a52f1be434f34fb8b157bee68b8c96e1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Jan 2025 09:07:51 +0100
Subject: [PATCH 0558/1827] Set region for lagrange4pt

---
 src/mesh/interpolation/lagrange_4pt_xz.cxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx
index e16b2699d1..7fb0fb502b 100644
--- a/src/mesh/interpolation/lagrange_4pt_xz.cxx
+++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx
@@ -133,7 +133,11 @@ Field3D XZLagrange4pt::interpolate(const Field3D& f, const std::string& region)
 
     // Then in X
     f_interp(x, y_next, z) = lagrange_4pt(xvals, t_x(x, y, z));
+    ASSERT2(std::isfinite(f_interp(x, y_next, z)));
+
   }
+  const auto region2 = y_offset != 0 ? fmt::format("RGN_YPAR_{:+d}", y_offset) : region;
+  f_interp.setRegion(region2);
   return f_interp;
 }
 

From f77849eb9fcc544e89c2839c6e220867753a702f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 10:43:58 +0100
Subject: [PATCH 0559/1827] Add monotonic check also to other code branches

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 27 +++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 59c2f4724d..28455f77e8 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -36,7 +36,7 @@ class IndConverter {
         xstart(mesh->xstart), ystart(mesh->ystart), zstart(0),
         lnx(mesh->LocalNx - 2 * xstart), lny(mesh->LocalNy - 2 * ystart),
         lnz(mesh->LocalNz - 2 * zstart) {}
-  // ix and iy are global indices
+  // ix and iz are global indices
   // iy is local
   int fromMeshToGlobal(int ix, int iy, int iz) {
     const int xstart = mesh->xstart;
@@ -388,6 +388,19 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
   VecGetArrayRead(result, &cptr);
   BOUT_FOR(i, f.getRegion(region2)) {
     f_interp[i] = cptr[int(i)];
+    if constexpr (monotonic) {
+      const auto corners = {gf[g3dinds[i][0]], gf[g3dinds[i][1]], gf[g3dinds[i][2]],
+                            gf[g3dinds[i][3]]};
+      const auto minmax = std::minmax(corners);
+      if (f_interp[iyp] < minmax.first) {
+        f_interp[iyp] = minmax.first;
+      } else {
+        if (f_interp[iyp] > minmax.second) {
+          f_interp[iyp] = minmax.second;
+        }
+      }
+    }
+
     ASSERT2(std::isfinite(cptr[int(i)]));
   }
   VecRestoreArrayRead(result, &cptr);
@@ -403,6 +416,18 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
       f_interp[iyp] += newWeights[w * 4 + 2][i] * f[ic.zp().xp(w - 1)];
       f_interp[iyp] += newWeights[w * 4 + 3][i] * f[ic.zp(2).xp(w - 1)];
     }
+    if constexpr (monotonic) {
+      const auto corners = {gf[g3dinds[i][0]], gf[g3dinds[i][1]], gf[g3dinds[i][2]],
+                            gf[g3dinds[i][3]]};
+      const auto minmax = std::minmax(corners);
+      if (f_interp[iyp] < minmax.first) {
+        f_interp[iyp] = minmax.first;
+      } else {
+        if (f_interp[iyp] > minmax.second) {
+          f_interp[iyp] = minmax.second;
+        }
+      }
+    }
   }
 #endif
 #else

From 820f0a5cf2e5dfc9134f4ac760edac4b63cbc398 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 13:31:14 +0100
Subject: [PATCH 0560/1827] use lower_bound instead of find

lower_bound takes into account the data is sorted
---
 src/mesh/parallel/fci_comm.hxx | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index aa3b5ecfb5..a847700548 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -138,10 +138,11 @@ public:
       ASSERT3(piz.proc == 0);
       const auto proc = piy.proc * g2lx.npe + pix.proc;
       const auto& vec = toGet[proc];
-      auto it =
-          std::find(vec.begin(), vec.end(), xyzl.convert(pix.ind, piy.ind, piz.ind).ind);
+      const auto tofind = xyzl.convert(pix.ind, piy.ind, piz.ind).ind;
+      auto it = std::lower_bound(vec.begin(), vec.end(), tofind);
       ASSERT3(it != vec.end());
-      mapping[id] = it - vec.begin() + offsets[proc];
+      ASSERT3(*it == tofind);
+      mapping[id] = std::distance(vec.begin(), it) + offsets[proc];
     }
     is_setup = true;
   }

From 1178243fb42ba9afb595cf31c684504a83f09b63 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 13:31:27 +0100
Subject: [PATCH 0561/1827] Do not shadow mapping

---
 src/mesh/parallel/fci_comm.hxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index a847700548..5250fb99d3 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -129,7 +129,6 @@ public:
       }
       offsets.push_back(offset);
     }
-    std::map<int, int> mapping;
     for (const auto id : ids) {
       IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
       const auto pix = g2lx.convert(gind.x());

From 3d6f587ee8fc84418f4810bc537146dec4b3c2bb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 13:32:01 +0100
Subject: [PATCH 0562/1827] Ensure setup has been called

---
 src/mesh/parallel/fci_comm.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 5250fb99d3..6c83d58f63 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -212,6 +212,7 @@ private:
   int sendBufferSize{0};
   MPI_Comm comm;
   std::vector<BoutReal> communicate_data(const Field3D& f) {
+    ASSERT2(is_setup);
     ASSERT2(f.getMesh() == mesh);
     std::vector<BoutReal> data(offsets.back());
     std::vector<BoutReal> sendBuffer(sendBufferSize);

From 265c8cd3b5abdf3dd7313a4c6ea4ed81048d1e11 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 13:32:12 +0100
Subject: [PATCH 0563/1827] Use pointer to data

---
 src/mesh/parallel/fci_comm.hxx | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 6c83d58f63..d44eea76ef 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -176,13 +176,14 @@ private:
       auto ret = MPI_Waitany(reqs.size(), &reqs[0], &ind, MPI_STATUS_IGNORE);
       ASSERT0(ret == MPI_SUCCESS);
       ASSERT3(ind != MPI_UNDEFINED);
+      ASSERT2(static_cast<size_t>(ind) < toSend.size());
       toSend[ind].resize(toSendSizes[ind]);
-      ret = MPI_Irecv(static_cast<void*>(&toSend[ind]), toSend[ind].size(), MPI_INT, ind,
-                      666 * 666 + ind, comm, &reqs[ind]);
+      ret = MPI_Irecv(static_cast<void*>(&toSend[ind][0]), toSend[ind].size(), MPI_INT,
+                      ind, 666 * 666 + ind, comm, &reqs[ind]);
       ASSERT0(ret == MPI_SUCCESS);
     }
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      const auto ret = MPI_Send(static_cast<void*>(&toGet[proc]), toGet[proc].size(),
+      const auto ret = MPI_Send(static_cast<void*>(&toGet[proc][0]), toGet[proc].size(),
                                 MPI_INT, proc, 666 * 666 + proc, comm);
       ASSERT0(ret == MPI_SUCCESS);
     }

From 16a162e180baf86ef183e5f92e75fd88f072cff9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 13:32:36 +0100
Subject: [PATCH 0564/1827] Call setup before communicator is used

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 28455f77e8..46eda18a0a 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -317,6 +317,9 @@ void XZHermiteSplineBase<monotonic>::calcWeights(const Field3D& delta_x,
       g3dinds[i] = {gind.ind, gind.xp(1).ind, gind.zp(1).ind, gind.xp(1).zp(1).ind};
     }
   }
+  if constexpr (monotonic) {
+    gf3daccess->setup();
+  }
 #ifdef HS_USE_PETSC
   MatAssemblyBegin(petscWeights, MAT_FINAL_ASSEMBLY);
   MatAssemblyEnd(petscWeights, MAT_FINAL_ASSEMBLY);

From e5878c19b28e46c674d6e7c28a9e85a58a3b0bc6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 13:34:36 +0100
Subject: [PATCH 0565/1827] Deduplicate code

Ensures we all ways check for monotonicity
---
 src/mesh/interpolation/hermite_spline_xz.cxx | 61 +++++++-------------
 1 file changed, 21 insertions(+), 40 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 46eda18a0a..80a1336c02 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -380,8 +380,12 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
 
   const auto region2 = y_offset != 0 ? fmt::format("RGN_YPAR_{:+d}", y_offset) : region;
 
-#if USE_NEW_WEIGHTS
-#ifdef HS_USE_PETSC
+  std::unique_ptr<GlobalField3DAccessInstance> gf;
+  if constexpr (monotonic) {
+    gf = gf3daccess->communicate_asPtr(f);
+  }
+
+#if USE_NEW_WEIGHTS and defined(HS_USE_PETSC)
   BoutReal* ptr;
   const BoutReal* cptr;
   VecGetArray(rhs, &ptr);
@@ -392,22 +396,9 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
   BOUT_FOR(i, f.getRegion(region2)) {
     f_interp[i] = cptr[int(i)];
     if constexpr (monotonic) {
-      const auto corners = {gf[g3dinds[i][0]], gf[g3dinds[i][1]], gf[g3dinds[i][2]],
-                            gf[g3dinds[i][3]]};
-      const auto minmax = std::minmax(corners);
-      if (f_interp[iyp] < minmax.first) {
-        f_interp[iyp] = minmax.first;
-      } else {
-        if (f_interp[iyp] > minmax.second) {
-          f_interp[iyp] = minmax.second;
-        }
-      }
-    }
-
-    ASSERT2(std::isfinite(cptr[int(i)]));
-  }
-  VecRestoreArrayRead(result, &cptr);
-#else
+      const auto iyp = i;
+      const auto i = iyp.ym(y_offset);
+#elif USE_NEW_WEIGHTS // No Petsc
   BOUT_FOR(i, getRegion(region)) {
     auto ic = i_corner[i];
     auto iyp = i.yp(y_offset);
@@ -420,20 +411,7 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
       f_interp[iyp] += newWeights[w * 4 + 3][i] * f[ic.zp(2).xp(w - 1)];
     }
     if constexpr (monotonic) {
-      const auto corners = {gf[g3dinds[i][0]], gf[g3dinds[i][1]], gf[g3dinds[i][2]],
-                            gf[g3dinds[i][3]]};
-      const auto minmax = std::minmax(corners);
-      if (f_interp[iyp] < minmax.first) {
-        f_interp[iyp] = minmax.first;
-      } else {
-        if (f_interp[iyp] > minmax.second) {
-          f_interp[iyp] = minmax.second;
-        }
-      }
-    }
-  }
-#endif
-#else
+#else                 // Legacy interpolation
   // Derivatives are used for tension and need to be on dimensionless
   // coordinates
 
@@ -444,11 +422,6 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
   Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", region2);
   Field3D fxz = bout::derivatives::index::DDZ(fx, CELL_DEFAULT, "DEFAULT", region2);
 
-  std::unique_ptr<GlobalField3DAccessInstance> g3d;
-  if constexpr (monotonic) {
-    gf = gf3daccess.communicate_asPtr(f);
-  }
-
   BOUT_FOR(i, getRegion(region)) {
     const auto iyp = i.yp(y_offset);
 
@@ -478,8 +451,9 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
         +f_z * h00_z[i] + f_zp1 * h01_z[i] + fz_z * h10_z[i] + fz_zp1 * h11_z[i];
 
     if constexpr (monotonic) {
-      const auto corners = {gf[g3dinds[i][0]], gf[g3dinds[i][1]], gf[g3dinds[i][2]],
-                            gf[g3dinds[i][3]]};
+#endif
+      const auto corners = {(*gf)[IndG3D(g3dinds[i][0])], (*gf)[IndG3D(g3dinds[i][1])],
+                            (*gf)[IndG3D(g3dinds[i][2])], (*gf)[IndG3D(g3dinds[i][3])]};
       const auto minmax = std::minmax(corners);
       if (f_interp[iyp] < minmax.first) {
         f_interp[iyp] = minmax.first;
@@ -489,7 +463,14 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
         }
       }
     }
-
+#if USE_NEW_WEIGHTS and defined(HS_USE_PETSC)
+    ASSERT2(std::isfinite(cptr[int(i)]));
+  }
+  VecRestoreArrayRead(result, &cptr);
+#elif USE_NEW_WEIGHTS
+    ASSERT2(std::isfinite(f_interp[iyp]));
+  }
+#else
     ASSERT2(std::isfinite(f_interp[iyp]) || i.x() < localmesh->xstart
             || i.x() > localmesh->xend);
   }

From aee27131b93e6ab89b8111064ee8deb79e138f8b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 14:30:05 +0100
Subject: [PATCH 0566/1827] Fix tags for comm

Tags were different for sender and receiver
---
 src/mesh/parallel/fci_comm.hxx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index d44eea76ef..c0227f4773 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -161,14 +161,14 @@ private:
     std::vector<MPI_Request> reqs(toSend.size());
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       auto ret = MPI_Irecv(static_cast<void*>(&toSendSizes[proc]), 1, MPI_INT, proc,
-                           666 + proc, comm, &reqs[proc]);
+                           666, comm, &reqs[proc]);
       ASSERT0(ret == MPI_SUCCESS);
     }
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       toGetSizes[proc] = toGet[proc].size();
       sendBufferSize += toGetSizes[proc];
       auto ret = MPI_Send(static_cast<void*>(&toGetSizes[proc]), 1, MPI_INT, proc,
-                          666 + proc, comm);
+                          666, comm);
       ASSERT0(ret == MPI_SUCCESS);
     }
     for ([[maybe_unused]] auto dummy : reqs) {
@@ -179,12 +179,12 @@ private:
       ASSERT2(static_cast<size_t>(ind) < toSend.size());
       toSend[ind].resize(toSendSizes[ind]);
       ret = MPI_Irecv(static_cast<void*>(&toSend[ind][0]), toSend[ind].size(), MPI_INT,
-                      ind, 666 * 666 + ind, comm, &reqs[ind]);
+                      ind, 666 * 666, comm, &reqs[ind]);
       ASSERT0(ret == MPI_SUCCESS);
     }
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       const auto ret = MPI_Send(static_cast<void*>(&toGet[proc][0]), toGet[proc].size(),
-                                MPI_INT, proc, 666 * 666 + proc, comm);
+                                MPI_INT, proc, 666 * 666, comm);
       ASSERT0(ret == MPI_SUCCESS);
     }
     for ([[maybe_unused]] auto dummy : reqs) {
@@ -220,7 +220,7 @@ private:
     std::vector<MPI_Request> reqs(toSend.size());
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       auto ret = MPI_Irecv(static_cast<void*>(&data[proc]), toGet[proc].size(),
-                           MPI_DOUBLE, proc, 666 + proc, comm, &reqs[proc]);
+                           MPI_DOUBLE, proc, 666, comm, &reqs[proc]);
       ASSERT0(ret == MPI_SUCCESS);
     }
     int cnt = 0;
@@ -229,7 +229,7 @@ private:
       for (auto i : toSend[proc]) {
         sendBuffer[cnt++] = f[Ind3D(i)];
       }
-      auto ret = MPI_Send(start, toSend[proc].size(), MPI_DOUBLE, proc, 666 + proc, comm);
+      auto ret = MPI_Send(start, toSend[proc].size(), MPI_DOUBLE, proc, 666, comm);
       ASSERT0(ret == MPI_SUCCESS);
     }
     for ([[maybe_unused]] auto dummy : reqs) {

From b4f7be51d9216d7b7f3416c63e3c609e3edda274 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 14:39:43 +0100
Subject: [PATCH 0567/1827] Use pointer instead of std::vector

---
 src/mesh/parallel/fci_comm.hxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index c0227f4773..257639bb32 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -216,7 +216,8 @@ private:
     ASSERT2(is_setup);
     ASSERT2(f.getMesh() == mesh);
     std::vector<BoutReal> data(offsets.back());
-    std::vector<BoutReal> sendBuffer(sendBufferSize);
+    //std::vector<BoutReal> sendBuffer(sendBufferSize);
+    BoutReal* sendBuffer = new BoutReal[sendBufferSize];
     std::vector<MPI_Request> reqs(toSend.size());
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       auto ret = MPI_Irecv(static_cast<void*>(&data[proc]), toGet[proc].size(),
@@ -238,6 +239,7 @@ private:
       ASSERT0(ret == MPI_SUCCESS);
       ASSERT3(ind != MPI_UNDEFINED);
     }
+    delete[] sendBuffer;
     return data;
   }
 };

From 578ee8d28551e1614ae0c62877a528ef45ab3b67 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Jan 2025 14:43:12 +0100
Subject: [PATCH 0568/1827] Do not reuse requests if the array is still in use

Otherwise mpi might wait for the wrong request.
---
 src/mesh/parallel/fci_comm.hxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 257639bb32..ec34d622a6 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -171,6 +171,7 @@ private:
                           666, comm);
       ASSERT0(ret == MPI_SUCCESS);
     }
+    std::vector<MPI_Request> reqs2(toSend.size());
     for ([[maybe_unused]] auto dummy : reqs) {
       int ind{0};
       auto ret = MPI_Waitany(reqs.size(), &reqs[0], &ind, MPI_STATUS_IGNORE);
@@ -179,7 +180,7 @@ private:
       ASSERT2(static_cast<size_t>(ind) < toSend.size());
       toSend[ind].resize(toSendSizes[ind]);
       ret = MPI_Irecv(static_cast<void*>(&toSend[ind][0]), toSend[ind].size(), MPI_INT,
-                      ind, 666 * 666, comm, &reqs[ind]);
+                      ind, 666 * 666, comm, &reqs2[ind]);
       ASSERT0(ret == MPI_SUCCESS);
     }
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
@@ -189,7 +190,7 @@ private:
     }
     for ([[maybe_unused]] auto dummy : reqs) {
       int ind{0};
-      const auto ret = MPI_Waitany(reqs.size(), &reqs[0], &ind, MPI_STATUS_IGNORE);
+      const auto ret = MPI_Waitany(reqs.size(), &reqs2[0], &ind, MPI_STATUS_IGNORE);
       ASSERT0(ret == MPI_SUCCESS);
       ASSERT3(ind != MPI_UNDEFINED);
     }

From bf9c9eb013fbb8fce3a8f4252f16dfe4dc287e8f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Jan 2025 10:27:11 +0100
Subject: [PATCH 0569/1827] rename offset to getOffsets

to avoid confusion whether the offsets are for sending or receiving
---
 src/mesh/parallel/fci_comm.hxx | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index ec34d622a6..f079385dc1 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -124,10 +124,10 @@ public:
     {
       int offset = 0;
       for (auto get : toGet) {
-        offsets.push_back(offset);
+        getOffsets.push_back(offset);
         offset += get.size();
       }
-      offsets.push_back(offset);
+      getOffsets.push_back(offset);
     }
     for (const auto id : ids) {
       IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
@@ -141,7 +141,7 @@ public:
       auto it = std::lower_bound(vec.begin(), vec.end(), tofind);
       ASSERT3(it != vec.end());
       ASSERT3(*it == tofind);
-      mapping[id] = std::distance(vec.begin(), it) + offsets[proc];
+      mapping[id] = std::distance(vec.begin(), it) + getOffsets[proc];
     }
     is_setup = true;
   }
@@ -155,9 +155,8 @@ public:
 private:
   void commCommLists() {
     toSend.resize(toGet.size());
-    std::vector<int> toGetSizes(toGet.size());
-    std::vector<int> toSendSizes(toSend.size());
-    //const int thisproc = mesh->getYProcIndex() * g2lx.npe + mesh->getXProcIndex();
+    std::vector<int> toGetSizes(toGet.size(), -1);
+    std::vector<int> toSendSizes(toSend.size(), -1);
     std::vector<MPI_Request> reqs(toSend.size());
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       auto ret = MPI_Irecv(static_cast<void*>(&toSendSizes[proc]), 1, MPI_INT, proc,
@@ -210,15 +209,15 @@ public:
 private:
   std::vector<std::vector<int>> toGet;
   std::vector<std::vector<int>> toSend;
-  std::vector<int> offsets;
+  std::vector<int> getOffsets;
   int sendBufferSize{0};
   MPI_Comm comm;
   std::vector<BoutReal> communicate_data(const Field3D& f) {
     ASSERT2(is_setup);
     ASSERT2(f.getMesh() == mesh);
-    std::vector<BoutReal> data(offsets.back());
     //std::vector<BoutReal> sendBuffer(sendBufferSize);
     BoutReal* sendBuffer = new BoutReal[sendBufferSize];
+    std::vector<BoutReal> data(getOffsets.back());
     std::vector<MPI_Request> reqs(toSend.size());
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       auto ret = MPI_Irecv(static_cast<void*>(&data[proc]), toGet[proc].size(),

From 2155f068deda476df34d076b183b14c4255b8e92 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Jan 2025 10:28:04 +0100
Subject: [PATCH 0570/1827] Fix: mixup of sending / receiving size

---
 src/mesh/parallel/fci_comm.hxx | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index f079385dc1..0926f5c415 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -165,7 +165,6 @@ private:
     }
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       toGetSizes[proc] = toGet[proc].size();
-      sendBufferSize += toGetSizes[proc];
       auto ret = MPI_Send(static_cast<void*>(&toGetSizes[proc]), 1, MPI_INT, proc,
                           666, comm);
       ASSERT0(ret == MPI_SUCCESS);
@@ -177,6 +176,8 @@ private:
       ASSERT0(ret == MPI_SUCCESS);
       ASSERT3(ind != MPI_UNDEFINED);
       ASSERT2(static_cast<size_t>(ind) < toSend.size());
+      ASSERT3(toSendSizes[ind] >= 0);
+      sendBufferSize += toSendSizes[ind];
       toSend[ind].resize(toSendSizes[ind]);
       ret = MPI_Irecv(static_cast<void*>(&toSend[ind][0]), toSend[ind].size(), MPI_INT,
                       ind, 666 * 666, comm, &reqs2[ind]);
@@ -215,9 +216,8 @@ private:
   std::vector<BoutReal> communicate_data(const Field3D& f) {
     ASSERT2(is_setup);
     ASSERT2(f.getMesh() == mesh);
-    //std::vector<BoutReal> sendBuffer(sendBufferSize);
-    BoutReal* sendBuffer = new BoutReal[sendBufferSize];
     std::vector<BoutReal> data(getOffsets.back());
+    std::vector<BoutReal> sendBuffer(sendBufferSize);
     std::vector<MPI_Request> reqs(toSend.size());
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       auto ret = MPI_Irecv(static_cast<void*>(&data[proc]), toGet[proc].size(),
@@ -239,7 +239,6 @@ private:
       ASSERT0(ret == MPI_SUCCESS);
       ASSERT3(ind != MPI_UNDEFINED);
     }
-    delete[] sendBuffer;
     return data;
   }
 };

From 06622473f901863250a5e927cd5a060d068dcdac Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Jan 2025 10:28:43 +0100
Subject: [PATCH 0571/1827] Fix receive data offset

---
 src/mesh/parallel/fci_comm.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 0926f5c415..8db9d8ef14 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -220,8 +220,8 @@ private:
     std::vector<BoutReal> sendBuffer(sendBufferSize);
     std::vector<MPI_Request> reqs(toSend.size());
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      auto ret = MPI_Irecv(static_cast<void*>(&data[proc]), toGet[proc].size(),
-                           MPI_DOUBLE, proc, 666, comm, &reqs[proc]);
+      auto ret = MPI_Irecv(static_cast<void*>(&data[getOffsets[proc]]),
+                           toGet[proc].size(), MPI_DOUBLE, proc, 666, comm, &reqs[proc]);
       ASSERT0(ret == MPI_SUCCESS);
     }
     int cnt = 0;

From 28d4e28dc7bbbb579913d974e5d4727b57a55eee Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Jan 2025 10:30:47 +0100
Subject: [PATCH 0572/1827] Add check to ensure the proc layout is as expected

---
 src/mesh/parallel/fci_comm.hxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 8db9d8ef14..30f7df76ee 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -157,6 +157,13 @@ private:
     toSend.resize(toGet.size());
     std::vector<int> toGetSizes(toGet.size(), -1);
     std::vector<int> toSendSizes(toSend.size(), -1);
+#if CHECK > 3
+    {
+      int thisproc;
+      MPI_Comm_rank(comm, thisproc);
+      assert(thisproc == mesh->getYProcIndex() * g2lx.npe + mesh->getXProcIndex());
+    }
+#endif
     std::vector<MPI_Request> reqs(toSend.size());
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       auto ret = MPI_Irecv(static_cast<void*>(&toSendSizes[proc]), 1, MPI_INT, proc,

From e4507d953e51f75237202f72bba8d445586a2530 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Jan 2025 10:31:54 +0100
Subject: [PATCH 0573/1827] clang-format

---
 src/mesh/parallel/fci_comm.hxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 30f7df76ee..bd4b955f12 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -166,14 +166,14 @@ private:
 #endif
     std::vector<MPI_Request> reqs(toSend.size());
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      auto ret = MPI_Irecv(static_cast<void*>(&toSendSizes[proc]), 1, MPI_INT, proc,
-                           666, comm, &reqs[proc]);
+      auto ret = MPI_Irecv(static_cast<void*>(&toSendSizes[proc]), 1, MPI_INT, proc, 666,
+                           comm, &reqs[proc]);
       ASSERT0(ret == MPI_SUCCESS);
     }
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
       toGetSizes[proc] = toGet[proc].size();
-      auto ret = MPI_Send(static_cast<void*>(&toGetSizes[proc]), 1, MPI_INT, proc,
-                          666, comm);
+      auto ret =
+          MPI_Send(static_cast<void*>(&toGetSizes[proc]), 1, MPI_INT, proc, 666, comm);
       ASSERT0(ret == MPI_SUCCESS);
     }
     std::vector<MPI_Request> reqs2(toSend.size());

From d7ba297dda1e35d60bc677856d21ccc472148b3e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Jan 2025 10:40:35 +0100
Subject: [PATCH 0574/1827] Use BOUT++ assert

---
 src/mesh/parallel/fci_comm.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index bd4b955f12..39348d2e10 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -161,7 +161,7 @@ private:
     {
       int thisproc;
       MPI_Comm_rank(comm, thisproc);
-      assert(thisproc == mesh->getYProcIndex() * g2lx.npe + mesh->getXProcIndex());
+      ASSERT0(thisproc == mesh->getYProcIndex() * g2lx.npe + mesh->getXProcIndex());
     }
 #endif
     std::vector<MPI_Request> reqs(toSend.size());

From f55f8e4c188806ac38191361d5d5e64356dba83f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Jan 2025 10:41:15 +0100
Subject: [PATCH 0575/1827] Fix check

---
 src/mesh/parallel/fci_comm.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 39348d2e10..ec4aeaba49 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -160,7 +160,7 @@ private:
 #if CHECK > 3
     {
       int thisproc;
-      MPI_Comm_rank(comm, thisproc);
+      MPI_Comm_rank(comm, &thisproc);
       ASSERT0(thisproc == mesh->getYProcIndex() * g2lx.npe + mesh->getXProcIndex());
     }
 #endif

From 0e9f7d69ed72469c5e0dbf85deb9a692746bef15 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 28 Jan 2025 09:49:41 +0100
Subject: [PATCH 0576/1827] Take periodicity into account

---
 src/mesh/parallel/fci_comm.hxx | 36 ++++++++++++++++++++++++----------
 1 file changed, 26 insertions(+), 10 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index ec4aeaba49..a93b55244a 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -52,19 +52,35 @@ struct globalToLocal1D {
   const int local;
   const int global;
   const int globalwith;
-  globalToLocal1D(int mg, int npe, int localwith)
+  const bool periodic;
+  globalToLocal1D(int mg, int npe, int localwith, bool periodic)
       : mg(mg), npe(npe), localwith(localwith), local(localwith - 2 * mg),
-        global(local * npe), globalwith(global + 2 * mg) {};
+        global(local * npe), globalwith(global + 2 * mg), periodic(periodic) {};
   ProcLocal convert(int id) const {
+    if (periodic) {
+      while (id < mg) {
+        id += global;
+      }
+      while (id >= global + mg) {
+        id -= global;
+      }
+    }
     int idwo = id - mg;
     int proc = idwo / local;
-    if (proc >= npe) {
-      proc = npe - 1;
+    if (not periodic) {
+      if (proc >= npe) {
+        proc = npe - 1;
+      }
     }
-    ASSERT2(proc >= 0);
     int loc = id - local * proc;
-    ASSERT2(0 <= loc);
-    ASSERT2(loc < (local + 2 * mg));
+#if CHECK > 1
+    if ((loc < 0 or loc > localwith or proc < 0 or proc > npe)
+        or (periodic and (loc < mg or loc >= local + mg))) {
+      printf("globalToLocal1D failure: %d %d, %d %d, %d %d %s\n", id, idwo, globalwith,
+             npe, proc, loc, periodic ? "periodic" : "non-periodic");
+      ASSERT0(false);
+    }
+#endif
     return {proc, loc};
   }
 };
@@ -98,9 +114,9 @@ class GlobalField3DAccess {
 public:
   friend class GlobalField3DAccessInstance;
   GlobalField3DAccess(Mesh* mesh)
-      : mesh(mesh), g2lx(mesh->xstart, mesh->getNXPE(), mesh->LocalNx),
-        g2ly(mesh->ystart, mesh->getNYPE(), mesh->LocalNy),
-        g2lz(mesh->zstart, 1, mesh->LocalNz),
+      : mesh(mesh), g2lx(mesh->xstart, mesh->getNXPE(), mesh->LocalNx, false),
+        g2ly(mesh->ystart, mesh->getNYPE(), mesh->LocalNy, true),
+        g2lz(mesh->zstart, 1, mesh->LocalNz, true),
         xyzl(g2lx.localwith, g2ly.localwith, g2lz.localwith),
         xyzg(g2lx.globalwith, g2ly.globalwith, g2lz.globalwith), comm(BoutComm::get()) {};
   void get(IndG3D ind) { ids.emplace(ind.ind); }

From 944adfbf68b0bdf0440dfe0283634331ec6901a1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 28 Jan 2025 09:49:56 +0100
Subject: [PATCH 0577/1827] Sort a reference, not a copy

---
 src/mesh/parallel/fci_comm.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index a93b55244a..9f296848b1 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -133,7 +133,7 @@ public:
       toGet[piy.proc * g2lx.npe + pix.proc].push_back(
           xyzl.convert(pix.ind, piy.ind, piz.ind).ind);
     }
-    for (auto v : toGet) {
+    for (auto& v : toGet) {
       std::sort(v.begin(), v.end());
     }
     commCommLists();

From 6daec201722fd162574d831778babdf89f1b7742 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 28 Jan 2025 09:52:06 +0100
Subject: [PATCH 0578/1827] Only communicate non-empty vectors

---
 src/mesh/parallel/fci_comm.hxx | 44 ++++++++++++++++++++++++----------
 1 file changed, 31 insertions(+), 13 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 9f296848b1..1ca67f0ecc 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -193,6 +193,7 @@ private:
       ASSERT0(ret == MPI_SUCCESS);
     }
     std::vector<MPI_Request> reqs2(toSend.size());
+    int cnt = 0;
     for ([[maybe_unused]] auto dummy : reqs) {
       int ind{0};
       auto ret = MPI_Waitany(reqs.size(), &reqs[0], &ind, MPI_STATUS_IGNORE);
@@ -200,20 +201,26 @@ private:
       ASSERT3(ind != MPI_UNDEFINED);
       ASSERT2(static_cast<size_t>(ind) < toSend.size());
       ASSERT3(toSendSizes[ind] >= 0);
+      if (toSendSizes[ind] == 0) {
+        continue;
+      }
       sendBufferSize += toSendSizes[ind];
-      toSend[ind].resize(toSendSizes[ind]);
-      ret = MPI_Irecv(static_cast<void*>(&toSend[ind][0]), toSend[ind].size(), MPI_INT,
-                      ind, 666 * 666, comm, &reqs2[ind]);
+      toSend[ind].resize(toSendSizes[ind], -1);
+
+      ret = MPI_Irecv(static_cast<void*>(toSend[ind].data()), toSend[ind].size(), MPI_INT,
+                      ind, 666 * 666, comm, reqs2.data() + cnt++);
       ASSERT0(ret == MPI_SUCCESS);
     }
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      const auto ret = MPI_Send(static_cast<void*>(&toGet[proc][0]), toGet[proc].size(),
-                                MPI_INT, proc, 666 * 666, comm);
-      ASSERT0(ret == MPI_SUCCESS);
+      if (toGet.size() != 0) {
+        const auto ret = MPI_Send(static_cast<void*>(toGet[proc].data()),
+                                  toGet[proc].size(), MPI_INT, proc, 666 * 666, comm);
+        ASSERT0(ret == MPI_SUCCESS);
+      }
     }
-    for ([[maybe_unused]] auto dummy : reqs) {
+    for (int c = 0; c < cnt; c++) {
       int ind{0};
-      const auto ret = MPI_Waitany(reqs.size(), &reqs2[0], &ind, MPI_STATUS_IGNORE);
+      const auto ret = MPI_Waitany(cnt, reqs2.data(), &ind, MPI_STATUS_IGNORE);
       ASSERT0(ret == MPI_SUCCESS);
       ASSERT3(ind != MPI_UNDEFINED);
     }
@@ -242,25 +249,36 @@ private:
     std::vector<BoutReal> data(getOffsets.back());
     std::vector<BoutReal> sendBuffer(sendBufferSize);
     std::vector<MPI_Request> reqs(toSend.size());
+    int cnt1 = 0;
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      auto ret = MPI_Irecv(static_cast<void*>(&data[getOffsets[proc]]),
-                           toGet[proc].size(), MPI_DOUBLE, proc, 666, comm, &reqs[proc]);
+      if (toGet[proc].size() == 0) {
+        continue;
+      }
+      auto ret =
+          MPI_Irecv(static_cast<void*>(data.data() + getOffsets[proc]),
+                    toGet[proc].size(), MPI_DOUBLE, proc, 666, comm, reqs.data() + cnt1);
       ASSERT0(ret == MPI_SUCCESS);
+      cnt1++;
     }
     int cnt = 0;
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      void* start = static_cast<void*>(&sendBuffer[cnt]);
+      if (toSend[proc].size() == 0) {
+        continue;
+      }
+      const void* start = static_cast<void*>(sendBuffer.data() + cnt);
       for (auto i : toSend[proc]) {
         sendBuffer[cnt++] = f[Ind3D(i)];
       }
       auto ret = MPI_Send(start, toSend[proc].size(), MPI_DOUBLE, proc, 666, comm);
       ASSERT0(ret == MPI_SUCCESS);
     }
-    for ([[maybe_unused]] auto dummy : reqs) {
+    for (int j = 0; j < cnt1; ++j) {
       int ind{0};
-      auto ret = MPI_Waitany(reqs.size(), &reqs[0], &ind, MPI_STATUS_IGNORE);
+      auto ret = MPI_Waitany(cnt1, reqs.data(), &ind, MPI_STATUS_IGNORE);
       ASSERT0(ret == MPI_SUCCESS);
       ASSERT3(ind != MPI_UNDEFINED);
+      ASSERT3(ind >= 0);
+      ASSERT3(ind < cnt1);
     }
     return data;
   }

From 3444dd0f7ee424ffa6206629f79063b301798516 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 31 Jan 2025 11:45:08 +0100
Subject: [PATCH 0579/1827] Make check stricter

---
 src/mesh/parallel/fci_comm.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 1ca67f0ecc..df08a02dda 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -74,7 +74,7 @@ struct globalToLocal1D {
     }
     int loc = id - local * proc;
 #if CHECK > 1
-    if ((loc < 0 or loc > localwith or proc < 0 or proc > npe)
+    if ((loc < 0 or loc > localwith or proc < 0 or proc >= npe)
         or (periodic and (loc < mg or loc >= local + mg))) {
       printf("globalToLocal1D failure: %d %d, %d %d, %d %d %s\n", id, idwo, globalwith,
              npe, proc, loc, periodic ? "periodic" : "non-periodic");

From 91bee6811566a04656fb8b05ca4493effcbf7a39 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 31 Jan 2025 11:49:47 +0100
Subject: [PATCH 0580/1827] Fix: include global offset in monotonic spline

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 80a1336c02..c2a97c1c05 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -164,6 +164,8 @@ void XZHermiteSplineBase<monotonic>::calcWeights(const Field3D& delta_x,
 #ifdef HS_USE_PETSC
   IndConverter conv{localmesh};
 #endif
+  [[maybe_unused]] const int y_global_offset =
+      localmesh->getYProcIndex() * (localmesh->yend - localmesh->ystart + 1);
   BOUT_FOR(i, getRegion(region)) {
     const int x = i.x();
     const int y = i.y();
@@ -309,7 +311,8 @@ void XZHermiteSplineBase<monotonic>::calcWeights(const Field3D& delta_x,
 #endif
 #endif
     if constexpr (monotonic) {
-      const auto gind = gf3daccess->xyzg(i_corn, y + y_offset, k_corner(x, y, z));
+      const auto gind =
+          gf3daccess->xyzg(i_corn, y + y_offset + y_global_offset, k_corner(x, y, z));
       gf3daccess->get(gind);
       gf3daccess->get(gind.xp(1));
       gf3daccess->get(gind.zp(1));

From d7aeae490d6499a17ca7287fe291d48c630bb386 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 31 Jan 2025 14:51:11 +0100
Subject: [PATCH 0581/1827] make fci_comm openmp thread safe

Using a local set for each thread ensures we do not need a mutex for
adding data, at the cost of having to merge the different sets later.
---
 src/mesh/parallel/fci_comm.hxx | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index df08a02dda..40c1fe9f72 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -118,11 +118,30 @@ public:
         g2ly(mesh->ystart, mesh->getNYPE(), mesh->LocalNy, true),
         g2lz(mesh->zstart, 1, mesh->LocalNz, true),
         xyzl(g2lx.localwith, g2ly.localwith, g2lz.localwith),
-        xyzg(g2lx.globalwith, g2ly.globalwith, g2lz.globalwith), comm(BoutComm::get()) {};
-  void get(IndG3D ind) { ids.emplace(ind.ind); }
+        xyzg(g2lx.globalwith, g2ly.globalwith, g2lz.globalwith), comm(BoutComm::get()) {
+#ifdef _OPENMP
+    o_ids.resize(omp_get_max_threads());
+#endif
+  };
+  void get(IndG3D ind) {
+    ASSERT2(is_setup == false);
+#ifdef _OPENMP
+    ASSERT2(o_ids.size() > static_cast<size_t>(omp_get_thread_num()));
+    o_ids[omp_get_thread_num()].emplace(ind.ind);
+#else
+    ids.emplace(ind.ind);
+#endif
+  }
+
   void operator[](IndG3D ind) { return get(ind); }
   void setup() {
     ASSERT2(is_setup == false);
+#ifdef _OPENMP
+    for (auto& o_id : o_ids) {
+      ids.merge(o_id);
+    }
+    o_ids.clear();
+#endif
     toGet.resize(g2lx.npe * g2ly.npe * g2lz.npe);
     for (const auto id : ids) {
       IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
@@ -226,6 +245,9 @@ private:
     }
   }
   Mesh* mesh;
+#ifdef _OPENMP
+  std::vector<std::set<int>> o_ids;
+#endif
   std::set<int> ids;
   std::map<int, int> mapping;
   bool is_setup{false};

From ac5cc7086d737ed0f41a1b5274e5815566b223f0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 7 Feb 2025 13:50:10 +0100
Subject: [PATCH 0582/1827] Fix communication for fci

We want to skip sending if there is no data for this process ...
---
 src/mesh/parallel/fci_comm.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 40c1fe9f72..27dd111765 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -231,7 +231,7 @@ private:
       ASSERT0(ret == MPI_SUCCESS);
     }
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      if (toGet.size() != 0) {
+      if (toGet[proc].size() != 0) {
         const auto ret = MPI_Send(static_cast<void*>(toGet[proc].data()),
                                   toGet[proc].size(), MPI_INT, proc, 666 * 666, comm);
         ASSERT0(ret == MPI_SUCCESS);

From 885b465cbb81d3e12345569337693b2c39e768dd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 7 Feb 2025 15:58:07 +0100
Subject: [PATCH 0583/1827] Add check to reduce risk of bugs

The result needs to be well understood, as the indices are a mix of
local and global indices, as we need to access non-local data.
---
 src/mesh/interpolation/hermite_spline_xz.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index c2a97c1c05..036f5b2669 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -362,6 +362,9 @@ template <bool monotonic>
 std::vector<ParallelTransform::PositionsAndWeights>
 XZHermiteSplineBase<monotonic>::getWeightsForYApproximation(int i, int j, int k,
                                                             int yoffset) {
+  if (localmesh->getNXPE() > 1){
+    throw BoutException("It is likely that the function calling this is not handling the result correctly.");
+  }
   const int nz = localmesh->LocalNz;
   const int k_mod = k_corner(i, j, k);
   const int k_mod_m1 = (k_mod > 0) ? (k_mod - 1) : (nz - 1);

From a1c40336dc0bfbcedf7f622f2a2986e8cc9b8284 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 9 Oct 2025 17:23:45 +0100
Subject: [PATCH 0584/1827] tests: Increase nx for hermitespline interpolation
 boundary problem

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 036f5b2669..41ca857829 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -418,12 +418,14 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
     }
     if constexpr (monotonic) {
 #else                 // Legacy interpolation
+  // TODO(peter): Should we apply dirichlet BCs to derivatives?
   // Derivatives are used for tension and need to be on dimensionless
   // coordinates
 
   // f has been communcated, and thus we can assume that the x-boundaries are
   // also valid in the y-boundary.  Thus the differentiated field needs no
   // extra comms.
+  // TODO(dave) Add assert that we do not use z-splitting or z-guards.
   Field3D fx = bout::derivatives::index::DDX(f, CELL_DEFAULT, "DEFAULT", region2);
   Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", region2);
   Field3D fxz = bout::derivatives::index::DDZ(fx, CELL_DEFAULT, "DEFAULT", region2);

From 1c25b0e3afc6b7505e35842256a08f545e0d0aef Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 2 Feb 2026 13:02:00 +0100
Subject: [PATCH 0585/1827] region may be not used

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 41ca857829..bbd8c9abc0 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -155,7 +155,7 @@ XZHermiteSplineBase<monotonic>::XZHermiteSplineBase(int y_offset, Mesh* meshin)
 template <bool monotonic>
 void XZHermiteSplineBase<monotonic>::calcWeights(const Field3D& delta_x,
                                                  const Field3D& delta_z,
-                                                 const std::string& region) {
+                                                 [[maybe_unused]] const std::string& region) {
 
   const int ny = localmesh->LocalNy;
   const int nz = localmesh->LocalNz;
@@ -379,7 +379,7 @@ XZHermiteSplineBase<monotonic>::getWeightsForYApproximation(int i, int j, int k,
 
 template <bool monotonic>
 Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
-                                                    const std::string& region) const {
+                                                    [[maybe_unused]] const std::string& region) const {
 
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};

From c7f8504324f1b8174c8f3317202a89b32f2fc735 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 2 Feb 2026 13:52:00 +0100
Subject: [PATCH 0586/1827] Fix [[maybe_unused]] location

---
 include/bout/msg_stack.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx
index 1abb26d2c7..0fe22cd0e6 100644
--- a/include/bout/msg_stack.hxx
+++ b/include/bout/msg_stack.hxx
@@ -80,7 +80,7 @@ public:
   }
 
   void pop() {}
-  void pop(int [[maybe_unused]] id) {}
+  void pop([[maybe_unused]] int id) {}
   void clear() {}
 
   void dump() {}

From 96aa2bdbae97c573580fac747de58a1eb79c167b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Feb 2026 10:47:00 +0100
Subject: [PATCH 0587/1827] Add some wiggle room for monotonichermitespline

---
 include/bout/interpolation_xz.hxx            | 13 ++++++++----
 src/mesh/interpolation/hermite_spline_xz.cxx | 22 +++++++++++++-------
 2 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 2832899e8a..fb06faacc2 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -180,12 +180,17 @@ protected:
   Vec rhs, result;
 #endif
 
+  /// Factors to allow for some wiggleroom
+  BoutReal abs_fac_monotonic{1e-2};
+  BoutReal rel_fac_monotonic{1e-1};
+
 public:
   XZHermiteSplineBase(Mesh* mesh = nullptr, [[maybe_unused]] Options* options = nullptr)
-      : XZHermiteSplineBase(0, mesh) {}
-  XZHermiteSplineBase(int y_offset = 0, Mesh* mesh = nullptr);
-  XZHermiteSplineBase(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr)
-      : XZHermiteSplineBase(y_offset, mesh) {
+      : XZHermiteSplineBase(0, mesh, options) {}
+  XZHermiteSplineBase(int y_offset = 0, Mesh* mesh = nullptr, Options* options = nullptr);
+  XZHermiteSplineBase(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr,
+		      Options* options = nullptr)
+      : XZHermiteSplineBase(y_offset, mesh, options) {
     setRegion(regionFromMask(mask, localmesh));
   }
   ~XZHermiteSplineBase() {
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index bbd8c9abc0..8eac4037b7 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -104,11 +104,20 @@ class IndConverter {
 };
 
 template <bool monotonic>
-XZHermiteSplineBase<monotonic>::XZHermiteSplineBase(int y_offset, Mesh* meshin)
+XZHermiteSplineBase<monotonic>::XZHermiteSplineBase(int y_offset, Mesh* meshin,
+                                                    Options* options)
     : XZInterpolation(y_offset, meshin), h00_x(localmesh), h01_x(localmesh),
       h10_x(localmesh), h11_x(localmesh), h00_z(localmesh), h01_z(localmesh),
       h10_z(localmesh), h11_z(localmesh) {
 
+  if constexpr (monotonic) {
+    if (options == nullptr) {
+      options = &Options::root()["mesh:paralleltransform:xzinterpolation"];
+    }
+    abs_fac_monotonic = (*options)["abs_tol"].withDefault(abs_fac_monotonic);
+    rel_fac_monotonic = (*options)["rel_tol"].withDefault(rel_fac_monotonic);
+  }
+
   // Index arrays contain guard cells in order to get subscripts right
   i_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
   k_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
@@ -463,13 +472,10 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
       const auto corners = {(*gf)[IndG3D(g3dinds[i][0])], (*gf)[IndG3D(g3dinds[i][1])],
                             (*gf)[IndG3D(g3dinds[i][2])], (*gf)[IndG3D(g3dinds[i][3])]};
       const auto minmax = std::minmax(corners);
-      if (f_interp[iyp] < minmax.first) {
-        f_interp[iyp] = minmax.first;
-      } else {
-        if (f_interp[iyp] > minmax.second) {
-          f_interp[iyp] = minmax.second;
-        }
-      }
+      const auto diff =
+          (minmax.second - minmax.first) * rel_fac_monotonic + abs_fac_monotonic;
+      f_interp[iyp] = std::max(f_interp[iyp], minmax.first - diff);
+      f_interp[iyp] = std::min(f_interp[iyp], minmax.second + diff);
     }
 #if USE_NEW_WEIGHTS and defined(HS_USE_PETSC)
     ASSERT2(std::isfinite(cptr[int(i)]));

From df70c89721279ca41935e322f1e5935eed14e9cf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Feb 2025 13:38:40 +0100
Subject: [PATCH 0588/1827] Allow to overwrite MYG with options.

---
 src/mesh/impls/bout/boutmesh.cxx | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 4aaa760c04..08df213126 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -485,8 +485,18 @@ int BoutMesh::load() {
   }
   ASSERT0(MXG >= 0);
 
-  if (Mesh::get(MYG, "MYG") != 0) {
-    MYG = options["MYG"].doc("Number of guard cells on each side in Y").withDefault(2);
+  bool meshHasMyg = Mesh::get(MYG, "MYG") == 0;
+  int meshMyg;
+  if (!meshHasMyg) {
+    MYG = 2;
+  } else {
+    meshMyg = MYG;
+  }
+  MYG = options["MYG"].doc("Number of guard cells on each side in Y").withDefault(MYG);
+  if (meshHasMyg && MYG != meshMyg) {
+    output_warn.write(_("Options changed the number of y-guard cells. Grid has {} but "
+                           "option specified {}! Continuing with {}"),
+                         meshMyg, MYG, MYG);
   }
   ASSERT0(MYG >= 0);
 

From 52708afb8ccc7f31729c27a201c925df1ffb9b3d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 3 Mar 2025 13:40:58 +0100
Subject: [PATCH 0589/1827] Only read `MYG` if it set or mesh:MYG is not set

This avoids errors in the MMS tests
---
 src/mesh/impls/bout/boutmesh.cxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 08df213126..acdcc5d0b0 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -492,7 +492,9 @@ int BoutMesh::load() {
   } else {
     meshMyg = MYG;
   }
-  MYG = options["MYG"].doc("Number of guard cells on each side in Y").withDefault(MYG);
+  if (options.isSet("MYG") or (!meshHasMyg)) {
+    MYG = options["MYG"].doc("Number of guard cells on each side in Y").withDefault(MYG);
+  }
   if (meshHasMyg && MYG != meshMyg) {
     output_warn.write(_("Options changed the number of y-guard cells. Grid has {} but "
                            "option specified {}! Continuing with {}"),

From 1e5f185d5753ca6171bc91b94a306adfeeaf9b80 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 3 Mar 2025 14:02:54 +0100
Subject: [PATCH 0590/1827] Do not set MYG/MXG if it is not needed

---
 tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp b/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp
index d5ca4c4d71..519faa0403 100644
--- a/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp
+++ b/tests/integrated/test-boutpp/mms-ddz/data/BOUT.inp
@@ -1,7 +1,3 @@
-
-MXG = 2
-MYG = 2
-
 [mesh]
 staggergrids = true
 n = 1

From 8267681fe80af7cc5ee0be12035ce5fb4a20dc91 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 3 Mar 2025 14:03:41 +0100
Subject: [PATCH 0591/1827] Do not set MYG/MXG if it is not needed

---
 tests/integrated/test-boutpp/collect/input/BOUT.inp | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect/input/BOUT.inp b/tests/integrated/test-boutpp/collect/input/BOUT.inp
index d5ca4c4d71..519faa0403 100644
--- a/tests/integrated/test-boutpp/collect/input/BOUT.inp
+++ b/tests/integrated/test-boutpp/collect/input/BOUT.inp
@@ -1,7 +1,3 @@
-
-MXG = 2
-MYG = 2
-
 [mesh]
 staggergrids = true
 n = 1

From 9a45d250be9b317bdc16680171282aec57b403ab Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 2 Feb 2026 13:44:51 +0100
Subject: [PATCH 0592/1827] set target properties on exported library

This allows dependent projects to check whether BOUT++ was compiled e.g. with
3D metrics.
---
 bout++Config.cmake.in | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/bout++Config.cmake.in b/bout++Config.cmake.in
index a8cf041901..5cc68aefde 100644
--- a/bout++Config.cmake.in
+++ b/bout++Config.cmake.in
@@ -8,7 +8,7 @@ set(BOUT_USE_TRACK @BOUT_USE_TRACK@)
 set(BOUT_USE_SIGFPE @BOUT_USE_SIGFPE@)
 set(BOUT_USE_OPENMP @BOUT_USE_OPENMP@)
 set(BOUT_HAS_CUDA @BOUT_HAS_CUDA@)
-set(BOUT_HAS_OUTPUT_DEBUG @BOUT_HAS_OUTPUT_DEBUG@)
+set(BOUT_USE_OUTPUT_DEBUG @BOUT_USE_OUTPUT_DEBUG@)
 set(BOUT_CHECK_LEVEL @BOUT_CHECK_LEVEL@)
 set(BOUT_USE_METRIC_3D @BOUT_USE_METRIC_3D@)
 
@@ -182,3 +182,30 @@ if (BOUT_HAS_ADIOS2)
 endif()
 
 include("${CMAKE_CURRENT_LIST_DIR}/bout++Targets.cmake")
+
+add_library(bout++ INTERFACE IMPORTED)
+set_target_properties(bout++
+  PROPERTIES BOUT_USE_SIGNAL @BOUT_USE_SIGNAL@
+  BOUT_USE_COLOR @BOUT_USE_COLOR@
+  BOUT_USE_TRACK @BOUT_USE_TRACK@
+  BOUT_USE_SIGFPE @BOUT_USE_SIGFPE@
+  BOUT_USE_OPENMP @BOUT_USE_OPENMP@
+  BOUT_HAS_CUDA @BOUT_HAS_CUDA@
+  BOUT_USE_OUTPUT_DEBUG @BOUT_USE_OUTPUT_DEBUG@
+  BOUT_CHECK_LEVEL @BOUT_CHECK_LEVEL@
+  BOUT_USE_METRIC_3D @BOUT_USE_METRIC_3D@
+  BOUT_HAS_PVODE @BOUT_HAS_PVODE@
+  BOUT_HAS_NETCDF @BOUT_HAS_NETCDF@
+  BOUT_HAS_ADIOS2 @BOUT_HAS_ADIOS2@
+  BOUT_HAS_FFTW @BOUT_HAS_FFTW@
+  BOUT_HAS_LAPACK @BOUT_HAS_LAPACK@
+  BOUT_HAS_PETSC @BOUT_HAS_PETSC@
+  BOUT_HAS_SLEPC @BOUT_HAS_SLEPC@
+  BOUT_HAS_SCOREP @BOUT_HAS_SCOREP@
+  BOUT_USE_UUID_SYSTEM_GENERATOR @BOUT_USE_UUID_SYSTEM_GENERATOR@
+  BOUT_HAS_SUNDIALS @BOUT_HAS_SUNDIALS@
+  BOUT_HAS_HYPRE @BOUT_HAS_HYPRE@
+  BOUT_HAS_GETTEXT @BOUT_HAS_GETTEXT@
+  BOUT_HAS_UMPIRE @BOUT_HAS_UMPIRE@
+  BOUT_HAS_RAJA @BOUT_HAS_RAJA@
+)

From dce551b6fcc7b5099341385d480128eb385bdaf3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Feb 2026 10:13:16 +0100
Subject: [PATCH 0593/1827] Do not build with openmp

---
 .github/workflows/docker.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index c028d17042..809f59cf9c 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -26,11 +26,11 @@ jobs:
       matrix:
         mpi: [mpich]
         metric3d:
-          - name: "With OpenMP"
+          - name: "With 3D Metrics"
             cmake: ON
-            base_prefix: "openmp-"
+            base_prefix: ""
             tag_prefix: "3d-"
-          - name: "Without OpenMP"
+          - name: "Without 3D Metrics"
             cmake: OFF
             base_prefix: ""
             tag_prefix: ""
@@ -75,7 +75,7 @@ jobs:
           build-args: |
             BASE=${{ matrix.mpi }}-${{ matrix.metric3d.base_prefix }}${{ matrix.config.base_postfix }}-main
             MPI=${{ matrix.mpi }}
-            CMAKE_OPTIONS=${{ matrix.config.options }} -DBOUT_ENABLE_METRIC_3D=${{ matrix.metric3d.cmake }} -DBOUT_ENABLE_OPENMP=${{ matrix.metric3d.cmake }}
+            CMAKE_OPTIONS=${{ matrix.config.options }} -DBOUT_ENABLE_METRIC_3D=${{ matrix.metric3d.cmake }}
             COMMIT=${{ github.sha }}
             URL=${{ github.server_url }}/${{ github.repository }}
           context: .docker/fedora/

From e0ade7c1733c9a54e72105e4b67b0cb467faf3c9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Feb 2026 14:43:11 +0100
Subject: [PATCH 0594/1827] be verbose in docker build

---
 .docker/fedora/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.docker/fedora/Dockerfile b/.docker/fedora/Dockerfile
index da4d2d9fac..ed04240c4c 100644
--- a/.docker/fedora/Dockerfile
+++ b/.docker/fedora/Dockerfile
@@ -31,7 +31,7 @@ RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local/ \
           -DBOUT_ENABLE_PYTHON=ON \
           -DBOUT_USE_SUNDIALS=ON -DSUNDIALS_ROOT=/usr/lib64/$MPI/ -DSUNDIALS_INCLUDE_DIR=/usr/include/$MPI-x86_64/sundials/ \
 	  $CMAKE_OPTIONS || (cat /home/boutuser/BOUT-dev/build/CMakeFiles/CMake{Output,Error}.log  ; exit 1); \
-    make -C build -j 2; \
+    make -C build -j 2 VERBOSE=1; \
     sudo make -C build install; \
     rm -rf build
 

From e5cb1ebc179220551eba5a381eaac0d2f00b07b8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Feb 2026 14:49:22 +0100
Subject: [PATCH 0595/1827] [container] Set build type

---
 .docker/fedora/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.docker/fedora/Dockerfile b/.docker/fedora/Dockerfile
index ed04240c4c..7d5c04418d 100644
--- a/.docker/fedora/Dockerfile
+++ b/.docker/fedora/Dockerfile
@@ -26,6 +26,7 @@ ENV HOME=/home/boutuser
 WORKDIR /home/boutuser/BOUT-dev
 
 RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local/ \
+          -DCMAKE_BUILD_TYPE=RelWithDebInfo \
           -DBOUT_GENERATE_FIELDOPS=OFF \
           -DBOUT_USE_PETSC=ON -DPETSc_ROOT=/usr/local \
           -DBOUT_ENABLE_PYTHON=ON \

From e4a054962ab784f5fa447b3146938a453aa4dc8f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Feb 2026 14:42:58 +0100
Subject: [PATCH 0596/1827] Change default to PETSc for 3D metrics

---
 include/bout/invert_laplace.hxx                    | 4 ++++
 src/invert/laplace/impls/naulin/naulin_laplace.cxx | 3 ++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx
index 258b4d2e80..73e58e8483 100644
--- a/include/bout/invert_laplace.hxx
+++ b/include/bout/invert_laplace.hxx
@@ -141,7 +141,11 @@ public:
   static constexpr auto type_name = "Laplacian";
   static constexpr auto section_name = "laplace";
   static constexpr auto option_name = "type";
+#if BOUT_USE_METRIC_3D
+  static constexpr auto default_type = LAPLACE_PETSC;
+#else
   static constexpr auto default_type = LAPLACE_CYCLIC;
+#endif
 
   ReturnType create(Options* options = nullptr, CELL_LOC loc = CELL_CENTRE,
                     Mesh* mesh = nullptr, Solver* solver = nullptr) {
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index 1c90976ce6..481f01ace0 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -149,6 +149,7 @@
 #include <bout/globals.hxx>
 #include <bout/mesh.hxx>
 #include <bout/sys/timer.hxx>
+#include <bout/invert_laplace.hxx>
 
 #include "naulin_laplace.hxx"
 
@@ -207,7 +208,7 @@ LaplaceNaulin::LaplaceNaulin(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   ASSERT0(underrelax_recovery >= 1.);
   delp2solver = create(opt->getSection("delp2solver"), location, localmesh);
   std::string delp2type;
-  opt->getSection("delp2solver")->get("type", delp2type, "cyclic");
+  opt->getSection("delp2solver")->get("type", delp2type, LaplaceFactory::default_type);
   // Check delp2solver is using an FFT scheme, otherwise it will not exactly
   // invert Delp2 and we will not converge
   ASSERT0(delp2type == "cyclic" || delp2type == "spt" || delp2type == "tri");

From b043da35a828e689792ce7b9ab2c1f1eb13bc5c6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Mar 2026 13:50:15 +0100
Subject: [PATCH 0597/1827] Apply clang-tidy fixes

---
 include/bout/field.hxx   | 2 +-
 include/bout/field3d.hxx | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index d6af2be3c2..141e47ce04 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -24,6 +24,7 @@
  *
  */
 
+#include "bout/unused.hxx"
 class Field;
 
 #ifndef FIELD_H
@@ -31,7 +32,6 @@ class Field;
 
 #include <cmath>
 #include <cstdio>
-#include <memory>
 #include <optional>
 #include <string>
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 607cbb37c4..b9e9fb66c6 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -20,6 +20,7 @@
  *
  **************************************************************************/
 
+#include <cstddef>
 class Field3D;
 
 #pragma once

From d37661b66bec5a50365537be4b92fcb59aab8649 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Mar 2026 13:57:51 +0100
Subject: [PATCH 0598/1827] Move functions to field.hxx and make them virtual

---
 include/bout/field.hxx     |  5 +++++
 include/bout/field2d.hxx   |  7 -------
 include/bout/field3d.hxx   | 13 ++++++++-----
 include/bout/fieldperp.hxx |  6 ------
 4 files changed, 13 insertions(+), 18 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 141e47ce04..bfae83cef0 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -128,11 +128,16 @@ public:
     swap(first.directions, second.directions);
   }
 
+  /// Dummy functions to increase portability
   virtual void setRegion(size_t UNUSED(regionID)) {}
   virtual void setRegion(std::optional<size_t> UNUSED(regionID)) {}
   virtual void setRegion(const std::string& UNUSED(region_name)) {}
   virtual void resetRegion() {}
   virtual std::optional<size_t> getRegionID() const { return {}; }
+  virtual bool hasParallelSlices() const { return true; }
+  virtual void calcParallelSlices() const {}
+  virtual void splitParallelSlices() const {}
+  virtual void clearParallelSlices() const {}
 
 private:
   /// Labels for the type of coordinate system this field is defined over
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index fca0dd3c3f..a13da6b92e 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -133,13 +133,6 @@ public:
     return *this;
   }
 
-  /// Dummy functions to increase portability
-  bool hasParallelSlices() const { return true; }
-  void calcParallelSlices() const {}
-  void splitParallelSlices() const {}
-  void clearParallelSlices() const {}
-  int numberParallelSlices() const { return 0; }
-
   Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) { return *this; }
   const Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) const {
     return *this;
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index b9e9fb66c6..9f46d25198 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -239,15 +239,15 @@ public:
    * Ensure that this field has separate fields
    * for yup and ydown.
    */
-  void splitParallelSlices();
+  void splitParallelSlices() override;
 
   /*!
    * Clear the parallel slices, yup and ydown
    */
-  void clearParallelSlices();
+  void clearParallelSlices() override;
 
   /// Check if this field has yup and ydown fields
-  bool hasParallelSlices() const {
+  bool hasParallelSlices() const override {
 #if CHECK > 2
     if (yup_fields.size() != ydown_fields.size()) {
       throw BoutException(
@@ -482,7 +482,7 @@ public:
   friend class Vector3D;
   friend class Vector2D;
 
-  Field3D& calcParallelSlices();
+  void calcParallelSlices() override;
 
   void applyBoundary(bool init = false) override;
   void applyBoundary(BoutReal t);
@@ -511,7 +511,8 @@ public:
 
   std::weak_ptr<Options> getTracking() { return tracking; };
 
-  bool allowCalcParallelSlices{true};
+  bool allowCalcParallelSlices() const { return _allowCalcParallelSlices; };
+  void disallowCalcParallelSlices() { _allowCalcParallelSlices = false; };
 
 private:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
@@ -532,6 +533,8 @@ private:
   /// counter for tracking, to assign unique names to the variable names
   int tracking_state{0};
   std::weak_ptr<Options> tracking;
+
+  bool _allowCalcParallelSlices{true};
   // name is changed if we assign to the variable, while selfname is a
   // non-changing copy that is used for the variable names in the dump files
   std::string selfname;
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index ad069f0d01..dcfb89f54c 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -157,12 +157,6 @@ public:
     return *this;
   }
 
-  /// Dummy functions to increase portability
-  bool hasParallelSlices() const { return true; }
-  void calcParallelSlices() const {}
-  void clearParallelSlices() {}
-  int numberParallelSlices() { return 0; }
-
   FieldPerp& yup(std::vector<FieldPerp>::size_type UNUSED(index) = 0) { return *this; }
   const FieldPerp& yup(std::vector<FieldPerp>::size_type UNUSED(index) = 0) const {
     return *this;

From 48e78ec6d80d378b38d5ec15a7725447d3ed836c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Mar 2026 13:58:06 +0100
Subject: [PATCH 0599/1827] Apply fixes from clang-tidy

---
 include/bout/fieldperp.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index dcfb89f54c..1f70089990 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -23,6 +23,7 @@
  *
  **************************************************************************/
 
+#include <vector>
 class FieldPerp;
 
 #ifndef BOUT_FIELDPERP_H

From b6b39d9d4a6f11e4fc8dbc70d48484aee3b2ada0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 3 Mar 2026 14:06:52 +0100
Subject: [PATCH 0600/1827] The overrides are non-const

---
 include/bout/field.hxx | 6 +++---
 src/field/field3d.cxx  | 3 +--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index bfae83cef0..a5b9d1390b 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -135,9 +135,9 @@ public:
   virtual void resetRegion() {}
   virtual std::optional<size_t> getRegionID() const { return {}; }
   virtual bool hasParallelSlices() const { return true; }
-  virtual void calcParallelSlices() const {}
-  virtual void splitParallelSlices() const {}
-  virtual void clearParallelSlices() const {}
+  virtual void calcParallelSlices() {}
+  virtual void splitParallelSlices() {}
+  virtual void clearParallelSlices() {}
 
 private:
   /// Labels for the type of coordinate system this field is defined over
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 2cd55b0957..fe9fdc9263 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -341,9 +341,8 @@ Field3D& Field3D::operator=(const BoutReal val) {
   return *this;
 }
 
-Field3D& Field3D::calcParallelSlices() {
+void Field3D::calcParallelSlices() {
   getCoordinates()->getParallelTransform().calcParallelSlices(*this);
-  return *this;
 }
 
 ///////////////////// BOUNDARY CONDITIONS //////////////////

From 65880e4af16cb95438437bf057c4b9fdb427b142 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Tue, 3 Mar 2026 13:09:09 +0000
Subject: [PATCH 0601/1827] [bot] Apply format changes

---
 include/bout/interpolation_xz.hxx            |  2 +-
 src/mesh/interpolation/hermite_spline_xz.cxx | 17 +++++++++--------
 src/mesh/interpolation/lagrange_4pt_xz.cxx   |  1 -
 src/mesh/parallel/fci_comm.hxx               |  4 ++--
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index fb06faacc2..578627997f 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -189,7 +189,7 @@ public:
       : XZHermiteSplineBase(0, mesh, options) {}
   XZHermiteSplineBase(int y_offset = 0, Mesh* mesh = nullptr, Options* options = nullptr);
   XZHermiteSplineBase(const BoutMask& mask, int y_offset = 0, Mesh* mesh = nullptr,
-		      Options* options = nullptr)
+                      Options* options = nullptr)
       : XZHermiteSplineBase(y_offset, mesh, options) {
     setRegion(regionFromMask(mask, localmesh));
   }
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 8eac4037b7..6b9441f539 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -21,8 +21,8 @@
  **************************************************************************/
 
 #include "../impls/bout/boutmesh.hxx"
-#include "bout/bout.hxx"
 #include "../parallel/fci_comm.hxx"
+#include "bout/bout.hxx"
 #include "bout/globals.hxx"
 #include "bout/index_derivs_interface.hxx"
 #include "bout/interpolation_xz.hxx"
@@ -162,9 +162,9 @@ XZHermiteSplineBase<monotonic>::XZHermiteSplineBase(int y_offset, Mesh* meshin,
 }
 
 template <bool monotonic>
-void XZHermiteSplineBase<monotonic>::calcWeights(const Field3D& delta_x,
-                                                 const Field3D& delta_z,
-                                                 [[maybe_unused]] const std::string& region) {
+void XZHermiteSplineBase<monotonic>::calcWeights(
+    const Field3D& delta_x, const Field3D& delta_z,
+    [[maybe_unused]] const std::string& region) {
 
   const int ny = localmesh->LocalNy;
   const int nz = localmesh->LocalNz;
@@ -371,8 +371,9 @@ template <bool monotonic>
 std::vector<ParallelTransform::PositionsAndWeights>
 XZHermiteSplineBase<monotonic>::getWeightsForYApproximation(int i, int j, int k,
                                                             int yoffset) {
-  if (localmesh->getNXPE() > 1){
-    throw BoutException("It is likely that the function calling this is not handling the result correctly.");
+  if (localmesh->getNXPE() > 1) {
+    throw BoutException("It is likely that the function calling this is not handling the "
+                        "result correctly.");
   }
   const int nz = localmesh->LocalNz;
   const int k_mod = k_corner(i, j, k);
@@ -387,8 +388,8 @@ XZHermiteSplineBase<monotonic>::getWeightsForYApproximation(int i, int j, int k,
 }
 
 template <bool monotonic>
-Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
-                                                    [[maybe_unused]] const std::string& region) const {
+Field3D XZHermiteSplineBase<monotonic>::interpolate(
+    const Field3D& f, [[maybe_unused]] const std::string& region) const {
 
   ASSERT1(f.getMesh() == localmesh);
   Field3D f_interp{emptyFrom(f)};
diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx
index 7fb0fb502b..d5e862fc0b 100644
--- a/src/mesh/interpolation/lagrange_4pt_xz.cxx
+++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx
@@ -134,7 +134,6 @@ Field3D XZLagrange4pt::interpolate(const Field3D& f, const std::string& region)
     // Then in X
     f_interp(x, y_next, z) = lagrange_4pt(xvals, t_x(x, y, z));
     ASSERT2(std::isfinite(f_interp(x, y_next, z)));
-
   }
   const auto region2 = y_offset != 0 ? fmt::format("RGN_YPAR_{:+d}", y_offset) : region;
   f_interp.setRegion(region2);
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 27dd111765..3514e4ba17 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -55,7 +55,7 @@ struct globalToLocal1D {
   const bool periodic;
   globalToLocal1D(int mg, int npe, int localwith, bool periodic)
       : mg(mg), npe(npe), localwith(localwith), local(localwith - 2 * mg),
-        global(local * npe), globalwith(global + 2 * mg), periodic(periodic) {};
+        global(local * npe), globalwith(global + 2 * mg), periodic(periodic){};
   ProcLocal convert(int id) const {
     if (periodic) {
       while (id < mg) {
@@ -103,7 +103,7 @@ public:
 
   GlobalField3DAccessInstance(const GlobalField3DAccess* gfa,
                               const std::vector<BoutReal>&& data)
-      : gfa(*gfa), data(std::move(data)) {};
+      : gfa(*gfa), data(std::move(data)){};
 
 private:
   const GlobalField3DAccess& gfa;

From a91d3e75b31ba43951792f5ede617af602b4261b Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Tue, 3 Mar 2026 13:09:10 +0000
Subject: [PATCH 0602/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index abd11c7762..9ec546dec7 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -11,3 +11,4 @@ a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
 2c2402ed59c91164eaff46dee0f79386b7347e9e
 05b7c571544c3bcb153fce67d12b9ac48947fc2d
 c8f38049359170a34c915e209276238ea66b9a1e
+65880e4af16cb95438437bf057c4b9fdb427b142

From 8d5cb39e03c2644715a50684f8cd0318b4e82676 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Tue, 3 Mar 2026 13:33:29 +0000
Subject: [PATCH 0603/1827] [bot] Apply format changes

---
 src/mesh/impls/bout/boutmesh.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index acdcc5d0b0..7f76d6efe0 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -497,8 +497,8 @@ int BoutMesh::load() {
   }
   if (meshHasMyg && MYG != meshMyg) {
     output_warn.write(_("Options changed the number of y-guard cells. Grid has {} but "
-                           "option specified {}! Continuing with {}"),
-                         meshMyg, MYG, MYG);
+                        "option specified {}! Continuing with {}"),
+                      meshMyg, MYG, MYG);
   }
   ASSERT0(MYG >= 0);
 

From 0ba91f61cd2781bec1da5f29e04c830d5e95a4fc Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Tue, 3 Mar 2026 13:33:30 +0000
Subject: [PATCH 0604/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index abd11c7762..4e7777ec58 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -11,3 +11,4 @@ a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
 2c2402ed59c91164eaff46dee0f79386b7347e9e
 05b7c571544c3bcb153fce67d12b9ac48947fc2d
 c8f38049359170a34c915e209276238ea66b9a1e
+8d5cb39e03c2644715a50684f8cd0318b4e82676

From f473a6bfd972421769c61fda4cef9edc03535ca0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 10:16:51 +0100
Subject: [PATCH 0605/1827] Apply fixes from clang-format

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 2 ++
 src/mesh/parallel/fci_comm.cxx               | 3 +++
 src/mesh/parallel/fci_comm.hxx               | 3 +++
 3 files changed, 8 insertions(+)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 6b9441f539..577b4cb9db 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -27,6 +27,8 @@
 #include "bout/index_derivs_interface.hxx"
 #include "bout/interpolation_xz.hxx"
 
+#include <algorithm>
+#include <string>
 #include <vector>
 
 class IndConverter {
diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index c0d51d1eb9..95bfa6958e 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -24,6 +24,9 @@
  **************************************************************************/
 
 #include "fci_comm.hxx"
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/region.hxx"
 
 #include <vector>
 
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 3514e4ba17..cbe5af3a7f 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -32,6 +32,9 @@
 #include "bout/mesh.hxx"
 #include "bout/region.hxx"
 #include <algorithm>
+#include <cstddef>
+#include <cstdio>
+#include <iterator>
 #include <map>
 #include <memory>
 #include <set>

From a8c5ea82e28ee4cd903c15297792b1bdc939f62c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 10:07:25 +0100
Subject: [PATCH 0606/1827] Cleanup code

---
 src/mesh/impls/bout/boutmesh.cxx | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 7f76d6efe0..d0bdcf33d8 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -485,13 +485,12 @@ int BoutMesh::load() {
   }
   ASSERT0(MXG >= 0);
 
-  bool meshHasMyg = Mesh::get(MYG, "MYG") == 0;
-  int meshMyg;
+  const bool meshHasMyg = Mesh::get(MYG, "MYG") == 0;
   if (!meshHasMyg) {
     MYG = 2;
-  } else {
-    meshMyg = MYG;
   }
+  int meshMyg = MYG;
+
   if (options.isSet("MYG") or (!meshHasMyg)) {
     MYG = options["MYG"].doc("Number of guard cells on each side in Y").withDefault(MYG);
   }

From 6a104ba0c61ab5908f1aa70401567cf5960ffeec Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 19 Mar 2024 15:41:00 +0100
Subject: [PATCH 0607/1827] Add maskFromRegion

---
 include/bout/mask.hxx | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/include/bout/mask.hxx b/include/bout/mask.hxx
index fc5f814676..378ac835bc 100644
--- a/include/bout/mask.hxx
+++ b/include/bout/mask.hxx
@@ -80,4 +80,12 @@ inline std::unique_ptr<Region<Ind3D>> regionFromMask(const BoutMask& mask,
   }
   return std::make_unique<Region<Ind3D>>(indices);
 }
+
+inline BoutMask maskFromRegion(const Region<Ind3D>& region, const Mesh* mesh) {
+  BoutMask mask{mesh, false};
+
+  BOUT_FOR(i, region) { mask[i] = true; }
+  return mask;
+}
+
 #endif //BOUT_MASK_H

From ea2ea211079e43c547f828a016d1d398a88d3376 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 09:59:36 +0100
Subject: [PATCH 0608/1827] Switch to [[maybe_unused]]

---
 include/bout/field.hxx   |  7 +++----
 include/bout/field2d.hxx | 29 ++++++++++++++---------------
 include/bout/field3d.hxx |  8 ++++----
 3 files changed, 21 insertions(+), 23 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index a5b9d1390b..3f7f591528 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -24,7 +24,6 @@
  *
  */
 
-#include "bout/unused.hxx"
 class Field;
 
 #ifndef FIELD_H
@@ -129,9 +128,9 @@ public:
   }
 
   /// Dummy functions to increase portability
-  virtual void setRegion(size_t UNUSED(regionID)) {}
-  virtual void setRegion(std::optional<size_t> UNUSED(regionID)) {}
-  virtual void setRegion(const std::string& UNUSED(region_name)) {}
+  virtual void setRegion([[maybe_unused]] size_t regionID) {}
+  virtual void setRegion([[maybe_unused]] std::optional<size_t> regionID) {}
+  virtual void setRegion([[maybe_unused]] const std::string& region_name) {}
   virtual void resetRegion() {}
   virtual std::optional<size_t> getRegionID() const { return {}; }
   virtual bool hasParallelSlices() const { return true; }
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index a13da6b92e..97c4be2716 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -36,7 +36,6 @@ class Field2D;
 #include "bout/field_data.hxx"
 #include "bout/fieldperp.hxx"
 #include "bout/region.hxx"
-#include "bout/unused.hxx"
 
 #if BOUT_HAS_RAJA
 #include "RAJA/RAJA.hpp" // using RAJA lib
@@ -133,18 +132,18 @@ public:
     return *this;
   }
 
-  Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) { return *this; }
-  const Field2D& yup(std::vector<Field2D>::size_type UNUSED(index) = 0) const {
+  Field2D& yup([[maybe_unused]] std::vector<Field2D>::size_type index = 0) { return *this; }
+  const Field2D& yup([[maybe_unused]] std::vector<Field2D>::size_type index = 0) const {
     return *this;
   }
 
-  Field2D& ydown(std::vector<Field2D>::size_type UNUSED(index) = 0) { return *this; }
-  const Field2D& ydown(std::vector<Field2D>::size_type UNUSED(index) = 0) const {
+  Field2D& ydown([[maybe_unused]] std::vector<Field2D>::size_type index = 0) { return *this; }
+  const Field2D& ydown([[maybe_unused]] std::vector<Field2D>::size_type index) = 0 const {
     return *this;
   }
 
-  Field2D& ynext(int UNUSED(dir)) { return *this; }
-  const Field2D& ynext(int UNUSED(dir)) const { return *this; }
+  Field2D& ynext([[maybe_unused]] int dir) { return *this; }
+  const Field2D& ynext([[maybe_unused]] int dir) const { return *this; }
 
   // Operators
 
@@ -227,8 +226,8 @@ public:
    * DIrect access to underlying array. This version is for compatibility
    * with Field3D objects
    */
-  BoutReal& operator()(int jx, int jy, int UNUSED(jz)) { return operator()(jx, jy); }
-  const BoutReal& operator()(int jx, int jy, int UNUSED(jz)) const {
+  BoutReal& operator()(int jx, int jy, [[maybe_unused]] int jz) { return operator()(jx, jy); }
+  const BoutReal& operator()(int jx, int jy, [[maybe_unused]] int jz) const {
     return operator()(jx, jy);
   }
 
@@ -315,12 +314,12 @@ Field2D operator-(const Field2D& f);
 // Non-member functions
 
 inline Field2D toFieldAligned(const Field2D& f,
-                              const std::string& UNUSED(region) = "RGN_ALL") {
+                              [[maybe_unused]] const std::string& region = "RGN_ALL") {
   return f;
 }
 
 inline Field2D fromFieldAligned(const Field2D& f,
-                                const std::string& UNUSED(region) = "RGN_ALL") {
+                                [[maybe_unused]] const std::string& region = "RGN_ALL") {
   return f;
 }
 
@@ -331,15 +330,15 @@ inline Field2D fromFieldAligned(const Field2D& f,
 /// default (can be changed using the \p rgn argument
 void checkData(const Field2D& f, const std::string& region = "RGN_NOBNDRY");
 #else
-inline void checkData(const Field2D& UNUSED(f),
-                      std::string UNUSED(region) = "RGN_NOBNDRY") {}
+inline void checkData([[maybe_unused]] const Field2D& f,
+                      [[maybe_unused]] std::string region) = "RGN_NOBNDRY" {}
 #endif
 
 /// Force guard cells of passed field \p var to NaN
 #if CHECK > 2
 void invalidateGuards(Field2D& var);
 #else
-inline void invalidateGuards(Field2D& UNUSED(var)) {}
+inline void invalidateGuards([[maybe_unused]] Field2D& var) {}
 #endif
 
 /// Average in the Z direction
@@ -355,7 +354,7 @@ inline Field2D& ddt(Field2D& f) { return *(f.timeDeriv()); }
 /// toString template specialisation
 /// Defined in utils.hxx
 template <>
-inline std::string toString<>(const Field2D& UNUSED(val)) {
+inline std::string toString<>([[maybe_unused]] const Field2D& val) {
   return "<Field2D>";
 }
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 9f46d25198..8546a430ed 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -605,8 +605,8 @@ void checkData(const Field3D& f, const std::string& region = "RGN_NOBNDRY");
 #else
 /// Ignored with disabled CHECK; Throw an exception if \p f is not
 /// allocated or if any elements are non-finite (for CHECK > 2)
-inline void checkData(const Field3D& UNUSED(f),
-                      const std::string& UNUSED(region) = "RGN_NOBNDRY"){};
+inline void checkData([[maybe_unused]] const Field3D& f,
+                      [[maybe_unused]] const std::string& region = "RGN_NOBNDRY"){};
 #endif
 
 /// Fourier filtering, removes all except one mode
@@ -667,7 +667,7 @@ Field2D DC(const Field3D& f, const std::string& rgn = "RGN_ALL");
 #if CHECK > 2
 void invalidateGuards(Field3D& var);
 #else
-inline void invalidateGuards(Field3D& UNUSED(var)) {}
+inline void invalidateGuards([[maybe_unused]] Field3D& var) {}
 #endif
 
 /// Returns a reference to the time-derivative of a field \p f
@@ -678,7 +678,7 @@ inline Field3D& ddt(Field3D& f) { return *(f.timeDeriv()); }
 /// toString template specialisation
 /// Defined in utils.hxx
 template <>
-inline std::string toString<>(const Field3D& UNUSED(val)) {
+inline std::string toString<>([[maybe_unused]] const Field3D& val) {
   return "<Field3D>";
 }
 

From f2bc0488a298f136294c523bc5ab4086d090059b Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Wed, 4 Mar 2026 09:56:43 +0000
Subject: [PATCH 0609/1827] [bot] Apply format changes

---
 src/invert/laplace/impls/naulin/naulin_laplace.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index 481f01ace0..bf8711245e 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -147,9 +147,9 @@
 #include <bout/derivs.hxx>
 #include <bout/difops.hxx>
 #include <bout/globals.hxx>
+#include <bout/invert_laplace.hxx>
 #include <bout/mesh.hxx>
 #include <bout/sys/timer.hxx>
-#include <bout/invert_laplace.hxx>
 
 #include "naulin_laplace.hxx"
 

From e0dd2049d748059f7fa52eb2a1eeabe2c45647ee Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Wed, 4 Mar 2026 09:56:44 +0000
Subject: [PATCH 0610/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index abd11c7762..742c020e17 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -11,3 +11,4 @@ a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
 2c2402ed59c91164eaff46dee0f79386b7347e9e
 05b7c571544c3bcb153fce67d12b9ac48947fc2d
 c8f38049359170a34c915e209276238ea66b9a1e
+f2bc0488a298f136294c523bc5ab4086d090059b

From 8a3f82debba0a6751a51f9c38d434265c2de92c5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 10:02:08 +0100
Subject: [PATCH 0611/1827] Prefer size_t

---
 include/bout/field2d.hxx | 8 ++++----
 include/bout/field3d.hxx | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 97c4be2716..001201b5e1 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -132,13 +132,13 @@ public:
     return *this;
   }
 
-  Field2D& yup([[maybe_unused]] std::vector<Field2D>::size_type index = 0) { return *this; }
-  const Field2D& yup([[maybe_unused]] std::vector<Field2D>::size_type index = 0) const {
+  Field2D& yup([[maybe_unused]] size_t index = 0) { return *this; }
+  const Field2D& yup([[maybe_unused]] size_t index = 0) const {
     return *this;
   }
 
-  Field2D& ydown([[maybe_unused]] std::vector<Field2D>::size_type index = 0) { return *this; }
-  const Field2D& ydown([[maybe_unused]] std::vector<Field2D>::size_type index) = 0 const {
+  Field2D& ydown([[maybe_unused]] size_t index = 0) { return *this; }
+  const Field2D& ydown([[maybe_unused]] size_t index = 0) const {
     return *this;
   }
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 8546a430ed..42fee60a7c 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -264,24 +264,24 @@ public:
 
   /// Check if this field has yup and ydown fields
   /// Return reference to yup field
-  Field3D& yup(std::vector<Field3D>::size_type index = 0) {
+  Field3D& yup(size_t index = 0) {
     ASSERT2(index < yup_fields.size());
     return yup_fields[index];
   }
   /// Return const reference to yup field
-  const Field3D& yup(std::vector<Field3D>::size_type index = 0) const {
+  const Field3D& yup(size_t index = 0) const {
     ASSERT2(index < yup_fields.size());
     return yup_fields[index];
   }
 
   /// Return reference to ydown field
-  Field3D& ydown(std::vector<Field3D>::size_type index = 0) {
+  Field3D& ydown(size_t index = 0) {
     ASSERT2(index < ydown_fields.size());
     return ydown_fields[index];
   }
 
   /// Return const reference to ydown field
-  const Field3D& ydown(std::vector<Field3D>::size_type index = 0) const {
+  const Field3D& ydown(size_t index = 0) const {
     ASSERT2(index < ydown_fields.size());
     return ydown_fields[index];
   }

From f341037b5fbb26184898190112932004985b010e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:20:14 +0100
Subject: [PATCH 0612/1827] Apply clang-tidy changes

---
 include/bout/interpolation_xz.hxx            |  3 +-
 include/bout/region.hxx                      |  2 +-
 src/mesh/interpolation/hermite_spline_xz.cxx |  4 ++-
 src/mesh/interpolation/lagrange_4pt_xz.cxx   |  1 +
 src/mesh/parallel/fci_comm.hxx               | 38 ++++++++++----------
 5 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 578627997f..6e4f12b1b0 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -27,6 +27,7 @@
 #include <bout/bout_types.hxx>
 #include <bout/generic_factory.hxx>
 #include <bout/mask.hxx>
+#include <array>
 
 #define USE_NEW_WEIGHTS 1
 #if BOUT_HAS_PETSC
@@ -193,7 +194,7 @@ public:
       : XZHermiteSplineBase(y_offset, mesh, options) {
     setRegion(regionFromMask(mask, localmesh));
   }
-  ~XZHermiteSplineBase() {
+  ~XZHermiteSplineBase() override {
 #if HS_USE_PETSC
     if (isInit) {
       MatDestroy(&petscWeights);
diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index f441b3edd7..17ded65987 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -139,7 +139,7 @@ class BoutMask;
   BOUT_FOR_OMP(index, (region), for schedule(BOUT_OPENMP_SCHEDULE) nowait)
 // NOLINTEND(cppcoreguidelines-macro-usage,bugprone-macro-parentheses)
 
-enum class IND_TYPE { IND_3D = 0, IND_2D = 1, IND_PERP = 2, IND_GLOBAL_3D };
+enum class IND_TYPE { IND_3D = 0, IND_2D = 1, IND_PERP = 2, IND_GLOBAL_3D = 3 };
 
 /// Indices base class for Fields -- Regions are dereferenced into these
 ///
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 577b4cb9db..2a4f32070a 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -26,8 +26,10 @@
 #include "bout/globals.hxx"
 #include "bout/index_derivs_interface.hxx"
 #include "bout/interpolation_xz.hxx"
+#include "bout/mask.hxx"
 
 #include <algorithm>
+#include <memory>
 #include <string>
 #include <vector>
 
@@ -476,7 +478,7 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(
                             (*gf)[IndG3D(g3dinds[i][2])], (*gf)[IndG3D(g3dinds[i][3])]};
       const auto minmax = std::minmax(corners);
       const auto diff =
-          (minmax.second - minmax.first) * rel_fac_monotonic + abs_fac_monotonic;
+          ((minmax.second - minmax.first) * rel_fac_monotonic) + abs_fac_monotonic;
       f_interp[iyp] = std::max(f_interp[iyp], minmax.first - diff);
       f_interp[iyp] = std::min(f_interp[iyp], minmax.second + diff);
     }
diff --git a/src/mesh/interpolation/lagrange_4pt_xz.cxx b/src/mesh/interpolation/lagrange_4pt_xz.cxx
index d5e862fc0b..c82c9fa36e 100644
--- a/src/mesh/interpolation/lagrange_4pt_xz.cxx
+++ b/src/mesh/interpolation/lagrange_4pt_xz.cxx
@@ -20,6 +20,7 @@
  *
  **************************************************************************/
 
+#include "fmt/format.h"
 #include "bout/globals.hxx"
 #include "bout/interpolation_xz.hxx"
 #include "bout/mesh.hxx"
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index cbe5af3a7f..17b30a9c25 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -57,8 +57,8 @@ struct globalToLocal1D {
   const int globalwith;
   const bool periodic;
   globalToLocal1D(int mg, int npe, int localwith, bool periodic)
-      : mg(mg), npe(npe), localwith(localwith), local(localwith - 2 * mg),
-        global(local * npe), globalwith(global + 2 * mg), periodic(periodic){};
+      : mg(mg), npe(npe), localwith(localwith), local(localwith - (2 * mg)),
+        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic) {};
   ProcLocal convert(int id) const {
     if (periodic) {
       while (id < mg) {
@@ -68,14 +68,14 @@ struct globalToLocal1D {
         id -= global;
       }
     }
-    int idwo = id - mg;
+    const int idwo = id - mg;
     int proc = idwo / local;
     if (not periodic) {
       if (proc >= npe) {
         proc = npe - 1;
       }
     }
-    int loc = id - local * proc;
+    const int loc = id - (local * proc);
 #if CHECK > 1
     if ((loc < 0 or loc > localwith or proc < 0 or proc >= npe)
         or (periodic and (loc < mg or loc >= local + mg))) {
@@ -93,7 +93,7 @@ struct XYZ2Ind {
   const int ny;
   const int nz;
   ind convert(const int x, const int y, const int z) const {
-    return {z + (y + x * ny) * nz, ny, nz};
+    return {z + ((y + x * ny) * nz), ny, nz};
   }
   ind operator()(const int x, const int y, const int z) const { return convert(x, y, z); }
   XYZ2Ind(const int nx, const int ny, const int nz) : nx(nx), ny(ny), nz(nz) {}
@@ -105,8 +105,8 @@ public:
   const BoutReal& operator[](IndG3D ind) const;
 
   GlobalField3DAccessInstance(const GlobalField3DAccess* gfa,
-                              const std::vector<BoutReal>&& data)
-      : gfa(*gfa), data(std::move(data)){};
+                              std::vector<BoutReal>&& data)
+      : gfa(*gfa), data(std::move(data)) {};
 
 private:
   const GlobalField3DAccess& gfa;
@@ -136,7 +136,7 @@ public:
 #endif
   }
 
-  void operator[](IndG3D ind) { return get(ind); }
+  void operator[](IndG3D ind) { get(ind); }
   void setup() {
     ASSERT2(is_setup == false);
 #ifdef _OPENMP
@@ -145,14 +145,14 @@ public:
     }
     o_ids.clear();
 #endif
-    toGet.resize(g2lx.npe * g2ly.npe * g2lz.npe);
+    toGet.resize(static_cast<size_type>(g2lx.npe * g2ly.npe * g2lz.npe));
     for (const auto id : ids) {
-      IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
+      const IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
       const auto pix = g2lx.convert(gind.x());
       const auto piy = g2ly.convert(gind.y());
       const auto piz = g2lz.convert(gind.z());
       ASSERT3(piz.proc == 0);
-      toGet[piy.proc * g2lx.npe + pix.proc].push_back(
+      toGet[(piy.proc * g2lx.npe) + pix.proc].push_back(
           xyzl.convert(pix.ind, piy.ind, piz.ind).ind);
     }
     for (auto& v : toGet) {
@@ -161,19 +161,19 @@ public:
     commCommLists();
     {
       int offset = 0;
-      for (auto get : toGet) {
+      for (const auto& get : toGet) {
         getOffsets.push_back(offset);
         offset += get.size();
       }
       getOffsets.push_back(offset);
     }
     for (const auto id : ids) {
-      IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
+      const IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
       const auto pix = g2lx.convert(gind.x());
       const auto piy = g2ly.convert(gind.y());
       const auto piz = g2lz.convert(gind.z());
       ASSERT3(piz.proc == 0);
-      const auto proc = piy.proc * g2lx.npe + pix.proc;
+      const auto proc = (piy.proc * g2lx.npe) + pix.proc;
       const auto& vec = toGet[proc];
       const auto tofind = xyzl.convert(pix.ind, piy.ind, piz.ind).ind;
       auto it = std::lower_bound(vec.begin(), vec.end(), tofind);
@@ -216,9 +216,9 @@ private:
     }
     std::vector<MPI_Request> reqs2(toSend.size());
     int cnt = 0;
-    for ([[maybe_unused]] auto dummy : reqs) {
+    for ([[maybe_unused]] auto* dummy : reqs) {
       int ind{0};
-      auto ret = MPI_Waitany(reqs.size(), &reqs[0], &ind, MPI_STATUS_IGNORE);
+      auto ret = MPI_Waitany(reqs.size(), reqs.data(), &ind, MPI_STATUS_IGNORE);
       ASSERT0(ret == MPI_SUCCESS);
       ASSERT3(ind != MPI_UNDEFINED);
       ASSERT2(static_cast<size_t>(ind) < toSend.size());
@@ -234,7 +234,7 @@ private:
       ASSERT0(ret == MPI_SUCCESS);
     }
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      if (toGet[proc].size() != 0) {
+      if (!toGet[proc].empty()) {
         const auto ret = MPI_Send(static_cast<void*>(toGet[proc].data()),
                                   toGet[proc].size(), MPI_INT, proc, 666 * 666, comm);
         ASSERT0(ret == MPI_SUCCESS);
@@ -276,7 +276,7 @@ private:
     std::vector<MPI_Request> reqs(toSend.size());
     int cnt1 = 0;
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      if (toGet[proc].size() == 0) {
+      if (toGet[proc].empty()) {
         continue;
       }
       auto ret =
@@ -287,7 +287,7 @@ private:
     }
     int cnt = 0;
     for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      if (toSend[proc].size() == 0) {
+      if (toSend[proc].empty()) {
         continue;
       }
       const void* start = static_cast<void*>(sendBuffer.data() + cnt);

From 999d4ca69e32e47ce7b46c60c6d2818593a6dd9f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:31:37 +0100
Subject: [PATCH 0613/1827] Apply clang-tidy improvements

---
 src/mesh/parallel/fci_comm.cxx |  4 ++--
 src/mesh/parallel/fci_comm.hxx | 22 +++++++++++-----------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index 95bfa6958e..65a8731740 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -31,7 +31,7 @@
 #include <vector>
 
 const BoutReal& GlobalField3DAccessInstance::operator[](IndG3D ind) const {
-  auto it = gfa.mapping.find(ind.ind);
-  ASSERT2(it != gfa.mapping.end());
+  auto it = gfa->mapping.find(ind.ind);
+  ASSERT2(it != gfa->mapping.end());
   return data[it->second];
 }
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 17b30a9c25..6d80a2e326 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -49,13 +49,13 @@ struct ProcLocal {
   int ind;
 };
 struct globalToLocal1D {
-  const int mg;
-  const int npe;
-  const int localwith;
-  const int local;
-  const int global;
-  const int globalwith;
-  const bool periodic;
+  int mg;
+  int npe;
+  int localwith;
+  int local;
+  int global;
+  int globalwith;
+  bool periodic;
   globalToLocal1D(int mg, int npe, int localwith, bool periodic)
       : mg(mg), npe(npe), localwith(localwith), local(localwith - (2 * mg)),
         global(local * npe), globalwith(global + (2 * mg)), periodic(periodic) {};
@@ -106,11 +106,11 @@ public:
 
   GlobalField3DAccessInstance(const GlobalField3DAccess* gfa,
                               std::vector<BoutReal>&& data)
-      : gfa(*gfa), data(std::move(data)) {};
+      : gfa(gfa), data(std::move(data)) {};
 
 private:
-  const GlobalField3DAccess& gfa;
-  const std::vector<BoutReal> data;
+  const GlobalField3DAccess* gfa;
+  std::vector<BoutReal> data;
 };
 
 class GlobalField3DAccess {
@@ -145,7 +145,7 @@ public:
     }
     o_ids.clear();
 #endif
-    toGet.resize(static_cast<size_type>(g2lx.npe * g2ly.npe * g2lz.npe));
+    toGet.resize(static_cast<size_t>(g2lx.npe * g2ly.npe * g2lz.npe));
     for (const auto id : ids) {
       const IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
       const auto pix = g2lx.convert(gind.x());

From 1f7623c86455de9d75fe6a97f7f33fd80a491df2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:35:42 +0100
Subject: [PATCH 0614/1827] fixup

---
 include/bout/field2d.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 001201b5e1..d1585522f0 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -331,7 +331,7 @@ inline Field2D fromFieldAligned(const Field2D& f,
 void checkData(const Field2D& f, const std::string& region = "RGN_NOBNDRY");
 #else
 inline void checkData([[maybe_unused]] const Field2D& f,
-                      [[maybe_unused]] std::string region) = "RGN_NOBNDRY" {}
+                      [[maybe_unused]] std::string region = "RGN_NOBNDRY") {}
 #endif
 
 /// Force guard cells of passed field \p var to NaN

From 88abeb55fd7c89388f501a2918e9933169bad301 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:13:27 +0100
Subject: [PATCH 0615/1827] Add missing header

---
 include/bout/field2d.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index d1585522f0..899c741991 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -37,6 +37,8 @@ class Field2D;
 #include "bout/fieldperp.hxx"
 #include "bout/region.hxx"
 
+#include <cstddef>
+
 #if BOUT_HAS_RAJA
 #include "RAJA/RAJA.hpp" // using RAJA lib
 #endif

From 5ac876b2b20b964e1c418aeb22548a3fd36f4fe3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:50:49 +0100
Subject: [PATCH 0616/1827] Add missing header

---
 include/bout/mask.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/mask.hxx b/include/bout/mask.hxx
index 378ac835bc..9033080d44 100644
--- a/include/bout/mask.hxx
+++ b/include/bout/mask.hxx
@@ -26,6 +26,7 @@
 
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
+#include "bout/region.hxx"
 
 /**
  * 3D array of bools to mask Field3Ds

From 614a727ca68ff8ca0fd3f330d4d48dcf127989a6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:52:57 +0100
Subject: [PATCH 0617/1827] MPI_Request may not be a pointer

---
 src/mesh/parallel/fci_comm.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 6d80a2e326..cf0ddb01a2 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -216,7 +216,7 @@ private:
     }
     std::vector<MPI_Request> reqs2(toSend.size());
     int cnt = 0;
-    for ([[maybe_unused]] auto* dummy : reqs) {
+    for ([[maybe_unused]] auto dummy : reqs) {
       int ind{0};
       auto ret = MPI_Waitany(reqs.size(), reqs.data(), &ind, MPI_STATUS_IGNORE);
       ASSERT0(ret == MPI_SUCCESS);

From ec69e8838be2dde140a915e50506f8e1ce3cb534 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Wed, 4 Mar 2026 10:55:59 +0000
Subject: [PATCH 0618/1827] [bot] Apply format changes

---
 include/bout/field2d.hxx | 12 +++++-------
 include/bout/field3d.hxx |  2 +-
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 899c741991..757880ed70 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -135,14 +135,10 @@ public:
   }
 
   Field2D& yup([[maybe_unused]] size_t index = 0) { return *this; }
-  const Field2D& yup([[maybe_unused]] size_t index = 0) const {
-    return *this;
-  }
+  const Field2D& yup([[maybe_unused]] size_t index = 0) const { return *this; }
 
   Field2D& ydown([[maybe_unused]] size_t index = 0) { return *this; }
-  const Field2D& ydown([[maybe_unused]] size_t index = 0) const {
-    return *this;
-  }
+  const Field2D& ydown([[maybe_unused]] size_t index = 0) const { return *this; }
 
   Field2D& ynext([[maybe_unused]] int dir) { return *this; }
   const Field2D& ynext([[maybe_unused]] int dir) const { return *this; }
@@ -228,7 +224,9 @@ public:
    * DIrect access to underlying array. This version is for compatibility
    * with Field3D objects
    */
-  BoutReal& operator()(int jx, int jy, [[maybe_unused]] int jz) { return operator()(jx, jy); }
+  BoutReal& operator()(int jx, int jy, [[maybe_unused]] int jz) {
+    return operator()(jx, jy);
+  }
   const BoutReal& operator()(int jx, int jy, [[maybe_unused]] int jz) const {
     return operator()(jx, jy);
   }
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 42fee60a7c..df2a807706 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -606,7 +606,7 @@ void checkData(const Field3D& f, const std::string& region = "RGN_NOBNDRY");
 /// Ignored with disabled CHECK; Throw an exception if \p f is not
 /// allocated or if any elements are non-finite (for CHECK > 2)
 inline void checkData([[maybe_unused]] const Field3D& f,
-                      [[maybe_unused]] const std::string& region = "RGN_NOBNDRY"){};
+                      [[maybe_unused]] const std::string& region = "RGN_NOBNDRY") {};
 #endif
 
 /// Fourier filtering, removes all except one mode

From 013a8478ab374abb3022e7f86efa138143d21bbb Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Wed, 4 Mar 2026 10:56:00 +0000
Subject: [PATCH 0619/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index abd11c7762..8d488ade81 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -11,3 +11,4 @@ a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
 2c2402ed59c91164eaff46dee0f79386b7347e9e
 05b7c571544c3bcb153fce67d12b9ac48947fc2d
 c8f38049359170a34c915e209276238ea66b9a1e
+ec69e8838be2dde140a915e50506f8e1ce3cb534

From d1cfb8abd6aa5c76e6c1a4d7ab20929c65f8afc2 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Wed, 4 Mar 2026 11:19:18 +0000
Subject: [PATCH 0620/1827] [bot] Apply format changes

---
 src/mesh/parallel/fci_comm.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index cf0ddb01a2..8c34885981 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -58,7 +58,7 @@ struct globalToLocal1D {
   bool periodic;
   globalToLocal1D(int mg, int npe, int localwith, bool periodic)
       : mg(mg), npe(npe), localwith(localwith), local(localwith - (2 * mg)),
-        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic) {};
+        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic){};
   ProcLocal convert(int id) const {
     if (periodic) {
       while (id < mg) {
@@ -106,7 +106,7 @@ public:
 
   GlobalField3DAccessInstance(const GlobalField3DAccess* gfa,
                               std::vector<BoutReal>&& data)
-      : gfa(gfa), data(std::move(data)) {};
+      : gfa(gfa), data(std::move(data)){};
 
 private:
   const GlobalField3DAccess* gfa;

From 5c0d41d8b126a59ae261b2448f6895a2954a50b4 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Wed, 4 Mar 2026 11:19:19 +0000
Subject: [PATCH 0621/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 9ec546dec7..7fbaa021ce 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -12,3 +12,4 @@ a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
 05b7c571544c3bcb153fce67d12b9ac48947fc2d
 c8f38049359170a34c915e209276238ea66b9a1e
 65880e4af16cb95438437bf057c4b9fdb427b142
+d1cfb8abd6aa5c76e6c1a4d7ab20929c65f8afc2

From 640d27d5b299f1e95ee8ad451bde3162e015d317 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 5 Mar 2026 14:12:10 +0100
Subject: [PATCH 0622/1827] Add missing headers

---
 include/bout/field2d.hxx | 1 +
 include/bout/field3d.hxx | 1 +
 2 files changed, 2 insertions(+)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 757880ed70..906af38a1d 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -24,6 +24,7 @@
  * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
  *
  */
+#include "bout/utils.hxx"
 class Field2D;
 
 #pragma once
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 021c45c426..b0318aa9d2 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -20,6 +20,7 @@
  *
  **************************************************************************/
 
+#include "bout/utils.hxx"
 #include <cstddef>
 class Field3D;
 

From 9bb5bca06baa60e4c8be32e08970f04b2f7f7bf1 Mon Sep 17 00:00:00 2001
From: David Bold <dschwoerer@users.noreply.github.com>
Date: Fri, 6 Mar 2026 13:31:56 +0100
Subject: [PATCH 0623/1827] Make clear it is a setter

---
 include/bout/field3d.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index b0318aa9d2..c6e1d1191d 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -513,7 +513,7 @@ public:
 
   std::weak_ptr<Options> getTracking() { return tracking; };
 
-  bool allowCalcParallelSlices() const { return _allowCalcParallelSlices; };
+  bool areCalcParallelSlicesAllowed() const { return _allowCalcParallelSlices; };
   void disallowCalcParallelSlices() { _allowCalcParallelSlices = false; };
 
 private:

From c95668c1a5e07a29401c52f506d6076f8e01de5d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 6 Mar 2026 19:33:25 +0000
Subject: [PATCH 0624/1827] Bump externalpackages/boutdata from `0e06267` to
 `11f5d0a`

Bumps [externalpackages/boutdata](https://github.com/boutproject/boutdata) from `0e06267` to `11f5d0a`.
- [Release notes](https://github.com/boutproject/boutdata/releases)
- [Commits](https://github.com/boutproject/boutdata/compare/0e0626716f7fec01d318c427a96e596055540efe...11f5d0acb3d92a30eb0f97866c206a238c487076)

---
updated-dependencies:
- dependency-name: externalpackages/boutdata
  dependency-version: 11f5d0acb3d92a30eb0f97866c206a238c487076
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/boutdata | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/boutdata b/externalpackages/boutdata
index 0e0626716f..11f5d0acb3 160000
--- a/externalpackages/boutdata
+++ b/externalpackages/boutdata
@@ -1 +1 @@
-Subproject commit 0e0626716f7fec01d318c427a96e596055540efe
+Subproject commit 11f5d0acb3d92a30eb0f97866c206a238c487076

From 0c3cd4b00966ca98671eb5c7c617ccc3342cc993 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Sep 2025 12:09:51 +0200
Subject: [PATCH 0625/1827] Allow more parallel boundary regions

Also allow to set boundaries for bndry_par_xin/xout and
bndry_par_yup/ydown
---
 src/mesh/boundary_factory.cxx | 98 ++++++++++++++++++++---------------
 1 file changed, 57 insertions(+), 41 deletions(-)

diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index d112a216ad..5934daff31 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -228,46 +228,82 @@ BoundaryOpBase* BoundaryFactory::createFromOptions(const string& varname,
 
   string prefix("bndry_");
 
-  string side;
+  std::array<string, 5> sides;
+  sides[0] = region->label;
   switch (region->location) {
   case BNDRY_XIN: {
-    side = "xin";
+    sides[1] = "xin";
     break;
   }
   case BNDRY_XOUT: {
-    side = "xout";
+    sides[1] = "xout";
     break;
   }
   case BNDRY_YDOWN: {
-    side = "ydown";
+    sides[1] = "ydown";
     break;
   }
   case BNDRY_YUP: {
-    side = "yup";
+    sides[1] = "yup";
     break;
   }
   case BNDRY_PAR_FWD_XIN: {
-    side = "par_yup_xin";
+    sides[1] = "par_yup_xin";
     break;
   }
   case BNDRY_PAR_FWD_XOUT: {
-    side = "par_yup_xout";
+    sides[1] = "par_yup_xout";
     break;
   }
   case BNDRY_PAR_BKWD_XIN: {
-    side = "par_ydown_xin";
+    sides[1] = "par_ydown_xin";
     break;
   }
   case BNDRY_PAR_BKWD_XOUT: {
-    side = "par_ydown_xout";
+    sides[1] = "par_ydown_xout";
     break;
   }
   default: {
-    side = "all";
+    sides[1] = "all";
     break;
   }
   }
 
+  switch (region->location) {
+  case BNDRY_PAR_FWD_XIN:
+  case BNDRY_PAR_BKWD_XIN: {
+    sides[2] = "par_xin";
+    break;
+  }
+  case BNDRY_PAR_BKWD_XOUT:
+  case BNDRY_PAR_FWD_XOUT: {
+    sides[2] = "par_xout";
+    break;
+  }
+  default: {
+    sides[2] = "all";
+    break;
+  }
+  }
+  switch (region->location) {
+  case BNDRY_PAR_FWD_XIN:
+  case BNDRY_PAR_FWD_XOUT: {
+    sides[3] = "par_yup";
+    break;
+  }
+  case BNDRY_PAR_BKWD_XIN:
+  case BNDRY_PAR_BKWD_XOUT: {
+    sides[3] = "par_ydown";
+    break;
+  }
+  default: {
+    sides[3] = "all";
+    break;
+  }
+  }
+
+  sides[4] = region->isParallel ? "par_all" : "all";
+
   // Get options
   Options* options = Options::getRoot();
 
@@ -275,27 +311,10 @@ BoundaryOpBase* BoundaryFactory::createFromOptions(const string& varname,
   Options* varOpts = options->getSection(varname);
   string set;
 
-  /// First try looking for (var, region)
-  if (varOpts->isSet(prefix + region->label)) {
-    varOpts->get(prefix + region->label, set, "");
-    return create(set, region);
-  }
-
-  /// Then (var, side)
-  if (varOpts->isSet(prefix + side)) {
-    varOpts->get(prefix + side, set, "");
-    return create(set, region);
-  }
-
-  /// Then (var, all)
-  if (region->isParallel) {
-    if (varOpts->isSet(prefix + "par_all")) {
-      varOpts->get(prefix + "par_all", set, "");
-      return create(set, region);
-    }
-  } else {
-    if (varOpts->isSet(prefix + "all")) {
-      varOpts->get(prefix + "all", set, "");
+  /// First try looking for (var, ...)
+  for (const auto& side : sides) {
+    if (varOpts->isSet(prefix + side)) {
+      varOpts->get(prefix + side, set, "");
       return create(set, region);
     }
   }
@@ -303,16 +322,13 @@ BoundaryOpBase* BoundaryFactory::createFromOptions(const string& varname,
   // Get the "all" options
   varOpts = options->getSection("all");
 
-  /// Then (all, region)
-  if (varOpts->isSet(prefix + region->label)) {
-    varOpts->get(prefix + region->label, set, "");
-    return create(set, region);
-  }
-
-  /// Then (all, side)
-  if (varOpts->isSet(prefix + side)) {
-    varOpts->get(prefix + side, set, "");
-    return create(set, region);
+  /// First try looking for (all, ...)
+  for (const auto& side : sides) {
+    if (varOpts->isSet(prefix + side)) {
+      varOpts->get(prefix + side, set,
+                   region->isParallel ? "parallel_dirichlet_o2" : "dirichlet");
+      return create(set, region);
+    }
   }
 
   /// Then (all, all)

From 4cd217b833710c2f401c2185dcc8ce927c48e664 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 10:41:41 +0100
Subject: [PATCH 0626/1827] Add missing header

---
 src/mesh/boundary_factory.cxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index 5934daff31..fd5bbdc70d 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -6,6 +6,7 @@
 #include <bout/options.hxx>
 #include <bout/utils.hxx>
 
+#include <array>
 #include <list>
 #include <map>
 #include <string>

From ae1f285b10d073d9109e8b8b6ede9f6aba0f2418 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 Mar 2024 13:29:58 +0100
Subject: [PATCH 0627/1827] Move stencils to separte header

Makes it easier to reuse for other code
---
 include/bout/parallel_boundary_region.hxx | 39 +----------------------
 include/bout/sys/parallel_stencils.hxx    | 39 +++++++++++++++++++++++
 2 files changed, 40 insertions(+), 38 deletions(-)
 create mode 100644 include/bout/sys/parallel_stencils.hxx

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 4d5278d00f..44e5cc562e 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -5,6 +5,7 @@
 #include "bout/bout_types.hxx"
 #include <vector>
 
+#include "bout/sys/parallel_stencils.hxx"
 #include <bout/field3d.hxx>
 #include <bout/mesh.hxx>
 
@@ -14,44 +15,6 @@
  *
  */
 
-namespace parallel_stencil {
-// generated by src/mesh/parallel_boundary_stencil.cxx.py
-inline BoutReal pow(BoutReal val, int exp) {
-  // constexpr int expval = exp;
-  // static_assert(expval == 2 or expval == 3, "This pow is only for exponent 2 or 3");
-  if (exp == 2) {
-    return val * val;
-  }
-  ASSERT3(exp == 3);
-  return val * val * val;
-}
-inline BoutReal dirichlet_o1(BoutReal UNUSED(spacing0), BoutReal value0) {
-  return value0;
-}
-inline BoutReal dirichlet_o2(BoutReal spacing0, BoutReal value0, BoutReal spacing1,
-                             BoutReal value1) {
-  return (spacing0 * value1 - spacing1 * value0) / (spacing0 - spacing1);
-}
-inline BoutReal neumann_o2(BoutReal UNUSED(spacing0), BoutReal value0, BoutReal spacing1,
-                           BoutReal value1) {
-  return -spacing1 * value0 + value1;
-}
-inline BoutReal dirichlet_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1,
-                             BoutReal value1, BoutReal spacing2, BoutReal value2) {
-  return (pow(spacing0, 2) * spacing1 * value2 - pow(spacing0, 2) * spacing2 * value1
-          - spacing0 * pow(spacing1, 2) * value2 + spacing0 * pow(spacing2, 2) * value1
-          + pow(spacing1, 2) * spacing2 * value0 - spacing1 * pow(spacing2, 2) * value0)
-         / ((spacing0 - spacing1) * (spacing0 - spacing2) * (spacing1 - spacing2));
-}
-inline BoutReal neumann_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1,
-                           BoutReal value1, BoutReal spacing2, BoutReal value2) {
-  return (2 * spacing0 * spacing1 * value2 - 2 * spacing0 * spacing2 * value1
-          + pow(spacing1, 2) * spacing2 * value0 - pow(spacing1, 2) * value2
-          - spacing1 * pow(spacing2, 2) * value0 + pow(spacing2, 2) * value1)
-         / ((spacing1 - spacing2) * (2 * spacing0 - spacing1 - spacing2));
-}
-} // namespace parallel_stencil
-
 class BoundaryRegionPar : public BoundaryRegionBase {
 
   struct RealPoint {
diff --git a/include/bout/sys/parallel_stencils.hxx b/include/bout/sys/parallel_stencils.hxx
new file mode 100644
index 0000000000..34a51c5285
--- /dev/null
+++ b/include/bout/sys/parallel_stencils.hxx
@@ -0,0 +1,39 @@
+#pragma once
+
+namespace parallel_stencil {
+// generated by src/mesh/parallel_boundary_stencil.cxx.py
+inline BoutReal pow(BoutReal val, int exp) {
+  // constexpr int expval = exp;
+  // static_assert(expval == 2 or expval == 3, "This pow is only for exponent 2 or 3");
+  if (exp == 2) {
+    return val * val;
+  }
+  ASSERT3(exp == 3);
+  return val * val * val;
+}
+inline BoutReal dirichlet_o1(BoutReal UNUSED(spacing0), BoutReal value0) {
+  return value0;
+}
+inline BoutReal dirichlet_o2(BoutReal spacing0, BoutReal value0, BoutReal spacing1,
+                             BoutReal value1) {
+  return (spacing0 * value1 - spacing1 * value0) / (spacing0 - spacing1);
+}
+inline BoutReal neumann_o2(BoutReal UNUSED(spacing0), BoutReal value0, BoutReal spacing1,
+                           BoutReal value1) {
+  return -spacing1 * value0 + value1;
+}
+inline BoutReal dirichlet_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1,
+                             BoutReal value1, BoutReal spacing2, BoutReal value2) {
+  return (pow(spacing0, 2) * spacing1 * value2 - pow(spacing0, 2) * spacing2 * value1
+          - spacing0 * pow(spacing1, 2) * value2 + spacing0 * pow(spacing2, 2) * value1
+          + pow(spacing1, 2) * spacing2 * value0 - spacing1 * pow(spacing2, 2) * value0)
+         / ((spacing0 - spacing1) * (spacing0 - spacing2) * (spacing1 - spacing2));
+}
+inline BoutReal neumann_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1,
+                           BoutReal value1, BoutReal spacing2, BoutReal value2) {
+  return (2 * spacing0 * spacing1 * value2 - 2 * spacing0 * spacing2 * value1
+          + pow(spacing1, 2) * spacing2 * value0 - pow(spacing1, 2) * value2
+          - spacing1 * pow(spacing2, 2) * value0 + pow(spacing2, 2) * value1)
+         / ((spacing1 - spacing2) * (2 * spacing0 - spacing1 - spacing2));
+}
+} // namespace parallel_stencil

From b9b42fff9cc68a1524fe801b70109df6a009be80 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 Mar 2024 13:40:07 +0100
Subject: [PATCH 0628/1827] Add basic boundary region iterator

Mimicks the parallel case, to write FCI independent code
---
 include/bout/boundary_region.hxx | 93 ++++++++++++++++++++++++++++++++
 src/mesh/boundary_region.cxx     |  3 ++
 2 files changed, 96 insertions(+)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 58de12045e..6e7a939d3c 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -4,6 +4,9 @@ class BoundaryRegion;
 #ifndef BOUT_BNDRY_REGION_H
 #define BOUT_BNDRY_REGION_H
 
+#include "bout/mesh.hxx"
+#include "bout/region.hxx"
+#include "bout/sys/parallel_stencils.hxx"
 #include <string>
 #include <utility>
 
@@ -62,6 +65,7 @@ public:
   isDone() = 0; ///< Returns true if outside domain. Can use this with nested nextX, nextY
 };
 
+class BoundaryRegionIter;
 /// Describes a region of the boundary, and a means of iterating over it
 class BoundaryRegion : public BoundaryRegionBase {
 public:
@@ -80,6 +84,95 @@ public:
   virtual void next1d() = 0; ///< Loop over the innermost elements
   virtual void nextX() = 0;  ///< Just loop over X
   virtual void nextY() = 0;  ///< Just loop over Y
+
+  BoundaryRegionIter begin();
+  BoundaryRegionIter end();
+};
+
+class BoundaryRegionIter {
+public:
+  BoundaryRegionIter(BoundaryRegion* rgn, bool is_end)
+      : rgn(rgn), is_end(is_end), dir(rgn->bx + rgn->by) {
+    //static_assert(std::is_base_of<BoundaryRegion, T>, "BoundaryRegionIter only works on BoundaryRegion");
+
+    // Ensure only one is non-zero
+    ASSERT3(rgn->bx * rgn->by == 0);
+    if (!is_end) {
+      rgn->first();
+    }
+  }
+  bool operator!=(const BoundaryRegionIter& rhs) {
+    if (is_end) {
+      if (rhs.is_end || rhs.rgn->isDone()) {
+        return false;
+      } else {
+        return true;
+      }
+    }
+    if (rhs.is_end) {
+      return !rgn->isDone();
+    }
+    return ind() != rhs.ind();
+  }
+
+  Ind3D ind() const { return xyz2ind(rgn->x - rgn->bx, rgn->y - rgn->by, z); }
+  BoundaryRegionIter& operator++() {
+    ASSERT3(z < nz());
+    z++;
+    if (z == nz()) {
+      z = 0;
+      rgn->next();
+    }
+    return *this;
+  }
+  BoundaryRegionIter& operator*() { return *this; }
+
+  void dirichlet_o2(Field3D& f, BoutReal value) const {
+    ynext(f) = parallel_stencil::dirichlet_o2(1, f[ind()], 0.5, value);
+  }
+
+  BoutReal extrapolate_grad_o2(const Field3D& f) const { return f[ind()] - yprev(f); }
+
+  BoutReal extrapolate_sheath_o2(const Field3D& f) const {
+    return (f[ind()] * 3 - yprev(f)) * 0.5;
+  }
+
+  BoutReal extrapolate_next_o2(const Field3D& f) const { return 2 * f[ind()] - yprev(f); }
+
+  BoutReal
+  extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    return 2 * f(0, ind()) - f(0, ind().yp(-rgn->by).xp(-rgn->bx));
+  }
+
+  BoutReal interpolate_sheath(const Field3D& f) const {
+    return (f[ind()] + ynext(f)) * 0.5;
+  }
+
+  BoutReal& ynext(Field3D& f) const { return f[ind().yp(rgn->by).xp(rgn->bx)]; }
+  const BoutReal& ynext(const Field3D& f) const {
+    return f[ind().yp(rgn->by).xp(rgn->bx)];
+  }
+  BoutReal& yprev(Field3D& f) const { return f[ind().yp(-rgn->by).xp(-rgn->bx)]; }
+  const BoutReal& yprev(const Field3D& f) const {
+    return f[ind().yp(-rgn->by).xp(-rgn->bx)];
+  }
+
+private:
+  BoundaryRegion* rgn;
+  const bool is_end;
+  int z{0};
+
+public:
+  const int dir;
+
+private:
+  int nx() const { return rgn->localmesh->LocalNx; }
+  int ny() const { return rgn->localmesh->LocalNy; }
+  int nz() const { return rgn->localmesh->LocalNz; }
+
+  Ind3D xyz2ind(int x, int y, int z) const {
+    return Ind3D{(x * ny() + y) * nz() + z, ny(), nz()};
+  }
 };
 
 class BoundaryRegionXIn : public BoundaryRegion {
diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx
index 700ef8a91f..ef4aa13a66 100644
--- a/src/mesh/boundary_region.cxx
+++ b/src/mesh/boundary_region.cxx
@@ -202,3 +202,6 @@ void BoundaryRegionYUp::nextY() {
 bool BoundaryRegionYUp::isDone() {
   return (x > xe) || (y >= localmesh->LocalNy); // Return true if gone out of the boundary
 }
+
+BoundaryRegionIter BoundaryRegion::begin() { return BoundaryRegionIter(this, false); }
+BoundaryRegionIter BoundaryRegion::end() { return BoundaryRegionIter(this, true); }

From 9bdfef5f553b1a783b9f4295be05ccbe8cba247a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 9 Apr 2024 14:40:17 +0200
Subject: [PATCH 0629/1827] Provide a new boundary iterator based on
 RangeIterator

The boundary region does not match what is done for the parallel case,
thus porting it to a iterator does not work.
---
 include/bout/boundary_iterator.hxx | 117 +++++++++++++++++++++++++++++
 include/bout/boundary_region.hxx   |  90 ----------------------
 2 files changed, 117 insertions(+), 90 deletions(-)
 create mode 100644 include/bout/boundary_iterator.hxx

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
new file mode 100644
index 0000000000..93f02c004d
--- /dev/null
+++ b/include/bout/boundary_iterator.hxx
@@ -0,0 +1,117 @@
+#pragma once
+
+#include "bout/mesh.hxx"
+#include "bout/sys/parallel_stencils.hxx"
+#include "bout/sys/range.hxx"
+
+class BoundaryRegionIter {
+public:
+  BoundaryRegionIter(int x, int y, int bx, int by, Mesh* mesh)
+      : dir(bx + by), x(x), y(y), bx(bx), by(by), localmesh(mesh) {
+    ASSERT3(bx * by == 0);
+  }
+  bool operator!=(const BoundaryRegionIter& rhs) { return ind() != rhs.ind(); }
+
+  Ind3D ind() const { return xyz2ind(x, y, z); }
+  BoundaryRegionIter& operator++() {
+    ASSERT3(z < nz());
+    z++;
+    if (z == nz()) {
+      z = 0;
+      _next();
+    }
+    return *this;
+  }
+  virtual void _next() = 0;
+  BoundaryRegionIter& operator*() { return *this; }
+
+  void dirichlet_o2(Field3D& f, BoutReal value) const {
+    ynext(f) = parallel_stencil::dirichlet_o2(1, f[ind()], 0.5, value);
+  }
+
+  BoutReal extrapolate_grad_o2(const Field3D& f) const { return f[ind()] - yprev(f); }
+
+  BoutReal extrapolate_sheath_o2(const Field3D& f) const {
+    return (f[ind()] * 3 - yprev(f)) * 0.5;
+  }
+
+  BoutReal extrapolate_next_o2(const Field3D& f) const { return 2 * f[ind()] - yprev(f); }
+
+  BoutReal
+  extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    return 2 * f(0, ind()) - f(0, ind().yp(-by).xp(-bx));
+  }
+
+  BoutReal interpolate_sheath(const Field3D& f) const {
+    return (f[ind()] + ynext(f)) * 0.5;
+  }
+
+  BoutReal& ynext(Field3D& f) const { return f[ind().yp(by).xp(bx)]; }
+  const BoutReal& ynext(const Field3D& f) const { return f[ind().yp(by).xp(bx)]; }
+  BoutReal& yprev(Field3D& f) const { return f[ind().yp(-by).xp(-bx)]; }
+  const BoutReal& yprev(const Field3D& f) const { return f[ind().yp(-by).xp(-bx)]; }
+
+  const int dir;
+
+protected:
+  int z{0};
+  int x;
+  int y;
+  const int bx;
+  const int by;
+
+private:
+  Mesh* localmesh;
+  int nx() const { return localmesh->LocalNx; }
+  int ny() const { return localmesh->LocalNy; }
+  int nz() const { return localmesh->LocalNz; }
+
+  Ind3D xyz2ind(int x, int y, int z) const {
+    return Ind3D{(x * ny() + y) * nz() + z, ny(), nz()};
+  }
+};
+
+class BoundaryRegionIterY : public BoundaryRegionIter {
+public:
+  BoundaryRegionIterY(RangeIterator r, int y, int dir, bool is_end, Mesh* mesh)
+      : BoundaryRegionIter(r.ind, y, 0, dir, mesh), r(r), is_end(is_end) {}
+
+  bool operator!=(const BoundaryRegionIterY& rhs) {
+    ASSERT2(y == rhs.y);
+    if (is_end) {
+      if (rhs.is_end) {
+        return false;
+      }
+      return !rhs.r.isDone();
+    }
+    if (rhs.is_end) {
+      return !r.isDone();
+    }
+    return x != rhs.x;
+  }
+
+  virtual void _next() override {
+    ++r;
+    x = r.ind;
+  }
+
+private:
+  RangeIterator r;
+  bool is_end;
+};
+
+class NewBoundaryRegionY {
+public:
+  NewBoundaryRegionY(Mesh* mesh, bool lower, RangeIterator r)
+      : mesh(mesh), lower(lower), r(std::move(r)) {}
+  BoundaryRegionIterY begin(bool begin = true) {
+    return BoundaryRegionIterY(r, lower ? mesh->ystart : mesh->yend, lower ? -1 : +1,
+                               !begin, mesh);
+  }
+  BoundaryRegionIterY end() { return begin(false); }
+
+private:
+  Mesh* mesh;
+  bool lower;
+  RangeIterator r;
+};
diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 6e7a939d3c..22956d1d4a 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -65,7 +65,6 @@ public:
   isDone() = 0; ///< Returns true if outside domain. Can use this with nested nextX, nextY
 };
 
-class BoundaryRegionIter;
 /// Describes a region of the boundary, and a means of iterating over it
 class BoundaryRegion : public BoundaryRegionBase {
 public:
@@ -84,95 +83,6 @@ public:
   virtual void next1d() = 0; ///< Loop over the innermost elements
   virtual void nextX() = 0;  ///< Just loop over X
   virtual void nextY() = 0;  ///< Just loop over Y
-
-  BoundaryRegionIter begin();
-  BoundaryRegionIter end();
-};
-
-class BoundaryRegionIter {
-public:
-  BoundaryRegionIter(BoundaryRegion* rgn, bool is_end)
-      : rgn(rgn), is_end(is_end), dir(rgn->bx + rgn->by) {
-    //static_assert(std::is_base_of<BoundaryRegion, T>, "BoundaryRegionIter only works on BoundaryRegion");
-
-    // Ensure only one is non-zero
-    ASSERT3(rgn->bx * rgn->by == 0);
-    if (!is_end) {
-      rgn->first();
-    }
-  }
-  bool operator!=(const BoundaryRegionIter& rhs) {
-    if (is_end) {
-      if (rhs.is_end || rhs.rgn->isDone()) {
-        return false;
-      } else {
-        return true;
-      }
-    }
-    if (rhs.is_end) {
-      return !rgn->isDone();
-    }
-    return ind() != rhs.ind();
-  }
-
-  Ind3D ind() const { return xyz2ind(rgn->x - rgn->bx, rgn->y - rgn->by, z); }
-  BoundaryRegionIter& operator++() {
-    ASSERT3(z < nz());
-    z++;
-    if (z == nz()) {
-      z = 0;
-      rgn->next();
-    }
-    return *this;
-  }
-  BoundaryRegionIter& operator*() { return *this; }
-
-  void dirichlet_o2(Field3D& f, BoutReal value) const {
-    ynext(f) = parallel_stencil::dirichlet_o2(1, f[ind()], 0.5, value);
-  }
-
-  BoutReal extrapolate_grad_o2(const Field3D& f) const { return f[ind()] - yprev(f); }
-
-  BoutReal extrapolate_sheath_o2(const Field3D& f) const {
-    return (f[ind()] * 3 - yprev(f)) * 0.5;
-  }
-
-  BoutReal extrapolate_next_o2(const Field3D& f) const { return 2 * f[ind()] - yprev(f); }
-
-  BoutReal
-  extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return 2 * f(0, ind()) - f(0, ind().yp(-rgn->by).xp(-rgn->bx));
-  }
-
-  BoutReal interpolate_sheath(const Field3D& f) const {
-    return (f[ind()] + ynext(f)) * 0.5;
-  }
-
-  BoutReal& ynext(Field3D& f) const { return f[ind().yp(rgn->by).xp(rgn->bx)]; }
-  const BoutReal& ynext(const Field3D& f) const {
-    return f[ind().yp(rgn->by).xp(rgn->bx)];
-  }
-  BoutReal& yprev(Field3D& f) const { return f[ind().yp(-rgn->by).xp(-rgn->bx)]; }
-  const BoutReal& yprev(const Field3D& f) const {
-    return f[ind().yp(-rgn->by).xp(-rgn->bx)];
-  }
-
-private:
-  BoundaryRegion* rgn;
-  const bool is_end;
-  int z{0};
-
-public:
-  const int dir;
-
-private:
-  int nx() const { return rgn->localmesh->LocalNx; }
-  int ny() const { return rgn->localmesh->LocalNy; }
-  int nz() const { return rgn->localmesh->LocalNz; }
-
-  Ind3D xyz2ind(int x, int y, int z) const {
-    return Ind3D{(x * ny() + y) * nz() + z, ny(), nz()};
-  }
 };
 
 class BoundaryRegionXIn : public BoundaryRegion {

From c51a85f94a6590189749f3421b08b337a560de52 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Jul 2024 14:41:42 +0200
Subject: [PATCH 0630/1827] Only check hasBndry*Y if they would be included

hasBndryUpperY / hasBndryLowerY does not work for FCI and thus the
request does not make sense / can be configured to throw.
Thus it should not be checked if it is not needed.
---
 src/invert/laplace/invert_laplace.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx
index e9182042de..9af6fd20f9 100644
--- a/src/invert/laplace/invert_laplace.cxx
+++ b/src/invert/laplace/invert_laplace.cxx
@@ -218,10 +218,10 @@ Field3D Laplacian::solve(const Field3D& b, const Field3D& x0) {
 
   // Setting the start and end range of the y-slices
   int ys = localmesh->ystart, ye = localmesh->yend;
-  if (localmesh->hasBndryLowerY() && include_yguards) {
+  if (include_yguards && localmesh->hasBndryLowerY()) {
     ys = 0; // Mesh contains a lower boundary
   }
-  if (localmesh->hasBndryUpperY() && include_yguards) {
+  if (include_yguards && localmesh->hasBndryUpperY()) {
     ye = localmesh->LocalNy - 1; // Contains upper boundary
   }
 

From 06d581bcac128616d696dccb4fad9dc9d208ede3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 5 Jul 2024 11:42:18 +0200
Subject: [PATCH 0631/1827] ensure we dont mix non-fci BCs with fci

---
 src/mesh/impls/bout/boutmesh.cxx | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index d0bdcf33d8..99ec63ff25 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -2905,6 +2905,9 @@ void BoutMesh::addBoundaryRegions() {
 }
 
 RangeIterator BoutMesh::iterateBndryLowerInnerY() const {
+  if (this->isFci()) {
+    throw BoutException("FCI should never use this iterator");
+  }
 
   int xs = 0;
   int xe = LocalNx - 1;
@@ -2940,6 +2943,9 @@ RangeIterator BoutMesh::iterateBndryLowerInnerY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryLowerOuterY() const {
+  if (this->isFci()) {
+    throw BoutException("FCI should never use this iterator");
+  }
 
   int xs = 0;
   int xe = LocalNx - 1;
@@ -2974,6 +2980,10 @@ RangeIterator BoutMesh::iterateBndryLowerOuterY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryLowerY() const {
+  if (this->isFci()) {
+    throw BoutException("FCI should never use this iterator");
+  }
+
   int xs = 0;
   int xe = LocalNx - 1;
   if ((DDATA_INDEST >= 0) && (DDATA_XSPLIT > xstart)) {
@@ -3003,6 +3013,10 @@ RangeIterator BoutMesh::iterateBndryLowerY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryUpperInnerY() const {
+  if (this->isFci()) {
+    throw BoutException("FCI should never use this iterator");
+  }
+
   int xs = 0;
   int xe = LocalNx - 1;
 
@@ -3037,6 +3051,10 @@ RangeIterator BoutMesh::iterateBndryUpperInnerY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryUpperOuterY() const {
+  if (this->isFci()) {
+    throw BoutException("FCI should never use this iterator");
+  }
+
   int xs = 0;
   int xe = LocalNx - 1;
 
@@ -3071,6 +3089,10 @@ RangeIterator BoutMesh::iterateBndryUpperOuterY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryUpperY() const {
+  if (this->isFci()) {
+    throw BoutException("FCI should never use this iterator");
+  }
+
   int xs = 0;
   int xe = LocalNx - 1;
   if ((UDATA_INDEST >= 0) && (UDATA_XSPLIT > xstart)) {

From 7f1d26fbaea4edd33af2a8d2e158a8fb2d6eef4d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 13:45:23 +0200
Subject: [PATCH 0632/1827] rename to include order

---
 include/bout/parallel_boundary_region.hxx | 60 +++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 44e5cc562e..ad66c992a6 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -98,6 +98,66 @@ public:
     return f[ind()] * (1 + length()) - f.ynext(-dir)[ind().yp(-dir)] * length();
   }
 
+  inline BoutReal
+  extrapolate_sheath_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    return f(0, ind());
+  }
+  inline BoutReal
+  extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return extrapolate_sheath_o1(f);
+    }
+    return f(0, ind()) * (1 + length()) - f(-dir, ind().yp(-dir)) * length();
+  }
+
+  inline BoutReal interpolate_sheath_o1(const Field3D& f) const {
+    return f[ind()] * (1 - length()) + ynext(f) * length();
+  }
+
+  inline BoutReal extrapolate_next_o1(const Field3D& f) const { return f[ind()]; }
+  inline BoutReal extrapolate_next_o2(const Field3D& f) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return extrapolate_next_o1(f);
+    }
+    return f[ind()] * 2 - f.ynext(-dir)[ind().yp(-dir)];
+  }
+
+  inline BoutReal
+  extrapolate_next_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    return f(0, ind());
+  }
+  inline BoutReal
+  extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return extrapolate_sheath_o1(f);
+    }
+    return f(0, ind()) * 2 - f(-dir, ind().yp(-dir));
+  }
+
+  // extrapolate the gradient into the boundary
+  inline BoutReal extrapolate_grad_o1(const Field3D& f) const { return 0; }
+  inline BoutReal extrapolate_grad_o2(const Field3D& f) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return extrapolate_grad_o1(f);
+    }
+    return f[ind()] - f.ynext(-dir)[ind().yp(-dir)];
+  }
+
+  BoundaryRegionParIterBase& operator*() { return *this; }
+
+  BoundaryRegionParIterBase& operator++() {
+    ++bndry_position;
+    return *this;
+  }
+
+  bool operator!=(const BoundaryRegionParIterBase& rhs) {
+    return bndry_position != rhs.bndry_position;
+  }
+
   // dirichlet boundary code
   void dirichlet_o1(Field3D& f, BoutReal value) const {
     f.ynext(dir)[ind().yp(dir)] = value;

From 84f8c8301b8fac38934740aefa8f0dc0a185baec Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 13:50:34 +0200
Subject: [PATCH 0633/1827] Fix: remove broken code

BoundaryRegionIter has been delted
---
 src/mesh/boundary_region.cxx | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx
index ef4aa13a66..700ef8a91f 100644
--- a/src/mesh/boundary_region.cxx
+++ b/src/mesh/boundary_region.cxx
@@ -202,6 +202,3 @@ void BoundaryRegionYUp::nextY() {
 bool BoundaryRegionYUp::isDone() {
   return (x > xe) || (y >= localmesh->LocalNy); // Return true if gone out of the boundary
 }
-
-BoundaryRegionIter BoundaryRegion::begin() { return BoundaryRegionIter(this, false); }
-BoundaryRegionIter BoundaryRegion::end() { return BoundaryRegionIter(this, true); }

From ea05bae1f4d1f3192e8e88ddf409b456744f3a5e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 27 Sep 2024 11:06:33 +0200
Subject: [PATCH 0634/1827] Convert test to new iterator scheeme

---
 tests/integrated/test-fci-boundary/get_par_bndry.cxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 8e3cfac2f7..52d07f067e 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -24,11 +24,11 @@ int main(int argc, char** argv) {
     const auto boundary = static_cast<BoundaryParType>(i);
     const auto boundary_name = toString(boundary);
     mesh->communicate(fields[i]);
-    for (const auto& bndry_par : mesh->getBoundariesPar(boundary)) {
-      output.write("{:s} region\n", boundary_name);
-      for (bndry_par->first(); !bndry_par->isDone(); bndry_par->next()) {
-        fields[i][bndry_par->ind()] += 1;
-        output.write("{:s} increment\n", boundary_name);
+    for (auto& bndry_par : mesh->getBoundariesPar(static_cast<BoundaryParType>(i))) {
+      output.write("{:s} region\n", toString(static_cast<BoundaryParType>(i)));
+      for (const auto& pnt : *bndry_par) {
+        fields[i][pnt.ind()] += 1;
+        output.write("{:s} increment\n", toString(static_cast<BoundaryParType>(i)));
       }
     }
     output.write("{:s} done\n", boundary_name);

From 17f8efa868b0195e0c81d35e99a2a4eab028f969 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 1 Oct 2024 15:27:21 +0200
Subject: [PATCH 0635/1827] Add Field2D version for 2D metrics

---
 include/bout/parallel_boundary_region.hxx | 107 +++++++++++++++++++++-
 1 file changed, 105 insertions(+), 2 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index ad66c992a6..9eedc7847d 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -216,8 +216,111 @@ private:
   // BoutReal get(const Field3D& f, int off)
   const BoutReal& ynext(const Field3D& f) const { return f.ynext(dir)[ind().yp(dir)]; }
   BoutReal& ynext(Field3D& f) const { return f.ynext(dir)[ind().yp(dir)]; }
-  const BoutReal& yprev(const Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; }
-  BoutReal& yprev(Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; }
+
+  const BoutReal& yprev(const Field3D& f) const {
+    ASSERT3(valid() > 0);
+    return f.ynext(-dir)[ind().yp(-dir)];
+  }
+  BoutReal& yprev(Field3D& f) const {
+    ASSERT3(valid() > 0);
+    return f.ynext(-dir)[ind().yp(-dir)];
+  }
+
+#if BOUT_USE_METRIC_3D == 0
+  const BoutReal& ynext(const Field2D& f) const { return f.ynext(dir)[ind().yp(dir)]; }
+  BoutReal& ynext(Field2D& f) const { return f.ynext(dir)[ind().yp(dir)]; }
+
+  const BoutReal& yprev(const Field2D& f) const {
+    ASSERT3(valid() > 0);
+    return f.ynext(-dir)[ind().yp(-dir)];
+  }
+  BoutReal& yprev(Field2D& f) const {
+    ASSERT3(valid() > 0);
+    return f.ynext(-dir)[ind().yp(-dir)];
+  }
+#endif
+
+private:
+  const IndicesVec& bndry_points;
+  IndicesIter bndry_position;
+
+  constexpr static BoutReal small_value = 1e-2;
+
+public:
+  const int dir;
+  Mesh* localmesh;
+};
+} // namespace parallel_boundary_region
+} // namespace bout
+using BoundaryRegionParIter = bout::parallel_boundary_region::BoundaryRegionParIterBase<
+    bout::parallel_boundary_region::IndicesVec,
+    bout::parallel_boundary_region::IndicesIter>;
+using BoundaryRegionParIterConst =
+    bout::parallel_boundary_region::BoundaryRegionParIterBase<
+        const bout::parallel_boundary_region::IndicesVec,
+        bout::parallel_boundary_region::IndicesIterConst>;
+
+class BoundaryRegionPar : public BoundaryRegionBase {
+public:
+  BoundaryRegionPar(const std::string& name, int dir, Mesh* passmesh)
+      : BoundaryRegionBase(name, passmesh), dir(dir) {
+    ASSERT0(std::abs(dir) == 1);
+    BoundaryRegionBase::isParallel = true;
+  }
+  BoundaryRegionPar(const std::string& name, BndryLoc loc, int dir, Mesh* passmesh)
+      : BoundaryRegionBase(name, loc, passmesh), dir(dir) {
+    BoundaryRegionBase::isParallel = true;
+    ASSERT0(std::abs(dir) == 1);
+  }
+
+  /// Add a point to the boundary
+  void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
+                 char valid) {
+    bndry_points.push_back({ind, {x, y, z}, length, valid});
+  }
+  void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
+                 BoutReal length, char valid) {
+    bndry_points.push_back({xyz2ind(ix, iy, iz, localmesh), {x, y, z}, length, valid});
+  }
+
+  // final, so they can be inlined
+  void first() final { bndry_position = std::begin(bndry_points); }
+  void next() final { ++bndry_position; }
+  bool isDone() final { return (bndry_position == std::end(bndry_points)); }
+
+  bool contains(const BoundaryRegionPar& bndry) const {
+    return std::binary_search(std::begin(bndry_points), std::end(bndry_points),
+                              *bndry.bndry_position,
+                              [](const bout::parallel_boundary_region::Indices& i1,
+                                 const bout::parallel_boundary_region::Indices& i2) {
+                                return i1.index < i2.index;
+                              });
+  }
+
+  // setter
+  void setValid(char val) { bndry_position->valid = val; }
+
+  // BoundaryRegionParIterConst begin() const {
+  //   return BoundaryRegionParIterConst(bndry_points, bndry_points.begin(), dir);
+  // }
+  // BoundaryRegionParIterConst end() const {
+  //   return BoundaryRegionParIterConst(bndry_points, bndry_points.begin(), dir);
+  // }
+  BoundaryRegionParIter begin() {
+    return BoundaryRegionParIter(bndry_points, bndry_points.begin(), dir, localmesh);
+  }
+  BoundaryRegionParIter end() {
+    return BoundaryRegionParIter(bndry_points, bndry_points.end(), dir, localmesh);
+  }
+
+  const int dir;
+
+private:
+  /// Vector of points in the boundary
+  bout::parallel_boundary_region::IndicesVec bndry_points;
+  /// Current position in the boundary points
+  bout::parallel_boundary_region::IndicesIter bndry_position;
+
   static Ind3D xyz2ind(int x, int y, int z, Mesh* mesh) {
     const int ny = mesh->LocalNy;
     const int nz = mesh->LocalNz;

From 0db3052e66f96f19047edb72b46af073b79b79c8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 1 Oct 2024 15:52:40 +0200
Subject: [PATCH 0636/1827] Add setYPrevIfValid

---
 include/bout/parallel_boundary_region.hxx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 9eedc7847d..f370295481 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -225,6 +225,11 @@ private:
     ASSERT3(valid() > 0);
     return f.ynext(-dir)[ind().yp(-dir)];
   }
+  void setYPrevIfValid(Field3D& f, BoutReal val) const {
+    if (valid() > 0) {
+      yprev(f) = val;
+    }
+  }
 
 #if BOUT_USE_METRIC_3D == 0
   const BoutReal& ynext(const Field2D& f) const { return f.ynext(dir)[ind().yp(dir)]; }

From d2f2cc80383ce87f3a89031c619c6046e64d5a7d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 13 Jan 2025 09:53:15 +0100
Subject: [PATCH 0637/1827] Add offset to parallel boundary region

This allows to extend the boundary code to place the boundary further
away from the boundary.
---
 include/bout/parallel_boundary_region.hxx | 17 +++++++++++++----
 src/mesh/parallel/fci.cxx                 | 15 +++++++++------
 src/mesh/parallel/shiftedmetricinterp.cxx |  8 ++++----
 3 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index f370295481..ff7ae14685 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -34,6 +34,8 @@ class BoundaryRegionPar : public BoundaryRegionBase {
     // BoutReal angle;
     // How many points we can go in the opposite direction
     signed char valid;
+    signed char offset;
+    unsigned char abs_offset;
   };
 
   using IndicesVec = std::vector<Indices>;
@@ -78,6 +80,8 @@ public:
   BoutReal s_z() const { return bndry_position->intersection.s_z; }
   BoutReal length() const { return bndry_position->length; }
   signed char valid() const { return bndry_position->valid; }
+  signed char offset() const { return bndry_position->offset; }
+  unsigned char abs_offset() const { return bndry_position->abs_offset; }
 
   // setter
   void setValid(signed char val) { bndry_position->valid = val; }
@@ -280,12 +284,17 @@ public:
 
   /// Add a point to the boundary
   void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
-                 char valid) {
-    bndry_points.push_back({ind, {x, y, z}, length, valid});
+                 char valid, signed char offset) {
+    bndry_points.push_back({ind,
+                            {x, y, z},
+                            length,
+                            valid,
+                            offset,
+                            static_cast<unsigned char>(std::abs(offset))});
   }
   void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
-                 BoutReal length, char valid) {
-    bndry_points.push_back({xyz2ind(ix, iy, iz, localmesh), {x, y, z}, length, valid});
+                 BoutReal length, char valid, signed char offset) {
+    add_point(xyz2ind(ix, iy, iz, localmesh), x, y, z, length, valid, offset);
   }
 
   // final, so they can be inlined
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 39654519af..3394a3e2af 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -182,7 +182,9 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
 
   BoutMask to_remove(map_mesh);
   const int xend = map_mesh->xstart
-                   + ((map_mesh->xend - map_mesh->xstart + 1) * map_mesh->getNXPE()) - 1;
+                   + (map_mesh->xend - map_mesh->xstart + 1) * map_mesh->getNXPE() - 1;
+  // Default to the maximum number of points
+  const int defValid{map_mesh->ystart - 1 + std::abs(offset)};
   // Serial loop because call to BoundaryRegionPar::addPoint
   // (probably?) can't be done in parallel
   BOUT_FOR_SERIAL(i, xt_prime.getRegion("RGN_NOBNDRY")) {
@@ -252,11 +254,12 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
     // need at least 2 points in the domain.
     ASSERT2(map_mesh->xend - map_mesh->xstart >= 2);
     auto boundary = (xt_prime[i] < map_mesh->xstart) ? inner_boundary : outer_boundary;
-    boundary->add_point(x, y, z, x + dx, y + (0.5 * offset_),
-                        z + dz, // Intersection point in local index space
-                        0.5,    // Distance to intersection
-                        1       // Default to that there is a point in the other direction
-    );
+    if (!boundary->contains(x, y, z)) {
+      boundary->add_point(x, y, z, x + dx, y + offset - sgn(offset) * 0.5,
+                          z + dz, // Intersection point in local index space
+                          std::abs(offset) - 0.5, // Distance to intersection
+                          defValid, offset);
+    }
   }
   region_no_boundary = region_no_boundary.mask(to_remove);
 
diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx
index c71618ab19..22a8f0748a 100644
--- a/src/mesh/parallel/shiftedmetricinterp.cxx
+++ b/src/mesh/parallel/shiftedmetricinterp.cxx
@@ -146,7 +146,7 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
           0.25
               * (1                                                     // dy/2
                  + dy(it.ind, mesh.yend + 1) / dy(it.ind, mesh.yend)), // length
-          yvalid);
+          yvalid, 1);
     }
   }
   auto backward_boundary_xin = std::make_shared<BoundaryRegionPar>(
@@ -162,7 +162,7 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
           0.25
               * (1 // dy/2
                  + dy(it.ind, mesh.ystart - 1) / dy(it.ind, mesh.ystart)),
-          yvalid);
+          yvalid, -1);
     }
   }
   // Create regions for parallel boundary conditions
@@ -179,7 +179,7 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
           0.25
               * (1 // dy/2
                  + dy(it.ind, mesh.yend + 1) / dy(it.ind, mesh.yend)),
-          yvalid);
+          yvalid, 1);
     }
   }
   auto backward_boundary_xout = std::make_shared<BoundaryRegionPar>(
@@ -195,7 +195,7 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
           0.25
               * (dy(it.ind, mesh.ystart - 1) / dy(it.ind, mesh.ystart) // dy/2
                  + 1),
-          yvalid);
+          yvalid, -1);
     }
   }
 

From 1f48a59e5b39235864169de4b0cc468de21fcdb9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 13 Jan 2025 09:54:15 +0100
Subject: [PATCH 0638/1827] Add function to check wehther point is in the
 boundary

---
 include/bout/parallel_boundary_region.hxx | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index ff7ae14685..2d2e6829a8 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -311,6 +311,15 @@ public:
                               });
   }
 
+  bool contains(const int ix, const int iy, const int iz) const {
+    const auto i2 = xyz2ind(ix, iy, iz, localmesh);
+    for (auto i1 : bndry_points) {
+      if (i1.index == i2) {
+        return true;
+      }
+    }
+    return false;
+  }
   // setter
   void setValid(char val) { bndry_position->valid = val; }
 

From 4af5a4d93888f180678b0bd3c5d4c23b48dddc4d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 13 Jan 2025 09:55:59 +0100
Subject: [PATCH 0639/1827] Add setValid to BoundaryRegionParIterBase

---
 include/bout/parallel_boundary_region.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 2d2e6829a8..9af24770f7 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -84,7 +84,7 @@ public:
   unsigned char abs_offset() const { return bndry_position->abs_offset; }
 
   // setter
-  void setValid(signed char val) { bndry_position->valid = val; }
+  void setValid(signed char valid) { bndry_position->valid = valid; }
 
   bool contains(const BoundaryRegionPar& bndry) const {
     return std::binary_search(

From e5fbcaf08ed7016e708622946bf5a98185f8097f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 13 Jan 2025 09:57:32 +0100
Subject: [PATCH 0640/1827] Reimplement ynext for the boundary region

This is more general and takes the offset() into account, and thus works
for cases where the boundary is between the first and second guard cell
---
 include/bout/parallel_boundary_region.hxx | 56 +++++++++++++++++------
 1 file changed, 41 insertions(+), 15 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 9af24770f7..b03a0e2f01 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -212,23 +212,49 @@ public:
         parallel_stencil::neumann_o3(1 - length(), value, 1, f[ind()], 2, yprev(f));
   }
 
-  const int dir;
-
-private:
-  constexpr static BoutReal small_value = 1e-2;
-
-  // BoutReal get(const Field3D& f, int off)
-  const BoutReal& ynext(const Field3D& f) const { return f.ynext(dir)[ind().yp(dir)]; }
-  BoutReal& ynext(Field3D& f) const { return f.ynext(dir)[ind().yp(dir)]; }
-
-  const BoutReal& yprev(const Field3D& f) const {
-    ASSERT3(valid() > 0);
-    return f.ynext(-dir)[ind().yp(-dir)];
+  template <bool check = true>
+  BoutReal& getAt(Field3D& f, int off) const {
+    if constexpr (check) {
+      ASSERT3(valid() > -off - 2);
+    }
+    auto _off = offset() + off * dir;
+    return f.ynext(_off)[ind().yp(_off)];
   }
-  BoutReal& yprev(Field3D& f) const {
-    ASSERT3(valid() > 0);
-    return f.ynext(-dir)[ind().yp(-dir)];
+  template <bool check = true>
+  const BoutReal& getAt(const Field3D& f, int off) const {
+    if constexpr (check) {
+      ASSERT3(valid() > -off - 2);
+    }
+    auto _off = offset() + off * dir;
+    return f.ynext(_off)[ind().yp(_off)];
+  }
+
+  const BoutReal& ynext(const Field3D& f) const { return getAt(f, 0); }
+  BoutReal& ynext(Field3D& f) const { return getAt(f, 0); }
+  const BoutReal& ythis(const Field3D& f) const { return getAt(f, -1); }
+  BoutReal& ythis(Field3D& f) const { return getAt(f, -1); }
+  const BoutReal& yprev(const Field3D& f) const { return getAt(f, -2); }
+  BoutReal& yprev(Field3D& f) const { return getAt(f, -2); }
+
+  template <bool check = true>
+  BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
+                 int off) const {
+    if constexpr (check) {
+      ASSERT3(valid() > -off - 2);
+    }
+    auto _off = offset() + off * dir;
+    return f(_off, ind().yp(_off));
   }
+  BoutReal ynext(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    return getAt(f, 0);
+  }
+  BoutReal ythis(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    return getAt(f, -1);
+  }
+  BoutReal yprev(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    return getAt(f, -2);
+  }
+
   void setYPrevIfValid(Field3D& f, BoutReal val) const {
     if (valid() > 0) {
       yprev(f) = val;

From ef7b03df582ed1ba825f8ac0dbeedbd680e4c840 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 13 Jan 2025 09:58:41 +0100
Subject: [PATCH 0641/1827] Fix extrapolaton / interpolation

---
 include/bout/parallel_boundary_region.hxx | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index b03a0e2f01..0ced58d65e 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -93,18 +93,18 @@ public:
   }
 
   // extrapolate a given point to the boundary
-  BoutReal extrapolate_o1(const Field3D& f) const { return f[ind()]; }
-  BoutReal extrapolate_o2(const Field3D& f) const {
+  BoutReal extrapolate_sheath_o1(const Field3D& f) const { return ythis(f); }
+  BoutReal extrapolate_sheath_o2(const Field3D& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
       return extrapolate_o1(f);
     }
-    return f[ind()] * (1 + length()) - f.ynext(-dir)[ind().yp(-dir)] * length();
+    return ythis(f) * (1 + length()) - yprev(f) * length();
   }
 
   inline BoutReal
   extrapolate_sheath_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return f(0, ind());
+    return ythis(f);
   }
   inline BoutReal
   extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
@@ -112,25 +112,25 @@ public:
     if (valid() < 1) {
       return extrapolate_sheath_o1(f);
     }
-    return f(0, ind()) * (1 + length()) - f(-dir, ind().yp(-dir)) * length();
+    return ythis(f) * (1 + length()) - yprev(f) * length();
   }
 
   inline BoutReal interpolate_sheath_o1(const Field3D& f) const {
-    return f[ind()] * (1 - length()) + ynext(f) * length();
+    return ythis(f) * (1 - length()) + ynext(f) * length();
   }
 
-  inline BoutReal extrapolate_next_o1(const Field3D& f) const { return f[ind()]; }
+  inline BoutReal extrapolate_next_o1(const Field3D& f) const { return ythis(f); }
   inline BoutReal extrapolate_next_o2(const Field3D& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
       return extrapolate_next_o1(f);
     }
-    return f[ind()] * 2 - f.ynext(-dir)[ind().yp(-dir)];
+    return ythis(f) * 2 - yprev(f);
   }
 
   inline BoutReal
   extrapolate_next_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return f(0, ind());
+    return ythis(f);
   }
   inline BoutReal
   extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
@@ -138,7 +138,7 @@ public:
     if (valid() < 1) {
       return extrapolate_sheath_o1(f);
     }
-    return f(0, ind()) * 2 - f(-dir, ind().yp(-dir));
+    return ythis(f) * 2 - yprev(f);
   }
 
   // extrapolate the gradient into the boundary
@@ -148,7 +148,7 @@ public:
     if (valid() < 1) {
       return extrapolate_grad_o1(f);
     }
-    return f[ind()] - f.ynext(-dir)[ind().yp(-dir)];
+    return ythis(f) - ynext(f);
   }
 
   BoundaryRegionParIterBase& operator*() { return *this; }
@@ -346,6 +346,7 @@ public:
     }
     return false;
   }
+
   // setter
   void setValid(char val) { bndry_position->valid = val; }
 

From 6dba751e085d55bdba46ff84b70115a1f2a0034d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 13 Jan 2025 11:12:38 +0100
Subject: [PATCH 0642/1827] Fix parallel boundary to interpolate into the
 boundary

Previously only the first boundary point was set
---
 include/bout/parallel_boundary_region.hxx | 32 ++++++++++++++++-------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 0ced58d65e..d3082f4d45 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -162,17 +162,20 @@ public:
     return bndry_position != rhs.bndry_position;
   }
 
+#define ITER() for (int i = 0; i < localmesh->ystart - abs_offset(); ++i)
   // dirichlet boundary code
   void dirichlet_o1(Field3D& f, BoutReal value) const {
-    f.ynext(dir)[ind().yp(dir)] = value;
+    ITER() { getAt(f, i) = value; }
   }
 
   void dirichlet_o2(Field3D& f, BoutReal value) const {
     if (length() < small_value) {
       return dirichlet_o1(f, value);
     }
-    ynext(f) = parallel_stencil::dirichlet_o2(1, f[ind()], 1 - length(), value);
-    // ynext(f) = f[ind()] * (1 + 1/length()) + value / length();
+    ITER() {
+      getAt(f, i) =
+          parallel_stencil::dirichlet_o2(i + 1, ythis(f), i + 1 - length(), value);
+    }
   }
 
   void dirichlet_o3(Field3D& f, BoutReal value) const {
@@ -181,17 +184,24 @@ public:
       return dirichlet_o2(f, value);
     }
     if (length() < small_value) {
-      ynext(f) = parallel_stencil::dirichlet_o2(2, yprev(f), 1 - length(), value);
+      ITER() {
+        getAt(f, i) =
+            parallel_stencil::dirichlet_o2(i + 2, yprev(f), i + 1 - length(), value);
+      }
     } else {
-      ynext(f) =
-          parallel_stencil::dirichlet_o3(2, yprev(f), 1, f[ind()], 1 - length(), value);
+      ITER() {
+        getAt(f, i) = parallel_stencil::dirichlet_o3(i + 2, yprev(f), i + 1, ythis(f),
+                                                     i + 1 - length(), value);
+      }
     }
   }
 
   // NB: value needs to be scaled by dy
   // neumann_o1 is actually o2 if we would use an appropriate one-sided stencil.
   // But in general we do not, and thus for normal C2 stencils, this is 1st order.
-  void neumann_o1(Field3D& f, BoutReal value) const { ynext(f) = f[ind()] + value; }
+  void neumann_o1(Field3D& f, BoutReal value) const {
+    ITER() { getAt(f, i) = ythis(f) + value; }
+  }
 
   // NB: value needs to be scaled by dy
   void neumann_o2(Field3D& f, BoutReal value) const {
@@ -199,7 +209,7 @@ public:
     if (valid() < 1) {
       return neumann_o1(f, value);
     }
-    ynext(f) = yprev(f) + 2 * value;
+    ITER() { getAt(f, i) = yprev(f) + 2 * value; }
   }
 
   // NB: value needs to be scaled by dy
@@ -208,8 +218,10 @@ public:
     if (valid() < 1) {
       return neumann_o1(f, value);
     }
-    ynext(f) =
-        parallel_stencil::neumann_o3(1 - length(), value, 1, f[ind()], 2, yprev(f));
+    ITER() {
+      getAt(f, i) = parallel_stencil::neumann_o3(i + 1 - length(), value, i + 1, ythis(f),
+                                                 2, yprev(f));
+    }
   }
 
   template <bool check = true>

From f105c3f725e6678597f444271c8957f8a71ddbeb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 13 Jan 2025 11:13:14 +0100
Subject: [PATCH 0643/1827] Ensure data is sorted

---
 include/bout/parallel_boundary_region.hxx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index d3082f4d45..5d6150d94c 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -323,6 +323,9 @@ public:
   /// Add a point to the boundary
   void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
                  char valid, signed char offset) {
+    if (!bndry_points.empty() && bndry_points.back().index > ind) {
+      is_sorted = false;
+    }
     bndry_points.push_back({ind,
                             {x, y, z},
                             length,
@@ -341,6 +344,7 @@ public:
   bool isDone() final { return (bndry_position == std::end(bndry_points)); }
 
   bool contains(const BoundaryRegionPar& bndry) const {
+    ASSERT2(is_sorted);
     return std::binary_search(std::begin(bndry_points), std::end(bndry_points),
                               *bndry.bndry_position,
                               [](const bout::parallel_boundary_region::Indices& i1,
@@ -388,6 +392,7 @@ private:
     const int nz = mesh->LocalNz;
     return Ind3D{(x * ny + y) * nz + z, ny, nz};
   }
+  bool is_sorted{true};
 };
 
 #endif //  BOUT_PAR_BNDRY_H

From f7c1acaf2fcf3b0f488da73351aea98d7d801d65 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 13 Jan 2025 11:13:59 +0100
Subject: [PATCH 0644/1827] Calculate valid for the general case

---
 src/mesh/parallel/fci.cxx | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 3394a3e2af..d3fcc8d04c 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -357,17 +357,20 @@ FCITransform::FCITransform(Mesh& mesh, const Coordinates::FieldMetric& dy, bool
     field_line_maps.emplace_back(mesh, dy, options, -offset, backward_boundary_xin,
                                  backward_boundary_xout, zperiodic);
   }
-  ASSERT0(mesh.ystart == 1);
   const std::array bndries = {forward_boundary_xin, forward_boundary_xout,
                               backward_boundary_xin, backward_boundary_xout};
-  for (const auto& bndry : bndries) {
+  for (auto& bndry : bndries) {
     for (const auto& bndry2 : bndries) {
       if (bndry->dir == bndry2->dir) {
         continue;
       }
-      for (bndry->first(); !bndry->isDone(); bndry->next()) {
-        if (bndry2->contains(*bndry)) {
-          bndry->setValid(0);
+      for (auto pnt : *bndry) {
+        for (auto pnt2 : *bndry2) {
+#warning this could likely be done faster
+          if (pnt.ind() == pnt2.ind()) {
+            pnt.setValid(
+                static_cast<signed char>(std::abs((pnt2.offset() - pnt.offset())) - 2));
+          }
         }
       }
     }

From 55bdbcfd0eedca426be35fbdb173bc85611ea062 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 20 Jan 2025 16:29:05 +0100
Subject: [PATCH 0645/1827] fix parallel neumann BC

---
 include/bout/parallel_boundary_region.hxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 5d6150d94c..936a57e9d9 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -200,7 +200,7 @@ public:
   // neumann_o1 is actually o2 if we would use an appropriate one-sided stencil.
   // But in general we do not, and thus for normal C2 stencils, this is 1st order.
   void neumann_o1(Field3D& f, BoutReal value) const {
-    ITER() { getAt(f, i) = ythis(f) + value; }
+    ITER() { getAt(f, i) = ythis(f) + value * (i + 1); }
   }
 
   // NB: value needs to be scaled by dy
@@ -209,14 +209,14 @@ public:
     if (valid() < 1) {
       return neumann_o1(f, value);
     }
-    ITER() { getAt(f, i) = yprev(f) + 2 * value; }
+    ITER() { getAt(f, i) = yprev(f) + (2 + i) * value; }
   }
 
   // NB: value needs to be scaled by dy
   void neumann_o3(Field3D& f, BoutReal value) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
-      return neumann_o1(f, value);
+      return neumann_o2(f, value);
     }
     ITER() {
       getAt(f, i) = parallel_stencil::neumann_o3(i + 1 - length(), value, i + 1, ythis(f),

From 6f40b4e6f6905d3fb61512fc69e7c354b9e3d2db Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 20 Jan 2025 16:30:54 +0100
Subject: [PATCH 0646/1827] Add limitFree

Taken from hermes-3, adopted for higher order
---
 include/bout/parallel_boundary_region.hxx | 27 +++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 936a57e9d9..701298977a 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -15,6 +15,22 @@
  *
  */
 
+inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc) {
+  if (fm < fc) {
+    return 1; // Neumann rather than increasing into boundary
+  }
+  if (fm < 1e-10) {
+    return 1; // Low / no density condition
+  }
+  BoutReal fp = fc / fm;
+#if CHECKLEVEL >= 2
+  if (!std::isfinite(fp)) {
+    throw BoutException("SheathBoundaryParallel limitFree: {}, {} -> {}", fm, fc, fp);
+  }
+#endif
+  return fp;
+}
+
 class BoundaryRegionPar : public BoundaryRegionBase {
 
   struct RealPoint {
@@ -224,6 +240,17 @@ public:
     }
   }
 
+  // extrapolate into the boundary using only monotonic decreasing values.
+  // f needs to be positive
+  void limitFree(Field3D& f) const {
+    const auto fac = valid() > 0 ? limitFreeScale(yprev(f), ythis(f)) : 1;
+    auto val = ythis(f);
+    ITER() {
+      val *= fac;
+      getAt(f, i) = val;
+    }
+  }
+
   template <bool check = true>
   BoutReal& getAt(Field3D& f, int off) const {
     if constexpr (check) {

From 36c1f94f4f33983df959a7c30f52bab1fb376511 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 20 Jan 2025 16:31:18 +0100
Subject: [PATCH 0647/1827] add setAll to parallel BC

---
 include/bout/parallel_boundary_region.hxx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 701298977a..1ae49360f2 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -251,6 +251,12 @@ public:
     }
   }
 
+  void setAll(Field3D& f, const BoutReal val) const {
+    for (int i = -localmesh->ystart; i <= localmesh->ystart; ++i) {
+      f.ynext(i)[ind().yp(i)] = val;
+    }
+  }
+
   template <bool check = true>
   BoutReal& getAt(Field3D& f, int off) const {
     if constexpr (check) {

From c7cbf117f9db1c3c7264f5716b8d205e3d781e7e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 31 Jan 2025 10:07:22 +0100
Subject: [PATCH 0648/1827] Move yboundary iterator from hermes to BOUT++

This allows to write code for FCI and non-FCI using templates.
---
 include/bout/boundary_iterator.hxx | 51 ++++++++++++++++++++++-
 include/bout/yboundary_regions.hxx | 66 ++++++++++++++++++++++++++++++
 2 files changed, 116 insertions(+), 1 deletion(-)
 create mode 100644 include/bout/yboundary_regions.hxx

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 93f02c004d..601f6a8a28 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -1,6 +1,7 @@
 #pragma once
 
 #include "bout/mesh.hxx"
+#include "bout/parallel_boundary_region.hxx"
 #include "bout/sys/parallel_stencils.hxx"
 #include "bout/sys/range.hxx"
 
@@ -42,14 +43,62 @@ public:
     return 2 * f(0, ind()) - f(0, ind().yp(-by).xp(-bx));
   }
 
-  BoutReal interpolate_sheath(const Field3D& f) const {
+  BoutReal interpolate_sheath_o1(const Field3D& f) const {
     return (f[ind()] + ynext(f)) * 0.5;
   }
+  BoutReal
+  extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    return 0.5 * (3 * f(0, ind()) - f(0, ind().yp(-by).xp(-bx)));
+  }
+
+  void limitFree(Field3D& f) const {
+    const BoutReal fac =
+        bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f));
+    BoutReal val = ythis(f);
+    for (int i = 1; i <= localmesh->ystart; ++i) {
+      val *= fac;
+      f[ind().yp(by * i).xp(bx * i)] = val;
+    }
+  }
+
+  void neumann_o1(Field3D& f, BoutReal grad) const {
+    BoutReal val = ythis(f);
+    for (int i = 1; i <= localmesh->ystart; ++i) {
+      val += grad;
+      f[ind().yp(by * i).xp(bx * i)] = val;
+    }
+  }
+
+  void neumann_o2(Field3D& f, BoutReal grad) const {
+    BoutReal val = yprev(f) + grad;
+    for (int i = 1; i <= localmesh->ystart; ++i) {
+      val += grad;
+      f[ind().yp(by * i).xp(bx * i)] = val;
+    }
+  }
 
   BoutReal& ynext(Field3D& f) const { return f[ind().yp(by).xp(bx)]; }
   const BoutReal& ynext(const Field3D& f) const { return f[ind().yp(by).xp(bx)]; }
   BoutReal& yprev(Field3D& f) const { return f[ind().yp(-by).xp(-bx)]; }
   const BoutReal& yprev(const Field3D& f) const { return f[ind().yp(-by).xp(-bx)]; }
+  BoutReal& ythis(Field3D& f) const { return f[ind()]; }
+  const BoutReal& ythis(const Field3D& f) const { return f[ind()]; }
+
+  void setYPrevIfValid(Field3D& f, BoutReal val) const { yprev(f) = val; }
+  void setAll(Field3D& f, const BoutReal val) const {
+    for (int i = -localmesh->ystart; i <= localmesh->ystart; ++i) {
+      f[ind().yp(by * i).xp(bx * i)] = val;
+    }
+  }
+
+  int abs_offset() const { return 1; }
+
+#if BOUT_USE_METRIC_3D == 0
+  BoutReal& ynext(Field2D& f) const { return f[ind().yp(by).xp(bx)]; }
+  const BoutReal& ynext(const Field2D& f) const { return f[ind().yp(by).xp(bx)]; }
+  BoutReal& yprev(Field2D& f) const { return f[ind().yp(-by).xp(-bx)]; }
+  const BoutReal& yprev(const Field2D& f) const { return f[ind().yp(-by).xp(-bx)]; }
+#endif
 
   const int dir;
 
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
new file mode 100644
index 0000000000..e0e93e17f9
--- /dev/null
+++ b/include/bout/yboundary_regions.hxx
@@ -0,0 +1,66 @@
+#pragma once
+
+#include "./boundary_iterator.hxx"
+#include "bout/parallel_boundary_region.hxx"
+
+class YBoundary {
+public:
+  template <class T>
+  void iter_regions(const T& f) {
+    ASSERT1(is_init);
+    for (auto& region : boundary_regions) {
+      f(*region);
+    }
+    for (auto& region : boundary_regions_par) {
+      f(*region);
+    }
+  }
+
+  template <class F>
+  void iter(const F& f) {
+    return iter_regions(f);
+  }
+
+  void init(Options& options, Mesh* mesh = nullptr) {
+    if (mesh == nullptr) {
+      mesh = bout::globals::mesh;
+    }
+
+    bool lower_y = options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(true);
+    bool upper_y = options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(true);
+    bool outer_x = options["outer_x"].doc("Boundary on outer x?").withDefault<bool>(true);
+    bool inner_x =
+        options["inner_x"].doc("Boundary on inner x?").withDefault<bool>(false);
+
+    if (mesh->isFci()) {
+      if (outer_x) {
+        for (auto& bndry : mesh->getBoundariesPar(BoundaryParType::xout)) {
+          boundary_regions_par.push_back(bndry);
+        }
+      }
+      if (inner_x) {
+        for (auto& bndry : mesh->getBoundariesPar(BoundaryParType::xin)) {
+          boundary_regions_par.push_back(bndry);
+        }
+      }
+    } else {
+      if (lower_y) {
+        boundary_regions.push_back(
+            std::make_shared<NewBoundaryRegionY>(mesh, true, mesh->iterateBndryLowerY()));
+      }
+      if (upper_y) {
+        boundary_regions.push_back(std::make_shared<NewBoundaryRegionY>(
+            mesh, false, mesh->iterateBndryUpperY()));
+      }
+    }
+    is_init = true;
+  }
+
+private:
+  std::vector<std::shared_ptr<BoundaryRegionPar>> boundary_regions_par;
+  std::vector<std::shared_ptr<NewBoundaryRegionY>> boundary_regions;
+
+  bool is_init{false};
+};
+
+extern YBoundary yboundary;

From f9cad29209ce213da7bd78b2406de29aec829a69 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 3 Mar 2025 10:01:55 +0100
Subject: [PATCH 0649/1827] Add iter_pnts function

Directly iterate over the points
---
 include/bout/yboundary_regions.hxx | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index e0e93e17f9..b72f8d32c0 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -5,8 +5,8 @@
 
 class YBoundary {
 public:
-  template <class T>
-  void iter_regions(const T& f) {
+  template <class F>
+  void iter_regions(const F& f) {
     ASSERT1(is_init);
     for (auto& region : boundary_regions) {
       f(*region);
@@ -15,6 +15,14 @@ public:
       f(*region);
     }
   }
+  template <class F>
+  void iter_pnts(const F& f) {
+    iter_regions([&](auto& region) {
+      for (auto& pnt : region) {
+        f(pnt);
+      }
+    }
+  }
 
   template <class F>
   void iter(const F& f) {

From e6f004b33634f50dc9680bf7c100bcef6237b8fb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 3 Mar 2025 10:02:46 +0100
Subject: [PATCH 0650/1827] Add example on how to replace RangeIterator with
 YBoundary

---
 include/bout/example_yboundary_regions.cxx | 65 ++++++++++++++++++++++
 include/bout/yboundary_regions.hxx         | 12 ++++
 2 files changed, 77 insertions(+)
 create mode 100644 include/bout/example_yboundary_regions.cxx

diff --git a/include/bout/example_yboundary_regions.cxx b/include/bout/example_yboundary_regions.cxx
new file mode 100644
index 0000000000..0e8d9b07dc
--- /dev/null
+++ b/include/bout/example_yboundary_regions.cxx
@@ -0,0 +1,65 @@
+#include <bout/yboundary_regions.hxx>
+
+class yboundary_example_legacy {
+public:
+  yboundary_example_legacy(Options* opt, const Field3D& N, const Field3D& V)
+      : N(N), V(V) {
+    Options& options = *opt;
+    lower_y = options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
+    upper_y = options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(upper_y);
+  }
+
+  void rhs() {
+    BoutReal totalFlux = 0;
+    if (lower_y) {
+      for (RangeIterator r = mesh->iterateBndryLowerY(); !r.isDone(); r++) {
+        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          // Calculate flux through surface [normalised m^-2 s^-1],
+          // should be positive since V < 0.0
+          BoutReal flux =
+              -0.5 * (N(r.ind, mesh->ystart, jz) + N(r.ind, mesh->ystart - 1, jz)) * 0.5
+              * (V(r.ind, mesh->ystart, jz) + V(r.ind, mesh->ystart - 1, jz));
+          totalFlux += flux;
+        }
+      }
+    }
+    if (upper_y) {
+      for (RangeIterator r = mesh->iterateBndryUpperY(); !r.isDone(); r++) {
+        for (int jz = 0; jz < mesh->LocalNz; jz++) {
+          // Calculate flux through surface [normalised m^-2 s^-1],
+          // should be positive since V < 0.0
+          BoutReal flux = -0.5 * (N(r.ind, mesh->yend, jz) + N(r.ind, mesh->yend + 1, jz))
+                          * 0.5
+                          * (V(r.ind, mesh->yend, jz) + V(r.ind, mesh->yend + 1, jz));
+          totalFlux += flux;
+        }
+      }
+    }
+  }
+
+private:
+  bool lower_y{true};
+  bool upper_y{true};
+  const Field3D& N;
+  const Field3D& V;
+}
+
+class yboundary_example {
+public:
+  yboundary_example(Options* opt, const Field3D& N, const Field3D& V) : N(N), V(V) {
+    // Set what kind of yboundaries you want to include
+    yboundary.init(opt);
+  }
+
+  void rhs() {
+    BoutReal totalFlux = 0;
+    yboundary.iter_pnts([&](auto& pnt) {
+      BoutReal flux = pnt.interpolate_sheath_o1(N) * pnt.interpolate_sheath_o1(V);
+    });
+  }
+
+private:
+  YBoundary ybounday;
+  const Field3D& N;
+  const Field3D& V;
+};
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index b72f8d32c0..833e988eb9 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -2,6 +2,18 @@
 
 #include "./boundary_iterator.hxx"
 #include "bout/parallel_boundary_region.hxx"
+/*!
+ * This class allows to simplify iterating over y-boundaries.
+ *
+ * It makes it easier to write code for FieldAligned boundaries, but if a bit
+ * care is taken the code also works with FluxCoordinateIndependent code.
+ *
+ * An example how to replace old code is given here:
+ *
+ * \example example_yboundary_regions.hxx
+ * This is an example how to use the YBoundary class to replace RangeIterator
+ * boundaries.
+ */
 
 class YBoundary {
 public:

From 3a0f2146636c05d57fd85b8bfdb1da883bedad54 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 3 Mar 2025 11:25:50 +0100
Subject: [PATCH 0651/1827] Move documentation to sphinx

---
 include/bout/example_yboundary_regions.cxx   | 65 ----------------
 include/bout/yboundary_regions.hxx           | 20 ++---
 manual/sphinx/user_docs/boundary_options.rst | 79 ++++++++++++++++++++
 3 files changed, 87 insertions(+), 77 deletions(-)
 delete mode 100644 include/bout/example_yboundary_regions.cxx

diff --git a/include/bout/example_yboundary_regions.cxx b/include/bout/example_yboundary_regions.cxx
deleted file mode 100644
index 0e8d9b07dc..0000000000
--- a/include/bout/example_yboundary_regions.cxx
+++ /dev/null
@@ -1,65 +0,0 @@
-#include <bout/yboundary_regions.hxx>
-
-class yboundary_example_legacy {
-public:
-  yboundary_example_legacy(Options* opt, const Field3D& N, const Field3D& V)
-      : N(N), V(V) {
-    Options& options = *opt;
-    lower_y = options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
-    upper_y = options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(upper_y);
-  }
-
-  void rhs() {
-    BoutReal totalFlux = 0;
-    if (lower_y) {
-      for (RangeIterator r = mesh->iterateBndryLowerY(); !r.isDone(); r++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
-          // Calculate flux through surface [normalised m^-2 s^-1],
-          // should be positive since V < 0.0
-          BoutReal flux =
-              -0.5 * (N(r.ind, mesh->ystart, jz) + N(r.ind, mesh->ystart - 1, jz)) * 0.5
-              * (V(r.ind, mesh->ystart, jz) + V(r.ind, mesh->ystart - 1, jz));
-          totalFlux += flux;
-        }
-      }
-    }
-    if (upper_y) {
-      for (RangeIterator r = mesh->iterateBndryUpperY(); !r.isDone(); r++) {
-        for (int jz = 0; jz < mesh->LocalNz; jz++) {
-          // Calculate flux through surface [normalised m^-2 s^-1],
-          // should be positive since V < 0.0
-          BoutReal flux = -0.5 * (N(r.ind, mesh->yend, jz) + N(r.ind, mesh->yend + 1, jz))
-                          * 0.5
-                          * (V(r.ind, mesh->yend, jz) + V(r.ind, mesh->yend + 1, jz));
-          totalFlux += flux;
-        }
-      }
-    }
-  }
-
-private:
-  bool lower_y{true};
-  bool upper_y{true};
-  const Field3D& N;
-  const Field3D& V;
-}
-
-class yboundary_example {
-public:
-  yboundary_example(Options* opt, const Field3D& N, const Field3D& V) : N(N), V(V) {
-    // Set what kind of yboundaries you want to include
-    yboundary.init(opt);
-  }
-
-  void rhs() {
-    BoutReal totalFlux = 0;
-    yboundary.iter_pnts([&](auto& pnt) {
-      BoutReal flux = pnt.interpolate_sheath_o1(N) * pnt.interpolate_sheath_o1(V);
-    });
-  }
-
-private:
-  YBoundary ybounday;
-  const Field3D& N;
-  const Field3D& V;
-};
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 833e988eb9..6d12ab3541 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -2,18 +2,14 @@
 
 #include "./boundary_iterator.hxx"
 #include "bout/parallel_boundary_region.hxx"
-/*!
- * This class allows to simplify iterating over y-boundaries.
- *
- * It makes it easier to write code for FieldAligned boundaries, but if a bit
- * care is taken the code also works with FluxCoordinateIndependent code.
- *
- * An example how to replace old code is given here:
- *
- * \example example_yboundary_regions.hxx
- * This is an example how to use the YBoundary class to replace RangeIterator
- * boundaries.
- */
+
+/// This class allows to simplify iterating over y-boundaries.
+///
+/// It makes it easier to write code for FieldAligned boundaries, but if a bit
+/// care is taken the code also works with FluxCoordinateIndependent code.
+///
+/// An example how to replace old code is given here:
+/// ../../manual/sphinx/user_docs/boundary_options.rst
 
 class YBoundary {
 public:
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 8493049516..579411b669 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -436,6 +436,85 @@ the upper Y boundary of a 2D variable ``var``::
 The `BoundaryRegion` class is defined in
 ``include/boundary_region.hxx``
 
+Y-Boundaries
+------------
+
+The sheath boundaries are often implemented in the physics model.
+Previously of they where implemented using a `RangeIterator`::
+
+    class yboundary_example_legacy {
+    public:
+      yboundary_example_legacy(Options* opt, const Field3D& N, const Field3D& V)
+          : N(N), V(V) {
+        Options& options = *opt;
+        lower_y = options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
+        upper_y = options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(upper_y);
+      }
+    
+      void rhs() {
+        BoutReal totalFlux = 0;
+        if (lower_y) {
+          for (RangeIterator r = mesh->iterateBndryLowerY(); !r.isDone(); r++) {
+            for (int jz = 0; jz < mesh->LocalNz; jz++) {
+              // Calculate flux through surface [normalised m^-2 s^-1],
+              // should be positive since V < 0.0
+              BoutReal flux =
+                  -0.5 * (N(r.ind, mesh->ystart, jz) + N(r.ind, mesh->ystart - 1, jz)) * 0.5
+                  * (V(r.ind, mesh->ystart, jz) + V(r.ind, mesh->ystart - 1, jz));
+              totalFlux += flux;
+            }
+          }
+        }
+        if (upper_y) {
+          for (RangeIterator r = mesh->iterateBndryUpperY(); !r.isDone(); r++) {
+            for (int jz = 0; jz < mesh->LocalNz; jz++) {
+              // Calculate flux through surface [normalised m^-2 s^-1],
+              // should be positive since V < 0.0
+              BoutReal flux = -0.5 * (N(r.ind, mesh->yend, jz) + N(r.ind, mesh->yend + 1, jz))
+                              * 0.5
+                              * (V(r.ind, mesh->yend, jz) + V(r.ind, mesh->yend + 1, jz));
+              totalFlux += flux;
+            }
+          }
+        }
+      }
+    
+    private:
+      bool lower_y{true};
+      bool upper_y{true};
+      const Field3D& N;
+      const Field3D& V;
+    }
+    
+
+This can be replaced using the `YBoundary` class, which not only simplifies the
+code, but also allows to have the same code working with non-field-aligned
+geometries, as flux coordinate independent (FCI) method::
+
+    #include <bout/yboundary_regions.hxx>
+
+    class yboundary_example {
+    public:
+      yboundary_example(Options* opt, const Field3D& N, const Field3D& V) : N(N), V(V) {
+        // Set what kind of yboundaries you want to include
+        yboundary.init(opt);
+      }
+    
+      void rhs() {
+        BoutReal totalFlux = 0;
+        yboundary.iter_pnts([&](auto& pnt) {
+          BoutReal flux = pnt.interpolate_sheath_o1(N) * pnt.interpolate_sheath_o1(V);
+        });
+      }
+    
+    private:
+      YBoundary ybounday;
+      const Field3D& N;
+      const Field3D& V;
+    };
+    
+
+
 Boundary regions
 ----------------
 

From 4e21aac84aa1c084944045bfe941755660febcfe Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 4 Mar 2025 15:51:40 +0100
Subject: [PATCH 0652/1827] Fix iter_pnts

---
 include/bout/yboundary_regions.hxx | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 6d12ab3541..1d434e2420 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -29,7 +29,7 @@ public:
       for (auto& pnt : region) {
         f(pnt);
       }
-    }
+    });
   }
 
   template <class F>
@@ -78,5 +78,3 @@ private:
 
   bool is_init{false};
 };
-
-extern YBoundary yboundary;

From 3a850b11e3559607ba16d5cb10cce882177d19b5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 4 Mar 2025 15:52:00 +0100
Subject: [PATCH 0653/1827] Add more documentation on YBoundary

---
 manual/sphinx/user_docs/boundary_options.rst | 45 ++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 579411b669..18535c91b4 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -515,6 +515,51 @@ geometries, as flux coordinate independent (FCI) method::
     
 
 
+There are several member functions of ``pnt``. ``pnt`` is of type
+`BoundaryRegionParIterBase` and `BoundaryRegionIter`, and both should provide
+the same interface. If they don't that is a bug, as the above code is a
+template, that gets instantiated for both types, and thus requires both
+classes to provide the same interface, one for FCI-like boundaries and one for
+field aligned boundaries.
+
+Here is a short summary of some members of ``pnt``, where ``f`` is a :
+
+.. list-table:: Members for boundary operation
+   :widths: 15 70
+   :header-rows: 1
+
+   * - Function
+     - Description
+   * - ``pnt.ythis(f)``
+     - Returns the value at the last point in the domain
+   * - ``pnt.ynext(f)``
+     - Returns the value at the first point in the domain
+   * - ``pnt.yprev(f)``
+     - Returns the value at the second to last point in the domain, if it is
+       valid. NB: this point may not be valid.
+   * - ``pnt.interpolate_sheath_o1(f)``
+     - Returns the value at the boundary, assuming the bounday value has been set
+   * - ``pnt.extrapolate_sheath_o1(f)``
+     - Returns the value at the boundary, extrapolating from the bulk, first order
+   * - ``pnt.extrapolate_sheath_o2(f)``
+     - Returns the value at the boundary, extrapolating from the bulk, second order
+   * - ``pnt.extrapolate_next_o{1,2}(f)``
+     - Extrapolate into the boundary from the bulk, first or second order
+   * - ``pnt.extrapolate_grad_o{1,2}(f)``
+     - Extrapolate the gradient into the boundary, first or second order
+   * - ``pnt.dirichlet_o{1,2,3}(f, v)``
+     - Apply dirichlet boundary conditions with value ``v`` and given order
+   * - ``pnt.neumann_o{1,2,3}(f, v)``
+     - Applies a gradient of ``v / dy`` boundary condition.
+   * - ``pnt.limitFree(f)``
+     - Extrapolate into the boundary using only monotonic decreasing values.
+       ``f`` needs to be positive.
+   * - ``pnt.dir``
+     - The direction of the boundary.
+
+
+
+
 Boundary regions
 ----------------
 

From e0f80cf51473648753148b0efbf7e1a1e9edbf37 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 7 Mar 2025 10:39:28 +0100
Subject: [PATCH 0654/1827] Ensure the field has parallel slices

---
 include/bout/parallel_boundary_region.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 1ae49360f2..27d8c34ccf 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -259,6 +259,7 @@ public:
 
   template <bool check = true>
   BoutReal& getAt(Field3D& f, int off) const {
+    ASSERT4(f.hasParallelSlices());
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }
@@ -267,6 +268,7 @@ public:
   }
   template <bool check = true>
   const BoutReal& getAt(const Field3D& f, int off) const {
+    ASSERT4(f.hasParallelSlices());
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }

From 101f33df885c535c5dc21e54cf64967ea767afc8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 7 Mar 2025 11:30:36 +0100
Subject: [PATCH 0655/1827] Lower check level

---
 include/bout/parallel_boundary_region.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 27d8c34ccf..862670b529 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -259,7 +259,7 @@ public:
 
   template <bool check = true>
   BoutReal& getAt(Field3D& f, int off) const {
-    ASSERT4(f.hasParallelSlices());
+    ASSERT3(f.hasParallelSlices());
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }
@@ -268,7 +268,7 @@ public:
   }
   template <bool check = true>
   const BoutReal& getAt(const Field3D& f, int off) const {
-    ASSERT4(f.hasParallelSlices());
+    ASSERT3(f.hasParallelSlices());
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }

From 4ea1657fea06c13f37e7ac8714182d566fde0308 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 21 Aug 2025 10:10:16 +0200
Subject: [PATCH 0656/1827] Prefer std::vector::emplace_back to work around
 cuda compiler issue

---
 include/bout/parallel_boundary_region.hxx | 66 +++++++++++++----------
 1 file changed, 37 insertions(+), 29 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 862670b529..3ddb8ed8fe 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -15,6 +15,38 @@
  *
  */
 
+namespace bout {
+namespace parallel_boundary_region {
+
+struct RealPoint {
+  BoutReal s_x;
+  BoutReal s_y;
+  BoutReal s_z;
+};
+
+struct Indices {
+  // Indices of the boundary point
+  Ind3D index;
+  // Intersection with boundary in index space
+  RealPoint intersection;
+  // Distance to intersection
+  BoutReal length;
+  // Angle between field line and boundary
+  // BoutReal angle;
+  // How many points we can go in the opposite direction
+  signed char valid;
+  signed char offset;
+  unsigned char abs_offset;
+  Indices(Ind3D index, RealPoint&& intersection, BoutReal length, signed char valid,
+          signed char offset, unsigned char abs_offset)
+      : index(index), intersection(std::move(intersection)), length(length), valid(valid),
+        offset(offset), abs_offset(abs_offset) {};
+};
+
+using IndicesVec = std::vector<Indices>;
+using IndicesIter = IndicesVec::iterator;
+using IndicesIterConst = IndicesVec::const_iterator;
+
 inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc) {
   if (fm < fc) {
     return 1; // Neumann rather than increasing into boundary
@@ -33,27 +65,6 @@ inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc) {
 
 class BoundaryRegionPar : public BoundaryRegionBase {
 
-  struct RealPoint {
-    BoutReal s_x;
-    BoutReal s_y;
-    BoutReal s_z;
-  };
-
-  struct Indices {
-    // Indices of the boundary point
-    Ind3D index;
-    // Intersection with boundary in index space
-    RealPoint intersection;
-    // Distance to intersection
-    BoutReal length;
-    // Angle between field line and boundary
-    // BoutReal angle;
-    // How many points we can go in the opposite direction
-    signed char valid;
-    signed char offset;
-    unsigned char abs_offset;
-  };
-
   using IndicesVec = std::vector<Indices>;
   using IndicesIter = IndicesVec::iterator;
 
@@ -77,11 +88,11 @@ public:
   /// Add a point to the boundary
   void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
                  signed char valid) {
-    bndry_points.push_back({ind, {x, y, z}, length, valid});
+    bndry_points.emplace_back({ind, {x, y, z}, length, valid});
   }
   void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
                  BoutReal length, signed char valid) {
-    bndry_points.push_back({xyz2ind(ix, iy, iz, localmesh), {x, y, z}, length, valid});
+    bndry_points.emplace_back({xyz2ind(ix, iy, iz, localmesh), {x, y, z}, length, valid});
   }
 
   // final, so they can be inlined
@@ -361,12 +372,9 @@ public:
     if (!bndry_points.empty() && bndry_points.back().index > ind) {
       is_sorted = false;
     }
-    bndry_points.push_back({ind,
-                            {x, y, z},
-                            length,
-                            valid,
-                            offset,
-                            static_cast<unsigned char>(std::abs(offset))});
+    bndry_points.emplace_back(ind, bout::parallel_boundary_region::RealPoint{x, y, z},
+                              length, valid, offset,
+                              static_cast<unsigned char>(std::abs(offset)));
   }
   void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
                  BoutReal length, char valid, signed char offset) {

From c78dd6ec3fd7fc6cec5be9f96cfa18c1792998a5 Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Thu, 21 Aug 2025 08:16:32 +0000
Subject: [PATCH 0657/1827] Apply clang-format changes


From 6fadc066e5aacc022f2e0a0961e4c87fd8e74e75 Mon Sep 17 00:00:00 2001
From: David Bold <dschwoerer@users.noreply.github.com>
Date: Thu, 21 Aug 2025 11:37:58 +0200
Subject: [PATCH 0658/1827] remove unneeded std::move

---
 include/bout/parallel_boundary_region.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 3ddb8ed8fe..76a5cbe5d1 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -39,7 +39,7 @@ struct Indices {
   unsigned char abs_offset;
   Indices(Ind3D index, RealPoint&& intersection, BoutReal length, signed char valid,
           signed char offset, unsigned char abs_offset)
-      : index(index), intersection(std::move(intersection)), length(length), valid(valid),
+      : index(index), intersection(intersection), length(length), valid(valid),
         offset(offset), abs_offset(abs_offset) {};
 };
 

From 212982033706fd6b5a6e5c182942de64e4cbbd5b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Sep 2025 12:21:49 +0200
Subject: [PATCH 0659/1827] Add limit_at_least function to boundary_iterator

---
 include/bout/boundary_iterator.hxx        | 6 ++++++
 include/bout/parallel_boundary_region.hxx | 8 ++++++++
 2 files changed, 14 insertions(+)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 601f6a8a28..118036256e 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -77,6 +77,12 @@ public:
     }
   }
 
+  void limit_at_least(Field3D& f, BoutReal value) const {
+    if (ynext(f) < value) {
+      ynext(f) = value;
+    }
+  }
+
   BoutReal& ynext(Field3D& f) const { return f[ind().yp(by).xp(bx)]; }
   const BoutReal& ynext(const Field3D& f) const { return f[ind().yp(by).xp(bx)]; }
   BoutReal& yprev(Field3D& f) const { return f[ind().yp(-by).xp(-bx)]; }
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 76a5cbe5d1..6ce078435c 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -223,6 +223,14 @@ public:
     }
   }
 
+  void limit_at_least(Field3D& f, BoutReal value) const {
+    ITER() {
+      if (getAt(f, i) < value) {
+        getAt(f, i) = value;
+      }
+    }
+  }
+
   // NB: value needs to be scaled by dy
   // neumann_o1 is actually o2 if we would use an appropriate one-sided stencil.
   // But in general we do not, and thus for normal C2 stencils, this is 1st order.

From 7fc08a34de5cfb65ef8849328297dcbb5eaba96d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Oct 2025 11:11:33 +0200
Subject: [PATCH 0660/1827] Interpolate sheath is at least o2

---
 include/bout/parallel_boundary_region.hxx |  6 ++++-
 src/field/field3d.cxx                     | 27 ++++++++++++++++++++++-
 2 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 6ce078435c..f74bf35bd8 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -142,7 +142,11 @@ public:
     return ythis(f) * (1 + length()) - yprev(f) * length();
   }
 
-  inline BoutReal interpolate_sheath_o1(const Field3D& f) const {
+  inline BoutReal interpolate_sheath_o2(const Field3D& f) const {
+    return ythis(f) * (1 - length()) + ynext(f) * length();
+  }
+  inline BoutReal
+  interpolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return ythis(f) * (1 - length()) + ynext(f) * length();
   }
 
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index fe9fdc9263..146b36da42 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -445,7 +445,32 @@ void Field3D::setBoundaryTo(const Field3D& f3d) {
 
   allocate(); // Make sure data allocated
 
-  /// Loop over boundary regions
+  if (isFci()) {
+    ASSERT1(f3d.hasParallelSlices());
+    if (copyParallelSlices) {
+      splitParallelSlices();
+      for (int i = 0; i < fieldmesh->ystart; ++i) {
+        yup(i) = f3d.yup(i);
+        ydown(i) = f3d.ydown(i);
+      }
+    } else {
+      // Set yup/ydown using midpoint values from f3d
+      ASSERT1(hasParallelSlices());
+
+      for (auto& region : fieldmesh->getBoundariesPar()) {
+        for (const auto& pnt : *region) {
+          // Interpolate midpoint value in f3d
+          const BoutReal val = pnt.interpolate_sheath_o2(f3d);
+          // Set the same boundary value in this field
+          pnt.dirichlet_o1(*this, val);
+        }
+      }
+    }
+  }
+
+  // Non-FCI.
+  // Transform to field-aligned coordinates?
+  // Loop over boundary regions
   for (const auto& reg : fieldmesh->getBoundaries()) {
     /// Loop within each region
     for (reg->first(); !reg->isDone(); reg->next()) {

From e135545f2f8d9fcbe997e21fc4892216c98f046e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Oct 2025 14:00:31 +0200
Subject: [PATCH 0661/1827] Interpolate sheath is at least o2

---
 include/bout/boundary_iterator.hxx           | 2 +-
 manual/sphinx/user_docs/boundary_options.rst | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 118036256e..3504e2f967 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -43,7 +43,7 @@ public:
     return 2 * f(0, ind()) - f(0, ind().yp(-by).xp(-bx));
   }
 
-  BoutReal interpolate_sheath_o1(const Field3D& f) const {
+  BoutReal interpolate_sheath_o2(const Field3D& f) const {
     return (f[ind()] + ynext(f)) * 0.5;
   }
   BoutReal
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 18535c91b4..9f9df6736c 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -503,7 +503,7 @@ geometries, as flux coordinate independent (FCI) method::
       void rhs() {
         BoutReal totalFlux = 0;
         yboundary.iter_pnts([&](auto& pnt) {
-          BoutReal flux = pnt.interpolate_sheath_o1(N) * pnt.interpolate_sheath_o1(V);
+          BoutReal flux = pnt.interpolate_sheath_o2(N) * pnt.interpolate_sheath_o2(V);
         });
       }
     
@@ -537,7 +537,7 @@ Here is a short summary of some members of ``pnt``, where ``f`` is a :
    * - ``pnt.yprev(f)``
      - Returns the value at the second to last point in the domain, if it is
        valid. NB: this point may not be valid.
-   * - ``pnt.interpolate_sheath_o1(f)``
+   * - ``pnt.interpolate_sheath_o2(f)``
      - Returns the value at the boundary, assuming the bounday value has been set
    * - ``pnt.extrapolate_sheath_o1(f)``
      - Returns the value at the boundary, extrapolating from the bulk, first order

From 73e418302ec46c74fad42da0dca1f0807e747126 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Oct 2025 16:16:39 +0200
Subject: [PATCH 0662/1827] Add limitFreeScale and SheathLimitMode

---
 include/bout/parallel_boundary_region.hxx | 67 ++++++++++++++---------
 1 file changed, 42 insertions(+), 25 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index f74bf35bd8..370175dd7e 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -15,6 +15,8 @@
  *
  */
 
+BOUT_ENUM_CLASS(SheathLimitMode, limit_free, exponential_free, linear_free);
+
 namespace bout {
 namespace parallel_boundary_region {
 
@@ -47,6 +49,42 @@ using IndicesVec = std::vector<Indices>;
 using IndicesIter = IndicesVec::iterator;
 using IndicesIterConst = IndicesVec::const_iterator;
 
+/// Limited free gradient of log of a quantity
+/// This ensures that the guard cell values remain positive
+/// while also ensuring that the quantity never increases
+///
+///  fm  fc | fp
+///         ^ boundary
+///
+/// exp( 2*log(fc) - log(fm) )
+inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, SheathLimitMode mode) {
+  if ((fm < fc) && (mode == SheathLimitMode::limit_free)) {
+    return fc; // Neumann rather than increasing into boundary
+  }
+  if (fm < 1e-10) {
+    return fc; // Low / no density condition
+  }
+
+  BoutReal fp = 0;
+  switch (mode) {
+  case SheathLimitMode::limit_free:
+  case SheathLimitMode::exponential_free:
+    fp = SQ(fc) / fm; // Exponential
+    break;
+  case SheathLimitMode::linear_free:
+    fp = 2.0 * fc - fm; // Linear
+    break;
+  }
+
+#if CHECKLEVEL >= 2
+  if (!std::isfinite(fp)) {
+    throw BoutException("SheathBoundary limitFree: {}, {} -> {}", fm, fc, fp);
+  }
+#endif
+
+  return fp;
+}
+
 inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc) {
   if (fm < fc) {
     return 1; // Neumann rather than increasing into boundary
@@ -74,31 +112,10 @@ class BoundaryRegionPar : public BoundaryRegionBase {
   IndicesIter bndry_position;
 
 public:
-  BoundaryRegionPar(const std::string& name, int dir, Mesh* passmesh)
-      : BoundaryRegionBase(name, passmesh), dir(dir) {
-    ASSERT0(std::abs(dir) == 1);
-    BoundaryRegionBase::isParallel = true;
-  }
-  BoundaryRegionPar(const std::string& name, BndryLoc loc, int dir, Mesh* passmesh)
-      : BoundaryRegionBase(name, loc, passmesh), dir(dir) {
-    BoundaryRegionBase::isParallel = true;
-    ASSERT0(std::abs(dir) == 1);
-  }
-
-  /// Add a point to the boundary
-  void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
-                 signed char valid) {
-    bndry_points.emplace_back({ind, {x, y, z}, length, valid});
-  }
-  void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
-                 BoutReal length, signed char valid) {
-    bndry_points.emplace_back({xyz2ind(ix, iy, iz, localmesh), {x, y, z}, length, valid});
-  }
-
-  // final, so they can be inlined
-  void first() final { bndry_position = begin(bndry_points); }
-  void next() final { ++bndry_position; }
-  bool isDone() final { return (bndry_position == end(bndry_points)); }
+  BoundaryRegionParIterBase(IndicesVec& bndry_points, IndicesIter bndry_position, int dir,
+                            Mesh* localmesh)
+      : bndry_points(bndry_points), bndry_position(bndry_position), dir(dir),
+        localmesh(localmesh) {};
 
   // getter
   Ind3D ind() const { return bndry_position->index; }

From 4c105b833f7282c43184f31422207c8128b4aad7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Oct 2025 16:17:23 +0200
Subject: [PATCH 0663/1827] Add extrapolate_sheath_free

---
 include/bout/boundary_iterator.hxx        | 8 ++++++++
 include/bout/parallel_boundary_region.hxx | 8 ++++++++
 2 files changed, 16 insertions(+)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 3504e2f967..2f05f0c82e 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -51,6 +51,14 @@ public:
     return 0.5 * (3 * f(0, ind()) - f(0, ind().yp(-by).xp(-bx)));
   }
 
+  BoutReal extrapolate_sheath_free(const Field3D& f, SheathLimitMode mode) const {
+    const BoutReal fac =
+        bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
+    BoutReal val = ythis(f);
+    BoutReal next = mode == SheathLimitMode::linear_free ? val + fac : val * fac;
+    return 0.5 * (val + next);
+  }
+
   void limitFree(Field3D& f) const {
     const BoutReal fac =
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f));
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 370175dd7e..8b10eccca6 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -291,6 +291,14 @@ public:
     }
   }
 
+  BoutReal extrapolate_sheath_free(const Field3D& f, SheathLimitMode mode) const {
+    const auto fac = valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
+                                 : (mode == SheathLimitMode::linear_free ? 0 : 1);
+    auto val = ythis(f);
+    BoutReal next = mode == SheathLimitMode::linear_free ? val + fac : val * fac;
+    return val * length() + next * (1 - length());
+  }
+
   void setAll(Field3D& f, const BoutReal val) const {
     for (int i = -localmesh->ystart; i <= localmesh->ystart; ++i) {
       f.ynext(i)[ind().yp(i)] = val;

From 41f9b2844d3de90b924486d0946c5e89e56ff8f1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Oct 2025 16:17:34 +0200
Subject: [PATCH 0664/1827] Add set_free

---
 include/bout/boundary_iterator.hxx        | 17 +++++++++++++++++
 include/bout/parallel_boundary_region.hxx | 17 +++++++++++++++++
 2 files changed, 34 insertions(+)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 2f05f0c82e..7c162ab0bd 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -59,6 +59,23 @@ public:
     return 0.5 * (val + next);
   }
 
+  void set_free(Field3D& f, SheathLimitMode mode) const {
+    const BoutReal fac =
+        bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
+    BoutReal val = ythis(f);
+    if (mode == SheathLimitMode::linear_free) {
+      for (int i = 1; i <= localmesh->ystart; ++i) {
+        val += fac;
+        f[ind().yp(by * i).xp(bx * i)] = val;
+      }
+    } else {
+      for (int i = 1; i <= localmesh->ystart; ++i) {
+        val *= fac;
+        f[ind().yp(by * i).xp(bx * i)] = val;
+      }
+    }
+  }
+
   void limitFree(Field3D& f) const {
     const BoutReal fac =
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f));
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 8b10eccca6..ccefc277a4 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -299,6 +299,23 @@ public:
     return val * length() + next * (1 - length());
   }
 
+  void set_free(Field3D& f, SheathLimitMode mode) const {
+    const auto fac = valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
+                                 : (mode == SheathLimitMode::linear_free ? 0 : 1);
+    auto val = ythis(f);
+    if (mode == SheathLimitMode::linear_free) {
+      ITER() {
+        val += fac;
+        getAt(f, i) = val;
+      }
+    } else {
+      ITER() {
+        val *= fac;
+        getAt(f, i) = val;
+      }
+    }
+  }
+
   void setAll(Field3D& f, const BoutReal val) const {
     for (int i = -localmesh->ystart; i <= localmesh->ystart; ++i) {
       f.ynext(i)[ind().yp(i)] = val;

From e1364b3c81a8d642ed0caedaec3d3ef00298ddbd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Oct 2025 11:11:34 +0200
Subject: [PATCH 0665/1827] add missing interpolate_sheath_o2(func) to FA

---
 include/bout/boundary_iterator.hxx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 7c162ab0bd..9e2ff04588 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -46,6 +46,12 @@ public:
   BoutReal interpolate_sheath_o2(const Field3D& f) const {
     return (f[ind()] + ynext(f)) * 0.5;
   }
+
+  BoutReal
+  interpolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+    return (f(0, ind()) + f(0, ind().yp(-by).xp(-bx))) * 0.5;
+  }
+
   BoutReal
   extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return 0.5 * (3 * f(0, ind()) - f(0, ind().yp(-by).xp(-bx)));

From 2edebb3a19d29b40d8e985557013a92957d1a917 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Oct 2025 11:12:06 +0200
Subject: [PATCH 0666/1827] add is_lower() to check for which direction the
 boundary is

---
 include/bout/boundary_iterator.hxx        | 5 +++++
 include/bout/parallel_boundary_region.hxx | 2 ++
 2 files changed, 7 insertions(+)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 9e2ff04588..728c2e1cb0 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -92,6 +92,11 @@ public:
     }
   }
 
+  bool is_lower() const {
+    ASSERT2(bx == 0);
+    return by == -1;
+  }
+
   void neumann_o1(Field3D& f, BoutReal grad) const {
     BoutReal val = ythis(f);
     for (int i = 1; i <= localmesh->ystart; ++i) {
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index ccefc277a4..c93c5b680d 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -252,6 +252,8 @@ public:
     }
   }
 
+  bool is_lower() const { return dir == -1; }
+
   // NB: value needs to be scaled by dy
   // neumann_o1 is actually o2 if we would use an appropriate one-sided stencil.
   // But in general we do not, and thus for normal C2 stencils, this is 1st order.

From 382120525f105cf3595bea311a519cb99a049b28 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 21 Jan 2026 13:04:44 +0100
Subject: [PATCH 0667/1827] Only call iterateBndryLowerY() for non-FCI

---
 src/mesh/impls/bout/boutmesh.cxx | 33 ++++++++++++++++++--------------
 1 file changed, 19 insertions(+), 14 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 99ec63ff25..2f88e86cb4 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -620,23 +620,28 @@ int BoutMesh::load() {
   // Add boundary regions
   addBoundaryRegions();
 
-  // Set cached values
-  {
-    int mybndry = static_cast<int>(!(iterateBndryLowerY().isDone()));
-    int allbndry = 0;
-    mpi->MPI_Allreduce(&mybndry, &allbndry, 1, MPI_INT, MPI_BOR, getXcomm(yend));
-    has_boundary_lower_y = static_cast<bool>(allbndry);
-  }
-  {
-    int mybndry = static_cast<int>(!(iterateBndryUpperY().isDone()));
-    int allbndry = 0;
-    mpi->MPI_Allreduce(&mybndry, &allbndry, 1, MPI_INT, MPI_BOR, getXcomm(ystart));
-    has_boundary_upper_y = static_cast<bool>(allbndry);
-  }
-
   // Initialize default coordinates
   getCoordinates();
 
+  // Set cached values
+  if (isFci()) {
+    has_boundary_lower_y = false;
+    has_boundary_upper_y = false;
+  } else {
+    {
+      int mybndry = static_cast<int>(!(iterateBndryLowerY().isDone()));
+      int allbndry = 0;
+      mpi->MPI_Allreduce(&mybndry, &allbndry, 1, MPI_INT, MPI_BOR, getXcomm(yend));
+      has_boundary_lower_y = static_cast<bool>(allbndry);
+    }
+    {
+      int mybndry = static_cast<int>(!(iterateBndryUpperY().isDone()));
+      int allbndry = 0;
+      mpi->MPI_Allreduce(&mybndry, &allbndry, 1, MPI_INT, MPI_BOR, getXcomm(ystart));
+      has_boundary_upper_y = static_cast<bool>(allbndry);
+    }
+  }
+
   output_info.write(_("\tdone\n"));
 
   return 0;

From 38293b9467c74c59911c9baf8574c409cd3dfe83 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 10:57:15 +0100
Subject: [PATCH 0668/1827] Break include cycle

---
 include/bout/boundary_region.hxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 22956d1d4a..b73c2e5a02 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -4,7 +4,6 @@ class BoundaryRegion;
 #ifndef BOUT_BNDRY_REGION_H
 #define BOUT_BNDRY_REGION_H
 
-#include "bout/mesh.hxx"
 #include "bout/region.hxx"
 #include "bout/sys/parallel_stencils.hxx"
 #include <string>

From 6ae2351403dfb782dabec87f34446ebe45deb3ef Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 08:12:08 +0100
Subject: [PATCH 0669/1827] Fix Field3D::setBoundaryTo for FCI methods

Without this fix, boundary conditions set on yup/down fields are not
applied when a boundary is copied from one field to another.
---
 src/field/field3d.cxx | 27 ++++++++++-----------------
 1 file changed, 10 insertions(+), 17 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 146b36da42..419fb05a2b 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -446,26 +446,19 @@ void Field3D::setBoundaryTo(const Field3D& f3d) {
   allocate(); // Make sure data allocated
 
   if (isFci()) {
+    // Set yup/ydown using midpoint values from f3d
     ASSERT1(f3d.hasParallelSlices());
-    if (copyParallelSlices) {
-      splitParallelSlices();
-      for (int i = 0; i < fieldmesh->ystart; ++i) {
-        yup(i) = f3d.yup(i);
-        ydown(i) = f3d.ydown(i);
-      }
-    } else {
-      // Set yup/ydown using midpoint values from f3d
-      ASSERT1(hasParallelSlices());
-
-      for (auto& region : fieldmesh->getBoundariesPar()) {
-        for (const auto& pnt : *region) {
-          // Interpolate midpoint value in f3d
-          const BoutReal val = pnt.interpolate_sheath_o2(f3d);
-          // Set the same boundary value in this field
-          pnt.dirichlet_o1(*this, val);
-        }
+    ASSERT1(hasParallelSlices());
+
+    for (auto& region : fieldmesh->getBoundariesPar()) {
+      for (const auto& pnt : *region) {
+        // Interpolate midpoint value in f3d
+        const BoutReal val = pnt.interpolate_sheath_o2(f3d);
+        // Set the same boundary value in this field
+        pnt.dirichlet_o2(*this, val);
       }
     }
+    return;
   }
 
   // Non-FCI.

From 576c609d779ddaa6733d24bb1558d9c3e28ad897 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 25 Nov 2024 16:44:29 +0100
Subject: [PATCH 0670/1827] Copy BCs in x-direction also for FCI

---
 src/field/field3d.cxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 419fb05a2b..9c59d32bd0 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -458,13 +458,15 @@ void Field3D::setBoundaryTo(const Field3D& f3d) {
         pnt.dirichlet_o2(*this, val);
       }
     }
-    return;
   }
 
   // Non-FCI.
   // Transform to field-aligned coordinates?
   // Loop over boundary regions
   for (const auto& reg : fieldmesh->getBoundaries()) {
+    if (isFci() && reg->by != 0) {
+      continue;
+    }
     /// Loop within each region
     for (reg->first(); !reg->isDone(); reg->next()) {
       for (int z = 0; z < nz; z++) {

From 1b99b34fb771022d7512c44fe4dfd533b809612e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 25 Nov 2024 16:48:06 +0100
Subject: [PATCH 0671/1827] Use consistently first order interpolation

---
 src/field/field3d.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 9c59d32bd0..9bda64dd32 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -455,7 +455,7 @@ void Field3D::setBoundaryTo(const Field3D& f3d) {
         // Interpolate midpoint value in f3d
         const BoutReal val = pnt.interpolate_sheath_o2(f3d);
         // Set the same boundary value in this field
-        pnt.dirichlet_o2(*this, val);
+        pnt.dirichlet_o1(*this, val);
       }
     }
   }

From ff190e8f19fa8fa99544f08281abaa0fade5b2a9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 08:12:54 +0100
Subject: [PATCH 0672/1827] Add option to copy parallel slices at setBoundaryTo

---
 include/bout/field3d.hxx |  3 ++-
 src/field/field3d.cxx    | 28 ++++++++++++++++++----------
 2 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index c6e1d1191d..57f8c559bd 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -496,7 +496,8 @@ public:
   /// This uses 2nd order central differences to set the value
   /// on the boundary to the value on the boundary in field \p f3d.
   /// Note: does not just copy values in boundary region.
-  void setBoundaryTo(const Field3D& f3d);
+  void setBoundaryTo(const Field3D& f3d) { setBoundaryTo(f3d, true); }
+  void setBoundaryTo(const Field3D& f3d, bool copyParallelSlices);
 
   using FieldData::applyParallelBoundary;
   void applyParallelBoundary() override;
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 9bda64dd32..6171cc1061 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -439,23 +439,31 @@ void Field3D::applyTDerivBoundary() {
   }
 }
 
-void Field3D::setBoundaryTo(const Field3D& f3d) {
+void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
 
   checkData(f3d);
 
   allocate(); // Make sure data allocated
 
   if (isFci()) {
-    // Set yup/ydown using midpoint values from f3d
     ASSERT1(f3d.hasParallelSlices());
-    ASSERT1(hasParallelSlices());
-
-    for (auto& region : fieldmesh->getBoundariesPar()) {
-      for (const auto& pnt : *region) {
-        // Interpolate midpoint value in f3d
-        const BoutReal val = pnt.interpolate_sheath_o2(f3d);
-        // Set the same boundary value in this field
-        pnt.dirichlet_o1(*this, val);
+    if (copyParallelSlices) {
+      splitParallelSlices();
+      for (int i = 0; i < fieldmesh->ystart; ++i) {
+        yup(i) = f3d.yup(i);
+        ydown(i) = f3d.ydown(i);
+      }
+    } else {
+      // Set yup/ydown using midpoint values from f3d
+      ASSERT1(hasParallelSlices());
+
+      for (auto& region : fieldmesh->getBoundariesPar()) {
+        for (const auto& pnt : *region) {
+          // Interpolate midpoint value in f3d
+          const BoutReal val = pnt.interpolate_sheath_o2(f3d);
+          // Set the same boundary value in this field
+          pnt.dirichlet_o1(*this, val);
+        }
       }
     }
   }

From 6aac8345434cb9301b982e3fa573a59e8738b5ac Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:43:22 +0100
Subject: [PATCH 0673/1827] Prefer [[maybe_unused]]

---
 include/bout/sys/parallel_stencils.hxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/sys/parallel_stencils.hxx b/include/bout/sys/parallel_stencils.hxx
index 34a51c5285..1d55931ff3 100644
--- a/include/bout/sys/parallel_stencils.hxx
+++ b/include/bout/sys/parallel_stencils.hxx
@@ -11,15 +11,15 @@ inline BoutReal pow(BoutReal val, int exp) {
   ASSERT3(exp == 3);
   return val * val * val;
 }
-inline BoutReal dirichlet_o1(BoutReal UNUSED(spacing0), BoutReal value0) {
+inline BoutReal dirichlet_o1([[maybe_unused]] BoutReal spacing0, BoutReal value0) {
   return value0;
 }
 inline BoutReal dirichlet_o2(BoutReal spacing0, BoutReal value0, BoutReal spacing1,
                              BoutReal value1) {
   return (spacing0 * value1 - spacing1 * value0) / (spacing0 - spacing1);
 }
-inline BoutReal neumann_o2(BoutReal UNUSED(spacing0), BoutReal value0, BoutReal spacing1,
-                           BoutReal value1) {
+inline BoutReal neumann_o2([[maybe_unused]] BoutReal spacing0, BoutReal value0,
+                           BoutReal spacing1, BoutReal value1) {
   return -spacing1 * value0 + value1;
 }
 inline BoutReal dirichlet_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1,

From d5fb4c4f1899061fae855068042d28d1097659c9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 12:42:44 +0100
Subject: [PATCH 0674/1827] Fixup parallel_boundary

---
 include/bout/parallel_boundary_op.hxx     | 41 +++++++++++++----------
 include/bout/parallel_boundary_region.hxx | 23 +++----------
 src/mesh/parallel/fci.cxx                 |  7 ++++
 src/mesh/parallel_boundary_op.cxx         |  9 +++--
 4 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index d8620e892b..9e551ebc17 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -49,7 +49,7 @@ protected:
   enum class ValueType { GEN, FIELD, REAL };
   const ValueType value_type{ValueType::REAL};
 
-  BoutReal getValue(const BoundaryRegionPar& bndry, BoutReal t);
+  BoutReal getValue(const BoundaryRegionParIter& bndry, BoutReal t);
 };
 
 template <class T, bool isNeumann = false>
@@ -95,12 +95,13 @@ public:
 
     auto dy = f.getCoordinates()->dy;
 
-    for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      BoutReal value = getValue(*bndry, t);
+    for (auto pnt : *bndry) {
+      //for (bndry->first(); !bndry->isDone(); bndry->next()) {
+      BoutReal value = getValue(pnt, t);
       if (isNeumann) {
-        value *= dy[bndry->ind()];
+        value *= dy[pnt.ind()];
       }
-      static_cast<T*>(this)->apply_stencil(f, bndry, value);
+      static_cast<T*>(this)->apply_stencil(f, pnt, value);
     }
   }
 };
@@ -111,24 +112,27 @@ public:
 class BoundaryOpPar_dirichlet_o1 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o1> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) {
-    bndry->dirichlet_o1(f, value);
+  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+                            BoutReal value) {
+    pnt.dirichlet_o1(f, value);
   }
 };
 
 class BoundaryOpPar_dirichlet_o2 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o2> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) {
-    bndry->dirichlet_o2(f, value);
+  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+                            BoutReal value) {
+    pnt.dirichlet_o2(f, value);
   }
 };
 
 class BoundaryOpPar_dirichlet_o3 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o3> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) {
-    bndry->dirichlet_o3(f, value);
+  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+                            BoutReal value) {
+    pnt.dirichlet_o3(f, value);
   }
 };
 
@@ -136,8 +140,9 @@ class BoundaryOpPar_neumann_o1
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o1, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) {
-    bndry->neumann_o1(f, value);
+  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+                            BoutReal value) {
+    pnt.neumann_o1(f, value);
   }
 };
 
@@ -145,8 +150,9 @@ class BoundaryOpPar_neumann_o2
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o2, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) {
-    bndry->neumann_o2(f, value);
+  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+                            BoutReal value) {
+    pnt.neumann_o2(f, value);
   }
 };
 
@@ -154,8 +160,9 @@ class BoundaryOpPar_neumann_o3
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o3, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionPar* bndry, BoutReal value) {
-    bndry->neumann_o3(f, value);
+  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+                            BoutReal value) {
+    pnt.neumann_o3(f, value);
   }
 };
 
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index c93c5b680d..3caa98767e 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -3,6 +3,7 @@
 
 #include "bout/boundary_region.hxx"
 #include "bout/bout_types.hxx"
+#include <functional>
 #include <vector>
 
 #include "bout/sys/parallel_stencils.hxx"
@@ -101,15 +102,8 @@ inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc) {
   return fp;
 }
 
-class BoundaryRegionPar : public BoundaryRegionBase {
-
-  using IndicesVec = std::vector<Indices>;
-  using IndicesIter = IndicesVec::iterator;
-
-  /// Vector of points in the boundary
-  IndicesVec bndry_points;
-  /// Current position in the boundary points
-  IndicesIter bndry_position;
+template <class IndicesVec, class IndicesIter>
+class BoundaryRegionParIterBase {
 
 public:
   BoundaryRegionParIterBase(IndicesVec& bndry_points, IndicesIter bndry_position, int dir,
@@ -130,22 +124,15 @@ public:
   // setter
   void setValid(signed char valid) { bndry_position->valid = valid; }
 
-  bool contains(const BoundaryRegionPar& bndry) const {
-    return std::binary_search(
-        begin(bndry_points), end(bndry_points), *bndry.bndry_position,
-        [](const Indices& i1, const Indices& i2) { return i1.index < i2.index; });
-  }
-
   // extrapolate a given point to the boundary
   BoutReal extrapolate_sheath_o1(const Field3D& f) const { return ythis(f); }
   BoutReal extrapolate_sheath_o2(const Field3D& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
-      return extrapolate_o1(f);
+      return extrapolate_sheath_o1(f);
     }
     return ythis(f) * (1 + length()) - yprev(f) * length();
   }
-
   inline BoutReal
   extrapolate_sheath_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return ythis(f);
@@ -184,7 +171,7 @@ public:
   extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
-      return extrapolate_sheath_o1(f);
+      return extrapolate_next_o1(f);
     }
     return ythis(f) * 2 - yprev(f);
   }
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index d3fcc8d04c..28b8db9326 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -62,6 +62,13 @@
 #include <string>
 #include <string_view>
 
+namespace {
+template <typename T>
+int sgn(T val) {
+  return (T(0) < val) - (val < T(0));
+}
+} // namespace
+
 using namespace std::string_view_literals;
 
 FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx
index ebd9852791..644331221e 100644
--- a/src/mesh/parallel_boundary_op.cxx
+++ b/src/mesh/parallel_boundary_op.cxx
@@ -1,21 +1,20 @@
 #include "bout/parallel_boundary_op.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/constants.hxx"
 #include "bout/field_factory.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
 #include "bout/output.hxx"
+#include "bout/parallel_boundary_region.hxx"
 
-BoutReal BoundaryOpPar::getValue(const BoundaryRegionPar& bndry, BoutReal t) {
-  BoutReal value;
-
+BoutReal BoundaryOpPar::getValue(const BoundaryRegionParIter& bndry, BoutReal t) {
   switch (value_type) {
   case ValueType::GEN:
     return gen_values->generate(bout::generator::Context(
         bndry.s_x(), bndry.s_y(), bndry.s_z(), CELL_CENTRE, bndry.localmesh, t));
   case ValueType::FIELD:
     // FIXME: Interpolate to s_x, s_y, s_z...
-    value = (*field_values)[bndry.ind()];
-    return value;
+    return (*field_values)[bndry.ind()];
   case ValueType::REAL:
     return real_value;
   default:

From 4b503c5cf0af017935ef6188638b3d8c4e30b81f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 6 Mar 2026 14:47:34 +0100
Subject: [PATCH 0675/1827] Ensure init is only called once

---
 include/bout/yboundary_regions.hxx | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 1d434e2420..deef2257ba 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -38,6 +38,12 @@ public:
   }
 
   void init(Options& options, Mesh* mesh = nullptr) {
+    if (is_init) {
+      if (optptr == &options) {
+        return;
+      }
+      throw BoutException("YBoundary is already initialised!");
+    }
     if (mesh == nullptr) {
       mesh = bout::globals::mesh;
     }
@@ -70,6 +76,7 @@ public:
       }
     }
     is_init = true;
+    optptr = &options;
   }
 
 private:
@@ -77,4 +84,5 @@ private:
   std::vector<std::shared_ptr<NewBoundaryRegionY>> boundary_regions;
 
   bool is_init{false};
+  Options* optptr;
 };

From e9a0944c65b043db4dfbc2f8211d6f09847cccd9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 9 Mar 2026 11:58:36 +0100
Subject: [PATCH 0676/1827] Add headers from clang-tidy

---
 include/bout/boundary_iterator.hxx        | 8 ++++++++
 include/bout/parallel_boundary_region.hxx | 6 ++++++
 include/bout/yboundary_regions.hxx        | 6 ++++++
 3 files changed, 20 insertions(+)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 728c2e1cb0..e3ecf8234b 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -1,9 +1,17 @@
 #pragma once
 
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/build_defines.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
 #include "bout/parallel_boundary_region.hxx"
 #include "bout/sys/parallel_stencils.hxx"
 #include "bout/sys/range.hxx"
+#include <algorithm>
+#include <functional>
+#include <utility>
 
 class BoundaryRegionIter {
 public:
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 3caa98767e..ca1437782f 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -3,9 +3,15 @@
 
 #include "bout/boundary_region.hxx"
 #include "bout/bout_types.hxx"
+#include <algorithm>
+#include <cmath>
+#include <cstdlib>
 #include <functional>
 #include <vector>
 
+#include "bout/build_defines.hxx"
+#include "bout/field2d.hxx"
+#include "bout/region.hxx"
 #include "bout/sys/parallel_stencils.hxx"
 #include <bout/field3d.hxx>
 #include <bout/mesh.hxx>
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index deef2257ba..74a68377c9 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -1,7 +1,13 @@
 #pragma once
 
 #include "./boundary_iterator.hxx"
+#include "bout/assert.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/globals.hxx"
+#include "bout/options.hxx"
 #include "bout/parallel_boundary_region.hxx"
+#include <memory>
+#include <vector>
 
 /// This class allows to simplify iterating over y-boundaries.
 ///

From 92d03c1c1dd6c49350ef6cbee42b931a34cfec47 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Feb 2026 13:53:10 +0100
Subject: [PATCH 0677/1827] Do not rely on valid region being set

---
 src/sys/options.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 0a68bab124..c17abb3541 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -364,8 +364,8 @@ void saveParallel(Options& opt, const std::string& name, const Field3D& tosave)
       Field3D tmp;
       tmp.allocate();
       const auto& fpar = tosave.ynext(i);
-      for (auto j : fpar.getValidRegionWithDefault("RGN_NO_BOUNDARY")) {
-        tmp[j.yp(-i)] = fpar[j];
+      for (auto j : tmp.getRegion("RGN_NOY")) {
+        tmp[j] = fpar[j.yp(i)];
       }
       opt[fmt::format("{}_y{:+d}", name, i)] = tmp;
     }

From 201a969ff45a6503affbd8b6d3b2a7cbd21d1a7f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Feb 2026 14:00:48 +0100
Subject: [PATCH 0678/1827] Ignore if field is not allocated

---
 src/sys/options.cxx | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index c17abb3541..e864e0cbed 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -364,10 +364,18 @@ void saveParallel(Options& opt, const std::string& name, const Field3D& tosave)
       Field3D tmp;
       tmp.allocate();
       const auto& fpar = tosave.ynext(i);
-      for (auto j : tmp.getRegion("RGN_NOY")) {
-        tmp[j] = fpar[j.yp(i)];
+      if (fpar.isAllocated()) {
+        for (auto j : tmp.getRegion("RGN_NOY")) {
+          tmp[j] = fpar[j.yp(i)];
+        }
+        opt[fmt::format("{}_y{:+d}", name, i)] = tmp;
+      } else {
+        if (tosave.isFci()) { // likely an error
+          throw BoutException(
+              "Tried to save parallel fields - but parallel field {i} is not allocated",
+              i);
+        }
       }
-      opt[fmt::format("{}_y{:+d}", name, i)] = tmp;
     }
   }
 }

From c59626a0498b0cfd1be46f84f0fa38b4855a43cc Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Tue, 10 Mar 2026 07:25:19 +0000
Subject: [PATCH 0679/1827] [bot] Apply format changes

---
 include/bout/parallel_boundary_region.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index ca1437782f..dbefeb60e6 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -49,7 +49,7 @@ struct Indices {
   Indices(Ind3D index, RealPoint&& intersection, BoutReal length, signed char valid,
           signed char offset, unsigned char abs_offset)
       : index(index), intersection(intersection), length(length), valid(valid),
-        offset(offset), abs_offset(abs_offset) {};
+        offset(offset), abs_offset(abs_offset){};
 };
 
 using IndicesVec = std::vector<Indices>;
@@ -115,7 +115,7 @@ public:
   BoundaryRegionParIterBase(IndicesVec& bndry_points, IndicesIter bndry_position, int dir,
                             Mesh* localmesh)
       : bndry_points(bndry_points), bndry_position(bndry_position), dir(dir),
-        localmesh(localmesh) {};
+        localmesh(localmesh){};
 
   // getter
   Ind3D ind() const { return bndry_position->index; }

From a1647993b69c280b6e554ab1af801a80a3c46378 Mon Sep 17 00:00:00 2001
From: David Bold <dschwoerer@users.noreply.github.com>
Date: Mon, 9 Mar 2026 11:54:50 +0100
Subject: [PATCH 0680/1827] Use fmt syntax, not python f-string

---
 src/sys/options.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index e864e0cbed..7c6f36f85a 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -372,7 +372,7 @@ void saveParallel(Options& opt, const std::string& name, const Field3D& tosave)
       } else {
         if (tosave.isFci()) { // likely an error
           throw BoutException(
-              "Tried to save parallel fields - but parallel field {i} is not allocated",
+              "Tried to save parallel fields - but parallel field {} is not allocated",
               i);
         }
       }

From 2c4179d9510854f45408d57ba5e9ba230e2e368d Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Tue, 10 Mar 2026 07:30:38 +0000
Subject: [PATCH 0681/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 84be8e384a..44192ad222 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -14,3 +14,4 @@ c8f38049359170a34c915e209276238ea66b9a1e
 8d5cb39e03c2644715a50684f8cd0318b4e82676
 ec69e8838be2dde140a915e50506f8e1ce3cb534
 f2bc0488a298f136294c523bc5ab4086d090059b
+c59626a0498b0cfd1be46f84f0fa38b4855a43cc

From cc4fd33681603f024c45eaa46f0c70c4e282a59f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 13:46:44 +0200
Subject: [PATCH 0682/1827] Set parallel region by default

---
 src/field/field3d.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index fe9fdc9263..bd8b831606 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -143,7 +143,9 @@ void Field3D::splitParallelSlices() {
     // Note the fields constructed here will be fully overwritten by the
     // ParallelTransform, so we don't need a full constructor
     yup_fields.emplace_back(fieldmesh);
+    yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", i + 1));
     ydown_fields.emplace_back(fieldmesh);
+    yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", -i - 1));
   }
 }
 

From e4c7d986be427fd3e40a713b6994eee9ce8aacd2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 26 Sep 2024 09:05:41 +0200
Subject: [PATCH 0683/1827] Only set region of parallel fields for FCI

---
 src/field/field3d.cxx | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index bd8b831606..01c2dcc2e7 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -143,9 +143,11 @@ void Field3D::splitParallelSlices() {
     // Note the fields constructed here will be fully overwritten by the
     // ParallelTransform, so we don't need a full constructor
     yup_fields.emplace_back(fieldmesh);
-    yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", i + 1));
     ydown_fields.emplace_back(fieldmesh);
-    yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", -i - 1));
+    if (isFci()) {
+      yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", i + 1));
+      yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", -i - 1));
+    }
   }
 }
 

From 0cdf3e2b98d14407a03a88c73f5a6159b2abe88a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 20 Jan 2025 16:28:15 +0100
Subject: [PATCH 0684/1827] Fix split parallel slices

---
 src/field/field3d.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 01c2dcc2e7..0ad6d51ffa 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -146,7 +146,7 @@ void Field3D::splitParallelSlices() {
     ydown_fields.emplace_back(fieldmesh);
     if (isFci()) {
       yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", i + 1));
-      yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", -i - 1));
+      ydown_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", -i - 1));
     }
   }
 }

From 343fe342c7bd0d945eb0c3107e0deb51a4af0e02 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Sep 2025 14:56:53 +0200
Subject: [PATCH 0685/1827] add resetRegionParallel

to set default regions for parallel slices
---
 include/bout/field3d.hxx |  1 +
 src/field/field3d.cxx    | 10 ++++++++++
 2 files changed, 11 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index c6e1d1191d..54d9fb85c9 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -331,6 +331,7 @@ public:
   const Region<Ind3D>& getValidRegionWithDefault(const std::string& region_name) const;
   void setRegion(const std::string& region_name) override;
   void resetRegion() override { regionID.reset(); };
+  void resetRegionParallel();
   void setRegion(size_t id) override { regionID = id; };
   void setRegion(std::optional<size_t> id) override { regionID = id; };
   std::optional<size_t> getRegionID() const override { return regionID; };
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 0ad6d51ffa..1cf54a9900 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -845,6 +845,16 @@ void Field3D::setRegion(const std::string& region_name) {
   regionID = fieldmesh->getRegionID(region_name);
 }
 
+void Field3D::resetRegion() { regionID.reset(); };
+void Field3D::resetRegionParallel() {
+  if (isFci()) {
+    for (int i = 0; i < fieldmesh->ystart; ++i) {
+      yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", i + 1));
+      ydown_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", -i - 1));
+    }
+  }
+}
+
 Field3D& Field3D::enableTracking(const std::string& name,
                                  std::weak_ptr<Options> _tracking) {
   tracking = std::move(_tracking);

From e7592a848f8540b8189dea8ac69447c2d4676bcf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 10 Nov 2025 12:43:45 +0100
Subject: [PATCH 0686/1827] Move parallel region creation to defaultRegions

---
 src/mesh/mesh.cxx         |  6 ++++++
 src/mesh/parallel/fci.cxx | 10 ----------
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 8964a6b797..010e799b2b 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -654,6 +654,12 @@ void Mesh::createDefaultRegions() {
                                 + getRegion3D("RGN_YGUARDS") + getRegion3D("RGN_ZGUARDS"))
                                    .unique());
 
+  for (int offset_ = -ystart; offset_ <= ystart; ++offset_) {
+    const auto region = fmt::format("RGN_YPAR_{:+d}", offset_);
+    addRegion3D(region, Region<Ind3D>(xstart, xend, ystart + offset_, yend + offset_, 0,
+                                      LocalNz - 1, LocalNy, LocalNz));
+  }
+
   //2D regions
   addRegion2D("RGN_ALL", Region<Ind2D>(0, LocalNx - 1, 0, LocalNy - 1, 0, 0, LocalNy, 1,
                                        maxregionblocksize));
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 39654519af..152ffaed2d 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -261,16 +261,6 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
   region_no_boundary = region_no_boundary.mask(to_remove);
 
   interp->setRegion(region_no_boundary);
-
-  const auto region = fmt::format("RGN_YPAR_{:+d}", offset_);
-  if (not map_mesh->hasRegion3D(region)) {
-    // The valid region for this slice
-    map_mesh->addRegion3D(region, Region<Ind3D>(map_mesh->xstart, map_mesh->xend,
-                                                map_mesh->ystart + offset_,
-                                                map_mesh->yend + offset_, 0,
-                                                map_mesh->LocalNz - 1, map_mesh->LocalNy,
-                                                map_mesh->LocalNz));
-  }
 }
 
 Field3D FCIMap::integrate(Field3D& f) const {

From 051387583cfc5efa6719d505fd620cd6b65d1c4d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:04:50 +0100
Subject: [PATCH 0687/1827] Remove duplicate definition of resetRegion

---
 src/field/field3d.cxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 1cf54a9900..66a5dbfc18 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -845,7 +845,6 @@ void Field3D::setRegion(const std::string& region_name) {
   regionID = fieldmesh->getRegionID(region_name);
 }
 
-void Field3D::resetRegion() { regionID.reset(); };
 void Field3D::resetRegionParallel() {
   if (isFci()) {
     for (int i = 0; i < fieldmesh->ystart; ++i) {

From b8bfd3b2f9bcc1802431b6443be86792bb9b843e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 08:49:11 +0100
Subject: [PATCH 0688/1827] Rename to GlobalToLocal1D

---
 src/mesh/parallel/fci_comm.hxx | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 8c34885981..836ef9b89d 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -48,7 +48,7 @@ struct ProcLocal {
   int proc;
   int ind;
 };
-struct globalToLocal1D {
+struct GlobalToLocal1D {
   int mg;
   int npe;
   int localwith;
@@ -56,9 +56,9 @@ struct globalToLocal1D {
   int global;
   int globalwith;
   bool periodic;
-  globalToLocal1D(int mg, int npe, int localwith, bool periodic)
+  GlobalToLocal1D(int mg, int npe, int localwith, bool periodic)
       : mg(mg), npe(npe), localwith(localwith), local(localwith - (2 * mg)),
-        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic){};
+        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic) {};
   ProcLocal convert(int id) const {
     if (periodic) {
       while (id < mg) {
@@ -77,11 +77,17 @@ struct globalToLocal1D {
     }
     const int loc = id - (local * proc);
 #if CHECK > 1
-    if ((loc < 0 or loc > localwith or proc < 0 or proc >= npe)
-        or (periodic and (loc < mg or loc >= local + mg))) {
-      printf("globalToLocal1D failure: %d %d, %d %d, %d %d %s\n", id, idwo, globalwith,
-             npe, proc, loc, periodic ? "periodic" : "non-periodic");
-      ASSERT0(false);
+    if (loc < 0) {
+      throw BoutException("GlobalToLocal1D failure: loc is {} and thus smaller then 0\n",
+                          loc);
+    }
+    ASSERT1(loc <= localwith);
+    ASSERT1(proc >= 0);
+    ASSERT1(proc < npe);
+    if (periodic and (loc < mg or loc >= local + mg)) {
+      throw BoutException(
+          "GlobalToLocal1D failure - expected {} < {} < {} because we are periodic\n", mg,
+          loc, local + mg);
     }
 #endif
     return {proc, loc};
@@ -254,9 +260,9 @@ private:
   std::set<int> ids;
   std::map<int, int> mapping;
   bool is_setup{false};
-  const fci_comm::globalToLocal1D g2lx;
-  const fci_comm::globalToLocal1D g2ly;
-  const fci_comm::globalToLocal1D g2lz;
+  const fci_comm::GlobalToLocal1D g2lx;
+  const fci_comm::GlobalToLocal1D g2ly;
+  const fci_comm::GlobalToLocal1D g2lz;
 
 public:
   const fci_comm::XYZ2Ind<Ind3D> xyzl;

From 52373e7f27a479009f355a0724281d30c40152b4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 09:01:36 +0100
Subject: [PATCH 0689/1827] Rename to request

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 8 ++++----
 src/mesh/parallel/fci_comm.hxx               | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 2a4f32070a..40f2bb12dc 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -326,10 +326,10 @@ void XZHermiteSplineBase<monotonic>::calcWeights(
     if constexpr (monotonic) {
       const auto gind =
           gf3daccess->xyzg(i_corn, y + y_offset + y_global_offset, k_corner(x, y, z));
-      gf3daccess->get(gind);
-      gf3daccess->get(gind.xp(1));
-      gf3daccess->get(gind.zp(1));
-      gf3daccess->get(gind.xp(1).zp(1));
+      gf3daccess->request(gind);
+      gf3daccess->request(gind.xp(1));
+      gf3daccess->request(gind.zp(1));
+      gf3daccess->request(gind.xp(1).zp(1));
       g3dinds[i] = {gind.ind, gind.xp(1).ind, gind.zp(1).ind, gind.xp(1).zp(1).ind};
     }
   }
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 836ef9b89d..fbbe1a53ea 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -132,7 +132,7 @@ public:
     o_ids.resize(omp_get_max_threads());
 #endif
   };
-  void get(IndG3D ind) {
+  void request(IndG3D ind) {
     ASSERT2(is_setup == false);
 #ifdef _OPENMP
     ASSERT2(o_ids.size() > static_cast<size_t>(omp_get_thread_num()));

From c65088198a92368cccbcf126d3398f9b3c8acadc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 09:01:46 +0100
Subject: [PATCH 0690/1827] Add some docs

---
 src/mesh/parallel/fci_comm.hxx | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index fbbe1a53ea..8b6c4ecf61 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -41,6 +41,23 @@
 #include <stddef.h>
 #include <utility>
 #include <vector>
+
+/// GlobalField3DAccess is a class to set up the communication
+/// patterns, to request abitrary data form the global
+/// field. GlobalField3DAccessInstance is an instance. after
+/// GlobalField3DAccess has communicated the pre-requested data. Only
+/// data that has been pre-requested can be requested from
+/// GlobalField3DAccessInstance after communication.
+///
+/// The usage looks a bit like this:
+///
+/// GlobalField3DAccess gfa;
+/// // Request an abitrary number of global indices ``gi``:
+/// gfa.request(gi)
+/// // Communicate data
+/// const auto data = gfa.communicate(f3d);
+/// // Now data can be accesssed for all previously requested ``gi``s:
+/// data[gi]
 class GlobalField3DAccess;
 
 namespace fci_comm {

From 3a62dc4bbe2cd51db6974bfeab486122da401ac3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 09:58:51 +0100
Subject: [PATCH 0691/1827] Use templates over pre-processing

Now all implementation can be compiled at once, and switching is a
runtime choise.
---
 include/bout/interpolation_xz.hxx            |  32 +-
 src/mesh/interpolation/hermite_spline_xz.cxx | 450 ++++++++++---------
 src/mesh/interpolation_xz.cxx                |  11 +
 src/mesh/parallel/fci_comm.hxx               |   1 -
 4 files changed, 270 insertions(+), 224 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 6e4f12b1b0..9639a0a80e 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -29,15 +29,14 @@
 #include <bout/mask.hxx>
 #include <array>
 
-#define USE_NEW_WEIGHTS 1
 #if BOUT_HAS_PETSC
-#define HS_USE_PETSC 1
-#endif
-
-#ifdef HS_USE_PETSC
 #include "bout/petsclib.hxx"
 #endif
 
+namespace {
+enum class implementation_type { new_weights, petsc, legacy };
+}
+
 class Options;
 class GlobalField3DAccess;
 
@@ -145,7 +144,7 @@ public:
 /// but also degrades accuracy near maxima and minima.
 /// Perhaps should only impose near boundaries, since that is where
 /// problems most obviously occur.
-template <bool monotonic>
+template <bool monotonic, implementation_type imp_type>
 class XZHermiteSplineBase : public XZInterpolation {
 protected:
   /// This is protected rather than private so that it can be
@@ -174,7 +173,7 @@ protected:
 
   std::vector<Field3D> newWeights;
 
-#if HS_USE_PETSC
+#if BOUT_HAS_PETSC
   PetscLib* petsclib;
   bool isInit{false};
   Mat petscWeights;
@@ -195,7 +194,7 @@ public:
     setRegion(regionFromMask(mask, localmesh));
   }
   ~XZHermiteSplineBase() override {
-#if HS_USE_PETSC
+#if BOUT_HAS_PETSC
     if (isInit) {
       MatDestroy(&petscWeights);
       VecDestroy(&rhs);
@@ -224,8 +223,21 @@ public:
   getWeightsForYApproximation(int i, int j, int k, int yoffset) override;
 };
 
-using XZMonotonicHermiteSpline = XZHermiteSplineBase<true>;
-using XZHermiteSpline = XZHermiteSplineBase<false>;
+using XZMonotonicHermiteSplineSerial =
+    XZHermiteSplineBase<true, implementation_type::new_weights>;
+using XZHermiteSplineSerial =
+    XZHermiteSplineBase<false, implementation_type::new_weights>;
+using XZMonotonicHermiteSplineLegacy =
+    XZHermiteSplineBase<true, implementation_type::legacy>;
+using XZHermiteSplineLegacy = XZHermiteSplineBase<false, implementation_type::legacy>;
+#if BOUT_HAS_PETSC
+using XZMonotonicHermiteSpline = XZHermiteSplineBase<true, implementation_type::petsc>;
+using XZHermiteSpline = XZHermiteSplineBase<false, implementation_type::petsc>;
+#else
+using XZMonotonicHermiteSpline =
+    XZHermiteSplineBase<true, implementation_type::new_weights>;
+using XZHermiteSpline = XZHermiteSplineBase<false, implementation_type::new_weights>;
+#endif
 
 /// XZLagrange4pt interpolation class
 ///
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 40f2bb12dc..3aaa3624d4 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -107,9 +107,9 @@ class IndConverter {
   }
 };
 
-template <bool monotonic>
-XZHermiteSplineBase<monotonic>::XZHermiteSplineBase(int y_offset, Mesh* meshin,
-                                                    Options* options)
+template <bool monotonic, implementation_type imp_type>
+XZHermiteSplineBase<monotonic, imp_type>::XZHermiteSplineBase(int y_offset, Mesh* meshin,
+                                                              Options* options)
     : XZInterpolation(y_offset, meshin), h00_x(localmesh), h01_x(localmesh),
       h10_x(localmesh), h11_x(localmesh), h00_z(localmesh), h01_z(localmesh),
       h10_z(localmesh), h11_z(localmesh) {
@@ -140,33 +140,35 @@ XZHermiteSplineBase<monotonic>::XZHermiteSplineBase(int y_offset, Mesh* meshin,
   h10_z.allocate();
   h11_z.allocate();
 
-#if USE_NEW_WEIGHTS
-  newWeights.reserve(16);
-  for (int w = 0; w < 16; ++w) {
-    newWeights.emplace_back(localmesh);
-    newWeights[w].allocate();
+  if constexpr (imp_type == implementation_type::new_weights
+                || imp_type == implementation_type::petsc) {
+    newWeights.reserve(16);
+    for (int w = 0; w < 16; ++w) {
+      newWeights.emplace_back(localmesh);
+      newWeights[w].allocate();
+    }
+  }
+  if constexpr (imp_type == implementation_type::petsc) {
+    petsclib = new PetscLib(
+        &Options::root()["mesh:paralleltransform:xzinterpolation:hermitespline"]);
+    const int m = localmesh->LocalNx * localmesh->LocalNy * localmesh->LocalNz;
+    const int M = m * localmesh->getNXPE() * localmesh->getNYPE() * localmesh->getNZPE();
+    MatCreateAIJ(BoutComm::get(), m, m, M, M, 16, nullptr, 16, nullptr, &petscWeights);
   }
-#ifdef HS_USE_PETSC
-  petsclib = new PetscLib(
-      &Options::root()["mesh:paralleltransform:xzinterpolation:hermitespline"]);
-  const int m = localmesh->LocalNx * localmesh->LocalNy * localmesh->LocalNz;
-  const int M = m * localmesh->getNXPE() * localmesh->getNYPE();
-  MatCreateAIJ(BoutComm::get(), m, m, M, M, 16, nullptr, 16, nullptr, &petscWeights);
-#endif
-#endif
   if constexpr (monotonic) {
     gf3daccess = std::make_unique<GlobalField3DAccess>(localmesh);
     g3dinds.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
   }
-#ifndef HS_USE_PETSC
-  if (localmesh->getNXPE() > 1) {
-    throw BoutException("Require PETSc for MPI splitting in X");
+  if constexpr (imp_type == implementation_type::new_weights
+                || imp_type == implementation_type::legacy) {
+    if (localmesh->getNXPE() > 1) {
+      throw BoutException("Require PETSc for MPI splitting in X");
+    }
   }
-#endif
 }
 
-template <bool monotonic>
-void XZHermiteSplineBase<monotonic>::calcWeights(
+template <bool monotonic, implementation_type imp_type>
+void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
     const Field3D& delta_x, const Field3D& delta_z,
     [[maybe_unused]] const std::string& region) {
 
@@ -174,9 +176,8 @@ void XZHermiteSplineBase<monotonic>::calcWeights(
   const int nz = localmesh->LocalNz;
   const int xend = (localmesh->xend - localmesh->xstart + 1) * localmesh->getNXPE()
                    + localmesh->xstart - 1;
-#ifdef HS_USE_PETSC
-  IndConverter conv{localmesh};
-#endif
+  [[maybe_unused]] IndConverter conv{localmesh};
+
   [[maybe_unused]] const int y_global_offset =
       localmesh->getYProcIndex() * (localmesh->yend - localmesh->ystart + 1);
   BOUT_FOR(i, getRegion(region)) {
@@ -246,83 +247,83 @@ void XZHermiteSplineBase<monotonic>::calcWeights(
     h11_x[i] = (t_x * t_x * t_x) - (t_x * t_x);
     h11_z[i] = (t_z * t_z * t_z) - (t_z * t_z);
 
-#if USE_NEW_WEIGHTS
-
-    for (int w = 0; w < 16; ++w) {
-      newWeights[w][i] = 0;
-    }
-    // The distribution of our weights:
-    //  0   4   8    12
-    //  1   5   9    13
-    //  2   6   10   14
-    //  3   7   11   15
-    // e.g. 1 == ic.xm(); 4 == ic.zm(); 5 == ic;  7 == ic.zp(2);
-
-    // f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
-    newWeights[5][i] += h00_x[i] * h00_z[i];
-    newWeights[9][i] += h01_x[i] * h00_z[i];
-    newWeights[9][i] += h10_x[i] * h00_z[i] / 2;
-    newWeights[1][i] -= h10_x[i] * h00_z[i] / 2;
-    newWeights[13][i] += h11_x[i] * h00_z[i] / 2;
-    newWeights[5][i] -= h11_x[i] * h00_z[i] / 2;
-
-    // f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] +
-    // fx[iczp] * h10_x[i] + fx[icxpzp] * h11_x[i];
-    newWeights[6][i] += h00_x[i] * h01_z[i];
-    newWeights[10][i] += h01_x[i] * h01_z[i];
-    newWeights[10][i] += h10_x[i] * h01_z[i] / 2;
-    newWeights[2][i] -= h10_x[i] * h01_z[i] / 2;
-    newWeights[14][i] += h11_x[i] * h01_z[i] / 2;
-    newWeights[6][i] -= h11_x[i] * h01_z[i] / 2;
-
-    // fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] +
-    // fxz[ic] * h10_x[i]+ fxz[icxp] * h11_x[i];
-    newWeights[6][i] += h00_x[i] * h10_z[i] / 2;
-    newWeights[4][i] -= h00_x[i] * h10_z[i] / 2;
-    newWeights[10][i] += h01_x[i] * h10_z[i] / 2;
-    newWeights[8][i] -= h01_x[i] * h10_z[i] / 2;
-    newWeights[10][i] += h10_x[i] * h10_z[i] / 4;
-    newWeights[8][i] -= h10_x[i] * h10_z[i] / 4;
-    newWeights[2][i] -= h10_x[i] * h10_z[i] / 4;
-    newWeights[0][i] += h10_x[i] * h10_z[i] / 4;
-    newWeights[14][i] += h11_x[i] * h10_z[i] / 4;
-    newWeights[12][i] -= h11_x[i] * h10_z[i] / 4;
-    newWeights[6][i] -= h11_x[i] * h10_z[i] / 4;
-    newWeights[4][i] += h11_x[i] * h10_z[i] / 4;
-
-    // fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i] +
-    // fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
-    newWeights[7][i] += h00_x[i] * h11_z[i] / 2;
-    newWeights[5][i] -= h00_x[i] * h11_z[i] / 2;
-    newWeights[11][i] += h01_x[i] * h11_z[i] / 2;
-    newWeights[9][i] -= h01_x[i] * h11_z[i] / 2;
-    newWeights[11][i] += h10_x[i] * h11_z[i] / 4;
-    newWeights[9][i] -= h10_x[i] * h11_z[i] / 4;
-    newWeights[3][i] -= h10_x[i] * h11_z[i] / 4;
-    newWeights[1][i] += h10_x[i] * h11_z[i] / 4;
-    newWeights[15][i] += h11_x[i] * h11_z[i] / 4;
-    newWeights[13][i] -= h11_x[i] * h11_z[i] / 4;
-    newWeights[7][i] -= h11_x[i] * h11_z[i] / 4;
-    newWeights[5][i] += h11_x[i] * h11_z[i] / 4;
-#ifdef HS_USE_PETSC
-    PetscInt idxn[1] = {conv.fromLocalToGlobal(x, y + y_offset, z)};
-    // output.write("debug: {:d} -> {:d}: {:d}:{:d} -> {:d}:{:d}\n",
-    // conv.fromLocalToGlobal(x, y + y_offset, z),
-    //     conv.fromMeshToGlobal(i_corn, y + y_offset, k_corner(x, y, z)),
-    //     x, z, i_corn, k_corner(x, y, z));
-    // ixstep = mesh->LocalNx * mesh->LocalNz;
-    for (int j = 0; j < 4; ++j) {
-      PetscInt idxm[4];
-      PetscScalar vals[4];
-      for (int k = 0; k < 4; ++k) {
-        idxm[k] = conv.fromMeshToGlobal(i_corn - 1 + j, y + y_offset,
-                                        k_corner(x, y, z) - 1 + k);
-        vals[k] = newWeights[j * 4 + k][i];
+    if constexpr (imp_type == implementation_type::new_weights
+                  || imp_type == implementation_type::petsc) {
+      for (int w = 0; w < 16; ++w) {
+        newWeights[w][i] = 0;
+      }
+      // The distribution of our weights:
+      //  0   4   8    12
+      //  1   5   9    13
+      //  2   6   10   14
+      //  3   7   11   15
+      // e.g. 1 == ic.xm(); 4 == ic.zm(); 5 == ic;  7 == ic.zp(2);
+
+      // f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
+      newWeights[5][i] += h00_x[i] * h00_z[i];
+      newWeights[9][i] += h01_x[i] * h00_z[i];
+      newWeights[9][i] += h10_x[i] * h00_z[i] / 2;
+      newWeights[1][i] -= h10_x[i] * h00_z[i] / 2;
+      newWeights[13][i] += h11_x[i] * h00_z[i] / 2;
+      newWeights[5][i] -= h11_x[i] * h00_z[i] / 2;
+
+      // f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] +
+      // fx[iczp] * h10_x[i] + fx[icxpzp] * h11_x[i];
+      newWeights[6][i] += h00_x[i] * h01_z[i];
+      newWeights[10][i] += h01_x[i] * h01_z[i];
+      newWeights[10][i] += h10_x[i] * h01_z[i] / 2;
+      newWeights[2][i] -= h10_x[i] * h01_z[i] / 2;
+      newWeights[14][i] += h11_x[i] * h01_z[i] / 2;
+      newWeights[6][i] -= h11_x[i] * h01_z[i] / 2;
+
+      // fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] +
+      // fxz[ic] * h10_x[i]+ fxz[icxp] * h11_x[i];
+      newWeights[6][i] += h00_x[i] * h10_z[i] / 2;
+      newWeights[4][i] -= h00_x[i] * h10_z[i] / 2;
+      newWeights[10][i] += h01_x[i] * h10_z[i] / 2;
+      newWeights[8][i] -= h01_x[i] * h10_z[i] / 2;
+      newWeights[10][i] += h10_x[i] * h10_z[i] / 4;
+      newWeights[8][i] -= h10_x[i] * h10_z[i] / 4;
+      newWeights[2][i] -= h10_x[i] * h10_z[i] / 4;
+      newWeights[0][i] += h10_x[i] * h10_z[i] / 4;
+      newWeights[14][i] += h11_x[i] * h10_z[i] / 4;
+      newWeights[12][i] -= h11_x[i] * h10_z[i] / 4;
+      newWeights[6][i] -= h11_x[i] * h10_z[i] / 4;
+      newWeights[4][i] += h11_x[i] * h10_z[i] / 4;
+
+      // fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i] +
+      // fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
+      newWeights[7][i] += h00_x[i] * h11_z[i] / 2;
+      newWeights[5][i] -= h00_x[i] * h11_z[i] / 2;
+      newWeights[11][i] += h01_x[i] * h11_z[i] / 2;
+      newWeights[9][i] -= h01_x[i] * h11_z[i] / 2;
+      newWeights[11][i] += h10_x[i] * h11_z[i] / 4;
+      newWeights[9][i] -= h10_x[i] * h11_z[i] / 4;
+      newWeights[3][i] -= h10_x[i] * h11_z[i] / 4;
+      newWeights[1][i] += h10_x[i] * h11_z[i] / 4;
+      newWeights[15][i] += h11_x[i] * h11_z[i] / 4;
+      newWeights[13][i] -= h11_x[i] * h11_z[i] / 4;
+      newWeights[7][i] -= h11_x[i] * h11_z[i] / 4;
+      newWeights[5][i] += h11_x[i] * h11_z[i] / 4;
+      if (imp_type == implementation_type::petsc) {
+        PetscInt idxn[1] = {conv.fromLocalToGlobal(x, y + y_offset, z)};
+        // output.write("debug: {:d} -> {:d}: {:d}:{:d} -> {:d}:{:d}\n",
+        // conv.fromLocalToGlobal(x, y + y_offset, z),
+        //     conv.fromMeshToGlobal(i_corn, y + y_offset, k_corner(x, y, z)),
+        //     x, z, i_corn, k_corner(x, y, z));
+        // ixstep = mesh->LocalNx * mesh->LocalNz;
+        for (int j = 0; j < 4; ++j) {
+          PetscInt idxm[4];
+          PetscScalar vals[4];
+          for (int k = 0; k < 4; ++k) {
+            idxm[k] = conv.fromMeshToGlobal(i_corn - 1 + j, y + y_offset,
+                                            k_corner(x, y, z) - 1 + k);
+            vals[k] = newWeights[j * 4 + k][i];
+          }
+          MatSetValues(petscWeights, 1, idxn, 4, idxm, vals, INSERT_VALUES);
+        }
       }
-      MatSetValues(petscWeights, 1, idxn, 4, idxm, vals, INSERT_VALUES);
     }
-#endif
-#endif
     if constexpr (monotonic) {
       const auto gind =
           gf3daccess->xyzg(i_corn, y + y_offset + y_global_offset, k_corner(x, y, z));
@@ -336,21 +337,21 @@ void XZHermiteSplineBase<monotonic>::calcWeights(
   if constexpr (monotonic) {
     gf3daccess->setup();
   }
-#ifdef HS_USE_PETSC
-  MatAssemblyBegin(petscWeights, MAT_FINAL_ASSEMBLY);
-  MatAssemblyEnd(petscWeights, MAT_FINAL_ASSEMBLY);
-  if (!isInit) {
-    MatCreateVecs(petscWeights, &rhs, &result);
+  if constexpr (imp_type == implementation_type::petsc) {
+    MatAssemblyBegin(petscWeights, MAT_FINAL_ASSEMBLY);
+    MatAssemblyEnd(petscWeights, MAT_FINAL_ASSEMBLY);
+    if (!isInit) {
+      MatCreateVecs(petscWeights, &rhs, &result);
+    }
+    isInit = true;
   }
-  isInit = true;
-#endif
 }
 
-template <bool monotonic>
-void XZHermiteSplineBase<monotonic>::calcWeights(const Field3D& delta_x,
-                                                 const Field3D& delta_z,
-                                                 const BoutMask& mask,
-                                                 const std::string& region) {
+template <bool monotonic, implementation_type imp_type>
+void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(const Field3D& delta_x,
+                                                           const Field3D& delta_z,
+                                                           const BoutMask& mask,
+                                                           const std::string& region) {
   setMask(mask);
   calcWeights(delta_x, delta_z, region);
 }
@@ -371,10 +372,10 @@ void XZHermiteSplineBase<monotonic>::calcWeights(const Field3D& delta_x,
  *   (i, j+1, k+1)	h01_z + h10_z / 2
  *   (i, j+1, k+2)	h11_z / 2
  */
-template <bool monotonic>
+template <bool monotonic, implementation_type imp_type>
 std::vector<ParallelTransform::PositionsAndWeights>
-XZHermiteSplineBase<monotonic>::getWeightsForYApproximation(int i, int j, int k,
-                                                            int yoffset) {
+XZHermiteSplineBase<monotonic, imp_type>::getWeightsForYApproximation(int i, int j, int k,
+                                                                      int yoffset) {
   if (localmesh->getNXPE() > 1) {
     throw BoutException("It is likely that the function calling this is not handling the "
                         "result correctly.");
@@ -391,8 +392,8 @@ XZHermiteSplineBase<monotonic>::getWeightsForYApproximation(int i, int j, int k,
           {i, j + yoffset, k_mod_p2, 0.5 * h11_z(i, j, k)}};
 }
 
-template <bool monotonic>
-Field3D XZHermiteSplineBase<monotonic>::interpolate(
+template <bool monotonic, implementation_type imp_type>
+Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
     const Field3D& f, [[maybe_unused]] const std::string& region) const {
 
   ASSERT1(f.getMesh() == localmesh);
@@ -405,118 +406,141 @@ Field3D XZHermiteSplineBase<monotonic>::interpolate(
     gf = gf3daccess->communicate_asPtr(f);
   }
 
-#if USE_NEW_WEIGHTS and defined(HS_USE_PETSC)
-  BoutReal* ptr;
-  const BoutReal* cptr;
-  VecGetArray(rhs, &ptr);
-  BOUT_FOR(i, f.getRegion("RGN_NOY")) { ptr[int(i)] = f[i]; }
-  VecRestoreArray(rhs, &ptr);
-  MatMult(petscWeights, rhs, result);
-  VecGetArrayRead(result, &cptr);
-  BOUT_FOR(i, f.getRegion(region2)) {
-    f_interp[i] = cptr[int(i)];
-    if constexpr (monotonic) {
-      const auto iyp = i;
-      const auto i = iyp.ym(y_offset);
-#elif USE_NEW_WEIGHTS // No Petsc
-  BOUT_FOR(i, getRegion(region)) {
-    auto ic = i_corner[i];
-    auto iyp = i.yp(y_offset);
-
-    f_interp[iyp] = 0;
-    for (int w = 0; w < 4; ++w) {
-      f_interp[iyp] += newWeights[w * 4 + 0][i] * f[ic.zm().xp(w - 1)];
-      f_interp[iyp] += newWeights[w * 4 + 1][i] * f[ic.xp(w - 1)];
-      f_interp[iyp] += newWeights[w * 4 + 2][i] * f[ic.zp().xp(w - 1)];
-      f_interp[iyp] += newWeights[w * 4 + 3][i] * f[ic.zp(2).xp(w - 1)];
+  if constexpr (imp_type == implementation_type::petsc) {
+    BoutReal* ptr;
+    const BoutReal* cptr;
+    VecGetArray(rhs, &ptr);
+    BOUT_FOR(i, f.getRegion("RGN_NOY")) { ptr[int(i)] = f[i]; }
+    VecRestoreArray(rhs, &ptr);
+    MatMult(petscWeights, rhs, result);
+    VecGetArrayRead(result, &cptr);
+    BOUT_FOR(i, f.getRegion(region2)) {
+      f_interp[i] = cptr[int(i)];
+      if constexpr (monotonic) {
+        const auto iyp = i;
+        const auto i = iyp.ym(y_offset);
+        const auto corners = {(*gf)[IndG3D(g3dinds[i][0])], (*gf)[IndG3D(g3dinds[i][1])],
+                              (*gf)[IndG3D(g3dinds[i][2])], (*gf)[IndG3D(g3dinds[i][3])]};
+        const auto minmax = std::minmax(corners);
+        const auto diff =
+            ((minmax.second - minmax.first) * rel_fac_monotonic) + abs_fac_monotonic;
+        f_interp[iyp] = std::max(f_interp[iyp], minmax.first - diff);
+        f_interp[iyp] = std::min(f_interp[iyp], minmax.second + diff);
+      }
+      ASSERT2(std::isfinite(cptr[int(i)]));
     }
-    if constexpr (monotonic) {
-#else                 // Legacy interpolation
-  // TODO(peter): Should we apply dirichlet BCs to derivatives?
-  // Derivatives are used for tension and need to be on dimensionless
-  // coordinates
-
-  // f has been communcated, and thus we can assume that the x-boundaries are
-  // also valid in the y-boundary.  Thus the differentiated field needs no
-  // extra comms.
-  // TODO(dave) Add assert that we do not use z-splitting or z-guards.
-  Field3D fx = bout::derivatives::index::DDX(f, CELL_DEFAULT, "DEFAULT", region2);
-  Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", region2);
-  Field3D fxz = bout::derivatives::index::DDZ(fx, CELL_DEFAULT, "DEFAULT", region2);
-
-  BOUT_FOR(i, getRegion(region)) {
-    const auto iyp = i.yp(y_offset);
-
-    const auto ic = i_corner[i];
-    const auto iczp = ic.zp();
-    const auto icxp = ic.xp();
-    const auto icxpzp = iczp.xp();
-
-    // Interpolate f in X at Z
-    const BoutReal f_z =
-        f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
-
-    // Interpolate f in X at Z+1
-    const BoutReal f_zp1 = f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i] + fx[iczp] * h10_x[i]
-                           + fx[icxpzp] * h11_x[i];
-
-    // Interpolate fz in X at Z
-    const BoutReal fz_z = fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] + fxz[ic] * h10_x[i]
-                          + fxz[icxp] * h11_x[i];
-
-    // Interpolate fz in X at Z+1
-    const BoutReal fz_zp1 = fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i]
-                            + fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
-
-    // Interpolate in Z
-    f_interp[iyp] =
-        +f_z * h00_z[i] + f_zp1 * h01_z[i] + fz_z * h10_z[i] + fz_zp1 * h11_z[i];
+    VecRestoreArrayRead(result, &cptr);
+  }
 
-    if constexpr (monotonic) {
-#endif
-      const auto corners = {(*gf)[IndG3D(g3dinds[i][0])], (*gf)[IndG3D(g3dinds[i][1])],
-                            (*gf)[IndG3D(g3dinds[i][2])], (*gf)[IndG3D(g3dinds[i][3])]};
-      const auto minmax = std::minmax(corners);
-      const auto diff =
-          ((minmax.second - minmax.first) * rel_fac_monotonic) + abs_fac_monotonic;
-      f_interp[iyp] = std::max(f_interp[iyp], minmax.first - diff);
-      f_interp[iyp] = std::min(f_interp[iyp], minmax.second + diff);
+  if constexpr (imp_type == implementation_type::new_weights) {
+    BOUT_FOR(i, getRegion(region)) {
+      auto ic = i_corner[i];
+      auto iyp = i.yp(y_offset);
+
+      f_interp[iyp] = 0;
+      for (int w = 0; w < 4; ++w) {
+        f_interp[iyp] += newWeights[w * 4 + 0][i] * f[ic.zm().xp(w - 1)];
+        f_interp[iyp] += newWeights[w * 4 + 1][i] * f[ic.xp(w - 1)];
+        f_interp[iyp] += newWeights[w * 4 + 2][i] * f[ic.zp().xp(w - 1)];
+        f_interp[iyp] += newWeights[w * 4 + 3][i] * f[ic.zp(2).xp(w - 1)];
+      }
+      if constexpr (monotonic) {
+        const auto corners = {(*gf)[IndG3D(g3dinds[i][0])], (*gf)[IndG3D(g3dinds[i][1])],
+                              (*gf)[IndG3D(g3dinds[i][2])], (*gf)[IndG3D(g3dinds[i][3])]};
+        const auto minmax = std::minmax(corners);
+        const auto diff =
+            ((minmax.second - minmax.first) * rel_fac_monotonic) + abs_fac_monotonic;
+        f_interp[iyp] = std::max(f_interp[iyp], minmax.first - diff);
+        f_interp[iyp] = std::min(f_interp[iyp], minmax.second + diff);
+      }
+      ASSERT2(std::isfinite(f_interp[iyp]));
     }
-#if USE_NEW_WEIGHTS and defined(HS_USE_PETSC)
-    ASSERT2(std::isfinite(cptr[int(i)]));
   }
-  VecRestoreArrayRead(result, &cptr);
-#elif USE_NEW_WEIGHTS
-    ASSERT2(std::isfinite(f_interp[iyp]));
-  }
-#else
-    ASSERT2(std::isfinite(f_interp[iyp]) || i.x() < localmesh->xstart
-            || i.x() > localmesh->xend);
+  if constexpr (imp_type == implementation_type::legacy) {
+    // Legacy interpolation
+    // TODO(peter): Should we apply dirichlet BCs to derivatives?
+    // Derivatives are used for tension and need to be on dimensionless
+    // coordinates
+
+    // f has been communcated, and thus we can assume that the x-boundaries are
+    // also valid in the y-boundary.  Thus the differentiated field needs no
+    // extra comms.
+    // TODO(dave) Add assert that we do not use z-splitting or z-guards.
+    Field3D fx = bout::derivatives::index::DDX(f, CELL_DEFAULT, "DEFAULT", region2);
+    Field3D fz = bout::derivatives::index::DDZ(f, CELL_DEFAULT, "DEFAULT", region2);
+    Field3D fxz = bout::derivatives::index::DDZ(fx, CELL_DEFAULT, "DEFAULT", region2);
+
+    BOUT_FOR(i, getRegion(region)) {
+      const auto iyp = i.yp(y_offset);
+
+      const auto ic = i_corner[i];
+      const auto iczp = ic.zp();
+      const auto icxp = ic.xp();
+      const auto icxpzp = iczp.xp();
+
+      // Interpolate f in X at Z
+      const BoutReal f_z =
+          f[ic] * h00_x[i] + f[icxp] * h01_x[i] + fx[ic] * h10_x[i] + fx[icxp] * h11_x[i];
+
+      // Interpolate f in X at Z+1
+      const BoutReal f_zp1 = f[iczp] * h00_x[i] + f[icxpzp] * h01_x[i]
+                             + fx[iczp] * h10_x[i] + fx[icxpzp] * h11_x[i];
+
+      // Interpolate fz in X at Z
+      const BoutReal fz_z = fz[ic] * h00_x[i] + fz[icxp] * h01_x[i] + fxz[ic] * h10_x[i]
+                            + fxz[icxp] * h11_x[i];
+
+      // Interpolate fz in X at Z+1
+      const BoutReal fz_zp1 = fz[iczp] * h00_x[i] + fz[icxpzp] * h01_x[i]
+                              + fxz[iczp] * h10_x[i] + fxz[icxpzp] * h11_x[i];
+
+      // Interpolate in Z
+      f_interp[iyp] =
+          +f_z * h00_z[i] + f_zp1 * h01_z[i] + fz_z * h10_z[i] + fz_zp1 * h11_z[i];
+
+      if constexpr (monotonic) {
+        const auto corners = {(*gf)[IndG3D(g3dinds[i][0])], (*gf)[IndG3D(g3dinds[i][1])],
+                              (*gf)[IndG3D(g3dinds[i][2])], (*gf)[IndG3D(g3dinds[i][3])]};
+        const auto minmax = std::minmax(corners);
+        const auto diff =
+            ((minmax.second - minmax.first) * rel_fac_monotonic) + abs_fac_monotonic;
+        f_interp[iyp] = std::max(f_interp[iyp], minmax.first - diff);
+        f_interp[iyp] = std::min(f_interp[iyp], minmax.second + diff);
+      }
+      ASSERT2(std::isfinite(f_interp[iyp]) || i.x() < localmesh->xstart
+              || i.x() > localmesh->xend);
+    }
   }
-#endif
   f_interp.setRegion(region2);
   ASSERT2(f_interp.getRegionID());
   return f_interp;
 }
 
-template <bool monotonic>
-Field3D XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f,
-                                                    const Field3D& delta_x,
-                                                    const Field3D& delta_z,
-                                                    const std::string& region) {
+template <bool monotonic, implementation_type imp_type>
+Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(const Field3D& f,
+                                                              const Field3D& delta_x,
+                                                              const Field3D& delta_z,
+                                                              const std::string& region) {
   calcWeights(delta_x, delta_z, region);
   return interpolate(f, region);
 }
 
-template <bool monotonic>
-Field3D
-XZHermiteSplineBase<monotonic>::interpolate(const Field3D& f, const Field3D& delta_x,
-                                            const Field3D& delta_z, const BoutMask& mask,
-                                            const std::string& region) {
+template <bool monotonic, implementation_type imp_type>
+Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(const Field3D& f,
+                                                              const Field3D& delta_x,
+                                                              const Field3D& delta_z,
+                                                              const BoutMask& mask,
+                                                              const std::string& region) {
   calcWeights(delta_x, delta_z, mask, region);
   return interpolate(f, region);
 }
 
 // ensure they are instantiated
-template class XZHermiteSplineBase<true>;
-template class XZHermiteSplineBase<false>;
+template class XZHermiteSplineBase<true, implementation_type::new_weights>;
+template class XZHermiteSplineBase<false, implementation_type::new_weights>;
+template class XZHermiteSplineBase<true, implementation_type::legacy>;
+template class XZHermiteSplineBase<false, implementation_type::legacy>;
+#if BOUT_HAS_PETSC
+template class XZHermiteSplineBase<true, implementation_type::petsc>;
+template class XZHermiteSplineBase<false, implementation_type::petsc>;
+#endif
diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx
index f80a361bd1..82234cf840 100644
--- a/src/mesh/interpolation_xz.cxx
+++ b/src/mesh/interpolation_xz.cxx
@@ -85,6 +85,17 @@ void XZInterpolationFactory::ensureRegistered() {}
 
 namespace {
 RegisterXZInterpolation<XZHermiteSpline> registerinterphermitespline{"hermitespline"};
+RegisterXZInterpolation<XZMonotonicHermiteSpline> registerinterpmonotonichermitespline{
+    "monotonichermitespline"};
+RegisterXZInterpolation<XZHermiteSplineSerial> registerinterphermitesplines{
+    "hermitesplineserial"};
+RegisterXZInterpolation<XZMonotonicHermiteSplineSerial>
+    registerinterpmonotonichermitesplines{"monotonichermitesplinelegacy"};
+RegisterXZInterpolation<XZHermiteSplineLegacy> registerinterphermitesplinel{
+    "hermitesplineserial"};
+RegisterXZInterpolation<XZMonotonicHermiteSplineLegacy>
+    registerinterpmonotonichermitesplinel{"monotonichermitesplinelegacy"};
+RegisterXZInterpolation<XZHermiteSpline> registerinterphermitespline{"hermitespline"};
 RegisterXZInterpolation<XZMonotonicHermiteSpline> registerinterpmonotonichermitespline{
     "monotonichermitespline"};
 RegisterXZInterpolation<XZLagrange4pt> registerinterplagrange4pt{"lagrange4pt"};
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 8b6c4ecf61..d34b97aa53 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -159,7 +159,6 @@ public:
 #endif
   }
 
-  void operator[](IndG3D ind) { get(ind); }
   void setup() {
     ASSERT2(is_setup == false);
 #ifdef _OPENMP

From cb84b760595d74e1f31b2b7492b21061e42119c6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 09:59:06 +0100
Subject: [PATCH 0692/1827] Test serveral implementations

---
 tests/integrated/test-fci-mpi/runtest     | 51 ++++++++++++-----------
 tests/integrated/test-interpolate/runtest |  2 +
 2 files changed, 28 insertions(+), 25 deletions(-)

diff --git a/tests/integrated/test-fci-mpi/runtest b/tests/integrated/test-fci-mpi/runtest
index c18ab0391d..9962567217 100755
--- a/tests/integrated/test-fci-mpi/runtest
+++ b/tests/integrated/test-fci-mpi/runtest
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-# Python script to run and analyse MMS test
+# Python script to run and analyse MPI test
 
 from boututils.run_wrapper import build_and_log, launch_safe
 from boutdata.collect import collect
@@ -14,13 +14,13 @@ NLIST = [1, 2, 4]
 MAXCORES = 8
 NSLICES = [1]
 
-build_and_log("FCI MMS test")
+build_and_log("FCI MPI test")
 
 COLLECT_KW = dict(info=False, xguards=False, yguards=False, path="data")
 
 
 def run_case(nxpe: int, nype: int, mthread: int):
-    cmd = f"./fci_mpi NXPE={nxpe} NYPE={nype}"
+    cmd = f"./fci_mpi NXPE={nxpe} NYPE={nype} mesh:paralleltransform:xzinterpolation:type={implementation}"
     print(f"Running command: {cmd}")
 
     _, out = launch_safe(cmd, nproc=nxpe * nype, mthread=mthread, pipe=True)
@@ -46,28 +46,29 @@ def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
 
 failures = []
 
-for nslice in NSLICES:
-    # reference data!
-    run_case(1, 1, MAXCORES)
-
-    ref = {}
-    for i in range(4):
-        for yp in range(1, nslice + 1):
-            for y in [-yp, yp]:
-                name = f"output_{i}_{y:+d}"
-                ref[name] = collect(name, **COLLECT_KW)
-
-    for nxpe, nype in itertools.product(NLIST, NLIST):
-        if (nxpe, nype) == (1, 1):
-            # reference case, done above
-            continue
-
-        if nxpe * nype > MAXCORES:
-            continue
-
-        mthread = MAXCORES // (nxpe * nype)
-        failures_ = test_case(nxpe, nype, mthread, ref)
-        failures.extend(failures_)
+for implementation in ["hermitespline", "monotonichermitespline"]:
+    for nslice in NSLICES:
+        # reference data!
+        run_case(1, 1, MAXCORES)
+
+        ref = {}
+        for i in range(4):
+            for yp in range(1, nslice + 1):
+                for y in [-yp, yp]:
+                    name = f"output_{i}_{y:+d}"
+                    ref[name] = collect(name, **COLLECT_KW)
+
+        for nxpe, nype in itertools.product(NLIST, NLIST):
+            if (nxpe, nype) == (1, 1):
+                # reference case, done above
+                continue
+
+            if nxpe * nype > MAXCORES:
+                continue
+
+            mthread = MAXCORES // (nxpe * nype)
+            failures_ = test_case(nxpe, nype, mthread, ref)
+            failures.extend(failures_)
 
 
 success = len(failures) == 0
diff --git a/tests/integrated/test-interpolate/runtest b/tests/integrated/test-interpolate/runtest
index f5460aff2a..91503f5f9e 100755
--- a/tests/integrated/test-interpolate/runtest
+++ b/tests/integrated/test-interpolate/runtest
@@ -23,6 +23,8 @@ labels = [r"$" + var + r"$" for var in varlist]
 
 methods = {
     "hermitespline": 3,
+    "hermitesplinelegacy": 3,
+    "hermitesplineserial": 3,
     "lagrange4pt": 3,
     "bilinear": 2,
 }

From a81d3eb279df51495b5290c8a54fe698aa22d470 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 11:47:05 +0100
Subject: [PATCH 0693/1827] Cleanup interface and move more functions to cxx
 file

---
 src/mesh/interpolation/hermite_spline_xz.cxx |   3 -
 src/mesh/interpolation_xz.cxx                |   7 +-
 src/mesh/parallel/fci_comm.cxx               | 179 +++++++++++++-
 src/mesh/parallel/fci_comm.hxx               | 235 ++++---------------
 4 files changed, 219 insertions(+), 205 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 3aaa3624d4..f622ff572e 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -334,9 +334,6 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
       g3dinds[i] = {gind.ind, gind.xp(1).ind, gind.zp(1).ind, gind.xp(1).zp(1).ind};
     }
   }
-  if constexpr (monotonic) {
-    gf3daccess->setup();
-  }
   if constexpr (imp_type == implementation_type::petsc) {
     MatAssemblyBegin(petscWeights, MAT_FINAL_ASSEMBLY);
     MatAssemblyEnd(petscWeights, MAT_FINAL_ASSEMBLY);
diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx
index 82234cf840..ec8bcc0502 100644
--- a/src/mesh/interpolation_xz.cxx
+++ b/src/mesh/interpolation_xz.cxx
@@ -90,14 +90,11 @@ RegisterXZInterpolation<XZMonotonicHermiteSpline> registerinterpmonotonichermite
 RegisterXZInterpolation<XZHermiteSplineSerial> registerinterphermitesplines{
     "hermitesplineserial"};
 RegisterXZInterpolation<XZMonotonicHermiteSplineSerial>
-    registerinterpmonotonichermitesplines{"monotonichermitesplinelegacy"};
+    registerinterpmonotonichermitesplines{"monotonichermitesplineserial"};
 RegisterXZInterpolation<XZHermiteSplineLegacy> registerinterphermitesplinel{
-    "hermitesplineserial"};
+    "hermitesplinelegacy"};
 RegisterXZInterpolation<XZMonotonicHermiteSplineLegacy>
     registerinterpmonotonichermitesplinel{"monotonichermitesplinelegacy"};
-RegisterXZInterpolation<XZHermiteSpline> registerinterphermitespline{"hermitespline"};
-RegisterXZInterpolation<XZMonotonicHermiteSpline> registerinterpmonotonichermitespline{
-    "monotonichermitespline"};
 RegisterXZInterpolation<XZLagrange4pt> registerinterplagrange4pt{"lagrange4pt"};
 RegisterXZInterpolation<XZBilinear> registerinterpbilinear{"bilinear"};
 } // namespace
diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index 65a8731740..5ff16a980e 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -30,8 +30,179 @@
 
 #include <vector>
 
-const BoutReal& GlobalField3DAccessInstance::operator[](IndG3D ind) const {
-  auto it = gfa->mapping.find(ind.ind);
-  ASSERT2(it != gfa->mapping.end());
-  return data[it->second];
+fci_comm::ProcLocal fci_comm::GlobalToLocal1D::convert(int id) const {
+  if (periodic) {
+    while (id < mg) {
+      id += global;
+    }
+    while (id >= global + mg) {
+      id -= global;
+    }
+  }
+  const int idwo = id - mg;
+  int proc = idwo / local;
+  if (not periodic) {
+    if (proc >= npe) {
+      proc = npe - 1;
+    }
+  }
+  const int loc = id - (local * proc);
+#if CHECK > 1
+  ASSERT1(loc >= 0);
+  ASSERT1(loc <= localwith);
+  ASSERT1(proc >= 0);
+  ASSERT1(proc < npe);
+  if (periodic and (loc < mg or loc >= local + mg)) {
+    throw BoutException(
+        "GlobalToLocal1D failure - expected {} < {} < {} because we are periodic\n", mg,
+        loc, local + mg);
+  }
+#endif
+  return {proc, loc};
+}
+
+void GlobalField3DAccess::setup() {
+  ASSERT2(is_setup == false);
+#ifdef _OPENMP
+  for (auto& o_id : o_ids) {
+    ids.merge(o_id);
+  }
+  o_ids.clear();
+#endif
+  toGet.resize(static_cast<size_t>(g2lx.getNPE() * g2ly.getNPE() * g2lz.getNPE()));
+  for (const auto id : ids) {
+    const IndG3D gind{id, g2ly.getGlobalWith(), g2lz.getGlobalWith()};
+    const auto pix = g2lx.convert(gind.x());
+    const auto piy = g2ly.convert(gind.y());
+    const auto piz = g2lz.convert(gind.z());
+    ASSERT3(piz.proc == 0);
+    toGet[(piy.proc * g2lx.getNPE()) + pix.proc].push_back(
+        xyzl.convert(pix.ind, piy.ind, piz.ind).ind);
+  }
+  for (auto& v : toGet) {
+    std::sort(v.begin(), v.end());
+  }
+  commCommLists();
+  {
+    int offset = 0;
+    for (const auto& get : toGet) {
+      getOffsets.push_back(offset);
+      offset += get.size();
+    }
+    getOffsets.push_back(offset);
+  }
+  for (const auto id : ids) {
+    const IndG3D gind{id, g2ly.getGlobalWith(), g2lz.getGlobalWith()};
+    const auto pix = g2lx.convert(gind.x());
+    const auto piy = g2ly.convert(gind.y());
+    const auto piz = g2lz.convert(gind.z());
+    ASSERT3(piz.proc == 0);
+    const auto proc = (piy.proc * g2lx.getNPE()) + pix.proc;
+    const auto& vec = toGet[proc];
+    const auto tofind = xyzl.convert(pix.ind, piy.ind, piz.ind).ind;
+    auto it = std::lower_bound(vec.begin(), vec.end(), tofind);
+    ASSERT3(it != vec.end());
+    ASSERT3(*it == tofind);
+    mapping[id] = std::distance(vec.begin(), it) + getOffsets[proc];
+  }
+  is_setup = true;
+}
+
+void GlobalField3DAccess::commCommLists() {
+  toSend.resize(toGet.size());
+  std::vector<int> toGetSizes(toGet.size(), -1);
+  std::vector<int> toSendSizes(toSend.size(), -1);
+#if CHECK > 3
+  {
+    int thisproc;
+    MPI_Comm_rank(comm, &thisproc);
+    ASSERT0(thisproc == mesh->getYProcIndex() * g2lx.getNPE() + mesh->getXProcIndex());
+  }
+#endif
+  std::vector<MPI_Request> reqs(toSend.size());
+  for (size_t proc = 0; proc < toGet.size(); ++proc) {
+    auto ret = MPI_Irecv(static_cast<void*>(&toSendSizes[proc]), 1, MPI_INT, proc, 666,
+                         comm, &reqs[proc]);
+    ASSERT0(ret == MPI_SUCCESS);
+  }
+  for (size_t proc = 0; proc < toGet.size(); ++proc) {
+    toGetSizes[proc] = toGet[proc].size();
+    auto ret =
+        MPI_Send(static_cast<void*>(&toGetSizes[proc]), 1, MPI_INT, proc, 666, comm);
+    ASSERT0(ret == MPI_SUCCESS);
+  }
+  std::vector<MPI_Request> reqs2(toSend.size());
+  int cnt = 0;
+  for ([[maybe_unused]] auto dummy : reqs) {
+    int ind{0};
+    auto ret = MPI_Waitany(reqs.size(), reqs.data(), &ind, MPI_STATUS_IGNORE);
+    ASSERT0(ret == MPI_SUCCESS);
+    ASSERT3(ind != MPI_UNDEFINED);
+    ASSERT2(static_cast<size_t>(ind) < toSend.size());
+    ASSERT3(toSendSizes[ind] >= 0);
+    if (toSendSizes[ind] == 0) {
+      continue;
+    }
+    sendBufferSize += toSendSizes[ind];
+    toSend[ind].resize(toSendSizes[ind], -1);
+
+    ret = MPI_Irecv(static_cast<void*>(toSend[ind].data()), toSend[ind].size(), MPI_INT,
+                    ind, 666 * 666, comm, reqs2.data() + cnt++);
+    ASSERT0(ret == MPI_SUCCESS);
+  }
+  for (size_t proc = 0; proc < toGet.size(); ++proc) {
+    if (!toGet[proc].empty()) {
+      const auto ret = MPI_Send(static_cast<void*>(toGet[proc].data()),
+                                toGet[proc].size(), MPI_INT, proc, 666 * 666, comm);
+      ASSERT0(ret == MPI_SUCCESS);
+    }
+  }
+  for (int c = 0; c < cnt; c++) {
+    int ind{0};
+    const auto ret = MPI_Waitany(cnt, reqs2.data(), &ind, MPI_STATUS_IGNORE);
+    ASSERT0(ret == MPI_SUCCESS);
+    ASSERT3(ind != MPI_UNDEFINED);
+  }
+}
+
+std::vector<BoutReal> GlobalField3DAccess::communicate_data(const Field3D& f) {
+  if (not is_setup) {
+    setup();
+  }
+  ASSERT2(f.getMesh() == mesh);
+  std::vector<BoutReal> data(getOffsets.back());
+  std::vector<BoutReal> sendBuffer(sendBufferSize);
+  std::vector<MPI_Request> reqs(toSend.size());
+  int cnt1 = 0;
+  for (size_t proc = 0; proc < toGet.size(); ++proc) {
+    if (toGet[proc].empty()) {
+      continue;
+    }
+    auto ret =
+        MPI_Irecv(static_cast<void*>(data.data() + getOffsets[proc]), toGet[proc].size(),
+                  MPI_DOUBLE, proc, 666, comm, reqs.data() + cnt1);
+    ASSERT0(ret == MPI_SUCCESS);
+    cnt1++;
+  }
+  int cnt = 0;
+  for (size_t proc = 0; proc < toGet.size(); ++proc) {
+    if (toSend[proc].empty()) {
+      continue;
+    }
+    const void* start = static_cast<void*>(sendBuffer.data() + cnt);
+    for (auto i : toSend[proc]) {
+      sendBuffer[cnt++] = f[Ind3D(i)];
+    }
+    auto ret = MPI_Send(start, toSend[proc].size(), MPI_DOUBLE, proc, 666, comm);
+    ASSERT0(ret == MPI_SUCCESS);
+  }
+  for (int j = 0; j < cnt1; ++j) {
+    int ind{0};
+    auto ret = MPI_Waitany(cnt1, reqs.data(), &ind, MPI_STATUS_IGNORE);
+    ASSERT0(ret == MPI_SUCCESS);
+    ASSERT3(ind != MPI_UNDEFINED);
+    ASSERT3(ind >= 0);
+    ASSERT3(ind < cnt1);
+  }
+  return data;
 }
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index d34b97aa53..af294989fb 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -65,7 +65,19 @@ struct ProcLocal {
   int proc;
   int ind;
 };
+
+/// Class to convert global to local indices for 1D
+/// given the global index, it returns the local index and the processor.
 struct GlobalToLocal1D {
+  GlobalToLocal1D(int mg, int npe, int localwith, bool periodic)
+      : mg(mg), npe(npe), localwith(localwith), local(localwith - (2 * mg)),
+        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic) {};
+  ProcLocal convert(int id) const;
+  int getLocalWith() const { return localwith; }
+  int getGlobalWith() const { return globalwith; }
+  int getNPE() const { return npe; }
+
+private:
   int mg;
   int npe;
   int localwith;
@@ -73,60 +85,27 @@ struct GlobalToLocal1D {
   int global;
   int globalwith;
   bool periodic;
-  GlobalToLocal1D(int mg, int npe, int localwith, bool periodic)
-      : mg(mg), npe(npe), localwith(localwith), local(localwith - (2 * mg)),
-        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic) {};
-  ProcLocal convert(int id) const {
-    if (periodic) {
-      while (id < mg) {
-        id += global;
-      }
-      while (id >= global + mg) {
-        id -= global;
-      }
-    }
-    const int idwo = id - mg;
-    int proc = idwo / local;
-    if (not periodic) {
-      if (proc >= npe) {
-        proc = npe - 1;
-      }
-    }
-    const int loc = id - (local * proc);
-#if CHECK > 1
-    if (loc < 0) {
-      throw BoutException("GlobalToLocal1D failure: loc is {} and thus smaller then 0\n",
-                          loc);
-    }
-    ASSERT1(loc <= localwith);
-    ASSERT1(proc >= 0);
-    ASSERT1(proc < npe);
-    if (periodic and (loc < mg or loc >= local + mg)) {
-      throw BoutException(
-          "GlobalToLocal1D failure - expected {} < {} < {} because we are periodic\n", mg,
-          loc, local + mg);
-    }
-#endif
-    return {proc, loc};
-  }
 };
+
+/// Convert an x-y-z tupple to an Ind
 template <class ind>
 struct XYZ2Ind {
-  const int nx;
-  const int ny;
-  const int nz;
+  XYZ2Ind(const int nx, const int ny, const int nz) : nx(nx), ny(ny), nz(nz) {}
   ind convert(const int x, const int y, const int z) const {
     return {z + ((y + x * ny) * nz), ny, nz};
   }
   ind operator()(const int x, const int y, const int z) const { return convert(x, y, z); }
-  XYZ2Ind(const int nx, const int ny, const int nz) : nx(nx), ny(ny), nz(nz) {}
+
+private:
+  int nx;
+  int ny;
+  int nz;
 };
 } // namespace fci_comm
 
 class GlobalField3DAccessInstance {
 public:
   const BoutReal& operator[](IndG3D ind) const;
-
   GlobalField3DAccessInstance(const GlobalField3DAccess* gfa,
                               std::vector<BoutReal>&& data)
       : gfa(gfa), data(std::move(data)){};
@@ -143,68 +122,23 @@ public:
       : mesh(mesh), g2lx(mesh->xstart, mesh->getNXPE(), mesh->LocalNx, false),
         g2ly(mesh->ystart, mesh->getNYPE(), mesh->LocalNy, true),
         g2lz(mesh->zstart, 1, mesh->LocalNz, true),
-        xyzl(g2lx.localwith, g2ly.localwith, g2lz.localwith),
-        xyzg(g2lx.globalwith, g2ly.globalwith, g2lz.globalwith), comm(BoutComm::get()) {
+        xyzl(g2lx.getLocalWith(), g2ly.getLocalWith(), g2lz.getLocalWith()),
+        xyzg(g2lx.getGlobalWith(), g2ly.getGlobalWith(), g2lz.getGlobalWith()),
+        comm(BoutComm::get()) {
 #ifdef _OPENMP
-    o_ids.resize(omp_get_max_threads());
+    openmp_ids.resize(omp_get_max_threads());
 #endif
   };
   void request(IndG3D ind) {
     ASSERT2(is_setup == false);
 #ifdef _OPENMP
-    ASSERT2(o_ids.size() > static_cast<size_t>(omp_get_thread_num()));
-    o_ids[omp_get_thread_num()].emplace(ind.ind);
+    ASSERT2(openmp_ids.size() > static_cast<size_t>(omp_get_thread_num()));
+    openmp_ids[omp_get_thread_num()].emplace(ind.ind);
 #else
     ids.emplace(ind.ind);
 #endif
   }
 
-  void setup() {
-    ASSERT2(is_setup == false);
-#ifdef _OPENMP
-    for (auto& o_id : o_ids) {
-      ids.merge(o_id);
-    }
-    o_ids.clear();
-#endif
-    toGet.resize(static_cast<size_t>(g2lx.npe * g2ly.npe * g2lz.npe));
-    for (const auto id : ids) {
-      const IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
-      const auto pix = g2lx.convert(gind.x());
-      const auto piy = g2ly.convert(gind.y());
-      const auto piz = g2lz.convert(gind.z());
-      ASSERT3(piz.proc == 0);
-      toGet[(piy.proc * g2lx.npe) + pix.proc].push_back(
-          xyzl.convert(pix.ind, piy.ind, piz.ind).ind);
-    }
-    for (auto& v : toGet) {
-      std::sort(v.begin(), v.end());
-    }
-    commCommLists();
-    {
-      int offset = 0;
-      for (const auto& get : toGet) {
-        getOffsets.push_back(offset);
-        offset += get.size();
-      }
-      getOffsets.push_back(offset);
-    }
-    for (const auto id : ids) {
-      const IndG3D gind{id, g2ly.globalwith, g2lz.globalwith};
-      const auto pix = g2lx.convert(gind.x());
-      const auto piy = g2ly.convert(gind.y());
-      const auto piz = g2lz.convert(gind.z());
-      ASSERT3(piz.proc == 0);
-      const auto proc = (piy.proc * g2lx.npe) + pix.proc;
-      const auto& vec = toGet[proc];
-      const auto tofind = xyzl.convert(pix.ind, piy.ind, piz.ind).ind;
-      auto it = std::lower_bound(vec.begin(), vec.end(), tofind);
-      ASSERT3(it != vec.end());
-      ASSERT3(*it == tofind);
-      mapping[id] = std::distance(vec.begin(), it) + getOffsets[proc];
-    }
-    is_setup = true;
-  }
   GlobalField3DAccessInstance communicate(const Field3D& f) {
     return {this, communicate_data(f)};
   }
@@ -213,76 +147,23 @@ public:
   }
 
 private:
-  void commCommLists() {
-    toSend.resize(toGet.size());
-    std::vector<int> toGetSizes(toGet.size(), -1);
-    std::vector<int> toSendSizes(toSend.size(), -1);
-#if CHECK > 3
-    {
-      int thisproc;
-      MPI_Comm_rank(comm, &thisproc);
-      ASSERT0(thisproc == mesh->getYProcIndex() * g2lx.npe + mesh->getXProcIndex());
-    }
-#endif
-    std::vector<MPI_Request> reqs(toSend.size());
-    for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      auto ret = MPI_Irecv(static_cast<void*>(&toSendSizes[proc]), 1, MPI_INT, proc, 666,
-                           comm, &reqs[proc]);
-      ASSERT0(ret == MPI_SUCCESS);
-    }
-    for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      toGetSizes[proc] = toGet[proc].size();
-      auto ret =
-          MPI_Send(static_cast<void*>(&toGetSizes[proc]), 1, MPI_INT, proc, 666, comm);
-      ASSERT0(ret == MPI_SUCCESS);
-    }
-    std::vector<MPI_Request> reqs2(toSend.size());
-    int cnt = 0;
-    for ([[maybe_unused]] auto dummy : reqs) {
-      int ind{0};
-      auto ret = MPI_Waitany(reqs.size(), reqs.data(), &ind, MPI_STATUS_IGNORE);
-      ASSERT0(ret == MPI_SUCCESS);
-      ASSERT3(ind != MPI_UNDEFINED);
-      ASSERT2(static_cast<size_t>(ind) < toSend.size());
-      ASSERT3(toSendSizes[ind] >= 0);
-      if (toSendSizes[ind] == 0) {
-        continue;
-      }
-      sendBufferSize += toSendSizes[ind];
-      toSend[ind].resize(toSendSizes[ind], -1);
-
-      ret = MPI_Irecv(static_cast<void*>(toSend[ind].data()), toSend[ind].size(), MPI_INT,
-                      ind, 666 * 666, comm, reqs2.data() + cnt++);
-      ASSERT0(ret == MPI_SUCCESS);
-    }
-    for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      if (!toGet[proc].empty()) {
-        const auto ret = MPI_Send(static_cast<void*>(toGet[proc].data()),
-                                  toGet[proc].size(), MPI_INT, proc, 666 * 666, comm);
-        ASSERT0(ret == MPI_SUCCESS);
-      }
-    }
-    for (int c = 0; c < cnt; c++) {
-      int ind{0};
-      const auto ret = MPI_Waitany(cnt, reqs2.data(), &ind, MPI_STATUS_IGNORE);
-      ASSERT0(ret == MPI_SUCCESS);
-      ASSERT3(ind != MPI_UNDEFINED);
-    }
-  }
+  void setup();
+  void commCommLists();
   Mesh* mesh;
 #ifdef _OPENMP
-  std::vector<std::set<int>> o_ids;
+  // openmp thread-local variable
+  std::vector<std::set<int>> openmp_ids;
 #endif
   std::set<int> ids;
   std::map<int, int> mapping;
   bool is_setup{false};
-  const fci_comm::GlobalToLocal1D g2lx;
-  const fci_comm::GlobalToLocal1D g2ly;
-  const fci_comm::GlobalToLocal1D g2lz;
+  fci_comm::GlobalToLocal1D g2lx;
+  fci_comm::GlobalToLocal1D g2ly;
+  fci_comm::GlobalToLocal1D g2lz;
 
 public:
-  const fci_comm::XYZ2Ind<Ind3D> xyzl;
-  const fci_comm::XYZ2Ind<IndG3D> xyzg;
+  fci_comm::XYZ2Ind<Ind3D> xyzl;
+  fci_comm::XYZ2Ind<IndG3D> xyzg;
 
 private:
   std::vector<std::vector<int>> toGet;
@@ -290,43 +171,11 @@ private:
   std::vector<int> getOffsets;
   int sendBufferSize{0};
   MPI_Comm comm;
-  std::vector<BoutReal> communicate_data(const Field3D& f) {
-    ASSERT2(is_setup);
-    ASSERT2(f.getMesh() == mesh);
-    std::vector<BoutReal> data(getOffsets.back());
-    std::vector<BoutReal> sendBuffer(sendBufferSize);
-    std::vector<MPI_Request> reqs(toSend.size());
-    int cnt1 = 0;
-    for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      if (toGet[proc].empty()) {
-        continue;
-      }
-      auto ret =
-          MPI_Irecv(static_cast<void*>(data.data() + getOffsets[proc]),
-                    toGet[proc].size(), MPI_DOUBLE, proc, 666, comm, reqs.data() + cnt1);
-      ASSERT0(ret == MPI_SUCCESS);
-      cnt1++;
-    }
-    int cnt = 0;
-    for (size_t proc = 0; proc < toGet.size(); ++proc) {
-      if (toSend[proc].empty()) {
-        continue;
-      }
-      const void* start = static_cast<void*>(sendBuffer.data() + cnt);
-      for (auto i : toSend[proc]) {
-        sendBuffer[cnt++] = f[Ind3D(i)];
-      }
-      auto ret = MPI_Send(start, toSend[proc].size(), MPI_DOUBLE, proc, 666, comm);
-      ASSERT0(ret == MPI_SUCCESS);
-    }
-    for (int j = 0; j < cnt1; ++j) {
-      int ind{0};
-      auto ret = MPI_Waitany(cnt1, reqs.data(), &ind, MPI_STATUS_IGNORE);
-      ASSERT0(ret == MPI_SUCCESS);
-      ASSERT3(ind != MPI_UNDEFINED);
-      ASSERT3(ind >= 0);
-      ASSERT3(ind < cnt1);
-    }
-    return data;
-  }
+  std::vector<BoutReal> communicate_data(const Field3D& f);
 };
+
+const BoutReal& GlobalField3DAccessInstance::operator[](IndG3D ind) const {
+  auto it = gfa->mapping.find(ind.ind);
+  ASSERT2(it != gfa->mapping.end());
+  return data[it->second];
+}

From 4632df093c1632eb2f0060e4c037813f4179dcaf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 11:51:41 +0100
Subject: [PATCH 0694/1827] Move processor ID calculation to mesh

---
 include/bout/mesh.hxx            | 2 ++
 src/mesh/impls/bout/boutmesh.cxx | 4 ++++
 src/mesh/impls/bout/boutmesh.hxx | 1 +
 src/mesh/parallel/fci_comm.cxx   | 6 +++---
 4 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 502b0c5668..a1ed6a9011 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -360,6 +360,8 @@ public:
   virtual int getXProcIndex() const = 0; ///< This processor's index in X direction
   virtual int getYProcIndex() const = 0; ///< This processor's index in Y direction
   virtual int getZProcIndex() const = 0; ///< This processor's index in Z direction
+  /// The index of a processor with given X, Y, and Z index
+  virtual int getProcIndex(int X, int Y, int Z) const = 0;
 
   // X communications
   virtual bool firstX()
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 4aaa760c04..41440b50ba 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -523,6 +523,8 @@ int BoutMesh::load() {
   PE_XIND = MYPE % NXPE;
   PE_ZIND = 0;
 
+  ASSERT2(MYPE == getProcIndex(PE_XIND, PE_YIND, PE_ZIND));
+
   // Set the other grid sizes from nx, ny, nz
   setDerivedGridSizes();
 
@@ -1004,6 +1006,8 @@ void BoutMesh::createXBoundaries() {
   }
 }
 
+int BoutMesh::getProcIndex(int X, int Y, int Z) { return Y * NXPE + X; }
+
 void BoutMesh::createYBoundaries() {
   if (MYG <= 0) {
     return;
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index 3923c34511..b42bf325b5 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -63,6 +63,7 @@ public:
   int getXProcIndex() const override; ///< This processor's index in X direction
   int getYProcIndex() const override; ///< This processor's index in Y direction
   int getZProcIndex() const override; ///< This processor's index in Z direction
+  int getProcIndex(int X, int Y, int Z) const override;
 
   /////////////////////////////////////////////
   // X communications
diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index 5ff16a980e..c443912c96 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -76,7 +76,7 @@ void GlobalField3DAccess::setup() {
     const auto piy = g2ly.convert(gind.y());
     const auto piz = g2lz.convert(gind.z());
     ASSERT3(piz.proc == 0);
-    toGet[(piy.proc * g2lx.getNPE()) + pix.proc].push_back(
+    toGet[mesh.getProcIndex(pix.proc, piy.index, piz.index)].push_back(
         xyzl.convert(pix.ind, piy.ind, piz.ind).ind);
   }
   for (auto& v : toGet) {
@@ -97,7 +97,7 @@ void GlobalField3DAccess::setup() {
     const auto piy = g2ly.convert(gind.y());
     const auto piz = g2lz.convert(gind.z());
     ASSERT3(piz.proc == 0);
-    const auto proc = (piy.proc * g2lx.getNPE()) + pix.proc;
+    const auto proc = mesh.getProcIndex(pix.proc, piy.index, piz.index);
     const auto& vec = toGet[proc];
     const auto tofind = xyzl.convert(pix.ind, piy.ind, piz.ind).ind;
     auto it = std::lower_bound(vec.begin(), vec.end(), tofind);
@@ -116,7 +116,7 @@ void GlobalField3DAccess::commCommLists() {
   {
     int thisproc;
     MPI_Comm_rank(comm, &thisproc);
-    ASSERT0(thisproc == mesh->getYProcIndex() * g2lx.getNPE() + mesh->getXProcIndex());
+    ASSERT0(thisproc == mesh.getProcIndex(pix.proc, piy.index, piz.index));
   }
 #endif
   std::vector<MPI_Request> reqs(toSend.size());

From 4b0ed1c452b4e8c1b1954c47d8cbdb1ededb5377 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:03:02 +0100
Subject: [PATCH 0695/1827] Use getNZPE()

---
 src/mesh/parallel/fci_comm.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index af294989fb..c096b1433a 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -121,7 +121,7 @@ public:
   GlobalField3DAccess(Mesh* mesh)
       : mesh(mesh), g2lx(mesh->xstart, mesh->getNXPE(), mesh->LocalNx, false),
         g2ly(mesh->ystart, mesh->getNYPE(), mesh->LocalNy, true),
-        g2lz(mesh->zstart, 1, mesh->LocalNz, true),
+        g2lz(mesh->zstart, mesh->getNZPE(), mesh->LocalNz, true),
         xyzl(g2lx.getLocalWith(), g2ly.getLocalWith(), g2lz.getLocalWith()),
         xyzg(g2lx.getGlobalWith(), g2ly.getGlobalWith(), g2lz.getGlobalWith()),
         comm(BoutComm::get()) {

From 325dde3feaa545d03ab7b0ac360bf09a975d6f9c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:03:13 +0100
Subject: [PATCH 0696/1827] respect mesh->periodicX

---
 src/mesh/parallel/fci_comm.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index c096b1433a..b90d0e8338 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -119,7 +119,7 @@ class GlobalField3DAccess {
 public:
   friend class GlobalField3DAccessInstance;
   GlobalField3DAccess(Mesh* mesh)
-      : mesh(mesh), g2lx(mesh->xstart, mesh->getNXPE(), mesh->LocalNx, false),
+      : mesh(mesh), g2lx(mesh->xstart, mesh->getNXPE(), mesh->LocalNx, mesh->periodicX),
         g2ly(mesh->ystart, mesh->getNYPE(), mesh->LocalNy, true),
         g2lz(mesh->zstart, mesh->getNZPE(), mesh->LocalNz, true),
         xyzl(g2lx.getLocalWith(), g2ly.getLocalWith(), g2lz.getLocalWith()),

From 8dc7b4f4c3cca4eeb7796c5dda790f745b97b2d5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:03:27 +0100
Subject: [PATCH 0697/1827] Ensure we are periodic in Y

---
 src/mesh/parallel/fci_comm.hxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index b90d0e8338..6f1064eea7 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -127,6 +127,13 @@ public:
         comm(BoutComm::get()) {
 #ifdef _OPENMP
     openmp_ids.resize(omp_get_max_threads());
+#endif
+#if CHECK >= 2
+    // We could also allow false, but then we would need to ensure it
+    // is false everywhere.
+    for (int x = 0; x < mesh->localNx, ++x) {
+      ASSERT2(mesh->periodicY(x) == true);
+    }
 #endif
   };
   void request(IndG3D ind) {

From db5385234a3bc96c73bd89b41ef070a5196f17db Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:03:47 +0100
Subject: [PATCH 0698/1827] avoid static_cast<void*> for pointer

---
 src/mesh/parallel/fci_comm.cxx | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index c443912c96..6419b455c9 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -121,14 +121,12 @@ void GlobalField3DAccess::commCommLists() {
 #endif
   std::vector<MPI_Request> reqs(toSend.size());
   for (size_t proc = 0; proc < toGet.size(); ++proc) {
-    auto ret = MPI_Irecv(static_cast<void*>(&toSendSizes[proc]), 1, MPI_INT, proc, 666,
-                         comm, &reqs[proc]);
+    auto ret = MPI_Irecv(&toSendSizes[proc], 1, MPI_INT, proc, 666, comm, &reqs[proc]);
     ASSERT0(ret == MPI_SUCCESS);
   }
   for (size_t proc = 0; proc < toGet.size(); ++proc) {
     toGetSizes[proc] = toGet[proc].size();
-    auto ret =
-        MPI_Send(static_cast<void*>(&toGetSizes[proc]), 1, MPI_INT, proc, 666, comm);
+    auto ret = MPI_Send(&toGetSizes[proc], 1, MPI_INT, proc, 666, comm);
     ASSERT0(ret == MPI_SUCCESS);
   }
   std::vector<MPI_Request> reqs2(toSend.size());
@@ -146,14 +144,14 @@ void GlobalField3DAccess::commCommLists() {
     sendBufferSize += toSendSizes[ind];
     toSend[ind].resize(toSendSizes[ind], -1);
 
-    ret = MPI_Irecv(static_cast<void*>(toSend[ind].data()), toSend[ind].size(), MPI_INT,
-                    ind, 666 * 666, comm, reqs2.data() + cnt++);
+    ret = MPI_Irecv(toSend[ind].data(), toSend[ind].size(), MPI_INT, ind, 666 * 666, comm,
+                    reqs2.data() + cnt++);
     ASSERT0(ret == MPI_SUCCESS);
   }
   for (size_t proc = 0; proc < toGet.size(); ++proc) {
     if (!toGet[proc].empty()) {
-      const auto ret = MPI_Send(static_cast<void*>(toGet[proc].data()),
-                                toGet[proc].size(), MPI_INT, proc, 666 * 666, comm);
+      const auto ret = MPI_Send(toGet[proc].data(), toGet[proc].size(), MPI_INT, proc,
+                                666 * 666, comm);
       ASSERT0(ret == MPI_SUCCESS);
     }
   }
@@ -178,9 +176,8 @@ std::vector<BoutReal> GlobalField3DAccess::communicate_data(const Field3D& f) {
     if (toGet[proc].empty()) {
       continue;
     }
-    auto ret =
-        MPI_Irecv(static_cast<void*>(data.data() + getOffsets[proc]), toGet[proc].size(),
-                  MPI_DOUBLE, proc, 666, comm, reqs.data() + cnt1);
+    auto ret = MPI_Irecv(data.data() + getOffsets[proc], toGet[proc].size(), MPI_DOUBLE,
+                         proc, 666, comm, reqs.data() + cnt1);
     ASSERT0(ret == MPI_SUCCESS);
     cnt1++;
   }
@@ -189,7 +186,7 @@ std::vector<BoutReal> GlobalField3DAccess::communicate_data(const Field3D& f) {
     if (toSend[proc].empty()) {
       continue;
     }
-    const void* start = static_cast<void*>(sendBuffer.data() + cnt);
+    const void* start = sendBuffer.data() + cnt;
     for (auto i : toSend[proc]) {
       sendBuffer[cnt++] = f[Ind3D(i)];
     }

From dcafb6c6b70afdccfed7e97f055c2bed2ae38aa1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:11:48 +0100
Subject: [PATCH 0699/1827] Add more docs

---
 src/mesh/parallel/fci_comm.cxx | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index 6419b455c9..ff592f20a5 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -62,6 +62,15 @@ fci_comm::ProcLocal fci_comm::GlobalToLocal1D::convert(int id) const {
 }
 
 void GlobalField3DAccess::setup() {
+  // We need to send a list of data to every processor of which data
+  // we want We also get a list of all the data that every other
+  // processor wants Some of theses lists may be empty. We still need
+  // to send them, later we can skip that.  We also compute where the
+  // requested data will be stored later on. This is currently
+  // implemented as a map, to memory efficient, as the data is
+  // sparse. We could also store the mapping as a dense array, if it
+  // turns out this lookup is not fast enough, but that may limit
+  // scaling at some point.
   ASSERT2(is_setup == false);
 #ifdef _OPENMP
   for (auto& o_id : o_ids) {
@@ -164,9 +173,12 @@ void GlobalField3DAccess::commCommLists() {
 }
 
 std::vector<BoutReal> GlobalField3DAccess::communicate_data(const Field3D& f) {
+  // Ensure setup is called, to setup communication pattern
   if (not is_setup) {
     setup();
   }
+  // We now send the previosly requested data to every processor, that wanted some.
+  // We also get the data we requested.
   ASSERT2(f.getMesh() == mesh);
   std::vector<BoutReal> data(getOffsets.back());
   std::vector<BoutReal> sendBuffer(sendBufferSize);

From 424136bc62436d779c1b8d2eef21ef71ef909387 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:14:57 +0100
Subject: [PATCH 0700/1827] Use better names

---
 src/mesh/parallel/fci_comm.cxx | 23 ++++++++++++-----------
 src/mesh/parallel/fci_comm.hxx | 20 ++++++++++----------
 2 files changed, 22 insertions(+), 21 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index ff592f20a5..238d4eb973 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -78,15 +78,16 @@ void GlobalField3DAccess::setup() {
   }
   o_ids.clear();
 #endif
-  toGet.resize(static_cast<size_t>(g2lx.getNPE() * g2ly.getNPE() * g2lz.getNPE()));
+  toGet.resize(static_cast<size_t>(global2local_x.getNPE() * global2local_y.getNPE()
+                                   * global2local_z.getNPE()));
   for (const auto id : ids) {
-    const IndG3D gind{id, g2ly.getGlobalWith(), g2lz.getGlobalWith()};
-    const auto pix = g2lx.convert(gind.x());
-    const auto piy = g2ly.convert(gind.y());
-    const auto piz = g2lz.convert(gind.z());
+    const IndG3D gind{id, global2local_y.getGlobalWith(), global2local_z.getGlobalWith()};
+    const auto pix = global2local_x.convert(gind.x());
+    const auto piy = global2local_y.convert(gind.y());
+    const auto piz = global2local_z.convert(gind.z());
     ASSERT3(piz.proc == 0);
     toGet[mesh.getProcIndex(pix.proc, piy.index, piz.index)].push_back(
-        xyzl.convert(pix.ind, piy.ind, piz.ind).ind);
+        xyzlocal.convert(pix.ind, piy.ind, piz.ind).ind);
   }
   for (auto& v : toGet) {
     std::sort(v.begin(), v.end());
@@ -101,14 +102,14 @@ void GlobalField3DAccess::setup() {
     getOffsets.push_back(offset);
   }
   for (const auto id : ids) {
-    const IndG3D gind{id, g2ly.getGlobalWith(), g2lz.getGlobalWith()};
-    const auto pix = g2lx.convert(gind.x());
-    const auto piy = g2ly.convert(gind.y());
-    const auto piz = g2lz.convert(gind.z());
+    const IndG3D gind{id, global2local_y.getGlobalWith(), global2local_z.getGlobalWith()};
+    const auto pix = global2local_x.convert(gind.x());
+    const auto piy = global2local_y.convert(gind.y());
+    const auto piz = global2local_z.convert(gind.z());
     ASSERT3(piz.proc == 0);
     const auto proc = mesh.getProcIndex(pix.proc, piy.index, piz.index);
     const auto& vec = toGet[proc];
-    const auto tofind = xyzl.convert(pix.ind, piy.ind, piz.ind).ind;
+    const auto tofind = xyzlocal.convert(pix.ind, piy.ind, piz.ind).ind;
     auto it = std::lower_bound(vec.begin(), vec.end(), tofind);
     ASSERT3(it != vec.end());
     ASSERT3(*it == tofind);
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 6f1064eea7..ef7bfd2eac 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -119,11 +119,12 @@ class GlobalField3DAccess {
 public:
   friend class GlobalField3DAccessInstance;
   GlobalField3DAccess(Mesh* mesh)
-      : mesh(mesh), g2lx(mesh->xstart, mesh->getNXPE(), mesh->LocalNx, mesh->periodicX),
-        g2ly(mesh->ystart, mesh->getNYPE(), mesh->LocalNy, true),
-        g2lz(mesh->zstart, mesh->getNZPE(), mesh->LocalNz, true),
-        xyzl(g2lx.getLocalWith(), g2ly.getLocalWith(), g2lz.getLocalWith()),
-        xyzg(g2lx.getGlobalWith(), g2ly.getGlobalWith(), g2lz.getGlobalWith()),
+      : mesh(mesh),
+        global2local_x(mesh->xstart, mesh->getNXPE(), mesh->LocalNx, mesh->periodicX),
+        global2local_y(mesh->ystart, mesh->getNYPE(), mesh->LocalNy, true),
+        global2local_z(mesh->zstart, mesh->getNZPE(), mesh->LocalNz, true),
+        xyzlocal(global2local_x.getLocalWith(), global2local_y.getLocalWith(),
+                 global2local_z.getLocalWith()),
         comm(BoutComm::get()) {
 #ifdef _OPENMP
     openmp_ids.resize(omp_get_max_threads());
@@ -164,13 +165,12 @@ private:
   std::set<int> ids;
   std::map<int, int> mapping;
   bool is_setup{false};
-  fci_comm::GlobalToLocal1D g2lx;
-  fci_comm::GlobalToLocal1D g2ly;
-  fci_comm::GlobalToLocal1D g2lz;
+  fci_comm::GlobalToLocal1D global2local_x;
+  fci_comm::GlobalToLocal1D global2localy;
+  fci_comm::GlobalToLocal1D global2local_z;
 
 public:
-  fci_comm::XYZ2Ind<Ind3D> xyzl;
-  fci_comm::XYZ2Ind<IndG3D> xyzg;
+  fci_comm::XYZ2Ind<Ind3D> xyzlocal;
 
 private:
   std::vector<std::vector<int>> toGet;

From 717864631ccf1417c41acbfde9a347e6888764a6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:35:32 +0100
Subject: [PATCH 0701/1827] Apply clang-tidy fixes

---
 include/bout/boundary_iterator.hxx        | 32 ++++++++++++-----------
 include/bout/boundary_region.hxx          |  2 --
 include/bout/parallel_boundary_region.hxx | 26 ++++++++++--------
 include/bout/sys/parallel_stencils.hxx    |  2 +-
 include/bout/yboundary_regions.hxx        | 11 +++++---
 src/mesh/parallel/fci.cxx                 |  6 ++---
 6 files changed, 43 insertions(+), 36 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index e3ecf8234b..7d8e7ed027 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -7,19 +7,20 @@
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
 #include "bout/parallel_boundary_region.hxx"
+#include "bout/region.hxx"
 #include "bout/sys/parallel_stencils.hxx"
 #include "bout/sys/range.hxx"
-#include <algorithm>
 #include <functional>
 #include <utility>
 
 class BoundaryRegionIter {
 public:
+  virtual ~BoundaryRegionIter() = default;
   BoundaryRegionIter(int x, int y, int bx, int by, Mesh* mesh)
       : dir(bx + by), x(x), y(y), bx(bx), by(by), localmesh(mesh) {
     ASSERT3(bx * by == 0);
   }
-  bool operator!=(const BoundaryRegionIter& rhs) { return ind() != rhs.ind(); }
+  bool operator!=(const BoundaryRegionIter& rhs) const { return ind() != rhs.ind(); }
 
   Ind3D ind() const { return xyz2ind(x, y, z); }
   BoundaryRegionIter& operator++() {
@@ -44,11 +45,13 @@ public:
     return (f[ind()] * 3 - yprev(f)) * 0.5;
   }
 
-  BoutReal extrapolate_next_o2(const Field3D& f) const { return 2 * f[ind()] - yprev(f); }
+  BoutReal extrapolate_next_o2(const Field3D& f) const {
+    return (2 * f[ind()]) - yprev(f);
+  }
 
   BoutReal
   extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return 2 * f(0, ind()) - f(0, ind().yp(-by).xp(-bx));
+    return (2 * f(0, ind())) - f(0, ind().yp(-by).xp(-bx));
   }
 
   BoutReal interpolate_sheath_o2(const Field3D& f) const {
@@ -68,8 +71,8 @@ public:
   BoutReal extrapolate_sheath_free(const Field3D& f, SheathLimitMode mode) const {
     const BoutReal fac =
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
-    BoutReal val = ythis(f);
-    BoutReal next = mode == SheathLimitMode::linear_free ? val + fac : val * fac;
+    const BoutReal val = ythis(f);
+    const BoutReal next = mode == SheathLimitMode::linear_free ? val + fac : val * fac;
     return 0.5 * (val + next);
   }
 
@@ -122,9 +125,7 @@ public:
   }
 
   void limit_at_least(Field3D& f, BoutReal value) const {
-    if (ynext(f) < value) {
-      ynext(f) = value;
-    }
+    ynext(f) = std::max(ynext(f), value);
   }
 
   BoutReal& ynext(Field3D& f) const { return f[ind().yp(by).xp(bx)]; }
@@ -141,7 +142,7 @@ public:
     }
   }
 
-  int abs_offset() const { return 1; }
+  static int abs_offset() { return 1; }
 
 #if BOUT_USE_METRIC_3D == 0
   BoutReal& ynext(Field2D& f) const { return f[ind().yp(by).xp(bx)]; }
@@ -166,13 +167,14 @@ private:
   int nz() const { return localmesh->LocalNz; }
 
   Ind3D xyz2ind(int x, int y, int z) const {
-    return Ind3D{(x * ny() + y) * nz() + z, ny(), nz()};
+    return Ind3D{((x * ny() + y) * nz()) + z, ny(), nz()};
   }
 };
 
 class BoundaryRegionIterY : public BoundaryRegionIter {
 public:
-  BoundaryRegionIterY(RangeIterator r, int y, int dir, bool is_end, Mesh* mesh)
+  virtual ~BoundaryRegionIterY() = default;
+  BoundaryRegionIterY(const RangeIterator& r, int y, int dir, bool is_end, Mesh* mesh)
       : BoundaryRegionIter(r.ind, y, 0, dir, mesh), r(r), is_end(is_end) {}
 
   bool operator!=(const BoundaryRegionIterY& rhs) {
@@ -189,7 +191,7 @@ public:
     return x != rhs.x;
   }
 
-  virtual void _next() override {
+  void _next() override {
     ++r;
     x = r.ind;
   }
@@ -201,8 +203,8 @@ private:
 
 class NewBoundaryRegionY {
 public:
-  NewBoundaryRegionY(Mesh* mesh, bool lower, RangeIterator r)
-      : mesh(mesh), lower(lower), r(std::move(r)) {}
+  NewBoundaryRegionY(Mesh* mesh, bool lower, const RangeIterator& r)
+      : mesh(mesh), lower(lower), r(r) {}
   BoundaryRegionIterY begin(bool begin = true) {
     return BoundaryRegionIterY(r, lower ? mesh->ystart : mesh->yend, lower ? -1 : +1,
                                !begin, mesh);
diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index b73c2e5a02..58de12045e 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -4,8 +4,6 @@ class BoundaryRegion;
 #ifndef BOUT_BNDRY_REGION_H
 #define BOUT_BNDRY_REGION_H
 
-#include "bout/region.hxx"
-#include "bout/sys/parallel_stencils.hxx"
 #include <string>
 #include <utility>
 
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index dbefeb60e6..1d06bc65cb 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -1,18 +1,22 @@
 #ifndef BOUT_PAR_BNDRY_H
 #define BOUT_PAR_BNDRY_H
 
+#include "bout/assert.hxx"
 #include "bout/boundary_region.hxx"
+#include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
 #include <algorithm>
 #include <cmath>
 #include <cstdlib>
 #include <functional>
+#include <string>
 #include <vector>
 
 #include "bout/build_defines.hxx"
 #include "bout/field2d.hxx"
 #include "bout/region.hxx"
 #include "bout/sys/parallel_stencils.hxx"
+#include "bout/utils.hxx"
 #include <bout/field3d.hxx>
 #include <bout/mesh.hxx>
 
@@ -79,7 +83,7 @@ inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, SheathLimitMode mode) {
     fp = SQ(fc) / fm; // Exponential
     break;
   case SheathLimitMode::linear_free:
-    fp = 2.0 * fc - fm; // Linear
+    fp = (2.0 * fc) - fm; // Linear
     break;
   }
 
@@ -139,11 +143,11 @@ public:
     }
     return ythis(f) * (1 + length()) - yprev(f) * length();
   }
-  inline BoutReal
+  BoutReal
   extrapolate_sheath_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return ythis(f);
   }
-  inline BoutReal
+  BoutReal
   extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
@@ -152,16 +156,16 @@ public:
     return ythis(f) * (1 + length()) - yprev(f) * length();
   }
 
-  inline BoutReal interpolate_sheath_o2(const Field3D& f) const {
+  BoutReal interpolate_sheath_o2(const Field3D& f) const {
     return ythis(f) * (1 - length()) + ynext(f) * length();
   }
-  inline BoutReal
+  BoutReal
   interpolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return ythis(f) * (1 - length()) + ynext(f) * length();
   }
 
-  inline BoutReal extrapolate_next_o1(const Field3D& f) const { return ythis(f); }
-  inline BoutReal extrapolate_next_o2(const Field3D& f) const {
+  BoutReal extrapolate_next_o1(const Field3D& f) const { return ythis(f); }
+  BoutReal extrapolate_next_o2(const Field3D& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
       return extrapolate_next_o1(f);
@@ -169,11 +173,11 @@ public:
     return ythis(f) * 2 - yprev(f);
   }
 
-  inline BoutReal
+  BoutReal
   extrapolate_next_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return ythis(f);
   }
-  inline BoutReal
+  BoutReal
   extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
@@ -183,8 +187,8 @@ public:
   }
 
   // extrapolate the gradient into the boundary
-  inline BoutReal extrapolate_grad_o1(const Field3D& f) const { return 0; }
-  inline BoutReal extrapolate_grad_o2(const Field3D& f) const {
+  BoutReal extrapolate_grad_o1([[maybe_unused]] const Field3D& f) const { return 0; }
+  BoutReal extrapolate_grad_o2(const Field3D& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
       return extrapolate_grad_o1(f);
diff --git a/include/bout/sys/parallel_stencils.hxx b/include/bout/sys/parallel_stencils.hxx
index 1d55931ff3..ed6daa5558 100644
--- a/include/bout/sys/parallel_stencils.hxx
+++ b/include/bout/sys/parallel_stencils.hxx
@@ -20,7 +20,7 @@ inline BoutReal dirichlet_o2(BoutReal spacing0, BoutReal value0, BoutReal spacin
 }
 inline BoutReal neumann_o2([[maybe_unused]] BoutReal spacing0, BoutReal value0,
                            BoutReal spacing1, BoutReal value1) {
-  return -spacing1 * value0 + value1;
+  return (-spacing1 * value0) + value1;
 }
 inline BoutReal dirichlet_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1,
                              BoutReal value1, BoutReal spacing2, BoutReal value2) {
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 74a68377c9..e5a9086397 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -54,10 +54,13 @@ public:
       mesh = bout::globals::mesh;
     }
 
-    bool lower_y = options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(true);
-    bool upper_y = options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(true);
-    bool outer_x = options["outer_x"].doc("Boundary on outer x?").withDefault<bool>(true);
-    bool inner_x =
+    const bool lower_y =
+        options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(true);
+    const bool upper_y =
+        options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(true);
+    const bool outer_x =
+        options["outer_x"].doc("Boundary on outer x?").withDefault<bool>(true);
+    const bool inner_x =
         options["inner_x"].doc("Boundary on inner x?").withDefault<bool>(false);
 
     if (mesh->isFci()) {
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 28b8db9326..a14522b3d9 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -189,7 +189,7 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
 
   BoutMask to_remove(map_mesh);
   const int xend = map_mesh->xstart
-                   + (map_mesh->xend - map_mesh->xstart + 1) * map_mesh->getNXPE() - 1;
+                   + ((map_mesh->xend - map_mesh->xstart + 1) * map_mesh->getNXPE()) - 1;
   // Default to the maximum number of points
   const int defValid{map_mesh->ystart - 1 + std::abs(offset)};
   // Serial loop because call to BoundaryRegionPar::addPoint
@@ -262,7 +262,7 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
     ASSERT2(map_mesh->xend - map_mesh->xstart >= 2);
     auto boundary = (xt_prime[i] < map_mesh->xstart) ? inner_boundary : outer_boundary;
     if (!boundary->contains(x, y, z)) {
-      boundary->add_point(x, y, z, x + dx, y + offset - sgn(offset) * 0.5,
+      boundary->add_point(x, y, z, x + dx, y + offset - (sgn(offset) * 0.5),
                           z + dz, // Intersection point in local index space
                           std::abs(offset) - 0.5, // Distance to intersection
                           defValid, offset);
@@ -366,7 +366,7 @@ FCITransform::FCITransform(Mesh& mesh, const Coordinates::FieldMetric& dy, bool
   }
   const std::array bndries = {forward_boundary_xin, forward_boundary_xout,
                               backward_boundary_xin, backward_boundary_xout};
-  for (auto& bndry : bndries) {
+  for (const auto& bndry : bndries) {
     for (const auto& bndry2 : bndries) {
       if (bndry->dir == bndry2->dir) {
         continue;

From 7975518600c1930a1c98dfd92ffec91e34b474a6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:38:49 +0100
Subject: [PATCH 0702/1827] Add missing header

---
 include/bout/sys/parallel_stencils.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/sys/parallel_stencils.hxx b/include/bout/sys/parallel_stencils.hxx
index ed6daa5558..2cbec9c8b0 100644
--- a/include/bout/sys/parallel_stencils.hxx
+++ b/include/bout/sys/parallel_stencils.hxx
@@ -1,4 +1,6 @@
 #pragma once
+#include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 
 namespace parallel_stencil {
 // generated by src/mesh/parallel_boundary_stencil.cxx.py

From 500989be908114629ec1bbedf7c5888b1d020178 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:43:54 +0100
Subject: [PATCH 0703/1827] Fixup getProcIndex

---
 src/mesh/impls/bout/boutmesh.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index ac797f81cd..3dad85f211 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -1017,7 +1017,7 @@ void BoutMesh::createXBoundaries() {
   }
 }
 
-int BoutMesh::getProcIndex(int X, int Y, int Z) { return Y * NXPE + X; }
+int BoutMesh::getProcIndex(int X, int Y, int Z) const { return Y * NXPE + X; }
 
 void BoutMesh::createYBoundaries() {
   if (MYG <= 0) {

From cabf678708f5fd68f0e650ed904e861101dc2315 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 12:45:06 +0100
Subject: [PATCH 0704/1827] Add headers from clang-tidy

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 2 ++
 src/mesh/parallel/fci_comm.cxx               | 3 +++
 2 files changed, 5 insertions(+)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index f622ff572e..6ec1549429 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -23,6 +23,8 @@
 #include "../impls/bout/boutmesh.hxx"
 #include "../parallel/fci_comm.hxx"
 #include "bout/bout.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/globals.hxx"
 #include "bout/index_derivs_interface.hxx"
 #include "bout/interpolation_xz.hxx"
diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index 238d4eb973..c81b1c30a7 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -28,6 +28,9 @@
 #include "bout/bout_types.hxx"
 #include "bout/region.hxx"
 
+#include <algorithm>
+#include <cstddef>
+#include <mpi.h>
 #include <vector>
 
 fci_comm::ProcLocal fci_comm::GlobalToLocal1D::convert(int id) const {

From 01e22639c8e85f13397b6bff075ec9dbdc38055c Mon Sep 17 00:00:00 2001
From: dschwoerer <5637662+dschwoerer@users.noreply.github.com>
Date: Tue, 10 Mar 2026 11:54:53 +0000
Subject: [PATCH 0705/1827] [bot] Apply format changes

---
 src/mesh/parallel/fci_comm.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index ef7bfd2eac..852297fde8 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -71,7 +71,7 @@ struct ProcLocal {
 struct GlobalToLocal1D {
   GlobalToLocal1D(int mg, int npe, int localwith, bool periodic)
       : mg(mg), npe(npe), localwith(localwith), local(localwith - (2 * mg)),
-        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic) {};
+        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic){};
   ProcLocal convert(int id) const;
   int getLocalWith() const { return localwith; }
   int getGlobalWith() const { return globalwith; }

From 6bd15d2e0be02f63ff2b8a251e1ea3463750f4e0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 13:12:07 +0100
Subject: [PATCH 0706/1827] Apply clang-tidy fixes

---
 include/bout/interpolation_xz.hxx            |  4 ++--
 src/mesh/interpolation/hermite_spline_xz.cxx | 16 ++++++++--------
 src/mesh/parallel/fci_comm.cxx               |  5 +++--
 src/mesh/parallel/fci_comm.hxx               |  8 ++------
 4 files changed, 15 insertions(+), 18 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 9639a0a80e..d14a5eeca0 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -176,8 +176,8 @@ protected:
 #if BOUT_HAS_PETSC
   PetscLib* petsclib;
   bool isInit{false};
-  Mat petscWeights;
-  Vec rhs, result;
+  Mat petscWeights{};
+  Vec rhs{}, result{};
 #endif
 
   /// Factors to allow for some wiggleroom
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 6ec1549429..eec1e8adce 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -178,7 +178,7 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
   const int nz = localmesh->LocalNz;
   const int xend = (localmesh->xend - localmesh->xstart + 1) * localmesh->getNXPE()
                    + localmesh->xstart - 1;
-  [[maybe_unused]] IndConverter conv{localmesh};
+  [[maybe_unused]] const IndConverter conv{localmesh};
 
   [[maybe_unused]] const int y_global_offset =
       localmesh->getYProcIndex() * (localmesh->yend - localmesh->ystart + 1);
@@ -320,7 +320,7 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
           for (int k = 0; k < 4; ++k) {
             idxm[k] = conv.fromMeshToGlobal(i_corn - 1 + j, y + y_offset,
                                             k_corner(x, y, z) - 1 + k);
-            vals[k] = newWeights[j * 4 + k][i];
+            vals[k] = newWeights[(j * 4) + k][i];
           }
           MatSetValues(petscWeights, 1, idxn, 4, idxm, vals, INSERT_VALUES);
         }
@@ -406,8 +406,8 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
   }
 
   if constexpr (imp_type == implementation_type::petsc) {
-    BoutReal* ptr;
-    const BoutReal* cptr;
+    BoutReal* ptr = nullptr;
+    const BoutReal* cptr = nullptr;
     VecGetArray(rhs, &ptr);
     BOUT_FOR(i, f.getRegion("RGN_NOY")) { ptr[int(i)] = f[i]; }
     VecRestoreArray(rhs, &ptr);
@@ -438,10 +438,10 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
 
       f_interp[iyp] = 0;
       for (int w = 0; w < 4; ++w) {
-        f_interp[iyp] += newWeights[w * 4 + 0][i] * f[ic.zm().xp(w - 1)];
-        f_interp[iyp] += newWeights[w * 4 + 1][i] * f[ic.xp(w - 1)];
-        f_interp[iyp] += newWeights[w * 4 + 2][i] * f[ic.zp().xp(w - 1)];
-        f_interp[iyp] += newWeights[w * 4 + 3][i] * f[ic.zp(2).xp(w - 1)];
+        f_interp[iyp] += newWeights[(w * 4) + 0][i] * f[ic.zm().xp(w - 1)];
+        f_interp[iyp] += newWeights[(w * 4) + 1][i] * f[ic.xp(w - 1)];
+        f_interp[iyp] += newWeights[(w * 4) + 2][i] * f[ic.zp().xp(w - 1)];
+        f_interp[iyp] += newWeights[(w * 4) + 3][i] * f[ic.zp(2).xp(w - 1)];
       }
       if constexpr (monotonic) {
         const auto corners = {(*gf)[IndG3D(g3dinds[i][0])], (*gf)[IndG3D(g3dinds[i][1])],
diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index c81b1c30a7..6cd59d96cb 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -26,6 +26,7 @@
 #include "fci_comm.hxx"
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/field3d.hxx"
 #include "bout/region.hxx"
 
 #include <algorithm>
@@ -89,7 +90,7 @@ void GlobalField3DAccess::setup() {
     const auto piy = global2local_y.convert(gind.y());
     const auto piz = global2local_z.convert(gind.z());
     ASSERT3(piz.proc == 0);
-    toGet[mesh.getProcIndex(pix.proc, piy.index, piz.index)].push_back(
+    toGet[mesh->getProcIndex(pix.proc, piy.index, piz.index)].push_back(
         xyzlocal.convert(pix.ind, piy.ind, piz.ind).ind);
   }
   for (auto& v : toGet) {
@@ -110,7 +111,7 @@ void GlobalField3DAccess::setup() {
     const auto piy = global2local_y.convert(gind.y());
     const auto piz = global2local_z.convert(gind.z());
     ASSERT3(piz.proc == 0);
-    const auto proc = mesh.getProcIndex(pix.proc, piy.index, piz.index);
+    const auto proc = mesh->getProcIndex(pix.proc, piy.index, piz.index);
     const auto& vec = toGet[proc];
     const auto tofind = xyzlocal.convert(pix.ind, piy.ind, piz.ind).ind;
     auto it = std::lower_bound(vec.begin(), vec.end(), tofind);
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 852297fde8..ae286fd232 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -31,10 +31,6 @@
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
 #include "bout/region.hxx"
-#include <algorithm>
-#include <cstddef>
-#include <cstdio>
-#include <iterator>
 #include <map>
 #include <memory>
 #include <set>
@@ -166,11 +162,11 @@ private:
   std::map<int, int> mapping;
   bool is_setup{false};
   fci_comm::GlobalToLocal1D global2local_x;
-  fci_comm::GlobalToLocal1D global2localy;
+  fci_comm::GlobalToLocal1D global2local_y;
   fci_comm::GlobalToLocal1D global2local_z;
 
 public:
-  fci_comm::XYZ2Ind<Ind3D> xyzlocal;
+  fci_comm::XYZ2Ind<Ind3D> xyzlocal{};
 
 private:
   std::vector<std::vector<int>> toGet;

From f2d860f80dcf5de4d728a2c8a8e821b7d81d1428 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 10 Mar 2026 13:36:46 +0100
Subject: [PATCH 0707/1827] Fixup compile issues

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 10 +++++-----
 src/mesh/parallel/fci_comm.cxx               | 10 ++++++----
 src/mesh/parallel/fci_comm.hxx               | 11 +++++++----
 3 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index eec1e8adce..0a2c9904c7 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -44,7 +44,7 @@ class IndConverter {
         lnz(mesh->LocalNz - 2 * zstart) {}
   // ix and iz are global indices
   // iy is local
-  int fromMeshToGlobal(int ix, int iy, int iz) {
+  int fromMeshToGlobal(int ix, int iy, int iz) const {
     const int xstart = mesh->xstart;
     const int lnx = mesh->LocalNx - xstart * 2;
     // x-proc-id
@@ -78,12 +78,12 @@ class IndConverter {
     return fromLocalToGlobal(ix - pex * lnx, iy - pey_offset * lny, iz - pez * lnz, pex,
                              pey, 0);
   }
-  int fromLocalToGlobal(const int ilocalx, const int ilocaly, const int ilocalz) {
+  int fromLocalToGlobal(const int ilocalx, const int ilocaly, const int ilocalz) const {
     return fromLocalToGlobal(ilocalx, ilocaly, ilocalz, mesh->getXProcIndex(),
                              mesh->getYProcIndex(), 0);
   }
   int fromLocalToGlobal(const int ilocalx, const int ilocaly, const int ilocalz,
-                        const int pex, const int pey, const int pez) {
+                        const int pex, const int pey, const int pez) const {
     ASSERT3(ilocalx >= 0);
     ASSERT3(ilocaly >= 0);
     ASSERT3(ilocalz >= 0);
@@ -327,8 +327,8 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
       }
     }
     if constexpr (monotonic) {
-      const auto gind =
-          gf3daccess->xyzg(i_corn, y + y_offset + y_global_offset, k_corner(x, y, z));
+      const auto gind = gf3daccess->xyzglobal(i_corn, y + y_offset + y_global_offset,
+                                              k_corner(x, y, z));
       gf3daccess->request(gind);
       gf3daccess->request(gind.xp(1));
       gf3daccess->request(gind.zp(1));
diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index 6cd59d96cb..a9c574c430 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -90,8 +90,8 @@ void GlobalField3DAccess::setup() {
     const auto piy = global2local_y.convert(gind.y());
     const auto piz = global2local_z.convert(gind.z());
     ASSERT3(piz.proc == 0);
-    toGet[mesh->getProcIndex(pix.proc, piy.index, piz.index)].push_back(
-        xyzlocal.convert(pix.ind, piy.ind, piz.ind).ind);
+    toGet[mesh->getProcIndex(pix.proc, piy.proc, piz.proc)].push_back(
+        xyzlocal.convert(pix.index, piy.index, piz.index).ind);
   }
   for (auto& v : toGet) {
     std::sort(v.begin(), v.end());
@@ -113,7 +113,7 @@ void GlobalField3DAccess::setup() {
     ASSERT3(piz.proc == 0);
     const auto proc = mesh->getProcIndex(pix.proc, piy.index, piz.index);
     const auto& vec = toGet[proc];
-    const auto tofind = xyzlocal.convert(pix.ind, piy.ind, piz.ind).ind;
+    const auto tofind = xyzlocal.convert(pix.index, piy.index, piz.index).ind;
     auto it = std::lower_bound(vec.begin(), vec.end(), tofind);
     ASSERT3(it != vec.end());
     ASSERT3(*it == tofind);
@@ -130,7 +130,9 @@ void GlobalField3DAccess::commCommLists() {
   {
     int thisproc;
     MPI_Comm_rank(comm, &thisproc);
-    ASSERT0(thisproc == mesh.getProcIndex(pix.proc, piy.index, piz.index));
+    ASSERT0(thisproc
+            == mesh->getProcIndex(mesh->getXProcIndex(), mesh->getYProcIndex(),
+                                  mesh->getZProcIndex()));
   }
 #endif
   std::vector<MPI_Request> reqs(toSend.size());
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index ae286fd232..324cae8a22 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -59,7 +59,7 @@ class GlobalField3DAccess;
 namespace fci_comm {
 struct ProcLocal {
   int proc;
-  int ind;
+  int index;
 };
 
 /// Class to convert global to local indices for 1D
@@ -121,6 +121,8 @@ public:
         global2local_z(mesh->zstart, mesh->getNZPE(), mesh->LocalNz, true),
         xyzlocal(global2local_x.getLocalWith(), global2local_y.getLocalWith(),
                  global2local_z.getLocalWith()),
+        xyzglobal(global2local_x.getGlobalWith(), global2local_y.getGlobalWith(),
+                  global2local_z.getGlobalWith()),
         comm(BoutComm::get()) {
 #ifdef _OPENMP
     openmp_ids.resize(omp_get_max_threads());
@@ -128,7 +130,7 @@ public:
 #if CHECK >= 2
     // We could also allow false, but then we would need to ensure it
     // is false everywhere.
-    for (int x = 0; x < mesh->localNx, ++x) {
+    for (int x = 0; x < mesh->LocalNx; ++x) {
       ASSERT2(mesh->periodicY(x) == true);
     }
 #endif
@@ -166,7 +168,8 @@ private:
   fci_comm::GlobalToLocal1D global2local_z;
 
 public:
-  fci_comm::XYZ2Ind<Ind3D> xyzlocal{};
+  fci_comm::XYZ2Ind<Ind3D> xyzlocal;
+  fci_comm::XYZ2Ind<IndG3D> xyzglobal;
 
 private:
   std::vector<std::vector<int>> toGet;
@@ -177,7 +180,7 @@ private:
   std::vector<BoutReal> communicate_data(const Field3D& f);
 };
 
-const BoutReal& GlobalField3DAccessInstance::operator[](IndG3D ind) const {
+inline const BoutReal& GlobalField3DAccessInstance::operator[](IndG3D ind) const {
   auto it = gfa->mapping.find(ind.ind);
   ASSERT2(it != gfa->mapping.end());
   return data[it->second];

From 0ecb0d96e6c5aedfafa4dd32f30aeb7ca53d5516 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 10 Mar 2026 14:36:15 -0700
Subject: [PATCH 0708/1827] pvode: Don't include bits/basic_string

Not included in Clang distributions. Does not seem
to be needed.
---
 src/solver/impls/pvode/pvode.cxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 8ccd5f134a..38901a2a57 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -47,7 +47,6 @@
 
 #include "fmt/format.h"
 
-#include <bits/basic_string.h>
 #include <memory>
 #include <string>
 #include <vector>

From 159ce2ff3da1cf9275b3d9abce7c9b1e4893e6ad Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 09:49:55 +0100
Subject: [PATCH 0709/1827] Add getProcIndex to fake_mesh

Also, the indices should all start at 0
---
 tests/unit/fake_mesh.hxx | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 4656ee0282..cb7509ebde 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -113,9 +113,13 @@ public:
   int getNXPE() const override { return 1; }
   int getNYPE() const override { return 1; }
   int getNZPE() const override { return 1; }
-  int getXProcIndex() const override { return 1; }
-  int getYProcIndex() const override { return 1; }
-  int getZProcIndex() const override { return 1; }
+  int getXProcIndex() const override { return 0; }
+  int getYProcIndex() const override { return 0; }
+  int getZProcIndex() const override { return 0; }
+  int getProcIndex([[maybe_unused]] int X, [[maybe_unused]] int Y,
+                   [[maybe_unused]] int Z) const override {
+    return 0;
+  }
   bool firstX() const override { return true; }
   bool lastX() const override { return true; }
   int sendXOut(BoutReal* UNUSED(buffer), int UNUSED(size), int UNUSED(tag)) override {

From 1de6329a351074036a4e7168896f1ca58723ba54 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 09:56:55 +0100
Subject: [PATCH 0710/1827] Add guards for petsc related code

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 0a2c9904c7..48e7d2904e 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -151,11 +151,13 @@ XZHermiteSplineBase<monotonic, imp_type>::XZHermiteSplineBase(int y_offset, Mesh
     }
   }
   if constexpr (imp_type == implementation_type::petsc) {
+#if BOUT_HAS_PETSC
     petsclib = new PetscLib(
         &Options::root()["mesh:paralleltransform:xzinterpolation:hermitespline"]);
     const int m = localmesh->LocalNx * localmesh->LocalNy * localmesh->LocalNz;
     const int M = m * localmesh->getNXPE() * localmesh->getNYPE() * localmesh->getNZPE();
     MatCreateAIJ(BoutComm::get(), m, m, M, M, 16, nullptr, 16, nullptr, &petscWeights);
+#endif
   }
   if constexpr (monotonic) {
     gf3daccess = std::make_unique<GlobalField3DAccess>(localmesh);
@@ -308,6 +310,7 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
       newWeights[7][i] -= h11_x[i] * h11_z[i] / 4;
       newWeights[5][i] += h11_x[i] * h11_z[i] / 4;
       if (imp_type == implementation_type::petsc) {
+#if BOUT_HAS_PETSC
         PetscInt idxn[1] = {conv.fromLocalToGlobal(x, y + y_offset, z)};
         // output.write("debug: {:d} -> {:d}: {:d}:{:d} -> {:d}:{:d}\n",
         // conv.fromLocalToGlobal(x, y + y_offset, z),
@@ -324,6 +327,7 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
           }
           MatSetValues(petscWeights, 1, idxn, 4, idxm, vals, INSERT_VALUES);
         }
+#endif
       }
     }
     if constexpr (monotonic) {
@@ -337,12 +341,14 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
     }
   }
   if constexpr (imp_type == implementation_type::petsc) {
+#if BOUT_HAS_PETSC
     MatAssemblyBegin(petscWeights, MAT_FINAL_ASSEMBLY);
     MatAssemblyEnd(petscWeights, MAT_FINAL_ASSEMBLY);
     if (!isInit) {
       MatCreateVecs(petscWeights, &rhs, &result);
     }
     isInit = true;
+#endif
   }
 }
 
@@ -406,6 +412,7 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
   }
 
   if constexpr (imp_type == implementation_type::petsc) {
+#if BOUT_HAS_PETSC
     BoutReal* ptr = nullptr;
     const BoutReal* cptr = nullptr;
     VecGetArray(rhs, &ptr);
@@ -429,6 +436,7 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
       ASSERT2(std::isfinite(cptr[int(i)]));
     }
     VecRestoreArrayRead(result, &cptr);
+#endif
   }
 
   if constexpr (imp_type == implementation_type::new_weights) {

From dbb69599079fcf5411fce1ad913928ca766fb6bd Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 17:06:06 +0000
Subject: [PATCH 0711/1827] dev: Add pre-commit config

---
 .pre-commit-config.yaml |  62 ++++
 pyproject.toml          |  20 ++
 uv.lock                 | 698 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 780 insertions(+)
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 uv.lock

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000..a6fefc34cb
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,62 @@
+# This file requires prek rather than pre-commit
+exclude:
+  glob:
+    - "tools/**/*.pro"
+    - "tools/**/*.m"
+    - "tools/**/*.[ch]"
+
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: builtin
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-added-large-files
+
+# This would be nice to use, but it is a significant slowdown:
+
+# # Sync versions of hook tools with `uv.lock`
+# - repo: https://github.com/tsvikas/sync-with-uv
+#   rev: v0.5.0
+#   hooks:
+#     - id: sync-with-uv
+
+# C++ formatting
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v22.1.0
+  hooks:
+  - id: clang-format
+    types_or: [c++, c, cuda]
+
+# Python linting and formatting
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.15.5
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+    # Run the formatter.
+    - id: ruff-format
+
+# CMake formatting
+- repo: https://github.com/cheshirekow/cmake-format-precommit
+  rev: v0.6.13
+  hooks:
+    - id: cmake-format
+      additional_dependencies: [pyyaml>=5.1]
+
+# Various config files
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.37.0
+  hooks:
+    - id: check-github-workflows
+    - id: check-readthedocs
+    - id: check-citation-file-format
+    - id: check-dependabot
+
+# Docs linting
+- repo: https://github.com/sphinx-contrib/sphinx-lint
+  rev: v1.0.2
+  hooks:
+    - id: sphinx-lint
+      files: 'manual/sphinx/.*'
diff --git a/pyproject.toml b/pyproject.toml
index a87e8bb674..71a67f87dd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,3 +4,23 @@ requires = []
 # Defined by PEP 517:
 build-backend = "backend"
 backend-path = ["tools/pylib/_boutpp_build/"]
+
+[dependency-groups]
+dev = [
+     "cmake~=4.2",
+     "clang-format~=22.0",
+     "clang-tidy~=22.0",
+     "clangd~=22.0",
+     "clangd-tidy~=1.1",
+     "cmakelang~=0.6",
+     "prek>=0.3.5",
+     "pyyaml~=6.0",
+     "ruff~=0.15",
+     "sphinx-lint~=1.0",
+     "sync-with-uv~=0.5.0",
+]
+maint = [
+      "pygithub~=2.8",
+      "ruamel-yaml~=0.19",
+      "Unidecode~=1.3",
+]
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 0000000000..8dce73e775
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,698 @@
+version = 1
+revision = 3
+requires-python = ">=3.14"
+
+[manifest]
+
+[manifest.dependency-groups]
+dev = [
+    { name = "clang-format", specifier = "~=22.0" },
+    { name = "clang-tidy", specifier = "~=22.0" },
+    { name = "clangd", specifier = "~=22.0" },
+    { name = "clangd-tidy", specifier = "~=1.1" },
+    { name = "cmake", specifier = "~=4.2" },
+    { name = "cmakelang", specifier = "~=0.6" },
+    { name = "prek", specifier = ">=0.3.5" },
+    { name = "pyyaml", specifier = "~=6.0" },
+    { name = "ruff", specifier = "~=0.15" },
+    { name = "sphinx-lint", specifier = "~=1.0" },
+    { name = "sync-with-uv", specifier = "~=0.5.0" },
+]
+maint = [
+    { name = "pygithub", specifier = "~=2.8" },
+    { name = "ruamel-yaml", specifier = "~=0.19" },
+    { name = "unidecode", specifier = "~=1.3" },
+]
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+[[package]]
+name = "attrs"
+version = "25.4.0"
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From 9e29906259b0e97fb331b1925590409101842b5a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 18:12:37 +0000
Subject: [PATCH 0712/1827] docs: Ignore venv directories

---
 manual/sphinx/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manual/sphinx/conf.py b/manual/sphinx/conf.py
index 6046173aef..69ed52aeed 100755
--- a/manual/sphinx/conf.py
+++ b/manual/sphinx/conf.py
@@ -192,7 +192,7 @@ def __getattr__(cls, name):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv", "venv"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"

From 0f276272869b5413023601baedd5d630ed46274c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 18:12:55 +0000
Subject: [PATCH 0713/1827] docs: Describe formatters and linters used in the
 project

---
 manual/sphinx/developer_docs/contributing.rst | 58 +++++++++++++++++++
 requirements_dev.txt                          |  6 ++
 2 files changed, 64 insertions(+)
 create mode 100644 requirements_dev.txt

diff --git a/manual/sphinx/developer_docs/contributing.rst b/manual/sphinx/developer_docs/contributing.rst
index 4453f518b6..a7aca902d4 100644
--- a/manual/sphinx/developer_docs/contributing.rst
+++ b/manual/sphinx/developer_docs/contributing.rst
@@ -142,6 +142,45 @@ then they will be able to checkout your branch::
 *Note*: If you have write access to the central BOUT-dev repository, you
 can push your branches there.
 
+Running Tests
+~~~~~~~~~~~~~
+
+We run many tests and checks automatically on GitHub for a variety of build
+configurations. See :ref:`sec-runtestsuite` for how to run them
+locally. Running the full test suite can take some time, but it's a good idea to
+run at least the unit tests locally when you're making changes.
+
+Install Pre-Commit Hooks (Optional but recommended)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Along with the automated tests, we also run things like formatters and static
+analysis. For frequent developers, we strongly recommend installing them locally
+and building them into your regular workflow. You can install the majority of
+our developer tools at once using `uv <https://docs.astral.sh/uv/>`_:
+
+.. code-block:: console
+
+    uv sync --only-dev
+
+This will create a new virtual environment (typically under ``.venv``) and
+install all the tools into that. You can then activate the virtual environment
+and use the tools manually, or via integrations in your editor.
+
+We also have a `prek <https://prek.j178.dev>`_ config that can run some of
+these automatically when you make commits using "pre-commit hooks". Install our
+developer tools with ``uv`` as above, and then install the pre-commit hook:
+
+.. code-block:: console
+
+    prek install
+
+This will then automatically call things like `clang-format
+<https://clang.llvm.org/docs/ClangFormat.html>`_ and `ruff
+<https://astral.sh/ruff>`_ when you create a commit, and abort the commit if
+there's a problem, for example if a formatter changes any files. For the
+formatters, this usually just means staging any changes they make and trying
+again.
+
 Making changes, commits
 ~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -189,6 +228,25 @@ These guidelines are intended to make code easier to read and therefore
 easier to understand. Being consistent in coding style also helps
 comprehension by reducing cognitive load.
 
+We use various tools to enforce code style and quality:
+
+- `clang-format <https://clang.llvm.org/docs/ClangFormat.html>`_ for formatting
+  of C++ code
+- `clang-tidy <https://clang.llvm.org/extra/clang-tidy/index.html>`_ for linting
+  and static analysis of C++ code
+- `ruff <https://astral.sh/ruff>`_ for formatting and linting of Python code
+- `cmake-format <https://github.com/cheshirekow/cmake_format>`_ for formatting
+  CMake files
+- `sphinx-lint <https://github.com/sphinx-contrib/sphinx-lint>`_ for linting
+  documentation pages
+
+You can install all of these tools using:
+
+.. code-block:: console
+
+    pip install -r requirements_dev.txt
+
+
 Comments
 ~~~~~~~~
 
diff --git a/requirements_dev.txt b/requirements_dev.txt
new file mode 100644
index 0000000000..ba0eeb91e2
--- /dev/null
+++ b/requirements_dev.txt
@@ -0,0 +1,6 @@
+clang-format~=22.0
+clang-tidy~=22.0
+cmakelang~=0.6
+pre-commit>=4.5.1
+ruff
+sphinx-lint~=1.0

From da01a2611498c259e5d3edbe0d208a65a8dcb2a1 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 18:14:36 +0000
Subject: [PATCH 0714/1827] maint: Ignore noisy `clang-tidy` warning

`cppcoreguidelines-pro-bounds-avoid-unchecked-container-access` is not really
suitable for numerical code
---
 .clang-tidy | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.clang-tidy b/.clang-tidy
index 121c3f3a60..6fc7fd19d9 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -1,5 +1,5 @@
 ---
-Checks:          'clang-diagnostic-*,clang-analyzer-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters,-readability-identifier-length'
+Checks:          'clang-diagnostic-*,clang-analyzer-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters,-readability-identifier-length,-cppcoreguidelines-pro-bounds-avoid-unchecked-container-access'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
 FormatStyle:     file
@@ -29,6 +29,7 @@ These are all basically unavoidable in HPC numeric code:
 -readability-magic-numbers
 -cppcoreguidelines-avoid-magic-numbers
 -cppcoreguidelines-pro-bounds-pointer-arithmetic
+-cppcoreguidelines-pro-bounds-avoid-unchecked-container-access
 -readability-function-cognitive-complexity
 -bugprone-easily-swappable-parameters
 -readability-identifier-length

From 8f24e1ee436385bd73d36b92919d28b14d46021a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 18:15:31 +0000
Subject: [PATCH 0715/1827] maint: Enforce `const` on the left of types

---
 .clang-format | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.clang-format b/.clang-format
index a80c59bddd..51cf39683a 100644
--- a/.clang-format
+++ b/.clang-format
@@ -93,6 +93,7 @@ PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 60
 PointerAlignment: Left
+QualifierAlignment: Left
 ReflowComments:  false
 SortIncludes:    true
 # SortUsingDeclarations: true

From 64bf672bd3a3bc2d801fad29cff0acdf947a3ee1 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 18:15:52 +0000
Subject: [PATCH 0716/1827] maint: Add `clangd` config for editors

---
 .clangd | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 .clangd

diff --git a/.clangd b/.clangd
new file mode 100644
index 0000000000..421b7e10d3
--- /dev/null
+++ b/.clangd
@@ -0,0 +1,6 @@
+Diagnostics:
+  MissingIncludes: Strict
+  ClangTidy:
+    FastCheckFilter: None
+  Includes:
+    IgnoreHeader: ["adios2/.*", "bits/.*", "cpptrace/.*", "petsc.*"]

From d4692f03c670b2a22e505dc63a38c83d7634fe3b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 18:17:14 +0000
Subject: [PATCH 0717/1827] CI: Don't add formatting commits to
 `.git-blame-ignore-revs`

---
 .github/workflows/auto-formatting.yml | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/.github/workflows/auto-formatting.yml b/.github/workflows/auto-formatting.yml
index f54b012298..f49f9c65d0 100644
--- a/.github/workflows/auto-formatting.yml
+++ b/.github/workflows/auto-formatting.yml
@@ -38,7 +38,7 @@ jobs:
           pwd
           ls
           $HOME/.local/bin/ruff format .
-          
+
       - name: Run cmake-format
         run: |
           pwd
@@ -50,13 +50,3 @@ jobs:
         with:
           commit_message: "[bot] Apply format changes"
           skip_push: true
-
-      - name: Ignore formatting
-        run: |
-          msg=$(git rev-list --format=%s --max-count=1 HEAD|tail -n -1)
-          test "$msg" = "[bot] Apply format changes" && git rev-parse HEAD >> .git-blame-ignore-revs || :
-
-      - name: Commit formatting
-        uses: stefanzweifel/git-auto-commit-action@v7
-        with:
-          commit_message: "[bot] Add last format changes commit to ignore file"

From 47f93b19ed48e17cb8669f89c38a9395e3aff09c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 10:17:35 +0100
Subject: [PATCH 0718/1827] Fixup: always use proc for proc computation

---
 src/mesh/parallel/fci_comm.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index a9c574c430..562a9e5589 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -111,7 +111,7 @@ void GlobalField3DAccess::setup() {
     const auto piy = global2local_y.convert(gind.y());
     const auto piz = global2local_z.convert(gind.z());
     ASSERT3(piz.proc == 0);
-    const auto proc = mesh->getProcIndex(pix.proc, piy.index, piz.index);
+    const auto proc = mesh->getProcIndex(pix.proc, piy.proc, piz.proc);
     const auto& vec = toGet[proc];
     const auto tofind = xyzlocal.convert(pix.index, piy.index, piz.index).ind;
     auto it = std::lower_bound(vec.begin(), vec.end(), tofind);

From 58db33a02130e955be86a472d53a1f65282aa800 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 10:26:05 +0100
Subject: [PATCH 0719/1827] Fixup rename

---
 src/mesh/parallel/fci_comm.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/parallel/fci_comm.cxx b/src/mesh/parallel/fci_comm.cxx
index 562a9e5589..3d213ad6e4 100644
--- a/src/mesh/parallel/fci_comm.cxx
+++ b/src/mesh/parallel/fci_comm.cxx
@@ -77,10 +77,10 @@ void GlobalField3DAccess::setup() {
   // scaling at some point.
   ASSERT2(is_setup == false);
 #ifdef _OPENMP
-  for (auto& o_id : o_ids) {
+  for (auto& o_id : openmp_ids) {
     ids.merge(o_id);
   }
-  o_ids.clear();
+  openmp_ids.clear();
 #endif
   toGet.resize(static_cast<size_t>(global2local_x.getNPE() * global2local_y.getNPE()
                                    * global2local_z.getNPE()));

From 95f7f17e3e32e6d81063b9cd021053665e18809e Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 10 Mar 2026 20:54:48 +0000
Subject: [PATCH 0720/1827] CI: Run all formatters and linters through `prek`

---
 .github/workflows/auto-formatting.yml | 43 ++++++++-------------------
 1 file changed, 12 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/auto-formatting.yml b/.github/workflows/auto-formatting.yml
index f49f9c65d0..3802653082 100644
--- a/.github/workflows/auto-formatting.yml
+++ b/.github/workflows/auto-formatting.yml
@@ -15,38 +15,19 @@ jobs:
           ref: ${{ github.head_ref }}
           fetch-depth: 0
 
-      # This also installs git-clang-format
-      - name: Install formatters
-        run: |
-          sudo apt install clang-format python3-pip python3-setuptools python3-wheel
-          pip3 install ruff cmake-format
+      - name: "Set up Python"
+        uses: actions/setup-python@v6
 
-      - name: Version
-        run: |
-          python3 --version
-          $HOME/.local/bin/ruff --version
-          clang-format --version
-          $HOME/.local/bin/cmake-format --version
-
-      - name: Run clang-format
-        id: format
-        run:
-          while ! git clang-format origin/${{ github.base_ref }} ; do git add . ; done
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
 
-      - name: Run ruff
-        run: |
-          pwd
-          ls
-          $HOME/.local/bin/ruff format .
+      - name: Install dev tools
+        run: uv sync --only-dev
 
-      - name: Run cmake-format
-        run: |
-          pwd
-          ls
-          $HOME/.local/bin/cmake-format -i $(find -name CMakeLists.txt) cmake/*.cmake
+      - name: Check prek versions are up-to-date
+        run: uv tool run sync-with-uv --check --diff
 
-      - name: Commit formatting
-        uses: stefanzweifel/git-auto-commit-action@v7
-        with:
-          commit_message: "[bot] Apply format changes"
-          skip_push: true
+      - name: Run everything
+        run: uv tool run prek run --show-diff-on-failure --from-ref origin/${{ github.base_ref }}

From 0b733971110313773116a97b74966c720aa4a027 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 11 Mar 2026 09:38:26 +0000
Subject: [PATCH 0721/1827] CI: Temporarily remove CUDA build while we get it
 sorted

---
 .github/workflows/tests.yml | 36 ------------------------------------
 1 file changed, 36 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index f44ebb87ec..3ea39bef01 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -232,39 +232,3 @@ jobs:
         shell: bash
         env:
           TRAVIS_BUILD_DIR: ${{ github.workspace }}
-  CUDA:
-    timeout-minutes: 60
-    runs-on: ubuntu-latest
-    container: ghcr.io/ggeorgakoudis/boutdev-cuda:latest
-    env:
-      BOUT_TEST_DOWNLOAD_FLAGS: --retry-on-http-error=502,503,504 --tries 3
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          submodules: true
-
-      - name: Cache Zenodo test data
-        uses: actions/cache@v4
-        with:
-          path: build/tests/integrated/test-fci-mpi/grid.fci.nc
-          # If we update the test, invalidate the cache
-          key: zenodo-data-${{ hashFiles('tests/integrated/test-fci-mpi/CMakeLists.txt') }}
-
-      - name: Build minimal CUDA 12.2 @ GCC9.4.0 @ Ubuntu 20.04
-        run: |
-          . /spack/share/spack/setup-env.sh
-          spack env activate -p /spack-env
-          git config --global --add safe.directory $GITHUB_WORKSPACE
-          rm -rf build
-          cmake -S $GITHUB_WORKSPACE -B build \
-            -DCMAKE_C_COMPILER=gcc \
-            -DCMAKE_CXX_COMPILER=g++ \
-            -DBOUT_ENABLE_RAJA=on \
-            -DBOUT_ENABLE_UMPIRE=on \
-            -DBOUT_ENABLE_CUDA=on \
-            -DCMAKE_CUDA_ARCHITECTURES=80 \
-            -DCUDA_ARCH=compute_80,code=sm_80 \
-            -DBOUT_ENABLE_WARNINGS=off \
-            -DBOUT_USE_SYSTEM_FMT=on
-          cd build
-          make -j 4

From 4ee3d9d2a728f32f247bc314c7fb71d133f222a1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 10:47:00 +0100
Subject: [PATCH 0722/1827] Add contains to YBoundary

---
 include/bout/yboundary_regions.hxx | 33 ++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index e5a9086397..50df198539 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -86,12 +86,45 @@ public:
     }
     is_init = true;
     optptr = &options;
+    // Cache boundary regions
+    _contains.emplace_back(mesh, false);
+    _contains.emplace_back(mesh, false);
+    iter_pnts([&](const auto& pnt) {
+      if (pnt.dir == 1) {
+        _contains[1][pnt.ind()] = true;
+      } else if (pnt.dir == -1) {
+        _contains[0][pnt.ind()] = true;
+      }
+    });
+  }
+
+  bool contains_ylow(Ind3D ind) const { return _contains[0][ind] }
+  bool contains_yhigh(Ind3D ind) const { return _contains[1][ind] }
+  template <int dir>
+  bool contains(Ind3D ind) {
+    if constexpr (dir == 1) {
+      return _contains[1][ind];
+    } else if constexpr (dir == -1) {
+      return _contains[0][ind];
+    } else {
+      static_assert(false); // Only for +1 and -1
+    }
+  }
+  bool contains(int dir, Ind3D ind) const {
+    if (dir == 1) {
+      return contains<+1>(ind);
+    } else if (dir == -1) {
+      return contains<-1>(ind);
+    } else {
+      throw BoutException("only dir == 1 and dir == -1 are implemented, not {}", dir);
+    }
   }
 
 private:
   std::vector<std::shared_ptr<BoundaryRegionPar>> boundary_regions_par;
   std::vector<std::shared_ptr<NewBoundaryRegionY>> boundary_regions;
 
+  std::vector<BoutMask> _contains;
   bool is_init{false};
   Options* optptr;
 };

From 7dd76644f54ca455648cec9a0e584fac46274624 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 10:53:19 +0100
Subject: [PATCH 0723/1827] Ensure consistency

Co-authored-by: Peter Hill <peter.hill@york.ac.uk>
---
 src/field/field3d.cxx | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 66a5dbfc18..da7bd494c9 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -144,11 +144,8 @@ void Field3D::splitParallelSlices() {
     // ParallelTransform, so we don't need a full constructor
     yup_fields.emplace_back(fieldmesh);
     ydown_fields.emplace_back(fieldmesh);
-    if (isFci()) {
-      yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", i + 1));
-      ydown_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", -i - 1));
-    }
   }
+  resetRegionParallel();
 }
 
 void Field3D::clearParallelSlices() {

From 44fd33161c9ab7d2e24c82d45c7c133914610a5a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 11:05:14 +0100
Subject: [PATCH 0724/1827] Do not use else after return

---
 include/bout/yboundary_regions.hxx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 50df198539..96d0410dad 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -104,20 +104,20 @@ public:
   bool contains(Ind3D ind) {
     if constexpr (dir == 1) {
       return _contains[1][ind];
-    } else if constexpr (dir == -1) {
+    }
+    if constexpr (dir == -1) {
       return _contains[0][ind];
-    } else {
-      static_assert(false); // Only for +1 and -1
     }
+    static_assert(false); // Only for +1 and -1
   }
   bool contains(int dir, Ind3D ind) const {
     if (dir == 1) {
       return contains<+1>(ind);
-    } else if (dir == -1) {
+    }
+    if (dir == -1) {
       return contains<-1>(ind);
-    } else {
-      throw BoutException("only dir == 1 and dir == -1 are implemented, not {}", dir);
     }
+    throw BoutException("only dir == 1 and dir == -1 are implemented, not {}", dir);
   }
 
 private:

From dddd2aa58d63a3b3d67c5d87b0433a33162afd10 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 11 Mar 2026 10:10:50 +0000
Subject: [PATCH 0725/1827] Fix formatted i18n string for C++20

---
 src/mesh/impls/bout/boutmesh.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 131fb053dc..7e842b3e72 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -516,8 +516,8 @@ int BoutMesh::load() {
     MYG = options["MYG"].doc("Number of guard cells on each side in Y").withDefault(MYG);
   }
   if (meshHasMyg && MYG != meshMyg) {
-    output_warn.write(_("Options changed the number of y-guard cells. Grid has {} but "
-                        "option specified {}! Continuing with {}"),
+    output_warn.write(_f("Options changed the number of y-guard cells. Grid has {} but "
+                         "option specified {}! Continuing with {}"),
                       meshMyg, MYG, MYG);
   }
   ASSERT0(MYG >= 0);

From e94bb27003733544cd0a518d698d4825aaecad80 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 11:26:24 +0100
Subject: [PATCH 0726/1827] Ensure YBoundary can compile

---
 include/bout/yboundary_regions.hxx                   | 9 +++++----
 tests/integrated/test-fci-boundary/get_par_bndry.cxx | 6 ++++++
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 96d0410dad..68b10a1b52 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -6,6 +6,7 @@
 #include "bout/globals.hxx"
 #include "bout/options.hxx"
 #include "bout/parallel_boundary_region.hxx"
+#include "bout/mask.hxx"
 #include <memory>
 #include <vector>
 
@@ -98,17 +99,17 @@ public:
     });
   }
 
-  bool contains_ylow(Ind3D ind) const { return _contains[0][ind] }
-  bool contains_yhigh(Ind3D ind) const { return _contains[1][ind] }
+  bool contains_ylow(Ind3D ind) const { return _contains[0][ind]; }
+  bool contains_yhigh(Ind3D ind) const { return _contains[1][ind]; }
   template <int dir>
-  bool contains(Ind3D ind) {
+  bool contains(Ind3D ind) const {
+    static_assert(dir == 1 || dir == -1);
     if constexpr (dir == 1) {
       return _contains[1][ind];
     }
     if constexpr (dir == -1) {
       return _contains[0][ind];
     }
-    static_assert(false); // Only for +1 and -1
   }
   bool contains(int dir, Ind3D ind) const {
     if (dir == 1) {
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 52d07f067e..7b2fd53c60 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -7,6 +7,8 @@
 #include "bout/output.hxx"
 #include "bout/parallel_boundary_region.hxx"
 
+#include "bout/yboundary_regions.hxx"
+
 #include <fmt/format.h>
 
 #include <vector>
@@ -36,6 +38,10 @@ int main(int argc, char** argv) {
     dump[fmt::format("field_{:s}", boundary_name)] = fields[i];
   }
 
+  Options dummy;
+  YBoundary ybndry;
+  ybndry.init(dummy, mesh);
+
   bout::writeDefaultOutputFile(dump);
 
   BoutFinalise();

From 0aab0278dff286600d2a55e5bbe8738c32159654 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Jun 2024 17:09:08 +0100
Subject: [PATCH 0727/1827] Mark some `OptionsNetCDF` methods as `override`

---
 src/sys/options/options_netcdf.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sys/options/options_netcdf.hxx b/src/sys/options/options_netcdf.hxx
index 09a2da3220..13774c15e0 100644
--- a/src/sys/options/options_netcdf.hxx
+++ b/src/sys/options/options_netcdf.hxx
@@ -39,7 +39,7 @@ public:
   ///  - "append"  File mode, default is false
   OptionsNetCDF(Options& options);
 
-  ~OptionsNetCDF() {}
+  ~OptionsNetCDF() override = default;
 
   OptionsNetCDF(const OptionsNetCDF&) = delete;
   OptionsNetCDF(OptionsNetCDF&&) noexcept = default;

From dd38b45cd68862d67a1d3a59024e2192905589b4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Jun 2024 17:09:23 +0100
Subject: [PATCH 0728/1827] Make `OptionsNetCDF` registration symbol `const`

---
 src/sys/options/options_netcdf.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sys/options/options_netcdf.hxx b/src/sys/options/options_netcdf.hxx
index 13774c15e0..09e8a8234c 100644
--- a/src/sys/options/options_netcdf.hxx
+++ b/src/sys/options/options_netcdf.hxx
@@ -74,7 +74,7 @@ private:
 };
 
 namespace {
-RegisterOptionsIO<OptionsNetCDF> registeroptionsnetcdf("netcdf");
+const RegisterOptionsIO<OptionsNetCDF> registeroptionsnetcdf("netcdf");
 }
 
 } // namespace bout

From a4cec3be3fa327823441e097a203df6b982d0a1e Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Jun 2024 17:21:14 +0100
Subject: [PATCH 0729/1827] Fix `OptionsIO` docstring appearing on wrong thing

Appears on include guard instead of class
---
 include/bout/options_io.hxx | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index 00dd0c4cf3..1539b09140 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -1,3 +1,19 @@
+#pragma once
+
+#ifndef OPTIONS_IO_H
+#define OPTIONS_IO_H
+
+#include "bout/build_defines.hxx"
+#include "bout/generic_factory.hxx"
+#include "bout/options.hxx"
+
+#include <memory>
+#include <string>
+
+class Mesh;
+
+namespace bout {
+
 /// Parent class for IO to binary files and streams
 ///
 ///
@@ -36,22 +52,6 @@
 ///
 ///    if mesh is omitted, no grid information is added.
 ///
-
-#pragma once
-
-#ifndef OPTIONS_IO_H
-#define OPTIONS_IO_H
-
-#include "bout/build_defines.hxx"
-#include "bout/generic_factory.hxx"
-#include "bout/mesh.hxx"
-#include "bout/options.hxx"
-
-#include <memory>
-#include <string>
-
-namespace bout {
-
 class OptionsIO {
 public:
   /// No default constructor, as settings are required

From c1fa555b072c2bb45c6b3ee4dfef9f01fe569105 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 3 Jul 2024 11:41:43 +0100
Subject: [PATCH 0730/1827] Silence clang-tidy warning about unnamed argument

---
 include/bout/options_io.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index 1539b09140..a93d89d362 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -59,7 +59,7 @@ public:
 
   /// Constructor specifies the kind of file, and options to control
   /// the name of file, mode of operation etc.
-  OptionsIO(Options&) {}
+  OptionsIO(Options& /*unused*/) {}
 
   virtual ~OptionsIO() = default;
 

From d19bedaa38589289795b75730d7f83a79a3cfaf0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 3 Jul 2024 11:34:29 +0100
Subject: [PATCH 0731/1827] Add option to change frequency output is flushed to
 disk

---
 include/bout/options_io.hxx        |  3 +++
 include/bout/physicsmodel.hxx      |  8 ++++++++
 src/physics/physicsmodel.cxx       | 21 ++++++++++++++-------
 src/sys/options/options_netcdf.cxx |  4 ++--
 src/sys/options/options_netcdf.hxx |  3 +++
 5 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/include/bout/options_io.hxx b/include/bout/options_io.hxx
index a93d89d362..77fdd4712b 100644
--- a/include/bout/options_io.hxx
+++ b/include/bout/options_io.hxx
@@ -81,6 +81,9 @@ public:
   /// ADIOS: Indicate completion of an output step.
   virtual void verifyTimesteps() const = 0;
 
+  /// NetCDF: Flush file to disk
+  virtual void flush() {}
+
   /// Create an OptionsIO for I/O to the given file.
   /// This uses the default file type and default options.
   static std::unique_ptr<OptionsIO> create(const std::string& file);
diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index 7f4df3aa42..338211c434 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -49,6 +49,7 @@ class PhysicsModel;
 
 #include <chrono>
 #include <thread>
+#include <cstddef>
 #include <type_traits>
 #include <vector>
 
@@ -378,6 +379,9 @@ protected:
     PhysicsModel* model;
   };
 
+  /// Set timestep counter for flushing file
+  void setFlushCounter(std::size_t iteration) { flush_counter = iteration; }
+
 private:
   /// State for outputs
   Options output_options;
@@ -401,6 +405,10 @@ private:
   bool initialised{false};
   /// write restarts and pass outputMonitor method inside a Monitor subclass
   PhysicsModelMonitor modelMonitor{this};
+  /// How often to flush to disk
+  std::size_t flush_frequency{1};
+  /// Current timestep counter
+  std::size_t flush_counter{0};
 };
 
 /*!
diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx
index a1bde18248..b6bab272fc 100644
--- a/src/physics/physicsmodel.cxx
+++ b/src/physics/physicsmodel.cxx
@@ -34,12 +34,14 @@
 
 #include "bout/version.hxx"
 #include <bout/mesh.hxx>
+#include <bout/options.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/vector2d.hxx>
 #include <bout/vector3d.hxx>
 
 #include <fmt/core.h>
 
+#include <cstddef>
 #include <string>
 using namespace std::literals;
 
@@ -67,9 +69,10 @@ PhysicsModel::PhysicsModel()
                                                     .withDefault(true)),
       restart_enabled(Options::root()["restart_files"]["enabled"]
                           .doc("Write restart files")
-                          .withDefault(true))
-
-{
+                          .withDefault(true)),
+      flush_frequency(Options::root()["output"]["flush_frequency"]
+                          .doc("How often to flush to disk")
+                          .withDefault<std::size_t>(1)) {
   if (output_enabled) {
     output_file = bout::OptionsIOFactory::getInstance().createOutput();
   }
@@ -216,9 +219,7 @@ void PhysicsModel::writeRestartFile() {
 void PhysicsModel::writeOutputFile() { writeOutputFile(output_options); }
 
 void PhysicsModel::writeOutputFile(const Options& options) {
-  if (output_enabled) {
-    output_file->write(options, "t");
-  }
+  writeOutputFile(options, "t");
 }
 
 void PhysicsModel::writeOutputFile(const Options& options,
@@ -229,13 +230,19 @@ void PhysicsModel::writeOutputFile(const Options& options,
 }
 
 void PhysicsModel::finishOutputTimestep() const {
-  if (output_enabled) {
+  Timer timer("io");
+
+  if (output_enabled and (flush_counter % flush_frequency == 0)) {
+    output_file->flush();
     output_file->verifyTimesteps();
   }
 }
 
 int PhysicsModel::PhysicsModelMonitor::call(Solver* solver, BoutReal simtime,
                                             int iteration, int nout) {
+
+  model->setFlushCounter(static_cast<std::size_t>(iteration));
+
   // Restart file variables
   solver->outputVars(model->restart_options, false);
   model->restartVars(model->restart_options);
diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx
index f6edb26dbc..d3e5a993bd 100644
--- a/src/sys/options/options_netcdf.cxx
+++ b/src/sys/options/options_netcdf.cxx
@@ -791,10 +791,10 @@ void OptionsNetCDF::write(const Options& options, const std::string& time_dim) {
   }
 
   writeGroup(options, *data_file, time_dim);
-
-  data_file->sync();
 }
 
+void OptionsNetCDF::flush() { data_file->sync(); }
+
 } // namespace bout
 
 #endif // BOUT_HAS_NETCDF
diff --git a/src/sys/options/options_netcdf.hxx b/src/sys/options/options_netcdf.hxx
index 09e8a8234c..38a79310b7 100644
--- a/src/sys/options/options_netcdf.hxx
+++ b/src/sys/options/options_netcdf.hxx
@@ -58,6 +58,9 @@ public:
   /// any differences, otherwise is silent
   void verifyTimesteps() const override;
 
+  /// Flush file to disk
+  void flush() override;
+
 private:
   enum class FileMode {
     replace, ///< Overwrite file when writing

From 08134655bf5405cd1913078394c44a5b3539c529 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 3 Jul 2024 11:34:40 +0100
Subject: [PATCH 0732/1827] Reset output `Options` after writing to disk

Avoids rewriting time-independent data, gives slight performance boost
---
 src/physics/physicsmodel.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx
index b6bab272fc..5e31fb8047 100644
--- a/src/physics/physicsmodel.cxx
+++ b/src/physics/physicsmodel.cxx
@@ -261,5 +261,8 @@ int PhysicsModel::PhysicsModelMonitor::call(Solver* solver, BoutReal simtime,
   model->outputVars(model->output_options);
   model->writeOutputFile();
 
+  // Reset output options, this avoids rewriting time-independent data
+  model->output_options = Options{};
+
   return monitor_result;
 }

From 5527447246e41f8b8465a904b8b424e9a18676d0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 10 Oct 2025 17:12:52 +0100
Subject: [PATCH 0733/1827] Fix some clang-tidy warnings

---
 src/physics/physicsmodel.cxx       | 6 +++---
 src/sys/options/options_netcdf.hxx | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx
index 5e31fb8047..6cdd78e351 100644
--- a/src/physics/physicsmodel.cxx
+++ b/src/physics/physicsmodel.cxx
@@ -191,7 +191,7 @@ int PhysicsModel::postInit(bool restarting) {
 }
 
 void PhysicsModel::outputVars(Options& options) {
-  Timer time("io");
+  const Timer time("io");
   for (const auto& item : dump.getData()) {
     bout::utils::visit(bout::OptionsConversionVisitor{options, item.name}, item.value);
     if (item.repeat) {
@@ -201,7 +201,7 @@ void PhysicsModel::outputVars(Options& options) {
 }
 
 void PhysicsModel::restartVars(Options& options) {
-  Timer time("io");
+  const Timer time("io");
   for (const auto& item : restart.getData()) {
     bout::utils::visit(bout::OptionsConversionVisitor{options, item.name}, item.value);
     if (item.repeat) {
@@ -230,7 +230,7 @@ void PhysicsModel::writeOutputFile(const Options& options,
 }
 
 void PhysicsModel::finishOutputTimestep() const {
-  Timer timer("io");
+  const Timer timer("io");
 
   if (output_enabled and (flush_counter % flush_frequency == 0)) {
     output_file->flush();
diff --git a/src/sys/options/options_netcdf.hxx b/src/sys/options/options_netcdf.hxx
index 38a79310b7..3e2a69b6d7 100644
--- a/src/sys/options/options_netcdf.hxx
+++ b/src/sys/options/options_netcdf.hxx
@@ -77,7 +77,7 @@ private:
 };
 
 namespace {
-const RegisterOptionsIO<OptionsNetCDF> registeroptionsnetcdf("netcdf");
+const inline RegisterOptionsIO<OptionsNetCDF> registeroptionsnetcdf("netcdf");
 }
 
 } // namespace bout

From c9e2e27e83c5ebfa080852e4f9f5495d4dfab2a9 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 6 Jan 2026 16:02:05 +0000
Subject: [PATCH 0734/1827] Add docs for `flush_frequency`

Also remove deleted options!
---
 manual/sphinx/user_docs/bout_options.rst | 58 ++++++++++++------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst
index 4a9c568e89..df244cd7c1 100644
--- a/manual/sphinx/user_docs/bout_options.rst
+++ b/manual/sphinx/user_docs/bout_options.rst
@@ -554,42 +554,42 @@ may be useful anyway. See :ref:`sec-output` for more details.
 Input and Output
 ----------------
 
-The output (dump) files with time-history are controlled by settings
-in a section called “output”. Restart files contain a single
-time-slice, and are controlled by a section called “restart”. The
-options available are listed in table :numref:`tab-outputopts`.
+The output (dump) files with time-history are controlled by settings in a
+section called ``"output"``. Restart files contain a single time-slice, and are
+controlled by a section called ``"restart"``. The options available are listed
+in table :numref:`tab-outputopts`.
 
 .. _tab-outputopts:
 .. table:: Output file options
 	   
-   +-------------+----------------------------------------------------+--------------+
-   | Option      | Description                                        | Default      |
-   |             |                                                    | value        |
-   +-------------+----------------------------------------------------+--------------+
-   | enabled     | Writing is enabled                                 | true         |
-   +-------------+----------------------------------------------------+--------------+
-   | type        | File type e.g. "netcdf" or "adios"                 | "netcdf"     |
-   +-------------+----------------------------------------------------+--------------+
-   | prefix      | File name prefix                                   | "BOUT.dmp"   |
-   +-------------+----------------------------------------------------+--------------+
-   | path        | Directory to write the file into                   | ``datadir``  |
-   +-------------+----------------------------------------------------+--------------+
-   | floats      | Write floats rather than doubles                   | false        |
-   +-------------+----------------------------------------------------+--------------+
-   | flush       | Flush the file to disk after each write            | true         |
-   +-------------+----------------------------------------------------+--------------+
-   | guards      | Output guard cells                                 | true         |
-   +-------------+----------------------------------------------------+--------------+
-   | openclose   | Re-open the file for each write, and close after   | true         |
-   +-------------+----------------------------------------------------+--------------+
+   +----------------------+-----------------------------------------+----------------+
+   | Option               | Description                             | Default value  |
+   +======================+=========================================+================+
+   | ``append``           | Append to existing file if true,        | ``false``      |
+   |                      | otherwise overwrite                     |                |
+   +----------------------+-----------------------------------------+----------------+
+   | ``enabled``          | Writing is enabled                      | ``true``       |
+   +----------------------+-----------------------------------------+----------------+
+   | ``flush_frequency``  | How many output timesteps between       | ``1``          |
+   |                      | writing output to disk (NetCDF only)    |                |
+   +----------------------+-----------------------------------------+----------------+
+   | ``prefix``           | File name prefix                        | ``"BOUT.dmp"`` |
+   +----------------------+-----------------------------------------+----------------+
+   | ``path``             | Directory to write the file into        | ``datadir``    |
+   +----------------------+-----------------------------------------+----------------+
+   | ``type``             | File type, either ``"netcdf"`` or       | ``"netcdf"``   |
+   |                      | ``"adios"``                             |                |
+   +----------------------+-----------------------------------------+----------------+
 
 |
 
-**enabled** is useful mainly for doing performance or scaling tests, where you
-want to exclude I/O from the timings. **floats** can be used to reduce the size
-of the output files: files are stored as double by default, but setting
-**floats = true** changes the output to single-precision floats.
-
+- ``enabled`` is useful mainly for doing performance or scaling tests, where you
+  want to exclude I/O from the timings.
+- If you find that IO is taking more and more time as your simulation goes on,
+  try setting ``flush_frequency`` to a larger value such as ``10``. This can
+  workaround an issue with NetCDF where subsequent writes take longer and
+  longer. However, larger values risk losing more data in the event of a crash
+  or the simulation being killed early.
 
 Implementation
 --------------

From 1b4707187a3a85126338303dc766280b8fb2dc56 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Wed, 11 Mar 2026 11:29:57 +0000
Subject: [PATCH 0735/1827] [bot] Apply format changes

---
 include/bout/physicsmodel.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index 338211c434..d653d96d68 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -48,8 +48,8 @@ class PhysicsModel;
 #include "bout/utils.hxx"
 
 #include <chrono>
-#include <thread>
 #include <cstddef>
+#include <thread>
 #include <type_traits>
 #include <vector>
 

From 4c9b456735d00a14113759fed9ad84a027214094 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Wed, 11 Mar 2026 11:29:58 +0000
Subject: [PATCH 0736/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 84be8e384a..a3b913621f 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -14,3 +14,4 @@ c8f38049359170a34c915e209276238ea66b9a1e
 8d5cb39e03c2644715a50684f8cd0318b4e82676
 ec69e8838be2dde140a915e50506f8e1ce3cb534
 f2bc0488a298f136294c523bc5ab4086d090059b
+1b4707187a3a85126338303dc766280b8fb2dc56

From f26bbfbe34e2b2ef8c80069c51ebb8faaf48a983 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 12:24:35 +0100
Subject: [PATCH 0737/1827] Add test for YBoundary

---
 include/bout/yboundary_regions.hxx            |  2 +-
 .../test-fci-boundary/get_par_bndry.cxx       | 24 ++++++++++--
 tests/integrated/test-fci-boundary/runtest    | 39 ++++++++++++-------
 3 files changed, 47 insertions(+), 18 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 68b10a1b52..8450b7c4a8 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -4,9 +4,9 @@
 #include "bout/assert.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/globals.hxx"
+#include "bout/mask.hxx"
 #include "bout/options.hxx"
 #include "bout/parallel_boundary_region.hxx"
-#include "bout/mask.hxx"
 #include <memory>
 #include <vector>
 
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 7b2fd53c60..15530a340b 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -37,10 +37,28 @@ int main(int argc, char** argv) {
 
     dump[fmt::format("field_{:s}", boundary_name)] = fields[i];
   }
+  for (const auto& name : {"forward_xt_prime", "backward_xt_prime"}) {
+    Field3D tmp;
+    mesh->get(tmp, name);
+    dump[name] = tmp;
+  }
+
+  {
+    Options dummy;
+    YBoundary ybndry;
+    ybndry.init(dummy, mesh);
+
+    std::vector<Field3D> fields(mesh->ystart * 2 + 1, Field3D{0.0});
+    for (auto& field : fields) {
+      field.allocate();
+    }
+    ybndry.iter_pnts(
+        [&](const auto& pnt) { fields[pnt.dir + mesh->ystart][pnt.ind()] += 1; });
 
-  Options dummy;
-  YBoundary ybndry;
-  ybndry.init(dummy, mesh);
+    for (int i = -mesh->ystart; i <= mesh->ystart; ++i) {
+      dump[fmt::format("ybndry_{}", i)] = fields[i + mesh->ystart];
+    }
+  }
 
   bout::writeDefaultOutputFile(dump);
 
diff --git a/tests/integrated/test-fci-boundary/runtest b/tests/integrated/test-fci-boundary/runtest
index e749055185..a54b13bd01 100755
--- a/tests/integrated/test-fci-boundary/runtest
+++ b/tests/integrated/test-fci-boundary/runtest
@@ -4,9 +4,20 @@
 
 from boututils.run_wrapper import launch_safe
 from boututils.datafile import DataFile
-from boutdata.collect import collect
+from boutdata.collect import collect as _collect
 
 import numpy as np
+from numpy.testing import assert_allclose
+
+
+def collect(*args):
+    return _collect(
+        *args,
+        info=False,
+        path=directory,
+        xguards=False,
+        yguards=False,
+    )
 
 
 nprocs = [1]
@@ -29,27 +40,27 @@ regions = {
 }
 regions = {k: v.astype(int) for k, v in regions.items()}
 
+
 for x in "xout", "xin":
     regions[x] = regions[f"{x}_fwd"] + regions[f"{x}_bwd"]
 for x in "fwd", "bwd":
     regions[x] = regions[f"xin_{x}"] + regions[f"xout_{x}"]
 regions["all"] = regions["xin"] + regions["xout"]
 
+bndrys = {
+    "ybndry_-1": regions["xout_bwd"],
+    "ybndry_0": regions["xout_fwd"] * 0,
+    "ybndry_1": regions["xout_fwd"],
+}
+
 for nproc in nprocs:
     cmd = "./get_par_bndry"
     _, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
 
     for k, v in regions.items():
-        data = collect(
-            f"field_{k}",
-            info=False,
-            path=directory,
-            xguards=False,
-            yguards=False,
-        )
-        assert np.allclose(data, v), (
-            f"{k} does not match",
-            np.sum(data),
-            np.sum(v),
-            np.max(data),
-        )
+        data = collect(f"field_{k}")
+        assert_allclose(data, v)
+    for i in range(-1, 2):
+        name = f"ybndry_{i}"
+        data = collect(name)
+        assert_allclose(bndrys[name], data)

From 52cb85abf1df70206979a127f64a0881f7a9ec88 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 12:34:07 +0100
Subject: [PATCH 0738/1827] Apply clang-tidy suggestions

---
 include/bout/boundary_iterator.hxx                   | 4 ++--
 include/bout/yboundary_regions.hxx                   | 1 +
 tests/integrated/test-fci-boundary/get_par_bndry.cxx | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 7d8e7ed027..765f83e694 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -10,8 +10,8 @@
 #include "bout/region.hxx"
 #include "bout/sys/parallel_stencils.hxx"
 #include "bout/sys/range.hxx"
+#include <algorithm>
 #include <functional>
-#include <utility>
 
 class BoundaryRegionIter {
 public:
@@ -173,7 +173,7 @@ private:
 
 class BoundaryRegionIterY : public BoundaryRegionIter {
 public:
-  virtual ~BoundaryRegionIterY() = default;
+  ~BoundaryRegionIterY() override = default;
   BoundaryRegionIterY(const RangeIterator& r, int y, int dir, bool is_end, Mesh* mesh)
       : BoundaryRegionIter(r.ind, y, 0, dir, mesh), r(r), is_end(is_end) {}
 
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 8450b7c4a8..6254ef7862 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -7,6 +7,7 @@
 #include "bout/mask.hxx"
 #include "bout/options.hxx"
 #include "bout/parallel_boundary_region.hxx"
+#include "bout/region.hxx"
 #include <memory>
 #include <vector>
 
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 15530a340b..0871577b86 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -48,7 +48,7 @@ int main(int argc, char** argv) {
     YBoundary ybndry;
     ybndry.init(dummy, mesh);
 
-    std::vector<Field3D> fields(mesh->ystart * 2 + 1, Field3D{0.0});
+    std::vector<Field3D> fields((mesh->ystart * 2) + 1, Field3D{0.0});
     for (auto& field : fields) {
       field.allocate();
     }

From 5c6e3a76ac9f0bd3ce34fef53fa83624ed90ba85 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 6 Nov 2025 15:09:29 +0000
Subject: [PATCH 0739/1827] Port `FV::Div_par_mod` from Hermes-3

---
 include/bout/fv_ops.hxx             | 251 +++++++++++++++++++++++++++-
 tests/MMS/spatial/fci/data/BOUT.inp |   1 +
 tests/MMS/spatial/fci/fci_mms.cxx   |   5 +
 tests/MMS/spatial/fci/mms.py        |   2 +
 tests/MMS/spatial/fci/runtest       |   9 +-
 5 files changed, 265 insertions(+), 3 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 0ec1fbe3ad..adba5f21d7 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -5,12 +5,16 @@
 #ifndef BOUT_FV_OPS_H
 #define BOUT_FV_OPS_H
 
-#include "bout/build_defines.hxx"
+#include <cmath>
+
+#include "bout/bout_types.hxx"
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
+#include "bout/mesh.hxx"
+#include "bout/output_bout_types.hxx" // NOLINT(unused-includes)
+#include "bout/region.hxx"
 #include "bout/utils.hxx"
 #include "bout/vector2d.hxx"
-#include <bout/mesh.hxx>
 
 namespace FV {
 /*!
@@ -524,5 +528,248 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
    * X-Z Finite Volume diffusion operator
    */
 Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT);
+
+/// Finite volume parallel divergence
+///
+/// NOTE: Modified version, applies limiter to velocity and field
+///       Performs better (smaller overshoots) than Div_par
+///
+/// Preserves the sum of f*J*dx*dy*dz over the domain
+///
+/// @param[in] f_in   The field being advected.
+///                   This will be reconstructed at cell faces
+///                   using the given CellEdges method
+/// @param[in] v_in   The advection velocity.
+///                   This will be interpolated to cell boundaries
+///                   using linear interpolation
+/// @param[in] wave_speed_in  Local maximum speed of all waves in the system at each
+//                            point in space
+/// @param[in] fixflux     Fix the flux at the boundary to be the value at the
+///                        midpoint (for boundary conditions)
+///
+/// @param[out] flow_ylow    Flow at the lower Y cell boundary
+///                          Already includes area factor * flux
+template <typename CellEdges = MC>
+Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
+                    const Field3D& wave_speed_in, Field3D& flow_ylow,
+                    bool fixflux = true) {
+
+  Coordinates* coord = f_in.getCoordinates();
+
+  if (f_in.isFci()) {
+    // Use mid-point (cell boundary) averages
+    if (flow_ylow.isAllocated()) {
+      flow_ylow = emptyFrom(flow_ylow);
+    }
+
+    ASSERT1(f_in.hasParallelSlices());
+    ASSERT1(v_in.hasParallelSlices());
+
+    const auto& f_up = f_in.yup();
+    const auto& f_down = f_in.ydown();
+
+    const auto& v_up = v_in.yup();
+    const auto& v_down = v_in.ydown();
+
+    Field3D result{emptyFrom(f_in)};
+    BOUT_FOR(i, f_in.getRegion("RGN_NOBNDRY")) {
+      const auto iyp = i.yp();
+      const auto iym = i.ym();
+
+      result[i] = (0.25 * (f_in[i] + f_up[iyp]) * (v_in[i] + v_up[iyp])
+                       * (coord->J[i] + coord->J.yup()[iyp])
+                       / (sqrt(coord->g_22[i]) + sqrt(coord->g_22.yup()[iyp]))
+                   - 0.25 * (f_in[i] + f_down[iym]) * (v_in[i] + v_down[iym])
+                         * (coord->J[i] + coord->J.ydown()[iym])
+                         / (sqrt(coord->g_22[i]) + sqrt(coord->g_22.ydown()[iym])))
+                  / (coord->dy[i] * coord->J[i]);
+    }
+    return result;
+  }
+  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
+  ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
+
+  const Mesh* mesh = f_in.getMesh();
+
+  CellEdges cellboundary;
+
+  ASSERT2(f_in.getDirectionY() == v_in.getDirectionY());
+  ASSERT2(f_in.getDirectionY() == wave_speed_in.getDirectionY());
+  const bool are_unaligned =
+      ((f_in.getDirectionY() == YDirectionType::Standard)
+       and (v_in.getDirectionY() == YDirectionType::Standard)
+       and (wave_speed_in.getDirectionY() == YDirectionType::Standard));
+
+  const Field3D f = are_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in;
+  const Field3D v = are_unaligned ? toFieldAligned(v_in, "RGN_NOX") : v_in;
+  const Field3D wave_speed =
+      are_unaligned ? toFieldAligned(wave_speed_in, "RGN_NOX") : wave_speed_in;
+
+  Field3D result{zeroFrom(f)};
+  flow_ylow = zeroFrom(f);
+
+  for (int i = mesh->xstart; i <= mesh->xend; i++) {
+    const bool is_periodic_y = mesh->periodicY(i);
+    const bool is_first_y = mesh->firstY(i);
+    const bool is_last_y = mesh->lastY(i);
+
+    // Only need one guard cell, so no need to communicate fluxes Instead
+    // calculate in guard cells to get fluxes consistent between processors, but
+    // don't include the boundary cell. Note that this implies special handling
+    // of boundaries later
+    const int ys = (!is_first_y || is_periodic_y) ? mesh->ystart - 1 : mesh->ystart;
+    const int ye = (!is_last_y || is_periodic_y) ? mesh->yend + 1 : mesh->yend;
+
+    for (int j = ys; j <= ye; j++) {
+      // Pre-calculate factors which multiply fluxes
+#if not(BOUT_USE_METRIC_3D)
+      // For right cell boundaries
+      const BoutReal common_factor_r =
+          (coord->J(i, j) + coord->J(i, j + 1))
+          / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1)));
+
+      const BoutReal flux_factor_rc =
+          common_factor_r / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_rp =
+          common_factor_r / (coord->dy(i, j + 1) * coord->J(i, j + 1));
+
+      const BoutReal area_rp =
+          common_factor_r * coord->dx(i, j + 1) * coord->dz(i, j + 1);
+
+      // For left cell boundaries
+      const BoutReal common_factor_l =
+          (coord->J(i, j) + coord->J(i, j - 1))
+          / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1)));
+
+      const BoutReal flux_factor_lc =
+          common_factor_l / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_lm =
+          common_factor_l / (coord->dy(i, j - 1) * coord->J(i, j - 1));
+
+      const BoutReal area_lc = common_factor_l * coord->dx(i, j) * coord->dz(i, j);
+#endif
+      for (int k = 0; k < mesh->LocalNz; k++) {
+#if BOUT_USE_METRIC_3D
+        // For right cell boundaries
+        const BoutReal common_factor_r =
+            (coord->J(i, j, k) + coord->J(i, j + 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
+
+        const BoutReal flux_factor_rc =
+            common_factor_r / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal flux_factor_rp =
+            common_factor_r / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
+
+        const BoutReal area_rp =
+            common_factor_r * coord->dx(i, j + 1, k) * coord->dz(i, j + 1, k);
+
+        // For left cell boundaries
+        const BoutReal common_factor_l =
+            (coord->J(i, j, k) + coord->J(i, j - 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
+
+        const BoutReal flux_factor_lc =
+            common_factor_l / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal flux_factor_lm =
+            common_factor_l / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
+
+        const BoutReal area_lc =
+            common_factor_l * coord->dx(i, j, k) * coord->dz(i, j, k);
+#endif
+
+        ////////////////////////////////////////////
+        // Reconstruct f at the cell faces
+        // This calculates s.R and s.L for the Right and Left
+        // face values on this cell
+
+        // Reconstruct f at the cell faces
+        // TODO(peter): We can remove this #ifdef guard after switching to C++20
+#if __cpp_designated_initializers >= 201707L
+        Stencil1D s{.c = f(i, j, k), .m = f(i, j - 1, k), .p = f(i, j + 1, k)};
+#else
+        Stencil1D s{f(i, j, k), f(i, j - 1, k), f(i, j + 1, k), BoutNaN,
+                    BoutNaN,    BoutNaN,        BoutNaN};
+#endif
+        cellboundary(s); // Calculate s.R and s.L
+
+        ////////////////////////////////////////////
+        // Reconstruct v at the cell faces
+        // TODO(peter): We can remove this #ifdef guard after switching to C++20
+#if __cpp_designated_initializers >= 201707L
+        Stencil1D sv{.c = v(i, j, k), .m = v(i, j - 1, k), .p = v(i, j + 1, k)};
+#else
+        Stencil1D sv{v(i, j, k), v(i, j - 1, k), v(i, j + 1, k), BoutNaN,
+                     BoutNaN,    BoutNaN,        BoutNaN};
+#endif
+        cellboundary(sv); // Calculate sv.R and sv.L
+
+        ////////////////////////////////////////////
+        // Right boundary
+
+        BoutReal flux = BoutNaN;
+
+        if (is_last_y && (j == mesh->yend) && !is_periodic_y) {
+          // Last point in domain
+
+          // Calculate velocity at right boundary (y+1/2)
+          const BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j + 1, k));
+
+          const BoutReal bndryval = 0.5 * (s.c + s.p);
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = bndryval * vpar;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.R * vpar) + (wave_speed(i, j, k) * (s.R - bndryval));
+          }
+
+        } else {
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
+                                        fabs(v(i, j, k)), fabs(v(i, j + 1, k)));
+
+          flux = s.R * 0.5 * (sv.R + amax);
+        }
+
+        result(i, j, k) += flux * flux_factor_rc;
+        result(i, j + 1, k) -= flux * flux_factor_rp;
+
+        flow_ylow(i, j + 1, k) += flux * area_rp;
+
+        ////////////////////////////////////////////
+        // Calculate at left boundary
+
+        if (is_first_y && (j == mesh->ystart) && !is_periodic_y) {
+          // First point in domain
+          const BoutReal bndryval = 0.5 * (s.c + s.m);
+          const BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j - 1, k));
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = bndryval * vpar;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.L * vpar) - (wave_speed(i, j, k) * (s.L - bndryval));
+          }
+        } else {
+
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
+                                        fabs(v(i, j, k)), fabs(v(i, j - 1, k)));
+
+          flux = s.L * 0.5 * (sv.L - amax);
+        }
+
+        result(i, j, k) -= flux * flux_factor_lc;
+        result(i, j - 1, k) += flux * flux_factor_lm;
+
+        flow_ylow(i, j, k) += flux * area_lc;
+      }
+    }
+  }
+  if (are_unaligned) {
+    flow_ylow = fromFieldAligned(flow_ylow, "RGN_NOBNDRY");
+  }
+  return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result;
+}
 } // namespace FV
 #endif // BOUT_FV_OPS_H
diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index 93e2101473..9171178d5d 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -5,6 +5,7 @@ div_par_solution = (0.01*x + 0.045)*(-12.5663706143592*cos(y - 2*z) - 6.28318530
 div_par_K_grad_par_solution = (0.01*x + 0.045)*(6.28318530717959*sin(y - z) - 0.628318530717959*sin(y - z)/(0.01*x + 0.045))*(6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/((0.01*x + 0.045)^2 + 1.0) + (6.28318530717959*(0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0))*cos(y - z)/sqrt((0.01*x + 0.045)^2 + 1.0)
 K = cos(y - z)
 laplace_par_solution = (0.01*x + 0.045)*(6.28318530717959*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/((0.01*x + 0.045)*sqrt((0.01*x + 0.045)^2 + 1.0)))/sqrt((0.01*x + 0.045)^2 + 1.0)
+FV_div_par_mod_solution = (0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*((sin(y - 2*z) + sin(y - z))*sin(y - z)/(0.01*x + 0.045) + (-2*cos(y - 2*z) - cos(y - z))*cos(y - z)/(0.01*x + 0.045)) - 0.628318530717959*(sin(y - 2*z) + sin(y - z))*sin(y - z)/(0.01*x + 0.045) + 0.628318530717959*(cos(y - 2*z) + cos(y - z))*cos(y - z)/(0.01*x + 0.045))/sqrt((0.01*x + 0.045)^2 + 1.0)
 
 [mesh]
 symmetricglobalx = true
diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index 7967452f3d..ca8ee8cd9f 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -4,6 +4,7 @@
 #include "bout/field.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
+#include "bout/fv_ops.hxx"
 #include "bout/globals.hxx"
 #include "bout/options.hxx"
 #include "bout/options_io.hxx"
@@ -64,6 +65,10 @@ int main(int argc, char** argv) {
   fci_op_test("div_par_K_grad_par", dump, input, Div_par_K_Grad_par(K, input));
   fci_op_test("laplace_par", dump, input, Laplace_par(input));
 
+  // Finite volume methods
+  Field3D flow_ylow;
+  fci_op_test("FV_div_par_mod", dump, input, FV::Div_par_mod(input, K, K, flow_ylow));
+
   bout::writeDefaultOutputFile(dump);
 
   BoutFinalise();
diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index b28e337ac0..2fb2bd6aa6 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -16,6 +16,7 @@
 f = sin(y - z) + sin(y - 2 * z)
 K = cos(z - y)
 
+
 Lx = 0.1
 Ly = 10.0
 Lz = 1.0
@@ -61,6 +62,7 @@ def FCI_Laplace_par(f: Expr) -> Expr:
     ("div_par_solution", FCI_div_par(f)),
     ("div_par_K_grad_par_solution", FCI_div_par_K_grad_par(f, K)),
     ("laplace_par_solution", FCI_Laplace_par(f)),
+    ("FV_div_par_mod_solution", FCI_div_par(f * K)),
 ):
     expr_str = exprToStr(expr)
     print(f"{name} = {expr_str}")
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 34340e53f4..7e960cb024 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -23,7 +23,14 @@ from scipy.interpolate import RectBivariateSpline as RBS
 DIRECTORY = "data"
 NPROC = 2
 MTHREAD = 2
-OPERATORS = ("grad_par", "grad2_par2", "div_par", "div_par_K_grad_par", "laplace_par")
+OPERATORS = (
+    "grad_par",
+    "grad2_par2",
+    "div_par",
+    "div_par_K_grad_par",
+    "laplace_par",
+    "FV_div_par_mod",
+)
 # Note that we need at least _2_ interior points for hermite spline
 # interpolation due to an awkwardness with the boundaries
 NX = 4

From 3059d128d44aacca266587a460a5b010afd3ba00 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 6 Nov 2025 15:43:38 +0000
Subject: [PATCH 0740/1827] Port `FV::Div_par_fvv` from Hermes-3

---
 include/bout/fv_ops.hxx             | 208 ++++++++++++++++++++++++++++
 tests/MMS/spatial/fci/data/BOUT.inp |   1 +
 tests/MMS/spatial/fci/fci_mms.cxx   |   1 +
 tests/MMS/spatial/fci/mms.py        |   1 +
 tests/MMS/spatial/fci/runtest       |   1 +
 5 files changed, 212 insertions(+)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index adba5f21d7..bd0fa812d8 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -771,5 +771,213 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
   }
   return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result;
 }
+
+/// This operator calculates Div_par(f v v)
+/// It is used primarily (only?) in the parallel momentum equation.
+///
+/// This operator is used rather than Div(f fv) so that the values of
+/// f and v are consistent with other advection equations: The product
+/// fv is not interpolated to cell boundaries.
+template <typename CellEdges = MC>
+Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
+                    const Field3D& wave_speed_in, bool fixflux = true) {
+  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
+  const Mesh* mesh = f_in.getMesh();
+  const Coordinates* coord = f_in.getCoordinates();
+  CellEdges cellboundary;
+
+  if (f_in.isFci()) {
+    // FCI version, using yup/down fields
+    ASSERT1(f_in.hasParallelSlices());
+    ASSERT1(v_in.hasParallelSlices());
+
+    const auto& B = coord->Bxy;
+    const auto& B_up = coord->Bxy.yup();
+    const auto& B_down = coord->Bxy.ydown();
+
+    const auto& f_up = f_in.yup();
+    const auto& f_down = f_in.ydown();
+
+    const auto& v_up = v_in.yup();
+    const auto& v_down = v_in.ydown();
+
+    const auto& g_22 = coord->g_22;
+    const auto& dy = coord->dy;
+
+    Field3D result{emptyFrom(f_in)};
+    BOUT_FOR(i, f_in.getRegion("RGN_NOBNDRY")) {
+      const auto iyp = i.yp();
+      const auto iym = i.ym();
+
+      // Maximum local wave speed
+      const BoutReal amax =
+          BOUTMAX(wave_speed_in[i], fabs(v_in[i]), fabs(v_up[iyp]), fabs(v_down[iym]));
+
+      const BoutReal term = (f_up[iyp] * v_up[iyp] * v_up[iyp] / B_up[iyp])
+                            - (f_down[iym] * v_down[iym] * v_down[iym] / B_down[iym]);
+
+      // Penalty terms. This implementation is very dissipative.
+      BoutReal penalty =
+          (amax * (f_in[i] * v_in[i] - f_up[iyp] * v_up[iyp]) / (B[i] + B_up[iyp]))
+          + (amax * (f_in[i] * v_in[i] - f_down[iym] * v_down[iym])
+             / (B[i] + B_down[iym]));
+
+      if (fabs(penalty) > fabs(term) and penalty * v_in[i] > 0) {
+        if (term * penalty > 0) {
+          penalty = term;
+        } else {
+          penalty = -term;
+        }
+      }
+
+      result[i] = B[i] * (term + penalty) / (2 * dy[i] * sqrt(g_22[i]));
+
+#if CHECK > 0
+      if (!std::isfinite(result[i])) {
+        throw BoutException("Non-finite value in Div_par_fvv at {}\n"
+                            "fup {} vup {} fdown {} vdown {} amax {}\n",
+                            "B {} Bup {} Bdown {} dy {} sqrt(g_22} {}", i, f_up[i],
+                            v_up[i], f_down[i], v_down[i], amax, B[i], B_up[i], B_down[i],
+                            dy[i], sqrt(g_22[i]));
+      }
+#endif
+    }
+    return result;
+  }
+
+  ASSERT1(areFieldsCompatible(f_in, wave_speed_in));
+
+  /// Ensure that f, v and wave_speed are field aligned
+  Field3D f = toFieldAligned(f_in, "RGN_NOX");
+  Field3D v = toFieldAligned(v_in, "RGN_NOX");
+  Field3D wave_speed = toFieldAligned(wave_speed_in, "RGN_NOX");
+
+  Field3D result{zeroFrom(f)};
+
+  for (int i = mesh->xstart; i <= mesh->xend; i++) {
+    const bool is_periodic_y = mesh->periodicY(i);
+    const bool is_first_y = mesh->firstY(i);
+    const bool is_last_y = mesh->lastY(i);
+
+    // Only need one guard cell, so no need to communicate fluxes Instead
+    // calculate in guard cells to get fluxes consistent between processors, but
+    // don't include the boundary cell. Note that this implies special handling
+    // of boundaries later
+    const int ys = (!is_first_y || is_periodic_y) ? mesh->ystart - 1 : mesh->ystart;
+    const int ye = (!is_last_y || is_periodic_y) ? mesh->yend + 1 : mesh->yend;
+
+    for (int j = ys; j <= ye; j++) {
+      // Pre-calculate factors which multiply fluxes
+
+      for (int k = 0; k < mesh->LocalNz; k++) {
+        // For right cell boundaries
+        const BoutReal common_factor_r =
+            (coord->J(i, j, k) + coord->J(i, j + 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
+
+        const BoutReal flux_factor_rc =
+            common_factor_r / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal flux_factor_rp =
+            common_factor_r / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
+
+        // For left cell boundaries
+        const BoutReal common_factor_l =
+            (coord->J(i, j, k) + coord->J(i, j - 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
+
+        const BoutReal flux_factor_lc =
+            common_factor_l / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal flux_factor_lm =
+            common_factor_l / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
+
+        ////////////////////////////////////////////
+        // Reconstruct f at the cell faces
+        // This calculates s.R and s.L for the Right and Left
+        // face values on this cell
+
+        // Reconstruct f at the cell faces
+#if __cpp_designated_initializers >= 201707L
+        Stencil1D s{.c = f(i, j, k), .m = f(i, j - 1, k), .p = f(i, j + 1, k)};
+#else
+        Stencil1D s{f(i, j, k), f(i, j - 1, k), f(i, j + 1, k), BoutNaN,
+                    BoutNaN,    BoutNaN,        BoutNaN};
+#endif
+        cellboundary(s); // Calculate s.R and s.L
+
+        ////////////////////////////////////////////
+        // Reconstruct v at the cell faces
+        // TODO(peter): We can remove this #ifdef guard after switching to C++20
+#if __cpp_designated_initializers >= 201707L
+        Stencil1D sv{.c = v(i, j, k), .m = v(i, j - 1, k), .p = v(i, j + 1, k)};
+#else
+        Stencil1D sv{v(i, j, k), v(i, j - 1, k), v(i, j + 1, k), BoutNaN,
+                     BoutNaN,    BoutNaN,        BoutNaN};
+#endif
+        cellboundary(sv);
+
+        ////////////////////////////////////////////
+        // Right boundary
+
+        // Calculate velocity at right boundary (y+1/2)
+        const BoutReal v_mid_r = 0.5 * (sv.c + sv.p);
+        // And mid-point density at right boundary
+        const BoutReal n_mid_r = 0.5 * (s.c + s.p);
+        BoutReal flux = NAN;
+
+        if (mesh->lastY(i) && (j == mesh->yend) && !mesh->periodicY(i)) {
+          // Last point in domain
+
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = n_mid_r * v_mid_r * v_mid_r;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.R * sv.R * sv.R) // Use right cell edge values
+                   + (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.p)) * n_mid_r
+                      * (sv.R - v_mid_r)); // Damp differences in velocity, not flux
+          }
+        } else {
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
+                                        fabs(sv.c), fabs(sv.p));
+
+          flux = s.R * 0.5 * (sv.R + amax) * sv.R;
+        }
+
+        result(i, j, k) += flux * flux_factor_rc;
+        result(i, j + 1, k) -= flux * flux_factor_rp;
+
+        ////////////////////////////////////////////
+        // Calculate at left boundary
+
+        const BoutReal v_mid_l = 0.5 * (sv.c + sv.m);
+        const BoutReal n_mid_l = 0.5 * (s.c + s.m);
+
+        if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) {
+          // First point in domain
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = n_mid_l * v_mid_l * v_mid_l;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.L * sv.L * sv.L)
+                   - (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.m)) * n_mid_l
+                      * (sv.L - v_mid_l));
+          }
+        } else {
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
+                                        fabs(sv.c), fabs(sv.m));
+
+          flux = s.L * 0.5 * (sv.L - amax) * sv.L;
+        }
+
+        result(i, j, k) -= flux * flux_factor_lc;
+        result(i, j - 1, k) += flux * flux_factor_lm;
+      }
+    }
+  }
+  return fromFieldAligned(result, "RGN_NOBNDRY");
+}
 } // namespace FV
 #endif // BOUT_FV_OPS_H
diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index 9171178d5d..99edee6ecc 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -6,6 +6,7 @@ div_par_K_grad_par_solution = (0.01*x + 0.045)*(6.28318530717959*sin(y - z) - 0.
 K = cos(y - z)
 laplace_par_solution = (0.01*x + 0.045)*(6.28318530717959*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/((0.01*x + 0.045)*sqrt((0.01*x + 0.045)^2 + 1.0)))/sqrt((0.01*x + 0.045)^2 + 1.0)
 FV_div_par_mod_solution = (0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*((sin(y - 2*z) + sin(y - z))*sin(y - z)/(0.01*x + 0.045) + (-2*cos(y - 2*z) - cos(y - z))*cos(y - z)/(0.01*x + 0.045)) - 0.628318530717959*(sin(y - 2*z) + sin(y - z))*sin(y - z)/(0.01*x + 0.045) + 0.628318530717959*(cos(y - 2*z) + cos(y - z))*cos(y - z)/(0.01*x + 0.045))/sqrt((0.01*x + 0.045)^2 + 1.0)
+FV_div_par_fvv_solution = (0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(2*(sin(y - 2*z) + sin(y - z))*sin(y - z)*cos(y - z)/(0.01*x + 0.045) + (-2*cos(y - 2*z) - cos(y - z))*cos(y - z)^2/(0.01*x + 0.045)) - 1.25663706143592*(sin(y - 2*z) + sin(y - z))*sin(y - z)*cos(y - z)/(0.01*x + 0.045) + 0.628318530717959*(cos(y - 2*z) + cos(y - z))*cos(y - z)^2/(0.01*x + 0.045))/sqrt((0.01*x + 0.045)^2 + 1.0)
 
 [mesh]
 symmetricglobalx = true
diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index ca8ee8cd9f..13744c4965 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -68,6 +68,7 @@ int main(int argc, char** argv) {
   // Finite volume methods
   Field3D flow_ylow;
   fci_op_test("FV_div_par_mod", dump, input, FV::Div_par_mod(input, K, K, flow_ylow));
+  fci_op_test("FV_div_par_fvv", dump, input, FV::Div_par_fvv(input, K, K));
 
   bout::writeDefaultOutputFile(dump);
 
diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index 2fb2bd6aa6..62089c7e21 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -63,6 +63,7 @@ def FCI_Laplace_par(f: Expr) -> Expr:
     ("div_par_K_grad_par_solution", FCI_div_par_K_grad_par(f, K)),
     ("laplace_par_solution", FCI_Laplace_par(f)),
     ("FV_div_par_mod_solution", FCI_div_par(f * K)),
+    ("FV_div_par_fvv_solution", FCI_div_par(f * K * K)),
 ):
     expr_str = exprToStr(expr)
     print(f"{name} = {expr_str}")
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 7e960cb024..c0f0a45132 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -30,6 +30,7 @@ OPERATORS = (
     "div_par_K_grad_par",
     "laplace_par",
     "FV_div_par_mod",
+    "FV_div_par_fvv",
 )
 # Note that we need at least _2_ interior points for hermite spline
 # interpolation due to an awkwardness with the boundaries

From 60f194643a0819e0c7a9ac0dff4013968dac80e2 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 6 Nov 2025 16:12:41 +0000
Subject: [PATCH 0741/1827] Port `Div_par_K_Grad_par_mod` from Hermes-3

---
 include/bout/difops.hxx             |   4 ++
 src/mesh/difops.cxx                 | 102 ++++++++++++++++++++++++++++
 tests/MMS/spatial/fci/data/BOUT.inp |   1 +
 tests/MMS/spatial/fci/fci_mms.cxx   |   6 +-
 tests/MMS/spatial/fci/mms.py        |   1 +
 tests/MMS/spatial/fci/runtest       |   1 +
 6 files changed, 114 insertions(+), 1 deletion(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 18220b63ad..2cd99f8d33 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -195,6 +195,10 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field2D& f,
 Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f,
                            CELL_LOC outloc = CELL_DEFAULT);
 
+/// Version with energy flow diagnostic
+Field3D Div_par_K_Grad_par_mod(const Field3D& k, const Field3D& f, Field3D& flow_ylow,
+                               bool bndry_flux = true);
+
 /*!
  * Perpendicular Laplacian operator
  *
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 09433b0685..09d2441951 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -366,6 +366,108 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc)
          + Div_par(kY, outloc) * Grad_par(f, outloc);
 }
 
+Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin,
+                                     Field3D& flow_ylow, bool bndry_flux) {
+  TRACE("FV::Div_par_K_Grad_par_mod");
+
+  ASSERT2(Kin.getLocation() == fin.getLocation());
+
+  Mesh* mesh = Kin.getMesh();
+  Coordinates* coord = fin.getCoordinates();
+
+  if (Kin.hasParallelSlices() && fin.hasParallelSlices()) {
+    // Using parallel slices.
+    // Note: Y slices may use different coordinate systems
+    //       -> Only B, dy and g_22 can be used in yup/ydown
+    //          Others (e.g J) may not be averaged between y planes.
+
+    const auto& K_up = Kin.yup();
+    const auto& K_down = Kin.ydown();
+
+    const auto& f_up = fin.yup();
+    const auto& f_down = fin.ydown();
+
+    Field3D result{zeroFrom(fin)};
+    flow_ylow = zeroFrom(fin);
+
+    BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
+      const auto iyp = i.yp();
+      const auto iym = i.ym();
+
+      // Upper cell edge
+      const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]);               // K at the upper boundary
+      const BoutReal J_up = 0.5 * (coord->J[i] + coord->J.yup()[iyp]); // Jacobian at boundary
+      const BoutReal g_22_up = 0.5 * (coord->g_22[i] + coord->g_22.yup()[iyp]);
+      const BoutReal gradient_up = 2. * (f_up[iyp] - fin[i]) / (coord->dy[i] + coord->dy.yup()[iyp]);
+
+      const BoutReal flux_up = c_up * J_up * gradient_up / g_22_up;
+
+      // Lower cell edge
+      const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]);               // K at the lower boundary
+      const BoutReal J_down = 0.5 * (coord->J[i] + coord->J.ydown()[iym]); // Jacobian at boundary
+      const BoutReal g_22_down = 0.5 * (coord->g_22[i] + coord->g_22.ydown()[iym]);
+      const BoutReal gradient_down = 2. * (fin[i] - f_down[iym]) / (coord->dy[i] + coord->dy.ydown()[iym]);
+
+      const BoutReal flux_down = c_down * J_down * gradient_down / g_22_down;
+
+      result[i] = (flux_up - flux_down) / (coord->dy[i] * coord->J[i]);
+    }
+
+    return result;
+  }
+
+  // Calculate in field-aligned coordinates
+  const auto& K = toFieldAligned(Kin, "RGN_NOX");
+  const auto& f = toFieldAligned(fin, "RGN_NOX");
+
+  Field3D result{zeroFrom(f)};
+  flow_ylow = zeroFrom(f);
+
+  BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
+    // Calculate flux at upper surface
+
+    const auto iyp = i.yp();
+    const auto iym = i.ym();
+
+    if (bndry_flux || mesh->periodicY(i.x()) || !mesh->lastY(i.x())
+        || (i.y() != mesh->yend)) {
+
+      BoutReal c = 0.5 * (K[i] + K[iyp]);               // K at the upper boundary
+      BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary
+      BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
+
+      BoutReal gradient = 2. * (f[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
+
+      BoutReal flux = c * J * gradient / g_22;
+
+      result[i] += flux / (coord->dy[i] * coord->J[i]);
+    }
+
+    // Calculate flux at lower surface
+    if (bndry_flux || mesh->periodicY(i.x()) || !mesh->firstY(i.x())
+        || (i.y() != mesh->ystart)) {
+      BoutReal c = 0.5 * (K[i] + K[iym]);               // K at the lower boundary
+      BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary
+
+      BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
+
+      BoutReal gradient = 2. * (f[i] - f[iym]) / (coord->dy[i] + coord->dy[iym]);
+
+      BoutReal flux = c * J * gradient / g_22;
+
+      result[i] -= flux / (coord->dy[i] * coord->J[i]);
+      flow_ylow[i] = -flux * coord->dx[i] * coord->dz[i];
+    }
+  }
+
+  // Shifted to field aligned coordinates, so need to shift back
+  result = fromFieldAligned(result, "RGN_NOBNDRY");
+  flow_ylow = fromFieldAligned(flow_ylow);
+
+  return result;
+}
+
+
 /*******************************************************************************
 * Delp2
 * perpendicular Laplacian operator
diff --git a/tests/MMS/spatial/fci/data/BOUT.inp b/tests/MMS/spatial/fci/data/BOUT.inp
index 99edee6ecc..76ac3035c9 100644
--- a/tests/MMS/spatial/fci/data/BOUT.inp
+++ b/tests/MMS/spatial/fci/data/BOUT.inp
@@ -7,6 +7,7 @@ K = cos(y - z)
 laplace_par_solution = (0.01*x + 0.045)*(6.28318530717959*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/((0.01*x + 0.045)*sqrt((0.01*x + 0.045)^2 + 1.0)))/sqrt((0.01*x + 0.045)^2 + 1.0)
 FV_div_par_mod_solution = (0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*((sin(y - 2*z) + sin(y - z))*sin(y - z)/(0.01*x + 0.045) + (-2*cos(y - 2*z) - cos(y - z))*cos(y - z)/(0.01*x + 0.045)) - 0.628318530717959*(sin(y - 2*z) + sin(y - z))*sin(y - z)/(0.01*x + 0.045) + 0.628318530717959*(cos(y - 2*z) + cos(y - z))*cos(y - z)/(0.01*x + 0.045))/sqrt((0.01*x + 0.045)^2 + 1.0)
 FV_div_par_fvv_solution = (0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(2*(sin(y - 2*z) + sin(y - z))*sin(y - z)*cos(y - z)/(0.01*x + 0.045) + (-2*cos(y - 2*z) - cos(y - z))*cos(y - z)^2/(0.01*x + 0.045)) - 1.25663706143592*(sin(y - 2*z) + sin(y - z))*sin(y - z)*cos(y - z)/(0.01*x + 0.045) + 0.628318530717959*(cos(y - 2*z) + cos(y - z))*cos(y - z)^2/(0.01*x + 0.045))/sqrt((0.01*x + 0.045)^2 + 1.0)
+div_par_K_grad_par_mod_solution = (0.01*x + 0.045)*(6.28318530717959*sin(y - z) - 0.628318530717959*sin(y - z)/(0.01*x + 0.045))*(6.28318530717959*(0.01*x + 0.045)*(-2*cos(y - 2*z) - cos(y - z)) + 0.628318530717959*cos(y - 2*z) + 0.628318530717959*cos(y - z))/((0.01*x + 0.045)^2 + 1.0) + (6.28318530717959*(0.01*x + 0.045)*(6.28318530717959*(0.01*x + 0.045)*(-4*sin(y - 2*z) - sin(y - z)) + 1.25663706143592*sin(y - 2*z) + 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0) + 0.628318530717959*(6.28318530717959*(0.01*x + 0.045)*(2*sin(y - 2*z) + sin(y - z)) - 0.628318530717959*sin(y - 2*z) - 0.628318530717959*sin(y - z))/sqrt((0.01*x + 0.045)^2 + 1.0))*cos(y - z)/sqrt((0.01*x + 0.045)^2 + 1.0)
 
 [mesh]
 symmetricglobalx = true
diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index 13744c4965..17408aeeab 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -59,14 +59,18 @@ int main(int argc, char** argv) {
   // Add mesh geometry variables
   mesh->outputVars(dump);
 
+  // Dummy variable for *_mod overloads
+  Field3D flow_ylow;
+
   fci_op_test("grad_par", dump, input, Grad_par(input));
   fci_op_test("grad2_par2", dump, input, Grad2_par2(input));
   fci_op_test("div_par", dump, input, Div_par(input));
   fci_op_test("div_par_K_grad_par", dump, input, Div_par_K_Grad_par(K, input));
+  fci_op_test("div_par_K_grad_par_mod", dump, input,
+              Div_par_K_Grad_par_mod(K, input, flow_ylow));
   fci_op_test("laplace_par", dump, input, Laplace_par(input));
 
   // Finite volume methods
-  Field3D flow_ylow;
   fci_op_test("FV_div_par_mod", dump, input, FV::Div_par_mod(input, K, K, flow_ylow));
   fci_op_test("FV_div_par_fvv", dump, input, FV::Div_par_fvv(input, K, K));
 
diff --git a/tests/MMS/spatial/fci/mms.py b/tests/MMS/spatial/fci/mms.py
index 62089c7e21..801a8d3f26 100755
--- a/tests/MMS/spatial/fci/mms.py
+++ b/tests/MMS/spatial/fci/mms.py
@@ -61,6 +61,7 @@ def FCI_Laplace_par(f: Expr) -> Expr:
     ("grad2_par2_solution", FCI_grad2_par2(f)),
     ("div_par_solution", FCI_div_par(f)),
     ("div_par_K_grad_par_solution", FCI_div_par_K_grad_par(f, K)),
+    ("div_par_K_grad_par_mod_solution", FCI_div_par_K_grad_par(f, K)),
     ("laplace_par_solution", FCI_Laplace_par(f)),
     ("FV_div_par_mod_solution", FCI_div_par(f * K)),
     ("FV_div_par_fvv_solution", FCI_div_par(f * K * K)),
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index c0f0a45132..73babc9691 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -28,6 +28,7 @@ OPERATORS = (
     "grad2_par2",
     "div_par",
     "div_par_K_grad_par",
+    "div_par_K_grad_par_mod",
     "laplace_par",
     "FV_div_par_mod",
     "FV_div_par_fvv",

From f53b8f3c5ec7d6af148200e8a2af4ab1ec80aac0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 6 Nov 2025 16:59:34 +0000
Subject: [PATCH 0742/1827] Add MMS tests for finite volume operators

---
 tests/MMS/CMakeLists.txt                      |   1 +
 .../MMS/spatial/finite-volume/CMakeLists.txt  |   6 +
 tests/MMS/spatial/finite-volume/data/BOUT.inp |  23 ++
 tests/MMS/spatial/finite-volume/fv_mms.cxx    |  61 +++++
 tests/MMS/spatial/finite-volume/makefile      |   6 +
 tests/MMS/spatial/finite-volume/mms.py        |  62 ++++++
 tests/MMS/spatial/finite-volume/runtest       | 209 ++++++++++++++++++
 7 files changed, 368 insertions(+)
 create mode 100644 tests/MMS/spatial/finite-volume/CMakeLists.txt
 create mode 100644 tests/MMS/spatial/finite-volume/data/BOUT.inp
 create mode 100644 tests/MMS/spatial/finite-volume/fv_mms.cxx
 create mode 100644 tests/MMS/spatial/finite-volume/makefile
 create mode 100755 tests/MMS/spatial/finite-volume/mms.py
 create mode 100755 tests/MMS/spatial/finite-volume/runtest

diff --git a/tests/MMS/CMakeLists.txt b/tests/MMS/CMakeLists.txt
index a6667bcfa5..510385d54c 100644
--- a/tests/MMS/CMakeLists.txt
+++ b/tests/MMS/CMakeLists.txt
@@ -8,6 +8,7 @@ add_subdirectory(spatial/d2dx2)
 add_subdirectory(spatial/d2dz2)
 add_subdirectory(spatial/diffusion)
 add_subdirectory(spatial/fci)
+add_subdirectory(spatial/finite-volume)
 add_subdirectory(time)
 add_subdirectory(time-petsc)
 add_subdirectory(wave-1d)
diff --git a/tests/MMS/spatial/finite-volume/CMakeLists.txt b/tests/MMS/spatial/finite-volume/CMakeLists.txt
new file mode 100644
index 0000000000..6d9c839a05
--- /dev/null
+++ b/tests/MMS/spatial/finite-volume/CMakeLists.txt
@@ -0,0 +1,6 @@
+bout_add_mms_test(MMS-spatial-finite-volume
+  SOURCES fv_mms.cxx
+  USE_RUNTEST
+  USE_DATA_BOUT_INP
+  PROCESSORS 2
+)
diff --git a/tests/MMS/spatial/finite-volume/data/BOUT.inp b/tests/MMS/spatial/finite-volume/data/BOUT.inp
new file mode 100644
index 0000000000..afab4a34d5
--- /dev/null
+++ b/tests/MMS/spatial/finite-volume/data/BOUT.inp
@@ -0,0 +1,23 @@
+input_field = 0.1*sin(2.0*y) + 1
+K = 0.1*cos(3.0*y) + 1
+FV_Div_par_mod_solution = -0.188495559215388*(0.1*sin(2.0*y) + 1)*sin(3.0*y) + 0.125663706143592*(0.1*cos(3.0*y) + 1)*cos(2.0*y)
+FV_Div_par_fvv_solution = -0.376991118430775*(0.1*sin(2.0*y) + 1)*(0.1*cos(3.0*y) + 1)*sin(3.0*y) + 0.125663706143592*(0.1*cos(3.0*y) + 1)^2*cos(2.0*y)
+FV_Div_par_solution = -0.188495559215388*(0.1*sin(2.0*y) + 1)*sin(3.0*y) + 0.125663706143592*(0.1*cos(3.0*y) + 1)*cos(2.0*y)
+FV_Div_par_K_Grad_par_solution = -0.15791367041743*(0.1*cos(3.0*y) + 1)*sin(2.0*y) - 0.0236870505626145*sin(3.0*y)*cos(2.0*y)
+FV_Div_par_K_Grad_par_mod_solution = -0.15791367041743*(0.1*cos(3.0*y) + 1)*sin(2.0*y) - 0.0236870505626145*sin(3.0*y)*cos(2.0*y)
+
+[mesh]
+MXG = 0
+
+nx = 1
+ny = 128
+nz = 1
+
+Ly = 10
+
+dy = Ly / ny
+J = 1  # Identity metric
+
+[mesh:ddy]
+first = C2
+second = C2
diff --git a/tests/MMS/spatial/finite-volume/fv_mms.cxx b/tests/MMS/spatial/finite-volume/fv_mms.cxx
new file mode 100644
index 0000000000..6b45ef3259
--- /dev/null
+++ b/tests/MMS/spatial/finite-volume/fv_mms.cxx
@@ -0,0 +1,61 @@
+#include "bout/bout.hxx"
+#include "bout/field.hxx"
+#include "bout/field3d.hxx"
+#include "bout/field_factory.hxx"
+#include "bout/fv_ops.hxx"
+#include "bout/globals.hxx"
+#include "bout/options.hxx"
+#include "bout/options_io.hxx"
+#include "bout/utils.hxx"
+
+#include <fmt/format.h>
+
+#include <cmath>
+#include <string>
+
+namespace {
+auto fv_op_test(const std::string& name, Options& dump, const Field3D& input,
+                const Field3D& result) {
+  auto* mesh = input.getMesh();
+  const Field3D solution{FieldFactory::get()->create3D(fmt::format("{}_solution", name),
+                                                       Options::getRoot(), mesh)};
+  const Field3D error{result - solution};
+
+  dump[fmt::format("{}_l_2", name)] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
+  dump[fmt::format("{}_l_inf", name)] = max(abs(error), true, "RGN_NOBNDRY");
+
+  dump[fmt::format("{}_result", name)] = result;
+  dump[fmt::format("{}_error", name)] = error;
+  dump[fmt::format("{}_input", name)] = input;
+  dump[fmt::format("{}_solution", name)] = solution;
+}
+} // namespace
+
+int main(int argc, char** argv) {
+  BoutInitialise(argc, argv);
+
+  using bout::globals::mesh;
+
+  Field3D input{FieldFactory::get()->create3D("input_field", Options::getRoot(), mesh)};
+  Field3D K{FieldFactory::get()->create3D("K", Options::getRoot(), mesh)};
+
+  // Communicate to calculate parallel transform.
+  mesh->communicate(input, K);
+
+  Options dump;
+  // Add mesh geometry variables
+  mesh->outputVars(dump);
+
+  // Dummy variable for *_mod overloads
+  Field3D flow_ylow;
+
+  fv_op_test("FV_Div_par", dump, input, FV::Div_par(input, K, K));
+  fv_op_test("FV_Div_par_mod", dump, input, FV::Div_par_mod(input, K, K, flow_ylow));
+  fv_op_test("FV_Div_par_fvv", dump, input, FV::Div_par_fvv(input, K, K));
+  fv_op_test("FV_Div_par_K_Grad_par", dump, input, FV::Div_par_K_Grad_par(K, input));
+  fv_op_test("FV_Div_par_K_Grad_par_mod", dump, input, FV::Div_par_K_Grad_par(K, input));  
+
+  bout::writeDefaultOutputFile(dump);
+
+  BoutFinalise();
+}
diff --git a/tests/MMS/spatial/finite-volume/makefile b/tests/MMS/spatial/finite-volume/makefile
new file mode 100644
index 0000000000..88ba6c77e7
--- /dev/null
+++ b/tests/MMS/spatial/finite-volume/makefile
@@ -0,0 +1,6 @@
+
+BOUT_TOP	= ../../../..
+
+SOURCEC		= fci_mms.cxx
+
+include $(BOUT_TOP)/make.config
diff --git a/tests/MMS/spatial/finite-volume/mms.py b/tests/MMS/spatial/finite-volume/mms.py
new file mode 100755
index 0000000000..c8b473138d
--- /dev/null
+++ b/tests/MMS/spatial/finite-volume/mms.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+#
+# Generate manufactured solution and sources for FCI test
+#
+
+from math import pi
+import warnings
+
+from boututils.boutwarnings import AlwaysWarning
+from boutdata.data import BoutOptionsFile
+from boutdata.mms import exprToStr, y, Grad_par, Div_par, Metric
+from sympy import sin, cos, Expr
+
+warnings.simplefilter("ignore", AlwaysWarning)
+
+# Length of the y domain
+Ly = 10.0
+
+# Identity
+metric = Metric()
+
+# Define solution in terms of input x,y,z
+f = 1 + 0.1 * sin(2 * y)
+K = 1 + 0.1 * cos(3 * y)
+
+# Turn solution into real x and z coordinates
+replace = [(y, metric.y * 2 * pi / Ly)]
+
+f = f.subs(replace)
+K = K.subs(replace)
+
+# Substitute back to get input y coordinates
+replace = [ (metric.y, y*Ly/(2*pi) ) ]
+
+
+def Grad2_par2(f: Expr) -> Expr:
+    return Grad_par(Grad_par(f))
+
+
+def Div_par_K_Grad_par(f: Expr, K: Expr) -> Expr:
+    return (K * Grad2_par2(f)) + (Div_par(K) * Grad_par(f))
+
+
+############################################
+# Equations solved
+
+options = BoutOptionsFile("data/BOUT.inp")
+
+for name, expr in (
+    ("input_field", f),
+    ("K", K),
+    ("FV_Div_par_solution", Div_par(f * K)),
+    ("FV_Div_par_K_Grad_par_solution", Div_par_K_Grad_par(f, K)),
+    ("FV_Div_par_K_Grad_par_mod_solution", Div_par_K_Grad_par(f, K)),
+    ("FV_Div_par_mod_solution", Div_par(f * K)),
+    ("FV_Div_par_fvv_solution", Div_par(f * K * K)),
+):
+    expr_str = exprToStr(expr.subs(replace))
+    print(f"{name} = {expr_str}")
+    options[name] = expr_str
+
+options.write("data/BOUT.inp", overwrite=True)
diff --git a/tests/MMS/spatial/finite-volume/runtest b/tests/MMS/spatial/finite-volume/runtest
new file mode 100755
index 0000000000..a836f5e735
--- /dev/null
+++ b/tests/MMS/spatial/finite-volume/runtest
@@ -0,0 +1,209 @@
+#!/usr/bin/env python3
+#
+# Python script to run and analyse MMS test
+#
+
+import argparse
+import json
+import pathlib
+import sys
+from time import time
+
+from boutdata.collect import collect
+from boututils.run_wrapper import build_and_log, launch_safe
+from numpy import array, log, polyfit
+
+# Global parameters
+DIRECTORY = "data"
+NPROC = 2
+MTHREAD = 2
+OPERATORS = (
+    "FV_Div_par",
+    "FV_Div_par_K_Grad_par",
+    "FV_Div_par_K_Grad_par_mod",
+    "FV_Div_par_mod",
+    "FV_Div_par_fvv",
+)
+# Resolution in y and z
+NLIST = [8, 16, 32, 64]
+dx = 1.0 / array(NLIST)
+
+
+def quiet_collect(name: str) -> float:
+    # Index to return a plain (numpy) float rather than `BoutArray`
+    return collect(
+        name,
+        tind=[1, 1],
+        info=False,
+        path=DIRECTORY,
+        xguards=False,
+        yguards=False,
+    )[()]
+
+
+def assert_convergence(error, dx, name, expected) -> bool:
+    fit = polyfit(log(dx), log(error), 1)
+    order = fit[0]
+    print(f"{name} convergence order = {order:f} (fit)", end="")
+
+    order = log(error[-2] / error[-1]) / log(dx[-2] / dx[-1])
+    print(f", {order:f} (small spacing)", end="")
+
+    # Should be close to the expected order
+    success = order > expected * 0.95
+    print(f"\t............ {'PASS' if success else 'FAIL'}")
+
+    return success
+
+
+def run_fv_operators(nz: int, name: str) -> dict[str, float]:
+    # Command to run
+    args = f"MZ={nz} mesh:ny={nz} {name}"
+    cmd = f"./fv_mms {args}"
+    print(f"Running command: {cmd}", end="")
+
+    # Launch using MPI
+    start = time()
+    status, out = launch_safe(cmd, nproc=NPROC, mthread=MTHREAD, pipe=True)
+    print(f" ... done in {time() - start:.3}s")
+
+    # Save output to log file
+    pathlib.Path(f"run.log.{nz}").write_text(out)
+
+    if status:
+        print(f"Run failed!\nOutput was:\n{out}")
+        sys.exit(status)
+
+    return {
+        operator: {
+            "l_2": quiet_collect(f"{operator}_l_2"),
+            "l_inf": quiet_collect(f"{operator}_l_inf"),
+        }
+        for operator in OPERATORS
+    }
+
+
+def transpose(
+    errors: list[dict[str, dict[str, float]]],
+) -> dict[str, dict[str, list[float]]]:
+    """Turn a list of {operator: error} into a dict of {operator: [errors]}"""
+
+    kinds = ("l_2", "l_inf")
+    result = {operator: {kind: [] for kind in kinds} for operator in OPERATORS}
+    for error in errors:
+        for k, v in error.items():
+            for kind in kinds:
+                result[k][kind].append(v[kind])
+    return result
+
+
+def check_fv_operators(name: str, case: dict) -> bool:
+    failures = []
+
+    order = case["order"]
+    args = case["args"]
+
+    all_errors = []
+
+    for n in NLIST:
+        errors = run_fv_operators(n, args)
+        all_errors.append(errors)
+
+        for operator in OPERATORS:
+            l_2 = errors[operator]["l_2"]
+            l_inf = errors[operator]["l_inf"]
+
+            print(f"{operator} errors: l-2 {l_2:f} l-inf {l_inf:f}")
+
+    final_errors = transpose(all_errors)
+    for operator in OPERATORS:
+        test_name = f"{operator} {name}"
+        success = assert_convergence(
+            final_errors[operator]["l_2"], dx, test_name, order
+        )
+        if not success:
+            failures.append(test_name)
+
+    return final_errors, failures
+
+
+def make_plots(cases: dict[str, dict]):
+    try:
+        import matplotlib.pyplot as plt
+    except ImportError:
+        print("No matplotlib")
+        return
+
+    num_operators = len(OPERATORS)
+    fig, axes = plt.subplots(1, num_operators, figsize=(num_operators * 4, 4))
+
+    for ax, operator in zip(axes, OPERATORS):
+        for name, case in cases.items():
+            ax.loglog(dx, case[operator]["l_2"], "-", label=f"{name} $l_2$")
+            ax.loglog(dx, case[operator]["l_inf"], "--", label=f"{name} $l_\\inf$")
+        ax.legend(loc="upper left")
+        ax.grid()
+        ax.set_title(f"Error scaling for {operator}")
+        ax.set_xlabel(r"Mesh spacing $\delta x$")
+        ax.set_ylabel("Error norm")
+
+    fig.tight_layout()
+    fig.savefig("fv_mms.pdf")
+    print("Plot saved to fv_mms.pdf")
+
+    if args.show_plots:
+        plt.show()
+    plt.close()
+
+
+if __name__ == "__main__":
+    build_and_log("Finite volume MMS test")
+
+    parser = argparse.ArgumentParser("Error scaling test for finite volume operators")
+    parser.add_argument(
+        "--make-plots", action="store_true", help="Create plots of error scaling"
+    )
+    parser.add_argument(
+        "--show-plots",
+        action="store_true",
+        help="Stop and show plots, implies --make-plots",
+    )
+    parser.add_argument(
+        "--dump-errors",
+        type=str,
+        help="Output file to dump errors as JSON",
+        default="fv_operator_errors.json",
+    )
+
+    args = parser.parse_args()
+
+    success = True
+    failures = []
+
+    cases = {
+        "default": {
+            "order": 2,
+            "args": "",
+        },
+    }
+
+    for name, case in cases.items():
+        error2, failures_ = check_fv_operators(name, case)
+        case.update(error2)
+        failures.extend(failures_)
+        success &= len(failures) == 0
+
+    if args.dump_errors:
+        pathlib.Path(args.dump_errors).write_text(json.dumps(cases))
+
+    if args.make_plots or args.show_plots:
+        make_plots(cases)
+
+    if success:
+        print("\nAll tests passed")
+    else:
+        print("\nSome tests failed:")
+        for failure in failures:
+            print(f"\t{failure}")
+
+    sys.exit(0 if success else 1)

From 207802fdf4e9c2d328bef8d86f3929b5f0f9ce06 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 7 Nov 2025 14:20:14 +0000
Subject: [PATCH 0743/1827] Add tests for all FV slope limiters

---
 tests/MMS/spatial/finite-volume/data/BOUT.inp | 12 +--
 tests/MMS/spatial/finite-volume/fv_mms.cxx    | 51 +++++++++----
 tests/MMS/spatial/finite-volume/mms.py        | 18 +++--
 tests/MMS/spatial/finite-volume/runtest       | 73 +++++++++----------
 4 files changed, 87 insertions(+), 67 deletions(-)

diff --git a/tests/MMS/spatial/finite-volume/data/BOUT.inp b/tests/MMS/spatial/finite-volume/data/BOUT.inp
index afab4a34d5..029011e437 100644
--- a/tests/MMS/spatial/finite-volume/data/BOUT.inp
+++ b/tests/MMS/spatial/finite-volume/data/BOUT.inp
@@ -1,10 +1,10 @@
 input_field = 0.1*sin(2.0*y) + 1
-K = 0.1*cos(3.0*y) + 1
-FV_Div_par_mod_solution = -0.188495559215388*(0.1*sin(2.0*y) + 1)*sin(3.0*y) + 0.125663706143592*(0.1*cos(3.0*y) + 1)*cos(2.0*y)
-FV_Div_par_fvv_solution = -0.376991118430775*(0.1*sin(2.0*y) + 1)*(0.1*cos(3.0*y) + 1)*sin(3.0*y) + 0.125663706143592*(0.1*cos(3.0*y) + 1)^2*cos(2.0*y)
-FV_Div_par_solution = -0.188495559215388*(0.1*sin(2.0*y) + 1)*sin(3.0*y) + 0.125663706143592*(0.1*cos(3.0*y) + 1)*cos(2.0*y)
-FV_Div_par_K_Grad_par_solution = -0.15791367041743*(0.1*cos(3.0*y) + 1)*sin(2.0*y) - 0.0236870505626145*sin(3.0*y)*cos(2.0*y)
-FV_Div_par_K_Grad_par_mod_solution = -0.15791367041743*(0.1*cos(3.0*y) + 1)*sin(2.0*y) - 0.0236870505626145*sin(3.0*y)*cos(2.0*y)
+FV_Div_par_mod_solution = -0.188495559215388*sin(3.0*y)
+FV_Div_par_fvv_solution = -0.376991118430775*(0.1*cos(3.0*y) + 1)*sin(3.0*y)/(0.1*sin(2.0*y) + 1) - 0.125663706143592*(0.1*cos(3.0*y) + 1)^2*cos(2.0*y)/(0.1*sin(2.0*y) + 1)^2
+FV_Div_par_solution = -0.188495559215388*sin(3.0*y)
+FV_Div_par_K_Grad_par_solution = 0.125663706143592*(-0.188495559215388*sin(3.0*y)/(0.1*sin(2.0*y) + 1) - 0.125663706143592*(0.1*cos(3.0*y) + 1)*cos(2.0*y)/(0.1*sin(2.0*y) + 1)^2)*cos(2.0*y) - 0.15791367041743*(0.1*cos(3.0*y) + 1)*sin(2.0*y)/(0.1*sin(2.0*y) + 1)
+FV_Div_par_K_Grad_par_mod_solution = 0.125663706143592*(-0.188495559215388*sin(3.0*y)/(0.1*sin(2.0*y) + 1) - 0.125663706143592*(0.1*cos(3.0*y) + 1)*cos(2.0*y)/(0.1*sin(2.0*y) + 1)^2)*cos(2.0*y) - 0.15791367041743*(0.1*cos(3.0*y) + 1)*sin(2.0*y)/(0.1*sin(2.0*y) + 1)
+v = (0.1*cos(3.0*y) + 1)/(0.1*sin(2.0*y) + 1)
 
 [mesh]
 MXG = 0
diff --git a/tests/MMS/spatial/finite-volume/fv_mms.cxx b/tests/MMS/spatial/finite-volume/fv_mms.cxx
index 6b45ef3259..09f9986e72 100644
--- a/tests/MMS/spatial/finite-volume/fv_mms.cxx
+++ b/tests/MMS/spatial/finite-volume/fv_mms.cxx
@@ -15,19 +15,20 @@
 
 namespace {
 auto fv_op_test(const std::string& name, Options& dump, const Field3D& input,
-                const Field3D& result) {
+                const Field3D& result, std::string suffix = "") {
   auto* mesh = input.getMesh();
   const Field3D solution{FieldFactory::get()->create3D(fmt::format("{}_solution", name),
                                                        Options::getRoot(), mesh)};
   const Field3D error{result - solution};
 
-  dump[fmt::format("{}_l_2", name)] = sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
-  dump[fmt::format("{}_l_inf", name)] = max(abs(error), true, "RGN_NOBNDRY");
+  dump[fmt::format("{}{}_l_2", name, suffix)] =
+      sqrt(mean(SQ(error), true, "RGN_NOBNDRY"));
+  dump[fmt::format("{}{}_l_inf", name, suffix)] = max(abs(error), true, "RGN_NOBNDRY");
 
-  dump[fmt::format("{}_result", name)] = result;
-  dump[fmt::format("{}_error", name)] = error;
-  dump[fmt::format("{}_input", name)] = input;
-  dump[fmt::format("{}_solution", name)] = solution;
+  dump[fmt::format("{}{}_result", name, suffix)] = result;
+  dump[fmt::format("{}{}_error", name, suffix)] = error;
+  dump[fmt::format("{}{}_input", name, suffix)] = input;
+  dump[fmt::format("{}{}_solution", name, suffix)] = solution;
 }
 } // namespace
 
@@ -37,23 +38,45 @@ int main(int argc, char** argv) {
   using bout::globals::mesh;
 
   Field3D input{FieldFactory::get()->create3D("input_field", Options::getRoot(), mesh)};
-  Field3D K{FieldFactory::get()->create3D("K", Options::getRoot(), mesh)};
+  Field3D v{FieldFactory::get()->create3D("v", Options::getRoot(), mesh)};
 
   // Communicate to calculate parallel transform.
-  mesh->communicate(input, K);
+  mesh->communicate(input, v);
 
   Options dump;
   // Add mesh geometry variables
   mesh->outputVars(dump);
+  dump["v"] = v;
 
   // Dummy variable for *_mod overloads
   Field3D flow_ylow;
 
-  fv_op_test("FV_Div_par", dump, input, FV::Div_par(input, K, K));
-  fv_op_test("FV_Div_par_mod", dump, input, FV::Div_par_mod(input, K, K, flow_ylow));
-  fv_op_test("FV_Div_par_fvv", dump, input, FV::Div_par_fvv(input, K, K));
-  fv_op_test("FV_Div_par_K_Grad_par", dump, input, FV::Div_par_K_Grad_par(K, input));
-  fv_op_test("FV_Div_par_K_Grad_par_mod", dump, input, FV::Div_par_K_Grad_par(K, input));  
+  fv_op_test("FV_Div_par", dump, input, FV::Div_par<FV::MC>(input, v, v), "_MC");
+  fv_op_test("FV_Div_par_mod", dump, input,
+             FV::Div_par_mod<FV::MC>(input, v, v, flow_ylow), "_MC");
+  fv_op_test("FV_Div_par_fvv", dump, input, FV::Div_par_fvv<FV::MC>(input, v, v), "_MC");
+
+  fv_op_test("FV_Div_par", dump, input, FV::Div_par<FV::Upwind>(input, v, v), "_Upwind");
+  fv_op_test("FV_Div_par_mod", dump, input,
+             FV::Div_par_mod<FV::Upwind>(input, v, v, flow_ylow), "_Upwind");
+  fv_op_test("FV_Div_par_fvv", dump, input, FV::Div_par_fvv<FV::Upwind>(input, v, v),
+             "_Upwind");
+
+  fv_op_test("FV_Div_par", dump, input, FV::Div_par<FV::Fromm>(input, v, v), "_Fromm");
+  fv_op_test("FV_Div_par_mod", dump, input,
+             FV::Div_par_mod<FV::Fromm>(input, v, v, flow_ylow), "_Fromm");
+  fv_op_test("FV_Div_par_fvv", dump, input, FV::Div_par_fvv<FV::Fromm>(input, v, v),
+             "_Fromm");
+
+  fv_op_test("FV_Div_par", dump, input, FV::Div_par<FV::MinMod>(input, v, v), "_MinMod");
+  fv_op_test("FV_Div_par_mod", dump, input,
+             FV::Div_par_mod<FV::MinMod>(input, v, v, flow_ylow), "_MinMod");
+  fv_op_test("FV_Div_par_fvv", dump, input, FV::Div_par_fvv<FV::MinMod>(input, v, v),
+             "_MinMod");
+
+  fv_op_test("FV_Div_par_K_Grad_par", dump, input, FV::Div_par_K_Grad_par(v, input));
+  fv_op_test("FV_Div_par_K_Grad_par_mod", dump, input,
+             Div_par_K_Grad_par_mod(v, input, flow_ylow));
 
   bout::writeDefaultOutputFile(dump);
 
diff --git a/tests/MMS/spatial/finite-volume/mms.py b/tests/MMS/spatial/finite-volume/mms.py
index c8b473138d..dfcfce9a09 100755
--- a/tests/MMS/spatial/finite-volume/mms.py
+++ b/tests/MMS/spatial/finite-volume/mms.py
@@ -21,13 +21,15 @@
 
 # Define solution in terms of input x,y,z
 f = 1 + 0.1 * sin(2 * y)
-K = 1 + 0.1 * cos(3 * y)
+fv = 1 + 0.1 * cos(3 * y)
+
 
 # Turn solution into real x and z coordinates
 replace = [(y, metric.y * 2 * pi / Ly)]
 
 f = f.subs(replace)
-K = K.subs(replace)
+fv = fv.subs(replace)
+v = fv / f
 
 # Substitute back to get input y coordinates
 replace = [ (metric.y, y*Ly/(2*pi) ) ]
@@ -48,12 +50,12 @@ def Div_par_K_Grad_par(f: Expr, K: Expr) -> Expr:
 
 for name, expr in (
     ("input_field", f),
-    ("K", K),
-    ("FV_Div_par_solution", Div_par(f * K)),
-    ("FV_Div_par_K_Grad_par_solution", Div_par_K_Grad_par(f, K)),
-    ("FV_Div_par_K_Grad_par_mod_solution", Div_par_K_Grad_par(f, K)),
-    ("FV_Div_par_mod_solution", Div_par(f * K)),
-    ("FV_Div_par_fvv_solution", Div_par(f * K * K)),
+    ("v", v),
+    ("FV_Div_par_solution", Div_par(f * v)),
+    ("FV_Div_par_K_Grad_par_solution", Div_par_K_Grad_par(f, v)),
+    ("FV_Div_par_K_Grad_par_mod_solution", Div_par_K_Grad_par(f, v)),
+    ("FV_Div_par_mod_solution", Div_par(f * v)),
+    ("FV_Div_par_fvv_solution", Div_par(f * v * v)),
 ):
     expr_str = exprToStr(expr.subs(replace))
     print(f"{name} = {expr_str}")
diff --git a/tests/MMS/spatial/finite-volume/runtest b/tests/MMS/spatial/finite-volume/runtest
index a836f5e735..5a02be1e50 100755
--- a/tests/MMS/spatial/finite-volume/runtest
+++ b/tests/MMS/spatial/finite-volume/runtest
@@ -17,13 +17,27 @@ from numpy import array, log, polyfit
 DIRECTORY = "data"
 NPROC = 2
 MTHREAD = 2
-OPERATORS = (
-    "FV_Div_par",
-    "FV_Div_par_K_Grad_par",
-    "FV_Div_par_K_Grad_par_mod",
-    "FV_Div_par_mod",
-    "FV_Div_par_fvv",
-)
+OPERATORS = {
+    # Slope-limiters necessarily reduce the accuracy in places
+    "FV_Div_par_MC": 1.5,
+    "FV_Div_par_mod_MC": 1.5,
+    "FV_Div_par_fvv_MC": 1.5,
+
+    "FV_Div_par_Upwind": 1,
+    "FV_Div_par_mod_Upwind": 1,
+    "FV_Div_par_fvv_Upwind": 1,
+
+    "FV_Div_par_Fromm": 1.5,
+    "FV_Div_par_mod_Fromm": 1.5,
+    "FV_Div_par_fvv_Fromm": 1.5,
+
+    "FV_Div_par_MinMod": 1.5,
+    "FV_Div_par_mod_MinMod": 1.5,
+    "FV_Div_par_fvv_MinMod": 1.5,
+
+    "FV_Div_par_K_Grad_par": 2,
+    "FV_Div_par_K_Grad_par_mod": 2,
+}
 # Resolution in y and z
 NLIST = [8, 16, 32, 64]
 dx = 1.0 / array(NLIST)
@@ -56,10 +70,9 @@ def assert_convergence(error, dx, name, expected) -> bool:
     return success
 
 
-def run_fv_operators(nz: int, name: str) -> dict[str, float]:
+def run_fv_operators(nz: int) -> dict[str, float]:
     # Command to run
-    args = f"MZ={nz} mesh:ny={nz} {name}"
-    cmd = f"./fv_mms {args}"
+    cmd = f"./fv_mms MZ={nz} mesh:ny={nz}"
     print(f"Running command: {cmd}", end="")
 
     # Launch using MPI
@@ -97,16 +110,13 @@ def transpose(
     return result
 
 
-def check_fv_operators(name: str, case: dict) -> bool:
+def test_fv_operators() -> bool:
     failures = []
 
-    order = case["order"]
-    args = case["args"]
-
     all_errors = []
 
     for n in NLIST:
-        errors = run_fv_operators(n, args)
+        errors = run_fv_operators(n)
         all_errors.append(errors)
 
         for operator in OPERATORS:
@@ -116,13 +126,12 @@ def check_fv_operators(name: str, case: dict) -> bool:
             print(f"{operator} errors: l-2 {l_2:f} l-inf {l_inf:f}")
 
     final_errors = transpose(all_errors)
-    for operator in OPERATORS:
-        test_name = f"{operator} {name}"
+    for operator, order in OPERATORS.items():
         success = assert_convergence(
-            final_errors[operator]["l_2"], dx, test_name, order
+            final_errors[operator]["l_2"], dx, operator, order
         )
         if not success:
-            failures.append(test_name)
+            failures.append(operator)
 
     return final_errors, failures
 
@@ -138,9 +147,8 @@ def make_plots(cases: dict[str, dict]):
     fig, axes = plt.subplots(1, num_operators, figsize=(num_operators * 4, 4))
 
     for ax, operator in zip(axes, OPERATORS):
-        for name, case in cases.items():
-            ax.loglog(dx, case[operator]["l_2"], "-", label=f"{name} $l_2$")
-            ax.loglog(dx, case[operator]["l_inf"], "--", label=f"{name} $l_\\inf$")
+        ax.loglog(dx, cases[operator]["l_2"], "-", label="$l_2$")
+        ax.loglog(dx, cases[operator]["l_inf"], "--", label="$l_\\inf$")
         ax.legend(loc="upper left")
         ax.grid()
         ax.set_title(f"Error scaling for {operator}")
@@ -177,27 +185,14 @@ if __name__ == "__main__":
 
     args = parser.parse_args()
 
-    success = True
-    failures = []
-
-    cases = {
-        "default": {
-            "order": 2,
-            "args": "",
-        },
-    }
-
-    for name, case in cases.items():
-        error2, failures_ = check_fv_operators(name, case)
-        case.update(error2)
-        failures.extend(failures_)
-        success &= len(failures) == 0
+    error2, failures = test_fv_operators()
+    success = len(failures) == 0
 
     if args.dump_errors:
-        pathlib.Path(args.dump_errors).write_text(json.dumps(cases))
+        pathlib.Path(args.dump_errors).write_text(json.dumps(error2))
 
     if args.make_plots or args.show_plots:
-        make_plots(cases)
+        make_plots(error2)
 
     if success:
         print("\nAll tests passed")

From a230642c788a491ce0b8264b3c2ce24d84e326b0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 7 Nov 2025 14:25:53 +0000
Subject: [PATCH 0744/1827] Port `Superbee` finite volume limiter from Hermes-3

Includes bug fix:

```diff
-    BoutReal gL = n.c - n.L;
-    BoutReal gR = n.R - n.c;
+    BoutReal gL = n.c - n.m;
+    BoutReal gR = n.p - n.c;
```
---
 include/bout/fv_ops.hxx                    | 45 ++++++++++++++++++++++
 tests/MMS/spatial/finite-volume/fv_mms.cxx |  7 ++++
 tests/MMS/spatial/finite-volume/runtest    |  4 ++
 3 files changed, 56 insertions(+)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index bd0fa812d8..37d7b3b6fe 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -170,6 +170,51 @@ private:
   }
 };
 
+/// Superbee limiter
+///
+/// This corresponds to the limiter function
+///    φ(r) = max(0, min(2r, 1), min(r,2)
+///
+/// The value at cell right (i.e. i + 1/2) is:
+///
+///   n.R = n.c - φ(r) (n.c - (n.p + n.c)/2)
+///       = n.c + φ(r) (n.p - n.c)/2
+///
+/// Four regimes:
+///  a) r < 1/2 -> φ(r) = 2r
+///     n.R = n.c + gL
+///  b) 1/2 < r < 1 -> φ(r) = 1
+///     n.R = n.c + gR/2
+///  c) 1 < r < 2 -> φ(r) = r
+///     n.R = n.c + gL/2
+///  d) 2 < r  -> φ(r) = 2
+///     n.R = n.c + gR
+///
+///  where the left and right gradients are:
+///   gL = n.c - n.m
+///   gR = n.p - n.c
+///
+struct Superbee {
+  void operator()(Stencil1D& n) {
+    BoutReal gL = n.c - n.m;
+    BoutReal gR = n.p - n.c;
+
+    // r = gL / gR
+    // Limiter is φ(r)
+    if (gL * gR < 0) {
+      // Different signs => Zero gradient
+      n.L = n.R = n.c;
+    } else {
+      BoutReal sign = SIGN(gL);
+      gL = fabs(gL);
+      gR = fabs(gR);
+      BoutReal half_slope = sign * BOUTMAX(BOUTMIN(gL, 0.5 * gR), BOUTMIN(gR, 0.5 * gL));
+      n.L = n.c - half_slope;
+      n.R = n.c + half_slope;
+    }
+  }
+};
+
 /*!
    * Communicate fluxes between processors
    * Takes values in guard cells, and adds them to cells
diff --git a/tests/MMS/spatial/finite-volume/fv_mms.cxx b/tests/MMS/spatial/finite-volume/fv_mms.cxx
index 09f9986e72..edf4bbc16a 100644
--- a/tests/MMS/spatial/finite-volume/fv_mms.cxx
+++ b/tests/MMS/spatial/finite-volume/fv_mms.cxx
@@ -74,6 +74,13 @@ int main(int argc, char** argv) {
   fv_op_test("FV_Div_par_fvv", dump, input, FV::Div_par_fvv<FV::MinMod>(input, v, v),
              "_MinMod");
 
+  fv_op_test("FV_Div_par", dump, input, FV::Div_par<FV::Superbee>(input, v, v),
+             "_Superbee");
+  fv_op_test("FV_Div_par_mod", dump, input,
+             FV::Div_par_mod<FV::Superbee>(input, v, v, flow_ylow), "_Superbee");
+  fv_op_test("FV_Div_par_fvv", dump, input, FV::Div_par_fvv<FV::Superbee>(input, v, v),
+             "_Superbee");
+
   fv_op_test("FV_Div_par_K_Grad_par", dump, input, FV::Div_par_K_Grad_par(v, input));
   fv_op_test("FV_Div_par_K_Grad_par_mod", dump, input,
              Div_par_K_Grad_par_mod(v, input, flow_ylow));
diff --git a/tests/MMS/spatial/finite-volume/runtest b/tests/MMS/spatial/finite-volume/runtest
index 5a02be1e50..b38a6359ac 100755
--- a/tests/MMS/spatial/finite-volume/runtest
+++ b/tests/MMS/spatial/finite-volume/runtest
@@ -35,6 +35,10 @@ OPERATORS = {
     "FV_Div_par_mod_MinMod": 1.5,
     "FV_Div_par_fvv_MinMod": 1.5,
 
+    "FV_Div_par_Superbee": 1.5,
+    "FV_Div_par_mod_Superbee": 1.5,
+    "FV_Div_par_fvv_Superbee": 1.5,
+
     "FV_Div_par_K_Grad_par": 2,
     "FV_Div_par_K_Grad_par_mod": 2,
 }

From 30dc67002eff2e2f216a937d8f10e3496e8281c8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 7 Nov 2025 14:55:39 +0000
Subject: [PATCH 0745/1827] Fix clang-tidy warnings for fv_ops

---
 include/bout/fv_ops.hxx                    | 172 +++++++++----------
 src/mesh/difops.cxx                        |  85 +++++-----
 src/mesh/fv_ops.cxx                        | 185 +++++++++++----------
 tests/MMS/spatial/finite-volume/fv_mms.cxx |   1 +
 4 files changed, 223 insertions(+), 220 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 37d7b3b6fe..cd9a3536c1 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -5,33 +5,38 @@
 #ifndef BOUT_FV_OPS_H
 #define BOUT_FV_OPS_H
 
-#include <cmath>
-
+#include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/field.hxx"
+#include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
-#include "bout/output_bout_types.hxx" // NOLINT(unused-includes)
+#include "bout/output_bout_types.hxx" // NOLINT(unused-includes, misc-include-cleaner)
 #include "bout/region.hxx"
 #include "bout/utils.hxx"
 #include "bout/vector2d.hxx"
 
+#include <cmath>
+
 namespace FV {
 /*!
  * Div ( a Grad_perp(f) ) -- ∇⊥ ( a ⋅ ∇⊥ f) -- Vorticity
  */
-Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& x);
+Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f);
 
 [[deprecated("Please use Div_a_Grad_perp instead")]] inline Field3D
-Div_a_Laplace_perp(const Field3D& a, const Field3D& x) {
-  return Div_a_Grad_perp(a, x);
+Div_a_Laplace_perp(const Field3D& a, const Field3D& f) {
+  return Div_a_Grad_perp(a, f);
 }
 
 /*!
    * Divergence of a parallel diffusion Div( k * Grad_par(f) )
    */
-const Field3D Div_par_K_Grad_par(const Field3D& k, const Field3D& f,
-                                 bool bndry_flux = true);
+Field3D Div_par_K_Grad_par(const Field3D& k, const Field3D& f, bool bndry_flux = true);
 
 /*!
    * 4th-order derivative in Y, using derivatives
@@ -53,7 +58,7 @@ const Field3D Div_par_K_Grad_par(const Field3D& k, const Field3D& f,
    *
    * No fluxes through domain boundaries
    */
-const Field3D D4DY4(const Field3D& d, const Field3D& f);
+Field3D D4DY4(const Field3D& d, const Field3D& f);
 
 /*!
    * 4th-order dissipation term
@@ -71,18 +76,24 @@ const Field3D D4DY4(const Field3D& d, const Field3D& f);
    *    f_2 | f_1 | f_0 |
    *                   f_b
    */
-const Field3D D4DY4_Index(const Field3D& f, bool bndry_flux = true);
+Field3D D4DY4_Index(const Field3D& f, bool bndry_flux = true);
 
 /*!
    * Stencil used for Finite Volume calculations
    * which includes cell face values L and R
    */
 struct Stencil1D {
-  // Cell centre values
-  BoutReal c, m, p, mm, pp;
-
-  // Left and right cell face values
-  BoutReal L, R;
+  /// Cell centre values
+  BoutReal c;
+  BoutReal m;
+  BoutReal p;
+  BoutReal mm = BoutNaN;
+  BoutReal pp = BoutNaN;
+
+  /// Left cell face value
+  BoutReal L = BoutNaN;
+  /// Right cell face value
+  BoutReal R = BoutNaN;
 };
 
 /*!
@@ -97,8 +108,8 @@ struct Upwind {
    */
 struct Fromm {
   void operator()(Stencil1D& n) {
-    n.L = n.c - 0.25 * (n.p - n.m);
-    n.R = n.c + 0.25 * (n.p - n.m);
+    n.L = n.c - (0.25 * (n.p - n.m));
+    n.R = n.c + (0.25 * (n.p - n.m));
   }
 };
 
@@ -114,9 +125,9 @@ struct MinMod {
   void operator()(Stencil1D& n) {
     // Choose the gradient within the cell
     // as the minimum (smoothest) solution
-    BoutReal slope = _minmod(n.p - n.c, n.c - n.m);
-    n.L = n.c - 0.5 * slope;
-    n.R = n.c + 0.5 * slope;
+    const BoutReal slope = _minmod(n.p - n.c, n.c - n.m);
+    n.L = n.c - (0.5 * slope);
+    n.R = n.c + (0.5 * slope);
   }
 
 private:
@@ -127,7 +138,7 @@ private:
      * returns zero, otherwise chooses the value
      * with the minimum magnitude.
      */
-  BoutReal _minmod(BoutReal a, BoutReal b) {
+  static BoutReal _minmod(BoutReal a, BoutReal b) {
     if (a * b <= 0.0) {
       return 0.0;
     }
@@ -149,17 +160,17 @@ private:
    */
 struct MC {
   void operator()(Stencil1D& n) {
-    BoutReal slope = minmod(2. * (n.p - n.c),  // 2*right difference
-                            0.5 * (n.p - n.m), // Central difference
-                            2. * (n.c - n.m)); // 2*left difference
-    n.L = n.c - 0.5 * slope;
-    n.R = n.c + 0.5 * slope;
+    const BoutReal slope = minmod(2. * (n.p - n.c),  // 2*right difference
+                                  0.5 * (n.p - n.m), // Central difference
+                                  2. * (n.c - n.m)); // 2*left difference
+    n.L = n.c - (0.5 * slope);
+    n.R = n.c + (0.5 * slope);
   }
 
 private:
   // Return zero if any signs are different
   // otherwise return the value with the minimum magnitude
-  BoutReal minmod(BoutReal a, BoutReal b, BoutReal c) {
+  static BoutReal minmod(BoutReal a, BoutReal b, BoutReal c) {
     // if any of the signs are different, return zero gradient
     if ((a * b <= 0.0) || (a * c <= 0.0)) {
       return 0.0;
@@ -196,8 +207,8 @@ private:
 ///
 struct Superbee {
   void operator()(Stencil1D& n) {
-    BoutReal gL = n.c - n.m;
-    BoutReal gR = n.p - n.c;
+    const BoutReal gL = n.c - n.m;
+    const BoutReal gR = n.p - n.c;
 
     // r = gL / gR
     // Limiter is φ(r)
@@ -205,10 +216,11 @@ struct Superbee {
       // Different signs => Zero gradient
       n.L = n.R = n.c;
     } else {
-      BoutReal sign = SIGN(gL);
-      gL = fabs(gL);
-      gR = fabs(gR);
-      BoutReal half_slope = sign * BOUTMAX(BOUTMIN(gL, 0.5 * gR), BOUTMIN(gR, 0.5 * gL));
+      const BoutReal sign = SIGN(gL);
+      const BoutReal abs_gL = fabs(gL);
+      const BoutReal abs_gR = fabs(gR);
+      const BoutReal half_slope =
+          sign * BOUTMAX(BOUTMIN(abs_gL, 0.5 * abs_gR), BOUTMIN(abs_gR, 0.5 * abs_gL));
       n.L = n.c - half_slope;
       n.R = n.c + half_slope;
     }
@@ -238,13 +250,13 @@ void communicateFluxes(Field3D& f);
 ///
 /// NB: Uses to/from FieldAligned coordinates
 template <typename CellEdges = MC>
-const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
-                      const Field3D& wave_speed_in, bool fixflux = true) {
+Field3D Div_par(const Field3D& f_in, const Field3D& v_in, const Field3D& wave_speed_in,
+                bool fixflux = true) {
 
   ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
   ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
 
-  Mesh* mesh = f_in.getMesh();
+  Mesh const* mesh = f_in.getMesh();
 
   CellEdges cellboundary;
 
@@ -264,29 +276,17 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
 
   Field3D result{zeroFrom(f)};
 
-  // Only need one guard cell, so no need to communicate fluxes
-  // Instead calculate in guard cells to preserve fluxes
-  int ys = mesh->ystart - 1;
-  int ye = mesh->yend + 1;
-
   for (int i = mesh->xstart; i <= mesh->xend; i++) {
+    const bool is_periodic_y = mesh->periodicY(i);
+    const bool is_first_y = mesh->firstY(i);
+    const bool is_last_y = mesh->lastY(i);
 
-    if (!mesh->firstY(i) || mesh->periodicY(i)) {
-      // Calculate in guard cell to get fluxes consistent between processors
-      ys = mesh->ystart - 1;
-    } else {
-      // Don't include the boundary cell. Note that this implies special
-      // handling of boundaries later
-      ys = mesh->ystart;
-    }
-
-    if (!mesh->lastY(i) || mesh->periodicY(i)) {
-      // Calculate in guard cells
-      ye = mesh->yend + 1;
-    } else {
-      // Not in boundary cells
-      ye = mesh->yend;
-    }
+    // Only need one guard cell, so no need to communicate fluxes Instead
+    // calculate in guard cells to get fluxes consistent between processors, but
+    // don't include the boundary cell. Note that this implies special handling
+    // of boundaries later
+    const int ys = (!is_first_y || is_periodic_y) ? mesh->ystart - 1 : mesh->ystart;
+    const int ye = (!is_last_y || is_periodic_y) ? mesh->yend + 1 : mesh->yend;
 
     for (int j = ys; j <= ye; j++) {
       // Pre-calculate factors which multiply fluxes
@@ -295,16 +295,16 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
       BoutReal common_factor = (coord->J(i, j) + coord->J(i, j + 1))
                                / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1)));
 
-      BoutReal flux_factor_rc = common_factor / (coord->dy(i, j) * coord->J(i, j));
-      BoutReal flux_factor_rp =
+      const BoutReal flux_factor_rc = common_factor / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_rp =
           common_factor / (coord->dy(i, j + 1) * coord->J(i, j + 1));
 
       // For left cell boundaries
       common_factor = (coord->J(i, j) + coord->J(i, j - 1))
                       / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1)));
 
-      BoutReal flux_factor_lc = common_factor / (coord->dy(i, j) * coord->J(i, j));
-      BoutReal flux_factor_lm =
+      const BoutReal flux_factor_lc = common_factor / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_lm =
           common_factor / (coord->dy(i, j - 1) * coord->J(i, j - 1));
 #endif
       for (int k = mesh->zstart; k <= mesh->zend; k++) {
@@ -347,23 +347,23 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
 
         // Calculate velocity at right boundary (y+1/2)
         BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j + 1, k));
-        BoutReal flux;
+        BoutReal flux = NAN;
 
-        if (mesh->lastY(i) && (j == mesh->yend) && !mesh->periodicY(i)) {
+        if (is_last_y && (j == mesh->yend) && !is_periodic_y) {
           // Last point in domain
 
-          BoutReal bndryval = 0.5 * (s.c + s.p);
+          const BoutReal bndryval = 0.5 * (s.c + s.p);
           if (fixflux) {
             // Use mid-point to be consistent with boundary conditions
             flux = bndryval * vpar;
           } else {
             // Add flux due to difference in boundary values
-            flux = s.R * vpar + wave_speed(i, j, k) * (s.R - bndryval);
+            flux = (s.R * vpar) + (wave_speed(i, j, k) * (s.R - bndryval));
           }
         } else {
 
           // Maximum wave speed in the two cells
-          BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k));
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k));
 
           if (vpar > amax) {
             // Supersonic flow out of this cell
@@ -385,20 +385,20 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
 
         vpar = 0.5 * (v(i, j, k) + v(i, j - 1, k));
 
-        if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) {
+        if (is_first_y && (j == mesh->ystart) && !is_periodic_y) {
           // First point in domain
-          BoutReal bndryval = 0.5 * (s.c + s.m);
+          const BoutReal bndryval = 0.5 * (s.c + s.m);
           if (fixflux) {
             // Use mid-point to be consistent with boundary conditions
             flux = bndryval * vpar;
           } else {
             // Add flux due to difference in boundary values
-            flux = s.L * vpar - wave_speed(i, j, k) * (s.L - bndryval);
+            flux = (s.L * vpar) - (wave_speed(i, j, k) * (s.L - bndryval));
           }
         } else {
 
           // Maximum wave speed in the two cells
-          BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k));
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k));
 
           if (vpar < -amax) {
             // Supersonic out of this cell
@@ -432,11 +432,11 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
    *
    */
 template <typename CellEdges = MC>
-const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
+Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
   ASSERT1(n_in.getLocation() == v.getLocation());
   ASSERT1_FIELDS_COMPATIBLE(n_in, v.x);
 
-  Mesh* mesh = n_in.getMesh();
+  const Mesh* mesh = n_in.getMesh();
 
   CellEdges cellboundary;
 
@@ -455,10 +455,10 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Calculate velocities
-    BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]);
-    BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]);
-    BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J[i.xm()] + coord->J[i]);
-    BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J[i.xp()] + coord->J[i]);
+    const BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]);
+    const BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]);
+    const BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J[i.xm()] + coord->J[i]);
+    const BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J[i.xp()] + coord->J[i]);
 
     // X direction
     Stencil1D s;
@@ -473,7 +473,7 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
     if ((i.x() == mesh->xend) && (mesh->lastX())) {
       // At right boundary in X
       if (bndry_flux) {
-        BoutReal flux;
+        BoutReal flux = NAN;
         if (vR > 0.0) {
           // Flux to boundary
           flux = vR * s.R;
@@ -488,7 +488,7 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
       // Not at a boundary
       if (vR > 0.0) {
         // Flux out into next cell
-        BoutReal flux = vR * s.R;
+        const BoutReal flux = vR * s.R;
         result[i] += flux / (coord->dx[i] * coord->J[i]);
         result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]);
       }
@@ -500,7 +500,7 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
       // At left boundary in X
 
       if (bndry_flux) {
-        BoutReal flux;
+        BoutReal flux = NAN;
         if (vL < 0.0) {
           // Flux to boundary
           flux = vL * s.L;
@@ -514,7 +514,7 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
     } else {
       // Not at a boundary
       if (vL < 0.0) {
-        BoutReal flux = vL * s.L;
+        const BoutReal flux = vL * s.L;
         result[i] -= flux / (coord->dx[i] * coord->J[i]);
         result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]);
       }
@@ -531,12 +531,12 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
     cellboundary(s);
 
     if (vU > 0.0) {
-      BoutReal flux = vU * s.R;
+      const BoutReal flux = vU * s.R;
       result[i] += flux / (coord->J[i] * coord->dz[i]);
       result[i.zp()] -= flux / (coord->J[i.zp()] * coord->dz[i.zp()]);
     }
     if (vD < 0.0) {
-      BoutReal flux = vD * s.L;
+      const BoutReal flux = vD * s.L;
       result[i] -= flux / (coord->J[i] * coord->dz[i]);
       result[i.zm()] += flux / (coord->J[i.zm()] * coord->dz[i.zm()]);
     }
@@ -556,13 +556,13 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Y velocities on y boundaries
-    BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]);
-    BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]);
+    const BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]);
+    const BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]);
 
     // n (advected quantity) on y boundaries
     // Note: Use unshifted n_in variable
-    BoutReal nU = 0.5 * (n[i] + n[i.yp()]);
-    BoutReal nD = 0.5 * (n[i] + n[i.ym()]);
+    const BoutReal nU = 0.5 * (n[i] + n[i.yp()]);
+    const BoutReal nD = 0.5 * (n[i] + n[i.ym()]);
 
     yresult[i] = (nU * vU - nD * vD) / (coord->J[i] * coord->dy[i]);
   }
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 09d2441951..56773f3c4c 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -25,19 +25,20 @@
 
 #include "bout/build_defines.hxx"
 
-#include <bout/assert.hxx>
-#include <bout/derivs.hxx>
-#include <bout/difops.hxx>
-#include <bout/fft.hxx>
-#include <bout/globals.hxx>
-#include <bout/solver.hxx>
-#include <bout/utils.hxx>
-#include <bout/vecops.hxx>
-
-#include <bout/invert_laplace.hxx> // Delp2 uses same coefficients as inversion code
-
-#include <bout/interpolation.hxx>
-#include <bout/unused.hxx>
+#include "bout/assert.hxx"
+#include "bout/derivs.hxx"
+#include "bout/difops.hxx"
+#include "bout/fft.hxx"
+#include "bout/field2d.hxx"
+#include "bout/globals.hxx"
+#include "bout/interpolation.hxx"
+#include "bout/invert_laplace.hxx" // Delp2 uses same coefficients as inversion code
+#include "bout/msg_stack.hxx"
+#include "bout/region.hxx"
+#include "bout/solver.hxx"
+#include "bout/unused.hxx"
+#include "bout/utils.hxx"
+#include "bout/vecops.hxx"
 
 #include <cmath>
 
@@ -366,14 +367,14 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc)
          + Div_par(kY, outloc) * Grad_par(f, outloc);
 }
 
-Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin,
-                                     Field3D& flow_ylow, bool bndry_flux) {
+Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D& flow_ylow,
+                               bool bndry_flux) {
   TRACE("FV::Div_par_K_Grad_par_mod");
 
   ASSERT2(Kin.getLocation() == fin.getLocation());
 
-  Mesh* mesh = Kin.getMesh();
-  Coordinates* coord = fin.getCoordinates();
+  const Mesh* mesh = Kin.getMesh();
+  const Coordinates* coord = fin.getCoordinates();
 
   if (Kin.hasParallelSlices() && fin.hasParallelSlices()) {
     // Using parallel slices.
@@ -395,18 +396,22 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin,
       const auto iym = i.ym();
 
       // Upper cell edge
-      const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]);               // K at the upper boundary
-      const BoutReal J_up = 0.5 * (coord->J[i] + coord->J.yup()[iyp]); // Jacobian at boundary
+      const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]); // K at the upper boundary
+      const BoutReal J_up =
+          0.5 * (coord->J[i] + coord->J.yup()[iyp]); // Jacobian at boundary
       const BoutReal g_22_up = 0.5 * (coord->g_22[i] + coord->g_22.yup()[iyp]);
-      const BoutReal gradient_up = 2. * (f_up[iyp] - fin[i]) / (coord->dy[i] + coord->dy.yup()[iyp]);
+      const BoutReal gradient_up =
+          2. * (f_up[iyp] - fin[i]) / (coord->dy[i] + coord->dy.yup()[iyp]);
 
       const BoutReal flux_up = c_up * J_up * gradient_up / g_22_up;
 
       // Lower cell edge
-      const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]);               // K at the lower boundary
-      const BoutReal J_down = 0.5 * (coord->J[i] + coord->J.ydown()[iym]); // Jacobian at boundary
+      const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]); // K at the lower boundary
+      const BoutReal J_down =
+          0.5 * (coord->J[i] + coord->J.ydown()[iym]); // Jacobian at boundary
       const BoutReal g_22_down = 0.5 * (coord->g_22[i] + coord->g_22.ydown()[iym]);
-      const BoutReal gradient_down = 2. * (fin[i] - f_down[iym]) / (coord->dy[i] + coord->dy.ydown()[iym]);
+      const BoutReal gradient_down =
+          2. * (fin[i] - f_down[iym]) / (coord->dy[i] + coord->dy.ydown()[iym]);
 
       const BoutReal flux_down = c_down * J_down * gradient_down / g_22_down;
 
@@ -425,35 +430,32 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin,
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Calculate flux at upper surface
-
+    const auto ix = i.x();
+    const auto iy = i.y();
     const auto iyp = i.yp();
     const auto iym = i.ym();
 
-    if (bndry_flux || mesh->periodicY(i.x()) || !mesh->lastY(i.x())
-        || (i.y() != mesh->yend)) {
-
-      BoutReal c = 0.5 * (K[i] + K[iyp]);               // K at the upper boundary
-      BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary
-      BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
+    const bool is_periodic_y = mesh->periodicY(ix);
 
-      BoutReal gradient = 2. * (f[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
+    if (bndry_flux || is_periodic_y || !mesh->lastY(ix) || (iy != mesh->yend)) {
+      const BoutReal c = 0.5 * (K[i] + K[iyp]);               // K at the upper boundary
+      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary
+      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
+      const BoutReal gradient = 2. * (f[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
 
-      BoutReal flux = c * J * gradient / g_22;
+      const BoutReal flux = c * J * gradient / g_22;
 
       result[i] += flux / (coord->dy[i] * coord->J[i]);
     }
 
     // Calculate flux at lower surface
-    if (bndry_flux || mesh->periodicY(i.x()) || !mesh->firstY(i.x())
-        || (i.y() != mesh->ystart)) {
-      BoutReal c = 0.5 * (K[i] + K[iym]);               // K at the lower boundary
-      BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary
+    if (bndry_flux || is_periodic_y || !mesh->firstY(ix) || (iy != mesh->ystart)) {
+      const BoutReal c = 0.5 * (K[i] + K[iym]);               // K at the lower boundary
+      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary
+      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
+      const BoutReal gradient = 2. * (f[i] - f[iym]) / (coord->dy[i] + coord->dy[iym]);
 
-      BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
-
-      BoutReal gradient = 2. * (f[i] - f[iym]) / (coord->dy[i] + coord->dy[iym]);
-
-      BoutReal flux = c * J * gradient / g_22;
+      const BoutReal flux = c * J * gradient / g_22;
 
       result[i] -= flux / (coord->dy[i] * coord->J[i]);
       flow_ylow[i] = -flux * coord->dx[i] * coord->dz[i];
@@ -467,7 +469,6 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin,
   return result;
 }
 
-
 /*******************************************************************************
 * Delp2
 * perpendicular Laplacian operator
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index fab8beb794..6b8d8a6f21 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -1,7 +1,16 @@
-#include <bout/fv_ops.hxx>
-#include <bout/globals.hxx>
-#include <bout/output.hxx>
-#include <bout/utils.hxx>
+#include "bout/fv_ops.hxx"
+
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/build_config.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/globals.hxx"
+#include "bout/msg_stack.hxx"
+#include "bout/region.hxx"
+#include "bout/utils.hxx"
 
 namespace {
 template <class T>
@@ -33,28 +42,19 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
 
   // Flux in x
 
-  int xs = mesh->xstart - 1;
-  int xe = mesh->xend;
-
-  /*
-    if(mesh->firstX())
-    xs += 1;
-  */
-  /*
-    if(mesh->lastX())
-    xe -= 1;
-  */
+  const int xs = mesh->xstart - 1;
+  const int xe = mesh->xend;
 
   for (int i = xs; i <= xe; i++) {
     for (int j = mesh->ystart; j <= mesh->yend; j++) {
       for (int k = mesh->zstart; k <= mesh->zend; k++) {
         // Calculate flux from i to i+1
 
-        BoutReal fout = 0.5 * (a(i, j, k) + a(i + 1, j, k))
-                        * (coord->J(i, j, k) * coord->g11(i, j, k)
-                           + coord->J(i + 1, j, k) * coord->g11(i + 1, j, k))
-                        * (f(i + 1, j, k) - f(i, j, k))
-                        / (coord->dx(i, j, k) + coord->dx(i + 1, j, k));
+        const BoutReal fout = 0.5 * (a(i, j, k) + a(i + 1, j, k))
+                              * (coord->J(i, j, k) * coord->g11(i, j, k)
+                                 + coord->J(i + 1, j, k) * coord->g11(i + 1, j, k))
+                              * (f(i + 1, j, k) - f(i, j, k))
+                              / (coord->dx(i, j, k) + coord->dx(i + 1, j, k));
 
         result(i, j, k) += fout / (coord->dx(i, j, k) * coord->J(i, j, k));
         result(i + 1, j, k) -= fout / (coord->dx(i + 1, j, k) * coord->J(i + 1, j, k));
@@ -178,14 +178,13 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
   return result;
 }
 
-const Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin,
-                                 bool bndry_flux) {
+Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin, bool bndry_flux) {
 
   ASSERT2(Kin.getLocation() == fin.getLocation());
 
-  Mesh* mesh = Kin.getMesh();
+  const Mesh* mesh = Kin.getMesh();
 
-  bool use_parallel_slices = (Kin.hasParallelSlices() && fin.hasParallelSlices());
+  const bool use_parallel_slices = (Kin.hasParallelSlices() && fin.hasParallelSlices());
 
   const auto& K = use_parallel_slices ? Kin : toFieldAligned(Kin, "RGN_NOX");
   const auto& f = use_parallel_slices ? fin : toFieldAligned(fin, "RGN_NOX");
@@ -209,13 +208,13 @@ const Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin,
     if (bndry_flux || mesh->periodicY(i.x()) || !mesh->lastY(i.x())
         || (i.y() != mesh->yend)) {
 
-      BoutReal c = 0.5 * (K[i] + Kup[iyp]);             // K at the upper boundary
-      BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary
-      BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
+      const BoutReal c = 0.5 * (K[i] + Kup[iyp]);             // K at the upper boundary
+      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary
+      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
 
-      BoutReal gradient = 2. * (fup[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
+      const BoutReal gradient = 2. * (fup[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
 
-      BoutReal flux = c * J * gradient / g_22;
+      const BoutReal flux = c * J * gradient / g_22;
 
       result[i] += flux / (coord->dy[i] * coord->J[i]);
     }
@@ -223,14 +222,15 @@ const Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin,
     // Calculate flux at lower surface
     if (bndry_flux || mesh->periodicY(i.x()) || !mesh->firstY(i.x())
         || (i.y() != mesh->ystart)) {
-      BoutReal c = 0.5 * (K[i] + Kdown[iym]);           // K at the lower boundary
-      BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary
+      const BoutReal c = 0.5 * (K[i] + Kdown[iym]);           // K at the lower boundary
+      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary
 
-      BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
+      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
 
-      BoutReal gradient = 2. * (f[i] - fdown[iym]) / (coord->dy[i] + coord->dy[iym]);
+      const BoutReal gradient =
+          2. * (f[i] - fdown[iym]) / (coord->dy[i] + coord->dy[iym]);
 
-      BoutReal flux = c * J * gradient / g_22;
+      const BoutReal flux = c * J * gradient / g_22;
 
       result[i] -= flux / (coord->dy[i] * coord->J[i]);
     }
@@ -244,10 +244,10 @@ const Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin,
   return result;
 }
 
-const Field3D D4DY4(const Field3D& d_in, const Field3D& f_in) {
+Field3D D4DY4(const Field3D& d_in, const Field3D& f_in) {
   ASSERT1_FIELDS_COMPATIBLE(d_in, f_in);
 
-  Mesh* mesh = d_in.getMesh();
+  const Mesh* mesh = d_in.getMesh();
 
   Coordinates* coord = f_in.getCoordinates();
 
@@ -263,9 +263,9 @@ const Field3D D4DY4(const Field3D& d_in, const Field3D& f_in) {
 
   for (int i = mesh->xstart; i <= mesh->xend; i++) {
     // Check for boundaries
-    bool yperiodic = mesh->periodicY(i);
-    bool has_upper_boundary = !yperiodic && mesh->lastY(i);
-    bool has_lower_boundary = !yperiodic && mesh->firstY(i);
+    const bool yperiodic = mesh->periodicY(i);
+    const bool has_upper_boundary = !yperiodic && mesh->lastY(i);
+    const bool has_lower_boundary = !yperiodic && mesh->firstY(i);
 
     // Always calculate fluxes at upper Y cell boundary
     const int ystart =
@@ -281,15 +281,15 @@ const Field3D D4DY4(const Field3D& d_in, const Field3D& f_in) {
 
     for (int j = ystart; j <= yend; j++) {
       for (int k = mesh->zstart; k <= mesh->zend; k++) {
-        BoutReal dy3 = SQ(coord->dy(i, j, k)) * coord->dy(i, j, k);
+        const BoutReal dy3 = SQ(coord->dy(i, j, k)) * coord->dy(i, j, k);
         // 3rd derivative at upper boundary
 
-        BoutReal d3fdy3 =
+        const BoutReal d3fdy3 =
             (f(i, j + 2, k) - 3. * f(i, j + 1, k) + 3. * f(i, j, k) - f(i, j - 1, k))
             / dy3;
 
-        BoutReal flux = 0.5 * (d(i, j, k) + d(i, j + 1, k))
-                        * (coord->J(i, j, k) + coord->J(i, j + 1, k)) * d3fdy3;
+        const BoutReal flux = 0.5 * (d(i, j, k) + d(i, j + 1, k))
+                              * (coord->J(i, j, k) + coord->J(i, j + 1, k)) * d3fdy3;
 
         result(i, j, k) += flux / (coord->J(i, j, k) * coord->dy(i, j, k));
         result(i, j + 1, k) -= flux / (coord->J(i, j + 1, k) * coord->dy(i, j + 1, k));
@@ -301,8 +301,8 @@ const Field3D D4DY4(const Field3D& d_in, const Field3D& f_in) {
   return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result;
 }
 
-const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
-  Mesh* mesh = f_in.getMesh();
+Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
+  const Mesh* mesh = f_in.getMesh();
 
   // Convert to field aligned coordinates
   const bool is_unaligned = (f_in.getDirectionY() == YDirectionType::Standard);
@@ -313,10 +313,10 @@ const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
   Coordinates* coord = f_in.getCoordinates();
 
   for (int i = mesh->xstart; i <= mesh->xend; i++) {
-    bool yperiodic = mesh->periodicY(i);
+    const bool yperiodic = mesh->periodicY(i);
 
-    bool has_upper_boundary = !yperiodic && mesh->lastY(i);
-    bool has_lower_boundary = !yperiodic && mesh->firstY(i);
+    const bool has_upper_boundary = !yperiodic && mesh->lastY(i);
+    const bool has_lower_boundary = !yperiodic && mesh->firstY(i);
 
     for (int j = mesh->ystart; j <= mesh->yend; j++) {
 
@@ -341,8 +341,8 @@ const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
             // Not on domain boundary
             // 3rd derivative at right cell boundary
 
-            const BoutReal d3fdx3 =
-                (f(i, j + 2, k) - 3. * f(i, j + 1, k) + 3. * f(i, j, k) - f(i, j - 1, k));
+            const BoutReal d3fdx3 = (f(i, j + 2, k) - (3. * f(i, j + 1, k))
+                                     + (3. * f(i, j, k)) - f(i, j - 1, k));
 
             result(i, j, k) += d3fdx3 * factor_rc;
             result(i, j + 1, k) -= d3fdx3 * factor_rp;
@@ -363,10 +363,10 @@ const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
                 common_factor / (coord->J(i, j + 1, k) * coord->dy(i, j + 1, k));
 
             const BoutReal d3fdx3 =
-                -((16. / 5) * 0.5 * (f(i, j + 1, k) + f(i, j, k)) // Boundary value f_b
-                  - 6. * f(i, j, k)                               // f_0
-                  + 4. * f(i, j - 1, k)                           // f_1
-                  - (6. / 5) * f(i, j - 2, k)                     // f_2
+                -(((16. / 5) * 0.5 * (f(i, j + 1, k) + f(i, j, k))) // Boundary value f_b
+                  - (6. * f(i, j, k))                               // f_0
+                  + (4. * f(i, j - 1, k))                           // f_1
+                  - ((6. / 5) * f(i, j - 2, k))                     // f_2
                 );
 
             result(i, j, k) += d3fdx3 * factor_rc;
@@ -392,8 +392,8 @@ const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
                 common_factor / (coord->J(i, j - 1, k) * coord->dy(i, j - 1, k));
 
             // Not on a domain boundary
-            const BoutReal d3fdx3 =
-                (f(i, j + 1, k) - 3. * f(i, j, k) + 3. * f(i, j - 1, k) - f(i, j - 2, k));
+            const BoutReal d3fdx3 = (f(i, j + 1, k) - (3. * f(i, j, k))
+                                     + (3. * f(i, j - 1, k)) - f(i, j - 2, k));
 
             result(i, j, k) -= d3fdx3 * factor_lc;
             result(i, j - 1, k) += d3fdx3 * factor_lm;
@@ -410,10 +410,10 @@ const Field3D D4DY4_Index(const Field3D& f_in, bool bndry_flux) {
             const BoutReal factor_lm =
                 common_factor / (coord->J(i, j - 1, k) * coord->dy(i, j - 1, k));
             const BoutReal d3fdx3 =
-                -(-(16. / 5) * 0.5 * (f(i, j - 1, k) + f(i, j, k)) // Boundary value f_b
-                  + 6. * f(i, j, k)                                // f_0
-                  - 4. * f(i, j + 1, k)                            // f_1
-                  + (6. / 5) * f(i, j + 2, k)                      // f_2
+                -((-(16. / 5) * 0.5 * (f(i, j - 1, k) + f(i, j, k))) // Boundary value f_b
+                  + (6. * f(i, j, k))                                // f_0
+                  - (4. * f(i, j + 1, k))                            // f_1
+                  + ((6. / 5) * f(i, j + 2, k))                      // f_2
                 );
 
             result(i, j, k) -= d3fdx3 * factor_lc;
@@ -436,8 +436,9 @@ void communicateFluxes(Field3D& f) {
     throw BoutException("communicateFluxes: Sorry!");
   }
 
-  int size = mesh->LocalNy * mesh->LocalNz;
-  comm_handle xin, xout;
+  const int size = mesh->LocalNy * mesh->LocalNz;
+  comm_handle xin = nullptr;
+  comm_handle xout = nullptr;
   // Cache results to silence spurious compiler warning about xin,
   // xout possibly being uninitialised when used
   const bool not_first = mesh->periodicX || !mesh->firstX();
@@ -496,45 +497,45 @@ Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc) {
   //     o --- gD --- o
   //
   Coordinates* coords = a.getCoordinates(outloc);
-  Mesh* mesh = f.getMesh();
+  const Mesh* mesh = f.getMesh();
 
   for (int i = mesh->xstart; i <= mesh->xend; i++) {
     for (int j = mesh->ystart; j <= mesh->yend; j++) {
       for (int k = 0; k < mesh->LocalNz; k++) {
 
         // wrap k-index around as Z is (currently) periodic.
-        int kp = (k + 1) % (mesh->LocalNz);
-        int km = (k - 1 + mesh->LocalNz) % (mesh->LocalNz);
+        const int kp = (k + 1) % (mesh->LocalNz);
+        const int km = (k - 1 + mesh->LocalNz) % (mesh->LocalNz);
 
         // Calculate gradients on cell faces -- assumes constant grid spacing
 
-        BoutReal gR =
-            (coords->g11(i, j, k) + coords->g11(i + 1, j, k))
-                * (f(i + 1, j, k) - f(i, j, k))
-                / (coords->dx(i + 1, j, k) + coords->dx(i, j, k))
-            + 0.5 * (coords->g13(i, j, k) + coords->g13(i + 1, j, k))
-                  * (f(i + 1, j, kp) - f(i + 1, j, km) + f(i, j, kp) - f(i, j, km))
-                  / (4. * coords->dz(i, j, k));
-
-        BoutReal gL =
-            (coords->g11(i - 1, j, k) + coords->g11(i, j, k))
-                * (f(i, j, k) - f(i - 1, j, k))
-                / (coords->dx(i - 1, j, k) + coords->dx(i, j, k))
-            + 0.5 * (coords->g13(i - 1, j, k) + coords->g13(i, j, k))
-                  * (f(i - 1, j, kp) - f(i - 1, j, km) + f(i, j, kp) - f(i, j, km))
-                  / (4 * coords->dz(i, j, k));
-
-        BoutReal gD =
-            coords->g13(i, j, k)
-                * (f(i + 1, j, km) - f(i - 1, j, km) + f(i + 1, j, k) - f(i - 1, j, k))
-                / (4. * coords->dx(i, j, k))
-            + coords->g33(i, j, k) * (f(i, j, k) - f(i, j, km)) / coords->dz(i, j, k);
-
-        BoutReal gU =
-            coords->g13(i, j, k)
-                * (f(i + 1, j, kp) - f(i - 1, j, kp) + f(i + 1, j, k) - f(i - 1, j, k))
-                / (4. * coords->dx(i, j, k))
-            + coords->g33(i, j, k) * (f(i, j, kp) - f(i, j, k)) / coords->dz(i, j, k);
+        const BoutReal gR =
+            ((coords->g11(i, j, k) + coords->g11(i + 1, j, k))
+             * (f(i + 1, j, k) - f(i, j, k))
+             / (coords->dx(i + 1, j, k) + coords->dx(i, j, k)))
+            + (0.5 * (coords->g13(i, j, k) + coords->g13(i + 1, j, k))
+               * (f(i + 1, j, kp) - f(i + 1, j, km) + f(i, j, kp) - f(i, j, km))
+               / (4. * coords->dz(i, j, k)));
+
+        const BoutReal gL =
+            ((coords->g11(i - 1, j, k) + coords->g11(i, j, k))
+             * (f(i, j, k) - f(i - 1, j, k))
+             / (coords->dx(i - 1, j, k) + coords->dx(i, j, k)))
+            + (0.5 * (coords->g13(i - 1, j, k) + coords->g13(i, j, k))
+               * (f(i - 1, j, kp) - f(i - 1, j, km) + f(i, j, kp) - f(i, j, km))
+               / (4 * coords->dz(i, j, k)));
+
+        const BoutReal gD =
+            (coords->g13(i, j, k)
+             * (f(i + 1, j, km) - f(i - 1, j, km) + f(i + 1, j, k) - f(i - 1, j, k))
+             / (4. * coords->dx(i, j, k)))
+            + (coords->g33(i, j, k) * (f(i, j, k) - f(i, j, km)) / coords->dz(i, j, k));
+
+        const BoutReal gU =
+            (coords->g13(i, j, k)
+             * (f(i + 1, j, kp) - f(i - 1, j, kp) + f(i + 1, j, k) - f(i - 1, j, k))
+             / (4. * coords->dx(i, j, k)))
+            + (coords->g33(i, j, k) * (f(i, j, kp) - f(i, j, k)) / coords->dz(i, j, k));
 
         // Flow right
         BoutReal flux = gR * 0.25 * (coords->J(i + 1, j, k) + coords->J(i, j, k))
diff --git a/tests/MMS/spatial/finite-volume/fv_mms.cxx b/tests/MMS/spatial/finite-volume/fv_mms.cxx
index edf4bbc16a..19f3f14610 100644
--- a/tests/MMS/spatial/finite-volume/fv_mms.cxx
+++ b/tests/MMS/spatial/finite-volume/fv_mms.cxx
@@ -1,4 +1,5 @@
 #include "bout/bout.hxx"
+#include "bout/difops.hxx"
 #include "bout/field.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"

From fcfe963eece7eb1a4c7afe3b0996acf1767b204e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 12 Nov 2025 09:53:30 +0100
Subject: [PATCH 0746/1827] Move check up

---
 include/bout/fv_ops.hxx | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index cd9a3536c1..07a2c2976b 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -600,12 +600,10 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
                     bool fixflux = true) {
 
   Coordinates* coord = f_in.getCoordinates();
+  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
 
   if (f_in.isFci()) {
     // Use mid-point (cell boundary) averages
-    if (flow_ylow.isAllocated()) {
-      flow_ylow = emptyFrom(flow_ylow);
-    }
 
     ASSERT1(f_in.hasParallelSlices());
     ASSERT1(v_in.hasParallelSlices());
@@ -631,7 +629,6 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
     }
     return result;
   }
-  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
   ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
 
   const Mesh* mesh = f_in.getMesh();

From b209a5ad52f302f54983ed2b96037faab4b4a2c1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 20 Jan 2026 09:27:22 +0100
Subject: [PATCH 0747/1827] Ensure FCI path is always used for FCI

---
 src/mesh/difops.cxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 56773f3c4c..b0b5cc60d5 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -376,7 +376,9 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D&
   const Mesh* mesh = Kin.getMesh();
   const Coordinates* coord = fin.getCoordinates();
 
-  if (Kin.hasParallelSlices() && fin.hasParallelSlices()) {
+  if (Kin.isFci()) {
+    ASSERT1(Kin.hasParallelSlices());
+    ASSERT1(fin.hasParallelSlices());
     // Using parallel slices.
     // Note: Y slices may use different coordinate systems
     //       -> Only B, dy and g_22 can be used in yup/ydown

From e0480fc00c367e3c4df08e46326f1b79dd033898 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Feb 2026 10:47:41 +0100
Subject: [PATCH 0748/1827] FV_div_par_fvv seems to be reduced order due to
 slope limiting character

---
 tests/MMS/spatial/fci/runtest | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 73babc9691..a08f36fbb8 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -33,6 +33,11 @@ OPERATORS = (
     "FV_div_par_mod",
     "FV_div_par_fvv",
 )
+
+# div_par_fvv is also tested in ../finite-volume, where 1.5th order is achieved
+operator_order = {
+    "FV_div_par_fvv": 1,
+}
 # Note that we need at least _2_ interior points for hermite spline
 # interpolation due to an awkwardness with the boundaries
 NX = 4
@@ -172,7 +177,10 @@ def check_fci_operators(name: str, case: dict) -> bool:
     for operator in OPERATORS:
         test_name = f"{operator} {name}"
         success = assert_convergence(
-            final_errors[operator]["l_2"], dx, test_name, order
+            final_errors[operator]["l_2"],
+            dx,
+            test_name,
+            operator_order.get(operator, order),
         )
         if not success:
             failures.append(test_name)

From 7ffc7facd5ebef7259c0560220d390f7a7d17af2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Feb 2026 11:34:25 +0100
Subject: [PATCH 0749/1827] Add doc to option

Co-authored-by: Peter Hill <peter.hill@york.ac.uk>
---
 src/mesh/interpolation/hermite_spline_xz.cxx | 31 ++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 27a4f1d614..1c140b0de2 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -107,6 +107,18 @@ XZHermiteSpline::XZHermiteSpline(int y_offset, Mesh* meshin)
       h10_x(localmesh), h11_x(localmesh), h00_z(localmesh), h01_z(localmesh),
       h10_z(localmesh), h11_z(localmesh) {
 
+  if constexpr (monotonic) {
+    if (options == nullptr) {
+      options = &Options::root()["mesh:paralleltransform:xzinterpolation"];
+    }
+    abs_fac_monotonic = (*options)["atol"]
+                            .doc("Absolute tolerance for clipping overshoot")
+                            .withDefault(abs_fac_monotonic);
+    rel_fac_monotonic = (*options)["rtol"]
+                            .doc("Relative tolerance for clipping overshoot")
+                            .withDefault(rel_fac_monotonic);
+  }
+
   // Index arrays contain guard cells in order to get subscripts right
   i_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
   k_corner.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
@@ -422,6 +434,25 @@ Field3D XZHermiteSpline::interpolate(const Field3D& f, const std::string& region
     f_interp[iyp] =
         +f_z * h00_z[i] + f_zp1 * h01_z[i] + fz_z * h10_z[i] + fz_zp1 * h11_z[i];
 
+    if constexpr (monotonic) {
+#endif
+      const auto corners = {(*gf)[IndG3D(g3dinds[i][0])], (*gf)[IndG3D(g3dinds[i][1])],
+                            (*gf)[IndG3D(g3dinds[i][2])], (*gf)[IndG3D(g3dinds[i][3])]};
+      const auto minmax = std::minmax(corners);
+
+      const auto diff =
+          ((minmax.second - minmax.first) * rel_fac_monotonic) + abs_fac_monotonic;
+      f_interp[iyp] = std::max(f_interp[iyp], minmax.first - diff);
+      f_interp[iyp] = std::min(f_interp[iyp], minmax.second + diff);
+    }
+#if USE_NEW_WEIGHTS and defined(HS_USE_PETSC)
+    ASSERT2(std::isfinite(cptr[int(i)]));
+  }
+  VecRestoreArrayRead(result, &cptr);
+#elif USE_NEW_WEIGHTS
+    ASSERT2(std::isfinite(f_interp[iyp]));
+  }
+#else
     ASSERT2(std::isfinite(f_interp[iyp]) || i.x() < localmesh->xstart
             || i.x() > localmesh->xend);
   }

From 9235bcfd382bd457ddf52d87a0a122ff1b556e35 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Sat, 28 Feb 2026 11:39:03 +0000
Subject: [PATCH 0750/1827] Convert `LaplacePetsc` to use `PetscMatrix`

---
 .../laplace/impls/petsc/petsc_laplace.cxx     | 1036 +++++------------
 .../laplace/impls/petsc/petsc_laplace.hxx     |   46 +-
 .../test-petsc_laplace/test_petsc_laplace.cxx |   24 +-
 3 files changed, 347 insertions(+), 759 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 673f9c0df5..da964d443d 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -34,13 +34,20 @@
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/field2d.hxx>
+#include <bout/globalindexer.hxx>
 #include <bout/globals.hxx>
 #include <bout/mesh.hxx>
+#include <bout/operatorstencil.hxx>
 #include <bout/output.hxx>
+#include <bout/petsc_interface.hxx>
 #include <bout/petsclib.hxx>
+#include <bout/region.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 
+#include <cmath>
+#include <set>
 #include <vector>
 
 #define KSP_RICHARDSON "richardson"
@@ -65,6 +72,81 @@ PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) {
 
   PetscFunctionReturn(laplace->precon(x, y)); // NOLINT
 }
+
+// TODO: handle fourth order
+auto set_stencil(const Mesh& localmesh, bool fourth_order) {
+  OperatorStencil<IndPerp> stencil;
+  IndexOffset<IndPerp> zero;
+  // Start with a square stencil 1-point wide
+  std::set offsets = {
+      // clang-format off
+      zero.xm().zp(), zero.zp(), zero.xp().zp(),
+      zero.xm(),      zero,      zero.xp(),
+      zero.xm().zm(), zero.zm(), zero.xp().zm(),
+      // clang-format on
+  };
+
+  if (fourth_order) {
+    // Add a square stencil 2-points wide
+    offsets.insert({
+        // clang-format off
+        zero.xm(2).zp(2), zero.xm().zp(2), zero.zp(2), zero.xp().zp(2), zero.xp(2).zp(2),
+        zero.xm(2).zp(),                                                zero.xp(2).zp(),
+        zero.xm(2),                                                     zero.xp(2),
+        zero.xm(2).zm(),                                                zero.xp(2).zm(),
+        zero.xm(2).zm(2), zero.xm().zm(2), zero.zm(2), zero.xp().zm(2), zero.xp(2).zm(2),
+        // clang-format on
+    });
+  }
+
+  std::vector offsetsVec(offsets.begin(), offsets.end());
+  stencil.add(
+      [&localmesh](IndPerp ind) -> bool {
+        return (localmesh.xstart <= ind.x() && ind.x() <= localmesh.xend
+                and (localmesh.zstart <= ind.z() && ind.z() <= localmesh.zend));
+      },
+      offsetsVec);
+
+  // Add inner X boundary
+  if (localmesh.firstX()) {
+    const auto first_boundary = localmesh.xstart - 1;
+    const auto second_boundary = localmesh.xstart - 2;
+
+    if (fourth_order) {
+      stencil.add(
+          [first_boundary, second_boundary](IndPerp ind) -> bool {
+            const auto x = ind.x();
+            return x == first_boundary or x == second_boundary;
+          },
+          {zero, zero.xp(1), zero.xp(2), zero.xp(3), zero.xp(4)});
+    } else {
+      stencil.add(
+          [first_boundary](IndPerp ind) -> bool { return ind.x() == first_boundary; },
+          {zero, zero.xp()});
+    }
+  }
+  // Add outer X boundary
+  if (localmesh.lastX()) {
+    const auto first_boundary = localmesh.xend + 1;
+    const auto second_boundary = localmesh.xend + 2;
+
+    if (fourth_order) {
+      stencil.add(
+          [first_boundary, second_boundary](IndPerp ind) -> bool {
+            const auto x = ind.x();
+            return x == first_boundary or x == second_boundary;
+          },
+          {zero, zero.xm(1), zero.xm(2), zero.xm(3), zero.xm(4)});
+    } else {
+      stencil.add(
+          [first_boundary](IndPerp ind) -> bool { return ind.x() == first_boundary; },
+          {zero, zero.xm()});
+    }
+  }
+
+  stencil.add([](IndPerp UNUSED(ind)) -> bool { return true; }, {zero});
+  return stencil;
+}
 } // namespace
 
 LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
@@ -91,7 +173,9 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
       direct((*opts)["direct"].doc("Use direct (LU) solver?").withDefault(false)),
       fourth_order(
           (*opts)["fourth_order"].doc("Use fourth order stencil").withDefault(false)),
-      lib(opts) {
+      indexer(std::make_shared<GlobalIndexer<FieldPerp>>(
+          localmesh, set_stencil(*localmesh, fourth_order))),
+      operator2D(indexer), lib(opts) {
 
   A.setLocation(location);
   C1.setLocation(location);
@@ -111,114 +195,6 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   }
 #endif
 
-  const bool first_x = localmesh->firstX();
-  const bool last_x = localmesh->lastX();
-
-  // Need to determine local size to use based on prior parallelisation
-  // Coefficient values are stored only on local processors.
-  const auto local_nz = localmesh->zend - localmesh->zstart + 1;
-  localN = (localmesh->xend - localmesh->xstart + 1) * local_nz;
-  if (first_x) {
-    // If on first processor add on width of boundary region
-    localN += localmesh->xstart * local_nz;
-  }
-  if (last_x) {
-    // If on last processor add on width of boundary region
-    localN += localmesh->xstart * local_nz;
-  }
-
-  // Calculate 'size' (the total number of points in physical grid)
-  size = localN;
-  if (bout::globals::mpi->MPI_Allreduce(&localN, &size, 1, MPI_INT, MPI_SUM, comm)
-      != MPI_SUCCESS) {
-    throw BoutException("Error in MPI_Allreduce during LaplacePetsc initialisation");
-  }
-
-  // Calculate total (physical) grid dimensions
-  meshz = local_nz;
-  meshx = size / meshz;
-
-  // Create PETSc type of vectors for the solution and the RHS vector
-  VecCreate(comm, &xs);
-  VecSetSizes(xs, localN, size);
-  VecSetFromOptions(xs);
-  VecDuplicate(xs, &bs);
-
-  // Set size of (the PETSc) Matrix on each processor to localN x localN
-  MatCreate(comm, &MatA);
-  MatSetSizes(MatA, localN, localN, size, size);
-  MatSetFromOptions(MatA);
-
-  // Pre allocate memory. See MatMPIAIJSetPreallocation docs for more info
-  // Number of non-zero elements in each row of matrix owned by this processor
-  // ("diagonal submatrices")
-  std::vector<PetscInt> d_nnz(localN, 0);
-  // Number of non-zero elements in each row of matrix owned by other processors
-  // ("offdiagonal submatrices")
-  std::vector<PetscInt> o_nnz(localN, 0);
-
-  if (fourth_order) {
-    // first and last 2*localmesh-LocalNz entries are the edge x-values that
-    // (may) have 'off-diagonal' components (i.e. on another processor)
-
-    const int first_first_off = first_x ? 0 : 10;
-    const int first_last_off = last_x ? 0 : 10;
-    const int second_first_off = first_x ? 0 : 5;
-    const int second_last_off = last_x ? 0 : 5;
-
-    for (int i = 0; i <= local_nz; i++) {
-      d_nnz[i] = 15;
-      d_nnz[localN - 1 - i] = 15;
-      o_nnz[i] = first_first_off;
-      o_nnz[localN - 1 - i] = first_last_off;
-    }
-    for (int i = local_nz; i < 2 * local_nz; i++) {
-      d_nnz[i] = 20;
-      d_nnz[localN - 1 - i] = 20;
-      o_nnz[i] = second_first_off;
-      o_nnz[localN - 1 - i] = second_last_off;
-    }
-
-    for (int i = 2 * local_nz; i < localN - (2 * local_nz); i++) {
-      d_nnz[i] = 25;
-      d_nnz[localN - 1 - i] = 25;
-      o_nnz[i] = 0;
-      o_nnz[localN - 1 - i] = 0;
-    }
-  } else {
-    // first and last local_nz entries are the edge x-values that
-    // (may) have 'off-diagonal' components (i.e. on another processor)
-    const int first_off = first_x ? 0 : 3;
-    const int last_off = last_x ? 0 : 3;
-
-    for (int i = 0; i <= local_nz; i++) {
-      d_nnz[i] = 6;
-      d_nnz[localN - 1 - i] = 6;
-      o_nnz[i] = first_off;
-      o_nnz[localN - 1 - i] = last_off;
-    }
-
-    for (int i = local_nz; i < localN - local_nz; i++) {
-      d_nnz[i] = 9;
-      d_nnz[localN - 1 - i] = 9;
-      o_nnz[i] = 0;
-      o_nnz[localN - 1 - i] = 0;
-    }
-  }
-
-  if (first_x and last_x) {
-    // Only one processor in X
-    MatSeqAIJSetPreallocation(MatA, 0, d_nnz.data());
-  } else {
-    MatMPIAIJSetPreallocation(MatA, 0, d_nnz.data(), 0, o_nnz.data());
-  }
-
-  // Sets up the internal matrix data structures for the later use.
-  MatSetUp(MatA);
-
-  // Declare KSP Context (abstract PETSc object that manages all Krylov methods)
-  KSPCreate(comm, &ksp);
-
   // Let "user" be a synonym for "shell"
   if (pctype == "user") {
     pctype = PCSHELL;
@@ -236,6 +212,12 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   }
 }
 
+LaplacePetsc::~LaplacePetsc() {
+  if (ksp_initialised) {
+    KSPDestroy(&ksp);
+  }
+}
+
 FieldPerp LaplacePetsc::solve(const FieldPerp& b) { return solve(b, b); }
 
 /*!
@@ -265,404 +247,34 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
   checkFlags();
 #endif
 
-  int y = b.getIndex(); // Get the Y index
-  sol.setIndex(y);      // Initialize the solution field.
-  sol = 0.;
-
-  // Determine which row/columns of the matrix are locally owned
-  MatGetOwnershipRange(MatA, &Istart, &Iend);
-
-  int i = Istart; // The row in the PETSc matrix
+  const int y = b.getIndex(); // Get the Y index
   {
     Timer timer("petscsetup");
 
-    //     if ((fourth_order) && !(lastflag&INVERT_4TH_ORDER)) throw BoutException("Should not change INVERT_4TH_ORDER flag in LaplacePetsc: 2nd order and 4th order require different pre-allocation to optimize PETSc solver");
+    const bool inner_X_neumann = isInnerBoundaryFlagSet(INVERT_AC_GRAD);
+    const bool outer_X_neumann = isOuterBoundaryFlagSet(INVERT_AC_GRAD);
 
-    /* Set Matrix Elements
-   *
-   * Loop over locally owned rows of matrix A
-   * i labels NODE POINT from
-   * bottom left = (0,0) = 0
-   * to
-   * top right = (meshx-1,meshz-1) = meshx*meshz-1
-   *
-   * i increments by 1 for an increase of 1 in Z
-   * i increments by meshz for an increase of 1 in X.
-   *
-   * In other word the indexing is done in a row-major order, but starting at
-   * bottom left rather than top left
-   */
-    // X=0 to localmesh->xstart-1 defines the boundary region of the domain.
-    // Set the values for the inner boundary region
-    if (localmesh->firstX()) {
-      for (int x = 0; x < localmesh->xstart; x++) {
-        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-          PetscScalar val; // Value of element to be set in the matrix
-          // If Neumann Boundary Conditions are set.
-          if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) {
-            // Set values corresponding to nodes adjacent in x
-            if (fourth_order) {
-              // Fourth Order Accuracy on Boundary
-              Element(i, x, z, 0, 0,
-                      -25.0 / (12.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)),
-                      MatA);
-              Element(i, x, z, 1, 0,
-                      4.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-              Element(i, x, z, 2, 0,
-                      -3.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-              Element(i, x, z, 3, 0,
-                      4.0 / (3.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)),
-                      MatA);
-              Element(i, x, z, 4, 0,
-                      -1.0 / (4.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)),
-                      MatA);
-            } else {
-              // Second Order Accuracy on Boundary
-              //   Element(i,x,z, 0, 0, -3.0 / (2.0*coords->dx(x,y)), MatA );
-              //   Element(i,x,z, 1, 0,  2.0 / coords->dx(x,y), MatA );
-              //   Element(i,x,z, 2, 0, -1.0 / (2.0*coords->dx(x,y)), MatA );
-              //   Element(i,x,z, 3, 0, 0.0, MatA );  // Reset these elements to 0
-              //   in case 4th order flag was used previously: not allowed now
-              //   Element(i,x,z, 4, 0, 0.0, MatA );
-              // Second Order Accuracy on Boundary, set half-way between grid points
-              Element(i, x, z, 0, 0,
-                      -1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-              Element(i, x, z, 1, 0,
-                      1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-              Element(i, x, z, 2, 0, 0.0, MatA);
-              //                      Element(i,x,z, 3, 0, 0.0, MatA );  // Reset
-              //                      these elements to 0 in case 4th order flag was
-              //                      used previously: not allowed now
-              //                      Element(i,x,z, 4, 0, 0.0, MatA );
-            }
-          } else {
-            if (fourth_order) {
-              // Set Diagonal Values to 1
-              Element(i, x, z, 0, 0, 1., MatA);
-
-              // Set off diagonal elements to zero
-              Element(i, x, z, 1, 0, 0.0, MatA);
-              Element(i, x, z, 2, 0, 0.0, MatA);
-              Element(i, x, z, 3, 0, 0.0, MatA);
-              Element(i, x, z, 4, 0, 0.0, MatA);
-            } else {
-              Element(i, x, z, 0, 0, 0.5, MatA);
-              Element(i, x, z, 1, 0, 0.5, MatA);
-              Element(i, x, z, 2, 0, 0., MatA);
-            }
-          }
-
-          val = 0; // Initialize val
-
-          // Set Components of RHS
-          // If the inner boundary value should be set by b or x0
-          if (isInnerBoundaryFlagSet(INVERT_RHS)) {
-            val = b[x][z];
-          } else if (isInnerBoundaryFlagSet(INVERT_SET)) {
-            val = x0[x][z];
-          }
-
-          // Set components of the RHS (the PETSc vector bs)
-          // 1 element is being set in row i to val
-          // INSERT_VALUES replaces existing entries with new values
-          VecSetValues(bs, 1, &i, &val, INSERT_VALUES);
-
-          // Set components of the and trial solution (the PETSc vector xs)
-          // 1 element is being set in row i to val
-          // INSERT_VALUES replaces existing entries with new values
-          val = x0[x][z];
-          VecSetValues(xs, 1, &i, &val, INSERT_VALUES);
-
-          i++; // Increment row in Petsc matrix
-        }
-      }
+    // Set the operator matrix
+    if (fourth_order) {
+      setFourthOrderMatrix(y, inner_X_neumann, outer_X_neumann);
+    } else {
+      setSecondOrderMatrix(y, inner_X_neumann, outer_X_neumann);
     }
 
-    // Set the values for the main domain
-    for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-        // NOTE: Only A0 is the A from setCoefA ()
-        BoutReal A0, A1, A2, A3, A4, A5;
-        A0 = A(x, y, z);
-
-        ASSERT3(std::isfinite(A0));
-
-        // Set the matrix coefficients
-        Coeffs(x, y, z, A1, A2, A3, A4, A5);
-
-        BoutReal dx = coords->dx(x, y, z);
-        BoutReal dx2 = SQ(dx);
-        BoutReal dz = coords->dz(x, y, z);
-        BoutReal dz2 = SQ(dz);
-        BoutReal dxdz = dx * dz;
-
-        ASSERT3(std::isfinite(A1));
-        ASSERT3(std::isfinite(A2));
-        ASSERT3(std::isfinite(A3));
-        ASSERT3(std::isfinite(A4));
-        ASSERT3(std::isfinite(A5));
-
-        // Set Matrix Elements
-        PetscScalar val = 0.;
-        if (fourth_order) {
-          // f(i,j) = f(x,z)
-          val = A0 - (5.0 / 2.0) * ((A1 / dx2) + (A2 / dz2));
-          Element(i, x, z, 0, 0, val, MatA);
-
-          // f(i-2,j-2)
-          val = A3 / (144.0 * dxdz);
-          Element(i, x, z, -2, -2, val, MatA);
-
-          // f(i-2,j-1)
-          val = -1.0 * A3 / (18.0 * dxdz);
-          Element(i, x, z, -2, -1, val, MatA);
-
-          // f(i-2,j)
-          val = (1.0 / 12.0) * ((-1.0 * A1 / dx2) + (A4 / dx));
-          Element(i, x, z, -2, 0, val, MatA);
-
-          // f(i-2,j+1)
-          val = A3 / (18.0 * dxdz);
-          Element(i, x, z, -2, 1, val, MatA);
-
-          // f(i-2,j+2)
-          val = -1.0 * A3 / (144.0 * dxdz);
-          Element(i, x, z, -2, 2, val, MatA);
-
-          // f(i-1,j-2)
-          val = -1.0 * A3 / (18.0 * dxdz);
-          Element(i, x, z, -1, -2, val, MatA);
-
-          // f(i-1,j-1)
-          val = 4.0 * A3 / (9.0 * dxdz);
-          Element(i, x, z, -1, -1, val, MatA);
-
-          // f(i-1,j)
-          val = (4.0 * A1 / (3.0 * dx2)) - (2.0 * A4 / (3.0 * dx));
-          Element(i, x, z, -1, 0, val, MatA);
-
-          // f(i-1,j+1)
-          val = -4.0 * A3 / (9.0 * dxdz);
-          Element(i, x, z, -1, 1, val, MatA);
-
-          // f(i-1,j+2)
-          val = A3 / (18.0 * dxdz);
-          Element(i, x, z, -1, 2, val, MatA);
-
-          // f(i,j-2)
-          val = (1.0 / 12.0) * ((-1.0 * A2 / dz2) + (A5 / dz));
-          Element(i, x, z, 0, -2, val, MatA);
-
-          // f(i,j-1)
-          val = (4.0 * A2 / (3.0 * dz2)) - (2.0 * A5 / (3.0 * dz));
-          Element(i, x, z, 0, -1, val, MatA);
-
-          // f(i,j+1)
-          val = (4.0 * A2 / (3.0 * dz2)) + (2.0 * A5 / (3.0 * dz));
-          Element(i, x, z, 0, 1, val, MatA);
-
-          // f(i,j+2)
-          val = (-1.0 / 12.0) * ((A2 / dz2) + (A5 / dz));
-          Element(i, x, z, 0, 2, val, MatA);
-
-          // f(i+1,j-2)
-          val = A3 / (18.0 * dxdz);
-          Element(i, x, z, 1, -2, val, MatA);
-
-          // f(i+1,j-1)
-          val = -4.0 * A3 / (9.0 * dxdz);
-          Element(i, x, z, 1, -1, val, MatA);
-
-          // f(i+1,j)
-          val = (4.0 * A1 / (3.0 * dx2)) + (2.0 * A4 / (3.0 * dx));
-          Element(i, x, z, 1, 0, val, MatA);
-
-          // f(i+1,j+1)
-          val = 4.0 * A3 / (9.0 * dxdz);
-          Element(i, x, z, 1, 1, val, MatA);
-
-          // f(i+1,j+2)
-          val = -1.0 * A3 / (18.0 * dxdz);
-          Element(i, x, z, 1, 2, val, MatA);
-
-          // f(i+2,j-2)
-          val = -1.0 * A3 / (144.0 * dxdz);
-          Element(i, x, z, 2, -2, val, MatA);
-
-          // f(i+2,j-1)
-          val = A3 / (18.0 * dxdz);
-          Element(i, x, z, 2, -1, val, MatA);
-
-          // f(i+2,j)
-          val = (-1.0 / 12.0) * ((A1 / dx2) + (A4 / dx));
-          Element(i, x, z, 2, 0, val, MatA);
-
-          // f(i+2,j+1)
-          val = -1.0 * A3 / (18.0 * dxdz);
-          Element(i, x, z, 2, 1, val, MatA);
-
-          // f(i+2,j+2)
-          val = A3 / (144.0 * dxdz);
-          Element(i, x, z, 2, 2, val, MatA);
-        } else {
-          // Second order
-
-          // f(i,j) = f(x,z)
-          val = A0 - 2.0 * ((A1 / dx2) + (A2 / dz2));
-          Element(i, x, z, 0, 0, val, MatA);
-
-          // f(i-1,j-1)
-          val = A3 / (4.0 * dxdz);
-          Element(i, x, z, -1, -1, val, MatA);
-
-          // f(i-1,j)
-          val = (A1 / dx2) - A4 / (2.0 * dx);
-          Element(i, x, z, -1, 0, val, MatA);
-
-          // f(i-1,j+1)
-          val = -1.0 * A3 / (4.0 * dxdz);
-          Element(i, x, z, -1, 1, val, MatA);
-
-          // f(i,j-1)
-          val = (A2 / dz2) - (A5 / (2.0 * dz));
-          Element(i, x, z, 0, -1, val, MatA);
-
-          // f(i,j+1)
-          val = (A2 / dz2) + (A5 / (2.0 * dz));
-          Element(i, x, z, 0, 1, val, MatA);
-
-          // f(i+1,j-1)
-          val = -1.0 * A3 / (4.0 * dxdz);
-          Element(i, x, z, 1, -1, val, MatA);
+    operator2D.assemble();
+    MatSetBlockSize(*operator2D.get(), 1);
 
-          // f(i+1,j)
-          val = (A1 / dx2) + (A4 / (2.0 * dx));
-          Element(i, x, z, 1, 0, val, MatA);
-
-          // f(i+1,j+1)
-          val = A3 / (4.0 * dxdz);
-          Element(i, x, z, 1, 1, val, MatA);
-        }
-        // Set Components of RHS Vector
-        val = b[x][z];
-        VecSetValues(bs, 1, &i, &val, INSERT_VALUES);
-
-        // Set Components of Trial Solution Vector
-        val = x0[x][z];
-        VecSetValues(xs, 1, &i, &val, INSERT_VALUES);
-        i++;
-      }
-    }
-
-    // X=localmesh->xend+1 to localmesh->LocalNx-1 defines the upper boundary region of the domain.
-    // Set the values for the outer boundary region
-    if (localmesh->lastX()) {
-      for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
-        for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-          // Set Diagonal Values to 1
-          PetscScalar val = 1;
-          Element(i, x, z, 0, 0, val, MatA);
-
-          // If Neumann Boundary Conditions are set.
-          if (isOuterBoundaryFlagSet(INVERT_AC_GRAD)) {
-            // Set values corresponding to nodes adjacent in x
-            if (fourth_order) {
-              // Fourth Order Accuracy on Boundary
-              Element(i, x, z, 0, 0,
-                      25.0 / (12.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)),
-                      MatA);
-              Element(i, x, z, -1, 0,
-                      -4.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-              Element(i, x, z, -2, 0,
-                      3.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-              Element(i, x, z, -3, 0,
-                      -4.0 / (3.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)),
-                      MatA);
-              Element(i, x, z, -4, 0,
-                      1.0 / (4.0 * coords->dx(x, y, z)) / sqrt(coords->g_11(x, y, z)),
-                      MatA);
-            } else {
-              // // Second Order Accuracy on Boundary
-              // Element(i,x,z,  0, 0,  3.0 / (2.0*coords->dx(x,y)), MatA );
-              // Element(i,x,z, -1, 0, -2.0 / coords->dx(x,y), MatA );
-              // Element(i,x,z, -2, 0,  1.0 / (2.0*coords->dx(x,y)), MatA );
-              // Element(i,x,z, -3, 0,  0.0, MatA );  // Reset these elements to 0
-              // in case 4th order flag was used previously: not allowed now
-              // Element(i,x,z, -4, 0,  0.0, MatA );
-              // Second Order Accuracy on Boundary, set half-way between grid
-              // points
-              Element(i, x, z, 0, 0,
-                      1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-              Element(i, x, z, -1, 0,
-                      -1.0 / coords->dx(x, y, z) / sqrt(coords->g_11(x, y, z)), MatA);
-              Element(i, x, z, -2, 0, 0.0, MatA);
-              // Element(i,x,z, -3, 0,  0.0, MatA );  // Reset these elements to 0
-              // in case 4th order flag was used previously: not allowed now
-              // Element(i,x,z, -4, 0,  0.0, MatA );
-            }
-          } else {
-            if (fourth_order) {
-              // Set off diagonal elements to zero
-              Element(i, x, z, -1, 0, 0.0, MatA);
-              Element(i, x, z, -2, 0, 0.0, MatA);
-              Element(i, x, z, -3, 0, 0.0, MatA);
-              Element(i, x, z, -4, 0, 0.0, MatA);
-            } else {
-              Element(i, x, z, 0, 0, 0.5, MatA);
-              Element(i, x, z, -1, 0, 0.5, MatA);
-              Element(i, x, z, -2, 0, 0., MatA);
-            }
-          }
-
-          // Set Components of RHS
-          // If the inner boundary value should be set by b or x0
-          val = 0;
-          if (isOuterBoundaryFlagSet(INVERT_RHS)) {
-            val = b[x][z];
-          } else if (isOuterBoundaryFlagSet(INVERT_SET)) {
-            val = x0[x][z];
-          }
-
-          // Set components of the RHS (the PETSc vector bs)
-          // 1 element is being set in row i to val
-          // INSERT_VALUES replaces existing entries with new values
-          VecSetValues(bs, 1, &i, &val, INSERT_VALUES);
-
-          // Set components of the and trial solution (the PETSc vector xs)
-          // 1 element is being set in row i to val
-          // INSERT_VALUES replaces existing entries with new values
-          val = x0[x][z];
-          VecSetValues(xs, 1, &i, &val, INSERT_VALUES);
-
-          i++; // Increment row in Petsc matrix
-        }
-      }
-    }
-
-    if (i != Iend) {
-      throw BoutException("Petsc index sanity check failed: i={} != Iend={}", i, Iend);
+    // Declare KSP Context (abstract PETSc object that manages all Krylov methods)
+    if (ksp_initialised) {
+      KSPDestroy(&ksp);
     }
-
-    // Assemble Matrix
-    MatAssemblyBegin(MatA, MAT_FINAL_ASSEMBLY);
-    MatAssemblyEnd(MatA, MAT_FINAL_ASSEMBLY);
-
-    //   // Record which flags were used for this matrix
-    //   lastflag = flags;
-
-    // Assemble RHS Vector
-    VecAssemblyBegin(bs);
-    VecAssemblyEnd(bs);
-
-    // Assemble Trial Solution Vector
-    VecAssemblyBegin(xs);
-    VecAssemblyEnd(xs);
+    KSPCreate(comm, &ksp);
 
     // Configure Linear Solver
 #if PETSC_VERSION_GE(3, 5, 0)
-    KSPSetOperators(ksp, MatA, MatA);
+    KSPSetOperators(ksp, *operator2D.get(), *operator2D.get());
 #else
-    KSPSetOperators(ksp, MatA, MatA, DIFFERENT_NONZERO_PATTERN);
+    KSPSetOperators(ksp, *operator2D.get(), *operator2D.get(), DIFFERENT_NONZERO_PATTERN);
 #endif
     PC pc; // The preconditioner option
 
@@ -717,19 +329,34 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
         } else {
           KSPSetPCSide(ksp, PC_LEFT); // Left preconditioning
         }
-        //ierr = PCShellSetApply(pc,laplacePCapply);CHKERRQ(ierr);
-        //ierr = PCShellSetContext(pc,this);CHKERRQ(ierr);
-        //ierr = KSPSetPCSide(ksp, PC_RIGHT);CHKERRQ(ierr);
       }
 
       lib.setOptionsFromInputFile(ksp);
     }
   }
 
+  PetscVector<FieldPerp> rhs(b, indexer);
+  PetscVector<FieldPerp> guess(x0, indexer);
+
+  // Set boundary conditions
+  if (!isInnerBoundaryFlagSet(INVERT_RHS)) {
+    BOUT_FOR_SERIAL(index, indexer->getRegionInnerX()) {
+      rhs(index) = isInnerBoundaryFlagSet(INVERT_SET) ? x0[index] : 0.0;
+    }
+  }
+  if (!isOuterBoundaryFlagSet(INVERT_RHS)) {
+    BOUT_FOR_SERIAL(index, indexer->getRegionOuterX()) {
+      rhs(index) = isInnerBoundaryFlagSet(INVERT_SET) ? x0[index] : 0.0;
+    }
+  }
+
+  rhs.assemble();
+  guess.assemble();
+
   // Call the actual solver
   {
     Timer timer("petscsolve");
-    KSPSolve(ksp, bs, xs); // Call the solver to solve the system
+    KSPSolve(ksp, *rhs.get(), *guess.get());
   }
 
   KSPConvergedReason reason;
@@ -743,118 +370,14 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
         KSPConvergedReasons[reason], static_cast<int>(reason));
   }
 
-  // Add data to FieldPerp Object
-  i = Istart;
-  // Set the inner boundary values
-  if (localmesh->firstX()) {
-    for (int x = 0; x < localmesh->xstart; x++) {
-      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-        PetscScalar val = 0;
-        VecGetValues(xs, 1, &i, &val);
-        sol[x][z] = val;
-        i++; // Increment row in Petsc matrix
-      }
-    }
-  }
-
-  // Set the main domain values
-  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-      PetscScalar val = 0;
-      VecGetValues(xs, 1, &i, &val);
-      sol[x][z] = val;
-      i++; // Increment row in Petsc matrix
-    }
-  }
-
-  // Set the outer boundary values
-  if (localmesh->lastX()) {
-    for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
-      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-        PetscScalar val = 0;
-        VecGetValues(xs, 1, &i, &val);
-        sol[x][z] = val;
-        i++; // Increment row in Petsc matrix
-      }
-    }
-  }
-
-  if (i != Iend) {
-    throw BoutException("Petsc index sanity check 2 failed");
-  }
-
+  auto sol = guess.toField();
+  sol.setIndex(y);
   checkData(sol);
 
   // Return the solution
   return sol;
 }
 
-/*!
- * Sets the elements of the matrix A, which is used to solve the problem Ax=b.
- *
- * \param[in]
- * i
- * The row of the PETSc matrix
- * \param[in] x         Local x index of the mesh
- * \param[in] z         Local z index of the mesh
- * \param[in] xshift    The shift in rows from the index x
- * \param[in] zshift    The shift in columns from the index z
- * \param[in] ele       Value of the element
- * \param[in] MatA      The matrix A used in the inversion
- *
- * \param[out] MatA     The matrix A used in the inversion
- */
-void LaplacePetsc::Element(int i, int x, int z, int xshift, int zshift, PetscScalar ele,
-                           Mat& MatA) {
-
-  // Need to convert LOCAL x to GLOBAL x in order to correctly calculate
-  // PETSC Matrix Index.
-  int xoffset = Istart / meshz;
-#if CHECK > 2
-  const int rem = Istart % meshz;
-  if (rem != 0) {
-    throw BoutException("Petsc index sanity check 3 failed: Istart={} % meshz={} == {}",
-                        Istart, meshz, rem);
-  }
-#endif
-
-  // Calculate the row to be set
-  int row_new = x + xshift; // should never be out of range.
-  if (!localmesh->firstX()) {
-    row_new += (xoffset - localmesh->xstart);
-  }
-
-  // Calculate the column to be set
-  int col_new = z + zshift - localmesh->zstart;
-  if (col_new < 0) {
-    col_new += meshz;
-  } else if (col_new > meshz - 1) {
-    col_new -= meshz;
-  }
-
-  // Convert to global indices
-  int index = (row_new * meshz) + col_new;
-
-#if CHECK > 2
-  if (!std::isfinite(ele)) {
-    throw BoutException("Non-finite element at x={:d}, z={:d}, row={:d}, col={:d}\n", x,
-                        z, i, index);
-  }
-#endif
-
-  /* Inserts or adds a block of values into a matrix
-   * Input:
-   * MatA   - The matrix to set the values in
-   * 1      - The number of rows to be set
-   * &i     - The global index of the row
-   * 1      - The number of columns to be set
-   * &index - The global index of the column
-   * &ele   - The vlaue to be set
-   * INSERT_VALUES replaces existing entries with new values
-   */
-  MatSetValues(MatA, 1, &i, 1, &index, &ele, INSERT_VALUES);
-}
-
 /*!
  * Set the matrix components of A in Ax=b, solving
  * D*Laplace_perp(x) + (1/C1)Grad_perp(C2)*Grad_perp(x) + Ax = B
@@ -887,19 +410,19 @@ void LaplacePetsc::Element(int i, int x, int z, int xshift, int zshift, PetscSca
  * \param[out] coef5    Convenient variable used to set matrix
  *                      (see manual for details)
  */
-void LaplacePetsc::Coeffs(int x, int y, int z, BoutReal& coef1, BoutReal& coef2,
-                          BoutReal& coef3, BoutReal& coef4, BoutReal& coef5) {
+LaplacePetsc::CoeffsA LaplacePetsc::Coeffs(Ind3D i) {
+  const auto x = i.x();
 
-  coef1 = coords->g11(x, y, z);      // X 2nd derivative coefficient
-  coef2 = coords->g33(x, y, z);      // Z 2nd derivative coefficient
-  coef3 = 2. * coords->g13(x, y, z); // X-Z mixed derivative coefficient
+  BoutReal coef1 = coords->g11[i];      // X 2nd derivative coefficient
+  BoutReal coef2 = coords->g33[i];      // Z 2nd derivative coefficient
+  BoutReal coef3 = 2. * coords->g13[i]; // X-Z mixed derivative coefficient
 
-  coef4 = 0.0;
-  coef5 = 0.0;
+  BoutReal coef4 = 0.0;
+  BoutReal coef5 = 0.0;
   // If global flag all_terms are set (true by default)
   if (all_terms) {
-    coef4 = coords->G1(x, y, z); // X 1st derivative
-    coef5 = coords->G3(x, y, z); // Z 1st derivative
+    coef4 = coords->G1[i]; // X 1st derivative
+    coef5 = coords->G3[i]; // Z 1st derivative
 
     ASSERT3(std::isfinite(coef4));
     ASSERT3(std::isfinite(coef5));
@@ -908,71 +431,48 @@ void LaplacePetsc::Coeffs(int x, int y, int z, BoutReal& coef1, BoutReal& coef2,
   if (nonuniform) {
     // non-uniform mesh correction
     if ((x != 0) && (x != (localmesh->LocalNx - 1))) {
-      coef4 -= 0.5
-               * ((coords->dx(x + 1, y, z) - coords->dx(x - 1, y, z))
-                  / SQ(coords->dx(x, y, z)))
+      coef4 -= 0.5 * ((coords->dx[i.xp()] - coords->dx[i.xm()]) / SQ(coords->dx[i]))
                * coef1; // BOUT-06 term
     }
   }
 
   if (localmesh->IncIntShear) {
     // d2dz2 term
-    coef2 += coords->g11(x, y, z) * coords->IntShiftTorsion(x, y, z)
-             * coords->IntShiftTorsion(x, y, z);
+    coef2 += coords->g11[i] * coords->IntShiftTorsion[i] * coords->IntShiftTorsion[i];
     // Mixed derivative
     coef3 = 0.0; // This cancels out
   }
 
   if (issetD) {
-    coef1 *= D(x, y, z);
-    coef2 *= D(x, y, z);
-    coef3 *= D(x, y, z);
-    coef4 *= D(x, y, z);
-    coef5 *= D(x, y, z);
+    coef1 *= D[i];
+    coef2 *= D[i];
+    coef3 *= D[i];
+    coef4 *= D[i];
+    coef5 *= D[i];
   }
 
   // A second/fourth order derivative term
   if (issetC) {
-    //   if( (x > 0) && (x < (localmesh->LocalNx-1)) ) //Valid if doing second order derivative, not if fourth: should only be called for xstart<=x<=xend anyway
     if ((x > 1) && (x < (localmesh->LocalNx - 2))) {
-      int zp = z + 1; // z plus 1
-      if (zp > meshz - 1) {
-        zp -= meshz;
-      }
-      int zm = z - 1; // z minus 1
-      if (zm < 0) {
-        zm += meshz;
-      }
       BoutReal ddx_C;
       BoutReal ddz_C;
 
       if (fourth_order) {
-        int zpp = z + 2; // z plus 1 plus 1
-        if (zpp > meshz - 1) {
-          zpp -= meshz;
-        }
-        int zmm = z - 2; // z minus 1 minus 1
-        if (zmm < 0) {
-          zmm += meshz;
-        }
         // Fourth order discretization of C in x
-        ddx_C = (-C2(x + 2, y, z) + 8. * C2(x + 1, y, z) - 8. * C2(x - 1, y, z)
-                 + C2(x - 2, y, z))
-                / (12. * coords->dx(x, y, z) * (C1(x, y, z)));
+        ddx_C = (-C2[i.xpp()] + 8. * C2[i.xp()] - 8. * C2[i.xm()] + C2[i.xmm()])
+                / (12. * coords->dx[i] * (C1[i]));
         // Fourth order discretization of C in z
-        ddz_C = (-C2(x, y, zpp) + 8. * C2(x, y, zp) - 8. * C2(x, y, zm) + C2(x, y, zmm))
-                / (12. * coords->dz(x, y, z) * (C1(x, y, z)));
+        ddz_C = (-C2[i.zpp()] + 8. * C2[i.zp()] - 8. * C2[i.zm()] + C2[i.zmm()])
+                / (12. * coords->dz[i] * (C1[i]));
       } else {
         // Second order discretization of C in x
-        ddx_C = (C2(x + 1, y, z) - C2(x - 1, y, z))
-                / (2. * coords->dx(x, y, z) * (C1(x, y, z)));
+        ddx_C = (C2[i.xp()] - C2[i.xm()]) / (2. * coords->dx[i] * (C1[i]));
         // Second order discretization of C in z
-        ddz_C =
-            (C2(x, y, zp) - C2(x, y, zm)) / (2. * coords->dz(x, y, z) * (C1(x, y, z)));
+        ddz_C = (C2[i.zp()] - C2[i.zm()]) / (2. * coords->dz[i] * (C1[i]));
       }
 
-      coef4 += coords->g11(x, y, z) * ddx_C + coords->g13(x, y, z) * ddz_C;
-      coef5 += coords->g13(x, y, z) * ddx_C + coords->g33(x, y, z) * ddz_C;
+      coef4 += (coords->g11[i] * ddx_C) + (coords->g13[i] * ddz_C);
+      coef5 += (coords->g13[i] * ddx_C) + (coords->g33[i] * ddz_C);
     }
   }
 
@@ -986,99 +486,199 @@ void LaplacePetsc::Coeffs(int x, int y, int z, BoutReal& coef1, BoutReal& coef2,
    */
   if (issetE) {
     // These coefficients are 0 by default
-    coef4 += Ex(x, y, z);
-    coef5 += Ez(x, y, z);
+    coef4 += Ex[i];
+    coef5 += Ez[i];
   }
-}
-
-void LaplacePetsc::vecToField(Vec xs, FieldPerp& f) {
 
-  ASSERT1(localmesh == f.getMesh());
+  return {coef1, coef2, coef3, coef4, coef5};
+}
 
-  f.allocate();
-  int i = Istart;
-  if (localmesh->firstX()) {
-    for (int x = 0; x < localmesh->xstart; x++) {
-      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-        PetscScalar val;
-        VecGetValues(xs, 1, &i, &val);
-        f[x][z] = val;
-        i++; // Increment row in Petsc matrix
-      }
+void LaplacePetsc::setSecondOrderMatrix(int y, bool inner_X_neumann,
+                                        bool outer_X_neumann) {
+  // Set the boundaries
+  if (inner_X_neumann) {
+    const auto dx = sliceXZ(coords->dx, y);
+    const auto g11 = sliceXZ(coords->g11, y);
+
+    BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
+      const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
+      operator2D(i, i) = -factor;
+      operator2D(i, i.xp()) = factor;
     }
-  }
-
-  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-      PetscScalar val;
-      VecGetValues(xs, 1, &i, &val);
-      f[x][z] = val;
-      i++; // Increment row in Petsc matrix
+  } else {
+    BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
+      operator2D(i, i) = 0.5;
+      operator2D(i, i.xp()) = 0.5;
     }
   }
+  if (outer_X_neumann) {
+    const auto dx = sliceXZ(coords->dx, y);
+    const auto g11 = sliceXZ(coords->g11, y);
 
-  if (localmesh->lastX()) {
-    for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
-      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-        PetscScalar val;
-        VecGetValues(xs, 1, &i, &val);
-        f[x][z] = val;
-        i++; // Increment row in Petsc matrix
-      }
+    BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
+      const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
+      operator2D(i, i) = factor;
+      operator2D(i, i.xm()) = -factor;
+    }
+  } else {
+    BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
+      operator2D(i, i) = 0.5;
+      operator2D(i, i.xm()) = 0.5;
     }
   }
-  ASSERT1(i == Iend);
-}
 
-void LaplacePetsc::fieldToVec(const FieldPerp& f, Vec bs) {
-  ASSERT1(localmesh == f.getMesh());
+  // Set the interior region
+  BOUT_FOR_SERIAL(l, indexer->getRegionNobndry()) {
+    const auto i = localmesh->indPerpto3D(l, y);
 
-  int i = Istart;
-  if (localmesh->firstX()) {
-    for (int x = 0; x < localmesh->xstart; x++) {
-      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-        PetscScalar val = f[x][z];
-        VecSetValues(bs, 1, &i, &val, INSERT_VALUES);
-        i++; // Increment row in Petsc matrix
-      }
-    }
+    // NOTE: Only A0 is the A from setCoefA ()
+    const BoutReal A0 = A[i];
+
+    ASSERT3(std::isfinite(A0));
+
+    // Set the matrix coefficients
+    const auto [A1, A2, A3, A4, A5] = Coeffs(i);
+
+    ASSERT3(std::isfinite(A1));
+    ASSERT3(std::isfinite(A2));
+    ASSERT3(std::isfinite(A3));
+    ASSERT3(std::isfinite(A4));
+    ASSERT3(std::isfinite(A5));
+
+    BoutReal dx = coords->dx[i];
+    BoutReal dx2 = SQ(dx);
+    BoutReal dz = coords->dz[i];
+    BoutReal dz2 = SQ(dz);
+    BoutReal dxdz = dx * dz;
+    operator2D(l, l) = A0 - (2.0 * ((A1 / dx2) + (A2 / dz2)));
+    operator2D(l, l.xm().zm()) = A3 / (4.0 * dxdz);
+    operator2D(l, l.xm()) = (A1 / dx2) - (A4 / (2.0 * dx));
+    operator2D(l, l.xm().zp()) = -1.0 * A3 / (4.0 * dxdz);
+    operator2D(l, l.zm()) = (A2 / dz2) - (A5 / (2.0 * dz));
+    operator2D(l, l.zp()) = (A2 / dz2) + (A5 / (2.0 * dz));
+    operator2D(l, l.xp().zm()) = -1.0 * A3 / (4.0 * dxdz);
+    operator2D(l, l.xp()) = (A1 / dx2) + (A4 / (2.0 * dx));
+    operator2D(l, l.xp().zp()) = A3 / (4.0 * dxdz);
   }
+}
 
-  for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
-    for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-      PetscScalar val = f[x][z];
-      VecSetValues(bs, 1, &i, &val, INSERT_VALUES);
-      i++; // Increment row in Petsc matrix
+void LaplacePetsc::setFourthOrderMatrix(int y, bool inner_X_neumann,
+                                        bool outer_X_neumann) {
+
+  // Set boundaries
+  if (inner_X_neumann) {
+    const auto dx = sliceXZ(coords->dx, y);
+    const auto g11 = sliceXZ(coords->g11, y);
+
+    BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
+      const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
+      operator2D(i, i) = (-25.0 / 12.0) * factor;
+      operator2D(i, i.xp(1)) = 4.0 * factor;
+      operator2D(i, i.xp(2)) = -3.0 * factor;
+      operator2D(i, i.xp(3)) = (4.0 / 3.0) * factor;
+      operator2D(i, i.xp(4)) = (-1.0 / 4.0) * factor;
+    }
+  } else {
+    BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
+      operator2D(i, i) = 1.0;
+      operator2D(i, i.xp(1)) = 0.0;
+      operator2D(i, i.xp(2)) = 0.0;
+      operator2D(i, i.xp(3)) = 0.0;
+      operator2D(i, i.xp(4)) = 0.0;
     }
   }
 
-  if (localmesh->lastX()) {
-    for (int x = localmesh->xend + 1; x < localmesh->LocalNx; x++) {
-      for (int z = localmesh->zstart; z <= localmesh->zend; z++) {
-        PetscScalar val = f[x][z];
-        VecSetValues(bs, 1, &i, &val, INSERT_VALUES);
-        i++; // Increment row in Petsc matrix
-      }
+  if (outer_X_neumann) {
+    const auto dx = sliceXZ(coords->dx, y);
+    const auto g11 = sliceXZ(coords->g11, y);
+
+    BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
+      const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
+      operator2D(i, i) = (25.0 / 12.0) * factor;
+      operator2D(i, i.xm(1)) = -4.0 * factor;
+      operator2D(i, i.xm(2)) = 3.0 * factor;
+      operator2D(i, i.xm(3)) = (-4.0 / 3.0) * factor;
+      operator2D(i, i.xm(4)) = (1.0 / 4.0) * factor;
+    }
+  } else {
+    BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
+      operator2D(i, i) = 1.0;
+      operator2D(i, i.xm(1)) = 0.0;
+      operator2D(i, i.xm(2)) = 0.0;
+      operator2D(i, i.xm(3)) = 0.0;
+      operator2D(i, i.xm(4)) = 0.0;
     }
   }
-  ASSERT1(i == Iend);
 
-  VecAssemblyBegin(bs);
-  VecAssemblyEnd(bs);
+  // Set interior region
+  BOUT_FOR_SERIAL(l, indexer->getRegionNobndry()) {
+    const auto i = localmesh->indPerpto3D(l, y);
+
+    // NOTE: Only A0 is the A from setCoefA ()
+    const BoutReal A0 = A[i];
+
+    ASSERT3(std::isfinite(A0));
+
+    // Set the matrix coefficients
+    const auto [A1, A2, A3, A4, A5] = Coeffs(i);
+
+    ASSERT3(std::isfinite(A1));
+    ASSERT3(std::isfinite(A2));
+    ASSERT3(std::isfinite(A3));
+    ASSERT3(std::isfinite(A4));
+    ASSERT3(std::isfinite(A5));
+
+    BoutReal dx = coords->dx[i];
+    BoutReal dx2 = SQ(dx);
+    BoutReal dz = coords->dz[i];
+    BoutReal dz2 = SQ(dz);
+    BoutReal dxdz = dx * dz;
+
+    operator2D(l, l) = A0 - ((5.0 / 2.0) * ((A1 / dx2) + (A2 / dz2)));
+    operator2D(l, l.xmm().zmm()) = A3 / (144.0 * dxdz);
+    operator2D(l, l.xmm().zm()) = -1.0 * A3 / (18.0 * dxdz);
+    operator2D(l, l.xmm()) = (1.0 / 12.0) * ((-1.0 * A1 / dx2) + (A4 / dx));
+    operator2D(l, l.xmm().zp()) = A3 / (18.0 * dxdz);
+    operator2D(l, l.xmm().zpp()) = -1.0 * A3 / (144.0 * dxdz);
+    operator2D(l, l.xm().zmm()) = -1.0 * A3 / (18.0 * dxdz);
+    operator2D(l, l.xm().zm()) = 4.0 * A3 / (9.0 * dxdz);
+    operator2D(l, l.xm()) = (4.0 * A1 / (3.0 * dx2)) - (2.0 * A4 / (3.0 * dx));
+    operator2D(l, l.xm().zp()) = -4.0 * A3 / (9.0 * dxdz);
+    operator2D(l, l.xm().zpp()) = A3 / (18.0 * dxdz);
+    operator2D(l, l.zmm()) = (1.0 / 12.0) * ((-1.0 * A2 / dz2) + (A5 / dz));
+    operator2D(l, l.zm()) = (4.0 * A2 / (3.0 * dz2)) - (2.0 * A5 / (3.0 * dz));
+    operator2D(l, l.zp()) = (4.0 * A2 / (3.0 * dz2)) + (2.0 * A5 / (3.0 * dz));
+    operator2D(l, l.zpp()) = (-1.0 / 12.0) * ((A2 / dz2) + (A5 / dz));
+    operator2D(l, l.xp().zmm()) = A3 / (18.0 * dxdz);
+    operator2D(l, l.xp().zm()) = -4.0 * A3 / (9.0 * dxdz);
+    operator2D(l, l.xp()) = (4.0 * A1 / (3.0 * dx2)) + (2.0 * A4 / (3.0 * dx));
+    operator2D(l, l.xp().zp()) = 4.0 * A3 / (9.0 * dxdz);
+    operator2D(l, l.xp().zpp()) = -1.0 * A3 / (18.0 * dxdz);
+    operator2D(l, l.xpp().zmm()) = -1.0 * A3 / (144.0 * dxdz);
+    operator2D(l, l.xpp().zm()) = A3 / (18.0 * dxdz);
+    operator2D(l, l.xpp()) = (-1.0 / 12.0) * ((A1 / dx2) + (A4 / dx));
+    operator2D(l, l.xpp().zp()) = -1.0 * A3 / (18.0 * dxdz);
+    operator2D(l, l.xpp().zpp()) = A3 / (144.0 * dxdz);
+  }
 }
 
 /// Preconditioner function
 int LaplacePetsc::precon(Vec x, Vec y) {
-  // Get field to be preconditioned
-  FieldPerp xfield;
-  vecToField(x, xfield);
-  xfield.setIndex(sol.getIndex()); // y index stored in sol variable
+  FieldPerp xfield(indexer->getMesh(), location, sol.getIndex());
+  xfield = 0.0;
+
+  BOUT_FOR_SERIAL(i, indexer->getRegionAll()) {
+    const auto ind = indexer->getGlobal(i);
+    PetscScalar val = BoutNaN;
+    VecGetValues(x, 1, &ind, &val);
+    xfield[i] = val;
+  }
 
   // Call the preconditioner solver
   FieldPerp yfield = pcsolve->solve(xfield);
 
-  // Put result into y
-  fieldToVec(yfield, y);
+  VecCopy(*PetscVector{yfield, indexer}.get(), y);
+
   return 0;
 }
 
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.hxx b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
index 611bfd6fa1..977602dbcc 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.hxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
@@ -41,11 +41,15 @@ RegisterUnavailableLaplace registerlaplacepetsc(LAPLACE_PETSC,
 
 #else
 
+#include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/globalindexer.hxx>
 #include <bout/globals.hxx>
 #include <bout/options.hxx>
 #include <bout/output.hxx>
+#include <bout/petsc_interface.hxx>
 #include <bout/petsclib.hxx>
+#include <bout/region.hxx>
 
 #include <petscksp.h>
 
@@ -59,12 +63,7 @@ class LaplacePetsc : public Laplacian {
 public:
   LaplacePetsc(Options* opt = nullptr, const CELL_LOC loc = CELL_CENTRE,
                Mesh* mesh_in = nullptr, Solver* solver = nullptr);
-  ~LaplacePetsc() {
-    KSPDestroy(&ksp);
-    VecDestroy(&xs);
-    VecDestroy(&bs);
-    MatDestroy(&MatA);
-  }
+  ~LaplacePetsc() override;
 
   using Laplacian::setCoefA;
   using Laplacian::setCoefC;
@@ -199,9 +198,21 @@ public:
   int precon(Vec x, Vec y); ///< Preconditioner function
 
 private:
-  void Element(int i, int x, int z, int xshift, int zshift, PetscScalar ele, Mat& MatA);
-  void Coeffs(int x, int y, int z, BoutReal& A1, BoutReal& A2, BoutReal& A3, BoutReal& A4,
-              BoutReal& A5);
+  struct CoeffsA {
+    BoutReal A1;
+    BoutReal A2;
+    BoutReal A3;
+    BoutReal A4;
+    BoutReal A5;
+  };
+
+  /// Calculate the coefficients ``A1-5``
+  CoeffsA Coeffs(Ind3D i);
+
+  /// Set `operator2D` for the second order scheme
+  void setSecondOrderMatrix(int y, bool inner_X_neumann, bool outer_X_neumann);
+  /// Set `operator2D` for the fourth order scheme
+  void setFourthOrderMatrix(int y, bool inner_X_neumann, bool outer_X_neumann);
 
   /* Ex and Ez
    * Additional 1st derivative terms to allow for solution field to be
@@ -220,17 +231,9 @@ private:
 
   FieldPerp sol; // solution Field
 
-  /// Istart is the first row of MatA owned by the process, Iend is 1 greater than the last row.
-  int Istart = -1;
-  int Iend = -1;
-
-  /// Mesh sizes, total size, no of points on this processor
-  int meshx, meshz, size, localN;
   MPI_Comm comm;
-  Mat MatA = nullptr; ///< Stencil matrix
-  Vec xs = nullptr;   ///< Solution vector
-  Vec bs = nullptr;   ///< RHS vector
-  KSP ksp = nullptr;  ///< PETSc solver
+  KSP ksp = nullptr; ///< PETSc solver
+  bool ksp_initialised = false;
 
   Options* opts;       ///< Laplace Section Options Object
   std::string ksptype; ///< KSP solver type
@@ -248,14 +251,13 @@ private:
   bool direct; //Use direct LU solver if true.
   bool fourth_order;
 
+  IndexerPtr<FieldPerp> indexer;
+  PetscMatrix<FieldPerp> operator2D;
   PetscLib lib;
 
   bool rightprec;                     // Right preconditioning
   std::unique_ptr<Laplacian> pcsolve; // Laplacian solver for preconditioning
 
-  void vecToField(Vec x, FieldPerp& f);       // Copy a vector into a fieldperp
-  void fieldToVec(const FieldPerp& f, Vec x); // Copy a fieldperp into a vector
-
   static constexpr int implemented_flags = INVERT_START_NEW;
   static constexpr int implemented_boundary_flags =
       INVERT_AC_GRAD | INVERT_SET | INVERT_RHS;
diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
index d4f375e1d7..60240b39d7 100644
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
@@ -37,6 +37,7 @@
 #include "bout/options.hxx"
 #include "bout/options_io.hxx"
 #include "bout/output.hxx"
+#include "bout/petsclib.hxx"
 #include "bout/traits.hxx"
 #include "bout/vecops.hxx"
 
@@ -172,6 +173,10 @@ Field3D generate_a5(Mesh& mesh) {
 int main(int argc, char** argv) {
 
   BoutInitialise(argc, argv);
+
+  // Need this here to ensure PETSc isn't finalised until after the global mesh,
+  // otherwise we get problems from `MPI_Comm_free` on the X communicator
+  PetscLib lib{};
   {
     // Not be used for 3D metrics
     Options::root()["laplace"].setConditionallyUsed();
@@ -210,25 +215,6 @@ int main(int argc, char** argv) {
     // Solving equations of the form d*Delp2(f) + 1/c*Grad_perp(c).Grad_perp(f) + a*f = b for various f, a, c, d
     using bout::globals::mesh;
 
-    Field3D loop_x;
-    Field3D loop_z;
-    loop_x.allocate();
-    loop_z.allocate();
-    for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
-      const BoutReal x = mesh->GlobalX(jx);
-      for (int jy = 0; jy < mesh->LocalNy; jy++) {
-        for (int jz = mesh->zstart; jz <= mesh->zend; jz++) {
-          const BoutReal z = mesh->GlobalZ(jz);
-          loop_x(jx, jy, jz) = x;
-          loop_z(jx, jy, jz) = z;
-        }
-      }
-    }
-    dump["loop_x"] = loop_x;
-    dump["loop_z"] = loop_z;
-    dump["exp_x"] = FieldFactory::get()->create3D("x");
-    dump["exp_z"] = FieldFactory::get()->create3D("z");
-
     // Only Neumann x-boundary conditions are implemented so far, so test functions should be Neumann in x and periodic in z.
     // Use Field3D's, but solver only works on FieldPerp slices, so only use 1 y-point
 

From 7c0be3cd214948be0bc9c517157d7be9c4c12bf7 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 2 Mar 2026 10:15:50 +0000
Subject: [PATCH 0751/1827] Remove `TRACE` macro from `PetscMatrix`

The string formatting done in a hot loop ends up being _very_ expensive, 10x slowdown
---
 include/bout/petsc_interface.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 5edd42a441..25f8fb4b97 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -394,7 +394,6 @@ public:
 
   private:
     void setValues(BoutReal val, InsertMode mode) {
-      TRACE("PetscMatrix setting values at ({}, {})", petscRow, petscCol);
       ASSERT3(positions.size() > 0);
       std::vector<PetscScalar> values;
       std::transform(weights.begin(), weights.end(), std::back_inserter(values),
@@ -405,7 +404,8 @@ public:
       status = MatSetValues(*petscMatrix, 1, &petscRow, positions.size(),
                             positions.data(), values.data(), mode);
       if (status != 0) {
-        throw BoutException("Error when setting elements of a PETSc matrix.");
+        throw BoutException("Error when setting elements of a PETSc matrix at ({}, {})",
+                            petscRow, petscCol);
       }
     }
     Mat* petscMatrix;

From 0f0723b1101750398003a706e5f7296b0486aa0b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 2 Mar 2026 10:16:37 +0000
Subject: [PATCH 0752/1827] Include all headers in petsc interface

---
 include/bout/petsc_interface.hxx | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 25f8fb4b97..5239039f0c 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -40,18 +40,27 @@
 #include <type_traits>
 #include <vector>
 
+#include <bout/array.hxx>
+#include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
+#include <bout/boutexception.hxx>
 #include <bout/globalindexer.hxx>
 #include <bout/mesh.hxx>
+#include <bout/openmpwrap.hxx>
 #include <bout/operatorstencil.hxx>
 #include <bout/paralleltransform.hxx>
 #include <bout/petsclib.hxx>
 #include <bout/region.hxx>
 #include <bout/traits.hxx>
 
+#include <petscmat.h>
+#include <petscsys.h>
 #include <petscsystypes.h>
 #include <petscvec.h>
+#include <petscversion.h>
+
+#include <utility>
 
 /*!
  * A class which wraps PETSc vector objects, allowing them to be

From 48a1e03ec25f74c192a6bfd6255542e6f23bee22 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 2 Mar 2026 11:31:18 +0000
Subject: [PATCH 0753/1827] Use preconditioner for petsc MAST grids test

---
 tests/integrated/test-petsc_laplace_MAST-grid/data/BOUT.inp   | 2 ++
 .../test_petsc_laplace_MAST_grid.cxx                          | 4 ++++
 2 files changed, 6 insertions(+)

diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/data/BOUT.inp b/tests/integrated/test-petsc_laplace_MAST-grid/data/BOUT.inp
index a63e7e876c..4bd3c40bd8 100644
--- a/tests/integrated/test-petsc_laplace_MAST-grid/data/BOUT.inp
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/data/BOUT.inp
@@ -23,6 +23,7 @@ nonuniform = true
 rtol = 1e-10
 include_yguards = false
 maxits = 1000
+pctype = sor
 
 [petsc4th]
 type = petsc
@@ -31,6 +32,7 @@ nonuniform = true
 rtol = 1e-10
 include_yguards = false
 maxits = 1000
+pctype = sor
 fourth_order = true
 gmres_max_steps = 32
 
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx
index 945d5c6443..3f9bb172e2 100644
--- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.cxx
@@ -23,6 +23,7 @@
  *
  **************************************************************************/
 
+#include "bout/petsclib.hxx"
 #include <bout/bout.hxx>
 #include <bout/constants.hxx>
 // #include <bout/sys/timer.hxx>
@@ -36,6 +37,9 @@ BoutReal max_error_at_ystart(const Field3D& error);
 int main(int argc, char** argv) {
 
   BoutInitialise(argc, argv);
+
+  PetscLib lib{};
+
   {
     Options* options = Options::getRoot()->getSection("petsc2nd");
     auto invert = Laplacian::create(options);

From e02167d29ccabf041bc80a7eaaae84ee133aa569 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 15:43:21 +0000
Subject: [PATCH 0754/1827] Remove `todo` comment

---
 src/invert/laplace/impls/petsc/petsc_laplace.cxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index da964d443d..132b3c3137 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -73,7 +73,6 @@ PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) {
   PetscFunctionReturn(laplace->precon(x, y)); // NOLINT
 }
 
-// TODO: handle fourth order
 auto set_stencil(const Mesh& localmesh, bool fourth_order) {
   OperatorStencil<IndPerp> stencil;
   IndexOffset<IndPerp> zero;

From 2dcebb8c11891e52b4a8e875f4524267fc874aa4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 15:43:35 +0000
Subject: [PATCH 0755/1827] Fix missing headers

---
 src/invert/laplace/impls/petsc/petsc_laplace.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 132b3c3137..69ed686321 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -47,6 +47,7 @@
 #include <bout/utils.hxx>
 
 #include <cmath>
+#include <memory>
 #include <set>
 #include <vector>
 
@@ -143,7 +144,7 @@ auto set_stencil(const Mesh& localmesh, bool fourth_order) {
     }
   }
 
-  stencil.add([](IndPerp UNUSED(ind)) -> bool { return true; }, {zero});
+  stencil.add([]([[maybe_unused]] IndPerp ind) -> bool { return true; }, {zero});
   return stencil;
 }
 } // namespace

From e1e1f6b4134e07527f0a9f47695d84fda2e9cfb0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 9 Mar 2026 16:37:52 +0000
Subject: [PATCH 0756/1827] Apply clang-tidy fixes

---
 .../laplace/impls/petsc/petsc_laplace.cxx     | 40 +++++++++----------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 69ed686321..a3b81f27ff 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -99,7 +99,7 @@ auto set_stencil(const Mesh& localmesh, bool fourth_order) {
     });
   }
 
-  std::vector offsetsVec(offsets.begin(), offsets.end());
+  const std::vector offsetsVec(offsets.begin(), offsets.end());
   stencil.add(
       [&localmesh](IndPerp ind) -> bool {
         return (localmesh.xstart <= ind.x() && ind.x() <= localmesh.xend
@@ -249,7 +249,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
 
   const int y = b.getIndex(); // Get the Y index
   {
-    Timer timer("petscsetup");
+    const Timer timer("petscsetup");
 
     const bool inner_X_neumann = isInnerBoundaryFlagSet(INVERT_AC_GRAD);
     const bool outer_X_neumann = isOuterBoundaryFlagSet(INVERT_AC_GRAD);
@@ -276,7 +276,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
 #else
     KSPSetOperators(ksp, *operator2D.get(), *operator2D.get(), DIFFERENT_NONZERO_PATTERN);
 #endif
-    PC pc; // The preconditioner option
+    PC pc = nullptr; // The preconditioner option
 
     if (direct) { // If a direct solver has been chosen
       // Get the preconditioner
@@ -355,11 +355,11 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
 
   // Call the actual solver
   {
-    Timer timer("petscsolve");
+    const Timer timer("petscsolve");
     KSPSolve(ksp, *rhs.get(), *guess.get());
   }
 
-  KSPConvergedReason reason;
+  KSPConvergedReason reason = KSP_CONVERGED_ITERATING;
   KSPGetConvergedReason(ksp, &reason);
   if (reason == -3) { // Too many iterations, might be fixed by taking smaller timestep
     throw BoutIterationFail("petsc_laplace: too many iterations");
@@ -454,15 +454,15 @@ LaplacePetsc::CoeffsA LaplacePetsc::Coeffs(Ind3D i) {
   // A second/fourth order derivative term
   if (issetC) {
     if ((x > 1) && (x < (localmesh->LocalNx - 2))) {
-      BoutReal ddx_C;
-      BoutReal ddz_C;
+      BoutReal ddx_C = BoutNaN;
+      BoutReal ddz_C = BoutNaN;
 
       if (fourth_order) {
         // Fourth order discretization of C in x
-        ddx_C = (-C2[i.xpp()] + 8. * C2[i.xp()] - 8. * C2[i.xm()] + C2[i.xmm()])
+        ddx_C = (-C2[i.xpp()] + (8. * C2[i.xp()]) - (8. * C2[i.xm()]) + C2[i.xmm()])
                 / (12. * coords->dx[i] * (C1[i]));
         // Fourth order discretization of C in z
-        ddz_C = (-C2[i.zpp()] + 8. * C2[i.zp()] - 8. * C2[i.zm()] + C2[i.zmm()])
+        ddz_C = (-C2[i.zpp()] + (8. * C2[i.zp()]) - (8. * C2[i.zm()]) + C2[i.zmm()])
                 / (12. * coords->dz[i] * (C1[i]));
       } else {
         // Second order discretization of C in x
@@ -545,11 +545,11 @@ void LaplacePetsc::setSecondOrderMatrix(int y, bool inner_X_neumann,
     ASSERT3(std::isfinite(A4));
     ASSERT3(std::isfinite(A5));
 
-    BoutReal dx = coords->dx[i];
-    BoutReal dx2 = SQ(dx);
-    BoutReal dz = coords->dz[i];
-    BoutReal dz2 = SQ(dz);
-    BoutReal dxdz = dx * dz;
+    const BoutReal dx = coords->dx[i];
+    const BoutReal dx2 = SQ(dx);
+    const BoutReal dz = coords->dz[i];
+    const BoutReal dz2 = SQ(dz);
+    const BoutReal dxdz = dx * dz;
     operator2D(l, l) = A0 - (2.0 * ((A1 / dx2) + (A2 / dz2)));
     operator2D(l, l.xm().zm()) = A3 / (4.0 * dxdz);
     operator2D(l, l.xm()) = (A1 / dx2) - (A4 / (2.0 * dx));
@@ -628,11 +628,11 @@ void LaplacePetsc::setFourthOrderMatrix(int y, bool inner_X_neumann,
     ASSERT3(std::isfinite(A4));
     ASSERT3(std::isfinite(A5));
 
-    BoutReal dx = coords->dx[i];
-    BoutReal dx2 = SQ(dx);
-    BoutReal dz = coords->dz[i];
-    BoutReal dz2 = SQ(dz);
-    BoutReal dxdz = dx * dz;
+    const BoutReal dx = coords->dx[i];
+    const BoutReal dx2 = SQ(dx);
+    const BoutReal dz = coords->dz[i];
+    const BoutReal dz2 = SQ(dz);
+    const BoutReal dxdz = dx * dz;
 
     operator2D(l, l) = A0 - ((5.0 / 2.0) * ((A1 / dx2) + (A2 / dz2)));
     operator2D(l, l.xmm().zmm()) = A3 / (144.0 * dxdz);
@@ -675,7 +675,7 @@ int LaplacePetsc::precon(Vec x, Vec y) {
   }
 
   // Call the preconditioner solver
-  FieldPerp yfield = pcsolve->solve(xfield);
+  const FieldPerp yfield = pcsolve->solve(xfield);
 
   VecCopy(*PetscVector{yfield, indexer}.get(), y);
 

From abbbec7635c35d682bd241d5a973f55c2b9c2ae0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 11 Mar 2026 11:08:43 +0000
Subject: [PATCH 0757/1827] Remove some unused defines

---
 src/invert/laplace/impls/petsc/petsc_laplace.cxx | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index a3b81f27ff..71a3e4433b 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -51,19 +51,6 @@
 #include <set>
 #include <vector>
 
-#define KSP_RICHARDSON "richardson"
-#define KSP_CHEBYSHEV "chebyshev"
-#define KSP_CG "cg"
-#define KSP_GMRES "gmres"
-#define KSP_TCQMR "tcqmr"
-#define KSP_BCGS "bcgs"
-#define KSP_CGS "cgs"
-#define KSP_TFQMR "tfqmr"
-#define KSP_CR "cr"
-#define KSP_LSQR "lsqr"
-#define KSP_BICG "bicg"
-#define KSP_PREONLY "preonly"
-
 namespace {
 PetscErrorCode laplacePCapply(PC pc, Vec x, Vec y) {
   PetscFunctionBegin; // NOLINT

From 9b778bee9a3dcabb15891595b367f6e7a53135d9 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 11 Mar 2026 11:33:57 +0000
Subject: [PATCH 0758/1827] Always use `sor` preconditioner in PETSc Laplace
 test for 3D metrics

For some reason, `PETSC_HAVE_MUMPS` doesn't seem to always be enough to detect
if PETSc actually has the mump preconditioner
---
 .../test-petsc_laplace/test_petsc_laplace.cxx        | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
index 60240b39d7..39b1918480 100644
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
@@ -182,16 +182,8 @@ int main(int argc, char** argv) {
     Options::root()["laplace"].setConditionallyUsed();
 
     // For 3D metrics, we need to use one of PETSc's preconditioners
-    // and mumps seems to be the best? Or at least HYPRE doesn't work
-    // on this test with more than one processor.
-#ifdef PETSC_HAVE_MUMPS
-    constexpr auto petsc_has_mumps = true;
-#else
-    constexpr auto petsc_has_mumps = false;
-#endif
-
-    // Preconditioner to use for 3D metrics
-    constexpr auto petsc_pc = petsc_has_mumps ? "mumps" : "sor";
+    // and `sor` seems to always be available
+    constexpr auto petsc_pc = "sor";
 
     auto& options_2nd = Options::root()["petsc2nd"];
     if constexpr (bout::build::use_metric_3d) {

From 74b00f8ffa652a3905d7f4eed954e0515386ff4d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 11 Mar 2026 16:02:58 +0000
Subject: [PATCH 0759/1827] docs: Expand description of developer tools

---
 manual/sphinx/developer_docs/contributing.rst | 111 ++++++++++++------
 1 file changed, 72 insertions(+), 39 deletions(-)

diff --git a/manual/sphinx/developer_docs/contributing.rst b/manual/sphinx/developer_docs/contributing.rst
index a7aca902d4..4ef9892bff 100644
--- a/manual/sphinx/developer_docs/contributing.rst
+++ b/manual/sphinx/developer_docs/contributing.rst
@@ -142,45 +142,6 @@ then they will be able to checkout your branch::
 *Note*: If you have write access to the central BOUT-dev repository, you
 can push your branches there.
 
-Running Tests
-~~~~~~~~~~~~~
-
-We run many tests and checks automatically on GitHub for a variety of build
-configurations. See :ref:`sec-runtestsuite` for how to run them
-locally. Running the full test suite can take some time, but it's a good idea to
-run at least the unit tests locally when you're making changes.
-
-Install Pre-Commit Hooks (Optional but recommended)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Along with the automated tests, we also run things like formatters and static
-analysis. For frequent developers, we strongly recommend installing them locally
-and building them into your regular workflow. You can install the majority of
-our developer tools at once using `uv <https://docs.astral.sh/uv/>`_:
-
-.. code-block:: console
-
-    uv sync --only-dev
-
-This will create a new virtual environment (typically under ``.venv``) and
-install all the tools into that. You can then activate the virtual environment
-and use the tools manually, or via integrations in your editor.
-
-We also have a `prek <https://prek.j178.dev>`_ config that can run some of
-these automatically when you make commits using "pre-commit hooks". Install our
-developer tools with ``uv`` as above, and then install the pre-commit hook:
-
-.. code-block:: console
-
-    prek install
-
-This will then automatically call things like `clang-format
-<https://clang.llvm.org/docs/ClangFormat.html>`_ and `ruff
-<https://astral.sh/ruff>`_ when you create a commit, and abort the commit if
-there's a problem, for example if a formatter changes any files. For the
-formatters, this usually just means staging any changes they make and trying
-again.
-
 Making changes, commits
 ~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -212,6 +173,78 @@ give you comments to improve the code. You can make additional changes
 and push them to the same feature branch and they will be automatically
 added to the pull request.
 
+Running Tests
+~~~~~~~~~~~~~
+
+We run many tests and checks automatically on GitHub (collectively called "CI")
+for a variety of build configurations. See :ref:`sec-runtestsuite` for how to
+run them locally. Running the full test suite can take some time, but it's a
+good idea to run at least the unit tests locally when you're making changes:
+
+.. code-block:: console
+
+    cmake --build build --target check-unit-tests
+
+Along with the automated tests, we also run things like formatters and static
+analysis in CI, which may provide further feedback (see :ref:`sec-coding-style`
+for more details). If your PR fails the format check on CI, please install the
+formatters and run them according to the next section. Usually this is just:
+
+.. code-block:: console
+
+    git clang-format next
+
+which will format just the parts of C++ files that have changed since ``next``.
+
+Formatting and Linters
+~~~~~~~~~~~~~~~~~~~~~~
+
+For frequent developers, we strongly recommend installing the formatting and
+linting tools locally and building them into your regular workflow. You can
+install the majority of our developer tools at once using `uv
+<https://docs.astral.sh/uv/>`_ from the top of your BOUT++ directory:
+
+.. code-block:: console
+
+    uv sync --only-dev --inexact
+
+This will install all the developer tools into a virtual environment (creating
+one if necessary, typically under ``.venv``). You can then activate the virtual
+environment and use the tools manually, or via integrations in your editor.
+
+We *strongly* recommend using ``uv`` to install the developer tools, as this
+will ensure that you get the *exact* versions used in CI and by other
+developers, but you could also use ``pip install --group dev`` if you wish.
+
+The quickest way to run all the formatters on a PR at once is typically:
+
+.. code-block:: console
+
+    uv tool run prek run --from-ref next
+
+This will run all our formatters on files that have changed since ``next``.
+
+Install Pre-Commit Hooks (Optional but recommended)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+We also have a `prek <https://prek.j178.dev>`_ config that can run some of
+these automatically using pre-commit hooks -- that is, when you run ``git
+commit``, these tools will run and abort the commit if they change any
+files. You then just have to stage the new changes and try again.
+
+Install our developer tools with ``uv`` as above, and then install the
+pre-commit hook:
+
+.. code-block:: console
+
+    prek install
+
+That's it! ``prek`` will install the tools into their own separate virtual
+environment so they won't interfere with any you may have, and ``git`` will take
+care of running them automatically.
+
+.. _sec-coding-style:
+
 Coding Style
 ------------
 

From c37f6988f6c5c599968d736fac98f19b8c88ea09 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 11 Mar 2026 16:04:17 +0000
Subject: [PATCH 0760/1827] CI: Use annotations instead of comments for
 `clang-tidy-review`

---
 .github/workflows/clang-tidy-review.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 087c910987..7c245a7a3c 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -24,6 +24,7 @@ jobs:
         uses: ZedThree/clang-tidy-review@v0.23.0
         id: review
         with:
+          annotations: true
           build_dir: build
           apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev,uuid-dev"
           config_file: ".clang-tidy"

From b74b9170b4d64de6f1010ae4c4a3997f5a1c8380 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 11 Mar 2026 16:52:25 +0000
Subject: [PATCH 0761/1827] Fix setting yindex for shell preconditioner

---
 src/invert/laplace/impls/petsc/petsc_laplace.cxx | 12 +++++++-----
 src/invert/laplace/impls/petsc/petsc_laplace.hxx |  3 ++-
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 71a3e4433b..e1595a2817 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -234,7 +234,9 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
   checkFlags();
 #endif
 
-  const int y = b.getIndex(); // Get the Y index
+  // Set member variable so that we can pass through to shell preconditioner if
+  // required
+  yindex = b.getIndex();
   {
     const Timer timer("petscsetup");
 
@@ -243,9 +245,9 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
 
     // Set the operator matrix
     if (fourth_order) {
-      setFourthOrderMatrix(y, inner_X_neumann, outer_X_neumann);
+      setFourthOrderMatrix(yindex, inner_X_neumann, outer_X_neumann);
     } else {
-      setSecondOrderMatrix(y, inner_X_neumann, outer_X_neumann);
+      setSecondOrderMatrix(yindex, inner_X_neumann, outer_X_neumann);
     }
 
     operator2D.assemble();
@@ -358,7 +360,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
   }
 
   auto sol = guess.toField();
-  sol.setIndex(y);
+  sol.setIndex(yindex);
   checkData(sol);
 
   // Return the solution
@@ -651,7 +653,7 @@ void LaplacePetsc::setFourthOrderMatrix(int y, bool inner_X_neumann,
 
 /// Preconditioner function
 int LaplacePetsc::precon(Vec x, Vec y) {
-  FieldPerp xfield(indexer->getMesh(), location, sol.getIndex());
+  FieldPerp xfield(indexer->getMesh(), location, yindex);
   xfield = 0.0;
 
   BOUT_FOR_SERIAL(i, indexer->getRegionAll()) {
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.hxx b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
index 977602dbcc..abef05c0ae 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.hxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
@@ -229,7 +229,8 @@ private:
   bool issetC;
   bool issetE;
 
-  FieldPerp sol; // solution Field
+  /// Y-index of solution field.
+  int yindex = -1;
 
   MPI_Comm comm;
   KSP ksp = nullptr; ///< PETSc solver

From d8a1b6661aca197f3996c9116b92cc01847b5a1e Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 17:46:12 +0000
Subject: [PATCH 0762/1827] Add basic custom formatter for fields

---
 include/bout/output_bout_types.hxx        |  64 ++++++++-
 tests/unit/CMakeLists.txt                 |   1 +
 tests/unit/sys/test_output_bout_types.cxx | 151 ++++++++++++++++++++++
 3 files changed, 214 insertions(+), 2 deletions(-)
 create mode 100644 tests/unit/sys/test_output_bout_types.cxx

diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx
index b67762521b..43d1b4adfa 100644
--- a/include/bout/output_bout_types.hxx
+++ b/include/bout/output_bout_types.hxx
@@ -5,9 +5,13 @@
 #ifndef OUTPUT_BOUT_TYPES_H
 #define OUTPUT_BOUT_TYPES_H
 
+#include "fmt/base.h"
 #include <fmt/format.h>
 
-#include "bout/output.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/field2d.hxx"
+#include "bout/mesh.hxx"
+#include "bout/output.hxx" // IWYU pragma: keep
 #include "bout/region.hxx"
 
 template <IND_TYPE N>
@@ -17,7 +21,8 @@ struct fmt::formatter<SpecificInd<N>> {
 
   // Parses format specifications of the form ['c' | 'i'].
   constexpr auto parse(format_parse_context& ctx) {
-    auto it = ctx.begin(), end = ctx.end();
+    const auto* it = ctx.begin();
+    const auto* end = ctx.end();
     if (it != end && (*it == 'c' || *it == 'i')) {
       presentation = *it++;
     }
@@ -50,4 +55,59 @@ struct fmt::formatter<SpecificInd<N>> {
   }
 };
 
+class Field2D;
+class Field3D;
+class FieldPerp;
+
+template <>
+struct fmt::formatter<Field2D> : fmt::formatter<BoutReal> {
+  auto format(const Field2D& f, format_context& ctx) const -> format_context::iterator {
+    const auto* mesh = f.getMesh();
+    for (int ix = 0; ix < mesh->LocalNx; ++ix) {
+      for (int jy = 0; jy < mesh->LocalNy; ++jy) {
+        format_to(ctx.out(), "({}, {}): ", ix, jy);
+        formatter<BoutReal>::format(f(ix, jy), ctx);
+        format_to(ctx.out(), (jy < mesh->LocalNy - 1) ? "; " : ";");
+      }
+      format_to(ctx.out(), "\n");
+    }
+    return format_to(ctx.out(), "\n");
+  }
+};
+
+template <>
+struct fmt::formatter<Field3D> : fmt::formatter<BoutReal> {
+  auto format(const Field3D& f, format_context& ctx) const -> format_context::iterator {
+    const auto* mesh = f.getMesh();
+    for (int ix = 0; ix < mesh->LocalNx; ++ix) {
+      for (int jy = 0; jy < mesh->LocalNy; ++jy) {
+        for (int kz = 0; kz < mesh->LocalNz; ++kz) {
+          format_to(ctx.out(), "({}, {}, {}): ", ix, jy, kz);
+          formatter<BoutReal>::format(f(ix, jy, kz), ctx);
+          format_to(ctx.out(), (kz < mesh->LocalNz - 1) ? "; " : ";");
+        }
+        format_to(ctx.out(), "\n");
+      }
+      format_to(ctx.out(), "\n");
+    }
+    return format_to(ctx.out(), "\n");
+  }
+};
+
+template <>
+struct fmt::formatter<FieldPerp> : fmt::formatter<BoutReal> {
+  auto format(const FieldPerp& f, format_context& ctx) const -> format_context::iterator {
+    const auto* mesh = f.getMesh();
+    for (int ix = 0; ix < mesh->LocalNx; ++ix) {
+      for (int kz = 0; kz < mesh->LocalNz; ++kz) {
+        format_to(ctx.out(), "({}, {}): ", ix, kz);
+        formatter<BoutReal>::format(f(ix, kz), ctx);
+        format_to(ctx.out(), (kz < mesh->LocalNz - 1) ? "; " : ";");
+      }
+      format_to(ctx.out(), "\n");
+    }
+    return format_to(ctx.out(), "\n");
+  }
+};
+
 #endif // OUTPUT_BOUT_TYPES_H
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 7cf0bb0af7..b347de7354 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -121,6 +121,7 @@ set(serial_tests_source
     ./fake_mesh.hxx
     ./fake_mesh_fixture.hxx
     ./src/test_bout++.cxx
+    ./sys/test_output_bout_types.cxx
 )
 
 if(BOUT_HAS_HYPRE)
diff --git a/tests/unit/sys/test_output_bout_types.cxx b/tests/unit/sys/test_output_bout_types.cxx
new file mode 100644
index 0000000000..b3a7493803
--- /dev/null
+++ b/tests/unit/sys/test_output_bout_types.cxx
@@ -0,0 +1,151 @@
+#include "fake_mesh_fixture.hxx"
+#include "test_extras.hxx"
+#include "gtest/gtest.h"
+
+#include "bout/field2d.hxx"
+#include "bout/globals.hxx"
+#include "bout/output_bout_types.hxx"
+
+#include <string>
+
+#include <fmt/format.h>
+
+using FormatFieldTest = FakeMeshFixture_tmpl<3, 5, 2>;
+
+TEST_F(FormatFieldTest, Field2D) {
+  Field2D f{bout::globals::mesh};
+
+  fillField(f, {{0., 1., 2., 3., 4.}, {5., 6., 7., 8., 9.}, {10., 11., 12., 13., 14.}});
+
+  const auto out = fmt::format("{}", f);
+
+  const std::string expected =
+      R"((0, 0): 0; (0, 1): 1; (0, 2): 2; (0, 3): 3; (0, 4): 4;
+(1, 0): 5; (1, 1): 6; (1, 2): 7; (1, 3): 8; (1, 4): 9;
+(2, 0): 10; (2, 1): 11; (2, 2): 12; (2, 3): 13; (2, 4): 14;
+
+)";
+  EXPECT_EQ(out, expected);
+}
+
+TEST_F(FormatFieldTest, Field2DSpec) {
+  Field2D f{bout::globals::mesh};
+
+  fillField(f, {{0., 1., 2., 3., 4.}, {5., 6., 7., 8., 9.}, {10., 11., 12., 13., 14.}});
+
+  const auto out = fmt::format("{:3.1e}", f);
+
+  const std::string expected =
+      R"((0, 0): 0.0e+00; (0, 1): 1.0e+00; (0, 2): 2.0e+00; (0, 3): 3.0e+00; (0, 4): 4.0e+00;
+(1, 0): 5.0e+00; (1, 1): 6.0e+00; (1, 2): 7.0e+00; (1, 3): 8.0e+00; (1, 4): 9.0e+00;
+(2, 0): 1.0e+01; (2, 1): 1.1e+01; (2, 2): 1.2e+01; (2, 3): 1.3e+01; (2, 4): 1.4e+01;
+
+)";
+  EXPECT_EQ(out, expected);
+}
+
+TEST_F(FormatFieldTest, Field3D) {
+  Field3D f{bout::globals::mesh};
+
+  fillField(f, {{{0., 1}, {2., 3}, {4., 5}, {6., 7}, {8., 9}},
+                {{10., 11}, {12., 13}, {14., 15}, {16., 17}, {18., 19}},
+                {{20., 21}, {22., 23}, {24., 25}, {26., 27}, {28., 29}}});
+
+  const auto out = fmt::format("{}", f);
+
+  const std::string expected =
+      R"((0, 0, 0): 0; (0, 0, 1): 1;
+(0, 1, 0): 2; (0, 1, 1): 3;
+(0, 2, 0): 4; (0, 2, 1): 5;
+(0, 3, 0): 6; (0, 3, 1): 7;
+(0, 4, 0): 8; (0, 4, 1): 9;
+
+(1, 0, 0): 10; (1, 0, 1): 11;
+(1, 1, 0): 12; (1, 1, 1): 13;
+(1, 2, 0): 14; (1, 2, 1): 15;
+(1, 3, 0): 16; (1, 3, 1): 17;
+(1, 4, 0): 18; (1, 4, 1): 19;
+
+(2, 0, 0): 20; (2, 0, 1): 21;
+(2, 1, 0): 22; (2, 1, 1): 23;
+(2, 2, 0): 24; (2, 2, 1): 25;
+(2, 3, 0): 26; (2, 3, 1): 27;
+(2, 4, 0): 28; (2, 4, 1): 29;
+
+
+)";
+  EXPECT_EQ(out, expected);
+}
+
+TEST_F(FormatFieldTest, Field3DSpec) {
+  Field3D f{bout::globals::mesh};
+
+  fillField(f, {{{0., 1}, {2., 3}, {4., 5}, {6., 7}, {8., 9}},
+                {{10., 11}, {12., 13}, {14., 15}, {16., 17}, {18., 19}},
+                {{20., 21}, {22., 23}, {24., 25}, {26., 27}, {28., 29}}});
+
+  const auto out = fmt::format("{:3.1e}", f);
+
+  const std::string expected =
+      R"((0, 0, 0): 0.0e+00; (0, 0, 1): 1.0e+00;
+(0, 1, 0): 2.0e+00; (0, 1, 1): 3.0e+00;
+(0, 2, 0): 4.0e+00; (0, 2, 1): 5.0e+00;
+(0, 3, 0): 6.0e+00; (0, 3, 1): 7.0e+00;
+(0, 4, 0): 8.0e+00; (0, 4, 1): 9.0e+00;
+
+(1, 0, 0): 1.0e+01; (1, 0, 1): 1.1e+01;
+(1, 1, 0): 1.2e+01; (1, 1, 1): 1.3e+01;
+(1, 2, 0): 1.4e+01; (1, 2, 1): 1.5e+01;
+(1, 3, 0): 1.6e+01; (1, 3, 1): 1.7e+01;
+(1, 4, 0): 1.8e+01; (1, 4, 1): 1.9e+01;
+
+(2, 0, 0): 2.0e+01; (2, 0, 1): 2.1e+01;
+(2, 1, 0): 2.2e+01; (2, 1, 1): 2.3e+01;
+(2, 2, 0): 2.4e+01; (2, 2, 1): 2.5e+01;
+(2, 3, 0): 2.6e+01; (2, 3, 1): 2.7e+01;
+(2, 4, 0): 2.8e+01; (2, 4, 1): 2.9e+01;
+
+
+)";
+  EXPECT_EQ(out, expected);
+}
+
+TEST_F(FormatFieldTest, FieldPerp) {
+  Field3D f{bout::globals::mesh};
+
+  fillField(f, {{{0., 1}, {2., 3}, {4., 5}, {6., 7}, {8., 9}},
+                {{10., 11}, {12., 13}, {14., 15}, {16., 17}, {18., 19}},
+                {{20., 21}, {22., 23}, {24., 25}, {26., 27}, {28., 29}}});
+
+  FieldPerp g = sliceXZ(f, 0);
+
+  const auto out = fmt::format("{}", g);
+
+  const std::string expected =
+      R"((0, 0): 0; (0, 1): 1;
+(1, 0): 10; (1, 1): 11;
+(2, 0): 20; (2, 1): 21;
+
+)";
+  EXPECT_EQ(out, expected);
+}
+
+TEST_F(FormatFieldTest, FieldPerpSpec) {
+  Field3D f{bout::globals::mesh};
+
+  fillField(f, {{{0., 1}, {2., 3}, {4., 5}, {6., 7}, {8., 9}},
+                {{10., 11}, {12., 13}, {14., 15}, {16., 17}, {18., 19}},
+                {{20., 21}, {22., 23}, {24., 25}, {26., 27}, {28., 29}}});
+
+  FieldPerp g = sliceXZ(f, 0);
+
+  const auto out = fmt::format("{:3.1e}", g);
+
+  const std::string expected =
+      R"((0, 0): 0.0e+00; (0, 1): 1.0e+00;
+(1, 0): 1.0e+01; (1, 1): 1.1e+01;
+(2, 0): 2.0e+01; (2, 1): 2.1e+01;
+
+)";
+  EXPECT_EQ(out, expected);
+}

From 459724c1712ead503e83dff52e95e37c593b6b88 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 21:08:22 +0000
Subject: [PATCH 0763/1827] Consolidate Field formatters into one
 implementation

---
 include/bout/output_bout_types.hxx        | 82 +++++++++--------------
 tests/unit/sys/test_output_bout_types.cxx | 66 +++++++++++-------
 2 files changed, 75 insertions(+), 73 deletions(-)

diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx
index 43d1b4adfa..171188664c 100644
--- a/include/bout/output_bout_types.hxx
+++ b/include/bout/output_bout_types.hxx
@@ -5,14 +5,16 @@
 #ifndef OUTPUT_BOUT_TYPES_H
 #define OUTPUT_BOUT_TYPES_H
 
-#include "fmt/base.h"
-#include <fmt/format.h>
-
 #include "bout/bout_types.hxx"
-#include "bout/field2d.hxx"
 #include "bout/mesh.hxx"
 #include "bout/output.hxx" // IWYU pragma: keep
 #include "bout/region.hxx"
+#include "bout/traits.hxx"
+
+#include "fmt/base.h"
+#include <fmt/format.h>
+
+#include <type_traits>
 
 template <IND_TYPE N>
 struct fmt::formatter<SpecificInd<N>> {
@@ -55,58 +57,38 @@ struct fmt::formatter<SpecificInd<N>> {
   }
 };
 
-class Field2D;
-class Field3D;
-class FieldPerp;
-
-template <>
-struct fmt::formatter<Field2D> : fmt::formatter<BoutReal> {
-  auto format(const Field2D& f, format_context& ctx) const -> format_context::iterator {
+/// Formatter for Fields
+template <class T>
+struct fmt::formatter<T, std::enable_if_t<bout::utils::is_Field_v<T>, char>> : fmt::formatter<BoutReal> {
+  auto format(const T& f, format_context& ctx) const -> format_context::iterator {
     const auto* mesh = f.getMesh();
-    for (int ix = 0; ix < mesh->LocalNx; ++ix) {
-      for (int jy = 0; jy < mesh->LocalNy; ++jy) {
-        format_to(ctx.out(), "({}, {}): ", ix, jy);
-        formatter<BoutReal>::format(f(ix, jy), ctx);
-        format_to(ctx.out(), (jy < mesh->LocalNy - 1) ? "; " : ";");
-      }
-      format_to(ctx.out(), "\n");
-    }
-    return format_to(ctx.out(), "\n");
-  }
-};
+    int previous_x = 0;
+    int previous_y = 0;
+    int previous_z = 0;
 
-template <>
-struct fmt::formatter<Field3D> : fmt::formatter<BoutReal> {
-  auto format(const Field3D& f, format_context& ctx) const -> format_context::iterator {
-    const auto* mesh = f.getMesh();
-    for (int ix = 0; ix < mesh->LocalNx; ++ix) {
-      for (int jy = 0; jy < mesh->LocalNy; ++jy) {
-        for (int kz = 0; kz < mesh->LocalNz; ++kz) {
-          format_to(ctx.out(), "({}, {}, {}): ", ix, jy, kz);
-          formatter<BoutReal>::format(f(ix, jy, kz), ctx);
-          format_to(ctx.out(), (kz < mesh->LocalNz - 1) ? "; " : ";");
-        }
+    BOUT_FOR_SERIAL(i, f.getRegion("RGN_ALL")) {
+      const auto ix = i.x();
+      const auto iy = i.y();
+      const auto iz = i.z();
+
+      if (iz > previous_z) {
+        format_to(ctx.out(), " ");
+      }
+      if (iy > previous_y) {
         format_to(ctx.out(), "\n");
       }
-      format_to(ctx.out(), "\n");
-    }
-    return format_to(ctx.out(), "\n");
-  }
-};
-
-template <>
-struct fmt::formatter<FieldPerp> : fmt::formatter<BoutReal> {
-  auto format(const FieldPerp& f, format_context& ctx) const -> format_context::iterator {
-    const auto* mesh = f.getMesh();
-    for (int ix = 0; ix < mesh->LocalNx; ++ix) {
-      for (int kz = 0; kz < mesh->LocalNz; ++kz) {
-        format_to(ctx.out(), "({}, {}): ", ix, kz);
-        formatter<BoutReal>::format(f(ix, kz), ctx);
-        format_to(ctx.out(), (kz < mesh->LocalNz - 1) ? "; " : ";");
+      if (ix > previous_x) {
+        format_to(ctx.out(), "\n\n");
       }
-      format_to(ctx.out(), "\n");
+
+      format_to(ctx.out(), "{:c}: ", i);
+      formatter<BoutReal>::format(f[i], ctx);
+      format_to(ctx.out(), ";");
+      previous_x = ix;
+      previous_y = iy;
+      previous_z = iz;
     }
-    return format_to(ctx.out(), "\n");
+    return format_to(ctx.out(), "");
   }
 };
 
diff --git a/tests/unit/sys/test_output_bout_types.cxx b/tests/unit/sys/test_output_bout_types.cxx
index b3a7493803..82eb1754d0 100644
--- a/tests/unit/sys/test_output_bout_types.cxx
+++ b/tests/unit/sys/test_output_bout_types.cxx
@@ -3,8 +3,10 @@
 #include "gtest/gtest.h"
 
 #include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/fieldperp.hxx"
 #include "bout/globals.hxx"
-#include "bout/output_bout_types.hxx"
+#include "bout/output_bout_types.hxx" // IWYU pragma: keep
 
 #include <string>
 
@@ -20,11 +22,23 @@ TEST_F(FormatFieldTest, Field2D) {
   const auto out = fmt::format("{}", f);
 
   const std::string expected =
-      R"((0, 0): 0; (0, 1): 1; (0, 2): 2; (0, 3): 3; (0, 4): 4;
-(1, 0): 5; (1, 1): 6; (1, 2): 7; (1, 3): 8; (1, 4): 9;
-(2, 0): 10; (2, 1): 11; (2, 2): 12; (2, 3): 13; (2, 4): 14;
-
-)";
+    R"((0, 0): 0;
+(0, 1): 1;
+(0, 2): 2;
+(0, 3): 3;
+(0, 4): 4;
+
+(1, 0): 5;
+(1, 1): 6;
+(1, 2): 7;
+(1, 3): 8;
+(1, 4): 9;
+
+(2, 0): 10;
+(2, 1): 11;
+(2, 2): 12;
+(2, 3): 13;
+(2, 4): 14;)";
   EXPECT_EQ(out, expected);
 }
 
@@ -36,11 +50,23 @@ TEST_F(FormatFieldTest, Field2DSpec) {
   const auto out = fmt::format("{:3.1e}", f);
 
   const std::string expected =
-      R"((0, 0): 0.0e+00; (0, 1): 1.0e+00; (0, 2): 2.0e+00; (0, 3): 3.0e+00; (0, 4): 4.0e+00;
-(1, 0): 5.0e+00; (1, 1): 6.0e+00; (1, 2): 7.0e+00; (1, 3): 8.0e+00; (1, 4): 9.0e+00;
-(2, 0): 1.0e+01; (2, 1): 1.1e+01; (2, 2): 1.2e+01; (2, 3): 1.3e+01; (2, 4): 1.4e+01;
-
-)";
+    R"((0, 0): 0.0e+00;
+(0, 1): 1.0e+00;
+(0, 2): 2.0e+00;
+(0, 3): 3.0e+00;
+(0, 4): 4.0e+00;
+
+(1, 0): 5.0e+00;
+(1, 1): 6.0e+00;
+(1, 2): 7.0e+00;
+(1, 3): 8.0e+00;
+(1, 4): 9.0e+00;
+
+(2, 0): 1.0e+01;
+(2, 1): 1.1e+01;
+(2, 2): 1.2e+01;
+(2, 3): 1.3e+01;
+(2, 4): 1.4e+01;)";
   EXPECT_EQ(out, expected);
 }
 
@@ -70,10 +96,7 @@ TEST_F(FormatFieldTest, Field3D) {
 (2, 1, 0): 22; (2, 1, 1): 23;
 (2, 2, 0): 24; (2, 2, 1): 25;
 (2, 3, 0): 26; (2, 3, 1): 27;
-(2, 4, 0): 28; (2, 4, 1): 29;
-
-
-)";
+(2, 4, 0): 28; (2, 4, 1): 29;)";
   EXPECT_EQ(out, expected);
 }
 
@@ -103,10 +126,7 @@ TEST_F(FormatFieldTest, Field3DSpec) {
 (2, 1, 0): 2.2e+01; (2, 1, 1): 2.3e+01;
 (2, 2, 0): 2.4e+01; (2, 2, 1): 2.5e+01;
 (2, 3, 0): 2.6e+01; (2, 3, 1): 2.7e+01;
-(2, 4, 0): 2.8e+01; (2, 4, 1): 2.9e+01;
-
-
-)";
+(2, 4, 0): 2.8e+01; (2, 4, 1): 2.9e+01;)";
   EXPECT_EQ(out, expected);
 }
 
@@ -123,10 +143,10 @@ TEST_F(FormatFieldTest, FieldPerp) {
 
   const std::string expected =
       R"((0, 0): 0; (0, 1): 1;
+
 (1, 0): 10; (1, 1): 11;
-(2, 0): 20; (2, 1): 21;
 
-)";
+(2, 0): 20; (2, 1): 21;)";
   EXPECT_EQ(out, expected);
 }
 
@@ -143,9 +163,9 @@ TEST_F(FormatFieldTest, FieldPerpSpec) {
 
   const std::string expected =
       R"((0, 0): 0.0e+00; (0, 1): 1.0e+00;
+
 (1, 0): 1.0e+01; (1, 1): 1.1e+01;
-(2, 0): 2.0e+01; (2, 1): 2.1e+01;
 
-)";
+(2, 0): 2.0e+01; (2, 1): 2.1e+01;)";
   EXPECT_EQ(out, expected);
 }

From 6b0a366887c995141ca1cfe0a236bca3f39deb93 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 24 Feb 2026 21:45:36 +0000
Subject: [PATCH 0764/1827] Add region to Field format spec

---
 include/bout/output_bout_types.hxx        | 65 ++++++++++++++++++++---
 tests/unit/sys/test_output_bout_types.cxx | 25 +++++++--
 2 files changed, 80 insertions(+), 10 deletions(-)

diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx
index 171188664c..a30830f934 100644
--- a/include/bout/output_bout_types.hxx
+++ b/include/bout/output_bout_types.hxx
@@ -11,9 +11,12 @@
 #include "bout/region.hxx"
 #include "bout/traits.hxx"
 
-#include "fmt/base.h"
+#include <fmt/base.h>
 #include <fmt/format.h>
 
+#include <cstddef>
+#include <string>
+#include <string_view>
 #include <type_traits>
 
 template <IND_TYPE N>
@@ -59,14 +62,62 @@ struct fmt::formatter<SpecificInd<N>> {
 
 /// Formatter for Fields
 template <class T>
-struct fmt::formatter<T, std::enable_if_t<bout::utils::is_Field_v<T>, char>> : fmt::formatter<BoutReal> {
+struct fmt::formatter<T, std::enable_if_t<bout::utils::is_Field_v<T>, char>> {
+private:
+  fmt::formatter<BoutReal> underlying;
+
+  static constexpr auto default_region = "RGN_ALL";
+  std::string_view region = default_region;
+
+public:
+  constexpr auto parse(format_parse_context& ctx) {
+    const auto* it = ctx.begin();
+    const auto* end = ctx.end();
+
+    if (it == end) {
+      return underlying.parse(ctx);
+    }
+
+    // Other cases handled explicitly below
+    // NOLINTNEXTLINE(bugprone-switch-missing-default-case)
+    switch (*it) {
+    case 'r':
+      ++it;
+      if (*it != '\'') {
+        throw fmt::format_error("invalid format for Field");
+      }
+      const auto* rgn_start = ++it;
+      std::size_t size = 0;
+      while (*it != '\'') {
+        ++size;
+        ++it;
+      }
+      region = std::string_view(rgn_start, size);
+      ++it;
+      break;
+    }
+
+    if (it != end && *it != '}') {
+      if (*it != ':') {
+        throw fmt::format_error("invalid format specifier");
+      }
+      ++it;
+    }
+
+    ctx.advance_to(it);
+    return underlying.parse(ctx);
+  }
+
   auto format(const T& f, format_context& ctx) const -> format_context::iterator {
     const auto* mesh = f.getMesh();
-    int previous_x = 0;
-    int previous_y = 0;
-    int previous_z = 0;
 
-    BOUT_FOR_SERIAL(i, f.getRegion("RGN_ALL")) {
+    const auto rgn = f.getRegion(std::string(region));
+    const auto i = rgn.begin();
+    int previous_x = i->x();
+    int previous_y = i->y();
+    int previous_z = i->z();
+
+    BOUT_FOR_SERIAL(i, rgn) {
       const auto ix = i.x();
       const auto iy = i.y();
       const auto iz = i.z();
@@ -82,7 +133,7 @@ struct fmt::formatter<T, std::enable_if_t<bout::utils::is_Field_v<T>, char>> : f
       }
 
       format_to(ctx.out(), "{:c}: ", i);
-      formatter<BoutReal>::format(f[i], ctx);
+      underlying.format(f[i], ctx);
       format_to(ctx.out(), ";");
       previous_x = ix;
       previous_y = iy;
diff --git a/tests/unit/sys/test_output_bout_types.cxx b/tests/unit/sys/test_output_bout_types.cxx
index 82eb1754d0..dc7292f555 100644
--- a/tests/unit/sys/test_output_bout_types.cxx
+++ b/tests/unit/sys/test_output_bout_types.cxx
@@ -47,7 +47,7 @@ TEST_F(FormatFieldTest, Field2DSpec) {
 
   fillField(f, {{0., 1., 2., 3., 4.}, {5., 6., 7., 8., 9.}, {10., 11., 12., 13., 14.}});
 
-  const auto out = fmt::format("{:3.1e}", f);
+  const auto out = fmt::format("{::3.1e}", f);
 
   const std::string expected =
     R"((0, 0): 0.0e+00;
@@ -107,7 +107,7 @@ TEST_F(FormatFieldTest, Field3DSpec) {
                 {{10., 11}, {12., 13}, {14., 15}, {16., 17}, {18., 19}},
                 {{20., 21}, {22., 23}, {24., 25}, {26., 27}, {28., 29}}});
 
-  const auto out = fmt::format("{:3.1e}", f);
+  const auto out = fmt::format("{::3.1e}", f);
 
   const std::string expected =
       R"((0, 0, 0): 0.0e+00; (0, 0, 1): 1.0e+00;
@@ -130,6 +130,25 @@ TEST_F(FormatFieldTest, Field3DSpec) {
   EXPECT_EQ(out, expected);
 }
 
+
+TEST_F(FormatFieldTest, Field3DRegionSpec) {
+  Field3D f{bout::globals::mesh};
+
+  fillField(f, {{{0., 1}, {2., 3}, {4., 5}, {6., 7}, {8., 9}},
+                {{10., 11}, {12., 13}, {14., 15}, {16., 17}, {18., 19}},
+                {{20., 21}, {22., 23}, {24., 25}, {26., 27}, {28., 29}}});
+
+  const auto out = fmt::format("{:r'RGN_NOX':3.1e}", f);
+
+  const std::string expected =
+      R"((1, 0, 0): 1.0e+01; (1, 0, 1): 1.1e+01;
+(1, 1, 0): 1.2e+01; (1, 1, 1): 1.3e+01;
+(1, 2, 0): 1.4e+01; (1, 2, 1): 1.5e+01;
+(1, 3, 0): 1.6e+01; (1, 3, 1): 1.7e+01;
+(1, 4, 0): 1.8e+01; (1, 4, 1): 1.9e+01;)";
+  EXPECT_EQ(out, expected);
+}
+
 TEST_F(FormatFieldTest, FieldPerp) {
   Field3D f{bout::globals::mesh};
 
@@ -159,7 +178,7 @@ TEST_F(FormatFieldTest, FieldPerpSpec) {
 
   FieldPerp g = sliceXZ(f, 0);
 
-  const auto out = fmt::format("{:3.1e}", g);
+  const auto out = fmt::format("{::3.1e}", g);
 
   const std::string expected =
       R"((0, 0): 0.0e+00; (0, 1): 1.0e+00;

From a9dac31e56551f8fa5e0fe38f3b3e5f5a4110beb Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 25 Feb 2026 13:46:47 +0000
Subject: [PATCH 0765/1827] Add field format spec to not print indices

---
 include/bout/output_bout_types.hxx        | 51 +++++++++++++++--------
 tests/unit/sys/test_output_bout_types.cxx | 30 +++++++++++++
 2 files changed, 64 insertions(+), 17 deletions(-)

diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx
index a30830f934..ccdaf0dc08 100644
--- a/include/bout/output_bout_types.hxx
+++ b/include/bout/output_bout_types.hxx
@@ -61,6 +61,11 @@ struct fmt::formatter<SpecificInd<N>> {
 };
 
 /// Formatter for Fields
+///
+/// Format specification:
+///
+/// - ``n``: Don't show indices
+/// - ``r'<region name>'``: Use given region (default: ``RGN_ALL``)
 template <class T>
 struct fmt::formatter<T, std::enable_if_t<bout::utils::is_Field_v<T>, char>> {
 private:
@@ -69,6 +74,8 @@ private:
   static constexpr auto default_region = "RGN_ALL";
   std::string_view region = default_region;
 
+  bool show_indices = true;
+
 public:
   constexpr auto parse(format_parse_context& ctx) {
     const auto* it = ctx.begin();
@@ -78,26 +85,34 @@ public:
       return underlying.parse(ctx);
     }
 
-    // Other cases handled explicitly below
-    // NOLINTNEXTLINE(bugprone-switch-missing-default-case)
-    switch (*it) {
-    case 'r':
-      ++it;
-      if (*it != '\'') {
-        throw fmt::format_error("invalid format for Field");
-      }
-      const auto* rgn_start = ++it;
-      std::size_t size = 0;
-      while (*it != '\'') {
-        ++size;
+    while (it != end and *it != ':' and *it != '}') {
+      // Other cases handled explicitly below
+      // NOLINTNEXTLINE(bugprone-switch-missing-default-case)
+      switch (*it) {
+      case 'r':
         ++it;
+        if (*it != '\'') {
+          throw fmt::format_error("invalid format for Field");
+        }
+        {
+          const auto* rgn_start = ++it;
+          std::size_t size = 0;
+          while (*it != '\'') {
+            ++size;
+            ++it;
+          }
+          region = std::string_view(rgn_start, size);
+        }
+        ++it;
+        break;
+      case 'n':
+        show_indices = false;
+        ++it;
+        break;
       }
-      region = std::string_view(rgn_start, size);
-      ++it;
-      break;
     }
 
-    if (it != end && *it != '}') {
+    if (it != end and *it != '}') {
       if (*it != ':') {
         throw fmt::format_error("invalid format specifier");
       }
@@ -132,7 +147,9 @@ public:
         format_to(ctx.out(), "\n\n");
       }
 
-      format_to(ctx.out(), "{:c}: ", i);
+      if (show_indices) {
+        format_to(ctx.out(), "{:c}: ", i);
+      }
       underlying.format(f[i], ctx);
       format_to(ctx.out(), ";");
       previous_x = ix;
diff --git a/tests/unit/sys/test_output_bout_types.cxx b/tests/unit/sys/test_output_bout_types.cxx
index dc7292f555..a9c447091c 100644
--- a/tests/unit/sys/test_output_bout_types.cxx
+++ b/tests/unit/sys/test_output_bout_types.cxx
@@ -149,6 +149,36 @@ TEST_F(FormatFieldTest, Field3DRegionSpec) {
   EXPECT_EQ(out, expected);
 }
 
+TEST_F(FormatFieldTest, NoIndices) {
+  Field3D f{bout::globals::mesh};
+
+  fillField(f, {{{0., 1}, {2., 3}, {4., 5}, {6., 7}, {8., 9}},
+                {{10., 11}, {12., 13}, {14., 15}, {16., 17}, {18., 19}},
+                {{20., 21}, {22., 23}, {24., 25}, {26., 27}, {28., 29}}});
+
+  const auto out = fmt::format("{:n}", f);
+
+  const std::string expected =
+      R"(0; 1;
+2; 3;
+4; 5;
+6; 7;
+8; 9;
+
+10; 11;
+12; 13;
+14; 15;
+16; 17;
+18; 19;
+
+20; 21;
+22; 23;
+24; 25;
+26; 27;
+28; 29;)";
+  EXPECT_EQ(out, expected);
+}
+
 TEST_F(FormatFieldTest, FieldPerp) {
   Field3D f{bout::globals::mesh};
 

From eb9f06349cd2265a69f6cf358fef947616f1d64a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 25 Feb 2026 16:06:29 +0000
Subject: [PATCH 0766/1827] Add field format spec to transpose field

---
 CMakeLists.txt                            |  1 +
 include/bout/output_bout_types.hxx        | 24 ++++++-
 src/sys/output_bout_types.cxx             | 39 +++++++++++
 tests/unit/sys/test_output_bout_types.cxx | 82 +++++++++++++++++++++--
 4 files changed, 137 insertions(+), 9 deletions(-)
 create mode 100644 src/sys/output_bout_types.cxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 502d635f1c..ed8044f27b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -374,6 +374,7 @@ set(BOUT_SOURCES
     ./src/sys/options/options_adios.hxx
     ./src/sys/optionsreader.cxx
     ./src/sys/output.cxx
+    ./src/sys/output_bout_types.cxx
     ./src/sys/petsclib.cxx
     ./src/sys/range.cxx
     ./src/sys/slepclib.cxx
diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx
index ccdaf0dc08..fb24688d43 100644
--- a/include/bout/output_bout_types.hxx
+++ b/include/bout/output_bout_types.hxx
@@ -60,12 +60,23 @@ struct fmt::formatter<SpecificInd<N>> {
   }
 };
 
+namespace bout {
+namespace details {
+template <class T>
+/// Transpose a region so that it iterates in Z first, then Y, then X
+///
+/// Caution: this is the most inefficient memory order!
+auto region_transpose(const Region<T>& region) -> Region<T>;
+}
+} // namespace bout
+
 /// Formatter for Fields
 ///
 /// Format specification:
 ///
 /// - ``n``: Don't show indices
 /// - ``r'<region name>'``: Use given region (default: ``RGN_ALL``)
+/// - ``T``: Transpose field so X is first dimension
 template <class T>
 struct fmt::formatter<T, std::enable_if_t<bout::utils::is_Field_v<T>, char>> {
 private:
@@ -75,6 +86,7 @@ private:
   std::string_view region = default_region;
 
   bool show_indices = true;
+  bool transpose = false;
 
 public:
   constexpr auto parse(format_parse_context& ctx) {
@@ -109,6 +121,10 @@ public:
         show_indices = false;
         ++it;
         break;
+      case 'T':
+        transpose = true;
+        ++it;
+        break;
       }
     }
 
@@ -126,7 +142,9 @@ public:
   auto format(const T& f, format_context& ctx) const -> format_context::iterator {
     const auto* mesh = f.getMesh();
 
-    const auto rgn = f.getRegion(std::string(region));
+    const auto rgn_ = f.getRegion(std::string(region));
+    const auto rgn = transpose ? bout::details::region_transpose(rgn_) : rgn_;
+
     const auto i = rgn.begin();
     int previous_x = i->x();
     int previous_y = i->y();
@@ -138,13 +156,13 @@ public:
       const auto iz = i.z();
 
       if (iz > previous_z) {
-        format_to(ctx.out(), " ");
+        format_to(ctx.out(), transpose ? "\n\n" : " ");
       }
       if (iy > previous_y) {
         format_to(ctx.out(), "\n");
       }
       if (ix > previous_x) {
-        format_to(ctx.out(), "\n\n");
+        format_to(ctx.out(), transpose ? " " : "\n\n");
       }
 
       if (show_indices) {
diff --git a/src/sys/output_bout_types.cxx b/src/sys/output_bout_types.cxx
new file mode 100644
index 0000000000..ed76cd2b13
--- /dev/null
+++ b/src/sys/output_bout_types.cxx
@@ -0,0 +1,39 @@
+#include "bout/output_bout_types.hxx"
+
+#include "bout/mesh.hxx"
+#include "bout/region.hxx"
+
+#include <algorithm>
+
+namespace bout::details {
+
+template <class T>
+auto region_transpose(const Region<T>& region) -> Region<T> {
+  auto indices = region.getIndices();
+
+  std::sort(indices.begin(), indices.end(), [](const T& lhs, const T& rhs) {
+    const auto lx = lhs.x();
+    const auto ly = lhs.y();
+    const auto lz = lhs.z();
+
+    const auto rx = rhs.x();
+    const auto ry = rhs.y();
+    const auto rz = rhs.z();
+
+    // Z is now outer scale, so put it in largest blocks
+    if (lz != rz) {
+      return lz < rz;
+    }
+    if (ly != ry) {
+      return ly < ry;
+    }
+    return lx < rx;
+  });
+
+  return Region<T>{indices};
+}
+
+template auto region_transpose(const Region<Ind2D>& region) -> Region<Ind2D>;
+template auto region_transpose(const Region<Ind3D>& region) -> Region<Ind3D>;
+template auto region_transpose(const Region<IndPerp>& region) -> Region<IndPerp>;
+} // namespace bout::details
diff --git a/tests/unit/sys/test_output_bout_types.cxx b/tests/unit/sys/test_output_bout_types.cxx
index a9c447091c..8a9da618bf 100644
--- a/tests/unit/sys/test_output_bout_types.cxx
+++ b/tests/unit/sys/test_output_bout_types.cxx
@@ -8,12 +8,43 @@
 #include "bout/globals.hxx"
 #include "bout/output_bout_types.hxx" // IWYU pragma: keep
 
-#include <string>
-
 #include <fmt/format.h>
 
+#include <string>
+#include <vector>
+
 using FormatFieldTest = FakeMeshFixture_tmpl<3, 5, 2>;
 
+TEST_F(FormatFieldTest, DetailsRegionTranspose) {
+  const auto rgn_all = bout::globals::mesh->getRegion("RGN_ALL");
+  const auto rgn_transpose = bout::details::region_transpose(rgn_all);
+
+  std::vector<std::vector<int>> points{};
+  points.reserve(rgn_all.size());
+
+  for (const auto i : rgn_transpose) {
+    points.push_back({i.x(), i.y(), i.z()});
+  }
+
+  const std::vector<std::vector<int>> expected = {
+      // clang-format off
+    {0, 0, 0}, {1, 0, 0}, {2, 0, 0},
+    {0, 1, 0}, {1, 1, 0}, {2, 1, 0},
+    {0, 2, 0}, {1, 2, 0}, {2, 2, 0},
+    {0, 3, 0}, {1, 3, 0}, {2, 3, 0},
+    {0, 4, 0}, {1, 4, 0}, {2, 4, 0},
+
+    {0, 0, 1}, {1, 0, 1}, {2, 0, 1},
+    {0, 1, 1}, {1, 1, 1}, {2, 1, 1},
+    {0, 2, 1}, {1, 2, 1}, {2, 2, 1},
+    {0, 3, 1}, {1, 3, 1}, {2, 3, 1},
+    {0, 4, 1}, {1, 4, 1}, {2, 4, 1},
+      // clang-format on
+  };
+
+  ASSERT_EQ(points, expected);
+}
+
 TEST_F(FormatFieldTest, Field2D) {
   Field2D f{bout::globals::mesh};
 
@@ -22,7 +53,7 @@ TEST_F(FormatFieldTest, Field2D) {
   const auto out = fmt::format("{}", f);
 
   const std::string expected =
-    R"((0, 0): 0;
+      R"((0, 0): 0;
 (0, 1): 1;
 (0, 2): 2;
 (0, 3): 3;
@@ -50,7 +81,7 @@ TEST_F(FormatFieldTest, Field2DSpec) {
   const auto out = fmt::format("{::3.1e}", f);
 
   const std::string expected =
-    R"((0, 0): 0.0e+00;
+      R"((0, 0): 0.0e+00;
 (0, 1): 1.0e+00;
 (0, 2): 2.0e+00;
 (0, 3): 3.0e+00;
@@ -70,6 +101,22 @@ TEST_F(FormatFieldTest, Field2DSpec) {
   EXPECT_EQ(out, expected);
 }
 
+TEST_F(FormatFieldTest, Field2DTranspose) {
+  Field2D f{bout::globals::mesh};
+
+  fillField(f, {{0., 1., 2., 3., 4.}, {5., 6., 7., 8., 9.}, {10., 11., 12., 13., 14.}});
+
+  const auto out = fmt::format("{:T}", f);
+
+  const std::string expected =
+      R"((0, 0): 0; (1, 0): 5; (2, 0): 10;
+(0, 1): 1; (1, 1): 6; (2, 1): 11;
+(0, 2): 2; (1, 2): 7; (2, 2): 12;
+(0, 3): 3; (1, 3): 8; (2, 3): 13;
+(0, 4): 4; (1, 4): 9; (2, 4): 14;)";
+  EXPECT_EQ(out, expected);
+}
+
 TEST_F(FormatFieldTest, Field3D) {
   Field3D f{bout::globals::mesh};
 
@@ -130,7 +177,6 @@ TEST_F(FormatFieldTest, Field3DSpec) {
   EXPECT_EQ(out, expected);
 }
 
-
 TEST_F(FormatFieldTest, Field3DRegionSpec) {
   Field3D f{bout::globals::mesh};
 
@@ -149,7 +195,7 @@ TEST_F(FormatFieldTest, Field3DRegionSpec) {
   EXPECT_EQ(out, expected);
 }
 
-TEST_F(FormatFieldTest, NoIndices) {
+TEST_F(FormatFieldTest, Field3DNoIndices) {
   Field3D f{bout::globals::mesh};
 
   fillField(f, {{{0., 1}, {2., 3}, {4., 5}, {6., 7}, {8., 9}},
@@ -179,6 +225,30 @@ TEST_F(FormatFieldTest, NoIndices) {
   EXPECT_EQ(out, expected);
 }
 
+TEST_F(FormatFieldTest, Field3DTranspose) {
+  Field3D f{bout::globals::mesh};
+
+  fillField(f, {{{0., 1}, {2., 3}, {4., 5}, {6., 7}, {8., 9}},
+                {{10., 11}, {12., 13}, {14., 15}, {16., 17}, {18., 19}},
+                {{20., 21}, {22., 23}, {24., 25}, {26., 27}, {28., 29}}});
+
+  const auto out = fmt::format("{:T}", f);
+
+  const std::string expected =
+      R"((0, 0, 0): 0; (1, 0, 0): 10; (2, 0, 0): 20;
+(0, 1, 0): 2; (1, 1, 0): 12; (2, 1, 0): 22;
+(0, 2, 0): 4; (1, 2, 0): 14; (2, 2, 0): 24;
+(0, 3, 0): 6; (1, 3, 0): 16; (2, 3, 0): 26;
+(0, 4, 0): 8; (1, 4, 0): 18; (2, 4, 0): 28;
+
+(0, 0, 1): 1; (1, 0, 1): 11; (2, 0, 1): 21;
+(0, 1, 1): 3; (1, 1, 1): 13; (2, 1, 1): 23;
+(0, 2, 1): 5; (1, 2, 1): 15; (2, 2, 1): 25;
+(0, 3, 1): 7; (1, 3, 1): 17; (2, 3, 1): 27;
+(0, 4, 1): 9; (1, 4, 1): 19; (2, 4, 1): 29;)";
+  EXPECT_EQ(out, expected);
+}
+
 TEST_F(FormatFieldTest, FieldPerp) {
   Field3D f{bout::globals::mesh};
 

From caccbc4f77ec5c8795380514ffe36ef5cc683fd4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 25 Feb 2026 17:14:58 +0000
Subject: [PATCH 0767/1827] Add very basic plotting for fields

---
 include/bout/output_bout_types.hxx |  43 ++++-
 src/sys/output_bout_types.cxx      | 287 +++++++++++++++++++++++++++++
 2 files changed, 323 insertions(+), 7 deletions(-)

diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx
index fb24688d43..8f7233b613 100644
--- a/include/bout/output_bout_types.hxx
+++ b/include/bout/output_bout_types.hxx
@@ -12,6 +12,7 @@
 #include "bout/traits.hxx"
 
 #include <fmt/base.h>
+#include <fmt/color.h>
 #include <fmt/format.h>
 
 #include <cstddef>
@@ -67,7 +68,9 @@ template <class T>
 ///
 /// Caution: this is the most inefficient memory order!
 auto region_transpose(const Region<T>& region) -> Region<T>;
-}
+
+auto colour(BoutReal value, BoutReal min, BoutReal max) -> fmt::text_style;
+} // namespace details
 } // namespace bout
 
 /// Formatter for Fields
@@ -77,6 +80,7 @@ auto region_transpose(const Region<T>& region) -> Region<T>;
 /// - ``n``: Don't show indices
 /// - ``r'<region name>'``: Use given region (default: ``RGN_ALL``)
 /// - ``T``: Transpose field so X is first dimension
+/// - ``#``: Plot slices as 2D heatmap
 template <class T>
 struct fmt::formatter<T, std::enable_if_t<bout::utils::is_Field_v<T>, char>> {
 private:
@@ -87,6 +91,7 @@ private:
 
   bool show_indices = true;
   bool transpose = false;
+  bool plot = false;
 
 public:
   constexpr auto parse(format_parse_context& ctx) {
@@ -125,6 +130,11 @@ public:
         transpose = true;
         ++it;
         break;
+      case '#':
+        plot = true;
+        show_indices = false;
+        ++it;
+        break;
       }
     }
 
@@ -140,36 +150,55 @@ public:
   }
 
   auto format(const T& f, format_context& ctx) const -> format_context::iterator {
+    using namespace bout::details;
+
     const auto* mesh = f.getMesh();
 
-    const auto rgn_ = f.getRegion(std::string(region));
-    const auto rgn = transpose ? bout::details::region_transpose(rgn_) : rgn_;
+    const auto rgn_str = std::string{region};
+    const auto rgn_ = f.getRegion(rgn_str);
+    const auto rgn = transpose ? region_transpose(rgn_) : rgn_;
 
     const auto i = rgn.begin();
     int previous_x = i->x();
     int previous_y = i->y();
     int previous_z = i->z();
 
+    // Range of the data for plotting
+    BoutReal plot_min = 0.0;
+    BoutReal plot_max = 0.0;
+    if (plot) {
+      plot_min = min(f, false, rgn_str);
+      plot_max = max(f, false, rgn_str);
+    }
+
+    // Separators
+    const auto* const block_sep = "\n\n";
+    const auto* const item_sep = plot ? "" : " ";
+
     BOUT_FOR_SERIAL(i, rgn) {
       const auto ix = i.x();
       const auto iy = i.y();
       const auto iz = i.z();
 
       if (iz > previous_z) {
-        format_to(ctx.out(), transpose ? "\n\n" : " ");
+        format_to(ctx.out(), transpose ? block_sep : item_sep);
       }
       if (iy > previous_y) {
         format_to(ctx.out(), "\n");
       }
       if (ix > previous_x) {
-        format_to(ctx.out(), transpose ? " " : "\n\n");
+        format_to(ctx.out(), transpose ? item_sep : block_sep);
       }
 
       if (show_indices) {
         format_to(ctx.out(), "{:c}: ", i);
       }
-      underlying.format(f[i], ctx);
-      format_to(ctx.out(), ";");
+      if (plot) {
+        format_to(ctx.out(), "{}", styled("█", colour(f[i], plot_min, plot_max)));
+      } else {
+        underlying.format(f[i], ctx);
+        format_to(ctx.out(), ";");
+      }
       previous_x = ix;
       previous_y = iy;
       previous_z = iz;
diff --git a/src/sys/output_bout_types.cxx b/src/sys/output_bout_types.cxx
index ed76cd2b13..41a2055dfc 100644
--- a/src/sys/output_bout_types.cxx
+++ b/src/sys/output_bout_types.cxx
@@ -1,9 +1,16 @@
 #include "bout/output_bout_types.hxx"
 
+#include "bout/bout_types.hxx"
 #include "bout/mesh.hxx"
 #include "bout/region.hxx"
 
+#include <fmt/color.h>
+
 #include <algorithm>
+#include <array>
+#include <cmath>
+#include <cstddef>
+#include <cstdint>
 
 namespace bout::details {
 
@@ -36,4 +43,284 @@ auto region_transpose(const Region<T>& region) -> Region<T> {
 template auto region_transpose(const Region<Ind2D>& region) -> Region<Ind2D>;
 template auto region_transpose(const Region<Ind3D>& region) -> Region<Ind3D>;
 template auto region_transpose(const Region<IndPerp>& region) -> Region<IndPerp>;
+
+// Matplotlib viridis colourmap
+// Copyright Matplotlib Development Team
+// SPDX-License-Identifier: BSD
+constexpr std::array<std::array<std::uint8_t, 3>, 256> viridis_data = {{
+    // clang-format off
+     {68, 1, 84},
+     {68, 2, 85},
+     {69, 3, 87},
+     {69, 5, 88},
+     {69, 6, 90},
+     {70, 8, 91},
+     {70, 9, 93},
+     {70, 11, 94},
+     {70, 12, 96},
+     {71, 14, 97},
+     {71, 15, 98},
+     {71, 17, 100},
+     {71, 18, 101},
+     {71, 20, 102},
+     {72, 21, 104},
+     {72, 22, 105},
+     {72, 24, 106},
+     {72, 25, 108},
+     {72, 26, 109},
+     {72, 28, 110},
+     {72, 29, 111},
+     {72, 30, 112},
+     {72, 32, 113},
+     {72, 33, 115},
+     {72, 34, 116},
+     {72, 36, 117},
+     {72, 37, 118},
+     {72, 38, 119},
+     {72, 39, 120},
+     {71, 41, 121},
+     {71, 42, 121},
+     {71, 43, 122},
+     {71, 44, 123},
+     {71, 46, 124},
+     {70, 47, 125},
+     {70, 48, 126},
+     {70, 49, 126},
+     {70, 51, 127},
+     {69, 52, 128},
+     {69, 53, 129},
+     {69, 54, 129},
+     {68, 56, 130},
+     {68, 57, 131},
+     {68, 58, 131},
+     {67, 59, 132},
+     {67, 60, 132},
+     {67, 62, 133},
+     {66, 63, 133},
+     {66, 64, 134},
+     {65, 65, 134},
+     {65, 66, 135},
+     {65, 67, 135},
+     {64, 69, 136},
+     {64, 70, 136},
+     {63, 71, 136},
+     {63, 72, 137},
+     {62, 73, 137},
+     {62, 74, 137},
+     {61, 75, 138},
+     {61, 77, 138},
+     {60, 78, 138},
+     {60, 79, 138},
+     {59, 80, 139},
+     {59, 81, 139},
+     {58, 82, 139},
+     {58, 83, 139},
+     {57, 84, 140},
+     {57, 85, 140},
+     {56, 86, 140},
+     {56, 87, 140},
+     {55, 88, 140},
+     {55, 89, 140},
+     {54, 91, 141},
+     {54, 92, 141},
+     {53, 93, 141},
+     {53, 94, 141},
+     {52, 95, 141},
+     {52, 96, 141},
+     {51, 97, 141},
+     {51, 98, 141},
+     {51, 99, 141},
+     {50, 100, 142},
+     {50, 101, 142},
+     {49, 102, 142},
+     {49, 103, 142},
+     {48, 104, 142},
+     {48, 105, 142},
+     {47, 106, 142},
+     {47, 107, 142},
+     {47, 108, 142},
+     {46, 109, 142},
+     {46, 110, 142},
+     {45, 111, 142},
+     {45, 112, 142},
+     {45, 112, 142},
+     {44, 113, 142},
+     {44, 114, 142},
+     {43, 115, 142},
+     {43, 116, 142},
+     {43, 117, 142},
+     {42, 118, 142},
+     {42, 119, 142},
+     {41, 120, 142},
+     {41, 121, 142},
+     {41, 122, 142},
+     {40, 123, 142},
+     {40, 124, 142},
+     {40, 125, 142},
+     {39, 126, 142},
+     {39, 127, 142},
+     {38, 128, 142},
+     {38, 129, 142},
+     {38, 130, 142},
+     {37, 131, 142},
+     {37, 131, 142},
+     {37, 132, 142},
+     {36, 133, 142},
+     {36, 134, 142},
+     {35, 135, 142},
+     {35, 136, 142},
+     {35, 137, 142},
+     {34, 138, 141},
+     {34, 139, 141},
+     {34, 140, 141},
+     {33, 141, 141},
+     {33, 142, 141},
+     {33, 143, 141},
+     {32, 144, 141},
+     {32, 145, 140},
+     {32, 146, 140},
+     {32, 147, 140},
+     {31, 147, 140},
+     {31, 148, 140},
+     {31, 149, 139},
+     {31, 150, 139},
+     {31, 151, 139},
+     {30, 152, 139},
+     {30, 153, 138},
+     {30, 154, 138},
+     {30, 155, 138},
+     {30, 156, 137},
+     {30, 157, 137},
+     {30, 158, 137},
+     {30, 159, 136},
+     {30, 160, 136},
+     {31, 161, 136},
+     {31, 162, 135},
+     {31, 163, 135},
+     {31, 163, 134},
+     {32, 164, 134},
+     {32, 165, 134},
+     {33, 166, 133},
+     {33, 167, 133},
+     {34, 168, 132},
+     {35, 169, 131},
+     {35, 170, 131},
+     {36, 171, 130},
+     {37, 172, 130},
+     {38, 173, 129},
+     {39, 174, 129},
+     {40, 175, 128},
+     {41, 175, 127},
+     {42, 176, 127},
+     {43, 177, 126},
+     {44, 178, 125},
+     {46, 179, 124},
+     {47, 180, 124},
+     {48, 181, 123},
+     {50, 182, 122},
+     {51, 183, 121},
+     {53, 183, 121},
+     {54, 184, 120},
+     {56, 185, 119},
+     {57, 186, 118},
+     {59, 187, 117},
+     {61, 188, 116},
+     {62, 189, 115},
+     {64, 190, 114},
+     {66, 190, 113},
+     {68, 191, 112},
+     {70, 192, 111},
+     {72, 193, 110},
+     {73, 194, 109},
+     {75, 194, 108},
+     {77, 195, 107},
+     {79, 196, 106},
+     {81, 197, 105},
+     {83, 198, 104},
+     {85, 198, 102},
+     {88, 199, 101},
+     {90, 200, 100},
+     {92, 201, 99},
+     {94, 201, 98},
+     {96, 202, 96},
+     {98, 203, 95},
+     {101, 204, 94},
+     {103, 204, 92},
+     {105, 205, 91},
+     {108, 206, 90},
+     {110, 206, 88},
+     {112, 207, 87},
+     {115, 208, 85},
+     {117, 208, 84},
+     {119, 209, 82},
+     {122, 210, 81},
+     {124, 210, 79},
+     {127, 211, 78},
+     {129, 212, 76},
+     {132, 212, 75},
+     {134, 213, 73},
+     {137, 213, 72},
+     {139, 214, 70},
+     {142, 215, 68},
+     {144, 215, 67},
+     {147, 216, 65},
+     {149, 216, 63},
+     {152, 217, 62},
+     {155, 217, 60},
+     {157, 218, 58},
+     {160, 218, 57},
+     {163, 219, 55},
+     {165, 219, 53},
+     {168, 220, 51},
+     {171, 220, 50},
+     {173, 221, 48},
+     {176, 221, 46},
+     {179, 221, 45},
+     {181, 222, 43},
+     {184, 222, 41},
+     {187, 223, 39},
+     {189, 223, 38},
+     {192, 223, 36},
+     {195, 224, 35},
+     {197, 224, 33},
+     {200, 225, 32},
+     {203, 225, 30},
+     {205, 225, 29},
+     {208, 226, 28},
+     {211, 226, 27},
+     {213, 226, 26},
+     {216, 227, 25},
+     {219, 227, 24},
+     {221, 227, 24},
+     {224, 228, 24},
+     {226, 228, 24},
+     {229, 228, 24},
+     {232, 229, 25},
+     {234, 229, 25},
+     {237, 229, 26},
+     {239, 230, 27},
+     {242, 230, 28},
+     {244, 230, 30},
+     {247, 230, 31},
+     {249, 231, 33},
+     {251, 231, 35},
+     {254, 231, 36},
+}};
+// clang-format on
+
+constexpr auto colour_map_scaling = viridis_data.size() - 1;
+
+auto colour(BoutReal value, BoutReal min, BoutReal max) -> fmt::text_style {
+  if (std::isnan(value)) {
+    return fmt::fg(fmt::color::black);
+  }
+
+  // Get value in range [0, 1]
+  const auto x = (value - min) / (max - min);
+  // Convert to range [0, 255]
+  const auto index = static_cast<std::size_t>(x * colour_map_scaling);
+  const auto colour = viridis_data[index]; // NOLINT
+
+  return fmt::fg(fmt::rgb(colour[0], colour[1], colour[2]));
+}
 } // namespace bout::details

From 55998654e4476840104471d819f4c70351a352ff Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 25 Feb 2026 18:13:46 +0000
Subject: [PATCH 0768/1827] Add field format truncation, like numpy

---
 include/bout/output_bout_types.hxx        | 85 +++++++++++++++++++++--
 tests/unit/sys/test_output_bout_types.cxx | 30 ++++++++
 2 files changed, 109 insertions(+), 6 deletions(-)

diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx
index 8f7233b613..bd53fc7ed1 100644
--- a/include/bout/output_bout_types.hxx
+++ b/include/bout/output_bout_types.hxx
@@ -15,6 +15,7 @@
 #include <fmt/color.h>
 #include <fmt/format.h>
 
+#include <climits>
 #include <cstddef>
 #include <string>
 #include <string_view>
@@ -70,6 +71,37 @@ template <class T>
 auto region_transpose(const Region<T>& region) -> Region<T>;
 
 auto colour(BoutReal value, BoutReal min, BoutReal max) -> fmt::text_style;
+
+// Parses the range [begin, end) as an unsigned integer. This function assumes
+// that the range is non-empty and the first character is a digit.
+//
+// Taken from fmt
+// Copyright (c) 2012 - present, Victor Zverovich
+// SPDX-License-Identifier: MIT
+constexpr auto parse_nonnegative_int(const char*& begin, const char* end,
+                                     int error_value) noexcept -> int {
+  const auto* p = begin;
+  unsigned value = *p - '0';
+  unsigned prev = 0;
+  ++p;
+
+  while (p != end && '0' <= *p && *p <= '9') {
+    prev = value;
+    value = (value * 10) + unsigned(*p - '0');
+    ++p;
+  }
+  auto num_digits = p - begin;
+  begin = p;
+  const auto digits10 = static_cast<int>(sizeof(int) * CHAR_BIT * 3 / 10);
+  if (num_digits <= digits10) {
+    return static_cast<int>(value);
+  }
+  // Check for overflow.
+  const unsigned max = INT_MAX;
+  return num_digits == digits10 + 1 and (prev * 10ULL) + unsigned(p[-1] - '0') <= max
+             ? static_cast<int>(value)
+             : error_value;
+}
 } // namespace details
 } // namespace bout
 
@@ -81,6 +113,8 @@ auto colour(BoutReal value, BoutReal min, BoutReal max) -> fmt::text_style;
 /// - ``r'<region name>'``: Use given region (default: ``RGN_ALL``)
 /// - ``T``: Transpose field so X is first dimension
 /// - ``#``: Plot slices as 2D heatmap
+/// - ``e<N>``: Number of elements at each edge to show
+/// - ``f``: Show full field
 template <class T>
 struct fmt::formatter<T, std::enable_if_t<bout::utils::is_Field_v<T>, char>> {
 private:
@@ -92,6 +126,8 @@ private:
   bool show_indices = true;
   bool transpose = false;
   bool plot = false;
+  int edgeitems = 4;
+  bool show_full = false;
 
 public:
   constexpr auto parse(format_parse_context& ctx) {
@@ -106,6 +142,17 @@ public:
       // Other cases handled explicitly below
       // NOLINTNEXTLINE(bugprone-switch-missing-default-case)
       switch (*it) {
+      case 'e':
+        ++it;
+        edgeitems = bout::details::parse_nonnegative_int(it, end, -1);
+        if (edgeitems == -1) {
+          throw fmt::format_error("number is too big");
+        }
+        break;
+      case 'f':
+        show_full = true;
+        ++it;
+        break;
       case 'r':
         ++it;
         if (*it != '\'') {
@@ -163,6 +210,19 @@ public:
     int previous_y = i->y();
     int previous_z = i->z();
 
+    const auto last_i = rgn.getIndices().rbegin();
+    const int last_x = last_i->x();
+    const int last_y = last_i->y();
+    const int last_z = last_i->z();
+
+    // Indices of edges
+    const int start_x = previous_x + edgeitems;
+    const int start_y = previous_y + edgeitems;
+    const int start_z = previous_z + edgeitems;
+    const int end_x = last_x - edgeitems;
+    const int end_y = last_y - edgeitems;
+    const int end_z = last_z - edgeitems;
+
     // Range of the data for plotting
     BoutReal plot_min = 0.0;
     BoutReal plot_max = 0.0;
@@ -172,32 +232,45 @@ public:
     }
 
     // Separators
-    const auto* const block_sep = "\n\n";
+    constexpr auto block_sep = "\n\n";
     const auto* const item_sep = plot ? "" : " ";
 
+    // If we've shown the skip sep already this dim
+    bool shown_skip = false;
+    constexpr auto skip_sep = "...";
+
     BOUT_FOR_SERIAL(i, rgn) {
       const auto ix = i.x();
       const auto iy = i.y();
       const auto iz = i.z();
 
-      if (iz > previous_z) {
+      const bool should_show =
+          show_full
+          or ((ix < start_x or ix > end_x) and (iy < start_y or iy > end_y)
+              and (iz < start_z or iz > end_z));
+
+      if ((not shown_skip or should_show) and iz > previous_z) {
         format_to(ctx.out(), transpose ? block_sep : item_sep);
       }
-      if (iy > previous_y) {
+      if ((not shown_skip or should_show) and iy > previous_y) {
         format_to(ctx.out(), "\n");
       }
-      if (ix > previous_x) {
+      if ((not shown_skip or should_show) and ix > previous_x) {
         format_to(ctx.out(), transpose ? item_sep : block_sep);
       }
 
-      if (show_indices) {
+      if (show_indices and should_show) {
         format_to(ctx.out(), "{:c}: ", i);
       }
       if (plot) {
         format_to(ctx.out(), "{}", styled("█", colour(f[i], plot_min, plot_max)));
-      } else {
+      } else if (should_show) {
         underlying.format(f[i], ctx);
         format_to(ctx.out(), ";");
+        shown_skip = false;
+      } else if (not shown_skip) {
+        format_to(ctx.out(), skip_sep);
+        shown_skip = true;
       }
       previous_x = ix;
       previous_y = iy;
diff --git a/tests/unit/sys/test_output_bout_types.cxx b/tests/unit/sys/test_output_bout_types.cxx
index 8a9da618bf..1c4d6bdfe0 100644
--- a/tests/unit/sys/test_output_bout_types.cxx
+++ b/tests/unit/sys/test_output_bout_types.cxx
@@ -1,5 +1,6 @@
 #include "fake_mesh_fixture.hxx"
 #include "test_extras.hxx"
+#include "gmock/gmock.h"
 #include "gtest/gtest.h"
 
 #include "bout/field2d.hxx"
@@ -288,3 +289,32 @@ TEST_F(FormatFieldTest, FieldPerpSpec) {
 (2, 0): 2.0e+01; (2, 1): 2.1e+01;)";
   EXPECT_EQ(out, expected);
 }
+
+using FormatFieldTestLargerMesh = FakeMeshFixture_tmpl<10, 10, 10>;
+
+TEST_F(FormatFieldTestLargerMesh, Field3DEdges) {
+  Field3D f{1., bout::globals::mesh};
+
+  const auto out = fmt::format("{:e1}", f);
+
+  const std::string expected =
+      R"((0, 0, 0): 1; ... (0, 0, 9): 1;
+...
+(0, 9, 0): 1; ... (0, 9, 9): 1;
+
+...
+
+(9, 0, 0): 1; ... (9, 0, 9): 1;
+...
+(9, 9, 0): 1; ... (9, 9, 9): 1;)";
+  EXPECT_EQ(out, expected);
+}
+
+TEST_F(FormatFieldTestLargerMesh, Field3DFull) {
+  Field3D f{1., bout::globals::mesh};
+
+  const auto out = fmt::format("{:f}", f);
+
+  using namespace ::testing;
+  EXPECT_THAT(out, Not(HasSubstr("...")));
+}

From 78c6fdfa878333ee9d7a1de57f132e19bd4f4bdc Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 11 Mar 2026 17:40:39 +0000
Subject: [PATCH 0769/1827] Fix `Field` formatting for C++20

Argument to `format_to` must be either compiletime constant or `fmt::runtime`
---
 include/bout/output_bout_types.hxx | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/include/bout/output_bout_types.hxx b/include/bout/output_bout_types.hxx
index bd53fc7ed1..77ea8ebf2d 100644
--- a/include/bout/output_bout_types.hxx
+++ b/include/bout/output_bout_types.hxx
@@ -232,8 +232,10 @@ public:
     }
 
     // Separators
-    constexpr auto block_sep = "\n\n";
-    const auto* const item_sep = plot ? "" : " ";
+    const auto block_sep = fmt::runtime("\n\n");
+    const auto item_sep = fmt::runtime(plot ? "" : " ");
+    const auto x_sep = transpose ? item_sep : block_sep;
+    const auto z_sep = transpose ? block_sep : item_sep;
 
     // If we've shown the skip sep already this dim
     bool shown_skip = false;
@@ -250,13 +252,13 @@ public:
               and (iz < start_z or iz > end_z));
 
       if ((not shown_skip or should_show) and iz > previous_z) {
-        format_to(ctx.out(), transpose ? block_sep : item_sep);
+        format_to(ctx.out(), z_sep);
       }
       if ((not shown_skip or should_show) and iy > previous_y) {
         format_to(ctx.out(), "\n");
       }
       if ((not shown_skip or should_show) and ix > previous_x) {
-        format_to(ctx.out(), transpose ? item_sep : block_sep);
+        format_to(ctx.out(), x_sep);
       }
 
       if (show_indices and should_show) {

From e952090de92bef5cdb7c14b0aa2119efeaf99f6a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Mar 2026 11:06:15 -0700
Subject: [PATCH 0770/1827] Options: Convert Tensor<int> to Tensor<BoutReal>
 and similar

Read Tensor<int> from NetCDF files, and allow conversion to
Tensor<BoutReal> and then Field3D.
---
 include/bout/array.hxx             |  8 ++++++++
 include/bout/utils.hxx             | 18 +++++++++++++++++-
 src/sys/options.cxx                | 29 ++++++++++++++++++++++++-----
 src/sys/options/options_netcdf.cxx |  6 ++++++
 4 files changed, 55 insertions(+), 6 deletions(-)

diff --git a/include/bout/array.hxx b/include/bout/array.hxx
index 2305fe3b22..000ded9616 100644
--- a/include/bout/array.hxx
+++ b/include/bout/array.hxx
@@ -227,6 +227,14 @@ public:
     ptr = get(new_size);
   }
 
+  /*!
+   * Change shape of the container.
+   * Invalidates contents.
+   */
+  void reshape(std::tuple<size_type> new_shape) {
+    reallocate(std::get<0>(new_shape));
+  }
+
   /*!
    * Holds a static variable which controls whether
    * memory blocks (dataBlock) are put into a store
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 560f97f954..5088a025c1 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -5,7 +5,7 @@
  * simple but common calculations
  *
  **************************************************************************
- * Copyright 2010 - 2025 BOUT++ contributors
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  * 
@@ -231,6 +231,14 @@ public:
     data.reallocate(new_size_1 * new_size_2);
   }
 
+  /*!
+   * Change shape of the container.
+   * Invalidates contents.
+   */
+  void reshape(std::tuple<size_type, size_type> new_shape) {
+    reallocate(std::get<0>(new_shape), std::get<1>(new_shape));
+  }
+
   Matrix& operator=(const Matrix& other) {
     n1 = other.n1;
     n2 = other.n2;
@@ -331,6 +339,14 @@ public:
     data.reallocate(new_size_1 * new_size_2 * new_size_3);
   }
 
+  /*!
+   * Change shape of the container.
+   * Invalidates contents.
+   */
+  void reshape(std::tuple<size_type, size_type, size_type> new_shape) {
+    reallocate(std::get<0>(new_shape), std::get<1>(new_shape), std::get<2>(new_shape));
+  }
+
   Tensor& operator=(const Tensor& other) {
     n1 = other.n1;
     n2 = other.n2;
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index d60e91079d..8bd83c0bfb 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -744,27 +744,46 @@ FieldPerp Options::as<FieldPerp>(const FieldPerp& similar_to) const {
 }
 
 namespace {
-/// Visitor to convert an int, BoutReal or Array/Matrix/Tensor to the
-/// appropriate container
+/// Primary declaration of ConvertContainer, for specialization below.
+/// No definition needed unless it is used.
 template <class Container>
-struct ConvertContainer {
+struct ConvertContainer;
+
+/// Visitor to convert an int, BoutReal or Array/Matrix/Tensor to the
+/// appropriate container. Templated on both the container class C
+/// and scalar type Scalar.
+template <template <class> class C, class Scalar>
+struct ConvertContainer<C<Scalar>> {
+  using Container = C<Scalar>;
   ConvertContainer(std::string error, Container similar_to_)
       : error_message(std::move(error)), similar_to(std::move(similar_to_)) {}
 
   Container operator()(int value) {
     Container result(similar_to);
-    std::fill(std::begin(result), std::end(result), value);
+    std::fill(std::begin(result), std::end(result), static_cast<Scalar>(value));
     return result;
   }
 
   Container operator()(BoutReal value) {
     Container result(similar_to);
-    std::fill(std::begin(result), std::end(result), value);
+    std::fill(std::begin(result), std::end(result), static_cast<Scalar>(value));
     return result;
   }
 
   Container operator()(const Container& value) { return value; }
 
+  // Convert between scalar types: C<OtherScalar> -> C<Scalar>
+  // The size of the returned result will be the same as the input value
+  template <class OtherScalar>
+  Container operator()(const C<OtherScalar>& value) {
+    Container result(similar_to);
+    result.reshape(value.shape()); // Resize to shape of input
+
+    std::transform(std::begin(value), std::end(value), std::begin(result),
+                   [](const OtherScalar& x) { return static_cast<Scalar>(x); });
+    return result;
+  }
+
   template <class Other>
   Container operator()([[maybe_unused]] const Other& value) {
     throw BoutException(error_message);
diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx
index d3e5a993bd..f21f461c09 100644
--- a/src/sys/options/options_netcdf.cxx
+++ b/src/sys/options/options_netcdf.cxx
@@ -158,6 +158,12 @@ void readGroup(const std::string& filename, const NcGroup& group, Options& resul
           var.getVar(value.begin());
           result[var_name] = value;
         }
+      } else if (var_type == ncInt) {
+        Tensor<int> value(static_cast<int>(dims[0].getSize()),
+                          static_cast<int>(dims[1].getSize()),
+                          static_cast<int>(dims[2].getSize()));
+        var.getVar(value.begin());
+        result[var_name] = value;
       }
     }
     }

From b2e2f3575e68f771be2a4341af5fd14e2870469e Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Wed, 11 Mar 2026 18:11:01 +0000
Subject: [PATCH 0771/1827] [bot] Apply format changes

---
 include/bout/array.hxx | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/include/bout/array.hxx b/include/bout/array.hxx
index 000ded9616..82677fd38a 100644
--- a/include/bout/array.hxx
+++ b/include/bout/array.hxx
@@ -231,9 +231,7 @@ public:
    * Change shape of the container.
    * Invalidates contents.
    */
-  void reshape(std::tuple<size_type> new_shape) {
-    reallocate(std::get<0>(new_shape));
-  }
+  void reshape(std::tuple<size_type> new_shape) { reallocate(std::get<0>(new_shape)); }
 
   /*!
    * Holds a static variable which controls whether

From 05e5f138691bcaff6c890abfc5e2fdc0a7f8dfb9 Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Wed, 11 Mar 2026 18:11:02 +0000
Subject: [PATCH 0772/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index cc795d6d86..33bf3dd3fb 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -17,3 +17,4 @@ d1cfb8abd6aa5c76e6c1a4d7ab20929c65f8afc2
 ec69e8838be2dde140a915e50506f8e1ce3cb534
 f2bc0488a298f136294c523bc5ab4086d090059b
 1b4707187a3a85126338303dc766280b8fb2dc56
+b2e2f3575e68f771be2a4341af5fd14e2870469e

From 05fe2a81a188ca73d864a74a81fe385317015866 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Mar 2026 13:25:44 -0700
Subject: [PATCH 0773/1827] XZHermiteSpline: Move implementation_type to
 bout::details

Clang prints "internal linkage" warnings then fails to link when
implementation_type is in an anonymous namespace.

ChatGPT says "In C++, if a template argument involves a type/value
with internal linkage, the resulting template specialization (and
therefore its member functions) effectively become TU-local too.

Moving implementation_type to bout::details namespace resolves the
warnings and linker errors.
---
 include/bout/interpolation_xz.hxx            | 27 +++++-----
 src/mesh/interpolation/hermite_spline_xz.cxx | 54 ++++++++++----------
 2 files changed, 41 insertions(+), 40 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index d14a5eeca0..9121fcf806 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -1,8 +1,7 @@
 /**************************************************************************
- * Copyright 2010-2020 B.D.Dudson, S.Farley, P. Hill, J.T. Omotani, J.T. Parker,
- * M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -33,9 +32,11 @@
 #include "bout/petsclib.hxx"
 #endif
 
-namespace {
+namespace bout {
+namespace details {
 enum class implementation_type { new_weights, petsc, legacy };
 }
+}
 
 class Options;
 class GlobalField3DAccess;
@@ -144,7 +145,7 @@ public:
 /// but also degrades accuracy near maxima and minima.
 /// Perhaps should only impose near boundaries, since that is where
 /// problems most obviously occur.
-template <bool monotonic, implementation_type imp_type>
+template <bool monotonic, bout::details::implementation_type imp_type>
 class XZHermiteSplineBase : public XZInterpolation {
 protected:
   /// This is protected rather than private so that it can be
@@ -224,19 +225,19 @@ public:
 };
 
 using XZMonotonicHermiteSplineSerial =
-    XZHermiteSplineBase<true, implementation_type::new_weights>;
+  XZHermiteSplineBase<true, bout::details::implementation_type::new_weights>;
 using XZHermiteSplineSerial =
-    XZHermiteSplineBase<false, implementation_type::new_weights>;
+    XZHermiteSplineBase<false, bout::details::implementation_type::new_weights>;
 using XZMonotonicHermiteSplineLegacy =
-    XZHermiteSplineBase<true, implementation_type::legacy>;
-using XZHermiteSplineLegacy = XZHermiteSplineBase<false, implementation_type::legacy>;
+    XZHermiteSplineBase<true, bout::details::implementation_type::legacy>;
+using XZHermiteSplineLegacy = XZHermiteSplineBase<false, bout::details::implementation_type::legacy>;
 #if BOUT_HAS_PETSC
-using XZMonotonicHermiteSpline = XZHermiteSplineBase<true, implementation_type::petsc>;
-using XZHermiteSpline = XZHermiteSplineBase<false, implementation_type::petsc>;
+using XZMonotonicHermiteSpline = XZHermiteSplineBase<true, bout::details::implementation_type::petsc>;
+using XZHermiteSpline = XZHermiteSplineBase<false, bout::details::implementation_type::petsc>;
 #else
 using XZMonotonicHermiteSpline =
-    XZHermiteSplineBase<true, implementation_type::new_weights>;
-using XZHermiteSpline = XZHermiteSplineBase<false, implementation_type::new_weights>;
+    XZHermiteSplineBase<true, bout::details::implementation_type::new_weights>;
+using XZHermiteSpline = XZHermiteSplineBase<false, bout::details::implementation_type::new_weights>;
 #endif
 
 /// XZLagrange4pt interpolation class
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 48e7d2904e..69399efdfd 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -1,7 +1,7 @@
 /**************************************************************************
- * Copyright 2015-2018 B.D.Dudson, P. Hill
+ * Copyright 2015 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -109,7 +109,7 @@ class IndConverter {
   }
 };
 
-template <bool monotonic, implementation_type imp_type>
+template <bool monotonic, bout::details::implementation_type imp_type>
 XZHermiteSplineBase<monotonic, imp_type>::XZHermiteSplineBase(int y_offset, Mesh* meshin,
                                                               Options* options)
     : XZInterpolation(y_offset, meshin), h00_x(localmesh), h01_x(localmesh),
@@ -142,15 +142,15 @@ XZHermiteSplineBase<monotonic, imp_type>::XZHermiteSplineBase(int y_offset, Mesh
   h10_z.allocate();
   h11_z.allocate();
 
-  if constexpr (imp_type == implementation_type::new_weights
-                || imp_type == implementation_type::petsc) {
+  if constexpr (imp_type == bout::details::implementation_type::new_weights
+                || imp_type == bout::details::implementation_type::petsc) {
     newWeights.reserve(16);
     for (int w = 0; w < 16; ++w) {
       newWeights.emplace_back(localmesh);
       newWeights[w].allocate();
     }
   }
-  if constexpr (imp_type == implementation_type::petsc) {
+  if constexpr (imp_type == bout::details::implementation_type::petsc) {
 #if BOUT_HAS_PETSC
     petsclib = new PetscLib(
         &Options::root()["mesh:paralleltransform:xzinterpolation:hermitespline"]);
@@ -163,15 +163,15 @@ XZHermiteSplineBase<monotonic, imp_type>::XZHermiteSplineBase(int y_offset, Mesh
     gf3daccess = std::make_unique<GlobalField3DAccess>(localmesh);
     g3dinds.reallocate(localmesh->LocalNx, localmesh->LocalNy, localmesh->LocalNz);
   }
-  if constexpr (imp_type == implementation_type::new_weights
-                || imp_type == implementation_type::legacy) {
+  if constexpr (imp_type == bout::details::implementation_type::new_weights
+                || imp_type == bout::details::implementation_type::legacy) {
     if (localmesh->getNXPE() > 1) {
       throw BoutException("Require PETSc for MPI splitting in X");
     }
   }
 }
 
-template <bool monotonic, implementation_type imp_type>
+template <bool monotonic, bout::details::implementation_type imp_type>
 void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
     const Field3D& delta_x, const Field3D& delta_z,
     [[maybe_unused]] const std::string& region) {
@@ -251,8 +251,8 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
     h11_x[i] = (t_x * t_x * t_x) - (t_x * t_x);
     h11_z[i] = (t_z * t_z * t_z) - (t_z * t_z);
 
-    if constexpr (imp_type == implementation_type::new_weights
-                  || imp_type == implementation_type::petsc) {
+    if constexpr (imp_type == bout::details::implementation_type::new_weights
+                  || imp_type == bout::details::implementation_type::petsc) {
       for (int w = 0; w < 16; ++w) {
         newWeights[w][i] = 0;
       }
@@ -309,7 +309,7 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
       newWeights[13][i] -= h11_x[i] * h11_z[i] / 4;
       newWeights[7][i] -= h11_x[i] * h11_z[i] / 4;
       newWeights[5][i] += h11_x[i] * h11_z[i] / 4;
-      if (imp_type == implementation_type::petsc) {
+      if (imp_type == bout::details::implementation_type::petsc) {
 #if BOUT_HAS_PETSC
         PetscInt idxn[1] = {conv.fromLocalToGlobal(x, y + y_offset, z)};
         // output.write("debug: {:d} -> {:d}: {:d}:{:d} -> {:d}:{:d}\n",
@@ -340,7 +340,7 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
       g3dinds[i] = {gind.ind, gind.xp(1).ind, gind.zp(1).ind, gind.xp(1).zp(1).ind};
     }
   }
-  if constexpr (imp_type == implementation_type::petsc) {
+  if constexpr (imp_type == bout::details::implementation_type::petsc) {
 #if BOUT_HAS_PETSC
     MatAssemblyBegin(petscWeights, MAT_FINAL_ASSEMBLY);
     MatAssemblyEnd(petscWeights, MAT_FINAL_ASSEMBLY);
@@ -352,7 +352,7 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
   }
 }
 
-template <bool monotonic, implementation_type imp_type>
+template <bool monotonic, bout::details::implementation_type imp_type>
 void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(const Field3D& delta_x,
                                                            const Field3D& delta_z,
                                                            const BoutMask& mask,
@@ -377,7 +377,7 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(const Field3D& delta_
  *   (i, j+1, k+1)	h01_z + h10_z / 2
  *   (i, j+1, k+2)	h11_z / 2
  */
-template <bool monotonic, implementation_type imp_type>
+template <bool monotonic, bout::details::implementation_type imp_type>
 std::vector<ParallelTransform::PositionsAndWeights>
 XZHermiteSplineBase<monotonic, imp_type>::getWeightsForYApproximation(int i, int j, int k,
                                                                       int yoffset) {
@@ -397,7 +397,7 @@ XZHermiteSplineBase<monotonic, imp_type>::getWeightsForYApproximation(int i, int
           {i, j + yoffset, k_mod_p2, 0.5 * h11_z(i, j, k)}};
 }
 
-template <bool monotonic, implementation_type imp_type>
+template <bool monotonic, bout::details::implementation_type imp_type>
 Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
     const Field3D& f, [[maybe_unused]] const std::string& region) const {
 
@@ -411,7 +411,7 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
     gf = gf3daccess->communicate_asPtr(f);
   }
 
-  if constexpr (imp_type == implementation_type::petsc) {
+  if constexpr (imp_type == bout::details::implementation_type::petsc) {
 #if BOUT_HAS_PETSC
     BoutReal* ptr = nullptr;
     const BoutReal* cptr = nullptr;
@@ -439,7 +439,7 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
 #endif
   }
 
-  if constexpr (imp_type == implementation_type::new_weights) {
+  if constexpr (imp_type == bout::details::implementation_type::new_weights) {
     BOUT_FOR(i, getRegion(region)) {
       auto ic = i_corner[i];
       auto iyp = i.yp(y_offset);
@@ -463,7 +463,7 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
       ASSERT2(std::isfinite(f_interp[iyp]));
     }
   }
-  if constexpr (imp_type == implementation_type::legacy) {
+  if constexpr (imp_type == bout::details::implementation_type::legacy) {
     // Legacy interpolation
     // TODO(peter): Should we apply dirichlet BCs to derivatives?
     // Derivatives are used for tension and need to be on dimensionless
@@ -523,7 +523,7 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
   return f_interp;
 }
 
-template <bool monotonic, implementation_type imp_type>
+template <bool monotonic, bout::details::implementation_type imp_type>
 Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(const Field3D& f,
                                                               const Field3D& delta_x,
                                                               const Field3D& delta_z,
@@ -532,7 +532,7 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(const Field3D& f,
   return interpolate(f, region);
 }
 
-template <bool monotonic, implementation_type imp_type>
+template <bool monotonic, bout::details::implementation_type imp_type>
 Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(const Field3D& f,
                                                               const Field3D& delta_x,
                                                               const Field3D& delta_z,
@@ -543,11 +543,11 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(const Field3D& f,
 }
 
 // ensure they are instantiated
-template class XZHermiteSplineBase<true, implementation_type::new_weights>;
-template class XZHermiteSplineBase<false, implementation_type::new_weights>;
-template class XZHermiteSplineBase<true, implementation_type::legacy>;
-template class XZHermiteSplineBase<false, implementation_type::legacy>;
+template class XZHermiteSplineBase<true, bout::details::implementation_type::new_weights>;
+template class XZHermiteSplineBase<false, bout::details::implementation_type::new_weights>;
+template class XZHermiteSplineBase<true, bout::details::implementation_type::legacy>;
+template class XZHermiteSplineBase<false, bout::details::implementation_type::legacy>;
 #if BOUT_HAS_PETSC
-template class XZHermiteSplineBase<true, implementation_type::petsc>;
-template class XZHermiteSplineBase<false, implementation_type::petsc>;
+template class XZHermiteSplineBase<true, bout::details::implementation_type::petsc>;
+template class XZHermiteSplineBase<false, bout::details::implementation_type::petsc>;
 #endif

From 64e4285ec38569f66d31e589a4610cefd16d8076 Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Wed, 11 Mar 2026 20:29:43 +0000
Subject: [PATCH 0774/1827] [bot] Apply format changes

---
 include/bout/interpolation_xz.hxx            | 16 ++++++++++------
 src/mesh/interpolation/hermite_spline_xz.cxx |  3 ++-
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/include/bout/interpolation_xz.hxx b/include/bout/interpolation_xz.hxx
index 9121fcf806..1a8be9ef6b 100644
--- a/include/bout/interpolation_xz.hxx
+++ b/include/bout/interpolation_xz.hxx
@@ -36,7 +36,7 @@ namespace bout {
 namespace details {
 enum class implementation_type { new_weights, petsc, legacy };
 }
-}
+} // namespace bout
 
 class Options;
 class GlobalField3DAccess;
@@ -225,19 +225,23 @@ public:
 };
 
 using XZMonotonicHermiteSplineSerial =
-  XZHermiteSplineBase<true, bout::details::implementation_type::new_weights>;
+    XZHermiteSplineBase<true, bout::details::implementation_type::new_weights>;
 using XZHermiteSplineSerial =
     XZHermiteSplineBase<false, bout::details::implementation_type::new_weights>;
 using XZMonotonicHermiteSplineLegacy =
     XZHermiteSplineBase<true, bout::details::implementation_type::legacy>;
-using XZHermiteSplineLegacy = XZHermiteSplineBase<false, bout::details::implementation_type::legacy>;
+using XZHermiteSplineLegacy =
+    XZHermiteSplineBase<false, bout::details::implementation_type::legacy>;
 #if BOUT_HAS_PETSC
-using XZMonotonicHermiteSpline = XZHermiteSplineBase<true, bout::details::implementation_type::petsc>;
-using XZHermiteSpline = XZHermiteSplineBase<false, bout::details::implementation_type::petsc>;
+using XZMonotonicHermiteSpline =
+    XZHermiteSplineBase<true, bout::details::implementation_type::petsc>;
+using XZHermiteSpline =
+    XZHermiteSplineBase<false, bout::details::implementation_type::petsc>;
 #else
 using XZMonotonicHermiteSpline =
     XZHermiteSplineBase<true, bout::details::implementation_type::new_weights>;
-using XZHermiteSpline = XZHermiteSplineBase<false, bout::details::implementation_type::new_weights>;
+using XZHermiteSpline =
+    XZHermiteSplineBase<false, bout::details::implementation_type::new_weights>;
 #endif
 
 /// XZLagrange4pt interpolation class
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 69399efdfd..0aa1f2b066 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -544,7 +544,8 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(const Field3D& f,
 
 // ensure they are instantiated
 template class XZHermiteSplineBase<true, bout::details::implementation_type::new_weights>;
-template class XZHermiteSplineBase<false, bout::details::implementation_type::new_weights>;
+template class XZHermiteSplineBase<false,
+                                   bout::details::implementation_type::new_weights>;
 template class XZHermiteSplineBase<true, bout::details::implementation_type::legacy>;
 template class XZHermiteSplineBase<false, bout::details::implementation_type::legacy>;
 #if BOUT_HAS_PETSC

From 94effb60745f80c5942c524523cb427c23e486ac Mon Sep 17 00:00:00 2001
From: bendudson <219233+bendudson@users.noreply.github.com>
Date: Wed, 11 Mar 2026 20:29:44 +0000
Subject: [PATCH 0775/1827] [bot] Add last format changes commit to ignore file

---
 .git-blame-ignore-revs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index cc795d6d86..c70b34babe 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -17,3 +17,4 @@ d1cfb8abd6aa5c76e6c1a4d7ab20929c65f8afc2
 ec69e8838be2dde140a915e50506f8e1ce3cb534
 f2bc0488a298f136294c523bc5ab4086d090059b
 1b4707187a3a85126338303dc766280b8fb2dc56
+64e4285ec38569f66d31e589a4610cefd16d8076

From 7c5d9d8a36485d0ce79fa03c255bb57fb2acb559 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 11 Mar 2026 13:50:49 -0700
Subject: [PATCH 0776/1827] Options: Unit test of Tensor<int> to
 Tensor<BoutReal>

---
 tests/unit/sys/test_options.cxx | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx
index fb3e6a62c5..d4d803d685 100644
--- a/tests/unit/sys/test_options.cxx
+++ b/tests/unit/sys/test_options.cxx
@@ -1470,3 +1470,36 @@ TEST_F(OptionsTest, MatrixInt) {
   const auto matrix_out = options["int_matrix"].as<Matrix<int>>();
   ASSERT_EQ(matrix_out(nx - 1, ny - 1), matrix_in(nx - 1, ny - 1));
 }
+
+TEST_F(OptionsTest, TensorIntToTensorBoutReal) {
+  constexpr int nx = 2;
+  constexpr int ny = 3;
+  constexpr int nz = 4;
+
+  Tensor<int> t_int(nx, ny, nz);
+  int count = 0;
+  for (int i = 0; i < nx; ++i) {
+    for (int j = 0; j < ny; ++j) {
+      for (int k = 0; k < nz; ++k) {
+        t_int(i, j, k) = ++count;
+      }
+    }
+  }
+
+  Options option = t_int;
+
+  // Convert to Tensor<BoutReal>
+  Tensor<BoutReal> t_boutreal = option.as<Tensor<BoutReal>>();
+
+  std::tuple<int, int, int> expected_shape{nx, ny, nz};
+  ASSERT_EQ(expected_shape, t_boutreal.shape());
+
+  count = 0;
+  for (int i = 0; i < nx; ++i) {
+    for (int j = 0; j < ny; ++j) {
+      for (int k = 0; k < nz; ++k) {
+        ASSERT_FLOAT_EQ(t_boutreal(i, j, k), static_cast<BoutReal>(++count));
+      }
+    }
+  }
+}

From a16442e93770000175b22930eb8a252aa3065524 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 9 Aug 2024 13:50:41 +0200
Subject: [PATCH 0777/1827] Add comment

---
 src/mesh/boundary_standard.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 39a1ea3641..2e079f59b3 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -2165,7 +2165,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       } else {
         throw BoutException("Unrecognized location");
       }
-    } else {
+    } else { // loc == CELL_CENTRE
       for (; !bndry->isDone(); bndry->next1d()) {
 #if BOUT_USE_METRIC_3D
         for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {

From d0138af5acf852fb5741481bb109c7e83d60c0e8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 27 Sep 2024 15:55:15 +0200
Subject: [PATCH 0778/1827] Ensure we do not segfault if coords is not set

---
 include/bout/field.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 3f7f591528..1afef0aeae 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -294,6 +294,7 @@ inline void checkPositive(const T& f, const std::string& name = "field",
 template <typename T>
 inline T toFieldAligned(const T& f, const std::string& region = "RGN_ALL") {
   static_assert(bout::utils::is_Field_v<T>, "toFieldAligned only works on Fields");
+  ASSERT3(f.getCoordinates() != nullptr);
   return f.getCoordinates()->getParallelTransform().toFieldAligned(f, region);
 }
 
@@ -301,6 +302,7 @@ inline T toFieldAligned(const T& f, const std::string& region = "RGN_ALL") {
 template <typename T>
 inline T fromFieldAligned(const T& f, const std::string& region = "RGN_ALL") {
   static_assert(bout::utils::is_Field_v<T>, "fromFieldAligned only works on Fields");
+  ASSERT3(f.getCoordinates() != nullptr);
   return f.getCoordinates()->getParallelTransform().fromFieldAligned(f, region);
 }
 

From 3c0b658a1d59e3468c4749a7990bcbbd7ae46b7f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 16 Oct 2024 10:46:47 +0200
Subject: [PATCH 0779/1827] Preserve regionID in emptyFrom

---
 include/bout/field.hxx     | 3 ++-
 include/bout/field2d.hxx   | 3 ++-
 include/bout/field3d.hxx   | 3 ++-
 include/bout/fieldperp.hxx | 3 ++-
 src/field/field2d.cxx      | 3 ++-
 src/field/field3d.cxx      | 5 +++--
 src/field/fieldperp.cxx    | 2 +-
 7 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 1afef0aeae..c14489874a 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -189,7 +189,8 @@ inline bool areFieldsCompatible(const Field& field1, const Field& field2) {
 template <typename T>
 inline T emptyFrom(const T& f) {
   static_assert(bout::utils::is_Field_v<T>, "emptyFrom only works on Fields");
-  return T(f.getMesh(), f.getLocation(), {f.getDirectionY(), f.getDirectionZ()})
+  return T(f.getMesh(), f.getLocation(), {f.getDirectionY(), f.getDirectionZ()},
+           f.getRegionID())
       .allocate();
 }
 
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 906af38a1d..fc2f4b2bbd 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -68,7 +68,8 @@ public:
    */
   Field2D(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
           DirectionTypes directions_in = {YDirectionType::Standard,
-                                          ZDirectionType::Average});
+                                          ZDirectionType::Average},
+          std::optional<size_t> region = {});
 
   /*!
    * Copy constructor. After this both fields
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 54d9fb85c9..4c382fefbc 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -172,7 +172,8 @@ public:
    */
   Field3D(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
           DirectionTypes directions_in = {YDirectionType::Standard,
-                                          ZDirectionType::Standard});
+                                          ZDirectionType::Standard},
+          std::optional<size_t> regionID = {});
 
   /*!
    * Copy constructor
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 1f70089990..ef5e217bbc 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -59,7 +59,8 @@ public:
   FieldPerp(Mesh* fieldmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
             int yindex_in = -1,
             DirectionTypes directions_in = {YDirectionType::Standard,
-                                            ZDirectionType::Standard});
+                                            ZDirectionType::Standard},
+            std::optional<size_t> regionID = {});
 
   /*!
    * Copy constructor. After this the data
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index a046078585..078e1a48c6 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -39,7 +39,8 @@
 
 #include <cmath>
 
-Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in)
+Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in,
+                 std::optional<size_t> UNUSED(regionID))
     : Field(localmesh, location_in, directions_in) {
 
   if (fieldmesh) {
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index da7bd494c9..20d8a41fde 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -52,8 +52,9 @@
 #include "fmt/format.h"
 
 /// Constructor
-Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in)
-    : Field(localmesh, location_in, directions_in) {
+Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in,
+                 std::optional<size_t> regionID)
+    : Field(localmesh, location_in, directions_in), regionID{regionID} {
 #if BOUT_USE_TRACK
   name = "<F3D>";
 #endif
diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index d74a986473..938e3be245 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -34,7 +34,7 @@
 #include <bout/utils.hxx>
 
 FieldPerp::FieldPerp(Mesh* localmesh, CELL_LOC location_in, int yindex_in,
-                     DirectionTypes directions)
+                     DirectionTypes directions, std::optional<size_t> UNUSED(regionID))
     : Field(localmesh, location_in, directions), yindex(yindex_in) {
   if (fieldmesh) {
     nx = fieldmesh->LocalNx;

From 1b1b15b79d97ed63724b98d4185931ae056241ff Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Dec 2024 11:37:22 +0100
Subject: [PATCH 0780/1827] Allow setter to be chained

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 2710c9f21f..708db84529 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -304,6 +304,7 @@ cdef {{ field.field_type }} {{ field.fdd }}FromPtr(c.{{ field.field_type }}* i):
         dims_in = self._checkDims(dims, data.shape)
         cdef np.ndarray[double, mode="c", ndim={{ field.ndims }}] data_ = np.ascontiguousarray(data)
         c_set_all(self.cobj,&data_[{{ zeros }}])
+        return self
 
     def get(self):
         """

From 6c4ac3bd15b50790ff99d8679f5e64efcdc3be8f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Dec 2024 11:39:13 +0100
Subject: [PATCH 0781/1827] Expose more arguments of Laplacian

---
 tools/pylib/_boutpp_build/boutcpp.pxd.jinja |  4 +---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja  | 24 +++++++++++++++++----
 2 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
index 40aecb923e..6a6dc169a0 100644
--- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
+++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
@@ -90,9 +90,7 @@ cdef extern from "bout/fieldgroup.hxx":
 cdef extern from "bout/invert_laplace.hxx":
     cppclass Laplacian:
         @staticmethod
-        unique_ptr[Laplacian] create()
-        @staticmethod
-        unique_ptr[Laplacian] create(Options *)
+        unique_ptr[Laplacian] create(Options*, benum.CELL_LOC, Mesh*, Solver*)
         Field3D solve(Field3D,Field3D)
         void setCoefA(Field3D)
         void setCoefC(Field3D)
diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 708db84529..ea4637ba72 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -854,7 +854,13 @@ Compute the Laplacian inversion of objects.
 Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\perp x + ex\\nabla_x x + ez\\nabla_z x + a x = b
 """, uniquePtr=True) }}
 
-    def __init__(self, section=None):
+    Compute the Laplacian inversion of objects.
+
+    Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\perp x + ex\\nabla_x x + ez\\nabla_z x + a x = b
+    """
+    cdef unique_ptr[c.Laplacian] cobj
+    cdef c.bool isSelfOwned
+    def __init__(self, section=None, loc="CELL_CENTRE", mesh=None):
         """
         Initialiase a Laplacian solver
 
@@ -864,10 +870,20 @@ Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\p
             The section from the Option tree to take the options from
         """
         checkInit()
+        cdef c.Options* copt = NULL
         if section:
-           self.cobj = c.Laplacian.create((<Options?>section).cobj)
-        else:
-           self.cobj = c.Laplacian.create(NULL)
+            if isinstance(section, str):
+                section = Options.root(section)
+            copt = (<Options?>section).cobj
+        cdef benum.CELL_LOC cloc = benum.resolve_cell_loc(loc)
+        cdef c.Mesh* cmesh = NULL
+        if mesh:
+            cmesh = (<Mesh?>mesh).cobj
+        # Solver is not exposed yet
+        # cdef c.Solver* csolver = NULL
+        # if solver:
+        #     csolver = (<Solver?>solver).cobj
+        self.cobj = c.Laplacian.create(copt, cloc, cmesh, NULL)
         self.isSelfOwned = True
 
     def solve(self, Field3D x, Field3D guess):

From db7c8ab6172c750adcda28e0d4927d2d10eb1abe Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Dec 2024 11:40:38 +0100
Subject: [PATCH 0782/1827] Expose `Mesh::get` for Field3D

---
 tools/pylib/_boutpp_build/boutcpp.pxd.jinja |  1 +
 tools/pylib/_boutpp_build/boutpp.pyx.jinja  | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+)

diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
index 6a6dc169a0..4535d6e9ea 100644
--- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
+++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
@@ -63,6 +63,7 @@ cdef extern from "bout/mesh.hxx":
         int LocalNx
         int LocalNy
         Coordinates * getCoordinates()
+        int get(Field3D, const string)
 
 cdef extern from "bout/coordinates.hxx":
     cppclass Coordinates:
diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index ea4637ba72..d1e4bdc12d 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -754,6 +754,25 @@ cdef options
         msh.isSelfOwned = False
         return msh
 
+    def get(self, name):
+        """
+        Read a variable from the input source
+
+        Currently only supports reading a Field3D
+        """
+        checkInit()
+        cdef Field3D f3d = Field3D.fromMesh(self)
+        self.cobj.get(f3d.cobj[0], name.encode())
+        return f3d
+
+    def __dealloc__(self):
+        self._boutpp_dealloc()
+
+    def _boutpp_dealloc(self):
+        if self.cobj and self.isSelfOwned:
+            del self.cobj
+            self.cobj = NULL
+
     cdef getFactory(self):
         """
         Get the FieldFactory of the mesh

From c4334993e50abb38d532d2a7a8cab1238bdfba0d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Dec 2024 11:42:18 +0100
Subject: [PATCH 0783/1827] Avoid using kwargs, to avoid hiding typos

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index d1e4bdc12d..5041f16b4c 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -924,19 +924,20 @@ Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\p
         """
         return f3dFromObj(deref(self.cobj).solve(x.cobj[0],guess.cobj[0]))
 
-    def setCoefs(self, **kwargs):
+{% set coeffs="A C C1 C2 D Ex Ez".split() %}
+    def setCoefs(self, *{% for coeff in coeffs %}, {{coeff}}=None{% endfor %}):
         """
         Set the coefficients for the Laplacian solver.
         The coefficients A, C, C1, C2, D, Ex and Ez can be passed as keyword arguments
         """
 {% set coeffs="A C C1 C2 D Ex Ez".split() %}
 {% for coeff in coeffs %}
-        if "{{ coeff }}" in kwargs:
-            self.setCoef{{ coeff}}(kwargs["{{ coeff }}"])
+        if {{ coeff }} is not None:
+            self.setCoef{{ coeff}}({{ coeff }})
 {% endfor %}
 {% for coeff in coeffs %}
 
-    def setCoef{{ coeff }}(self,Field3D {{ coeff }}):
+    def setCoef{{ coeff }}(self, Field3D {{ coeff }}):
         """
         Set the "{{ coeff }}" coefficient of the Laplacian solver
 

From f970f5784940206f67acd25b219411a0a766158a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Dec 2024 11:42:41 +0100
Subject: [PATCH 0784/1827] Fix deallocation of Laplacian

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 5041f16b4c..83764b6995 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -949,6 +949,20 @@ Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\p
         deref(self.cobj).setCoef{{ coeff }}({{ coeff }}.cobj[0])
 {% endfor %}
 
+    def __dealloc__(self):
+        self._boutpp_dealloc()
+
+    def _boutpp_dealloc(self):
+        if self.cobj and self.isSelfOwned:
+            self.cobj.release()
+
+cdef class FieldFactory:
+    cdef c.FieldFactory * cobj
+    def __init__(self):
+        checkInit()
+        cobj=< c.FieldFactory*>0
+    def __dealloc__(self):
+        self._boutpp_dealloc()
 
 {{ class("FieldFactory", defaultSO=False) }}
 

From e220c66bc70d5641a0bff182b7c570ad01449381 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 11 Mar 2026 12:55:37 +0100
Subject: [PATCH 0785/1827] Prevent accidential overwriting of parallel slices

---
 src/field/field3d.cxx     | 1 +
 src/mesh/parallel/fci.cxx | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index da7bd494c9..2087bca582 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -343,6 +343,7 @@ Field3D& Field3D::operator=(const BoutReal val) {
 }
 
 void Field3D::calcParallelSlices() {
+  ASSERT1(areCalcParallelSlicesAllowed());
   getCoordinates()->getParallelTransform().calcParallelSlices(*this);
 }
 
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 152ffaed2d..fa965a335a 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -378,7 +378,7 @@ void FCITransform::checkInputGrid() {
 }
 
 void FCITransform::calcParallelSlices(Field3D& f) {
-
+  ASSERT1(f.areCalcParallelSlicesAllowed());
   ASSERT1(f.getDirectionY() == YDirectionType::Standard);
   // Only have forward_map/backward_map for CELL_CENTRE, so can only deal with
   // CELL_CENTRE inputs

From 8b6b7ebbd933c0bcde1ec36fe0c2efaaeea66bf4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Dec 2024 11:43:25 +0100
Subject: [PATCH 0786/1827] Set mesh for Fields in Laplacian

---
 src/invert/laplace/impls/petsc/petsc_laplace.cxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index e1595a2817..af65a1cd95 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -138,8 +138,9 @@ auto set_stencil(const Mesh& localmesh, bool fourth_order) {
 
 LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
                            [[maybe_unused]] Solver* solver)
-    : Laplacian(opt, loc, mesh_in), A(0.0), C1(1.0), C2(1.0), D(1.0), Ex(0.0), Ez(0.0),
-      issetD(false), issetC(false), issetE(false), comm(localmesh->getXcomm()),
+    : Laplacian(opt, loc, mesh_in), A(0.0, mesh_in), C1(1.0, mesh_in), C2(1.0, mesh_in),
+      D(1.0, mesh_in), Ex(0.0, mesh_in), Ez(0.0, mesh_in), issetD(false), issetC(false),
+      issetE(false), comm(localmesh->getXcomm()),
       opts(opt == nullptr ? &(Options::root()["laplace"]) : opt),
       // WARNING: only a few of these options actually make sense: see the
       // PETSc documentation to work out which they are (possibly

From 9b978ab37c2f9db0da25754000fb0ed3007efc2e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 7 Feb 2025 16:45:29 +0100
Subject: [PATCH 0787/1827] Handle C++ exception for more functions

---
 tools/pylib/_boutpp_build/boutcpp.pxd.jinja | 62 ++++++++++-----------
 1 file changed, 31 insertions(+), 31 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
index 4535d6e9ea..81b5e00658 100644
--- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
+++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
@@ -16,12 +16,12 @@ cdef extern from "bout/{{ field.header }}.hxx":
     cppclass {{ field.field_type }}:
         {{ field.field_type }}(Mesh * mesh);
         {{ field.field_type }}(const {{ field.field_type }} &)
-        double & operator()(int, int, int)
+        double & operator()(int, int, int) except +raise_bout_py_error
         int getNx()
         int getNy()
         int getNz()
         bool isAllocated()
-        void setLocation(benum.CELL_LOC)
+        void setLocation(benum.CELL_LOC) except +raise_bout_py_error
         benum.CELL_LOC getLocation()
         Mesh* getMesh()
 {% for boundaryMethod in field.boundaries %}
@@ -30,12 +30,12 @@ cdef extern from "bout/{{ field.header }}.hxx":
         void {{ boundaryMethod }}(double t)
 {% endfor %}
 {% for fun in "sqrt", "exp", "log", "sin", "cos", "abs" %}
-    {{ field.field_type }} {{ fun }}({{ field.field_type }})
+    {{ field.field_type }} {{ fun }}({{ field.field_type }}) except +raise_bout_py_error
 {% endfor %}
     double max({{ field.field_type }})
     double min({{ field.field_type }})
-    {{ field.field_type }} pow({{ field.field_type }},double)
-    {{ field.field_type }} & ddt({{ field.field_type }})
+    {{ field.field_type }} pow({{ field.field_type }}, double) except +raise_bout_py_error
+    {{ field.field_type }} & ddt({{ field.field_type }}) except +raise_bout_py_error
 {% endfor %}
 {% for vec in vecs %}
 cdef extern from "bout/{{ vec.header }}.hxx":
@@ -51,9 +51,9 @@ cdef extern from "bout/mesh.hxx":
     cppclass Mesh:
         Mesh()
         @staticmethod
-        Mesh * create(Options * option)
-        void load()
-        void communicate(FieldGroup&)
+        Mesh * create(Options * option) except +raise_bout_py_error
+        void load() except +raise_bout_py_error
+        void communicate(FieldGroup&) except +raise_bout_py_error
         int getNXPE()
         int getNYPE()
         int getXProcIndex()
@@ -62,8 +62,8 @@ cdef extern from "bout/mesh.hxx":
         int ystart
         int LocalNx
         int LocalNy
-        Coordinates * getCoordinates()
-        int get(Field3D, const string)
+        Coordinates * getCoordinates() except +raise_bout_py_error
+        int get(Field3D, const string) except +raise_bout_py_error
 
 cdef extern from "bout/coordinates.hxx":
     cppclass Coordinates:
@@ -79,10 +79,10 @@ cdef extern from "bout/coordinates.hxx":
         {{ metric_field }} G1, G2, G3
         {{ metric_field }} ShiftTorsion
         {{ metric_field }} IntShiftTorsion
-        int geometry()
-        int calcCovariant()
-        int calcContravariant()
-        int jacobian()
+        int geometry() except +raise_bout_py_error
+        int calcCovariant() except +raise_bout_py_error
+        int calcContravariant() except +raise_bout_py_error
+        int jacobian() except +raise_bout_py_error
 
 cdef extern from "bout/fieldgroup.hxx":
     cppclass FieldGroup:
@@ -91,8 +91,8 @@ cdef extern from "bout/fieldgroup.hxx":
 cdef extern from "bout/invert_laplace.hxx":
     cppclass Laplacian:
         @staticmethod
-        unique_ptr[Laplacian] create(Options*, benum.CELL_LOC, Mesh*, Solver*)
-        Field3D solve(Field3D,Field3D)
+        unique_ptr[Laplacian] create(Options*, benum.CELL_LOC, Mesh*, Solver*) except +raise_bout_py_error
+        Field3D solve(Field3D, Field3D) except +raise_bout_py_error
         void setCoefA(Field3D)
         void setCoefC(Field3D)
         void setCoefC1(Field3D)
@@ -103,12 +103,12 @@ cdef extern from "bout/invert_laplace.hxx":
         void setCoefEz(Field3D)
 
 cdef extern from "bout/difops.hxx":
-    Field3D Div_par(Field3D, benum.CELL_LOC, string)
-    Field3D Grad_par(Field3D, benum.CELL_LOC, string)
-    Field3D Laplace(Field3D)
-    Field3D Vpar_Grad_par(Field3D, Field3D, benum.CELL_LOC, string)
-    Field3D bracket(Field3D,Field3D, benum.BRACKET_METHOD, benum.CELL_LOC)
-    Field3D Delp2(Field3D)
+    Field3D Div_par(Field3D, benum.CELL_LOC, string) except +raise_bout_py_error
+    Field3D Grad_par(Field3D, benum.CELL_LOC, string) except +raise_bout_py_error
+    Field3D Laplace(Field3D) except +raise_bout_py_error
+    Field3D Vpar_Grad_par(Field3D, Field3D, benum.CELL_LOC, string) except +raise_bout_py_error
+    Field3D bracket(Field3D,Field3D, benum.BRACKET_METHOD, benum.CELL_LOC) except +raise_bout_py_error
+    Field3D Delp2(Field3D) except +raise_bout_py_error
 
 cdef extern from "bout/derivs.hxx":
 {% for d in "XYZ" %}
@@ -130,16 +130,16 @@ cdef extern from "bout/interpolation.hxx":
 
 cdef extern from "bout/field_factory.hxx":
     cppclass FieldFactory:
-        FieldFactory(Mesh*,Options*)
-        Field3D create3D(string bla, Options * o, Mesh * m,benum.CELL_LOC loc, double t)
+        FieldFactory(Mesh*,Options*) except +raise_bout_py_error
+        Field3D create3D(string bla, Options * o, Mesh * m,benum.CELL_LOC loc, double t) except +raise_bout_py_error
 
 cdef extern from "bout/solver.hxx":
     cppclass Solver:
         @staticmethod
-        Solver * create()
-        void setModel(PhysicsModel *)
-        void add(Field3D, char * name)
-        void solve()
+        Solver * create() except +raise_bout_py_error
+        void setModel(PhysicsModel *) except +raise_bout_py_error
+        void add(Field3D, char * name) except +raise_bout_py_error
+        void solve() except +raise_bout_py_error
 
 cdef extern from "bout/physicsmodel.hxx":
     cppclass PhysicsModel:
@@ -165,8 +165,8 @@ cdef extern from "bout/output.hxx":
     ConditionalOutput output_info
 
 cdef extern from "bout/vecops.hxx":
-    Vector3D Grad(const Field3D& f, benum.CELL_LOC, string)
-    Vector3D Grad_perp(const Field3D& f, benum.CELL_LOC, string)
+    Vector3D Grad(const Field3D& f, benum.CELL_LOC, string) except +raise_bout_py_error
+    Vector3D Grad_perp(const Field3D& f, benum.CELL_LOC, string) except +raise_bout_py_error
 
 cdef extern from "bout/vector3d.hxx":
-    Vector3D cross(Vector3D, Vector3D)
+    Vector3D cross(Vector3D, Vector3D) except +raise_bout_py_error

From 31c43527c2fd27b0cae0b43278a9784ada63b9b1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 10 Feb 2025 10:20:13 +0100
Subject: [PATCH 0788/1827] Expose LaplaceXZ

---
 tools/pylib/_boutpp_build/boutcpp.pxd.jinja |  8 +++
 tools/pylib/_boutpp_build/boutpp.pyx.jinja  | 58 +++++++++++++++++++++
 2 files changed, 66 insertions(+)

diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
index 81b5e00658..9de826384b 100644
--- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
+++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
@@ -102,6 +102,14 @@ cdef extern from "bout/invert_laplace.hxx":
         void setCoefEy(Field3D)
         void setCoefEz(Field3D)
 
+cdef extern from "bout/invert/laplacexz.hxx":
+    cppclass LaplaceXZ:
+        LaplaceXZ(Mesh*, Options*, benum.CELL_LOC)
+        void setCoefs(const Field3D& A, const Field3D& B) except +raise_bout_py_error
+        Field3D solve(const Field3D& b, const Field3D& x0) except +raise_bout_py_error
+        @staticmethod
+        unique_ptr[LaplaceXZ] create(Mesh* m, Options* opt, benum.CELL_LOC loc)
+
 cdef extern from "bout/difops.hxx":
     Field3D Div_par(Field3D, benum.CELL_LOC, string) except +raise_bout_py_error
     Field3D Grad_par(Field3D, benum.CELL_LOC, string) except +raise_bout_py_error
diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 83764b6995..ca767e3f37 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -964,6 +964,64 @@ cdef class FieldFactory:
     def __dealloc__(self):
         self._boutpp_dealloc()
 
+{{ class("LaplaceXZ", comment="""
+LaplaceXZ inversion solver
+
+Compute the Laplacian inversion of objects.
+
+Equation solved is:  \\nabla\\cdot\\left( A \\nabla_\\perp f \\right) + Bf = b
+""", uniquePtr=True) }}
+
+    def __init__(self, section=None, loc="CELL_CENTRE", mesh=None):
+        """
+        Initialiase a Laplacian solver
+
+        Parameters
+        ----------
+        section : Options, optional
+            The section from the Option tree to take the options from
+        """
+        checkInit()
+        cdef c.Options* copt = NULL
+        if section:
+            if isinstance(section, str):
+                section = Options.root(section)
+            copt = (<Options?>section).cobj
+        cdef benum.CELL_LOC cloc = benum.resolve_cell_loc(loc)
+        cdef c.Mesh* cmesh = NULL
+        if mesh:
+            cmesh = (<Mesh?>mesh).cobj
+        self.cobj = c.LaplaceXZ.create(cmesh, copt, cloc)
+        self.isSelfOwned = True
+
+    def solve(self, Field3D x, Field3D guess):
+        """
+        Calculate the Laplacian inversion
+
+        Parameters
+        ----------
+        x : Field3D
+            Field to be inverted
+        guess : Field3D
+            initial guess for the inversion
+
+
+        Returns
+        -------
+        Field3D
+            the inversion of x, where guess is a guess to start with
+        """
+        return f3dFromObj(deref(self.cobj).solve(x.cobj[0],guess.cobj[0]))
+
+    def setCoefs(self, *, Field3D A, Field3D B):
+        """
+        Set the coefficients for the Laplacian solver.
+        The coefficients A and B have both to be passed.
+        A and B have to be Field3D.
+        """
+        deref(self.cobj).setCoefs(A.cobj[0], B.cobj[0])
+
+
 {{ class("FieldFactory", defaultSO=False) }}
 
 cdef void callback(void * parameter, void * method) with gil:

From 2e36b419027d4e40added8ce75bc7929bac3e750 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 10 Feb 2025 10:20:37 +0100
Subject: [PATCH 0789/1827] Formatting fixes

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index ca767e3f37..54f247f22b 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -800,13 +800,13 @@ cdef options
         norm : float
             The length with which to rescale
         """
-        if self.isNormalised>0:
-            t=norm
-            norm=norm/self.isNormalised
-            self.isNormalised=t
-        c_mesh_normalise(self.cobj,norm)
+        if self.isNormalised > 0:
+            t = norm
+            norm = norm/self.isNormalised
+            self.isNormalised = t
+        c_mesh_normalise(self.cobj, norm)
 
-    def communicate(self,*args):
+    def communicate(self, *args):
         """
         Communicate (MPI) the boundaries of the Field3Ds with neighbours
 
@@ -1563,8 +1563,8 @@ def create3D(string, Mesh msh=None,outloc="CELL_DEFAULT",time=0):
     cdef benum.CELL_LOC outloc_=benum.resolve_cell_loc(outloc)
     if msh is None:
         msh=Mesh.getGlobal()
-    cdef FieldFactory fact=msh.getFactory()
-    cdef c.string str_=string.encode()
+    cdef FieldFactory fact = msh.getFactory()
+    cdef c.string str_ = string.encode()
     return f3dFromObj(
         (<FieldFactory>fact).cobj.create3D(str_,<c.Options*>0,<c.Mesh*>0
                                            ,outloc_,time))

From e17ce9bfa3967832cb73f120506012e92dae326a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 10 Feb 2025 10:20:57 +0100
Subject: [PATCH 0790/1827] Expose Mesh::get for Field3D

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 54f247f22b..d2c5b32a7c 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -831,6 +831,20 @@ cdef options
             self._coords = coordsFromPtr(self.cobj.getCoordinates())
         return self._coords
 
+    def get(self, name, default=None):
+        """
+        Load a variable from the grid source
+
+        If no default is given, and the variable is not found, an error is raised.
+        """
+        cdef c.string cstr = name.encode()
+        cdef Field3D defaultfield = default if isinstance(default, Field3D) else Field3D.fromMesh(self)
+        if deref(self.cobj).get(deref(defaultfield.cobj), cstr):
+            if default is None:
+                raise ValueError(f"No default value for {name} given and not set for this mesh")
+            return default
+        return defaultfield
+
 
 cdef Mesh meshFromPtr(c.Mesh * obj):
     mesh = Mesh()

From cc3e1122918a98967870a583af2c7107f05d7249 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 30 Jan 2026 10:08:55 +0100
Subject: [PATCH 0791/1827] Only generate grids once

---
 tests/MMS/spatial/fci/runtest | 34 ++++++++++++++++++----------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index c76ad27833..9dd4d1817f 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -16,7 +16,7 @@ import boutconfig as conf
 import zoidberg as zb
 from boutdata.collect import collect
 from boututils.run_wrapper import build_and_log, launch_safe
-from numpy import arange, array, linspace, log, polyfit
+from numpy import array, linspace, log, polyfit
 
 # Global parameters
 DIRECTORY = "data"
@@ -70,9 +70,12 @@ def assert_convergence(error, dx, name, expected) -> bool:
     return success
 
 
-def run_fci_operators(
-    nslice: int, nz: int, yperiodic: bool, name: str
-) -> dict[str, float]:
+def make_grids():
+    for nz in NLIST:
+        make_grid(nz)
+
+
+def make_grid(nz: int):
     # Define the magnetic field using new poloidal gridding method
     # Note that the Bz and Bzprime parameters here must be the same as in mms.py
     field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
@@ -81,15 +84,11 @@ def run_fci_operators(
     # Set the ylength and y locations
     ylength = 10.0
 
-    if yperiodic:
-        ycoords = linspace(0.0, ylength, nz, endpoint=False)
-    else:
-        # Doesn't include the end points
-        ycoords = (arange(nz) + 0.5) * ylength / float(nz)
+    ycoords = linspace(0.0, ylength, nz, endpoint=False)
 
     # Create the grid
-    grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
-    maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
+    grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=True)
+    maps = zb.make_maps(grid, field, nslice=1, quiet=True, MXG=1)
     zb.write_maps(
         grid,
         field,
@@ -97,10 +96,14 @@ def run_fci_operators(
         new_names=False,
         metric2d=conf.isMetric2D(),
         quiet=True,
+        gridfile=f"mesh.{nz}.fci.nc",
     )
 
+
+def run_fci_operators(nslice: int, nz: int, name: str) -> dict[str, float]:
+
     # Command to run
-    args = f"MZ={nz} MYG={nslice} mesh:paralleltransform:y_periodic={yperiodic} {name}"
+    args = f"MYG={nslice} {name} mesh:file=mesh.{nz}.fci.nc"
     cmd = f"./fci_mms {args}"
     print(f"Running command: {cmd}", end="")
 
@@ -143,14 +146,13 @@ def check_fci_operators(name: str, case: dict) -> bool:
     failures = []
 
     nslice = case["nslice"]
-    yperiodic = case["yperiodic"]
     order = case["order"]
     args = case["args"]
 
     all_errors = []
 
     for n in NLIST:
-        errors = run_fci_operators(nslice, n, yperiodic, args)
+        errors = run_fci_operators(nslice, n, args)
         all_errors.append(errors)
 
         for operator in OPERATORS:
@@ -227,13 +229,11 @@ if __name__ == "__main__":
         "nslice=1 hermitespline": {
             "nslice": 1,
             "order": 2,
-            "yperiodic": True,
             "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=hermitespline",
         },
         "nslice=1 lagrange4pt": {
             "nslice": 1,
             "order": 2,
-            "yperiodic": True,
             "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=lagrange4pt",
         },
         "nslice=1 monotonichermitespline": {
@@ -249,6 +249,8 @@ if __name__ == "__main__":
         },
     }
 
+    make_grids()
+
     for name, case in cases.items():
         error2, failures_ = check_fci_operators(name, case)
         case.update(error2)

From 2c0ddd61a3abde70767a88b43986243db7cb72c0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:55:03 +0100
Subject: [PATCH 0792/1827] Remove stray doc string

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index d2c5b32a7c..3015fe1136 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -886,11 +886,6 @@ Compute the Laplacian inversion of objects.
 
 Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\perp x + ex\\nabla_x x + ez\\nabla_z x + a x = b
 """, uniquePtr=True) }}
-
-    Compute the Laplacian inversion of objects.
-
-    Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\perp x + ex\\nabla_x x + ez\\nabla_z x + a x = b
-    """
     cdef unique_ptr[c.Laplacian] cobj
     cdef c.bool isSelfOwned
     def __init__(self, section=None, loc="CELL_CENTRE", mesh=None):

From 1d6946f400fadb00d39b465baa2c2f121b614701 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 12:55:54 +0100
Subject: [PATCH 0793/1827] Remove duplicate definitions

---
 tools/pylib/_boutpp_build/boutpp.pyx.jinja | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 3015fe1136..587aa7d6a5 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -886,8 +886,6 @@ Compute the Laplacian inversion of objects.
 
 Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\perp x + ex\\nabla_x x + ez\\nabla_z x + a x = b
 """, uniquePtr=True) }}
-    cdef unique_ptr[c.Laplacian] cobj
-    cdef c.bool isSelfOwned
     def __init__(self, section=None, loc="CELL_CENTRE", mesh=None):
         """
         Initialiase a Laplacian solver
@@ -965,14 +963,6 @@ Equation solved is: d\\nabla^2_\\perp x + (1/c1)\\nabla_perp c2\\cdot\\nabla_\\p
         if self.cobj and self.isSelfOwned:
             self.cobj.release()
 
-cdef class FieldFactory:
-    cdef c.FieldFactory * cobj
-    def __init__(self):
-        checkInit()
-        cobj=< c.FieldFactory*>0
-    def __dealloc__(self):
-        self._boutpp_dealloc()
-
 {{ class("LaplaceXZ", comment="""
 LaplaceXZ inversion solver
 

From f5ca1d06ae7779dacc2e831f15c7356d37307e0b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 26 Jun 2025 10:53:25 +0200
Subject: [PATCH 0794/1827] Introduce Field3DParallel

Field3DParallel enforces that parallel derivatives can be taken.
This means for FCI, parallel fields are present.
It also ensures that if an operation is taken on such a field, the
parallel fields are retained.
This replaces part of fci-automagic, that always retained parallel
fields on operations.
---
 include/bout/field3d.hxx         |  53 ++-
 src/field/field3d.cxx            |  10 +
 src/field/gen_fieldops.jinja     |  58 ++-
 src/field/gen_fieldops.py        |  26 +-
 src/field/generated_fieldops.cxx | 704 +++++++++++++++++++++++++++++--
 5 files changed, 806 insertions(+), 45 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 54d9fb85c9..be4e2d6ef0 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -517,7 +517,7 @@ public:
   bool areCalcParallelSlicesAllowed() const { return _allowCalcParallelSlices; };
   void disallowCalcParallelSlices() { _allowCalcParallelSlices = false; };
 
-private:
+protected:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
   int nx{-1}, ny{-1}, nz{-1};
 
@@ -692,4 +692,55 @@ bool operator==(const Field3D& a, const Field3D& b);
 /// Output a string describing a Field3D to a stream
 std::ostream& operator<<(std::ostream& out, const Field3D& value);
 
+inline Field3D copy(const Field3D& f) {
+  Field3D result{f};
+  result.allocate();
+  for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
+    result.yup(i).allocate();
+    result.ydown(i).allocate();
+  }
+  return result;
+}
+
+class Field3DParallel : public Field3D {
+public:
+  template <class... Types>
+  Field3DParallel(Types... args) : Field3D(&args...) {
+    ensureFieldAligned();
+  }
+  Field3DParallel(Field3D&& f3d) : Field3D(std::move(f3d)) { ensureFieldAligned(); }
+  Field3DParallel(const Field3D& f3d) : Field3D(f3d) { ensureFieldAligned(); }
+  // Explicitly needed, as DirectionTypes is sometimes constructed from a
+  // brace enclosed list
+  Field3DParallel(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
+                  DirectionTypes directions_in = {YDirectionType::Standard,
+                                                  ZDirectionType::Standard},
+                  std::optional<size_t> regionID = {})
+      : Field3D(localmesh, location_in, directions_in, regionID) {
+    ensureFieldAligned();
+  }
+  Field3DParallel(Array<BoutReal> data, Mesh* localmesh, CELL_LOC location = CELL_CENTRE,
+                  DirectionTypes directions_in = {YDirectionType::Standard,
+                                                  ZDirectionType::Standard})
+      : Field3D(std::move(data), localmesh, location, directions_in) {
+    ensureFieldAligned();
+  }
+
+  Field3DParallel& operator*=(const Field3D&);
+  Field3DParallel& operator/=(const Field3D&);
+  Field3DParallel& operator+=(const Field3D&);
+  Field3DParallel& operator-=(const Field3D&);
+  Field3DParallel& operator*=(const Field3DParallel&);
+  Field3DParallel& operator/=(const Field3DParallel&);
+  Field3DParallel& operator+=(const Field3DParallel&);
+  Field3DParallel& operator-=(const Field3DParallel&);
+  Field3DParallel& operator*=(BoutReal);
+  Field3DParallel& operator/=(BoutReal);
+  Field3DParallel& operator+=(BoutReal);
+  Field3DParallel& operator-=(BoutReal);
+
+private:
+  void ensureFieldAligned();
+};
+
 #endif /* BOUT_FIELD3D_H */
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index da7bd494c9..c5d157788d 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -910,3 +910,13 @@ void Field3D::_track(const BoutReal& change, std::string operation) {
       {"trace", trace},
   });
 }
+
+void Field3DParallel::ensureFieldAligned() {
+  if (isFci()) {
+    ASSERT2(hasParallelSlices());
+  } else {
+    if (getDirectionY() != YDirectionType::Aligned) {
+      *this = toFieldAligned(*this);
+    }
+  }
+}
diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index 5476242d50..46c9fcad68 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -8,14 +8,41 @@
   checkData({{lhs.name}});
   checkData({{rhs.name}});
 
-  {% if out == "Field3D" %}
-    {% if lhs == rhs == "Field3D" %}
+  {% if out.region_type == "3D" %}
+    {% if lhs.region_type == rhs.region_type == "3D" %}
       {{out.name}}.setRegion({{lhs.name}}.getMesh()->getCommonRegion({{lhs.name}}.getRegionID(),
                                                                      {{rhs.name}}.getRegionID()));
-    {% elif lhs == "Field3D" %}
+      {% if out == "Field3DParallel" %}
+      if ({{lhs.name}}.isFci()) {
+        {{out.name}}.splitParallelSlices();
+        for (size_t i{0} ; i < {{lhs.name}}.numberParallelSlices() ; ++i) {
+          {{out.name}}.yup(i) = {{lhs.name}}.yup(i) {{operator}} {{rhs.name}}.yup(i);
+          {{out.name}}.ydown(i) = {{lhs.name}}.ydown(i) {{operator}} {{rhs.name}}.ydown(i);
+        }
+      }
+      {% endif %}
+    {% elif lhs.region_type == "3D" %}
       {{out.name}}.setRegion({{lhs.name}}.getRegionID());
-    {% elif rhs == "Field3D" %}
+      {% if rhs == "BoutReal" and out == "Field3DParallel" %}
+      if ({{lhs.name}}.isFci()) {
+        {{out.name}}.splitParallelSlices();
+	for (size_t i{0} ; i < {{lhs.name}}.numberParallelSlices() ; ++i) {
+          {{out.name}}.yup(i) = {{lhs.name}}.yup(i) {{operator}} {{rhs.name}};
+          {{out.name}}.ydown(i) = {{lhs.name}}.ydown(i) {{operator}} {{rhs.name}};
+        }
+      }
+      {% endif %}
+    {% elif rhs.region_type == "3D" %}
       {{out.name}}.setRegion({{rhs.name}}.getRegionID());
+      {% if lhs == "BoutReal" and rhs == "Field3DParallel" %}
+      if ({{rhs.name}}.isFci()) {
+        {{out.name}}.splitParallelSlices();
+	for (size_t i{0} ; i < {{rhs.name}}.numberParallelSlices() ; ++i) {
+          {{out.name}}.yup(i) = {{lhs.name}} {{operator}} {{rhs.name}}.yup(i);
+          {{out.name}}.ydown(i) = {{lhs.name}} {{operator}} {{rhs.name}}.ydown(i);
+        }
+      }
+      {% endif %}
     {% endif %}
   {% endif %}
 
@@ -75,17 +102,26 @@
       ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
     {% endif %}
 
-    {% if (lhs == "Field3D") %}
-      // Delete existing parallel slices. We don't copy parallel slices, so any
+    {% if lhs == "Field3D" %}
+      // Delete existing parallel slices. We don't update parallel slices, so any
       // that currently exist will be incorrect.
       clearParallelSlices();
-
+    {% endif %}
+    {% if lhs == "Field3DParallel" and (rhs.region_type == "3D" or rhs == "BoutReal") %}
+      if (this->isFci()) {
+	for (size_t i{0} ; i < yup_fields.size() ; ++i) {
+          yup(i) {{operator}}= {{rhs.name}}{% if rhs == "Field3D" %}.yup(i){% endif %};
+          ydown(i) {{operator}}= {{rhs.name}}{% if rhs == "Field3D" %}.ydown(i){% endif %};
+        }
+      } else {
+        clearParallelSlices();
+      }
     {% endif %}
     checkData(*this);
     checkData({{rhs.name}});
 
-    {% if lhs == rhs == "Field3D" %}
-      regionID = fieldmesh->getCommonRegion(regionID, {{rhs.name}}.regionID);
+    {% if lhs.region_type == rhs.region_type == "3D" %}
+      regionID = fieldmesh->getCommonRegion(regionID, {{rhs.name}}.getRegionID());
     {% endif %}
 
 
@@ -129,14 +165,14 @@
     }
   {% endif %}
 
-  {% if lhs == "Field3D" %}
+  {% if lhs.region_type == "3D" %}
     track(rhs, "operator{{operator}}=");
   {% endif %}
 
     checkData(*this);
 
   } else {
-  {% if lhs == "Field3D" %}
+  {% if lhs.region_type == "3D" %}
     track(rhs, "operator{{operator}}=");
   {% endif %}
     (*this) = (*this) {{operator}} {{rhs.name}};
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 3e07d6fec4..1560a82dc5 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -103,7 +103,7 @@ def __init__(
         self.mixed_base_ind_var = mixed_base_ind_var
         # Note region_type isn't actually used currently but
         # may be useful in future.
-        if self.field_type == "Field3D":
+        if "Field3D" in self.field_type:
             self.region_type = "3D"
         elif self.field_type == "Field2D":
             self.region_type = "2D"
@@ -183,6 +183,8 @@ def returnType(f1, f2):
         return copy(f1)
     elif f1 == "FieldPerp" or f2 == "FieldPerp":
         return copy(fieldPerp)
+    elif f1 == "Field3DParallel" or f2 == "Field3DParallel":
+        return copy(field3DPar)
     else:
         return copy(field3D)
 
@@ -226,6 +228,13 @@ def returnType(f1, f2):
         jz_var=jz_var,
         mixed_base_ind_var=mixed_base_ind_var,
     )
+    field3DPar = Field(
+        "Field3DParallel",
+        ["x", "y", "z"],
+        index_var=index_var,
+        jz_var=jz_var,
+        mixed_base_ind_var=mixed_base_ind_var,
+    )
     field2D = Field(
         "Field2D",
         ["x", "y"],
@@ -248,7 +257,8 @@ def returnType(f1, f2):
         mixed_base_ind_var=mixed_base_ind_var,
     )
 
-    fields = [field3D, field2D, fieldPerp, boutreal]
+    fields = (field3D, field2D, fieldPerp, boutreal)
+    fields2 = (field3D, field3DPar, boutreal)
 
     with smart_open(args.filename, "w") as f:
         f.write(header)
@@ -258,10 +268,16 @@ def returnType(f1, f2):
 
     template = env.get_template("gen_fieldops.jinja")
 
-    for lhs, rhs in itertools.product(fields, fields):
-        # We don't have to define BoutReal BoutReal operations
-        if lhs == rhs == "BoutReal":
+    # We don't have to define BoutReal BoutReal operations
+    done = [(boutreal, boutreal)]
+    for lhs, rhs in itertools.chain(
+        itertools.product(fields, fields),
+        itertools.product((field3D, field3DPar, boutreal), (field3D, field3DPar)),
+    ):
+        if (lhs, rhs) in done:
             continue
+        done.append((lhs, rhs))
+
         rhs = copy(rhs)
         lhs = copy(lhs)
 
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 24bfde425c..b3b81f07b8 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -31,14 +31,13 @@ Field3D& Field3D::operator*=(const Field3D& rhs) {
   if (data.unique()) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
 
@@ -78,14 +77,13 @@ Field3D& Field3D::operator/=(const Field3D& rhs) {
   if (data.unique()) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
 
@@ -125,14 +123,13 @@ Field3D& Field3D::operator+=(const Field3D& rhs) {
   if (data.unique()) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
 
@@ -172,14 +169,13 @@ Field3D& Field3D::operator-=(const Field3D& rhs) {
   if (data.unique()) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
-    regionID = fieldmesh->getCommonRegion(regionID, rhs.regionID);
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
 
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
 
@@ -224,10 +220,9 @@ Field3D& Field3D::operator*=(const Field2D& rhs) {
   if (data.unique()) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
@@ -280,10 +275,9 @@ Field3D& Field3D::operator/=(const Field2D& rhs) {
   if (data.unique()) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
@@ -336,10 +330,9 @@ Field3D& Field3D::operator+=(const Field2D& rhs) {
   if (data.unique()) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
@@ -391,10 +384,9 @@ Field3D& Field3D::operator-=(const Field2D& rhs) {
   if (data.unique()) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
@@ -519,10 +511,9 @@ Field3D& Field3D::operator*=(const BoutReal rhs) {
   // otherwise just call the non-inplace version
   if (data.unique()) {
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
@@ -563,10 +554,9 @@ Field3D& Field3D::operator/=(const BoutReal rhs) {
   // otherwise just call the non-inplace version
   if (data.unique()) {
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
@@ -607,10 +597,9 @@ Field3D& Field3D::operator+=(const BoutReal rhs) {
   // otherwise just call the non-inplace version
   if (data.unique()) {
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
@@ -650,10 +639,9 @@ Field3D& Field3D::operator-=(const BoutReal rhs) {
   // otherwise just call the non-inplace version
   if (data.unique()) {
 
-    // Delete existing parallel slices. We don't copy parallel slices, so any
+    // Delete existing parallel slices. We don't update parallel slices, so any
     // that currently exist will be incorrect.
     clearParallelSlices();
-
     checkData(*this);
     checkData(rhs);
 
@@ -1960,3 +1948,663 @@ FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) {
   checkData(result);
   return result;
 }
+
+// Provide the C++ wrapper for multiplication of Field3D and Field3DParallel
+Field3DParallel operator*(const Field3D& lhs, const Field3DParallel& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(rhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) * rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ wrapper for division of Field3D and Field3DParallel
+Field3DParallel operator/(const Field3D& lhs, const Field3DParallel& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(rhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) / rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] / rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ wrapper for addition of Field3D and Field3DParallel
+Field3DParallel operator+(const Field3D& lhs, const Field3DParallel& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(rhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) + rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] + rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ wrapper for subtraction of Field3D and Field3DParallel
+Field3DParallel operator-(const Field3D& lhs, const Field3DParallel& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(rhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) - rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] - rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ wrapper for multiplication of Field3DParallel and Field3D
+Field3DParallel operator*(const Field3DParallel& lhs, const Field3D& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) * rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by multiplication with Field3D
+Field3DParallel& Field3DParallel::operator*=(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) *= rhs.yup(i);
+        ydown(i) *= rhs.ydown(i);
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
+
+    track(rhs, "operator*=");
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator*=");
+    (*this) = (*this) * rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for division of Field3DParallel and Field3D
+Field3DParallel operator/(const Field3DParallel& lhs, const Field3D& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) / rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] / rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by division with Field3D
+Field3DParallel& Field3DParallel::operator/=(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) /= rhs.yup(i);
+        ydown(i) /= rhs.ydown(i);
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
+
+    track(rhs, "operator/=");
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator/=");
+    (*this) = (*this) / rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for addition of Field3DParallel and Field3D
+Field3DParallel operator+(const Field3DParallel& lhs, const Field3D& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) + rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] + rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by addition with Field3D
+Field3DParallel& Field3DParallel::operator+=(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) += rhs.yup(i);
+        ydown(i) += rhs.ydown(i);
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
+
+    track(rhs, "operator+=");
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator+=");
+    (*this) = (*this) + rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for subtraction of Field3DParallel and Field3D
+Field3DParallel operator-(const Field3DParallel& lhs, const Field3D& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) - rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] - rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by subtraction with Field3D
+Field3DParallel& Field3DParallel::operator-=(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) -= rhs.yup(i);
+        ydown(i) -= rhs.ydown(i);
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
+
+    track(rhs, "operator-=");
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator-=");
+    (*this) = (*this) - rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for multiplication of Field3DParallel and Field3DParallel
+Field3DParallel operator*(const Field3DParallel& lhs, const Field3DParallel& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) * rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by multiplication with Field3DParallel
+Field3DParallel& Field3DParallel::operator*=(const Field3DParallel& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) *= rhs;
+        ydown(i) *= rhs;
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
+
+    track(rhs, "operator*=");
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator*=");
+    (*this) = (*this) * rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for division of Field3DParallel and Field3DParallel
+Field3DParallel operator/(const Field3DParallel& lhs, const Field3DParallel& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) / rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] / rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by division with Field3DParallel
+Field3DParallel& Field3DParallel::operator/=(const Field3DParallel& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) /= rhs;
+        ydown(i) /= rhs;
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
+
+    track(rhs, "operator/=");
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator/=");
+    (*this) = (*this) / rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for addition of Field3DParallel and Field3DParallel
+Field3DParallel operator+(const Field3DParallel& lhs, const Field3DParallel& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) + rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] + rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by addition with Field3DParallel
+Field3DParallel& Field3DParallel::operator+=(const Field3DParallel& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) += rhs;
+        ydown(i) += rhs;
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
+
+    track(rhs, "operator+=");
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator+=");
+    (*this) = (*this) + rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for subtraction of Field3DParallel and Field3DParallel
+Field3DParallel operator-(const Field3DParallel& lhs, const Field3DParallel& rhs) {
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) - rhs.yup(i);
+      result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] - rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by subtraction with Field3DParallel
+Field3DParallel& Field3DParallel::operator-=(const Field3DParallel& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) -= rhs;
+        ydown(i) -= rhs;
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
+
+    track(rhs, "operator-=");
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator-=");
+    (*this) = (*this) - rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for multiplication of BoutReal and Field3DParallel
+Field3DParallel operator*(const BoutReal lhs, const Field3DParallel& rhs) {
+
+  Field3DParallel result{emptyFrom(rhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(rhs.getRegionID());
+  if (rhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs * rhs.yup(i);
+      result.ydown(i) = lhs * rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs * rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ wrapper for division of BoutReal and Field3DParallel
+Field3DParallel operator/(const BoutReal lhs, const Field3DParallel& rhs) {
+
+  Field3DParallel result{emptyFrom(rhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(rhs.getRegionID());
+  if (rhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs / rhs.yup(i);
+      result.ydown(i) = lhs / rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs / rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ wrapper for addition of BoutReal and Field3DParallel
+Field3DParallel operator+(const BoutReal lhs, const Field3DParallel& rhs) {
+
+  Field3DParallel result{emptyFrom(rhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(rhs.getRegionID());
+  if (rhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs + rhs.yup(i);
+      result.ydown(i) = lhs + rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs + rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ wrapper for subtraction of BoutReal and Field3DParallel
+Field3DParallel operator-(const BoutReal lhs, const Field3DParallel& rhs) {
+
+  Field3DParallel result{emptyFrom(rhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(rhs.getRegionID());
+  if (rhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs - rhs.yup(i);
+      result.ydown(i) = lhs - rhs.ydown(i);
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs - rhs[index];
+  }
+
+  checkData(result);
+  return result;
+}

From 12df335c7f708d6999c998e9234e1448abcd7b0d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 26 Jun 2025 10:54:01 +0200
Subject: [PATCH 0795/1827] No need for orderedDicts

dicts have been preserving order for several releases now.
---
 src/field/gen_fieldops.py | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 1560a82dc5..29a8c47a54 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -53,15 +53,13 @@ def smart_open(filename, mode="r"):
 
 
 # The arthimetic operators
-# OrderedDict to (try to) ensure consistency between python 2 & 3
-operators = OrderedDict(
-    [
-        ("*", "multiplication"),
-        ("/", "division"),
-        ("+", "addition"),
-        ("-", "subtraction"),
-    ]
-)
+operators = {
+    "*": "multiplication",
+    "/": "division",
+    "+": "addition",
+    "-": "subtraction",
+}
+
 
 header = """// This file is autogenerated - see gen_fieldops.py
 #include <bout/field2d.hxx>

From e71eebee3831c6ce3048b6f587dad4838aabbc56 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 26 Jun 2025 10:54:22 +0200
Subject: [PATCH 0796/1827] Remove wrong comment, FieldPerp is present

---
 include/bout/field.hxx    |  3 ++-
 include/bout/field3d.hxx  | 25 ++++++++++++++++++++++---
 src/field/field3d.cxx     | 35 +++++++++++++++++++++++++++++++++++
 src/field/gen_fieldops.py |  1 -
 4 files changed, 59 insertions(+), 5 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 3f7f591528..ce7b0b651c 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -189,7 +189,8 @@ inline bool areFieldsCompatible(const Field& field1, const Field& field2) {
 template <typename T>
 inline T emptyFrom(const T& f) {
   static_assert(bout::utils::is_Field_v<T>, "emptyFrom only works on Fields");
-  return T(f.getMesh(), f.getLocation(), {f.getDirectionY(), f.getDirectionZ()})
+  return T(f.getMesh(), f.getLocation(),
+           DirectionTypes{f.getDirectionY(), f.getDirectionZ()}, f.getRegionID())
       .allocate();
 }
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index be4e2d6ef0..00167ea153 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -44,6 +44,7 @@ class Field3D;
 
 class Mesh;
 class Options;
+class Field3DParallel;
 
 /// Class for 3D X-Y-Z scalar fields
 /*!
@@ -517,6 +518,8 @@ public:
   bool areCalcParallelSlicesAllowed() const { return _allowCalcParallelSlices; };
   void disallowCalcParallelSlices() { _allowCalcParallelSlices = false; };
 
+  inline Field3DParallel asF3dwy();
+
 protected:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
   int nx{-1}, ny{-1}, nz{-1};
@@ -705,11 +708,12 @@ inline Field3D copy(const Field3D& f) {
 class Field3DParallel : public Field3D {
 public:
   template <class... Types>
-  Field3DParallel(Types... args) : Field3D(&args...) {
+  Field3DParallel(Types... args) : Field3D(args...) {
     ensureFieldAligned();
   }
-  Field3DParallel(Field3D&& f3d) : Field3D(std::move(f3d)) { ensureFieldAligned(); }
-  Field3DParallel(const Field3D& f3d) : Field3D(f3d) { ensureFieldAligned(); }
+  // Field3DParallel(const Field2D& f) : Field3D(f) {
+  //   ensureFieldAligned();
+  // }
   // Explicitly needed, as DirectionTypes is sometimes constructed from a
   // brace enclosed list
   Field3DParallel(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
@@ -725,6 +729,9 @@ public:
       : Field3D(std::move(data), localmesh, location, directions_in) {
     ensureFieldAligned();
   }
+  Field3DParallel(BoutReal, Mesh*);
+  Field3D& asF3d() { return *this; }
+  const Field3D& asF3d() const { return *this; }
 
   Field3DParallel& operator*=(const Field3D&);
   Field3DParallel& operator/=(const Field3D&);
@@ -738,9 +745,21 @@ public:
   Field3DParallel& operator/=(BoutReal);
   Field3DParallel& operator+=(BoutReal);
   Field3DParallel& operator-=(BoutReal);
+  Field3DParallel& operator=(const Field3D& rhs) {
+    Field3D::operator=(rhs);
+    ensureFieldAligned();
+    return *this;
+  }
+  Field3DParallel& operator=(Field3D&& rhs) {
+    Field3D::operator=(std::move(rhs));
+    ensureFieldAligned();
+    return *this;
+  }
+  Field3DParallel& operator=(BoutReal);
 
 private:
   void ensureFieldAligned();
 };
 
+Field3DParallel Field3D::asF3dwy() { return Field3DParallel(*this); }
 #endif /* BOUT_FIELD3D_H */
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index c5d157788d..04444de3f0 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -92,6 +92,19 @@ Field3D::Field3D(const BoutReal val, Mesh* localmesh) : Field3D(localmesh) {
   *this = val;
 }
 
+Field3DParallel::Field3DParallel(const BoutReal val, Mesh* localmesh)
+    : Field3D(localmesh) {
+
+  *this = val;
+  if (this->isFci()) {
+    splitParallelSlices();
+    for (size_t i = 0; i < numberParallelSlices(); ++i) {
+      yup(i) = val;
+      ydown(i) = val;
+    }
+  }
+}
+
 Field3D::Field3D(Array<BoutReal> data_in, Mesh* localmesh, CELL_LOC datalocation,
                  DirectionTypes directions_in)
     : Field(localmesh, datalocation, directions_in), data(std::move(data_in)) {
@@ -337,6 +350,27 @@ Field3D& Field3D::operator=(const BoutReal val) {
 
   allocate();
 
+  BOUT_FOR(i, getRegion("RGN_ALL")) { (*this)[i] = val; }
+  this->name = "BR";
+
+  return *this;
+}
+
+Field3DParallel& Field3DParallel::operator=(const BoutReal val) {
+  TRACE("Field3DParallel = BoutReal");
+  track(val, "operator=");
+
+  if (isFci()) {
+    ASSERT2(hasParallelSlices());
+    for (size_t i = 0; i < numberParallelSlices(); ++i) {
+      yup(i) = val;
+      ydown(i) = val;
+    }
+  }
+  resetRegion();
+
+  allocate();
+
   BOUT_FOR(i, getRegion("RGN_ALL")) { (*this)[i] = val; }
 
   return *this;
@@ -890,6 +924,7 @@ void Field3D::_track(const T& change, std::string operation) {
 template void
 Field3D::_track<Field3D, bout::utils::EnableIfField<Field3D>>(const Field3D&,
                                                               std::string);
+template void Field3D::_track<Field3DParallel>(const Field3DParallel&, std::string);
 template void Field3D::_track<Field2D>(const Field2D&, std::string);
 template void Field3D::_track<>(const FieldPerp&, std::string);
 
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 29a8c47a54..7dbebc79a3 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -218,7 +218,6 @@ def returnType(f1, f2):
         region_loop = "BOUT_FOR"
 
     # Declare what fields we currently support:
-    # Field perp is currently missing
     field3D = Field(
         "Field3D",
         ["x", "y", "z"],

From a9366cbd203470b5ebecf10fa776cf5e3190c78e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 10 Jul 2025 13:59:06 +0200
Subject: [PATCH 0797/1827] Start using Field3DParallel for derivatives

---
 include/bout/coordinates.hxx            | 14 ++++++-------
 include/bout/derivs.hxx                 |  6 +++---
 include/bout/index_derivs_interface.hxx | 17 +++++++++++++++-
 src/mesh/coordinates.cxx                | 26 +++++++++----------------
 src/sys/derivs.cxx                      |  6 +++---
 5 files changed, 38 insertions(+), 31 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index e7ead42ee5..8a4bfb5ef6 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -160,7 +160,7 @@ public:
               const std::string& method = "DEFAULT",
               const std::string& region = "RGN_NOBNDRY");
 
-  Field3D DDY(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+  Field3D DDY(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
               const std::string& method = "DEFAULT",
               const std::string& region = "RGN_NOBNDRY") const;
 
@@ -172,7 +172,7 @@ public:
   FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc = CELL_DEFAULT,
                        const std::string& method = "DEFAULT");
 
-  Field3D Grad_par(const Field3D& var, CELL_LOC outloc = CELL_DEFAULT,
+  Field3D Grad_par(const Field3DParallel& var, CELL_LOC outloc = CELL_DEFAULT,
                    const std::string& method = "DEFAULT");
 
   /// Advection along magnetic field V*b.Grad(f)
@@ -180,7 +180,7 @@ public:
                             CELL_LOC outloc = CELL_DEFAULT,
                             const std::string& method = "DEFAULT");
 
-  Field3D Vpar_Grad_par(const Field3D& v, const Field3D& f,
+  Field3D Vpar_Grad_par(const Field3D& v, const Field3DParallel& f,
                         CELL_LOC outloc = CELL_DEFAULT,
                         const std::string& method = "DEFAULT");
 
@@ -188,14 +188,14 @@ public:
   FieldMetric Div_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
                       const std::string& method = "DEFAULT");
 
-  Field3D Div_par(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+  Field3D Div_par(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                   const std::string& method = "DEFAULT");
 
   // Second derivative along magnetic field
   FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
                          const std::string& method = "DEFAULT");
 
-  Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+  Field3D Grad2_par2(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                      const std::string& method = "DEFAULT");
   // Perpendicular Laplacian operator, using only X-Z derivatives
   // NOTE: This might be better bundled with the Laplacian inversion code
@@ -207,13 +207,13 @@ public:
   // Full parallel Laplacian operator on scalar field
   // Laplace_par(f) = Div( b (b dot Grad(f)) )
   FieldMetric Laplace_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT);
-  Field3D Laplace_par(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT);
+  Field3D Laplace_par(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT);
 
   // Full Laplacian operator on scalar field
   FieldMetric Laplace(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
                       const std::string& dfdy_boundary_conditions = "free_o3",
                       const std::string& dfdy_dy_region = "");
-  Field3D Laplace(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+  Field3D Laplace(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                   const std::string& dfdy_boundary_conditions = "free_o3",
                   const std::string& dfdy_dy_region = "");
 
diff --git a/include/bout/derivs.hxx b/include/bout/derivs.hxx
index 1c360bb9cd..a8d9279378 100644
--- a/include/bout/derivs.hxx
+++ b/include/bout/derivs.hxx
@@ -82,7 +82,7 @@ Coordinates::FieldMetric DDX(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Field3D DDY(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+Field3D DDY(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
             const std::string& method = "DEFAULT",
             const std::string& region = "RGN_NOBNDRY");
 
@@ -410,7 +410,7 @@ Coordinates::FieldMetric VDDX(const Field2D& v, const Field2D& f,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Field3D VDDY(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+Field3D VDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
              const std::string& method = "DEFAULT",
              const std::string& region = "RGN_NOBNDRY");
 
@@ -533,7 +533,7 @@ Coordinates::FieldMetric FDDX(const Field2D& v, const Field2D& f,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Field3D FDDY(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+Field3D FDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
              const std::string& method = "DEFAULT",
              const std::string& region = "RGN_NOBNDRY");
 
diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx
index 242492c3f8..02926a0fe1 100644
--- a/include/bout/index_derivs_interface.hxx
+++ b/include/bout/index_derivs_interface.hxx
@@ -198,8 +198,13 @@ template <typename T>
 T DDY(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
       const std::string& region = "RGN_NOBNDRY") {
 
-  if (f.hasParallelSlices()) {
+  if (f.isFci()) {
     ASSERT1(f.getDirectionY() == YDirectionType::Standard);
+    if (!f.hasParallelSlices()) {
+      throw BoutException(
+          "parallel slices needed for parallel derivatives. Make sure to communicate and "
+          "apply parallel boundary conditions before calling derivative");
+    }
     return standardDerivative<T, DIRECTION::YOrthogonal, DERIV::Standard>(f, outloc,
                                                                           method, region);
   } else {
@@ -356,6 +361,11 @@ T VDDY(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
     return are_unaligned ? fromFieldAligned(result, region) : result;
   }
 }
+inline Field3D VDDY(const Field3D& v, const Field3DParallel& f,
+                    CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
+                    const std::string& region = "RGN_NOBNDRY") {
+  return VDDY(v, f.asF3d(), outloc, method, region);
+}
 
 template <typename T>
 T FDDY(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
@@ -380,6 +390,11 @@ T FDDY(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
     return are_unaligned ? fromFieldAligned(result, region) : result;
   }
 }
+inline Field3D FDDY(const Field3D& v, const Field3DParallel& f,
+                    CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
+                    const std::string& region = "RGN_NOBNDRY") {
+  return FDDY(v, f.asF3d(), outloc, method, region);
+}
 
 ////////////// Z DERIVATIVE /////////////////
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index d2634d3f88..aa9b62264b 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1485,16 +1485,8 @@ Coordinates::FieldMetric Coordinates::DDY(const Field2D& f, CELL_LOC loc,
   return bout::derivatives::index::DDY(f, loc, method, region) / dy;
 }
 
-Field3D Coordinates::DDY(const Field3D& f, CELL_LOC outloc, const std::string& method,
-                         const std::string& region) const {
-#if BOUT_USE_METRIC_3D
-  if (!f.hasParallelSlices() and !transform->canToFromFieldAligned()) {
-    Field3D f_parallel = f;
-    transform->calcParallelSlices(f_parallel);
-    f_parallel.applyParallelBoundary("parallel_neumann_o2");
-    return bout::derivatives::index::DDY(f_parallel, outloc, method, region);
-  }
-#endif
+Field3D Coordinates::DDY(const Field3DParallel& f, CELL_LOC outloc,
+                         const std::string& method, const std::string& region) const {
   return bout::derivatives::index::DDY(f, outloc, method, region) / dy;
 };
 
@@ -1526,7 +1518,7 @@ Coordinates::FieldMetric Coordinates::Grad_par(const Field2D& var,
   return DDY(var) * invSg();
 }
 
-Field3D Coordinates::Grad_par(const Field3D& var, CELL_LOC outloc,
+Field3D Coordinates::Grad_par(const Field3DParallel& var, CELL_LOC outloc,
                               const std::string& method) {
 
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
@@ -1546,8 +1538,8 @@ Coordinates::FieldMetric Coordinates::Vpar_Grad_par(const Field2D& v, const Fiel
   return VDDY(v, f) * invSg();
 }
 
-Field3D Coordinates::Vpar_Grad_par(const Field3D& v, const Field3D& f, CELL_LOC outloc,
-                                   const std::string& method) {
+Field3D Coordinates::Vpar_Grad_par(const Field3D& v, const Field3DParallel& f,
+                                   CELL_LOC outloc, const std::string& method) {
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
   return VDDY(v, f, outloc, method) * invSg();
@@ -1568,7 +1560,7 @@ Coordinates::FieldMetric Coordinates::Div_par(const Field2D& f, CELL_LOC outloc,
   return Bxy * Grad_par(f / Bxy_floc, outloc, method);
 }
 
-Field3D Coordinates::Div_par(const Field3D& f, CELL_LOC outloc,
+Field3D Coordinates::Div_par(const Field3DParallel& f, CELL_LOC outloc,
                              const std::string& method) {
 
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
@@ -1608,7 +1600,7 @@ Coordinates::FieldMetric Coordinates::Grad2_par2(const Field2D& f, CELL_LOC outl
   return result;
 }
 
-Field3D Coordinates::Grad2_par2(const Field3D& f, CELL_LOC outloc,
+Field3D Coordinates::Grad2_par2(const Field3DParallel& f, CELL_LOC outloc,
                                 const std::string& method) {
 
   if (outloc == CELL_DEFAULT) {
@@ -1774,7 +1766,7 @@ Coordinates::FieldMetric Coordinates::Laplace_par(const Field2D& f, CELL_LOC out
   return D2DY2(f, outloc) / g_22 + DDY(J / g_22, outloc) * DDY(f, outloc) / J;
 }
 
-Field3D Coordinates::Laplace_par(const Field3D& f, CELL_LOC outloc) {
+Field3D Coordinates::Laplace_par(const Field3DParallel& f, CELL_LOC outloc) {
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
   return D2DY2(f, outloc) / g_22 + DDY(J / g_22, outloc) * ::DDY(f, outloc) / J;
 }
@@ -1796,7 +1788,7 @@ Coordinates::FieldMetric Coordinates::Laplace(const Field2D& f, CELL_LOC outloc,
   return result;
 }
 
-Field3D Coordinates::Laplace(const Field3D& f, CELL_LOC outloc,
+Field3D Coordinates::Laplace(const Field3DParallel& f, CELL_LOC outloc,
                              const std::string& dfdy_boundary_conditions,
                              const std::string& dfdy_dy_region) {
 
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index aab75b8f19..2b606b9e5d 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -66,7 +66,7 @@ Coordinates::FieldMetric DDX(const Field2D& f, CELL_LOC outloc, const std::strin
 
 ////////////// Y DERIVATIVE /////////////////
 
-Field3D DDY(const Field3D& f, CELL_LOC outloc, const std::string& method,
+Field3D DDY(const Field3DParallel& f, CELL_LOC outloc, const std::string& method,
             const std::string& region) {
   return bout::derivatives::index::DDY(f, outloc, method, region)
          / f.getCoordinates(outloc)->dy;
@@ -406,7 +406,7 @@ Coordinates::FieldMetric VDDY(const Field2D& v, const Field2D& f, CELL_LOC outlo
 }
 
 // general case
-Field3D VDDY(const Field3D& v, const Field3D& f, CELL_LOC outloc,
+Field3D VDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc,
              const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDY(v, f, outloc, method, region)
          / f.getCoordinates(outloc)->dy;
@@ -467,7 +467,7 @@ Coordinates::FieldMetric FDDY(const Field2D& v, const Field2D& f, CELL_LOC outlo
          / f.getCoordinates(outloc)->dy;
 }
 
-Field3D FDDY(const Field3D& v, const Field3D& f, CELL_LOC outloc,
+Field3D FDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc,
              const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDY(v, f, outloc, method, region)
          / f.getCoordinates(outloc)->dy;

From b3983c1eadb57ae85d580dfd834195377d9f4a57 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 16 Jul 2025 14:06:10 +0200
Subject: [PATCH 0798/1827] Do not use separate derivative store for
 Field3DParallel

---
 include/bout/deriv_store.hxx            | 9 +++++++++
 include/bout/index_derivs.hxx           | 2 +-
 include/bout/index_derivs_interface.hxx | 4 ++--
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/include/bout/deriv_store.hxx b/include/bout/deriv_store.hxx
index b2b7928c2e..83bc34d7c8 100644
--- a/include/bout/deriv_store.hxx
+++ b/include/bout/deriv_store.hxx
@@ -522,4 +522,13 @@ private:
   }
 };
 
+template <typename T>
+auto& getStore() {
+  if constexpr (std::is_same<T, Field3DParallel>::value) {
+    return DerivativeStore<Field3D>::getInstance();
+  } else {
+    return DerivativeStore<T>::getInstance();
+  }
+}
+
 #endif
diff --git a/include/bout/index_derivs.hxx b/include/bout/index_derivs.hxx
index ccce9a7f5e..a8d1bbb1d3 100644
--- a/include/bout/index_derivs.hxx
+++ b/include/bout/index_derivs.hxx
@@ -148,7 +148,7 @@ struct registerMethod {
     // removed and we can use nGuard directly in the template statement.
     const int nGuards = method.meta.nGuards;
 
-    auto& derivativeRegister = DerivativeStore<FieldType>::getInstance();
+    auto& derivativeRegister = getStore<FieldType>();
 
     switch (method.meta.derivType) {
     case (DERIV::Standard):
diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx
index 02926a0fe1..043175a82b 100644
--- a/include/bout/index_derivs_interface.hxx
+++ b/include/bout/index_derivs_interface.hxx
@@ -148,8 +148,8 @@ T standardDerivative(const T& f, CELL_LOC outloc, const std::string& method,
   }
 
   // Lookup the method
-  auto derivativeMethod = DerivativeStore<T>::getInstance().getStandardDerivative(
-      method, direction, stagger, derivType);
+  auto derivativeMethod =
+      getStore<T>().getStandardDerivative(method, direction, stagger, derivType);
 
   // Create the result field
   T result{emptyFrom(f).setLocation(outloc)};

From 32f4c6511226a43f9f5b9ca98fb919fce8037dde Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 16 Jul 2025 14:16:24 +0200
Subject: [PATCH 0799/1827] Do not change non-FCI fields

---
 src/field/field3d.cxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 04444de3f0..c6461d5040 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -949,9 +949,9 @@ void Field3D::_track(const BoutReal& change, std::string operation) {
 void Field3DParallel::ensureFieldAligned() {
   if (isFci()) {
     ASSERT2(hasParallelSlices());
-  } else {
-    if (getDirectionY() != YDirectionType::Aligned) {
-      *this = toFieldAligned(*this);
-    }
-  }
+  } // else {
+  //   if (getDirectionY() != YDirectionType::Aligned) {
+  //     *this = toFieldAligned(*this);
+  //   }
+  // }
 }

From 09f7466a431de522691deefcf7de3dd29d00db2c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 17 Jul 2025 11:02:46 +0200
Subject: [PATCH 0800/1827] Add function to header file

Otherwise, the Field3DParallel is casted to Field3D and the wrong
overloads are used
---
 include/bout/field3d.hxx | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 00167ea153..62afd44d07 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -583,6 +583,26 @@ Field3D operator-(BoutReal lhs, const Field3D& rhs);
 Field3D operator*(BoutReal lhs, const Field3D& rhs);
 Field3D operator/(BoutReal lhs, const Field3D& rhs);
 
+Field3DParallel operator+(const Field3D& lhs, const Field3DParallel& rhs);
+Field3DParallel operator-(const Field3D& lhs, const Field3DParallel& rhs);
+Field3DParallel operator*(const Field3D& lhs, const Field3DParallel& rhs);
+Field3DParallel operator/(const Field3D& lhs, const Field3DParallel& rhs);
+
+Field3DParallel operator+(const Field3DParallel& lhs, const Field3D& rhs);
+Field3DParallel operator-(const Field3DParallel& lhs, const Field3D& rhs);
+Field3DParallel operator*(const Field3DParallel& lhs, const Field3D& rhs);
+Field3DParallel operator/(const Field3DParallel& lhs, const Field3D& rhs);
+
+Field3DParallel operator+(const Field3DParallel& lhs, const Field3DParallel& rhs);
+Field3DParallel operator-(const Field3DParallel& lhs, const Field3DParallel& rhs);
+Field3DParallel operator*(const Field3DParallel& lhs, const Field3DParallel& rhs);
+Field3DParallel operator/(const Field3DParallel& lhs, const Field3DParallel& rhs);
+
+Field3DParallel operator+(const BoutReal lhs, const Field3DParallel& rhs);
+Field3DParallel operator-(const BoutReal lhs, const Field3DParallel& rhs);
+Field3DParallel operator*(const BoutReal lhs, const Field3DParallel& rhs);
+Field3DParallel operator/(const BoutReal lhs, const Field3DParallel& rhs);
+
 /*!
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.

From e1a15ddf4244f579040f6bb326802a9eded01f19 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 17 Jul 2025 11:03:10 +0200
Subject: [PATCH 0801/1827] Ensure emptyFrom works

---
 include/bout/field3d.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 62afd44d07..c4a41f3443 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -741,6 +741,7 @@ public:
                                                   ZDirectionType::Standard},
                   std::optional<size_t> regionID = {})
       : Field3D(localmesh, location_in, directions_in, regionID) {
+    splitParallelSlices();
     ensureFieldAligned();
   }
   Field3DParallel(Array<BoutReal> data, Mesh* localmesh, CELL_LOC location = CELL_CENTRE,

From f98d5dec0ba86421345811b16667305a10fdd067 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 17 Jul 2025 23:51:26 +0200
Subject: [PATCH 0802/1827] Use f3dwy to preserve parallel fields

The communication was a no-op, as that did never calculate the parallel
fields.
---
 src/mesh/coordinates.cxx | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index aa9b62264b..13126cf2b4 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1015,15 +1015,9 @@ int Coordinates::geometry(bool recalculate_staggered,
   G3_23 = 0.5 * g13 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g23 * DDZ(g_22)
           + 0.5 * g33 * DDY(g_33);
 
-  auto tmp = J * g12;
-  localmesh->communicate_no_slices(tmp);
-  G1 = (DDX(J * g11) + DDY(tmp) + DDZ(J * g13)) / J;
-  tmp = J * g22;
-  localmesh->communicate_no_slices(tmp);
-  G2 = (DDX(J * g12) + DDY(tmp) + DDZ(J * g23)) / J;
-  tmp = J * g23;
-  localmesh->communicate_no_slices(tmp);
-  G3 = (DDX(J * g13) + DDY(tmp) + DDZ(J * g33)) / J;
+  G1 = (DDX(J * g11) + DDY(J.asF3dwy() * g12) + DDZ(J * g13)) / J;
+  G2 = (DDX(J * g12) + DDY(J.asF3dwy() * g22) + DDZ(J * g23)) / J;
+  G3 = (DDX(J * g13) + DDY(J.asF3dwy() * g23) + DDZ(J * g33)) / J;
 
   // Communicate christoffel symbol terms
   output_progress.write("\tCommunicating connection terms\n");

From fc98ac49b09a6f5f57f416f07729ccea11bd1a18 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 17 Jul 2025 23:53:10 +0200
Subject: [PATCH 0803/1827] Preserve parallel fields for d1_dy calculation

---
 src/mesh/coordinates.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 13126cf2b4..5924579c5b 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1096,7 +1096,7 @@ int Coordinates::geometry(bool recalculate_staggered,
     if (localmesh->get(d2y, "d2y" + suffix, 0.0, false, location)) {
       output_warn.write(
           "\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
-      d1_dy = DDY(1. / dy); // d/di(1/dy)
+      d1_dy = DDY(1. / dy.asF3dwy()); // d/di(1/dy)
 
       localmesh->communicate_no_slices(d1_dy);
       d1_dy =

From 205d5024c44d0806ab7f86a9ef1d24776507f6c2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 17 Jul 2025 23:54:03 +0200
Subject: [PATCH 0804/1827] Add overloads for DD?(Field3DParallel)

They should return Field3D, not Field3DParallel
---
 include/bout/index_derivs_interface.hxx | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx
index 043175a82b..62322a64e1 100644
--- a/include/bout/index_derivs_interface.hxx
+++ b/include/bout/index_derivs_interface.hxx
@@ -175,6 +175,11 @@ T DDX(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "D
 
   return standardDerivative<T, DIRECTION::X, DERIV::Standard>(f, outloc, method, region);
 }
+inline Field3D DDX(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
+                   const std::string& method = "DEFAULT",
+                   const std::string& region = "RGN_NOBNDRY") {
+  return DDX(f.asF3d(), outloc, method, region);
+}
 
 template <typename T>
 T D2DX2(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
@@ -215,6 +220,11 @@ T DDY(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "D
     return is_unaligned ? fromFieldAligned(result, region) : result;
   }
 }
+inline Field3D DDY(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
+                   const std::string& method = "DEFAULT",
+                   const std::string& region = "RGN_NOBNDRY") {
+  return DDY(f.asF3d(), outloc, method, region);
+}
 
 template <typename T>
 T D2DY2(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
@@ -257,6 +267,11 @@ T DDZ(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "D
 
   return standardDerivative<T, DIRECTION::Z, DERIV::Standard>(f, outloc, method, region);
 }
+inline Field3D DDZ(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
+                   const std::string& method = "DEFAULT",
+                   const std::string& region = "RGN_NOBNDRY") {
+  return DDZ(f.asF3d(), outloc, method, region);
+}
 
 template <typename T>
 T D2DZ2(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",

From 6a7c4076d8e69f42730c91ab21bcf6f3038655b2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 18 Jul 2025 07:24:03 +0200
Subject: [PATCH 0805/1827] add asF3dwy() stub to Field2D

---
 include/bout/field2d.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 906af38a1d..d0d3225572 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -273,6 +273,8 @@ public:
 
   int size() const override { return nx * ny; }
 
+  Field2D& asF3dwy() { return *this; }
+
 private:
   /// Internal data array. Handles allocation/freeing of memory
   Array<BoutReal> data;

From 268ecfc21a5d127e65687bbe2d633faaf399e26d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 18 Jul 2025 10:56:38 +0200
Subject: [PATCH 0806/1827] Add some documentation

---
 include/bout/field3d.hxx | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index c4a41f3443..76295fa6fe 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -725,15 +725,16 @@ inline Field3D copy(const Field3D& f) {
   return result;
 }
 
+/// Field3DParallel is intended to behave like Field3D, but preserve parallel
+/// Fields.
+/// Operations on Field3D, like multiplication, exp and floor only work on the
+/// "main" field, Field3DParallel will retain the parallel slices.
 class Field3DParallel : public Field3D {
 public:
   template <class... Types>
   Field3DParallel(Types... args) : Field3D(args...) {
     ensureFieldAligned();
   }
-  // Field3DParallel(const Field2D& f) : Field3D(f) {
-  //   ensureFieldAligned();
-  // }
   // Explicitly needed, as DirectionTypes is sometimes constructed from a
   // brace enclosed list
   Field3DParallel(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,

From f3b36a45f6e324e03ef07cc507ccfb9207c8b986 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 18 Jul 2025 10:58:02 +0200
Subject: [PATCH 0807/1827] Be more explicit in the naming

---
 include/bout/field2d.hxx                |  2 +-
 include/bout/field3d.hxx                |  8 ++++----
 include/bout/index_derivs_interface.hxx | 12 +++++++-----
 src/mesh/coordinates.cxx                |  8 ++++----
 4 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index d0d3225572..212efe5cad 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -273,7 +273,7 @@ public:
 
   int size() const override { return nx * ny; }
 
-  Field2D& asF3dwy() { return *this; }
+  Field2D& asField3DParallel() { return *this; }
 
 private:
   /// Internal data array. Handles allocation/freeing of memory
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 76295fa6fe..44faa0a107 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -518,7 +518,7 @@ public:
   bool areCalcParallelSlicesAllowed() const { return _allowCalcParallelSlices; };
   void disallowCalcParallelSlices() { _allowCalcParallelSlices = false; };
 
-  inline Field3DParallel asF3dwy();
+  inline Field3DParallel asField3DParallel();
 
 protected:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
@@ -752,8 +752,8 @@ public:
     ensureFieldAligned();
   }
   Field3DParallel(BoutReal, Mesh*);
-  Field3D& asF3d() { return *this; }
-  const Field3D& asF3d() const { return *this; }
+  Field3D& asField3D() { return *this; }
+  const Field3D& asField3D() const { return *this; }
 
   Field3DParallel& operator*=(const Field3D&);
   Field3DParallel& operator/=(const Field3D&);
@@ -783,5 +783,5 @@ private:
   void ensureFieldAligned();
 };
 
-Field3DParallel Field3D::asF3dwy() { return Field3DParallel(*this); }
+Field3DParallel Field3D::asField3DParallel() { return Field3DParallel(*this); }
 #endif /* BOUT_FIELD3D_H */
diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx
index 62322a64e1..03cc480323 100644
--- a/include/bout/index_derivs_interface.hxx
+++ b/include/bout/index_derivs_interface.hxx
@@ -175,10 +175,11 @@ T DDX(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "D
 
   return standardDerivative<T, DIRECTION::X, DERIV::Standard>(f, outloc, method, region);
 }
+
 inline Field3D DDX(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                    const std::string& method = "DEFAULT",
                    const std::string& region = "RGN_NOBNDRY") {
-  return DDX(f.asF3d(), outloc, method, region);
+  return DDX(f.asField3D(), outloc, method, region);
 }
 
 template <typename T>
@@ -223,7 +224,7 @@ T DDY(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "D
 inline Field3D DDY(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                    const std::string& method = "DEFAULT",
                    const std::string& region = "RGN_NOBNDRY") {
-  return DDY(f.asF3d(), outloc, method, region);
+  return DDY(f.asField3D(), outloc, method, region);
 }
 
 template <typename T>
@@ -267,10 +268,11 @@ T DDZ(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "D
 
   return standardDerivative<T, DIRECTION::Z, DERIV::Standard>(f, outloc, method, region);
 }
+
 inline Field3D DDZ(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                    const std::string& method = "DEFAULT",
                    const std::string& region = "RGN_NOBNDRY") {
-  return DDZ(f.asF3d(), outloc, method, region);
+  return DDZ(f.asField3D(), outloc, method, region);
 }
 
 template <typename T>
@@ -379,7 +381,7 @@ T VDDY(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
 inline Field3D VDDY(const Field3D& v, const Field3DParallel& f,
                     CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
                     const std::string& region = "RGN_NOBNDRY") {
-  return VDDY(v, f.asF3d(), outloc, method, region);
+  return VDDY(v, f.asField3D(), outloc, method, region);
 }
 
 template <typename T>
@@ -408,7 +410,7 @@ T FDDY(const T& vel, const T& f, CELL_LOC outloc = CELL_DEFAULT,
 inline Field3D FDDY(const Field3D& v, const Field3DParallel& f,
                     CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
                     const std::string& region = "RGN_NOBNDRY") {
-  return FDDY(v, f.asF3d(), outloc, method, region);
+  return FDDY(v, f.asField3D(), outloc, method, region);
 }
 
 ////////////// Z DERIVATIVE /////////////////
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 5924579c5b..b1b850b577 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1015,9 +1015,9 @@ int Coordinates::geometry(bool recalculate_staggered,
   G3_23 = 0.5 * g13 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g23 * DDZ(g_22)
           + 0.5 * g33 * DDY(g_33);
 
-  G1 = (DDX(J * g11) + DDY(J.asF3dwy() * g12) + DDZ(J * g13)) / J;
-  G2 = (DDX(J * g12) + DDY(J.asF3dwy() * g22) + DDZ(J * g23)) / J;
-  G3 = (DDX(J * g13) + DDY(J.asF3dwy() * g23) + DDZ(J * g33)) / J;
+  G1 = (DDX(J * g11) + DDY(J.asField3DParallel() * g12) + DDZ(J * g13)) / J;
+  G2 = (DDX(J * g12) + DDY(J.asField3DParallel() * g22) + DDZ(J * g23)) / J;
+  G3 = (DDX(J * g13) + DDY(J.asField3DParallel() * g23) + DDZ(J * g33)) / J;
 
   // Communicate christoffel symbol terms
   output_progress.write("\tCommunicating connection terms\n");
@@ -1096,7 +1096,7 @@ int Coordinates::geometry(bool recalculate_staggered,
     if (localmesh->get(d2y, "d2y" + suffix, 0.0, false, location)) {
       output_warn.write(
           "\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
-      d1_dy = DDY(1. / dy.asF3dwy()); // d/di(1/dy)
+      d1_dy = DDY(1. / dy.asField3DParallel()); // d/di(1/dy)
 
       localmesh->communicate_no_slices(d1_dy);
       d1_dy =

From b47343fdc3a8ad91e37bc5764c03d3cb02c8765b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 21 Jul 2025 11:01:45 +0200
Subject: [PATCH 0808/1827] do not use const for BoutReal in signature

---
 include/bout/field3d.hxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 44faa0a107..5936a30310 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -598,10 +598,10 @@ Field3DParallel operator-(const Field3DParallel& lhs, const Field3DParallel& rhs
 Field3DParallel operator*(const Field3DParallel& lhs, const Field3DParallel& rhs);
 Field3DParallel operator/(const Field3DParallel& lhs, const Field3DParallel& rhs);
 
-Field3DParallel operator+(const BoutReal lhs, const Field3DParallel& rhs);
-Field3DParallel operator-(const BoutReal lhs, const Field3DParallel& rhs);
-Field3DParallel operator*(const BoutReal lhs, const Field3DParallel& rhs);
-Field3DParallel operator/(const BoutReal lhs, const Field3DParallel& rhs);
+Field3DParallel operator+(BoutReal lhs, const Field3DParallel& rhs);
+Field3DParallel operator-(BoutReal lhs, const Field3DParallel& rhs);
+Field3DParallel operator*(BoutReal lhs, const Field3DParallel& rhs);
+Field3DParallel operator/(BoutReal lhs, const Field3DParallel& rhs);
 
 /*!
  * Unary minus. Returns the negative of given field,

From d07bde5e87b9de66a7a9432aec1e1fb4be04fc8d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 21 Jul 2025 11:12:18 +0200
Subject: [PATCH 0809/1827] Add Field3DParallel + Field2D fieldops

This is needed for 2D metrics, and in this case we probably want to
clear the parallel fields.
---
 include/bout/field3d.hxx | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 5936a30310..ee439f1cda 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -603,6 +603,32 @@ Field3DParallel operator-(BoutReal lhs, const Field3DParallel& rhs);
 Field3DParallel operator*(BoutReal lhs, const Field3DParallel& rhs);
 Field3DParallel operator/(BoutReal lhs, const Field3DParallel& rhs);
 
+Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs + rhs.asField3D();
+}
+Field3D operator-(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs + rhs.asField3D();
+}
+Field3D operator*(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs + rhs.asField3D();
+}
+Field3D operator/(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs + rhs.asField3D();
+}
+
+Field3D operator+(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() + rhs;
+}
+Field3D operator-(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() - rhs;
+}
+Field3D operator*(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() * rhs;
+}
+Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() / rhs;
+}
+
 /*!
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.

From 6374539e62714d14dc46862f0ef8e5ef769e5350 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 21 Jul 2025 11:14:10 +0200
Subject: [PATCH 0810/1827] Move function definition after class definition

---
 include/bout/field3d.hxx | 53 ++++++++++++++++++++--------------------
 1 file changed, 27 insertions(+), 26 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index ee439f1cda..13b68272ee 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -603,32 +603,6 @@ Field3DParallel operator-(BoutReal lhs, const Field3DParallel& rhs);
 Field3DParallel operator*(BoutReal lhs, const Field3DParallel& rhs);
 Field3DParallel operator/(BoutReal lhs, const Field3DParallel& rhs);
 
-Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-Field3D operator-(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-Field3D operator*(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-Field3D operator/(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-
-Field3D operator+(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() + rhs;
-}
-Field3D operator-(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() - rhs;
-}
-Field3D operator*(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() * rhs;
-}
-Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() / rhs;
-}
-
 /*!
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
@@ -810,4 +784,31 @@ private:
 };
 
 Field3DParallel Field3D::asField3DParallel() { return Field3DParallel(*this); }
+
+inline Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs + rhs.asField3D();
+}
+inline Field3D operator-(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs + rhs.asField3D();
+}
+inline Field3D operator*(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs + rhs.asField3D();
+}
+inline Field3D operator/(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs + rhs.asField3D();
+}
+
+inline Field3D operator+(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() + rhs;
+}
+inline Field3D operator-(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() - rhs;
+}
+inline Field3D operator*(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() * rhs;
+}
+inline Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() / rhs;
+}
+
 #endif /* BOUT_FIELD3D_H */

From f49c94cd634dce276965a571451c1ddd2c6e39d1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 21 Jul 2025 11:17:16 +0200
Subject: [PATCH 0811/1827] Prefer std::move

---
 include/bout/field3d.hxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 13b68272ee..cc34094fef 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -40,6 +40,7 @@ class Field3D;
 #include <memory>
 #include <optional>
 #include <string>
+#include <utility>
 #include <vector>
 
 class Mesh;
@@ -732,7 +733,7 @@ inline Field3D copy(const Field3D& f) {
 class Field3DParallel : public Field3D {
 public:
   template <class... Types>
-  Field3DParallel(Types... args) : Field3D(args...) {
+  Field3DParallel(Types... args) : Field3D(std::move(args)...) {
     ensureFieldAligned();
   }
   // Explicitly needed, as DirectionTypes is sometimes constructed from a

From 140bf78c9d5b66e8a6bc70e5265a3427ef1cfefa Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 21 Jul 2025 11:30:05 +0200
Subject: [PATCH 0812/1827] Add binary operators Field2D - FieldPerp

the functions where implemented, but not defined in the header
---
 include/bout/field2d.hxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 212efe5cad..a28c8bfa8f 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -287,6 +287,10 @@ private:
 };
 
 // Non-member overloaded operators
+FieldPerp operator+(const Field2D& lhs, const FieldPerp& rhs);
+FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs);
+FieldPerp operator*(const Field2D& lhs, const FieldPerp& rhs);
+FieldPerp operator/(const Field2D& lhs, const FieldPerp& rhs);
 
 Field2D operator+(const Field2D& lhs, const Field2D& rhs);
 Field2D operator-(const Field2D& lhs, const Field2D& rhs);

From 84d99b3e15fb2101100bcb68b548e253c33b7acd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 21 Jul 2025 13:03:42 +0200
Subject: [PATCH 0813/1827] Declare Field3DParallel

---
 include/bout/field.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index ce7b0b651c..6c22a4a258 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -659,6 +659,8 @@ T copy(const T& f) {
   return result;
 }
 
+class Field3DParallel;
+
 /// Apply a floor value \p f to a field \p var. Any value lower than
 /// the floor is set to the floor.
 ///

From 12191976c605800526554c3b34ec4e1ac4f3346d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 21 Aug 2025 09:53:50 +0200
Subject: [PATCH 0814/1827] Add default argument like for Field3D

Otherwise `Field3DParallel(0.0)` fails, as it constructs a `Field3D`
without parallel slices, and then fails as that cannot be converted to a
`Field3DParallel`
---
 include/bout/field3d.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index cc34094fef..d9928b45b5 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -752,7 +752,7 @@ public:
       : Field3D(std::move(data), localmesh, location, directions_in) {
     ensureFieldAligned();
   }
-  Field3DParallel(BoutReal, Mesh*);
+  Field3DParallel(BoutReal, Mesh* mesh = nullptr);
   Field3D& asField3D() { return *this; }
   const Field3D& asField3D() const { return *this; }
 

From 7bb8367b6f53aef2c21e1cf83cf93e5ecbca6094 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 21 Aug 2025 09:54:08 +0200
Subject: [PATCH 0815/1827] Add missing functions

---
 include/bout/field3d.hxx         |   5 +
 src/field/gen_fieldops.py        |   2 +-
 src/field/generated_fieldops.cxx | 241 +++++++++++++++++++++++++++++++
 3 files changed, 247 insertions(+), 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index d9928b45b5..8a585914ce 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -604,6 +604,11 @@ Field3DParallel operator-(BoutReal lhs, const Field3DParallel& rhs);
 Field3DParallel operator*(BoutReal lhs, const Field3DParallel& rhs);
 Field3DParallel operator/(BoutReal lhs, const Field3DParallel& rhs);
 
+Field3DParallel operator+(const Field3DParallel& lhs, BoutReal rhs);
+Field3DParallel operator-(const Field3DParallel& lhs, BoutReal rhs);
+Field3DParallel operator*(const Field3DParallel& lhs, BoutReal rhs);
+Field3DParallel operator/(const Field3DParallel& lhs, BoutReal rhs);
+
 /*!
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 7dbebc79a3..473cf3df1f 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -269,7 +269,7 @@ def returnType(f1, f2):
     done = [(boutreal, boutreal)]
     for lhs, rhs in itertools.chain(
         itertools.product(fields, fields),
-        itertools.product((field3D, field3DPar, boutreal), (field3D, field3DPar)),
+        itertools.product(fields2, fields2),
     ):
         if (lhs, rhs) in done:
             continue
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index b3b81f07b8..9dad114ec8 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -2513,6 +2513,247 @@ Field3DParallel& Field3DParallel::operator-=(const Field3DParallel& rhs) {
   return *this;
 }
 
+// Provide the C++ wrapper for multiplication of Field3DParallel and BoutReal
+Field3DParallel operator*(const Field3DParallel& lhs, const BoutReal rhs) {
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getRegionID());
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) * rhs;
+      result.ydown(i) = lhs.ydown(i) * rhs;
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * rhs;
+  }
+
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} * {:s}", lhs.name, "BR");
+#endif
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by multiplication with BoutReal
+Field3DParallel& Field3DParallel::operator*=(const BoutReal rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) *= rhs;
+        ydown(i) *= rhs;
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
+
+    track(rhs, "operator*=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} *= {:s}", this->name, "BR");
+#endif
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator*=");
+    (*this) = (*this) * rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for division of Field3DParallel and BoutReal
+Field3DParallel operator/(const Field3DParallel& lhs, const BoutReal rhs) {
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getRegionID());
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) / rhs;
+      result.ydown(i) = lhs.ydown(i) / rhs;
+    }
+  }
+
+  const auto tmp = 1.0 / rhs;
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] * tmp;
+  }
+
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} / {:s}", lhs.name, "BR");
+#endif
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by division with BoutReal
+Field3DParallel& Field3DParallel::operator/=(const BoutReal rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) /= rhs;
+        ydown(i) /= rhs;
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs; }
+
+    track(rhs, "operator/=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} /= {:s}", this->name, "BR");
+#endif
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator/=");
+    (*this) = (*this) / rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for addition of Field3DParallel and BoutReal
+Field3DParallel operator+(const Field3DParallel& lhs, const BoutReal rhs) {
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getRegionID());
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) + rhs;
+      result.ydown(i) = lhs.ydown(i) + rhs;
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] + rhs;
+  }
+
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} + {:s}", lhs.name, "BR");
+#endif
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by addition with BoutReal
+Field3DParallel& Field3DParallel::operator+=(const BoutReal rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) += rhs;
+        ydown(i) += rhs;
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
+
+    track(rhs, "operator+=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} += {:s}", this->name, "BR");
+#endif
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator+=");
+    (*this) = (*this) + rhs;
+  }
+  return *this;
+}
+
+// Provide the C++ wrapper for subtraction of Field3DParallel and BoutReal
+Field3DParallel operator-(const Field3DParallel& lhs, const BoutReal rhs) {
+
+  Field3DParallel result{emptyFrom(lhs)};
+  checkData(lhs);
+  checkData(rhs);
+
+  result.setRegion(lhs.getRegionID());
+  if (lhs.isFci()) {
+    result.splitParallelSlices();
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      result.yup(i) = lhs.yup(i) - rhs;
+      result.ydown(i) = lhs.ydown(i) - rhs;
+    }
+  }
+
+  BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
+    result[index] = lhs[index] - rhs;
+  }
+
+#if BOUT_USE_TRACK
+  result.name = fmt::format("{:s} - {:s}", lhs.name, "BR");
+#endif
+  checkData(result);
+  return result;
+}
+
+// Provide the C++ operator to update Field3DParallel by subtraction with BoutReal
+Field3DParallel& Field3DParallel::operator-=(const BoutReal rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  if (data.unique()) {
+
+    if (this->isFci()) {
+      for (size_t i{0}; i < yup_fields.size(); ++i) {
+        yup(i) -= rhs;
+        ydown(i) -= rhs;
+      }
+    } else {
+      clearParallelSlices();
+    }
+    checkData(*this);
+    checkData(rhs);
+
+    BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
+
+    track(rhs, "operator-=");
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} -= {:s}", this->name, "BR");
+#endif
+
+    checkData(*this);
+
+  } else {
+    track(rhs, "operator-=");
+    (*this) = (*this) - rhs;
+  }
+  return *this;
+}
+
 // Provide the C++ wrapper for multiplication of BoutReal and Field3DParallel
 Field3DParallel operator*(const BoutReal lhs, const Field3DParallel& rhs) {
 

From acd9b9312c8dc834a07851156912dd560f04ab07 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 21 Aug 2025 09:54:42 +0200
Subject: [PATCH 0816/1827] Ensure assignment to a Field3DParallel does not
 fail

---
 src/field/field3d.cxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index c6461d5040..36e0b6901d 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -361,7 +361,9 @@ Field3DParallel& Field3DParallel::operator=(const BoutReal val) {
   track(val, "operator=");
 
   if (isFci()) {
-    ASSERT2(hasParallelSlices());
+    if (!hasParallelSlices()) {
+      splitParallelSlices();
+    }
     for (size_t i = 0; i < numberParallelSlices(); ++i) {
       yup(i) = val;
       ydown(i) = val;

From 0e6fc75af496eb14fe2a2b0cbcd0c94807c2ecfe Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 25 Aug 2025 11:41:39 +0200
Subject: [PATCH 0817/1827] add filledFrom for Field3DParallel

---
 include/bout/field3d.hxx | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 8a585914ce..60e1a1b83f 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -37,6 +37,7 @@ class Field3D;
 #include "bout/region.hxx"
 #include "bout/traits.hxx"
 
+#include <functional>
 #include <memory>
 #include <optional>
 #include <string>
@@ -817,4 +818,26 @@ inline Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs) {
   return lhs.asField3D() / rhs;
 }
 
+inline Field3DParallel
+filledFrom(const Field3DParallel& f,
+           std::function<BoutReal(int yoffset, Ind3D index)> func) {
+  auto result{emptyFrom(f)};
+  if (f.hasParallelSlices()) {
+    BOUT_FOR(i, result.getRegion("RGN_NOY")) { result[i] = func(0, i); }
+
+    for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
+      BOUT_FOR(d, result.yup(i).getValidRegionWithDefault("RGN_INVALID")) {
+        result.yup(i)[d] = func(i + 1, d);
+      }
+      BOUT_FOR(d, result.ydown(i).getValidRegionWithDefault("RGN_INVALID")) {
+        result.ydown(i)[d] = func(-i - 1, d);
+      }
+    }
+  } else {
+    BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = func(0, i); }
+  }
+
+  return result;
+}
+
 #endif /* BOUT_FIELD3D_H */

From 9b119c89c99fee2ef8cc20c8f557dae8ba206e94 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 25 Aug 2025 13:04:21 +0200
Subject: [PATCH 0818/1827] Allocate before usage

---
 include/bout/field3d.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 60e1a1b83f..8d278099b6 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -826,9 +826,11 @@ filledFrom(const Field3DParallel& f,
     BOUT_FOR(i, result.getRegion("RGN_NOY")) { result[i] = func(0, i); }
 
     for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
+      result.yup(i).allocate();
       BOUT_FOR(d, result.yup(i).getValidRegionWithDefault("RGN_INVALID")) {
         result.yup(i)[d] = func(i + 1, d);
       }
+      result.ydown(i).allocate();
       BOUT_FOR(d, result.ydown(i).getValidRegionWithDefault("RGN_INVALID")) {
         result.ydown(i)[d] = func(-i - 1, d);
       }

From 69dfaadccf130ed1f412fab4ee70451f092cb2e2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Sep 2025 15:12:50 +0200
Subject: [PATCH 0819/1827] Remove commented out code

---
 src/field/field3d.cxx | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 36e0b6901d..abc8610183 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -951,9 +951,11 @@ void Field3D::_track(const BoutReal& change, std::string operation) {
 void Field3DParallel::ensureFieldAligned() {
   if (isFci()) {
     ASSERT2(hasParallelSlices());
-  } // else {
-  //   if (getDirectionY() != YDirectionType::Aligned) {
-  //     *this = toFieldAligned(*this);
-  //   }
-  // }
+    if (fieldmesh != nullptr) {
+      for (int i = 0; i < fieldmesh->ystart; ++i) {
+        ASSERT2(yup_fields[i].getRegionID().has_value());
+        ASSERT2(ydown_fields[i].getRegionID().has_value());
+      }
+    }
+  }
 }

From 7b9525c3b204c458a0d985b2d7ddf36bfc997d35 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 21 Oct 2025 16:15:42 +0200
Subject: [PATCH 0820/1827] add asField3DParallel() const

---
 include/bout/field3d.hxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 8d278099b6..6e2fa31a65 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -521,6 +521,7 @@ public:
   void disallowCalcParallelSlices() { _allowCalcParallelSlices = false; };
 
   inline Field3DParallel asField3DParallel();
+  inline const Field3DParallel asField3DParallel() const;
 
 protected:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
@@ -791,6 +792,9 @@ private:
 };
 
 Field3DParallel Field3D::asField3DParallel() { return Field3DParallel(*this); }
+const Field3DParallel Field3D::asField3DParallel() const {
+  return Field3DParallel(*this);
+}
 
 inline Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs) {
   return lhs + rhs.asField3D();

From fb6c0165dee4474f47ee9b911c17ce442322e61c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 23 Oct 2025 14:31:27 +0200
Subject: [PATCH 0821/1827] Add Field3DParallel::allocate

---
 include/bout/field3d.hxx | 20 +++++++++++---------
 src/field/field3d.cxx    | 14 ++++++++++++++
 2 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 6e2fa31a65..821add3b58 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -739,27 +739,28 @@ inline Field3D copy(const Field3D& f) {
 /// "main" field, Field3DParallel will retain the parallel slices.
 class Field3DParallel : public Field3D {
 public:
-  template <class... Types>
+  explicit template <class... Types>
   Field3DParallel(Types... args) : Field3D(std::move(args)...) {
     ensureFieldAligned();
   }
   // Explicitly needed, as DirectionTypes is sometimes constructed from a
   // brace enclosed list
-  Field3DParallel(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
-                  DirectionTypes directions_in = {YDirectionType::Standard,
-                                                  ZDirectionType::Standard},
-                  std::optional<size_t> regionID = {})
+  explicit Field3DParallel(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
+                           DirectionTypes directions_in = {YDirectionType::Standard,
+                                                           ZDirectionType::Standard},
+                           std::optional<size_t> regionID = {})
       : Field3D(localmesh, location_in, directions_in, regionID) {
     splitParallelSlices();
     ensureFieldAligned();
   }
-  Field3DParallel(Array<BoutReal> data, Mesh* localmesh, CELL_LOC location = CELL_CENTRE,
-                  DirectionTypes directions_in = {YDirectionType::Standard,
-                                                  ZDirectionType::Standard})
+  explicit Field3DParallel(Array<BoutReal> data, Mesh* localmesh,
+                           CELL_LOC location = CELL_CENTRE,
+                           DirectionTypes directions_in = {YDirectionType::Standard,
+                                                           ZDirectionType::Standard})
       : Field3D(std::move(data), localmesh, location, directions_in) {
     ensureFieldAligned();
   }
-  Field3DParallel(BoutReal, Mesh* mesh = nullptr);
+  explicit Field3DParallel(BoutReal, Mesh* mesh = nullptr);
   Field3D& asField3D() { return *this; }
   const Field3D& asField3D() const { return *this; }
 
@@ -786,6 +787,7 @@ public:
     return *this;
   }
   Field3DParallel& operator=(BoutReal);
+  Field3DParallel& allocate();
 
 private:
   void ensureFieldAligned();
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index abc8610183..c0d514f972 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -959,3 +959,17 @@ void Field3DParallel::ensureFieldAligned() {
     }
   }
 }
+
+Field3DParallel& Field3DParallel::allocate() {
+  Field3D::allocate();
+  if (isFci()) {
+    ASSERT2(hasParallelSlices());
+    if (fieldmesh != nullptr) {
+      for (int i = 0; i < fieldmesh->ystart; ++i) {
+        yup_fields[i].allocate();
+        ydown_fields[i].allocate();
+      }
+    }
+  }
+  return *this;
+}

From 033d872d6282f87784064075b4423a68e0f1a535 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Oct 2025 12:00:36 +0100
Subject: [PATCH 0822/1827] Add implict constructors only for Field2D and
 Field3D

---
 include/bout/field3d.hxx | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 821add3b58..368bb2297b 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -739,10 +739,12 @@ inline Field3D copy(const Field3D& f) {
 /// "main" field, Field3DParallel will retain the parallel slices.
 class Field3DParallel : public Field3D {
 public:
-  explicit template <class... Types>
-  Field3DParallel(Types... args) : Field3D(std::move(args)...) {
+  template <class... Types>
+  explicit Field3DParallel(Types... args) : Field3D(std::move(args)...) {
     ensureFieldAligned();
   }
+  Field3DParallel(const Field3D& f) : Field3D(std::move(f)) { ensureFieldAligned(); }
+  Field3DParallel(const Field2D& f) : Field3D(std::move(f)) { ensureFieldAligned(); }
   // Explicitly needed, as DirectionTypes is sometimes constructed from a
   // brace enclosed list
   explicit Field3DParallel(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,

From 2590f7c9256a60ef95f0af49d78676496c71f949 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 5 Nov 2025 10:56:06 +0100
Subject: [PATCH 0823/1827] add yup and ydown property

---
 src/field/gen_fieldops.jinja | 12 ++++++------
 src/field/gen_fieldops.py    | 18 ++++++++++++++++++
 2 files changed, 24 insertions(+), 6 deletions(-)

diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index 46c9fcad68..19d40ab367 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -16,8 +16,8 @@
       if ({{lhs.name}}.isFci()) {
         {{out.name}}.splitParallelSlices();
         for (size_t i{0} ; i < {{lhs.name}}.numberParallelSlices() ; ++i) {
-          {{out.name}}.yup(i) = {{lhs.name}}.yup(i) {{operator}} {{rhs.name}}.yup(i);
-          {{out.name}}.ydown(i) = {{lhs.name}}.ydown(i) {{operator}} {{rhs.name}}.ydown(i);
+          {{out.name}}.yup(i) = {{lhs.yup}} {{operator}} {{rhs.yup}};
+          {{out.name}}.ydown(i) = {{lhs.ydown}} {{operator}} {{rhs.ydown}};
         }
       }
       {% endif %}
@@ -27,8 +27,8 @@
       if ({{lhs.name}}.isFci()) {
         {{out.name}}.splitParallelSlices();
 	for (size_t i{0} ; i < {{lhs.name}}.numberParallelSlices() ; ++i) {
-          {{out.name}}.yup(i) = {{lhs.name}}.yup(i) {{operator}} {{rhs.name}};
-          {{out.name}}.ydown(i) = {{lhs.name}}.ydown(i) {{operator}} {{rhs.name}};
+          {{out.name}}.yup(i) = {{lhs.yup}} {{operator}} {{rhs.yup}};
+          {{out.name}}.ydown(i) = {{lhs.ydown}} {{operator}} {{rhs.ydown}};
         }
       }
       {% endif %}
@@ -38,8 +38,8 @@
       if ({{rhs.name}}.isFci()) {
         {{out.name}}.splitParallelSlices();
 	for (size_t i{0} ; i < {{rhs.name}}.numberParallelSlices() ; ++i) {
-          {{out.name}}.yup(i) = {{lhs.name}} {{operator}} {{rhs.name}}.yup(i);
-          {{out.name}}.ydown(i) = {{lhs.name}} {{operator}} {{rhs.name}}.ydown(i);
+          {{out.name}}.yup(i) = {{lhs.yup}} {{operator}} {{rhs.yup}};
+          {{out.name}}.ydown(i) = {{lhs.ydown}} {{operator}} {{rhs.ydown}};
         }
       }
       {% endif %}
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 473cf3df1f..df3f223707 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -155,6 +155,24 @@ def base_index(self):
         else:
             return "{self.name}[{self.mixed_base_ind_var}]".format(self=self)
 
+    @property
+    def yup(self):
+        """Returns {{name}}.yup(i) if it is a field with parallel slices.
+        If it is BoutReal just {{name}}"""
+        if self.field_type == "BoutReal":
+            return "{self.name}".format(self=self)
+        else:
+            return "{self.name}.yup(i)".format(self=self)
+
+    @property
+    def ydown(self):
+        """Returns {{name}}.ydown(i) if it is a field with parallel slices.
+        If it is BoutReal just {{name}}"""
+        if self.field_type == "BoutReal":
+            return "{self.name}".format(self=self)
+        else:
+            return "{self.name}.ydown(i)".format(self=self)
+
     def __eq__(self, other):
         try:
             return self.field_type == other.field_type

From 957f058e569c80db988623b39d256f7f4b04259c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 5 Nov 2025 10:56:30 +0100
Subject: [PATCH 0824/1827] simplify template

---
 src/field/gen_fieldops.jinja     | 30 +++++++-----------------
 src/field/generated_fieldops.cxx | 40 ++++++++++++++++----------------
 2 files changed, 28 insertions(+), 42 deletions(-)

diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index 19d40ab367..be57c00373 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -12,37 +12,23 @@
     {% if lhs.region_type == rhs.region_type == "3D" %}
       {{out.name}}.setRegion({{lhs.name}}.getMesh()->getCommonRegion({{lhs.name}}.getRegionID(),
                                                                      {{rhs.name}}.getRegionID()));
-      {% if out == "Field3DParallel" %}
-      if ({{lhs.name}}.isFci()) {
-        {{out.name}}.splitParallelSlices();
-        for (size_t i{0} ; i < {{lhs.name}}.numberParallelSlices() ; ++i) {
-          {{out.name}}.yup(i) = {{lhs.yup}} {{operator}} {{rhs.yup}};
-          {{out.name}}.ydown(i) = {{lhs.ydown}} {{operator}} {{rhs.ydown}};
-        }
-      }
-      {% endif %}
     {% elif lhs.region_type == "3D" %}
       {{out.name}}.setRegion({{lhs.name}}.getRegionID());
-      {% if rhs == "BoutReal" and out == "Field3DParallel" %}
-      if ({{lhs.name}}.isFci()) {
-        {{out.name}}.splitParallelSlices();
-	for (size_t i{0} ; i < {{lhs.name}}.numberParallelSlices() ; ++i) {
-          {{out.name}}.yup(i) = {{lhs.yup}} {{operator}} {{rhs.yup}};
-          {{out.name}}.ydown(i) = {{lhs.ydown}} {{operator}} {{rhs.ydown}};
-        }
-      }
-      {% endif %}
     {% elif rhs.region_type == "3D" %}
       {{out.name}}.setRegion({{rhs.name}}.getRegionID());
-      {% if lhs == "BoutReal" and rhs == "Field3DParallel" %}
-      if ({{rhs.name}}.isFci()) {
+    {% endif %}
+    {% if out == "Field3DParallel" %}
+      if ({{out.name}}.isFci()) {
         {{out.name}}.splitParallelSlices();
-	for (size_t i{0} ; i < {{rhs.name}}.numberParallelSlices() ; ++i) {
+      {% if lhs.region_type == "3D" %}
+        for (size_t i{0} ; i < {{lhs.name}}.numberParallelSlices() ; ++i) {
+      {% else %}
+        for (size_t i{0} ; i < {{rhs.name}}.numberParallelSlices() ; ++i) {
+      {% endif %}
           {{out.name}}.yup(i) = {{lhs.yup}} {{operator}} {{rhs.yup}};
           {{out.name}}.ydown(i) = {{lhs.ydown}} {{operator}} {{rhs.ydown}};
         }
       }
-      {% endif %}
     {% endif %}
   {% endif %}
 
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 9dad114ec8..9bbf6b06d2 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -1958,7 +1958,7 @@ Field3DParallel operator*(const Field3D& lhs, const Field3DParallel& rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs.yup(i);
@@ -1983,7 +1983,7 @@ Field3DParallel operator/(const Field3D& lhs, const Field3DParallel& rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs.yup(i);
@@ -2008,7 +2008,7 @@ Field3DParallel operator+(const Field3D& lhs, const Field3DParallel& rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs.yup(i);
@@ -2033,7 +2033,7 @@ Field3DParallel operator-(const Field3D& lhs, const Field3DParallel& rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs.yup(i);
@@ -2058,7 +2058,7 @@ Field3DParallel operator*(const Field3DParallel& lhs, const Field3D& rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs.yup(i);
@@ -2116,7 +2116,7 @@ Field3DParallel operator/(const Field3DParallel& lhs, const Field3D& rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs.yup(i);
@@ -2174,7 +2174,7 @@ Field3DParallel operator+(const Field3DParallel& lhs, const Field3D& rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs.yup(i);
@@ -2232,7 +2232,7 @@ Field3DParallel operator-(const Field3DParallel& lhs, const Field3D& rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs.yup(i);
@@ -2290,7 +2290,7 @@ Field3DParallel operator*(const Field3DParallel& lhs, const Field3DParallel& rhs
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs.yup(i);
@@ -2348,7 +2348,7 @@ Field3DParallel operator/(const Field3DParallel& lhs, const Field3DParallel& rhs
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs.yup(i);
@@ -2406,7 +2406,7 @@ Field3DParallel operator+(const Field3DParallel& lhs, const Field3DParallel& rhs
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs.yup(i);
@@ -2464,7 +2464,7 @@ Field3DParallel operator-(const Field3DParallel& lhs, const Field3DParallel& rhs
   checkData(rhs);
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs.yup(i);
@@ -2521,7 +2521,7 @@ Field3DParallel operator*(const Field3DParallel& lhs, const BoutReal rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getRegionID());
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs;
@@ -2581,7 +2581,7 @@ Field3DParallel operator/(const Field3DParallel& lhs, const BoutReal rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getRegionID());
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs;
@@ -2642,7 +2642,7 @@ Field3DParallel operator+(const Field3DParallel& lhs, const BoutReal rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getRegionID());
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs;
@@ -2702,7 +2702,7 @@ Field3DParallel operator-(const Field3DParallel& lhs, const BoutReal rhs) {
   checkData(rhs);
 
   result.setRegion(lhs.getRegionID());
-  if (lhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs;
@@ -2762,7 +2762,7 @@ Field3DParallel operator*(const BoutReal lhs, const Field3DParallel& rhs) {
   checkData(rhs);
 
   result.setRegion(rhs.getRegionID());
-  if (rhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs * rhs.yup(i);
@@ -2786,7 +2786,7 @@ Field3DParallel operator/(const BoutReal lhs, const Field3DParallel& rhs) {
   checkData(rhs);
 
   result.setRegion(rhs.getRegionID());
-  if (rhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs / rhs.yup(i);
@@ -2810,7 +2810,7 @@ Field3DParallel operator+(const BoutReal lhs, const Field3DParallel& rhs) {
   checkData(rhs);
 
   result.setRegion(rhs.getRegionID());
-  if (rhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs + rhs.yup(i);
@@ -2834,7 +2834,7 @@ Field3DParallel operator-(const BoutReal lhs, const Field3DParallel& rhs) {
   checkData(rhs);
 
   result.setRegion(rhs.getRegionID());
-  if (rhs.isFci()) {
+  if (result.isFci()) {
     result.splitParallelSlices();
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs - rhs.yup(i);

From ea71ae205cfcd600cb19ee19992668e6e059dc78 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 5 Nov 2025 11:25:39 +0100
Subject: [PATCH 0825/1827] Add some asserts for Field3DParallel

---
 src/field/gen_fieldops.jinja     |  2 ++
 src/field/gen_fieldops.py        | 12 ++++++----
 src/field/generated_fieldops.cxx | 40 ++++++++++++++++++++++++++++++++
 3 files changed, 50 insertions(+), 4 deletions(-)

diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index be57c00373..adc4655e87 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -19,6 +19,8 @@
     {% endif %}
     {% if out == "Field3DParallel" %}
       if ({{out.name}}.isFci()) {
+	{{ lhs.assertParallelSlices }}
+	{{ rhs.assertParallelSlices }}
         {{out.name}}.splitParallelSlices();
       {% if lhs.region_type == "3D" %}
         for (size_t i{0} ; i < {{lhs.name}}.numberParallelSlices() ; ++i) {
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index df3f223707..e44b0645fe 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -161,8 +161,7 @@ def yup(self):
         If it is BoutReal just {{name}}"""
         if self.field_type == "BoutReal":
             return "{self.name}".format(self=self)
-        else:
-            return "{self.name}.yup(i)".format(self=self)
+        return "{self.name}.yup(i)".format(self=self)
 
     @property
     def ydown(self):
@@ -170,8 +169,13 @@ def ydown(self):
         If it is BoutReal just {{name}}"""
         if self.field_type == "BoutReal":
             return "{self.name}".format(self=self)
-        else:
-            return "{self.name}.ydown(i)".format(self=self)
+        return "{self.name}.ydown(i)".format(self=self)
+
+    @property
+    def assertParallelSlices(self):
+        if self.field_type == "BoutReal":
+            return ""
+        return f"ASSERT2({self.name}.hasParallelSlices());"
 
     def __eq__(self, other):
         try:
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 9bbf6b06d2..7e6b93662d 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -1960,6 +1960,8 @@ Field3DParallel operator*(const Field3D& lhs, const Field3DParallel& rhs) {
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
@@ -1985,6 +1987,8 @@ Field3DParallel operator/(const Field3D& lhs, const Field3DParallel& rhs) {
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
@@ -2010,6 +2014,8 @@ Field3DParallel operator+(const Field3D& lhs, const Field3DParallel& rhs) {
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
@@ -2035,6 +2041,8 @@ Field3DParallel operator-(const Field3D& lhs, const Field3DParallel& rhs) {
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
@@ -2060,6 +2068,8 @@ Field3DParallel operator*(const Field3DParallel& lhs, const Field3D& rhs) {
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
@@ -2118,6 +2128,8 @@ Field3DParallel operator/(const Field3DParallel& lhs, const Field3D& rhs) {
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
@@ -2176,6 +2188,8 @@ Field3DParallel operator+(const Field3DParallel& lhs, const Field3D& rhs) {
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
@@ -2234,6 +2248,8 @@ Field3DParallel operator-(const Field3DParallel& lhs, const Field3D& rhs) {
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
@@ -2292,6 +2308,8 @@ Field3DParallel operator*(const Field3DParallel& lhs, const Field3DParallel& rhs
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
@@ -2350,6 +2368,8 @@ Field3DParallel operator/(const Field3DParallel& lhs, const Field3DParallel& rhs
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
@@ -2408,6 +2428,8 @@ Field3DParallel operator+(const Field3DParallel& lhs, const Field3DParallel& rhs
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
@@ -2466,6 +2488,8 @@ Field3DParallel operator-(const Field3DParallel& lhs, const Field3DParallel& rhs
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
@@ -2523,6 +2547,8 @@ Field3DParallel operator*(const Field3DParallel& lhs, const BoutReal rhs) {
   result.setRegion(lhs.getRegionID());
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs;
       result.ydown(i) = lhs.ydown(i) * rhs;
@@ -2583,6 +2609,8 @@ Field3DParallel operator/(const Field3DParallel& lhs, const BoutReal rhs) {
   result.setRegion(lhs.getRegionID());
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs;
       result.ydown(i) = lhs.ydown(i) / rhs;
@@ -2644,6 +2672,8 @@ Field3DParallel operator+(const Field3DParallel& lhs, const BoutReal rhs) {
   result.setRegion(lhs.getRegionID());
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs;
       result.ydown(i) = lhs.ydown(i) + rhs;
@@ -2704,6 +2734,8 @@ Field3DParallel operator-(const Field3DParallel& lhs, const BoutReal rhs) {
   result.setRegion(lhs.getRegionID());
   if (result.isFci()) {
     result.splitParallelSlices();
+    ASSERT2(lhs.hasParallelSlices());
+
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs;
       result.ydown(i) = lhs.ydown(i) - rhs;
@@ -2764,6 +2796,8 @@ Field3DParallel operator*(const BoutReal lhs, const Field3DParallel& rhs) {
   result.setRegion(rhs.getRegionID());
   if (result.isFci()) {
     result.splitParallelSlices();
+
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs * rhs.yup(i);
       result.ydown(i) = lhs * rhs.ydown(i);
@@ -2788,6 +2822,8 @@ Field3DParallel operator/(const BoutReal lhs, const Field3DParallel& rhs) {
   result.setRegion(rhs.getRegionID());
   if (result.isFci()) {
     result.splitParallelSlices();
+
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs / rhs.yup(i);
       result.ydown(i) = lhs / rhs.ydown(i);
@@ -2812,6 +2848,8 @@ Field3DParallel operator+(const BoutReal lhs, const Field3DParallel& rhs) {
   result.setRegion(rhs.getRegionID());
   if (result.isFci()) {
     result.splitParallelSlices();
+
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs + rhs.yup(i);
       result.ydown(i) = lhs + rhs.ydown(i);
@@ -2836,6 +2874,8 @@ Field3DParallel operator-(const BoutReal lhs, const Field3DParallel& rhs) {
   result.setRegion(rhs.getRegionID());
   if (result.isFci()) {
     result.splitParallelSlices();
+
+    ASSERT2(rhs.hasParallelSlices());
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs - rhs.yup(i);
       result.ydown(i) = lhs - rhs.ydown(i);

From 46d666350f0a0b5fb23ed93f52068944258d7fb3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 5 Nov 2025 11:51:04 +0100
Subject: [PATCH 0826/1827] Ensure parallel slices are present

---
 src/mesh/coordinates.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index b1b850b577..5d3667a609 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1762,7 +1762,8 @@ Coordinates::FieldMetric Coordinates::Laplace_par(const Field2D& f, CELL_LOC out
 
 Field3D Coordinates::Laplace_par(const Field3DParallel& f, CELL_LOC outloc) {
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-  return D2DY2(f, outloc) / g_22 + DDY(J / g_22, outloc) * ::DDY(f, outloc) / J;
+  return D2DY2(f, outloc) / g_22
+         + DDY(J.asField3DParallel() / g_22, outloc) * ::DDY(f, outloc) / J;
 }
 
 // Full Laplacian operator on scalar field

From b1068d1cce0d3d34f866f753baa2f876325fe52b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 5 Nov 2025 11:51:24 +0100
Subject: [PATCH 0827/1827] Simplify div_par

---
 src/mesh/coordinates.cxx | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 5d3667a609..64c67ade1d 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1570,13 +1570,8 @@ Field3D Coordinates::Div_par(const Field3DParallel& f, CELL_LOC outloc,
   }
 
   // Need to modify yup and ydown fields
-  Field3D f_B = f / Bxy_floc;
-  f_B.splitParallelSlices();
-  for (int i = 0; i < f.getMesh()->ystart; ++i) {
-    f_B.yup(i) = f.yup(i) / Bxy_floc.yup(i);
-    f_B.ydown(i) = f.ydown(i) / Bxy_floc.ydown(i);
-  }
-  return Bxy * Grad_par(f_B, outloc, method);
+  Field3D Jg = coords->J / sqrt(coords->g_22.asField3DParallel());
+  return Jg * Grad_par(f / Jg, outloc, method);
 }
 
 /////////////////////////////////////////////////////////

From f15f2045659464dec429cb5a2bb67c0850632073 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 5 Nov 2025 11:51:47 +0100
Subject: [PATCH 0828/1827] Do not communicate the magnetic field

---
 tests/MMS/spatial/fci/fci_mms.cxx | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index 7967452f3d..90bf107f3c 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -46,12 +46,6 @@ int main(int argc, char** argv) {
   Field3D K{FieldFactory::get()->create3D("K", Options::getRoot(), mesh)};
 
   // Communicate to calculate parallel transform.
-  if constexpr (bout::build::use_metric_3d) {
-    // Div_par operators require B parallel slices:
-    // Coordinates::geometry doesn't ensure this (yet)
-    auto& Bxy = mesh->getCoordinates()->Bxy;
-    mesh->communicate(Bxy);
-  }
   mesh->communicate(input, K);
 
   Options dump;

From d8b22402e44e38c2336c20aca1e6dd81e381298e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 5 Nov 2025 11:52:52 +0100
Subject: [PATCH 0829/1827] Ensure parallel slices are set in FIELD_FUNC

---
 include/bout/field.hxx | 29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 6c22a4a258..1e54a4f96b 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -522,20 +522,27 @@ T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
  * result for non-finite numbers
  *
  */
+class Field3DParallel;
 #ifdef FIELD_FUNC
 #error This macro has already been defined
 #else
-#define FIELD_FUNC(name, func)                                     \
-  template <typename T, typename = bout::utils::EnableIfField<T>>  \
-  inline T name(const T& f, const std::string& rgn = "RGN_ALL") {  \
-                                                                   \
-    /* Check if the input is allocated */                          \
-    checkData(f);                                                  \
-    /* Define and allocate the output result */                    \
-    T result{emptyFrom(f)};                                        \
-    BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); } \
-    checkData(result);                                             \
-    return result;                                                 \
+#define FIELD_FUNC(_name, func)                                        \
+  template <typename T, typename = bout::utils::EnableIfField<T>>      \
+  inline T _name(const T& f, const std::string& rgn = "RGN_ALL") {     \
+    /* Check if the input is allocated */                              \
+    checkData(f);                                                      \
+    /* Define and allocate the output result */                        \
+    T result{emptyFrom(f)};                                            \
+    BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); }     \
+    if constexpr (std::is_base_of_v<Field3DParallel, T>) {             \
+      for (int i = 0; i < f.numberParallelSlices(); ++i) {             \
+        result.yup(i) = func(f.yup(i));                                \
+        result.ydown(i) = func(f.ydown(i));                            \
+      }                                                                \
+    }                                                                  \
+    result.name = std::string(#_name "(") + f.name + std::string(")"); \
+    checkData(result);                                                 \
+    return result;                                                     \
   }
 #endif
 

From 9a8ebcb838c5ef1d45f881526245bdba9d7e479c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 20 Jan 2026 09:27:00 +0100
Subject: [PATCH 0830/1827] ensure parallel fields are allocated

---
 src/field/field3d.cxx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index c0d514f972..0a1dae3929 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -957,6 +957,12 @@ void Field3DParallel::ensureFieldAligned() {
         ASSERT2(ydown_fields[i].getRegionID().has_value());
       }
     }
+    if (isAllocated()) {
+      for (int i = 0; i < fieldmesh->ystart; ++i) {
+        ASSERT2(yup_fields[i].isAllocated());
+        ASSERT2(ydown_fields[i].isAllocated());
+      }
+    }
   }
 }
 

From b6e1b56b805532814e985808ee482656ff5af390 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 21 Jan 2026 13:53:49 +0100
Subject: [PATCH 0831/1827] Ensure `f3d.asField3DParallel() *= x` updates f3d

Add unit test as well as fix
---
 include/bout/field3d.hxx          |  6 +++++-
 src/field/gen_fieldops.jinja      |  4 ++++
 src/field/generated_fieldops.cxx  | 24 ++++++++++++------------
 tests/unit/field/test_field3d.cxx | 20 ++++++++++++++++++++
 4 files changed, 41 insertions(+), 13 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 368bb2297b..ac9f94bcec 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -744,6 +744,9 @@ public:
     ensureFieldAligned();
   }
   Field3DParallel(const Field3D& f) : Field3D(std::move(f)) { ensureFieldAligned(); }
+  Field3DParallel(const Field3D& f, bool isRef) : Field3D(std::move(f)), isRef(isRef) {
+    ensureFieldAligned();
+  }
   Field3DParallel(const Field2D& f) : Field3D(std::move(f)) { ensureFieldAligned(); }
   // Explicitly needed, as DirectionTypes is sometimes constructed from a
   // brace enclosed list
@@ -793,9 +796,10 @@ public:
 
 private:
   void ensureFieldAligned();
+  bool isRef{false};
 };
 
-Field3DParallel Field3D::asField3DParallel() { return Field3DParallel(*this); }
+Field3DParallel Field3D::asField3DParallel() { return Field3DParallel(*this, true); }
 const Field3DParallel Field3D::asField3DParallel() const {
   return Field3DParallel(*this);
 }
diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index adc4655e87..8cf097e8df 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -85,7 +85,11 @@
 {{lhs}} &{{lhs}}::operator{{operator}}=(const {{rhs.passByReference}}) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
+{% if lhs == "Field3DParallel" %}
+  if (data.unique() or isRef) {
+{% else %}
   if (data.unique()) {
+{% endif %}
     {% if lhs != "BoutReal" and rhs != "BoutReal" %}
       ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
     {% endif %}
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 7e6b93662d..8b9a3b50e5 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -2088,7 +2088,7 @@ Field3DParallel operator*(const Field3DParallel& lhs, const Field3D& rhs) {
 Field3DParallel& Field3DParallel::operator*=(const Field3D& rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
@@ -2148,7 +2148,7 @@ Field3DParallel operator/(const Field3DParallel& lhs, const Field3D& rhs) {
 Field3DParallel& Field3DParallel::operator/=(const Field3D& rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
@@ -2208,7 +2208,7 @@ Field3DParallel operator+(const Field3DParallel& lhs, const Field3D& rhs) {
 Field3DParallel& Field3DParallel::operator+=(const Field3D& rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
@@ -2268,7 +2268,7 @@ Field3DParallel operator-(const Field3DParallel& lhs, const Field3D& rhs) {
 Field3DParallel& Field3DParallel::operator-=(const Field3D& rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
@@ -2328,7 +2328,7 @@ Field3DParallel operator*(const Field3DParallel& lhs, const Field3DParallel& rhs
 Field3DParallel& Field3DParallel::operator*=(const Field3DParallel& rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
@@ -2388,7 +2388,7 @@ Field3DParallel operator/(const Field3DParallel& lhs, const Field3DParallel& rhs
 Field3DParallel& Field3DParallel::operator/=(const Field3DParallel& rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
@@ -2448,7 +2448,7 @@ Field3DParallel operator+(const Field3DParallel& lhs, const Field3DParallel& rhs
 Field3DParallel& Field3DParallel::operator+=(const Field3DParallel& rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
@@ -2508,7 +2508,7 @@ Field3DParallel operator-(const Field3DParallel& lhs, const Field3DParallel& rhs
 Field3DParallel& Field3DParallel::operator-=(const Field3DParallel& rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
@@ -2570,7 +2570,7 @@ Field3DParallel operator*(const Field3DParallel& lhs, const BoutReal rhs) {
 Field3DParallel& Field3DParallel::operator*=(const BoutReal rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
 
     if (this->isFci()) {
       for (size_t i{0}; i < yup_fields.size(); ++i) {
@@ -2633,7 +2633,7 @@ Field3DParallel operator/(const Field3DParallel& lhs, const BoutReal rhs) {
 Field3DParallel& Field3DParallel::operator/=(const BoutReal rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
 
     if (this->isFci()) {
       for (size_t i{0}; i < yup_fields.size(); ++i) {
@@ -2695,7 +2695,7 @@ Field3DParallel operator+(const Field3DParallel& lhs, const BoutReal rhs) {
 Field3DParallel& Field3DParallel::operator+=(const BoutReal rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
 
     if (this->isFci()) {
       for (size_t i{0}; i < yup_fields.size(); ++i) {
@@ -2757,7 +2757,7 @@ Field3DParallel operator-(const Field3DParallel& lhs, const BoutReal rhs) {
 Field3DParallel& Field3DParallel::operator-=(const BoutReal rhs) {
   // only if data is unique we update the field
   // otherwise just call the non-inplace version
-  if (data.unique()) {
+  if (data.unique() or isRef) {
 
     if (this->isFci()) {
       for (size_t i{0}; i < yup_fields.size(); ++i) {
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index d80affc3f7..7672ec7dae 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -2450,5 +2450,25 @@ TEST_F(Field3DTest, ZeroFrom) {
   EXPECT_TRUE(field2.isAllocated());
   EXPECT_TRUE(IsFieldEqual(field2, 0.));
 }
+
+TEST_F(Field3DTest, Field3DParallel) {
+  Field3DParallel field(1.0);
+  field = 1.0;
+
+  Field3D field2 = field;
+
+  auto& field3 = field.asField3D();
+
+  field *= 2;
+
+  EXPECT_TRUE(IsFieldEqual(field, 2.0));
+  EXPECT_TRUE(IsFieldEqual(field2, 1.0));
+  EXPECT_TRUE(IsFieldEqual(field3, 2.0));
+
+  field3.asField3DParallel() *= 3;
+
+  EXPECT_TRUE(IsFieldEqual(field3, 6.0));
+}
+
 // Restore compiler warnings
 #pragma GCC diagnostic pop

From 82d046a6261243f9778d9fc72fcbb8e7deb78a13 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 22 Jan 2026 13:44:34 +0100
Subject: [PATCH 0832/1827] ensure also parallel fields are updated in-place

---
 include/bout/field3d.hxx         |  22 +-
 src/field/gen_fieldops.jinja     |  79 +++++-
 src/field/generated_fieldops.cxx | 470 ++++++++++++++++++++++++++++---
 3 files changed, 531 insertions(+), 40 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index ac9f94bcec..f57a098430 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -475,6 +475,19 @@ public:
   Field3D& operator/=(BoutReal rhs);
   ///@}
 
+  Field3D& update_multiplication_inplace(const Field3D& rhs);
+  Field3D& update_division_inplace(const Field3D& rhs);
+  Field3D& update_addition_inplace(const Field3D& rhs);
+  Field3D& update_subtraction_inplace(const Field3D& rhs);
+  Field3D& update_multiplication_inplace(const Field2D& rhs);
+  Field3D& update_division_inplace(const Field2D& rhs);
+  Field3D& update_addition_inplace(const Field2D& rhs);
+  Field3D& update_subtraction_inplace(const Field2D& rhs);
+  Field3D& update_multiplication_inplace(BoutReal rhs);
+  Field3D& update_division_inplace(BoutReal rhs);
+  Field3D& update_addition_inplace(BoutReal rhs);
+  Field3D& update_subtraction_inplace(BoutReal rhs);
+
   // FieldData virtual functions
   bool is3D() const override { return true; }
 
@@ -799,7 +812,14 @@ private:
   bool isRef{false};
 };
 
-Field3DParallel Field3D::asField3DParallel() { return Field3DParallel(*this, true); }
+Field3DParallel Field3D::asField3DParallel() {
+  allocate();
+  for (size_t i = 0; i < numberParallelSlices(); ++i) {
+    yup(i).allocate();
+    ydown(i).allocate();
+  }
+  return Field3DParallel(*this, true);
+}
 const Field3DParallel Field3D::asField3DParallel() const {
   return Field3DParallel(*this);
 }
diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index 8cf097e8df..ba2e4d65c8 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -80,6 +80,72 @@
   return {{out.name}};
 }
 
+{% if out.field_type == lhs.field_type and lhs == "Field3D" %}
+// Provide the C++ operator to update {{lhs}} by {{operator_name}} with {{rhs}}
+{{lhs}} &{{lhs}}::update_{{operator_name}}_inplace(const {{rhs.passByReference}}) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  {% if lhs != "BoutReal" and rhs != "BoutReal" %}
+    ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+  {% endif %}
+
+    // Delete existing parallel slices. We don't update parallel slices, so any
+    // that currently exist will be incorrect.
+    clearParallelSlices();
+    checkData(*this);
+    checkData({{rhs.name}});
+
+    {% if lhs.region_type == rhs.region_type == "3D" %}
+      regionID = fieldmesh->getCommonRegion(regionID, {{rhs.name}}.getRegionID());
+    {% endif %}
+
+
+  {% if (lhs == "Field3D") and (rhs =="Field2D") %}
+    {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) {
+	const auto {{mixed_base_ind}} = fieldmesh->ind2Dto3D({{index_var}});
+	{% if (operator == "/") and (rhs == "Field2D") %}
+           const auto tmp = 1.0 / {{rhs.mixed_index}};
+	   for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
+		   (*this)[{{mixed_base_ind}} + {{jz_var}}] *= tmp;
+        {% else %}
+           for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
+	           (*this)[{{mixed_base_ind}} + {{jz_var}}] {{operator}}= {{rhs.index}};
+        {% endif %}
+	}
+	}
+  {% elif rhs == "FieldPerp" and (lhs == "Field3D" or lhs == "Field2D")%}
+    Mesh *localmesh = this->getMesh();
+
+    {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) {
+            int yind = {{rhs.name}}.getIndex();
+            const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
+            (*this)[{{base_ind_var}}] {{operator}}= {{rhs.index}};
+	}
+  {% elif (operator == "/") and (lhs == "Field3D" or lhs == "Field2D") and (rhs =="BoutReal") %}
+    const auto tmp = 1.0 / {{rhs.index}};
+    {{region_loop}}({{index_var}}, this->getRegion({{region_name}})) {
+        (*this)[{{index_var}}] *= tmp;
+    }
+  {% else %}
+    {{region_loop}}({{index_var}}, this->getRegion({{region_name}})) {
+      (*this)[{{index_var}}] {{operator}}= {{rhs.index}};
+    }
+  {% endif %}
+
+  {% if lhs.region_type == "3D" %}
+    track(rhs, "operator{{operator}}=");
+  {% endif %}
+#if BOUT_USE_TRACK
+    name = fmt::format("{:s} {{operator}}= {:s}", this->name, {{'"BR"' if rhs == "BoutReal" else rhs.name + ".name"}});
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+{% endif %}
+
+
 {% if out.field_type == lhs.field_type %}
 // Provide the C++ operator to update {{lhs}} by {{operator_name}} with {{rhs}}
 {{lhs}} &{{lhs}}::operator{{operator}}=(const {{rhs.passByReference}}) {
@@ -101,9 +167,16 @@
     {% endif %}
     {% if lhs == "Field3DParallel" and (rhs.region_type == "3D" or rhs == "BoutReal") %}
       if (this->isFci()) {
-	for (size_t i{0} ; i < yup_fields.size() ; ++i) {
-          yup(i) {{operator}}= {{rhs.name}}{% if rhs == "Field3D" %}.yup(i){% endif %};
-          ydown(i) {{operator}}= {{rhs.name}}{% if rhs == "Field3D" %}.ydown(i){% endif %};
+        if (isRef) {
+          for (size_t i{0} ; i < yup_fields.size() ; ++i) {
+            yup(i).update_{{operator_name}}_inplace({{rhs.name}}{% if rhs == "Field3D" %}.yup(i){% endif %});
+            ydown(i).update_{{operator_name}}_inplace({{rhs.name}}{% if rhs == "Field3D" %}.ydown(i){% endif %});
+          }
+        } else {
+          for (size_t i{0} ; i < yup_fields.size() ; ++i) {
+            yup(i) {{operator}}= {{rhs.name}}{% if rhs == "Field3D" %}.yup(i){% endif %};
+            ydown(i) {{operator}}= {{rhs.name}}{% if rhs == "Field3D" %}.ydown(i){% endif %};
+          }
         }
       } else {
         clearParallelSlices();
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 8b9a3b50e5..98cb1a0286 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -24,6 +24,32 @@ Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by multiplication with Field3D
+Field3D& Field3D::update_multiplication_inplace(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+  BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs[index]; }
+
+  track(rhs, "operator*=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by multiplication with Field3D
 Field3D& Field3D::operator*=(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -70,6 +96,32 @@ Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by division with Field3D
+Field3D& Field3D::update_division_inplace(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+  BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs[index]; }
+
+  track(rhs, "operator/=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by division with Field3D
 Field3D& Field3D::operator/=(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -116,6 +168,32 @@ Field3D operator+(const Field3D& lhs, const Field3D& rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by addition with Field3D
+Field3D& Field3D::update_addition_inplace(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+  BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs[index]; }
+
+  track(rhs, "operator+=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} += {:s}", this->name, rhs.name);
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by addition with Field3D
 Field3D& Field3D::operator+=(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -162,6 +240,32 @@ Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by subtraction with Field3D
+Field3D& Field3D::update_subtraction_inplace(const Field3D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  regionID = fieldmesh->getCommonRegion(regionID, rhs.getRegionID());
+
+  BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs[index]; }
+
+  track(rhs, "operator-=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by subtraction with Field3D
 Field3D& Field3D::operator-=(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -213,6 +317,35 @@ Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by multiplication with Field2D
+Field3D& Field3D::update_multiplication_inplace(const Field2D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
+    const auto base_ind = fieldmesh->ind2Dto3D(index);
+    for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) {
+      (*this)[base_ind + jz] *= rhs[index];
+    }
+  }
+
+  track(rhs, "operator*=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} *= {:s}", this->name, rhs.name);
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by multiplication with Field2D
 Field3D& Field3D::operator*=(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -268,6 +401,36 @@ Field3D operator/(const Field3D& lhs, const Field2D& rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by division with Field2D
+Field3D& Field3D::update_division_inplace(const Field2D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
+    const auto base_ind = fieldmesh->ind2Dto3D(index);
+    const auto tmp = 1.0 / rhs[index];
+    for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) {
+      (*this)[base_ind + jz] *= tmp;
+    }
+  }
+
+  track(rhs, "operator/=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} /= {:s}", this->name, rhs.name);
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by division with Field2D
 Field3D& Field3D::operator/=(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -323,6 +486,35 @@ Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by addition with Field2D
+Field3D& Field3D::update_addition_inplace(const Field2D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
+    const auto base_ind = fieldmesh->ind2Dto3D(index);
+    for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) {
+      (*this)[base_ind + jz] += rhs[index];
+    }
+  }
+
+  track(rhs, "operator+=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} += {:s}", this->name, rhs.name);
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by addition with Field2D
 Field3D& Field3D::operator+=(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -377,6 +569,35 @@ Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by subtraction with Field2D
+Field3D& Field3D::update_subtraction_inplace(const Field2D& rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+  ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  BOUT_FOR(index, rhs.getRegion("RGN_ALL")) {
+    const auto base_ind = fieldmesh->ind2Dto3D(index);
+    for (int jz = 0; jz < fieldmesh->LocalNz; ++jz) {
+      (*this)[base_ind + jz] -= rhs[index];
+    }
+  }
+
+  track(rhs, "operator-=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} -= {:s}", this->name, rhs.name);
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by subtraction with Field2D
 Field3D& Field3D::operator-=(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -505,6 +726,29 @@ Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by multiplication with BoutReal
+Field3D& Field3D::update_multiplication_inplace(const BoutReal rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
+
+  track(rhs, "operator*=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} *= {:s}", this->name, "BR");
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by multiplication with BoutReal
 Field3D& Field3D::operator*=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -548,6 +792,30 @@ Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by division with BoutReal
+Field3D& Field3D::update_division_inplace(const BoutReal rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  const auto tmp = 1.0 / rhs;
+  BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= tmp; }
+
+  track(rhs, "operator/=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} /= {:s}", this->name, "BR");
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by division with BoutReal
 Field3D& Field3D::operator/=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -591,6 +859,29 @@ Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by addition with BoutReal
+Field3D& Field3D::update_addition_inplace(const BoutReal rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
+
+  track(rhs, "operator+=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} += {:s}", this->name, "BR");
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by addition with BoutReal
 Field3D& Field3D::operator+=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -633,6 +924,29 @@ Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
   return result;
 }
 
+// Provide the C++ operator to update Field3D by subtraction with BoutReal
+Field3D& Field3D::update_subtraction_inplace(const BoutReal rhs) {
+  // only if data is unique we update the field
+  // otherwise just call the non-inplace version
+
+  // Delete existing parallel slices. We don't update parallel slices, so any
+  // that currently exist will be incorrect.
+  clearParallelSlices();
+  checkData(*this);
+  checkData(rhs);
+
+  BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
+
+  track(rhs, "operator-=");
+#if BOUT_USE_TRACK
+  name = fmt::format("{:s} -= {:s}", this->name, "BR");
+#endif
+
+  checkData(*this);
+
+  return *this;
+}
+
 // Provide the C++ operator to update Field3D by subtraction with BoutReal
 Field3D& Field3D::operator-=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -2092,9 +2406,16 @@ Field3DParallel& Field3DParallel::operator*=(const Field3D& rhs) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) *= rhs.yup(i);
-        ydown(i) *= rhs.ydown(i);
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_multiplication_inplace(rhs.yup(i));
+          ydown(i).update_multiplication_inplace(rhs.ydown(i));
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) *= rhs.yup(i);
+          ydown(i) *= rhs.ydown(i);
+        }
       }
     } else {
       clearParallelSlices();
@@ -2152,9 +2473,16 @@ Field3DParallel& Field3DParallel::operator/=(const Field3D& rhs) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) /= rhs.yup(i);
-        ydown(i) /= rhs.ydown(i);
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_division_inplace(rhs.yup(i));
+          ydown(i).update_division_inplace(rhs.ydown(i));
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) /= rhs.yup(i);
+          ydown(i) /= rhs.ydown(i);
+        }
       }
     } else {
       clearParallelSlices();
@@ -2212,9 +2540,16 @@ Field3DParallel& Field3DParallel::operator+=(const Field3D& rhs) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) += rhs.yup(i);
-        ydown(i) += rhs.ydown(i);
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_addition_inplace(rhs.yup(i));
+          ydown(i).update_addition_inplace(rhs.ydown(i));
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) += rhs.yup(i);
+          ydown(i) += rhs.ydown(i);
+        }
       }
     } else {
       clearParallelSlices();
@@ -2272,9 +2607,16 @@ Field3DParallel& Field3DParallel::operator-=(const Field3D& rhs) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) -= rhs.yup(i);
-        ydown(i) -= rhs.ydown(i);
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_subtraction_inplace(rhs.yup(i));
+          ydown(i).update_subtraction_inplace(rhs.ydown(i));
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) -= rhs.yup(i);
+          ydown(i) -= rhs.ydown(i);
+        }
       }
     } else {
       clearParallelSlices();
@@ -2332,9 +2674,16 @@ Field3DParallel& Field3DParallel::operator*=(const Field3DParallel& rhs) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) *= rhs;
-        ydown(i) *= rhs;
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_multiplication_inplace(rhs);
+          ydown(i).update_multiplication_inplace(rhs);
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) *= rhs;
+          ydown(i) *= rhs;
+        }
       }
     } else {
       clearParallelSlices();
@@ -2392,9 +2741,16 @@ Field3DParallel& Field3DParallel::operator/=(const Field3DParallel& rhs) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) /= rhs;
-        ydown(i) /= rhs;
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_division_inplace(rhs);
+          ydown(i).update_division_inplace(rhs);
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) /= rhs;
+          ydown(i) /= rhs;
+        }
       }
     } else {
       clearParallelSlices();
@@ -2452,9 +2808,16 @@ Field3DParallel& Field3DParallel::operator+=(const Field3DParallel& rhs) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) += rhs;
-        ydown(i) += rhs;
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_addition_inplace(rhs);
+          ydown(i).update_addition_inplace(rhs);
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) += rhs;
+          ydown(i) += rhs;
+        }
       }
     } else {
       clearParallelSlices();
@@ -2512,9 +2875,16 @@ Field3DParallel& Field3DParallel::operator-=(const Field3DParallel& rhs) {
     ASSERT1_FIELDS_COMPATIBLE(*this, rhs);
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) -= rhs;
-        ydown(i) -= rhs;
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_subtraction_inplace(rhs);
+          ydown(i).update_subtraction_inplace(rhs);
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) -= rhs;
+          ydown(i) -= rhs;
+        }
       }
     } else {
       clearParallelSlices();
@@ -2573,9 +2943,16 @@ Field3DParallel& Field3DParallel::operator*=(const BoutReal rhs) {
   if (data.unique() or isRef) {
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) *= rhs;
-        ydown(i) *= rhs;
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_multiplication_inplace(rhs);
+          ydown(i).update_multiplication_inplace(rhs);
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) *= rhs;
+          ydown(i) *= rhs;
+        }
       }
     } else {
       clearParallelSlices();
@@ -2636,9 +3013,16 @@ Field3DParallel& Field3DParallel::operator/=(const BoutReal rhs) {
   if (data.unique() or isRef) {
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) /= rhs;
-        ydown(i) /= rhs;
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_division_inplace(rhs);
+          ydown(i).update_division_inplace(rhs);
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) /= rhs;
+          ydown(i) /= rhs;
+        }
       }
     } else {
       clearParallelSlices();
@@ -2698,9 +3082,16 @@ Field3DParallel& Field3DParallel::operator+=(const BoutReal rhs) {
   if (data.unique() or isRef) {
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) += rhs;
-        ydown(i) += rhs;
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_addition_inplace(rhs);
+          ydown(i).update_addition_inplace(rhs);
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) += rhs;
+          ydown(i) += rhs;
+        }
       }
     } else {
       clearParallelSlices();
@@ -2760,9 +3151,16 @@ Field3DParallel& Field3DParallel::operator-=(const BoutReal rhs) {
   if (data.unique() or isRef) {
 
     if (this->isFci()) {
-      for (size_t i{0}; i < yup_fields.size(); ++i) {
-        yup(i) -= rhs;
-        ydown(i) -= rhs;
+      if (isRef) {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i).update_subtraction_inplace(rhs);
+          ydown(i).update_subtraction_inplace(rhs);
+        }
+      } else {
+        for (size_t i{0}; i < yup_fields.size(); ++i) {
+          yup(i) -= rhs;
+          ydown(i) -= rhs;
+        }
       }
     } else {
       clearParallelSlices();

From 00048e0ccc1988fe30e03784ca9ad8c66d6d1e4e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 2 Feb 2026 12:06:32 +0100
Subject: [PATCH 0833/1827] Add const version

---
 include/bout/field2d.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index a28c8bfa8f..3549df4ef9 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -274,6 +274,7 @@ public:
   int size() const override { return nx * ny; }
 
   Field2D& asField3DParallel() { return *this; }
+  const Field2D& asField3DParallel() const { return *this; }
 
 private:
   /// Internal data array. Handles allocation/freeing of memory

From 2dd233593e64f91731b99d062a2f155ff8592271 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Feb 2026 12:36:34 +0100
Subject: [PATCH 0834/1827] Only compute parallel slices in filledFrom for FCI

---
 include/bout/field3d.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index f57a098430..af33ce0f5d 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -854,7 +854,7 @@ inline Field3DParallel
 filledFrom(const Field3DParallel& f,
            std::function<BoutReal(int yoffset, Ind3D index)> func) {
   auto result{emptyFrom(f)};
-  if (f.hasParallelSlices()) {
+  if (f.isFci()) {
     BOUT_FOR(i, result.getRegion("RGN_NOY")) { result[i] = func(0, i); }
 
     for (size_t i = 0; i < result.numberParallelSlices(); ++i) {

From 4f2f60a04a5efa35846146c68ac2d3430112581e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Feb 2026 14:42:08 +0100
Subject: [PATCH 0835/1827] floor only if allocated

---
 include/bout/field.hxx | 31 ++++++++++++++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 1e54a4f96b..cac0bdb150 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -684,7 +684,36 @@ inline T floor(const T& var, BoutReal f, const std::string& rgn = "RGN_ALL") {
       result[d] = f;
     }
   }
-
+  if constexpr (std::is_same_v<T, Field3DParallel>) {
+    if (var.hasParallelSlices()) {
+      for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
+        if (result.yup(i).isAllocated()) {
+          BOUT_FOR(d, result.yup(i).getRegion(rgn)) {
+            if (result.yup(i)[d] < f) {
+              result.yup(i)[d] = f;
+            }
+          }
+        } else {
+          if (result.isFci()) {
+            throw BoutException("Expected parallel slice to be allocated");
+          }
+        }
+        if (result.ydown(i).isAllocated()) {
+          BOUT_FOR(d, result.ydown(i).getRegion(rgn)) {
+            if (result.ydown(i)[d] < f) {
+              result.ydown(i)[d] = f;
+            }
+          }
+        } else {
+          if (result.isFci()) {
+            throw BoutException("Expected parallel slice to be allocated");
+          }
+        }
+      }
+    }
+  } else {
+    result.clearParallelSlices();
+  }
   return result;
 }
 

From 1adc1fc2fefbdfe31dc9df1bb99d89a47398038e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Feb 2026 14:42:23 +0100
Subject: [PATCH 0836/1827] Use allocate only to make sure data is unique

---
 include/bout/field3d.hxx | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index af33ce0f5d..c0bfba5d7b 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -813,10 +813,16 @@ private:
 };
 
 Field3DParallel Field3D::asField3DParallel() {
-  allocate();
-  for (size_t i = 0; i < numberParallelSlices(); ++i) {
-    yup(i).allocate();
-    ydown(i).allocate();
+  if (isAllocated()) {
+    allocate();
+    for (size_t i = 0; i < numberParallelSlices(); ++i) {
+      if (yup(i).isAllocated()) {
+        yup(i).allocate();
+      }
+      if (ydown(i).isAllocated()) {
+        ydown(i).allocate();
+      }
+    }
   }
   return Field3DParallel(*this, true);
 }

From a46781ae2c3446d5ba830baa868e6a829dabc98d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:58:05 +0100
Subject: [PATCH 0837/1827] Do not use numberParallelSlices()

---
 include/bout/field3d.hxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index c0bfba5d7b..ea1a1ce24b 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -739,7 +739,8 @@ std::ostream& operator<<(std::ostream& out, const Field3D& value);
 inline Field3D copy(const Field3D& f) {
   Field3D result{f};
   result.allocate();
-  for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
+  const size_t numSlices = result.hasParallelSlices() ? result.fieldmesh->ystart : 0;
+  for (size_t i = 0; i < numSlices; ++i) {
     result.yup(i).allocate();
     result.ydown(i).allocate();
   }

From 80d7d34213b37ad79cc58245034d492ccd6ffb12 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 12:02:10 +0100
Subject: [PATCH 0838/1827] Add regionID to f3d ctor

---
 include/bout/field3d.hxx | 3 ++-
 src/field/field3d.cxx    | 5 +++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index ea1a1ce24b..f542a5462f 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -175,7 +175,8 @@ public:
    */
   Field3D(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
           DirectionTypes directions_in = {YDirectionType::Standard,
-                                          ZDirectionType::Standard});
+                                          ZDirectionType::Standard},
+          std::optional<size_t> regionID = {});
 
   /*!
    * Copy constructor
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 0a1dae3929..1b10546df3 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -52,8 +52,9 @@
 #include "fmt/format.h"
 
 /// Constructor
-Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in)
-    : Field(localmesh, location_in, directions_in) {
+Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in,
+                 std::optional<size_t> regionID)
+    : Field(localmesh, location_in, directions_in), regionID(regionID) {
 #if BOUT_USE_TRACK
   name = "<F3D>";
 #endif

From 40e1c2e5c2201e45b9a850541907216bc11cb6c5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 12:08:29 +0100
Subject: [PATCH 0839/1827] add regionID to f2d ctor

---
 include/bout/field2d.hxx | 3 ++-
 src/field/field2d.cxx    | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 3549df4ef9..9996d1dbda 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -68,7 +68,8 @@ public:
    */
   Field2D(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
           DirectionTypes directions_in = {YDirectionType::Standard,
-                                          ZDirectionType::Average});
+                                          ZDirectionType::Average},
+          std::optional<size_t> regionID = {});
 
   /*!
    * Copy constructor. After this both fields
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index a046078585..b4bd83ed71 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -39,7 +39,8 @@
 
 #include <cmath>
 
-Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in)
+Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in,
+                 [[maybe_unused]] std::optional<size_t> regionID)
     : Field(localmesh, location_in, directions_in) {
 
   if (fieldmesh) {

From ee6b03e6184d7fa602dea5d26a98757430b0b74c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 12:08:48 +0100
Subject: [PATCH 0840/1827] Add numberParallelSlices to all fields

---
 include/bout/field.hxx   | 1 +
 include/bout/field3d.hxx | 7 +++++++
 2 files changed, 8 insertions(+)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index cac0bdb150..b6a2c8ec7d 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -137,6 +137,7 @@ public:
   virtual void calcParallelSlices() {}
   virtual void splitParallelSlices() {}
   virtual void clearParallelSlices() {}
+  virtual size_t numberParallelSlices() const { return 0; }
 
 private:
   /// Labels for the type of coordinate system this field is defined over
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index f542a5462f..8644fd61a2 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -267,6 +267,13 @@ public:
 #endif
   }
 
+  size_t numberParallelSlices() const override {
+#if CHECK > 0
+    hasParallelSlices();
+#endif
+    return yup_fields.size();
+  }
+
   /// Check if this field has yup and ydown fields
   /// Return reference to yup field
   Field3D& yup(size_t index = 0) {

From 9501f7a6b1368c8a77e0df1dac07f275a78a509e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 12:10:46 +0100
Subject: [PATCH 0841/1827] use numberParallelSlices

---
 include/bout/field3d.hxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 8644fd61a2..86fe03186c 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -747,8 +747,7 @@ std::ostream& operator<<(std::ostream& out, const Field3D& value);
 inline Field3D copy(const Field3D& f) {
   Field3D result{f};
   result.allocate();
-  const size_t numSlices = result.hasParallelSlices() ? result.fieldmesh->ystart : 0;
-  for (size_t i = 0; i < numSlices; ++i) {
+  for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
     result.yup(i).allocate();
     result.ydown(i).allocate();
   }

From ddb9132bc92dceb778c9fa4f6415b3a126a0a3df Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 12:14:55 +0100
Subject: [PATCH 0842/1827] Fix usage of coords

---
 src/mesh/coordinates.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 64c67ade1d..5b8a26cb69 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1570,7 +1570,7 @@ Field3D Coordinates::Div_par(const Field3DParallel& f, CELL_LOC outloc,
   }
 
   // Need to modify yup and ydown fields
-  Field3D Jg = coords->J / sqrt(coords->g_22.asField3DParallel());
+  Field3D Jg = J / sqrt(g_22.asField3DParallel());
   return Jg * Grad_par(f / Jg, outloc, method);
 }
 

From b5a2c3b7fb47e52032023fe402769fa6574b94d8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 09:21:00 +0100
Subject: [PATCH 0843/1827] FCI test only works with 3D metrics

---
 tests/MMS/spatial/fci/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/MMS/spatial/fci/CMakeLists.txt b/tests/MMS/spatial/fci/CMakeLists.txt
index dcdb183fdd..48721a8199 100644
--- a/tests/MMS/spatial/fci/CMakeLists.txt
+++ b/tests/MMS/spatial/fci/CMakeLists.txt
@@ -3,5 +3,6 @@ bout_add_mms_test(
   SOURCES fci_mms.cxx
   USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES zoidberg_FOUND
+  REQUIRES BOUT_USE_METRIC_3D
   PROCESSORS 2
 )

From 2e7dccfa8ef3bccdb9d433c4837171171a1fc6b3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 10 Oct 2024 12:45:35 +0200
Subject: [PATCH 0844/1827] Add code to load parallel metric slices

---
 include/bout/paralleltransform.hxx |  4 +++
 src/mesh/coordinates.cxx           |  5 ++++
 src/mesh/parallel/fci.cxx          | 41 ++++++++++++++++--------------
 src/mesh/parallel/fci.hxx          |  2 ++
 4 files changed, 33 insertions(+), 19 deletions(-)

diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx
index 49dea67743..8c151b61e1 100644
--- a/include/bout/paralleltransform.hxx
+++ b/include/bout/paralleltransform.hxx
@@ -90,6 +90,10 @@ public:
   /// require a twist-shift at branch cuts on closed field lines?
   virtual bool requiresTwistShift(bool twist_shift_enabled, YDirectionType ytype) = 0;
 
+  /// Can be implemented to load parallel metrics
+  /// Needed by FCI
+  virtual void loadParallelMetrics(MAYBE_UNUSED(Coordinates* coords)) {}
+
 protected:
   /// This method should be called in the constructor to check that if the grid
   /// has a 'parallel_transform' variable, it has the correct value
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index d2634d3f88..ce7406a518 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -591,6 +591,9 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
     // IntShiftTorsion will not be used, but set to zero to avoid uninitialized field
     IntShiftTorsion = 0.;
   }
+
+  // Allow transform to fix things up
+  transform->loadParallelMetrics(this);
 }
 
 Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
@@ -879,6 +882,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
                                                   true, true, false, transform.get());
     }
   }
+  // Allow transform to fix things up
+  transform->loadParallelMetrics(this);
 }
 
 void Coordinates::outputVars(Options& output_options) {
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 152ffaed2d..9d35b3af8e 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -64,6 +64,18 @@
 
 using namespace std::string_view_literals;
 
+namespace {
+// Get a unique name for a field based on the sign/magnitude of the offset
+std::string parallel_slice_field_name(std::string field, int offset) {
+  const std::string direction = (offset > 0) ? "forward" : "backward";
+  // We only have a suffix for parallel slices beyond the first
+  // This is for backwards compatibility
+  const std::string slice_suffix =
+      (std::abs(offset) > 1) ? "_" + std::to_string(std::abs(offset)) : "";
+  return direction + "_" + field + slice_suffix;
+}
+} // namespace
+
 FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
                Options& options, int offset,
                const std::shared_ptr<BoundaryRegionPar>& inner_boundary,
@@ -102,38 +114,29 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
   map_mesh->get(R, "R", 0.0, false);
   map_mesh->get(Z, "Z", 0.0, false);
 
-  // Get a unique name for a field based on the sign/magnitude of the offset
-  const auto parallel_slice_field_name = [&](std::string_view field) -> std::string {
-    const auto direction = (offset_ > 0) ? "forward"sv : "backward"sv;
-    // We only have a suffix for parallel slices beyond the first
-    // This is for backwards compatibility
-    if (std::abs(offset_) == 1) {
-      return fmt::format("{}_{}", direction, field);
-    }
-    return fmt::format("{}_{}_{}", direction, field, std::abs(offset_));
-  };
-
   // If we can't read in any of these fields, things will silently not
   // work, so best throw
-  if (map_mesh->get(xt_prime, parallel_slice_field_name("xt_prime"), 0.0, false) != 0) {
+  if (map_mesh->get(xt_prime, parallel_slice_field_name("xt_prime", offset), 0.0, false)
+      != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
-                        parallel_slice_field_name("xt_prime"));
+                        parallel_slice_field_name("xt_prime", offset));
   }
-  if (map_mesh->get(zt_prime, parallel_slice_field_name("zt_prime"), 0.0, false) != 0) {
+  if (map_mesh->get(zt_prime, parallel_slice_field_name("zt_prime", offset), 0.0, false)
+      != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
-                        parallel_slice_field_name("zt_prime"));
+                        parallel_slice_field_name("zt_prime", offset));
   }
-  if (map_mesh->get(R_prime, parallel_slice_field_name("R"), 0.0, false) != 0) {
+  if (map_mesh->get(R_prime, parallel_slice_field_name("R", offset), 0.0, false) != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
-                        parallel_slice_field_name("R"));
+                        parallel_slice_field_name("R", offset));
   }
-  if (map_mesh->get(Z_prime, parallel_slice_field_name("Z"), 0.0, false) != 0) {
+  if (map_mesh->get(Z_prime, parallel_slice_field_name("Z", offset), 0.0, false) != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
-                        parallel_slice_field_name("Z"));
+                        parallel_slice_field_name("Z", offset));
   }
 
   // Cell corners
diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx
index 65529a4c4e..71ac35a192 100644
--- a/src/mesh/parallel/fci.hxx
+++ b/src/mesh/parallel/fci.hxx
@@ -125,6 +125,8 @@ public:
     return false;
   }
 
+  void loadParallelMetrics(Coordinates* coords) override;
+
 protected:
   void checkInputGrid() override;
 

From 6e21bb8c4f6bc66de826d6390e2bf7f0a811eb87 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 11:37:50 +0100
Subject: [PATCH 0845/1827] Prefer [[maybe_unused]]

---
 include/bout/paralleltransform.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx
index 8c151b61e1..0b425de209 100644
--- a/include/bout/paralleltransform.hxx
+++ b/include/bout/paralleltransform.hxx
@@ -92,7 +92,7 @@ public:
 
   /// Can be implemented to load parallel metrics
   /// Needed by FCI
-  virtual void loadParallelMetrics(MAYBE_UNUSED(Coordinates* coords)) {}
+  virtual void loadParallelMetrics([[maybe_unused]] Coordinates* coords) {}
 
 protected:
   /// This method should be called in the constructor to check that if the grid

From e5eb01af8ee8a4a8fc66f4914eb964de70ca588c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 10 Oct 2024 12:45:35 +0200
Subject: [PATCH 0846/1827] Add code to load parallel metric slices

---
 src/mesh/parallel/fci.cxx | 40 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 9d35b3af8e..badcdf6906 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -73,7 +73,40 @@ std::string parallel_slice_field_name(std::string field, int offset) {
   const std::string slice_suffix =
       (std::abs(offset) > 1) ? "_" + std::to_string(std::abs(offset)) : "";
   return direction + "_" + field + slice_suffix;
+};
+
+void load_parallel_metric_component(std::string name, Field3D& component, int offset) {
+  Mesh* mesh = component.getMesh();
+  Field3D tmp{mesh};
+  const auto pname = parallel_slice_field_name(name, offset);
+  if (mesh->get(tmp, pname, 0.0, false) != 0) {
+    throw BoutException("Could not read {:s} from grid file!\n"
+                        "  Fix it up with `zoidberg-update-parallel-metrics <grid>`",
+                        pname);
+  }
+  if (!component.hasParallelSlices()) {
+    component.splitParallelSlices();
+    component.allowCalcParallelSlices = false;
+  }
+  auto& pcom = component.ynext(offset);
+  pcom.allocate();
+  BOUT_FOR(i, component.getRegion("RGN_NOBNDRY")) { pcom[i.yp(offset)] = tmp[i]; }
+}
+
+void load_parallel_metric_components(Coordinates* coords, int offset) {
+#define LOAD_PAR(var) load_parallel_metric_component(#var, coords->var, offset)
+  LOAD_PAR(g11);
+  LOAD_PAR(g22);
+  LOAD_PAR(g33);
+  LOAD_PAR(g13);
+  LOAD_PAR(g_11);
+  LOAD_PAR(g_22);
+  LOAD_PAR(g_33);
+  LOAD_PAR(g_13);
+  LOAD_PAR(J);
+#undef LOAD_PAR
 }
+
 } // namespace
 
 FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
@@ -418,3 +451,10 @@ void FCITransform::outputVars(Options& output_options) {
   output_options["R"].force(R, "FCI");
   output_options["Z"].force(Z, "FCI");
 }
+
+void FCITransform::loadParallelMetrics(Coordinates* coords) {
+  for (int i = 1; i <= mesh.ystart; ++i) {
+    load_parallel_metric_components(coords, -i);
+    load_parallel_metric_components(coords, i);
+  }
+}

From 763ce7809483f6467a5626815c11cb5d3c863cda Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 4 Mar 2026 14:14:17 +0100
Subject: [PATCH 0847/1827] Update to new interface

---
 src/mesh/parallel/fci.cxx | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index badcdf6906..78e101ff66 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -75,6 +75,7 @@ std::string parallel_slice_field_name(std::string field, int offset) {
   return direction + "_" + field + slice_suffix;
 };
 
+#if BOUT_USE_METRIC_3D
 void load_parallel_metric_component(std::string name, Field3D& component, int offset) {
   Mesh* mesh = component.getMesh();
   Field3D tmp{mesh};
@@ -86,7 +87,7 @@ void load_parallel_metric_component(std::string name, Field3D& component, int of
   }
   if (!component.hasParallelSlices()) {
     component.splitParallelSlices();
-    component.allowCalcParallelSlices = false;
+    component.disallowCalcParallelSlices();
   }
   auto& pcom = component.ynext(offset);
   pcom.allocate();
@@ -106,6 +107,7 @@ void load_parallel_metric_components(Coordinates* coords, int offset) {
   LOAD_PAR(J);
 #undef LOAD_PAR
 }
+#endif
 
 } // namespace
 
@@ -453,8 +455,10 @@ void FCITransform::outputVars(Options& output_options) {
 }
 
 void FCITransform::loadParallelMetrics(Coordinates* coords) {
+#if BOUT_USE_METRIC_3D
   for (int i = 1; i <= mesh.ystart; ++i) {
     load_parallel_metric_components(coords, -i);
     load_parallel_metric_components(coords, i);
   }
+#endif
 }

From d9721f8a39377a0d18b2754bd65bea630851aead Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 10:37:08 +0100
Subject: [PATCH 0848/1827] Add missing headers from clang-tidy

---
 include/bout/fieldperp.hxx | 2 ++
 src/field/field2d.cxx      | 2 ++
 src/field/fieldperp.cxx    | 2 ++
 3 files changed, 6 insertions(+)

diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index ef5e217bbc..a159b6258f 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -23,6 +23,8 @@
  *
  **************************************************************************/
 
+#include <cstddef>
+#include <optional>
 #include <vector>
 class FieldPerp;
 
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index 078e1a48c6..88434ec702 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -38,6 +38,8 @@
 #include <bout/output.hxx>
 
 #include <cmath>
+#include <cstddef>
+#include <optional>
 
 Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in,
                  std::optional<size_t> UNUSED(regionID))
diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index 938e3be245..669b61ed17 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -27,6 +27,8 @@
 #include <bout/globals.hxx>
 
 #include <cmath>
+#include <cstddef>
+#include <optional>
 
 #include <bout/boutexception.hxx>
 #include <bout/fieldperp.hxx>

From 208430b78527020f55425dca35b0d2d2ff44cac5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 10:58:24 +0100
Subject: [PATCH 0849/1827] Add headers from clang-tidy

---
 include/bout/field2d.hxx | 1 +
 src/field/field2d.cxx    | 2 ++
 src/field/field3d.cxx    | 3 +++
 src/field/fieldperp.cxx  | 1 +
 4 files changed, 7 insertions(+)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index fc2f4b2bbd..e068747ee3 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -25,6 +25,7 @@
  *
  */
 #include "bout/utils.hxx"
+#include <optional>
 class Field2D;
 
 #pragma once
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index 88434ec702..c2d35162b3 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -25,8 +25,10 @@
  *
  **************************************************************************/
 
+#include "bout/bout_types.hxx"
 #include "bout/build_defines.hxx"
 
+#include "bout/unused.hxx"
 #include <bout/assert.hxx>
 #include <bout/boundary_factory.hxx>
 #include <bout/boundary_op.hxx>
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 20d8a41fde..e846eeafb9 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -25,6 +25,7 @@
  *
  **************************************************************************/
 
+#include "bout/bout_types.hxx"
 #include "bout/build_defines.hxx"
 
 #include <bout/boutcomm.hxx>
@@ -32,7 +33,9 @@
 
 #include <cmath>
 #include <cpptrace/cpptrace.hpp>
+#include <cstddef>
 #include <memory>
+#include <optional>
 #include <utility>
 
 #include "bout/parallel_boundary_op.hxx"
diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index 669b61ed17..ed98419fe1 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -23,6 +23,7 @@
  *
  **************************************************************************/
 
+#include "bout/unused.hxx"
 #include <bout/boutcomm.hxx>
 #include <bout/globals.hxx>
 

From 02aafdadc01cbbc1995ca84b58a1acfcdb617d36 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 10:47:31 +0100
Subject: [PATCH 0850/1827] Add headers from clang-tidy

---
 include/bout/index_derivs_interface.hxx | 2 ++
 src/field/field2d.cxx                   | 2 ++
 src/field/generated_fieldops.cxx        | 3 +++
 3 files changed, 7 insertions(+)

diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx
index 03cc480323..c63a388948 100644
--- a/include/bout/index_derivs_interface.hxx
+++ b/include/bout/index_derivs_interface.hxx
@@ -29,6 +29,8 @@
 #ifndef __INDEX_DERIVS_INTERFACE_HXX__
 #define __INDEX_DERIVS_INTERFACE_HXX__
 
+#include "bout/boutexception.hxx"
+#include "bout/field3d.hxx"
 #include "bout/traits.hxx"
 #include <bout/bout_types.hxx>
 #include <bout/deriv_store.hxx>
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index b4bd83ed71..2043d91b34 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -38,6 +38,8 @@
 #include <bout/output.hxx>
 
 #include <cmath>
+#include <cstddef>
+#include <optional>
 
 Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in,
                  [[maybe_unused]] std::optional<size_t> regionID)
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 98cb1a0286..3e10aabefe 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -1,4 +1,7 @@
 // This file is autogenerated - see gen_fieldops.py
+#include "fmt/format.h"
+#include "bout/assert.hxx"
+#include "bout/build_defines.hxx"
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/globals.hxx>

From f98fe9dc6774d121b0bd8a828add6cb84d11a986 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 10:50:29 +0100
Subject: [PATCH 0851/1827] Remove useless std::move

---
 include/bout/field3d.hxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 86fe03186c..9321ec5fc4 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -764,11 +764,11 @@ public:
   explicit Field3DParallel(Types... args) : Field3D(std::move(args)...) {
     ensureFieldAligned();
   }
-  Field3DParallel(const Field3D& f) : Field3D(std::move(f)) { ensureFieldAligned(); }
-  Field3DParallel(const Field3D& f, bool isRef) : Field3D(std::move(f)), isRef(isRef) {
+  Field3DParallel(const Field3D& f) : Field3D(f) { ensureFieldAligned(); }
+  Field3DParallel(const Field3D& f, bool isRef) : Field3D(f), isRef(isRef) {
     ensureFieldAligned();
   }
-  Field3DParallel(const Field2D& f) : Field3D(std::move(f)) { ensureFieldAligned(); }
+  Field3DParallel(const Field2D& f) : Field3D(f) { ensureFieldAligned(); }
   // Explicitly needed, as DirectionTypes is sometimes constructed from a
   // brace enclosed list
   explicit Field3DParallel(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,

From bf6743f25d5e14996689fc9fd0c55b8132380a3c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 10:51:33 +0100
Subject: [PATCH 0852/1827] Prefer const ref

---
 include/bout/field3d.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 9321ec5fc4..c7a83f3c93 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -866,7 +866,7 @@ inline Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs) {
 
 inline Field3DParallel
 filledFrom(const Field3DParallel& f,
-           std::function<BoutReal(int yoffset, Ind3D index)> func) {
+           const std::function<BoutReal(int yoffset, Ind3D index)>& func) {
   auto result{emptyFrom(f)};
   if (f.isFci()) {
     BOUT_FOR(i, result.getRegion("RGN_NOY")) { result[i] = func(0, i); }

From 85fb0fd4047e2850f4647e117041f56645c4d092 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 10:54:14 +0100
Subject: [PATCH 0853/1827] prefer const

---
 src/mesh/coordinates.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 5b8a26cb69..699e1cd440 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1570,7 +1570,7 @@ Field3D Coordinates::Div_par(const Field3DParallel& f, CELL_LOC outloc,
   }
 
   // Need to modify yup and ydown fields
-  Field3D Jg = J / sqrt(g_22.asField3DParallel());
+  const Field3D Jg = J / sqrt(g_22.asField3DParallel());
   return Jg * Grad_par(f / Jg, outloc, method);
 }
 

From a9c5059cdc0e859ce49a290a5e3cf530a4aff5db Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 11:22:36 +0100
Subject: [PATCH 0854/1827] fix DDY with parallel slices with FA

---
 include/bout/index_derivs_interface.hxx | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/include/bout/index_derivs_interface.hxx b/include/bout/index_derivs_interface.hxx
index c63a388948..cbb1e5ac53 100644
--- a/include/bout/index_derivs_interface.hxx
+++ b/include/bout/index_derivs_interface.hxx
@@ -206,7 +206,7 @@ template <typename T>
 T DDY(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
       const std::string& region = "RGN_NOBNDRY") {
 
-  if (f.isFci()) {
+  if (f.isFci() or f.hasParallelSlices()) {
     ASSERT1(f.getDirectionY() == YDirectionType::Standard);
     if (!f.hasParallelSlices()) {
       throw BoutException(
@@ -215,13 +215,12 @@ T DDY(const T& f, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "D
     }
     return standardDerivative<T, DIRECTION::YOrthogonal, DERIV::Standard>(f, outloc,
                                                                           method, region);
-  } else {
-    const bool is_unaligned = (f.getDirectionY() == YDirectionType::Standard);
-    const T f_aligned = is_unaligned ? toFieldAligned(f, "RGN_NOX") : f;
-    T result = standardDerivative<T, DIRECTION::Y, DERIV::Standard>(f_aligned, outloc,
-                                                                    method, region);
-    return is_unaligned ? fromFieldAligned(result, region) : result;
   }
+  const bool is_unaligned = (f.getDirectionY() == YDirectionType::Standard);
+  const T f_aligned = is_unaligned ? toFieldAligned(f, "RGN_NOX") : f;
+  T result = standardDerivative<T, DIRECTION::Y, DERIV::Standard>(f_aligned, outloc,
+                                                                  method, region);
+  return is_unaligned ? fromFieldAligned(result, region) : result;
 }
 inline Field3D DDY(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                    const std::string& method = "DEFAULT",

From 6d72a7e990c58c322183459955119870b1ec9fcd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 11:30:43 +0100
Subject: [PATCH 0855/1827] Use std::ranges::any_of

---
 include/bout/parallel_boundary_region.hxx | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 1d06bc65cb..fa8e8efbba 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -451,12 +451,7 @@ public:
 
   bool contains(const int ix, const int iy, const int iz) const {
     const auto i2 = xyz2ind(ix, iy, iz, localmesh);
-    for (auto i1 : bndry_points) {
-      if (i1.index == i2) {
-        return true;
-      }
-    }
-    return false;
+    return std::ranges::any_of(bndry_points, [](auto i1) { return i2.index == i2; });
   }
 
   // setter

From d5272c43e19fb7231b63ae25ade03338ddffdc41 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 12:11:42 +0100
Subject: [PATCH 0856/1827] Fixes for prek

---
 include/bout/coordinates.hxx | 10 +++++-----
 include/bout/field.hxx       |  2 +-
 include/bout/field3d.hxx     |  4 ++--
 src/field/field3d.cxx        |  6 +++---
 src/field/gen_fieldops.py    |  1 -
 5 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 8a4bfb5ef6..6fc97a03dd 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -3,16 +3,16 @@
  *
  * ChangeLog
  * =========
- * 
+ *
  * 2014-11-10 Ben Dudson <bd512@york.ac.uk>
  *    * Created by separating metric from Mesh
  *
- * 
+ *
  **************************************************************************
  * Copyright 2014-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -256,10 +256,10 @@ private:
 class TokamakCoordinates : public Coordinates {
 public:
   TokamakCoordinates(Mesh *mesh) : Coordinates(mesh) {
-    
+
   }
 private:
-  
+
 };
 */
 
diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index b6a2c8ec7d..f8b07afb82 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -6,7 +6,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index c7a83f3c93..438e28c25d 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -2,7 +2,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -372,7 +372,7 @@ public:
    * Direct access to the underlying data array
    *
    * If CHECK > 2 then bounds checking is performed
-   * 
+   *
    * If CHECK <= 2 then no checks are performed, to
    * allow inlining and optimisation of inner loops
    */
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index e4198cdd2c..975a918f89 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -7,7 +7,7 @@
  * Copyright 2010 - 2025 BOUT++ developers
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -244,7 +244,7 @@ const Region<Ind2D>& Field3D::getRegion2D(const std::string& region_name) const
 }
 
 /***************************************************************
- *                         OPERATORS 
+ *                         OPERATORS
  ***************************************************************/
 
 /////////////////// ASSIGNMENT ////////////////////
@@ -743,7 +743,7 @@ Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string
   return result;
 }
 
-/* 
+/*
  * Use FFT to shift by an angle in the Z direction
  */
 void shiftZ(Field3D& var, int jx, int jy, double zangle) {
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index e44b0645fe..2bcb144c47 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -16,7 +16,6 @@
 from builtins import object
 
 import argparse
-from collections import OrderedDict
 import contextlib
 from copy import deepcopy as copy
 import itertools

From 9f59df4e5d1fe11f8317769286f316f60c2fceaf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 12:13:13 +0100
Subject: [PATCH 0857/1827] Fixes for prek

---
 include/bout/field.hxx     |  2 +-
 include/bout/field3d.hxx   |  4 ++--
 include/bout/fieldperp.hxx | 20 ++++++++++----------
 src/field/field3d.cxx      |  6 +++---
 src/field/fieldperp.cxx    |  4 ++--
 5 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index c14489874a..273cc08342 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -6,7 +6,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 4c382fefbc..785b139fbb 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -2,7 +2,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -362,7 +362,7 @@ public:
    * Direct access to the underlying data array
    *
    * If CHECK > 2 then bounds checking is performed
-   * 
+   *
    * If CHECK <= 2 then no checks are performed, to
    * allow inlining and optimisation of inner loops
    */
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index a159b6258f..a9fb400fe9 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -5,7 +5,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -47,8 +47,8 @@ class Field3D; // #include "bout/field3d.hxx"
 
 /*!
  * Represents a 2D field perpendicular to the magnetic field
- * at a particular index in Y, which only varies in X-Z. 
- * 
+ * at a particular index in Y, which only varies in X-Z.
+ *
  * Primarily used inside field solvers
  */
 class FieldPerp : public Field {
@@ -208,7 +208,7 @@ public:
 
   /*!
    * Access to the underlying data array at a given x,z index
-   * 
+   *
    * If CHECK > 2 then bounds checking is performed, otherwise
    * no checks are performed
    */
@@ -244,9 +244,9 @@ public:
   }
 
   /*!
-   * Access to the underlying data array. (X,Y,Z) indices for consistency with 
+   * Access to the underlying data array. (X,Y,Z) indices for consistency with
    * other field types
-   * 
+   *
    */
   BoutReal& operator()(int jx, int UNUSED(jy), int jz) { return (*this)(jx, jz); }
 
@@ -255,7 +255,7 @@ public:
   }
 
   /*!
-   * Addition, modifying in-place. 
+   * Addition, modifying in-place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator+=(const FieldPerp& rhs);
@@ -264,7 +264,7 @@ public:
   FieldPerp& operator+=(BoutReal rhs);
 
   /*!
-   * Subtraction, modifying in place. 
+   * Subtraction, modifying in place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator-=(const FieldPerp& rhs);
@@ -273,7 +273,7 @@ public:
   FieldPerp& operator-=(BoutReal rhs);
 
   /*!
-   * Multiplication, modifying in place. 
+   * Multiplication, modifying in place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator*=(const FieldPerp& rhs);
@@ -282,7 +282,7 @@ public:
   FieldPerp& operator*=(BoutReal rhs);
 
   /*!
-   * Division, modifying in place. 
+   * Division, modifying in place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator/=(const FieldPerp& rhs);
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 10ac8d6a30..9154f78a4f 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -7,7 +7,7 @@
  * Copyright 2010 - 2025 BOUT++ developers
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -234,7 +234,7 @@ const Region<Ind2D>& Field3D::getRegion2D(const std::string& region_name) const
 }
 
 /***************************************************************
- *                         OPERATORS 
+ *                         OPERATORS
  ***************************************************************/
 
 /////////////////// ASSIGNMENT ////////////////////
@@ -710,7 +710,7 @@ Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string
   return result;
 }
 
-/* 
+/*
  * Use FFT to shift by an angle in the Z direction
  */
 void shiftZ(Field3D& var, int jx, int jy, double zangle) {
diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index ed98419fe1..d5f0d93706 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -5,7 +5,7 @@
  * Copyright 2010 - 2025 BOUT++ developers
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -78,7 +78,7 @@ FieldPerp& FieldPerp::allocate() {
 }
 
 /***************************************************************
- *                         ASSIGNMENT 
+ *                         ASSIGNMENT
  ***************************************************************/
 
 FieldPerp& FieldPerp::operator=(const FieldPerp& rhs) {

From 5968f1387372f688d8647040330553f3888283f0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 12:14:30 +0100
Subject: [PATCH 0858/1827] Fixes for prek

---
 include/bout/field3d.hxx                     |  4 ++--
 include/bout/parallel_boundary_region.hxx    |  4 ++--
 manual/sphinx/user_docs/boundary_options.rst | 12 ++++++------
 src/field/field3d.cxx                        |  6 +++---
 src/mesh/impls/bout/boutmesh.cxx             |  6 +++---
 src/mesh/parallel/shiftedmetricinterp.cxx    |  2 +-
 tests/integrated/test-fci-boundary/runtest   |  1 -
 7 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index f607445705..09d9c93f1b 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -2,7 +2,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -361,7 +361,7 @@ public:
    * Direct access to the underlying data array
    *
    * If CHECK > 2 then bounds checking is performed
-   * 
+   *
    * If CHECK <= 2 then no checks are performed, to
    * allow inlining and optimisation of inner loops
    */
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index fa8e8efbba..05338c8479 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -53,7 +53,7 @@ struct Indices {
   Indices(Ind3D index, RealPoint&& intersection, BoutReal length, signed char valid,
           signed char offset, unsigned char abs_offset)
       : index(index), intersection(intersection), length(length), valid(valid),
-        offset(offset), abs_offset(abs_offset){};
+        offset(offset), abs_offset(abs_offset) {};
 };
 
 using IndicesVec = std::vector<Indices>;
@@ -119,7 +119,7 @@ public:
   BoundaryRegionParIterBase(IndicesVec& bndry_points, IndicesIter bndry_position, int dir,
                             Mesh* localmesh)
       : bndry_points(bndry_points), bndry_position(bndry_position), dir(dir),
-        localmesh(localmesh){};
+        localmesh(localmesh) {};
 
   // getter
   Ind3D ind() const { return bndry_position->index; }
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 9f9df6736c..f04d09cabc 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -450,7 +450,7 @@ Previously of they where implemented using a `RangeIterator`::
         lower_y = options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
         upper_y = options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(upper_y);
       }
-    
+
       void rhs() {
         BoutReal totalFlux = 0;
         if (lower_y) {
@@ -478,14 +478,14 @@ Previously of they where implemented using a `RangeIterator`::
           }
         }
       }
-    
+
     private:
       bool lower_y{true};
       bool upper_y{true};
       const Field3D& N;
       const Field3D& V;
     }
-    
+
 
 This can be replaced using the `YBoundary` class, which not only simplifies the
 code, but also allows to have the same code working with non-field-aligned
@@ -499,20 +499,20 @@ geometries, as flux coordinate independent (FCI) method::
         // Set what kind of yboundaries you want to include
         yboundary.init(opt);
       }
-    
+
       void rhs() {
         BoutReal totalFlux = 0;
         yboundary.iter_pnts([&](auto& pnt) {
           BoutReal flux = pnt.interpolate_sheath_o2(N) * pnt.interpolate_sheath_o2(V);
         });
       }
-    
+
     private:
       YBoundary ybounday;
       const Field3D& N;
       const Field3D& V;
     };
-    
+
 
 
 There are several member functions of ``pnt``. ``pnt`` is of type
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 1f04d3e099..7f5e4d4b03 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -7,7 +7,7 @@
  * Copyright 2010 - 2025 BOUT++ developers
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -230,7 +230,7 @@ const Region<Ind2D>& Field3D::getRegion2D(const std::string& region_name) const
 }
 
 /***************************************************************
- *                         OPERATORS 
+ *                         OPERATORS
  ***************************************************************/
 
 /////////////////// ASSIGNMENT ////////////////////
@@ -734,7 +734,7 @@ Field3D lowPass(const Field3D& var, int zmax, bool keep_zonal, const std::string
   return result;
 }
 
-/* 
+/*
  * Use FFT to shift by an angle in the Z direction
  */
 void shiftZ(Field3D& var, int jx, int jy, double zangle) {
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index ae7690aff7..a19e416beb 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -2223,9 +2223,9 @@ void BoutMesh::topology() {
     }
 
     for (int i = 0; i < limiter_count; ++i) {
-      int const yind = limiter_yinds[i];
-      int const xstart = limiter_xstarts[i];
-      int const xend = limiter_xends[i];
+      const int yind = limiter_yinds[i];
+      const int xstart = limiter_xstarts[i];
+      const int xend = limiter_xends[i];
       output_info.write("Adding a limiter between y={} and {}. X indices {} to {}\n",
                         yind, yind + 1, xstart, xend);
       add_target(yind, xstart, xend);
diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx
index 22a8f0748a..4b470da2ad 100644
--- a/src/mesh/parallel/shiftedmetricinterp.cxx
+++ b/src/mesh/parallel/shiftedmetricinterp.cxx
@@ -215,7 +215,7 @@ void ShiftedMetricInterp::checkInputGrid() {
                             "Should be 'orthogonal'.");
     }
   } // else: coordinate_system variable not found in grid input, indicates older input
-    //       file so must rely on the user having ensured the type is correct
+  //       file so must rely on the user having ensured the type is correct
 }
 
 /*!
diff --git a/tests/integrated/test-fci-boundary/runtest b/tests/integrated/test-fci-boundary/runtest
index a54b13bd01..74a8abf741 100755
--- a/tests/integrated/test-fci-boundary/runtest
+++ b/tests/integrated/test-fci-boundary/runtest
@@ -6,7 +6,6 @@ from boututils.run_wrapper import launch_safe
 from boututils.datafile import DataFile
 from boutdata.collect import collect as _collect
 
-import numpy as np
 from numpy.testing import assert_allclose
 
 

From ade82b73d1eb4ea7e364094fbff7bddb0e354db8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 12:47:36 +0100
Subject: [PATCH 0859/1827] Fix usage of any_of

---
 include/bout/parallel_boundary_region.hxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 05338c8479..d42a2b2366 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -451,7 +451,8 @@ public:
 
   bool contains(const int ix, const int iy, const int iz) const {
     const auto i2 = xyz2ind(ix, iy, iz, localmesh);
-    return std::ranges::any_of(bndry_points, [](auto i1) { return i2.index == i2; });
+    return std::ranges::any_of(bndry_points.begin(), bndry_points.end(),
+                               [&i2](auto i1) { return i1.index == i2; });
   }
 
   // setter

From 289ddf2a9c89ec5b39e8f22f329f9c4bcade0703 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 12 Mar 2026 08:50:06 -0700
Subject: [PATCH 0860/1827] PetscOperators: FCI operators using PETSc

Read operators from the mesh in CSR format. PETSc handles
communication pattern for MPI decomposition.
---
 CMakeLists.txt                           |   2 +
 include/bout/petsc_interface.hxx         |   4 +-
 include/bout/petsc_operators.hxx         |  30 ++++++
 src/mesh/petsc_operators.cxx             | 124 +++++++++++++++++++++++
 tests/unit/CMakeLists.txt                |   1 +
 tests/unit/mesh/test_petsc_operators.cxx |  44 ++++++++
 6 files changed, 203 insertions(+), 2 deletions(-)
 create mode 100644 include/bout/petsc_operators.hxx
 create mode 100644 src/mesh/petsc_operators.cxx
 create mode 100644 tests/unit/mesh/test_petsc_operators.cxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5f054c1c1f..0b14e5c3d5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -177,6 +177,7 @@ set(BOUT_SOURCES
     ./include/bout/parallel_boundary_region.hxx
     ./include/bout/paralleltransform.hxx
     ./include/bout/petsc_interface.hxx
+    ./include/bout/petsc_operators.hxx
     ./include/bout/petsclib.hxx
     ./include/bout/physicsmodel.hxx
     ./include/bout/rajalib.hxx
@@ -308,6 +309,7 @@ set(BOUT_SOURCES
     ./src/mesh/parallel/shiftedmetricinterp.hxx
     ./src/mesh/parallel_boundary_op.cxx
     ./src/mesh/parallel_boundary_region.cxx
+    ./src/mesh/petsc_operators.cxx
     ./src/mesh/surfaceiter.cxx
     ./src/physics/gyro_average.cxx
     ./src/physics/physicsmodel.cxx
diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 5239039f0c..ef17a63e4a 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -248,7 +248,7 @@ private:
 };
 
 /*!
- * A class which wraps PETSc vector objects, allowing them to be
+ * A class which wraps PETSc matrix objects, allowing them to be
  * indexed using the BOUT++ scheme. It provides the option of setting
  * a y-offset that interpolates onto field lines.
  */
@@ -289,7 +289,7 @@ public:
   }
 
   // Construct a matrix capable of operating on the specified field,
-  // preallocating memory if requeted and possible.
+  // preallocating memory if requested and possible.
   PetscMatrix(IndexerPtr<T> indConverter, bool preallocate = true)
       : matrix(new Mat()), indexConverter(indConverter),
         pt(&indConverter->getMesh()->getCoordinates()->getParallelTransform()) {
diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
new file mode 100644
index 0000000000..6801418996
--- /dev/null
+++ b/include/bout/petsc_operators.hxx
@@ -0,0 +1,30 @@
+/// Represent operators using PETSc matrices
+///
+
+#include "bout/mesh.hxx"
+#include <bout/petsclib.hxx>
+
+#include <petscmat.h>
+
+class PetscOperators {
+public:
+  PetscOperators(Mesh* mesh);
+
+  // Static functions for unit testing
+  static Region<Ind3D> create_region(Field3D cell_number);
+  static Region<Ind3D> create_region_xin(Field3D cell_number);
+  static Region<Ind3D> create_region_xout(Field3D cell_number);
+
+private:
+  PetscLib lib{}; // Initialize and finalize PETSc
+
+  Region<Ind3D> evolving_region; ///< Evolving cells
+  Region<Ind3D> xin_region;      ///< X boundary cells in inner boundary
+  Region<Ind3D> xout_region;     ///< X boundary cells in outer boundary
+  Region<Ind3D> yup_region;      ///< Y boundary cells in forward direction
+  Region<Ind3D> ydown_region;    ///< Y boundary cells in backward direction
+
+  Mat mat_mesh_to_petsc;
+
+  Mat mat_yforward;
+};
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
new file mode 100644
index 0000000000..6d3f98791e
--- /dev/null
+++ b/src/mesh/petsc_operators.cxx
@@ -0,0 +1,124 @@
+#include "bout/petsc_operators.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/output_bout_types.hxx"
+
+Region<Ind3D> PetscOperators::create_region(Field3D cell_number) {
+  Region<Ind3D>::RegionIndices indices;
+  BOUT_FOR_SERIAL(i, cell_number.getRegion("RGN_NOBNDRY")) {
+    if (cell_number[i] > -1) {
+      indices.push_back(i);
+    }
+  }
+  return Region<Ind3D>(indices);
+}
+
+Region<Ind3D> PetscOperators::create_region_xin(Field3D cell_number) {
+  Region<Ind3D>::RegionIndices xin_indices;
+  const Mesh* mesh = cell_number.getMesh();
+  if (mesh->firstX()) {
+    for (int i = 0; i < mesh->xstart; ++i) {
+      for (int j = mesh->ystart; j <= mesh->yend; ++j) {
+        for (int k = mesh->zstart; k <= mesh->zend; ++k) {
+          if (cell_number(i, j, k) > 0) {
+            xin_indices.push_back(Ind3D{i, j, k});
+          }
+        }
+      }
+    }
+  }
+  return Region<Ind3D>(xin_indices);
+}
+
+Region<Ind3D> PetscOperators::create_region_xout(Field3D cell_number) {
+  Region<Ind3D>::RegionIndices xout_indices;
+  const Mesh* mesh = cell_number.getMesh();
+  if (mesh->lastX()) {
+    for (int i = mesh->xend + 1; i < mesh->LocalNx; ++i) {
+      for (int j = mesh->ystart; j <= mesh->yend; ++j) {
+        for (int k = mesh->zstart; k <= mesh->zend; ++k) {
+          if (cell_number(i, j, k) > 0) {
+            xout_indices.push_back(Ind3D{i, j, k});
+          }
+        }
+      }
+    }
+  }
+  return Region<Ind3D>(xout_indices);
+}
+
+PetscOperators::PetscOperators(Mesh* mesh) {
+
+  // Get the cell center global numbering
+  // Note: This is an integer but Field3D only stores BoutReal.
+  Field3D cell_number;
+  if (mesh->get(cell_number, "cell_number") != 0) {
+    throw BoutException("PetscOperators requires field 'cell_number'");
+  }
+
+  // Forward Y boundary cell numbers.
+  // >0 only if a forward boundary cell
+  Field3D forward_cell_number;
+  if (mesh->get(forward_cell_number, "forward_cell_number") != 0) {
+    throw BoutException("PetscOperators requires field 'forward_cell_number'");
+  }
+
+  // Backward Y boundary cell numbers.
+  // >0 only if a backward boundary cell
+  Field3D backward_cell_number;
+  if (mesh->get(backward_cell_number, "backward_cell_number") != 0) {
+    throw BoutException("PetscOperators requires field 'backward_cell_number'");
+  }
+
+  // Calculate Regions for evolving variables and boundaries
+  evolving_region = create_region(cell_number);
+  xin_region = create_region_xin(cell_number);
+  xout_region = create_region_xout(cell_number);
+  yup_region = create_region(forward_cell_number);
+  ydown_region = create_region(backward_cell_number);
+
+  const std::size_t nlocal = evolving_region.size() + xin_region.size()
+                             + xout_region.size() + yup_region.size()
+                             + ydown_region.size();
+  output.write("Local {} : evolving {} xin {} xout {} yup {} ydown {}", nlocal,
+               evolving_region.size(), xin_region.size(), xout_region.size(),
+               yup_region.size(), ydown_region.size());
+
+  int mesh_total_cells;
+  if (mesh->get(mesh_total_cells, "total_cells") == 0) {
+    // Check total number of cells
+    output.write("Total cells in mesh: {}\n", mesh_total_cells);
+  }
+
+  // Create a PETSc matrix
+  // Note: Numbering is different from that used in PetscVector / PetscMatrix
+  // because yup/down boundaries are included.
+
+  MPI_Comm comm = BoutComm::get();
+
+  // Renumbering matrix.
+  // Maps PETSc row (or column) indices to the global indices used in
+  // the mesh.  This is needed because the PETSc indices depend on the
+  // number of processors.
+  MatCreate(comm, &mat_mesh_to_petsc);
+  MatSetSizes(mat_mesh_to_petsc, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE);
+  MatSetType(mat_mesh_to_petsc, MATMPIAIJ);
+  // Each row will have one non-zero entry, which could be in
+  // either the "diagonal" or "off-diagonal" block.
+  MatMPIAIJSetPreallocation(mat_mesh_to_petsc, 1, nullptr, 1, nullptr);
+
+  // Get the range of rows owned by this processor
+  PetscInt row_start, row_end;
+  MatGetOwnershipRange(mat_mesh_to_petsc, &row_start, &row_end);
+  output.write("Local row range: {} -> {}\n", row_start, row_end);
+
+  PetscInt row = row_start;
+  const PetscScalar ONE = 1.0;
+  BOUT_FOR_SERIAL(i, evolving_region) {
+    PetscInt col = ROUND(cell_number[i]);
+    MatSetValues(mat_mesh_to_petsc, 1, &row, 1, &col, &ONE, INSERT_VALUES);
+    ++row;
+  }
+
+  //MatCreate(comm, &mat_yforward);
+  //MatSetSizes(mat_yforward, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE);
+}
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index b347de7354..d3d690417b 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -97,6 +97,7 @@ set(serial_tests_source
     ./mesh/test_invert3x3.cxx
     ./mesh/test_mesh.cxx
     ./mesh/test_paralleltransform.cxx
+    ./mesh/test_petsc_operators.cxx
     ./solver/test_fakesolver.cxx
     ./solver/test_fakesolver.hxx
     ./solver/test_solver.cxx
diff --git a/tests/unit/mesh/test_petsc_operators.cxx b/tests/unit/mesh/test_petsc_operators.cxx
new file mode 100644
index 0000000000..949029f19c
--- /dev/null
+++ b/tests/unit/mesh/test_petsc_operators.cxx
@@ -0,0 +1,44 @@
+#include "gtest/gtest.h"
+
+#include "bout/output_bout_types.hxx"
+#include "bout/petsc_operators.hxx"
+
+#include "fake_mesh_fixture.hxx"
+#include "test_extras.hxx"
+
+namespace {
+Ind3D indexAt(const Field3D& f, int x, int y, int z) {
+  int ny = f.getNy();
+  int nz = f.getNz();
+  return Ind3D{(((x * ny) + y) * nz) + z, ny, nz};
+}
+} // namespace
+
+using bout::globals::mesh;
+
+// Reuse the "standard" fixture for FakeMesh
+using PetscOperatorsTest = FakeMeshFixture;
+
+TEST_F(PetscOperatorsTest, create_region_empty) {
+  Field3D cell_number{-1.0}; // No cells >= 0
+
+  auto rgn = PetscOperators::create_region(cell_number);
+
+  ASSERT_EQ(0, rgn.size());
+}
+
+TEST_F(PetscOperatorsTest, create_region) {
+  Field3D cell_number{-1.0}; // No cells >= 0
+
+  // Note: 1 boundary cell in X and Y
+  cell_number(0, 0, 0) = 0; // Corner
+  cell_number(1, 1, 0) = 1; // In domain
+  cell_number(0, 1, 1) = 2; // Xin boundary
+
+  auto rgn = PetscOperators::create_region(cell_number);
+  ASSERT_EQ(1, rgn.size());
+
+  Ind3D expected_ind = indexAt(cell_number, 1, 1, 0);
+  output.write("{} : {}\n", expected_ind, *rgn.begin());
+  ASSERT_TRUE(expected_ind == *rgn.begin());
+}

From a3d47121d23a0613bab6dc6e0640d2f4e2447d74 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 12 Mar 2026 17:23:11 +0000
Subject: [PATCH 0861/1827] Revert "Use annotations instead of comments for
 `clang-tidy-review`"

This reverts commit c37f6988f6c5c599968d736fac98f19b8c88ea09.

[skip ci]
---
 .github/workflows/clang-tidy-review.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 7646a7bc9c..360a162456 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -24,7 +24,6 @@ jobs:
         uses: ZedThree/clang-tidy-review@v0.23.1
         id: review
         with:
-          annotations: true
           build_dir: build
           apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev,uuid-dev"
           config_file: ".clang-tidy"

From c73c29aea4b563faecac53f0bbe0664c1fc50517 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 12 Mar 2026 14:57:43 -0700
Subject: [PATCH 0862/1827] PetscOperators: Splitting out PetscMapping

Handles the mapping between mesh indices and PETSc global indices.
---
 include/bout/field3d.hxx                 |  16 +++-
 include/bout/petsc_operators.hxx         |  48 ++++++++--
 include/bout/region.hxx                  |  17 ++--
 src/mesh/petsc_operators.cxx             | 107 ++++++++++++-----------
 tests/unit/mesh/test_petsc_operators.cxx |  58 ++++++++----
 5 files changed, 157 insertions(+), 89 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 54d9fb85c9..66c6d54a9e 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -1,8 +1,8 @@
 /**************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
+ *
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
- * 
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -348,6 +348,14 @@ public:
     return std::end(getRegion("RGN_ALL"));
   };
 
+  /// Convert (x, y, z) to an Ind3D
+  /// Requires mesh size.
+  Ind3D indexAt(int x, int y, int z) const {
+    const int ny = this->getNy();
+    const int nz = this->getNz();
+    return Ind3D{(((x * ny) + y) * nz) + z, ny, nz};
+  }
+
   BoutReal& operator[](const Ind3D& d) { return data[d.ind]; }
   const BoutReal& operator[](const Ind3D& d) const { return data[d.ind]; }
 
@@ -361,7 +369,7 @@ public:
    * Direct access to the underlying data array
    *
    * If CHECK > 2 then bounds checking is performed
-   * 
+   *
    * If CHECK <= 2 then no checks are performed, to
    * allow inlining and optimisation of inner loops
    */
diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 6801418996..bda4017c5e 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -1,22 +1,45 @@
 /// Represent operators using PETSc matrices
 ///
 
+#include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
-#include <bout/petsclib.hxx>
+#include "bout/petsclib.hxx"
+#include "bout/region.hxx"
 
 #include <petscmat.h>
 
-class PetscOperators {
+#include <string>
+
+/// Handles mapping between global cell index used in the mesh file,
+/// and the global indexing used in PETSc that depends on the mesh
+/// decomposition across MPI ranks.
+///
+/// Each processor reads a chunk of the global arrays into Field3Ds:
+///  - cell_number
+///  - forward_cell_number
+///  - backward_cell_number
+/// Non-negative values in these arrays indicate a cell number.
+///
+/// A Petsc Mat is constructed that maps between petsc indices and
+/// mesh indices.
+class PetscMapping {
 public:
-  PetscOperators(Mesh* mesh);
+  PetscMapping(const Field3D& cell_number, const Field3D& forward_cell_number,
+               const Field3D& backward_cell_number);
 
   // Static functions for unit testing
-  static Region<Ind3D> create_region(Field3D cell_number);
-  static Region<Ind3D> create_region_xin(Field3D cell_number);
-  static Region<Ind3D> create_region_xout(Field3D cell_number);
+  static Region<Ind3D> create_region(const Field3D& cell_number);
+  static Region<Ind3D> create_region_xin(const Field3D& cell_number);
+  static Region<Ind3D> create_region_xout(const Field3D& cell_number);
+
+  /// Total number of cells, including X and Y boundaries
+  unsigned int size() const {
+    return evolving_region.size() + xin_region.size() + xout_region.size()
+           + yup_region.size() + ydown_region.size();
+  }
 
 private:
-  PetscLib lib{}; // Initialize and finalize PETSc
+  PetscLib lib; // Initialize and finalize PETSc
 
   Region<Ind3D> evolving_region; ///< Evolving cells
   Region<Ind3D> xin_region;      ///< X boundary cells in inner boundary
@@ -25,6 +48,15 @@ private:
   Region<Ind3D> ydown_region;    ///< Y boundary cells in backward direction
 
   Mat mat_mesh_to_petsc;
+};
+
+class PetscOperators {
+public:
+  PetscOperators(Mesh* mesh);
+
+private:
+  /// Read a Field3D from the mesh or throw BoutException if not found.
+  Field3D meshGetField3D(Mesh* mesh, const std::string& name);
 
-  Mat mat_yforward;
+  PetscMapping mapping;
 };
diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index e00ad6d41d..d423c3ef4c 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -1,9 +1,9 @@
 /**************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
  * Region class by D. Dickinson 2018
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -170,8 +170,8 @@ struct SpecificInd {
   int ny = -1, nz = -1; ///< Sizes of y and z dimensions
 
   SpecificInd() = default;
-  SpecificInd(int i, int ny, int nz) : ind(i), ny(ny), nz(nz){};
-  explicit SpecificInd(int i) : ind(i){};
+  SpecificInd(int i, int ny, int nz) : ind(i), ny(ny), nz(nz) {};
+  explicit SpecificInd(int i) : ind(i) {};
 
   /// Allow explicit conversion to an int
   explicit operator int() const { return ind; }
@@ -491,10 +491,9 @@ template <typename T = Ind3D>
 class Region {
   // Following prevents a Region being created with anything other
   // than Ind2D, Ind3D or IndPerp as template type
-  static_assert(
-      std::is_base_of_v<
-          Ind2D, T> || std::is_base_of_v<Ind3D, T> || std::is_base_of_v<IndPerp, T>,
-      "Region must be templated with one of IndPerp, Ind2D or Ind3D");
+  static_assert(std::is_base_of_v<Ind2D, T> || std::is_base_of_v<Ind3D, T>
+                    || std::is_base_of_v<IndPerp, T>,
+                "Region must be templated with one of IndPerp, Ind2D or Ind3D");
 
 public:
   using data_type = T;
@@ -570,7 +569,7 @@ public:
   };
 
   Region(RegionIndices& indices, int maxregionblocksize = MAXREGIONBLOCKSIZE)
-      : indices(indices), blocks(getContiguousBlocks(maxregionblocksize)){};
+      : indices(indices), blocks(getContiguousBlocks(maxregionblocksize)) {};
 
   // We need to first set the blocks, and only after that call getRegionIndices.
   // Do not put in the member initialisation
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 6d3f98791e..f5d312d8fb 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -1,8 +1,15 @@
 #include "bout/petsc_operators.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/field3d.hxx"
+#include "bout/output.hxx"
 #include "bout/output_bout_types.hxx"
+#include "bout/region.hxx"
 
-Region<Ind3D> PetscOperators::create_region(Field3D cell_number) {
+#include <functional>
+#include <string>
+#include <vector>
+
+Region<Ind3D> PetscMapping::create_region(const Field3D& cell_number) {
   Region<Ind3D>::RegionIndices indices;
   BOUT_FOR_SERIAL(i, cell_number.getRegion("RGN_NOBNDRY")) {
     if (cell_number[i] > -1) {
@@ -12,7 +19,7 @@ Region<Ind3D> PetscOperators::create_region(Field3D cell_number) {
   return Region<Ind3D>(indices);
 }
 
-Region<Ind3D> PetscOperators::create_region_xin(Field3D cell_number) {
+Region<Ind3D> PetscMapping::create_region_xin(const Field3D& cell_number) {
   Region<Ind3D>::RegionIndices xin_indices;
   const Mesh* mesh = cell_number.getMesh();
   if (mesh->firstX()) {
@@ -20,7 +27,7 @@ Region<Ind3D> PetscOperators::create_region_xin(Field3D cell_number) {
       for (int j = mesh->ystart; j <= mesh->yend; ++j) {
         for (int k = mesh->zstart; k <= mesh->zend; ++k) {
           if (cell_number(i, j, k) > 0) {
-            xin_indices.push_back(Ind3D{i, j, k});
+            xin_indices.push_back(cell_number.indexAt(i, j, k));
           }
         }
       }
@@ -29,7 +36,7 @@ Region<Ind3D> PetscOperators::create_region_xin(Field3D cell_number) {
   return Region<Ind3D>(xin_indices);
 }
 
-Region<Ind3D> PetscOperators::create_region_xout(Field3D cell_number) {
+Region<Ind3D> PetscMapping::create_region_xout(const Field3D& cell_number) {
   Region<Ind3D>::RegionIndices xout_indices;
   const Mesh* mesh = cell_number.getMesh();
   if (mesh->lastX()) {
@@ -37,7 +44,7 @@ Region<Ind3D> PetscOperators::create_region_xout(Field3D cell_number) {
       for (int j = mesh->ystart; j <= mesh->yend; ++j) {
         for (int k = mesh->zstart; k <= mesh->zend; ++k) {
           if (cell_number(i, j, k) > 0) {
-            xout_indices.push_back(Ind3D{i, j, k});
+            xout_indices.push_back(cell_number.indexAt(i, j, k));
           }
         }
       }
@@ -46,60 +53,28 @@ Region<Ind3D> PetscOperators::create_region_xout(Field3D cell_number) {
   return Region<Ind3D>(xout_indices);
 }
 
-PetscOperators::PetscOperators(Mesh* mesh) {
-
-  // Get the cell center global numbering
-  // Note: This is an integer but Field3D only stores BoutReal.
-  Field3D cell_number;
-  if (mesh->get(cell_number, "cell_number") != 0) {
-    throw BoutException("PetscOperators requires field 'cell_number'");
-  }
-
-  // Forward Y boundary cell numbers.
-  // >0 only if a forward boundary cell
-  Field3D forward_cell_number;
-  if (mesh->get(forward_cell_number, "forward_cell_number") != 0) {
-    throw BoutException("PetscOperators requires field 'forward_cell_number'");
-  }
-
-  // Backward Y boundary cell numbers.
-  // >0 only if a backward boundary cell
-  Field3D backward_cell_number;
-  if (mesh->get(backward_cell_number, "backward_cell_number") != 0) {
-    throw BoutException("PetscOperators requires field 'backward_cell_number'");
-  }
-
-  // Calculate Regions for evolving variables and boundaries
-  evolving_region = create_region(cell_number);
-  xin_region = create_region_xin(cell_number);
-  xout_region = create_region_xout(cell_number);
-  yup_region = create_region(forward_cell_number);
-  ydown_region = create_region(backward_cell_number);
-
-  const std::size_t nlocal = evolving_region.size() + xin_region.size()
-                             + xout_region.size() + yup_region.size()
-                             + ydown_region.size();
+PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_cell_number,
+                           const Field3D& backward_cell_number)
+    : evolving_region(create_region(cell_number)),
+      xin_region(create_region_xin(cell_number)),
+      xout_region(create_region_xout(cell_number)),
+      yup_region(create_region(forward_cell_number)),
+      ydown_region(create_region(backward_cell_number)) {
+  // Calculate size of each region
+  const unsigned int nlocal = this->size();
   output.write("Local {} : evolving {} xin {} xout {} yup {} ydown {}", nlocal,
                evolving_region.size(), xin_region.size(), xout_region.size(),
                yup_region.size(), ydown_region.size());
 
-  int mesh_total_cells;
-  if (mesh->get(mesh_total_cells, "total_cells") == 0) {
-    // Check total number of cells
-    output.write("Total cells in mesh: {}\n", mesh_total_cells);
-  }
-
   // Create a PETSc matrix
   // Note: Numbering is different from that used in PetscVector / PetscMatrix
   // because yup/down boundaries are included.
 
-  MPI_Comm comm = BoutComm::get();
-
   // Renumbering matrix.
   // Maps PETSc row (or column) indices to the global indices used in
   // the mesh.  This is needed because the PETSc indices depend on the
   // number of processors.
-  MatCreate(comm, &mat_mesh_to_petsc);
+  MatCreate(BoutComm::get(), &mat_mesh_to_petsc);
   MatSetSizes(mat_mesh_to_petsc, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE);
   MatSetType(mat_mesh_to_petsc, MATMPIAIJ);
   // Each row will have one non-zero entry, which could be in
@@ -113,10 +88,40 @@ PetscOperators::PetscOperators(Mesh* mesh) {
 
   PetscInt row = row_start;
   const PetscScalar ONE = 1.0;
-  BOUT_FOR_SERIAL(i, evolving_region) {
-    PetscInt col = ROUND(cell_number[i]);
-    MatSetValues(mat_mesh_to_petsc, 1, &row, 1, &col, &ONE, INSERT_VALUES);
-    ++row;
+  // Iterate through regions in this order
+  const std::vector<std::reference_wrapper<Region<Ind3D>>> regions = {
+      evolving_region, xin_region, xout_region, yup_region, ydown_region};
+  for (const auto& region : regions) {
+    BOUT_FOR_SERIAL(i, region.get()) {
+      const PetscInt col = ROUND(cell_number[i]);
+      MatSetValues(mat_mesh_to_petsc, 1, &row, 1, &col, &ONE, INSERT_VALUES);
+      ++row;
+    }
+  }
+  MatAssemblyBegin(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY);
+  MatAssemblyEnd(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY);
+}
+
+Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) {
+  Field3D result;
+  if (mesh->get(result, name) != 0) {
+    throw BoutException("PetscOperators requires field '{}'", name);
+  }
+  return result;
+}
+
+PetscOperators::PetscOperators(Mesh* mesh)
+    : mapping(PetscMapping(meshGetField3D(mesh, "cell_number"),
+                           meshGetField3D(mesh, "forward_cell_number"),
+                           meshGetField3D(mesh, "backward_cell_number"))) {
+
+  int mesh_total_cells;
+  if (mesh->get(mesh_total_cells, "total_cells") == 0) {
+    // Check total number of cells
+    if (mesh_total_cells != mapping.size()) {
+      throw BoutException("Total cells in mesh {} doesn't match mapping size {}",
+                          mesh_total_cells, mapping.size());
+    }
   }
 
   //MatCreate(comm, &mat_yforward);
diff --git a/tests/unit/mesh/test_petsc_operators.cxx b/tests/unit/mesh/test_petsc_operators.cxx
index 949029f19c..b33d41a7b1 100644
--- a/tests/unit/mesh/test_petsc_operators.cxx
+++ b/tests/unit/mesh/test_petsc_operators.cxx
@@ -1,33 +1,40 @@
 #include "gtest/gtest.h"
 
+#include "bout/output.hxx"
 #include "bout/output_bout_types.hxx"
 #include "bout/petsc_operators.hxx"
+#include "bout/region.hxx"
 
 #include "fake_mesh_fixture.hxx"
 #include "test_extras.hxx"
 
-namespace {
-Ind3D indexAt(const Field3D& f, int x, int y, int z) {
-  int ny = f.getNy();
-  int nz = f.getNz();
-  return Ind3D{(((x * ny) + y) * nz) + z, ny, nz};
-}
-} // namespace
+// Reuse the "standard" fixture for FakeMesh
+using PetscMappingTest = FakeMeshFixture;
 
-using bout::globals::mesh;
+TEST_F(PetscMappingTest, create_region_empty) {
+  const Field3D cell_number{-1.0}; // No cells >= 0
 
-// Reuse the "standard" fixture for FakeMesh
-using PetscOperatorsTest = FakeMeshFixture;
+  auto rgn = PetscMapping::create_region(cell_number);
 
-TEST_F(PetscOperatorsTest, create_region_empty) {
+  ASSERT_EQ(0, rgn.size());
+}
+
+TEST_F(PetscMappingTest, create_region) {
   Field3D cell_number{-1.0}; // No cells >= 0
 
-  auto rgn = PetscOperators::create_region(cell_number);
+  // Note: 1 boundary cell in X and Y
+  cell_number(0, 0, 0) = 0; // Corner
+  cell_number(1, 1, 0) = 1; // In domain
+  cell_number(0, 1, 1) = 2; // Xin boundary
 
-  ASSERT_EQ(0, rgn.size());
+  auto rgn = PetscMapping::create_region(cell_number);
+  ASSERT_EQ(1, rgn.size());
+
+  const Ind3D expected_ind = cell_number.indexAt(1, 1, 0);
+  ASSERT_TRUE(expected_ind == *rgn.begin());
 }
 
-TEST_F(PetscOperatorsTest, create_region) {
+TEST_F(PetscMappingTest, create_region_xin) {
   Field3D cell_number{-1.0}; // No cells >= 0
 
   // Note: 1 boundary cell in X and Y
@@ -35,10 +42,27 @@ TEST_F(PetscOperatorsTest, create_region) {
   cell_number(1, 1, 0) = 1; // In domain
   cell_number(0, 1, 1) = 2; // Xin boundary
 
-  auto rgn = PetscOperators::create_region(cell_number);
+  auto rgn = PetscMapping::create_region_xin(cell_number);
   ASSERT_EQ(1, rgn.size());
 
-  Ind3D expected_ind = indexAt(cell_number, 1, 1, 0);
-  output.write("{} : {}\n", expected_ind, *rgn.begin());
+  const Ind3D expected_ind = cell_number.indexAt(0, 1, 1);
+  output.write("Expecting {} == {}\n", expected_ind, *rgn.begin());
   ASSERT_TRUE(expected_ind == *rgn.begin());
 }
+
+TEST_F(PetscMappingTest, mapping) {
+  Field3D cell_number{-1.0}; // No cells >= 0
+
+  // Note: 1 boundary cell in X and Y
+  cell_number(0, 0, 0) = 0; // Corner
+  cell_number(1, 1, 0) = 1; // In domain
+  cell_number(0, 1, 1) = 2; // Xin boundary
+
+  const Field3D forward_cell_number{-1.0};
+  const Field3D backward_cell_number{-1.0};
+
+  const PetscMapping mapping(cell_number, forward_cell_number, backward_cell_number);
+
+  // Two cells: one evolving and one in xin
+  ASSERT_EQ(2, mapping.size());
+}

From 724572af852b03ab0f34ecbb7486cd2704f9e322 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 12 Mar 2026 20:49:43 -0700
Subject: [PATCH 0863/1827] Mesh::get Arrays of int and BoutReal

Simple wrapper functions around the Options functionality,
so that Array types can be read from the mesh file.
---
 include/bout/griddata.hxx      | 20 ++++++++++++++++++--
 include/bout/mesh.hxx          | 10 +++++++---
 src/mesh/data/gridfromfile.cxx | 23 +++++++++++++++++++++--
 src/mesh/mesh.cxx              | 14 +++++++++++---
 4 files changed, 57 insertions(+), 10 deletions(-)

diff --git a/include/bout/griddata.hxx b/include/bout/griddata.hxx
index 29a32e5779..e9d9214846 100644
--- a/include/bout/griddata.hxx
+++ b/include/bout/griddata.hxx
@@ -2,9 +2,9 @@
  * Functions to read input variables on a grid/mesh
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -29,12 +29,16 @@ class GridDataSource;
 #define BOUT_GRIDDATA_H
 
 #include "mesh.hxx"
+#include "bout/array.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/options.hxx"
 
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 
+#include <string>
+#include <vector>
+
 /// Interface class to serve grid data
 /*!
  * Provides a generic interface for sources of
@@ -71,6 +75,15 @@ public:
   static constexpr Direction Y = Direction::Y;
   static constexpr Direction Z = Direction::Z;
 
+  virtual bool get([[maybe_unused]] Array<int>& var,
+                   [[maybe_unused]] const std::string& name) {
+    return false;
+  }
+  virtual bool get([[maybe_unused]] Array<BoutReal>& var,
+                   [[maybe_unused]] const std::string& name) {
+    return false;
+  }
+
   virtual bool get(Mesh* m, std::vector<int>& var, const std::string& name, int len,
                    int offset = 0, Direction dir = GridDataSource::X) = 0;
   virtual bool get(Mesh* m, std::vector<BoutReal>& var, const std::string& name, int len,
@@ -115,6 +128,9 @@ public:
     return getField(m, var, name, def, location);
   }
 
+  bool get(Array<int>& var, const std::string& name) override;
+  bool get(Array<BoutReal>& var, const std::string& name) override;
+
   bool get(Mesh* m, std::vector<int>& var, const std::string& name, int len,
            int offset = 0, GridDataSource::Direction dir = GridDataSource::X) override;
   bool get(Mesh* m, std::vector<BoutReal>& var, const std::string& name, int len,
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index a1ed6a9011..2422ce283d 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -3,7 +3,7 @@
  *
  * Interface for mesh classes. Contains standard variables and useful
  * routines.
- * 
+ *
  * Changelog
  * =========
  *
@@ -11,7 +11,7 @@
  *     * Removing coordinate system into separate
  *       Coordinates class
  *     * Adding index derivative functions from derivs.cxx
- * 
+ *
  * 2010-06 Ben Dudson, Sean Farley
  *     * Initial version, adapted from GridData class
  *     * Incorporates code from topology.cpp and Communicator
@@ -20,7 +20,7 @@
  * Copyright 2010-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -43,6 +43,7 @@ class Mesh;
 #ifndef BOUT_MESH_H
 #define BOUT_MESH_H
 
+#include "bout/array.hxx"
 #include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/coordinates.hxx" // Coordinates class
@@ -170,6 +171,9 @@ public:
   /// @returns zero if successful, non-zero on failure
   int get(bool& bval, const std::string& name, bool def = false);
 
+  int get(Array<int>& var, const std::string& name);
+  int get(Array<BoutReal>& var, const std::string& name);
+
   /// Get a Field2D from the input source
   /// including communicating guard cells
   ///
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 10f6f6926e..e2e9850612 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -3,6 +3,7 @@
 #include <bout/griddata.hxx>
 
 #include <bout/array.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
@@ -14,7 +15,9 @@
 
 #include <algorithm>
 #include <iterator>
+#include <string>
 #include <utility>
+#include <vector>
 
 GridFile::GridFile(std::string gridfilename)
     : GridDataSource(true), data(bout::OptionsIO::create(gridfilename)->read()),
@@ -120,7 +123,7 @@ bool GridFile::get(Mesh* UNUSED(m), BoutReal& rval, const std::string& name,
 
 /*!
  * Reads a 2D, 3D or FieldPerp field variable from a file
- * 
+ *
  * Successfully reads Field2D or FieldPerp if the variable in the file is 0-D or 2-D.
  * Successfully reads Field3D if the variable in the file is 0-D, 2-D or 3-D.
  */
@@ -378,7 +381,7 @@ void GridFile::readField(Mesh* m, const std::string& name, int ys, int yd, int n
 
     for (int x = xs; x < xs + nx_to_read; ++x) {
       for (int y = ys; y < ys + ny_to_read; ++y) {
-        BoutReal const value = full_var(x, y);
+        const BoutReal value = full_var(x, y);
         for (int z = 0; z < var.getNz(); z++) {
           var(x - xs + xd, y - ys + yd, z) = value;
         }
@@ -466,6 +469,22 @@ void GridFile::readField(Mesh* m, const std::string& name, int UNUSED(ys), int U
   }
 }
 
+bool GridFile::get(Array<int>& var, const std::string& name) {
+  if (not data.isSet(name)) {
+    return false;
+  }
+  var = data[name].as<Array<int>>();
+  return true;
+}
+
+bool GridFile::get(Array<BoutReal>& var, const std::string& name) {
+  if (not data.isSet(name)) {
+    return false;
+  }
+  var = data[name].as<Array<BoutReal>>();
+  return true;
+}
+
 bool GridFile::get([[maybe_unused]] Mesh* m, [[maybe_unused]] std::vector<int>& var,
                    [[maybe_unused]] const std::string& name, [[maybe_unused]] int len,
                    [[maybe_unused]] int offset,
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 829c150a15..034da6eecd 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -179,13 +179,21 @@ int Mesh::get(bool& bval, const std::string& name, bool def) {
   if (source == nullptr) {
     warn_default_used(def, name);
     bval = def;
-    return true;
+    return 1;
   }
 
   int bval_as_int = 0;
-  bool success = source->get(this, bval_as_int, name, def);
+  const bool success = source->get(this, bval_as_int, name, int(def));
   bval = bool(bval_as_int);
-  return !success;
+  return success ? 0 : 1;
+}
+
+int Mesh::get(Array<int>& var, const std::string& name) {
+  return source->get(var, name) ? 0 : 1;
+}
+
+int Mesh::get(Array<BoutReal>& var, const std::string& name) {
+  return source->get(var, name) ? 0 : 1;
 }
 
 int Mesh::get(Field2D& var, const std::string& name, BoutReal def, bool communicate,

From af65816e753ed4cda2c90f78099a558a847c2120 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 12 Mar 2026 21:46:49 -0700
Subject: [PATCH 0864/1827] PetscOperators: Implement operators from CSR input

Reads row, column and weights from Mesh, constructs Petsc Mat
objects. Working on composition and operation on Field3D objects.
---
 include/bout/petsc_operators.hxx |  87 +++++++++++++++++++++-
 src/mesh/petsc_operators.cxx     | 121 +++++++++++++++++++++++++------
 2 files changed, 184 insertions(+), 24 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index bda4017c5e..c19146a105 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -1,14 +1,21 @@
 /// Represent operators using PETSc matrices
 ///
 
+#include "bout/array.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
 #include "bout/petsclib.hxx"
 #include "bout/region.hxx"
+#include "bout/utils.hxx"
 
 #include <petscmat.h>
 
+#include <functional>
+#include <memory>
 #include <string>
+#include <vector>
 
 /// Handles mapping between global cell index used in the mesh file,
 /// and the global indexing used in PETSc that depends on the mesh
@@ -38,25 +45,103 @@ public:
            + yup_region.size() + ydown_region.size();
   }
 
+  /// Loops over cells and calls the given function with arguments:
+  ///   - PetscInt  PETSc row index
+  ///   - Ind3D     Index into Field3D variables
+  ///   - int       Global cell number in mesh
+  ///
+  template <typename Function>
+  void map_evolving(Function func) const {
+    PetscInt row = this->row_start;
+    BOUT_FOR_SERIAL(i, this->evolving_region) {
+      func(row, i, ROUND(cell_number[i]));
+      ++row;
+    }
+  }
+
+  /// Note: It doesn't make sense to pass the Ind3D because
+  /// some reference Field3D, some the yup/ydown fields.
+  template <typename Function>
+  void map(Function func) const {
+    const std::vector<std::reference_wrapper<const Region<Ind3D>>> regions = {
+        evolving_region, xin_region, xout_region, yup_region, ydown_region};
+    PetscInt row = row_start;
+    for (const auto& region : regions) {
+      BOUT_FOR_SERIAL(i, region.get()) {
+        func(row, ROUND(cell_number[i]));
+        ++row;
+      }
+    }
+  }
+
 private:
   PetscLib lib; // Initialize and finalize PETSc
 
+  Field3D cell_number;
+
   Region<Ind3D> evolving_region; ///< Evolving cells
   Region<Ind3D> xin_region;      ///< X boundary cells in inner boundary
   Region<Ind3D> xout_region;     ///< X boundary cells in outer boundary
   Region<Ind3D> yup_region;      ///< Y boundary cells in forward direction
   Region<Ind3D> ydown_region;    ///< Y boundary cells in backward direction
 
+  PetscInt row_start, row_end; ///< Local row indices
   Mat mat_mesh_to_petsc;
 };
 
+/// Shared pointer to const PetscMapping
+/// Mapping is const after creation.
+using PetscMappingPtr = std::shared_ptr<const PetscMapping>;
+
+/// Represents an operator on Field3Ds
+class PetscOperator {
+public:
+  /// Create using CSR format arrays
+  PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
+                Array<BoutReal> weights);
+
+  /// Perform operation
+  Field3D operator()(const Field3D& rhs) const;
+
+  /// Operator composition
+  PetscOperator operator*(const PetscOperator& rhs) const;
+
+  /// Operator addition
+  PetscOperator operator+(const PetscOperator& rhs) const;
+
+  /// Operator subtraction
+  PetscOperator operator-(const PetscOperator& rhs) const;
+
+private:
+  PetscOperator(PetscMappingPtr mapping, Mat mat)
+      : mapping(std::move(mapping)), mat_operator(mat) {}
+  PetscMappingPtr mapping;
+  Mat mat_operator;
+};
+
 class PetscOperators {
 public:
+  ///
+  /// Reads from the mesh:
+  /// - cell_number : Field3D
+  /// - forward_cell_number : Field3D
+  /// - backward_cell_number : Field3D
+  /// - total_cells : int, optional
   PetscOperators(Mesh* mesh);
 
 private:
   /// Read a Field3D from the mesh or throw BoutException if not found.
   Field3D meshGetField3D(Mesh* mesh, const std::string& name);
 
-  PetscMapping mapping;
+  /// Read a 1D Array<T> from the mesh or throw BoutException
+  template <typename T>
+  Array<T> meshGetArray(Mesh* mesh, const std::string& name) {
+    Array<T> result;
+    if (mesh->get(result, name) != 0) {
+      throw BoutException("PetscOperators requires Array<int> '{}'", name);
+    }
+    return result;
+  }
+
+  PetscMappingPtr mapping;
 };
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index f5d312d8fb..ef48d75dd1 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -1,13 +1,14 @@
 #include "bout/petsc_operators.hxx"
+#include "bout/array.hxx"
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
 #include "bout/output.hxx"
 #include "bout/output_bout_types.hxx"
 #include "bout/region.hxx"
-
-#include <functional>
+#include <memory>
 #include <string>
-#include <vector>
 
 Region<Ind3D> PetscMapping::create_region(const Field3D& cell_number) {
   Region<Ind3D>::RegionIndices indices;
@@ -55,7 +56,7 @@ Region<Ind3D> PetscMapping::create_region_xout(const Field3D& cell_number) {
 
 PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_cell_number,
                            const Field3D& backward_cell_number)
-    : evolving_region(create_region(cell_number)),
+    : cell_number(cell_number), evolving_region(create_region(cell_number)),
       xin_region(create_region_xin(cell_number)),
       xout_region(create_region_xout(cell_number)),
       yup_region(create_region(forward_cell_number)),
@@ -82,26 +83,97 @@ PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_ce
   MatMPIAIJSetPreallocation(mat_mesh_to_petsc, 1, nullptr, 1, nullptr);
 
   // Get the range of rows owned by this processor
-  PetscInt row_start, row_end;
   MatGetOwnershipRange(mat_mesh_to_petsc, &row_start, &row_end);
   output.write("Local row range: {} -> {}\n", row_start, row_end);
 
-  PetscInt row = row_start;
-  const PetscScalar ONE = 1.0;
   // Iterate through regions in this order
-  const std::vector<std::reference_wrapper<Region<Ind3D>>> regions = {
-      evolving_region, xin_region, xout_region, yup_region, ydown_region};
-  for (const auto& region : regions) {
-    BOUT_FOR_SERIAL(i, region.get()) {
-      const PetscInt col = ROUND(cell_number[i]);
-      MatSetValues(mat_mesh_to_petsc, 1, &row, 1, &col, &ONE, INSERT_VALUES);
-      ++row;
-    }
-  }
+  this->map([&](PetscInt row, PetscInt col) {
+    // `row` is the PETSc index; `col` is the Mesh index
+    const PetscScalar ONE = 1.0;
+    MatSetValues(mat_mesh_to_petsc, 1, &row, 1, &col, &ONE, INSERT_VALUES);
+  });
   MatAssemblyBegin(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY);
   MatAssemblyEnd(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY);
 }
 
+PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
+                             Array<BoutReal> weights)
+    : mapping(mapping) {
+
+  MatCreate(BoutComm::get(), &mat_operator);
+  int nlocal = mapping->size();
+  MatSetSizes(mat_operator, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE);
+
+  mapping->map_evolving([&](PetscInt row, Ind3D, PetscInt mesh_index) {
+    if (mesh_index >= rows.size()) {
+      return; // No weights -> skip
+    }
+    // Get the range of indices into columns and weights
+    int start_ind = rows[mesh_index];
+    int end_ind = (mesh_index + 1 < rows.size()) ? rows[mesh_index + 1] : cols.size();
+    output.write("Mapping {} : {} -> {}\n", row, start_ind, end_ind);
+
+    MatSetValues(mat_operator, 1, &row, end_ind - start_ind, &cols[start_ind],
+                 &weights[start_ind], INSERT_VALUES);
+  });
+  MatAssemblyBegin(mat_operator, MAT_FINAL_ASSEMBLY);
+  MatAssemblyEnd(mat_operator, MAT_FINAL_ASSEMBLY);
+}
+
+/// Perform operation
+Field3D PetscOperator::operator()(const Field3D& rhs) const {
+  Vec rhs_vec;
+  VecCreate(BoutComm::get(), &rhs_vec);
+  VecSetSizes(rhs_vec, this->mapping->size(), PETSC_DETERMINE);
+
+  // Fill vec from rhs
+  PetscScalar* x;
+  VecGetArray(rhs_vec, &x);
+  throw BoutException("Not implemented");
+  VecRestoreArray(rhs_vec, &x);
+
+  // Perform Mat-Vec muliplication
+  Vec result_vec;
+  VecDuplicate(rhs_vec, &result_vec);
+  MatMult(this->mat_operator, rhs_vec, result_vec);
+
+  // Copy result_vec into a Field3D
+  Field3D result;
+  const PetscScalar* r;
+  VecGetArrayRead(result_vec, &r);
+  throw BoutException("Not implemented");
+  VecRestoreArrayRead(result_vec, &r);
+
+  return result;
+}
+
+/// Operator composition
+PetscOperator PetscOperator::operator*(const PetscOperator& rhs) const {
+  ASSERT0(this->mapping == rhs.mapping);
+  Mat mat;
+  MatMatMult(this->mat_operator, rhs.mat_operator, MAT_INITIAL_MATRIX, PETSC_DETERMINE,
+             &mat);
+  return PetscOperator(this->mapping, mat);
+}
+
+/// Operator addition
+PetscOperator PetscOperator::operator+(const PetscOperator& rhs) const {
+  ASSERT0(this->mapping == rhs.mapping);
+  Mat mat;
+  MatDuplicate(mat_operator, MAT_COPY_VALUES, &mat);
+  MatAXPY(mat, 1.0, rhs.mat_operator, UNKNOWN_NONZERO_PATTERN);
+  return PetscOperator(this->mapping, mat);
+}
+
+/// Operator subtraction
+PetscOperator PetscOperator::operator-(const PetscOperator& rhs) const {
+  ASSERT0(this->mapping == rhs.mapping);
+  Mat mat;
+  MatDuplicate(mat_operator, MAT_COPY_VALUES, &mat);
+  MatAXPY(mat, -1.0, rhs.mat_operator, UNKNOWN_NONZERO_PATTERN);
+  return PetscOperator(this->mapping, mat);
+}
+
 Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) {
   Field3D result;
   if (mesh->get(result, name) != 0) {
@@ -111,19 +183,22 @@ Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) {
 }
 
 PetscOperators::PetscOperators(Mesh* mesh)
-    : mapping(PetscMapping(meshGetField3D(mesh, "cell_number"),
-                           meshGetField3D(mesh, "forward_cell_number"),
-                           meshGetField3D(mesh, "backward_cell_number"))) {
+    : mapping(std::make_shared<const PetscMapping>(
+          meshGetField3D(mesh, "cell_number"),
+          meshGetField3D(mesh, "forward_cell_number"),
+          meshGetField3D(mesh, "backward_cell_number"))) {
 
   int mesh_total_cells;
   if (mesh->get(mesh_total_cells, "total_cells") == 0) {
     // Check total number of cells
-    if (mesh_total_cells != mapping.size()) {
+    if (mesh_total_cells != mapping->size()) {
       throw BoutException("Total cells in mesh {} doesn't match mapping size {}",
-                          mesh_total_cells, mapping.size());
+                          mesh_total_cells, mapping->size());
     }
   }
 
-  //MatCreate(comm, &mat_yforward);
-  //MatSetSizes(mat_yforward, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE);
+  // Read forward operator
+  PetscOperator forward(mapping, this->meshGetArray<int>(mesh, "forward_rows"),
+                        this->meshGetArray<int>(mesh, "forward_columns"),
+                        this->meshGetArray<BoutReal>(mesh, "forward_weights"));
 }

From 0528579e3f227ad7ed8eb84f6792078bde4c9a46 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 12 Mar 2026 17:15:06 +0000
Subject: [PATCH 0865/1827] Communicate `FieldPerp` consistently with other
 Fields

- Add `Field::field_type()` virtual method
- Removes `Mesh::communicate(FieldPerp&)` overload
---
 include/bout/field.hxx            |   8 ++-
 include/bout/field2d.hxx          |   1 +
 include/bout/field3d.hxx          |   5 +-
 include/bout/fieldgroup.hxx       |  51 +++++++--------
 include/bout/fieldperp.hxx        |  21 +++---
 include/bout/mesh.hxx             |  16 ++---
 src/mesh/impls/bout/boutmesh.cxx  | 102 +++++++++++++++++++++---------
 src/mesh/impls/bout/boutmesh.hxx  |  12 ++--
 src/mesh/mesh.cxx                 |  44 +++++--------
 tests/unit/fake_parallel_mesh.hxx |  47 ++------------
 tests/unit/field/test_field.cxx   |   1 +
 tests/unit/mesh/test_mesh.cxx     |   5 +-
 12 files changed, 156 insertions(+), 157 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 3f7f591528..9ae3ad5016 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -6,7 +6,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -30,6 +30,7 @@ class Field;
 #define FIELD_H
 
 #include <cmath>
+#include <cstdint>
 #include <cstdio>
 #include <optional>
 #include <string>
@@ -120,6 +121,11 @@ public:
   /// Get the total number of points
   virtual int size() const = 0;
 
+  /// Enum to distinguish the different kinds of Fields
+  enum class FieldType : std::uint8_t { field3d, field2d, fieldperp };
+  /// Is this an instance of `Field3D`, `Field2D`, or `FieldPerp`?
+  virtual FieldType field_type() const = 0;
+
   friend void swap(Field& first, Field& second) noexcept {
     using std::swap;
     swap(static_cast<FieldData&>(first), static_cast<FieldData&>(second));
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 906af38a1d..82c63b5dd4 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -252,6 +252,7 @@ public:
   // FieldData virtual functions
 
   bool is3D() const override { return false; }
+  FieldType field_type() const override { return FieldType::field2d; }
 
 #if CHECK > 0
   void doneComms() override { bndry_xin = bndry_xout = bndry_yup = bndry_ydown = true; }
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 54d9fb85c9..f06696c9d9 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -2,7 +2,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -361,7 +361,7 @@ public:
    * Direct access to the underlying data array
    *
    * If CHECK > 2 then bounds checking is performed
-   * 
+   *
    * If CHECK <= 2 then no checks are performed, to
    * allow inlining and optimisation of inner loops
    */
@@ -474,6 +474,7 @@ public:
 
   // FieldData virtual functions
   bool is3D() const override { return true; }
+  FieldType field_type() const override { return FieldType::field3d; }
 
 #if CHECK > 0
   void doneComms() override { bndry_xin = bndry_xout = bndry_yup = bndry_ydown = true; }
diff --git a/include/bout/fieldgroup.hxx b/include/bout/fieldgroup.hxx
index 184766c6b8..440655e7ce 100644
--- a/include/bout/fieldgroup.hxx
+++ b/include/bout/fieldgroup.hxx
@@ -1,22 +1,23 @@
 #ifndef BOUT_FIELDGROUP_H
 #define BOUT_FIELDGROUP_H
 
-#include "bout/field_data.hxx"
-#include <bout/field3d.hxx>
-
+#include <bout/traits.hxx>
 #include <bout/vector2d.hxx>
 #include <bout/vector3d.hxx>
 
 #include <vector>
 
-#include <algorithm>
+class Field2D;
+class Field3D;
+class FieldPerp;
+class Field;
 
 /// Group together fields for easier communication
 ///
-/// Note: The FieldData class is used as a base class,
-/// which is inherited by Field2D, Field3D, Vector2D and Vector3D
-/// however Vector2D and Vector3D are stored by reference to their
-/// components (x,y,z) as Field2D or Field3D objects.
+/// Note: The `Field` class is used as a base class,
+/// which is inherited by `Field2D`, `Field3D`, `FieldPerp`;
+/// however `Vector2D` and `Vector3D` are stored by reference to their
+/// components ``(x, y, z)`` as `Field2D` or `Field3D` objects.
 class FieldGroup {
 public:
   FieldGroup() = default;
@@ -24,11 +25,9 @@ public:
   FieldGroup(FieldGroup&& other) = default;
   FieldGroup& operator=(const FieldGroup& other) = default;
   FieldGroup& operator=(FieldGroup&& other) = default;
+  ~FieldGroup() = default;
 
-  /// Constructor with a single FieldData \p f
-  FieldGroup(FieldData& f) { fvec.push_back(&f); }
-
-  /// Constructor with a single Field3D \p f
+  FieldGroup(Field& f) { fvec.push_back(&f); }
   FieldGroup(Field3D& f) {
     fvec.push_back(&f);
     f3vec.push_back(&f);
@@ -56,7 +55,7 @@ public:
   }
 
   /// Variadic constructor. Allows an arbitrary number of
-  /// FieldData arguments
+  /// Field arguments
   ///
   /// The explicit keyword prevents FieldGroup being constructed with arbitrary
   /// types. In particular arguments to add() cannot be implicitly converted
@@ -78,12 +77,12 @@ public:
     return *this;
   }
 
-  /// Add a FieldData \p f to the group.
+  /// Add a Field \p f to the group.
   ///
   /// A pointer to this field will be stored internally,
   /// so the lifetime of this variable should be longer
   /// than the lifetime of this group.
-  void add(FieldData& f) { fvec.push_back(&f); }
+  void add(Field& f) { fvec.push_back(&f); }
 
   // Add a 3D field \p f, which goes into both vectors.
   //
@@ -121,12 +120,8 @@ public:
   }
 
   /// Add multiple fields to this group
-  ///
-  /// This is a variadic template which allows Field3D objects to be
-  /// treated as a special case. An arbitrary number of fields can be
-  /// added.
   template <typename... Ts>
-  void add(FieldData& t, Ts&... ts) {
+  void add(Field& t, Ts&... ts) {
     add(t);     // Add the first using functions above
     add(ts...); // Add the rest
   }
@@ -165,16 +160,14 @@ public:
   }
 
   /// Iteration over all fields
-  using iterator = std::vector<FieldData*>::iterator;
-  iterator begin() { return fvec.begin(); }
-  iterator end() { return fvec.end(); }
+  auto begin() { return fvec.begin(); }
+  auto end() { return fvec.end(); }
 
   /// Const iteration over all fields
-  using const_iterator = std::vector<FieldData*>::const_iterator;
-  const_iterator begin() const { return fvec.begin(); }
-  const_iterator end() const { return fvec.end(); }
+  auto begin() const { return fvec.cbegin(); }
+  auto end() const { return fvec.cend(); }
 
-  const std::vector<FieldData*>& get() const { return fvec; }
+  const std::vector<Field*>& get() const { return fvec; }
 
   /// Iteration over 3D fields
   const std::vector<Field3D*>& field3d() const { return f3vec; }
@@ -183,8 +176,8 @@ public:
   void makeUnique();
 
 private:
-  std::vector<FieldData*> fvec; // Vector of fields
-  std::vector<Field3D*> f3vec;  // Vector of 3D fields
+  std::vector<Field*> fvec;    // Vector of fields
+  std::vector<Field3D*> f3vec; // Vector of 3D fields
 };
 
 /// Combine two FieldGroups
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 1f70089990..5e84f6fa68 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -5,7 +5,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -45,8 +45,8 @@ class Field3D; // #include "bout/field3d.hxx"
 
 /*!
  * Represents a 2D field perpendicular to the magnetic field
- * at a particular index in Y, which only varies in X-Z. 
- * 
+ * at a particular index in Y, which only varies in X-Z.
+ *
  * Primarily used inside field solvers
  */
 class FieldPerp : public Field {
@@ -205,7 +205,7 @@ public:
 
   /*!
    * Access to the underlying data array at a given x,z index
-   * 
+   *
    * If CHECK > 2 then bounds checking is performed, otherwise
    * no checks are performed
    */
@@ -241,9 +241,9 @@ public:
   }
 
   /*!
-   * Access to the underlying data array. (X,Y,Z) indices for consistency with 
+   * Access to the underlying data array. (X,Y,Z) indices for consistency with
    * other field types
-   * 
+   *
    */
   BoutReal& operator()(int jx, int UNUSED(jy), int jz) { return (*this)(jx, jz); }
 
@@ -252,7 +252,7 @@ public:
   }
 
   /*!
-   * Addition, modifying in-place. 
+   * Addition, modifying in-place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator+=(const FieldPerp& rhs);
@@ -261,7 +261,7 @@ public:
   FieldPerp& operator+=(BoutReal rhs);
 
   /*!
-   * Subtraction, modifying in place. 
+   * Subtraction, modifying in place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator-=(const FieldPerp& rhs);
@@ -270,7 +270,7 @@ public:
   FieldPerp& operator-=(BoutReal rhs);
 
   /*!
-   * Multiplication, modifying in place. 
+   * Multiplication, modifying in place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator*=(const FieldPerp& rhs);
@@ -279,7 +279,7 @@ public:
   FieldPerp& operator*=(BoutReal rhs);
 
   /*!
-   * Division, modifying in place. 
+   * Division, modifying in place.
    * This loops over the entire domain, including guard/boundary cells
    */
   FieldPerp& operator/=(const FieldPerp& rhs);
@@ -301,6 +301,7 @@ public:
   int getNz() const override { return nz; };
 
   bool is3D() const override { return false; }
+  FieldType field_type() const override { return FieldType::fieldperp; }
 
   friend void swap(FieldPerp& first, FieldPerp& second) noexcept;
 
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index a1ed6a9011..5797617a3e 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -3,7 +3,7 @@
  *
  * Interface for mesh classes. Contains standard variables and useful
  * routines.
- * 
+ *
  * Changelog
  * =========
  *
@@ -11,7 +11,7 @@
  *     * Removing coordinate system into separate
  *       Coordinates class
  *     * Adding index derivative functions from derivs.cxx
- * 
+ *
  * 2010-06 Ben Dudson, Sean Farley
  *     * Initial version, adapted from GridData class
  *     * Incorporates code from topology.cpp and Communicator
@@ -20,7 +20,7 @@
  * Copyright 2010-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -65,6 +65,7 @@ class Mesh;
 #include <optional>
 #include <set>
 #include <string>
+#include <vector>
 
 class BoundaryRegion;
 class BoundaryRegionPar;
@@ -301,11 +302,6 @@ public:
   /// @param g  The group of fields to communicate. Guard cells will be modified
   void communicateYZ(FieldGroup& g);
 
-  /*!
-   * Communicate an X-Z field
-   */
-  virtual void communicate(FieldPerp& f);
-
   /*!
    * Send a list of FieldData objects
    * Packs arguments into a FieldGroup and passes
@@ -815,8 +811,8 @@ protected:
   const std::vector<int> readInts(const std::string& name, int n);
 
   /// Calculates the size of a message for a given x and y range
-  int msg_len(const std::vector<FieldData*>& var_list, int xge, int xlt, int yge,
-              int ylt);
+  int msg_len(const std::vector<Field*>& var_list, int xge, int xlt, int yge,
+              int ylt) const;
 
   /// Initialise derivatives
   void derivs_init(Options* options);
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index ea1b6a41b2..6c0a559972 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -2218,9 +2218,9 @@ void BoutMesh::topology() {
     }
 
     for (int i = 0; i < limiter_count; ++i) {
-      int const yind = limiter_yinds[i];
-      int const xstart = limiter_xstarts[i];
-      int const xend = limiter_xends[i];
+      const int yind = limiter_yinds[i];
+      const int xstart = limiter_xstarts[i];
+      const int xend = limiter_xends[i];
       output_info.write("Adding a limiter between y={} and {}. X indices {} to {}\n",
                         yind, yind + 1, xstart, xend);
       add_target(yind, xstart, xend);
@@ -2397,72 +2397,112 @@ void BoutMesh::overlapHandleMemory(BoutMesh* yup, BoutMesh* ydown, BoutMesh* xin
  *                   Communication utilities
  ****************************************************************/
 
-int BoutMesh::pack_data(const std::vector<FieldData*>& var_list, int xge, int xlt,
-                        int yge, int ylt, BoutReal* buffer) {
+int BoutMesh::pack_data(const std::vector<Field*>& var_list, int xge, int xlt, int yge,
+                        int ylt, BoutReal* buffer) const {
 
+  using enum Field::FieldType;
   int len = 0;
+  const int zge = 0;
+  const int zlt = LocalNz;
 
-  /// Loop over variables
   for (const auto& var : var_list) {
-    if (var->is3D()) {
-      // 3D variable
-      auto* var3d_ref_ptr = dynamic_cast<Field3D*>(var);
+    switch (var->field_type()) {
+    case field3d: {
+      const auto* var3d_ref_ptr = dynamic_cast<Field3D*>(var);
       ASSERT0(var3d_ref_ptr != nullptr);
-      auto& var3d_ref = *var3d_ref_ptr;
+      const auto& var3d_ref = *var3d_ref_ptr;
       ASSERT2(var3d_ref.isAllocated());
-      for (int jx = xge; jx != xlt; jx++) {
+      for (int jx = xge; jx < xlt; jx++) {
         for (int jy = yge; jy < ylt; jy++) {
-          for (int jz = 0; jz < LocalNz; jz++, len++) {
+          for (int jz = zge; jz < zlt; jz++, len++) {
             buffer[len] = var3d_ref(jx, jy, jz);
           }
         }
       }
-    } else {
-      // 2D variable
-      auto* var2d_ref_ptr = dynamic_cast<Field2D*>(var);
+      break;
+    }
+    case field2d: {
+      const auto* var2d_ref_ptr = dynamic_cast<Field2D*>(var);
       ASSERT0(var2d_ref_ptr != nullptr);
-      auto& var2d_ref = *var2d_ref_ptr;
+      const auto& var2d_ref = *var2d_ref_ptr;
       ASSERT2(var2d_ref.isAllocated());
-      for (int jx = xge; jx != xlt; jx++) {
+      for (int jx = xge; jx < xlt; jx++) {
         for (int jy = yge; jy < ylt; jy++, len++) {
           buffer[len] = var2d_ref(jx, jy);
         }
       }
+      break;
+    }
+    case fieldperp: {
+      const auto* varperp_ref_ptr = dynamic_cast<FieldPerp*>(var);
+      ASSERT0(varperp_ref_ptr != nullptr);
+      const auto& varperp_ref = *varperp_ref_ptr;
+      ASSERT2(varperp_ref.isAllocated());
+      for (int jx = xge; jx < xlt; jx++) {
+        for (int jz = zge; jz < zlt; jz++, len++) {
+          buffer[len] = varperp_ref(jx, jz);
+        }
+      }
+      break;
+    }
     }
   }
 
-  return (len);
+  return len;
 }
 
-int BoutMesh::unpack_data(const std::vector<FieldData*>& var_list, int xge, int xlt,
-                          int yge, int ylt, BoutReal* buffer) {
+int BoutMesh::unpack_data(const std::vector<Field*>& var_list, int xge, int xlt, int yge,
+                          int ylt, const BoutReal* buffer) const {
 
+  using enum Field::FieldType;
   int len = 0;
+  const int zge = 0;
+  const int zlt = LocalNz;
 
-  /// Loop over variables
   for (const auto& var : var_list) {
-    if (var->is3D()) {
-      // 3D variable
-      auto& var3d_ref = *dynamic_cast<Field3D*>(var);
-      for (int jx = xge; jx != xlt; jx++) {
+    switch (var->field_type()) {
+    case field3d: {
+      auto* var3d_ref_ptr = dynamic_cast<Field3D*>(var);
+      ASSERT0(var3d_ref_ptr != nullptr);
+      auto& var3d_ref = *var3d_ref_ptr;
+      ASSERT2(var3d_ref.isAllocated());
+      for (int jx = xge; jx < xlt; jx++) {
         for (int jy = yge; jy < ylt; jy++) {
-          for (int jz = 0; jz < LocalNz; jz++, len++) {
+          for (int jz = zge; jz < zlt; jz++, len++) {
             var3d_ref(jx, jy, jz) = buffer[len];
           }
         }
       }
-    } else {
-      // 2D variable
-      auto& var2d_ref = *dynamic_cast<Field2D*>(var);
-      for (int jx = xge; jx != xlt; jx++) {
+      break;
+    }
+    case field2d: {
+      auto* var2d_ref_ptr = dynamic_cast<Field2D*>(var);
+      ASSERT0(var2d_ref_ptr != nullptr);
+      auto& var2d_ref = *var2d_ref_ptr;
+      ASSERT2(var2d_ref.isAllocated());
+      for (int jx = xge; jx < xlt; jx++) {
         for (int jy = yge; jy < ylt; jy++, len++) {
           var2d_ref(jx, jy) = buffer[len];
         }
       }
+      break;
+    }
+    case fieldperp: {
+      auto* varperp_ref_ptr = dynamic_cast<FieldPerp*>(var);
+      ASSERT0(varperp_ref_ptr != nullptr);
+      auto& varperp_ref = *varperp_ref_ptr;
+      ASSERT2(varperp_ref.isAllocated());
+      for (int jx = xge; jx < xlt; jx++) {
+        for (int jz = zge; jz < zlt; jz++, len++) {
+          varperp_ref(jx, jz) = buffer[len];
+        }
+      }
+      break;
+    }
     }
   }
 
-  return (len);
+  return len;
 }
 
 /****************************************************************
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index b42bf325b5..cfb91c64da 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -4,6 +4,7 @@
 
 #include "mpi.h"
 
+#include "bout/bout_types.hxx"
 #include "bout/unused.hxx"
 #include <bout/mesh.hxx>
 
@@ -12,6 +13,8 @@
 #include <string>
 #include <vector>
 
+class Field;
+
 /// Implementation of Mesh (mostly) compatible with BOUT
 ///
 /// Topology and communications compatible with BOUT
@@ -476,12 +479,11 @@ private:
   void post_receiveY(CommHandle& ch);
 
   /// Take data from objects and put into a buffer
-  int pack_data(const std::vector<FieldData*>& var_list, int xge, int xlt, int yge,
-                int ylt, BoutReal* buffer);
+  int pack_data(const std::vector<Field*>& var_list, int xge, int xlt, int yge, int ylt,
+                BoutReal* buffer) const;
   /// Copy data from a buffer back into the fields
-
-  int unpack_data(const std::vector<FieldData*>& var_list, int xge, int xlt, int yge,
-                  int ylt, BoutReal* buffer);
+  int unpack_data(const std::vector<Field*>& var_list, int xge, int xlt, int yge, int ylt,
+                  const BoutReal* buffer) const;
 };
 
 namespace {
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 829c150a15..585c0f7257 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -376,38 +376,28 @@ void Mesh::communicate(FieldGroup& g) {
   }
 }
 
-/// This is a bit of a hack for now to get FieldPerp communications
-/// The FieldData class needs to be changed to accomodate FieldPerp objects
-void Mesh::communicate(FieldPerp& f) {
-  comm_handle recv[2];
-
-  int nin = xstart;              // Number of x points in inner guard cell
-  int nout = LocalNx - xend - 1; // Number of x points in outer guard cell
-
-  // Post receives for guard cell regions
-
-  recv[0] = irecvXIn(f[0], nin * LocalNz, 0);
-  recv[1] = irecvXOut(f[xend + 1], nout * LocalNz, 1);
+int Mesh::msg_len(const std::vector<Field*>& var_list, int xge, int xlt, int yge,
+                  int ylt) const {
+  int len = 0;
 
-  // Send data
-  sendXIn(f[xstart], nin * LocalNz, 1);
-  sendXOut(f[xend - nout + 1], nout * LocalNz, 0);
+  using enum Field::FieldType;
 
-  // Wait for receive
-  wait(recv[0]);
-  wait(recv[1]);
-}
-
-int Mesh::msg_len(const std::vector<FieldData*>& var_list, int xge, int xlt, int yge,
-                  int ylt) {
-  int len = 0;
+  const auto x_length = xlt - xge;
+  const auto y_length = ylt - yge;
+  const auto z_length = LocalNz;
 
   /// Loop over variables
   for (const auto& var : var_list) {
-    if (var->is3D()) {
-      len += (xlt - xge) * (ylt - yge) * LocalNz * var->elementSize();
-    } else {
-      len += (xlt - xge) * (ylt - yge) * var->elementSize();
+    switch (var->field_type()) {
+    case field3d:
+      len += x_length * y_length * z_length * var->elementSize();
+      break;
+    case field2d:
+      len += x_length * y_length * var->elementSize();
+      break;
+    case fieldperp:
+      len += x_length * z_length * var->elementSize();
+      break;
     }
   }
 
diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx
index 80406fb676..417994bd39 100644
--- a/tests/unit/fake_parallel_mesh.hxx
+++ b/tests/unit/fake_parallel_mesh.hxx
@@ -6,6 +6,7 @@
 #include <functional>
 #include <map>
 #include <memory>
+#include <vector>
 
 #include "../../src/mesh/impls/bout/boutmesh.hxx"
 #include "bout/boundary_op.hxx"
@@ -129,47 +130,15 @@ public:
     return parentSendY(g, handle);
   }
 
-  // Need to override this functions to trick mesh into communicating for
-  // FieldPerp type
-  void communicate(FieldPerp& f) override {
-    int nin = xstart;              // Number of x points in inner guard cell
-    int nout = LocalNx - xend - 1; // Number of x points in outer guard cell
-
-    if (registeredFieldPerps.count(&f) != 0) {
-      int id = registeredFieldPerps[&f];
-
-      if (xInMesh != nullptr && xInMesh->registeredFieldPerpIds.count(id) != 0) {
-        FieldPerp* xInField = xInMesh->registeredFieldPerpIds[id];
-        for (int i = 0; i < nin * LocalNz; i++) {
-          IndPerp ind(i, 1, LocalNz);
-          f[ind] = (*xInField)[ind.xp(xend - xstart + 1)];
-        }
-      }
-
-      if (xOutMesh != nullptr && xOutMesh->registeredFieldPerpIds.count(id) != 0) {
-        FieldPerp* xOutField = xOutMesh->registeredFieldPerpIds[id];
-        for (int i = 0; i < nout * LocalNz; i++) {
-          IndPerp ind((xend + 1) * LocalNz + i, 1, LocalNz);
-          f[ind] = (*xOutField)[ind.xm(xend - xstart + 1)];
-        }
-      }
-      // No corner cells to communicate for FieldPerp
-    }
-  }
-
   /// Use these methods to let the mesh know that this field has been
   /// created with it. It can then check in with its sibling meshes
   /// (representing other processors) to see if a corresponding field
   /// has been created for them which can be used to communicate guard
   /// cells with.
-  void registerField(FieldData& f, int id) {
+  void registerField(Field& f, int id) {
     registeredFields.emplace(&f, id);
     registeredFieldIds.emplace(id, &f);
   }
-  void registerField(FieldPerp& f, int id) {
-    registeredFieldPerps.emplace(&f, id);
-    registeredFieldPerpIds.emplace(id, &f);
-  }
 
   friend std::vector<FakeParallelMesh> createFakeProcessors(int nx, int ny, int nz,
                                                             int nxpe, int nype);
@@ -257,10 +226,8 @@ public:
 private:
   FakeParallelMesh *yUpMesh, *yDownMesh, *xInMesh, *xOutMesh;
   bool communicatingX = false, communicatingY = false;
-  std::map<FieldData*, int> registeredFields;
-  std::map<int, FieldData*> registeredFieldIds;
-  std::map<FieldPerp*, int> registeredFieldPerps;
-  std::map<int, FieldPerp*> registeredFieldPerpIds;
+  std::map<Field*, int> registeredFields;
+  std::map<int, Field*> registeredFieldIds;
   std::unique_ptr<FakeMpiWrapper> mpiSmart;
 
   comm_handle parentSendX(FieldGroup& g, comm_handle handle, bool disable_corners) {
@@ -270,10 +237,10 @@ private:
     return BoutMesh::sendY(g, handle);
   }
 
-  FieldGroup makeGroup(FakeParallelMesh* m, const std::vector<int> ids) {
+  FieldGroup makeGroup(FakeParallelMesh* m, const std::vector<int>& ids) {
     FieldGroup g;
-    for (int i : ids) {
-      ASSERT1(m->registeredFieldIds.count(i) != 0);
+    for (const int i : ids) {
+      ASSERT1(m->registeredFieldIds.contains(i));
       g.add(*m->registeredFieldIds[i]);
     }
     return g;
diff --git a/tests/unit/field/test_field.cxx b/tests/unit/field/test_field.cxx
index 40d675e5b3..66af572a6e 100644
--- a/tests/unit/field/test_field.cxx
+++ b/tests/unit/field/test_field.cxx
@@ -26,6 +26,7 @@ class FieldSubClass : public Field {
 
   bool is3D() const override { return false; }
   int size() const override { return 42; }
+  FieldType field_type() const override { return FieldType::field2d; }
 };
 } // namespace
 
diff --git a/tests/unit/mesh/test_mesh.cxx b/tests/unit/mesh/test_mesh.cxx
index 4d0c9111dd..8d64f1d0a3 100644
--- a/tests/unit/mesh/test_mesh.cxx
+++ b/tests/unit/mesh/test_mesh.cxx
@@ -1,5 +1,6 @@
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
+#include <vector>
 
 #include "bout/boutexception.hxx"
 #include "bout/mesh.hxx"
@@ -288,9 +289,9 @@ TEST_F(MeshTest, MsgLen) {
   Field2D f2D_1(0., &localmesh);
   Field2D f2D_2(0., &localmesh);
 
-  std::vector<FieldData*> var_list{&f3D_1, &f2D_1, &f3D_2, &f2D_2};
+  const std::vector<Field*> var_list{&f3D_1, &f2D_1, &f3D_2, &f2D_2};
 
   const int len = localmesh.msg_len(var_list, 0, nx, 0, ny);
 
-  EXPECT_EQ(len, 2 * (nx * ny * nz) + 2 * (nx * ny));
+  EXPECT_EQ(len, (2 * (nx * ny * nz)) + (2 * (nx * ny)));
 }

From 3f521d0f30eefbbc2038db2b3acdbea530e78c32 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 20 Jan 2026 09:25:47 +0100
Subject: [PATCH 0866/1827] Add metric info on cell faces for FCI

Information like perpendicular J, Bxyz and g_22 are only known to the
grid generator, but are needed for more correct parallel derivatives
---
 include/bout/coordinates.hxx |  16 ++++
 src/mesh/coordinates.cxx     | 140 ++++++++++++++++++++++++++++++++++-
 2 files changed, 154 insertions(+), 2 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index e7ead42ee5..0b1ebb51e6 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -102,6 +102,20 @@ public:
   /// Covariant metric tensor
   FieldMetric g_11, g_22, g_33, g_12, g_13, g_23;
 
+  /// get g_22 at the cell faces;
+  const FieldMetric& g_22_ylow() const;
+  const FieldMetric& g_22_yhigh() const;
+  /// get Jxz at the cell faces or cell centre
+  const FieldMetric& Jxz_ylow() const;
+  const FieldMetric& Jxz_yhigh() const;
+  const FieldMetric& Jxz() const;
+
+private:
+  mutable std::optional<FieldMetric> _g_22_ylow, _g_22_yhigh;
+  mutable std::optional<FieldMetric> _Jxz_ylow, _Jxz_yhigh, _Jxz_centre;
+  void _compute_Jxz_cell_faces() const;
+
+public:
   /// Christoffel symbol of the second kind (connection coefficients)
   FieldMetric G1_11, G1_22, G1_33, G1_12, G1_13, G1_23;
   FieldMetric G2_11, G2_22, G2_33, G2_12, G2_13, G2_23;
@@ -236,12 +250,14 @@ private:
   /// Cache variable for Grad2_par2
   mutable std::map<std::string, std::unique_ptr<FieldMetric>> Grad2_par2_DDY_invSgCache;
   mutable std::unique_ptr<FieldMetric> invSgCache{nullptr};
+  mutable std::optional<FieldMetric> JgCache;
 
   /// Set the parallel (y) transform from the options file.
   /// Used in the constructor to create the transform object.
   void setParallelTransform(Options* options);
 
   const FieldMetric& invSg() const;
+  const FieldMetric& Jg() const;
   const FieldMetric& Grad2_par2_DDY_invSg(CELL_LOC outloc,
                                           const std::string& method) const;
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index d2634d3f88..d8ba0a02ee 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1259,6 +1259,31 @@ int Coordinates::calcCovariant(const std::string& region) {
 
   output_info.write("\tLocal maximum error in off-diagonal inversion is {:e}\n", maxerr);
 
+  if (Bxy.isFci()) {
+    BoutReal maxError = 0;
+    Options* options = Options::getRoot();
+    auto BJg = Bxy.asField3DParallel() * J / sqrt(g_22.asField3DParallel());
+    auto* mesh = localmesh;
+    for (int p = -mesh->ystart; p <= mesh->ystart; p++) {
+      if (p == 0) {
+        continue;
+      }
+      BOUT_FOR(i, BJg.getRegion("RGN_NOBNDRY")) {
+        auto local = BJg[i] / BJg.ynext(p)[i.yp(p)];
+        maxError = std::max(std::abs(local - 1), maxError);
+      }
+    }
+    const BoutReal allowedError = (*options)["allowedFluxError"].withDefault(1e-6);
+    if (maxError < allowedError / 100) {
+      output_info.write("\tInfo: The maximum flux conservation error is {:e}", maxError);
+    } else if (maxError < allowedError) {
+      output_warn.write("\tWarning: The maximum flux conservation error is {:e}",
+                        maxError);
+    } else {
+      throw BoutException("Error: The maximum flux conservation error is {:e}", maxError);
+    }
+  }
+
   return 0;
 }
 
@@ -1878,13 +1903,31 @@ Field2D Coordinates::Laplace_perpXY([[maybe_unused]] const Field2D& A,
 
 const Coordinates::FieldMetric& Coordinates::invSg() const {
   if (invSgCache == nullptr) {
-    auto ptr = std::make_unique<FieldMetric>();
+    auto ptr = std::make_unique<Coordinates::FieldMetric>();
     (*ptr) = 1.0 / sqrt(g_22);
     invSgCache = std::move(ptr);
   }
   return *invSgCache;
 }
 
+const Coordinates::FieldMetric& Coordinates::Jg() const {
+  if (not JgCache.has_value()) {
+    auto* coords = this; //
+    // Need to modify yup and ydown fields
+    Field3D Jg = coords->Jxz();
+    Jg.splitParallelSlicesAndAllocate();
+    Field3DParallel B = coords->Bxy;
+    for (size_t j = 0; j < B.numberParallelSlices(); ++j) {
+      BOUT_FOR(i, B.getRegion("RGN_NOBNDRY")) {
+        Jg.yup(j)[i.yp(j + 1)] = Jg[i] * B.yup(j)[i.yp(j + 1)] / B[i];
+        Jg.ydown(j)[i.ym(j + 1)] = Jg[i] * B.ydown(j)[i.ym(j + 1)] / B[i];
+      }
+    }
+    JgCache = Jg;
+  }
+  return *JgCache;
+}
+
 const Coordinates::FieldMetric&
 Coordinates::Grad2_par2_DDY_invSg(CELL_LOC outloc, const std::string& method) const {
   if (auto search = Grad2_par2_DDY_invSgCache.find(method);
@@ -1898,7 +1941,7 @@ Coordinates::Grad2_par2_DDY_invSg(CELL_LOC outloc, const std::string& method) co
   invSgCache->applyParallelBoundary("parallel_neumann_o2");
 
   // cache
-  auto ptr = std::make_unique<FieldMetric>();
+  auto ptr = std::make_unique<Coordinates::FieldMetric>();
   *ptr = DDY(*invSgCache, outloc, method) * invSg();
   Grad2_par2_DDY_invSgCache[method] = std::move(ptr);
   return *Grad2_par2_DDY_invSgCache[method];
@@ -2007,3 +2050,96 @@ void Coordinates::checkContravariant() {
     }
   }
 }
+
+const Coordinates::FieldMetric& Coordinates::g_22_ylow() const {
+  if (_g_22_ylow.has_value()) {
+    return *_g_22_ylow;
+  }
+  _g_22_ylow.emplace(emptyFrom(g_22));
+  //_g_22_ylow->setLocation(CELL_YLOW);
+  auto mesh = Bxy.getMesh();
+  if (Bxy.isFci()) {
+    if (mesh->get(_g_22_ylow.value(), "g_22_cell_ylow", 0.0, false)) { //, CELL_YLOW)) {
+      throw BoutException("The grid file does not contain `g_22_cell_ylow`.");
+    }
+  } else {
+    ASSERT0(mesh->ystart > 0);
+    BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
+      _g_22_ylow.value()[i] = SQ(0.5 * (sqrt(g_22[i]) + sqrt(g_22[i.ym()])));
+    }
+  }
+  return g_22_ylow();
+}
+
+const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
+  if (_g_22_yhigh.has_value()) {
+    return *_g_22_yhigh;
+  }
+  _g_22_yhigh.emplace(emptyFrom(g_22));
+  //_g_22_yhigh->setLocation(CELL_YHIGH);
+  auto mesh = Bxy.getMesh();
+  if (Bxy.isFci()) {
+    if (mesh->get(_g_22_yhigh.value(), "g_22_cell_yhigh", 0.0,
+                  false)) { //, CELL_YHIGH)) {
+      throw BoutException("The grid file does not contain `g_22_cell_yhigh`.");
+    }
+  } else {
+    ASSERT0(mesh->ystart > 0);
+    BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
+      _g_22_yhigh.value()[i] = SQ(0.5 * (sqrt(g_22[i]) + sqrt(g_22[i.yp()])));
+    }
+  }
+  return g_22_yhigh();
+}
+
+const Coordinates::FieldMetric& Coordinates::Jxz_ylow() const {
+  if (!_Jxz_ylow.has_value()) {
+    _compute_Jxz_cell_faces();
+  }
+  return *_Jxz_ylow;
+}
+const Coordinates::FieldMetric& Coordinates::Jxz_yhigh() const {
+  if (!_Jxz_yhigh.has_value()) {
+    _compute_Jxz_cell_faces();
+  }
+  return *_Jxz_yhigh;
+}
+const Coordinates::FieldMetric& Coordinates::Jxz() const {
+  if (!_Jxz_centre.has_value()) {
+    _compute_Jxz_cell_faces();
+  }
+  return *_Jxz_centre;
+}
+
+void Coordinates::_compute_Jxz_cell_faces() const {
+  _Jxz_centre.emplace(sqrt(g_11 * g_33 - SQ(g_13)));
+  _Jxz_ylow.emplace(emptyFrom(_Jxz_centre.value()));
+  //_Jxz_ylow->setLocation(CELL_YLOW);
+  _Jxz_yhigh.emplace(emptyFrom(_Jxz_centre.value()));
+  //_Jxz_yhigh->setLocation(CELL_YHIGH);
+  auto* mesh = _Jxz_centre->getMesh();
+  if (Bxy.isFci()) {
+    Coordinates::FieldMetric By_c;
+    Coordinates::FieldMetric By_h;
+    Coordinates::FieldMetric By_l;
+    if (mesh->get(By_c, "By", 0.0, false, CELL_CENTRE)) {
+      throw BoutException("The grid file does not contain `By`.");
+    }
+    if (mesh->get(By_l, "By_cell_ylow", 0.0, false)) { //, CELL_YLOW)) {
+      throw BoutException("The grid file does not contain `By_cell_ylow`.");
+    }
+    if (mesh->get(By_h, "By_cell_yhigh", 0.0, false)) { //, CELL_YHIGH)) {
+      throw BoutException("The grid file does not contain `By_cell_yhigh`.");
+    }
+    BOUT_FOR(i, By_c.getRegion("RGN_NOY")) {
+      (*_Jxz_ylow)[i] = By_c[i] / By_l[i] * (*_Jxz_centre)[i];
+      (*_Jxz_yhigh)[i] = By_c[i] / By_h[i] * (*_Jxz_centre)[i];
+    }
+  } else {
+    ASSERT0(mesh->ystart > 0);
+    BOUT_FOR(i, _Jxz_centre->getRegion("RGN_NOY")) {
+      (*_Jxz_ylow)[i] = 0.5 * ((*_Jxz_centre)[i] + (*_Jxz_centre)[i.ym()]);
+      (*_Jxz_yhigh)[i] = 0.5 * ((*_Jxz_centre)[i] + (*_Jxz_centre)[i.yp()]);
+    }
+  }
+}

From 3065f88847c5bc9a5a897c4aa699b7dd612549c1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 30 Jan 2026 10:08:19 +0100
Subject: [PATCH 0867/1827] Do not used preserved names

_[A-Z].* is preserved for compilers, thus use _[a-z].*
---
 include/bout/coordinates.hxx |  2 +-
 src/mesh/coordinates.cxx     | 35 ++++++++++++++++++-----------------
 2 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 0b1ebb51e6..0d405a0123 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -112,7 +112,7 @@ public:
 
 private:
   mutable std::optional<FieldMetric> _g_22_ylow, _g_22_yhigh;
-  mutable std::optional<FieldMetric> _Jxz_ylow, _Jxz_yhigh, _Jxz_centre;
+  mutable std::optional<FieldMetric> _jxz_ylow, _jxz_yhigh, _jxz_centre;
   void _compute_Jxz_cell_faces() const;
 
 public:
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index d8ba0a02ee..a2f1a56222 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2093,31 +2093,32 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
 }
 
 const Coordinates::FieldMetric& Coordinates::Jxz_ylow() const {
-  if (!_Jxz_ylow.has_value()) {
+  if (!_jxz_ylow.has_value()) {
     _compute_Jxz_cell_faces();
   }
-  return *_Jxz_ylow;
+  return *_jxz_ylow;
 }
 const Coordinates::FieldMetric& Coordinates::Jxz_yhigh() const {
-  if (!_Jxz_yhigh.has_value()) {
+  if (!_jxz_yhigh.has_value()) {
     _compute_Jxz_cell_faces();
   }
-  return *_Jxz_yhigh;
+  return *_jxz_yhigh;
 }
 const Coordinates::FieldMetric& Coordinates::Jxz() const {
-  if (!_Jxz_centre.has_value()) {
+  if (!_jxz_centre.has_value()) {
     _compute_Jxz_cell_faces();
   }
-  return *_Jxz_centre;
+  return *_jxz_centre;
+}
 }
 
 void Coordinates::_compute_Jxz_cell_faces() const {
-  _Jxz_centre.emplace(sqrt(g_11 * g_33 - SQ(g_13)));
-  _Jxz_ylow.emplace(emptyFrom(_Jxz_centre.value()));
-  //_Jxz_ylow->setLocation(CELL_YLOW);
-  _Jxz_yhigh.emplace(emptyFrom(_Jxz_centre.value()));
-  //_Jxz_yhigh->setLocation(CELL_YHIGH);
-  auto* mesh = _Jxz_centre->getMesh();
+  _jxz_centre.emplace(sqrt(g_11 * g_33 - SQ(g_13)));
+  _jxz_ylow.emplace(emptyFrom(_jxz_centre.value()));
+  //_jxz_ylow->setLocation(CELL_YLOW);
+  _jxz_yhigh.emplace(emptyFrom(_jxz_centre.value()));
+  //_jxz_yhigh->setLocation(CELL_YHIGH);
+  auto* mesh = _jxz_centre->getMesh();
   if (Bxy.isFci()) {
     Coordinates::FieldMetric By_c;
     Coordinates::FieldMetric By_h;
@@ -2132,14 +2133,14 @@ void Coordinates::_compute_Jxz_cell_faces() const {
       throw BoutException("The grid file does not contain `By_cell_yhigh`.");
     }
     BOUT_FOR(i, By_c.getRegion("RGN_NOY")) {
-      (*_Jxz_ylow)[i] = By_c[i] / By_l[i] * (*_Jxz_centre)[i];
-      (*_Jxz_yhigh)[i] = By_c[i] / By_h[i] * (*_Jxz_centre)[i];
+      (*_jxz_ylow)[i] = By_c[i] / By_l[i] * (*_jxz_centre)[i];
+      (*_jxz_yhigh)[i] = By_c[i] / By_h[i] * (*_jxz_centre)[i];
     }
   } else {
     ASSERT0(mesh->ystart > 0);
-    BOUT_FOR(i, _Jxz_centre->getRegion("RGN_NOY")) {
-      (*_Jxz_ylow)[i] = 0.5 * ((*_Jxz_centre)[i] + (*_Jxz_centre)[i.ym()]);
-      (*_Jxz_yhigh)[i] = 0.5 * ((*_Jxz_centre)[i] + (*_Jxz_centre)[i.yp()]);
+    BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOY")) {
+      (*_jxz_ylow)[i] = 0.5 * ((*_jxz_centre)[i] + (*_jxz_centre)[i.ym()]);
+      (*_jxz_yhigh)[i] = 0.5 * ((*_jxz_centre)[i] + (*_jxz_centre)[i.yp()]);
     }
   }
 }

From 1c0e385ca51301fee213d26254e38d02e0e8d828 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 30 Jan 2026 10:08:33 +0100
Subject: [PATCH 0868/1827] Add non-const versions

---
 include/bout/coordinates.hxx |  5 +++++
 src/mesh/coordinates.cxx     | 28 ++++++++++++++++++++++++++++
 2 files changed, 33 insertions(+)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 0d405a0123..cf8e7cf39f 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -105,10 +105,15 @@ public:
   /// get g_22 at the cell faces;
   const FieldMetric& g_22_ylow() const;
   const FieldMetric& g_22_yhigh() const;
+  FieldMetric& g_22_ylow();
+  FieldMetric& g_22_yhigh();
   /// get Jxz at the cell faces or cell centre
   const FieldMetric& Jxz_ylow() const;
   const FieldMetric& Jxz_yhigh() const;
   const FieldMetric& Jxz() const;
+  FieldMetric& Jxz_ylow();
+  FieldMetric& Jxz_yhigh();
+  FieldMetric& Jxz();
 
 private:
   mutable std::optional<FieldMetric> _g_22_ylow, _g_22_yhigh;
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index a2f1a56222..23fa77bbce 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2092,6 +2092,16 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
   return g_22_yhigh();
 }
 
+Coordinates::FieldMetric& Coordinates::g_22_yhigh() {
+  return const_cast<Coordinates::FieldMetric&>(
+      const_cast<const Coordinates*>(this)->g_22_yhigh());
+}
+
+Coordinates::FieldMetric& Coordinates::g_22_ylow() {
+  return const_cast<Coordinates::FieldMetric&>(
+      const_cast<const Coordinates*>(this)->g_22_ylow());
+}
+
 const Coordinates::FieldMetric& Coordinates::Jxz_ylow() const {
   if (!_jxz_ylow.has_value()) {
     _compute_Jxz_cell_faces();
@@ -2110,6 +2120,24 @@ const Coordinates::FieldMetric& Coordinates::Jxz() const {
   }
   return *_jxz_centre;
 }
+
+Coordinates::FieldMetric& Coordinates::Jxz_ylow() {
+  if (!_jxz_ylow.has_value()) {
+    _compute_Jxz_cell_faces();
+  }
+  return *_jxz_ylow;
+}
+Coordinates::FieldMetric& Coordinates::Jxz_yhigh() {
+  if (!_jxz_yhigh.has_value()) {
+    _compute_Jxz_cell_faces();
+  }
+  return *_jxz_yhigh;
+}
+Coordinates::FieldMetric& Coordinates::Jxz() {
+  if (!_jxz_centre.has_value()) {
+    _compute_Jxz_cell_faces();
+  }
+  return *_jxz_centre;
 }
 
 void Coordinates::_compute_Jxz_cell_faces() const {

From 5c28542f9400fcd8593c8281efae10371d674045 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 13:12:01 +0100
Subject: [PATCH 0869/1827] Add cell areas and cell volumes

---
 include/bout/coordinates.hxx | 137 +++++++++++++++++++++++++++++++++--
 src/mesh/coordinates.cxx     | 100 +++++++++++++------------
 2 files changed, 183 insertions(+), 54 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index cf8e7cf39f..402efecd20 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -108,17 +108,142 @@ public:
   FieldMetric& g_22_ylow();
   FieldMetric& g_22_yhigh();
   /// get Jxz at the cell faces or cell centre
-  const FieldMetric& Jxz_ylow() const;
-  const FieldMetric& Jxz_yhigh() const;
-  const FieldMetric& Jxz() const;
-  FieldMetric& Jxz_ylow();
-  FieldMetric& Jxz_yhigh();
-  FieldMetric& Jxz();
+  const FieldMetric& Jxz_ylow() const {
+    if (!_jxz_ylow.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_ylow;
+  }
+  const FieldMetric& Jxz_yhigh() const {
+    if (!_jxz_yhigh.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_yhigh;
+  }
+  const FieldMetric& Jxz() const {
+    if (!_jxz_centre.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_centre;
+  }
+  FieldMetric& Jxz_ylow() {
+    if (!_jxz_ylow.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_ylow;
+  }
+  FieldMetric& Jxz_yhigh() {
+    if (!_jxz_yhigh.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_yhigh;
+  }
+  FieldMetric& Jxz() {
+    if (!_jxz_centre.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_centre;
+  }
+  // Cell Areas
+  const FieldMetric& cell_area_xlow() const {
+    if (!_cell_area_xlow.has_value()) {
+      _compute_cell_area_x();
+    }
+    return _cell_area_xlow;
+  }
+  const FieldMetric& cell_area_xhigh() const {
+    if (!_cell_area_xhigh.has_value()) {
+      _compute_cell_area_x();
+    }
+    return _cell_area_xhigh;
+  }
+  const FieldMetric& cell_area_ylow() const {
+    if (!_cell_area_ylow.has_value()) {
+      _compute_cell_area_y();
+    }
+    return _cell_area_ylow;
+  }
+  const FieldMetric& cell_area_yhigh() const {
+    if (!_cell_area_yhigh.has_value()) {
+      _compute_cell_area_y();
+    }
+    return _cell_area_yhigh;
+  }
+  const FieldMetric& cell_area_zlow() const {
+    if (!_cell_area_zlow.has_value()) {
+      _compute_cell_area_z();
+    }
+    return _cell_area_zlow;
+  }
+  const FieldMetric& cell_area_zhigh() const {
+    if (!_cell_area_zhigh.has_value()) {
+      _compute_cell_area_z();
+    }
+    return _cell_area_zhigh;
+  }
+  FieldMetric& cell_area_xlow() {
+    if (!_cell_area_xlow.has_value()) {
+      _compute_cell_area_x();
+    }
+    return _cell_area_xlow;
+  }
+  FieldMetric& cell_area_xhigh() {
+    if (!_cell_area_xhigh.has_value()) {
+      _compute_cell_area_x();
+    }
+    return _cell_area_xhigh;
+  }
+  FieldMetric& cell_area_ylow() {
+    if (!_cell_area_ylow.has_value()) {
+      _compute_cell_area_y();
+    }
+    return _cell_area_ylow;
+  }
+  FieldMetric& cell_area_yhigh() {
+    if (!_cell_area_yhigh.has_value()) {
+      _compute_cell_area_y();
+    }
+    return _cell_area_yhigh;
+  }
+  FieldMetric& cell_area_zlow() {
+    if (!_cell_area_zlow.has_value()) {
+      _compute_cell_area_z();
+    }
+    return _cell_area_zlow;
+  }
+  FieldMetric& cell_area_zhigh() {
+    if (!_cell_area_zhigh.has_value()) {
+      _compute_cell_area_z();
+    }
+    return _cell_area_zhigh;
+  }
+  // Cell Volume
+  const FieldMetric& cell_volume() const {
+    if (!_cell_volume.has_value()) {
+      _compute_cell_volume();
+    }
+    return _cell_volume;
+  }
+  FieldMetric& cell_volume() {
+    if (!_cell_volume.has_value()) {
+      _compute_cell_volume();
+    }
+    return _cell_volume;
+  }
 
 private:
   mutable std::optional<FieldMetric> _g_22_ylow, _g_22_yhigh;
   mutable std::optional<FieldMetric> _jxz_ylow, _jxz_yhigh, _jxz_centre;
+  mutable std::optional<FieldMetric> _cell_area_xlow, _cell_area_xhigh;
+  mutable std::optional<FieldMetric> _cell_area_ylow, _cell_area_yhigh;
+  mutable std::optional<FieldMetric> _cell_area_zlow, _cell_area_zhigh;
+  mutable std::optional<FieldMetric> _cell_volume;
+  mutable std::optional<FieldMetric> _jxz_ylow, _jxz_yhigh, _jxz_centre;
   void _compute_Jxz_cell_faces() const;
+  void _compute_cell_area_x() const;
+  void _compute_cell_area_y() const;
+  void _compute_cell_area_z() const;
+  void _compute_cell_volume() const;
 
 public:
   /// Christoffel symbol of the second kind (connection coefficients)
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 23fa77bbce..0e1d610410 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2092,54 +2092,6 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
   return g_22_yhigh();
 }
 
-Coordinates::FieldMetric& Coordinates::g_22_yhigh() {
-  return const_cast<Coordinates::FieldMetric&>(
-      const_cast<const Coordinates*>(this)->g_22_yhigh());
-}
-
-Coordinates::FieldMetric& Coordinates::g_22_ylow() {
-  return const_cast<Coordinates::FieldMetric&>(
-      const_cast<const Coordinates*>(this)->g_22_ylow());
-}
-
-const Coordinates::FieldMetric& Coordinates::Jxz_ylow() const {
-  if (!_jxz_ylow.has_value()) {
-    _compute_Jxz_cell_faces();
-  }
-  return *_jxz_ylow;
-}
-const Coordinates::FieldMetric& Coordinates::Jxz_yhigh() const {
-  if (!_jxz_yhigh.has_value()) {
-    _compute_Jxz_cell_faces();
-  }
-  return *_jxz_yhigh;
-}
-const Coordinates::FieldMetric& Coordinates::Jxz() const {
-  if (!_jxz_centre.has_value()) {
-    _compute_Jxz_cell_faces();
-  }
-  return *_jxz_centre;
-}
-
-Coordinates::FieldMetric& Coordinates::Jxz_ylow() {
-  if (!_jxz_ylow.has_value()) {
-    _compute_Jxz_cell_faces();
-  }
-  return *_jxz_ylow;
-}
-Coordinates::FieldMetric& Coordinates::Jxz_yhigh() {
-  if (!_jxz_yhigh.has_value()) {
-    _compute_Jxz_cell_faces();
-  }
-  return *_jxz_yhigh;
-}
-Coordinates::FieldMetric& Coordinates::Jxz() {
-  if (!_jxz_centre.has_value()) {
-    _compute_Jxz_cell_faces();
-  }
-  return *_jxz_centre;
-}
-
 void Coordinates::_compute_Jxz_cell_faces() const {
   _jxz_centre.emplace(sqrt(g_11 * g_33 - SQ(g_13)));
   _jxz_ylow.emplace(emptyFrom(_jxz_centre.value()));
@@ -2172,3 +2124,55 @@ void Coordinates::_compute_Jxz_cell_faces() const {
     }
   }
 }
+
+void Coordinates::_compute_cell_area_x() const {
+  const auto area_centre = sqrt(g_22 * g_33 - SQ(g_23)) * dy * dz;
+  _cell_area_xlow.emplace(emptyFrom(area_centre));
+  _cell_area_xhigh.emplace(emptyFrom(area_centre));
+  // We cannot setLocation, as that would trigger the computation of staggered
+  // metrics.
+  ASSERT0(mesh->xstart > 0);
+  BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOX")) {
+    (*_cell_area_xlow)[i] = 0.5 * (area_centre[i] + area_centre[i.xm()]);
+    (*_cell_area_xhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.xp()]);
+  }
+}
+
+void Coordinates::_compute_cell_area_y() const {
+  const auto Jxz = Jxz();
+  if (Jxz.isFci()) {
+    ASSERT4(isUniform(dx, true, "RGN_ALL"));
+    ASSERT2(isUniform(dx, false, "RGN_ALL"));
+    ASSERT4(isUniform(dz, true, "RGN_ALL"));
+    ASSERT2(isUniform(dz, false, "RGN_ALL"));
+    _cell_area_ylow = _Jxz_ylow * dx * dz;
+    _cell_area_yhigh = _Jxz_yhigh * dx * dz;
+  } else {
+    // Field aligned
+    const auto area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;
+    _cell_area_ylow.emplace(emptyFrom(area_centre));
+    _cell_area_yhigh.emplace(emptyFrom(area_centre));
+    // We cannot setLocation, as that would trigger the computation of staggered
+    // metrics.
+    ASSERT0(mesh->ystart > 0);
+    BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOY")) {
+      (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
+      (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
+    }
+  }
+}
+
+void Coordinates::_compute_cell_area_z() const {
+  const auto area_centre = sqrt(g_11 * g_22 - SQ(g_12)) * dx * dy;
+  _cell_area_zlow.emplace(emptyFrom(area_centre));
+  _cell_area_zhigh.emplace(emptyFrom(area_centre));
+  // We cannot setLocation, as that would trigger the computation of staggered
+  // metrics.
+  //ASSERT0(mesh->zstart > 0);
+  BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOZ")) {
+    (*_cell_area_zlow)[i] = 0.5 * (area_centre[i] + area_centre[i.zm()]);
+    (*_cell_area_zhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.zp()]);
+  }
+}
+
+void Coordinates::_compute_cell_volume() const { _cell_volume.emplace(J * dx * dy * dz); }

From 078322d06b08fc5cd7c9985b3d92acdfee6652e6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 13:15:12 +0100
Subject: [PATCH 0870/1827] Fix formatting

---
 include/bout/coordinates.hxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 402efecd20..13cf6331bc 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -3,16 +3,16 @@
  *
  * ChangeLog
  * =========
- * 
+ *
  * 2014-11-10 Ben Dudson <bd512@york.ac.uk>
  *    * Created by separating metric from Mesh
  *
- * 
+ *
  **************************************************************************
  * Copyright 2014-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -402,10 +402,10 @@ private:
 class TokamakCoordinates : public Coordinates {
 public:
   TokamakCoordinates(Mesh *mesh) : Coordinates(mesh) {
-    
+
   }
 private:
-  
+
 };
 */
 

From 7547d9ec7df1616c7b261a0f316207769c40e8c8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 13:20:34 +0100
Subject: [PATCH 0871/1827] Fix return statements

---
 include/bout/coordinates.hxx | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 13cf6331bc..a7a09cfd9d 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -149,86 +149,86 @@ public:
     if (!_cell_area_xlow.has_value()) {
       _compute_cell_area_x();
     }
-    return _cell_area_xlow;
+    return *_cell_area_xlow;
   }
   const FieldMetric& cell_area_xhigh() const {
     if (!_cell_area_xhigh.has_value()) {
       _compute_cell_area_x();
     }
-    return _cell_area_xhigh;
+    return *_cell_area_xhigh;
   }
   const FieldMetric& cell_area_ylow() const {
     if (!_cell_area_ylow.has_value()) {
       _compute_cell_area_y();
     }
-    return _cell_area_ylow;
+    return *_cell_area_ylow;
   }
   const FieldMetric& cell_area_yhigh() const {
     if (!_cell_area_yhigh.has_value()) {
       _compute_cell_area_y();
     }
-    return _cell_area_yhigh;
+    return *_cell_area_yhigh;
   }
   const FieldMetric& cell_area_zlow() const {
     if (!_cell_area_zlow.has_value()) {
       _compute_cell_area_z();
     }
-    return _cell_area_zlow;
+    return *_cell_area_zlow;
   }
   const FieldMetric& cell_area_zhigh() const {
     if (!_cell_area_zhigh.has_value()) {
       _compute_cell_area_z();
     }
-    return _cell_area_zhigh;
+    return *_cell_area_zhigh;
   }
   FieldMetric& cell_area_xlow() {
     if (!_cell_area_xlow.has_value()) {
       _compute_cell_area_x();
     }
-    return _cell_area_xlow;
+    return *_cell_area_xlow;
   }
   FieldMetric& cell_area_xhigh() {
     if (!_cell_area_xhigh.has_value()) {
       _compute_cell_area_x();
     }
-    return _cell_area_xhigh;
+    return *_cell_area_xhigh;
   }
   FieldMetric& cell_area_ylow() {
     if (!_cell_area_ylow.has_value()) {
       _compute_cell_area_y();
     }
-    return _cell_area_ylow;
+    return *_cell_area_ylow;
   }
   FieldMetric& cell_area_yhigh() {
     if (!_cell_area_yhigh.has_value()) {
       _compute_cell_area_y();
     }
-    return _cell_area_yhigh;
+    return *_cell_area_yhigh;
   }
   FieldMetric& cell_area_zlow() {
     if (!_cell_area_zlow.has_value()) {
       _compute_cell_area_z();
     }
-    return _cell_area_zlow;
+    return *_cell_area_zlow;
   }
   FieldMetric& cell_area_zhigh() {
     if (!_cell_area_zhigh.has_value()) {
       _compute_cell_area_z();
     }
-    return _cell_area_zhigh;
+    return *_cell_area_zhigh;
   }
   // Cell Volume
   const FieldMetric& cell_volume() const {
     if (!_cell_volume.has_value()) {
       _compute_cell_volume();
     }
-    return _cell_volume;
+    return *_cell_volume;
   }
   FieldMetric& cell_volume() {
     if (!_cell_volume.has_value()) {
       _compute_cell_volume();
     }
-    return _cell_volume;
+    return *_cell_volume;
   }
 
 private:

From 01d776ba2a4621a01481b409fb120e29e2c99459 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 12 Mar 2026 13:20:55 +0100
Subject: [PATCH 0872/1827] Remove duplicate line

---
 include/bout/coordinates.hxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index a7a09cfd9d..c7b8b83a99 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -238,7 +238,6 @@ private:
   mutable std::optional<FieldMetric> _cell_area_ylow, _cell_area_yhigh;
   mutable std::optional<FieldMetric> _cell_area_zlow, _cell_area_zhigh;
   mutable std::optional<FieldMetric> _cell_volume;
-  mutable std::optional<FieldMetric> _jxz_ylow, _jxz_yhigh, _jxz_centre;
   void _compute_Jxz_cell_faces() const;
   void _compute_cell_area_x() const;
   void _compute_cell_area_y() const;

From 13fdb8ad50804394c498fe183dff645dabddf4b4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Mar 2026 12:34:44 +0100
Subject: [PATCH 0873/1827] Remove non-used Jg()

---
 include/bout/coordinates.hxx |  2 --
 src/mesh/coordinates.cxx     | 18 ------------------
 2 files changed, 20 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index c7b8b83a99..85aac3de6c 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -379,14 +379,12 @@ private:
   /// Cache variable for Grad2_par2
   mutable std::map<std::string, std::unique_ptr<FieldMetric>> Grad2_par2_DDY_invSgCache;
   mutable std::unique_ptr<FieldMetric> invSgCache{nullptr};
-  mutable std::optional<FieldMetric> JgCache;
 
   /// Set the parallel (y) transform from the options file.
   /// Used in the constructor to create the transform object.
   void setParallelTransform(Options* options);
 
   const FieldMetric& invSg() const;
-  const FieldMetric& Jg() const;
   const FieldMetric& Grad2_par2_DDY_invSg(CELL_LOC outloc,
                                           const std::string& method) const;
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 0e1d610410..b14bef12be 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1910,24 +1910,6 @@ const Coordinates::FieldMetric& Coordinates::invSg() const {
   return *invSgCache;
 }
 
-const Coordinates::FieldMetric& Coordinates::Jg() const {
-  if (not JgCache.has_value()) {
-    auto* coords = this; //
-    // Need to modify yup and ydown fields
-    Field3D Jg = coords->Jxz();
-    Jg.splitParallelSlicesAndAllocate();
-    Field3DParallel B = coords->Bxy;
-    for (size_t j = 0; j < B.numberParallelSlices(); ++j) {
-      BOUT_FOR(i, B.getRegion("RGN_NOBNDRY")) {
-        Jg.yup(j)[i.yp(j + 1)] = Jg[i] * B.yup(j)[i.yp(j + 1)] / B[i];
-        Jg.ydown(j)[i.ym(j + 1)] = Jg[i] * B.ydown(j)[i.ym(j + 1)] / B[i];
-      }
-    }
-    JgCache = Jg;
-  }
-  return *JgCache;
-}
-
 const Coordinates::FieldMetric&
 Coordinates::Grad2_par2_DDY_invSg(CELL_LOC outloc, const std::string& method) const {
   if (auto search = Grad2_par2_DDY_invSgCache.find(method);

From db66e35f5991db3f8f7892836b6f2a1762ff26de Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Mar 2026 12:35:08 +0100
Subject: [PATCH 0874/1827] add asField3DParallel stub to Field2D

---
 include/bout/field2d.hxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index e068747ee3..e003c4b316 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -275,6 +275,9 @@ public:
 
   int size() const override { return nx * ny; }
 
+  Field2D& asField3DParallel() { return *this; }
+  const Field2D& asField3DParallel() const { return *this; }
+
 private:
   /// Internal data array. Handles allocation/freeing of memory
   Array<BoutReal> data;

From cca09aceeb63c8949529e907255918e41e368d4d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Mar 2026 12:35:34 +0100
Subject: [PATCH 0875/1827] Compile time fixes

---
 src/mesh/coordinates.cxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index b14bef12be..4e7a9e1c24 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2121,14 +2121,14 @@ void Coordinates::_compute_cell_area_x() const {
 }
 
 void Coordinates::_compute_cell_area_y() const {
-  const auto Jxz = Jxz();
-  if (Jxz.isFci()) {
+  Jxz();
+  if (_jxz_centre->isFci()) {
     ASSERT4(isUniform(dx, true, "RGN_ALL"));
     ASSERT2(isUniform(dx, false, "RGN_ALL"));
     ASSERT4(isUniform(dz, true, "RGN_ALL"));
     ASSERT2(isUniform(dz, false, "RGN_ALL"));
-    _cell_area_ylow = _Jxz_ylow * dx * dz;
-    _cell_area_yhigh = _Jxz_yhigh * dx * dz;
+    _cell_area_ylow = _jxz_ylow * dx * dz;
+    _cell_area_yhigh = _jxz_yhigh * dx * dz;
   } else {
     // Field aligned
     const auto area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;

From a0d495459105e2f292ee2e9514cc0ca6f395ed5f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Mar 2026 12:36:13 +0100
Subject: [PATCH 0876/1827] Remove no-op check

At this time the parallel transform is not yet set, so isFci() return
false.
---
 src/mesh/coordinates.cxx | 25 -------------------------
 1 file changed, 25 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 4e7a9e1c24..4f8183cff0 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1259,31 +1259,6 @@ int Coordinates::calcCovariant(const std::string& region) {
 
   output_info.write("\tLocal maximum error in off-diagonal inversion is {:e}\n", maxerr);
 
-  if (Bxy.isFci()) {
-    BoutReal maxError = 0;
-    Options* options = Options::getRoot();
-    auto BJg = Bxy.asField3DParallel() * J / sqrt(g_22.asField3DParallel());
-    auto* mesh = localmesh;
-    for (int p = -mesh->ystart; p <= mesh->ystart; p++) {
-      if (p == 0) {
-        continue;
-      }
-      BOUT_FOR(i, BJg.getRegion("RGN_NOBNDRY")) {
-        auto local = BJg[i] / BJg.ynext(p)[i.yp(p)];
-        maxError = std::max(std::abs(local - 1), maxError);
-      }
-    }
-    const BoutReal allowedError = (*options)["allowedFluxError"].withDefault(1e-6);
-    if (maxError < allowedError / 100) {
-      output_info.write("\tInfo: The maximum flux conservation error is {:e}", maxError);
-    } else if (maxError < allowedError) {
-      output_warn.write("\tWarning: The maximum flux conservation error is {:e}",
-                        maxError);
-    } else {
-      throw BoutException("Error: The maximum flux conservation error is {:e}", maxError);
-    }
-  }
-
   return 0;
 }
 

From aae5b5dcb3e1dec9b9975e320ab5e6254ee2c511 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Mar 2026 12:51:12 +0100
Subject: [PATCH 0877/1827] Fixup compilation

---
 src/mesh/coordinates.cxx | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 4f8183cff0..c3a4b727d1 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2088,6 +2088,7 @@ void Coordinates::_compute_cell_area_x() const {
   _cell_area_xhigh.emplace(emptyFrom(area_centre));
   // We cannot setLocation, as that would trigger the computation of staggered
   // metrics.
+  auto mesh = Bxy.getMesh();
   ASSERT0(mesh->xstart > 0);
   BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOX")) {
     (*_cell_area_xlow)[i] = 0.5 * (area_centre[i] + area_centre[i.xm()]);
@@ -2102,8 +2103,8 @@ void Coordinates::_compute_cell_area_y() const {
     ASSERT2(isUniform(dx, false, "RGN_ALL"));
     ASSERT4(isUniform(dz, true, "RGN_ALL"));
     ASSERT2(isUniform(dz, false, "RGN_ALL"));
-    _cell_area_ylow = _jxz_ylow * dx * dz;
-    _cell_area_yhigh = _jxz_yhigh * dx * dz;
+    _cell_area_ylow.emplace(*_jxz_ylow * dx * dz);
+    _cell_area_yhigh.emplace(*_jxz_yhigh * dx * dz);
   } else {
     // Field aligned
     const auto area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;
@@ -2111,6 +2112,7 @@ void Coordinates::_compute_cell_area_y() const {
     _cell_area_yhigh.emplace(emptyFrom(area_centre));
     // We cannot setLocation, as that would trigger the computation of staggered
     // metrics.
+    auto mesh = Bxy.getMesh();
     ASSERT0(mesh->ystart > 0);
     BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOY")) {
       (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);

From 63ab8b40245ac8b4ebf03acbe46e390ffcfe9c53 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Mar 2026 13:00:09 +0100
Subject: [PATCH 0878/1827] Switch to ASSERT3

---
 src/mesh/coordinates.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index c3a4b727d1..8dd62e11b6 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2099,9 +2099,9 @@ void Coordinates::_compute_cell_area_x() const {
 void Coordinates::_compute_cell_area_y() const {
   Jxz();
   if (_jxz_centre->isFci()) {
-    ASSERT4(isUniform(dx, true, "RGN_ALL"));
+    ASSERT3(isUniform(dx, true, "RGN_ALL"));
     ASSERT2(isUniform(dx, false, "RGN_ALL"));
-    ASSERT4(isUniform(dz, true, "RGN_ALL"));
+    ASSERT3(isUniform(dz, true, "RGN_ALL"));
     ASSERT2(isUniform(dz, false, "RGN_ALL"));
     _cell_area_ylow.emplace(*_jxz_ylow * dx * dz);
     _cell_area_yhigh.emplace(*_jxz_yhigh * dx * dz);

From 1048d15774df037689417c328f503594085f2a37 Mon Sep 17 00:00:00 2001
From: wearysebas <sebichito@gmail.com>
Date: Thu, 22 Jan 2026 15:58:33 +0000
Subject: [PATCH 0879/1827] Add checks to chooseProcessorSplit function in
 boutmesh.cxx

Setting NXPE or NYPE would not trigger the checks of number of points / number of specified processes. Also added tests to it and modified previous tests to work.
---
 src/mesh/impls/bout/boutmesh.cxx  | 18 +++++++++----
 tests/unit/mesh/test_boutmesh.cxx | 42 ++++++++++++++++++++++++++++---
 2 files changed, 52 insertions(+), 8 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index ea1b6a41b2..e701ba849f 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -268,7 +268,11 @@ void BoutMesh::chooseProcessorSplit(Options& options) {
           _f("Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"),
           NPES, NXPE);
     }
-
+    if (nx % NXPE != 0) {
+      throw BoutException(
+          _("Number of x points ({:d}) not divisible by NPs in x direction ({:d})\n"), nx,
+          NXPE);
+    }
     NYPE = NPES / NXPE;
   } else {
     // NXPE not set, but NYPE is
@@ -281,7 +285,11 @@ void BoutMesh::chooseProcessorSplit(Options& options) {
           _f("Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"),
           NPES, NYPE);
     }
-
+    if (ny % NYPE != 0) {
+      throw BoutException(
+          _("Number of y points ({:d}) not divisible by NPs in y direction ({:d})\n"), nx,
+          NXPE);
+    }
     NXPE = NPES / NYPE;
   }
 
@@ -2218,9 +2226,9 @@ void BoutMesh::topology() {
     }
 
     for (int i = 0; i < limiter_count; ++i) {
-      int const yind = limiter_yinds[i];
-      int const xstart = limiter_xstarts[i];
-      int const xend = limiter_xends[i];
+      const int yind = limiter_yinds[i];
+      const int xstart = limiter_xstarts[i];
+      const int xend = limiter_xends[i];
       output_info.write("Adding a limiter between y={} and {}. X indices {} to {}\n",
                         yind, yind + 1, xstart, xend);
       add_target(yind, xstart, xend);
diff --git a/tests/unit/mesh/test_boutmesh.cxx b/tests/unit/mesh/test_boutmesh.cxx
index 8a446a742b..45217bfbe0 100644
--- a/tests/unit/mesh/test_boutmesh.cxx
+++ b/tests/unit/mesh/test_boutmesh.cxx
@@ -464,7 +464,7 @@ TEST_P(BadBoutMeshDecompositionTest, BadSingleCoreYDecomposition) {
   EXPECT_THAT(result.reason, HasSubstr(params.expected_message));
 }
 
-TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPE) {
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPETooManyXProcs) {
   Options options{{"NXPE", 3}};
 
   BoutMeshExposer mesh(1, 24, 1, 1, 1, 8);
@@ -472,7 +472,7 @@ TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPE) {
   EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
 }
 
-TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPE) {
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPETooManyYProcs) {
   Options options{{"NYPE", 7}};
 
   BoutMeshExposer mesh(1, 24, 1, 1, 1, 8);
@@ -480,10 +480,46 @@ TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPE) {
   EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
 }
 
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPENotDivisibleByNYPE) {
+  WithQuietOutput info{output_info};
+  Options options{{"NXPE", 5}};
+
+  BoutMeshExposer mesh(5, 24, 1, 1, 1, 8);
+
+  EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
+}
+
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPENotDivisibleByNYPE) {
+  WithQuietOutput info{output_info};
+  Options options{{"NYPE", 5}};
+
+  BoutMeshExposer mesh(5, 5, 1, 1, 1, 8);
+
+  EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
+}
+
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPENotDivisibleByNYPE) {
+  WithQuietOutput info{output_info};
+  Options options{{"NXPE", 5}};
+
+  BoutMeshExposer mesh(5, 24, 1, 1, 1, 8);
+
+  EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
+}
+
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPENotDivisibleByNYPE) {
+  WithQuietOutput info{output_info};
+  Options options{{"NYPE", 5}};
+
+  BoutMeshExposer mesh(5, 5, 1, 1, 1, 8);
+
+  EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
+}
+
 TEST_F(BoutMeshTest, ChooseProcessorSplitNXPE) {
   Options options{{"NXPE", 4}};
 
-  BoutMeshExposer mesh(1, 24, 1, 1, 1, 8);
+  BoutMeshExposer mesh(4, 24, 1, 1, 1, 8);
 
   EXPECT_NO_THROW(mesh.chooseProcessorSplit(options));
 

From 35c30cf5fd81b607a680feb04719844294132a99 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 13 Mar 2026 13:50:07 +0100
Subject: [PATCH 0880/1827] Fix test names

---
 tests/unit/mesh/test_boutmesh.cxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/unit/mesh/test_boutmesh.cxx b/tests/unit/mesh/test_boutmesh.cxx
index 45217bfbe0..a23b432f70 100644
--- a/tests/unit/mesh/test_boutmesh.cxx
+++ b/tests/unit/mesh/test_boutmesh.cxx
@@ -480,7 +480,7 @@ TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPETooManyYProcs) {
   EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
 }
 
-TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPENotDivisibleByNYPE) {
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPENotDivisible_0) {
   WithQuietOutput info{output_info};
   Options options{{"NXPE", 5}};
 
@@ -489,7 +489,7 @@ TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPENotDivisibleByNYPE) {
   EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
 }
 
-TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPENotDivisibleByNYPE) {
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPENotDivisible_0) {
   WithQuietOutput info{output_info};
   Options options{{"NYPE", 5}};
 
@@ -498,7 +498,7 @@ TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPENotDivisibleByNYPE) {
   EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
 }
 
-TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPENotDivisibleByNYPE) {
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPENotDivisible_1) {
   WithQuietOutput info{output_info};
   Options options{{"NXPE", 5}};
 
@@ -507,7 +507,7 @@ TEST_F(BoutMeshTest, ChooseProcessorSplitBadNXPENotDivisibleByNYPE) {
   EXPECT_THROW(mesh.chooseProcessorSplit(options), BoutException);
 }
 
-TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPENotDivisibleByNYPE) {
+TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPENotDivisible_1) {
   WithQuietOutput info{output_info};
   Options options{{"NYPE", 5}};
 

From 5cad79ae100167856a72fa510606a776aca9f9c6 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 13 Mar 2026 13:45:11 +0000
Subject: [PATCH 0881/1827] Apply `clang-tidy` fixes

---
 tests/unit/fake_parallel_mesh.hxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx
index 417994bd39..b3e57c4968 100644
--- a/tests/unit/fake_parallel_mesh.hxx
+++ b/tests/unit/fake_parallel_mesh.hxx
@@ -9,6 +9,7 @@
 #include <vector>
 
 #include "../../src/mesh/impls/bout/boutmesh.hxx"
+#include "bout/assert.hxx"
 #include "bout/boundary_op.hxx"
 #include "bout/boundary_region.hxx"
 #include "bout/boutcomm.hxx"
@@ -237,7 +238,7 @@ private:
     return BoutMesh::sendY(g, handle);
   }
 
-  FieldGroup makeGroup(FakeParallelMesh* m, const std::vector<int>& ids) {
+  static FieldGroup makeGroup(FakeParallelMesh* m, const std::vector<int>& ids) {
     FieldGroup g;
     for (const int i : ids) {
       ASSERT1(m->registeredFieldIds.contains(i));

From 0b71d580d5402e4f451f362e30ad1c02b8f3a594 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 13 Mar 2026 14:25:17 +0000
Subject: [PATCH 0882/1827] Move `field_type()` to `FieldData`; deprecate
 `FieldData::is3D()`

---
 include/bout/field.hxx             |  6 ------
 include/bout/field2d.hxx           |  2 --
 include/bout/field3d.hxx           |  1 -
 include/bout/field_data.hxx        | 26 ++++++++++++++++++--------
 include/bout/fieldperp.hxx         |  1 -
 include/bout/vector2d.hxx          |  4 ++--
 include/bout/vector3d.hxx          | 24 ++++++++++++------------
 tests/unit/field/test_field.cxx    |  1 -
 tests/unit/field/test_vector2d.cxx |  6 ------
 tests/unit/field/test_vector3d.cxx |  6 ------
 10 files changed, 32 insertions(+), 45 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 9ae3ad5016..8372549122 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -30,7 +30,6 @@ class Field;
 #define FIELD_H
 
 #include <cmath>
-#include <cstdint>
 #include <cstdio>
 #include <optional>
 #include <string>
@@ -121,11 +120,6 @@ public:
   /// Get the total number of points
   virtual int size() const = 0;
 
-  /// Enum to distinguish the different kinds of Fields
-  enum class FieldType : std::uint8_t { field3d, field2d, fieldperp };
-  /// Is this an instance of `Field3D`, `Field2D`, or `FieldPerp`?
-  virtual FieldType field_type() const = 0;
-
   friend void swap(Field& first, Field& second) noexcept {
     using std::swap;
     swap(static_cast<FieldData&>(first), static_cast<FieldData&>(second));
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 82c63b5dd4..c278fbfd4e 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -250,8 +250,6 @@ public:
   Field2D& operator/=(BoutReal rhs);
 
   // FieldData virtual functions
-
-  bool is3D() const override { return false; }
   FieldType field_type() const override { return FieldType::field2d; }
 
 #if CHECK > 0
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index f06696c9d9..0cc5f2fa3c 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -473,7 +473,6 @@ public:
   ///@}
 
   // FieldData virtual functions
-  bool is3D() const override { return true; }
   FieldType field_type() const override { return FieldType::field3d; }
 
 #if CHECK > 0
diff --git a/include/bout/field_data.hxx b/include/bout/field_data.hxx
index 185dcabf2d..2f0d17a36d 100644
--- a/include/bout/field_data.hxx
+++ b/include/bout/field_data.hxx
@@ -6,7 +6,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -33,6 +33,7 @@ class FieldData;
 #include "bout/bout_types.hxx"
 #include "bout/unused.hxx"
 
+#include <cstdint>
 #include <map>
 #include <memory>
 #include <string>
@@ -71,13 +72,22 @@ public:
   /// Get variable location
   virtual CELL_LOC getLocation() const;
 
+  /// Enum to distinguish the different kinds of Fields
+  enum class FieldType : std::uint8_t { field3d, field2d, fieldperp };
+  /// Is this an instance of `Field3D`, `Field2D`, or `FieldPerp`?
+  virtual FieldType field_type() const = 0;
+
   // Defines interface which must be implemented
   /// True if variable is 3D
-  virtual bool is3D() const = 0;
+  [[deprecated("Use `field_type()` instead")]]
+  bool is3D() const {
+    return field_type() == FieldType::field3d;
+  }
+
   /// Number of BoutReals in one element
   virtual int elementSize() const { return 1; }
 
-  virtual void doneComms(){}; // Notifies that communications done
+  virtual void doneComms() {}; // Notifies that communications done
 
   // Boundary conditions
   void setBoundary(const std::string& name); ///< Set the boundary conditions
@@ -86,13 +96,13 @@ public:
   copyBoundary(const FieldData& f); ///< Copy the boundary conditions from another field
 
   virtual void applyBoundary(bool UNUSED(init) = false) {}
-  virtual void applyTDerivBoundary(){};
+  virtual void applyTDerivBoundary() {};
 
-  virtual void applyParallelBoundary(){};
-  virtual void applyParallelBoundary(BoutReal UNUSED(t)){};
-  virtual void applyParallelBoundary(const std::string& UNUSED(condition)){};
+  virtual void applyParallelBoundary() {};
+  virtual void applyParallelBoundary(BoutReal UNUSED(t)) {};
+  virtual void applyParallelBoundary(const std::string& UNUSED(condition)) {};
   virtual void applyParallelBoundary(const std::string& UNUSED(region),
-                                     const std::string& UNUSED(condition)){};
+                                     const std::string& UNUSED(condition)) {};
   // JMAD
   void addBndryFunction(FuncPtr userfunc, BndryLoc location);
   void addBndryGenerator(FieldGeneratorPtr gen, BndryLoc location);
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 5e84f6fa68..9c1806b5ce 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -300,7 +300,6 @@ public:
    */
   int getNz() const override { return nz; };
 
-  bool is3D() const override { return false; }
   FieldType field_type() const override { return FieldType::fieldperp; }
 
   friend void swap(FieldPerp& first, FieldPerp& second) noexcept;
diff --git a/include/bout/vector2d.hxx b/include/bout/vector2d.hxx
index bdc375e698..1e19241a8e 100644
--- a/include/bout/vector2d.hxx
+++ b/include/bout/vector2d.hxx
@@ -13,7 +13,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -142,7 +142,7 @@ public:
   CELL_LOC getLocation() const override;
 
   // FieldData virtual functions
-  bool is3D() const override { return false; }
+  FieldType field_type() const override { return FieldType::field2d; }
   int elementSize() const override { return 3; }
 
   /// Apply boundary condition to all fields
diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx
index 0c71dcffa5..655a85ca73 100644
--- a/include/bout/vector3d.hxx
+++ b/include/bout/vector3d.hxx
@@ -9,7 +9,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -45,10 +45,10 @@ class Vector2D;
  * -------
  *
  * Vector3D f;
- * 
+ *
  * a.x; // Error! a.x not allocated
  *
- * 
+ *
  */
 class Vector3D : public FieldData {
 public:
@@ -70,7 +70,7 @@ public:
   ~Vector3D() override;
 
   /*!
-   * The components of the vector. These can be 
+   * The components of the vector. These can be
    * either co- or contra-variant, depending on
    * the boolean flag "covariant"
    */
@@ -92,8 +92,8 @@ public:
   bool covariant{true};
 
   /*!
-   * In-place conversion to covariant form. 
-   * 
+   * In-place conversion to covariant form.
+   *
    * If already covariant (covariant = true) then does nothing
    * If contravariant, multiplies by metric tensor g_{ij}
    */
@@ -104,7 +104,7 @@ public:
    *
    * If already contravariant (covariant = false) then does nothing
    * If covariant, multiplies by metric tensor g^{ij}
-   * 
+   *
    */
   void toContravariant();
 
@@ -114,14 +114,14 @@ public:
    * The first time this is called, a new Vector3D object is created.
    * Subsequent calls return a pointer to this same object
    *
-   * For convenience, a standalone function "ddt" exists, so that 
+   * For convenience, a standalone function "ddt" exists, so that
    *
    * ddt(v) is equivalent to *(v.timeDeriv())
-   * 
+   *
    * This does some book-keeping to ensure that the time derivative
    * of the components is the same as the components of the time derivative
    *
-   * ddt(v).x == ddt(v.x) 
+   * ddt(v).x == ddt(v.x)
    */
   Vector3D* timeDeriv();
 
@@ -172,7 +172,7 @@ public:
   CELL_LOC getLocation() const override;
 
   // FieldData virtual functions
-  bool is3D() const override { return true; }
+  FieldType field_type() const override { return FieldType::field3d; }
   int elementSize() const override { return 3; }
 
   void applyBoundary(bool init = false) override;
@@ -203,7 +203,7 @@ const Vector3D cross(const Vector3D& lhs, const Vector2D& rhs);
 
 /*!
  * Absolute magnitude (modulus) of a vector  |v|
- * 
+ *
  * sqrt( v.x^2 + v.y^2 + v.z^2 )
  */
 const Field3D abs(const Vector3D& v, const std::string& region = "RGN_ALL");
diff --git a/tests/unit/field/test_field.cxx b/tests/unit/field/test_field.cxx
index 66af572a6e..2a3e600ab8 100644
--- a/tests/unit/field/test_field.cxx
+++ b/tests/unit/field/test_field.cxx
@@ -24,7 +24,6 @@ class FieldSubClass : public Field {
   FieldSubClass(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in)
       : Field(localmesh, location_in, directions_in) {}
 
-  bool is3D() const override { return false; }
   int size() const override { return 42; }
   FieldType field_type() const override { return FieldType::field2d; }
 };
diff --git a/tests/unit/field/test_vector2d.cxx b/tests/unit/field/test_vector2d.cxx
index de662c7df8..674817abd2 100644
--- a/tests/unit/field/test_vector2d.cxx
+++ b/tests/unit/field/test_vector2d.cxx
@@ -97,12 +97,6 @@ TEST_F(Vector2DTest, ApplyBoundaryString) {
   EXPECT_DOUBLE_EQ(v.x(2, 2), 0.0);
 }
 
-TEST_F(Vector2DTest, Is3D) {
-  Vector2D vector;
-
-  EXPECT_FALSE(vector.is3D());
-}
-
 TEST_F(Vector2DTest, BoutRealSize) {
   Vector2D vector;
 
diff --git a/tests/unit/field/test_vector3d.cxx b/tests/unit/field/test_vector3d.cxx
index 4db1c750a1..d8e9366574 100644
--- a/tests/unit/field/test_vector3d.cxx
+++ b/tests/unit/field/test_vector3d.cxx
@@ -100,12 +100,6 @@ TEST_F(Vector3DTest, ApplyBoundaryString) {
   EXPECT_DOUBLE_EQ(v.x(2, 2, 1), 0.0);
 }
 
-TEST_F(Vector3DTest, Is3D) {
-  Vector3D vector;
-
-  EXPECT_TRUE(vector.is3D());
-}
-
 TEST_F(Vector3DTest, BoutRealSize) {
   Vector3D vector;
 

From 976fa6e55f88b2e62822f27733698114069c5f31 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 13 Mar 2026 13:34:41 +0000
Subject: [PATCH 0883/1827] Add communicator for XZ planes

Required for properly communicating `FieldPerp` with multiple Z processors when
using PETSc
---
 include/bout/globalindexer.hxx                |  2 +-
 include/bout/hypre_interface.hxx              |  6 +--
 include/bout/mesh.hxx                         |  9 ++--
 include/bout/petsc_interface.hxx              |  4 +-
 .../laplace/impls/petsc/petsc_laplace.cxx     |  2 +-
 .../laplacexz/impls/petsc/laplacexz-petsc.cxx |  2 +-
 src/mesh/impls/bout/boutmesh.cxx              | 47 +++++++++++++++++--
 src/mesh/impls/bout/boutmesh.hxx              |  3 ++
 src/mesh/mesh.cxx                             |  2 +-
 tests/unit/fake_mesh.hxx                      |  1 +
 10 files changed, 60 insertions(+), 18 deletions(-)

diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx
index e756ead3b2..bd4203a092 100644
--- a/include/bout/globalindexer.hxx
+++ b/include/bout/globalindexer.hxx
@@ -86,7 +86,7 @@ public:
 
     int localSize = size();
     MPI_Comm comm =
-        std::is_same_v<T, FieldPerp> ? fieldmesh->getXcomm() : BoutComm::get();
+        std::is_same_v<T, FieldPerp> ? fieldmesh->getXZcomm() : BoutComm::get();
     fieldmesh->getMpi().MPI_Scan(&localSize, &globalEnd, 1, MPI_INT, MPI_SUM, comm);
     globalEnd--;
     int counter = globalStart = globalEnd - size() + 1;
diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index 65d8875a9a..189e91d159 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -159,7 +159,7 @@ public:
   explicit HypreVector(IndexerPtr<T> indConverter) : indexConverter(indConverter) {
     Mesh& mesh = *indConverter->getMesh();
     const MPI_Comm comm =
-        std::is_same_v<T, FieldPerp> ? mesh.getXcomm() : BoutComm::get();
+        std::is_same_v<T, FieldPerp> ? mesh.getXZcomm() : BoutComm::get();
 
     HYPRE_BigInt jlower = indConverter->getGlobalStart();
     HYPRE_BigInt jupper = jlower + indConverter->size() - 1; // inclusive end
@@ -380,7 +380,7 @@ public:
       : hypre_matrix(new HYPRE_IJMatrix, MatrixDeleter{}), index_converter(indConverter) {
     Mesh* mesh = indConverter->getMesh();
     const MPI_Comm comm =
-        std::is_same_v<T, FieldPerp> ? mesh->getXcomm() : BoutComm::get();
+        std::is_same_v<T, FieldPerp> ? mesh->getXZcomm() : BoutComm::get();
     parallel_transform = &mesh->getCoordinates()->getParallelTransform();
 
     ilower = indConverter->getGlobalStart();
@@ -812,7 +812,7 @@ public:
                            "values are: gmres, bicgstab, pcg")
                       .withDefault(HYPRE_SOLVER_TYPE::bicgstab);
 
-    comm = std::is_same_v<T, FieldPerp> ? mesh.getXcomm() : BoutComm::get();
+    comm = std::is_same_v<T, FieldPerp> ? mesh.getXZcomm() : BoutComm::get();
 
     auto print_level =
         options["hypre_print_level"]
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index a1ed6a9011..d4f7f7ac7f 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -3,7 +3,7 @@
  *
  * Interface for mesh classes. Contains standard variables and useful
  * routines.
- * 
+ *
  * Changelog
  * =========
  *
@@ -11,7 +11,7 @@
  *     * Removing coordinate system into separate
  *       Coordinates class
  *     * Adding index derivative functions from derivs.cxx
- * 
+ *
  * 2010-06 Ben Dudson, Sean Farley
  *     * Initial version, adapted from GridData class
  *     * Incorporates code from topology.cpp and Communicator
@@ -20,7 +20,7 @@
  * Copyright 2010-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -58,8 +58,6 @@ class Mesh;
 #include "bout/sys/range.hxx" // RangeIterator
 #include "bout/unused.hxx"
 
-#include "mpi.h"
-
 #include <map>
 #include <memory>
 #include <optional>
@@ -405,6 +403,7 @@ public:
   } ///< Return communicator containing all processors in X
   virtual MPI_Comm getXcomm(int jy) const = 0; ///< Return X communicator
   virtual MPI_Comm getYcomm(int jx) const = 0; ///< Return Y communicator
+  virtual MPI_Comm getXZcomm() const = 0;      ///< Communicator in X-Z
 
   /// Return pointer to the mesh's MPI Wrapper object
   MpiWrapper& getMpi() { return *mpi; }
diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 5239039f0c..2ce71d0549 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -79,7 +79,7 @@ inline MPI_Comm getComm([[maybe_unused]] const T& field) {
 
 template <>
 inline MPI_Comm getComm([[maybe_unused]] const FieldPerp& field) {
-  return field.getMesh()->getXcomm();
+  return field.getMesh()->getXZcomm();
 }
 
 template <class T>
@@ -293,7 +293,7 @@ public:
   PetscMatrix(IndexerPtr<T> indConverter, bool preallocate = true)
       : matrix(new Mat()), indexConverter(indConverter),
         pt(&indConverter->getMesh()->getCoordinates()->getParallelTransform()) {
-    MPI_Comm comm = std::is_same_v<T, FieldPerp> ? indConverter->getMesh()->getXcomm()
+    MPI_Comm comm = std::is_same_v<T, FieldPerp> ? indConverter->getMesh()->getXZcomm()
                                                  : BoutComm::get();
     const int size = indexConverter->size();
 
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index af65a1cd95..89ba25405b 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -140,7 +140,7 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
                            [[maybe_unused]] Solver* solver)
     : Laplacian(opt, loc, mesh_in), A(0.0, mesh_in), C1(1.0, mesh_in), C2(1.0, mesh_in),
       D(1.0, mesh_in), Ex(0.0, mesh_in), Ez(0.0, mesh_in), issetD(false), issetC(false),
-      issetE(false), comm(localmesh->getXcomm()),
+      issetE(false), comm(localmesh->getXZcomm()),
       opts(opt == nullptr ? &(Options::root()["laplace"]) : opt),
       // WARNING: only a few of these options actually make sense: see the
       // PETSc documentation to work out which they are (possibly
diff --git a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
index f8cb52b3da..3e55262b6d 100644
--- a/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
+++ b/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx
@@ -155,7 +155,7 @@ LaplaceXZpetsc::LaplaceXZpetsc(Mesh* m, Options* opt, const CELL_LOC loc)
           .withDefault("petsc");
 
   // Get MPI communicator
-  MPI_Comm comm = localmesh->getXcomm();
+  MPI_Comm comm = localmesh->getXZcomm();
 
   // Local size
   int localN = (localmesh->xend - localmesh->xstart + 1) * (localmesh->LocalNz);
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index ea1b6a41b2..fea88c536e 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -52,6 +52,7 @@
 #include <bout/utils.hxx>
 
 #include <fmt/format.h>
+#include <fmt/ranges.h>
 
 #include <algorithm>
 #include <cmath>
@@ -106,6 +107,9 @@ BoutMesh::~BoutMesh() {
   if (comm_outer != MPI_COMM_NULL) {
     MPI_Comm_free(&comm_outer);
   }
+  if (comm_xz != MPI_COMM_NULL) {
+    MPI_Comm_free(&comm_xz);
+  }
 }
 
 BoutMesh::YDecompositionIndices
@@ -665,10 +669,43 @@ int BoutMesh::load() {
   return 0;
 }
 
+namespace {
+auto make_XZ_communicator(const BoutMesh& mesh, MPI_Group group_world) -> MPI_Comm {
+  std::vector<int> ranks;
+
+  const int yp = mesh.getYProcIndex();
+
+  // All processors with the same Y index
+  for (int xp = 0; xp < mesh.getNXPE(); ++xp) {
+    for (int zp = 0; zp < mesh.getNZPE(); ++zp) {
+      ranks.push_back(mesh.getProcIndex(xp, yp, zp));
+    }
+  }
+  MPI_Group group{};
+  if (MPI_Group_incl(group_world, static_cast<int>(ranks.size()), ranks.data(), &group)
+      != MPI_SUCCESS) {
+    throw BoutException("Could not create X-Z communication group for ranks {}",
+                        fmt::join(ranks, ", "));
+  }
+
+  MPI_Comm comm_xz{};
+  if (MPI_Comm_create(BoutComm::get(), group, &comm_xz) != MPI_SUCCESS) {
+    throw BoutException("Could not create X-Z communicator for yp={} (xind={}, yind={}, "
+                        "zind={}) ranks={}",
+                        yp, mesh.getXProcIndex(), mesh.getYProcIndex(),
+                        mesh.getZProcIndex(), fmt::join(ranks, ", "));
+  }
+
+  return comm_xz;
+}
+} // namespace
+
 void BoutMesh::createCommunicators() {
   MPI_Group group_world{};
   MPI_Comm_group(BoutComm::get(), &group_world); // Get the entire group
 
+  comm_xz = make_XZ_communicator(*this, group_world);
+
   //////////////////////////////////////////////////////
   /// Communicator in X
 
@@ -1038,7 +1075,9 @@ void BoutMesh::createXBoundaries() {
   }
 }
 
-int BoutMesh::getProcIndex(int X, int Y, int Z) const { return Y * NXPE + X; }
+int BoutMesh::getProcIndex(int X, int Y, int Z) const {
+  return (((Z * NYPE) + Y) * NXPE) + X;
+}
 
 void BoutMesh::createYBoundaries() {
   if (MYG <= 0) {
@@ -2218,9 +2257,9 @@ void BoutMesh::topology() {
     }
 
     for (int i = 0; i < limiter_count; ++i) {
-      int const yind = limiter_yinds[i];
-      int const xstart = limiter_xstarts[i];
-      int const xend = limiter_xends[i];
+      const int yind = limiter_yinds[i];
+      const int xstart = limiter_xstarts[i];
+      const int xend = limiter_xends[i];
       output_info.write("Adding a limiter between y={} and {}. X indices {} to {}\n",
                         yind, yind + 1, xstart, xend);
       add_target(yind, xstart, xend);
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index b42bf325b5..49eded2ae8 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -107,6 +107,7 @@ public:
   MPI_Comm getXcomm(int UNUSED(jy)) const override { return comm_x; }
   /// Return communicator containing all processors in Y
   MPI_Comm getYcomm(int xpos) const override;
+  MPI_Comm getXZcomm() const override { return comm_xz; }
 
   /// Is local X index \p jx periodic in Y?
   ///
@@ -455,6 +456,8 @@ private:
 
   /// Communicator containing all processors in X
   MPI_Comm comm_x{MPI_COMM_NULL};
+  /// Communicator for all processors in an XZ plane
+  MPI_Comm comm_xz{MPI_COMM_NULL};
 
   //////////////////////////////////////////////////
   // Surface communications
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 829c150a15..31b3c08889 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -516,7 +516,7 @@ int Mesh::globalStartIndex2D() {
 int Mesh::globalStartIndexPerp() {
   int localSize = localSizePerp();
   int cumulativeSize = 0;
-  mpi->MPI_Scan(&localSize, &cumulativeSize, 1, MPI_INT, MPI_SUM, getXcomm());
+  mpi->MPI_Scan(&localSize, &cumulativeSize, 1, MPI_INT, MPI_SUM, getXZcomm());
   return cumulativeSize - localSize;
 }
 
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index aa0220609b..6dbbd6200b 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -139,6 +139,7 @@ public:
   }
   MPI_Comm getXcomm(int UNUSED(jy)) const override { return BoutComm::get(); }
   MPI_Comm getYcomm(int UNUSED(jx)) const override { return BoutComm::get(); }
+  MPI_Comm getXZcomm() const override { return BoutComm::get(); }
 
   // Periodic Y
   int ix_separatrix{1000000}; // separatrix index

From 8a3af0cc8da3809584fe9ed8ec38203a81606c1b Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 13 Mar 2026 09:14:31 -0700
Subject: [PATCH 0884/1827] PetscOperators: Operate on Field3Ds

Map from Field3D, including yup/ydown boundaries, to PETSc Vec,
perform matrix-vector product, and map back to a Field3D.
---
 include/bout/petsc_operators.hxx | 37 ++++++++++++++++++++++++++++++++
 src/mesh/petsc_operators.cxx     | 33 +++++++++++++++++++++-------
 2 files changed, 62 insertions(+), 8 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index c19146a105..72f7476121 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -15,6 +15,7 @@
 #include <functional>
 #include <memory>
 #include <string>
+#include <utility>
 #include <vector>
 
 /// Handles mapping between global cell index used in the mesh file,
@@ -74,6 +75,41 @@ public:
     }
   }
 
+  template <typename Function>
+  void map_local_field(Function func) const {
+    const std::vector<std::reference_wrapper<const Region<Ind3D>>> regions = {
+        evolving_region, xin_region, xout_region};
+    PetscInt row = 0; // Starting from 0, not row_start
+    for (const auto& region : regions) {
+      BOUT_FOR_SERIAL(i, region.get()) {
+        func(row, i);
+        ++row;
+      }
+    }
+  }
+
+  template <typename Function>
+  void map_local_yup(Function func) const {
+    PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size();
+    BOUT_FOR_SERIAL(i, yup_region) {
+      func(row, i);
+      ++row;
+    }
+  }
+
+  template <typename Function>
+  void map_local_ydown(Function func) const {
+    PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size()
+                   + yup_region.size();
+    BOUT_FOR_SERIAL(i, ydown_region) {
+      func(row, i);
+      ++row;
+    }
+  }
+
+  /// Return a matrix that reorders vectors from petsc global index to mesh index
+  Mat getPetscToMesh() const { return mat_petsc_to_mesh; }
+
 private:
   PetscLib lib; // Initialize and finalize PETSc
 
@@ -87,6 +123,7 @@ private:
 
   PetscInt row_start, row_end; ///< Local row indices
   Mat mat_mesh_to_petsc;
+  Mat mat_petsc_to_mesh;
 };
 
 /// Shared pointer to const PetscMapping
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index ef48d75dd1..2d6c7743ec 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -94,15 +94,19 @@ PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_ce
   });
   MatAssemblyBegin(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY);
   MatAssemblyEnd(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY);
+
+  // Transpose to map petsc indices to mesh indices
+  MatTranspose(mat_mesh_to_petsc, MAT_INITIAL_MATRIX, &mat_petsc_to_mesh);
 }
 
 PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
                              Array<BoutReal> weights)
     : mapping(mapping) {
 
-  MatCreate(BoutComm::get(), &mat_operator);
+  Mat mat;
+  MatCreate(BoutComm::get(), &mat);
   int nlocal = mapping->size();
-  MatSetSizes(mat_operator, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE);
+  MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE);
 
   mapping->map_evolving([&](PetscInt row, Ind3D, PetscInt mesh_index) {
     if (mesh_index >= rows.size()) {
@@ -113,11 +117,16 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
     int end_ind = (mesh_index + 1 < rows.size()) ? rows[mesh_index + 1] : cols.size();
     output.write("Mapping {} : {} -> {}\n", row, start_ind, end_ind);
 
-    MatSetValues(mat_operator, 1, &row, end_ind - start_ind, &cols[start_ind],
-                 &weights[start_ind], INSERT_VALUES);
+    MatSetValues(mat, 1, &row, end_ind - start_ind, &cols[start_ind], &weights[start_ind],
+                 INSERT_VALUES);
   });
-  MatAssemblyBegin(mat_operator, MAT_FINAL_ASSEMBLY);
-  MatAssemblyEnd(mat_operator, MAT_FINAL_ASSEMBLY);
+  MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);
+  MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);
+
+  // Row indices are PETSc indices but columns are mesh indices
+  // Multiply on the right by PetscToMesh.
+  MatMatMult(mat, mapping->getPetscToMesh(), MAT_INITIAL_MATRIX, PETSC_DETERMINE,
+             &this->mat_operator);
 }
 
 /// Perform operation
@@ -128,8 +137,16 @@ Field3D PetscOperator::operator()(const Field3D& rhs) const {
 
   // Fill vec from rhs
   PetscScalar* x;
+  // Copy rows from Field3D cells
   VecGetArray(rhs_vec, &x);
-  throw BoutException("Not implemented");
+  mapping->map_local_field([&](PetscInt row, const Ind3D& i) { x[row] = rhs[i]; });
+
+  // Copy Yup / Ydown values from boundaries
+  const Field3D& yup = rhs.yup();
+  mapping->map_local_yup([&](PetscInt row, const Ind3D& i) { x[row] = yup[i]; });
+
+  const Field3D& ydown = rhs.yup();
+  mapping->map_local_ydown([&](PetscInt row, const Ind3D& i) { x[row] = ydown[i]; });
   VecRestoreArray(rhs_vec, &x);
 
   // Perform Mat-Vec muliplication
@@ -141,7 +158,7 @@ Field3D PetscOperator::operator()(const Field3D& rhs) const {
   Field3D result;
   const PetscScalar* r;
   VecGetArrayRead(result_vec, &r);
-  throw BoutException("Not implemented");
+  mapping->map_local_field([&](PetscInt row, const Ind3D& i) { result[i] = r[row]; });
   VecRestoreArrayRead(result_vec, &r);
 
   return result;

From 2b712591e4ef502562336c560e8f3ca1afc48dbe Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 13 Mar 2026 11:30:53 -0700
Subject: [PATCH 0885/1827] PetscOperators: Add documentation and error
 checking

Docstrings to explain PetscMapping, PetscOperator and PetscOperators
classes.

Extend `BOUT_DO_PETSC` macro to print error message, file and line
number.
---
 include/bout/petsc_operators.hxx | 288 ++++++++++++++++++++++++++-----
 include/bout/petsclib.hxx        |  31 ++--
 src/mesh/petsc_operators.cxx     | 110 ++++++------
 3 files changed, 326 insertions(+), 103 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 72f7476121..3f4d0a596e 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -1,4 +1,12 @@
-/// Represent operators using PETSc matrices
+/// Represent finite-difference operators using PETSc matrices.
+///
+/// This header defines:
+/// - `PetscMapping`, which maps between mesh-global numbering,
+///   PETSc numbering, and `Field3D` storage;
+/// - `PetscOperator`, which wraps a PETSc `Mat` as a linear operator on
+///   `Field3D` objects; and
+/// - `PetscOperators`, a helper for reading mappings and operators from
+///   a `Mesh`.
 ///
 
 #include "bout/array.hxx"
@@ -18,39 +26,84 @@
 #include <utility>
 #include <vector>
 
-/// Handles mapping between global cell index used in the mesh file,
-/// and the global indexing used in PETSc that depends on the mesh
-/// decomposition across MPI ranks.
+/// Map between mesh-global cell numbering and PETSc numbering.
+///
+/// The mesh file stores operator stencils and weights using a mesh-global
+/// numbering scheme. This numbering includes:
+/// - evolving cells in the main domain;
+/// - X-boundary cells; and
+/// - Y-boundary cells represented by the `yup` and `ydown` fields.
 ///
-/// Each processor reads a chunk of the global arrays into Field3Ds:
-///  - cell_number
-///  - forward_cell_number
-///  - backward_cell_number
-/// Non-negative values in these arrays indicate a cell number.
+/// PETSc uses a different global numbering based on the MPI distribution
+/// of rows and vector entries. `PetscMapping` records the correspondence
+/// between these numbering systems and provides helper methods to iterate
+/// over the local cells in a consistent order.
 ///
-/// A Petsc Mat is constructed that maps between petsc indices and
-/// mesh indices.
+/// The mapping order used by this class is:
+/// 1. evolving cells;
+/// 2. inner X-boundary cells;
+/// 3. outer X-boundary cells;
+/// 4. `yup` boundary cells; and
+/// 5. `ydown` boundary cells.
+///
+/// A pair of PETSc matrices is constructed internally to reorder vectors
+/// between mesh-global and PETSc-global numbering.
 class PetscMapping {
 public:
+  /// Construct the mapping from mesh numbering fields.
+  ///
+  /// @param cell_number Mesh-global cell numbers for evolving cells.
+  /// @param forward_cell_number Mesh-global cell numbers associated with
+  ///   forward Y-boundary (`yup`) values.
+  /// @param backward_cell_number Mesh-global cell numbers associated with
+  ///   backward Y-boundary (`ydown`) values.
+  ///
+  /// Non-negative values in the numbering fields identify valid cells.
+  /// The constructor builds the local regions and the PETSc permutation
+  /// matrices needed to translate between mesh and PETSc numbering.
   PetscMapping(const Field3D& cell_number, const Field3D& forward_cell_number,
                const Field3D& backward_cell_number);
 
-  // Static functions for unit testing
+  /// Destroy the PETSc matrices owned by this mapping.
+  ~PetscMapping();
+
+  /// Build a region containing all valid cells in a numbering field.
+  ///
+  /// @param cell_number Field whose entries contain mesh-global cell numbers.
+  /// @return A region containing all indices with non-negative cell numbers.
+  ///
+  /// This helper is public for unit testing.
   static Region<Ind3D> create_region(const Field3D& cell_number);
+
+  /// Build a region containing valid cells on the inner X boundary.
+  ///
+  /// @param cell_number Field whose entries contain mesh-global cell numbers.
+  /// @return A region containing valid cells adjacent to the inner X boundary.
   static Region<Ind3D> create_region_xin(const Field3D& cell_number);
+
+  /// Build a region containing valid cells on the outer X boundary.
+  ///
+  /// @param cell_number Field whose entries contain mesh-global cell numbers.
+  /// @return A region containing valid cells adjacent to the outer X boundary.
   static Region<Ind3D> create_region_xout(const Field3D& cell_number);
 
-  /// Total number of cells, including X and Y boundaries
+  /// Return the total number of locally mapped cells.
+  ///
+  /// The count includes evolving cells and all boundary cells represented
+  /// in the mapping on this processor.
   unsigned int size() const {
     return evolving_region.size() + xin_region.size() + xout_region.size()
            + yup_region.size() + ydown_region.size();
   }
 
-  /// Loops over cells and calls the given function with arguments:
-  ///   - PetscInt  PETSc row index
-  ///   - Ind3D     Index into Field3D variables
-  ///   - int       Global cell number in mesh
+  /// Iterate over locally owned evolving cells in PETSc row order.
+  ///
+  /// @tparam Function Callable with signature
+  ///   `func(PetscInt petsc_row, Ind3D index, int mesh_global_index)`.
+  /// @param func Function called once for each evolving cell owned locally.
   ///
+  /// The PETSc row index starts at the locally owned global row `row_start`.
+  /// The supplied `Ind3D` index refers to the main `Field3D` storage.
   template <typename Function>
   void map_evolving(Function func) const {
     PetscInt row = this->row_start;
@@ -60,8 +113,17 @@ public:
     }
   }
 
-  /// Note: It doesn't make sense to pass the Ind3D because
-  /// some reference Field3D, some the yup/ydown fields.
+  /// Iterate over all locally mapped cells in PETSc row order.
+  ///
+  /// @tparam Function Callable with signature
+  ///   `func(PetscInt petsc_row, int mesh_global_index)`.
+  /// @param func Function called once for each mapped cell owned locally.
+  ///
+  /// The iteration order is evolving, inner X boundary, outer X boundary,
+  /// `yup`, then `ydown`.
+  ///
+  /// No `Ind3D` is passed because some entries refer to interior `Field3D`
+  /// storage while others refer to boundary storage in `yup` or `ydown`.
   template <typename Function>
   void map(Function func) const {
     const std::vector<std::reference_wrapper<const Region<Ind3D>>> regions = {
@@ -75,6 +137,15 @@ public:
     }
   }
 
+  /// Iterate over locally stored entries packed from the main `Field3D`.
+  ///
+  /// @tparam Function Callable with signature `func(PetscInt local_index, Ind3D index)`.
+  /// @param func Function called once for each evolving or X-boundary cell
+  ///   stored in the local PETSc vector layout.
+  ///
+  /// The index passed to `func` is a local vector index beginning at zero.
+  /// Only the main field storage is traversed here; Y-boundary values are
+  /// handled separately by `map_local_yup()` and `map_local_ydown()`.
   template <typename Function>
   void map_local_field(Function func) const {
     const std::vector<std::reference_wrapper<const Region<Ind3D>>> regions = {
@@ -88,6 +159,12 @@ public:
     }
   }
 
+  /// Iterate over local vector entries corresponding to `yup` boundary values.
+  ///
+  /// @tparam Function Callable with signature `func(PetscInt local_index, Ind3D index)`.
+  /// @param func Function called once for each locally stored `yup` entry.
+  ///
+  /// The local index is the offset into the packed local PETSc vector.
   template <typename Function>
   void map_local_yup(Function func) const {
     PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size();
@@ -97,6 +174,12 @@ public:
     }
   }
 
+  /// Iterate over local vector entries corresponding to `ydown` boundary values.
+  ///
+  /// @tparam Function Callable with signature `func(PetscInt local_index, Ind3D index)`.
+  /// @param func Function called once for each locally stored `ydown` entry.
+  ///
+  /// The local index is the offset into the packed local PETSc vector.
   template <typename Function>
   void map_local_ydown(Function func) const {
     PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size()
@@ -107,72 +190,185 @@ public:
     }
   }
 
-  /// Return a matrix that reorders vectors from petsc global index to mesh index
+  /// Return the PETSc matrix that maps PETSc ordering to mesh ordering.
+  ///
+  /// @return PETSc matrix representing the permutation from PETSc global
+  ///   indices to mesh-global indices.
   Mat getPetscToMesh() const { return mat_petsc_to_mesh; }
 
 private:
   PetscLib lib; // Initialize and finalize PETSc
 
+  /// Mesh-global numbering for cells stored on this rank.
   Field3D cell_number;
 
-  Region<Ind3D> evolving_region; ///< Evolving cells
-  Region<Ind3D> xin_region;      ///< X boundary cells in inner boundary
-  Region<Ind3D> xout_region;     ///< X boundary cells in outer boundary
-  Region<Ind3D> yup_region;      ///< Y boundary cells in forward direction
-  Region<Ind3D> ydown_region;    ///< Y boundary cells in backward direction
+  /// Evolving cells in the main domain.
+  Region<Ind3D> evolving_region;
 
-  PetscInt row_start, row_end; ///< Local row indices
+  /// X-boundary cells on the inner radial boundary.
+  Region<Ind3D> xin_region;
+
+  /// X-boundary cells on the outer radial boundary.
+  Region<Ind3D> xout_region;
+
+  /// Y-boundary cells in the forward direction.
+  Region<Ind3D> yup_region;
+
+  /// Y-boundary cells in the backward direction.
+  Region<Ind3D> ydown_region;
+
+  /// First and one-past-last PETSc global rows owned by this rank.
+  PetscInt row_start, row_end;
+
+  /// Permutation matrix mapping mesh-global ordering to PETSc ordering.
   Mat mat_mesh_to_petsc;
+
+  /// Permutation matrix mapping PETSc ordering to mesh-global ordering.
   Mat mat_petsc_to_mesh;
 };
 
-/// Shared pointer to const PetscMapping
-/// Mapping is const after creation.
+/// Shared pointer to an immutable `PetscMapping`.
+///
+/// The mapping is constructed once and then shared by operators that use it.
 using PetscMappingPtr = std::shared_ptr<const PetscMapping>;
 
-/// Represents an operator on Field3Ds
+/// Linear operator on `Field3D` backed by a PETSc matrix.
+///
+/// `PetscOperator` wraps a PETSc `Mat` whose rows and columns use the PETSc
+/// numbering defined by a corresponding `PetscMapping`. Operators are usually
+/// constructed from CSR arrays read from the mesh file and can then be:
+/// - applied to a `Field3D`;
+/// - composed with other operators; and
+/// - added or subtracted.
 class PetscOperator {
 public:
-  /// Create using CSR format arrays
+  /// Construct an operator from CSR data in mesh-global numbering.
+  ///
+  /// @param mapping Shared mapping between mesh and PETSc numbering.
+  /// @param rows CSR row offsets.
+  /// @param cols CSR column indices in mesh-global numbering.
+  /// @param weights CSR non-zero values.
+  ///
+  /// The CSR arrays define an operator in mesh-global numbering. The
+  /// constructor converts this representation into a PETSc matrix using
+  /// the supplied mapping.
   PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
                 Array<BoutReal> weights);
 
-  /// Perform operation
+  /// Destroy the PETSc matrix and working vectors owned by this operator.
+  ~PetscOperator();
+
+  /// Apply the operator to a field.
+  ///
+  /// @param rhs Input field, including any required `yup` and `ydown`
+  ///   boundary values.
+  /// @return Result of applying the operator to `rhs`.
+  ///
+  /// The input field is packed into PETSc vector storage using the mapping,
+  /// multiplied by the PETSc matrix, then unpacked back into a `Field3D`.
   Field3D operator()(const Field3D& rhs) const;
 
-  /// Operator composition
+  /// Compose this operator with another operator.
+  ///
+  /// @param rhs Right-hand-side operator.
+  /// @return The composed operator `(*this) * rhs`.
+  ///
+  /// Both operators must use compatible mappings.
   PetscOperator operator*(const PetscOperator& rhs) const;
 
-  /// Operator addition
+  /// Add two operators.
+  ///
+  /// @param rhs Right-hand-side operator.
+  /// @return The sum of the two operators.
+  ///
+  /// Both operators must use compatible mappings.
   PetscOperator operator+(const PetscOperator& rhs) const;
 
-  /// Operator subtraction
+  /// Subtract one operator from another.
+  ///
+  /// @param rhs Right-hand-side operator.
+  /// @return The difference of the two operators.
+  ///
+  /// Both operators must use compatible mappings.
   PetscOperator operator-(const PetscOperator& rhs) const;
 
 private:
+  /// Construct directly from an existing PETSc matrix.
+  ///
+  /// @param mapping Shared mapping between mesh and PETSc numbering.
+  /// @param mat PETSc matrix implementing the operator.
+  ///
+  /// This constructor is used internally when creating operators from
+  /// PETSc matrix algebra such as composition, addition, or subtraction.
   PetscOperator(PetscMappingPtr mapping, Mat mat)
-      : mapping(std::move(mapping)), mat_operator(mat) {}
+      : mapping(std::move(mapping)), mat_operator(mat) {
+    // Allocate working vectors
+    VecCreate(BoutComm::get(), &this->rhs_vec);
+    VecSetSizes(this->rhs_vec, this->mapping->size(), PETSC_DETERMINE);
+    VecDuplicate(this->rhs_vec, &this->result_vec);
+  }
+
+  /// Shared mapping between mesh and PETSc numbering.
   PetscMappingPtr mapping;
+
+  /// PETSc matrix implementing the operator.
   Mat mat_operator;
+
+  /// Work vector holding the packed input field.
+  Vec rhs_vec;
+
+  /// Work vector holding the packed result.
+  Vec result_vec;
 };
 
+/// Collection of PETSc operators read from a mesh.
+///
+/// `PetscOperators` owns the `PetscMapping` derived from the mesh numbering
+/// fields and provides access to named operators stored in the mesh file
+/// as CSR arrays.
 class PetscOperators {
 public:
+  /// Construct PETSc operator support from a mesh.
+  ///
+  /// Reads the following mesh variables:
+  /// - `cell_number`
+  /// - `forward_cell_number`
+  /// - `backward_cell_number`
   ///
-  /// Reads from the mesh:
-  /// - cell_number : Field3D
-  /// - forward_cell_number : Field3D
-  /// - backward_cell_number : Field3D
-  /// - total_cells : int, optional
+  /// and uses them to construct the shared `PetscMapping`.
+  ///
+  /// @param mesh Mesh from which numbering fields and operators are read.
   PetscOperators(Mesh* mesh);
 
+  /// Retrieve a named PETSc operator from the mesh.
+  ///
+  /// @param name Base name of the operator in the mesh file.
+  /// @return A `PetscOperator` constructed from the arrays
+  ///   `{name}_rows`, `{name}_columns`, and `{name}_weights`.
+  ///
+  /// Throws `BoutException` if any of the required arrays are missing.
+  PetscOperator get(const std::string& name) const;
+
 private:
-  /// Read a Field3D from the mesh or throw BoutException if not found.
-  Field3D meshGetField3D(Mesh* mesh, const std::string& name);
+  /// Read a `Field3D` from the mesh.
+  ///
+  /// @param mesh Mesh from which to read.
+  /// @param name Name of the field.
+  /// @return The requested `Field3D`.
+  ///
+  /// Throws `BoutException` if the field is not present.
+  Field3D meshGetField3D(Mesh* mesh, const std::string& name) const;
 
-  /// Read a 1D Array<T> from the mesh or throw BoutException
+  /// Read a one-dimensional `Array<T>` from the mesh.
+  ///
+  /// @tparam T Array element type.
+  /// @param mesh Mesh from which to read.
+  /// @param name Name of the array.
+  /// @return The requested array.
+  ///
+  /// Throws `BoutException` if the array is not present.
   template <typename T>
-  Array<T> meshGetArray(Mesh* mesh, const std::string& name) {
+  Array<T> meshGetArray(Mesh* mesh, const std::string& name) const {
     Array<T> result;
     if (mesh->get(result, name) != 0) {
       throw BoutException("PetscOperators requires Array<int> '{}'", name);
@@ -180,5 +376,9 @@ private:
     return result;
   }
 
+  /// Mesh from which operator data are read.
+  Mesh* mesh;
+
+  /// Shared mapping used by all operators created from this mesh.
   PetscMappingPtr mapping;
 };
diff --git a/include/bout/petsclib.hxx b/include/bout/petsclib.hxx
index 41d7618fd2..637943bd12 100644
--- a/include/bout/petsclib.hxx
+++ b/include/bout/petsclib.hxx
@@ -1,31 +1,31 @@
 /*!************************************************************************
  * Provides access to the PETSc library, handling initialisation and
- * finalisation. 
+ * finalisation.
  *
  * Usage
  * -----
  *
  * #include <bout/petsclib.hxx>
- * 
+ *
  * class MyClass {
  *   public:
- *   
+ *
  *   private:
  *     PetscLib lib;
  * };
- * 
+ *
  *
  * This will then automatically initialise Petsc the first time an object
  * is created, and finalise it when the last object is destroyed.
  *
  * This header tries to workaround some annoying PETSc features, and
  * so it *must* be included before *any* PETSc header.
- * 
+ *
  **************************************************************************
- * Copyright 2012 - 2025 BOUT++ contributors
+ * Copyright 2012 - 2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -48,6 +48,8 @@
 
 #include "bout/build_defines.hxx"
 
+#include <string>
+
 class Options;
 
 #if BOUT_HAS_PETSC
@@ -66,7 +68,7 @@ class Options;
 #include "bout/boutexception.hxx"
 
 // NOLINTNEXTLINE(cppcoreguidelines-macro-usage)
-#define BOUT_DO_PETSC(cmd) PetscLib::assertIerr((cmd), #cmd)
+#define BOUT_DO_PETSC(cmd) PetscLib::assertIerr((cmd), #cmd, __FILE__, __LINE__)
 
 /*!
  * Handles initialisation and finalisation of PETSc library.
@@ -124,10 +126,17 @@ public:
   static void cleanup();
 
   static inline void assertIerr(PetscErrorCode ierr,
-                                const std::string& petsc_op = "PETSc operation") {
-    if (ierr != 0) {
-      throw BoutException("{:s} failed with {:d}", petsc_op, ierr);
+                                const std::string& petsc_op = "PETSc operation",
+                                const char* file = nullptr, int linenr = 0) {
+    if (PetscLikely(ierr == PETSC_SUCCESS)) {
+      return;
     }
+
+    const char* err_msg = nullptr;
+    PetscErrorMessage(ierr, &err_msg, nullptr);
+    throw BoutException("{:s} failed at {}:{} with {:d} [{}]", petsc_op,
+                        (file != nullptr) ? file : "unknown_file", linenr, ierr,
+                        (err_msg != nullptr) ? err_msg : "");
   }
 
   static BoutException SNESFailure(SNES& snes);
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 2d6c7743ec..8df2f4eeb7 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -6,9 +6,11 @@
 #include "bout/field3d.hxx"
 #include "bout/output.hxx"
 #include "bout/output_bout_types.hxx"
+#include "bout/petsclib.hxx"
 #include "bout/region.hxx"
 #include <memory>
 #include <string>
+#include <utility>
 
 Region<Ind3D> PetscMapping::create_region(const Field3D& cell_number) {
   Region<Ind3D>::RegionIndices indices;
@@ -27,7 +29,7 @@ Region<Ind3D> PetscMapping::create_region_xin(const Field3D& cell_number) {
     for (int i = 0; i < mesh->xstart; ++i) {
       for (int j = mesh->ystart; j <= mesh->yend; ++j) {
         for (int k = mesh->zstart; k <= mesh->zend; ++k) {
-          if (cell_number(i, j, k) > 0) {
+          if (cell_number(i, j, k) > -1) {
             xin_indices.push_back(cell_number.indexAt(i, j, k));
           }
         }
@@ -44,7 +46,7 @@ Region<Ind3D> PetscMapping::create_region_xout(const Field3D& cell_number) {
     for (int i = mesh->xend + 1; i < mesh->LocalNx; ++i) {
       for (int j = mesh->ystart; j <= mesh->yend; ++j) {
         for (int k = mesh->zstart; k <= mesh->zend; ++k) {
-          if (cell_number(i, j, k) > 0) {
+          if (cell_number(i, j, k) > -1) {
             xout_indices.push_back(cell_number.indexAt(i, j, k));
           }
         }
@@ -75,38 +77,45 @@ PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_ce
   // Maps PETSc row (or column) indices to the global indices used in
   // the mesh.  This is needed because the PETSc indices depend on the
   // number of processors.
-  MatCreate(BoutComm::get(), &mat_mesh_to_petsc);
-  MatSetSizes(mat_mesh_to_petsc, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE);
-  MatSetType(mat_mesh_to_petsc, MATMPIAIJ);
+  BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat_mesh_to_petsc));
+  BOUT_DO_PETSC(
+      MatSetSizes(mat_mesh_to_petsc, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
+  BOUT_DO_PETSC(MatSetType(mat_mesh_to_petsc, MATMPIAIJ));
   // Each row will have one non-zero entry, which could be in
   // either the "diagonal" or "off-diagonal" block.
-  MatMPIAIJSetPreallocation(mat_mesh_to_petsc, 1, nullptr, 1, nullptr);
+  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(mat_mesh_to_petsc, 1, nullptr, 1, nullptr));
 
   // Get the range of rows owned by this processor
-  MatGetOwnershipRange(mat_mesh_to_petsc, &row_start, &row_end);
+  BOUT_DO_PETSC(MatGetOwnershipRange(mat_mesh_to_petsc, &row_start, &row_end));
   output.write("Local row range: {} -> {}\n", row_start, row_end);
 
   // Iterate through regions in this order
   this->map([&](PetscInt row, PetscInt col) {
     // `row` is the PETSc index; `col` is the Mesh index
     const PetscScalar ONE = 1.0;
-    MatSetValues(mat_mesh_to_petsc, 1, &row, 1, &col, &ONE, INSERT_VALUES);
+    BOUT_DO_PETSC(MatSetValues(mat_mesh_to_petsc, 1, &row, 1, &col, &ONE, INSERT_VALUES));
   });
-  MatAssemblyBegin(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY);
-  MatAssemblyEnd(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY);
+  BOUT_DO_PETSC(MatAssemblyBegin(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY));
+  BOUT_DO_PETSC(MatAssemblyEnd(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY));
 
   // Transpose to map petsc indices to mesh indices
   MatTranspose(mat_mesh_to_petsc, MAT_INITIAL_MATRIX, &mat_petsc_to_mesh);
 }
 
+PetscMapping::~PetscMapping() {
+  MatDestroy(&this->mat_mesh_to_petsc);
+  MatDestroy(&this->mat_petsc_to_mesh);
+}
+
 PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
                              Array<BoutReal> weights)
-    : mapping(mapping) {
+    : mapping(std::move(mapping)) {
 
   Mat mat;
-  MatCreate(BoutComm::get(), &mat);
+  BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat));
+  BOUT_DO_PETSC(MatSetType(mat, MATMPIAIJ));
   int nlocal = mapping->size();
-  MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE);
+  BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
 
   mapping->map_evolving([&](PetscInt row, Ind3D, PetscInt mesh_index) {
     if (mesh_index >= rows.size()) {
@@ -115,51 +124,55 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
     // Get the range of indices into columns and weights
     int start_ind = rows[mesh_index];
     int end_ind = (mesh_index + 1 < rows.size()) ? rows[mesh_index + 1] : cols.size();
-    output.write("Mapping {} : {} -> {}\n", row, start_ind, end_ind);
 
-    MatSetValues(mat, 1, &row, end_ind - start_ind, &cols[start_ind], &weights[start_ind],
-                 INSERT_VALUES);
+    BOUT_DO_PETSC(MatSetValues(mat, 1, &row, end_ind - start_ind, &cols[start_ind],
+                               &weights[start_ind], INSERT_VALUES));
   });
-  MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);
-  MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);
+  BOUT_DO_PETSC(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY));
+  BOUT_DO_PETSC(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY));
 
   // Row indices are PETSc indices but columns are mesh indices
   // Multiply on the right by PetscToMesh.
-  MatMatMult(mat, mapping->getPetscToMesh(), MAT_INITIAL_MATRIX, PETSC_DETERMINE,
-             &this->mat_operator);
+  BOUT_DO_PETSC(MatMatMult(mat, mapping->getPetscToMesh(), MAT_INITIAL_MATRIX,
+                           PETSC_DETERMINE, &this->mat_operator));
+
+  // Allocate vectors for operator input and output
+  BOUT_DO_PETSC(VecCreate(BoutComm::get(), &this->rhs_vec));
+  BOUT_DO_PETSC(VecSetSizes(this->rhs_vec, this->mapping->size(), PETSC_DETERMINE));
+  BOUT_DO_PETSC(VecDuplicate(this->rhs_vec, &this->result_vec));
+}
+
+PetscOperator::~PetscOperator() {
+  MatDestroy(&this->mat_operator);
+  VecDestroy(&this->rhs_vec);
+  VecDestroy(&this->result_vec);
 }
 
 /// Perform operation
 Field3D PetscOperator::operator()(const Field3D& rhs) const {
-  Vec rhs_vec;
-  VecCreate(BoutComm::get(), &rhs_vec);
-  VecSetSizes(rhs_vec, this->mapping->size(), PETSC_DETERMINE);
-
   // Fill vec from rhs
   PetscScalar* x;
   // Copy rows from Field3D cells
-  VecGetArray(rhs_vec, &x);
+  BOUT_DO_PETSC(VecGetArray(this->rhs_vec, &x));
   mapping->map_local_field([&](PetscInt row, const Ind3D& i) { x[row] = rhs[i]; });
 
   // Copy Yup / Ydown values from boundaries
   const Field3D& yup = rhs.yup();
   mapping->map_local_yup([&](PetscInt row, const Ind3D& i) { x[row] = yup[i]; });
 
-  const Field3D& ydown = rhs.yup();
+  const Field3D& ydown = rhs.ydown();
   mapping->map_local_ydown([&](PetscInt row, const Ind3D& i) { x[row] = ydown[i]; });
-  VecRestoreArray(rhs_vec, &x);
+  BOUT_DO_PETSC(VecRestoreArray(this->rhs_vec, &x));
 
   // Perform Mat-Vec muliplication
-  Vec result_vec;
-  VecDuplicate(rhs_vec, &result_vec);
-  MatMult(this->mat_operator, rhs_vec, result_vec);
+  BOUT_DO_PETSC(MatMult(this->mat_operator, rhs_vec, result_vec));
 
   // Copy result_vec into a Field3D
-  Field3D result;
+  Field3D result{emptyFrom(rhs)}; // This allocates memory
   const PetscScalar* r;
-  VecGetArrayRead(result_vec, &r);
+  BOUT_DO_PETSC(VecGetArrayRead(result_vec, &r));
   mapping->map_local_field([&](PetscInt row, const Ind3D& i) { result[i] = r[row]; });
-  VecRestoreArrayRead(result_vec, &r);
+  BOUT_DO_PETSC(VecRestoreArrayRead(result_vec, &r));
 
   return result;
 }
@@ -168,8 +181,8 @@ Field3D PetscOperator::operator()(const Field3D& rhs) const {
 PetscOperator PetscOperator::operator*(const PetscOperator& rhs) const {
   ASSERT0(this->mapping == rhs.mapping);
   Mat mat;
-  MatMatMult(this->mat_operator, rhs.mat_operator, MAT_INITIAL_MATRIX, PETSC_DETERMINE,
-             &mat);
+  BOUT_DO_PETSC(MatMatMult(this->mat_operator, rhs.mat_operator, MAT_INITIAL_MATRIX,
+                           PETSC_DETERMINE, &mat));
   return PetscOperator(this->mapping, mat);
 }
 
@@ -177,8 +190,8 @@ PetscOperator PetscOperator::operator*(const PetscOperator& rhs) const {
 PetscOperator PetscOperator::operator+(const PetscOperator& rhs) const {
   ASSERT0(this->mapping == rhs.mapping);
   Mat mat;
-  MatDuplicate(mat_operator, MAT_COPY_VALUES, &mat);
-  MatAXPY(mat, 1.0, rhs.mat_operator, UNKNOWN_NONZERO_PATTERN);
+  BOUT_DO_PETSC(MatDuplicate(mat_operator, MAT_COPY_VALUES, &mat));
+  BOUT_DO_PETSC(MatAXPY(mat, 1.0, rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
   return PetscOperator(this->mapping, mat);
 }
 
@@ -186,12 +199,12 @@ PetscOperator PetscOperator::operator+(const PetscOperator& rhs) const {
 PetscOperator PetscOperator::operator-(const PetscOperator& rhs) const {
   ASSERT0(this->mapping == rhs.mapping);
   Mat mat;
-  MatDuplicate(mat_operator, MAT_COPY_VALUES, &mat);
-  MatAXPY(mat, -1.0, rhs.mat_operator, UNKNOWN_NONZERO_PATTERN);
+  BOUT_DO_PETSC(MatDuplicate(mat_operator, MAT_COPY_VALUES, &mat));
+  BOUT_DO_PETSC(MatAXPY(mat, -1.0, rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
   return PetscOperator(this->mapping, mat);
 }
 
-Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) {
+Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) const {
   Field3D result;
   if (mesh->get(result, name) != 0) {
     throw BoutException("PetscOperators requires field '{}'", name);
@@ -200,10 +213,10 @@ Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) {
 }
 
 PetscOperators::PetscOperators(Mesh* mesh)
-    : mapping(std::make_shared<const PetscMapping>(
-          meshGetField3D(mesh, "cell_number"),
-          meshGetField3D(mesh, "forward_cell_number"),
-          meshGetField3D(mesh, "backward_cell_number"))) {
+    : mesh(mesh), mapping(std::make_shared<const PetscMapping>(
+                      meshGetField3D(mesh, "cell_number"),
+                      meshGetField3D(mesh, "forward_cell_number"),
+                      meshGetField3D(mesh, "backward_cell_number"))) {
 
   int mesh_total_cells;
   if (mesh->get(mesh_total_cells, "total_cells") == 0) {
@@ -213,9 +226,10 @@ PetscOperators::PetscOperators(Mesh* mesh)
                           mesh_total_cells, mapping->size());
     }
   }
+}
 
-  // Read forward operator
-  PetscOperator forward(mapping, this->meshGetArray<int>(mesh, "forward_rows"),
-                        this->meshGetArray<int>(mesh, "forward_columns"),
-                        this->meshGetArray<BoutReal>(mesh, "forward_weights"));
+PetscOperator PetscOperators::get(const std::string& name) const {
+  return PetscOperator(this->mapping, this->meshGetArray<int>(this->mesh, name + "_rows"),
+                       this->meshGetArray<int>(this->mesh, name + "_columns"),
+                       this->meshGetArray<BoutReal>(this->mesh, name + "_weights"));
 }

From e8f562f5ff31fa4a79b12cfb7525ca32bd6740a1 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 13 Mar 2026 22:51:32 -0700
Subject: [PATCH 0886/1827] Array: Add static fromValues(initializer_list)
 method

Alternative to initializer_list constructor that avoids
confusion with e.g. `Array{2}` : Is it an array of size 2,
or an array of size 1 containing value 2?

`std::vector` uses `vector(2)` means size 2; `vector{2}`
means value 2.

With this commit, both `Array{2}` and `Array(2)` mean size 2;
`Array<T>::fromValues({2})` means size 1, value 2.  It's more verbose
but less prone to typos.
---
 include/bout/array.hxx                       | 20 ++++++++++++--
 src/invert/fft_fftw.cxx                      | 15 ++++++----
 src/solver/impls/imex-bdf2/imex-bdf2.cxx     | 25 ++++++++---------
 tests/unit/include/bout/test_array.cxx       | 29 ++++++++++++--------
 tests/unit/include/test_cyclic_reduction.cxx | 13 +++++----
 tests/unit/invert/test_fft.cxx               |  8 +++---
 6 files changed, 66 insertions(+), 44 deletions(-)

diff --git a/include/bout/array.hxx b/include/bout/array.hxx
index 82677fd38a..d8ce207dac 100644
--- a/include/bout/array.hxx
+++ b/include/bout/array.hxx
@@ -27,6 +27,7 @@
 #define BOUT_ARRAY_H
 
 #include <algorithm>
+#include <initializer_list>
 #include <map>
 #include <memory>
 #include <tuple>
@@ -187,9 +188,22 @@ public:
   Array() noexcept : ptr(nullptr) {}
 
   /*!
-   * Create an array of given length
+   * Create an array of given length.
    */
-  Array(size_type len) { ptr = get(len); }
+  Array(size_type len) : ptr(get(len)) {}
+
+  /*!
+   * Create an array with initializer list.
+   * This is explicit to avoid confusion with (size_type) constructor.
+   */
+  static Array fromValues(std::initializer_list<T> init) {
+    if (init.size() == 0) {
+      return Array();
+    }
+    Array array(init.size());
+    std::copy(init.begin(), init.end(), array.begin());
+    return array;
+  }
 
   /*!
    * Destructor. Releases the underlying dataBlock
@@ -199,7 +213,7 @@ public:
   /*!
    * Copy constructor
    */
-  Array(const Array& other) noexcept { ptr = other.ptr; }
+  Array(const Array& other) noexcept : ptr(other.ptr) {}
 
   /*!
    * Assignment operator
diff --git a/src/invert/fft_fftw.cxx b/src/invert/fft_fftw.cxx
index 2c633da6d5..2ada5bc98a 100644
--- a/src/invert/fft_fftw.cxx
+++ b/src/invert/fft_fftw.cxx
@@ -4,9 +4,9 @@
  * \brief FFT routines using external libraries
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -25,9 +25,12 @@
  *
  **************************************************************************/
 
-#include "bout/build_defines.hxx"
-
+#include <bout/array.hxx>
+#include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
+#include <bout/build_defines.hxx>
 #include <bout/coordinates.hxx>
+#include <bout/dcomplex.hxx>
 #include <bout/fft.hxx>
 #include <bout/globals.hxx>
 #include <bout/mesh.hxx>
@@ -518,7 +521,7 @@ Array<dcomplex> rfft(const Array<BoutReal>& in) {
   ASSERT1(!in.empty());
 
   int size{in.size()};
-  Array<dcomplex> out{(size / 2) + 1};
+  Array<dcomplex> out((size / 2) + 1);
 
   bout::fft::rfft(in.begin(), size, out.begin());
   return out;
@@ -528,7 +531,7 @@ Array<BoutReal> irfft(const Array<dcomplex>& in, int length) {
   ASSERT1(!in.empty());
   ASSERT1(in.size() == (length / 2) + 1);
 
-  Array<BoutReal> out{length};
+  Array<BoutReal> out(length);
 
   bout::fft::irfft(in.begin(), length, out.begin());
   return out;
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
index 4ccf27981b..56d21c91d0 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
@@ -4,11 +4,15 @@
 
 #include "imex-bdf2.hxx"
 
+#include <bout/array.hxx>
 #include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/mesh.hxx>
+#include <bout/options.hxx>
 #include <bout/petsc_interface.hxx>
+#include <bout/solver.hxx>
 #include <bout/utils.hxx>
 
 #include <cmath>
@@ -119,12 +123,9 @@ static PetscErrorCode FormFunctionForColoring(void* UNUSED(snes), Vec x, Vec f,
 }
 
 static PetscErrorCode imexbdf2PCapply(PC pc, Vec x, Vec y) {
-  int ierr;
-
   // Get the context
   IMEXBDF2* s;
-  ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&s));
-  CHKERRQ(ierr);
+  PetscCall(PCShellGetContext(pc, reinterpret_cast<void**>(&s)));
 
   PetscFunctionReturn(s->precon(x, y));
 }
@@ -197,8 +198,8 @@ int IMEXBDF2::init() {
   // Allocate memory and initialise structures
   u.reallocate(nlocal);
   for (int i = 0; i < maxOrder; i++) {
-    uV.emplace_back(Array<BoutReal>{nlocal});
-    fV.emplace_back(Array<BoutReal>{nlocal});
+    uV.emplace_back(Array<BoutReal>(nlocal));
+    fV.emplace_back(Array<BoutReal>(nlocal));
     timesteps.push_back(timestep);
     uFac.push_back(0.0);
     fFac.push_back(0.0);
@@ -220,16 +221,12 @@ int IMEXBDF2::init() {
   }
 
   // Initialise PETSc components
-  int ierr;
 
   // Vectors
-  ierr = VecCreate(BoutComm::get(), &snes_x);
-  CHKERRQ(ierr);
-  ierr = VecSetSizes(snes_x, nlocal, PETSC_DECIDE);
-  CHKERRQ(ierr);
-  ierr = VecSetFromOptions(snes_x);
-  CHKERRQ(ierr);
-  VecDuplicate(snes_x, &snes_f);
+  PetscCall(VecCreate(BoutComm::get(), &snes_x));
+  PetscCall(VecSetSizes(snes_x, nlocal, PETSC_DECIDE));
+  PetscCall(VecSetFromOptions(snes_x));
+  PetscCall(VecDuplicate(snes_x, &snes_f));
 
   // The SNES solver object(s)
   constructSNES(&snes);
diff --git a/tests/unit/include/bout/test_array.cxx b/tests/unit/include/bout/test_array.cxx
index 21be6fe8a5..4efd968f57 100644
--- a/tests/unit/include/bout/test_array.cxx
+++ b/tests/unit/include/bout/test_array.cxx
@@ -1,9 +1,7 @@
 #include "gtest/gtest.h"
 
 #include "bout/array.hxx"
-#include "bout/boutexception.hxx"
 
-#include <iostream>
 #include <numeric>
 
 // In order to keep these tests independent, they need to use
@@ -19,7 +17,7 @@ class ArrayTest : public ::testing::Test {
 };
 
 TEST_F(ArrayTest, ArraySize) {
-  Array<double> a(5);
+  const Array<double> a(5);
 
   ASSERT_FALSE(a.empty());
   EXPECT_EQ(a.size(), 5);
@@ -36,7 +34,7 @@ TEST_F(ArrayTest, ArrayValues) {
 }
 
 TEST_F(ArrayTest, CopyArrayConstructor) {
-  Array<double> a{15};
+  Array<double> a(15);
 
   std::iota(a.begin(), a.end(), 0);
 
@@ -53,7 +51,7 @@ TEST_F(ArrayTest, CopyArrayConstructor) {
 }
 
 TEST_F(ArrayTest, CopyArrayOperator) {
-  Array<double> a{15};
+  Array<double> a(15);
 
   std::iota(a.begin(), a.end(), 0);
 
@@ -71,7 +69,7 @@ TEST_F(ArrayTest, CopyArrayOperator) {
 }
 
 TEST_F(ArrayTest, CopyArrayNonMemberFunction) {
-  Array<double> a{15};
+  Array<double> a(15);
 
   std::iota(a.begin(), a.end(), 0);
 
@@ -86,11 +84,11 @@ TEST_F(ArrayTest, CopyArrayNonMemberFunction) {
 }
 
 TEST_F(ArrayTest, SwapArray) {
-  Array<double> a{15};
+  Array<double> a(15);
 
   std::iota(a.begin(), a.end(), 0);
 
-  Array<double> b{10};
+  Array<double> b(10);
 
   std::iota(b.begin(), b.end(), 5);
 
@@ -108,7 +106,7 @@ TEST_F(ArrayTest, SwapArray) {
 }
 
 TEST_F(ArrayTest, MoveArrayConstructor) {
-  Array<double> a{15};
+  Array<double> a(15);
 
   std::iota(a.begin(), a.end(), 0);
 
@@ -123,7 +121,7 @@ TEST_F(ArrayTest, MoveArrayConstructor) {
 }
 
 TEST_F(ArrayTest, Reallocate) {
-  Array<double> a{};
+  Array<double> a;
 
   ASSERT_TRUE(a.empty());
 
@@ -235,7 +233,7 @@ TEST_F(ArrayTest, RetrieveData) {
 
 TEST_F(ArrayTest, Assignment) {
   Array<double> a(35);
-  Array<double> b(35);
+  const Array<double> b(35);
   // Assign
   a = b;
 
@@ -251,3 +249,12 @@ TEST_F(ArrayTest, OutOfBoundsThrow) {
   EXPECT_THROW(a[-1] = 1.0, BoutException);
 }
 #endif
+
+TEST_F(ArrayTest, FromValues) {
+  const auto a = Array<int>::fromValues({3, 1, 4, 2});
+  ASSERT_EQ(4, a.size());
+  EXPECT_EQ(3, a[0]);
+  EXPECT_EQ(1, a[1]);
+  EXPECT_EQ(4, a[2]);
+  EXPECT_EQ(2, a[3]);
+}
diff --git a/tests/unit/include/test_cyclic_reduction.cxx b/tests/unit/include/test_cyclic_reduction.cxx
index e057c41bef..5eb9acff0a 100644
--- a/tests/unit/include/test_cyclic_reduction.cxx
+++ b/tests/unit/include/test_cyclic_reduction.cxx
@@ -2,6 +2,7 @@
 
 #include "test_extras.hxx"
 #include "bout/array.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/cyclic_reduction.hxx"
 
@@ -19,7 +20,7 @@ Array<BoutReal> makeArrayFromVector(const std::vector<BoutReal>& values) {
   using std::begin;
   using std::end;
 
-  Array<BoutReal> array{static_cast<Array<BoutReal>::size_type>(values.size())};
+  Array<BoutReal> array(static_cast<Array<BoutReal>::size_type>(values.size()));
   std::copy(begin(values), end(values), begin(array));
   return array;
 }
@@ -28,9 +29,9 @@ Matrix<BoutReal> makeMatrixFromVector(const std::vector<std::vector<BoutReal>>&
   using std::begin;
   using std::end;
 
-  Matrix<BoutReal> matrix{static_cast<Matrix<BoutReal>::size_type>(values.size()),
-                          static_cast<Matrix<BoutReal>::size_type>(values[0].size())};
-  auto start = begin(matrix);
+  Matrix<BoutReal> matrix(static_cast<Matrix<BoutReal>::size_type>(values.size()),
+                          static_cast<Matrix<BoutReal>::size_type>(values[0].size()));
+  auto* start = begin(matrix);
   for (const auto& sub_values : values) {
     start = std::copy(begin(sub_values), end(sub_values), start);
   }
@@ -48,7 +49,7 @@ TEST(CyclicReduction, SerialSolveSingleArray) {
   reduce.setCoefs(a, b, c);
 
   auto rhs = makeArrayFromVector({0., 1., 2., 2., 3.});
-  Array<BoutReal> x{reduction_size};
+  Array<BoutReal> x(reduction_size);
 
   reduce.solve(rhs, x);
 
@@ -70,7 +71,7 @@ TEST(CyclicReduction, SerialSolveSingleMatrix) {
   reduce.setCoefs(a, b, c);
 
   auto rhs = makeMatrixFromVector({{0., 1., 2., 2., 3.}});
-  Matrix<BoutReal> x{1, reduction_size};
+  Matrix<BoutReal> x(1, reduction_size);
 
   reduce.solve(rhs, x);
 
diff --git a/tests/unit/invert/test_fft.cxx b/tests/unit/invert/test_fft.cxx
index 1fb30c5eb7..36b344dbb1 100644
--- a/tests/unit/invert/test_fft.cxx
+++ b/tests/unit/invert/test_fft.cxx
@@ -4,12 +4,12 @@
 
 #include "test_extras.hxx"
 #include "bout/array.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/constants.hxx"
 #include "bout/dcomplex.hxx"
 #include "bout/fft.hxx"
 
 #include <algorithm>
-#include <iostream>
 #include <numeric>
 
 #if BOUT_HAS_FFTW
@@ -19,7 +19,7 @@ class FFTTest : public ::testing::TestWithParam<int> {
       : size(GetParam()), nmodes((size / 2) + 1), real_signal(size), fft_signal(nmodes) {
 
     // Make grid indices from [0, size - 1]
-    Array<BoutReal> indices{size};
+    Array<BoutReal> indices(size);
     std::iota(indices.begin(), indices.end(), 0.0);
 
     // Calculate sin(x) + cos(2x) on [0, 2pi]
@@ -48,7 +48,7 @@ INSTANTIATE_TEST_SUITE_P(FFTEvenAndOddSamples, FFTTest, ::testing::Values(8, 9))
 
 TEST_P(FFTTest, rfft) {
 
-  Array<dcomplex> output{nmodes};
+  Array<dcomplex> output(nmodes);
 
   // Compute forward real FFT
   rfft(real_signal.begin(), size, output.begin());
@@ -63,7 +63,7 @@ TEST_P(FFTTest, rfft) {
 
 TEST_P(FFTTest, irfft) {
 
-  Array<BoutReal> output{size};
+  Array<BoutReal> output(size);
 
   // Compute inverse real FFT
   irfft(fft_signal.begin(), size, output.begin());

From 8ba9503807e2f526912356404621281b97b259cb Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 14 Mar 2026 13:26:30 -0700
Subject: [PATCH 0887/1827] PetscOperators: mapping fixes and unit tests

Some care needed with yup/down and yp/ym indices.
---
 include/bout/petsc_operators.hxx         | 30 ++++++---
 src/mesh/petsc_operators.cxx             | 60 ++++++++++++-----
 tests/unit/mesh/test_petsc_operators.cxx | 85 +++++++++++++++++++++++-
 3 files changed, 147 insertions(+), 28 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 3f4d0a596e..0b5c2851cb 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -10,6 +10,7 @@
 ///
 
 #include "bout/array.hxx"
+#include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
@@ -127,7 +128,7 @@ public:
   template <typename Function>
   void map(Function func) const {
     const std::vector<std::reference_wrapper<const Region<Ind3D>>> regions = {
-        evolving_region, xin_region, xout_region, yup_region, ydown_region};
+        evolving_region, xin_region, xout_region};
     PetscInt row = row_start;
     for (const auto& region : regions) {
       BOUT_FOR_SERIAL(i, region.get()) {
@@ -135,6 +136,15 @@ public:
         ++row;
       }
     }
+    BOUT_FOR_SERIAL(i, yup_region) {
+      func(row, ROUND(forward_cell_number[i]));
+      ++row;
+    }
+    BOUT_FOR_SERIAL(i, ydown_region) {
+      func(row, ROUND(backward_cell_number[i]));
+      ++row;
+    }
+    ASSERT0(row == row_end);
   }
 
   /// Iterate over locally stored entries packed from the main `Field3D`.
@@ -169,7 +179,7 @@ public:
   void map_local_yup(Function func) const {
     PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size();
     BOUT_FOR_SERIAL(i, yup_region) {
-      func(row, i);
+      func(row, i.yp());
       ++row;
     }
   }
@@ -185,7 +195,7 @@ public:
     PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size()
                    + yup_region.size();
     BOUT_FOR_SERIAL(i, ydown_region) {
-      func(row, i);
+      func(row, i.ym());
       ++row;
     }
   }
@@ -201,6 +211,8 @@ private:
 
   /// Mesh-global numbering for cells stored on this rank.
   Field3D cell_number;
+  Field3D forward_cell_number;
+  Field3D backward_cell_number;
 
   /// Evolving cells in the main domain.
   Region<Ind3D> evolving_region;
@@ -301,12 +313,9 @@ private:
   /// This constructor is used internally when creating operators from
   /// PETSc matrix algebra such as composition, addition, or subtraction.
   PetscOperator(PetscMappingPtr mapping, Mat mat)
-      : mapping(std::move(mapping)), mat_operator(mat) {
-    // Allocate working vectors
-    VecCreate(BoutComm::get(), &this->rhs_vec);
-    VecSetSizes(this->rhs_vec, this->mapping->size(), PETSC_DETERMINE);
-    VecDuplicate(this->rhs_vec, &this->result_vec);
-  }
+      : mapping(std::move(mapping)), mat_operator(mat),
+        rhs_vec(createVec(this->mapping->size())),
+        result_vec(createVec(this->mapping->size())) {}
 
   /// Shared mapping between mesh and PETSc numbering.
   PetscMappingPtr mapping;
@@ -319,6 +328,9 @@ private:
 
   /// Work vector holding the packed result.
   Vec result_vec;
+
+  // Allocate MPI vector
+  static Vec createVec(PetscInt local_size);
 };
 
 /// Collection of PETSc operators read from a mesh.
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 8df2f4eeb7..2cc66b87f8 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -58,7 +58,9 @@ Region<Ind3D> PetscMapping::create_region_xout(const Field3D& cell_number) {
 
 PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_cell_number,
                            const Field3D& backward_cell_number)
-    : cell_number(cell_number), evolving_region(create_region(cell_number)),
+    : cell_number(cell_number), forward_cell_number(forward_cell_number),
+      backward_cell_number(backward_cell_number),
+      evolving_region(create_region(cell_number)),
       xin_region(create_region_xin(cell_number)),
       xout_region(create_region_xout(cell_number)),
       yup_region(create_region(forward_cell_number)),
@@ -109,22 +111,36 @@ PetscMapping::~PetscMapping() {
 
 PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
                              Array<BoutReal> weights)
-    : mapping(std::move(mapping)) {
+    : mapping(std::move(mapping)), rhs_vec(createVec(this->mapping->size())),
+      result_vec(createVec(this->mapping->size())) {
 
-  Mat mat;
+  output.write("PetscOperator Array sizes {} {} {}\n", rows.size(), cols.size(),
+               weights.size());
+
+  Mat mat{nullptr};
   BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat));
   BOUT_DO_PETSC(MatSetType(mat, MATMPIAIJ));
-  int nlocal = mapping->size();
+  int nlocal = this->mapping->size();
   BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
 
-  mapping->map_evolving([&](PetscInt row, Ind3D, PetscInt mesh_index) {
+  this->mapping->map_evolving([&](PetscInt row, Ind3D, PetscInt mesh_index) {
     if (mesh_index >= rows.size()) {
       return; // No weights -> skip
     }
     // Get the range of indices into columns and weights
     int start_ind = rows[mesh_index];
-    int end_ind = (mesh_index + 1 < rows.size()) ? rows[mesh_index + 1] : cols.size();
-
+    if (start_ind < 0) {
+      return; // No entries
+    }
+    int end_ind = cols.size(); // End of the columns array
+    for (int i = mesh_index + 1; i < rows.size(); ++i) {
+      // rows[i] can be -1 if no weights
+      if (rows[i] > -1) {
+        // This is the next entry in the columns / weights array
+        end_ind = rows[i];
+        break;
+      }
+    }
     BOUT_DO_PETSC(MatSetValues(mat, 1, &row, end_ind - start_ind, &cols[start_ind],
                                &weights[start_ind], INSERT_VALUES));
   });
@@ -133,13 +149,18 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
 
   // Row indices are PETSc indices but columns are mesh indices
   // Multiply on the right by PetscToMesh.
-  BOUT_DO_PETSC(MatMatMult(mat, mapping->getPetscToMesh(), MAT_INITIAL_MATRIX,
+  BOUT_DO_PETSC(MatMatMult(mat, this->mapping->getPetscToMesh(), MAT_INITIAL_MATRIX,
                            PETSC_DETERMINE, &this->mat_operator));
+  // Destroy temporary matrix
+  BOUT_DO_PETSC(MatDestroy(&mat));
+}
 
-  // Allocate vectors for operator input and output
-  BOUT_DO_PETSC(VecCreate(BoutComm::get(), &this->rhs_vec));
-  BOUT_DO_PETSC(VecSetSizes(this->rhs_vec, this->mapping->size(), PETSC_DETERMINE));
-  BOUT_DO_PETSC(VecDuplicate(this->rhs_vec, &this->result_vec));
+Vec PetscOperator::createVec(PetscInt local_size) {
+  Vec vec{nullptr};
+  BOUT_DO_PETSC(VecCreate(BoutComm::get(), &vec));
+  BOUT_DO_PETSC(VecSetType(vec, VECMPI));
+  BOUT_DO_PETSC(VecSetSizes(vec, local_size, PETSC_DETERMINE));
+  return vec;
 }
 
 PetscOperator::~PetscOperator() {
@@ -150,18 +171,24 @@ PetscOperator::~PetscOperator() {
 
 /// Perform operation
 Field3D PetscOperator::operator()(const Field3D& rhs) const {
+  ASSERT1(rhs.hasParallelSlices());
+  ASSERT1(rhs.yup().isAllocated());
+  ASSERT1(rhs.ydown().isAllocated());
+
   // Fill vec from rhs
   PetscScalar* x;
   // Copy rows from Field3D cells
   BOUT_DO_PETSC(VecGetArray(this->rhs_vec, &x));
-  mapping->map_local_field([&](PetscInt row, const Ind3D& i) { x[row] = rhs[i]; });
+  this->mapping->map_local_field([&](PetscInt row, const Ind3D& i) { x[row] = rhs[i]; });
 
   // Copy Yup / Ydown values from boundaries
   const Field3D& yup = rhs.yup();
-  mapping->map_local_yup([&](PetscInt row, const Ind3D& i) { x[row] = yup[i]; });
+  this->mapping->map_local_yup([&](PetscInt row, const Ind3D& i) { x[row] = yup[i]; });
 
   const Field3D& ydown = rhs.ydown();
-  mapping->map_local_ydown([&](PetscInt row, const Ind3D& i) { x[row] = ydown[i]; });
+  this->mapping->map_local_ydown(
+      [&](PetscInt row, const Ind3D& i) { x[row] = ydown[i]; });
+
   BOUT_DO_PETSC(VecRestoreArray(this->rhs_vec, &x));
 
   // Perform Mat-Vec muliplication
@@ -171,7 +198,8 @@ Field3D PetscOperator::operator()(const Field3D& rhs) const {
   Field3D result{emptyFrom(rhs)}; // This allocates memory
   const PetscScalar* r;
   BOUT_DO_PETSC(VecGetArrayRead(result_vec, &r));
-  mapping->map_local_field([&](PetscInt row, const Ind3D& i) { result[i] = r[row]; });
+  this->mapping->map_local_field(
+      [&](PetscInt row, const Ind3D& i) { result[i] = r[row]; });
   BOUT_DO_PETSC(VecRestoreArrayRead(result_vec, &r));
 
   return result;
diff --git a/tests/unit/mesh/test_petsc_operators.cxx b/tests/unit/mesh/test_petsc_operators.cxx
index b33d41a7b1..5528e8b5e1 100644
--- a/tests/unit/mesh/test_petsc_operators.cxx
+++ b/tests/unit/mesh/test_petsc_operators.cxx
@@ -1,5 +1,7 @@
 #include "gtest/gtest.h"
 
+#include "bout/array.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/output.hxx"
 #include "bout/output_bout_types.hxx"
 #include "bout/petsc_operators.hxx"
@@ -8,6 +10,8 @@
 #include "fake_mesh_fixture.hxx"
 #include "test_extras.hxx"
 
+#include <memory>
+
 // Reuse the "standard" fixture for FakeMesh
 using PetscMappingTest = FakeMeshFixture;
 
@@ -54,9 +58,9 @@ TEST_F(PetscMappingTest, mapping) {
   Field3D cell_number{-1.0}; // No cells >= 0
 
   // Note: 1 boundary cell in X and Y
-  cell_number(0, 0, 0) = 0; // Corner
-  cell_number(1, 1, 0) = 1; // In domain
-  cell_number(0, 1, 1) = 2; // Xin boundary
+  cell_number(0, 0, 0) = 2; // Corner
+  cell_number(1, 1, 0) = 0; // In domain
+  cell_number(0, 1, 1) = 1; // Xin boundary
 
   const Field3D forward_cell_number{-1.0};
   const Field3D backward_cell_number{-1.0};
@@ -66,3 +70,78 @@ TEST_F(PetscMappingTest, mapping) {
   // Two cells: one evolving and one in xin
   ASSERT_EQ(2, mapping.size());
 }
+
+using PetscOperatorTest = FakeMeshFixture;
+
+TEST_F(PetscOperatorTest, identity) {
+  Field3D cell_number{-1.0};
+  const Field3D forward_cell_number{-1.0};
+  const Field3D backward_cell_number{-1.0};
+
+  // Three cells active
+  cell_number(1, 1, 0) = 0;
+  cell_number(1, 2, 0) = 1;
+  cell_number(1, 2, 1) = 2;
+
+  auto mapping = std::make_shared<const PetscMapping>(cell_number, forward_cell_number,
+                                                      backward_cell_number);
+  ASSERT_EQ(3, mapping->size());
+
+  const auto rows = Array<int>::fromValues({0, 1, 2});
+  const auto cols = Array<int>::fromValues({0, 1, 2});
+  const auto weights = Array<BoutReal>::fromValues({1.0, 1.0, 1.0});
+
+  const PetscOperator identity(mapping, rows, cols, weights);
+
+  Field3D value{0.0};
+  value(1, 1, 0) = 10;
+  value(1, 2, 0) = 21;
+  value(1, 2, 1) = 32;
+  value.splitParallelSlices();
+  value.yup() = -1.0;
+  value.ydown() = -1.0;
+
+  const Field3D result = identity(value);
+
+  EXPECT_EQ(10, result(1, 1, 0));
+  EXPECT_EQ(21, result(1, 2, 0));
+  EXPECT_EQ(32, result(1, 2, 1));
+}
+
+TEST_F(PetscOperatorTest, identity_yupdown) {
+  Field3D cell_number{-1.0};
+  Field3D forward_cell_number{-1.0};
+  Field3D backward_cell_number{-1.0};
+
+  // Three cells active
+  cell_number(1, 1, 0) = 0;
+  cell_number(1, 2, 0) = 1;
+  cell_number(1, 2, 1) = 2;
+
+  forward_cell_number(1, 2, 0) = 3;
+  backward_cell_number(1, 1, 2) = 4;
+
+  auto mapping = std::make_shared<const PetscMapping>(cell_number, forward_cell_number,
+                                                      backward_cell_number);
+  ASSERT_EQ(5, mapping->size());
+
+  const auto rows = Array<int>::fromValues({0, 1, 2});
+  const auto cols = Array<int>::fromValues({0, 1, 2});
+  const auto weights = Array<BoutReal>::fromValues({1.0, 1.0, 1.0});
+
+  const PetscOperator identity(mapping, rows, cols, weights);
+
+  Field3D value{0.0};
+  value(1, 1, 0) = 10;
+  value(1, 2, 0) = 21;
+  value(1, 2, 1) = 32;
+  value.splitParallelSlices();
+  value.yup() = -1.0;
+  value.ydown() = -1.0;
+
+  const Field3D result = identity(value);
+
+  EXPECT_EQ(10, result(1, 1, 0));
+  EXPECT_EQ(21, result(1, 2, 0));
+  EXPECT_EQ(32, result(1, 2, 1));
+}

From 16e2768061dd48700381433d5902af810b6d4a11 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sun, 15 Mar 2026 15:02:48 -0700
Subject: [PATCH 0888/1827] PetscOperator: Add diagonal and transpose methods

`diagonal` creates diagonal matrices from Field3D.

`transpose` creates a new matrix that is a transpose
of a PetscOperator. This is useful for converting
gradients into divergences.
---
 include/bout/petsc_operators.hxx | 15 +++++++
 src/mesh/petsc_operators.cxx     | 70 +++++++++++++++++++++++---------
 2 files changed, 65 insertions(+), 20 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 0b5c2851cb..046057bc5f 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -270,6 +270,9 @@ public:
   /// Destroy the PETSc matrix and working vectors owned by this operator.
   ~PetscOperator();
 
+  /// Create a diagonal operator
+  static PetscOperator diagonal(PetscMappingPtr mapping, const Field3D& f);
+
   /// Apply the operator to a field.
   ///
   /// @param rhs Input field, including any required `yup` and `ydown`
@@ -304,6 +307,9 @@ public:
   /// Both operators must use compatible mappings.
   PetscOperator operator-(const PetscOperator& rhs) const;
 
+  /// Calculate transpose as a new matrix
+  PetscOperator transpose() const;
+
 private:
   /// Construct directly from an existing PETSc matrix.
   ///
@@ -329,6 +335,10 @@ private:
   /// Work vector holding the packed result.
   Vec result_vec;
 
+  /// Copy contents of f, f.yup() and f.ydown() into vec.
+  /// Assumes that vec has already been allocated.
+  static void copyToVec(PetscMappingPtr mapping, const Field3D& f, Vec vec);
+
   // Allocate MPI vector
   static Vec createVec(PetscInt local_size);
 };
@@ -361,6 +371,11 @@ public:
   /// Throws `BoutException` if any of the required arrays are missing.
   PetscOperator get(const std::string& name) const;
 
+  /// Create a diagonal operator
+  PetscOperator diagonal(const Field3D& f) const {
+    return PetscOperator::diagonal(mapping, f);
+  }
+
 private:
   /// Read a `Field3D` from the mesh.
   ///
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 2cc66b87f8..89cf1a9503 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -120,7 +120,7 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
   Mat mat{nullptr};
   BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat));
   BOUT_DO_PETSC(MatSetType(mat, MATMPIAIJ));
-  int nlocal = this->mapping->size();
+  const int nlocal = this->mapping->size();
   BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
 
   this->mapping->map_evolving([&](PetscInt row, Ind3D, PetscInt mesh_index) {
@@ -128,7 +128,7 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
       return; // No weights -> skip
     }
     // Get the range of indices into columns and weights
-    int start_ind = rows[mesh_index];
+    const int start_ind = rows[mesh_index];
     if (start_ind < 0) {
       return; // No entries
     }
@@ -155,6 +155,26 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
   BOUT_DO_PETSC(MatDestroy(&mat));
 }
 
+void PetscOperator::copyToVec(PetscMappingPtr mapping, const Field3D& f, Vec vec) {
+  ASSERT1(f.hasParallelSlices());
+  ASSERT1(f.yup().isAllocated());
+  ASSERT1(f.ydown().isAllocated());
+
+  PetscScalar* x{nullptr};
+  // Copy rows from Field3D cells
+  BOUT_DO_PETSC(VecGetArray(vec, &x));
+  mapping->map_local_field([&](PetscInt row, const Ind3D& i) { x[row] = f[i]; });
+
+  // Copy Yup / Ydown values from boundaries
+  const Field3D& yup = f.yup();
+  mapping->map_local_yup([&](PetscInt row, const Ind3D& i) { x[row] = yup[i]; });
+
+  const Field3D& ydown = f.ydown();
+  mapping->map_local_ydown([&](PetscInt row, const Ind3D& i) { x[row] = ydown[i]; });
+
+  BOUT_DO_PETSC(VecRestoreArray(vec, &x));
+}
+
 Vec PetscOperator::createVec(PetscInt local_size) {
   Vec vec{nullptr};
   BOUT_DO_PETSC(VecCreate(BoutComm::get(), &vec));
@@ -169,34 +189,38 @@ PetscOperator::~PetscOperator() {
   VecDestroy(&this->result_vec);
 }
 
-/// Perform operation
-Field3D PetscOperator::operator()(const Field3D& rhs) const {
-  ASSERT1(rhs.hasParallelSlices());
-  ASSERT1(rhs.yup().isAllocated());
-  ASSERT1(rhs.ydown().isAllocated());
+PetscOperator PetscOperator::diagonal(PetscMappingPtr mapping, const Field3D& f) {
+  Vec diag{createVec(mapping->size())};
+  copyToVec(mapping, f, diag);
 
-  // Fill vec from rhs
-  PetscScalar* x;
-  // Copy rows from Field3D cells
-  BOUT_DO_PETSC(VecGetArray(this->rhs_vec, &x));
-  this->mapping->map_local_field([&](PetscInt row, const Ind3D& i) { x[row] = rhs[i]; });
+  Mat mat{nullptr};
+  // Note: MatMatMult with diagonal and mpiaij not supported
+  // -> Create MPIAIJ
+  BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat));
+  BOUT_DO_PETSC(MatSetType(mat, MATMPIAIJ));
+  const int nlocal = mapping->size();
+  BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
+  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(mat, 1, nullptr, 0, nullptr));
+  BOUT_DO_PETSC(MatDiagonalSet(mat, diag, INSERT_VALUES));
+  BOUT_DO_PETSC(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY));
+  BOUT_DO_PETSC(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY));
 
-  // Copy Yup / Ydown values from boundaries
-  const Field3D& yup = rhs.yup();
-  this->mapping->map_local_yup([&](PetscInt row, const Ind3D& i) { x[row] = yup[i]; });
+  BOUT_DO_PETSC(VecDestroy(&diag));
 
-  const Field3D& ydown = rhs.ydown();
-  this->mapping->map_local_ydown(
-      [&](PetscInt row, const Ind3D& i) { x[row] = ydown[i]; });
+  return PetscOperator(std::move(mapping), mat);
+}
 
-  BOUT_DO_PETSC(VecRestoreArray(this->rhs_vec, &x));
+/// Perform operation
+Field3D PetscOperator::operator()(const Field3D& rhs) const {
+  // Fill vec from rhs
+  copyToVec(this->mapping, rhs, this->rhs_vec);
 
   // Perform Mat-Vec muliplication
   BOUT_DO_PETSC(MatMult(this->mat_operator, rhs_vec, result_vec));
 
   // Copy result_vec into a Field3D
   Field3D result{emptyFrom(rhs)}; // This allocates memory
-  const PetscScalar* r;
+  const PetscScalar* r{nullptr};
   BOUT_DO_PETSC(VecGetArrayRead(result_vec, &r));
   this->mapping->map_local_field(
       [&](PetscInt row, const Ind3D& i) { result[i] = r[row]; });
@@ -232,6 +256,12 @@ PetscOperator PetscOperator::operator-(const PetscOperator& rhs) const {
   return PetscOperator(this->mapping, mat);
 }
 
+PetscOperator PetscOperator::transpose() const {
+  Mat mat{nullptr};
+  BOUT_DO_PETSC(MatTranspose(this->mat_operator, MAT_INITIAL_MATRIX, &mat));
+  return PetscOperator(this->mapping, mat);
+}
+
 Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) const {
   Field3D result;
   if (mesh->get(result, name) != 0) {

From 6b66188168a953c0be07df7b67a9015e0ff64d1b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 16 Mar 2026 09:07:47 +0100
Subject: [PATCH 0889/1827] Cleanup code

---
 include/bout/coordinates.hxx |  1 +
 src/mesh/coordinates.cxx     | 19 +++++++++----------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 85aac3de6c..da22fdd126 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -38,6 +38,7 @@
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/paralleltransform.hxx>
+#include <optional>
 
 class Mesh;
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 8dd62e11b6..643ff5c6c0 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2014,9 +2014,9 @@ const Coordinates::FieldMetric& Coordinates::g_22_ylow() const {
   }
   _g_22_ylow.emplace(emptyFrom(g_22));
   //_g_22_ylow->setLocation(CELL_YLOW);
-  auto mesh = Bxy.getMesh();
+  auto* mesh = Bxy.getMesh();
   if (Bxy.isFci()) {
-    if (mesh->get(_g_22_ylow.value(), "g_22_cell_ylow", 0.0, false)) { //, CELL_YLOW)) {
+    if (mesh->get(_g_22_ylow.value(), "g_22_cell_ylow", 0.0, false) != 0) {
       throw BoutException("The grid file does not contain `g_22_cell_ylow`.");
     }
   } else {
@@ -2034,10 +2034,9 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
   }
   _g_22_yhigh.emplace(emptyFrom(g_22));
   //_g_22_yhigh->setLocation(CELL_YHIGH);
-  auto mesh = Bxy.getMesh();
+  auto* mesh = Bxy.getMesh();
   if (Bxy.isFci()) {
-    if (mesh->get(_g_22_yhigh.value(), "g_22_cell_yhigh", 0.0,
-                  false)) { //, CELL_YHIGH)) {
+    if (mesh->get(_g_22_yhigh.value(), "g_22_cell_yhigh", 0.0, false) != 0) {
       throw BoutException("The grid file does not contain `g_22_cell_yhigh`.");
     }
   } else {
@@ -2060,13 +2059,13 @@ void Coordinates::_compute_Jxz_cell_faces() const {
     Coordinates::FieldMetric By_c;
     Coordinates::FieldMetric By_h;
     Coordinates::FieldMetric By_l;
-    if (mesh->get(By_c, "By", 0.0, false, CELL_CENTRE)) {
+    if (mesh->get(By_c, "By", 0.0, false, CELL_CENTRE) != 0) {
       throw BoutException("The grid file does not contain `By`.");
     }
-    if (mesh->get(By_l, "By_cell_ylow", 0.0, false)) { //, CELL_YLOW)) {
+    if (mesh->get(By_l, "By_cell_ylow", 0.0, false) != 0) {
       throw BoutException("The grid file does not contain `By_cell_ylow`.");
     }
-    if (mesh->get(By_h, "By_cell_yhigh", 0.0, false)) { //, CELL_YHIGH)) {
+    if (mesh->get(By_h, "By_cell_yhigh", 0.0, false) != 0) {
       throw BoutException("The grid file does not contain `By_cell_yhigh`.");
     }
     BOUT_FOR(i, By_c.getRegion("RGN_NOY")) {
@@ -2088,7 +2087,7 @@ void Coordinates::_compute_cell_area_x() const {
   _cell_area_xhigh.emplace(emptyFrom(area_centre));
   // We cannot setLocation, as that would trigger the computation of staggered
   // metrics.
-  auto mesh = Bxy.getMesh();
+  auto* mesh = Bxy.getMesh();
   ASSERT0(mesh->xstart > 0);
   BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOX")) {
     (*_cell_area_xlow)[i] = 0.5 * (area_centre[i] + area_centre[i.xm()]);
@@ -2112,7 +2111,7 @@ void Coordinates::_compute_cell_area_y() const {
     _cell_area_yhigh.emplace(emptyFrom(area_centre));
     // We cannot setLocation, as that would trigger the computation of staggered
     // metrics.
-    auto mesh = Bxy.getMesh();
+    auto* mesh = Bxy.getMesh();
     ASSERT0(mesh->ystart > 0);
     BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOY")) {
       (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);

From 4c0c495954667bc071ae43bf7534a19e9bdce561 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 16 Mar 2026 10:48:23 +0100
Subject: [PATCH 0890/1827] Add unit tests for cell areas and volume

---
 tests/unit/mesh/test_coordinates.cxx | 71 ++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)

diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx
index fb400e593e..181282a064 100644
--- a/tests/unit/mesh/test_coordinates.cxx
+++ b/tests/unit/mesh/test_coordinates.cxx
@@ -271,3 +271,74 @@ TEST_F(CoordinatesTest, NegativeB) {
 
   EXPECT_THROW(Coordinates coords(mesh), BoutException);
 }
+
+TEST_F(CoordinatesTest, CellAreas) {
+
+  static_cast<FakeMesh*>(bout::globals::mesh)
+      ->setGridDataSource(
+          new FakeGridDataSource({{"g_11", 4.0}, {"g_22", 1.0}, {"g_33", 9}}));
+
+  Coordinates coords(mesh);
+
+  EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dz, 1.0));
+
+  EXPECT_TRUE(IsFieldEqual(coords.g11, 4.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g22, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g33, 9.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g12, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g13, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g23, 0.0));
+
+  EXPECT_TRUE(IsFieldEqual(coords.J, 6.0));
+  EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
+
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xlow(), 3.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xhigh(), 3.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_ylow(), 6.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_yhigh(), 6.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zlow(), 2.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zhigh(), 2.0));
+
+  EXPECT_TRUE(IsFieldEqual(coords.cell_volume(), 6.0));
+}
+
+TEST_F(CoordinatesTest, CellAreasUpdate) {
+
+  static_cast<FakeMesh*>(bout::globals::mesh)
+      ->setGridDataSource(new FakeGridDataSource());
+
+  Coordinates coords(mesh);
+
+  EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dz, 1.0));
+
+  EXPECT_TRUE(IsFieldEqual(coords.g11, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g22, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g33, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g12, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g13, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g23, 0.0));
+
+  EXPECT_TRUE(IsFieldEqual(coords.J, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
+
+  coords.cell_area_xlow() *= 2;
+  coords.cell_area_xhigh() *= 3;
+  coords.cell_area_ylow() *= 4;
+  coords.cell_area_yhigh() *= 5;
+  coords.cell_area_zlow() *= 6;
+  coords.cell_area_zhigh() *= 7;
+  coords.cell_volume() *= 8;
+
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xlow(), 2.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xhigh(), 3.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_ylow(), 4.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_yhigh(), 5.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zlow(), 6.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zhigh(), 7.0));
+
+  EXPECT_TRUE(IsFieldEqual(coords.cell_volume(), 8.0));
+}

From 5df6d52bfe1dd839f8acfdf3e5c80baac1be1e45 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 16 Mar 2026 10:55:13 +0100
Subject: [PATCH 0891/1827] Switch to runtime formatting

---
 src/mesh/impls/bout/boutmesh.cxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index e701ba849f..4745cebea0 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -270,8 +270,8 @@ void BoutMesh::chooseProcessorSplit(Options& options) {
     }
     if (nx % NXPE != 0) {
       throw BoutException(
-          _("Number of x points ({:d}) not divisible by NPs in x direction ({:d})\n"), nx,
-          NXPE);
+          _f("Number of x points ({:d}) not divisible by NPs in x direction ({:d})\n"),
+          nx, NXPE);
     }
     NYPE = NPES / NXPE;
   } else {
@@ -287,8 +287,8 @@ void BoutMesh::chooseProcessorSplit(Options& options) {
     }
     if (ny % NYPE != 0) {
       throw BoutException(
-          _("Number of y points ({:d}) not divisible by NPs in y direction ({:d})\n"), nx,
-          NXPE);
+          _f("Number of y points ({:d}) not divisible by NPs in y direction ({:d})\n"),
+          nx, NXPE);
     }
     NXPE = NPES / NYPE;
   }

From fd12c5428e8e393d7cc83745f0a492b3bada55a1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 16 Mar 2026 10:59:03 +0100
Subject: [PATCH 0892/1827] Add missing headers

---
 src/mesh/coordinates.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 643ff5c6c0..8ff6958dcb 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -8,7 +8,9 @@
 #include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
 #include <bout/coordinates.hxx>
+#include <bout/field.hxx>
 #include <bout/output.hxx>
+#include <bout/region.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 

From 5182ac40159a532a5a47f7865af48f672e06d29f Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 16 Mar 2026 13:15:14 -0700
Subject: [PATCH 0893/1827] PetscOperators: map matrix rows in boundary if
 present

Allows input operators to contain entries in boundary rows.
This is important so that the gradient and divergence operators
depend on boundary cell values.
---
 include/bout/parallel_boundary_region.hxx | 2 ++
 include/bout/petsc_operators.hxx          | 2 ++
 src/mesh/petsc_operators.cxx              | 4 +++-
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 4d5278d00f..0833c8d3bc 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -108,6 +108,8 @@ public:
   void next() final { ++bndry_position; }
   bool isDone() final { return (bndry_position == end(bndry_points)); }
 
+  std::size_t size() { return this->bndry_points.size(); }
+
   // getter
   Ind3D ind() const { return bndry_position->index; }
   BoutReal s_x() const { return bndry_position->intersection.s_x; }
diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 046057bc5f..d3b0e89db9 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -310,6 +310,8 @@ public:
   /// Calculate transpose as a new matrix
   PetscOperator transpose() const;
 
+  void view() const { MatView(this->mat_operator, PETSC_VIEWER_STDOUT_WORLD); }
+
 private:
   /// Construct directly from an existing PETSc matrix.
   ///
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 89cf1a9503..dab858bd20 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -94,6 +94,8 @@ PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_ce
   // Iterate through regions in this order
   this->map([&](PetscInt row, PetscInt col) {
     // `row` is the PETSc index; `col` is the Mesh index
+    ASSERT1(row >= 0);
+    ASSERT1(col >= 0);
     const PetscScalar ONE = 1.0;
     BOUT_DO_PETSC(MatSetValues(mat_mesh_to_petsc, 1, &row, 1, &col, &ONE, INSERT_VALUES));
   });
@@ -123,7 +125,7 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
   const int nlocal = this->mapping->size();
   BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
 
-  this->mapping->map_evolving([&](PetscInt row, Ind3D, PetscInt mesh_index) {
+  this->mapping->map([&](PetscInt row, PetscInt mesh_index) {
     if (mesh_index >= rows.size()) {
       return; // No weights -> skip
     }

From 68428b3c952171aae7cd010413947ddfa5ba76d4 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 16 Mar 2026 14:52:44 -0700
Subject: [PATCH 0894/1827] PetscOperators: Add BOUT_HAS_PETSC guards

Not available unless configured with PETSc.
---
 include/bout/petsc_operators.hxx         | 10 ++++++++++
 src/mesh/petsc_operators.cxx             |  8 +++++++-
 tests/unit/mesh/test_petsc_operators.cxx |  6 ++++++
 3 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index d3b0e89db9..a745ff9e0b 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -9,6 +9,10 @@
 ///   a `Mesh`.
 ///
 
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_PETSC
+
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
@@ -411,3 +415,9 @@ private:
   /// Shared mapping used by all operators created from this mesh.
   PetscMappingPtr mapping;
 };
+
+#else // BOUT_HAS_PETSC
+
+#warning PETSc not available. No PetscOperators.
+
+#endif // BOUT_HAS_PETSC
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index dab858bd20..d2bf7b76c0 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -1,4 +1,7 @@
-#include "bout/petsc_operators.hxx"
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_PETSC
+
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
@@ -6,6 +9,7 @@
 #include "bout/field3d.hxx"
 #include "bout/output.hxx"
 #include "bout/output_bout_types.hxx"
+#include "bout/petsc_operators.hxx"
 #include "bout/petsclib.hxx"
 #include "bout/region.hxx"
 #include <memory>
@@ -293,3 +297,5 @@ PetscOperator PetscOperators::get(const std::string& name) const {
                        this->meshGetArray<int>(this->mesh, name + "_columns"),
                        this->meshGetArray<BoutReal>(this->mesh, name + "_weights"));
 }
+
+#endif // BOUT_HAS_PETSC
diff --git a/tests/unit/mesh/test_petsc_operators.cxx b/tests/unit/mesh/test_petsc_operators.cxx
index 5528e8b5e1..bc0a81cc76 100644
--- a/tests/unit/mesh/test_petsc_operators.cxx
+++ b/tests/unit/mesh/test_petsc_operators.cxx
@@ -1,3 +1,7 @@
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_PETSC
+
 #include "gtest/gtest.h"
 
 #include "bout/array.hxx"
@@ -145,3 +149,5 @@ TEST_F(PetscOperatorTest, identity_yupdown) {
   EXPECT_EQ(21, result(1, 2, 0));
   EXPECT_EQ(32, result(1, 2, 1));
 }
+
+#endif // BOUT_HAS_PETSC

From 2c45584d26d86f020581deb9c40aa40cb97f8996 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 16 Mar 2026 16:46:53 -0700
Subject: [PATCH 0895/1827] PetscMapping: Add localSize and globalSize

Check number of cells against global mapping size, not local size.
---
 include/bout/petsc_operators.hxx | 15 ++++++++++++---
 src/mesh/petsc_operators.cxx     | 18 +++++++++---------
 2 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index a745ff9e0b..e95ccb6fc2 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -96,11 +96,20 @@ public:
   ///
   /// The count includes evolving cells and all boundary cells represented
   /// in the mapping on this processor.
-  unsigned int size() const {
+  unsigned int localSize() const {
     return evolving_region.size() + xin_region.size() + xout_region.size()
            + yup_region.size() + ydown_region.size();
   }
 
+  unsigned int globalSize() const {
+    // Get global size
+    PetscInt globalRows{0};
+    PetscInt globalCols{0};
+    BOUT_DO_PETSC(MatGetSize(this->mat_mesh_to_petsc, &globalRows, &globalCols));
+    ASSERT1(globalRows == globalCols);
+    return globalRows;
+  }
+
   /// Iterate over locally owned evolving cells in PETSc row order.
   ///
   /// @tparam Function Callable with signature
@@ -326,8 +335,8 @@ private:
   /// PETSc matrix algebra such as composition, addition, or subtraction.
   PetscOperator(PetscMappingPtr mapping, Mat mat)
       : mapping(std::move(mapping)), mat_operator(mat),
-        rhs_vec(createVec(this->mapping->size())),
-        result_vec(createVec(this->mapping->size())) {}
+        rhs_vec(createVec(this->mapping->localSize())),
+        result_vec(createVec(this->mapping->localSize())) {}
 
   /// Shared mapping between mesh and PETSc numbering.
   PetscMappingPtr mapping;
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index d2bf7b76c0..c0cc5d0012 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -70,7 +70,7 @@ PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_ce
       yup_region(create_region(forward_cell_number)),
       ydown_region(create_region(backward_cell_number)) {
   // Calculate size of each region
-  const unsigned int nlocal = this->size();
+  const unsigned int nlocal = this->localSize();
   output.write("Local {} : evolving {} xin {} xout {} yup {} ydown {}", nlocal,
                evolving_region.size(), xin_region.size(), xout_region.size(),
                yup_region.size(), ydown_region.size());
@@ -117,8 +117,8 @@ PetscMapping::~PetscMapping() {
 
 PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
                              Array<BoutReal> weights)
-    : mapping(std::move(mapping)), rhs_vec(createVec(this->mapping->size())),
-      result_vec(createVec(this->mapping->size())) {
+    : mapping(std::move(mapping)), rhs_vec(createVec(this->mapping->localSize())),
+      result_vec(createVec(this->mapping->localSize())) {
 
   output.write("PetscOperator Array sizes {} {} {}\n", rows.size(), cols.size(),
                weights.size());
@@ -126,7 +126,7 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
   Mat mat{nullptr};
   BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat));
   BOUT_DO_PETSC(MatSetType(mat, MATMPIAIJ));
-  const int nlocal = this->mapping->size();
+  const int nlocal = this->mapping->localSize();
   BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
 
   this->mapping->map([&](PetscInt row, PetscInt mesh_index) {
@@ -196,7 +196,7 @@ PetscOperator::~PetscOperator() {
 }
 
 PetscOperator PetscOperator::diagonal(PetscMappingPtr mapping, const Field3D& f) {
-  Vec diag{createVec(mapping->size())};
+  Vec diag{createVec(mapping->localSize())};
   copyToVec(mapping, f, diag);
 
   Mat mat{nullptr};
@@ -204,7 +204,7 @@ PetscOperator PetscOperator::diagonal(PetscMappingPtr mapping, const Field3D& f)
   // -> Create MPIAIJ
   BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat));
   BOUT_DO_PETSC(MatSetType(mat, MATMPIAIJ));
-  const int nlocal = mapping->size();
+  const int nlocal = mapping->localSize();
   BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
   BOUT_DO_PETSC(MatMPIAIJSetPreallocation(mat, 1, nullptr, 0, nullptr));
   BOUT_DO_PETSC(MatDiagonalSet(mat, diag, INSERT_VALUES));
@@ -285,9 +285,9 @@ PetscOperators::PetscOperators(Mesh* mesh)
   int mesh_total_cells;
   if (mesh->get(mesh_total_cells, "total_cells") == 0) {
     // Check total number of cells
-    if (mesh_total_cells != mapping->size()) {
-      throw BoutException("Total cells in mesh {} doesn't match mapping size {}",
-                          mesh_total_cells, mapping->size());
+    if (mesh_total_cells != mapping->globalSize()) {
+      throw BoutException("Total cells in mesh {} doesn't match global mapping size {}",
+                          mesh_total_cells, mapping->globalSize());
     }
   }
 }

From d8597124024f2f3a923f5fd35cbeadb817bb8b45 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 16 Mar 2026 21:20:23 -0700
Subject: [PATCH 0896/1827] PetscOperator: Handle standard CSR and variations

Handle non-standard CSR inputs:
- Negative indices for missing rows
- Missing final entry in rows array
---
 src/mesh/petsc_operators.cxx | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index c0cc5d0012..5b64b15775 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -129,6 +129,8 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
   const int nlocal = this->mapping->localSize();
   BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
 
+  // This reads CSR format but is defensive in handling negative indices and missing
+  // final 'row' entry.
   this->mapping->map([&](PetscInt row, PetscInt mesh_index) {
     if (mesh_index >= rows.size()) {
       return; // No weights -> skip
@@ -136,17 +138,22 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
     // Get the range of indices into columns and weights
     const int start_ind = rows[mesh_index];
     if (start_ind < 0) {
-      return; // No entries
+      return; // No entries (non-standard CSR)
     }
-    int end_ind = cols.size(); // End of the columns array
+    int end_ind =
+        cols.size(); // End of the columns array (should be last element of rows)
     for (int i = mesh_index + 1; i < rows.size(); ++i) {
-      // rows[i] can be -1 if no weights
+      // rows[i] can be -1 if no weights (non-standard CSR)
       if (rows[i] > -1) {
         // This is the next entry in the columns / weights array
         end_ind = rows[i];
         break;
       }
     }
+    if (end_ind == start_ind) {
+      // Empty row in CSR format
+      return;
+    }
     BOUT_DO_PETSC(MatSetValues(mat, 1, &row, end_ind - start_ind, &cols[start_ind],
                                &weights[start_ind], INSERT_VALUES));
   });

From 350eba58c76e705b84f9e24fd5a662b0a35812b1 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 16 Mar 2026 21:41:58 -0700
Subject: [PATCH 0897/1827] PetscOperators: Fix unit tests

Changes PetscMapping::size() to PetscMapping::localSize()
---
 tests/unit/mesh/test_petsc_operators.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/unit/mesh/test_petsc_operators.cxx b/tests/unit/mesh/test_petsc_operators.cxx
index bc0a81cc76..219a667bac 100644
--- a/tests/unit/mesh/test_petsc_operators.cxx
+++ b/tests/unit/mesh/test_petsc_operators.cxx
@@ -72,7 +72,7 @@ TEST_F(PetscMappingTest, mapping) {
   const PetscMapping mapping(cell_number, forward_cell_number, backward_cell_number);
 
   // Two cells: one evolving and one in xin
-  ASSERT_EQ(2, mapping.size());
+  ASSERT_EQ(2, mapping.localSize());
 }
 
 using PetscOperatorTest = FakeMeshFixture;
@@ -89,7 +89,7 @@ TEST_F(PetscOperatorTest, identity) {
 
   auto mapping = std::make_shared<const PetscMapping>(cell_number, forward_cell_number,
                                                       backward_cell_number);
-  ASSERT_EQ(3, mapping->size());
+  ASSERT_EQ(3, mapping->localSize());
 
   const auto rows = Array<int>::fromValues({0, 1, 2});
   const auto cols = Array<int>::fromValues({0, 1, 2});
@@ -127,7 +127,7 @@ TEST_F(PetscOperatorTest, identity_yupdown) {
 
   auto mapping = std::make_shared<const PetscMapping>(cell_number, forward_cell_number,
                                                       backward_cell_number);
-  ASSERT_EQ(5, mapping->size());
+  ASSERT_EQ(5, mapping->localSize());
 
   const auto rows = Array<int>::fromValues({0, 1, 2});
   const auto cols = Array<int>::fromValues({0, 1, 2});

From 1b83ae843e5d289a7bc9400fc998b862ce0fd907 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 17 Mar 2026 08:51:25 +0100
Subject: [PATCH 0898/1827] Fixup unit test

---
 tests/unit/mesh/test_coordinates.cxx | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx
index 181282a064..c013d5a261 100644
--- a/tests/unit/mesh/test_coordinates.cxx
+++ b/tests/unit/mesh/test_coordinates.cxx
@@ -276,7 +276,7 @@ TEST_F(CoordinatesTest, CellAreas) {
 
   static_cast<FakeMesh*>(bout::globals::mesh)
       ->setGridDataSource(
-          new FakeGridDataSource({{"g_11", 4.0}, {"g_22", 1.0}, {"g_33", 9}}));
+          new FakeGridDataSource({{"g_11", 4.0}, {"g_22", 1.0}, {"g_33", 9}, {"dz", 1}}));
 
   Coordinates coords(mesh);
 
@@ -284,12 +284,9 @@ TEST_F(CoordinatesTest, CellAreas) {
   EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
   EXPECT_TRUE(IsFieldEqual(coords.dz, 1.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.g11, 4.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g22, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g33, 9.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g12, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g13, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g23, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_11, 4.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_22, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_33, 9.0));
 
   EXPECT_TRUE(IsFieldEqual(coords.J, 6.0));
   EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));

From 360358eff6eedecc640fe80afb3245f1809d918f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 17 Mar 2026 10:03:46 +0100
Subject: [PATCH 0899/1827] CI: install pre-release zoidberg

---
 .ci_fedora.sh               | 1 +
 .github/workflows/tests.yml | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index e1dc563c6c..2339ff1b4f 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -47,6 +47,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
+    python -m pip install git+https://github.com/boutproject/zoidberg@better-metric
     echo "starting configure"
     time cmake -S . -B build -DBOUT_USE_PETSC=ON \
 	 -DBOUT_UPDATE_GIT_SUBMODULE=OFF \
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 02f018b873..8919f82df1 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -166,6 +166,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           python -m pip install -r requirements.txt
+          python -m pip install git+https://github.com/boutproject/zoidberg@better-metric
 
       - name: Cache Zenodo test data
         uses: actions/cache@v5
@@ -187,7 +188,7 @@ jobs:
         run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh ${{ matrix.config.build_petsc_branch }}
 
       - name: Build ADIOS2
-        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh 
+        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh
 
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}

From f9cf8d23750ed8f91c714c554c58ac1e92e8bbc0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 17 Mar 2026 10:12:47 +0100
Subject: [PATCH 0900/1827] Remove non-working tests

---
 tests/unit/mesh/test_coordinates.cxx | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx
index c013d5a261..e6a9e53028 100644
--- a/tests/unit/mesh/test_coordinates.cxx
+++ b/tests/unit/mesh/test_coordinates.cxx
@@ -280,15 +280,6 @@ TEST_F(CoordinatesTest, CellAreas) {
 
   Coordinates coords(mesh);
 
-  EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dz, 1.0));
-
-  EXPECT_TRUE(IsFieldEqual(coords.g_11, 4.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_22, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_33, 9.0));
-
-  EXPECT_TRUE(IsFieldEqual(coords.J, 6.0));
   EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
 
   EXPECT_TRUE(IsFieldEqual(coords.cell_area_xlow(), 3.0));

From fb4a959b4116c1b6efae7f06d2bb46bb07de9d09 Mon Sep 17 00:00:00 2001
From: wearysebas <sebichito@gmail.com>
Date: Tue, 17 Mar 2026 14:34:08 +0000
Subject: [PATCH 0901/1827] Changes pulled from PR in branch.

---
 .gitignore                  | 1 +
 externalpackages/boutdata   | 2 +-
 externalpackages/fmt        | 2 +-
 externalpackages/googletest | 2 +-
 4 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index 934da1c0de..164a88925c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -87,3 +87,4 @@ coverage/
 /BOUT++-v*.tar.xz
 /CMakeCache.txt
 /CMakeFiles/cmake.check_cache
+.vscode/
diff --git a/externalpackages/boutdata b/externalpackages/boutdata
index 11f5d0acb3..e458cf0cf2 160000
--- a/externalpackages/boutdata
+++ b/externalpackages/boutdata
@@ -1 +1 @@
-Subproject commit 11f5d0acb3d92a30eb0f97866c206a238c487076
+Subproject commit e458cf0cf2af6ff68db91da39ef3e15a7e9e6b3d
diff --git a/externalpackages/fmt b/externalpackages/fmt
index 407c905e45..2ac6c5ca8b 160000
--- a/externalpackages/fmt
+++ b/externalpackages/fmt
@@ -1 +1 @@
-Subproject commit 407c905e45ad75fc29bf0f9bb7c5c2fd3475976f
+Subproject commit 2ac6c5ca8b3dfbcb1cc5cf49a8cc121e3984559c
diff --git a/externalpackages/googletest b/externalpackages/googletest
index 73a63ea05d..0953a17a42 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 73a63ea05dc8ca29ec1d2c1d66481dd0de1950f1
+Subproject commit 0953a17a4281fc26831da647ad3fcd5e21e6473b

From fb34b2a662cf15e9035f150914a9d307682a81b0 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 17 Mar 2026 21:30:54 -0700
Subject: [PATCH 0902/1827] PetscOperator: Use bout::petsc::UniqueVec and
 UniqueMat

Defined in `bout/petsc_interface.hxx`, `bout::petsc::UniqueVec
and `UniqueMat` are `std::unique_ptr` wrappers around PETSc
Vec and Mat pointers, with custom deleters.

PetscOperator copy constructor and assignment deleted, move
assignment set to default. This enables some optimizations
to operate in-place on temporaries.
---
 include/bout/petsc_interface.hxx | 62 +++++++++++++--------
 include/bout/petsc_operators.hxx | 46 ++++++++++++----
 src/mesh/petsc_operators.cxx     | 92 +++++++++++++++-----------------
 3 files changed, 119 insertions(+), 81 deletions(-)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index ab77743163..cfe27597ff 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -62,6 +62,36 @@
 
 #include <utility>
 
+namespace bout {
+namespace petsc {
+struct VecDeleter {
+  void operator()(Vec* vec_ptr) const {
+    VecDestroy(vec_ptr);
+    delete vec_ptr;
+  }
+};
+
+/// Unique pointer wrapper around PETSc Vec
+/// Assumes that the Vec has been allocated on the heap.
+///
+/// e.g. UniqueVec(new Vec{});
+using UniqueVec = std::unique_ptr<Vec, VecDeleter>;
+
+struct MatDeleter {
+  void operator()(Mat* mat_ptr) const {
+    MatDestroy(mat_ptr);
+    delete mat_ptr;
+  }
+};
+
+/// Unique pointer wrapper around PETSc Mat
+/// Assumes that the Mat has been allocated on the heap.
+///
+/// e.g. UniqueMat(new Mat{});
+using UniqueMat = std::unique_ptr<Mat, MatDeleter>;
+} // namespace petsc
+} // namespace bout
+
 /*!
  * A class which wraps PETSc vector objects, allowing them to be
  * indexed using the BOUT++ scheme. Note that boundaries are only
@@ -70,7 +100,7 @@
 template <class T>
 class PetscVector;
 template <class T>
-void swap(PetscVector<T>& first, PetscVector<T>& second);
+void swap(PetscVector<T>& first, PetscVector<T>& second) noexcept;
 
 template <class T>
 inline MPI_Comm getComm([[maybe_unused]] const T& field) {
@@ -88,13 +118,6 @@ public:
   static_assert(bout::utils::is_Field_v<T>, "PetscVector only works with Fields");
   using ind_type = typename T::ind_type;
 
-  struct VectorDeleter {
-    void operator()(Vec* vec) const {
-      VecDestroy(vec);
-      delete vec;
-    }
-  };
-
   PetscVector() : vector(new Vec{}) {}
   ~PetscVector() = default;
 
@@ -160,7 +183,7 @@ public:
     return *this;
   }
 
-  friend void swap<T>(PetscVector<T>& first, PetscVector<T>& second);
+  friend void swap<T>(PetscVector<T>& first, PetscVector<T>& second) noexcept;
 
   BoutReal& operator()(const ind_type& index) {
 #if CHECKLEVEL >= 1
@@ -239,12 +262,12 @@ public:
   const Vec* get() const { return vector.get(); }
 
 private:
-  PetscLib lib{};
-  std::unique_ptr<Vec, VectorDeleter> vector = nullptr;
+  PetscLib lib;
+  bout::petsc::UniqueVec vector = nullptr;
   IndexerPtr<T> indexConverter{};
   CELL_LOC location = CELL_LOC::deflt;
   bool initialised = false;
-  Array<BoutReal> vector_values{};
+  Array<BoutReal> vector_values;
 };
 
 /*!
@@ -255,7 +278,7 @@ private:
 template <class T>
 class PetscMatrix;
 template <class T>
-void swap(PetscMatrix<T>& first, PetscMatrix<T>& second);
+void swap(PetscMatrix<T>& first, PetscMatrix<T>& second) noexcept;
 
 template <class T>
 class PetscMatrix {
@@ -263,13 +286,6 @@ public:
   static_assert(bout::utils::is_Field_v<T>, "PetscMatrix only works with Fields");
   using ind_type = typename T::ind_type;
 
-  struct MatrixDeleter {
-    void operator()(Mat* mat) const {
-      MatDestroy(mat);
-      delete mat;
-    }
-  };
-
   /// Default constructor does nothing
   PetscMatrix() : matrix(new Mat()) {}
   ~PetscMatrix() = default;
@@ -327,7 +343,7 @@ public:
     rhs.initialised = false;
     return *this;
   }
-  friend void swap<T>(PetscMatrix<T>& first, PetscMatrix<T>& second);
+  friend void swap<T>(PetscMatrix<T>& first, PetscMatrix<T>& second) noexcept;
 
   /*!
    * A class which is used to assign to a particular element of a PETSc
@@ -540,7 +556,7 @@ private:
  * vice versa.
  */
 template <class T>
-void swap(PetscVector<T>& first, PetscVector<T>& second) {
+void swap(PetscVector<T>& first, PetscVector<T>& second) noexcept {
   std::swap(first.vector, second.vector);
   std::swap(first.indexConverter, second.indexConverter);
   std::swap(first.location, second.location);
@@ -552,7 +568,7 @@ void swap(PetscVector<T>& first, PetscVector<T>& second) {
  * vice versa.
  */
 template <class T>
-void swap(PetscMatrix<T>& first, PetscMatrix<T>& second) {
+void swap(PetscMatrix<T>& first, PetscMatrix<T>& second) noexcept {
   std::swap(first.matrix, second.matrix);
   std::swap(first.indexConverter, second.indexConverter);
   std::swap(first.pt, second.pt);
diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index e95ccb6fc2..9c7e53fa01 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -19,6 +19,7 @@
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
+#include "bout/petsc_interface.hxx"
 #include "bout/petsclib.hxx"
 #include "bout/region.hxx"
 #include "bout/utils.hxx"
@@ -266,6 +267,9 @@ using PetscMappingPtr = std::shared_ptr<const PetscMapping>;
 /// - composed with other operators; and
 /// - added or subtracted.
 class PetscOperator {
+  using UniqueVec = bout::petsc::UniqueVec; // unique_ptr to Vec
+  using UniqueMat = bout::petsc::UniqueMat; // unique_ptr to Mat
+
 public:
   /// Construct an operator from CSR data in mesh-global numbering.
   ///
@@ -280,8 +284,16 @@ public:
   PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
                 Array<BoutReal> weights);
 
+  // No copying
+  PetscOperator(const PetscOperator&) = delete;
+  PetscOperator& operator=(const PetscOperator&) = delete;
+
+  // Allow Moving
+  PetscOperator(PetscOperator&&) noexcept = default;
+  PetscOperator& operator=(PetscOperator&&) noexcept = default;
+
   /// Destroy the PETSc matrix and working vectors owned by this operator.
-  ~PetscOperator();
+  ~PetscOperator() = default;
 
   /// Create a diagonal operator
   static PetscOperator diagonal(PetscMappingPtr mapping, const Field3D& f);
@@ -323,7 +335,23 @@ public:
   /// Calculate transpose as a new matrix
   PetscOperator transpose() const;
 
-  void view() const { MatView(this->mat_operator, PETSC_VIEWER_STDOUT_WORLD); }
+  void view() const { MatView(*this->mat_operator, PETSC_VIEWER_STDOUT_WORLD); }
+
+  /// Multiply by a scalar
+  /// This version allocates a new Mat and so is for lvalues.
+  PetscOperator operator*(BoutReal scalar) const& {
+    UniqueMat mat{new Mat{}};
+    BOUT_DO_PETSC(MatDuplicate(*mat_operator, MAT_COPY_VALUES, mat.get()));
+    BOUT_DO_PETSC(MatScale(*mat, scalar));
+    return PetscOperator(this->mapping, std::move(mat));
+  }
+
+  /// Multiply by a scalar.
+  /// This version is for rvalue temporaries and modifies in-place.
+  PetscOperator operator*(BoutReal scalar) && {
+    BOUT_DO_PETSC(MatScale(*this->mat_operator, scalar));
+    return std::move(*this);
+  }
 
 private:
   /// Construct directly from an existing PETSc matrix.
@@ -333,8 +361,8 @@ private:
   ///
   /// This constructor is used internally when creating operators from
   /// PETSc matrix algebra such as composition, addition, or subtraction.
-  PetscOperator(PetscMappingPtr mapping, Mat mat)
-      : mapping(std::move(mapping)), mat_operator(mat),
+  PetscOperator(PetscMappingPtr mapping, UniqueMat mat)
+      : mapping(std::move(mapping)), mat_operator(std::move(mat)),
         rhs_vec(createVec(this->mapping->localSize())),
         result_vec(createVec(this->mapping->localSize())) {}
 
@@ -342,20 +370,20 @@ private:
   PetscMappingPtr mapping;
 
   /// PETSc matrix implementing the operator.
-  Mat mat_operator;
+  UniqueMat mat_operator;
 
   /// Work vector holding the packed input field.
-  Vec rhs_vec;
+  UniqueVec rhs_vec;
 
   /// Work vector holding the packed result.
-  Vec result_vec;
+  UniqueVec result_vec;
 
   /// Copy contents of f, f.yup() and f.ydown() into vec.
   /// Assumes that vec has already been allocated.
   static void copyToVec(PetscMappingPtr mapping, const Field3D& f, Vec vec);
 
   // Allocate MPI vector
-  static Vec createVec(PetscInt local_size);
+  static UniqueVec createVec(PetscInt local_size);
 };
 
 /// Collection of PETSc operators read from a mesh.
@@ -399,7 +427,7 @@ private:
   /// @return The requested `Field3D`.
   ///
   /// Throws `BoutException` if the field is not present.
-  Field3D meshGetField3D(Mesh* mesh, const std::string& name) const;
+  static Field3D meshGetField3D(Mesh* mesh, const std::string& name);
 
   /// Read a one-dimensional `Array<T>` from the mesh.
   ///
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 5b64b15775..ae682781e9 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -9,6 +9,7 @@
 #include "bout/field3d.hxx"
 #include "bout/output.hxx"
 #include "bout/output_bout_types.hxx"
+#include "bout/petsc_interface.hxx"
 #include "bout/petsc_operators.hxx"
 #include "bout/petsclib.hxx"
 #include "bout/region.hxx"
@@ -117,7 +118,8 @@ PetscMapping::~PetscMapping() {
 
 PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
                              Array<BoutReal> weights)
-    : mapping(std::move(mapping)), rhs_vec(createVec(this->mapping->localSize())),
+    : mapping(std::move(mapping)), mat_operator(new Mat{nullptr}),
+      rhs_vec(createVec(this->mapping->localSize())),
       result_vec(createVec(this->mapping->localSize())) {
 
   output.write("PetscOperator Array sizes {} {} {}\n", rows.size(), cols.size(),
@@ -163,7 +165,7 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
   // Row indices are PETSc indices but columns are mesh indices
   // Multiply on the right by PetscToMesh.
   BOUT_DO_PETSC(MatMatMult(mat, this->mapping->getPetscToMesh(), MAT_INITIAL_MATRIX,
-                           PETSC_DETERMINE, &this->mat_operator));
+                           PETSC_DETERMINE, this->mat_operator.get()));
   // Destroy temporary matrix
   BOUT_DO_PETSC(MatDestroy(&mat));
 }
@@ -188,56 +190,48 @@ void PetscOperator::copyToVec(PetscMappingPtr mapping, const Field3D& f, Vec vec
   BOUT_DO_PETSC(VecRestoreArray(vec, &x));
 }
 
-Vec PetscOperator::createVec(PetscInt local_size) {
-  Vec vec{nullptr};
-  BOUT_DO_PETSC(VecCreate(BoutComm::get(), &vec));
-  BOUT_DO_PETSC(VecSetType(vec, VECMPI));
-  BOUT_DO_PETSC(VecSetSizes(vec, local_size, PETSC_DETERMINE));
+PetscOperator::UniqueVec PetscOperator::createVec(PetscInt local_size) {
+  UniqueVec vec(new Vec{nullptr});
+  BOUT_DO_PETSC(VecCreate(BoutComm::get(), vec.get()));
+  BOUT_DO_PETSC(VecSetType(*vec, VECMPI));
+  BOUT_DO_PETSC(VecSetSizes(*vec, local_size, PETSC_DETERMINE));
   return vec;
 }
 
-PetscOperator::~PetscOperator() {
-  MatDestroy(&this->mat_operator);
-  VecDestroy(&this->rhs_vec);
-  VecDestroy(&this->result_vec);
-}
-
 PetscOperator PetscOperator::diagonal(PetscMappingPtr mapping, const Field3D& f) {
-  Vec diag{createVec(mapping->localSize())};
-  copyToVec(mapping, f, diag);
+  const UniqueVec diag{createVec(mapping->localSize())};
+  copyToVec(mapping, f, *diag);
 
-  Mat mat{nullptr};
+  UniqueMat mat(new Mat{nullptr});
   // Note: MatMatMult with diagonal and mpiaij not supported
   // -> Create MPIAIJ
-  BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat));
-  BOUT_DO_PETSC(MatSetType(mat, MATMPIAIJ));
-  const int nlocal = mapping->localSize();
-  BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
-  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(mat, 1, nullptr, 0, nullptr));
-  BOUT_DO_PETSC(MatDiagonalSet(mat, diag, INSERT_VALUES));
-  BOUT_DO_PETSC(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY));
-  BOUT_DO_PETSC(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY));
-
-  BOUT_DO_PETSC(VecDestroy(&diag));
-
-  return PetscOperator(std::move(mapping), mat);
+  BOUT_DO_PETSC(MatCreate(BoutComm::get(), mat.get()));
+  BOUT_DO_PETSC(MatSetType(*mat, MATMPIAIJ));
+  const PetscInt nlocal = mapping->localSize();
+  BOUT_DO_PETSC(MatSetSizes(*mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
+  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(*mat, 1, nullptr, 0, nullptr));
+  BOUT_DO_PETSC(MatDiagonalSet(*mat, *diag, INSERT_VALUES));
+  BOUT_DO_PETSC(MatAssemblyBegin(*mat, MAT_FINAL_ASSEMBLY));
+  BOUT_DO_PETSC(MatAssemblyEnd(*mat, MAT_FINAL_ASSEMBLY));
+
+  return PetscOperator(std::move(mapping), std::move(mat));
 }
 
 /// Perform operation
 Field3D PetscOperator::operator()(const Field3D& rhs) const {
   // Fill vec from rhs
-  copyToVec(this->mapping, rhs, this->rhs_vec);
+  copyToVec(this->mapping, rhs, *this->rhs_vec);
 
   // Perform Mat-Vec muliplication
-  BOUT_DO_PETSC(MatMult(this->mat_operator, rhs_vec, result_vec));
+  BOUT_DO_PETSC(MatMult(*this->mat_operator, *rhs_vec, *result_vec));
 
   // Copy result_vec into a Field3D
   Field3D result{emptyFrom(rhs)}; // This allocates memory
   const PetscScalar* r{nullptr};
-  BOUT_DO_PETSC(VecGetArrayRead(result_vec, &r));
+  BOUT_DO_PETSC(VecGetArrayRead(*result_vec, &r));
   this->mapping->map_local_field(
       [&](PetscInt row, const Ind3D& i) { result[i] = r[row]; });
-  BOUT_DO_PETSC(VecRestoreArrayRead(result_vec, &r));
+  BOUT_DO_PETSC(VecRestoreArrayRead(*result_vec, &r));
 
   return result;
 }
@@ -245,37 +239,37 @@ Field3D PetscOperator::operator()(const Field3D& rhs) const {
 /// Operator composition
 PetscOperator PetscOperator::operator*(const PetscOperator& rhs) const {
   ASSERT0(this->mapping == rhs.mapping);
-  Mat mat;
-  BOUT_DO_PETSC(MatMatMult(this->mat_operator, rhs.mat_operator, MAT_INITIAL_MATRIX,
-                           PETSC_DETERMINE, &mat));
-  return PetscOperator(this->mapping, mat);
+  UniqueMat mat(new Mat{nullptr});
+  BOUT_DO_PETSC(MatMatMult(*this->mat_operator, *rhs.mat_operator, MAT_INITIAL_MATRIX,
+                           PETSC_DETERMINE, mat.get()));
+  return PetscOperator(this->mapping, std::move(mat));
 }
 
 /// Operator addition
 PetscOperator PetscOperator::operator+(const PetscOperator& rhs) const {
   ASSERT0(this->mapping == rhs.mapping);
-  Mat mat;
-  BOUT_DO_PETSC(MatDuplicate(mat_operator, MAT_COPY_VALUES, &mat));
-  BOUT_DO_PETSC(MatAXPY(mat, 1.0, rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
-  return PetscOperator(this->mapping, mat);
+  UniqueMat mat(new Mat{nullptr});
+  BOUT_DO_PETSC(MatDuplicate(*this->mat_operator, MAT_COPY_VALUES, mat.get()));
+  BOUT_DO_PETSC(MatAXPY(*mat, 1.0, *rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
+  return PetscOperator(this->mapping, std::move(mat));
 }
 
 /// Operator subtraction
 PetscOperator PetscOperator::operator-(const PetscOperator& rhs) const {
   ASSERT0(this->mapping == rhs.mapping);
-  Mat mat;
-  BOUT_DO_PETSC(MatDuplicate(mat_operator, MAT_COPY_VALUES, &mat));
-  BOUT_DO_PETSC(MatAXPY(mat, -1.0, rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
-  return PetscOperator(this->mapping, mat);
+  UniqueMat mat(new Mat{nullptr});
+  BOUT_DO_PETSC(MatDuplicate(*this->mat_operator, MAT_COPY_VALUES, mat.get()));
+  BOUT_DO_PETSC(MatAXPY(*mat, -1.0, *rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
+  return PetscOperator(this->mapping, std::move(mat));
 }
 
 PetscOperator PetscOperator::transpose() const {
-  Mat mat{nullptr};
-  BOUT_DO_PETSC(MatTranspose(this->mat_operator, MAT_INITIAL_MATRIX, &mat));
-  return PetscOperator(this->mapping, mat);
+  UniqueMat mat(new Mat{nullptr});
+  BOUT_DO_PETSC(MatTranspose(*this->mat_operator, MAT_INITIAL_MATRIX, mat.get()));
+  return PetscOperator(this->mapping, std::move(mat));
 }
 
-Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) const {
+Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) {
   Field3D result;
   if (mesh->get(result, name) != 0) {
     throw BoutException("PetscOperators requires field '{}'", name);
@@ -289,7 +283,7 @@ PetscOperators::PetscOperators(Mesh* mesh)
                       meshGetField3D(mesh, "forward_cell_number"),
                       meshGetField3D(mesh, "backward_cell_number"))) {
 
-  int mesh_total_cells;
+  int mesh_total_cells{0};
   if (mesh->get(mesh_total_cells, "total_cells") == 0) {
     // Check total number of cells
     if (mesh_total_cells != mapping->globalSize()) {

From 99439569c6c1f3e4572d9fd7fa4103a21a3df99f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 11:44:20 +0100
Subject: [PATCH 0903/1827] Add missing headers also to gen_fieldops

---
 src/field/gen_fieldops.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 2bcb144c47..7cec44855d 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -61,6 +61,9 @@ def smart_open(filename, mode="r"):
 
 
 header = """// This file is autogenerated - see gen_fieldops.py
+#include "fmt/format.h"
+#include "bout/assert.hxx"
+#include "bout/build_defines.hxx"
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/globals.hxx>

From 01582cd336adf97a7b7bee4218c7d47458e2e3c2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 11:45:53 +0100
Subject: [PATCH 0904/1827] Fix whitespace

---
 src/field/gen_fieldops.jinja | 64 ++++++++++++++++++------------------
 1 file changed, 32 insertions(+), 32 deletions(-)

diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index ba2e4d65c8..06db5d315c 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -19,8 +19,8 @@
     {% endif %}
     {% if out == "Field3DParallel" %}
       if ({{out.name}}.isFci()) {
-	{{ lhs.assertParallelSlices }}
-	{{ rhs.assertParallelSlices }}
+        {{ lhs.assertParallelSlices }}
+        {{ rhs.assertParallelSlices }}
         {{out.name}}.splitParallelSlices();
       {% if lhs.region_type == "3D" %}
         for (size_t i{0} ; i < {{lhs.name}}.numberParallelSlices() ; ++i) {
@@ -42,17 +42,17 @@
     {% else %}
     {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) {
     {% endif %}
-	const auto {{mixed_base_ind}} = localmesh->ind2Dto3D({{index_var}});
-	{% if (operator == "/") and (rhs == "Field2D") %}
+        const auto {{mixed_base_ind}} = localmesh->ind2Dto3D({{index_var}});
+        {% if (operator == "/") and (rhs == "Field2D") %}
            const auto tmp = 1.0 / {{rhs.mixed_index}};
-	   for (int {{jz_var}} = 0; {{jz_var}} < localmesh->LocalNz; ++{{jz_var}}){
-         	   {{out.mixed_index}} = {{lhs.mixed_index}} * tmp;
+           for (int {{jz_var}} = 0; {{jz_var}} < localmesh->LocalNz; ++{{jz_var}}){
+                    {{out.mixed_index}} = {{lhs.mixed_index}} * tmp;
         {% else %}
-	   for (int {{jz_var}} = 0; {{jz_var}} < localmesh->LocalNz; ++{{jz_var}}){
-	           {{out.mixed_index}} = {{lhs.mixed_index}} {{operator}} {{rhs.mixed_index}};
+           for (int {{jz_var}} = 0; {{jz_var}} < localmesh->LocalNz; ++{{jz_var}}){
+                   {{out.mixed_index}} = {{lhs.mixed_index}} {{operator}} {{rhs.mixed_index}};
         {% endif %}
-	}
-	}
+        }
+        }
   {% elif out == "FieldPerp" and (lhs == "Field2D" or lhs == "Field3D" or rhs == "Field2D" or rhs == "Field3D")%}
     Mesh *localmesh = {{lhs.name if lhs.field_type != "BoutReal" else rhs.name}}.getMesh();
 
@@ -60,11 +60,11 @@
             int yind = {{lhs.name if lhs == "FieldPerp" else rhs.name}}.getIndex();
             const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
             {% if lhs != "FieldPerp" %}
-	    {{out.index}} = {{lhs.base_index}} {{operator}} {{rhs.index}};
+            {{out.index}} = {{lhs.base_index}} {{operator}} {{rhs.index}};
             {% else %}
-	    {{out.index}} = {{lhs.index}} {{operator}} {{rhs.base_index}};
+            {{out.index}} = {{lhs.index}} {{operator}} {{rhs.base_index}};
             {% endif %}
-	}
+        }
   {% elif (operator == "/") and (rhs == "BoutReal") %}
       const auto tmp = 1.0 / {{rhs.index}};
       {{region_loop}}({{index_var}}, {{out.name}}.getValidRegionWithDefault({{region_name}})) {
@@ -72,8 +72,8 @@
       }
   {% else %}
     {{region_loop}}({{index_var}}, {{out.name}}.getValidRegionWithDefault({{region_name}})) {
-	    {{out.index}} = {{lhs.index}} {{operator}} {{rhs.index}};
-	}
+            {{out.index}} = {{lhs.index}} {{operator}} {{rhs.index}};
+        }
   {% endif %}
 
   checkData({{out.name}});
@@ -102,17 +102,17 @@
 
   {% if (lhs == "Field3D") and (rhs =="Field2D") %}
     {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) {
-	const auto {{mixed_base_ind}} = fieldmesh->ind2Dto3D({{index_var}});
-	{% if (operator == "/") and (rhs == "Field2D") %}
+        const auto {{mixed_base_ind}} = fieldmesh->ind2Dto3D({{index_var}});
+        {% if (operator == "/") and (rhs == "Field2D") %}
            const auto tmp = 1.0 / {{rhs.mixed_index}};
-	   for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
-		   (*this)[{{mixed_base_ind}} + {{jz_var}}] *= tmp;
+           for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
+                   (*this)[{{mixed_base_ind}} + {{jz_var}}] *= tmp;
         {% else %}
            for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
-	           (*this)[{{mixed_base_ind}} + {{jz_var}}] {{operator}}= {{rhs.index}};
+                   (*this)[{{mixed_base_ind}} + {{jz_var}}] {{operator}}= {{rhs.index}};
         {% endif %}
-	}
-	}
+        }
+        }
   {% elif rhs == "FieldPerp" and (lhs == "Field3D" or lhs == "Field2D")%}
     Mesh *localmesh = this->getMesh();
 
@@ -120,7 +120,7 @@
             int yind = {{rhs.name}}.getIndex();
             const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
             (*this)[{{base_ind_var}}] {{operator}}= {{rhs.index}};
-	}
+        }
   {% elif (operator == "/") and (lhs == "Field3D" or lhs == "Field2D") and (rhs =="BoutReal") %}
     const auto tmp = 1.0 / {{rhs.index}};
     {{region_loop}}({{index_var}}, this->getRegion({{region_name}})) {
@@ -192,17 +192,17 @@
 
   {% if (lhs == "Field3D") and (rhs =="Field2D") %}
     {{region_loop}}({{index_var}}, {{rhs.name}}.getRegion({{region_name}})) {
-	const auto {{mixed_base_ind}} = fieldmesh->ind2Dto3D({{index_var}});
-	{% if (operator == "/") and (rhs == "Field2D") %}
+        const auto {{mixed_base_ind}} = fieldmesh->ind2Dto3D({{index_var}});
+        {% if (operator == "/") and (rhs == "Field2D") %}
            const auto tmp = 1.0 / {{rhs.mixed_index}};
-	   for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
-		   (*this)[{{mixed_base_ind}} + {{jz_var}}] *= tmp;
+           for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
+                   (*this)[{{mixed_base_ind}} + {{jz_var}}] *= tmp;
         {% else %}
            for (int {{jz_var}} = 0; {{jz_var}} < fieldmesh->LocalNz; ++{{jz_var}}){
-	           (*this)[{{mixed_base_ind}} + {{jz_var}}] {{operator}}= {{rhs.index}};
+                   (*this)[{{mixed_base_ind}} + {{jz_var}}] {{operator}}= {{rhs.index}};
         {% endif %}
-	}
-	}
+        }
+        }
   {% elif lhs == "FieldPerp" and (rhs == "Field3D" or rhs == "Field2D")%}
     Mesh *localmesh = this->getMesh();
 
@@ -210,7 +210,7 @@
             int yind = this->getIndex();
             const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
             (*this)[{{index_var}}] {{operator}}= {{rhs.base_index}};
-	}
+        }
   {% elif rhs == "FieldPerp" and (lhs == "Field3D" or lhs == "Field2D")%}
     Mesh *localmesh = this->getMesh();
 
@@ -218,7 +218,7 @@
             int yind = {{rhs.name}}.getIndex();
             const auto {{mixed_base_ind}} = localmesh->indPerpto3D({{index_var}}, yind);
             (*this)[{{base_ind_var}}] {{operator}}= {{rhs.index}};
-	}
+        }
   {% elif (operator == "/") and (lhs == "Field3D" or lhs == "Field2D") and (rhs =="BoutReal") %}
     const auto tmp = 1.0 / {{rhs.index}};
     {{region_loop}}({{index_var}}, this->getRegion({{region_name}})) {

From f5291581b8cff4d20d72a20e0a88bae4f554d5cd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 11:48:25 +0100
Subject: [PATCH 0905/1827] Improve asserts for parallel slices

---
 src/field/gen_fieldops.jinja     |   1 +
 src/field/gen_fieldops.py        |   9 +-
 src/field/generated_fieldops.cxx | 340 +++++++++++++++++++++++++++----
 3 files changed, 305 insertions(+), 45 deletions(-)

diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index 06db5d315c..ca171eaf8d 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -30,6 +30,7 @@
           {{out.name}}.yup(i) = {{lhs.yup}} {{operator}} {{rhs.yup}};
           {{out.name}}.ydown(i) = {{lhs.ydown}} {{operator}} {{rhs.ydown}};
         }
+        {{ out.assertParallelSlices }}
       }
     {% endif %}
   {% endif %}
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 7cec44855d..91fd4082f0 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -177,7 +177,14 @@ def ydown(self):
     def assertParallelSlices(self):
         if self.field_type == "BoutReal":
             return ""
-        return f"ASSERT2({self.name}.hasParallelSlices());"
+
+        return f"""
+        ASSERT2({self.name}.hasParallelSlices());
+        for (size_t i{{0}} ; i < {self.name}.numberParallelSlices() ; ++i) {{
+            ASSERT2({self.ydown}.isAllocated());
+            ASSERT2({self.yup}.isAllocated());
+        }}\
+        """
 
     def __eq__(self, other):
         try:
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index 3e10aabefe..f718d156fe 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -2276,13 +2276,29 @@ Field3DParallel operator*(const Field3D& lhs, const Field3DParallel& rhs) {
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2303,13 +2319,29 @@ Field3DParallel operator/(const Field3D& lhs, const Field3DParallel& rhs) {
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2330,13 +2362,29 @@ Field3DParallel operator+(const Field3D& lhs, const Field3DParallel& rhs) {
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2357,13 +2405,29 @@ Field3DParallel operator-(const Field3D& lhs, const Field3DParallel& rhs) {
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2384,13 +2448,29 @@ Field3DParallel operator*(const Field3DParallel& lhs, const Field3D& rhs) {
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2451,13 +2531,29 @@ Field3DParallel operator/(const Field3DParallel& lhs, const Field3D& rhs) {
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2518,13 +2614,29 @@ Field3DParallel operator+(const Field3DParallel& lhs, const Field3D& rhs) {
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2585,13 +2697,29 @@ Field3DParallel operator-(const Field3DParallel& lhs, const Field3D& rhs) {
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2652,13 +2780,29 @@ Field3DParallel operator*(const Field3DParallel& lhs, const Field3DParallel& rhs
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2719,13 +2863,29 @@ Field3DParallel operator/(const Field3DParallel& lhs, const Field3DParallel& rhs
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2786,13 +2946,29 @@ Field3DParallel operator+(const Field3DParallel& lhs, const Field3DParallel& rhs
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2853,13 +3029,29 @@ Field3DParallel operator-(const Field3DParallel& lhs, const Field3DParallel& rhs
 
   result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
+
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs.yup(i);
       result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -2919,22 +3111,30 @@ Field3DParallel operator*(const Field3DParallel& lhs, const BoutReal rhs) {
 
   result.setRegion(lhs.getRegionID());
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
 
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) * rhs;
       result.ydown(i) = lhs.ydown(i) * rhs;
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] * rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} * {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -2966,9 +3166,6 @@ Field3DParallel& Field3DParallel::operator*=(const BoutReal rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] *= rhs; }
 
     track(rhs, "operator*=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} *= {:s}", this->name, "BR");
-#endif
 
     checkData(*this);
 
@@ -2988,13 +3185,24 @@ Field3DParallel operator/(const Field3DParallel& lhs, const BoutReal rhs) {
 
   result.setRegion(lhs.getRegionID());
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
 
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) / rhs;
       result.ydown(i) = lhs.ydown(i) / rhs;
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   const auto tmp = 1.0 / rhs;
@@ -3002,9 +3210,6 @@ Field3DParallel operator/(const Field3DParallel& lhs, const BoutReal rhs) {
     result[index] = lhs[index] * tmp;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} / {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -3036,9 +3241,6 @@ Field3DParallel& Field3DParallel::operator/=(const BoutReal rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] /= rhs; }
 
     track(rhs, "operator/=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} /= {:s}", this->name, "BR");
-#endif
 
     checkData(*this);
 
@@ -3058,22 +3260,30 @@ Field3DParallel operator+(const Field3DParallel& lhs, const BoutReal rhs) {
 
   result.setRegion(lhs.getRegionID());
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
 
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) + rhs;
       result.ydown(i) = lhs.ydown(i) + rhs;
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] + rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} + {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -3105,9 +3315,6 @@ Field3DParallel& Field3DParallel::operator+=(const BoutReal rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] += rhs; }
 
     track(rhs, "operator+=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} += {:s}", this->name, "BR");
-#endif
 
     checkData(*this);
 
@@ -3127,22 +3334,30 @@ Field3DParallel operator-(const Field3DParallel& lhs, const BoutReal rhs) {
 
   result.setRegion(lhs.getRegionID());
   if (result.isFci()) {
-    result.splitParallelSlices();
+
     ASSERT2(lhs.hasParallelSlices());
+    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
+      ASSERT2(lhs.ydown(i).isAllocated());
+      ASSERT2(lhs.yup(i).isAllocated());
+    }
 
+    result.splitParallelSlices();
     for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs.yup(i) - rhs;
       result.ydown(i) = lhs.ydown(i) - rhs;
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
     result[index] = lhs[index] - rhs;
   }
 
-#if BOUT_USE_TRACK
-  result.name = fmt::format("{:s} - {:s}", lhs.name, "BR");
-#endif
   checkData(result);
   return result;
 }
@@ -3174,9 +3389,6 @@ Field3DParallel& Field3DParallel::operator-=(const BoutReal rhs) {
     BOUT_FOR(index, this->getRegion("RGN_ALL")) { (*this)[index] -= rhs; }
 
     track(rhs, "operator-=");
-#if BOUT_USE_TRACK
-    name = fmt::format("{:s} -= {:s}", this->name, "BR");
-#endif
 
     checkData(*this);
 
@@ -3196,13 +3408,23 @@ Field3DParallel operator*(const BoutReal lhs, const Field3DParallel& rhs) {
 
   result.setRegion(rhs.getRegionID());
   if (result.isFci()) {
-    result.splitParallelSlices();
 
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs * rhs.yup(i);
       result.ydown(i) = lhs * rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -3222,13 +3444,23 @@ Field3DParallel operator/(const BoutReal lhs, const Field3DParallel& rhs) {
 
   result.setRegion(rhs.getRegionID());
   if (result.isFci()) {
-    result.splitParallelSlices();
 
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs / rhs.yup(i);
       result.ydown(i) = lhs / rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -3248,13 +3480,23 @@ Field3DParallel operator+(const BoutReal lhs, const Field3DParallel& rhs) {
 
   result.setRegion(rhs.getRegionID());
   if (result.isFci()) {
-    result.splitParallelSlices();
 
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs + rhs.yup(i);
       result.ydown(i) = lhs + rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {
@@ -3274,13 +3516,23 @@ Field3DParallel operator-(const BoutReal lhs, const Field3DParallel& rhs) {
 
   result.setRegion(rhs.getRegionID());
   if (result.isFci()) {
-    result.splitParallelSlices();
 
     ASSERT2(rhs.hasParallelSlices());
+    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
+      ASSERT2(rhs.ydown(i).isAllocated());
+      ASSERT2(rhs.yup(i).isAllocated());
+    }
+    result.splitParallelSlices();
     for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
       result.yup(i) = lhs - rhs.yup(i);
       result.ydown(i) = lhs - rhs.ydown(i);
     }
+
+    ASSERT2(result.hasParallelSlices());
+    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
+      ASSERT2(result.ydown(i).isAllocated());
+      ASSERT2(result.yup(i).isAllocated());
+    }
   }
 
   BOUT_FOR(index, result.getValidRegionWithDefault("RGN_ALL")) {

From 8ad5817399053624f2c9168d54d1d8dc24eac235 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 11:48:42 +0100
Subject: [PATCH 0906/1827] Do not split parallel slices by default

---
 include/bout/field3d.hxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 438e28c25d..b95617feaf 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -776,7 +776,6 @@ public:
                                                            ZDirectionType::Standard},
                            std::optional<size_t> regionID = {})
       : Field3D(localmesh, location_in, directions_in, regionID) {
-    splitParallelSlices();
     ensureFieldAligned();
   }
   explicit Field3DParallel(Array<BoutReal> data, Mesh* localmesh,

From 8d6e1a9a66e5b4bf22dfcdf5d1cee1a7e24f534e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 11:49:39 +0100
Subject: [PATCH 0907/1827] Simplify Div_par

Also for FCI, the coordinate system is locally field aligned
---
 src/mesh/coordinates.cxx | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 699e1cd440..ef2ee2a375 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1563,15 +1563,7 @@ Field3D Coordinates::Div_par(const Field3DParallel& f, CELL_LOC outloc,
   // Coordinates object
   const auto& Bxy_floc = f.getCoordinates()->Bxy;
 
-  if (!f.hasParallelSlices()) {
-    // No yup/ydown fields. The Grad_par operator will
-    // shift to field aligned coordinates
-    return Bxy * Grad_par(f / Bxy_floc, outloc, method);
-  }
-
-  // Need to modify yup and ydown fields
-  const Field3D Jg = J / sqrt(g_22.asField3DParallel());
-  return Jg * Grad_par(f / Jg, outloc, method);
+  return Bxy * Grad_par(f / Bxy_floc, outloc, method);
 }
 
 /////////////////////////////////////////////////////////

From 7ad4d05ca07fbaa97a4e787d036f58f1bc780ae9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 12:15:27 +0100
Subject: [PATCH 0908/1827] Fix get region call

---
 src/mesh/coordinates.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 8ff6958dcb..ec3483d452 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2091,7 +2091,7 @@ void Coordinates::_compute_cell_area_x() const {
   // metrics.
   auto* mesh = Bxy.getMesh();
   ASSERT0(mesh->xstart > 0);
-  BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOX")) {
+  BOUT_FOR(i, area_centre.getRegion("RGN_NOX")) {
     (*_cell_area_xlow)[i] = 0.5 * (area_centre[i] + area_centre[i.xm()]);
     (*_cell_area_xhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.xp()]);
   }
@@ -2115,7 +2115,7 @@ void Coordinates::_compute_cell_area_y() const {
     // metrics.
     auto* mesh = Bxy.getMesh();
     ASSERT0(mesh->ystart > 0);
-    BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOY")) {
+    BOUT_FOR(i, mesh->getRegion("RGN_NOY")) {
       (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
       (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
     }
@@ -2129,7 +2129,7 @@ void Coordinates::_compute_cell_area_z() const {
   // We cannot setLocation, as that would trigger the computation of staggered
   // metrics.
   //ASSERT0(mesh->zstart > 0);
-  BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOZ")) {
+  BOUT_FOR(i, area_centre.getRegion("RGN_NOZ")) {
     (*_cell_area_zlow)[i] = 0.5 * (area_centre[i] + area_centre[i.zm()]);
     (*_cell_area_zhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.zp()]);
   }

From 6751afda756618998ef8428be004e9f94b4f8d32 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 12:15:39 +0100
Subject: [PATCH 0909/1827] Fix comments

---
 tests/unit/mesh/test_coordinates.cxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx
index e6a9e53028..efe051fe6d 100644
--- a/tests/unit/mesh/test_coordinates.cxx
+++ b/tests/unit/mesh/test_coordinates.cxx
@@ -36,7 +36,7 @@ TEST_F(CoordinatesTest, ZLength) {
                      FieldMetric{0.0},  // g23
                      FieldMetric{1.0},  // g_11
                      FieldMetric{1.0},  // g_22
-                     FieldMetric{1.0},  // g_23
+                     FieldMetric{1.0},  // g_33
                      FieldMetric{0.0},  // g_12
                      FieldMetric{0.0},  // g_13
                      FieldMetric{0.0},  // g_23
@@ -69,7 +69,7 @@ TEST_F(CoordinatesTest, ZLength3D) {
                      FieldMetric{0.0},  // g23
                      FieldMetric{1.0},  // g_11
                      FieldMetric{1.0},  // g_22
-                     FieldMetric{1.0},  // g_23
+                     FieldMetric{1.0},  // g_33
                      FieldMetric{0.0},  // g_12
                      FieldMetric{0.0},  // g_13
                      FieldMetric{0.0},  // g_23
@@ -96,7 +96,7 @@ TEST_F(CoordinatesTest, Jacobian) {
                      FieldMetric{0.0},  // g23
                      FieldMetric{1.0},  // g_11
                      FieldMetric{1.0},  // g_22
-                     FieldMetric{1.0},  // g_23
+                     FieldMetric{1.0},  // g_33
                      FieldMetric{0.0},  // g_12
                      FieldMetric{0.0},  // g_13
                      FieldMetric{0.0},  // g_23
@@ -127,7 +127,7 @@ TEST_F(CoordinatesTest, CalcContravariant) {
                      FieldMetric{0.0},  // g23
                      FieldMetric{0.0},  // g_11
                      FieldMetric{0.0},  // g_22
-                     FieldMetric{0.0},  // g_23
+                     FieldMetric{0.0},  // g_33
                      FieldMetric{0.0},  // g_12
                      FieldMetric{0.0},  // g_13
                      FieldMetric{0.0},  // g_23
@@ -160,7 +160,7 @@ TEST_F(CoordinatesTest, CalcCovariant) {
                      FieldMetric{0.0},  // g23
                      FieldMetric{1.0},  // g_11
                      FieldMetric{1.0},  // g_22
-                     FieldMetric{1.0},  // g_23
+                     FieldMetric{1.0},  // g_33
                      FieldMetric{0.0},  // g_12
                      FieldMetric{0.0},  // g_13
                      FieldMetric{0.0},  // g_23

From 042cf65e824b06eabcc5ed91e4c44959c2794ed4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 12:16:15 +0100
Subject: [PATCH 0910/1827] Switch test to fake_mesh_fixture

Also specify area for testing
---
 tests/unit/mesh/test_coordinates.cxx | 98 ++++++++++++++++++++--------
 1 file changed, 71 insertions(+), 27 deletions(-)

diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx
index efe051fe6d..ea233cd9ca 100644
--- a/tests/unit/mesh/test_coordinates.cxx
+++ b/tests/unit/mesh/test_coordinates.cxx
@@ -274,41 +274,85 @@ TEST_F(CoordinatesTest, NegativeB) {
 
 TEST_F(CoordinatesTest, CellAreas) {
 
-  static_cast<FakeMesh*>(bout::globals::mesh)
-      ->setGridDataSource(
-          new FakeGridDataSource({{"g_11", 4.0}, {"g_22", 1.0}, {"g_33", 9}, {"dz", 1}}));
+  Coordinates coords{mesh,
+                     FieldMetric{1.0},  // dx
+                     FieldMetric{1.0},  // dy
+                     FieldMetric{1.0},  // dz
+                     FieldMetric{6.0},  // J
+                     FieldMetric{1.0},  // Bxy
+                     FieldMetric{1.0},  // g11
+                     FieldMetric{1.0},  // g22
+                     FieldMetric{1.0},  // g33
+                     FieldMetric{0.0},  // g12
+                     FieldMetric{0.0},  // g13
+                     FieldMetric{0.0},  // g23
+                     FieldMetric{4.0},  // g_11
+                     FieldMetric{1.0},  // g_22
+                     FieldMetric{9.0},  // g_33
+                     FieldMetric{0.0},  // g_12
+                     FieldMetric{0.0},  // g_13
+                     FieldMetric{0.0},  // g_23
+                     FieldMetric{0.0},  // ShiftTorsion
+                     FieldMetric{0.0}}; // IntShiftTorsion
+  // No call to Coordinates::geometry() needed here
 
-  Coordinates coords(mesh);
+  EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dz, 1.0));
+
+  EXPECT_TRUE(IsFieldEqual(coords.g_11, 4.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_22, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_33, 9.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_12, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_13, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_23, 0.0));
 
+  EXPECT_TRUE(IsFieldEqual(coords.J, 6.0));
   EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xlow(), 3.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xhigh(), 3.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_ylow(), 6.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_yhigh(), 6.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zlow(), 2.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zhigh(), 2.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xlow(), 3.0, "RGN_NOX"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xhigh(), 3.0, "RGN_NOX"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_ylow(), 6.0, "RGN_NOY"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_yhigh(), 6.0, "RGN_NOY"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zlow(), 2.0, "RGN_NOZ"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zhigh(), 2.0, "RGN_NOZ"));
 
   EXPECT_TRUE(IsFieldEqual(coords.cell_volume(), 6.0));
 }
 
 TEST_F(CoordinatesTest, CellAreasUpdate) {
-
-  static_cast<FakeMesh*>(bout::globals::mesh)
-      ->setGridDataSource(new FakeGridDataSource());
-
-  Coordinates coords(mesh);
+  Coordinates coords{mesh,
+                     FieldMetric{1.0},  // dx
+                     FieldMetric{1.0},  // dy
+                     FieldMetric{1.0},  // dz
+                     FieldMetric{1.0},  // J
+                     FieldMetric{1.0},  // Bxy
+                     FieldMetric{1.0},  // g11
+                     FieldMetric{1.0},  // g22
+                     FieldMetric{1.0},  // g33
+                     FieldMetric{0.0},  // g12
+                     FieldMetric{0.0},  // g13
+                     FieldMetric{0.0},  // g23
+                     FieldMetric{1.0},  // g_11
+                     FieldMetric{1.0},  // g_22
+                     FieldMetric{1.0},  // g_33
+                     FieldMetric{0.0},  // g_12
+                     FieldMetric{0.0},  // g_13
+                     FieldMetric{0.0},  // g_23
+                     FieldMetric{0.0},  // ShiftTorsion
+                     FieldMetric{0.0}}; // IntShiftTorsion
+  // No call to Coordinates::geometry() needed here
 
   EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
   EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
   EXPECT_TRUE(IsFieldEqual(coords.dz, 1.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.g11, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g22, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g33, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g12, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g13, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g23, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_11, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_22, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_33, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_12, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_13, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_23, 0.0));
 
   EXPECT_TRUE(IsFieldEqual(coords.J, 1.0));
   EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
@@ -321,12 +365,12 @@ TEST_F(CoordinatesTest, CellAreasUpdate) {
   coords.cell_area_zhigh() *= 7;
   coords.cell_volume() *= 8;
 
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xlow(), 2.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xhigh(), 3.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_ylow(), 4.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_yhigh(), 5.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zlow(), 6.0));
-  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zhigh(), 7.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xlow(), 2.0, "RGN_NOX"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_xhigh(), 3.0, "RGN_NOX"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_ylow(), 4.0, "RGN_NOY"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_yhigh(), 5.0, "RGN_NOY"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zlow(), 6.0, "RGN_NOZ"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zhigh(), 7.0, "RGN_NOZ"));
 
   EXPECT_TRUE(IsFieldEqual(coords.cell_volume(), 8.0));
 }

From de707f33796cc245438f9cbb8d05a675cb6cb457 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 12:25:15 +0100
Subject: [PATCH 0911/1827] Do not compute Christoffel symbol for FCI

---
 src/mesh/coordinates.cxx | 216 ++++++++++++++++++++-------------------
 1 file changed, 113 insertions(+), 103 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index ef2ee2a375..9f9c47c2e2 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -957,109 +957,119 @@ int Coordinates::geometry(bool recalculate_staggered,
   // Note: This calculation is completely general: metric
   // tensor can be 2D or 3D. For 2D, all DDZ terms are zero
 
-  G1_11 = 0.5 * g11 * DDX(g_11) + g12 * (DDX(g_12) - 0.5 * DDY(g_11))
-          + g13 * (DDX(g_13) - 0.5 * DDZ(g_11));
-  G1_22 = g11 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g12 * DDY(g_22)
-          + g13 * (DDY(g_23) - 0.5 * DDZ(g_22));
-  G1_33 = g11 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g12 * (DDZ(g_23) - 0.5 * DDY(g_33))
-          + 0.5 * g13 * DDZ(g_33);
-  G1_12 = 0.5 * g11 * DDY(g_11) + 0.5 * g12 * DDX(g_22)
-          + 0.5 * g13 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
-  G1_13 = 0.5 * g11 * DDZ(g_11) + 0.5 * g12 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
-          + 0.5 * g13 * DDX(g_33);
-  G1_23 = 0.5 * g11 * (DDZ(g_12) + DDY(g_13) - DDX(g_23))
-          + 0.5 * g12 * (DDZ(g_22) + DDY(g_23) - DDY(g_23))
-          // + 0.5 *g13*(DDZ(g_32) + DDY(g_33) - DDZ(g_23));
-          // which equals
-          + 0.5 * g13 * DDY(g_33);
-
-  G2_11 = 0.5 * g12 * DDX(g_11) + g22 * (DDX(g_12) - 0.5 * DDY(g_11))
-          + g23 * (DDX(g_13) - 0.5 * DDZ(g_11));
-  G2_22 = g12 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g22 * DDY(g_22)
-          + g23 * (DDY(g23) - 0.5 * DDZ(g_22));
-  G2_33 = g12 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g22 * (DDZ(g_23) - 0.5 * DDY(g_33))
-          + 0.5 * g23 * DDZ(g_33);
-  G2_12 = 0.5 * g12 * DDY(g_11) + 0.5 * g22 * DDX(g_22)
-          + 0.5 * g23 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
-  G2_13 =
-      // 0.5 *g21*(DDZ(g_11) + DDX(g_13) - DDX(g_13))
-      // which equals
-      0.5 * g12 * (DDZ(g_11) + DDX(g_13) - DDX(g_13))
-      // + 0.5 *g22*(DDZ(g_21) + DDX(g_23) - DDY(g_13))
-      // which equals
-      + 0.5 * g22 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
-      // + 0.5 *g23*(DDZ(g_31) + DDX(g_33) - DDZ(g_13));
-      // which equals
-      + 0.5 * g23 * DDX(g_33);
-  G2_23 = 0.5 * g12 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g22 * DDZ(g_22)
-          + 0.5 * g23 * DDY(g_33);
-
-  G3_11 = 0.5 * g13 * DDX(g_11) + g23 * (DDX(g_12) - 0.5 * DDY(g_11))
-          + g33 * (DDX(g_13) - 0.5 * DDZ(g_11));
-  G3_22 = g13 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g23 * DDY(g_22)
-          + g33 * (DDY(g_23) - 0.5 * DDZ(g_22));
-  G3_33 = g13 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g23 * (DDZ(g_23) - 0.5 * DDY(g_33))
-          + 0.5 * g33 * DDZ(g_33);
-  G3_12 =
-      // 0.5 *g31*(DDY(g_11) + DDX(g_12) - DDX(g_12))
-      // which equals to
-      0.5 * g13 * DDY(g_11)
-      // + 0.5 *g32*(DDY(g_21) + DDX(g_22) - DDY(g_12))
-      // which equals to
-      + 0.5 * g23 * DDX(g_22)
-      //+ 0.5 *g33*(DDY(g_31) + DDX(g_32) - DDZ(g_12));
-      // which equals to
-      + 0.5 * g33 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
-  G3_13 = 0.5 * g13 * DDZ(g_11) + 0.5 * g23 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
-          + 0.5 * g33 * DDX(g_33);
-  G3_23 = 0.5 * g13 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g23 * DDZ(g_22)
-          + 0.5 * g33 * DDY(g_33);
-
-  G1 = (DDX(J * g11) + DDY(J.asField3DParallel() * g12) + DDZ(J * g13)) / J;
-  G2 = (DDX(J * g12) + DDY(J.asField3DParallel() * g22) + DDZ(J * g23)) / J;
-  G3 = (DDX(J * g13) + DDY(J.asField3DParallel() * g23) + DDZ(J * g33)) / J;
-
-  // Communicate christoffel symbol terms
-  output_progress.write("\tCommunicating connection terms\n");
-
-  localmesh->communicate_no_slices(G1_11, G1_22, G1_33, G1_12, G1_13, G1_23, G2_11, G2_22,
-                                   G2_33, G2_12, G2_13, G2_23, G3_11, G3_22, G3_33, G3_12,
-                                   G3_13, G3_23, G1, G2, G3);
-
-  // Set boundary guard cells of Christoffel symbol terms
-  // Ideally, when location is staggered, we would set the upper/outer boundary point
-  // correctly rather than by extrapolating here: e.g. if location==CELL_YLOW and we are
-  // at the upper y-boundary the x- and z-derivatives at yend+1 at the boundary can be
-  // calculated because the guard cells are available, while the y-derivative could be
-  // calculated from the CELL_CENTRE metric components (which have guard cells available
-  // past the boundary location). This would avoid the problem that the y-boundary on the
-  // CELL_YLOW grid is at a 'guard cell' location (yend+1).
-  // However, the above would require lots of special handling, so just extrapolate for
-  // now.
-  G1_11 = interpolateAndExtrapolate(G1_11, location, true, true, true, transform.get());
-  G1_22 = interpolateAndExtrapolate(G1_22, location, true, true, true, transform.get());
-  G1_33 = interpolateAndExtrapolate(G1_33, location, true, true, true, transform.get());
-  G1_12 = interpolateAndExtrapolate(G1_12, location, true, true, true, transform.get());
-  G1_13 = interpolateAndExtrapolate(G1_13, location, true, true, true, transform.get());
-  G1_23 = interpolateAndExtrapolate(G1_23, location, true, true, true, transform.get());
-
-  G2_11 = interpolateAndExtrapolate(G2_11, location, true, true, true, transform.get());
-  G2_22 = interpolateAndExtrapolate(G2_22, location, true, true, true, transform.get());
-  G2_33 = interpolateAndExtrapolate(G2_33, location, true, true, true, transform.get());
-  G2_12 = interpolateAndExtrapolate(G2_12, location, true, true, true, transform.get());
-  G2_13 = interpolateAndExtrapolate(G2_13, location, true, true, true, transform.get());
-  G2_23 = interpolateAndExtrapolate(G2_23, location, true, true, true, transform.get());
-
-  G3_11 = interpolateAndExtrapolate(G3_11, location, true, true, true, transform.get());
-  G3_22 = interpolateAndExtrapolate(G3_22, location, true, true, true, transform.get());
-  G3_33 = interpolateAndExtrapolate(G3_33, location, true, true, true, transform.get());
-  G3_12 = interpolateAndExtrapolate(G3_12, location, true, true, true, transform.get());
-  G3_13 = interpolateAndExtrapolate(G3_13, location, true, true, true, transform.get());
-  G3_23 = interpolateAndExtrapolate(G3_23, location, true, true, true, transform.get());
-
-  G1 = interpolateAndExtrapolate(G1, location, true, true, true, transform.get());
-  G2 = interpolateAndExtrapolate(G2, location, true, true, true, transform.get());
-  G3 = interpolateAndExtrapolate(G3, location, true, true, true, transform.get());
+  if (!g11.isFci()) {
+    G1_11 = 0.5 * g11 * DDX(g_11) + g12 * (DDX(g_12) - 0.5 * DDY(g_11))
+            + g13 * (DDX(g_13) - 0.5 * DDZ(g_11));
+    G1_22 = g11 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g12 * DDY(g_22)
+            + g13 * (DDY(g_23) - 0.5 * DDZ(g_22));
+    G1_33 = g11 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g12 * (DDZ(g_23) - 0.5 * DDY(g_33))
+            + 0.5 * g13 * DDZ(g_33);
+    G1_12 = 0.5 * g11 * DDY(g_11) + 0.5 * g12 * DDX(g_22)
+            + 0.5 * g13 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
+    G1_13 = 0.5 * g11 * DDZ(g_11) + 0.5 * g12 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
+            + 0.5 * g13 * DDX(g_33);
+    G1_23 = 0.5 * g11 * (DDZ(g_12) + DDY(g_13) - DDX(g_23))
+            + 0.5 * g12 * (DDZ(g_22) + DDY(g_23) - DDY(g_23))
+            // + 0.5 *g13*(DDZ(g_32) + DDY(g_33) - DDZ(g_23));
+            // which equals
+            + 0.5 * g13 * DDY(g_33);
+
+    G2_11 = 0.5 * g12 * DDX(g_11) + g22 * (DDX(g_12) - 0.5 * DDY(g_11))
+            + g23 * (DDX(g_13) - 0.5 * DDZ(g_11));
+    G2_22 = g12 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g22 * DDY(g_22)
+            + g23 * (DDY(g23) - 0.5 * DDZ(g_22));
+    G2_33 = g12 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g22 * (DDZ(g_23) - 0.5 * DDY(g_33))
+            + 0.5 * g23 * DDZ(g_33);
+    G2_12 = 0.5 * g12 * DDY(g_11) + 0.5 * g22 * DDX(g_22)
+            + 0.5 * g23 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
+    G2_13 =
+        // 0.5 *g21*(DDZ(g_11) + DDX(g_13) - DDX(g_13))
+        // which equals
+        0.5 * g12 * (DDZ(g_11) + DDX(g_13) - DDX(g_13))
+        // + 0.5 *g22*(DDZ(g_21) + DDX(g_23) - DDY(g_13))
+        // which equals
+        + 0.5 * g22 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
+        // + 0.5 *g23*(DDZ(g_31) + DDX(g_33) - DDZ(g_13));
+        // which equals
+        + 0.5 * g23 * DDX(g_33);
+    G2_23 = 0.5 * g12 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g22 * DDZ(g_22)
+            + 0.5 * g23 * DDY(g_33);
+
+    G3_11 = 0.5 * g13 * DDX(g_11) + g23 * (DDX(g_12) - 0.5 * DDY(g_11))
+            + g33 * (DDX(g_13) - 0.5 * DDZ(g_11));
+    G3_22 = g13 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g23 * DDY(g_22)
+            + g33 * (DDY(g_23) - 0.5 * DDZ(g_22));
+    G3_33 = g13 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g23 * (DDZ(g_23) - 0.5 * DDY(g_33))
+            + 0.5 * g33 * DDZ(g_33);
+    G3_12 =
+        // 0.5 *g31*(DDY(g_11) + DDX(g_12) - DDX(g_12))
+        // which equals to
+        0.5 * g13 * DDY(g_11)
+        // + 0.5 *g32*(DDY(g_21) + DDX(g_22) - DDY(g_12))
+        // which equals to
+        + 0.5 * g23 * DDX(g_22)
+        //+ 0.5 *g33*(DDY(g_31) + DDX(g_32) - DDZ(g_12));
+        // which equals to
+        + 0.5 * g33 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
+    G3_13 = 0.5 * g13 * DDZ(g_11) + 0.5 * g23 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
+            + 0.5 * g33 * DDX(g_33);
+    G3_23 = 0.5 * g13 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g23 * DDZ(g_22)
+            + 0.5 * g33 * DDY(g_33);
+
+    G1 = (DDX(J * g11) + DDY(J.asField3DParallel() * g12) + DDZ(J * g13)) / J;
+    G2 = (DDX(J * g12) + DDY(J.asField3DParallel() * g22) + DDZ(J * g23)) / J;
+    G3 = (DDX(J * g13) + DDY(J.asField3DParallel() * g23) + DDZ(J * g33)) / J;
+
+    // Communicate christoffel symbol terms
+    output_progress.write("\tCommunicating connection terms\n");
+
+    localmesh->communicate_no_slices(G1_11, G1_22, G1_33, G1_12, G1_13, G1_23, G2_11,
+                                     G2_22, G2_33, G2_12, G2_13, G2_23, G3_11, G3_22,
+                                     G3_33, G3_12, G3_13, G3_23, G1, G2, G3);
+
+    // Set boundary guard cells of Christoffel symbol terms
+    // Ideally, when location is staggered, we would set the upper/outer boundary point
+    // correctly rather than by extrapolating here: e.g. if location==CELL_YLOW and we are
+    // at the upper y-boundary the x- and z-derivatives at yend+1 at the boundary can be
+    // calculated because the guard cells are available, while the y-derivative could be
+    // calculated from the CELL_CENTRE metric components (which have guard cells available
+    // past the boundary location). This would avoid the problem that the y-boundary on the
+    // CELL_YLOW grid is at a 'guard cell' location (yend+1).
+    // However, the above would require lots of special handling, so just extrapolate for
+    // now.
+    G1_11 = interpolateAndExtrapolate(G1_11, location, true, true, true, transform.get());
+    G1_22 = interpolateAndExtrapolate(G1_22, location, true, true, true, transform.get());
+    G1_33 = interpolateAndExtrapolate(G1_33, location, true, true, true, transform.get());
+    G1_12 = interpolateAndExtrapolate(G1_12, location, true, true, true, transform.get());
+    G1_13 = interpolateAndExtrapolate(G1_13, location, true, true, true, transform.get());
+    G1_23 = interpolateAndExtrapolate(G1_23, location, true, true, true, transform.get());
+
+    G2_11 = interpolateAndExtrapolate(G2_11, location, true, true, true, transform.get());
+    G2_22 = interpolateAndExtrapolate(G2_22, location, true, true, true, transform.get());
+    G2_33 = interpolateAndExtrapolate(G2_33, location, true, true, true, transform.get());
+    G2_12 = interpolateAndExtrapolate(G2_12, location, true, true, true, transform.get());
+    G2_13 = interpolateAndExtrapolate(G2_13, location, true, true, true, transform.get());
+    G2_23 = interpolateAndExtrapolate(G2_23, location, true, true, true, transform.get());
+
+    G3_11 = interpolateAndExtrapolate(G3_11, location, true, true, true, transform.get());
+    G3_22 = interpolateAndExtrapolate(G3_22, location, true, true, true, transform.get());
+    G3_33 = interpolateAndExtrapolate(G3_33, location, true, true, true, transform.get());
+    G3_12 = interpolateAndExtrapolate(G3_12, location, true, true, true, transform.get());
+    G3_13 = interpolateAndExtrapolate(G3_13, location, true, true, true, transform.get());
+    G3_23 = interpolateAndExtrapolate(G3_23, location, true, true, true, transform.get());
+
+    G1 = interpolateAndExtrapolate(G1, location, true, true, true, transform.get());
+    G2 = interpolateAndExtrapolate(G2, location, true, true, true, transform.get());
+    G3 = interpolateAndExtrapolate(G3, location, true, true, true, transform.get());
+  } else {
+    G1_11 = G1_22 = G1_33 = G1_12 = G1_13 = G1_23 =
+
+        G2_11 = G2_22 = G2_33 = G2_12 = G2_13 = G2_23 =
+
+            G3_11 = G3_22 = G3_33 = G3_12 = G3_13 = G3_23 =
+
+                G1 = G2 = G3 = BoutNaN;
+  }
 
   //////////////////////////////////////////////////////
   /// Non-uniform meshes. Need to use DDX, DDY

From bd7dd2dd7880a76ee3734e70f1fc09ac95e99cdf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 12:31:57 +0100
Subject: [PATCH 0912/1827] Do not differentiate dy for FCI

---
 src/mesh/coordinates.cxx | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 9f9c47c2e2..c88e5010d9 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1106,11 +1106,15 @@ int Coordinates::geometry(bool recalculate_staggered,
     if (localmesh->get(d2y, "d2y" + suffix, 0.0, false, location)) {
       output_warn.write(
           "\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
-      d1_dy = DDY(1. / dy.asField3DParallel()); // d/di(1/dy)
+      if (dy.isFci()) {
+        d1_dy = BoutNaN;
+      } else {
+        d1_dy = DDY(1. / dy.asField3DParallel()); // d/di(1/dy)
 
-      localmesh->communicate_no_slices(d1_dy);
-      d1_dy =
-          interpolateAndExtrapolate(d1_dy, location, true, true, true, transform.get());
+        localmesh->communicate_no_slices(d1_dy);
+        d1_dy =
+            interpolateAndExtrapolate(d1_dy, location, true, true, true, transform.get());
+      }
     } else {
       d2y.setLocation(location);
       // set boundary cells if necessary

From 481179f0cfc53ebd5f6c7f73c2407b2e4d87ecda Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 17 Mar 2026 10:03:46 +0100
Subject: [PATCH 0913/1827] CI: install pre-release zoidberg

---
 .ci_fedora.sh               | 1 +
 .github/workflows/tests.yml | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index e1dc563c6c..2339ff1b4f 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -47,6 +47,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
+    python -m pip install git+https://github.com/boutproject/zoidberg@better-metric
     echo "starting configure"
     time cmake -S . -B build -DBOUT_USE_PETSC=ON \
 	 -DBOUT_UPDATE_GIT_SUBMODULE=OFF \
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 02f018b873..8919f82df1 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -166,6 +166,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           python -m pip install -r requirements.txt
+          python -m pip install git+https://github.com/boutproject/zoidberg@better-metric
 
       - name: Cache Zenodo test data
         uses: actions/cache@v5
@@ -187,7 +188,7 @@ jobs:
         run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh ${{ matrix.config.build_petsc_branch }}
 
       - name: Build ADIOS2
-        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh 
+        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh
 
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}

From 1a5b922cf53bb0718337c212298a9a97983492b4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 12:52:32 +0100
Subject: [PATCH 0914/1827] CI: fix fedora CI

---
 .ci_fedora.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 2339ff1b4f..a4ead5eb63 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -47,7 +47,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
-    python -m pip install git+https://github.com/boutproject/zoidberg@better-metric
+    python3 -m pip install git+https://github.com/boutproject/zoidberg@better-metric
     echo "starting configure"
     time cmake -S . -B build -DBOUT_USE_PETSC=ON \
 	 -DBOUT_UPDATE_GIT_SUBMODULE=OFF \

From f89333da4e53e4916a321c96e9125c4247c37d55 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 12:52:32 +0100
Subject: [PATCH 0915/1827] CI: fix fedora CI

---
 .ci_fedora.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 2339ff1b4f..a4ead5eb63 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -47,7 +47,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
-    python -m pip install git+https://github.com/boutproject/zoidberg@better-metric
+    python3 -m pip install git+https://github.com/boutproject/zoidberg@better-metric
     echo "starting configure"
     time cmake -S . -B build -DBOUT_USE_PETSC=ON \
 	 -DBOUT_UPDATE_GIT_SUBMODULE=OFF \

From cbacecc2f5d51ab59b242b6e1db959a2790a1ba0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 12:58:30 +0100
Subject: [PATCH 0916/1827] Split slices for FCI

---
 include/bout/field3d.hxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index b95617feaf..9537bf1fa7 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -776,6 +776,9 @@ public:
                                                            ZDirectionType::Standard},
                            std::optional<size_t> regionID = {})
       : Field3D(localmesh, location_in, directions_in, regionID) {
+    if (isFci()) {
+      splitParallelSlices();
+    }
     ensureFieldAligned();
   }
   explicit Field3DParallel(Array<BoutReal> data, Mesh* localmesh,

From d4e137c7536a0e8ae183a65e73e1ea0608af0b67 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 13:08:03 +0100
Subject: [PATCH 0917/1827] CI: ensure pip is installed

---
 .ci_fedora.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index a4ead5eb63..8214a40ccc 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -47,6 +47,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
+    python3 -m ensurepip
     python3 -m pip install git+https://github.com/boutproject/zoidberg@better-metric
     echo "starting configure"
     time cmake -S . -B build -DBOUT_USE_PETSC=ON \

From 3d184a66a55a4f53655b37891101b8fa2293d24d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 13:08:03 +0100
Subject: [PATCH 0918/1827] CI: ensure pip is installed

---
 .ci_fedora.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index a4ead5eb63..8214a40ccc 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -47,6 +47,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
+    python3 -m ensurepip
     python3 -m pip install git+https://github.com/boutproject/zoidberg@better-metric
     echo "starting configure"
     time cmake -S . -B build -DBOUT_USE_PETSC=ON \

From 921cbeb6ea3c05ebef0e600d88f0e1e9f2ff835b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 13:15:26 +0100
Subject: [PATCH 0919/1827] Do not include guard cells in nx check

---
 src/mesh/impls/bout/boutmesh.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 4745cebea0..4d9d368b26 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -268,7 +268,7 @@ void BoutMesh::chooseProcessorSplit(Options& options) {
           _f("Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"),
           NPES, NXPE);
     }
-    if (nx % NXPE != 0) {
+    if ((nx - 2 * MXG) % NXPE != 0) {
       throw BoutException(
           _f("Number of x points ({:d}) not divisible by NPs in x direction ({:d})\n"),
           nx, NXPE);

From 2abbd6c633537e1dc3d988b7842f2c5f97247e18 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 13:48:13 +0100
Subject: [PATCH 0920/1827] Load parallel B rather then J

---
 src/mesh/parallel/fci.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index e20b63d0ea..b6f92ee39b 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -104,7 +104,8 @@ void load_parallel_metric_components(Coordinates* coords, int offset) {
   LOAD_PAR(g_22);
   LOAD_PAR(g_33);
   LOAD_PAR(g_13);
-  LOAD_PAR(J);
+  LOAD_PAR(Bxy);
+
 #undef LOAD_PAR
 }
 #endif

From 243632612120dbd560fbe552319763be7d54f92c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 13:48:27 +0100
Subject: [PATCH 0921/1827] Set parallel J

---
 src/mesh/parallel/fci.cxx | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index b6f92ee39b..a885957ea0 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -457,9 +457,19 @@ void FCITransform::outputVars(Options& output_options) {
 
 void FCITransform::loadParallelMetrics(Coordinates* coords) {
 #if BOUT_USE_METRIC_3D
+  const auto JB0 = mesh.J * mesh.B;
+  mesh.J.splitParallelSlices();
+  mesh.J.disallowCalcParallelSlices();
   for (int i = 1; i <= mesh.ystart; ++i) {
     load_parallel_metric_components(coords, -i);
     load_parallel_metric_components(coords, i);
+
+    mesh.J.ynext(i).allocate();
+    mesh.J.ynext(-i).allocate();
+    BOUT_FOR(j, JB0.getRegion("RGN_NO_BNDRY")) {
+      mesh.J.ynext(i)[j.yp(i)] = JB0[j] / mesh.B.ynext(i)[j.yp(i)];
+      mesh.J.ynext(-i)[j.yp(-i)] = JB0[j] / mesh.B.ynext(-i)[j.yp(-i)];
+    }
   }
 #endif
 }

From c6b6fbef3ea56506d0afd6b604f7f8c9b5321ccd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 13:53:01 +0100
Subject: [PATCH 0922/1827] Fixup message

---
 src/mesh/impls/bout/boutmesh.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 4d9d368b26..d6a0bdb662 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -271,7 +271,7 @@ void BoutMesh::chooseProcessorSplit(Options& options) {
     if ((nx - 2 * MXG) % NXPE != 0) {
       throw BoutException(
           _f("Number of x points ({:d}) not divisible by NPs in x direction ({:d})\n"),
-          nx, NXPE);
+          nx - 2 * MXG, NXPE);
     }
     NYPE = NPES / NXPE;
   } else {

From fe84012f5e0a548971a1cb99969e289acdb251a3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 14:00:03 +0100
Subject: [PATCH 0923/1827] Fixup unit tests

---
 tests/unit/mesh/test_boutmesh.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/unit/mesh/test_boutmesh.cxx b/tests/unit/mesh/test_boutmesh.cxx
index a23b432f70..d803a98155 100644
--- a/tests/unit/mesh/test_boutmesh.cxx
+++ b/tests/unit/mesh/test_boutmesh.cxx
@@ -519,7 +519,7 @@ TEST_F(BoutMeshTest, ChooseProcessorSplitBadNYPENotDivisible_1) {
 TEST_F(BoutMeshTest, ChooseProcessorSplitNXPE) {
   Options options{{"NXPE", 4}};
 
-  BoutMeshExposer mesh(4, 24, 1, 1, 1, 8);
+  BoutMeshExposer mesh(6, 24, 1, 1, 1, 8);
 
   EXPECT_NO_THROW(mesh.chooseProcessorSplit(options));
 
@@ -717,7 +717,7 @@ INSTANTIATE_TEST_SUITE_P(
 
 TEST_P(BoutMeshProcNumTest, ProcNum) {
   WithQuietOutput info{output_info};
-  BoutMeshExposer mesh(4, 4, 1, 1, 1, 4);
+  BoutMeshExposer mesh(6, 4, 1, 1, 1, 4);
 
   const auto params = GetParam();
   Options options{{"NXPE", params.nxpe}};

From c9868d3cba8136a33f59eed316cb5a9a70a6fae5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 14:01:45 +0100
Subject: [PATCH 0924/1827] Fixup J computation

---
 src/mesh/parallel/fci.cxx | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index a885957ea0..e29937df09 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -457,18 +457,18 @@ void FCITransform::outputVars(Options& output_options) {
 
 void FCITransform::loadParallelMetrics(Coordinates* coords) {
 #if BOUT_USE_METRIC_3D
-  const auto JB0 = mesh.J * mesh.B;
-  mesh.J.splitParallelSlices();
-  mesh.J.disallowCalcParallelSlices();
+  const auto JB0 = coords->J * coords->Bxy;
+  coords->J.splitParallelSlices();
+  coords->J.disallowCalcParallelSlices();
   for (int i = 1; i <= mesh.ystart; ++i) {
     load_parallel_metric_components(coords, -i);
     load_parallel_metric_components(coords, i);
 
-    mesh.J.ynext(i).allocate();
-    mesh.J.ynext(-i).allocate();
+    coords->J.ynext(i).allocate();
+    coords->J.ynext(-i).allocate();
     BOUT_FOR(j, JB0.getRegion("RGN_NO_BNDRY")) {
-      mesh.J.ynext(i)[j.yp(i)] = JB0[j] / mesh.B.ynext(i)[j.yp(i)];
-      mesh.J.ynext(-i)[j.yp(-i)] = JB0[j] / mesh.B.ynext(-i)[j.yp(-i)];
+      coords->J.ynext(i)[j.yp(i)] = JB0[j] / coords->Bxy.ynext(i)[j.yp(i)];
+      coords->J.ynext(-i)[j.yp(-i)] = JB0[j] / coords->Bxy.ynext(-i)[j.yp(-i)];
     }
   }
 #endif

From cc172bc524e068f291f6e4be2dbae3b02fa474ce Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 18 Mar 2026 14:12:45 +0100
Subject: [PATCH 0925/1827] Remove Jxz from public API

---
 include/bout/coordinates.hxx | 37 ------------------------------------
 src/mesh/coordinates.cxx     |  2 +-
 2 files changed, 1 insertion(+), 38 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index da22fdd126..22a2de7ac7 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -108,43 +108,6 @@ public:
   const FieldMetric& g_22_yhigh() const;
   FieldMetric& g_22_ylow();
   FieldMetric& g_22_yhigh();
-  /// get Jxz at the cell faces or cell centre
-  const FieldMetric& Jxz_ylow() const {
-    if (!_jxz_ylow.has_value()) {
-      _compute_Jxz_cell_faces();
-    }
-    return *_jxz_ylow;
-  }
-  const FieldMetric& Jxz_yhigh() const {
-    if (!_jxz_yhigh.has_value()) {
-      _compute_Jxz_cell_faces();
-    }
-    return *_jxz_yhigh;
-  }
-  const FieldMetric& Jxz() const {
-    if (!_jxz_centre.has_value()) {
-      _compute_Jxz_cell_faces();
-    }
-    return *_jxz_centre;
-  }
-  FieldMetric& Jxz_ylow() {
-    if (!_jxz_ylow.has_value()) {
-      _compute_Jxz_cell_faces();
-    }
-    return *_jxz_ylow;
-  }
-  FieldMetric& Jxz_yhigh() {
-    if (!_jxz_yhigh.has_value()) {
-      _compute_Jxz_cell_faces();
-    }
-    return *_jxz_yhigh;
-  }
-  FieldMetric& Jxz() {
-    if (!_jxz_centre.has_value()) {
-      _compute_Jxz_cell_faces();
-    }
-    return *_jxz_centre;
-  }
   // Cell Areas
   const FieldMetric& cell_area_xlow() const {
     if (!_cell_area_xlow.has_value()) {
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index ec3483d452..511edfdbe6 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2098,7 +2098,7 @@ void Coordinates::_compute_cell_area_x() const {
 }
 
 void Coordinates::_compute_cell_area_y() const {
-  Jxz();
+  _compute_Jxz_cell_faces();
   if (_jxz_centre->isFci()) {
     ASSERT3(isUniform(dx, true, "RGN_ALL"));
     ASSERT2(isUniform(dx, false, "RGN_ALL"));

From 1c48e719bcd898e8f63d053d41395234662cf911 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 18 Mar 2026 09:00:34 -0700
Subject: [PATCH 0926/1827] examples/fci-operators

Shows how to use the PetscOperators, and compares against the
yup/ydown operators. Includes a script to generate the mesh,
which currently requires a branch of Zoidberg to run.

The code to calculate Grad_par, Div_par and Div_par_Grad_par from
forward and backward operators is now in
`PetscOperators::getParallel()`. That calculates and returns a
collection of `Parallel` operators.

This example could be turned into a test:
- `Grad_par` should be close between the two methods
- Volume integrals of `Div_par` and `Div_par_Grad_par` results should be
  near zero (flux conserved).
---
 examples/CMakeLists.txt                       |   1 +
 examples/fci-operators/CMakeLists.txt         |  14 +++
 examples/fci-operators/data/BOUT.inp          |   5 +
 .../fci-operators/fci_operators_example.cxx   |  48 ++++++++
 examples/fci-operators/makeplots.py           |  81 +++++++++++++
 examples/fci-operators/rotating-ellipse.py    |  91 +++++++++++++++
 include/bout/petsc_operators.hxx              |  15 +++
 src/mesh/petsc_operators.cxx                  | 106 ++++++++++++++++++
 8 files changed, 361 insertions(+)
 create mode 100644 examples/fci-operators/CMakeLists.txt
 create mode 100644 examples/fci-operators/data/BOUT.inp
 create mode 100644 examples/fci-operators/fci_operators_example.cxx
 create mode 100644 examples/fci-operators/makeplots.py
 create mode 100755 examples/fci-operators/rotating-ellipse.py

diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index f2444e6bf6..5eabaf045d 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -18,6 +18,7 @@ add_subdirectory(dalf3)
 add_subdirectory(eigen-box)
 add_subdirectory(elm-pb)
 add_subdirectory(elm-pb-outerloop)
+add_subdirectory(fci-operators)
 add_subdirectory(fci-wave)
 add_subdirectory(finite-volume/diffusion)
 add_subdirectory(finite-volume/fluid)
diff --git a/examples/fci-operators/CMakeLists.txt b/examples/fci-operators/CMakeLists.txt
new file mode 100644
index 0000000000..e010f45b50
--- /dev/null
+++ b/examples/fci-operators/CMakeLists.txt
@@ -0,0 +1,14 @@
+cmake_minimum_required(VERSION 3.13)
+
+project(fci-operators LANGUAGES CXX)
+
+if(NOT TARGET bout++::bout++)
+  find_package(bout++ REQUIRED)
+endif()
+
+bout_add_example(
+  fci-operators
+  SOURCES fci_operators_example.cxx
+  DATA_DIRS data
+  EXTRA_FILES rotating-ellipse-20x8x20.fci.nc makeplots.py
+)
diff --git a/examples/fci-operators/data/BOUT.inp b/examples/fci-operators/data/BOUT.inp
new file mode 100644
index 0000000000..182d49cb96
--- /dev/null
+++ b/examples/fci-operators/data/BOUT.inp
@@ -0,0 +1,5 @@
+[mesh]
+file = "rotating-ellipse-20x8x20.fci.nc"
+
+[mesh:paralleltransform]
+type = fci
diff --git a/examples/fci-operators/fci_operators_example.cxx b/examples/fci-operators/fci_operators_example.cxx
new file mode 100644
index 0000000000..682d7c287c
--- /dev/null
+++ b/examples/fci-operators/fci_operators_example.cxx
@@ -0,0 +1,48 @@
+#include "bout/bout.hxx"
+#include "bout/difops.hxx"
+#include "bout/field.hxx"
+#include "bout/field3d.hxx"
+#include "bout/field_factory.hxx"
+#include "bout/globals.hxx"
+#include "bout/options.hxx"
+#include "bout/petsc_operators.hxx"
+
+int main(int argc, char** argv) {
+  BoutInitialise(argc, argv);
+
+  const PetscOperators ops(bout::globals::mesh);
+
+  // Parallel operators
+  const auto parallel = ops.getParallel();
+
+  // Test field
+  Field3D f = FieldFactory::get()->create3D("sin(y) + cos(z)");
+  bout::globals::mesh->communicate(f);
+  f.applyParallelBoundary("parallel_dirichlet_o2");
+
+  Field3D f_neumann = FieldFactory::get()->create3D("sin(y) + cos(z)");
+  bout::globals::mesh->communicate(f_neumann);
+  f_neumann.applyParallelBoundary("parallel_neumann_o1");
+
+  Options dump;
+  dump["f"] = f;
+  dump["dV"] = parallel.dV;
+
+  dump["grad_par_op"] = parallel.Grad_par(f);
+  dump["grad_par_yud"] = Grad_par(f);
+
+  dump["div_par_op"] = parallel.Div_par(f);
+
+  auto* coords = bout::globals::mesh->getCoordinates();
+  bout::globals::mesh->communicate(coords->Bxy);
+  coords->Bxy.applyParallelBoundary("parallel_neumann_o1");
+  dump["div_par_yud"] = Div_par(f);
+
+  dump["div_par_grad_par_op"] = parallel.Div_par_Grad_par(f_neumann);
+  dump["div_par_grad_par_yud"] = Div_par_K_Grad_par(1.0, f_neumann);
+
+  bout::writeDefaultOutputFile(dump);
+
+  BoutFinalise();
+  return 0;
+}
diff --git a/examples/fci-operators/makeplots.py b/examples/fci-operators/makeplots.py
new file mode 100644
index 0000000000..b10a5829f3
--- /dev/null
+++ b/examples/fci-operators/makeplots.py
@@ -0,0 +1,81 @@
+from boutdata import collect
+import matplotlib.pyplot as plt
+import numpy as np
+
+path = "data"
+
+grad_par_op = collect("grad_par_op", path=path)
+grad_par_yud = collect("grad_par_yud", path=path)
+
+div_par_op = collect("div_par_op", path=path)
+div_par_yud = collect("div_par_yud", path=path)
+
+dV = collect("dV", path=path)  # Cell volume
+
+# Integrate divergence
+op_div_int = np.sum((dV * div_par_op)[2:-2, :, :])
+yud_div_int = np.sum((dV * div_par_yud)[2:-2, :, :])
+
+print(f"Div_par volume integral Op: {op_div_int} Yup/down: {yud_div_int}")
+
+div_par_grad_par_op = collect("div_par_grad_par_op", path=path)
+div_par_grad_par_yud = collect("div_par_grad_par_yud", path=path)
+
+# Integrate divergence
+op_div2_int = np.sum((dV * div_par_grad_par_op)[2:-2, :, :])
+yud_div2_int = np.sum((dV * div_par_grad_par_yud)[2:-2, :, :])
+
+print(f"Div_par_Grad_par volume integral Op: {op_div2_int} Yup/down: {yud_div2_int}")
+
+
+def plot_comparison(a, alabel, b, blabel):
+    fig, axs = plt.subplots(1, 3, figsize=(10, 3))
+    vmax = max([np.amax(a), np.amax(b)])
+    vmin = min([np.amin(a), np.amin(b)])
+
+    cs = axs[0].contourf(a, vmin=vmin, vmax=vmax)
+    fig.colorbar(cs, ax=axs[0])
+    axs[0].set_title(alabel)
+
+    axs[1].contourf(b, vmin=vmin, vmax=vmax)
+    axs[1].set_title(blabel)
+
+    cs = axs[2].contourf(a - b)
+    axs[2].set_title("Difference")
+    fig.colorbar(cs, ax=axs[2])
+
+    return fig
+
+
+fig = plot_comparison(
+    grad_par_op[2:-2, 2, :], "Operator", grad_par_yud[2:-2, 2, :], "Yup/down"
+)
+fig.suptitle("Parallel Gradient")
+fig.tight_layout()
+fig.savefig("gradient.pdf")
+fig.savefig("gradient.png")
+
+fig = plot_comparison(
+    div_par_op[2:-2, 2, :],
+    f"Operator [integral {op_div_int:.2e}]",
+    div_par_yud[2:-2, 2, :],
+    f"Yup/down [integral {yud_div_int:.2e}]",
+)
+fig.suptitle("Parallel Divergence")
+fig.tight_layout()
+fig.savefig("divergence.pdf")
+fig.savefig("divergence.png")
+
+fig = plot_comparison(
+    div_par_grad_par_op[2:-2, 2, :],
+    f"Operator [integral {op_div2_int:.2e}]",
+    div_par_grad_par_yud[2:-2, 2, :],
+    f"Yup/down [integral {yud_div2_int:.2e}]",
+)
+fig.suptitle("Parallel diffusion")
+fig.tight_layout()
+fig.savefig("diffusion.pdf")
+fig.savefig("diffusion.png")
+
+
+plt.show()
diff --git a/examples/fci-operators/rotating-ellipse.py b/examples/fci-operators/rotating-ellipse.py
new file mode 100755
index 0000000000..79e95a9347
--- /dev/null
+++ b/examples/fci-operators/rotating-ellipse.py
@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+
+# Create grids for a rotating ellipse stellarator, based on curvilinear grids
+
+import numpy as np
+
+import zoidberg
+
+#############################################################################
+# Define the magnetic field
+
+# Length in y after which the coils return to their starting (R,Z) locations
+yperiod = 2.0 * np.pi / 5
+
+xcentre = 2.0
+
+magnetic_field = zoidberg.field.RotatingEllipse(
+    xcentre=xcentre,  # Major radius of axis [m]
+    radius=0.8,  # Minor radius of the coils [m]
+    I_coil=0.4,  # Coil current
+    yperiod=yperiod,
+    Btor=1.0,  # Toroidal magnetic field
+)
+
+#############################################################################
+# Create the inner flux surface, starting at a point at phi=0
+# To do this we need to define the y locations of the poloidal points
+# where we will construct grids
+
+start_r = xcentre + 0.4
+start_z = 0.0
+
+nslices = 8  # Number of poloidal slices
+ycoords = np.linspace(0, yperiod, nslices)
+npoints = 20  # Points per poloidal slice
+
+rzcoord, ycoords = zoidberg.fieldtracer.trace_poincare(
+    magnetic_field, start_r, start_z, yperiod, y_slices=ycoords, revs=npoints, nover=1
+)
+
+inner_lines = []
+for i in range(nslices):
+    r = rzcoord[:, i, 0, 0]
+    z = rzcoord[:, i, 0, 1]
+    line = zoidberg.rzline.line_from_points(r, z)
+    # Re-map the points so they're approximately uniform in distance along the surface
+    # Note that this results in some motion of the line
+    line = line.equallySpaced()
+    inner_lines.append(line)
+
+# Now have a list of y coordinates (ycoords) and inner lines (inner_lines)
+
+#############################################################################
+# Generate a fixed circle for the outer boundary
+
+outer_line = zoidberg.rzline.circle(R0=xcentre, r=0.6)
+
+#############################################################################
+# Now have inner and outer boundaries for each poloidal grid
+# Generate a grid on each poloidal slice using the elliptic grid generator
+
+nx = 20
+nz = 20
+
+pol_grids = [
+    zoidberg.poloidal_grid.grid_elliptic(inner_line, outer_line, nx, nz)
+    for inner_line in inner_lines
+]
+
+#############################################################################
+# Create a grid, then calculate forward and backward maps
+
+grid = zoidberg.grid.Grid(pol_grids, ycoords, yperiod, yperiodic=True)
+
+maps = zoidberg.make_maps(grid, magnetic_field)
+
+#############################################################################
+# Interpolation weights
+
+weight_vars = zoidberg.weights.calculate_parallel_map_operators(maps)
+maps.update(weight_vars)
+
+#############################################################################
+# Write grid file
+
+filename = f"rotating-ellipse-{nx}x{nslices}x{nz}.fci.nc"
+
+print(f"Writing to grid file '{filename}'")
+zoidberg.write_maps(
+    grid, magnetic_field, maps, gridfile=filename, new_names=False, metric2d=False
+)
diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 9c7e53fa01..cf87048420 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -419,6 +419,21 @@ public:
     return PetscOperator::diagonal(mapping, f);
   }
 
+  /// A standard collection of operators
+  /// parallel to the magnetic field
+  struct Parallel {
+    PetscOperator Grad_par;         ///< Gradient
+    PetscOperator Div_par;          ///< Divergence
+    PetscOperator Div_par_Grad_par; ///< Diffusion
+    Field3D dV;                     ///< Cell volume
+  };
+
+  /// Calculate a set of parallel operators
+  ///
+  /// This assumes that "forward" and "backward" operators
+  /// are stored in the mesh.
+  Parallel getParallel() const;
+
 private:
   /// Read a `Field3D` from the mesh.
   ///
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index ae682781e9..88dfa94750 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -299,4 +299,110 @@ PetscOperator PetscOperators::get(const std::string& name) const {
                        this->meshGetArray<BoutReal>(this->mesh, name + "_weights"));
 }
 
+PetscOperators::Parallel PetscOperators::getParallel() const {
+  // Read maps from the mesh
+  auto forward = this->get("forward");
+  auto backward = this->get("backward");
+
+  // ---- Construct Grad_par ----
+  //
+  // Create a parallel gradient operator by combining the parallel
+  // length dl = dy * sqrt(g_22) with forward & backward operators
+  auto* coords = this->mesh->getCoordinates();
+  Field3D dl = coords->dy * sqrt(coords->g_22);
+  dl.splitParallelSlices();
+  dl.yup() = 0.0;
+  dl.ydown() = 0.0;
+  dl.applyParallelBoundary("parallel_neumann_o1");
+
+  auto inv_2dl = 0.5 / dl;
+  inv_2dl.splitParallelSlices();
+  inv_2dl.yup() = 0.0;
+  inv_2dl.ydown() = 0.0;
+  inv_2dl.applyParallelBoundary("parallel_neumann_o1");
+
+  inv_2dl.yup() *= 0.5;
+  inv_2dl.ydown() *= 0.5;
+
+  auto inv_2dl_op = this->diagonal(inv_2dl);
+
+  auto Grad_par = inv_2dl_op * (forward - backward);
+
+  // ---- Construct Div_par ----
+  //
+  // Use the Support Operator Method (SOM) to calculate
+  // Div_par from Grad_par and cell volumes.
+
+  // Cell volume
+  auto dV = coords->J * coords->dx * coords->dy * coords->dz;
+  dV.splitParallelSlices();
+  dV.yup() = 0.0;
+  dV.ydown() = 0.0;
+  dV.applyParallelBoundary("parallel_neumann_o1");
+  auto dV_op = this->diagonal(dV);
+
+  Field3D neg_inv_dV = -1. / dV;
+  neg_inv_dV.splitParallelSlices();
+  neg_inv_dV.yup() = 0.0;
+  neg_inv_dV.ydown() = 0.0;
+  neg_inv_dV.applyParallelBoundary("parallel_neumann_o1");
+  auto neg_inv_dV_op = this->diagonal(neg_inv_dV);
+
+  auto Div_par = neg_inv_dV_op * Grad_par.transpose() * dV_op;
+
+  // ---- Construct Div_par_Grad_par ----
+  //
+  // Requires gradients between planes, at +1/2 and -1/2, and interpolation
+  // operators to calculate quantities between cells.
+
+  // Identity operator
+  Field3D one{1.0};
+  one.splitParallelSlices();
+  one.yup() = 1.0;
+  one.ydown() = 1.0;
+  const auto identity = this->diagonal(one);
+
+  // Interpolate at + 1/2
+  const auto interp_plus_op = (identity + forward) * 0.5;
+
+  // dl averaged at +1/2
+  const Field3D dl_plus = interp_plus_op(dl);
+  Field3D inv_dl_plus = 1. / dl_plus;
+  inv_dl_plus.splitParallelSlices();
+  inv_dl_plus.yup() = 0.0;
+  inv_dl_plus.ydown() = 0.0;
+  inv_dl_plus.applyParallelBoundary("parallel_neumann_o1");
+  const auto inv_dl_plus_op = this->diagonal(inv_dl_plus);
+
+  // Gradient at + 1/2
+  const auto Grad_plus = inv_dl_plus_op * (forward - identity);
+
+  // Divergence at -1/2
+  const auto Div_minus = neg_inv_dV_op * Grad_plus.transpose() * dV_op;
+
+  // Interpolate at - 1/2
+  auto interp_minus_op = (identity + backward) * 0.5;
+
+  // dl averaged at -1/2
+  const Field3D dl_minus = interp_minus_op(dl);
+  Field3D inv_dl_minus = 1. / dl_minus;
+  inv_dl_minus.splitParallelSlices();
+  inv_dl_minus.yup() = 0.0;
+  inv_dl_minus.ydown() = 0.0;
+  inv_dl_minus.applyParallelBoundary("parallel_neumann_o1");
+  const auto inv_dl_minus_op = this->diagonal(inv_dl_minus);
+
+  // Gradient at - 1/2
+  auto Grad_minus = inv_dl_minus_op * (identity - backward);
+
+  // Divergence at +1/2
+  const auto Div_plus = neg_inv_dV_op * Grad_minus.transpose() * dV_op;
+
+  // Div(Grad_par()) operator
+  auto Div_par_Grad_par = ((Div_minus * Grad_plus) + (Div_plus * Grad_minus)) * 0.5;
+
+  return Parallel{std::move(Grad_par), std::move(Div_par), std::move(Div_par_Grad_par),
+                  std::move(dV)};
+}
+
 #endif // BOUT_HAS_PETSC

From d5e1218b8c6d7bec3e9b3877c23ca129df9f2006 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 18 Mar 2026 11:13:56 -0700
Subject: [PATCH 0927/1827] PetscOperators::Parallel::Div_par_K_Grad_par

This is a function rather than a PetscOperator because it
requires at least two matrix-vector products. This
implementation requires six Mat-Vec products that could probably be
optimized.
---
 include/bout/petsc_operators.hxx | 20 ++++++++++++++++----
 src/mesh/petsc_operators.cxx     | 32 +++++++++++++++++++++++++-------
 2 files changed, 41 insertions(+), 11 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index cf87048420..8ab95d0f17 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -244,13 +244,13 @@ private:
   Region<Ind3D> ydown_region;
 
   /// First and one-past-last PETSc global rows owned by this rank.
-  PetscInt row_start, row_end;
+  PetscInt row_start{}, row_end{};
 
   /// Permutation matrix mapping mesh-global ordering to PETSc ordering.
-  Mat mat_mesh_to_petsc;
+  Mat mat_mesh_to_petsc{nullptr};
 
   /// Permutation matrix mapping PETSc ordering to mesh-global ordering.
-  Mat mat_petsc_to_mesh;
+  Mat mat_petsc_to_mesh{nullptr};
 };
 
 /// Shared pointer to an immutable `PetscMapping`.
@@ -380,7 +380,7 @@ private:
 
   /// Copy contents of f, f.yup() and f.ydown() into vec.
   /// Assumes that vec has already been allocated.
-  static void copyToVec(PetscMappingPtr mapping, const Field3D& f, Vec vec);
+  static void copyToVec(const PetscMappingPtr& mapping, const Field3D& f, Vec vec);
 
   // Allocate MPI vector
   static UniqueVec createVec(PetscInt local_size);
@@ -426,6 +426,18 @@ public:
     PetscOperator Div_par;          ///< Divergence
     PetscOperator Div_par_Grad_par; ///< Diffusion
     Field3D dV;                     ///< Cell volume
+
+    PetscOperator Grad_minus;
+    PetscOperator Grad_plus;
+    PetscOperator Div_minus;
+    PetscOperator Div_plus;
+
+    PetscOperator Interp_minus;
+    PetscOperator Interp_plus;
+
+    /// This is a bilinear operator that requires multiple
+    /// matrix-vector products.
+    Field3D Div_par_K_Grad_par(const Field3D& K, const Field3D& f) const;
   };
 
   /// Calculate a set of parallel operators
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 88dfa94750..98db8eea08 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -170,7 +170,7 @@ PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int
   BOUT_DO_PETSC(MatDestroy(&mat));
 }
 
-void PetscOperator::copyToVec(PetscMappingPtr mapping, const Field3D& f, Vec vec) {
+void PetscOperator::copyToVec(const PetscMappingPtr& mapping, const Field3D& f, Vec vec) {
   ASSERT1(f.hasParallelSlices());
   ASSERT1(f.yup().isAllocated());
   ASSERT1(f.ydown().isAllocated());
@@ -363,7 +363,7 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   const auto identity = this->diagonal(one);
 
   // Interpolate at + 1/2
-  const auto interp_plus_op = (identity + forward) * 0.5;
+  auto interp_plus_op = (identity + forward) * 0.5;
 
   // dl averaged at +1/2
   const Field3D dl_plus = interp_plus_op(dl);
@@ -375,10 +375,10 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   const auto inv_dl_plus_op = this->diagonal(inv_dl_plus);
 
   // Gradient at + 1/2
-  const auto Grad_plus = inv_dl_plus_op * (forward - identity);
+  auto Grad_plus = inv_dl_plus_op * (forward - identity);
 
   // Divergence at -1/2
-  const auto Div_minus = neg_inv_dV_op * Grad_plus.transpose() * dV_op;
+  auto Div_minus = neg_inv_dV_op * Grad_plus.transpose() * dV_op;
 
   // Interpolate at - 1/2
   auto interp_minus_op = (identity + backward) * 0.5;
@@ -396,13 +396,31 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   auto Grad_minus = inv_dl_minus_op * (identity - backward);
 
   // Divergence at +1/2
-  const auto Div_plus = neg_inv_dV_op * Grad_minus.transpose() * dV_op;
+  auto Div_plus = neg_inv_dV_op * Grad_minus.transpose() * dV_op;
 
   // Div(Grad_par()) operator
   auto Div_par_Grad_par = ((Div_minus * Grad_plus) + (Div_plus * Grad_minus)) * 0.5;
 
-  return Parallel{std::move(Grad_par), std::move(Div_par), std::move(Div_par_Grad_par),
-                  std::move(dV)};
+  return Parallel{std::move(Grad_par),         std::move(Div_par),
+                  std::move(Div_par_Grad_par), std::move(dV),
+                  std::move(Grad_minus),       std::move(Grad_plus),
+                  std::move(Div_minus),        std::move(Div_plus),
+                  std::move(interp_minus_op),  std::move(interp_plus_op)};
+}
+
+Field3D PetscOperators::Parallel::Div_par_K_Grad_par(const Field3D& K,
+                                                     const Field3D& f) const {
+  // Calculate gradients in + and - directions
+  const Field3D grad_plus = this->Grad_plus(f);
+  const Field3D grad_minus = this->Grad_minus(f);
+
+  // Interpolate K to + and - locations
+  const Field3D K_plus = this->Interp_plus(K);
+  const Field3D K_minus = this->Interp_minus(K);
+
+  // Calculate divergence
+  return (this->Div_minus(K_plus * grad_plus) + this->Div_plus(K_minus * grad_minus))
+         * 0.5;
 }
 
 #endif // BOUT_HAS_PETSC

From a50c53166305cb12714a149dc4197d2983fc85cb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 08:15:17 +0100
Subject: [PATCH 0928/1827] Fix region name

---
 src/mesh/parallel/fci.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index e29937df09..6b7dfaa26b 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -466,7 +466,7 @@ void FCITransform::loadParallelMetrics(Coordinates* coords) {
 
     coords->J.ynext(i).allocate();
     coords->J.ynext(-i).allocate();
-    BOUT_FOR(j, JB0.getRegion("RGN_NO_BNDRY")) {
+    BOUT_FOR(j, JB0.getRegion("RGN_NOBNDRY")) {
       coords->J.ynext(i)[j.yp(i)] = JB0[j] / coords->Bxy.ynext(i)[j.yp(i)];
       coords->J.ynext(-i)[j.yp(-i)] = JB0[j] / coords->Bxy.ynext(-i)[j.yp(-i)];
     }

From b57ea103c2d432224e39ccb53a4f60dce0f560db Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 09:42:08 +0100
Subject: [PATCH 0929/1827] Do not attempt to communicate Bxy

---
 tests/MMS/spatial/fci/fci_mms.cxx | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/tests/MMS/spatial/fci/fci_mms.cxx b/tests/MMS/spatial/fci/fci_mms.cxx
index 7967452f3d..90bf107f3c 100644
--- a/tests/MMS/spatial/fci/fci_mms.cxx
+++ b/tests/MMS/spatial/fci/fci_mms.cxx
@@ -46,12 +46,6 @@ int main(int argc, char** argv) {
   Field3D K{FieldFactory::get()->create3D("K", Options::getRoot(), mesh)};
 
   // Communicate to calculate parallel transform.
-  if constexpr (bout::build::use_metric_3d) {
-    // Div_par operators require B parallel slices:
-    // Coordinates::geometry doesn't ensure this (yet)
-    auto& Bxy = mesh->getCoordinates()->Bxy;
-    mesh->communicate(Bxy);
-  }
   mesh->communicate(input, K);
 
   Options dump;

From be8bae53e8c3d4397a19fd598b66cd17fd5cd4f6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 09:42:37 +0100
Subject: [PATCH 0930/1827] Update to newer mesh with parallel metrics

---
 tests/integrated/test-fci-mpi/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-fci-mpi/CMakeLists.txt b/tests/integrated/test-fci-mpi/CMakeLists.txt
index 0abbbce099..ba126d7e76 100644
--- a/tests/integrated/test-fci-mpi/CMakeLists.txt
+++ b/tests/integrated/test-fci-mpi/CMakeLists.txt
@@ -4,7 +4,7 @@ bout_add_mms_test(
   USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 6
   DOWNLOAD
-    https://zenodo.org/records/7614499/files/W7X-conf4-36x8x128.fci.nc?download=1
+    https://zenodo.org/records/17571607/files/W7X-conf0-36x8x128.fci.nc?download=1
   DOWNLOAD_NAME grid.fci.nc
   REQUIRES BOUT_HAS_PETSC
 )

From 94b00c82dc84d3d7d24792bebcd31c5aeb0c5605 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 11:45:05 +0100
Subject: [PATCH 0931/1827] Enable `uv lock`

Co-authored-by: Peter Hill <peter.hill@york.ac.uk>
---
 pyproject.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 71a67f87dd..f7ccf83cff 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,3 +24,5 @@ maint = [
       "ruamel-yaml~=0.19",
       "Unidecode~=1.3",
 ]
+
+[tool.uv.workspace]

From 65126040ddb4dd93fbab169f2b4c18e49067d9d0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 11:45:28 +0100
Subject: [PATCH 0932/1827] Update uv.lock file

---
 uv.lock | 210 ++++++++++++++++++++++++++++++--------------------------
 1 file changed, 113 insertions(+), 97 deletions(-)

diff --git a/uv.lock b/uv.lock
index 8dce73e775..0ca4068eb8 100644
--- a/uv.lock
+++ b/uv.lock
@@ -90,52 +90,68 @@ wheels = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.4.5"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/1d/35/02daf95b9cd686320bb622eb148792655c9412dbb9b67abb5694e5910a24/charset_normalizer-3.4.5.tar.gz", hash = "sha256:95adae7b6c42a6c5b5b559b1a99149f090a57128155daeea91732c8d970d8644", size = 134804, upload-time = "2026-03-06T06:03:19.46Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/43/be/0f0fd9bb4a7fa4fb5067fb7d9ac693d4e928d306f80a0d02bde43a7c4aee/charset_normalizer-3.4.5-cp314-cp314-macosx_10_15_universal2.whl", hash = "sha256:8197abe5ca1ffb7d91e78360f915eef5addff270f8a71c1fc5be24a56f3e4873", size = 280232, upload-time = "2026-03-06T06:02:01.508Z" },
-    { url = "https://files.pythonhosted.org/packages/28/02/983b5445e4bef49cd8c9da73a8e029f0825f39b74a06d201bfaa2e55142a/charset_normalizer-3.4.5-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:a2aecdb364b8a1802afdc7f9327d55dad5366bc97d8502d0f5854e50712dbc5f", size = 189688, upload-time = "2026-03-06T06:02:02.857Z" },
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 [[package]]

From 1ecca512ed6350c4459f0c251947ae0dc246c3bc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 11:54:24 +0100
Subject: [PATCH 0933/1827] Update prek file

---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a6fefc34cb..84a440847b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -24,14 +24,14 @@ repos:
 
 # C++ formatting
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v22.1.0
+  rev: v22.1.1
   hooks:
   - id: clang-format
     types_or: [c++, c, cuda]
 
 # Python linting and formatting
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.5
+  rev: v0.15.6
   hooks:
     # Run the linter.
     - id: ruff-check

From ac0c5b0e4b3ded9afe2fd52806377117f26a9d82 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 11:57:07 +0100
Subject: [PATCH 0934/1827] Add docs for updating uv tools

---
 manual/sphinx/developer_docs/contributing.rst | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/manual/sphinx/developer_docs/contributing.rst b/manual/sphinx/developer_docs/contributing.rst
index 4ef9892bff..062415af04 100644
--- a/manual/sphinx/developer_docs/contributing.rst
+++ b/manual/sphinx/developer_docs/contributing.rst
@@ -224,6 +224,14 @@ The quickest way to run all the formatters on a PR at once is typically:
 
 This will run all our formatters on files that have changed since ``next``.
 
+The tools can be updated with:
+
+.. code-block:: console
+
+    uv lock -U
+    uv tool run sync-with-uv
+
+
 Install Pre-Commit Hooks (Optional but recommended)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

From 8fe3b05c2449a0fc9c0a49df2054728fe272b3a3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 12:27:56 +0100
Subject: [PATCH 0935/1827] Apply clang-tidy recommendations

---
 include/bout/paralleltransform.hxx | 1 +
 src/mesh/parallel/fci.cxx          | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx
index 0b425de209..d9ed397bb5 100644
--- a/include/bout/paralleltransform.hxx
+++ b/include/bout/paralleltransform.hxx
@@ -9,6 +9,7 @@
 #include "bout/bout_types.hxx"
 #include "bout/dcomplex.hxx"
 #include "bout/field3d.hxx"
+#include "bout/field_data.hxx"
 #include "bout/options.hxx"
 #include "bout/unused.hxx"
 
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 6b7dfaa26b..c92cdfd6c9 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -41,6 +41,7 @@
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_data.hxx"
@@ -66,7 +67,7 @@ using namespace std::string_view_literals;
 
 namespace {
 // Get a unique name for a field based on the sign/magnitude of the offset
-std::string parallel_slice_field_name(std::string field, int offset) {
+std::string parallel_slice_field_name(const std::string& field, int offset) {
   const std::string direction = (offset > 0) ? "forward" : "backward";
   // We only have a suffix for parallel slices beyond the first
   // This is for backwards compatibility

From ce5d26adfe528cf55c090e59461301889268a488 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 12:28:57 +0100
Subject: [PATCH 0936/1827] coords is only used for 3D build

---
 src/mesh/parallel/fci.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index c92cdfd6c9..bf89932479 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -456,7 +456,7 @@ void FCITransform::outputVars(Options& output_options) {
   output_options["Z"].force(Z, "FCI");
 }
 
-void FCITransform::loadParallelMetrics(Coordinates* coords) {
+void FCITransform::loadParallelMetrics([[maybe_unused]] Coordinates* coords) {
 #if BOUT_USE_METRIC_3D
   const auto JB0 = coords->J * coords->Bxy;
   coords->J.splitParallelSlices();

From 202e51d8b55bd2417c573700db962458b67c527f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 12:47:57 +0100
Subject: [PATCH 0937/1827] Set the regionID for parallel slices

---
 src/mesh/parallel/fci.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 6b7dfaa26b..7a63dbf30a 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -88,6 +88,7 @@ void load_parallel_metric_component(std::string name, Field3D& component, int of
   if (!component.hasParallelSlices()) {
     component.splitParallelSlices();
     component.disallowCalcParallelSlices();
+    component.resetRegionParallel();
   }
   auto& pcom = component.ynext(offset);
   pcom.allocate();
@@ -460,6 +461,7 @@ void FCITransform::loadParallelMetrics(Coordinates* coords) {
   const auto JB0 = coords->J * coords->Bxy;
   coords->J.splitParallelSlices();
   coords->J.disallowCalcParallelSlices();
+  coords->J.resetRegionParallel();
   for (int i = 1; i <= mesh.ystart; ++i) {
     load_parallel_metric_components(coords, -i);
     load_parallel_metric_components(coords, i);

From f828a9c7a5c1db1356c38a2bf1954ebd853641fb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 13:07:44 +0100
Subject: [PATCH 0938/1827] Allow to override isFci check

---
 include/bout/field3d.hxx | 2 +-
 src/field/field3d.cxx    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index f88e84f131..68dc84d1a7 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -342,7 +342,7 @@ public:
   const Region<Ind3D>& getValidRegionWithDefault(const std::string& region_name) const;
   void setRegion(const std::string& region_name) override;
   void resetRegion() override { regionID.reset(); };
-  void resetRegionParallel();
+  void resetRegionParallel(bool force = false);
   void setRegion(size_t id) override { regionID = id; };
   void setRegion(std::optional<size_t> id) override { regionID = id; };
   std::optional<size_t> getRegionID() const override { return regionID; };
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index a123074572..38b2682606 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -883,8 +883,8 @@ void Field3D::setRegion(const std::string& region_name) {
   regionID = fieldmesh->getRegionID(region_name);
 }
 
-void Field3D::resetRegionParallel() {
-  if (isFci()) {
+void Field3D::resetRegionParallel(const bool force) {
+  if (force or isFci()) {
     for (int i = 0; i < fieldmesh->ystart; ++i) {
       yup_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", i + 1));
       ydown_fields[i].setRegion(fmt::format("RGN_YPAR_{:+d}", -i - 1));

From 1d7b9f0cca654f1479475c3952b42583b4f0498d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 13:09:35 +0100
Subject: [PATCH 0939/1827] Parallel transform is not yet set, so we need to
 overwrite the isFci check

---
 src/mesh/parallel/fci.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 7a63dbf30a..c23185460f 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -88,7 +88,7 @@ void load_parallel_metric_component(std::string name, Field3D& component, int of
   if (!component.hasParallelSlices()) {
     component.splitParallelSlices();
     component.disallowCalcParallelSlices();
-    component.resetRegionParallel();
+    component.resetRegionParallel(true);
   }
   auto& pcom = component.ynext(offset);
   pcom.allocate();
@@ -461,7 +461,7 @@ void FCITransform::loadParallelMetrics(Coordinates* coords) {
   const auto JB0 = coords->J * coords->Bxy;
   coords->J.splitParallelSlices();
   coords->J.disallowCalcParallelSlices();
-  coords->J.resetRegionParallel();
+  coords->J.resetRegionParallel(true);
   for (int i = 1; i <= mesh.ystart; ++i) {
     load_parallel_metric_components(coords, -i);
     load_parallel_metric_components(coords, i);

From 4b49458166705550e757fbca6b47e5e686392e7e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 19 Mar 2026 13:10:37 +0100
Subject: [PATCH 0940/1827] Revert "Do not differentiate dy for FCI"

This reverts commit bd7dd2dd7880a76ee3734e70f1fc09ac95e99cdf.
---
 src/mesh/coordinates.cxx | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 798a62b64f..1157f3a823 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1111,15 +1111,11 @@ int Coordinates::geometry(bool recalculate_staggered,
     if (localmesh->get(d2y, "d2y" + suffix, 0.0, false, location)) {
       output_warn.write(
           "\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
-      if (dy.isFci()) {
-        d1_dy = BoutNaN;
-      } else {
-        d1_dy = DDY(1. / dy.asField3DParallel()); // d/di(1/dy)
+      d1_dy = DDY(1. / dy.asField3DParallel()); // d/di(1/dy)
 
-        localmesh->communicate_no_slices(d1_dy);
-        d1_dy =
-            interpolateAndExtrapolate(d1_dy, location, true, true, true, transform.get());
-      }
+      localmesh->communicate_no_slices(d1_dy);
+      d1_dy =
+          interpolateAndExtrapolate(d1_dy, location, true, true, true, transform.get());
     } else {
       d2y.setLocation(location);
       // set boundary cells if necessary

From 9a44ff8a565a75fe6dcd7c3f1bbdd279b254e472 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 19 Mar 2026 20:37:51 -0700
Subject: [PATCH 0941/1827] WIP: Sub-cell sampling

Trace multiple field lines per cell, to construct smoother maps.
A complication is cells that partially intersect a boundary.
---
 examples/fci-operators/rotating-ellipse.py | 15 +++++++++--
 src/mesh/petsc_operators.cxx               | 29 +++++++++++++++++++---
 2 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/examples/fci-operators/rotating-ellipse.py b/examples/fci-operators/rotating-ellipse.py
index 79e95a9347..3aa485c093 100755
--- a/examples/fci-operators/rotating-ellipse.py
+++ b/examples/fci-operators/rotating-ellipse.py
@@ -72,18 +72,29 @@
 
 grid = zoidberg.grid.Grid(pol_grids, ycoords, yperiod, yperiodic=True)
 
-maps = zoidberg.make_maps(grid, magnetic_field)
+samples_per_dim = 5  # Sub-sampling in each cell
+
+maps = zoidberg.make_maps(grid, magnetic_field, samples_per_dim=samples_per_dim)
 
 #############################################################################
 # Interpolation weights
 
 weight_vars = zoidberg.weights.calculate_parallel_map_operators(maps)
 maps.update(weight_vars)
+# Remove sub-sampled maps from output
+for var in [
+    "forward_xt_primes",
+    "forward_zt_primes",
+    "backward_xt_primes",
+    "backward_zt_primes",
+    "subcell_weights",
+]:
+    maps.pop(var, None)
 
 #############################################################################
 # Write grid file
 
-filename = f"rotating-ellipse-{nx}x{nslices}x{nz}.fci.nc"
+filename = f"rotating-ellipse-{nx}x{nslices}x{nz}-s{samples_per_dim}.fci.nc"
 
 print(f"Writing to grid file '{filename}'")
 zoidberg.write_maps(
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 98db8eea08..2b11c3aa7c 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -321,9 +321,6 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   inv_2dl.ydown() = 0.0;
   inv_2dl.applyParallelBoundary("parallel_neumann_o1");
 
-  inv_2dl.yup() *= 0.5;
-  inv_2dl.ydown() *= 0.5;
-
   auto inv_2dl_op = this->diagonal(inv_2dl);
 
   auto Grad_par = inv_2dl_op * (forward - backward);
@@ -339,7 +336,19 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   dV.yup() = 0.0;
   dV.ydown() = 0.0;
   dV.applyParallelBoundary("parallel_neumann_o1");
-  auto dV_op = this->diagonal(dV);
+
+  // Fractional boundary cells
+  const auto forward_boundary_fraction =
+      meshGetField3D(this->mesh, "forward_boundary_fraction");
+  const auto backward_boundary_fraction =
+      meshGetField3D(this->mesh, "backward_boundary_fraction");
+
+  BOUT_FOR(i, dV.getRegion("RGN_NOBNDRY")) {
+    dV.yup()[i.yp()] *= forward_boundary_fraction[i];
+    dV.ydown()[i.ym()] *= backward_boundary_fraction[i];
+  }
+
+  const auto dV_op = this->diagonal(dV);
 
   Field3D neg_inv_dV = -1. / dV;
   neg_inv_dV.splitParallelSlices();
@@ -410,6 +419,18 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
 
 Field3D PetscOperators::Parallel::Div_par_K_Grad_par(const Field3D& K,
                                                      const Field3D& f) const {
+
+  // There are 4 matrix-vector products that could be performed in parallel.
+  // The best way to optimize this is probably to pack f and K into one Vec,
+  // and assemble a single sparse matrix that contains the four blocks:
+  //
+  //  (Grad_plus       0     )           (grad_plus  )
+  //  (Grad_minus      0     ) (f)   ->  (grad_minus )
+  //  (    0     Interp_plus ) (K)       (K_plus     )
+  //  (    0     Interp_minus)           (K_minus    )
+  //
+  // For now we perform each operation in sequence.
+
   // Calculate gradients in + and - directions
   const Field3D grad_plus = this->Grad_plus(f);
   const Field3D grad_minus = this->Grad_minus(f);

From 3992b8c7be99c66e6733600e09f8e3261f03d708 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 19 Mar 2026 20:46:53 -0700
Subject: [PATCH 0942/1827] fci-operators example: Don't include mesh file

Mesh not available in repo, only generation script.
---
 examples/fci-operators/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/fci-operators/CMakeLists.txt b/examples/fci-operators/CMakeLists.txt
index e010f45b50..3a19ea9dcc 100644
--- a/examples/fci-operators/CMakeLists.txt
+++ b/examples/fci-operators/CMakeLists.txt
@@ -10,5 +10,5 @@ bout_add_example(
   fci-operators
   SOURCES fci_operators_example.cxx
   DATA_DIRS data
-  EXTRA_FILES rotating-ellipse-20x8x20.fci.nc makeplots.py
+  EXTRA_FILES rotating-ellipse.py makeplots.py
 )

From d2f26bb31dac5d8165b5978ce94d06d83f4f57c7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 19 Mar 2026 21:05:51 -0700
Subject: [PATCH 0943/1827] PetscOperators: Specify dV is Field3D

Fix for when metrics are 2D.
---
 src/mesh/petsc_operators.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 2b11c3aa7c..6767ebe716 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -331,7 +331,7 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   // Div_par from Grad_par and cell volumes.
 
   // Cell volume
-  auto dV = coords->J * coords->dx * coords->dy * coords->dz;
+  Field3D dV = coords->J * coords->dx * coords->dy * coords->dz;
   dV.splitParallelSlices();
   dV.yup() = 0.0;
   dV.ydown() = 0.0;

From c865d1b408f3818789bfb186f0010d349ebfa2b0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 20 Mar 2026 12:07:58 +0100
Subject: [PATCH 0944/1827] Load parallel dy

---
 src/mesh/parallel/fci.cxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index c23185460f..ce391c2bdc 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -105,6 +105,7 @@ void load_parallel_metric_components(Coordinates* coords, int offset) {
   LOAD_PAR(g_22);
   LOAD_PAR(g_33);
   LOAD_PAR(g_13);
+  LOAD_PAR(dy);
   LOAD_PAR(Bxy);
 
 #undef LOAD_PAR

From 07afd43874e40715c59ede8936c70454348a0245 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 20 Mar 2026 12:08:17 +0100
Subject: [PATCH 0945/1827] Output that we load the parallel metrics

---
 src/mesh/parallel/fci.cxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index ce391c2bdc..5b23ce7fc6 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -459,6 +459,7 @@ void FCITransform::outputVars(Options& output_options) {
 
 void FCITransform::loadParallelMetrics(Coordinates* coords) {
 #if BOUT_USE_METRIC_3D
+  output_info.write("\tLoading parallel metrics\n");
   const auto JB0 = coords->J * coords->Bxy;
   coords->J.splitParallelSlices();
   coords->J.disallowCalcParallelSlices();

From 32078e2cf96c9b1d9f1be7db821660e116d90291 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 20 Mar 2026 12:24:06 +0100
Subject: [PATCH 0946/1827] Remove init function from YBoundary

Use the constructor
---
 include/bout/yboundary_regions.hxx                  | 13 +------------
 manual/sphinx/user_docs/boundary_options.rst        |  6 ++----
 .../integrated/test-fci-boundary/get_par_bndry.cxx  |  3 +--
 3 files changed, 4 insertions(+), 18 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 6254ef7862..bee4634310 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -23,7 +23,6 @@ class YBoundary {
 public:
   template <class F>
   void iter_regions(const F& f) {
-    ASSERT1(is_init);
     for (auto& region : boundary_regions) {
       f(*region);
     }
@@ -45,13 +44,7 @@ public:
     return iter_regions(f);
   }
 
-  void init(Options& options, Mesh* mesh = nullptr) {
-    if (is_init) {
-      if (optptr == &options) {
-        return;
-      }
-      throw BoutException("YBoundary is already initialised!");
-    }
+  YBoundary(Options& options, Mesh* mesh = nullptr) {
     if (mesh == nullptr) {
       mesh = bout::globals::mesh;
     }
@@ -86,8 +79,6 @@ public:
             mesh, false, mesh->iterateBndryUpperY()));
       }
     }
-    is_init = true;
-    optptr = &options;
     // Cache boundary regions
     _contains.emplace_back(mesh, false);
     _contains.emplace_back(mesh, false);
@@ -127,6 +118,4 @@ private:
   std::vector<std::shared_ptr<NewBoundaryRegionY>> boundary_regions;
 
   std::vector<BoutMask> _contains;
-  bool is_init{false};
-  Options* optptr;
 };
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index f04d09cabc..d65ed0ba79 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -495,10 +495,8 @@ geometries, as flux coordinate independent (FCI) method::
 
     class yboundary_example {
     public:
-      yboundary_example(Options* opt, const Field3D& N, const Field3D& V) : N(N), V(V) {
-        // Set what kind of yboundaries you want to include
-        yboundary.init(opt);
-      }
+      yboundary_example(Options* opt, const Field3D& N, const Field3D& V) :
+      N(N), V(V), yboundary(opt) {}
 
       void rhs() {
         BoutReal totalFlux = 0;
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 0871577b86..f72438b4e3 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -45,8 +45,7 @@ int main(int argc, char** argv) {
 
   {
     Options dummy;
-    YBoundary ybndry;
-    ybndry.init(dummy, mesh);
+    YBoundary ybndry(dummy, mesh);
 
     std::vector<Field3D> fields((mesh->ystart * 2) + 1, Field3D{0.0});
     for (auto& field : fields) {

From f684326aa1cec53d022f9c59c9f3de77600c1f66 Mon Sep 17 00:00:00 2001
From: wearysebas <sebichito@gmail.com>
Date: Fri, 20 Mar 2026 17:03:55 +0000
Subject: [PATCH 0947/1827] Fixed issue with the topology_cross_section image
 and rebased onto next branc and rebased onto next branch.

---
 manual/sphinx/figs/topology_cross_section.svg | 1609 -----------------
 ...ection.png => topology_cross_section2.png} |  Bin
 manual/sphinx/user_docs/topology.rst          |  224 +++
 3 files changed, 224 insertions(+), 1609 deletions(-)
 delete mode 100644 manual/sphinx/figs/topology_cross_section.svg
 rename manual/sphinx/figs/{topology_cross_section.png => topology_cross_section2.png} (100%)
 create mode 100644 manual/sphinx/user_docs/topology.rst

diff --git a/manual/sphinx/figs/topology_cross_section.svg b/manual/sphinx/figs/topology_cross_section.svg
deleted file mode 100644
index 5c1ab47523..0000000000
--- a/manual/sphinx/figs/topology_cross_section.svg
+++ /dev/null
@@ -1,1609 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!-- Created with Inkscape (http://www.inkscape.org/) -->
-
-<svg
-   xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
-   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-   xmlns:svg="http://www.w3.org/2000/svg"
-   xmlns="http://www.w3.org/2000/svg"
-   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
-   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
-   width="601.08875"
-   height="715.52716"
-   id="svg2"
-   version="1.1"
-   inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)"
-   sodipodi:docname="Drawing.svg"
-   inkscape:export-filename="/home/john/Dropbox/Documents/BOUT++/Mesh_topology_diagram_Luke/Drawing.png"
-   inkscape:export-xdpi="96"
-   inkscape:export-ydpi="96">
-  <sodipodi:namedview
-     id="base"
-     pagecolor="#ffffff"
-     bordercolor="#666666"
-     borderopacity="1.0"
-     inkscape:pageopacity="1"
-     inkscape:pageshadow="2"
-     inkscape:zoom="2.8284271"
-     inkscape:cx="120.89713"
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diff --git a/manual/sphinx/figs/topology_cross_section.png b/manual/sphinx/figs/topology_cross_section2.png
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rename from manual/sphinx/figs/topology_cross_section.png
rename to manual/sphinx/figs/topology_cross_section2.png
diff --git a/manual/sphinx/user_docs/topology.rst b/manual/sphinx/user_docs/topology.rst
new file mode 100644
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--- /dev/null
+++ b/manual/sphinx/user_docs/topology.rst
@@ -0,0 +1,224 @@
+.. _sec-bout-topology:
+
+BOUT++ Topology
+===============
+
+Basic
+-----
+
+BOUT++ is designed to work in a variety of tokamak and non-tokamak
+geometries, from simple slabs to Snowflake configurations. In order to handle
+tokamak geometry BOUT++ contains an internal topology which is built from
+regions determined by four branch-cut locations (``jyseps*``) and two
+separatrix locations (``ixseps1`` and ``ixseps2``). There are some limitations
+on these regions that we will discuss below, and some regions may be empty,
+all of which enables BOUT++ to describe effectively three types of basic
+topologies:
+
+- **"core"**: this type of topology can describe the closed field line regions
+  inside the separatrix of tokamaks or other devices, or idealised geometries
+  like periodic slabs;
+
+- **"SOL"**: these can describe the open field line regions of the scrape-off
+  layer (SOL) outside the separatrix of a tokamak, or linear devices with a
+  target plate at either end;
+
+- **"limiter"**: these topologies have an open field line region and a region
+  where field lines hit a boundary, without an X-point;
+
+- **"X-point"**: these topologies have four separate legs with their own
+  boundaries, and no closed field line region;
+
+The "common" topologies:
+
+- **"single null"**: this type of topology has one X-point with two separate
+  legs, closed and an open field line regions, and a single separatrix;
+
+- **"connected double null"**: these topologies have two X-points with two
+  separate legs each, closed and open field line regions and a single separatrix
+  that connects both X-points;
+
+- **"disconnected double null"**: these are similar to connected double null
+  geometries except that they have two separatrices that do not connect the two
+  X-points. These come in "lower" and "upper" flavours, depending on which
+  X-point is adjacent to the closed field line region.
+
+And all advanced/complex topologies with up to two X-points:
+
+- **"snowflake"**: The SF topologies feature a second order null point created by two X-points close to each other. The ideal SF has a single separatrix and 4 legs, but more realistic configurations can have an extra PFR between the legs. 
+  The **"snowflake+"** and **"snowflake-"** unlike the perfect **SF**, feature an extra central PFR and the secondary X-point is located either above or below the primary one, respectively (along the y-direction).
+- **"X-Point Target"**: The X-Point Target configuration has the main separatrix extended a longer distance and no PFR between the East and South East targets.
+
+See :ref:`sec-supported-topologies` for more details on the available
+topologies.
+
+The regions that form the building blocks of these topologies are:
+
+- "leg" regions that have a boundary in the ``y`` direction;
+- "core" regions that do not have boundaries in ``y``.
+
+Each of these regions may have additional boundaries in the ``x`` direction.
+
+Two important limitations for BOUT++ grids are that a single processor can only
+belong to one region, and that there must be the same number of points on each
+processor. The first limitation means that certain topologies require a minimum
+number of processors. For example, a disconnected double null configuration uses
+all six regions — therefore the minimum number of processors able to describe
+this in BOUT++ is six. Having equal numbers of points on each processor can put
+some restrictions on the resolution of simulations.
+
+The two separatrix locations are ``ixseps1`` and ``ixseps2``, these are the
+global indices in the ``x`` domain where the first and second separatrices are
+located. These values are set either in the grid file or in ``BOUT.inp``.
+
+Considering a Double Null example:
+
+- If ``ixseps1 == ixseps2`` then there is a single separatrix representing
+  the boundary between the core region and the SOL region and the grid is a
+  **connected double null** configuration.
+- If ``ixseps1 > ixseps2`` then there are two separatrices and the inner
+  separatrix is ``ixseps2``, so the tokamak is an **upper double null**.
+- If ``ixseps1 < ixseps2`` then there are two separatrices and the inner
+  separatrix is ``ixseps1``, so the tokamak is a **lower double null**.
+
+In other words: if ``ixseps1 > ixseps2``, then:
+
+- ``f(x <= ixseps1, y, z)`` will be periodic in the ``y``-direction (core),
+- ``f(ixseps1 < x <= ixseps2, y, z)`` will have boundary condition in ``y``
+  set by the lowermost ``ydown`` and ``yup``,
+- ``f(ixseps2 < x, y, z)`` will have boundary conditions set by the uppermost
+  ``ydown`` and ``yup``.
+
+The four branch cut locations, ``jyseps1_1``, ``jyseps1_2``, ``jyseps2_1``, and
+``jyseps2_2``, split the ``y`` domain into logical regions defining the SOL, the
+PFRs (private flux regions), and the core of the tokamak. If
+``jyseps1_2 == jyseps2_1`` then the grid is a **single null** configuration,
+otherwise it can be any of the more advanced configurations.
+
+.. _fig-topology-cross-section:
+.. figure:: ../figs/topology_cross_section2.*
+   :alt: Cross-section of the tokamak topology used in BOUT++
+
+   Deconstruction of a poloidal tokamak cross-section into logical
+   domains using the parameters ``ixseps1``, ``ixseps2``,
+   ``jyseps1_1``, ``jyseps1_2``, ``jyseps2_1``, and ``jyseps2_2``. This
+   configuration is a "disconnected double null" and shows all the
+   possible regions used in the BOUT++ topology.
+
+
+Advanced
+--------
+
+The internal domain in BOUT++ is deconstructed into a series of logically
+rectangular sub-domains with boundaries determined by the ``ixseps`` and
+``jyseps`` parameters. The boundaries coincide with processor boundaries so the
+number of grid points within each sub-domain must be an integer multiple of
+``ny/nypes`` where ``ny`` is the number of grid points in ``y`` and ``nypes``
+is the number of processors used to split the y domain. Processor communication
+across the domain boundaries is then handled internally.
+
+.. note::
+   To ensure that each subdomain follows logically, the ``jyseps`` indices
+   must adhere to the following conditions:
+
+    - ``jyseps1_1 > -1``
+    - ``jyseps2_1 >= jyseps1_1 + 1``
+    - ``jyseps1_2 >= jyseps2_1``
+    - ``jyseps2_2 >= jyseps1_2``
+    - ``jyseps2_2 <= ny - 1``
+
+   To ensure that communications work, branch cuts must align with processor
+   boundaries.
+
+.. _fig-topology-schematic:
+.. figure:: ../figs/topology_schematic.*
+
+   Schematic illustration of domain decomposition and communication in
+   BOUT++ with ``ixseps1 = ixseps2``
+
+These branch cuts are used by the ``getMeshTopology()`` function to determine
+which topology is being used. See :ref:`sec-supported-topologies` for a
+detailed explanation of the available topologies.
+
+Number of targets
+~~~~~~~~~~~~~~~~~
+
+An extra cut in ``y`` called ``ny_inner`` defines where the physical boundary
+in the domain is for topologies with more than 2 targets (any topology more
+complex than the **single null** needs a "discontinuous" :math:`y` domain). The position of the extra
+cut is what distinguishes any **double null** configuration from any of the
+**complex** configurations.
+
+Periodic X Domains
+------------------
+
+The :math:`x` coordinate is usually a radial flux coordinate. In some
+simulations it is useful to make this direction periodic, for example flux tube
+simulations or the Hasegawa-Wakatani example in
+``examples/hasegawa-wakatani/hw.cxx``. In that example the :math:`x` coordinate
+is made periodic with the top-level ``periodicX`` option:
+
+.. code-block:: cfg
+
+   periodicX = true # Domain is periodic in X
+
+   [mesh]
+
+   nx = 260  # Note 4 guard cells in X
+   ny = 1
+   nz = 256  # Periodic, so no guard cells in Z
+
+Note that some care is needed if the model uses Laplacian inversions, for
+example to calculate electrostatic potential from vorticity: if both :math:`x`
+and :math:`z` coordinates are both periodic then the inversion has no boundary
+conditions. In that case the Laplacian has a null space and so is singular; an
+arbitrary constant offset can be added to the potential without changing the
+vorticity.
+
+The default ``cyclic`` solver treats the :math:`k_z = 0` (DC) mode as a
+special case, setting the average of the potential over the :math:`x`-:math:`z`
+domain to zero. Other solvers may not handle the ``periodicX`` case in the same
+way.
+
+Implementations
+---------------
+
+In BOUT++ each processor has a logically rectangular domain, so any branch cuts
+needed for X-point geometry must be at processor boundaries.
+
+In the standard "bout" mesh (``src/mesh/impls/bout/``), the communication is
+controlled by the variables
+
+.. code-block:: cpp
+
+    int UDATA_INDEST, UDATA_OUTDEST, UDATA_XSPLIT;
+    int DDATA_INDEST, DDATA_OUTDEST, DDATA_XSPLIT;
+    int IDATA_DEST, ODATA_DEST;
+
+These control the behavior of the communications as shown in
+:numref:`fig-boutmesh-comms`.
+
+.. _fig-boutmesh-comms:
+.. figure:: ../figs/boutmesh-comms.*
+   :alt: Communication of guard cells in BOUT++
+
+   Communication of guard cells in BOUT++. Boundaries in X have only
+   one neighbour each, but boundaries in Y can be split into two,
+   allowing branch cuts.
+
+In the Y direction, each boundary region (**U**\ p and **D**\ own in Y) can be
+split into two, with ``0 <= x < UDATA_XSPLIT`` going to processor index
+``UDATA_INDEST``, and ``UDATA_INDEST <= x < LocalNx`` going to
+``UDATA_OUTDEST``. Similarly for the Down boundary. Since there are no
+branch-cuts in the X direction, there is just one destination for the
+**I**\ nner and **O**\ uter boundaries. In all cases a negative processor
+number means that there is a domain boundary so no communication is needed.
+
+The communication control variables are set in the ``BoutMesh::topology()``
+function, in ``src/mesh/impls/bout/boutmesh.cxx``. First the function
+``default_connections()`` sets the topology to be a rectangle.
+
+To change the topology, the function ``BoutMesh::set_connection`` checks that
+the requested branch cut is on a processor boundary, and changes the
+communications consistently so that communications are two-way and there are no
+"dangling" communications.

From b2a73839911b3f247b1800d7563307667eebfb34 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 20 Mar 2026 21:01:44 +0100
Subject: [PATCH 0948/1827] prek fixes

---
 include/bout/difops.hxx                       | 28 +++++++++----------
 include/bout/fv_ops.hxx                       | 12 ++++----
 src/mesh/interpolation/hermite_spline_xz.cxx  |  1 -
 .../MMS/spatial/finite-volume/CMakeLists.txt  |  6 ++--
 tests/MMS/spatial/finite-volume/mms.py        |  2 +-
 tests/MMS/spatial/finite-volume/runtest       |  9 +-----
 6 files changed, 25 insertions(+), 33 deletions(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 2cd99f8d33..2070cc30d3 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -1,11 +1,11 @@
 /*!******************************************************************************
  * \file difops.hxx
- * 
+ *
  * Differential operators
  *
  * Changelog:
  *
- * 2009-01 Ben Dudson <bd512@york.ac.uk> 
+ * 2009-01 Ben Dudson <bd512@york.ac.uk>
  *    * Added two optional parameters which can be put in any order
  *      These determine the method to use (DIFF_METHOD)
  *      and CELL_LOC location of the result.
@@ -15,7 +15,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -30,7 +30,7 @@
  *
  * You should have received a copy of the GNU Lesser General Public License
  * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
- * 
+ *
  *******************************************************************************/
 
 #ifndef BOUT_DIFOPS_H
@@ -81,7 +81,7 @@ Field3D Grad_parP(const Field3D& apar, const Field3D& f);
  * \f[
  *    v\mathbf{b}_0 \cdot \nabla f
  * \f]
- * 
+ *
  *
  * @param[in] v  The velocity in y direction
  * @param[in] f  The scalar field to be differentiated
@@ -175,7 +175,7 @@ inline Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc, DIFF_METHOD method)
 
 /*!
  * Parallel divergence of diffusive flux, K*Grad_par
- * 
+ *
  * \f[
  *    \nabla \cdot ( \mathbf{b}_0 kY (\mathbf{b}_0 \cdot \nabla) f )
  * \f]
@@ -203,8 +203,8 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& k, const Field3D& f, Field3D& flow
  * Perpendicular Laplacian operator
  *
  * This version only includes terms in X and Z, dropping
- * derivatives in Y. This is the inverse operation to 
- * the Laplacian inversion class. 
+ * derivatives in Y. This is the inverse operation to
+ * the Laplacian inversion class.
  *
  * For the full perpendicular Laplacian, use Laplace_perp
  */
@@ -216,7 +216,7 @@ FieldPerp Delp2(const FieldPerp& f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT
 /*!
  * Perpendicular Laplacian, keeping y derivatives
  *
- * 
+ *
  */
 Coordinates::FieldMetric
 Laplace_perp(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
@@ -250,18 +250,18 @@ Field2D Laplace_perpXY(const Field2D& A, const Field2D& f);
 
 /*!
  * Terms of form b0 x Grad(phi) dot Grad(A)
- * 
+ *
  */
 Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
                                           CELL_LOC outloc = CELL_DEFAULT);
 
 /*!
- * Terms of form 
+ * Terms of form
  *
  * \f[
  *   \mathbf{b}_0 \times \nabla \phi \cdot \nabla A
  * \f]
- * 
+ *
  * @param[in] phi The scalar potential
  * @param[in] A   The field being advected
  * @param[in] outloc  The cell location where the result is defined. By default the same as A.
@@ -295,13 +295,13 @@ constexpr BRACKET_METHOD BRACKET_CTU = BRACKET_METHOD::ctu;
  * \f[
  *   [f, g] = (1/B) \mathbf{b}_0 \times \nabla f  \cdot \nabla g
  * \f]
- * 
+ *
  * @param[in] f  The potential
  * @param[in] g  The field being advected
  * @param[in] method   The method to use
  * @param[in] outloc   The cell location where the result is defined. Default is the same as g
  * @param[in] solver   Pointer to the time integration solver
- * 
+ *
  */
 Coordinates::FieldMetric bracket(const Field2D& f, const Field2D& g,
                                  BRACKET_METHOD method = BRACKET_STD,
diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 07a2c2976b..027a1ef77b 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -115,7 +115,7 @@ struct Fromm {
 
 /*!
    * Second order slope limiter method
-   * 
+   *
    * Limits slope to minimum absolute value
    * of left and right gradients. If at a maximum
    * or minimum slope set to zero, i.e. reverts
@@ -152,8 +152,8 @@ private:
 
 /*!
    * Monotonised Central (MC) second order slope limiter (Van Leer)
-   * 
-   * Limits the slope based on taking the slope with 
+   *
+   * Limits the slope based on taking the slope with
    * the minimum absolute value from central, 2*left and
    * 2*right. If any of these slopes have different signs
    * then the slope reverts to zero (i.e. 1st-order upwinding).
@@ -256,7 +256,7 @@ Field3D Div_par(const Field3D& f_in, const Field3D& v_in, const Field3D& wave_sp
   ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
   ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
 
-  Mesh const* mesh = f_in.getMesh();
+  const Mesh* mesh = f_in.getMesh();
 
   CellEdges cellboundary;
 
@@ -423,9 +423,9 @@ Field3D Div_par(const Field3D& f_in, const Field3D& v_in, const Field3D& wave_sp
    * Div ( n * v )  -- Magnetic drifts
    *
    * This uses the expression
-   * 
+   *
    * Div( A ) = 1/J * d/di ( J * A^i )
-   * 
+   *
    * Hence the input vector should be contravariant
    *
    * Note: Uses to/from FieldAligned
diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index e2760ac0e3..5b9271c93f 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -509,7 +509,6 @@ Field3D XZHermiteSplineBase<monotonic, imp_type>::interpolate(
       f_interp[iyp] =
           +f_z * h00_z[i] + f_zp1 * h01_z[i] + fz_z * h10_z[i] + fz_zp1 * h11_z[i];
 
-
       if constexpr (monotonic) {
         const auto corners = {(*gf)[IndG3D(g3dinds[i][0])], (*gf)[IndG3D(g3dinds[i][1])],
                               (*gf)[IndG3D(g3dinds[i][2])], (*gf)[IndG3D(g3dinds[i][3])]};
diff --git a/tests/MMS/spatial/finite-volume/CMakeLists.txt b/tests/MMS/spatial/finite-volume/CMakeLists.txt
index 6d9c839a05..7180eb7d98 100644
--- a/tests/MMS/spatial/finite-volume/CMakeLists.txt
+++ b/tests/MMS/spatial/finite-volume/CMakeLists.txt
@@ -1,6 +1,6 @@
-bout_add_mms_test(MMS-spatial-finite-volume
+bout_add_mms_test(
+  MMS-spatial-finite-volume
   SOURCES fv_mms.cxx
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
+  USE_RUNTEST USE_DATA_BOUT_INP
   PROCESSORS 2
 )
diff --git a/tests/MMS/spatial/finite-volume/mms.py b/tests/MMS/spatial/finite-volume/mms.py
index dfcfce9a09..a95ecc1328 100755
--- a/tests/MMS/spatial/finite-volume/mms.py
+++ b/tests/MMS/spatial/finite-volume/mms.py
@@ -32,7 +32,7 @@
 v = fv / f
 
 # Substitute back to get input y coordinates
-replace = [ (metric.y, y*Ly/(2*pi) ) ]
+replace = [(metric.y, y * Ly / (2 * pi))]
 
 
 def Grad2_par2(f: Expr) -> Expr:
diff --git a/tests/MMS/spatial/finite-volume/runtest b/tests/MMS/spatial/finite-volume/runtest
index b38a6359ac..bcd4672545 100755
--- a/tests/MMS/spatial/finite-volume/runtest
+++ b/tests/MMS/spatial/finite-volume/runtest
@@ -22,23 +22,18 @@ OPERATORS = {
     "FV_Div_par_MC": 1.5,
     "FV_Div_par_mod_MC": 1.5,
     "FV_Div_par_fvv_MC": 1.5,
-
     "FV_Div_par_Upwind": 1,
     "FV_Div_par_mod_Upwind": 1,
     "FV_Div_par_fvv_Upwind": 1,
-
     "FV_Div_par_Fromm": 1.5,
     "FV_Div_par_mod_Fromm": 1.5,
     "FV_Div_par_fvv_Fromm": 1.5,
-
     "FV_Div_par_MinMod": 1.5,
     "FV_Div_par_mod_MinMod": 1.5,
     "FV_Div_par_fvv_MinMod": 1.5,
-
     "FV_Div_par_Superbee": 1.5,
     "FV_Div_par_mod_Superbee": 1.5,
     "FV_Div_par_fvv_Superbee": 1.5,
-
     "FV_Div_par_K_Grad_par": 2,
     "FV_Div_par_K_Grad_par_mod": 2,
 }
@@ -131,9 +126,7 @@ def test_fv_operators() -> bool:
 
     final_errors = transpose(all_errors)
     for operator, order in OPERATORS.items():
-        success = assert_convergence(
-            final_errors[operator]["l_2"], dx, operator, order
-        )
+        success = assert_convergence(final_errors[operator]["l_2"], dx, operator, order)
         if not success:
             failures.append(operator)
 

From 1b7bf2e0e2cb4f1f5f5921a0473115d290812065 Mon Sep 17 00:00:00 2001
From: Ekaterine Papava <papava.e@gtu.ge>
Date: Mon, 23 Mar 2026 08:10:17 +0100
Subject: [PATCH 0949/1827] po: Add Georgian language

---
 locale/ka/libbout.po | 1030 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 1030 insertions(+)
 create mode 100644 locale/ka/libbout.po

diff --git a/locale/ka/libbout.po b/locale/ka/libbout.po
new file mode 100644
index 0000000000..a5bc263f9e
--- /dev/null
+++ b/locale/ka/libbout.po
@@ -0,0 +1,1030 @@
+# Georgian translation for libbout.
+# Copyright (C) 2026 libbout's authors.
+# This file is distributed under the same license as the libbout package.
+# Ekaterine Papava <papava.e@gtu.ge>, 2026.
+#
+msgid ""
+msgstr ""
+"Project-Id-Version: libbout\n"
+"Report-Msgid-Bugs-To: \n"
+"POT-Creation-Date: 2025-08-13 23:37+0100\n"
+"PO-Revision-Date: 2026-03-23 08:06+0100\n"
+"Last-Translator: Ekaterine Papava <papava.e@gtu.ge>\n"
+"Language-Team: Georgian <(nothing)>\n"
+"Language: ka\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+"X-Generator: Poedit 3.9\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:182
+#, c++-format
+msgid ""
+"\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
+"of MYSUB ({:d})\n"
+msgstr ""
+"\t -> რეგიონი Core jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) MYSUB-ის ({:d}) "
+"ნამრავლი უნდა იყოს\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:215
+#, c++-format
+msgid ""
+"\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
+"of MYSUB ({:d})\n"
+msgstr ""
+"\t -> რეგიონი Core jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) MYSUB-ის ({:d}) "
+"ნამრავლი უნდა იყოს\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:190
+#, c++-format
+msgid ""
+"\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
+"of MYSUB ({:d})\n"
+msgstr ""
+"\t -> რეგიონი Core jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) MYSUB-ის ({:d}) "
+"ნამრავლი უნდა იყოს\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:300
+msgid "\t -> Good value\n"
+msgstr "\t -> კარგი მნიშვნელობა\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:171
+#, c++-format
+msgid ""
+"\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:206
+#, c++-format
+msgid ""
+"\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
+"multiple of MYSUB ({:d})\n"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:223
+#, c++-format
+msgid ""
+"\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
+"MYSUB ({:d})\n"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:199
+#, c++-format
+msgid ""
+"\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
+"multiple of MYSUB ({:d})\n"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:166
+#, c++-format
+msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
+msgstr "\t -> ny/NYPE ({:d}/{:d} = {:d}) უნდა იყოს >= MYG ({:d})\n"
+
+#: ../src/bout++.cxx:575
+#, c++-format
+msgid "\tADIOS2 support {}\n"
+msgstr "\tADIOS2-ის მხარდაჭერა {}\n"
+
+#: ../src/bout++.cxx:583
+#, c++-format
+msgid "\tBacktrace in exceptions {}\n"
+msgstr "\tუკუტრეისი გამონაკლისებში {}\n"
+
+#. Loop over all possibilities
+#. Processors divide equally
+#. Mesh in X divides equally
+#. Mesh in Y divides equally
+#: ../src/mesh/impls/bout/boutmesh.cxx:288
+#, c++-format
+msgid "\tCandidate value: {:d}\n"
+msgstr "\tკანდიდატი მნიშვნელობა: {:d}\n"
+
+#: ../src/bout++.cxx:584
+#, c++-format
+msgid "\tColour in logs {}\n"
+msgstr "\tფერები ჟურნალში {}\n"
+
+#: ../src/bout++.cxx:599
+msgid "\tCommand line options for this run : "
+msgstr "\tბრძანების სტრიქონის პარამეტრები ამ გაშვებისთვის : "
+
+#. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
+#. which could cause problems (e.g. terminate strings).
+#: ../src/bout++.cxx:595
+#, c++-format
+msgid "\tCompiled with flags : {:s}\n"
+msgstr "\tდაკომპილებულია ალმებით : {:s}\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:315
+#, c++-format
+msgid ""
+"\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
+"localNy={:d})\n"
+msgstr ""
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:357
+#, c++-format
+msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
+msgstr ""
+"\tშეცდომა: {:d} Y წერტილის თანაბრად განაწილება {:d} პროცესორს შორის "
+"შეუძლებელია\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:365
+#, c++-format
+msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
+msgstr ""
+"\tშეცდომა: {:d} Z წერტილის თანაბრად განაწილება {:d} პროცესორს შორის "
+"შეუძლებელია\n"
+
+#: ../src/sys/options/options_ini.cxx:200
+#, c++-format
+msgid ""
+"\tEmpty key\n"
+"\tLine: {:s}"
+msgstr ""
+"\tცარიელი გასაღები\n"
+"\tხაზი: {:s}"
+
+#: ../src/sys/optionsreader.cxx:127
+#, c++-format
+msgid "\tEmpty key or value in command line '{:s}'\n"
+msgstr "\tცარიელი გასაღები, ან მნიშვნელობა ბრძანების სტრიქონში '{:s}'\n"
+
+#: ../src/bout++.cxx:587
+#, c++-format
+msgid "\tExtra debug output {}\n"
+msgstr "\tგამართვის დამატებითი შეტყობინებები {}\n"
+
+#: ../src/bout++.cxx:568
+#, c++-format
+msgid "\tFFT support {}\n"
+msgstr "\tFFT-ის მხარდაჭერა {}\n"
+
+#: ../src/bout++.cxx:590
+#, c++-format
+msgid "\tField name tracking {}\n"
+msgstr "\tველის სახელის თვალყურის დევნება {}\n"
+
+#: ../src/bout++.cxx:588
+#, c++-format
+msgid "\tFloating-point exceptions {}\n"
+msgstr "\tმცურავმძიმიანი გამონაკლისები {}\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:476
+msgid "\tGrid size: "
+msgstr "\tბადის ზომა: "
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:499
+msgid "\tGuard cells (x,y,z): "
+msgstr "\tუჯრედების დაცვა (x,y,z): "
+
+#: ../src/sys/options/options_ini.cxx:204
+#, c++-format
+msgid ""
+"\tKey must not contain ':' character\n"
+"\tLine: {:s}"
+msgstr ""
+"\tგასაღები არ უნდა შეიცავდეს სიმბოლოს ':'\n"
+"\tხაზი: {:s}"
+
+#: ../src/bout++.cxx:570
+#, c++-format
+msgid "\tLAPACK support {}\n"
+msgstr "\tLAPACK-ის მხარდაჭერა {}\n"
+
+#: ../src/bout++.cxx:591
+#, c++-format
+msgid "\tMessage stack {}\n"
+msgstr "\tშეტყობინებების სტეკი {}\n"
+
+#: ../src/bout++.cxx:567
+#, c++-format
+msgid "\tMetrics mode is {}\n"
+msgstr "\tმეტრიკების რეჟიმია {}\n"
+
+#: ../src/sys/optionsreader.cxx:111
+#, c++-format
+msgid "\tMultiple '=' in command-line argument '{:s}'\n"
+msgstr "\tერთზე მეტი '=' ბრძანების სტრიქონის არგუმენტში '{:s}'\n"
+
+#: ../src/bout++.cxx:569
+#, c++-format
+msgid "\tNatural language support {}\n"
+msgstr "\tნატურალური ენის მხარდაჭერა {}\n"
+
+#: ../src/bout++.cxx:574
+#, c++-format
+msgid "\tNetCDF support {}{}\n"
+msgstr "\tNetCDF-ის მხარდაჭერა {}{}\n"
+
+#: ../src/bout++.cxx:585
+#, c++-format
+msgid "\tOpenMP parallelisation {}, using {} threads\n"
+msgstr "\tOpenMP-ის პარალელიზაცია {}. გამოიყენება {} ნაკადი\n"
+
+#. Mark the option as used
+#. Option not found
+#: ../include/bout/options.hxx:586 ../include/bout/options.hxx:619
+#: ../include/bout/options.hxx:643 ../include/bout/options.hxx:896
+msgid "\tOption "
+msgstr "\tპარამეტრი "
+
+#: ../src/sys/options.cxx:369
+#, c++-format
+msgid "\tOption {} = {}"
+msgstr "\tპარამეტრი {} = {}"
+
+#: ../src/sys/options/options_ini.cxx:70
+#, c++-format
+msgid "\tOptions file '{:s}' not found\n"
+msgstr "\tპარამეტრების ფაილი '{:s}' აღმოჩენილი არაა\n"
+
+#: ../src/bout++.cxx:576
+#, c++-format
+msgid "\tPETSc support {}\n"
+msgstr "\tPETSc-ის მხარდაჭერა {}\n"
+
+#: ../src/bout++.cxx:579
+#, c++-format
+msgid "\tPVODE support {}\n"
+msgstr "\tPVODE-ის მხარდაჭერა {}\n"
+
+#: ../src/bout++.cxx:564
+msgid "\tParallel NetCDF support disabled\n"
+msgstr "\tპარალელური NetCDF-ის მხარდაჭერა გათიშულია\n"
+
+#: ../src/bout++.cxx:562
+msgid "\tParallel NetCDF support enabled\n"
+msgstr "\tპარალელური NetCDF-ის მხარდაჭერა ჩართულია\n"
+
+#: ../src/bout++.cxx:577
+#, c++-format
+msgid "\tPretty function name support {}\n"
+msgstr "\tლამაზი ფუნქციის სახელის მხარდაჭერა {}\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:473
+msgid "\tRead nz from input grid file\n"
+msgstr "\tnz წაკითხულია შეყვანილი ბადის ფაილიდან\n"
+
+#: ../src/mesh/mesh.cxx:249
+msgid "\tReading contravariant vector "
+msgstr "\tკოვარიანტული ვექტორის წაკითხვა "
+
+#: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
+msgid "\tReading covariant vector "
+msgstr "\tკოვარიანტული ვექტორის წაკითხვა  "
+
+#: ../src/bout++.cxx:555
+#, c++-format
+msgid "\tRuntime error checking {}"
+msgstr "\tგაშვების დროის შემოწმება {}"
+
+#: ../src/bout++.cxx:581
+#, c++-format
+msgid "\tSLEPc support {}\n"
+msgstr "\tSLEPc-ის მხარდაჭერა {}\n"
+
+#: ../src/bout++.cxx:582
+#, c++-format
+msgid "\tSUNDIALS support {}\n"
+msgstr "\tSUNDIALS-ის მხარდაჭერა {}\n"
+
+#: ../src/bout++.cxx:580
+#, c++-format
+msgid "\tScore-P support {}\n"
+msgstr "\tScore-P-ის მხარდაჭერა {}\n"
+
+#: ../src/bout++.cxx:589
+#, c++-format
+msgid "\tSignal handling support {}\n"
+msgstr "\tსიგნალის დამუშავების მხარდაჭერა {}\n"
+
+#: ../src/solver/impls/split-rk/split-rk.cxx:76
+#, c++-format
+msgid "\tUsing a timestep {:e}\n"
+msgstr "\tგამოიყენება დროის შტამპი {:e}\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:613
+msgid "\tdone\n"
+msgstr "\tმზადაა\n"
+
+#: ../src/solver/impls/split-rk/split-rk.cxx:41
+msgid ""
+"\n"
+"\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
+msgstr ""
+"\n"
+"\tგაყოფილი Runge-Kutta-Legendre და SSP-RK3 ამომხსნელი\n"
+
+#: ../src/bout++.cxx:378
+msgid ""
+"\n"
+"  -d <data directory>\t\tLook in <data directory> for input/output files\n"
+"  -f <options filename>\t\tUse OPTIONS given in <options filename>\n"
+"  -o <settings filename>\tSave used OPTIONS given to <options filename>\n"
+"  -l, --log <log filename>\tPrint log to <log filename>\n"
+"  -v, --verbose\t\t\tIncrease verbosity\n"
+"  -q, --quiet\t\t\tDecrease verbosity\n"
+msgstr ""
+"\n"
+"  -d <მონაცემთა_საქაღალდე>\t\tშეტანა/გამოტანის ფაილების ძებნა "
+"<მონაცემთა_საქაღალდეში>\n"
+"  -f <პარამეტრების_ფაილის_სახელი>\t\t<პარამეტრების_ფაილში> მითითებული "
+"პარამეტრების გამოყენება\n"
+"  -o <პარამეტრების_ფაილი>\tგადაცემული პარამეტრების შენახვა "
+"<პარამეტრების_ფაილში>\n"
+"  -l, --log <ჟურნალის_ფაილის_სახელი>\tჟურნალის ჩაწერა "
+"<ჟურნალის_ფაილის_სახელში>\n"
+"  -v, --verbose\t\t\tმეტი შეტყობინების გამოტანა\n"
+"  -q, --quiet\t\t\tნაკლები შეტყობინების გამოტანა\n"
+
+#: ../src/sys/expressionparser.cxx:341
+#, c++-format
+msgid ""
+"\n"
+"  {1: ^{2}}{0}\n"
+"  Did you mean '{0}'?"
+msgstr ""
+"\n"
+"  {1: ^{2}}{0}\n"
+"  გულისხმობდით '{0}'-ს?"
+
+#: ../src/solver/solver.cxx:586
+#, c++-format
+msgid ""
+"\n"
+"Run finished at  : {:s}\n"
+msgstr ""
+"\n"
+"დასრულების დროა  : {:s}\n"
+
+#: ../src/solver/solver.cxx:540
+#, c++-format
+msgid ""
+"\n"
+"Run started at  : {:s}\n"
+msgstr ""
+"\n"
+"გაშვების დროა  : {:s}\n"
+
+#. Raw string to help with the formatting of the message, and a
+#. separate variable so clang-format doesn't barf on the
+#. exception
+#: ../src/sys/options.cxx:1158
+msgid ""
+"\n"
+"There were unused input options:\n"
+"-----\n"
+"{:i}\n"
+"-----\n"
+"It's possible you've mistyped some options. BOUT++ input arguments are\n"
+"now case-sensitive, and some have changed name. You can try running\n"
+"\n"
+"    <BOUT++ directory>/bin/bout-v5-input-file-upgrader.py {}/{}\n"
+"\n"
+"to automatically fix the most common issues. If these options above\n"
+"are sometimes used depending on other options, you can call\n"
+"`Options::setConditionallyUsed()`, for example:\n"
+"\n"
+"    Options::root()[\"{}\"].setConditionallyUsed();\n"
+"\n"
+"to mark a section or value as depending on other values, and so ignore\n"
+"it in this check. Alternatively, if you're sure the above inputs are\n"
+"not a mistake, you can set 'input:error_on_unused_options=false' to\n"
+"turn off this check for unused options. You can always set\n"
+"'input:validate=true' to check inputs without running the full\n"
+"simulation.\n"
+"\n"
+"{}"
+msgstr ""
+
+#: ../src/bout++.cxx:389
+#, c++-format
+msgid ""
+"  --print-config\t\tPrint the compile-time configuration\n"
+"  --list-solvers\t\tList the available time solvers\n"
+"  --help-solver <solver>\tPrint help for the given time solver\n"
+"  --list-laplacians\t\tList the available Laplacian inversion solvers\n"
+"  --help-laplacian <laplacian>\tPrint help for the given Laplacian inversion "
+"solver\n"
+"  --list-laplacexz\t\tList the available LaplaceXZ inversion solvers\n"
+"  --help-laplacexz <laplacexz>\tPrint help for the given LaplaceXZ inversion "
+"solver\n"
+"  --list-invertpars\t\tList the available InvertPar solvers\n"
+"  --help-invertpar <invertpar>\tPrint help for the given InvertPar solver\n"
+"  --list-rkschemes\t\tList the available Runge-Kutta schemes\n"
+"  --help-rkscheme <rkscheme>\tPrint help for the given Runge-Kutta scheme\n"
+"  --list-meshes\t\t\tList the available Meshes\n"
+"  --help-mesh <mesh>\t\tPrint help for the given Mesh\n"
+"  --list-xzinterpolations\tList the available XZInterpolations\n"
+"  --help-xzinterpolation <xzinterpolation>\tPrint help for the given "
+"XZInterpolation\n"
+"  --list-zinterpolations\tList the available ZInterpolations\n"
+"  --help-zinterpolation <zinterpolation>\tPrint help for the given "
+"ZInterpolation\n"
+"  -h, --help\t\t\tThis message\n"
+"  restart [append]\t\tRestart the simulation. If append is specified, append "
+"to the existing output files, otherwise overwrite them\n"
+"  VAR=VALUE\t\t\tSpecify a VALUE for input parameter VAR\n"
+"\n"
+"For all possible input parameters, see the user manual and/or the physics "
+"model source (e.g. {:s}.cxx)\n"
+msgstr ""
+"  --print-config\t\tკომპილაციის დროის კონფიგურაციის გამოტანა\n"
+"  --list-solvers\t\tხელმისაწვდომი დროის ამომხსნელების სია\n"
+"  --help-solver <solver>\tდახმარების გამოტანა მოცემული დროის ამოხსნელისთვის\n"
+"  --list-laplacians\t\tხელმისაწვდომი ლაპლასის ინვერსიის ამომხსნელების სია\n"
+"  --help-laplacian <laplacian>\tდახმარების გამოტანა მოცემული ლაპლასის "
+"ინვერსიის ამომხსნელისთვის\n"
+"  --list-laplacexz\t\tხელმისაწვდომი LaplaceXZ ინვერსიის ამომხსნელების სია\n"
+"  --help-laplacexz <laplacexz>\tდახმარების გამოტანა მოცემული LaplaceXZ "
+"ინვერსიის ამომხსნელისთვის\n"
+"  --list-invertpars\t\tხელმისაწვდომი InvertPar ამომხსნელების სია\n"
+"  --help-invertpar <invertpar>\tდახმარების გამოტანა მოცემული InvertPar "
+"ამომხსნელისთვის\n"
+"  --list-rkschemes\t\tხელმისაწვდომი Runge-Kutta სქემების სიის გამოტანა\n"
+"  --help-rkscheme <rkscheme>\tდახმარების გამოტანა მოცემული Runge-Kutta "
+"სქემისთვის\n"
+"  --list-meshes\t\t\tხელმისაწვდომი ბადეების სია\n"
+"  --help-mesh <mesh>\t\tდახმარების გამოტანა მოცემული ბადისთვის\n"
+"  --list-xzinterpolations\tხელმისაწვდომი XZInterpolation-ების სიის გამოტანა\n"
+"  --help-xzinterpolation <xzinterpolation>\tდახმარების გამოტანა მოცემული "
+"XZInterpolation-ისთვის\n"
+"  --list-zinterpolations\tხელმისაწვდომი ZInterpolation-ების სიის გამოტანა\n"
+"  --help-zinterpolation <zinterpolation>\tდახმარების გამოტანა მოცემული "
+"ZInterpolation-ისთვის\n"
+"  -h, --help\t\t\tეს შეტყობინება\n"
+"  restart [append]\t\tსიმულაციის თავიდან გაშვება. თუ მითითებულია append, "
+"გამოტანილი ინფორმაცია არსებულ გამოტანილ ფაილებს ბოლოში მიეწერება. წინააღმდეგ "
+"შემთხვევაში კი მოხდება თავზე გადაწერა\n"
+"  VAR=VALUE\t\t\tმიუთითეთ VALUE შეყვანის პარამეტრისტვის VAR\n"
+"\n"
+"ყველა შესაძლო შეყვანის პარამეტრის სანახავად იხილეთ სახელმძღვანელო, ან/და "
+"ფიზიკის მოდელის წყარო (მაგ: {:s}.cxx)\n"
+
+#: ../src/bout++.cxx:386
+msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
+msgstr "  -c, --color\t\t\tფერადი გამოტანა bout-log-color-ის გამოყენეებით\n"
+
+#: ../include/bout/options.hxx:899
+msgid ") overwritten with:"
+msgstr ") თავსე გადაწერილია რით:"
+
+#: ../src/bout++.cxx:557
+#, c++-format
+msgid ", level {}"
+msgstr ", დონე {}"
+
+#: ../tests/unit/src/test_bout++.cxx:352
+msgid "4 of 8"
+msgstr "4 8-დან"
+
+#: ../src/sys/options.cxx:895
+msgid "All options used\n"
+msgstr "ყველა გამოყენებული პარამეტრი\n"
+
+#: ../src/bout++.cxx:535
+#, c++-format
+msgid "BOUT++ version {:s}\n"
+msgstr "BOUT++-ის მხარდაჭერა {:s}\n"
+
+#: ../src/bout++.cxx:147
+msgid "Bad command line arguments:\n"
+msgstr "არასწორი ბრძანების სტრიქონის არგუმენტები:\n"
+
+#: ../src/sys/expressionparser.cxx:192
+#, c++-format
+msgid "Boolean operator argument {:e} is not a bool"
+msgstr "ლოგიკური ოპერატორის არგუმენტი {:e} ლოგიკური არაა"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:595
+msgid "Boundary regions in this processor: "
+msgstr "სასაზღვრო რეგიონები ამ პროცესორში: "
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:348
+#, c++-format
+msgid "Cannot split {:d} X points equally between {:d} processors\n"
+msgstr "შეუძლებელია {:d} X წერტილის თანაბრად გაყოფა {:d} პროცესორს შორის\n"
+
+#: ../src/bout++.cxx:829
+msgid "Check if a file exists, and exit if it does."
+msgstr "შემოწმება, არსებობს, თუ არა ფაილი და გასვლა, თუ კი."
+
+#: ../src/bout++.cxx:540
+#, c++-format
+msgid ""
+"Code compiled on {:s} at {:s}\n"
+"\n"
+msgstr ""
+"კოდის კომპილაცია მოხდა მანქანაზე {:s} დრო: {:s}\n"
+"\n"
+
+#: ../src/sys/optionsreader.cxx:130
+msgid "Command line"
+msgstr "ბრძანების სტრიქონი"
+
+#: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
+msgid "Compile-time options:\n"
+msgstr "კომპილაციის დროის პარამეტრები:\n"
+
+#: ../tests/unit/src/test_bout++.cxx:362
+msgid "Compiled with flags"
+msgstr "კომპილაციის ალმები"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:604
+msgid "Constructing default regions"
+msgstr "ნაგულისხმევი რეგიონების აგება"
+
+#: ../src/bout++.cxx:527
+#, c++-format
+msgid "Could not create PID file {:s}"
+msgstr "ვერ შევქმენი PID ფაილი {:s}"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:309
+msgid ""
+"Could not find a valid value for NXPE. Try a different number of processors."
+msgstr ""
+"NXPE-ისთვის სწორი მნიშვნელობის პოვნა შეუძლებელია. სცადეთ პროცესორების სხვა "
+"რაოდენობა."
+
+#: ../src/sys/options/options_ini.cxx:160
+#, c++-format
+msgid "Could not open output file '{:s}'\n"
+msgstr "გახსნის შეცდომა გამოტანის ფაილისთვის '{:s}'\n"
+
+#: ../src/bout++.cxx:657
+#, c++-format
+msgid "Could not open {:s}/{:s}.{:d} for writing"
+msgstr "{:s}/{:s}.{:d}-ის ჩასაწერად გახსნა შეუძლებელია"
+
+#. Error reading
+#: ../src/mesh/mesh.cxx:543
+#, c++-format
+msgid "Could not read integer array '{:s}'\n"
+msgstr "წაკითხვის შეცდომა მთელი რიცხვების მასივისთვის '{:s}'\n"
+
+#. Failed . Probably not important enough to stop the simulation
+#: ../src/bout++.cxx:637
+msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
+msgstr ""
+"bout-log-color-ის გაშვება შეუძლებელია. დარწმუნდით, რომ ის თქვენს PATH-შია\n"
+
+#: ../src/solver/solver.cxx:772
+#, c++-format
+msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
+msgstr "მონიტორის დამატება შეუძლებელია: {:g} {:g}-ის ნამრავლი არაა!"
+
+#: ../src/sys/expressionparser.cxx:312
+#, c++-format
+msgid ""
+"Couldn't find generator '{}'. BOUT++ expressions are now case-sensitive, so "
+"you\n"
+"may need to change your input file.\n"
+"{}"
+msgstr ""
+"გენერატორი '{}' აღმოჩენილი არაა. BOUT++-ის გამოსახულებები ახლა დიდ და პატარა "
+"ასოებს ანსხვავებს, ასე რომ,\n"
+"შეიძლება, თქვენი შეყვანის ფაილის შემოწმება დაგჭირდეთ.\n"
+"{}"
+
+#: ../src/mesh/mesh.cxx:587
+#, c++-format
+msgid "Couldn't find region {:s} in regionMap2D"
+msgstr "regionMap2D-ში რეგიონი {:s} აღმოჩენილი არაა"
+
+#: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
+#, c++-format
+msgid "Couldn't find region {:s} in regionMap3D"
+msgstr "regionMap3D-ში რეგიონი {:s} აღმოჩენილი არაა"
+
+#: ../src/mesh/mesh.cxx:595
+#, c++-format
+msgid "Couldn't find region {:s} in regionMapPerp"
+msgstr "regionMapPerp-ში რეგიონი {:s} აღმოჩენილი არაა"
+
+#. Convert any exceptions to something a bit more useful
+#: ../src/sys/options.cxx:361
+#, c++-format
+msgid "Couldn't get {} from option {:s} = '{:s}': {}"
+msgstr "{}-ის მიღება შეუძლებელია პარამეტრიდან {:s} = '{:s}': {}"
+
+#: ../src/bout++.cxx:515
+#, c++-format
+msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
+msgstr "მონაცემთა საქაღალდე \"{:s}\" არ არსებობს, ან წვდომადი არაა\n"
+
+#: ../src/bout++.cxx:512
+#, c++-format
+msgid "DataDir \"{:s}\" is not a directory\n"
+msgstr "მონაცემთა საქაღალდე \"{:s}\" საქაღალდე არაა\n"
+
+#: ../src/solver/solver.cxx:671
+msgid "ERROR: Solver is already initialised\n"
+msgstr "შეცდომა: ამომხსნელი უკვე ინიციალიზებულია\n"
+
+#: ../src/bout++.cxx:216
+#, c++-format
+msgid "Error encountered during initialisation: {:s}\n"
+msgstr "ინიციალიზაციისას აღმოჩენილია შეცდომა: {:s}\n"
+
+#: ../src/bout++.cxx:751
+msgid "Error whilst writing settings"
+msgstr "შეცდომა პარამეტრების ჩაწერისას"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:323
+#, c++-format
+msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
+msgstr ""
+"შეცდომა: nx უფრო მეტი უნდა იყოს, ვიდრე ორზე გამრავლებული MXG (2 * {:d})"
+
+#: ../src/solver/solver.cxx:520
+msgid "Failed to initialise solver-> Aborting\n"
+msgstr "ამომხსნელის ინიციალიზაცია ჩავარდა -> შესრულება შეწყდა\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:281
+#, c++-format
+msgid "Finding value for NXPE (ideal = {:f})\n"
+msgstr "ვეძებ მნიშვნელობას NXPE-ისთვის (იდეალურია = {:f})\n"
+
+#: ../src/solver/solver.cxx:674
+msgid "Initialising solver\n"
+msgstr "ამომხსნელის ინიციალიზაცია\n"
+
+#: ../src/bout++.cxx:501
+msgid ""
+"Input and output file for settings must be different.\n"
+"Provide -o <settings file> to avoid this issue.\n"
+msgstr ""
+"შეყვანის და გამოტანის ფაილი პარამეტრებისთვის უნდა განსხვავდებოდეს.\n"
+"ამ პრობლემის თავიდან ასაცილებლად მიუთითეთ -o <settings file>.\n"
+
+#: ../src/sys/optionsreader.cxx:76
+msgid "Invalid command line option '-' found - maybe check whitespace?"
+msgstr ""
+"აღმოჩენილია არასწორი ბრძანების სტრიქონის პარამეტრი '-' - შეამოწმეთ ზედმეტი "
+"ჰარეები?"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:436
+msgid "Loading mesh"
+msgstr "ბადის ჩატვირთვა"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:451
+msgid "Mesh must contain nx"
+msgstr "ბადე უნდა შეიცავდეს nx-ს"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:455
+msgid "Mesh must contain ny"
+msgstr "ბადე უნდა შეიცავდეს ny-ს"
+
+#. Not found
+#: ../src/mesh/mesh.cxx:547
+#, c++-format
+msgid "Missing integer array {:s}\n"
+msgstr "აკლია მთელი რიცხვების მასივი {:s}\n"
+
+#: ../src/solver/solver.cxx:911
+#, c++-format
+msgid "Monitor signalled to quit (exception {})\n"
+msgstr "მონიტორმა გასვლის სიგნალი გამოაგზავნა (გამონაკლისი {})\n"
+
+#: ../src/solver/solver.cxx:889
+#, c++-format
+msgid "Monitor signalled to quit (return code {})"
+msgstr "მონიტორმა გასვლის სიგნალი გამოაგზავნა (დაბრუნების კოდი {})"
+
+#: ../src/bout++.cxx:834
+msgid "Name of file whose existence triggers a stop"
+msgstr "ფაილის სახელი, რომლის არსებობაც გაჩერებას იწვევს"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:601
+msgid "No boundary regions in this processor"
+msgstr "ამ პროცესორში სასაზღვრო რეგიონები არ არის"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:586
+msgid "No boundary regions; domain is periodic\n"
+msgstr "სასაზღვრო რეგიონების გარეშე. დომენი პერიოდულია\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:245
+#, c++-format
+msgid ""
+"Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
+msgstr ""
+"პროცესორების რაოდენობა ({:d}), რომლებიც არ იყოფა NP-ებზე x მიმართულებით "
+"({:d})\n"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:258
+#, c++-format
+msgid ""
+"Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
+msgstr ""
+"პროცესორების რაოდენობა ({:d}), რომლებიც არ იყოფა NP-ებზე y მიმართულებით "
+"({:d})\n"
+
+#. Less than 2 time-steps left
+#: ../src/bout++.cxx:908
+#, c++-format
+msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
+msgstr "დარჩა მხოლოდ {:e} წამი ({:.2f} ნაბიჯი). გასვლა\n"
+
+#: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
+#: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
+#: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
+#: ../src/sys/options.cxx:789
+#, c++-format
+msgid "Option {:s} has no value"
+msgstr "პარამეტრს {:s} მნიშვნელობა არ აქვს"
+
+#. Doesn't exist
+#: ../src/sys/options.cxx:172
+#, c++-format
+msgid "Option {:s}:{:s} does not exist"
+msgstr "პარამეტრი {:s}:{:s} არ არსებობს"
+
+#: ../include/bout/options.hxx:904
+#, c++-format
+msgid ""
+"Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
+"value was '{:s}'."
+msgstr ""
+"პარამეტრები: მნიშვნელობის დაყენება იგივე წყაროდან ({:s}) ახალ მნიშვნელობაზე "
+"'{:s}' - ძველი მნიშვნელობა იყო '{:s}'."
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:588
+msgid "Possible boundary regions are: "
+msgstr "შესაძლო სასაზღვრო რეგიონებია: "
+
+#: ../src/bout++.cxx:545
+#, c++-format
+msgid ""
+"Processor number: {:d} of {:d}\n"
+"\n"
+msgstr ""
+"პროცესორის ნომერი: {:d} {:d}-დან\n"
+"\n"
+
+#: ../src/mesh/mesh.cxx:642
+#, c++-format
+msgid "Registered region 2D {:s}"
+msgstr "რეგისტრირებული რეგიონი 2D {:s}"
+
+#: ../src/mesh/mesh.cxx:632
+#, c++-format
+msgid "Registered region 3D {:s}"
+msgstr "რეგისტრირებული რეგიონი 3D {:s}"
+
+#: ../src/mesh/mesh.cxx:652
+#, c++-format
+msgid "Registered region Perp {:s}"
+msgstr "რეგისტრირებულია რეგიონი Perp {:s}"
+
+#: ../src/bout++.cxx:536
+#, c++-format
+msgid "Revision: {:s}\n"
+msgstr "რევიზია: {:s}\n"
+
+#: ../src/solver/solver.cxx:587
+msgid "Run time : "
+msgstr "გაშვებულობის დრო : "
+
+#. / Run the solver
+#: ../src/solver/solver.cxx:533
+msgid ""
+"Running simulation\n"
+"\n"
+msgstr ""
+"სიმულაციის გაშვება\n"
+"\n"
+
+#: ../tests/unit/src/test_bout++.cxx:359
+msgid "Signal"
+msgstr "სიგნალი"
+
+#: ../src/bout++.cxx:876
+msgid ""
+"Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
+"\n"
+msgstr ""
+
+#: ../src/bout++.cxx:879
+msgid ""
+"Sim Time  |  RHS_e evals  | RHS_I evals  | Wall Time |  Calc    Inv   "
+"Comm    I/O   SOLVER\n"
+"\n"
+msgstr ""
+
+#: ../src/solver/solver.cxx:514
+#, c++-format
+msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
+msgstr ""
+"ამომხსნელი გაშვებულია {:d} გამოტანისთვის მონიტორინგის დროის ნაბიჯით {:e}\n"
+
+#: ../src/solver/solver.cxx:510
+#, c++-format
+msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
+msgstr ""
+"ამომხსნელი გაშვებულია {:d} გამოტანისთვის გამოტანის დროის ნაბიჯით {:e}\n"
+
+#: ../src/solver/solver.cxx:788
+#, c++-format
+msgid ""
+"Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
+"called!"
+msgstr ""
+"Solver::addMonitor: init-ის გამოძახების შემდეგ დროის ნაბიჯს ({:g}-და {:g}-"
+"ზე) ვერ შეამცირებთ!"
+
+#: ../src/solver/solver.cxx:1289
+#, c++-format
+msgid ""
+"Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
+"for field '{:s}'\n"
+msgstr ""
+
+#: ../src/solver/solver.cxx:1494
+#, c++-format
+msgid "Time derivative for variable '{:s}' not set"
+msgstr "ცვლადისთვის '{:s}' დროის წარმოებული დაყენებული არაა"
+
+#: ../src/mesh/mesh.cxx:638
+#, c++-format
+msgid "Trying to add an already existing region {:s} to regionMap2D"
+msgstr "მცდელობა, დაემატოს უკვე არსებული რეგიონი {:s} regionMap2D-ს"
+
+#: ../src/mesh/mesh.cxx:614
+#, c++-format
+msgid "Trying to add an already existing region {:s} to regionMap3D"
+msgstr "მცდელობა, დაემატოს უკვე არსებული რეგიონი {:s} regionMap3D-ს"
+
+#: ../src/mesh/mesh.cxx:649
+#, c++-format
+msgid "Trying to add an already existing region {:s} to regionMapPerp"
+msgstr "მცდელობა, დაემატოს უკვე არსებული რეგიონი {:s} regionMapPerp-ს"
+
+#: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
+#, c++-format
+msgid ""
+"Trying to index Option '{0}' with '{1}', but '{0}' is a value, not a "
+"section.\n"
+"This is likely the result of clashing input options, and you may have to "
+"rename one of them.\n"
+msgstr ""
+
+#: ../src/mesh/coordinates.cxx:1464
+msgid ""
+"Unrecognised paralleltransform option.\n"
+"Valid choices are 'identity', 'shifted', 'fci'"
+msgstr ""
+
+#: ../src/sys/options.cxx:899
+msgid "Unused options:\n"
+msgstr "გამოიყენებელი პარამეტრები:\n"
+
+#: ../src/bout++.cxx:446
+#, c++-format
+msgid "Usage is {:s} -d <data directory>\n"
+msgstr "გამოყენება: {:s} -d <მონაცემების_სააღალდე>\n"
+
+#: ../src/bout++.cxx:455
+#, c++-format
+msgid "Usage is {:s} -f <options filename>\n"
+msgstr "გამოყენება: {:s} -f <პარამეტრების_ფაილის_სახელი>\n"
+
+#: ../src/bout++.cxx:473
+#, c++-format
+msgid "Usage is {:s} -l <log filename>\n"
+msgstr "გამოყენება: {:s} -l <ჟურნალის_ფაილის_სახელი>\n"
+
+#: ../src/bout++.cxx:464
+#, c++-format
+msgid "Usage is {:s} -o <settings filename>\n"
+msgstr "გამოყენება: {:s} -o <პარამეტრების_ფაილის_სახელი>\n"
+
+#: ../src/bout++.cxx:360
+#, c++-format
+msgid "Usage is {} {} <name>\n"
+msgstr "გამოყენება: {} {} <სახელი>\n"
+
+#: ../tests/unit/src/test_bout++.cxx:32 ../tests/unit/src/test_bout++.cxx:46
+msgid "Usage:"
+msgstr "გამოყენება:"
+
+#. Print help message -- note this will be displayed once per processor as we've not
+#. started MPI yet.
+#: ../src/bout++.cxx:374
+#, c++-format
+msgid ""
+"Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
+"[VAR=VALUE]\n"
+msgstr ""
+"გამოყენება: {:s} [-d <მონაცემთა_საქაღალდე>] [-f "
+"<პარამეტრების_ფაილის_სახელი>] [restart [append]] [VAR=VALUE]\n"
+
+#. restart file should be written by physics model
+#: ../src/solver/solver.cxx:927
+msgid "User signalled to quit. Returning\n"
+msgstr "მომხმარებელმა მიგვანიშნა, მუშაობა დაგვემთავრებინა\n"
+
+#: ../src/sys/options.cxx:486
+#, c++-format
+msgid "Value for option {:s} = {:e} is not a bool"
+msgstr "მნიშვნელობა პარამეტრისთვის {:s} = {:e} ლოგიკური არაა"
+
+#: ../src/sys/options.cxx:426
+#, c++-format
+msgid "Value for option {:s} = {:e} is not an integer"
+msgstr "მნიშვნელობა პარამეტრისთვის {:s} = {:e} მთელი რიცხვი არაა"
+
+#: ../src/sys/options.cxx:456
+#, c++-format
+msgid "Value for option {:s} cannot be converted to a BoutReal"
+msgstr "მნიშვნელობა პარამეტრისთვის {:s} BoutReal-ში გადაყვანილი ვერ იქნება"
+
+#: ../src/sys/options.cxx:623
+#, c++-format
+msgid "Value for option {:s} cannot be converted to a Field2D"
+msgstr "მნიშვნელობა პარამეტრისთვის {:s} Field2D-ში გადაყვანილი ვერ იქნება"
+
+#: ../src/sys/options.cxx:571
+#, c++-format
+msgid "Value for option {:s} cannot be converted to a Field3D"
+msgstr "მნიშვნელობა პარამეტრისთვის {:s} Field3D-ში გადაყვანილი ვერ იქნება"
+
+#: ../src/sys/options.cxx:705
+#, c++-format
+msgid "Value for option {:s} cannot be converted to a FieldPerp"
+msgstr "მნიშვნელობა პარამეტრისთვის {:s} FieldPerp-ში გადაყვანილი ვერ იქნება"
+
+#: ../src/sys/options.cxx:491
+#, c++-format
+msgid "Value for option {:s} cannot be converted to a bool"
+msgstr "მნიშვნელობა პარამეტრისთვის {:s} bool-ში გადაყვანილი ვერ იქნება"
+
+#: ../src/sys/options.cxx:751
+#, c++-format
+msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
+msgstr ""
+"მნიშვნელობა პარამეტრისთვის {:s} Array<BoutReal>-ში გადაყვანილი ვერ იქნება"
+
+#: ../src/sys/options.cxx:773
+#, c++-format
+msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
+msgstr ""
+"მნიშვნელობა პარამეტრისთვის {:s} Matrix<BoutReal>-ში გადაყვანილი ვერ იქნება"
+
+#: ../src/sys/options.cxx:795
+#, c++-format
+msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
+msgstr ""
+"მნიშვნელობა პარამეტრისთვის {:s} Tensor<BoutReal>-ში გადაყვანილი ვერ იქნება"
+
+#. Another type which can't be converted
+#: ../src/sys/options.cxx:418
+#, c++-format
+msgid "Value for option {:s} is not an integer"
+msgstr "მნიშვნელობა პარამეტრისთვის {:s} მთელი რიცხვი არაა"
+
+#: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
+#, c++-format
+msgid "Variable '{:s}' not initialised"
+msgstr "ცვლადი '{:s}' ინიციალიზებული არაა"
+
+#: ../src/mesh/impls/bout/boutmesh.cxx:467
+#, c++-format
+msgid ""
+"WARNING: Number of toroidal points should be 2^n for efficient FFT "
+"performance -- consider changing MZ ({:d}) if using FFTs\n"
+msgstr ""
+
+#: ../src/mesh/coordinates.cxx:635
+msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
+msgstr ""
+
+#: ../src/mesh/coordinates.cxx:412
+msgid ""
+"WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
+"option extrapolate_x=false to disable this.\n"
+msgstr ""
+
+#: ../src/mesh/coordinates.cxx:640
+msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
+msgstr ""
+
+#: ../src/mesh/coordinates.cxx:417
+msgid ""
+"WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
+"option extrapolate_y=false to disable this.\n"
+msgstr ""
+
+#: ../src/bout++.cxx:825
+msgid "Wall time limit in hours. By default (< 0), no limit"
+msgstr ""
+
+#: ../src/sys/optionsreader.cxx:42
+#, c++-format
+msgid "Writing options to file {:s}\n"
+msgstr "პარამეტრების ჩაწერა ფაილში {:s}\n"
+
+#. / The source label given to default values
+#: ../src/sys/options.cxx:34
+msgid "default"
+msgstr "ნაგულისხმევი"

From ebf4cf8bc1166d3b90357e5ffe152eac65fe745d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 23 Mar 2026 19:32:33 +0000
Subject: [PATCH 0950/1827] Update pygithub requirement from ~=2.8 to ~=2.9

Updates the requirements on [pygithub](https://github.com/pygithub/pygithub) to permit the latest version.
- [Release notes](https://github.com/pygithub/pygithub/releases)
- [Changelog](https://github.com/PyGithub/PyGithub/blob/main/doc/changes.rst)
- [Commits](https://github.com/pygithub/pygithub/compare/v2.8.0...v2.9.0)

---
updated-dependencies:
- dependency-name: pygithub
  dependency-version: 2.9.0
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements_maint.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements_maint.txt b/requirements_maint.txt
index 05375dd39e..be76672fd4 100644
--- a/requirements_maint.txt
+++ b/requirements_maint.txt
@@ -1,3 +1,3 @@
-pygithub~=2.8
+pygithub~=2.9
 ruamel-yaml~=0.19
 Unidecode~=1.3

From ed56609095b1aba1b8ac50d168f1ba566b3e8453 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 23 Mar 2026 15:18:06 -0700
Subject: [PATCH 0951/1827] PetscOperators: Change to use C, L+ and L- spaces

More consistent treatment of where values are defined: On cells (C),
forward (L+) and backward (L-) legs. Uses typed vectors and operators
to ensure that quantities are used consistently.

Coauthor: ChatGPT.
---
 include/bout/petsc_operators.hxx | 744 ++++++++++++++++---------------
 src/mesh/petsc_operators.cxx     | 605 +++++++++++--------------
 2 files changed, 643 insertions(+), 706 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 8ab95d0f17..b9d35a9793 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -1,14 +1,3 @@
-/// Represent finite-difference operators using PETSc matrices.
-///
-/// This header defines:
-/// - `PetscMapping`, which maps between mesh-global numbering,
-///   PETSc numbering, and `Field3D` storage;
-/// - `PetscOperator`, which wraps a PETSc `Mat` as a linear operator on
-///   `Field3D` objects; and
-/// - `PetscOperators`, a helper for reading mappings and operators from
-///   a `Mesh`.
-///
-
 #include "bout/build_defines.hxx"
 
 #if BOUT_HAS_PETSC
@@ -25,156 +14,103 @@
 #include "bout/utils.hxx"
 
 #include <petscmat.h>
+#include <petscvec.h>
 
 #include <functional>
 #include <memory>
 #include <string>
+#include <type_traits>
+#include <unordered_map>
 #include <utility>
 #include <vector>
 
-/// Map between mesh-global cell numbering and PETSc numbering.
-///
-/// The mesh file stores operator stencils and weights using a mesh-global
-/// numbering scheme. This numbering includes:
-/// - evolving cells in the main domain;
-/// - X-boundary cells; and
-/// - Y-boundary cells represented by the `yup` and `ydown` fields.
-///
-/// PETSc uses a different global numbering based on the MPI distribution
-/// of rows and vector entries. `PetscMapping` records the correspondence
-/// between these numbering systems and provides helper methods to iterate
-/// over the local cells in a consistent order.
-///
-/// The mapping order used by this class is:
-/// 1. evolving cells;
-/// 2. inner X-boundary cells;
-/// 3. outer X-boundary cells;
-/// 4. `yup` boundary cells; and
-/// 5. `ydown` boundary cells.
+/// Tag type for the cell space C.
+struct CellSpaceTag {};
+
+/// Tag type for the forward leg space L+.
+struct ForwardLegSpaceTag {};
+
+/// Tag type for the backward leg space L-.
+struct BackwardLegSpaceTag {};
+
+/// Mapping between stored indices in a mesh file and PETSc row ownership.
 ///
-/// A pair of PETSc matrices is constructed internally to reorder vectors
-/// between mesh-global and PETSc-global numbering.
-class PetscMapping {
+/// Every space is defined by a global stored numbering written to the mesh file.
+/// PETSc distributes rows contiguously across MPI ranks, so this class stores the
+/// local owned stored indices in row order and a permutation matrix that maps
+/// from stored numbering to PETSc numbering.
+class PetscIndexMapping {
 public:
-  /// Construct the mapping from mesh numbering fields.
-  ///
-  /// @param cell_number Mesh-global cell numbers for evolving cells.
-  /// @param forward_cell_number Mesh-global cell numbers associated with
-  ///   forward Y-boundary (`yup`) values.
-  /// @param backward_cell_number Mesh-global cell numbers associated with
-  ///   backward Y-boundary (`ydown`) values.
-  ///
-  /// Non-negative values in the numbering fields identify valid cells.
-  /// The constructor builds the local regions and the PETSc permutation
-  /// matrices needed to translate between mesh and PETSc numbering.
-  PetscMapping(const Field3D& cell_number, const Field3D& forward_cell_number,
-               const Field3D& backward_cell_number);
-
-  /// Destroy the PETSc matrices owned by this mapping.
-  ~PetscMapping();
-
-  /// Build a region containing all valid cells in a numbering field.
-  ///
-  /// @param cell_number Field whose entries contain mesh-global cell numbers.
-  /// @return A region containing all indices with non-negative cell numbers.
-  ///
-  /// This helper is public for unit testing.
-  static Region<Ind3D> create_region(const Field3D& cell_number);
+  PetscIndexMapping() = default;
+  virtual ~PetscIndexMapping();
 
-  /// Build a region containing valid cells on the inner X boundary.
-  ///
-  /// @param cell_number Field whose entries contain mesh-global cell numbers.
-  /// @return A region containing valid cells adjacent to the inner X boundary.
-  static Region<Ind3D> create_region_xin(const Field3D& cell_number);
+  PetscIndexMapping(const PetscIndexMapping&) = delete;
+  PetscIndexMapping& operator=(const PetscIndexMapping&) = delete;
+  PetscIndexMapping(PetscIndexMapping&&) = delete;
+  PetscIndexMapping& operator=(PetscIndexMapping&&) = delete;
 
-  /// Build a region containing valid cells on the outer X boundary.
-  ///
-  /// @param cell_number Field whose entries contain mesh-global cell numbers.
-  /// @return A region containing valid cells adjacent to the outer X boundary.
-  static Region<Ind3D> create_region_xout(const Field3D& cell_number);
-
-  /// Return the total number of locally mapped cells.
-  ///
-  /// The count includes evolving cells and all boundary cells represented
-  /// in the mapping on this processor.
-  unsigned int localSize() const {
-    return evolving_region.size() + xin_region.size() + xout_region.size()
-           + yup_region.size() + ydown_region.size();
+  /// Number of rows owned locally by this MPI rank.
+  PetscInt localSize() const {
+    return static_cast<PetscInt>(local_stored_indices.size());
   }
 
-  unsigned int globalSize() const {
-    // Get global size
-    PetscInt globalRows{0};
-    PetscInt globalCols{0};
-    BOUT_DO_PETSC(MatGetSize(this->mat_mesh_to_petsc, &globalRows, &globalCols));
-    ASSERT1(globalRows == globalCols);
-    return globalRows;
-  }
+  /// Global number of rows in this space.
+  PetscInt globalSize() const { return global_size; }
 
-  /// Iterate over locally owned evolving cells in PETSc row order.
-  ///
-  /// @tparam Function Callable with signature
-  ///   `func(PetscInt petsc_row, Ind3D index, int mesh_global_index)`.
-  /// @param func Function called once for each evolving cell owned locally.
-  ///
-  /// The PETSc row index starts at the locally owned global row `row_start`.
-  /// The supplied `Ind3D` index refers to the main `Field3D` storage.
-  template <typename Function>
-  void map_evolving(Function func) const {
-    PetscInt row = this->row_start;
-    BOUT_FOR_SERIAL(i, this->evolving_region) {
-      func(row, i, ROUND(cell_number[i]));
-      ++row;
-    }
-  }
+  /// First global PETSc row owned by this MPI rank.
+  PetscInt rowStart() const { return row_start; }
+
+  /// One-past-last global PETSc row owned by this MPI rank.
+  PetscInt rowEnd() const { return row_end; }
+
+  /// Stored indices owned locally in PETSc row order.
+  const std::vector<int>& localStoredIndices() const { return local_stored_indices; }
+
+  /// Map a locally owned stored index to a PETSc global row.
+  PetscInt storedToPetsc(int stored_index) const;
+
+  /// Permutation matrix mapping PETSc ordering to stored numbering.
+  Mat getPetscToStored() const { return mat_petsc_to_stored; }
+
+protected:
+  PetscLib lib;
+
+  void buildPermutation(PetscInt nlocal, PetscInt nglobal,
+                        const std::vector<int>& stored_indices);
+
+  PetscInt global_size{0};
+  PetscInt row_start{0};
+  PetscInt row_end{0};
+  std::vector<int> local_stored_indices;
+  std::unordered_map<int, PetscInt> local_stored_to_petsc;
+  Mat mat_stored_to_petsc{nullptr};
+  Mat mat_petsc_to_stored{nullptr};
+};
+
+/// Cell-space mapping between stored cell numbers, PETSc numbering, and Field3D.
+class PetscCellMapping : public PetscIndexMapping {
+public:
+  PetscCellMapping(const Field3D& cell_number, const Field3D& forward_cell_number,
+                   const Field3D& backward_cell_number, int total_cells);
+
+  static Region<Ind3D> create_region(const Field3D& cell_number);
+  static Region<Ind3D> create_region_xin(const Field3D& cell_number);
+  static Region<Ind3D> create_region_xout(const Field3D& cell_number);
 
-  /// Iterate over all locally mapped cells in PETSc row order.
-  ///
-  /// @tparam Function Callable with signature
-  ///   `func(PetscInt petsc_row, int mesh_global_index)`.
-  /// @param func Function called once for each mapped cell owned locally.
-  ///
-  /// The iteration order is evolving, inner X boundary, outer X boundary,
-  /// `yup`, then `ydown`.
-  ///
-  /// No `Ind3D` is passed because some entries refer to interior `Field3D`
-  /// storage while others refer to boundary storage in `yup` or `ydown`.
   template <typename Function>
-  void map(Function func) const {
-    const std::vector<std::reference_wrapper<const Region<Ind3D>>> regions = {
-        evolving_region, xin_region, xout_region};
-    PetscInt row = row_start;
-    for (const auto& region : regions) {
-      BOUT_FOR_SERIAL(i, region.get()) {
-        func(row, ROUND(cell_number[i]));
-        ++row;
-      }
-    }
-    BOUT_FOR_SERIAL(i, yup_region) {
-      func(row, ROUND(forward_cell_number[i]));
-      ++row;
-    }
-    BOUT_FOR_SERIAL(i, ydown_region) {
-      func(row, ROUND(backward_cell_number[i]));
+  void mapOwnedInteriorCells(Function func) const {
+    PetscInt row = rowStart();
+    BOUT_FOR_SERIAL(i, evolving_region) {
+      func(row, i, ROUND(cell_number[i]));
       ++row;
     }
-    ASSERT0(row == row_end);
   }
 
-  /// Iterate over locally stored entries packed from the main `Field3D`.
-  ///
-  /// @tparam Function Callable with signature `func(PetscInt local_index, Ind3D index)`.
-  /// @param func Function called once for each evolving or X-boundary cell
-  ///   stored in the local PETSc vector layout.
-  ///
-  /// The index passed to `func` is a local vector index beginning at zero.
-  /// Only the main field storage is traversed here; Y-boundary values are
-  /// handled separately by `map_local_yup()` and `map_local_ydown()`.
   template <typename Function>
-  void map_local_field(Function func) const {
+  void mapLocalField(Function func) const {
+    PetscInt row = 0;
     const std::vector<std::reference_wrapper<const Region<Ind3D>>> regions = {
         evolving_region, xin_region, xout_region};
-    PetscInt row = 0; // Starting from 0, not row_start
     for (const auto& region : regions) {
       BOUT_FOR_SERIAL(i, region.get()) {
         func(row, i);
@@ -183,14 +119,8 @@ public:
     }
   }
 
-  /// Iterate over local vector entries corresponding to `yup` boundary values.
-  ///
-  /// @tparam Function Callable with signature `func(PetscInt local_index, Ind3D index)`.
-  /// @param func Function called once for each locally stored `yup` entry.
-  ///
-  /// The local index is the offset into the packed local PETSc vector.
   template <typename Function>
-  void map_local_yup(Function func) const {
+  void mapLocalYup(Function func) const {
     PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size();
     BOUT_FOR_SERIAL(i, yup_region) {
       func(row, i.yp());
@@ -198,14 +128,8 @@ public:
     }
   }
 
-  /// Iterate over local vector entries corresponding to `ydown` boundary values.
-  ///
-  /// @tparam Function Callable with signature `func(PetscInt local_index, Ind3D index)`.
-  /// @param func Function called once for each locally stored `ydown` entry.
-  ///
-  /// The local index is the offset into the packed local PETSc vector.
   template <typename Function>
-  void map_local_ydown(Function func) const {
+  void mapLocalYdown(Function func) const {
     PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size()
                    + yup_region.size();
     BOUT_FOR_SERIAL(i, ydown_region) {
@@ -214,274 +138,372 @@ public:
     }
   }
 
-  /// Return the PETSc matrix that maps PETSc ordering to mesh ordering.
-  ///
-  /// @return PETSc matrix representing the permutation from PETSc global
-  ///   indices to mesh-global indices.
-  Mat getPetscToMesh() const { return mat_petsc_to_mesh; }
-
 private:
-  PetscLib lib; // Initialize and finalize PETSc
-
-  /// Mesh-global numbering for cells stored on this rank.
   Field3D cell_number;
   Field3D forward_cell_number;
   Field3D backward_cell_number;
-
-  /// Evolving cells in the main domain.
   Region<Ind3D> evolving_region;
-
-  /// X-boundary cells on the inner radial boundary.
   Region<Ind3D> xin_region;
-
-  /// X-boundary cells on the outer radial boundary.
   Region<Ind3D> xout_region;
-
-  /// Y-boundary cells in the forward direction.
   Region<Ind3D> yup_region;
-
-  /// Y-boundary cells in the backward direction.
   Region<Ind3D> ydown_region;
+};
+
+/// Mapping for forward or backward leg spaces.
+class PetscLegMapping : public PetscIndexMapping {
+public:
+  PetscLegMapping(int total_legs, std::vector<int> local_leg_indices);
+};
+
+using PetscCellMappingPtr = std::shared_ptr<const PetscCellMapping>;
+using PetscLegMappingPtr = std::shared_ptr<const PetscLegMapping>;
+
+/// Wrapper around a PETSc Vec with a compile-time space tag.
+template <typename SpaceTag>
+class PetscSpaceVector {
+  using UniqueVec = bout::petsc::UniqueVec;
+
+public:
+  PetscSpaceVector() = default;
+
+  explicit PetscSpaceVector(std::shared_ptr<const PetscIndexMapping> mapping)
+      : mapping(std::move(mapping)),
+        vec(createVec(this->mapping->localSize(), this->mapping->globalSize())) {}
+
+  PetscSpaceVector(std::shared_ptr<const PetscIndexMapping> mapping, UniqueVec vec)
+      : mapping(std::move(mapping)), vec(std::move(vec)) {}
+
+  PetscSpaceVector(const PetscSpaceVector&) = delete;
+  PetscSpaceVector& operator=(const PetscSpaceVector&) = delete;
+  PetscSpaceVector(PetscSpaceVector&&) noexcept = default;
+  PetscSpaceVector& operator=(PetscSpaceVector&&) noexcept = default;
+
+  Vec raw() const { return *this->vec; }
+  const std::shared_ptr<const PetscIndexMapping>& getMapping() const { return mapping; }
+
+  PetscSpaceVector duplicate() const {
+    UniqueVec out{new Vec{nullptr}};
+    BOUT_DO_PETSC(VecDuplicate(*this->vec, out.get()));
+    return PetscSpaceVector(this->mapping, std::move(out));
+  }
+
+  PetscSpaceVector operator*(BoutReal scalar) const {
+    auto out = this->duplicate();
+    BOUT_DO_PETSC(VecScale(out.raw(), scalar));
+    return out;
+  }
+
+  PetscSpaceVector operator+(const PetscSpaceVector& rhs) const {
+    ASSERT0(mapping == rhs.mapping);
+    auto out = this->duplicate();
+    BOUT_DO_PETSC(VecAXPY(out.raw(), 1.0, rhs.raw()));
+    return out;
+  }
+
+  PetscSpaceVector operator-(const PetscSpaceVector& rhs) const {
+    ASSERT0(mapping == rhs.mapping);
+    auto out = this->duplicate();
+    BOUT_DO_PETSC(VecAXPY(out.raw(), -1.0, rhs.raw()));
+    return out;
+  }
+
+  static PetscSpaceVector pointwiseMultiply(const PetscSpaceVector& lhs,
+                                            const PetscSpaceVector& rhs) {
+    ASSERT0(lhs.mapping == rhs.mapping);
+    auto out = lhs.duplicate();
+    BOUT_DO_PETSC(VecPointwiseMult(out.raw(), lhs.raw(), rhs.raw()));
+    return out;
+  }
 
-  /// First and one-past-last PETSc global rows owned by this rank.
-  PetscInt row_start{}, row_end{};
+  static PetscSpaceVector reciprocal(const PetscSpaceVector& in) {
+    auto out = in.duplicate();
+    BOUT_DO_PETSC(VecReciprocal(out.raw()));
+    return out;
+  }
 
-  /// Permutation matrix mapping mesh-global ordering to PETSc ordering.
-  Mat mat_mesh_to_petsc{nullptr};
+private:
+  static UniqueVec createVec(PetscInt local_size, PetscInt global_size) {
+    UniqueVec out{new Vec{nullptr}};
+    BOUT_DO_PETSC(VecCreate(BoutComm::get(), out.get()));
+    BOUT_DO_PETSC(VecSetType(*out, VECMPI));
+    BOUT_DO_PETSC(VecSetSizes(*out, local_size, global_size));
+    return out;
+  }
 
-  /// Permutation matrix mapping PETSc ordering to mesh-global ordering.
-  Mat mat_petsc_to_mesh{nullptr};
+  std::shared_ptr<const PetscIndexMapping> mapping;
+  UniqueVec vec;
 };
 
-/// Shared pointer to an immutable `PetscMapping`.
-///
-/// The mapping is constructed once and then shared by operators that use it.
-using PetscMappingPtr = std::shared_ptr<const PetscMapping>;
+// Tagged vectors provide compile-time check of compatible operations
+using PetscCellVector = PetscSpaceVector<CellSpaceTag>;
+using PetscForwardLegVector = PetscSpaceVector<ForwardLegSpaceTag>;
+using PetscBackwardLegVector = PetscSpaceVector<BackwardLegSpaceTag>;
 
-/// Linear operator on `Field3D` backed by a PETSc matrix.
-///
-/// `PetscOperator` wraps a PETSc `Mat` whose rows and columns use the PETSc
-/// numbering defined by a corresponding `PetscMapping`. Operators are usually
-/// constructed from CSR arrays read from the mesh file and can then be:
-/// - applied to a `Field3D`;
-/// - composed with other operators; and
-/// - added or subtracted.
+PetscCellVector makePetscCellVector(const PetscCellMappingPtr& mapping,
+                                    const Field3D& field);
+Field3D toField3D(const PetscCellVector& vec, const Field3D& prototype);
+
+/// Typed linear operator between two spaces.
+template <typename OutSpaceTag, typename InSpaceTag>
 class PetscOperator {
-  using UniqueVec = bout::petsc::UniqueVec; // unique_ptr to Vec
-  using UniqueMat = bout::petsc::UniqueMat; // unique_ptr to Mat
+  using UniqueMat = bout::petsc::UniqueMat;
 
 public:
-  /// Construct an operator from CSR data in mesh-global numbering.
-  ///
-  /// @param mapping Shared mapping between mesh and PETSc numbering.
-  /// @param rows CSR row offsets.
-  /// @param cols CSR column indices in mesh-global numbering.
-  /// @param weights CSR non-zero values.
-  ///
-  /// The CSR arrays define an operator in mesh-global numbering. The
-  /// constructor converts this representation into a PETSc matrix using
-  /// the supplied mapping.
-  PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
-                Array<BoutReal> weights);
-
-  // No copying
+  PetscOperator() = default;
+  ~PetscOperator() = default;
+
+  PetscOperator(std::shared_ptr<const PetscIndexMapping> out_mapping,
+                std::shared_ptr<const PetscIndexMapping> in_mapping, Array<int> rows,
+                Array<int> cols, Array<BoutReal> weights)
+      : out_mapping(std::move(out_mapping)), in_mapping(std::move(in_mapping)) {
+    assembleFromCSR(rows, cols, weights);
+  }
+
+  PetscOperator(std::shared_ptr<const PetscIndexMapping> out_mapping,
+                std::shared_ptr<const PetscIndexMapping> in_mapping, UniqueMat mat)
+      : out_mapping(std::move(out_mapping)), in_mapping(std::move(in_mapping)),
+        mat_operator(std::move(mat)) {}
+
+  // Cannot be copied but can be moved
   PetscOperator(const PetscOperator&) = delete;
   PetscOperator& operator=(const PetscOperator&) = delete;
-
-  // Allow Moving
   PetscOperator(PetscOperator&&) noexcept = default;
   PetscOperator& operator=(PetscOperator&&) noexcept = default;
 
-  /// Destroy the PETSc matrix and working vectors owned by this operator.
-  ~PetscOperator() = default;
+  PetscSpaceVector<OutSpaceTag>
+  operator()(const PetscSpaceVector<InSpaceTag>& rhs) const {
+    ASSERT0(in_mapping == rhs.getMapping());
+    PetscSpaceVector<OutSpaceTag> result(out_mapping);
+    BOUT_DO_PETSC(MatMult(*this->mat_operator, rhs.raw(), result.raw()));
+    return result;
+  }
+
+  template <typename T = InSpaceTag,
+            typename = std::enable_if_t<std::is_same_v<T, CellSpaceTag>>>
+  PetscSpaceVector<OutSpaceTag> operator()(const Field3D& rhs) const {
+    auto in = makePetscCellVector(
+        std::static_pointer_cast<const PetscCellMapping>(in_mapping), rhs);
+    return (*this)(in);
+  }
+
+  template <typename T = OutSpaceTag,
+            typename = std::enable_if_t<std::is_same_v<T, CellSpaceTag>>>
+  Field3D applyToField(const PetscSpaceVector<InSpaceTag>& rhs,
+                       const Field3D& prototype) const {
+    auto out = (*this)(rhs);
+    return toField3D(out, prototype);
+  }
+
+  template <typename T = InSpaceTag, typename U = OutSpaceTag,
+            typename = std::enable_if_t<std::is_same_v<T, CellSpaceTag>
+                                        && std::is_same_v<U, CellSpaceTag>>>
+  Field3D operator()(const Field3D& rhs, const Field3D& prototype) const {
+    return applyToField((*this)(rhs), prototype);
+  }
+
+  PetscOperator<InSpaceTag, OutSpaceTag> transpose() const {
+    UniqueMat out{new Mat{nullptr}};
+    BOUT_DO_PETSC(MatTranspose(*mat_operator, MAT_INITIAL_MATRIX, out.get()));
+    return PetscOperator<InSpaceTag, OutSpaceTag>(in_mapping, out_mapping,
+                                                  std::move(out));
+  }
+
+  PetscOperator operator+(const PetscOperator& rhs) const {
+    ASSERT0(out_mapping == rhs.out_mapping);
+    ASSERT0(in_mapping == rhs.in_mapping);
+    UniqueMat out{new Mat{nullptr}};
+    BOUT_DO_PETSC(MatDuplicate(*this->mat_operator, MAT_COPY_VALUES, out.get()));
+    BOUT_DO_PETSC(MatAXPY(*out, 1.0, *rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
+    return PetscOperator(out_mapping, in_mapping, std::move(out));
+  }
+
+  PetscOperator operator-(const PetscOperator& rhs) const {
+    ASSERT0(out_mapping == rhs.out_mapping);
+    ASSERT0(in_mapping == rhs.in_mapping);
+    UniqueMat out{new Mat{nullptr}};
+    BOUT_DO_PETSC(MatDuplicate(*this->mat_operator, MAT_COPY_VALUES, out.get()));
+    BOUT_DO_PETSC(MatAXPY(*out, -1.0, *rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
+    return PetscOperator(out_mapping, in_mapping, std::move(out));
+  }
 
-  /// Create a diagonal operator
-  static PetscOperator diagonal(PetscMappingPtr mapping, const Field3D& f);
-
-  /// Apply the operator to a field.
-  ///
-  /// @param rhs Input field, including any required `yup` and `ydown`
-  ///   boundary values.
-  /// @return Result of applying the operator to `rhs`.
-  ///
-  /// The input field is packed into PETSc vector storage using the mapping,
-  /// multiplied by the PETSc matrix, then unpacked back into a `Field3D`.
-  Field3D operator()(const Field3D& rhs) const;
-
-  /// Compose this operator with another operator.
-  ///
-  /// @param rhs Right-hand-side operator.
-  /// @return The composed operator `(*this) * rhs`.
-  ///
-  /// Both operators must use compatible mappings.
-  PetscOperator operator*(const PetscOperator& rhs) const;
-
-  /// Add two operators.
-  ///
-  /// @param rhs Right-hand-side operator.
-  /// @return The sum of the two operators.
-  ///
-  /// Both operators must use compatible mappings.
-  PetscOperator operator+(const PetscOperator& rhs) const;
-
-  /// Subtract one operator from another.
-  ///
-  /// @param rhs Right-hand-side operator.
-  /// @return The difference of the two operators.
-  ///
-  /// Both operators must use compatible mappings.
-  PetscOperator operator-(const PetscOperator& rhs) const;
-
-  /// Calculate transpose as a new matrix
-  PetscOperator transpose() const;
-
-  void view() const { MatView(*this->mat_operator, PETSC_VIEWER_STDOUT_WORLD); }
-
-  /// Multiply by a scalar
-  /// This version allocates a new Mat and so is for lvalues.
   PetscOperator operator*(BoutReal scalar) const& {
-    UniqueMat mat{new Mat{}};
-    BOUT_DO_PETSC(MatDuplicate(*mat_operator, MAT_COPY_VALUES, mat.get()));
-    BOUT_DO_PETSC(MatScale(*mat, scalar));
-    return PetscOperator(this->mapping, std::move(mat));
+    UniqueMat out{new Mat{nullptr}};
+    BOUT_DO_PETSC(MatDuplicate(*this->mat_operator, MAT_COPY_VALUES, out.get()));
+    BOUT_DO_PETSC(MatScale(*out, scalar));
+    return PetscOperator(out_mapping, in_mapping, std::move(out));
   }
 
-  /// Multiply by a scalar.
-  /// This version is for rvalue temporaries and modifies in-place.
   PetscOperator operator*(BoutReal scalar) && {
     BOUT_DO_PETSC(MatScale(*this->mat_operator, scalar));
     return std::move(*this);
   }
 
+  Mat raw() const { return *this->mat_operator; }
+
+  static PetscOperator diagonal(std::shared_ptr<const PetscIndexMapping> mapping,
+                                const PetscSpaceVector<OutSpaceTag>& diag) {
+    static_assert(std::is_same_v<OutSpaceTag, InSpaceTag>,
+                  "Diagonal operators require the same input and output space");
+    UniqueMat out{new Mat{nullptr}};
+    BOUT_DO_PETSC(MatCreate(BoutComm::get(), out.get()));
+    BOUT_DO_PETSC(MatSetType(*out, MATMPIAIJ));
+    BOUT_DO_PETSC(MatSetSizes(*out, mapping->localSize(), mapping->localSize(),
+                              mapping->globalSize(), mapping->globalSize()));
+    BOUT_DO_PETSC(MatMPIAIJSetPreallocation(*out, 1, nullptr, 0, nullptr));
+    BOUT_DO_PETSC(MatDiagonalSet(*out, diag.raw(), INSERT_VALUES));
+    BOUT_DO_PETSC(MatAssemblyBegin(*out, MAT_FINAL_ASSEMBLY));
+    BOUT_DO_PETSC(MatAssemblyEnd(*out, MAT_FINAL_ASSEMBLY));
+    return PetscOperator(mapping, mapping, std::move(out));
+  }
+
 private:
-  /// Construct directly from an existing PETSc matrix.
-  ///
-  /// @param mapping Shared mapping between mesh and PETSc numbering.
-  /// @param mat PETSc matrix implementing the operator.
-  ///
-  /// This constructor is used internally when creating operators from
-  /// PETSc matrix algebra such as composition, addition, or subtraction.
-  PetscOperator(PetscMappingPtr mapping, UniqueMat mat)
-      : mapping(std::move(mapping)), mat_operator(std::move(mat)),
-        rhs_vec(createVec(this->mapping->localSize())),
-        result_vec(createVec(this->mapping->localSize())) {}
-
-  /// Shared mapping between mesh and PETSc numbering.
-  PetscMappingPtr mapping;
-
-  /// PETSc matrix implementing the operator.
-  UniqueMat mat_operator;
-
-  /// Work vector holding the packed input field.
-  UniqueVec rhs_vec;
-
-  /// Work vector holding the packed result.
-  UniqueVec result_vec;
-
-  /// Copy contents of f, f.yup() and f.ydown() into vec.
-  /// Assumes that vec has already been allocated.
-  static void copyToVec(const PetscMappingPtr& mapping, const Field3D& f, Vec vec);
-
-  // Allocate MPI vector
-  static UniqueVec createVec(PetscInt local_size);
+  void assembleFromCSR(const Array<int>& rows, const Array<int>& cols,
+                       const Array<BoutReal>& weights) {
+    UniqueMat temp{new Mat{nullptr}};
+    BOUT_DO_PETSC(MatCreate(BoutComm::get(), temp.get()));
+    BOUT_DO_PETSC(MatSetType(*temp, MATMPIAIJ));
+    BOUT_DO_PETSC(MatSetSizes(*temp, out_mapping->localSize(), PETSC_DECIDE,
+                              out_mapping->globalSize(), in_mapping->globalSize()));
+
+    const auto& local_rows = out_mapping->localStoredIndices();
+    for (PetscInt local_row = 0; local_row < static_cast<PetscInt>(local_rows.size());
+         ++local_row) {
+      const int stored_row = local_rows[local_row];
+      if (stored_row < 0 || stored_row + 1 >= static_cast<int>(rows.size())) {
+        continue;
+      }
+      const int start = rows[stored_row];
+      const int end = rows[stored_row + 1];
+      if (end <= start) {
+        continue;
+      }
+      const PetscInt petsc_row = out_mapping->rowStart() + local_row;
+      BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, end - start, &cols[start],
+                                 &weights[start], INSERT_VALUES));
+    }
+    BOUT_DO_PETSC(MatAssemblyBegin(*temp, MAT_FINAL_ASSEMBLY));
+    BOUT_DO_PETSC(MatAssemblyEnd(*temp, MAT_FINAL_ASSEMBLY));
+
+    UniqueMat out{new Mat{nullptr}};
+    BOUT_DO_PETSC(MatMatMult(*temp, in_mapping->getPetscToStored(), MAT_INITIAL_MATRIX,
+                             PETSC_DETERMINE, out.get()));
+    mat_operator = std::move(out);
+  }
+
+  std::shared_ptr<const PetscIndexMapping> out_mapping;
+  std::shared_ptr<const PetscIndexMapping> in_mapping;
+  UniqueMat mat_operator{new Mat{nullptr}};
+
+  template <typename O, typename M, typename I>
+  friend PetscOperator<O, I> operator*(const PetscOperator<O, M>& lhs,
+                                       const PetscOperator<M, I>& rhs);
 };
 
-/// Collection of PETSc operators read from a mesh.
-///
-/// `PetscOperators` owns the `PetscMapping` derived from the mesh numbering
-/// fields and provides access to named operators stored in the mesh file
-/// as CSR arrays.
+template <typename OutSpaceTag, typename MidSpaceTag, typename InSpaceTag>
+PetscOperator<OutSpaceTag, InSpaceTag>
+operator*(const PetscOperator<OutSpaceTag, MidSpaceTag>& lhs,
+          const PetscOperator<MidSpaceTag, InSpaceTag>& rhs) {
+  ASSERT0(lhs.in_mapping == rhs.out_mapping);
+  typename PetscOperator<OutSpaceTag, InSpaceTag>::UniqueMat out{new Mat{nullptr}};
+  BOUT_DO_PETSC(
+      MatMatMult(lhs.raw(), rhs.raw(), MAT_INITIAL_MATRIX, PETSC_DETERMINE, out.get()));
+  return PetscOperator<OutSpaceTag, InSpaceTag>(lhs.out_mapping, rhs.in_mapping,
+                                                std::move(out));
+}
+
+using PetscForwardOperator = PetscOperator<ForwardLegSpaceTag, CellSpaceTag>;
+using PetscBackwardOperator = PetscOperator<BackwardLegSpaceTag, CellSpaceTag>;
+using PetscForwardToCellOperator = PetscOperator<CellSpaceTag, ForwardLegSpaceTag>;
+using PetscBackwardToCellOperator = PetscOperator<CellSpaceTag, BackwardLegSpaceTag>;
+using PetscCellOperator = PetscOperator<CellSpaceTag, CellSpaceTag>;
+using PetscForwardLegOperator = PetscOperator<ForwardLegSpaceTag, ForwardLegSpaceTag>;
+using PetscBackwardLegOperator = PetscOperator<BackwardLegSpaceTag, BackwardLegSpaceTag>;
+
+/// Factory for operators defined on cell and leg spaces.
 class PetscOperators {
 public:
-  /// Construct PETSc operator support from a mesh.
-  ///
-  /// Reads the following mesh variables:
-  /// - `cell_number`
-  /// - `forward_cell_number`
-  /// - `backward_cell_number`
-  ///
-  /// and uses them to construct the shared `PetscMapping`.
-  ///
-  /// @param mesh Mesh from which numbering fields and operators are read.
-  PetscOperators(Mesh* mesh);
-
-  /// Retrieve a named PETSc operator from the mesh.
-  ///
-  /// @param name Base name of the operator in the mesh file.
-  /// @return A `PetscOperator` constructed from the arrays
-  ///   `{name}_rows`, `{name}_columns`, and `{name}_weights`.
-  ///
-  /// Throws `BoutException` if any of the required arrays are missing.
-  PetscOperator get(const std::string& name) const;
-
-  /// Create a diagonal operator
-  PetscOperator diagonal(const Field3D& f) const {
-    return PetscOperator::diagonal(mapping, f);
-  }
+  explicit PetscOperators(Mesh* mesh);
 
-  /// A standard collection of operators
-  /// parallel to the magnetic field
-  struct Parallel {
-    PetscOperator Grad_par;         ///< Gradient
-    PetscOperator Div_par;          ///< Divergence
-    PetscOperator Div_par_Grad_par; ///< Diffusion
-    Field3D dV;                     ///< Cell volume
+  PetscForwardOperator forward() const;
+  PetscBackwardOperator backward() const;
 
-    PetscOperator Grad_minus;
-    PetscOperator Grad_plus;
-    PetscOperator Div_minus;
-    PetscOperator Div_plus;
+  PetscForwardOperator injectForward() const;
+  PetscBackwardOperator injectBackward() const;
 
-    PetscOperator Interp_minus;
-    PetscOperator Interp_plus;
+  PetscForwardLegVector forwardLegWeights() const;
+  PetscBackwardLegVector backwardLegWeights() const;
+
+  PetscCellOperator diagonal(const Field3D& f) const;
+  PetscForwardLegOperator diagonal(const PetscForwardLegVector& v) const;
+  PetscBackwardLegOperator diagonal(const PetscBackwardLegVector& v) const;
+
+  struct Parallel {
+    PetscForwardOperator Forward;
+    PetscBackwardOperator Backward;
+    PetscForwardOperator Inject_plus;
+    PetscBackwardOperator Inject_minus;
+    PetscForwardOperator Interp_plus;
+    PetscBackwardOperator Interp_minus;
+    PetscForwardOperator Grad_plus;
+    PetscBackwardOperator Grad_minus;
+    PetscForwardToCellOperator Div_minus;
+    PetscBackwardToCellOperator Div_plus;
+    PetscCellOperator Div_par_Grad_par;
+    Field3D dV;
 
-    /// This is a bilinear operator that requires multiple
-    /// matrix-vector products.
     Field3D Div_par_K_Grad_par(const Field3D& K, const Field3D& f) const;
   };
 
-  /// Calculate a set of parallel operators
-  ///
-  /// This assumes that "forward" and "backward" operators
-  /// are stored in the mesh.
   Parallel getParallel() const;
 
 private:
-  /// Read a `Field3D` from the mesh.
-  ///
-  /// @param mesh Mesh from which to read.
-  /// @param name Name of the field.
-  /// @return The requested `Field3D`.
-  ///
-  /// Throws `BoutException` if the field is not present.
   static Field3D meshGetField3D(Mesh* mesh, const std::string& name);
 
-  /// Read a one-dimensional `Array<T>` from the mesh.
-  ///
-  /// @tparam T Array element type.
-  /// @param mesh Mesh from which to read.
-  /// @param name Name of the array.
-  /// @return The requested array.
-  ///
-  /// Throws `BoutException` if the array is not present.
   template <typename T>
-  Array<T> meshGetArray(Mesh* mesh, const std::string& name) const {
+  Array<T> meshGetArray(const std::string& name) const {
     Array<T> result;
     if (mesh->get(result, name) != 0) {
-      throw BoutException("PetscOperators requires Array<int> '{}'", name);
+      throw BoutException("PetscOperators requires array '{}'", name);
     }
     return result;
   }
 
-  /// Mesh from which operator data are read.
-  Mesh* mesh;
+  int meshGetInt(const std::string& name) const;
+
+  template <typename LegTag>
+  PetscOperator<LegTag, CellSpaceTag>
+  buildInjection(const Field3D& interior_leg_number, const Field3D& boundary_leg_number,
+                 std::shared_ptr<const PetscLegMapping> leg_mapping) const;
+
+  template <typename LegVector>
+  LegVector loadLegWeights(const std::string& name,
+                           std::shared_ptr<const PetscLegMapping> mapping) const {
+    auto values = meshGetArray<BoutReal>(name);
+    LegVector out(mapping);
+    PetscScalar* x{nullptr};
+    BOUT_DO_PETSC(VecGetArray(out.raw(), &x));
+    const auto& local = mapping->localStoredIndices();
+    for (PetscInt i = 0; i < static_cast<PetscInt>(local.size()); ++i) {
+      const int stored = local[i];
+      x[i] = (stored >= 0 && stored < static_cast<int>(values.size())) ? values[stored]
+                                                                       : 0.0;
+    }
+    BOUT_DO_PETSC(VecRestoreArray(out.raw(), &x));
+    return out;
+  }
 
-  /// Shared mapping used by all operators created from this mesh.
-  PetscMappingPtr mapping;
+  Mesh* mesh{nullptr};
+  PetscCellMappingPtr cell_mapping;
+  PetscLegMappingPtr forward_leg_mapping;
+  PetscLegMappingPtr backward_leg_mapping;
+  Field3D forward_leg_interior_number;
+  Field3D forward_leg_boundary_number;
+  Field3D backward_leg_interior_number;
+  Field3D backward_leg_boundary_number;
 };
 
-#else // BOUT_HAS_PETSC
+#else
 
 #warning PETSc not available. No PetscOperators.
 
-#endif // BOUT_HAS_PETSC
+#endif
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 6767ebe716..d3682d2b00 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -2,67 +2,99 @@
 
 #if BOUT_HAS_PETSC
 
-#include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
-#include "bout/output.hxx"
-#include "bout/output_bout_types.hxx"
-#include "bout/petsc_interface.hxx"
 #include "bout/petsc_operators.hxx"
-#include "bout/petsclib.hxx"
 #include "bout/region.hxx"
+#include "bout/utils.hxx"
+
+#include <algorithm>
 #include <memory>
 #include <string>
 #include <utility>
+#include <vector>
+
+PetscIndexMapping::~PetscIndexMapping() {
+  if (mat_stored_to_petsc != nullptr) {
+    MatDestroy(&mat_stored_to_petsc);
+  }
+  if (mat_petsc_to_stored != nullptr) {
+    MatDestroy(&mat_petsc_to_stored);
+  }
+}
 
-Region<Ind3D> PetscMapping::create_region(const Field3D& cell_number) {
+PetscInt PetscIndexMapping::storedToPetsc(int stored_index) const {
+  auto it = local_stored_to_petsc.find(stored_index);
+  if (it == local_stored_to_petsc.end()) {
+    throw BoutException("Stored index {} is not owned locally", stored_index);
+  }
+  return it->second;
+}
+
+void PetscIndexMapping::buildPermutation(PetscInt nlocal, PetscInt nglobal,
+                                         const std::vector<int>& stored_indices) {
+  global_size = nglobal;
+  local_stored_indices = stored_indices;
+
+  BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat_stored_to_petsc));
+  BOUT_DO_PETSC(MatSetSizes(mat_stored_to_petsc, nlocal, nlocal, nglobal, nglobal));
+  BOUT_DO_PETSC(MatSetType(mat_stored_to_petsc, MATMPIAIJ));
+  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(mat_stored_to_petsc, 1, nullptr, 1, nullptr));
+  BOUT_DO_PETSC(MatGetOwnershipRange(mat_stored_to_petsc, &row_start, &row_end));
+  ASSERT1(row_end - row_start == nlocal);
+
+  const PetscScalar one = 1.0;
+  for (PetscInt i = 0; i < nlocal; ++i) {
+    const PetscInt petsc_row = row_start + i;
+    const PetscInt stored_col = stored_indices[i];
+    ASSERT1(stored_col >= 0);
+    local_stored_to_petsc[static_cast<int>(stored_col)] = petsc_row;
+    BOUT_DO_PETSC(MatSetValues(mat_stored_to_petsc, 1, &petsc_row, 1, &stored_col, &one,
+                               INSERT_VALUES));
+  }
+  BOUT_DO_PETSC(MatAssemblyBegin(mat_stored_to_petsc, MAT_FINAL_ASSEMBLY));
+  BOUT_DO_PETSC(MatAssemblyEnd(mat_stored_to_petsc, MAT_FINAL_ASSEMBLY));
+  BOUT_DO_PETSC(
+      MatTranspose(mat_stored_to_petsc, MAT_INITIAL_MATRIX, &mat_petsc_to_stored));
+}
+
+Region<Ind3D> PetscCellMapping::create_region(const Field3D& cell_number) {
   Region<Ind3D>::RegionIndices indices;
-  BOUT_FOR_SERIAL(i, cell_number.getRegion("RGN_NOBNDRY")) {
-    if (cell_number[i] > -1) {
+  BOUT_FOR(i, cell_number.getRegion("RGN_NOBNDRY")) {
+    if (cell_number[i] >= 0) {
       indices.push_back(i);
     }
   }
   return Region<Ind3D>(indices);
 }
 
-Region<Ind3D> PetscMapping::create_region_xin(const Field3D& cell_number) {
-  Region<Ind3D>::RegionIndices xin_indices;
-  const Mesh* mesh = cell_number.getMesh();
-  if (mesh->firstX()) {
-    for (int i = 0; i < mesh->xstart; ++i) {
-      for (int j = mesh->ystart; j <= mesh->yend; ++j) {
-        for (int k = mesh->zstart; k <= mesh->zend; ++k) {
-          if (cell_number(i, j, k) > -1) {
-            xin_indices.push_back(cell_number.indexAt(i, j, k));
-          }
-        }
-      }
+Region<Ind3D> PetscCellMapping::create_region_xin(const Field3D& cell_number) {
+  Region<Ind3D>::RegionIndices indices;
+  const auto& region = cell_number.getRegion("RGN_INNER_X");
+  BOUT_FOR(i, region) {
+    if (cell_number[i] >= 0) {
+      indices.push_back(i);
     }
   }
-  return Region<Ind3D>(xin_indices);
+  return Region<Ind3D>(indices);
 }
 
-Region<Ind3D> PetscMapping::create_region_xout(const Field3D& cell_number) {
-  Region<Ind3D>::RegionIndices xout_indices;
-  const Mesh* mesh = cell_number.getMesh();
-  if (mesh->lastX()) {
-    for (int i = mesh->xend + 1; i < mesh->LocalNx; ++i) {
-      for (int j = mesh->ystart; j <= mesh->yend; ++j) {
-        for (int k = mesh->zstart; k <= mesh->zend; ++k) {
-          if (cell_number(i, j, k) > -1) {
-            xout_indices.push_back(cell_number.indexAt(i, j, k));
-          }
-        }
-      }
+Region<Ind3D> PetscCellMapping::create_region_xout(const Field3D& cell_number) {
+  Region<Ind3D>::RegionIndices indices;
+  const auto& region = cell_number.getRegion("RGN_OUTER_X");
+  BOUT_FOR(i, region) {
+    if (cell_number[i] >= 0) {
+      indices.push_back(i);
     }
   }
-  return Region<Ind3D>(xout_indices);
+  return Region<Ind3D>(indices);
 }
 
-PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_cell_number,
-                           const Field3D& backward_cell_number)
+PetscCellMapping::PetscCellMapping(const Field3D& cell_number,
+                                   const Field3D& forward_cell_number,
+                                   const Field3D& backward_cell_number, int total_cells)
     : cell_number(cell_number), forward_cell_number(forward_cell_number),
       backward_cell_number(backward_cell_number),
       evolving_region(create_region(cell_number)),
@@ -70,378 +102,261 @@ PetscMapping::PetscMapping(const Field3D& cell_number, const Field3D& forward_ce
       xout_region(create_region_xout(cell_number)),
       yup_region(create_region(forward_cell_number)),
       ydown_region(create_region(backward_cell_number)) {
-  // Calculate size of each region
-  const unsigned int nlocal = this->localSize();
-  output.write("Local {} : evolving {} xin {} xout {} yup {} ydown {}", nlocal,
-               evolving_region.size(), xin_region.size(), xout_region.size(),
-               yup_region.size(), ydown_region.size());
-
-  // Create a PETSc matrix
-  // Note: Numbering is different from that used in PetscVector / PetscMatrix
-  // because yup/down boundaries are included.
-
-  // Renumbering matrix.
-  // Maps PETSc row (or column) indices to the global indices used in
-  // the mesh.  This is needed because the PETSc indices depend on the
-  // number of processors.
-  BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat_mesh_to_petsc));
-  BOUT_DO_PETSC(
-      MatSetSizes(mat_mesh_to_petsc, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
-  BOUT_DO_PETSC(MatSetType(mat_mesh_to_petsc, MATMPIAIJ));
-  // Each row will have one non-zero entry, which could be in
-  // either the "diagonal" or "off-diagonal" block.
-  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(mat_mesh_to_petsc, 1, nullptr, 1, nullptr));
-
-  // Get the range of rows owned by this processor
-  BOUT_DO_PETSC(MatGetOwnershipRange(mat_mesh_to_petsc, &row_start, &row_end));
-  output.write("Local row range: {} -> {}\n", row_start, row_end);
-
-  // Iterate through regions in this order
-  this->map([&](PetscInt row, PetscInt col) {
-    // `row` is the PETSc index; `col` is the Mesh index
-    ASSERT1(row >= 0);
-    ASSERT1(col >= 0);
-    const PetscScalar ONE = 1.0;
-    BOUT_DO_PETSC(MatSetValues(mat_mesh_to_petsc, 1, &row, 1, &col, &ONE, INSERT_VALUES));
-  });
-  BOUT_DO_PETSC(MatAssemblyBegin(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY));
-  BOUT_DO_PETSC(MatAssemblyEnd(mat_mesh_to_petsc, MAT_FINAL_ASSEMBLY));
+  std::vector<int> local_indices;
+  const auto push_region = [&](const Region<Ind3D>& region, const Field3D& values) {
+    BOUT_FOR_SERIAL(i, region) { local_indices.push_back(ROUND(values[i])); }
+  };
+  push_region(evolving_region, this->cell_number);
+  push_region(xin_region, this->cell_number);
+  push_region(xout_region, this->cell_number);
+  push_region(yup_region, this->forward_cell_number);
+  push_region(ydown_region, this->backward_cell_number);
+  buildPermutation(static_cast<PetscInt>(local_indices.size()), total_cells,
+                   local_indices);
+}
+
+PetscLegMapping::PetscLegMapping(int total_legs, std::vector<int> local_leg_indices) {
+  std::sort(local_leg_indices.begin(), local_leg_indices.end());
+  local_leg_indices.erase(std::unique(local_leg_indices.begin(), local_leg_indices.end()),
+                          local_leg_indices.end());
+  buildPermutation(static_cast<PetscInt>(local_leg_indices.size()), total_legs,
+                   local_leg_indices);
+}
+
+PetscCellVector makePetscCellVector(const PetscCellMappingPtr& mapping,
+                                    const Field3D& field) {
+  ASSERT1(field.hasParallelSlices());
+  ASSERT1(field.yup().isAllocated());
+  ASSERT1(field.ydown().isAllocated());
+  PetscCellVector out(mapping);
+  PetscScalar* x{nullptr};
+  BOUT_DO_PETSC(VecGetArray(out.raw(), &x));
+  mapping->mapLocalField([&](PetscInt row, const Ind3D& i) { x[row] = field[i]; });
+  const auto& yup = field.yup();
+  mapping->mapLocalYup([&](PetscInt row, const Ind3D& i) { x[row] = yup[i]; });
+  const auto& ydown = field.ydown();
+  mapping->mapLocalYdown([&](PetscInt row, const Ind3D& i) { x[row] = ydown[i]; });
+  BOUT_DO_PETSC(VecRestoreArray(out.raw(), &x));
+  return out;
+}
 
-  // Transpose to map petsc indices to mesh indices
-  MatTranspose(mat_mesh_to_petsc, MAT_INITIAL_MATRIX, &mat_petsc_to_mesh);
+Field3D toField3D(const PetscCellVector& vec, const Field3D& prototype) {
+  auto mapping = std::static_pointer_cast<const PetscCellMapping>(vec.getMapping());
+  Field3D result{emptyFrom(prototype)};
+  const PetscScalar* x{nullptr};
+  BOUT_DO_PETSC(VecGetArrayRead(vec.raw(), &x));
+  mapping->mapLocalField([&](PetscInt row, const Ind3D& i) { result[i] = x[row]; });
+  mapping->mapLocalYup([&](PetscInt row, const Ind3D& i) { result.yup()[i] = x[row]; });
+  mapping->mapLocalYdown(
+      [&](PetscInt row, const Ind3D& i) { result.ydown()[i] = x[row]; });
+  BOUT_DO_PETSC(VecRestoreArrayRead(vec.raw(), &x));
+  return result;
 }
 
-PetscMapping::~PetscMapping() {
-  MatDestroy(&this->mat_mesh_to_petsc);
-  MatDestroy(&this->mat_petsc_to_mesh);
+Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) {
+  Field3D result;
+  if (mesh->get(result, name) != 0) {
+    throw BoutException("PetscOperators requires field '{}'", name);
+  }
+  return result;
+}
+
+int PetscOperators::meshGetInt(const std::string& name) const {
+  int result{0};
+  if (mesh->get(result, name) != 0) {
+    throw BoutException("PetscOperators requires int '{}'", name);
+  }
+  return result;
 }
 
-PetscOperator::PetscOperator(PetscMappingPtr mapping, Array<int> rows, Array<int> cols,
-                             Array<BoutReal> weights)
-    : mapping(std::move(mapping)), mat_operator(new Mat{nullptr}),
-      rhs_vec(createVec(this->mapping->localSize())),
-      result_vec(createVec(this->mapping->localSize())) {
-
-  output.write("PetscOperator Array sizes {} {} {}\n", rows.size(), cols.size(),
-               weights.size());
-
-  Mat mat{nullptr};
-  BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat));
-  BOUT_DO_PETSC(MatSetType(mat, MATMPIAIJ));
-  const int nlocal = this->mapping->localSize();
-  BOUT_DO_PETSC(MatSetSizes(mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
-
-  // This reads CSR format but is defensive in handling negative indices and missing
-  // final 'row' entry.
-  this->mapping->map([&](PetscInt row, PetscInt mesh_index) {
-    if (mesh_index >= rows.size()) {
-      return; // No weights -> skip
+PetscOperators::PetscOperators(Mesh* mesh)
+    : mesh(mesh),
+      cell_mapping(std::make_shared<PetscCellMapping>(
+          meshGetField3D(mesh, "cell_number"),
+          meshGetField3D(mesh, "forward_cell_number"),
+          meshGetField3D(mesh, "backward_cell_number"), meshGetInt("total_cells"))),
+      forward_leg_interior_number(meshGetField3D(mesh, "forward_leg_interior_number")),
+      forward_leg_boundary_number(meshGetField3D(mesh, "forward_leg_boundary_number")),
+      backward_leg_interior_number(meshGetField3D(mesh, "backward_leg_interior_number")),
+      backward_leg_boundary_number(meshGetField3D(mesh, "backward_leg_boundary_number")) {
+  std::vector<int> local_forward_legs;
+  std::vector<int> local_backward_legs;
+  cell_mapping->mapOwnedInteriorCells([&](PetscInt, const Ind3D& i, int) {
+    const int f_int = ROUND(forward_leg_interior_number[i]);
+    const int f_bnd = ROUND(forward_leg_boundary_number[i]);
+    const int b_int = ROUND(backward_leg_interior_number[i]);
+    const int b_bnd = ROUND(backward_leg_boundary_number[i]);
+    if (f_int >= 0) {
+      local_forward_legs.push_back(f_int);
     }
-    // Get the range of indices into columns and weights
-    const int start_ind = rows[mesh_index];
-    if (start_ind < 0) {
-      return; // No entries (non-standard CSR)
+    if (f_bnd >= 0) {
+      local_forward_legs.push_back(f_bnd);
     }
-    int end_ind =
-        cols.size(); // End of the columns array (should be last element of rows)
-    for (int i = mesh_index + 1; i < rows.size(); ++i) {
-      // rows[i] can be -1 if no weights (non-standard CSR)
-      if (rows[i] > -1) {
-        // This is the next entry in the columns / weights array
-        end_ind = rows[i];
-        break;
-      }
+    if (b_int >= 0) {
+      local_backward_legs.push_back(b_int);
     }
-    if (end_ind == start_ind) {
-      // Empty row in CSR format
-      return;
+    if (b_bnd >= 0) {
+      local_backward_legs.push_back(b_bnd);
     }
-    BOUT_DO_PETSC(MatSetValues(mat, 1, &row, end_ind - start_ind, &cols[start_ind],
-                               &weights[start_ind], INSERT_VALUES));
   });
-  BOUT_DO_PETSC(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY));
-  BOUT_DO_PETSC(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY));
-
-  // Row indices are PETSc indices but columns are mesh indices
-  // Multiply on the right by PetscToMesh.
-  BOUT_DO_PETSC(MatMatMult(mat, this->mapping->getPetscToMesh(), MAT_INITIAL_MATRIX,
-                           PETSC_DETERMINE, this->mat_operator.get()));
-  // Destroy temporary matrix
-  BOUT_DO_PETSC(MatDestroy(&mat));
-}
-
-void PetscOperator::copyToVec(const PetscMappingPtr& mapping, const Field3D& f, Vec vec) {
-  ASSERT1(f.hasParallelSlices());
-  ASSERT1(f.yup().isAllocated());
-  ASSERT1(f.ydown().isAllocated());
-
-  PetscScalar* x{nullptr};
-  // Copy rows from Field3D cells
-  BOUT_DO_PETSC(VecGetArray(vec, &x));
-  mapping->map_local_field([&](PetscInt row, const Ind3D& i) { x[row] = f[i]; });
 
-  // Copy Yup / Ydown values from boundaries
-  const Field3D& yup = f.yup();
-  mapping->map_local_yup([&](PetscInt row, const Ind3D& i) { x[row] = yup[i]; });
-
-  const Field3D& ydown = f.ydown();
-  mapping->map_local_ydown([&](PetscInt row, const Ind3D& i) { x[row] = ydown[i]; });
-
-  BOUT_DO_PETSC(VecRestoreArray(vec, &x));
+  forward_leg_mapping = std::make_shared<PetscLegMapping>(meshGetInt("n_forward_legs"),
+                                                          std::move(local_forward_legs));
+  backward_leg_mapping = std::make_shared<PetscLegMapping>(
+      meshGetInt("n_backward_legs"), std::move(local_backward_legs));
 }
 
-PetscOperator::UniqueVec PetscOperator::createVec(PetscInt local_size) {
-  UniqueVec vec(new Vec{nullptr});
-  BOUT_DO_PETSC(VecCreate(BoutComm::get(), vec.get()));
-  BOUT_DO_PETSC(VecSetType(*vec, VECMPI));
-  BOUT_DO_PETSC(VecSetSizes(*vec, local_size, PETSC_DETERMINE));
-  return vec;
+PetscForwardOperator PetscOperators::forward() const {
+  return PetscForwardOperator(
+      forward_leg_mapping, cell_mapping, meshGetArray<int>("forward_rows"),
+      meshGetArray<int>("forward_columns"), meshGetArray<BoutReal>("forward_weights"));
 }
 
-PetscOperator PetscOperator::diagonal(PetscMappingPtr mapping, const Field3D& f) {
-  const UniqueVec diag{createVec(mapping->localSize())};
-  copyToVec(mapping, f, *diag);
+PetscBackwardOperator PetscOperators::backward() const {
+  return PetscBackwardOperator(
+      backward_leg_mapping, cell_mapping, meshGetArray<int>("backward_rows"),
+      meshGetArray<int>("backward_columns"), meshGetArray<BoutReal>("backward_weights"));
+}
 
-  UniqueMat mat(new Mat{nullptr});
-  // Note: MatMatMult with diagonal and mpiaij not supported
-  // -> Create MPIAIJ
+template <typename LegTag>
+PetscOperator<LegTag, CellSpaceTag>
+PetscOperators::buildInjection(const Field3D& interior_leg_number,
+                               const Field3D& boundary_leg_number,
+                               std::shared_ptr<const PetscLegMapping> leg_mapping) const {
+  using Op = PetscOperator<LegTag, CellSpaceTag>;
+  bout::petsc::UniqueMat mat{new Mat{nullptr}};
   BOUT_DO_PETSC(MatCreate(BoutComm::get(), mat.get()));
   BOUT_DO_PETSC(MatSetType(*mat, MATMPIAIJ));
-  const PetscInt nlocal = mapping->localSize();
-  BOUT_DO_PETSC(MatSetSizes(*mat, nlocal, nlocal, PETSC_DECIDE, PETSC_DECIDE));
-  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(*mat, 1, nullptr, 0, nullptr));
-  BOUT_DO_PETSC(MatDiagonalSet(*mat, *diag, INSERT_VALUES));
+  BOUT_DO_PETSC(MatSetSizes(*mat, leg_mapping->localSize(), cell_mapping->localSize(),
+                            leg_mapping->globalSize(), cell_mapping->globalSize()));
+  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(*mat, 1, nullptr, 1, nullptr));
+  const PetscScalar one = 1.0;
+  cell_mapping->mapOwnedInteriorCells([&](PetscInt cell_row, const Ind3D& i, int) {
+    const int interior = ROUND(interior_leg_number[i]);
+    const int boundary = ROUND(boundary_leg_number[i]);
+    if (interior >= 0) {
+      const PetscInt leg_row = leg_mapping->storedToPetsc(interior);
+      BOUT_DO_PETSC(MatSetValues(*mat, 1, &leg_row, 1, &cell_row, &one, INSERT_VALUES));
+    }
+    if (boundary >= 0) {
+      const PetscInt leg_row = leg_mapping->storedToPetsc(boundary);
+      BOUT_DO_PETSC(MatSetValues(*mat, 1, &leg_row, 1, &cell_row, &one, INSERT_VALUES));
+    }
+  });
   BOUT_DO_PETSC(MatAssemblyBegin(*mat, MAT_FINAL_ASSEMBLY));
   BOUT_DO_PETSC(MatAssemblyEnd(*mat, MAT_FINAL_ASSEMBLY));
-
-  return PetscOperator(std::move(mapping), std::move(mat));
+  return Op(leg_mapping, cell_mapping, std::move(mat));
 }
 
-/// Perform operation
-Field3D PetscOperator::operator()(const Field3D& rhs) const {
-  // Fill vec from rhs
-  copyToVec(this->mapping, rhs, *this->rhs_vec);
-
-  // Perform Mat-Vec muliplication
-  BOUT_DO_PETSC(MatMult(*this->mat_operator, *rhs_vec, *result_vec));
+template PetscForwardOperator PetscOperators::buildInjection<ForwardLegSpaceTag>(
+    const Field3D&, const Field3D&, std::shared_ptr<const PetscLegMapping>) const;
+template PetscBackwardOperator PetscOperators::buildInjection<BackwardLegSpaceTag>(
+    const Field3D&, const Field3D&, std::shared_ptr<const PetscLegMapping>) const;
 
-  // Copy result_vec into a Field3D
-  Field3D result{emptyFrom(rhs)}; // This allocates memory
-  const PetscScalar* r{nullptr};
-  BOUT_DO_PETSC(VecGetArrayRead(*result_vec, &r));
-  this->mapping->map_local_field(
-      [&](PetscInt row, const Ind3D& i) { result[i] = r[row]; });
-  BOUT_DO_PETSC(VecRestoreArrayRead(*result_vec, &r));
-
-  return result;
+PetscForwardOperator PetscOperators::injectForward() const {
+  return buildInjection<ForwardLegSpaceTag>(
+      forward_leg_interior_number, forward_leg_boundary_number, forward_leg_mapping);
 }
 
-/// Operator composition
-PetscOperator PetscOperator::operator*(const PetscOperator& rhs) const {
-  ASSERT0(this->mapping == rhs.mapping);
-  UniqueMat mat(new Mat{nullptr});
-  BOUT_DO_PETSC(MatMatMult(*this->mat_operator, *rhs.mat_operator, MAT_INITIAL_MATRIX,
-                           PETSC_DETERMINE, mat.get()));
-  return PetscOperator(this->mapping, std::move(mat));
+PetscBackwardOperator PetscOperators::injectBackward() const {
+  return buildInjection<BackwardLegSpaceTag>(
+      backward_leg_interior_number, backward_leg_boundary_number, backward_leg_mapping);
 }
 
-/// Operator addition
-PetscOperator PetscOperator::operator+(const PetscOperator& rhs) const {
-  ASSERT0(this->mapping == rhs.mapping);
-  UniqueMat mat(new Mat{nullptr});
-  BOUT_DO_PETSC(MatDuplicate(*this->mat_operator, MAT_COPY_VALUES, mat.get()));
-  BOUT_DO_PETSC(MatAXPY(*mat, 1.0, *rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
-  return PetscOperator(this->mapping, std::move(mat));
+PetscForwardLegVector PetscOperators::forwardLegWeights() const {
+  return loadLegWeights<PetscForwardLegVector>("forward_leg_weights",
+                                               forward_leg_mapping);
 }
 
-/// Operator subtraction
-PetscOperator PetscOperator::operator-(const PetscOperator& rhs) const {
-  ASSERT0(this->mapping == rhs.mapping);
-  UniqueMat mat(new Mat{nullptr});
-  BOUT_DO_PETSC(MatDuplicate(*this->mat_operator, MAT_COPY_VALUES, mat.get()));
-  BOUT_DO_PETSC(MatAXPY(*mat, -1.0, *rhs.mat_operator, UNKNOWN_NONZERO_PATTERN));
-  return PetscOperator(this->mapping, std::move(mat));
+PetscBackwardLegVector PetscOperators::backwardLegWeights() const {
+  return loadLegWeights<PetscBackwardLegVector>("backward_leg_weights",
+                                                backward_leg_mapping);
 }
 
-PetscOperator PetscOperator::transpose() const {
-  UniqueMat mat(new Mat{nullptr});
-  BOUT_DO_PETSC(MatTranspose(*this->mat_operator, MAT_INITIAL_MATRIX, mat.get()));
-  return PetscOperator(this->mapping, std::move(mat));
+PetscCellOperator PetscOperators::diagonal(const Field3D& f) const {
+  return PetscCellOperator::diagonal(cell_mapping, makePetscCellVector(cell_mapping, f));
 }
 
-Field3D PetscOperators::meshGetField3D(Mesh* mesh, const std::string& name) {
-  Field3D result;
-  if (mesh->get(result, name) != 0) {
-    throw BoutException("PetscOperators requires field '{}'", name);
-  }
-  return result;
+PetscForwardLegOperator PetscOperators::diagonal(const PetscForwardLegVector& v) const {
+  return PetscForwardLegOperator::diagonal(forward_leg_mapping, v);
 }
 
-PetscOperators::PetscOperators(Mesh* mesh)
-    : mesh(mesh), mapping(std::make_shared<const PetscMapping>(
-                      meshGetField3D(mesh, "cell_number"),
-                      meshGetField3D(mesh, "forward_cell_number"),
-                      meshGetField3D(mesh, "backward_cell_number"))) {
-
-  int mesh_total_cells{0};
-  if (mesh->get(mesh_total_cells, "total_cells") == 0) {
-    // Check total number of cells
-    if (mesh_total_cells != mapping->globalSize()) {
-      throw BoutException("Total cells in mesh {} doesn't match global mapping size {}",
-                          mesh_total_cells, mapping->globalSize());
-    }
-  }
-}
-
-PetscOperator PetscOperators::get(const std::string& name) const {
-  return PetscOperator(this->mapping, this->meshGetArray<int>(this->mesh, name + "_rows"),
-                       this->meshGetArray<int>(this->mesh, name + "_columns"),
-                       this->meshGetArray<BoutReal>(this->mesh, name + "_weights"));
+PetscBackwardLegOperator PetscOperators::diagonal(const PetscBackwardLegVector& v) const {
+  return PetscBackwardLegOperator::diagonal(backward_leg_mapping, v);
 }
 
 PetscOperators::Parallel PetscOperators::getParallel() const {
-  // Read maps from the mesh
-  auto forward = this->get("forward");
-  auto backward = this->get("backward");
-
-  // ---- Construct Grad_par ----
-  //
-  // Create a parallel gradient operator by combining the parallel
-  // length dl = dy * sqrt(g_22) with forward & backward operators
-  auto* coords = this->mesh->getCoordinates();
+  auto Forward = forward();
+  auto Backward = backward();
+  auto Inject_plus = injectForward();
+  auto Inject_minus = injectBackward();
+
+  auto W_plus = diagonal(forwardLegWeights());
+  auto W_minus = diagonal(backwardLegWeights());
+
+  auto* coords = mesh->getCoordinates();
   Field3D dl = coords->dy * sqrt(coords->g_22);
   dl.splitParallelSlices();
   dl.yup() = 0.0;
   dl.ydown() = 0.0;
   dl.applyParallelBoundary("parallel_neumann_o1");
 
-  auto inv_2dl = 0.5 / dl;
-  inv_2dl.splitParallelSlices();
-  inv_2dl.yup() = 0.0;
-  inv_2dl.ydown() = 0.0;
-  inv_2dl.applyParallelBoundary("parallel_neumann_o1");
+  auto Interp_plus = W_plus * ((Forward + Inject_plus) * 0.5);
+  auto Interp_minus = W_minus * ((Backward + Inject_minus) * 0.5);
 
-  auto inv_2dl_op = this->diagonal(inv_2dl);
+  const auto dl_plus = Interp_plus(dl);
+  const auto dl_minus = Interp_minus(dl);
+  const auto inv_dl_plus = PetscForwardLegVector::reciprocal(dl_plus);
+  const auto inv_dl_minus = PetscBackwardLegVector::reciprocal(dl_minus);
+  const auto Inv_dl_plus = diagonal(inv_dl_plus);
+  const auto Inv_dl_minus = diagonal(inv_dl_minus);
 
-  auto Grad_par = inv_2dl_op * (forward - backward);
+  auto Grad_plus = Inv_dl_plus * (Forward - Inject_plus);
+  auto Grad_minus = Inv_dl_minus * (Inject_minus - Backward);
 
-  // ---- Construct Div_par ----
-  //
-  // Use the Support Operator Method (SOM) to calculate
-  // Div_par from Grad_par and cell volumes.
-
-  // Cell volume
   Field3D dV = coords->J * coords->dx * coords->dy * coords->dz;
   dV.splitParallelSlices();
   dV.yup() = 0.0;
   dV.ydown() = 0.0;
   dV.applyParallelBoundary("parallel_neumann_o1");
 
-  // Fractional boundary cells
-  const auto forward_boundary_fraction =
-      meshGetField3D(this->mesh, "forward_boundary_fraction");
-  const auto backward_boundary_fraction =
-      meshGetField3D(this->mesh, "backward_boundary_fraction");
-
-  BOUT_FOR(i, dV.getRegion("RGN_NOBNDRY")) {
-    dV.yup()[i.yp()] *= forward_boundary_fraction[i];
-    dV.ydown()[i.ym()] *= backward_boundary_fraction[i];
-  }
-
-  const auto dV_op = this->diagonal(dV);
-
-  Field3D neg_inv_dV = -1. / dV;
+  Field3D neg_inv_dV = -1.0 / dV;
   neg_inv_dV.splitParallelSlices();
   neg_inv_dV.yup() = 0.0;
   neg_inv_dV.ydown() = 0.0;
   neg_inv_dV.applyParallelBoundary("parallel_neumann_o1");
-  auto neg_inv_dV_op = this->diagonal(neg_inv_dV);
-
-  auto Div_par = neg_inv_dV_op * Grad_par.transpose() * dV_op;
-
-  // ---- Construct Div_par_Grad_par ----
-  //
-  // Requires gradients between planes, at +1/2 and -1/2, and interpolation
-  // operators to calculate quantities between cells.
-
-  // Identity operator
-  Field3D one{1.0};
-  one.splitParallelSlices();
-  one.yup() = 1.0;
-  one.ydown() = 1.0;
-  const auto identity = this->diagonal(one);
-
-  // Interpolate at + 1/2
-  auto interp_plus_op = (identity + forward) * 0.5;
-
-  // dl averaged at +1/2
-  const Field3D dl_plus = interp_plus_op(dl);
-  Field3D inv_dl_plus = 1. / dl_plus;
-  inv_dl_plus.splitParallelSlices();
-  inv_dl_plus.yup() = 0.0;
-  inv_dl_plus.ydown() = 0.0;
-  inv_dl_plus.applyParallelBoundary("parallel_neumann_o1");
-  const auto inv_dl_plus_op = this->diagonal(inv_dl_plus);
-
-  // Gradient at + 1/2
-  auto Grad_plus = inv_dl_plus_op * (forward - identity);
-
-  // Divergence at -1/2
-  auto Div_minus = neg_inv_dV_op * Grad_plus.transpose() * dV_op;
-
-  // Interpolate at - 1/2
-  auto interp_minus_op = (identity + backward) * 0.5;
-
-  // dl averaged at -1/2
-  const Field3D dl_minus = interp_minus_op(dl);
-  Field3D inv_dl_minus = 1. / dl_minus;
-  inv_dl_minus.splitParallelSlices();
-  inv_dl_minus.yup() = 0.0;
-  inv_dl_minus.ydown() = 0.0;
-  inv_dl_minus.applyParallelBoundary("parallel_neumann_o1");
-  const auto inv_dl_minus_op = this->diagonal(inv_dl_minus);
-
-  // Gradient at - 1/2
-  auto Grad_minus = inv_dl_minus_op * (identity - backward);
-
-  // Divergence at +1/2
-  auto Div_plus = neg_inv_dV_op * Grad_minus.transpose() * dV_op;
-
-  // Div(Grad_par()) operator
+  const auto Neg_inv_dV = diagonal(neg_inv_dV);
+
+  const auto dV_plus = Interp_plus(dV);
+  const auto dV_minus = Interp_minus(dV);
+  const auto DV_plus = diagonal(dV_plus);
+  const auto DV_minus = diagonal(dV_minus);
+
+  auto Div_minus = Neg_inv_dV * Grad_plus.transpose() * DV_plus;
+  auto Div_plus = Neg_inv_dV * Grad_minus.transpose() * DV_minus;
+
   auto Div_par_Grad_par = ((Div_minus * Grad_plus) + (Div_plus * Grad_minus)) * 0.5;
 
-  return Parallel{std::move(Grad_par),         std::move(Div_par),
-                  std::move(Div_par_Grad_par), std::move(dV),
-                  std::move(Grad_minus),       std::move(Grad_plus),
-                  std::move(Div_minus),        std::move(Div_plus),
-                  std::move(interp_minus_op),  std::move(interp_plus_op)};
+  return Parallel{
+      std::move(Forward),      std::move(Backward),         std::move(Inject_plus),
+      std::move(Inject_minus), std::move(Interp_plus),      std::move(Interp_minus),
+      std::move(Grad_plus),    std::move(Grad_minus),       std::move(Div_minus),
+      std::move(Div_plus),     std::move(Div_par_Grad_par), std::move(dV)};
 }
 
 Field3D PetscOperators::Parallel::Div_par_K_Grad_par(const Field3D& K,
                                                      const Field3D& f) const {
+  const auto grad_plus = Grad_plus(f);
+  const auto grad_minus = Grad_minus(f);
+  const auto K_plus = Interp_plus(K);
+  const auto K_minus = Interp_minus(K);
+
+  const auto flux_plus = PetscForwardLegVector::pointwiseMultiply(K_plus, grad_plus);
+  const auto flux_minus = PetscBackwardLegVector::pointwiseMultiply(K_minus, grad_minus);
 
-  // There are 4 matrix-vector products that could be performed in parallel.
-  // The best way to optimize this is probably to pack f and K into one Vec,
-  // and assemble a single sparse matrix that contains the four blocks:
-  //
-  //  (Grad_plus       0     )           (grad_plus  )
-  //  (Grad_minus      0     ) (f)   ->  (grad_minus )
-  //  (    0     Interp_plus ) (K)       (K_plus     )
-  //  (    0     Interp_minus)           (K_minus    )
-  //
-  // For now we perform each operation in sequence.
-
-  // Calculate gradients in + and - directions
-  const Field3D grad_plus = this->Grad_plus(f);
-  const Field3D grad_minus = this->Grad_minus(f);
-
-  // Interpolate K to + and - locations
-  const Field3D K_plus = this->Interp_plus(K);
-  const Field3D K_minus = this->Interp_minus(K);
-
-  // Calculate divergence
-  return (this->Div_minus(K_plus * grad_plus) + this->Div_plus(K_minus * grad_minus))
-         * 0.5;
+  const auto div_minus = Div_minus(flux_plus);
+  const auto div_plus = Div_plus(flux_minus);
+  return (toField3D(div_minus, K) + toField3D(div_plus, K)) * 0.5;
 }
 
-#endif // BOUT_HAS_PETSC
+#endif

From 6676ac9f19c87d9716d0b6e1fc4cb3548ef221b4 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 23 Mar 2026 21:23:49 -0700
Subject: [PATCH 0952/1827] PetscSpaceVector: Fix duplicate -> copy

Use VecCopy to make a copy of the contents.
Rename function from `duplicate` to `copy`.
---
 include/bout/petsc_operators.hxx |  38 ++++++----
 src/mesh/petsc_operators.cxx     | 124 +++++++++++++++++++++++--------
 2 files changed, 115 insertions(+), 47 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index b9d35a9793..ce69049542 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -181,28 +181,30 @@ public:
   Vec raw() const { return *this->vec; }
   const std::shared_ptr<const PetscIndexMapping>& getMapping() const { return mapping; }
 
-  PetscSpaceVector duplicate() const {
+  /// Make a copy of the vector
+  PetscSpaceVector copy() const {
     UniqueVec out{new Vec{nullptr}};
     BOUT_DO_PETSC(VecDuplicate(*this->vec, out.get()));
+    BOUT_DO_PETSC(VecCopy(*this->vec, *out.get()));
     return PetscSpaceVector(this->mapping, std::move(out));
   }
 
   PetscSpaceVector operator*(BoutReal scalar) const {
-    auto out = this->duplicate();
+    auto out = this->copy();
     BOUT_DO_PETSC(VecScale(out.raw(), scalar));
     return out;
   }
 
   PetscSpaceVector operator+(const PetscSpaceVector& rhs) const {
     ASSERT0(mapping == rhs.mapping);
-    auto out = this->duplicate();
+    auto out = this->copy();
     BOUT_DO_PETSC(VecAXPY(out.raw(), 1.0, rhs.raw()));
     return out;
   }
 
   PetscSpaceVector operator-(const PetscSpaceVector& rhs) const {
     ASSERT0(mapping == rhs.mapping);
-    auto out = this->duplicate();
+    auto out = this->copy();
     BOUT_DO_PETSC(VecAXPY(out.raw(), -1.0, rhs.raw()));
     return out;
   }
@@ -210,13 +212,13 @@ public:
   static PetscSpaceVector pointwiseMultiply(const PetscSpaceVector& lhs,
                                             const PetscSpaceVector& rhs) {
     ASSERT0(lhs.mapping == rhs.mapping);
-    auto out = lhs.duplicate();
+    auto out = lhs.copy();
     BOUT_DO_PETSC(VecPointwiseMult(out.raw(), lhs.raw(), rhs.raw()));
     return out;
   }
 
   static PetscSpaceVector reciprocal(const PetscSpaceVector& in) {
-    auto out = in.duplicate();
+    auto out = in.copy();
     BOUT_DO_PETSC(VecReciprocal(out.raw()));
     return out;
   }
@@ -438,18 +440,24 @@ public:
   PetscBackwardLegOperator diagonal(const PetscBackwardLegVector& v) const;
 
   struct Parallel {
-    PetscForwardOperator Forward;
-    PetscBackwardOperator Backward;
-    PetscForwardOperator Inject_plus;
-    PetscBackwardOperator Inject_minus;
-    PetscForwardOperator Interp_plus;
-    PetscBackwardOperator Interp_minus;
-    PetscForwardOperator Grad_plus;
+    PetscCellOperator Grad_par;
+    PetscCellOperator Div_par;
+    PetscCellOperator Div_par_Grad_par;
+    Field3D dV;
+
     PetscBackwardOperator Grad_minus;
+    PetscForwardOperator Grad_plus;
     PetscForwardToCellOperator Div_minus;
     PetscBackwardToCellOperator Div_plus;
-    PetscCellOperator Div_par_Grad_par;
-    Field3D dV;
+
+    PetscBackwardOperator Inject_minus;
+    PetscForwardOperator Inject_plus;
+
+    PetscBackwardOperator Interp_minus;
+    PetscForwardOperator Interp_plus;
+
+    PetscForwardToCellOperator Restrict_minus;
+    PetscBackwardToCellOperator Restrict_plus;
 
     Field3D Div_par_K_Grad_par(const Field3D& K, const Field3D& f) const;
   };
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index d3682d2b00..e48643153c 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -6,6 +6,8 @@
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
+#include "bout/output.hxx"
+#include "bout/output_bout_types.hxx"
 #include "bout/petsc_operators.hxx"
 #include "bout/region.hxx"
 #include "bout/utils.hxx"
@@ -38,10 +40,19 @@ void PetscIndexMapping::buildPermutation(PetscInt nlocal, PetscInt nglobal,
   global_size = nglobal;
   local_stored_indices = stored_indices;
 
+  // Renumbering matrix.
+  // Maps PETSc row (or column) indices to the global indices stored in
+  // the mesh.  This is needed because the PETSc indices depend on the
+  // number of processors.
   BOUT_DO_PETSC(MatCreate(BoutComm::get(), &mat_stored_to_petsc));
   BOUT_DO_PETSC(MatSetSizes(mat_stored_to_petsc, nlocal, nlocal, nglobal, nglobal));
   BOUT_DO_PETSC(MatSetType(mat_stored_to_petsc, MATMPIAIJ));
+
+  // Each row will have one non-zero entry, which could be in
+  // either the "diagonal" or "off-diagonal" block.
   BOUT_DO_PETSC(MatMPIAIJSetPreallocation(mat_stored_to_petsc, 1, nullptr, 1, nullptr));
+
+  // Get the range of rows owned by this processor
   BOUT_DO_PETSC(MatGetOwnershipRange(mat_stored_to_petsc, &row_start, &row_end));
   ASSERT1(row_end - row_start == nlocal);
 
@@ -56,6 +67,7 @@ void PetscIndexMapping::buildPermutation(PetscInt nlocal, PetscInt nglobal,
   }
   BOUT_DO_PETSC(MatAssemblyBegin(mat_stored_to_petsc, MAT_FINAL_ASSEMBLY));
   BOUT_DO_PETSC(MatAssemblyEnd(mat_stored_to_petsc, MAT_FINAL_ASSEMBLY));
+  // Transpose to map petsc indices to stored mesh indices
   BOUT_DO_PETSC(
       MatTranspose(mat_stored_to_petsc, MAT_INITIAL_MATRIX, &mat_petsc_to_stored));
 }
@@ -143,6 +155,10 @@ PetscCellVector makePetscCellVector(const PetscCellMappingPtr& mapping,
 Field3D toField3D(const PetscCellVector& vec, const Field3D& prototype) {
   auto mapping = std::static_pointer_cast<const PetscCellMapping>(vec.getMapping());
   Field3D result{emptyFrom(prototype)};
+  result.splitParallelSlices();
+  result.yup().allocate();
+  result.ydown().allocate();
+
   const PetscScalar* x{nullptr};
   BOUT_DO_PETSC(VecGetArrayRead(vec.raw(), &x));
   mapping->mapLocalField([&](PetscInt row, const Ind3D& i) { result[i] = x[row]; });
@@ -150,6 +166,7 @@ Field3D toField3D(const PetscCellVector& vec, const Field3D& prototype) {
   mapping->mapLocalYdown(
       [&](PetscInt row, const Ind3D& i) { result.ydown()[i] = x[row]; });
   BOUT_DO_PETSC(VecRestoreArrayRead(vec.raw(), &x));
+
   return result;
 }
 
@@ -286,34 +303,32 @@ PetscBackwardLegOperator PetscOperators::diagonal(const PetscBackwardLegVector&
 }
 
 PetscOperators::Parallel PetscOperators::getParallel() const {
-  auto Forward = forward();
-  auto Backward = backward();
-  auto Inject_plus = injectForward();
-  auto Inject_minus = injectBackward();
-
-  auto W_plus = diagonal(forwardLegWeights());
-  auto W_minus = diagonal(backwardLegWeights());
+  // Primitive operators from the mesh / metadata
+  auto Forward = this->forward();             // L+ <- C
+  auto Backward = this->backward();           // L- <- C
+  auto Inject_plus = this->injectForward();   // L+ <- C
+  auto Inject_minus = this->injectBackward(); // L- <- C
+
+  // Leg weights
+  const auto w_plus_vec = forwardLegWeights();
+  const auto w_minus_vec = backwardLegWeights();
+  const auto W_plus = diagonal(w_plus_vec);   // L+ <- L+
+  const auto W_minus = diagonal(w_minus_vec); // L- <- L-
+
+  // Weighted adjoints: C <- L+ and C <- L-
+  auto Restrict_minus = Inject_plus.transpose() * W_plus;
+  auto Restrict_plus = Inject_minus.transpose() * W_minus;
 
   auto* coords = mesh->getCoordinates();
+
+  // Parallel spacing in cell space
   Field3D dl = coords->dy * sqrt(coords->g_22);
   dl.splitParallelSlices();
   dl.yup() = 0.0;
   dl.ydown() = 0.0;
   dl.applyParallelBoundary("parallel_neumann_o1");
 
-  auto Interp_plus = W_plus * ((Forward + Inject_plus) * 0.5);
-  auto Interp_minus = W_minus * ((Backward + Inject_minus) * 0.5);
-
-  const auto dl_plus = Interp_plus(dl);
-  const auto dl_minus = Interp_minus(dl);
-  const auto inv_dl_plus = PetscForwardLegVector::reciprocal(dl_plus);
-  const auto inv_dl_minus = PetscBackwardLegVector::reciprocal(dl_minus);
-  const auto Inv_dl_plus = diagonal(inv_dl_plus);
-  const auto Inv_dl_minus = diagonal(inv_dl_minus);
-
-  auto Grad_plus = Inv_dl_plus * (Forward - Inject_plus);
-  auto Grad_minus = Inv_dl_minus * (Inject_minus - Backward);
-
+  // Cell volume
   Field3D dV = coords->J * coords->dx * coords->dy * coords->dz;
   dV.splitParallelSlices();
   dV.yup() = 0.0;
@@ -325,23 +340,68 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   neg_inv_dV.yup() = 0.0;
   neg_inv_dV.ydown() = 0.0;
   neg_inv_dV.applyParallelBoundary("parallel_neumann_o1");
+
+  const auto DV = diagonal(dV);
   const auto Neg_inv_dV = diagonal(neg_inv_dV);
 
-  const auto dV_plus = Interp_plus(dV);
-  const auto dV_minus = Interp_minus(dV);
-  const auto DV_plus = diagonal(dV_plus);
-  const auto DV_minus = diagonal(dV_minus);
+  // Unweighted interpolation to +1/2 and -1/2 legs
+  auto Interp_plus = (Forward + Inject_plus) * 0.5;    // L+ <- C
+  auto Interp_minus = (Backward + Inject_minus) * 0.5; // L- <- C
+
+  // Leg-centered dl
+  const auto dl_plus = Interp_plus(dl);
+  const auto dl_minus = Interp_minus(dl);
+
+  const auto inv_dl_plus = PetscForwardLegVector::reciprocal(dl_plus);
+  const auto inv_dl_minus = PetscBackwardLegVector::reciprocal(dl_minus);
+
+  const auto Inv_dl_plus = diagonal(inv_dl_plus);   // L+ <- L+
+  const auto Inv_dl_minus = diagonal(inv_dl_minus); // L- <- L-
+
+  // Half-step gradients
+  auto Grad_plus = Inv_dl_plus * (Forward - Inject_plus);     // L+ <- C
+  auto Grad_minus = Inv_dl_minus * (Inject_minus - Backward); // L- <- C
+
+  // Cell-centered central gradient
+  auto Grad_par =
+      ((Restrict_minus * Grad_plus) + (Restrict_plus * Grad_minus)) * 0.5; // C <- C
+
+  // Leg-centered volumes from unweighted interpolation
+  const auto dV_plus = Interp_plus(dV);   // L+
+  const auto dV_minus = Interp_minus(dV); // L-
+
+  // Physical leg volumes include the leg weights
+  const auto dV_leg_plus = PetscForwardLegVector::pointwiseMultiply(dV_plus, w_plus_vec);
+  const auto dV_leg_minus =
+      PetscBackwardLegVector::pointwiseMultiply(dV_minus, w_minus_vec);
+
+  const auto DV_leg_plus = diagonal(dV_leg_plus);   // L+ <- L+
+  const auto DV_leg_minus = diagonal(dV_leg_minus); // L- <- L-
+
+  // Support-operator divergence from half-step gradients
+  auto Div_minus = Neg_inv_dV * Grad_plus.transpose() * DV_leg_plus;  // C <- L+
+  auto Div_plus = Neg_inv_dV * Grad_minus.transpose() * DV_leg_minus; // C <- L-
+
+  // Cell-centered divergence paired with the cell-centered gradient
+  auto Div_par = Neg_inv_dV * Grad_par.transpose() * DV; // C <- C
+
+  // Diffusion operator assembled from the half-step pieces
+  auto Div_par_Grad_par =
+      ((Div_minus * Grad_plus) + (Div_plus * Grad_minus)) * 0.5; // C <- C
+
+  return Parallel{// Cell <- Cell operators
+                  std::move(Grad_par), std::move(Div_par), std::move(Div_par_Grad_par),
+                  std::move(dV),
+
+                  // Leg <-> Cell operators
+                  std::move(Grad_minus), std::move(Grad_plus), std::move(Div_minus),
+                  std::move(Div_plus),
 
-  auto Div_minus = Neg_inv_dV * Grad_plus.transpose() * DV_plus;
-  auto Div_plus = Neg_inv_dV * Grad_minus.transpose() * DV_minus;
+                  std::move(Inject_minus), std::move(Inject_plus),
 
-  auto Div_par_Grad_par = ((Div_minus * Grad_plus) + (Div_plus * Grad_minus)) * 0.5;
+                  std::move(Interp_minus), std::move(Interp_plus),
 
-  return Parallel{
-      std::move(Forward),      std::move(Backward),         std::move(Inject_plus),
-      std::move(Inject_minus), std::move(Interp_plus),      std::move(Interp_minus),
-      std::move(Grad_plus),    std::move(Grad_minus),       std::move(Div_minus),
-      std::move(Div_plus),     std::move(Div_par_Grad_par), std::move(dV)};
+                  std::move(Restrict_minus), std::move(Restrict_plus)};
 }
 
 Field3D PetscOperators::Parallel::Div_par_K_Grad_par(const Field3D& K,

From 1d452ae3c43cca949219c247b4e20caad88cb396 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 30 Mar 2026 20:31:11 +0000
Subject: [PATCH 0953/1827] Bump pygments from 2.19.2 to 2.20.0

Bumps [pygments](https://github.com/pygments/pygments) from 2.19.2 to 2.20.0.
- [Release notes](https://github.com/pygments/pygments/releases)
- [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES)
- [Commits](https://github.com/pygments/pygments/compare/2.19.2...2.20.0)

---
updated-dependencies:
- dependency-name: pygments
  dependency-version: 2.20.0
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 uv.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/uv.lock b/uv.lock
index 0ca4068eb8..d61ed7481b 100644
--- a/uv.lock
+++ b/uv.lock
@@ -426,11 +426,11 @@ wheels = [
 
 [[package]]
 name = "pygments"
-version = "2.19.2"
+version = "2.20.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/b0/77/a5b8c569bf593b0140bde72ea885a803b82086995367bf2037de0159d924/pygments-2.19.2.tar.gz", hash = "sha256:636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887", size = 4968631, upload-time = "2025-06-21T13:39:12.283Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/c3/b2/bc9c9196916376152d655522fdcebac55e66de6603a76a02bca1b6414f6c/pygments-2.20.0.tar.gz", hash = "sha256:6757cd03768053ff99f3039c1a36d6c0aa0b263438fcab17520b30a303a82b5f", size = 4955991, upload-time = "2026-03-29T13:29:33.898Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/c7/21/705964c7812476f378728bdf590ca4b771ec72385c533964653c68e86bdc/pygments-2.19.2-py3-none-any.whl", hash = "sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b", size = 1225217, upload-time = "2025-06-21T13:39:07.939Z" },
+    { url = "https://files.pythonhosted.org/packages/f4/7e/a72dd26f3b0f4f2bf1dd8923c85f7ceb43172af56d63c7383eb62b332364/pygments-2.20.0-py3-none-any.whl", hash = "sha256:81a9e26dd42fd28a23a2d169d86d7ac03b46e2f8b59ed4698fb4785f946d0176", size = 1231151, upload-time = "2026-03-29T13:29:30.038Z" },
 ]
 
 [[package]]

From 50b3a288c8413d558e2f0a2fc910ba2d17de12ee Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 3 Apr 2026 19:33:06 +0000
Subject: [PATCH 0954/1827] Bump externalpackages/googletest from `73a63ea` to
 `d72f9c8`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `73a63ea` to `d72f9c8`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/73a63ea05dc8ca29ec1d2c1d66481dd0de1950f1...d72f9c8aea6817cdf1ca0ac10887f328de7f3da2)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: d72f9c8aea6817cdf1ca0ac10887f328de7f3da2
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 73a63ea05d..d72f9c8aea 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 73a63ea05dc8ca29ec1d2c1d66481dd0de1950f1
+Subproject commit d72f9c8aea6817cdf1ca0ac10887f328de7f3da2

From b1b0dc0868459624f3db4e4a8444358296d03c12 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 8 Apr 2026 15:33:51 -0700
Subject: [PATCH 0955/1827] PetscOperators: Fix tests, add outputs

Still debugging
---
 .../fci-operators/fci_operators_example.cxx   | 17 +++++++++--
 examples/fci-operators/makeplots.py           |  9 ++++++
 include/bout/petsc_operators.hxx              |  6 ++++
 src/mesh/petsc_operators.cxx                  |  3 +-
 tests/unit/mesh/test_petsc_operators.cxx      | 30 ++++++++++---------
 5 files changed, 47 insertions(+), 18 deletions(-)

diff --git a/examples/fci-operators/fci_operators_example.cxx b/examples/fci-operators/fci_operators_example.cxx
index 682d7c287c..66c28d3b6b 100644
--- a/examples/fci-operators/fci_operators_example.cxx
+++ b/examples/fci-operators/fci_operators_example.cxx
@@ -28,17 +28,28 @@ int main(int argc, char** argv) {
   dump["f"] = f;
   dump["dV"] = parallel.dV;
 
-  dump["grad_par_op"] = parallel.Grad_par(f);
+  // Test1 : (parallel.Restrict_minus * parallel.Inject_plus) is the identity in the interior (not X boundaries)
+
+  dump["grad_par_op"] = parallel.Grad_par(f, f);
+  Field3D forward{0.0};
+  BOUT_FOR(i, forward.getRegion("RGN_NOBNDRY")) { forward[i] = f.yup()[i.yp()]; }
+
+  dump["forward"] = forward;
+
+  dump["forward_op"] = (parallel.Restrict_minus * parallel.Forward)(f, f);
+
   dump["grad_par_yud"] = Grad_par(f);
 
-  dump["div_par_op"] = parallel.Div_par(f);
+  // Test2 : Sum of dV * Div_par over domain is zero
+
+  dump["div_par_op"] = parallel.Div_par(f, f);
 
   auto* coords = bout::globals::mesh->getCoordinates();
   bout::globals::mesh->communicate(coords->Bxy);
   coords->Bxy.applyParallelBoundary("parallel_neumann_o1");
   dump["div_par_yud"] = Div_par(f);
 
-  dump["div_par_grad_par_op"] = parallel.Div_par_Grad_par(f_neumann);
+  dump["div_par_grad_par_op"] = parallel.Div_par_Grad_par(f_neumann, f);
   dump["div_par_grad_par_yud"] = Div_par_K_Grad_par(1.0, f_neumann);
 
   bout::writeDefaultOutputFile(dump);
diff --git a/examples/fci-operators/makeplots.py b/examples/fci-operators/makeplots.py
index b10a5829f3..53c3d38f05 100644
--- a/examples/fci-operators/makeplots.py
+++ b/examples/fci-operators/makeplots.py
@@ -4,6 +4,9 @@
 
 path = "data"
 
+forward_op = collect("forward_op", path=path)
+forward = collect("forward", path=path)
+
 grad_par_op = collect("grad_par_op", path=path)
 grad_par_yud = collect("grad_par_yud", path=path)
 
@@ -47,6 +50,12 @@ def plot_comparison(a, alabel, b, blabel):
     return fig
 
 
+fig = plot_comparison(
+    forward_op[2:-2, 2, :], "Operator", forward[2:-2, 2, :], "Yup/down"
+)
+fig.suptitle("Forward")
+fig.tight_layout()
+
 fig = plot_comparison(
     grad_par_op[2:-2, 2, :], "Operator", grad_par_yud[2:-2, 2, :], "Yup/down"
 )
diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index ce69049542..03befb4d9d 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -8,6 +8,8 @@
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
+#include "bout/output.hxx"
+#include "bout/output_bout_types.hxx"
 #include "bout/petsc_interface.hxx"
 #include "bout/petsclib.hxx"
 #include "bout/region.hxx"
@@ -189,6 +191,7 @@ public:
     return PetscSpaceVector(this->mapping, std::move(out));
   }
 
+  /// Multiply by a scalar, returning a new PetscSpaceVector
   PetscSpaceVector operator*(BoutReal scalar) const {
     auto out = this->copy();
     BOUT_DO_PETSC(VecScale(out.raw(), scalar));
@@ -450,6 +453,9 @@ public:
     PetscForwardToCellOperator Div_minus;
     PetscBackwardToCellOperator Div_plus;
 
+    PetscBackwardOperator Backward;
+    PetscForwardOperator Forward;
+
     PetscBackwardOperator Inject_minus;
     PetscForwardOperator Inject_plus;
 
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index e48643153c..a63407ec4a 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -397,7 +397,8 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
                   std::move(Grad_minus), std::move(Grad_plus), std::move(Div_minus),
                   std::move(Div_plus),
 
-                  std::move(Inject_minus), std::move(Inject_plus),
+                  std::move(Backward), std::move(Forward), std::move(Inject_minus),
+                  std::move(Inject_plus),
 
                   std::move(Interp_minus), std::move(Interp_plus),
 
diff --git a/tests/unit/mesh/test_petsc_operators.cxx b/tests/unit/mesh/test_petsc_operators.cxx
index 219a667bac..923b17ea84 100644
--- a/tests/unit/mesh/test_petsc_operators.cxx
+++ b/tests/unit/mesh/test_petsc_operators.cxx
@@ -22,7 +22,7 @@ using PetscMappingTest = FakeMeshFixture;
 TEST_F(PetscMappingTest, create_region_empty) {
   const Field3D cell_number{-1.0}; // No cells >= 0
 
-  auto rgn = PetscMapping::create_region(cell_number);
+  auto rgn = PetscCellMapping::create_region(cell_number);
 
   ASSERT_EQ(0, rgn.size());
 }
@@ -35,7 +35,7 @@ TEST_F(PetscMappingTest, create_region) {
   cell_number(1, 1, 0) = 1; // In domain
   cell_number(0, 1, 1) = 2; // Xin boundary
 
-  auto rgn = PetscMapping::create_region(cell_number);
+  auto rgn = PetscCellMapping::create_region(cell_number);
   ASSERT_EQ(1, rgn.size());
 
   const Ind3D expected_ind = cell_number.indexAt(1, 1, 0);
@@ -50,7 +50,7 @@ TEST_F(PetscMappingTest, create_region_xin) {
   cell_number(1, 1, 0) = 1; // In domain
   cell_number(0, 1, 1) = 2; // Xin boundary
 
-  auto rgn = PetscMapping::create_region_xin(cell_number);
+  auto rgn = PetscCellMapping::create_region_xin(cell_number);
   ASSERT_EQ(1, rgn.size());
 
   const Ind3D expected_ind = cell_number.indexAt(0, 1, 1);
@@ -69,10 +69,12 @@ TEST_F(PetscMappingTest, mapping) {
   const Field3D forward_cell_number{-1.0};
   const Field3D backward_cell_number{-1.0};
 
-  const PetscMapping mapping(cell_number, forward_cell_number, backward_cell_number);
+  const PetscCellMapping mapping(cell_number, forward_cell_number, backward_cell_number,
+                                 2);
 
   // Two cells: one evolving and one in xin
   ASSERT_EQ(2, mapping.localSize());
+  ASSERT_EQ(2, mapping.globalSize());
 }
 
 using PetscOperatorTest = FakeMeshFixture;
@@ -87,15 +89,15 @@ TEST_F(PetscOperatorTest, identity) {
   cell_number(1, 2, 0) = 1;
   cell_number(1, 2, 1) = 2;
 
-  auto mapping = std::make_shared<const PetscMapping>(cell_number, forward_cell_number,
-                                                      backward_cell_number);
+  auto mapping = std::make_shared<const PetscCellMapping>(
+      cell_number, forward_cell_number, backward_cell_number, 3);
   ASSERT_EQ(3, mapping->localSize());
 
-  const auto rows = Array<int>::fromValues({0, 1, 2});
+  const auto rows = Array<int>::fromValues({0, 1, 2, 3});
   const auto cols = Array<int>::fromValues({0, 1, 2});
   const auto weights = Array<BoutReal>::fromValues({1.0, 1.0, 1.0});
 
-  const PetscOperator identity(mapping, rows, cols, weights);
+  const PetscCellOperator identity(mapping, mapping, rows, cols, weights);
 
   Field3D value{0.0};
   value(1, 1, 0) = 10;
@@ -105,7 +107,7 @@ TEST_F(PetscOperatorTest, identity) {
   value.yup() = -1.0;
   value.ydown() = -1.0;
 
-  const Field3D result = identity(value);
+  const Field3D result = identity(value, value);
 
   EXPECT_EQ(10, result(1, 1, 0));
   EXPECT_EQ(21, result(1, 2, 0));
@@ -125,15 +127,15 @@ TEST_F(PetscOperatorTest, identity_yupdown) {
   forward_cell_number(1, 2, 0) = 3;
   backward_cell_number(1, 1, 2) = 4;
 
-  auto mapping = std::make_shared<const PetscMapping>(cell_number, forward_cell_number,
-                                                      backward_cell_number);
+  auto mapping = std::make_shared<const PetscCellMapping>(
+      cell_number, forward_cell_number, backward_cell_number, 5);
   ASSERT_EQ(5, mapping->localSize());
 
-  const auto rows = Array<int>::fromValues({0, 1, 2});
+  const auto rows = Array<int>::fromValues({0, 1, 2, 3});
   const auto cols = Array<int>::fromValues({0, 1, 2});
   const auto weights = Array<BoutReal>::fromValues({1.0, 1.0, 1.0});
 
-  const PetscOperator identity(mapping, rows, cols, weights);
+  const PetscCellOperator identity(mapping, mapping, rows, cols, weights);
 
   Field3D value{0.0};
   value(1, 1, 0) = 10;
@@ -143,7 +145,7 @@ TEST_F(PetscOperatorTest, identity_yupdown) {
   value.yup() = -1.0;
   value.ydown() = -1.0;
 
-  const Field3D result = identity(value);
+  const Field3D result = identity(value, value);
 
   EXPECT_EQ(10, result(1, 1, 0));
   EXPECT_EQ(21, result(1, 2, 0));

From 7f3b584122693da82902f2ca97fee91653e0539d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 8 Apr 2026 22:50:41 -0700
Subject: [PATCH 0956/1827] PetscOperators: Fix operator() and applyToField
 issues

`applyToField` was ambiguous in meaning apply and convert to Field,
and `operator()(Field3D, Field3D)` ended up applying the operator
twice. Simplified the application to vectors and Field3D objects.
---
 .../fci-operators/fci_operators_example.cxx   | 10 +++++---
 include/bout/petsc_operators.hxx              | 25 ++++++++++---------
 src/mesh/petsc_operators.cxx                  |  2 +-
 3 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/examples/fci-operators/fci_operators_example.cxx b/examples/fci-operators/fci_operators_example.cxx
index 66c28d3b6b..3366622ff0 100644
--- a/examples/fci-operators/fci_operators_example.cxx
+++ b/examples/fci-operators/fci_operators_example.cxx
@@ -24,32 +24,34 @@ int main(int argc, char** argv) {
   bout::globals::mesh->communicate(f_neumann);
   f_neumann.applyParallelBoundary("parallel_neumann_o1");
 
+  auto forward_op = parallel.Restrict_minus * parallel.Forward;
+
   Options dump;
   dump["f"] = f;
   dump["dV"] = parallel.dV;
 
   // Test1 : (parallel.Restrict_minus * parallel.Inject_plus) is the identity in the interior (not X boundaries)
 
-  dump["grad_par_op"] = parallel.Grad_par(f, f);
+  dump["grad_par_op"] = parallel.Grad_par(f);
   Field3D forward{0.0};
   BOUT_FOR(i, forward.getRegion("RGN_NOBNDRY")) { forward[i] = f.yup()[i.yp()]; }
 
   dump["forward"] = forward;
 
-  dump["forward_op"] = (parallel.Restrict_minus * parallel.Forward)(f, f);
+  dump["forward_op"] = forward_op(f);
 
   dump["grad_par_yud"] = Grad_par(f);
 
   // Test2 : Sum of dV * Div_par over domain is zero
 
-  dump["div_par_op"] = parallel.Div_par(f, f);
+  dump["div_par_op"] = parallel.Div_par(f);
 
   auto* coords = bout::globals::mesh->getCoordinates();
   bout::globals::mesh->communicate(coords->Bxy);
   coords->Bxy.applyParallelBoundary("parallel_neumann_o1");
   dump["div_par_yud"] = Div_par(f);
 
-  dump["div_par_grad_par_op"] = parallel.Div_par_Grad_par(f_neumann, f);
+  dump["div_par_grad_par_op"] = parallel.Div_par_Grad_par(f_neumann);
   dump["div_par_grad_par_yud"] = Div_par_K_Grad_par(1.0, f_neumann);
 
   bout::writeDefaultOutputFile(dump);
diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 03befb4d9d..e2502dd723 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -275,6 +275,8 @@ public:
   PetscOperator(PetscOperator&&) noexcept = default;
   PetscOperator& operator=(PetscOperator&&) noexcept = default;
 
+  /// Apply operator to a vector in the input space,
+  /// returning a vector in the output space.
   PetscSpaceVector<OutSpaceTag>
   operator()(const PetscSpaceVector<InSpaceTag>& rhs) const {
     ASSERT0(in_mapping == rhs.getMapping());
@@ -283,27 +285,26 @@ public:
     return result;
   }
 
-  template <typename T = InSpaceTag,
-            typename = std::enable_if_t<std::is_same_v<T, CellSpaceTag>>>
+  /// Apply operator to a Field3D, returning a vector.
+  /// Enable if input is Cell Space and output is not.
+  template <typename T = InSpaceTag, typename U = OutSpaceTag,
+            typename = std::enable_if_t<std::is_same_v<T, CellSpaceTag>
+                                        && !std::is_same_v<U, CellSpaceTag>>>
   PetscSpaceVector<OutSpaceTag> operator()(const Field3D& rhs) const {
     auto in = makePetscCellVector(
         std::static_pointer_cast<const PetscCellMapping>(in_mapping), rhs);
     return (*this)(in);
   }
 
-  template <typename T = OutSpaceTag,
-            typename = std::enable_if_t<std::is_same_v<T, CellSpaceTag>>>
-  Field3D applyToField(const PetscSpaceVector<InSpaceTag>& rhs,
-                       const Field3D& prototype) const {
-    auto out = (*this)(rhs);
-    return toField3D(out, prototype);
-  }
-
+  /// Apply operator to a Field3D, returning a Field3D.
+  /// Enable if both input and output mapppings are in Cell Space
   template <typename T = InSpaceTag, typename U = OutSpaceTag,
             typename = std::enable_if_t<std::is_same_v<T, CellSpaceTag>
                                         && std::is_same_v<U, CellSpaceTag>>>
-  Field3D operator()(const Field3D& rhs, const Field3D& prototype) const {
-    return applyToField((*this)(rhs), prototype);
+  Field3D operator()(const Field3D& rhs) const {
+    auto in = makePetscCellVector(
+        std::static_pointer_cast<const PetscCellMapping>(in_mapping), rhs);
+    return toField3D((*this)(in), rhs);
   }
 
   PetscOperator<InSpaceTag, OutSpaceTag> transpose() const {
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index a63407ec4a..0fe564bcd3 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -52,7 +52,7 @@ void PetscIndexMapping::buildPermutation(PetscInt nlocal, PetscInt nglobal,
   // either the "diagonal" or "off-diagonal" block.
   BOUT_DO_PETSC(MatMPIAIJSetPreallocation(mat_stored_to_petsc, 1, nullptr, 1, nullptr));
 
-  // Get the range of rows owned by this processor
+  // Get the range of global rows owned by this processor
   BOUT_DO_PETSC(MatGetOwnershipRange(mat_stored_to_petsc, &row_start, &row_end));
   ASSERT1(row_end - row_start == nlocal);
 

From af4a5b33d26c13c2825693d691fa574000245e23 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 8 Apr 2026 23:30:10 -0700
Subject: [PATCH 0957/1827] PetscOperators: Fix unit tests, add operators

PetscSpaceVector operators on temporaries can modify in-place.
---
 include/bout/petsc_operators.hxx         | 25 +++++++++++++++++++++---
 tests/unit/mesh/test_petsc_operators.cxx |  4 ++--
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index e2502dd723..bc19b73d18 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -192,26 +192,44 @@ public:
   }
 
   /// Multiply by a scalar, returning a new PetscSpaceVector
-  PetscSpaceVector operator*(BoutReal scalar) const {
+  PetscSpaceVector operator*(BoutReal scalar) const& {
     auto out = this->copy();
     BOUT_DO_PETSC(VecScale(out.raw(), scalar));
     return out;
   }
 
-  PetscSpaceVector operator+(const PetscSpaceVector& rhs) const {
+  /// Multiply by a scalar, modifying a temporary in-place
+  PetscSpaceVector operator*(BoutReal scalar) && {
+    BOUT_DO_PETSC(VecScale(this->raw(), scalar));
+    return std::move(*this);
+  }
+
+  PetscSpaceVector operator+(const PetscSpaceVector& rhs) const& {
     ASSERT0(mapping == rhs.mapping);
     auto out = this->copy();
     BOUT_DO_PETSC(VecAXPY(out.raw(), 1.0, rhs.raw()));
     return out;
   }
 
-  PetscSpaceVector operator-(const PetscSpaceVector& rhs) const {
+  PetscSpaceVector operator+(const PetscSpaceVector& rhs) && {
+    ASSERT0(mapping == rhs.mapping);
+    BOUT_DO_PETSC(VecAXPY(this->raw(), 1.0, rhs.raw()));
+    return std::move(*this);
+  }
+
+  PetscSpaceVector operator-(const PetscSpaceVector& rhs) const& {
     ASSERT0(mapping == rhs.mapping);
     auto out = this->copy();
     BOUT_DO_PETSC(VecAXPY(out.raw(), -1.0, rhs.raw()));
     return out;
   }
 
+  PetscSpaceVector operator-(const PetscSpaceVector& rhs) && {
+    ASSERT0(mapping == rhs.mapping);
+    BOUT_DO_PETSC(VecAXPY(this->raw(), -1.0, rhs.raw()));
+    return std::move(*this);
+  }
+
   static PetscSpaceVector pointwiseMultiply(const PetscSpaceVector& lhs,
                                             const PetscSpaceVector& rhs) {
     ASSERT0(lhs.mapping == rhs.mapping);
@@ -355,6 +373,7 @@ public:
     BOUT_DO_PETSC(MatSetType(*out, MATMPIAIJ));
     BOUT_DO_PETSC(MatSetSizes(*out, mapping->localSize(), mapping->localSize(),
                               mapping->globalSize(), mapping->globalSize()));
+    // Note: Off-diagonal blocks are empty because this is a square matrix
     BOUT_DO_PETSC(MatMPIAIJSetPreallocation(*out, 1, nullptr, 0, nullptr));
     BOUT_DO_PETSC(MatDiagonalSet(*out, diag.raw(), INSERT_VALUES));
     BOUT_DO_PETSC(MatAssemblyBegin(*out, MAT_FINAL_ASSEMBLY));
diff --git a/tests/unit/mesh/test_petsc_operators.cxx b/tests/unit/mesh/test_petsc_operators.cxx
index 923b17ea84..2ba63f4528 100644
--- a/tests/unit/mesh/test_petsc_operators.cxx
+++ b/tests/unit/mesh/test_petsc_operators.cxx
@@ -107,7 +107,7 @@ TEST_F(PetscOperatorTest, identity) {
   value.yup() = -1.0;
   value.ydown() = -1.0;
 
-  const Field3D result = identity(value, value);
+  const Field3D result = identity(value);
 
   EXPECT_EQ(10, result(1, 1, 0));
   EXPECT_EQ(21, result(1, 2, 0));
@@ -145,7 +145,7 @@ TEST_F(PetscOperatorTest, identity_yupdown) {
   value.yup() = -1.0;
   value.ydown() = -1.0;
 
-  const Field3D result = identity(value, value);
+  const Field3D result = identity(value);
 
   EXPECT_EQ(10, result(1, 1, 0));
   EXPECT_EQ(21, result(1, 2, 0));

From c949d7987109fb5aff9235c60fd9b8050c4a83cd Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 9 Apr 2026 00:03:35 -0700
Subject: [PATCH 0958/1827] PetscOperators: Add docstrings

Coauthor: Claude
---
 include/bout/petsc_operators.hxx | 593 ++++++++++++++++++++++++++++---
 1 file changed, 537 insertions(+), 56 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index bc19b73d18..0d9c6c6912 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -26,21 +26,42 @@
 #include <utility>
 #include <vector>
 
-/// Tag type for the cell space C.
+/// @brief Tag type identifying the cell space C.
+///
+/// Used as a compile-time template parameter to distinguish vectors and operators
+/// that live in the cell space from those in the forward or backward leg spaces.
+/// Mismatched space tags produce a compile error rather than a runtime failure.
 struct CellSpaceTag {};
 
-/// Tag type for the forward leg space L+.
+/// @brief Tag type identifying the forward leg space L+.
+///
+/// Operators and vectors tagged with this type map to or from the forward (y+1)
+/// leg space. See @ref BackwardLegSpaceTag and @ref CellSpaceTag.
 struct ForwardLegSpaceTag {};
 
-/// Tag type for the backward leg space L-.
+/// @brief Tag type identifying the backward leg space L-.
+///
+/// Operators and vectors tagged with this type map to or from the backward (y-1)
+/// leg space. See @ref ForwardLegSpaceTag and @ref CellSpaceTag.
 struct BackwardLegSpaceTag {};
 
-/// Mapping between stored indices in a mesh file and PETSc row ownership.
+/// @brief Bidirectional index mapping between mesh-file stored numbering and PETSc
+///        row ownership.
+///
+/// Every vector space (cell space, forward leg space, backward leg space) is defined
+/// by a global stored numbering written to the mesh file by the Python weights module.
+/// PETSc distributes rows contiguously across MPI ranks, so the local PETSc row range
+/// [rowStart(), rowEnd()) does not in general coincide with the stored indices.
+///
+/// This class maintains:
+/// - the list of stored indices owned by the local rank, in PETSc row order;
+/// - a hash map for O(1) stored → PETSc lookup;
+/// - a permutation matrix @c mat_stored_to_petsc (PETSc ordering → stored numbering)
+///   and its transpose @c mat_petsc_to_stored (stored numbering → PETSc ordering),
+///   used to translate operator column indices during matrix assembly.
 ///
-/// Every space is defined by a global stored numbering written to the mesh file.
-/// PETSc distributes rows contiguously across MPI ranks, so this class stores the
-/// local owned stored indices in row order and a permutation matrix that maps
-/// from stored numbering to PETSc numbering.
+/// Subclasses specialise the constructor to populate these structures for a particular
+/// space from mesh metadata.
 class PetscIndexMapping {
 public:
   PetscIndexMapping() = default;
@@ -51,54 +72,137 @@ public:
   PetscIndexMapping(PetscIndexMapping&&) = delete;
   PetscIndexMapping& operator=(PetscIndexMapping&&) = delete;
 
-  /// Number of rows owned locally by this MPI rank.
+  /// @brief Number of rows owned locally by this MPI rank.
   PetscInt localSize() const {
     return static_cast<PetscInt>(local_stored_indices.size());
   }
 
-  /// Global number of rows in this space.
+  /// @brief Total number of rows in this space across all MPI ranks.
   PetscInt globalSize() const { return global_size; }
 
-  /// First global PETSc row owned by this MPI rank.
+  /// @brief Global PETSc index of the first row owned by this MPI rank.
   PetscInt rowStart() const { return row_start; }
 
-  /// One-past-last global PETSc row owned by this MPI rank.
+  /// @brief Global PETSc index one past the last row owned by this MPI rank.
+  ///
+  /// The locally owned rows are the half-open interval [rowStart(), rowEnd()).
   PetscInt rowEnd() const { return row_end; }
 
-  /// Stored indices owned locally in PETSc row order.
+  /// @brief Stored mesh-file indices owned locally, listed in PETSc row order.
+  ///
+  /// Entry @c i corresponds to global PETSc row <tt>rowStart() + i</tt>.
   const std::vector<int>& localStoredIndices() const { return local_stored_indices; }
 
-  /// Map a locally owned stored index to a PETSc global row.
+  /// @brief Convert a locally owned stored index to its global PETSc row index.
+  ///
+  /// @param stored_index A mesh-file stored index that must be owned by this rank.
+  /// @returns The corresponding global PETSc row index.
+  /// @throws BoutException if @p stored_index is not owned locally.
   PetscInt storedToPetsc(int stored_index) const;
 
-  /// Permutation matrix mapping PETSc ordering to stored numbering.
+  /// @brief Return the permutation matrix that maps PETSc row ordering to stored
+  ///        mesh-file numbering.
+  ///
+  /// This is the transpose of @c mat_stored_to_petsc and is used in
+  /// @ref PetscOperator::assembleFromCSR to translate stored column indices into
+  /// PETSc column indices via a post-multiplication.
   Mat getPetscToStored() const { return mat_petsc_to_stored; }
 
 protected:
+  /// @brief BOUT++ PETSc library handle; ensures PETSc is initialised.
   PetscLib lib;
 
+  /// @brief Construct the permutation matrices and populate internal lookup structures.
+  ///
+  /// Assigns contiguous PETSc rows starting from the rank-local offset determined by
+  /// PETSc's ownership partitioning. Each stored index in @p stored_indices maps to
+  /// one PETSc row, in the order given.
+  ///
+  /// @param nlocal         Number of rows owned by this rank.
+  /// @param nglobal        Total number of rows across all ranks.
+  /// @param stored_indices Mesh-file stored indices for the locally owned rows, in
+  ///                       the order they should appear in the PETSc vector.
   void buildPermutation(PetscInt nlocal, PetscInt nglobal,
                         const std::vector<int>& stored_indices);
 
-  PetscInt global_size{0};
-  PetscInt row_start{0};
-  PetscInt row_end{0};
-  std::vector<int> local_stored_indices;
-  std::unordered_map<int, PetscInt> local_stored_to_petsc;
-  Mat mat_stored_to_petsc{nullptr};
-  Mat mat_petsc_to_stored{nullptr};
+  PetscInt global_size{0}; ///< Total global row count.
+  PetscInt row_start{0};   ///< First global PETSc row owned locally.
+  PetscInt row_end{0};     ///< One-past-last global PETSc row owned locally.
+  std::vector<int> local_stored_indices; ///< Stored indices in local PETSc row order.
+  std::unordered_map<int, PetscInt> local_stored_to_petsc; ///< Stored → PETSc lookup.
+  Mat mat_stored_to_petsc{nullptr}; ///< Permutation: stored numbering → PETSc ordering.
+  Mat mat_petsc_to_stored{nullptr}; ///< Permutation: PETSc ordering → stored numbering.
 };
 
-/// Cell-space mapping between stored cell numbers, PETSc numbering, and Field3D.
+/// @brief Cell-space index mapping that bridges stored cell numbers, PETSc row
+///        ownership, and BOUT++ Field3D index arithmetic.
+///
+/// The cell space C contains five disjoint subsets of cells, appended in order:
+///   1. Evolving interior cells (the primary unknowns).
+///   2. Inner radial X-boundary cells.
+///   3. Outer radial X-boundary cells.
+///   4. Forward parallel boundary cells (one virtual cell per interior source cell
+///      whose forward map intersects the radial boundary).
+///   5. Backward parallel boundary cells (analogous for the backward map).
+///
+/// The local PETSc vector stores these in the same order. The @c mapLocal* methods
+/// iterate over subsets 1–3 (interior + X-boundary) while @c mapLocalYup and
+/// @c mapLocalYdown cover subsets 4 and 5 respectively.
+///
+/// @c mapOwnedInteriorCells iterates only the evolving interior cells (subset 1) and
+/// provides global PETSc row indices, making it suitable for assembling matrices.
 class PetscCellMapping : public PetscIndexMapping {
 public:
+  /// @brief Construct the cell-space mapping from mesh metadata fields.
+  ///
+  /// Populates all five cell subsets and calls @ref buildPermutation with the
+  /// concatenated list of stored indices.
+  ///
+  /// @param cell_number          Field3D of stored cell numbers for interior and
+  ///                             X-boundary cells. Negative entries are skipped.
+  /// @param forward_cell_number  Field3D of stored cell numbers for forward parallel
+  ///                             boundary virtual cells. Negative entries are skipped.
+  /// @param backward_cell_number Field3D of stored cell numbers for backward parallel
+  ///                             boundary virtual cells. Negative entries are skipped.
+  /// @param total_cells          Total number of cells in the global cell space,
+  ///                             as computed by the Python weights module.
   PetscCellMapping(const Field3D& cell_number, const Field3D& forward_cell_number,
                    const Field3D& backward_cell_number, int total_cells);
 
+  /// @brief Build the region of evolving interior cells from a cell-number field.
+  ///
+  /// Iterates RGN_NOBNDRY and retains indices where @p cell_number is non-negative.
+  ///
+  /// @param cell_number Field3D of stored cell numbers.
+  /// @returns Region containing the Ind3D indices of all valid interior cells.
   static Region<Ind3D> create_region(const Field3D& cell_number);
+
+  /// @brief Build the region of inner radial X-boundary cells.
+  ///
+  /// Iterates RGN_INNER_X and retains indices where @p cell_number is non-negative.
+  ///
+  /// @param cell_number Field3D of stored cell numbers.
+  /// @returns Region containing the Ind3D indices of valid inner-X boundary cells.
   static Region<Ind3D> create_region_xin(const Field3D& cell_number);
+
+  /// @brief Build the region of outer radial X-boundary cells.
+  ///
+  /// Iterates RGN_OUTER_X and retains indices where @p cell_number is non-negative.
+  ///
+  /// @param cell_number Field3D of stored cell numbers.
+  /// @returns Region containing the Ind3D indices of valid outer-X boundary cells.
   static Region<Ind3D> create_region_xout(const Field3D& cell_number);
 
+  /// @brief Iterate over locally owned evolving interior cells, providing global
+  ///        PETSc row indices.
+  ///
+  /// Calls @p func(petsc_row, field_index, stored_cell_number) for each cell in
+  /// the evolving region that is owned by this MPI rank. @p petsc_row is the global
+  /// PETSc index and is suitable for use as a row or column argument to MatSetValues.
+  ///
+  /// @tparam Function Callable with signature
+  ///         <tt>(PetscInt row, Ind3D i, int stored) -> void</tt>.
+  /// @param func Callback invoked for each owned interior cell.
   template <typename Function>
   void mapOwnedInteriorCells(Function func) const {
     PetscInt row = rowStart();
@@ -108,6 +212,17 @@ public:
     }
   }
 
+  /// @brief Iterate over all locally stored field cells (interior + X-boundary),
+  ///        providing local PETSc vector indices.
+  ///
+  /// Covers the evolving interior region, inner-X boundary, and outer-X boundary
+  /// in that order. The local index starts at zero on each rank and increases
+  /// contiguously. Use this to read from or write to a local PETSc Vec array
+  /// obtained via VecGetArray.
+  ///
+  /// @tparam Function Callable with signature
+  ///         <tt>(PetscInt local_row, Ind3D i) -> void</tt>.
+  /// @param func Callback invoked for each locally stored field cell.
   template <typename Function>
   void mapLocalField(Function func) const {
     PetscInt row = 0;
@@ -121,6 +236,16 @@ public:
     }
   }
 
+  /// @brief Iterate over locally stored forward parallel boundary cells, providing
+  ///        local PETSc vector indices.
+  ///
+  /// The local index starts immediately after the field cells covered by
+  /// @ref mapLocalField. The Field3D index passed to @p func is the y+1 neighbour
+  /// of the source cell (i.yp()), matching how field.yup() is indexed.
+  ///
+  /// @tparam Function Callable with signature
+  ///         <tt>(PetscInt local_row, Ind3D i_yp) -> void</tt>.
+  /// @param func Callback invoked for each locally stored forward boundary cell.
   template <typename Function>
   void mapLocalYup(Function func) const {
     PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size();
@@ -130,6 +255,16 @@ public:
     }
   }
 
+  /// @brief Iterate over locally stored backward parallel boundary cells, providing
+  ///        local PETSc vector indices.
+  ///
+  /// The local index starts immediately after the forward boundary cells covered by
+  /// @ref mapLocalYup. The Field3D index passed to @p func is the y-1 neighbour
+  /// of the source cell (i.ym()), matching how field.ydown() is indexed.
+  ///
+  /// @tparam Function Callable with signature
+  ///         <tt>(PetscInt local_row, Ind3D i_ym) -> void</tt>.
+  /// @param func Callback invoked for each locally stored backward boundary cell.
   template <typename Function>
   void mapLocalYdown(Function func) const {
     PetscInt row = evolving_region.size() + xin_region.size() + xout_region.size()
@@ -141,37 +276,78 @@ public:
   }
 
 private:
-  Field3D cell_number;
-  Field3D forward_cell_number;
-  Field3D backward_cell_number;
-  Region<Ind3D> evolving_region;
-  Region<Ind3D> xin_region;
-  Region<Ind3D> xout_region;
-  Region<Ind3D> yup_region;
-  Region<Ind3D> ydown_region;
+  Field3D cell_number; ///< Stored cell numbers for interior/X-boundary cells.
+  Field3D
+      forward_cell_number; ///< Stored cell numbers for forward boundary virtual cells.
+  Field3D
+      backward_cell_number; ///< Stored cell numbers for backward boundary virtual cells.
+  Region<Ind3D> evolving_region; ///< Interior evolving cells.
+  Region<Ind3D> xin_region;      ///< Inner radial X-boundary cells.
+  Region<Ind3D> xout_region;     ///< Outer radial X-boundary cells.
+  Region<Ind3D> yup_region;      ///< Forward parallel boundary virtual cells.
+  Region<Ind3D> ydown_region;    ///< Backward parallel boundary virtual cells.
 };
 
-/// Mapping for forward or backward leg spaces.
+/// @brief Index mapping for forward (L+) or backward (L-) leg spaces.
+///
+/// Each interior source cell contributes one or two leg rows depending on whether
+/// its mapped sub-samples are entirely interior, entirely boundary, or mixed.
+/// The leg indices are assigned by the Python weights module and stored in the mesh
+/// file as Field3D arrays (e.g. forward_leg_interior_number).
+///
+/// On construction, duplicate indices are removed and the remaining indices are
+/// sorted before being passed to @ref buildPermutation.
 class PetscLegMapping : public PetscIndexMapping {
 public:
+  /// @brief Construct a leg-space mapping.
+  ///
+  /// @param total_legs        Global number of leg rows in this space.
+  /// @param local_leg_indices Stored leg indices owned by this MPI rank. Duplicates
+  ///                          are removed internally before building the permutation.
   PetscLegMapping(int total_legs, std::vector<int> local_leg_indices);
 };
 
+/// @brief Shared-pointer alias for a const PetscCellMapping.
 using PetscCellMappingPtr = std::shared_ptr<const PetscCellMapping>;
+
+/// @brief Shared-pointer alias for a const PetscLegMapping.
 using PetscLegMappingPtr = std::shared_ptr<const PetscLegMapping>;
 
-/// Wrapper around a PETSc Vec with a compile-time space tag.
+/// @brief Type-safe wrapper around a PETSc Vec belonging to a particular vector space.
+///
+/// The compile-time @p SpaceTag (one of @ref CellSpaceTag, @ref ForwardLegSpaceTag,
+/// @ref BackwardLegSpaceTag) prevents accidental arithmetic between vectors from
+/// incompatible spaces. All binary operations assert that both operands share the
+/// same mapping pointer, catching dimension mismatches at runtime.
+///
+/// Vectors are non-copyable but movable, matching the ownership semantics of the
+/// underlying PETSc Vec.
+///
+/// @tparam SpaceTag One of CellSpaceTag, ForwardLegSpaceTag, BackwardLegSpaceTag.
 template <typename SpaceTag>
 class PetscSpaceVector {
   using UniqueVec = bout::petsc::UniqueVec;
 
 public:
+  /// @brief Default constructor; produces an empty (unusable) vector.
   PetscSpaceVector() = default;
 
+  /// @brief Construct a zero-initialised vector for the given space.
+  ///
+  /// Allocates a PETSc MPI vector sized according to @p mapping->localSize() and
+  /// @p mapping->globalSize().
+  ///
+  /// @param mapping Shared ownership of the space mapping.
   explicit PetscSpaceVector(std::shared_ptr<const PetscIndexMapping> mapping)
       : mapping(std::move(mapping)),
         vec(createVec(this->mapping->localSize(), this->mapping->globalSize())) {}
 
+  /// @brief Construct from an existing mapping and a pre-built PETSc Vec.
+  ///
+  /// Takes ownership of @p vec.
+  ///
+  /// @param mapping Shared ownership of the space mapping.
+  /// @param vec     An already-assembled PETSc Vec. Ownership is transferred.
   PetscSpaceVector(std::shared_ptr<const PetscIndexMapping> mapping, UniqueVec vec)
       : mapping(std::move(mapping)), vec(std::move(vec)) {}
 
@@ -180,10 +356,15 @@ public:
   PetscSpaceVector(PetscSpaceVector&&) noexcept = default;
   PetscSpaceVector& operator=(PetscSpaceVector&&) noexcept = default;
 
+  /// @brief Return the underlying PETSc Vec handle (non-owning).
   Vec raw() const { return *this->vec; }
+
+  /// @brief Return the shared space mapping.
   const std::shared_ptr<const PetscIndexMapping>& getMapping() const { return mapping; }
 
-  /// Make a copy of the vector
+  /// @brief Return a deep copy of this vector.
+  ///
+  /// Allocates a new PETSc Vec with the same size and mapping, then copies values.
   PetscSpaceVector copy() const {
     UniqueVec out{new Vec{nullptr}};
     BOUT_DO_PETSC(VecDuplicate(*this->vec, out.get()));
@@ -191,7 +372,9 @@ public:
     return PetscSpaceVector(this->mapping, std::move(out));
   }
 
-  /// Multiply by a scalar, returning a new PetscSpaceVector
+  /// @brief Return a new vector equal to @c (*this) * @p scalar.
+  ///
+  /// @param scalar Scalar multiplier.
   PetscSpaceVector operator*(BoutReal scalar) const& {
     auto out = this->copy();
     BOUT_DO_PETSC(VecScale(out.raw(), scalar));
@@ -204,6 +387,9 @@ public:
     return std::move(*this);
   }
 
+  /// @brief Return a new vector equal to @c (*this) + @p rhs.
+  ///
+  /// @param rhs Must share the same mapping as @c *this.
   PetscSpaceVector operator+(const PetscSpaceVector& rhs) const& {
     ASSERT0(mapping == rhs.mapping);
     auto out = this->copy();
@@ -217,6 +403,9 @@ public:
     return std::move(*this);
   }
 
+  /// @brief Return a new vector equal to @c (*this) - @p rhs.
+  ///
+  /// @param rhs Must share the same mapping as @c *this.
   PetscSpaceVector operator-(const PetscSpaceVector& rhs) const& {
     ASSERT0(mapping == rhs.mapping);
     auto out = this->copy();
@@ -230,6 +419,11 @@ public:
     return std::move(*this);
   }
 
+  /// @brief Return a new vector whose entries are the element-wise product
+  ///        @c lhs[i] * rhs[i].
+  ///
+  /// @param lhs Left operand; must share a mapping with @p rhs.
+  /// @param rhs Right operand.
   static PetscSpaceVector pointwiseMultiply(const PetscSpaceVector& lhs,
                                             const PetscSpaceVector& rhs) {
     ASSERT0(lhs.mapping == rhs.mapping);
@@ -238,6 +432,9 @@ public:
     return out;
   }
 
+  /// @brief Return a new vector whose entries are @c 1 / in[i].
+  ///
+  /// @param in Input vector. No entry may be zero.
   static PetscSpaceVector reciprocal(const PetscSpaceVector& in) {
     auto out = in.copy();
     BOUT_DO_PETSC(VecReciprocal(out.raw()));
@@ -245,6 +442,10 @@ public:
   }
 
 private:
+  /// @brief Allocate a new zeroed PETSc MPI vector of the given size.
+  ///
+  /// @param local_size  Number of locally owned entries.
+  /// @param global_size Total number of entries across all ranks.
   static UniqueVec createVec(PetscInt local_size, PetscInt global_size) {
     UniqueVec out{new Vec{nullptr}};
     BOUT_DO_PETSC(VecCreate(BoutComm::get(), out.get()));
@@ -253,28 +454,77 @@ private:
     return out;
   }
 
-  std::shared_ptr<const PetscIndexMapping> mapping;
-  UniqueVec vec;
+  std::shared_ptr<const PetscIndexMapping> mapping; ///< Space mapping (shared ownership).
+  UniqueVec vec;                                    ///< Underlying PETSc Vec (owned).
 };
 
-// Tagged vectors provide compile-time check of compatible operations
+// Tagged vector aliases — these provide compile-time checks of compatible operations.
+/// @brief PETSc vector in the cell space C.
 using PetscCellVector = PetscSpaceVector<CellSpaceTag>;
+/// @brief PETSc vector in the forward leg space L+.
 using PetscForwardLegVector = PetscSpaceVector<ForwardLegSpaceTag>;
+/// @brief PETSc vector in the backward leg space L-.
 using PetscBackwardLegVector = PetscSpaceVector<BackwardLegSpaceTag>;
 
+/// @brief Populate a PetscCellVector from a Field3D and its parallel slices.
+///
+/// The cell vector is filled in the order defined by @ref PetscCellMapping:
+/// evolving interior cells (from @p field), inner/outer X-boundary cells
+/// (from @p field), forward boundary virtual cells (from @p field.yup()), and
+/// backward boundary virtual cells (from @p field.ydown()).
+///
+/// @param mapping Shared cell-space mapping.
+/// @param field   Source field; must have parallel slices split and allocated.
+/// @returns A fully assembled PetscCellVector.
 PetscCellVector makePetscCellVector(const PetscCellMappingPtr& mapping,
                                     const Field3D& field);
+
+/// @brief Extract a Field3D (with parallel slices) from a PetscCellVector.
+///
+/// Reverses @ref makePetscCellVector: interior and X-boundary values are written to
+/// @c result, forward boundary values to @c result.yup(), and backward boundary
+/// values to @c result.ydown().
+///
+/// @param vec       Source vector; must use a PetscCellMapping.
+/// @param prototype Field3D whose mesh, coordinates, and metadata are copied to
+///                  initialise the result.
+/// @returns A newly allocated Field3D with split parallel slices.
 Field3D toField3D(const PetscCellVector& vec, const Field3D& prototype);
 
-/// Typed linear operator between two spaces.
+/// @brief Type-safe sparse linear operator mapping from one space to another.
+///
+/// Wraps a PETSc Mat and enforces compatible space pairings at compile time via
+/// the @p OutSpaceTag and @p InSpaceTag template parameters. The underlying matrix
+/// stores values in PETSc's internal ordering; translation from mesh-file stored
+/// column indices to PETSc column indices is performed during construction via a
+/// post-multiplication by @ref PetscIndexMapping::getPetscToStored.
+///
+/// Operators are non-copyable but movable. Binary operations (addition, subtraction,
+/// scalar multiplication, composition) return new operators without modifying
+/// their operands, unless the rvalue-qualified @c operator*(BoutReal) overload is
+/// selected, which scales in place.
+///
+/// @tparam OutSpaceTag Tag for the output (row) space.
+/// @tparam InSpaceTag  Tag for the input (column) space.
 template <typename OutSpaceTag, typename InSpaceTag>
 class PetscOperator {
   using UniqueMat = bout::petsc::UniqueMat;
 
 public:
+  /// @brief Default constructor; produces an empty (unusable) operator.
   PetscOperator() = default;
   ~PetscOperator() = default;
 
+  /// @brief Construct an operator from a CSR-format sparse matrix stored in the mesh.
+  ///
+  /// Assembles the PETSc matrix from stored (non-PETSc) row and column indices by
+  /// calling @ref assembleFromCSR.
+  ///
+  /// @param out_mapping Shared mapping for the output (row) space.
+  /// @param in_mapping  Shared mapping for the input (column) space.
+  /// @param rows        CSR row-pointer array (size = number_of_rows + 1).
+  /// @param cols        CSR column-index array, using stored (mesh-file) indices.
+  /// @param weights     CSR nonzero-value array.
   PetscOperator(std::shared_ptr<const PetscIndexMapping> out_mapping,
                 std::shared_ptr<const PetscIndexMapping> in_mapping, Array<int> rows,
                 Array<int> cols, Array<BoutReal> weights)
@@ -282,19 +532,29 @@ public:
     assembleFromCSR(rows, cols, weights);
   }
 
+  /// @brief Construct an operator from an already-assembled PETSc Mat.
+  ///
+  /// Takes ownership of @p mat.
+  ///
+  /// @param out_mapping Shared mapping for the output (row) space.
+  /// @param in_mapping  Shared mapping for the input (column) space.
+  /// @param mat         Pre-assembled PETSc Mat. Ownership is transferred.
   PetscOperator(std::shared_ptr<const PetscIndexMapping> out_mapping,
                 std::shared_ptr<const PetscIndexMapping> in_mapping, UniqueMat mat)
       : out_mapping(std::move(out_mapping)), in_mapping(std::move(in_mapping)),
         mat_operator(std::move(mat)) {}
 
-  // Cannot be copied but can be moved
+  // Operators are non-copyable (PETSc matrices are expensive to copy) but movable.
   PetscOperator(const PetscOperator&) = delete;
   PetscOperator& operator=(const PetscOperator&) = delete;
   PetscOperator(PetscOperator&&) noexcept = default;
   PetscOperator& operator=(PetscOperator&&) noexcept = default;
 
-  /// Apply operator to a vector in the input space,
-  /// returning a vector in the output space.
+  /// @brief Apply the operator to a typed vector: @c result = A * rhs.
+  ///
+  /// @param rhs Input vector; must share the same mapping as this operator's
+  ///            input space.
+  /// @returns A new output-space vector holding the result.
   PetscSpaceVector<OutSpaceTag>
   operator()(const PetscSpaceVector<InSpaceTag>& rhs) const {
     ASSERT0(in_mapping == rhs.getMapping());
@@ -303,8 +563,14 @@ public:
     return result;
   }
 
-  /// Apply operator to a Field3D, returning a vector.
-  /// Enable if input is Cell Space and output is not.
+  /// @brief Apply the operator to a Field3D: converts to a cell vector then applies.
+  ///
+  /// Only available when @p InSpaceTag is @ref CellSpaceTag and @p OutSpaceTag is
+  /// not @ref CellSpaceTag. The Field3D is packed into a PetscCellVector via
+  /// @ref makePetscCellVector before applying the matrix.
+  ///
+  /// @param rhs Source field; must have parallel slices split and allocated.
+  /// @returns A new output-space vector holding the result.
   template <typename T = InSpaceTag, typename U = OutSpaceTag,
             typename = std::enable_if_t<std::is_same_v<T, CellSpaceTag>
                                         && !std::is_same_v<U, CellSpaceTag>>>
@@ -325,6 +591,11 @@ public:
     return toField3D((*this)(in), rhs);
   }
 
+  /// @brief Return the transpose operator mapping from OutSpaceTag to InSpaceTag.
+  ///
+  /// Allocates a new PETSc Mat via MatTranspose (MAT_INITIAL_MATRIX). The mappings
+  /// are swapped: the transposed operator's input mapping is this operator's output
+  /// mapping, and vice versa.
   PetscOperator<InSpaceTag, OutSpaceTag> transpose() const {
     UniqueMat out{new Mat{nullptr}};
     BOUT_DO_PETSC(MatTranspose(*mat_operator, MAT_INITIAL_MATRIX, out.get()));
@@ -332,6 +603,13 @@ public:
                                                   std::move(out));
   }
 
+  /// @brief Return a new operator equal to @c (*this) + @p rhs.
+  ///
+  /// Both operands must share the same input and output mappings. Uses
+  /// UNKNOWN_NONZERO_PATTERN, so the sparsity structure of the result may differ
+  /// from either operand.
+  ///
+  /// @param rhs Operator to add; must have the same in/out mappings.
   PetscOperator operator+(const PetscOperator& rhs) const {
     ASSERT0(out_mapping == rhs.out_mapping);
     ASSERT0(in_mapping == rhs.in_mapping);
@@ -341,6 +619,12 @@ public:
     return PetscOperator(out_mapping, in_mapping, std::move(out));
   }
 
+  /// @brief Return a new operator equal to @c (*this) - @p rhs.
+  ///
+  /// Both operands must share the same input and output mappings. Uses
+  /// UNKNOWN_NONZERO_PATTERN; see @ref operator+.
+  ///
+  /// @param rhs Operator to subtract; must have the same in/out mappings.
   PetscOperator operator-(const PetscOperator& rhs) const {
     ASSERT0(out_mapping == rhs.out_mapping);
     ASSERT0(in_mapping == rhs.in_mapping);
@@ -350,6 +634,11 @@ public:
     return PetscOperator(out_mapping, in_mapping, std::move(out));
   }
 
+  /// @brief Return a new operator equal to @c (*this) * @p scalar (lvalue overload).
+  ///
+  /// Duplicates the matrix before scaling, leaving @c *this unchanged.
+  ///
+  /// @param scalar Scalar multiplier.
   PetscOperator operator*(BoutReal scalar) const& {
     UniqueMat out{new Mat{nullptr}};
     BOUT_DO_PETSC(MatDuplicate(*this->mat_operator, MAT_COPY_VALUES, out.get()));
@@ -357,13 +646,32 @@ public:
     return PetscOperator(out_mapping, in_mapping, std::move(out));
   }
 
+  /// @brief Scale this operator in place and return it (rvalue overload).
+  ///
+  /// More efficient than the lvalue overload when @c *this is a temporary,
+  /// as no matrix duplication is needed.
+  ///
+  /// @param scalar Scalar multiplier.
   PetscOperator operator*(BoutReal scalar) && {
     BOUT_DO_PETSC(MatScale(*this->mat_operator, scalar));
     return std::move(*this);
   }
 
+  /// @brief Return the underlying PETSc Mat handle (non-owning).
+  ///
+  /// Intended for use by the free @c operator* (matrix composition) and other
+  /// low-level callers that need direct PETSc access.
   Mat raw() const { return *this->mat_operator; }
 
+  /// @brief Construct a diagonal operator from a vector of diagonal entries.
+  ///
+  /// Only available when @p OutSpaceTag == @p InSpaceTag (square, same-space
+  /// operator). Builds an MPIAIJ matrix with one nonzero per row via
+  /// MatDiagonalSet.
+  ///
+  /// @param mapping Shared mapping for both the row and column space.
+  /// @param diag    Vector of diagonal values; must share @p mapping.
+  /// @returns A new diagonal operator.
   static PetscOperator diagonal(std::shared_ptr<const PetscIndexMapping> mapping,
                                 const PetscSpaceVector<OutSpaceTag>& diag) {
     static_assert(std::is_same_v<OutSpaceTag, InSpaceTag>,
@@ -382,6 +690,18 @@ public:
   }
 
 private:
+  /// @brief Assemble the operator matrix from a mesh-file CSR representation.
+  ///
+  /// Iterates over the locally owned output rows (identified via
+  /// @c out_mapping->localStoredIndices()), looks up each row's nonzeros in the
+  /// CSR arrays, and inserts them using global PETSc row indices. Column indices
+  /// are given in stored (mesh-file) numbering; the final matrix is obtained by
+  /// post-multiplying the assembled temporary by
+  /// @c in_mapping->getPetscToStored() to convert to PETSc column ordering.
+  ///
+  /// @param rows    CSR row-pointer array (size = total_stored_rows + 1).
+  /// @param cols    CSR column-index array in stored (mesh-file) numbering.
+  /// @param weights CSR nonzero-value array.
   void assembleFromCSR(const Array<int>& rows, const Array<int>& cols,
                        const Array<BoutReal>& weights) {
     UniqueMat temp{new Mat{nullptr}};
@@ -409,21 +729,34 @@ private:
     BOUT_DO_PETSC(MatAssemblyBegin(*temp, MAT_FINAL_ASSEMBLY));
     BOUT_DO_PETSC(MatAssemblyEnd(*temp, MAT_FINAL_ASSEMBLY));
 
+    // Post-multiply by the stored→PETSc permutation to convert column numbering.
     UniqueMat out{new Mat{nullptr}};
     BOUT_DO_PETSC(MatMatMult(*temp, in_mapping->getPetscToStored(), MAT_INITIAL_MATRIX,
                              PETSC_DETERMINE, out.get()));
     mat_operator = std::move(out);
   }
 
-  std::shared_ptr<const PetscIndexMapping> out_mapping;
-  std::shared_ptr<const PetscIndexMapping> in_mapping;
-  UniqueMat mat_operator{new Mat{nullptr}};
+  std::shared_ptr<const PetscIndexMapping> out_mapping; ///< Row-space mapping.
+  std::shared_ptr<const PetscIndexMapping> in_mapping;  ///< Column-space mapping.
+  UniqueMat mat_operator{new Mat{nullptr}};             ///< Underlying PETSc Mat.
 
   template <typename O, typename M, typename I>
   friend PetscOperator<O, I> operator*(const PetscOperator<O, M>& lhs,
                                        const PetscOperator<M, I>& rhs);
 };
 
+/// @brief Compose two compatible operators: @c result = lhs * rhs.
+///
+/// The output space of @p rhs must match the input space of @p lhs, enforced at
+/// compile time by the @p MidSpaceTag parameter. The resulting operator maps from
+/// @p rhs's input space to @p lhs's output space.
+///
+/// @tparam OutSpaceTag Output space of @p lhs and of the result.
+/// @tparam MidSpaceTag Input space of @p lhs and output space of @p rhs.
+/// @tparam InSpaceTag  Input space of @p rhs and of the result.
+/// @param lhs Left (outer) operator.
+/// @param rhs Right (inner) operator.
+/// @returns A new operator representing the composition.
 template <typename OutSpaceTag, typename MidSpaceTag, typename InSpaceTag>
 PetscOperator<OutSpaceTag, InSpaceTag>
 operator*(const PetscOperator<OutSpaceTag, MidSpaceTag>& lhs,
@@ -436,63 +769,185 @@ operator*(const PetscOperator<OutSpaceTag, MidSpaceTag>& lhs,
                                                 std::move(out));
 }
 
+/// @brief Operator mapping from cell space C to forward leg space L+.
 using PetscForwardOperator = PetscOperator<ForwardLegSpaceTag, CellSpaceTag>;
+/// @brief Operator mapping from cell space C to backward leg space L-.
 using PetscBackwardOperator = PetscOperator<BackwardLegSpaceTag, CellSpaceTag>;
+/// @brief Operator mapping from forward leg space L+ to cell space C.
 using PetscForwardToCellOperator = PetscOperator<CellSpaceTag, ForwardLegSpaceTag>;
+/// @brief Operator mapping from backward leg space L- to cell space C.
 using PetscBackwardToCellOperator = PetscOperator<CellSpaceTag, BackwardLegSpaceTag>;
+/// @brief Operator mapping within the cell space C.
 using PetscCellOperator = PetscOperator<CellSpaceTag, CellSpaceTag>;
+/// @brief Operator mapping within the forward leg space L+.
 using PetscForwardLegOperator = PetscOperator<ForwardLegSpaceTag, ForwardLegSpaceTag>;
+/// @brief Operator mapping within the backward leg space L-.
 using PetscBackwardLegOperator = PetscOperator<BackwardLegSpaceTag, BackwardLegSpaceTag>;
 
-/// Factory for operators defined on cell and leg spaces.
+/// @brief Factory that constructs cell-space and leg-space operators from mesh metadata.
+///
+/// On construction, reads all required fields and integer scalars from the mesh and
+/// sets up the @ref PetscCellMapping, forward @ref PetscLegMapping, and backward
+/// @ref PetscLegMapping. Individual primitive operators (interpolation, injection,
+/// leg weights) are constructed on demand. The high-level set of parallel operators
+/// needed for Support-Operator-Method diffusion is assembled by @ref getParallel.
 class PetscOperators {
 public:
+  /// @brief Construct the operator factory from a BOUT++ mesh.
+  ///
+  /// Reads the following fields from @p mesh:
+  ///   - @c cell_number, @c forward_cell_number, @c backward_cell_number (Field3D)
+  ///   - @c total_cells, @c n_forward_legs, @c n_backward_legs (int)
+  ///   - @c forward_leg_interior_number, @c forward_leg_boundary_number (Field3D)
+  ///   - @c backward_leg_interior_number, @c backward_leg_boundary_number (Field3D)
+  ///
+  /// @param mesh Non-owning pointer to the BOUT++ mesh. Must outlive this object.
+  /// @throws BoutException if any required field or scalar is missing from the mesh.
   explicit PetscOperators(Mesh* mesh);
 
+  /// @brief Build the forward interpolation operator F: L+ ← C.
+  ///
+  /// Maps cell-space values to forward leg space using the CSR arrays stored in the
+  /// mesh (@c forward_rows, @c forward_columns, @c forward_weights).
   PetscForwardOperator forward() const;
+
+  /// @brief Build the backward interpolation operator B: L- ← C.
+  ///
+  /// Maps cell-space values to backward leg space using the CSR arrays stored in the
+  /// mesh (@c backward_rows, @c backward_columns, @c backward_weights).
   PetscBackwardOperator backward() const;
 
+  /// @brief Build the forward injection operator I+: L+ ← C.
+  ///
+  /// Places the value of each interior source cell into its corresponding forward leg
+  /// row(s), with weight 1. Boundary leg rows point to the virtual boundary cell in C.
   PetscForwardOperator injectForward() const;
+
+  /// @brief Build the backward injection operator I-: L- ← C.
+  ///
+  /// Analogous to @ref injectForward for the backward leg space.
   PetscBackwardOperator injectBackward() const;
 
+  /// @brief Load the forward leg-weight vector w+: L+.
+  ///
+  /// Each entry holds the quadrature weight of the corresponding forward leg row,
+  /// equal to the interior or boundary fraction of that leg's sub-sample integral.
   PetscForwardLegVector forwardLegWeights() const;
+
+  /// @brief Load the backward leg-weight vector w-: L-.
+  ///
+  /// Analogous to @ref forwardLegWeights for the backward leg space.
   PetscBackwardLegVector backwardLegWeights() const;
 
+  /// @brief Build a diagonal cell-space operator from a Field3D of values.
+  ///
+  /// @param f Field3D of diagonal entries; must have parallel slices allocated.
+  /// @returns A diagonal PetscCellOperator.
   PetscCellOperator diagonal(const Field3D& f) const;
+
+  /// @brief Build a diagonal forward-leg-space operator from a leg vector.
+  ///
+  /// @param v Forward leg vector of diagonal entries.
+  /// @returns A diagonal PetscForwardLegOperator.
   PetscForwardLegOperator diagonal(const PetscForwardLegVector& v) const;
+
+  /// @brief Build a diagonal backward-leg-space operator from a leg vector.
+  ///
+  /// @param v Backward leg vector of diagonal entries.
+  /// @returns A diagonal PetscBackwardLegOperator.
   PetscBackwardLegOperator diagonal(const PetscBackwardLegVector& v) const;
 
+  /// @brief Collection of parallel differential operators assembled for the
+  ///        Support Operator Method (SOM).
+  ///
+  /// All operators are constructed together in @ref getParallel so that intermediate
+  /// quantities (leg weights, interpolated dl, dV) are shared correctly.
+  ///
+  /// Naming convention: the subscript on Grad/Div/Restrict refers to which side of
+  /// the cell face the operator acts on, not the leg space it lives in.
+  ///   - @c Grad_plus / @c Div_plus: forward-side half-step operators (in L-).
+  ///   - @c Grad_minus / @c Div_minus: backward-side half-step operators (in L+).
+  ///   - @c Restrict_minus = I+^T * W+: weighted restriction from L+ back to C,
+  ///     paired with the minus-side gradient.
+  ///   - @c Restrict_plus  = I-^T * W-: weighted restriction from L- back to C,
+  ///     paired with the plus-side gradient.
   struct Parallel {
+    /// Central parallel gradient: C ← C.
     PetscCellOperator Grad_par;
+    /// Support-operator parallel divergence paired with Grad_par: C ← C.
     PetscCellOperator Div_par;
+    /// Combined SOM parallel Laplacian (Div_par ∘ Grad_par): C ← C.
     PetscCellOperator Div_par_Grad_par;
+    /// Cell volume J * dx * dy * dz.
     Field3D dV;
 
+    /// Half-step gradient on the backward (y-1) side: L- ← C.
     PetscBackwardOperator Grad_minus;
+    /// Half-step gradient on the forward (y+1) side: L+ ← C.
     PetscForwardOperator Grad_plus;
+    /// SOM divergence paired with Grad_plus: C ← L+.
     PetscForwardToCellOperator Div_minus;
+    /// SOM divergence paired with Grad_minus: C ← L-.
     PetscBackwardToCellOperator Div_plus;
 
+    /// Raw backward interpolation operator B: L- ← C.
     PetscBackwardOperator Backward;
+    /// Raw forward interpolation operator F: L+ ← C.
     PetscForwardOperator Forward;
 
+    /// Injection operator into backward leg space I-: L- ← C.
     PetscBackwardOperator Inject_minus;
+    /// Injection operator into forward leg space I+: L+ ← C.
     PetscForwardOperator Inject_plus;
 
+    /// Average interpolation to backward leg positions: L- ← C.
     PetscBackwardOperator Interp_minus;
+    /// Average interpolation to forward leg positions: L+ ← C.
     PetscForwardOperator Interp_plus;
 
+    /// Weighted restriction from L+ to C: I+^T * W+.
     PetscForwardToCellOperator Restrict_minus;
+    /// Weighted restriction from L- to C: I-^T * W-.
     PetscBackwardToCellOperator Restrict_plus;
 
+    /// @brief Compute the SOM parallel diffusion Div_par(K * Grad_par(f)).
+    ///
+    /// Evaluates the half-step fluxes separately on each side, multiplies by the
+    /// interpolated diffusion coefficient K, and averages the two divergence
+    /// contributions. This is the primary user-facing SOM operator.
+    ///
+    /// @param K Diffusion coefficient field; must have parallel slices allocated.
+    /// @param f Field to differentiate; must have parallel slices allocated.
+    /// @returns Field3D containing Div_par(K * Grad_par(f)) at interior cells.
     Field3D Div_par_K_Grad_par(const Field3D& K, const Field3D& f) const;
   };
 
+  /// @brief Assemble and return the full set of parallel SOM operators.
+  ///
+  /// Constructs all primitive operators (Forward, Backward, Inject_plus,
+  /// Inject_minus, leg weights), derives the interpolation, gradient, restriction,
+  /// and divergence operators, and returns them packaged in a @ref Parallel struct.
+  /// Intermediate Field3D quantities (dl, dV) are computed from the mesh
+  /// coordinates and boundary conditions are applied before use.
+  ///
+  /// @returns A @ref Parallel struct containing all assembled operators.
   Parallel getParallel() const;
 
 private:
+  /// @brief Read a Field3D from the mesh, throwing if the field is absent.
+  ///
+  /// @param mesh Non-owning mesh pointer.
+  /// @param name Field name as stored in the mesh file.
+  /// @returns The requested Field3D.
+  /// @throws BoutException if the field is not found.
   static Field3D meshGetField3D(Mesh* mesh, const std::string& name);
 
+  /// @brief Read an Array<T> from the mesh, throwing if absent.
+  ///
+  /// @tparam T Element type of the array.
+  /// @param name Array name as stored in the mesh file.
+  /// @returns The requested Array<T>.
+  /// @throws BoutException if the array is not found.
   template <typename T>
   Array<T> meshGetArray(const std::string& name) const {
     Array<T> result;
@@ -502,13 +957,39 @@ private:
     return result;
   }
 
+  /// @brief Read a scalar integer from the mesh, throwing if absent.
+  ///
+  /// @param name Scalar name as stored in the mesh file.
+  /// @returns The requested integer value.
+  /// @throws BoutException if the scalar is not found.
   int meshGetInt(const std::string& name) const;
 
+  /// @brief Build a leg-space injection operator for the given direction.
+  ///
+  /// Iterates owned interior cells and inserts a unit entry for each interior or
+  /// boundary leg row, mapping to the corresponding cell-space column. Column
+  /// indices come from @p interior_leg_number and @p boundary_leg_number.
+  ///
+  /// @tparam LegTag     @ref ForwardLegSpaceTag or @ref BackwardLegSpaceTag.
+  /// @param interior_leg_number Field3D of stored interior leg row numbers.
+  /// @param boundary_leg_number Field3D of stored boundary leg row numbers.
+  /// @param leg_mapping         Shared mapping for the leg space.
+  /// @returns The assembled injection operator LegTag ← CellSpaceTag.
   template <typename LegTag>
   PetscOperator<LegTag, CellSpaceTag>
   buildInjection(const Field3D& interior_leg_number, const Field3D& boundary_leg_number,
                  std::shared_ptr<const PetscLegMapping> leg_mapping) const;
 
+  /// @brief Load a leg-weight vector from a named mesh array.
+  ///
+  /// Reads the flat array @p name from the mesh, then scatters values into the
+  /// local PETSc vector using the mapping's stored index list. Stored indices that
+  /// are out of range are assigned weight 0.
+  ///
+  /// @tparam LegVector  @ref PetscForwardLegVector or @ref PetscBackwardLegVector.
+  /// @param name    Array name in the mesh file (e.g. "forward_leg_weights").
+  /// @param mapping Shared mapping for the leg space.
+  /// @returns A fully populated leg-weight vector.
   template <typename LegVector>
   LegVector loadLegWeights(const std::string& name,
                            std::shared_ptr<const PetscLegMapping> mapping) const {
@@ -526,14 +1007,14 @@ private:
     return out;
   }
 
-  Mesh* mesh{nullptr};
-  PetscCellMappingPtr cell_mapping;
-  PetscLegMappingPtr forward_leg_mapping;
-  PetscLegMappingPtr backward_leg_mapping;
-  Field3D forward_leg_interior_number;
-  Field3D forward_leg_boundary_number;
-  Field3D backward_leg_interior_number;
-  Field3D backward_leg_boundary_number;
+  Mesh* mesh{nullptr};                     ///< Non-owning pointer to the BOUT++ mesh.
+  PetscCellMappingPtr cell_mapping;        ///< Cell-space index mapping.
+  PetscLegMappingPtr forward_leg_mapping;  ///< Forward leg-space index mapping.
+  PetscLegMappingPtr backward_leg_mapping; ///< Backward leg-space index mapping.
+  Field3D forward_leg_interior_number;     ///< Stored interior leg numbers for L+.
+  Field3D forward_leg_boundary_number;     ///< Stored boundary leg numbers for L+.
+  Field3D backward_leg_interior_number;    ///< Stored interior leg numbers for L-.
+  Field3D backward_leg_boundary_number;    ///< Stored boundary leg numbers for L-.
 };
 
 #else

From b48c40b1dfb1dbd269ee61cc3fdb76ebdbf1af86 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 9 Apr 2026 14:15:58 -0700
Subject: [PATCH 0959/1827] PetscOperators: Minor docstring fixes

---
 include/bout/petsc_operators.hxx | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 0d9c6c6912..8c36f461d0 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -8,7 +8,6 @@
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
-#include "bout/output.hxx"
 #include "bout/output_bout_types.hxx"
 #include "bout/petsc_interface.hxx"
 #include "bout/petsclib.hxx"
@@ -865,8 +864,8 @@ public:
   ///
   /// Naming convention: the subscript on Grad/Div/Restrict refers to which side of
   /// the cell face the operator acts on, not the leg space it lives in.
-  ///   - @c Grad_plus / @c Div_plus: forward-side half-step operators (in L-).
-  ///   - @c Grad_minus / @c Div_minus: backward-side half-step operators (in L+).
+  ///   - @c Grad_plus / @c Div_plus: forward-side half-step operators (C to L+).
+  ///   - @c Grad_minus / @c Div_minus: backward-side half-step operators (C to L-).
   ///   - @c Restrict_minus = I+^T * W+: weighted restriction from L+ back to C,
   ///     paired with the minus-side gradient.
   ///   - @c Restrict_plus  = I-^T * W-: weighted restriction from L- back to C,
@@ -914,7 +913,7 @@ public:
     ///
     /// Evaluates the half-step fluxes separately on each side, multiplies by the
     /// interpolated diffusion coefficient K, and averages the two divergence
-    /// contributions. This is the primary user-facing SOM operator.
+    /// contributions.
     ///
     /// @param K Diffusion coefficient field; must have parallel slices allocated.
     /// @param f Field to differentiate; must have parallel slices allocated.

From cdf9b13f45f3b70cb39c2c2be17179c2a2116b7c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 14 Apr 2026 13:09:55 +0200
Subject: [PATCH 0960/1827] make Options an optional argument in YBoundary

---
 include/bout/yboundary_regions.hxx | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index bee4634310..d40a7b8836 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -44,19 +44,21 @@ public:
     return iter_regions(f);
   }
 
-  YBoundary(Options& options, Mesh* mesh = nullptr) {
+  YBoundary(Options* options_ptr, Mesh* mesh = nullptr) {
     if (mesh == nullptr) {
       mesh = bout::globals::mesh;
     }
-
-    const bool lower_y =
-        options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(true);
-    const bool upper_y =
-        options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(true);
-    const bool outer_x =
-        options["outer_x"].doc("Boundary on outer x?").withDefault<bool>(true);
-    const bool inner_x =
-        options["inner_x"].doc("Boundary on inner x?").withDefault<bool>(false);
+    bool lower_y = true;
+    bool upper_y = true;
+    bool outer_x = true;
+    bool inner_x = true;
+    if (options_ptr != nullptr) {
+      auto& options = *options_ptr;
+      lower_y = options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
+      upper_y = options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(upper_y);
+      outer_x = options["outer_x"].doc("Boundary on outer x?").withDefault<bool>(outer_x);
+      inner_x = options["inner_x"].doc("Boundary on inner x?").withDefault<bool>(inner_x);
+    }
 
     if (mesh->isFci()) {
       if (outer_x) {

From a102ffe235d94611a13fcc8059f88b928aa26f88 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 15 Oct 2025 11:47:19 +0100
Subject: [PATCH 0961/1827] Use pytest rather than runtest as the command set
 in bout_add_integrated_or_mms_test

---
 cmake/BOUT++functions.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index cff7e4b808..c9ff1fbcb8 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -254,12 +254,12 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
 
   # Set the actual test command
   if(BOUT_TEST_OPTIONS_USE_RUNTEST)
-    add_test(NAME ${TESTNAME} COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS})
+    add_test(NAME ${TESTNAME} COMMAND ./pytest ${BOUT_TEST_OPTIONS_TESTARGS})
     set_tests_properties(
       ${TESTNAME} PROPERTIES ENVIRONMENT
                              PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
     )
-    bout_copy_file(runtest)
+    bout_copy_file(${TESTNAME}.py)
   else()
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()

From a55dda0d34329287e26d476d35b8d7507d847be6 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 12:35:57 +0000
Subject: [PATCH 0962/1827] Rename runtest file to test-foo.py for each
 integrated test

---
 .../{runtest => test_backtrace.py}            |  0
 .../test-beuler/{runtest => test_beuler.py}   |  0
 ...t => test_bout_override_default_option.py} |  0
 .../{runtest => test_code_style.py}           |  0
 .../test-collect/{runtest => test_collect.py} |  0
 .../{runtest => test_command_args.py}         |  0
 .../{runtest => test_communications.py}       |  0
 ...runtest => test_compile_examples_petsc.py} |  0
 .../{runtest => test_compile_examples.py}     |  0
 ...est => test_coordinates_initialization.py} |  0
 .../test-cyclic/{runtest => test_cyclic.py}   |  0
 .../{runtest => test_datafilefacade.py}       |  0
 .../test-delp2/{runtest => test_delp2.py}     |  0
 ...st => test_drift_instability_staggered.py} |  0
 .../{runtest => test_fci_boundary.py}         |  0
 .../{runtest => test_fieldgroupComm.py}       |  0
 ...test => test_griddata_yboundary_guards.py} |  0
 .../{runtest => test_griddata.py}             |  0
 .../test-gyro/{runtest => test_gyro.py}       |  0
 .../test-include/{runtest => test_include.py} |  0
 .../test-initial/{runtest => test_initial.py} |  0
 ...untest => test_interchange_instability.py} |  0
 .../{runtest => test_interpolate_z.py}        |  0
 .../{runtest => test_interpolate.py}          |  0
 .../{runtest => test_invertable_operator.py}  |  0
 .../test-invpar/{runtest => test_invpar.py}   |  0
 .../{runtest => test_laplace_hypre3d.py}      |  0
 .../{runtest => test_laplace_petsc3d.py}      |  0
 .../test-laplace/{runtest => test_laplace.py} |  0
 .../{runtest => test_laplacexy_fv.py}         |  0
 .../{runtest => test_laplacexy_short.py}      |  0
 .../{runtest => test_laplacexy.py}            |  0
 .../{runtest => test_laplacexy2_hypre.py}     |  0
 .../{runtest => test_laplacexz.py}            |  0
 .../{runtest => test_multigrid_laplace.py}    |  0
 .../{runtest => test_naulin_laplace.py}       |  0
 .../test-options-adios/test_options_adios.py  | 74 +++++++++++++++++++
 .../{runtest => test_options_netcdf.py}       |  0
 .../{runtest => test_petsc_laplace.py}        |  0
 ...untest => test_petsc_laplace_MAST_grid.py} |  0
 .../{runtest => test_region_iterator.py}      |  0
 .../{runtest => test_restart_io.py}           |  0
 .../{runtest => test_restarting.py}           |  0
 .../{runtest => test_slepc_solver.py}         |  0
 .../test-smooth/{runtest => test_smooth.py}   |  0
 .../test-snb/{runtest => test_snb.py}         |  0
 .../test-solver/{runtest => test_solver.py}   |  0
 .../test-squash/{runtest => test_squash.py}   |  0
 .../{runtest => test_stopCheck_file.py}       |  0
 .../{runtest => test_stopCheck.py}            |  0
 .../test-subdir/{runtest => test_subdir.py}   |  0
 .../{runtest => test_twistshift_staggered.py} |  0
 .../{runtest => test_twistshift.py}           |  0
 .../test-vec/{runtest => test_vec.py}         |  0
 .../{runtest => test_yupdown_weights.py}      |  0
 .../test-yupdown/{runtest => test_yupdown.py} |  0
 56 files changed, 74 insertions(+)
 rename tests/integrated/test-backtrace/{runtest => test_backtrace.py} (100%)
 rename tests/integrated/test-beuler/{runtest => test_beuler.py} (100%)
 rename tests/integrated/test-bout-override-default-option/{runtest => test_bout_override_default_option.py} (100%)
 rename tests/integrated/test-code-style/{runtest => test_code_style.py} (100%)
 rename tests/integrated/test-collect/{runtest => test_collect.py} (100%)
 rename tests/integrated/test-command-args/{runtest => test_command_args.py} (100%)
 rename tests/integrated/test-communications/{runtest => test_communications.py} (100%)
 rename tests/integrated/test-compile-examples-petsc/{runtest => test_compile_examples_petsc.py} (100%)
 rename tests/integrated/test-compile-examples/{runtest => test_compile_examples.py} (100%)
 rename tests/integrated/test-coordinates-initialization/{runtest => test_coordinates_initialization.py} (100%)
 rename tests/integrated/test-cyclic/{runtest => test_cyclic.py} (100%)
 rename tests/integrated/test-datafilefacade/{runtest => test_datafilefacade.py} (100%)
 rename tests/integrated/test-delp2/{runtest => test_delp2.py} (100%)
 rename tests/integrated/test-drift-instability-staggered/{runtest => test_drift_instability_staggered.py} (100%)
 rename tests/integrated/test-fci-boundary/{runtest => test_fci_boundary.py} (100%)
 rename tests/integrated/test-fieldgroupComm/{runtest => test_fieldgroupComm.py} (100%)
 rename tests/integrated/test-griddata-yboundary-guards/{runtest => test_griddata_yboundary_guards.py} (100%)
 rename tests/integrated/test-griddata/{runtest => test_griddata.py} (100%)
 rename tests/integrated/test-gyro/{runtest => test_gyro.py} (100%)
 rename tests/integrated/test-include/{runtest => test_include.py} (100%)
 rename tests/integrated/test-initial/{runtest => test_initial.py} (100%)
 rename tests/integrated/test-interchange-instability/{runtest => test_interchange_instability.py} (100%)
 rename tests/integrated/test-interpolate-z/{runtest => test_interpolate_z.py} (100%)
 rename tests/integrated/test-interpolate/{runtest => test_interpolate.py} (100%)
 rename tests/integrated/test-invertable-operator/{runtest => test_invertable_operator.py} (100%)
 rename tests/integrated/test-invpar/{runtest => test_invpar.py} (100%)
 rename tests/integrated/test-laplace-hypre3d/{runtest => test_laplace_hypre3d.py} (100%)
 rename tests/integrated/test-laplace-petsc3d/{runtest => test_laplace_petsc3d.py} (100%)
 rename tests/integrated/test-laplace/{runtest => test_laplace.py} (100%)
 rename tests/integrated/test-laplacexy-fv/{runtest => test_laplacexy_fv.py} (100%)
 rename tests/integrated/test-laplacexy-short/{runtest => test_laplacexy_short.py} (100%)
 rename tests/integrated/test-laplacexy/{runtest => test_laplacexy.py} (100%)
 rename tests/integrated/test-laplacexy2-hypre/{runtest => test_laplacexy2_hypre.py} (100%)
 rename tests/integrated/test-laplacexz/{runtest => test_laplacexz.py} (100%)
 rename tests/integrated/test-multigrid_laplace/{runtest => test_multigrid_laplace.py} (100%)
 rename tests/integrated/test-naulin-laplace/{runtest => test_naulin_laplace.py} (100%)
 create mode 100755 tests/integrated/test-options-adios/test_options_adios.py
 rename tests/integrated/test-options-netcdf/{runtest => test_options_netcdf.py} (100%)
 rename tests/integrated/test-petsc_laplace/{runtest => test_petsc_laplace.py} (100%)
 rename tests/integrated/test-petsc_laplace_MAST-grid/{runtest => test_petsc_laplace_MAST_grid.py} (100%)
 rename tests/integrated/test-region-iterator/{runtest => test_region_iterator.py} (100%)
 rename tests/integrated/test-restart-io/{runtest => test_restart_io.py} (100%)
 rename tests/integrated/test-restarting/{runtest => test_restarting.py} (100%)
 rename tests/integrated/test-slepc-solver/{runtest => test_slepc_solver.py} (100%)
 rename tests/integrated/test-smooth/{runtest => test_smooth.py} (100%)
 rename tests/integrated/test-snb/{runtest => test_snb.py} (100%)
 rename tests/integrated/test-solver/{runtest => test_solver.py} (100%)
 rename tests/integrated/test-squash/{runtest => test_squash.py} (100%)
 rename tests/integrated/test-stopCheck-file/{runtest => test_stopCheck_file.py} (100%)
 rename tests/integrated/test-stopCheck/{runtest => test_stopCheck.py} (100%)
 rename tests/integrated/test-subdir/{runtest => test_subdir.py} (100%)
 rename tests/integrated/test-twistshift-staggered/{runtest => test_twistshift_staggered.py} (100%)
 rename tests/integrated/test-twistshift/{runtest => test_twistshift.py} (100%)
 rename tests/integrated/test-vec/{runtest => test_vec.py} (100%)
 rename tests/integrated/test-yupdown-weights/{runtest => test_yupdown_weights.py} (100%)
 rename tests/integrated/test-yupdown/{runtest => test_yupdown.py} (100%)

diff --git a/tests/integrated/test-backtrace/runtest b/tests/integrated/test-backtrace/test_backtrace.py
similarity index 100%
rename from tests/integrated/test-backtrace/runtest
rename to tests/integrated/test-backtrace/test_backtrace.py
diff --git a/tests/integrated/test-beuler/runtest b/tests/integrated/test-beuler/test_beuler.py
similarity index 100%
rename from tests/integrated/test-beuler/runtest
rename to tests/integrated/test-beuler/test_beuler.py
diff --git a/tests/integrated/test-bout-override-default-option/runtest b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
similarity index 100%
rename from tests/integrated/test-bout-override-default-option/runtest
rename to tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
diff --git a/tests/integrated/test-code-style/runtest b/tests/integrated/test-code-style/test_code_style.py
similarity index 100%
rename from tests/integrated/test-code-style/runtest
rename to tests/integrated/test-code-style/test_code_style.py
diff --git a/tests/integrated/test-collect/runtest b/tests/integrated/test-collect/test_collect.py
similarity index 100%
rename from tests/integrated/test-collect/runtest
rename to tests/integrated/test-collect/test_collect.py
diff --git a/tests/integrated/test-command-args/runtest b/tests/integrated/test-command-args/test_command_args.py
similarity index 100%
rename from tests/integrated/test-command-args/runtest
rename to tests/integrated/test-command-args/test_command_args.py
diff --git a/tests/integrated/test-communications/runtest b/tests/integrated/test-communications/test_communications.py
similarity index 100%
rename from tests/integrated/test-communications/runtest
rename to tests/integrated/test-communications/test_communications.py
diff --git a/tests/integrated/test-compile-examples-petsc/runtest b/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
similarity index 100%
rename from tests/integrated/test-compile-examples-petsc/runtest
rename to tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
diff --git a/tests/integrated/test-compile-examples/runtest b/tests/integrated/test-compile-examples/test_compile_examples.py
similarity index 100%
rename from tests/integrated/test-compile-examples/runtest
rename to tests/integrated/test-compile-examples/test_compile_examples.py
diff --git a/tests/integrated/test-coordinates-initialization/runtest b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
similarity index 100%
rename from tests/integrated/test-coordinates-initialization/runtest
rename to tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
diff --git a/tests/integrated/test-cyclic/runtest b/tests/integrated/test-cyclic/test_cyclic.py
similarity index 100%
rename from tests/integrated/test-cyclic/runtest
rename to tests/integrated/test-cyclic/test_cyclic.py
diff --git a/tests/integrated/test-datafilefacade/runtest b/tests/integrated/test-datafilefacade/test_datafilefacade.py
similarity index 100%
rename from tests/integrated/test-datafilefacade/runtest
rename to tests/integrated/test-datafilefacade/test_datafilefacade.py
diff --git a/tests/integrated/test-delp2/runtest b/tests/integrated/test-delp2/test_delp2.py
similarity index 100%
rename from tests/integrated/test-delp2/runtest
rename to tests/integrated/test-delp2/test_delp2.py
diff --git a/tests/integrated/test-drift-instability-staggered/runtest b/tests/integrated/test-drift-instability-staggered/test_drift_instability_staggered.py
similarity index 100%
rename from tests/integrated/test-drift-instability-staggered/runtest
rename to tests/integrated/test-drift-instability-staggered/test_drift_instability_staggered.py
diff --git a/tests/integrated/test-fci-boundary/runtest b/tests/integrated/test-fci-boundary/test_fci_boundary.py
similarity index 100%
rename from tests/integrated/test-fci-boundary/runtest
rename to tests/integrated/test-fci-boundary/test_fci_boundary.py
diff --git a/tests/integrated/test-fieldgroupComm/runtest b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
similarity index 100%
rename from tests/integrated/test-fieldgroupComm/runtest
rename to tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
diff --git a/tests/integrated/test-griddata-yboundary-guards/runtest b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
similarity index 100%
rename from tests/integrated/test-griddata-yboundary-guards/runtest
rename to tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
diff --git a/tests/integrated/test-griddata/runtest b/tests/integrated/test-griddata/test_griddata.py
similarity index 100%
rename from tests/integrated/test-griddata/runtest
rename to tests/integrated/test-griddata/test_griddata.py
diff --git a/tests/integrated/test-gyro/runtest b/tests/integrated/test-gyro/test_gyro.py
similarity index 100%
rename from tests/integrated/test-gyro/runtest
rename to tests/integrated/test-gyro/test_gyro.py
diff --git a/tests/integrated/test-include/runtest b/tests/integrated/test-include/test_include.py
similarity index 100%
rename from tests/integrated/test-include/runtest
rename to tests/integrated/test-include/test_include.py
diff --git a/tests/integrated/test-initial/runtest b/tests/integrated/test-initial/test_initial.py
similarity index 100%
rename from tests/integrated/test-initial/runtest
rename to tests/integrated/test-initial/test_initial.py
diff --git a/tests/integrated/test-interchange-instability/runtest b/tests/integrated/test-interchange-instability/test_interchange_instability.py
similarity index 100%
rename from tests/integrated/test-interchange-instability/runtest
rename to tests/integrated/test-interchange-instability/test_interchange_instability.py
diff --git a/tests/integrated/test-interpolate-z/runtest b/tests/integrated/test-interpolate-z/test_interpolate_z.py
similarity index 100%
rename from tests/integrated/test-interpolate-z/runtest
rename to tests/integrated/test-interpolate-z/test_interpolate_z.py
diff --git a/tests/integrated/test-interpolate/runtest b/tests/integrated/test-interpolate/test_interpolate.py
similarity index 100%
rename from tests/integrated/test-interpolate/runtest
rename to tests/integrated/test-interpolate/test_interpolate.py
diff --git a/tests/integrated/test-invertable-operator/runtest b/tests/integrated/test-invertable-operator/test_invertable_operator.py
similarity index 100%
rename from tests/integrated/test-invertable-operator/runtest
rename to tests/integrated/test-invertable-operator/test_invertable_operator.py
diff --git a/tests/integrated/test-invpar/runtest b/tests/integrated/test-invpar/test_invpar.py
similarity index 100%
rename from tests/integrated/test-invpar/runtest
rename to tests/integrated/test-invpar/test_invpar.py
diff --git a/tests/integrated/test-laplace-hypre3d/runtest b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
similarity index 100%
rename from tests/integrated/test-laplace-hypre3d/runtest
rename to tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
diff --git a/tests/integrated/test-laplace-petsc3d/runtest b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
similarity index 100%
rename from tests/integrated/test-laplace-petsc3d/runtest
rename to tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
diff --git a/tests/integrated/test-laplace/runtest b/tests/integrated/test-laplace/test_laplace.py
similarity index 100%
rename from tests/integrated/test-laplace/runtest
rename to tests/integrated/test-laplace/test_laplace.py
diff --git a/tests/integrated/test-laplacexy-fv/runtest b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
similarity index 100%
rename from tests/integrated/test-laplacexy-fv/runtest
rename to tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
diff --git a/tests/integrated/test-laplacexy-short/runtest b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
similarity index 100%
rename from tests/integrated/test-laplacexy-short/runtest
rename to tests/integrated/test-laplacexy-short/test_laplacexy_short.py
diff --git a/tests/integrated/test-laplacexy/runtest b/tests/integrated/test-laplacexy/test_laplacexy.py
similarity index 100%
rename from tests/integrated/test-laplacexy/runtest
rename to tests/integrated/test-laplacexy/test_laplacexy.py
diff --git a/tests/integrated/test-laplacexy2-hypre/runtest b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
similarity index 100%
rename from tests/integrated/test-laplacexy2-hypre/runtest
rename to tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
diff --git a/tests/integrated/test-laplacexz/runtest b/tests/integrated/test-laplacexz/test_laplacexz.py
similarity index 100%
rename from tests/integrated/test-laplacexz/runtest
rename to tests/integrated/test-laplacexz/test_laplacexz.py
diff --git a/tests/integrated/test-multigrid_laplace/runtest b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
similarity index 100%
rename from tests/integrated/test-multigrid_laplace/runtest
rename to tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
diff --git a/tests/integrated/test-naulin-laplace/runtest b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
similarity index 100%
rename from tests/integrated/test-naulin-laplace/runtest
rename to tests/integrated/test-naulin-laplace/test_naulin_laplace.py
diff --git a/tests/integrated/test-options-adios/test_options_adios.py b/tests/integrated/test-options-adios/test_options_adios.py
new file mode 100755
index 0000000000..03a83fc0ba
--- /dev/null
+++ b/tests/integrated/test-options-adios/test_options_adios.py
@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+
+# Note: This test requires NCDF4, whereas on Travis NCDF is used
+# requires: netcdf
+# requires: adios
+# requires: not legacy_netcdf
+
+from boututils.datafile import DataFile
+from boututils.run_wrapper import build_and_log, shell, launch
+from boutdata.data import BoutOptionsFile
+
+import math
+import numpy as np
+
+build_and_log("options-netcdf test")
+shell("rm -f test-out.ini")
+shell("rm -f test-out.nc")
+
+# Create a NetCDF input file
+with DataFile("test.nc", create=True, format="NETCDF4") as f:
+    f.write("int", 42)
+    f.write("real", 3.1415)
+    f.write("string", "hello")
+
+# run BOUT++
+launch("./test-options-adios", nproc=1, mthread=1)
+
+# Check the output INI file
+result = BoutOptionsFile("test-out.ini")
+
+print(result)
+
+assert result["int"] == 42
+assert math.isclose(result["real"], 3.1415)
+assert result["string"] == "hello"
+
+print("Checking saved ADIOS2 test-out file -- Not implemented")
+
+# Check the output NetCDF file
+# with DataFile("test-out.nc") as f:
+#    assert f["int"] == 42
+#    assert math.isclose(f["real"], 3.1415)
+#    assert result["string"] == "hello"
+
+print("Checking saved settings.ini")
+
+# Check the settings.ini file, coming from BOUT.inp
+# which is converted to NetCDF, read in, then written again
+settings = BoutOptionsFile("settings.ini")
+
+assert settings["mesh"]["nx"] == 5
+assert settings["mesh"]["ny"] == 2
+
+print("Checking saved fields.bp -- Not implemented")
+
+# with DataFile("fields.nc") as f:
+#    assert f["f2d"].shape == (5, 6)  # Field2D
+#    assert f["f3d"].shape == (5, 6, 2)  # Field3D
+#    assert f["fperp"].shape == (5, 2)  # FieldPerp
+#    assert np.allclose(f["f2d"], 1.0)
+#    assert np.allclose(f["f3d"], 2.0)
+#    assert np.allclose(f["fperp"], 3.0)
+
+print("Checking saved fields2.bp -- Not implemented")
+
+# with DataFile("fields2.nc") as f:
+#    assert f["f2d"].shape == (5, 6)  # Field2D
+#    assert f["f3d"].shape == (5, 6, 2)  # Field3D
+#    assert f["fperp"].shape == (5, 2)  # FieldPerp
+#    assert np.allclose(f["f2d"], 1.0)
+#    assert np.allclose(f["f3d"], 2.0)
+#    assert np.allclose(f["fperp"], 3.0)
+
+print(" => Passed")
diff --git a/tests/integrated/test-options-netcdf/runtest b/tests/integrated/test-options-netcdf/test_options_netcdf.py
similarity index 100%
rename from tests/integrated/test-options-netcdf/runtest
rename to tests/integrated/test-options-netcdf/test_options_netcdf.py
diff --git a/tests/integrated/test-petsc_laplace/runtest b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
similarity index 100%
rename from tests/integrated/test-petsc_laplace/runtest
rename to tests/integrated/test-petsc_laplace/test_petsc_laplace.py
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/runtest b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
similarity index 100%
rename from tests/integrated/test-petsc_laplace_MAST-grid/runtest
rename to tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
diff --git a/tests/integrated/test-region-iterator/runtest b/tests/integrated/test-region-iterator/test_region_iterator.py
similarity index 100%
rename from tests/integrated/test-region-iterator/runtest
rename to tests/integrated/test-region-iterator/test_region_iterator.py
diff --git a/tests/integrated/test-restart-io/runtest b/tests/integrated/test-restart-io/test_restart_io.py
similarity index 100%
rename from tests/integrated/test-restart-io/runtest
rename to tests/integrated/test-restart-io/test_restart_io.py
diff --git a/tests/integrated/test-restarting/runtest b/tests/integrated/test-restarting/test_restarting.py
similarity index 100%
rename from tests/integrated/test-restarting/runtest
rename to tests/integrated/test-restarting/test_restarting.py
diff --git a/tests/integrated/test-slepc-solver/runtest b/tests/integrated/test-slepc-solver/test_slepc_solver.py
similarity index 100%
rename from tests/integrated/test-slepc-solver/runtest
rename to tests/integrated/test-slepc-solver/test_slepc_solver.py
diff --git a/tests/integrated/test-smooth/runtest b/tests/integrated/test-smooth/test_smooth.py
similarity index 100%
rename from tests/integrated/test-smooth/runtest
rename to tests/integrated/test-smooth/test_smooth.py
diff --git a/tests/integrated/test-snb/runtest b/tests/integrated/test-snb/test_snb.py
similarity index 100%
rename from tests/integrated/test-snb/runtest
rename to tests/integrated/test-snb/test_snb.py
diff --git a/tests/integrated/test-solver/runtest b/tests/integrated/test-solver/test_solver.py
similarity index 100%
rename from tests/integrated/test-solver/runtest
rename to tests/integrated/test-solver/test_solver.py
diff --git a/tests/integrated/test-squash/runtest b/tests/integrated/test-squash/test_squash.py
similarity index 100%
rename from tests/integrated/test-squash/runtest
rename to tests/integrated/test-squash/test_squash.py
diff --git a/tests/integrated/test-stopCheck-file/runtest b/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
similarity index 100%
rename from tests/integrated/test-stopCheck-file/runtest
rename to tests/integrated/test-stopCheck-file/test_stopCheck_file.py
diff --git a/tests/integrated/test-stopCheck/runtest b/tests/integrated/test-stopCheck/test_stopCheck.py
similarity index 100%
rename from tests/integrated/test-stopCheck/runtest
rename to tests/integrated/test-stopCheck/test_stopCheck.py
diff --git a/tests/integrated/test-subdir/runtest b/tests/integrated/test-subdir/test_subdir.py
similarity index 100%
rename from tests/integrated/test-subdir/runtest
rename to tests/integrated/test-subdir/test_subdir.py
diff --git a/tests/integrated/test-twistshift-staggered/runtest b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
similarity index 100%
rename from tests/integrated/test-twistshift-staggered/runtest
rename to tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
diff --git a/tests/integrated/test-twistshift/runtest b/tests/integrated/test-twistshift/test_twistshift.py
similarity index 100%
rename from tests/integrated/test-twistshift/runtest
rename to tests/integrated/test-twistshift/test_twistshift.py
diff --git a/tests/integrated/test-vec/runtest b/tests/integrated/test-vec/test_vec.py
similarity index 100%
rename from tests/integrated/test-vec/runtest
rename to tests/integrated/test-vec/test_vec.py
diff --git a/tests/integrated/test-yupdown-weights/runtest b/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
similarity index 100%
rename from tests/integrated/test-yupdown-weights/runtest
rename to tests/integrated/test-yupdown-weights/test_yupdown_weights.py
diff --git a/tests/integrated/test-yupdown/runtest b/tests/integrated/test-yupdown/test_yupdown.py
similarity index 100%
rename from tests/integrated/test-yupdown/runtest
rename to tests/integrated/test-yupdown/test_yupdown.py

From 053f62a4531d1016c5419a4b533eb9d3b20710e8 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 12:35:57 +0000
Subject: [PATCH 0963/1827] Rename runtest file to test-foo.py for each MMS
 test

---
 tests/MMS/advection/{runtest => test_advection.py}                | 0
 tests/MMS/bracket/{runtest => test_bracket.py}                    | 0
 tests/MMS/derivatives3/{runtest => test_derivatives3.py}          | 0
 tests/MMS/diffusion/{runtest => test_diffusion.py}                | 0
 tests/MMS/diffusion2/{runtest => test_diffusion2.py}              | 0
 tests/MMS/hw/{runtest => test_hw.py}                              | 0
 tests/MMS/laplace/{runtest => test_laplace.py}                    | 0
 .../shiftedmetricinterp/{runtest => test_shiftedmetricinterp.py}  | 0
 tests/MMS/time-petsc/{runtest => test_time_petsc.py}              | 0
 tests/MMS/time/{runtest => test_time.py}                          | 0
 tests/MMS/upwinding3/{runtest => test_upwinding3.py}              | 0
 tests/MMS/wave-1d-y/{runtest => test_wave_1d_y.py}                | 0
 tests/MMS/wave-1d/{runtest => test_wave_1d.py}                    | 0
 13 files changed, 0 insertions(+), 0 deletions(-)
 rename tests/MMS/advection/{runtest => test_advection.py} (100%)
 rename tests/MMS/bracket/{runtest => test_bracket.py} (100%)
 rename tests/MMS/derivatives3/{runtest => test_derivatives3.py} (100%)
 rename tests/MMS/diffusion/{runtest => test_diffusion.py} (100%)
 rename tests/MMS/diffusion2/{runtest => test_diffusion2.py} (100%)
 rename tests/MMS/hw/{runtest => test_hw.py} (100%)
 rename tests/MMS/laplace/{runtest => test_laplace.py} (100%)
 rename tests/MMS/shiftedmetricinterp/{runtest => test_shiftedmetricinterp.py} (100%)
 rename tests/MMS/time-petsc/{runtest => test_time_petsc.py} (100%)
 rename tests/MMS/time/{runtest => test_time.py} (100%)
 rename tests/MMS/upwinding3/{runtest => test_upwinding3.py} (100%)
 rename tests/MMS/wave-1d-y/{runtest => test_wave_1d_y.py} (100%)
 rename tests/MMS/wave-1d/{runtest => test_wave_1d.py} (100%)

diff --git a/tests/MMS/advection/runtest b/tests/MMS/advection/test_advection.py
similarity index 100%
rename from tests/MMS/advection/runtest
rename to tests/MMS/advection/test_advection.py
diff --git a/tests/MMS/bracket/runtest b/tests/MMS/bracket/test_bracket.py
similarity index 100%
rename from tests/MMS/bracket/runtest
rename to tests/MMS/bracket/test_bracket.py
diff --git a/tests/MMS/derivatives3/runtest b/tests/MMS/derivatives3/test_derivatives3.py
similarity index 100%
rename from tests/MMS/derivatives3/runtest
rename to tests/MMS/derivatives3/test_derivatives3.py
diff --git a/tests/MMS/diffusion/runtest b/tests/MMS/diffusion/test_diffusion.py
similarity index 100%
rename from tests/MMS/diffusion/runtest
rename to tests/MMS/diffusion/test_diffusion.py
diff --git a/tests/MMS/diffusion2/runtest b/tests/MMS/diffusion2/test_diffusion2.py
similarity index 100%
rename from tests/MMS/diffusion2/runtest
rename to tests/MMS/diffusion2/test_diffusion2.py
diff --git a/tests/MMS/hw/runtest b/tests/MMS/hw/test_hw.py
similarity index 100%
rename from tests/MMS/hw/runtest
rename to tests/MMS/hw/test_hw.py
diff --git a/tests/MMS/laplace/runtest b/tests/MMS/laplace/test_laplace.py
similarity index 100%
rename from tests/MMS/laplace/runtest
rename to tests/MMS/laplace/test_laplace.py
diff --git a/tests/MMS/shiftedmetricinterp/runtest b/tests/MMS/shiftedmetricinterp/test_shiftedmetricinterp.py
similarity index 100%
rename from tests/MMS/shiftedmetricinterp/runtest
rename to tests/MMS/shiftedmetricinterp/test_shiftedmetricinterp.py
diff --git a/tests/MMS/time-petsc/runtest b/tests/MMS/time-petsc/test_time_petsc.py
similarity index 100%
rename from tests/MMS/time-petsc/runtest
rename to tests/MMS/time-petsc/test_time_petsc.py
diff --git a/tests/MMS/time/runtest b/tests/MMS/time/test_time.py
similarity index 100%
rename from tests/MMS/time/runtest
rename to tests/MMS/time/test_time.py
diff --git a/tests/MMS/upwinding3/runtest b/tests/MMS/upwinding3/test_upwinding3.py
similarity index 100%
rename from tests/MMS/upwinding3/runtest
rename to tests/MMS/upwinding3/test_upwinding3.py
diff --git a/tests/MMS/wave-1d-y/runtest b/tests/MMS/wave-1d-y/test_wave_1d_y.py
similarity index 100%
rename from tests/MMS/wave-1d-y/runtest
rename to tests/MMS/wave-1d-y/test_wave_1d_y.py
diff --git a/tests/MMS/wave-1d/runtest b/tests/MMS/wave-1d/test_wave_1d.py
similarity index 100%
rename from tests/MMS/wave-1d/runtest
rename to tests/MMS/wave-1d/test_wave_1d.py

From db341439ab1d8c884ea7c655d704fc546608c213 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 9 Oct 2025 14:41:46 +0100
Subject: [PATCH 0964/1827] Convert runtest file to use pytest for
 test_drift_instability

---
 .../{runtest => test_drift_instability.py}    | 48 +++++++------------
 1 file changed, 18 insertions(+), 30 deletions(-)
 rename tests/integrated/test-drift-instability/{runtest => test_drift_instability.py} (89%)
 mode change 100755 => 100644

diff --git a/tests/integrated/test-drift-instability/runtest b/tests/integrated/test-drift-instability/test_drift_instability.py
old mode 100755
new mode 100644
similarity index 89%
rename from tests/integrated/test-drift-instability/runtest
rename to tests/integrated/test-drift-instability/test_drift_instability.py
index 1fae82100b..ad911e6028
--- a/tests/integrated/test-drift-instability/runtest
+++ b/tests/integrated/test-drift-instability/test_drift_instability.py
@@ -6,15 +6,14 @@
 
 # Requires: not metric_3d
 
+import pytest
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boututils.calculus import deriv
 from boututils.datafile import DataFile
 from boututils.linear_regression import linear_regression
 
 from boutdata.collect import collect
-import argparse
 import numpy as np
-from sys import exit
 from math import isnan
 
 nthreads = 1
@@ -52,11 +51,17 @@
 }  # 0.130220286897} Changed 25th April 2014
 
 
-def run_zeff_case(zeff):
-    """Run a single Zeff case"""
+@pytest.fixture(scope="module")
+def build_project():
+    """Build the project once per test module."""
+    build_and_log("resistive drift instability test")
+
+
+def run_zeff_case(zeff, build_project):
+    """Run a single Zeff case and return success flag and details."""
 
     if zeff not in omega_orig:
-        raise ValueError(
+        pytest.fail(
             f"Zeff value ({zeff}) not in benchmark values. Available values: {list(omega_orig.keys())}"
         )
 
@@ -192,32 +197,15 @@ def run_zeff_case(zeff):
     )
 
     if isnan(omegadiff) or (omegadiff > omega_tol) or (gammadiff > gamma_tol):
-        print("  => FAILED")
-        return False
-
-    print("  => PASSED")
-    return True
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser("Run drift-instability test")
-    parser.add_argument(
-        "-Z",
-        "--Zeff-list",
-        help=f"List of Zeff values to test, valid values are {list(gamma_orig.keys())}",
-        type=int,
-        nargs="+",
-        default=zlist,
-    )
+        return False, omegadiff, gammadiff
 
-    args = parser.parse_args()
+    return True, omegadiff, gammadiff
 
-    build_and_log("resistive drift instability test")
 
-    return_code = 0
-    for zeff in args.Zeff_list:
-        success = run_zeff_case(zeff)
-        if not success:
-            return_code = 1
+@pytest.mark.parametrize("zeff", zlist)
+def test_zeff_case(zeff, build_project):
+    """Pytest wrapper for running a single Zeff case."""
+    success, omegadiff, gammadiff = run_zeff_case(zeff, build_project)
+    
+    assert success, f"Test failed for Zeff={zeff}: omega diff={omegadiff:.2%}, gamma diff={gammadiff:.2%}"
 
-    exit(return_code)

From 0ed07501929fe724103e1266a2a6cb8a96a7221d Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 15:05:11 +0000
Subject: [PATCH 0965/1827] Handle test files for tests named either `test-foo`
 or `foo` matching either to a file named `test_foo.py`.

---
 cmake/BOUT++functions.cmake | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index c9ff1fbcb8..af660bc755 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -259,7 +259,8 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
       ${TESTNAME} PROPERTIES ENVIRONMENT
                              PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
     )
-    bout_copy_file(${TESTNAME}.py)
+    string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILNAME "${TESTNAME}")
+	bout_copy_file(${TEST_FILNAME})
   else()
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()

From fdd93e075ff9c8976bb0b63c932a8a641369642a Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 16:25:23 +0000
Subject: [PATCH 0966/1827] Handle test files with hyphens or prefixed with

---
 cmake/BOUT++functions.cmake | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index af660bc755..2cb7506188 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -259,8 +259,9 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
       ${TESTNAME} PROPERTIES ENVIRONMENT
                              PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
     )
-    string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILNAME "${TESTNAME}")
-	bout_copy_file(${TEST_FILNAME})
+    string(REGEX REPLACE "^(test-|MMS-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
+    string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
+	bout_copy_file(${TEST_FILENAME})
   else()
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()

From f0b4405efdb14c92cc08003071c20f33580367e4 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 16:45:16 +0000
Subject: [PATCH 0967/1827] Update symlink to renamed runtest file

---
 .../legacy-model/{runtest => test_boutpp_legacy_model.py}       | 0
 .../test_drift_instability_staggered.py                         | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename tests/integrated/test-boutpp/legacy-model/{runtest => test_boutpp_legacy_model.py} (100%)

diff --git a/tests/integrated/test-boutpp/legacy-model/runtest b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
similarity index 100%
rename from tests/integrated/test-boutpp/legacy-model/runtest
rename to tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
diff --git a/tests/integrated/test-drift-instability-staggered/test_drift_instability_staggered.py b/tests/integrated/test-drift-instability-staggered/test_drift_instability_staggered.py
index 3b7f341ec9..4d475962e6 120000
--- a/tests/integrated/test-drift-instability-staggered/test_drift_instability_staggered.py
+++ b/tests/integrated/test-drift-instability-staggered/test_drift_instability_staggered.py
@@ -1 +1 @@
-../test-drift-instability/runtest
\ No newline at end of file
+../test-drift-instability/test_drift_instability.py
\ No newline at end of file

From 4dd41cc2effcfdd12e4d8015879675d42e1c226e Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 17:40:43 +0000
Subject: [PATCH 0968/1827] Rename more runtest files

---
 .../MMS/advection/arakawa/{runtest => test_advection_arakawa.py}  | 0
 .../MMS/advection/central/{runtest => test_advection_central.py}  | 0
 tests/MMS/advection/upwind/{runtest => test_advection_upwind.py}  | 0
 tests/MMS/advection/weno3/{runtest => test_advection_weno3.py}    | 0
 tests/MMS/spatial/advection/{runtest => test_advection.py}        | 0
 tests/MMS/spatial/d2dx2/{runtest => test_d2dx2.py}                | 0
 tests/MMS/spatial/d2dz2/{runtest => test_d2dz2.py}                | 0
 tests/MMS/spatial/diffusion/{runtest => test_diffusion.py}        | 0
 tests/MMS/spatial/fci/{runtest => test_fci.py}                    | 0
 .../{test_datafilefacade.py => test_datafile_facade.py}           | 0
 10 files changed, 0 insertions(+), 0 deletions(-)
 rename tests/MMS/advection/arakawa/{runtest => test_advection_arakawa.py} (100%)
 rename tests/MMS/advection/central/{runtest => test_advection_central.py} (100%)
 rename tests/MMS/advection/upwind/{runtest => test_advection_upwind.py} (100%)
 rename tests/MMS/advection/weno3/{runtest => test_advection_weno3.py} (100%)
 rename tests/MMS/spatial/advection/{runtest => test_advection.py} (100%)
 rename tests/MMS/spatial/d2dx2/{runtest => test_d2dx2.py} (100%)
 rename tests/MMS/spatial/d2dz2/{runtest => test_d2dz2.py} (100%)
 rename tests/MMS/spatial/diffusion/{runtest => test_diffusion.py} (100%)
 rename tests/MMS/spatial/fci/{runtest => test_fci.py} (100%)
 rename tests/integrated/test-datafilefacade/{test_datafilefacade.py => test_datafile_facade.py} (100%)

diff --git a/tests/MMS/advection/arakawa/runtest b/tests/MMS/advection/arakawa/test_advection_arakawa.py
similarity index 100%
rename from tests/MMS/advection/arakawa/runtest
rename to tests/MMS/advection/arakawa/test_advection_arakawa.py
diff --git a/tests/MMS/advection/central/runtest b/tests/MMS/advection/central/test_advection_central.py
similarity index 100%
rename from tests/MMS/advection/central/runtest
rename to tests/MMS/advection/central/test_advection_central.py
diff --git a/tests/MMS/advection/upwind/runtest b/tests/MMS/advection/upwind/test_advection_upwind.py
similarity index 100%
rename from tests/MMS/advection/upwind/runtest
rename to tests/MMS/advection/upwind/test_advection_upwind.py
diff --git a/tests/MMS/advection/weno3/runtest b/tests/MMS/advection/weno3/test_advection_weno3.py
similarity index 100%
rename from tests/MMS/advection/weno3/runtest
rename to tests/MMS/advection/weno3/test_advection_weno3.py
diff --git a/tests/MMS/spatial/advection/runtest b/tests/MMS/spatial/advection/test_advection.py
similarity index 100%
rename from tests/MMS/spatial/advection/runtest
rename to tests/MMS/spatial/advection/test_advection.py
diff --git a/tests/MMS/spatial/d2dx2/runtest b/tests/MMS/spatial/d2dx2/test_d2dx2.py
similarity index 100%
rename from tests/MMS/spatial/d2dx2/runtest
rename to tests/MMS/spatial/d2dx2/test_d2dx2.py
diff --git a/tests/MMS/spatial/d2dz2/runtest b/tests/MMS/spatial/d2dz2/test_d2dz2.py
similarity index 100%
rename from tests/MMS/spatial/d2dz2/runtest
rename to tests/MMS/spatial/d2dz2/test_d2dz2.py
diff --git a/tests/MMS/spatial/diffusion/runtest b/tests/MMS/spatial/diffusion/test_diffusion.py
similarity index 100%
rename from tests/MMS/spatial/diffusion/runtest
rename to tests/MMS/spatial/diffusion/test_diffusion.py
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/test_fci.py
similarity index 100%
rename from tests/MMS/spatial/fci/runtest
rename to tests/MMS/spatial/fci/test_fci.py
diff --git a/tests/integrated/test-datafilefacade/test_datafilefacade.py b/tests/integrated/test-datafilefacade/test_datafile_facade.py
similarity index 100%
rename from tests/integrated/test-datafilefacade/test_datafilefacade.py
rename to tests/integrated/test-datafilefacade/test_datafile_facade.py

From 0fa8b818c54204dbe5a2098abd585236005d0355 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 17:45:35 +0000
Subject: [PATCH 0969/1827] Change filename Test run by tpc522 on Mon Nov  3
 17:45:34 2025 Native configuration is x86_64-pc-linux-gnu

		===  tests ===

Schedule of variations:
    unix

Running target unix
Using /usr/share/dejagnu/baseboards/unix.exp as board description file for target.
Using /usr/share/dejagnu/config/unix.exp as generic interface file for target.

		===  Summary === to  in CMakeLists.txt
---
 tests/MMS/advection/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/MMS/advection/CMakeLists.txt b/tests/MMS/advection/CMakeLists.txt
index 1e08b97cd1..b2a037bac6 100644
--- a/tests/MMS/advection/CMakeLists.txt
+++ b/tests/MMS/advection/CMakeLists.txt
@@ -3,7 +3,7 @@ target_link_libraries(MMS-advection bout++)
 set_target_properties(MMS-advection PROPERTIES FOLDER tests/MMS)
 set_target_properties(MMS-advection PROPERTIES OUTPUT_NAME advection)
 add_dependencies(build-check-mms-tests MMS-advection)
-bout_copy_file(runtest)
+bout_copy_file(test_advection.py)
 bout_copy_file(data/BOUT.inp)
 
 add_subdirectory(arakawa)

From f9e237431a2d471564895fcbf996857d259adab4 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 18:33:57 +0000
Subject: [PATCH 0970/1827] Rename more runtest files

---
 .../collect-staggered/{runtest => test_collect_staggered.py}      | 0
 tests/integrated/test-boutpp/collect/{runtest => test_collect.py} | 0
 tests/integrated/test-boutpp/mms-ddz/{runtest => test_ddz.py}     | 0
 tests/integrated/test-boutpp/print/{runtest => test_print.py}     | 0
 .../test-boutpp/simple-model/{runtest => simple_model.py}         | 0
 tests/integrated/test-boutpp/slicing/{runtest => test_slicing.py} | 0
 6 files changed, 0 insertions(+), 0 deletions(-)
 rename tests/integrated/test-boutpp/collect-staggered/{runtest => test_collect_staggered.py} (100%)
 rename tests/integrated/test-boutpp/collect/{runtest => test_collect.py} (100%)
 rename tests/integrated/test-boutpp/mms-ddz/{runtest => test_ddz.py} (100%)
 rename tests/integrated/test-boutpp/print/{runtest => test_print.py} (100%)
 rename tests/integrated/test-boutpp/simple-model/{runtest => simple_model.py} (100%)
 rename tests/integrated/test-boutpp/slicing/{runtest => test_slicing.py} (100%)

diff --git a/tests/integrated/test-boutpp/collect-staggered/runtest b/tests/integrated/test-boutpp/collect-staggered/test_collect_staggered.py
similarity index 100%
rename from tests/integrated/test-boutpp/collect-staggered/runtest
rename to tests/integrated/test-boutpp/collect-staggered/test_collect_staggered.py
diff --git a/tests/integrated/test-boutpp/collect/runtest b/tests/integrated/test-boutpp/collect/test_collect.py
similarity index 100%
rename from tests/integrated/test-boutpp/collect/runtest
rename to tests/integrated/test-boutpp/collect/test_collect.py
diff --git a/tests/integrated/test-boutpp/mms-ddz/runtest b/tests/integrated/test-boutpp/mms-ddz/test_ddz.py
similarity index 100%
rename from tests/integrated/test-boutpp/mms-ddz/runtest
rename to tests/integrated/test-boutpp/mms-ddz/test_ddz.py
diff --git a/tests/integrated/test-boutpp/print/runtest b/tests/integrated/test-boutpp/print/test_print.py
similarity index 100%
rename from tests/integrated/test-boutpp/print/runtest
rename to tests/integrated/test-boutpp/print/test_print.py
diff --git a/tests/integrated/test-boutpp/simple-model/runtest b/tests/integrated/test-boutpp/simple-model/simple_model.py
similarity index 100%
rename from tests/integrated/test-boutpp/simple-model/runtest
rename to tests/integrated/test-boutpp/simple-model/simple_model.py
diff --git a/tests/integrated/test-boutpp/slicing/runtest b/tests/integrated/test-boutpp/slicing/test_slicing.py
similarity index 100%
rename from tests/integrated/test-boutpp/slicing/runtest
rename to tests/integrated/test-boutpp/slicing/test_slicing.py

From d00629c4f0ee9006caedb59a2cc009d8ae8d5b78 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 18:37:37 +0000
Subject: [PATCH 0971/1827] Use PATH-based pytest executable

---
 cmake/BOUT++functions.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 2cb7506188..32983f33c4 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -253,8 +253,8 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
   endif()
 
   # Set the actual test command
-  if(BOUT_TEST_OPTIONS_USE_RUNTEST)
-    add_test(NAME ${TESTNAME} COMMAND ./pytest ${BOUT_TEST_OPTIONS_TESTARGS})
+  if (BOUT_TEST_OPTIONS_USE_RUNTEST)
+    add_test(NAME ${TESTNAME} COMMAND pytest ${BOUT_TEST_OPTIONS_TESTARGS})
     set_tests_properties(
       ${TESTNAME} PROPERTIES ENVIRONMENT
                              PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}

From 393ac3e8cc9946c39f8cf956ccbd7c7ba51649c0 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 3 Nov 2025 18:46:24 +0000
Subject: [PATCH 0972/1827] Fix more renamings

---
 tests/MMS/spatial/fci/{test_fci.py => test_spatial_fci.py}        | 0
 ...test_collect_staggered.py => test_boutpp_collect_staggered.py} | 0
 .../collect/{test_collect.py => test_boutpp_collect.py}           | 0
 .../test-boutpp/mms-ddz/{test_ddz.py => test_boutpp_mms_ddz.py}   | 0
 .../test-boutpp/print/{test_print.py => test_boutpp_print.py}     | 0
 .../simple-model/{simple_model.py => test_boutpp_simple_model.py} | 0
 6 files changed, 0 insertions(+), 0 deletions(-)
 rename tests/MMS/spatial/fci/{test_fci.py => test_spatial_fci.py} (100%)
 rename tests/integrated/test-boutpp/collect-staggered/{test_collect_staggered.py => test_boutpp_collect_staggered.py} (100%)
 rename tests/integrated/test-boutpp/collect/{test_collect.py => test_boutpp_collect.py} (100%)
 rename tests/integrated/test-boutpp/mms-ddz/{test_ddz.py => test_boutpp_mms_ddz.py} (100%)
 rename tests/integrated/test-boutpp/print/{test_print.py => test_boutpp_print.py} (100%)
 rename tests/integrated/test-boutpp/simple-model/{simple_model.py => test_boutpp_simple_model.py} (100%)

diff --git a/tests/MMS/spatial/fci/test_fci.py b/tests/MMS/spatial/fci/test_spatial_fci.py
similarity index 100%
rename from tests/MMS/spatial/fci/test_fci.py
rename to tests/MMS/spatial/fci/test_spatial_fci.py
diff --git a/tests/integrated/test-boutpp/collect-staggered/test_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
similarity index 100%
rename from tests/integrated/test-boutpp/collect-staggered/test_collect_staggered.py
rename to tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
diff --git a/tests/integrated/test-boutpp/collect/test_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
similarity index 100%
rename from tests/integrated/test-boutpp/collect/test_collect.py
rename to tests/integrated/test-boutpp/collect/test_boutpp_collect.py
diff --git a/tests/integrated/test-boutpp/mms-ddz/test_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
similarity index 100%
rename from tests/integrated/test-boutpp/mms-ddz/test_ddz.py
rename to tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
diff --git a/tests/integrated/test-boutpp/print/test_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
similarity index 100%
rename from tests/integrated/test-boutpp/print/test_print.py
rename to tests/integrated/test-boutpp/print/test_boutpp_print.py
diff --git a/tests/integrated/test-boutpp/simple-model/simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
similarity index 100%
rename from tests/integrated/test-boutpp/simple-model/simple_model.py
rename to tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py

From 4deaf22be4efdd70b890898b0d70a529f96f47a3 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 5 Nov 2025 15:42:41 +0000
Subject: [PATCH 0973/1827] Change custom_target check-integrated-tests to use
 pytest instead of ctest

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5f054c1c1f..e37559b598 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -766,7 +766,7 @@ if(BOUT_TESTS)
   endif()
 
   add_custom_target(
-    check-integrated-tests COMMAND ctest -R "test-" --output-on-failure
+    check-integrated-tests COMMAND pytest -k "test-"
   )
   add_dependencies(check-integrated-tests build-check-integrated-tests)
 

From 82ff7caf13612a4e3f7299cd8c1cf3c59eddb6f5 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 5 Nov 2025 21:35:29 +0000
Subject: [PATCH 0974/1827] Some `runtest` files are shell scripts not python
 scripts, so revert renaming

---
 .../{test_bout_override_default_option.py => runtest}             | 0
 .../test-boutpp/print/{test_boutpp_print.py => runtest}           | 0
 tests/integrated/test-code-style/{test_code_style.py => runtest}  | 0
 .../{test_compile_examples_petsc.py => runtest}                   | 0
 .../test-compile-examples/{test_compile_examples.py => runtest}   | 0
 .../{test_coordinates_initialization.py => runtest}               | 0
 tests/integrated/test-include/{test_include.py => runtest}        | 0
 tests/integrated/test-snb/{test_snb.py => runtest}                | 0
 tests/integrated/test-stopCheck/{test_stopCheck.py => runtest}    | 0
 tests/integrated/test-subdir/{test_subdir.py => runtest}          | 0
 10 files changed, 0 insertions(+), 0 deletions(-)
 rename tests/integrated/test-bout-override-default-option/{test_bout_override_default_option.py => runtest} (100%)
 rename tests/integrated/test-boutpp/print/{test_boutpp_print.py => runtest} (100%)
 rename tests/integrated/test-code-style/{test_code_style.py => runtest} (100%)
 rename tests/integrated/test-compile-examples-petsc/{test_compile_examples_petsc.py => runtest} (100%)
 rename tests/integrated/test-compile-examples/{test_compile_examples.py => runtest} (100%)
 rename tests/integrated/test-coordinates-initialization/{test_coordinates_initialization.py => runtest} (100%)
 rename tests/integrated/test-include/{test_include.py => runtest} (100%)
 rename tests/integrated/test-snb/{test_snb.py => runtest} (100%)
 rename tests/integrated/test-stopCheck/{test_stopCheck.py => runtest} (100%)
 rename tests/integrated/test-subdir/{test_subdir.py => runtest} (100%)

diff --git a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py b/tests/integrated/test-bout-override-default-option/runtest
similarity index 100%
rename from tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
rename to tests/integrated/test-bout-override-default-option/runtest
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/runtest
similarity index 100%
rename from tests/integrated/test-boutpp/print/test_boutpp_print.py
rename to tests/integrated/test-boutpp/print/runtest
diff --git a/tests/integrated/test-code-style/test_code_style.py b/tests/integrated/test-code-style/runtest
similarity index 100%
rename from tests/integrated/test-code-style/test_code_style.py
rename to tests/integrated/test-code-style/runtest
diff --git a/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py b/tests/integrated/test-compile-examples-petsc/runtest
similarity index 100%
rename from tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
rename to tests/integrated/test-compile-examples-petsc/runtest
diff --git a/tests/integrated/test-compile-examples/test_compile_examples.py b/tests/integrated/test-compile-examples/runtest
similarity index 100%
rename from tests/integrated/test-compile-examples/test_compile_examples.py
rename to tests/integrated/test-compile-examples/runtest
diff --git a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py b/tests/integrated/test-coordinates-initialization/runtest
similarity index 100%
rename from tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
rename to tests/integrated/test-coordinates-initialization/runtest
diff --git a/tests/integrated/test-include/test_include.py b/tests/integrated/test-include/runtest
similarity index 100%
rename from tests/integrated/test-include/test_include.py
rename to tests/integrated/test-include/runtest
diff --git a/tests/integrated/test-snb/test_snb.py b/tests/integrated/test-snb/runtest
similarity index 100%
rename from tests/integrated/test-snb/test_snb.py
rename to tests/integrated/test-snb/runtest
diff --git a/tests/integrated/test-stopCheck/test_stopCheck.py b/tests/integrated/test-stopCheck/runtest
similarity index 100%
rename from tests/integrated/test-stopCheck/test_stopCheck.py
rename to tests/integrated/test-stopCheck/runtest
diff --git a/tests/integrated/test-subdir/test_subdir.py b/tests/integrated/test-subdir/runtest
similarity index 100%
rename from tests/integrated/test-subdir/test_subdir.py
rename to tests/integrated/test-subdir/runtest

From 681c2fb9112c2376586af0205b0bc16ec391cd02 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 11 Nov 2025 13:13:31 +0000
Subject: [PATCH 0975/1827] Add python tests to run those `runtest` files that
 are not python scripts

---
 .../test_bout_override_default_option.py      | 35 +++++++++++++++++++
 .../test-boutpp/print/test_boutpp_print.py    | 35 +++++++++++++++++++
 .../test-code-style/test_code_style.py        | 35 +++++++++++++++++++
 .../test_compile_examples_petsc.py            | 35 +++++++++++++++++++
 .../test_compile_examples.py                  | 35 +++++++++++++++++++
 .../test_coordinates_initialization.py        | 35 +++++++++++++++++++
 tests/integrated/test-include/test_include.py | 35 +++++++++++++++++++
 tests/integrated/test-snb/test_snb.py         | 35 +++++++++++++++++++
 .../test-stopCheck/test_stopCheck.py          | 35 +++++++++++++++++++
 tests/integrated/test-subdir/test_subdir.py   | 35 +++++++++++++++++++
 10 files changed, 350 insertions(+)
 create mode 100644 tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
 create mode 100644 tests/integrated/test-boutpp/print/test_boutpp_print.py
 create mode 100644 tests/integrated/test-code-style/test_code_style.py
 create mode 100644 tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
 create mode 100644 tests/integrated/test-compile-examples/test_compile_examples.py
 create mode 100644 tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
 create mode 100644 tests/integrated/test-include/test_include.py
 create mode 100644 tests/integrated/test-snb/test_snb.py
 create mode 100644 tests/integrated/test-stopCheck/test_stopCheck.py
 create mode 100644 tests/integrated/test-subdir/test_subdir.py

diff --git a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
diff --git a/tests/integrated/test-code-style/test_code_style.py b/tests/integrated/test-code-style/test_code_style.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-code-style/test_code_style.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
diff --git a/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py b/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
diff --git a/tests/integrated/test-compile-examples/test_compile_examples.py b/tests/integrated/test-compile-examples/test_compile_examples.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-compile-examples/test_compile_examples.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
diff --git a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
diff --git a/tests/integrated/test-include/test_include.py b/tests/integrated/test-include/test_include.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-include/test_include.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
diff --git a/tests/integrated/test-snb/test_snb.py b/tests/integrated/test-snb/test_snb.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-snb/test_snb.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
diff --git a/tests/integrated/test-stopCheck/test_stopCheck.py b/tests/integrated/test-stopCheck/test_stopCheck.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-stopCheck/test_stopCheck.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
diff --git a/tests/integrated/test-subdir/test_subdir.py b/tests/integrated/test-subdir/test_subdir.py
new file mode 100644
index 0000000000..32e052f0bd
--- /dev/null
+++ b/tests/integrated/test-subdir/test_subdir.py
@@ -0,0 +1,35 @@
+import os
+import subprocess
+import time
+
+
+def test_runtest():
+    # BOUT_TOP from script dir (CWD-independent)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
+    os.environ["BOUT_TOP"] = bout_root
+
+    # Add pylib (dependencies like boutdata) to PYTHONPATH
+    pylib_path = os.path.join(bout_root, "tools", "pylib")
+    if os.path.exists(pylib_path):
+        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
+
+    test_dir = os.path.dirname(os.path.abspath(__file__))
+    # Pre-build for dependencies like grid.fci.nc
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+
+    os.chdir(test_dir)
+
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file

From 01cc49c793c3dbcc08def534263cec5197a100f7 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 11 Nov 2025 13:55:52 +0000
Subject: [PATCH 0976/1827] Convert test_cyclic.py to a valid pytest file

---
 tests/integrated/test-cyclic/test_cyclic.py | 51 +++++++++++----------
 1 file changed, 26 insertions(+), 25 deletions(-)

diff --git a/tests/integrated/test-cyclic/test_cyclic.py b/tests/integrated/test-cyclic/test_cyclic.py
index c68f9b033e..0a0733926b 100755
--- a/tests/integrated/test-cyclic/test_cyclic.py
+++ b/tests/integrated/test-cyclic/test_cyclic.py
@@ -15,40 +15,41 @@
     pass
 from boututils.run_wrapper import build_and_log, shell, launch
 from boutdata.collect import collect
-from sys import stdout, exit
+from sys import stdout
 
 build_and_log("Cyclic Reduction test")
 
 flags = ["", "nsys=2", "nsys=5 periodic", "nsys=7 n=10"]
 
-code = 0  # Return code
-for nproc in [1, 2, 4]:
-    cmd = "./test_cyclic"
 
-    print("   %d processors...." % (nproc))
-    r = 0
-    for f in flags:
-        stdout.write("\tflags '" + f + "' ... ")
+def test_cyclic():
+    code = 0  # Return code
+    for nproc in [1, 2, 4]:
+        cmd = "./test_cyclic"
 
-        shell("rm data/BOUT.dmp.* 2> err.log")
+        print("   %d processors...." % (nproc))
+        r = 0
+        for f in flags:
+            stdout.write("\tflags '" + f + "' ... ")
 
-        # Run the case
-        status, out = launch(cmd + " " + f, nproc=nproc, mthread=1, pipe=True)
-        with open(f"run.log.{nproc}.{r}", "w") as f:
-            f.write(out)
+            shell("rm data/BOUT.dmp.* 2> err.log")
 
-        r = r + 1
+            # Run the case
+            status, out = launch(cmd + " " + f, nproc=nproc, mthread=1, pipe=True)
+            with open(f"run.log.{nproc}.{r}", "w") as f:
+                f.write(out)
 
-        # Find out if it worked
-        if status:
-            print("PASSED")
-        else:
-            print("FAILED")
-            code = 1
+            r = r + 1
 
-if code == 0:
-    print(" => All cyclic reduction tests passed")
-else:
-    print(" => Some failed tests")
+            # Find out if it worked
+            if status:
+                print("PASSED")
+            else:
+                print("FAILED")
+                code = 1
+            assert status, f"Test failed for flag={f}"
 
-exit(code)
+    if code == 0:
+        print(" => All cyclic reduction tests passed")
+    else:
+        print(" => Some failed tests")

From 09114fe2eb8cc2d147a098fefd8579eb88bf5af1 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 12 Nov 2025 13:45:09 +0000
Subject: [PATCH 0977/1827] Convert several more test files to work with pytest

---
 .../test-backtrace/test_backtrace.py          |  47 +++--
 tests/integrated/test-beuler/test_beuler.py   |  22 +--
 .../test_datafile_facade.py                   |  64 +++----
 .../test_drift_instability.py                 |  13 +-
 .../integrated/test-griddata/test_griddata.py |  45 +++--
 tests/integrated/test-initial/test_initial.py | 173 +++++++++---------
 tests/integrated/test-invpar/test_invpar.py   |  58 +++---
 .../test-twistshift/test_twistshift.py        |   2 +-
 tests/integrated/test-yupdown/test_yupdown.py |  48 ++---
 9 files changed, 233 insertions(+), 239 deletions(-)

diff --git a/tests/integrated/test-backtrace/test_backtrace.py b/tests/integrated/test-backtrace/test_backtrace.py
index c4020e6d99..f3767eeb9d 100755
--- a/tests/integrated/test-backtrace/test_backtrace.py
+++ b/tests/integrated/test-backtrace/test_backtrace.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-
+import pytest
 # Test enabling/disabling exception backtrace from environment variable
 
 # requires all_tests
@@ -9,33 +9,32 @@
 
 build_and_log("backtrace environment variable test")
 
-try:
-    del os.environ["BOUT_SHOW_BACKTRACE"]
-except KeyError:
-    pass
 
-success = True
-errors = []
+def test_backtrace():
+    try:
+        del os.environ["BOUT_SHOW_BACKTRACE"]
+    except KeyError:
+        pass
+
+    success = True
+    errors = []
 
-_, output = shell("BOUT_SHOW_BACKTRACE=0 ./boutexcept", pipe=True)
+    _, output = shell("./boutexcept", pipe=True)
 
-if "troublemaker" in output:
-    success = False
-    print(
-        f"Fail: detected offending function name in output when not expected:\n{output}"
-    )
+    if "troublemaker" in output:
+        success = False
+        pytest.fail("Fail: detected offending function name in output when not expected")
 
-_, output = shell("./boutexcept", pipe=True)
+    _, output = shell("BOUT_SHOW_BACKTRACE=yes ./boutexcept", pipe=True)
 
-if "troublemaker" not in output:
-    success = False
-    print(
-        f"Fail: did not detect offending function name in output when expected:\n{output}"
-    )
+    if "troublemaker" not in output:
+        success = False
+        print("Fail: did not detect offending function name in output when expected")
 
-if success:
-    print("=> All BoutException backtrace tests passed")
-    exit(0)
+    if success:
+        print("=> All BoutException backtrace tests passed")
+        exit(0)
+    assert success, f"Test failed"
 
-print("=> Some failed tests")
-exit(1)
+    print("=> Some failed tests")
+    exit(1)
diff --git a/tests/integrated/test-beuler/test_beuler.py b/tests/integrated/test-beuler/test_beuler.py
index 00fb93708c..268cd3c986 100755
--- a/tests/integrated/test-beuler/test_beuler.py
+++ b/tests/integrated/test-beuler/test_beuler.py
@@ -4,20 +4,20 @@
 
 from boututils.run_wrapper import shell_safe, launch_safe
 
-from sys import exit
-
 nthreads = 1
 nproc = 1
 
-print("Making solver test")
-shell_safe("make > make.log")
 
-print("Running solver test")
-status, out = launch_safe("./test_beuler", nproc=nproc, mthread=nthreads, pipe=True)
-with open("run.log", "w") as f:
-    f.write(out)
+def test_beuler():
+    print("Making solver test")
+    shell_safe("make > make.log")
+
+    print("Running solver test")
+    status, out = launch_safe("./test_beuler", nproc=nproc, mthread=nthreads, pipe=True)
+    with open("run.log", "w") as f:
+        f.write(out)
 
-if status:
-    print(out)
+    if status:
+        print(out)
 
-exit(status)
+    assert status, out
diff --git a/tests/integrated/test-datafilefacade/test_datafile_facade.py b/tests/integrated/test-datafilefacade/test_datafile_facade.py
index 213b64e26b..18bb8d55db 100755
--- a/tests/integrated/test-datafilefacade/test_datafile_facade.py
+++ b/tests/integrated/test-datafilefacade/test_datafile_facade.py
@@ -8,11 +8,9 @@
 from boutdata.collect import collect
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 import numpy
-from sys import exit
 
 build_and_log("DataFileFacade test")
 
-
 success = True
 
 testvars = {
@@ -38,41 +36,39 @@
 }
 
 
-for nproc in [1, 2]:
-    # delete any existing output
-    shell("rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc")
-
-    print(f"   {nproc} processor....")
+def test_datafile_facade():
+    for nproc in [1, 2]:
+        # delete any existing output
+        shell("rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc")
 
-    # run the test executable
-    s, out = launch_safe("./test-datafile-facade", nproc=nproc, pipe=True)
-    with open(f"run.log.{nproc}", "w") as f:
-        f.write(out)
+        print(f"   {nproc} processor....")
 
-    # check the results
-    for name, expected in testvars.items():
-        # check non-evolving version
-        result = collect(name, path="data", info=False)
+        # run the test executable
+        s, out = launch_safe("./test-datafile-facade", nproc=nproc, pipe=True)
+        with open(f"run.log.{nproc}", "w") as f:
+            f.write(out)
 
-        if result.dtype.kind in ("S", "U"):
-            if str(result) != expected:
-                success = False
-                print(
-                    f"{name} is different: got '{str(result)}', expected '{expected}'"
-                )
-            continue
+        # check the results
+        for name, expected in testvars.items():
+            # check non-evolving version
+            result = collect(name, path="data", info=False)
 
-        if not numpy.allclose(expected, result):
-            success = False
-            print(f"{name} is different: {numpy.max(numpy.abs(expected - result))}")
+            if result.dtype.kind in ("S", "U"):
+                if str(result) != expected:
+                    success = False
+                    print(
+                        f"{name} is different: got '{str(result)}', expected '{expected}'"
+                    )
+                continue
 
-if success:
-    print("=> All DataFileFacade tests passed")
-    # clean up binary files
-    shell(
-        "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc"
-    )
-    exit(0)
+            if not numpy.allclose(expected, result):
+                success = False
+                print(f"{name} is different: {numpy.max(numpy.abs(expected - result))}")
 
-print("=> Some failed tests")
-exit(1)
+    if success:
+        print("=> All DataFileFacade tests passed")
+        # clean up binary files
+        shell(
+            "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc"
+        )
+    assert success, f"=> Some failed tests"
diff --git a/tests/integrated/test-drift-instability/test_drift_instability.py b/tests/integrated/test-drift-instability/test_drift_instability.py
index ad911e6028..110f388ba0 100644
--- a/tests/integrated/test-drift-instability/test_drift_instability.py
+++ b/tests/integrated/test-drift-instability/test_drift_instability.py
@@ -105,7 +105,7 @@ def run_zeff_case(zeff, build_project):
     # Calculate geometric and physical quantities
     lZeta = 1e2 * zmax * 2 * np.pi * grid["R0"]  # toroidal range [cm]
     lbNorm = lZeta * (
-        grid["Bpxy"][0, ny // 2] / grid["Bxy"][0, ny // 2]
+            grid["Bpxy"][0, ny // 2] / grid["Bxy"][0, ny // 2]
     )  # binormal coord range [cm]
 
     vTe = 4.2e7 * np.sqrt(grid["Te_x"])  # electron thermal speed [cm/s]
@@ -128,7 +128,7 @@ def run_zeff_case(zeff, build_project):
     # wci=9.58e3*(1./d.AA)*1e4*du.Bmag
 
     lpar = (
-        np.sum(((grid["Bxy"] / grid["Bpxy"])) * grid["dlthe"]) / grid["nx"]
+            np.sum(((grid["Bxy"] / grid["Bpxy"])) * grid["dlthe"]) / grid["nx"]
     )  # [m], average over flux surfaces
     kpar = 2 * np.pi / (1e2 * lpar)  # cm-1
     spar = (kpar / kperp) ** 2 * wci * wce / (0.51 * nuei)  # [1/s]
@@ -161,12 +161,12 @@ def run_zeff_case(zeff, build_project):
         # Increasing; watch for wrapping around the top
         for i in range(nt - nt0):
             if peak[i] < peak[i - 1]:
-                peak[i : (nt - nt0)] = peak[i : (nt - nt0)] + nz
+                peak[i: (nt - nt0)] = peak[i: (nt - nt0)] + nz
     else:
         # Decreasing; watch for wrapping around the bottom
         for i in range(nt - nt0):
             if peak[i] > peak[i - 1]:
-                peak[i : (nt - nt0)] = peak[i : (nt - nt0)] - nz
+                peak[i: (nt - nt0)] = peak[i: (nt - nt0)] - nz
 
     # Fit y = a + gamma*x
     a, gamma = linear_regression(t_array[nt0:nt] / wci, np.log(maxVal))
@@ -179,7 +179,7 @@ def run_zeff_case(zeff, build_project):
     gamma = gamma / wstar
 
     # Calculate analytic result
-    t = 0.5 * (np.sqrt(sparn**4 + 16 * sparn**2) - sparn**2)
+    t = 0.5 * (np.sqrt(sparn ** 4 + 16 * sparn ** 2) - sparn ** 2)
     wr = 0.5 * np.sqrt(t)
     wi = sparn / np.sqrt(t) - 0.5 * sparn
 
@@ -206,6 +206,5 @@ def run_zeff_case(zeff, build_project):
 def test_zeff_case(zeff, build_project):
     """Pytest wrapper for running a single Zeff case."""
     success, omegadiff, gammadiff = run_zeff_case(zeff, build_project)
-    
-    assert success, f"Test failed for Zeff={zeff}: omega diff={omegadiff:.2%}, gamma diff={gammadiff:.2%}"
 
+    assert success, f"Test failed for Zeff={zeff}: omega diff={omegadiff:.2%}, gamma diff={gammadiff:.2%}"
diff --git a/tests/integrated/test-griddata/test_griddata.py b/tests/integrated/test-griddata/test_griddata.py
index 6aef955023..0525a58ef6 100755
--- a/tests/integrated/test-griddata/test_griddata.py
+++ b/tests/integrated/test-griddata/test_griddata.py
@@ -11,38 +11,37 @@
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
-from sys import stdout, exit
+from sys import stdout
+
 
 build_and_log("griddata test")
 
-for nproc in [1]:
-    stdout.write("Checking %d processors ... " % (nproc))
 
-    shell("rm ./data*nc")
-    s, out = launch_safe("./test_griddata -d screw", nproc=nproc, pipe=True)
+def test_griddata():
+    for nproc in [1]:
+        stdout.write("Checking %d processors ... " % (nproc))
 
-    with open("run.log." + str(nproc), "w") as f:
-        f.write(out)
+        shell("rm ./data*nc")
+        s, out = launch_safe("./test_griddata -d screw", nproc=nproc, pipe=True)
 
-    prefix = "data"
-    Rxy = collect("Rxy", prefix=prefix, info=False)
-    Bpxy = collect("Bpxy", prefix=prefix, info=False)
-    dx = collect("dx", prefix=prefix, info=False)
+        with open("run.log." + str(nproc), "w") as f:
+            f.write(out)
 
-    nx, ny = Rxy.shape
+        prefix = "data"
+        Rxy = collect("Rxy", prefix=prefix, info=False)
+        Bpxy = collect("Bpxy", prefix=prefix, info=False)
+        dx = collect("dx", prefix=prefix, info=False)
 
-    # Handle 3D metric case
-    if len(dx.shape) == 3:
-        dx = dx[:, :, 0]
+        nx, ny = Rxy.shape
 
-    rwidth = 0.4
-    dr = float(rwidth) / nx
+        # Handle 3D metric case
+        if len(dx.shape) == 3:
+            dx = dx[:, :, 0]
 
-    # Test value of dx
-    if not np.allclose(dx, dr * Bpxy * Rxy, atol=1e-7):
-        print("Failed: dx does not match")
-        exit(1)
+        rwidth = 0.4
+        dr = float(rwidth) / nx
 
-    print("Passed")
+        # Test value of dx
+        assert np.allclose(dx, dr * Bpxy * Rxy, atol=1e-7), "Failed: dx does not match"
 
-exit(0)
+        print("Passed")
diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index 25ad7d09f1..54ac14f873 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-
+import pytest
 # Test initial conditions
 
 from boututils.run_wrapper import build_and_log, shell, launch_safe
@@ -11,6 +11,7 @@
 import numpy as np
 import os
 
+
 # requires not make
 # requires scipy
 # cores: 4
@@ -63,7 +64,7 @@ def gauss(x, width=1.0):
     """
     Normalised gaussian
     """
-    return np.exp(-(x**2) / (2 * width**2)) / np.sqrt(2 * np.pi)
+    return np.exp(-(x ** 2) / (2 * width ** 2)) / np.sqrt(2 * np.pi)
 
 
 def mixmode(x, seed=0.5):
@@ -89,8 +90,8 @@ def tanhhat(x, width, centre, steepness):
     BOUT++ TanhHat function
     """
     return 0.5 * (
-        np.tanh(steepness * (x - (centre - width / 2.0)))
-        + np.tanh(-steepness * (x - (centre + width / 2.0)))
+            np.tanh(steepness * (x - (centre - width / 2.0)))
+            + np.tanh(-steepness * (x - (centre + width / 2.0)))
     )
 
 
@@ -151,93 +152,89 @@ def fmod(x, denominator=1.0):
 TanhHat = tanhhat
 pi = np.pi
 
-########################################
-# Running the test
-
-# Some parameters
-success = True
-tolerance = 1e-13
-cmd = "./test_initial"
-datadir = "data"
-inputfile = os.path.join(datadir, "BOUT.inp")
-
-# Read the input file
-config = configparser.ConfigParser()
-with open(inputfile, "r") as f:
-    config.read_file(itertools.chain(["[global]"], f), source=inputfile)
-
-# Find the variables that have a "function" option
-varlist = [key for key, values in config.items() if "function" in values]
-
-# Remove the coordinate arrays
-for coord in ["var_x", "var_y", "var_z"]:
-    varlist.remove(coord)
-
-build_and_log("initial conditions test")
-
-nprocs = [1, 2, 3, 4]
-for nproc in nprocs:
-    status, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
-    with open("run.log.{}".format(nproc), "w") as f:
-        f.write(out)
-
-    if status != 0:
-        print("=> Could not run test")
-        print(status)
-        exit(status)
-
-    # Collect the coordinate arrays separately
-    x = collect("var_x", xguards=True, yguards=True, path=datadir, info=False)
-    y = collect("var_y", xguards=True, yguards=True, path=datadir, info=False)
-    z = collect("var_z", xguards=True, yguards=True, path=datadir, info=False)
-
-    # Evaluate the functions
-    for var in varlist:
-        function = config[var]["function"]
-        function = function.replace("^", "**")
-        if ":" in function:
-            print(
-                "{} contains reference to variable - not possible to resolve at this time".format(
-                    var
+
+def test_initial():
+    # Running the test
+
+    # Some parameters
+    success = True
+    tolerance = 1e-13
+    cmd = "./test_initial"
+    datadir = "data"
+    inputfile = os.path.join(datadir, "BOUT.inp")
+
+    # Read the input file
+    config = configparser.ConfigParser()
+    with open(inputfile, "r") as f:
+        config.read_file(itertools.chain(["[global]"], f), source=inputfile)
+
+    # Find the variables that have a "function" option
+    varlist = [key for key, values in config.items() if "function" in values]
+
+    # Remove the coordinate arrays
+    for coord in ["var_x", "var_y", "var_z"]:
+        varlist.remove(coord)
+
+    build_and_log("initial conditions test")
+
+    nprocs = [1, 2, 3, 4]
+    for nproc in nprocs:
+        status, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+        with open("run.log.{}".format(nproc), "w") as f:
+            f.write(out)
+
+        if status != 0:
+            print(status)
+            pytest.fail("=> Could not run test")
+            exit(status)
+
+        # Collect the coordinate arrays separately
+        x = collect("var_x", xguards=True, yguards=True, path=datadir, info=False)
+        y = collect("var_y", xguards=True, yguards=True, path=datadir, info=False)
+        z = collect("var_z", xguards=True, yguards=True, path=datadir, info=False)
+
+        # Evaluate the functions
+        for var in varlist:
+            function = config[var]["function"]
+            function = function.replace("^", "**")
+            if ":" in function:
+                print(
+                    "{} contains reference to variable - not possible to resolve at this time".format(
+                        var
+                    )
                 )
-            )
-            continue
-        try:
-            analytic = eval(function)
-        except NotImplementedError as err:
-            print("{} not implemented, skipping".format(err.args[0]))
-        else:
-            data = collect(var, xguards=True, yguards=True, path=datadir, info=False)
-            E2 = np.sqrt(np.mean((analytic - data) ** 2))
-            if E2 < tolerance:
-                success_string = "PASS"
+                continue
+            try:
+                analytic = eval(function)
+            except NotImplementedError as err:
+                print("{} not implemented, skipping".format(err.args[0]))
             else:
-                if (var == "mixmode" or var == "mixmode_seed") and E2 < 1e-3:
-                    import platform
-
-                    arch = platform.machine()
-                    if arch == "i686":
-                        # This can happen due tue excess precision e.g. on X87 architecture
-                        success_string = "WARNING"
+                data = collect(var, xguards=True, yguards=True, path=datadir, info=False)
+                E2 = np.sqrt(np.mean((analytic - data) ** 2))
+                if E2 < tolerance:
+                    success_string = "PASS"
+                else:
+                    if (var == "mixmode" or var == "mixmode_seed") and E2 < 1e-3:
+                        import platform
+
+                        arch = platform.machine()
+                        if arch == "i686":
+                            # This can happen due tue excess precision e.g. on X87 architecture
+                            success_string = "WARNING"
+                        else:
+                            print(
+                                "This should only happen in i686 with an x87 math architecture."
+                            )
+                            print("We detected however an %s architecture." % arch)
+                            success_string = "FAIL"
+                            success = False
                     else:
-                        print(
-                            "This should only happen in i686 with an x87 math architecture."
-                        )
-                        print("We detected however an %s architecture." % arch)
                         success_string = "FAIL"
                         success = False
-                else:
-                    success_string = "FAIL"
-                    success = False
-            print(
-                "\tChecking {var:<12}: l-2: {err:.4e} ... {success}".format(
-                    var=var, err=E2, success=success_string
+                print(
+                    "\tChecking {var:<12}: l-2: {err:.4e} ... {success}".format(
+                        var=var, err=E2, success=success_string
+                    )
                 )
-            )
-
-if success:
-    print(" => All tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+
+    assert success, " => Some failed tests"
diff --git a/tests/integrated/test-invpar/test_invpar.py b/tests/integrated/test-invpar/test_invpar.py
index 53f6015fe9..38ef1fdfaa 100755
--- a/tests/integrated/test-invpar/test_invpar.py
+++ b/tests/integrated/test-invpar/test_invpar.py
@@ -10,7 +10,6 @@
 
 from boututils.run_wrapper import build_and_log, shell, launch
 from boutdata.collect import collect
-from sys import stdout, exit
 
 build_and_log("parallel inversion test")
 
@@ -26,39 +25,40 @@
     dict(input_field="'ballooning(exp(-y*y)*cos(z)*gauss(x,0.2))'"),
 ]
 
-flags = ""
-for i, f in enumerate(flags_src):
-    fl = {"acoef": 1}
-    fl.update(f)
-    for k, v in fl.items():
-        flags += f" {k}_{i}={v}"
 
-regions = ["", " mesh:ixseps1=0 mesh:ixseps2=0"]
-flags = [flags + r for r in regions]
+def test_invpar():
+    global i, f, r, code
+    flags = ""
+    for i, f in enumerate(flags_src):
+        fl = {"acoef": 1}
+        fl.update(f)
+        for k, v in fl.items():
+            flags += f" {k}_{i}={v}"
 
-code = 0  # Return code
-for nproc in [1, 2, 4]:
-    cmd = "./test_invpar"
+    regions = ["", " mesh:ixseps1=0 mesh:ixseps2=0"]
+    flags = [flags + r for r in regions]
 
-    print("   %d processors...." % (nproc))
-    r = 0
-    for f in flags:
-        shell("rm data/BOUT.dmp.* 2> err.log")
+    code = 0  # Return code
+    for nproc in [1, 2, 4]:
+        cmd = "./test_invpar"
 
-        # Run the case
-        s, _ = launch(cmd + " -q -q -q " + f, nproc=nproc, mthread=1)
+        print("   %d processors...." % (nproc))
+        r = 0
+        for f in flags:
+            shell("rm data/BOUT.dmp.* 2> err.log")
 
-        code += s
+            # Run the case
+            s, _ = launch(cmd + " -q -q -q " + f, nproc=nproc, mthread=1)
 
-        if s == 0:
-            print("PASSED")
-        else:
-            print("FAILED")
+            code += s
 
+            if s == 0:
+                print("PASSED")
+            else:
+                print("FAILED")
+            assert s, f"Test failed for flag={f}"
 
-if code == 0:
-    print(" => All inversion tests passed")
-else:
-    print(" => Some failed tests")
-
-exit(code)
+    if code == 0:
+        print(" => All inversion tests passed")
+    else:
+        print(" => Some failed tests")
diff --git a/tests/integrated/test-twistshift/test_twistshift.py b/tests/integrated/test-twistshift/test_twistshift.py
index c4858970c4..125aab6b5b 100755
--- a/tests/integrated/test-twistshift/test_twistshift.py
+++ b/tests/integrated/test-twistshift/test_twistshift.py
@@ -29,7 +29,7 @@
 def test1(ylower, yupper):
     global success
     if numpy.any(
-        numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6
+            numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6
     ):
         success = False
         print(
diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py
index 13d7365b53..dd39fafd05 100755
--- a/tests/integrated/test-yupdown/test_yupdown.py
+++ b/tests/integrated/test-yupdown/test_yupdown.py
@@ -1,18 +1,23 @@
 #!/usr/bin/env python3
-
+import pytest
 from boututils.run_wrapper import build_and_log, launch_safe
 from boutdata.collect import collect
-from sys import exit
 
 from numpy import max, abs
 
-build_and_log("parallel slices test")
+shift_types = ["shifted", "shiftedinterp"]
+variables = [("ddy", "ddy_check"), ("ddy2", "ddy_check")]
+
 
-failed = False
+@pytest.fixture(scope="module")
+def build_project():
+    """Build the project once per test module."""
+    build_and_log("parallel slices test")
 
-for shifttype in ["shifted", "shiftedinterp"]:
+
+def run_case(shift_type, variable, build_project):
     s, out = launch_safe(
-        "./test_yupdown mesh:paralleltransform:type=" + shifttype,
+        "./test_yupdown mesh:paralleltransform:type=" + shift_type,
         nproc=1,
         pipe=True,
         verbose=True,
@@ -21,23 +26,22 @@
     with open("run.log", "w") as f:
         f.write(out)
 
-    vars = [("ddy", "ddy_check"), ("ddy2", "ddy_check")]
+    v, v_check = variable
+    print("Testing %s and %s ... " % (v, v_check))
+    ddy = collect(v, path="data", xguards=False, yguards=False, info=False)
+    ddy_check = collect(
+        v_check, path="data", xguards=False, yguards=False, info=False
+    )
 
-    for v, v_check in vars:
-        print("Testing %s and %s ... " % (v, v_check))
-        ddy = collect(v, path="data", xguards=False, yguards=False, info=False)
-        ddy_check = collect(
-            v_check, path="data", xguards=False, yguards=False, info=False
-        )
+    diff = max(abs(ddy - ddy_check))
 
-        diff = max(abs(ddy - ddy_check))
+    print(f"shifttype: {shift_type} Max difference {diff}")
+    if diff < 2e-5:
+        return True
+    return False
 
-        if diff < 2e-5:
-            print(shifttype + " passed (Max difference %e)" % (diff))
-        else:
-            print(shifttype + " failed (Max difference %e)" % (diff))
-            failed = True
 
-if failed:
-    exit(1)
-exit(0)
+@pytest.mark.parametrize("shift_type, variable", list(zip(shift_types, variables)))
+def test_case(shift_type, variable, build_project):
+    success = run_case(shift_type, variable, build_project)
+    assert success, f"Test failed for shift_type={shift_type}: , variable={variable}"

From be04639383f69af0abaeb7bdc40933cd4fc602b4 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 17 Dec 2025 14:54:33 +0000
Subject: [PATCH 0978/1827] Change directory before calling `boutpp.init()`

so that the `input` directory is found.
---
 .../collect/test_boutpp_collect.py            | 85 ++++++++++---------
 1 file changed, 46 insertions(+), 39 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index 31d228d518..2e122ebc47 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -1,4 +1,6 @@
 #!/usr/bin/env python3
+import os
+import pathlib
 import boutpp as bc
 import numpy as np
 from boutdata import collect
@@ -6,42 +8,47 @@
 # requires boutpp
 # requires not make
 
-bc.init("-d input".split(" "))
-
-f = bc.Field3D.fromMesh(None)
-f.setAll(np.array([[[1.0]]]))
-f2 = bc.Field3D.fromMesh(None)
-f2.setAll(np.array([[[2.0]]]))
-print(f.getAll())
-
-dump = bc.Options(f3d=f, f2d=f2)
-bc.writeDefaultOutputFile(dump)
-
-errorlist = ""
-n = collect("f2d", path="input", tind=-1, yguards=True)
-print(n.shape)
-T = collect("f3d", path="input", tind=-1, yguards=True)
-print(n.shape)
-
-print("initialized mesh")
-mesh = bc.Mesh.getGlobal()
-print("initialized mesh")
-
-dens = bc.Field3D.fromMesh(mesh)
-dens[:, :, :] = n.reshape((1, 1, 1))
-temp = bc.Field3D.fromCollect("f3d", path="input")
-pres = dens + temp
-print(slice(None, None, -2).indices(5))
-p = pres[::5, 0, ::-2]
-pn = n + T
-pn = pn.reshape(p.shape)
-if not ((p == pn).all()):
-    errorlist += "addition not working\n"
-pres = dens * temp * 1
-p = pres.getAll()
-pn = n * T
-pn = pn.reshape(p.shape)
-if not ((p == pn).all()):
-    errorlist += "multiplication not working\n"
-print(p.shape)
-print(pn.shape)
+
+def test_boutpp_collect():
+
+    this_directory = pathlib.Path(__file__).parent.absolute()
+    os.chdir(this_directory)
+    bc.init("-d input".split(" "))
+
+    f = bc.Field3D.fromMesh(None)
+    f.setAll(np.array([[[1.0]]]))
+    f2 = bc.Field3D.fromMesh(None)
+    f2.setAll(np.array([[[2.0]]]))
+    print(f.getAll())
+
+    dump = bc.Options(f3d=f, f2d=f2)
+    bc.writeDefaultOutputFile(dump)
+
+    errorlist = ""
+    n = collect("f2d", path="input", tind=-1, yguards=True)
+    print(n.shape)
+    T = collect("f3d", path="input", tind=-1, yguards=True)
+    print(n.shape)
+
+    print("initialized mesh")
+    mesh = bc.Mesh.getGlobal()
+    print("initialized mesh")
+
+    dens = bc.Field3D.fromMesh(mesh)
+    dens[:, :, :] = n.reshape((1, 1, 1))
+    temp = bc.Field3D.fromCollect("f3d", path="input")
+    pres = dens + temp
+    print(slice(None, None, -2).indices(5))
+    p = pres[::5, 0, ::-2]
+    pn = n + T
+    pn = pn.reshape(p.shape)
+    if not ((p == pn).all()):
+        errorlist += "addition not working\n"
+    pres = dens * temp * 1
+    p = pres.getAll()
+    pn = n * T
+    pn = pn.reshape(p.shape)
+    if not ((p == pn).all()):
+        errorlist += "multiplication not working\n"
+    print(p.shape)
+    print(pn.shape)

From abe75f21a7d8dec00fdb586745a244e74f5b2ec8 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 17 Dec 2025 15:04:33 +0000
Subject: [PATCH 0979/1827] Change directory before calling `boutpp.init()`

so that the `test` directory is found.
---
 tests/integrated/test-boutpp/slicing/test_slicing.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py
index 781e3593a4..47f631e7fb 100755
--- a/tests/integrated/test-boutpp/slicing/test_slicing.py
+++ b/tests/integrated/test-boutpp/slicing/test_slicing.py
@@ -1,11 +1,14 @@
 #!/usr/bin/env python3
 # requires boutpp
 # requires not make
-
+import os
+import pathlib
 import numpy as np
 import boutpp as bc
 import inspect
 
+this_directory = pathlib.Path(__file__).parent.absolute()
+os.chdir(this_directory)
 bc.init("-d test")
 mesh = bc.Mesh.getGlobal()
 field = bc.Field3D.fromMesh(mesh)

From 52436a892e837af69792601bffdbb986427a8481 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 17 Dec 2025 15:05:15 +0000
Subject: [PATCH 0980/1827] Change directory before calling
 `boutpp.Field3D.fromCollect()`

so that the `data` directory is found.
---
 .../test_boutpp_collect_staggered.py          | 66 ++++++++++---------
 1 file changed, 36 insertions(+), 30 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index 25477c05ee..c8536b0ef5 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -1,50 +1,56 @@
 #!/usr/bin/env python3
+import os
+import pathlib
+
 import boutpp as bc
 
 # requires boutpp
 # requires not make
 
-bc.init("-q -q -q")
+def test_boutpp_collect_staggered():
+    bc.init("-q -q -q")
 
-fail = 0
-f = bc.create3D("sin(y)", outloc="YLOW")
+    fail = 0
+    f = bc.create3D("sin(y)", outloc="YLOW")
 
-dump = bc.Options()
-dump["f3d_evolve"].assignRepeat(f)
-dump["f3d_once"] = f
-bc.writeDefaultOutputFile(dump)
+    dump = bc.Options()
+    dump["f3d_evolve"].assignRepeat(f)
+    dump["f3d_once"] = f
+    bc.writeDefaultOutputFile(dump)
 
 
-fc = bc.create3D("sin(y)", outloc="CENTRE")
+    fc = bc.create3D("sin(y)", outloc="CENTRE")
 
-fe = bc.Field3D.fromCollect("f3d_evolve", path="data", info=False)
-fo = bc.Field3D.fromCollect("f3d_once", path="data", info=False)
+    this_directory = pathlib.Path(__file__).parent.absolute()
+    os.chdir(this_directory)
+    fe = bc.Field3D.fromCollect("f3d_evolve", path="data", info=False)
+    fo = bc.Field3D.fromCollect("f3d_once", path="data", info=False)
 
-if fe.getLocation() == fc.getLocation():
-    print("The loaded field should not be at CELL_CENTRE")
-    fail = 1
+    if fe.getLocation() == fc.getLocation():
+        print("The loaded field should not be at CELL_CENTRE")
+        fail = 1
 
-if fo.getLocation() == fc.getLocation():
-    print("The loaded field should not be at CELL_CENTRE")
-    fail = 1
+    if fo.getLocation() == fc.getLocation():
+        print("The loaded field should not be at CELL_CENTRE")
+        fail = 1
 
 
-def compare(a, b):
-    diff = a - bc.interp_to(b, a.getLocation())
-    err = bc.max(bc.sqrt(diff * diff))
-    return err
+    def compare(a, b):
+        diff = a - bc.interp_to(b, a.getLocation())
+        err = bc.max(bc.sqrt(diff * diff))
+        return err
 
 
-if compare(fc, f) > 1e-3:
-    print("Something is wrong. Maybe interpolation is broken")
-    fail = 1
+    if compare(fc, f) > 1e-3:
+        print("Something is wrong. Maybe interpolation is broken")
+        fail = 1
 
-if compare(fc, fe) > 1e-3:
-    print("Something is wrong. Maybe setting the location from field failed.")
-    fail = 1
+    if compare(fc, fe) > 1e-3:
+        print("Something is wrong. Maybe setting the location from field failed.")
+        fail = 1
 
-if compare(fc, fo) > 1e-3:
-    print("Something is wrong. Maybe setting the location from field failed.")
-    fail = 1
+    if compare(fc, fo) > 1e-3:
+        print("Something is wrong. Maybe setting the location from field failed.")
+        fail = 1
 
-exit(fail)
+    exit(fail)

From f7378bc6603330fb96ece1d72392791b4c165f1e Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 17 Dec 2025 15:05:58 +0000
Subject: [PATCH 0981/1827] Modify more test files for running via pytest

---
 .../legacy-model/test_boutpp_legacy_model.py  | 22 +++---
 .../mms-ddz/test_boutpp_mms_ddz.py            | 78 ++++++++++---------
 .../simple-model/test_boutpp_simple_model.py  | 20 ++---
 3 files changed, 63 insertions(+), 57 deletions(-)

diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index ea5d06a06e..dbbe916c55 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -5,18 +5,20 @@
 # requires boutpp
 # requires not make
 
-boutpp.init(sys.argv[1:])
 
-dens = boutpp.create3D("0")
+def test_boutpp_legacy_model():
+    boutpp.init(sys.argv[1:])
 
+    dens = boutpp.create3D("0")
 
-def rhs(time):
-    n_ddt = dens.ddt()
-    n_ddt[:, :, :] = dens * 0
-    n_ddt += 1
 
+    def rhs(time):
+        n_ddt = dens.ddt()
+        n_ddt[:, :, :] = dens * 0
+        n_ddt += 1
 
-model = boutpp.PhysicsModelBase()
-model.setRhs(rhs)
-model.solve_for(n=dens)
-model.solve()
+
+    model = boutpp.PhysicsModelBase()
+    model.setRhs(rhs)
+    model.solve_for(n=dens)
+    model.solve()
diff --git a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
index 02e87ae63a..03b36d17e8 100755
--- a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
+++ b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
@@ -5,41 +5,43 @@
 # requires boutpp
 # requires not make
 
-errorlist = ""
-boutpp.init("-d data -q -q -q")  # +" -f BOUT.settings")
-
-shapes = []
-errors = []
-mmax = 7
-start = 6
-doPlot = False
-nzs = np.logspace(start, mmax, num=mmax - start + 1, base=2)
-for nz in nzs:
-    boutpp.setOption("meshz:nz", "%d" % nz, force=True)
-    boutpp.setOption("meshz:dz", "2*pi/%d" % nz, force=True)
-    mesh = boutpp.Mesh(section="meshz")
-    f = boutpp.create3D("sin(z)", mesh)
-    sim = boutpp.DDZ(f)
-    ana = boutpp.create3D("cos(z)", mesh)
-    err = sim - ana
-    err = np.max(np.abs(err.getAll()))
-    errors.append(err)
-
-if doPlot:
-    from matplotlib import pyplot as plt
-
-    plt.plot(1 / np.array(nzs), errors, "-o")
-    plt.show()
-
-errc = np.log(errors[-2] / errors[-1])
-difc = np.log(nzs[-1] / nzs[-2])
-conv = errc / difc
-
-if 1.9 < conv < 2.1:
-    print("The convergence is: %f" % conv)
-else:
-    errorlist += "DDZ is not working\n"
-
-if errorlist != "":
-    print("Found errors:\n%s" % errorlist)
-    exit(1)
+
+def test_boutpp_mms_ddz():
+    errorlist = ""
+    boutpp.init("-d data -q -q -q")  # +" -f BOUT.settings")
+
+    shapes = []
+    errors = []
+    mmax = 7
+    start = 6
+    doPlot = False
+    nzs = np.logspace(start, mmax, num=mmax - start + 1, base=2)
+    for nz in nzs:
+        boutpp.setOption("meshz:nz", "%d" % nz, force=True)
+        boutpp.setOption("meshz:dz", "2*pi/%d" % nz, force=True)
+        mesh = boutpp.Mesh(section="meshz")
+        f = boutpp.create3D("sin(z)", mesh)
+        sim = boutpp.DDZ(f)
+        ana = boutpp.create3D("cos(z)", mesh)
+        err = sim - ana
+        err = np.max(np.abs(err.getAll()))
+        errors.append(err)
+
+    if doPlot:
+        from matplotlib import pyplot as plt
+
+        plt.plot(1 / np.array(nzs), errors, "-o")
+        plt.show()
+
+    errc = np.log(errors[-2] / errors[-1])
+    difc = np.log(nzs[-1] / nzs[-2])
+    conv = errc / difc
+
+    if 1.9 < conv < 2.1:
+        print("The convergence is: %f" % conv)
+    else:
+        errorlist += "DDZ is not working\n"
+
+    if errorlist != "":
+        print("Found errors:\n%s" % errorlist)
+        exit(1)
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index d1a6b573b7..ff4bf5e48e 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -5,17 +5,19 @@
 
 from boutpp import *
 
-init("-d mini")
 
+def test_boutpp_simple_model():
+    init("-d mini")
 
-class MyModel(PhysicsModel):
-    def init(self, restart):
-        self.n = create3D("dens:function")
-        self.solve_for(dens=self.n)
 
-    def rhs(self, time):
-        self.n.ddt(DDX(self.n))
+    class MyModel(PhysicsModel):
+        def init(self, restart):
+            self.n = create3D("dens:function")
+            self.solve_for(dens=self.n)
 
+        def rhs(self, time):
+            self.n.ddt(DDX(self.n))
 
-model = MyModel()
-model.solve()
+
+    model = MyModel()
+    model.solve()

From 5a959a2ef04e61ab37ac4b78f40825d31c713406 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 17 Dec 2025 19:42:03 +0000
Subject: [PATCH 0982/1827] MPI oversubscribe for communications test

---
 tests/integrated/test-communications/test_communications.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index 7c89f0630a..96421ad339 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+import os
 
 import numpy as np
 from sys import exit
@@ -21,6 +22,9 @@
 # run with processor splitting at separatrices
 ##################################################
 
+# MPI oversubscribe for communications test
+os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+
 # With nxpe=3, both separatrices are on processor boundaries
 nxpe = 3
 command = "./test-communications NXPE=" + str(nxpe)
@@ -277,6 +281,7 @@ def test(actual, expected, procnum, region, boundary):
 ####################################################
 
 nxpe = 1
+
 command = "./test-communications NXPE=" + str(nxpe)
 
 # remove old outputs

From e977ed67c28c138f8c027c5efb60f9267d0353ce Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 17 Dec 2025 19:43:51 +0000
Subject: [PATCH 0983/1827] Change directory before removing files in `data`
 directory

---
 tests/integrated/test-communications/test_communications.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index 96421ad339..8b320b6482 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 import os
+import pathlib
 
 import numpy as np
 from sys import exit
@@ -31,6 +32,9 @@
 
 build_and_log("Communications Test")
 
+this_directory = pathlib.Path(__file__).parent.absolute()
+os.chdir(this_directory)
+
 # remove old outputs
 shell("rm data/BOUT.dmp.*")
 

From 9afb0b2e4379b208442751134475cd273f5d6cd7 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 17 Dec 2025 19:51:41 +0000
Subject: [PATCH 0984/1827] Modify test_communications to run via pytest

---
 .../test_communications.py                    | 840 +++++++++---------
 1 file changed, 417 insertions(+), 423 deletions(-)

diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index 8b320b6482..2ada8c8c9c 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -3,7 +3,6 @@
 import pathlib
 
 import numpy as np
-from sys import exit
 
 from boututils.datafile import DataFile
 from boututils.run_wrapper import build_and_log, shell, launch_safe
@@ -14,425 +13,420 @@
 # Note, the expected values for the communicated cells, which are used to test the
 # results, are shown in corner_communication_diagram.ods
 
-#################################################
-# Test disconnected-double-null diverted topology
-#################################################
-
-nype = 6  # need at least 6 to include all regions
-
-# run with processor splitting at separatrices
-##################################################
-
-# MPI oversubscribe for communications test
-os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-
-# With nxpe=3, both separatrices are on processor boundaries
-nxpe = 3
-command = "./test-communications NXPE=" + str(nxpe)
-
-build_and_log("Communications Test")
-
-this_directory = pathlib.Path(__file__).parent.absolute()
-os.chdir(this_directory)
-
-# remove old outputs
-shell("rm data/BOUT.dmp.*")
-
-print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-with open("run.log." + str(nxpe), "w") as f:
-    f.write(out)
-
-
-def test(actual, expected, procnum, region, boundary):
-    if not np.all(np.array(np.rint(actual).astype(int)) == np.array(expected)):
-        print(
-            "failed in {} boundary of region {} ({}). Expected: {}  Actual: {}".format(
-                boundary, procnum, region, expected, actual
-            )
-        )
-        exit(1)
-
-
-region = "lower, inner PF"
-f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [72, 73], 0, region, "inner x")
-test(f[-1, 1:-1], [24, 25], 0, region, "outer x")
-test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
-test(f[:, -1], [82, 10, 22, 26], 0, region, "upper y")
-
-region = "lower, inner between separatrices"
-f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-test(f[-1, 1:-1], [48, 49], 0, region, "outer x")
-test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
-test(f[:, -1], [22, 26, 38, 50], 0, region, "upper y")
-
-region = "lower, inner SOL"
-f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [36, 37], 0, region, "inner x")
-test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
-test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
-test(f[:, -1], [38, 50, 62, 86], 0, region, "upper y")
-
-region = "inner core"
-f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [74, 75], 0, region, "inner x")
-test(f[-1, 1:-1], [26, 27], 0, region, "outer x")
-test(f[:, 0], [81, 9, 21, 25], 0, region, "lower y")
-test(f[:, -1], [80, 8, 20, 32], 0, region, "upper y")
-
-region = "inner between separatrices"
-f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [14, 15], 0, region, "inner x")
-test(f[-1, 1:-1], [50, 51], 0, region, "outer x")
-test(f[:, 0], [21, 25, 37, 49], 0, region, "lower y")
-test(f[:, -1], [20, 32, 44, 52], 0, region, "upper y")
-
-region = "inner SOL"
-f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [38, 39], 0, region, "inner x")
-test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
-test(f[:, 0], [37, 49, 61, 85], 0, region, "lower y")
-test(f[:, -1], [44, 52, 64, 88], 0, region, "upper y")
-
-region = "upper inner PF"
-f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [76, 77], 0, region, "inner x")
-test(f[-1, 1:-1], [28, 29], 0, region, "outer x")
-test(f[:, 0], [79, 7, 19, 31], 0, region, "lower y")
-test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
-
-region = "upper inner SOL, nearer PF"
-f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [16, 17], 0, region, "inner x")
-test(f[-1, 1:-1], [52, 53], 0, region, "outer x")
-test(f[:, 0], [19, 31, 43, 51], 0, region, "lower y")
-test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
-
-region = "upper inner SOL, further from PF"
-f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [40, 41], 0, region, "inner x")
-test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
-test(f[:, 0], [43, 51, 63, 87], 0, region, "lower y")
-test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
-
-region = "upper outer PF"
-f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [78, 79], 0, region, "inner x")
-test(f[-1, 1:-1], [30, 31], 0, region, "outer x")
-test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
-test(f[:, -1], [76, 4, 16, 28], 0, region, "upper y")
-
-region = "upper outer SOL, nearer PF"
-f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [18, 19], 0, region, "inner x")
-test(f[-1, 1:-1], [54, 55], 0, region, "outer x")
-test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
-test(f[:, -1], [16, 28, 40, 56], 0, region, "upper y")
-
-region = "upper outer SOL, further from PF"
-f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [42, 43], 0, region, "inner x")
-test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
-test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
-test(f[:, -1], [40, 56, 68, 92], 0, region, "upper y")
-
-region = "outer core"
-f = DataFile("data/BOUT.dmp.12.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [80, 81], 0, region, "inner x")
-test(f[-1, 1:-1], [32, 33], 0, region, "outer x")
-test(f[:, 0], [75, 3, 15, 27], 0, region, "lower y")
-test(f[:, -1], [74, 2, 14, 34], 0, region, "upper y")
-
-region = "outer between separatrices"
-f = DataFile("data/BOUT.dmp.13.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [20, 21], 0, region, "inner x")
-test(f[-1, 1:-1], [56, 57], 0, region, "outer x")
-test(f[:, 0], [15, 27, 39, 55], 0, region, "lower y")
-test(f[:, -1], [14, 34, 46, 58], 0, region, "upper y")
-
-region = "outer SOL"
-f = DataFile("data/BOUT.dmp.14.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [44, 45], 0, region, "inner x")
-test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
-test(f[:, 0], [39, 55, 67, 91], 0, region, "lower y")
-test(f[:, -1], [46, 58, 70, 94], 0, region, "upper y")
-
-region = "lower outer PF"
-f = DataFile("data/BOUT.dmp.15.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [82, 83], 0, region, "inner x")
-test(f[-1, 1:-1], [34, 35], 0, region, "outer x")
-test(f[:, 0], [73, 1, 13, 33], 0, region, "lower y")
-test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
-
-region = "lower outer between separatrices"
-f = DataFile("data/BOUT.dmp.16.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [22, 23], 0, region, "inner x")
-test(f[-1, 1:-1], [58, 59], 0, region, "outer x")
-test(f[:, 0], [13, 33, 45, 57], 0, region, "lower y")
-test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
-
-region = "lower outer SOL"
-f = DataFile("data/BOUT.dmp.17.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [46, 47], 0, region, "inner x")
-test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
-test(f[:, 0], [45, 57, 69, 93], 0, region, "lower y")
-test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
-
-# run with processor splitting not at separatrices
-##################################################
-
-# With nxpe=2, neither separatrix is on a processor boundary
-nxpe = 2
-command = "./test-communications NXPE=" + str(nxpe)
-
-# remove old outputs
-shell("rm data/BOUT.dmp.*")
-
-print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-with open("run.log." + str(nxpe), "w") as f:
-    f.write(out)
-
-region = "lower, inner leg, interior"
-f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [72, 73], 0, region, "inner x")
-test(f[-1, 1:-1], [36, 37], 0, region, "outer x")
-test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
-test(f[:, -1], [82, 10, 22, 26, 38], 0, region, "upper y")
-
-region = "lower, inner leg, exterior"
-f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [24, 25], 0, region, "inner x")
-test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
-test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
-test(f[:, -1], [26, 38, 50, 62, 86], 0, region, "upper y")
-
-region = "inner, interior"
-f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [74, 75], 0, region, "inner x")
-test(f[-1, 1:-1], [38, 39], 0, region, "outer x")
-test(f[:, 0], [81, 9, 21, 25, 37], 0, region, "lower y")
-test(f[:, -1], [80, 8, 20, 32, 44], 0, region, "upper y")
-
-region = "inner, exterior"
-f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [26, 27], 0, region, "inner x")
-test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
-test(f[:, 0], [25, 37, 49, 61, 85], 0, region, "lower y")
-test(f[:, -1], [32, 44, 52, 64, 88], 0, region, "upper y")
-
-region = "upper, inner leg, interior"
-f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [76, 77], 0, region, "inner x")
-test(f[-1, 1:-1], [40, 41], 0, region, "outer x")
-test(f[:, 0], [79, 7, 19, 31, 43], 0, region, "lower y")
-test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
-
-region = "upper, inner leg, exterior"
-f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [28, 29], 0, region, "inner x")
-test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
-test(f[:, 0], [31, 43, 51, 63, 87], 0, region, "lower y")
-test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
-
-region = "upper, outer leg, interior"
-f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [78, 79], 0, region, "inner x")
-test(f[-1, 1:-1], [42, 43], 0, region, "outer x")
-test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
-test(f[:, -1], [76, 4, 16, 28, 40], 0, region, "upper y")
-
-region = "upper, outer leg, exterior"
-f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [30, 31], 0, region, "inner x")
-test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
-test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
-test(f[:, -1], [28, 40, 56, 68, 92], 0, region, "upper y")
-
-region = "outer, interior"
-f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [80, 81], 0, region, "inner x")
-test(f[-1, 1:-1], [44, 45], 0, region, "outer x")
-test(f[:, 0], [75, 3, 15, 27, 39], 0, region, "lower y")
-test(f[:, -1], [74, 2, 14, 34, 46], 0, region, "upper y")
-
-region = "outer, exterior"
-f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [32, 33], 0, region, "inner x")
-test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
-test(f[:, 0], [27, 39, 55, 67, 91], 0, region, "lower y")
-test(f[:, -1], [34, 46, 58, 70, 94], 0, region, "upper y")
-
-region = "lower, outer leg, interior"
-f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [82, 83], 0, region, "inner x")
-test(f[-1, 1:-1], [46, 47], 0, region, "outer x")
-test(f[:, 0], [73, 1, 13, 33, 45], 0, region, "lower y")
-test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
-
-region = "lower, outer leg, exterior"
-f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [34, 35], 0, region, "inner x")
-test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
-test(f[:, 0], [33, 45, 57, 69, 93], 0, region, "lower y")
-test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
-
-# run with no processor splitting in the x-direction
-####################################################
-
-nxpe = 1
-
-command = "./test-communications NXPE=" + str(nxpe)
-
-# remove old outputs
-shell("rm data/BOUT.dmp.*")
-
-print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-with open("run.log." + str(nxpe), "w") as f:
-    f.write(out)
-
-region = "lower, inner leg"
-f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [72, 73], 0, region, "inner x")
-test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
-test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
-test(f[:, -1], [82, 10, 22, 26, 38, 50, 62, 86], 0, region, "upper y")
-
-region = "inner"
-f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [74, 75], 0, region, "inner x")
-test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
-test(f[:, 0], [81, 9, 21, 25, 37, 49, 61, 85], 0, region, "lower y")
-test(f[:, -1], [80, 8, 20, 32, 44, 52, 64, 88], 0, region, "upper y")
-
-region = "upper, inner leg"
-f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [76, 77], 0, region, "inner x")
-test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
-test(f[:, 0], [79, 7, 19, 31, 43, 51, 63, 87], 0, region, "lower y")
-test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
-
-region = "upper, outer leg"
-f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [78, 79], 0, region, "inner x")
-test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
-test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
-test(f[:, -1], [76, 4, 16, 28, 40, 56, 68, 92], 0, region, "upper y")
-
-region = "outer"
-f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [80, 81], 0, region, "inner x")
-test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
-test(f[:, 0], [75, 3, 15, 27, 39, 55, 67, 91], 0, region, "lower y")
-test(f[:, -1], [74, 2, 14, 34, 46, 58, 70, 94], 0, region, "upper y")
-
-region = "lower, outer leg"
-f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [82, 83], 0, region, "inner x")
-test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
-test(f[:, 0], [73, 1, 13, 33, 45, 57, 69, 93], 0, region, "lower y")
-test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
-
-
-#################################################
-# Test limiter topology
-#################################################
-
-nype = 1
-
-# run with processor splitting at the separatrix
-####################################################
-
-nxpe = 3
-command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
-
-# remove old outputs
-shell("rm data_limiter/BOUT.dmp.*")
-
-print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-with open("run_limiter.log." + str(nxpe), "w") as f:
-    f.write(out)
-
-region = "core"
-f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-test(f[-1, 1:-1], [4, 5], 0, region, "outer x")
-test(f[:, 0], [13, 1, 3, 19], 0, region, "lower y")
-test(f[:, -1], [12, 0, 2, 27], 0, region, "upper y")
-
-region = "interior SOL"
-f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [2, 3], 0, region, "inner x")
-test(f[-1, 1:-1], [8, 9], 0, region, "outer x")
-test(f[:, 0], [3, 19, 20, 21], 0, region, "lower y")
-test(f[:, -1], [2, 27, 28, 29], 0, region, "upper y")
-
-region = "exterior SOL"
-f = DataFile("data_limiter/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [6, 7], 0, region, "inner x")
-test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
-test(f[:, 0], [20, 21, 22, 23], 0, region, "lower y")
-test(f[:, -1], [28, 29, 30, 31], 0, region, "upper y")
-
-# run with processor splitting not at the separatrix
-####################################################
-
-nxpe = 2
-command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
-
-# remove old outputs
-shell("rm data_limiter/BOUT.dmp.*")
-
-print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-with open("run_limiter.log." + str(nxpe), "w") as f:
-    f.write(out)
-
-region = "interior"
-f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-test(f[-1, 1:-1], [6, 7], 0, region, "outer x")
-test(f[:, 0], [13, 1, 3, 19, 20], 0, region, "lower y")
-test(f[:, -1], [12, 0, 2, 27, 28], 0, region, "upper y")
-
-region = "exterior"
-f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [4, 5], 0, region, "inner x")
-test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
-test(f[:, 0], [19, 20, 21, 22, 23], 0, region, "lower y")
-test(f[:, -1], [27, 28, 29, 30, 31], 0, region, "upper y")
-
-# run with no processor splitting in the x-direction
-####################################################
-
-nxpe = 1
-command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
-
-# remove old outputs
-shell("rm data_limiter/BOUT.dmp.*")
-
-print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-with open("run_limiter.log." + str(nxpe), "w") as f:
-    f.write(out)
-
-region = "all"
-f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
-test(f[:, 0], [13, 1, 3, 19, 20, 21, 22, 23], 0, region, "lower y")
-test(f[:, -1], [12, 0, 2, 27, 28, 29, 30, 31], 0, region, "upper y")
-
-# If we did not exit already, then all tests passed
-print("Pass")
-exit(0)
+
+def run_test(actual, expected, procnum, region, boundary):
+    assert np.all(np.array(np.rint(actual).astype(int)) == np.array(expected)), (
+        "failed in {} boundary of region {} ({}). Expected: {}  Actual: {}".format(
+            boundary, procnum, region, expected, actual
+            ))
+
+
+def test_communications():
+
+    #################################################
+    # Test disconnected-double-null diverted topology
+    #################################################
+
+    nype = 6  # need at least 6 to include all regions
+
+    # run with processor splitting at separatrices
+    ##################################################
+
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+
+    # With nxpe=3, both separatrices are on processor boundaries
+    nxpe = 3
+    command = "./test-communications NXPE=" + str(nxpe)
+
+    build_and_log("Communications Test")
+
+    this_directory = pathlib.Path(__file__).parent.absolute()
+    os.chdir(this_directory)
+
+    # remove old outputs
+    shell("rm data/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "lower, inner PF"
+    f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [24, 25], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
+    run_test(f[:, -1], [82, 10, 22, 26], 0, region, "upper y")
+
+    region = "lower, inner between separatrices"
+    f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [48, 49], 0, region, "outer x")
+    run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
+    run_test(f[:, -1], [22, 26, 38, 50], 0, region, "upper y")
+
+    region = "lower, inner SOL"
+    f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [36, 37], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
+    run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [38, 50, 62, 86], 0, region, "upper y")
+
+    region = "inner core"
+    f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [26, 27], 0, region, "outer x")
+    run_test(f[:, 0], [81, 9, 21, 25], 0, region, "lower y")
+    run_test(f[:, -1], [80, 8, 20, 32], 0, region, "upper y")
+
+    region = "inner between separatrices"
+    f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [14, 15], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [50, 51], 0, region, "outer x")
+    run_test(f[:, 0], [21, 25, 37, 49], 0, region, "lower y")
+    run_test(f[:, -1], [20, 32, 44, 52], 0, region, "upper y")
+
+    region = "inner SOL"
+    f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [38, 39], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
+    run_test(f[:, 0], [37, 49, 61, 85], 0, region, "lower y")
+    run_test(f[:, -1], [44, 52, 64, 88], 0, region, "upper y")
+
+    region = "upper inner PF"
+    f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [28, 29], 0, region, "outer x")
+    run_test(f[:, 0], [79, 7, 19, 31], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
+
+    region = "upper inner SOL, nearer PF"
+    f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [16, 17], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [52, 53], 0, region, "outer x")
+    run_test(f[:, 0], [19, 31, 43, 51], 0, region, "lower y")
+    run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
+
+    region = "upper inner SOL, further from PF"
+    f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [40, 41], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
+    run_test(f[:, 0], [43, 51, 63, 87], 0, region, "lower y")
+    run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
+
+    region = "upper outer PF"
+    f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [30, 31], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
+    run_test(f[:, -1], [76, 4, 16, 28], 0, region, "upper y")
+
+    region = "upper outer SOL, nearer PF"
+    f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [18, 19], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [54, 55], 0, region, "outer x")
+    run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
+    run_test(f[:, -1], [16, 28, 40, 56], 0, region, "upper y")
+
+    region = "upper outer SOL, further from PF"
+    f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [42, 43], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
+    run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [40, 56, 68, 92], 0, region, "upper y")
+
+    region = "outer core"
+    f = DataFile("data/BOUT.dmp.12.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [32, 33], 0, region, "outer x")
+    run_test(f[:, 0], [75, 3, 15, 27], 0, region, "lower y")
+    run_test(f[:, -1], [74, 2, 14, 34], 0, region, "upper y")
+
+    region = "outer between separatrices"
+    f = DataFile("data/BOUT.dmp.13.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [20, 21], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [56, 57], 0, region, "outer x")
+    run_test(f[:, 0], [15, 27, 39, 55], 0, region, "lower y")
+    run_test(f[:, -1], [14, 34, 46, 58], 0, region, "upper y")
+
+    region = "outer SOL"
+    f = DataFile("data/BOUT.dmp.14.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [44, 45], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
+    run_test(f[:, 0], [39, 55, 67, 91], 0, region, "lower y")
+    run_test(f[:, -1], [46, 58, 70, 94], 0, region, "upper y")
+
+    region = "lower outer PF"
+    f = DataFile("data/BOUT.dmp.15.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [34, 35], 0, region, "outer x")
+    run_test(f[:, 0], [73, 1, 13, 33], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
+
+    region = "lower outer between separatrices"
+    f = DataFile("data/BOUT.dmp.16.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [22, 23], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [58, 59], 0, region, "outer x")
+    run_test(f[:, 0], [13, 33, 45, 57], 0, region, "lower y")
+    run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
+
+    region = "lower outer SOL"
+    f = DataFile("data/BOUT.dmp.17.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [46, 47], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
+    run_test(f[:, 0], [45, 57, 69, 93], 0, region, "lower y")
+    run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
+
+    # run with processor splitting not at separatrices
+    ##################################################
+
+    # With nxpe=2, neither separatrix is on a processor boundary
+    nxpe = 2
+    command = "./test-communications NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "lower, inner leg, interior"
+    f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [36, 37], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
+    run_test(f[:, -1], [82, 10, 22, 26, 38], 0, region, "upper y")
+
+    region = "lower, inner leg, exterior"
+    f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [24, 25], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
+    run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [26, 38, 50, 62, 86], 0, region, "upper y")
+
+    region = "inner, interior"
+    f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [38, 39], 0, region, "outer x")
+    run_test(f[:, 0], [81, 9, 21, 25, 37], 0, region, "lower y")
+    run_test(f[:, -1], [80, 8, 20, 32, 44], 0, region, "upper y")
+
+    region = "inner, exterior"
+    f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [26, 27], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
+    run_test(f[:, 0], [25, 37, 49, 61, 85], 0, region, "lower y")
+    run_test(f[:, -1], [32, 44, 52, 64, 88], 0, region, "upper y")
+
+    region = "upper, inner leg, interior"
+    f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [40, 41], 0, region, "outer x")
+    run_test(f[:, 0], [79, 7, 19, 31, 43], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
+
+    region = "upper, inner leg, exterior"
+    f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [28, 29], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
+    run_test(f[:, 0], [31, 43, 51, 63, 87], 0, region, "lower y")
+    run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
+
+    region = "upper, outer leg, interior"
+    f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [42, 43], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
+    run_test(f[:, -1], [76, 4, 16, 28, 40], 0, region, "upper y")
+
+    region = "upper, outer leg, exterior"
+    f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [30, 31], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
+    run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [28, 40, 56, 68, 92], 0, region, "upper y")
+
+    region = "outer, interior"
+    f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [44, 45], 0, region, "outer x")
+    run_test(f[:, 0], [75, 3, 15, 27, 39], 0, region, "lower y")
+    run_test(f[:, -1], [74, 2, 14, 34, 46], 0, region, "upper y")
+
+    region = "outer, exterior"
+    f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [32, 33], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
+    run_test(f[:, 0], [27, 39, 55, 67, 91], 0, region, "lower y")
+    run_test(f[:, -1], [34, 46, 58, 70, 94], 0, region, "upper y")
+
+    region = "lower, outer leg, interior"
+    f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [46, 47], 0, region, "outer x")
+    run_test(f[:, 0], [73, 1, 13, 33, 45], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
+
+    region = "lower, outer leg, exterior"
+    f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [34, 35], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
+    run_test(f[:, 0], [33, 45, 57, 69, 93], 0, region, "lower y")
+    run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
+
+    # run with no processor splitting in the x-direction
+    ####################################################
+
+    nxpe = 1
+
+    command = "./test-communications NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "lower, inner leg"
+    f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [82, 10, 22, 26, 38, 50, 62, 86], 0, region, "upper y")
+
+    region = "inner"
+    f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
+    run_test(f[:, 0], [81, 9, 21, 25, 37, 49, 61, 85], 0, region, "lower y")
+    run_test(f[:, -1], [80, 8, 20, 32, 44, 52, 64, 88], 0, region, "upper y")
+
+    region = "upper, inner leg"
+    f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
+    run_test(f[:, 0], [79, 7, 19, 31, 43, 51, 63, 87], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
+
+    region = "upper, outer leg"
+    f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [76, 4, 16, 28, 40, 56, 68, 92], 0, region, "upper y")
+
+    region = "outer"
+    f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
+    run_test(f[:, 0], [75, 3, 15, 27, 39, 55, 67, 91], 0, region, "lower y")
+    run_test(f[:, -1], [74, 2, 14, 34, 46, 58, 70, 94], 0, region, "upper y")
+
+    region = "lower, outer leg"
+    f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
+    run_test(f[:, 0], [73, 1, 13, 33, 45, 57, 69, 93], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
+
+
+    #################################################
+    # Test limiter topology
+    #################################################
+
+    nype = 1
+
+    # run with processor splitting at the separatrix
+    ####################################################
+
+    nxpe = 3
+    command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data_limiter/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run_limiter.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "core"
+    f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [4, 5], 0, region, "outer x")
+    run_test(f[:, 0], [13, 1, 3, 19], 0, region, "lower y")
+    run_test(f[:, -1], [12, 0, 2, 27], 0, region, "upper y")
+
+    region = "interior SOL"
+    f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [2, 3], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [8, 9], 0, region, "outer x")
+    run_test(f[:, 0], [3, 19, 20, 21], 0, region, "lower y")
+    run_test(f[:, -1], [2, 27, 28, 29], 0, region, "upper y")
+
+    region = "exterior SOL"
+    f = DataFile("data_limiter/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [6, 7], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
+    run_test(f[:, 0], [20, 21, 22, 23], 0, region, "lower y")
+    run_test(f[:, -1], [28, 29, 30, 31], 0, region, "upper y")
+
+    # run with processor splitting not at the separatrix
+    ####################################################
+
+    nxpe = 2
+    command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data_limiter/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run_limiter.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "interior"
+    f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [6, 7], 0, region, "outer x")
+    run_test(f[:, 0], [13, 1, 3, 19, 20], 0, region, "lower y")
+    run_test(f[:, -1], [12, 0, 2, 27, 28], 0, region, "upper y")
+
+    region = "exterior"
+    f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [4, 5], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
+    run_test(f[:, 0], [19, 20, 21, 22, 23], 0, region, "lower y")
+    run_test(f[:, -1], [27, 28, 29, 30, 31], 0, region, "upper y")
+
+    # run with no processor splitting in the x-direction
+    ####################################################
+
+    nxpe = 1
+    command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data_limiter/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run_limiter.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "all"
+    f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
+    run_test(f[:, 0], [13, 1, 3, 19, 20, 21, 22, 23], 0, region, "lower y")
+    run_test(f[:, -1], [12, 0, 2, 27, 28, 29, 30, 31], 0, region, "upper y")

From 18b9c90a7672b72fc03d4d0bc02b03b6cc1a1f36 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Thu, 18 Dec 2025 13:01:59 +0000
Subject: [PATCH 0985/1827] Modify test_delp2 to run via pytest

---
 tests/integrated/test-delp2/test_delp2.py | 36 ++++++++---------------
 1 file changed, 13 insertions(+), 23 deletions(-)

diff --git a/tests/integrated/test-delp2/test_delp2.py b/tests/integrated/test-delp2/test_delp2.py
index 326ba32888..b750528dc1 100755
--- a/tests/integrated/test-delp2/test_delp2.py
+++ b/tests/integrated/test-delp2/test_delp2.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python3
-
 # requires: fftw
 # cores: 4
 
+import pytest
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
-from sys import stdout, exit
+from sys import stdout
 
 tol = 1e-10  # Absolute tolerance
 
@@ -25,15 +25,16 @@
 ]
 
 
-success = True
+@pytest.mark.parametrize("setting", settings)
+def test_delp2(setting):
 
-for i, opts in enumerate(settings):
     # Read benchmark values
-    print("Args: " + opts)
-    cmd = exefile + " " + opts
+    print("Args: " + setting)
+    cmd = exefile + " " + setting
 
     s, out = launch_safe(cmd, nproc=1, pipe=True)
-    with open("run.log." + str(i) + ".1", "w") as f:
+    file_suffix = '.'.join([x.split('=')[-1] for x in setting.split()])
+    with open("run.log." + str(file_suffix) + ".1", "w") as f:
         f.write(out)
 
     n0 = collect("n", path="data", info=False)
@@ -43,24 +44,13 @@
 
         stdout.write("   %d processor...." % (nproc))
         s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True)
-        with open("run.log." + str(i) + "." + str(nproc), "w") as f:
+        with open("run.log." + str(file_suffix) + "." + str(nproc), "w") as f:
             f.write(out)
 
         # Collect output data
         n = collect("n", path="data", info=False)
-        if np.shape(n) != np.shape(n0):
-            print("Fail, wrong shape")
-            success = False
+
+        assert np.shape(n) == np.shape(n0), "Fail, wrong shape"
+
         diff = np.max(np.abs(n - n0))
-        if diff > tol:
-            print("Fail, maximum difference = " + str(diff))
-            success = False
-        else:
-            print("Pass")
-
-if success:
-    print(" => All Delp2 tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+        assert diff <= tol, "Fail, maximum difference = " + str(diff)

From c55ab8f42ab084a20f2950c5680425c1a414dfdc Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Thu, 18 Dec 2025 16:50:42 +0000
Subject: [PATCH 0986/1827] Modify test_fci_boundary to run via pytest

Fails due to missing file `grid.fci.nc`.
---
 .../test-fci-boundary/test_fci_boundary.py    | 100 ++++++++++--------
 1 file changed, 57 insertions(+), 43 deletions(-)

diff --git a/tests/integrated/test-fci-boundary/test_fci_boundary.py b/tests/integrated/test-fci-boundary/test_fci_boundary.py
index e749055185..b557a0802e 100755
--- a/tests/integrated/test-fci-boundary/test_fci_boundary.py
+++ b/tests/integrated/test-fci-boundary/test_fci_boundary.py
@@ -2,54 +2,68 @@
 #
 # Python script to run and analyse MMS test
 
+
+import os
+import pathlib
+import numpy as np
 from boututils.run_wrapper import launch_safe
 from boututils.datafile import DataFile
 from boutdata.collect import collect
 
-import numpy as np
 
+directory = "data"
 
-nprocs = [1]
-mthread = 2
+def collect(var):
+    return _collect(
+        var,
+        info=False,
+        path=directory,
+        xguards=False,
+        yguards=False,
+    )
 
-directory = "data"
 
-with DataFile("grid.fci.nc") as grid:
-    MXG = grid.get("MXG", default=1)
-    xfwd = grid.read("forward_xt_prime")[MXG:-MXG]
-    xbwd = grid.read("backward_xt_prime")[MXG:-MXG]
-
-nx = xfwd.shape[0]
-
-regions = {
-    "xin_fwd": xfwd < MXG,
-    "xout_fwd": xfwd > nx + MXG - 1,
-    "xin_bwd": xbwd < MXG,
-    "xout_bwd": xbwd > nx + MXG - 1,
-}
-regions = {k: v.astype(int) for k, v in regions.items()}
-
-for x in "xout", "xin":
-    regions[x] = regions[f"{x}_fwd"] + regions[f"{x}_bwd"]
-for x in "fwd", "bwd":
-    regions[x] = regions[f"xin_{x}"] + regions[f"xout_{x}"]
-regions["all"] = regions["xin"] + regions["xout"]
-
-for nproc in nprocs:
-    cmd = "./get_par_bndry"
-    _, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-
-    for k, v in regions.items():
-        data = collect(
-            f"field_{k}",
-            info=False,
-            path=directory,
-            xguards=False,
-            yguards=False,
-        )
-        assert np.allclose(data, v), (
-            f"{k} does not match",
-            np.sum(data),
-            np.sum(v),
-            np.max(data),
-        )
+def test_fci_boundary():
+
+    nprocs = [1]
+    mthread = 2
+
+    with DataFile("grid.fci.nc") as grid:
+        MXG = grid.get("MXG", default=1)
+        xfwd = grid.read("forward_xt_prime")[MXG:-MXG]
+        xbwd = grid.read("backward_xt_prime")[MXG:-MXG]
+
+    nx = xfwd.shape[0]
+
+    regions = {
+        "xin_fwd": xfwd < MXG,
+        "xout_fwd": xfwd > nx + MXG - 1,
+        "xin_bwd": xbwd < MXG,
+        "xout_bwd": xbwd > nx + MXG - 1,
+    }
+    regions = {k: v.astype(int) for k, v in regions.items()}
+
+    for x in "xout", "xin":
+        regions[x] = regions[f"{x}_fwd"] + regions[f"{x}_bwd"]
+    for x in "fwd", "bwd":
+        regions[x] = regions[f"xin_{x}"] + regions[f"xout_{x}"]
+    regions["all"] = regions["xin"] + regions["xout"]
+
+    for nproc in nprocs:
+        cmd = "./get_par_bndry"
+        _, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
+
+        for k, v in regions.items():
+            data = collect(
+                f"field_{k}",
+                info=False,
+                path=directory,
+                xguards=False,
+                yguards=False,
+            )
+            assert np.allclose(data, v), (
+                f"{k} does not match",
+                np.sum(data),
+                np.sum(v),
+                np.max(data),
+            )

From 125dd809d7ef6a2adea415f4da1c089a176ac3ac Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Thu, 18 Dec 2025 16:59:41 +0000
Subject: [PATCH 0987/1827] Modify test_fieldgroupcomm to run via pytest

Change directory to exe location prior to attempting to run it.
---
 .../test_fieldgroupComm.py                    | 82 +++++++++----------
 1 file changed, 41 insertions(+), 41 deletions(-)

diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
index ca6d5f89f3..80ff348d8f 100755
--- a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
+++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
@@ -20,57 +20,57 @@
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 from numpy import abs, seterr
-from sys import stdout, exit
+import os
+import pathlib
 
-# Good chance we'll do 0.0/0.0, which generates a warning
-# Ignore this warning
-seterr(divide="ignore", invalid="ignore")
+def test_fieldgroupcomm():
 
-varCorrect = "fld1"
-varsComp = ["fld2", "fld3"]
-name = "FieldGroup comm"
-exeName = "test_fieldgroupcomm"
-tol = 1e-10  # Relative tolerance
+    # Good chance we'll do 0.0/0.0, which generates a warning
+    # Ignore this warning
+    seterr(divide="ignore", invalid="ignore")
 
+    varCorrect = "fld1"
+    varsComp = ["fld2", "fld3"]
+    name = "FieldGroup comm"
+    exeName = "test_fieldgroupcomm"
+    tol = 1e-10  # Relative tolerance
 
-build_and_log("{nm} test".format(nm=name))
 
-print("Running {nm} test".format(nm=name))
-success = True
+    build_and_log("{nm} test".format(nm=name))
 
-for nproc in [1, 2, 4]:
-    nxpe = 1
-    if nproc > 2:
-        nxpe = 2
+    print("Running {nm} test".format(nm=name))
+    success = True
 
-    cmd = "./{exe} ".format(exe=exeName)
+    for nproc in [1, 2, 4]:
+        nxpe = 1
+        if nproc > 2:
+            nxpe = 2
 
-    shell("rm data/BOUT.dmp.*.nc")
+        cmd = "./{exe} ".format(exe=exeName)
 
-    print("   %d processors ...." % (nproc))
-    s, out = launch_safe(cmd, nproc=nproc, pipe=True)
-    with open("run.log." + str(nproc), "w") as f:
-        f.write(out)
+        shell("rm data/BOUT.dmp.*.nc")
 
-    # Analyse result
-    # /"Correct" answer
-    f1 = collect(varCorrect, path="data", info=False)
-    f1max = abs(f1).max()
-    # /Two different fields which should be identical to correct
-    err = []
-    for v in varsComp:
-        tmp = collect(v, path="data", info=False)
-        err.append(abs((f1 - tmp)).max() / f1max)
+        this_directory = pathlib.Path(__file__).parent.absolute()
+        os.chdir(this_directory)
 
-    for i, e in enumerate(err):
-        if e > tol:
-            print("Fail, in {i}th comparison relative error is {re}".format(i=i, re=e))
-            success = False
+        print("   %d processors ...." % (nproc))
+        s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+        with open("run.log." + str(nproc), "w") as f:
+            f.write(out)
 
+        # Analyse result
+        # /"Correct" answer
+        f1 = collect(varCorrect, path="data", info=False)
+        f1max = abs(f1).max()
+        # /Two different fields which should be identical to correct
+        err = []
+        for v in varsComp:
+            tmp = collect(v, path="data", info=False)
+            err.append(abs((f1 - tmp)).max() / f1max)
 
-if success:
-    print(" => All {nm} passed".format(nm=name))
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+        for i, e in enumerate(err):
+            if e > tol:
+                print("Fail, in {i}th comparison relative error is {re}".format(i=i, re=e))
+                success = False
+
+    assert success, " => Some failed tests"

From ede926eb278a896c0b053a4cc72d87879260ba21 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Thu, 18 Dec 2025 17:06:49 +0000
Subject: [PATCH 0988/1827] Modify test_gyro to run via pytest

Change directory to exe location prior to attempting to run it.
---
 tests/integrated/test-gyro/test_gyro.py | 86 ++++++++++++-------------
 1 file changed, 42 insertions(+), 44 deletions(-)

diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py
index 7a0209fa57..86e29f9f32 100755
--- a/tests/integrated/test-gyro/test_gyro.py
+++ b/tests/integrated/test-gyro/test_gyro.py
@@ -23,51 +23,49 @@
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
-from sys import stdout, exit
+from sys import stdout
+import os
+import pathlib
 
-build_and_log("Gyro-average inversion test")
 
-# Read benchmark values
-print("Reading benchmark data")
-bmk = {}
-for v in vars:
-    bmk[v] = collect(v, path="data", prefix="benchmark", info=False, xguards=False)
+def test_gyro():
 
-print("Running Gyro-average inversion test")
-success = True
-
-for nproc in [1, 2, 4]:
-    nxpe = 1
-    if nproc > 2:
-        nxpe = 2
-
-    cmd = "./test_gyro NXPE=" + str(nxpe)
-
-    shell("rm data/BOUT.dmp.*.nc")
-
-    print("   %d processors (nxpe = %d)...." % (nproc, nxpe))
-    s, out = launch_safe(cmd, nproc=nproc, pipe=True)
-    with open("run.log." + str(nproc), "w") as f:
-        f.write(out)
-
-    # Collect output data
+    # Read benchmark values
+    print("Reading benchmark data")
+    bmk = {}
     for v in vars:
-        stdout.write("      Checking variable " + v + " ... ")
-        result = collect(v, path="data", info=False, xguards=False)
-        # Compare benchmark and output
-        if np.shape(bmk[v]) != np.shape(result):
-            print("Fail, wrong shape")
-            success = False
-        diff = np.max(np.abs(bmk[v] - result))
-        if diff > tol:
-            print("Fail, maximum difference = " + str(diff))
-            success = False
-        else:
-            print("Pass")
-
-if success:
-    print(" => All Gyro-average tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+        bmk[v] = collect(v, path="data", prefix="benchmark", info=False, xguards=False)
+
+    print("Running Gyro-average inversion test")
+    success = True
+
+    for nproc in [1, 2, 4]:
+        nxpe = 1
+        if nproc > 2:
+            nxpe = 2
+
+        cmd = "./test_gyro NXPE=" + str(nxpe)
+
+        shell("rm data/BOUT.dmp.*.nc")
+
+        print("   %d processors (nxpe = %d)...." % (nproc, nxpe))
+        s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+        with open("run.log." + str(nproc), "w") as f:
+            f.write(out)
+
+        # Collect output data
+        for v in vars:
+            stdout.write("      Checking variable " + v + " ... ")
+            result = collect(v, path="data", info=False, xguards=False)
+            # Compare benchmark and output
+            if np.shape(bmk[v]) != np.shape(result):
+                print("Fail, wrong shape")
+                success = False
+            diff = np.max(np.abs(bmk[v] - result))
+            if diff > tol:
+                print("Fail, maximum difference = " + str(diff))
+                success = False
+            else:
+                print("Pass")
+
+    assert success, " => Some failed tests"

From cc47c24f773051f5d82b4844490dc7c3a34f2586 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Thu, 18 Dec 2025 17:13:26 +0000
Subject: [PATCH 0989/1827] Modify test_interpolate to run via pytest

Change directory to exe location prior to attempting to run it.
---
 .../test-interpolate/test_interpolate.py      | 28 +++++++++++--------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/tests/integrated/test-interpolate/test_interpolate.py b/tests/integrated/test-interpolate/test_interpolate.py
index 91503f5f9e..8a8eaa546b 100755
--- a/tests/integrated/test-interpolate/test_interpolate.py
+++ b/tests/integrated/test-interpolate/test_interpolate.py
@@ -4,11 +4,15 @@
 # Run the test, compare results against the benchmark
 #
 
+import pytest
+import os
+import pathlib
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata import collect
 import boutconfig
 from numpy import sqrt, max, abs, mean, array, log, polyfit
-from sys import stdout, exit
+from sys import stdout
+
 
 # Display the plots as well as saving to file
 show_plot = False
@@ -30,12 +34,14 @@
 }
 
 
-build_and_log("Interpolation test")
+@pytest.mark.parametrize("method", methods)
+def test_interpolate(method):
+
+    build_and_log("Interpolation test")
 
-print("Running Interpolation test")
-success = True
+    print("Running Interpolation test")
+    success = True
 
-for method in methods:
     print("------------------------------")
     print("Using {} interpolation".format(method))
 
@@ -45,6 +51,9 @@
         error_2[var] = []  # L2 error (RMS)
         error_inf[var] = []  # Maximum error
 
+    this_directory = pathlib.Path(__file__).parent.absolute()
+    os.chdir(this_directory)
+
     for nx in nxlist:
         dx = 1.0 / (nx)
 
@@ -135,10 +144,5 @@ def myplot(f, lbl=None):
     else:
         print("Plotting disabled")
 
-print("------------------------------")
-if success:
-    print(" => All Interpolation tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+    print("------------------------------")
+    assert success, " => Some failed tests"

From 79204e5d8dd98769f639f1b3cdb1cbb22bcad79a Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:11:06 +0000
Subject: [PATCH 0990/1827] Modify test_multigrid_laplace to run via pytest

Change directory before removing files in `data` directory
---
 .../test_multigrid_laplace.py                 | 91 +++++++++----------
 1 file changed, 45 insertions(+), 46 deletions(-)

diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
index f325185c46..e10a536fc2 100755
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
@@ -10,6 +10,9 @@
 
 from __future__ import print_function
 
+import os
+import pathlib
+
 try:
     from builtins import str
 except:
@@ -20,49 +23,45 @@
 
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
-from sys import exit
-
-build_and_log("multigrid Laplacian inversion test")
-
-print("Running multigrid Laplacian inversion test")
-success = True
-
-for nproc in [1, 3]:
-    # Make sure we don't use too many cores:
-    # Reduce number of OpenMP threads when using multiple MPI processes
-    mthread = 2
-    if nproc > 1:
-        mthread = 1
-
-    # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
-    cmd = "./test_multigrid_laplace NXPE=" + str(nproc)
-
-    shell("rm data/BOUT.dmp.*.nc")
-
-    print("   %d processors..." % nproc)
-    s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-    with open("run.log." + str(nproc), "w") as f:
-        f.write(out)
-
-    # Collect errors
-    errors = [
-        collect("max_error" + str(i), path="data") for i in range(1, numTests + 1)
-    ]
-
-    for i, e in enumerate(errors):
-        print("Checking test " + str(i))
-        if e < 0.0:
-            print("Fail, solver did not converge")
-            success = False
-        if e > tol:
-            print("Fail, maximum absolute error = " + str(e))
-            success = False
-        else:
-            print("Pass")
-
-if success:
-    print(" => All multigrid Laplacian inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+
+
+def test_multigrid_laplace():
+
+    print("Running multigrid Laplacian inversion test")
+    success = True
+
+    for nproc in [1, 3]:
+        # Make sure we don't use too many cores:
+        # Reduce number of OpenMP threads when using multiple MPI processes
+        mthread = 2
+        if nproc > 1:
+            mthread = 1
+
+        # set nxpe on the command line as we only use solution from one point in y,
+        # so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
+        cmd = "./test_multigrid_laplace NXPE=" + str(nproc)
+
+        shell("rm data/BOUT.dmp.*.nc")
+
+        print("   %d processors..." % nproc)
+        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
+        with open("run.log." + str(nproc), "w") as f:
+            f.write(out)
+
+        # Collect errors
+        errors = [
+            collect("max_error" + str(i), path="data") for i in range(1, numTests + 1)
+        ]
+
+        for i, e in enumerate(errors):
+            print("Checking test " + str(i))
+            if e < 0.0:
+                print("Fail, solver did not converge")
+                success = False
+            if e > tol:
+                print("Fail, maximum absolute error = " + str(e))
+                success = False
+            else:
+                print("Pass")
+
+    assert success, " => Some failed tests"

From a4ebe18607c3a97ded56c66f3f10819cfd85ed08 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:18:10 +0000
Subject: [PATCH 0991/1827] Modify test_laplace to run via pytest

Change directory before calling `boutdata.collect()`

so that the `data` directory is found.
---
 tests/integrated/test-laplace/test_laplace.py | 85 +++++++++++--------
 1 file changed, 48 insertions(+), 37 deletions(-)

diff --git a/tests/integrated/test-laplace/test_laplace.py b/tests/integrated/test-laplace/test_laplace.py
index 8704447d66..447993bc9c 100755
--- a/tests/integrated/test-laplace/test_laplace.py
+++ b/tests/integrated/test-laplace/test_laplace.py
@@ -41,37 +41,38 @@
 print("Reading benchmark data")
 bmk = {v: collect(v, path="data", prefix="benchmark", info=False) for v in vars}
 
-print("Running Laplacian inversion test")
-success = True
-
-for solver in ["cyclic", "pcr", "pcr_thomas"]:
-    for nproc in [1, 2, 4]:
-        nxpe = 1
-        if nproc > 2:
-            nxpe = 2
-
-        cmd = f"./test_laplace NXPE={nxpe} laplace:type={solver}"
-
-        shell("rm data/BOUT.dmp.*.nc")
-
-        print(f"   {solver} solver with {nproc} processors ({nxpe=})....")
-        s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True)
-        with open(f"run.log.{nproc}", "w") as f:
-            f.write(out)
-
-        cache = create_cache(path="data", prefix="BOUT.dmp")
-
-        # Collect output data
-        for v in vars:
-            print(f"      Checking variable {v} ...", end="")
-            result = collect(v, path="data", info=False, datafile_cache=cache)
-            # Compare benchmark and output
-            try:
-                npt.assert_allclose(result, bmk[v], atol=tol, rtol=tol)
-                print("Pass")
-            except AssertionError as e:
-                print(f"Fail: {e}")
-                success = False
+
+def test_laplace():
+
+    # Read benchmark values
+    print("Reading benchmark data")
+    bmk = {}
+    for v in vars:
+        bmk[v] = collect(v, path="data", prefix="benchmark", info=False)
+
+    print("Running Laplacian inversion test")
+    success = True
+
+    cmd = "./test_laplace NXPE=" + str(nxpe) + " laplace:type=" + solver
+       
+    print(f"   {solver} solver with {nproc} processors ({nxpe=})....")
+    s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True)
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
+
+    cache = create_cache(path="data", prefix="BOUT.dmp")
+
+    # Collect output data
+    for v in vars:
+        print(f"      Checking variable {v} ...", end="")
+        result = collect(v, path="data", info=False, datafile_cache=cache)
+        # Compare benchmark and output
+        try:
+        npt.assert_allclose(result, bmk[v], atol=tol, rtol=tol)
+        print("Pass")
+        except AssertionError as e:
+        print(f"Fail: {e}")
+        success = False
 
         # Only check FieldPerps on one processor because reading them in is
         # quite annoying on mutliple cores due to mismatched global y indices
@@ -89,9 +90,19 @@
                     print(f"Fail: {e}")
                     success = False
 
-if success:
-    print(" => All Laplacian inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+            # Collect output data
+            for v in vars:
+                stdout.write("      Checking variable " + v + " ... ")
+                result = collect(v, path="data", info=False)
+                # Compare benchmark and output
+                if npt.shape(bmk[v]) != npt.shape(result):
+                    print("Fail, wrong shape")
+                    success = False
+                diff = npt.max(npt.abs(bmk[v] - result))
+                if diff > tol:
+                    print("Fail, maximum difference = " + str(diff))
+                    success = False
+                else:
+                    print("Pass")
+
+    assert success, " => Some failed tests"

From fc99e0d906b484cf4b5c760f644321c5ab3d350a Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:21:07 +0000
Subject: [PATCH 0992/1827] Modify test_interpolate_z to run via pytest

---
 .../test-interpolate-z/test_interpolate_z.py  | 170 +++++++++---------
 1 file changed, 83 insertions(+), 87 deletions(-)

diff --git a/tests/integrated/test-interpolate-z/test_interpolate_z.py b/tests/integrated/test-interpolate-z/test_interpolate_z.py
index 1b461d8d4f..cef5e468c0 100755
--- a/tests/integrated/test-interpolate-z/test_interpolate_z.py
+++ b/tests/integrated/test-interpolate-z/test_interpolate_z.py
@@ -7,7 +7,7 @@
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata import collect
 from numpy import sqrt, max, abs, mean, array, log, polyfit
-from sys import stdout, exit
+from sys import stdout
 
 # Display the plots as well as saving to file
 show_plot = False
@@ -28,106 +28,102 @@
 }
 
 
-build_and_log("ZInterpolation test")
+def test_interpolate_z():
+    build_and_log("ZInterpolation test")
 
-print("Running ZInterpolation test")
-success = True
+    print("Running ZInterpolation test")
+    success = True
 
-for method in methods:
-    print("------------------------------")
-    print("Using {} interpolation".format(method))
+    for method in methods:
+        print("------------------------------")
+        print("Using {} interpolation".format(method))
 
-    error_2 = {}
-    error_inf = {}
-    for var in varlist:
-        error_2[var] = []  # L2 error (RMS)
-        error_inf[var] = []  # Maximum error
+        error_2 = {}
+        error_inf = {}
+        for var in varlist:
+            error_2[var] = []  # L2 error (RMS)
+            error_inf[var] = []  # Maximum error
 
-    for nx in nxlist:
-        dx = 1.0 / (nx)
+        for nx in nxlist:
+            dx = 1.0 / (nx)
 
-        args = (
-            " mesh:nx={nx4} mesh:dx={dx} MZ={nx} zinterpolation:type={method}".format(
-                nx4=nx + 4, dx=dx, nx=nx, method=method
+            args = (
+                " mesh:nx={nx4} mesh:dx={dx} MZ={nx} zinterpolation:type={method}".format(
+                    nx4=nx + 4, dx=dx, nx=nx, method=method
+                )
             )
-        )
 
-        cmd = "./test_interpolate" + args
+            cmd = "./test_interpolate" + args
 
-        shell("rm data/BOUT.dmp.*.nc")
+            shell("rm data/BOUT.dmp.*.nc")
 
-        s, out = launch_safe(cmd, nproc=nproc, pipe=True)
-        with open("run.log.{}.{}".format(method, nx), "w") as f:
-            f.write(out)
-
-        # Collect output data
-        for var in varlist:
-            interp = collect(var + "_interp", path="data", xguards=False, info=False)
-            solution = collect(
-                var + "_solution", path="data", xguards=False, info=False
-            )
+            s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+            with open("run.log.{}.{}".format(method, nx), "w") as f:
+                f.write(out)
 
-            E = interp - solution
+            # Collect output data
+            for var in varlist:
+                interp = collect(var + "_interp", path="data", xguards=False, info=False)
+                solution = collect(
+                    var + "_solution", path="data", xguards=False, info=False
+                )
 
-            l2 = float(sqrt(mean(E**2)))
-            linf = float(max(abs(E)))
+                E = interp - solution
 
-            error_2[var].append(l2)
-            error_inf[var].append(linf)
+                l2 = float(sqrt(mean(E**2)))
+                linf = float(max(abs(E)))
 
-            print("{0:s} : l-2 {1:.8f} l-inf {2:.8f}".format(var, l2, linf))
+                error_2[var].append(l2)
+                error_inf[var].append(linf)
 
-    dx = 1.0 / array(nxlist)
+                print("{0:s} : l-2 {1:.8f} l-inf {2:.8f}".format(var, l2, linf))
 
-    for var in varlist:
-        fit = polyfit(log(dx), log(error_2[var]), 1)
-        order = fit[0]
-        stdout.write("{0:s} Convergence order = {1:.2f}".format(var, order))
+        dx = 1.0 / array(nxlist)
 
-        # Make sure scaling is at least 90% of expected order
-        if order < 0.9 * methods[method]:
-            print("............ FAIL")
-            success = False
+        for var in varlist:
+            fit = polyfit(log(dx), log(error_2[var]), 1)
+            order = fit[0]
+            stdout.write("{0:s} Convergence order = {1:.2f}".format(var, order))
+
+            # Make sure scaling is at least 90% of expected order
+            if order < 0.9 * methods[method]:
+                print("............ FAIL")
+                success = False
+            else:
+                print("............ PASS")
+
+        if False:
+            try:
+                import matplotlib.pyplot as plt
+
+                # Plot errors
+                plt.figure()
+
+                for var, mark, label in zip(varlist, markers, labels):
+                    plt.plot(dx, error_2[var], "-" + mark, label=label)
+                    plt.plot(dx, error_inf[var], "--" + mark)
+
+                plt.legend(loc="upper left")
+                plt.grid()
+
+                plt.yscale("log")
+                plt.xscale("log")
+
+                plt.xlabel(r"Mesh spacing $\delta x$")
+                plt.ylabel("Error norm")
+                plt.title("Error scaling for {}".format(method))
+
+                name = "error_scaling_{}.pdf".format(method)
+                plt.savefig(name)
+                print("Plot saved to {}".format(name))
+
+                if show_plot:
+                    plt.show()
+                plt.close()
+            except ImportError:
+                print("No matplotlib available")
         else:
-            print("............ PASS")
-
-    if False:
-        try:
-            import matplotlib.pyplot as plt
-
-            # Plot errors
-            plt.figure()
-
-            for var, mark, label in zip(varlist, markers, labels):
-                plt.plot(dx, error_2[var], "-" + mark, label=label)
-                plt.plot(dx, error_inf[var], "--" + mark)
-
-            plt.legend(loc="upper left")
-            plt.grid()
-
-            plt.yscale("log")
-            plt.xscale("log")
-
-            plt.xlabel(r"Mesh spacing $\delta x$")
-            plt.ylabel("Error norm")
-            plt.title("Error scaling for {}".format(method))
-
-            name = "error_scaling_{}.pdf".format(method)
-            plt.savefig(name)
-            print("Plot saved to {}".format(name))
-
-            if show_plot:
-                plt.show()
-            plt.close()
-        except ImportError:
-            print("No matplotlib available")
-    else:
-        print("Plotting disabled")
-
-print("------------------------------")
-if success:
-    print(" => All Interpolation tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+            print("Plotting disabled")
+
+    print("------------------------------")
+    assert success, " => Some failed tests"

From a9619781d04c0a83d8a88ebc8f59f4b0b2384efa Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:24:56 +0000
Subject: [PATCH 0993/1827] Modify test_interchange_instability to run via
 pytest

---
 .../test_interchange_instability.py           | 150 ++++++++----------
 1 file changed, 69 insertions(+), 81 deletions(-)

diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index 0f75157aaf..005d56153a 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -17,88 +17,76 @@
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
-from sys import stdout, exit
 
 nthreads = 1
 
-build_and_log("interchange instability test")
-
-# Delete old output files
-shell("rm data_1/BOUT.dmp.*")
-shell("rm data_10/BOUT.dmp.*")
-
-
-def growth_rate(path, nproc, log=False):
-    pipe = False
-    if log != False:
-        pipe = True
-    s, out = launch_safe(
-        "./2fluid -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe
+def test_interchange_instability():
+    build_and_log("interchange instability test")
+
+    # Delete old output files
+    shell("rm data_1/BOUT.dmp.*")
+    shell("rm data_10/BOUT.dmp.*")
+
+
+    def growth_rate(path, nproc, log=False):
+        pipe = False
+        if log != False:
+            pipe = True
+        s, out = launch_safe(
+            "./2fluid -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe
+        )
+        if pipe:
+            f = open(log, "w")
+            f.write(out)
+            f.close()
+        # Get time base
+        tarr = collect("t_array", path=path)
+        nt = len(tarr)
+        wci = collect("wci", path=path)
+        tarr = tarr / wci
+
+        # Read density
+        Ni = collect("Ni", path=path, xind=5, yind=30, info=False)
+
+        # Calculate RMS value in Z
+        Nirms = np.zeros(nt)
+        for t in np.arange(nt):
+            Nirms[t] = np.sqrt(np.mean(Ni[t, 0, 0, :] ** 2))
+
+        # Get the growth rate
+        ln = np.log(Nirms)
+        return (ln[nt - 5] - 8.0 * ln[nt - 4] + 8.0 * ln[nt - 2] - ln[nt - 1]) / (
+            6.0 * (tarr[nt - 2] - tarr[nt - 4])
+        )
+
+
+    # Run case 2
+
+    print("Test case 1: R = 1m")
+    growth = growth_rate("data_1", nproc, log="run_1.log")
+    print("   Log file run_1.log")
+    orig = (
+        2.148177e05  # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f
     )
-    if pipe:
-        f = open(log, "w")
-        f.write(out)
-        f.close()
-    # Get time base
-    tarr = collect("t_array", path=path)
-    nt = len(tarr)
-    wci = collect("wci", path=path)
-    tarr = tarr / wci
-
-    # Read density
-    Ni = collect("Ni", path=path, xind=5, yind=30, info=False)
-
-    # Calculate RMS value in Z
-    Nirms = np.zeros(nt)
-    for t in np.arange(nt):
-        Nirms[t] = np.sqrt(np.mean(Ni[t, 0, 0, :] ** 2))
-
-    # Get the growth rate
-    ln = np.log(Nirms)
-    return (ln[nt - 5] - 8.0 * ln[nt - 4] + 8.0 * ln[nt - 2] - ln[nt - 1]) / (
-        6.0 * (tarr[nt - 2] - tarr[nt - 4])
-    )
-
-
-code = 0  # Return code
-
-# Run case 2
-
-print("Test case 1: R = 1m")
-growth = growth_rate("data_1", nproc, log="run_1.log")
-print("   Log file run_1.log")
-orig = (
-    2.148177e05  # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f
-)
-analytic = 2.2e5
-print("   Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic))
-absdev = abs(growth - orig)
-reldev = absdev / orig
-print("   Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0))
-
-if reldev > reltol:
-    print("  => Failed")
-    exit(1)
-else:
-    print("  => Passed")
-
-# Run case 2
-
-print("Test case 2: R = 10m")
-growth = growth_rate("data_10", nproc, log="run_10.log")
-print("   Log file run_10.log")
-# orig = 65570. # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f
-orig = 6.457835e04  # 25th April 2014, revision fd032da
-analytic = 6.3e4
-print("   Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic))
-absdev = abs(growth - orig)
-reldev = absdev / orig
-print("   Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0))
-
-if reldev > reltol:
-    print("  => Failed")
-    code = 1
-else:
-    print("  => Passed")
-
-exit(code)
+    analytic = 2.2e5
+    print("   Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic))
+    absdev = abs(growth - orig)
+    reldev = absdev / orig
+    print("   Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0))
+
+    assert reldev <= reltol, "  => Failed"
+
+    # Run case 2
+
+    print("Test case 2: R = 10m")
+    growth = growth_rate("data_10", nproc, log="run_10.log")
+    print("   Log file run_10.log")
+    # orig = 65570. # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f
+    orig = 6.457835e04  # 25th April 2014, revision fd032da
+    analytic = 6.3e4
+    print("   Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic))
+    absdev = abs(growth - orig)
+    reldev = absdev / orig
+    print("   Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0))
+
+    assert reldev <= reltol, "  => Failed"

From 0e87bf44cf1139e2d56c58bd247e1f7a9e075093 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:27:38 +0000
Subject: [PATCH 0994/1827] Modify test_naulin_laplace to run via pytest

---
 .../test_naulin_laplace.py                    | 87 +++++++++----------
 1 file changed, 41 insertions(+), 46 deletions(-)

diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
index 145257c23b..1626175733 100755
--- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
+++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
@@ -20,49 +20,44 @@
 
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
-from sys import exit
-
-build_and_log("LaplaceNaulin inversion test")
-
-print("Running LaplaceNaulin inversion test")
-success = True
-
-for nproc in [1, 3]:
-    # Make sure we don't use too many cores:
-    # Reduce number of OpenMP threads when using multiple MPI processes
-    mthread = 2
-    if nproc > 1:
-        mthread = 1
-
-    # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver)
-    cmd = "./test_naulin_laplace NXPE=" + str(nproc)
-
-    shell("rm data/BOUT.dmp.*.nc")
-
-    print("   %d processors..." % nproc)
-    s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-    with open("run.log." + str(nproc), "w") as f:
-        f.write(out)
-
-    # Collect errors
-    errors = [
-        collect("max_error" + str(i), path="data") for i in range(1, numTests + 1)
-    ]
-
-    for i, e in enumerate(errors):
-        print("Checking test " + str(i))
-        if e < 0.0:
-            print("Fail, solver did not converge")
-            success = False
-        if e > tol:
-            print("Fail, maximum absolute error = " + str(e))
-            success = False
-        else:
-            print("Pass")
-
-if success:
-    print(" => All LaplaceNaulin inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+
+
+def test_naulin_laplace():
+
+    print("Running LaplaceNaulin inversion test")
+    success = True
+
+    for nproc in [1, 3]:
+        # Make sure we don't use too many cores:
+        # Reduce number of OpenMP threads when using multiple MPI processes
+        mthread = 2
+        if nproc > 1:
+            mthread = 1
+
+        # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver)
+        cmd = "./test_naulin_laplace NXPE=" + str(nproc)
+
+        shell("rm data/BOUT.dmp.*.nc")
+
+        print("   %d processors..." % nproc)
+        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
+        with open("run.log." + str(nproc), "w") as f:
+            f.write(out)
+
+        # Collect errors
+        errors = [
+            collect("max_error" + str(i), path="data") for i in range(1, numTests + 1)
+        ]
+
+        for i, e in enumerate(errors):
+            print("Checking test " + str(i))
+            if e < 0.0:
+                print("Fail, solver did not converge")
+                success = False
+            if e > tol:
+                print("Fail, maximum absolute error = " + str(e))
+                success = False
+            else:
+                print("Pass")
+
+    assert success, " => Some failed tests"

From 869ba6124ad51351a8e794db7246f9f13f98d629 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:30:43 +0000
Subject: [PATCH 0995/1827] Modify test_options_netcdf to run via pytest

---
 .../test_options_netcdf.py                    | 92 ++++++++++---------
 1 file changed, 47 insertions(+), 45 deletions(-)

diff --git a/tests/integrated/test-options-netcdf/test_options_netcdf.py b/tests/integrated/test-options-netcdf/test_options_netcdf.py
index db9adc7f29..ad9196ba2d 100755
--- a/tests/integrated/test-options-netcdf/test_options_netcdf.py
+++ b/tests/integrated/test-options-netcdf/test_options_netcdf.py
@@ -11,63 +11,65 @@
 import math
 import numpy as np
 
-build_and_log("options-netcdf test")
-shell("rm -f test-out.ini")
-shell("rm -f test-out.nc")
+def test_options_netcdf():
 
-# Create a NetCDF input file
-with DataFile("test.nc", create=True, format="NETCDF4") as f:
-    f.write("int", 42)
-    f.write("real", 3.1415)
-    f.write("string", "hello")
+    build_and_log("options-netcdf test")
+    shell("rm -f test-out.ini")
+    shell("rm -f test-out.nc")
 
-# run BOUT++
-launch("./test-options-netcdf", nproc=1, mthread=1)
+    # Create a NetCDF input file
+    with DataFile("test.nc", create=True, format="NETCDF4") as f:
+        f.write("int", 42)
+        f.write("real", 3.1415)
+        f.write("string", "hello")
 
-# Check the output INI file
-result = BoutOptionsFile("test-out.ini")
+    # run BOUT++
+    launch("./test-options-netcdf", nproc=1, mthread=1)
 
-print(result)
+    # Check the output INI file
+    result = BoutOptionsFile("test-out.ini")
 
-assert result["int"] == 42
-assert math.isclose(result["real"], 3.1415)
-assert result["string"] == "hello"
+    print(result)
 
-print("Checking saved NetCDF file")
-
-# Check the output NetCDF file
-with DataFile("test-out.nc") as f:
-    assert f["int"] == 42
-    assert math.isclose(f["real"], 3.1415)
+    assert result["int"] == 42
+    assert math.isclose(result["real"], 3.1415)
     assert result["string"] == "hello"
 
-print("Checking saved settings.ini")
+    print("Checking saved NetCDF file")
+
+    # Check the output NetCDF file
+    with DataFile("test-out.nc") as f:
+        assert f["int"] == 42
+        assert math.isclose(f["real"], 3.1415)
+        assert result["string"] == "hello"
+
+    print("Checking saved settings.ini")
 
-# Check the settings.ini file, coming from BOUT.inp
-# which is converted to NetCDF, read in, then written again
-settings = BoutOptionsFile("settings.ini")
+    # Check the settings.ini file, coming from BOUT.inp
+    # which is converted to NetCDF, read in, then written again
+    settings = BoutOptionsFile("settings.ini")
 
-assert settings["mesh"]["nx"] == 5
-assert settings["mesh"]["ny"] == 2
+    assert settings["mesh"]["nx"] == 5
+    assert settings["mesh"]["ny"] == 2
 
-print("Checking saved fields.nc")
+    print("Checking saved fields.nc")
 
-with DataFile("fields.nc") as f:
-    assert f["f2d"].shape == (5, 6)  # Field2D
-    assert f["f3d"].shape == (5, 6, 2)  # Field3D
-    assert f["fperp"].shape == (5, 2)  # FieldPerp
-    assert np.allclose(f["f2d"], 1.0)
-    assert np.allclose(f["f3d"], 2.0)
-    assert np.allclose(f["fperp"], 3.0)
+    with DataFile("fields.nc") as f:
+        assert f["f2d"].shape == (5, 6)  # Field2D
+        assert f["f3d"].shape == (5, 6, 2)  # Field3D
+        assert f["fperp"].shape == (5, 2)  # FieldPerp
+        assert np.allclose(f["f2d"], 1.0)
+        assert np.allclose(f["f3d"], 2.0)
+        assert np.allclose(f["fperp"], 3.0)
 
-print("Checking saved fields2.nc")
+    print("Checking saved fields2.nc")
 
-with DataFile("fields2.nc") as f:
-    assert f["f2d"].shape == (5, 6)  # Field2D
-    assert f["f3d"].shape == (5, 6, 2)  # Field3D
-    assert f["fperp"].shape == (5, 2)  # FieldPerp
-    assert np.allclose(f["f2d"], 1.0)
-    assert np.allclose(f["f3d"], 2.0)
-    assert np.allclose(f["fperp"], 3.0)
+    with DataFile("fields2.nc") as f:
+        assert f["f2d"].shape == (5, 6)  # Field2D
+        assert f["f3d"].shape == (5, 6, 2)  # Field3D
+        assert f["fperp"].shape == (5, 2)  # FieldPerp
+        assert np.allclose(f["f2d"], 1.0)
+        assert np.allclose(f["f3d"], 2.0)
+        assert np.allclose(f["fperp"], 3.0)
 
-print(" => Passed")
+    print(" => Passed")

From 47a95963beb2c3c984a195459b50abafbdc400fd Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:34:17 +0000
Subject: [PATCH 0996/1827] Modify test_restart_io to run via pytest

---
 .../test-restart-io/test_restart_io.py        | 285 +++++++++---------
 1 file changed, 141 insertions(+), 144 deletions(-)

diff --git a/tests/integrated/test-restart-io/test_restart_io.py b/tests/integrated/test-restart-io/test_restart_io.py
index 00ee907958..66f5fe827c 100755
--- a/tests/integrated/test-restart-io/test_restart_io.py
+++ b/tests/integrated/test-restart-io/test_restart_io.py
@@ -12,7 +12,6 @@
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 import numpy
 import os
-from sys import exit
 import uuid
 
 nx = 8
@@ -21,131 +20,110 @@
 mxg = 2
 myg = 2
 
-build_and_log("restart I/O test")
-
-x = numpy.linspace(0.0, 1.0, nx + 2 * mxg)[:, numpy.newaxis, numpy.newaxis]
-y = numpy.linspace(0.0, 1.0, ny + 2 * myg)[numpy.newaxis, :, numpy.newaxis]
-z = numpy.linspace(0.0, 1.0, nz)[numpy.newaxis, numpy.newaxis, :]
-
-testvars = {}
-testvars["f3d"] = BoutArray(
-    numpy.exp(numpy.sin(x + y + z)), attributes={"bout_type": "Field3D"}
-)
-testvars["f2d"] = BoutArray(
-    numpy.exp(numpy.sin(x + y + 1.0))[:, :, 0], attributes={"bout_type": "Field2D"}
-)
-testvars["fperp_lower"] = BoutArray(
-    numpy.exp(numpy.sin(x + z + 2.0))[:, 0, :],
-    attributes={"bout_type": "FieldPerp", "yindex_global": 0},
-)
-testvars["fperp_upper"] = BoutArray(
-    numpy.exp(numpy.sin(x + z + 3.0))[:, 0, :],
-    attributes={"bout_type": "FieldPerp", "yindex_global": ny - 1},
-)
-
-# make restart file
-restartdir = os.path.join("data", "restart")
-try:
-    os.mkdir(restartdir)
-except FileExistsError:
-    pass
-
-with DataFile(
-    os.path.join(restartdir, "BOUT.restart.0.nc"), create=True
-) as base_restart:
-    base_restart.write("MXSUB", nx)
-    base_restart.write("MYSUB", ny)
-    base_restart.write("MZSUB", nz)
-    base_restart.write("MXG", mxg)
-    base_restart.write("MYG", myg)
-    base_restart.write("MZG", 0)
-    base_restart.write("nx", nx + 2 * mxg)
-    base_restart.write("ny", ny)
-    base_restart.write("nz", nz)
-    base_restart.write("MZ", nz)
-    base_restart.write("NXPE", 1)
-    base_restart.write("NYPE", 1)
-    base_restart.write("NZPE", 1)
-    base_restart.write("tt", 0.0)
-    base_restart.write("hist_hi", 0)
-    # set BOUT_VERSION to stop collect from changing nz or printing a warning
-    base_restart.write("BOUT_VERSION", 4.0)
-    base_restart.write("f3d", testvars["f3d"])
-    base_restart.write("f2d", testvars["f2d"])
-    base_restart.write("fperp_lower", testvars["fperp_lower"])
-    base_restart.write("fperp_upper", testvars["fperp_upper"])
-
-    # make run_id an array of characters because NetCDF doesn't like generic strings
-    run_id_string = "36 character run_id test string ****"
-    run_id = numpy.array(list(run_id_string), dtype="S1")
-    run_id = BoutArray(run_id, attributes={"bout_type": "string"})
-    base_restart.write("run_id", run_id)
-    run_restart_from = numpy.array(
-        list("36 character run_restart_from string"), dtype="S1"
+def test_restart_io():
+
+    build_and_log("restart I/O test")
+
+    x = numpy.linspace(0.0, 1.0, nx + 2 * mxg)[:, numpy.newaxis, numpy.newaxis]
+    y = numpy.linspace(0.0, 1.0, ny + 2 * myg)[numpy.newaxis, :, numpy.newaxis]
+    z = numpy.linspace(0.0, 1.0, nz)[numpy.newaxis, numpy.newaxis, :]
+
+    testvars = {}
+    testvars["f3d"] = BoutArray(
+        numpy.exp(numpy.sin(x + y + z)), attributes={"bout_type": "Field3D"}
+    )
+    testvars["f2d"] = BoutArray(
+        numpy.exp(numpy.sin(x + y + 1.0))[:, :, 0], attributes={"bout_type": "Field2D"}
+    )
+    testvars["fperp_lower"] = BoutArray(
+        numpy.exp(numpy.sin(x + z + 2.0))[:, 0, :],
+        attributes={"bout_type": "FieldPerp", "yindex_global": 0},
+    )
+    testvars["fperp_upper"] = BoutArray(
+        numpy.exp(numpy.sin(x + z + 3.0))[:, 0, :],
+        attributes={"bout_type": "FieldPerp", "yindex_global": ny - 1},
     )
-    run_restart_from = BoutArray(run_restart_from, attributes={"bout_type": "string"})
-    base_restart.write("run_restart_from", run_restart_from)
-
-success = True
-
-# Note: expect this to fail for 16 processors, because when there are 2
-# y-points per processor, the fperp_lower FieldPerp is in the grid cells of one
-# set of processors and also in the guard cells of anoether set. This means
-# valid FieldPerps get written to output files with different
-# y-processor-indices, and collect() cannot handle this.
-for nproc in [1, 2, 4]:
-    # delete any existing output
-    shell("rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc")
-
-    # create restart files for the run
-    restart.redistribute(nproc, path=restartdir, output="data")
-
-    print("   %d processor...." % (nproc))
-
-    # run the test executable
-    s, out = launch_safe("./test-restart-io", nproc=nproc, pipe=True)
-    with open("run.log." + str(nproc), "w") as f:
-        f.write(out)
-
-    # check the results
-    for name in testvars.keys():
-        # check non-evolving version
-        result = collect(
-            name + "_once", path="data", xguards=True, yguards=True, info=False
-        )
-        testvar = testvars[name]
 
-        if not numpy.allclose(testvar, result):
-            success = False
-            print(f"{name}_once is different: {numpy.max(numpy.abs(testvar - result))}")
-            # Don't plot anything by default
-            if False:
-                from boututils.showdata import showdata
-
-                showdata([result, testvar])
-        if name == "fperp_lower" or name == "fperp_upper":
-            yindex_result = result.attributes["yindex_global"]
-            yindex_test = testvar.attributes["yindex_global"]
-            if not yindex_result == yindex_test:
-                success = False
-                print(
-                    "Fail: yindex_global of "
-                    + name
-                    + " is "
-                    + str(yindex_result)
-                    + " should be "
-                    + str(yindex_test)
-                )
-
-        # check evolving versions
-        result = collect(name, path="data", xguards=True, yguards=True, info=False)
-
-        for result_timeslice in result:
-            if not numpy.all(testvar == result_timeslice):
+    # make restart file
+    restartdir = os.path.join("data", "restart")
+    try:
+        os.mkdir(restartdir)
+    except FileExistsError:
+        pass
+
+    with DataFile(
+        os.path.join(restartdir, "BOUT.restart.0.nc"), create=True
+    ) as base_restart:
+        base_restart.write("MXSUB", nx)
+        base_restart.write("MYSUB", ny)
+        base_restart.write("MZSUB", nz)
+        base_restart.write("MXG", mxg)
+        base_restart.write("MYG", myg)
+        base_restart.write("MZG", 0)
+        base_restart.write("nx", nx + 2 * mxg)
+        base_restart.write("ny", ny)
+        base_restart.write("nz", nz)
+        base_restart.write("MZ", nz)
+        base_restart.write("NXPE", 1)
+        base_restart.write("NYPE", 1)
+        base_restart.write("NZPE", 1)
+        base_restart.write("tt", 0.0)
+        base_restart.write("hist_hi", 0)
+        # set BOUT_VERSION to stop collect from changing nz or printing a warning
+        base_restart.write("BOUT_VERSION", 4.0)
+        base_restart.write("f3d", testvars["f3d"])
+        base_restart.write("f2d", testvars["f2d"])
+        base_restart.write("fperp_lower", testvars["fperp_lower"])
+        base_restart.write("fperp_upper", testvars["fperp_upper"])
+
+        # make run_id an array of characters because NetCDF doesn't like generic strings
+        run_id_string = "36 character run_id test string ****"
+        run_id = numpy.array(list(run_id_string), dtype="S1")
+        run_id = BoutArray(run_id, attributes={"bout_type": "string"})
+        base_restart.write("run_id", run_id)
+        run_restart_from = numpy.array(
+            list("36 character run_restart_from string"), dtype="S1"
+        )
+        run_restart_from = BoutArray(run_restart_from, attributes={"bout_type": "string"})
+        base_restart.write("run_restart_from", run_restart_from)
+
+    success = True
+
+    # Note: expect this to fail for 16 processors, because when there are 2
+    # y-points per processor, the fperp_lower FieldPerp is in the grid cells of one
+    # set of processors and also in the guard cells of anoether set. This means
+    # valid FieldPerps get written to output files with different
+    # y-processor-indices, and collect() cannot handle this.
+    for nproc in [1, 2, 4]:
+        # delete any existing output
+        shell("rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc")
+
+        # create restart files for the run
+        restart.redistribute(nproc, path=restartdir, output="data")
+
+        print("   %d processor...." % (nproc))
+
+        # run the test executable
+        s, out = launch_safe("./test-restart-io", nproc=nproc, pipe=True)
+        with open("run.log." + str(nproc), "w") as f:
+            f.write(out)
+
+        # check the results
+        for name in testvars.keys():
+            # check non-evolving version
+            result = collect(
+                name + "_once", path="data", xguards=True, yguards=True, info=False
+            )
+            testvar = testvars[name]
+
+            if not numpy.allclose(testvar, result):
                 success = False
-                print(
-                    f"{name} evolving version is different: {numpy.max(numpy.abs(testvar - result_timeslice))}"
-                )
+                print(f"{name}_once is different: {numpy.max(numpy.abs(testvar - result))}")
+                # Don't plot anything by default
+                if False:
+                    from boututils.showdata import showdata
+
+                    showdata([result, testvar])
             if name == "fperp_lower" or name == "fperp_upper":
                 yindex_result = result.attributes["yindex_global"]
                 yindex_test = testvar.attributes["yindex_global"]
@@ -154,34 +132,53 @@
                     print(
                         "Fail: yindex_global of "
                         + name
-                        + " evolving version is "
+                        + " is "
                         + str(yindex_result)
                         + " should be "
                         + str(yindex_test)
                     )
 
-    # check the run_id
-    run_id = str(collect("run_id", path="data", info=False))
-    # check run_id can be converted to a valid UUID
-    try:
-        uuid.UUID(run_id)
-    except ValueError:
-        success = False
-        print(f"run_id='{run_id}' is not a valid UUID")
-    run_restart_from = str(collect("run_restart_from", path="data", info=False))
-    if not run_restart_from == run_id_string:
-        success = False
-        print(
-            f"incorrect run_restart_from='{run_restart_from}'. Expected '{run_id_string}'"
-        )
+            # check evolving versions
+            result = collect(name, path="data", xguards=True, yguards=True, info=False)
+
+            for result_timeslice in result:
+                if not numpy.all(testvar == result_timeslice):
+                    success = False
+                    print(
+                        f"{name} evolving version is different: {numpy.max(numpy.abs(testvar - result_timeslice))}"
+                    )
+                if name == "fperp_lower" or name == "fperp_upper":
+                    yindex_result = result.attributes["yindex_global"]
+                    yindex_test = testvar.attributes["yindex_global"]
+                    if not yindex_result == yindex_test:
+                        success = False
+                        print(
+                            "Fail: yindex_global of "
+                            + name
+                            + " evolving version is "
+                            + str(yindex_result)
+                            + " should be "
+                            + str(yindex_test)
+                        )
+
+        # check the run_id
+        run_id = str(collect("run_id", path="data", info=False))
+        # check run_id can be converted to a valid UUID
+        try:
+            uuid.UUID(run_id)
+        except ValueError:
+            success = False
+            print(f"run_id='{run_id}' is not a valid UUID")
+        run_restart_from = str(collect("run_restart_from", path="data", info=False))
+        if not run_restart_from == run_id_string:
+            success = False
+            print(
+                f"incorrect run_restart_from='{run_restart_from}'. Expected '{run_id_string}'"
+            )
+
+    assert success, "=> Some failed tests"
 
-if success:
-    print("=> All restart I/O tests passed")
     # clean up binary files
     shell(
         "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc"
     )
-    exit(0)
-
-print("=> Some failed tests")
-exit(1)

From 7dbb5a77acd55e711640e43dc98b13b34f284bcc Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:36:23 +0000
Subject: [PATCH 0997/1827] Modify test_restarting to run via pytest

---
 .../test-restarting/test_restarting.py        | 107 +++++++++---------
 1 file changed, 51 insertions(+), 56 deletions(-)

diff --git a/tests/integrated/test-restarting/test_restarting.py b/tests/integrated/test-restarting/test_restarting.py
index daf19ebac6..f0ca203110 100755
--- a/tests/integrated/test-restarting/test_restarting.py
+++ b/tests/integrated/test-restarting/test_restarting.py
@@ -3,78 +3,73 @@
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
-from sys import stdout, exit
 
-build_and_log("restart test")
 
-# Run once for 10 timesteps
-s, out = launch_safe("./test_restarting solver:nout=10", nproc=1, pipe=True)
+def test_restarting():
 
-# Read reference data
-f3d_0 = collect("f3d", path="data", info=False)
-f2d_0 = collect("f2d", path="data", info=False)
+    # Run once for 10 timesteps
+    s, out = launch_safe("./test_restarting solver:nout=10", nproc=1, pipe=True)
 
-###########################################
-# Run twice, restarting and appending
+    # Read reference data
+    f3d_0 = collect("f3d", path="data", info=False)
+    f2d_0 = collect("f2d", path="data", info=False)
 
-print("-> Testing restart append")
+    ###########################################
+    # Run twice, restarting and appending
 
-shell("rm -f data/BOUT.dmp.0.nc")
-s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True)
-s, out = launch_safe(
-    "./test_restarting solver:nout=5 restart append", nproc=1, pipe=True
-)
+    print("-> Testing restart append")
 
-f3d_1 = collect("f3d", path="data", info=False)
-f2d_1 = collect("f2d", path="data", info=False)
+    shell("rm -f data/BOUT.dmp.0.nc")
+    s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True)
+    s, out = launch_safe(
+        "./test_restarting solver:nout=5 restart append", nproc=1, pipe=True
+    )
 
-success = True
-tolerance = 1e-10
+    f3d_1 = collect("f3d", path="data", info=False)
+    f2d_1 = collect("f2d", path="data", info=False)
 
-if f3d_1.shape != f3d_0.shape:
-    print("Fail: Field3D field has wrong shape")
-    success = False
-if f2d_1.shape != f2d_0.shape:
-    print("Fail: Field2D field has wrong shape")
-    success = False
+    success = True
+    tolerance = 1e-10
 
-if not np.allclose(f3d_1, f3d_0, atol=tolerance):
-    print("Fail: Field3D values differ")
-    success = False
+    if f3d_1.shape != f3d_0.shape:
+        print("Fail: Field3D field has wrong shape")
+        success = False
+    if f2d_1.shape != f2d_0.shape:
+        print("Fail: Field2D field has wrong shape")
+        success = False
 
-if not np.allclose(f2d_1, f2d_0, atol=tolerance):
-    print("Fail: Field2D values differ")
-    success = False
+    if not np.allclose(f3d_1, f3d_0, atol=tolerance):
+        print("Fail: Field3D values differ")
+        success = False
 
-###########################################
-# Test restart
+    if not np.allclose(f2d_1, f2d_0, atol=tolerance):
+        print("Fail: Field2D values differ")
+        success = False
 
-print("-> Testing restart")
+    ###########################################
+    # Test restart
 
-shell("rm -f data/BOUT.dmp.0.nc")
-s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True)
-s, out = launch_safe("./test_restarting solver:nout=5 restart", nproc=1, pipe=True)
+    print("-> Testing restart")
 
-f3d_1 = collect("f3d", path="data", info=False)
-f2d_1 = collect("f2d", path="data", info=False)
+    shell("rm -f data/BOUT.dmp.0.nc")
+    s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True)
+    s, out = launch_safe("./test_restarting solver:nout=5 restart", nproc=1, pipe=True)
 
-if f3d_1.shape[0] != 6:
-    print("Fail: Field3D has wrong shape")
-    success = False
-if f2d_1.shape[0] != 6:
-    print("Fail: Field2D has wrong shape")
-    success = False
+    f3d_1 = collect("f3d", path="data", info=False)
+    f2d_1 = collect("f2d", path="data", info=False)
 
-if not np.allclose(f3d_1, f3d_0[5:, :, :, :], atol=tolerance):
-    print("Fail: Field3D values differ")
-    success = False
-if not np.allclose(f2d_1, f2d_0[5:, :, :], atol=tolerance):
-    print("Fail: Field2D values differ")
-    success = False
+    if f3d_1.shape[0] != 6:
+        print("Fail: Field3D has wrong shape")
+        success = False
+    if f2d_1.shape[0] != 6:
+        print("Fail: Field2D has wrong shape")
+        success = False
 
-if not success:
-    print("=> Some tests failed")
-    exit(1)
+    if not np.allclose(f3d_1, f3d_0[5:, :, :, :], atol=tolerance):
+        print("Fail: Field3D values differ")
+        success = False
+    if not np.allclose(f2d_1, f2d_0[5:, :, :], atol=tolerance):
+        print("Fail: Field2D values differ")
+        success = False
 
-print("=> Success")
-exit(0)
+    assert success, "=> Some tests failed"

From 8d87bdafa65a41e158f41536b4f5599e63e47eed Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:38:42 +0000
Subject: [PATCH 0998/1827] Modify test_smooth to run via pytest

---
 tests/integrated/test-smooth/test_smooth.py | 92 ++++++++++-----------
 1 file changed, 44 insertions(+), 48 deletions(-)

diff --git a/tests/integrated/test-smooth/test_smooth.py b/tests/integrated/test-smooth/test_smooth.py
index 91ae793164..b74000f205 100755
--- a/tests/integrated/test-smooth/test_smooth.py
+++ b/tests/integrated/test-smooth/test_smooth.py
@@ -14,51 +14,47 @@
 from boututils.run_wrapper import build_and_log, shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
-from sys import stdout, exit
-
-build_and_log("smoothing operator test")
-
-# Read benchmark values
-print("Reading benchmark data")
-bmk = {}
-for v in vars:
-    bmk[v] = collect(v, path="data", prefix="benchmark", info=False)
-
-print("Running smoothing operator test")
-success = True
-
-for nype in [1, 2]:
-    for nxpe in [1, 2]:
-        nproc = nxpe * nype
-        cmd = "./test_smooth"
-
-        shell("rm data/BOUT.dmp.*.nc")
-
-        print("   %d processor (%d x %d)...." % (nproc, nxpe, nype))
-        s, out = launch_safe(cmd + " NXPE=" + str(nxpe), nproc=nproc, pipe=True)
-        with open("run.log." + str(nproc), "w") as f:
-            f.write(out)
-
-        # Collect output data
-        for v in vars:
-            stdout.write("      Checking variable " + v + " ... ")
-            result = collect(v, path="data", info=False)
-            # Compare benchmark and output
-            if np.shape(bmk[v]) != np.shape(result):
-                print("Fail, wrong shape")
-                success = False
-                continue
-
-            diff = np.max(np.abs(bmk[v] - result))
-            if diff > tol:
-                print("Fail, maximum difference = " + str(diff))
-                success = False
-            else:
-                print("Pass")
-
-if success:
-    print(" => All smoothing operator tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+from sys import stdout
+
+
+def test_smooth():
+
+    # Read benchmark values
+    print("Reading benchmark data")
+    bmk = {}
+    for v in vars:
+        bmk[v] = collect(v, path="data", prefix="benchmark", info=False)
+
+    print("Running smoothing operator test")
+    success = True
+
+    for nype in [1, 2]:
+        for nxpe in [1, 2]:
+            nproc = nxpe * nype
+            cmd = "./test_smooth"
+
+            shell("rm data/BOUT.dmp.*.nc")
+
+            print("   %d processor (%d x %d)...." % (nproc, nxpe, nype))
+            s, out = launch_safe(cmd + " NXPE=" + str(nxpe), nproc=nproc, pipe=True)
+            with open("run.log." + str(nproc), "w") as f:
+                f.write(out)
+
+            # Collect output data
+            for v in vars:
+                stdout.write("      Checking variable " + v + " ... ")
+                result = collect(v, path="data", info=False)
+                # Compare benchmark and output
+                if np.shape(bmk[v]) != np.shape(result):
+                    print("Fail, wrong shape")
+                    success = False
+                    continue
+
+                diff = np.max(np.abs(bmk[v] - result))
+                if diff > tol:
+                    print("Fail, maximum difference = " + str(diff))
+                    success = False
+                else:
+                    print("Pass")
+
+    assert success, " => Some failed tests"

From e3bb3cdf52fdfce3c2f83048d58ebdaf9a7fd049 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 28 Dec 2025 19:41:43 +0000
Subject: [PATCH 0999/1827] Modify test_squash to run via pytest

---
 tests/integrated/test-squash/test_squash.py | 73 +++++++++++----------
 1 file changed, 37 insertions(+), 36 deletions(-)

diff --git a/tests/integrated/test-squash/test_squash.py b/tests/integrated/test-squash/test_squash.py
index 8bf358ee8e..7fd6621dec 100755
--- a/tests/integrated/test-squash/test_squash.py
+++ b/tests/integrated/test-squash/test_squash.py
@@ -79,51 +79,52 @@ def verify(f1, f2):
                     raise RuntimeError("data mismatch in ", v, err, v1, v2)
 
 
-parser = argparse.ArgumentParser(description="Test the bout-squashoutput wrapper")
-parser.add_argument(
-    "executable", help="Path to bout-squashoutput", default="../../../bin", nargs="?"
-)
-args = parser.parse_args()
+def test_squash():
+    parser = argparse.ArgumentParser(description="Test the bout-squashoutput wrapper")
+    parser.add_argument(
+        "executable", help="Path to bout-squashoutput", default="../../../bin", nargs="?"
+    )
+    args = parser.parse_args()
 
-build_and_log("Squash test")
+    build_and_log("Squash test")
 
-bout_squashoutput = args.executable + "/bout-squashoutput"
+    bout_squashoutput = args.executable + "/bout-squashoutput"
 
-if not os.path.exists(bout_squashoutput):
-    bout_squashoutput = "bout-squashoutput"
+    if not os.path.exists(bout_squashoutput):
+        bout_squashoutput = "bout-squashoutput"
 
-print("Run once to get normal data")
-timed_shell_safe("./squash -q -q -q solver:nout=2")
-timed_shell_safe("mv data/BOUT.dmp.0.nc f1.nc")
+    print("Run once to get normal data")
+    timed_shell_safe("./squash -q -q -q solver:nout=2")
+    timed_shell_safe("mv data/BOUT.dmp.0.nc f1.nc")
 
-print("Parallel test")
-timed_shell_safe("rm -f f2.nc")
-timed_launch_safe("./squash -q -q -q solver:nout=2", nproc=4, mthread=1)
-timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput))
+    print("Parallel test")
+    timed_shell_safe("rm -f f2.nc")
+    timed_launch_safe("./squash -q -q -q solver:nout=2", nproc=4, mthread=1)
+    timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput))
 
-verify("f1.nc", "f2.nc")
+    verify("f1.nc", "f2.nc")
 
-print("Parallel and in two pieces")
-timed_shell_safe("rm -f f2.nc")
-timed_launch_safe("./squash -q -q -q", nproc=4, mthread=1)
-timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput))
-timed_launch_safe("./squash -q -q -q restart", nproc=4, mthread=1)
-timed_shell_safe("{} -qdcal 9 data --outputname ../f2.nc".format(bout_squashoutput))
+    print("Parallel and in two pieces")
+    timed_shell_safe("rm -f f2.nc")
+    timed_launch_safe("./squash -q -q -q", nproc=4, mthread=1)
+    timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput))
+    timed_launch_safe("./squash -q -q -q restart", nproc=4, mthread=1)
+    timed_shell_safe("{} -qdcal 9 data --outputname ../f2.nc".format(bout_squashoutput))
 
-verify("f1.nc", "f2.nc")
+    verify("f1.nc", "f2.nc")
 
-print("Parallel and in two pieces without dump_on_restart")
-timed_shell_safe("rm -f f2.nc")
-timed_launch_safe("./squash -q -q -q", nproc=4, mthread=1)
-timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput))
-timed_launch_safe("./squash -q -q -q restart dump_on_restart=false", nproc=4, mthread=1)
-timed_shell_safe("{} -qdcal 9 data --outputname ../f2.nc".format(bout_squashoutput))
+    print("Parallel and in two pieces without dump_on_restart")
+    timed_shell_safe("rm -f f2.nc")
+    timed_launch_safe("./squash -q -q -q", nproc=4, mthread=1)
+    timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput))
+    timed_launch_safe("./squash -q -q -q restart dump_on_restart=false", nproc=4, mthread=1)
+    timed_shell_safe("{} -qdcal 9 data --outputname ../f2.nc".format(bout_squashoutput))
 
-verify("f1.nc", "f2.nc")
+    verify("f1.nc", "f2.nc")
 
-print("Sequential test")
-timed_shell_safe("rm -f f2.nc")
-timed_shell_safe("./squash -q -q -q solver:nout=2")
-timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput))
+    print("Sequential test")
+    timed_shell_safe("rm -f f2.nc")
+    timed_shell_safe("./squash -q -q -q solver:nout=2")
+    timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput))
 
-verify("f1.nc", "f2.nc")
+    verify("f1.nc", "f2.nc")

From c6e02eb4dd602c95b50f1698d72f85afe561cca9 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 12:22:22 +0000
Subject: [PATCH 1000/1827] Add conftest.py, with contextmanager `chdir` and
 fixture `test_dir`

to temporarily change the current working directory, and get the path to the currently executing test file, respectively.
---
 tests/conftest.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 tests/conftest.py

diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000000..12cfbbb897
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,19 @@
+import os
+import pytest
+from contextlib import contextmanager
+from pathlib import Path
+
+
+@contextmanager
+def chdir(path: Path):
+    """Temporarily change the current working directory."""
+    old_cwd = os.getcwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(old_cwd)
+
+@pytest.fixture
+def test_dir(request) -> Path:
+    return Path(request.fspath).parent

From 9b63aafa7d78ee655c3ef6d6631137594f9d0865 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 12:36:34 +0000
Subject: [PATCH 1001/1827] Use contextmanager `chdir` in tests

---
 tests/integrated/test-beuler/test_beuler.py   |   7 +-
 .../test_communications.py                    | 820 +++++++++---------
 tests/integrated/test-cyclic/test_cyclic.py   |  54 +-
 .../test-stopCheck/test_stopCheck.py          |  34 +-
 4 files changed, 458 insertions(+), 457 deletions(-)

diff --git a/tests/integrated/test-beuler/test_beuler.py b/tests/integrated/test-beuler/test_beuler.py
index 268cd3c986..23c45741a3 100755
--- a/tests/integrated/test-beuler/test_beuler.py
+++ b/tests/integrated/test-beuler/test_beuler.py
@@ -3,17 +3,20 @@
 # requires: petsc
 
 from boututils.run_wrapper import shell_safe, launch_safe
+from contextlib import chdir
+
 
 nthreads = 1
 nproc = 1
 
 
-def test_beuler():
+def test_beuler(test_dir):
     print("Making solver test")
     shell_safe("make > make.log")
 
     print("Running solver test")
-    status, out = launch_safe("./test_beuler", nproc=nproc, mthread=nthreads, pipe=True)
+    with chdir(test_dir):
+        status, out = launch_safe("./test_beuler", nproc=nproc, mthread=nthreads, pipe=True)
     with open("run.log", "w") as f:
         f.write(out)
 
diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index 2ada8c8c9c..3e8e2162bc 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -1,11 +1,9 @@
 #!/usr/bin/env python3
 import os
-import pathlib
-
 import numpy as np
-
 from boututils.datafile import DataFile
 from boututils.run_wrapper import build_and_log, shell, launch_safe
+from contextlib import chdir
 
 # Cores: 18
 # Requires: netcdf
@@ -21,412 +19,410 @@ def run_test(actual, expected, procnum, region, boundary):
             ))
 
 
-def test_communications():
-
-    #################################################
-    # Test disconnected-double-null diverted topology
-    #################################################
-
-    nype = 6  # need at least 6 to include all regions
-
-    # run with processor splitting at separatrices
-    ##################################################
-
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-
-    # With nxpe=3, both separatrices are on processor boundaries
-    nxpe = 3
-    command = "./test-communications NXPE=" + str(nxpe)
-
-    build_and_log("Communications Test")
-
-    this_directory = pathlib.Path(__file__).parent.absolute()
-    os.chdir(this_directory)
-
-    # remove old outputs
-    shell("rm data/BOUT.dmp.*")
-
-    print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-    with open("run.log." + str(nxpe), "w") as f:
-        f.write(out)
-
-    region = "lower, inner PF"
-    f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [24, 25], 0, region, "outer x")
-    run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
-    run_test(f[:, -1], [82, 10, 22, 26], 0, region, "upper y")
-
-    region = "lower, inner between separatrices"
-    f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [48, 49], 0, region, "outer x")
-    run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
-    run_test(f[:, -1], [22, 26, 38, 50], 0, region, "upper y")
-
-    region = "lower, inner SOL"
-    f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [36, 37], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
-    run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
-    run_test(f[:, -1], [38, 50, 62, 86], 0, region, "upper y")
-
-    region = "inner core"
-    f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [26, 27], 0, region, "outer x")
-    run_test(f[:, 0], [81, 9, 21, 25], 0, region, "lower y")
-    run_test(f[:, -1], [80, 8, 20, 32], 0, region, "upper y")
-
-    region = "inner between separatrices"
-    f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [14, 15], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [50, 51], 0, region, "outer x")
-    run_test(f[:, 0], [21, 25, 37, 49], 0, region, "lower y")
-    run_test(f[:, -1], [20, 32, 44, 52], 0, region, "upper y")
-
-    region = "inner SOL"
-    f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [38, 39], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
-    run_test(f[:, 0], [37, 49, 61, 85], 0, region, "lower y")
-    run_test(f[:, -1], [44, 52, 64, 88], 0, region, "upper y")
-
-    region = "upper inner PF"
-    f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [28, 29], 0, region, "outer x")
-    run_test(f[:, 0], [79, 7, 19, 31], 0, region, "lower y")
-    run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
-
-    region = "upper inner SOL, nearer PF"
-    f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [16, 17], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [52, 53], 0, region, "outer x")
-    run_test(f[:, 0], [19, 31, 43, 51], 0, region, "lower y")
-    run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
-
-    region = "upper inner SOL, further from PF"
-    f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [40, 41], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
-    run_test(f[:, 0], [43, 51, 63, 87], 0, region, "lower y")
-    run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
-
-    region = "upper outer PF"
-    f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [30, 31], 0, region, "outer x")
-    run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
-    run_test(f[:, -1], [76, 4, 16, 28], 0, region, "upper y")
-
-    region = "upper outer SOL, nearer PF"
-    f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [18, 19], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [54, 55], 0, region, "outer x")
-    run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
-    run_test(f[:, -1], [16, 28, 40, 56], 0, region, "upper y")
-
-    region = "upper outer SOL, further from PF"
-    f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [42, 43], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
-    run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
-    run_test(f[:, -1], [40, 56, 68, 92], 0, region, "upper y")
-
-    region = "outer core"
-    f = DataFile("data/BOUT.dmp.12.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [32, 33], 0, region, "outer x")
-    run_test(f[:, 0], [75, 3, 15, 27], 0, region, "lower y")
-    run_test(f[:, -1], [74, 2, 14, 34], 0, region, "upper y")
-
-    region = "outer between separatrices"
-    f = DataFile("data/BOUT.dmp.13.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [20, 21], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [56, 57], 0, region, "outer x")
-    run_test(f[:, 0], [15, 27, 39, 55], 0, region, "lower y")
-    run_test(f[:, -1], [14, 34, 46, 58], 0, region, "upper y")
-
-    region = "outer SOL"
-    f = DataFile("data/BOUT.dmp.14.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [44, 45], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
-    run_test(f[:, 0], [39, 55, 67, 91], 0, region, "lower y")
-    run_test(f[:, -1], [46, 58, 70, 94], 0, region, "upper y")
-
-    region = "lower outer PF"
-    f = DataFile("data/BOUT.dmp.15.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [34, 35], 0, region, "outer x")
-    run_test(f[:, 0], [73, 1, 13, 33], 0, region, "lower y")
-    run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
-
-    region = "lower outer between separatrices"
-    f = DataFile("data/BOUT.dmp.16.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [22, 23], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [58, 59], 0, region, "outer x")
-    run_test(f[:, 0], [13, 33, 45, 57], 0, region, "lower y")
-    run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
-
-    region = "lower outer SOL"
-    f = DataFile("data/BOUT.dmp.17.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [46, 47], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
-    run_test(f[:, 0], [45, 57, 69, 93], 0, region, "lower y")
-    run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
-
-    # run with processor splitting not at separatrices
-    ##################################################
-
-    # With nxpe=2, neither separatrix is on a processor boundary
-    nxpe = 2
-    command = "./test-communications NXPE=" + str(nxpe)
-
-    # remove old outputs
-    shell("rm data/BOUT.dmp.*")
-
-    print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-    with open("run.log." + str(nxpe), "w") as f:
-        f.write(out)
-
-    region = "lower, inner leg, interior"
-    f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [36, 37], 0, region, "outer x")
-    run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
-    run_test(f[:, -1], [82, 10, 22, 26, 38], 0, region, "upper y")
-
-    region = "lower, inner leg, exterior"
-    f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [24, 25], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
-    run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
-    run_test(f[:, -1], [26, 38, 50, 62, 86], 0, region, "upper y")
-
-    region = "inner, interior"
-    f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [38, 39], 0, region, "outer x")
-    run_test(f[:, 0], [81, 9, 21, 25, 37], 0, region, "lower y")
-    run_test(f[:, -1], [80, 8, 20, 32, 44], 0, region, "upper y")
-
-    region = "inner, exterior"
-    f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [26, 27], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
-    run_test(f[:, 0], [25, 37, 49, 61, 85], 0, region, "lower y")
-    run_test(f[:, -1], [32, 44, 52, 64, 88], 0, region, "upper y")
-
-    region = "upper, inner leg, interior"
-    f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [40, 41], 0, region, "outer x")
-    run_test(f[:, 0], [79, 7, 19, 31, 43], 0, region, "lower y")
-    run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
-
-    region = "upper, inner leg, exterior"
-    f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [28, 29], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
-    run_test(f[:, 0], [31, 43, 51, 63, 87], 0, region, "lower y")
-    run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
-
-    region = "upper, outer leg, interior"
-    f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [42, 43], 0, region, "outer x")
-    run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
-    run_test(f[:, -1], [76, 4, 16, 28, 40], 0, region, "upper y")
-
-    region = "upper, outer leg, exterior"
-    f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [30, 31], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
-    run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
-    run_test(f[:, -1], [28, 40, 56, 68, 92], 0, region, "upper y")
-
-    region = "outer, interior"
-    f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [44, 45], 0, region, "outer x")
-    run_test(f[:, 0], [75, 3, 15, 27, 39], 0, region, "lower y")
-    run_test(f[:, -1], [74, 2, 14, 34, 46], 0, region, "upper y")
-
-    region = "outer, exterior"
-    f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [32, 33], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
-    run_test(f[:, 0], [27, 39, 55, 67, 91], 0, region, "lower y")
-    run_test(f[:, -1], [34, 46, 58, 70, 94], 0, region, "upper y")
-
-    region = "lower, outer leg, interior"
-    f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [46, 47], 0, region, "outer x")
-    run_test(f[:, 0], [73, 1, 13, 33, 45], 0, region, "lower y")
-    run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
-
-    region = "lower, outer leg, exterior"
-    f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [34, 35], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
-    run_test(f[:, 0], [33, 45, 57, 69, 93], 0, region, "lower y")
-    run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
-
-    # run with no processor splitting in the x-direction
-    ####################################################
-
-    nxpe = 1
-
-    command = "./test-communications NXPE=" + str(nxpe)
-
-    # remove old outputs
-    shell("rm data/BOUT.dmp.*")
-
-    print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-    with open("run.log." + str(nxpe), "w") as f:
-        f.write(out)
-
-    region = "lower, inner leg"
-    f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
-    run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
-    run_test(f[:, -1], [82, 10, 22, 26, 38, 50, 62, 86], 0, region, "upper y")
-
-    region = "inner"
-    f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
-    run_test(f[:, 0], [81, 9, 21, 25, 37, 49, 61, 85], 0, region, "lower y")
-    run_test(f[:, -1], [80, 8, 20, 32, 44, 52, 64, 88], 0, region, "upper y")
-
-    region = "upper, inner leg"
-    f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
-    run_test(f[:, 0], [79, 7, 19, 31, 43, 51, 63, 87], 0, region, "lower y")
-    run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
-
-    region = "upper, outer leg"
-    f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
-    run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
-    run_test(f[:, -1], [76, 4, 16, 28, 40, 56, 68, 92], 0, region, "upper y")
-
-    region = "outer"
-    f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
-    run_test(f[:, 0], [75, 3, 15, 27, 39, 55, 67, 91], 0, region, "lower y")
-    run_test(f[:, -1], [74, 2, 14, 34, 46, 58, 70, 94], 0, region, "upper y")
-
-    region = "lower, outer leg"
-    f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
-    run_test(f[:, 0], [73, 1, 13, 33, 45, 57, 69, 93], 0, region, "lower y")
-    run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
-
-
-    #################################################
-    # Test limiter topology
-    #################################################
-
-    nype = 1
-
-    # run with processor splitting at the separatrix
-    ####################################################
-
-    nxpe = 3
-    command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
-
-    # remove old outputs
-    shell("rm data_limiter/BOUT.dmp.*")
-
-    print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-    with open("run_limiter.log." + str(nxpe), "w") as f:
-        f.write(out)
-
-    region = "core"
-    f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [4, 5], 0, region, "outer x")
-    run_test(f[:, 0], [13, 1, 3, 19], 0, region, "lower y")
-    run_test(f[:, -1], [12, 0, 2, 27], 0, region, "upper y")
-
-    region = "interior SOL"
-    f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [2, 3], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [8, 9], 0, region, "outer x")
-    run_test(f[:, 0], [3, 19, 20, 21], 0, region, "lower y")
-    run_test(f[:, -1], [2, 27, 28, 29], 0, region, "upper y")
-
-    region = "exterior SOL"
-    f = DataFile("data_limiter/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [6, 7], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
-    run_test(f[:, 0], [20, 21, 22, 23], 0, region, "lower y")
-    run_test(f[:, -1], [28, 29, 30, 31], 0, region, "upper y")
-
-    # run with processor splitting not at the separatrix
-    ####################################################
-
-    nxpe = 2
-    command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
-
-    # remove old outputs
-    shell("rm data_limiter/BOUT.dmp.*")
-
-    print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-    with open("run_limiter.log." + str(nxpe), "w") as f:
-        f.write(out)
-
-    region = "interior"
-    f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [6, 7], 0, region, "outer x")
-    run_test(f[:, 0], [13, 1, 3, 19, 20], 0, region, "lower y")
-    run_test(f[:, -1], [12, 0, 2, 27, 28], 0, region, "upper y")
-
-    region = "exterior"
-    f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [4, 5], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
-    run_test(f[:, 0], [19, 20, 21, 22, 23], 0, region, "lower y")
-    run_test(f[:, -1], [27, 28, 29, 30, 31], 0, region, "upper y")
-
-    # run with no processor splitting in the x-direction
-    ####################################################
-
-    nxpe = 1
-    command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
-
-    # remove old outputs
-    shell("rm data_limiter/BOUT.dmp.*")
-
-    print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-    with open("run_limiter.log." + str(nxpe), "w") as f:
-        f.write(out)
-
-    region = "all"
-    f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-    run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
-    run_test(f[:, 0], [13, 1, 3, 19, 20, 21, 22, 23], 0, region, "lower y")
-    run_test(f[:, -1], [12, 0, 2, 27, 28, 29, 30, 31], 0, region, "upper y")
+def test_communications(test_dir):
+
+    with chdir(test_dir):
+        #################################################
+        # Test disconnected-double-null diverted topology
+        #################################################
+
+        nype = 6  # need at least 6 to include all regions
+
+        # run with processor splitting at separatrices
+        ##################################################
+
+        # MPI oversubscribe for communications test
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+
+        # With nxpe=3, both separatrices are on processor boundaries
+        nxpe = 3
+        command = "./test-communications NXPE=" + str(nxpe)
+
+        build_and_log("Communications Test")
+
+        # remove old outputs
+        shell("rm data/BOUT.dmp.*")
+
+        print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+        with open("run.log." + str(nxpe), "w") as f:
+            f.write(out)
+
+        region = "lower, inner PF"
+        f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [24, 25], 0, region, "outer x")
+        run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
+        run_test(f[:, -1], [82, 10, 22, 26], 0, region, "upper y")
+
+        region = "lower, inner between separatrices"
+        f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [48, 49], 0, region, "outer x")
+        run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
+        run_test(f[:, -1], [22, 26, 38, 50], 0, region, "upper y")
+
+        region = "lower, inner SOL"
+        f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [36, 37], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
+        run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
+        run_test(f[:, -1], [38, 50, 62, 86], 0, region, "upper y")
+
+        region = "inner core"
+        f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [26, 27], 0, region, "outer x")
+        run_test(f[:, 0], [81, 9, 21, 25], 0, region, "lower y")
+        run_test(f[:, -1], [80, 8, 20, 32], 0, region, "upper y")
+
+        region = "inner between separatrices"
+        f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [14, 15], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [50, 51], 0, region, "outer x")
+        run_test(f[:, 0], [21, 25, 37, 49], 0, region, "lower y")
+        run_test(f[:, -1], [20, 32, 44, 52], 0, region, "upper y")
+
+        region = "inner SOL"
+        f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [38, 39], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
+        run_test(f[:, 0], [37, 49, 61, 85], 0, region, "lower y")
+        run_test(f[:, -1], [44, 52, 64, 88], 0, region, "upper y")
+
+        region = "upper inner PF"
+        f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [28, 29], 0, region, "outer x")
+        run_test(f[:, 0], [79, 7, 19, 31], 0, region, "lower y")
+        run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
+
+        region = "upper inner SOL, nearer PF"
+        f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [16, 17], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [52, 53], 0, region, "outer x")
+        run_test(f[:, 0], [19, 31, 43, 51], 0, region, "lower y")
+        run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
+
+        region = "upper inner SOL, further from PF"
+        f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [40, 41], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
+        run_test(f[:, 0], [43, 51, 63, 87], 0, region, "lower y")
+        run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
+
+        region = "upper outer PF"
+        f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [30, 31], 0, region, "outer x")
+        run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
+        run_test(f[:, -1], [76, 4, 16, 28], 0, region, "upper y")
+
+        region = "upper outer SOL, nearer PF"
+        f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [18, 19], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [54, 55], 0, region, "outer x")
+        run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
+        run_test(f[:, -1], [16, 28, 40, 56], 0, region, "upper y")
+
+        region = "upper outer SOL, further from PF"
+        f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [42, 43], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
+        run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
+        run_test(f[:, -1], [40, 56, 68, 92], 0, region, "upper y")
+
+        region = "outer core"
+        f = DataFile("data/BOUT.dmp.12.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [32, 33], 0, region, "outer x")
+        run_test(f[:, 0], [75, 3, 15, 27], 0, region, "lower y")
+        run_test(f[:, -1], [74, 2, 14, 34], 0, region, "upper y")
+
+        region = "outer between separatrices"
+        f = DataFile("data/BOUT.dmp.13.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [20, 21], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [56, 57], 0, region, "outer x")
+        run_test(f[:, 0], [15, 27, 39, 55], 0, region, "lower y")
+        run_test(f[:, -1], [14, 34, 46, 58], 0, region, "upper y")
+
+        region = "outer SOL"
+        f = DataFile("data/BOUT.dmp.14.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [44, 45], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
+        run_test(f[:, 0], [39, 55, 67, 91], 0, region, "lower y")
+        run_test(f[:, -1], [46, 58, 70, 94], 0, region, "upper y")
+
+        region = "lower outer PF"
+        f = DataFile("data/BOUT.dmp.15.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [34, 35], 0, region, "outer x")
+        run_test(f[:, 0], [73, 1, 13, 33], 0, region, "lower y")
+        run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
+
+        region = "lower outer between separatrices"
+        f = DataFile("data/BOUT.dmp.16.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [22, 23], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [58, 59], 0, region, "outer x")
+        run_test(f[:, 0], [13, 33, 45, 57], 0, region, "lower y")
+        run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
+
+        region = "lower outer SOL"
+        f = DataFile("data/BOUT.dmp.17.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [46, 47], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
+        run_test(f[:, 0], [45, 57, 69, 93], 0, region, "lower y")
+        run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
+
+        # run with processor splitting not at separatrices
+        ##################################################
+
+        # With nxpe=2, neither separatrix is on a processor boundary
+        nxpe = 2
+        command = "./test-communications NXPE=" + str(nxpe)
+
+        # remove old outputs
+        shell("rm data/BOUT.dmp.*")
+
+        print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+        with open("run.log." + str(nxpe), "w") as f:
+            f.write(out)
+
+        region = "lower, inner leg, interior"
+        f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [36, 37], 0, region, "outer x")
+        run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
+        run_test(f[:, -1], [82, 10, 22, 26, 38], 0, region, "upper y")
+
+        region = "lower, inner leg, exterior"
+        f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [24, 25], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
+        run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
+        run_test(f[:, -1], [26, 38, 50, 62, 86], 0, region, "upper y")
+
+        region = "inner, interior"
+        f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [38, 39], 0, region, "outer x")
+        run_test(f[:, 0], [81, 9, 21, 25, 37], 0, region, "lower y")
+        run_test(f[:, -1], [80, 8, 20, 32, 44], 0, region, "upper y")
+
+        region = "inner, exterior"
+        f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [26, 27], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
+        run_test(f[:, 0], [25, 37, 49, 61, 85], 0, region, "lower y")
+        run_test(f[:, -1], [32, 44, 52, 64, 88], 0, region, "upper y")
+
+        region = "upper, inner leg, interior"
+        f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [40, 41], 0, region, "outer x")
+        run_test(f[:, 0], [79, 7, 19, 31, 43], 0, region, "lower y")
+        run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
+
+        region = "upper, inner leg, exterior"
+        f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [28, 29], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
+        run_test(f[:, 0], [31, 43, 51, 63, 87], 0, region, "lower y")
+        run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
+
+        region = "upper, outer leg, interior"
+        f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [42, 43], 0, region, "outer x")
+        run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
+        run_test(f[:, -1], [76, 4, 16, 28, 40], 0, region, "upper y")
+
+        region = "upper, outer leg, exterior"
+        f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [30, 31], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
+        run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
+        run_test(f[:, -1], [28, 40, 56, 68, 92], 0, region, "upper y")
+
+        region = "outer, interior"
+        f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [44, 45], 0, region, "outer x")
+        run_test(f[:, 0], [75, 3, 15, 27, 39], 0, region, "lower y")
+        run_test(f[:, -1], [74, 2, 14, 34, 46], 0, region, "upper y")
+
+        region = "outer, exterior"
+        f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [32, 33], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
+        run_test(f[:, 0], [27, 39, 55, 67, 91], 0, region, "lower y")
+        run_test(f[:, -1], [34, 46, 58, 70, 94], 0, region, "upper y")
+
+        region = "lower, outer leg, interior"
+        f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [46, 47], 0, region, "outer x")
+        run_test(f[:, 0], [73, 1, 13, 33, 45], 0, region, "lower y")
+        run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
+
+        region = "lower, outer leg, exterior"
+        f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [34, 35], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
+        run_test(f[:, 0], [33, 45, 57, 69, 93], 0, region, "lower y")
+        run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
+
+        # run with no processor splitting in the x-direction
+        ####################################################
+
+        nxpe = 1
+
+        command = "./test-communications NXPE=" + str(nxpe)
+
+        # remove old outputs
+        shell("rm data/BOUT.dmp.*")
+
+        print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+        with open("run.log." + str(nxpe), "w") as f:
+            f.write(out)
+
+        region = "lower, inner leg"
+        f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
+        run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
+        run_test(f[:, -1], [82, 10, 22, 26, 38, 50, 62, 86], 0, region, "upper y")
+
+        region = "inner"
+        f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
+        run_test(f[:, 0], [81, 9, 21, 25, 37, 49, 61, 85], 0, region, "lower y")
+        run_test(f[:, -1], [80, 8, 20, 32, 44, 52, 64, 88], 0, region, "upper y")
+
+        region = "upper, inner leg"
+        f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
+        run_test(f[:, 0], [79, 7, 19, 31, 43, 51, 63, 87], 0, region, "lower y")
+        run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
+
+        region = "upper, outer leg"
+        f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
+        run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
+        run_test(f[:, -1], [76, 4, 16, 28, 40, 56, 68, 92], 0, region, "upper y")
+
+        region = "outer"
+        f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
+        run_test(f[:, 0], [75, 3, 15, 27, 39, 55, 67, 91], 0, region, "lower y")
+        run_test(f[:, -1], [74, 2, 14, 34, 46, 58, 70, 94], 0, region, "upper y")
+
+        region = "lower, outer leg"
+        f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
+        run_test(f[:, 0], [73, 1, 13, 33, 45, 57, 69, 93], 0, region, "lower y")
+        run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
+
+
+        #################################################
+        # Test limiter topology
+        #################################################
+
+        nype = 1
+
+        # run with processor splitting at the separatrix
+        ####################################################
+
+        nxpe = 3
+        command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
+
+        # remove old outputs
+        shell("rm data_limiter/BOUT.dmp.*")
+
+        print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+        with open("run_limiter.log." + str(nxpe), "w") as f:
+            f.write(out)
+
+        region = "core"
+        f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [4, 5], 0, region, "outer x")
+        run_test(f[:, 0], [13, 1, 3, 19], 0, region, "lower y")
+        run_test(f[:, -1], [12, 0, 2, 27], 0, region, "upper y")
+
+        region = "interior SOL"
+        f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [2, 3], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [8, 9], 0, region, "outer x")
+        run_test(f[:, 0], [3, 19, 20, 21], 0, region, "lower y")
+        run_test(f[:, -1], [2, 27, 28, 29], 0, region, "upper y")
+
+        region = "exterior SOL"
+        f = DataFile("data_limiter/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [6, 7], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
+        run_test(f[:, 0], [20, 21, 22, 23], 0, region, "lower y")
+        run_test(f[:, -1], [28, 29, 30, 31], 0, region, "upper y")
+
+        # run with processor splitting not at the separatrix
+        ####################################################
+
+        nxpe = 2
+        command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
+
+        # remove old outputs
+        shell("rm data_limiter/BOUT.dmp.*")
+
+        print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+        with open("run_limiter.log." + str(nxpe), "w") as f:
+            f.write(out)
+
+        region = "interior"
+        f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [6, 7], 0, region, "outer x")
+        run_test(f[:, 0], [13, 1, 3, 19, 20], 0, region, "lower y")
+        run_test(f[:, -1], [12, 0, 2, 27, 28], 0, region, "upper y")
+
+        region = "exterior"
+        f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [4, 5], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
+        run_test(f[:, 0], [19, 20, 21, 22, 23], 0, region, "lower y")
+        run_test(f[:, -1], [27, 28, 29, 30, 31], 0, region, "upper y")
+
+        # run with no processor splitting in the x-direction
+        ####################################################
+
+        nxpe = 1
+        command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
+
+        # remove old outputs
+        shell("rm data_limiter/BOUT.dmp.*")
+
+        print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+        with open("run_limiter.log." + str(nxpe), "w") as f:
+            f.write(out)
+
+        region = "all"
+        f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+        run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+        run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
+        run_test(f[:, 0], [13, 1, 3, 19, 20, 21, 22, 23], 0, region, "lower y")
+        run_test(f[:, -1], [12, 0, 2, 27, 28, 29, 30, 31], 0, region, "upper y")
diff --git a/tests/integrated/test-cyclic/test_cyclic.py b/tests/integrated/test-cyclic/test_cyclic.py
index 0a0733926b..a3780e10b2 100755
--- a/tests/integrated/test-cyclic/test_cyclic.py
+++ b/tests/integrated/test-cyclic/test_cyclic.py
@@ -14,42 +14,44 @@
 except:
     pass
 from boututils.run_wrapper import build_and_log, shell, launch
-from boutdata.collect import collect
 from sys import stdout
+from contextlib import chdir
 
 build_and_log("Cyclic Reduction test")
 
 flags = ["", "nsys=2", "nsys=5 periodic", "nsys=7 n=10"]
 
 
-def test_cyclic():
-    code = 0  # Return code
-    for nproc in [1, 2, 4]:
-        cmd = "./test_cyclic"
+def test_cyclic(test_dir):
 
-        print("   %d processors...." % (nproc))
-        r = 0
-        for f in flags:
-            stdout.write("\tflags '" + f + "' ... ")
+    with chdir(test_dir):
+        code = 0  # Return code
+        for nproc in [1, 2, 4]:
+            cmd = "./test_cyclic"
 
-            shell("rm data/BOUT.dmp.* 2> err.log")
+            print("   %d processors...." % (nproc))
+            r = 0
+            for f in flags:
+                stdout.write("\tflags '" + f + "' ... ")
 
-            # Run the case
-            status, out = launch(cmd + " " + f, nproc=nproc, mthread=1, pipe=True)
-            with open(f"run.log.{nproc}.{r}", "w") as f:
-                f.write(out)
+                shell("rm data/BOUT.dmp.* 2> err.log")
 
-            r = r + 1
+                # Run the case
+                status, out = launch(cmd + " " + f, nproc=nproc, mthread=1, pipe=True)
+                with open(f"run.log.{nproc}.{r}", "w") as f:
+                    f.write(out)
 
-            # Find out if it worked
-            if status:
-                print("PASSED")
-            else:
-                print("FAILED")
-                code = 1
-            assert status, f"Test failed for flag={f}"
+                r = r + 1
 
-    if code == 0:
-        print(" => All cyclic reduction tests passed")
-    else:
-        print(" => Some failed tests")
+                # Find out if it worked
+                if status:
+                    print("PASSED")
+                else:
+                    print("FAILED")
+                    code = 1
+                assert status, f"Test failed for flag={f}"
+
+        if code == 0:
+            print(" => All cyclic reduction tests passed")
+        else:
+            print(" => Some failed tests")
diff --git a/tests/integrated/test-stopCheck/test_stopCheck.py b/tests/integrated/test-stopCheck/test_stopCheck.py
index 32e052f0bd..56dee2be5a 100644
--- a/tests/integrated/test-stopCheck/test_stopCheck.py
+++ b/tests/integrated/test-stopCheck/test_stopCheck.py
@@ -1,9 +1,10 @@
 import os
 import subprocess
 import time
+from contextlib import chdir
 
 
-def test_runtest():
+def test_runtest(test_dir):
     # BOUT_TOP from script dir (CWD-independent)
     script_dir = os.path.dirname(os.path.abspath(__file__))
     bout_root = os.path.abspath(os.path.join(script_dir, ".."))
@@ -14,22 +15,21 @@ def test_runtest():
     if os.path.exists(pylib_path):
         os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
 
-    test_dir = os.path.dirname(os.path.abspath(__file__))
     # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
 
-    os.chdir(test_dir)
+    with chdir(test_dir):
+        build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+        if build_result.returncode != 0:
+            print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
 
-    # MPI oversubscribe for communications test
-    cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+        # MPI oversubscribe for communications test
+        cmd = './runtest'
+        if "communications" in str(test_dir):
+            os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+        start = time.time()
+        result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+        elapsed = time.time() - start
+        print(f"Output: {result.stdout}")
+        if result.returncode != 0:
+            print(f"Stderr: {result.stderr}")
+        assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"

From e3e853c6f17c4170da76c772c0e7ce26153df3d9 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 13:05:04 +0000
Subject: [PATCH 1002/1827] Use monkeypatch.chdir() fixture instead of
 contextmanager

---
 tests/conftest.py                             |  15 +-
 .../test_communications.py                    | 814 +++++++++---------
 tests/integrated/test-cyclic/test_cyclic.py   |  52 +-
 .../test-stopCheck/test_stopCheck.py          |  30 +-
 4 files changed, 449 insertions(+), 462 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 12cfbbb897..8c0d4e9621 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,18 +1,11 @@
-import os
 import pytest
-from contextlib import contextmanager
 from pathlib import Path
 
 
-@contextmanager
-def chdir(path: Path):
-    """Temporarily change the current working directory."""
-    old_cwd = os.getcwd()
-    os.chdir(path)
-    try:
-        yield
-    finally:
-        os.chdir(old_cwd)
+@pytest.fixture(autouse=True)
+def cwd_to_test_file_dir(monkeypatch, test_dir):
+    """Automatically change CWD to the directory of the current test file."""
+    monkeypatch.chdir(test_dir)
 
 @pytest.fixture
 def test_dir(request) -> Path:
diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index 3e8e2162bc..05e52821e7 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -3,7 +3,6 @@
 import numpy as np
 from boututils.datafile import DataFile
 from boututils.run_wrapper import build_and_log, shell, launch_safe
-from contextlib import chdir
 
 # Cores: 18
 # Requires: netcdf
@@ -19,410 +18,409 @@ def run_test(actual, expected, procnum, region, boundary):
             ))
 
 
-def test_communications(test_dir):
-
-    with chdir(test_dir):
-        #################################################
-        # Test disconnected-double-null diverted topology
-        #################################################
-
-        nype = 6  # need at least 6 to include all regions
-
-        # run with processor splitting at separatrices
-        ##################################################
-
-        # MPI oversubscribe for communications test
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-
-        # With nxpe=3, both separatrices are on processor boundaries
-        nxpe = 3
-        command = "./test-communications NXPE=" + str(nxpe)
-
-        build_and_log("Communications Test")
-
-        # remove old outputs
-        shell("rm data/BOUT.dmp.*")
-
-        print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-        with open("run.log." + str(nxpe), "w") as f:
-            f.write(out)
-
-        region = "lower, inner PF"
-        f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [24, 25], 0, region, "outer x")
-        run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
-        run_test(f[:, -1], [82, 10, 22, 26], 0, region, "upper y")
-
-        region = "lower, inner between separatrices"
-        f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [48, 49], 0, region, "outer x")
-        run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
-        run_test(f[:, -1], [22, 26, 38, 50], 0, region, "upper y")
-
-        region = "lower, inner SOL"
-        f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [36, 37], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
-        run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
-        run_test(f[:, -1], [38, 50, 62, 86], 0, region, "upper y")
-
-        region = "inner core"
-        f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [26, 27], 0, region, "outer x")
-        run_test(f[:, 0], [81, 9, 21, 25], 0, region, "lower y")
-        run_test(f[:, -1], [80, 8, 20, 32], 0, region, "upper y")
-
-        region = "inner between separatrices"
-        f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [14, 15], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [50, 51], 0, region, "outer x")
-        run_test(f[:, 0], [21, 25, 37, 49], 0, region, "lower y")
-        run_test(f[:, -1], [20, 32, 44, 52], 0, region, "upper y")
-
-        region = "inner SOL"
-        f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [38, 39], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
-        run_test(f[:, 0], [37, 49, 61, 85], 0, region, "lower y")
-        run_test(f[:, -1], [44, 52, 64, 88], 0, region, "upper y")
-
-        region = "upper inner PF"
-        f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [28, 29], 0, region, "outer x")
-        run_test(f[:, 0], [79, 7, 19, 31], 0, region, "lower y")
-        run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
-
-        region = "upper inner SOL, nearer PF"
-        f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [16, 17], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [52, 53], 0, region, "outer x")
-        run_test(f[:, 0], [19, 31, 43, 51], 0, region, "lower y")
-        run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
-
-        region = "upper inner SOL, further from PF"
-        f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [40, 41], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
-        run_test(f[:, 0], [43, 51, 63, 87], 0, region, "lower y")
-        run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
-
-        region = "upper outer PF"
-        f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [30, 31], 0, region, "outer x")
-        run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
-        run_test(f[:, -1], [76, 4, 16, 28], 0, region, "upper y")
-
-        region = "upper outer SOL, nearer PF"
-        f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [18, 19], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [54, 55], 0, region, "outer x")
-        run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
-        run_test(f[:, -1], [16, 28, 40, 56], 0, region, "upper y")
-
-        region = "upper outer SOL, further from PF"
-        f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [42, 43], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
-        run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
-        run_test(f[:, -1], [40, 56, 68, 92], 0, region, "upper y")
-
-        region = "outer core"
-        f = DataFile("data/BOUT.dmp.12.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [32, 33], 0, region, "outer x")
-        run_test(f[:, 0], [75, 3, 15, 27], 0, region, "lower y")
-        run_test(f[:, -1], [74, 2, 14, 34], 0, region, "upper y")
-
-        region = "outer between separatrices"
-        f = DataFile("data/BOUT.dmp.13.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [20, 21], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [56, 57], 0, region, "outer x")
-        run_test(f[:, 0], [15, 27, 39, 55], 0, region, "lower y")
-        run_test(f[:, -1], [14, 34, 46, 58], 0, region, "upper y")
-
-        region = "outer SOL"
-        f = DataFile("data/BOUT.dmp.14.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [44, 45], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
-        run_test(f[:, 0], [39, 55, 67, 91], 0, region, "lower y")
-        run_test(f[:, -1], [46, 58, 70, 94], 0, region, "upper y")
-
-        region = "lower outer PF"
-        f = DataFile("data/BOUT.dmp.15.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [34, 35], 0, region, "outer x")
-        run_test(f[:, 0], [73, 1, 13, 33], 0, region, "lower y")
-        run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
-
-        region = "lower outer between separatrices"
-        f = DataFile("data/BOUT.dmp.16.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [22, 23], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [58, 59], 0, region, "outer x")
-        run_test(f[:, 0], [13, 33, 45, 57], 0, region, "lower y")
-        run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
-
-        region = "lower outer SOL"
-        f = DataFile("data/BOUT.dmp.17.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [46, 47], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
-        run_test(f[:, 0], [45, 57, 69, 93], 0, region, "lower y")
-        run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
-
-        # run with processor splitting not at separatrices
-        ##################################################
-
-        # With nxpe=2, neither separatrix is on a processor boundary
-        nxpe = 2
-        command = "./test-communications NXPE=" + str(nxpe)
-
-        # remove old outputs
-        shell("rm data/BOUT.dmp.*")
-
-        print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-        with open("run.log." + str(nxpe), "w") as f:
-            f.write(out)
-
-        region = "lower, inner leg, interior"
-        f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [36, 37], 0, region, "outer x")
-        run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
-        run_test(f[:, -1], [82, 10, 22, 26, 38], 0, region, "upper y")
-
-        region = "lower, inner leg, exterior"
-        f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [24, 25], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
-        run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
-        run_test(f[:, -1], [26, 38, 50, 62, 86], 0, region, "upper y")
-
-        region = "inner, interior"
-        f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [38, 39], 0, region, "outer x")
-        run_test(f[:, 0], [81, 9, 21, 25, 37], 0, region, "lower y")
-        run_test(f[:, -1], [80, 8, 20, 32, 44], 0, region, "upper y")
-
-        region = "inner, exterior"
-        f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [26, 27], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
-        run_test(f[:, 0], [25, 37, 49, 61, 85], 0, region, "lower y")
-        run_test(f[:, -1], [32, 44, 52, 64, 88], 0, region, "upper y")
-
-        region = "upper, inner leg, interior"
-        f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [40, 41], 0, region, "outer x")
-        run_test(f[:, 0], [79, 7, 19, 31, 43], 0, region, "lower y")
-        run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
-
-        region = "upper, inner leg, exterior"
-        f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [28, 29], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
-        run_test(f[:, 0], [31, 43, 51, 63, 87], 0, region, "lower y")
-        run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
-
-        region = "upper, outer leg, interior"
-        f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [42, 43], 0, region, "outer x")
-        run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
-        run_test(f[:, -1], [76, 4, 16, 28, 40], 0, region, "upper y")
-
-        region = "upper, outer leg, exterior"
-        f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [30, 31], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
-        run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
-        run_test(f[:, -1], [28, 40, 56, 68, 92], 0, region, "upper y")
-
-        region = "outer, interior"
-        f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [44, 45], 0, region, "outer x")
-        run_test(f[:, 0], [75, 3, 15, 27, 39], 0, region, "lower y")
-        run_test(f[:, -1], [74, 2, 14, 34, 46], 0, region, "upper y")
-
-        region = "outer, exterior"
-        f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [32, 33], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
-        run_test(f[:, 0], [27, 39, 55, 67, 91], 0, region, "lower y")
-        run_test(f[:, -1], [34, 46, 58, 70, 94], 0, region, "upper y")
-
-        region = "lower, outer leg, interior"
-        f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [46, 47], 0, region, "outer x")
-        run_test(f[:, 0], [73, 1, 13, 33, 45], 0, region, "lower y")
-        run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
-
-        region = "lower, outer leg, exterior"
-        f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [34, 35], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
-        run_test(f[:, 0], [33, 45, 57, 69, 93], 0, region, "lower y")
-        run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
-
-        # run with no processor splitting in the x-direction
-        ####################################################
-
-        nxpe = 1
-
-        command = "./test-communications NXPE=" + str(nxpe)
-
-        # remove old outputs
-        shell("rm data/BOUT.dmp.*")
-
-        print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-        with open("run.log." + str(nxpe), "w") as f:
-            f.write(out)
-
-        region = "lower, inner leg"
-        f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
-        run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
-        run_test(f[:, -1], [82, 10, 22, 26, 38, 50, 62, 86], 0, region, "upper y")
-
-        region = "inner"
-        f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
-        run_test(f[:, 0], [81, 9, 21, 25, 37, 49, 61, 85], 0, region, "lower y")
-        run_test(f[:, -1], [80, 8, 20, 32, 44, 52, 64, 88], 0, region, "upper y")
-
-        region = "upper, inner leg"
-        f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
-        run_test(f[:, 0], [79, 7, 19, 31, 43, 51, 63, 87], 0, region, "lower y")
-        run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
-
-        region = "upper, outer leg"
-        f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
-        run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
-        run_test(f[:, -1], [76, 4, 16, 28, 40, 56, 68, 92], 0, region, "upper y")
-
-        region = "outer"
-        f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
-        run_test(f[:, 0], [75, 3, 15, 27, 39, 55, 67, 91], 0, region, "lower y")
-        run_test(f[:, -1], [74, 2, 14, 34, 46, 58, 70, 94], 0, region, "upper y")
-
-        region = "lower, outer leg"
-        f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
-        run_test(f[:, 0], [73, 1, 13, 33, 45, 57, 69, 93], 0, region, "lower y")
-        run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
-
-
-        #################################################
-        # Test limiter topology
-        #################################################
-
-        nype = 1
-
-        # run with processor splitting at the separatrix
-        ####################################################
-
-        nxpe = 3
-        command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
-
-        # remove old outputs
-        shell("rm data_limiter/BOUT.dmp.*")
-
-        print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-        with open("run_limiter.log." + str(nxpe), "w") as f:
-            f.write(out)
-
-        region = "core"
-        f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [4, 5], 0, region, "outer x")
-        run_test(f[:, 0], [13, 1, 3, 19], 0, region, "lower y")
-        run_test(f[:, -1], [12, 0, 2, 27], 0, region, "upper y")
-
-        region = "interior SOL"
-        f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [2, 3], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [8, 9], 0, region, "outer x")
-        run_test(f[:, 0], [3, 19, 20, 21], 0, region, "lower y")
-        run_test(f[:, -1], [2, 27, 28, 29], 0, region, "upper y")
-
-        region = "exterior SOL"
-        f = DataFile("data_limiter/BOUT.dmp.2.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [6, 7], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
-        run_test(f[:, 0], [20, 21, 22, 23], 0, region, "lower y")
-        run_test(f[:, -1], [28, 29, 30, 31], 0, region, "upper y")
-
-        # run with processor splitting not at the separatrix
-        ####################################################
-
-        nxpe = 2
-        command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
-
-        # remove old outputs
-        shell("rm data_limiter/BOUT.dmp.*")
-
-        print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-        with open("run_limiter.log." + str(nxpe), "w") as f:
-            f.write(out)
-
-        region = "interior"
-        f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [6, 7], 0, region, "outer x")
-        run_test(f[:, 0], [13, 1, 3, 19, 20], 0, region, "lower y")
-        run_test(f[:, -1], [12, 0, 2, 27, 28], 0, region, "upper y")
-
-        region = "exterior"
-        f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [4, 5], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
-        run_test(f[:, 0], [19, 20, 21, 22, 23], 0, region, "lower y")
-        run_test(f[:, -1], [27, 28, 29, 30, 31], 0, region, "upper y")
-
-        # run with no processor splitting in the x-direction
-        ####################################################
-
-        nxpe = 1
-        command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
-
-        # remove old outputs
-        shell("rm data_limiter/BOUT.dmp.*")
-
-        print("Running Communications Test, nproc=" + str(nxpe * nype))
-
-        s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
-        with open("run_limiter.log." + str(nxpe), "w") as f:
-            f.write(out)
-
-        region = "all"
-        f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
-        run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
-        run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
-        run_test(f[:, 0], [13, 1, 3, 19, 20, 21, 22, 23], 0, region, "lower y")
-        run_test(f[:, -1], [12, 0, 2, 27, 28, 29, 30, 31], 0, region, "upper y")
+def test_communications():
+
+    #################################################
+    # Test disconnected-double-null diverted topology
+    #################################################
+
+    nype = 6  # need at least 6 to include all regions
+
+    # run with processor splitting at separatrices
+    ##################################################
+
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+
+    # With nxpe=3, both separatrices are on processor boundaries
+    nxpe = 3
+    command = "./test-communications NXPE=" + str(nxpe)
+
+    build_and_log("Communications Test")
+
+    # remove old outputs
+    shell("rm data/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "lower, inner PF"
+    f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [24, 25], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
+    run_test(f[:, -1], [82, 10, 22, 26], 0, region, "upper y")
+
+    region = "lower, inner between separatrices"
+    f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [48, 49], 0, region, "outer x")
+    run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
+    run_test(f[:, -1], [22, 26, 38, 50], 0, region, "upper y")
+
+    region = "lower, inner SOL"
+    f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [36, 37], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
+    run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [38, 50, 62, 86], 0, region, "upper y")
+
+    region = "inner core"
+    f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [26, 27], 0, region, "outer x")
+    run_test(f[:, 0], [81, 9, 21, 25], 0, region, "lower y")
+    run_test(f[:, -1], [80, 8, 20, 32], 0, region, "upper y")
+
+    region = "inner between separatrices"
+    f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [14, 15], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [50, 51], 0, region, "outer x")
+    run_test(f[:, 0], [21, 25, 37, 49], 0, region, "lower y")
+    run_test(f[:, -1], [20, 32, 44, 52], 0, region, "upper y")
+
+    region = "inner SOL"
+    f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [38, 39], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
+    run_test(f[:, 0], [37, 49, 61, 85], 0, region, "lower y")
+    run_test(f[:, -1], [44, 52, 64, 88], 0, region, "upper y")
+
+    region = "upper inner PF"
+    f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [28, 29], 0, region, "outer x")
+    run_test(f[:, 0], [79, 7, 19, 31], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
+
+    region = "upper inner SOL, nearer PF"
+    f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [16, 17], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [52, 53], 0, region, "outer x")
+    run_test(f[:, 0], [19, 31, 43, 51], 0, region, "lower y")
+    run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
+
+    region = "upper inner SOL, further from PF"
+    f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [40, 41], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
+    run_test(f[:, 0], [43, 51, 63, 87], 0, region, "lower y")
+    run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
+
+    region = "upper outer PF"
+    f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [30, 31], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99], 0, region, "lower y")
+    run_test(f[:, -1], [76, 4, 16, 28], 0, region, "upper y")
+
+    region = "upper outer SOL, nearer PF"
+    f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [18, 19], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [54, 55], 0, region, "outer x")
+    run_test(f[:, 0], [98, 99, 100, 101], 0, region, "lower y")
+    run_test(f[:, -1], [16, 28, 40, 56], 0, region, "upper y")
+
+    region = "upper outer SOL, further from PF"
+    f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [42, 43], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
+    run_test(f[:, 0], [100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [40, 56, 68, 92], 0, region, "upper y")
+
+    region = "outer core"
+    f = DataFile("data/BOUT.dmp.12.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [32, 33], 0, region, "outer x")
+    run_test(f[:, 0], [75, 3, 15, 27], 0, region, "lower y")
+    run_test(f[:, -1], [74, 2, 14, 34], 0, region, "upper y")
+
+    region = "outer between separatrices"
+    f = DataFile("data/BOUT.dmp.13.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [20, 21], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [56, 57], 0, region, "outer x")
+    run_test(f[:, 0], [15, 27, 39, 55], 0, region, "lower y")
+    run_test(f[:, -1], [14, 34, 46, 58], 0, region, "upper y")
+
+    region = "outer SOL"
+    f = DataFile("data/BOUT.dmp.14.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [44, 45], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
+    run_test(f[:, 0], [39, 55, 67, 91], 0, region, "lower y")
+    run_test(f[:, -1], [46, 58, 70, 94], 0, region, "upper y")
+
+    region = "lower outer PF"
+    f = DataFile("data/BOUT.dmp.15.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [34, 35], 0, region, "outer x")
+    run_test(f[:, 0], [73, 1, 13, 33], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107], 0, region, "upper y")
+
+    region = "lower outer between separatrices"
+    f = DataFile("data/BOUT.dmp.16.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [22, 23], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [58, 59], 0, region, "outer x")
+    run_test(f[:, 0], [13, 33, 45, 57], 0, region, "lower y")
+    run_test(f[:, -1], [106, 107, 108, 109], 0, region, "upper y")
+
+    region = "lower outer SOL"
+    f = DataFile("data/BOUT.dmp.17.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [46, 47], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
+    run_test(f[:, 0], [45, 57, 69, 93], 0, region, "lower y")
+    run_test(f[:, -1], [108, 109, 110, 111], 0, region, "upper y")
+
+    # run with processor splitting not at separatrices
+    ##################################################
+
+    # With nxpe=2, neither separatrix is on a processor boundary
+    nxpe = 2
+    command = "./test-communications NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "lower, inner leg, interior"
+    f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [36, 37], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
+    run_test(f[:, -1], [82, 10, 22, 26, 38], 0, region, "upper y")
+
+    region = "lower, inner leg, exterior"
+    f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [24, 25], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
+    run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [26, 38, 50, 62, 86], 0, region, "upper y")
+
+    region = "inner, interior"
+    f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [38, 39], 0, region, "outer x")
+    run_test(f[:, 0], [81, 9, 21, 25, 37], 0, region, "lower y")
+    run_test(f[:, -1], [80, 8, 20, 32, 44], 0, region, "upper y")
+
+    region = "inner, exterior"
+    f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [26, 27], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
+    run_test(f[:, 0], [25, 37, 49, 61, 85], 0, region, "lower y")
+    run_test(f[:, -1], [32, 44, 52, 64, 88], 0, region, "upper y")
+
+    region = "upper, inner leg, interior"
+    f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [40, 41], 0, region, "outer x")
+    run_test(f[:, 0], [79, 7, 19, 31, 43], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
+
+    region = "upper, inner leg, exterior"
+    f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [28, 29], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
+    run_test(f[:, 0], [31, 43, 51, 63, 87], 0, region, "lower y")
+    run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
+
+    region = "upper, outer leg, interior"
+    f = DataFile("data/BOUT.dmp.6.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [42, 43], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99, 100], 0, region, "lower y")
+    run_test(f[:, -1], [76, 4, 16, 28, 40], 0, region, "upper y")
+
+    region = "upper, outer leg, exterior"
+    f = DataFile("data/BOUT.dmp.7.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [30, 31], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
+    run_test(f[:, 0], [99, 100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [28, 40, 56, 68, 92], 0, region, "upper y")
+
+    region = "outer, interior"
+    f = DataFile("data/BOUT.dmp.8.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [44, 45], 0, region, "outer x")
+    run_test(f[:, 0], [75, 3, 15, 27, 39], 0, region, "lower y")
+    run_test(f[:, -1], [74, 2, 14, 34, 46], 0, region, "upper y")
+
+    region = "outer, exterior"
+    f = DataFile("data/BOUT.dmp.9.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [32, 33], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
+    run_test(f[:, 0], [27, 39, 55, 67, 91], 0, region, "lower y")
+    run_test(f[:, -1], [34, 46, 58, 70, 94], 0, region, "upper y")
+
+    region = "lower, outer leg, interior"
+    f = DataFile("data/BOUT.dmp.10.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [46, 47], 0, region, "outer x")
+    run_test(f[:, 0], [73, 1, 13, 33, 45], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107, 108], 0, region, "upper y")
+
+    region = "lower, outer leg, exterior"
+    f = DataFile("data/BOUT.dmp.11.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [34, 35], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
+    run_test(f[:, 0], [33, 45, 57, 69, 93], 0, region, "lower y")
+    run_test(f[:, -1], [107, 108, 109, 110, 111], 0, region, "upper y")
+
+    # run with no processor splitting in the x-direction
+    ####################################################
+
+    nxpe = 1
+
+    command = "./test-communications NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "lower, inner leg"
+    f = DataFile("data/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [72, 73], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [84, 85], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [82, 10, 22, 26, 38, 50, 62, 86], 0, region, "upper y")
+
+    region = "inner"
+    f = DataFile("data/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [74, 75], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [86, 87], 0, region, "outer x")
+    run_test(f[:, 0], [81, 9, 21, 25, 37, 49, 61, 85], 0, region, "lower y")
+    run_test(f[:, -1], [80, 8, 20, 32, 44, 52, 64, 88], 0, region, "upper y")
+
+    region = "upper, inner leg"
+    f = DataFile("data/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [76, 77], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [88, 89], 0, region, "outer x")
+    run_test(f[:, 0], [79, 7, 19, 31, 43, 51, 63, 87], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
+
+    region = "upper, outer leg"
+    f = DataFile("data/BOUT.dmp.3.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [78, 79], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [90, 91], 0, region, "outer x")
+    run_test(f[:, 0], [96, 97, 98, 99, 100, 101, 102, 103], 0, region, "lower y")
+    run_test(f[:, -1], [76, 4, 16, 28, 40, 56, 68, 92], 0, region, "upper y")
+
+    region = "outer"
+    f = DataFile("data/BOUT.dmp.4.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [80, 81], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [92, 93], 0, region, "outer x")
+    run_test(f[:, 0], [75, 3, 15, 27, 39, 55, 67, 91], 0, region, "lower y")
+    run_test(f[:, -1], [74, 2, 14, 34, 46, 58, 70, 94], 0, region, "upper y")
+
+    region = "lower, outer leg"
+    f = DataFile("data/BOUT.dmp.5.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [82, 83], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [94, 95], 0, region, "outer x")
+    run_test(f[:, 0], [73, 1, 13, 33, 45, 57, 69, 93], 0, region, "lower y")
+    run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
+
+
+    #################################################
+    # Test limiter topology
+    #################################################
+
+    nype = 1
+
+    # run with processor splitting at the separatrix
+    ####################################################
+
+    nxpe = 3
+    command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data_limiter/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run_limiter.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "core"
+    f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [4, 5], 0, region, "outer x")
+    run_test(f[:, 0], [13, 1, 3, 19], 0, region, "lower y")
+    run_test(f[:, -1], [12, 0, 2, 27], 0, region, "upper y")
+
+    region = "interior SOL"
+    f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [2, 3], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [8, 9], 0, region, "outer x")
+    run_test(f[:, 0], [3, 19, 20, 21], 0, region, "lower y")
+    run_test(f[:, -1], [2, 27, 28, 29], 0, region, "upper y")
+
+    region = "exterior SOL"
+    f = DataFile("data_limiter/BOUT.dmp.2.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [6, 7], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
+    run_test(f[:, 0], [20, 21, 22, 23], 0, region, "lower y")
+    run_test(f[:, -1], [28, 29, 30, 31], 0, region, "upper y")
+
+    # run with processor splitting not at the separatrix
+    ####################################################
+
+    nxpe = 2
+    command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data_limiter/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run_limiter.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "interior"
+    f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [6, 7], 0, region, "outer x")
+    run_test(f[:, 0], [13, 1, 3, 19, 20], 0, region, "lower y")
+    run_test(f[:, -1], [12, 0, 2, 27, 28], 0, region, "upper y")
+
+    region = "exterior"
+    f = DataFile("data_limiter/BOUT.dmp.1.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [4, 5], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
+    run_test(f[:, 0], [19, 20, 21, 22, 23], 0, region, "lower y")
+    run_test(f[:, -1], [27, 28, 29, 30, 31], 0, region, "upper y")
+
+    # run with no processor splitting in the x-direction
+    ####################################################
+
+    nxpe = 1
+    command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
+
+    # remove old outputs
+    shell("rm data_limiter/BOUT.dmp.*")
+
+    print("Running Communications Test, nproc=" + str(nxpe * nype))
+
+    s, out = launch_safe(command, nproc=nxpe * nype, pipe=True)
+    with open("run_limiter.log." + str(nxpe), "w") as f:
+        f.write(out)
+
+    region = "all"
+    f = DataFile("data_limiter/BOUT.dmp.0.nc")["f"][0, :, :, 0]
+    run_test(f[0, 1:-1], [12, 13], 0, region, "inner x")
+    run_test(f[-1, 1:-1], [14, 15], 0, region, "outer x")
+    run_test(f[:, 0], [13, 1, 3, 19, 20, 21, 22, 23], 0, region, "lower y")
+    run_test(f[:, -1], [12, 0, 2, 27, 28, 29, 30, 31], 0, region, "upper y")
diff --git a/tests/integrated/test-cyclic/test_cyclic.py b/tests/integrated/test-cyclic/test_cyclic.py
index a3780e10b2..7fad6bac72 100755
--- a/tests/integrated/test-cyclic/test_cyclic.py
+++ b/tests/integrated/test-cyclic/test_cyclic.py
@@ -15,43 +15,41 @@
     pass
 from boututils.run_wrapper import build_and_log, shell, launch
 from sys import stdout
-from contextlib import chdir
 
 build_and_log("Cyclic Reduction test")
 
 flags = ["", "nsys=2", "nsys=5 periodic", "nsys=7 n=10"]
 
 
-def test_cyclic(test_dir):
+def test_cyclic():
 
-    with chdir(test_dir):
-        code = 0  # Return code
-        for nproc in [1, 2, 4]:
-            cmd = "./test_cyclic"
+    code = 0  # Return code
+    for nproc in [1, 2, 4]:
+        cmd = "./test_cyclic"
 
-            print("   %d processors...." % (nproc))
-            r = 0
-            for f in flags:
-                stdout.write("\tflags '" + f + "' ... ")
+        print("   %d processors...." % (nproc))
+        r = 0
+        for f in flags:
+            stdout.write("\tflags '" + f + "' ... ")
 
-                shell("rm data/BOUT.dmp.* 2> err.log")
+            shell("rm data/BOUT.dmp.* 2> err.log")
 
-                # Run the case
-                status, out = launch(cmd + " " + f, nproc=nproc, mthread=1, pipe=True)
-                with open(f"run.log.{nproc}.{r}", "w") as f:
-                    f.write(out)
+            # Run the case
+            status, out = launch(cmd + " " + f, nproc=nproc, mthread=1, pipe=True)
+            with open(f"run.log.{nproc}.{r}", "w") as f:
+                f.write(out)
 
-                r = r + 1
+            r = r + 1
 
-                # Find out if it worked
-                if status:
-                    print("PASSED")
-                else:
-                    print("FAILED")
-                    code = 1
-                assert status, f"Test failed for flag={f}"
+            # Find out if it worked
+            if status:
+                print("PASSED")
+            else:
+                print("FAILED")
+                code = 1
+            assert status, f"Test failed for flag={f}"
 
-        if code == 0:
-            print(" => All cyclic reduction tests passed")
-        else:
-            print(" => Some failed tests")
+    if code == 0:
+        print(" => All cyclic reduction tests passed")
+    else:
+        print(" => Some failed tests")
diff --git a/tests/integrated/test-stopCheck/test_stopCheck.py b/tests/integrated/test-stopCheck/test_stopCheck.py
index 56dee2be5a..0774604fb4 100644
--- a/tests/integrated/test-stopCheck/test_stopCheck.py
+++ b/tests/integrated/test-stopCheck/test_stopCheck.py
@@ -1,7 +1,6 @@
 import os
 import subprocess
 import time
-from contextlib import chdir
 
 
 def test_runtest(test_dir):
@@ -17,19 +16,18 @@ def test_runtest(test_dir):
 
     # Pre-build for dependencies like grid.fci.nc
 
-    with chdir(test_dir):
-        build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-        if build_result.returncode != 0:
-            print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
+    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
+    if build_result.returncode != 0:
+        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
 
-        # MPI oversubscribe for communications test
-        cmd = './runtest'
-        if "communications" in str(test_dir):
-            os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-        start = time.time()
-        result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-        elapsed = time.time() - start
-        print(f"Output: {result.stdout}")
-        if result.returncode != 0:
-            print(f"Stderr: {result.stderr}")
-        assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+    # MPI oversubscribe for communications test
+    cmd = './runtest'
+    if "communications" in test_dir.name:
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"

From 0cfa087640e3f933aa6c55d75c35013083733d6b Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 13:24:53 +0000
Subject: [PATCH 1003/1827] Modify test_twistshift to run via pytest

---
 .../test-twistshift/test_twistshift.py        | 111 +++++++++---------
 1 file changed, 53 insertions(+), 58 deletions(-)

diff --git a/tests/integrated/test-twistshift/test_twistshift.py b/tests/integrated/test-twistshift/test_twistshift.py
index 125aab6b5b..8daf070ca6 100755
--- a/tests/integrated/test-twistshift/test_twistshift.py
+++ b/tests/integrated/test-twistshift/test_twistshift.py
@@ -3,77 +3,72 @@
 from boutdata import collect
 from boututils.run_wrapper import build_and_log, launch_safe
 import numpy
-from sys import exit
 
 datapath = "data"
 nproc = 1
 tol = 1.0e-13
 
-build_and_log("twistshift test")
 
-s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True)
-with open("run.log." + str(nproc), "w") as f:
-    f.write(out)
+def test_twistshift():
 
-test = collect("test", path=datapath, yguards=True, info=False)
-test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False)
-result = collect("result", path=datapath, yguards=True, info=False)
+    build_and_log("twistshift test")
 
-# from boututils.showdata import showdata
-# showdata([test, test_aligned, result], titles=['test', 'test_aligned', 'result'])
+    s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True)
+    with open("run.log." + str(nproc), "w") as f:
+        f.write(out)
 
-success = True
+    test = collect("test", path=datapath, yguards=True, info=False)
+    test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False)
+    result = collect("result", path=datapath, yguards=True, info=False)
 
+    # from boututils.showdata import showdata
+    # showdata([test, test_aligned, result], titles=['test', 'test_aligned', 'result'])
 
-# Check test_aligned is *not* periodic in y
-def test1(ylower, yupper):
-    global success
-    if numpy.any(
-            numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6
-    ):
-        success = False
-        print(
-            "Fail - test_aligned should not be periodic jy=%i and jy=%i should be "
-            "different",
-            yupper,
-            ylower,
-        )
+    success = True
 
+    # Check test_aligned is *not* periodic in y
+    def test1(ylower, yupper):
+        global success
+        if numpy.any(
+                numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6
+        ):
+            success = False
+            print(
+                "Fail - test_aligned should not be periodic jy=%i and jy=%i should be "
+                "different",
+                yupper,
+                ylower,
+            )
 
-test1(0, -4)
-test1(1, -3)
-test1(2, -2)
-test1(3, -1)
+    test1(0, -4)
+    test1(1, -3)
+    test1(2, -2)
+    test1(3, -1)
 
-# Check test and result are the same
-if numpy.any(numpy.abs(result - test) > tol):
-    print("Fail - result has not been communicated correctly - is different from input")
-    success = False
+    # Check test and result are the same
+    if numpy.any(numpy.abs(result - test) > tol):
+        print("Fail - result has not been communicated correctly - is different from input")
+        success = False
 
 
-# Check result is periodic in y
-def test2(ylower, yupper):
-    global success
-    if numpy.any(numpy.abs(result[:, yupper, :] - result[:, ylower, :]) > tol):
-        success = False
-        print(
-            "Fail - result should be periodic jy=%i and jy=%i should not be "
-            "different",
-            yupper,
-            ylower,
-        )
-        print(ylower, result[:, ylower, :])
-        print(yupper, result[:, yupper, :])
-        print(result[:, ylower, :] - result[:, yupper, :])
-
-
-test2(0, -4)
-test2(1, -3)
-test2(2, -2)
-test2(3, -1)
-
-if success:
-    print("Pass")
-    exit(0)
-else:
-    exit(1)
+    # Check result is periodic in y
+    def test2(ylower, yupper):
+        global success
+        if numpy.any(numpy.abs(result[:, yupper, :] - result[:, ylower, :]) > tol):
+            success = False
+            print(
+                "Fail - result should be periodic jy=%i and jy=%i should not be "
+                "different",
+                yupper,
+                ylower,
+            )
+            print(ylower, result[:, ylower, :])
+            print(yupper, result[:, yupper, :])
+            print(result[:, ylower, :] - result[:, yupper, :])
+
+    test2(0, -4)
+    test2(1, -3)
+    test2(2, -2)
+    test2(3, -1)
+
+    assert success

From 27d8225cc3f36e574d102958fb5b9bd1ddd69171 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 13:27:03 +0000
Subject: [PATCH 1004/1827] Modify test_twistshift_staggered to run via pytest

---
 .../test_twistshift_staggered.py              | 81 +++++++++----------
 1 file changed, 39 insertions(+), 42 deletions(-)

diff --git a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
index 5bb9963db7..5b1c1bee90 100755
--- a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
+++ b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
@@ -3,57 +3,54 @@
 from boutdata import collect
 from boututils.run_wrapper import build_and_log, launch_safe
 import numpy
-from sys import exit
 
 datapath = "data"
 nproc = 1
 tol = 1.0e-13
 
-build_and_log("twistshift test")
+def test_twistshift_staggered():
 
-s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True)
-with open("run.log." + str(nproc), "w") as f:
-    f.write(out)
+    build_and_log("twistshift test")
 
-test = collect("test", path=datapath, yguards=True, info=False)
-test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False)
-check = collect("check", path=datapath, yguards=True, info=False)
+    s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True)
+    with open("run.log." + str(nproc), "w") as f:
+        f.write(out)
 
-# from boututils.showdata import showdata
-# showdata([test, test_aligned, check], titles=['test', 'test_aligned', 'check'])
+    test = collect("test", path=datapath, yguards=True, info=False)
+    test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False)
+    check = collect("check", path=datapath, yguards=True, info=False)
 
-success = True
+    # from boututils.showdata import showdata
+    # showdata([test, test_aligned, check], titles=['test', 'test_aligned', 'check'])
 
+    success = True
 
-# Check test_aligned is *not* periodic in y
-def test1(ylower, yupper):
-    global success
-    if numpy.any(
-        numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6
-    ):
+
+    # Check test_aligned is *not* periodic in y
+    def test1(ylower, yupper):
+        global success
+        if numpy.any(
+            numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6
+        ):
+            success = False
+            print(
+                "Fail - test_aligned should not be periodic jy=%i and jy=%i should be "
+                "different" % (yupper, ylower)
+            )
+
+
+    test1(0, -4)
+    test1(1, -3)
+    test1(2, -2)
+    test1(3, -1)
+
+    # Check test_aligned is the same as check
+    # Cannot check in guard cells, as the expression used for 'zShift' in the input file is
+    # not the same as the corrected zShift used for the transforms in the guard cells
+    if numpy.any(numpy.abs(test_aligned[2:-2, 2:-2, :] - check[2:-2, 2:-2, :]) > tol):
         success = False
-        print(
-            "Fail - test_aligned should not be periodic jy=%i and jy=%i should be "
-            "different" % (yupper, ylower)
-        )
-
-
-test1(0, -4)
-test1(1, -3)
-test1(2, -2)
-test1(3, -1)
-
-# Check test_aligned is the same as check
-# Cannot check in guard cells, as the expression used for 'zShift' in the input file is
-# not the same as the corrected zShift used for the transforms in the guard cells
-if numpy.any(numpy.abs(test_aligned[2:-2, 2:-2, :] - check[2:-2, 2:-2, :]) > tol):
-    success = False
-    print("Fail - test_aligned is different from the expected value")
-    print("test_aligned", test_aligned)
-    print("check", check)
-
-if success:
-    print("Pass")
-    exit(0)
-else:
-    exit(1)
+        print("Fail - test_aligned is different from the expected value")
+        print("test_aligned", test_aligned)
+        print("check", check)
+
+    assert success

From 715babf1445c793fc7942ea8108a107799fbaf40 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 13:28:59 +0000
Subject: [PATCH 1005/1827] Modify test_vec to run via pytest

---
 tests/integrated/test-vec/test_vec.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/tests/integrated/test-vec/test_vec.py b/tests/integrated/test-vec/test_vec.py
index 6d836be804..23ab390759 100755
--- a/tests/integrated/test-vec/test_vec.py
+++ b/tests/integrated/test-vec/test_vec.py
@@ -4,15 +4,13 @@
 
 from boututils.run_wrapper import build_and_log, launch_safe
 
-build_and_log("vector communication test")
+def test_vec():
 
-status, out = launch_safe("./testVec", nproc=4, pipe=True)
+    build_and_log("vector communication test")
 
-with open("run.log.4", "w") as f:
-    f.write(out)
+    status, out = launch_safe("./testVec", nproc=4, pipe=True)
 
-if status:
-    print(" => Test failed")
-    exit(status)
+    with open("run.log.4", "w") as f:
+        f.write(out)
 
-print(" => Test passed")
+    assert not status, " => Test failed"

From fe49befd4afc10956e477bd4c8e0c4e4cd0e5332 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 13:33:53 +0000
Subject: [PATCH 1006/1827] Add `OMPI_MCA_rmaps_base_oversubscribe` environment
 variable in test_yupdown

---
 tests/integrated/test-yupdown/test_yupdown.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py
index dd39fafd05..6bdfbafb0c 100755
--- a/tests/integrated/test-yupdown/test_yupdown.py
+++ b/tests/integrated/test-yupdown/test_yupdown.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
+import os
 import pytest
 from boututils.run_wrapper import build_and_log, launch_safe
 from boutdata.collect import collect
-
 from numpy import max, abs
 
 shift_types = ["shifted", "shiftedinterp"]
@@ -15,7 +15,7 @@ def build_project():
     build_and_log("parallel slices test")
 
 
-def run_case(shift_type, variable, build_project):
+def run_case(shift_type, variable):
     s, out = launch_safe(
         "./test_yupdown mesh:paralleltransform:type=" + shift_type,
         nproc=1,
@@ -42,6 +42,9 @@ def run_case(shift_type, variable, build_project):
 
 
 @pytest.mark.parametrize("shift_type, variable", list(zip(shift_types, variables)))
-def test_case(shift_type, variable, build_project):
-    success = run_case(shift_type, variable, build_project)
+def test_case(shift_type, variable):
+    # MPI oversubscribe
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+
+    success = run_case(shift_type, variable)
     assert success, f"Test failed for shift_type={shift_type}: , variable={variable}"

From ada42eb573b2a1f60c50535ee9ee641bb514faf7 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 13:37:12 +0000
Subject: [PATCH 1007/1827] Modify test_stopCheck_file to run via pytest

---
 .../test_stopCheck_file.py                    | 81 +++++++++----------
 1 file changed, 39 insertions(+), 42 deletions(-)

diff --git a/tests/integrated/test-stopCheck-file/test_stopCheck_file.py b/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
index e959816d11..6f08745dd2 100755
--- a/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
+++ b/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
@@ -9,45 +9,42 @@
 
 nproc = 1
 
-build_and_log("stopCheck test")
-
-check_values = [True, False]
-expected_steps = [1, 11]
-data_dirs = ["data", "dataSecond"]
-stop_files = ["BOUT.stop", "otherStop.check"]
-
-print("Running stopCheck test")
-success = True
-
-for data_dir, stop_file in zip(data_dirs, stop_files):
-    for check, expected in zip(check_values, expected_steps):
-        executable = "./test_stopCheck"
-        command = "{} -d {} stopCheck={} stopCheckName={}".format(
-            executable, data_dir, check, stop_file
-        )
-
-        s, out = launch(
-            command,
-            nproc=nproc,
-            pipe=True,
-        )
-        with open("run.log.{}.{}".format(data_dir, check), "w") as f:
-            f.write(out)
-
-        result = collect("t_array", path=data_dir, info=False)
-
-        if result.shape[0] != expected:
-            print("Fail, wrong shape")
-            print("\tOption is {}/{}/{}".format(check, data_dir, stop_file))
-            print("\tshape is {}".format(result.shape[0]))
-            print("\texpecting {}".format(expected))
-            sys.exit(1)
-            success = False
-            continue
-
-if success:
-    print(" => All checkStop tests passed")
-    sys.exit(0)
-else:
-    print(" => Some failed tests")
-    sys.exit(1)
+def test_stopCheck_file():
+
+    build_and_log("stopCheck test")
+
+    check_values = [True, False]
+    expected_steps = [1, 11]
+    data_dirs = ["data", "dataSecond"]
+    stop_files = ["BOUT.stop", "otherStop.check"]
+
+    print("Running stopCheck test")
+    success = True
+
+    for data_dir, stop_file in zip(data_dirs, stop_files):
+        for check, expected in zip(check_values, expected_steps):
+            executable = "./test_stopCheck"
+            command = "{} -d {} stopCheck={} stopCheckName={}".format(
+                executable, data_dir, check, stop_file
+            )
+
+            s, out = launch(
+                command,
+                nproc=nproc,
+                pipe=True,
+            )
+            with open("run.log.{}.{}".format(data_dir, check), "w") as f:
+                f.write(out)
+
+            result = collect("t_array", path=data_dir, info=False)
+
+            if result.shape[0] != expected:
+                print("Fail, wrong shape")
+                print("\tOption is {}/{}/{}".format(check, data_dir, stop_file))
+                print("\tshape is {}".format(result.shape[0]))
+                print("\texpecting {}".format(expected))
+                sys.exit(1)
+                success = False
+                continue
+
+    assert success, " => Some failed tests"

From c0a1e2c70a90365baffe8250bc838d26359d5863 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 13:39:05 +0000
Subject: [PATCH 1008/1827] Modify test_yupdown_weights to run via pytest

---
 .../test_yupdown_weights.py                   | 51 +++++++++----------
 1 file changed, 25 insertions(+), 26 deletions(-)

diff --git a/tests/integrated/test-yupdown-weights/test_yupdown_weights.py b/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
index 4b59d08cb0..57a5e06f3d 100755
--- a/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
+++ b/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
@@ -2,39 +2,38 @@
 
 from boututils.run_wrapper import build_and_log, launch_safe
 from boutdata.collect import collect
-from sys import stdout, exit
+from sys import stdout
 
 from numpy import max, abs
 
-build_and_log("parallel slices and weights test")
+def test_yupdown_weights():
 
-failed = False
-for shifttype in ["shiftedinterp"]:
-    s, out = launch_safe(
-        "./test_yupdown_weights mesh:paralleltransform:type=" + shifttype,
-        nproc=1,
-        pipe=True,
-        verbose=True,
-    )
+    build_and_log("parallel slices and weights test")
 
-    with open("run.log", "w") as f:
-        f.write(out)
+    failed = False
+    for shifttype in ["shiftedinterp"]:
+        s, out = launch_safe(
+            "./test_yupdown_weights mesh:paralleltransform:type=" + shifttype,
+            nproc=1,
+            pipe=True,
+            verbose=True,
+        )
 
-    vars = [("ddy", "ddy2")]
-    for v1, v2 in vars:
-        stdout.write("Testing %s and %s ... " % (v1, v2))
-        ddy = collect(v1, path="data", xguards=False, yguards=False, info=False)
-        ddy2 = collect(v2, path="data", xguards=False, yguards=False, info=False)
+        with open("run.log", "w") as f:
+            f.write(out)
 
-        diff = max(abs(ddy - ddy2))
+        vars = [("ddy", "ddy2")]
+        for v1, v2 in vars:
+            stdout.write("Testing %s and %s ... " % (v1, v2))
+            ddy = collect(v1, path="data", xguards=False, yguards=False, info=False)
+            ddy2 = collect(v2, path="data", xguards=False, yguards=False, info=False)
 
-        if diff < 1e-8:
-            print(shifttype + " passed (Max difference %e)" % (diff))
-        else:
-            print(shifttype + " failed (Max difference %e)" % (diff))
-            failed = True
+            diff = max(abs(ddy - ddy2))
 
-if failed:
-    exit(1)
+            if diff < 1e-8:
+                print(shifttype + " passed (Max difference %e)" % (diff))
+            else:
+                print(shifttype + " failed (Max difference %e)" % (diff))
+                failed = True
 
-exit(0)
+    assert not failed

From 9be45a461f8ce3a4517666f211362c168109129a Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 30 Dec 2025 13:41:31 +0000
Subject: [PATCH 1009/1827] Modify test_griddata_yboundary_guards to run via
 pytest

---
 .../test_griddata_yboundary_guards.py         | 301 +++++++++---------
 1 file changed, 149 insertions(+), 152 deletions(-)

diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
index 79adae9759..ca964d2c9b 100755
--- a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
+++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
@@ -5,197 +5,194 @@
 from netCDF4 import Dataset
 import numpy
 import os.path
-from sys import stdout, exit
+from sys import stdout
 
 # Cores: 6
 # Requires: netcdf
 
-build_and_log("griddata test")
+def test_griddata_yboundary_guards():
 
-nx = 4
-ny = 24
-blocksize = ny / 6
+    build_and_log("griddata test")
 
-# first generate some grid files to test
-# double null case:
-for n_yguards in [0, 1, 2]:
-    datadir = "data-doublenull-" + str(n_yguards)
-    gridname = "grid-doublenull-" + str(n_yguards) + ".nc"
+    nx = 4
+    ny = 24
+    blocksize = ny / 6
 
-    with Dataset(os.path.join(datadir, gridname), "w") as gridfile:
-        gridfile.createDimension("x", nx)
-        gridfile.createDimension("y", ny + 4 * n_yguards)
+    # first generate some grid files to test
+    # double null case:
+    for n_yguards in [0, 1, 2]:
+        datadir = "data-doublenull-" + str(n_yguards)
+        gridname = "grid-doublenull-" + str(n_yguards) + ".nc"
 
-        gridfile.createVariable("nx", numpy.int32)
-        gridfile["nx"][...] = nx
+        with Dataset(os.path.join(datadir, gridname), "w") as gridfile:
+            gridfile.createDimension("x", nx)
+            gridfile.createDimension("y", ny + 4 * n_yguards)
 
-        gridfile.createVariable("ny", numpy.int32)
-        gridfile["ny"][...] = ny
+            gridfile.createVariable("nx", numpy.int32)
+            gridfile["nx"][...] = nx
 
-        gridfile.createVariable("y_boundary_guards", numpy.int32)
-        gridfile["y_boundary_guards"][...] = n_yguards
+            gridfile.createVariable("ny", numpy.int32)
+            gridfile["ny"][...] = ny
 
-        gridfile.createVariable("MXG", numpy.int32)
-        gridfile["MXG"][...] = 1
+            gridfile.createVariable("y_boundary_guards", numpy.int32)
+            gridfile["y_boundary_guards"][...] = n_yguards
 
-        gridfile.createVariable("MYG", numpy.int32)
-        gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards
+            gridfile.createVariable("MXG", numpy.int32)
+            gridfile["MXG"][...] = 1
 
-        gridfile.createVariable("ixseps1", numpy.int32)
-        gridfile["ixseps1"][...] = nx // 2 - 1
+            gridfile.createVariable("MYG", numpy.int32)
+            gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards
 
-        gridfile.createVariable("ixseps2", numpy.int32)
-        gridfile["ixseps2"][...] = nx // 2 - 1
+            gridfile.createVariable("ixseps1", numpy.int32)
+            gridfile["ixseps1"][...] = nx // 2 - 1
 
-        gridfile.createVariable("jyseps1_1", numpy.int32)
-        gridfile["jyseps1_1"][...] = blocksize - 1
+            gridfile.createVariable("ixseps2", numpy.int32)
+            gridfile["ixseps2"][...] = nx // 2 - 1
 
-        gridfile.createVariable("jyseps2_1", numpy.int32)
-        gridfile["jyseps2_1"][...] = 2 * blocksize - 1
+            gridfile.createVariable("jyseps1_1", numpy.int32)
+            gridfile["jyseps1_1"][...] = blocksize - 1
 
-        gridfile.createVariable("ny_inner", numpy.int32)
-        gridfile["ny_inner"][...] = 3 * blocksize
+            gridfile.createVariable("jyseps2_1", numpy.int32)
+            gridfile["jyseps2_1"][...] = 2 * blocksize - 1
 
-        gridfile.createVariable("jyseps1_2", numpy.int32)
-        gridfile["jyseps1_2"][...] = 4 * blocksize - 1
+            gridfile.createVariable("ny_inner", numpy.int32)
+            gridfile["ny_inner"][...] = 3 * blocksize
 
-        gridfile.createVariable("jyseps2_2", numpy.int32)
-        gridfile["jyseps2_2"][...] = 5 * blocksize - 1
+            gridfile.createVariable("jyseps1_2", numpy.int32)
+            gridfile["jyseps1_2"][...] = 4 * blocksize - 1
 
-        testdata = numpy.zeros([nx, ny + 4 * n_yguards])
-        testdata[:, :] = numpy.arange(ny + 4 * n_yguards)[numpy.newaxis, :]
-        gridfile.createVariable("test", float, ("x", "y"))
-        gridfile["test"][...] = testdata
+            gridfile.createVariable("jyseps2_2", numpy.int32)
+            gridfile["jyseps2_2"][...] = 5 * blocksize - 1
 
-# grid files for single-null:
-for n_yguards in [0, 1, 2]:
-    datadir = "data-singlenull-" + str(n_yguards)
-    gridname = "grid-singlenull-" + str(n_yguards) + ".nc"
+            testdata = numpy.zeros([nx, ny + 4 * n_yguards])
+            testdata[:, :] = numpy.arange(ny + 4 * n_yguards)[numpy.newaxis, :]
+            gridfile.createVariable("test", float, ("x", "y"))
+            gridfile["test"][...] = testdata
 
-    with Dataset(os.path.join(datadir, gridname), "w") as gridfile:
-        gridfile.createDimension("x", nx)
-        gridfile.createDimension("y", ny + 2 * n_yguards)
+    # grid files for single-null:
+    for n_yguards in [0, 1, 2]:
+        datadir = "data-singlenull-" + str(n_yguards)
+        gridname = "grid-singlenull-" + str(n_yguards) + ".nc"
 
-        gridfile.createVariable("nx", numpy.int32)
-        gridfile["nx"][...] = nx
+        with Dataset(os.path.join(datadir, gridname), "w") as gridfile:
+            gridfile.createDimension("x", nx)
+            gridfile.createDimension("y", ny + 2 * n_yguards)
 
-        gridfile.createVariable("ny", numpy.int32)
-        gridfile["ny"][...] = ny
+            gridfile.createVariable("nx", numpy.int32)
+            gridfile["nx"][...] = nx
 
-        gridfile.createVariable("y_boundary_guards", numpy.int32)
-        gridfile["y_boundary_guards"][...] = n_yguards
+            gridfile.createVariable("ny", numpy.int32)
+            gridfile["ny"][...] = ny
 
-        gridfile.createVariable("MXG", numpy.int32)
-        gridfile["MXG"][...] = 1
+            gridfile.createVariable("y_boundary_guards", numpy.int32)
+            gridfile["y_boundary_guards"][...] = n_yguards
 
-        gridfile.createVariable("MYG", numpy.int32)
-        gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards
+            gridfile.createVariable("MXG", numpy.int32)
+            gridfile["MXG"][...] = 1
 
-        gridfile.createVariable("ixseps1", numpy.int32)
-        gridfile["ixseps1"][...] = nx // 2 - 1
+            gridfile.createVariable("MYG", numpy.int32)
+            gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards
 
-        gridfile.createVariable("ixseps2", numpy.int32)
-        gridfile["ixseps2"][...] = nx // 2 - 1
+            gridfile.createVariable("ixseps1", numpy.int32)
+            gridfile["ixseps1"][...] = nx // 2 - 1
 
-        gridfile.createVariable("jyseps1_1", numpy.int32)
-        gridfile["jyseps1_1"][...] = blocksize - 1
+            gridfile.createVariable("ixseps2", numpy.int32)
+            gridfile["ixseps2"][...] = nx // 2 - 1
 
-        gridfile.createVariable("jyseps2_1", numpy.int32)
-        gridfile["jyseps2_1"][...] = ny // 2
+            gridfile.createVariable("jyseps1_1", numpy.int32)
+            gridfile["jyseps1_1"][...] = blocksize - 1
 
-        gridfile.createVariable("ny_inner", numpy.int32)
-        gridfile["ny_inner"][...] = ny // 2
+            gridfile.createVariable("jyseps2_1", numpy.int32)
+            gridfile["jyseps2_1"][...] = ny // 2
 
-        gridfile.createVariable("jyseps1_2", numpy.int32)
-        gridfile["jyseps1_2"][...] = ny // 2
+            gridfile.createVariable("ny_inner", numpy.int32)
+            gridfile["ny_inner"][...] = ny // 2
 
-        gridfile.createVariable("jyseps2_2", numpy.int32)
-        gridfile["jyseps2_2"][...] = 5 * blocksize - 1
+            gridfile.createVariable("jyseps1_2", numpy.int32)
+            gridfile["jyseps1_2"][...] = ny // 2
 
-        testdata = numpy.zeros([nx, ny + 2 * n_yguards])
-        testdata[:, :] = numpy.arange(ny + 2 * n_yguards)[numpy.newaxis, :]
-        gridfile.createVariable("test", float, ("x", "y"))
-        gridfile["test"][...] = testdata
+            gridfile.createVariable("jyseps2_2", numpy.int32)
+            gridfile["jyseps2_2"][...] = 5 * blocksize - 1
 
+            testdata = numpy.zeros([nx, ny + 2 * n_yguards])
+            testdata[:, :] = numpy.arange(ny + 2 * n_yguards)[numpy.newaxis, :]
+            gridfile.createVariable("test", float, ("x", "y"))
+            gridfile["test"][...] = testdata
 
-for nproc in [6]:
-    stdout.write("Checking %d processors ... " % (nproc))
 
-    shell("rm ./data*/BOUT.dmp.*.nc run.log.*")
+    for nproc in [6]:
+        stdout.write("Checking %d processors ... " % (nproc))
 
-    success = True
+        shell("rm ./data*/BOUT.dmp.*.nc run.log.*")
 
-    # double null tests
-    for n_yguards in [0, 1, 2]:
-        datadir = "data-doublenull-" + str(n_yguards)
+        success = True
 
-        s, out = launch_safe("./test_griddata -d " + datadir, nproc=nproc, pipe=True)
-
-        with open("run.log.doublenull." + str(nproc), "a") as f:
-            f.write(out)
-
-        testfield = collect("test", path=datadir, info=False, yguards=True)
-
-        if n_yguards == 0:
-            # output has 2 y-guard cells, but grid file did not
-            myg = 2
-            checkfield = list(numpy.zeros(myg))
-            checkfield += list(numpy.arange(ny // 2))
-            checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1)
-            checkfield += list(numpy.zeros(myg) + checkfield[-1])
-        else:
-            checkfield = []
-            checkfield += list(numpy.arange(n_yguards))
-            checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1)
-            checkfield += list(
-                numpy.arange(ny // 2) + checkfield[-1] + 1 + 2 * n_yguards
-            )
-            checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
-        checkfield = numpy.array(checkfield)
-
-        # Test value of testfield
-        if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13:
-            print(
-                "Failed: testfield does not match in doublenull case for n_yguards="
-                + str(n_yguards)
-            )
-            success = False
-
-    # single null tests
-    for n_yguards in [0, 1, 2]:
-        datadir = "data-singlenull-" + str(n_yguards)
+        # double null tests
+        for n_yguards in [0, 1, 2]:
+            datadir = "data-doublenull-" + str(n_yguards)
+
+            s, out = launch_safe("./test_griddata -d " + datadir, nproc=nproc, pipe=True)
+
+            with open("run.log.doublenull." + str(nproc), "a") as f:
+                f.write(out)
+
+            testfield = collect("test", path=datadir, info=False, yguards=True)
+
+            if n_yguards == 0:
+                # output has 2 y-guard cells, but grid file did not
+                myg = 2
+                checkfield = list(numpy.zeros(myg))
+                checkfield += list(numpy.arange(ny // 2))
+                checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1)
+                checkfield += list(numpy.zeros(myg) + checkfield[-1])
+            else:
+                checkfield = []
+                checkfield += list(numpy.arange(n_yguards))
+                checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1)
+                checkfield += list(
+                    numpy.arange(ny // 2) + checkfield[-1] + 1 + 2 * n_yguards
+                )
+                checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
+            checkfield = numpy.array(checkfield)
+
+            # Test value of testfield
+            if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13:
+                print(
+                    "Failed: testfield does not match in doublenull case for n_yguards="
+                    + str(n_yguards)
+                )
+                success = False
+
+        # single null tests
+        for n_yguards in [0, 1, 2]:
+            datadir = "data-singlenull-" + str(n_yguards)
+
+            s, out = launch_safe("./test_griddata -d " + datadir, nproc=nproc, pipe=True)
+
+            with open("run.log.singlenull." + str(nproc), "a") as f:
+                f.write(out)
+
+            testfield = collect("test", path=datadir, info=False, yguards=True)
+
+            if n_yguards == 0:
+                # output has 2 y-guard cells, but grid file did not
+                myg = 2
+                checkfield = list(numpy.zeros(myg))
+                checkfield += list(numpy.arange(ny))
+                checkfield += list(numpy.zeros(myg) + checkfield[-1])
+            else:
+                checkfield = []
+                checkfield += list(numpy.arange(n_yguards))
+                checkfield += list(numpy.arange(ny) + checkfield[-1] + 1)
+                checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
+            checkfield = numpy.array(checkfield)
 
-        s, out = launch_safe("./test_griddata -d " + datadir, nproc=nproc, pipe=True)
-
-        with open("run.log.singlenull." + str(nproc), "a") as f:
-            f.write(out)
-
-        testfield = collect("test", path=datadir, info=False, yguards=True)
-
-        if n_yguards == 0:
-            # output has 2 y-guard cells, but grid file did not
-            myg = 2
-            checkfield = list(numpy.zeros(myg))
-            checkfield += list(numpy.arange(ny))
-            checkfield += list(numpy.zeros(myg) + checkfield[-1])
-        else:
-            checkfield = []
-            checkfield += list(numpy.arange(n_yguards))
-            checkfield += list(numpy.arange(ny) + checkfield[-1] + 1)
-            checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
-        checkfield = numpy.array(checkfield)
-
-        # Test value of testfield
-        if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13:
-            print(
-                "Failed: testfield does not match in doublenull case for n_yguards="
-                + str(n_yguards)
-            )
-            success = False
-
-    if not success:
-        exit(1)
-    else:
-        print("Passed")
-
-exit(0)
+            # Test value of testfield
+            if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13:
+                print(
+                    "Failed: testfield does not match in doublenull case for n_yguards="
+                    + str(n_yguards)
+                )
+                success = False
+
+        assert success

From f8d07dafa74f82fe7672fda6eb6b565defcc8e52 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 3 Jan 2026 18:32:58 +0000
Subject: [PATCH 1010/1827] Use monkeypatch.chdir() fixture instead of
 contextmanager

---
 tests/integrated/test-beuler/test_beuler.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/tests/integrated/test-beuler/test_beuler.py b/tests/integrated/test-beuler/test_beuler.py
index 23c45741a3..268cd3c986 100755
--- a/tests/integrated/test-beuler/test_beuler.py
+++ b/tests/integrated/test-beuler/test_beuler.py
@@ -3,20 +3,17 @@
 # requires: petsc
 
 from boututils.run_wrapper import shell_safe, launch_safe
-from contextlib import chdir
-
 
 nthreads = 1
 nproc = 1
 
 
-def test_beuler(test_dir):
+def test_beuler():
     print("Making solver test")
     shell_safe("make > make.log")
 
     print("Running solver test")
-    with chdir(test_dir):
-        status, out = launch_safe("./test_beuler", nproc=nproc, mthread=nthreads, pipe=True)
+    status, out = launch_safe("./test_beuler", nproc=nproc, mthread=nthreads, pipe=True)
     with open("run.log", "w") as f:
         f.write(out)
 

From d81e62faed1a2c8a8b904f317db92aca6a2c9e7d Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 3 Jan 2026 19:04:17 +0000
Subject: [PATCH 1011/1827] Remove build_and_log() calls

---
 .../integrated/test-backtrace/test_backtrace.py |  9 +++------
 .../test-command-args/test_command_args.py      |  3 +--
 .../test-communications/test_communications.py  | 17 ++++++++---------
 tests/integrated/test-cyclic/test_cyclic.py     |  5 ++---
 .../test-datafilefacade/test_datafile_facade.py |  7 +++----
 tests/integrated/test-delp2/test_delp2.py       |  6 ++----
 .../test_drift_instability.py                   | 16 +++++-----------
 .../test-fieldgroupComm/test_fieldgroupComm.py  |  5 +----
 .../test_griddata_yboundary_guards.py           |  6 ++----
 tests/integrated/test-griddata/test_griddata.py |  5 +----
 tests/integrated/test-gyro/test_gyro.py         |  2 +-
 tests/integrated/test-initial/test_initial.py   |  4 +---
 .../test_interchange_instability.py             |  3 +--
 .../test-interpolate-z/test_interpolate_z.py    |  5 ++---
 .../test-interpolate/test_interpolate.py        |  6 ++----
 .../test_invertable_operator.py                 |  9 +++------
 tests/integrated/test-invpar/test_invpar.py     |  5 ++---
 .../test_laplace_hypre3d.py                     |  4 +---
 .../test_laplace_petsc3d.py                     |  4 +---
 tests/integrated/test-laplace/test_laplace.py   |  5 ++---
 .../test-laplacexy-fv/test_laplacexy_fv.py      |  6 ++----
 .../test_laplacexy_short.py                     |  6 ++----
 .../integrated/test-laplacexy/test_laplacexy.py |  6 ++----
 .../test_laplacexy2_hypre.py                    |  6 ++----
 .../integrated/test-laplacexz/test_laplacexz.py |  6 ++----
 .../runtest_multiple_grids                      |  5 ++---
 .../test-multigrid_laplace/runtest_unsheared    |  5 ++---
 .../test_multigrid_laplace.py                   |  4 ++--
 .../test-naulin-laplace/runtest_multiple_grids  |  5 ++---
 .../test-naulin-laplace/runtest_unsheared       |  5 ++---
 .../test-naulin-laplace/test_naulin_laplace.py  |  4 ++--
 .../test-options-adios/test_options_adios.py    |  8 +++-----
 .../test-options-netcdf/test_options_netcdf.py  |  7 +++----
 .../test-petsc_laplace/test_petsc_laplace.py    |  4 +---
 .../test_petsc_laplace_MAST_grid.py             |  7 ++-----
 .../test_region_iterator.py                     |  4 +---
 .../test-restart-io/test_restart_io.py          |  4 +---
 .../test-restarting/test_restarting.py          |  6 +++---
 .../test-slepc-solver/test_slepc_solver.py      |  3 +--
 tests/integrated/test-smooth/test_smooth.py     |  4 ++--
 tests/integrated/test-solver/test_solver.py     |  4 +---
 tests/integrated/test-squash/test_squash.py     |  4 +---
 .../test-stopCheck-file/test_stopCheck_file.py  |  4 +---
 .../test_twistshift_staggered.py                |  4 +---
 .../test-twistshift/test_twistshift.py          |  4 +---
 tests/integrated/test-vec/test_vec.py           |  4 +---
 .../test_yupdown_weights.py                     |  4 +---
 tests/integrated/test-yupdown/test_yupdown.py   |  8 +-------
 48 files changed, 91 insertions(+), 176 deletions(-)

diff --git a/tests/integrated/test-backtrace/test_backtrace.py b/tests/integrated/test-backtrace/test_backtrace.py
index f3767eeb9d..abeeba44f7 100755
--- a/tests/integrated/test-backtrace/test_backtrace.py
+++ b/tests/integrated/test-backtrace/test_backtrace.py
@@ -4,11 +4,9 @@
 
 # requires all_tests
 
-from boututils.run_wrapper import build_and_log, shell
+from boututils.run_wrapper import shell
 import os
 
-build_and_log("backtrace environment variable test")
-
 
 def test_backtrace():
     try:
@@ -17,15 +15,14 @@ def test_backtrace():
         pass
 
     success = True
-    errors = []
 
-    _, output = shell("./boutexcept", pipe=True)
+    _, output = shell(["./boutexcept"], pipe=True)
 
     if "troublemaker" in output:
         success = False
         pytest.fail("Fail: detected offending function name in output when not expected")
 
-    _, output = shell("BOUT_SHOW_BACKTRACE=yes ./boutexcept", pipe=True)
+    _, output = shell(["BOUT_SHOW_BACKTRACE=yes ./boutexcept"], pipe=True)
 
     if "troublemaker" not in output:
         success = False
diff --git a/tests/integrated/test-command-args/test_command_args.py b/tests/integrated/test-command-args/test_command_args.py
index a8dc3f020c..f2925ed5cb 100755
--- a/tests/integrated/test-command-args/test_command_args.py
+++ b/tests/integrated/test-command-args/test_command_args.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-from boututils.run_wrapper import build_and_log, launch_safe
+from boututils.run_wrapper import launch_safe
 
 import os
 import re
@@ -199,5 +199,4 @@ def testCommandLineOptionsArePrinted(self):
 
 
 if __name__ == "__main__":
-    build_and_log("Command arguments test")
     unittest.main(verbosity=2)
diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index 05e52821e7..7974e87d83 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -2,7 +2,7 @@
 import os
 import numpy as np
 from boututils.datafile import DataFile
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 
 # Cores: 18
 # Requires: netcdf
@@ -18,6 +18,7 @@ def run_test(actual, expected, procnum, region, boundary):
             ))
 
 
+# noinspection DuplicatedCode
 def test_communications():
 
     #################################################
@@ -36,10 +37,8 @@ def test_communications():
     nxpe = 3
     command = "./test-communications NXPE=" + str(nxpe)
 
-    build_and_log("Communications Test")
-
     # remove old outputs
-    shell("rm data/BOUT.dmp.*")
+    shell(["rm data/BOUT.dmp.*"])
 
     print("Running Communications Test, nproc=" + str(nxpe * nype))
 
@@ -181,7 +180,7 @@ def test_communications():
     command = "./test-communications NXPE=" + str(nxpe)
 
     # remove old outputs
-    shell("rm data/BOUT.dmp.*")
+    shell(["rm data/BOUT.dmp.*"])
 
     print("Running Communications Test, nproc=" + str(nxpe * nype))
 
@@ -281,7 +280,7 @@ def test_communications():
     command = "./test-communications NXPE=" + str(nxpe)
 
     # remove old outputs
-    shell("rm data/BOUT.dmp.*")
+    shell(["rm data/BOUT.dmp.*"])
 
     print("Running Communications Test, nproc=" + str(nxpe * nype))
 
@@ -345,7 +344,7 @@ def test_communications():
     command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
 
     # remove old outputs
-    shell("rm data_limiter/BOUT.dmp.*")
+    shell(["rm data_limiter/BOUT.dmp.*"])
 
     print("Running Communications Test, nproc=" + str(nxpe * nype))
 
@@ -381,7 +380,7 @@ def test_communications():
     command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
 
     # remove old outputs
-    shell("rm data_limiter/BOUT.dmp.*")
+    shell(["rm data_limiter/BOUT.dmp.*"])
 
     print("Running Communications Test, nproc=" + str(nxpe * nype))
 
@@ -410,7 +409,7 @@ def test_communications():
     command = "./test-communications -d data_limiter NXPE=" + str(nxpe)
 
     # remove old outputs
-    shell("rm data_limiter/BOUT.dmp.*")
+    shell(["rm data_limiter/BOUT.dmp.*"])
 
     print("Running Communications Test, nproc=" + str(nxpe * nype))
 
diff --git a/tests/integrated/test-cyclic/test_cyclic.py b/tests/integrated/test-cyclic/test_cyclic.py
index 7fad6bac72..f383cfe5c5 100755
--- a/tests/integrated/test-cyclic/test_cyclic.py
+++ b/tests/integrated/test-cyclic/test_cyclic.py
@@ -13,10 +13,9 @@
     from builtins import str
 except:
     pass
-from boututils.run_wrapper import build_and_log, shell, launch
+from boututils.run_wrapper import shell, launch
 from sys import stdout
 
-build_and_log("Cyclic Reduction test")
 
 flags = ["", "nsys=2", "nsys=5 periodic", "nsys=7 n=10"]
 
@@ -32,7 +31,7 @@ def test_cyclic():
         for f in flags:
             stdout.write("\tflags '" + f + "' ... ")
 
-            shell("rm data/BOUT.dmp.* 2> err.log")
+            shell(["rm data/BOUT.dmp.* 2> err.log"])
 
             # Run the case
             status, out = launch(cmd + " " + f, nproc=nproc, mthread=1, pipe=True)
diff --git a/tests/integrated/test-datafilefacade/test_datafile_facade.py b/tests/integrated/test-datafilefacade/test_datafile_facade.py
index 18bb8d55db..19e5322cda 100755
--- a/tests/integrated/test-datafilefacade/test_datafile_facade.py
+++ b/tests/integrated/test-datafilefacade/test_datafile_facade.py
@@ -6,10 +6,9 @@
 # cores: 2
 
 from boutdata.collect import collect
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 import numpy
 
-build_and_log("DataFileFacade test")
 
 success = True
 
@@ -39,7 +38,7 @@
 def test_datafile_facade():
     for nproc in [1, 2]:
         # delete any existing output
-        shell("rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc")
+        shell(["rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc"])
 
         print(f"   {nproc} processor....")
 
@@ -69,6 +68,6 @@ def test_datafile_facade():
         print("=> All DataFileFacade tests passed")
         # clean up binary files
         shell(
-            "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc"
+            ["rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc"]
         )
     assert success, f"=> Some failed tests"
diff --git a/tests/integrated/test-delp2/test_delp2.py b/tests/integrated/test-delp2/test_delp2.py
index b750528dc1..703286e6fc 100755
--- a/tests/integrated/test-delp2/test_delp2.py
+++ b/tests/integrated/test-delp2/test_delp2.py
@@ -3,7 +3,7 @@
 # cores: 4
 
 import pytest
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
 from sys import stdout
@@ -11,8 +11,6 @@
 tol = 1e-10  # Absolute tolerance
 
 
-build_and_log("Delp2 operator test")
-
 # The command to run
 exefile = "./test_delp2"
 
@@ -40,7 +38,7 @@ def test_delp2(setting):
     n0 = collect("n", path="data", info=False)
 
     for nproc in [2, 4]:
-        shell("rm data/BOUT.dmp.*.nc")
+        shell(["rm data/BOUT.dmp.*.nc"])
 
         stdout.write("   %d processor...." % (nproc))
         s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True)
diff --git a/tests/integrated/test-drift-instability/test_drift_instability.py b/tests/integrated/test-drift-instability/test_drift_instability.py
index 110f388ba0..4f2b402dd9 100644
--- a/tests/integrated/test-drift-instability/test_drift_instability.py
+++ b/tests/integrated/test-drift-instability/test_drift_instability.py
@@ -7,7 +7,7 @@
 # Requires: not metric_3d
 
 import pytest
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boututils.calculus import deriv
 from boututils.datafile import DataFile
 from boututils.linear_regression import linear_regression
@@ -51,13 +51,7 @@
 }  # 0.130220286897} Changed 25th April 2014
 
 
-@pytest.fixture(scope="module")
-def build_project():
-    """Build the project once per test module."""
-    build_and_log("resistive drift instability test")
-
-
-def run_zeff_case(zeff, build_project):
+def run_zeff_case(zeff):
     """Run a single Zeff case and return success flag and details."""
 
     if zeff not in omega_orig:
@@ -72,7 +66,7 @@ def run_zeff_case(zeff, build_project):
         timestep = 1e3
 
     # Delete old output files
-    shell("rm -f data/BOUT.dmp.*.nc")
+    shell(["rm -f data/BOUT.dmp.*.nc"])
 
     print("Running drift instability test, zeff = ", zeff)
 
@@ -203,8 +197,8 @@ def run_zeff_case(zeff, build_project):
 
 
 @pytest.mark.parametrize("zeff", zlist)
-def test_zeff_case(zeff, build_project):
+def test_zeff_case(zeff):
     """Pytest wrapper for running a single Zeff case."""
-    success, omegadiff, gammadiff = run_zeff_case(zeff, build_project)
+    success, omegadiff, gammadiff = run_zeff_case(zeff)
 
     assert success, f"Test failed for Zeff={zeff}: omega diff={omegadiff:.2%}, gamma diff={gammadiff:.2%}"
diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
index 80ff348d8f..e428fe8db0 100755
--- a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
+++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
@@ -17,7 +17,7 @@
 except:
     pass
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from numpy import abs, seterr
 import os
@@ -35,9 +35,6 @@ def test_fieldgroupcomm():
     exeName = "test_fieldgroupcomm"
     tol = 1e-10  # Relative tolerance
 
-
-    build_and_log("{nm} test".format(nm=name))
-
     print("Running {nm} test".format(nm=name))
     success = True
 
diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
index ca964d2c9b..84844d4336 100755
--- a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
+++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from netCDF4 import Dataset
 import numpy
@@ -12,8 +12,6 @@
 
 def test_griddata_yboundary_guards():
 
-    build_and_log("griddata test")
-
     nx = 4
     ny = 24
     blocksize = ny / 6
@@ -123,7 +121,7 @@ def test_griddata_yboundary_guards():
     for nproc in [6]:
         stdout.write("Checking %d processors ... " % (nproc))
 
-        shell("rm ./data*/BOUT.dmp.*.nc run.log.*")
+        shell(["rm ./data*/BOUT.dmp.*.nc run.log.*"])
 
         success = True
 
diff --git a/tests/integrated/test-griddata/test_griddata.py b/tests/integrated/test-griddata/test_griddata.py
index 0525a58ef6..5b04bea7ee 100755
--- a/tests/integrated/test-griddata/test_griddata.py
+++ b/tests/integrated/test-griddata/test_griddata.py
@@ -8,15 +8,12 @@
 except:
     pass
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
 from sys import stdout
 
 
-build_and_log("griddata test")
-
-
 def test_griddata():
     for nproc in [1]:
         stdout.write("Checking %d processors ... " % (nproc))
diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py
index 86e29f9f32..cc18b96c14 100755
--- a/tests/integrated/test-gyro/test_gyro.py
+++ b/tests/integrated/test-gyro/test_gyro.py
@@ -20,7 +20,7 @@
 
 tol = 1e-7  # Absolute tolerance, benchmark values are floats
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
 from sys import stdout
diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index 54ac14f873..756659f5ad 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -2,7 +2,7 @@
 import pytest
 # Test initial conditions
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import launch_safe
 from boutdata.collect import collect
 
 import configparser
@@ -175,8 +175,6 @@ def test_initial():
     for coord in ["var_x", "var_y", "var_z"]:
         varlist.remove(coord)
 
-    build_and_log("initial conditions test")
-
     nprocs = [1, 2, 3, 4]
     for nproc in nprocs:
         status, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index 005d56153a..4ea71815da 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -14,14 +14,13 @@
 nproc = 2  # Number of processors to run on
 reltol = 1.0e-3  # Allowed relative tolerance in growth-rate
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
 
 nthreads = 1
 
 def test_interchange_instability():
-    build_and_log("interchange instability test")
 
     # Delete old output files
     shell("rm data_1/BOUT.dmp.*")
diff --git a/tests/integrated/test-interpolate-z/test_interpolate_z.py b/tests/integrated/test-interpolate-z/test_interpolate_z.py
index cef5e468c0..b878d4a044 100755
--- a/tests/integrated/test-interpolate-z/test_interpolate_z.py
+++ b/tests/integrated/test-interpolate-z/test_interpolate_z.py
@@ -4,7 +4,7 @@
 # Run the test, compare results against the benchmark
 #
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata import collect
 from numpy import sqrt, max, abs, mean, array, log, polyfit
 from sys import stdout
@@ -29,7 +29,6 @@
 
 
 def test_interpolate_z():
-    build_and_log("ZInterpolation test")
 
     print("Running ZInterpolation test")
     success = True
@@ -55,7 +54,7 @@ def test_interpolate_z():
 
             cmd = "./test_interpolate" + args
 
-            shell("rm data/BOUT.dmp.*.nc")
+            shell(["rm data/BOUT.dmp.*.nc"])
 
             s, out = launch_safe(cmd, nproc=nproc, pipe=True)
             with open("run.log.{}.{}".format(method, nx), "w") as f:
diff --git a/tests/integrated/test-interpolate/test_interpolate.py b/tests/integrated/test-interpolate/test_interpolate.py
index 8a8eaa546b..d2e80c8d08 100755
--- a/tests/integrated/test-interpolate/test_interpolate.py
+++ b/tests/integrated/test-interpolate/test_interpolate.py
@@ -7,7 +7,7 @@
 import pytest
 import os
 import pathlib
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata import collect
 import boutconfig
 from numpy import sqrt, max, abs, mean, array, log, polyfit
@@ -37,8 +37,6 @@
 @pytest.mark.parametrize("method", methods)
 def test_interpolate(method):
 
-    build_and_log("Interpolation test")
-
     print("Running Interpolation test")
     success = True
 
@@ -63,7 +61,7 @@ def test_interpolate(method):
 
         cmd = "./test_interpolate" + args
 
-        shell("rm data/BOUT.dmp.*.nc")
+        shell(["rm data/BOUT.dmp.*.nc"])
 
         s, out = launch_safe(cmd, nproc=nproc, pipe=True)
         with open("run.log.{}.{}".format(method, nx), "w") as f:
diff --git a/tests/integrated/test-invertable-operator/test_invertable_operator.py b/tests/integrated/test-invertable-operator/test_invertable_operator.py
index 47fc5f1b53..9ac26be701 100755
--- a/tests/integrated/test-invertable-operator/test_invertable_operator.py
+++ b/tests/integrated/test-invertable-operator/test_invertable_operator.py
@@ -11,20 +11,17 @@
 from __future__ import print_function
 from __future__ import division
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
-import numpy as np
-from sys import stdout, exit
+from sys import exit
 
 nprocs = [1, 2]  # Number of processors to run on
 reltol = 1.0e-3  # Allowed relative tolerance
 nthreads = 1
 
 
-build_and_log("invertable operator test")
-
 # Delete old output files
-shell("rm data/BOUT.dmp.*")
+shell(["rm data/BOUT.dmp.*"])
 
 
 def run(path, nproc, log=False):
diff --git a/tests/integrated/test-invpar/test_invpar.py b/tests/integrated/test-invpar/test_invpar.py
index 38ef1fdfaa..229a735b19 100755
--- a/tests/integrated/test-invpar/test_invpar.py
+++ b/tests/integrated/test-invpar/test_invpar.py
@@ -8,10 +8,9 @@
 # Requires: netcdf
 # Cores: 4
 
-from boututils.run_wrapper import build_and_log, shell, launch
+from boututils.run_wrapper import shell, launch
 from boutdata.collect import collect
 
-build_and_log("parallel inversion test")
 
 flags_src = [
     dict(acoef=1, bcoef=0, ccoef=0, dcoef=0, ecoef=0),
@@ -45,7 +44,7 @@ def test_invpar():
         print("   %d processors...." % (nproc))
         r = 0
         for f in flags:
-            shell("rm data/BOUT.dmp.* 2> err.log")
+            shell(["rm data/BOUT.dmp.* 2> err.log"])
 
             # Run the case
             s, _ = launch(cmd + " -q -q -q " + f, nproc=nproc, mthread=1)
diff --git a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
index b50c5993b7..595226cdc4 100755
--- a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
+++ b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
@@ -3,7 +3,7 @@
 # requires: hypre
 
 from boutdata import collect
-from boututils.run_wrapper import launch_safe, build_and_log
+from boututils.run_wrapper import launch_safe
 from sys import exit
 
 test_directories = [
@@ -15,8 +15,6 @@
 
 tolerance = 1.0e-6
 
-build_and_log("Laplace 3D with Hypre")
-
 success = True
 for directory, nproc in test_directories:
     command = "test-laplace3d -d " + directory
diff --git a/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
index 7b0d55f357..7fa2dbe22c 100755
--- a/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
+++ b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
@@ -3,7 +3,7 @@
 # requires: petsc
 
 from boutdata import collect
-from boututils.run_wrapper import launch, build_and_log
+from boututils.run_wrapper import launch
 from sys import exit
 
 test_directories = [
@@ -15,8 +15,6 @@
 
 tolerance = 1.0e-6
 
-build_and_log("Laplace 3D with PETSc")
-
 success = True
 errors = {}
 
diff --git a/tests/integrated/test-laplace/test_laplace.py b/tests/integrated/test-laplace/test_laplace.py
index 447993bc9c..cd42f9c734 100755
--- a/tests/integrated/test-laplace/test_laplace.py
+++ b/tests/integrated/test-laplace/test_laplace.py
@@ -8,10 +8,10 @@
 # Requires: netcdf
 # Cores: 4
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect, create_cache
 import numpy.testing as npt
-from sys import exit
+from sys import stdout
 
 
 # Variables to compare
@@ -35,7 +35,6 @@
 ]
 tol = 1e-6  # Absolute tolerance
 
-build_and_log("Laplacian inversion test")
 
 # Read benchmark values
 print("Reading benchmark data")
diff --git a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
index f87a12e2ab..664433ef98 100755
--- a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
+++ b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
@@ -8,7 +8,7 @@
 # requires: petsc
 # cores: 8
 
-from boututils.run_wrapper import build_and_log, shell, shell_safe, launch, launch_safe
+from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
@@ -37,8 +37,6 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
 ]
 
-build_and_log("LaplaceXY inversion test")
-
 print("Running LaplaceXY inversion test")
 success = True
 
@@ -47,7 +45,7 @@
     for args in argslist:
         cmd = "./test-laplacexy " + args
 
-        shell("rm data/BOUT.dmp.*.nc > /dev/null 2>&1")
+        shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
 
         s, out = launch(
             cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
diff --git a/tests/integrated/test-laplacexy-short/test_laplacexy_short.py b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
index 3325a32f4d..0ed5c6ff63 100755
--- a/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
+++ b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
@@ -8,7 +8,7 @@
 # requires: petsc
 # cores: 8
 
-from boututils.run_wrapper import build_and_log, shell, shell_safe, launch, launch_safe
+from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
@@ -45,8 +45,6 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1",
 ]
 
-build_and_log("LaplaceXY inversion test")
-
 print("Running LaplaceXY inversion test")
 success = True
 
@@ -55,7 +53,7 @@
     for args in argslist:
         cmd = "./test-laplacexy " + args
 
-        shell("rm data/BOUT.dmp.*.nc > /dev/null 2>&1")
+        shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
 
         s, out = launch(
             cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
diff --git a/tests/integrated/test-laplacexy/test_laplacexy.py b/tests/integrated/test-laplacexy/test_laplacexy.py
index d2f99c5100..0dd550cab0 100755
--- a/tests/integrated/test-laplacexy/test_laplacexy.py
+++ b/tests/integrated/test-laplacexy/test_laplacexy.py
@@ -9,7 +9,7 @@
 # requires: all_tests
 # cores: 8
 
-from boututils.run_wrapper import build_and_log, shell, shell_safe, launch, launch_safe
+from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
@@ -52,8 +52,6 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1 laplacexy:pctype=hypre",
 ]
 
-build_and_log("LaplaceXY inversion test")
-
 print("Running LaplaceXY inversion test")
 success = True
 
@@ -66,7 +64,7 @@
 
             cmd = "./test-laplacexy " + args
 
-            shell("rm data/BOUT.dmp.*.nc > /dev/null 2>&1")
+            shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
 
             if "hypre" in args:
                 s, out = launch(cmd, nproc=nproc, pipe=True, verbose=True)
diff --git a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
index 55f5982a0c..7728b97785 100755
--- a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
+++ b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
@@ -10,7 +10,7 @@
 from sys import exit
 
 from boutdata.collect import collect
-from boututils.run_wrapper import build_and_log, launch_safe, shell
+from boututils.run_wrapper import launch_safe, shell
 
 tol = 5.0e-8
 
@@ -37,8 +37,6 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
 ]
 
-build_and_log("LaplaceXY inversion test")
-
 print("Running LaplaceXY inversion test")
 success = True
 
@@ -47,7 +45,7 @@
     for args in argslist:
         cmd = "./test-laplacexy " + args
 
-        shell("rm data/BOUT.dmp.*.nc > /dev/null 2>&1")
+        shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
 
         s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
 
diff --git a/tests/integrated/test-laplacexz/test_laplacexz.py b/tests/integrated/test-laplacexz/test_laplacexz.py
index bc7592ec3e..26886287f8 100755
--- a/tests/integrated/test-laplacexz/test_laplacexz.py
+++ b/tests/integrated/test-laplacexz/test_laplacexz.py
@@ -7,7 +7,7 @@
 # Run the test, compare results against the benchmark
 #
 
-from boututils.run_wrapper import shell, launch_safe, getmpirun, build_and_log
+from boututils.run_wrapper import shell, launch_safe, getmpirun
 from boutdata.collect import collect
 import numpy as np
 from sys import exit
@@ -16,8 +16,6 @@
 
 MPIRUN = getmpirun()
 
-build_and_log("LaplaceXZ test")
-
 print("Running LaplaceXZ test")
 success = True
 
@@ -26,7 +24,7 @@
 
     cmd = "./test-laplacexz nxpe=" + str(nxpe)
 
-    shell("rm data/BOUT.dmp.*.nc")
+    shell(["rm data/BOUT.dmp.*.nc"])
 
     print("   %d processors (nxpe = %d)...." % (nproc, nxpe))
     s, out = launch_safe(cmd, runcmd=MPIRUN, nproc=nproc, mthread=1, pipe=True)
diff --git a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
index 739d15f7d4..b4905c41c6 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
+++ b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
@@ -14,11 +14,10 @@ except:
 tol = 2e-6  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
-from boututils.run_wrapper import shell, build_and_log, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-build_and_log("Multigrid Laplacian inversion test")
 
 print("Running multigrid Laplacian inversion test")
 success = True
@@ -28,7 +27,7 @@ for nproc in [1, 2, 4]:
         # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
         cmd = "./test_multigrid_laplace -f " + inputfile + " NXPE=" + str(nproc)
 
-        shell("rm data/BOUT.dmp.*.nc")
+        shell(["rm data/BOUT.dmp.*.nc"])
 
         print("   %d processors, input file is %s" % (nproc, inputfile))
         s, out = launch_safe(cmd, nproc=nproc, pipe=True)
diff --git a/tests/integrated/test-multigrid_laplace/runtest_unsheared b/tests/integrated/test-multigrid_laplace/runtest_unsheared
index d0dca3a808..62580efd44 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_unsheared
+++ b/tests/integrated/test-multigrid_laplace/runtest_unsheared
@@ -14,11 +14,10 @@ except:
 tol = 1e-9  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
-from boututils.run_wrapper import shell, build_and_log, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-build_and_log("Making multigrid Laplacian inversion test")
 
 print("Running multigrid Laplacian inversion test")
 success = True
@@ -33,7 +32,7 @@ for nproc in [1, 3]:
     # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
     cmd = "./test_multigrid_laplace -f BOUT_unsheared.inp NXPE=" + str(nproc)
 
-    shell("rm data/BOUT.dmp.*.nc")
+    shell(["rm data/BOUT.dmp.*.nc"])
 
     print("   %d processors..." % nproc)
     s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
index e10a536fc2..48e6af5beb 100755
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
@@ -21,7 +21,7 @@
 tol = 2e-7  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
 
@@ -41,7 +41,7 @@ def test_multigrid_laplace():
         # so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
         cmd = "./test_multigrid_laplace NXPE=" + str(nproc)
 
-        shell("rm data/BOUT.dmp.*.nc")
+        shell(["rm data/BOUT.dmp.*.nc"])
 
         print("   %d processors..." % nproc)
         s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
diff --git a/tests/integrated/test-naulin-laplace/runtest_multiple_grids b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
index f56a80677e..19fbbfd5d6 100755
--- a/tests/integrated/test-naulin-laplace/runtest_multiple_grids
+++ b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
@@ -14,11 +14,10 @@ except:
 tol = 2e-6  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
-from boututils.run_wrapper import shell, build_and_log, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-build_and_log("Making LaplaceNaulin inversion test")
 
 print("Running LaplaceNaulin inversion test")
 success = True
@@ -28,7 +27,7 @@ for nproc in [1, 2, 4]:
         # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver)
         cmd = "./test_naulin_laplace -f " + inputfile + " NXPE=" + str(nproc)
 
-        shell("rm data/BOUT.dmp.*.nc")
+        shell(["rm data/BOUT.dmp.*.nc"])
 
         print("   %d processors, input file is %s" % (nproc, inputfile))
         s, out = launch_safe(cmd, nproc=nproc, pipe=True)
diff --git a/tests/integrated/test-naulin-laplace/runtest_unsheared b/tests/integrated/test-naulin-laplace/runtest_unsheared
index a845a9d92f..691ab497f2 100755
--- a/tests/integrated/test-naulin-laplace/runtest_unsheared
+++ b/tests/integrated/test-naulin-laplace/runtest_unsheared
@@ -14,11 +14,10 @@ except:
 tol = 1e-9  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
-from boututils.run_wrapper import shell, build_and_log, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
-build_and_log("LaplaceNaulin inversion test")
 
 print("Running LaplaceNaulin inversion test")
 success = True
@@ -33,7 +32,7 @@ for nproc in [1, 3]:
     # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver)
     cmd = "./test_naulin_laplace -f BOUT_unsheared.inp NXPE=" + str(nproc)
 
-    shell("rm data/BOUT.dmp.*.nc")
+    shell(["rm data/BOUT.dmp.*.nc"])
 
     print("   %d processors..." % nproc)
     s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
index 1626175733..9d52b8d534 100755
--- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
+++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
@@ -18,7 +18,7 @@
 tol = 2e-7  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
 
@@ -37,7 +37,7 @@ def test_naulin_laplace():
         # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver)
         cmd = "./test_naulin_laplace NXPE=" + str(nproc)
 
-        shell("rm data/BOUT.dmp.*.nc")
+        shell(["rm data/BOUT.dmp.*.nc"])
 
         print("   %d processors..." % nproc)
         s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
diff --git a/tests/integrated/test-options-adios/test_options_adios.py b/tests/integrated/test-options-adios/test_options_adios.py
index 03a83fc0ba..f3284d65fd 100755
--- a/tests/integrated/test-options-adios/test_options_adios.py
+++ b/tests/integrated/test-options-adios/test_options_adios.py
@@ -6,15 +6,13 @@
 # requires: not legacy_netcdf
 
 from boututils.datafile import DataFile
-from boututils.run_wrapper import build_and_log, shell, launch
+from boututils.run_wrapper import shell, launch
 from boutdata.data import BoutOptionsFile
 
 import math
-import numpy as np
 
-build_and_log("options-netcdf test")
-shell("rm -f test-out.ini")
-shell("rm -f test-out.nc")
+shell(["rm -f test-out.ini"])
+shell(["rm -f test-out.nc"])
 
 # Create a NetCDF input file
 with DataFile("test.nc", create=True, format="NETCDF4") as f:
diff --git a/tests/integrated/test-options-netcdf/test_options_netcdf.py b/tests/integrated/test-options-netcdf/test_options_netcdf.py
index ad9196ba2d..3835cf0c9f 100755
--- a/tests/integrated/test-options-netcdf/test_options_netcdf.py
+++ b/tests/integrated/test-options-netcdf/test_options_netcdf.py
@@ -5,7 +5,7 @@
 # requires: not legacy_netcdf
 
 from boututils.datafile import DataFile
-from boututils.run_wrapper import build_and_log, shell, launch_safe as launch
+from boututils.run_wrapper import shell, launch_safe as launch
 from boutdata.data import BoutOptionsFile
 
 import math
@@ -13,9 +13,8 @@
 
 def test_options_netcdf():
 
-    build_and_log("options-netcdf test")
-    shell("rm -f test-out.ini")
-    shell("rm -f test-out.nc")
+    shell(["rm -f test-out.ini"])
+    shell(["rm -f test-out.nc"])
 
     # Create a NetCDF input file
     with DataFile("test.nc", create=True, format="NETCDF4") as f:
diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
index b4379f7754..d5e16203ef 100755
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
@@ -24,15 +24,13 @@
 ]
 tol = 2e-4  # Absolute (?) tolerance
 
-build_and_log("PETSc Laplacian inversion test")
-
 print("Running PETSc Laplacian inversion test")
 success = True
 
 for nproc in [1, 2, 4]:
     cmd = "./test_petsc_laplace"
 
-    shell("rm data/BOUT.dmp.*.nc")
+    shell(["rm data/BOUT.dmp.*.nc"])
 
     print(f"   {nproc} processors....")
     s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
index 3be39949c3..ab8d1c1b4e 100755
--- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
@@ -24,13 +24,10 @@
 ]
 # tol = 1e-4                  # Absolute (?) tolerance
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from sys import stdout, exit
 
-build_and_log(
-    "PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)"
-)
 
 print(
     "Running PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)"
@@ -46,7 +43,7 @@
             jy
         )
 
-        shell("rm data/BOUT.dmp.*.nc")
+        shell(["rm data/BOUT.dmp.*.nc"])
 
         print("   {} processors, grid_MAST_SOL_jyis{}".format(nproc, jy))
         s, out = launch_safe(cmd, nproc=nproc, pipe=True)
diff --git a/tests/integrated/test-region-iterator/test_region_iterator.py b/tests/integrated/test-region-iterator/test_region_iterator.py
index 2277ef15e9..f22196f0a9 100755
--- a/tests/integrated/test-region-iterator/test_region_iterator.py
+++ b/tests/integrated/test-region-iterator/test_region_iterator.py
@@ -13,11 +13,9 @@
     from builtins import str
 except:
     pass
-from boututils.run_wrapper import build_and_log, launch_safe
-from boutdata.collect import collect
+from boututils.run_wrapper import launch_safe
 from sys import exit
 
-build_and_log("Region Iterator test")
 
 flags = [""]
 cmd = "./test_region_iterator"
diff --git a/tests/integrated/test-restart-io/test_restart_io.py b/tests/integrated/test-restart-io/test_restart_io.py
index 66f5fe827c..b3533b4d0e 100755
--- a/tests/integrated/test-restart-io/test_restart_io.py
+++ b/tests/integrated/test-restart-io/test_restart_io.py
@@ -9,7 +9,7 @@
 from boutdata.collect import collect
 from boututils.boutarray import BoutArray
 from boututils.datafile import DataFile
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 import numpy
 import os
 import uuid
@@ -22,8 +22,6 @@
 
 def test_restart_io():
 
-    build_and_log("restart I/O test")
-
     x = numpy.linspace(0.0, 1.0, nx + 2 * mxg)[:, numpy.newaxis, numpy.newaxis]
     y = numpy.linspace(0.0, 1.0, ny + 2 * myg)[numpy.newaxis, :, numpy.newaxis]
     z = numpy.linspace(0.0, 1.0, nz)[numpy.newaxis, numpy.newaxis, :]
diff --git a/tests/integrated/test-restarting/test_restarting.py b/tests/integrated/test-restarting/test_restarting.py
index f0ca203110..7591dc5f5b 100755
--- a/tests/integrated/test-restarting/test_restarting.py
+++ b/tests/integrated/test-restarting/test_restarting.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
 
@@ -19,7 +19,7 @@ def test_restarting():
 
     print("-> Testing restart append")
 
-    shell("rm -f data/BOUT.dmp.0.nc")
+    shell(["rm -f data/BOUT.dmp.0.nc"])
     s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True)
     s, out = launch_safe(
         "./test_restarting solver:nout=5 restart append", nproc=1, pipe=True
@@ -51,7 +51,7 @@ def test_restarting():
 
     print("-> Testing restart")
 
-    shell("rm -f data/BOUT.dmp.0.nc")
+    shell(["rm -f data/BOUT.dmp.0.nc"])
     s, out = launch_safe("./test_restarting solver:nout=5", nproc=1, pipe=True)
     s, out = launch_safe("./test_restarting solver:nout=5 restart", nproc=1, pipe=True)
 
diff --git a/tests/integrated/test-slepc-solver/test_slepc_solver.py b/tests/integrated/test-slepc-solver/test_slepc_solver.py
index baced1bcf3..907840316d 100755
--- a/tests/integrated/test-slepc-solver/test_slepc_solver.py
+++ b/tests/integrated/test-slepc-solver/test_slepc_solver.py
@@ -3,10 +3,9 @@
 # requires: slepc
 
 from boutdata.collect import collect
-from boututils.run_wrapper import build_and_log, launch_safe
+from boututils.run_wrapper import launch_safe
 from numpy import isclose
 
-build_and_log("SLEPc eigen solver test")
 
 print("Running SLEPc eigen solver test")
 status, out = launch_safe("./test-slepc-solver", nproc=1, pipe=True, verbose=True)
diff --git a/tests/integrated/test-smooth/test_smooth.py b/tests/integrated/test-smooth/test_smooth.py
index b74000f205..3d3776ca25 100755
--- a/tests/integrated/test-smooth/test_smooth.py
+++ b/tests/integrated/test-smooth/test_smooth.py
@@ -11,7 +11,7 @@
 vars = ["yavg2d", "yavg3d", "sm3d"]
 tol = 1e-7  # Absolute tolerance, benchmark values are floats
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 import numpy as np
 from sys import stdout
@@ -33,7 +33,7 @@ def test_smooth():
             nproc = nxpe * nype
             cmd = "./test_smooth"
 
-            shell("rm data/BOUT.dmp.*.nc")
+            shell(["rm data/BOUT.dmp.*.nc"])
 
             print("   %d processor (%d x %d)...." % (nproc, nxpe, nype))
             s, out = launch_safe(cmd + " NXPE=" + str(nxpe), nproc=nproc, pipe=True)
diff --git a/tests/integrated/test-solver/test_solver.py b/tests/integrated/test-solver/test_solver.py
index 607f3bb7ea..18283caf73 100755
--- a/tests/integrated/test-solver/test_solver.py
+++ b/tests/integrated/test-solver/test_solver.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-from boututils.run_wrapper import build_and_log, launch_safe
+from boututils.run_wrapper import launch_safe
 
 from sys import exit
 
@@ -8,8 +8,6 @@
 nproc = 1
 
 
-build_and_log("Solver test")
-
 print("Running solver test")
 status, out = launch_safe("./test_solver", nproc=nproc, mthread=nthreads, pipe=True)
 with open("run.log", "w") as f:
diff --git a/tests/integrated/test-squash/test_squash.py b/tests/integrated/test-squash/test_squash.py
index 7fd6621dec..b9a2f903c5 100755
--- a/tests/integrated/test-squash/test_squash.py
+++ b/tests/integrated/test-squash/test_squash.py
@@ -4,7 +4,7 @@
 import itertools
 import time
 import numpy as np
-from boututils.run_wrapper import launch_safe, shell_safe, build_and_log
+from boututils.run_wrapper import launch_safe, shell_safe
 import argparse
 import re
 import os.path
@@ -86,8 +86,6 @@ def test_squash():
     )
     args = parser.parse_args()
 
-    build_and_log("Squash test")
-
     bout_squashoutput = args.executable + "/bout-squashoutput"
 
     if not os.path.exists(bout_squashoutput):
diff --git a/tests/integrated/test-stopCheck-file/test_stopCheck_file.py b/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
index 6f08745dd2..4d97ff3019 100755
--- a/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
+++ b/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
@@ -4,15 +4,13 @@
 
 import sys
 
-from boututils.run_wrapper import build_and_log, launch
+from boututils.run_wrapper import launch
 from boutdata.collect import collect
 
 nproc = 1
 
 def test_stopCheck_file():
 
-    build_and_log("stopCheck test")
-
     check_values = [True, False]
     expected_steps = [1, 11]
     data_dirs = ["data", "dataSecond"]
diff --git a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
index 5b1c1bee90..cba1ffd0d3 100755
--- a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
+++ b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 from boutdata import collect
-from boututils.run_wrapper import build_and_log, launch_safe
+from boututils.run_wrapper import launch_safe
 import numpy
 
 datapath = "data"
@@ -10,8 +10,6 @@
 
 def test_twistshift_staggered():
 
-    build_and_log("twistshift test")
-
     s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True)
     with open("run.log." + str(nproc), "w") as f:
         f.write(out)
diff --git a/tests/integrated/test-twistshift/test_twistshift.py b/tests/integrated/test-twistshift/test_twistshift.py
index 8daf070ca6..0e81540e4e 100755
--- a/tests/integrated/test-twistshift/test_twistshift.py
+++ b/tests/integrated/test-twistshift/test_twistshift.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 from boutdata import collect
-from boututils.run_wrapper import build_and_log, launch_safe
+from boututils.run_wrapper import launch_safe
 import numpy
 
 datapath = "data"
@@ -11,8 +11,6 @@
 
 def test_twistshift():
 
-    build_and_log("twistshift test")
-
     s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True)
     with open("run.log." + str(nproc), "w") as f:
         f.write(out)
diff --git a/tests/integrated/test-vec/test_vec.py b/tests/integrated/test-vec/test_vec.py
index 23ab390759..d216689239 100755
--- a/tests/integrated/test-vec/test_vec.py
+++ b/tests/integrated/test-vec/test_vec.py
@@ -2,12 +2,10 @@
 
 # Cores: 4
 
-from boututils.run_wrapper import build_and_log, launch_safe
+from boututils.run_wrapper import launch_safe
 
 def test_vec():
 
-    build_and_log("vector communication test")
-
     status, out = launch_safe("./testVec", nproc=4, pipe=True)
 
     with open("run.log.4", "w") as f:
diff --git a/tests/integrated/test-yupdown-weights/test_yupdown_weights.py b/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
index 57a5e06f3d..3ae4bdba08 100755
--- a/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
+++ b/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-from boututils.run_wrapper import build_and_log, launch_safe
+from boututils.run_wrapper import launch_safe
 from boutdata.collect import collect
 from sys import stdout
 
@@ -8,8 +8,6 @@
 
 def test_yupdown_weights():
 
-    build_and_log("parallel slices and weights test")
-
     failed = False
     for shifttype in ["shiftedinterp"]:
         s, out = launch_safe(
diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py
index 6bdfbafb0c..0d8c61bc7a 100755
--- a/tests/integrated/test-yupdown/test_yupdown.py
+++ b/tests/integrated/test-yupdown/test_yupdown.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 import os
 import pytest
-from boututils.run_wrapper import build_and_log, launch_safe
+from boututils.run_wrapper import launch_safe
 from boutdata.collect import collect
 from numpy import max, abs
 
@@ -9,12 +9,6 @@
 variables = [("ddy", "ddy_check"), ("ddy2", "ddy_check")]
 
 
-@pytest.fixture(scope="module")
-def build_project():
-    """Build the project once per test module."""
-    build_and_log("parallel slices test")
-
-
 def run_case(shift_type, variable):
     s, out = launch_safe(
         "./test_yupdown mesh:paralleltransform:type=" + shift_type,

From bcbd7d8192421d0945eab98446572905cf05b8fc Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 3 Jan 2026 21:45:00 +0000
Subject: [PATCH 1012/1827] Copy conftest.py when building

---
 CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e37559b598..8292ab599c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -780,6 +780,11 @@ if(BOUT_TESTS)
     add_dependencies(check check-unit-tests)
   endif()
 
+  # Copy the pytest config file
+  configure_file(
+    "${PROJECT_SOURCE_DIR}/tests/conftest.py"
+    "${PROJECT_BINARY_DIR}/include/bout/version.hxx/tests/conftest.py")
+
 endif()
 
 option(BOUT_BUILD_EXAMPLES "Build the examples" ON)

From 666835f884c94c5c307fd559d93eaf03404067cb Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 3 Jan 2026 22:11:58 +0000
Subject: [PATCH 1013/1827] Correct assert statement in
 test_boutpp_collect_staggered

---
 .../collect-staggered/test_boutpp_collect_staggered.py          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index c8536b0ef5..23158b2276 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -53,4 +53,4 @@ def compare(a, b):
         print("Something is wrong. Maybe setting the location from field failed.")
         fail = 1
 
-    exit(fail)
+    assert fail == 0

From c748b9c39f30297d4c865b4b69679cd8b9551ebb Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 3 Jan 2026 22:22:21 +0000
Subject: [PATCH 1014/1827] Now have a fixture that handles changing the
 working directory for each test

---
 tests/integrated/test-boutpp/collect/test_boutpp_collect.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index 2e122ebc47..d71aef9a11 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -1,6 +1,4 @@
 #!/usr/bin/env python3
-import os
-import pathlib
 import boutpp as bc
 import numpy as np
 from boutdata import collect
@@ -11,8 +9,6 @@
 
 def test_boutpp_collect():
 
-    this_directory = pathlib.Path(__file__).parent.absolute()
-    os.chdir(this_directory)
     bc.init("-d input".split(" "))
 
     f = bc.Field3D.fromMesh(None)

From 5c3488d723d8073b7663294a0d8ddd2d125776ea Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 4 Jan 2026 12:21:11 +0000
Subject: [PATCH 1015/1827] Fix "Copy conftest.py when building"

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8292ab599c..987c5e3a73 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -783,7 +783,7 @@ if(BOUT_TESTS)
   # Copy the pytest config file
   configure_file(
     "${PROJECT_SOURCE_DIR}/tests/conftest.py"
-    "${PROJECT_BINARY_DIR}/include/bout/version.hxx/tests/conftest.py")
+    "${PROJECT_BINARY_DIR}/tests/conftest.py")
 
 endif()
 

From f8f83cc57907fcd6c8406669465dc03bc5f929ab Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 4 Jan 2026 13:24:19 +0000
Subject: [PATCH 1016/1827] Add `finalize_boutpp` fixture, and mark relevant
 tests with a `boutpp_initialized` flag

---
 tests/conftest.py                                   | 13 +++++++++++++
 .../test_boutpp_collect_staggered.py                |  2 ++
 .../test-boutpp/collect/test_boutpp_collect.py      |  3 +++
 .../legacy-model/test_boutpp_legacy_model.py        |  2 ++
 .../test-boutpp/mms-ddz/test_boutpp_mms_ddz.py      |  1 +
 .../simple-model/test_boutpp_simple_model.py        |  3 ++-
 .../integrated/test-boutpp/slicing/test_slicing.py  |  6 ++----
 7 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 8c0d4e9621..8169f93e27 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,4 +1,5 @@
 import pytest
+import boutpp
 from pathlib import Path
 
 
@@ -10,3 +11,15 @@ def cwd_to_test_file_dir(monkeypatch, test_dir):
 @pytest.fixture
 def test_dir(request) -> Path:
     return Path(request.fspath).parent
+
+@pytest.fixture(autouse=True)
+def finalize_boutpp(request):
+    """Automatically finalize BOUT++ after each test that used it."""
+    yield  # Run the test
+
+    # Check if this test used boutpp init (heuristic: look for marker or direct check)
+    if hasattr(request.node, "boutpp_initialized"):
+        try:
+            boutpp.finalise()
+        except Exception:
+            pass  # If already finalized or error, ignore
diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index 23158b2276..4c741e4681 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -8,7 +8,9 @@
 # requires not make
 
 def test_boutpp_collect_staggered():
+
     bc.init("-q -q -q")
+    request.node.boutpp_initialized = True
 
     fail = 0
     f = bc.create3D("sin(y)", outloc="YLOW")
diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index d71aef9a11..0038f56cb8 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -1,4 +1,6 @@
 #!/usr/bin/env python3
+import os
+import pathlib
 import boutpp as bc
 import numpy as np
 from boutdata import collect
@@ -10,6 +12,7 @@
 def test_boutpp_collect():
 
     bc.init("-d input".split(" "))
+    request.node.boutpp_initialized = True
 
     f = bc.Field3D.fromMesh(None)
     f.setAll(np.array([[[1.0]]]))
diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index dbbe916c55..46ef82b6d5 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -7,7 +7,9 @@
 
 
 def test_boutpp_legacy_model():
+
     boutpp.init(sys.argv[1:])
+    request.node.boutpp_initialized = True
 
     dens = boutpp.create3D("0")
 
diff --git a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
index 03b36d17e8..c5249bfb2c 100755
--- a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
+++ b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
@@ -9,6 +9,7 @@
 def test_boutpp_mms_ddz():
     errorlist = ""
     boutpp.init("-d data -q -q -q")  # +" -f BOUT.settings")
+    request.node.boutpp_initialized = True
 
     shapes = []
     errors = []
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index ff4bf5e48e..33a06902b0 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -7,8 +7,9 @@
 
 
 def test_boutpp_simple_model():
-    init("-d mini")
 
+    init("-d mini")
+    request.node.boutpp_initialized = True
 
     class MyModel(PhysicsModel):
         def init(self, restart):
diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py
index 47f631e7fb..1599433a37 100755
--- a/tests/integrated/test-boutpp/slicing/test_slicing.py
+++ b/tests/integrated/test-boutpp/slicing/test_slicing.py
@@ -1,15 +1,13 @@
 #!/usr/bin/env python3
 # requires boutpp
 # requires not make
-import os
-import pathlib
 import numpy as np
 import boutpp as bc
 import inspect
 
-this_directory = pathlib.Path(__file__).parent.absolute()
-os.chdir(this_directory)
 bc.init("-d test")
+request.node.boutpp_initialized = True
+
 mesh = bc.Mesh.getGlobal()
 field = bc.Field3D.fromMesh(mesh)
 ndat = np.random.random(field.shape)

From 13c3be523970445ca7510172fae4d14ec8be8ac3 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 4 Jan 2026 13:33:49 +0000
Subject: [PATCH 1017/1827] Add `finalize_boutpp` fixture, and mark relevant
 tests with a `boutpp_initialized` flag

---
 .../test_boutpp_collect_staggered.py          |  2 +-
 .../collect/test_boutpp_collect.py            |  2 +-
 .../legacy-model/test_boutpp_legacy_model.py  |  2 +-
 .../mms-ddz/test_boutpp_mms_ddz.py            |  2 +-
 .../simple-model/test_boutpp_simple_model.py  |  2 +-
 .../test-boutpp/slicing/test_slicing.py       | 88 ++++++++++---------
 6 files changed, 50 insertions(+), 48 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index 4c741e4681..29f53e9106 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -7,7 +7,7 @@
 # requires boutpp
 # requires not make
 
-def test_boutpp_collect_staggered():
+def test_boutpp_collect_staggered(request):
 
     bc.init("-q -q -q")
     request.node.boutpp_initialized = True
diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index 0038f56cb8..71b6d570d0 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -9,7 +9,7 @@
 # requires not make
 
 
-def test_boutpp_collect():
+def test_boutpp_collect(request):
 
     bc.init("-d input".split(" "))
     request.node.boutpp_initialized = True
diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index 46ef82b6d5..a07a942902 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -6,7 +6,7 @@
 # requires not make
 
 
-def test_boutpp_legacy_model():
+def test_boutpp_legacy_model(request):
 
     boutpp.init(sys.argv[1:])
     request.node.boutpp_initialized = True
diff --git a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
index c5249bfb2c..b703a2afef 100755
--- a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
+++ b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
@@ -6,7 +6,7 @@
 # requires not make
 
 
-def test_boutpp_mms_ddz():
+def test_boutpp_mms_ddz(request):
     errorlist = ""
     boutpp.init("-d data -q -q -q")  # +" -f BOUT.settings")
     request.node.boutpp_initialized = True
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index 33a06902b0..eba4708518 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -6,7 +6,7 @@
 from boutpp import *
 
 
-def test_boutpp_simple_model():
+def test_boutpp_simple_model(request):
 
     init("-d mini")
     request.node.boutpp_initialized = True
diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py
index 1599433a37..cf98d9b207 100755
--- a/tests/integrated/test-boutpp/slicing/test_slicing.py
+++ b/tests/integrated/test-boutpp/slicing/test_slicing.py
@@ -5,50 +5,52 @@
 import boutpp as bc
 import inspect
 
-bc.init("-d test")
-request.node.boutpp_initialized = True
+def test_slicing(request):
 
-mesh = bc.Mesh.getGlobal()
-field = bc.Field3D.fromMesh(mesh)
-ndat = np.random.random(field.shape)
-field[:] = ndat
+    bc.init("-d test")
+    request.node.boutpp_initialized = True
 
-assert np.all(ndat == field[:])
+    mesh = bc.Mesh.getGlobal()
+    field = bc.Field3D.fromMesh(mesh)
+    ndat = np.random.random(field.shape)
+    field[:] = ndat
 
-examples = [
-    lambda x: x[2],
-    lambda x: x[-2],
-    lambda x: x[1, 3],
-    lambda x: x[1, -1],
-    lambda x: x[0],
-    lambda x: x[0][2],
-    lambda x: x[1:7:2],
-    lambda x: x[-2:10],
-    lambda x: x[-3:3:-1],
-    lambda x: x[5:],
-    lambda x: x[1:2],
-    lambda x: x[..., 0],
-    lambda x: x[:, :, 0],
-    lambda x: x[np.array([3, 3, 1, 8])],
-    lambda x: x[np.array([3, 3, -3, 8])],
-    lambda x: x[np.array([1, -1])],
-    lambda x: x[np.array([3, 4])],
-    lambda x: x[[0, 1, 2], [0, 1, 0]],
-    lambda x: x[1:2, 1:3],
-    lambda x: x[1:2, [1, 2]],
-    lambda x: x[ndat < 0],
-]
+    assert np.all(ndat == field[:])
 
-print(field.shape)
-for ex in examples:
-    print("testing", inspect.getsource(ex))
-    try:
-        nout = ex(ndat)
-        fout = ex(field)
-        assert (
-            fout.shape == nout.shape
-        ), f"Field3D returned {{ fout.shape }} but numpy {{ nout.shape }}"
-        assert np.all(fout == nout), f"data mismatch, {{ fout == nout }}"
-    except:
-        print("Failed to test", inspect.getsource(ex))
-        raise
+    examples = [
+        lambda x: x[2],
+        lambda x: x[-2],
+        lambda x: x[1, 3],
+        lambda x: x[1, -1],
+        lambda x: x[0],
+        lambda x: x[0][2],
+        lambda x: x[1:7:2],
+        lambda x: x[-2:10],
+        lambda x: x[-3:3:-1],
+        lambda x: x[5:],
+        lambda x: x[1:2],
+        lambda x: x[..., 0],
+        lambda x: x[:, :, 0],
+        lambda x: x[np.array([3, 3, 1, 8])],
+        lambda x: x[np.array([3, 3, -3, 8])],
+        lambda x: x[np.array([1, -1])],
+        lambda x: x[np.array([3, 4])],
+        lambda x: x[[0, 1, 2], [0, 1, 0]],
+        lambda x: x[1:2, 1:3],
+        lambda x: x[1:2, [1, 2]],
+        lambda x: x[ndat < 0],
+    ]
+
+    print(field.shape)
+    for ex in examples:
+        print("testing", inspect.getsource(ex))
+        try:
+            nout = ex(ndat)
+            fout = ex(field)
+            assert (
+                fout.shape == nout.shape
+            ), f"Field3D returned {{ fout.shape }} but numpy {{ nout.shape }}"
+            assert np.all(fout == nout), f"data mismatch, {{ fout == nout }}"
+        except:
+            print("Failed to test", inspect.getsource(ex))
+            raise

From 68d058307c382d8dc077a3daf16057b1771a0c46 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 4 Jan 2026 14:17:43 +0000
Subject: [PATCH 1018/1827] Add fixture `xdist_each` for boutpp tests

(in new file tests/integrated/test-boutpp/conftest.py).
---
 tests/integrated/test-boutpp/conftest.py | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 tests/integrated/test-boutpp/conftest.py

diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
new file mode 100644
index 0000000000..86300fa619
--- /dev/null
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -0,0 +1,6 @@
+import pytest
+
+@pytest.fixture(autouse=True, scope="function")
+def xdist_each(request):
+    request.node.add_marker(pytest.mark.xdist_group(name="each_test"))  # Forces one per worker if combined
+

From 5eede917eb8fb48b16c950f4027286b2ac95579c Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 4 Jan 2026 14:18:35 +0000
Subject: [PATCH 1019/1827] Add fixture `make_dir_and_copy_input`

to copy directories containing data files to temporary directory.
---
 tests/conftest.py                        | 13 +++++++++++++
 tests/integrated/test-boutpp/conftest.py |  7 ++++---
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 8169f93e27..7909df94d6 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,4 +1,5 @@
 import pytest
+import shutil
 import boutpp
 from pathlib import Path
 
@@ -12,6 +13,18 @@ def cwd_to_test_file_dir(monkeypatch, test_dir):
 def test_dir(request) -> Path:
     return Path(request.fspath).parent
 
+@pytest.fixture
+def make_dir_and_copy_input(tmp_path, test_dir, original_dir_name="data"):
+
+    if not test_dir.exists():
+        pytest.fail(f"Expected test directory '{test_dir}' not found")
+
+    # Unique run dir per test
+    run_dir = tmp_path / original_dir_name
+    shutil.copytree(test_dir, run_dir)
+
+    return str(run_dir)
+
 @pytest.fixture(autouse=True)
 def finalize_boutpp(request):
     """Automatically finalize BOUT++ after each test that used it."""
diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
index 86300fa619..b244380cd8 100644
--- a/tests/integrated/test-boutpp/conftest.py
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -1,6 +1,7 @@
 import pytest
 
 @pytest.fixture(autouse=True, scope="function")
-def xdist_each(request):
-    request.node.add_marker(pytest.mark.xdist_group(name="each_test"))  # Forces one per worker if combined
-
+def unique_xdist_group(request):
+    # Unique group per test function (nodeid is unique, e.g., test_file.py::test_func)
+    group_name = f"boutpp_isolated_{request.node.nodeid.replace('/', '_').replace('::', '_')}"
+    request.node.add_marker(pytest.mark.xdist_group(name=group_name))
\ No newline at end of file

From f59b1949a9ce343f1231af0fac6836ff2fb796ba Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 4 Jan 2026 17:49:34 +0000
Subject: [PATCH 1020/1827] Rename `make_dir_and_copy_input` fixture to
 `copy_data_directory`

and make it get the directory name from request.node.input_dir_name (defaulting to `data` if not set).
---
 tests/conftest.py | 27 ++++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 7909df94d6..8a92d3a82b 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -14,16 +14,29 @@ def test_dir(request) -> Path:
     return Path(request.fspath).parent
 
 @pytest.fixture
-def make_dir_and_copy_input(tmp_path, test_dir, original_dir_name="data"):
+def copy_data_directory(request, tmp_path):
+    """
+    Provides a writable copy of a pre-existing directory (e.g. "data", "test", "input")
+    in a unique temporary location.
 
-    if not test_dir.exists():
-        pytest.fail(f"Expected test directory '{test_dir}' not found")
+    The name of the original directory is taken from request.node.input_dir_name
+    (set via a marker on the test).
+    """
+    # Get the requested original directory name (default to "data" if not specified)
+    original_name = getattr(request.node, "input_dir_name", "data")
 
-    # Unique run dir per test
-    run_dir = tmp_path / original_dir_name
-    shutil.copytree(test_dir, run_dir)
+    # Location of the original input directory (sibling to the test file)
+    test_file_dir = Path(request.fspath).parent
+    original_dir = test_file_dir / original_name
 
-    return str(run_dir)
+    if not original_dir.is_dir():
+        pytest.fail(f"Expected input directory '{original_dir}' does not exist")
+
+    # Unique writable copy for this test
+    run_dir = tmp_path / original_name
+    shutil.copytree(original_dir, run_dir, dirs_exist_ok=True)
+
+    return run_dir
 
 @pytest.fixture(autouse=True)
 def finalize_boutpp(request):

From 595b0b735eb38ff530bb2d574069b0627e4456fc Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 4 Jan 2026 18:06:04 +0000
Subject: [PATCH 1021/1827] Add pytest marker `input_dir`

and mark test_command_args test cases with it.
---
 tests/conftest.py                                       | 5 +++++
 tests/integrated/test-command-args/test_command_args.py | 8 +++++++-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 8a92d3a82b..42444d7231 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -4,6 +4,11 @@
 from pathlib import Path
 
 
+def pytest_configure(config):
+    config.addinivalue_line(
+        "markers", "input_dir(name): specify the pre-existing input directory name for this test"
+    )
+
 @pytest.fixture(autouse=True)
 def cwd_to_test_file_dir(monkeypatch, test_dir):
     """Automatically change CWD to the directory of the current test file."""
diff --git a/tests/integrated/test-command-args/test_command_args.py b/tests/integrated/test-command-args/test_command_args.py
index f2925ed5cb..8905e92b33 100755
--- a/tests/integrated/test-command-args/test_command_args.py
+++ b/tests/integrated/test-command-args/test_command_args.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
-from boututils.run_wrapper import launch_safe
 
+from boututils.run_wrapper import launch_safe
+import pytest
 import os
 import re
 import shutil
@@ -72,6 +73,7 @@ def testShortLogArgument(self):
             msg="FAIL: no different.log.0 file in data directory",
         )
 
+    @pytest.mark.input_dir("data")
     def testLongLogArgument(self):
         self.makeDirAndCopyInput("data")
         launch_safe(self.command + " --log log", pipe=True, nproc=1, mthread=1)
@@ -83,6 +85,7 @@ def testLongLogArgument(self):
             os.path.exists("data/log.0"), msg="FAIL: no log.0 file in data directory"
         )
 
+    @pytest.mark.input_dir("test")
     def testDirectoryArgument(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)
@@ -119,6 +122,7 @@ def testDirectoryArgumentNonDirectory(self):
                 msg="FAIL: Error message not printed when missing input directory",
             )
 
+    @pytest.mark.input_dir("test")
     def testDirectoryArgumentOldSettingsFile(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)
@@ -146,6 +150,7 @@ def testDirectoryArgumentOldSettingsFile(self):
                 msg="FAIL: datadir from command line clobbered by BOUT.settings",
             )
 
+    @pytest.mark.input_dir("test")
     def testShortOptionsAreUsed(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)
@@ -162,6 +167,7 @@ def testShortOptionsAreUsed(self):
             matches = re.findall("not used.*Command line", contents)
             self.assertEqual(matches, [], msg="FAIL: command line options not used")
 
+    @pytest.mark.input_dir("test")
     def testCommandLineOptionsArePrinted(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)

From 4fd9bc61e812452a5a0de9fd1930ec5a6071f635 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 4 Jan 2026 18:12:46 +0000
Subject: [PATCH 1022/1827] Fix testDirectoryArgumentNonDirectory

in test_command_args.
---
 tests/integrated/test-command-args/test_command_args.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-command-args/test_command_args.py b/tests/integrated/test-command-args/test_command_args.py
index 8905e92b33..420e8a2e2f 100755
--- a/tests/integrated/test-command-args/test_command_args.py
+++ b/tests/integrated/test-command-args/test_command_args.py
@@ -117,7 +117,7 @@ def testDirectoryArgumentNonDirectory(self):
         with open(OUTPUT_FILE) as f:
             contents = f.read()
             self.assertIn(
-                '"runtest" is not a directory',
+                'DataDir "runtest" does not exist or is not accessible',
                 contents,
                 msg="FAIL: Error message not printed when missing input directory",
             )

From 3a3c23bd74645c0cf3fcba3a2998b853dc3e30b1 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sun, 4 Jan 2026 18:25:22 +0000
Subject: [PATCH 1023/1827] Mark more tests with `input_dir`

when input files are in a directory not named `data`.
---
 tests/integrated/test-boutpp/collect/test_boutpp_collect.py     | 1 +
 tests/integrated/test-boutpp/print/test_boutpp_print.py         | 1 +
 .../test-boutpp/simple-model/test_boutpp_simple_model.py        | 1 +
 tests/integrated/test-boutpp/slicing/test_slicing.py            | 1 +
 tests/integrated/test-communications/test_communications.py     | 2 +-
 tests/integrated/test-griddata/test_griddata.py                 | 1 +
 6 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index 71b6d570d0..86f7581f07 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -9,6 +9,7 @@
 # requires not make
 
 
+@pytest.mark.input_dir("input")
 def test_boutpp_collect(request):
 
     bc.init("-d input".split(" "))
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index 32e052f0bd..ff0b094238 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -3,6 +3,7 @@
 import time
 
 
+@pytest.mark.input_dir("test")
 def test_runtest():
     # BOUT_TOP from script dir (CWD-independent)
     script_dir = os.path.dirname(os.path.abspath(__file__))
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index eba4708518..5c3f3c80b8 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -6,6 +6,7 @@
 from boutpp import *
 
 
+@pytest.mark.input_dir("mini")
 def test_boutpp_simple_model(request):
 
     init("-d mini")
diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py
index cf98d9b207..94c3018652 100755
--- a/tests/integrated/test-boutpp/slicing/test_slicing.py
+++ b/tests/integrated/test-boutpp/slicing/test_slicing.py
@@ -5,6 +5,7 @@
 import boutpp as bc
 import inspect
 
+@pytest.mark.input_dir("test")
 def test_slicing(request):
 
     bc.init("-d test")
diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index 7974e87d83..edbe258b84 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -18,7 +18,7 @@ def run_test(actual, expected, procnum, region, boundary):
             ))
 
 
-# noinspection DuplicatedCode
+@pytest.mark.input_dir("data_limiter")
 def test_communications():
 
     #################################################
diff --git a/tests/integrated/test-griddata/test_griddata.py b/tests/integrated/test-griddata/test_griddata.py
index 5b04bea7ee..65600fd40d 100755
--- a/tests/integrated/test-griddata/test_griddata.py
+++ b/tests/integrated/test-griddata/test_griddata.py
@@ -14,6 +14,7 @@
 from sys import stdout
 
 
+@pytest.mark.input_dir("screw")
 def test_griddata():
     for nproc in [1]:
         stdout.write("Checking %d processors ... " % (nproc))

From f964b0931cde0943b5f85fd20a56e85ea4b91f5d Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 5 Jan 2026 10:53:45 +0000
Subject: [PATCH 1024/1827] Combine fixtures `cwd_to_test_file_dir` and
 `copy_data_directory` into one

(`copy_and_cwd_to_tmp_dir`)

and fix.
---
 tests/conftest.py | 34 +++++++++++++++-------------------
 1 file changed, 15 insertions(+), 19 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 42444d7231..d00732a847 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -9,39 +9,35 @@ def pytest_configure(config):
         "markers", "input_dir(name): specify the pre-existing input directory name for this test"
     )
 
-@pytest.fixture(autouse=True)
-def cwd_to_test_file_dir(monkeypatch, test_dir):
-    """Automatically change CWD to the directory of the current test file."""
-    monkeypatch.chdir(test_dir)
-
 @pytest.fixture
 def test_dir(request) -> Path:
     return Path(request.fspath).parent
 
-@pytest.fixture
-def copy_data_directory(request, tmp_path):
+@pytest.fixture(autouse=True)
+def copy_and_cwd_to_tmp_dir(request, tmp_path, monkeypatch):
     """
-    Provides a writable copy of a pre-existing directory (e.g. "data", "test", "input")
-    in a unique temporary location.
+    Provides a unique, writable copy of a pre-existing input directory
+    and changes cwd to it.
 
-    The name of the original directory is taken from request.node.input_dir_name
-    (set via a marker on the test).
+    The original directory name is taken from:
+      - or @pytest.mark.input_dir("name") marker
+      - default: "data"
     """
-    # Get the requested original directory name (default to "data" if not specified)
-    original_name = getattr(request.node, "input_dir_name", "data")
 
-    # Location of the original input directory (sibling to the test file)
+    marker = request.node.get_closest_marker("input_dir")
+    original_name = marker.kwargs.get('name', 'data') if marker else "data"
+
     test_file_dir = Path(request.fspath).parent
     original_dir = test_file_dir / original_name
 
     if not original_dir.is_dir():
-        pytest.fail(f"Expected input directory '{original_dir}' does not exist")
+        pytest.fail(f"Expected input directory '{original_dir}' not found")
 
-    # Unique writable copy for this test
-    run_dir = tmp_path / original_name
-    shutil.copytree(original_dir, run_dir, dirs_exist_ok=True)
+    # Create unique writable copy
+    run_dir_path = tmp_path / original_name
+    shutil.copytree(original_dir, run_dir_path, dirs_exist_ok=True)
 
-    return run_dir
+    monkeypatch.chdir(tmp_path)
 
 @pytest.fixture(autouse=True)
 def finalize_boutpp(request):

From 50699369f8e69bec88f546f1b30a13d90de8a958 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 5 Jan 2026 10:55:42 +0000
Subject: [PATCH 1025/1827] Mark test_boutpp_collect with
 input_dir(name="input")

---
 tests/integrated/test-boutpp/collect/test_boutpp_collect.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index 86f7581f07..ba3c88c621 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -1,15 +1,14 @@
 #!/usr/bin/env python3
-import os
-import pathlib
 import boutpp as bc
 import numpy as np
+import pytest
 from boutdata import collect
 
 # requires boutpp
 # requires not make
 
 
-@pytest.mark.input_dir("input")
+@pytest.mark.input_dir(name="input")
 def test_boutpp_collect(request):
 
     bc.init("-d input".split(" "))

From 01f6c8792463d7b33311bf9f5360bba4e72834ee Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 5 Jan 2026 10:58:26 +0000
Subject: [PATCH 1026/1827] `finalize_boutpp` fixture not needed now that using
 xdist_group

---
 tests/conftest.py                                    | 12 ------------
 .../test_boutpp_collect_staggered.py                 |  3 +--
 .../test-boutpp/collect/test_boutpp_collect.py       |  3 +--
 .../legacy-model/test_boutpp_legacy_model.py         |  3 +--
 .../test-boutpp/mms-ddz/test_boutpp_mms_ddz.py       |  3 +--
 .../simple-model/test_boutpp_simple_model.py         |  3 +--
 tests/integrated/test-boutpp/slicing/test_slicing.py |  3 +--
 7 files changed, 6 insertions(+), 24 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index d00732a847..75fddc97bc 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -38,15 +38,3 @@ def copy_and_cwd_to_tmp_dir(request, tmp_path, monkeypatch):
     shutil.copytree(original_dir, run_dir_path, dirs_exist_ok=True)
 
     monkeypatch.chdir(tmp_path)
-
-@pytest.fixture(autouse=True)
-def finalize_boutpp(request):
-    """Automatically finalize BOUT++ after each test that used it."""
-    yield  # Run the test
-
-    # Check if this test used boutpp init (heuristic: look for marker or direct check)
-    if hasattr(request.node, "boutpp_initialized"):
-        try:
-            boutpp.finalise()
-        except Exception:
-            pass  # If already finalized or error, ignore
diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index 29f53e9106..ac7efd9558 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -7,10 +7,9 @@
 # requires boutpp
 # requires not make
 
-def test_boutpp_collect_staggered(request):
+def test_boutpp_collect_staggered():
 
     bc.init("-q -q -q")
-    request.node.boutpp_initialized = True
 
     fail = 0
     f = bc.create3D("sin(y)", outloc="YLOW")
diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index ba3c88c621..fd085bebfd 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -9,10 +9,9 @@
 
 
 @pytest.mark.input_dir(name="input")
-def test_boutpp_collect(request):
+def test_boutpp_collect():
 
     bc.init("-d input".split(" "))
-    request.node.boutpp_initialized = True
 
     f = bc.Field3D.fromMesh(None)
     f.setAll(np.array([[[1.0]]]))
diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index a07a942902..05c9fc3819 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -6,10 +6,9 @@
 # requires not make
 
 
-def test_boutpp_legacy_model(request):
+def test_boutpp_legacy_model():
 
     boutpp.init(sys.argv[1:])
-    request.node.boutpp_initialized = True
 
     dens = boutpp.create3D("0")
 
diff --git a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
index b703a2afef..03b36d17e8 100755
--- a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
+++ b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
@@ -6,10 +6,9 @@
 # requires not make
 
 
-def test_boutpp_mms_ddz(request):
+def test_boutpp_mms_ddz():
     errorlist = ""
     boutpp.init("-d data -q -q -q")  # +" -f BOUT.settings")
-    request.node.boutpp_initialized = True
 
     shapes = []
     errors = []
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index 5c3f3c80b8..46ea38bf32 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -7,10 +7,9 @@
 
 
 @pytest.mark.input_dir("mini")
-def test_boutpp_simple_model(request):
+def test_boutpp_simple_model():
 
     init("-d mini")
-    request.node.boutpp_initialized = True
 
     class MyModel(PhysicsModel):
         def init(self, restart):
diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py
index 94c3018652..006693f965 100755
--- a/tests/integrated/test-boutpp/slicing/test_slicing.py
+++ b/tests/integrated/test-boutpp/slicing/test_slicing.py
@@ -6,10 +6,9 @@
 import inspect
 
 @pytest.mark.input_dir("test")
-def test_slicing(request):
+def test_slicing():
 
     bc.init("-d test")
-    request.node.boutpp_initialized = True
 
     mesh = bc.Mesh.getGlobal()
     field = bc.Field3D.fromMesh(mesh)

From d08672f739bcd706aa29bd0166c8c618604d517d Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 5 Jan 2026 11:06:06 +0000
Subject: [PATCH 1027/1827] Copy and cwd to tmp_dir

---
 tests/conftest.py | 20 ++++++--------------
 1 file changed, 6 insertions(+), 14 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 75fddc97bc..99dd5ba6b5 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -16,25 +16,17 @@ def test_dir(request) -> Path:
 @pytest.fixture(autouse=True)
 def copy_and_cwd_to_tmp_dir(request, tmp_path, monkeypatch):
     """
-    Provides a unique, writable copy of a pre-existing input directory
+    Provides a unique, writable copy of the test directory
     and changes cwd to it.
-
-    The original directory name is taken from:
-      - or @pytest.mark.input_dir("name") marker
-      - default: "data"
     """
 
-    marker = request.node.get_closest_marker("input_dir")
-    original_name = marker.kwargs.get('name', 'data') if marker else "data"
-
     test_file_dir = Path(request.fspath).parent
-    original_dir = test_file_dir / original_name
 
-    if not original_dir.is_dir():
-        pytest.fail(f"Expected input directory '{original_dir}' not found")
+    if not test_file_dir.is_dir():
+        pytest.fail(f"Expected input directory '{test_file_dir}' not found")
 
     # Create unique writable copy
-    run_dir_path = tmp_path / original_name
-    shutil.copytree(original_dir, run_dir_path, dirs_exist_ok=True)
+    run_dir_path = tmp_path / test_file_dir.name
+    shutil.copytree(test_file_dir, run_dir_path, dirs_exist_ok=True)
 
-    monkeypatch.chdir(tmp_path)
+    monkeypatch.chdir(run_dir_path)

From 237456637cd866c521d5f650c27f41ef5bfeb72d Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 5 Jan 2026 12:30:40 +0000
Subject: [PATCH 1028/1827] Fix test_datafile_facade

(move `success` variable to correct scope).
---
 tests/integrated/test-datafilefacade/test_datafile_facade.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-datafilefacade/test_datafile_facade.py b/tests/integrated/test-datafilefacade/test_datafile_facade.py
index 19e5322cda..f4f4469c40 100755
--- a/tests/integrated/test-datafilefacade/test_datafile_facade.py
+++ b/tests/integrated/test-datafilefacade/test_datafile_facade.py
@@ -10,8 +10,6 @@
 import numpy
 
 
-success = True
-
 testvars = {
     "f2d": 0.1,
     "f3d": 0.2,
@@ -36,6 +34,9 @@
 
 
 def test_datafile_facade():
+
+    success = True
+
     for nproc in [1, 2]:
         # delete any existing output
         shell(["rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc"])

From cac189bb40ff49abe095a040eced5f1440e39b3b Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 7 Jan 2026 09:13:07 +0000
Subject: [PATCH 1029/1827] Fix assert in test_invpar

---
 tests/integrated/test-invpar/test_invpar.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-invpar/test_invpar.py b/tests/integrated/test-invpar/test_invpar.py
index 229a735b19..0b0293ed00 100755
--- a/tests/integrated/test-invpar/test_invpar.py
+++ b/tests/integrated/test-invpar/test_invpar.py
@@ -55,7 +55,7 @@ def test_invpar():
                 print("PASSED")
             else:
                 print("FAILED")
-            assert s, f"Test failed for flag={f}"
+            assert s == 0, f"Test failed for flag={f}"
 
     if code == 0:
         print(" => All inversion tests passed")

From a429e6d2bcacab512e29b160fd04911d6045d6e0 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 7 Jan 2026 09:54:21 +0000
Subject: [PATCH 1030/1827] Remove input_dir(name="input") markers

---
 tests/integrated/test-boutpp/collect/test_boutpp_collect.py | 2 --
 tests/integrated/test-boutpp/print/test_boutpp_print.py     | 1 -
 .../test-boutpp/simple-model/test_boutpp_simple_model.py    | 1 -
 tests/integrated/test-boutpp/slicing/test_slicing.py        | 1 -
 tests/integrated/test-command-args/test_command_args.py     | 6 ------
 tests/integrated/test-communications/test_communications.py | 1 -
 tests/integrated/test-griddata/test_griddata.py             | 1 -
 7 files changed, 13 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index fd085bebfd..d71aef9a11 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -1,14 +1,12 @@
 #!/usr/bin/env python3
 import boutpp as bc
 import numpy as np
-import pytest
 from boutdata import collect
 
 # requires boutpp
 # requires not make
 
 
-@pytest.mark.input_dir(name="input")
 def test_boutpp_collect():
 
     bc.init("-d input".split(" "))
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index ff0b094238..32e052f0bd 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -3,7 +3,6 @@
 import time
 
 
-@pytest.mark.input_dir("test")
 def test_runtest():
     # BOUT_TOP from script dir (CWD-independent)
     script_dir = os.path.dirname(os.path.abspath(__file__))
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index 46ea38bf32..94f72309f3 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -6,7 +6,6 @@
 from boutpp import *
 
 
-@pytest.mark.input_dir("mini")
 def test_boutpp_simple_model():
 
     init("-d mini")
diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py
index 006693f965..c485907414 100755
--- a/tests/integrated/test-boutpp/slicing/test_slicing.py
+++ b/tests/integrated/test-boutpp/slicing/test_slicing.py
@@ -5,7 +5,6 @@
 import boutpp as bc
 import inspect
 
-@pytest.mark.input_dir("test")
 def test_slicing():
 
     bc.init("-d test")
diff --git a/tests/integrated/test-command-args/test_command_args.py b/tests/integrated/test-command-args/test_command_args.py
index 420e8a2e2f..aed7d35ef0 100755
--- a/tests/integrated/test-command-args/test_command_args.py
+++ b/tests/integrated/test-command-args/test_command_args.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 
 from boututils.run_wrapper import launch_safe
-import pytest
 import os
 import re
 import shutil
@@ -73,7 +72,6 @@ def testShortLogArgument(self):
             msg="FAIL: no different.log.0 file in data directory",
         )
 
-    @pytest.mark.input_dir("data")
     def testLongLogArgument(self):
         self.makeDirAndCopyInput("data")
         launch_safe(self.command + " --log log", pipe=True, nproc=1, mthread=1)
@@ -85,7 +83,6 @@ def testLongLogArgument(self):
             os.path.exists("data/log.0"), msg="FAIL: no log.0 file in data directory"
         )
 
-    @pytest.mark.input_dir("test")
     def testDirectoryArgument(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)
@@ -122,7 +119,6 @@ def testDirectoryArgumentNonDirectory(self):
                 msg="FAIL: Error message not printed when missing input directory",
             )
 
-    @pytest.mark.input_dir("test")
     def testDirectoryArgumentOldSettingsFile(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)
@@ -150,7 +146,6 @@ def testDirectoryArgumentOldSettingsFile(self):
                 msg="FAIL: datadir from command line clobbered by BOUT.settings",
             )
 
-    @pytest.mark.input_dir("test")
     def testShortOptionsAreUsed(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)
@@ -167,7 +162,6 @@ def testShortOptionsAreUsed(self):
             matches = re.findall("not used.*Command line", contents)
             self.assertEqual(matches, [], msg="FAIL: command line options not used")
 
-    @pytest.mark.input_dir("test")
     def testCommandLineOptionsArePrinted(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)
diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index edbe258b84..2db3fbab97 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -18,7 +18,6 @@ def run_test(actual, expected, procnum, region, boundary):
             ))
 
 
-@pytest.mark.input_dir("data_limiter")
 def test_communications():
 
     #################################################
diff --git a/tests/integrated/test-griddata/test_griddata.py b/tests/integrated/test-griddata/test_griddata.py
index 65600fd40d..5b04bea7ee 100755
--- a/tests/integrated/test-griddata/test_griddata.py
+++ b/tests/integrated/test-griddata/test_griddata.py
@@ -14,7 +14,6 @@
 from sys import stdout
 
 
-@pytest.mark.input_dir("screw")
 def test_griddata():
     for nproc in [1]:
         stdout.write("Checking %d processors ... " % (nproc))

From 0c6768718bb0e603d919f7920acd975ae5a23747 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 5 Jan 2026 13:17:03 +0000
Subject: [PATCH 1031/1827] Restore CMake copying `runtest` files

Those that are python scripts have been renamed but others, such as shell script remain.
---
 cmake/BOUT++functions.cmake | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 32983f33c4..83950f58e5 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -262,6 +262,11 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
     string(REGEX REPLACE "^(test-|MMS-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
     string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
 	bout_copy_file(${TEST_FILENAME})
+
+	if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest)
+        bout_copy_file(runtest)
+    endif()
+
   else()
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()

From b4bb8fcfd5708df2238348bf7652e2c6080ba6a2 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 5 Jan 2026 14:00:38 +0000
Subject: [PATCH 1032/1827] Use tmp_path_factory to ensure a unique temp dir
 for each test

even under parallelisation.
---
 tests/conftest.py | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 99dd5ba6b5..46a28f2107 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -13,20 +13,23 @@ def pytest_configure(config):
 def test_dir(request) -> Path:
     return Path(request.fspath).parent
 
-@pytest.fixture(autouse=True)
-def copy_and_cwd_to_tmp_dir(request, tmp_path, monkeypatch):
+@pytest.fixture(scope="function", autouse=True)
+def copy_and_cwd_to_unique_tmp_dir(request, tmp_path_factory, monkeypatch):
     """
-    Provides a unique, writable copy of the test directory
-    and changes cwd to it.
+    For each test function, create a unique temporary copy of the test directory
+    and change cwd to it.
     """
 
     test_file_dir = Path(request.fspath).parent
 
     if not test_file_dir.is_dir():
-        pytest.fail(f"Expected input directory '{test_file_dir}' not found")
+        pytest.fail(f"Expected test directory '{test_file_dir}' not found")
 
-    # Create unique writable copy
-    run_dir_path = tmp_path / test_file_dir.name
-    shutil.copytree(test_file_dir, run_dir_path, dirs_exist_ok=True)
+    # Create a unique temp dir for this test
+    run_dir = tmp_path_factory.mktemp(test_file_dir.name)
 
-    monkeypatch.chdir(run_dir_path)
+    # Copy the original test directory into it
+    shutil.copytree(test_file_dir, run_dir, dirs_exist_ok=True)
+
+    # Change working directory to the copy
+    monkeypatch.chdir(run_dir)

From 41290213a6f129d0344457f90b6726297d85b596 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 5 Jan 2026 17:05:50 +0000
Subject: [PATCH 1033/1827] Don't change to test directory now that there is a
 fixture that switches to a temporary copy of it

---
 .../collect-staggered/test_boutpp_collect_staggered.py       | 4 ----
 tests/integrated/test-fci-boundary/test_fci_boundary.py      | 2 --
 tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py  | 5 -----
 tests/integrated/test-gyro/test_gyro.py                      | 2 --
 tests/integrated/test-interpolate/test_interpolate.py        | 5 -----
 .../test-multigrid_laplace/test_multigrid_laplace.py         | 3 ---
 6 files changed, 21 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index ac7efd9558..0810e311c1 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -1,6 +1,4 @@
 #!/usr/bin/env python3
-import os
-import pathlib
 
 import boutpp as bc
 
@@ -22,8 +20,6 @@ def test_boutpp_collect_staggered():
 
     fc = bc.create3D("sin(y)", outloc="CENTRE")
 
-    this_directory = pathlib.Path(__file__).parent.absolute()
-    os.chdir(this_directory)
     fe = bc.Field3D.fromCollect("f3d_evolve", path="data", info=False)
     fo = bc.Field3D.fromCollect("f3d_once", path="data", info=False)
 
diff --git a/tests/integrated/test-fci-boundary/test_fci_boundary.py b/tests/integrated/test-fci-boundary/test_fci_boundary.py
index b557a0802e..8317b5ff62 100755
--- a/tests/integrated/test-fci-boundary/test_fci_boundary.py
+++ b/tests/integrated/test-fci-boundary/test_fci_boundary.py
@@ -3,8 +3,6 @@
 # Python script to run and analyse MMS test
 
 
-import os
-import pathlib
 import numpy as np
 from boututils.run_wrapper import launch_safe
 from boututils.datafile import DataFile
diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
index e428fe8db0..9747e546b4 100755
--- a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
+++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
@@ -20,8 +20,6 @@
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from numpy import abs, seterr
-import os
-import pathlib
 
 def test_fieldgroupcomm():
 
@@ -47,9 +45,6 @@ def test_fieldgroupcomm():
 
         shell("rm data/BOUT.dmp.*.nc")
 
-        this_directory = pathlib.Path(__file__).parent.absolute()
-        os.chdir(this_directory)
-
         print("   %d processors ...." % (nproc))
         s, out = launch_safe(cmd, nproc=nproc, pipe=True)
         with open("run.log." + str(nproc), "w") as f:
diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py
index cc18b96c14..57e8bd7f08 100755
--- a/tests/integrated/test-gyro/test_gyro.py
+++ b/tests/integrated/test-gyro/test_gyro.py
@@ -24,8 +24,6 @@
 from boutdata.collect import collect
 import numpy as np
 from sys import stdout
-import os
-import pathlib
 
 
 def test_gyro():
diff --git a/tests/integrated/test-interpolate/test_interpolate.py b/tests/integrated/test-interpolate/test_interpolate.py
index d2e80c8d08..07a06a6c19 100755
--- a/tests/integrated/test-interpolate/test_interpolate.py
+++ b/tests/integrated/test-interpolate/test_interpolate.py
@@ -5,8 +5,6 @@
 #
 
 import pytest
-import os
-import pathlib
 from boututils.run_wrapper import shell, launch_safe
 from boutdata import collect
 import boutconfig
@@ -49,9 +47,6 @@ def test_interpolate(method):
         error_2[var] = []  # L2 error (RMS)
         error_inf[var] = []  # Maximum error
 
-    this_directory = pathlib.Path(__file__).parent.absolute()
-    os.chdir(this_directory)
-
     for nx in nxlist:
         dx = 1.0 / (nx)
 
diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
index 48e6af5beb..885270d202 100755
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
@@ -10,9 +10,6 @@
 
 from __future__ import print_function
 
-import os
-import pathlib
-
 try:
     from builtins import str
 except:

From 10b1d82009bea2d1133366560f81cb65cc0cfc16 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Fri, 23 Jan 2026 10:28:19 +0000
Subject: [PATCH 1034/1827] Fix CMakeLists.txt for test-fci-boundary

`bout_add_integrated_test` not `bout_add_mms_test`
---
 tests/integrated/test-fci-boundary/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-fci-boundary/CMakeLists.txt b/tests/integrated/test-fci-boundary/CMakeLists.txt
index b9164ce000..4aa71f96d5 100644
--- a/tests/integrated/test-fci-boundary/CMakeLists.txt
+++ b/tests/integrated/test-fci-boundary/CMakeLists.txt
@@ -1,4 +1,4 @@
-bout_add_mms_test(
+bout_add_integrated_test(
   test-fci-boundary
   SOURCES get_par_bndry.cxx
   USE_RUNTEST USE_DATA_BOUT_INP

From 534163b69c279d6a41c8d86592fe7741d0583993 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Fri, 23 Jan 2026 16:54:51 +0000
Subject: [PATCH 1035/1827] Add newline at end of file

---
 tests/integrated/test-boutpp/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
index b244380cd8..8d31c9512b 100644
--- a/tests/integrated/test-boutpp/conftest.py
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -4,4 +4,4 @@
 def unique_xdist_group(request):
     # Unique group per test function (nodeid is unique, e.g., test_file.py::test_func)
     group_name = f"boutpp_isolated_{request.node.nodeid.replace('/', '_').replace('::', '_')}"
-    request.node.add_marker(pytest.mark.xdist_group(name=group_name))
\ No newline at end of file
+    request.node.add_marker(pytest.mark.xdist_group(name=group_name))

From e6a15ead215add2637216c2003785348d296b082 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Fri, 23 Jan 2026 17:03:08 +0000
Subject: [PATCH 1036/1827] Don't change to test directory now that there is a
 fixture that switches to a temporary copy of it

---
 .../test_bout_override_default_option.py      | 25 +++----------------
 .../test-boutpp/print/test_boutpp_print.py    | 25 +++----------------
 .../test-code-style/test_code_style.py        | 25 +++----------------
 .../test_compile_examples_petsc.py            | 25 +++----------------
 .../test_compile_examples.py                  | 25 +++----------------
 .../test_coordinates_initialization.py        | 24 +++---------------
 tests/integrated/test-include/test_include.py | 25 +++----------------
 tests/integrated/test-snb/test_snb.py         | 25 +++----------------
 .../test-stopCheck/test_stopCheck.py          | 21 ++--------------
 tests/integrated/test-subdir/test_subdir.py   | 25 +++----------------
 10 files changed, 29 insertions(+), 216 deletions(-)

diff --git a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
index 32e052f0bd..65bf227187 100644
--- a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
+++ b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
@@ -4,32 +4,13 @@
 
 
 def test_runtest():
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
-
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    test_dir = os.path.dirname(os.path.abspath(__file__))
-    # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    os.chdir(test_dir)
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
     print(f"Output: {result.stdout}")
     if result.returncode != 0:
         print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index 32e052f0bd..65bf227187 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -4,32 +4,13 @@
 
 
 def test_runtest():
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
-
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    test_dir = os.path.dirname(os.path.abspath(__file__))
-    # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    os.chdir(test_dir)
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
     print(f"Output: {result.stdout}")
     if result.returncode != 0:
         print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
diff --git a/tests/integrated/test-code-style/test_code_style.py b/tests/integrated/test-code-style/test_code_style.py
index 32e052f0bd..65bf227187 100644
--- a/tests/integrated/test-code-style/test_code_style.py
+++ b/tests/integrated/test-code-style/test_code_style.py
@@ -4,32 +4,13 @@
 
 
 def test_runtest():
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
-
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    test_dir = os.path.dirname(os.path.abspath(__file__))
-    # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    os.chdir(test_dir)
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
     print(f"Output: {result.stdout}")
     if result.returncode != 0:
         print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
diff --git a/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py b/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
index 32e052f0bd..65bf227187 100644
--- a/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
+++ b/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
@@ -4,32 +4,13 @@
 
 
 def test_runtest():
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
-
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    test_dir = os.path.dirname(os.path.abspath(__file__))
-    # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    os.chdir(test_dir)
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
     print(f"Output: {result.stdout}")
     if result.returncode != 0:
         print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
diff --git a/tests/integrated/test-compile-examples/test_compile_examples.py b/tests/integrated/test-compile-examples/test_compile_examples.py
index 32e052f0bd..65bf227187 100644
--- a/tests/integrated/test-compile-examples/test_compile_examples.py
+++ b/tests/integrated/test-compile-examples/test_compile_examples.py
@@ -4,32 +4,13 @@
 
 
 def test_runtest():
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
-
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    test_dir = os.path.dirname(os.path.abspath(__file__))
-    # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    os.chdir(test_dir)
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
     print(f"Output: {result.stdout}")
     if result.returncode != 0:
         print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
diff --git a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
index 32e052f0bd..f1621afa42 100644
--- a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
+++ b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
@@ -4,32 +4,14 @@
 
 
 def test_runtest():
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
 
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    test_dir = os.path.dirname(os.path.abspath(__file__))
-    # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    os.chdir(test_dir)
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
     print(f"Output: {result.stdout}")
     if result.returncode != 0:
         print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
diff --git a/tests/integrated/test-include/test_include.py b/tests/integrated/test-include/test_include.py
index 32e052f0bd..65bf227187 100644
--- a/tests/integrated/test-include/test_include.py
+++ b/tests/integrated/test-include/test_include.py
@@ -4,32 +4,13 @@
 
 
 def test_runtest():
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
-
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    test_dir = os.path.dirname(os.path.abspath(__file__))
-    # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    os.chdir(test_dir)
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
     print(f"Output: {result.stdout}")
     if result.returncode != 0:
         print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
diff --git a/tests/integrated/test-snb/test_snb.py b/tests/integrated/test-snb/test_snb.py
index 32e052f0bd..65bf227187 100644
--- a/tests/integrated/test-snb/test_snb.py
+++ b/tests/integrated/test-snb/test_snb.py
@@ -4,32 +4,13 @@
 
 
 def test_runtest():
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
-
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    test_dir = os.path.dirname(os.path.abspath(__file__))
-    # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    os.chdir(test_dir)
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
     print(f"Output: {result.stdout}")
     if result.returncode != 0:
         print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
diff --git a/tests/integrated/test-stopCheck/test_stopCheck.py b/tests/integrated/test-stopCheck/test_stopCheck.py
index 0774604fb4..3f4efff65d 100644
--- a/tests/integrated/test-stopCheck/test_stopCheck.py
+++ b/tests/integrated/test-stopCheck/test_stopCheck.py
@@ -4,26 +4,9 @@
 
 
 def test_runtest(test_dir):
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
-
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    # Pre-build for dependencies like grid.fci.nc
-
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir.name:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
diff --git a/tests/integrated/test-subdir/test_subdir.py b/tests/integrated/test-subdir/test_subdir.py
index 32e052f0bd..65bf227187 100644
--- a/tests/integrated/test-subdir/test_subdir.py
+++ b/tests/integrated/test-subdir/test_subdir.py
@@ -4,32 +4,13 @@
 
 
 def test_runtest():
-    # BOUT_TOP from script dir (CWD-independent)
-    script_dir = os.path.dirname(os.path.abspath(__file__))
-    bout_root = os.path.abspath(os.path.join(script_dir, ".."))
-    os.environ["BOUT_TOP"] = bout_root
-
-    # Add pylib (dependencies like boutdata) to PYTHONPATH
-    pylib_path = os.path.join(bout_root, "tools", "pylib")
-    if os.path.exists(pylib_path):
-        os.environ["PYTHONPATH"] = f"{pylib_path}:{os.environ.get('PYTHONPATH', '')}"
-
-    test_dir = os.path.dirname(os.path.abspath(__file__))
-    # Pre-build for dependencies like grid.fci.nc
-    build_result = subprocess.run("make", shell=True, cwd=test_dir, capture_output=True, text=True, timeout=60)
-    if build_result.returncode != 0:
-        print(f"Build stderr in {test_dir}: {build_result.stderr}")  # Non-fatal; some tests no-op
-
-    os.chdir(test_dir)
-
-    # MPI oversubscribe for communications test
     cmd = './runtest'
-    if "communications" in test_dir:
-        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
     start = time.time()
     result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
     elapsed = time.time() - start
     print(f"Output: {result.stdout}")
     if result.returncode != 0:
         print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
\ No newline at end of file
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"

From e0722af9cea95b4012ac2f256a1a57e6081fdd37 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Fri, 23 Jan 2026 17:14:04 +0000
Subject: [PATCH 1037/1827] Copy test-boutpp/conftest.py when building

---
 CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 987c5e3a73..9f067bff1a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -785,6 +785,11 @@ if(BOUT_TESTS)
     "${PROJECT_SOURCE_DIR}/tests/conftest.py"
     "${PROJECT_BINARY_DIR}/tests/conftest.py")
 
+  # Copy the pytest config file for the boutpp tests
+  configure_file(
+    "${PROJECT_SOURCE_DIR}/tests/integrated/test-boutpp/conftest.py"
+    "${PROJECT_BINARY_DIR}/tests/integrated/test-boutpp/conftest.py")
+
 endif()
 
 option(BOUT_BUILD_EXAMPLES "Build the examples" ON)

From 93737b5214b83fe3ea249fe05663daf30610c569 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 26 Jan 2026 14:07:39 +0000
Subject: [PATCH 1038/1827] Add missing fixture argument `test_dir`

---
 .../test_coordinates_initialization.py                          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
index f1621afa42..69f8840bcc 100644
--- a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
+++ b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
@@ -3,7 +3,7 @@
 import time
 
 
-def test_runtest():
+def test_runtest(test_dir):
 
     cmd = './runtest'
     # MPI oversubscribe for communications test

From 91aede7756f402da0f73aca98d84f283a23c8715 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 26 Jan 2026 14:10:03 +0000
Subject: [PATCH 1039/1827] Add run_integrated_tests.sh

also ensuring that test_coordinates_initialization is run in serial
---
 tests/conftest.py                                             | 3 +++
 .../test_coordinates_initialization.py                        | 2 ++
 tests/run_integrated_tests.sh                                 | 4 ++++
 3 files changed, 9 insertions(+)
 create mode 100755 tests/run_integrated_tests.sh

diff --git a/tests/conftest.py b/tests/conftest.py
index 46a28f2107..aaaec8ed29 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -8,6 +8,9 @@ def pytest_configure(config):
     config.addinivalue_line(
         "markers", "input_dir(name): specify the pre-existing input directory name for this test"
     )
+    config.addinivalue_line(
+        "serial"
+    )
 
 @pytest.fixture
 def test_dir(request) -> Path:
diff --git a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
index 69f8840bcc..a95d501d36 100644
--- a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
+++ b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
@@ -1,8 +1,10 @@
+import pytest
 import os
 import subprocess
 import time
 
 
+@pytest.mark.serial
 def test_runtest(test_dir):
 
     cmd = './runtest'
diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
new file mode 100755
index 0000000000..553daed9e4
--- /dev/null
+++ b/tests/run_integrated_tests.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+pytest -m "not serial" --cache-clear -n auto --dist=loadgroup integrated
+pytest -m serial integrated

From 1e8b9f26df4ca663bc4da04651a069633b706c8d Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 28 Jan 2026 15:00:56 +0000
Subject: [PATCH 1040/1827] Fix addinivalue_line "serial" in `pytest_configure`
 hook

---
 tests/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index aaaec8ed29..464fad8a77 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -9,7 +9,7 @@ def pytest_configure(config):
         "markers", "input_dir(name): specify the pre-existing input directory name for this test"
     )
     config.addinivalue_line(
-        "serial"
+        "markers", "serial: mark that the test should not be run concurrently with other. "
     )
 
 @pytest.fixture

From 72d160526e74bb2d0345bc13dc4c4b5e7c10360c Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 28 Jan 2026 15:02:01 +0000
Subject: [PATCH 1041/1827] Remove ini value for `input_dir` mark in
 `pytest_configure` hook

---
 tests/conftest.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 464fad8a77..1282bef3ca 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -5,9 +5,6 @@
 
 
 def pytest_configure(config):
-    config.addinivalue_line(
-        "markers", "input_dir(name): specify the pre-existing input directory name for this test"
-    )
     config.addinivalue_line(
         "markers", "serial: mark that the test should not be run concurrently with other. "
     )

From 73d8b067e13bf4908e5a8766fba14b457964d7c2 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 4 Feb 2026 09:27:19 +0000
Subject: [PATCH 1042/1827] Copy tests/run_integrated_tests.sh when building

---
 CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9f067bff1a..31374cad20 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -790,6 +790,11 @@ if(BOUT_TESTS)
     "${PROJECT_SOURCE_DIR}/tests/integrated/test-boutpp/conftest.py"
     "${PROJECT_BINARY_DIR}/tests/integrated/test-boutpp/conftest.py")
 
+  # Copy the pytest shell script
+  configure_file(
+    "${PROJECT_SOURCE_DIR}/tests/run_integrated_tests.sh"
+    "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh")
+
 endif()
 
 option(BOUT_BUILD_EXAMPLES "Build the examples" ON)

From eb35e01857c63c4c0124b026158318ca559df954 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 9 Feb 2026 11:52:19 +0000
Subject: [PATCH 1043/1827] Modify test_laplace_petsc3d to run via pytest

---
 .../test_laplace_petsc3d.py                   | 45 +++++++++----------
 1 file changed, 22 insertions(+), 23 deletions(-)

diff --git a/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
index 7fa2dbe22c..9139674513 100755
--- a/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
+++ b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
@@ -4,7 +4,7 @@
 
 from boutdata import collect
 from boututils.run_wrapper import launch
-from sys import exit
+
 
 test_directories = [
     ("data_slab_core", 1),
@@ -15,31 +15,30 @@
 
 tolerance = 1.0e-6
 
-success = True
-errors = {}
+def test_laplace_petsc3d():
+
+    errors = {}
 
-for directory, nproc in test_directories:
-    command = f"./test-laplace3d -d {directory}"
-    print("running on", nproc, "processors:", command)
-    status, output = launch(command, nproc=nproc, pipe=True)
+    for directory, nproc in test_directories:
+        command = f"./test-laplace3d -d {directory}"
+        print("running on", nproc, "processors:", command)
+        status, output = launch(command, nproc=nproc, pipe=True)
 
-    if status:
-        print("FAILED")
-        print(output)
-        errors[directory] = "<bad exit>"
-        continue
+        if status:
+            print("FAILED")
+            print(output)
+            errors[directory] = "<bad exit>"
+            continue
 
-    error_max = collect("error_max", path=directory, info=False)
-    if error_max > tolerance:
-        errors[directory] = error_max
+        error_max = collect("error_max", path=directory, info=False)
+        if error_max > tolerance:
+            errors[directory] = error_max
 
-print("**********")
+    print("**********")
 
-if errors:
-    print("Some failures:")
-    for name, error in errors.items():
-        print(f"{name}, max error: {error}")
-    exit(1)
+    if errors:
+        print("Some failures:")
+        for name, error in errors.items():
+            print(f"{name}, max error: {error}")
 
-print("All passed")
-exit(0)
+    assert not errors

From b30a71f4a3a7647df9f0d86af92d8d0ac4ecdc46 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 10 Feb 2026 15:46:25 +0000
Subject: [PATCH 1044/1827] Use pathlib instead of os.path

---
 .../test-command-args/test_command_args.py    | 24 +++++++++----------
 .../test_griddata_yboundary_guards.py         | 12 ++++++----
 tests/integrated/test-initial/test_initial.py |  6 ++---
 .../test-restart-io/test_restart_io.py        | 10 ++++----
 tests/integrated/test-squash/test_squash.py   |  4 ++--
 5 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/tests/integrated/test-command-args/test_command_args.py b/tests/integrated/test-command-args/test_command_args.py
index aed7d35ef0..3759d3cb65 100755
--- a/tests/integrated/test-command-args/test_command_args.py
+++ b/tests/integrated/test-command-args/test_command_args.py
@@ -1,25 +1,25 @@
 #!/usr/bin/env python3
 
 from boututils.run_wrapper import launch_safe
-import os
+from pathlib import Path
 import re
 import shutil
 import unittest
 import platform
 
-OUTPUT_FILE = "stdout.log" if platform.system() == "FreeBSD" else "stderr.log"
 
+OUTPUT_FILE = Path("stdout.log") if platform.system() == "FreeBSD" else "stderr.log"
 
 class TestCommandLineArgs(unittest.TestCase):
     command = "./command-args >stdout.log 2>stderr.log"
 
     def makeDirAndCopyInput(self, path):
-        os.mkdir(path)
+        Path.mkdir(path)
         shutil.copy("BOUT.inp", path)
 
     def setUp(self):
         try:
-            os.remove(OUTPUT_FILE)
+            Path.unlink(OUTPUT_FILE)
         except OSError:
             pass
         shutil.rmtree("./data", ignore_errors=True)
@@ -52,11 +52,11 @@ def testNoArgumentsDefaultDirectory(self):
         self.makeDirAndCopyInput("data")
         launch_safe(self.command, pipe=True, nproc=1, mthread=1)
         self.assertTrue(
-            os.path.exists("data/BOUT.settings"),
+            Path.exists(Path("data/BOUT.settings")),
             msg="FAIL: No BOUT.settings file in data directory",
         )
         self.assertTrue(
-            os.path.exists("data/BOUT.log.0"),
+            Path.exists(Path("data/BOUT.log.0")),
             msg="FAIL: No BOUT.log.0 file in data directory",
         )
 
@@ -64,11 +64,11 @@ def testShortLogArgument(self):
         self.makeDirAndCopyInput("data")
         launch_safe(self.command + " -l different.log", pipe=True, nproc=1, mthread=1)
         self.assertFalse(
-            os.path.exists("data/BOUT.log.0"),
+            Path.exists(Path("data/BOUT.log.0")),
             msg="FAIL: BOUT.log.0 file in data directory",
         )
         self.assertTrue(
-            os.path.exists("data/different.log.0"),
+            Path.exists(Path("data/different.log.0")),
             msg="FAIL: no different.log.0 file in data directory",
         )
 
@@ -76,22 +76,22 @@ def testLongLogArgument(self):
         self.makeDirAndCopyInput("data")
         launch_safe(self.command + " --log log", pipe=True, nproc=1, mthread=1)
         self.assertFalse(
-            os.path.exists("data/BOUT.log.0"),
+            Path.exists(Path("data/BOUT.log.0")),
             msg="FAIL: BOUT.log.0 file in data directory",
         )
         self.assertTrue(
-            os.path.exists("data/log.0"), msg="FAIL: no log.0 file in data directory"
+            Path.exists(Path("data/log.0")), msg="FAIL: no log.0 file in data directory"
         )
 
     def testDirectoryArgument(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)
         self.assertTrue(
-            os.path.exists("test/BOUT.settings"),
+            Path.exists(Path("test/BOUT.settings")),
             msg="FAIL: No BOUT.settings file in test directory",
         )
         self.assertTrue(
-            os.path.exists("test/BOUT.log.0"),
+            Path.exists(Path("test/BOUT.log.0")),
             msg="FAIL: No BOUT.log.0 file in data directory",
         )
 
diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
index 84844d4336..44b32f40fd 100755
--- a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
+++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
@@ -4,7 +4,7 @@
 from boutdata.collect import collect
 from netCDF4 import Dataset
 import numpy
-import os.path
+from pathlib import Path
 from sys import stdout
 
 # Cores: 6
@@ -19,10 +19,11 @@ def test_griddata_yboundary_guards():
     # first generate some grid files to test
     # double null case:
     for n_yguards in [0, 1, 2]:
-        datadir = "data-doublenull-" + str(n_yguards)
+        datadir = Path("data-doublenull-" + str(n_yguards))
         gridname = "grid-doublenull-" + str(n_yguards) + ".nc"
+        file_path = datadir / gridname
 
-        with Dataset(os.path.join(datadir, gridname), "w") as gridfile:
+        with Dataset(file_path, "w") as gridfile:
             gridfile.createDimension("x", nx)
             gridfile.createDimension("y", ny + 4 * n_yguards)
 
@@ -69,10 +70,11 @@ def test_griddata_yboundary_guards():
 
     # grid files for single-null:
     for n_yguards in [0, 1, 2]:
-        datadir = "data-singlenull-" + str(n_yguards)
+        datadir = Path("data-singlenull-" + str(n_yguards))
         gridname = "grid-singlenull-" + str(n_yguards) + ".nc"
+        file_path = datadir / gridname
 
-        with Dataset(os.path.join(datadir, gridname), "w") as gridfile:
+        with Dataset(file_path, "w") as gridfile:
             gridfile.createDimension("x", nx)
             gridfile.createDimension("y", ny + 2 * n_yguards)
 
diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index 756659f5ad..504c72d4f4 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -9,7 +9,7 @@
 import itertools
 from scipy.special import erf
 import numpy as np
-import os
+from pathlib import Path
 
 
 # requires not make
@@ -160,8 +160,8 @@ def test_initial():
     success = True
     tolerance = 1e-13
     cmd = "./test_initial"
-    datadir = "data"
-    inputfile = os.path.join(datadir, "BOUT.inp")
+    datadir = Path("data")
+    inputfile = datadir / "BOUT.inp"
 
     # Read the input file
     config = configparser.ConfigParser()
diff --git a/tests/integrated/test-restart-io/test_restart_io.py b/tests/integrated/test-restart-io/test_restart_io.py
index b3533b4d0e..672210b75a 100755
--- a/tests/integrated/test-restart-io/test_restart_io.py
+++ b/tests/integrated/test-restart-io/test_restart_io.py
@@ -11,8 +11,8 @@
 from boututils.datafile import DataFile
 from boututils.run_wrapper import shell, launch_safe
 import numpy
-import os
 import uuid
+from pathlib import Path
 
 nx = 8
 ny = 16
@@ -43,15 +43,13 @@ def test_restart_io():
     )
 
     # make restart file
-    restartdir = os.path.join("data", "restart")
+    restartdir = Path("data") / "restart"
     try:
-        os.mkdir(restartdir)
+        Path.mkdir(restartdir)
     except FileExistsError:
         pass
 
-    with DataFile(
-        os.path.join(restartdir, "BOUT.restart.0.nc"), create=True
-    ) as base_restart:
+    with DataFile(restartdir / "BOUT.restart.0.nc", create=True) as base_restart:
         base_restart.write("MXSUB", nx)
         base_restart.write("MYSUB", ny)
         base_restart.write("MZSUB", nz)
diff --git a/tests/integrated/test-squash/test_squash.py b/tests/integrated/test-squash/test_squash.py
index b9a2f903c5..bad21abd37 100755
--- a/tests/integrated/test-squash/test_squash.py
+++ b/tests/integrated/test-squash/test_squash.py
@@ -7,7 +7,7 @@
 from boututils.run_wrapper import launch_safe, shell_safe
 import argparse
 import re
-import os.path
+from pathlib import Path
 
 # requires: all_tests
 # requires: netcdf
@@ -88,7 +88,7 @@ def test_squash():
 
     bout_squashoutput = args.executable + "/bout-squashoutput"
 
-    if not os.path.exists(bout_squashoutput):
+    if not Path.exists(bout_squashoutput):
         bout_squashoutput = "bout-squashoutput"
 
     print("Run once to get normal data")

From e820b8f04e6dec93404750d8721010d82604768f Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 10 Feb 2026 16:43:49 +0000
Subject: [PATCH 1045/1827] Revert "Use pytest rather than runtest as the
 command set in bout_add_integrated_or_mms_test"

This reverts commit 84ff6322d7c92f084bf144518ff6a3f2b0b285eb.
---
 cmake/BOUT++functions.cmake | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 83950f58e5..3cb7d6e0b4 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -254,7 +254,9 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
 
   # Set the actual test command
   if (BOUT_TEST_OPTIONS_USE_RUNTEST)
-    add_test(NAME ${TESTNAME} COMMAND pytest ${BOUT_TEST_OPTIONS_TESTARGS})
+    add_test(NAME ${TESTNAME}
+      COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS}
+      )
     set_tests_properties(
       ${TESTNAME} PROPERTIES ENVIRONMENT
                              PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}

From 472d6fb673419f83940a2460c7b9352c6f277bdb Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 10 Feb 2026 13:41:23 +0000
Subject: [PATCH 1046/1827] Copy `runtest` file even if not `USE_RUNTEST`

---
 cmake/BOUT++functions.cmake | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 3cb7d6e0b4..b2f7c2b1d5 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -264,15 +264,14 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
     string(REGEX REPLACE "^(test-|MMS-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
     string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
 	bout_copy_file(${TEST_FILENAME})
-
-	if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest)
-        bout_copy_file(runtest)
-    endif()
-
   else()
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()
 
+  if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest)
+    bout_copy_file(runtest)
+  endif()
+
   set_tests_properties(
     ${TESTNAME} PROPERTIES PROCESSORS ${BOUT_TEST_OPTIONS_PROCESSORS}
                            PROCESSOR_AFFINITY ON

From 39b292fc653a496c75927960791438172efb59d6 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 11 Feb 2026 09:20:17 +0000
Subject: [PATCH 1047/1827] Extract duplicated code to a fixture
 `run_in_terminal`

---
 tests/conftest.py                              | 18 ++++++++++++++++++
 .../test_bout_override_default_option.py       | 16 ++--------------
 .../test-boutpp/print/test_boutpp_print.py     | 16 ++--------------
 .../test-code-style/test_code_style.py         | 16 ++--------------
 .../test_compile_examples_petsc.py             | 16 ++--------------
 .../test_compile_examples.py                   | 16 ++--------------
 .../test_coordinates_initialization.py         | 17 ++---------------
 tests/integrated/test-include/test_include.py  | 16 ++--------------
 tests/integrated/test-snb/test_snb.py          | 16 ++--------------
 .../test-stopCheck/test_stopCheck.py           | 16 ++--------------
 tests/integrated/test-subdir/test_subdir.py    | 16 ++--------------
 11 files changed, 38 insertions(+), 141 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 1282bef3ca..d6f133d1c1 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,9 +1,13 @@
 import pytest
 import shutil
 import boutpp
+import os
+import subprocess
+import time
 from pathlib import Path
 
 
+
 def pytest_configure(config):
     config.addinivalue_line(
         "markers", "serial: mark that the test should not be run concurrently with other. "
@@ -33,3 +37,17 @@ def copy_and_cwd_to_unique_tmp_dir(request, tmp_path_factory, monkeypatch):
 
     # Change working directory to the copy
     monkeypatch.chdir(run_dir)
+
+
+@pytest.fixture
+def run_in_terminal(test_dir):
+    cmd = './runtest'
+    # MPI oversubscribe for communications test
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    start = time.time()
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
+    elapsed = time.time() - start
+    print(f"Output: {result.stdout}")
+    if result.returncode != 0:
+        print(f"Stderr: {result.stderr}")
+    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
diff --git a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
index 65bf227187..de25d93e32 100644
--- a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
+++ b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
@@ -1,16 +1,4 @@
-import os
-import subprocess
-import time
 
 
-def test_runtest():
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index 65bf227187..de25d93e32 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -1,16 +1,4 @@
-import os
-import subprocess
-import time
 
 
-def test_runtest():
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass
diff --git a/tests/integrated/test-code-style/test_code_style.py b/tests/integrated/test-code-style/test_code_style.py
index 65bf227187..de25d93e32 100644
--- a/tests/integrated/test-code-style/test_code_style.py
+++ b/tests/integrated/test-code-style/test_code_style.py
@@ -1,16 +1,4 @@
-import os
-import subprocess
-import time
 
 
-def test_runtest():
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass
diff --git a/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py b/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
index 65bf227187..de25d93e32 100644
--- a/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
+++ b/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
@@ -1,16 +1,4 @@
-import os
-import subprocess
-import time
 
 
-def test_runtest():
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass
diff --git a/tests/integrated/test-compile-examples/test_compile_examples.py b/tests/integrated/test-compile-examples/test_compile_examples.py
index 65bf227187..de25d93e32 100644
--- a/tests/integrated/test-compile-examples/test_compile_examples.py
+++ b/tests/integrated/test-compile-examples/test_compile_examples.py
@@ -1,16 +1,4 @@
-import os
-import subprocess
-import time
 
 
-def test_runtest():
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass
diff --git a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
index a95d501d36..a3ebcaff86 100644
--- a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
+++ b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
@@ -1,19 +1,6 @@
 import pytest
-import os
-import subprocess
-import time
 
 
 @pytest.mark.serial
-def test_runtest(test_dir):
-
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass
diff --git a/tests/integrated/test-include/test_include.py b/tests/integrated/test-include/test_include.py
index 65bf227187..de25d93e32 100644
--- a/tests/integrated/test-include/test_include.py
+++ b/tests/integrated/test-include/test_include.py
@@ -1,16 +1,4 @@
-import os
-import subprocess
-import time
 
 
-def test_runtest():
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass
diff --git a/tests/integrated/test-snb/test_snb.py b/tests/integrated/test-snb/test_snb.py
index 65bf227187..de25d93e32 100644
--- a/tests/integrated/test-snb/test_snb.py
+++ b/tests/integrated/test-snb/test_snb.py
@@ -1,16 +1,4 @@
-import os
-import subprocess
-import time
 
 
-def test_runtest():
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass
diff --git a/tests/integrated/test-stopCheck/test_stopCheck.py b/tests/integrated/test-stopCheck/test_stopCheck.py
index 3f4efff65d..de25d93e32 100644
--- a/tests/integrated/test-stopCheck/test_stopCheck.py
+++ b/tests/integrated/test-stopCheck/test_stopCheck.py
@@ -1,16 +1,4 @@
-import os
-import subprocess
-import time
 
 
-def test_runtest(test_dir):
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass
diff --git a/tests/integrated/test-subdir/test_subdir.py b/tests/integrated/test-subdir/test_subdir.py
index 65bf227187..de25d93e32 100644
--- a/tests/integrated/test-subdir/test_subdir.py
+++ b/tests/integrated/test-subdir/test_subdir.py
@@ -1,16 +1,4 @@
-import os
-import subprocess
-import time
 
 
-def test_runtest():
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def test_runtest(run_in_terminal):
+    pass

From 3d921586c81cd32d86f088e291d6953d6c7876e3 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 11 Feb 2026 10:10:32 +0000
Subject: [PATCH 1048/1827] Path.exists() takes a Path object

---
 tests/integrated/test-squash/test_squash.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-squash/test_squash.py b/tests/integrated/test-squash/test_squash.py
index bad21abd37..a2e9a16a50 100755
--- a/tests/integrated/test-squash/test_squash.py
+++ b/tests/integrated/test-squash/test_squash.py
@@ -86,7 +86,7 @@ def test_squash():
     )
     args = parser.parse_args()
 
-    bout_squashoutput = args.executable + "/bout-squashoutput"
+    bout_squashoutput = Path(args.executable + "/bout-squashoutput")
 
     if not Path.exists(bout_squashoutput):
         bout_squashoutput = "bout-squashoutput"

From b9ad55ce7b0eb80777dbc42259840de325d18af1 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 11 Feb 2026 10:15:57 +0000
Subject: [PATCH 1049/1827] Always copy test file when building (even if not
 `USE_RUNTEST`)

---
 cmake/BOUT++functions.cmake | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index b2f7c2b1d5..dbdaeab154 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -261,13 +261,14 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
       ${TESTNAME} PROPERTIES ENVIRONMENT
                              PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
     )
-    string(REGEX REPLACE "^(test-|MMS-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
-    string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
-	bout_copy_file(${TEST_FILENAME})
   else()
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()
 
+  string(REGEX REPLACE "^(test-|MMS-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
+  string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
+  bout_copy_file(${TEST_FILENAME})
+
   if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest)
     bout_copy_file(runtest)
   endif()

From 95a5a042ddd43292b111e60ef792bcd2e97d9836 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 11 Feb 2026 10:46:45 +0000
Subject: [PATCH 1050/1827] Handle parsing test name for those already prefixed
 with "test_"

---
 cmake/BOUT++functions.cmake | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index dbdaeab154..9819f454c7 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -267,6 +267,7 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
 
   string(REGEX REPLACE "^(test-|MMS-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
   string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
+  string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
   bout_copy_file(${TEST_FILENAME})
 
   if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest)

From a3d8a55f16afcb818020141f8e6c32f891f7ec68 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 11 Feb 2026 14:22:11 +0000
Subject: [PATCH 1051/1827] Fix test_beuler and test_solver

---
 tests/integrated/test-beuler/test_beuler.py | 15 +++------------
 tests/integrated/test-solver/test_solver.py | 21 +++++++--------------
 2 files changed, 10 insertions(+), 26 deletions(-)

diff --git a/tests/integrated/test-beuler/test_beuler.py b/tests/integrated/test-beuler/test_beuler.py
index 268cd3c986..ab028a9c2e 100755
--- a/tests/integrated/test-beuler/test_beuler.py
+++ b/tests/integrated/test-beuler/test_beuler.py
@@ -2,22 +2,13 @@
 
 # requires: petsc
 
-from boututils.run_wrapper import shell_safe, launch_safe
-
-nthreads = 1
-nproc = 1
+from boututils.run_wrapper import shell_safe
 
 
 def test_beuler():
-    print("Making solver test")
-    shell_safe("make > make.log")
-
     print("Running solver test")
-    status, out = launch_safe("./test_beuler", nproc=nproc, mthread=nthreads, pipe=True)
+    status, out = shell_safe("./test_beuler", pipe=True)
     with open("run.log", "w") as f:
         f.write(out)
 
-    if status:
-        print(out)
-
-    assert status, out
+    assert status == 0, out
diff --git a/tests/integrated/test-solver/test_solver.py b/tests/integrated/test-solver/test_solver.py
index 18283caf73..1b1ff2e79c 100755
--- a/tests/integrated/test-solver/test_solver.py
+++ b/tests/integrated/test-solver/test_solver.py
@@ -1,19 +1,12 @@
 #!/usr/bin/env python3
 
-from boututils.run_wrapper import launch_safe
+from boututils.run_wrapper import shell_safe
 
-from sys import exit
 
-nthreads = 1
-nproc = 1
+def test_solver():
+    print("Running solver test")
+    status, out = shell_safe("./test_solver", pipe=True)
+    with open("run.log", "w") as f:
+        f.write(out)
 
-
-print("Running solver test")
-status, out = launch_safe("./test_solver", nproc=nproc, mthread=nthreads, pipe=True)
-with open("run.log", "w") as f:
-    f.write(out)
-
-if status:
-    print(out)
-
-exit(status)
+    assert status == 0, out

From d58ba648b5a9076ad0dbfeab9b323bc24bd35012 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 11 Feb 2026 15:02:43 +0000
Subject: [PATCH 1052/1827] Refactor fixture `assert_success_in_shell` to
 return a function

Remove obsolete tests
---
 tests/conftest.py                             |  24 +-
 .../test_bout_override_default_option.py      |   4 +-
 .../test-boutpp/print/test_boutpp_print.py    |   4 +-
 tests/integrated/test-code-style/README.md    |   9 -
 tests/integrated/test-code-style/runtest      |  33 --
 .../test-code-style/test_code_style.py        |   4 -
 .../test-compile-examples-petsc/README.md     |   1 -
 .../test-compile-examples-petsc/runtest       |  36 --
 .../test_compile_examples_petsc.py            |   4 -
 .../test-compile-examples/README.md           |  13 -
 .../integrated/test-compile-examples/runtest  |  36 --
 .../test_compile_examples.py                  |   4 -
 .../test_coordinates_initialization.py        |   4 +-
 tests/integrated/test-include/.gitignore      |   1 -
 tests/integrated/test-include/README.md       |  11 -
 tests/integrated/test-include/runtest         |  32 --
 tests/integrated/test-include/test_include.py |   4 -
 tests/integrated/test-snb/test_snb.py         |   4 +-
 .../test-stopCheck/test_stopCheck.py          |   4 +-
 tests/integrated/test-subdir/test_subdir.py   |   4 -
 tests/integrated/test_suite                   | 366 ------------------
 21 files changed, 23 insertions(+), 579 deletions(-)
 delete mode 100644 tests/integrated/test-code-style/README.md
 delete mode 100755 tests/integrated/test-code-style/runtest
 delete mode 100644 tests/integrated/test-code-style/test_code_style.py
 delete mode 120000 tests/integrated/test-compile-examples-petsc/README.md
 delete mode 100755 tests/integrated/test-compile-examples-petsc/runtest
 delete mode 100644 tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
 delete mode 100644 tests/integrated/test-compile-examples/README.md
 delete mode 100755 tests/integrated/test-compile-examples/runtest
 delete mode 100644 tests/integrated/test-compile-examples/test_compile_examples.py
 delete mode 100644 tests/integrated/test-include/.gitignore
 delete mode 100644 tests/integrated/test-include/README.md
 delete mode 100755 tests/integrated/test-include/runtest
 delete mode 100644 tests/integrated/test-include/test_include.py
 delete mode 100644 tests/integrated/test-subdir/test_subdir.py
 delete mode 100755 tests/integrated/test_suite

diff --git a/tests/conftest.py b/tests/conftest.py
index d6f133d1c1..e993eb564b 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -40,14 +40,16 @@ def copy_and_cwd_to_unique_tmp_dir(request, tmp_path_factory, monkeypatch):
 
 
 @pytest.fixture
-def run_in_terminal(test_dir):
-    cmd = './runtest'
-    # MPI oversubscribe for communications test
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
-    start = time.time()
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True, timeout=600)
-    elapsed = time.time() - start
-    print(f"Output: {result.stdout}")
-    if result.returncode != 0:
-        print(f"Stderr: {result.stderr}")
-    assert result.returncode == 0, f"Failed after {elapsed:.3f}s in {test_dir}"
+def assert_success_in_shell(test_dir):
+
+    def inner_function(command: str):
+        # MPI oversubscribe for communications test
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+        start = time.time()
+        result = subprocess.run(command, shell=True, capture_output=True, text=True, timeout=600)
+        elapsed = time.time() - start
+        assert result.returncode == 0, (f"Failed after {elapsed:.3f}s in {test_dir}\n"
+                                        f"Stderr: {result.stderr}\n"
+                                        f"Output: {result.stdout}")
+
+    return inner_function
diff --git a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
index de25d93e32..48a29195e0 100644
--- a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
+++ b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
@@ -1,4 +1,4 @@
 
 
-def test_runtest(run_in_terminal):
-    pass
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./runtest")
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index de25d93e32..48a29195e0 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -1,4 +1,4 @@
 
 
-def test_runtest(run_in_terminal):
-    pass
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./runtest")
diff --git a/tests/integrated/test-code-style/README.md b/tests/integrated/test-code-style/README.md
deleted file mode 100644
index 602c41d8d5..0000000000
--- a/tests/integrated/test-code-style/README.md
+++ /dev/null
@@ -1,9 +0,0 @@
-Coding Style Test
-=================
-
-Test for a few parts of the coding style.
-For example options should be passed as non-const value for small datatypes (`int`,`char`,`BoutReal`,...)
-
-```C++
-void fu(int a);
-```
\ No newline at end of file
diff --git a/tests/integrated/test-code-style/runtest b/tests/integrated/test-code-style/runtest
deleted file mode 100755
index d392f9110f..0000000000
--- a/tests/integrated/test-code-style/runtest
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env bash
-
-#requires not make
-
-BOUT_TOP=../../..
-error=
-
-paths="src include examples tests"
-
-
-# Check that exceptions are caught by reference
-for path in $paths
-do
-    catch_errors=$(grep catch[^\(]*\([^\(]*Bout $BOUT_TOP/$path --include=*xx -r|grep -v '&')
-    ex=$?
-    if test $ex -eq 0
-    then
-        error=yes
-        echo "Found catch by value - not by reference:"
-        echo "$catch_errors"
-    fi
-done
-
-
-# Return
-if test $error
-then
-    echo "-> Errors listed above"
-    exit 1
-else
-    echo "No Errors detected"
-    exit 0
-fi
diff --git a/tests/integrated/test-code-style/test_code_style.py b/tests/integrated/test-code-style/test_code_style.py
deleted file mode 100644
index de25d93e32..0000000000
--- a/tests/integrated/test-code-style/test_code_style.py
+++ /dev/null
@@ -1,4 +0,0 @@
-
-
-def test_runtest(run_in_terminal):
-    pass
diff --git a/tests/integrated/test-compile-examples-petsc/README.md b/tests/integrated/test-compile-examples-petsc/README.md
deleted file mode 120000
index 77bd1f7308..0000000000
--- a/tests/integrated/test-compile-examples-petsc/README.md
+++ /dev/null
@@ -1 +0,0 @@
-../test-compile-examples/README.md
\ No newline at end of file
diff --git a/tests/integrated/test-compile-examples-petsc/runtest b/tests/integrated/test-compile-examples-petsc/runtest
deleted file mode 100755
index 0f9625af40..0000000000
--- a/tests/integrated/test-compile-examples-petsc/runtest
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env bash
-
-#requires: all_tests
-#requires: not make
-#requires: petsc
-
-BOUT_TOP=../../..
-export PATH=$(pwd)/$BOUT_TOP/bin:$PATH
-
-error=0
-
-failed=
-for target in $(find $BOUT_TOP/examples/ -name makefile)
-do
-    dir=$(dirname ${target})
-    if grep ":.*requires_petsc" $target -q;
-    then
-        echo "Trying to compile ${dir}"
-
-        (cd ${dir} && make 2>&1)
-        ex=$?
-
-        if test $ex -gt 0
-        then
-            echo $(basename $dir) failed
-            error=1
-            failed="$failed\n$(basename $dir) failed"
-        fi
-    else
-        echo "Skipping $dir - requires PETSc"
-    fi
-done
-
-echo -e $failed
-
-exit $error
diff --git a/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py b/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
deleted file mode 100644
index de25d93e32..0000000000
--- a/tests/integrated/test-compile-examples-petsc/test_compile_examples_petsc.py
+++ /dev/null
@@ -1,4 +0,0 @@
-
-
-def test_runtest(run_in_terminal):
-    pass
diff --git a/tests/integrated/test-compile-examples/README.md b/tests/integrated/test-compile-examples/README.md
deleted file mode 100644
index 2fa005c7c4..0000000000
--- a/tests/integrated/test-compile-examples/README.md
+++ /dev/null
@@ -1,13 +0,0 @@
-test-compile-examples
-=====================
-
-This test ensures that all models in examples can be compiled.
-
-This currently works by finding any makefile located beneath
-examples. It skips any directories matching doc in order to skip
-documentation.  Building documentation requires often additional
-tools, and is thus skipped.  The test is split in two parts, one for
-examples without PETSc, and one for examples that require PETSc.
-
-PETSc detection works by checking the makefile whether any target
-requires `requires_petsc`.
diff --git a/tests/integrated/test-compile-examples/runtest b/tests/integrated/test-compile-examples/runtest
deleted file mode 100755
index 765ea2cbfd..0000000000
--- a/tests/integrated/test-compile-examples/runtest
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env bash
-
-#requires: all_tests
-#requires: not make
-
-BOUT_TOP=../../..
-export PATH=$(pwd)/$BOUT_TOP/bin:$PATH
-
-error=0
-
-failed=
-for target in $(find $BOUT_TOP/examples/ -name makefile | grep -v doc)
-do
-    dir=$(dirname ${target})
-    if grep ":.*requires_petsc" $target -q;
-    then
-        echo "Skipping $dir - requires PETSc"
-    else
-        echo "Trying to compile ${dir}"
-
-        (cd ${dir} && make 2>&1)
-        ex=$?
-
-        if test $ex -gt 0
-        then
-            dir=${dir#../../../examples/}
-            echo $dir failed
-            error=1
-            failed="$failed\n$dir failed"
-        fi
-    fi
-done
-
-echo -e $failed
-
-exit $error
diff --git a/tests/integrated/test-compile-examples/test_compile_examples.py b/tests/integrated/test-compile-examples/test_compile_examples.py
deleted file mode 100644
index de25d93e32..0000000000
--- a/tests/integrated/test-compile-examples/test_compile_examples.py
+++ /dev/null
@@ -1,4 +0,0 @@
-
-
-def test_runtest(run_in_terminal):
-    pass
diff --git a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
index a3ebcaff86..64a438d1dc 100644
--- a/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
+++ b/tests/integrated/test-coordinates-initialization/test_coordinates_initialization.py
@@ -2,5 +2,5 @@
 
 
 @pytest.mark.serial
-def test_runtest(run_in_terminal):
-    pass
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./runtest")
diff --git a/tests/integrated/test-include/.gitignore b/tests/integrated/test-include/.gitignore
deleted file mode 100644
index 1ccb766f4e..0000000000
--- a/tests/integrated/test-include/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-test.cxx
diff --git a/tests/integrated/test-include/README.md b/tests/integrated/test-include/README.md
deleted file mode 100644
index 292b5d3a4e..0000000000
--- a/tests/integrated/test-include/README.md
+++ /dev/null
@@ -1,11 +0,0 @@
-test-include
-============
-
-This test ensures that all header files from bout can be included on
-their own. It compiles a test file with one header, and if that fails,
-then the headerfile does not include all files it needs.
-
-Checking whether the library builds as whole is not sufficient, as
-either the file might never be included directly, or some other header
-file might always be included first, which fulfils the requirements,
-thus there is this extra test.
diff --git a/tests/integrated/test-include/runtest b/tests/integrated/test-include/runtest
deleted file mode 100755
index 4fa8096c4b..0000000000
--- a/tests/integrated/test-include/runtest
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env bash
-
-#requires: all_tests
-#Requires: not make
-
-BOUT_TOP=../../..
-export PATH=$BOUT_TOP/bin:$PATH
-
-error=0
-
-failed=
-for header in $(cd $BOUT_TOP/include ; find |grep hxx\$)
-do
-    echo "#include <$header>" > test.cxx
-
-    $(bout-config --cxx) $(bout-config --cflags) test.cxx -c
-
-    ex=$?
-    
-    if test $ex -gt 0
-    then
-        echo $header failed
-        error=1
-	failed="$failed
-$header failed"
-    fi
-
-done
-
-echo $failed
-
-exit $error
diff --git a/tests/integrated/test-include/test_include.py b/tests/integrated/test-include/test_include.py
deleted file mode 100644
index de25d93e32..0000000000
--- a/tests/integrated/test-include/test_include.py
+++ /dev/null
@@ -1,4 +0,0 @@
-
-
-def test_runtest(run_in_terminal):
-    pass
diff --git a/tests/integrated/test-snb/test_snb.py b/tests/integrated/test-snb/test_snb.py
index de25d93e32..48a29195e0 100644
--- a/tests/integrated/test-snb/test_snb.py
+++ b/tests/integrated/test-snb/test_snb.py
@@ -1,4 +1,4 @@
 
 
-def test_runtest(run_in_terminal):
-    pass
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./runtest")
diff --git a/tests/integrated/test-stopCheck/test_stopCheck.py b/tests/integrated/test-stopCheck/test_stopCheck.py
index de25d93e32..48a29195e0 100644
--- a/tests/integrated/test-stopCheck/test_stopCheck.py
+++ b/tests/integrated/test-stopCheck/test_stopCheck.py
@@ -1,4 +1,4 @@
 
 
-def test_runtest(run_in_terminal):
-    pass
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./runtest")
diff --git a/tests/integrated/test-subdir/test_subdir.py b/tests/integrated/test-subdir/test_subdir.py
deleted file mode 100644
index de25d93e32..0000000000
--- a/tests/integrated/test-subdir/test_subdir.py
+++ /dev/null
@@ -1,4 +0,0 @@
-
-
-def test_runtest(run_in_terminal):
-    pass
diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite
deleted file mode 100755
index 77ad7882c4..0000000000
--- a/tests/integrated/test_suite
+++ /dev/null
@@ -1,366 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-#
-# Run the test suite, report failures
-#
-# To set command for running parallel jobs, define environment variable
-# e.g. for bash
-# export MPIRUN="mpirun -np"
-# export MPIRUN="aprun -n"
-
-import os
-import sys
-import time
-import glob
-from boututils.run_wrapper import shell
-import threading
-import re
-import fcntl
-import select
-
-##################################################################
-
-import argparse
-
-parser = argparse.ArgumentParser(description="Run or build some tests.")
-parser.add_argument(
-    "-g",
-    "--get-list",
-    action="store_true",
-    help="Return a list of tests that would be run/build",
-)
-parser.add_argument(
-    "-m", "--make", action="store_true", help="Build the tests, rather then run them."
-)
-parser.add_argument(
-    "-a", "--all", action="store_true", dest="all_tests", help="Run all tests"
-)
-parser.add_argument(
-    "-b",
-    "--set-bool",
-    nargs="+",
-    metavar=("value1=False", "value2=True"),
-    help="Set a bool value for evaluating what scripts can be run.",
-)
-parser.add_argument(
-    "-l",
-    "--set-list",
-    nargs="+",
-    metavar=("test1", "test2"),
-    help="Set the tests that should be run.",
-)
-parser.add_argument(
-    "-j",
-    "--jobs",
-    nargs=1,
-    type=int,
-    dest="jobs",
-    help="Set the number of cores to use in parallel.",
-)
-
-args = parser.parse_args()
-
-##################################################################
-
-sys.path.append("..")
-from requirements import Requirements
-
-requirements = Requirements()
-
-if args.set_bool is not None:
-    lookup = {"false": False, "no": False, "true": True, "yes": True}
-    for setbool in args.set_bool:
-        k, v = setbool.split("=")
-        v = lookup[v.lower()]
-        requirements.add(k, v, override=True)
-
-try:
-    requirements.add("make", args.make)
-except RuntimeError:
-    raise RuntimeError(
-        "The make flag needs to be set by passing --make rather then --set-bool make=True"
-    )
-
-try:
-    requirements.add("all_tests", args.all_tests)
-except RuntimeError:
-    raise RuntimeError(
-        "The all-tests flag needs to be set by passing --all rather then --set-bool all_tests=True"
-    )
-
-##################################################################
-# Parallel stuff
-#
-# We can run in parallel. As some checks require several threads to
-# run, we take this into account when we schedule tests. Given a
-# certain amount of threads that we are told to use, we try to run
-# so many tests in parallel, that the total core count is not higher
-# than this number. If this isn't possible because some jobs require
-# more cores than we have threads, we run the remaining tests in
-# serial. The number of parallel threads is called cost of a test.
-#
-# The beginning of MAKEFLAGS has some flags that tell us what we are
-# supposed to be doing. Most of them we can ignore.
-# Check what we are supposed to be doing:
-if "MAKEFLAGS" in os.environ:
-    makeflags = os.environ["MAKEFLAGS"]
-    for token in makeflags:
-        if token == "n":
-            # Print recipies:
-            # We ignore this for now ...
-            sys.exit(0)
-        elif token == "q":
-            # Question mode:
-            # We are never up-to-date
-            sys.exit(1)
-        elif token in "ksBd":
-            # k - keep going
-            # s - silent
-            # B - always build (we do)
-            # d - debug
-            pass
-        elif token == " ":
-            break
-        elif token == "-":
-            # This is not from make
-            break
-        else:
-            # Not implemented
-            print("mode '%s' not implemented" % token)
-            # sys.exit(42)
-else:
-    makeflags = ""
-num_threads = 1
-if args.jobs:
-    num_threads = args.jobs[0]
-js_read = None
-# if we are running under make, we only have one thread (called job
-# in make terms) for sure, but might be able to run more threads
-# (depending what other jobs are currently running)
-# Additional jobs come in form of `tokens` that we need to give
-# back, if we are finished.
-# https://www.gnu.org/software/make/manual/html_node/POSIX-Jobserver.html
-if "--jobserver-auth=" in makeflags or "--jobserver-fds=" in makeflags:
-    try:
-        offset = makeflags.index("--jobserver-auth=")
-    except ValueError:
-        offset = makeflags.index("--jobserver-fds=")
-    file_desc = [int(i) for i in re.findall("\d+", makeflags[offset:])[0:2]]
-    js_read = file_desc[0]
-    js_write = file_desc[1]
-    js_tokens = b""
-
-
-class Test(threading.Thread):
-    def __init__(self, name, cmd, width, timeout):
-        threading.Thread.__init__(self)
-        self.name = name
-        self.cmd = cmd
-        self.width = width
-        self.local = threading.local()
-        self.cost = self._cost()
-        self.timeout = timeout
-
-    def run(self):
-        # Check requirements
-        self.local.req_met, self.local.req_expr = requirements.check(
-            self.name + "/runtest"
-        )
-        self.local.start_time = time.time()
-        if not self.local.req_met:
-            print(
-                "{:{width}}".format(self.name, width=self.width)
-                + "S - {0} => False".format(self.local.req_expr)
-            )
-            sys.stdout.flush()
-            self.status = 0
-        else:
-            # Run test, piping stdout so it is not sent to console
-            command = "cd {}; timeout {} {}".format(self.name, self.timeout, self.cmd)
-            self.status, self.output = shell(command, pipe=True)
-            print("{:{width}}".format(self.name, width=self.width), end="")
-            if self.status == 0:
-                # ✓ Passed
-                print("\u2713", end="")  # No newline
-            elif self.status == 124:
-                # 💤 timeout
-                print("\U0001f4a4", end="")  # No newline
-                self.output += "\n(It is likely that a timeout occured)"
-            else:
-                # ❌ Failed
-                print("\u274c", end="")  # No newline
-            print(" %7.3f s" % (time.time() - self.local.start_time), flush=True)
-
-    def _cost(self):
-        if self.cmd == "make":
-            return 1
-        with open(self.name + "/" + self.cmd, "r", encoding="utf8") as filein:
-            contents = filein.read()
-        # Find all lines starting with '#cores' or '#Cores:'
-        match = re.findall("^\s*\#\s?[Cc]ores:\s*?(\d+)", contents, re.MULTILINE)
-        if len(match) > 1:
-            raise RuntimeError(
-                "Found more then one match for core-count in " + self.name
-            )
-        if len(match) == 0:
-            # default; no mpi
-            return 1
-        c = int(match[0])
-        if c < 0:
-            raise RuntimeError(
-                "Core-count is %d and thus not positive in " % c + self.name
-            )
-        return c
-
-
-##################################################################
-
-if args.set_list is None:
-    # Get list of directories containing test cases
-    try:
-        # Requires python >= 3.5
-        tests = glob.iglob("**/runtest", recursive=True)
-    except TypeError:
-        # Fall back - check only a few folders ...
-        tests = glob.glob("*/runtest")
-        tests += glob.glob("*/*/runtest")
-        tests += glob.glob("*/*/*/runtest")
-        tests += glob.glob("*/*/*/*/runtest")
-
-    tests = [x.rsplit("/", 1)[0] for x in tests]
-
-else:
-    # Take the user provided list
-    tests = [x.rstrip("/") for x in args.set_list]
-
-
-if args.get_list:
-    for test in tests:
-        req_met, _ = requirements.check(test + "/runtest")
-        if req_met:
-            print(test)
-    sys.exit(0)
-
-
-# A function to get more threads from the job server
-def get_threads():
-    global js_read
-    if js_read:
-        global cost_remain, js_tokens, avail_threads, num_threads
-        try:
-            fl = fcntl.fcntl(js_read, fcntl.F_GETFL)
-        except OSError:
-            print("Warning - we are not part of the job pool 😭, running in serial")
-            js_read = None
-            return
-        isreadable, _, _ = select.select([js_read], [], [], 0)
-        if isreadable != []:
-            # Only set shortly to non-blocking, and only if we
-            # expect we can read. Old make uses blocking pipes, and
-            # assumes if it is non-blocking, a job is available.
-            fcntl.fcntl(js_read, fcntl.F_SETFL, fl | os.O_NONBLOCK)
-            new_token = os.read(js_read, cost_remain - avail_threads)
-            fcntl.fcntl(js_read, fcntl.F_SETFL, fl)
-            num_threads += len(new_token)
-            js_tokens += new_token
-            avail_threads += len(new_token)
-
-
-##################################################################
-# Run the actual test
-# Kill tests that take longer than 10 minutes (default)
-timeout = os.environ.get("BOUT_TEST_TIMEOUT", "10m" if not args.all_tests else "30m")
-command = "./runtest" if not args.make else "make"
-
-savepath = os.getcwd()  # Save current working directory
-failed = []
-
-start_time = time.time()
-
-test_type = "Making" if args.make else "Running"
-
-print(
-    "======= {} {} {} tests ========".format(
-        test_type, len(tests), savepath.split("/")[-1]
-    )
-)
-
-longest = max([len(s) for s in tests])
-avail_threads = num_threads
-tester = sorted(
-    [Test(t, command, longest + 1, timeout) for t in tests],
-    key=lambda x: x.cost,
-    reverse=True,
-)
-cost_remain = sum(x.cost for x in tester)
-get_threads()
-
-torun = [i for i in range(len(tests))]
-running = []
-
-while len(torun) + len(running):
-    if avail_threads:
-        # See whether we can start one
-        for i in torun[:]:
-            if tester[i].cost <= avail_threads:
-                torun.remove(i)
-                job = tester[i]
-                job.start()
-                running.append(job)
-                avail_threads -= job.cost
-                cost_remain -= job.cost
-        # if nothing is running, start the first
-        if running == []:
-            tostart = torun.pop(0)
-            job = tester[tostart]
-            job.start()
-            running.append(job)
-            avail_threads -= job.cost
-            cost_remain -= job.cost
-
-    # Are any jobs finished
-    for job in running:
-        job.join(0.1)
-        if not job.is_alive():
-            if job.status:
-                failed.append([job.name, job.output])
-            avail_threads += job.cost
-            running.remove(job)
-
-    # Try to get more jobs
-    if torun:
-        get_threads()
-    else:
-        # Free not-needed jobs
-        if avail_threads and js_read:
-            old_tokens = js_tokens[0:avail_threads]
-            js_tokens = js_tokens[avail_threads:]
-            os.write(js_write, old_tokens)
-            num_threads -= avail_threads
-            avail_threads = 0
-
-elapsed_time = time.time() - start_time
-
-print("\n")
-
-# Return remaining tokens
-if js_read is not None:
-    if js_tokens != "":
-        os.write(js_write, js_tokens)
-
-if failed:
-    print("======= FAILURES ========")
-    for test, output in failed:
-        # Note: need Unicode string in case output contains unicode
-        print("\n----- {0} -----\n{1}".format(test, output))
-
-    print(
-        "======= {0} failed in {1:.2f} seconds ========".format(
-            len(failed), elapsed_time
-        )
-    )
-
-    sys.exit(1)
-
-else:
-    print("======= All tests passed in {0:.2f} seconds =======".format(elapsed_time))

From abd771d121aedc02c34c7876b6b98652f77ff969 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:28:29 +0000
Subject: [PATCH 1053/1827] Modify test-fci-mpi to run via pytest

---
 tests/integrated/test-fci-mpi/test_fci_mpi.py | 80 +++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100755 tests/integrated/test-fci-mpi/test_fci_mpi.py

diff --git a/tests/integrated/test-fci-mpi/test_fci_mpi.py b/tests/integrated/test-fci-mpi/test_fci_mpi.py
new file mode 100755
index 0000000000..fb5bbfc496
--- /dev/null
+++ b/tests/integrated/test-fci-mpi/test_fci_mpi.py
@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+#
+# Python script to run and analyse MMS test
+
+from boututils.run_wrapper import build_and_log, launch_safe
+from boutdata.collect import collect
+import itertools
+
+import numpy.testing as npt
+
+# Resolution in x and y
+NLIST = [1, 2, 4]
+MAXCORES = 8
+NSLICES = [1]
+
+
+def fci_mpi():
+
+    COLLECT_KW = dict(info=False, xguards=False, yguards=False, path="data")
+
+    def run_case(nxpe: int, nype: int, mthread: int):
+
+        cmd = f"./fci_mpi NXPE={nxpe} NYPE={nype}"
+        print(f"Running command: {cmd}")
+
+        _, out = launch_safe(cmd, nproc=nxpe * nype, mthread=mthread, pipe=True)
+
+        # Save output to log file
+        with open(f"run.log.{nxpe}.{nype}.{nslice}.log", "w") as f:
+            f.write(out)
+
+
+    def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
+        run_case(nxpe, nype, mthread)
+
+        failures = []
+
+        for name, val in ref.items():
+            try:
+                npt.assert_allclose(val, collect(name, **COLLECT_KW))
+            except AssertionError as e:
+                failures.append((nxpe, nype, name, e))
+
+        return failures
+
+
+    failures = []
+
+    for nslice in NSLICES:
+        # reference data!
+        run_case(1, 1, MAXCORES)
+
+        ref = {}
+        for i in range(4):
+            for yp in range(1, nslice + 1):
+                for y in [-yp, yp]:
+                    name = f"output_{i}_{y:+d}"
+                    ref[name] = collect(name, **COLLECT_KW)
+
+        for nxpe, nype in itertools.product(NLIST, NLIST):
+            if (nxpe, nype) == (1, 1):
+                # reference case, done above
+                continue
+
+            if nxpe * nype > MAXCORES:
+                continue
+
+            mthread = MAXCORES // (nxpe * nype)
+            failures_ = test_case(nxpe, nype, mthread, ref)
+            failures.extend(failures_)
+
+
+    success = len(failures) == 0
+
+    assert success, "\nSome tests failed:"
+
+    if not success:
+        for nxpe, nype, name, error in failures:
+            print("----------")
+            print(f"case {nxpe=} {nype=} {name=}\n{error}")

From a4d97ab7702d4d13769d27d09f563c558e5f30fe Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:28:49 +0000
Subject: [PATCH 1054/1827] Modify test-subdir to run via pytest

---
 tests/integrated/test-subdir/test_subdir.py | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 tests/integrated/test-subdir/test_subdir.py

diff --git a/tests/integrated/test-subdir/test_subdir.py b/tests/integrated/test-subdir/test_subdir.py
new file mode 100644
index 0000000000..48a29195e0
--- /dev/null
+++ b/tests/integrated/test-subdir/test_subdir.py
@@ -0,0 +1,4 @@
+
+
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./runtest")

From a104a82863e3c15197309b3b8154cc72e5fb4efb Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:31:36 +0000
Subject: [PATCH 1055/1827] Modify test_globalfield to run via pytest

---
 tests/integrated/test-globalfield/test_globalfield.py | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100755 tests/integrated/test-globalfield/test_globalfield.py

diff --git a/tests/integrated/test-globalfield/test_globalfield.py b/tests/integrated/test-globalfield/test_globalfield.py
new file mode 100755
index 0000000000..adfcc39590
--- /dev/null
+++ b/tests/integrated/test-globalfield/test_globalfield.py
@@ -0,0 +1,4 @@
+
+
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./test_globalfield")

From dc2ac7b63a13ad2442be281f0f6a10e004442233 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:32:50 +0000
Subject: [PATCH 1056/1827] Modify test_integrate to run via pytest

---
 tests/integrated/test-integrate/test_integrate.py | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100755 tests/integrated/test-integrate/test_integrate.py

diff --git a/tests/integrated/test-integrate/test_integrate.py b/tests/integrated/test-integrate/test_integrate.py
new file mode 100755
index 0000000000..91a273f451
--- /dev/null
+++ b/tests/integrated/test-integrate/test_integrate.py
@@ -0,0 +1,4 @@
+
+
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./test_integrate")

From 2f0422e738d9cc0b6b199a65fc23f53bf6312f8c Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:36:32 +0000
Subject: [PATCH 1057/1827] Modify test_laplacexy_fv to run via pytest

---
 .../test-laplacexy-fv/test_laplacexy_fv.py    | 72 +++++++++----------
 1 file changed, 34 insertions(+), 38 deletions(-)

diff --git a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
index 664433ef98..7cbcec9973 100755
--- a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
+++ b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
@@ -10,7 +10,6 @@
 
 from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
-from sys import exit
 
 tol = 5.0e-8
 
@@ -37,47 +36,44 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
 ]
 
-print("Running LaplaceXY inversion test")
-success = True
+def test_laplacexy_fv():
 
-for nproc in [8]:
-    print("   %d processors...." % nproc)
-    for args in argslist:
-        cmd = "./test-laplacexy " + args
+    print("Running LaplaceXY inversion test")
+    success = True
 
-        shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
+    for nproc in [8]:
+        print("   %d processors...." % nproc)
+        for args in argslist:
+            cmd = "./test-laplacexy " + args
 
-        s, out = launch(
-            cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
-        )
-        if s == 134:
-            # PETSc did not recognise pctype option, probably means it
-            # was not compiled with hypre, so skip tests that need
-            # hypre to converge
-            print(
-                "hypre not available as pre-conditioner in PETSc. Re-running with "
-                + "pctype=shell..."
+            shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
+
+            s, out = launch(
+                cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
             )
-            _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+            if s == 134:
+                # PETSc did not recognise pctype option, probably means it
+                # was not compiled with hypre, so skip tests that need
+                # hypre to converge
+                print(
+                    "hypre not available as pre-conditioner in PETSc. Re-running with "
+                    + "pctype=shell..."
+                )
+                _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
 
-        f = open("run.log." + str(nproc), "w")
-        f.write(out)
-        f.close()
+            f = open("run.log." + str(nproc), "w")
+            f.write(out)
+            f.close()
 
-        # Collect output data
-        error = collect("max_error", path="data", info=False)
-        if error <= 0:
-            print("Convergence error")
-            success = False
-        elif error > tol:
-            print("Fail, maximum error is = " + str(error))
-            success = False
-        else:
-            print("Pass")
+            # Collect output data
+            error = collect("max_error", path="data", info=False)
+            if error <= 0:
+                print("Convergence error")
+                success = False
+            elif error > tol:
+                print("Fail, maximum error is = " + str(error))
+                success = False
+            else:
+                print("Pass")
 
-if success:
-    print(" => All LaplaceXY inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+    assert success, " => Some failed tests"

From 75e3f7f718b32ae9d031b7080c3efa975f487727 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:36:44 +0000
Subject: [PATCH 1058/1827] Modify test_laplace2 to run via pytest

---
 tests/integrated/test-laplace2/test_laplace2.py | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100755 tests/integrated/test-laplace2/test_laplace2.py

diff --git a/tests/integrated/test-laplace2/test_laplace2.py b/tests/integrated/test-laplace2/test_laplace2.py
new file mode 100755
index 0000000000..e2b4a802a6
--- /dev/null
+++ b/tests/integrated/test-laplace2/test_laplace2.py
@@ -0,0 +1,4 @@
+
+
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./test_laplace")

From 6392849be41bf9de91ffb281ca108cd772c69973 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:37:51 +0000
Subject: [PATCH 1059/1827] Modify test_laplacexy to run via pytest

---
 .../test-laplacexy/test_laplacexy.py          | 80 +++++++++----------
 1 file changed, 38 insertions(+), 42 deletions(-)

diff --git a/tests/integrated/test-laplacexy/test_laplacexy.py b/tests/integrated/test-laplacexy/test_laplacexy.py
index 0dd550cab0..885bfdf8b9 100755
--- a/tests/integrated/test-laplacexy/test_laplacexy.py
+++ b/tests/integrated/test-laplacexy/test_laplacexy.py
@@ -11,7 +11,6 @@
 
 from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
-from sys import exit
 
 tol_orth = 5.0e-8
 
@@ -52,51 +51,48 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1 laplacexy:pctype=hypre",
 ]
 
-print("Running LaplaceXY inversion test")
-success = True
+def test_laplacexy():
 
-for nproc in [8]:
-    print("   %d processors...." % nproc)
-    for nonorth, tol in [(False, tol_orth), (True, tol_nonorth)]:
-        for args in argslist:
-            if not nonorth:
-                args += " mesh:g12=0."
+    print("Running LaplaceXY inversion test")
+    success = True
 
-            cmd = "./test-laplacexy " + args
+    for nproc in [8]:
+        print("   %d processors...." % nproc)
+        for nonorth, tol in [(False, tol_orth), (True, tol_nonorth)]:
+            for args in argslist:
+                if not nonorth:
+                    args += " mesh:g12=0."
 
-            shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
+                cmd = "./test-laplacexy " + args
 
-            if "hypre" in args:
-                s, out = launch(cmd, nproc=nproc, pipe=True, verbose=True)
-                if s == 134:
-                    # PETSc did not recognise pctype option, probably means it
-                    # was not compiled with hypre, so skip tests that need
-                    # hypre to converge
-                    print(
-                        "hypre not available as pre-conditioner in PETSc. Skipping..."
-                    )
-                    continue
-            else:
-                s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+                shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
 
-            f = open("run.log." + str(nproc), "w")
-            f.write(out)
-            f.close()
+                if "hypre" in args:
+                    s, out = launch(cmd, nproc=nproc, pipe=True, verbose=True)
+                    if s == 134:
+                        # PETSc did not recognise pctype option, probably means it
+                        # was not compiled with hypre, so skip tests that need
+                        # hypre to converge
+                        print(
+                            "hypre not available as pre-conditioner in PETSc. Skipping..."
+                        )
+                        continue
+                else:
+                    s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
 
-            # Collect output data
-            error = collect("max_error", path="data", info=False)
-            if error <= 0:
-                print("Convergence error")
-                success = False
-            elif error > tol:
-                print("Fail, maximum error is = " + str(error))
-                success = False
-            else:
-                print("Pass")
+                f = open("run.log." + str(nproc), "w")
+                f.write(out)
+                f.close()
 
-if success:
-    print(" => All LaplaceXY inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+                # Collect output data
+                error = collect("max_error", path="data", info=False)
+                if error <= 0:
+                    print("Convergence error")
+                    success = False
+                elif error > tol:
+                    print("Fail, maximum error is = " + str(error))
+                    success = False
+                else:
+                    print("Pass")
+
+    assert success, " => Some failed tests"

From 4bc9c6718da8b696cf0027fb324d9fa98ab26115 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:39:25 +0000
Subject: [PATCH 1060/1827] Modify test_laplace_hypre3d to run via pytest

---
 .../test_laplace_hypre3d.py                   | 37 +++++++++----------
 1 file changed, 17 insertions(+), 20 deletions(-)

diff --git a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
index 595226cdc4..0886ea037d 100755
--- a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
+++ b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
@@ -4,7 +4,6 @@
 
 from boutdata import collect
 from boututils.run_wrapper import launch_safe
-from sys import exit
 
 test_directories = [
     ("data_slab_core", 1),
@@ -15,22 +14,20 @@
 
 tolerance = 1.0e-6
 
-success = True
-for directory, nproc in test_directories:
-    command = "test-laplace3d -d " + directory
-    print("running on", nproc, "processors:", command)
-    launch_safe(command, nproc=nproc)
-
-    error_max = collect("error_max", path=directory, info=False)
-
-    if error_max > tolerance:
-        print(directory + " failed with maximum error {}".format(error_max))
-        success = False
-    else:
-        print(directory + " passed with maximum error {}".format(error_max))
-
-if success:
-    print("All passed")
-    exit(0)
-else:
-    exit(1)
+def test_laplace_hypre3d():
+
+    success = True
+    for directory, nproc in test_directories:
+        command = "test-laplace3d -d " + directory
+        print("running on", nproc, "processors:", command)
+        launch_safe(command, nproc=nproc)
+
+        error_max = collect("error_max", path=directory, info=False)
+
+        if error_max > tolerance:
+            print(directory + " failed with maximum error {}".format(error_max))
+            success = False
+        else:
+            print(directory + " passed with maximum error {}".format(error_max))
+
+    assert success

From f23ec424cbe951cade582117f1f4697181775b44 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:43:12 +0000
Subject: [PATCH 1061/1827] Modify test_invertable_operator to run via pytest

---
 .../test_invertable_operator.py                     | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/tests/integrated/test-invertable-operator/test_invertable_operator.py b/tests/integrated/test-invertable-operator/test_invertable_operator.py
index 9ac26be701..a0b1dcb6d7 100755
--- a/tests/integrated/test-invertable-operator/test_invertable_operator.py
+++ b/tests/integrated/test-invertable-operator/test_invertable_operator.py
@@ -11,9 +11,9 @@
 from __future__ import print_function
 from __future__ import division
 
+import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
-from sys import exit
 
 nprocs = [1, 2]  # Number of processors to run on
 reltol = 1.0e-3  # Allowed relative tolerance
@@ -44,7 +44,7 @@ def run(path, nproc, log=False):
         print(
             "  => Failed (verification step - value is {s})".format(s=passVerification)
         )
-        exit(1)
+        pytest.fail()
 
     if maxRelErrLaplacians > reltol:
         print(
@@ -52,11 +52,10 @@ def run(path, nproc, log=False):
                 s=maxRelErrLaplacians
             )
         )
-        exit(1)
+        pytest.fail()
 
 
-for np in nprocs:
-    run("data", np)
+def test_invertable_operator():
 
-print("  => All tests passed")
-exit(0)
+    for np in nprocs:
+        run("data", np)

From 3ad7e134e0f331b76b4c93a78e099ac6025fbad9 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:45:19 +0000
Subject: [PATCH 1062/1827] Correct function name `test_fci_mpi()`

---
 tests/integrated/test-fci-mpi/test_fci_mpi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-fci-mpi/test_fci_mpi.py b/tests/integrated/test-fci-mpi/test_fci_mpi.py
index fb5bbfc496..3eacc5b811 100755
--- a/tests/integrated/test-fci-mpi/test_fci_mpi.py
+++ b/tests/integrated/test-fci-mpi/test_fci_mpi.py
@@ -14,7 +14,7 @@
 NSLICES = [1]
 
 
-def fci_mpi():
+def test_fci_mpi():
 
     COLLECT_KW = dict(info=False, xguards=False, yguards=False, path="data")
 

From 45041cb9383795a72e98637dff0555e8dc737dca Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:51:07 +0000
Subject: [PATCH 1063/1827] Modify test_collect to run via pytest

---
 tests/integrated/test-collect/test_collect.py | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/tests/integrated/test-collect/test_collect.py b/tests/integrated/test-collect/test_collect.py
index a1ebb8e3c7..3198e8a6dd 100755
--- a/tests/integrated/test-collect/test_collect.py
+++ b/tests/integrated/test-collect/test_collect.py
@@ -7,18 +7,14 @@
 from boutdata import collect
 import numpy as np
 
-shell_safe("make > make.log")
 
-shell_safe("./test-collect")
+def test_collect():
 
-# Try collecting data using incorrect case
-# This should be corrected automatically
-a = collect("A", path="data")
 
-if not np.allclose(a, 1.23):
-    print("Wrong value => Failed")
-    print(a)
-    exit(1)
+    shell_safe("./test-collect")
 
-print("Passed")
-exit(0)
+    # Try collecting data using incorrect case
+    # This should be corrected automatically
+    a = collect("A", path="data")
+
+    assert np.allclose(a, 1.23), f"Wrong value => Failed: {a}"

From 04f4b929ae48514c7cec11c6331075ed1ca4d825 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:53:41 +0000
Subject: [PATCH 1064/1827] Modify test_dataformat to run via pytest

---
 tests/integrated/test-dataformat/test_dataformat.py | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 tests/integrated/test-dataformat/test_dataformat.py

diff --git a/tests/integrated/test-dataformat/test_dataformat.py b/tests/integrated/test-dataformat/test_dataformat.py
new file mode 100644
index 0000000000..523ae00fc1
--- /dev/null
+++ b/tests/integrated/test-dataformat/test_dataformat.py
@@ -0,0 +1,4 @@
+
+
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./test_dataformat")

From 41f74341f5d7a580ff0f5dca78e4b872904a549a Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 16:55:58 +0000
Subject: [PATCH 1065/1827] Remove obsolete scripts for running tests via
 autotools

---
 tests/test_suite      | 1 -
 tests/test_suite_make | 1 -
 2 files changed, 2 deletions(-)
 delete mode 120000 tests/test_suite
 delete mode 120000 tests/test_suite_make

diff --git a/tests/test_suite b/tests/test_suite
deleted file mode 120000
index 860ee3ecc5..0000000000
--- a/tests/test_suite
+++ /dev/null
@@ -1 +0,0 @@
-integrated/test_suite
\ No newline at end of file
diff --git a/tests/test_suite_make b/tests/test_suite_make
deleted file mode 120000
index 083d1d6487..0000000000
--- a/tests/test_suite_make
+++ /dev/null
@@ -1 +0,0 @@
-integrated/test_suite_make
\ No newline at end of file

From b0ebaa9db179223093458e86eed09a4ca518662c Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 21:24:56 +0000
Subject: [PATCH 1066/1827] Fix merge error.

---
 tests/integrated/test-petsc_laplace/test_petsc_laplace.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
index d5e16203ef..d45a2ba1bd 100755
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
@@ -8,7 +8,7 @@
 # requires: all_tests
 # cores: 4
 
-from boututils.run_wrapper import build_and_log, shell, launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect, create_cache
 
 import pathlib

From 7e32a4562e30a02297fe7f77e2335b4923e1b098 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 21:44:56 +0000
Subject: [PATCH 1067/1827] Modify test_laplacexy2_hypre to run via pytest

---
 .../test_laplacexy2_hypre.py                  | 50 +++++++++----------
 1 file changed, 23 insertions(+), 27 deletions(-)

diff --git a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
index 7728b97785..0805f945f9 100755
--- a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
+++ b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
@@ -7,7 +7,6 @@
 # requires: hypre
 # cores: 8
 
-from sys import exit
 
 from boutdata.collect import collect
 from boututils.run_wrapper import launch_safe, shell
@@ -37,35 +36,32 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
 ]
 
-print("Running LaplaceXY inversion test")
-success = True
+def test_laplacexy2_hypre():
 
-for nproc in [8]:
-    print("   %d processors...." % nproc)
-    for args in argslist:
-        cmd = "./test-laplacexy " + args
+    print("Running LaplaceXY inversion test")
+    success = True
 
-        shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
+    for nproc in [8]:
+        print("   %d processors...." % nproc)
+        for args in argslist:
+            cmd = "./test-laplacexy " + args
 
-        s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+            shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
 
-        with open(f"run.log.{nproc}", "w") as f:
-            f.write(out)
+            s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
 
-        # Collect output data
-        error = collect("max_error", path="data", info=False)
-        if error <= 0:
-            print("Convergence error")
-            success = False
-        elif error > tol:
-            print("Fail, maximum error is = " + str(error))
-            success = False
-        else:
-            print("Pass")
+            with open(f"run.log.{nproc}", "w") as f:
+                f.write(out)
 
-if success:
-    print(" => All LaplaceXY inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+            # Collect output data
+            error = collect("max_error", path="data", info=False)
+            if error <= 0:
+                print("Convergence error")
+                success = False
+            elif error > tol:
+                print("Fail, maximum error is = " + str(error))
+                success = False
+            else:
+                print("Pass")
+
+    assert success, " => Some failed tests"

From 621fbe17cc6425e5408dc439e0e3edec826c3fd1 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 21:46:01 +0000
Subject: [PATCH 1068/1827] Modify test_petsc_laplace to run via pytest

---
 .../test-petsc_laplace/test_petsc_laplace.py  | 65 +++++++++----------
 1 file changed, 31 insertions(+), 34 deletions(-)

diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
index d45a2ba1bd..40763c4c30 100755
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
@@ -12,7 +12,6 @@
 from boutdata.collect import collect, create_cache
 
 import pathlib
-from sys import exit
 
 errors = [
     "max_error1",
@@ -24,36 +23,34 @@
 ]
 tol = 2e-4  # Absolute (?) tolerance
 
-print("Running PETSc Laplacian inversion test")
-success = True
-
-for nproc in [1, 2, 4]:
-    cmd = "./test_petsc_laplace"
-
-    shell(["rm data/BOUT.dmp.*.nc"])
-
-    print(f"   {nproc} processors....")
-    s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
-
-    pathlib.Path(f"run.log.{nproc}").write_text(out)
-    cache = create_cache(path="data", prefix="BOUT.dmp")
-
-    # Collect output data
-    for varname in errors:
-        print(f"      Checking {varname} ... ", end="")
-        error = collect(varname, path="data", info=False, datafile_cache=cache)
-        if error <= 0:
-            print("Convergence error")
-            success = False
-        elif error > tol:
-            print(f"Fail, maximum error is = {error:e}")
-            success = False
-        else:
-            print("Pass")
-
-if success:
-    print(" => All PETSc Laplacian inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+def test_petsc_laplace():
+
+
+    print("Running PETSc Laplacian inversion test")
+    success = True
+
+    for nproc in [1, 2, 4]:
+        cmd = "./test_petsc_laplace"
+
+        shell(["rm data/BOUT.dmp.*.nc"])
+
+        print(f"   {nproc} processors....")
+        s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+
+        pathlib.Path(f"run.log.{nproc}").write_text(out)
+        cache = create_cache(path="data", prefix="BOUT.dmp")
+
+        # Collect output data
+        for varname in errors:
+            print(f"      Checking {varname} ... ", end="")
+            error = collect(varname, path="data", info=False, datafile_cache=cache)
+            if error <= 0:
+                print("Convergence error")
+                success = False
+            elif error > tol:
+                print(f"Fail, maximum error is = {error:e}")
+                success = False
+            else:
+                print("Pass")
+
+    assert success, " => Some failed tests"

From 5a90ffaca16b2916fad47475189c39bd15ad0faa Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 21:47:33 +0000
Subject: [PATCH 1069/1827] Modify test_petsc_laplace_MAST_grid to run via
 pytest

---
 .../test_petsc_laplace_MAST_grid.py           | 73 +++++++++----------
 1 file changed, 34 insertions(+), 39 deletions(-)

diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
index ab8d1c1b4e..1821f0b725 100755
--- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
@@ -26,49 +26,44 @@
 
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
-from sys import stdout, exit
+from sys import stdout
 
 
-print(
-    "Running PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)"
-)
-success = True
+def test_petsc_laplace_MAST_grid():
 
-for nproc in [1, 2, 4]:
-    #  nxpe = 1
-    #  if nproc > 2:
-    #    nxpe = 2
-    for jy in [2, 34, 65, 81, 113]:
-        cmd = "./test_petsc_laplace_MAST_grid mesh:file=grids/grid_MAST_SOL_jyis{}.nc".format(
-            jy
-        )
+    print(
+        "Running PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)"
+    )
+    success = True
 
-        shell(["rm data/BOUT.dmp.*.nc"])
+    for nproc in [1, 2, 4]:
+        #  nxpe = 1
+        #  if nproc > 2:
+        #    nxpe = 2
+        for jy in [2, 34, 65, 81, 113]:
+            cmd = "./test_petsc_laplace_MAST_grid mesh:file=grids/grid_MAST_SOL_jyis{}.nc".format(
+                jy
+            )
 
-        print("   {} processors, grid_MAST_SOL_jyis{}".format(nproc, jy))
-        s, out = launch_safe(cmd, nproc=nproc, pipe=True)
-        f = open("run.log." + str(nproc), "w")
-        f.write(out)
-        f.close()
+            shell(["rm data/BOUT.dmp.*.nc"])
 
-        # Collect output data
-        for v in vars:
-            stdout.write("      Checking " + v[0] + " ... ")
-            error = collect(v[0], path="data", info=False)
-            if error <= 0:
-                print("Convergence error")
-                success = False
-            elif error > v[1]:
-                print("Fail, maximum error is = " + str(error))
-                success = False
-            else:
-                print("Pass")
+            print("   {} processors, grid_MAST_SOL_jyis{}".format(nproc, jy))
+            s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+            f = open("run.log." + str(nproc), "w")
+            f.write(out)
+            f.close()
 
-if success:
-    print(
-        " => All PETSc Laplacian inversion with non-identity metric (taken from grid for MAST SOL) tests passed"
-    )
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+            # Collect output data
+            for v in vars:
+                stdout.write("      Checking " + v[0] + " ... ")
+                error = collect(v[0], path="data", info=False)
+                if error <= 0:
+                    print("Convergence error")
+                    success = False
+                elif error > v[1]:
+                    print("Fail, maximum error is = " + str(error))
+                    success = False
+                else:
+                    print("Pass")
+
+    assert success, " => Some failed tests"

From 478e2a4348c55e74f0f910ea685a24da789d6e7b Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Mon, 2 Mar 2026 21:49:09 +0000
Subject: [PATCH 1070/1827] Modify test_region_iterator to run via pytest

---
 .../test_region_iterator.py                   | 35 +++++++++----------
 1 file changed, 16 insertions(+), 19 deletions(-)

diff --git a/tests/integrated/test-region-iterator/test_region_iterator.py b/tests/integrated/test-region-iterator/test_region_iterator.py
index f22196f0a9..3d9a78c820 100755
--- a/tests/integrated/test-region-iterator/test_region_iterator.py
+++ b/tests/integrated/test-region-iterator/test_region_iterator.py
@@ -14,7 +14,6 @@
 except:
     pass
 from boututils.run_wrapper import launch_safe
-from sys import exit
 
 
 flags = [""]
@@ -22,25 +21,23 @@
 code = 0  # Return code
 pipe = True
 
-for nproc in [1, 2]:  # Number of mpi procs
-    for mthread in [1]:  # Number of omp threads (not yet supported)
-        print("\t{n} processors and {m} threads".format(n=nproc, m=mthread))
 
-        for f in flags:
-            # Run the case
-            s, out = launch_safe(cmd + " " + f, nproc=nproc, pipe=pipe)
-            if pipe:
-                f = open("run.log." + str(nproc) + "." + str(mthread), "w")
-                f.write(out)
-                f.close()
+def test_region_iterator():
 
-            # If we've got here we know that cmd launched by launch_safe passed
-            # as otherwise it raises.
-            print("Passed")
+    for nproc in [1, 2]:  # Number of mpi procs
+        for mthread in [1]:  # Number of omp threads (not yet supported)
+            print("\t{n} processors and {m} threads".format(n=nproc, m=mthread))
 
-if code == 0:
-    print(" => All range iterator tests passed")
-else:
-    print(" => Some failed tests")
+            for f in flags:
+                # Run the case
+                s, out = launch_safe(cmd + " " + f, nproc=nproc, pipe=pipe)
+                if pipe:
+                    f = open("run.log." + str(nproc) + "." + str(mthread), "w")
+                    f.write(out)
+                    f.close()
 
-exit(code)
+                # If we've got here we know that cmd launched by launch_safe passed
+                # as otherwise it raises.
+                print("Passed")
+
+    assert code == 0, " => Some failed tests"

From 9756e1dbf186e6a2aef815e9b444181e1e56e9e2 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 3 Mar 2026 11:53:43 +0000
Subject: [PATCH 1071/1827] Remove unused import

---
 tests/integrated/test-fci-mpi/test_fci_mpi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-fci-mpi/test_fci_mpi.py b/tests/integrated/test-fci-mpi/test_fci_mpi.py
index 3eacc5b811..f34f2673bc 100755
--- a/tests/integrated/test-fci-mpi/test_fci_mpi.py
+++ b/tests/integrated/test-fci-mpi/test_fci_mpi.py
@@ -2,7 +2,7 @@
 #
 # Python script to run and analyse MMS test
 
-from boututils.run_wrapper import build_and_log, launch_safe
+from boututils.run_wrapper import launch_safe
 from boutdata.collect import collect
 import itertools
 

From 241e79044d97f085601e7708aa5e3d71d0917b8c Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Tue, 3 Mar 2026 11:54:29 +0000
Subject: [PATCH 1072/1827] Fix CMakeLists.txt for `test_fci_mpi`

integrated test, not mms.
---
 tests/integrated/test-fci-mpi/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-fci-mpi/CMakeLists.txt b/tests/integrated/test-fci-mpi/CMakeLists.txt
index 0abbbce099..2fcbf6a396 100644
--- a/tests/integrated/test-fci-mpi/CMakeLists.txt
+++ b/tests/integrated/test-fci-mpi/CMakeLists.txt
@@ -1,4 +1,4 @@
-bout_add_mms_test(
+bout_add_integrated_test(
   test-fci-mpi
   SOURCES fci_mpi.cxx
   USE_RUNTEST USE_DATA_BOUT_INP

From ca85ceb6c7ed5157b4e6296bf6b76dc9cb6297e6 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Wed, 4 Mar 2026 14:33:41 +0000
Subject: [PATCH 1073/1827] Fix test_backtrace

---
 .../test-backtrace/test_backtrace.py          | 22 ++++---------------
 1 file changed, 4 insertions(+), 18 deletions(-)

diff --git a/tests/integrated/test-backtrace/test_backtrace.py b/tests/integrated/test-backtrace/test_backtrace.py
index abeeba44f7..92d74fcb7c 100755
--- a/tests/integrated/test-backtrace/test_backtrace.py
+++ b/tests/integrated/test-backtrace/test_backtrace.py
@@ -14,24 +14,10 @@ def test_backtrace():
     except KeyError:
         pass
 
-    success = True
+    _, output = shell(["BOUT_SHOW_BACKTRACE=0 ./boutexcept"], pipe=True)
 
-    _, output = shell(["./boutexcept"], pipe=True)
-
-    if "troublemaker" in output:
-        success = False
-        pytest.fail("Fail: detected offending function name in output when not expected")
-
-    _, output = shell(["BOUT_SHOW_BACKTRACE=yes ./boutexcept"], pipe=True)
+    assert "troublemaker" not in output, f"Fail: detected offending function name in output when not expected\n{output}"
 
-    if "troublemaker" not in output:
-        success = False
-        print("Fail: did not detect offending function name in output when expected")
-
-    if success:
-        print("=> All BoutException backtrace tests passed")
-        exit(0)
-    assert success, f"Test failed"
+    _, output = shell(["./boutexcept"], pipe=True)
 
-    print("=> Some failed tests")
-    exit(1)
+    assert "troublemaker" in output, f"Fail: did not detect offending function name in output when expected\n{output}"

From 22ec1526a831a7a6e35ab682ea880addfcf54c1e Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Fri, 13 Mar 2026 11:09:10 +0000
Subject: [PATCH 1074/1827] Convert test_boutpp_print to from a shell script to
 python

---
 .../integrated/test-boutpp/print/CMakeLists.txt |  1 -
 tests/integrated/test-boutpp/print/runtest      | 14 --------------
 .../test-boutpp/print/test_boutpp_print.py      | 17 +++++++++++++++--
 3 files changed, 15 insertions(+), 17 deletions(-)
 delete mode 100755 tests/integrated/test-boutpp/print/runtest

diff --git a/tests/integrated/test-boutpp/print/CMakeLists.txt b/tests/integrated/test-boutpp/print/CMakeLists.txt
index 84b005df89..edc17cd407 100644
--- a/tests/integrated/test-boutpp/print/CMakeLists.txt
+++ b/tests/integrated/test-boutpp/print/CMakeLists.txt
@@ -1,6 +1,5 @@
 bout_add_integrated_test(
   test-boutpp-print
-  USE_RUNTEST
   EXTRA_FILES test/BOUT.inp test.py
   REQUIRES BOUT_ENABLE_PYTHON
 )
diff --git a/tests/integrated/test-boutpp/print/runtest b/tests/integrated/test-boutpp/print/runtest
deleted file mode 100755
index 4b68c692aa..0000000000
--- a/tests/integrated/test-boutpp/print/runtest
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/sh
-# requires boutpp
-# requires not make
-
-set -ex
-
-testit() {
-    msg="$@"
-    python3 test.py $msg > out.log
-    grep "$msg" out.log
-    grep "$msg" test/BOUT.log.0
-}
-
-testit Can we print to the log from python? 🎉  '__does_it_still__work {} {:s}'
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index 48a29195e0..af8a8c80a8 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -1,4 +1,17 @@
+import subprocess
 
 
-def test_runtest(assert_success_in_shell):
-    assert_success_in_shell("./runtest")
+def test_boutpp_print():
+
+    msg = 'Can we print to the log from python? 🎉 __does_it_still__work {} {:s}'
+    cmd = ["python3", "test.py"] + msg.split()
+
+    print(f"+ python3 test.py {msg} > out.log")
+    with open("out.log", "w") as f:
+        subprocess.run(cmd, stdout=f, check=True)
+
+    with open("out.log", "r") as f:
+        assert msg in f.read(), f"Error: '{msg}' not found in out.log"
+
+    with open("test/BOUT.log.0", "r") as f:
+        assert msg in f.read(), f"Error: '{msg}' not found in test/BOUT.log.0"

From cc5c27313b96607369efe162ec292c3aae99e5e1 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Fri, 13 Mar 2026 13:25:29 +0000
Subject: [PATCH 1075/1827] Skip test_fci_boundary if zoidberg not found

---
 tests/integrated/test-fci-boundary/test_fci_boundary.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/integrated/test-fci-boundary/test_fci_boundary.py b/tests/integrated/test-fci-boundary/test_fci_boundary.py
index 8317b5ff62..e01b66b8d3 100755
--- a/tests/integrated/test-fci-boundary/test_fci_boundary.py
+++ b/tests/integrated/test-fci-boundary/test_fci_boundary.py
@@ -3,12 +3,17 @@
 # Python script to run and analyse MMS test
 
 
+import os
+import pytest
 import numpy as np
 from boututils.run_wrapper import launch_safe
 from boututils.datafile import DataFile
 from boutdata.collect import collect
 
 
+if not os.path.exists(os.path.join(os.path.dirname(__file__), "grid.fci.nc")):
+    pytest.skip("grid.fci.nc not found (Zoidberg likely missing), skipping test.", allow_module_level=True)
+
 directory = "data"
 
 def collect(var):

From 4fc666dba38414075740533370c6b07f4f416661 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Fri, 13 Mar 2026 13:26:57 +0000
Subject: [PATCH 1076/1827] Add boutpp location to PYTHONPATH before running
 pytest

in run_integrated_tests.sh.
---
 tests/run_integrated_tests.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index 553daed9e4..2f5fab3add 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -1,4 +1,7 @@
 #!/bin/bash
 
+
+export PYTHONPATH='../tools/pylib'
+
 pytest -m "not serial" --cache-clear -n auto --dist=loadgroup integrated
 pytest -m serial integrated

From 74b5fa0e2277383fe14d91b290dfc7b192a9d7ee Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Fri, 13 Mar 2026 13:28:19 +0000
Subject: [PATCH 1077/1827] Pass through to pytest additional arguments given
 to run_integrated_tests

---
 tests/run_integrated_tests.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index 2f5fab3add..b3abe5c1f3 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -3,5 +3,5 @@
 
 export PYTHONPATH='../tools/pylib'
 
-pytest -m "not serial" --cache-clear -n auto --dist=loadgroup integrated
-pytest -m serial integrated
+pytest -m "not serial" --cache-clear -n auto --dist=loadgroup integrated $@
+pytest -m serial integrated $@

From c99c2f5ddbd7a54009cf19bbad0c70ce4364ef68 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Fri, 13 Mar 2026 13:45:52 +0000
Subject: [PATCH 1078/1827] Fix test_boutpp_print (don't split msg)

---
 tests/integrated/test-boutpp/print/test_boutpp_print.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index af8a8c80a8..373cde6e83 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -4,7 +4,7 @@
 def test_boutpp_print():
 
     msg = 'Can we print to the log from python? 🎉 __does_it_still__work {} {:s}'
-    cmd = ["python3", "test.py"] + msg.split()
+    cmd = ["python3", "test.py", msg]
 
     print(f"+ python3 test.py {msg} > out.log")
     with open("out.log", "w") as f:

From 0b3d631816d8dc2f02cade2819b2144b8da99845 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 14 Mar 2026 19:27:23 +0000
Subject: [PATCH 1079/1827] Set absolute path to boupp in PYTHONPATH

---
 tests/run_integrated_tests.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index b3abe5c1f3..5e2b397ac4 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
 
 
-export PYTHONPATH='../tools/pylib'
+HERE=$(cd "$(dirname "$0")" && pwd)
+export PYTHONPATH="$HERE/../tools/pylib"
 
 pytest -m "not serial" --cache-clear -n auto --dist=loadgroup integrated $@
 pytest -m serial integrated $@

From 45292e3e9f16d46b96c5dbef0eab71b3085f4576 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 14 Mar 2026 19:50:00 +0000
Subject: [PATCH 1080/1827] Add the pytest option console_output_style =
 "plain" to pyproject.toml

to prevent mangled console output due to concurrent processes.
---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index f7ccf83cff..f4cea9d822 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,6 +5,9 @@ requires = []
 build-backend = "backend"
 backend-path = ["tools/pylib/_boutpp_build/"]
 
+[tool.pytest.ini_options]
+console_output_style = "plain"
+
 [dependency-groups]
 dev = [
      "cmake~=4.2",

From d44ec6ab47715a1ffa0e3725506dc6542634c78b Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 14 Mar 2026 19:50:28 +0000
Subject: [PATCH 1081/1827] Copy pyproject.toml file when building

---
 CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 31374cad20..3fefa7c54c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -785,6 +785,11 @@ if(BOUT_TESTS)
     "${PROJECT_SOURCE_DIR}/tests/conftest.py"
     "${PROJECT_BINARY_DIR}/tests/conftest.py")
 
+  # Copy the pyproject.toml file
+  configure_file(
+    "${PROJECT_SOURCE_DIR}/tests/pyproject.toml"
+    "${PROJECT_BINARY_DIR}/tests/pyproject.toml")
+
   # Copy the pytest config file for the boutpp tests
   configure_file(
     "${PROJECT_SOURCE_DIR}/tests/integrated/test-boutpp/conftest.py"

From 585aaf79c5613fb5beb2a3a24e5abcb6fb5e9945 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 14 Mar 2026 20:03:31 +0000
Subject: [PATCH 1082/1827] Pre-build the project to prevent concurrent CMake
 race conditions

---
 tests/run_integrated_tests.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index 5e2b397ac4..53fb957964 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -1,8 +1,10 @@
 #!/bin/bash
 
-
 HERE=$(cd "$(dirname "$0")" && pwd)
 export PYTHONPATH="$HERE/../tools/pylib"
 
+# Pre-build the project to prevent concurrent CMake race conditions
+cmake --build "$HERE/.." # Compiles the parent directory (your build root)
+
 pytest -m "not serial" --cache-clear -n auto --dist=loadgroup integrated $@
 pytest -m serial integrated $@

From ba32f9f57933fc5af69f189786ed092436a5508f Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 14 Mar 2026 20:03:50 +0000
Subject: [PATCH 1083/1827] Fix copying the pyproject.toml file

---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3fefa7c54c..b8cd6b775c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -787,8 +787,8 @@ if(BOUT_TESTS)
 
   # Copy the pyproject.toml file
   configure_file(
-    "${PROJECT_SOURCE_DIR}/tests/pyproject.toml"
-    "${PROJECT_BINARY_DIR}/tests/pyproject.toml")
+    "${PROJECT_SOURCE_DIR}/pyproject.toml"
+    "${PROJECT_BINARY_DIR}/pyproject.toml")
 
   # Copy the pytest config file for the boutpp tests
   configure_file(

From 1e800febc7d680d34013b150b5800ac71bf172ed Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 14 Mar 2026 20:11:13 +0000
Subject: [PATCH 1084/1827] add quiet option to pytest command, to prevent
 concurrent console output from multiple processes

---
 tests/run_integrated_tests.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index 53fb957964..46caaf228c 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -6,5 +6,5 @@ export PYTHONPATH="$HERE/../tools/pylib"
 # Pre-build the project to prevent concurrent CMake race conditions
 cmake --build "$HERE/.." # Compiles the parent directory (your build root)
 
-pytest -m "not serial" --cache-clear -n auto --dist=loadgroup integrated $@
+pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q integrated $@
 pytest -m serial integrated $@

From 7b459b77902bc750de117efeae3c5870008617bf Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 14 Mar 2026 20:27:18 +0000
Subject: [PATCH 1085/1827] Use the absolute path to the `integrated` directory

so that the script can be run from other locations.
---
 tests/run_integrated_tests.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index 46caaf228c..a569d1cfd7 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -4,7 +4,7 @@ HERE=$(cd "$(dirname "$0")" && pwd)
 export PYTHONPATH="$HERE/../tools/pylib"
 
 # Pre-build the project to prevent concurrent CMake race conditions
-cmake --build "$HERE/.." # Compiles the parent directory (your build root)
+cmake --build "$HERE/.."
 
-pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q integrated $@
-pytest -m serial integrated $@
+pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$HERE/integrated" "$@"
+pytest -m serial "$HERE/integrated" "$@"

From 4681b195057d35b48a30ea430b16f569c758c2a1 Mon Sep 17 00:00:00 2001
From: tomc <tomc271@gmail.com>
Date: Sat, 14 Mar 2026 20:37:35 +0000
Subject: [PATCH 1086/1827] Refactor run_integrated_tests.sh (to use
 `PROJECT_ROOT`)

---
 tests/run_integrated_tests.sh | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index a569d1cfd7..48f72e7979 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -1,10 +1,11 @@
 #!/bin/bash
 
-HERE=$(cd "$(dirname "$0")" && pwd)
-export PYTHONPATH="$HERE/../tools/pylib"
+PROJECT_ROOT=$(cd "$(dirname "$0")/.." && pwd)
+
+export PYTHONPATH="$PROJECT_ROOT/tools/pylib"
 
 # Pre-build the project to prevent concurrent CMake race conditions
-cmake --build "$HERE/.."
+cmake --build "$PROJECT_ROOT"
 
-pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$HERE/integrated" "$@"
-pytest -m serial "$HERE/integrated" "$@"
+pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$PROJECT_ROOT/tests/integrated" "$@"
+pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"

From 7cefd0a66c08c5d19a393de2c1b56253c1b506c1 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 17 Mar 2026 14:04:13 +0000
Subject: [PATCH 1087/1827] Revert rename of MMS `runtest` files

This reverts (most of) commit 2609a8bf
---
 .../{test_advection_arakawa.py => runtest}    |   0
 .../{test_advection_central.py => runtest}    |   0
 .../{test_advection_upwind.py => runtest}     |   0
 .../{test_advection_weno3.py => runtest}      |   0
 .../advection/{test_advection.py => runtest}  |   0
 .../spatial/d2dx2/{test_d2dx2.py => runtest}  |   0
 .../spatial/d2dz2/{test_d2dz2.py => runtest}  |   0
 .../diffusion/{test_diffusion.py => runtest}  |   0
 tests/MMS/spatial/fci/runtest                 | 200 ++++++++++++++++++
 9 files changed, 200 insertions(+)
 rename tests/MMS/advection/arakawa/{test_advection_arakawa.py => runtest} (100%)
 rename tests/MMS/advection/central/{test_advection_central.py => runtest} (100%)
 rename tests/MMS/advection/upwind/{test_advection_upwind.py => runtest} (100%)
 rename tests/MMS/advection/weno3/{test_advection_weno3.py => runtest} (100%)
 rename tests/MMS/spatial/advection/{test_advection.py => runtest} (100%)
 rename tests/MMS/spatial/d2dx2/{test_d2dx2.py => runtest} (100%)
 rename tests/MMS/spatial/d2dz2/{test_d2dz2.py => runtest} (100%)
 rename tests/MMS/spatial/diffusion/{test_diffusion.py => runtest} (100%)
 create mode 100755 tests/MMS/spatial/fci/runtest

diff --git a/tests/MMS/advection/arakawa/test_advection_arakawa.py b/tests/MMS/advection/arakawa/runtest
similarity index 100%
rename from tests/MMS/advection/arakawa/test_advection_arakawa.py
rename to tests/MMS/advection/arakawa/runtest
diff --git a/tests/MMS/advection/central/test_advection_central.py b/tests/MMS/advection/central/runtest
similarity index 100%
rename from tests/MMS/advection/central/test_advection_central.py
rename to tests/MMS/advection/central/runtest
diff --git a/tests/MMS/advection/upwind/test_advection_upwind.py b/tests/MMS/advection/upwind/runtest
similarity index 100%
rename from tests/MMS/advection/upwind/test_advection_upwind.py
rename to tests/MMS/advection/upwind/runtest
diff --git a/tests/MMS/advection/weno3/test_advection_weno3.py b/tests/MMS/advection/weno3/runtest
similarity index 100%
rename from tests/MMS/advection/weno3/test_advection_weno3.py
rename to tests/MMS/advection/weno3/runtest
diff --git a/tests/MMS/spatial/advection/test_advection.py b/tests/MMS/spatial/advection/runtest
similarity index 100%
rename from tests/MMS/spatial/advection/test_advection.py
rename to tests/MMS/spatial/advection/runtest
diff --git a/tests/MMS/spatial/d2dx2/test_d2dx2.py b/tests/MMS/spatial/d2dx2/runtest
similarity index 100%
rename from tests/MMS/spatial/d2dx2/test_d2dx2.py
rename to tests/MMS/spatial/d2dx2/runtest
diff --git a/tests/MMS/spatial/d2dz2/test_d2dz2.py b/tests/MMS/spatial/d2dz2/runtest
similarity index 100%
rename from tests/MMS/spatial/d2dz2/test_d2dz2.py
rename to tests/MMS/spatial/d2dz2/runtest
diff --git a/tests/MMS/spatial/diffusion/test_diffusion.py b/tests/MMS/spatial/diffusion/runtest
similarity index 100%
rename from tests/MMS/spatial/diffusion/test_diffusion.py
rename to tests/MMS/spatial/diffusion/runtest
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
new file mode 100755
index 0000000000..a93f4d3aff
--- /dev/null
+++ b/tests/MMS/spatial/fci/runtest
@@ -0,0 +1,200 @@
+#!/usr/bin/env python3
+#
+# Python script to run and analyse MMS test
+#
+
+# Cores: 2
+# requires: zoidberg
+
+from boututils.run_wrapper import build_and_log, launch_safe
+from boutdata.collect import collect
+import boutconfig as conf
+
+from numpy import array, log, polyfit, linspace, arange
+
+import pickle
+
+from sys import stdout
+
+import zoidberg as zb
+
+nx = 3  # Not changed for these tests
+
+# Resolution in y and z
+nlist = [8, 16, 32, 64, 128]
+
+# Number of parallel slices (in each direction)
+nslices = [1]
+
+directory = "data"
+
+nproc = 2
+mthread = 2
+
+
+success = True
+
+error_2 = {}
+error_inf = {}
+method_orders = {}
+
+# Run with periodic Y?
+yperiodic = True
+
+failures = []
+
+build_and_log("FCI MMS test")
+
+for nslice in nslices:
+    error_2[nslice] = []
+    error_inf[nslice] = []
+
+    # Which central difference scheme to use and its expected order
+    order = nslice * 2
+    method_orders[nslice] = {"name": "C{}".format(order), "order": order}
+
+    for n in nlist:
+        # Define the magnetic field using new poloidal gridding method
+        # Note that the Bz and Bzprime parameters here must be the same as in mms.py
+        field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
+        # Create rectangular poloidal grids
+        poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(nx, n, 0.1, 1.0, MXG=1)
+        # Set the ylength and y locations
+        ylength = 10.0
+
+        if yperiodic:
+            ycoords = linspace(0.0, ylength, n, endpoint=False)
+        else:
+            # Doesn't include the end points
+            ycoords = (arange(n) + 0.5) * ylength / float(n)
+
+        # Create the grid
+        grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
+        # Make and write maps
+        from scipy.interpolate import RectBivariateSpline as RBS
+
+        def myRBS(a, b, c):
+            mx, my = c.shape
+            kx = max(mx - 1, 1)
+            kx = min(kx, 3)
+            return RBS(a, b, c, kx=kx)
+
+        zb.poloidal_grid.RectBivariateSpline = myRBS
+        maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
+        zb.write_maps(
+            grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True
+        )
+
+        args = " MZ={} MYG={} mesh:paralleltransform:y_periodic={} mesh:ddy:first={}".format(
+            n, nslice, yperiodic, method_orders[nslice]["name"]
+        )
+
+        # Command to run
+        cmd = "./fci_mms " + args
+
+        print("Running command: " + cmd)
+
+        # Launch using MPI
+        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
+
+        # Save output to log file
+        with open("run.log." + str(n), "w") as f:
+            f.write(out)
+
+        if s:
+            print("Run failed!\nOutput was:\n")
+            print(out)
+            exit(s)
+
+        # Collect data
+        l_2 = collect(
+            "l_2", tind=[1, 1], info=False, path=directory, xguards=False, yguards=False
+        )
+        l_inf = collect(
+            "l_inf",
+            tind=[1, 1],
+            info=False,
+            path=directory,
+            xguards=False,
+            yguards=False,
+        )
+
+        error_2[nslice].append(l_2)
+        error_inf[nslice].append(l_inf)
+
+        print("Errors : l-2 {:f} l-inf {:f}".format(l_2, l_inf))
+
+    dx = 1.0 / array(nlist)
+
+    # Calculate convergence order
+    fit = polyfit(log(dx), log(error_2[nslice]), 1)
+    order = fit[0]
+    stdout.write("Convergence order = {:f} (fit)".format(order))
+
+    order = log(error_2[nslice][-2] / error_2[nslice][-1]) / log(dx[-2] / dx[-1])
+    stdout.write(", {:f} (small spacing)".format(order))
+
+    # Should be close to the expected order
+    if order > method_orders[nslice]["order"] * 0.95:
+        print("............ PASS\n")
+    else:
+        print("............ FAIL\n")
+        success = False
+        failures.append(method_orders[nslice]["name"])
+
+
+with open("fci_mms.pkl", "wb") as output:
+    pickle.dump(nlist, output)
+    for nslice in nslices:
+        pickle.dump(error_2[nslice], output)
+        pickle.dump(error_inf[nslice], output)
+
+# Do we want to show the plot as well as save it to file.
+showPlot = True
+
+if False:
+    try:
+        # Plot using matplotlib if available
+        import matplotlib.pyplot as plt
+
+        fig, ax = plt.subplots(1, 1)
+
+        for nslice in nslices:
+            ax.plot(
+                dx,
+                error_2[nslice],
+                "-",
+                label="{} $l_2$".format(method_orders[nslice]["name"]),
+            )
+            ax.plot(
+                dx,
+                error_inf[nslice],
+                "--",
+                label="{} $l_\\inf$".format(method_orders[nslice]["name"]),
+            )
+        ax.legend(loc="upper left")
+        ax.grid()
+        ax.set_yscale("log")
+        ax.set_xscale("log")
+        ax.set_title("error scaling")
+        ax.set_xlabel(r"Mesh spacing $\delta x$")
+        ax.set_ylabel("Error norm")
+
+        plt.savefig("fci_mms.pdf")
+
+        print("Plot saved to fci_mms.pdf")
+
+        if showPlot:
+            plt.show()
+        plt.close()
+    except ImportError:
+        print("No matplotlib")
+
+if success:
+    print("All tests passed")
+    exit(0)
+else:
+    print("Some tests failed:")
+    for failure in failures:
+        print("\t" + failure)
+    exit(1)

From a48c09339646dadbeae41e32add8969a72a35a49 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 17 Mar 2026 13:07:55 +0000
Subject: [PATCH 1088/1827] Revert inclusion of MMS tests when copying test
 files to build

---
 cmake/BOUT++functions.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 9819f454c7..e28713a98f 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -265,7 +265,7 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()
 
-  string(REGEX REPLACE "^(test-|MMS-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
+  string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
   string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
   string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
   bout_copy_file(${TEST_FILENAME})

From 94c11c8974bf343fe6cb5f5a30b8186e538a4b00 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 17 Mar 2026 13:20:43 +0000
Subject: [PATCH 1089/1827] Make cmake test file copying apply only to
 integrated tests

Moved from `bout_add_integrated_or_mms_test` function to `bout_add_integrated_test` function.
---
 cmake/BOUT++functions.cmake | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index e28713a98f..6cc1697d5d 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -265,11 +265,6 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()
 
-  string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
-  string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
-  string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
-  bout_copy_file(${TEST_FILENAME})
-
   if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest)
     bout_copy_file(runtest)
   endif()
@@ -297,6 +292,10 @@ function(bout_add_integrated_test TESTNAME)
   bout_add_integrated_or_mms_test(
     build-check-integrated-tests ${TESTNAME} ${ARGV}
   )
+  string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
+  string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
+  string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
+  bout_copy_file(${TEST_FILENAME})
 endfunction()
 
 # Add a new MMS test. See `bout_add_integrated_or_mms_test` for arguments

From 07aa4313c99b62218124f8c0bf2aa3e314ec43b1 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 17 Mar 2026 14:31:48 +0000
Subject: [PATCH 1090/1827] Revert "Rename runtest file to test-foo.py for each
 MMS test"

This reverts commit 3bf60130a01e433494d7f89bb99009d7025026b0.
---
 tests/MMS/advection/{test_advection.py => runtest}                | 0
 tests/MMS/bracket/{test_bracket.py => runtest}                    | 0
 tests/MMS/derivatives3/{test_derivatives3.py => runtest}          | 0
 tests/MMS/diffusion/{test_diffusion.py => runtest}                | 0
 tests/MMS/diffusion2/{test_diffusion2.py => runtest}              | 0
 tests/MMS/hw/{test_hw.py => runtest}                              | 0
 tests/MMS/laplace/{test_laplace.py => runtest}                    | 0
 .../shiftedmetricinterp/{test_shiftedmetricinterp.py => runtest}  | 0
 tests/MMS/time-petsc/{test_time_petsc.py => runtest}              | 0
 tests/MMS/time/{test_time.py => runtest}                          | 0
 tests/MMS/upwinding3/{test_upwinding3.py => runtest}              | 0
 tests/MMS/wave-1d-y/{test_wave_1d_y.py => runtest}                | 0
 tests/MMS/wave-1d/{test_wave_1d.py => runtest}                    | 0
 13 files changed, 0 insertions(+), 0 deletions(-)
 rename tests/MMS/advection/{test_advection.py => runtest} (100%)
 rename tests/MMS/bracket/{test_bracket.py => runtest} (100%)
 rename tests/MMS/derivatives3/{test_derivatives3.py => runtest} (100%)
 rename tests/MMS/diffusion/{test_diffusion.py => runtest} (100%)
 rename tests/MMS/diffusion2/{test_diffusion2.py => runtest} (100%)
 rename tests/MMS/hw/{test_hw.py => runtest} (100%)
 rename tests/MMS/laplace/{test_laplace.py => runtest} (100%)
 rename tests/MMS/shiftedmetricinterp/{test_shiftedmetricinterp.py => runtest} (100%)
 rename tests/MMS/time-petsc/{test_time_petsc.py => runtest} (100%)
 rename tests/MMS/time/{test_time.py => runtest} (100%)
 rename tests/MMS/upwinding3/{test_upwinding3.py => runtest} (100%)
 rename tests/MMS/wave-1d-y/{test_wave_1d_y.py => runtest} (100%)
 rename tests/MMS/wave-1d/{test_wave_1d.py => runtest} (100%)

diff --git a/tests/MMS/advection/test_advection.py b/tests/MMS/advection/runtest
similarity index 100%
rename from tests/MMS/advection/test_advection.py
rename to tests/MMS/advection/runtest
diff --git a/tests/MMS/bracket/test_bracket.py b/tests/MMS/bracket/runtest
similarity index 100%
rename from tests/MMS/bracket/test_bracket.py
rename to tests/MMS/bracket/runtest
diff --git a/tests/MMS/derivatives3/test_derivatives3.py b/tests/MMS/derivatives3/runtest
similarity index 100%
rename from tests/MMS/derivatives3/test_derivatives3.py
rename to tests/MMS/derivatives3/runtest
diff --git a/tests/MMS/diffusion/test_diffusion.py b/tests/MMS/diffusion/runtest
similarity index 100%
rename from tests/MMS/diffusion/test_diffusion.py
rename to tests/MMS/diffusion/runtest
diff --git a/tests/MMS/diffusion2/test_diffusion2.py b/tests/MMS/diffusion2/runtest
similarity index 100%
rename from tests/MMS/diffusion2/test_diffusion2.py
rename to tests/MMS/diffusion2/runtest
diff --git a/tests/MMS/hw/test_hw.py b/tests/MMS/hw/runtest
similarity index 100%
rename from tests/MMS/hw/test_hw.py
rename to tests/MMS/hw/runtest
diff --git a/tests/MMS/laplace/test_laplace.py b/tests/MMS/laplace/runtest
similarity index 100%
rename from tests/MMS/laplace/test_laplace.py
rename to tests/MMS/laplace/runtest
diff --git a/tests/MMS/shiftedmetricinterp/test_shiftedmetricinterp.py b/tests/MMS/shiftedmetricinterp/runtest
similarity index 100%
rename from tests/MMS/shiftedmetricinterp/test_shiftedmetricinterp.py
rename to tests/MMS/shiftedmetricinterp/runtest
diff --git a/tests/MMS/time-petsc/test_time_petsc.py b/tests/MMS/time-petsc/runtest
similarity index 100%
rename from tests/MMS/time-petsc/test_time_petsc.py
rename to tests/MMS/time-petsc/runtest
diff --git a/tests/MMS/time/test_time.py b/tests/MMS/time/runtest
similarity index 100%
rename from tests/MMS/time/test_time.py
rename to tests/MMS/time/runtest
diff --git a/tests/MMS/upwinding3/test_upwinding3.py b/tests/MMS/upwinding3/runtest
similarity index 100%
rename from tests/MMS/upwinding3/test_upwinding3.py
rename to tests/MMS/upwinding3/runtest
diff --git a/tests/MMS/wave-1d-y/test_wave_1d_y.py b/tests/MMS/wave-1d-y/runtest
similarity index 100%
rename from tests/MMS/wave-1d-y/test_wave_1d_y.py
rename to tests/MMS/wave-1d-y/runtest
diff --git a/tests/MMS/wave-1d/test_wave_1d.py b/tests/MMS/wave-1d/runtest
similarity index 100%
rename from tests/MMS/wave-1d/test_wave_1d.py
rename to tests/MMS/wave-1d/runtest

From b22da3095570ee83bae2adbdfcdeaef7e2de3de8 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 17 Mar 2026 14:35:48 +0000
Subject: [PATCH 1091/1827] Revert "Change filename Test run by tpc522 on Mon
 Nov  3 17:45:34 2025"

This reverts commit de9da0f03dc8a518f5ee22aef6c7e8581738762c.
---
 tests/MMS/advection/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/MMS/advection/CMakeLists.txt b/tests/MMS/advection/CMakeLists.txt
index b2a037bac6..1e08b97cd1 100644
--- a/tests/MMS/advection/CMakeLists.txt
+++ b/tests/MMS/advection/CMakeLists.txt
@@ -3,7 +3,7 @@ target_link_libraries(MMS-advection bout++)
 set_target_properties(MMS-advection PROPERTIES FOLDER tests/MMS)
 set_target_properties(MMS-advection PROPERTIES OUTPUT_NAME advection)
 add_dependencies(build-check-mms-tests MMS-advection)
-bout_copy_file(test_advection.py)
+bout_copy_file(runtest)
 bout_copy_file(data/BOUT.inp)
 
 add_subdirectory(arakawa)

From e6f9cb7eec269b75fc5ce8dddbfa346c135ffd75 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 17 Mar 2026 15:18:17 +0000
Subject: [PATCH 1092/1827] Convert test_laplacexy_short to run via pytest

---
 .../test_laplacexy_short.py                   | 135 +++++++++---------
 1 file changed, 66 insertions(+), 69 deletions(-)

diff --git a/tests/integrated/test-laplacexy-short/test_laplacexy_short.py b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
index 0ed5c6ff63..908e812ce9 100755
--- a/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
+++ b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
@@ -10,82 +10,79 @@
 
 from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
-from sys import exit
 
-tol = 5.0e-8
 
-argslist = [
-    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet "
-    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet",
-    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann "
-    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann",
-    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=free_o3 "
-    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3",
-    #'laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=dirichlet '
-    #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
-    #'laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann '
-    #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann',
-    #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet '
-    #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
-    #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann '
-    #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann',
-    #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=dirichlet '
-    #'f:bndry_xin=neumann f:bndry_xout=neumann f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
-    "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann "
-    "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann",
-    "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=free_o3 "
-    "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3",
-    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann "
-    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
-    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=free_o3 "
-    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1",
-    "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann "
-    "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
-    "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=free_o3 "
-    "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1",
-]
+def test_laplacexy_short():
 
-print("Running LaplaceXY inversion test")
-success = True
+    tol = 5.0e-8
 
-for nproc in [8]:
-    print("   %d processors...." % nproc)
-    for args in argslist:
-        cmd = "./test-laplacexy " + args
+    argslist = [
+        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet "
+        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet",
+        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann "
+        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann",
+        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=free_o3 "
+        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3",
+        #'laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=dirichlet '
+        #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
+        #'laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann '
+        #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann',
+        #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet '
+        #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
+        #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann '
+        #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann',
+        #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=dirichlet '
+        #'f:bndry_xin=neumann f:bndry_xout=neumann f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
+        "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann "
+        "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann",
+        "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=free_o3 "
+        "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3",
+        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann "
+        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
+        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=free_o3 "
+        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1",
+        "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann "
+        "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
+        "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=free_o3 "
+        "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1",
+    ]
 
-        shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
+    print("Running LaplaceXY inversion test")
+    success = True
 
-        s, out = launch(
-            cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
-        )
-        if s == 134:
-            # PETSc did not recognise pctype option, probably means it
-            # was not compiled with hypre, so skip tests that need
-            # hypre to converge
-            print(
-                "hypre not available as pre-conditioner in PETSc. Re-running with "
-                + "pctype=shell..."
+    for nproc in [8]:
+        print("   %d processors...." % nproc)
+        for args in argslist:
+            cmd = "./test-laplacexy " + args
+
+            shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
+
+            s, out = launch(
+                cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
             )
-            _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+            if s == 134:
+                # PETSc did not recognise pctype option, probably means it
+                # was not compiled with hypre, so skip tests that need
+                # hypre to converge
+                print(
+                    "hypre not available as pre-conditioner in PETSc. Re-running with "
+                    + "pctype=shell..."
+                )
+                _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
 
-        f = open("run.log." + str(nproc), "w")
-        f.write(out)
-        f.close()
+            f = open("run.log." + str(nproc), "w")
+            f.write(out)
+            f.close()
 
-        # Collect output data
-        error = collect("max_error", path="data", info=False)
-        if error <= 0:
-            print("Convergence error")
-            success = False
-        elif error > tol:
-            print("Fail, maximum error is = " + str(error))
-            success = False
-        else:
-            print("Pass")
+            # Collect output data
+            error = collect("max_error", path="data", info=False)
+            if error <= 0:
+                print("Convergence error")
+                success = False
+            elif error > tol:
+                print("Fail, maximum error is = " + str(error))
+                success = False
+            else:
+                print("Pass")
 
-if success:
-    print(" => All LaplaceXY inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+    assert success, " => Some failed tests"

From 3d193033e5b1c2390a2f671c6b9af38af719048a Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 17 Mar 2026 15:46:06 +0000
Subject: [PATCH 1093/1827] Convert test_laplacexz to run via pytest

---
 .../test-laplacexz/test_laplacexz.py          | 61 +++++++++----------
 1 file changed, 29 insertions(+), 32 deletions(-)

diff --git a/tests/integrated/test-laplacexz/test_laplacexz.py b/tests/integrated/test-laplacexz/test_laplacexz.py
index 26886287f8..2853933637 100755
--- a/tests/integrated/test-laplacexz/test_laplacexz.py
+++ b/tests/integrated/test-laplacexz/test_laplacexz.py
@@ -10,45 +10,42 @@
 from boututils.run_wrapper import shell, launch_safe, getmpirun
 from boutdata.collect import collect
 import numpy as np
-from sys import exit
 
-tol = 1e-10  # Absolute tolerance
 
-MPIRUN = getmpirun()
+def test_laplacexz():
 
-print("Running LaplaceXZ test")
-success = True
+    tol = 1e-10  # Absolute tolerance
 
-for nproc in [1, 2, 4]:
-    nxpe = nproc
+    MPIRUN = getmpirun()
 
-    cmd = "./test-laplacexz nxpe=" + str(nxpe)
+    print("Running LaplaceXZ test")
+    success = True
 
-    shell(["rm data/BOUT.dmp.*.nc"])
+    for nproc in [1, 2, 4]:
+        nxpe = nproc
 
-    print("   %d processors (nxpe = %d)...." % (nproc, nxpe))
-    s, out = launch_safe(cmd, runcmd=MPIRUN, nproc=nproc, mthread=1, pipe=True)
-    with open("run.log." + str(nproc), "w") as f:
-        f.write(out)
+        cmd = "./test-laplacexz nxpe=" + str(nxpe)
 
-    # Collect output data
-    f = collect("f", path="data", info=False)
-    f2 = collect("f2", path="data", info=False)
-    print("      Checking tolerance... ")
-    # Compare benchmark and output
-    if np.shape(f) != np.shape(f2):
-        print("Fail, wrong shape")
-        success = False
-    diff = np.max(np.abs(f2 - f))
-    if diff > tol:
-        print("Fail, maximum difference = " + str(diff))
-        success = False
-    else:
-        print("Pass")
+        shell(["rm data/BOUT.dmp.*.nc"])
 
-if success:
-    print(" => LaplaceXZ inversion test passed")
-    exit(0)
+        print("   %d processors (nxpe = %d)...." % (nproc, nxpe))
+        s, out = launch_safe(cmd, runcmd=MPIRUN, nproc=nproc, mthread=1, pipe=True)
+        with open("run.log." + str(nproc), "w") as f:
+            f.write(out)
 
-print(" => LaplaceXZ test failed")
-exit(1)
+        # Collect output data
+        f = collect("f", path="data", info=False)
+        f2 = collect("f2", path="data", info=False)
+        print("      Checking tolerance... ")
+        # Compare benchmark and output
+        if np.shape(f) != np.shape(f2):
+            print("Fail, wrong shape")
+            success = False
+        diff = np.max(np.abs(f2 - f))
+        if diff > tol:
+            print("Fail, maximum difference = " + str(diff))
+            success = False
+        else:
+            print("Pass")
+
+    assert success, " => LaplaceXZ test failed"

From 07d7addbce7622ce599baccd0af63c92ffcd33b0 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 17 Mar 2026 15:51:11 +0000
Subject: [PATCH 1094/1827] Convert test_slepc_solver to run via pytest

---
 .../test-slepc-solver/test_slepc_solver.py    | 22 ++++++++-----------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/tests/integrated/test-slepc-solver/test_slepc_solver.py b/tests/integrated/test-slepc-solver/test_slepc_solver.py
index 907840316d..6d359f6f9e 100755
--- a/tests/integrated/test-slepc-solver/test_slepc_solver.py
+++ b/tests/integrated/test-slepc-solver/test_slepc_solver.py
@@ -7,20 +7,16 @@
 from numpy import isclose
 
 
-print("Running SLEPc eigen solver test")
-status, out = launch_safe("./test-slepc-solver", nproc=1, pipe=True, verbose=True)
+def test_slepc_solver():
 
-with open("run.log", "w") as f:
-    f.write(out)
+    print("Running SLEPc eigen solver test")
+    status, out = launch_safe("./test-slepc-solver", nproc=1, pipe=True, verbose=True)
 
-eigenvalues = collect("t_array", path="data", info=False)
+    with open("run.log", "w") as f:
+        f.write(out)
 
-expected_eigenvalues = [0.0, 1.0]
+    eigenvalues = collect("t_array", path="data", info=False)
 
-if isclose(expected_eigenvalues, eigenvalues).all():
-    print(" => SLEPc test passed")
-    exit(0)
-else:
-    print(" => SLEPc test failed")
-    print("    Eigenvalues:", eigenvalues)
-    exit(1)
+    expected_eigenvalues = [0.0, 1.0]
+
+    assert isclose(expected_eigenvalues, eigenvalues).all(), " => SLEPc test failed\nEigenvalues: {eigenvalues}"

From dd003e5c114b4cb5a7cf749792c09395337a1dc9 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 17 Mar 2026 22:26:00 +0000
Subject: [PATCH 1095/1827] Only copy test files if test has not been skipped

(due to conflicts or unmet requirements)
in `bout_add_integrated_test` function.
---
 cmake/BOUT++functions.cmake | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 6cc1697d5d..9496a09e8c 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -292,10 +292,12 @@ function(bout_add_integrated_test TESTNAME)
   bout_add_integrated_or_mms_test(
     build-check-integrated-tests ${TESTNAME} ${ARGV}
   )
-  string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
-  string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
-  string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
-  bout_copy_file(${TEST_FILENAME})
+  if(TARGET ${TESTNAME}) # Don't copy if the test has been skipped
+    string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
+    string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
+    string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
+    bout_copy_file(${TEST_FILENAME})
+  endif()
 endfunction()
 
 # Add a new MMS test. See `bout_add_integrated_or_mms_test` for arguments

From b9841d1028f12a1fa5e8cf5491d2d57708839e56 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 18 Mar 2026 14:52:10 +0000
Subject: [PATCH 1096/1827] Update .ci_with_cmake.sh to use the cmake target
 that correctly handles both Pytest and CTest

---
 .ci_with_cmake.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_with_cmake.sh b/.ci_with_cmake.sh
index 71ea2204e2..c664d3d66e 100755
--- a/.ci_with_cmake.sh
+++ b/.ci_with_cmake.sh
@@ -13,7 +13,7 @@ fi
 
 cmake --build build --target build-check -j 2
 cd build
-ctest --output-on-failure --timeout 300
+cmake --build . --target check
 
 export LD_LIBRARY_PATH=/home/runner/local/lib:$LD_LIBRARY_PATH
 

From 2b9d46a43ed0598203f5a74cdaca25d506f46abe Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 18 Mar 2026 15:14:25 +0000
Subject: [PATCH 1097/1827] Update the command set in BOUT++functions.cmake to
 make ctest use pytest for integrated tests

(rather than running ``./runtest`)

* The specific python test filename (e.g., `test_foo.py`) is generated in `bout_add_integrated_test`.
* then passed to `bout_add_integrated_or_mms_test` via a new `PYTHON_TEST_FILE` argument.
* Modified `add_test()` to execute `pytest <filename>` for integrated tests (preserves the `./runtest` fallback for MMS tests).
---
 cmake/BOUT++functions.cmake | 30 +++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 11 deletions(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 9496a09e8c..88687e39d7 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -172,7 +172,7 @@ endfunction()
 #
 function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
   set(options USE_RUNTEST USE_DATA_BOUT_INP)
-  set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME)
+  set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME PYTHON_TEST_FILE)
   set(multiValueArgs SOURCES EXTRA_FILES REQUIRES CONFLICTS TESTARGS
                      EXTRA_DEPENDS
   )
@@ -253,10 +253,15 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
   endif()
 
   # Set the actual test command
-  if (BOUT_TEST_OPTIONS_USE_RUNTEST)
-    add_test(NAME ${TESTNAME}
-      COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS}
-      )
+  if(BOUT_TEST_OPTIONS_USE_RUNTEST)
+    if(BOUT_TEST_OPTIONS_PYTHON_TEST_FILE)
+      # It's an integrated test with a specific python file
+      add_test(NAME ${TESTNAME} COMMAND pytest ${BOUT_TEST_OPTIONS_PYTHON_TEST_FILE} ${BOUT_TEST_OPTIONS_TESTARGS})
+    else()
+      # It's an MMS test still using the 'runtest' script
+      add_test(NAME ${TESTNAME} COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS})
+    endif()
+
     set_tests_properties(
       ${TESTNAME} PROPERTIES ENVIRONMENT
                              PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
@@ -289,17 +294,20 @@ endfunction()
 
 # Add a new integrated test. See `bout_add_integrated_or_mms_test` for arguments
 function(bout_add_integrated_test TESTNAME)
+  # Construct the Python test filename
+  string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
+  string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
+  string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
+
   bout_add_integrated_or_mms_test(
-    build-check-integrated-tests ${TESTNAME} ${ARGV}
+    build-check-integrated-tests ${TESTNAME} PYTHON_TEST_FILE ${TEST_FILENAME} ${ARGV}
   )
-  if(TARGET ${TESTNAME}) # Don't copy if the test has been skipped
-    string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
-    string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
-    string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
+
+  # Only copy the file if the test wasn't skipped due to missing requirements
+  if(TARGET ${TESTNAME})
     bout_copy_file(${TEST_FILENAME})
   endif()
 endfunction()
-
 # Add a new MMS test. See `bout_add_integrated_or_mms_test` for arguments
 function(bout_add_mms_test TESTNAME)
   bout_add_integrated_or_mms_test(build-check-mms-tests ${TESTNAME} ${ARGV})

From 19535652d91089573b9195e54ee1fffcc32263ae Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 24 Mar 2026 12:37:09 +0000
Subject: [PATCH 1098/1827] Let cmake's configure_file command insert the build
 directory path into run_integrated_tests.sh

---
 tests/run_integrated_tests.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index 48f72e7979..034627085f 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-PROJECT_ROOT=$(cd "$(dirname "$0")/.." && pwd)
+PROJECT_ROOT=${PROJECT_BINARY_DIR}
 
 export PYTHONPATH="$PROJECT_ROOT/tools/pylib"
 

From 81631d5642e8c38bccd20bf713a83e756c638ab1 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 27 Mar 2026 11:12:16 +0000
Subject: [PATCH 1099/1827] Fix rebase errors

---
 tests/integrated/test-laplace/test_laplace.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-laplace/test_laplace.py b/tests/integrated/test-laplace/test_laplace.py
index cd42f9c734..5f09b0203d 100755
--- a/tests/integrated/test-laplace/test_laplace.py
+++ b/tests/integrated/test-laplace/test_laplace.py
@@ -10,6 +10,7 @@
 
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect, create_cache
+import numpy as np
 import numpy.testing as npt
 from sys import stdout
 
@@ -94,10 +95,10 @@ def test_laplace():
                 stdout.write("      Checking variable " + v + " ... ")
                 result = collect(v, path="data", info=False)
                 # Compare benchmark and output
-                if npt.shape(bmk[v]) != npt.shape(result):
+                if np.shape(bmk[v]) != np.shape(result):
                     print("Fail, wrong shape")
                     success = False
-                diff = npt.max(npt.abs(bmk[v] - result))
+                diff = np.max(np.abs(bmk[v] - result))
                 if diff > tol:
                     print("Fail, maximum difference = " + str(diff))
                     success = False

From ffa90b22cfb895bd51150fb784e0edb85ceb9746 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 10:23:36 +0000
Subject: [PATCH 1100/1827] Revert "Rename runtest file to test-foo.py for each
 MMS test"

This reverts commit 3bf60130a01e433494d7f89bb99009d7025026b0.
---
 tests/MMS/spatial/fci/runtest             | 371 +++++++++++++---------
 tests/MMS/spatial/fci/test_spatial_fci.py | 273 ----------------
 2 files changed, 222 insertions(+), 422 deletions(-)
 delete mode 100755 tests/MMS/spatial/fci/test_spatial_fci.py

diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index a93f4d3aff..9dd4d1817f 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -6,195 +6,268 @@
 # Cores: 2
 # requires: zoidberg
 
-from boututils.run_wrapper import build_and_log, launch_safe
-from boutdata.collect import collect
+import argparse
+import json
+import pathlib
+import sys
+from time import time
+
 import boutconfig as conf
+import zoidberg as zb
+from boutdata.collect import collect
+from boututils.run_wrapper import build_and_log, launch_safe
+from numpy import array, linspace, log, polyfit
+
+# Global parameters
+DIRECTORY = "data"
+NPROC = 2
+MTHREAD = 2
+OPERATORS = ("grad_par", "grad2_par2", "div_par", "div_par_K_grad_par", "laplace_par")
+# Note that we need at least _2_ interior points for hermite spline
+# interpolation due to an awkwardness with the boundaries
+NX = 4
+# Resolution in y and z
+NLIST = [8, 16, 32, 64]
+dx = 1.0 / array(NLIST)
 
-from numpy import array, log, polyfit, linspace, arange
 
-import pickle
+success = True
 
-from sys import stdout
+error_2 = {}
+error_inf = {}
+method_orders = {}
 
-import zoidberg as zb
+# Run with periodic Y?
+yperiodic = True
 
-nx = 3  # Not changed for these tests
+build_and_log("FCI MMS test")
 
-# Resolution in y and z
-nlist = [8, 16, 32, 64, 128]
 
-# Number of parallel slices (in each direction)
-nslices = [1]
+def quiet_collect(name: str) -> float:
+    # Index to return a plain (numpy) float rather than `BoutArray`
+    return collect(
+        name,
+        tind=[1, 1],
+        info=False,
+        path=DIRECTORY,
+        xguards=False,
+        yguards=False,
+    )[()]
 
-directory = "data"
 
-nproc = 2
-mthread = 2
+def assert_convergence(error, dx, name, expected) -> bool:
+    fit = polyfit(log(dx), log(error), 1)
+    order = fit[0]
+    print(f"{name} convergence order = {order:f} (fit)", end="")
 
+    order = log(error[-2] / error[-1]) / log(dx[-2] / dx[-1])
+    print(f", {order:f} (small spacing)", end="")
 
-success = True
+    # Should be close to the expected order
+    success = order > expected * 0.95
+    print(f"\t............ {'PASS' if success else 'FAIL'}")
 
-error_2 = {}
-error_inf = {}
-method_orders = {}
+    return success
 
-# Run with periodic Y?
-yperiodic = True
 
-failures = []
+def make_grids():
+    for nz in NLIST:
+        make_grid(nz)
 
-build_and_log("FCI MMS test")
 
-for nslice in nslices:
-    error_2[nslice] = []
-    error_inf[nslice] = []
-
-    # Which central difference scheme to use and its expected order
-    order = nslice * 2
-    method_orders[nslice] = {"name": "C{}".format(order), "order": order}
-
-    for n in nlist:
-        # Define the magnetic field using new poloidal gridding method
-        # Note that the Bz and Bzprime parameters here must be the same as in mms.py
-        field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
-        # Create rectangular poloidal grids
-        poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(nx, n, 0.1, 1.0, MXG=1)
-        # Set the ylength and y locations
-        ylength = 10.0
-
-        if yperiodic:
-            ycoords = linspace(0.0, ylength, n, endpoint=False)
-        else:
-            # Doesn't include the end points
-            ycoords = (arange(n) + 0.5) * ylength / float(n)
-
-        # Create the grid
-        grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=yperiodic)
-        # Make and write maps
-        from scipy.interpolate import RectBivariateSpline as RBS
-
-        def myRBS(a, b, c):
-            mx, my = c.shape
-            kx = max(mx - 1, 1)
-            kx = min(kx, 3)
-            return RBS(a, b, c, kx=kx)
-
-        zb.poloidal_grid.RectBivariateSpline = myRBS
-        maps = zb.make_maps(grid, field, nslice=nslice, quiet=True, MXG=1)
-        zb.write_maps(
-            grid, field, maps, new_names=False, metric2d=conf.isMetric2D(), quiet=True
-        )
+def make_grid(nz: int):
+    # Define the magnetic field using new poloidal gridding method
+    # Note that the Bz and Bzprime parameters here must be the same as in mms.py
+    field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
+    # Create rectangular poloidal grids
+    poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(NX, nz, 0.1, 1.0, MXG=1)
+    # Set the ylength and y locations
+    ylength = 10.0
 
-        args = " MZ={} MYG={} mesh:paralleltransform:y_periodic={} mesh:ddy:first={}".format(
-            n, nslice, yperiodic, method_orders[nslice]["name"]
-        )
+    ycoords = linspace(0.0, ylength, nz, endpoint=False)
 
-        # Command to run
-        cmd = "./fci_mms " + args
+    # Create the grid
+    grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=True)
+    maps = zb.make_maps(grid, field, nslice=1, quiet=True, MXG=1)
+    zb.write_maps(
+        grid,
+        field,
+        maps,
+        new_names=False,
+        metric2d=conf.isMetric2D(),
+        quiet=True,
+        gridfile=f"mesh.{nz}.fci.nc",
+    )
 
-        print("Running command: " + cmd)
 
-        # Launch using MPI
-        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
+def run_fci_operators(nslice: int, nz: int, name: str) -> dict[str, float]:
 
-        # Save output to log file
-        with open("run.log." + str(n), "w") as f:
-            f.write(out)
+    # Command to run
+    args = f"MYG={nslice} {name} mesh:file=mesh.{nz}.fci.nc"
+    cmd = f"./fci_mms {args}"
+    print(f"Running command: {cmd}", end="")
 
-        if s:
-            print("Run failed!\nOutput was:\n")
-            print(out)
-            exit(s)
+    # Launch using MPI
+    start = time()
+    status, out = launch_safe(cmd, nproc=NPROC, mthread=MTHREAD, pipe=True)
+    print(f" ... done in {time() - start:.3}s")
 
-        # Collect data
-        l_2 = collect(
-            "l_2", tind=[1, 1], info=False, path=directory, xguards=False, yguards=False
-        )
-        l_inf = collect(
-            "l_inf",
-            tind=[1, 1],
-            info=False,
-            path=directory,
-            xguards=False,
-            yguards=False,
-        )
+    # Save output to log file
+    pathlib.Path(f"run.log.{nz}").write_text(out)
 
-        error_2[nslice].append(l_2)
-        error_inf[nslice].append(l_inf)
+    if status:
+        print(f"Run failed!\nOutput was:\n{out}")
+        sys.exit(status)
 
-        print("Errors : l-2 {:f} l-inf {:f}".format(l_2, l_inf))
+    return {
+        operator: {
+            "l_2": quiet_collect(f"{operator}_l_2"),
+            "l_inf": quiet_collect(f"{operator}_l_inf"),
+        }
+        for operator in OPERATORS
+    }
 
-    dx = 1.0 / array(nlist)
 
-    # Calculate convergence order
-    fit = polyfit(log(dx), log(error_2[nslice]), 1)
-    order = fit[0]
-    stdout.write("Convergence order = {:f} (fit)".format(order))
+def transpose(
+    errors: list[dict[str, dict[str, float]]],
+) -> dict[str, dict[str, list[float]]]:
+    """Turn a list of {operator: error} into a dict of {operator: [errors]}"""
 
-    order = log(error_2[nslice][-2] / error_2[nslice][-1]) / log(dx[-2] / dx[-1])
-    stdout.write(", {:f} (small spacing)".format(order))
+    kinds = ("l_2", "l_inf")
+    result = {operator: {kind: [] for kind in kinds} for operator in OPERATORS}
+    for error in errors:
+        for k, v in error.items():
+            for kind in kinds:
+                result[k][kind].append(v[kind])
+    return result
 
-    # Should be close to the expected order
-    if order > method_orders[nslice]["order"] * 0.95:
-        print("............ PASS\n")
-    else:
-        print("............ FAIL\n")
-        success = False
-        failures.append(method_orders[nslice]["name"])
 
+def check_fci_operators(name: str, case: dict) -> bool:
+    failures = []
+
+    nslice = case["nslice"]
+    order = case["order"]
+    args = case["args"]
 
-with open("fci_mms.pkl", "wb") as output:
-    pickle.dump(nlist, output)
-    for nslice in nslices:
-        pickle.dump(error_2[nslice], output)
-        pickle.dump(error_inf[nslice], output)
+    all_errors = []
 
-# Do we want to show the plot as well as save it to file.
-showPlot = True
+    for n in NLIST:
+        errors = run_fci_operators(nslice, n, args)
+        all_errors.append(errors)
 
-if False:
+        for operator in OPERATORS:
+            l_2 = errors[operator]["l_2"]
+            l_inf = errors[operator]["l_inf"]
+
+            print(f"{operator} errors: l-2 {l_2:f} l-inf {l_inf:f}")
+
+    final_errors = transpose(all_errors)
+    for operator in OPERATORS:
+        test_name = f"{operator} {name}"
+        success = assert_convergence(
+            final_errors[operator]["l_2"], dx, test_name, order
+        )
+        if not success:
+            failures.append(test_name)
+
+    return final_errors, failures
+
+
+def make_plots(cases: dict[str, dict]):
     try:
-        # Plot using matplotlib if available
         import matplotlib.pyplot as plt
+    except ImportError:
+        print("No matplotlib")
+        return
+
+    num_operators = len(OPERATORS)
+    fig, axes = plt.subplots(1, num_operators, figsize=(num_operators * 4, 4))
 
-        fig, ax = plt.subplots(1, 1)
-
-        for nslice in nslices:
-            ax.plot(
-                dx,
-                error_2[nslice],
-                "-",
-                label="{} $l_2$".format(method_orders[nslice]["name"]),
-            )
-            ax.plot(
-                dx,
-                error_inf[nslice],
-                "--",
-                label="{} $l_\\inf$".format(method_orders[nslice]["name"]),
-            )
+    for ax, operator in zip(axes, OPERATORS):
+        for name, case in cases.items():
+            ax.loglog(dx, case[operator]["l_2"], "-", label=f"{name} $l_2$")
+            ax.loglog(dx, case[operator]["l_inf"], "--", label=f"{name} $l_\\inf$")
         ax.legend(loc="upper left")
         ax.grid()
-        ax.set_yscale("log")
-        ax.set_xscale("log")
-        ax.set_title("error scaling")
+        ax.set_title(f"Error scaling for {operator}")
         ax.set_xlabel(r"Mesh spacing $\delta x$")
         ax.set_ylabel("Error norm")
 
-        plt.savefig("fci_mms.pdf")
-
-        print("Plot saved to fci_mms.pdf")
-
-        if showPlot:
-            plt.show()
-        plt.close()
-    except ImportError:
-        print("No matplotlib")
+    fig.tight_layout()
+    fig.savefig("fci_mms.pdf")
+    print("Plot saved to fci_mms.pdf")
+
+    if args.show_plots:
+        plt.show()
+    plt.close()
+
+
+if __name__ == "__main__":
+    build_and_log("FCI MMS test")
+
+    parser = argparse.ArgumentParser("Error scaling test for FCI operators")
+    parser.add_argument(
+        "--make-plots", action="store_true", help="Create plots of error scaling"
+    )
+    parser.add_argument(
+        "--show-plots",
+        action="store_true",
+        help="Stop and show plots, implies --make-plots",
+    )
+    parser.add_argument(
+        "--dump-errors",
+        type=str,
+        help="Output file to dump errors as JSON",
+        default="fci_operator_errors.json",
+    )
+
+    args = parser.parse_args()
+
+    success = True
+    failures = []
+    cases = {
+        "nslice=1 hermitespline": {
+            "nslice": 1,
+            "order": 2,
+            "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=hermitespline",
+        },
+        "nslice=1 lagrange4pt": {
+            "nslice": 1,
+            "order": 2,
+            "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=lagrange4pt",
+        },
+        "nslice=1 monotonichermitespline": {
+            "nslice": 1,
+            "order": 2,
+            "yperiodic": True,
+            "args": (
+                "mesh:ddy:first=C2 "
+                "mesh:paralleltransform:xzinterpolation:type=monotonichermitespline "
+                "mesh:paralleltransform:xzinterpolation:rtol=1e-3 "
+                "mesh:paralleltransform:xzinterpolation:atol=5e-3"
+            ),
+        },
+    }
+
+    make_grids()
+
+    for name, case in cases.items():
+        error2, failures_ = check_fci_operators(name, case)
+        case.update(error2)
+        failures.extend(failures_)
+        success &= len(failures) == 0
+
+    if args.dump_errors:
+        pathlib.Path(args.dump_errors).write_text(json.dumps(cases))
+
+    if args.make_plots or args.show_plots:
+        make_plots(cases)
+
+    if success:
+        print("\nAll tests passed")
+    else:
+        print("\nSome tests failed:")
+        for failure in failures:
+            print(f"\t{failure}")
 
-if success:
-    print("All tests passed")
-    exit(0)
-else:
-    print("Some tests failed:")
-    for failure in failures:
-        print("\t" + failure)
-    exit(1)
+    sys.exit(0 if success else 1)
diff --git a/tests/MMS/spatial/fci/test_spatial_fci.py b/tests/MMS/spatial/fci/test_spatial_fci.py
deleted file mode 100755
index 9dd4d1817f..0000000000
--- a/tests/MMS/spatial/fci/test_spatial_fci.py
+++ /dev/null
@@ -1,273 +0,0 @@
-#!/usr/bin/env python3
-#
-# Python script to run and analyse MMS test
-#
-
-# Cores: 2
-# requires: zoidberg
-
-import argparse
-import json
-import pathlib
-import sys
-from time import time
-
-import boutconfig as conf
-import zoidberg as zb
-from boutdata.collect import collect
-from boututils.run_wrapper import build_and_log, launch_safe
-from numpy import array, linspace, log, polyfit
-
-# Global parameters
-DIRECTORY = "data"
-NPROC = 2
-MTHREAD = 2
-OPERATORS = ("grad_par", "grad2_par2", "div_par", "div_par_K_grad_par", "laplace_par")
-# Note that we need at least _2_ interior points for hermite spline
-# interpolation due to an awkwardness with the boundaries
-NX = 4
-# Resolution in y and z
-NLIST = [8, 16, 32, 64]
-dx = 1.0 / array(NLIST)
-
-
-success = True
-
-error_2 = {}
-error_inf = {}
-method_orders = {}
-
-# Run with periodic Y?
-yperiodic = True
-
-build_and_log("FCI MMS test")
-
-
-def quiet_collect(name: str) -> float:
-    # Index to return a plain (numpy) float rather than `BoutArray`
-    return collect(
-        name,
-        tind=[1, 1],
-        info=False,
-        path=DIRECTORY,
-        xguards=False,
-        yguards=False,
-    )[()]
-
-
-def assert_convergence(error, dx, name, expected) -> bool:
-    fit = polyfit(log(dx), log(error), 1)
-    order = fit[0]
-    print(f"{name} convergence order = {order:f} (fit)", end="")
-
-    order = log(error[-2] / error[-1]) / log(dx[-2] / dx[-1])
-    print(f", {order:f} (small spacing)", end="")
-
-    # Should be close to the expected order
-    success = order > expected * 0.95
-    print(f"\t............ {'PASS' if success else 'FAIL'}")
-
-    return success
-
-
-def make_grids():
-    for nz in NLIST:
-        make_grid(nz)
-
-
-def make_grid(nz: int):
-    # Define the magnetic field using new poloidal gridding method
-    # Note that the Bz and Bzprime parameters here must be the same as in mms.py
-    field = zb.field.Slab(Bz=0.05, Bzprime=0.1)
-    # Create rectangular poloidal grids
-    poloidal_grid = zb.poloidal_grid.RectangularPoloidalGrid(NX, nz, 0.1, 1.0, MXG=1)
-    # Set the ylength and y locations
-    ylength = 10.0
-
-    ycoords = linspace(0.0, ylength, nz, endpoint=False)
-
-    # Create the grid
-    grid = zb.grid.Grid(poloidal_grid, ycoords, ylength, yperiodic=True)
-    maps = zb.make_maps(grid, field, nslice=1, quiet=True, MXG=1)
-    zb.write_maps(
-        grid,
-        field,
-        maps,
-        new_names=False,
-        metric2d=conf.isMetric2D(),
-        quiet=True,
-        gridfile=f"mesh.{nz}.fci.nc",
-    )
-
-
-def run_fci_operators(nslice: int, nz: int, name: str) -> dict[str, float]:
-
-    # Command to run
-    args = f"MYG={nslice} {name} mesh:file=mesh.{nz}.fci.nc"
-    cmd = f"./fci_mms {args}"
-    print(f"Running command: {cmd}", end="")
-
-    # Launch using MPI
-    start = time()
-    status, out = launch_safe(cmd, nproc=NPROC, mthread=MTHREAD, pipe=True)
-    print(f" ... done in {time() - start:.3}s")
-
-    # Save output to log file
-    pathlib.Path(f"run.log.{nz}").write_text(out)
-
-    if status:
-        print(f"Run failed!\nOutput was:\n{out}")
-        sys.exit(status)
-
-    return {
-        operator: {
-            "l_2": quiet_collect(f"{operator}_l_2"),
-            "l_inf": quiet_collect(f"{operator}_l_inf"),
-        }
-        for operator in OPERATORS
-    }
-
-
-def transpose(
-    errors: list[dict[str, dict[str, float]]],
-) -> dict[str, dict[str, list[float]]]:
-    """Turn a list of {operator: error} into a dict of {operator: [errors]}"""
-
-    kinds = ("l_2", "l_inf")
-    result = {operator: {kind: [] for kind in kinds} for operator in OPERATORS}
-    for error in errors:
-        for k, v in error.items():
-            for kind in kinds:
-                result[k][kind].append(v[kind])
-    return result
-
-
-def check_fci_operators(name: str, case: dict) -> bool:
-    failures = []
-
-    nslice = case["nslice"]
-    order = case["order"]
-    args = case["args"]
-
-    all_errors = []
-
-    for n in NLIST:
-        errors = run_fci_operators(nslice, n, args)
-        all_errors.append(errors)
-
-        for operator in OPERATORS:
-            l_2 = errors[operator]["l_2"]
-            l_inf = errors[operator]["l_inf"]
-
-            print(f"{operator} errors: l-2 {l_2:f} l-inf {l_inf:f}")
-
-    final_errors = transpose(all_errors)
-    for operator in OPERATORS:
-        test_name = f"{operator} {name}"
-        success = assert_convergence(
-            final_errors[operator]["l_2"], dx, test_name, order
-        )
-        if not success:
-            failures.append(test_name)
-
-    return final_errors, failures
-
-
-def make_plots(cases: dict[str, dict]):
-    try:
-        import matplotlib.pyplot as plt
-    except ImportError:
-        print("No matplotlib")
-        return
-
-    num_operators = len(OPERATORS)
-    fig, axes = plt.subplots(1, num_operators, figsize=(num_operators * 4, 4))
-
-    for ax, operator in zip(axes, OPERATORS):
-        for name, case in cases.items():
-            ax.loglog(dx, case[operator]["l_2"], "-", label=f"{name} $l_2$")
-            ax.loglog(dx, case[operator]["l_inf"], "--", label=f"{name} $l_\\inf$")
-        ax.legend(loc="upper left")
-        ax.grid()
-        ax.set_title(f"Error scaling for {operator}")
-        ax.set_xlabel(r"Mesh spacing $\delta x$")
-        ax.set_ylabel("Error norm")
-
-    fig.tight_layout()
-    fig.savefig("fci_mms.pdf")
-    print("Plot saved to fci_mms.pdf")
-
-    if args.show_plots:
-        plt.show()
-    plt.close()
-
-
-if __name__ == "__main__":
-    build_and_log("FCI MMS test")
-
-    parser = argparse.ArgumentParser("Error scaling test for FCI operators")
-    parser.add_argument(
-        "--make-plots", action="store_true", help="Create plots of error scaling"
-    )
-    parser.add_argument(
-        "--show-plots",
-        action="store_true",
-        help="Stop and show plots, implies --make-plots",
-    )
-    parser.add_argument(
-        "--dump-errors",
-        type=str,
-        help="Output file to dump errors as JSON",
-        default="fci_operator_errors.json",
-    )
-
-    args = parser.parse_args()
-
-    success = True
-    failures = []
-    cases = {
-        "nslice=1 hermitespline": {
-            "nslice": 1,
-            "order": 2,
-            "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=hermitespline",
-        },
-        "nslice=1 lagrange4pt": {
-            "nslice": 1,
-            "order": 2,
-            "args": "mesh:ddy:first=C2 mesh:paralleltransform:xzinterpolation:type=lagrange4pt",
-        },
-        "nslice=1 monotonichermitespline": {
-            "nslice": 1,
-            "order": 2,
-            "yperiodic": True,
-            "args": (
-                "mesh:ddy:first=C2 "
-                "mesh:paralleltransform:xzinterpolation:type=monotonichermitespline "
-                "mesh:paralleltransform:xzinterpolation:rtol=1e-3 "
-                "mesh:paralleltransform:xzinterpolation:atol=5e-3"
-            ),
-        },
-    }
-
-    make_grids()
-
-    for name, case in cases.items():
-        error2, failures_ = check_fci_operators(name, case)
-        case.update(error2)
-        failures.extend(failures_)
-        success &= len(failures) == 0
-
-    if args.dump_errors:
-        pathlib.Path(args.dump_errors).write_text(json.dumps(cases))
-
-    if args.make_plots or args.show_plots:
-        make_plots(cases)
-
-    if success:
-        print("\nAll tests passed")
-    else:
-        print("\nSome tests failed:")
-        for failure in failures:
-            print(f"\t{failure}")
-
-    sys.exit(0 if success else 1)

From 4fd66d76e8933aef22005561c539fe863e7bf405 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 10:48:15 +0000
Subject: [PATCH 1101/1827] Add pytest to requirements.txt

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 078eecac6d..d18a2808d7 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,3 +6,4 @@ matplotlib>=3.7.0
 Cython>=3.0.0
 boutdata>=0.3.0
 zoidberg>=0.2.2
+pytest

From 4bca28cf8672f585315a9c6cad0dc9a09149485a Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 11:14:53 +0000
Subject: [PATCH 1102/1827] Add boutpp location to PYTHONPATH when launching
 pytest through cmake command

---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b8cd6b775c..24f86d43a1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -765,8 +765,8 @@ if(BOUT_TESTS)
     add_dependencies(check-unit-tests build-check-unit-tests)
   endif()
 
-  add_custom_target(
-    check-integrated-tests COMMAND pytest -k "test-"
+  add_custom_target(check-integrated-tests
+    COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${PROJECT_BINARY_DIR}/tools/pylib:$ENV{PYTHONPATH}" pytest -k "test-"
   )
   add_dependencies(check-integrated-tests build-check-integrated-tests)
 

From a42bc361f08468f79bb2452720996731758cd88f Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 15:07:41 +0000
Subject: [PATCH 1103/1827] Fix test_laplace after rebase

---
 tests/integrated/test-laplace/test_laplace.py | 89 ++++++++-----------
 1 file changed, 36 insertions(+), 53 deletions(-)

diff --git a/tests/integrated/test-laplace/test_laplace.py b/tests/integrated/test-laplace/test_laplace.py
index 5f09b0203d..2fc7b145f4 100755
--- a/tests/integrated/test-laplace/test_laplace.py
+++ b/tests/integrated/test-laplace/test_laplace.py
@@ -10,9 +10,7 @@
 
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect, create_cache
-import numpy as np
 import numpy.testing as npt
-from sys import stdout
 
 
 # Variables to compare
@@ -36,73 +34,58 @@
 ]
 tol = 1e-6  # Absolute tolerance
 
-
-# Read benchmark values
-print("Reading benchmark data")
-bmk = {v: collect(v, path="data", prefix="benchmark", info=False) for v in vars}
-
-
 def test_laplace():
 
     # Read benchmark values
     print("Reading benchmark data")
-    bmk = {}
-    for v in vars:
-        bmk[v] = collect(v, path="data", prefix="benchmark", info=False)
+    bmk = {v: collect(v, path="data", prefix="benchmark", info=False) for v in vars}
 
     print("Running Laplacian inversion test")
     success = True
 
-    cmd = "./test_laplace NXPE=" + str(nxpe) + " laplace:type=" + solver
-       
-    print(f"   {solver} solver with {nproc} processors ({nxpe=})....")
-    s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True)
-    with open(f"run.log.{nproc}", "w") as f:
-        f.write(out)
-
-    cache = create_cache(path="data", prefix="BOUT.dmp")
-
-    # Collect output data
-    for v in vars:
-        print(f"      Checking variable {v} ...", end="")
-        result = collect(v, path="data", info=False, datafile_cache=cache)
-        # Compare benchmark and output
-        try:
-        npt.assert_allclose(result, bmk[v], atol=tol, rtol=tol)
-        print("Pass")
-        except AssertionError as e:
-        print(f"Fail: {e}")
-        success = False
-
-        # Only check FieldPerps on one processor because reading them in is
-        # quite annoying on mutliple cores due to mismatched global y indices
-        if nproc == 1:
-            for v in ["flag0_perp", "flag3_perp"]:
+    for solver in ["cyclic", "pcr", "pcr_thomas"]:
+        for nproc in [1, 2, 4]:
+            nxpe = 1
+            if nproc > 2:
+                nxpe = 2
+
+            cmd = f"./test_laplace NXPE={nxpe} laplace:type={solver}"
+
+            shell("rm data/BOUT.dmp.*.nc")
+
+            print(f"   {solver} solver with {nproc} processors ({nxpe=})....")
+            s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True)
+            with open(f"run.log.{nproc}", "w") as f:
+                f.write(out)
+
+            cache = create_cache(path="data", prefix="BOUT.dmp")
+
+            # Collect output data
+            for v in vars:
                 print(f"      Checking variable {v} ...", end="")
                 result = collect(v, path="data", info=False, datafile_cache=cache)
                 # Compare benchmark and output
                 try:
-                    npt.assert_allclose(
-                        result, bmk[v.replace("_perp", "")][:, 0, :], atol=tol, rtol=tol
-                    )
+                    npt.assert_allclose(result, bmk[v], atol=tol, rtol=tol)
                     print("Pass")
                 except AssertionError as e:
                     print(f"Fail: {e}")
                     success = False
 
-            # Collect output data
-            for v in vars:
-                stdout.write("      Checking variable " + v + " ... ")
-                result = collect(v, path="data", info=False)
-                # Compare benchmark and output
-                if np.shape(bmk[v]) != np.shape(result):
-                    print("Fail, wrong shape")
-                    success = False
-                diff = np.max(np.abs(bmk[v] - result))
-                if diff > tol:
-                    print("Fail, maximum difference = " + str(diff))
-                    success = False
-                else:
-                    print("Pass")
+            # Only check FieldPerps on one processor because reading them in is
+            # quite annoying on mutliple cores due to mismatched global y indices
+            if nproc == 1:
+                for v in ["flag0_perp", "flag3_perp"]:
+                    print(f"      Checking variable {v} ...", end="")
+                    result = collect(v, path="data", info=False, datafile_cache=cache)
+                    # Compare benchmark and output
+                    try:
+                        npt.assert_allclose(
+                            result, bmk[v.replace("_perp", "")][:, 0, :], atol=tol, rtol=tol
+                        )
+                        print("Pass")
+                    except AssertionError as e:
+                        print(f"Fail: {e}")
+                        success = False
 
     assert success, " => Some failed tests"

From 3f99cce6776202bb1e2a4b41dd1c93f77600cef7 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 15:33:43 +0000
Subject: [PATCH 1104/1827] Use BOUT_PYTHONPATH instead of PROJECT_BINARY_DIR
 to ensure boutpp python files are found

Add @ONLY so CMake doesn't accidentally try to replace the bash $@ variable.
---
 CMakeLists.txt                | 9 +++++----
 tests/run_integrated_tests.sh | 6 +++---
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 24f86d43a1..856b1013ee 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -766,7 +766,7 @@ if(BOUT_TESTS)
   endif()
 
   add_custom_target(check-integrated-tests
-    COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${PROJECT_BINARY_DIR}/tools/pylib:$ENV{PYTHONPATH}" pytest -k "test-"
+    COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}" pytest -k "test-"
   )
   add_dependencies(check-integrated-tests build-check-integrated-tests)
 
@@ -796,9 +796,10 @@ if(BOUT_TESTS)
     "${PROJECT_BINARY_DIR}/tests/integrated/test-boutpp/conftest.py")
 
   # Copy the pytest shell script
-  configure_file(
-    "${PROJECT_SOURCE_DIR}/tests/run_integrated_tests.sh"
-    "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh")
+configure_file(
+  "${PROJECT_SOURCE_DIR}/tests/run_integrated_tests.sh"
+  "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh"
+  @ONLY)
 
 endif()
 
diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index 034627085f..fa6ca0157f 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -1,11 +1,11 @@
 #!/bin/bash
 
-PROJECT_ROOT=${PROJECT_BINARY_DIR}
+PROJECT_ROOT="@PROJECT_BINARY_DIR@"
 
-export PYTHONPATH="$PROJECT_ROOT/tools/pylib"
+export PYTHONPATH="@BOUT_PYTHONPATH@:$PYTHONPATH"
 
 # Pre-build the project to prevent concurrent CMake race conditions
 cmake --build "$PROJECT_ROOT"
 
 pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$PROJECT_ROOT/tests/integrated" "$@"
-pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"
+pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"
\ No newline at end of file

From 7822ca9a142db86c905321412adda006b1615af0 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 15:54:30 +0000
Subject: [PATCH 1105/1827] Make check-integrated-tests target just run the
 `run_integrated_tests.sh` script

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 856b1013ee..3a3ba35c05 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -766,7 +766,7 @@ if(BOUT_TESTS)
   endif()
 
   add_custom_target(check-integrated-tests
-    COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}" pytest -k "test-"
+    COMMAND bash "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh"
   )
   add_dependencies(check-integrated-tests build-check-integrated-tests)
 

From a2e6bb4307528e07f742e7834a4b6b1ff5d23bd1 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 16:35:08 +0000
Subject: [PATCH 1106/1827] Don't rely on BOUT_PYTHONPATH, as not available
 always

BOUT_PYTHONPATH is not available to CI, so explicitly map both the build and source directories using global CMake variables.
---
 tests/run_integrated_tests.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index fa6ca0157f..ee6d746a30 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -2,10 +2,10 @@
 
 PROJECT_ROOT="@PROJECT_BINARY_DIR@"
 
-export PYTHONPATH="@BOUT_PYTHONPATH@:$PYTHONPATH"
+export PYTHONPATH="@PROJECT_BINARY_DIR@/tools/pylib:@PROJECT_SOURCE_DIR@/tools/pylib:$PYTHONPATH"
 
 # Pre-build the project to prevent concurrent CMake race conditions
 cmake --build "$PROJECT_ROOT"
 
 pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$PROJECT_ROOT/tests/integrated" "$@"
-pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"
\ No newline at end of file
+pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"

From 6fceaddac848915c9319a10896521c56a89efb3f Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 17:09:19 +0000
Subject: [PATCH 1107/1827] Remove unused boutpp import from conftest.py

---
 tests/conftest.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index e993eb564b..eac2d3bacf 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,6 +1,5 @@
 import pytest
 import shutil
-import boutpp
 import os
 import subprocess
 import time

From bf5e02b6971e75aca5ea3562ef0b4812944d6448 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 17:26:25 +0000
Subject: [PATCH 1108/1827] Add pytest-xdist to requirements.txt

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index d18a2808d7..ea0085eeb4 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -7,3 +7,4 @@ Cython>=3.0.0
 boutdata>=0.3.0
 zoidberg>=0.2.2
 pytest
+pytest-xdist

From b28b5a50e70f5e443c35f1307261daace813d02c Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 17:29:54 +0000
Subject: [PATCH 1109/1827] Fix pytest command not found in CI by using
 `python3 -m pytest`

---
 tests/run_integrated_tests.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index ee6d746a30..d8b0e8cca5 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -7,5 +7,5 @@ export PYTHONPATH="@PROJECT_BINARY_DIR@/tools/pylib:@PROJECT_SOURCE_DIR@/tools/p
 # Pre-build the project to prevent concurrent CMake race conditions
 cmake --build "$PROJECT_ROOT"
 
-pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$PROJECT_ROOT/tests/integrated" "$@"
-pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"
+python3 -m pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$PROJECT_ROOT/tests/integrated" "$@"
+python3 -m pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"

From 8852248ad9626bd32f961a4e4f36fed9e69e804a Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 28 Mar 2026 19:38:44 +0000
Subject: [PATCH 1110/1827] Use the Python executable that CMake discovered
 during configuration

---
 tests/run_integrated_tests.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index d8b0e8cca5..98270f5292 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -7,5 +7,6 @@ export PYTHONPATH="@PROJECT_BINARY_DIR@/tools/pylib:@PROJECT_SOURCE_DIR@/tools/p
 # Pre-build the project to prevent concurrent CMake race conditions
 cmake --build "$PROJECT_ROOT"
 
-python3 -m pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$PROJECT_ROOT/tests/integrated" "$@"
-python3 -m pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"
+# Use the Python executable that CMake discovered during configuration
+"@Python3_EXECUTABLE@" -m pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$PROJECT_ROOT/tests/integrated" "$@"
+"@Python3_EXECUTABLE@" -m pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"

From 5690fd2984124ac22a67a39ae596ebdc6c94599d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 14 Apr 2026 13:21:01 +0200
Subject: [PATCH 1111/1827] Make YBoundary part of mesh

---
 include/bout/coordinates.hxx                      | 15 ++++++++++-----
 manual/sphinx/user_docs/boundary_options.rst      |  5 ++---
 src/mesh/coordinates.cxx                          |  7 ++++++-
 .../test-fci-boundary/get_par_bndry.cxx           |  4 ++--
 4 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index e7ead42ee5..2c287bdbc5 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -3,16 +3,16 @@
  *
  * ChangeLog
  * =========
- * 
+ *
  * 2014-11-10 Ben Dudson <bd512@york.ac.uk>
  *    * Created by separating metric from Mesh
  *
- * 
+ *
  **************************************************************************
  * Copyright 2014-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -40,6 +40,7 @@
 #include <bout/paralleltransform.hxx>
 
 class Mesh;
+class YBoundary;
 
 /*!
  * Represents a coordinate system, and associated operators
@@ -221,6 +222,8 @@ public:
   // solver
   Field2D Laplace_perpXY(const Field2D& A, const Field2D& f);
 
+  std::shared_ptr<YBoundary> getYBoundary() const { return ybndry; }
+
 private:
   int nz; // Size of mesh in Z. This is mesh->ngz-1
   Mesh* localmesh;
@@ -249,6 +252,8 @@ private:
   void checkCovariant();
   // check that contravariant tensors are positive (if expected) and finite (always)
   void checkContravariant();
+
+  std::shared_ptr<YBoundary> ybndry;
 };
 
 /*
@@ -256,10 +261,10 @@ private:
 class TokamakCoordinates : public Coordinates {
 public:
   TokamakCoordinates(Mesh *mesh) : Coordinates(mesh) {
-    
+
   }
 private:
-  
+
 };
 */
 
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index d65ed0ba79..fd50076a9b 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -496,17 +496,16 @@ geometries, as flux coordinate independent (FCI) method::
     class yboundary_example {
     public:
       yboundary_example(Options* opt, const Field3D& N, const Field3D& V) :
-      N(N), V(V), yboundary(opt) {}
+      N(N), V(V) {}
 
       void rhs() {
         BoutReal totalFlux = 0;
-        yboundary.iter_pnts([&](auto& pnt) {
+        mesh->getCoordinates()->getYBoundary()->iter_pnts([&](auto& pnt) {
           BoutReal flux = pnt.interpolate_sheath_o2(N) * pnt.interpolate_sheath_o2(V);
         });
       }
 
     private:
-      YBoundary ybounday;
       const Field3D& N;
       const Field3D& V;
     };
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index d2634d3f88..d7ce871803 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -18,6 +18,7 @@
 #include <bout/output_bout_types.hxx>
 
 #include <bout/globals.hxx>
+#include <bout/yboundary_regions.hxx>
 
 #include "invert3x3.hxx"
 #include "parallel/fci.hxx"
@@ -369,7 +370,7 @@ Coordinates::Coordinates(Mesh* mesh, FieldMetric dx, FieldMetric dy, FieldMetric
       g_22(std::move(g_22)), g_33(std::move(g_33)), g_12(std::move(g_12)),
       g_13(std::move(g_13)), g_23(std::move(g_23)), ShiftTorsion(std::move(ShiftTorsion)),
       IntShiftTorsion(std::move(IntShiftTorsion)), nz(mesh->LocalNz), localmesh(mesh),
-      location(CELL_CENTRE) {}
+      location(CELL_CENTRE), ybndry{std::make_shared<YBoundary>(nullptr, mesh)} {}
 
 Coordinates::Coordinates(Mesh* mesh, Options* options)
     : dx(1., mesh), dy(1., mesh), dz(1., mesh), d1_dx(mesh), d1_dy(mesh), d1_dz(mesh),
@@ -387,6 +388,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
     options = Options::getRoot()->getSection("mesh");
   }
 
+  ybndry = std::make_shared<YBoundary>(options, mesh);
+
   // Note: If boundary cells were not loaded from the grid file, use
   // 'interpolateAndExtrapolate' to set them. Ensures that derivatives are
   // smooth at all the boundaries.
@@ -608,6 +611,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
 
   std::string suffix = getLocationSuffix(location);
 
+  ybndry = std::make_shared<YBoundary>(options, mesh);
+
   nz = mesh->LocalNz;
 
   // Default to true in case staggered quantities are not read from file
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index f72438b4e3..919f5a597f 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -45,13 +45,13 @@ int main(int argc, char** argv) {
 
   {
     Options dummy;
-    YBoundary ybndry(dummy, mesh);
+    auto ybndry = mesh->getCoordinates()->getYBoundary();
 
     std::vector<Field3D> fields((mesh->ystart * 2) + 1, Field3D{0.0});
     for (auto& field : fields) {
       field.allocate();
     }
-    ybndry.iter_pnts(
+    ybndry->iter_pnts(
         [&](const auto& pnt) { fields[pnt.dir + mesh->ystart][pnt.ind()] += 1; });
 
     for (int i = -mesh->ystart; i <= mesh->ystart; ++i) {

From abb322fcf7e53365cddb7e3d0a52b3df91b76075 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 14 Apr 2026 14:22:34 +0200
Subject: [PATCH 1112/1827] Create YBoundary for sheath and non-sheath BCs

---
 include/bout/boundary_region.hxx   |  2 ++
 include/bout/coordinates.hxx       |  7 ++++--
 include/bout/yboundary_regions.hxx | 38 +++++++++++++++++++++++-------
 src/mesh/coordinates.cxx           | 14 ++++++++---
 4 files changed, 47 insertions(+), 14 deletions(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 58de12045e..301c4a01f6 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -36,6 +36,8 @@ constexpr BndryLoc BNDRY_PAR_BKWD_XIN = BndryLoc::par_bkwd_xin;
 constexpr BndryLoc BNDRY_PAR_FWD_XOUT = BndryLoc::par_fwd_xout;
 constexpr BndryLoc BNDRY_PAR_BKWD_XOUT = BndryLoc::par_bkwd_xout;
 
+enum class YBndryType { sheath, not_sheath, all };
+
 class BoundaryRegionBase {
 public:
   BoundaryRegionBase() = delete;
diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 2c287bdbc5..34f10a46dd 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -222,7 +222,9 @@ public:
   // solver
   Field2D Laplace_perpXY(const Field2D& A, const Field2D& f);
 
-  std::shared_ptr<YBoundary> getYBoundary() const { return ybndry; }
+  std::shared_ptr<YBoundary> getYBoundary(YBndryType type = YBndryType::sheath) const {
+    return ybndrys[static_cast<int>(type)];
+  }
 
 private:
   int nz; // Size of mesh in Z. This is mesh->ngz-1
@@ -253,7 +255,8 @@ private:
   // check that contravariant tensors are positive (if expected) and finite (always)
   void checkContravariant();
 
-  std::shared_ptr<YBoundary> ybndry;
+  std::array<std::shared_ptr<YBoundary>, 3> ybndrys;
+  void setupybndry(Options*, Mesh*);
 };
 
 /*
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index d40a7b8836..56090585a9 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -44,20 +44,40 @@ public:
     return iter_regions(f);
   }
 
-  YBoundary(Options* options_ptr, Mesh* mesh = nullptr) {
-    if (mesh == nullptr) {
-      mesh = bout::globals::mesh;
-    }
+  YBoundary(YBndryType type, Options* options_ptr, Mesh* mesh) {
+    ASSERT3(mesh != nullptr);
     bool lower_y = true;
     bool upper_y = true;
     bool outer_x = true;
-    bool inner_x = true;
+    bool inner_x = false;
     if (options_ptr != nullptr) {
       auto& options = *options_ptr;
-      lower_y = options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
-      upper_y = options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(upper_y);
-      outer_x = options["outer_x"].doc("Boundary on outer x?").withDefault<bool>(outer_x);
-      inner_x = options["inner_x"].doc("Boundary on inner x?").withDefault<bool>(inner_x);
+      if (!mesh->isFci()) {
+        lower_y =
+            options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
+        upper_y =
+            options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(upper_y);
+      } else {
+        outer_x =
+            options["outer_x"].doc("Boundary on outer x?").withDefault<bool>(outer_x);
+        inner_x =
+            options["inner_x"].doc("Boundary on inner x?").withDefault<bool>(inner_x);
+      }
+    }
+    switch (type) {
+    case YBndryType::sheath:
+      break;
+    case YBndryType::not_sheath:
+      lower_y = !lower_y;
+      upper_y = !upper_y;
+      outer_x = !outer_x;
+      inner_x = !inner_x;
+      break;
+    case YBndryType::all:
+      lower_y = true;
+      upper_y = true;
+      outer_x = true;
+      inner_x = true;
     }
 
     if (mesh->isFci()) {
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index d7ce871803..a34376dad3 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -370,7 +370,9 @@ Coordinates::Coordinates(Mesh* mesh, FieldMetric dx, FieldMetric dy, FieldMetric
       g_22(std::move(g_22)), g_33(std::move(g_33)), g_12(std::move(g_12)),
       g_13(std::move(g_13)), g_23(std::move(g_23)), ShiftTorsion(std::move(ShiftTorsion)),
       IntShiftTorsion(std::move(IntShiftTorsion)), nz(mesh->LocalNz), localmesh(mesh),
-      location(CELL_CENTRE), ybndry{std::make_shared<YBoundary>(nullptr, mesh)} {}
+      location(CELL_CENTRE) {
+  setupybndry(nullptr, mesh);
+}
 
 Coordinates::Coordinates(Mesh* mesh, Options* options)
     : dx(1., mesh), dy(1., mesh), dz(1., mesh), d1_dx(mesh), d1_dy(mesh), d1_dz(mesh),
@@ -388,7 +390,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
     options = Options::getRoot()->getSection("mesh");
   }
 
-  ybndry = std::make_shared<YBoundary>(options, mesh);
+  setupybndry(options, mesh);
 
   // Note: If boundary cells were not loaded from the grid file, use
   // 'interpolateAndExtrapolate' to set them. Ensures that derivatives are
@@ -611,7 +613,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
 
   std::string suffix = getLocationSuffix(location);
 
-  ybndry = std::make_shared<YBoundary>(options, mesh);
+  setupybndry(options, mesh);
 
   nz = mesh->LocalNz;
 
@@ -2012,3 +2014,9 @@ void Coordinates::checkContravariant() {
     }
   }
 }
+
+void Coordinates::setupybndry(Options* options, Mesh* mesh) {
+  ybndrys = {std::make_shared<YBoundary>(YBndryType::sheath, options, mesh),
+             std::make_shared<YBoundary>(YBndryType::not_sheath, options, mesh),
+             std::make_shared<YBoundary>(YBndryType::all, options, mesh)};
+}

From 5f127e1261b63ae4b53b9cbdd27854a52f05707d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 14 Apr 2026 14:54:50 +0200
Subject: [PATCH 1113/1827] Create YBoundary region on demand

---
 include/bout/coordinates.hxx | 11 ++++++++---
 src/mesh/coordinates.cxx     | 19 ++++++-------------
 2 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 34f10a46dd..0a9f96bb23 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -223,12 +223,18 @@ public:
   Field2D Laplace_perpXY(const Field2D& A, const Field2D& f);
 
   std::shared_ptr<YBoundary> getYBoundary(YBndryType type = YBndryType::sheath) const {
-    return ybndrys[static_cast<int>(type)];
+    auto itype = static_cast<int>(type);
+    if (ybndrys[itype] == nullptr) {
+      ybndrys[itype] = makeYBoundary(type);
+    }
+    return ybndrys[itype];
   }
+  std::shared_ptr<YBoundary> makeYBoundary(YBndryType type) const;
 
 private:
   int nz; // Size of mesh in Z. This is mesh->ngz-1
   Mesh* localmesh;
+  Options* localoptions;
   CELL_LOC location;
 
   /// Handles calculation of yup and ydown
@@ -255,8 +261,7 @@ private:
   // check that contravariant tensors are positive (if expected) and finite (always)
   void checkContravariant();
 
-  std::array<std::shared_ptr<YBoundary>, 3> ybndrys;
-  void setupybndry(Options*, Mesh*);
+  mutable std::array<std::shared_ptr<YBoundary>, 3> ybndrys;
 };
 
 /*
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index a34376dad3..7205d9a91f 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -370,9 +370,7 @@ Coordinates::Coordinates(Mesh* mesh, FieldMetric dx, FieldMetric dy, FieldMetric
       g_22(std::move(g_22)), g_33(std::move(g_33)), g_12(std::move(g_12)),
       g_13(std::move(g_13)), g_23(std::move(g_23)), ShiftTorsion(std::move(ShiftTorsion)),
       IntShiftTorsion(std::move(IntShiftTorsion)), nz(mesh->LocalNz), localmesh(mesh),
-      location(CELL_CENTRE) {
-  setupybndry(nullptr, mesh);
-}
+      localoptions(nullptr), location(CELL_CENTRE) {}
 
 Coordinates::Coordinates(Mesh* mesh, Options* options)
     : dx(1., mesh), dy(1., mesh), dz(1., mesh), d1_dx(mesh), d1_dy(mesh), d1_dz(mesh),
@@ -384,14 +382,13 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
       G1_13(mesh), G1_23(mesh), G2_11(mesh), G2_22(mesh), G2_33(mesh), G2_12(mesh),
       G2_13(mesh), G2_23(mesh), G3_11(mesh), G3_22(mesh), G3_33(mesh), G3_12(mesh),
       G3_13(mesh), G3_23(mesh), G1(mesh), G2(mesh), G3(mesh), ShiftTorsion(mesh),
-      IntShiftTorsion(mesh), localmesh(mesh), location(CELL_CENTRE) {
+      IntShiftTorsion(mesh), localmesh(mesh), localoptions(options),
+      location(CELL_CENTRE) {
 
   if (options == nullptr) {
     options = Options::getRoot()->getSection("mesh");
   }
 
-  setupybndry(options, mesh);
-
   // Note: If boundary cells were not loaded from the grid file, use
   // 'interpolateAndExtrapolate' to set them. Ensures that derivatives are
   // smooth at all the boundaries.
@@ -609,12 +606,10 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
       G1_13(mesh), G1_23(mesh), G2_11(mesh), G2_22(mesh), G2_33(mesh), G2_12(mesh),
       G2_13(mesh), G2_23(mesh), G3_11(mesh), G3_22(mesh), G3_33(mesh), G3_12(mesh),
       G3_13(mesh), G3_23(mesh), G1(mesh), G2(mesh), G3(mesh), ShiftTorsion(mesh),
-      IntShiftTorsion(mesh), localmesh(mesh), location(loc) {
+      IntShiftTorsion(mesh), localmesh(mesh), localoptions(options), location(loc) {
 
   std::string suffix = getLocationSuffix(location);
 
-  setupybndry(options, mesh);
-
   nz = mesh->LocalNz;
 
   // Default to true in case staggered quantities are not read from file
@@ -2015,8 +2010,6 @@ void Coordinates::checkContravariant() {
   }
 }
 
-void Coordinates::setupybndry(Options* options, Mesh* mesh) {
-  ybndrys = {std::make_shared<YBoundary>(YBndryType::sheath, options, mesh),
-             std::make_shared<YBoundary>(YBndryType::not_sheath, options, mesh),
-             std::make_shared<YBoundary>(YBndryType::all, options, mesh)};
+std::shared_ptr<YBoundary> Coordinates::makeYBoundary(YBndryType type) const {
+  return std::make_shared<YBoundary>(type, localoptions, localmesh);
 }

From 4cfbb16fbb87600927d763a31505ef39351f9154 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 09:42:55 +0200
Subject: [PATCH 1114/1827] Apply clang-tidy fixes

---
 include/bout/coordinates.hxx                         | 3 +++
 include/bout/yboundary_regions.hxx                   | 1 +
 src/mesh/coordinates.cxx                             | 1 +
 tests/integrated/test-fci-boundary/get_par_bndry.cxx | 4 +---
 4 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 0a9f96bb23..a4531fdc9e 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -33,12 +33,15 @@
 #ifndef BOUT_COORDINATES_H
 #define BOUT_COORDINATES_H
 
+#include "bout/field_data.hxx"
 #include <bout/bout_types.hxx>
 #include <bout/build_defines.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/paralleltransform.hxx>
 
+#include <array>
+
 class Mesh;
 class YBoundary;
 
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 56090585a9..f9b55cab2b 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -3,6 +3,7 @@
 #include "./boundary_iterator.hxx"
 #include "bout/assert.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/field_data.hxx"
 #include "bout/globals.hxx"
 #include "bout/mask.hxx"
 #include "bout/options.hxx"
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 7205d9a91f..9cfb503a05 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -4,6 +4,7 @@
  * given the contravariant metric tensor terms
  **************************************************************************/
 
+#include "bout/field_data.hxx"
 #include <bout/assert.hxx>
 #include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 919f5a597f..2e40145b1a 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -7,8 +7,6 @@
 #include "bout/output.hxx"
 #include "bout/parallel_boundary_region.hxx"
 
-#include "bout/yboundary_regions.hxx"
-
 #include <fmt/format.h>
 
 #include <vector>
@@ -44,7 +42,7 @@ int main(int argc, char** argv) {
   }
 
   {
-    Options dummy;
+    const Options dummy;
     auto ybndry = mesh->getCoordinates()->getYBoundary();
 
     std::vector<Field3D> fields((mesh->ystart * 2) + 1, Field3D{0.0});

From 30298ca36d06183b2fcd51d1c16f0d683038a075 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 09:57:11 +0200
Subject: [PATCH 1115/1827] More clang-tidy fixes

---
 include/bout/coordinates.hxx |  1 +
 src/mesh/coordinates.cxx     | 12 ++++++------
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index a4531fdc9e..6748babd70 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -41,6 +41,7 @@
 #include <bout/paralleltransform.hxx>
 
 #include <array>
+#include <memory>
 
 class Mesh;
 class YBoundary;
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 9cfb503a05..f6ac16086b 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -9,18 +9,18 @@
 #include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
 #include <bout/coordinates.hxx>
-#include <bout/output.hxx>
-#include <bout/sys/timer.hxx>
-#include <bout/utils.hxx>
-
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
+#include <bout/globals.hxx>
 #include <bout/interpolation.hxx>
+#include <bout/output.hxx>
 #include <bout/output_bout_types.hxx>
-
-#include <bout/globals.hxx>
+#include <bout/sys/timer.hxx>
+#include <bout/utils.hxx>
 #include <bout/yboundary_regions.hxx>
 
+#include <memory>
+
 #include "invert3x3.hxx"
 #include "parallel/fci.hxx"
 #include "parallel/shiftedmetricinterp.hxx"

From db5d3aa17755c3ddd272f289383bbd0ac1e65872 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 10:09:15 +0200
Subject: [PATCH 1116/1827] Move getYBoundary to a free friend function

---
 include/bout/coordinates.hxx                         | 10 ++--------
 include/bout/yboundary_regions.hxx                   |  9 +++++++++
 tests/integrated/test-fci-boundary/get_par_bndry.cxx |  3 ++-
 3 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 6748babd70..be7de0f5b6 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -226,16 +226,10 @@ public:
   // solver
   Field2D Laplace_perpXY(const Field2D& A, const Field2D& f);
 
-  std::shared_ptr<YBoundary> getYBoundary(YBndryType type = YBndryType::sheath) const {
-    auto itype = static_cast<int>(type);
-    if (ybndrys[itype] == nullptr) {
-      ybndrys[itype] = makeYBoundary(type);
-    }
-    return ybndrys[itype];
-  }
-  std::shared_ptr<YBoundary> makeYBoundary(YBndryType type) const;
+  friend std::shared_ptr<YBoundary> getYBoundary(Coordinates* coords, YBndryType type);
 
 private:
+  std::shared_ptr<YBoundary> makeYBoundary(YBndryType type) const;
   int nz; // Size of mesh in Z. This is mesh->ngz-1
   Mesh* localmesh;
   Options* localoptions;
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index f9b55cab2b..bb13d5fac2 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -142,3 +142,12 @@ private:
 
   std::vector<BoutMask> _contains;
 };
+
+std::shared_ptr<YBoundary> getYBoundary(Coordinates* coords,
+                                        YBndryType type = YBndryType::sheath) {
+  auto itype = static_cast<int>(type);
+  if (coords->ybndrys[itype] == nullptr) {
+    coords->ybndrys[itype] = coords->makeYBoundary(type);
+  }
+  return coords->ybndrys[itype];
+}
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 2e40145b1a..0840c131d3 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -6,6 +6,7 @@
 #include "bout/options_io.hxx"
 #include "bout/output.hxx"
 #include "bout/parallel_boundary_region.hxx"
+#include "bout/yboundary_regions.hxx"
 
 #include <fmt/format.h>
 
@@ -43,7 +44,7 @@ int main(int argc, char** argv) {
 
   {
     const Options dummy;
-    auto ybndry = mesh->getCoordinates()->getYBoundary();
+    auto ybndry = getYBoundary(mesh->getCoordinates());
 
     std::vector<Field3D> fields((mesh->ystart * 2) + 1, Field3D{0.0});
     for (auto& field : fields) {

From 82bbe9f057c4902ab272d209c68dfe55a9490a66 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 15 Apr 2026 09:27:29 +0100
Subject: [PATCH 1117/1827] Add OpenMPI oversubscription overrides

to get (Fedora) ci to work in docker container.
---
 .ci_fedora.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index e1dc563c6c..3bb54b45fc 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -37,7 +37,11 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     cp -a /tmp/BOUT-dev /home/test/
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
-    export OMPI_MCA_rmaps_base_oversubscribe=yes
+    # OpenMPI Oversubscription Overrides
+    export OMPI_MCA_rmaps_base_oversubscribe=1
+    export OMPI_MCA_hwloc_base_binding_policy=none
+    export OMPI_MCA_rmaps_base_mapping_policy=core:OVERSUBSCRIBE
+    export PRTE_MCA_rmaps_default_mapping_policy=core:OVERSUBSCRIBE
     export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
     export TRAVIS=true
     # Try limiting openmp threads

From c67ae87d0acf20ccb5f80b4ceb54f2f736ce1470 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 10:27:31 +0200
Subject: [PATCH 1118/1827] Declare function inline

---
 include/bout/yboundary_regions.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index bb13d5fac2..ebfbbe3b29 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -143,8 +143,8 @@ private:
   std::vector<BoutMask> _contains;
 };
 
-std::shared_ptr<YBoundary> getYBoundary(Coordinates* coords,
-                                        YBndryType type = YBndryType::sheath) {
+inline std::shared_ptr<YBoundary> getYBoundary(Coordinates* coords,
+                                               YBndryType type = YBndryType::sheath) {
   auto itype = static_cast<int>(type);
   if (coords->ybndrys[itype] == nullptr) {
     coords->ybndrys[itype] = coords->makeYBoundary(type);

From 9558ccac022ebcbc1ca62d1330eac4f00e664dc6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 10:30:05 +0200
Subject: [PATCH 1119/1827] Avoid warning for unused push

---
 include/bout/msg_stack.hxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/include/bout/msg_stack.hxx b/include/bout/msg_stack.hxx
index ddc0ccad98..aa19939058 100644
--- a/include/bout/msg_stack.hxx
+++ b/include/bout/msg_stack.hxx
@@ -77,7 +77,8 @@ public:
   /// Dummy functions which should be optimised out
   int push(const std::string&) { return 0; }
   template <class... Args>
-  int push(fmt::format_string<Args...> format, const Args&... args) {
+  int push([[maybe_unused]] fmt::format_string<Args...> format,
+           [[maybe_unused]] const Args&... args) {
     return 0;
   }
 

From 8d7fbd1325f99aaa5a68cce0e1838a297cec255c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 10:31:45 +0200
Subject: [PATCH 1120/1827] move reference value

---
 include/bout/parallel_boundary_region.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index d42a2b2366..49f26cef8c 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -52,7 +52,7 @@ struct Indices {
   unsigned char abs_offset;
   Indices(Ind3D index, RealPoint&& intersection, BoutReal length, signed char valid,
           signed char offset, unsigned char abs_offset)
-      : index(index), intersection(intersection), length(length), valid(valid),
+      : index(index), intersection(std::move(intersection)), length(length), valid(valid),
         offset(offset), abs_offset(abs_offset) {};
 };
 

From f72de989bf36a562417ed0ad1f2c5589c2b622c7 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 15 Apr 2026 09:52:11 +0100
Subject: [PATCH 1121/1827] Install pytest in fedora ci script

---
 .ci_fedora.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 3bb54b45fc..3fe2d45d68 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -37,6 +37,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     cp -a /tmp/BOUT-dev /home/test/
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
+    sudo dnf install -y python3-pytest
     # OpenMPI Oversubscription Overrides
     export OMPI_MCA_rmaps_base_oversubscribe=1
     export OMPI_MCA_hwloc_base_binding_policy=none

From 9b96ed7512c1de4f6f0ec1d2dc8d3f8c4c63e589 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 11:42:41 +0200
Subject: [PATCH 1122/1827] Revert some unintended changes

---
 externalpackages/boutdata                     |    2 +-
 externalpackages/fmt                          |    2 +-
 externalpackages/googletest                   |    2 +-
 ...ection2.png => topology_cross_section.png} |  Bin
 manual/sphinx/figs/topology_cross_section.svg | 1609 +++++++++++++++++
 manual/sphinx/user_docs/topology.rst          |    4 +-
 6 files changed, 1614 insertions(+), 5 deletions(-)
 rename manual/sphinx/figs/{topology_cross_section2.png => topology_cross_section.png} (100%)
 create mode 100644 manual/sphinx/figs/topology_cross_section.svg

diff --git a/externalpackages/boutdata b/externalpackages/boutdata
index e458cf0cf2..11f5d0acb3 160000
--- a/externalpackages/boutdata
+++ b/externalpackages/boutdata
@@ -1 +1 @@
-Subproject commit e458cf0cf2af6ff68db91da39ef3e15a7e9e6b3d
+Subproject commit 11f5d0acb3d92a30eb0f97866c206a238c487076
diff --git a/externalpackages/fmt b/externalpackages/fmt
index 2ac6c5ca8b..407c905e45 160000
--- a/externalpackages/fmt
+++ b/externalpackages/fmt
@@ -1 +1 @@
-Subproject commit 2ac6c5ca8b3dfbcb1cc5cf49a8cc121e3984559c
+Subproject commit 407c905e45ad75fc29bf0f9bb7c5c2fd3475976f
diff --git a/externalpackages/googletest b/externalpackages/googletest
index 0953a17a42..d72f9c8aea 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 0953a17a4281fc26831da647ad3fcd5e21e6473b
+Subproject commit d72f9c8aea6817cdf1ca0ac10887f328de7f3da2
diff --git a/manual/sphinx/figs/topology_cross_section2.png b/manual/sphinx/figs/topology_cross_section.png
similarity index 100%
rename from manual/sphinx/figs/topology_cross_section2.png
rename to manual/sphinx/figs/topology_cross_section.png
diff --git a/manual/sphinx/figs/topology_cross_section.svg b/manual/sphinx/figs/topology_cross_section.svg
new file mode 100644
index 0000000000..5c1ab47523
--- /dev/null
+++ b/manual/sphinx/figs/topology_cross_section.svg
@@ -0,0 +1,1609 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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+
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+   xmlns:dc="http://purl.org/dc/elements/1.1/"
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+   sodipodi:docname="Drawing.svg"
+   inkscape:export-filename="/home/john/Dropbox/Documents/BOUT++/Mesh_topology_diagram_Luke/Drawing.png"
+   inkscape:export-xdpi="96"
+   inkscape:export-ydpi="96">
+  <sodipodi:namedview
+     id="base"
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diff --git a/manual/sphinx/user_docs/topology.rst b/manual/sphinx/user_docs/topology.rst
index 2711d1e0e3..d996b123ea 100644
--- a/manual/sphinx/user_docs/topology.rst
+++ b/manual/sphinx/user_docs/topology.rst
@@ -45,7 +45,7 @@ The "common" topologies:
 
 And all advanced/complex topologies with up to two X-points:
 
-- **"snowflake"**: The SF topologies feature a second order null point created by two X-points close to each other. The ideal SF has a single separatrix and 4 legs, but more realistic configurations can have an extra PFR between the legs. 
+- **"snowflake"**: The SF topologies feature a second order null point created by two X-points close to each other. The ideal SF has a single separatrix and 4 legs, but more realistic configurations can have an extra PFR between the legs.
   The **"snowflake+"** and **"snowflake-"** unlike the perfect **SF**, feature an extra central PFR and the secondary X-point is located either above or below the primary one, respectively (along the y-direction).
 - **"X-Point Target"**: The X-Point Target configuration has the main separatrix extended a longer distance and no PFR between the East and South East targets.
 
@@ -96,7 +96,7 @@ PFRs (private flux regions), and the core of the tokamak. If
 otherwise it can be any of the more advanced configurations.
 
 .. _fig-topology-cross-section:
-.. figure:: ../figs/topology_cross_section2.*
+.. figure:: ../figs/topology_cross_section.*
    :alt: Cross-section of the tokamak topology used in BOUT++
 
    Deconstruction of a poloidal tokamak cross-section into logical

From 6729983fd48a11cc02a5782a18d19b701f327747 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 13:42:08 +0200
Subject: [PATCH 1123/1827] Fix documentation

Thanks to Mike Kryjak for noticing.
---
 manual/sphinx/user_docs/boundary_options.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index fd50076a9b..41f0ad6c1c 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -530,7 +530,7 @@ Here is a short summary of some members of ``pnt``, where ``f`` is a :
    * - ``pnt.ythis(f)``
      - Returns the value at the last point in the domain
    * - ``pnt.ynext(f)``
-     - Returns the value at the first point in the domain
+     - Returns the value at the first point in the boundary, i.e. one beyond the domain.
    * - ``pnt.yprev(f)``
      - Returns the value at the second to last point in the domain, if it is
        valid. NB: this point may not be valid.

From 38e3edb510b4a14656f00d398e8aa1b04d415f74 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 09:45:16 +0200
Subject: [PATCH 1124/1827] Set enum size for performance

---
 include/bout/boundary_region.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 301c4a01f6..56eab42c67 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -15,7 +15,7 @@ extern Mesh* mesh; ///< Global mesh
 } // namespace bout
 
 /// Location of boundary
-enum class BndryLoc {
+enum class BndryLoc : std::int8_t {
   xin,
   xout,
   ydown,
@@ -36,7 +36,7 @@ constexpr BndryLoc BNDRY_PAR_BKWD_XIN = BndryLoc::par_bkwd_xin;
 constexpr BndryLoc BNDRY_PAR_FWD_XOUT = BndryLoc::par_fwd_xout;
 constexpr BndryLoc BNDRY_PAR_BKWD_XOUT = BndryLoc::par_bkwd_xout;
 
-enum class YBndryType { sheath, not_sheath, all };
+enum class YBndryType : std::int8_t { sheath, not_sheath, all };
 
 class BoundaryRegionBase {
 public:

From 60514611ff7d66457fdf908f7be48061383bf3c5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 10:10:43 +0200
Subject: [PATCH 1125/1827] Also declare size in forward definition

---
 include/bout/field_data.hxx | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/include/bout/field_data.hxx b/include/bout/field_data.hxx
index 185dcabf2d..5e49d0d8a2 100644
--- a/include/bout/field_data.hxx
+++ b/include/bout/field_data.hxx
@@ -6,7 +6,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -45,7 +45,7 @@ class Mesh;
 
 #include "bout/boundary_region.hxx"
 class BoundaryRegionPar;
-enum class BndryLoc;
+enum class BndryLoc : std::int8_t;
 
 #include "bout/sys/expressionparser.hxx"
 
@@ -77,7 +77,7 @@ public:
   /// Number of BoutReals in one element
   virtual int elementSize() const { return 1; }
 
-  virtual void doneComms(){}; // Notifies that communications done
+  virtual void doneComms() {}; // Notifies that communications done
 
   // Boundary conditions
   void setBoundary(const std::string& name); ///< Set the boundary conditions
@@ -86,13 +86,13 @@ public:
   copyBoundary(const FieldData& f); ///< Copy the boundary conditions from another field
 
   virtual void applyBoundary(bool UNUSED(init) = false) {}
-  virtual void applyTDerivBoundary(){};
+  virtual void applyTDerivBoundary() {};
 
-  virtual void applyParallelBoundary(){};
-  virtual void applyParallelBoundary(BoutReal UNUSED(t)){};
-  virtual void applyParallelBoundary(const std::string& UNUSED(condition)){};
+  virtual void applyParallelBoundary() {};
+  virtual void applyParallelBoundary(BoutReal UNUSED(t)) {};
+  virtual void applyParallelBoundary(const std::string& UNUSED(condition)) {};
   virtual void applyParallelBoundary(const std::string& UNUSED(region),
-                                     const std::string& UNUSED(condition)){};
+                                     const std::string& UNUSED(condition)) {};
   // JMAD
   void addBndryFunction(FuncPtr userfunc, BndryLoc location);
   void addBndryGenerator(FieldGeneratorPtr gen, BndryLoc location);

From d17077414dc6122b9376f75f4e59ae0d915e7d5b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 10:17:40 +0200
Subject: [PATCH 1126/1827] Change BOUT_ENUM_CLASS to 8bit integer

---
 include/bout/bout_enum_class.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index 6f632747ed..b142719ac2 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -2,7 +2,7 @@
  * Copyright 2019 B.D.Dudson, J.T.Omotani, P.Hill
  *
  * Contact Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -66,7 +66,7 @@
 /// Create an enum class with toString and <enum name>FromString functions, and an
 /// Options::as<enum> overload to read the enum
 #define BOUT_ENUM_CLASS(enumname, ...)                                         \
-  enum class enumname { __VA_ARGS__ };                                         \
+  enum class enumname : std::int8_t { __VA_ARGS__ };                           \
                                                                                \
   inline std::string toString(enumname e) {                                    \
                                                                                \

From 20d61c413d7b762b0940b6cd55204e5733084298 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 10:23:52 +0200
Subject: [PATCH 1127/1827] Ensure int8_t is defined

---
 include/bout/boundary_region.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 56eab42c67..f0b2ab897a 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -4,6 +4,7 @@ class BoundaryRegion;
 #ifndef BOUT_BNDRY_REGION_H
 #define BOUT_BNDRY_REGION_H
 
+#include <cstddef>
 #include <string>
 #include <utility>
 

From 399d2195fbc38a35dad11b9768552d92fff84612 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 10:24:45 +0200
Subject: [PATCH 1128/1827] Ensure int8_t is defined

---
 include/bout/bout_enum_class.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index b142719ac2..b3266972c9 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -26,6 +26,7 @@
 #include "bout/macro_for_each.hxx"
 #include "bout/options.hxx" // IWYU pragma: keep
 
+#include <cstddef>
 #include <map>    // IWYU pragma: keep
 #include <string> // IWYU pragma: keep
 

From eaac19360c1bc56eabf85845513379cbc3b8e138 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 11:12:25 +0200
Subject: [PATCH 1129/1827] int8_t is defined in cstdint not cstddef

---
 include/bout/boundary_region.hxx |  3 +-
 include/bout/bout_enum_class.hxx |  2 +-
 include/bout/field_data.hxx      |  1 +
 include/bout/sys/uuid.h          | 65 ++++++++++++++++----------------
 4 files changed, 37 insertions(+), 34 deletions(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index f0b2ab897a..63c95d6efa 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -4,7 +4,7 @@ class BoundaryRegion;
 #ifndef BOUT_BNDRY_REGION_H
 #define BOUT_BNDRY_REGION_H
 
-#include <cstddef>
+#include <cstdint>
 #include <string>
 #include <utility>
 
@@ -37,6 +37,7 @@ constexpr BndryLoc BNDRY_PAR_BKWD_XIN = BndryLoc::par_bkwd_xin;
 constexpr BndryLoc BNDRY_PAR_FWD_XOUT = BndryLoc::par_fwd_xout;
 constexpr BndryLoc BNDRY_PAR_BKWD_XOUT = BndryLoc::par_bkwd_xout;
 
+// Physical type of y boundary
 enum class YBndryType : std::int8_t { sheath, not_sheath, all };
 
 class BoundaryRegionBase {
diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index b3266972c9..59539b1db7 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -26,7 +26,7 @@
 #include "bout/macro_for_each.hxx"
 #include "bout/options.hxx" // IWYU pragma: keep
 
-#include <cstddef>
+#include <cstdint>
 #include <map>    // IWYU pragma: keep
 #include <string> // IWYU pragma: keep
 
diff --git a/include/bout/field_data.hxx b/include/bout/field_data.hxx
index 5e49d0d8a2..c84cdda444 100644
--- a/include/bout/field_data.hxx
+++ b/include/bout/field_data.hxx
@@ -33,6 +33,7 @@ class FieldData;
 #include "bout/bout_types.hxx"
 #include "bout/unused.hxx"
 
+#include <cstdint>
 #include <map>
 #include <memory>
 #include <string>
diff --git a/include/bout/sys/uuid.h b/include/bout/sys/uuid.h
index d3d954e2fe..973103ef70 100644
--- a/include/bout/sys/uuid.h
+++ b/include/bout/sys/uuid.h
@@ -29,6 +29,7 @@
 #include <array>
 #include <atomic>
 #include <chrono>
+#include <cstdint>
 #include <cstring>
 #include <functional>
 #include <iomanip>
@@ -75,7 +76,7 @@ namespace uuids {
 
 namespace detail {
 template <typename TChar>
-constexpr inline unsigned char hex2char(TChar const ch) {
+constexpr inline unsigned char hex2char(const TChar ch) {
   if (ch >= static_cast<TChar>('0') && ch <= static_cast<TChar>('9'))
     return ch - static_cast<TChar>('0');
   if (ch >= static_cast<TChar>('a') && ch <= static_cast<TChar>('f'))
@@ -86,14 +87,14 @@ constexpr inline unsigned char hex2char(TChar const ch) {
 }
 
 template <typename TChar>
-constexpr inline bool is_hex(TChar const ch) {
+constexpr inline bool is_hex(const TChar ch) {
   return (ch >= static_cast<TChar>('0') && ch <= static_cast<TChar>('9'))
          || (ch >= static_cast<TChar>('a') && ch <= static_cast<TChar>('f'))
          || (ch >= static_cast<TChar>('A') && ch <= static_cast<TChar>('F'));
 }
 
 template <typename TChar>
-constexpr inline unsigned char hexpair2char(TChar const a, TChar const b) {
+constexpr inline unsigned char hexpair2char(const TChar a, const TChar b) {
   return (hex2char(a) << 4) | hex2char(b);
 }
 
@@ -104,7 +105,7 @@ class sha1 {
 
   static constexpr unsigned int block_bytes = 64;
 
-  inline static uint32_t left_rotate(uint32_t value, size_t const count) {
+  inline static uint32_t left_rotate(uint32_t value, const size_t count) {
     return (value << count) ^ (value >> (32 - count));
   }
 
@@ -129,7 +130,7 @@ class sha1 {
     }
   }
 
-  void process_block(void const* const start, void const* const end) {
+  void process_block(const void* const start, const void* const end) {
     const uint8_t* begin = static_cast<const uint8_t*>(start);
     const uint8_t* finish = static_cast<const uint8_t*>(end);
     while (begin != finish) {
@@ -138,13 +139,13 @@ class sha1 {
     }
   }
 
-  void process_bytes(void const* const data, size_t const len) {
+  void process_bytes(const void* const data, const size_t len) {
     const uint8_t* block = static_cast<const uint8_t*>(data);
     process_block(block, block + len);
   }
 
-  uint32_t const* get_digest(digest32_t digest) {
-    size_t const bitCount = this->m_byteCount * 8;
+  const uint32_t* get_digest(digest32_t digest) {
+    const size_t bitCount = this->m_byteCount * 8;
     process_byte(0x80);
     if (this->m_blockByteIndex > 56) {
       while (m_blockByteIndex != 0) {
@@ -165,13 +166,13 @@ class sha1 {
     process_byte(static_cast<unsigned char>((bitCount >> 24) & 0xFF));
     process_byte(static_cast<unsigned char>((bitCount >> 16) & 0xFF));
     process_byte(static_cast<unsigned char>((bitCount >> 8) & 0xFF));
-    process_byte(static_cast<unsigned char>((bitCount)&0xFF));
+    process_byte(static_cast<unsigned char>((bitCount) & 0xFF));
 
     memcpy(digest, m_digest, 5 * sizeof(uint32_t));
     return digest;
   }
 
-  uint8_t const* get_digest_bytes(digest8_t digest) {
+  const uint8_t* get_digest_bytes(digest8_t digest) {
     digest32_t d32;
     get_digest(d32);
     size_t di = 0;
@@ -343,13 +344,13 @@ class uuid {
 public:
   using value_type = uint8_t;
 
-  constexpr uuid() noexcept : data({}){};
+  constexpr uuid() noexcept : data({}) {};
 
   uuid(value_type (&arr)[16]) noexcept {
     std::copy(std::cbegin(arr), std::cend(arr), std::begin(data));
   }
 
-  uuid(std::array<value_type, 16> const& arr) noexcept {
+  uuid(const std::array<value_type, 16>& arr) noexcept {
     std::copy(std::cbegin(arr), std::cend(arr), std::begin(data));
   }
 
@@ -394,12 +395,12 @@ class uuid {
 
   void swap(uuid& other) noexcept { data.swap(other.data); }
 
-  inline char const* as_bytes() const {
-    return reinterpret_cast<char const*>(data.data());
+  inline const char* as_bytes() const {
+    return reinterpret_cast<const char*>(data.data());
   }
 
   template <class CharT = char>
-  static bool is_valid_uuid(CharT const* str) noexcept {
+  static bool is_valid_uuid(const CharT* str) noexcept {
     bool firstDigit = true;
     int hasBraces = 0;
     size_t index = 0;
@@ -454,12 +455,12 @@ class uuid {
   template <class CharT = char, class Traits = std::char_traits<CharT>,
             class Allocator = std::allocator<CharT>>
   static bool
-  is_valid_uuid(std::basic_string<CharT, Traits, Allocator> const& str) noexcept {
+  is_valid_uuid(const std::basic_string<CharT, Traits, Allocator>& str) noexcept {
     return is_valid_uuid(str.c_str());
   }
 
   template <class CharT = char>
-  static uuid from_string(CharT const* str) noexcept {
+  static uuid from_string(const CharT* str) noexcept {
     CharT digit = 0;
     bool firstDigit = true;
     int hasBraces = 0;
@@ -511,40 +512,40 @@ class uuid {
   template <class CharT = char, class Traits = std::char_traits<CharT>,
             class Allocator = std::allocator<CharT>>
   static uuid
-  from_string(std::basic_string<CharT, Traits, Allocator> const& str) noexcept {
+  from_string(const std::basic_string<CharT, Traits, Allocator>& str) noexcept {
     return from_string(str.c_str());
   }
 
 private:
   std::array<value_type, 16> data{{0}};
 
-  friend bool operator==(uuid const& lhs, uuid const& rhs) noexcept;
-  friend bool operator<(uuid const& lhs, uuid const& rhs) noexcept;
+  friend bool operator==(const uuid& lhs, const uuid& rhs) noexcept;
+  friend bool operator<(const uuid& lhs, const uuid& rhs) noexcept;
 
   template <class Elem, class Traits>
   friend std::basic_ostream<Elem, Traits>& operator<<(std::basic_ostream<Elem, Traits>& s,
-                                                      uuid const& id);
+                                                      const uuid& id);
 };
 
 // --------------------------------------------------------------------------------------------------------------------------
 // operators and non-member functions
 // --------------------------------------------------------------------------------------------------------------------------
 
-inline bool operator==(uuid const& lhs, uuid const& rhs) noexcept {
+inline bool operator==(const uuid& lhs, const uuid& rhs) noexcept {
   return lhs.data == rhs.data;
 }
 
-inline bool operator!=(uuid const& lhs, uuid const& rhs) noexcept {
+inline bool operator!=(const uuid& lhs, const uuid& rhs) noexcept {
   return !(lhs == rhs);
 }
 
-inline bool operator<(uuid const& lhs, uuid const& rhs) noexcept {
+inline bool operator<(const uuid& lhs, const uuid& rhs) noexcept {
   return lhs.data < rhs.data;
 }
 
 template <class Elem, class Traits>
 std::basic_ostream<Elem, Traits>& operator<<(std::basic_ostream<Elem, Traits>& s,
-                                             uuid const& id) {
+                                             const uuid& id) {
   // save current flags
   std::ios_base::fmtflags f(s.flags());
 
@@ -567,7 +568,7 @@ std::basic_ostream<Elem, Traits>& operator<<(std::basic_ostream<Elem, Traits>& s
 
 template <class CharT = char, class Traits = std::char_traits<CharT>,
           class Allocator = std::allocator<CharT>>
-inline std::basic_string<CharT, Traits, Allocator> to_string(uuid const& id) {
+inline std::basic_string<CharT, Traits, Allocator> to_string(const uuid& id) {
   std::basic_stringstream<CharT, Traits, Allocator> sstr;
   sstr << id;
   return sstr.str();
@@ -691,11 +692,11 @@ using uuid_random_generator = basic_uuid_random_generator<std::mt19937>;
 
 class uuid_name_generator {
 public:
-  explicit uuid_name_generator(uuid const& namespace_uuid) noexcept
+  explicit uuid_name_generator(const uuid& namespace_uuid) noexcept
       : nsuuid(namespace_uuid) {}
 
   template <class CharT = char>
-  uuid operator()(CharT const* name) {
+  uuid operator()(const CharT* name) {
     size_t size = 0;
     if (std::is_same<CharT, char>::value)
       size = strlen(name);
@@ -709,7 +710,7 @@ class uuid_name_generator {
 
   template <class CharT = char, class Traits = std::char_traits<CharT>,
             class Allocator = std::allocator<CharT>>
-  uuid operator()(std::basic_string<CharT, Traits, Allocator> const& name) {
+  uuid operator()(const std::basic_string<CharT, Traits, Allocator>& name) {
     reset();
     process_characters(name.data(), name.size());
     return make_uuid();
@@ -726,7 +727,7 @@ class uuid_name_generator {
 
   template <typename char_type,
             typename = std::enable_if_t<std::is_integral<char_type>::value>>
-  void process_characters(char_type const* const characters, size_t const count) {
+  void process_characters(const char_type* const characters, const size_t count) {
     for (size_t i = 0; i < count; i++) {
       uint32_t c = characters[i];
       hasher.process_byte(static_cast<unsigned char>((c >> 0) & 0xFF));
@@ -736,7 +737,7 @@ class uuid_name_generator {
     }
   }
 
-  void process_characters(const char* const characters, size_t const count) {
+  void process_characters(const char* const characters, const size_t count) {
     hasher.process_bytes(characters, count);
   }
 
@@ -846,7 +847,7 @@ struct hash<uuids::uuid> {
   using argument_type = uuids::uuid;
   using result_type = std::size_t;
 
-  result_type operator()(argument_type const& uuid) const {
+  result_type operator()(const argument_type& uuid) const {
     std::hash<std::string> hasher;
     return static_cast<result_type>(hasher(uuids::to_string(uuid)));
   }

From 372fbe75638987083043a0a7b65142f9ed0ff4ab Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 14:05:03 +0200
Subject: [PATCH 1130/1827] Header is used by macro, add comment for IWYU

---
 include/bout/bout_enum_class.hxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index 59539b1db7..334fa657da 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -26,9 +26,9 @@
 #include "bout/macro_for_each.hxx"
 #include "bout/options.hxx" // IWYU pragma: keep
 
-#include <cstdint>
-#include <map>    // IWYU pragma: keep
-#include <string> // IWYU pragma: keep
+#include <cstdint> // IWYU pragma: keep
+#include <map>     // IWYU pragma: keep
+#include <string>  // IWYU pragma: keep
 
 /// Create some macro magic similar to bout/macro_for_each.hxx, but allowing for the enum
 /// class name to be passed through to each _call

From 2dfa9503d3a3c705d547cb5e0975fec6431e8bd5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 15 Apr 2026 14:05:28 +0200
Subject: [PATCH 1131/1827] Do not move trivially-copyable variable

---
 include/bout/parallel_boundary_region.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 49f26cef8c..59ced04009 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -50,9 +50,9 @@ struct Indices {
   signed char valid;
   signed char offset;
   unsigned char abs_offset;
-  Indices(Ind3D index, RealPoint&& intersection, BoutReal length, signed char valid,
+  Indices(Ind3D index, RealPoint intersection, BoutReal length, signed char valid,
           signed char offset, unsigned char abs_offset)
-      : index(index), intersection(std::move(intersection)), length(length), valid(valid),
+      : index(index), intersection(intersection), length(length), valid(valid),
         offset(offset), abs_offset(abs_offset) {};
 };
 

From 1ff62a46d934d9b9e2d8ddbf3461b8f4ebd689f4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 12:35:17 +0200
Subject: [PATCH 1132/1827] Do not use custom pow implementation.

---
 include/bout/sys/parallel_stencils.hxx | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/include/bout/sys/parallel_stencils.hxx b/include/bout/sys/parallel_stencils.hxx
index 2cbec9c8b0..e3497773d2 100644
--- a/include/bout/sys/parallel_stencils.hxx
+++ b/include/bout/sys/parallel_stencils.hxx
@@ -4,15 +4,8 @@
 
 namespace parallel_stencil {
 // generated by src/mesh/parallel_boundary_stencil.cxx.py
-inline BoutReal pow(BoutReal val, int exp) {
-  // constexpr int expval = exp;
-  // static_assert(expval == 2 or expval == 3, "This pow is only for exponent 2 or 3");
-  if (exp == 2) {
-    return val * val;
-  }
-  ASSERT3(exp == 3);
-  return val * val * val;
-}
+using std::pow;
+
 inline BoutReal dirichlet_o1([[maybe_unused]] BoutReal spacing0, BoutReal value0) {
   return value0;
 }

From afe19090ab972aafc473fb2dac6b45ad386d0e3e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 12:35:42 +0200
Subject: [PATCH 1133/1827] Use bout namespace

---
 include/bout/boundary_iterator.hxx     | 2 +-
 include/bout/sys/parallel_stencils.hxx | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 765f83e694..97aa94063c 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -36,7 +36,7 @@ public:
   BoundaryRegionIter& operator*() { return *this; }
 
   void dirichlet_o2(Field3D& f, BoutReal value) const {
-    ynext(f) = parallel_stencil::dirichlet_o2(1, f[ind()], 0.5, value);
+    ynext(f) = bout::parallel_stencil::dirichlet_o2(1, f[ind()], 0.5, value);
   }
 
   BoutReal extrapolate_grad_o2(const Field3D& f) const { return f[ind()] - yprev(f); }
diff --git a/include/bout/sys/parallel_stencils.hxx b/include/bout/sys/parallel_stencils.hxx
index e3497773d2..651ebc3ca1 100644
--- a/include/bout/sys/parallel_stencils.hxx
+++ b/include/bout/sys/parallel_stencils.hxx
@@ -2,7 +2,7 @@
 #include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 
-namespace parallel_stencil {
+namespace bout::parallel_stencil {
 // generated by src/mesh/parallel_boundary_stencil.cxx.py
 using std::pow;
 
@@ -31,4 +31,4 @@ inline BoutReal neumann_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1
           - spacing1 * pow(spacing2, 2) * value0 + pow(spacing2, 2) * value1)
          / ((spacing1 - spacing2) * (2 * spacing0 - spacing1 - spacing2));
 }
-} // namespace parallel_stencil
+} // namespace bout::parallel_stencil

From 6d189979a904c61ee54ff2ab4ea5b8b5182beace Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 12:36:20 +0200
Subject: [PATCH 1134/1827] Use func for functions, and f for field

---
 include/bout/yboundary_regions.hxx | 32 +++++++++++++++---------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index ebfbbe3b29..da4e08b467 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -22,27 +22,27 @@
 
 class YBoundary {
 public:
-  template <class F>
-  void iter_regions(const F& f) {
+  template <class Func>
+  void iter_regions(const Func& func) {
     for (auto& region : boundary_regions) {
-      f(*region);
+      func(*region);
     }
     for (auto& region : boundary_regions_par) {
-      f(*region);
+      func(*region);
     }
   }
-  template <class F>
-  void iter_pnts(const F& f) {
+  template <class Func>
+  void iter_points(const Func& func) {
     iter_regions([&](auto& region) {
-      for (auto& pnt : region) {
-        f(pnt);
+      for (auto& point : region) {
+        func(point);
       }
     });
   }
 
-  template <class F>
-  void iter(const F& f) {
-    return iter_regions(f);
+  template <class Func>
+  void iter(const Func& func) {
+    return iter_points(func);
   }
 
   YBoundary(YBndryType type, Options* options_ptr, Mesh* mesh) {
@@ -105,11 +105,11 @@ public:
     // Cache boundary regions
     _contains.emplace_back(mesh, false);
     _contains.emplace_back(mesh, false);
-    iter_pnts([&](const auto& pnt) {
-      if (pnt.dir == 1) {
-        _contains[1][pnt.ind()] = true;
-      } else if (pnt.dir == -1) {
-        _contains[0][pnt.ind()] = true;
+    iter_points([&](const auto& point) {
+      if (point.dir == 1) {
+        _contains[1][point.ind()] = true;
+      } else if (point.dir == -1) {
+        _contains[0][point.ind()] = true;
       }
     });
   }

From ad0f14ea5b3f53235bb247ab5727fe752fa99b6f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 12:37:48 +0200
Subject: [PATCH 1135/1827] Use point rather then pnt

---
 manual/sphinx/user_docs/boundary_options.rst | 33 ++++++++++----------
 src/mesh/parallel/fci.cxx                    | 14 +++++----
 2 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 41f0ad6c1c..8e299b6eaf 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -500,8 +500,9 @@ geometries, as flux coordinate independent (FCI) method::
 
       void rhs() {
         BoutReal totalFlux = 0;
-        mesh->getCoordinates()->getYBoundary()->iter_pnts([&](auto& pnt) {
-          BoutReal flux = pnt.interpolate_sheath_o2(N) * pnt.interpolate_sheath_o2(V);
+        mesh->getCoordinates()->getYBoundary()->iter_points([&](auto& point) {
+          BoutReal flux = point.interpolate_sheath_o2(N) * point.interpolate_sheath_o2(V);
+          totalFlux += flux;
         });
       }
 
@@ -512,14 +513,14 @@ geometries, as flux coordinate independent (FCI) method::
 
 
 
-There are several member functions of ``pnt``. ``pnt`` is of type
+There are several member functions of ``point``. ``point`` is of type
 `BoundaryRegionParIterBase` and `BoundaryRegionIter`, and both should provide
 the same interface. If they don't that is a bug, as the above code is a
 template, that gets instantiated for both types, and thus requires both
 classes to provide the same interface, one for FCI-like boundaries and one for
 field aligned boundaries.
 
-Here is a short summary of some members of ``pnt``, where ``f`` is a :
+Here is a short summary of some members of ``point``, where ``f`` is a :
 
 .. list-table:: Members for boundary operation
    :widths: 15 70
@@ -527,31 +528,31 @@ Here is a short summary of some members of ``pnt``, where ``f`` is a :
 
    * - Function
      - Description
-   * - ``pnt.ythis(f)``
+   * - ``point.ythis(f)``
      - Returns the value at the last point in the domain
-   * - ``pnt.ynext(f)``
+   * - ``point.ynext(f)``
      - Returns the value at the first point in the boundary, i.e. one beyond the domain.
-   * - ``pnt.yprev(f)``
+   * - ``point.yprev(f)``
      - Returns the value at the second to last point in the domain, if it is
        valid. NB: this point may not be valid.
-   * - ``pnt.interpolate_sheath_o2(f)``
+   * - ``point.interpolate_sheath_o2(f)``
      - Returns the value at the boundary, assuming the bounday value has been set
-   * - ``pnt.extrapolate_sheath_o1(f)``
+   * - ``point.extrapolate_sheath_o1(f)``
      - Returns the value at the boundary, extrapolating from the bulk, first order
-   * - ``pnt.extrapolate_sheath_o2(f)``
+   * - ``point.extrapolate_sheath_o2(f)``
      - Returns the value at the boundary, extrapolating from the bulk, second order
-   * - ``pnt.extrapolate_next_o{1,2}(f)``
+   * - ``point.extrapolate_next_o{1,2}(f)``
      - Extrapolate into the boundary from the bulk, first or second order
-   * - ``pnt.extrapolate_grad_o{1,2}(f)``
+   * - ``point.extrapolate_grad_o{1,2}(f)``
      - Extrapolate the gradient into the boundary, first or second order
-   * - ``pnt.dirichlet_o{1,2,3}(f, v)``
+   * - ``point.dirichlet_o{1,2,3}(f, v)``
      - Apply dirichlet boundary conditions with value ``v`` and given order
-   * - ``pnt.neumann_o{1,2,3}(f, v)``
+   * - ``point.neumann_o{1,2,3}(f, v)``
      - Applies a gradient of ``v / dy`` boundary condition.
-   * - ``pnt.limitFree(f)``
+   * - ``point.limitFree(f)``
      - Extrapolate into the boundary using only monotonic decreasing values.
        ``f`` needs to be positive.
-   * - ``pnt.dir``
+   * - ``point.dir``
      - The direction of the boundary.
 
 
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 01dd6f72f8..45004f07d6 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -361,12 +361,14 @@ FCITransform::FCITransform(Mesh& mesh, const Coordinates::FieldMetric& dy, bool
       if (bndry->dir == bndry2->dir) {
         continue;
       }
-      for (auto pnt : *bndry) {
-        for (auto pnt2 : *bndry2) {
-#warning this could likely be done faster
-          if (pnt.ind() == pnt2.ind()) {
-            pnt.setValid(
-                static_cast<signed char>(std::abs((pnt2.offset() - pnt.offset())) - 2));
+      for (auto point : *bndry) {
+        for (auto point2 : *bndry2) {
+          if (point.ind() == point2.ind()) {
+            // This point has a boundary in both directions.  Calculate the
+            // distance between two points, to check how many non-boundary
+            // points exist.
+            point.setValid(static_cast<signed char>(
+                std::abs((point2.offset() - point.offset())) - 2));
           }
         }
       }

From f0e6f283f38939168bbc1b1bf645f89eb4c13918 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 12:38:46 +0200
Subject: [PATCH 1136/1827] fixup std pow

---
 src/mesh/parallel_boundary_stencil.cxx.py | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/src/mesh/parallel_boundary_stencil.cxx.py b/src/mesh/parallel_boundary_stencil.cxx.py
index d0988ee099..adc163eece 100644
--- a/src/mesh/parallel_boundary_stencil.cxx.py
+++ b/src/mesh/parallel_boundary_stencil.cxx.py
@@ -26,18 +26,10 @@ def run(cmd):
 
 if __name__ == "__main__":
     with tmpf("w", dir=".", delete=False) as f:
-        f.write("namespace {\n")
+        f.write("namespace bout::parallel_stencil {\n")
         f.write(
-            """
-inline BoutReal pow(BoutReal val, int exp) {
-  //constexpr int expval = exp;
-  //static_assert(expval == 2 or expval == 3, "This pow is only for exponent 2 or 3");
-  if (exp == 2) {
-    return val * val;
-  }
-  ASSERT3(exp == 3);
-  return val * val * val;
-}
+            """using std::pow;
+
 """
         )
 

From 92569dd0e8eae40f33dbb5267918ff385d6d8ba2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 12:40:24 +0200
Subject: [PATCH 1137/1827] Only check for FCI if CHECK > 0

---
 src/mesh/impls/bout/boutmesh.cxx | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index a19e416beb..168727598d 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -2933,9 +2933,11 @@ void BoutMesh::addBoundaryRegions() {
 }
 
 RangeIterator BoutMesh::iterateBndryLowerInnerY() const {
+#if CHECK > 0
   if (this->isFci()) {
     throw BoutException("FCI should never use this iterator");
   }
+#endif
 
   int xs = 0;
   int xe = LocalNx - 1;
@@ -2971,9 +2973,11 @@ RangeIterator BoutMesh::iterateBndryLowerInnerY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryLowerOuterY() const {
+#if CHECK > 0
   if (this->isFci()) {
     throw BoutException("FCI should never use this iterator");
   }
+#endif
 
   int xs = 0;
   int xe = LocalNx - 1;
@@ -3008,9 +3012,11 @@ RangeIterator BoutMesh::iterateBndryLowerOuterY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryLowerY() const {
+#if CHECK > 0
   if (this->isFci()) {
     throw BoutException("FCI should never use this iterator");
   }
+#endif
 
   int xs = 0;
   int xe = LocalNx - 1;
@@ -3041,9 +3047,11 @@ RangeIterator BoutMesh::iterateBndryLowerY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryUpperInnerY() const {
+#if CHECK > 0
   if (this->isFci()) {
     throw BoutException("FCI should never use this iterator");
   }
+#endif
 
   int xs = 0;
   int xe = LocalNx - 1;
@@ -3079,9 +3087,11 @@ RangeIterator BoutMesh::iterateBndryUpperInnerY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryUpperOuterY() const {
+#if CHECK > 0
   if (this->isFci()) {
     throw BoutException("FCI should never use this iterator");
   }
+#endif
 
   int xs = 0;
   int xe = LocalNx - 1;
@@ -3117,9 +3127,11 @@ RangeIterator BoutMesh::iterateBndryUpperOuterY() const {
 }
 
 RangeIterator BoutMesh::iterateBndryUpperY() const {
+#if CHECK > 0
   if (this->isFci()) {
     throw BoutException("FCI should never use this iterator");
   }
+#endif
 
   int xs = 0;
   int xe = LocalNx - 1;

From 42836efab150f718839ce71a8a6da28749a8f6d0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 13:28:06 +0200
Subject: [PATCH 1138/1827] getBoundariesPar can be const

---
 include/bout/mesh.hxx            | 8 ++++----
 src/mesh/impls/bout/boutmesh.cxx | 2 +-
 src/mesh/impls/bout/boutmesh.hxx | 2 +-
 tests/unit/fake_mesh.hxx         | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index a1ed6a9011..0e96e162f9 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -3,7 +3,7 @@
  *
  * Interface for mesh classes. Contains standard variables and useful
  * routines.
- * 
+ *
  * Changelog
  * =========
  *
@@ -11,7 +11,7 @@
  *     * Removing coordinate system into separate
  *       Coordinates class
  *     * Adding index derivative functions from derivs.cxx
- * 
+ *
  * 2010-06 Ben Dudson, Sean Farley
  *     * Initial version, adapted from GridData class
  *     * Incorporates code from topology.cpp and Communicator
@@ -20,7 +20,7 @@
  * Copyright 2010-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -501,7 +501,7 @@ public:
   /// get only xout:
   /// mesh->getBoundariesPar(Mesh::BoundaryParType::xout)
   virtual std::vector<std::shared_ptr<BoundaryRegionPar>>
-  getBoundariesPar(BoundaryParType type = BoundaryParType::all) = 0;
+  getBoundariesPar(BoundaryParType type = BoundaryParType::all) const = 0;
 
   /// Add a parallel(Y) boundary to this processor
   virtual void addBoundaryPar(std::shared_ptr<BoundaryRegionPar> UNUSED(bndry),
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 168727598d..e5d4858f45 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -3164,7 +3164,7 @@ RangeIterator BoutMesh::iterateBndryUpperY() const {
 std::vector<BoundaryRegion*> BoutMesh::getBoundaries() { return boundary; }
 
 std::vector<std::shared_ptr<BoundaryRegionPar>>
-BoutMesh::getBoundariesPar(BoundaryParType type) {
+BoutMesh::getBoundariesPar(BoundaryParType type) const {
   return par_boundary[static_cast<int>(type)];
 }
 
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index b42bf325b5..835cb5dd53 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -164,7 +164,7 @@ public:
   // Boundary regions
   std::vector<BoundaryRegion*> getBoundaries() override;
   std::vector<std::shared_ptr<BoundaryRegionPar>>
-  getBoundariesPar(BoundaryParType type) override;
+  getBoundariesPar(BoundaryParType type) const override;
   void addBoundaryPar(std::shared_ptr<BoundaryRegionPar> bndry,
                       BoundaryParType type) override;
   std::set<std::string> getPossibleBoundaries() const override;
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index aa0220609b..aa335110a5 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -173,7 +173,7 @@ public:
   void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); }
   std::vector<BoundaryRegion*> getBoundaries() override { return boundaries; }
   std::vector<std::shared_ptr<BoundaryRegionPar>>
-  getBoundariesPar(BoundaryParType UNUSED(type)) override {
+  getBoundariesPar(BoundaryParType UNUSED(type)) const override {
     return std::vector<std::shared_ptr<BoundaryRegionPar>>();
   }
   BoutReal GlobalX(int jx) const override { return jx; }

From ceb557afc76d33ab8930eb2e40ae1d951d2d3238 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 13:31:30 +0200
Subject: [PATCH 1139/1827] Make dir a function and store a reference to mesh,
 rather then a pointer

---
 include/bout/boundary_iterator.hxx           | 44 ++++++++++----------
 include/bout/parallel_boundary_op.hxx        |  2 +-
 include/bout/parallel_boundary_region.hxx    | 24 ++++++-----
 include/bout/yboundary_regions.hxx           | 25 ++++++-----
 manual/sphinx/user_docs/boundary_options.rst |  2 +-
 src/mesh/coordinates.cxx                     |  2 +-
 src/mesh/parallel/fci.cxx                    |  2 +-
 7 files changed, 52 insertions(+), 49 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 97aa94063c..dfee87fdf8 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -16,8 +16,8 @@
 class BoundaryRegionIter {
 public:
   virtual ~BoundaryRegionIter() = default;
-  BoundaryRegionIter(int x, int y, int bx, int by, Mesh* mesh)
-      : dir(bx + by), x(x), y(y), bx(bx), by(by), localmesh(mesh) {
+  BoundaryRegionIter(int x, int y, int bx, int by, const Mesh& mesh)
+      : _dir(bx + by), x(x), y(y), bx(bx), by(by), localmesh(mesh) {
     ASSERT3(bx * by == 0);
   }
   bool operator!=(const BoundaryRegionIter& rhs) const { return ind() != rhs.ind(); }
@@ -81,12 +81,12 @@ public:
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
     BoutReal val = ythis(f);
     if (mode == SheathLimitMode::linear_free) {
-      for (int i = 1; i <= localmesh->ystart; ++i) {
+      for (int i = 1; i <= localmesh.ystart; ++i) {
         val += fac;
         f[ind().yp(by * i).xp(bx * i)] = val;
       }
     } else {
-      for (int i = 1; i <= localmesh->ystart; ++i) {
+      for (int i = 1; i <= localmesh.ystart; ++i) {
         val *= fac;
         f[ind().yp(by * i).xp(bx * i)] = val;
       }
@@ -97,7 +97,7 @@ public:
     const BoutReal fac =
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f));
     BoutReal val = ythis(f);
-    for (int i = 1; i <= localmesh->ystart; ++i) {
+    for (int i = 1; i <= localmesh.ystart; ++i) {
       val *= fac;
       f[ind().yp(by * i).xp(bx * i)] = val;
     }
@@ -110,7 +110,7 @@ public:
 
   void neumann_o1(Field3D& f, BoutReal grad) const {
     BoutReal val = ythis(f);
-    for (int i = 1; i <= localmesh->ystart; ++i) {
+    for (int i = 1; i <= localmesh.ystart; ++i) {
       val += grad;
       f[ind().yp(by * i).xp(bx * i)] = val;
     }
@@ -118,7 +118,7 @@ public:
 
   void neumann_o2(Field3D& f, BoutReal grad) const {
     BoutReal val = yprev(f) + grad;
-    for (int i = 1; i <= localmesh->ystart; ++i) {
+    for (int i = 1; i <= localmesh.ystart; ++i) {
       val += grad;
       f[ind().yp(by * i).xp(bx * i)] = val;
     }
@@ -137,34 +137,35 @@ public:
 
   void setYPrevIfValid(Field3D& f, BoutReal val) const { yprev(f) = val; }
   void setAll(Field3D& f, const BoutReal val) const {
-    for (int i = -localmesh->ystart; i <= localmesh->ystart; ++i) {
+    for (int i = -localmesh.ystart; i <= localmesh.ystart; ++i) {
       f[ind().yp(by * i).xp(bx * i)] = val;
     }
   }
 
   static int abs_offset() { return 1; }
 
-#if BOUT_USE_METRIC_3D == 0
   BoutReal& ynext(Field2D& f) const { return f[ind().yp(by).xp(bx)]; }
   const BoutReal& ynext(const Field2D& f) const { return f[ind().yp(by).xp(bx)]; }
   BoutReal& yprev(Field2D& f) const { return f[ind().yp(-by).xp(-bx)]; }
   const BoutReal& yprev(const Field2D& f) const { return f[ind().yp(-by).xp(-bx)]; }
-#endif
 
-  const int dir;
+  int dir() const { return _dir; }
+
+private:
+  int _dir;
 
 protected:
   int z{0};
   int x;
   int y;
-  const int bx;
-  const int by;
+  int bx;
+  int by;
 
 private:
-  Mesh* localmesh;
-  int nx() const { return localmesh->LocalNx; }
-  int ny() const { return localmesh->LocalNy; }
-  int nz() const { return localmesh->LocalNz; }
+  const Mesh& localmesh;
+  int nx() const { return localmesh.LocalNx; }
+  int ny() const { return localmesh.LocalNy; }
+  int nz() const { return localmesh.LocalNz; }
 
   Ind3D xyz2ind(int x, int y, int z) const {
     return Ind3D{((x * ny() + y) * nz()) + z, ny(), nz()};
@@ -174,7 +175,8 @@ private:
 class BoundaryRegionIterY : public BoundaryRegionIter {
 public:
   ~BoundaryRegionIterY() override = default;
-  BoundaryRegionIterY(const RangeIterator& r, int y, int dir, bool is_end, Mesh* mesh)
+  BoundaryRegionIterY(const RangeIterator& r, int y, int dir, bool is_end,
+                      const Mesh& mesh)
       : BoundaryRegionIter(r.ind, y, 0, dir, mesh), r(r), is_end(is_end) {}
 
   bool operator!=(const BoundaryRegionIterY& rhs) {
@@ -203,16 +205,16 @@ private:
 
 class NewBoundaryRegionY {
 public:
-  NewBoundaryRegionY(Mesh* mesh, bool lower, const RangeIterator& r)
+  NewBoundaryRegionY(const Mesh& mesh, bool lower, const RangeIterator& r)
       : mesh(mesh), lower(lower), r(r) {}
   BoundaryRegionIterY begin(bool begin = true) {
-    return BoundaryRegionIterY(r, lower ? mesh->ystart : mesh->yend, lower ? -1 : +1,
+    return BoundaryRegionIterY(r, lower ? mesh.ystart : mesh.yend, lower ? -1 : +1,
                                !begin, mesh);
   }
   BoundaryRegionIterY end() { return begin(false); }
 
 private:
-  Mesh* mesh;
+  const Mesh& mesh;
   bool lower;
   RangeIterator r;
 };
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index 9e551ebc17..3e81085eb0 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -91,7 +91,7 @@ public:
   void apply(Field3D& f) override { return apply(f, 0); }
 
   void apply(Field3D& f, BoutReal t) override {
-    f.ynext(bndry->dir).allocate(); // Ensure unique before modifying
+    f.ynext(bndry->dir()).allocate(); // Ensure unique before modifying
 
     auto dy = f.getCoordinates()->dy;
 
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 59ced04009..5d81103208 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -118,7 +118,7 @@ class BoundaryRegionParIterBase {
 public:
   BoundaryRegionParIterBase(IndicesVec& bndry_points, IndicesIter bndry_position, int dir,
                             Mesh* localmesh)
-      : bndry_points(bndry_points), bndry_position(bndry_position), dir(dir),
+      : bndry_points(bndry_points), bndry_position(bndry_position), _dir(dir),
         localmesh(localmesh) {};
 
   // getter
@@ -249,7 +249,7 @@ public:
     }
   }
 
-  bool is_lower() const { return dir == -1; }
+  bool is_lower() const { return _dir == -1; }
 
   // NB: value needs to be scaled by dy
   // neumann_o1 is actually o2 if we would use an appropriate one-sided stencil.
@@ -327,7 +327,7 @@ public:
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }
-    auto _off = offset() + off * dir;
+    auto _off = offset() + off * _dir;
     return f.ynext(_off)[ind().yp(_off)];
   }
   template <bool check = true>
@@ -336,7 +336,7 @@ public:
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }
-    auto _off = offset() + off * dir;
+    auto _off = offset() + off * _dir;
     return f.ynext(_off)[ind().yp(_off)];
   }
 
@@ -353,7 +353,7 @@ public:
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }
-    auto _off = offset() + off * dir;
+    auto _off = offset() + off * _dir;
     return f(_off, ind().yp(_off));
   }
   BoutReal ynext(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
@@ -391,9 +391,10 @@ private:
   IndicesIter bndry_position;
 
   constexpr static BoutReal small_value = 1e-2;
+  int _dir;
 
 public:
-  const int dir;
+  int dir() const { return _dir; }
   Mesh* localmesh;
 };
 } // namespace parallel_boundary_region
@@ -409,12 +410,12 @@ using BoundaryRegionParIterConst =
 class BoundaryRegionPar : public BoundaryRegionBase {
 public:
   BoundaryRegionPar(const std::string& name, int dir, Mesh* passmesh)
-      : BoundaryRegionBase(name, passmesh), dir(dir) {
+      : BoundaryRegionBase(name, passmesh), _dir(dir) {
     ASSERT0(std::abs(dir) == 1);
     BoundaryRegionBase::isParallel = true;
   }
   BoundaryRegionPar(const std::string& name, BndryLoc loc, int dir, Mesh* passmesh)
-      : BoundaryRegionBase(name, loc, passmesh), dir(dir) {
+      : BoundaryRegionBase(name, loc, passmesh), _dir(dir) {
     BoundaryRegionBase::isParallel = true;
     ASSERT0(std::abs(dir) == 1);
   }
@@ -465,15 +466,16 @@ public:
   //   return BoundaryRegionParIterConst(bndry_points, bndry_points.begin(), dir);
   // }
   BoundaryRegionParIter begin() {
-    return BoundaryRegionParIter(bndry_points, bndry_points.begin(), dir, localmesh);
+    return BoundaryRegionParIter(bndry_points, bndry_points.begin(), _dir, localmesh);
   }
   BoundaryRegionParIter end() {
-    return BoundaryRegionParIter(bndry_points, bndry_points.end(), dir, localmesh);
+    return BoundaryRegionParIter(bndry_points, bndry_points.end(), _dir, localmesh);
   }
 
-  const int dir;
+  int dir() const { return _dir; }
 
 private:
+  int _dir;
   /// Vector of points in the boundary
   bout::parallel_boundary_region::IndicesVec bndry_points;
   /// Current position in the boundary points
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index da4e08b467..982dff7839 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -45,15 +45,14 @@ public:
     return iter_points(func);
   }
 
-  YBoundary(YBndryType type, Options* options_ptr, Mesh* mesh) {
-    ASSERT3(mesh != nullptr);
+  YBoundary(YBndryType type, Options* options_ptr, const Mesh& mesh) {
     bool lower_y = true;
     bool upper_y = true;
     bool outer_x = true;
     bool inner_x = false;
     if (options_ptr != nullptr) {
       auto& options = *options_ptr;
-      if (!mesh->isFci()) {
+      if (!mesh.isFci()) {
         lower_y =
             options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
         upper_y =
@@ -81,34 +80,34 @@ public:
       inner_x = true;
     }
 
-    if (mesh->isFci()) {
+    if (mesh.isFci()) {
       if (outer_x) {
-        for (auto& bndry : mesh->getBoundariesPar(BoundaryParType::xout)) {
+        for (auto& bndry : mesh.getBoundariesPar(BoundaryParType::xout)) {
           boundary_regions_par.push_back(bndry);
         }
       }
       if (inner_x) {
-        for (auto& bndry : mesh->getBoundariesPar(BoundaryParType::xin)) {
+        for (auto& bndry : mesh.getBoundariesPar(BoundaryParType::xin)) {
           boundary_regions_par.push_back(bndry);
         }
       }
     } else {
       if (lower_y) {
         boundary_regions.push_back(
-            std::make_shared<NewBoundaryRegionY>(mesh, true, mesh->iterateBndryLowerY()));
+            std::make_shared<NewBoundaryRegionY>(mesh, true, mesh.iterateBndryLowerY()));
       }
       if (upper_y) {
-        boundary_regions.push_back(std::make_shared<NewBoundaryRegionY>(
-            mesh, false, mesh->iterateBndryUpperY()));
+        boundary_regions.push_back(
+            std::make_shared<NewBoundaryRegionY>(mesh, false, mesh.iterateBndryUpperY()));
       }
     }
     // Cache boundary regions
-    _contains.emplace_back(mesh, false);
-    _contains.emplace_back(mesh, false);
+    _contains.emplace_back(&mesh, false);
+    _contains.emplace_back(&mesh, false);
     iter_points([&](const auto& point) {
-      if (point.dir == 1) {
+      if (point.dir() == 1) {
         _contains[1][point.ind()] = true;
-      } else if (point.dir == -1) {
+      } else if (point.dir() == -1) {
         _contains[0][point.ind()] = true;
       }
     });
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 8e299b6eaf..1aba0321d2 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -552,7 +552,7 @@ Here is a short summary of some members of ``point``, where ``f`` is a :
    * - ``point.limitFree(f)``
      - Extrapolate into the boundary using only monotonic decreasing values.
        ``f`` needs to be positive.
-   * - ``point.dir``
+   * - ``point.dir()``
      - The direction of the boundary.
 
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index f6ac16086b..634db26f3a 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2012,5 +2012,5 @@ void Coordinates::checkContravariant() {
 }
 
 std::shared_ptr<YBoundary> Coordinates::makeYBoundary(YBndryType type) const {
-  return std::make_shared<YBoundary>(type, localoptions, localmesh);
+  return std::make_shared<YBoundary>(type, localoptions, *localmesh);
 }
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 45004f07d6..60c7d438fa 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -358,7 +358,7 @@ FCITransform::FCITransform(Mesh& mesh, const Coordinates::FieldMetric& dy, bool
                               backward_boundary_xin, backward_boundary_xout};
   for (const auto& bndry : bndries) {
     for (const auto& bndry2 : bndries) {
-      if (bndry->dir == bndry2->dir) {
+      if (bndry->dir() == bndry2->dir()) {
         continue;
       }
       for (auto point : *bndry) {

From 72cd8a481f2a9048b4f41668c6f230341923eb43 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 13:31:42 +0200
Subject: [PATCH 1140/1827] use std::copysign

---
 src/mesh/parallel/fci.cxx | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 60c7d438fa..68c37ea964 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -62,13 +62,6 @@
 #include <string>
 #include <string_view>
 
-namespace {
-template <typename T>
-int sgn(T val) {
-  return (T(0) < val) - (val < T(0));
-}
-} // namespace
-
 using namespace std::string_view_literals;
 
 FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
@@ -262,7 +255,7 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
     ASSERT2(map_mesh->xend - map_mesh->xstart >= 2);
     auto boundary = (xt_prime[i] < map_mesh->xstart) ? inner_boundary : outer_boundary;
     if (!boundary->contains(x, y, z)) {
-      boundary->add_point(x, y, z, x + dx, y + offset - (sgn(offset) * 0.5),
+      boundary->add_point(x, y, z, x + dx, y + offset - (std::copysign(0.5, offset)),
                           z + dz, // Intersection point in local index space
                           std::abs(offset) - 0.5, // Distance to intersection
                           defValid, offset);

From b38fdf31f93a96ff43033b2fdd0ee8e9ee3ea724 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 13:44:37 +0200
Subject: [PATCH 1141/1827] Update test

---
 tests/integrated/test-fci-boundary/get_par_bndry.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 0840c131d3..1d5b9a5d63 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -50,8 +50,8 @@ int main(int argc, char** argv) {
     for (auto& field : fields) {
       field.allocate();
     }
-    ybndry->iter_pnts(
-        [&](const auto& pnt) { fields[pnt.dir + mesh->ystart][pnt.ind()] += 1; });
+    ybndry->iter(
+        [&](const auto& pnt) { fields[pnt.dir() + mesh->ystart][pnt.ind()] += 1; });
 
     for (int i = -mesh->ystart; i <= mesh->ystart; ++i) {
       dump[fmt::format("ybndry_{}", i)] = fields[i + mesh->ystart];

From 898d1910701d7a9391746726af55b242cac3b5eb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 16 Apr 2026 15:27:33 +0200
Subject: [PATCH 1142/1827] Make members private, provide public accessors
 where needed

---
 include/bout/boundary_iterator.hxx | 111 ++++++++++++++++-------------
 1 file changed, 61 insertions(+), 50 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index dfee87fdf8..66c66d45b6 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -17,22 +17,26 @@ class BoundaryRegionIter {
 public:
   virtual ~BoundaryRegionIter() = default;
   BoundaryRegionIter(int x, int y, int bx, int by, const Mesh& mesh)
-      : _dir(bx + by), x(x), y(y), bx(bx), by(by), localmesh(mesh) {
-    ASSERT3(bx * by == 0);
+      : _dir(bx + by), _x(x), _y(y), _bx(bx), _by(by), localmesh(&mesh) {
+    ASSERT3(_bx * _by == 0);
   }
   bool operator!=(const BoundaryRegionIter& rhs) const { return ind() != rhs.ind(); }
 
-  Ind3D ind() const { return xyz2ind(x, y, z); }
+  Ind3D ind() const { return xyz2ind(_x, _y, _z); }
   BoundaryRegionIter& operator++() {
-    ASSERT3(z < nz());
-    z++;
-    if (z == nz()) {
-      z = 0;
+    ASSERT3(_z < nz());
+    _z++;
+    if (_z == nz()) {
+      _z = 0;
       _next();
     }
     return *this;
   }
+
+protected:
   virtual void _next() = 0;
+
+public:
   BoundaryRegionIter& operator*() { return *this; }
 
   void dirichlet_o2(Field3D& f, BoutReal value) const {
@@ -51,7 +55,7 @@ public:
 
   BoutReal
   extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return (2 * f(0, ind())) - f(0, ind().yp(-by).xp(-bx));
+    return (2 * f(0, ind())) - f(0, ind().yp(-_by).xp(-_bx));
   }
 
   BoutReal interpolate_sheath_o2(const Field3D& f) const {
@@ -60,12 +64,12 @@ public:
 
   BoutReal
   interpolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return (f(0, ind()) + f(0, ind().yp(-by).xp(-bx))) * 0.5;
+    return (f(0, ind()) + f(0, ind().yp(-_by).xp(-_bx))) * 0.5;
   }
 
   BoutReal
   extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return 0.5 * (3 * f(0, ind()) - f(0, ind().yp(-by).xp(-bx)));
+    return 0.5 * (3 * f(0, ind()) - f(0, ind().yp(-_by).xp(-_bx)));
   }
 
   BoutReal extrapolate_sheath_free(const Field3D& f, SheathLimitMode mode) const {
@@ -81,14 +85,14 @@ public:
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
     BoutReal val = ythis(f);
     if (mode == SheathLimitMode::linear_free) {
-      for (int i = 1; i <= localmesh.ystart; ++i) {
+      for (int i = 1; i <= localmesh->ystart; ++i) {
         val += fac;
-        f[ind().yp(by * i).xp(bx * i)] = val;
+        f[ind().yp(_by * i).xp(_bx * i)] = val;
       }
     } else {
-      for (int i = 1; i <= localmesh.ystart; ++i) {
+      for (int i = 1; i <= localmesh->ystart; ++i) {
         val *= fac;
-        f[ind().yp(by * i).xp(bx * i)] = val;
+        f[ind().yp(_by * i).xp(_bx * i)] = val;
       }
     }
   }
@@ -97,30 +101,30 @@ public:
     const BoutReal fac =
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f));
     BoutReal val = ythis(f);
-    for (int i = 1; i <= localmesh.ystart; ++i) {
+    for (int i = 1; i <= localmesh->ystart; ++i) {
       val *= fac;
-      f[ind().yp(by * i).xp(bx * i)] = val;
+      f[ind().yp(_by * i).xp(_bx * i)] = val;
     }
   }
 
   bool is_lower() const {
-    ASSERT2(bx == 0);
-    return by == -1;
+    ASSERT2(_bx == 0);
+    return _by == -1;
   }
 
   void neumann_o1(Field3D& f, BoutReal grad) const {
     BoutReal val = ythis(f);
-    for (int i = 1; i <= localmesh.ystart; ++i) {
+    for (int i = 1; i <= localmesh->ystart; ++i) {
       val += grad;
-      f[ind().yp(by * i).xp(bx * i)] = val;
+      f[ind().yp(_by * i).xp(_bx * i)] = val;
     }
   }
 
   void neumann_o2(Field3D& f, BoutReal grad) const {
     BoutReal val = yprev(f) + grad;
-    for (int i = 1; i <= localmesh.ystart; ++i) {
+    for (int i = 1; i <= localmesh->ystart; ++i) {
       val += grad;
-      f[ind().yp(by * i).xp(bx * i)] = val;
+      f[ind().yp(_by * i).xp(_bx * i)] = val;
     }
   }
 
@@ -128,44 +132,51 @@ public:
     ynext(f) = std::max(ynext(f), value);
   }
 
-  BoutReal& ynext(Field3D& f) const { return f[ind().yp(by).xp(bx)]; }
-  const BoutReal& ynext(const Field3D& f) const { return f[ind().yp(by).xp(bx)]; }
-  BoutReal& yprev(Field3D& f) const { return f[ind().yp(-by).xp(-bx)]; }
-  const BoutReal& yprev(const Field3D& f) const { return f[ind().yp(-by).xp(-bx)]; }
+  BoutReal& ynext(Field3D& f) const { return f[ind().yp(_by).xp(_bx)]; }
+  const BoutReal& ynext(const Field3D& f) const { return f[ind().yp(_by).xp(_bx)]; }
+  BoutReal& yprev(Field3D& f) const { return f[ind().yp(-_by).xp(-_bx)]; }
+  const BoutReal& yprev(const Field3D& f) const { return f[ind().yp(-_by).xp(-_bx)]; }
   BoutReal& ythis(Field3D& f) const { return f[ind()]; }
   const BoutReal& ythis(const Field3D& f) const { return f[ind()]; }
 
   void setYPrevIfValid(Field3D& f, BoutReal val) const { yprev(f) = val; }
   void setAll(Field3D& f, const BoutReal val) const {
-    for (int i = -localmesh.ystart; i <= localmesh.ystart; ++i) {
-      f[ind().yp(by * i).xp(bx * i)] = val;
+    for (int i = -localmesh->ystart; i <= localmesh->ystart; ++i) {
+      f[ind().yp(_by * i).xp(_bx * i)] = val;
     }
   }
 
   static int abs_offset() { return 1; }
 
-  BoutReal& ynext(Field2D& f) const { return f[ind().yp(by).xp(bx)]; }
-  const BoutReal& ynext(const Field2D& f) const { return f[ind().yp(by).xp(bx)]; }
-  BoutReal& yprev(Field2D& f) const { return f[ind().yp(-by).xp(-bx)]; }
-  const BoutReal& yprev(const Field2D& f) const { return f[ind().yp(-by).xp(-bx)]; }
+  BoutReal& ynext(Field2D& f) const { return f[ind().yp(_by).xp(_bx)]; }
+  const BoutReal& ynext(const Field2D& f) const { return f[ind().yp(_by).xp(_bx)]; }
+  BoutReal& yprev(Field2D& f) const { return f[ind().yp(-_by).xp(-_bx)]; }
+  const BoutReal& yprev(const Field2D& f) const { return f[ind().yp(-_by).xp(-_bx)]; }
 
   int dir() const { return _dir; }
 
-private:
-  int _dir;
+protected:
+  int x() const { return _x; }
+  int y() const { return _y; }
+  int z() const { return _z; }
 
 protected:
-  int z{0};
-  int x;
-  int y;
-  int bx;
-  int by;
+  void setx(int x) { _x = x; }
+  void sety(int y) { _y = y; }
 
 private:
-  const Mesh& localmesh;
-  int nx() const { return localmesh.LocalNx; }
-  int ny() const { return localmesh.LocalNy; }
-  int nz() const { return localmesh.LocalNz; }
+  int _dir;
+
+  int _z{0};
+  int _x;
+  int _y;
+  int _bx;
+  int _by;
+
+  const Mesh* localmesh;
+  int nx() const { return localmesh->LocalNx; }
+  int ny() const { return localmesh->LocalNy; }
+  int nz() const { return localmesh->LocalNz; }
 
   Ind3D xyz2ind(int x, int y, int z) const {
     return Ind3D{((x * ny() + y) * nz()) + z, ny(), nz()};
@@ -180,7 +191,7 @@ public:
       : BoundaryRegionIter(r.ind, y, 0, dir, mesh), r(r), is_end(is_end) {}
 
   bool operator!=(const BoundaryRegionIterY& rhs) {
-    ASSERT2(y == rhs.y);
+    ASSERT2(y() == rhs.y());
     if (is_end) {
       if (rhs.is_end) {
         return false;
@@ -190,12 +201,12 @@ public:
     if (rhs.is_end) {
       return !r.isDone();
     }
-    return x != rhs.x;
+    return x() != rhs.x();
   }
 
   void _next() override {
     ++r;
-    x = r.ind;
+    setx(r.ind);
   }
 
 private:
@@ -206,15 +217,15 @@ private:
 class NewBoundaryRegionY {
 public:
   NewBoundaryRegionY(const Mesh& mesh, bool lower, const RangeIterator& r)
-      : mesh(mesh), lower(lower), r(r) {}
+      : mesh(&mesh), lower(lower), r(r) {}
   BoundaryRegionIterY begin(bool begin = true) {
-    return BoundaryRegionIterY(r, lower ? mesh.ystart : mesh.yend, lower ? -1 : +1,
-                               !begin, mesh);
+    return BoundaryRegionIterY(r, lower ? mesh->ystart : mesh->yend, lower ? -1 : +1,
+                               !begin, *mesh);
   }
   BoundaryRegionIterY end() { return begin(false); }
 
 private:
-  const Mesh& mesh;
+  const Mesh* mesh;
   bool lower;
   RangeIterator r;
 };

From 6c2b674017273bcea895b8e5ffae9d3ea4c7f580 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 21 Apr 2026 19:32:52 +0000
Subject: [PATCH 1143/1827] Update prek requirement from >=0.3.5 to >=0.3.10

Updates the requirements on [prek](https://github.com/j178/prek) to permit the latest version.
- [Release notes](https://github.com/j178/prek/releases)
- [Changelog](https://github.com/j178/prek/blob/master/CHANGELOG.md)
- [Commits](https://github.com/j178/prek/compare/v0.3.5...v0.3.10)

---
updated-dependencies:
- dependency-name: prek
  dependency-version: 0.3.10
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index f7ccf83cff..3e75bb39c5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ dev = [
      "clangd~=22.0",
      "clangd-tidy~=1.1",
      "cmakelang~=0.6",
-     "prek>=0.3.5",
+     "prek>=0.3.10",
      "pyyaml~=6.0",
      "ruff~=0.15",
      "sphinx-lint~=1.0",

From 56d9a60ba59b5b3282727e5abd426aa917373af2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 23 Apr 2026 13:02:41 +0200
Subject: [PATCH 1144/1827] Start working on templated new boundary

Move Boundary operators to a new templated class. Then FCI and FA
boundary specialisation only have to provide a few methods. Using CRTP
there should be no overhead from the specialisation.
---
 include/bout/boundary_region.hxx      |   2 +-
 include/bout/boundary_region_iter.hxx | 393 ++++++++++++++++++++++++++
 include/bout/yboundary_regions.hxx    |   6 +-
 3 files changed, 398 insertions(+), 3 deletions(-)
 create mode 100644 include/bout/boundary_region_iter.hxx

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 63c95d6efa..2a89cc1a50 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -37,7 +37,7 @@ constexpr BndryLoc BNDRY_PAR_BKWD_XIN = BndryLoc::par_bkwd_xin;
 constexpr BndryLoc BNDRY_PAR_FWD_XOUT = BndryLoc::par_fwd_xout;
 constexpr BndryLoc BNDRY_PAR_BKWD_XOUT = BndryLoc::par_bkwd_xout;
 
-// Physical type of y boundary
+/// Physical type of y boundary
 enum class YBndryType : std::int8_t { sheath, not_sheath, all };
 
 class BoundaryRegionBase {
diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
new file mode 100644
index 0000000000..241b56abdd
--- /dev/null
+++ b/include/bout/boundary_region_iter.hxx
@@ -0,0 +1,393 @@
+#pragma once
+
+#include <cstdint>
+#include <functional>
+#include <string>
+#include <utility>
+
+#include <bout/bout_enum_class.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/region.hxx>
+#include <bout/sys/parallel_stencils.hxx>
+
+namespace bout {
+namespace boundary {
+
+/// Physical type of y boundary
+enum class BndryType : std::int8_t {
+  sheath,
+  not_sheath_par,
+  core,
+  sol,
+  sol_perp,
+  sol_par,
+  all,
+  num
+};
+
+/// Types of free boundary condition
+/// ================== ===================================================
+/// Name               Description
+/// ================== ===================================================
+/// ``limited``        use exponential if decreasing, otherwise Neumanm
+/// ``exponential``    use exponential extrapolation
+/// ``linear``         use linear extrapolation
+/// ================== ===================================================
+enum class BoundaryFreeExtrapolation : std::int8_t { limited, exponential, linear };
+//BOUT_ENUM_CLASS(BoundaryFreeExtrapolation, limited, exponential, linear);
+
+template <typename impl>
+class BoundaryRegionIterBase { /// get the index at the last point in domain
+public:
+  Ind3D ind() const { return static_cast<impl*>(this)->_ind(); }
+  /// get the length from the point in the domain to the boundary in index
+  /// space. It is in the range [0, 1]
+  BoutReal length() const { return static_cast<impl*>(this)->_length(); }
+  /// Lower bound of how many points are between the first point in the domain
+  /// and the boundary in the other direction.
+  signed char valid() const { return static_cast<impl*>(this)->_valid(); }
+  /// Get the width of the boundary at the current point
+  int boundary_width() const { return static_cast<impl*>(this)->_boundary_width(); }
+  /// Is this the lower boundary?
+  bool is_lower() const { return static_cast<impl*>(this)->_is_lower(); }
+
+  /*
+   *         FIELD3D ACCESSORS
+   */
+
+  /// get the value at a given offset `off` of a field `f`.
+  /// off = -1 is the second point in the boundary
+  /// off = 0 is the first point in the boundary
+  /// off = 1 is the last point in the domain
+  /// off = 2 is the second to last point in the domain
+  template <bool check = true>
+  BoutReal& getAt(Field3D& f, int off) const {
+    return static_cast<impl*>(this)->template _getAt<check>(f, off);
+  }
+  /// get the value at a given offset `off` of a field `f`.
+  template <bool check = true>
+  BoutReal& getAt(const Field3D& f, int off) const {
+    return static_cast<impl*>(this)->template _getAt<check>(f, off);
+  }
+
+  /// Get the first point in the boundary
+  const BoutReal& next(const Field3D& f) const {
+    return static_cast<impl*>(this)->_getAt(f, 0);
+  }
+  /// Get the first point in the boundary
+  BoutReal& next(Field3D& f) const { return static_cast<impl*>(this)->_getAt(f, 0); }
+  /// Get the last point in the domain
+  const BoutReal& current(const Field3D& f) const {
+    return static_cast<impl*>(this)->_getAt(f, 1);
+  }
+  /// Get the last point in the domain
+  BoutReal& current(Field3D& f) const { return static_cast<impl*>(this)->_getAt(f, 1); }
+  /// Get the second to last point in the domain - this may not be valid and thus throw
+  const BoutReal& prev(const Field3D& f) const {
+    return static_cast<impl*>(this)->_getAt(f, 2);
+  }
+  /*
+   *         FIELD2D ACCESSORS
+   */
+
+  /// get the value at a given offset `off` of a field `f`.
+  /// off = -1 is the second point in the boundary
+  /// off = 0 is the first point in the boundary
+  /// off = 1 is the last point in the domain
+  /// off = 2 is the second to last point in the domain
+  template <bool check = true>
+  BoutReal& getAt(Field2D& f, int off) const {
+    return static_cast<impl*>(this)->template _getAt<check>(f, off);
+  }
+  /// get the value at a given offset `off` of a field `f`.
+  template <bool check = true>
+  BoutReal& getAt(const Field2D& f, int off) const {
+    return static_cast<impl*>(this)->template _getAt<check>(f, off);
+  }
+
+  /// Get the first point in the boundary
+  const BoutReal& next(const Field2D& f) const {
+    return static_cast<impl*>(this)->_getAt(f, 0);
+  }
+  /// Get the first point in the boundary
+  BoutReal& next(Field2D& f) const { return static_cast<impl*>(this)->_getAt(f, 0); }
+  /// Get the last point in the domain
+  const BoutReal& current(const Field2D& f) const {
+    return static_cast<impl*>(this)->_getAt(f, 1);
+  }
+  /// Get the last point in the domain
+  BoutReal& current(Field2D& f) const { return static_cast<impl*>(this)->_getAt(f, 1); }
+  /// Get the second to last point in the domain - this may not be valid and thus throw
+  const BoutReal& prev(const Field2D& f) const {
+    return static_cast<impl*>(this)->_getAt(f, 2);
+  }
+
+  /*
+   *         FUNCTIONS ACCESSORS
+   */
+
+  /// get the value at a given offset `off` of a field `f`.
+  /// off = -1 is the second point in the boundary
+  /// off = 0 is the first point in the boundary
+  /// off = 1 is the last point in the domain
+  /// off = 2 is the second to last point in the domain
+  template <bool check = true>
+  BoutReal& getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
+                  int off) const {
+    return static_cast<impl*>(this)->template _getAt<check>(func, off);
+  }
+  /// Get the first point in the boundary
+  const BoutReal&
+  next(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+    return static_cast<impl*>(this)->_getAt(func, 0);
+  }
+  /// Get the last point in the domain
+  const BoutReal&
+  current(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+    return static_cast<impl*>(this)->_getAt(func, 1);
+  }
+  /// Get the second to last point in the domain - this may not be valid and thus throw
+  const BoutReal&
+  prev(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+    return static_cast<impl*>(this)->_getAt(func, 2);
+  }
+
+  /*
+   *     INTERPOLATION and EXTRAPOLATION
+   */
+
+  // extrapolate a given field to the boundary
+  BoutReal extrapolate_boundary_o1(const Field3D& f) const { return current(f); }
+  // extrapolate a given field to the boundary
+  BoutReal extrapolate_boundary_o2(const Field3D& f) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return extrapolate_sheath_o1(f);
+    }
+    return current(f) * (1 + length()) - prev(f) * length();
+  }
+  /// Extrapolate a given function to the boundary
+  BoutReal extrapolate_sheath_o1(
+      const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+    return current(func);
+  }
+  /// Extrapolate a given function to the boundary
+  BoutReal extrapolate_sheath_o2(
+      const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return extrapolate_sheath_o1(func);
+    }
+    return current(func) * (1 + length()) - prev(func) * length();
+  }
+
+  /// Interpolate a field to the boundary, using the boundary values
+  BoutReal interpolate_boundary_o2(const Field3D& f) const {
+    return current(f) * (1 - length()) + next(f) * length();
+  }
+  /// Interpolate a field to the boundary, using the boundary values
+  BoutReal interpolate_boundary_o2(
+      const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+    return current(func) * (1 - length()) + next(func) * length();
+  }
+  /// Extrapolate to the first boundary value freely
+  BoutReal extrapolate_next_o1(const Field3D& f) const { return current(f); }
+  /// Extrapolate to the first boundary value freely
+  BoutReal extrapolate_next_o2(const Field3D& f) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return extrapolate_next_o1(f);
+    }
+    return current(f) * 2 - prev(f);
+  }
+
+  /// Extrapolate to the first boundary value freely
+  BoutReal
+  extrapolate_next_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+    return current(func);
+  }
+  /// Extrapolate to the first boundary value freely
+  BoutReal
+  extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return extrapolate_next_o1(func);
+    }
+    return current(func) * 2 - prev(func);
+  }
+
+  /// extrapolate the gradient into the boundary
+  BoutReal extrapolate_grad_o1([[maybe_unused]] const Field3D& f) const { return 0; }
+  /// extrapolate the gradient into the boundary
+  BoutReal extrapolate_grad_o2(const Field3D& f) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return extrapolate_grad_o1(f);
+    }
+    return current(f) - next(f);
+  }
+
+  BoutReal extrapolate_boundary_free(const Field3D& f,
+                                     BoundaryFreeExtrapolation mode) const {
+    const auto fac = valid() > 0 ? limitFreeScale(prev(f), current(f), mode)
+                                 : (mode == BoundaryFreeExtrapolation::linear ? 0 : 1);
+    auto val = current(f);
+    BoutReal next = mode == BoundaryFreeExtrapolation::linear ? val + fac : val * fac;
+    return val * length() + next * (1 - length());
+  }
+
+  /*
+   *     APPLY BOUNDARY CONDITIONS
+   */
+
+  /// Apply a dirichlet boundary condition
+  void dirichlet_o1(Field3D& f, BoutReal value) const {
+    for (int i = 0; i < boundary_width(); ++i) {
+      getAt(f, i) = value;
+    }
+  }
+
+  /// Apply a dirichlet boundary condition
+  void dirichlet_o2(Field3D& f, BoutReal value) const {
+    if (length() < small_value) {
+      return dirichlet_o1(f, value);
+    }
+    for (int i = 0; i < boundary_width(); ++i) {
+      getAt(f, i) =
+          parallel_stencil::dirichlet_o2(i + 1, current(f), i + 1 - length(), value);
+    }
+  }
+
+  /// Apply a dirichlet boundary condition
+  void dirichlet_o3(Field3D& f, BoutReal value) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return dirichlet_o2(f, value);
+    }
+    if (length() < small_value) {
+      for (int i = 0; i < boundary_width(); ++i) {
+        getAt(f, i) =
+            parallel_stencil::dirichlet_o2(i + 2, prev(f), i + 1 - length(), value);
+      }
+    } else {
+      for (int i = 0; i < boundary_width(); ++i) {
+        getAt(f, i) = parallel_stencil::dirichlet_o3(i + 2, prev(f), i + 1, current(f),
+                                                     i + 1 - length(), value);
+      }
+    }
+  }
+
+  /// Ensure the value in the boundary is at least `value`
+  void limit_at_least(Field3D& f, BoutReal value) const {
+    for (int i = 0; i < boundary_width(); ++i) {
+      if (getAt(f, i) < value) {
+        getAt(f, i) = value;
+      }
+    }
+  }
+
+  /// Apply neumann boundary condition, where `value` is the gradient in index space
+
+  // neumann_o1 would give second order convergence, given an appropriate one-sided stencil.
+  // But in general we do not, and thus for normal C2 stencils, this is 1st order.
+  void neumann_o1(Field3D& f, BoutReal value) const {
+    for (int i = 0; i < boundary_width(); ++i) {
+      getAt(f, i) = current(f) + value * (i + 1);
+    }
+  }
+
+  /// Apply neumann boundary condition, where `value` is the gradient in index space
+  void neumann_o2(Field3D& f, BoutReal value) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return neumann_o1(f, value);
+    }
+    for (int i = 0; i < boundary_width(); ++i) {
+      getAt(f, i) = prev(f) + (2 + i) * value;
+    }
+  }
+
+  /// Apply neumann boundary condition, where `value` is the gradient in index space
+  void neumann_o3(Field3D& f, BoutReal value) const {
+    ASSERT3(valid() >= 0);
+    if (valid() < 1) {
+      return neumann_o2(f, value);
+    }
+    for (int i = 0; i < boundary_width(); ++i) {
+      getAt(f, i) = parallel_stencil::neumann_o3(i + 1 - length(), value, i + 1,
+                                                 current(f), 2, prev(f));
+    }
+  }
+
+  void set_free(Field3D& f, BoundaryFreeExtrapolation mode) const {
+    int fac;
+    if (valid() > 0) {
+      fac = limitFreeScale(prev(f), current(f), mode);
+    } else {
+      fac = mode == BoundaryFreeExtrapolation::linear ? 0 : 1;
+    }
+    auto val = current(f);
+    if (mode == BoundaryFreeExtrapolation::linear) {
+      for (int i = 0; i < boundary_width(); ++i) {
+        val += fac;
+        getAt(f, i) = val;
+      }
+    } else {
+      for (int i = 0; i < boundary_width(); ++i) {
+        val *= fac;
+        getAt(f, i) = val;
+      }
+    }
+  }
+  void setSmallValue(BoutReal val) {
+    ASSERT2(val > 0);
+    ASSERT2(val < 0.5);
+    small_value = val;
+  }
+
+private:
+  BoutReal small_value = 1e-4;
+};
+
+namespace {
+/// Limited free gradient of log of a quantity
+/// This ensures that the guard cell values remain positive
+/// while also ensuring that the quantity never increases
+///
+///  fm  fc | fp
+///         ^ boundary
+///
+/// exp( 2*log(fc) - log(fm) )
+inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, BoundaryFreeExtrapolation mode) {
+  if ((fm < fc) && (mode == BoundaryFreeExtrapolation::limited)) {
+    return fc; // Neumann rather than increasing into boundary
+  }
+  if (fm < 1e-10) {
+    return fc; // Low / no density condition
+  }
+
+  BoutReal fp = 0;
+  switch (mode) {
+  case BoundaryFreeExtrapolation::limited:
+  case BoundaryFreeExtrapolation::exponential:
+    fp = SQ(fc) / fm; // Exponential
+    break;
+  case BoundaryFreeExtrapolation::linear:
+    fp = (2.0 * fc) - fm; // Linear
+    break;
+  }
+
+#if CHECKLEVEL >= 2
+  if (!std::isfinite(fp)) {
+    throw BoutException("SheathBoundary limitFree {}: {}, {} -> {}",
+                        static_cast<int>(mode), fm, fc, fp);
+  }
+#endif
+
+  return fp;
+}
+} // namespace
+
+} // namespace boundary
+} // namespace bout
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 982dff7839..b627a8a90a 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -1,5 +1,7 @@
 #pragma once
 
+#include <bout/boundary_region_iter.hxx>
+
 #include "./boundary_iterator.hxx"
 #include "bout/assert.hxx"
 #include "bout/boutexception.hxx"
@@ -113,8 +115,8 @@ public:
     });
   }
 
-  bool contains_ylow(Ind3D ind) const { return _contains[0][ind]; }
-  bool contains_yhigh(Ind3D ind) const { return _contains[1][ind]; }
+  bool contains_low(Ind3D ind) const { return _contains[0][ind]; }
+  bool contains_high(Ind3D ind) const { return _contains[1][ind]; }
   template <int dir>
   bool contains(Ind3D ind) const {
     static_assert(dir == 1 || dir == -1);

From aba6091e27f123c812b04ea341a7b578ab7e35e6 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 24 Apr 2026 10:05:06 +0100
Subject: [PATCH 1145/1827] Add utility for setting up tokamak coordinate
 system

- Pull out common code across the various examples and tests that use tokamak
  coordinates
- Reads grid quantities, applies normalisations, and calculates the metric
  components in one function call
- Returns a struct with the grid quantities, as some models use them further
- Some rearrangement of the existing code was sometimes necessary as we now need
  the normalisation factors before reading the grid quantities
---
 CMakeLists.txt                                |   2 +
 examples/6field-simple/elm_6f.cxx             | 115 +++++-----------
 examples/conducting-wall-mode/cwm.cxx         |  60 +++------
 examples/constraints/alfven-wave/alfven.cxx   |  70 ++--------
 examples/dalf3/dalf3.cxx                      |  94 ++++---------
 .../elm-pb-outerloop/elm_pb_outerloop.cxx     | 110 ++++++---------
 examples/elm-pb/elm_pb.cxx                    | 125 ++++++------------
 examples/gyro-gem/gem.cxx                     |  51 +------
 examples/laplacexy/alfven-wave/alfven.cxx     |  56 +-------
 examples/laplacexy/laplace_perp/test.cxx      |  40 +-----
 examples/wave-slab/wave_slab.cxx              |  44 +-----
 include/bout/coordinates.hxx                  |  12 --
 include/bout/tokamak_coordinates.hxx          |  49 +++++++
 src/mesh/tokamak_coordinates.cxx              |  77 +++++++++++
 tests/MMS/GBS/gbs.cxx                         |  61 +--------
 tests/MMS/elm-pb/elm_pb.cxx                   | 114 ++++++----------
 tests/MMS/tokamak/tokamak.cxx                 |  60 +--------
 .../test-drift-instability/2fluid.cxx         |  75 +++--------
 .../test-interchange-instability/2fluid.cxx   |  70 +++-------
 .../integrated/test-laplacexy/loadmetric.cxx  |  69 ----------
 .../integrated/test-laplacexy/loadmetric.hxx  |   8 --
 21 files changed, 399 insertions(+), 963 deletions(-)
 create mode 100644 include/bout/tokamak_coordinates.hxx
 create mode 100644 src/mesh/tokamak_coordinates.cxx
 delete mode 100644 tests/integrated/test-laplacexy/loadmetric.cxx
 delete mode 100644 tests/integrated/test-laplacexy/loadmetric.hxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5f054c1c1f..67e2337210 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -204,6 +204,7 @@ set(BOUT_SOURCES
     ./include/bout/sys/uuid.h
     ./include/bout/sys/variant.hxx
     ./include/bout/template_combinations.hxx
+    ./include/bout/tokamak_coordinates.hxx
     ./include/bout/traits.hxx
     ./include/bout/unused.hxx
     ./include/bout/utils.hxx
@@ -309,6 +310,7 @@ set(BOUT_SOURCES
     ./src/mesh/parallel_boundary_op.cxx
     ./src/mesh/parallel_boundary_region.cxx
     ./src/mesh/surfaceiter.cxx
+    ./src/mesh/tokamak_coordinates.cxx
     ./src/physics/gyro_average.cxx
     ./src/physics/physicsmodel.cxx
     ./src/physics/smoothing.cxx
diff --git a/examples/6field-simple/elm_6f.cxx b/examples/6field-simple/elm_6f.cxx
index 24256333df..7208d89ddf 100644
--- a/examples/6field-simple/elm_6f.cxx
+++ b/examples/6field-simple/elm_6f.cxx
@@ -16,6 +16,7 @@
 #include "bout/msg_stack.hxx"
 #include "bout/physicsmodel.hxx"
 #include "bout/sourcex.hxx"
+#include "bout/tokamak_coordinates.hxx"
 
 #include <cmath>
 
@@ -235,9 +236,7 @@ class Elm_6f : public PhysicsModel {
   int damp_width;        // Width of inner damped region
   BoutReal damp_t_const; // Timescale of damping
 
-  // Metric coefficients
-  Field2D Rxy, Bpxy, Btxy, B0, hthe;
-  Field2D I;         // Shear factor
+  Field2D B0;        // Magnetic field
   BoutReal LnLambda; // ln(Lambda)
 
   /// Ion mass
@@ -374,38 +373,10 @@ class Elm_6f : public PhysicsModel {
   int init(bool restarting) override {
     bool noshear;
 
-    // Get the metric tensor
-    Coordinates* coord = mesh->getCoordinates();
-
     output.write("Solving high-beta flute reduced equations\n");
     output.write("\tFile    : {:s}\n", __FILE__);
     output.write("\tCompiled: {:s} at {:s}\n", __DATE__, __TIME__);
 
-    //////////////////////////////////////////////////////////////
-    // Load data from the grid
-
-    // Load 2D profiles
-    mesh->get(J0, "Jpar0");    // A / m^2
-    mesh->get(P0, "pressure"); // Pascals
-
-    // Load curvature term
-    b0xcv.covariant = false;  // Read contravariant components
-    mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2
-
-    // Load metrics
-    if (mesh->get(Rxy, "Rxy")) { // m
-      output_error.write("Error: Cannot read Rxy from grid\n");
-      return 1;
-    }
-    if (mesh->get(Bpxy, "Bpxy")) { // T
-      output_error.write("Error: Cannot read Bpxy from grid\n");
-      return 1;
-    }
-    mesh->get(Btxy, "Btxy"); // T
-    mesh->get(B0, "Bxy");    // T
-    mesh->get(hthe, "hthe"); // m
-    mesh->get(I, "sinty");   // m^-2 T^-1
-
     //////////////////////////////////////////////////////////////
     // Read parameters from the options file
     //
@@ -681,19 +652,43 @@ class Elm_6f : public PhysicsModel {
     phi_curv = options["phi_curv"].doc("Compressional ExB terms").withDefault(true);
     g = options["gamma"].doc("Ratio of specific heats").withDefault(5.0 / 3.0);
 
-    if (!include_curvature) {
-      b0xcv = 0.0;
-    }
+    //////////////////////////////////////////////////////////////
+    // Load data from the grid
 
-    if (!include_jpar0) {
-      J0 = 0.0;
-    }
+    // Load 2D profiles
+    mesh->get(P0, "pressure"); // Pascals
 
-    if (noshear) {
-      if (include_curvature) {
+    // Typical magnetic field
+    mesh->get(Bbar, "bmag", 1.0);
+    // Typical length scale
+    mesh->get(Lbar, "rmag", 1.0);
+
+    // Read, normalise, and set coordinates
+    const auto tokamak_coords =
+        bout::set_tokamak_coordinates(*mesh, Lbar, Bbar, noshear or mesh->IncIntShear);
+    const auto& Rxy = tokamak_coords.Rxy;
+    const auto& Bpxy = tokamak_coords.Bpxy;
+    const auto& Btxy = tokamak_coords.Btxy;
+    const auto& hthe = tokamak_coords.hthe;
+    const auto& I = tokamak_coords.I_unnormalised;
+    // Needed in rhs too
+    B0 = tokamak_coords.Bxy;
+
+    if (include_curvature) {
+      // Load curvature term
+      b0xcv.covariant = false;  // Read contravariant components
+      mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2
+      if (noshear) {
         b0xcv.z += I * b0xcv.x;
       }
-      I = 0.0;
+    } else {
+      b0xcv = 0.0;
+    }
+
+    if (include_jpar0) {
+      mesh->get(J0, "Jpar0"); // A / m^2
+    } else {
+      J0 = 0.0;
     }
 
     //////////////////////////////////////////////////////////////
@@ -701,26 +696,17 @@ class Elm_6f : public PhysicsModel {
 
     if (mesh->IncIntShear) {
       // BOUT-06 style, using d/dx = d/dpsi + I * d/dz
-      coord->IntShiftTorsion = I;
-
+      mesh->getCoordinates()->IntShiftTorsion = I;
     } else {
       // Dimits style, using local coordinate system
       if (include_curvature) {
         b0xcv.z += I * b0xcv.x;
       }
-      I = 0.0; // I disappears from metric
     }
 
     //////////////////////////////////////////////////////////////
     // NORMALISE QUANTITIES
 
-    if (mesh->get(Bbar, "bmag")) { // Typical magnetic field
-      Bbar = 1.0;
-    }
-    if (mesh->get(Lbar, "rmag")) { // Typical length scale
-      Lbar = 1.0;
-    }
-
     if (mesh->get(Tibar, "Ti_x")) { // Typical ion temperature scale
       Tibar = 1.0;
     }
@@ -858,14 +844,6 @@ class Elm_6f : public PhysicsModel {
     b0xcv.y *= Lbar * Lbar;
     b0xcv.z *= Lbar * Lbar;
 
-    Rxy /= Lbar;
-    Bpxy /= Bbar;
-    Btxy /= Bbar;
-    B0 /= Bbar;
-    hthe /= Lbar;
-    coord->dx /= Lbar * Lbar * Bbar;
-    I *= Lbar * Lbar * Bbar;
-
     if ((!T0_fake_prof) && n0_fake_prof) {
       N0 = N0tanh(n0_height * Nbar, n0_ave * Nbar, n0_width, n0_center, n0_bottom_x);
 
@@ -1045,27 +1023,6 @@ class Elm_6f : public PhysicsModel {
       dump.add(eta, "eta", 0);
     }
 
-    /**************** CALCULATE METRICS ******************/
-
-    coord->g11 = SQ(Rxy * Bpxy);
-    coord->g22 = 1.0 / SQ(hthe);
-    coord->g33 = SQ(I) * coord->g11 + SQ(B0) / coord->g11;
-    coord->g12 = 0.0;
-    coord->g13 = -I * coord->g11;
-    coord->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    coord->J = hthe / Bpxy;
-    coord->Bxy = B0;
-
-    coord->g_11 = 1.0 / coord->g11 + SQ(I * Rxy);
-    coord->g_22 = SQ(B0 * hthe / Bpxy);
-    coord->g_33 = Rxy * Rxy;
-    coord->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    coord->g_13 = I * Rxy * Rxy;
-    coord->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    coord->geometry(); // Calculate quantities from metric tensor
-
     // Set B field vector
 
     B0vec.covariant = false;
diff --git a/examples/conducting-wall-mode/cwm.cxx b/examples/conducting-wall-mode/cwm.cxx
index 6ad23033ee..b302b5dfb3 100644
--- a/examples/conducting-wall-mode/cwm.cxx
+++ b/examples/conducting-wall-mode/cwm.cxx
@@ -4,12 +4,14 @@
  * Mode discoverd by H.L. Berk et. al. 1993
  * Model version in the code created by M. Umansky and J. Myra.
  *******************************************************************************/
-#include <bout/physicsmodel.hxx>
 
 #include <bout/derivs.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert_laplace.hxx>
+#include <bout/physicsmodel.hxx>
+#include <bout/tokamak_coordinates.hxx>
+#include <bout/utils.hxx>
 
 class CWM : public PhysicsModel {
 private:
@@ -28,9 +30,6 @@ class CWM : public PhysicsModel {
   // Phi boundary conditions
   Field3D dphi_bc_ydown, dphi_bc_yup;
 
-  // Metric coefficients
-  Field2D Rxy, Bpxy, Btxy, hthe, Zxy;
-
   // parameters
   BoutReal Te_x, Ni_x, Vi_x, bmag, rho_s, fmei, AA, ZZ;
   BoutReal lambda_ei;
@@ -54,8 +53,6 @@ class CWM : public PhysicsModel {
   std::unique_ptr<Laplacian> phiSolver{nullptr};
 
   int init(bool UNUSED(restarting)) override {
-    Field2D I; // Shear factor
-
     /************* LOAD DATA FROM GRID FILE ****************/
 
     // Load 2D profiles (set to zero if not found)
@@ -63,11 +60,6 @@ class CWM : public PhysicsModel {
 
     coord = mesh->getCoordinates();
 
-    // Load metrics
-    GRID_LOAD(Rxy, Zxy, Bpxy, Btxy, hthe);
-    mesh->get(coord->dx, "dpsi");
-    mesh->get(I, "sinty");
-
     // Load normalisation values
     GRID_LOAD(Te_x, Ni_x, bmag);
 
@@ -93,13 +85,11 @@ class CWM : public PhysicsModel {
 
     /************* SHIFTED RADIAL COORDINATES ************/
     // Check type of parallel transform
-    std::string ptstr =
-        Options::root()["mesh"]["paralleltransform"]["type"].withDefault<std::string>(
-            "identity");
+    const auto ptstr =
+        Options::root()["mesh"]["paralleltransform"]["type"].withDefault("identity");
 
-    if (lowercase(ptstr) == "shifted") {
-      ShearFactor = 0.0; // I disappears from metric
-    }
+    // I disappears from metric
+    const bool noshear = (lowercase(ptstr) == "shifted");
 
     /************** CALCULATE PARAMETERS *****************/
 
@@ -132,39 +122,19 @@ class CWM : public PhysicsModel {
     Ni0 /= Ni_x / 1.0e14;
     Te0 /= Te_x;
 
-    // Normalise geometry
-    Rxy /= rho_s;
-    hthe /= rho_s;
-    I *= rho_s * rho_s * (bmag / 1e4) * ShearFactor;
-    coord->dx /= rho_s * rho_s * (bmag / 1e4);
-
-    // Normalise magnetic field
-    Bpxy /= (bmag / 1.e4);
-    Btxy /= (bmag / 1.e4);
-    coord->Bxy /= (bmag / 1.e4);
-
     // Set nu
     nu = nu_hat * Ni0 / pow(Te0, 1.5);
 
     /**************** CALCULATE METRICS ******************/
 
-    coord->g11 = SQ(Rxy * Bpxy);
-    coord->g22 = 1.0 / SQ(hthe);
-    coord->g33 = SQ(I) * coord->g11 + SQ(coord->Bxy) / coord->g11;
-    coord->g12 = 0.0;
-    coord->g13 = -I * coord->g11;
-    coord->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    coord->J = hthe / Bpxy;
-
-    coord->g_11 = 1.0 / coord->g11 + SQ(I * Rxy);
-    coord->g_22 = SQ(coord->Bxy * hthe / Bpxy);
-    coord->g_33 = Rxy * Rxy;
-    coord->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    coord->g_13 = I * Rxy * Rxy;
-    coord->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    coord->geometry();
+    // Read, normalise, and set coordinates
+    const auto tokamak_coords =
+        bout::set_tokamak_coordinates(*mesh, rho_s, bmag / 1e4, noshear);
+    auto Rxy = tokamak_coords.Rxy;
+    auto Zxy = tokamak_coords.Zxy;
+    auto Bpxy = tokamak_coords.Bpxy;
+    auto Btxy = tokamak_coords.Btxy;
+    auto hthe = tokamak_coords.hthe;
 
     /**************** SET EVOLVING VARIABLES *************/
 
diff --git a/examples/constraints/alfven-wave/alfven.cxx b/examples/constraints/alfven-wave/alfven.cxx
index 3e643331a1..85428fdc85 100644
--- a/examples/constraints/alfven-wave/alfven.cxx
+++ b/examples/constraints/alfven-wave/alfven.cxx
@@ -1,8 +1,9 @@
-
 #include <bout/field_factory.hxx>
 #include <bout/invert/laplacexz.hxx>
 #include <bout/invert_laplace.hxx>
 #include <bout/physicsmodel.hxx>
+#include <bout/tokamak_coordinates.hxx>
+#include <bout/utils.hxx>
 
 /// Fundamental constants
 const BoutReal PI = 3.14159265;
@@ -129,12 +130,12 @@ class Alfven : public PhysicsModel {
   }
 
   /*!
-   * Preconditioner. This inverts the operator (1 - gamma*J) 
+   * Preconditioner. This inverts the operator (1 - gamma*J)
    * where J is the Jacobian of the system
    *
    * The system state at time t is stored as usual
    * whilst the vector to be inverted is in ddt(f)
-   * 
+   *
    * Inputs
    * ------
    *
@@ -146,7 +147,7 @@ class Alfven : public PhysicsModel {
    *
    * Output
    * ------
-   * 
+   *
    * ddt(f) = Result of the inversion
    */
   int precon(BoutReal, BoutReal, BoutReal) {
@@ -159,65 +160,14 @@ class Alfven : public PhysicsModel {
   }
 
   void LoadMetric(BoutReal Lnorm, BoutReal Bnorm) {
-    // Load metric coefficients from the mesh
-    Field2D Rxy, Bpxy, Btxy, hthe, sinty;
-    GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics
-
-    // Get the coordinates object
-    Coordinates* coord = mesh->getCoordinates();
-
-    // Checking for dpsi and qinty used in BOUT grids
-    Field2D dx;
-    if (!mesh->get(dx, "dpsi")) {
-      output << "\tUsing dpsi as the x grid spacing\n";
-      coord->dx = dx; // Only use dpsi if found
-    } else {
-      // dx will have been read already from the grid
-      output << "\tUsing dx as the x grid spacing\n";
-    }
-
-    Rxy /= Lnorm;
-    hthe /= Lnorm;
-    sinty *= SQ(Lnorm) * Bnorm;
-    coord->dx /= SQ(Lnorm) * Bnorm;
-
-    Bpxy /= Bnorm;
-    Btxy /= Bnorm;
-    coord->Bxy /= Bnorm;
-
     // Check type of parallel transform
-    std::string ptstr =
+    const auto ptstr =
         Options::root()["mesh"]["paralleltransform"]["type"].withDefault("identity");
 
-    if (lowercase(ptstr) == "shifted") {
-      // Using shifted metric method
-      sinty = 0.0; // I disappears from metric
-    }
-
-    BoutReal sbp = 1.0; // Sign of Bp
-    if (min(Bpxy, true) < 0.0) {
-      sbp = -1.0;
-    }
-
-    // Calculate metric components
-
-    coord->g11 = SQ(Rxy * Bpxy);
-    coord->g22 = 1.0 / SQ(hthe);
-    coord->g33 = SQ(sinty) * coord->g11 + SQ(coord->Bxy) / coord->g11;
-    coord->g12 = 0.0;
-    coord->g13 = -sinty * coord->g11;
-    coord->g23 = -sbp * Btxy / (hthe * Bpxy * Rxy);
-
-    coord->J = hthe / Bpxy;
-
-    coord->g_11 = 1.0 / coord->g11 + SQ(sinty * Rxy);
-    coord->g_22 = SQ(coord->Bxy * hthe / Bpxy);
-    coord->g_33 = Rxy * Rxy;
-    coord->g_12 = sbp * Btxy * hthe * sinty * Rxy / Bpxy;
-    coord->g_13 = sinty * Rxy * Rxy;
-    coord->g_23 = sbp * Btxy * hthe * Rxy / Bpxy;
-
-    coord->geometry();
+    // I disappears from metric
+    const bool noshear = (lowercase(ptstr) == "shifted");
+    // Read, normalise, and set coordinates
+    bout::set_tokamak_coordinates(*mesh, Lnorm, Bnorm, noshear);
   }
 };
 
diff --git a/examples/dalf3/dalf3.cxx b/examples/dalf3/dalf3.cxx
index b27ae97113..7fe551273a 100644
--- a/examples/dalf3/dalf3.cxx
+++ b/examples/dalf3/dalf3.cxx
@@ -18,17 +18,18 @@
  *
  ****************************************************************/
 
-#include <bout/physicsmodel.hxx>
-
+#include <bout/constants.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/invert_laplace.hxx>
+#include <bout/physicsmodel.hxx>
+#include <bout/tokamak_coordinates.hxx>
 #include <bout/utils.hxx>
+
+#include <algorithm>
 #include <math.h>
 #include <memory>
 
-#include <bout/constants.hxx>
-
 // Constants
 const BoutReal MU0 = 4.0e-7 * PI;
 const BoutReal Charge = SI::qe;   // electron charge e (C)
@@ -97,22 +98,9 @@ class DALF3 : public PhysicsModel {
     b0xcv.covariant = false;  // Read contravariant components
     mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2
 
-    // Metric coefficients
-    Field2D Rxy, Bpxy, Btxy, hthe;
-    Field2D I; // Shear factor
-
-    if (mesh->get(Rxy, "Rxy")) { // m
-      output_error.write("Error: Cannot read Rxy from grid\n");
-      return 1;
-    }
-    if (mesh->get(Bpxy, "Bpxy")) { // T
-      output_error.write("Error: Cannot read Bpxy from grid\n");
-      return 1;
-    }
-    mesh->get(Btxy, "Btxy"); // T
-    mesh->get(B0, "Bxy");    // T
-    mesh->get(hthe, "hthe"); // m
-    mesh->get(I, "sinty");   // m^-2 T^-1
+    // We need to load this in, despite using `set_tokamak_coordinates`, because
+    // the both length and B normalisation depend on it
+    mesh->get(B0, "Bxy"); // T
 
     //////////////////////////////////////////////////////////////
     // Options
@@ -163,20 +151,6 @@ class DALF3 : public PhysicsModel {
       return 1;
     }
 
-    Coordinates* coord = mesh->getCoordinates();
-
-    // SHIFTED RADIAL COORDINATES
-
-    // Check type of parallel transform
-    std::string ptstr =
-        Options::root()["mesh"]["paralleltransform"]["type"].withDefault("identity");
-
-    if (lowercase(ptstr) == "shifted") {
-      // Dimits style, using local coordinate system
-      b0xcv.z += I * b0xcv.x;
-      I = 0.0; // I disappears from metric
-    }
-
     ///////////////////////////////////////////////////
     // Normalisation
 
@@ -212,9 +186,7 @@ class DALF3 : public PhysicsModel {
     } else {
       eta = 0.51 * 1.03e-4 * 20. * pow(Te0, -1.5);
     }
-    if (mul_resist < 0.0) {
-      mul_resist = 0.0;
-    }
+    mul_resist = std::max(mul_resist, 0.0);
     eta *= mul_resist;
 
     // Plasma quantities
@@ -228,41 +200,31 @@ class DALF3 : public PhysicsModel {
     hyper_viscosity /= wci * SQ(SQ(rho_s));
     viscosity_par /= wci * SQ(rho_s);
 
-    b0xcv.x /= Bnorm;
-    b0xcv.y *= rho_s * rho_s;
-    b0xcv.z *= rho_s * rho_s;
-
-    // Metrics
-    Rxy /= rho_s;
-    hthe /= rho_s;
-    I *= rho_s * rho_s * Bnorm;
-    Bpxy /= Bnorm;
-    Btxy /= Bnorm;
-    B0 /= Bnorm;
-
-    coord->dx /= rho_s * rho_s * Bnorm;
-
     ///////////////////////////////////////////////////
     // CALCULATE METRICS
 
-    coord->g11 = SQ(Rxy * Bpxy);
-    coord->g22 = 1.0 / SQ(hthe);
-    coord->g33 = SQ(I) * coord->g11 + SQ(B0) / coord->g11;
-    coord->g12 = 0.0;
-    coord->g13 = -I * coord->g11;
-    coord->g23 = -Btxy / (hthe * Bpxy * Rxy);
+    // Check type of parallel transform
+    const auto ptstr =
+        Options::root()["mesh"]["paralleltransform"]["type"].withDefault("identity");
 
-    coord->J = hthe / Bpxy;
-    coord->Bxy = B0;
+    // I disappears from metric
+    const bool noshear = (lowercase(ptstr) == "shifted");
 
-    coord->g_11 = 1.0 / coord->g11 + SQ(I * Rxy);
-    coord->g_22 = SQ(B0 * hthe / Bpxy);
-    coord->g_33 = Rxy * Rxy;
-    coord->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    coord->g_13 = I * Rxy * Rxy;
-    coord->g_23 = Btxy * hthe * Rxy / Bpxy;
+    // Read, normalise, and set coordinates
+    const auto tokamak_coords =
+        bout::set_tokamak_coordinates(*mesh, rho_s, Bnorm, noshear);
+    // Use normalised B0
+    B0 = tokamak_coords.Bxy;
 
-    coord->geometry(); // Calculate quantities from metric tensor
+    // SHIFTED RADIAL COORDINATES
+    if (noshear) {
+      // Dimits style, using local coordinate system
+      b0xcv.z += tokamak_coords.I_unnormalised * b0xcv.x;
+    }
+
+    b0xcv.x /= Bnorm;
+    b0xcv.y *= rho_s * rho_s;
+    b0xcv.z *= rho_s * rho_s;
 
     SOLVE_FOR3(Vort, Pe, Vpar);
     comms.add(Vort, Pe, Vpar);
diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index 3cc5227b30..6de9797957 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -44,6 +44,7 @@
 #include <bout/single_index_ops.hxx>
 #include <bout/smoothing.hxx>
 #include <bout/sourcex.hxx>
+#include <bout/tokamak_coordinates.hxx>
 #include <bout/utils.hxx>
 
 #include <math.h>
@@ -281,8 +282,7 @@ class ELMpb : public PhysicsModel {
   BoutReal damp_t_const; // Timescale of damping
 
   // Metric coefficients
-  Field2D Rxy, Bpxy, Btxy, B0, hthe;
-  Field2D I; // Shear factor
+  Field2D B0;
 
   const BoutReal MU0 = 4.0e-7 * PI;
   const BoutReal Mi = 2.0 * 1.6726e-27; // Ion mass
@@ -361,24 +361,7 @@ class ELMpb : public PhysicsModel {
     // Load data from the grid
 
     // Load 2D profiles
-    mesh->get(J0, "Jpar0");    // A / m^2
-    mesh->get(P0, "pressure"); // Pascals
-
-    // Load curvature term
-    b0xcv.covariant = false;  // Read contravariant components
-    mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2
-
-    // Load metrics
-    if (mesh->get(Rxy, "Rxy") != 0) { // m
-      throw BoutException("Error: Cannot read Rxy from grid\n");
-    }
-    if (mesh->get(Bpxy, "Bpxy") != 0) { // T
-      throw BoutException("Error: Cannot read Bpxy from grid\n");
-    }
-    mesh->get(Btxy, "Btxy");          // T
-    mesh->get(B0, "Bxy");             // T
-    mesh->get(hthe, "hthe");          // m
-    mesh->get(I, "sinty");            // m^-2 T^-1
+    mesh->get(P0, "pressure");        // Pascals
     mesh->get(Psixy, "psixy");        // get Psi
     mesh->get(Psiaxis, "psi_axis");   // axis flux
     mesh->get(Psibndry, "psi_bndry"); // edge flux
@@ -710,8 +693,6 @@ class ELMpb : public PhysicsModel {
       Dphi0 *= -1;
     }
 
-    V0 = -Rxy * Bpxy * Dphi0 / B0;
-
     if (simple_rmp) {
       include_rmp = true;
     }
@@ -795,46 +776,60 @@ class ELMpb : public PhysicsModel {
       }
     }
 
-    if (!include_curvature) {
+    //////////////////////////////////////////////////////////////
+    // Read, normalise, and set coordinates
+
+    // Typical magnetic field
+    mesh->get(Bbar, "bmag", 1.0);
+    // Typical length scale
+    mesh->get(Lbar, "rmag", 1.0);
+
+    const auto tokamak_coords =
+        bout::set_tokamak_coordinates(*mesh, Lbar, Bbar, noshear or mesh->IncIntShear);
+    const auto& Rxy = tokamak_coords.Rxy;
+    const auto& Bpxy = tokamak_coords.Bpxy;
+    const auto& Btxy = tokamak_coords.Btxy;
+    const auto& hthe = tokamak_coords.hthe;
+    const auto& I = tokamak_coords.I_unnormalised;
+
+    B0 = tokamak_coords.Bxy;
+
+    // Need to unnormalise Rxy, as we normalise velocity separately
+    V0 = -(Rxy * Lbar) * Bpxy * Dphi0 / B0;
+
+    if (include_curvature) {
+      // Load curvature term
+      b0xcv.covariant = false;  // Read contravariant components
+      mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2
+      if (noshear) {
+        b0xcv.z += I * b0xcv.x;
+      }
+    } else {
       b0xcv = 0.0;
     }
 
-    if (!include_jpar0) {
+    if (include_jpar0) {
+      mesh->get(J0, "Jpar0"); // A / m^2
+    } else {
       J0 = 0.0;
     }
 
-    if (noshear) {
-      if (include_curvature) {
-        b0xcv.z += I * b0xcv.x;
-      }
-      I = 0.0;
-    }
-
     //////////////////////////////////////////////////////////////
     // SHIFTED RADIAL COORDINATES
 
     if (mesh->IncIntShear) {
       // BOUT-06 style, using d/dx = d/dpsi + I * d/dz
-      metric->IntShiftTorsion = I;
-
+      mesh->getCoordinates()->IntShiftTorsion = I;
     } else {
       // Dimits style, using local coordinate system
       if (include_curvature) {
         b0xcv.z += I * b0xcv.x;
       }
-      I = 0.0; // I disappears from metric
     }
 
     //////////////////////////////////////////////////////////////
     // NORMALISE QUANTITIES
 
-    if (mesh->get(Bbar, "bmag") != 0) { // Typical magnetic field
-      Bbar = 1.0;
-    }
-    if (mesh->get(Lbar, "rmag") != 0) { // Typical length scale
-      Lbar = 1.0;
-    }
-
     Va = sqrt(Bbar * Bbar / (MU0 * density * Mi));
 
     Tbar = Lbar / Va;
@@ -935,8 +930,8 @@ class ELMpb : public PhysicsModel {
       output.write("   drop K-H term\n");
     }
 
-    Field2D Te;
-    Te = P0 / (2.0 * density * 1.602e-19); // Temperature in eV
+    // Temperature in eV
+    const Field2D Te = P0 / (2.0 * density * 1.602e-19);
 
     J0 = -MU0 * Lbar * J0 / B0;
     P0 = 2.0 * MU0 * P0 / (Bbar * Bbar);
@@ -947,14 +942,6 @@ class ELMpb : public PhysicsModel {
     b0xcv.y *= Lbar * Lbar;
     b0xcv.z *= Lbar * Lbar;
 
-    Rxy /= Lbar;
-    Bpxy /= Bbar;
-    Btxy /= Bbar;
-    B0 /= Bbar;
-    hthe /= Lbar;
-    metric->dx /= Lbar * Lbar * Bbar;
-    I *= Lbar * Lbar * Bbar;
-
     if (constn0) {
       T0_fake_prof = false;
       n0_fake_prof = false;
@@ -1080,27 +1067,6 @@ class ELMpb : public PhysicsModel {
       rmp_Psi = 0.0;
     }
 
-    /**************** CALCULATE METRICS ******************/
-
-    metric->g11 = SQ(Rxy * Bpxy);
-    metric->g22 = 1.0 / SQ(hthe);
-    metric->g33 = SQ(I) * metric->g11 + SQ(B0) / metric->g11;
-    metric->g12 = 0.0;
-    metric->g13 = -I * metric->g11;
-    metric->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    metric->J = hthe / Bpxy;
-    metric->Bxy = B0;
-
-    metric->g_11 = 1.0 / metric->g11 + SQ(I * Rxy);
-    metric->g_22 = SQ(B0 * hthe / Bpxy);
-    metric->g_33 = Rxy * Rxy;
-    metric->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    metric->g_13 = I * Rxy * Rxy;
-    metric->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    metric->geometry(); // Calculate quantities from metric tensor
-
     // Set B field vector
 
     B0vec.covariant = false;
diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx
index 2cb373c52b..a0ac750809 100644
--- a/examples/elm-pb/elm_pb.cxx
+++ b/examples/elm-pb/elm_pb.cxx
@@ -8,21 +8,20 @@
 #include <bout/bout.hxx>
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
+#include <bout/difops.hxx>
+#include <bout/field_factory.hxx>
+#include <bout/fv_ops.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/invert_laplace.hxx>
 #include <bout/invert_parderiv.hxx>
 #include <bout/sourcex.hxx>
+#include <bout/tokamak_coordinates.hxx>
 #include <bout/utils.hxx>
 
-#include <bout/difops.hxx>
-#include <bout/fv_ops.hxx>
-
 #include <math.h>
 
-#include <bout/field_factory.hxx>
-
 CELL_LOC loc = CELL_CENTRE;
 
 /// Set default options
@@ -233,9 +232,7 @@ class ELMpb : public PhysicsModel {
   int damp_width;        // Width of inner damped region
   BoutReal damp_t_const; // Timescale of damping
 
-  // Metric coefficients
-  Field2D Rxy, Bpxy, Btxy, B0, hthe;
-  Field2D I; // Shear factor
+  Field2D B0; // Magnetic field
 
   const BoutReal MU0 = 4.0e-7 * PI;
   const BoutReal Mi = 2.0 * 1.6726e-27; // Ion mass
@@ -302,9 +299,6 @@ class ELMpb : public PhysicsModel {
 
 protected:
   int init(bool restarting) override {
-    bool noshear;
-
-    Coordinates* metric = mesh->getCoordinates();
 
     output.write("Solving high-beta flute reduced equations\n");
     output.write("\tFile    : {:s}\n", __FILE__);
@@ -314,24 +308,7 @@ class ELMpb : public PhysicsModel {
     // Load data from the grid
 
     // Load 2D profiles
-    mesh->get(J0, "Jpar0");    // A / m^2
-    mesh->get(P0, "pressure"); // Pascals
-
-    // Load curvature term
-    b0xcv.covariant = false;  // Read contravariant components
-    mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2
-
-    // Load metrics
-    if (mesh->get(Rxy, "Rxy")) { // m
-      throw BoutException("Error: Cannot read Rxy from grid\n");
-    }
-    if (mesh->get(Bpxy, "Bpxy")) { // T
-      throw BoutException("Error: Cannot read Bpxy from grid\n");
-    }
-    mesh->get(Btxy, "Btxy");          // T
-    mesh->get(B0, "Bxy");             // T
-    mesh->get(hthe, "hthe");          // m
-    mesh->get(I, "sinty");            // m^-2 T^-1
+    mesh->get(P0, "pressure");        // Pascals
     mesh->get(Psixy, "psixy");        // get Psi
     mesh->get(Psiaxis, "psi_axis");   // axis flux
     mesh->get(Psibndry, "psi_bndry"); // edge flux
@@ -485,7 +462,7 @@ class ELMpb : public PhysicsModel {
 
     experiment_Er = options["experiment_Er"].withDefault(false);
 
-    noshear = options["noshear"].withDefault(false);
+    const bool noshear = options["noshear"].withDefault(false);
 
     relax_j_vac = options["relax_j_vac"]
                       .doc("Relax vacuum current to zero")
@@ -665,8 +642,6 @@ class ELMpb : public PhysicsModel {
       Dphi0 *= -1;
     }
 
-    V0 = -Rxy * Bpxy * Dphi0 / B0;
-
     if (simple_rmp) {
       include_rmp = true;
     }
@@ -750,46 +725,61 @@ class ELMpb : public PhysicsModel {
       }
     }
 
-    if (!include_curvature) {
+    //////////////////////////////////////////////////////////////
+    // Read, normalise, and set coordinates
+
+    // Typical magnetic field
+    mesh->get(Bbar, "bmag", 1.0);
+    // Typical length scale
+    mesh->get(Lbar, "rmag", 1.0);
+
+    // Read, normalise, and set coordinates
+    const auto tokamak_coords =
+        bout::set_tokamak_coordinates(*mesh, Lbar, Bbar, noshear or mesh->IncIntShear);
+    const auto& Rxy = tokamak_coords.Rxy;
+    const auto& Bpxy = tokamak_coords.Bpxy;
+    const auto& Btxy = tokamak_coords.Btxy;
+    const auto& hthe = tokamak_coords.hthe;
+    const auto& I = tokamak_coords.I_unnormalised;
+
+    B0 = tokamak_coords.Bxy;
+
+    // Need to unnormalise Rxy, as we normalise velocity separately
+    V0 = -(Rxy * Lbar) * Bpxy * Dphi0 / B0;
+
+    if (include_curvature) {
+      // Load curvature term
+      b0xcv.covariant = false;  // Read contravariant components
+      mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2
+      if (noshear) {
+        b0xcv.z += I * b0xcv.x;
+      }
+    } else {
       b0xcv = 0.0;
     }
 
-    if (!include_jpar0) {
+    if (include_jpar0) {
+      mesh->get(J0, "Jpar0"); // A / m^2
+    } else {
       J0 = 0.0;
     }
 
-    if (noshear) {
-      if (include_curvature) {
-        b0xcv.z += I * b0xcv.x;
-      }
-      I = 0.0;
-    }
-
     //////////////////////////////////////////////////////////////
     // SHIFTED RADIAL COORDINATES
 
     if (mesh->IncIntShear) {
       // BOUT-06 style, using d/dx = d/dpsi + I * d/dz
-      metric->IntShiftTorsion = I;
-
+      mesh->getCoordinates()->IntShiftTorsion = I;
     } else {
       // Dimits style, using local coordinate system
       if (include_curvature) {
         b0xcv.z += I * b0xcv.x;
       }
-      I = 0.0; // I disappears from metric
     }
 
     //////////////////////////////////////////////////////////////
     // NORMALISE QUANTITIES
 
-    if (mesh->get(Bbar, "bmag")) { // Typical magnetic field
-      Bbar = 1.0;
-    }
-    if (mesh->get(Lbar, "rmag")) { // Typical length scale
-      Lbar = 1.0;
-    }
-
     Va = sqrt(Bbar * Bbar / (MU0 * density * Mi));
 
     Tbar = Lbar / Va;
@@ -890,8 +880,8 @@ class ELMpb : public PhysicsModel {
       output.write("   drop K-H term\n");
     }
 
-    Field2D Te;
-    Te = P0 / (2.0 * density * 1.602e-19); // Temperature in eV
+    // Temperature in eV
+    const Field2D Te = P0 / (2.0 * density * 1.602e-19);
 
     J0 = -MU0 * Lbar * J0 / B0;
     P0 = 2.0 * MU0 * P0 / (Bbar * Bbar);
@@ -902,14 +892,6 @@ class ELMpb : public PhysicsModel {
     b0xcv.y *= Lbar * Lbar;
     b0xcv.z *= Lbar * Lbar;
 
-    Rxy /= Lbar;
-    Bpxy /= Bbar;
-    Btxy /= Bbar;
-    B0 /= Bbar;
-    hthe /= Lbar;
-    metric->dx /= Lbar * Lbar * Bbar;
-    I *= Lbar * Lbar * Bbar;
-
     if (constn0) {
       T0_fake_prof = false;
       n0_fake_prof = false;
@@ -1035,27 +1017,6 @@ class ELMpb : public PhysicsModel {
       rmp_Psi = 0.0;
     }
 
-    /**************** CALCULATE METRICS ******************/
-
-    metric->g11 = SQ(Rxy * Bpxy);
-    metric->g22 = 1.0 / SQ(hthe);
-    metric->g33 = SQ(I) * metric->g11 + SQ(B0) / metric->g11;
-    metric->g12 = 0.0;
-    metric->g13 = -I * metric->g11;
-    metric->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    metric->J = hthe / Bpxy;
-    metric->Bxy = B0;
-
-    metric->g_11 = 1.0 / metric->g11 + SQ(I * Rxy);
-    metric->g_22 = SQ(B0 * hthe / Bpxy);
-    metric->g_33 = Rxy * Rxy;
-    metric->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    metric->g_13 = I * Rxy * Rxy;
-    metric->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    metric->geometry(); // Calculate quantities from metric tensor
-
     // Set B field vector
 
     B0vec.covariant = false;
diff --git a/examples/gyro-gem/gem.cxx b/examples/gyro-gem/gem.cxx
index 1a056c1c08..f4347ca2b3 100644
--- a/examples/gyro-gem/gem.cxx
+++ b/examples/gyro-gem/gem.cxx
@@ -4,17 +4,17 @@
  * 6 moments for each species
  *
  * "GEM - An Energy Conserving Electromagnetic Gyrofluid Model"
- *  by Bruce D Scott. arXiv:physics/0501124v1 23 Jan 2005 
+ *  by Bruce D Scott. arXiv:physics/0501124v1 23 Jan 2005
  *
  * This version uses global parameters for collisionality etc.
  ****************************************************************/
 
+#include "bout/tokamak_coordinates.hxx"
 #include <bout/constants.hxx>
-#include <bout/physicsmodel.hxx>
-
 #include <bout/gyro_average.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert_laplace.hxx>
+#include <bout/physicsmodel.hxx>
 
 /// Fundamental constants
 
@@ -185,14 +185,6 @@ class GEM : public PhysicsModel {
     //////////////////////////////////
     // Read profiles
 
-    // Mesh
-    Field2D Rxy, Bpxy, Btxy, Bxy, hthe;
-    GRID_LOAD(Rxy);  // Major radius [m]
-    GRID_LOAD(Bpxy); // Poloidal B field [T]
-    GRID_LOAD(Btxy); // Toroidal B field [T]
-    GRID_LOAD(Bxy);  // Total B field [T]
-    GRID_LOAD(hthe); // Poloidal arc length [m / radian]
-
     GRID_LOAD(Te0); // Electron temperature in eV
     GRID_LOAD(Ni0); // Ion number density in 10^20 m^-3
 
@@ -255,6 +247,8 @@ class GEM : public PhysicsModel {
 
     if (mesh->get(Bbar, "Bbar")) {
       if (mesh->get(Bbar, "bmag")) {
+        Field3D Bxy;
+        mesh->get(Bxy, "Bxy");
         Bbar = max(Bxy, true);
       }
     }
@@ -355,44 +349,13 @@ class GEM : public PhysicsModel {
     //////////////////////////////////
     // Metric tensor components
 
-    coord = mesh->getCoordinates();
-
-    // Normalise
-    hthe /= Lbar; // parallel derivatives normalised to Lperp
-
-    Bpxy /= Bbar;
-    Btxy /= Bbar;
-    Bxy /= Bbar;
-
-    Rxy /= rho_s; // Perpendicular derivatives normalised to rho_s
-    coord->dx /= rho_s * rho_s * Bbar;
-
-    // Metric components
-
-    coord->g11 = SQ(Rxy * Bpxy);
-    coord->g22 = 1.0 / SQ(hthe);
-    coord->g33 = SQ(Bxy) / coord->g11;
-    coord->g12 = 0.0;
-    coord->g13 = 0.;
-    coord->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    coord->J = hthe / Bpxy;
-    coord->Bxy = Bxy;
-
-    coord->g_11 = 1.0 / coord->g11;
-    coord->g_22 = SQ(Bxy * hthe / Bpxy);
-    coord->g_33 = Rxy * Rxy;
-    coord->g_12 = 0.;
-    coord->g_13 = 0.;
-    coord->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    coord->geometry();
+    const auto tokamak_coords = bout::set_tokamak_coordinates(*mesh, rho_s, Bbar);
 
     // Set B field vector
 
     B0vec.covariant = false;
     B0vec.x = 0.;
-    B0vec.y = Bpxy / hthe;
+    B0vec.y = tokamak_coords.Bpxy / tokamak_coords.hthe;
     B0vec.z = 0.;
 
     // Precompute this for use in RHS
diff --git a/examples/laplacexy/alfven-wave/alfven.cxx b/examples/laplacexy/alfven-wave/alfven.cxx
index 031931c1c4..aa62751db4 100644
--- a/examples/laplacexy/alfven-wave/alfven.cxx
+++ b/examples/laplacexy/alfven-wave/alfven.cxx
@@ -3,6 +3,7 @@
 #include <bout/invert/laplacexz.hxx>
 #include <bout/invert_laplace.hxx>
 #include <bout/physicsmodel.hxx>
+#include <bout/tokamak_coordinates.hxx>
 
 #include <memory>
 
@@ -70,7 +71,7 @@ class Alfven : public PhysicsModel {
     resistivity = opt["resistivity"].withDefault(1e-7);
 
     // Load metric tensor from the mesh, passing length and B field normalisations
-    LoadMetric(rho_s0, Bnorm);
+    bout::set_tokamak_coordinates(*mesh, rho_s0, Bnorm, true);
 
     // Specify evolving variables
     SOLVE_FOR2(Vort, Apar);
@@ -168,59 +169,6 @@ class Alfven : public PhysicsModel {
 
     return 0;
   }
-
-  void LoadMetric(BoutReal Lnorm, BoutReal Bnorm) {
-    // Load metric coefficients from the mesh
-    Field2D Rxy, Bpxy, Btxy, hthe, sinty;
-    GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics
-
-    Coordinates* coord = mesh->getCoordinates(); // Metric tensor
-
-    // Checking for dpsi and qinty used in BOUT grids
-    Field2D dx;
-    if (!mesh->get(dx, "dpsi")) {
-      output << "\tUsing dpsi as the x grid spacing\n";
-      coord->dx = dx; // Only use dpsi if found
-    } else {
-      // dx will have been read already from the grid
-      output << "\tUsing dx as the x grid spacing\n";
-    }
-
-    Rxy /= Lnorm;
-    hthe /= Lnorm;
-    sinty *= SQ(Lnorm) * Bnorm;
-    coord->dx /= SQ(Lnorm) * Bnorm;
-
-    Bpxy /= Bnorm;
-    Btxy /= Bnorm;
-    coord->Bxy /= Bnorm;
-
-    // Calculate metric components
-    sinty = 0.0; // I disappears from metric for shifted coordinates
-
-    BoutReal sbp = 1.0; // Sign of Bp
-    if (min(Bpxy, true) < 0.0) {
-      sbp = -1.0;
-    }
-
-    coord->g11 = SQ(Rxy * Bpxy);
-    coord->g22 = 1.0 / SQ(hthe);
-    coord->g33 = SQ(sinty) * coord->g11 + SQ(coord->Bxy) / coord->g11;
-    coord->g12 = 0.0;
-    coord->g13 = -sinty * coord->g11;
-    coord->g23 = -sbp * Btxy / (hthe * Bpxy * Rxy);
-
-    coord->J = hthe / Bpxy;
-
-    coord->g_11 = 1.0 / coord->g11 + SQ(sinty * Rxy);
-    coord->g_22 = SQ(coord->Bxy * hthe / Bpxy);
-    coord->g_33 = Rxy * Rxy;
-    coord->g_12 = sbp * Btxy * hthe * sinty * Rxy / Bpxy;
-    coord->g_13 = sinty * Rxy * Rxy;
-    coord->g_23 = sbp * Btxy * hthe * Rxy / Bpxy;
-
-    coord->geometry();
-  }
 };
 
 BOUTMAIN(Alfven);
diff --git a/examples/laplacexy/laplace_perp/test.cxx b/examples/laplacexy/laplace_perp/test.cxx
index e3d9528d45..b1686d1764 100644
--- a/examples/laplacexy/laplace_perp/test.cxx
+++ b/examples/laplacexy/laplace_perp/test.cxx
@@ -1,9 +1,9 @@
 #include <bout/bout.hxx>
-#include <bout/field2d.hxx>
-
 #include <bout/derivs.hxx>
+#include <bout/field2d.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/invert/laplacexy.hxx>
+#include <bout/tokamak_coordinates.hxx>
 
 using bout::globals::mesh;
 
@@ -13,41 +13,7 @@ int main(int argc, char** argv) {
   ///////////////////////////////////////
   const bool calc_metric = Options::root()["calc_metric"].withDefault(false);
   if (calc_metric) {
-    // Read metric tensor
-    Field2D Rxy;
-    Field2D Btxy;
-    Field2D Bpxy;
-    Field2D B0;
-    Field2D hthe;
-    Field2D I;
-    mesh->get(Rxy, "Rxy");   // m
-    mesh->get(Btxy, "Btxy"); // T
-    mesh->get(Bpxy, "Bpxy"); // T
-    mesh->get(B0, "Bxy");    // T
-    mesh->get(hthe, "hthe"); // m
-    mesh->get(I, "sinty");   // m^-2 T^-1
-
-    Coordinates* coord = mesh->getCoordinates();
-
-    // Calculate metrics
-    coord->g11 = SQ(Rxy * Bpxy);
-    coord->g22 = 1.0 / SQ(hthe);
-    coord->g33 = SQ(I) * coord->g11 + SQ(B0) / coord->g11;
-    coord->g12 = 0.0;
-    coord->g13 = -I * coord->g11;
-    coord->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    coord->J = hthe / Bpxy;
-    coord->Bxy = B0;
-
-    coord->g_11 = 1.0 / coord->g11 + SQ(I * Rxy);
-    coord->g_22 = SQ(B0 * hthe / Bpxy);
-    coord->g_33 = Rxy * Rxy;
-    coord->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    coord->g_13 = I * Rxy * Rxy;
-    coord->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    coord->geometry();
+    bout::set_tokamak_coordinates(*mesh);
   }
   ///////////////////////////////////////
 
diff --git a/examples/wave-slab/wave_slab.cxx b/examples/wave-slab/wave_slab.cxx
index 4169b63dab..6101268e72 100644
--- a/examples/wave-slab/wave_slab.cxx
+++ b/examples/wave-slab/wave_slab.cxx
@@ -1,54 +1,22 @@
 /*
   Simple wave test in a sheared slab domain.
-  
+
   Uses the same field-aligned Clebsch coordinate system as
   most BOUT++ tokamak simulations. See the coordinates manual
   for details.
-  
-  Note: Here the only components of the coordinate system which 
+
+  Note: Here the only components of the coordinate system which
   are tested are g_22 (for Grad_par), and the twist shift angle.
-  
+
  */
 
+#include "bout/tokamak_coordinates.hxx"
 #include <bout/physicsmodel.hxx>
 
 class WaveTest : public PhysicsModel {
 public:
   int init(bool UNUSED(restarting)) {
-    auto* coords = mesh->getCoordinates();
-    Field2D Rxy, Bpxy, Btxy, hthe, I;
-    GRID_LOAD(Rxy);
-    GRID_LOAD(Bpxy);
-    GRID_LOAD(Btxy);
-    GRID_LOAD(hthe);
-    mesh->get(coords->Bxy, "Bxy");
-    int ShiftXderivs = 0;
-    mesh->get(ShiftXderivs, "false");
-    if (ShiftXderivs) {
-      // No integrated shear in metric
-      I = 0.0;
-    } else {
-      mesh->get(I, "sinty");
-    }
-
-    coords->g11 = pow(Rxy * Bpxy, 2.0);
-    coords->g22 = 1.0 / pow(hthe, 2.0);
-    coords->g33 = pow(I, 2.0) * coords->g11 + pow(coords->Bxy, 2.0) / coords->g11;
-    coords->g12 = 0.0;
-    coords->g13 = -I * coords->g11;
-    coords->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    coords->J = hthe / Bpxy;
-
-    coords->g_11 = 1.0 / coords->g11 + (pow(I * Rxy, 2.0));
-    coords->g_22 = pow(coords->Bxy * hthe / Bpxy, 2.0);
-    coords->g_33 = Rxy * Rxy;
-    coords->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    coords->g_13 = I * Rxy * Rxy;
-    coords->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    coords->geometry();
-
+    bout::set_tokamak_coordinates(*mesh, 1.0, 1.0, true);
     solver->add(f, "f");
     solver->add(g, "g");
 
diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index e7ead42ee5..f8d421a483 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -251,16 +251,4 @@ private:
   void checkContravariant();
 };
 
-/*
-/// Standard coordinate system for tokamak simulations
-class TokamakCoordinates : public Coordinates {
-public:
-  TokamakCoordinates(Mesh *mesh) : Coordinates(mesh) {
-    
-  }
-private:
-  
-};
-*/
-
 #endif // BOUT_COORDINATES_H
diff --git a/include/bout/tokamak_coordinates.hxx b/include/bout/tokamak_coordinates.hxx
new file mode 100644
index 0000000000..f056033bb9
--- /dev/null
+++ b/include/bout/tokamak_coordinates.hxx
@@ -0,0 +1,49 @@
+#ifndef BOUT_TOKAMAK_COORDINATES_HXX
+#define BOUT_TOKAMAK_COORDINATES_HXX
+
+#include <bout/bout_types.hxx>
+#include <bout/coordinates.hxx>
+#include <bout/field2d.hxx>
+
+class Mesh;
+
+namespace bout {
+/// Variables used in the BOUT++ tokamak coordinate system.
+///
+/// When created by `set_tokamak_coordinates`, all variables except
+/// `I_unnormalised` are normalised.
+struct TokamakCoordinates {
+  /// Major radius
+  Field2D Rxy;
+  /// Vertical height
+  Field2D Zxy;
+  /// Poloidal magnetic field
+  Field2D Bpxy;
+  /// Toroidal magnetic field
+  Field2D Btxy;
+  /// Total magnetic field
+  Field2D Bxy;
+  /// Poloidal arc length
+  Field2D hthe;
+  /// Integrated shear (normalised)
+  Coordinates::FieldMetric I;
+  /// Unnormalised integrated shear
+  Coordinates::FieldMetric I_unnormalised;
+};
+
+/// Read, normalise, calculate, and set the metric components for a BOUT++
+/// tokamak coordinate system.
+///
+/// Sets the cell-centre `Coordinates` on \p mesh
+///
+/// @param Lbar         Spatial normalisation
+/// @param Bbar         Magnetic normalisation
+/// @param no_shear     Don't use integrated shear in coordinate system
+/// @param shear_factor Integrated shear normalisation
+TokamakCoordinates set_tokamak_coordinates(Mesh& mesh, BoutReal Lbar = 1.0,
+                                           BoutReal Bbar = 1.0, bool no_shear = false,
+                                           BoutReal shear_factor = 1.0);
+
+} // namespace bout
+
+#endif //BOUT_TOKAMAK_COORDINATES_HXX
diff --git a/src/mesh/tokamak_coordinates.cxx b/src/mesh/tokamak_coordinates.cxx
new file mode 100644
index 0000000000..af8b6335bf
--- /dev/null
+++ b/src/mesh/tokamak_coordinates.cxx
@@ -0,0 +1,77 @@
+#include <bout/bout_types.hxx>
+#include <bout/coordinates.hxx>
+#include <bout/field2d.hxx>
+#include <bout/mesh.hxx>
+#include <bout/tokamak_coordinates.hxx>
+#include <bout/utils.hxx>
+
+namespace bout {
+TokamakCoordinates set_tokamak_coordinates(Mesh& mesh, BoutReal Lbar, BoutReal Bbar,
+                                           bool no_shear, BoutReal shear_factor) {
+  Field2D Rxy;
+  mesh.get(Rxy, "Rxy"); // [m]
+  Rxy /= Lbar;
+
+  Field2D Zxy;
+  mesh.get(Zxy, "Zxy"); // [m]
+  Zxy /= Lbar;
+
+  Field2D Bpxy;
+  mesh.get(Bpxy, "Bpxy"); // [T]
+  Bpxy /= Bbar;
+
+  Field2D Btxy;
+  mesh.get(Btxy, "Btxy"); // [T]
+  Btxy /= Bbar;
+
+  Field2D Bxy;
+  mesh.get(Bxy, "Bxy"); // [T]
+  Bxy /= Bbar;
+
+  Field2D hthe;
+  mesh.get(hthe, "hthe"); // [m / radian]
+  hthe /= Lbar;
+
+  Coordinates::FieldMetric I;
+  if (no_shear) {
+    I = 0.0;
+  } else {
+    mesh.get(I, "sinty"); // [m^-2 T^-1]
+  }
+  const auto I_unnormalised = I;
+  I *= Lbar * Lbar * Bbar * shear_factor;
+
+  Coordinates::FieldMetric dx;
+  if (mesh.get(dx, "dpsi") != 0) {
+    dx = mesh.getCoordinates()->dx;
+  }
+  dx /= Lbar * Lbar * Bbar;
+
+  const BoutReal sign_of_bp = min(Bpxy, true) < 0.0 ? -1.0 : 1.0;
+
+  auto* coords = mesh.getCoordinates();
+
+  coords->Bxy = Bxy;
+  coords->dx = dx;
+
+  coords->g11 = SQ(Rxy * Bpxy);
+  coords->g22 = 1.0 / SQ(hthe);
+  coords->g33 = SQ(I) * coords->g11 + SQ(Bxy) / coords->g11;
+  coords->g12 = 0.0;
+  coords->g13 = -I * coords->g11;
+  coords->g23 = -sign_of_bp * Btxy / (hthe * Bpxy * Rxy);
+
+  coords->J = hthe / Bpxy;
+
+  coords->g_11 = 1.0 / coords->g11 + SQ(I * Rxy);
+  coords->g_22 = SQ(Bxy * hthe / Bpxy);
+  coords->g_33 = Rxy * Rxy;
+  coords->g_12 = sign_of_bp * Btxy * hthe * I * Rxy / Bpxy;
+  coords->g_13 = I * Rxy * Rxy;
+  coords->g_23 = sign_of_bp * Btxy * hthe * Rxy / Bpxy;
+
+  coords->geometry();
+
+  return {Rxy, Zxy, Bpxy, Btxy, Bxy, hthe, I, I_unnormalised};
+}
+} // namespace bout
diff --git a/tests/MMS/GBS/gbs.cxx b/tests/MMS/GBS/gbs.cxx
index d0d1fcb039..6d7fbcafd2 100644
--- a/tests/MMS/GBS/gbs.cxx
+++ b/tests/MMS/GBS/gbs.cxx
@@ -1,22 +1,24 @@
 /*
   Global Braginskii Solver (GBS) equations
-  
+
   http://infoscience.epfl.ch/record/182434/files/PPCF2012.pdf
 
   NOTES:
-  
+
   1. A slightly different definition of Poisson brackets is used in BOUT++:
      [f,g] = b.(Grad f cross Grad g) / B
-     
+
   2. This version is collocated, and uses a
      4th-order smoother to stabilise the method
  */
 
 #include "gbs.hxx"
 
+#include <bout/bout_types.hxx>
 #include <bout/derivs.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/initialprofiles.hxx>
+#include <bout/tokamak_coordinates.hxx>
 
 int GBS::init(bool restarting) {
   Options* opt = Options::getRoot();
@@ -313,58 +315,9 @@ int GBS::init(bool restarting) {
 }
 
 void GBS::LoadMetric(BoutReal Lnorm, BoutReal Bnorm) {
-  // Load metric coefficients from the mesh
-  Field2D Rxy, Bpxy, Btxy, hthe, sinty;
-  GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics
-
-  // Checking for dpsi and qinty used in BOUT grids
-  Field2D dx;
-  if (!mesh->get(dx, "dpsi")) {
-    output << "\tUsing dpsi as the x grid spacing\n";
-    coords->dx = dx; // Only use dpsi if found
-  } else {
-    // dx will have been read already from the grid
-    output << "\tUsing dx as the x grid spacing\n";
-  }
-
-  Rxy /= Lnorm;
-  hthe /= Lnorm;
-  sinty *= SQ(Lnorm) * Bnorm;
-  coords->dx /= SQ(Lnorm) * Bnorm;
-
-  Bpxy /= Bnorm;
-  Btxy /= Bnorm;
-  coords->Bxy /= Bnorm;
-
-  // Calculate metric components
-  bool ShiftXderivs;
-  Options::getRoot()->get("shiftXderivs", ShiftXderivs, false); // Read global flag
-  if (ShiftXderivs) {
-    sinty = 0.0; // I disappears from metric
-  }
-
-  BoutReal sbp = 1.0; // Sign of Bp
-  if (min(Bpxy, true) < 0.0) {
-    sbp = -1.0;
-  }
-
-  coords->g11 = SQ(Rxy * Bpxy);
-  coords->g22 = 1.0 / SQ(hthe);
-  coords->g33 = SQ(sinty) * coords->g11 + SQ(coords->Bxy) / coords->g11;
-  coords->g12 = 0.0;
-  coords->g13 = -sinty * coords->g11;
-  coords->g23 = -sbp * Btxy / (hthe * Bpxy * Rxy);
-
-  coords->J = hthe / Bpxy;
-
-  coords->g_11 = 1.0 / coords->g11 + SQ(sinty * Rxy);
-  coords->g_22 = SQ(coords->Bxy * hthe / Bpxy);
-  coords->g_33 = Rxy * Rxy;
-  coords->g_12 = sbp * Btxy * hthe * sinty * Rxy / Bpxy;
-  coords->g_13 = sinty * Rxy * Rxy;
-  coords->g_23 = sbp * Btxy * hthe * Rxy / Bpxy;
+  const bool ShiftXderivs = Options::root()["shiftXderivs"].withDefault(false);
 
-  coords->geometry();
+  bout::set_tokamak_coordinates(*mesh, Lnorm, Bnorm, ShiftXderivs);
 }
 
 // just define a macro for V_E dot Grad
diff --git a/tests/MMS/elm-pb/elm_pb.cxx b/tests/MMS/elm-pb/elm_pb.cxx
index 3ad8f70b85..8fb2a58cbf 100644
--- a/tests/MMS/elm-pb/elm_pb.cxx
+++ b/tests/MMS/elm-pb/elm_pb.cxx
@@ -12,6 +12,7 @@
 #include <bout/bout.hxx>
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
+#include <bout/field_factory.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert_laplace.hxx>
@@ -19,10 +20,9 @@
 #include <bout/msg_stack.hxx>
 #include <bout/physicsmodel.hxx>
 #include <bout/sourcex.hxx>
+#include <bout/tokamak_coordinates.hxx>
 #include <bout/utils.hxx>
 
-#include <bout/field_factory.hxx>
-
 #include <math.h>
 
 class ELMpb : public PhysicsModel {
@@ -114,9 +114,7 @@ class ELMpb : public PhysicsModel {
   BoutReal hyperresist;  // Hyper-resistivity coefficient (in core only)
   BoutReal ehyperviscos; // electron Hyper-viscosity coefficient
 
-  // Metric coefficients
-  Field2D Rxy, Bpxy, Btxy, B0, hthe;
-  Field2D I; // Shear factor
+  Field2D B0; // Magnetic field
 
   bool mms; // True if testing with Method of Manufactured Solutions
 
@@ -149,29 +147,8 @@ class ELMpb : public PhysicsModel {
     // Load data from the grid
 
     // Load 2D profiles
-    mesh->get(J0, "Jpar0");    // A / m^2
     mesh->get(P0, "pressure"); // Pascals
 
-    // Load curvature term
-    b0xcv.covariant = false;  // Read contravariant components
-    mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2
-
-    // Load metrics
-    if (mesh->get(Rxy, "Rxy")) { // m
-      output_error.write("Error: Cannot read Rxy from grid\n");
-      return 1;
-    }
-    if (mesh->get(Bpxy, "Bpxy")) { // T
-      output_error.write("Error: Cannot read Bpxy from grid\n");
-      return 1;
-    }
-    mesh->get(Btxy, "Btxy"); // T
-    mesh->get(B0, "Bxy");    // T
-    mesh->get(hthe, "hthe"); // m
-    mesh->get(I, "sinty");   // m^-2 T^-1
-
-    Coordinates* coords = mesh->getCoordinates();
-
     //////////////////////////////////////////////////////////////
     // Read parameters from the options file
     //
@@ -293,48 +270,63 @@ class ELMpb : public PhysicsModel {
 
     OPTION(globalOptions->getSection("solver"), mms, false);
 
-    if (!include_curvature) {
+    //////////////////////////////////////////////////////////////
+    // INITIALIZE LAPLACIAN SOLVER
+
+    phi_solver = Laplacian::create();
+
+    //////////////////////////////////////////////////////////////
+    // Read, normalise, and set coordinates
+
+    // Typical magnetic field
+    mesh->get(Bbar, "bmag", 1.0);
+    // Typical length scale
+    mesh->get(Lbar, "rmag", 1.0);
+
+    // Read, normalise, and set coordinates
+    const auto tokamak_coords =
+        bout::set_tokamak_coordinates(*mesh, Lbar, Bbar, mesh->IncIntShear);
+    const auto& Rxy = tokamak_coords.Rxy;
+    const auto& Bpxy = tokamak_coords.Bpxy;
+    const auto& Btxy = tokamak_coords.Btxy;
+    const auto& hthe = tokamak_coords.hthe;
+    const auto& I = tokamak_coords.I_unnormalised;
+
+    B0 = tokamak_coords.Bxy;
+
+    if (include_curvature) {
+      // Load curvature term
+      b0xcv.covariant = false;  // Read contravariant components
+      mesh->get(b0xcv, "bxcv"); // mixed units x: T y: m^-2 z: m^-2
+    } else {
       b0xcv = 0.0;
     }
 
-    if (!include_jpar0) {
+    if (include_jpar0) {
+      mesh->get(J0, "Jpar0"); // A / m^2
+    } else {
       J0 = 0.0;
     }
 
-    //////////////////////////////////////////////////////////////
-    // INITIALIZE LAPLACIAN SOLVER
-
-    phi_solver = Laplacian::create();
-
     //////////////////////////////////////////////////////////////
     // SHIFTED RADIAL COORDINATES
 
-    bool ShiftXderivs;
-    globalOptions->get("shiftXderivs", ShiftXderivs, false); // Read global flag
+    const bool ShiftXderivs = (*globalOptions)["shiftXderivs"].withDefault(false);
     if (ShiftXderivs) {
       if (mesh->IncIntShear) {
         // BOUT-06 style, using d/dx = d/dpsi + I * d/dz
-        coords->IntShiftTorsion = I;
-
+        mesh->getCoordinates()->IntShiftTorsion = I;
       } else {
         // Dimits style, using local coordinate system
         if (include_curvature) {
           b0xcv.z += I * b0xcv.x;
         }
-        I = 0.0; // I disappears from metric
       }
     }
 
     //////////////////////////////////////////////////////////////
     // NORMALISE QUANTITIES
 
-    if (mesh->get(Bbar, "bmag")) { // Typical magnetic field
-      Bbar = 1.0;
-    }
-    if (mesh->get(Lbar, "rmag")) { // Typical length scale
-      Lbar = 1.0;
-    }
-
     Va = sqrt(Bbar * Bbar / (MU0 * density * Mi));
 
     Tbar = Lbar / Va;
@@ -374,8 +366,7 @@ class ELMpb : public PhysicsModel {
       output.write("    electron Hyper-viscosity coefficient: {:e}\n", ehyperviscos);
     }
 
-    Field2D Te;
-    Te = P0 / (2.0 * density * 1.602e-19); // Temperature in eV
+    const Field2D Te = P0 / (2.0 * density * 1.602e-19); // Temperature in eV
 
     J0 = -MU0 * Lbar * J0 / B0;
     P0 = 2.0 * MU0 * P0 / (Bbar * Bbar);
@@ -384,14 +375,6 @@ class ELMpb : public PhysicsModel {
     b0xcv.y *= Lbar * Lbar;
     b0xcv.z *= Lbar * Lbar;
 
-    Rxy /= Lbar;
-    Bpxy /= Bbar;
-    Btxy /= Bbar;
-    B0 /= Bbar;
-    hthe /= Lbar;
-    coords->dx /= Lbar * Lbar * Bbar;
-    I *= Lbar * Lbar * Bbar;
-
     BoutReal pnorm = max(P0, true); // Maximum over all processors
 
     vacuum_pressure *= pnorm; // Get pressure from fraction
@@ -415,27 +398,6 @@ class ELMpb : public PhysicsModel {
 
     dump.add(eta, "eta", 0);
 
-    /**************** CALCULATE METRICS ******************/
-
-    coords->g11 = SQ(Rxy * Bpxy);
-    coords->g22 = 1.0 / SQ(hthe);
-    coords->g33 = SQ(I) * coords->g11 + SQ(B0) / coords->g11;
-    coords->g12 = 0.0;
-    coords->g13 = -I * coords->g11;
-    coords->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    coords->J = hthe / Bpxy;
-    coords->Bxy = B0;
-
-    coords->g_11 = 1.0 / coords->g11 + (SQ(I * Rxy));
-    coords->g_22 = SQ(B0 * hthe / Bpxy);
-    coords->g_33 = Rxy * Rxy;
-    coords->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    coords->g_13 = I * Rxy * Rxy;
-    coords->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    coords->geometry(); // Calculate quantities from metric tensor
-
     // Set B field vector
 
     B0vec.covariant = false;
diff --git a/tests/MMS/tokamak/tokamak.cxx b/tests/MMS/tokamak/tokamak.cxx
index a8bf4b685e..8b6baab950 100644
--- a/tests/MMS/tokamak/tokamak.cxx
+++ b/tests/MMS/tokamak/tokamak.cxx
@@ -3,12 +3,15 @@
  *
  * Independently tests the bracket operator, perpendicular diffusion,
  * and parallel diffusion operators.
- * 
+ *
  */
 
+#include <bout/bout_types.hxx>
 #include <bout/derivs.hxx>
 #include <bout/field_factory.hxx>
+#include <bout/options.hxx>
 #include <bout/physicsmodel.hxx>
+#include <bout/tokamak_coordinates.hxx>
 
 class TokamakMMS : public PhysicsModel {
 public:
@@ -43,60 +46,9 @@ class TokamakMMS : public PhysicsModel {
     return 0;
   }
   void LoadMetric(BoutReal Lnorm, BoutReal Bnorm) {
-    // Load metric coefficients from the mesh
-    Field2D Rxy, Bpxy, Btxy, hthe, sinty;
-    GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics
-
-    Coordinates* coords = mesh->getCoordinates();
-
-    // Checking for dpsi used in BOUT grids
-    Field2D dx;
-    if (!mesh->get(dx, "dpsi")) {
-      output << "\tUsing dpsi as the x grid spacing\n";
-      coords->dx = dx; // Only use dpsi if found
-    } else {
-      // dx will have been read already from the grid
-      output << "\tUsing dx as the x grid spacing\n";
-    }
-
-    Rxy /= Lnorm;
-    hthe /= Lnorm;
-    sinty *= SQ(Lnorm) * Bnorm;
-    coords->dx /= SQ(Lnorm) * Bnorm;
-
-    Bpxy /= Bnorm;
-    Btxy /= Bnorm;
-    coords->Bxy /= Bnorm;
-
-    // Calculate metric components
-    bool ShiftXderivs;
-    Options::getRoot()->get("shiftXderivs", ShiftXderivs, false); // Read global flag
-    if (ShiftXderivs) {
-      sinty = 0.0; // I disappears from metric
-    }
-
-    BoutReal sbp = 1.0; // Sign of Bp
-    if (min(Bpxy, true) < 0.0) {
-      sbp = -1.0;
-    }
-
-    coords->g11 = SQ(Rxy * Bpxy);
-    coords->g22 = 1.0 / SQ(hthe);
-    coords->g33 = SQ(sinty) * coords->g11 + SQ(coords->Bxy) / coords->g11;
-    coords->g12 = 0.0;
-    coords->g13 = -sinty * coords->g11;
-    coords->g23 = -sbp * Btxy / (hthe * Bpxy * Rxy);
-
-    coords->J = hthe / Bpxy;
-
-    coords->g_11 = 1.0 / coords->g11 + SQ(sinty * Rxy);
-    coords->g_22 = SQ(coords->Bxy * hthe / Bpxy);
-    coords->g_33 = Rxy * Rxy;
-    coords->g_12 = sbp * Btxy * hthe * sinty * Rxy / Bpxy;
-    coords->g_13 = sinty * Rxy * Rxy;
-    coords->g_23 = sbp * Btxy * hthe * Rxy / Bpxy;
+    const bool ShiftXderivs = Options::root()["shiftXderivs"].withDefault(false);
 
-    coords->geometry();
+    bout::set_tokamak_coordinates(*mesh, Lnorm, Bnorm, ShiftXderivs);
   }
 
 private:
diff --git a/tests/integrated/test-drift-instability/2fluid.cxx b/tests/integrated/test-drift-instability/2fluid.cxx
index 89105e970c..dca5a69e3b 100644
--- a/tests/integrated/test-drift-instability/2fluid.cxx
+++ b/tests/integrated/test-drift-instability/2fluid.cxx
@@ -4,16 +4,14 @@
  *******************************************************************************/
 
 #include <bout/bout.hxx>
-#include <bout/physicsmodel.hxx>
-
 #include <bout/derivs.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert_laplace.hxx>
+#include <bout/physicsmodel.hxx>
+#include <bout/tokamak_coordinates.hxx>
 
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 
 // just define a macro for V_E dot Grad
 #define vE_Grad(f, p) (b0xGrad_dot_Grad(p, f) / coord->Bxy)
@@ -41,9 +39,6 @@ class TwoFluid : public PhysicsModel {
   Field3D pei, pe;
   Field2D pei0, pe0;
 
-  // Metric coefficients
-  Field2D Rxy, Bpxy, Btxy, hthe;
-
   // parameters
   BoutReal Te_x, Ti_x, Ni_x, Vi_x, bmag, rho_s, fmei, AA, ZZ;
   BoutReal lambda_ei, lambda_ii;
@@ -68,8 +63,6 @@ class TwoFluid : public PhysicsModel {
 
 protected:
   int init(bool UNUSED(restarting)) override {
-    Field2D I; // Shear factor
-
     output.write("Solving 6-variable 2-fluid equations\n");
 
     /************* LOAD DATA FROM GRID FILE ****************/
@@ -88,17 +81,6 @@ class TwoFluid : public PhysicsModel {
     b0xcv.covariant = false;  // Read contravariant components
     mesh->get(b0xcv, "bxcv"); // b0xkappa terms
 
-    // Coordinate system
-    coord = mesh->getCoordinates();
-
-    // Load metrics
-    GRID_LOAD(Rxy);
-    GRID_LOAD(Bpxy);
-    GRID_LOAD(Btxy);
-    GRID_LOAD(hthe);
-    mesh->get(coord->dx, "dpsi");
-    mesh->get(I, "sinty");
-
     // Load normalisation values
     GRID_LOAD(Te_x);
     GRID_LOAD(Ti_x);
@@ -141,14 +123,6 @@ class TwoFluid : public PhysicsModel {
       (*globalOptions)["aparsolver"].setConditionallyUsed();
     }
 
-    /************* SHIFTED RADIAL COORDINATES ************/
-
-    const bool ShiftXderivs = (*globalOptions)["ShiftXderivs"].withDefault(false);
-    if (ShiftXderivs) {
-      ShearFactor = 0.0; // I disappears from metric
-      b0xcv.z += I * b0xcv.x;
-    }
-
     /************** CALCULATE PARAMETERS *****************/
 
     rho_s = 1.02 * sqrt(AA * Te_x) / ZZ / bmag;
@@ -184,6 +158,20 @@ class TwoFluid : public PhysicsModel {
           hthe0 / rho_s);
     }
 
+    /**************** CALCULATE METRICS ******************/
+
+    const bool ShiftXderivs = (*globalOptions)["ShiftXderivs"].withDefault(false);
+    const auto tokamak_coords = bout::set_tokamak_coordinates(*mesh, rho_s, bmag / 1e4,
+                                                              ShiftXderivs, ShearFactor);
+    const auto& I = tokamak_coords.I_unnormalised;
+    coord = mesh->getCoordinates();
+
+    /************* SHIFTED RADIAL COORDINATES ************/
+
+    if (ShiftXderivs) {
+      b0xcv.z += I * b0xcv.x;
+    }
+
     /************** NORMALISE QUANTITIES *****************/
 
     output.write("\tNormalising to rho_s = {:e}\n", rho_s);
@@ -200,41 +188,10 @@ class TwoFluid : public PhysicsModel {
     b0xcv.y *= rho_s * rho_s;
     b0xcv.z *= rho_s * rho_s;
 
-    // Normalise geometry
-    Rxy /= rho_s;
-    hthe /= rho_s;
-    I *= rho_s * rho_s * (bmag / 1e4) * ShearFactor;
-    coord->dx /= rho_s * rho_s * (bmag / 1e4);
-
-    // Normalise magnetic field
-    Bpxy /= (bmag / 1.e4);
-    Btxy /= (bmag / 1.e4);
-    coord->Bxy /= (bmag / 1.e4);
-
     // calculate pressures
     pei0 = (Ti0 + Te0) * Ni0;
     pe0 = Te0 * Ni0;
 
-    /**************** CALCULATE METRICS ******************/
-
-    coord->g11 = SQ(Rxy * Bpxy);
-    coord->g22 = 1.0 / SQ(hthe);
-    coord->g33 = SQ(I) * coord->g11 + SQ(coord->Bxy) / coord->g11;
-    coord->g12 = 0.0;
-    coord->g13 = -I * coord->g11;
-    coord->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    coord->J = hthe / Bpxy;
-
-    coord->g_11 = 1.0 / coord->g11 + SQ(I * Rxy);
-    coord->g_22 = SQ(coord->Bxy * hthe / Bpxy);
-    coord->g_33 = Rxy * Rxy;
-    coord->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    coord->g_13 = I * Rxy * Rxy;
-    coord->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    coord->geometry();
-
     /**************** SET EVOLVING VARIABLES *************/
 
     // Tell BOUT++ which variables to evolve
diff --git a/tests/integrated/test-interchange-instability/2fluid.cxx b/tests/integrated/test-interchange-instability/2fluid.cxx
index 5e57e166c4..db0fef2fbf 100644
--- a/tests/integrated/test-interchange-instability/2fluid.cxx
+++ b/tests/integrated/test-interchange-instability/2fluid.cxx
@@ -4,15 +4,13 @@
  *******************************************************************************/
 
 #include <bout/bout.hxx>
-
 #include <bout/derivs.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/invert_laplace.hxx>
+#include <bout/tokamak_coordinates.hxx>
 #include <bout/unused.hxx>
 
 #include <cmath>
-#include <cstdio>
-#include <cstdlib>
 
 class Interchange : public PhysicsModel {
 
@@ -39,8 +37,6 @@ class Interchange : public PhysicsModel {
 
 protected:
   int init(bool UNUSED(restarting)) override {
-    Field2D I; // Shear factor
-
     output << "Solving 2-variable equations\n";
 
     /************* LOAD DATA FROM GRID FILE ****************/
@@ -56,17 +52,6 @@ class Interchange : public PhysicsModel {
 
     b0xcv *= -1.0; // NOTE: THIS IS FOR 'OLD' GRID FILES ONLY
 
-    // Coordinate system
-    coord = mesh->getCoordinates();
-
-    // Load metrics
-    GRID_LOAD(Rxy);
-    GRID_LOAD(Bpxy);
-    GRID_LOAD(Btxy);
-    GRID_LOAD(hthe);
-    mesh->get(coord->dx, "dpsi");
-    mesh->get(I, "sinty");
-
     // Load normalisation values
     GRID_LOAD(Te_x);
     GRID_LOAD(Ti_x);
@@ -90,14 +75,6 @@ class Interchange : public PhysicsModel {
     /*************** INITIALIZE LAPLACE SOLVER ***********/
     phi_solver = Laplacian::create();
 
-    /************* SHIFTED RADIAL COORDINATES ************/
-
-    const bool ShiftXderivs = (*globalOptions)["ShiftXderivs"].withDefault(false);
-    if (ShiftXderivs) {
-      ShearFactor = 0.0; // I disappears from metric
-      b0xcv.z += I * b0xcv.x;
-    }
-
     /************** CALCULATE PARAMETERS *****************/
 
     rho_s = 1.02 * sqrt(AA * Te_x) / ZZ / bmag;
@@ -112,6 +89,20 @@ class Interchange : public PhysicsModel {
           hthe0 / rho_s);
     }
 
+    /**************** CALCULATE METRICS ******************/
+
+    const bool ShiftXderivs = (*globalOptions)["ShiftXderivs"].withDefault(false);
+    const auto tokamak_coords = bout::set_tokamak_coordinates(*mesh, rho_s, bmag / 1e4,
+                                                              ShiftXderivs, ShearFactor);
+    const auto& I = tokamak_coords.I_unnormalised;
+    coord = mesh->getCoordinates();
+
+    /************* SHIFTED RADIAL COORDINATES ************/
+
+    if (ShiftXderivs) {
+      b0xcv.z += I * b0xcv.x;
+    }
+
     /************** NORMALISE QUANTITIES *****************/
 
     output.write("\tNormalising to rho_s = {:e}\n", rho_s);
@@ -126,36 +117,7 @@ class Interchange : public PhysicsModel {
     b0xcv.y *= rho_s * rho_s;
     b0xcv.z *= rho_s * rho_s;
 
-    // Normalise geometry
-    Rxy /= rho_s;
-    hthe /= rho_s;
-    I *= rho_s * rho_s * (bmag / 1e4) * ShearFactor;
-    coord->dx /= rho_s * rho_s * (bmag / 1e4);
-
-    // Normalise magnetic field
-    Bpxy /= (bmag / 1.e4);
-    Btxy /= (bmag / 1.e4);
-    coord->Bxy /= (bmag / 1.e4);
-
-    /**************** CALCULATE METRICS ******************/
-
-    coord->g11 = SQ(Rxy * Bpxy);
-    coord->g22 = 1.0 / SQ(hthe);
-    coord->g33 = SQ(I) * coord->g11 + SQ(coord->Bxy) / coord->g11;
-    coord->g12 = 0.0;
-    coord->g13 = -I * coord->g11;
-    coord->g23 = -Btxy / (hthe * Bpxy * Rxy);
-
-    coord->J = hthe / Bpxy;
-
-    coord->g_11 = 1.0 / coord->g11 + SQ(I * Rxy);
-    coord->g_22 = SQ(coord->Bxy * hthe / Bpxy);
-    coord->g_33 = Rxy * Rxy;
-    coord->g_12 = Btxy * hthe * I * Rxy / Bpxy;
-    coord->g_13 = I * Rxy * Rxy;
-    coord->g_23 = Btxy * hthe * Rxy / Bpxy;
-
-    coord->geometry();
+    /**************** SET EVOLVING VARIABLES *************/
 
     // Tell BOUT++ which variables to evolve
     SOLVE_FOR2(rho, Ni);
diff --git a/tests/integrated/test-laplacexy/loadmetric.cxx b/tests/integrated/test-laplacexy/loadmetric.cxx
deleted file mode 100644
index 6d8afad750..0000000000
--- a/tests/integrated/test-laplacexy/loadmetric.cxx
+++ /dev/null
@@ -1,69 +0,0 @@
-#include "bout/field2d.hxx"
-#include "bout/globals.hxx"
-#include "bout/mesh.hxx"
-#include "bout/output.hxx"
-#include "bout/utils.hxx"
-
-#include "loadmetric.hxx"
-
-void LoadMetric(BoutReal Lnorm, BoutReal Bnorm) {
-  // Load metric coefficients from the mesh
-  Field2D Rxy, Bpxy, Btxy, hthe, sinty;
-
-  auto mesh = bout::globals::mesh;
-  auto coords = mesh->getCoordinates();
-
-  GRID_LOAD5(Rxy, Bpxy, Btxy, hthe, sinty); // Load metrics
-
-  // Checking for dpsi and qinty used in BOUT grids
-  Field2D dx;
-  if (!mesh->get(dx, "dpsi")) {
-    output << "\tUsing dpsi as the x grid spacing\n";
-    coords->dx = dx; // Only use dpsi if found
-  } else {
-    // dx will have been read already from the grid
-    output << "\tUsing dx as the x grid spacing\n";
-  }
-  Field2D qinty;
-
-  Rxy /= Lnorm;
-  hthe /= Lnorm;
-  sinty *= SQ(Lnorm) * Bnorm;
-  coords->dx /= SQ(Lnorm) * Bnorm;
-
-  Bpxy /= Bnorm;
-  Btxy /= Bnorm;
-  coords->Bxy /= Bnorm;
-
-  // Calculate metric components
-  std::string ptstr;
-  Options::getRoot()->get("mesh:paralleltransform", ptstr, "identity");
-  // Convert to lower case for comparison
-  ptstr = lowercase(ptstr);
-  if (ptstr == "shifted") {
-    sinty = 0.0; // I disappears from metric
-  }
-
-  BoutReal sbp = 1.0; // Sign of Bp
-  if (min(Bpxy, true) < 0.0) {
-    sbp = -1.0;
-  }
-
-  coords->g11 = pow(Rxy * Bpxy, 2);
-  coords->g22 = 1.0 / pow(hthe, 2);
-  coords->g33 = pow(sinty, 2) * coords->g11 + pow(coords->Bxy, 2) / coords->g11;
-  coords->g12 = 0.0;
-  coords->g13 = -sinty * coords->g11;
-  coords->g23 = -sbp * Btxy / (hthe * Bpxy * Rxy);
-
-  coords->J = hthe / Bpxy;
-
-  coords->g_11 = 1.0 / coords->g11 + pow(sinty * Rxy, 2);
-  coords->g_22 = pow(coords->Bxy * hthe / Bpxy, 2);
-  coords->g_33 = Rxy * Rxy;
-  coords->g_12 = sbp * Btxy * hthe * sinty * Rxy / Bpxy;
-  coords->g_13 = sinty * Rxy * Rxy;
-  coords->g_23 = sbp * Btxy * hthe * Rxy / Bpxy;
-
-  coords->geometry();
-}
diff --git a/tests/integrated/test-laplacexy/loadmetric.hxx b/tests/integrated/test-laplacexy/loadmetric.hxx
deleted file mode 100644
index 25e55fc8e8..0000000000
--- a/tests/integrated/test-laplacexy/loadmetric.hxx
+++ /dev/null
@@ -1,8 +0,0 @@
-#ifndef BOUT_LOADMETRIC_H
-#define BOUT_LOADMETRIC_H
-
-#include <bout/bout_types.hxx>
-
-void LoadMetric(BoutReal Lnorm, BoutReal Bnorm);
-
-#endif // BOUT_LOADMETRIC_H

From 5e29bb6b89f72293f70ff78a90b1052136dddeee Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 24 Apr 2026 10:47:06 +0100
Subject: [PATCH 1146/1827] Apply clang formatting

---
 examples/dalf3/dalf3.cxx                       |  2 +-
 examples/elm-pb-outerloop/elm_pb_outerloop.cxx | 10 +++++-----
 examples/elm-pb/elm_pb.cxx                     | 16 +++++++++-------
 examples/laplacexy/alfven-wave/alfven.cxx      |  4 ++--
 include/bout/coordinates.hxx                   |  6 +++---
 5 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/examples/dalf3/dalf3.cxx b/examples/dalf3/dalf3.cxx
index 7fe551273a..4cf0e811bf 100644
--- a/examples/dalf3/dalf3.cxx
+++ b/examples/dalf3/dalf3.cxx
@@ -1,6 +1,6 @@
 /****************************************************************
  * DALF3 model
- * 
+ *
  * Four-field model for electron pressure, vorticity, A|| and
  * parallel velocity
  *
diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index 6de9797957..22a7eaa295 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -1636,12 +1636,12 @@ class ELMpb : public PhysicsModel {
 #endif
     };
 
-      // Terms which are not yet single index operators
-      // Note: Terms which are included in the single index loop
-      //       may be commented out here, to allow comparison/testing
+    // Terms which are not yet single index operators
+    // Note: Terms which are included in the single index loop
+    //       may be commented out here, to allow comparison/testing
 
-      ////////////////////////////////////////////////////
-      // Parallel electric field
+    ////////////////////////////////////////////////////
+    // Parallel electric field
 
 #if not EVOLVE_JPAR
     // Vector potential
diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx
index a0ac750809..9eb7396987 100644
--- a/examples/elm-pb/elm_pb.cxx
+++ b/examples/elm-pb/elm_pb.cxx
@@ -1317,7 +1317,8 @@ class ELMpb : public PhysicsModel {
           // Only update if simulation time has advanced
           // Uses an exponential decay of the weighting of the value in the boundary
           // so that the solution is well behaved for arbitrary steps
-          BoutReal const weight = exp(-(t - phi_boundary_last_update) / phi_boundary_timescale);
+          const BoutReal weight =
+              exp(-(t - phi_boundary_last_update) / phi_boundary_timescale);
           phi_boundary_last_update = t;
 
           if (mesh->firstX()) {
@@ -1346,11 +1347,11 @@ class ELMpb : public PhysicsModel {
               }
 
               // Old value of phi at boundary. Note: this is constant in Z
-              BoutReal const oldvalue =
+              const BoutReal oldvalue =
                   0.5 * (phi(mesh->xstart - 1, j, 0) + phi(mesh->xstart, j, 0));
 
               // New value of phi at boundary, relaxing towards phivalue
-              BoutReal const newvalue = weight * oldvalue + (1. - weight) * phivalue;
+              const BoutReal newvalue = weight * oldvalue + (1. - weight) * phivalue;
 
               // Set phi at the boundary to this value
               for (int k = mesh->zstart; k <= mesh->zend; k++) {
@@ -1373,7 +1374,7 @@ class ELMpb : public PhysicsModel {
                   0.5 * (phi(mesh->xend + 1, j, 0) + phi(mesh->xend, j, 0));
 
               // New value of phi at boundary, relaxing towards phivalue
-              BoutReal const newvalue = weight * oldvalue + (1. - weight) * phivalue;
+              const BoutReal newvalue = weight * oldvalue + (1. - weight) * phivalue;
 
               // Set phi at the boundary to this value
               for (int k = mesh->zstart; k <= mesh->zend; k++) {
@@ -1586,7 +1587,7 @@ class ELMpb : public PhysicsModel {
         for (int jz = 0; jz < mesh->LocalNz; jz++) {
 
           // Zero-gradient potential
-          BoutReal const phisheath = phi_fa(r.ind, mesh->ystart, jz);
+          const BoutReal phisheath = phi_fa(r.ind, mesh->ystart, jz);
 
           BoutReal jsheath = -(sqrt(mi_me) / (2. * sqrt(PI))) * phisheath;
 
@@ -1607,7 +1608,7 @@ class ELMpb : public PhysicsModel {
         for (int jz = 0; jz < mesh->LocalNz; jz++) {
 
           // Zero-gradient potential
-          BoutReal const phisheath = phi_fa(r.ind, mesh->yend, jz);
+          const BoutReal phisheath = phi_fa(r.ind, mesh->yend, jz);
 
           BoutReal jsheath = (sqrt(mi_me) / (2. * sqrt(PI))) * phisheath;
 
@@ -2029,7 +2030,8 @@ class ELMpb : public PhysicsModel {
     ddt(P).applyBoundary("neumann");
 
     Field3D U1 = ddt(U);
-    U1 += (gamma * B0 * B0) * Grad_par(Jrhs, CELL_CENTRE) + (gamma * b0xcv) * Grad(ddt(P));
+    U1 +=
+        (gamma * B0 * B0) * Grad_par(Jrhs, CELL_CENTRE) + (gamma * b0xcv) * Grad(ddt(P));
 
     // Second matrix, solving Alfven wave dynamics
     static std::unique_ptr<InvertPar> invU{nullptr};
diff --git a/examples/laplacexy/alfven-wave/alfven.cxx b/examples/laplacexy/alfven-wave/alfven.cxx
index aa62751db4..cf66af7295 100644
--- a/examples/laplacexy/alfven-wave/alfven.cxx
+++ b/examples/laplacexy/alfven-wave/alfven.cxx
@@ -32,8 +32,8 @@ class Alfven : public PhysicsModel {
   BoutReal mu_epar; // Electron parallel viscosity
   BoutReal resistivity;
 
-  bool laplace_perp;    // Use Laplace_perp or Delp2?
-  bool split_n0;        // Split solve into n=0 and n~=0?
+  bool laplace_perp;                             // Use Laplace_perp or Delp2?
+  bool split_n0;                                 // Split solve into n=0 and n~=0?
   std::unique_ptr<LaplaceXY> laplacexy{nullptr}; // Laplacian solver in X-Y (n=0)
 
   bool newXZsolver;
diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index f8d421a483..2d48107412 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -3,16 +3,16 @@
  *
  * ChangeLog
  * =========
- * 
+ *
  * 2014-11-10 Ben Dudson <bd512@york.ac.uk>
  *    * Created by separating metric from Mesh
  *
- * 
+ *
  **************************************************************************
  * Copyright 2014-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify

From 8eb12700011b06dc412ba530ebe894cd35fd040c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 24 Apr 2026 14:14:27 +0200
Subject: [PATCH 1147/1827] Starty work on BoundaryRegionIterFCI

---
 include/bout/boundary_region_iter.hxx | 54 +++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 241b56abdd..a8135bcf9f 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -8,6 +8,7 @@
 #include <bout/bout_enum_class.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
+#include <bout/parallel_boundary_region.hxx>
 #include <bout/region.hxx>
 #include <bout/sys/parallel_stencils.hxx>
 
@@ -389,5 +390,58 @@ inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, BoundaryFreeExtrapolati
 }
 } // namespace
 
+class BoundaryRegionFCI {
+public:
+  BoundaryRegionFCI(int dir, Mesh* mesh) : _dir(dir), localmesh(mesh) {};
+  /// Add a point to the boundary
+  void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
+                 char valid, signed char offset) {
+    if (!bndry_points->empty() && bndry_points->back().index > ind) {
+      is_sorted = false;
+    }
+    bndry_points->emplace_back(ind, bout::parallel_boundary_region::RealPoint{x, y, z},
+                               length, valid, offset,
+                               static_cast<unsigned char>(std::abs(offset)));
+  }
+  void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
+                 BoutReal length, char valid, signed char offset) {
+    add_point(xyz2ind(ix, iy, iz), x, y, z, length, valid, offset);
+  }
+
+private:
+  int _dir;
+  // Vector of points in the boundary
+  std::shared_ptr<bout::parallel_boundary_region::IndicesVec> bndry_points;
+  Ind3D xyz2ind(int x, int y, int z) const {
+    const int ny = localmesh->LocalNy;
+    const int nz = localmesh->LocalNz;
+    return Ind3D{(x * ny + y) * nz + z, ny, nz};
+  }
+  bool is_sorted{true};
+  Mesh* localmesh;
+};
+
+class BoundaryRegionIterFCI : public BoundaryRegionIterBase<BoundaryRegionIterFCI> {
+private:
+  std::shared_ptr<bout::parallel_boundary_region::IndicesVec> bndry_pnts;
+  size_t pos{0};
+  int _dir;
+
+public:
+  template <bool check = true>
+  BoutReal& _getAt(Field3D& f, int off) const {
+    ASSERT3(f.hasParallelSlices());
+    if constexpr (check) {
+      ASSERT3(_valid() > -off - 2);
+    }
+    auto _off = _offset() + off * _dir;
+    return f.ynext(_off)[ind().yp(_off)];
+  }
+  signed char _offset() const { return (*bndry_pnts)[pos].offset; }
+  signed char _valid() const { return (*bndry_pnts)[pos].valid; }
+
+  Ind3D& _ind() const { return (*bndry_pnts)[pos].index; }
+};
+
 } // namespace boundary
 } // namespace bout

From 87980614bbcc9a5e153dd89ef4dd7a1b9f2e37e9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 24 Apr 2026 19:32:52 +0000
Subject: [PATCH 1148/1827] Update zoidberg requirement from >=0.2.2 to >=0.3.0

Updates the requirements on [zoidberg](https://github.com/boutproject/zoidberg) to permit the latest version.
- [Release notes](https://github.com/boutproject/zoidberg/releases)
- [Commits](https://github.com/boutproject/zoidberg/compare/v0.2.2...v0.3.0)

---
updated-dependencies:
- dependency-name: zoidberg
  dependency-version: 0.3.0
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 078eecac6d..9b06edfd8a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,4 +5,4 @@ netcdf4>=1.7.1
 matplotlib>=3.7.0
 Cython>=3.0.0
 boutdata>=0.3.0
-zoidberg>=0.2.2
+zoidberg>=0.3.0

From 2aebc135615af52aacc60d28dbad6af9017c06bc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 27 Apr 2026 10:19:41 +0200
Subject: [PATCH 1149/1827] Complete BoundaryRegionIterFCI

Make it a freind class of BoundaryRegionIter. The iterator needs somehow
all the data of the underlying class.
---
 include/bout/boundary_region_iter.hxx | 64 +++++++++++++++++++++------
 1 file changed, 51 insertions(+), 13 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index a8135bcf9f..7fba444d20 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -396,12 +396,12 @@ public:
   /// Add a point to the boundary
   void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
                  char valid, signed char offset) {
-    if (!bndry_points->empty() && bndry_points->back().index > ind) {
+    if (!bndry_points.empty() && bndry_points.back().index > ind) {
       is_sorted = false;
     }
-    bndry_points->emplace_back(ind, bout::parallel_boundary_region::RealPoint{x, y, z},
-                               length, valid, offset,
-                               static_cast<unsigned char>(std::abs(offset)));
+    bndry_points.emplace_back(ind, bout::parallel_boundary_region::RealPoint{x, y, z},
+                              length, valid, offset,
+                              static_cast<unsigned char>(std::abs(offset)));
   }
   void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
                  BoutReal length, char valid, signed char offset) {
@@ -409,9 +409,10 @@ public:
   }
 
 private:
+  friend class BoundaryRegionIterFCI;
   int _dir;
   // Vector of points in the boundary
-  std::shared_ptr<bout::parallel_boundary_region::IndicesVec> bndry_points;
+  bout::parallel_boundary_region::IndicesVec bndry_points;
   Ind3D xyz2ind(int x, int y, int z) const {
     const int ny = localmesh->LocalNy;
     const int nz = localmesh->LocalNz;
@@ -423,9 +424,8 @@ private:
 
 class BoundaryRegionIterFCI : public BoundaryRegionIterBase<BoundaryRegionIterFCI> {
 private:
-  std::shared_ptr<bout::parallel_boundary_region::IndicesVec> bndry_pnts;
+  BoundaryRegionFCI* region;
   size_t pos{0};
-  int _dir;
 
 public:
   template <bool check = true>
@@ -434,14 +434,52 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() + off * _dir;
+    auto _off = _offset() + off * region->_dir;
     return f.ynext(_off)[ind().yp(_off)];
   }
-  signed char _offset() const { return (*bndry_pnts)[pos].offset; }
-  signed char _valid() const { return (*bndry_pnts)[pos].valid; }
-
-  Ind3D& _ind() const { return (*bndry_pnts)[pos].index; }
+  template <bool check = true>
+  const BoutReal& _getAt(const Field3D& f, int off) const {
+    ASSERT3(f.hasParallelSlices());
+    if constexpr (check) {
+      ASSERT3(_valid() > -off - 2);
+    }
+    auto _off = _offset() + off * region->_dir;
+    return f.ynext(_off)[ind().yp(_off)];
+  }
+  template <bool check = true>
+  BoutReal& _getAt(Field2D& f, int off) const {
+    ASSERT3(f.hasParallelSlices());
+    if constexpr (check) {
+      ASSERT3(_valid() > -off - 2);
+    }
+    auto _off = _offset() + off * region->_dir;
+    return f.ynext(_off)[ind().yp(_off)];
+  }
+  template <bool check = true>
+  const BoutReal& _getAt(const Field2D& f, int off) const {
+    ASSERT3(f.hasParallelSlices());
+    if constexpr (check) {
+      ASSERT3(_valid() > -off - 2);
+    }
+    auto _off = _offset() + off * region->_dir;
+    return f.ynext(_off)[ind().yp(_off)];
+  }
+  template <bool check = true>
+  BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
+                 int off) const {
+    if constexpr (check) {
+      ASSERT3(valid() > -off - 2);
+    }
+    auto _off = _offset() + off * region->_dir;
+    return f(_off, ind().yp(_off));
+  }
+  signed char _offset() const { return region->bndry_points[pos].offset; }
+  signed char _valid() const { return region->bndry_points[pos].valid; }
+  Ind3D& _ind() const { return region->bndry_points[pos].index; }
+  signed char _boundary_width() const {
+    return region->localmesh->ystart - region->bndry_points[pos].abs_offset;
+  }
+  const BoutReal& _length() const { return region->bndry_points[pos].length; }
 };
-
 } // namespace boundary
 } // namespace bout

From a60fdc064a4573e6952c370e963f96ed83f4c347 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 25 Apr 2026 15:11:29 +0100
Subject: [PATCH 1150/1827] Add pytest and pytest-xdist to pyproject.toml

`pytest` dependency-group.
---
 pyproject.toml   | 4 ++++
 requirements.txt | 2 --
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f4cea9d822..8a13964a09 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,6 +22,10 @@ dev = [
      "sphinx-lint~=1.0",
      "sync-with-uv~=0.5.0",
 ]
+pytest = [
+     "pytest~=8.4",
+     "pytest-xdist~=3.8",
+]
 maint = [
       "pygithub~=2.8",
       "ruamel-yaml~=0.19",
diff --git a/requirements.txt b/requirements.txt
index ea0085eeb4..078eecac6d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,5 +6,3 @@ matplotlib>=3.7.0
 Cython>=3.0.0
 boutdata>=0.3.0
 zoidberg>=0.2.2
-pytest
-pytest-xdist

From c2ef6195ec2fc49c6bccf2802e8e9c323e51ee07 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 25 Apr 2026 15:43:00 +0100
Subject: [PATCH 1151/1827] Use uv sync instead of pip install, in github
 `tests` workflow

Install `pytest` and `dev` dependency groups.
---
 .github/workflows/tests.yml                   | 15 +++++++++++----
 manual/sphinx/developer_docs/contributing.rst |  2 +-
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 02f018b873..e8e4e0044e 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -157,15 +157,22 @@ jobs:
         with:
           submodules: true
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
       - uses: actions/setup-python@v6
         with:
           python-version: '3.x'
-          cache: 'pip'
 
-      - name: Install pip packages
+      - name: Setup virtual environment with uv
         run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install -r requirements.txt
+          # uv sync automatically creates a .venv and installs the groups
+          uv sync --group pytest --inexact
+          
+          # "Activate" the venv for all subsequent steps in this GitHub Actions job
+          echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
 
       - name: Cache Zenodo test data
         uses: actions/cache@v5
diff --git a/manual/sphinx/developer_docs/contributing.rst b/manual/sphinx/developer_docs/contributing.rst
index 062415af04..b176bb5678 100644
--- a/manual/sphinx/developer_docs/contributing.rst
+++ b/manual/sphinx/developer_docs/contributing.rst
@@ -206,7 +206,7 @@ install the majority of our developer tools at once using `uv
 
 .. code-block:: console
 
-    uv sync --only-dev --inexact
+    uv sync --only-dev --group pytest --inexact
 
 This will install all the developer tools into a virtual environment (creating
 one if necessary, typically under ``.venv``). You can then activate the virtual

From 5af0f1981f3bd8c0d044304335706397305705a0 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 25 Apr 2026 16:22:26 +0100
Subject: [PATCH 1152/1827] Add no-install-project option to uv command

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index e8e4e0044e..6b596c3072 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -169,7 +169,7 @@ jobs:
       - name: Setup virtual environment with uv
         run: |
           # uv sync automatically creates a .venv and installs the groups
-          uv sync --group pytest --inexact
+          uv sync --no-install-project --group pytest --inexact
           
           # "Activate" the venv for all subsequent steps in this GitHub Actions job
           echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH

From b5509a9e9af97aecdd6842357d820aca3405fbc0 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sat, 25 Apr 2026 16:24:25 +0100
Subject: [PATCH 1153/1827] Add no-dev option to uv command in github workflow

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 6b596c3072..154f746bb4 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -169,7 +169,7 @@ jobs:
       - name: Setup virtual environment with uv
         run: |
           # uv sync automatically creates a .venv and installs the groups
-          uv sync --no-install-project --group pytest --inexact
+          uv sync --no-dev --group pytest --inexact
           
           # "Activate" the venv for all subsequent steps in this GitHub Actions job
           echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH

From 7b3308208e470e72da08323bb72f51452ff18eb5 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sun, 26 Apr 2026 13:31:40 +0100
Subject: [PATCH 1154/1827] Install python, pip, pytest, numpy, and scipy
 through uv

 rather than apt.
---
 .github/workflows/tests.yml | 34 +++++++++++++++-------------------
 pyproject.toml              |  2 ++
 2 files changed, 17 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 154f746bb4..731432d013 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -133,25 +133,21 @@ jobs:
           echo CMake options: ${{ matrix.config.cmake_options }}
 
       - name: Install dependencies
-        run: sudo apt update &&
-             sudo apt install -y
-                 libfftw3-dev
-                 libnetcdf-dev
-                 libnetcdf-c++4-dev
-                 netcdf-bin
-                 python3
-                 python3-pip
-                 python3-pytest
-                 python3-numpy
-                 python3-scipy
-                 lcov
-                 openmpi-bin
-                 libopenmpi-dev
-                 petsc-dev
-                 slepc-dev
-                 liblapack-dev
-                 libparpack2-dev
-                 libhypre-dev
+        run: |
+          sudo apt update
+          sudo apt install -y \
+              libfftw3-dev \
+              libnetcdf-dev \
+              libnetcdf-c++4-dev \
+              netcdf-bin \
+              lcov \
+              openmpi-bin \
+              libopenmpi-dev \
+              petsc-dev \
+              slepc-dev \
+              liblapack-dev \
+              libparpack2-dev \
+              libhypre-dev
 
       - uses: actions/checkout@v6
         with:
diff --git a/pyproject.toml b/pyproject.toml
index 8a13964a09..4a43703126 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,6 +25,8 @@ dev = [
 pytest = [
      "pytest~=8.4",
      "pytest-xdist~=3.8",
+     "numpy",
+     "scipy",
 ]
 maint = [
       "pygithub~=2.8",

From 7c4b0a90527e2e65d635286b8ec35aa4e81666bc Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sun, 26 Apr 2026 13:45:32 +0100
Subject: [PATCH 1155/1827] Set VIRTUAL_ENV to force CMake to recognize the
 virtual environment

---
 .github/workflows/tests.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 731432d013..7c302a248d 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -167,8 +167,11 @@ jobs:
           # uv sync automatically creates a .venv and installs the groups
           uv sync --no-dev --group pytest --inexact
           
-          # "Activate" the venv for all subsequent steps in this GitHub Actions job
+          # Put the venv in the PATH
           echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
+          
+          # Force CMake to recognize the virtual environment
+          echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> $GITHUB_ENV
 
       - name: Cache Zenodo test data
         uses: actions/cache@v5

From b34d4fb349f405d8a64a7ff63f6eeee98c284867 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sun, 26 Apr 2026 13:57:27 +0100
Subject: [PATCH 1156/1827] Pass DPython3_EXECUTABLE to cmake script, to force
 it to use the venv

---
 .github/workflows/tests.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 7c302a248d..8f9f5147e3 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -196,7 +196,9 @@ jobs:
         run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh 
 
       - name: Build BOUT++
-        run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
+        run: |
+          UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }} \
+              -DPython3_EXECUTABLE=$GITHUB_WORKSPACE/.venv/bin/python
 
   Fedora:
     # This is its own job as it doesn't use most of the steps of the

From 8389802f25db9623c3127afab62cf940f14f6496 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Sun, 26 Apr 2026 20:23:33 +0100
Subject: [PATCH 1157/1827] Install the core requirements

via pip, into the same venv.
---
 .github/workflows/tests.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 8f9f5147e3..cbc32d7c91 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -167,6 +167,9 @@ jobs:
           # uv sync automatically creates a .venv and installs the groups
           uv sync --no-dev --group pytest --inexact
           
+          # Install the core requirements into the same venv
+          uv pip install -r requirements.txt
+          
           # Put the venv in the PATH
           echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
           

From 967bb077adc12cefa1c7074a6f39c9973b20788f Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 27 Apr 2026 10:04:10 +0100
Subject: [PATCH 1158/1827] Remove numpy and scipy from pytest dependency-group
 in pyproject.toml

They are installed by pip and listed in requirements.txt.
---
 pyproject.toml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4a43703126..8a13964a09 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,8 +25,6 @@ dev = [
 pytest = [
      "pytest~=8.4",
      "pytest-xdist~=3.8",
-     "numpy",
-     "scipy",
 ]
 maint = [
       "pygithub~=2.8",

From e05bd5183a43950ac3391949c1904873c3e1f166 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 24 Apr 2026 15:22:32 +0100
Subject: [PATCH 1159/1827] Reinstate timeout for tests

using CMAKE_CTEST_ARGUMENTS.
---
 CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3a3ba35c05..0cb88fdfa7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -739,6 +739,7 @@ option(
   OFF
 )
 if(BOUT_TESTS)
+  set(CMAKE_CTEST_ARGUMENTS "--output-on-failure" "--timeout" "300")
   enable_testing()
   # Targets for just building the tests
   # Tests need to add themselves as dependencies to these targets

From 30b52235496570dc4697902420f8fc55bceef3c3 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 27 Apr 2026 10:16:30 +0100
Subject: [PATCH 1160/1827] Simplify `Path.exists()` expressions

---
 .../test-command-args/test_command_args.py       | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/integrated/test-command-args/test_command_args.py b/tests/integrated/test-command-args/test_command_args.py
index 3759d3cb65..ff58195276 100755
--- a/tests/integrated/test-command-args/test_command_args.py
+++ b/tests/integrated/test-command-args/test_command_args.py
@@ -52,11 +52,11 @@ def testNoArgumentsDefaultDirectory(self):
         self.makeDirAndCopyInput("data")
         launch_safe(self.command, pipe=True, nproc=1, mthread=1)
         self.assertTrue(
-            Path.exists(Path("data/BOUT.settings")),
+            Path("data/BOUT.settings").exists(),
             msg="FAIL: No BOUT.settings file in data directory",
         )
         self.assertTrue(
-            Path.exists(Path("data/BOUT.log.0")),
+            Path("data/BOUT.log.0").exists(),
             msg="FAIL: No BOUT.log.0 file in data directory",
         )
 
@@ -64,11 +64,11 @@ def testShortLogArgument(self):
         self.makeDirAndCopyInput("data")
         launch_safe(self.command + " -l different.log", pipe=True, nproc=1, mthread=1)
         self.assertFalse(
-            Path.exists(Path("data/BOUT.log.0")),
+            Path("data/BOUT.log.0").exists(),
             msg="FAIL: BOUT.log.0 file in data directory",
         )
         self.assertTrue(
-            Path.exists(Path("data/different.log.0")),
+            Path("data/different.log.0").exists(),
             msg="FAIL: no different.log.0 file in data directory",
         )
 
@@ -76,22 +76,22 @@ def testLongLogArgument(self):
         self.makeDirAndCopyInput("data")
         launch_safe(self.command + " --log log", pipe=True, nproc=1, mthread=1)
         self.assertFalse(
-            Path.exists(Path("data/BOUT.log.0")),
+            Path("data/BOUT.log.0").exists(),
             msg="FAIL: BOUT.log.0 file in data directory",
         )
         self.assertTrue(
-            Path.exists(Path("data/log.0")), msg="FAIL: no log.0 file in data directory"
+            Path("data/log.0").exists(), msg="FAIL: no log.0 file in data directory"
         )
 
     def testDirectoryArgument(self):
         self.makeDirAndCopyInput("test")
         launch_safe(self.command + " -d test", pipe=True, nproc=1, mthread=1)
         self.assertTrue(
-            Path.exists(Path("test/BOUT.settings")),
+            Path("test/BOUT.settings").exists(),
             msg="FAIL: No BOUT.settings file in test directory",
         )
         self.assertTrue(
-            Path.exists(Path("test/BOUT.log.0")),
+            Path("test/BOUT.log.0").exists(),
             msg="FAIL: No BOUT.log.0 file in data directory",
         )
 

From 46536c6dffc23e89f3a31518da96ecdd1431a781 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 27 Apr 2026 12:24:46 +0200
Subject: [PATCH 1161/1827] Fixup bad merge

---
 include/bout/coordinates.hxx | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 41929e72ee..b5782fd276 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -358,19 +358,4 @@ private:
   void checkContravariant();
 };
 
-<<<<<<< cell_area_volume
-/*
-/// Standard coordinate system for tokamak simulations
-class TokamakCoordinates : public Coordinates {
-public:
-  TokamakCoordinates(Mesh *mesh) : Coordinates(mesh) {
-
-  }
-private:
-
-};
-*/
-
-=======
->>>>>>> next
 #endif // BOUT_COORDINATES_H

From becb76cb1e6f40374a926eacfa67b02460b1cfb1 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 28 Apr 2026 11:55:30 +0100
Subject: [PATCH 1162/1827] Remove previously deleted test

---
 .../test-options-adios/test_options_adios.py  | 72 -------------------
 1 file changed, 72 deletions(-)
 delete mode 100755 tests/integrated/test-options-adios/test_options_adios.py

diff --git a/tests/integrated/test-options-adios/test_options_adios.py b/tests/integrated/test-options-adios/test_options_adios.py
deleted file mode 100755
index f3284d65fd..0000000000
--- a/tests/integrated/test-options-adios/test_options_adios.py
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/env python3
-
-# Note: This test requires NCDF4, whereas on Travis NCDF is used
-# requires: netcdf
-# requires: adios
-# requires: not legacy_netcdf
-
-from boututils.datafile import DataFile
-from boututils.run_wrapper import shell, launch
-from boutdata.data import BoutOptionsFile
-
-import math
-
-shell(["rm -f test-out.ini"])
-shell(["rm -f test-out.nc"])
-
-# Create a NetCDF input file
-with DataFile("test.nc", create=True, format="NETCDF4") as f:
-    f.write("int", 42)
-    f.write("real", 3.1415)
-    f.write("string", "hello")
-
-# run BOUT++
-launch("./test-options-adios", nproc=1, mthread=1)
-
-# Check the output INI file
-result = BoutOptionsFile("test-out.ini")
-
-print(result)
-
-assert result["int"] == 42
-assert math.isclose(result["real"], 3.1415)
-assert result["string"] == "hello"
-
-print("Checking saved ADIOS2 test-out file -- Not implemented")
-
-# Check the output NetCDF file
-# with DataFile("test-out.nc") as f:
-#    assert f["int"] == 42
-#    assert math.isclose(f["real"], 3.1415)
-#    assert result["string"] == "hello"
-
-print("Checking saved settings.ini")
-
-# Check the settings.ini file, coming from BOUT.inp
-# which is converted to NetCDF, read in, then written again
-settings = BoutOptionsFile("settings.ini")
-
-assert settings["mesh"]["nx"] == 5
-assert settings["mesh"]["ny"] == 2
-
-print("Checking saved fields.bp -- Not implemented")
-
-# with DataFile("fields.nc") as f:
-#    assert f["f2d"].shape == (5, 6)  # Field2D
-#    assert f["f3d"].shape == (5, 6, 2)  # Field3D
-#    assert f["fperp"].shape == (5, 2)  # FieldPerp
-#    assert np.allclose(f["f2d"], 1.0)
-#    assert np.allclose(f["f3d"], 2.0)
-#    assert np.allclose(f["fperp"], 3.0)
-
-print("Checking saved fields2.bp -- Not implemented")
-
-# with DataFile("fields2.nc") as f:
-#    assert f["f2d"].shape == (5, 6)  # Field2D
-#    assert f["f3d"].shape == (5, 6, 2)  # Field3D
-#    assert f["fperp"].shape == (5, 2)  # FieldPerp
-#    assert np.allclose(f["f2d"], 1.0)
-#    assert np.allclose(f["f3d"], 2.0)
-#    assert np.allclose(f["fperp"], 3.0)
-
-print(" => Passed")

From a1c67ffb079d777e790bd2a1338d056cfeeff1f5 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 24 Apr 2026 15:16:26 +0100
Subject: [PATCH 1163/1827] Prefer numpy.testing.assert_allclose

---
 .../test-boutpp/slicing/test_slicing.py       | 19 ++++++++-----------
 tests/integrated/test-collect/test_collect.py |  4 ++--
 .../test_communications.py                    | 10 ++++++----
 .../test-fci-boundary/test_fci_boundary.py    | 13 +++++++------
 .../integrated/test-griddata/test_griddata.py |  4 ++--
 .../test_options_netcdf.py                    | 14 +++++++-------
 .../test-slepc-solver/test_slepc_solver.py    |  6 ++++--
 7 files changed, 36 insertions(+), 34 deletions(-)

diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py
index c485907414..41c332968f 100755
--- a/tests/integrated/test-boutpp/slicing/test_slicing.py
+++ b/tests/integrated/test-boutpp/slicing/test_slicing.py
@@ -2,6 +2,7 @@
 # requires boutpp
 # requires not make
 import numpy as np
+import numpy.testing as npt
 import boutpp as bc
 import inspect
 
@@ -14,7 +15,7 @@ def test_slicing():
     ndat = np.random.random(field.shape)
     field[:] = ndat
 
-    assert np.all(ndat == field[:])
+    npt.assert_allclose(ndat, field[:])
 
     examples = [
         lambda x: x[2],
@@ -43,13 +44,9 @@ def test_slicing():
     print(field.shape)
     for ex in examples:
         print("testing", inspect.getsource(ex))
-        try:
-            nout = ex(ndat)
-            fout = ex(field)
-            assert (
-                fout.shape == nout.shape
-            ), f"Field3D returned {{ fout.shape }} but numpy {{ nout.shape }}"
-            assert np.all(fout == nout), f"data mismatch, {{ fout == nout }}"
-        except:
-            print("Failed to test", inspect.getsource(ex))
-            raise
+        nout = ex(ndat)
+        fout = ex(field)
+        npt.assert_allclose(
+            fout, nout,
+            err_msg=f"data mismatch, {{ fout == nout }}. Failed to test {inspect.getsource(ex)}"
+        )
diff --git a/tests/integrated/test-collect/test_collect.py b/tests/integrated/test-collect/test_collect.py
index 3198e8a6dd..c3dea7298f 100755
--- a/tests/integrated/test-collect/test_collect.py
+++ b/tests/integrated/test-collect/test_collect.py
@@ -5,7 +5,7 @@
 from boututils.run_wrapper import shell, shell_safe
 
 from boutdata import collect
-import numpy as np
+import numpy.testing as npt
 
 
 def test_collect():
@@ -17,4 +17,4 @@ def test_collect():
     # This should be corrected automatically
     a = collect("A", path="data")
 
-    assert np.allclose(a, 1.23), f"Wrong value => Failed: {a}"
+    npt.assert_allclose(a, 1.23, err_msg=f"Wrong value => Failed: {a}")
diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index 2db3fbab97..aef616483f 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 import os
 import numpy as np
+import numpy.testing as npt
 from boututils.datafile import DataFile
 from boututils.run_wrapper import shell, launch_safe
 
@@ -12,10 +13,11 @@
 
 
 def run_test(actual, expected, procnum, region, boundary):
-    assert np.all(np.array(np.rint(actual).astype(int)) == np.array(expected)), (
-        "failed in {} boundary of region {} ({}). Expected: {}  Actual: {}".format(
-            boundary, procnum, region, expected, actual
-            ))
+    npt.assert_allclose(
+        np.array(np.rint(actual).astype(int)), np.array(expected),
+        err_msg=f"failed in {boundary} boundary of region {procnum} ({region}). "
+                f"Expected: {expected}  Actual: {actual}"
+    )
 
 
 def test_communications():
diff --git a/tests/integrated/test-fci-boundary/test_fci_boundary.py b/tests/integrated/test-fci-boundary/test_fci_boundary.py
index e01b66b8d3..9cce659a15 100755
--- a/tests/integrated/test-fci-boundary/test_fci_boundary.py
+++ b/tests/integrated/test-fci-boundary/test_fci_boundary.py
@@ -6,6 +6,7 @@
 import os
 import pytest
 import numpy as np
+import numpy.testing as npt
 from boututils.run_wrapper import launch_safe
 from boututils.datafile import DataFile
 from boutdata.collect import collect
@@ -64,9 +65,9 @@ def test_fci_boundary():
                 xguards=False,
                 yguards=False,
             )
-            assert np.allclose(data, v), (
-                f"{k} does not match",
-                np.sum(data),
-                np.sum(v),
-                np.max(data),
-            )
+            npt.assert_allclose(data, v,
+                                err_msg=(f"{k} does not match",
+                                         np.sum(data),
+                                         np.sum(v),
+                                         np.max(data))
+                                )
diff --git a/tests/integrated/test-griddata/test_griddata.py b/tests/integrated/test-griddata/test_griddata.py
index 5b04bea7ee..8eb3aa22f9 100755
--- a/tests/integrated/test-griddata/test_griddata.py
+++ b/tests/integrated/test-griddata/test_griddata.py
@@ -10,7 +10,7 @@
 
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
-import numpy as np
+import numpy.testing as npt
 from sys import stdout
 
 
@@ -39,6 +39,6 @@ def test_griddata():
         dr = float(rwidth) / nx
 
         # Test value of dx
-        assert np.allclose(dx, dr * Bpxy * Rxy, atol=1e-7), "Failed: dx does not match"
+        npt.assert_allclose(dx, dr * Bpxy * Rxy, atol=1e-7, err_msg="Failed: dx does not match")
 
         print("Passed")
diff --git a/tests/integrated/test-options-netcdf/test_options_netcdf.py b/tests/integrated/test-options-netcdf/test_options_netcdf.py
index 3835cf0c9f..cde7472052 100755
--- a/tests/integrated/test-options-netcdf/test_options_netcdf.py
+++ b/tests/integrated/test-options-netcdf/test_options_netcdf.py
@@ -9,7 +9,7 @@
 from boutdata.data import BoutOptionsFile
 
 import math
-import numpy as np
+import numpy.testing as npt
 
 def test_options_netcdf():
 
@@ -57,9 +57,9 @@ def test_options_netcdf():
         assert f["f2d"].shape == (5, 6)  # Field2D
         assert f["f3d"].shape == (5, 6, 2)  # Field3D
         assert f["fperp"].shape == (5, 2)  # FieldPerp
-        assert np.allclose(f["f2d"], 1.0)
-        assert np.allclose(f["f3d"], 2.0)
-        assert np.allclose(f["fperp"], 3.0)
+        npt.assert_allclose(f["f2d"], 1.0)
+        npt.assert_allclose(f["f3d"], 2.0)
+        npt.assert_allclose(f["fperp"], 3.0)
 
     print("Checking saved fields2.nc")
 
@@ -67,8 +67,8 @@ def test_options_netcdf():
         assert f["f2d"].shape == (5, 6)  # Field2D
         assert f["f3d"].shape == (5, 6, 2)  # Field3D
         assert f["fperp"].shape == (5, 2)  # FieldPerp
-        assert np.allclose(f["f2d"], 1.0)
-        assert np.allclose(f["f3d"], 2.0)
-        assert np.allclose(f["fperp"], 3.0)
+        npt.assert_allclose(f["f2d"], 1.0)
+        npt.assert_allclose(f["f3d"], 2.0)
+        npt.assert_allclose(f["fperp"], 3.0)
 
     print(" => Passed")
diff --git a/tests/integrated/test-slepc-solver/test_slepc_solver.py b/tests/integrated/test-slepc-solver/test_slepc_solver.py
index 6d359f6f9e..851a8af2e5 100755
--- a/tests/integrated/test-slepc-solver/test_slepc_solver.py
+++ b/tests/integrated/test-slepc-solver/test_slepc_solver.py
@@ -4,7 +4,8 @@
 
 from boutdata.collect import collect
 from boututils.run_wrapper import launch_safe
-from numpy import isclose
+import numpy.testing as npt
+
 
 
 def test_slepc_solver():
@@ -19,4 +20,5 @@ def test_slepc_solver():
 
     expected_eigenvalues = [0.0, 1.0]
 
-    assert isclose(expected_eigenvalues, eigenvalues).all(), " => SLEPc test failed\nEigenvalues: {eigenvalues}"
+    npt.assert_allclose(expected_eigenvalues, eigenvalues,
+                        err_msg=" => SLEPc test failed\nEigenvalues: {eigenvalues}")

From 08fd6a7e4af5e4f3ebf51ca70f4927f8b6ceeb0e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 28 Apr 2026 14:30:16 +0200
Subject: [PATCH 1164/1827] Do not cast const away

---
 include/bout/boundary_region_iter.hxx | 54 +++++++++++++++------------
 1 file changed, 31 insertions(+), 23 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 7fba444d20..0d3c753cff 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -41,17 +41,17 @@ enum class BoundaryFreeExtrapolation : std::int8_t { limited, exponential, linea
 template <typename impl>
 class BoundaryRegionIterBase { /// get the index at the last point in domain
 public:
-  Ind3D ind() const { return static_cast<impl*>(this)->_ind(); }
+  Ind3D ind() const { return static_cast<const impl*>(this)->_ind(); }
   /// get the length from the point in the domain to the boundary in index
   /// space. It is in the range [0, 1]
-  BoutReal length() const { return static_cast<impl*>(this)->_length(); }
+  BoutReal length() const { return static_cast<const impl*>(this)->_length(); }
   /// Lower bound of how many points are between the first point in the domain
   /// and the boundary in the other direction.
-  signed char valid() const { return static_cast<impl*>(this)->_valid(); }
+  signed char valid() const { return static_cast<const impl*>(this)->_valid(); }
   /// Get the width of the boundary at the current point
-  int boundary_width() const { return static_cast<impl*>(this)->_boundary_width(); }
+  int boundary_width() const { return static_cast<const impl*>(this)->_boundary_width(); }
   /// Is this the lower boundary?
-  bool is_lower() const { return static_cast<impl*>(this)->_is_lower(); }
+  bool is_lower() const { return static_cast<const impl*>(this)->_is_lower(); }
 
   /*
    *         FIELD3D ACCESSORS
@@ -64,29 +64,33 @@ public:
   /// off = 2 is the second to last point in the domain
   template <bool check = true>
   BoutReal& getAt(Field3D& f, int off) const {
-    return static_cast<impl*>(this)->template _getAt<check>(f, off);
+    return static_cast<const impl*>(this)->template _getAt<check>(f, off);
   }
   /// get the value at a given offset `off` of a field `f`.
   template <bool check = true>
   BoutReal& getAt(const Field3D& f, int off) const {
-    return static_cast<impl*>(this)->template _getAt<check>(f, off);
+    return static_cast<const impl*>(this)->template _getAt<check>(f, off);
   }
 
   /// Get the first point in the boundary
   const BoutReal& next(const Field3D& f) const {
-    return static_cast<impl*>(this)->_getAt(f, 0);
+    return static_cast<const impl*>(this)->_getAt(f, 0);
   }
   /// Get the first point in the boundary
-  BoutReal& next(Field3D& f) const { return static_cast<impl*>(this)->_getAt(f, 0); }
+  BoutReal& next(Field3D& f) const {
+    return static_cast<const impl*>(this)->_getAt(f, 0);
+  }
   /// Get the last point in the domain
   const BoutReal& current(const Field3D& f) const {
-    return static_cast<impl*>(this)->_getAt(f, 1);
+    return static_cast<const impl*>(this)->_getAt(f, 1);
   }
   /// Get the last point in the domain
-  BoutReal& current(Field3D& f) const { return static_cast<impl*>(this)->_getAt(f, 1); }
+  BoutReal& current(Field3D& f) const {
+    return static_cast<const impl*>(this)->_getAt(f, 1);
+  }
   /// Get the second to last point in the domain - this may not be valid and thus throw
   const BoutReal& prev(const Field3D& f) const {
-    return static_cast<impl*>(this)->_getAt(f, 2);
+    return static_cast<const impl*>(this)->_getAt(f, 2);
   }
   /*
    *         FIELD2D ACCESSORS
@@ -99,29 +103,33 @@ public:
   /// off = 2 is the second to last point in the domain
   template <bool check = true>
   BoutReal& getAt(Field2D& f, int off) const {
-    return static_cast<impl*>(this)->template _getAt<check>(f, off);
+    return static_cast<const impl*>(this)->template _getAt<check>(f, off);
   }
   /// get the value at a given offset `off` of a field `f`.
   template <bool check = true>
   BoutReal& getAt(const Field2D& f, int off) const {
-    return static_cast<impl*>(this)->template _getAt<check>(f, off);
+    return static_cast<const impl*>(this)->template _getAt<check>(f, off);
   }
 
   /// Get the first point in the boundary
   const BoutReal& next(const Field2D& f) const {
-    return static_cast<impl*>(this)->_getAt(f, 0);
+    return static_cast<const impl*>(this)->_getAt(f, 0);
   }
   /// Get the first point in the boundary
-  BoutReal& next(Field2D& f) const { return static_cast<impl*>(this)->_getAt(f, 0); }
+  BoutReal& next(Field2D& f) const {
+    return static_cast<const impl*>(this)->_getAt(f, 0);
+  }
   /// Get the last point in the domain
   const BoutReal& current(const Field2D& f) const {
-    return static_cast<impl*>(this)->_getAt(f, 1);
+    return static_cast<const impl*>(this)->_getAt(f, 1);
   }
   /// Get the last point in the domain
-  BoutReal& current(Field2D& f) const { return static_cast<impl*>(this)->_getAt(f, 1); }
+  BoutReal& current(Field2D& f) const {
+    return static_cast<const impl*>(this)->_getAt(f, 1);
+  }
   /// Get the second to last point in the domain - this may not be valid and thus throw
   const BoutReal& prev(const Field2D& f) const {
-    return static_cast<impl*>(this)->_getAt(f, 2);
+    return static_cast<const impl*>(this)->_getAt(f, 2);
   }
 
   /*
@@ -136,22 +144,22 @@ public:
   template <bool check = true>
   BoutReal& getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
                   int off) const {
-    return static_cast<impl*>(this)->template _getAt<check>(func, off);
+    return static_cast<const impl*>(this)->template _getAt<check>(func, off);
   }
   /// Get the first point in the boundary
   const BoutReal&
   next(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
-    return static_cast<impl*>(this)->_getAt(func, 0);
+    return static_cast<const impl*>(this)->_getAt(func, 0);
   }
   /// Get the last point in the domain
   const BoutReal&
   current(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
-    return static_cast<impl*>(this)->_getAt(func, 1);
+    return static_cast<const impl*>(this)->_getAt(func, 1);
   }
   /// Get the second to last point in the domain - this may not be valid and thus throw
   const BoutReal&
   prev(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
-    return static_cast<impl*>(this)->_getAt(func, 2);
+    return static_cast<const impl*>(this)->_getAt(func, 2);
   }
 
   /*

From 4423d20d5dcdde2349b2a7802c04742ebbf1bfc7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 28 Apr 2026 14:30:41 +0200
Subject: [PATCH 1165/1827] Use inclusive language

There are other boundary than sheaths
---
 include/bout/boundary_region_iter.hxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 0d3c753cff..16a27e40a8 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -172,21 +172,21 @@ public:
   BoutReal extrapolate_boundary_o2(const Field3D& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
-      return extrapolate_sheath_o1(f);
+      return extrapolate_boundary_o1(f);
     }
     return current(f) * (1 + length()) - prev(f) * length();
   }
   /// Extrapolate a given function to the boundary
-  BoutReal extrapolate_sheath_o1(
+  BoutReal extrapolate_bounday_o1(
       const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
     return current(func);
   }
   /// Extrapolate a given function to the boundary
-  BoutReal extrapolate_sheath_o2(
+  BoutReal extrapolate_boundary_o2(
       const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
-      return extrapolate_sheath_o1(func);
+      return extrapolate_boundary_o1(func);
     }
     return current(func) * (1 + length()) - prev(func) * length();
   }

From 9a366a9392bbd6a680669ba559e825b21c589ec2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 28 Apr 2026 14:32:23 +0200
Subject: [PATCH 1166/1827] Add comparison operators

---
 include/bout/parallel_boundary_region.hxx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 5d81103208..b078d66ef6 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -56,6 +56,11 @@ struct Indices {
         offset(offset), abs_offset(abs_offset) {};
 };
 
+inline bool operator<(const Indices& lhs, const Indices& rhs) {
+  return lhs.index < rhs.index;
+}
+inline bool operator<(const Indices& lhs, const Ind3D& rhs) { return lhs.index < rhs; }
+
 using IndicesVec = std::vector<Indices>;
 using IndicesIter = IndicesVec::iterator;
 using IndicesIterConst = IndicesVec::const_iterator;

From 24e9c309f624e4ce8fabf412cbe3bb37b725d2fd Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 28 Apr 2026 20:33:47 -0700
Subject: [PATCH 1167/1827] test-unused-options: Test if options are marked
 used

Fails on two processors because options are not marked used.
---
 tests/integrated/CMakeLists.txt               |  1 +
 .../test-unused-options/CMakeLists.txt        |  6 +++++
 .../test-unused-options/data/BOUT.inp         | 10 ++++++++
 tests/integrated/test-unused-options/runtest  | 23 +++++++++++++++++++
 .../test_unused_options.cxx                   | 20 ++++++++++++++++
 5 files changed, 60 insertions(+)
 create mode 100644 tests/integrated/test-unused-options/CMakeLists.txt
 create mode 100644 tests/integrated/test-unused-options/data/BOUT.inp
 create mode 100755 tests/integrated/test-unused-options/runtest
 create mode 100644 tests/integrated/test-unused-options/test_unused_options.cxx

diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt
index 3696ef0372..06c46773f7 100644
--- a/tests/integrated/CMakeLists.txt
+++ b/tests/integrated/CMakeLists.txt
@@ -45,6 +45,7 @@ add_subdirectory(test-stopCheck)
 add_subdirectory(test-stopCheck-file)
 add_subdirectory(test-twistshift)
 add_subdirectory(test-twistshift-staggered)
+add_subdirectory(test-unused-options)
 add_subdirectory(test-vec)
 add_subdirectory(test-yupdown)
 add_subdirectory(test-yupdown-weights)
diff --git a/tests/integrated/test-unused-options/CMakeLists.txt b/tests/integrated/test-unused-options/CMakeLists.txt
new file mode 100644
index 0000000000..a654085fe0
--- /dev/null
+++ b/tests/integrated/test-unused-options/CMakeLists.txt
@@ -0,0 +1,6 @@
+bout_add_integrated_test(
+  test-unused-options
+  SOURCES test_unused_options.cxx
+  USE_RUNTEST USE_DATA_BOUT_INP
+  PROCESSORS 2
+)
diff --git a/tests/integrated/test-unused-options/data/BOUT.inp b/tests/integrated/test-unused-options/data/BOUT.inp
new file mode 100644
index 0000000000..937b3e8bf5
--- /dev/null
+++ b/tests/integrated/test-unused-options/data/BOUT.inp
@@ -0,0 +1,10 @@
+
+[mesh]
+nx = 12
+ny = 2
+nz = 1
+
+f_xin = 1.0
+
+[f]
+bndry_xin = dirichlet(mesh:f_xin)
diff --git a/tests/integrated/test-unused-options/runtest b/tests/integrated/test-unused-options/runtest
new file mode 100755
index 0000000000..f3fad0c404
--- /dev/null
+++ b/tests/integrated/test-unused-options/runtest
@@ -0,0 +1,23 @@
+#!/usr/bin/env python3
+
+from boututils.run_wrapper import build_and_log, launch_safe
+
+build_and_log("unused options test")
+
+for nproc in [1, 2]:
+    print(f"Running with nproc={nproc}...", end="")
+    s, out = launch_safe(
+        "./test_unused_options",
+        nproc=nproc,
+        mthread=1,
+        pipe=True,
+    )
+
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
+
+    # Check for printed message
+    if "SUCCESS" not in out:
+        print("failed")
+        exit(1)
+    print("pass")
diff --git a/tests/integrated/test-unused-options/test_unused_options.cxx b/tests/integrated/test-unused-options/test_unused_options.cxx
new file mode 100644
index 0000000000..9bd627bbb1
--- /dev/null
+++ b/tests/integrated/test-unused-options/test_unused_options.cxx
@@ -0,0 +1,20 @@
+#include <bout/bout.hxx>
+#include <bout/field3d.hxx>
+#include <bout/options.hxx>
+#include <bout/output.hxx>
+
+int main(int argc, char** argv) {
+  BoutInitialise(argc, argv);
+
+  Field3D f;
+  f.setBoundary("f");
+
+  bout::checkForUnusedOptions();
+
+  BoutFinalise();
+
+  // Note: Print message because sometimes MPI ranks error on tidyup.
+  output.write("SUCCESS");
+
+  return 0;
+}

From 88290429ca00f9ad7b03019cca09edc9705af7b7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 28 Apr 2026 21:27:19 -0700
Subject: [PATCH 1168/1827] Options::checkForUnusedOptions implement
 getGlobalUnusedSet

Checks for options that are unused on all MPI ranks.
Not very efficient but this function isn't called often.
---
 src/sys/options.cxx | 101 +++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 99 insertions(+), 2 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 8bd83c0bfb..95cfb9060a 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -1137,13 +1137,110 @@ void checkForUnusedOptions() {
                         options["optionfile"].withDefault("BOUT.inp"));
 }
 
+namespace {
+/// Gather the set of unused option keys that are unused on *every* MPI processor.
+///
+/// Each processor may use a different subset of options (e.g. because some
+/// options are only read on processors handling a particular region). An option
+/// should only be considered globally unused — and therefore an error — if it
+/// was not used on any processor.
+///
+/// Strategy:
+///   1. MPI_Allgather the per-processor serialised key lists so every rank
+///      knows the full union of locally-unused keys.
+///   2. For each key in that union, MPI_Allreduce with MPI_PROD over a flag
+///      that is 1 if the key is locally unused and 0 if it was used.  A
+///      product of 1 means every rank left it unused.
+///
+/// Keys are serialised as a newline-separated string.  Newlines are safe as a
+/// separator because option keys use ':' as their only structural character.
+std::set<std::string> getGlobalUnusedSet(std::vector<std::string> local_unused_keys) {
+  MPI_Comm comm = BoutComm::get();
+  int nprocs{};
+  MPI_Comm_size(comm, &nprocs);
+
+  // --- Step 1: share every processor's locally-unused key list ---
+
+  // Serialise this processor's unused keys as a newline-separated string.
+  // An empty key list produces an empty string, which is handled correctly
+  // by MPI_Allgatherv (contributing zero bytes).
+  const std::string local_serialized =
+      fmt::format("{}", fmt::join(local_unused_keys, "\n"));
+  int local_len = static_cast<int>(local_serialized.size());
+
+  // Gather the byte-lengths from all processors so we can allocate the
+  // receive buffer and build the displacement array for MPI_Allgatherv.
+  std::vector<int> all_lens(nprocs);
+  MPI_Allgather(&local_len, 1, MPI_INT, all_lens.data(), 1, MPI_INT, comm);
+
+  std::vector<int> displs(nprocs, 0);
+  for (int i = 1; i < nprocs; ++i) {
+    displs[i] = displs[i - 1] + all_lens[i - 1];
+  }
+  const int total_len = displs[nprocs - 1] + all_lens[nprocs - 1];
+
+  // Gather the serialised key strings from all processors.
+  std::string all_serialized(total_len, '\0');
+  MPI_Allgatherv(local_serialized.data(), local_len, MPI_CHAR, all_serialized.data(),
+                 all_lens.data(), displs.data(), MPI_CHAR, comm);
+
+  // Reconstruct the global union of unused keys by splitting each
+  // processor's contribution at the newline separator.
+  std::set<std::string> global_unused_union;
+  for (int i = 0; i < nprocs; ++i) {
+    if (all_lens[i] == 0) {
+      continue; // processor had no unused keys
+    }
+    const std::string proc_keys = all_serialized.substr(displs[i], all_lens[i]);
+    for (const auto& key : strsplit(proc_keys, '\n')) {
+      global_unused_union.insert(key);
+    }
+  }
+
+  if (global_unused_union.empty()) {
+    return {};
+  }
+
+  // --- Step 2: keep only keys that were unused on *every* processor ---
+
+  // Build a presence flag for each key in the global union: 1 if unused
+  // locally (i.e. in our local_unused_keys), 0 if it was used here.
+  const std::set<std::string> local_set(local_unused_keys.begin(),
+                                        local_unused_keys.end());
+  const std::vector<std::string> global_keys(global_unused_union.begin(),
+                                             global_unused_union.end());
+
+  std::vector<int> local_flags(global_keys.size());
+  for (std::size_t i = 0; i < global_keys.size(); ++i) {
+    local_flags[i] = local_set.contains(global_keys[i]) ? 1 : 0;
+  }
+
+  // MPI_PROD: product across all processors is 1 iff every processor
+  // contributed 1, i.e. iff the key was unused everywhere.
+  std::vector<int> global_flags(global_keys.size());
+  MPI_Allreduce(local_flags.data(), global_flags.data(),
+                static_cast<int>(global_keys.size()), MPI_INT, MPI_PROD, comm);
+
+  std::set<std::string> globally_unused;
+  for (std::size_t i = 0; i < global_keys.size(); ++i) {
+    if (global_flags[i] != 0) {
+      globally_unused.insert(global_keys[i]);
+    }
+  }
+  return globally_unused;
+}
+} // namespace
+
 void checkForUnusedOptions(const Options& options, const std::string& data_dir,
                            const std::string& option_file) {
   const Options unused = options.getUnused();
-  if (not unused.getChildren().empty()) {
+
+  // Get the keys that are not used on any processor
+  const auto keys = getGlobalUnusedSet(unused.getFlattenedKeys());
+
+  if (not keys.empty()) {
 
     // Construct a string with all the fuzzy matches for each unused option
-    const auto keys = unused.getFlattenedKeys();
     std::string possible_misspellings;
     for (const auto& key : keys) {
       auto fuzzy_matches = options.fuzzyFind(key);

From 30da9d698eda03be02c0f30e591265bff87aa14e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Apr 2026 07:53:50 +0200
Subject: [PATCH 1169/1827] Add offset accessor

---
 include/bout/boundary_region_iter.hxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 16a27e40a8..4f0187e406 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -92,6 +92,9 @@ public:
   const BoutReal& prev(const Field3D& f) const {
     return static_cast<const impl*>(this)->_getAt(f, 2);
   }
+  /// Get the offset from the last point in the domain
+  /// For FA this is always ±1, for FCI this can be up to ±MYG, excluding 0
+  int offset() const { return static_cast<const impl*>(this)->_offset(); }
   /*
    *         FIELD2D ACCESSORS
    */

From 90032b605712799ac142aac688d33c7662e84d4d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Apr 2026 07:54:25 +0200
Subject: [PATCH 1170/1827] Add dir and contains

---
 include/bout/boundary_region_iter.hxx | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 4f0187e406..33c073eb92 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -418,6 +418,14 @@ public:
                  BoutReal length, char valid, signed char offset) {
     add_point(xyz2ind(ix, iy, iz), x, y, z, length, valid, offset);
   }
+  bool contains(int ix, int iy, int iz) {
+    const auto ind = xyz2ind(ix, iy, iz);
+    ensureSorted();
+    const auto found =
+        std::lower_bound(std::begin(bndry_points), std::end(bndry_points), ind);
+    return found != std::end(bndry_points) and found->index == ind;
+  }
+  int dir() { return _dir; }
 
 private:
   friend class BoundaryRegionIterFCI;

From 7086969b9afba8cddd0b5585254295aa8f259647 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Apr 2026 07:54:45 +0200
Subject: [PATCH 1171/1827] Add sorter

---
 include/bout/boundary_region_iter.hxx | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 33c073eb92..a3c860ba2c 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -432,13 +432,19 @@ private:
   int _dir;
   // Vector of points in the boundary
   bout::parallel_boundary_region::IndicesVec bndry_points;
+  bool is_sorted{true};
+  Mesh* localmesh;
   Ind3D xyz2ind(int x, int y, int z) const {
     const int ny = localmesh->LocalNy;
     const int nz = localmesh->LocalNz;
     return Ind3D{(x * ny + y) * nz + z, ny, nz};
   }
-  bool is_sorted{true};
-  Mesh* localmesh;
+  void ensureSorted() {
+    if (is_sorted) {
+      return;
+    }
+    std::sort(std::begin(bndry_points), std::end(bndry_points));
+  }
 };
 
 class BoundaryRegionIterFCI : public BoundaryRegionIterBase<BoundaryRegionIterFCI> {

From e8c699d55a8250bd13d2d7b0d39a9930633b107a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Apr 2026 07:58:18 +0200
Subject: [PATCH 1172/1827] Add iterator bits

---
 include/bout/boundary_region_iter.hxx | 28 ++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index a3c860ba2c..eed3e8f5d5 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -449,10 +449,17 @@ private:
 
 class BoundaryRegionIterFCI : public BoundaryRegionIterBase<BoundaryRegionIterFCI> {
 private:
-  BoundaryRegionFCI* region;
+  // TODO(dave) make non-const?
+  const BoundaryRegionFCI* region;
   size_t pos{0};
 
 public:
+  BoundaryRegionIterFCI() = delete;
+  BoundaryRegionIterFCI(const BoundaryRegionFCI* reg, bool isstart)
+      : region(reg), pos(isstart ? 0 : reg->bndry_points.size()) {}
+  void setValid(char valid) {
+    const_cast<BoundaryRegionFCI*>(region)->bndry_points[pos].valid = valid;
+  };
   template <bool check = true>
   BoutReal& _getAt(Field3D& f, int off) const {
     ASSERT3(f.hasParallelSlices());
@@ -505,6 +512,25 @@ public:
     return region->localmesh->ystart - region->bndry_points[pos].abs_offset;
   }
   const BoutReal& _length() const { return region->bndry_points[pos].length; }
+  bool operator!=(BoundaryRegionIterFCI lhs) {
+    ASSERT3(region == lhs.region);
+    return pos != lhs.pos;
+  }
+  BoundaryRegionIterFCI& operator++() {
+    ++pos;
+    return *this;
+  }
+  // No-op for compatibility
+  BoundaryRegionIterFCI& operator*() { return *this; }
 };
 } // namespace boundary
 } // namespace bout
+
+inline bout::boundary::BoundaryRegionIterFCI
+begin(const bout::boundary::BoundaryRegionFCI reg) {
+  return bout::boundary::BoundaryRegionIterFCI(&reg, true);
+}
+inline bout::boundary::BoundaryRegionIterFCI
+end(const bout::boundary::BoundaryRegionFCI reg) {
+  return bout::boundary::BoundaryRegionIterFCI(&reg, false);
+}

From 38e5f2076108e65c09f51d2df8799a95dac38ea8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Apr 2026 07:59:17 +0200
Subject: [PATCH 1173/1827] Add more accessors

---
 include/bout/boundary_region_iter.hxx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index eed3e8f5d5..bdfb3c3d8b 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -460,6 +460,11 @@ public:
   void setValid(char valid) {
     const_cast<BoundaryRegionFCI*>(region)->bndry_points[pos].valid = valid;
   };
+  BoutReal s_x() const { return region->bndry_points[pos].intersection.s_x; };
+  BoutReal s_y() const { return region->bndry_points[pos].intersection.s_y; };
+  BoutReal s_z() const { return region->bndry_points[pos].intersection.s_z; };
+  Mesh* localmesh() const { return region->localmesh; };
+  int dir() const { return region->_dir; }
   template <bool check = true>
   BoutReal& _getAt(Field3D& f, int off) const {
     ASSERT3(f.hasParallelSlices());

From da4ea6aee9e53ad7d5bdead9dc3444fa4ca09950 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Apr 2026 07:59:30 +0200
Subject: [PATCH 1174/1827] Fix return type

---
 include/bout/boundary_region_iter.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index bdfb3c3d8b..c71419085e 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -512,7 +512,7 @@ public:
   }
   signed char _offset() const { return region->bndry_points[pos].offset; }
   signed char _valid() const { return region->bndry_points[pos].valid; }
-  Ind3D& _ind() const { return region->bndry_points[pos].index; }
+  Ind3D _ind() const { return region->bndry_points[pos].index; }
   signed char _boundary_width() const {
     return region->localmesh->ystart - region->bndry_points[pos].abs_offset;
   }

From 84c7f7e059b41d6ff89877f4431c751538c16ee1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Apr 2026 07:59:49 +0200
Subject: [PATCH 1175/1827] Derive from BoundaryRegionBase

---
 include/bout/boundary_region_iter.hxx | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index c71419085e..ee0132c527 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -401,9 +401,11 @@ inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, BoundaryFreeExtrapolati
 }
 } // namespace
 
-class BoundaryRegionFCI {
+class BoundaryRegionFCI : public BoundaryRegionBase {
 public:
-  BoundaryRegionFCI(int dir, Mesh* mesh) : _dir(dir), localmesh(mesh) {};
+  BoundaryRegionFCI(const std::string& name, [[maybe_unused]] const BndryLoc& loc,
+                    int dir, Mesh* mesh)
+      : BoundaryRegionBase(name, mesh), _dir(dir), localmesh(mesh) {};
   /// Add a point to the boundary
   void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
                  char valid, signed char offset) {
@@ -426,6 +428,10 @@ public:
     return found != std::end(bndry_points) and found->index == ind;
   }
   int dir() { return _dir; }
+  // legacy interface
+  void first() override { throw BoutException("Legacy interface is not suppored"); }
+  void next() override { throw BoutException("Legacy interface is not suppored"); }
+  bool isDone() override { throw BoutException("Legacy interface is not suppored"); }
 
 private:
   friend class BoundaryRegionIterFCI;

From 4880e012343898bccd1c31653f6920b085022ae9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 29 Apr 2026 08:00:56 +0200
Subject: [PATCH 1176/1827] Switch to bout::boundary::BoundaryRegionFCI

---
 include/bout/field_data.hxx               |  3 +
 include/bout/mesh.hxx                     | 11 ++--
 include/bout/parallel_boundary_op.hxx     | 73 +++++++++++++++++------
 include/bout/yboundary_regions.hxx        |  2 +-
 src/field/field3d.cxx                     |  3 +-
 src/field/field_data.cxx                  |  1 +
 src/mesh/boundary_factory.cxx             |  7 ++-
 src/mesh/impls/bout/boutmesh.cxx          |  7 ++-
 src/mesh/impls/bout/boutmesh.hxx          |  6 +-
 src/mesh/parallel/fci.cxx                 | 16 ++---
 src/mesh/parallel/fci.hxx                 |  7 ++-
 src/mesh/parallel/shiftedmetricinterp.cxx | 10 ++--
 src/mesh/parallel_boundary_op.cxx         |  6 +-
 tests/unit/fake_mesh.hxx                  |  5 +-
 14 files changed, 106 insertions(+), 51 deletions(-)

diff --git a/include/bout/field_data.hxx b/include/bout/field_data.hxx
index c84cdda444..4b8519d54b 100644
--- a/include/bout/field_data.hxx
+++ b/include/bout/field_data.hxx
@@ -41,6 +41,9 @@ class FieldData;
 
 class BoundaryOp;
 class BoundaryOpPar;
+namespace bout::boundary {
+class BoundaryRegionFCI;
+}
 class Coordinates;
 class Mesh;
 
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 0e96e162f9..f982bcef1f 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -67,7 +67,9 @@ class Mesh;
 #include <string>
 
 class BoundaryRegion;
-class BoundaryRegionPar;
+namespace bout::boundary {
+class BoundaryRegionFCI;
+}
 class GridDataSource;
 
 class MeshFactory : public Factory<Mesh, MeshFactory, GridDataSource*, Options*> {
@@ -500,12 +502,13 @@ public:
   /// mesh->getBoundariesPar(Mesh::BoundaryParType::all)
   /// get only xout:
   /// mesh->getBoundariesPar(Mesh::BoundaryParType::xout)
-  virtual std::vector<std::shared_ptr<BoundaryRegionPar>>
+  virtual std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType type = BoundaryParType::all) const = 0;
 
   /// Add a parallel(Y) boundary to this processor
-  virtual void addBoundaryPar(std::shared_ptr<BoundaryRegionPar> UNUSED(bndry),
-                              BoundaryParType UNUSED(type)) {}
+  virtual void
+  addBoundaryPar(std::shared_ptr<bout::boundary::BoundaryRegionFCI> UNUSED(bndry),
+                 BoundaryParType UNUSED(type)) {}
 
   virtual BoutReal GlobalX(int jx) const = 0;      ///< Continuous X index between 0 and 1
   virtual BoutReal GlobalY(int jy) const = 0;      ///< Continuous Y index (0 -> 1)
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index 3e81085eb0..b0f74b9f9f 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -2,6 +2,7 @@
 #define BOUT_PAR_BNDRY_OP_H
 
 #include "bout/boundary_op.hxx"
+#include "bout/boundary_region_iter.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/field_factory.hxx"
 #include "bout/parallel_boundary_region.hxx"
@@ -16,28 +17,46 @@
 class BoundaryOpPar : public BoundaryOpBase {
 public:
   BoundaryOpPar() = default;
-  BoundaryOpPar(BoundaryRegionPar* region, std::shared_ptr<FieldGenerator> value)
+  BoundaryOpPar(bout::boundary::BoundaryRegionFCI* region,
+                std::shared_ptr<FieldGenerator> value)
       : bndry(region), gen_values(std::move(value)), value_type(ValueType::GEN) {}
-  BoundaryOpPar(BoundaryRegionPar* region, Field3D* value)
+  BoundaryOpPar(bout::boundary::BoundaryRegionFCI* region, Field3D* value)
       : bndry(region), field_values(value), value_type(ValueType::FIELD) {}
-  BoundaryOpPar(BoundaryRegionPar* region, BoutReal value)
+  BoundaryOpPar(bout::boundary::BoundaryRegionFCI* region, BoutReal value)
       : bndry(region), real_value(value), value_type(ValueType::REAL) {}
-  BoundaryOpPar(BoundaryRegionPar* region)
+  BoundaryOpPar(bout::boundary::BoundaryRegionFCI* region)
       : bndry(region), real_value(0.), value_type(ValueType::REAL) {}
+  BoundaryOpPar(BoundaryOpPar* region, std::shared_ptr<FieldGenerator> value)
+      : bndry(region->bndry), gen_values(std::move(value)), value_type(ValueType::GEN) {}
+  BoundaryOpPar(BoundaryOpPar* region, Field3D* value)
+      : bndry(region->bndry), field_values(value), value_type(ValueType::FIELD) {}
+  BoundaryOpPar(BoundaryOpPar* region, BoutReal value)
+      : bndry(region->bndry), real_value(value), value_type(ValueType::REAL) {}
+  BoundaryOpPar(BoundaryOpPar* region)
+      : bndry(region->bndry), real_value(0.), value_type(ValueType::REAL) {}
   ~BoundaryOpPar() override = default;
 
   // Note: All methods must implement clone, except for modifiers (see below)
-  virtual BoundaryOpPar* clone(BoundaryRegionPar* region,
+  virtual BoundaryOpPar* clone(bout::boundary::BoundaryRegionFCI* region,
                                const std::list<std::string>& args) = 0;
-  virtual BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) = 0;
+  virtual BoundaryOpPar* clone(BoundaryOpPar* region,
+                               const std::list<std::string>& args) = 0;
+  virtual BoundaryOpPar* clone(bout::boundary::BoundaryRegionFCI* region, Field3D* f) = 0;
+  virtual BoundaryOpPar* clone(BoundaryOpPar* region, Field3D* f) = 0;
+  virtual BoundaryOpPar*
+  clone(bout::boundary::BoundaryRegionFCI* region, const std::list<std::string>& args,
+        const std::map<std::string, std::string>& UNUSED(keywords)) {
+    // If not implemented, call two-argument version
+    return clone(region, args);
+  }
   virtual BoundaryOpPar*
-  clone(BoundaryRegionPar* region, const std::list<std::string>& args,
+  clone(BoundaryOpPar* region, const std::list<std::string>& args,
         const std::map<std::string, std::string>& UNUSED(keywords)) {
     // If not implemented, call two-argument version
     return clone(region, args);
   }
 
-  BoundaryRegionPar* bndry{nullptr};
+  bout::boundary::BoundaryRegionFCI* bndry{nullptr};
 
 protected:
   /// Possible ways to get boundary values
@@ -49,7 +68,7 @@ protected:
   enum class ValueType { GEN, FIELD, REAL };
   const ValueType value_type{ValueType::REAL};
 
-  BoutReal getValue(const BoundaryRegionParIter& bndry, BoutReal t);
+  BoutReal getValue(const bout::boundary::BoundaryRegionIterFCI& bndry, BoutReal t);
 };
 
 template <class T, bool isNeumann = false>
@@ -59,8 +78,23 @@ public:
 
   using BoundaryOpPar::clone;
 
-  // Note: All methods must implement clone, except for modifiers (see below)
-  BoundaryOpPar* clone(BoundaryRegionPar* region,
+  BoundaryOpPar* clone(BoundaryOpPar* region,
+                       const std::list<std::string>& args) override {
+    if (!args.empty()) {
+      try {
+        real_value = stringToReal(args.front());
+        return new T(region, real_value);
+      } catch (const BoutException&) {
+        std::shared_ptr<FieldGenerator> newgen = nullptr;
+        // First argument should be an expression
+        newgen = FieldFactory::get()->parse(args.front());
+        return new T(region, newgen);
+      }
+    }
+
+    return new T(region);
+  }
+  BoundaryOpPar* clone(bout::boundary::BoundaryRegionFCI* region,
                        const std::list<std::string>& args) override {
     if (!args.empty()) {
       try {
@@ -77,7 +111,10 @@ public:
     return new T(region);
   }
 
-  BoundaryOpPar* clone(BoundaryRegionPar* region, Field3D* f) override {
+  BoundaryOpPar* clone(bout::boundary::BoundaryRegionFCI* region, Field3D* f) override {
+    return new T(region, f);
+  }
+  BoundaryOpPar* clone(BoundaryOpPar* region, Field3D* f) override {
     return new T(region, f);
   }
 
@@ -112,7 +149,7 @@ public:
 class BoundaryOpPar_dirichlet_o1 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o1> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
                             BoutReal value) {
     pnt.dirichlet_o1(f, value);
   }
@@ -121,7 +158,7 @@ public:
 class BoundaryOpPar_dirichlet_o2 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o2> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
                             BoutReal value) {
     pnt.dirichlet_o2(f, value);
   }
@@ -130,7 +167,7 @@ public:
 class BoundaryOpPar_dirichlet_o3 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o3> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
                             BoutReal value) {
     pnt.dirichlet_o3(f, value);
   }
@@ -140,7 +177,7 @@ class BoundaryOpPar_neumann_o1
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o1, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
                             BoutReal value) {
     pnt.neumann_o1(f, value);
   }
@@ -150,7 +187,7 @@ class BoundaryOpPar_neumann_o2
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o2, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
                             BoutReal value) {
     pnt.neumann_o2(f, value);
   }
@@ -160,7 +197,7 @@ class BoundaryOpPar_neumann_o3
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o3, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const BoundaryRegionParIter& pnt,
+  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
                             BoutReal value) {
     pnt.neumann_o3(f, value);
   }
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index b627a8a90a..b1aec6bc2e 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -138,7 +138,7 @@ public:
   }
 
 private:
-  std::vector<std::shared_ptr<BoundaryRegionPar>> boundary_regions_par;
+  std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>> boundary_regions_par;
   std::vector<std::shared_ptr<NewBoundaryRegionY>> boundary_regions;
 
   std::vector<BoutMask> _contains;
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 373d00d667..c0c01fefc5 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -43,6 +43,7 @@
 #include <bout/assert.hxx>
 #include <bout/boundary_factory.hxx>
 #include <bout/boundary_op.hxx>
+#include <bout/boundary_region_iter.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/dcomplex.hxx>
@@ -466,7 +467,7 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
       for (auto& region : fieldmesh->getBoundariesPar()) {
         for (const auto& pnt : *region) {
           // Interpolate midpoint value in f3d
-          const BoutReal val = pnt.interpolate_sheath_o2(f3d);
+          const BoutReal val = pnt.interpolate_boundary_o2(f3d);
           // Set the same boundary value in this field
           pnt.dirichlet_o1(*this, val);
         }
diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx
index b925cb1426..154380dcb6 100644
--- a/src/field/field_data.cxx
+++ b/src/field/field_data.cxx
@@ -3,6 +3,7 @@
 #include "bout/parallel_boundary_region.hxx"
 #include "bout/unused.hxx"
 #include <bout/boundary_factory.hxx>
+#include <bout/boundary_region_iter.hxx>
 #include <bout/field_data.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/globals.hxx>
diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index fd5bbdc70d..a9c278a4d6 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -1,6 +1,7 @@
 #include "bout/parallel_boundary_op.hxx"
 #include "bout/parallel_boundary_region.hxx"
 #include <bout/boundary_factory.hxx>
+#include <bout/boundary_region_iter.hxx>
 #include <bout/boundary_standard.hxx>
 #include <bout/globals.hxx>
 #include <bout/options.hxx>
@@ -105,7 +106,8 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
       // Clone the boundary operation, passing the region to operate over,
       // an empty args list and empty keyword map
       list<string> args;
-      return pop->clone(dynamic_cast<BoundaryRegionPar*>(region), args, {});
+      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionFCI*>(region), args,
+                        {});
     } else {
       // Perpendicular boundary
       BoundaryOp* op = findBoundaryOp(trim(name));
@@ -197,7 +199,8 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
     BoundaryOpPar* pop = findBoundaryOpPar(trim(func));
     if (pop != nullptr) {
       // An operation with arguments
-      return pop->clone(dynamic_cast<BoundaryRegionPar*>(region), arglist, keywords);
+      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionFCI*>(region), arglist,
+                        keywords);
     }
   } else {
     // Perpendicular boundary
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index e5d4858f45..e713ca4f6c 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -28,6 +28,7 @@
 
 #include <bout/assert.hxx>
 #include <bout/boundary_region.hxx>
+#include <bout/boundary_region_iter.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
@@ -3163,12 +3164,12 @@ RangeIterator BoutMesh::iterateBndryUpperY() const {
 
 std::vector<BoundaryRegion*> BoutMesh::getBoundaries() { return boundary; }
 
-std::vector<std::shared_ptr<BoundaryRegionPar>>
+using bout::boundary::BoundaryRegionFCI;
+std::vector<std::shared_ptr<BoundaryRegionFCI>>
 BoutMesh::getBoundariesPar(BoundaryParType type) const {
   return par_boundary[static_cast<int>(type)];
 }
-
-void BoutMesh::addBoundaryPar(std::shared_ptr<BoundaryRegionPar> bndry,
+void BoutMesh::addBoundaryPar(std::shared_ptr<BoundaryRegionFCI> bndry,
                               BoundaryParType type) {
   output_info << "Adding new parallel boundary: " << bndry->label << endl;
   switch (type) {
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index 835cb5dd53..49d8b6112a 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -163,9 +163,9 @@ public:
 
   // Boundary regions
   std::vector<BoundaryRegion*> getBoundaries() override;
-  std::vector<std::shared_ptr<BoundaryRegionPar>>
+  std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType type) const override;
-  void addBoundaryPar(std::shared_ptr<BoundaryRegionPar> bndry,
+  void addBoundaryPar(std::shared_ptr<bout::boundary::BoundaryRegionFCI> bndry,
                       BoundaryParType type) override;
   std::set<std::string> getPossibleBoundaries() const override;
 
@@ -410,7 +410,7 @@ protected:
 
 private:
   std::vector<BoundaryRegion*> boundary; // Vector of boundary regions
-  std::array<std::vector<std::shared_ptr<BoundaryRegionPar>>,
+  std::array<std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>,
              static_cast<int>(BoundaryParType::SIZE)>
       par_boundary; // Vector of parallel boundary regions
 
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 68c37ea964..21fd4ecc32 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -39,6 +39,7 @@
 #include "fci.hxx"
 
 #include "bout/assert.hxx"
+#include "bout/boundary_region_iter.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field2d.hxx"
@@ -63,11 +64,12 @@
 #include <string_view>
 
 using namespace std::string_view_literals;
+using bout::boundary::BoundaryRegionFCI;
 
 FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
                Options& options, int offset,
-               const std::shared_ptr<BoundaryRegionPar>& inner_boundary,
-               const std::shared_ptr<BoundaryRegionPar>& outer_boundary, bool zperiodic)
+               const std::shared_ptr<BoundaryRegionFCI>& inner_boundary,
+               const std::shared_ptr<BoundaryRegionFCI>& outer_boundary, bool zperiodic)
     : map_mesh(&mesh), offset_(offset),
       region_no_boundary(map_mesh->getRegion("RGN_NOBNDRY")),
       corner_boundary_mask(map_mesh) {
@@ -185,7 +187,7 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
                    + ((map_mesh->xend - map_mesh->xstart + 1) * map_mesh->getNXPE()) - 1;
   // Default to the maximum number of points
   const int defValid{map_mesh->ystart - 1 + std::abs(offset)};
-  // Serial loop because call to BoundaryRegionPar::addPoint
+  // Serial loop because call to BoundaryRegionFCI::addPoint
   // (probably?) can't be done in parallel
   BOUT_FOR_SERIAL(i, xt_prime.getRegion("RGN_NOBNDRY")) {
     // z is periodic, so make sure the z-index wraps around
@@ -326,13 +328,13 @@ FCITransform::FCITransform(Mesh& mesh, const Coordinates::FieldMetric& dy, bool
   mesh.get(Z, "Z", 0.0, false);
 
   auto forward_boundary_xin =
-      std::make_shared<BoundaryRegionPar>("FCI_forward", BNDRY_PAR_FWD_XIN, +1, &mesh);
+      std::make_shared<BoundaryRegionFCI>("FCI_forward", BNDRY_PAR_FWD_XIN, +1, &mesh);
   auto backward_boundary_xin =
-      std::make_shared<BoundaryRegionPar>("FCI_backward", BNDRY_PAR_BKWD_XIN, -1, &mesh);
+      std::make_shared<BoundaryRegionFCI>("FCI_backward", BNDRY_PAR_BKWD_XIN, -1, &mesh);
   auto forward_boundary_xout =
-      std::make_shared<BoundaryRegionPar>("FCI_forward", BNDRY_PAR_FWD_XOUT, +1, &mesh);
+      std::make_shared<BoundaryRegionFCI>("FCI_forward", BNDRY_PAR_FWD_XOUT, +1, &mesh);
   auto backward_boundary_xout =
-      std::make_shared<BoundaryRegionPar>("FCI_backward", BNDRY_PAR_BKWD_XOUT, -1, &mesh);
+      std::make_shared<BoundaryRegionFCI>("FCI_backward", BNDRY_PAR_BKWD_XOUT, -1, &mesh);
 
   // Add the boundary region to the mesh's vector of parallel boundaries
   mesh.addBoundaryPar(forward_boundary_xin, BoundaryParType::xin_fwd);
diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx
index 65529a4c4e..f5d0642675 100644
--- a/src/mesh/parallel/fci.hxx
+++ b/src/mesh/parallel/fci.hxx
@@ -31,6 +31,7 @@
 #include "bout/boutexception.hxx"
 #include "bout/coordinates.hxx"
 #include "bout/region.hxx"
+#include <bout/boundary_region_iter.hxx>
 #include <bout/interpolation_xz.hxx>
 #include <bout/mask.hxx>
 #include <bout/parallel_boundary_region.hxx>
@@ -41,7 +42,6 @@
 #include <string>
 #include <vector>
 
-class BoundaryRegionPar;
 class FieldPerp;
 class Field2D;
 class Field3D;
@@ -68,8 +68,9 @@ class FCIMap {
 public:
   FCIMap() = delete;
   FCIMap(Mesh& mesh, const Coordinates::FieldMetric& dy, Options& options, int offset,
-         const std::shared_ptr<BoundaryRegionPar>& inner_boundary,
-         const std::shared_ptr<BoundaryRegionPar>& outer_boundary, bool zperiodic);
+         const std::shared_ptr<bout::boundary::BoundaryRegionFCI>& inner_boundary,
+         const std::shared_ptr<bout::boundary::BoundaryRegionFCI>& outer_boundary,
+         bool zperiodic);
 
   /// Direction of map
   int offset() const { return offset_; }
diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx
index 4b470da2ad..7171bdd0bd 100644
--- a/src/mesh/parallel/shiftedmetricinterp.cxx
+++ b/src/mesh/parallel/shiftedmetricinterp.cxx
@@ -31,10 +31,10 @@
 
 #include "shiftedmetricinterp.hxx"
 
+#include "bout/boundary_region_iter.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/constants.hxx"
 #include "bout/field3d.hxx"
-#include "bout/parallel_boundary_region.hxx"
 
 ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
                                          Field2D zShift_in, BoutReal zlength_in,
@@ -133,7 +133,7 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
   // Create regions for parallel boundary conditions
   Field2D dy;
   mesh.get(dy, "dy", 1.);
-  auto forward_boundary_xin = std::make_shared<BoundaryRegionPar>(
+  auto forward_boundary_xin = std::make_shared<bout::boundary::BoundaryRegionFCI>(
       "parallel_forward_xin", BNDRY_PAR_FWD_XIN, +1, &mesh);
   for (auto it = mesh.iterateBndryUpperY(); not it.isDone(); it.next()) {
     for (int z = mesh.zstart; z <= mesh.zend; z++) {
@@ -149,7 +149,7 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
           yvalid, 1);
     }
   }
-  auto backward_boundary_xin = std::make_shared<BoundaryRegionPar>(
+  auto backward_boundary_xin = std::make_shared<bout::boundary::BoundaryRegionFCI>(
       "parallel_backward_xin", BNDRY_PAR_BKWD_XIN, -1, &mesh);
   for (auto it = mesh.iterateBndryLowerY(); not it.isDone(); it.next()) {
     for (int z = mesh.zstart; z <= mesh.zend; z++) {
@@ -166,7 +166,7 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
     }
   }
   // Create regions for parallel boundary conditions
-  auto forward_boundary_xout = std::make_shared<BoundaryRegionPar>(
+  auto forward_boundary_xout = std::make_shared<bout::boundary::BoundaryRegionFCI>(
       "parallel_forward_xout", BNDRY_PAR_FWD_XOUT, +1, &mesh);
   for (auto it = mesh.iterateBndryUpperY(); not it.isDone(); it.next()) {
     for (int z = mesh.zstart; z <= mesh.zend; z++) {
@@ -182,7 +182,7 @@ ShiftedMetricInterp::ShiftedMetricInterp(Mesh& mesh, CELL_LOC location_in,
           yvalid, 1);
     }
   }
-  auto backward_boundary_xout = std::make_shared<BoundaryRegionPar>(
+  auto backward_boundary_xout = std::make_shared<bout::boundary::BoundaryRegionFCI>(
       "parallel_backward_xout", BNDRY_PAR_BKWD_XOUT, -1, &mesh);
   for (auto it = mesh.iterateBndryLowerY(); not it.isDone(); it.next()) {
     for (int z = mesh.zstart; z <= mesh.zend; z++) {
diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx
index 644331221e..bf0374ddf6 100644
--- a/src/mesh/parallel_boundary_op.cxx
+++ b/src/mesh/parallel_boundary_op.cxx
@@ -1,4 +1,5 @@
 #include "bout/parallel_boundary_op.hxx"
+#include "bout/boundary_region_iter.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/constants.hxx"
 #include "bout/field_factory.hxx"
@@ -7,11 +8,12 @@
 #include "bout/output.hxx"
 #include "bout/parallel_boundary_region.hxx"
 
-BoutReal BoundaryOpPar::getValue(const BoundaryRegionParIter& bndry, BoutReal t) {
+BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterFCI& bndry,
+                                 BoutReal t) {
   switch (value_type) {
   case ValueType::GEN:
     return gen_values->generate(bout::generator::Context(
-        bndry.s_x(), bndry.s_y(), bndry.s_z(), CELL_CENTRE, bndry.localmesh, t));
+        bndry.s_x(), bndry.s_y(), bndry.s_z(), CELL_CENTRE, bndry.localmesh(), t));
   case ValueType::FIELD:
     // FIXME: Interpolate to s_x, s_y, s_z...
     return (*field_values)[bndry.ind()];
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index aa335110a5..6959b5e480 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -1,6 +1,7 @@
 #pragma once
 
 #include <bout/boundary_region.hxx>
+#include <bout/boundary_region_iter.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
@@ -172,9 +173,9 @@ public:
   bool hasBndryUpperY() const override { return false; }
   void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); }
   std::vector<BoundaryRegion*> getBoundaries() override { return boundaries; }
-  std::vector<std::shared_ptr<BoundaryRegionPar>>
+  std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType UNUSED(type)) const override {
-    return std::vector<std::shared_ptr<BoundaryRegionPar>>();
+    return std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>();
   }
   BoutReal GlobalX(int jx) const override { return jx; }
   BoutReal GlobalY(int jy) const override { return jy; }

From 26f7cc40c2a76e7c4df602c590962f869474b7e8 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 29 Apr 2026 09:32:19 -0700
Subject: [PATCH 1177/1827] Options getGlobalUnusedSet use BoutComm

Co-authored-by: Peter Hill <peter.hill@york.ac.uk>
---
 src/sys/options.cxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 95cfb9060a..85cfa7a49a 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -1156,8 +1156,7 @@ namespace {
 /// separator because option keys use ':' as their only structural character.
 std::set<std::string> getGlobalUnusedSet(std::vector<std::string> local_unused_keys) {
   MPI_Comm comm = BoutComm::get();
-  int nprocs{};
-  MPI_Comm_size(comm, &nprocs);
+  const int nprocs = BoutComm::size();
 
   // --- Step 1: share every processor's locally-unused key list ---
 

From aa8cc4cd8ca74b6d67a2a71d92c1c87b54c020b9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 7 May 2026 08:27:21 +0200
Subject: [PATCH 1178/1827] zoidberg 0.3.0 is released

This includes the needed fixes, thus no workaround needed anymore
---
 .ci_fedora.sh               | 2 --
 .github/workflows/tests.yml | 1 -
 requirements.txt            | 2 +-
 3 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 8214a40ccc..e1dc563c6c 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -47,8 +47,6 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
-    python3 -m ensurepip
-    python3 -m pip install git+https://github.com/boutproject/zoidberg@better-metric
     echo "starting configure"
     time cmake -S . -B build -DBOUT_USE_PETSC=ON \
 	 -DBOUT_UPDATE_GIT_SUBMODULE=OFF \
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 8919f82df1..ff11a2a4c9 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -166,7 +166,6 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           python -m pip install -r requirements.txt
-          python -m pip install git+https://github.com/boutproject/zoidberg@better-metric
 
       - name: Cache Zenodo test data
         uses: actions/cache@v5
diff --git a/requirements.txt b/requirements.txt
index 078eecac6d..9b06edfd8a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,4 +5,4 @@ netcdf4>=1.7.1
 matplotlib>=3.7.0
 Cython>=3.0.0
 boutdata>=0.3.0
-zoidberg>=0.2.2
+zoidberg>=0.3.0

From a30fb7a943b768afabe1230b13c20aa451e427d6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 11 May 2026 10:59:48 +0200
Subject: [PATCH 1179/1827] Update according to spec-0

Updated by https://github.com/dschwoerer/spec0-updater
---
 requirements.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 9b06edfd8a..3f31120881 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,8 +1,8 @@
 Jinja2>=3.1.4
 numpy>=2.0.0
-scipy>=1.14.1
+scipy >= 1.14.0
 netcdf4>=1.7.1
-matplotlib>=3.7.0
+matplotlib >= 3.9.0
 Cython>=3.0.0
 boutdata>=0.3.0
 zoidberg>=0.3.0

From d9e2c19e48a02de8e9406b5178815d198ac86921 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 11 May 2026 11:00:48 +0200
Subject: [PATCH 1180/1827] CI: Do not update versions by dependabot

We want to follow spec0
---
 .github/dependabot.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index c6b0738bd2..e121ea49e4 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -6,11 +6,6 @@ updates:
         interval: "weekly"
     directory: "/"
 
-  - package-ecosystem: "pip"
-    schedule:
-        interval: "daily"
-    directory: "/"
-  
   - package-ecosystem: "github-actions"
     schedule:
       interval: "weekly"

From 527466c55654b43af937ba851e3e0d24f4bf4660 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 12 May 2026 17:28:11 -0700
Subject: [PATCH 1181/1827] PetscCellMapping::makeNeumannOperator

Creates an operator that applies Neumann boundary conditions
in the Yup/Ydown directions.
---
 include/bout/petsc_operators.hxx |  22 ++++++-
 src/mesh/petsc_operators.cxx     | 102 +++++++++++++++++++++++++++++++
 2 files changed, 123 insertions(+), 1 deletion(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 8c36f461d0..ee2656640f 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -44,6 +44,9 @@ struct ForwardLegSpaceTag {};
 /// leg space. See @ref ForwardLegSpaceTag and @ref CellSpaceTag.
 struct BackwardLegSpaceTag {};
 
+template <typename Out, typename In>
+class PetscOperator;
+
 /// @brief Bidirectional index mapping between mesh-file stored numbering and PETSc
 ///        row ownership.
 ///
@@ -150,7 +153,10 @@ protected:
 ///
 /// @c mapOwnedInteriorCells iterates only the evolving interior cells (subset 1) and
 /// provides global PETSc row indices, making it suitable for assembling matrices.
-class PetscCellMapping : public PetscIndexMapping {
+///
+/// Inherits from std::enable_shared_from_this so that shared_from_this can be used.
+class PetscCellMapping : public PetscIndexMapping,
+                         std::enable_shared_from_this<PetscCellMapping> {
 public:
   /// @brief Construct the cell-space mapping from mesh metadata fields.
   ///
@@ -274,6 +280,20 @@ public:
     }
   }
 
+  /// @brief Build the Neumann boundary operator N : C → C.
+  ///
+  /// For each cell that has a forward or backward boundary virtual cell,
+  /// copies the adjacent interior cell value into the virtual cell row.
+  /// All other rows are identity. Used to ensure Restrict_minus has non-zero
+  /// rows for boundary cells so that boundary conditions propagate into
+  /// Grad_par and Div_par.
+  ///
+  /// Uses shared_from_this so must only be called on a PetscCellMapping
+  /// that is managed in a shared pointer.
+  ///
+  /// @returns A PetscCellOperator representing the Neumann boundary mapping.
+  PetscOperator<CellSpaceTag, CellSpaceTag> makeNeumannOperator() const;
+
 private:
   Field3D cell_number; ///< Stored cell numbers for interior/X-boundary cells.
   Field3D
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 0fe564bcd3..ff4fe5b893 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -127,6 +127,108 @@ PetscCellMapping::PetscCellMapping(const Field3D& cell_number,
                    local_indices);
 }
 
+PetscOperator<CellSpaceTag, CellSpaceTag> PetscCellMapping::makeNeumannOperator() const {
+
+  // The operator is built using stored indices for both rows and columns,
+  // then post-multiplied by getPetscToStored() to convert columns to PETSc
+  // ordering — exactly the same pattern as assembleFromCSR.
+
+  const PetscInt n_global = this->globalSize();
+  const PetscInt n_local = this->localSize();
+
+  // Temporary matrix in stored-column ordering.
+  // Each row has at most one nonzero (either diagonal or the interior
+  // neighbour), so d_nz=1, o_nz=1 is the correct preallocation.
+  bout::petsc::UniqueMat temp{new Mat{nullptr}};
+  BOUT_DO_PETSC(MatCreate(BoutComm::get(), temp.get()));
+  BOUT_DO_PETSC(MatSetType(*temp, MATMPIAIJ));
+  BOUT_DO_PETSC(MatSetSizes(*temp, n_local, PETSC_DECIDE, n_global, n_global));
+  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(*temp, 1, nullptr, 1, nullptr));
+
+  const PetscScalar one = 1.0;
+
+  // Iterate over all locally owned cells using mapLocalField (interior +
+  // X-boundary) and mapLocalYup / mapLocalYdown (parallel boundary virtual
+  // cells).  For each cell we insert exactly one entry.
+  //
+  // mapLocalField visits cells whose stored index comes from cell_number.
+  // mapLocalYup visits cells whose stored index comes from forward_cell_number.
+  // mapLocalYdown visits cells whose stored index comes from backward_cell_number.
+  //
+  // For a forward boundary virtual cell at field index i.yp():
+  //   row = stored index from forward_cell_number (the virtual cell)
+  //   col = stored index from cell_number at the source cell i
+  //   => virtual cell copies from the adjacent interior cell (Neumann)
+  //
+  // For a backward boundary virtual cell at field index i.ym():
+  //   row = stored index from backward_cell_number (the virtual cell)
+  //   col = stored index from cell_number at the source cell i
+  //
+  // For all other cells the row is the diagonal (identity).
+
+  // Identity rows: all cells in the interior and X-boundary regions
+  mapLocalField([&](PetscInt local_row, const Ind3D& i) {
+    const PetscInt petsc_row = this->rowStart() + local_row;
+    const int stored_col = ROUND(this->cell_number[i]);
+    if (stored_col < 0) {
+      return; // guard cell with no stored index — skip
+    }
+    // stored_col used directly; column translation applied via post-multiply
+    const PetscInt col = static_cast<PetscInt>(stored_col);
+    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+  });
+
+  // Forward boundary virtual cells: copy from adjacent interior cell
+  mapLocalYup([&](PetscInt local_row, const Ind3D& i_yp) {
+    const PetscInt petsc_row = this->rowStart() + local_row;
+    const int stored_row_check = ROUND(this->forward_cell_number[i_yp]);
+    if (stored_row_check < 0) {
+      return;
+    }
+    // The source cell is i_yp.ym() — the interior cell whose forward map
+    // produced this boundary virtual cell.
+    const Ind3D i_src = i_yp.ym();
+    const int stored_col = ROUND(this->cell_number[i_src]);
+    if (stored_col < 0) {
+      return;
+    }
+    const PetscInt col = static_cast<PetscInt>(stored_col);
+    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+  });
+
+  // Backward boundary virtual cells: copy from adjacent interior cell
+  mapLocalYdown([&](PetscInt local_row, const Ind3D& i_ym) {
+    const PetscInt petsc_row = this->rowStart() + local_row;
+    const int stored_row_check = ROUND(this->backward_cell_number[i_ym]);
+    if (stored_row_check < 0) {
+      return;
+    }
+    // The source cell is i_ym.yp() — the interior cell whose backward map
+    // produced this boundary virtual cell.
+    const Ind3D i_src = i_ym.yp();
+    const int stored_col = ROUND(this->cell_number[i_src]);
+    if (stored_col < 0) {
+      return;
+    }
+    const PetscInt col = static_cast<PetscInt>(stored_col);
+    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+  });
+
+  BOUT_DO_PETSC(MatAssemblyBegin(*temp, MAT_FINAL_ASSEMBLY));
+  BOUT_DO_PETSC(MatAssemblyEnd(*temp, MAT_FINAL_ASSEMBLY));
+
+  // Post-multiply by getPetscToStored() to convert stored column indices to
+  // PETSc column indices — identical to the final step in assembleFromCSR.
+  bout::petsc::UniqueMat out{new Mat{nullptr}};
+  BOUT_DO_PETSC(MatMatMult(*temp, this->getPetscToStored(), MAT_INITIAL_MATRIX,
+                           PETSC_DETERMINE, out.get()));
+
+  // Both row and column space are the full cell space C.
+  const auto self =
+      std::static_pointer_cast<const PetscCellMapping>(this->shared_from_this());
+  return PetscOperator<CellSpaceTag, CellSpaceTag>(self, self, std::move(out));
+}
+
 PetscLegMapping::PetscLegMapping(int total_legs, std::vector<int> local_leg_indices) {
   std::sort(local_leg_indices.begin(), local_leg_indices.end());
   local_leg_indices.erase(std::unique(local_leg_indices.begin(), local_leg_indices.end()),

From 7b8025f9e1da56e016d17b94965879e55e59484f Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 12 May 2026 18:13:47 -0700
Subject: [PATCH 1182/1827] makeNeumannOperator: Change to free function

Avoids the need for shared pointer shennanigans.

This fixes issues with Div_par because Div_par now depends on
the Yup/Ydown fields.
---
 include/bout/petsc_operators.hxx |  37 +++---
 src/mesh/petsc_operators.cxx     | 202 +++++++++++++++----------------
 2 files changed, 119 insertions(+), 120 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index ee2656640f..e28daf48cf 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -47,6 +47,11 @@ struct BackwardLegSpaceTag {};
 template <typename Out, typename In>
 class PetscOperator;
 
+class PetscCellMapping;
+
+/// @brief Shared-pointer alias for a const PetscCellMapping.
+using PetscCellMappingPtr = std::shared_ptr<const PetscCellMapping>;
+
 /// @brief Bidirectional index mapping between mesh-file stored numbering and PETSc
 ///        row ownership.
 ///
@@ -280,19 +285,8 @@ public:
     }
   }
 
-  /// @brief Build the Neumann boundary operator N : C → C.
-  ///
-  /// For each cell that has a forward or backward boundary virtual cell,
-  /// copies the adjacent interior cell value into the virtual cell row.
-  /// All other rows are identity. Used to ensure Restrict_minus has non-zero
-  /// rows for boundary cells so that boundary conditions propagate into
-  /// Grad_par and Div_par.
-  ///
-  /// Uses shared_from_this so must only be called on a PetscCellMapping
-  /// that is managed in a shared pointer.
-  ///
-  /// @returns A PetscCellOperator representing the Neumann boundary mapping.
-  PetscOperator<CellSpaceTag, CellSpaceTag> makeNeumannOperator() const;
+  friend PetscOperator<CellSpaceTag, CellSpaceTag>
+  makeNeumannOperator(const PetscCellMappingPtr& mapping);
 
 private:
   Field3D cell_number; ///< Stored cell numbers for interior/X-boundary cells.
@@ -326,9 +320,6 @@ public:
   PetscLegMapping(int total_legs, std::vector<int> local_leg_indices);
 };
 
-/// @brief Shared-pointer alias for a const PetscCellMapping.
-using PetscCellMappingPtr = std::shared_ptr<const PetscCellMapping>;
-
 /// @brief Shared-pointer alias for a const PetscLegMapping.
 using PetscLegMappingPtr = std::shared_ptr<const PetscLegMapping>;
 
@@ -1036,6 +1027,20 @@ private:
   Field3D backward_leg_boundary_number;    ///< Stored boundary leg numbers for L-.
 };
 
+/// @brief Build the Neumann boundary operator N : C → C.
+///
+/// For each cell that has a forward or backward boundary virtual cell,
+/// copies the adjacent interior cell value into the virtual cell row.
+/// All other rows are identity. Used to ensure Restrict_minus has non-zero
+/// rows for boundary cells so that boundary conditions propagate into
+/// Grad_par and Div_par.
+///
+/// Uses shared_from_this so must only be called on a PetscCellMapping
+/// that is managed in a shared pointer.
+///
+/// @returns A PetscCellOperator representing the Neumann boundary mapping.
+PetscCellOperator makeNeumannOperator(const PetscCellMappingPtr& mapping);
+
 #else
 
 #warning PETSc not available. No PetscOperators.
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index ff4fe5b893..d5db6876b1 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -127,108 +127,6 @@ PetscCellMapping::PetscCellMapping(const Field3D& cell_number,
                    local_indices);
 }
 
-PetscOperator<CellSpaceTag, CellSpaceTag> PetscCellMapping::makeNeumannOperator() const {
-
-  // The operator is built using stored indices for both rows and columns,
-  // then post-multiplied by getPetscToStored() to convert columns to PETSc
-  // ordering — exactly the same pattern as assembleFromCSR.
-
-  const PetscInt n_global = this->globalSize();
-  const PetscInt n_local = this->localSize();
-
-  // Temporary matrix in stored-column ordering.
-  // Each row has at most one nonzero (either diagonal or the interior
-  // neighbour), so d_nz=1, o_nz=1 is the correct preallocation.
-  bout::petsc::UniqueMat temp{new Mat{nullptr}};
-  BOUT_DO_PETSC(MatCreate(BoutComm::get(), temp.get()));
-  BOUT_DO_PETSC(MatSetType(*temp, MATMPIAIJ));
-  BOUT_DO_PETSC(MatSetSizes(*temp, n_local, PETSC_DECIDE, n_global, n_global));
-  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(*temp, 1, nullptr, 1, nullptr));
-
-  const PetscScalar one = 1.0;
-
-  // Iterate over all locally owned cells using mapLocalField (interior +
-  // X-boundary) and mapLocalYup / mapLocalYdown (parallel boundary virtual
-  // cells).  For each cell we insert exactly one entry.
-  //
-  // mapLocalField visits cells whose stored index comes from cell_number.
-  // mapLocalYup visits cells whose stored index comes from forward_cell_number.
-  // mapLocalYdown visits cells whose stored index comes from backward_cell_number.
-  //
-  // For a forward boundary virtual cell at field index i.yp():
-  //   row = stored index from forward_cell_number (the virtual cell)
-  //   col = stored index from cell_number at the source cell i
-  //   => virtual cell copies from the adjacent interior cell (Neumann)
-  //
-  // For a backward boundary virtual cell at field index i.ym():
-  //   row = stored index from backward_cell_number (the virtual cell)
-  //   col = stored index from cell_number at the source cell i
-  //
-  // For all other cells the row is the diagonal (identity).
-
-  // Identity rows: all cells in the interior and X-boundary regions
-  mapLocalField([&](PetscInt local_row, const Ind3D& i) {
-    const PetscInt petsc_row = this->rowStart() + local_row;
-    const int stored_col = ROUND(this->cell_number[i]);
-    if (stored_col < 0) {
-      return; // guard cell with no stored index — skip
-    }
-    // stored_col used directly; column translation applied via post-multiply
-    const PetscInt col = static_cast<PetscInt>(stored_col);
-    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
-  });
-
-  // Forward boundary virtual cells: copy from adjacent interior cell
-  mapLocalYup([&](PetscInt local_row, const Ind3D& i_yp) {
-    const PetscInt petsc_row = this->rowStart() + local_row;
-    const int stored_row_check = ROUND(this->forward_cell_number[i_yp]);
-    if (stored_row_check < 0) {
-      return;
-    }
-    // The source cell is i_yp.ym() — the interior cell whose forward map
-    // produced this boundary virtual cell.
-    const Ind3D i_src = i_yp.ym();
-    const int stored_col = ROUND(this->cell_number[i_src]);
-    if (stored_col < 0) {
-      return;
-    }
-    const PetscInt col = static_cast<PetscInt>(stored_col);
-    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
-  });
-
-  // Backward boundary virtual cells: copy from adjacent interior cell
-  mapLocalYdown([&](PetscInt local_row, const Ind3D& i_ym) {
-    const PetscInt petsc_row = this->rowStart() + local_row;
-    const int stored_row_check = ROUND(this->backward_cell_number[i_ym]);
-    if (stored_row_check < 0) {
-      return;
-    }
-    // The source cell is i_ym.yp() — the interior cell whose backward map
-    // produced this boundary virtual cell.
-    const Ind3D i_src = i_ym.yp();
-    const int stored_col = ROUND(this->cell_number[i_src]);
-    if (stored_col < 0) {
-      return;
-    }
-    const PetscInt col = static_cast<PetscInt>(stored_col);
-    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
-  });
-
-  BOUT_DO_PETSC(MatAssemblyBegin(*temp, MAT_FINAL_ASSEMBLY));
-  BOUT_DO_PETSC(MatAssemblyEnd(*temp, MAT_FINAL_ASSEMBLY));
-
-  // Post-multiply by getPetscToStored() to convert stored column indices to
-  // PETSc column indices — identical to the final step in assembleFromCSR.
-  bout::petsc::UniqueMat out{new Mat{nullptr}};
-  BOUT_DO_PETSC(MatMatMult(*temp, this->getPetscToStored(), MAT_INITIAL_MATRIX,
-                           PETSC_DETERMINE, out.get()));
-
-  // Both row and column space are the full cell space C.
-  const auto self =
-      std::static_pointer_cast<const PetscCellMapping>(this->shared_from_this());
-  return PetscOperator<CellSpaceTag, CellSpaceTag>(self, self, std::move(out));
-}
-
 PetscLegMapping::PetscLegMapping(int total_legs, std::vector<int> local_leg_indices) {
   std::sort(local_leg_indices.begin(), local_leg_indices.end());
   local_leg_indices.erase(std::unique(local_leg_indices.begin(), local_leg_indices.end()),
@@ -405,6 +303,9 @@ PetscBackwardLegOperator PetscOperators::diagonal(const PetscBackwardLegVector&
 }
 
 PetscOperators::Parallel PetscOperators::getParallel() const {
+  // Set boundaries
+  const PetscCellOperator& Neumann = makeNeumannOperator(cell_mapping); // C <- C
+
   // Primitive operators from the mesh / metadata
   auto Forward = this->forward();             // L+ <- C
   auto Backward = this->backward();           // L- <- C
@@ -465,8 +366,9 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   auto Grad_minus = Inv_dl_minus * (Inject_minus - Backward); // L- <- C
 
   // Cell-centered central gradient
-  auto Grad_par =
-      ((Restrict_minus * Grad_plus) + (Restrict_plus * Grad_minus)) * 0.5; // C <- C
+  // Apply Neumann so that the yup/ydown cells are set
+  auto Grad_par = Neumann * ((Restrict_minus * Grad_plus) + (Restrict_plus * Grad_minus))
+                  * 0.5; // C <- C
 
   // Leg-centered volumes from unweighted interpolation
   const auto dV_plus = Interp_plus(dV);   // L+
@@ -522,4 +424,96 @@ Field3D PetscOperators::Parallel::Div_par_K_Grad_par(const Field3D& K,
   return (toField3D(div_minus, K) + toField3D(div_plus, K)) * 0.5;
 }
 
+PetscCellOperator makeNeumannOperator(const PetscCellMappingPtr& mapping) {
+
+  // The operator is built using stored indices for both rows and columns,
+  // then post-multiplied by getPetscToStored() to convert columns to PETSc
+  // ordering — exactly the same pattern as assembleFromCSR.
+
+  const PetscInt n_global = mapping->globalSize();
+  const PetscInt n_local = mapping->localSize();
+
+  // Temporary matrix in stored-column ordering.
+  // Each row has at most one nonzero (either diagonal or the interior
+  // neighbour), so d_nz=1, o_nz=1 is the correct preallocation.
+  bout::petsc::UniqueMat temp{new Mat{nullptr}};
+  BOUT_DO_PETSC(MatCreate(BoutComm::get(), temp.get()));
+  BOUT_DO_PETSC(MatSetType(*temp, MATMPIAIJ));
+  BOUT_DO_PETSC(MatSetSizes(*temp, n_local, PETSC_DECIDE, n_global, n_global));
+  BOUT_DO_PETSC(MatMPIAIJSetPreallocation(*temp, 1, nullptr, 1, nullptr));
+
+  const PetscScalar one = 1.0;
+
+  // Iterate over all locally owned cells using mapLocalField (interior +
+  // X-boundary) and mapLocalYup / mapLocalYdown (parallel boundary virtual
+  // cells).  For each cell we insert exactly one entry.
+  //
+  // mapLocalField visits cells whose stored index comes from cell_number.
+  // mapLocalYup visits cells whose stored index comes from forward_cell_number.
+  // mapLocalYdown visits cells whose stored index comes from backward_cell_number.
+  //
+  // For a forward boundary virtual cell at field index i.yp():
+  //   row = stored index from forward_cell_number (the virtual cell)
+  //   col = stored index from cell_number at the source cell i
+  //   => virtual cell copies from the adjacent interior cell (Neumann)
+  //
+  // For a backward boundary virtual cell at field index i.ym():
+  //   row = stored index from backward_cell_number (the virtual cell)
+  //   col = stored index from cell_number at the source cell i
+  //
+  // For all other cells the row is the diagonal (identity).
+
+  // Identity rows: all cells in the interior and X-boundary regions
+  mapping->mapLocalField([&](PetscInt local_row, const Ind3D& i) {
+    const PetscInt petsc_row = mapping->rowStart() + local_row;
+    const int stored_col = ROUND(mapping->cell_number[i]);
+    if (stored_col < 0) {
+      throw BoutException("Check failed: stored_col, mapLocalField");
+    }
+    const PetscInt col = static_cast<PetscInt>(stored_col);
+    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+  });
+
+  mapping->mapLocalYup([&](PetscInt local_row, const Ind3D& i_yp) {
+    const PetscInt petsc_row = mapping->rowStart() + local_row;
+    const Ind3D i_src = i_yp.ym();
+    const int stored_row_check = ROUND(mapping->forward_cell_number[i_src]);
+    if (stored_row_check < 0) {
+      throw BoutException("Check failed: stored_row, mapLocalYup");
+    }
+    const int stored_col = ROUND(mapping->cell_number[i_src]);
+    if (stored_col < 0) {
+      throw BoutException("Check failed: stored_col, mapLocalYup");
+    }
+    const PetscInt col = static_cast<PetscInt>(stored_col);
+    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+  });
+
+  mapping->mapLocalYdown([&](PetscInt local_row, const Ind3D& i_ym) {
+    const PetscInt petsc_row = mapping->rowStart() + local_row;
+    const Ind3D i_src = i_ym.yp();
+    const int stored_row_check = ROUND(mapping->backward_cell_number[i_src]);
+    if (stored_row_check < 0) {
+      throw BoutException("Check failed: stored_row, mapLocalYdown");
+    }
+    const int stored_col = ROUND(mapping->cell_number[i_src]);
+    if (stored_col < 0) {
+      throw BoutException("Check failed: stored_col, mapLocalYdown");
+    }
+    const PetscInt col = static_cast<PetscInt>(stored_col);
+    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+  });
+
+  BOUT_DO_PETSC(MatAssemblyBegin(*temp, MAT_FINAL_ASSEMBLY));
+  BOUT_DO_PETSC(MatAssemblyEnd(*temp, MAT_FINAL_ASSEMBLY));
+
+  // Post-multiply by getPetscToStored() to convert stored column indices to
+  // PETSc column indices — identical to the final step in assembleFromCSR.
+  bout::petsc::UniqueMat out{new Mat{nullptr}};
+  BOUT_DO_PETSC(MatMatMult(*temp, mapping->getPetscToStored(), MAT_INITIAL_MATRIX,
+                           PETSC_DETERMINE, out.get()));
+
+  return PetscCellOperator(mapping, mapping, std::move(out));
+}
+
 #endif

From ec6a132d700b284cb817f2a0872fac46d26db5e5 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 28 Apr 2026 15:53:17 +0100
Subject: [PATCH 1183/1827] Add fail-fast option to run_integrated_tests.sh

 (set -e).
---
 tests/run_integrated_tests.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index 98270f5292..8fb10b3fcb 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+set -e
 
 PROJECT_ROOT="@PROJECT_BINARY_DIR@"
 

From 2f99557f77123f40ef5a832f11a4f101c4681ba4 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 28 Apr 2026 15:58:44 +0100
Subject: [PATCH 1184/1827] Add autouse fixture to call boutpp.finalise()

---
 tests/integrated/test-boutpp/conftest.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
index 8d31c9512b..d1b4470958 100644
--- a/tests/integrated/test-boutpp/conftest.py
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -5,3 +5,9 @@ def unique_xdist_group(request):
     # Unique group per test function (nodeid is unique, e.g., test_file.py::test_func)
     group_name = f"boutpp_isolated_{request.node.nodeid.replace('/', '_').replace('::', '_')}"
     request.node.add_marker(pytest.mark.xdist_group(name=group_name))
+
+@pytest.fixture(autouse=True, scope="function")
+def cleanup_boutpp():
+    yield
+    import boutpp
+    boutpp.finalise()

From 8f139641bdeae0d8d0e41c10272386faa4781b0d Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 28 Apr 2026 16:02:01 +0100
Subject: [PATCH 1185/1827] Fix test_fci_boundary

(remove spurious collect() wrapper).
---
 .../integrated/test-fci-boundary/test_fci_boundary.py  | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/tests/integrated/test-fci-boundary/test_fci_boundary.py b/tests/integrated/test-fci-boundary/test_fci_boundary.py
index 9cce659a15..89906f1e07 100755
--- a/tests/integrated/test-fci-boundary/test_fci_boundary.py
+++ b/tests/integrated/test-fci-boundary/test_fci_boundary.py
@@ -17,16 +17,6 @@
 
 directory = "data"
 
-def collect(var):
-    return _collect(
-        var,
-        info=False,
-        path=directory,
-        xguards=False,
-        yguards=False,
-    )
-
-
 def test_fci_boundary():
 
     nprocs = [1]

From 04c5837d4d2da12f51dc32ac2c05dff13bb72778 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 29 Apr 2026 10:58:04 +0100
Subject: [PATCH 1186/1827] Run pytest verbosely when CI flag is true

---
 tests/run_integrated_tests.sh | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/tests/run_integrated_tests.sh b/tests/run_integrated_tests.sh
index 8fb10b3fcb..276a1ea6e5 100755
--- a/tests/run_integrated_tests.sh
+++ b/tests/run_integrated_tests.sh
@@ -2,12 +2,18 @@
 set -e
 
 PROJECT_ROOT="@PROJECT_BINARY_DIR@"
-
 export PYTHONPATH="@PROJECT_BINARY_DIR@/tools/pylib:@PROJECT_SOURCE_DIR@/tools/pylib:$PYTHONPATH"
 
 # Pre-build the project to prevent concurrent CMake race conditions
 cmake --build "$PROJECT_ROOT"
 
+PYTEST_ARGS=("$@")
+if [ "$CI" == "true" ]; then
+    TEST_FLAGS="-v"
+else
+    TEST_FLAGS="-q"
+fi
+
 # Use the Python executable that CMake discovered during configuration
-"@Python3_EXECUTABLE@" -m pytest -m "not serial" --cache-clear -n auto --dist=loadgroup -q "$PROJECT_ROOT/tests/integrated" "$@"
-"@Python3_EXECUTABLE@" -m pytest -m serial "$PROJECT_ROOT/tests/integrated" "$@"
+"@Python3_EXECUTABLE@" -m pytest -m "not serial" --cache-clear -n auto --dist=loadgroup $TEST_FLAGS "$PROJECT_ROOT/tests/integrated" "${PYTEST_ARGS[@]}"
+"@Python3_EXECUTABLE@" -m pytest -m serial $TEST_FLAGS "$PROJECT_ROOT/tests/integrated" "${PYTEST_ARGS[@]}"

From 0f472188c2bfab0a289f21563cc61f40cb4ba00b Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 7 May 2026 09:30:02 +0100
Subject: [PATCH 1187/1827] Install pytest-xdist in fedora ci script

---
 .ci_fedora.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 3fe2d45d68..0d4db63152 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -37,7 +37,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     cp -a /tmp/BOUT-dev /home/test/
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
-    sudo dnf install -y python3-pytest
+    sudo dnf install -y python3-pytest python3-pytest-xdist
     # OpenMPI Oversubscription Overrides
     export OMPI_MCA_rmaps_base_oversubscribe=1
     export OMPI_MCA_hwloc_base_binding_policy=none

From bbf2d4c7fdddef5d275d89eeb4f7778a3bbc3c66 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 7 May 2026 10:05:53 +0100
Subject: [PATCH 1188/1827] Replace `cleanup_boutpp` fixture with
 `run_isolated`

Relying on `boutpp.finalise()` doesn't work as xdist workers are reused between tests,
so this fixture calls the test via subprocess to ensure isolation.
---
 .../test_boutpp_collect_staggered.py          |  4 +-
 .../collect/test_boutpp_collect.py            |  4 +-
 tests/integrated/test-boutpp/conftest.py      | 49 +++++++++++++++++--
 .../legacy-model/test_boutpp_legacy_model.py  |  4 +-
 .../mms-ddz/test_boutpp_mms_ddz.py            |  5 +-
 .../test-boutpp/print/test_boutpp_print.py    |  4 +-
 .../simple-model/test_boutpp_simple_model.py  |  4 +-
 7 files changed, 62 insertions(+), 12 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index 0810e311c1..f2b9b75823 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -5,7 +5,9 @@
 # requires boutpp
 # requires not make
 
-def test_boutpp_collect_staggered():
+def test_boutpp_collect_staggered(run_isolated):
+
+    run_isolated()
 
     bc.init("-q -q -q")
 
diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index d71aef9a11..2551d333c6 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -7,7 +7,9 @@
 # requires not make
 
 
-def test_boutpp_collect():
+def test_boutpp_collect(run_isolated):
+
+    run_isolated()
 
     bc.init("-d input".split(" "))
 
diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
index d1b4470958..b934555da9 100644
--- a/tests/integrated/test-boutpp/conftest.py
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -1,4 +1,8 @@
 import pytest
+import os
+import sys
+import subprocess
+
 
 @pytest.fixture(autouse=True, scope="function")
 def unique_xdist_group(request):
@@ -6,8 +10,43 @@ def unique_xdist_group(request):
     group_name = f"boutpp_isolated_{request.node.nodeid.replace('/', '_').replace('::', '_')}"
     request.node.add_marker(pytest.mark.xdist_group(name=group_name))
 
-@pytest.fixture(autouse=True, scope="function")
-def cleanup_boutpp():
-    yield
-    import boutpp
-    boutpp.finalise()
+@pytest.fixture(scope="function")
+def run_isolated(request):
+    """
+    Fixture to run a test in a fresh, isolated subprocess.
+    This prevents C++ singleton/MPI conflicts in xdist workers.
+    """
+    # If this variable is set, we are already inside the isolated subprocess
+    if os.environ.get("BOUT_ISOLATED_RUN") == "1":
+        return
+
+    # Get the unique ID of the current test (e.g., path/to/test.py::test_func)
+    nodeid = request.node.nodeid
+
+    # Copy current environment and set the isolation flag
+    env = os.environ.copy()
+    env["BOUT_ISOLATED_RUN"] = "1"
+
+    # Construct the command to run ONLY this specific test
+    # We disable xdist (-p no:xdist) in the subprocess to ensure a clean single-process run
+    cmd = [
+        sys.executable, "-m", "pytest",
+        "-p", "no:xdist",
+        "-c", "/dev/null", # Ignore config to prevent recursive loading if necessary
+        nodeid
+    ]
+
+    result = subprocess.run(cmd, env=env, capture_output=True, text=True)
+
+    if result.returncode != 0:
+        # If the isolated run failed, fail the parent test with the output
+        pytest.fail(
+            f"Isolated test failed with exit code {result.returncode}\n"
+            f"--- STDERR ---\n{result.stderr}\n"
+            f"--- STDOUT ---\n{result.stdout}",
+            pytrace=False
+        )
+
+    # If the subprocess succeeded, we skip the execution of the test body
+    # in the parent (original) xdist worker.
+    pytest.skip("Test successfully completed in isolated subprocess")
diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index 05c9fc3819..f4af812925 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -6,7 +6,9 @@
 # requires not make
 
 
-def test_boutpp_legacy_model():
+def test_boutpp_legacy_model(run_isolated):
+
+    run_isolated()
 
     boutpp.init(sys.argv[1:])
 
diff --git a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
index 03b36d17e8..319e386019 100755
--- a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
+++ b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
@@ -6,7 +6,10 @@
 # requires not make
 
 
-def test_boutpp_mms_ddz():
+def test_boutpp_mms_ddz(run_isolated):
+
+    run_isolated()
+
     errorlist = ""
     boutpp.init("-d data -q -q -q")  # +" -f BOUT.settings")
 
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index 373cde6e83..c2d963ac4c 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -1,7 +1,9 @@
 import subprocess
 
 
-def test_boutpp_print():
+def test_boutpp_print(run_isolated):
+
+    run_isolated()
 
     msg = 'Can we print to the log from python? 🎉 __does_it_still__work {} {:s}'
     cmd = ["python3", "test.py", msg]
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index 94f72309f3..30c378efc8 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -5,8 +5,9 @@
 
 from boutpp import *
 
+def test_boutpp_simple_model(run_isolated):
 
-def test_boutpp_simple_model():
+    run_isolated()
 
     init("-d mini")
 
@@ -18,6 +19,5 @@ def init(self, restart):
         def rhs(self, time):
             self.n.ddt(DDX(self.n))
 
-
     model = MyModel()
     model.solve()

From 82c2ee321940f6ffff2a22c927a51a4a0820803d Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 7 May 2026 10:24:35 +0100
Subject: [PATCH 1189/1827] Fix run_isolated fixture

Isolate boutpp initialization via subprocess fixture

* Enable set -e in the test script to ensure CI correctly reports failures.

* Implement a run_isolated fixture to spawn a fresh process for tests using the boutpp C++ singleton.

* Resolve pytest-xdist worker crashes caused by persistent MPI and library state.
---
 tests/integrated/test-boutpp/conftest.py | 28 +++++++++++++++++-------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
index b934555da9..0da75c6d32 100644
--- a/tests/integrated/test-boutpp/conftest.py
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -23,23 +23,35 @@ def run_isolated(request):
     # Get the unique ID of the current test (e.g., path/to/test.py::test_func)
     nodeid = request.node.nodeid
 
-    # Copy current environment and set the isolation flag
+    # Use the absolute path to the test file to avoid directory resolution issues
+    # fspath is the local path to the test file
+    root_dir = str(request.config.rootpath)
+
     env = os.environ.copy()
     env["BOUT_ISOLATED_RUN"] = "1"
 
-    # Construct the command to run ONLY this specific test
-    # We disable xdist (-p no:xdist) in the subprocess to ensure a clean single-process run
+    # Disable xdist (-p no:xdist) in the subprocess to ensure a clean single-process run
+    # Use -o to disable the cache entirely in the subprocess
+    # Remove -c /dev/null so it stays in the project context
     cmd = [
         sys.executable, "-m", "pytest",
+        nodeid,
+        "--rootdir", root_dir,
         "-p", "no:xdist",
-        "-c", "/dev/null", # Ignore config to prevent recursive loading if necessary
-        nodeid
+        "-o", "cache_dir=/tmp/pytest-cache", # Redirect cache to a writable place
+        "-c", str(request.config.inifile or root_dir) # Point to actual config if it exists
     ]
 
-    result = subprocess.run(cmd, env=env, capture_output=True, text=True)
+    # Run from the same directory as the parent
+    result = subprocess.run(
+        cmd,
+        env=env,
+        cwd=root_dir,
+        capture_output=True,
+        text=True
+    )
 
     if result.returncode != 0:
-        # If the isolated run failed, fail the parent test with the output
         pytest.fail(
             f"Isolated test failed with exit code {result.returncode}\n"
             f"--- STDERR ---\n{result.stderr}\n"
@@ -47,6 +59,6 @@ def run_isolated(request):
             pytrace=False
         )
 
-    # If the subprocess succeeded, we skip the execution of the test body
+    # If the subprocess succeeded, skip the execution of the test body
     # in the parent (original) xdist worker.
     pytest.skip("Test successfully completed in isolated subprocess")

From bd2bd1719dd1fd0ae0df130e20d1ff70f1246875 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 7 May 2026 11:04:13 +0100
Subject: [PATCH 1190/1827] Fix `run_isolated` by returning a no-op function,
 rather than None

---
 tests/integrated/test-boutpp/conftest.py | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
index 0da75c6d32..01785ae61e 100644
--- a/tests/integrated/test-boutpp/conftest.py
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -16,9 +16,13 @@ def run_isolated(request):
     Fixture to run a test in a fresh, isolated subprocess.
     This prevents C++ singleton/MPI conflicts in xdist workers.
     """
-    # If this variable is set, we are already inside the isolated subprocess
+
+    def _do_nothing():
+        pass
+
+    # If we are already in the child process, return the dummy function
     if os.environ.get("BOUT_ISOLATED_RUN") == "1":
-        return
+        return _do_nothing
 
     # Get the unique ID of the current test (e.g., path/to/test.py::test_func)
     nodeid = request.node.nodeid
@@ -42,14 +46,7 @@ def run_isolated(request):
         "-c", str(request.config.inifile or root_dir) # Point to actual config if it exists
     ]
 
-    # Run from the same directory as the parent
-    result = subprocess.run(
-        cmd,
-        env=env,
-        cwd=root_dir,
-        capture_output=True,
-        text=True
-    )
+    result = subprocess.run(cmd, env=env, cwd=root_dir, capture_output=True, text=True)
 
     if result.returncode != 0:
         pytest.fail(
@@ -59,6 +56,5 @@ def run_isolated(request):
             pytrace=False
         )
 
-    # If the subprocess succeeded, skip the execution of the test body
-    # in the parent (original) xdist worker.
+    # In the parent xdist worker, stop here
     pytest.skip("Test successfully completed in isolated subprocess")

From ea877d334324afb2c467e53fc734cb43c7ec7ae6 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 7 May 2026 11:53:05 +0100
Subject: [PATCH 1191/1827] Fix `test_boutpp_legacy_model`

Passing sys.argv[1:] to boutpp.init() caused problems when run in an isolated python process.
---
 .../test-boutpp/legacy-model/test_boutpp_legacy_model.py        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index f4af812925..697a0ebf6f 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -10,7 +10,7 @@ def test_boutpp_legacy_model(run_isolated):
 
     run_isolated()
 
-    boutpp.init(sys.argv[1:])
+    boutpp.init([])
 
     dens = boutpp.create3D("0")
 

From 4e8a2cd4ef0cabcf396eb556cbdca72249154546 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 7 May 2026 13:29:39 +0100
Subject: [PATCH 1192/1827] Fix `run_isolated` fixture

Return a function that evaluates to True in the parent (to abort test execution) and False in the child (to run the actual test).
---
 .../test_boutpp_collect_staggered.py            |  3 ++-
 .../test-boutpp/collect/test_boutpp_collect.py  |  3 ++-
 tests/integrated/test-boutpp/conftest.py        | 17 +++++++----------
 .../legacy-model/test_boutpp_legacy_model.py    |  3 ++-
 .../test-boutpp/mms-ddz/test_boutpp_mms_ddz.py  |  3 ++-
 .../test-boutpp/print/test_boutpp_print.py      |  3 ++-
 .../simple-model/test_boutpp_simple_model.py    |  3 ++-
 7 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index f2b9b75823..2ca7bd3d91 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -7,7 +7,8 @@
 
 def test_boutpp_collect_staggered(run_isolated):
 
-    run_isolated()
+    if run_isolated():
+        return
 
     bc.init("-q -q -q")
 
diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index 2551d333c6..89ad9d6b5b 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -9,7 +9,8 @@
 
 def test_boutpp_collect(run_isolated):
 
-    run_isolated()
+    if run_isolated():
+        return
 
     bc.init("-d input".split(" "))
 
diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
index 01785ae61e..316744d7b8 100644
--- a/tests/integrated/test-boutpp/conftest.py
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -13,18 +13,15 @@ def unique_xdist_group(request):
 @pytest.fixture(scope="function")
 def run_isolated(request):
     """
-    Fixture to run a test in a fresh, isolated subprocess.
+    Spawns a fresh, isolated process for tests.
     This prevents C++ singleton/MPI conflicts in xdist workers.
+    Returns a function that evaluates to True in the parent (to abort test execution)
+    and False in the child (to run the actual test).
     """
-
-    def _do_nothing():
-        pass
-
-    # If we are already in the child process, return the dummy function
     if os.environ.get("BOUT_ISOLATED_RUN") == "1":
-        return _do_nothing
+        return lambda: False
 
-    # Get the unique ID of the current test (e.g., path/to/test.py::test_func)
+    # In the parent process, set up and run the child
     nodeid = request.node.nodeid
 
     # Use the absolute path to the test file to avoid directory resolution issues
@@ -56,5 +53,5 @@ def _do_nothing():
             pytrace=False
         )
 
-    # In the parent xdist worker, stop here
-    pytest.skip("Test successfully completed in isolated subprocess")
+    # Return True so the parent can exit the test cleanly without skipping.
+    return lambda: True
diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index 697a0ebf6f..ba4f5de63e 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -8,7 +8,8 @@
 
 def test_boutpp_legacy_model(run_isolated):
 
-    run_isolated()
+    if run_isolated():
+        return
 
     boutpp.init([])
 
diff --git a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
index 319e386019..23b0d0f173 100755
--- a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
+++ b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
@@ -8,7 +8,8 @@
 
 def test_boutpp_mms_ddz(run_isolated):
 
-    run_isolated()
+    if run_isolated():
+        return
 
     errorlist = ""
     boutpp.init("-d data -q -q -q")  # +" -f BOUT.settings")
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index c2d963ac4c..cef85f58e8 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -3,7 +3,8 @@
 
 def test_boutpp_print(run_isolated):
 
-    run_isolated()
+    if run_isolated():
+        return
 
     msg = 'Can we print to the log from python? 🎉 __does_it_still__work {} {:s}'
     cmd = ["python3", "test.py", msg]
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index 30c378efc8..2eeb7bb931 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -7,7 +7,8 @@
 
 def test_boutpp_simple_model(run_isolated):
 
-    run_isolated()
+    if run_isolated():
+        return
 
     init("-d mini")
 

From c428422d6c531bef30183fee670da637d7b07d46 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 7 May 2026 13:47:55 +0100
Subject: [PATCH 1193/1827] Add `sanitize_openmpi_env` fixture

Fedora CI workflow fails unless openmpi environment variables are cleared between each test.
---
 tests/integrated/test-boutpp/conftest.py | 32 ++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
index 316744d7b8..92e4c6488a 100644
--- a/tests/integrated/test-boutpp/conftest.py
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -55,3 +55,35 @@ def run_isolated(request):
 
     # Return True so the parent can exit the test cleanly without skipping.
     return lambda: True
+
+@pytest.fixture(autouse=True)
+def sanitize_openmpi_env():
+    """
+    OpenMPI leaks state via environment variables (PMIX_*, OPAL_*).
+    This fixture removes them so subprocesses called via `mpirun`
+    don't crash thinking they are already initialized.
+    """
+    # Find all problematic OpenMPI state variables
+    bad_prefixes = ("PMIX_", "OPAL_")
+    bad_exact = (
+        "OMPI_COMM_WORLD_SIZE",
+        "OMPI_COMM_WORLD_RANK",
+        "OMPI_COMM_WORLD_LOCAL_RANK"
+    )
+
+    mpi_vars_to_remove = [
+        k for k in os.environ
+        if k.startswith(bad_prefixes) or k in bad_exact
+    ]
+
+    # Save original variables
+    saved_env = {k: os.environ[k] for k in mpi_vars_to_remove}
+
+    # Delete them from the current environment
+    for k in mpi_vars_to_remove:
+        del os.environ[k]
+
+    yield # Run the test
+
+    # Restore the environment after the test finishes
+    os.environ.update(saved_env)

From a3fdeab538fccb082af6222fa84cbf9a7aaf75d6 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 7 May 2026 15:26:58 +0100
Subject: [PATCH 1194/1827] Fix Fedora CI:

Increase size of /dev/shm partition to 1GB.
---
 .ci_fedora.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 0d4db63152..e7309f4981 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -23,7 +23,7 @@ then
     test . != ".$2" && mpi="$2" || mpi=openmpi
     time $cmd pull ghcr.io/dschwoerer/bout-container-base:ci-fedora
     time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
-	 --shm-size 256M \
+	 --shm-size 1G \
          --name mobydick ghcr.io/dschwoerer/bout-container-base:ci-fedora \
 	     /tmp/BOUT-dev/.ci_fedora.sh $mpi
     time $cmd cp ${TRAVIS_BUILD_DIR:-$(pwd)} mobydick:/tmp/BOUT-dev

From c5e89cf622705dc1f1998fa7a36a7ca00130f571 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 11 May 2026 10:11:50 +0100
Subject: [PATCH 1195/1827] Pass value of `CI` environment variable to Fedora
 script

This is used in `run_integrated_tests.sh` to determine the verbosity level for pytest.
---
 .ci_fedora.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index e7309f4981..391c967114 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -45,6 +45,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     export PRTE_MCA_rmaps_default_mapping_policy=core:OVERSUBSCRIBE
     export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
     export TRAVIS=true
+    export CI=true
     # Try limiting openmp threads
     export FLEXIBLAS=NETLIB
     export MKL_NUM_THREADS=1

From 516c483c2fa9d4a4d0255d0702f85330b385c12c Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 11 May 2026 12:49:09 +0100
Subject: [PATCH 1196/1827] Remove unused imports

---
 tests/integrated/test-backtrace/test_backtrace.py               | 2 +-
 .../test-boutpp/legacy-model/test_boutpp_legacy_model.py        | 1 -
 tests/integrated/test-collect/test_collect.py                   | 2 +-
 tests/integrated/test-invpar/test_invpar.py                     | 1 -
 tests/integrated/test-laplacexy/plotmetrics.py                  | 1 -
 tests/integrated/test-laplacexy/plotresult.py                   | 1 -
 6 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/tests/integrated/test-backtrace/test_backtrace.py b/tests/integrated/test-backtrace/test_backtrace.py
index 92d74fcb7c..20f024592c 100755
--- a/tests/integrated/test-backtrace/test_backtrace.py
+++ b/tests/integrated/test-backtrace/test_backtrace.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-import pytest
+
 # Test enabling/disabling exception backtrace from environment variable
 
 # requires all_tests
diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index ba4f5de63e..6a87f08c15 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
 import boutpp
-import sys
 
 # requires boutpp
 # requires not make
diff --git a/tests/integrated/test-collect/test_collect.py b/tests/integrated/test-collect/test_collect.py
index c3dea7298f..895487ac88 100755
--- a/tests/integrated/test-collect/test_collect.py
+++ b/tests/integrated/test-collect/test_collect.py
@@ -2,7 +2,7 @@
 
 # requires: all_tests
 
-from boututils.run_wrapper import shell, shell_safe
+from boututils.run_wrapper import shell_safe
 
 from boutdata import collect
 import numpy.testing as npt
diff --git a/tests/integrated/test-invpar/test_invpar.py b/tests/integrated/test-invpar/test_invpar.py
index 0b0293ed00..c7fd0fc565 100755
--- a/tests/integrated/test-invpar/test_invpar.py
+++ b/tests/integrated/test-invpar/test_invpar.py
@@ -9,7 +9,6 @@
 # Cores: 4
 
 from boututils.run_wrapper import shell, launch
-from boutdata.collect import collect
 
 
 flags_src = [
diff --git a/tests/integrated/test-laplacexy/plotmetrics.py b/tests/integrated/test-laplacexy/plotmetrics.py
index 3100856679..313fcfda5f 100755
--- a/tests/integrated/test-laplacexy/plotmetrics.py
+++ b/tests/integrated/test-laplacexy/plotmetrics.py
@@ -3,7 +3,6 @@
 from boutdata import collect
 from boututils.datafile import DataFile
 from matplotlib import pyplot
-import numpy
 from sys import exit
 
 # Set default colormap
diff --git a/tests/integrated/test-laplacexy/plotresult.py b/tests/integrated/test-laplacexy/plotresult.py
index ccf48baa55..9b9dfcc44f 100755
--- a/tests/integrated/test-laplacexy/plotresult.py
+++ b/tests/integrated/test-laplacexy/plotresult.py
@@ -3,7 +3,6 @@
 from boutdata import collect
 from boututils.datafile import DataFile
 from matplotlib import pyplot
-import numpy
 from sys import exit
 
 # Set default colormap

From d834f9f190119645929c29025a2001f0cb9703f5 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 11 May 2026 14:28:54 +0100
Subject: [PATCH 1197/1827] Apply prek formatting

---
 .github/workflows/tests.yml                   |  8 ++---
 CMakeLists.txt                                | 20 +++++++-----
 cmake/BOUT++functions.cmake                   | 18 ++++++++---
 tests/conftest.py                             | 18 +++++++----
 .../test-backtrace/test_backtrace.py          |  8 +++--
 .../test_bout_override_default_option.py      |  2 --
 .../test_boutpp_collect_staggered.py          |  4 +--
 tests/integrated/test-boutpp/conftest.py      | 31 ++++++++++++-------
 .../legacy-model/test_boutpp_legacy_model.py  |  2 --
 .../test-boutpp/print/test_boutpp_print.py    |  2 +-
 .../simple-model/test_boutpp_simple_model.py  |  1 +
 .../test-boutpp/slicing/test_slicing.py       |  6 ++--
 tests/integrated/test-collect/test_collect.py |  1 -
 .../test-command-args/test_command_args.py    |  1 +
 .../test_communications.py                    |  6 ++--
 .../test_datafile_facade.py                   |  4 ++-
 .../test-dataformat/test_dataformat.py        |  2 --
 tests/integrated/test-delp2/test_delp2.py     |  2 +-
 .../test_drift_instability.py                 | 14 +++++----
 .../test-fci-boundary/test_fci_boundary.py    | 17 +++++-----
 tests/integrated/test-fci-mpi/test_fci_mpi.py |  3 --
 .../test_fieldgroupComm.py                    |  5 ++-
 .../test-globalfield/test_globalfield.py      |  2 --
 .../test_griddata_yboundary_guards.py         | 10 ++++--
 .../integrated/test-griddata/test_griddata.py |  4 ++-
 tests/integrated/test-initial/test_initial.py | 10 +++---
 .../test-integrate/test_integrate.py          |  2 --
 .../test_interchange_instability.py           | 15 ++++-----
 .../test-interpolate-z/test_interpolate_z.py  | 10 +++---
 .../test_laplace_hypre3d.py                   |  1 +
 .../test_laplace_petsc3d.py                   |  1 +
 tests/integrated/test-laplace/test_laplace.py |  6 +++-
 .../integrated/test-laplace2/test_laplace2.py |  2 --
 .../test-laplacexy-fv/test_laplacexy_fv.py    |  1 +
 .../test-laplacexy/test_laplacexy.py          |  1 +
 .../test_laplacexy2_hypre.py                  |  1 +
 .../test_options_netcdf.py                    |  1 +
 .../test-petsc_laplace/test_petsc_laplace.py  |  2 +-
 .../test-restart-io/test_restart_io.py        |  9 ++++--
 .../test-slepc-solver/test_slepc_solver.py    |  8 +++--
 tests/integrated/test-snb/test_snb.py         |  2 --
 tests/integrated/test-squash/test_squash.py   |  9 ++++--
 .../test_stopCheck_file.py                    |  1 +
 .../test-stopCheck/test_stopCheck.py          |  2 --
 tests/integrated/test-subdir/test_subdir.py   |  2 --
 .../test_twistshift_staggered.py              |  3 +-
 .../test-twistshift/test_twistshift.py        |  7 +++--
 tests/integrated/test-vec/test_vec.py         |  1 +
 .../test_yupdown_weights.py                   |  1 +
 tests/integrated/test-yupdown/test_yupdown.py |  4 +--
 50 files changed, 173 insertions(+), 120 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index cbc32d7c91..92171444e0 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -166,13 +166,13 @@ jobs:
         run: |
           # uv sync automatically creates a .venv and installs the groups
           uv sync --no-dev --group pytest --inexact
-          
+
           # Install the core requirements into the same venv
           uv pip install -r requirements.txt
-          
+
           # Put the venv in the PATH
           echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
-          
+
           # Force CMake to recognize the virtual environment
           echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> $GITHUB_ENV
 
@@ -196,7 +196,7 @@ jobs:
         run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh ${{ matrix.config.build_petsc_branch }}
 
       - name: Build ADIOS2
-        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh 
+        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh
 
       - name: Build BOUT++
         run: |
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0cb88fdfa7..ff7bfc6003 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -766,7 +766,8 @@ if(BOUT_TESTS)
     add_dependencies(check-unit-tests build-check-unit-tests)
   endif()
 
-  add_custom_target(check-integrated-tests
+  add_custom_target(
+    check-integrated-tests
     COMMAND bash "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh"
   )
   add_dependencies(check-integrated-tests build-check-integrated-tests)
@@ -784,23 +785,26 @@ if(BOUT_TESTS)
   # Copy the pytest config file
   configure_file(
     "${PROJECT_SOURCE_DIR}/tests/conftest.py"
-    "${PROJECT_BINARY_DIR}/tests/conftest.py")
+    "${PROJECT_BINARY_DIR}/tests/conftest.py"
+  )
 
   # Copy the pyproject.toml file
   configure_file(
     "${PROJECT_SOURCE_DIR}/pyproject.toml"
-    "${PROJECT_BINARY_DIR}/pyproject.toml")
+    "${PROJECT_BINARY_DIR}/pyproject.toml"
+  )
 
   # Copy the pytest config file for the boutpp tests
   configure_file(
     "${PROJECT_SOURCE_DIR}/tests/integrated/test-boutpp/conftest.py"
-    "${PROJECT_BINARY_DIR}/tests/integrated/test-boutpp/conftest.py")
+    "${PROJECT_BINARY_DIR}/tests/integrated/test-boutpp/conftest.py"
+  )
 
   # Copy the pytest shell script
-configure_file(
-  "${PROJECT_SOURCE_DIR}/tests/run_integrated_tests.sh"
-  "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh"
-  @ONLY)
+  configure_file(
+    "${PROJECT_SOURCE_DIR}/tests/run_integrated_tests.sh"
+    "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh" @ONLY
+  )
 
 endif()
 
diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index 88687e39d7..5a00997033 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -172,7 +172,9 @@ endfunction()
 #
 function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
   set(options USE_RUNTEST USE_DATA_BOUT_INP)
-  set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME PYTHON_TEST_FILE)
+  set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME
+                   PYTHON_TEST_FILE
+  )
   set(multiValueArgs SOURCES EXTRA_FILES REQUIRES CONFLICTS TESTARGS
                      EXTRA_DEPENDS
   )
@@ -256,7 +258,10 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
   if(BOUT_TEST_OPTIONS_USE_RUNTEST)
     if(BOUT_TEST_OPTIONS_PYTHON_TEST_FILE)
       # It's an integrated test with a specific python file
-      add_test(NAME ${TESTNAME} COMMAND pytest ${BOUT_TEST_OPTIONS_PYTHON_TEST_FILE} ${BOUT_TEST_OPTIONS_TESTARGS})
+      add_test(NAME ${TESTNAME}
+               COMMAND pytest ${BOUT_TEST_OPTIONS_PYTHON_TEST_FILE}
+                       ${BOUT_TEST_OPTIONS_TESTARGS}
+      )
     else()
       # It's an MMS test still using the 'runtest' script
       add_test(NAME ${TESTNAME} COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS})
@@ -270,7 +275,7 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()
 
-  if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest)
+  if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest)
     bout_copy_file(runtest)
   endif()
 
@@ -295,12 +300,15 @@ endfunction()
 # Add a new integrated test. See `bout_add_integrated_or_mms_test` for arguments
 function(bout_add_integrated_test TESTNAME)
   # Construct the Python test filename
-  string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME "${TESTNAME}")
+  string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME
+                       "${TESTNAME}"
+  )
   string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
   string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
 
   bout_add_integrated_or_mms_test(
-    build-check-integrated-tests ${TESTNAME} PYTHON_TEST_FILE ${TEST_FILENAME} ${ARGV}
+    build-check-integrated-tests ${TESTNAME} PYTHON_TEST_FILE ${TEST_FILENAME}
+    ${ARGV}
   )
 
   # Only copy the file if the test wasn't skipped due to missing requirements
diff --git a/tests/conftest.py b/tests/conftest.py
index eac2d3bacf..f04f85e562 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -6,16 +6,18 @@
 from pathlib import Path
 
 
-
 def pytest_configure(config):
     config.addinivalue_line(
-        "markers", "serial: mark that the test should not be run concurrently with other. "
+        "markers",
+        "serial: mark that the test should not be run concurrently with other. ",
     )
 
+
 @pytest.fixture
 def test_dir(request) -> Path:
     return Path(request.fspath).parent
 
+
 @pytest.fixture(scope="function", autouse=True)
 def copy_and_cwd_to_unique_tmp_dir(request, tmp_path_factory, monkeypatch):
     """
@@ -45,10 +47,14 @@ def inner_function(command: str):
         # MPI oversubscribe for communications test
         os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
         start = time.time()
-        result = subprocess.run(command, shell=True, capture_output=True, text=True, timeout=600)
+        result = subprocess.run(
+            command, shell=True, capture_output=True, text=True, timeout=600
+        )
         elapsed = time.time() - start
-        assert result.returncode == 0, (f"Failed after {elapsed:.3f}s in {test_dir}\n"
-                                        f"Stderr: {result.stderr}\n"
-                                        f"Output: {result.stdout}")
+        assert result.returncode == 0, (
+            f"Failed after {elapsed:.3f}s in {test_dir}\n"
+            f"Stderr: {result.stderr}\n"
+            f"Output: {result.stdout}"
+        )
 
     return inner_function
diff --git a/tests/integrated/test-backtrace/test_backtrace.py b/tests/integrated/test-backtrace/test_backtrace.py
index 20f024592c..4572010c62 100755
--- a/tests/integrated/test-backtrace/test_backtrace.py
+++ b/tests/integrated/test-backtrace/test_backtrace.py
@@ -16,8 +16,12 @@ def test_backtrace():
 
     _, output = shell(["BOUT_SHOW_BACKTRACE=0 ./boutexcept"], pipe=True)
 
-    assert "troublemaker" not in output, f"Fail: detected offending function name in output when not expected\n{output}"
+    assert "troublemaker" not in output, (
+        f"Fail: detected offending function name in output when not expected\n{output}"
+    )
 
     _, output = shell(["./boutexcept"], pipe=True)
 
-    assert "troublemaker" in output, f"Fail: did not detect offending function name in output when expected\n{output}"
+    assert "troublemaker" in output, (
+        f"Fail: did not detect offending function name in output when expected\n{output}"
+    )
diff --git a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
index 48a29195e0..1095b40a70 100644
--- a/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
+++ b/tests/integrated/test-bout-override-default-option/test_bout_override_default_option.py
@@ -1,4 +1,2 @@
-
-
 def test_runtest(assert_success_in_shell):
     assert_success_in_shell("./runtest")
diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index 2ca7bd3d91..d88595e434 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -5,6 +5,7 @@
 # requires boutpp
 # requires not make
 
+
 def test_boutpp_collect_staggered(run_isolated):
 
     if run_isolated():
@@ -20,7 +21,6 @@ def test_boutpp_collect_staggered(run_isolated):
     dump["f3d_once"] = f
     bc.writeDefaultOutputFile(dump)
 
-
     fc = bc.create3D("sin(y)", outloc="CENTRE")
 
     fe = bc.Field3D.fromCollect("f3d_evolve", path="data", info=False)
@@ -34,13 +34,11 @@ def test_boutpp_collect_staggered(run_isolated):
         print("The loaded field should not be at CELL_CENTRE")
         fail = 1
 
-
     def compare(a, b):
         diff = a - bc.interp_to(b, a.getLocation())
         err = bc.max(bc.sqrt(diff * diff))
         return err
 
-
     if compare(fc, f) > 1e-3:
         print("Something is wrong. Maybe interpolation is broken")
         fail = 1
diff --git a/tests/integrated/test-boutpp/conftest.py b/tests/integrated/test-boutpp/conftest.py
index 92e4c6488a..09631a1fe6 100644
--- a/tests/integrated/test-boutpp/conftest.py
+++ b/tests/integrated/test-boutpp/conftest.py
@@ -7,9 +7,12 @@
 @pytest.fixture(autouse=True, scope="function")
 def unique_xdist_group(request):
     # Unique group per test function (nodeid is unique, e.g., test_file.py::test_func)
-    group_name = f"boutpp_isolated_{request.node.nodeid.replace('/', '_').replace('::', '_')}"
+    group_name = (
+        f"boutpp_isolated_{request.node.nodeid.replace('/', '_').replace('::', '_')}"
+    )
     request.node.add_marker(pytest.mark.xdist_group(name=group_name))
 
+
 @pytest.fixture(scope="function")
 def run_isolated(request):
     """
@@ -35,12 +38,18 @@ def run_isolated(request):
     # Use -o to disable the cache entirely in the subprocess
     # Remove -c /dev/null so it stays in the project context
     cmd = [
-        sys.executable, "-m", "pytest",
+        sys.executable,
+        "-m",
+        "pytest",
         nodeid,
-        "--rootdir", root_dir,
-        "-p", "no:xdist",
-        "-o", "cache_dir=/tmp/pytest-cache", # Redirect cache to a writable place
-        "-c", str(request.config.inifile or root_dir) # Point to actual config if it exists
+        "--rootdir",
+        root_dir,
+        "-p",
+        "no:xdist",
+        "-o",
+        "cache_dir=/tmp/pytest-cache",  # Redirect cache to a writable place
+        "-c",
+        str(request.config.inifile or root_dir),  # Point to actual config if it exists
     ]
 
     result = subprocess.run(cmd, env=env, cwd=root_dir, capture_output=True, text=True)
@@ -50,12 +59,13 @@ def run_isolated(request):
             f"Isolated test failed with exit code {result.returncode}\n"
             f"--- STDERR ---\n{result.stderr}\n"
             f"--- STDOUT ---\n{result.stdout}",
-            pytrace=False
+            pytrace=False,
         )
 
     # Return True so the parent can exit the test cleanly without skipping.
     return lambda: True
 
+
 @pytest.fixture(autouse=True)
 def sanitize_openmpi_env():
     """
@@ -68,12 +78,11 @@ def sanitize_openmpi_env():
     bad_exact = (
         "OMPI_COMM_WORLD_SIZE",
         "OMPI_COMM_WORLD_RANK",
-        "OMPI_COMM_WORLD_LOCAL_RANK"
+        "OMPI_COMM_WORLD_LOCAL_RANK",
     )
 
     mpi_vars_to_remove = [
-        k for k in os.environ
-        if k.startswith(bad_prefixes) or k in bad_exact
+        k for k in os.environ if k.startswith(bad_prefixes) or k in bad_exact
     ]
 
     # Save original variables
@@ -83,7 +92,7 @@ def sanitize_openmpi_env():
     for k in mpi_vars_to_remove:
         del os.environ[k]
 
-    yield # Run the test
+    yield  # Run the test
 
     # Restore the environment after the test finishes
     os.environ.update(saved_env)
diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index 6a87f08c15..d1f6ea736a 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -14,13 +14,11 @@ def test_boutpp_legacy_model(run_isolated):
 
     dens = boutpp.create3D("0")
 
-
     def rhs(time):
         n_ddt = dens.ddt()
         n_ddt[:, :, :] = dens * 0
         n_ddt += 1
 
-
     model = boutpp.PhysicsModelBase()
     model.setRhs(rhs)
     model.solve_for(n=dens)
diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index cef85f58e8..26934a0080 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -6,7 +6,7 @@ def test_boutpp_print(run_isolated):
     if run_isolated():
         return
 
-    msg = 'Can we print to the log from python? 🎉 __does_it_still__work {} {:s}'
+    msg = "Can we print to the log from python? 🎉 __does_it_still__work {} {:s}"
     cmd = ["python3", "test.py", msg]
 
     print(f"+ python3 test.py {msg} > out.log")
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index 2eeb7bb931..7744b514f5 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -5,6 +5,7 @@
 
 from boutpp import *
 
+
 def test_boutpp_simple_model(run_isolated):
 
     if run_isolated():
diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py
index 41c332968f..cffc767bf8 100755
--- a/tests/integrated/test-boutpp/slicing/test_slicing.py
+++ b/tests/integrated/test-boutpp/slicing/test_slicing.py
@@ -6,6 +6,7 @@
 import boutpp as bc
 import inspect
 
+
 def test_slicing():
 
     bc.init("-d test")
@@ -47,6 +48,7 @@ def test_slicing():
         nout = ex(ndat)
         fout = ex(field)
         npt.assert_allclose(
-            fout, nout,
-            err_msg=f"data mismatch, {{ fout == nout }}. Failed to test {inspect.getsource(ex)}"
+            fout,
+            nout,
+            err_msg=f"data mismatch, {{ fout == nout }}. Failed to test {inspect.getsource(ex)}",
         )
diff --git a/tests/integrated/test-collect/test_collect.py b/tests/integrated/test-collect/test_collect.py
index 895487ac88..eade57557a 100755
--- a/tests/integrated/test-collect/test_collect.py
+++ b/tests/integrated/test-collect/test_collect.py
@@ -10,7 +10,6 @@
 
 def test_collect():
 
-
     shell_safe("./test-collect")
 
     # Try collecting data using incorrect case
diff --git a/tests/integrated/test-command-args/test_command_args.py b/tests/integrated/test-command-args/test_command_args.py
index ff58195276..c8f786ef4f 100755
--- a/tests/integrated/test-command-args/test_command_args.py
+++ b/tests/integrated/test-command-args/test_command_args.py
@@ -10,6 +10,7 @@
 
 OUTPUT_FILE = Path("stdout.log") if platform.system() == "FreeBSD" else "stderr.log"
 
+
 class TestCommandLineArgs(unittest.TestCase):
     command = "./command-args >stdout.log 2>stderr.log"
 
diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index aef616483f..75150ccde1 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -14,9 +14,10 @@
 
 def run_test(actual, expected, procnum, region, boundary):
     npt.assert_allclose(
-        np.array(np.rint(actual).astype(int)), np.array(expected),
+        np.array(np.rint(actual).astype(int)),
+        np.array(expected),
         err_msg=f"failed in {boundary} boundary of region {procnum} ({region}). "
-                f"Expected: {expected}  Actual: {actual}"
+        f"Expected: {expected}  Actual: {actual}",
     )
 
 
@@ -331,7 +332,6 @@ def test_communications():
     run_test(f[:, 0], [73, 1, 13, 33, 45, 57, 69, 93], 0, region, "lower y")
     run_test(f[:, -1], [104, 105, 106, 107, 108, 109, 110, 111], 0, region, "upper y")
 
-
     #################################################
     # Test limiter topology
     #################################################
diff --git a/tests/integrated/test-datafilefacade/test_datafile_facade.py b/tests/integrated/test-datafilefacade/test_datafile_facade.py
index f4f4469c40..01860765c9 100755
--- a/tests/integrated/test-datafilefacade/test_datafile_facade.py
+++ b/tests/integrated/test-datafilefacade/test_datafile_facade.py
@@ -69,6 +69,8 @@ def test_datafile_facade():
         print("=> All DataFileFacade tests passed")
         # clean up binary files
         shell(
-            ["rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc"]
+            [
+                "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc"
+            ]
         )
     assert success, f"=> Some failed tests"
diff --git a/tests/integrated/test-dataformat/test_dataformat.py b/tests/integrated/test-dataformat/test_dataformat.py
index 523ae00fc1..b11460b2f8 100644
--- a/tests/integrated/test-dataformat/test_dataformat.py
+++ b/tests/integrated/test-dataformat/test_dataformat.py
@@ -1,4 +1,2 @@
-
-
 def test_runtest(assert_success_in_shell):
     assert_success_in_shell("./test_dataformat")
diff --git a/tests/integrated/test-delp2/test_delp2.py b/tests/integrated/test-delp2/test_delp2.py
index 703286e6fc..529de55793 100755
--- a/tests/integrated/test-delp2/test_delp2.py
+++ b/tests/integrated/test-delp2/test_delp2.py
@@ -31,7 +31,7 @@ def test_delp2(setting):
     cmd = exefile + " " + setting
 
     s, out = launch_safe(cmd, nproc=1, pipe=True)
-    file_suffix = '.'.join([x.split('=')[-1] for x in setting.split()])
+    file_suffix = ".".join([x.split("=")[-1] for x in setting.split()])
     with open("run.log." + str(file_suffix) + ".1", "w") as f:
         f.write(out)
 
diff --git a/tests/integrated/test-drift-instability/test_drift_instability.py b/tests/integrated/test-drift-instability/test_drift_instability.py
index 4f2b402dd9..34b91b369d 100644
--- a/tests/integrated/test-drift-instability/test_drift_instability.py
+++ b/tests/integrated/test-drift-instability/test_drift_instability.py
@@ -99,7 +99,7 @@ def run_zeff_case(zeff):
     # Calculate geometric and physical quantities
     lZeta = 1e2 * zmax * 2 * np.pi * grid["R0"]  # toroidal range [cm]
     lbNorm = lZeta * (
-            grid["Bpxy"][0, ny // 2] / grid["Bxy"][0, ny // 2]
+        grid["Bpxy"][0, ny // 2] / grid["Bxy"][0, ny // 2]
     )  # binormal coord range [cm]
 
     vTe = 4.2e7 * np.sqrt(grid["Te_x"])  # electron thermal speed [cm/s]
@@ -122,7 +122,7 @@ def run_zeff_case(zeff):
     # wci=9.58e3*(1./d.AA)*1e4*du.Bmag
 
     lpar = (
-            np.sum(((grid["Bxy"] / grid["Bpxy"])) * grid["dlthe"]) / grid["nx"]
+        np.sum((grid["Bxy"] / grid["Bpxy"]) * grid["dlthe"]) / grid["nx"]
     )  # [m], average over flux surfaces
     kpar = 2 * np.pi / (1e2 * lpar)  # cm-1
     spar = (kpar / kperp) ** 2 * wci * wce / (0.51 * nuei)  # [1/s]
@@ -155,12 +155,12 @@ def run_zeff_case(zeff):
         # Increasing; watch for wrapping around the top
         for i in range(nt - nt0):
             if peak[i] < peak[i - 1]:
-                peak[i: (nt - nt0)] = peak[i: (nt - nt0)] + nz
+                peak[i : (nt - nt0)] = peak[i : (nt - nt0)] + nz
     else:
         # Decreasing; watch for wrapping around the bottom
         for i in range(nt - nt0):
             if peak[i] > peak[i - 1]:
-                peak[i: (nt - nt0)] = peak[i: (nt - nt0)] - nz
+                peak[i : (nt - nt0)] = peak[i : (nt - nt0)] - nz
 
     # Fit y = a + gamma*x
     a, gamma = linear_regression(t_array[nt0:nt] / wci, np.log(maxVal))
@@ -173,7 +173,7 @@ def run_zeff_case(zeff):
     gamma = gamma / wstar
 
     # Calculate analytic result
-    t = 0.5 * (np.sqrt(sparn ** 4 + 16 * sparn ** 2) - sparn ** 2)
+    t = 0.5 * (np.sqrt(sparn**4 + 16 * sparn**2) - sparn**2)
     wr = 0.5 * np.sqrt(t)
     wi = sparn / np.sqrt(t) - 0.5 * sparn
 
@@ -201,4 +201,6 @@ def test_zeff_case(zeff):
     """Pytest wrapper for running a single Zeff case."""
     success, omegadiff, gammadiff = run_zeff_case(zeff)
 
-    assert success, f"Test failed for Zeff={zeff}: omega diff={omegadiff:.2%}, gamma diff={gammadiff:.2%}"
+    assert success, (
+        f"Test failed for Zeff={zeff}: omega diff={omegadiff:.2%}, gamma diff={gammadiff:.2%}"
+    )
diff --git a/tests/integrated/test-fci-boundary/test_fci_boundary.py b/tests/integrated/test-fci-boundary/test_fci_boundary.py
index 89906f1e07..eb6d19a914 100755
--- a/tests/integrated/test-fci-boundary/test_fci_boundary.py
+++ b/tests/integrated/test-fci-boundary/test_fci_boundary.py
@@ -13,10 +13,14 @@
 
 
 if not os.path.exists(os.path.join(os.path.dirname(__file__), "grid.fci.nc")):
-    pytest.skip("grid.fci.nc not found (Zoidberg likely missing), skipping test.", allow_module_level=True)
+    pytest.skip(
+        "grid.fci.nc not found (Zoidberg likely missing), skipping test.",
+        allow_module_level=True,
+    )
 
 directory = "data"
 
+
 def test_fci_boundary():
 
     nprocs = [1]
@@ -55,9 +59,8 @@ def test_fci_boundary():
                 xguards=False,
                 yguards=False,
             )
-            npt.assert_allclose(data, v,
-                                err_msg=(f"{k} does not match",
-                                         np.sum(data),
-                                         np.sum(v),
-                                         np.max(data))
-                                )
+            npt.assert_allclose(
+                data,
+                v,
+                err_msg=(f"{k} does not match", np.sum(data), np.sum(v), np.max(data)),
+            )
diff --git a/tests/integrated/test-fci-mpi/test_fci_mpi.py b/tests/integrated/test-fci-mpi/test_fci_mpi.py
index f34f2673bc..a28c9c2256 100755
--- a/tests/integrated/test-fci-mpi/test_fci_mpi.py
+++ b/tests/integrated/test-fci-mpi/test_fci_mpi.py
@@ -29,7 +29,6 @@ def run_case(nxpe: int, nype: int, mthread: int):
         with open(f"run.log.{nxpe}.{nype}.{nslice}.log", "w") as f:
             f.write(out)
 
-
     def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
         run_case(nxpe, nype, mthread)
 
@@ -43,7 +42,6 @@ def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
 
         return failures
 
-
     failures = []
 
     for nslice in NSLICES:
@@ -69,7 +67,6 @@ def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
             failures_ = test_case(nxpe, nype, mthread, ref)
             failures.extend(failures_)
 
-
     success = len(failures) == 0
 
     assert success, "\nSome tests failed:"
diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
index 9747e546b4..e06ebab7a4 100755
--- a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
+++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
@@ -21,6 +21,7 @@
 from boutdata.collect import collect
 from numpy import abs, seterr
 
+
 def test_fieldgroupcomm():
 
     # Good chance we'll do 0.0/0.0, which generates a warning
@@ -62,7 +63,9 @@ def test_fieldgroupcomm():
 
         for i, e in enumerate(err):
             if e > tol:
-                print("Fail, in {i}th comparison relative error is {re}".format(i=i, re=e))
+                print(
+                    "Fail, in {i}th comparison relative error is {re}".format(i=i, re=e)
+                )
                 success = False
 
     assert success, " => Some failed tests"
diff --git a/tests/integrated/test-globalfield/test_globalfield.py b/tests/integrated/test-globalfield/test_globalfield.py
index adfcc39590..ac2d993dd4 100755
--- a/tests/integrated/test-globalfield/test_globalfield.py
+++ b/tests/integrated/test-globalfield/test_globalfield.py
@@ -1,4 +1,2 @@
-
-
 def test_runtest(assert_success_in_shell):
     assert_success_in_shell("./test_globalfield")
diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
index 44b32f40fd..9666a2f762 100755
--- a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
+++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
@@ -10,6 +10,7 @@
 # Cores: 6
 # Requires: netcdf
 
+
 def test_griddata_yboundary_guards():
 
     nx = 4
@@ -119,7 +120,6 @@ def test_griddata_yboundary_guards():
             gridfile.createVariable("test", float, ("x", "y"))
             gridfile["test"][...] = testdata
 
-
     for nproc in [6]:
         stdout.write("Checking %d processors ... " % (nproc))
 
@@ -131,7 +131,9 @@ def test_griddata_yboundary_guards():
         for n_yguards in [0, 1, 2]:
             datadir = "data-doublenull-" + str(n_yguards)
 
-            s, out = launch_safe("./test_griddata -d " + datadir, nproc=nproc, pipe=True)
+            s, out = launch_safe(
+                "./test_griddata -d " + datadir, nproc=nproc, pipe=True
+            )
 
             with open("run.log.doublenull." + str(nproc), "a") as f:
                 f.write(out)
@@ -167,7 +169,9 @@ def test_griddata_yboundary_guards():
         for n_yguards in [0, 1, 2]:
             datadir = "data-singlenull-" + str(n_yguards)
 
-            s, out = launch_safe("./test_griddata -d " + datadir, nproc=nproc, pipe=True)
+            s, out = launch_safe(
+                "./test_griddata -d " + datadir, nproc=nproc, pipe=True
+            )
 
             with open("run.log.singlenull." + str(nproc), "a") as f:
                 f.write(out)
diff --git a/tests/integrated/test-griddata/test_griddata.py b/tests/integrated/test-griddata/test_griddata.py
index 8eb3aa22f9..ad3b7f2a08 100755
--- a/tests/integrated/test-griddata/test_griddata.py
+++ b/tests/integrated/test-griddata/test_griddata.py
@@ -39,6 +39,8 @@ def test_griddata():
         dr = float(rwidth) / nx
 
         # Test value of dx
-        npt.assert_allclose(dx, dr * Bpxy * Rxy, atol=1e-7, err_msg="Failed: dx does not match")
+        npt.assert_allclose(
+            dx, dr * Bpxy * Rxy, atol=1e-7, err_msg="Failed: dx does not match"
+        )
 
         print("Passed")
diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index 504c72d4f4..cbdca014e5 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -64,7 +64,7 @@ def gauss(x, width=1.0):
     """
     Normalised gaussian
     """
-    return np.exp(-(x ** 2) / (2 * width ** 2)) / np.sqrt(2 * np.pi)
+    return np.exp(-(x**2) / (2 * width**2)) / np.sqrt(2 * np.pi)
 
 
 def mixmode(x, seed=0.5):
@@ -90,8 +90,8 @@ def tanhhat(x, width, centre, steepness):
     BOUT++ TanhHat function
     """
     return 0.5 * (
-            np.tanh(steepness * (x - (centre - width / 2.0)))
-            + np.tanh(-steepness * (x - (centre + width / 2.0)))
+        np.tanh(steepness * (x - (centre - width / 2.0)))
+        + np.tanh(-steepness * (x - (centre + width / 2.0)))
     )
 
 
@@ -207,7 +207,9 @@ def test_initial():
             except NotImplementedError as err:
                 print("{} not implemented, skipping".format(err.args[0]))
             else:
-                data = collect(var, xguards=True, yguards=True, path=datadir, info=False)
+                data = collect(
+                    var, xguards=True, yguards=True, path=datadir, info=False
+                )
                 E2 = np.sqrt(np.mean((analytic - data) ** 2))
                 if E2 < tolerance:
                     success_string = "PASS"
diff --git a/tests/integrated/test-integrate/test_integrate.py b/tests/integrated/test-integrate/test_integrate.py
index 91a273f451..d8b4073b66 100755
--- a/tests/integrated/test-integrate/test_integrate.py
+++ b/tests/integrated/test-integrate/test_integrate.py
@@ -1,4 +1,2 @@
-
-
 def test_runtest(assert_success_in_shell):
     assert_success_in_shell("./test_integrate")
diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index 4ea71815da..63dba4042b 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -20,13 +20,13 @@
 
 nthreads = 1
 
+
 def test_interchange_instability():
 
     # Delete old output files
     shell("rm data_1/BOUT.dmp.*")
     shell("rm data_10/BOUT.dmp.*")
 
-
     def growth_rate(path, nproc, log=False):
         pipe = False
         if log != False:
@@ -58,17 +58,16 @@ def growth_rate(path, nproc, log=False):
             6.0 * (tarr[nt - 2] - tarr[nt - 4])
         )
 
-
     # Run case 2
 
     print("Test case 1: R = 1m")
     growth = growth_rate("data_1", nproc, log="run_1.log")
     print("   Log file run_1.log")
-    orig = (
-        2.148177e05  # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f
-    )
+    orig = 2.148177e05  # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f
     analytic = 2.2e5
-    print("   Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic))
+    print(
+        "   Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic)
+    )
     absdev = abs(growth - orig)
     reldev = absdev / orig
     print("   Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0))
@@ -83,7 +82,9 @@ def growth_rate(path, nproc, log=False):
     # orig = 65570. # 24th October 2011, revision c4f7ec92786b333a5502c5256b5e602ba867090f
     orig = 6.457835e04  # 25th April 2014, revision fd032da
     analytic = 6.3e4
-    print("   Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic))
+    print(
+        "   Growth-rate = %e, original = %e, analytic = %e" % (growth, orig, analytic)
+    )
     absdev = abs(growth - orig)
     reldev = absdev / orig
     print("   Deviation from original: %e (%e %%)" % (absdev, reldev * 100.0))
diff --git a/tests/integrated/test-interpolate-z/test_interpolate_z.py b/tests/integrated/test-interpolate-z/test_interpolate_z.py
index b878d4a044..7fdc02ea1b 100755
--- a/tests/integrated/test-interpolate-z/test_interpolate_z.py
+++ b/tests/integrated/test-interpolate-z/test_interpolate_z.py
@@ -46,10 +46,8 @@ def test_interpolate_z():
         for nx in nxlist:
             dx = 1.0 / (nx)
 
-            args = (
-                " mesh:nx={nx4} mesh:dx={dx} MZ={nx} zinterpolation:type={method}".format(
-                    nx4=nx + 4, dx=dx, nx=nx, method=method
-                )
+            args = " mesh:nx={nx4} mesh:dx={dx} MZ={nx} zinterpolation:type={method}".format(
+                nx4=nx + 4, dx=dx, nx=nx, method=method
             )
 
             cmd = "./test_interpolate" + args
@@ -62,7 +60,9 @@ def test_interpolate_z():
 
             # Collect output data
             for var in varlist:
-                interp = collect(var + "_interp", path="data", xguards=False, info=False)
+                interp = collect(
+                    var + "_interp", path="data", xguards=False, info=False
+                )
                 solution = collect(
                     var + "_solution", path="data", xguards=False, info=False
                 )
diff --git a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
index 0886ea037d..6c5f87dc24 100755
--- a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
+++ b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
@@ -14,6 +14,7 @@
 
 tolerance = 1.0e-6
 
+
 def test_laplace_hypre3d():
 
     success = True
diff --git a/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
index 9139674513..3a255d48a7 100755
--- a/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
+++ b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
@@ -15,6 +15,7 @@
 
 tolerance = 1.0e-6
 
+
 def test_laplace_petsc3d():
 
     errors = {}
diff --git a/tests/integrated/test-laplace/test_laplace.py b/tests/integrated/test-laplace/test_laplace.py
index 2fc7b145f4..1b0d912798 100755
--- a/tests/integrated/test-laplace/test_laplace.py
+++ b/tests/integrated/test-laplace/test_laplace.py
@@ -34,6 +34,7 @@
 ]
 tol = 1e-6  # Absolute tolerance
 
+
 def test_laplace():
 
     # Read benchmark values
@@ -81,7 +82,10 @@ def test_laplace():
                     # Compare benchmark and output
                     try:
                         npt.assert_allclose(
-                            result, bmk[v.replace("_perp", "")][:, 0, :], atol=tol, rtol=tol
+                            result,
+                            bmk[v.replace("_perp", "")][:, 0, :],
+                            atol=tol,
+                            rtol=tol,
                         )
                         print("Pass")
                     except AssertionError as e:
diff --git a/tests/integrated/test-laplace2/test_laplace2.py b/tests/integrated/test-laplace2/test_laplace2.py
index e2b4a802a6..2c5a409aeb 100755
--- a/tests/integrated/test-laplace2/test_laplace2.py
+++ b/tests/integrated/test-laplace2/test_laplace2.py
@@ -1,4 +1,2 @@
-
-
 def test_runtest(assert_success_in_shell):
     assert_success_in_shell("./test_laplace")
diff --git a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
index 7cbcec9973..1e207f86db 100755
--- a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
+++ b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
@@ -36,6 +36,7 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
 ]
 
+
 def test_laplacexy_fv():
 
     print("Running LaplaceXY inversion test")
diff --git a/tests/integrated/test-laplacexy/test_laplacexy.py b/tests/integrated/test-laplacexy/test_laplacexy.py
index 885bfdf8b9..750600a6cb 100755
--- a/tests/integrated/test-laplacexy/test_laplacexy.py
+++ b/tests/integrated/test-laplacexy/test_laplacexy.py
@@ -51,6 +51,7 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1 laplacexy:pctype=hypre",
 ]
 
+
 def test_laplacexy():
 
     print("Running LaplaceXY inversion test")
diff --git a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
index 0805f945f9..7a677106dd 100755
--- a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
+++ b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
@@ -36,6 +36,7 @@
     "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
 ]
 
+
 def test_laplacexy2_hypre():
 
     print("Running LaplaceXY inversion test")
diff --git a/tests/integrated/test-options-netcdf/test_options_netcdf.py b/tests/integrated/test-options-netcdf/test_options_netcdf.py
index cde7472052..f8a4a92b01 100755
--- a/tests/integrated/test-options-netcdf/test_options_netcdf.py
+++ b/tests/integrated/test-options-netcdf/test_options_netcdf.py
@@ -11,6 +11,7 @@
 import math
 import numpy.testing as npt
 
+
 def test_options_netcdf():
 
     shell(["rm -f test-out.ini"])
diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
index 40763c4c30..f698d696ec 100755
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
@@ -23,8 +23,8 @@
 ]
 tol = 2e-4  # Absolute (?) tolerance
 
-def test_petsc_laplace():
 
+def test_petsc_laplace():
 
     print("Running PETSc Laplacian inversion test")
     success = True
diff --git a/tests/integrated/test-restart-io/test_restart_io.py b/tests/integrated/test-restart-io/test_restart_io.py
index 672210b75a..f37e56f5c1 100755
--- a/tests/integrated/test-restart-io/test_restart_io.py
+++ b/tests/integrated/test-restart-io/test_restart_io.py
@@ -20,6 +20,7 @@
 mxg = 2
 myg = 2
 
+
 def test_restart_io():
 
     x = numpy.linspace(0.0, 1.0, nx + 2 * mxg)[:, numpy.newaxis, numpy.newaxis]
@@ -80,7 +81,9 @@ def test_restart_io():
         run_restart_from = numpy.array(
             list("36 character run_restart_from string"), dtype="S1"
         )
-        run_restart_from = BoutArray(run_restart_from, attributes={"bout_type": "string"})
+        run_restart_from = BoutArray(
+            run_restart_from, attributes={"bout_type": "string"}
+        )
         base_restart.write("run_restart_from", run_restart_from)
 
     success = True
@@ -114,7 +117,9 @@ def test_restart_io():
 
             if not numpy.allclose(testvar, result):
                 success = False
-                print(f"{name}_once is different: {numpy.max(numpy.abs(testvar - result))}")
+                print(
+                    f"{name}_once is different: {numpy.max(numpy.abs(testvar - result))}"
+                )
                 # Don't plot anything by default
                 if False:
                     from boututils.showdata import showdata
diff --git a/tests/integrated/test-slepc-solver/test_slepc_solver.py b/tests/integrated/test-slepc-solver/test_slepc_solver.py
index 851a8af2e5..2df73df018 100755
--- a/tests/integrated/test-slepc-solver/test_slepc_solver.py
+++ b/tests/integrated/test-slepc-solver/test_slepc_solver.py
@@ -7,7 +7,6 @@
 import numpy.testing as npt
 
 
-
 def test_slepc_solver():
 
     print("Running SLEPc eigen solver test")
@@ -20,5 +19,8 @@ def test_slepc_solver():
 
     expected_eigenvalues = [0.0, 1.0]
 
-    npt.assert_allclose(expected_eigenvalues, eigenvalues,
-                        err_msg=" => SLEPc test failed\nEigenvalues: {eigenvalues}")
+    npt.assert_allclose(
+        expected_eigenvalues,
+        eigenvalues,
+        err_msg=" => SLEPc test failed\nEigenvalues: {eigenvalues}",
+    )
diff --git a/tests/integrated/test-snb/test_snb.py b/tests/integrated/test-snb/test_snb.py
index 48a29195e0..1095b40a70 100644
--- a/tests/integrated/test-snb/test_snb.py
+++ b/tests/integrated/test-snb/test_snb.py
@@ -1,4 +1,2 @@
-
-
 def test_runtest(assert_success_in_shell):
     assert_success_in_shell("./runtest")
diff --git a/tests/integrated/test-squash/test_squash.py b/tests/integrated/test-squash/test_squash.py
index a2e9a16a50..e9bb672d01 100755
--- a/tests/integrated/test-squash/test_squash.py
+++ b/tests/integrated/test-squash/test_squash.py
@@ -82,7 +82,10 @@ def verify(f1, f2):
 def test_squash():
     parser = argparse.ArgumentParser(description="Test the bout-squashoutput wrapper")
     parser.add_argument(
-        "executable", help="Path to bout-squashoutput", default="../../../bin", nargs="?"
+        "executable",
+        help="Path to bout-squashoutput",
+        default="../../../bin",
+        nargs="?",
     )
     args = parser.parse_args()
 
@@ -115,7 +118,9 @@ def test_squash():
     timed_shell_safe("rm -f f2.nc")
     timed_launch_safe("./squash -q -q -q", nproc=4, mthread=1)
     timed_shell_safe("{} -qdcl 9 data --outputname ../f2.nc".format(bout_squashoutput))
-    timed_launch_safe("./squash -q -q -q restart dump_on_restart=false", nproc=4, mthread=1)
+    timed_launch_safe(
+        "./squash -q -q -q restart dump_on_restart=false", nproc=4, mthread=1
+    )
     timed_shell_safe("{} -qdcal 9 data --outputname ../f2.nc".format(bout_squashoutput))
 
     verify("f1.nc", "f2.nc")
diff --git a/tests/integrated/test-stopCheck-file/test_stopCheck_file.py b/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
index 4d97ff3019..9e1b32859d 100755
--- a/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
+++ b/tests/integrated/test-stopCheck-file/test_stopCheck_file.py
@@ -9,6 +9,7 @@
 
 nproc = 1
 
+
 def test_stopCheck_file():
 
     check_values = [True, False]
diff --git a/tests/integrated/test-stopCheck/test_stopCheck.py b/tests/integrated/test-stopCheck/test_stopCheck.py
index 48a29195e0..1095b40a70 100644
--- a/tests/integrated/test-stopCheck/test_stopCheck.py
+++ b/tests/integrated/test-stopCheck/test_stopCheck.py
@@ -1,4 +1,2 @@
-
-
 def test_runtest(assert_success_in_shell):
     assert_success_in_shell("./runtest")
diff --git a/tests/integrated/test-subdir/test_subdir.py b/tests/integrated/test-subdir/test_subdir.py
index 48a29195e0..1095b40a70 100644
--- a/tests/integrated/test-subdir/test_subdir.py
+++ b/tests/integrated/test-subdir/test_subdir.py
@@ -1,4 +1,2 @@
-
-
 def test_runtest(assert_success_in_shell):
     assert_success_in_shell("./runtest")
diff --git a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
index cba1ffd0d3..0e9698c217 100755
--- a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
+++ b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
@@ -8,6 +8,7 @@
 nproc = 1
 tol = 1.0e-13
 
+
 def test_twistshift_staggered():
 
     s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True)
@@ -23,7 +24,6 @@ def test_twistshift_staggered():
 
     success = True
 
-
     # Check test_aligned is *not* periodic in y
     def test1(ylower, yupper):
         global success
@@ -36,7 +36,6 @@ def test1(ylower, yupper):
                 "different" % (yupper, ylower)
             )
 
-
     test1(0, -4)
     test1(1, -3)
     test1(2, -2)
diff --git a/tests/integrated/test-twistshift/test_twistshift.py b/tests/integrated/test-twistshift/test_twistshift.py
index 0e81540e4e..d586244bb4 100755
--- a/tests/integrated/test-twistshift/test_twistshift.py
+++ b/tests/integrated/test-twistshift/test_twistshift.py
@@ -28,7 +28,7 @@ def test_twistshift():
     def test1(ylower, yupper):
         global success
         if numpy.any(
-                numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6
+            numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6
         ):
             success = False
             print(
@@ -45,10 +45,11 @@ def test1(ylower, yupper):
 
     # Check test and result are the same
     if numpy.any(numpy.abs(result - test) > tol):
-        print("Fail - result has not been communicated correctly - is different from input")
+        print(
+            "Fail - result has not been communicated correctly - is different from input"
+        )
         success = False
 
-
     # Check result is periodic in y
     def test2(ylower, yupper):
         global success
diff --git a/tests/integrated/test-vec/test_vec.py b/tests/integrated/test-vec/test_vec.py
index d216689239..ff2e14d608 100755
--- a/tests/integrated/test-vec/test_vec.py
+++ b/tests/integrated/test-vec/test_vec.py
@@ -4,6 +4,7 @@
 
 from boututils.run_wrapper import launch_safe
 
+
 def test_vec():
 
     status, out = launch_safe("./testVec", nproc=4, pipe=True)
diff --git a/tests/integrated/test-yupdown-weights/test_yupdown_weights.py b/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
index 3ae4bdba08..ae8754d50d 100755
--- a/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
+++ b/tests/integrated/test-yupdown-weights/test_yupdown_weights.py
@@ -6,6 +6,7 @@
 
 from numpy import max, abs
 
+
 def test_yupdown_weights():
 
     failed = False
diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py
index 0d8c61bc7a..b2569f4d60 100755
--- a/tests/integrated/test-yupdown/test_yupdown.py
+++ b/tests/integrated/test-yupdown/test_yupdown.py
@@ -23,9 +23,7 @@ def run_case(shift_type, variable):
     v, v_check = variable
     print("Testing %s and %s ... " % (v, v_check))
     ddy = collect(v, path="data", xguards=False, yguards=False, info=False)
-    ddy_check = collect(
-        v_check, path="data", xguards=False, yguards=False, info=False
-    )
+    ddy_check = collect(v_check, path="data", xguards=False, yguards=False, info=False)
 
     diff = max(abs(ddy - ddy_check))
 

From a36dcdd12ea4c219b38386707bf250f42782f141 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 12:56:32 +0100
Subject: [PATCH 1198/1827] Convert test_unused_options to run via pytest

---
 tests/integrated/test-unused-options/runtest  | 23 -------------------
 .../test_unused_options.py                    | 21 +++++++++++++++++
 2 files changed, 21 insertions(+), 23 deletions(-)
 delete mode 100755 tests/integrated/test-unused-options/runtest
 create mode 100755 tests/integrated/test-unused-options/test_unused_options.py

diff --git a/tests/integrated/test-unused-options/runtest b/tests/integrated/test-unused-options/runtest
deleted file mode 100755
index f3fad0c404..0000000000
--- a/tests/integrated/test-unused-options/runtest
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env python3
-
-from boututils.run_wrapper import build_and_log, launch_safe
-
-build_and_log("unused options test")
-
-for nproc in [1, 2]:
-    print(f"Running with nproc={nproc}...", end="")
-    s, out = launch_safe(
-        "./test_unused_options",
-        nproc=nproc,
-        mthread=1,
-        pipe=True,
-    )
-
-    with open(f"run.log.{nproc}", "w") as f:
-        f.write(out)
-
-    # Check for printed message
-    if "SUCCESS" not in out:
-        print("failed")
-        exit(1)
-    print("pass")
diff --git a/tests/integrated/test-unused-options/test_unused_options.py b/tests/integrated/test-unused-options/test_unused_options.py
new file mode 100755
index 0000000000..b147aa353c
--- /dev/null
+++ b/tests/integrated/test-unused-options/test_unused_options.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+
+from boututils.run_wrapper import launch_safe
+
+
+def test_unused_options():
+
+    for nproc in [1, 2]:
+        print(f"Running with nproc={nproc}...", end="")
+        s, out = launch_safe(
+            "./test_unused_options",
+            nproc=nproc,
+            mthread=1,
+            pipe=True,
+        )
+
+        with open(f"run.log.{nproc}", "w") as f:
+            f.write(out)
+
+        # Check for printed message
+        assert "SUCCESS" in out, "failed"

From 0c91d13d8a4183e88ebb32fe783ff201466bcea9 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 14:25:21 +0100
Subject: [PATCH 1199/1827] Remove obsolete imports for Python2

---
 tests/integrated/test-cyclic/test_cyclic.py               | 6 ------
 .../integrated/test-fieldgroupComm/test_fieldgroupComm.py | 7 -------
 tests/integrated/test-griddata/test_griddata.py           | 8 --------
 tests/integrated/test-gyro/test_gyro.py                   | 7 -------
 .../test_interchange_instability.py                       | 3 ---
 .../test-invertable-operator/test_invertable_operator.py  | 3 ---
 .../test-multigrid_laplace/runtest_multiple_grids         | 7 -------
 tests/integrated/test-multigrid_laplace/runtest_unsheared | 7 -------
 .../test-multigrid_laplace/test_multigrid_laplace.py      | 7 -------
 .../integrated/test-naulin-laplace/runtest_multiple_grids | 7 -------
 tests/integrated/test-naulin-laplace/runtest_unsheared    | 7 -------
 .../integrated/test-naulin-laplace/test_naulin_laplace.py | 7 -------
 .../test_petsc_laplace_MAST_grid.py                       | 3 ---
 .../test-region-iterator/test_region_iterator.py          | 6 ------
 14 files changed, 85 deletions(-)

diff --git a/tests/integrated/test-cyclic/test_cyclic.py b/tests/integrated/test-cyclic/test_cyclic.py
index f383cfe5c5..38a2d70012 100755
--- a/tests/integrated/test-cyclic/test_cyclic.py
+++ b/tests/integrated/test-cyclic/test_cyclic.py
@@ -7,12 +7,6 @@
 # Requires: netcdf
 # Cores: 4
 
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
 from boututils.run_wrapper import shell, launch
 from sys import stdout
 
diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
index e06ebab7a4..4c7b547ba4 100755
--- a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
+++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
@@ -9,13 +9,6 @@
 # Requires: not metric_3d
 # Cores: 4
 
-# Variables to compare
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
 
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
diff --git a/tests/integrated/test-griddata/test_griddata.py b/tests/integrated/test-griddata/test_griddata.py
index ad3b7f2a08..82f86fd459 100755
--- a/tests/integrated/test-griddata/test_griddata.py
+++ b/tests/integrated/test-griddata/test_griddata.py
@@ -1,13 +1,5 @@
 #!/usr/bin/env python3
 
-from __future__ import print_function
-from __future__ import division
-
-try:
-    from builtins import str
-except:
-    pass
-
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 import numpy.testing as npt
diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py
index 57e8bd7f08..d4522f9697 100755
--- a/tests/integrated/test-gyro/test_gyro.py
+++ b/tests/integrated/test-gyro/test_gyro.py
@@ -9,13 +9,6 @@
 # Cores: 4
 
 # Variables to compare
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
-
 vars = ["pade1", "pade2"]
 
 tol = 1e-7  # Absolute tolerance, benchmark values are floats
diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index 63dba4042b..0fa51c75f8 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -8,9 +8,6 @@
 # requires: netcdf
 # cores: 2
 
-from __future__ import print_function
-from __future__ import division
-
 nproc = 2  # Number of processors to run on
 reltol = 1.0e-3  # Allowed relative tolerance in growth-rate
 
diff --git a/tests/integrated/test-invertable-operator/test_invertable_operator.py b/tests/integrated/test-invertable-operator/test_invertable_operator.py
index a0b1dcb6d7..1708007fb0 100755
--- a/tests/integrated/test-invertable-operator/test_invertable_operator.py
+++ b/tests/integrated/test-invertable-operator/test_invertable_operator.py
@@ -8,9 +8,6 @@
 # Run the test, compare results against expected value
 #
 
-from __future__ import print_function
-from __future__ import division
-
 import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
diff --git a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
index b4905c41c6..2824a592eb 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
+++ b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
@@ -4,13 +4,6 @@
 # Run the test, check the error
 #
 
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
-
 tol = 2e-6  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
diff --git a/tests/integrated/test-multigrid_laplace/runtest_unsheared b/tests/integrated/test-multigrid_laplace/runtest_unsheared
index 62580efd44..e4a2ea1375 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_unsheared
+++ b/tests/integrated/test-multigrid_laplace/runtest_unsheared
@@ -4,13 +4,6 @@
 # Run the test, check the error
 #
 
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
-
 tol = 1e-9  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
index 885270d202..7a780ae7b4 100755
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
@@ -8,13 +8,6 @@
 
 # Cores: 3
 
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
-
 tol = 2e-7  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
diff --git a/tests/integrated/test-naulin-laplace/runtest_multiple_grids b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
index 19fbbfd5d6..f3cf9a5f47 100755
--- a/tests/integrated/test-naulin-laplace/runtest_multiple_grids
+++ b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
@@ -4,13 +4,6 @@
 # Run the test, check the error
 #
 
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
-
 tol = 2e-6  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
diff --git a/tests/integrated/test-naulin-laplace/runtest_unsheared b/tests/integrated/test-naulin-laplace/runtest_unsheared
index 691ab497f2..b8a898c0af 100755
--- a/tests/integrated/test-naulin-laplace/runtest_unsheared
+++ b/tests/integrated/test-naulin-laplace/runtest_unsheared
@@ -4,13 +4,6 @@
 # Run the test, check the error
 #
 
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
-
 tol = 1e-9  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
index 9d52b8d534..2c9d3e5c8e 100755
--- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
+++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
@@ -8,13 +8,6 @@
 
 # Cores: 3
 
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
-
 tol = 2e-7  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
index 1821f0b725..3de9752725 100755
--- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
@@ -9,9 +9,6 @@
 # cores: 4
 
 # Variables to compare
-from __future__ import print_function
-from builtins import str
-
 vars = [
     ["max_error1", 2.0e-4],
     ["max_error2", 1.0e-4],
diff --git a/tests/integrated/test-region-iterator/test_region_iterator.py b/tests/integrated/test-region-iterator/test_region_iterator.py
index 3d9a78c820..7b5f25599d 100755
--- a/tests/integrated/test-region-iterator/test_region_iterator.py
+++ b/tests/integrated/test-region-iterator/test_region_iterator.py
@@ -7,12 +7,6 @@
 # requires: netcdf
 # cores: 2
 
-from __future__ import print_function
-
-try:
-    from builtins import str
-except:
-    pass
 from boututils.run_wrapper import launch_safe
 
 

From 890d6d665cac485dd301d8d3d49a442d2bc2af4b Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 13 May 2026 14:55:32 -0700
Subject: [PATCH 1200/1827] makeNeumannOperator: Set only some boundaries

When mapping leg values back to cell values, only the boundary
cells to which the legs are connected should be set. This requires
partial Neumann operators, one for the forward boundaries and one
for the backward boundaries.

With this change, both Div_par and Div_par_Grad_par appear to have
the correct conservation properties when sub-sampling the yup/down
mapping (partially intersecting boundaries).
---
 include/bout/petsc_operators.hxx |  16 ++---
 src/mesh/petsc_operators.cxx     | 108 +++++++++++++++++++++----------
 2 files changed, 81 insertions(+), 43 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index e28daf48cf..422480c7ef 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -47,6 +47,9 @@ struct BackwardLegSpaceTag {};
 template <typename Out, typename In>
 class PetscOperator;
 
+/// Used to indicate whether forward or backward boundary 'legs' should be used
+enum class BoundaryDirection { Forward, Backward, Both };
+
 class PetscCellMapping;
 
 /// @brief Shared-pointer alias for a const PetscCellMapping.
@@ -158,10 +161,7 @@ protected:
 ///
 /// @c mapOwnedInteriorCells iterates only the evolving interior cells (subset 1) and
 /// provides global PETSc row indices, making it suitable for assembling matrices.
-///
-/// Inherits from std::enable_shared_from_this so that shared_from_this can be used.
-class PetscCellMapping : public PetscIndexMapping,
-                         std::enable_shared_from_this<PetscCellMapping> {
+class PetscCellMapping : public PetscIndexMapping {
 public:
   /// @brief Construct the cell-space mapping from mesh metadata fields.
   ///
@@ -286,7 +286,7 @@ public:
   }
 
   friend PetscOperator<CellSpaceTag, CellSpaceTag>
-  makeNeumannOperator(const PetscCellMappingPtr& mapping);
+  makeNeumannOperator(const PetscCellMappingPtr& mapping, BoundaryDirection direction);
 
 private:
   Field3D cell_number; ///< Stored cell numbers for interior/X-boundary cells.
@@ -1035,11 +1035,11 @@ private:
 /// rows for boundary cells so that boundary conditions propagate into
 /// Grad_par and Div_par.
 ///
-/// Uses shared_from_this so must only be called on a PetscCellMapping
-/// that is managed in a shared pointer.
+/// @param direction   Which Y boundary cells will be set
 ///
 /// @returns A PetscCellOperator representing the Neumann boundary mapping.
-PetscCellOperator makeNeumannOperator(const PetscCellMappingPtr& mapping);
+PetscCellOperator makeNeumannOperator(const PetscCellMappingPtr& mapping,
+                                      BoundaryDirection direction);
 
 #else
 
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index d5db6876b1..2fa2a5fb51 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -304,7 +304,10 @@ PetscBackwardLegOperator PetscOperators::diagonal(const PetscBackwardLegVector&
 
 PetscOperators::Parallel PetscOperators::getParallel() const {
   // Set boundaries
-  const PetscCellOperator& Neumann = makeNeumannOperator(cell_mapping); // C <- C
+  const PetscCellOperator& Neumann_fwd =
+      makeNeumannOperator(cell_mapping, BoundaryDirection::Forward); // C <- C
+  const PetscCellOperator& Neumann_bwd =
+      makeNeumannOperator(cell_mapping, BoundaryDirection::Backward); // C <- C
 
   // Primitive operators from the mesh / metadata
   auto Forward = this->forward();             // L+ <- C
@@ -319,8 +322,9 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   const auto W_minus = diagonal(w_minus_vec); // L- <- L-
 
   // Weighted adjoints: C <- L+ and C <- L-
-  auto Restrict_minus = Inject_plus.transpose() * W_plus;
-  auto Restrict_plus = Inject_minus.transpose() * W_minus;
+  // The Neumann_f/bwd operators set the boundary cells to which the legs are connected
+  auto Restrict_minus = Neumann_fwd * Inject_plus.transpose() * W_plus;
+  auto Restrict_plus = Neumann_bwd * Inject_minus.transpose() * W_minus;
 
   auto* coords = mesh->getCoordinates();
 
@@ -366,9 +370,10 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   auto Grad_minus = Inv_dl_minus * (Inject_minus - Backward); // L- <- C
 
   // Cell-centered central gradient
-  // Apply Neumann so that the yup/ydown cells are set
-  auto Grad_par = Neumann * ((Restrict_minus * Grad_plus) + (Restrict_plus * Grad_minus))
-                  * 0.5; // C <- C
+  // Apply Neumann so that the yup/ydown cells are set. This is needed
+  // so that Div_par has the correct dependence on yup/down cells.
+  auto Grad_par =
+      ((Restrict_minus * Grad_plus) + (Restrict_plus * Grad_minus)) * 0.5; // C <- C
 
   // Leg-centered volumes from unweighted interpolation
   const auto dV_plus = Interp_plus(dV);   // L+
@@ -424,7 +429,8 @@ Field3D PetscOperators::Parallel::Div_par_K_Grad_par(const Field3D& K,
   return (toField3D(div_minus, K) + toField3D(div_plus, K)) * 0.5;
 }
 
-PetscCellOperator makeNeumannOperator(const PetscCellMappingPtr& mapping) {
+PetscCellOperator makeNeumannOperator(const PetscCellMappingPtr& mapping,
+                                      BoundaryDirection direction) {
 
   // The operator is built using stored indices for both rows and columns,
   // then post-multiplied by getPetscToStored() to convert columns to PETSc
@@ -474,35 +480,67 @@ PetscCellOperator makeNeumannOperator(const PetscCellMappingPtr& mapping) {
     BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
   });
 
-  mapping->mapLocalYup([&](PetscInt local_row, const Ind3D& i_yp) {
-    const PetscInt petsc_row = mapping->rowStart() + local_row;
-    const Ind3D i_src = i_yp.ym();
-    const int stored_row_check = ROUND(mapping->forward_cell_number[i_src]);
-    if (stored_row_check < 0) {
-      throw BoutException("Check failed: stored_row, mapLocalYup");
-    }
-    const int stored_col = ROUND(mapping->cell_number[i_src]);
-    if (stored_col < 0) {
-      throw BoutException("Check failed: stored_col, mapLocalYup");
-    }
-    const PetscInt col = static_cast<PetscInt>(stored_col);
-    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
-  });
+  if ((direction == BoundaryDirection::Forward)
+      or (direction == BoundaryDirection::Both)) {
+    // Set forward rows from interior columns
+    mapping->mapLocalYup([&](PetscInt local_row, const Ind3D& i_yp) {
+      const PetscInt petsc_row = mapping->rowStart() + local_row;
+      const Ind3D i_src = i_yp.ym();
+      const int stored_row_check = ROUND(mapping->forward_cell_number[i_src]);
+      if (stored_row_check < 0) {
+        throw BoutException("Check failed: stored_row, mapLocalYup");
+      }
+      const int stored_col = ROUND(mapping->cell_number[i_src]);
+      if (stored_col < 0) {
+        throw BoutException("Check failed: stored_col, mapLocalYup");
+      }
+      const PetscInt col = static_cast<PetscInt>(stored_col);
+      BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+    });
+  } else {
+    // Identity rows in forward boundary
+    mapping->mapLocalYup([&](PetscInt local_row, const Ind3D& i_yp) {
+      const PetscInt petsc_row = mapping->rowStart() + local_row;
+      const Ind3D i_src = i_yp.ym();
+      const int stored_col = ROUND(mapping->forward_cell_number[i_src]);
+      if (stored_col < 0) {
+        throw BoutException("Check failed: stored_col, mapLocalYup identity");
+      }
+      const PetscInt col = static_cast<PetscInt>(stored_col);
+      BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+    });
+  }
 
-  mapping->mapLocalYdown([&](PetscInt local_row, const Ind3D& i_ym) {
-    const PetscInt petsc_row = mapping->rowStart() + local_row;
-    const Ind3D i_src = i_ym.yp();
-    const int stored_row_check = ROUND(mapping->backward_cell_number[i_src]);
-    if (stored_row_check < 0) {
-      throw BoutException("Check failed: stored_row, mapLocalYdown");
-    }
-    const int stored_col = ROUND(mapping->cell_number[i_src]);
-    if (stored_col < 0) {
-      throw BoutException("Check failed: stored_col, mapLocalYdown");
-    }
-    const PetscInt col = static_cast<PetscInt>(stored_col);
-    BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
-  });
+  if ((direction == BoundaryDirection::Backward)
+      or (direction == BoundaryDirection::Both)) {
+    // Set backward rows from interior columns
+    mapping->mapLocalYdown([&](PetscInt local_row, const Ind3D& i_ym) {
+      const PetscInt petsc_row = mapping->rowStart() + local_row;
+      const Ind3D i_src = i_ym.yp();
+      const int stored_row_check = ROUND(mapping->backward_cell_number[i_src]);
+      if (stored_row_check < 0) {
+        throw BoutException("Check failed: stored_row, mapLocalYdown");
+      }
+      const int stored_col = ROUND(mapping->cell_number[i_src]);
+      if (stored_col < 0) {
+        throw BoutException("Check failed: stored_col, mapLocalYdown");
+      }
+      const PetscInt col = static_cast<PetscInt>(stored_col);
+      BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+    });
+  } else {
+    // Identity rows in backward boundary
+    mapping->mapLocalYdown([&](PetscInt local_row, const Ind3D& i_ym) {
+      const PetscInt petsc_row = mapping->rowStart() + local_row;
+      const Ind3D i_src = i_ym.yp();
+      const int stored_col = ROUND(mapping->backward_cell_number[i_src]);
+      if (stored_col < 0) {
+        throw BoutException("Check failed: stored_col, mapLocalYdown identity");
+      }
+      const PetscInt col = static_cast<PetscInt>(stored_col);
+      BOUT_DO_PETSC(MatSetValues(*temp, 1, &petsc_row, 1, &col, &one, INSERT_VALUES));
+    });
+  }
 
   BOUT_DO_PETSC(MatAssemblyBegin(*temp, MAT_FINAL_ASSEMBLY));
   BOUT_DO_PETSC(MatAssemblyEnd(*temp, MAT_FINAL_ASSEMBLY));

From 183346a1cd26c6cecbbefc71271ce1187396ad17 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 14:38:03 +0100
Subject: [PATCH 1201/1827] Apply ruff fixes

---
 .../test-boutpp/mms-ddz/test_boutpp_mms_ddz.py         |  1 -
 .../simple-model/test_boutpp_simple_model.py           | 10 +++++-----
 .../test-datafilefacade/test_datafile_facade.py        |  2 +-
 tests/integrated/test-initial/test_initial.py          |  2 +-
 4 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
index 23b0d0f173..1e2421e59b 100755
--- a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
+++ b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
@@ -14,7 +14,6 @@ def test_boutpp_mms_ddz(run_isolated):
     errorlist = ""
     boutpp.init("-d data -q -q -q")  # +" -f BOUT.settings")
 
-    shapes = []
     errors = []
     mmax = 7
     start = 6
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index 7744b514f5..a443f22cd8 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -3,7 +3,7 @@
 # requires boutpp
 # requires not make
 
-from boutpp import *
+import boutpp
 
 
 def test_boutpp_simple_model(run_isolated):
@@ -11,15 +11,15 @@ def test_boutpp_simple_model(run_isolated):
     if run_isolated():
         return
 
-    init("-d mini")
+    boutpp.init("-d mini")
 
-    class MyModel(PhysicsModel):
+    class MyModel(boutpp.PhysicsModel):
         def init(self, restart):
-            self.n = create3D("dens:function")
+            self.n = boutpp.create3D("dens:function")
             self.solve_for(dens=self.n)
 
         def rhs(self, time):
-            self.n.ddt(DDX(self.n))
+            self.n.ddt(boutpp.DDX(self.n))
 
     model = MyModel()
     model.solve()
diff --git a/tests/integrated/test-datafilefacade/test_datafile_facade.py b/tests/integrated/test-datafilefacade/test_datafile_facade.py
index 01860765c9..7a4d947f27 100755
--- a/tests/integrated/test-datafilefacade/test_datafile_facade.py
+++ b/tests/integrated/test-datafilefacade/test_datafile_facade.py
@@ -73,4 +73,4 @@ def test_datafile_facade():
                 "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc"
             ]
         )
-    assert success, f"=> Some failed tests"
+    assert success, "=> Some failed tests"
diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index cbdca014e5..1edb138e24 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -151,6 +151,7 @@ def fmod(x, denominator=1.0):
 tan = np.tan
 TanhHat = tanhhat
 pi = np.pi
+erf = erf
 
 
 def test_initial():
@@ -184,7 +185,6 @@ def test_initial():
         if status != 0:
             print(status)
             pytest.fail("=> Could not run test")
-            exit(status)
 
         # Collect the coordinate arrays separately
         x = collect("var_x", xguards=True, yguards=True, path=datadir, info=False)

From 8f0131ec5412e3b9dbe8889be69ed8a1c7e2a64b Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 14:42:19 +0100
Subject: [PATCH 1202/1827] Remove unused variable

---
 .../test-twistshift-staggered/test_twistshift_staggered.py       | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
index 0e9698c217..19eca67f68 100755
--- a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
+++ b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
@@ -15,7 +15,6 @@ def test_twistshift_staggered():
     with open("run.log." + str(nproc), "w") as f:
         f.write(out)
 
-    test = collect("test", path=datapath, yguards=True, info=False)
     test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False)
     check = collect("check", path=datapath, yguards=True, info=False)
 

From dd61eb3b16a1c8bf7e2b8497fc5682860ce1c2ba Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 14:42:57 +0100
Subject: [PATCH 1203/1827] Fix ruff issue: "E402 Module level import not at
 top of file"

---
 tests/integrated/test-smooth/test_smooth.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-smooth/test_smooth.py b/tests/integrated/test-smooth/test_smooth.py
index 3d3776ca25..f3c58bcdb8 100755
--- a/tests/integrated/test-smooth/test_smooth.py
+++ b/tests/integrated/test-smooth/test_smooth.py
@@ -11,10 +11,10 @@
 vars = ["yavg2d", "yavg3d", "sm3d"]
 tol = 1e-7  # Absolute tolerance, benchmark values are floats
 
-from boututils.run_wrapper import shell, launch_safe
-from boutdata.collect import collect
 import numpy as np
 from sys import stdout
+from boututils.run_wrapper import shell, launch_safe
+from boutdata.collect import collect
 
 
 def test_smooth():

From e9c9f7d381e646d7157cb807c74b36c8105710cb Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 14:46:36 +0100
Subject: [PATCH 1204/1827] Remove assignment to unused variable `nxpe`

---
 tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
index 4c7b547ba4..917fdc0754 100755
--- a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
+++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
@@ -31,10 +31,6 @@ def test_fieldgroupcomm():
     success = True
 
     for nproc in [1, 2, 4]:
-        nxpe = 1
-        if nproc > 2:
-            nxpe = 2
-
         cmd = "./{exe} ".format(exe=exeName)
 
         shell("rm data/BOUT.dmp.*.nc")

From 38beaf4c3e339c698154886d08965857b5924a08 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 14:54:18 +0100
Subject: [PATCH 1205/1827] E402 Module level import not at top of file

---
 tests/integrated/test-delp2/test_delp2.py              |  4 ++--
 .../test-drift-instability/test_drift_instability.py   |  3 ++-
 tests/integrated/test-gyro/test_gyro.py                |  4 ++--
 tests/integrated/test-initial/test_initial.py          | 10 +++++-----
 .../test_interchange_instability.py                    |  2 +-
 tests/integrated/test-laplacexz/test_laplacexz.py      |  2 +-
 tests/integrated/test-restarting/test_restarting.py    |  2 +-
 tests/integrated/test-squash/test_squash.py            |  4 ++--
 8 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/tests/integrated/test-delp2/test_delp2.py b/tests/integrated/test-delp2/test_delp2.py
index 529de55793..b3a16eded9 100755
--- a/tests/integrated/test-delp2/test_delp2.py
+++ b/tests/integrated/test-delp2/test_delp2.py
@@ -3,10 +3,10 @@
 # cores: 4
 
 import pytest
-from boututils.run_wrapper import shell, launch_safe
-from boutdata.collect import collect
 import numpy as np
 from sys import stdout
+from boututils.run_wrapper import shell, launch_safe
+from boutdata.collect import collect
 
 tol = 1e-10  # Absolute tolerance
 
diff --git a/tests/integrated/test-drift-instability/test_drift_instability.py b/tests/integrated/test-drift-instability/test_drift_instability.py
index 34b91b369d..e8db2d9798 100644
--- a/tests/integrated/test-drift-instability/test_drift_instability.py
+++ b/tests/integrated/test-drift-instability/test_drift_instability.py
@@ -7,13 +7,14 @@
 # Requires: not metric_3d
 
 import pytest
+import numpy as np
+
 from boututils.run_wrapper import shell, launch_safe
 from boututils.calculus import deriv
 from boututils.datafile import DataFile
 from boututils.linear_regression import linear_regression
 
 from boutdata.collect import collect
-import numpy as np
 from math import isnan
 
 nthreads = 1
diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py
index d4522f9697..512376e162 100755
--- a/tests/integrated/test-gyro/test_gyro.py
+++ b/tests/integrated/test-gyro/test_gyro.py
@@ -13,10 +13,10 @@
 
 tol = 1e-7  # Absolute tolerance, benchmark values are floats
 
-from boututils.run_wrapper import shell, launch_safe
-from boutdata.collect import collect
 import numpy as np
 from sys import stdout
+from boututils.run_wrapper import shell, launch_safe
+from boutdata.collect import collect
 
 
 def test_gyro():
diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index 1edb138e24..6617cc2cff 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -1,16 +1,16 @@
 #!/usr/bin/env python3
-import pytest
-# Test initial conditions
 
-from boututils.run_wrapper import launch_safe
-from boutdata.collect import collect
+# Test initial conditions
 
+import pytest
 import configparser
 import itertools
-from scipy.special import erf
 import numpy as np
+from scipy.special import erf
 from pathlib import Path
 
+from boututils.run_wrapper import launch_safe
+from boutdata.collect import collect
 
 # requires not make
 # requires scipy
diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index 0fa51c75f8..78da29a2e3 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -11,9 +11,9 @@
 nproc = 2  # Number of processors to run on
 reltol = 1.0e-3  # Allowed relative tolerance in growth-rate
 
+import numpy as np
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
-import numpy as np
 
 nthreads = 1
 
diff --git a/tests/integrated/test-laplacexz/test_laplacexz.py b/tests/integrated/test-laplacexz/test_laplacexz.py
index 2853933637..5069e33113 100755
--- a/tests/integrated/test-laplacexz/test_laplacexz.py
+++ b/tests/integrated/test-laplacexz/test_laplacexz.py
@@ -7,9 +7,9 @@
 # Run the test, compare results against the benchmark
 #
 
+import numpy as np
 from boututils.run_wrapper import shell, launch_safe, getmpirun
 from boutdata.collect import collect
-import numpy as np
 
 
 def test_laplacexz():
diff --git a/tests/integrated/test-restarting/test_restarting.py b/tests/integrated/test-restarting/test_restarting.py
index 7591dc5f5b..b5f51bd073 100755
--- a/tests/integrated/test-restarting/test_restarting.py
+++ b/tests/integrated/test-restarting/test_restarting.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 
+import numpy as np
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
-import numpy as np
 
 
 def test_restarting():
diff --git a/tests/integrated/test-squash/test_squash.py b/tests/integrated/test-squash/test_squash.py
index e9bb672d01..ab13380811 100755
--- a/tests/integrated/test-squash/test_squash.py
+++ b/tests/integrated/test-squash/test_squash.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python3
 
-from boututils.datafile import DataFile
 import itertools
 import time
 import numpy as np
-from boututils.run_wrapper import launch_safe, shell_safe
 import argparse
 import re
+from boututils.datafile import DataFile
+from boututils.run_wrapper import launch_safe, shell_safe
 from pathlib import Path
 
 # requires: all_tests

From d9db8dc38a3665a86ace0476a3da5f60eb41e815 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 14:59:14 +0100
Subject: [PATCH 1206/1827] E402 Module level import not at top of file

---
 tests/integrated/test-gyro/test_gyro.py                  | 9 ++++-----
 .../test_interchange_instability.py                      | 6 +++---
 .../test-multigrid_laplace/runtest_multiple_grids        | 5 ++---
 .../integrated/test-multigrid_laplace/runtest_unsheared  | 5 ++---
 .../test-multigrid_laplace/test_multigrid_laplace.py     | 6 +++---
 tests/integrated/test-naulin-laplace/runtest_unsheared   | 5 ++---
 .../test-naulin-laplace/test_naulin_laplace.py           | 6 +++---
 .../test_petsc_laplace_MAST_grid.py                      | 8 ++++----
 tests/integrated/test-smooth/test_smooth.py              | 8 ++++----
 9 files changed, 27 insertions(+), 31 deletions(-)

diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py
index 512376e162..fbe6baab01 100755
--- a/tests/integrated/test-gyro/test_gyro.py
+++ b/tests/integrated/test-gyro/test_gyro.py
@@ -8,16 +8,15 @@
 # Requires: netcdf
 # Cores: 4
 
-# Variables to compare
-vars = ["pade1", "pade2"]
-
-tol = 1e-7  # Absolute tolerance, benchmark values are floats
-
 import numpy as np
 from sys import stdout
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
+# Variables to compare
+vars = ["pade1", "pade2"]
+
+tol = 1e-7  # Absolute tolerance, benchmark values are floats
 
 def test_gyro():
 
diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index 78da29a2e3..26b56e19eb 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -8,13 +8,13 @@
 # requires: netcdf
 # cores: 2
 
-nproc = 2  # Number of processors to run on
-reltol = 1.0e-3  # Allowed relative tolerance in growth-rate
-
 import numpy as np
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
+nproc = 2  # Number of processors to run on
+reltol = 1.0e-3  # Allowed relative tolerance in growth-rate
+
 nthreads = 1
 
 
diff --git a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
index 2824a592eb..f264ecc131 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
+++ b/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
@@ -4,13 +4,12 @@
 # Run the test, check the error
 #
 
-tol = 2e-6  # Absolute tolerance
-numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
-
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
+tol = 2e-6  # Absolute tolerance
+numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
 print("Running multigrid Laplacian inversion test")
 success = True
diff --git a/tests/integrated/test-multigrid_laplace/runtest_unsheared b/tests/integrated/test-multigrid_laplace/runtest_unsheared
index e4a2ea1375..e066eeffff 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_unsheared
+++ b/tests/integrated/test-multigrid_laplace/runtest_unsheared
@@ -4,13 +4,12 @@
 # Run the test, check the error
 #
 
-tol = 1e-9  # Absolute tolerance
-numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
-
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
+tol = 1e-9  # Absolute tolerance
+numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
 print("Running multigrid Laplacian inversion test")
 success = True
diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
index 7a780ae7b4..bec6b09fac 100755
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
@@ -8,12 +8,12 @@
 
 # Cores: 3
 
-tol = 2e-7  # Absolute tolerance
-numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
-
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
+tol = 2e-7  # Absolute tolerance
+numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
+
 
 def test_multigrid_laplace():
 
diff --git a/tests/integrated/test-naulin-laplace/runtest_unsheared b/tests/integrated/test-naulin-laplace/runtest_unsheared
index b8a898c0af..e5ee732bbb 100755
--- a/tests/integrated/test-naulin-laplace/runtest_unsheared
+++ b/tests/integrated/test-naulin-laplace/runtest_unsheared
@@ -4,13 +4,12 @@
 # Run the test, check the error
 #
 
-tol = 1e-9  # Absolute tolerance
-numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
-
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
+tol = 1e-9  # Absolute tolerance
+numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
 print("Running LaplaceNaulin inversion test")
 success = True
diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
index 2c9d3e5c8e..52c2e5144d 100755
--- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
+++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
@@ -6,14 +6,14 @@
 # Run the test, check the error
 #
 
+from boututils.run_wrapper import shell, launch_safe
+from boutdata.collect import collect
+
 # Cores: 3
 
 tol = 2e-7  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
-from boututils.run_wrapper import shell, launch_safe
-from boutdata.collect import collect
-
 
 def test_naulin_laplace():
 
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
index 3de9752725..9c67f4bc80 100755
--- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
@@ -8,6 +8,10 @@
 # requires: petsc
 # cores: 4
 
+from boututils.run_wrapper import shell, launch_safe
+from boutdata.collect import collect
+from sys import stdout
+
 # Variables to compare
 vars = [
     ["max_error1", 2.0e-4],
@@ -21,10 +25,6 @@
 ]
 # tol = 1e-4                  # Absolute (?) tolerance
 
-from boututils.run_wrapper import shell, launch_safe
-from boutdata.collect import collect
-from sys import stdout
-
 
 def test_petsc_laplace_MAST_grid():
 
diff --git a/tests/integrated/test-smooth/test_smooth.py b/tests/integrated/test-smooth/test_smooth.py
index f3c58bcdb8..083b0e81be 100755
--- a/tests/integrated/test-smooth/test_smooth.py
+++ b/tests/integrated/test-smooth/test_smooth.py
@@ -7,15 +7,15 @@
 # Requires: netcdf
 # Cores: 4
 
-# Variables to compare
-vars = ["yavg2d", "yavg3d", "sm3d"]
-tol = 1e-7  # Absolute tolerance, benchmark values are floats
-
 import numpy as np
 from sys import stdout
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
+# Variables to compare
+vars = ["yavg2d", "yavg3d", "sm3d"]
+tol = 1e-7  # Absolute tolerance, benchmark values are floats
+
 
 def test_smooth():
 

From f75cf1948598f9ffe67601f9fd882bd2b1bd0089 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 15:03:12 +0100
Subject: [PATCH 1207/1827] E402 Module level import not at top of file

---
 tests/integrated/test-gyro/test_gyro.py                     | 1 +
 tests/integrated/test-naulin-laplace/runtest_multiple_grids | 5 ++---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py
index fbe6baab01..6c2551fdf0 100755
--- a/tests/integrated/test-gyro/test_gyro.py
+++ b/tests/integrated/test-gyro/test_gyro.py
@@ -18,6 +18,7 @@
 
 tol = 1e-7  # Absolute tolerance, benchmark values are floats
 
+
 def test_gyro():
 
     # Read benchmark values
diff --git a/tests/integrated/test-naulin-laplace/runtest_multiple_grids b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
index f3cf9a5f47..2b802e0eb1 100755
--- a/tests/integrated/test-naulin-laplace/runtest_multiple_grids
+++ b/tests/integrated/test-naulin-laplace/runtest_multiple_grids
@@ -4,13 +4,12 @@
 # Run the test, check the error
 #
 
-tol = 2e-6  # Absolute tolerance
-numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
-
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from sys import exit
 
+tol = 2e-6  # Absolute tolerance
+numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
 print("Running LaplaceNaulin inversion test")
 success = True

From a59b93bff940084da6a77bf17c3338ff96439b18 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 15:04:33 +0100
Subject: [PATCH 1208/1827] E712 Avoid inequality comparisons to `False`; use
 `log:` for truth checks

---
 .../test_interchange_instability.py                             | 2 +-
 .../test-invertable-operator/test_invertable_operator.py        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index 26b56e19eb..2bc9b1c461 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -26,7 +26,7 @@ def test_interchange_instability():
 
     def growth_rate(path, nproc, log=False):
         pipe = False
-        if log != False:
+        if log:
             pipe = True
         s, out = launch_safe(
             "./2fluid -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe
diff --git a/tests/integrated/test-invertable-operator/test_invertable_operator.py b/tests/integrated/test-invertable-operator/test_invertable_operator.py
index 1708007fb0..3a8379f323 100755
--- a/tests/integrated/test-invertable-operator/test_invertable_operator.py
+++ b/tests/integrated/test-invertable-operator/test_invertable_operator.py
@@ -23,7 +23,7 @@
 
 def run(path, nproc, log=False):
     pipe = False
-    if log != False:
+    if log:
         pipe = True
     s, out = launch_safe(
         "./invertable_operator -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe

From b6b4e1cbb250ffe313c0f2c66f7125deba066bcd Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 12 May 2026 15:16:59 +0100
Subject: [PATCH 1209/1827] Explicitly pass x, y, z as a dictionary to eval()

to prevent type-checker warnings.
---
 tests/integrated/test-initial/test_initial.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index 6617cc2cff..cf61514fac 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -202,8 +202,10 @@ def test_initial():
                     )
                 )
                 continue
+
+            context = {"x": x, "y": y, "z": z}
             try:
-                analytic = eval(function)
+                analytic = eval(function, globals(), context)
             except NotImplementedError as err:
                 print("{} not implemented, skipping".format(err.args[0]))
             else:

From 760d9a3636513843d11e27d2caa9e4ea07ac8eb9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 15 May 2026 19:33:17 +0000
Subject: [PATCH 1210/1827] Bump externalpackages/googletest from `d72f9c8` to
 `dc3c9ed`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `d72f9c8` to `dc3c9ed`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/d72f9c8aea6817cdf1ca0ac10887f328de7f3da2...dc3c9eda2f02ba32de9329dd27ace7e527f492dc)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: dc3c9eda2f02ba32de9329dd27ace7e527f492dc
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index d72f9c8aea..dc3c9eda2f 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit d72f9c8aea6817cdf1ca0ac10887f328de7f3da2
+Subproject commit dc3c9eda2f02ba32de9329dd27ace7e527f492dc

From 4c517d2d5e8c111b4c4ab9aba3680d8e60609434 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 19 May 2026 23:29:31 -0700
Subject: [PATCH 1211/1827] Testing: Convert fci-operators example to
 test-petsc-operators

Since correctness depends on a combination of mesh generation
and BOUT++ implementation, this integrated test installs
Zoidberg in a virtual environment to generate a mesh.

Uses pytest for forward compatibility
---
 examples/CMakeLists.txt                       |   1 -
 examples/fci-operators/CMakeLists.txt         |  14 --
 examples/fci-operators/makeplots.py           |  90 -----------
 tests/integrated/CMakeLists.txt               |   1 +
 .../test-petsc-operators/CMakeLists.txt       |   7 +
 .../test-petsc-operators}/data/BOUT.inp       |   2 +-
 .../test-petsc-operators}/rotating-ellipse.py |  64 ++++----
 tests/integrated/test-petsc-operators/runtest |   5 +
 .../test_petsc_operators.cxx                  |   0
 .../test_petsc_operators.py                   | 151 ++++++++++++++++++
 10 files changed, 198 insertions(+), 137 deletions(-)
 delete mode 100644 examples/fci-operators/CMakeLists.txt
 delete mode 100644 examples/fci-operators/makeplots.py
 create mode 100644 tests/integrated/test-petsc-operators/CMakeLists.txt
 rename {examples/fci-operators => tests/integrated/test-petsc-operators}/data/BOUT.inp (50%)
 rename {examples/fci-operators => tests/integrated/test-petsc-operators}/rotating-ellipse.py (64%)
 create mode 100755 tests/integrated/test-petsc-operators/runtest
 rename examples/fci-operators/fci_operators_example.cxx => tests/integrated/test-petsc-operators/test_petsc_operators.cxx (100%)
 create mode 100644 tests/integrated/test-petsc-operators/test_petsc_operators.py

diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index 5eabaf045d..f2444e6bf6 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -18,7 +18,6 @@ add_subdirectory(dalf3)
 add_subdirectory(eigen-box)
 add_subdirectory(elm-pb)
 add_subdirectory(elm-pb-outerloop)
-add_subdirectory(fci-operators)
 add_subdirectory(fci-wave)
 add_subdirectory(finite-volume/diffusion)
 add_subdirectory(finite-volume/fluid)
diff --git a/examples/fci-operators/CMakeLists.txt b/examples/fci-operators/CMakeLists.txt
deleted file mode 100644
index 3a19ea9dcc..0000000000
--- a/examples/fci-operators/CMakeLists.txt
+++ /dev/null
@@ -1,14 +0,0 @@
-cmake_minimum_required(VERSION 3.13)
-
-project(fci-operators LANGUAGES CXX)
-
-if(NOT TARGET bout++::bout++)
-  find_package(bout++ REQUIRED)
-endif()
-
-bout_add_example(
-  fci-operators
-  SOURCES fci_operators_example.cxx
-  DATA_DIRS data
-  EXTRA_FILES rotating-ellipse.py makeplots.py
-)
diff --git a/examples/fci-operators/makeplots.py b/examples/fci-operators/makeplots.py
deleted file mode 100644
index 53c3d38f05..0000000000
--- a/examples/fci-operators/makeplots.py
+++ /dev/null
@@ -1,90 +0,0 @@
-from boutdata import collect
-import matplotlib.pyplot as plt
-import numpy as np
-
-path = "data"
-
-forward_op = collect("forward_op", path=path)
-forward = collect("forward", path=path)
-
-grad_par_op = collect("grad_par_op", path=path)
-grad_par_yud = collect("grad_par_yud", path=path)
-
-div_par_op = collect("div_par_op", path=path)
-div_par_yud = collect("div_par_yud", path=path)
-
-dV = collect("dV", path=path)  # Cell volume
-
-# Integrate divergence
-op_div_int = np.sum((dV * div_par_op)[2:-2, :, :])
-yud_div_int = np.sum((dV * div_par_yud)[2:-2, :, :])
-
-print(f"Div_par volume integral Op: {op_div_int} Yup/down: {yud_div_int}")
-
-div_par_grad_par_op = collect("div_par_grad_par_op", path=path)
-div_par_grad_par_yud = collect("div_par_grad_par_yud", path=path)
-
-# Integrate divergence
-op_div2_int = np.sum((dV * div_par_grad_par_op)[2:-2, :, :])
-yud_div2_int = np.sum((dV * div_par_grad_par_yud)[2:-2, :, :])
-
-print(f"Div_par_Grad_par volume integral Op: {op_div2_int} Yup/down: {yud_div2_int}")
-
-
-def plot_comparison(a, alabel, b, blabel):
-    fig, axs = plt.subplots(1, 3, figsize=(10, 3))
-    vmax = max([np.amax(a), np.amax(b)])
-    vmin = min([np.amin(a), np.amin(b)])
-
-    cs = axs[0].contourf(a, vmin=vmin, vmax=vmax)
-    fig.colorbar(cs, ax=axs[0])
-    axs[0].set_title(alabel)
-
-    axs[1].contourf(b, vmin=vmin, vmax=vmax)
-    axs[1].set_title(blabel)
-
-    cs = axs[2].contourf(a - b)
-    axs[2].set_title("Difference")
-    fig.colorbar(cs, ax=axs[2])
-
-    return fig
-
-
-fig = plot_comparison(
-    forward_op[2:-2, 2, :], "Operator", forward[2:-2, 2, :], "Yup/down"
-)
-fig.suptitle("Forward")
-fig.tight_layout()
-
-fig = plot_comparison(
-    grad_par_op[2:-2, 2, :], "Operator", grad_par_yud[2:-2, 2, :], "Yup/down"
-)
-fig.suptitle("Parallel Gradient")
-fig.tight_layout()
-fig.savefig("gradient.pdf")
-fig.savefig("gradient.png")
-
-fig = plot_comparison(
-    div_par_op[2:-2, 2, :],
-    f"Operator [integral {op_div_int:.2e}]",
-    div_par_yud[2:-2, 2, :],
-    f"Yup/down [integral {yud_div_int:.2e}]",
-)
-fig.suptitle("Parallel Divergence")
-fig.tight_layout()
-fig.savefig("divergence.pdf")
-fig.savefig("divergence.png")
-
-fig = plot_comparison(
-    div_par_grad_par_op[2:-2, 2, :],
-    f"Operator [integral {op_div2_int:.2e}]",
-    div_par_grad_par_yud[2:-2, 2, :],
-    f"Yup/down [integral {yud_div2_int:.2e}]",
-)
-fig.suptitle("Parallel diffusion")
-fig.tight_layout()
-fig.savefig("diffusion.pdf")
-fig.savefig("diffusion.png")
-
-
-plt.show()
diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt
index 3696ef0372..a31fe551da 100644
--- a/tests/integrated/CMakeLists.txt
+++ b/tests/integrated/CMakeLists.txt
@@ -34,6 +34,7 @@ add_subdirectory(test-naulin-laplace)
 add_subdirectory(test-options-netcdf)
 add_subdirectory(test-petsc_laplace)
 add_subdirectory(test-petsc_laplace_MAST-grid)
+add_subdirectory(test-petsc-operators)
 add_subdirectory(test-restart-io)
 add_subdirectory(test-restarting)
 add_subdirectory(test-slepc-solver)
diff --git a/tests/integrated/test-petsc-operators/CMakeLists.txt b/tests/integrated/test-petsc-operators/CMakeLists.txt
new file mode 100644
index 0000000000..7191a39a30
--- /dev/null
+++ b/tests/integrated/test-petsc-operators/CMakeLists.txt
@@ -0,0 +1,7 @@
+bout_add_integrated_test(
+  test_petsc_operators
+  SOURCES test_petsc_operators.cxx
+  USE_RUNTEST USE_DATA_BOUT_INP
+  REQUIRES BOUT_HAS_PETSC
+  EXTRA_FILES rotating-ellipse.py test_petsc_operators.py
+)
diff --git a/examples/fci-operators/data/BOUT.inp b/tests/integrated/test-petsc-operators/data/BOUT.inp
similarity index 50%
rename from examples/fci-operators/data/BOUT.inp
rename to tests/integrated/test-petsc-operators/data/BOUT.inp
index 182d49cb96..72907d3fc9 100644
--- a/examples/fci-operators/data/BOUT.inp
+++ b/tests/integrated/test-petsc-operators/data/BOUT.inp
@@ -1,5 +1,5 @@
 [mesh]
-file = "rotating-ellipse-20x8x20.fci.nc"
+file = "rotating-ellipse-20x8x20-s5.fci.nc"
 
 [mesh:paralleltransform]
 type = fci
diff --git a/examples/fci-operators/rotating-ellipse.py b/tests/integrated/test-petsc-operators/rotating-ellipse.py
similarity index 64%
rename from examples/fci-operators/rotating-ellipse.py
rename to tests/integrated/test-petsc-operators/rotating-ellipse.py
index 3aa485c093..2482d580c9 100755
--- a/examples/fci-operators/rotating-ellipse.py
+++ b/tests/integrated/test-petsc-operators/rotating-ellipse.py
@@ -1,11 +1,34 @@
 #!/usr/bin/env python
 
-# Create grids for a rotating ellipse stellarator, based on curvilinear grids
-
+import argparse
 import numpy as np
-
 import zoidberg
 
+parser = argparse.ArgumentParser(
+    prog="RotatingEllipse",
+    description="Create grids for a rotating ellipse stellarator, based on curvilinear grids.",
+)
+parser.add_argument(
+    "-nx", type=int, default=20, help="Number of radial (x) cells including boundaries"
+)
+parser.add_argument(
+    "-ny", "--nslices", type=int, default=8, help="Number of parallel (y) slices"
+)
+parser.add_argument("-nz", type=int, default=20, help="Number of poloidal (z) cells")
+parser.add_argument(
+    "-ns",
+    "--nsamples-per-dim",
+    type=int,
+    default=1,
+    help="Number of samples per dimension",
+)
+parser.add_argument("-pb", "--partial-boundaries", action="store_true", default=True)
+parser.add_argument("-o", "--output", type=str, default="")
+args = parser.parse_args()
+
+if args.output == "":
+    args.output = f"rotating-ellipse-{args.nx}x{args.nslices}x{args.nz}-s{args.nsamples_per_dim}{'-npb' if not args.partial_boundaries else ''}.fci.nc"
+
 #############################################################################
 # Define the magnetic field
 
@@ -30,8 +53,7 @@
 start_r = xcentre + 0.4
 start_z = 0.0
 
-nslices = 8  # Number of poloidal slices
-ycoords = np.linspace(0, yperiod, nslices)
+ycoords = np.linspace(0, yperiod, args.nslices, endpoint=False)
 npoints = 20  # Points per poloidal slice
 
 rzcoord, ycoords = zoidberg.fieldtracer.trace_poincare(
@@ -39,7 +61,7 @@
 )
 
 inner_lines = []
-for i in range(nslices):
+for i in range(args.nslices):
     r = rzcoord[:, i, 0, 0]
     z = rzcoord[:, i, 0, 1]
     line = zoidberg.rzline.line_from_points(r, z)
@@ -59,11 +81,8 @@
 # Now have inner and outer boundaries for each poloidal grid
 # Generate a grid on each poloidal slice using the elliptic grid generator
 
-nx = 20
-nz = 20
-
 pol_grids = [
-    zoidberg.poloidal_grid.grid_elliptic(inner_line, outer_line, nx, nz)
+    zoidberg.poloidal_grid.grid_elliptic(inner_line, outer_line, args.nx, args.nz)
     for inner_line in inner_lines
 ]
 
@@ -72,31 +91,14 @@
 
 grid = zoidberg.grid.Grid(pol_grids, ycoords, yperiod, yperiodic=True)
 
-samples_per_dim = 5  # Sub-sampling in each cell
+maps = zoidberg.make_maps(grid, magnetic_field, samples_per_dim=args.nsamples_per_dim)
 
-maps = zoidberg.make_maps(grid, magnetic_field, samples_per_dim=samples_per_dim)
-
-#############################################################################
-# Interpolation weights
-
-weight_vars = zoidberg.weights.calculate_parallel_map_operators(maps)
-maps.update(weight_vars)
-# Remove sub-sampled maps from output
-for var in [
-    "forward_xt_primes",
-    "forward_zt_primes",
-    "backward_xt_primes",
-    "backward_zt_primes",
-    "subcell_weights",
-]:
-    maps.pop(var, None)
+maps = zoidberg.weights.modify_maps(maps, partial_boundaries=args.partial_boundaries)
 
 #############################################################################
 # Write grid file
 
-filename = f"rotating-ellipse-{nx}x{nslices}x{nz}-s{samples_per_dim}.fci.nc"
-
-print(f"Writing to grid file '{filename}'")
+print(f"Writing to grid file '{args.output}'")
 zoidberg.write_maps(
-    grid, magnetic_field, maps, gridfile=filename, new_names=False, metric2d=False
+    grid, magnetic_field, maps, gridfile=args.output, new_names=False, metric2d=False
 )
diff --git a/tests/integrated/test-petsc-operators/runtest b/tests/integrated/test-petsc-operators/runtest
new file mode 100755
index 0000000000..9b28e48157
--- /dev/null
+++ b/tests/integrated/test-petsc-operators/runtest
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+#
+# requires: petsc
+
+pytest .
diff --git a/examples/fci-operators/fci_operators_example.cxx b/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
similarity index 100%
rename from examples/fci-operators/fci_operators_example.cxx
rename to tests/integrated/test-petsc-operators/test_petsc_operators.cxx
diff --git a/tests/integrated/test-petsc-operators/test_petsc_operators.py b/tests/integrated/test-petsc-operators/test_petsc_operators.py
new file mode 100644
index 0000000000..9ece74b9a0
--- /dev/null
+++ b/tests/integrated/test-petsc-operators/test_petsc_operators.py
@@ -0,0 +1,151 @@
+import pytest
+import venv
+import subprocess
+import sys
+import numpy as np
+import warnings
+
+from boututils.run_wrapper import build_and_log, launch_safe
+
+
+def analyse_path(path, plot=False, tol=1e-12):
+    from boutdata import collect
+
+    forward_op = collect("forward_op", path=path)
+    forward = collect("forward", path=path)
+
+    grad_par_op = collect("grad_par_op", path=path)
+    grad_par_yud = collect("grad_par_yud", path=path)
+
+    div_par_op = collect("div_par_op", path=path)
+    div_par_yud = collect("div_par_yud", path=path)
+
+    dV = collect("dV", path=path)  # Cell volume
+
+    # Integrate divergence
+    op_div_int = np.sum((dV * div_par_op)[2:-2, :, :])
+    yud_div_int = np.sum((dV * div_par_yud)[2:-2, :, :])
+
+    if np.abs(op_div_int) > tol:
+        raise ValueError(f"Div_par operator has integral {op_div_int} > {tol}")
+
+    print(f"Div_par volume integral Op: {op_div_int} Yup/down: {yud_div_int}")
+
+    div_par_grad_par_op = collect("div_par_grad_par_op", path=path)
+    div_par_grad_par_yud = collect("div_par_grad_par_yud", path=path)
+
+    # Integrate divergence
+    op_div2_int = np.sum((dV * div_par_grad_par_op)[2:-2, :, :])
+    yud_div2_int = np.sum((dV * div_par_grad_par_yud)[2:-2, :, :])
+
+    if np.abs(op_div2_int) > tol:
+        raise ValueError(
+            f"Div_par_Grad_par operator has integral {op_div2_int} > {tol}"
+        )
+
+    if plot:
+        import matplotlib.pyplot as plt
+
+        def plot_comparison(a, alabel, b, blabel):
+            fig, axs = plt.subplots(1, 3, figsize=(10, 3))
+            vmax = max([np.amax(a), np.amax(b)])
+            vmin = min([np.amin(a), np.amin(b)])
+
+            cs = axs[0].contourf(a, vmin=vmin, vmax=vmax)
+            fig.colorbar(cs, ax=axs[0])
+            axs[0].set_title(alabel)
+
+            axs[1].contourf(b, vmin=vmin, vmax=vmax)
+            axs[1].set_title(blabel)
+
+            cs = axs[2].contourf(a - b)
+            axs[2].set_title("Difference")
+            fig.colorbar(cs, ax=axs[2])
+
+            return fig
+
+        fig = plot_comparison(
+            forward_op[2:-2, 2, :], "Operator", forward[2:-2, 2, :], "Yup/down"
+        )
+        fig.suptitle("Forward")
+        fig.tight_layout()
+
+        fig = plot_comparison(
+            grad_par_op[2:-2, 2, :], "Operator", grad_par_yud[2:-2, 2, :], "Yup/down"
+        )
+        fig.suptitle("Parallel Gradient")
+        fig.tight_layout()
+        fig.savefig("gradient.pdf")
+        fig.savefig("gradient.png")
+
+        fig = plot_comparison(
+            div_par_op[2:-2, 2, :],
+            f"Operator [integral {op_div_int:.2e}]",
+            div_par_yud[2:-2, 2, :],
+            f"Yup/down [integral {yud_div_int:.2e}]",
+        )
+        fig.suptitle("Parallel Divergence")
+        fig.tight_layout()
+        fig.savefig("divergence.pdf")
+        fig.savefig("divergence.png")
+
+        fig = plot_comparison(
+            div_par_grad_par_op[2:-2, 2, :],
+            f"Operator [integral {op_div2_int:.2e}]",
+            div_par_grad_par_yud[2:-2, 2, :],
+            f"Yup/down [integral {yud_div2_int:.2e}]",
+        )
+        fig.suptitle("Parallel diffusion")
+        fig.tight_layout()
+        fig.savefig("diffusion.pdf")
+        fig.savefig("diffusion.png")
+
+
+@pytest.fixture(scope="session")
+def temporary_venv(tmp_path_factory):
+    # Create a venv
+    venv_dir = tmp_path_factory.mktemp("venv")
+    venv.create(venv_dir, with_pip=True, symlinks=True)
+
+    # Determine the correct python path (platform dependent)
+    python_exe = str(
+        venv_dir / ("Scripts" if sys.platform == "win32" else "bin") / "python"
+    )
+
+    # Clone and install latest version of Zoidberg
+    zoidberg_dir = tmp_path_factory.mktemp("zoidberg")
+    subprocess.check_call(
+        [
+            "git",
+            "clone",
+            "https://github.com/boutproject/zoidberg.git",
+            str(zoidberg_dir),
+        ]
+    )
+    subprocess.check_call([python_exe, "-m", "pip", "install", str(zoidberg_dir)])
+
+    return python_exe
+
+
+def test_petsc_operators(temporary_venv):
+    grid_path = "grid.fci.nc"
+
+    # Generate grid file and store in temporary path
+    subprocess.check_call([temporary_venv, "rotating-ellipse.py", "-o", grid_path])
+
+    # Build executable
+    build_and_log("test_petsc_operators")
+
+    nproc = 1
+
+    try:
+        s, out = launch_safe(
+            f"./test_petsc_operators -d data mesh:file={grid_path}",
+            nproc=nproc,
+            pipe=True,
+        )
+    except Exception as e:
+        # May throw after run
+        warnings.warn(f"Caught exception: {e}", RuntimeWarning)
+
+    analyse_path("data")

From 5fb45f6481d462770ee6b4daff16b026b30ef493 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 20 May 2026 09:16:28 +0200
Subject: [PATCH 1212/1827] Do not copy

---
 include/bout/boundary_region_iter.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index ee0132c527..323956f16f 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -538,10 +538,10 @@ public:
 } // namespace bout
 
 inline bout::boundary::BoundaryRegionIterFCI
-begin(const bout::boundary::BoundaryRegionFCI reg) {
+begin(const bout::boundary::BoundaryRegionFCI& reg) {
   return bout::boundary::BoundaryRegionIterFCI(&reg, true);
 }
 inline bout::boundary::BoundaryRegionIterFCI
-end(const bout::boundary::BoundaryRegionFCI reg) {
+end(const bout::boundary::BoundaryRegionFCI& reg) {
   return bout::boundary::BoundaryRegionIterFCI(&reg, false);
 }

From 9c7b904275292dba4c3fbbd74fbbf8f39f7ff0ca Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 20 May 2026 09:17:47 +0200
Subject: [PATCH 1213/1827] Avoid some warnings

---
 src/invert/laplace/impls/pcr/pcr.cxx                 |  2 --
 src/mesh/data/gridfromfile.cxx                       | 10 ++--------
 src/mesh/impls/bout/boutmesh.cxx                     |  4 +++-
 src/solver/impls/adams_bashforth/adams_bashforth.cxx |  8 +++++---
 4 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx
index eb786afa2c..93fbf09cdb 100644
--- a/src/invert/laplace/impls/pcr/pcr.cxx
+++ b/src/invert/laplace/impls/pcr/pcr.cxx
@@ -560,7 +560,6 @@ void LaplacePCR ::pcr_forward_single_row(Matrix<dcomplex>& a, Matrix<dcomplex>&
   const int nlevel = log2(nprocs);
   const int nhprocs = nprocs / 2;
   int dist_rank = 1;
-  int dist2_rank = 2;
 
   /// Parallel cyclic reduction continues until 2x2 matrix are made between a pair of
   /// rank, (myrank, myrank+nhprocs).
@@ -678,7 +677,6 @@ void LaplacePCR ::pcr_forward_single_row(Matrix<dcomplex>& a, Matrix<dcomplex>&
     }
 
     dist_rank *= 2;
-    dist2_rank *= 2;
   }
 
   /// Solving 2x2 matrix. All pair of ranks, myrank and myrank+nhprocs, solves it
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 10f6f6926e..27ad9411c2 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -120,7 +120,7 @@ bool GridFile::get(Mesh* UNUSED(m), BoutReal& rval, const std::string& name,
 
 /*!
  * Reads a 2D, 3D or FieldPerp field variable from a file
- * 
+ *
  * Successfully reads Field2D or FieldPerp if the variable in the file is 0-D or 2-D.
  * Successfully reads Field3D if the variable in the file is 0-D, 2-D or 3-D.
  */
@@ -207,9 +207,6 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def,
   // we pass
   int ys = m->OffsetY;
 
-  // Total number of y-boundary cells in grid file, used for check later.
-  // Value depends on if we are double-null or not.
-  int total_grid_yguards = 2 * grid_yguards;
   if (m->numberOfXPoints > 1) {
     ASSERT1(m->numberOfXPoints == 2);
     // Need to check if we are before or after the target in the middle of the
@@ -219,9 +216,6 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def,
       // Note: neither ny_inner nor OffsetY include guard cells
       ys += 2 * grid_yguards;
     }
-
-    // Add y-boundary guard cells at upper target
-    total_grid_yguards += 2 * grid_yguards;
   }
 
   // Index offsets into destination
@@ -378,7 +372,7 @@ void GridFile::readField(Mesh* m, const std::string& name, int ys, int yd, int n
 
     for (int x = xs; x < xs + nx_to_read; ++x) {
       for (int y = ys; y < ys + ny_to_read; ++y) {
-        BoutReal const value = full_var(x, y);
+        const BoutReal value = full_var(x, y);
         for (int z = 0; z < var.getNz(); z++) {
           var(x - xs + xd, y - ys + yd, z) = value;
         }
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index e713ca4f6c..bc9994ed2c 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -1044,7 +1044,9 @@ void BoutMesh::createXBoundaries() {
   }
 }
 
-int BoutMesh::getProcIndex(int X, int Y, int Z) const { return Y * NXPE + X; }
+int BoutMesh::getProcIndex(int X, int Y, [[maybe_unused]] int Z) const {
+  return Y * NXPE + X;
+}
 
 void BoutMesh::createYBoundaries() {
   if (MYG <= 0) {
diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
index 51fff4fe6a..00bd8f4ff2 100644
--- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx
+++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
@@ -352,8 +352,8 @@ void AdamsBashforthSolver::resetInternalFields() {
 int AdamsBashforthSolver::run() {
 
   // Just for developer diagnostics
-  int nwasted = 0;
-  int nwasted_following_fail = 0;
+  [[maybe_unused]] int nwasted = 0;
+  [[maybe_unused]] int nwasted_following_fail = 0;
 
   for (int s = 0; s < getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
@@ -373,7 +373,7 @@ int AdamsBashforthSolver::run() {
 
       // Just for developer diagnostics - set to true when the previous
       // attempt at a time step failed.
-      bool previous_fail = false;
+      [[maybe_unused]] bool previous_fail = false;
 
       // Flag to indicate if we want to use a lower order method
       bool use_lower = false;
@@ -488,12 +488,14 @@ int AdamsBashforthSolver::run() {
         // Be more conservative if we've failed;
         timestep = 0.9 * dt_lim;
 
+#if CHECK > 4
         // For developers
         if (previous_fail) {
           nwasted_following_fail++;
         }
         previous_fail = true;
         nwasted++;
+#endif
       }
 
       // Ditch last history point if we have enough

From 51fc4aa60d26b28e3004df9659ac593977ceca62 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 20 May 2026 10:32:11 +0200
Subject: [PATCH 1214/1827] Ensure isParallel is set

---
 include/bout/boundary_region_iter.hxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 323956f16f..98706905d6 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -405,7 +405,9 @@ class BoundaryRegionFCI : public BoundaryRegionBase {
 public:
   BoundaryRegionFCI(const std::string& name, [[maybe_unused]] const BndryLoc& loc,
                     int dir, Mesh* mesh)
-      : BoundaryRegionBase(name, mesh), _dir(dir), localmesh(mesh) {};
+      : BoundaryRegionBase(name, mesh), _dir(dir), localmesh(mesh) {
+    isParallel = true;
+  };
   /// Add a point to the boundary
   void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
                  char valid, signed char offset) {

From 9faef5c80899bb7cd683d22172814635024f7938 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 20 May 2026 11:15:49 +0200
Subject: [PATCH 1215/1827] Use system cpptrace on fedora

---
 .ci_fedora.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index e1dc563c6c..8262d032cc 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -52,7 +52,8 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
 	 -DBOUT_UPDATE_GIT_SUBMODULE=OFF \
 	 -DBOUT_USE_SYSTEM_FMT=ON \
 	 -DBOUT_USE_SYSTEM_MPARK_VARIANT=ON \
-	 -DBOUT_USE_SUNDIALS=ON
+	 -DBOUT_USE_SUNDIALS=ON \
+	 -DBOUT_USE_SYSTEM_CPPTRACE=ON
 
     time make -C build build-check -j 2
     time make -C build check

From 490d054bf4cf031de466daeec8aca0af99713cde Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 21 May 2026 00:59:15 +0200
Subject: [PATCH 1216/1827] fix sign error

---
 include/bout/boundary_region_iter.hxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 98706905d6..d85afa754a 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -479,7 +479,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() + off * region->_dir;
+    auto _off = _offset() - off * region->_dir;
     return f.ynext(_off)[ind().yp(_off)];
   }
   template <bool check = true>
@@ -488,7 +488,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() + off * region->_dir;
+    auto _off = _offset() - off * region->_dir;
     return f.ynext(_off)[ind().yp(_off)];
   }
   template <bool check = true>
@@ -497,7 +497,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() + off * region->_dir;
+    auto _off = _offset() - off * region->_dir;
     return f.ynext(_off)[ind().yp(_off)];
   }
   template <bool check = true>
@@ -506,7 +506,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() + off * region->_dir;
+    auto _off = _offset() - off * region->_dir;
     return f.ynext(_off)[ind().yp(_off)];
   }
   template <bool check = true>

From ca3f5efa295f747e9aaebea3042339f8edfff415 Mon Sep 17 00:00:00 2001
From: wearysebas <sebichito@gmail.com>
Date: Thu, 21 May 2026 16:02:00 +0100
Subject: [PATCH 1217/1827] Add remaining topology documentation (images +
 supported_topologies)

---
 .../figs/Topologies/CDN/CDN_Geometry.png      | Bin 0 -> 186058 bytes
 .../figs/Topologies/CDN/CDN_processors.png    | Bin 0 -> 51458 bytes
 .../figs/Topologies/CDN/CDN_regions.png       | Bin 0 -> 54130 bytes
 .../figs/Topologies/CDN/CDN_topology.png      | Bin 0 -> 59072 bytes
 .../figs/Topologies/SF/SF_processors.png      | Bin 0 -> 62763 bytes
 .../sphinx/figs/Topologies/SF/SF_regions.png  | Bin 0 -> 82422 bytes
 .../sphinx/figs/Topologies/SF/SF_topology.png | Bin 0 -> 78287 bytes
 .../figs/Topologies/SF/SFminus_Geometry.png   | Bin 0 -> 683587 bytes
 .../figs/Topologies/SF/SFplus_Geometry.png    | Bin 0 -> 201865 bytes
 .../sphinx/figs/Topologies/SN/SN_Geometry.png | Bin 0 -> 149799 bytes
 .../figs/Topologies/SN/SN_processors.png      | Bin 0 -> 57104 bytes
 .../sphinx/figs/Topologies/SN/SN_regions.png  | Bin 0 -> 56739 bytes
 .../sphinx/figs/Topologies/SN/SN_topology.png | Bin 0 -> 50811 bytes
 .../figs/Topologies/UDN/UDN_Geometry.png      | Bin 0 -> 212195 bytes
 .../figs/Topologies/UDN/UDN_processors.png    | Bin 0 -> 63291 bytes
 .../figs/Topologies/UDN/UDN_regions.png       | Bin 0 -> 190467 bytes
 .../figs/Topologies/UDN/UDN_topology.png      | Bin 0 -> 70752 bytes
 manual/sphinx/figs/topology_cross_section.png | Bin 115905 -> 99460 bytes
 manual/sphinx/index.rst                       |   8 +
 manual/sphinx/requirements.txt                |   2 +-
 manual/sphinx/user_docs/input_grids.rst       | 244 ++----------------
 .../sphinx/user_docs/supported_topologies.rst | 201 +++++++++++++++
 manual/sphinx/user_docs/topology.rst          |   4 +-
 23 files changed, 232 insertions(+), 227 deletions(-)
 create mode 100644 manual/sphinx/figs/Topologies/CDN/CDN_Geometry.png
 create mode 100644 manual/sphinx/figs/Topologies/CDN/CDN_processors.png
 create mode 100644 manual/sphinx/figs/Topologies/CDN/CDN_regions.png
 create mode 100644 manual/sphinx/figs/Topologies/CDN/CDN_topology.png
 create mode 100644 manual/sphinx/figs/Topologies/SF/SF_processors.png
 create mode 100644 manual/sphinx/figs/Topologies/SF/SF_regions.png
 create mode 100644 manual/sphinx/figs/Topologies/SF/SF_topology.png
 create mode 100644 manual/sphinx/figs/Topologies/SF/SFminus_Geometry.png
 create mode 100644 manual/sphinx/figs/Topologies/SF/SFplus_Geometry.png
 create mode 100644 manual/sphinx/figs/Topologies/SN/SN_Geometry.png
 create mode 100644 manual/sphinx/figs/Topologies/SN/SN_processors.png
 create mode 100644 manual/sphinx/figs/Topologies/SN/SN_regions.png
 create mode 100644 manual/sphinx/figs/Topologies/SN/SN_topology.png
 create mode 100644 manual/sphinx/figs/Topologies/UDN/UDN_Geometry.png
 create mode 100644 manual/sphinx/figs/Topologies/UDN/UDN_processors.png
 create mode 100644 manual/sphinx/figs/Topologies/UDN/UDN_regions.png
 create mode 100644 manual/sphinx/figs/Topologies/UDN/UDN_topology.png
 create mode 100644 manual/sphinx/user_docs/supported_topologies.rst

diff --git a/manual/sphinx/figs/Topologies/CDN/CDN_Geometry.png b/manual/sphinx/figs/Topologies/CDN/CDN_Geometry.png
new file mode 100644
index 0000000000000000000000000000000000000000..ae68ace00482953537db90147627f3bcdd0eb12e
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diff --git a/manual/sphinx/index.rst b/manual/sphinx/index.rst
index c150273285..9408d05057 100644
--- a/manual/sphinx/index.rst
+++ b/manual/sphinx/index.rst
@@ -85,6 +85,14 @@ The documentation is divided into the following sections:
    user_docs/preconditioning
    user_docs/BOUT_Gradperp_op
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Topology Handling
+   :name: topologies
+
+   user_docs/topology
+   user_docs/supported_topologies
+
 .. toctree::
    :maxdepth: 1
    :caption: Developer Documentation
diff --git a/manual/sphinx/requirements.txt b/manual/sphinx/requirements.txt
index e09943ad07..52a1764023 100644
--- a/manual/sphinx/requirements.txt
+++ b/manual/sphinx/requirements.txt
@@ -1,4 +1,4 @@
-breathe>=4.30
+#breathe>=4.30
 Jinja2>=2.11.3
 numpy>=1.21.1
 netcdf4>=1.5.6
diff --git a/manual/sphinx/user_docs/input_grids.rst b/manual/sphinx/user_docs/input_grids.rst
index 3d6be2cf77..402fb30d06 100644
--- a/manual/sphinx/user_docs/input_grids.rst
+++ b/manual/sphinx/user_docs/input_grids.rst
@@ -155,237 +155,27 @@ The only quantities which are required are the sizes of the grid. If
 these are the only quantities specified, then the coordinates revert to
 Cartesian.
 
-This section describes how to generate inputs for tokamak equilibria. If
-you’re not interested in tokamaks then you can skip to the next section.
-
-The directory ``tokamak_grids`` contains code to generate input grid
-files for tokamaks. These can be used by, for example, the ``2fluid`` and
-``highbeta_reduced`` modules.
-
-.. _sec-bout-topology:
-
-BOUT++ Topology
----------------
-
-Basic
-~~~~~
-
-BOUT++ is designed to work in a variety of tokamak and non-tokamak
-geometries, from simple slabs to disconnected double-null
-configurations. In order to handle tokamak geometry BOUT++ contains an
-internal topology which is built from six regions determined by four
-branch-cut locations and two separatrix locations (``ixseps1`` and
-``ixseps2``). There are some limitations on these regions that we will
-discuss below, and some regions may be empty, all of which enables
-BOUT++ to describe effectively seven types of topology:
-
-- "core": this type of topology can describe the closed field line
-  regions inside the separatrix of tokamaks or other devices, or
-  idealised geometries like periodic slabs;
-
-- "SOL": these can describe the open field line regions of the
-  scrape-off layer (SOL) outside the separatrix of a tokamak, or linear
-  devices with a target plate at either end;
-
-- "limiter": these topologies have an open field line region and a
-  region where field lines hit a boundary, without an X-point;
-
-- "X-point": these topologies have four separate legs with their own
-  boundaries, and no closed field line region;
-
-- "single null": this type of topology has one X-point with two separate
-  legs, closed and an open field line regions, and a single separatrix;
-
-- "connected double null": these topologies have two X-points with two
-  separate legs each, closed and open field line regions and a single
-  separatrix that connects both X-points;
-
-- "disconnected double null": finally, these are similar to connected
-  double null geometries except that they have two separatrices that do
-  not connect the two X-points. These come in "lower" and "upper"
-  flavours, depending on which X-point is adjacent to the closed field
-  line region.
-
-The six regions that form the building blocks of these topologies are:
-
-- four separate "leg" regions that have a boundary in the ``y``
-  direction;
-
-- two "core" regions that do not have boundaries in ``y``.
-
-Each of these regions may have additional boundaries in the ``x``
-direction. The separate regions are illustrated in
-:numref:`fig-topology-cross-section`: the grey dashed lines show the
-region partitions, with the sections labelled 1, 2, and 3 forming one
-leg; 4, 5, and 6 forming one core region, and so on. The internal names
-for these separate regions use "inner" and "outer" in reference to the
-major radius -- that is, "inner" regions correspond to the left-hand
-side of :numref:`fig-topology-cross-section` and "outer" regions to the
-right-hand side.
-
-Two important limitations for BOUT++ grids are that a single processor
-can only belong to one region, and that there must be the same number of
-points on each processor. The first limitation means that certain
-topologies require a minimum number of processors. For example, a
-disconnected double null configuration uses all six regions -- therefore
-the minimum number of processors able to describe this in BOUT++ is
-six. Having equal numbers of points on each processor can put some
-restrictions on the resolution of simulations.
-
-The two separatrix locations are ``ixseps1`` and ``ixseps2``, these are
-the global indices in the ``x`` domain where the first and second
-separatrices are located. These values are set either in the grid file
-or in ``BOUT.inp``.  :numref:`fig-topology-cross-section` shows
-schematically how ``ixseps`` is used.
-
-If ``ixseps1 == ixseps2`` then there is a single separatrix representing
-the boundary between the core region and the SOL region and the grid is
-a connected double null configuration. If ``ixseps1 > ixseps2`` then
-there are two separatrices and the inner separatrix is ``ixseps2`` so
-the tokamak is an upper double null. If ``ixseps1 < ixseps2`` then there
-are two separatrices and the inner separatrix is ``ixseps1`` so the
-tokamak is a lower double null.
-
-In other words: Let us for illustrative purposes say that ``ixseps1 >
-ixseps2`` (see :numref:`fig-topology-cross-section`). Let us say that we
-have a field ``f(x,y,z)`` with a global ``x``-index which includes ghost
-points. ``f(x <= ixseps1, y, z)``) will then be periodic in the
-``y``-direction, ``f(ixspes1 < x <= ixseps2, y, z)``) will have boundary
-condition in the ``y``-direction set by the lowermost ``ydown`` and
-``yup``. If ``f(ixspes2 < x, y, z)``) the boundary condition in the
-``y``-direction will be set by the uppermost ``ydown`` and ``yup``. As
-for now, there is no difference between the two sets of upper and lower
-``ydown`` and ``yup`` boundary conditions (unless manually specified,
-see :ref:`sec-custom-BC`).
-
-The four branch cut locations, ``jyseps1_1``, ``jyseps1_2``,
-``jyseps2_1``, and ``jyseps2_2``, split the ``y`` domain into logical
-regions defining the SOL, the PFR (private flux region) and the core of
-the tokamak. This is illustrated also in
-:numref:`fig-topology-cross-section`. If ``jyseps1_2 == jyseps2_1`` then
-the grid is a single null configuration, otherwise the grid is a double
-null configuration.
-
-.. _fig-topology-cross-section:
-.. figure:: ../figs/topology_cross_section.*
-   :alt: Cross-section of the tokamak topology used in BOUT++
-
-   Deconstruction of a poloidal tokamak cross-section into logical
-   domains using the parameters ``ixseps1``, ``ixseps2``,
-   ``jyseps1_1``, ``jyseps1_2``, ``jyseps2_1``, and ``jyseps2_2``. This
-   configuration is a "disconnected double null" and shows all the
-   possible regions used in the BOUT++ topology.
-
-Advanced
-~~~~~~~~
-
-The internal domain in BOUT++ is deconstructed into a series of
-logically rectangular sub-domains with boundaries determined by the
-``ixseps`` and ``jyseps`` parameters. The boundaries coincide with
-processor boundaries so the number of grid points within each sub-domain
-must be an integer multiple of ``ny/nypes`` where ``ny`` is the number
-of grid points in ``y`` and ``nypes`` is the number of processors used
-to split the y domain. Processor communication across the domain
-boundaries is then handled internally. :numref:`fig-topology-schematic`
-shows schematically how the different regions of a double null tokamak
-with ``ixseps1 = ixseps2`` are connected together via communications.
-
-.. note::
-   To ensure that each subdomain follows logically, the
-   ``jyseps`` indices must adhere to the following conditions:
-
-    - ``jyseps1_1 > -1``
-    - ``jyseps2_1 >= jyseps1_1 + 1``
-    - ``jyseps1_2 >= jyseps2_1``
-    - ``jyseps2_2 >= jyseps1_2``
-    - ``jyseps2_2 <= ny - 1``
-
-   To ensure that communications work branch cuts must align with
-   processor boundaries.
-
-.. _fig-topology-schematic:
-.. figure:: ../figs/topology_schematic.*
-
-   Schematic illustration of domain decomposition and communication in
-   BOUT++ with ``ixseps1 = ixseps2``
-
-Periodic X domains
-~~~~~~~~~~~~~~~~~~
-
-The :math:`x` coordinate is usually a radial flux coordinate. In some
-simulations it is useful to make this direction periodic, for example
-flux tube simulations or the Hasegawa-Wakatani example in
-``examples/hasegawa-wakatani/hw.cxx``. In that example the :math:`x`
-coordinate is made periodic with the top-level ``periodicX`` option:
+You can read additional quantities from the grid and make them available in
+expressions in the input file by listing them in the ``input:grid_variables``
+section, with the key being the name in the grid file (``mesh:file``) and the
+value being the type (one of ``field3d``, ``field2d``, ``boutreal``):
 
 .. code-block:: cfg
 
-   periodicX = true # Domain is periodic in X
+   [input:grid_variables]
+   rho = field2d
+   theta = field2d
+   scale = boutreal
 
    [mesh]
+   B = (scale / rho) * cos(theta)
 
-   nx = 260  # Note 4 guard cells in X
-   ny = 1
-   nz = 256  # Periodic, so no guard cells in Z
-
-Note that some care is now needed if the model uses Laplacian
-inversions, for example to calculate electrostatic potential from
-vorticity: If both :math:`x` and :math:`z` coordinates are both
-periodic then the inversion has no boundary conditions. In that case
-the laplacian has a null space and so is singular; an arbitrary
-constant offset can be added to the potential without changing the
-vorticity.
-
-The default ``cyclic`` solver treats the :math:`k_z =
-0` (DC) mode as a special case, setting the average of the potential
-over the :math:`x-z` domain to zero. Other solvers may not
-handle the ``periodicX`` case in the same way.
-
-Implementations
-~~~~~~~~~~~~~~~
-
-In BOUT++ each processor has a logically rectangular domain, so any
-branch cuts needed for X-point geometry (see
-:numref:`fig-topology-schematic`) must be at processor boundaries.
-
-In the standard “bout” mesh (``src/mesh/impls/bout/``), the
-communication is controlled by the variables
-
-.. code-block:: cpp
-
-    int UDATA_INDEST, UDATA_OUTDEST, UDATA_XSPLIT;
-    int DDATA_INDEST, DDATA_OUTDEST, DDATA_XSPLIT;
-    int IDATA_DEST, ODATA_DEST;
-
-These control the behavior of the communications as shown in
-:numref:`fig-boutmesh-comms`.
-
-.. _fig-boutmesh-comms:
-.. figure:: ../figs/boutmesh-comms.*
-   :alt: Communication of guard cells in BOUT++
-
-   Communication of guard cells in BOUT++. Boundaries in X have only
-   one neighbour each, but boundaries in Y can be split into two,
-   allowing branch cuts
-
-In the Y direction, each boundary region (**U**\ p and **D**\ own in Y)
-can be split into two, with ``0 <= x < UDATA_XSPLIT`` going to the
-processor index ``UDATA_INDEST``, and ``UDATA_INDEST <= x < LocalNx`` going
-to ``UDATA_OUTDEST``. Similarly for the Down boundary. Since there are
-no branch-cuts in the X direction, there is just one destination for the
-**I**\ nner and **O**\ uter boundaries. In all cases a negative
-processor number means that there’s a domain boundary so no
-communication is needed.
-
-The communication control variables are set in the
-`BoutMesh::topology()` function, in
-``src/mesh/impls/bout/boutmesh.cxx``. First the function
-`default_connections()` sets the topology to be a rectangle.
+This section describes how to generate inputs for tokamak equilibria. If
+you’re not interested in tokamaks then you can skip to the next section.
 
-To change the topology, the function `BoutMesh::set_connection` checks
-that the requested branch cut is on a processor boundary, and changes
-the communications consistently so that communications are two-way and
-there are no “dangling” communications.
+The directory ``tokamak_grids`` contains code to generate input grid
+files for tokamaks. These can be used by, for example, the ``2fluid`` and
+``highbeta_reduced`` modules.
 
 3D variables
 ------------
@@ -431,6 +221,12 @@ has been developed to create BOUT++ input files from R-Z equilibria. This can re
 (geqdsk) files, find flux surfaces, and calculate metric
 coefficients. 
 
+From GRIDUE files
+--------------
+
+A separate tool (in python) called `INGRID <https://github.com/llnl/INGRID>`_ has been modified to be able to output BOUT++ input files too. It can read EFIT ’g’ (geqdsk) files, find flux surfaces, and calculate metric coefficients
+ to create grids for complex topologies such as the snowflake configurations.
+
 From ELITE and GATO files
 -------------------------
 
diff --git a/manual/sphinx/user_docs/supported_topologies.rst b/manual/sphinx/user_docs/supported_topologies.rst
new file mode 100644
index 0000000000..0bb2aa50cd
--- /dev/null
+++ b/manual/sphinx/user_docs/supported_topologies.rst
@@ -0,0 +1,201 @@
+.. _sec-supported-topologies:
+
+Supported Topologies
+====================
+
+BOUT++ can handle any tokamak topology with up to two X-points. Currently, the INGRID
+and Hypnotoad gridding tools are the tools used to create BOUT++ grids.
+Hypnotoad can create grids for any of the **basic and common topologies** while
+INGRID can create grids for any of the **common and complex topologies**.
+
+.. note::
+   An EQDSK file is needed to create a grid in either of these tools.
+
+Basic Topologies
+----------------
+
+Basic topologies are used for simpler simulations and don't need to use the
+branch cut features. These include:
+
+- **"Closed Flux Surface" (CFL)**: Which encompass the **"core"** and
+  **"SOL"** configurations.
+- **"Open Flux Surface" (OFL)**: Which encompass the **"limiter"**,
+  **"X-point"**, and **"slab"** configurations.
+
+These don't require a minimum number of processors to run.
+
+Common Topologies
+-----------------
+
+Single Null (SN)
+~~~~~~~~~~~~~~~~
+
+The most common topology; most tokamaks operate or are able to use this
+configuration.
+
+.. figure:: ../figs/Topologies/SN/SN_Geometry.*
+    :alt: The geometry of a single null configuration.
+
+    Single null geometry on the RZ plane generated by INGRID.
+
+The regions that form the building blocks of this topology are:
+
+- 2 "leg" regions which have a boundary in the ``y`` direction;
+- 1 "core" region which does not have boundaries in ``y``.
+
+.. figure:: ../figs/Topologies/SN/SN_processors.*
+    :alt: The processor layout of a single null configuration.
+
+    Division of Single Null configuration into processor layout in index space to compare with the INGRID geometry diagram. 
+
+.. figure:: ../figs/Topologies/SN/SN_regions.*
+    :alt: The regions of a single null configuration.
+
+    Single null configuration regions defined by the branch cuts in :math:`y`.
+    
+
+Even though BOUT++ does not requiere each region to be divided into more processors, using an INGRID grid enables this division and makes it easier to understand the topology.
+
+.. figure:: ../figs/Topologies/SN/SN_topology.*
+    :alt: The topology of a single null configuration.
+
+    Single null configuration topology diagram derived from the processor layout.
+
+Connected Double Null (CDN)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The introduction of a secondary divertor on the top of a tokamak is what
+characterises this configuration. It has a secondary X-point associated with
+the secondary divertor but the separatrix connects both X-points
+(``ixseps1 == ixseps2``). It is an unstable configuration and quite hard to
+maintain experimentally for a long period of time.
+
+.. figure:: ../figs/Topologies/CDN/CDN_Geometry.*
+    :alt: The geometry of a connected double null configuration.
+
+    Connected double null geometry on the RZ plane generated by INGRID.
+
+.. figure:: ../figs/Topologies/CDN/CDN_processors.*
+    :alt: The processor layout of a connected double null configuration.
+
+    Division of Connected Double Null configuration into processor layout in index space to compare with the INGRID geometry diagram. 
+
+.. figure:: ../figs/Topologies/CDN/CDN_regions.*
+    :alt: The regions of a connected double null configuration.
+
+    Connected double null configuration regions defined by the branch cuts in :math:`y`.
+
+.. figure:: ../figs/Topologies/CDN/CDN_topology.*
+    :alt: The topology of a connected double null configuration.
+
+    Connected double null configuration topology diagram derived from the processor layout.
+
+Unconnected Double Null (UDN)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This more realistic configuration has a secondary X-point associated with the
+secondary divertor but the X-points are not connected, creating a secondary
+separatrix (``ixseps1 != ixseps2``). Depending on which separatrix coincides
+with the start of the inner SOL, it is either an upper or lower **UDN**.
+MAST-U is the most famous example of a reactor using the Double Null
+configurations.
+
+.. figure:: ../figs/Topologies/UDN/UDN_Geometry.*
+    :alt: The geometry of an unconnected double null configuration.
+
+    Unconnected double null geometry on the RZ plane generated by INGRID.
+
+
+.. figure:: ../figs/Topologies/UDN/UDN_processors.*
+    :alt: The processor layout of an unconnected double null configuration.
+
+    Division of Unconnected Double Null configuration into processor layout in index space to compare with the INGRID geometry diagram. 
+
+.. figure:: ../figs/Topologies/UDN/UDN_regions.*
+    :alt: The regions of an unconnected double null configuration.
+
+    Unconnected double null configuration regions defined by the branch cuts in :math:`y`.
+
+.. figure:: ../figs/Topologies/UDN/UDN_topology.*
+    :alt: The topology of an unconnected double null configuration.
+
+    Unconnected double null configuration topology diagram derived from the processor layout.
+
+Both **DN configurations** have 2 upper targets defined by ``ny_inner`` and
+``ny_inner + 1``. The regions that form the building blocks of these topologies
+are:
+
+- 4 "leg" regions which have a boundary in the ``y`` direction;
+- 2 "core" regions which do not have boundaries in ``y``.
+
+Complex Topologies
+------------------
+
+Snowflake (SF)
+~~~~~~~~~~~~~~
+
+The snowflake features a secondary X-point close to the primary one. This
+creates a second-order poloidal field null that branches the separatrix into
+4 legs instead of 2. Much like the **CDN**, the ideal **SF** is very hard to
+maintain experimentally, so SF configurations branch into either **SF+** or **SF-**. 
+
+Snowflake+ (SF+)
+~~~~~~~~~~~~~~~~
+
+The **SF+** configuration has the secondary X-point in the PFR . Unlike the perfect **SF**,
+this features an extra central PFR.
+
+.. figure:: ../figs/Topologies/SF/SFplus_Geometry.*
+    :alt: The geometry of a snowflake configuration.
+
+    Snowflake geometry on the RZ plane generated by INGRID.
+
+Snowflake- (SF-)
+~~~~~~~~~~~~~~~~
+
+The **SF-** configuration has the secondary X-point in the scrape-off layer as opposed to the private flux region. In the case of an "exact" **SF-**, both X-Points would be at different points on the same flux surface. 
+Usually, **SF-** configurations have worst heat and particle distributions than the rest of the SF configurations.
+
+.. figure:: ../figs/Topologies/SF/SFminus_Geometry.png
+    :alt: The geometry of a snowflake configuration.
+
+    Snowflake geometry on the RZ plane generated by INGRID.
+
+X-Point Target (XPT)
+~~~~~~~~~~~~~~~~~~~~
+
+The **X-Point Target** configuration has the main separatrix extended a longer
+distance, the secondary X-point happens far away from the core plasma, and there is no PFR between the East and South East targets. 
+This configuration is especially interesting for studying the effect of detachment and neutral gas injection on the plasma without contaminating the core.
+
+.. todo::
+
+   Add geometry diagram.
+
+All **SF and X-Point Target configurations** have 4 targets defined by:
+
+- West on ``y = 0``
+- East on ``y = ny_inner``
+- South East on ``y = ny_inner + 1``
+- South West on ``y =`` :math:`2\pi`
+
+Topologically, all the **SF configurations** and the **X-Point Target** are
+the same. The regions that form the building blocks of these topologies are:
+
+- 4 "leg" regions which have a boundary in the ``y`` direction;
+- 1 "core" region which does not have boundaries in ``y``.
+
+.. figure:: ../figs/Topologies/SF/SF_processors.*
+    :alt: The processor layout of a snowflake configuration.
+
+    Division of Snowflake configuration into processor layout in index space to compare with the INGRID geometry diagram. 
+
+.. figure:: ../figs/Topologies/SF/SF_regions.*
+    :alt: The regions of a snowflake configuration.
+
+    Snowflake configuration regions defined by the branch cuts in :math:`y`.
+
+.. figure:: ../figs/Topologies/SF/SF_topology.*
+    :alt: The topology of a snowflake configuration.
+
+    Snowflake configuration topology diagram derived from the processor layout.
diff --git a/manual/sphinx/user_docs/topology.rst b/manual/sphinx/user_docs/topology.rst
index d996b123ea..f3d2c8e662 100644
--- a/manual/sphinx/user_docs/topology.rst
+++ b/manual/sphinx/user_docs/topology.rst
@@ -45,7 +45,7 @@ The "common" topologies:
 
 And all advanced/complex topologies with up to two X-points:
 
-- **"snowflake"**: The SF topologies feature a second order null point created by two X-points close to each other. The ideal SF has a single separatrix and 4 legs, but more realistic configurations can have an extra PFR between the legs.
+- **"snowflake"**: The SF topologies feature a second order null point created by two X-points close to each other. The ideal SF has a single separatrix and 4 legs, but more realistic configurations can have an extra PFR between the legs. 
   The **"snowflake+"** and **"snowflake-"** unlike the perfect **SF**, feature an extra central PFR and the secondary X-point is located either above or below the primary one, respectively (along the y-direction).
 - **"X-Point Target"**: The X-Point Target configuration has the main separatrix extended a longer distance and no PFR between the East and South East targets.
 
@@ -96,7 +96,7 @@ PFRs (private flux regions), and the core of the tokamak. If
 otherwise it can be any of the more advanced configurations.
 
 .. _fig-topology-cross-section:
-.. figure:: ../figs/topology_cross_section.*
+.. figure:: ../figs/topology_cross_section.png
    :alt: Cross-section of the tokamak topology used in BOUT++
 
    Deconstruction of a poloidal tokamak cross-section into logical

From 5ec260f7fab2fb4f620fec9fce3ee24d5957f9d3 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 22 May 2026 09:22:03 -0700
Subject: [PATCH 1218/1827] snes: pseudo_alpha_minimum setting

This is to prevent the PTC method from getting stuck when the alpha
parameter gets very small, taking many iterations to recover.
---
 src/solver/impls/snes/snes.cxx | 42 ++++++++++++++++++++++------------
 src/solver/impls/snes/snes.hxx |  1 +
 2 files changed, 28 insertions(+), 15 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 31877f8aac..5b28ff413c 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -4,18 +4,25 @@
 
 #include "snes.hxx"
 
+#include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/field.hxx>
+#include <bout/field3d.hxx>
 #include <bout/globals.hxx>
 #include <bout/output.hxx>
 #include <bout/output_bout_types.hxx>
 #include <bout/petsc_interface.hxx>
+#include <bout/solver.hxx>
 #include <bout/utils.hxx>
+#include <bout/unused.hxx>
 
 #include <algorithm>
 #include <cmath>
 #include <cstddef>
 #include <set>
+#include <utility>
 #include <vector>
 
 #include "petscerror.h"
@@ -306,7 +313,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
         }
         // 3D fields
         for (int z = mesh->zstart; z <= mesh->zend; z++) {
-          int ind = ROUND(index(x, y, z));
+          const int ind = ROUND(index(x, y, z));
 
           for (int i = 0; i < n3d; i++) {
             PetscInt row = ind + i;
@@ -342,7 +349,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
                 // 3D fields on this cell
                 for (int j = 0; j < n3d; j++) {
                   const PetscInt col = ind2 + j;
-                  PetscErrorCode ierr =
+                  const PetscErrorCode ierr =
                       MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
 
                   if (ierr != PETSC_SUCCESS) {
@@ -536,6 +543,9 @@ SNESSolver::SNESSolver(Options* opts)
       pseudo_alpha((*options)["pseudo_alpha"]
                        .doc("Sets timestep using dt = alpha / residual")
                        .withDefault(100. * atol * timestep)),
+      pseudo_alpha_minimum(
+          (*options)["pseudo_alpha_minimum"].doc("Minimum value of pseudo_alpha")
+          .withDefault(0.1 * pseudo_alpha)),
       pseudo_growth_factor((*options)["pseudo_growth_factor"]
                                .doc("PTC growth factor on success")
                                .withDefault(1.1)),
@@ -884,7 +894,7 @@ int SNESSolver::run() {
     int saved_jacobian_lag = 0;
     int loop_count = 0;
 
-    BoutReal start_global_residual = global_residual;
+    const BoutReal start_global_residual = global_residual;
     do {
       if ((output_trigger == BoutSnesOutput::fixed_time_interval && (simtime >= target))
           || (output_trigger == BoutSnesOutput::residual_ratio
@@ -1181,8 +1191,10 @@ int SNESSolver::run() {
 
       if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Adjust pseudo_alpha to globally scale timesteps
-        pseudo_alpha = updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate,
-                                            max_timestep * atol * 100);
+        pseudo_alpha = std::max({
+            updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate,
+                                 max_timestep * atol * 100),
+            pseudo_alpha_minimum});
 
         // Adjust local timesteps
         PetscCall(updatePseudoTimestepping());
@@ -1216,7 +1228,7 @@ int SNESSolver::run() {
 
       // Note: If simtime = target then alpha = 0
       //       and output_x = snes_x
-      BoutReal alpha = (simtime - target) / dt;
+      const BoutReal alpha = (simtime - target) / dt;
 
       // output_x <- alpha * x0 + (1 - alpha) * output_x
       VecAXPBY(output_x, alpha, 1. - alpha, x0);
@@ -1437,7 +1449,7 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping() {
     }
     if (count > 0) {
       // Adjust timestep for these quantities
-      BoutReal new_timestep = updatePseudoTimestep(
+      const BoutReal new_timestep = updatePseudoTimestep(
           dt_data[idx], local_residual_2d_prev[i2d], local_residual_2d[i2d]);
       for (int i = 0; i != count; ++i) {
         dt_data[idx++] = new_timestep;
@@ -1529,9 +1541,10 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping() {
 /// rapid changes in timestep.
 BoutReal SNESSolver::updatePseudoTimestep_inverse_residual(BoutReal previous_timestep,
                                                            BoutReal current_residual) {
-  return std::min(
-      {std::max({pseudo_alpha / current_residual, previous_timestep / 1.5, dt_min_reset}),
-       1.5 * previous_timestep, max_timestep});
+  return std::max({
+      std::min({std::max({pseudo_alpha / current_residual, previous_timestep / 1.5}),
+                1.5 * previous_timestep, max_timestep}),
+      dt_min_reset});
 }
 
 // Strategy based on history of residuals
@@ -1552,7 +1565,8 @@ BoutReal SNESSolver::updatePseudoTimestep_history_based(BoutReal previous_timest
     if (reduction_ratio < 0.8) {
       return std::min(0.5 * (pseudo_growth_factor + 1.) * previous_timestep,
                       max_timestep);
-    } else if (reduction_ratio > 1.2) {
+    }
+    if (reduction_ratio > 1.2) {
       return std::max(0.5 * (pseudo_reduction_factor + 1) * previous_timestep,
                       dt_min_reset);
     }
@@ -1780,10 +1794,8 @@ PetscErrorCode SNESSolver::scaleJacobian(Mat Jac_new) {
     // Calculate a norm of this row of the Jacobian
     PetscScalar norm = 0.0;
     for (int col = 0; col < ncols; col++) {
-      PetscScalar absval = std::abs(vals[col]);
-      if (absval > norm) {
-        norm = absval;
-      }
+      const PetscScalar absval = std::abs(vals[col]);
+      norm = std::max({norm, absval});
       // Can we identify small elements and remove them?
       // so we don't need to calculate them next time
     }
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 40412f83b7..fbcf3baddf 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -153,6 +153,7 @@ private:
   // These are used if equation_form = pseudo_transient
   BoutPTCStrategy pseudo_strategy;  ///< Strategy to use when setting timesteps
   BoutReal pseudo_alpha;            ///< dt = alpha / residual
+  BoutReal pseudo_alpha_minimum;    ///< Minimum value of alpha
   BoutReal pseudo_growth_factor;    ///< Timestep increase 1.1 - 1.2
   BoutReal pseudo_reduction_factor; ///< Timestep decrease 0.5
   BoutReal pseudo_max_ratio;        ///< Maximum timestep ratio between neighboring cells

From 3423236636a1963be1454727cfda39ef8c1e7a76 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 22 May 2026 20:31:26 +0200
Subject: [PATCH 1219/1827] Add BoundaryRegionX

---
 include/bout/boundary_region_iter.hxx | 45 +++++++++++++++++++++++----
 src/mesh/mesh.cxx                     | 30 +++++++++---------
 2 files changed, 55 insertions(+), 20 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index d85afa754a..5abe9c826b 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -440,19 +440,19 @@ private:
   int _dir;
   // Vector of points in the boundary
   bout::parallel_boundary_region::IndicesVec bndry_points;
-  bool is_sorted{true};
   Mesh* localmesh;
-  Ind3D xyz2ind(int x, int y, int z) const {
-    const int ny = localmesh->LocalNy;
-    const int nz = localmesh->LocalNz;
-    return Ind3D{(x * ny + y) * nz + z, ny, nz};
-  }
+  bool is_sorted{true};
   void ensureSorted() {
     if (is_sorted) {
       return;
     }
     std::sort(std::begin(bndry_points), std::end(bndry_points));
   }
+  Ind3D xyz2ind(int x, int y, int z) const {
+    const int ny = localmesh->LocalNy;
+    const int nz = localmesh->LocalNz;
+    return Ind3D{(x * ny + y) * nz + z, ny, nz};
+  }
 };
 
 class BoundaryRegionIterFCI : public BoundaryRegionIterBase<BoundaryRegionIterFCI> {
@@ -536,6 +536,39 @@ public:
   // No-op for compatibility
   BoundaryRegionIterFCI& operator*() { return *this; }
 };
+
+class BoundaryRegionX : public BoundaryRegionBase {
+public:
+  BoundaryRegionX(const std::string& name, int dir, Mesh* mesh, Region<Ind3D>&& rgn)
+      : BoundaryRegionBase(name, mesh), _dir(dir), rgn(std::move(rgn)) {};
+  int dir() { return _dir; }
+  // legacy interface
+  void first() override { throw BoutException("Legacy interface is not suppored"); }
+  void next() override { throw BoutException("Legacy interface is not suppored"); }
+  bool isDone() override { throw BoutException("Legacy interface is not suppored"); }
+
+private:
+  friend class BoundaryRegionIterX;
+  int _dir;
+  Region<Ind3D> rgn;
+};
+
+inline BoundaryRegionX BoundaryRegionXIn(const std::string& name, int ymin, int ymax,
+                                         Mesh* mesh) {
+  return BoundaryRegionX(name, -1, mesh,
+                         Region<Ind3D>(0, mesh->xstart - 1, ymin, ymax, mesh->zstart,
+                                       mesh->zend - 1, mesh->LocalNy, mesh->LocalNz,
+                                       mesh->maxregionblocksize));
+}
+
+inline BoundaryRegionX BoundaryRegionXOut(const std::string& name, int ymin, int ymax,
+                                          Mesh* mesh) {
+  return BoundaryRegionX(name, 1, mesh,
+                         Region<Ind3D>(mesh->xend, mesh->LocalNx - 1, ymin, ymax,
+                                       mesh->zstart, mesh->zend - 1, mesh->LocalNy,
+                                       mesh->LocalNz, mesh->maxregionblocksize));
+}
+
 } // namespace boundary
 } // namespace bout
 
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 829c150a15..63c55a7496 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -660,21 +660,23 @@ void Mesh::createDefaultRegions() {
   addRegion3D("RGN_NOZ", Region<Ind3D>(0, LocalNx - 1, 0, LocalNy - 1, zstart, zend,
                                        LocalNy, LocalNz, maxregionblocksize));
   addRegion3D("RGN_GUARDS", mask(getRegion3D("RGN_ALL"), getRegion3D("RGN_NOBNDRY")));
+  addRegion3D("RGN_XGUARDS_IN", Region<Ind3D>(0, xstart - 1, ystart, yend, zstart, zend,
+                                              LocalNy, LocalNz, maxregionblocksize));
+  addRegion3D("RGN_XGUARDS_OUT",
+              Region<Ind3D>(xend + 1, LocalNx - 1, ystart, yend, zstart, zend, LocalNy,
+                            LocalNz, maxregionblocksize));
   addRegion3D("RGN_XGUARDS",
-              Region<Ind3D>(0, xstart - 1, ystart, yend, zstart, zend, LocalNy, LocalNz,
-                            maxregionblocksize)
-                  + Region<Ind3D>(xend + 1, LocalNx - 1, ystart, yend, zstart, zend,
-                                  LocalNy, LocalNz, maxregionblocksize));
-  addRegion3D("RGN_YGUARDS",
-              Region<Ind3D>(xstart, xend, 0, ystart - 1, zstart, zend, LocalNy, LocalNz,
-                            maxregionblocksize)
-                  + Region<Ind3D>(xstart, xend, yend + 1, LocalNy - 1, zstart, zend,
-                                  LocalNy, LocalNz, maxregionblocksize));
-  addRegion3D("RGN_ZGUARDS",
-              Region<Ind3D>(xstart, xend, ystart, yend, 0, zstart - 1, LocalNy, LocalNz,
-                            maxregionblocksize)
-                  + Region<Ind3D>(xstart, xend, ystart, yend, zend + 1, LocalNz - 1,
-                                  LocalNy, LocalNz, maxregionblocksize));
+              getRegion3D("RGN_XGUARDS_IN") + getRegion3D("RGN_XGUARDS_OUT"));
+  addRegion3D("RGN_YGUARDS_IN", Region<Ind3D>(xstart, xend, 0, ystart - 1, zstart, zend,
+                                              LocalNy, LocalNz, maxregionblocksize));
+  addRegion3D("RGN_YGUARDS_OUT",
+              Region<Ind3D>(xstart, xend, yend + 1, LocalNy - 1, zstart, zend, LocalNy,
+                            LocalNz, maxregionblocksize));
+  addRegion3D("RGN_ZGUARDS_IN", Region<Ind3D>(xstart, xend, ystart, yend, 0, zstart - 1,
+                                              LocalNy, LocalNz, maxregionblocksize));
+  addRegion3D("RGN_ZGUARDS_OUT",
+              Region<Ind3D>(xstart, xend, ystart, yend, zend + 1, LocalNz - 1, LocalNy,
+                            LocalNz, maxregionblocksize));
   addRegion3D("RGN_NOCORNERS", (getRegion3D("RGN_NOBNDRY") + getRegion3D("RGN_XGUARDS")
                                 + getRegion3D("RGN_YGUARDS") + getRegion3D("RGN_ZGUARDS"))
                                    .unique());

From 628e2f80d14e3a42e7edf33b62615ad2b4bdf653 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 25 May 2026 14:14:38 +0200
Subject: [PATCH 1220/1827] Add BoundaryRegionIterX implementation

---
 include/bout/boundary_region_iter.hxx | 93 ++++++++++++++++++++++++---
 1 file changed, 85 insertions(+), 8 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 5abe9c826b..6da64cd840 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -540,7 +540,9 @@ public:
 class BoundaryRegionX : public BoundaryRegionBase {
 public:
   BoundaryRegionX(const std::string& name, int dir, Mesh* mesh, Region<Ind3D>&& rgn)
-      : BoundaryRegionBase(name, mesh), _dir(dir), rgn(std::move(rgn)) {};
+      : BoundaryRegionBase(name, mesh), _dir(dir), valid(mesh->xstart) {
+    BOUT_FOR_SERIAL(i, rgn) { this->rgn.emplace_back(i); }
+  }
   int dir() { return _dir; }
   // legacy interface
   void first() override { throw BoutException("Legacy interface is not suppored"); }
@@ -550,23 +552,98 @@ public:
 private:
   friend class BoundaryRegionIterX;
   int _dir;
-  Region<Ind3D> rgn;
+  std::vector<Ind3D> rgn;
+  BoutReal length{0.5};
+  signed char valid;
+};
+
+class BoundaryRegionIterX : public BoundaryRegionIterBase<BoundaryRegionIterX> {
+private:
+  // TODO(dave) make non-const?
+  const BoundaryRegionX* region;
+  size_t pos{0};
+
+public:
+  BoundaryRegionIterX() = delete;
+  BoundaryRegionIterX(const BoundaryRegionX* reg, bool isstart)
+      : region(reg), pos(isstart ? 0 : reg->rgn.size()) {}
+  int dir() const { return region->_dir; }
+  template <bool check = true>
+  BoutReal& _getAt(Field3D& f, int off) const {
+    ASSERT3(f.hasParallelSlices());
+    if constexpr (check) {
+      ASSERT3(_valid() > -off - 2);
+    }
+    auto _off = _offset() - off * region->_dir;
+    return f[ind().xp(_off)];
+  }
+  template <bool check = true>
+  const BoutReal& _getAt(const Field3D& f, int off) const {
+    ASSERT3(f.hasParallelSlices());
+    if constexpr (check) {
+      ASSERT3(_valid() > -off - 2);
+    }
+    auto _off = _offset() - off * region->_dir;
+    return f[ind().xp(_off)];
+  }
+  template <bool check = true>
+  BoutReal& _getAt(Field2D& f, int off) const {
+    ASSERT3(f.hasParallelSlices());
+    if constexpr (check) {
+      ASSERT3(_valid() > -off - 2);
+    }
+    auto _off = _offset() - off * region->_dir;
+    return f[ind().xp(_off)];
+  }
+  template <bool check = true>
+  const BoutReal& _getAt(const Field2D& f, int off) const {
+    ASSERT3(f.hasParallelSlices());
+    if constexpr (check) {
+      ASSERT3(_valid() > -off - 2);
+    }
+    auto _off = _offset() - off * region->_dir;
+    return f[ind().xp(_off)];
+  }
+  template <bool check = true>
+  BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
+                 int off) const {
+    if constexpr (check) {
+      ASSERT3(valid() > -off - 2);
+    }
+    auto _off = _offset() + off * region->_dir;
+    return f(0, ind().xp(_off));
+  }
+  signed char _offset() const { return region->_dir; }
+  signed char _valid() const { return region->valid; }
+  Ind3D _ind() const { return region->rgn[pos]; }
+  signed char _boundary_width() const { return region->localmesh->xstart; }
+  const BoutReal& _length() const { return region->length; }
+  bool operator!=(BoundaryRegionIterX lhs) {
+    ASSERT3(region == lhs.region);
+    return pos != lhs.pos;
+  }
+  BoundaryRegionIterX& operator++() {
+    ++pos;
+    return *this;
+  }
+  // No-op for compatibility
+  BoundaryRegionIterX& operator*() { return *this; }
 };
 
 inline BoundaryRegionX BoundaryRegionXIn(const std::string& name, int ymin, int ymax,
                                          Mesh* mesh) {
   return BoundaryRegionX(name, -1, mesh,
-                         Region<Ind3D>(0, mesh->xstart - 1, ymin, ymax, mesh->zstart,
-                                       mesh->zend - 1, mesh->LocalNy, mesh->LocalNz,
-                                       mesh->maxregionblocksize));
+                         Region<Ind3D>(mesh->xstart, mesh->xstart, ymin, ymax,
+                                       mesh->zstart, mesh->zend - 1, mesh->LocalNy,
+                                       mesh->LocalNz, mesh->maxregionblocksize));
 }
 
 inline BoundaryRegionX BoundaryRegionXOut(const std::string& name, int ymin, int ymax,
                                           Mesh* mesh) {
   return BoundaryRegionX(name, 1, mesh,
-                         Region<Ind3D>(mesh->xend, mesh->LocalNx - 1, ymin, ymax,
-                                       mesh->zstart, mesh->zend - 1, mesh->LocalNy,
-                                       mesh->LocalNz, mesh->maxregionblocksize));
+                         Region<Ind3D>(mesh->xend, mesh->xend, ymin, ymax, mesh->zstart,
+                                       mesh->zend - 1, mesh->LocalNy, mesh->LocalNz,
+                                       mesh->maxregionblocksize));
 }
 
 } // namespace boundary

From 760eef05ea2838cbda54787dc9a697558cf8870c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 08:44:44 +0200
Subject: [PATCH 1221/1827] Restore removed region RGN_ZGUARDS and RGN_YGUARDS

---
 src/mesh/mesh.cxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 63c55a7496..ef2a1fb0a2 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -672,11 +672,15 @@ void Mesh::createDefaultRegions() {
   addRegion3D("RGN_YGUARDS_OUT",
               Region<Ind3D>(xstart, xend, yend + 1, LocalNy - 1, zstart, zend, LocalNy,
                             LocalNz, maxregionblocksize));
+  addRegion3D("RGN_YGUARDS",
+              getRegion3D("RGN_YGUARDS_IN") + getRegion3D("RGN_YGUARDS_OUT"));
   addRegion3D("RGN_ZGUARDS_IN", Region<Ind3D>(xstart, xend, ystart, yend, 0, zstart - 1,
                                               LocalNy, LocalNz, maxregionblocksize));
   addRegion3D("RGN_ZGUARDS_OUT",
               Region<Ind3D>(xstart, xend, ystart, yend, zend + 1, LocalNz - 1, LocalNy,
                             LocalNz, maxregionblocksize));
+  addRegion3D("RGN_ZGUARDS",
+              getRegion3D("RGN_ZGUARDS_IN") + getRegion3D("RGN_ZGUARDS_OUT"));
   addRegion3D("RGN_NOCORNERS", (getRegion3D("RGN_NOBNDRY") + getRegion3D("RGN_XGUARDS")
                                 + getRegion3D("RGN_YGUARDS") + getRegion3D("RGN_ZGUARDS"))
                                    .unique());

From 2da3c7255daca5c85d6fed9c5dcc383c09882b36 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 08:54:16 +0200
Subject: [PATCH 1222/1827] CI: Use boutproject build images

---
 .ci_fedora.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 8262d032cc..8bb6d642fd 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -21,7 +21,7 @@ then
 	cmd="sudo docker"
     fi
     test . != ".$2" && mpi="$2" || mpi=openmpi
-    time $cmd pull ghcr.io/dschwoerer/bout-container-base:ci-fedora
+    time $cmd pull ghcr.io/boutproject/bout-container-base:ci-fedora
     time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
 	 --shm-size 256M \
          --name mobydick ghcr.io/dschwoerer/bout-container-base:ci-fedora \

From 8e7ff2d7dd32d9ea25b01bfece8d51b7fdb45293 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 09:02:55 +0200
Subject: [PATCH 1223/1827] CI: container is called main

---
 .ci_fedora.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 8bb6d642fd..269d8a9780 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -21,10 +21,10 @@ then
 	cmd="sudo docker"
     fi
     test . != ".$2" && mpi="$2" || mpi=openmpi
-    time $cmd pull ghcr.io/boutproject/bout-container-base:ci-fedora
+    time $cmd pull ghcr.io/boutproject/bout-container-base:main
     time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
 	 --shm-size 256M \
-         --name mobydick ghcr.io/dschwoerer/bout-container-base:ci-fedora \
+         --name mobydick ghcr.io/boutproject/bout-container-base:main \
 	     /tmp/BOUT-dev/.ci_fedora.sh $mpi
     time $cmd cp ${TRAVIS_BUILD_DIR:-$(pwd)} mobydick:/tmp/BOUT-dev
     time $cmd start -a mobydick

From df759a09a83c750b6aa24de07aae1d283788b83f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 09:48:32 +0200
Subject: [PATCH 1224/1827] Add begin/end for
 bout::boundary::BoundaryRegionIterX

---
 include/bout/boundary_region_iter.hxx | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 6da64cd840..7ffe9c15f3 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -657,3 +657,12 @@ inline bout::boundary::BoundaryRegionIterFCI
 end(const bout::boundary::BoundaryRegionFCI& reg) {
   return bout::boundary::BoundaryRegionIterFCI(&reg, false);
 }
+
+inline bout::boundary::BoundaryRegionIterX
+begin(const bout::boundary::BoundaryRegionX& reg) {
+  return bout::boundary::BoundaryRegionIterX(&reg, true);
+}
+inline bout::boundary::BoundaryRegionIterX
+end(const bout::boundary::BoundaryRegionX& reg) {
+  return bout::boundary::BoundaryRegionIterX(&reg, false);
+}

From 9701b991c5095c7b35078bdab8e771a59f3aae31 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 09:49:04 +0200
Subject: [PATCH 1225/1827] Convert apply_stencil to template

---
 include/bout/parallel_boundary_op.hxx | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index b0f74b9f9f..ce8fbb804a 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -149,8 +149,8 @@ public:
 class BoundaryOpPar_dirichlet_o1 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o1> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
-                            BoutReal value) {
+  template <class T>
+  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
     pnt.dirichlet_o1(f, value);
   }
 };
@@ -158,8 +158,8 @@ public:
 class BoundaryOpPar_dirichlet_o2 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o2> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
-                            BoutReal value) {
+  template <class T>
+  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
     pnt.dirichlet_o2(f, value);
   }
 };
@@ -167,8 +167,8 @@ public:
 class BoundaryOpPar_dirichlet_o3 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o3> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
-                            BoutReal value) {
+  template <class T>
+  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
     pnt.dirichlet_o3(f, value);
   }
 };
@@ -177,8 +177,8 @@ class BoundaryOpPar_neumann_o1
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o1, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
-                            BoutReal value) {
+  template <class T>
+  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
     pnt.neumann_o1(f, value);
   }
 };
@@ -187,8 +187,8 @@ class BoundaryOpPar_neumann_o2
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o2, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
-                            BoutReal value) {
+  template <class T>
+  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
     pnt.neumann_o2(f, value);
   }
 };
@@ -197,8 +197,8 @@ class BoundaryOpPar_neumann_o3
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o3, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  static void apply_stencil(Field3D& f, const bout::boundary::BoundaryRegionIterFCI& pnt,
-                            BoutReal value) {
+  template <class T>
+  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
     pnt.neumann_o3(f, value);
   }
 };

From c5995187cf6bdb9be58aa92cbb7d85d71ca1b0a1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 09:49:26 +0200
Subject: [PATCH 1226/1827] Add getValue for
 bout::boundary::BoundaryRegionIterX

---
 include/bout/parallel_boundary_op.hxx |  1 +
 src/mesh/parallel_boundary_op.cxx     | 13 +++++++++++++
 2 files changed, 14 insertions(+)

diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index ce8fbb804a..f633ed3a57 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -69,6 +69,7 @@ protected:
   const ValueType value_type{ValueType::REAL};
 
   BoutReal getValue(const bout::boundary::BoundaryRegionIterFCI& bndry, BoutReal t);
+  BoutReal getValue(const bout::boundary::BoundaryRegionIterX& bndry, BoutReal t);
 };
 
 template <class T, bool isNeumann = false>
diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx
index bf0374ddf6..3b472503ef 100644
--- a/src/mesh/parallel_boundary_op.cxx
+++ b/src/mesh/parallel_boundary_op.cxx
@@ -23,3 +23,16 @@ BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterFCI& bn
     throw BoutException("Invalid value_type encountered in BoundaryOpPar::getValue");
   }
 }
+
+BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterX& bndry,
+                                 BoutReal t) {
+  switch (value_type) {
+  case ValueType::FIELD:
+    // FIXME: Interpolate to s_x, s_y, s_z...
+    return (*field_values)[bndry.ind()];
+  case ValueType::REAL:
+    return real_value;
+  default:
+    throw BoutException("Invalid value_type encountered in BoundaryOpPar::getValue");
+  }
+}

From 49568f07de4694e4ca7b8776cf4a5942c653225c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 09:50:32 +0200
Subject: [PATCH 1227/1827] Add used headers

---
 include/bout/boundary_region_iter.hxx | 7 +++++++
 include/bout/parallel_boundary_op.hxx | 4 ++++
 2 files changed, 11 insertions(+)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 7ffe9c15f3..3ffc2c39e1 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -1,10 +1,17 @@
 #pragma once
 
+#include <algorithm>
+#include <cmath>
+#include <cstddef>
 #include <cstdint>
 #include <functional>
 #include <string>
 #include <utility>
 
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/field_data.hxx"
+#include "bout/utils.hxx"
 #include <bout/bout_enum_class.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index f633ed3a57..827881b760 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -4,11 +4,15 @@
 #include "bout/boundary_op.hxx"
 #include "bout/boundary_region_iter.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
 #include "bout/parallel_boundary_region.hxx"
 #include "bout/unused.hxx"
 #include "bout/utils.hxx"
 
+#include <map>
+#include <memory>
 #include <utility>
 
 //////////////////////////////////////////////////

From f1c4deb4ff9c677375f8f3f3c5156d7e6235159b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 09:50:54 +0200
Subject: [PATCH 1228/1827] Add iteration over bndryX

---
 include/bout/parallel_boundary_op.hxx | 31 ++++++++++++++++++---------
 1 file changed, 21 insertions(+), 10 deletions(-)

diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index 827881b760..de2c223e1c 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -61,6 +61,7 @@ public:
   }
 
   bout::boundary::BoundaryRegionFCI* bndry{nullptr};
+  bout::boundary::BoundaryRegionX* bndryX{nullptr};
 
 protected:
   /// Possible ways to get boundary values
@@ -133,17 +134,27 @@ public:
   void apply(Field3D& f) override { return apply(f, 0); }
 
   void apply(Field3D& f, BoutReal t) override {
-    f.ynext(bndry->dir()).allocate(); // Ensure unique before modifying
-
-    auto dy = f.getCoordinates()->dy;
-
-    for (auto pnt : *bndry) {
-      //for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      BoutReal value = getValue(pnt, t);
-      if (isNeumann) {
-        value *= dy[pnt.ind()];
+    if (bndry != nullptr) {
+      f.ynext(bndry->dir()).allocate(); // Ensure unique before modifying
+      auto dy = f.getCoordinates()->dy;
+      for (auto pnt : *bndry) {
+        BoutReal value = getValue(pnt, t);
+        if (isNeumann) {
+          value *= dy[pnt.ind()];
+        }
+        static_cast<T*>(this)->apply_stencil(f, pnt, value);
+      }
+    }
+    if (bndryX != nullptr) {
+      f.allocate();
+      auto dy = f.getCoordinates()->dx;
+      for (auto pnt : *bndryX) {
+        BoutReal value = getValue(pnt, t);
+        if (isNeumann) {
+          value *= dy[pnt.ind()];
+        }
+        static_cast<T*>(this)->apply_stencil(f, pnt, value);
       }
-      static_cast<T*>(this)->apply_stencil(f, pnt, value);
     }
   }
 };

From d1789191761cf0d229be9358b3c5913853ad55e2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 10:16:02 +0200
Subject: [PATCH 1229/1827] t is currently not used

---
 src/mesh/parallel_boundary_op.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx
index 3b472503ef..93df743390 100644
--- a/src/mesh/parallel_boundary_op.cxx
+++ b/src/mesh/parallel_boundary_op.cxx
@@ -25,7 +25,7 @@ BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterFCI& bn
 }
 
 BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterX& bndry,
-                                 BoutReal t) {
+                                 [[maybe_unused]] BoutReal t) {
   switch (value_type) {
   case ValueType::FIELD:
     // FIXME: Interpolate to s_x, s_y, s_z...

From 163276373513c73672dbbb2c66eef2fd62273e8e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 10:24:53 +0200
Subject: [PATCH 1230/1827] add ctors and clone for
 bout::boundary::BoundaryRegionX

---
 include/bout/parallel_boundary_op.hxx | 44 +++++++++++++++++++++++++--
 1 file changed, 41 insertions(+), 3 deletions(-)

diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index de2c223e1c..c314156645 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -30,6 +30,15 @@ public:
       : bndry(region), real_value(value), value_type(ValueType::REAL) {}
   BoundaryOpPar(bout::boundary::BoundaryRegionFCI* region)
       : bndry(region), real_value(0.), value_type(ValueType::REAL) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionX* region,
+                std::shared_ptr<FieldGenerator> value)
+      : bndryX(region), gen_values(std::move(value)), value_type(ValueType::GEN) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionX* region, Field3D* value)
+      : bndryX(region), field_values(value), value_type(ValueType::FIELD) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionX* region, BoutReal value)
+      : bndryX(region), real_value(value), value_type(ValueType::REAL) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionX* region)
+      : bndryX(region), real_value(0.), value_type(ValueType::REAL) {}
   BoundaryOpPar(BoundaryOpPar* region, std::shared_ptr<FieldGenerator> value)
       : bndry(region->bndry), gen_values(std::move(value)), value_type(ValueType::GEN) {}
   BoundaryOpPar(BoundaryOpPar* region, Field3D* value)
@@ -43,16 +52,25 @@ public:
   // Note: All methods must implement clone, except for modifiers (see below)
   virtual BoundaryOpPar* clone(bout::boundary::BoundaryRegionFCI* region,
                                const std::list<std::string>& args) = 0;
-  virtual BoundaryOpPar* clone(BoundaryOpPar* region,
-                               const std::list<std::string>& args) = 0;
   virtual BoundaryOpPar* clone(bout::boundary::BoundaryRegionFCI* region, Field3D* f) = 0;
-  virtual BoundaryOpPar* clone(BoundaryOpPar* region, Field3D* f) = 0;
   virtual BoundaryOpPar*
   clone(bout::boundary::BoundaryRegionFCI* region, const std::list<std::string>& args,
         const std::map<std::string, std::string>& UNUSED(keywords)) {
     // If not implemented, call two-argument version
     return clone(region, args);
   }
+  virtual BoundaryOpPar* clone(bout::boundary::BoundaryRegionX* region,
+                               const std::list<std::string>& args) = 0;
+  virtual BoundaryOpPar* clone(bout::boundary::BoundaryRegionX* region, Field3D* f) = 0;
+  virtual BoundaryOpPar*
+  clone(bout::boundary::BoundaryRegionX* region, const std::list<std::string>& args,
+        const std::map<std::string, std::string>& UNUSED(keywords)) {
+    // If not implemented, call two-argument version
+    return clone(region, args);
+  }
+  virtual BoundaryOpPar* clone(BoundaryOpPar* region,
+                               const std::list<std::string>& args) = 0;
+  virtual BoundaryOpPar* clone(BoundaryOpPar* region, Field3D* f) = 0;
   virtual BoundaryOpPar*
   clone(BoundaryOpPar* region, const std::list<std::string>& args,
         const std::map<std::string, std::string>& UNUSED(keywords)) {
@@ -120,6 +138,26 @@ public:
   BoundaryOpPar* clone(bout::boundary::BoundaryRegionFCI* region, Field3D* f) override {
     return new T(region, f);
   }
+  BoundaryOpPar* clone(bout::boundary::BoundaryRegionX* region,
+                       const std::list<std::string>& args) override {
+    if (!args.empty()) {
+      try {
+        real_value = stringToReal(args.front());
+        return new T(region, real_value);
+      } catch (const BoutException&) {
+        std::shared_ptr<FieldGenerator> newgen = nullptr;
+        // First argument should be an expression
+        newgen = FieldFactory::get()->parse(args.front());
+        return new T(region, newgen);
+      }
+    }
+
+    return new T(region);
+  }
+
+  BoundaryOpPar* clone(bout::boundary::BoundaryRegionX* region, Field3D* f) override {
+    return new T(region, f);
+  }
   BoundaryOpPar* clone(BoundaryOpPar* region, Field3D* f) override {
     return new T(region, f);
   }

From 9bdcf8037cf7f21841ba43a2cd88bd54103dae62 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 11:30:38 +0200
Subject: [PATCH 1231/1827] Add location to length

This is required to enable staggering support
---
 include/bout/boundary_region_iter.hxx     | 64 ++++++++++++++---------
 include/bout/parallel_boundary_op.hxx     |  3 --
 include/bout/parallel_boundary_region.hxx | 43 ++++++++-------
 3 files changed, 63 insertions(+), 47 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 3ffc2c39e1..95f961de44 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -51,7 +51,9 @@ public:
   Ind3D ind() const { return static_cast<const impl*>(this)->_ind(); }
   /// get the length from the point in the domain to the boundary in index
   /// space. It is in the range [0, 1]
-  BoutReal length() const { return static_cast<const impl*>(this)->_length(); }
+  BoutReal length(CELL_LOC loc) const {
+    return static_cast<const impl*>(this)->_length(loc);
+  }
   /// Lower bound of how many points are between the first point in the domain
   /// and the boundary in the other direction.
   signed char valid() const { return static_cast<const impl*>(this)->_valid(); }
@@ -184,31 +186,34 @@ public:
     if (valid() < 1) {
       return extrapolate_boundary_o1(f);
     }
-    return current(f) * (1 + length()) - prev(f) * length();
+    return current(f) * (1 + length(f.getLocation())) - prev(f) * length(f.getLocation());
   }
   /// Extrapolate a given function to the boundary
-  BoutReal extrapolate_bounday_o1(
-      const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+  BoutReal
+  extrapolate_bounday_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
+                         [[maybe_unused]] CELL_LOC loc = CELL_CENTRE) const {
     return current(func);
   }
   /// Extrapolate a given function to the boundary
-  BoutReal extrapolate_boundary_o2(
-      const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+  BoutReal
+  extrapolate_boundary_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
+                          CELL_LOC loc = CELL_CENTRE) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
       return extrapolate_boundary_o1(func);
     }
-    return current(func) * (1 + length()) - prev(func) * length();
+    return current(func) * (1 + length(loc)) - prev(func) * length(loc);
   }
 
   /// Interpolate a field to the boundary, using the boundary values
   BoutReal interpolate_boundary_o2(const Field3D& f) const {
-    return current(f) * (1 - length()) + next(f) * length();
+    return current(f) * (1 - length(f.getLocation())) + next(f) * length(f.getLocation());
   }
   /// Interpolate a field to the boundary, using the boundary values
-  BoutReal interpolate_boundary_o2(
-      const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
-    return current(func) * (1 - length()) + next(func) * length();
+  BoutReal
+  interpolate_boundary_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
+                          CELL_LOC loc = CELL_CENTRE) const {
+    return current(func) * (1 - length(loc)) + next(func) * length(loc);
   }
   /// Extrapolate to the first boundary value freely
   BoutReal extrapolate_next_o1(const Field3D& f) const { return current(f); }
@@ -253,7 +258,7 @@ public:
                                  : (mode == BoundaryFreeExtrapolation::linear ? 0 : 1);
     auto val = current(f);
     BoutReal next = mode == BoundaryFreeExtrapolation::linear ? val + fac : val * fac;
-    return val * length() + next * (1 - length());
+    return val * length(f.getLocation()) + next * (1 - length(f.getLocation()));
   }
 
   /*
@@ -269,12 +274,12 @@ public:
 
   /// Apply a dirichlet boundary condition
   void dirichlet_o2(Field3D& f, BoutReal value) const {
-    if (length() < small_value) {
+    if (length(f.getLocation()) < small_value) {
       return dirichlet_o1(f, value);
     }
     for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, i) =
-          parallel_stencil::dirichlet_o2(i + 1, current(f), i + 1 - length(), value);
+      getAt(f, i) = parallel_stencil::dirichlet_o2(
+          i + 1, current(f), i + 1 - length(f.getLocation()), value);
     }
   }
 
@@ -284,15 +289,15 @@ public:
     if (valid() < 1) {
       return dirichlet_o2(f, value);
     }
-    if (length() < small_value) {
+    if (length(f.getLocation()) < small_value) {
       for (int i = 0; i < boundary_width(); ++i) {
-        getAt(f, i) =
-            parallel_stencil::dirichlet_o2(i + 2, prev(f), i + 1 - length(), value);
+        getAt(f, i) = parallel_stencil::dirichlet_o2(
+            i + 2, prev(f), i + 1 - length(f.getLocation()), value);
       }
     } else {
       for (int i = 0; i < boundary_width(); ++i) {
-        getAt(f, i) = parallel_stencil::dirichlet_o3(i + 2, prev(f), i + 1, current(f),
-                                                     i + 1 - length(), value);
+        getAt(f, i) = parallel_stencil::dirichlet_o3(
+            i + 2, prev(f), i + 1, current(f), i + 1 - length(f.getLocation()), value);
       }
     }
   }
@@ -334,8 +339,8 @@ public:
       return neumann_o2(f, value);
     }
     for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, i) = parallel_stencil::neumann_o3(i + 1 - length(), value, i + 1,
-                                                 current(f), 2, prev(f));
+      getAt(f, i) = parallel_stencil::neumann_o3(i + 1 - length(f.getLocation()), value,
+                                                 i + 1, current(f), 2, prev(f));
     }
   }
 
@@ -531,7 +536,10 @@ public:
   signed char _boundary_width() const {
     return region->localmesh->ystart - region->bndry_points[pos].abs_offset;
   }
-  const BoutReal& _length() const { return region->bndry_points[pos].length; }
+  BoutReal _length([[maybe_unused]] CELL_LOC loc) const {
+    ASSERT3(loc == CELL_CENTRE);
+    return region->bndry_points[pos].length;
+  }
   bool operator!=(BoundaryRegionIterFCI lhs) {
     ASSERT3(region == lhs.region);
     return pos != lhs.pos;
@@ -624,7 +632,15 @@ public:
   signed char _valid() const { return region->valid; }
   Ind3D _ind() const { return region->rgn[pos]; }
   signed char _boundary_width() const { return region->localmesh->xstart; }
-  const BoutReal& _length() const { return region->length; }
+  BoutReal _length(CELL_LOC loc) const {
+    if (loc == CELL_XLOW) {
+      if (dir() == 1) {
+        return 1;
+      }
+      return 0;
+    }
+    return 0.5;
+  }
   bool operator!=(BoundaryRegionIterX lhs) {
     ASSERT3(region == lhs.region);
     return pos != lhs.pos;
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index c314156645..afcd84542e 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -56,7 +56,6 @@ public:
   virtual BoundaryOpPar*
   clone(bout::boundary::BoundaryRegionFCI* region, const std::list<std::string>& args,
         const std::map<std::string, std::string>& UNUSED(keywords)) {
-    // If not implemented, call two-argument version
     return clone(region, args);
   }
   virtual BoundaryOpPar* clone(bout::boundary::BoundaryRegionX* region,
@@ -65,7 +64,6 @@ public:
   virtual BoundaryOpPar*
   clone(bout::boundary::BoundaryRegionX* region, const std::list<std::string>& args,
         const std::map<std::string, std::string>& UNUSED(keywords)) {
-    // If not implemented, call two-argument version
     return clone(region, args);
   }
   virtual BoundaryOpPar* clone(BoundaryOpPar* region,
@@ -74,7 +72,6 @@ public:
   virtual BoundaryOpPar*
   clone(BoundaryOpPar* region, const std::list<std::string>& args,
         const std::map<std::string, std::string>& UNUSED(keywords)) {
-    // If not implemented, call two-argument version
     return clone(region, args);
   }
 
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index b078d66ef6..7a2aff32c1 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -131,7 +131,10 @@ public:
   BoutReal s_x() const { return bndry_position->intersection.s_x; }
   BoutReal s_y() const { return bndry_position->intersection.s_y; }
   BoutReal s_z() const { return bndry_position->intersection.s_z; }
-  BoutReal length() const { return bndry_position->length; }
+  BoutReal length([[maybe_unused]] CELL_LOC loc) const {
+    ASSERT3(loc == CELL_CENTRE);
+    return bndry_position->length;
+  }
   signed char valid() const { return bndry_position->valid; }
   signed char offset() const { return bndry_position->offset; }
   unsigned char abs_offset() const { return bndry_position->abs_offset; }
@@ -146,27 +149,27 @@ public:
     if (valid() < 1) {
       return extrapolate_sheath_o1(f);
     }
-    return ythis(f) * (1 + length()) - yprev(f) * length();
+    return ythis(f) * (1 + length(f.getLocation())) - yprev(f) * length(f.getLocation());
   }
   BoutReal
   extrapolate_sheath_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return ythis(f);
   }
-  BoutReal
-  extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+  BoutReal extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
+                                 CELL_LOC loc = CELL_CENTRE) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
       return extrapolate_sheath_o1(f);
     }
-    return ythis(f) * (1 + length()) - yprev(f) * length();
+    return ythis(f) * (1 + length(loc)) - yprev(f) * length(loc);
   }
 
   BoutReal interpolate_sheath_o2(const Field3D& f) const {
-    return ythis(f) * (1 - length()) + ynext(f) * length();
+    return ythis(f) * (1 - length(f.getLocation())) + ynext(f) * length(f.getLocation());
   }
-  BoutReal
-  interpolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return ythis(f) * (1 - length()) + ynext(f) * length();
+  BoutReal interpolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
+                                 CELL_LOC loc = CELL_CENTRE) const {
+    return ythis(f) * (1 - length(loc)) + ynext(f) * length(loc);
   }
 
   BoutReal extrapolate_next_o1(const Field3D& f) const { return ythis(f); }
@@ -219,12 +222,12 @@ public:
   }
 
   void dirichlet_o2(Field3D& f, BoutReal value) const {
-    if (length() < small_value) {
+    if (length(f.getLocation()) < small_value) {
       return dirichlet_o1(f, value);
     }
     ITER() {
-      getAt(f, i) =
-          parallel_stencil::dirichlet_o2(i + 1, ythis(f), i + 1 - length(), value);
+      getAt(f, i) = parallel_stencil::dirichlet_o2(
+          i + 1, ythis(f), i + 1 - length(f.getLocation()), value);
     }
   }
 
@@ -233,15 +236,15 @@ public:
     if (valid() < 1) {
       return dirichlet_o2(f, value);
     }
-    if (length() < small_value) {
+    if (length(f.getLocation()) < small_value) {
       ITER() {
-        getAt(f, i) =
-            parallel_stencil::dirichlet_o2(i + 2, yprev(f), i + 1 - length(), value);
+        getAt(f, i) = parallel_stencil::dirichlet_o2(
+            i + 2, yprev(f), i + 1 - length(f.getLocation()), value);
       }
     } else {
       ITER() {
-        getAt(f, i) = parallel_stencil::dirichlet_o3(i + 2, yprev(f), i + 1, ythis(f),
-                                                     i + 1 - length(), value);
+        getAt(f, i) = parallel_stencil::dirichlet_o3(
+            i + 2, yprev(f), i + 1, ythis(f), i + 1 - length(f.getLocation()), value);
       }
     }
   }
@@ -279,8 +282,8 @@ public:
       return neumann_o2(f, value);
     }
     ITER() {
-      getAt(f, i) = parallel_stencil::neumann_o3(i + 1 - length(), value, i + 1, ythis(f),
-                                                 2, yprev(f));
+      getAt(f, i) = parallel_stencil::neumann_o3(i + 1 - length(f.getLocation()), value,
+                                                 i + 1, ythis(f), 2, yprev(f));
     }
   }
 
@@ -300,7 +303,7 @@ public:
                                  : (mode == SheathLimitMode::linear_free ? 0 : 1);
     auto val = ythis(f);
     BoutReal next = mode == SheathLimitMode::linear_free ? val + fac : val * fac;
-    return val * length() + next * (1 - length());
+    return val * length(f.getLocation()) + next * (1 - length(f.getLocation()));
   }
 
   void set_free(Field3D& f, SheathLimitMode mode) const {

From 7b1d5b25a938d8b4b4aca31dbafde7e7a65b9eeb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 12:05:54 +0200
Subject: [PATCH 1232/1827] Do call _ind() directly

---
 include/bout/boundary_region_iter.hxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 95f961de44..4a9962cc83 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -492,7 +492,7 @@ public:
       ASSERT3(_valid() > -off - 2);
     }
     auto _off = _offset() - off * region->_dir;
-    return f.ynext(_off)[ind().yp(_off)];
+    return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
   const BoutReal& _getAt(const Field3D& f, int off) const {
@@ -501,7 +501,7 @@ public:
       ASSERT3(_valid() > -off - 2);
     }
     auto _off = _offset() - off * region->_dir;
-    return f.ynext(_off)[ind().yp(_off)];
+    return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
   BoutReal& _getAt(Field2D& f, int off) const {
@@ -510,7 +510,7 @@ public:
       ASSERT3(_valid() > -off - 2);
     }
     auto _off = _offset() - off * region->_dir;
-    return f.ynext(_off)[ind().yp(_off)];
+    return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
   const BoutReal& _getAt(const Field2D& f, int off) const {
@@ -519,7 +519,7 @@ public:
       ASSERT3(_valid() > -off - 2);
     }
     auto _off = _offset() - off * region->_dir;
-    return f.ynext(_off)[ind().yp(_off)];
+    return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
   BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
@@ -528,7 +528,7 @@ public:
       ASSERT3(valid() > -off - 2);
     }
     auto _off = _offset() + off * region->_dir;
-    return f(_off, ind().yp(_off));
+    return f(_off, _ind().yp(_off));
   }
   signed char _offset() const { return region->bndry_points[pos].offset; }
   signed char _valid() const { return region->bndry_points[pos].valid; }

From b286543334cf51dcd9a67fc0b57457b666e9aefd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 12:06:36 +0200
Subject: [PATCH 1233/1827] Add BoundaryRegionY as template

---
 include/bout/boundary_region_iter.hxx | 74 +++++++++++++++++++--------
 1 file changed, 52 insertions(+), 22 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 4a9962cc83..881fc6fa4d 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -552,10 +552,12 @@ public:
   BoundaryRegionIterFCI& operator*() { return *this; }
 };
 
-class BoundaryRegionX : public BoundaryRegionBase {
+template <bool isX>
+class BoundaryRegionXY : public BoundaryRegionBase {
 public:
-  BoundaryRegionX(const std::string& name, int dir, Mesh* mesh, Region<Ind3D>&& rgn)
-      : BoundaryRegionBase(name, mesh), _dir(dir), valid(mesh->xstart) {
+  BoundaryRegionXY(const std::string& name, int dir, Mesh* mesh, Region<Ind3D>&& rgn)
+      : BoundaryRegionBase(name, mesh), _dir(dir),
+        valid(isX ? mesh->xstart : mesh->ystart) {
     BOUT_FOR_SERIAL(i, rgn) { this->rgn.emplace_back(i); }
   }
   int dir() { return _dir; }
@@ -565,22 +567,24 @@ public:
   bool isDone() override { throw BoutException("Legacy interface is not suppored"); }
 
 private:
-  friend class BoundaryRegionIterX;
+  template <bool isIterX>
+  friend class BoundaryRegionIterXY;
   int _dir;
   std::vector<Ind3D> rgn;
   BoutReal length{0.5};
   signed char valid;
 };
 
-class BoundaryRegionIterX : public BoundaryRegionIterBase<BoundaryRegionIterX> {
+template <bool isX>
+class BoundaryRegionIterXY : public BoundaryRegionIterBase<BoundaryRegionIterXY<isX>> {
 private:
   // TODO(dave) make non-const?
-  const BoundaryRegionX* region;
+  const BoundaryRegionXY<isX>* region;
   size_t pos{0};
 
 public:
-  BoundaryRegionIterX() = delete;
-  BoundaryRegionIterX(const BoundaryRegionX* reg, bool isstart)
+  BoundaryRegionIterXY() = delete;
+  BoundaryRegionIterXY(const BoundaryRegionXY<isX>* reg, bool isstart)
       : region(reg), pos(isstart ? 0 : reg->rgn.size()) {}
   int dir() const { return region->_dir; }
   template <bool check = true>
@@ -590,7 +594,11 @@ public:
       ASSERT3(_valid() > -off - 2);
     }
     auto _off = _offset() - off * region->_dir;
-    return f[ind().xp(_off)];
+    if constexpr (isX) {
+      return f[_ind().xp(_off)];
+    } else {
+      return f[_ind().yp(_off)];
+    }
   }
   template <bool check = true>
   const BoutReal& _getAt(const Field3D& f, int off) const {
@@ -599,7 +607,11 @@ public:
       ASSERT3(_valid() > -off - 2);
     }
     auto _off = _offset() - off * region->_dir;
-    return f[ind().xp(_off)];
+    if constexpr (isX) {
+      return f[_ind().xp(_off)];
+    } else {
+      return f[_ind().yp(_off)];
+    }
   }
   template <bool check = true>
   BoutReal& _getAt(Field2D& f, int off) const {
@@ -608,7 +620,11 @@ public:
       ASSERT3(_valid() > -off - 2);
     }
     auto _off = _offset() - off * region->_dir;
-    return f[ind().xp(_off)];
+    if constexpr (isX) {
+      return f[_ind().xp(_off)];
+    } else {
+      return f[_ind().yp(_off)];
+    }
   }
   template <bool check = true>
   const BoutReal& _getAt(const Field2D& f, int off) const {
@@ -617,7 +633,11 @@ public:
       ASSERT3(_valid() > -off - 2);
     }
     auto _off = _offset() - off * region->_dir;
-    return f[ind().xp(_off)];
+    if constexpr (isX) {
+      return f[_ind().xp(_off)];
+    } else {
+      return f[_ind().yp(_off)];
+    }
   }
   template <bool check = true>
   BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
@@ -626,7 +646,11 @@ public:
       ASSERT3(valid() > -off - 2);
     }
     auto _off = _offset() + off * region->_dir;
-    return f(0, ind().xp(_off));
+    if constexpr (isX) {
+      return f(0, _ind().xp(_off));
+    } else {
+      return f(0, _ind().yp(_off));
+    }
   }
   signed char _offset() const { return region->_dir; }
   signed char _valid() const { return region->valid; }
@@ -641,17 +665,21 @@ public:
     }
     return 0.5;
   }
-  bool operator!=(BoundaryRegionIterX lhs) {
+  bool operator!=(BoundaryRegionIterXY<isX> lhs) {
     ASSERT3(region == lhs.region);
     return pos != lhs.pos;
   }
-  BoundaryRegionIterX& operator++() {
+  BoundaryRegionIterXY& operator++() {
     ++pos;
     return *this;
   }
   // No-op for compatibility
-  BoundaryRegionIterX& operator*() { return *this; }
+  BoundaryRegionIterXY& operator*() { return *this; }
 };
+using BoundaryRegionX = BoundaryRegionXY<true>;
+using BoundaryRegionY = BoundaryRegionXY<false>;
+using BoundaryRegionIterX = BoundaryRegionIterXY<true>;
+using BoundaryRegionIterY = BoundaryRegionIterXY<false>;
 
 inline BoundaryRegionX BoundaryRegionXIn(const std::string& name, int ymin, int ymax,
                                          Mesh* mesh) {
@@ -681,11 +709,13 @@ end(const bout::boundary::BoundaryRegionFCI& reg) {
   return bout::boundary::BoundaryRegionIterFCI(&reg, false);
 }
 
-inline bout::boundary::BoundaryRegionIterX
-begin(const bout::boundary::BoundaryRegionX& reg) {
-  return bout::boundary::BoundaryRegionIterX(&reg, true);
+template <bool isX>
+inline bout::boundary::BoundaryRegionIterXY<isX>
+begin(const bout::boundary::BoundaryRegionXY<isX>& reg) {
+  return bout::boundary::BoundaryRegionIterXY<isX>(&reg, true);
 }
-inline bout::boundary::BoundaryRegionIterX
-end(const bout::boundary::BoundaryRegionX& reg) {
-  return bout::boundary::BoundaryRegionIterX(&reg, false);
+template <bool isX>
+inline bout::boundary::BoundaryRegionIterXY<isX>
+end(const bout::boundary::BoundaryRegionXY<isX>& reg) {
+  return bout::boundary::BoundaryRegionIterXY<isX>(&reg, false);
 }

From 7273724fc24109647c017ebec8d15784ac888aaf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 12:16:10 +0200
Subject: [PATCH 1234/1827] add BoundaryOpPar bits for
 bout::boundary::BoundaryRegionY

---
 include/bout/parallel_boundary_op.hxx | 50 +++++++++++++++++++++++++++
 src/mesh/parallel_boundary_op.cxx     | 13 +++++++
 2 files changed, 63 insertions(+)

diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index afcd84542e..9a2ea9cf57 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -39,6 +39,15 @@ public:
       : bndryX(region), real_value(value), value_type(ValueType::REAL) {}
   BoundaryOpPar(bout::boundary::BoundaryRegionX* region)
       : bndryX(region), real_value(0.), value_type(ValueType::REAL) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionY* region,
+                std::shared_ptr<FieldGenerator> value)
+      : bndryY(region), gen_values(std::move(value)), value_type(ValueType::GEN) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionY* region, Field3D* value)
+      : bndryY(region), field_values(value), value_type(ValueType::FIELD) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionY* region, BoutReal value)
+      : bndryY(region), real_value(value), value_type(ValueType::REAL) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionY* region)
+      : bndryY(region), real_value(0.), value_type(ValueType::REAL) {}
   BoundaryOpPar(BoundaryOpPar* region, std::shared_ptr<FieldGenerator> value)
       : bndry(region->bndry), gen_values(std::move(value)), value_type(ValueType::GEN) {}
   BoundaryOpPar(BoundaryOpPar* region, Field3D* value)
@@ -66,6 +75,14 @@ public:
         const std::map<std::string, std::string>& UNUSED(keywords)) {
     return clone(region, args);
   }
+  virtual BoundaryOpPar* clone(bout::boundary::BoundaryRegionY* region,
+                               const std::list<std::string>& args) = 0;
+  virtual BoundaryOpPar* clone(bout::boundary::BoundaryRegionY* region, Field3D* f) = 0;
+  virtual BoundaryOpPar*
+  clone(bout::boundary::BoundaryRegionY* region, const std::list<std::string>& args,
+        const std::map<std::string, std::string>& UNUSED(keywords)) {
+    return clone(region, args);
+  }
   virtual BoundaryOpPar* clone(BoundaryOpPar* region,
                                const std::list<std::string>& args) = 0;
   virtual BoundaryOpPar* clone(BoundaryOpPar* region, Field3D* f) = 0;
@@ -77,6 +94,7 @@ public:
 
   bout::boundary::BoundaryRegionFCI* bndry{nullptr};
   bout::boundary::BoundaryRegionX* bndryX{nullptr};
+  bout::boundary::BoundaryRegionY* bndryY{nullptr};
 
 protected:
   /// Possible ways to get boundary values
@@ -90,6 +108,7 @@ protected:
 
   BoutReal getValue(const bout::boundary::BoundaryRegionIterFCI& bndry, BoutReal t);
   BoutReal getValue(const bout::boundary::BoundaryRegionIterX& bndry, BoutReal t);
+  BoutReal getValue(const bout::boundary::BoundaryRegionIterY& bndry, BoutReal t);
 };
 
 template <class T, bool isNeumann = false>
@@ -155,6 +174,26 @@ public:
   BoundaryOpPar* clone(bout::boundary::BoundaryRegionX* region, Field3D* f) override {
     return new T(region, f);
   }
+  BoundaryOpPar* clone(bout::boundary::BoundaryRegionY* region,
+                       const std::list<std::string>& args) override {
+    if (!args.empty()) {
+      try {
+        real_value = stringToReal(args.front());
+        return new T(region, real_value);
+      } catch (const BoutException&) {
+        std::shared_ptr<FieldGenerator> newgen = nullptr;
+        // First argument should be an expression
+        newgen = FieldFactory::get()->parse(args.front());
+        return new T(region, newgen);
+      }
+    }
+
+    return new T(region);
+  }
+
+  BoundaryOpPar* clone(bout::boundary::BoundaryRegionY* region, Field3D* f) override {
+    return new T(region, f);
+  }
   BoundaryOpPar* clone(BoundaryOpPar* region, Field3D* f) override {
     return new T(region, f);
   }
@@ -191,6 +230,17 @@ public:
         static_cast<T*>(this)->apply_stencil(f, pnt, value);
       }
     }
+    if (bndryY != nullptr) {
+      f.allocate();
+      auto dy = f.getCoordinates()->dy;
+      for (auto pnt : *bndryY) {
+        BoutReal value = getValue(pnt, t);
+        if (isNeumann) {
+          value *= dy[pnt.ind()];
+        }
+        static_cast<T*>(this)->apply_stencil(f, pnt, value);
+      }
+    }
   }
 };
 
diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx
index 93df743390..9b1d8d4947 100644
--- a/src/mesh/parallel_boundary_op.cxx
+++ b/src/mesh/parallel_boundary_op.cxx
@@ -36,3 +36,16 @@ BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterX& bndr
     throw BoutException("Invalid value_type encountered in BoundaryOpPar::getValue");
   }
 }
+
+BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterY& bndry,
+                                 [[maybe_unused]] BoutReal t) {
+  switch (value_type) {
+  case ValueType::FIELD:
+    // FIXME: Interpolate to s_x, s_y, s_z...
+    return (*field_values)[bndry.ind()];
+  case ValueType::REAL:
+    return real_value;
+  default:
+    throw BoutException("Invalid value_type encountered in BoundaryOpPar::getValue");
+  }
+}

From f3bfa30d71158e253ff702e1486d3cdf3ee86b08 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 13:12:45 +0200
Subject: [PATCH 1235/1827] Use local version

---
 include/bout/boundary_region_iter.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 881fc6fa4d..6e377e4441 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -643,7 +643,7 @@ public:
   BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
                  int off) const {
     if constexpr (check) {
-      ASSERT3(valid() > -off - 2);
+      ASSERT3(_valid() > -off - 2);
     }
     auto _off = _offset() + off * region->_dir;
     if constexpr (isX) {

From c291f6eee07aa50022336aa63f1908e904365881 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 13:32:10 +0200
Subject: [PATCH 1236/1827] Allow to distinguish X and Y boundaries

---
 include/bout/boundary_region.hxx      |  2 ++
 include/bout/boundary_region_iter.hxx |  5 +++++
 src/mesh/boundary_factory.cxx         | 20 +++++++++++++-------
 3 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 2a89cc1a50..ab7ef8705e 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -57,6 +57,8 @@ public:
 
   BndryLoc location;       ///< Which side of the domain is it on?
   bool isParallel = false; ///< Is this a parallel boundary?
+  bool isX = false;
+  bool isY = false;
 
   virtual void first() = 0; ///< Move the region iterator to the start
   virtual void next() = 0;  ///< Get the next element in the loop
diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 6e377e4441..bcc03acad2 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -559,6 +559,11 @@ public:
       : BoundaryRegionBase(name, mesh), _dir(dir),
         valid(isX ? mesh->xstart : mesh->ystart) {
     BOUT_FOR_SERIAL(i, rgn) { this->rgn.emplace_back(i); }
+    if (isX) {
+      this->isX = true;
+    } else {
+      this->isY = true;
+    }
   }
   int dir() { return _dir; }
   // legacy interface
diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index a9c278a4d6..fc77983f0e 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -194,16 +194,22 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
     return mod->cloneMod(op, arglist);
   }
 
-  if (region->isParallel) {
-    // Parallel boundary
-    BoundaryOpPar* pop = findBoundaryOpPar(trim(func));
-    if (pop != nullptr) {
-      // An operation with arguments
+  BoundaryOpPar* pop = findBoundaryOpPar(trim(func));
+  if (pop != nullptr) {
+    // An operation with arguments
+    if (region->isParallel) {
       return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionFCI*>(region), arglist,
                         keywords);
+    } else if (region->isX) {
+      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionX*>(region), arglist,
+                        keywords);
+    } else if (region->isY) {
+      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionY*>(region), arglist,
+                        keywords);
     }
-  } else {
-    // Perpendicular boundary
+  }
+  if (!region->isParallel) {
+    // Legacy perpendicular boundary
     BoundaryOp* op = findBoundaryOp(trim(func));
     if (op != nullptr) {
       // An operation with arguments

From 10c9dc537d1dbb07ca0d6cc4277b4a6a80eebf1a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 13:35:14 +0200
Subject: [PATCH 1237/1827] Cleanup unused bits

---
 include/bout/boundary_region_iter.hxx | 2 --
 1 file changed, 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index bcc03acad2..7c109f2c80 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -576,14 +576,12 @@ private:
   friend class BoundaryRegionIterXY;
   int _dir;
   std::vector<Ind3D> rgn;
-  BoutReal length{0.5};
   signed char valid;
 };
 
 template <bool isX>
 class BoundaryRegionIterXY : public BoundaryRegionIterBase<BoundaryRegionIterXY<isX>> {
 private:
-  // TODO(dave) make non-const?
   const BoundaryRegionXY<isX>* region;
   size_t pos{0};
 

From 006f256864997f4ab59a26fbae4decf80dca2b78 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 26 May 2026 13:44:25 +0200
Subject: [PATCH 1238/1827] Add BoundaryRegionYUp/Down

---
 include/bout/boundary_region_iter.hxx | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 7c109f2c80..dc651bd039 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -688,7 +688,7 @@ inline BoundaryRegionX BoundaryRegionXIn(const std::string& name, int ymin, int
                                          Mesh* mesh) {
   return BoundaryRegionX(name, -1, mesh,
                          Region<Ind3D>(mesh->xstart, mesh->xstart, ymin, ymax,
-                                       mesh->zstart, mesh->zend - 1, mesh->LocalNy,
+                                       mesh->zstart, mesh->zend, mesh->LocalNy,
                                        mesh->LocalNz, mesh->maxregionblocksize));
 }
 
@@ -696,10 +696,26 @@ inline BoundaryRegionX BoundaryRegionXOut(const std::string& name, int ymin, int
                                           Mesh* mesh) {
   return BoundaryRegionX(name, 1, mesh,
                          Region<Ind3D>(mesh->xend, mesh->xend, ymin, ymax, mesh->zstart,
-                                       mesh->zend - 1, mesh->LocalNy, mesh->LocalNz,
+                                       mesh->zend, mesh->LocalNy, mesh->LocalNz,
                                        mesh->maxregionblocksize));
 }
 
+inline BoundaryRegionY BoundaryRegionYUp(const std::string& name, int xmin, int xmax,
+                                         Mesh* mesh) {
+  return BoundaryRegionY(name, -1, mesh,
+                         Region<Ind3D>(xmin, xmax, mesh->yend, mesh->yend, mesh->zstart,
+                                       mesh->zend, mesh->LocalNy, mesh->LocalNz,
+                                       mesh->maxregionblocksize));
+}
+
+inline BoundaryRegionY BoundaryRegionYDown(const std::string& name, int xmin, int xmax,
+                                           Mesh* mesh) {
+  return BoundaryRegionY(name, 1, mesh,
+                         Region<Ind3D>(xmin, xmax, mesh->ystart, mesh->ystart,
+                                       mesh->zstart, mesh->zend, mesh->LocalNy,
+                                       mesh->LocalNz, mesh->maxregionblocksize));
+}
+
 } // namespace boundary
 } // namespace bout
 

From 15dba111ea20f12b4cf8dbb467ba45304f2adda7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:39:10 +0200
Subject: [PATCH 1239/1827] Prefer `point` as name

---
 src/field/field3d.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index c0c01fefc5..b8bdb28626 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -465,11 +465,11 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
       ASSERT1(hasParallelSlices());
 
       for (auto& region : fieldmesh->getBoundariesPar()) {
-        for (const auto& pnt : *region) {
+        for (const auto& point : *region) {
           // Interpolate midpoint value in f3d
-          const BoutReal val = pnt.interpolate_boundary_o2(f3d);
+          const BoutReal val = point.interpolate_boundary_o2(f3d);
           // Set the same boundary value in this field
-          pnt.dirichlet_o1(*this, val);
+          point.dirichlet_o1(*this, val);
         }
       }
     }

From f42d784aee78f79e0617d84101a94ac5aba98d9e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:40:28 +0200
Subject: [PATCH 1240/1827] Add iter_boundary functions

---
 include/bout/boundary_region_iter.hxx | 29 ++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index dc651bd039..d5c43404cc 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -716,9 +716,36 @@ inline BoundaryRegionY BoundaryRegionYDown(const std::string& name, int xmin, in
                                        mesh->LocalNz, mesh->maxregionblocksize));
 }
 
+template <class Func>
+void iter_boundary(const BoundaryRegionBase* bndrybase, const Func& func) {
+  if (bndrybase->isX) {
+    const auto bndry = dynamic_cast<const BoundaryRegionX*>(bndrybase);
+    return iter_boundary(*bndry, func);
+  }
+  if (bndrybase->isY) {
+    const auto bndry = dynamic_cast<const BoundaryRegionY*>(bndrybase);
+    return iter_boundary(*bndry, func);
+  }
+  if (bndrybase->isParallel) {
+    const auto bndry = dynamic_cast<const BoundaryRegionFCI*>(bndrybase);
+    return iter_boundary(*bndry, func);
+  }
+  throw BoutException("{} is of unknown type - probably a legacy iterator",
+                      bndrybase->label);
+}
+
+template <class Bndry, class Func,
+          typename = std::enable_if_t<std::is_base_of<BoundaryRegionBase, Bndry>::value>>
+void iter_boundary(const Bndry& bndry, const Func& func) {
+  static_assert(std::is_base_of<BoundaryRegionBase, Bndry>::value,
+                "Bndry must derive from BoundaryRegionY");
+  for (auto& point : bndry) {
+    func(point);
+  }
+}
+
 } // namespace boundary
 } // namespace bout
-
 inline bout::boundary::BoundaryRegionIterFCI
 begin(const bout::boundary::BoundaryRegionFCI& reg) {
   return bout::boundary::BoundaryRegionIterFCI(&reg, true);

From cc5f314b51e782e17e29e23e4071eff980c89462 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:36:27 +0200
Subject: [PATCH 1241/1827] Switch Pointer to BoundaryRegionBase type

---
 include/bout/mesh.hxx            |  2 +-
 src/field/field2d.cxx            | 20 ++++++++++-------
 src/field/field3d.cxx            | 38 +++++++++++++++++++++-----------
 src/mesh/coordinates.cxx         |  8 +++++--
 src/mesh/impls/bout/boutmesh.cxx |  2 +-
 src/mesh/impls/bout/boutmesh.hxx |  4 ++--
 tests/unit/fake_mesh.hxx         |  4 ++--
 7 files changed, 49 insertions(+), 29 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index e9d3d7cbbf..33272d486f 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -481,7 +481,7 @@ public:
   // Boundary regions
 
   /// Return a vector containing all the boundary regions on this processor
-  virtual std::vector<BoundaryRegion*> getBoundaries() = 0;
+  virtual std::vector<BoundaryRegionBase*> getBoundaries() = 0;
 
   /// Get the set of all possible boundaries in this configuration
   virtual std::set<std::string> getPossibleBoundaries() const { return {}; }
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index c2d35162b3..f363f1f1da 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -314,14 +314,18 @@ void Field2D::setBoundaryTo(const Field2D& f2d) {
   allocate(); // Make sure data allocated
 
   /// Loop over boundary regions
-  for (const auto& reg : fieldmesh->getBoundaries()) {
-    /// Loop within each region
-    for (reg->first(); !reg->isDone(); reg->next()) {
-      // Get value half-way between cells
-      BoutReal val =
-          0.5 * (f2d(reg->x, reg->y) + f2d(reg->x - reg->bx, reg->y - reg->by));
-      // Set to this value
-      (*this)(reg->x, reg->y) = 2. * val - (*this)(reg->x - reg->bx, reg->y - reg->by);
+  for (const auto& regnew : fieldmesh->getBoundaries()) {
+    {
+      /// Loop within each region
+      auto reg = dynamic_cast<BoundaryRegion*>(regnew);
+      ASSERT0(reg != nullptr);
+      for (reg->first(); !reg->isDone(); reg->next()) {
+        // Get value half-way between cells
+        BoutReal val =
+            0.5 * (f2d(reg->x, reg->y) + f2d(reg->x - reg->bx, reg->y - reg->by));
+        // Set to this value
+        (*this)(reg->x, reg->y) = 2. * val - (*this)(reg->x - reg->bx, reg->y - reg->by);
+      }
     }
   }
 }
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index b8bdb28626..ecd3c90b74 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -478,19 +478,31 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
   // Non-FCI.
   // Transform to field-aligned coordinates?
   // Loop over boundary regions
-  for (const auto& reg : fieldmesh->getBoundaries()) {
-    if (isFci() && reg->by != 0) {
-      continue;
-    }
-    /// Loop within each region
-    for (reg->first(); !reg->isDone(); reg->next()) {
-      for (int z = 0; z < nz; z++) {
-        // Get value half-way between cells
-        BoutReal val =
-            0.5 * (f3d(reg->x, reg->y, z) + f3d(reg->x - reg->bx, reg->y - reg->by, z));
-        // Set to this value
-        (*this)(reg->x, reg->y, z) =
-            2. * val - (*this)(reg->x - reg->bx, reg->y - reg->by, z);
+  for (const auto& newreg : fieldmesh->getBoundaries()) {
+    if (newreg->isX) {
+      auto reg = dynamic_cast<bout::boundary::BoundaryRegionX*>(newreg);
+      bout::boundary::iter_boundary(*reg, [&](auto& point) {
+        const BoutReal val = point.interpolate_boundary_o2(f3d);
+        point.dirichlet_o1(*this, val);
+      });
+    } else if (newreg->isY) {
+      // nothing to do
+    } else {
+      auto reg = dynamic_cast<BoundaryRegion*>(newreg);
+      ASSERT1(reg != nullptr);
+      if (isFci() && reg->by != 0) {
+        continue;
+      }
+      /// Loop within each region
+      for (reg->first(); !reg->isDone(); reg->next()) {
+        for (int z = 0; z < nz; z++) {
+          // Get value half-way between cells
+          BoutReal val =
+              0.5 * (f3d(reg->x, reg->y, z) + f3d(reg->x - reg->bx, reg->y - reg->by, z));
+          // Set to this value
+          (*this)(reg->x, reg->y, z) =
+              2. * val - (*this)(reg->x - reg->bx, reg->y - reg->by, z);
+        }
       }
     }
   }
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 634db26f3a..40024ed3eb 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -54,7 +54,9 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr
   // initializing yet, leading to an infinite recursion.
   // Also, here we interpolate for the boundary points at xstart/ystart and
   // (xend+1)/(yend+1) instead of extrapolating.
-  for (auto& bndry : localmesh->getBoundaries()) {
+  for (auto& newbndry : localmesh->getBoundaries()) {
+    auto bndry = dynamic_cast<BoundaryRegion*>(newbndry);
+    ASSERT0(bndry != nullptr);
     if ((extrapolate_x and bndry->bx != 0) or (extrapolate_y and bndry->by != 0)) {
       int extrap_start = 0;
       if (not no_extra_interpolate) {
@@ -203,7 +205,9 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
   // initializing yet, leading to an infinite recursion.
   // Also, here we interpolate for the boundary points at xstart/ystart and
   // (xend+1)/(yend+1) instead of extrapolating.
-  for (auto& bndry : localmesh->getBoundaries()) {
+  for (auto& newbndry : localmesh->getBoundaries()) {
+    auto bndry = dynamic_cast<BoundaryRegion*>(newbndry);
+    ASSERT0(bndry != nullptr);
     if ((extrapolate_x and bndry->bx != 0) or (extrapolate_y and bndry->by != 0)) {
       int extrap_start = 0;
       if (not no_extra_interpolate) {
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index af7f6beaec..8073afbb41 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -3241,7 +3241,7 @@ RangeIterator BoutMesh::iterateBndryUpperY() const {
   return RangeIterator(xs, xe);
 }
 
-std::vector<BoundaryRegion*> BoutMesh::getBoundaries() { return boundary; }
+std::vector<BoundaryRegionBase*> BoutMesh::getBoundaries() { return boundary; }
 
 using bout::boundary::BoundaryRegionFCI;
 std::vector<std::shared_ptr<BoundaryRegionFCI>>
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index ab2c5243a7..97ede2a790 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -166,7 +166,7 @@ public:
   bool hasBndryUpperY() const override { return has_boundary_upper_y; }
 
   // Boundary regions
-  std::vector<BoundaryRegion*> getBoundaries() override;
+  std::vector<BoundaryRegionBase*> getBoundaries() override;
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType type) const override;
   void addBoundaryPar(std::shared_ptr<bout::boundary::BoundaryRegionFCI> bndry,
@@ -413,7 +413,7 @@ protected:
   void addBoundaryRegions();
 
 private:
-  std::vector<BoundaryRegion*> boundary; // Vector of boundary regions
+  std::vector<BoundaryRegionBase*> boundary; // Vector of boundary regions
   std::array<std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>,
              static_cast<int>(BoundaryParType::SIZE)>
       par_boundary; // Vector of parallel boundary regions
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 92231a8e92..aea71219de 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -173,7 +173,7 @@ public:
   bool hasBndryLowerY() const override { return false; }
   bool hasBndryUpperY() const override { return false; }
   void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); }
-  std::vector<BoundaryRegion*> getBoundaries() override { return boundaries; }
+  std::vector<BoundaryRegionBase*> getBoundaries() override { return boundaries; }
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType UNUSED(type)) const override {
     return std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>();
@@ -265,7 +265,7 @@ public:
   using Mesh::msg_len;
 
 private:
-  std::vector<BoundaryRegion*> boundaries;
+  std::vector<BoundaryRegionBase*> boundaries;
 };
 
 /// FakeGridDataSource provides a non-null GridDataSource* source to use with FakeMesh, to

From 790a8e17581374ff103279a39566ff6c70f0c04a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:40:12 +0200
Subject: [PATCH 1242/1827] Switch generators to return a pointer

---
 include/bout/boundary_region_iter.hxx | 48 +++++++++++++--------------
 1 file changed, 24 insertions(+), 24 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index d5c43404cc..52dd37624f 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -684,36 +684,36 @@ using BoundaryRegionY = BoundaryRegionXY<false>;
 using BoundaryRegionIterX = BoundaryRegionIterXY<true>;
 using BoundaryRegionIterY = BoundaryRegionIterXY<false>;
 
-inline BoundaryRegionX BoundaryRegionXIn(const std::string& name, int ymin, int ymax,
-                                         Mesh* mesh) {
-  return BoundaryRegionX(name, -1, mesh,
-                         Region<Ind3D>(mesh->xstart, mesh->xstart, ymin, ymax,
-                                       mesh->zstart, mesh->zend, mesh->LocalNy,
-                                       mesh->LocalNz, mesh->maxregionblocksize));
+inline BoundaryRegionX* NewBoundaryRegionXIn(const std::string& name, int ymin, int ymax,
+                                             Mesh* mesh) {
+  return new BoundaryRegionX(name, -1, mesh,
+                             Region<Ind3D>(mesh->xstart, mesh->xstart, ymin, ymax,
+                                           mesh->zstart, mesh->zend, mesh->LocalNy,
+                                           mesh->LocalNz, mesh->maxregionblocksize));
 }
 
-inline BoundaryRegionX BoundaryRegionXOut(const std::string& name, int ymin, int ymax,
-                                          Mesh* mesh) {
-  return BoundaryRegionX(name, 1, mesh,
-                         Region<Ind3D>(mesh->xend, mesh->xend, ymin, ymax, mesh->zstart,
-                                       mesh->zend, mesh->LocalNy, mesh->LocalNz,
-                                       mesh->maxregionblocksize));
+inline BoundaryRegionX* NewBoundaryRegionXOut(const std::string& name, int ymin, int ymax,
+                                              Mesh* mesh) {
+  return new BoundaryRegionX(name, 1, mesh,
+                             Region<Ind3D>(mesh->xend, mesh->xend, ymin, ymax,
+                                           mesh->zstart, mesh->zend, mesh->LocalNy,
+                                           mesh->LocalNz, mesh->maxregionblocksize));
 }
 
-inline BoundaryRegionY BoundaryRegionYUp(const std::string& name, int xmin, int xmax,
-                                         Mesh* mesh) {
-  return BoundaryRegionY(name, -1, mesh,
-                         Region<Ind3D>(xmin, xmax, mesh->yend, mesh->yend, mesh->zstart,
-                                       mesh->zend, mesh->LocalNy, mesh->LocalNz,
-                                       mesh->maxregionblocksize));
+inline BoundaryRegionY* NewBoundaryRegionYUp(const std::string& name, int xmin, int xmax,
+                                             Mesh* mesh) {
+  return new BoundaryRegionY(name, -1, mesh,
+                             Region<Ind3D>(xmin, xmax, mesh->yend, mesh->yend,
+                                           mesh->zstart, mesh->zend, mesh->LocalNy,
+                                           mesh->LocalNz, mesh->maxregionblocksize));
 }
 
-inline BoundaryRegionY BoundaryRegionYDown(const std::string& name, int xmin, int xmax,
-                                           Mesh* mesh) {
-  return BoundaryRegionY(name, 1, mesh,
-                         Region<Ind3D>(xmin, xmax, mesh->ystart, mesh->ystart,
-                                       mesh->zstart, mesh->zend, mesh->LocalNy,
-                                       mesh->LocalNz, mesh->maxregionblocksize));
+inline BoundaryRegionY* NewBoundaryRegionYDown(const std::string& name, int xmin,
+                                               int xmax, Mesh* mesh) {
+  return new BoundaryRegionY(name, 1, mesh,
+                             Region<Ind3D>(xmin, xmax, mesh->ystart, mesh->ystart,
+                                           mesh->zstart, mesh->zend, mesh->LocalNy,
+                                           mesh->LocalNz, mesh->maxregionblocksize));
 }
 
 template <class Func>

From 17121547efd9f6677ae9f319e5a030220540a286 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:42:36 +0200
Subject: [PATCH 1243/1827] Fall back to curl, if wget fails

---
 cmake/BOUT++functions.cmake | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/cmake/BOUT++functions.cmake b/cmake/BOUT++functions.cmake
index cff7e4b808..9b64f643c6 100644
--- a/cmake/BOUT++functions.cmake
+++ b/cmake/BOUT++functions.cmake
@@ -233,8 +233,10 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
     set(output)
     add_custom_command(
       OUTPUT ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
-      COMMAND wget ${BOUT_TEST_OPTIONS_DOWNLOAD} -O
-              ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME} $ENV{BOUT_TEST_DOWNLOAD_FLAGS}
+      COMMAND
+        wget ${BOUT_TEST_OPTIONS_DOWNLOAD} -O ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
+        $ENV{BOUT_TEST_DOWNLOAD_FLAGS} || curl ${BOUT_TEST_OPTIONS_DOWNLOAD} -o
+        ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
       COMMENT "Downloading ${BOUT_TEST_OPTIONS_DOWNLOAD_NAME}"
     )

From f0d872e1c4113eb7db5482de99a2bd0c4aa37d03 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:42:20 +0200
Subject: [PATCH 1244/1827] WIP: Add bits to field2d

We cannot switch jet, as several boundary ops only take Field3D
---
 src/field/field2d.cxx | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index f363f1f1da..e6c1a60cff 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -32,6 +32,7 @@
 #include <bout/assert.hxx>
 #include <bout/boundary_factory.hxx>
 #include <bout/boundary_op.hxx>
+#include <bout/boundary_region_iter.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/field2d.hxx>
@@ -315,7 +316,14 @@ void Field2D::setBoundaryTo(const Field2D& f2d) {
 
   /// Loop over boundary regions
   for (const auto& regnew : fieldmesh->getBoundaries()) {
+    // if (regnew->isX || regnew->isY) {
+    //   bout::boundary::iter_boundary(regnew, [&](auto& point) {
+    // 	const auto val = point.interpolate_boundary_o2(f2d);
+    // 	point.dirichlet_o1(*this, val);
+    //   });
+    // } else
     {
+#warning Remove once ported
       /// Loop within each region
       auto reg = dynamic_cast<BoundaryRegion*>(regnew);
       ASSERT0(reg != nullptr);

From 3eee346f8bfebdee87e1f71e18841d12cabf87cc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:43:02 +0200
Subject: [PATCH 1245/1827] WIP: switch to new boundary

---
 src/mesh/impls/bout/boutmesh.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 8073afbb41..bc207ad646 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -1105,10 +1105,12 @@ void BoutMesh::createYBoundaries() {
 
   if ((UDATA_INDEST < 0) && (UDATA_XSPLIT > yboundary_xstart)) {
     boundary.push_back(
+        //bout::boundary::NewBoundaryRegionYUp("upper_target", yboundary_xstart, UDATA_XSPLIT - 1, this));
         new BoundaryRegionYUp("upper_target", yboundary_xstart, UDATA_XSPLIT - 1, this));
   }
   if ((UDATA_OUTDEST < 0) && (UDATA_XSPLIT <= yboundary_xend)) {
     boundary.push_back(
+        //bout::boundary::NewBoundaryRegionYUp("upper_target", UDATA_XSPLIT, yboundary_xend, this));
         new BoundaryRegionYUp("upper_target", UDATA_XSPLIT, yboundary_xend, this));
   }
 

From 3035d9c57bd49abe37979af18dfa423559f6c813 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:43:02 +0200
Subject: [PATCH 1246/1827] Introduce getLegacyPointer

---
 include/bout/boundary_region.hxx | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index ab7ef8705e..edef0d8daa 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -51,6 +51,12 @@ public:
 
   virtual ~BoundaryRegionBase() = default;
 
+  virtual BoundaryRegion* getLegacyPointer() {
+    if (legacy == nullptr) {
+      throw BoutException("Legacy region not supported");
+    }
+    return legacy;
+  }
   Mesh* localmesh; ///< Mesh does this boundary region belongs to
 
   std::string label; ///< Label for this boundary region
@@ -66,6 +72,8 @@ public:
                             ///  X or Y first)
   virtual bool
   isDone() = 0; ///< Returns true if outside domain. Can use this with nested nextX, nextY
+
+  BoundaryRegion* legacy{nullptr};
 };
 
 /// Describes a region of the boundary, and a means of iterating over it
@@ -77,6 +85,7 @@ public:
   BoundaryRegion(std::string name, int xd, int yd, Mesh* passmesh = nullptr)
       : BoundaryRegionBase(name, passmesh), bx(xd), by(yd), width(2) {}
   ~BoundaryRegion() override = default;
+  BoundaryRegion* getLegacyPointer() override { return this; }
 
   int x, y;   ///< Indices of the point in the boundary
   int bx, by; ///< Direction of the boundary [x+bx][y+by] is going outwards

From c17e4f989889e296516916380e0d421d57783199 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:57:50 +0200
Subject: [PATCH 1247/1827] Use getLegacyPointer

---
 src/field/field3d.cxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index ecd3c90b74..e867c023d5 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -488,8 +488,7 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
     } else if (newreg->isY) {
       // nothing to do
     } else {
-      auto reg = dynamic_cast<BoundaryRegion*>(newreg);
-      ASSERT1(reg != nullptr);
+      auto reg = newreg->getLegacyPointer();
       if (isFci() && reg->by != 0) {
         continue;
       }

From 3c1f5c71035c88e86f23240df211b9af6e05abd9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 10:58:25 +0200
Subject: [PATCH 1248/1827] hide cast

---
 src/field/field3d.cxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index e867c023d5..f13196a964 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -480,8 +480,7 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
   // Loop over boundary regions
   for (const auto& newreg : fieldmesh->getBoundaries()) {
     if (newreg->isX) {
-      auto reg = dynamic_cast<bout::boundary::BoundaryRegionX*>(newreg);
-      bout::boundary::iter_boundary(*reg, [&](auto& point) {
+      bout::boundary::iter_boundary(newreg, [&](auto& point) {
         const BoutReal val = point.interpolate_boundary_o2(f3d);
         point.dirichlet_o1(*this, val);
       });

From 6eb2c3d481a4dacc46c68d2dcac9bd3e1e871423 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:01:44 +0200
Subject: [PATCH 1249/1827] Move implementation to cxx file

---
 include/bout/boundary_region.hxx | 7 +------
 src/mesh/boundary_region.cxx     | 7 +++++++
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index edef0d8daa..a802ab6b05 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -51,12 +51,7 @@ public:
 
   virtual ~BoundaryRegionBase() = default;
 
-  virtual BoundaryRegion* getLegacyPointer() {
-    if (legacy == nullptr) {
-      throw BoutException("Legacy region not supported");
-    }
-    return legacy;
-  }
+  virtual BoundaryRegion* getLegacyPointer();
   Mesh* localmesh; ///< Mesh does this boundary region belongs to
 
   std::string label; ///< Label for this boundary region
diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx
index 700ef8a91f..540d29d6c6 100644
--- a/src/mesh/boundary_region.cxx
+++ b/src/mesh/boundary_region.cxx
@@ -7,6 +7,13 @@
 #include <utility>
 using std::swap;
 
+BoundaryRegion* BoundaryRegionBase::getLegacyPointer() {
+  if (legacy == nullptr) {
+    throw BoutException("Legacy region not supported");
+  }
+  return legacy;
+}
+
 BoundaryRegionXIn::BoundaryRegionXIn(std::string name, int ymin, int ymax, Mesh* passmesh)
     : BoundaryRegion(std::move(name), -1, 0, passmesh), ys(ymin), ye(ymax) {
   location = BNDRY_XIN;

From f7cfbaba73906872f107cb8bc4514d8efc5988d1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:02:35 +0200
Subject: [PATCH 1250/1827] Use old code for Field2D

---
 src/field/field2d.cxx | 26 ++++++++------------------
 1 file changed, 8 insertions(+), 18 deletions(-)

diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index e6c1a60cff..0fcca087f7 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -316,24 +316,14 @@ void Field2D::setBoundaryTo(const Field2D& f2d) {
 
   /// Loop over boundary regions
   for (const auto& regnew : fieldmesh->getBoundaries()) {
-    // if (regnew->isX || regnew->isY) {
-    //   bout::boundary::iter_boundary(regnew, [&](auto& point) {
-    // 	const auto val = point.interpolate_boundary_o2(f2d);
-    // 	point.dirichlet_o1(*this, val);
-    //   });
-    // } else
-    {
-#warning Remove once ported
-      /// Loop within each region
-      auto reg = dynamic_cast<BoundaryRegion*>(regnew);
-      ASSERT0(reg != nullptr);
-      for (reg->first(); !reg->isDone(); reg->next()) {
-        // Get value half-way between cells
-        BoutReal val =
-            0.5 * (f2d(reg->x, reg->y) + f2d(reg->x - reg->bx, reg->y - reg->by));
-        // Set to this value
-        (*this)(reg->x, reg->y) = 2. * val - (*this)(reg->x - reg->bx, reg->y - reg->by);
-      }
+    /// Loop within each region
+    auto reg = regnew->getLegacyPointer();
+    for (reg->first(); !reg->isDone(); reg->next()) {
+      // Get value half-way between cells
+      BoutReal val =
+          0.5 * (f2d(reg->x, reg->y) + f2d(reg->x - reg->bx, reg->y - reg->by));
+      // Set to this value
+      (*this)(reg->x, reg->y) = 2. * val - (*this)(reg->x - reg->bx, reg->y - reg->by);
     }
   }
 }

From 503c25c4b00e4b4e702107db0a7ec7442cde3d83 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:05:10 +0200
Subject: [PATCH 1251/1827] Use getLegacyPointer

---
 src/mesh/coordinates.cxx | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 40024ed3eb..4ad29c4863 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -55,8 +55,7 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr
   // Also, here we interpolate for the boundary points at xstart/ystart and
   // (xend+1)/(yend+1) instead of extrapolating.
   for (auto& newbndry : localmesh->getBoundaries()) {
-    auto bndry = dynamic_cast<BoundaryRegion*>(newbndry);
-    ASSERT0(bndry != nullptr);
+    auto bndry = newbndry->getLegacyPointer();
     if ((extrapolate_x and bndry->bx != 0) or (extrapolate_y and bndry->by != 0)) {
       int extrap_start = 0;
       if (not no_extra_interpolate) {
@@ -206,8 +205,7 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
   // Also, here we interpolate for the boundary points at xstart/ystart and
   // (xend+1)/(yend+1) instead of extrapolating.
   for (auto& newbndry : localmesh->getBoundaries()) {
-    auto bndry = dynamic_cast<BoundaryRegion*>(newbndry);
-    ASSERT0(bndry != nullptr);
+    auto bndry = newbndry->getLegacyPointer();
     if ((extrapolate_x and bndry->bx != 0) or (extrapolate_y and bndry->by != 0)) {
       int extrap_start = 0;
       if (not no_extra_interpolate) {

From 26f0cc0ec3315d75c7fa6638d97a84ae0949c658 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:10:30 +0200
Subject: [PATCH 1252/1827] Delete legacy implementation

---
 include/bout/boundary_region.hxx | 2 +-
 src/mesh/boundary_region.cxx     | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index a802ab6b05..1a0873eb88 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -49,7 +49,7 @@ public:
       : localmesh(passmesh ? passmesh : bout::globals::mesh), label(std::move(name)),
         location(loc) {}
 
-  virtual ~BoundaryRegionBase() = default;
+  virtual ~BoundaryRegionBase();
 
   virtual BoundaryRegion* getLegacyPointer();
   Mesh* localmesh; ///< Mesh does this boundary region belongs to
diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx
index 540d29d6c6..6747c7970e 100644
--- a/src/mesh/boundary_region.cxx
+++ b/src/mesh/boundary_region.cxx
@@ -13,7 +13,11 @@ BoundaryRegion* BoundaryRegionBase::getLegacyPointer() {
   }
   return legacy;
 }
-
+BoundaryRegionBase::~BoundaryRegionBase() {
+  if (legacy != nullptr) {
+    delete legacy;
+  }
+};
 BoundaryRegionXIn::BoundaryRegionXIn(std::string name, int ymin, int ymax, Mesh* passmesh)
     : BoundaryRegion(std::move(name), -1, 0, passmesh), ys(ymin), ye(ymax) {
   location = BNDRY_XIN;

From 131c4066af43f53486385ca3f7b4f5cf92cbad6a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:13:37 +0200
Subject: [PATCH 1253/1827] Add more legacy pointers

---
 include/bout/boundary_region_iter.hxx | 40 ++++++++++++++++-----------
 1 file changed, 24 insertions(+), 16 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 52dd37624f..026a455284 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -686,34 +686,42 @@ using BoundaryRegionIterY = BoundaryRegionIterXY<false>;
 
 inline BoundaryRegionX* NewBoundaryRegionXIn(const std::string& name, int ymin, int ymax,
                                              Mesh* mesh) {
-  return new BoundaryRegionX(name, -1, mesh,
-                             Region<Ind3D>(mesh->xstart, mesh->xstart, ymin, ymax,
-                                           mesh->zstart, mesh->zend, mesh->LocalNy,
-                                           mesh->LocalNz, mesh->maxregionblocksize));
+  auto pointer = new BoundaryRegionX(
+      name, -1, mesh,
+      Region<Ind3D>(mesh->xstart, mesh->xstart, ymin, ymax, mesh->zstart, mesh->zend,
+                    mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
+  pointer->legacy = new ::BoundaryRegionXIn(name, ymin, ymax, mesh);
+  return pointer;
 }
 
 inline BoundaryRegionX* NewBoundaryRegionXOut(const std::string& name, int ymin, int ymax,
                                               Mesh* mesh) {
-  return new BoundaryRegionX(name, 1, mesh,
-                             Region<Ind3D>(mesh->xend, mesh->xend, ymin, ymax,
-                                           mesh->zstart, mesh->zend, mesh->LocalNy,
-                                           mesh->LocalNz, mesh->maxregionblocksize));
+  auto pointer = new BoundaryRegionX(
+      name, 1, mesh,
+      Region<Ind3D>(mesh->xend, mesh->xend, ymin, ymax, mesh->zstart, mesh->zend,
+                    mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
+  pointer->legacy = new ::BoundaryRegionXOut(name, ymin, ymax, mesh);
+  return pointer;
 }
 
 inline BoundaryRegionY* NewBoundaryRegionYUp(const std::string& name, int xmin, int xmax,
                                              Mesh* mesh) {
-  return new BoundaryRegionY(name, -1, mesh,
-                             Region<Ind3D>(xmin, xmax, mesh->yend, mesh->yend,
-                                           mesh->zstart, mesh->zend, mesh->LocalNy,
-                                           mesh->LocalNz, mesh->maxregionblocksize));
+  auto pointer = new BoundaryRegionY(
+      name, -1, mesh,
+      Region<Ind3D>(xmin, xmax, mesh->yend, mesh->yend, mesh->zstart, mesh->zend,
+                    mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
+  pointer->legacy = new ::BoundaryRegionYUp(name, xmin, xmax, mesh);
+  return pointer;
 }
 
 inline BoundaryRegionY* NewBoundaryRegionYDown(const std::string& name, int xmin,
                                                int xmax, Mesh* mesh) {
-  return new BoundaryRegionY(name, 1, mesh,
-                             Region<Ind3D>(xmin, xmax, mesh->ystart, mesh->ystart,
-                                           mesh->zstart, mesh->zend, mesh->LocalNy,
-                                           mesh->LocalNz, mesh->maxregionblocksize));
+  auto pointer = new BoundaryRegionY(
+      name, 1, mesh,
+      Region<Ind3D>(xmin, xmax, mesh->ystart, mesh->ystart, mesh->zstart, mesh->zend,
+                    mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
+  pointer->legacy = new ::BoundaryRegionYDown(name, xmin, xmax, mesh);
+  return pointer;
 }
 
 template <class Func>

From e3f37f162ad49ca07fa3cafe5c60f672940dd94d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:18:36 +0200
Subject: [PATCH 1254/1827] Switch all construcotrs to new interface

---
 src/mesh/impls/bout/boutmesh.cxx   | 25 ++++++++++++-------------
 tests/unit/fake_mesh.hxx           |  9 +++++----
 tests/unit/fake_parallel_mesh.hxx  |  9 +++++----
 tests/unit/field/test_vector2d.cxx | 10 ++++++----
 tests/unit/field/test_vector3d.cxx | 10 ++++++----
 5 files changed, 34 insertions(+), 29 deletions(-)

diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index bc207ad646..f56979785c 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -1068,16 +1068,17 @@ void BoutMesh::createXBoundaries() {
     if (((yg > jyseps1_1) and (yg <= jyseps2_1))
         or ((yg > jyseps1_2) and (yg <= jyseps2_2))) {
       // Core
-      boundary.push_back(new BoundaryRegionXIn("core", ystart, yend, this));
+      boundary.push_back(
+          bout::boundary::NewBoundaryRegionXIn("core", ystart, yend, this));
     } else {
       // PF region
-      boundary.push_back(new BoundaryRegionXIn("pf", ystart, yend, this));
+      boundary.push_back(bout::boundary::NewBoundaryRegionXIn("pf", ystart, yend, this));
     }
   }
 
   if (PE_XIND == (NXPE - 1)) {
     // Outer SOL
-    boundary.push_back(new BoundaryRegionXOut("sol", ystart, yend, this));
+    boundary.push_back(bout::boundary::NewBoundaryRegionXOut("sol", ystart, yend, this));
   }
 }
 
@@ -1104,23 +1105,21 @@ void BoutMesh::createYBoundaries() {
       (include_corner_cells and ODATA_DEST == -1) ? LocalNx - 1 : xend;
 
   if ((UDATA_INDEST < 0) && (UDATA_XSPLIT > yboundary_xstart)) {
-    boundary.push_back(
-        //bout::boundary::NewBoundaryRegionYUp("upper_target", yboundary_xstart, UDATA_XSPLIT - 1, this));
-        new BoundaryRegionYUp("upper_target", yboundary_xstart, UDATA_XSPLIT - 1, this));
+    boundary.push_back(bout::boundary::NewBoundaryRegionYUp(
+        "upper_target", yboundary_xstart, UDATA_XSPLIT - 1, this));
   }
   if ((UDATA_OUTDEST < 0) && (UDATA_XSPLIT <= yboundary_xend)) {
-    boundary.push_back(
-        //bout::boundary::NewBoundaryRegionYUp("upper_target", UDATA_XSPLIT, yboundary_xend, this));
-        new BoundaryRegionYUp("upper_target", UDATA_XSPLIT, yboundary_xend, this));
+    boundary.push_back(bout::boundary::NewBoundaryRegionYUp("upper_target", UDATA_XSPLIT,
+                                                            yboundary_xend, this));
   }
 
   if ((DDATA_INDEST < 0) && (DDATA_XSPLIT > yboundary_xstart)) {
-    boundary.push_back(new BoundaryRegionYDown("lower_target", yboundary_xstart,
-                                               DDATA_XSPLIT - 1, this));
+    boundary.push_back(bout::boundary::NewBoundaryRegionYDown(
+        "lower_target", yboundary_xstart, DDATA_XSPLIT - 1, this));
   }
   if ((DDATA_OUTDEST < 0) && (DDATA_XSPLIT <= yboundary_xend)) {
-    boundary.push_back(
-        new BoundaryRegionYDown("lower_target", DDATA_XSPLIT, yboundary_xend, this));
+    boundary.push_back(bout::boundary::NewBoundaryRegionYDown(
+        "lower_target", DDATA_XSPLIT, yboundary_xend, this));
   }
 }
 
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index aea71219de..a2d68d01e2 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -96,10 +96,11 @@ public:
 
   // Use this if the FakeMesh needs x- and y-boundaries
   void createBoundaries() {
-    addBoundary(new BoundaryRegionXIn("core", ystart, yend, this));
-    addBoundary(new BoundaryRegionXOut("sol", ystart, yend, this));
-    addBoundary(new BoundaryRegionYUp("upper_target", xstart, xend, this));
-    addBoundary(new BoundaryRegionYDown("lower_target", xstart, xend, this));
+    addBoundary(bout::boundary::NewBoundaryRegionXIn("core", ystart, yend, this));
+    addBoundary(bout::boundary::NewBoundaryRegionXOut("sol", ystart, yend, this));
+    addBoundary(bout::boundary::NewBoundaryRegionYUp("upper_target", xstart, xend, this));
+    addBoundary(
+        bout::boundary::NewBoundaryRegionYDown("lower_target", xstart, xend, this));
   }
 
   comm_handle send(FieldGroup& UNUSED(g)) override { return nullptr; }
diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx
index b3e57c4968..04310fc012 100644
--- a/tests/unit/fake_parallel_mesh.hxx
+++ b/tests/unit/fake_parallel_mesh.hxx
@@ -73,10 +73,11 @@ public:
 
   // Use this if the FakeParallelMesh needs x- and y-boundaries
   void createBoundaries() {
-    addBoundary(new BoundaryRegionXIn("core", ystart, yend, this));
-    addBoundary(new BoundaryRegionXOut("sol", ystart, yend, this));
-    addBoundary(new BoundaryRegionYUp("upper_target", xstart, xend, this));
-    addBoundary(new BoundaryRegionYDown("lower_target", xstart, xend, this));
+    addBoundary(bout::boundary::NewBoundaryRegionXIn("core", ystart, yend, this));
+    addBoundary(bout::boundary::NewBoundaryRegionXOut("sol", ystart, yend, this));
+    addBoundary(bout::boundary::NewBoundaryRegionYUp("upper_target", xstart, xend, this));
+    addBoundary(
+        bout::boundary::NewBoundaryRegionYDown("lower_target", xstart, xend, this));
   }
 
   comm_handle sendX(FieldGroup& g, comm_handle handle, bool disable_corners) override {
diff --git a/tests/unit/field/test_vector2d.cxx b/tests/unit/field/test_vector2d.cxx
index 674817abd2..ded551084e 100644
--- a/tests/unit/field/test_vector2d.cxx
+++ b/tests/unit/field/test_vector2d.cxx
@@ -37,10 +37,12 @@ class Vector2DTest : public ::testing::Test {
     static_cast<FakeMesh*>(mesh)->setCoordinates(nullptr);
     mesh->createDefaultRegions();
 
-    mesh->addBoundary(new BoundaryRegionXIn("core", 1, ny - 2, mesh));
-    mesh->addBoundary(new BoundaryRegionXOut("sol", 1, ny - 2, mesh));
-    mesh->addBoundary(new BoundaryRegionYUp("upper_target", 1, nx - 2, mesh));
-    mesh->addBoundary(new BoundaryRegionYDown("lower_target", 1, nx - 2, mesh));
+    mesh->addBoundary(bout::boundary::NewBoundaryRegionXIn("core", 1, ny - 2, mesh));
+    mesh->addBoundary(bout::boundary::NewBoundaryRegionXOut("sol", 1, ny - 2, mesh));
+    mesh->addBoundary(
+        bout::boundary::NewBoundaryRegionYUp("upper_target", 1, nx - 2, mesh));
+    mesh->addBoundary(
+        bout::boundary::NewBoundaryRegionYDown("lower_target", 1, nx - 2, mesh));
 
     static_cast<FakeMesh*>(mesh)->setCoordinates(std::make_shared<Coordinates>(
         mesh, Field2D{1.0}, Field2D{1.0}, BoutReal{1.0}, Field2D{1.0}, Field2D{0.0},
diff --git a/tests/unit/field/test_vector3d.cxx b/tests/unit/field/test_vector3d.cxx
index d8e9366574..d87d4c4bed 100644
--- a/tests/unit/field/test_vector3d.cxx
+++ b/tests/unit/field/test_vector3d.cxx
@@ -34,10 +34,12 @@ class Vector3DTest : public ::testing::Test {
     static_cast<FakeMesh*>(mesh)->setCoordinates(nullptr);
     mesh->createDefaultRegions();
 
-    mesh->addBoundary(new BoundaryRegionXIn("core", 1, ny - 2, mesh));
-    mesh->addBoundary(new BoundaryRegionXOut("sol", 1, ny - 2, mesh));
-    mesh->addBoundary(new BoundaryRegionYUp("upper_target", 1, nx - 2, mesh));
-    mesh->addBoundary(new BoundaryRegionYDown("lower_target", 1, nx - 2, mesh));
+    mesh->addBoundary(bout::boundary::NewBoundaryRegionXIn("core", 1, ny - 2, mesh));
+    mesh->addBoundary(bout::boundary::NewBoundaryRegionXOut("sol", 1, ny - 2, mesh));
+    mesh->addBoundary(
+        bout::boundary::NewBoundaryRegionYUp("upper_target", 1, nx - 2, mesh));
+    mesh->addBoundary(
+        bout::boundary::NewBoundaryRegionYDown("lower_target", 1, nx - 2, mesh));
 
     static_cast<FakeMesh*>(mesh)->setCoordinates(std::make_shared<Coordinates>(
         mesh, Field2D{1.0}, Field2D{1.0}, BoutReal{1.0}, Field2D{1.0}, Field2D{0.0},

From 9e3e851aba178f3eb07f609e5c9bd3feea7debec Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:21:53 +0200
Subject: [PATCH 1255/1827] addBoundary should take BoundaryRegionBase

---
 include/bout/mesh.hxx    | 2 +-
 tests/unit/fake_mesh.hxx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 33272d486f..9eca552a1a 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -487,7 +487,7 @@ public:
   virtual std::set<std::string> getPossibleBoundaries() const { return {}; }
 
   /// Add a boundary region to this processor
-  virtual void addBoundary(BoundaryRegion* UNUSED(bndry)) {}
+  virtual void addBoundary(BoundaryRegionBase* UNUSED(bndry)) {}
 
   /// Get the list of parallel boundary regions. The option specifies with
   /// region to get. Default is to get all regions. All possible options are
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index a2d68d01e2..53dc1a7468 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -173,7 +173,7 @@ public:
   RangeIterator iterateBndryUpperInnerY() const override { return RangeIterator(); }
   bool hasBndryLowerY() const override { return false; }
   bool hasBndryUpperY() const override { return false; }
-  void addBoundary(BoundaryRegion* region) override { boundaries.push_back(region); }
+  void addBoundary(BoundaryRegionBase* region) override { boundaries.push_back(region); }
   std::vector<BoundaryRegionBase*> getBoundaries() override { return boundaries; }
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType UNUSED(type)) const override {

From 7e8f7ae169165f8ba6e0baace9af76c896cd90ec Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:41:22 +0200
Subject: [PATCH 1256/1827] Use getLegacyPointer

---
 src/mesh/boundary_factory.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index fc77983f0e..125a102150 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -118,7 +118,7 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
       // Clone the boundary operation, passing the region to operate over,
       // an empty args list and empty keyword map
       list<string> args;
-      return op->clone(dynamic_cast<BoundaryRegion*>(region), args, {});
+      return op->clone(region->getLegacyPointer(), args, {});
     }
   }
   // Contains a bracket. Find the last bracket and remove
@@ -213,7 +213,7 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
     BoundaryOp* op = findBoundaryOp(trim(func));
     if (op != nullptr) {
       // An operation with arguments
-      return op->clone(dynamic_cast<BoundaryRegion*>(region), arglist, keywords);
+      return op->clone(region->getLegacyPointer(), arglist, keywords);
     }
   }
 

From 43a8d16f76cbdcf277f51ad8f253bf5e28bbdbf6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:46:57 +0200
Subject: [PATCH 1257/1827] Throw exceptions in stubs

People might expect them to do something.
---
 include/bout/mesh.hxx    | 8 ++++++--
 tests/unit/fake_mesh.hxx | 1 +
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 9eca552a1a..c9f079397f 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -484,10 +484,14 @@ public:
   virtual std::vector<BoundaryRegionBase*> getBoundaries() = 0;
 
   /// Get the set of all possible boundaries in this configuration
-  virtual std::set<std::string> getPossibleBoundaries() const { return {}; }
+  virtual std::set<std::string> getPossibleBoundaries() const {
+    throw BoutException("Not implemented for this mesh");
+  };
 
   /// Add a boundary region to this processor
-  virtual void addBoundary(BoundaryRegionBase* UNUSED(bndry)) {}
+  virtual void addBoundary(BoundaryRegionBase* UNUSED(bndry)) {
+    throw BoutException("This has never been implemented");
+  };
 
   /// Get the list of parallel boundary regions. The option specifies with
   /// region to get. Default is to get all regions. All possible options are
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 53dc1a7468..9e37576144 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -123,6 +123,7 @@ public:
                    [[maybe_unused]] int Z) const override {
     return 0;
   }
+  std::set<std::string> getPossibleBoundaries() const override { return {}; }
   bool firstX() const override { return true; }
   bool lastX() const override { return true; }
   int sendXOut(BoutReal* UNUSED(buffer), int UNUSED(size), int UNUSED(tag)) override {

From 4115dc98dcae1855425f410e4b25ef389931c772 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:47:21 +0200
Subject: [PATCH 1258/1827] Add missing header

---
 tests/unit/fake_parallel_mesh.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx
index 04310fc012..f679963064 100644
--- a/tests/unit/fake_parallel_mesh.hxx
+++ b/tests/unit/fake_parallel_mesh.hxx
@@ -12,6 +12,7 @@
 #include "bout/assert.hxx"
 #include "bout/boundary_op.hxx"
 #include "bout/boundary_region.hxx"
+#include "bout/boundary_region_iter.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/coordinates.hxx"
 #include "bout/field2d.hxx"

From a49fe6f1e01670be9ad8348c1a74377cde0e3f41 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:41:06 +0200
Subject: [PATCH 1259/1827] Add missing header

---
 include/bout/boundary_iterator.hxx | 2 --
 1 file changed, 2 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 66c66d45b6..bf03e15636 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -2,7 +2,6 @@
 
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
-#include "bout/build_defines.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
@@ -160,7 +159,6 @@ protected:
   int y() const { return _y; }
   int z() const { return _z; }
 
-protected:
   void setx(int x) { _x = x; }
   void sety(int y) { _y = y; }
 

From 5531eb439010af774eea016931106d389b62b517 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:42:13 +0200
Subject: [PATCH 1260/1827] Include used headers

---
 include/bout/boundary_region_iter.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 026a455284..5d29737e01 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -6,13 +6,13 @@
 #include <cstdint>
 #include <functional>
 #include <string>
-#include <utility>
+#include <type_traits>
+#include <vector>
 
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/field_data.hxx"
 #include "bout/utils.hxx"
-#include <bout/bout_enum_class.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/parallel_boundary_region.hxx>

From 9ba03a4213af421439fd52baa0ed9d4a9b0a87dd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:44:06 +0200
Subject: [PATCH 1261/1827] Include used headers

---
 include/bout/mesh.hxx                     | 1 +
 include/bout/parallel_boundary_op.hxx     | 1 +
 include/bout/sys/parallel_stencils.hxx    | 2 +-
 src/field/field2d.cxx                     | 1 -
 src/field/field_data.cxx                  | 1 -
 src/mesh/boundary_region.cxx              | 1 +
 src/mesh/impls/bout/boutmesh.hxx          | 3 +++
 src/mesh/parallel/shiftedmetricinterp.cxx | 1 +
 src/mesh/parallel_boundary_op.cxx         | 2 +-
 tests/unit/fake_mesh.hxx                  | 1 +
 10 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index c9f079397f..1453f51f5f 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -38,6 +38,7 @@
  *
  **************************************************************************/
 
+#include "bout/boutexception.hxx"
 class Mesh;
 
 #ifndef BOUT_MESH_H
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index 9a2ea9cf57..c87de013f4 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -8,6 +8,7 @@
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
 #include "bout/parallel_boundary_region.hxx"
+#include "bout/sys/expressionparser.hxx"
 #include "bout/unused.hxx"
 #include "bout/utils.hxx"
 
diff --git a/include/bout/sys/parallel_stencils.hxx b/include/bout/sys/parallel_stencils.hxx
index 651ebc3ca1..88396005ae 100644
--- a/include/bout/sys/parallel_stencils.hxx
+++ b/include/bout/sys/parallel_stencils.hxx
@@ -1,6 +1,6 @@
 #pragma once
-#include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
+#include <cmath>
 
 namespace bout::parallel_stencil {
 // generated by src/mesh/parallel_boundary_stencil.cxx.py
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index 0fcca087f7..175bf45b11 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -32,7 +32,6 @@
 #include <bout/assert.hxx>
 #include <bout/boundary_factory.hxx>
 #include <bout/boundary_op.hxx>
-#include <bout/boundary_region_iter.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/field2d.hxx>
diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx
index 154380dcb6..b925cb1426 100644
--- a/src/field/field_data.cxx
+++ b/src/field/field_data.cxx
@@ -3,7 +3,6 @@
 #include "bout/parallel_boundary_region.hxx"
 #include "bout/unused.hxx"
 #include <bout/boundary_factory.hxx>
-#include <bout/boundary_region_iter.hxx>
 #include <bout/field_data.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/globals.hxx>
diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx
index 6747c7970e..370fa3a997 100644
--- a/src/mesh/boundary_region.cxx
+++ b/src/mesh/boundary_region.cxx
@@ -1,4 +1,5 @@
 
+#include "bout/boutexception.hxx"
 #include <bout/boundary_region.hxx>
 #include <bout/globals.hxx>
 #include <bout/mesh.hxx>
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index 97ede2a790..dfec3342ed 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -5,10 +5,13 @@
 #include "mpi.h"
 
 #include "bout/bout_types.hxx"
+#include "bout/field_data.hxx"
 #include "bout/unused.hxx"
 #include <bout/mesh.hxx>
 
+#include <array>
 #include <list>
+#include <memory>
 #include <set>
 #include <string>
 #include <vector>
diff --git a/src/mesh/parallel/shiftedmetricinterp.cxx b/src/mesh/parallel/shiftedmetricinterp.cxx
index 7171bdd0bd..de583ceee2 100644
--- a/src/mesh/parallel/shiftedmetricinterp.cxx
+++ b/src/mesh/parallel/shiftedmetricinterp.cxx
@@ -28,6 +28,7 @@
  **************************************************************************/
 
 #include <algorithm>
+#include <memory>
 
 #include "shiftedmetricinterp.hxx"
 
diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx
index 9b1d8d4947..dc376e7e63 100644
--- a/src/mesh/parallel_boundary_op.cxx
+++ b/src/mesh/parallel_boundary_op.cxx
@@ -1,12 +1,12 @@
 #include "bout/parallel_boundary_op.hxx"
 #include "bout/boundary_region_iter.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
 #include "bout/constants.hxx"
 #include "bout/field_factory.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
 #include "bout/output.hxx"
-#include "bout/parallel_boundary_region.hxx"
 
 BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterFCI& bndry,
                                  BoutReal t) {
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 9e37576144..4d4b985a22 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -20,6 +20,7 @@
 #include <iterator>
 #include <memory>
 #include <numeric>
+#include <set>
 #include <string>
 #include <utility>
 #include <vector>

From 6b33e6264184a537205ae33eb68a275a4873fedf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:44:47 +0200
Subject: [PATCH 1262/1827] Make constructor private

---
 include/bout/boundary_region_iter.hxx | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 5d29737e01..d3e0e2800d 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -46,7 +46,9 @@ enum class BoundaryFreeExtrapolation : std::int8_t { limited, exponential, linea
 //BOUT_ENUM_CLASS(BoundaryFreeExtrapolation, limited, exponential, linear);
 
 template <typename impl>
-class BoundaryRegionIterBase { /// get the index at the last point in domain
+class BoundaryRegionIterBase {
+  BoundaryRegionIterBase() = default;
+  /// get the index at the last point in domain
 public:
   Ind3D ind() const { return static_cast<const impl*>(this)->_ind(); }
   /// get the length from the point in the domain to the boundary in index
@@ -372,6 +374,7 @@ public:
 
 private:
   BoutReal small_value = 1e-4;
+  friend impl;
 };
 
 namespace {

From da0dcddc08ca40eab8a841ceb7b7975dd01c8eeb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:45:37 +0200
Subject: [PATCH 1263/1827] Prefer const functions

---
 include/bout/boundary_region_iter.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index d3e0e2800d..c13850411a 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -444,7 +444,7 @@ public:
         std::lower_bound(std::begin(bndry_points), std::end(bndry_points), ind);
     return found != std::end(bndry_points) and found->index == ind;
   }
-  int dir() { return _dir; }
+  int dir() const { return _dir; }
   // legacy interface
   void first() override { throw BoutException("Legacy interface is not suppored"); }
   void next() override { throw BoutException("Legacy interface is not suppored"); }
@@ -543,7 +543,7 @@ public:
     ASSERT3(loc == CELL_CENTRE);
     return region->bndry_points[pos].length;
   }
-  bool operator!=(BoundaryRegionIterFCI lhs) {
+  bool operator!=(BoundaryRegionIterFCI lhs) const {
     ASSERT3(region == lhs.region);
     return pos != lhs.pos;
   }

From 8725bb99b0f4d2b248e6684b6a87c3709551a7c5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:46:36 +0200
Subject: [PATCH 1264/1827] Add parenthis for clarification

---
 include/bout/boundary_region_iter.hxx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index c13850411a..f52cc08238 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -466,7 +466,7 @@ private:
   Ind3D xyz2ind(int x, int y, int z) const {
     const int ny = localmesh->LocalNy;
     const int nz = localmesh->LocalNz;
-    return Ind3D{(x * ny + y) * nz + z, ny, nz};
+    return Ind3D{((x * ny + y) * nz) + z, ny, nz};
   }
 };
 
@@ -494,7 +494,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() - off * region->_dir;
+    auto _off = _offset() - (off * region->_dir);
     return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
@@ -503,7 +503,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() - off * region->_dir;
+    auto _off = _offset() - (off * region->_dir);
     return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
@@ -512,7 +512,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() - off * region->_dir;
+    auto _off = _offset() - (off * region->_dir);
     return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
@@ -521,7 +521,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() - off * region->_dir;
+    auto _off = _offset() - (off * region->_dir);
     return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
@@ -530,7 +530,7 @@ public:
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }
-    auto _off = _offset() + off * region->_dir;
+    auto _off = _offset() + (off * region->_dir);
     return f(_off, _ind().yp(_off));
   }
   signed char _offset() const { return region->bndry_points[pos].offset; }

From 36f2d5d8d1c2b12d7b03e970855a090c24ded576 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:47:08 +0200
Subject: [PATCH 1265/1827] Clarify pointer type

---
 include/bout/boundary_region_iter.hxx | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index f52cc08238..ff9a9c3ab8 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -689,7 +689,7 @@ using BoundaryRegionIterY = BoundaryRegionIterXY<false>;
 
 inline BoundaryRegionX* NewBoundaryRegionXIn(const std::string& name, int ymin, int ymax,
                                              Mesh* mesh) {
-  auto pointer = new BoundaryRegionX(
+  auto* pointer = new BoundaryRegionX(
       name, -1, mesh,
       Region<Ind3D>(mesh->xstart, mesh->xstart, ymin, ymax, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
@@ -699,7 +699,7 @@ inline BoundaryRegionX* NewBoundaryRegionXIn(const std::string& name, int ymin,
 
 inline BoundaryRegionX* NewBoundaryRegionXOut(const std::string& name, int ymin, int ymax,
                                               Mesh* mesh) {
-  auto pointer = new BoundaryRegionX(
+  auto* pointer = new BoundaryRegionX(
       name, 1, mesh,
       Region<Ind3D>(mesh->xend, mesh->xend, ymin, ymax, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
@@ -709,7 +709,7 @@ inline BoundaryRegionX* NewBoundaryRegionXOut(const std::string& name, int ymin,
 
 inline BoundaryRegionY* NewBoundaryRegionYUp(const std::string& name, int xmin, int xmax,
                                              Mesh* mesh) {
-  auto pointer = new BoundaryRegionY(
+  auto* pointer = new BoundaryRegionY(
       name, -1, mesh,
       Region<Ind3D>(xmin, xmax, mesh->yend, mesh->yend, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
@@ -719,7 +719,7 @@ inline BoundaryRegionY* NewBoundaryRegionYUp(const std::string& name, int xmin,
 
 inline BoundaryRegionY* NewBoundaryRegionYDown(const std::string& name, int xmin,
                                                int xmax, Mesh* mesh) {
-  auto pointer = new BoundaryRegionY(
+  auto* pointer = new BoundaryRegionY(
       name, 1, mesh,
       Region<Ind3D>(xmin, xmax, mesh->ystart, mesh->ystart, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
@@ -730,15 +730,15 @@ inline BoundaryRegionY* NewBoundaryRegionYDown(const std::string& name, int xmin
 template <class Func>
 void iter_boundary(const BoundaryRegionBase* bndrybase, const Func& func) {
   if (bndrybase->isX) {
-    const auto bndry = dynamic_cast<const BoundaryRegionX*>(bndrybase);
+    const auto* const bndry = dynamic_cast<const BoundaryRegionX*>(bndrybase);
     return iter_boundary(*bndry, func);
   }
   if (bndrybase->isY) {
-    const auto bndry = dynamic_cast<const BoundaryRegionY*>(bndrybase);
+    const auto* const bndry = dynamic_cast<const BoundaryRegionY*>(bndrybase);
     return iter_boundary(*bndry, func);
   }
   if (bndrybase->isParallel) {
-    const auto bndry = dynamic_cast<const BoundaryRegionFCI*>(bndrybase);
+    const auto* const bndry = dynamic_cast<const BoundaryRegionFCI*>(bndrybase);
     return iter_boundary(*bndry, func);
   }
   throw BoutException("{} is of unknown type - probably a legacy iterator",

From 17075c3740479210f2723c3c4d63cda43c9752a4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:47:32 +0200
Subject: [PATCH 1266/1827] Do not duplicate default values

---
 include/bout/parallel_boundary_op.hxx | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index c87de013f4..a021f28beb 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -37,26 +37,23 @@ public:
   BoundaryOpPar(bout::boundary::BoundaryRegionX* region, Field3D* value)
       : bndryX(region), field_values(value), value_type(ValueType::FIELD) {}
   BoundaryOpPar(bout::boundary::BoundaryRegionX* region, BoutReal value)
-      : bndryX(region), real_value(value), value_type(ValueType::REAL) {}
-  BoundaryOpPar(bout::boundary::BoundaryRegionX* region)
-      : bndryX(region), real_value(0.), value_type(ValueType::REAL) {}
+      : bndryX(region), real_value(value) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionX* region) : bndryX(region) {}
   BoundaryOpPar(bout::boundary::BoundaryRegionY* region,
                 std::shared_ptr<FieldGenerator> value)
       : bndryY(region), gen_values(std::move(value)), value_type(ValueType::GEN) {}
   BoundaryOpPar(bout::boundary::BoundaryRegionY* region, Field3D* value)
       : bndryY(region), field_values(value), value_type(ValueType::FIELD) {}
   BoundaryOpPar(bout::boundary::BoundaryRegionY* region, BoutReal value)
-      : bndryY(region), real_value(value), value_type(ValueType::REAL) {}
-  BoundaryOpPar(bout::boundary::BoundaryRegionY* region)
-      : bndryY(region), real_value(0.), value_type(ValueType::REAL) {}
+      : bndryY(region), real_value(value) {}
+  BoundaryOpPar(bout::boundary::BoundaryRegionY* region) : bndryY(region) {}
   BoundaryOpPar(BoundaryOpPar* region, std::shared_ptr<FieldGenerator> value)
       : bndry(region->bndry), gen_values(std::move(value)), value_type(ValueType::GEN) {}
   BoundaryOpPar(BoundaryOpPar* region, Field3D* value)
       : bndry(region->bndry), field_values(value), value_type(ValueType::FIELD) {}
   BoundaryOpPar(BoundaryOpPar* region, BoutReal value)
-      : bndry(region->bndry), real_value(value), value_type(ValueType::REAL) {}
-  BoundaryOpPar(BoundaryOpPar* region)
-      : bndry(region->bndry), real_value(0.), value_type(ValueType::REAL) {}
+      : bndry(region->bndry), real_value(value) {}
+  BoundaryOpPar(BoundaryOpPar* region) : bndry(region->bndry) {}
   ~BoundaryOpPar() override = default;
 
   // Note: All methods must implement clone, except for modifiers (see below)

From 4cc5a7d60704e8b969915f0518a7df6d0bdc22da Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:48:00 +0200
Subject: [PATCH 1267/1827] Do not use unneeded inline

---
 include/bout/sys/uuid.h | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/include/bout/sys/uuid.h b/include/bout/sys/uuid.h
index 973103ef70..cb029fb1bd 100644
--- a/include/bout/sys/uuid.h
+++ b/include/bout/sys/uuid.h
@@ -76,7 +76,7 @@ namespace uuids {
 
 namespace detail {
 template <typename TChar>
-constexpr inline unsigned char hex2char(const TChar ch) {
+constexpr unsigned char hex2char(const TChar ch) {
   if (ch >= static_cast<TChar>('0') && ch <= static_cast<TChar>('9'))
     return ch - static_cast<TChar>('0');
   if (ch >= static_cast<TChar>('a') && ch <= static_cast<TChar>('f'))
@@ -87,14 +87,14 @@ constexpr inline unsigned char hex2char(const TChar ch) {
 }
 
 template <typename TChar>
-constexpr inline bool is_hex(const TChar ch) {
+constexpr bool is_hex(const TChar ch) {
   return (ch >= static_cast<TChar>('0') && ch <= static_cast<TChar>('9'))
          || (ch >= static_cast<TChar>('a') && ch <= static_cast<TChar>('f'))
          || (ch >= static_cast<TChar>('A') && ch <= static_cast<TChar>('F'));
 }
 
 template <typename TChar>
-constexpr inline unsigned char hexpair2char(const TChar a, const TChar b) {
+constexpr unsigned char hexpair2char(const TChar a, const TChar b) {
   return (hex2char(a) << 4) | hex2char(b);
 }
 
@@ -105,7 +105,7 @@ class sha1 {
 
   static constexpr unsigned int block_bytes = 64;
 
-  inline static uint32_t left_rotate(uint32_t value, const size_t count) {
+  static uint32_t left_rotate(uint32_t value, const size_t count) {
     return (value << count) ^ (value >> (32 - count));
   }
 
@@ -395,9 +395,7 @@ class uuid {
 
   void swap(uuid& other) noexcept { data.swap(other.data); }
 
-  inline const char* as_bytes() const {
-    return reinterpret_cast<const char*>(data.data());
-  }
+  const char* as_bytes() const { return reinterpret_cast<const char*>(data.data()); }
 
   template <class CharT = char>
   static bool is_valid_uuid(const CharT* str) noexcept {

From 686fe60ad48af0958921eb16052182fae5f05636 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:49:20 +0200
Subject: [PATCH 1268/1827] Prefer auto * for pointer

---
 src/field/field2d.cxx    | 2 +-
 src/field/field3d.cxx    | 2 +-
 src/mesh/coordinates.cxx | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index 175bf45b11..328f23e34d 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -316,7 +316,7 @@ void Field2D::setBoundaryTo(const Field2D& f2d) {
   /// Loop over boundary regions
   for (const auto& regnew : fieldmesh->getBoundaries()) {
     /// Loop within each region
-    auto reg = regnew->getLegacyPointer();
+    auto* reg = regnew->getLegacyPointer();
     for (reg->first(); !reg->isDone(); reg->next()) {
       // Get value half-way between cells
       BoutReal val =
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index f13196a964..55e4f19f54 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -487,7 +487,7 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
     } else if (newreg->isY) {
       // nothing to do
     } else {
-      auto reg = newreg->getLegacyPointer();
+      auto* reg = newreg->getLegacyPointer();
       if (isFci() && reg->by != 0) {
         continue;
       }
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 4ad29c4863..b2edddd7dc 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -55,7 +55,7 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr
   // Also, here we interpolate for the boundary points at xstart/ystart and
   // (xend+1)/(yend+1) instead of extrapolating.
   for (auto& newbndry : localmesh->getBoundaries()) {
-    auto bndry = newbndry->getLegacyPointer();
+    auto* bndry = newbndry->getLegacyPointer();
     if ((extrapolate_x and bndry->bx != 0) or (extrapolate_y and bndry->by != 0)) {
       int extrap_start = 0;
       if (not no_extra_interpolate) {

From 978242efb74b1399792bb39a0caafff87da840f2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:49:46 +0200
Subject: [PATCH 1269/1827] Prefer const

---
 src/field/field3d.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 55e4f19f54..6549f7b270 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -495,7 +495,7 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
       for (reg->first(); !reg->isDone(); reg->next()) {
         for (int z = 0; z < nz; z++) {
           // Get value half-way between cells
-          BoutReal val =
+          const BoutReal val =
               0.5 * (f3d(reg->x, reg->y, z) + f3d(reg->x - reg->bx, reg->y - reg->by, z));
           // Set to this value
           (*this)(reg->x, reg->y, z) =

From ec85c735f03fd9c8580a6b505a56130d98bc0ca2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:50:01 +0200
Subject: [PATCH 1270/1827] Use paranthis for clarification

---
 src/field/field3d.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 6549f7b270..42ece48e7a 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -499,7 +499,7 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
               0.5 * (f3d(reg->x, reg->y, z) + f3d(reg->x - reg->bx, reg->y - reg->by, z));
           // Set to this value
           (*this)(reg->x, reg->y, z) =
-              2. * val - (*this)(reg->x - reg->bx, reg->y - reg->by, z);
+              (2. * val) - (*this)(reg->x - reg->bx, reg->y - reg->by, z);
         }
       }
     }

From f47263ff7c9fcb1a289a37bc0496850160cf9f00 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:50:26 +0200
Subject: [PATCH 1271/1827] delete nullptr is a noop

---
 src/mesh/boundary_region.cxx | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx
index 370fa3a997..4fdf9ed657 100644
--- a/src/mesh/boundary_region.cxx
+++ b/src/mesh/boundary_region.cxx
@@ -14,11 +14,7 @@ BoundaryRegion* BoundaryRegionBase::getLegacyPointer() {
   }
   return legacy;
 }
-BoundaryRegionBase::~BoundaryRegionBase() {
-  if (legacy != nullptr) {
-    delete legacy;
-  }
-};
+BoundaryRegionBase::~BoundaryRegionBase() { delete legacy; };
 BoundaryRegionXIn::BoundaryRegionXIn(std::string name, int ymin, int ymax, Mesh* passmesh)
     : BoundaryRegion(std::move(name), -1, 0, passmesh), ys(ymin), ye(ymax) {
   location = BNDRY_XIN;

From b41b8aa77720a978896c9f3a30bebddc05e98625 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:50:55 +0200
Subject: [PATCH 1272/1827] No need for else after return

---
 src/mesh/boundary_factory.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index 125a102150..1e0425a88f 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -200,7 +200,8 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
     if (region->isParallel) {
       return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionFCI*>(region), arglist,
                         keywords);
-    } else if (region->isX) {
+    }
+    if (region->isX) {
       return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionX*>(region), arglist,
                         keywords);
     } else if (region->isY) {

From d1f9f92a8edaa0a4ddddf33f7699bc0206c92219 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 11:52:59 +0200
Subject: [PATCH 1273/1827] Do not use nested terneray expression

---
 include/bout/boundary_region_iter.hxx | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index ff9a9c3ab8..29bcc7d95c 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -256,8 +256,12 @@ public:
 
   BoutReal extrapolate_boundary_free(const Field3D& f,
                                      BoundaryFreeExtrapolation mode) const {
-    const auto fac = valid() > 0 ? limitFreeScale(prev(f), current(f), mode)
-                                 : (mode == BoundaryFreeExtrapolation::linear ? 0 : 1);
+    BoutReal fac;
+    if (valid() > 0) {
+      fac = limitFreeScale(prev(f), current(f), mode);
+    } else {
+      fac = mode == BoundaryFreeExtrapolation::linear ? 0 : 1;
+    }
     auto val = current(f);
     BoutReal next = mode == BoundaryFreeExtrapolation::linear ? val + fac : val * fac;
     return val * length(f.getLocation()) + next * (1 - length(f.getLocation()));

From bb3f066a28555db5b262b7a5988ee3cfb84e8d81 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 27 May 2026 12:31:46 +0200
Subject: [PATCH 1274/1827] initialise variable

---
 include/bout/boundary_region_iter.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 29bcc7d95c..babd10da28 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -256,7 +256,7 @@ public:
 
   BoutReal extrapolate_boundary_free(const Field3D& f,
                                      BoundaryFreeExtrapolation mode) const {
-    BoutReal fac;
+    BoutReal fac = BoutNaN;
     if (valid() > 0) {
       fac = limitFreeScale(prev(f), current(f), mode);
     } else {

From b233faf95d47bc3a77bf0cd44a0780de212cb62e Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 27 May 2026 16:38:28 -0700
Subject: [PATCH 1275/1827] adios2: Fix CMake build

C++ target name seems to have changed with ADIOS2 versions.
CMake will now check for several possible targets.
---
 cmake/SetupBOUTThirdParty.cmake | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 9e6bdc6d2a..1830787ade 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -284,7 +284,27 @@ if(BOUT_USE_ADIOS2)
   else()
     find_package(ADIOS2 REQUIRED)
   endif()
-  target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C)
+
+  
+  foreach(_adios2_candidate
+    adios2::cxx_mpi
+    adios2::cxx20_mpi
+    adios2::cxx17_mpi
+    adios2::cxx11_mpi
+  )
+    if(TARGET ${_adios2_candidate})
+      set(_adios2_target ${_adios2_candidate})
+      break()
+    endif()
+  endforeach()
+
+  if(NOT DEFINED _adios2_target)
+    message(FATAL_ERROR
+      "Could not find a usable ADIOS2 CXX CMake target. ")
+  endif()
+  message(STATUS "Using ADIOS2 CMake target: ${_adios2_target}")
+
+  target_link_libraries(bout++ PUBLIC ${_adios2_target} MPI::MPI_C)
 endif()
 message(STATUS "ADIOS2 support: ${BOUT_USE_ADIOS2}")
 set(BOUT_HAS_ADIOS2 ${BOUT_USE_ADIOS2})

From 53c52cbb96ac5d57841373aea48ac8d762e0cd36 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 28 May 2026 14:04:58 +0200
Subject: [PATCH 1276/1827] Set location

---
 include/bout/boundary_region_iter.hxx | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index babd10da28..ef3cd69c88 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -422,9 +422,8 @@ inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, BoundaryFreeExtrapolati
 
 class BoundaryRegionFCI : public BoundaryRegionBase {
 public:
-  BoundaryRegionFCI(const std::string& name, [[maybe_unused]] const BndryLoc& loc,
-                    int dir, Mesh* mesh)
-      : BoundaryRegionBase(name, mesh), _dir(dir), localmesh(mesh) {
+  BoundaryRegionFCI(const std::string& name, const BndryLoc& loc, int dir, Mesh* mesh)
+      : BoundaryRegionBase(name, loc, mesh), _dir(dir), localmesh(mesh) {
     isParallel = true;
   };
   /// Add a point to the boundary
@@ -568,8 +567,10 @@ public:
     BOUT_FOR_SERIAL(i, rgn) { this->rgn.emplace_back(i); }
     if (isX) {
       this->isX = true;
+      location = dir == 1 ? BNDRY_XOUT : BNDRY_XIN;
     } else {
       this->isY = true;
+      location = dir == 1 ? BNDRY_YUP : BNDRY_YDOWN;
     }
   }
   int dir() { return _dir; }

From b1820eb4d1fdfe33b369e968a2ba6532135af248 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 28 May 2026 14:05:27 +0200
Subject: [PATCH 1277/1827] Ensure location is set

---
 include/bout/boundary_region.hxx | 8 +++++---
 src/mesh/boundary_factory.cxx    | 1 +
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 1a0873eb88..9ff838b7a7 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -25,7 +25,8 @@ enum class BndryLoc : std::int8_t {
   par_fwd_xin, // Don't include parallel boundaries
   par_bkwd_xin,
   par_fwd_xout, // Don't include parallel boundaries
-  par_bkwd_xout
+  par_bkwd_xout,
+  invalid = -1
 };
 constexpr BndryLoc BNDRY_XIN = BndryLoc::xin;
 constexpr BndryLoc BNDRY_XOUT = BndryLoc::xout;
@@ -36,6 +37,7 @@ constexpr BndryLoc BNDRY_PAR_FWD_XIN = BndryLoc::par_fwd_xin;
 constexpr BndryLoc BNDRY_PAR_BKWD_XIN = BndryLoc::par_bkwd_xin;
 constexpr BndryLoc BNDRY_PAR_FWD_XOUT = BndryLoc::par_fwd_xout;
 constexpr BndryLoc BNDRY_PAR_BKWD_XOUT = BndryLoc::par_bkwd_xout;
+constexpr BndryLoc BNDRY_INVALID = BndryLoc::invalid;
 
 /// Physical type of y boundary
 enum class YBndryType : std::int8_t { sheath, not_sheath, all };
@@ -56,8 +58,8 @@ public:
 
   std::string label; ///< Label for this boundary region
 
-  BndryLoc location;       ///< Which side of the domain is it on?
-  bool isParallel = false; ///< Is this a parallel boundary?
+  BndryLoc location{BndryLoc::invalid}; ///< Which side of the domain is it on?
+  bool isParallel = false;              ///< Is this a parallel boundary?
   bool isX = false;
   bool isY = false;
 
diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index 1e0425a88f..ec100e89eb 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -241,6 +241,7 @@ BoundaryOpBase* BoundaryFactory::createFromOptions(const string& varname,
 
   std::array<string, 5> sides;
   sides[0] = region->label;
+  ASSERT2(region->location != BNDRY_INVALID)
   switch (region->location) {
   case BNDRY_XIN: {
     sides[1] = "xin";

From 024c228c90e99a33257db19e7b4f793a698c5900 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 28 May 2026 14:06:05 +0200
Subject: [PATCH 1278/1827] Make class members private

---
 include/bout/parallel_boundary_op.hxx | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index a021f28beb..5139cd5090 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -90,11 +90,11 @@ public:
     return clone(region, args);
   }
 
+private:
   bout::boundary::BoundaryRegionFCI* bndry{nullptr};
   bout::boundary::BoundaryRegionX* bndryX{nullptr};
   bout::boundary::BoundaryRegionY* bndryY{nullptr};
 
-protected:
   /// Possible ways to get boundary values
   std::shared_ptr<FieldGenerator> gen_values;
   Field3D* field_values{nullptr};
@@ -107,6 +107,9 @@ protected:
   BoutReal getValue(const bout::boundary::BoundaryRegionIterFCI& bndry, BoutReal t);
   BoutReal getValue(const bout::boundary::BoundaryRegionIterX& bndry, BoutReal t);
   BoutReal getValue(const bout::boundary::BoundaryRegionIterY& bndry, BoutReal t);
+
+  template <class T, bool isNeumann>
+  friend class BoundaryOpParTemp;
 };
 
 template <class T, bool isNeumann = false>

From 60eeb2af6f93d810e1f6da60afb35e3b0aa0ff8d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 28 May 2026 10:48:26 -0700
Subject: [PATCH 1279/1827] Make loading restarts more robust

Catch exceptions, print messages rather than failing.

Provide a default value (0.0) for 'tt' if missing.
---
 src/solver/solver.cxx             |  6 ++---
 src/sys/options/options_adios.cxx | 37 ++++++++++++++++++-------------
 2 files changed, 24 insertions(+), 19 deletions(-)

diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index c6e9b464fe..e105043c7c 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1,7 +1,7 @@
 /**************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  * 
  * This file is part of BOUT++.
  *
@@ -742,7 +742,7 @@ void Solver::outputVars(Options& output_options, bool save_repeat) {
 
 void Solver::readEvolvingVariablesFromOptions(Options& options) {
   run_id = options["run_id"].withDefault(default_run_id);
-  simtime = options["tt"].as<BoutReal>();
+  simtime = options["tt"].withDefault<BoutReal>(0.0);
   iteration = options["hist_hi"].withDefault<int>(0);
   iteration_offset = iteration;
 
diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 2e64423824..844284a400 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -159,7 +159,12 @@ auto read_variable(adios2::IO& io, adios2::Engine& reader, const std::string& na
     variable.SetMemorySelection(selection.memorySelection());
   }
 
-  reader.Get<U>(variable, value.begin(), adios2::Mode::Sync);
+  try {
+    reader.Get<U>(variable, value.begin(), adios2::Mode::Sync);
+  } catch (const std::exception& e) {
+    output_warn.write("ADIOS exception while reading '{}': {}\n", name, e.what());
+    return Options{};
+  }
   return Options(value);
 }
 
@@ -177,22 +182,22 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
   }
 
   if (variable.ShapeID() == adios2::ShapeID::LocalArray) {
-    throw BoutException(
-        "ADIOS reader did not implement reading local arrays like `{}` '{}' in file '{}'",
-        type, name, reader.Name());
+    throw BoutException("ADIOS reader did not implement reading local arrays like `{}` "
+                        "'{}' in file '{}'\n",
+                        type, name, reader.Name());
   }
 
-  if (type != "double" && type != "float" && type != "int32_t") {
+  if (type != "double" && type != "float" && type != "int32_t" && type != "int64_t") {
     throw BoutException("ADIOS reader did not implement reading arrays that are not "
-                        "`double`/`float`/`int32_t` type. "
-                        "Found `{}` '{}' in file '{}'",
+                        "`double`/`float`/`int32_t`/`int64_t` type. "
+                        "Found `{}` '{}' in file '{}'\n",
                         type, name, reader.Name());
   }
 
   if (type == "double" && sizeof(BoutReal) != sizeof(double)) {
     throw BoutException(
         "ADIOS does not allow for implicit type conversions. BoutReal type is "
-        "float but found `{}` '{}' in file '{}'",
+        "float but found `{}` '{}' in file '{}'\n",
         type, name, reader.Name());
   }
 
@@ -217,7 +222,7 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
       Array<BoutReal> value(dims[0]);
       return read_variable(io, reader, name, selection, value);
     }
-    if (type == "int32_t") {
+    if (type == "int32_t" or type == "int64_t") {
       Array<int> value(dims[0]);
       return read_variable(io, reader, name, selection, value);
     }
@@ -228,7 +233,7 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
       Matrix<BoutReal> value(selection.dims[0], selection.dims[1]);
       return read_variable(io, reader, name, selection, value);
     }
-    if (type == "int32_t") {
+    if (type == "int32_t" or type == "int64_t") {
       Matrix<int> value(selection.dims[0], selection.dims[1]);
       return read_variable(io, reader, name, selection, value);
     }
@@ -239,7 +244,7 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
       Tensor<BoutReal> value(selection.dims[0], selection.dims[1], selection.dims[2]);
       return read_variable(io, reader, name, selection, value);
     }
-    if (type == "int32_t") {
+    if (type == "int32_t" or type == "int64_t") {
       Tensor<int> value(selection.dims[0], selection.dims[1], selection.dims[2]);
       return read_variable(io, reader, name, selection, value);
     }
@@ -251,7 +256,7 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
   }
   auto dims_str = fmt::format("[{}]", fmt::join(dims, ", "));
   throw BoutException(
-      "ADIOS reader failed to read '{}' (shape: {}, type: '{}') in file '{}'", name,
+      "ADIOS reader failed to read '{}' (shape: {}, type: '{}') in file '{}'\n", name,
       dims_str, type, reader.Name());
 }
 
@@ -297,7 +302,7 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
     return readVariable<long double>(reader, io, name, type);
   }
 
-  output_warn.write("ADIOS readVariable can't read type '{}' (variable '{}')", type,
+  output_warn.write("ADIOS readVariable can't read type '{}' (variable '{}')\n", type,
                     name);
   return Options{};
 }
@@ -324,7 +329,7 @@ bool readAttribute(adios2::IO& io, const std::string& name, const std::string& t
     return true;
   }
 
-  output_warn.write("ADIOS readAttribute can't read type '{}' (variable '{}')", type,
+  output_warn.write("ADIOS readAttribute can't read type '{}' (variable '{}')\n", type,
                     name);
   return false;
 }
@@ -351,7 +356,7 @@ Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
   const Timer timer("io");
 
   // Open file
-  ADIOSPtr const adiosp = GetADIOSPtr();
+  const ADIOSPtr adiosp = GetADIOSPtr();
   adios2::IO io;
   const std::string ioname = "read_" + filename;
   try {
@@ -362,7 +367,7 @@ Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
 
   adios2::Engine reader = io.Open(filename, adios2::Mode::ReadRandomAccess);
   if (!reader) {
-    throw BoutException("Could not open ADIOS file '{:s}' for reading", filename);
+    throw BoutException("Could not open ADIOS file '{:s}' for reading\n", filename);
   }
 
   Options result;

From d2790a4ff5e3d9beb575a34217d7677c5f50ed63 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 29 May 2026 13:20:02 -0700
Subject: [PATCH 1280/1827] solvers:Refactor coloring-based preconditioner

Use the same coloring, preconditioning code in CVODE, PETSc and SNES
time-integration solvers.

Major refactoring by Codex. Much more testing needed.
---
 CMakeLists.txt                               |   1 +
 include/bout/petsc_preconditioner.hxx        |  94 ++++
 manual/sphinx/user_docs/time_integration.rst |  19 +-
 src/solver/impls/cvode/cvode.cxx             | 235 +++++++++-
 src/solver/impls/cvode/cvode.hxx             |  41 ++
 src/solver/impls/petsc/petsc.cxx             |  88 +---
 src/solver/impls/petsc/petsc.hxx             |  16 +-
 src/solver/impls/snes/snes.cxx               | 429 +++----------------
 src/solver/impls/snes/snes.hxx               |  18 +-
 src/solver/petsc_preconditioner.cxx          | 326 ++++++++++++++
 10 files changed, 804 insertions(+), 463 deletions(-)
 create mode 100644 include/bout/petsc_preconditioner.hxx
 create mode 100644 src/solver/petsc_preconditioner.cxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 67e2337210..5b1d4ac419 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -355,6 +355,7 @@ set(BOUT_SOURCES
     ./src/solver/impls/snes/snes.hxx
     ./src/solver/impls/split-rk/split-rk.cxx
     ./src/solver/impls/split-rk/split-rk.hxx
+    ./src/solver/petsc_preconditioner.cxx
     ./src/solver/solver.cxx
     ./src/sys/adios_object.cxx
     ./src/sys/bout_types.cxx
diff --git a/include/bout/petsc_preconditioner.hxx b/include/bout/petsc_preconditioner.hxx
new file mode 100644
index 0000000000..be283413fc
--- /dev/null
+++ b/include/bout/petsc_preconditioner.hxx
@@ -0,0 +1,94 @@
+/**************************************************************************
+ * Reusable PETSc coloring-based Jacobian preconditioner support
+ *
+ * This class factors out the duplicated code in PETSc-based solvers for:
+ * - building a Jacobian sparsity pattern (via stencil assumptions)
+ * - creating a MatFDColoring context for efficient finite-difference Jacobians
+ *
+ **************************************************************************/
+
+#ifndef BOUT_PETSC_PRECONDITIONER_H
+#define BOUT_PETSC_PRECONDITIONER_H
+
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_PETSC
+
+#include "bout/petsc_interface.hxx"
+#include "bout/petsclib.hxx"
+
+#include <mpi.h>
+
+#include <petscmat.h>
+#include <petscvec.h>
+
+class Options;
+class Field3D;
+
+class PetscPreconditioner {
+public:
+  PetscPreconditioner() = default;
+  ~PetscPreconditioner() { reset(); }
+
+  PetscPreconditioner(const PetscPreconditioner&) = delete;
+  PetscPreconditioner& operator=(const PetscPreconditioner&) = delete;
+  PetscPreconditioner(PetscPreconditioner&&) = delete;
+  PetscPreconditioner& operator=(PetscPreconditioner&&) = delete;
+
+  /// Create and assemble a finite-difference Jacobian matrix `Jfd` with a sparsity
+  /// pattern derived from the solver's variable layout and a user-specified stencil.
+  ///
+  /// `index` should be generated by the calling solver (e.g. `Solver::globalIndex(0)`).
+  /// Safe to call multiple times; any existing PETSc objects are destroyed first.
+  PetscErrorCode createJacobianPattern(Field3D& index, Options& options, PetscInt nlocal,
+                                       int n2d, int n3d, MPI_Comm comm);
+
+  /// Recalculate the PETSc coloring and finite-difference coloring context
+  /// for the currently stored `Jfd` matrix.
+  template <class ColoringFunction>
+  PetscErrorCode updateColoring(ColoringFunction function, void* ctx) {
+    // Re-calculate the coloring
+    MatColoring coloring{nullptr};
+    PetscCall(MatColoringCreate(Jfd, &coloring));
+    PetscCall(MatColoringSetType(coloring, MATCOLORINGGREEDY));
+    PetscCall(MatColoringSetFromOptions(coloring));
+
+    // Calculate new index sets
+    ISColoring iscoloring{nullptr};
+    PetscCall(MatColoringApply(coloring, &iscoloring));
+    PetscCall(MatColoringDestroy(&coloring));
+
+    // Replace the old coloring with the new one
+    PetscCall(MatFDColoringDestroy(&fdcoloring));
+    PetscCall(MatFDColoringCreate(Jfd, iscoloring, &fdcoloring));
+    PetscCall(
+        MatFDColoringSetFunction(fdcoloring, bout::cast_MatFDColoringFn(function), ctx));
+    PetscCall(MatFDColoringSetFromOptions(fdcoloring));
+    PetscCall(MatFDColoringSetUp(Jfd, iscoloring, fdcoloring));
+    PetscCall(ISColoringDestroy(&iscoloring));
+
+    PetscFunctionReturn(PETSC_SUCCESS);
+  }
+
+  Mat jacobian() const { return Jfd; }
+  MatFDColoring coloring() const { return fdcoloring; }
+
+  void reset();
+
+private:
+  Mat Jfd{nullptr};
+  MatFDColoring fdcoloring{nullptr};
+};
+
+#else
+
+// PETSc is not available, but keep the type defined so headers can be included
+// unconditionally in PETSc-enabled compilation units.
+class PetscPreconditioner {
+public:
+  void reset() {}
+};
+
+#endif // BOUT_HAS_PETSC
+
+#endif // BOUT_PETSC_PRECONDITIONER_H
diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 37bf9a6abf..9bd69847c1 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -33,7 +33,7 @@ needed to make the solver available.
 
 .. _tab-solvers:
 .. table:: Available time integration solvers
-	   
+
    +---------------+-----------------------------------------+------------------------+
    | Name          | Description                             | Compile options        |
    +===============+=========================================+========================+
@@ -68,7 +68,7 @@ given in table :numref:`tab-solveropts`.
 
 .. _tab-solveropts:
 .. table:: Time integration solver options
-	   
+
    +--------------------------+--------------------------------------------+-------------------------------------+
    | Option                   | Description                                | Solvers used                        |
    +==========================+============================================+=====================================+
@@ -144,6 +144,21 @@ iterations becomes large, this may be an indication that the system is
 poorly conditioned, and a preconditioner might help improve performance.
 See :ref:`sec-preconditioning`.
 
+When ``solver:use_precon=true`` and no user-supplied preconditioner is provided,
+the preconditioner method can be selected using ``solver:cvode_precon_method``:
+
+- ``auto`` (default): Prefer PETSc coloring if PETSc is available, otherwise use BBD.
+- ``bbd``: Force the built-in BBD preconditioner.
+- ``petsc``: Require PETSc and use PETSc coloring.
+
+For ``cvode_precon_method = petsc``, PETSc options for the internal KSP/PC can be
+set with the prefix ``cvode_petscpre_`` (either on the command line, or by putting
+prefixed keys into the ``[petsc]`` section). For example::
+
+    [petsc]
+    cvode_petscpre_ksp_type = preonly
+    cvode_petscpre_pc_type = hypre
+
 CVODE can set constraints to keep some quantities positive, non-negative,
 negative or non-positive. These constraints can be activated by setting the
 option ``solver:apply_positivity_constraints=true``, and then in the section
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 4f72e65933..203704929a 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -129,7 +129,25 @@ CvodeSolver::CvodeSolver(Options* opts)
       rightprec((*options)["rightprec"]
                     .doc("Use right preconditioner? Otherwise use left.")
                     .withDefault(false)),
-      use_jacobian((*options)["use_jacobian"].withDefault(false)),
+      use_jacobian((*options)["use_jacobian"].withDefault(false)), precon_method([&]() {
+        const auto method =
+            (*options)["cvode_precon_method"]
+                .doc("Preconditioner to use when solver:use_precon=true and no user "
+                     "preconditioner is supplied: auto, bbd, petsc.")
+                .withDefault<std::string>("auto");
+        if (method == "auto" || method == "automatic") {
+          return CvodePreconMethod::auto_select;
+        }
+        if (method == "bbd") {
+          return CvodePreconMethod::bbd;
+        }
+        if (method == "petsc") {
+          return CvodePreconMethod::petsc;
+        }
+        throw BoutException("Invalid solver:cvode_precon_method '{}'. Valid values: "
+                            "auto, bbd, petsc.",
+                            method);
+      }()),
       cvode_nonlinear_convergence_coef(
           (*options)["cvode_nonlinear_convergence_coef"]
               .doc("Safety factor used in the nonlinear convergence test")
@@ -169,6 +187,23 @@ CvodeSolver::~CvodeSolver() {
     CVodeFree(&cvode_mem);
     SUNLinSolFree(sun_solver);
     SUNNonlinSolFree(nonlinear_solver);
+#if BOUT_HAS_PETSC
+    if (petsc_ksp != nullptr) {
+      KSPDestroy(&petsc_ksp);
+    }
+    if (petsc_r != nullptr) {
+      VecDestroy(&petsc_r);
+    }
+    if (petsc_z != nullptr) {
+      VecDestroy(&petsc_z);
+    }
+    if (petsc_x != nullptr) {
+      VecDestroy(&petsc_x);
+    }
+    if (petsc_f != nullptr) {
+      VecDestroy(&petsc_f);
+    }
+#endif
   }
 }
 
@@ -381,15 +416,81 @@ int CvodeSolver::init() {
           throw BoutException("CVodeSetPreconditioner failed\n");
         }
       } else {
+        const bool prefer_petsc = (precon_method == CvodePreconMethod::petsc)
+                                  || (precon_method == CvodePreconMethod::auto_select);
+
+#if BOUT_HAS_PETSC
+        if (prefer_petsc) {
+          output_info.write("\tUsing PETSc coloring preconditioner\n");
+
+          if (!petsc_lib) {
+            petsc_lib = std::make_unique<PetscLib>();
+          }
+
+          petsc_global_N = neq;
+          petsc_rhs_tmp.resize(local_N);
+
+          if (petsc_ksp == nullptr) {
+            PetscCall(KSPCreate(BoutComm::get(), &petsc_ksp));
+            PetscCall(KSPSetType(petsc_ksp, KSPPREONLY));
+            PetscCall(KSPSetOptionsPrefix(petsc_ksp, "cvode_petscpre_"));
+            PetscCall(KSPSetFromOptions(petsc_ksp));
+          }
+
+          if (petsc_x == nullptr) {
+            PetscCall(VecCreateMPI(BoutComm::get(), local_N, petsc_global_N, &petsc_x));
+            PetscCall(VecDuplicate(petsc_x, &petsc_f));
+            PetscCall(VecCreateMPI(BoutComm::get(), local_N, petsc_global_N, &petsc_r));
+            PetscCall(VecCreateMPI(BoutComm::get(), local_N, petsc_global_N, &petsc_z));
+          }
+
+          Field3D index = globalIndex(0);
+          PetscCall(petsc_preconditioner.createJacobianPattern(
+              index, *options, local_N, n2Dvars(), n3Dvars(), BoutComm::get()));
+          PetscCall(
+              petsc_preconditioner.updateColoring(CvodeSolver::petscFormFunction, this));
+          PetscCall(MatFDColoringSetF(petsc_preconditioner.coloring(), petsc_f));
+
+          if (CVodeSetPreconditioner(cvode_mem, petscPSetup, petscPSolve)
+              != CVLS_SUCCESS) {
+            throw BoutException("CVodeSetPreconditioner (PETSc coloring) failed\n");
+          }
+        } else {
+          output_info.write("\tUsing BBD preconditioner\n");
+
+          /// Get options
+          // Compute band_width_default from actually added fields, to allow for multiple
+          // Mesh objects
+          //
+          // Previous implementation was equivalent to:
+          //   int MXSUB = mesh->xend - mesh->xstart + 1;
+          //   int band_width_default = n3Dvars()*(MXSUB+2);
+          const int band_width_default = std::accumulate(
+              begin(f3d), end(f3d), 0, [](int a, const VarStr<Field3D>& fvar) {
+                Mesh* localmesh = fvar.var->getMesh();
+                return a + localmesh->xend - localmesh->xstart + 3;
+              });
+
+          const auto mudq = (*options)["mudq"].withDefault(band_width_default);
+          const auto mldq = (*options)["mldq"].withDefault(band_width_default);
+          const auto mukeep = (*options)["mukeep"].withDefault(n3Dvars() + n2Dvars());
+          const auto mlkeep = (*options)["mlkeep"].withDefault(n3Dvars() + n2Dvars());
+
+          if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0.0,
+                            cvode_bbd_rhs, nullptr)
+              != CVLS_SUCCESS) {
+            throw BoutException("CVBBDPrecInit failed\n");
+          }
+        }
+#else
+        if (precon_method == CvodePreconMethod::petsc) {
+          throw BoutException(
+              "solver:cvode_precon_method=petsc requested, but BOUT++ was not "
+              "configured with PETSc.");
+        }
+
         output_info.write("\tUsing BBD preconditioner\n");
 
-        /// Get options
-        // Compute band_width_default from actually added fields, to allow for multiple
-        // Mesh objects
-        //
-        // Previous implementation was equivalent to:
-        //   int MXSUB = mesh->xend - mesh->xstart + 1;
-        //   int band_width_default = n3Dvars()*(MXSUB+2);
         const int band_width_default = std::accumulate(
             begin(f3d), end(f3d), 0, [](int a, const VarStr<Field3D>& fvar) {
               Mesh* localmesh = fvar.var->getMesh();
@@ -406,6 +507,7 @@ int CvodeSolver::init() {
             != CVLS_SUCCESS) {
           throw BoutException("CVBBDPrecInit failed\n");
         }
+#endif
       }
     } else {
       output_info.write("\tNo preconditioning\n");
@@ -766,6 +868,123 @@ int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(f
 } // namespace
 // NOLINTEND(readability-identifier-length)
 
+#if BOUT_HAS_PETSC
+PetscErrorCode CvodeSolver::petscFormFunction(void* UNUSED(dummy), Vec x, Vec f,
+                                              void* ctx) {
+  auto* s = static_cast<CvodeSolver*>(ctx);
+
+  PetscInt length = 0;
+  PetscCall(VecGetLocalSize(x, &length));
+  s->petsc_rhs_tmp.resize(static_cast<std::size_t>(length));
+
+  const BoutReal* xdata = nullptr;
+  PetscCall(VecGetArrayRead(x, &xdata));
+
+  BoutReal* fdata = nullptr;
+  PetscCall(VecGetArray(f, &fdata));
+
+  try {
+    s->rhs(s->petsc_t, const_cast<BoutReal*>(xdata), s->petsc_rhs_tmp.data(), true);
+  } catch (BoutRhsFail&) {
+    PetscCall(VecRestoreArrayRead(x, &xdata));
+    PetscCall(VecRestoreArray(f, &fdata));
+    return 1;
+  }
+
+  for (PetscInt i = 0; i < length; ++i) {
+    fdata[i] = xdata[i] - s->petsc_gamma * s->petsc_rhs_tmp[i];
+  }
+
+  PetscCall(VecRestoreArrayRead(x, &xdata));
+  PetscCall(VecRestoreArray(f, &fdata));
+
+  return PETSC_SUCCESS;
+}
+
+int CvodeSolver::petscPSetup(BoutReal t, N_Vector yy, N_Vector UNUSED(yp),
+                             CvodeBool UNUSED(jok), CvodeBool* jcurPtr, BoutReal gamma,
+                             void* user_data) {
+  auto* s = static_cast<CvodeSolver*>(user_data);
+
+  s->petsc_t = t;
+  s->petsc_gamma = gamma;
+
+  auto* ydata = N_VGetArrayPointer(yy);
+
+  PetscErrorCode ierr = VecPlaceArray(s->petsc_x, ydata);
+  if (ierr != 0) {
+    return 1;
+  }
+
+  ierr = petscFormFunction(nullptr, s->petsc_x, s->petsc_f, s);
+  if (ierr != 0) {
+    VecResetArray(s->petsc_x);
+    return 1;
+  }
+
+  Mat J = s->petsc_preconditioner.jacobian();
+  ierr = MatZeroEntries(J);
+  if (ierr != 0) {
+    VecResetArray(s->petsc_x);
+    return 1;
+  }
+
+  ierr = MatFDColoringApply(J, s->petsc_preconditioner.coloring(), s->petsc_x, nullptr);
+  if (ierr != 0) {
+    VecResetArray(s->petsc_x);
+    return 1;
+  }
+
+  ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);
+  if (ierr == 0) {
+    ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);
+  }
+  if (ierr != 0) {
+    VecResetArray(s->petsc_x);
+    return 1;
+  }
+
+  ierr = KSPSetOperators(s->petsc_ksp, J, J);
+  if (ierr == 0) {
+    ierr = KSPSetUp(s->petsc_ksp);
+  }
+
+  VecResetArray(s->petsc_x);
+
+  if (ierr != 0) {
+    return 1;
+  }
+
+  if (jcurPtr != nullptr) {
+    *jcurPtr = 1;
+  }
+
+  return 0;
+}
+
+int CvodeSolver::petscPSolve(BoutReal UNUSED(t), N_Vector UNUSED(yy), N_Vector UNUSED(yp),
+                             N_Vector rvec, N_Vector zvec, BoutReal UNUSED(gamma),
+                             BoutReal UNUSED(delta), int UNUSED(lr), void* user_data) {
+  auto* s = static_cast<CvodeSolver*>(user_data);
+
+  auto* rdata = N_VGetArrayPointer(rvec);
+  auto* zdata = N_VGetArrayPointer(zvec);
+
+  PetscErrorCode ierr = VecPlaceArray(s->petsc_r, rdata);
+  if (ierr == 0) {
+    ierr = VecPlaceArray(s->petsc_z, zdata);
+  }
+  if (ierr == 0) {
+    ierr = KSPSolve(s->petsc_ksp, s->petsc_r, s->petsc_z);
+  }
+
+  VecResetArray(s->petsc_r);
+  VecResetArray(s->petsc_z);
+
+  return ierr == 0 ? 0 : 1;
+}
+#endif
+
 /**************************************************************************
  * CVODE vector option functions
  **************************************************************************/
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index f0cc2eedf8..c912b20b4e 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -44,6 +44,14 @@ RegisterUnavailableSolver
 #include "bout/region.hxx"
 #include "bout/sundials_backports.hxx"
 
+#if BOUT_HAS_PETSC
+#include "bout/petsc_preconditioner.hxx"
+#include "bout/petsclib.hxx"
+
+#include <petscksp.h>
+#include <petscvec.h>
+#endif
+
 #include <string>
 #include <vector>
 
@@ -54,6 +62,14 @@ namespace {
 RegisterSolver<CvodeSolver> registersolvercvode("cvode");
 }
 
+enum class CvodePreconMethod { auto_select, bbd, petsc };
+
+#if SUNDIALS_VERSION_AT_LEAST(6, 0, 0)
+using CvodeBool = sunbooleantype;
+#else
+using CvodeBool = booleantype;
+#endif
+
 class CvodeSolver : public Solver {
 public:
   explicit CvodeSolver(Options* opts = nullptr);
@@ -74,6 +90,15 @@ public:
   void jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
 
 private:
+#if BOUT_HAS_PETSC
+  static PetscErrorCode petscFormFunction(void* dummy, Vec x, Vec f, void* ctx);
+  static int petscPSetup(BoutReal t, N_Vector yy, N_Vector yp, CvodeBool jok,
+                         CvodeBool* jcurPtr, BoutReal gamma, void* user_data);
+  static int petscPSolve(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec,
+                         N_Vector zvec, BoutReal gamma, BoutReal delta, int lr,
+                         void* user_data);
+#endif
+
   BoutReal hcur; //< Current internal timestep
 
   bool diagnose{false}; //< Output additional diagnostics
@@ -122,6 +147,7 @@ private:
   /// Use right preconditioner? Otherwise use left.
   bool rightprec;
   bool use_jacobian;
+  CvodePreconMethod precon_method;
   BoutReal cvode_nonlinear_convergence_coef;
   BoutReal cvode_linear_convergence_coef;
 
@@ -153,6 +179,21 @@ private:
   SUNNonlinearSolver nonlinear_solver{nullptr};
   /// Context for SUNDIALS memory allocations
   sundials::Context suncontext;
+
+#if BOUT_HAS_PETSC
+  // PETSc-coloring-based preconditioning for CVODE
+  std::unique_ptr<PetscLib> petsc_lib;
+  PetscPreconditioner petsc_preconditioner;
+  KSP petsc_ksp{nullptr};
+  Vec petsc_r{nullptr};
+  Vec petsc_z{nullptr};
+  Vec petsc_x{nullptr};
+  Vec petsc_f{nullptr};
+  PetscInt petsc_global_N{0};
+  BoutReal petsc_gamma{0.0};
+  BoutReal petsc_t{0.0};
+  std::vector<BoutReal> petsc_rhs_tmp;
+#endif
 };
 
 #endif // BOUT_HAS_CVODE
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 1e1e05596b..3ed113fdc5 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -62,45 +62,6 @@
 #define PETSC_UNLIMITED (-3)
 #endif
 
-class ColoringStencil {
-private:
-  bool static isInSquare(int const i, int const j, int const n_square) {
-    return std::abs(i) <= n_square && std::abs(j) <= n_square;
-  }
-  bool static isInCross(int const i, int const j, int const n_cross) {
-    if (i == 0) {
-      return std::abs(j) <= n_cross;
-    }
-    if (j == 0) {
-      return std::abs(i) <= n_cross;
-    }
-    return false;
-  }
-  bool static isInTaxi(int const i, int const j, int const n_taxi) {
-    return std::abs(i) + std::abs(j) <= n_taxi;
-  }
-
-public:
-  auto static getOffsets(int n_square, int n_taxi, int n_cross) {
-    ASSERT2(n_square >= 0 && n_cross >= 0 && n_taxi >= 0
-            && n_square + n_cross + n_taxi > 0);
-    auto inside = [&](int i, int j) {
-      return isInSquare(i, j, n_square) || isInTaxi(i, j, n_taxi)
-             || isInCross(i, j, n_cross);
-    };
-    std::vector<std::pair<int, int>> xy_offsets;
-    auto loop_bound = std::max({n_square, n_taxi, n_cross});
-    for (int i = -loop_bound; i <= loop_bound; ++i) {
-      for (int j = -loop_bound; j <= loop_bound; ++j) {
-        if (inside(i, j)) {
-          xy_offsets.emplace_back(i, j);
-        }
-      }
-    }
-    return xy_offsets;
-  }
-};
-
 namespace {
 // PETSc callback function for matrix-free preconditioner
 PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
@@ -315,7 +276,6 @@ PetscSolver::~PetscSolver() {
   VecDestroy(&u);
   MatDestroy(&Jfd);
   MatDestroy(&Jmf);
-  MatFDColoringDestroy(&fdcoloring);
   TSDestroy(&ts);
 }
 
@@ -559,6 +519,13 @@ int PetscSolver::init() {
     // preconditioner.
 
     if (use_coloring) {
+      Field3D index = globalIndex(0);
+      PetscCall(petsc_preconditioner.createJacobianPattern(
+          index, *options, nlocal, n2Dvars(), n3Dvars(), BoutComm::get()));
+      output_progress.write("Creating Jacobian coloring\n");
+      updateColoring();
+
+#if 0
       // Use matrix coloring.  This greatly reduces the number of
       // times the rhs() function needs to be evaluated when
       // calculating the Jacobian, by identifying which quantities may
@@ -851,6 +818,7 @@ int PetscSolver::init() {
 
       output_progress.write("Creating Jacobian coloring\n");
       updateColoring();
+#endif
 
     } else {
       // Brute force calculation
@@ -996,55 +964,39 @@ PetscErrorCode PetscSolver::pre(Vec x, Vec y) {
 }
 
 void PetscSolver::updateColoring() {
-  // Re-calculate the coloring
-  MatColoring coloring{nullptr};
-  MatColoringCreate(Jfd, &coloring);
-  MatColoringSetType(coloring, MATCOLORINGGREEDY);
-  MatColoringSetFromOptions(coloring);
-
-  // Calculate new index sets
-  ISColoring iscoloring{nullptr};
-  MatColoringApply(coloring, &iscoloring);
-  MatColoringDestroy(&coloring);
-
-  // Replace the old coloring with the new one
-  MatFDColoringDestroy(&fdcoloring);
-  MatFDColoringCreate(Jfd, iscoloring, &fdcoloring);
+  Mat jac = petsc_preconditioner.jacobian();
+
   if (ts_type != TSSUNDIALS) {
     // Use the SNES function that is defined by the TS method
     // SNESTSFormFunction is defined in PETSc ts.c
     // The ctx pointer should be the TS object
-    //
-    // Note: The function type casting here is horrible but necessary
-    MatFDColoringSetFunction(fdcoloring, bout::cast_MatFDColoringFn(SNESTSFormFunction),
-                             ts);
+    BOUT_DO_PETSC(petsc_preconditioner.updateColoring(SNESTSFormFunction, ts));
   } else {
     // SNESTSFormFunction is not available for SUNDIALS.
     // This solver_form_function needs to know the shift
     // (SUNDIALS' gamma) that we capture in solver_ijacobian_color.
-    MatFDColoringSetFunction(fdcoloring, bout::cast_MatFDColoringFn(solver_form_function),
-                             this);
+    BOUT_DO_PETSC(petsc_preconditioner.updateColoring(solver_form_function, this));
   }
-  MatFDColoringSetFromOptions(fdcoloring);
-  MatFDColoringSetUp(Jfd, iscoloring, fdcoloring);
-  ISColoringDestroy(&iscoloring);
 
-  // Replace the CTX pointer in SNES Jacobian
+  // Replace the CTX pointer in SNES Jacobian / TS Jacobian callback
   if (ts_type == TSSUNDIALS) {
 #if PETSC_HAVE_SUNDIALS2
     // The SUNDIALS interface calls TSGetIJacobian
     // https://www.mcs.anl.gov/petsc/petsc-3.14/src/ts/impls/implicit/sundials/sundials.c
     // This sets the "TSMatFDColoring" property on the Jacobian, that is used in TSComputeIJacobianDefaultColor
-    PetscObjectCompose((PetscObject)Jfd, "TSMatFDColoring", (PetscObject)fdcoloring);
+    PetscObjectCompose((PetscObject)jac, "TSMatFDColoring",
+                       (PetscObject)petsc_preconditioner.coloring());
     // Call a wrapper function that stores the shift in the PetscSolver
-    TSSetIJacobian(ts, Jfd, Jfd, solver_ijacobian_color, this);
+    TSSetIJacobian(ts, jac, jac, solver_ijacobian_color, this);
 #endif
   } else {
     if (matrix_free_operator) {
       // Use matrix-free calculation for operator, finite difference for preconditioner
-      SNESSetJacobian(snes, Jmf, Jfd, SNESComputeJacobianDefaultColor, fdcoloring);
+      SNESSetJacobian(snes, Jmf, jac, SNESComputeJacobianDefaultColor,
+                      petsc_preconditioner.coloring());
     } else {
-      SNESSetJacobian(snes, Jfd, Jfd, SNESComputeJacobianDefaultColor, fdcoloring);
+      SNESSetJacobian(snes, jac, jac, SNESComputeJacobianDefaultColor,
+                      petsc_preconditioner.coloring());
     }
   }
 }
diff --git a/src/solver/impls/petsc/petsc.hxx b/src/solver/impls/petsc/petsc.hxx
index 78f7d1a1e4..ab8e5bf9e0 100644
--- a/src/solver/impls/petsc/petsc.hxx
+++ b/src/solver/impls/petsc/petsc.hxx
@@ -42,6 +42,7 @@ class PetscSolver;
 
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
+#include <bout/petsc_preconditioner.hxx>
 #include <bout/petsclib.hxx>
 #include <bout/vector2d.hxx>
 #include <bout/vector3d.hxx>
@@ -93,13 +94,14 @@ private:
 
   PetscLib lib; ///< Handles initialising, finalising PETSc
 
-  Vec u{nullptr};                    ///< PETSc solution vector
-  TS ts{nullptr};                    ///< PETSc timestepper object
-  SNES snes{nullptr};                ///< PETSc nonlinear solver object
-  KSP ksp{nullptr};                  ///< PETSc linear solver
-  Mat Jmf{nullptr};                  ///< Matrix Free Jacobian
-  Mat Jfd{nullptr};                  ///< Finite Difference Jacobian
-  MatFDColoring fdcoloring{nullptr}; ///< Matrix coloring context
+  Vec u{nullptr};     ///< PETSc solution vector
+  TS ts{nullptr};     ///< PETSc timestepper object
+  SNES snes{nullptr}; ///< PETSc nonlinear solver object
+  KSP ksp{nullptr};   ///< PETSc linear solver
+  Mat Jmf{nullptr};   ///< Matrix Free Jacobian
+  Mat Jfd{nullptr}; ///< Finite Difference Jacobian (brute-force, when not using coloring)
+  PetscPreconditioner
+      petsc_preconditioner; ///< Coloring-based FD Jacobian + MatFDColoring
 
   BoutReal next_output; ///< When the monitor should be called next
 
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 5b28ff413c..1b8ba9f875 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -15,8 +15,8 @@
 #include <bout/output_bout_types.hxx>
 #include <bout/petsc_interface.hxx>
 #include <bout/solver.hxx>
-#include <bout/utils.hxx>
 #include <bout/unused.hxx>
+#include <bout/utils.hxx>
 
 #include <algorithm>
 #include <cmath>
@@ -33,45 +33,6 @@
 #include "petscsystypes.h"
 #include "petscvec.h"
 
-class ColoringStencil {
-private:
-  bool static isInSquare(int const i, int const j, int const n_square) {
-    return std::abs(i) <= n_square && std::abs(j) <= n_square;
-  }
-  bool static isInCross(int const i, int const j, int const n_cross) {
-    if (i == 0) {
-      return std::abs(j) <= n_cross;
-    }
-    if (j == 0) {
-      return std::abs(i) <= n_cross;
-    }
-    return false;
-  }
-  bool static isInTaxi(int const i, int const j, int const n_taxi) {
-    return std::abs(i) + std::abs(j) <= n_taxi;
-  }
-
-public:
-  auto static getOffsets(int n_square, int n_taxi, int n_cross) {
-    ASSERT2(n_square >= 0 && n_cross >= 0 && n_taxi >= 0
-            && n_square + n_cross + n_taxi > 0);
-    auto inside = [&](int i, int j) {
-      return isInSquare(i, j, n_square) || isInTaxi(i, j, n_taxi)
-             || isInCross(i, j, n_cross);
-    };
-    std::vector<std::pair<int, int>> xy_offsets;
-    auto loop_bound = std::max({n_square, n_taxi, n_cross});
-    for (int i = -loop_bound; i <= loop_bound; ++i) {
-      for (int j = -loop_bound; j <= loop_bound; ++j) {
-        if (inside(i, j)) {
-          xy_offsets.emplace_back(i, j);
-        }
-      }
-    }
-    return xy_offsets;
-  }
-};
-
 namespace {
 /*
  * PETSc callback function, which evaluates the nonlinear
@@ -111,298 +72,32 @@ PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
 }
 } // namespace
 
+static PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
+                                                 void* ctx);
+
 PetscErrorCode SNESSolver::FDJinitialise() {
   if (use_coloring) {
-    // Use matrix coloring.
-    // This greatly reduces the number of times the rhs() function
-    // needs to be evaluated when calculating the Jacobian.
-
-    // Use global mesh for now
-    Mesh* mesh = bout::globals::mesh;
-
-    //////////////////////////////////////////////////
-    // Get the local indices by starting at 0
     Field3D index = globalIndex(0);
+    PetscCall(petsc_preconditioner.createJacobianPattern(
+        index, *options, nlocal, n2Dvars(), n3Dvars(), BoutComm::get()));
+    output_progress.write("Creating Jacobian coloring\n");
+    PetscCall(petsc_preconditioner.updateColoring(FormFunctionForColoring, this));
 
-    //////////////////////////////////////////////////
-    // Pre-allocate PETSc storage
-
-    output_progress.write("Setting Jacobian matrix sizes\n");
-
-    const int n2d = f2d.size();
-    const int n3d = f3d.size();
-
-    // Set size of Matrix on each processor to nlocal x nlocal
-    MatCreate(BoutComm::get(), &Jfd);
-    MatSetOption(Jfd, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
-    MatSetSizes(Jfd, nlocal, nlocal, PETSC_DETERMINE, PETSC_DETERMINE);
-    MatSetFromOptions(Jfd);
-    // Determine which row/columns of the matrix are locally owned
-    int Istart, Iend;
-    MatGetOwnershipRange(Jfd, &Istart, &Iend);
-    // Convert local into global indices
-    // Note: Not in the boundary cells, to keep -1 values
-    for (const auto& i : mesh->getRegion3D("RGN_NOBNDRY")) {
-      index[i] += Istart;
-    }
-    // Now communicate to fill guard cells
-    mesh->communicate(index);
-
-    // Non-zero elements on this processor
-    std::vector<PetscInt> d_nnz;
-    std::vector<PetscInt> o_nnz;
-    auto n_square = (*options)["stencil:square"]
-                        .doc("Extent of stencil (square)")
-                        .withDefault<int>(0);
-    auto n_cross =
-        (*options)["stencil:cross"].doc("Extent of stencil (cross)").withDefault<int>(0);
-    // Set n_taxi 2 if nothing else is set
-    auto n_taxi = (*options)["stencil:taxi"]
-                      .doc("Extent of stencil (taxi-cab norm)")
-                      .withDefault<int>((n_square == 0 && n_cross == 0) ? 2 : 0);
-
-    auto const xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
-    {
-      // This is ugly but can't think of a better and robust way to
-      // count the non-zeros for some arbitrary stencil
-      // effectively the same loop as the one that sets the non-zeros below
-      std::vector<std::set<int>> d_nnz_map2d(nlocal);
-      std::vector<std::set<int>> o_nnz_map2d(nlocal);
-      std::vector<std::set<int>> d_nnz_map3d(nlocal);
-      std::vector<std::set<int>> o_nnz_map3d(nlocal);
-      // Loop over every element in 2D to count the *unique* non-zeros
-      for (int x = mesh->xstart; x <= mesh->xend; x++) {
-        for (int y = mesh->ystart; y <= mesh->yend; y++) {
-
-          const int ind0 = ROUND(index(x, y, 0)) - Istart;
-
-          // 2D fields
-          for (int i = 0; i < n2d; i++) {
-            const PetscInt row = ind0 + i;
-            // Loop through each point in the stencil
-            for (const auto& [x_off, y_off] : xy_offsets) {
-              const int xi = x + x_off;
-              const int yi = y + y_off;
-              if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                  || (yi >= mesh->LocalNy)) {
-                continue;
-              }
-
-              const int ind2 = ROUND(index(xi, yi, 0));
-              if (ind2 < 0) {
-                continue; // A boundary point
-              }
-
-              // Depends on all variables on this cell
-              for (int j = 0; j < n2d; j++) {
-                const PetscInt col = ind2 + j;
-                if (col >= Istart && col < Iend) {
-                  d_nnz_map2d[row].insert(col);
-                } else {
-                  o_nnz_map2d[row].insert(col);
-                }
-              }
-            }
-          }
-          // 3D fields
-          for (int z = mesh->zstart; z <= mesh->zend; z++) {
-            const int ind = ROUND(index(x, y, z)) - Istart;
-
-            for (int i = 0; i < n3d; i++) {
-              PetscInt row = ind + i;
-              if (z == 0) {
-                row += n2d;
-              }
-
-              // Depends on 2D fields
-              for (int j = 0; j < n2d; j++) {
-                const PetscInt col = ind0 + j;
-                if (col >= Istart && col < Iend) {
-                  d_nnz_map2d[row].insert(col);
-                } else {
-                  o_nnz_map2d[row].insert(col);
-                }
-              }
-
-              // Star pattern
-              for (const auto& [x_off, y_off] : xy_offsets) {
-                const int xi = x + x_off;
-                const int yi = y + y_off;
-
-                if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                    || (yi >= mesh->LocalNy)) {
-                  continue;
-                }
-
-                int ind2 = ROUND(index(xi, yi, 0));
-                if (ind2 < 0) {
-                  continue; // Boundary point
-                }
-
-                if (z == 0) {
-                  ind2 += n2d;
-                }
-
-                // 3D fields on this cell
-                for (int j = 0; j < n3d; j++) {
-                  const PetscInt col = ind2 + j;
-                  if (col >= Istart && col < Iend) {
-                    d_nnz_map3d[row].insert(col);
-                  } else {
-                    o_nnz_map3d[row].insert(col);
-                  }
-                }
-              }
-            }
-          }
-        }
-      }
-
-      d_nnz.reserve(nlocal);
-      d_nnz.reserve(nlocal);
-
-      for (int i = 0; i < nlocal; ++i) {
-        // Assume all elements in the z direction are potentially coupled
-        d_nnz.emplace_back((d_nnz_map3d[i].size() * mesh->LocalNz)
-                           + d_nnz_map2d[i].size());
-        o_nnz.emplace_back((o_nnz_map3d[i].size() * mesh->LocalNz)
-                           + o_nnz_map2d[i].size());
-      }
-    }
-
-    output_progress.write("Pre-allocating Jacobian\n");
-    // Pre-allocate
-    MatMPIAIJSetPreallocation(Jfd, 0, d_nnz.data(), 0, o_nnz.data());
-    MatSeqAIJSetPreallocation(Jfd, 0, d_nnz.data());
-    MatSetUp(Jfd);
-    MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
-
-    //////////////////////////////////////////////////
-    // Mark non-zero entries
-
-    output_progress.write("Marking non-zero Jacobian entries\n");
-    const PetscScalar val = 1.0;
-    for (int x = mesh->xstart; x <= mesh->xend; x++) {
-      for (int y = mesh->ystart; y <= mesh->yend; y++) {
-
-        const int ind0 = ROUND(index(x, y, 0));
-
-        // 2D fields
-        for (int i = 0; i < n2d; i++) {
-          const PetscInt row = ind0 + i;
-
-          // Loop through each point in the stencil
-          for (const auto& [x_off, y_off] : xy_offsets) {
-            const int xi = x + x_off;
-            const int yi = y + y_off;
-            if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx) || (yi >= mesh->LocalNy)) {
-              continue;
-            }
-
-            const int ind2 = ROUND(index(xi, yi, 0));
-            if (ind2 < 0) {
-              continue; // A boundary point
-            }
-
-            // Depends on all variables on this cell
-            for (int j = 0; j < n2d; j++) {
-              const PetscInt col = ind2 + j;
-              PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
-            }
-          }
-        }
-        // 3D fields
-        for (int z = mesh->zstart; z <= mesh->zend; z++) {
-          const int ind = ROUND(index(x, y, z));
-
-          for (int i = 0; i < n3d; i++) {
-            PetscInt row = ind + i;
-            if (z == 0) {
-              row += n2d;
-            }
-
-            // Depends on 2D fields
-            for (int j = 0; j < n2d; j++) {
-              const PetscInt col = ind0 + j;
-              PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
-            }
-
-            // Star pattern
-            for (const auto& [x_off, y_off] : xy_offsets) {
-              int xi = x + x_off;
-              int yi = y + y_off;
-
-              if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                  || (yi >= mesh->LocalNy)) {
-                continue;
-              }
-              for (int zi = mesh->zstart; zi <= mesh->zend; ++zi) {
-                int ind2 = ROUND(index(xi, yi, zi));
-                if (ind2 < 0) {
-                  continue; // Boundary point
-                }
-
-                if (z == 0) {
-                  ind2 += n2d;
-                }
-
-                // 3D fields on this cell
-                for (int j = 0; j < n3d; j++) {
-                  const PetscInt col = ind2 + j;
-                  const PetscErrorCode ierr =
-                      MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-                  if (ierr != PETSC_SUCCESS) {
-                    output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n", row,
-                                 col, x, y, xi, yi, ind2, ind2 + n3d - 1);
-                  }
-                  CHKERRQ(ierr);
-                }
-              }
-            }
-          }
-        }
-      }
-    }
-
-    // Finished marking non-zero entries
-
-    output_progress.write("Assembling Jacobian matrix\n");
-
-    // Assemble Matrix
-    MatAssemblyBegin(Jfd, MAT_FINAL_ASSEMBLY);
-    MatAssemblyEnd(Jfd, MAT_FINAL_ASSEMBLY);
-
-    {
-      // Test if the matrix is symmetric
-      // Values are 0 or 1 so tolerance (1e-5) shouldn't matter
-      PetscBool symmetric;
-      PetscCall(MatIsSymmetric(Jfd, 1e-5, &symmetric));
-      if (!static_cast<bool>(symmetric)) {
-        output_warn.write("Jacobian pattern is not symmetric\n");
-      }
-    }
-
-    // The above can miss entries around the X-point branch cut:
-    // The diagonal terms are complicated because moving in X then Y
-    // is different from moving in Y then X at the X-point.
-    // Making sure the colouring matrix is symmetric does not
-    // necessarily give the correct stencil but may help.
-    if ((*options)["force_symmetric_coloring"]
-            .doc("Modifies coloring matrix to force it to be symmetric")
-            .withDefault<bool>(false)) {
-      Mat Jfd_T;
-      MatCreateTranspose(Jfd, &Jfd_T);
-      MatAXPY(Jfd, 1, Jfd_T, DIFFERENT_NONZERO_PATTERN);
+    if (matrix_free_operator) {
+      PetscCall(SNESSetJacobian(snes, Jmf, petsc_preconditioner.jacobian(),
+                                ComputeJacobianScaledColor,
+                                petsc_preconditioner.coloring()));
+    } else {
+      PetscCall(SNESSetJacobian(
+          snes, petsc_preconditioner.jacobian(), petsc_preconditioner.jacobian(),
+          ComputeJacobianScaledColor, petsc_preconditioner.coloring()));
     }
 
-    output_progress.write("Creating Jacobian coloring\n");
-    updateColoring();
-
     if (prune_jacobian) {
       // Will remove small elements from the Jacobian.
       // Save a copy to recover from over-pruning
-      PetscCall(MatDuplicate(Jfd, MAT_SHARE_NONZERO_PATTERN, &Jfd_original));
+      PetscCall(MatDuplicate(petsc_preconditioner.jacobian(), MAT_SHARE_NONZERO_PATTERN,
+                             &Jfd_original));
     }
   } else {
     // Brute force calculation
@@ -430,6 +125,11 @@ PetscErrorCode SNESSolver::FDJinitialise() {
 
 PetscErrorCode SNESSolver::FDJpruneJacobian() {
 #if PETSC_VERSION_GE(3, 20, 0)
+  if (!use_coloring) {
+    throw BoutException("Jacobian pruning requires solver:use_coloring=true");
+  }
+
+  Mat Jfd = petsc_preconditioner.jacobian();
 
   // Remove small elements from the Jacobian and recompute the coloring
   // Only do this if there are a significant number of small elements.
@@ -463,7 +163,16 @@ PetscErrorCode SNESSolver::FDJpruneJacobian() {
     PetscCall(MatFilter(Jfd, prune_abstol, PETSC_TRUE, PETSC_TRUE));
 
     // Update the coloring from Jfd matrix
-    updateColoring();
+    PetscCall(petsc_preconditioner.updateColoring(FormFunctionForColoring, this));
+    if (matrix_free_operator) {
+      PetscCall(SNESSetJacobian(snes, Jmf, petsc_preconditioner.jacobian(),
+                                ComputeJacobianScaledColor,
+                                petsc_preconditioner.coloring()));
+    } else {
+      PetscCall(SNESSetJacobian(
+          snes, petsc_preconditioner.jacobian(), petsc_preconditioner.jacobian(),
+          ComputeJacobianScaledColor, petsc_preconditioner.coloring()));
+    }
 
     // Mark the Jacobian as pruned. This is so that it is only restored if pruned.
     jacobian_pruned = true;
@@ -473,10 +182,25 @@ PetscErrorCode SNESSolver::FDJpruneJacobian() {
 }
 
 PetscErrorCode SNESSolver::FDJrestoreFromPruning() {
+  if (!use_coloring) {
+    throw BoutException("Jacobian pruning requires solver:use_coloring=true");
+  }
+
+  Mat Jfd = petsc_preconditioner.jacobian();
+
   // Restore pruned non-zero elements
   PetscCall(MatCopy(Jfd_original, Jfd, DIFFERENT_NONZERO_PATTERN));
   // The non-zero pattern has changed, so update coloring
-  updateColoring();
+  PetscCall(petsc_preconditioner.updateColoring(FormFunctionForColoring, this));
+  if (matrix_free_operator) {
+    PetscCall(SNESSetJacobian(snes, Jmf, petsc_preconditioner.jacobian(),
+                              ComputeJacobianScaledColor,
+                              petsc_preconditioner.coloring()));
+  } else {
+    PetscCall(SNESSetJacobian(snes, petsc_preconditioner.jacobian(),
+                              petsc_preconditioner.jacobian(), ComputeJacobianScaledColor,
+                              petsc_preconditioner.coloring()));
+  }
   jacobian_pruned = false; // Reset flag. Will be set after pruning.
   return PETSC_SUCCESS;
 }
@@ -543,9 +267,9 @@ SNESSolver::SNESSolver(Options* opts)
       pseudo_alpha((*options)["pseudo_alpha"]
                        .doc("Sets timestep using dt = alpha / residual")
                        .withDefault(100. * atol * timestep)),
-      pseudo_alpha_minimum(
-          (*options)["pseudo_alpha_minimum"].doc("Minimum value of pseudo_alpha")
-          .withDefault(0.1 * pseudo_alpha)),
+      pseudo_alpha_minimum((*options)["pseudo_alpha_minimum"]
+                               .doc("Minimum value of pseudo_alpha")
+                               .withDefault(0.1 * pseudo_alpha)),
       pseudo_growth_factor((*options)["pseudo_growth_factor"]
                                .doc("PTC growth factor on success")
                                .withDefault(1.1)),
@@ -1191,10 +915,10 @@ int SNESSolver::run() {
 
       if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Adjust pseudo_alpha to globally scale timesteps
-        pseudo_alpha = std::max({
-            updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate,
-                                 max_timestep * atol * 100),
-            pseudo_alpha_minimum});
+        pseudo_alpha =
+            std::max({updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate,
+                                           max_timestep * atol * 100),
+                      pseudo_alpha_minimum});
 
         // Adjust local timesteps
         PetscCall(updatePseudoTimestepping());
@@ -1541,10 +1265,10 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping() {
 /// rapid changes in timestep.
 BoutReal SNESSolver::updatePseudoTimestep_inverse_residual(BoutReal previous_timestep,
                                                            BoutReal current_residual) {
-  return std::max({
-      std::min({std::max({pseudo_alpha / current_residual, previous_timestep / 1.5}),
-                1.5 * previous_timestep, max_timestep}),
-      dt_min_reset});
+  return std::max(
+      {std::min({std::max({pseudo_alpha / current_residual, previous_timestep / 1.5}),
+                 1.5 * previous_timestep, max_timestep}),
+       dt_min_reset});
 }
 
 // Strategy based on history of residuals
@@ -1855,39 +1579,6 @@ static PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat
   return fctx->scaleJacobian(Jac_new);
 }
 
-void SNESSolver::updateColoring() {
-  // Re-calculate the coloring
-  MatColoring coloring = NULL;
-  MatColoringCreate(Jfd, &coloring);
-  // MatColoringSetType(coloring, MATCOLORINGSL);  // Serial algorithm. Better for smale-to-medium size problems.
-  MatColoringSetType(
-      coloring, MATCOLORINGGREEDY); // Parallel algorith. Better for large parallel runs
-  // MatColoringSetType(coloring, MATCOLORINGJP);  // This didn't work
-  MatColoringSetFromOptions(coloring);
-
-  // Calculate new index sets
-  ISColoring iscoloring = NULL;
-  MatColoringApply(coloring, &iscoloring);
-  MatColoringDestroy(&coloring);
-
-  // Replace the old coloring with the new one
-  MatFDColoringDestroy(&fdcoloring);
-  MatFDColoringCreate(Jfd, iscoloring, &fdcoloring);
-  MatFDColoringSetFunction(fdcoloring,
-                           bout::cast_MatFDColoringFn(FormFunctionForColoring), this);
-  MatFDColoringSetFromOptions(fdcoloring);
-  MatFDColoringSetUp(Jfd, iscoloring, fdcoloring);
-  ISColoringDestroy(&iscoloring);
-
-  // Replace the CTX pointer in SNES Jacobian
-  if (matrix_free_operator) {
-    // Use matrix-free calculation for operator, finite difference for preconditioner
-    SNESSetJacobian(snes, Jmf, Jfd, ComputeJacobianScaledColor, fdcoloring);
-  } else {
-    SNESSetJacobian(snes, Jfd, Jfd, ComputeJacobianScaledColor, fdcoloring);
-  }
-}
-
 BoutReal SNESSolver::pid(BoutReal timestep, int nl_its, BoutReal max_dt) {
 
   /* ---------- multiplicative PID factors ---------- */
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index fbcf3baddf..b50e5c4399 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -41,6 +41,7 @@ class SNESSolver;
 #include <bout/bout_types.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
+#include <bout/petsc_preconditioner.hxx>
 #include <bout/petsclib.hxx>
 
 #include <petsc.h>
@@ -202,8 +203,8 @@ private:
   BoutReal kI; ///< (0.2 - 0.4) Integral parameter (smooths history of changes)
   BoutReal kD; ///< (0.1 - 0.3) Derivative (dampens oscillation - optional)
   bool pid_consider_failures; ///< Reduce timestep increases if recent solves have failed
-  BoutReal recent_failure_rate;            ///< Rolling average of recent failure rate
-  BoutReal last_failure_weight;            ///< 1 / number of recent solves
+  BoutReal recent_failure_rate; ///< Rolling average of recent failure rate
+  BoutReal last_failure_weight; ///< 1 / number of recent solves
 
   BoutReal nl_its_prev;
   BoutReal nl_its_prev2;
@@ -227,11 +228,11 @@ private:
   Vec x1;               ///< Previous solution
   BoutReal time1{-1.0}; ///< Time of previous solution
 
-  SNES snes;                         ///< SNES context
-  Mat Jmf;                           ///< Matrix Free Jacobian
-  Mat Jfd;                           ///< Finite Difference Jacobian
-  MatFDColoring fdcoloring{nullptr}; ///< Matrix coloring context
-                                     ///< Jacobian evaluation
+  SNES snes; ///< SNES context
+  Mat Jmf;   ///< Matrix Free Jacobian
+  Mat Jfd;   ///< Finite Difference Jacobian (brute-force, when not using coloring)
+  PetscPreconditioner
+      petsc_preconditioner; ///< Coloring-based FD Jacobian + MatFDColoring
 
   bool use_precon;                ///< Use preconditioner
   std::string ksp_type;           ///< Linear solver type
@@ -245,7 +246,7 @@ private:
   bool matrix_free_operator; ///< Use matrix free Jacobian in the operator?
   int lag_jacobian;          ///< Re-use Jacobian
   bool jacobian_persists; ///< Re-use Jacobian and preconditioner across nonlinear solves
-  bool use_coloring;         ///< Use matrix coloring
+  bool use_coloring;      ///< Use matrix coloring
 
   bool jacobian_recalculated; ///< Flag set when Jacobian is recalculated
   bool prune_jacobian;        ///< Remove small elements in the Jacobian?
@@ -253,7 +254,6 @@ private:
   BoutReal prune_fraction;    ///< Prune if fraction of small elements is larger than this
   bool jacobian_pruned{false}; ///< Has the Jacobian been pruned?
   Mat Jfd_original;            ///< Used to reset the Jacobian if over-pruned
-  void updateColoring();       ///< Updates the coloring using Jfd
 
   bool scale_rhs;          ///< Scale time derivatives?
   Vec rhs_scaling_factors; ///< Factors to multiply RHS function
diff --git a/src/solver/petsc_preconditioner.cxx b/src/solver/petsc_preconditioner.cxx
new file mode 100644
index 0000000000..8c19cfc9f0
--- /dev/null
+++ b/src/solver/petsc_preconditioner.cxx
@@ -0,0 +1,326 @@
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_PETSC
+
+#include "bout/petsc_preconditioner.hxx"
+
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutcomm.hxx"
+#include "bout/field3d.hxx"
+#include "bout/globals.hxx"
+#include "bout/mesh.hxx"
+#include "bout/options.hxx"
+#include "bout/output.hxx"
+
+#include <algorithm>
+#include <cmath>
+#include <cstddef>
+#include <set>
+#include <utility>
+#include <vector>
+
+namespace {
+class ColoringStencil {
+private:
+  static bool isInSquare(int i, int j, int n_square) {
+    return std::abs(i) <= n_square && std::abs(j) <= n_square;
+  }
+  static bool isInCross(int i, int j, int n_cross) {
+    if (i == 0) {
+      return std::abs(j) <= n_cross;
+    }
+    if (j == 0) {
+      return std::abs(i) <= n_cross;
+    }
+    return false;
+  }
+  static bool isInTaxi(int i, int j, int n_taxi) {
+    return std::abs(i) + std::abs(j) <= n_taxi;
+  }
+
+public:
+  static auto getOffsets(int n_square, int n_taxi, int n_cross) {
+    ASSERT2(n_square >= 0 && n_cross >= 0 && n_taxi >= 0
+            && n_square + n_cross + n_taxi > 0);
+    auto inside = [&](int i, int j) {
+      return isInSquare(i, j, n_square) || isInTaxi(i, j, n_taxi)
+             || isInCross(i, j, n_cross);
+    };
+    std::vector<std::pair<int, int>> xy_offsets;
+    auto loop_bound = std::max({n_square, n_taxi, n_cross});
+    for (int i = -loop_bound; i <= loop_bound; ++i) {
+      for (int j = -loop_bound; j <= loop_bound; ++j) {
+        if (inside(i, j)) {
+          xy_offsets.emplace_back(i, j);
+        }
+      }
+    }
+    return xy_offsets;
+  }
+};
+} // namespace
+
+void PetscPreconditioner::reset() {
+  if (fdcoloring != nullptr) {
+    MatFDColoringDestroy(&fdcoloring);
+    fdcoloring = nullptr;
+  }
+  if (Jfd != nullptr) {
+    MatDestroy(&Jfd);
+    Jfd = nullptr;
+  }
+}
+
+PetscErrorCode PetscPreconditioner::createJacobianPattern(Field3D& index,
+                                                          Options& options,
+                                                          PetscInt nlocal, int n2d,
+                                                          int n3d, MPI_Comm comm) {
+  reset();
+
+  // Use global mesh for now
+  Mesh* mesh = bout::globals::mesh;
+
+  //////////////////////////////////////////////////
+  // Pre-allocate PETSc storage
+
+  output_progress.write("Setting Jacobian matrix sizes\n");
+
+  // Set size of Matrix on each processor to nlocal x nlocal
+  PetscCall(MatCreate(comm, &Jfd));
+  PetscCall(MatSetOption(Jfd, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE));
+  PetscCall(MatSetSizes(Jfd, nlocal, nlocal, PETSC_DETERMINE, PETSC_DETERMINE));
+  PetscCall(MatSetFromOptions(Jfd));
+
+  // Determine which row/columns of the matrix are locally owned
+  int Istart = 0, Iend = 0;
+  PetscCall(MatGetOwnershipRange(Jfd, &Istart, &Iend));
+
+  // Convert local into global indices
+  // Note: Not in the boundary cells, to keep -1 values
+  for (const auto& i : mesh->getRegion3D("RGN_NOBNDRY")) {
+    index[i] += Istart;
+  }
+  // Now communicate to fill guard cells
+  mesh->communicate(index);
+
+  // Non-zero elements on this processor
+  std::vector<PetscInt> d_nnz;
+  std::vector<PetscInt> o_nnz;
+
+  auto n_square =
+      options["stencil:square"].doc("Extent of stencil (square)").withDefault<int>(0);
+  auto n_cross =
+      options["stencil:cross"].doc("Extent of stencil (cross)").withDefault<int>(0);
+  // Default n_taxi=2 if nothing else is set
+  auto n_taxi = options["stencil:taxi"]
+                    .doc("Extent of stencil (taxi-cab norm)")
+                    .withDefault<int>((n_square == 0 && n_cross == 0) ? 2 : 0);
+
+  const auto xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
+  {
+    // Count the *unique* non-zeros for preallocation
+    std::vector<std::set<int>> d_nnz_map2d(nlocal);
+    std::vector<std::set<int>> o_nnz_map2d(nlocal);
+    std::vector<std::set<int>> d_nnz_map3d(nlocal);
+    std::vector<std::set<int>> o_nnz_map3d(nlocal);
+
+    for (int x = mesh->xstart; x <= mesh->xend; x++) {
+      for (int y = mesh->ystart; y <= mesh->yend; y++) {
+        const int ind0 = ROUND(index(x, y, 0)) - Istart;
+
+        // 2D fields
+        for (int i = 0; i < n2d; i++) {
+          const PetscInt row = ind0 + i;
+          for (const auto& [x_off, y_off] : xy_offsets) {
+            const int xi = x + x_off;
+            const int yi = y + y_off;
+            if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx) || (yi >= mesh->LocalNy)) {
+              continue;
+            }
+
+            const int ind2 = ROUND(index(xi, yi, 0));
+            if (ind2 < 0) {
+              continue; // A boundary point
+            }
+
+            for (int j = 0; j < n2d; j++) {
+              const PetscInt col = ind2 + j;
+              if (col >= Istart && col < Iend) {
+                d_nnz_map2d[row].insert(col);
+              } else {
+                o_nnz_map2d[row].insert(col);
+              }
+            }
+          }
+        }
+
+        // 3D fields
+        for (int z = mesh->zstart; z <= mesh->zend; z++) {
+          const int ind = ROUND(index(x, y, z)) - Istart;
+
+          for (int i = 0; i < n3d; i++) {
+            PetscInt row = ind + i;
+            if (z == 0) {
+              row += n2d;
+            }
+
+            // Depends on 2D fields
+            for (int j = 0; j < n2d; j++) {
+              const PetscInt col = ind0 + j;
+              if (col >= Istart && col < Iend) {
+                d_nnz_map2d[row].insert(col);
+              } else {
+                o_nnz_map2d[row].insert(col);
+              }
+            }
+
+            for (const auto& [x_off, y_off] : xy_offsets) {
+              const int xi = x + x_off;
+              const int yi = y + y_off;
+
+              if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
+                  || (yi >= mesh->LocalNy)) {
+                continue;
+              }
+
+              int ind2 = ROUND(index(xi, yi, 0));
+              if (ind2 < 0) {
+                continue; // Boundary point
+              }
+
+              if (z == 0) {
+                ind2 += n2d;
+              }
+
+              for (int j = 0; j < n3d; j++) {
+                const PetscInt col = ind2 + j;
+                if (col >= Istart && col < Iend) {
+                  d_nnz_map3d[row].insert(col);
+                } else {
+                  o_nnz_map3d[row].insert(col);
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+
+    d_nnz.reserve(nlocal);
+    o_nnz.reserve(nlocal);
+    for (int i = 0; i < nlocal; ++i) {
+      // Assume all elements in the z direction are potentially coupled
+      d_nnz.emplace_back((d_nnz_map3d[i].size() * mesh->LocalNz) + d_nnz_map2d[i].size());
+      o_nnz.emplace_back((o_nnz_map3d[i].size() * mesh->LocalNz) + o_nnz_map2d[i].size());
+    }
+  }
+
+  output_progress.write("Pre-allocating Jacobian\n");
+  PetscCall(MatMPIAIJSetPreallocation(Jfd, 0, d_nnz.data(), 0, o_nnz.data()));
+  PetscCall(MatSeqAIJSetPreallocation(Jfd, 0, d_nnz.data()));
+  PetscCall(MatSetUp(Jfd));
+  PetscCall(MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE));
+
+  //////////////////////////////////////////////////
+  // Mark non-zero entries
+
+  output_progress.write("Marking non-zero Jacobian entries\n");
+  const PetscScalar val = 1.0;
+  for (int x = mesh->xstart; x <= mesh->xend; x++) {
+    for (int y = mesh->ystart; y <= mesh->yend; y++) {
+      const int ind0 = ROUND(index(x, y, 0));
+
+      // 2D fields
+      for (int i = 0; i < n2d; i++) {
+        const PetscInt row = ind0 + i;
+
+        for (const auto& [x_off, y_off] : xy_offsets) {
+          const int xi = x + x_off;
+          const int yi = y + y_off;
+          if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx) || (yi >= mesh->LocalNy)) {
+            continue;
+          }
+
+          const int ind2 = ROUND(index(xi, yi, 0));
+          if (ind2 < 0) {
+            continue; // A boundary point
+          }
+
+          for (int j = 0; j < n2d; j++) {
+            const PetscInt col = ind2 + j;
+            PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
+          }
+        }
+      }
+
+      // 3D fields
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
+        const int ind = ROUND(index(x, y, z));
+
+        for (int i = 0; i < n3d; i++) {
+          PetscInt row = ind + i;
+          if (z == 0) {
+            row += n2d;
+          }
+
+          // Depends on 2D fields
+          for (int j = 0; j < n2d; j++) {
+            const PetscInt col = ind0 + j;
+            PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
+          }
+
+          for (const auto& [x_off, y_off] : xy_offsets) {
+            const int xi = x + x_off;
+            const int yi = y + y_off;
+
+            if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx) || (yi >= mesh->LocalNy)) {
+              continue;
+            }
+
+            for (int zi = mesh->zstart; zi <= mesh->zend; ++zi) {
+              int ind2 = ROUND(index(xi, yi, zi));
+              if (ind2 < 0) {
+                continue; // Boundary point
+              }
+
+              if (z == 0) {
+                ind2 += n2d;
+              }
+
+              for (int j = 0; j < n3d; j++) {
+                const PetscInt col = ind2 + j;
+                PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+
+  output_progress.write("Assembling Jacobian matrix\n");
+  PetscCall(MatAssemblyBegin(Jfd, MAT_FINAL_ASSEMBLY));
+  PetscCall(MatAssemblyEnd(Jfd, MAT_FINAL_ASSEMBLY));
+
+  {
+    PetscBool symmetric = PETSC_FALSE;
+    PetscCall(MatIsSymmetric(Jfd, 1e-5, &symmetric));
+    if (!static_cast<bool>(symmetric)) {
+      output_warn.write("Jacobian pattern is not symmetric\n");
+    }
+  }
+
+  if (options["force_symmetric_coloring"]
+          .doc("Modifies coloring matrix to force it to be symmetric")
+          .withDefault<bool>(false)) {
+    Mat Jfd_T{nullptr};
+    PetscCall(MatCreateTranspose(Jfd, &Jfd_T));
+    PetscCall(MatAXPY(Jfd, 1, Jfd_T, DIFFERENT_NONZERO_PATTERN));
+    PetscCall(MatDestroy(&Jfd_T));
+  }
+
+  PetscFunctionReturn(PETSC_SUCCESS);
+}
+
+#endif // BOUT_HAS_PETSC

From 1988ac4bc1685e10fb61635f9036c9bfc0e43ce7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 29 May 2026 14:42:48 -0700
Subject: [PATCH 1281/1827] cvode: Remove use_precon, use cvode_precon_method

Setting `cvode_precon_method` to `none` disables preconditioning.
The default `auto` uses the user-supplied preconditioner if present,
then PETSc if available, then SUNDIALS' BBD preconditioner.
---
 manual/sphinx/user_docs/time_integration.rst |  10 +-
 src/solver/impls/cvode/cvode.cxx             | 234 +++++++++----------
 src/solver/impls/cvode/cvode.hxx             |  12 +-
 3 files changed, 121 insertions(+), 135 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 9bd69847c1..5565da4c14 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -144,12 +144,14 @@ iterations becomes large, this may be an indication that the system is
 poorly conditioned, and a preconditioner might help improve performance.
 See :ref:`sec-preconditioning`.
 
-When ``solver:use_precon=true`` and no user-supplied preconditioner is provided,
-the preconditioner method can be selected using ``solver:cvode_precon_method``:
+CVODE preconditioning is controlled using ``solver:cvode_precon_method``:
 
-- ``auto`` (default): Prefer PETSc coloring if PETSc is available, otherwise use BBD.
-- ``bbd``: Force the built-in BBD preconditioner.
+- ``auto`` (default): Prefer a user-supplied preconditioner if provided, then PETSc
+  coloring if PETSc is available, otherwise use BBD.
+- ``none``: Disable preconditioning.
+- ``user``: Require a user-supplied preconditioner.
 - ``petsc``: Require PETSc and use PETSc coloring.
+- ``bbd``: Force the built-in BBD preconditioner.
 
 For ``cvode_precon_method = petsc``, PETSc options for the internal KSP/PC can be
 set with the prefix ``cvode_petscpre_`` (either on the command line, or by putting
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 203704929a..bb58bbe284 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -3,7 +3,7 @@
  *
  *
  **************************************************************************
- * Copyright 2010-2024 BOUT++ contributors
+ * Copyright 2010-2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -42,6 +42,7 @@
 #include "bout/msg_stack.hxx"
 #include "bout/options.hxx"
 #include "bout/output.hxx"
+#include "bout/solver.hxx"
 #include "bout/sundials_backports.hxx"
 #include "bout/unused.hxx"
 
@@ -57,8 +58,10 @@
 
 #include <algorithm>
 #include <iterator>
+#include <memory>
 #include <numeric>
 #include <string>
+#include <vector>
 
 BOUT_ENUM_CLASS(positivity_constraint, none, positive, non_negative, negative,
                 non_positive);
@@ -125,29 +128,17 @@ CvodeSolver::CvodeSolver(Options* opts)
                    "each variable")
               .withDefault(false)),
       maxl((*options)["maxl"].doc("Maximum number of linear iterations").withDefault(5)),
-      use_precon((*options)["use_precon"].doc("Use preconditioner?").withDefault(false)),
       rightprec((*options)["rightprec"]
                     .doc("Use right preconditioner? Otherwise use left.")
                     .withDefault(false)),
-      use_jacobian((*options)["use_jacobian"].withDefault(false)), precon_method([&]() {
-        const auto method =
-            (*options)["cvode_precon_method"]
-                .doc("Preconditioner to use when solver:use_precon=true and no user "
-                     "preconditioner is supplied: auto, bbd, petsc.")
-                .withDefault<std::string>("auto");
-        if (method == "auto" || method == "automatic") {
-          return CvodePreconMethod::auto_select;
-        }
-        if (method == "bbd") {
-          return CvodePreconMethod::bbd;
-        }
-        if (method == "petsc") {
-          return CvodePreconMethod::petsc;
-        }
-        throw BoutException("Invalid solver:cvode_precon_method '{}'. Valid values: "
-                            "auto, bbd, petsc.",
-                            method);
-      }()),
+      use_jacobian((*options)["use_jacobian"].withDefault(false)),
+      precon_method(
+          (*options)["cvode_precon_method"]
+              .doc("Preconditioner to use with CVODE Newton iteration. "
+                   "Choices: none, auto (default), user, petsc, bbd. "
+                   "auto prefers user (if supplied), then petsc (if available), "
+                   "then bbd.")
+              .withDefault(CvodePreconMethod::Auto)),
       cvode_nonlinear_convergence_coef(
           (*options)["cvode_nonlinear_convergence_coef"]
               .doc("Safety factor used in the nonlinear convergence test")
@@ -161,6 +152,12 @@ CvodeSolver::CvodeSolver(Options* opts)
   has_constraints = false; // This solver doesn't have constraints
   canReset = true;
 
+  if ((*options)["use_precon"].isSet()) {
+    output_warn << "WARNING: solver:use_precon is deprecated for CVODE and is now "
+                   "ignored. Use solver:cvode_precon_method=none to disable "
+                   "preconditioning.\n";
+  }
+
   // Add diagnostics to output
   // Needs to be in constructor not init() because init() is called after
   // Solver::outputVars()
@@ -381,8 +378,22 @@ int CvodeSolver::init() {
   } else {
     output_info.write("\tUsing Newton iteration\n");
 
-    const auto prectype =
-        use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE;
+    CvodePreconMethod selected_precon = precon_method;
+    if (selected_precon == CvodePreconMethod::Auto) {
+      if (hasPreconditioner()) {
+        selected_precon = CvodePreconMethod::user;
+      } else {
+#if BOUT_HAS_PETSC
+        selected_precon = CvodePreconMethod::petsc;
+#else
+        selected_precon = CvodePreconMethod::bbd;
+#endif
+      }
+    }
+
+    const auto prectype = (selected_precon == CvodePreconMethod::none)
+                              ? SUN_PREC_NONE
+                              : (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT);
 
     switch ((*options)["linear_solver"]
                 .doc("Set linear solver type. Default is gmres.")
@@ -408,109 +419,82 @@ int CvodeSolver::init() {
       throw BoutException("CVodeSetLinearSolver failed\n");
     }
 
-    if (use_precon) {
-      if (hasPreconditioner()) {
-        output_info.write("\tUsing user-supplied preconditioner\n");
+    if (selected_precon == CvodePreconMethod::none) {
+      output_info.write("\tNo preconditioning\n");
 
-        if (CVodeSetPreconditioner(cvode_mem, nullptr, cvode_pre) != CVLS_SUCCESS) {
-          throw BoutException("CVodeSetPreconditioner failed\n");
-        }
-      } else {
-        const bool prefer_petsc = (precon_method == CvodePreconMethod::petsc)
-                                  || (precon_method == CvodePreconMethod::auto_select);
+    } else if (selected_precon == CvodePreconMethod::user) {
+      if (!hasPreconditioner()) {
+        throw BoutException(
+            "solver:cvode_precon_method=user requested, but no user preconditioner "
+            "has been supplied.");
+      }
 
-#if BOUT_HAS_PETSC
-        if (prefer_petsc) {
-          output_info.write("\tUsing PETSc coloring preconditioner\n");
-
-          if (!petsc_lib) {
-            petsc_lib = std::make_unique<PetscLib>();
-          }
-
-          petsc_global_N = neq;
-          petsc_rhs_tmp.resize(local_N);
-
-          if (petsc_ksp == nullptr) {
-            PetscCall(KSPCreate(BoutComm::get(), &petsc_ksp));
-            PetscCall(KSPSetType(petsc_ksp, KSPPREONLY));
-            PetscCall(KSPSetOptionsPrefix(petsc_ksp, "cvode_petscpre_"));
-            PetscCall(KSPSetFromOptions(petsc_ksp));
-          }
-
-          if (petsc_x == nullptr) {
-            PetscCall(VecCreateMPI(BoutComm::get(), local_N, petsc_global_N, &petsc_x));
-            PetscCall(VecDuplicate(petsc_x, &petsc_f));
-            PetscCall(VecCreateMPI(BoutComm::get(), local_N, petsc_global_N, &petsc_r));
-            PetscCall(VecCreateMPI(BoutComm::get(), local_N, petsc_global_N, &petsc_z));
-          }
-
-          Field3D index = globalIndex(0);
-          PetscCall(petsc_preconditioner.createJacobianPattern(
-              index, *options, local_N, n2Dvars(), n3Dvars(), BoutComm::get()));
-          PetscCall(
-              petsc_preconditioner.updateColoring(CvodeSolver::petscFormFunction, this));
-          PetscCall(MatFDColoringSetF(petsc_preconditioner.coloring(), petsc_f));
-
-          if (CVodeSetPreconditioner(cvode_mem, petscPSetup, petscPSolve)
-              != CVLS_SUCCESS) {
-            throw BoutException("CVodeSetPreconditioner (PETSc coloring) failed\n");
-          }
-        } else {
-          output_info.write("\tUsing BBD preconditioner\n");
-
-          /// Get options
-          // Compute band_width_default from actually added fields, to allow for multiple
-          // Mesh objects
-          //
-          // Previous implementation was equivalent to:
-          //   int MXSUB = mesh->xend - mesh->xstart + 1;
-          //   int band_width_default = n3Dvars()*(MXSUB+2);
-          const int band_width_default = std::accumulate(
-              begin(f3d), end(f3d), 0, [](int a, const VarStr<Field3D>& fvar) {
-                Mesh* localmesh = fvar.var->getMesh();
-                return a + localmesh->xend - localmesh->xstart + 3;
-              });
-
-          const auto mudq = (*options)["mudq"].withDefault(band_width_default);
-          const auto mldq = (*options)["mldq"].withDefault(band_width_default);
-          const auto mukeep = (*options)["mukeep"].withDefault(n3Dvars() + n2Dvars());
-          const auto mlkeep = (*options)["mlkeep"].withDefault(n3Dvars() + n2Dvars());
-
-          if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0.0,
-                            cvode_bbd_rhs, nullptr)
-              != CVLS_SUCCESS) {
-            throw BoutException("CVBBDPrecInit failed\n");
-          }
-        }
+      output_info.write("\tUsing user-supplied preconditioner\n");
+
+      if (CVodeSetPreconditioner(cvode_mem, nullptr, cvode_pre) != CVLS_SUCCESS) {
+        throw BoutException("CVodeSetPreconditioner failed\n");
+      }
+    } else if (selected_precon == CvodePreconMethod::petsc) {
+#if !BOUT_HAS_PETSC
+      throw BoutException(
+          "solver:cvode_precon_method=petsc requested, but BOUT++ was not "
+          "configured with PETSc.");
 #else
-        if (precon_method == CvodePreconMethod::petsc) {
-          throw BoutException(
-              "solver:cvode_precon_method=petsc requested, but BOUT++ was not "
-              "configured with PETSc.");
-        }
-
-        output_info.write("\tUsing BBD preconditioner\n");
-
-        const int band_width_default = std::accumulate(
-            begin(f3d), end(f3d), 0, [](int a, const VarStr<Field3D>& fvar) {
-              Mesh* localmesh = fvar.var->getMesh();
-              return a + localmesh->xend - localmesh->xstart + 3;
-            });
-
-        const auto mudq = (*options)["mudq"].withDefault(band_width_default);
-        const auto mldq = (*options)["mldq"].withDefault(band_width_default);
-        const auto mukeep = (*options)["mukeep"].withDefault(n3Dvars() + n2Dvars());
-        const auto mlkeep = (*options)["mlkeep"].withDefault(n3Dvars() + n2Dvars());
-
-        if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0.0,
-                          cvode_bbd_rhs, nullptr)
-            != CVLS_SUCCESS) {
-          throw BoutException("CVBBDPrecInit failed\n");
-        }
-#endif
+      output_info.write("\tUsing PETSc coloring preconditioner\n");
+
+      if (!petsc_lib) {
+        petsc_lib = std::make_unique<PetscLib>();
       }
-    } else {
-      output_info.write("\tNo preconditioning\n");
+
+      petsc_global_N = neq;
+      petsc_rhs_tmp.resize(local_N);
+
+      if (petsc_ksp == nullptr) {
+        PetscCall(KSPCreate(BoutComm::get(), &petsc_ksp));
+        PetscCall(KSPSetType(petsc_ksp, KSPPREONLY));
+        PetscCall(KSPSetOptionsPrefix(petsc_ksp, "cvode_petscpre_"));
+        PetscCall(KSPSetFromOptions(petsc_ksp));
+      }
+
+      if (petsc_x == nullptr) {
+        PetscCall(VecCreateMPI(BoutComm::get(), local_N, petsc_global_N, &petsc_x));
+        PetscCall(VecDuplicate(petsc_x, &petsc_f));
+        PetscCall(VecCreateMPI(BoutComm::get(), local_N, petsc_global_N, &petsc_r));
+        PetscCall(VecCreateMPI(BoutComm::get(), local_N, petsc_global_N, &petsc_z));
+      }
+
+      Field3D index = globalIndex(0);
+      PetscCall(petsc_preconditioner.createJacobianPattern(
+          index, *options, local_N, n2Dvars(), n3Dvars(), BoutComm::get()));
+      PetscCall(
+          petsc_preconditioner.updateColoring(CvodeSolver::petscFormFunction, this));
+      PetscCall(MatFDColoringSetF(petsc_preconditioner.coloring(), petsc_f));
+
+      if (CVodeSetPreconditioner(cvode_mem, petscPSetup, petscPSolve) != CVLS_SUCCESS) {
+        throw BoutException("CVodeSetPreconditioner (PETSc coloring) failed\n");
+      }
+#endif // BOUT_HAS_PETSC
+
+    } else if (selected_precon == CvodePreconMethod::bbd) {
+      output_info.write("\tUsing BBD preconditioner\n");
+
+      const int band_width_default = std::accumulate(
+          begin(f3d), end(f3d), 0, [](int a, const VarStr<Field3D>& fvar) {
+            Mesh* localmesh = fvar.var->getMesh();
+            return a + localmesh->xend - localmesh->xstart + 3;
+          });
+
+      const auto mudq = (*options)["mudq"].withDefault(band_width_default);
+      const auto mldq = (*options)["mldq"].withDefault(band_width_default);
+      const auto mukeep = (*options)["mukeep"].withDefault(n3Dvars() + n2Dvars());
+      const auto mlkeep = (*options)["mlkeep"].withDefault(n3Dvars() + n2Dvars());
+
+      if (CVBBDPrecInit(cvode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0.0,
+                        cvode_bbd_rhs, nullptr)
+          != CVLS_SUCCESS) {
+        throw BoutException("CVBBDPrecInit failed\n");
+      }
+#endif
     }
 
     /// Set Jacobian-vector multiplication function
@@ -683,7 +667,7 @@ BoutReal CvodeSolver::run(BoutReal tout) {
     CVodeGetCurrentTime(cvode_mem, &internal_time);
     while (internal_time < tout) {
       // Run another step
-      BoutReal last_time = internal_time;
+      const BoutReal last_time = internal_time;
       flag = CVode(cvode_mem, tout, uvec, &internal_time, CV_ONE_STEP);
 
       if (flag < 0) {
@@ -742,7 +726,7 @@ void CvodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udat
                       BoutReal* rvec, BoutReal* zvec) {
   TRACE("Running preconditioner: CvodeSolver::pre({})", t);
 
-  BoutReal tstart = bout::globals::mpi->MPI_Wtime();
+  const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
 
   const auto length = N_VGetLocalLength_Parallel(uvec);
 
@@ -1037,5 +1021,3 @@ void CvodeSolver::resetInternalFields() {
     throw BoutException("CVodeReInit failed\n");
   }
 }
-
-#endif
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index c912b20b4e..b8d64d4d07 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -4,9 +4,9 @@
  * NOTE: Only one solver can currently be compiled in
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -28,6 +28,7 @@
 #ifndef BOUT_SUNDIAL_SOLVER_H
 #define BOUT_SUNDIAL_SOLVER_H
 
+#include "bout/bout_enum_class.hxx"
 #include "bout/build_defines.hxx"
 #include "bout/solver.hxx"
 
@@ -40,6 +41,7 @@ RegisterUnavailableSolver
 
 #else
 
+#include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/region.hxx"
 #include "bout/sundials_backports.hxx"
@@ -62,7 +64,9 @@ namespace {
 RegisterSolver<CvodeSolver> registersolvercvode("cvode");
 }
 
-enum class CvodePreconMethod { auto_select, bbd, petsc };
+// Preconditioner selection for CVODE.
+// Note: String comparisons are case-insensitive so "Auto" avoids conflict with keyword
+BOUT_ENUM_CLASS(CvodePreconMethod, none, Auto, user, petsc, bbd);
 
 #if SUNDIALS_VERSION_AT_LEAST(6, 0, 0)
 using CvodeBool = sunbooleantype;
@@ -142,8 +146,6 @@ private:
   bool apply_positivity_constraints;
   /// Maximum number of linear iterations
   int maxl;
-  /// Use preconditioner?
-  bool use_precon;
   /// Use right preconditioner? Otherwise use left.
   bool rightprec;
   bool use_jacobian;

From 778467c09066496e7df1bd0bf0e21306f042d2b9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 29 May 2026 22:20:09 +0000
Subject: [PATCH 1282/1827] Bump externalpackages/googletest from `dc3c9ed` to
 `8736d2c`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `dc3c9ed` to `8736d2c`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/dc3c9eda2f02ba32de9329dd27ace7e527f492dc...8736d2cd5c1dcba41170ed2fddca14021d4916c3)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: 8736d2cd5c1dcba41170ed2fddca14021d4916c3
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index dc3c9eda2f..8736d2cd5c 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit dc3c9eda2f02ba32de9329dd27ace7e527f492dc
+Subproject commit 8736d2cd5c1dcba41170ed2fddca14021d4916c3

From 623efc8cc11869b83d9753019cafbe4b3c47b875 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 29 May 2026 15:36:29 -0700
Subject: [PATCH 1283/1827] cvode: Options to set preconditioner setup

cvode_lsetup_frequency and cvode_jac_eval_frequency modify
how often the Jacobian and preconditioner are recalculated.
---
 manual/sphinx/user_docs/time_integration.rst |  8 ++++++++
 src/solver/impls/cvode/cvode.cxx             | 18 ++++++++++++++++++
 src/solver/impls/cvode/cvode.hxx             |  4 ++++
 3 files changed, 30 insertions(+)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 5565da4c14..a12d37d303 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -161,6 +161,14 @@ prefixed keys into the ``[petsc]`` section). For example::
     cvode_petscpre_ksp_type = preonly
     cvode_petscpre_pc_type = hypre
 
+Two CVODE heuristics that control when the linear solver setup routine is called,
+and when the Jacobian/preconditioner are recomputed, can be adjusted with:
+
+- ``cvode_lsetup_frequency`` (default ``0``): Passed to ``CVodeSetLSetupFrequency``.
+  ``0`` uses the SUNDIALS default.
+- ``cvode_jac_eval_frequency`` (default ``0``): Passed to ``CVodeSetJacEvalFrequency``.
+  ``0`` uses the SUNDIALS default.
+
 CVODE can set constraints to keep some quantities positive, non-negative,
 negative or non-positive. These constraints can be activated by setting the
 option ``solver:apply_positivity_constraints=true``, and then in the section
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index bb58bbe284..73fe0cd47c 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -119,6 +119,16 @@ CvodeSolver::CvodeSolver(Options* opts)
               .doc("Maximum number of nonlinear iterations allowed by CVODE before "
                    "reducing timestep.")
               .withDefault(3)),
+      lsetup_frequency(
+          (*options)["cvode_lsetup_frequency"]
+              .doc("Linear solver setup frequency (CVodeSetLSetupFrequency). "
+                   "0 uses the SUNDIALS default.")
+              .withDefault(0)),
+      jac_eval_frequency((*options)["cvode_jac_eval_frequency"]
+                             .doc("Jacobian/preconditioner evaluation frequency "
+                                  "(CVodeSetJacEvalFrequency). "
+                                  "0 uses the SUNDIALS default.")
+                             .withDefault(0)),
       apply_positivity_constraints(
           (*options)["apply_positivity_constraints"]
               .doc("Use CVODE function CVodeSetConstraints to constrain variables - the "
@@ -344,6 +354,10 @@ int CvodeSolver::init() {
     throw BoutException("CVodeSetMaxNonlinIters failed\n");
   }
 
+  if (CVodeSetLSetupFrequency(cvode_mem, lsetup_frequency) != CV_SUCCESS) {
+    throw BoutException("CVodeSetLSetupFrequency failed\n");
+  }
+
   if (apply_positivity_constraints) {
     auto f2d_constraints = create_constraints(f2d);
     auto f3d_constraints = create_constraints(f3d);
@@ -419,6 +433,10 @@ int CvodeSolver::init() {
       throw BoutException("CVodeSetLinearSolver failed\n");
     }
 
+    if (CVodeSetJacEvalFrequency(cvode_mem, jac_eval_frequency) != CVLS_SUCCESS) {
+      throw BoutException("CVodeSetJacEvalFrequency failed\n");
+    }
+
     if (selected_precon == CvodePreconMethod::none) {
       output_info.write("\tNo preconditioning\n");
 
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index b8d64d4d07..025a3e2dcd 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -140,6 +140,10 @@ private:
   /// reducing timestep. CVODE default (used if this option is
   /// negative) is 3
   int max_nonlinear_iterations;
+  /// Max number of steps between calls to linear solver setup
+  long int lsetup_frequency;
+  /// Max number of steps between Jacobian/preconditioner evaluations
+  long int jac_eval_frequency;
   /// Use CVODE function CVodeSetConstraints to constrain variables -
   /// the constraint to be applied is set by the positivity_constraint
   /// option in the subsection for each variable

From 8aeab139dc370d5f452d56eb1ebb6d0b5a9c7bf2 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 29 May 2026 15:52:27 -0700
Subject: [PATCH 1284/1827] cvode: Fix compile guard location

---
 src/solver/impls/cvode/cvode.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 73fe0cd47c..9c23fca0e3 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -512,7 +512,6 @@ int CvodeSolver::init() {
           != CVLS_SUCCESS) {
         throw BoutException("CVBBDPrecInit failed\n");
       }
-#endif
     }
 
     /// Set Jacobian-vector multiplication function
@@ -1039,3 +1038,4 @@ void CvodeSolver::resetInternalFields() {
     throw BoutException("CVodeReInit failed\n");
   }
 }
+#endif

From 2ca57216b76473a9f3cfbc49beeef1532567f1b7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 29 May 2026 19:35:20 -0700
Subject: [PATCH 1285/1827] cvode: Version guards around CVode calls

`CVodeSetLSetupFrequency` and `CVodeSetJacEvalFrequency` are not
available in Sundials version 4.1.0 on CI.
---
 src/solver/impls/cvode/cvode.cxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 9c23fca0e3..92533b1896 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -354,9 +354,11 @@ int CvodeSolver::init() {
     throw BoutException("CVodeSetMaxNonlinIters failed\n");
   }
 
+#if SUNDIALS_VERSION_MAJOR >= 6
   if (CVodeSetLSetupFrequency(cvode_mem, lsetup_frequency) != CV_SUCCESS) {
     throw BoutException("CVodeSetLSetupFrequency failed\n");
   }
+#endif
 
   if (apply_positivity_constraints) {
     auto f2d_constraints = create_constraints(f2d);
@@ -433,9 +435,11 @@ int CvodeSolver::init() {
       throw BoutException("CVodeSetLinearSolver failed\n");
     }
 
+#if SUNDIALS_VERSION_MAJOR >= 6
     if (CVodeSetJacEvalFrequency(cvode_mem, jac_eval_frequency) != CVLS_SUCCESS) {
       throw BoutException("CVodeSetJacEvalFrequency failed\n");
     }
+#endif
 
     if (selected_precon == CvodePreconMethod::none) {
       output_info.write("\tNo preconditioning\n");

From 5667c0555c637e7496e564f6b1b60e3c92869111 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 30 May 2026 09:49:18 -0700
Subject: [PATCH 1286/1827] cvode: Set default preconditioning to none

test-delp2 answer changes slightly (~1e-6) if preconditioning
is enabled.
---
 src/solver/impls/cvode/cvode.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 92533b1896..3a3fa02c4b 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -145,10 +145,10 @@ CvodeSolver::CvodeSolver(Options* opts)
       precon_method(
           (*options)["cvode_precon_method"]
               .doc("Preconditioner to use with CVODE Newton iteration. "
-                   "Choices: none, auto (default), user, petsc, bbd. "
+                   "Choices: none (default), auto, user, petsc, bbd. "
                    "auto prefers user (if supplied), then petsc (if available), "
                    "then bbd.")
-              .withDefault(CvodePreconMethod::Auto)),
+              .withDefault(CvodePreconMethod::none)),
       cvode_nonlinear_convergence_coef(
           (*options)["cvode_nonlinear_convergence_coef"]
               .doc("Safety factor used in the nonlinear convergence test")

From 8d734c2d69904618f37af7dc09fa823ba5c7aead Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 30 May 2026 23:30:11 -0700
Subject: [PATCH 1287/1827] cvode/snes: Initialise PetscLib early, tidying

Hermes-3 braginskii_conduction creates a "type" subsection
in every section of options. PetscLib throws an exception when
the "petsc" section contains a subsection.
---
 src/solver/impls/cvode/cvode.cxx    | 18 +++++++++++++++---
 src/solver/impls/snes/snes.cxx      |  4 +---
 src/solver/impls/snes/snes.hxx      |  2 +-
 src/solver/petsc_preconditioner.cxx |  4 +---
 4 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 3a3fa02c4b..e479a5be01 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -42,6 +42,7 @@
 #include "bout/msg_stack.hxx"
 #include "bout/options.hxx"
 #include "bout/output.hxx"
+#include "bout/region.hxx"
 #include "bout/solver.hxx"
 #include "bout/sundials_backports.hxx"
 #include "bout/unused.hxx"
@@ -168,6 +169,16 @@ CvodeSolver::CvodeSolver(Options* opts)
                    "preconditioning.\n";
   }
 
+#if BOUT_HAS_PETSC
+  // This is a temporary fix to initialise PetscLib early, working
+  // around a bug in Hermes-3 braginskii_conduction that creates a
+  // "petsc:type" subsection.
+  if (precon_method == CvodePreconMethod::petsc
+      || ((precon_method == CvodePreconMethod::Auto) && !this->hasPreconditioner())) {
+    petsc_lib = std::make_unique<PetscLib>();
+  }
+#endif
+
   // Add diagnostics to output
   // Needs to be in constructor not init() because init() is called after
   // Solver::outputVars()
@@ -228,9 +239,10 @@ int CvodeSolver::init() {
   const int local_N = getLocalN();
 
   // Get total problem size
-  int neq;
+  int neq{0};
   if (bout::globals::mpi->MPI_Allreduce(&local_N, &neq, 1, MPI_INT, MPI_SUM,
-                                        BoutComm::get())) {
+                                        BoutComm::get())
+      != 0) {
     throw BoutException("Allreduce localN -> GlobalN failed!\n");
   }
 
@@ -661,7 +673,7 @@ int CvodeSolver::run() {
 
     /// Call the monitor function
 
-    if (call_monitors(simtime, i, getNumberOutputSteps())) {
+    if (call_monitors(simtime, i, getNumberOutputSteps()) != 0) {
       // User signalled to quit
       break;
     }
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 1b8ba9f875..45e037bbd2 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -21,8 +21,6 @@
 #include <algorithm>
 #include <cmath>
 #include <cstddef>
-#include <set>
-#include <utility>
 #include <vector>
 
 #include "petscerror.h"
@@ -1274,7 +1272,7 @@ BoutReal SNESSolver::updatePseudoTimestep_inverse_residual(BoutReal previous_tim
 // Strategy based on history of residuals
 BoutReal SNESSolver::updatePseudoTimestep_history_based(BoutReal previous_timestep,
                                                         BoutReal previous_residual,
-                                                        BoutReal current_residual) {
+                                                        BoutReal current_residual) const {
   const BoutReal converged_threshold = 10 * atol;
   const BoutReal transition_threshold = 100 * atol;
 
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index b50e5c4399..dc05e77e1c 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -185,7 +185,7 @@ private:
                                                  BoutReal current_residual);
   BoutReal updatePseudoTimestep_history_based(BoutReal previous_timestep,
                                               BoutReal previous_residual,
-                                              BoutReal current_residual);
+                                              BoutReal current_residual) const;
 
   Field3D pseudo_timestep;
 
diff --git a/src/solver/petsc_preconditioner.cxx b/src/solver/petsc_preconditioner.cxx
index 8c19cfc9f0..21ebae67e7 100644
--- a/src/solver/petsc_preconditioner.cxx
+++ b/src/solver/petsc_preconditioner.cxx
@@ -5,17 +5,15 @@
 #include "bout/petsc_preconditioner.hxx"
 
 #include "bout/assert.hxx"
-#include "bout/bout_types.hxx"
-#include "bout/boutcomm.hxx"
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
 #include "bout/options.hxx"
 #include "bout/output.hxx"
+#include "bout/utils.hxx"
 
 #include <algorithm>
 #include <cmath>
-#include <cstddef>
 #include <set>
 #include <utility>
 #include <vector>

From 928f37e92b7caf20f65e858db1a7ed09a6195889 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sun, 31 May 2026 14:09:41 -0700
Subject: [PATCH 1288/1827] cvode/snes: Minor tidying, update manual

---
 manual/sphinx/user_docs/time_integration.rst | 4 ++--
 src/solver/impls/cvode/cvode.cxx             | 1 +
 src/solver/impls/petsc/petsc.cxx             | 5 -----
 src/solver/impls/snes/snes.hxx               | 2 +-
 src/solver/petsc_preconditioner.cxx          | 3 ++-
 5 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index a12d37d303..8dd16f9c7b 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -146,9 +146,9 @@ See :ref:`sec-preconditioning`.
 
 CVODE preconditioning is controlled using ``solver:cvode_precon_method``:
 
-- ``auto`` (default): Prefer a user-supplied preconditioner if provided, then PETSc
+- ``none`` (default): Disable preconditioning.
+- ``auto``: Prefer a user-supplied preconditioner if provided, then PETSc
   coloring if PETSc is available, otherwise use BBD.
-- ``none``: Disable preconditioning.
 - ``user``: Require a user-supplied preconditioner.
 - ``petsc``: Require PETSc and use PETSc coloring.
 - ``bbd``: Force the built-in BBD preconditioner.
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index e479a5be01..ac049265b7 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -42,6 +42,7 @@
 #include "bout/msg_stack.hxx"
 #include "bout/options.hxx"
 #include "bout/output.hxx"
+#include "bout/petsclib.hxx"
 #include "bout/region.hxx"
 #include "bout/solver.hxx"
 #include "bout/sundials_backports.hxx"
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 3ed113fdc5..b48ea46b58 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -29,11 +29,6 @@
 
 #include "petsc.hxx"
 
-#include <algorithm>
-#include <cmath>
-#include <utility>
-#include <vector>
-
 #include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index dc05e77e1c..ddb447e865 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -106,7 +106,7 @@ public:
   /// and update the internal RHS scaling factors
   /// This is called by SNESComputeJacobianScaledColor with the
   /// finite difference approximated Jacobian.
-  PetscErrorCode scaleJacobian(Mat B);
+  PetscErrorCode scaleJacobian(Mat Jac_new);
 
   /// Save diagnostics to output
   void outputVars(Options& output_options, bool save_repeat = true) override;
diff --git a/src/solver/petsc_preconditioner.cxx b/src/solver/petsc_preconditioner.cxx
index 21ebae67e7..433d63f5ad 100644
--- a/src/solver/petsc_preconditioner.cxx
+++ b/src/solver/petsc_preconditioner.cxx
@@ -91,7 +91,8 @@ PetscErrorCode PetscPreconditioner::createJacobianPattern(Field3D& index,
   PetscCall(MatSetFromOptions(Jfd));
 
   // Determine which row/columns of the matrix are locally owned
-  int Istart = 0, Iend = 0;
+  int Istart = 0;
+  int Iend = 0;
   PetscCall(MatGetOwnershipRange(Jfd, &Istart, &Iend));
 
   // Convert local into global indices

From c7c60be8906e390749720e8eef8297e49f1cf416 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 10:48:15 +0200
Subject: [PATCH 1289/1827] Do not shadow template parameter

---
 include/bout/boundary_region_iter.hxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index ef3cd69c88..03f43537d1 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -558,14 +558,14 @@ public:
   BoundaryRegionIterFCI& operator*() { return *this; }
 };
 
-template <bool isX>
+template <bool isXtemp>
 class BoundaryRegionXY : public BoundaryRegionBase {
 public:
   BoundaryRegionXY(const std::string& name, int dir, Mesh* mesh, Region<Ind3D>&& rgn)
       : BoundaryRegionBase(name, mesh), _dir(dir),
-        valid(isX ? mesh->xstart : mesh->ystart) {
+        valid(isXtemp ? mesh->xstart : mesh->ystart) {
     BOUT_FOR_SERIAL(i, rgn) { this->rgn.emplace_back(i); }
-    if (isX) {
+    if constexpr (isXtemp) {
       this->isX = true;
       location = dir == 1 ? BNDRY_XOUT : BNDRY_XIN;
     } else {

From 9d9a856136d80f22b7087bf6f8909dd76031cabd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 10:48:37 +0200
Subject: [PATCH 1290/1827] Ensure at compile time clone is implemented

---
 include/bout/boundary_op.hxx | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/include/bout/boundary_op.hxx b/include/bout/boundary_op.hxx
index 1a9aa1ad68..b91282cf74 100644
--- a/include/bout/boundary_op.hxx
+++ b/include/bout/boundary_op.hxx
@@ -55,9 +55,7 @@ public:
 
   // Note: All methods must implement clone, except for modifiers (see below)
   virtual BoundaryOp* clone(BoundaryRegion* UNUSED(region),
-                            const std::list<std::string>& UNUSED(args)) {
-    throw BoutException("BoundaryOp::clone not implemented");
-  }
+                            const std::list<std::string>& UNUSED(args)) = 0;
 
   /// Clone using positional args and keywords
   /// If not implemented, check if keywords are passed, then call two-argument version
@@ -88,6 +86,10 @@ public:
   BoundaryModifier() = default;
   BoundaryModifier(BoundaryOp* operation) : BoundaryOp(operation->bndry), op(operation) {}
   virtual BoundaryOp* cloneMod(BoundaryOp* op, const std::list<std::string>& args) = 0;
+  virtual BoundaryOp* clone(BoundaryRegion* UNUSED(region),
+                            const std::list<std::string>& UNUSED(args)) {
+    throw BoutException("This must not be used!");
+  }
 
 protected:
   BoundaryOp* op{nullptr};

From 26a9a4c7feb9c2fddb0c8718566476e9e432ce74 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 10:52:45 +0200
Subject: [PATCH 1291/1827] Fix y locations

---
 include/bout/boundary_region_iter.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 03f43537d1..2ca7197e2e 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -570,7 +570,7 @@ public:
       location = dir == 1 ? BNDRY_XOUT : BNDRY_XIN;
     } else {
       this->isY = true;
-      location = dir == 1 ? BNDRY_YUP : BNDRY_YDOWN;
+      location = dir == 1 ? BNDRY_YDOWN : BNDRY_YUP;
     }
   }
   int dir() { return _dir; }

From 04b7bc36701a80cdd852315e22e13026139f3b01 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 10:49:01 +0200
Subject: [PATCH 1292/1827] Ensure legacy region matches new region

---
 src/mesh/boundary_region.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx
index 4fdf9ed657..aab7168806 100644
--- a/src/mesh/boundary_region.cxx
+++ b/src/mesh/boundary_region.cxx
@@ -12,6 +12,9 @@ BoundaryRegion* BoundaryRegionBase::getLegacyPointer() {
   if (legacy == nullptr) {
     throw BoutException("Legacy region not supported");
   }
+  ASSERT3(legacy->location == location);
+  ASSERT3(legacy->label == label);
+  ASSERT3(legacy->localmesh == localmesh);
   return legacy;
 }
 BoundaryRegionBase::~BoundaryRegionBase() { delete legacy; };

From 86bdab4cabc499a0b466448a1df03ca2720e4690 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 10:56:01 +0200
Subject: [PATCH 1293/1827] Speedup diffusion MMS test

---
 tests/MMS/diffusion/data/BOUT.inp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/MMS/diffusion/data/BOUT.inp b/tests/MMS/diffusion/data/BOUT.inp
index 25ec5adfd1..e735eee536 100644
--- a/tests/MMS/diffusion/data/BOUT.inp
+++ b/tests/MMS/diffusion/data/BOUT.inp
@@ -5,7 +5,7 @@ ZMIN = 0.0
 ZMAX = 0.15915494309189535# dz = 2*pi(zmax-zmin)/(mz-1)in fraction of 2 \pi:  2*pi*1.59 = 1
 
 #number of guard cells
-MYG = 1  #noy comm for now
+MYG = 0  #noy comm for now
 MXG = 1
 
 [mesh]

From 8b4aa1c83c66279cfc6f67d2b25790adbadc9be9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 11:16:42 +0200
Subject: [PATCH 1294/1827] Implement clone

---
 tests/unit/mesh/test_boundary_factory.cxx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/unit/mesh/test_boundary_factory.cxx b/tests/unit/mesh/test_boundary_factory.cxx
index a36b7da9d9..fd0100b755 100644
--- a/tests/unit/mesh/test_boundary_factory.cxx
+++ b/tests/unit/mesh/test_boundary_factory.cxx
@@ -18,6 +18,12 @@ class TestBoundary : public BoundaryOp {
     testboundary->keywords = keywords;
     return testboundary;
   }
+  BoundaryOp* clone(BoundaryRegion* UNUSED(region),
+                    const std::list<std::string>& args) override {
+    auto* testboundary = new TestBoundary();
+    testboundary->args = args;
+    return testboundary;
+  }
   std::list<std::string> args;
   std::map<std::string, std::string> keywords;
 

From 6806b9de885f4ab5c86387bcd67e09e4933fd6cc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 11:17:12 +0200
Subject: [PATCH 1295/1827] delete default constructor

---
 include/bout/boundary_region_iter.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 2ca7197e2e..f329fee7e2 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -561,6 +561,7 @@ public:
 template <bool isXtemp>
 class BoundaryRegionXY : public BoundaryRegionBase {
 public:
+  BoundaryRegionXY() = delete;
   BoundaryRegionXY(const std::string& name, int dir, Mesh* mesh, Region<Ind3D>&& rgn)
       : BoundaryRegionBase(name, mesh), _dir(dir),
         valid(isXtemp ? mesh->xstart : mesh->ystart) {

From 657f88c41982b94cd4cbebed1ae28ed4619c8708 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 12:07:15 +0200
Subject: [PATCH 1296/1827] prefer override

---
 include/bout/boundary_op.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_op.hxx b/include/bout/boundary_op.hxx
index b91282cf74..e4d2c459bf 100644
--- a/include/bout/boundary_op.hxx
+++ b/include/bout/boundary_op.hxx
@@ -86,8 +86,8 @@ public:
   BoundaryModifier() = default;
   BoundaryModifier(BoundaryOp* operation) : BoundaryOp(operation->bndry), op(operation) {}
   virtual BoundaryOp* cloneMod(BoundaryOp* op, const std::list<std::string>& args) = 0;
-  virtual BoundaryOp* clone(BoundaryRegion* UNUSED(region),
-                            const std::list<std::string>& UNUSED(args)) {
+  BoundaryOp* clone(BoundaryRegion* UNUSED(region),
+                    const std::list<std::string>& UNUSED(args)) override {
     throw BoutException("This must not be used!");
   }
 

From ad3da0725b7ce3109b941268c5aef3453ec0780e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 12:07:29 +0200
Subject: [PATCH 1297/1827] Explicitly number all enums

---
 include/bout/boundary_region.hxx | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 9ff838b7a7..739d06f11f 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -17,15 +17,15 @@ extern Mesh* mesh; ///< Global mesh
 
 /// Location of boundary
 enum class BndryLoc : std::int8_t {
-  xin,
-  xout,
-  ydown,
-  yup,
-  all,
-  par_fwd_xin, // Don't include parallel boundaries
-  par_bkwd_xin,
-  par_fwd_xout, // Don't include parallel boundaries
-  par_bkwd_xout,
+  xin = 0,
+  xout = 1,
+  ydown = 2,
+  yup = 3,
+  all = 4,
+  par_fwd_xin = 5, // Don't include parallel boundaries
+  par_bkwd_xin = 6,
+  par_fwd_xout = 7, // Don't include parallel boundaries
+  par_bkwd_xout = 8,
   invalid = -1
 };
 constexpr BndryLoc BNDRY_XIN = BndryLoc::xin;

From 38df9b1f29861b2d09b8ee2b58106ed54074824c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 12:07:57 +0200
Subject: [PATCH 1298/1827] Do not use else after return

---
 src/mesh/boundary_factory.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index ec100e89eb..5596456898 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -204,7 +204,8 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
     if (region->isX) {
       return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionX*>(region), arglist,
                         keywords);
-    } else if (region->isY) {
+    }
+    if (region->isY) {
       return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionY*>(region), arglist,
                         keywords);
     }

From 4a4ce5c48b3087980ba6ddc67fe2f6ed98de38e7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 12:08:08 +0200
Subject: [PATCH 1299/1827] Add missing headers

---
 src/mesh/boundary_factory.cxx | 1 +
 src/mesh/boundary_region.cxx  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index 5596456898..988fcfce9b 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -1,3 +1,4 @@
+#include "bout/assert.hxx"
 #include "bout/parallel_boundary_op.hxx"
 #include "bout/parallel_boundary_region.hxx"
 #include <bout/boundary_factory.hxx>
diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx
index aab7168806..2dc64fc88f 100644
--- a/src/mesh/boundary_region.cxx
+++ b/src/mesh/boundary_region.cxx
@@ -1,4 +1,5 @@
 
+#include "bout/assert.hxx"
 #include "bout/boutexception.hxx"
 #include <bout/boundary_region.hxx>
 #include <bout/globals.hxx>

From 02e2df0aaed90e67b5283e9c927c9804e968804e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 12:09:59 +0200
Subject: [PATCH 1300/1827] fix fac to be of type double

---
 include/bout/boundary_region_iter.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index f329fee7e2..7bc86926fc 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -351,7 +351,7 @@ public:
   }
 
   void set_free(Field3D& f, BoundaryFreeExtrapolation mode) const {
-    int fac;
+    BoutReal fac = BoutNaN;
     if (valid() > 0) {
       fac = limitFreeScale(prev(f), current(f), mode);
     } else {

From 04a07ff4286f3f38e7c2d7ac9d0bd68f95a1d749 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 1 Jun 2026 12:10:46 +0200
Subject: [PATCH 1301/1827] Remove FCI asserts for FA code

---
 include/bout/boundary_region_iter.hxx | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 7bc86926fc..d871fe6be7 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -601,7 +601,6 @@ public:
   int dir() const { return region->_dir; }
   template <bool check = true>
   BoutReal& _getAt(Field3D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
@@ -614,7 +613,6 @@ public:
   }
   template <bool check = true>
   const BoutReal& _getAt(const Field3D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
@@ -627,7 +625,6 @@ public:
   }
   template <bool check = true>
   BoutReal& _getAt(Field2D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
@@ -640,7 +637,6 @@ public:
   }
   template <bool check = true>
   const BoutReal& _getAt(const Field2D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }

From 3d9b5fd77ae5e2fffcec30fcaada77f9184210de Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 1 Jun 2026 14:51:33 -0700
Subject: [PATCH 1302/1827] petsc_operators: wip debugging CI failures

Test passes locally, fails in CI.

One error occurs when allocating:
```
  	Option total_cells = 4828 (grid.fci.nc)
  	Option backward_cell_number = Tensor<BoutReal> (grid.fci.nc)
  	Option  backward_cell_number = Tensor<BoutReal> (grid.fci.nc)
  	Option forward_cell_number = Tensor<BoutReal> (grid.fci.nc)
  	Option  forward_cell_number = Tensor<BoutReal> (grid.fci.nc)
  	Option cell_number = Tensor<BoutReal> (grid.fci.nc)
  	Option  cell_number = Tensor<BoutReal> (grid.fci.nc)

  STDERR:
  terminate called after throwing an instance of 'std::bad_array_new_length'
    what():  std::bad_array_new_length
  [runnervm3jyl0:12838] *** Process received signal ***
  [runnervm3jyl0:12838] Signal: Aborted (6)
  [runnervm3jyl0:12838] Signal code:  (-6)
  malloc(): invalid size (unsorted)
```

A second error is due to missing `netCDF4` library
```
 FAILED test_petsc_operators.py::test_petsc_operators - ImportError:
 DataFile: No supported NetCDF modules available -- requires netCDF4
```

but netCDF4 seems to be installed:
```
Successfully installed boutdata-0.4.0 certifi-2026.5.20 cftime-1.6.5 contourpy-1.3.3 cycler-0.12.1 fonttools-4.63.0 fortranformat-2.0.3 freeqdsk-0.5.2 kiwisolver-1.5.0 matplotlib-3.10.9 mpmath-1.3.0 natsort-8.4.0 netCDF4-1.7.4 numpy-2.4.6 packaging-26.2 pillow-12.2.0 pyparsing-3.3.2 python-dateutil-2.9.0.post0 scipy-1.17.1 shapely-2.1.2 six-1.17.0 sympy-1.14.0 zoidberg-0.3.1.dev3+gfc5e428
```
---
 include/bout/utils.hxx                        | 30 +++++++++----------
 .../test_petsc_operators.py                   |  2 +-
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 5088a025c1..b2d822475c 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -8,7 +8,7 @@
  * Copyright 2010 - 2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -313,9 +313,9 @@ public:
   Tensor(Tensor&&) noexcept = default;
   Tensor& operator=(Tensor&&) noexcept = default;
   Tensor(size_type n1, size_type n2, size_type n3) : n1(n1), n2(n2), n3(n3) {
-    ASSERT2(n1 >= 0);
-    ASSERT2(n2 >= 0);
-    ASSERT2(n3 >= 0);
+    ASSERT0(n1 >= 0);
+    ASSERT0(n2 >= 0);
+    ASSERT0(n3 >= 0);
     data.reallocate(n1 * n2 * n3);
   }
   Tensor(const Tensor& other)
@@ -329,9 +329,9 @@ public:
   ///
   /// Note that this invalidates the existing data!
   void reallocate(size_type new_size_1, size_type new_size_2, size_type new_size_3) {
-    ASSERT2(new_size_1 >= 0);
-    ASSERT2(new_size_2 >= 0);
-    ASSERT2(new_size_3 >= 0);
+    ASSERT0(new_size_1 >= 0);
+    ASSERT0(new_size_2 >= 0);
+    ASSERT0(new_size_3 >= 0);
 
     n1 = new_size_1;
     n2 = new_size_2;
@@ -484,7 +484,7 @@ inline bool is_pow2(int x) { return x && !((x - 1) & x); }
 
 /*!
  * Return the sign of a number \p a
- * by testing if a > 0 
+ * by testing if a > 0
  */
 template <typename T>
 T SIGN(T a) { // Return +1 or -1 (0 -> +1)
@@ -511,7 +511,7 @@ inline void checkData(BoutReal f) {
 }
 #else
 /// Ignored with disabled CHECK; Throw an exception if \p f is not finite
-inline void checkData(BoutReal UNUSED(f)){};
+inline void checkData(BoutReal UNUSED(f)) {};
 #endif
 
 /*!
@@ -587,7 +587,7 @@ BoutReal stringToReal(const std::string& s);
 
 /*!
  * Convert a string to an int
- * 
+ *
  * Throws BoutException if can't be done
  */
 int stringToInt(const std::string& s);
@@ -604,7 +604,7 @@ std::list<std::string>& strsplit(const std::string& s, char delim,
 
 /*!
  * Split a string on a given delimiter
- * 
+ *
  * @param[in] s     The string to split (not modified by call)
  * @param[in] delim The delimiter to split on (single char)
  */
@@ -612,7 +612,7 @@ std::list<std::string> strsplit(const std::string& s, char delim);
 
 /*!
  * Strips leading and trailing spaces from a string
- * 
+ *
  * @param[in] s   The string to trim (not modified)
  * @param[in] c   Collection of characters to remove
  */
@@ -620,7 +620,7 @@ std::string trim(const std::string& s, const std::string& c = " \t\r");
 
 /*!
  * Strips leading spaces from a string
- * 
+ *
  * @param[in] s   The string to trim (not modified)
  * @param[in] c   Collection of characters to remove
  */
@@ -628,7 +628,7 @@ std::string trimLeft(const std::string& s, const std::string& c = " \t");
 
 /*!
  * Strips leading spaces from a string
- * 
+ *
  * @param[in] s   The string to trim (not modified)
  * @param[in] c   Collection of characters to remove
  */
@@ -636,7 +636,7 @@ std::string trimRight(const std::string& s, const std::string& c = " \t\r");
 
 /*!
  * Strips the comments from a string
- * 
+ *
  * @param[in] s   The string to trim (not modified)
  * @param[in] c   Collection of characters to remove
  */
diff --git a/tests/integrated/test-petsc-operators/test_petsc_operators.py b/tests/integrated/test-petsc-operators/test_petsc_operators.py
index 9ece74b9a0..01bae1a541 100644
--- a/tests/integrated/test-petsc-operators/test_petsc_operators.py
+++ b/tests/integrated/test-petsc-operators/test_petsc_operators.py
@@ -6,10 +6,10 @@
 import warnings
 
 from boututils.run_wrapper import build_and_log, launch_safe
+from boutdata import collect
 
 
 def analyse_path(path, plot=False, tol=1e-12):
-    from boutdata import collect
 
     forward_op = collect("forward_op", path=path)
     forward = collect("forward", path=path)

From 1b64f348e9503a4258d7d67960b686cdedc7b8a7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 1 Jun 2026 15:31:36 -0700
Subject: [PATCH 1303/1827] petsc-operators: Use python -m pytest

Attempting to resolve netCDF4 issue
---
 tests/integrated/test-petsc-operators/runtest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-petsc-operators/runtest b/tests/integrated/test-petsc-operators/runtest
index 9b28e48157..12d6e07fc8 100755
--- a/tests/integrated/test-petsc-operators/runtest
+++ b/tests/integrated/test-petsc-operators/runtest
@@ -2,4 +2,4 @@
 #
 # requires: petsc
 
-pytest .
+python -m pytest .

From 5886820ea3cc2d110ee5f366c87aaf3220ff79f0 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 1 Jun 2026 16:04:08 -0700
Subject: [PATCH 1304/1827] petsc-operators: More pytest issues

---
 requirements.txt                              | 1 +
 tests/integrated/test-petsc-operators/runtest | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 078eecac6d..d18a2808d7 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,3 +6,4 @@ matplotlib>=3.7.0
 Cython>=3.0.0
 boutdata>=0.3.0
 zoidberg>=0.2.2
+pytest
diff --git a/tests/integrated/test-petsc-operators/runtest b/tests/integrated/test-petsc-operators/runtest
index 12d6e07fc8..63d8b931e3 100755
--- a/tests/integrated/test-petsc-operators/runtest
+++ b/tests/integrated/test-petsc-operators/runtest
@@ -2,4 +2,4 @@
 #
 # requires: petsc
 
-python -m pytest .
+python3 -m pytest .

From 045eac40f3e09497f7e31f9d6e932386f1ea942f Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 1 Jun 2026 17:06:09 -0700
Subject: [PATCH 1305/1827] github: Add debug flags to 3D tests

Trying to get stack trace on allocation failure.
---
 .github/workflows/tests.yml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 02f018b873..e6506b4c26 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -42,7 +42,9 @@ jobs:
         config:
           - name: "PETSc unreleased, ADIOS2, 3D metrics"
             os: ubuntu-24.04
-            cmake_options: "-DBUILD_SHARED_LIBS=ON
+            cmake_options: "-DCHECK=2
+                            -DCMAKE_BUILD_TYPE=Debug
+                            -DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
                             -DBOUT_ENABLE_OPENMP=ON
                             -DBOUT_USE_PETSC=ON
@@ -109,7 +111,9 @@ jobs:
 
           - name: "Shared, OpenMP, 3D metrics"
             os: ubuntu-latest
-            cmake_options: "-DBUILD_SHARED_LIBS=ON
+            cmake_options: "-DCHECK=2
+                            -DCMAKE_BUILD_TYPE=Debug
+                            -DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
                             -DBOUT_ENABLE_OPENMP=ON
                             -DBOUT_USE_PETSC=ON
@@ -187,7 +191,7 @@ jobs:
         run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh ${{ matrix.config.build_petsc_branch }}
 
       - name: Build ADIOS2
-        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh 
+        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh
 
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}

From 9092b6ed9a000102ded18047f4afd91e7162a89d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 1 Jun 2026 18:27:32 -0700
Subject: [PATCH 1306/1827] test-petsc-operators: clean up before BoutFinalise

Enclose PetscOperators in a scope that ends before BoutFinalise
is called, so that the last PetscLib destructor is called before
MPI_Finalize.
---
 .../test_petsc_operators.cxx                  | 62 ++++++++++---------
 1 file changed, 32 insertions(+), 30 deletions(-)

diff --git a/tests/integrated/test-petsc-operators/test_petsc_operators.cxx b/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
index 3366622ff0..31a17aa5d5 100644
--- a/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
+++ b/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
@@ -10,51 +10,53 @@
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
-  const PetscOperators ops(bout::globals::mesh);
+  {
+    const PetscOperators ops(bout::globals::mesh);
 
-  // Parallel operators
-  const auto parallel = ops.getParallel();
+    // Parallel operators
+    const auto parallel = ops.getParallel();
 
-  // Test field
-  Field3D f = FieldFactory::get()->create3D("sin(y) + cos(z)");
-  bout::globals::mesh->communicate(f);
-  f.applyParallelBoundary("parallel_dirichlet_o2");
+    // Test field
+    Field3D f = FieldFactory::get()->create3D("sin(y) + cos(z)");
+    bout::globals::mesh->communicate(f);
+    f.applyParallelBoundary("parallel_dirichlet_o2");
 
-  Field3D f_neumann = FieldFactory::get()->create3D("sin(y) + cos(z)");
-  bout::globals::mesh->communicate(f_neumann);
-  f_neumann.applyParallelBoundary("parallel_neumann_o1");
+    Field3D f_neumann = FieldFactory::get()->create3D("sin(y) + cos(z)");
+    bout::globals::mesh->communicate(f_neumann);
+    f_neumann.applyParallelBoundary("parallel_neumann_o1");
 
-  auto forward_op = parallel.Restrict_minus * parallel.Forward;
+    auto forward_op = parallel.Restrict_minus * parallel.Forward;
 
-  Options dump;
-  dump["f"] = f;
-  dump["dV"] = parallel.dV;
+    Options dump;
+    dump["f"] = f;
+    dump["dV"] = parallel.dV;
 
-  // Test1 : (parallel.Restrict_minus * parallel.Inject_plus) is the identity in the interior (not X boundaries)
+    // Test1 : (parallel.Restrict_minus * parallel.Inject_plus) is the identity in the interior (not X boundaries)
 
-  dump["grad_par_op"] = parallel.Grad_par(f);
-  Field3D forward{0.0};
-  BOUT_FOR(i, forward.getRegion("RGN_NOBNDRY")) { forward[i] = f.yup()[i.yp()]; }
+    dump["grad_par_op"] = parallel.Grad_par(f);
+    Field3D forward{0.0};
+    BOUT_FOR(i, forward.getRegion("RGN_NOBNDRY")) { forward[i] = f.yup()[i.yp()]; }
 
-  dump["forward"] = forward;
+    dump["forward"] = forward;
 
-  dump["forward_op"] = forward_op(f);
+    dump["forward_op"] = forward_op(f);
 
-  dump["grad_par_yud"] = Grad_par(f);
+    dump["grad_par_yud"] = Grad_par(f);
 
-  // Test2 : Sum of dV * Div_par over domain is zero
+    // Test2 : Sum of dV * Div_par over domain is zero
 
-  dump["div_par_op"] = parallel.Div_par(f);
+    dump["div_par_op"] = parallel.Div_par(f);
 
-  auto* coords = bout::globals::mesh->getCoordinates();
-  bout::globals::mesh->communicate(coords->Bxy);
-  coords->Bxy.applyParallelBoundary("parallel_neumann_o1");
-  dump["div_par_yud"] = Div_par(f);
+    auto* coords = bout::globals::mesh->getCoordinates();
+    bout::globals::mesh->communicate(coords->Bxy);
+    coords->Bxy.applyParallelBoundary("parallel_neumann_o1");
+    dump["div_par_yud"] = Div_par(f);
 
-  dump["div_par_grad_par_op"] = parallel.Div_par_Grad_par(f_neumann);
-  dump["div_par_grad_par_yud"] = Div_par_K_Grad_par(1.0, f_neumann);
+    dump["div_par_grad_par_op"] = parallel.Div_par_Grad_par(f_neumann);
+    dump["div_par_grad_par_yud"] = Div_par_K_Grad_par(1.0, f_neumann);
 
-  bout::writeDefaultOutputFile(dump);
+    bout::writeDefaultOutputFile(dump);
+  }
 
   BoutFinalise();
   return 0;

From 87845eacf8efccbaa7bd4f05826da18f3d5d47b8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Jun 2026 07:28:52 +0200
Subject: [PATCH 1307/1827] Fix sign error for extrapolation into sheath

---
 include/bout/boundary_region_iter.hxx | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index d871fe6be7..c90719815d 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -274,7 +274,7 @@ public:
   /// Apply a dirichlet boundary condition
   void dirichlet_o1(Field3D& f, BoutReal value) const {
     for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, i) = value;
+      getAt(f, -i) = value;
     }
   }
 
@@ -284,7 +284,7 @@ public:
       return dirichlet_o1(f, value);
     }
     for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, i) = parallel_stencil::dirichlet_o2(
+      getAt(f, -i) = parallel_stencil::dirichlet_o2(
           i + 1, current(f), i + 1 - length(f.getLocation()), value);
     }
   }
@@ -297,12 +297,12 @@ public:
     }
     if (length(f.getLocation()) < small_value) {
       for (int i = 0; i < boundary_width(); ++i) {
-        getAt(f, i) = parallel_stencil::dirichlet_o2(
+        getAt(f, -i) = parallel_stencil::dirichlet_o2(
             i + 2, prev(f), i + 1 - length(f.getLocation()), value);
       }
     } else {
       for (int i = 0; i < boundary_width(); ++i) {
-        getAt(f, i) = parallel_stencil::dirichlet_o3(
+        getAt(f, -i) = parallel_stencil::dirichlet_o3(
             i + 2, prev(f), i + 1, current(f), i + 1 - length(f.getLocation()), value);
       }
     }
@@ -311,8 +311,8 @@ public:
   /// Ensure the value in the boundary is at least `value`
   void limit_at_least(Field3D& f, BoutReal value) const {
     for (int i = 0; i < boundary_width(); ++i) {
-      if (getAt(f, i) < value) {
-        getAt(f, i) = value;
+      if (getAt(f, -i) < value) {
+        getAt(f, -i) = value;
       }
     }
   }
@@ -323,7 +323,7 @@ public:
   // But in general we do not, and thus for normal C2 stencils, this is 1st order.
   void neumann_o1(Field3D& f, BoutReal value) const {
     for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, i) = current(f) + value * (i + 1);
+      getAt(f, -i) = current(f) + value * (i + 1);
     }
   }
 
@@ -334,7 +334,7 @@ public:
       return neumann_o1(f, value);
     }
     for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, i) = prev(f) + (2 + i) * value;
+      getAt(f, -i) = prev(f) + (2 + i) * value;
     }
   }
 
@@ -345,8 +345,8 @@ public:
       return neumann_o2(f, value);
     }
     for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, i) = parallel_stencil::neumann_o3(i + 1 - length(f.getLocation()), value,
-                                                 i + 1, current(f), 2, prev(f));
+      getAt(f, -i) = parallel_stencil::neumann_o3(i + 1 - length(f.getLocation()), value,
+                                                  i + 1, current(f), 2, prev(f));
     }
   }
 
@@ -361,12 +361,12 @@ public:
     if (mode == BoundaryFreeExtrapolation::linear) {
       for (int i = 0; i < boundary_width(); ++i) {
         val += fac;
-        getAt(f, i) = val;
+        getAt(f, -i) = val;
       }
     } else {
       for (int i = 0; i < boundary_width(); ++i) {
         val *= fac;
-        getAt(f, i) = val;
+        getAt(f, -i) = val;
       }
     }
   }

From 13cccd91ba3cb9e1a2567640d43fe90b8c7837d2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Jun 2026 07:29:07 +0200
Subject: [PATCH 1308/1827] Simplify offset calculation

---
 include/bout/boundary_region_iter.hxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index c90719815d..f91fa055fa 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -604,7 +604,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() - off * region->_dir;
+    auto _off = (1 - off) * region->_dir;
     if constexpr (isX) {
       return f[_ind().xp(_off)];
     } else {
@@ -616,7 +616,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() - off * region->_dir;
+    auto _off = (1 - off) * region->_dir;
     if constexpr (isX) {
       return f[_ind().xp(_off)];
     } else {
@@ -628,7 +628,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() - off * region->_dir;
+    auto _off = (1 - off) * region->_dir;
     if constexpr (isX) {
       return f[_ind().xp(_off)];
     } else {
@@ -640,7 +640,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() - off * region->_dir;
+    auto _off = (1 - off) * region->_dir;
     if constexpr (isX) {
       return f[_ind().xp(_off)];
     } else {
@@ -653,7 +653,7 @@ public:
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }
-    auto _off = _offset() + off * region->_dir;
+    auto _off = (1 - off) * region->_dir;
     if constexpr (isX) {
       return f(0, _ind().xp(_off));
     } else {

From 425b9162b1356e020cbc43ce61b9650dbe0b4267 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Jun 2026 07:29:28 +0200
Subject: [PATCH 1309/1827] Fix boundary_width for y boundaries

---
 include/bout/boundary_region_iter.hxx | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index f91fa055fa..296d1c8e53 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -663,7 +663,12 @@ public:
   signed char _offset() const { return region->_dir; }
   signed char _valid() const { return region->valid; }
   Ind3D _ind() const { return region->rgn[pos]; }
-  signed char _boundary_width() const { return region->localmesh->xstart; }
+  signed char _boundary_width() const {
+    if constexpr (isX) {
+      return region->localmesh->xstart;
+    }
+    return region->localmesh->ystart;
+  }
   BoutReal _length(CELL_LOC loc) const {
     if (loc == CELL_XLOW) {
       if (dir() == 1) {

From 14a4877a34bc69b3c24be64c9f5265c4013c4c27 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Jun 2026 07:30:39 +0200
Subject: [PATCH 1310/1827] Interpolate second order

---
 src/field/field3d.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 42ece48e7a..eec61ce078 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -482,7 +482,7 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
     if (newreg->isX) {
       bout::boundary::iter_boundary(newreg, [&](auto& point) {
         const BoutReal val = point.interpolate_boundary_o2(f3d);
-        point.dirichlet_o1(*this, val);
+        point.dirichlet_o2(*this, val);
       });
     } else if (newreg->isY) {
       // nothing to do

From 15c04265cddfcf65a0e1894ad8d89556600ebc92 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Jun 2026 07:31:53 +0200
Subject: [PATCH 1311/1827] Add option to keep old behaviour

---
 include/bout/field3d.hxx                      |  3 ++-
 src/field/field3d.cxx                         | 22 ++++++++++++++++++-
 .../invertable_operator.cxx                   |  2 +-
 3 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 7458066fb1..db24202542 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -499,7 +499,8 @@ public:
   /// on the boundary to the value on the boundary in field \p f3d.
   /// Note: does not just copy values in boundary region.
   void setBoundaryTo(const Field3D& f3d) { setBoundaryTo(f3d, true); }
-  void setBoundaryTo(const Field3D& f3d, bool copyParallelSlices);
+  void setBoundaryTo(const Field3D& f3d, bool copyParallelSlices,
+                     bool forceLegacy = false);
 
   using FieldData::applyParallelBoundary;
   void applyParallelBoundary() override;
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index eec61ce078..81402223d3 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -446,7 +446,8 @@ void Field3D::applyTDerivBoundary() {
   }
 }
 
-void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
+void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices,
+                            bool forceLegacy) {
 
   checkData(f3d);
 
@@ -484,6 +485,25 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices) {
         const BoutReal val = point.interpolate_boundary_o2(f3d);
         point.dirichlet_o2(*this, val);
       });
+      if (forceLegacy) {
+        // get the old, potentially wrong behaviour
+        auto* reg = newreg->getLegacyPointer();
+        if (isFci() && reg->by != 0) {
+          continue;
+        }
+        /// Loop within each region
+        for (reg->first(); !reg->isDone(); reg->next()) {
+          for (int z = 0; z < nz; z++) {
+            // Get value half-way between cells
+            const BoutReal val =
+                0.5
+                * (f3d(reg->x, reg->y, z) + f3d(reg->x - reg->bx, reg->y - reg->by, z));
+            // Set to this value
+            (*this)(reg->x, reg->y, z) =
+                ((2. * val) - (*this)(reg->x - reg->bx, reg->y - reg->by, z));
+          }
+        }
+      }
     } else if (newreg->isY) {
       // nothing to do
     } else {
diff --git a/tests/integrated/test-invertable-operator/invertable_operator.cxx b/tests/integrated/test-invertable-operator/invertable_operator.cxx
index 9f00fad304..ed81d78b04 100644
--- a/tests/integrated/test-invertable-operator/invertable_operator.cxx
+++ b/tests/integrated/test-invertable-operator/invertable_operator.cxx
@@ -19,7 +19,7 @@ class InvertableOperatorTest : public PhysicsModel {
       Field3D result = A * input + D * Delp2(input);
 
       // Ensure boundary points are set appropriately as given by the input field.
-      result.setBoundaryTo(input);
+      result.setBoundaryTo(input, true, true);
 
       return result;
     };

From aa5b9da5f279582e9b730231645af76e8792a59f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Jun 2026 10:36:49 +0200
Subject: [PATCH 1312/1827] PETSc is not thread safe

---
 src/mesh/interpolation/hermite_spline_xz.cxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/mesh/interpolation/hermite_spline_xz.cxx b/src/mesh/interpolation/hermite_spline_xz.cxx
index 0aa1f2b066..afbd336bb2 100644
--- a/src/mesh/interpolation/hermite_spline_xz.cxx
+++ b/src/mesh/interpolation/hermite_spline_xz.cxx
@@ -184,7 +184,11 @@ void XZHermiteSplineBase<monotonic, imp_type>::calcWeights(
 
   [[maybe_unused]] const int y_global_offset =
       localmesh->getYProcIndex() * (localmesh->yend - localmesh->ystart + 1);
+#if BOUT_HAS_PETSC
+  BOUT_FOR_SERIAL(i, getRegion(region)) {
+#else
   BOUT_FOR(i, getRegion(region)) {
+#endif
     const int x = i.x();
     const int y = i.y();
     const int z = i.z();

From a6f2f25d7f54e55963947475ad925d56326b5597 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 06:31:03 +0200
Subject: [PATCH 1313/1827] Add missing headers

---
 include/bout/deriv_store.hxx       | 2 ++
 include/bout/paralleltransform.hxx | 1 +
 src/field/field3d.cxx              | 1 +
 src/field/generated_fieldops.cxx   | 1 +
 src/mesh/coordinates.cxx           | 1 +
 src/mesh/parallel/fci.cxx          | 1 +
 6 files changed, 7 insertions(+)

diff --git a/include/bout/deriv_store.hxx b/include/bout/deriv_store.hxx
index 83bc34d7c8..7c08802cae 100644
--- a/include/bout/deriv_store.hxx
+++ b/include/bout/deriv_store.hxx
@@ -33,8 +33,10 @@
 #include <functional>
 #include <map>
 #include <set>
+#include <type_traits>
 #include <unordered_map>
 
+#include "bout/field3d.hxx"
 #include <bout/scorepwrapper.hxx>
 
 #include <bout/bout_types.hxx>
diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx
index 0b425de209..d9ed397bb5 100644
--- a/include/bout/paralleltransform.hxx
+++ b/include/bout/paralleltransform.hxx
@@ -9,6 +9,7 @@
 #include "bout/bout_types.hxx"
 #include "bout/dcomplex.hxx"
 #include "bout/field3d.hxx"
+#include "bout/field_data.hxx"
 #include "bout/options.hxx"
 #include "bout/unused.hxx"
 
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 2b9ebf1107..154d9291f9 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -28,6 +28,7 @@
 #include "bout/bout_types.hxx"
 #include "bout/build_defines.hxx"
 
+#include "bout/index_derivs_interface.hxx"
 #include <bout/boutcomm.hxx>
 #include <bout/globals.hxx>
 
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index f718d156fe..181c15c709 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -8,6 +8,7 @@
 #include <bout/interpolation.hxx>
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
+#include <cstddef>
 
 // Provide the C++ wrapper for multiplication of Field3D and Field3D
 Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 709ce168e1..836f0e8ce3 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -4,6 +4,7 @@
  * given the contravariant metric tensor terms
  **************************************************************************/
 
+#include "bout/field3d.hxx"
 #include "bout/field_data.hxx"
 #include <bout/assert.hxx>
 #include <bout/build_defines.hxx>
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 094d7884f9..e3aaea2bab 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -42,6 +42,7 @@
 #include "bout/boundary_region_iter.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_data.hxx"

From c44416b66311bd458281e451c1843e1bc1923bef Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 06:31:12 +0200
Subject: [PATCH 1314/1827] prefer const ref

---
 src/mesh/parallel/fci.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index e3aaea2bab..0b4ea5f6d1 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -69,7 +69,7 @@ using bout::boundary::BoundaryRegionFCI;
 
 namespace {
 // Get a unique name for a field based on the sign/magnitude of the offset
-std::string parallel_slice_field_name(std::string field, int offset) {
+std::string parallel_slice_field_name(const std::string& field, int offset) {
   const std::string direction = (offset > 0) ? "forward" : "backward";
   // We only have a suffix for parallel slices beyond the first
   // This is for backwards compatibility

From e191ce73e786537c5dd1448c9a214d627b93b235 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 07:21:08 +0200
Subject: [PATCH 1315/1827] better-metric branch has been released as version
 0.3.0 of zoidberg

---
 .ci_fedora.sh               | 2 +-
 .github/workflows/tests.yml | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 27a28df468..c865e8a0aa 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -48,7 +48,7 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     cd
     cd BOUT-dev
     python3 -m ensurepip
-    python3 -m pip install git+https://github.com/boutproject/zoidberg@better-metric
+    python3 -m pip install -r requirements.txt
     echo "starting configure"
     time cmake -S . -B build -DBOUT_USE_PETSC=ON \
 	 -DBOUT_UPDATE_GIT_SUBMODULE=OFF \
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 8919f82df1..ff11a2a4c9 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -166,7 +166,6 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           python -m pip install -r requirements.txt
-          python -m pip install git+https://github.com/boutproject/zoidberg@better-metric
 
       - name: Cache Zenodo test data
         uses: actions/cache@v5

From 55b7957773262c3d12e68f15029c9686f14c9ae5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 07:48:51 +0200
Subject: [PATCH 1316/1827] Use released zoidberg

---
 requirements.txt                              |  2 +-
 .../test_petsc_operators.py                   | 32 ++-----------------
 2 files changed, 3 insertions(+), 31 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index d18a2808d7..2ba339d786 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,5 +5,5 @@ netcdf4>=1.7.1
 matplotlib>=3.7.0
 Cython>=3.0.0
 boutdata>=0.3.0
-zoidberg>=0.2.2
+zoidberg>=0.3.1
 pytest
diff --git a/tests/integrated/test-petsc-operators/test_petsc_operators.py b/tests/integrated/test-petsc-operators/test_petsc_operators.py
index 01bae1a541..08cee39fd6 100644
--- a/tests/integrated/test-petsc-operators/test_petsc_operators.py
+++ b/tests/integrated/test-petsc-operators/test_petsc_operators.py
@@ -1,5 +1,3 @@
-import pytest
-import venv
 import subprocess
 import sys
 import numpy as np
@@ -101,37 +99,11 @@ def plot_comparison(a, alabel, b, blabel):
         fig.savefig("diffusion.png")
 
 
-@pytest.fixture(scope="session")
-def temporary_venv(tmp_path_factory):
-    # Create a venv
-    venv_dir = tmp_path_factory.mktemp("venv")
-    venv.create(venv_dir, with_pip=True, symlinks=True)
-
-    # Determine the correct python path (platform dependent)
-    python_exe = str(
-        venv_dir / ("Scripts" if sys.platform == "win32" else "bin") / "python"
-    )
-
-    # Clone and install latest version of Zoidberg
-    zoidberg_dir = tmp_path_factory.mktemp("zoidberg")
-    subprocess.check_call(
-        [
-            "git",
-            "clone",
-            "https://github.com/boutproject/zoidberg.git",
-            str(zoidberg_dir),
-        ]
-    )
-    subprocess.check_call([python_exe, "-m", "pip", "install", str(zoidberg_dir)])
-
-    return python_exe
-
-
-def test_petsc_operators(temporary_venv):
+def test_petsc_operators():
     grid_path = "grid.fci.nc"
 
     # Generate grid file and store in temporary path
-    subprocess.check_call([temporary_venv, "rotating-ellipse.py", "-o", grid_path])
+    subprocess.check_call([sys.executable, "rotating-ellipse.py", "-o", grid_path])
 
     # Build executable
     build_and_log("test_petsc_operators")

From b7aa4fbf0fa81d957a5cf17216965b533db45d4b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:14:58 +0200
Subject: [PATCH 1317/1827] Avoid unused arguments warning for dummy function

---
 src/mesh/boundary_standard.cxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 2e079f59b3..141cab0a43 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -1727,13 +1727,13 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
   void BoundaryNeumann::apply(Field2D & f) { BoundaryNeumann::apply(f, 0.); }
 
+#if not(BOUT_USE_METRIC_3D)
   void BoundaryNeumann::apply(Field2D & f, BoutReal t) {
     // Set (at 2nd order / 3rd order) the value at the mid-point between
     // the guard cell and the grid cell to be val
     // N.B. First guard cells (closest to the grid) is 2nd order, while
     // 2nd is 3rd order
 
-#if not(BOUT_USE_METRIC_3D)
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
     Coordinates* metric = f.getCoordinates();
@@ -1930,6 +1930,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       }
     }
 #else
+
+void BoundaryNeumann::apply([[maybe_unused]] Field2D& f, [[maybe_unused]] BoutReal t) {
   throw BoutException("Applying boundary condition 'neumann' to Field2D "
                       "not compatible with 3D metrics in all cases.");
 #endif

From 1e7199a8f50c039e8a57fe97a62d36ad4ab7aac3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:20:29 +0200
Subject: [PATCH 1318/1827] std::vector::push_back is not thread safe

---
 src/mesh/petsc_operators.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 2fa2a5fb51..1c8fa7680c 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -74,7 +74,7 @@ void PetscIndexMapping::buildPermutation(PetscInt nlocal, PetscInt nglobal,
 
 Region<Ind3D> PetscCellMapping::create_region(const Field3D& cell_number) {
   Region<Ind3D>::RegionIndices indices;
-  BOUT_FOR(i, cell_number.getRegion("RGN_NOBNDRY")) {
+  BOUT_FOR_SERIAL(i, cell_number.getRegion("RGN_NOBNDRY")) {
     if (cell_number[i] >= 0) {
       indices.push_back(i);
     }
@@ -85,7 +85,7 @@ Region<Ind3D> PetscCellMapping::create_region(const Field3D& cell_number) {
 Region<Ind3D> PetscCellMapping::create_region_xin(const Field3D& cell_number) {
   Region<Ind3D>::RegionIndices indices;
   const auto& region = cell_number.getRegion("RGN_INNER_X");
-  BOUT_FOR(i, region) {
+  BOUT_FOR_SERIAL(i, region) {
     if (cell_number[i] >= 0) {
       indices.push_back(i);
     }
@@ -96,7 +96,7 @@ Region<Ind3D> PetscCellMapping::create_region_xin(const Field3D& cell_number) {
 Region<Ind3D> PetscCellMapping::create_region_xout(const Field3D& cell_number) {
   Region<Ind3D>::RegionIndices indices;
   const auto& region = cell_number.getRegion("RGN_OUTER_X");
-  BOUT_FOR(i, region) {
+  BOUT_FOR_SERIAL(i, region) {
     if (cell_number[i] >= 0) {
       indices.push_back(i);
     }

From 209f0090de41d9bc096ad6a6a2a13d2d230d147b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:22:49 +0200
Subject: [PATCH 1319/1827] Fail test if the run fails

---
 .../test-petsc-operators/test_petsc_operators.py  | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/tests/integrated/test-petsc-operators/test_petsc_operators.py b/tests/integrated/test-petsc-operators/test_petsc_operators.py
index 08cee39fd6..1ff3b4cd41 100644
--- a/tests/integrated/test-petsc-operators/test_petsc_operators.py
+++ b/tests/integrated/test-petsc-operators/test_petsc_operators.py
@@ -1,7 +1,6 @@
 import subprocess
 import sys
 import numpy as np
-import warnings
 
 from boututils.run_wrapper import build_and_log, launch_safe
 from boutdata import collect
@@ -110,14 +109,10 @@ def test_petsc_operators():
 
     nproc = 1
 
-    try:
-        s, out = launch_safe(
-            f"./test_petsc_operators -d data mesh:file={grid_path}",
-            nproc=nproc,
-            pipe=True,
-        )
-    except Exception as e:
-        # May throw after run
-        warnings.warn(f"Caught exception: {e}", RuntimeWarning)
+    _, out = launch_safe(
+        f"./test_petsc_operators -d data mesh:file={grid_path}",
+        nproc=nproc,
+        pipe=True,
+    )
 
     analyse_path("data")

From b47b90406eb6bd16be5fb90369c0224f61bc5a72 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:23:18 +0200
Subject: [PATCH 1320/1827] Allow running with default args

---
 tests/integrated/test-petsc-operators/data/BOUT.inp           | 2 +-
 tests/integrated/test-petsc-operators/test_petsc_operators.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-petsc-operators/data/BOUT.inp b/tests/integrated/test-petsc-operators/data/BOUT.inp
index 72907d3fc9..4702f9617f 100644
--- a/tests/integrated/test-petsc-operators/data/BOUT.inp
+++ b/tests/integrated/test-petsc-operators/data/BOUT.inp
@@ -1,5 +1,5 @@
 [mesh]
-file = "rotating-ellipse-20x8x20-s5.fci.nc"
+file = "grid.fci.nc"
 
 [mesh:paralleltransform]
 type = fci
diff --git a/tests/integrated/test-petsc-operators/test_petsc_operators.py b/tests/integrated/test-petsc-operators/test_petsc_operators.py
index 1ff3b4cd41..cf8da3d290 100644
--- a/tests/integrated/test-petsc-operators/test_petsc_operators.py
+++ b/tests/integrated/test-petsc-operators/test_petsc_operators.py
@@ -110,7 +110,7 @@ def test_petsc_operators():
     nproc = 1
 
     _, out = launch_safe(
-        f"./test_petsc_operators -d data mesh:file={grid_path}",
+        "./test_petsc_operators",
         nproc=nproc,
         pipe=True,
     )

From 4d07c00d047566740478f0d75aac3d6aedf1e48f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:34:49 +0200
Subject: [PATCH 1321/1827] Add missing headers

---
 src/solver/impls/petsc/petsc.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index b48ea46b58..ba6e061e55 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -24,6 +24,8 @@
  **************************************************************************/
 
 #include "bout/build_defines.hxx"
+#include "bout/field3d.hxx"
+#include "bout/petsclib.hxx"
 
 #if BOUT_HAS_PETSC
 

From fe92b56b76f0f32ba70c954493ba82d8863fbd10 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:48:13 +0200
Subject: [PATCH 1322/1827] Prefer anonymous namespace

---
 src/solver/impls/snes/snes.cxx | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 45e037bbd2..9a53aabfcb 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -68,10 +68,10 @@ PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
 
   PetscFunctionReturn(s->precon(x, y));
 }
-} // namespace
 
-static PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
-                                                 void* ctx);
+PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
+                                          void* ctx);
+} // namespace
 
 PetscErrorCode SNESSolver::FDJinitialise() {
   if (use_coloring) {
@@ -1548,6 +1548,7 @@ PetscErrorCode SNESSolver::scaleJacobian(Mat Jac_new) {
   return PETSC_SUCCESS;
 }
 
+namespace {
 ///
 /// Input Parameters:
 ///   snes - nonlinear solver object
@@ -1558,8 +1559,8 @@ PetscErrorCode SNESSolver::scaleJacobian(Mat Jac_new) {
 ///   Jac - Jacobian matrix (not altered in this routine)
 ///   Jac_new - newly computed Jacobian matrix to use with preconditioner (generally the same as
 ///   Jac)
-static PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
-                                                 void* ctx) {
+PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
+                                          void* ctx) {
   PetscErrorCode err = SNESComputeJacobianDefaultColor(snes, x1, Jac, Jac_new, ctx);
   CHKERRQ(err);
 
@@ -1576,6 +1577,7 @@ static PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat
   // Call the SNESSolver function
   return fctx->scaleJacobian(Jac_new);
 }
+} // namespace
 
 BoutReal SNESSolver::pid(BoutReal timestep, int nl_its, BoutReal max_dt) {
 

From 6491e3367afd52311c4cbeea5f5c1b9301aaabea Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:42:21 +0200
Subject: [PATCH 1323/1827] Add missing header

---
 src/solver/petsc_preconditioner.cxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/solver/petsc_preconditioner.cxx b/src/solver/petsc_preconditioner.cxx
index 433d63f5ad..508d001fd3 100644
--- a/src/solver/petsc_preconditioner.cxx
+++ b/src/solver/petsc_preconditioner.cxx
@@ -5,6 +5,7 @@
 #include "bout/petsc_preconditioner.hxx"
 
 #include "bout/assert.hxx"
+#include "bout/boutcomm.hxx"
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"

From 59934f6ef0395934a28a0e250b985e4da394e783 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:42:50 +0200
Subject: [PATCH 1324/1827] Avoid nested conditional operator

---
 src/solver/impls/cvode/cvode.cxx | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index ac049265b7..a1e4284eab 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -420,9 +420,14 @@ int CvodeSolver::init() {
       }
     }
 
-    const auto prectype = (selected_precon == CvodePreconMethod::none)
-                              ? SUN_PREC_NONE
-                              : (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT);
+    auto prectype = SUN_PREC_NONE;
+    if (selected_precon != CvodePreconMethod::none) {
+      if (rightprec) {
+        prectype = SUN_PREC_RIGHT;
+      } else {
+        prectype = SUN_PREC_LEFT;
+      }
+    }
 
     switch ((*options)["linear_solver"]
                 .doc("Set linear solver type. Default is gmres.")

From 4ea2d47827da4c601a2f16820edfcdd6ad5514d3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:56:36 +0200
Subject: [PATCH 1325/1827] Update used headers

---
 src/solver/impls/cvode/cvode.cxx | 1 +
 src/solver/impls/cvode/cvode.hxx | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index a1e4284eab..66a6b353b8 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -25,6 +25,7 @@
  **************************************************************************/
 
 #include "bout/build_defines.hxx"
+#include <cstddef>
 
 #include "cvode.hxx"
 
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index 025a3e2dcd..d1409ad9a3 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -31,6 +31,7 @@
 #include "bout/bout_enum_class.hxx"
 #include "bout/build_defines.hxx"
 #include "bout/solver.hxx"
+#include <memory>
 
 #if not BOUT_HAS_CVODE
 
@@ -41,7 +42,6 @@ RegisterUnavailableSolver
 
 #else
 
-#include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/region.hxx"
 #include "bout/sundials_backports.hxx"

From a950cfa2ec673d52273e13bad1f8938b65078836 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 08:57:23 +0200
Subject: [PATCH 1326/1827] Apply clang-tidy cleanups

---
 src/solver/impls/cvode/cvode.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 66a6b353b8..5cc5cae59a 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -521,7 +521,7 @@ int CvodeSolver::init() {
 
       const int band_width_default = std::accumulate(
           begin(f3d), end(f3d), 0, [](int a, const VarStr<Field3D>& fvar) {
-            Mesh* localmesh = fvar.var->getMesh();
+            const Mesh* localmesh = fvar.var->getMesh();
             return a + localmesh->xend - localmesh->xstart + 3;
           });
 
@@ -916,7 +916,7 @@ PetscErrorCode CvodeSolver::petscFormFunction(void* UNUSED(dummy), Vec x, Vec f,
   }
 
   for (PetscInt i = 0; i < length; ++i) {
-    fdata[i] = xdata[i] - s->petsc_gamma * s->petsc_rhs_tmp[i];
+    fdata[i] = xdata[i] - (s->petsc_gamma * s->petsc_rhs_tmp[i]);
   }
 
   PetscCall(VecRestoreArrayRead(x, &xdata));

From 0bcaf31c32abe7f203095783525c144642414683 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 3 Jun 2026 09:27:34 +0200
Subject: [PATCH 1327/1827] Remove `#if 0`'ed code

---
 src/solver/impls/petsc/petsc.cxx | 296 -------------------------------
 1 file changed, 296 deletions(-)

diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index ba6e061e55..146e8e5361 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -521,302 +521,6 @@ int PetscSolver::init() {
           index, *options, nlocal, n2Dvars(), n3Dvars(), BoutComm::get()));
       output_progress.write("Creating Jacobian coloring\n");
       updateColoring();
-
-#if 0
-      // Use matrix coloring.  This greatly reduces the number of
-      // times the rhs() function needs to be evaluated when
-      // calculating the Jacobian, by identifying which quantities may
-      // be simultaneously perturbed.
-
-      // Use global mesh for now
-      Mesh* mesh = bout::globals::mesh;
-
-      //////////////////////////////////////////////////
-      // Get the local indices by starting at 0
-      Field3D index = globalIndex(0);
-
-      //////////////////////////////////////////////////
-      // Pre-allocate PETSc storage
-
-      output_progress.write("Setting Jacobian matrix sizes\n");
-
-      const int n2d = f2d.size();
-      const int n3d = f3d.size();
-
-      // Set size of Matrix on each processor to nlocal x nlocal
-      MatCreate(BoutComm::get(), &Jfd);
-      MatSetOption(Jfd, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
-      MatSetSizes(Jfd, nlocal, nlocal, PETSC_DETERMINE, PETSC_DETERMINE);
-      MatSetFromOptions(Jfd);
-      // Determine which row/columns of the matrix are locally owned
-      int Istart, Iend;
-      MatGetOwnershipRange(Jfd, &Istart, &Iend);
-      // Convert local into global indices
-      // Note: Not in the boundary cells, to keep -1 values
-      for (const auto& i : mesh->getRegion3D("RGN_NOBNDRY")) {
-        index[i] += Istart;
-      }
-      // Now communicate to fill guard cells
-      mesh->communicate(index);
-
-      // Non-zero elements on this processor
-      std::vector<PetscInt> d_nnz;
-      std::vector<PetscInt> o_nnz;
-      auto n_square = (*options)["stencil:square"]
-                          .doc("Extent of stencil (square)")
-                          .withDefault<int>(0);
-      auto n_taxi = (*options)["stencil:taxi"]
-                        .doc("Extent of stencil (taxi-cab norm)")
-                        .withDefault<int>(0);
-      auto n_cross = (*options)["stencil:cross"]
-                         .doc("Extent of stencil (cross)")
-                         .withDefault<int>(0);
-      // Set n_taxi 2 if nothing else is set
-      // Probably a better way to do this
-      if (n_square == 0 && n_taxi == 0 && n_cross == 0) {
-        output_info.write("Setting solver:stencil:taxi = 2\n");
-        n_taxi = 2;
-      }
-
-      auto const xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
-      {
-        // This is ugly but can't think of a better and robust way to
-        // count the non-zeros for some arbitrary stencil
-        // effectively the same loop as the one that sets the non-zeros below
-        std::vector<std::set<int>> d_nnz_map2d(nlocal);
-        std::vector<std::set<int>> o_nnz_map2d(nlocal);
-        std::vector<std::set<int>> d_nnz_map3d(nlocal);
-        std::vector<std::set<int>> o_nnz_map3d(nlocal);
-        // Loop over every element in 2D to count the *unique* non-zeros
-        for (int x = mesh->xstart; x <= mesh->xend; x++) {
-          for (int y = mesh->ystart; y <= mesh->yend; y++) {
-
-            const int ind0 = ROUND(index(x, y, 0)) - Istart;
-
-            // 2D fields
-            for (int i = 0; i < n2d; i++) {
-              const PetscInt row = ind0 + i;
-              // Loop through each point in the stencil
-              for (const auto& [x_off, y_off] : xy_offsets) {
-                const int xi = x + x_off;
-                const int yi = y + y_off;
-                if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                    || (yi >= mesh->LocalNy)) {
-                  continue;
-                }
-
-                const int ind2 = ROUND(index(xi, yi, 0));
-                if (ind2 < 0) {
-                  continue; // A boundary point
-                }
-
-                // Depends on all variables on this cell
-                for (int j = 0; j < n2d; j++) {
-                  const PetscInt col = ind2 + j;
-                  if (col >= Istart && col < Iend) {
-                    d_nnz_map2d[row].insert(col);
-                  } else {
-                    o_nnz_map2d[row].insert(col);
-                  }
-                }
-              }
-            }
-            // 3D fields
-            for (int z = mesh->zstart; z <= mesh->zend; z++) {
-              const int ind = ROUND(index(x, y, z)) - Istart;
-
-              for (int i = 0; i < n3d; i++) {
-                PetscInt row = ind + i;
-                if (z == 0) {
-                  row += n2d;
-                }
-
-                // Depends on 2D fields
-                for (int j = 0; j < n2d; j++) {
-                  const PetscInt col = ind0 + j;
-                  if (col >= Istart && col < Iend) {
-                    d_nnz_map2d[row].insert(col);
-                  } else {
-                    o_nnz_map2d[row].insert(col);
-                  }
-                }
-
-                // Star pattern
-                for (const auto& [x_off, y_off] : xy_offsets) {
-                  const int xi = x + x_off;
-                  const int yi = y + y_off;
-
-                  if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                      || (yi >= mesh->LocalNy)) {
-                    continue;
-                  }
-
-                  int ind2 = ROUND(index(xi, yi, 0));
-                  if (ind2 < 0) {
-                    continue; // Boundary point
-                  }
-
-                  if (z == 0) {
-                    ind2 += n2d;
-                  }
-
-                  // 3D fields on this cell
-                  for (int j = 0; j < n3d; j++) {
-                    const PetscInt col = ind2 + j;
-                    if (col >= Istart && col < Iend) {
-                      d_nnz_map3d[row].insert(col);
-                    } else {
-                      o_nnz_map3d[row].insert(col);
-                    }
-                  }
-                }
-              }
-            }
-          }
-        }
-
-        d_nnz.reserve(nlocal);
-        d_nnz.reserve(nlocal);
-
-        for (int i = 0; i < nlocal; ++i) {
-          // Assume all elements in the z direction are potentially coupled
-          d_nnz.emplace_back((d_nnz_map3d[i].size() * mesh->LocalNz)
-                             + d_nnz_map2d[i].size());
-          o_nnz.emplace_back((o_nnz_map3d[i].size() * mesh->LocalNz)
-                             + o_nnz_map2d[i].size());
-        }
-      }
-
-      output_progress.write("Pre-allocating Jacobian\n");
-      // Pre-allocate
-      MatMPIAIJSetPreallocation(Jfd, 0, d_nnz.data(), 0, o_nnz.data());
-      MatSeqAIJSetPreallocation(Jfd, 0, d_nnz.data());
-      MatSetUp(Jfd);
-      MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
-
-      //////////////////////////////////////////////////
-      // Mark non-zero entries
-
-      output_progress.write("Marking non-zero Jacobian entries\n");
-      PetscScalar const val = 1.0;
-      for (int x = mesh->xstart; x <= mesh->xend; x++) {
-        for (int y = mesh->ystart; y <= mesh->yend; y++) {
-
-          const int ind0 = ROUND(index(x, y, 0));
-
-          // 2D fields
-          for (int i = 0; i < n2d; i++) {
-            const PetscInt row = ind0 + i;
-
-            // Loop through each point in the stencil
-            for (const auto& [x_off, y_off] : xy_offsets) {
-              const int xi = x + x_off;
-              const int yi = y + y_off;
-              if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                  || (yi >= mesh->LocalNy)) {
-                continue;
-              }
-
-              int const ind2 = ROUND(index(xi, yi, 0));
-              if (ind2 < 0) {
-                continue; // A boundary point
-              }
-
-              // Depends on all variables on this cell
-              for (int j = 0; j < n2d; j++) {
-                PetscInt const col = ind2 + j;
-                PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
-              }
-            }
-          }
-          // 3D fields
-          for (int z = mesh->zstart; z <= mesh->zend; z++) {
-            int const ind = ROUND(index(x, y, z));
-
-            for (int i = 0; i < n3d; i++) {
-              PetscInt row = ind + i;
-              if (z == 0) {
-                row += n2d;
-              }
-
-              // Depends on 2D fields
-              for (int j = 0; j < n2d; j++) {
-                PetscInt const col = ind0 + j;
-                PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
-              }
-
-              // Star pattern
-              for (const auto& [x_off, y_off] : xy_offsets) {
-                int xi = x + x_off;
-                int yi = y + y_off;
-
-                if ((xi < 0) || (yi < 0) || (xi >= mesh->LocalNx)
-                    || (yi >= mesh->LocalNy)) {
-                  continue;
-                }
-                for (int zi = mesh->zstart; zi <= mesh->zend; ++zi) {
-                  int ind2 = ROUND(index(xi, yi, zi));
-                  if (ind2 < 0) {
-                    continue; // Boundary point
-                  }
-
-                  if (z == 0) {
-                    ind2 += n2d;
-                  }
-
-                  // 3D fields on this cell
-                  for (int j = 0; j < n3d; j++) {
-                    PetscInt const col = ind2 + j;
-                    int ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
-
-                    if (ierr != 0) {
-                      output.write("ERROR: {} {} : ({}, {}) -> ({}, {}) : {} -> {}\n",
-                                   row, col, x, y, xi, yi, ind2, ind2 + n3d - 1);
-                    }
-                    CHKERRQ(ierr);
-                  }
-                }
-              }
-            }
-          }
-        }
-      }
-
-      // Finished marking non-zero entries
-
-      output_progress.write("Assembling Jacobian matrix\n");
-
-      // Assemble Matrix
-      MatAssemblyBegin(Jfd, MAT_FINAL_ASSEMBLY);
-      MatAssemblyEnd(Jfd, MAT_FINAL_ASSEMBLY);
-
-      {
-        // Test if the matrix is symmetric
-        // Values are 0 or 1 so tolerance (1e-5) shouldn't matter
-        PetscBool symmetric;
-        PetscCall(MatIsSymmetric(Jfd, 1e-5, &symmetric));
-        if (!symmetric) {
-          output_warn.write("Jacobian pattern is not symmetric\n");
-        }
-      }
-
-      // The above can miss entries around the X-point branch cut:
-      // The diagonal terms are complicated because moving in X then Y
-      // is different from moving in Y then X at the X-point.
-      // Making sure the colouring matrix is symmetric does not
-      // necessarily give the correct stencil but may help.
-      if ((*options)["force_symmetric_coloring"]
-              .doc("Modifies coloring matrix to force it to be symmetric")
-              .withDefault<bool>(false)) {
-        Mat Jfd_T;
-        MatCreateTranspose(Jfd, &Jfd_T);
-        MatAXPY(Jfd, 1, Jfd_T, DIFFERENT_NONZERO_PATTERN);
-      }
-
-      output_progress.write("Creating Jacobian coloring\n");
-      updateColoring();
-#endif
-
     } else {
       // Brute force calculation
       // There is usually no reason to use this, except as a check of

From d4caff6d2903039307aeccaec3fa5ae7bb5ba712 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 4 Jun 2026 10:23:01 -0700
Subject: [PATCH 1328/1827] petsc-operators: Include guards

---
 include/bout/petsc_operators.hxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 422480c7ef..78196b2e29 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -1,3 +1,8 @@
+#pragma once
+
+#ifndef BOUT_PETSC_OPERATORS
+#define BOUT_PETSC_OPERATORS
+
 #include "bout/build_defines.hxx"
 
 #if BOUT_HAS_PETSC
@@ -1046,3 +1051,5 @@ PetscCellOperator makeNeumannOperator(const PetscCellMappingPtr& mapping,
 #warning PETSc not available. No PetscOperators.
 
 #endif
+
+#endif // BOUT_PETSC_OPERATORS

From 7066e3f9ae144cc5ab1708abea70f2c03739951c Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 4 Jun 2026 11:12:08 -0700
Subject: [PATCH 1329/1827] field2d: Comment asField3DParallel, tidying

Add missing includes, add comment to potentially confusing
`asField3DParallel` method that returns `Field2D`.
---
 include/bout/field2d.hxx | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 025285b84a..329d636932 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -4,9 +4,9 @@
  * \brief Definition of 2D scalar field class
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -33,13 +33,17 @@ class Field2D;
 #define BOUT_FIELD2D_H
 
 #include "bout/array.hxx"
-#include "bout/build_config.hxx"
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/field.hxx"
 #include "bout/field_data.hxx"
 #include "bout/fieldperp.hxx"
 #include "bout/region.hxx"
 
 #include <cstddef>
+#include <ostream>
+#include <string>
 
 #if BOUT_HAS_RAJA
 #include "RAJA/RAJA.hpp" // using RAJA lib
@@ -206,7 +210,7 @@ public:
     }
 #endif
 
-    return data[jx * ny + jy];
+    return data[(jx * ny) + jy];
   }
   inline const BoutReal& operator()(int jx, int jy) const {
 #if CHECK > 2 && !BOUT_HAS_CUDA
@@ -220,7 +224,7 @@ public:
     }
 #endif
 
-    return data[jx * ny + jy];
+    return data[(jx * ny) + jy];
   }
 
   /*!
@@ -274,6 +278,8 @@ public:
 
   int size() const override { return nx * ny; }
 
+  /// Return a field that can be used to perform parallel (Y) derivatives.
+  /// This is used to write generic FA/FCI code.
   Field2D& asField3DParallel() { return *this; }
   const Field2D& asField3DParallel() const { return *this; }
 

From 86945d5b480cd4459c7c63c8a93dc3d74afac523 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 4 Jun 2026 11:22:39 -0700
Subject: [PATCH 1330/1827] field3d: Clang tidy suggestions

---
 include/bout/field3d.hxx | 20 ++++++++++----------
 src/field/field3d.cxx    |  4 ++--
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 457119546a..361faea2e8 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -1,7 +1,7 @@
 /**************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -33,6 +33,7 @@ class Field3D;
 #include "bout/bout_types.hxx"
 #include "bout/field.hxx"
 #include "bout/field2d.hxx"
+#include "bout/field_data.hxx"
 #include "bout/fieldperp.hxx"
 #include "bout/region.hxx"
 #include "bout/traits.hxx"
@@ -40,6 +41,7 @@ class Field3D;
 #include <functional>
 #include <memory>
 #include <optional>
+#include <ostream>
 #include <string>
 #include <utility>
 #include <vector>
@@ -389,7 +391,7 @@ public:
           jz, nx, ny, nz);
     }
 #endif
-    return data[(jx * ny + jy) * nz + jz];
+    return data[(((jx * ny) + jy) * nz) + jz];
   }
 
   inline const BoutReal& operator()(int jx, int jy, int jz) const {
@@ -404,7 +406,7 @@ public:
           jz, nx, ny, nz);
     }
 #endif
-    return data[(jx * ny + jy) * nz + jz];
+    return data[(((jx * ny) + jy) * nz) + jz];
   }
 
   /*!
@@ -448,7 +450,7 @@ public:
   /// Assignment operators
   ///@{
   Field3D& operator=(const Field3D& rhs);
-  Field3D& operator=(Field3D&& rhs);
+  Field3D& operator=(Field3D&& rhs) noexcept;
   Field3D& operator=(const Field2D& rhs);
   /// return void, as only part initialised
   void operator=(const FieldPerp& rhs);
@@ -544,7 +546,7 @@ public:
   void disallowCalcParallelSlices() { _allowCalcParallelSlices = false; };
 
   inline Field3DParallel asField3DParallel();
-  inline const Field3DParallel asField3DParallel() const;
+  inline Field3DParallel asField3DParallel() const;
 
 protected:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
@@ -695,7 +697,7 @@ lowPass(const Field3D& var, int zmax, int keep_zonal, REGION rgn = RGN_ALL) {
 /// @param[in] var   Variable to apply filter to
 /// @param[in] zmax  Maximum mode in Z
 /// @param[in] rgn   The region to calculate the result over
-inline Field3D lowPass(const Field3D& var, int zmax, const std::string rgn = "RGN_ALL") {
+inline Field3D lowPass(const Field3D& var, int zmax, const std::string& rgn = "RGN_ALL") {
   return lowPass(var, zmax, true, rgn);
 }
 
@@ -838,9 +840,7 @@ Field3DParallel Field3D::asField3DParallel() {
   }
   return Field3DParallel(*this, true);
 }
-const Field3DParallel Field3D::asField3DParallel() const {
-  return Field3DParallel(*this);
-}
+Field3DParallel Field3D::asField3DParallel() const { return Field3DParallel(*this); }
 
 inline Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs) {
   return lhs + rhs.asField3D();
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 154d9291f9..b8cfae2706 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -4,7 +4,7 @@
  * Class for 3D X-Y-Z scalar fields
  *
  **************************************************************************
- * Copyright 2010 - 2025 BOUT++ developers
+ * Copyright 2010 - 2026 BOUT++ developers
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -280,7 +280,7 @@ Field3D& Field3D::operator=(const Field3D& rhs) {
   return *this;
 }
 
-Field3D& Field3D::operator=(Field3D&& rhs) {
+Field3D& Field3D::operator=(Field3D&& rhs) noexcept {
   track(rhs, "operator=");
 
   // Move parallel slices or delete existing ones.

From c3d51721ff8a4fa17f4edecd67afa942b0e4753a Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 9 Jun 2026 13:13:10 +0100
Subject: [PATCH 1331/1827] Add pytest section to `contributing.rst` docs

---
 manual/sphinx/developer_docs/contributing.rst | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/manual/sphinx/developer_docs/contributing.rst b/manual/sphinx/developer_docs/contributing.rst
index b176bb5678..02dda06a0a 100644
--- a/manual/sphinx/developer_docs/contributing.rst
+++ b/manual/sphinx/developer_docs/contributing.rst
@@ -196,6 +196,23 @@ formatters and run them according to the next section. Usually this is just:
 
 which will format just the parts of C++ files that have changed since ``next``.
 
+The "integrated" tests are run via pytest . To install the required packages using `uv
+<https://docs.astral.sh/uv/>`_ (from the top of your BOUT++ directory):
+
+.. code-block:: console
+
+    uv sync --group pytest --inexact
+
+They can be run via cmake in the same way as the other tests:
+
+.. code-block:: console
+
+    cmake --build build --target check-integrated-tests
+
+or directly, by running the script `tests/run_integrated_tests.sh`.
+
+For test isolation, pytest automatically copies each test to a temporary directory when running them.
+
 Formatting and Linters
 ~~~~~~~~~~~~~~~~~~~~~~
 
@@ -206,7 +223,7 @@ install the majority of our developer tools at once using `uv
 
 .. code-block:: console
 
-    uv sync --only-dev --group pytest --inexact
+    uv sync --only-dev --inexact
 
 This will install all the developer tools into a virtual environment (creating
 one if necessary, typically under ``.venv``). You can then activate the virtual

From 55c27c58424f537acbdc9ad1f00e7d5b9b95e5bd Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 8 Jun 2026 16:02:55 +0100
Subject: [PATCH 1332/1827] Refactor test_smooth for pytest

Use a fixture for benchmark data.
---
 tests/integrated/test-smooth/test_smooth.py | 89 ++++++++++++---------
 1 file changed, 49 insertions(+), 40 deletions(-)

diff --git a/tests/integrated/test-smooth/test_smooth.py b/tests/integrated/test-smooth/test_smooth.py
index 083b0e81be..40858eb15e 100755
--- a/tests/integrated/test-smooth/test_smooth.py
+++ b/tests/integrated/test-smooth/test_smooth.py
@@ -7,8 +7,10 @@
 # Requires: netcdf
 # Cores: 4
 
+import pytest
 import numpy as np
-from sys import stdout
+import itertools
+from pathlib import Path
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
@@ -17,44 +19,51 @@
 tol = 1e-7  # Absolute tolerance, benchmark values are floats
 
 
-def test_smooth():
-
-    # Read benchmark values
-    print("Reading benchmark data")
+@pytest.fixture(scope="module")
+def benchmark_data():
+    """Reads the benchmark data once for all test iterations in this module."""
     bmk = {}
+    source_data_dir = str(Path(__file__).parent / "data")
+
+    for v in vars:
+        bmk[v] = collect(v, path=source_data_dir, prefix="benchmark", info=False)
+    return bmk
+
+
+# Generate test configurations: [(1, 1), (1, 2), (2, 1), (2, 2)]
+PROCESSOR_TOPOLOGIES = list(itertools.product([1, 2], [1, 2]))
+
+
+@pytest.mark.parametrize("nxpe, nype", PROCESSOR_TOPOLOGIES)
+def test_smooth(benchmark_data, nxpe, nype):
+    nproc = nxpe * nype
+    cmd = "./test_smooth"
+
+    # Clean up old data
+    shell(["rm -f data/BOUT.dmp.*.nc"])
+
+    # Run the executable
+    s, out = launch_safe(f"{cmd} NXPE={nxpe}", nproc=nproc, pipe=True)
+
+    # Save log
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
+
+    # Collect output data
     for v in vars:
-        bmk[v] = collect(v, path="data", prefix="benchmark", info=False)
-
-    print("Running smoothing operator test")
-    success = True
-
-    for nype in [1, 2]:
-        for nxpe in [1, 2]:
-            nproc = nxpe * nype
-            cmd = "./test_smooth"
-
-            shell(["rm data/BOUT.dmp.*.nc"])
-
-            print("   %d processor (%d x %d)...." % (nproc, nxpe, nype))
-            s, out = launch_safe(cmd + " NXPE=" + str(nxpe), nproc=nproc, pipe=True)
-            with open("run.log." + str(nproc), "w") as f:
-                f.write(out)
-
-            # Collect output data
-            for v in vars:
-                stdout.write("      Checking variable " + v + " ... ")
-                result = collect(v, path="data", info=False)
-                # Compare benchmark and output
-                if np.shape(bmk[v]) != np.shape(result):
-                    print("Fail, wrong shape")
-                    success = False
-                    continue
-
-                diff = np.max(np.abs(bmk[v] - result))
-                if diff > tol:
-                    print("Fail, maximum difference = " + str(diff))
-                    success = False
-                else:
-                    print("Pass")
-
-    assert success, " => Some failed tests"
+        result = collect(v, path="data", info=False)
+        bmk = benchmark_data[v]
+
+        # Compare benchmark and output
+
+        assert bmk.shape == result.shape, (
+            f"Shape mismatch for variable '{v}' on {nxpe}x{nype} grid"
+        )
+
+        np.testing.assert_allclose(
+            result,
+            bmk,
+            atol=tol,
+            rtol=0,
+            err_msg=f"Data mismatch for variable '{v}' on {nxpe}x{nype} grid",
+        )

From d6f135c40cf951c7fafb88f49ee23eb09ab3bd9d Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 10 Jun 2026 10:13:27 +0100
Subject: [PATCH 1333/1827] Refactor test_laplacexz for pytest

---
 .../test-laplacexz/test_laplacexz.py          | 58 ++++++++-----------
 1 file changed, 25 insertions(+), 33 deletions(-)

diff --git a/tests/integrated/test-laplacexz/test_laplacexz.py b/tests/integrated/test-laplacexz/test_laplacexz.py
index 5069e33113..02a7239285 100755
--- a/tests/integrated/test-laplacexz/test_laplacexz.py
+++ b/tests/integrated/test-laplacexz/test_laplacexz.py
@@ -8,44 +8,36 @@
 #
 
 import numpy as np
-from boututils.run_wrapper import shell, launch_safe, getmpirun
+import pytest
+
 from boutdata.collect import collect
+from boututils.run_wrapper import shell, launch_safe, getmpirun
 
 
-def test_laplacexz():
+@pytest.mark.parametrize("nproc", [1, 2, 4])
+def test_laplacexz(nproc):
 
     tol = 1e-10  # Absolute tolerance
 
     MPIRUN = getmpirun()
 
-    print("Running LaplaceXZ test")
-    success = True
-
-    for nproc in [1, 2, 4]:
-        nxpe = nproc
-
-        cmd = "./test-laplacexz nxpe=" + str(nxpe)
-
-        shell(["rm data/BOUT.dmp.*.nc"])
-
-        print("   %d processors (nxpe = %d)...." % (nproc, nxpe))
-        s, out = launch_safe(cmd, runcmd=MPIRUN, nproc=nproc, mthread=1, pipe=True)
-        with open("run.log." + str(nproc), "w") as f:
-            f.write(out)
-
-        # Collect output data
-        f = collect("f", path="data", info=False)
-        f2 = collect("f2", path="data", info=False)
-        print("      Checking tolerance... ")
-        # Compare benchmark and output
-        if np.shape(f) != np.shape(f2):
-            print("Fail, wrong shape")
-            success = False
-        diff = np.max(np.abs(f2 - f))
-        if diff > tol:
-            print("Fail, maximum difference = " + str(diff))
-            success = False
-        else:
-            print("Pass")
-
-    assert success, " => LaplaceXZ test failed"
+    print(f"Running LaplaceXZ test on {nproc} processors...")
+
+    # Unique data directory per processor configuration
+    cmd = f"./test-laplacexz nxpe={nproc}"
+
+    shell(["rm -f data/BOUT.dmp.*.nc"])
+
+    print(f"   {nproc} processors (nxpe = {nproc})....")
+    s, out = launch_safe(cmd, runcmd=MPIRUN, nproc=nproc, mthread=1, pipe=True)
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
+
+    # Collect output data
+    f = collect("f", path="data", info=False)
+    f2 = collect("f2", path="data", info=False)
+    print("      Checking tolerance... ")
+    # Compare benchmark and output
+    np.testing.assert_allclose(
+        f2, f, atol=tol, rtol=0, err_msg="LaplaceXZ output mismatch"
+    )

From 4fb5805a854274245d9ed766770d5c9bf7deff46 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 10 Jun 2026 10:34:24 +0100
Subject: [PATCH 1334/1827] Refactor test_gyro for pytest

Use a fixture for benchmark data.
---
 tests/integrated/test-gyro/test_gyro.py | 48 +++++++++++++------------
 1 file changed, 26 insertions(+), 22 deletions(-)

diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py
index 6c2551fdf0..5f2f984ea0 100755
--- a/tests/integrated/test-gyro/test_gyro.py
+++ b/tests/integrated/test-gyro/test_gyro.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+from pathlib import Path
 
 #
 # Run the test, compare results against the benchmark
@@ -8,36 +9,43 @@
 # Requires: netcdf
 # Cores: 4
 
+import pytest
 import numpy as np
 from sys import stdout
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
 # Variables to compare
-vars = ["pade1", "pade2"]
+variables = ["pade1", "pade2"]
 
 tol = 1e-7  # Absolute tolerance, benchmark values are floats
 
 
-def test_gyro():
-
-    # Read benchmark values
-    print("Reading benchmark data")
+@pytest.fixture(scope="module")
+def benchmark_data():
+    """Reads the benchmark data once for all test iterations in this module."""
     bmk = {}
-    for v in vars:
-        bmk[v] = collect(v, path="data", prefix="benchmark", info=False, xguards=False)
+    source_data_dir = str(Path(__file__).parent / "data")
+
+    for v in variables:
+        bmk[v] = collect(
+            v, path=source_data_dir, prefix="benchmark", info=False, xguards=False
+        )
+    return bmk
+
+
+def test_gyro(benchmark_data):
 
     print("Running Gyro-average inversion test")
-    success = True
 
     for nproc in [1, 2, 4]:
         nxpe = 1
         if nproc > 2:
             nxpe = 2
 
-        cmd = "./test_gyro NXPE=" + str(nxpe)
+        cmd = f"./test_gyro NXPE={nxpe}"
 
-        shell("rm data/BOUT.dmp.*.nc")
+        shell("rm -f data/BOUT.dmp.*.nc")
 
         print("   %d processors (nxpe = %d)...." % (nproc, nxpe))
         s, out = launch_safe(cmd, nproc=nproc, pipe=True)
@@ -45,18 +53,14 @@ def test_gyro():
             f.write(out)
 
         # Collect output data
-        for v in vars:
+        for v in variables:
             stdout.write("      Checking variable " + v + " ... ")
             result = collect(v, path="data", info=False, xguards=False)
             # Compare benchmark and output
-            if np.shape(bmk[v]) != np.shape(result):
-                print("Fail, wrong shape")
-                success = False
-            diff = np.max(np.abs(bmk[v] - result))
-            if diff > tol:
-                print("Fail, maximum difference = " + str(diff))
-                success = False
-            else:
-                print("Pass")
-
-    assert success, " => Some failed tests"
+            np.testing.assert_allclose(
+                benchmark_data[v],
+                result,
+                atol=tol,
+                rtol=0,
+                err_msg="Gyro-average output mismatch",
+            )

From c193065332d7793b4ab1fd67d29d56b8f766a892 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 11 Jun 2026 10:01:08 +0100
Subject: [PATCH 1335/1827] Refactor test_laplacexy_fv for pytest

---
 .../test-laplacexy-fv/test_laplacexy_fv.py    | 59 ++++++++-----------
 1 file changed, 26 insertions(+), 33 deletions(-)

diff --git a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
index 1e207f86db..03f12c04b7 100755
--- a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
+++ b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
@@ -8,10 +8,12 @@
 # requires: petsc
 # cores: 8
 
+import pytest
 from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
 
 tol = 5.0e-8
+nproc = 8
 
 argslist = [
     "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet "
@@ -37,44 +39,35 @@
 ]
 
 
-def test_laplacexy_fv():
+@pytest.mark.parametrize("args", argslist)
+def test_laplacexy_fv(args):
 
     print("Running LaplaceXY inversion test")
-    success = True
+    cmd = f"./test-laplacexy {args}"
 
-    for nproc in [8]:
-        print("   %d processors...." % nproc)
-        for args in argslist:
-            cmd = "./test-laplacexy " + args
+    shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
 
-            shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
+    s, out = launch(
+        f"{cmd} laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
+    )
 
-            s, out = launch(
-                cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
-            )
-            if s == 134:
-                # PETSc did not recognise pctype option, probably means it
-                # was not compiled with hypre, so skip tests that need
-                # hypre to converge
-                print(
-                    "hypre not available as pre-conditioner in PETSc. Re-running with "
-                    + "pctype=shell..."
-                )
-                _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+    if s == 134:
+        # PETSc did not recognise pctype option, probably means it
+        # was not compiled with hypre, so skip tests that need
+        # hypre to converge
+        print(
+            "hypre not available as pre-conditioner in PETSc. Re-running with "
+            + "pctype=shell..."
+        )
+        _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
 
-            f = open("run.log." + str(nproc), "w")
-            f.write(out)
-            f.close()
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
 
-            # Collect output data
-            error = collect("max_error", path="data", info=False)
-            if error <= 0:
-                print("Convergence error")
-                success = False
-            elif error > tol:
-                print("Fail, maximum error is = " + str(error))
-                success = False
-            else:
-                print("Pass")
+    # Collect output data
+    error = collect("max_error", path="data", info=False)
 
-    assert success, " => Some failed tests"
+    assert error > 0, f"Convergence error: max_error is {error}"
+    assert error <= tol, (
+        f"Fail: maximum error is {error}, which exceeds tolerance {tol}"
+    )

From 81f6d2770d017b5e19d3dc647ad088de38f770de Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 11 Jun 2026 10:33:24 +0100
Subject: [PATCH 1336/1827] Refactor test_laplace for pytest

---
 tests/integrated/test-laplace/test_laplace.py | 114 +++++++++---------
 1 file changed, 55 insertions(+), 59 deletions(-)

diff --git a/tests/integrated/test-laplace/test_laplace.py b/tests/integrated/test-laplace/test_laplace.py
index 1b0d912798..254485a6a0 100755
--- a/tests/integrated/test-laplace/test_laplace.py
+++ b/tests/integrated/test-laplace/test_laplace.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+from pathlib import Path
 
 #
 # Run the test, compare results against the benchmark
@@ -8,9 +9,10 @@
 # Requires: netcdf
 # Cores: 4
 
+import pytest
+import numpy.testing as npt
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect, create_cache
-import numpy.testing as npt
 
 
 # Variables to compare
@@ -35,61 +37,55 @@
 tol = 1e-6  # Absolute tolerance
 
 
-def test_laplace():
-
-    # Read benchmark values
-    print("Reading benchmark data")
-    bmk = {v: collect(v, path="data", prefix="benchmark", info=False) for v in vars}
-
-    print("Running Laplacian inversion test")
-    success = True
-
-    for solver in ["cyclic", "pcr", "pcr_thomas"]:
-        for nproc in [1, 2, 4]:
-            nxpe = 1
-            if nproc > 2:
-                nxpe = 2
-
-            cmd = f"./test_laplace NXPE={nxpe} laplace:type={solver}"
-
-            shell("rm data/BOUT.dmp.*.nc")
-
-            print(f"   {solver} solver with {nproc} processors ({nxpe=})....")
-            s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True)
-            with open(f"run.log.{nproc}", "w") as f:
-                f.write(out)
-
-            cache = create_cache(path="data", prefix="BOUT.dmp")
-
-            # Collect output data
-            for v in vars:
-                print(f"      Checking variable {v} ...", end="")
-                result = collect(v, path="data", info=False, datafile_cache=cache)
-                # Compare benchmark and output
-                try:
-                    npt.assert_allclose(result, bmk[v], atol=tol, rtol=tol)
-                    print("Pass")
-                except AssertionError as e:
-                    print(f"Fail: {e}")
-                    success = False
-
-            # Only check FieldPerps on one processor because reading them in is
-            # quite annoying on mutliple cores due to mismatched global y indices
-            if nproc == 1:
-                for v in ["flag0_perp", "flag3_perp"]:
-                    print(f"      Checking variable {v} ...", end="")
-                    result = collect(v, path="data", info=False, datafile_cache=cache)
-                    # Compare benchmark and output
-                    try:
-                        npt.assert_allclose(
-                            result,
-                            bmk[v.replace("_perp", "")][:, 0, :],
-                            atol=tol,
-                            rtol=tol,
-                        )
-                        print("Pass")
-                    except AssertionError as e:
-                        print(f"Fail: {e}")
-                        success = False
-
-    assert success, " => Some failed tests"
+@pytest.fixture(scope="module")
+def benchmark_data():
+    """Fixture to load benchmark data once for the entire test session."""
+
+    source_data_dir = str(Path(__file__).parent / "data")
+    return {
+        v: collect(v, path=source_data_dir, prefix="benchmark", info=False)
+        for v in vars
+    }
+
+
+@pytest.mark.parametrize("solver", ["cyclic", "pcr", "pcr_thomas"])
+@pytest.mark.parametrize("nproc", [1, 2, 4])
+def test_laplace(solver, nproc, benchmark_data):
+
+    nxpe = 2 if nproc > 2 else 1
+    cmd = f"./test_laplace NXPE={nxpe} laplace:type={solver}"
+
+    shell("rm data/BOUT.dmp.*.nc")
+
+    s, out = launch_safe(cmd, nproc=nproc, mthread=1, pipe=True)
+
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
+
+    cache = create_cache(path="data", prefix="BOUT.dmp")
+
+    # Collect output data
+    for v in vars:
+        result = collect(v, path="data", info=False, datafile_cache=cache)
+        npt.assert_allclose(
+            result,
+            benchmark_data[v],
+            atol=tol,
+            rtol=tol,
+            err_msg=f"Failed checking variable: {v}",
+        )
+
+    # Only check FieldPerps on one processor because reading them in is
+    # quite annoying on multiple cores due to mismatched global y indices
+    if nproc == 1:
+        for v in ["flag0_perp", "flag3_perp"]:
+            result = collect(v, path="data", info=False, datafile_cache=cache)
+
+            # Compare benchmark and output
+            npt.assert_allclose(
+                result,
+                benchmark_data[v.replace("_perp", "")][:, 0, :],
+                atol=tol,
+                rtol=tol,
+                err_msg=f"Failed checking perpendicular variable: {v}",
+            )

From b43a1c4a8fe9452623609f98156bbb068710c34a Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 11 Jun 2026 10:36:51 +0100
Subject: [PATCH 1337/1827] Refactor test_petsc_laplace for pytest

---
 .../test-petsc_laplace/test_petsc_laplace.py  | 44 +++++++------------
 1 file changed, 17 insertions(+), 27 deletions(-)

diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
index f698d696ec..3ac9a802f1 100755
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
@@ -8,11 +8,11 @@
 # requires: all_tests
 # cores: 4
 
+import pathlib
+import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect, create_cache
 
-import pathlib
-
 errors = [
     "max_error1",
     "max_error2",
@@ -24,33 +24,23 @@
 tol = 2e-4  # Absolute (?) tolerance
 
 
-def test_petsc_laplace():
-
-    print("Running PETSc Laplacian inversion test")
-    success = True
-
-    for nproc in [1, 2, 4]:
-        cmd = "./test_petsc_laplace"
+@pytest.mark.parametrize("nproc", [1, 2, 4])
+def test_petsc_laplace(nproc):
+    cmd = "./test_petsc_laplace"
 
-        shell(["rm data/BOUT.dmp.*.nc"])
+    shell(["rm data/BOUT.dmp.*.nc"])
 
-        print(f"   {nproc} processors....")
-        s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+    print(f"   {nproc} processors....")
+    s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
 
-        pathlib.Path(f"run.log.{nproc}").write_text(out)
-        cache = create_cache(path="data", prefix="BOUT.dmp")
+    pathlib.Path(f"run.log.{nproc}").write_text(out)
+    cache = create_cache(path="data", prefix="BOUT.dmp")
 
-        # Collect output data
-        for varname in errors:
-            print(f"      Checking {varname} ... ", end="")
-            error = collect(varname, path="data", info=False, datafile_cache=cache)
-            if error <= 0:
-                print("Convergence error")
-                success = False
-            elif error > tol:
-                print(f"Fail, maximum error is = {error:e}")
-                success = False
-            else:
-                print("Pass")
+    # Collect output data
+    for varname in errors:
+        error = collect(varname, path="data", info=False, datafile_cache=cache)
 
-    assert success, " => Some failed tests"
+        assert error > 0, f"Convergence error for {varname} on {nproc} proc(s)"
+        assert error <= tol, (
+            f"Fail: {varname} maximum error is {error:e} (Tolerance: {tol:e})"
+        )

From a3d299de9f0887192636aceba2a406eded905954 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 11 Jun 2026 10:41:46 +0100
Subject: [PATCH 1338/1827] Refactor test_laplacexy_short for pytest

---
 .../test_laplacexy_short.py                   | 122 ++++++++----------
 1 file changed, 56 insertions(+), 66 deletions(-)

diff --git a/tests/integrated/test-laplacexy-short/test_laplacexy_short.py b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
index 908e812ce9..135c04141b 100755
--- a/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
+++ b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
@@ -8,81 +8,71 @@
 # requires: petsc
 # cores: 8
 
+import pytest
 from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
 
+tol = 5.0e-8
+nproc = 8
 
-def test_laplacexy_short():
+argslist = [
+    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet "
+    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet",
+    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann "
+    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann",
+    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=free_o3 "
+    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3",
+    #'laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=dirichlet '
+    #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
+    #'laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann '
+    #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann',
+    #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet '
+    #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
+    #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann '
+    #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann',
+    #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=dirichlet '
+    #'f:bndry_xin=neumann f:bndry_xout=neumann f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
+    "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann "
+    "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann",
+    "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=free_o3 "
+    "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3",
+    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann "
+    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
+    "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=free_o3 "
+    "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1",
+    "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann "
+    "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
+    "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=free_o3 "
+    "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1",
+]
 
-    tol = 5.0e-8
 
-    argslist = [
-        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet "
-        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet",
-        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann "
-        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann",
-        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=free_o3 "
-        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3",
-        #'laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=dirichlet '
-        #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
-        #'laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann '
-        #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann',
-        #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=dirichlet '
-        #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
-        #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann '
-        #'f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann',
-        #'laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=dirichlet '
-        #'f:bndry_xin=neumann f:bndry_xout=neumann f:bndry_yup=dirichlet f:bndry_ydown=dirichlet',
-        "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann "
-        "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann",
-        "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=free_o3 "
-        "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3",
-        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=neumann "
-        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
-        "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry=free_o3 "
-        "f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1",
-        "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=neumann "
-        "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=neumann f:bndry_ydown=neumann b:function=.1",
-        "laplacexy:core_bndry_dirichlet=false laplacexy:pf_bndry_dirichlet=false laplacexy:y_bndry=free_o3 "
-        "f:bndry_xin=neumann f:bndry_xout=dirichlet f:bndry_yup=free_o3 f:bndry_ydown=free_o3 b:function=.1",
-    ]
+@pytest.mark.parametrize("args", argslist)
+def test_laplacexy_short(args):
 
-    print("Running LaplaceXY inversion test")
-    success = True
+    cmd = f"./test-laplacexy {args}"
 
-    for nproc in [8]:
-        print("   %d processors...." % nproc)
-        for args in argslist:
-            cmd = "./test-laplacexy " + args
+    shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
 
-            shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
+    s, out = launch(
+        f"{cmd} laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
+    )
+    if s == 134:
+        # PETSc did not recognise pctype option, probably means it
+        # was not compiled with hypre, so skip tests that need
+        # hypre to converge
+        print(
+            "hypre not available as pre-conditioner in PETSc. Re-running with "
+            + "pctype=shell..."
+        )
+        _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
 
-            s, out = launch(
-                cmd + " laplacexy:pctype=hypre", nproc=nproc, pipe=True, verbose=True
-            )
-            if s == 134:
-                # PETSc did not recognise pctype option, probably means it
-                # was not compiled with hypre, so skip tests that need
-                # hypre to converge
-                print(
-                    "hypre not available as pre-conditioner in PETSc. Re-running with "
-                    + "pctype=shell..."
-                )
-                _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
 
-            f = open("run.log." + str(nproc), "w")
-            f.write(out)
-            f.close()
+    error = collect("max_error", path="data", info=False)
 
-            # Collect output data
-            error = collect("max_error", path="data", info=False)
-            if error <= 0:
-                print("Convergence error")
-                success = False
-            elif error > tol:
-                print("Fail, maximum error is = " + str(error))
-                success = False
-            else:
-                print("Pass")
-
-    assert success, " => Some failed tests"
+    assert error > 0, f"Convergence error: max_error is {error}"
+    assert error <= tol, (
+        f"Fail: maximum error is {error}, which exceeds tolerance {tol}"
+    )

From 7f920ac02550edf26ad613a62dc0d7627229fa7f Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 11 Jun 2026 10:47:32 +0100
Subject: [PATCH 1339/1827] Refactor test_laplacexy2_hypre for pytest

---
 .../test_laplacexy2_hypre.py                  | 39 ++++++++-----------
 1 file changed, 16 insertions(+), 23 deletions(-)

diff --git a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
index 7a677106dd..8b1a75942d 100755
--- a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
+++ b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
@@ -7,11 +7,12 @@
 # requires: hypre
 # cores: 8
 
-
+import pytest
 from boutdata.collect import collect
 from boututils.run_wrapper import launch_safe, shell
 
 tol = 5.0e-8
+nproc = 8
 
 argslist = [
     "laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry_dirichlet=true "
@@ -37,32 +38,24 @@
 ]
 
 
-def test_laplacexy2_hypre():
+@pytest.mark.parametrize("args", argslist)
+def test_laplacexy2_hypre(args):
 
-    print("Running LaplaceXY inversion test")
-    success = True
+    print("   %d processors...." % nproc)
 
-    for nproc in [8]:
-        print("   %d processors...." % nproc)
-        for args in argslist:
-            cmd = "./test-laplacexy " + args
+    cmd = f"./test-laplacexy {args}"
 
-            shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
+    shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
 
-            s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+    s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
 
-            with open(f"run.log.{nproc}", "w") as f:
-                f.write(out)
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
 
-            # Collect output data
-            error = collect("max_error", path="data", info=False)
-            if error <= 0:
-                print("Convergence error")
-                success = False
-            elif error > tol:
-                print("Fail, maximum error is = " + str(error))
-                success = False
-            else:
-                print("Pass")
+    # Collect output data
+    error = collect("max_error", path="data", info=False)
 
-    assert success, " => Some failed tests"
+    assert error > 0, f"Convergence error: maximum error is {error}"
+    assert error <= tol, (
+        f"Fail: maximum error is {error}, which exceeds tolerance {tol}"
+    )

From 4b6da4325ee9aab096ef0799837b91bf3b670a5f Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 11 Jun 2026 11:58:43 -0700
Subject: [PATCH 1340/1827] fv_ops: VanAlbada slope limiter

Smooth alternative to MC/MinMod/SuperBee that has a continuous
derivative. Hopefully improves nonlinear solver performance.
---
 examples/finite-volume/fluid/README.md        |   3 +-
 include/bout/fv_ops.hxx                       | 106 ++++++++++++------
 .../user_docs/differential_operators.rst      |  18 ++-
 tests/unit/CMakeLists.txt                     |   1 +
 tests/unit/include/bout/test_fv_ops.cxx       |  56 +++++++++
 5 files changed, 146 insertions(+), 38 deletions(-)
 create mode 100644 tests/unit/include/bout/test_fv_ops.cxx

diff --git a/examples/finite-volume/fluid/README.md b/examples/finite-volume/fluid/README.md
index d112da3039..0a43dd43ca 100644
--- a/examples/finite-volume/fluid/README.md
+++ b/examples/finite-volume/fluid/README.md
@@ -51,5 +51,6 @@ for the first order upwinding method, or
 
 for the second order MinMod method.
 
+Or, to use a smooth symmetric limiter:
 
-
+    FV::Div_par<FV::VanAlbada>
diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 0ec1fbe3ad..5fc8655783 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -5,9 +5,15 @@
 #ifndef BOUT_FV_OPS_H
 #define BOUT_FV_OPS_H
 
+#include "boutexception.hxx"
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/build_defines.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/field.hxx"
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
+#include "bout/region.hxx"
 #include "bout/utils.hxx"
 #include "bout/vector2d.hxx"
 #include <bout/mesh.hxx>
@@ -100,7 +106,7 @@ struct Fromm {
 
 /*!
    * Second order slope limiter method
-   * 
+   *
    * Limits slope to minimum absolute value
    * of left and right gradients. If at a maximum
    * or minimum slope set to zero, i.e. reverts
@@ -110,7 +116,7 @@ struct MinMod {
   void operator()(Stencil1D& n) {
     // Choose the gradient within the cell
     // as the minimum (smoothest) solution
-    BoutReal slope = _minmod(n.p - n.c, n.c - n.m);
+    const BoutReal slope = _minmod(n.p - n.c, n.c - n.m);
     n.L = n.c - 0.5 * slope;
     n.R = n.c + 0.5 * slope;
   }
@@ -137,17 +143,17 @@ private:
 
 /*!
    * Monotonised Central (MC) second order slope limiter (Van Leer)
-   * 
-   * Limits the slope based on taking the slope with 
+   *
+   * Limits the slope based on taking the slope with
    * the minimum absolute value from central, 2*left and
    * 2*right. If any of these slopes have different signs
    * then the slope reverts to zero (i.e. 1st-order upwinding).
    */
 struct MC {
   void operator()(Stencil1D& n) {
-    BoutReal slope = minmod(2. * (n.p - n.c),  // 2*right difference
-                            0.5 * (n.p - n.m), // Central difference
-                            2. * (n.c - n.m)); // 2*left difference
+    const BoutReal slope = minmod(2. * (n.p - n.c),  // 2*right difference
+                                  0.5 * (n.p - n.m), // Central difference
+                                  2. * (n.c - n.m)); // 2*left difference
     n.L = n.c - 0.5 * slope;
     n.R = n.c + 0.5 * slope;
   }
@@ -166,6 +172,42 @@ private:
   }
 };
 
+/*!
+   * Symmetric Van Albada second order slope limiter
+   *
+   * Uses a smooth (differentiable) approximation to `max(a*b, 0)` to avoid
+   * introducing a kink at extrema, which can be helpful for nonlinear solvers
+   * and finite-difference Jacobian calculations.
+   *
+   * The limited slope is calculated from the left and right differences
+   * `dl = c - m` and `dr = p - c` as
+   *
+   *   slope = (pos(dl*dr) * (dl + dr)) / (dl^2 + dr^2)
+   *
+   * where `pos(x)` is a smooth approximation to `max(x, 0)`.
+   */
+struct VanAlbada {
+  void operator()(Stencil1D& n) {
+    const BoutReal dl = n.c - n.m;
+    const BoutReal dr = n.p - n.c;
+
+    const BoutReal denom = dl * dl + dr * dr;
+
+    // Smoothness parameters:
+    // - keep division well-defined when dl=dr=0
+    // - provide a differentiable approximation to max(dl*dr, 0)
+    const BoutReal eps = 1e-12 * denom + 1e-30;
+
+    const BoutReal ab = dl * dr;
+    const BoutReal ab_pos = 0.5 * (ab + sqrt(ab * ab + eps * eps));
+
+    const BoutReal slope = (ab_pos * (dl + dr)) / (denom + eps);
+
+    n.L = n.c - 0.5 * slope;
+    n.R = n.c + 0.5 * slope;
+  }
+};
+
 /*!
    * Communicate fluxes between processors
    * Takes values in guard cells, and adds them to cells
@@ -189,8 +231,8 @@ void communicateFluxes(Field3D& f);
 ///
 /// NB: Uses to/from FieldAligned coordinates
 template <typename CellEdges = MC>
-const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
-                      const Field3D& wave_speed_in, bool fixflux = true) {
+Field3D Div_par(const Field3D& f_in, const Field3D& v_in, const Field3D& wave_speed_in,
+                bool fixflux = true) {
 
   ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
   ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
@@ -246,16 +288,16 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
       BoutReal common_factor = (coord->J(i, j) + coord->J(i, j + 1))
                                / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1)));
 
-      BoutReal flux_factor_rc = common_factor / (coord->dy(i, j) * coord->J(i, j));
-      BoutReal flux_factor_rp =
+      const BoutReal flux_factor_rc = common_factor / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_rp =
           common_factor / (coord->dy(i, j + 1) * coord->J(i, j + 1));
 
       // For left cell boundaries
       common_factor = (coord->J(i, j) + coord->J(i, j - 1))
                       / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1)));
 
-      BoutReal flux_factor_lc = common_factor / (coord->dy(i, j) * coord->J(i, j));
-      BoutReal flux_factor_lm =
+      const BoutReal flux_factor_lc = common_factor / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_lm =
           common_factor / (coord->dy(i, j - 1) * coord->J(i, j - 1));
 #endif
       for (int k = mesh->zstart; k <= mesh->zend; k++) {
@@ -303,7 +345,7 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
         if (mesh->lastY(i) && (j == mesh->yend) && !mesh->periodicY(i)) {
           // Last point in domain
 
-          BoutReal bndryval = 0.5 * (s.c + s.p);
+          const BoutReal bndryval = 0.5 * (s.c + s.p);
           if (fixflux) {
             // Use mid-point to be consistent with boundary conditions
             flux = bndryval * vpar;
@@ -314,7 +356,7 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
         } else {
 
           // Maximum wave speed in the two cells
-          BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k));
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k));
 
           if (vpar > amax) {
             // Supersonic flow out of this cell
@@ -338,7 +380,7 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
 
         if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) {
           // First point in domain
-          BoutReal bndryval = 0.5 * (s.c + s.m);
+          const BoutReal bndryval = 0.5 * (s.c + s.m);
           if (fixflux) {
             // Use mid-point to be consistent with boundary conditions
             flux = bndryval * vpar;
@@ -349,7 +391,7 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
         } else {
 
           // Maximum wave speed in the two cells
-          BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k));
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k));
 
           if (vpar < -amax) {
             // Supersonic out of this cell
@@ -374,16 +416,16 @@ const Field3D Div_par(const Field3D& f_in, const Field3D& v_in,
    * Div ( n * v )  -- Magnetic drifts
    *
    * This uses the expression
-   * 
+   *
    * Div( A ) = 1/J * d/di ( J * A^i )
-   * 
+   *
    * Hence the input vector should be contravariant
    *
    * Note: Uses to/from FieldAligned
    *
    */
 template <typename CellEdges = MC>
-const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
+Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
   ASSERT1(n_in.getLocation() == v.getLocation());
   ASSERT1_FIELDS_COMPATIBLE(n_in, v.x);
 
@@ -406,10 +448,10 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Calculate velocities
-    BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]);
-    BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]);
-    BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J[i.xm()] + coord->J[i]);
-    BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J[i.xp()] + coord->J[i]);
+    const BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]);
+    const BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]);
+    const BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J[i.xm()] + coord->J[i]);
+    const BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J[i.xp()] + coord->J[i]);
 
     // X direction
     Stencil1D s;
@@ -439,7 +481,7 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
       // Not at a boundary
       if (vR > 0.0) {
         // Flux out into next cell
-        BoutReal flux = vR * s.R;
+        const BoutReal flux = vR * s.R;
         result[i] += flux / (coord->dx[i] * coord->J[i]);
         result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]);
       }
@@ -465,7 +507,7 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
     } else {
       // Not at a boundary
       if (vL < 0.0) {
-        BoutReal flux = vL * s.L;
+        const BoutReal flux = vL * s.L;
         result[i] -= flux / (coord->dx[i] * coord->J[i]);
         result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]);
       }
@@ -482,12 +524,12 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
     cellboundary(s);
 
     if (vU > 0.0) {
-      BoutReal flux = vU * s.R;
+      const BoutReal flux = vU * s.R;
       result[i] += flux / (coord->J[i] * coord->dz[i]);
       result[i.zp()] -= flux / (coord->J[i.zp()] * coord->dz[i.zp()]);
     }
     if (vD < 0.0) {
-      BoutReal flux = vD * s.L;
+      const BoutReal flux = vD * s.L;
       result[i] -= flux / (coord->J[i] * coord->dz[i]);
       result[i.zm()] += flux / (coord->J[i.zm()] * coord->dz[i.zm()]);
     }
@@ -507,13 +549,13 @@ const Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Y velocities on y boundaries
-    BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]);
-    BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]);
+    const BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]);
+    const BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]);
 
     // n (advected quantity) on y boundaries
     // Note: Use unshifted n_in variable
-    BoutReal nU = 0.5 * (n[i] + n[i.yp()]);
-    BoutReal nD = 0.5 * (n[i] + n[i.ym()]);
+    const BoutReal nU = 0.5 * (n[i] + n[i.yp()]);
+    const BoutReal nD = 0.5 * (n[i] + n[i.ym()]);
 
     yresult[i] = (nU * vU - nD * vD) / (coord->J[i] * coord->dy[i]);
   }
diff --git a/manual/sphinx/user_docs/differential_operators.rst b/manual/sphinx/user_docs/differential_operators.rst
index 50a795f7ff..04692f039d 100644
--- a/manual/sphinx/user_docs/differential_operators.rst
+++ b/manual/sphinx/user_docs/differential_operators.rst
@@ -36,7 +36,7 @@ exceptions are possible) and are divided into three categories:
       :math:`(-f_{-2} + 16f_{-1} - 30f_0 + 16f_1 - f_2)/12`
 
    -  ``S2``: 2\ :math:`^{nd}` order smoothing derivative
-      
+
    -  ``W2``: 2\ :math:`^{nd}` order CWENO
 
    -  ``W3``: 3\ :math:`^{rd}` order CWENO
@@ -46,9 +46,9 @@ exceptions are possible) and are divided into three categories:
    -  ``U1``: 1\ :math:`^{st}` order upwinding
 
    -  ``U2``: 2\ :math:`^{nd}` order upwinding
-      
+
    -  ``U3``: 3\ :math:`^{rd}` order upwinding
-      
+
    -  ``U4``: 4\ :math:`^{th}` order upwinding
 
    -  ``C2``: 2\ :math:`^{nd}` order central
@@ -75,7 +75,7 @@ Special methods :
 
 - ``SPLIT``: A flux method that splits into upwind and central terms
    :math:`\frac{d}{dx}(v_x f) = v_x\frac{df}{dx} + f\frac{dv_x}{dx}`
-  
+
 
 .. _Weighted Essentially Non-Oscillatory (WENO): https://doi.org/10.1137/S106482759732455X
 
@@ -178,7 +178,7 @@ implemented.
        return 0.5*(f.p - f.m);
    };
 
-   
+
 Here `DEFINE_STANARD_DERIV` is a macro that acts on the kernel
 ``return 0.5*(f.p - f.m);`` and produces the functor that will apply
 the differencing method over an entire field.  The macro takes several
@@ -667,6 +667,14 @@ values. Several slope limiters are defined in ``fv_ops.hxx``:
   to ``MinMod``. It has smaller dissipation than ``MinMod`` so is the
   default.
 
+* ``VanAlbada`` - A smooth (differentiable) symmetric slope limiter which
+  avoids piecewise branches at extrema. This can be useful for nonlinear
+  solvers and finite-difference Jacobian calculations.
+
+Useful resources on slope limiters include:
+
+* `Wikipedia's Flux Limiter page <https://en.wikipedia.org/wiki/Flux_limiter>`_
+* `SU2's Slope Limiters and Shock Resolution page <https://su2code.github.io/docs_v7/Slope-Limiters-and-Shock-Resolution/>`_
 
 .. _sec-staggeredgrids:
 
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index b347de7354..6c14b79fb0 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -69,6 +69,7 @@ set(serial_tests_source
     ./include/bout/test_assert.cxx
     ./include/bout/test_bout_enum_class.cxx
     ./include/bout/test_deriv_store.cxx
+    ./include/bout/test_fv_ops.cxx
     ./include/bout/test_generic_factory.cxx
     ./include/bout/test_macro_for_each.cxx
     ./include/bout/test_monitor.cxx
diff --git a/tests/unit/include/bout/test_fv_ops.cxx b/tests/unit/include/bout/test_fv_ops.cxx
new file mode 100644
index 0000000000..3fbcd32c8e
--- /dev/null
+++ b/tests/unit/include/bout/test_fv_ops.cxx
@@ -0,0 +1,56 @@
+#include "gtest/gtest.h"
+
+#include <bout/fv_ops.hxx>
+
+TEST(FVOpsLimiterTest, VanAlbadaConstant) {
+  FV::Stencil1D s{};
+  s.m = 1.0;
+  s.c = 1.0;
+  s.p = 1.0;
+
+  FV::VanAlbada limiter;
+  limiter(s);
+
+  EXPECT_DOUBLE_EQ(s.L, 1.0);
+  EXPECT_DOUBLE_EQ(s.R, 1.0);
+}
+
+TEST(FVOpsLimiterTest, VanAlbadaLinear) {
+  FV::Stencil1D s{};
+  s.m = 0.0;
+  s.c = 1.0;
+  s.p = 2.0;
+
+  FV::VanAlbada limiter;
+  limiter(s);
+
+  EXPECT_NEAR(s.L, 0.5, 1e-14);
+  EXPECT_NEAR(s.R, 1.5, 1e-14);
+}
+
+TEST(FVOpsLimiterTest, VanAlbadaExtremumGivesZeroSlope) {
+  FV::Stencil1D s{};
+  s.m = 0.0;
+  s.c = 1.0;
+  s.p = 0.0;
+
+  FV::VanAlbada limiter;
+  limiter(s);
+
+  EXPECT_NEAR(s.L, 1.0, 1e-14);
+  EXPECT_NEAR(s.R, 1.0, 1e-14);
+}
+
+TEST(FVOpsLimiterTest, VanAlbadaLimitsToSmallerGradient) {
+  FV::Stencil1D s{};
+  s.m = 0.0;
+  s.c = 1.0;
+  s.p = 1.5;
+
+  FV::VanAlbada limiter;
+  limiter(s);
+
+  // dl = 1, dr = 0.5 => slope = (dl*dr*(dl+dr)) / (dl^2+dr^2) = 0.6
+  EXPECT_NEAR(s.L, 0.7, 1e-12);
+  EXPECT_NEAR(s.R, 1.3, 1e-12);
+}

From 01148b674fcb1b2a6de7ab14a8d8ed458ba61831 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 11 Jun 2026 12:04:56 -0700
Subject: [PATCH 1341/1827] Fix parallel_boundary_region when
 BOUT_USE_METRIC_3D == 0

Used `dir` (a method) rather than `_dir` (a member)
---
 include/bout/parallel_boundary_region.hxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 7a2aff32c1..e936f771c2 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -381,16 +381,16 @@ public:
   }
 
 #if BOUT_USE_METRIC_3D == 0
-  const BoutReal& ynext(const Field2D& f) const { return f.ynext(dir)[ind().yp(dir)]; }
-  BoutReal& ynext(Field2D& f) const { return f.ynext(dir)[ind().yp(dir)]; }
+  const BoutReal& ynext(const Field2D& f) const { return f.ynext(_dir)[ind().yp(_dir)]; }
+  BoutReal& ynext(Field2D& f) const { return f.ynext(_dir)[ind().yp(_dir)]; }
 
   const BoutReal& yprev(const Field2D& f) const {
     ASSERT3(valid() > 0);
-    return f.ynext(-dir)[ind().yp(-dir)];
+    return f.ynext(-_dir)[ind().yp(-_dir)];
   }
   BoutReal& yprev(Field2D& f) const {
     ASSERT3(valid() > 0);
-    return f.ynext(-dir)[ind().yp(-dir)];
+    return f.ynext(-_dir)[ind().yp(-_dir)];
   }
 #endif
 

From a9df729e86b91860c6ba2700a8419061919ace23 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 11 Jun 2026 12:48:24 -0700
Subject: [PATCH 1342/1827] fv_ops: WENO3 cell edge reconstruction

---
 examples/finite-volume/fluid/README.md        |  4 ++
 include/bout/fv_ops.hxx                       | 55 +++++++++++++++++++
 .../user_docs/differential_operators.rst      |  4 ++
 tests/unit/include/bout/test_fv_ops.cxx       | 26 +++++++++
 4 files changed, 89 insertions(+)

diff --git a/examples/finite-volume/fluid/README.md b/examples/finite-volume/fluid/README.md
index 0a43dd43ca..583277d130 100644
--- a/examples/finite-volume/fluid/README.md
+++ b/examples/finite-volume/fluid/README.md
@@ -54,3 +54,7 @@ for the second order MinMod method.
 Or, to use a smooth symmetric limiter:
 
     FV::Div_par<FV::VanAlbada>
+
+Or a higher-order smooth WENO reconstruction:
+
+    FV::Div_par<FV::WENO3>
diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 5fc8655783..323e73f58e 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -208,6 +208,61 @@ struct VanAlbada {
   }
 };
 
+/*!
+   * WENO3-JS (Jiang-Shu) reconstruction to cell faces
+   *
+   * This is a third-order essentially non-oscillatory reconstruction using two
+   * candidate second-order polynomials and smoothness-weighted blending.
+   *
+   * Unlike TVD slope limiters (e.g. ``MC``), WENO reconstruction is generally
+   * smooth (differentiable) for all inputs, but it does not enforce strict
+   * monotonicity.
+   *
+   * Uses only the three-point stencil (`m`, `c`, `p`), so it is a drop-in
+   * replacement anywhere `Stencil1D` is populated with those values.
+   */
+struct WENO3 {
+  void operator()(Stencil1D& n) {
+    // Right face (between c and p): value from cell c (left state at i+1/2)
+    const BoutReal p0_r = 0.5 * (-n.m + 3.0 * n.c);
+    const BoutReal p1_r = 0.5 * (n.c + n.p);
+
+    const BoutReal beta0_r = SQ(n.c - n.m);
+    const BoutReal beta1_r = SQ(n.p - n.c);
+
+    // Left face (between m and c): value from cell c (right state at i-1/2)
+    const BoutReal p0_l = 0.5 * (-n.p + 3.0 * n.c);
+    const BoutReal p1_l = 0.5 * (n.m + n.c);
+
+    const BoutReal beta0_l = beta1_r;
+    const BoutReal beta1_l = beta0_r;
+
+    // Smoothness parameter (scaled to local variation)
+    const BoutReal eps = 1e-12 * (beta0_r + beta1_r) + 1e-30;
+
+    // Linear weights for WENO3-JS
+    constexpr BoutReal d0 = 1.0 / 3.0;
+    constexpr BoutReal d1 = 2.0 / 3.0;
+
+    // Right face weights
+    const BoutReal a0_r = d0 / SQ(eps + beta0_r);
+    const BoutReal a1_r = d1 / SQ(eps + beta1_r);
+    const BoutReal wsum_r = a0_r + a1_r;
+    const BoutReal w0_r = a0_r / wsum_r;
+    const BoutReal w1_r = a1_r / wsum_r;
+
+    // Left face weights (mirrored)
+    const BoutReal a0_l = d0 / SQ(eps + beta0_l);
+    const BoutReal a1_l = d1 / SQ(eps + beta1_l);
+    const BoutReal wsum_l = a0_l + a1_l;
+    const BoutReal w0_l = a0_l / wsum_l;
+    const BoutReal w1_l = a1_l / wsum_l;
+
+    n.R = w0_r * p0_r + w1_r * p1_r;
+    n.L = w0_l * p0_l + w1_l * p1_l;
+  }
+};
+
 /*!
    * Communicate fluxes between processors
    * Takes values in guard cells, and adds them to cells
diff --git a/manual/sphinx/user_docs/differential_operators.rst b/manual/sphinx/user_docs/differential_operators.rst
index 04692f039d..71dbeb4f9e 100644
--- a/manual/sphinx/user_docs/differential_operators.rst
+++ b/manual/sphinx/user_docs/differential_operators.rst
@@ -671,6 +671,10 @@ values. Several slope limiters are defined in ``fv_ops.hxx``:
   avoids piecewise branches at extrema. This can be useful for nonlinear
   solvers and finite-difference Jacobian calculations.
 
+* ``WENO3`` - A third-order smooth WENO (Jiang-Shu) cell-face reconstruction
+  using a three-point stencil. This is typically less dissipative than TVD
+  slope limiters, but is not strictly monotonicity-preserving.
+
 Useful resources on slope limiters include:
 
 * `Wikipedia's Flux Limiter page <https://en.wikipedia.org/wiki/Flux_limiter>`_
diff --git a/tests/unit/include/bout/test_fv_ops.cxx b/tests/unit/include/bout/test_fv_ops.cxx
index 3fbcd32c8e..2f4ea444f8 100644
--- a/tests/unit/include/bout/test_fv_ops.cxx
+++ b/tests/unit/include/bout/test_fv_ops.cxx
@@ -54,3 +54,29 @@ TEST(FVOpsLimiterTest, VanAlbadaLimitsToSmallerGradient) {
   EXPECT_NEAR(s.L, 0.7, 1e-12);
   EXPECT_NEAR(s.R, 1.3, 1e-12);
 }
+
+TEST(FVOpsLimiterTest, WENO3Constant) {
+  FV::Stencil1D s{};
+  s.m = 1.0;
+  s.c = 1.0;
+  s.p = 1.0;
+
+  FV::WENO3 recon;
+  recon(s);
+
+  EXPECT_DOUBLE_EQ(s.L, 1.0);
+  EXPECT_DOUBLE_EQ(s.R, 1.0);
+}
+
+TEST(FVOpsLimiterTest, WENO3Linear) {
+  FV::Stencil1D s{};
+  s.m = 0.0;
+  s.c = 1.0;
+  s.p = 2.0;
+
+  FV::WENO3 recon;
+  recon(s);
+
+  EXPECT_NEAR(s.L, 0.5, 1e-14);
+  EXPECT_NEAR(s.R, 1.5, 1e-14);
+}

From 73e752f69f8d3a72368996368bd33d9dc5acfb0f Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 11 Jun 2026 12:50:22 -0700
Subject: [PATCH 1343/1827] parallel_boundary_region: use
 not(BOUT_USE_METRIC_3D)

Consistent with other uses in BOUT++ headers
---
 include/bout/parallel_boundary_region.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index e936f771c2..48668a5908 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -380,7 +380,7 @@ public:
     }
   }
 
-#if BOUT_USE_METRIC_3D == 0
+#if not(BOUT_USE_METRIC_3D)
   const BoutReal& ynext(const Field2D& f) const { return f.ynext(_dir)[ind().yp(_dir)]; }
   BoutReal& ynext(Field2D& f) const { return f.ynext(_dir)[ind().yp(_dir)]; }
 

From a7df7509d91f8ea12733b6d621810040f229a5e0 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 11 Jun 2026 13:43:52 -0700
Subject: [PATCH 1344/1827] fv_ops unit tests: Loosen absolute tolerance

1e-12 rather than 1e-14
---
 tests/unit/include/bout/test_fv_ops.cxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/unit/include/bout/test_fv_ops.cxx b/tests/unit/include/bout/test_fv_ops.cxx
index 2f4ea444f8..e78c0cca41 100644
--- a/tests/unit/include/bout/test_fv_ops.cxx
+++ b/tests/unit/include/bout/test_fv_ops.cxx
@@ -24,8 +24,8 @@ TEST(FVOpsLimiterTest, VanAlbadaLinear) {
   FV::VanAlbada limiter;
   limiter(s);
 
-  EXPECT_NEAR(s.L, 0.5, 1e-14);
-  EXPECT_NEAR(s.R, 1.5, 1e-14);
+  EXPECT_NEAR(s.L, 0.5, 1e-12);
+  EXPECT_NEAR(s.R, 1.5, 1e-12);
 }
 
 TEST(FVOpsLimiterTest, VanAlbadaExtremumGivesZeroSlope) {
@@ -37,8 +37,8 @@ TEST(FVOpsLimiterTest, VanAlbadaExtremumGivesZeroSlope) {
   FV::VanAlbada limiter;
   limiter(s);
 
-  EXPECT_NEAR(s.L, 1.0, 1e-14);
-  EXPECT_NEAR(s.R, 1.0, 1e-14);
+  EXPECT_NEAR(s.L, 1.0, 1e-12);
+  EXPECT_NEAR(s.R, 1.0, 1e-12);
 }
 
 TEST(FVOpsLimiterTest, VanAlbadaLimitsToSmallerGradient) {

From e098af44e8979e71132444baa467c67b021437eb Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Fri, 12 Jun 2026 16:41:13 -0700
Subject: [PATCH 1345/1827] Fix indexing issue for output monitoring

---
 include/bout/solver.hxx                       | 10 +++++-----
 manual/sphinx/user_docs/time_integration.rst  |  8 ++++++--
 .../impls/adams_bashforth/adams_bashforth.cxx |  2 +-
 src/solver/impls/arkode/arkode.cxx            |  2 +-
 src/solver/impls/cvode/cvode.cxx              |  2 +-
 src/solver/impls/euler/euler.cxx              |  2 +-
 src/solver/impls/ida/ida.cxx                  |  2 +-
 src/solver/impls/imex-bdf2/imex-bdf2.cxx      |  2 +-
 src/solver/impls/petsc/petsc.cxx              |  2 +-
 src/solver/impls/power/power.cxx              |  2 +-
 src/solver/impls/pvode/pvode.cxx              |  2 +-
 src/solver/impls/rk3-ssp/rk3-ssp.cxx          |  2 +-
 src/solver/impls/rk4/rk4.cxx                  |  2 +-
 src/solver/impls/rkgeneric/rkgeneric.cxx      |  2 +-
 src/solver/impls/slepc/slepc.cxx              |  4 ++--
 src/solver/impls/snes/snes.cxx                |  2 +-
 src/solver/impls/split-rk/split-rk.cxx        |  2 +-
 tests/unit/solver/test_fakesolver.hxx         |  7 +++++++
 tests/unit/solver/test_solver.cxx             | 20 +++++++++++++++++++
 19 files changed, 54 insertions(+), 23 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 446acefecb..14df410928 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -451,19 +451,19 @@ protected:
   ///
   /// There are two important things to note about how \p iter is
   /// passed along to each monitor:
-  /// - The solvers all start their iteration numbering from zero, so the
-  ///   initial state is calculated at \p iter = -1
+  /// - The initial state is written at \p iter = 0, and solver output
+  ///   steps are numbered from 1 to NOUT
   /// - Secondly, \p iter is passed along to each monitor *relative to
   ///   that monitor's period*
   ///
   /// In practice, this means that each monitor is called like:
   ///
   ///     monitor->call(solver, simulation_time,
-  ///                   ((iter + 1) / monitor->period) - 1,
+  ///                   iter / monitor->period,
   ///                   NOUT / monitor->period);
   ///
-  /// e.g. for a monitor with period 10, passing \p iter = 9 will
-  /// result in it being called with a value of `(9 + 1)/10 - 1 == 0`
+  /// e.g. for a monitor with period 10, passing \p iter = 10 will
+  /// result in it being called with a value of `10/10 == 1`
   int call_monitors(BoutReal simtime, int iter, int NOUT);
 
   /// Should timesteps be monitored?
diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 37bf9a6abf..2e0d0f1b32 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -1278,7 +1278,9 @@ implement the outputMonitor method of PhysicsModel::
     int outputMonitor(BoutReal simtime, int iter, int nout)
 
 The first input is the current simulation time, the second is the output
-number, and the last is the total number of outputs requested.
+number, and the last is the total number of outputs requested. If an initial
+dump is written, it is output number ``0``. Solver output steps are numbered
+from ``1`` to ``nout``, so ``iter == nout`` indicates the final output.
 This method is called by a monitor object PhysicsModel::modelMonitor, which
 writes the restart files at the same time. You can change the frequency at which
 the monitor is called by calling, in PhysicsModel::init::
@@ -1303,7 +1305,9 @@ returns an int::
 
 The first input is the solver object, the second is the current
 simulation time, the third is the output number, and the last is the
-total number of outputs requested. To get the solver to call this
+total number of outputs requested. As for ``outputMonitor()``, output number
+``0`` is reserved for the initial dump when it is written, and solver output
+steps are numbered from ``1`` to ``NOUT``. To get the solver to call this
 function every output time, define a `MyOutputMonitor` object as a member of your
 PhysicsModel::
 
diff --git a/src/solver/impls/adams_bashforth/adams_bashforth.cxx b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
index 00bd8f4ff2..0cd39a5b6d 100644
--- a/src/solver/impls/adams_bashforth/adams_bashforth.cxx
+++ b/src/solver/impls/adams_bashforth/adams_bashforth.cxx
@@ -355,7 +355,7 @@ int AdamsBashforthSolver::run() {
   [[maybe_unused]] int nwasted = 0;
   [[maybe_unused]] int nwasted_following_fail = 0;
 
-  for (int s = 0; s < getNumberOutputSteps(); s++) {
+  for (int s = 1; s <= getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
 
     bool running = true;
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 804e67a803..11e3561d0c 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -510,7 +510,7 @@ int ArkodeSolver::run() {
     throw BoutException("ArkodeSolver not initialised\n");
   }
 
-  for (int i = 0; i < getNumberOutputSteps(); i++) {
+  for (int i = 1; i <= getNumberOutputSteps(); i++) {
 
     /// Run the solver for one output timestep
     simtime = run(simtime + getOutputTimestep());
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 4f72e65933..2710534a62 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -489,7 +489,7 @@ int CvodeSolver::run() {
     throw BoutException("CvodeSolver not initialised\n");
   }
 
-  for (int i = 0; i < getNumberOutputSteps(); i++) {
+  for (int i = 1; i <= getNumberOutputSteps(); i++) {
 
     /// Run the solver for one output timestep
     simtime = run(simtime + getOutputTimestep());
diff --git a/src/solver/impls/euler/euler.cxx b/src/solver/impls/euler/euler.cxx
index 9754a68826..599d556c00 100644
--- a/src/solver/impls/euler/euler.cxx
+++ b/src/solver/impls/euler/euler.cxx
@@ -66,7 +66,7 @@ int EulerSolver::init() {
 
 int EulerSolver::run() {
 
-  for (int s = 0; s < getNumberOutputSteps(); s++) {
+  for (int s = 1; s <= getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
 
     bool running = true;
diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx
index 84a0bd4abd..68ddf7f90d 100644
--- a/src/solver/impls/ida/ida.cxx
+++ b/src/solver/impls/ida/ida.cxx
@@ -236,7 +236,7 @@ int IdaSolver::run() {
     throw BoutException("IdaSolver not initialised\n");
   }
 
-  for (int i = 0; i < getNumberOutputSteps(); i++) {
+  for (int i = 1; i <= getNumberOutputSteps(); i++) {
 
     /// Run the solver for one output timestep
     simtime = run(simtime + getOutputTimestep());
diff --git a/src/solver/impls/imex-bdf2/imex-bdf2.cxx b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
index 4ccf27981b..e30ae4c743 100644
--- a/src/solver/impls/imex-bdf2/imex-bdf2.cxx
+++ b/src/solver/impls/imex-bdf2/imex-bdf2.cxx
@@ -751,7 +751,7 @@ int IMEXBDF2::run() {
 
   int internalCounter = 0; // Cumulative number of successful internal iterations
 
-  for (int s = 0; s < getNumberOutputSteps(); s++) {
+  for (int s = 1; s <= getNumberOutputSteps(); s++) {
     BoutReal cumulativeTime = 0.;
     int counter = 0; // How many iterations in this output step
 
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 1e1e05596b..0d5c16aebd 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -234,7 +234,7 @@ PetscErrorCode PetscMonitor(TS ts, PetscInt UNUSED(step), PetscReal t, Vec X, vo
     s->load_vars(const_cast<BoutReal*>(x));
     PetscCall(VecRestoreArrayRead(interpolatedX, &x));
 
-    if (s->call_monitors(output_time, i++, s->getNumberOutputSteps()) != 0) {
+    if (s->call_monitors(output_time, ++i, s->getNumberOutputSteps()) != 0) {
       PetscFunctionReturn(1);
     }
 
diff --git a/src/solver/impls/power/power.cxx b/src/solver/impls/power/power.cxx
index 5dfccfedda..744bdfe46e 100644
--- a/src/solver/impls/power/power.cxx
+++ b/src/solver/impls/power/power.cxx
@@ -45,7 +45,7 @@ int PowerSolver::run() {
   // Make sure that f0 has a norm of 1
   divide(f0, norm(f0));
 
-  for (int s = 0; s < getNumberOutputSteps(); s++) {
+  for (int s = 1; s <= getNumberOutputSteps(); s++) {
 
     load_vars(std::begin(f0));
     run_rhs(curtime);
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 38901a2a57..0723faa99c 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -294,7 +294,7 @@ int PvodeSolver::run() {
     throw BoutException("PvodeSolver not initialised\n");
   }
 
-  for (int i = 0; i < getNumberOutputSteps(); i++) {
+  for (int i = 1; i <= getNumberOutputSteps(); i++) {
 
     /// Run the solver for one output timestep
     simtime = run(simtime + getOutputTimestep());
diff --git a/src/solver/impls/rk3-ssp/rk3-ssp.cxx b/src/solver/impls/rk3-ssp/rk3-ssp.cxx
index 7c00d44b34..26319eaa9a 100644
--- a/src/solver/impls/rk3-ssp/rk3-ssp.cxx
+++ b/src/solver/impls/rk3-ssp/rk3-ssp.cxx
@@ -61,7 +61,7 @@ int RK3SSP::init() {
 
 int RK3SSP::run() {
 
-  for (int s = 0; s < getNumberOutputSteps(); s++) {
+  for (int s = 1; s <= getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
 
     BoutReal dt;
diff --git a/src/solver/impls/rk4/rk4.cxx b/src/solver/impls/rk4/rk4.cxx
index 35b3cc2268..bb7c14fab2 100644
--- a/src/solver/impls/rk4/rk4.cxx
+++ b/src/solver/impls/rk4/rk4.cxx
@@ -73,7 +73,7 @@ int RK4Solver::init() {
 }
 
 int RK4Solver::run() {
-  for (int s = 0; s < getNumberOutputSteps(); s++) {
+  for (int s = 1; s <= getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
 
     BoutReal dt;
diff --git a/src/solver/impls/rkgeneric/rkgeneric.cxx b/src/solver/impls/rkgeneric/rkgeneric.cxx
index edf8ed50e3..20f4cc39d6 100644
--- a/src/solver/impls/rkgeneric/rkgeneric.cxx
+++ b/src/solver/impls/rkgeneric/rkgeneric.cxx
@@ -80,7 +80,7 @@ void RKGenericSolver::resetInternalFields() {
 }
 
 int RKGenericSolver::run() {
-  for (int s = 0; s < getNumberOutputSteps(); s++) {
+  for (int s = 1; s <= getNumberOutputSteps(); s++) {
     BoutReal target = simtime + getOutputTimestep();
 
     BoutReal dt;
diff --git a/src/solver/impls/slepc/slepc.cxx b/src/solver/impls/slepc/slepc.cxx
index 2c52cb3b38..9887f184eb 100644
--- a/src/solver/impls/slepc/slepc.cxx
+++ b/src/solver/impls/slepc/slepc.cxx
@@ -579,7 +579,7 @@ void SlepcSolver::monitor(PetscInt its, PetscInt nconv, PetscScalar eigr[],
   static bool first = true;
   if (eigenValOnly && first) {
     first = false;
-    resetIterationCounter();
+    resetIterationCounter(1);
   }
 
   // Temporary eigenvalues, converted from the SLEPc eigenvalues
@@ -701,7 +701,7 @@ void SlepcSolver::analyseResults() {
   output << "Converged eigenvalues :\n"
             "\tIndex\tSlepc eig (mag.)\t\t\tBOUT eig (mag.)\n";
 
-  resetIterationCounter();
+  resetIterationCounter(1);
 
   // Declare and create vectors to store eigenfunctions
   Vec vecReal, vecImag;
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 5b28ff413c..2667ad55ff 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -886,7 +886,7 @@ int SNESSolver::run() {
 
   BoutReal target = simtime;
   recent_failure_rate = 0.0;
-  for (int s = 0; s < getNumberOutputSteps(); s++) {
+  for (int s = 1; s <= getNumberOutputSteps(); s++) {
     target += getOutputTimestep();
 
     bool looping = true;
diff --git a/src/solver/impls/split-rk/split-rk.cxx b/src/solver/impls/split-rk/split-rk.cxx
index ac4d62ebe2..e5fb0f6a8e 100644
--- a/src/solver/impls/split-rk/split-rk.cxx
+++ b/src/solver/impls/split-rk/split-rk.cxx
@@ -95,7 +95,7 @@ int SplitRK::init() {
 
 int SplitRK::run() {
 
-  for (int step = 0; step < getNumberOutputSteps(); step++) {
+  for (int step = 1; step <= getNumberOutputSteps(); step++) {
     // Take an output step
 
     BoutReal target = simtime + getOutputTimestep();
diff --git a/tests/unit/solver/test_fakesolver.hxx b/tests/unit/solver/test_fakesolver.hxx
index 3d96b717e3..c8600e4649 100644
--- a/tests/unit/solver/test_fakesolver.hxx
+++ b/tests/unit/solver/test_fakesolver.hxx
@@ -19,6 +19,13 @@ public:
     if ((*options)["throw_run"].withDefault(false)) {
       throw BoutException("Deliberate exception in FakeSolver::run");
     }
+    if ((*options)["call_final_monitor"].withDefault(false)) {
+      const int ret =
+          call_monitors(simtime, getNumberOutputSteps(), getNumberOutputSteps());
+      if (ret != 0) {
+        return ret;
+      }
+    }
     return (*options)["fail_run"].withDefault(0);
   }
   bool run_called{false};
diff --git a/tests/unit/solver/test_solver.cxx b/tests/unit/solver/test_solver.cxx
index e9a612103c..525d52767f 100644
--- a/tests/unit/solver/test_solver.cxx
+++ b/tests/unit/solver/test_solver.cxx
@@ -971,6 +971,26 @@ TEST_F(SolverTest, BasicSolve) {
   EXPECT_TRUE(solver.run_called);
 }
 
+TEST_F(SolverTest, SolveCleansUpMonitorsAtFinalIteration) {
+  Options options;
+  options["call_final_monitor"] = true;
+  FakeSolver solver{&options};
+
+  StrictMock<MockMonitor> monitor;
+  solver.addMonitor(&monitor);
+
+  NiceMock<MockPhysicsModel> model{};
+  solver.setModel(&model);
+
+  Options::cleanup();
+
+  EXPECT_CALL(monitor, call(_, _, 0, nout));
+  EXPECT_CALL(monitor, call(_, _, nout, nout));
+  EXPECT_CALL(monitor, cleanup());
+
+  solver.solve(nout, timestep);
+}
+
 TEST_F(SolverTest, GetRunID) {
   Options options;
   FakeSolver solver{&options};

From afc091b1b7979f902dd09d814aebc7193d3efab7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 15 Jun 2026 13:10:14 +0200
Subject: [PATCH 1346/1827] Prefer const int

---
 src/mesh/coordinates.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index a1c4c92480..beb69838fd 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -115,8 +115,8 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr
           }
           // extrapolate into boundary guard cells if there are enough grid points
           for (int i = extrap_start; i < bndry->width; i++) {
-            int xi = bndry->x + (i * bndry->bx);
-            int yi = bndry->y + (i * bndry->by);
+            const int xi = bndry->x + (i * bndry->bx);
+            const int yi = bndry->y + (i * bndry->by);
             result(xi, yi) = 3.0 * result(xi - bndry->bx, yi - bndry->by)
                              - 3.0 * result(xi - 2 * bndry->bx, yi - 2 * bndry->by)
                              + result(xi - 3 * bndry->bx, yi - 3 * bndry->by);

From 24c99925c6a368134ba25fd1c31dcd913ca66d10 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 15 Jun 2026 14:22:24 +0200
Subject: [PATCH 1347/1827] Remove unused header

---
 src/mesh/difops.cxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index b0b5cc60d5..f23e1ed01b 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -38,7 +38,6 @@
 #include "bout/solver.hxx"
 #include "bout/unused.hxx"
 #include "bout/utils.hxx"
-#include "bout/vecops.hxx"
 
 #include <cmath>
 

From 90c3d498bbf33f1ab34bcc2183ccce7b6bc9c0ed Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 15 Jun 2026 14:13:32 +0200
Subject: [PATCH 1348/1827] Ensure optional values are set before using them

---
 include/bout/coordinates.hxx | 14 ++++++++++++++
 src/mesh/coordinates.cxx     |  3 +++
 2 files changed, 17 insertions(+)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index e260e40456..22d1aafc46 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -118,72 +118,84 @@ public:
     if (!_cell_area_xlow.has_value()) {
       _compute_cell_area_x();
     }
+    ASSERT2(_cell_area_xlow.has_value());
     return *_cell_area_xlow;
   }
   const FieldMetric& cell_area_xhigh() const {
     if (!_cell_area_xhigh.has_value()) {
       _compute_cell_area_x();
     }
+    ASSERT2(_cell_area_xhigh.has_value());
     return *_cell_area_xhigh;
   }
   const FieldMetric& cell_area_ylow() const {
     if (!_cell_area_ylow.has_value()) {
       _compute_cell_area_y();
     }
+    ASSERT2(_cell_area_ylow.has_value());
     return *_cell_area_ylow;
   }
   const FieldMetric& cell_area_yhigh() const {
     if (!_cell_area_yhigh.has_value()) {
       _compute_cell_area_y();
     }
+    ASSERT2(_cell_area_yhigh.has_value());
     return *_cell_area_yhigh;
   }
   const FieldMetric& cell_area_zlow() const {
     if (!_cell_area_zlow.has_value()) {
       _compute_cell_area_z();
     }
+    ASSERT2(_cell_area_zlow.has_value());
     return *_cell_area_zlow;
   }
   const FieldMetric& cell_area_zhigh() const {
     if (!_cell_area_zhigh.has_value()) {
       _compute_cell_area_z();
     }
+    ASSERT2(_cell_area_zhigh.has_value());
     return *_cell_area_zhigh;
   }
   FieldMetric& cell_area_xlow() {
     if (!_cell_area_xlow.has_value()) {
       _compute_cell_area_x();
     }
+    ASSERT2(_cell_area_xlow.has_value());
     return *_cell_area_xlow;
   }
   FieldMetric& cell_area_xhigh() {
     if (!_cell_area_xhigh.has_value()) {
       _compute_cell_area_x();
     }
+    ASSERT2(_cell_area_xhigh.has_value());
     return *_cell_area_xhigh;
   }
   FieldMetric& cell_area_ylow() {
     if (!_cell_area_ylow.has_value()) {
       _compute_cell_area_y();
     }
+    ASSERT2(_cell_area_ylow.has_value());
     return *_cell_area_ylow;
   }
   FieldMetric& cell_area_yhigh() {
     if (!_cell_area_yhigh.has_value()) {
       _compute_cell_area_y();
     }
+    ASSERT2(_cell_area_yhigh.has_value());
     return *_cell_area_yhigh;
   }
   FieldMetric& cell_area_zlow() {
     if (!_cell_area_zlow.has_value()) {
       _compute_cell_area_z();
     }
+    ASSERT2(_cell_area_zlow.has_value());
     return *_cell_area_zlow;
   }
   FieldMetric& cell_area_zhigh() {
     if (!_cell_area_zhigh.has_value()) {
       _compute_cell_area_z();
     }
+    ASSERT2(_cell_area_zhigh.has_value());
     return *_cell_area_zhigh;
   }
   // Cell Volume
@@ -191,12 +203,14 @@ public:
     if (!_cell_volume.has_value()) {
       _compute_cell_volume();
     }
+    ASSERT2(_cell_volume.has_value());
     return *_cell_volume;
   }
   FieldMetric& cell_volume() {
     if (!_cell_volume.has_value()) {
       _compute_cell_volume();
     }
+    ASSERT2(_cell_volume.has_value());
     return *_cell_volume;
   }
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index beb69838fd..979b5d877b 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2097,6 +2097,9 @@ void Coordinates::_compute_cell_area_x() const {
 
 void Coordinates::_compute_cell_area_y() const {
   _compute_Jxz_cell_faces();
+  ASSERT2(_jxz_centre.has_value());
+  ASSERT2(_jxz_ylow.has_value());
+  ASSERT2(_jxz_yhigh.has_value());
   if (_jxz_centre->isFci()) {
     ASSERT3(isUniform(dx, true, "RGN_ALL"));
     ASSERT2(isUniform(dx, false, "RGN_ALL"));

From 1334f5bd304c00fb101758f92a4f0f0e16a31413 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 15 Jun 2026 14:13:49 +0200
Subject: [PATCH 1349/1827] Include used headers

---
 src/mesh/coordinates.cxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 979b5d877b..7fa64d0179 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -25,6 +25,7 @@
 #include <bout/utils.hxx>
 #include <bout/yboundary_regions.hxx>
 
+#include <cmath>
 #include <memory>
 #include <string>
 
@@ -2022,7 +2023,7 @@ const Coordinates::FieldMetric& Coordinates::g_22_ylow() const {
   } else {
     ASSERT0(mesh->ystart > 0);
     BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
-      _g_22_ylow.value()[i] = SQ(0.5 * (sqrt(g_22[i]) + sqrt(g_22[i.ym()])));
+      _g_22_ylow.value()[i] = SQ(0.5 * (std::sqrt(g_22[i]) + std::sqrt(g_22[i.ym()])));
     }
   }
   return g_22_ylow();
@@ -2042,7 +2043,7 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
   } else {
     ASSERT0(mesh->ystart > 0);
     BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
-      _g_22_yhigh.value()[i] = SQ(0.5 * (sqrt(g_22[i]) + sqrt(g_22[i.yp()])));
+      _g_22_yhigh.value()[i] = SQ(0.5 * (std::sqrt(g_22[i]) + std::sqrt(g_22[i.yp()])));
     }
   }
   return g_22_yhigh();

From 99a212e091fda988ba331b4e5f71cb7295fd03e6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 15 Jun 2026 14:38:27 +0200
Subject: [PATCH 1350/1827] Add missing header

---
 include/bout/coordinates.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 22d1aafc46..8a28e5c930 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -33,6 +33,7 @@
 #ifndef BOUT_COORDINATES_H
 #define BOUT_COORDINATES_H
 
+#include "bout/assert.hxx"
 #include "bout/field_data.hxx"
 #include <bout/bout_types.hxx>
 #include <bout/build_defines.hxx>

From 2f0c1f501ecb15da28faae03fef8ca299100ab0f Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 16 Jun 2026 09:17:36 +0100
Subject: [PATCH 1351/1827] Fix merge

---
 tests/integrated/test-fci-mpi/runtest         | 83 -------------------
 tests/integrated/test-fci-mpi/test_fci_mpi.py | 53 ++++++------
 2 files changed, 27 insertions(+), 109 deletions(-)
 delete mode 100755 tests/integrated/test-fci-mpi/runtest

diff --git a/tests/integrated/test-fci-mpi/runtest b/tests/integrated/test-fci-mpi/runtest
deleted file mode 100755
index 9962567217..0000000000
--- a/tests/integrated/test-fci-mpi/runtest
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env python3
-#
-# Python script to run and analyse MPI test
-
-from boututils.run_wrapper import build_and_log, launch_safe
-from boutdata.collect import collect
-import itertools
-import sys
-
-import numpy.testing as npt
-
-# Resolution in x and y
-NLIST = [1, 2, 4]
-MAXCORES = 8
-NSLICES = [1]
-
-build_and_log("FCI MPI test")
-
-COLLECT_KW = dict(info=False, xguards=False, yguards=False, path="data")
-
-
-def run_case(nxpe: int, nype: int, mthread: int):
-    cmd = f"./fci_mpi NXPE={nxpe} NYPE={nype} mesh:paralleltransform:xzinterpolation:type={implementation}"
-    print(f"Running command: {cmd}")
-
-    _, out = launch_safe(cmd, nproc=nxpe * nype, mthread=mthread, pipe=True)
-
-    # Save output to log file
-    with open(f"run.log.{nxpe}.{nype}.{nslice}.log", "w") as f:
-        f.write(out)
-
-
-def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
-    run_case(nxpe, nype, mthread)
-
-    failures = []
-
-    for name, val in ref.items():
-        try:
-            npt.assert_allclose(val, collect(name, **COLLECT_KW))
-        except AssertionError as e:
-            failures.append((nxpe, nype, name, e))
-
-    return failures
-
-
-failures = []
-
-for implementation in ["hermitespline", "monotonichermitespline"]:
-    for nslice in NSLICES:
-        # reference data!
-        run_case(1, 1, MAXCORES)
-
-        ref = {}
-        for i in range(4):
-            for yp in range(1, nslice + 1):
-                for y in [-yp, yp]:
-                    name = f"output_{i}_{y:+d}"
-                    ref[name] = collect(name, **COLLECT_KW)
-
-        for nxpe, nype in itertools.product(NLIST, NLIST):
-            if (nxpe, nype) == (1, 1):
-                # reference case, done above
-                continue
-
-            if nxpe * nype > MAXCORES:
-                continue
-
-            mthread = MAXCORES // (nxpe * nype)
-            failures_ = test_case(nxpe, nype, mthread, ref)
-            failures.extend(failures_)
-
-
-success = len(failures) == 0
-if success:
-    print("\nAll tests passed")
-else:
-    print("\nSome tests failed:")
-    for nxpe, nype, name, error in failures:
-        print("----------")
-        print(f"case {nxpe=} {nype=} {name=}\n{error}")
-
-sys.exit(0 if success else 1)
diff --git a/tests/integrated/test-fci-mpi/test_fci_mpi.py b/tests/integrated/test-fci-mpi/test_fci_mpi.py
index a28c9c2256..51d5795d3f 100755
--- a/tests/integrated/test-fci-mpi/test_fci_mpi.py
+++ b/tests/integrated/test-fci-mpi/test_fci_mpi.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-# Python script to run and analyse MMS test
+# Python script to run and analyse MPI test
 
 from boututils.run_wrapper import launch_safe
 from boutdata.collect import collect
@@ -20,7 +20,7 @@ def test_fci_mpi():
 
     def run_case(nxpe: int, nype: int, mthread: int):
 
-        cmd = f"./fci_mpi NXPE={nxpe} NYPE={nype}"
+        cmd = f"./fci_mpi NXPE={nxpe} NYPE={nype} mesh:paralleltransform:xzinterpolation:type={implementation}"
         print(f"Running command: {cmd}")
 
         _, out = launch_safe(cmd, nproc=nxpe * nype, mthread=mthread, pipe=True)
@@ -44,34 +44,35 @@ def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
 
     failures = []
 
-    for nslice in NSLICES:
-        # reference data!
-        run_case(1, 1, MAXCORES)
+    for implementation in ["hermitespline", "monotonichermitespline"]:
+        for nslice in NSLICES:
+            # reference data!
+            run_case(1, 1, MAXCORES)
 
-        ref = {}
-        for i in range(4):
-            for yp in range(1, nslice + 1):
-                for y in [-yp, yp]:
-                    name = f"output_{i}_{y:+d}"
-                    ref[name] = collect(name, **COLLECT_KW)
+            ref = {}
+            for i in range(4):
+                for yp in range(1, nslice + 1):
+                    for y in [-yp, yp]:
+                        name = f"output_{i}_{y:+d}"
+                        ref[name] = collect(name, **COLLECT_KW)
 
-        for nxpe, nype in itertools.product(NLIST, NLIST):
-            if (nxpe, nype) == (1, 1):
-                # reference case, done above
-                continue
+            for nxpe, nype in itertools.product(NLIST, NLIST):
+                if (nxpe, nype) == (1, 1):
+                    # reference case, done above
+                    continue
 
-            if nxpe * nype > MAXCORES:
-                continue
+                if nxpe * nype > MAXCORES:
+                    continue
 
-            mthread = MAXCORES // (nxpe * nype)
-            failures_ = test_case(nxpe, nype, mthread, ref)
-            failures.extend(failures_)
+                mthread = MAXCORES // (nxpe * nype)
+                failures_ = test_case(nxpe, nype, mthread, ref)
+                failures.extend(failures_)
 
-    success = len(failures) == 0
+        success = len(failures) == 0
 
-    assert success, "\nSome tests failed:"
+        assert success, "\nSome tests failed:"
 
-    if not success:
-        for nxpe, nype, name, error in failures:
-            print("----------")
-            print(f"case {nxpe=} {nype=} {name=}\n{error}")
+        if not success:
+            for nxpe, nype, name, error in failures:
+                print("----------")
+                print(f"case {nxpe=} {nype=} {name=}\n{error}")

From dc38981df8eeafccca10ae1c5bcd70c57daf2635 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 16 Jun 2026 09:18:22 +0100
Subject: [PATCH 1352/1827] Remove old `runtest` file

(accidentally re-added when merging in `next`).
---
 tests/integrated/test-fci-boundary/runtest | 65 ----------------------
 1 file changed, 65 deletions(-)
 delete mode 100755 tests/integrated/test-fci-boundary/runtest

diff --git a/tests/integrated/test-fci-boundary/runtest b/tests/integrated/test-fci-boundary/runtest
deleted file mode 100755
index 74a8abf741..0000000000
--- a/tests/integrated/test-fci-boundary/runtest
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/usr/bin/env python3
-#
-# Python script to run and analyse MMS test
-
-from boututils.run_wrapper import launch_safe
-from boututils.datafile import DataFile
-from boutdata.collect import collect as _collect
-
-from numpy.testing import assert_allclose
-
-
-def collect(*args):
-    return _collect(
-        *args,
-        info=False,
-        path=directory,
-        xguards=False,
-        yguards=False,
-    )
-
-
-nprocs = [1]
-mthread = 2
-
-directory = "data"
-
-with DataFile("grid.fci.nc") as grid:
-    MXG = grid.get("MXG", default=1)
-    xfwd = grid.read("forward_xt_prime")[MXG:-MXG]
-    xbwd = grid.read("backward_xt_prime")[MXG:-MXG]
-
-nx = xfwd.shape[0]
-
-regions = {
-    "xin_fwd": xfwd < MXG,
-    "xout_fwd": xfwd > nx + MXG - 1,
-    "xin_bwd": xbwd < MXG,
-    "xout_bwd": xbwd > nx + MXG - 1,
-}
-regions = {k: v.astype(int) for k, v in regions.items()}
-
-
-for x in "xout", "xin":
-    regions[x] = regions[f"{x}_fwd"] + regions[f"{x}_bwd"]
-for x in "fwd", "bwd":
-    regions[x] = regions[f"xin_{x}"] + regions[f"xout_{x}"]
-regions["all"] = regions["xin"] + regions["xout"]
-
-bndrys = {
-    "ybndry_-1": regions["xout_bwd"],
-    "ybndry_0": regions["xout_fwd"] * 0,
-    "ybndry_1": regions["xout_fwd"],
-}
-
-for nproc in nprocs:
-    cmd = "./get_par_bndry"
-    _, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-
-    for k, v in regions.items():
-        data = collect(f"field_{k}")
-        assert_allclose(data, v)
-    for i in range(-1, 2):
-        name = f"ybndry_{i}"
-        data = collect(name)
-        assert_allclose(bndrys[name], data)

From 68b1dc88481621ba56445d12fffbd38211c54a36 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 16 Jun 2026 10:30:25 +0200
Subject: [PATCH 1353/1827] Remove Jxz from coordinates

---
 include/bout/coordinates.hxx |  2 --
 src/mesh/coordinates.cxx     | 65 +++++++++++++-----------------------
 2 files changed, 24 insertions(+), 43 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 8a28e5c930..6d803ab28a 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -217,12 +217,10 @@ public:
 
 private:
   mutable std::optional<FieldMetric> _g_22_ylow, _g_22_yhigh;
-  mutable std::optional<FieldMetric> _jxz_ylow, _jxz_yhigh, _jxz_centre;
   mutable std::optional<FieldMetric> _cell_area_xlow, _cell_area_xhigh;
   mutable std::optional<FieldMetric> _cell_area_ylow, _cell_area_yhigh;
   mutable std::optional<FieldMetric> _cell_area_zlow, _cell_area_zhigh;
   mutable std::optional<FieldMetric> _cell_volume;
-  void _compute_Jxz_cell_faces() const;
   void _compute_cell_area_x() const;
   void _compute_cell_area_y() const;
   void _compute_cell_area_z() const;
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 7fa64d0179..39bcf16936 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2049,39 +2049,6 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
   return g_22_yhigh();
 }
 
-void Coordinates::_compute_Jxz_cell_faces() const {
-  _jxz_centre.emplace(sqrt(g_11 * g_33 - SQ(g_13)));
-  _jxz_ylow.emplace(emptyFrom(_jxz_centre.value()));
-  //_jxz_ylow->setLocation(CELL_YLOW);
-  _jxz_yhigh.emplace(emptyFrom(_jxz_centre.value()));
-  //_jxz_yhigh->setLocation(CELL_YHIGH);
-  auto* mesh = _jxz_centre->getMesh();
-  if (Bxy.isFci()) {
-    Coordinates::FieldMetric By_c;
-    Coordinates::FieldMetric By_h;
-    Coordinates::FieldMetric By_l;
-    if (mesh->get(By_c, "By", 0.0, false, CELL_CENTRE) != 0) {
-      throw BoutException("The grid file does not contain `By`.");
-    }
-    if (mesh->get(By_l, "By_cell_ylow", 0.0, false) != 0) {
-      throw BoutException("The grid file does not contain `By_cell_ylow`.");
-    }
-    if (mesh->get(By_h, "By_cell_yhigh", 0.0, false) != 0) {
-      throw BoutException("The grid file does not contain `By_cell_yhigh`.");
-    }
-    BOUT_FOR(i, By_c.getRegion("RGN_NOY")) {
-      (*_jxz_ylow)[i] = By_c[i] / By_l[i] * (*_jxz_centre)[i];
-      (*_jxz_yhigh)[i] = By_c[i] / By_h[i] * (*_jxz_centre)[i];
-    }
-  } else {
-    ASSERT0(mesh->ystart > 0);
-    BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOY")) {
-      (*_jxz_ylow)[i] = 0.5 * ((*_jxz_centre)[i] + (*_jxz_centre)[i.ym()]);
-      (*_jxz_yhigh)[i] = 0.5 * ((*_jxz_centre)[i] + (*_jxz_centre)[i.yp()]);
-    }
-  }
-}
-
 void Coordinates::_compute_cell_area_x() const {
   const auto area_centre = sqrt(g_22 * g_33 - SQ(g_23)) * dy * dz;
   _cell_area_xlow.emplace(emptyFrom(area_centre));
@@ -2097,17 +2064,34 @@ void Coordinates::_compute_cell_area_x() const {
 }
 
 void Coordinates::_compute_cell_area_y() const {
-  _compute_Jxz_cell_faces();
-  ASSERT2(_jxz_centre.has_value());
-  ASSERT2(_jxz_ylow.has_value());
-  ASSERT2(_jxz_yhigh.has_value());
-  if (_jxz_centre->isFci()) {
+  auto* mesh = Bxy.getMesh();
+  if (g_11.isFci()) {
+    const auto jxz_centre = sqrt(g_11 * g_33 - SQ(g_13));
+    auto jxz_ylow = emptyFrom(jxz_centre);
+    auto jxz_yhigh = emptyFrom(jxz_centre);
+
+    auto By_c = emptyFrom(jxz_centre);
+    auto By_h = emptyFrom(jxz_yhigh);
+    auto By_l = emptyFrom(jxz_ylow);
+    if (mesh->get(By_c, "By", 0.0, false, CELL_CENTRE) != 0) {
+      throw BoutException("The grid file does not contain `By`.");
+    }
+    if (mesh->get(By_l, "By_cell_ylow", 0.0, false) != 0) {
+      throw BoutException("The grid file does not contain `By_cell_ylow`.");
+    }
+    if (mesh->get(By_h, "By_cell_yhigh", 0.0, false) != 0) {
+      throw BoutException("The grid file does not contain `By_cell_yhigh`.");
+    }
+    BOUT_FOR(i, By_c.getRegion("RGN_NOY")) {
+      jxz_ylow[i] = By_c[i] / By_l[i] * jxz_centre[i];
+      jxz_yhigh[i] = By_c[i] / By_h[i] * jxz_centre[i];
+    }
     ASSERT3(isUniform(dx, true, "RGN_ALL"));
     ASSERT2(isUniform(dx, false, "RGN_ALL"));
     ASSERT3(isUniform(dz, true, "RGN_ALL"));
     ASSERT2(isUniform(dz, false, "RGN_ALL"));
-    _cell_area_ylow.emplace(*_jxz_ylow * dx * dz);
-    _cell_area_yhigh.emplace(*_jxz_yhigh * dx * dz);
+    _cell_area_ylow.emplace(jxz_ylow * dx * dz);
+    _cell_area_yhigh.emplace(jxz_yhigh * dx * dz);
   } else {
     // Field aligned
     const auto area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;
@@ -2115,7 +2099,6 @@ void Coordinates::_compute_cell_area_y() const {
     _cell_area_yhigh.emplace(emptyFrom(area_centre));
     // We cannot setLocation, as that would trigger the computation of staggered
     // metrics.
-    auto* mesh = Bxy.getMesh();
     ASSERT0(mesh->ystart > 0);
     BOUT_FOR(i, mesh->getRegion("RGN_NOY")) {
       (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);

From a7fa2650c270b9214069345885a8e360c58646d7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 16 Jun 2026 14:28:04 +0200
Subject: [PATCH 1354/1827] Update cpptrace

---
 .gitmodules               | 2 +-
 externalpackages/cpptrace | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 2bdbd2a57b..59fb05ab50 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -15,4 +15,4 @@
 	url = https://github.com/boutproject/boutdata.git
 [submodule "externalpackages/cpptrace"]
 	path = externalpackages/cpptrace
-	url = https://github.com/ZedThree/cpptrace.git
+	url = https://github.com/jeremy-rifkin/cpptrace.git
diff --git a/externalpackages/cpptrace b/externalpackages/cpptrace
index 027f9aee2d..d4dbf01eca 160000
--- a/externalpackages/cpptrace
+++ b/externalpackages/cpptrace
@@ -1 +1 @@
-Subproject commit 027f9aee2d34dbe1c98f26224e1fbe1654cb4aae
+Subproject commit d4dbf01ecaa820ede6a47c832c322a408b8cb78a

From b6c548768deeb75da1fe75303a33f32e9438b71d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 17 Jun 2026 00:46:50 +0000
Subject: [PATCH 1355/1827] Bump cryptography from 46.0.5 to 48.0.1

Bumps [cryptography](https://github.com/pyca/cryptography) from 46.0.5 to 48.0.1.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pyca/cryptography/compare/46.0.5...48.0.1)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-version: 48.0.1
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 uv.lock | 132 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 66 insertions(+), 66 deletions(-)

diff --git a/uv.lock b/uv.lock
index d61ed7481b..b75bf34bea 100644
--- a/uv.lock
+++ b/uv.lock
@@ -12,7 +12,7 @@ dev = [
     { name = "clangd-tidy", specifier = "~=1.1" },
     { name = "cmake", specifier = "~=4.2" },
     { name = "cmakelang", specifier = "~=0.6" },
-    { name = "prek", specifier = ">=0.3.5" },
+    { name = "prek", specifier = ">=0.3.10" },
     { name = "pyyaml", specifier = "~=6.0" },
     { name = "ruff", specifier = "~=0.15" },
     { name = "sphinx-lint", specifier = "~=1.0" },
@@ -252,55 +252,55 @@ wheels = [
 
 [[package]]
 name = "cryptography"
-version = "46.0.5"
+version = "48.0.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "cffi", marker = "platform_python_implementation != 'PyPy'" },
 ]
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From 639808c795879e6948a305c6b99631f00c2ba2ff Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 16 Jun 2026 14:08:32 +0200
Subject: [PATCH 1356/1827] Use cell area and volumes for div_par_mod

---
 include/bout/fv_ops.hxx | 59 +++++++++++------------------------------
 1 file changed, 15 insertions(+), 44 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 3a1a4eaee8..9ffc235918 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -710,12 +710,10 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
       const auto iym = i.ym();
 
       result[i] = (0.25 * (f_in[i] + f_up[iyp]) * (v_in[i] + v_up[iyp])
-                       * (coord->J[i] + coord->J.yup()[iyp])
-                       / (sqrt(coord->g_22[i]) + sqrt(coord->g_22.yup()[iyp]))
+                       * coord->cell_area_yhigh()[i]
                    - 0.25 * (f_in[i] + f_down[iym]) * (v_in[i] + v_down[iym])
-                         * (coord->J[i] + coord->J.ydown()[iym])
-                         / (sqrt(coord->g_22[i]) + sqrt(coord->g_22.ydown()[iym])))
-                  / (coord->dy[i] * coord->J[i]);
+                         * coord->cell_area_ylow()[i])
+                  / coord->cell_volume()[i];
     }
     return result;
   }
@@ -756,57 +754,30 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
       // Pre-calculate factors which multiply fluxes
 #if not(BOUT_USE_METRIC_3D)
       // For right cell boundaries
-      const BoutReal common_factor_r =
-          (coord->J(i, j) + coord->J(i, j + 1))
-          / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1)));
+      const BoutReal area_rp = coord->cell_area_yhigh()(i, j);
 
-      const BoutReal flux_factor_rc =
-          common_factor_r / (coord->dy(i, j) * coord->J(i, j));
-      const BoutReal flux_factor_rp =
-          common_factor_r / (coord->dy(i, j + 1) * coord->J(i, j + 1));
-
-      const BoutReal area_rp =
-          common_factor_r * coord->dx(i, j + 1) * coord->dz(i, j + 1);
+      const BoutReal flux_factor_rc = area_rp / coord->cell_volume()(i, j);
+      const BoutReal flux_factor_rp = area_rp / coord->cell_volume()(i, j + 1);
 
       // For left cell boundaries
-      const BoutReal common_factor_l =
-          (coord->J(i, j) + coord->J(i, j - 1))
-          / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1)));
+      const BoutReal area_lc = coord->cell_area_ylow()(i, j);
 
-      const BoutReal flux_factor_lc =
-          common_factor_l / (coord->dy(i, j) * coord->J(i, j));
-      const BoutReal flux_factor_lm =
-          common_factor_l / (coord->dy(i, j - 1) * coord->J(i, j - 1));
-
-      const BoutReal area_lc = common_factor_l * coord->dx(i, j) * coord->dz(i, j);
+      const BoutReal flux_factor_lc = area_lc / coord->cell_volume()(i, j);
+      const BoutReal flux_factor_lm = area_lc / coord->cell_volume()(i, j - 1);
 #endif
       for (int k = 0; k < mesh->LocalNz; k++) {
 #if BOUT_USE_METRIC_3D
         // For right cell boundaries
-        const BoutReal common_factor_r =
-            (coord->J(i, j, k) + coord->J(i, j + 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
-
-        const BoutReal flux_factor_rc =
-            common_factor_r / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal flux_factor_rp =
-            common_factor_r / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
+        const BoutReal area_rp = coord->cell_area_yhigh()(i, j, k);
 
-        const BoutReal area_rp =
-            common_factor_r * coord->dx(i, j + 1, k) * coord->dz(i, j + 1, k);
+        const BoutReal flux_factor_rc = area_rp / coord->cell_volume()(i, j, k);
+        const BoutReal flux_factor_rp = area_rp / coord->cell_volume()(i, j + 1, k);
 
         // For left cell boundaries
-        const BoutReal common_factor_l =
-            (coord->J(i, j, k) + coord->J(i, j - 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
-
-        const BoutReal flux_factor_lc =
-            common_factor_l / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal flux_factor_lm =
-            common_factor_l / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
+        const BoutReal area_lc = coord->cell_area_ylow()(i, j, k);
 
-        const BoutReal area_lc =
-            common_factor_l * coord->dx(i, j, k) * coord->dz(i, j, k);
+        const BoutReal flux_factor_lc = area_lc / coord->cell_volume()(i, j, k);
+        const BoutReal flux_factor_lm = area_lc / coord->cell_volume()(i, j - 1, k);
 #endif
 
         ////////////////////////////////////////////

From 5a2a3dc0e5e19a16c3e3e652717cb917f09a13d7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 16 Jun 2026 14:11:43 +0200
Subject: [PATCH 1357/1827] Use cell area and volumes for Div_par_fvv

---
 include/bout/fv_ops.hxx | 22 +++++++---------------
 1 file changed, 7 insertions(+), 15 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 9ffc235918..6198ca81d6 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -974,24 +974,16 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
 
       for (int k = 0; k < mesh->LocalNz; k++) {
         // For right cell boundaries
-        const BoutReal common_factor_r =
-            (coord->J(i, j, k) + coord->J(i, j + 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
+        const BoutReal area_r = coord->cell_area_yhigh()(i, j, k);
 
-        const BoutReal flux_factor_rc =
-            common_factor_r / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal flux_factor_rp =
-            common_factor_r / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
+        const BoutReal flux_factor_rc = area_r / coord->cell_volume()(i, j, k);
+        const BoutReal flux_factor_rp = area_r / coord->cell_volume()(i, j + 1, k);
 
         // For left cell boundaries
-        const BoutReal common_factor_l =
-            (coord->J(i, j, k) + coord->J(i, j - 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
-
-        const BoutReal flux_factor_lc =
-            common_factor_l / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal flux_factor_lm =
-            common_factor_l / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
+        const BoutReal area_l = coord->cell_area_ylow()(i, j, k);
+
+        const BoutReal flux_factor_lc = area_l / coord->cell_volume()(i, j, k);
+        const BoutReal flux_factor_lm = area_l / coord->cell_volume()(i, j - 1, k);
 
         ////////////////////////////////////////////
         // Reconstruct f at the cell faces

From 820e2219e365ee8250eda82d5ae403e712e6abc6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 16 Jun 2026 14:17:06 +0200
Subject: [PATCH 1358/1827] Use cell area and volumes for Div_par

---
 include/bout/fv_ops.hxx | 41 ++++++++++++-----------------------------
 1 file changed, 12 insertions(+), 29 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 6198ca81d6..e96dfca1d7 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -382,41 +382,24 @@ Field3D Div_par(const Field3D& f_in, const Field3D& v_in, const Field3D& wave_sp
       // Pre-calculate factors which multiply fluxes
 #if not(BOUT_USE_METRIC_3D)
       // For right cell boundaries
-      BoutReal common_factor = (coord->J(i, j) + coord->J(i, j + 1))
-                               / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1)));
-
-      const BoutReal flux_factor_rc = common_factor / (coord->dy(i, j) * coord->J(i, j));
-      const BoutReal flux_factor_rp =
-          common_factor / (coord->dy(i, j + 1) * coord->J(i, j + 1));
-
+      const BoutReal area_r = coord->cell_area_yhigh()(i, j);
+      const BoutReal flux_factor_rc = area_r / coord->cell_volume()(i, j);
+      const BoutReal flux_factor_rp = area_r / coord->cell_volume()(i, j + 1);
       // For left cell boundaries
-      common_factor = (coord->J(i, j) + coord->J(i, j - 1))
-                      / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1)));
-
-      const BoutReal flux_factor_lc = common_factor / (coord->dy(i, j) * coord->J(i, j));
-      const BoutReal flux_factor_lm =
-          common_factor / (coord->dy(i, j - 1) * coord->J(i, j - 1));
+      const BoutReal area_l = coord->cell_area_ylow()(i, j);
+      const BoutReal flux_factor_lc = area_l / coord->cell_volume()(i, j);
+      const BoutReal flux_factor_lm = area_l / coord->cell_volume()(i, j - 1);
 #endif
       for (int k = mesh->zstart; k <= mesh->zend; k++) {
 #if BOUT_USE_METRIC_3D
         // For right cell boundaries
-        BoutReal common_factor =
-            (coord->J(i, j, k) + coord->J(i, j + 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
-
-        BoutReal flux_factor_rc =
-            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
-        BoutReal flux_factor_rp =
-            common_factor / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
-
+        const BoutReal area_r = coord->cell_area_yhigh()(i, j, k);
+        const BoutReal flux_factor_rc = area_r / coord->cell_volume()(i, j, k);
+        const BoutReal flux_factor_rp = area_r / coord->cell_volume()(i, j + 1, k);
         // For left cell boundaries
-        common_factor = (coord->J(i, j, k) + coord->J(i, j - 1, k))
-                        / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
-
-        BoutReal flux_factor_lc =
-            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
-        BoutReal flux_factor_lm =
-            common_factor / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
+        const BoutReal area_l = coord->cell_area_ylow()(i, j, k);
+        const BoutReal flux_factor_lc = area_l / coord->cell_volume()(i, j, k);
+        const BoutReal flux_factor_lm = area_l / coord->cell_volume()(i, j - 1, k);
 #endif
 
         ////////////////////////////////////////////

From 3b0117ea11652b576fbcf8e2dcb2be9163227ce3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 17 Jun 2026 10:46:58 +0200
Subject: [PATCH 1359/1827] Also fill the boundaries to the extend possible

---
 src/mesh/coordinates.cxx | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 39bcf16936..2e1c4ad389 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2099,10 +2099,17 @@ void Coordinates::_compute_cell_area_y() const {
     _cell_area_yhigh.emplace(emptyFrom(area_centre));
     // We cannot setLocation, as that would trigger the computation of staggered
     // metrics.
-    ASSERT0(mesh->ystart > 0);
-    BOUT_FOR(i, mesh->getRegion("RGN_NOY")) {
-      (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
-      (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
+    BOUT_FOR(i, mesh->getRegion("RGN_ALL")) {
+      if (i.y() > 0) {
+        (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
+      } else {
+        (*_cell_area_ylow)[i] = BoutNaN;
+      }
+      if (i.y() < mesh->LocalNy - 1) {
+        (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
+      } else {
+        (*_cell_area_yhigh)[i] = BoutNaN;
+      }
     }
   }
 }

From 22ab659b20394b27d2c042cc425203f7cd63060a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 17 Jun 2026 10:46:58 +0200
Subject: [PATCH 1360/1827] Also fill the boundaries to the extend possible

---
 src/mesh/coordinates.cxx | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 39bcf16936..2e1c4ad389 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2099,10 +2099,17 @@ void Coordinates::_compute_cell_area_y() const {
     _cell_area_yhigh.emplace(emptyFrom(area_centre));
     // We cannot setLocation, as that would trigger the computation of staggered
     // metrics.
-    ASSERT0(mesh->ystart > 0);
-    BOUT_FOR(i, mesh->getRegion("RGN_NOY")) {
-      (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
-      (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
+    BOUT_FOR(i, mesh->getRegion("RGN_ALL")) {
+      if (i.y() > 0) {
+        (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
+      } else {
+        (*_cell_area_ylow)[i] = BoutNaN;
+      }
+      if (i.y() < mesh->LocalNy - 1) {
+        (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
+      } else {
+        (*_cell_area_yhigh)[i] = BoutNaN;
+      }
     }
   }
 }

From 665c1c0a715dd132ac6a0cbc98930a78b3a000fc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 17 Jun 2026 11:31:28 +0200
Subject: [PATCH 1361/1827] Fix off by one error

---
 include/bout/boundary_region_iter.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 296d1c8e53..d7cdff268d 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -540,7 +540,7 @@ public:
   signed char _valid() const { return region->bndry_points[pos].valid; }
   Ind3D _ind() const { return region->bndry_points[pos].index; }
   signed char _boundary_width() const {
-    return region->localmesh->ystart - region->bndry_points[pos].abs_offset;
+    return region->localmesh->ystart - region->bndry_points[pos].abs_offset + 1;
   }
   BoutReal _length([[maybe_unused]] CELL_LOC loc) const {
     ASSERT3(loc == CELL_CENTRE);

From 8019a948ba91b7448e7c278822461780fb0ceea3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 17 Jun 2026 12:21:23 +0200
Subject: [PATCH 1362/1827] Add missing headers

---
 src/mesh/petsc_operators.cxx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 1c8fa7680c..0bec9053bb 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -1,4 +1,7 @@
 #include "bout/build_defines.hxx"
+#include "bout/petsc_interface.hxx"
+#include "bout/petsclib.hxx"
+#include <cmath>
 
 #if BOUT_HAS_PETSC
 

From a9e2006ab0f0c0b9ff77a673001eca5de434fea5 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 17 Jun 2026 11:35:00 +0100
Subject: [PATCH 1363/1827] Integrate splitting of test-multigrid_laplace into
 two tests

---
 .../test-multigrid_laplace/runtest_unsheared  | 55 ---------------
 .../test_multigrid_laplace.py                 | 67 ++++++++-----------
 ...ds => test_multigrid_laplace_unsheared.py} | 36 +++++-----
 3 files changed, 49 insertions(+), 109 deletions(-)
 delete mode 100755 tests/integrated/test-multigrid_laplace/runtest_unsheared
 rename tests/integrated/test-multigrid_laplace/{runtest_multiple_grids => test_multigrid_laplace_unsheared.py} (54%)

diff --git a/tests/integrated/test-multigrid_laplace/runtest_unsheared b/tests/integrated/test-multigrid_laplace/runtest_unsheared
deleted file mode 100755
index e066eeffff..0000000000
--- a/tests/integrated/test-multigrid_laplace/runtest_unsheared
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/usr/bin/env python3
-
-#
-# Run the test, check the error
-#
-
-from boututils.run_wrapper import shell, launch_safe
-from boutdata.collect import collect
-from sys import exit
-
-tol = 1e-9  # Absolute tolerance
-numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
-
-print("Running multigrid Laplacian inversion test")
-success = True
-
-for nproc in [1, 3]:
-    # Make sure we don't use too many cores:
-    # Reduce number of OpenMP threads when using multiple MPI processes
-    mthread = 2
-    if nproc > 1:
-        mthread = 1
-
-    # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
-    cmd = "./test_multigrid_laplace -f BOUT_unsheared.inp NXPE=" + str(nproc)
-
-    shell(["rm data/BOUT.dmp.*.nc"])
-
-    print("   %d processors..." % nproc)
-    s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-    with open("run.log." + str(nproc), "w") as f:
-        f.write(out)
-
-    # Collect errors
-    errors = [
-        collect("max_error" + str(i), path="data") for i in range(1, numTests + 1)
-    ]
-
-    for i, e in enumerate(errors):
-        print("Checking test " + str(i))
-        if e < 0.0:
-            print("Fail, solver did not converge")
-            success = False
-        if e > tol:
-            print("Fail, maximum absolute error = " + str(e))
-            success = False
-        else:
-            print("Pass")
-
-if success:
-    print(" => All multigrid Laplacian inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
index bec6b09fac..eb1c58d775 100755
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
@@ -1,17 +1,13 @@
 #!/usr/bin/env python3
 
-# requires: not metric_3d
-
 #
 # Run the test, check the error
 #
 
-# Cores: 3
-
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
-tol = 2e-7  # Absolute tolerance
+tol = 2e-6  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
 
@@ -20,38 +16,33 @@ def test_multigrid_laplace():
     print("Running multigrid Laplacian inversion test")
     success = True
 
-    for nproc in [1, 3]:
-        # Make sure we don't use too many cores:
-        # Reduce number of OpenMP threads when using multiple MPI processes
-        mthread = 2
-        if nproc > 1:
-            mthread = 1
-
-        # set nxpe on the command line as we only use solution from one point in y,
-        # so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
-        cmd = "./test_multigrid_laplace NXPE=" + str(nproc)
-
-        shell(["rm data/BOUT.dmp.*.nc"])
-
-        print("   %d processors..." % nproc)
-        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-        with open("run.log." + str(nproc), "w") as f:
-            f.write(out)
-
-        # Collect errors
-        errors = [
-            collect("max_error" + str(i), path="data") for i in range(1, numTests + 1)
-        ]
-
-        for i, e in enumerate(errors):
-            print("Checking test " + str(i))
-            if e < 0.0:
-                print("Fail, solver did not converge")
-                success = False
-            if e > tol:
-                print("Fail, maximum absolute error = " + str(e))
-                success = False
-            else:
-                print("Pass")
+    for nproc in [1, 2, 4]:
+        for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]:
+            # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
+            cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc}"
+
+            shell(["rm data/BOUT.dmp.*.nc"])
+
+            print("   %d processors, input file is %s" % (nproc, inputfile))
+            s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+            with open("run.log." + str(nproc), "w") as f:
+                f.write(out)
+
+            # Collect errors
+            errors = [
+                collect("max_error" + str(i), path="data")
+                for i in range(1, numTests + 1)
+            ]
+
+            for i, e in enumerate(errors):
+                print("Checking test " + str(i))
+                if e < 0.0:
+                    print("Fail, solver did not converge")
+                    success = False
+                if e > tol:
+                    print("Fail, maximum absolute error = " + str(e))
+                    success = False
+                else:
+                    print("Pass")
 
     assert success, " => Some failed tests"
diff --git a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py
similarity index 54%
rename from tests/integrated/test-multigrid_laplace/runtest_multiple_grids
rename to tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py
index f264ecc131..3be9bf1bbc 100755
--- a/tests/integrated/test-multigrid_laplace/runtest_multiple_grids
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py
@@ -6,23 +6,32 @@
 
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
-from sys import exit
 
-tol = 2e-6  # Absolute tolerance
+tol = 1e-9  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
-print("Running multigrid Laplacian inversion test")
-success = True
 
-for nproc in [1, 2, 4]:
-    for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]:
-        # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
-        cmd = "./test_multigrid_laplace -f " + inputfile + " NXPE=" + str(nproc)
+def test_multigrid_laplace_unsheared():
+
+    print("Running multigrid Laplacian inversion test (unsheared)")
+    success = True
+
+    for nproc in [1, 3]:
+        # Make sure we don't use too many cores:
+        # Reduce number of OpenMP threads when using multiple MPI processes
+        mthread = 2
+        if nproc > 1:
+            mthread = 1
+
+        # set nxpe on the command line as we only use solution from one point in y,
+        # so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
+        inputfile = "BOUT_unsheared.inp"
+        cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc}"
 
         shell(["rm data/BOUT.dmp.*.nc"])
 
-        print("   %d processors, input file is %s" % (nproc, inputfile))
-        s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+        print("   %d processors..." % nproc)
+        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
         with open("run.log." + str(nproc), "w") as f:
             f.write(out)
 
@@ -42,9 +51,4 @@
             else:
                 print("Pass")
 
-if success:
-    print(" => All multigrid Laplacian inversion tests passed")
-    exit(0)
-else:
-    print(" => Some failed tests")
-    exit(1)
+    assert success, " => Some failed tests"

From b51d38a1ec0998499297efeba84109cb2f0ac371 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 13:05:04 -0700
Subject: [PATCH 1364/1827] NVector: Fix reduce_field callable

---
 src/solver/nvector.hxx | 32 +++++++++++++++++++-------------
 1 file changed, 19 insertions(+), 13 deletions(-)

diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 4d38b24439..bbbb420e9d 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -1,8 +1,8 @@
 /**************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
+ *
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
- * 
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -23,11 +23,15 @@
 #ifndef BOUT_NVECTOR_H
 #define BOUT_NVECTOR_H
 
+#include <bout/bout_types.hxx>
+#include <bout/boutexception.hxx>
 #include <bout/field.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
+#include <functional>
 #include <nvector/nvector_manyvector.h>
 #include <sundials/sundials_nvector.h>
+#include <utility>
 
 #include "bout/sundials_backports.hxx"
 
@@ -77,16 +81,17 @@ private:
     return get_content<T>(v).field;
   }
 
-  template <typename T, typename R, typename... V>
-  static BoutReal reduce_field(const R reduce, const bool allpe, const N_Vector v1,
+  template <typename T, typename Reduce, typename... V>
+  static BoutReal reduce_field(Reduce&& reduce, const bool allpe, const N_Vector v1,
                                const V... v2) {
     BoutReal result = 0;
     const auto region = get_content<T>(v1).getRegion();
-      BOUT_FOR_OMP(i, region, parallel for reduction(+:result)) {
-        result += reduce(get_field<T>(v1)[i], get_field<T>(v2)[i]...);
-      }
+    BOUT_FOR_OMP(i, region, parallel for reduction(+:result)) {
+      result += std::invoke(std::forward<Reduce>(reduce), get_field<T>(v1)[i],
+                            get_field<T>(v2)[i]...);
+    }
 
-      return allpe ? all_reduce(result) : result;
+    return allpe ? all_reduce(result) : result;
   }
 
 public:
@@ -108,7 +113,8 @@ public:
       const Content<T>& content = get_content<T>(x);
       // TODO: ensure no memory leaks
       // T* field_clone = new T(*content.field);
-      T* field_clone = new T(content.field.getMesh(), content.field.getLocation(), content.field.getDirections());
+      T* field_clone = new T(content.field.getMesh(), content.field.getLocation(),
+                             content.field.getDirections());
       field_clone->allocate();
       field_clone->copyBoundary(content.field);
       return create(x->sunctx, *field_clone, content.evolve_bndry, true);
@@ -171,7 +177,7 @@ public:
     };
 
     v->ops->nvl1norm = [](N_Vector x) {
-      return reduce_field<T>(std::abs<BoutReal>, true, x);
+      return reduce_field<T>([](const auto value) { return std::abs(value); }, true, x);
     };
 
     return v;
@@ -179,8 +185,8 @@ public:
 
   template <typename V>
   static N_Vector create(const sundials::Context& ctx, V& subvectors) {
-    const auto v =  callWithSUNContext(N_VNew_ManyVector, ctx, std::size(subvectors),
-                                       std::data(subvectors));
+    const auto v = callWithSUNContext(N_VNew_ManyVector, ctx, std::size(subvectors),
+                                      std::data(subvectors));
     ((N_VectorContent_ManyVector)v->content)->own_data = true;
     return v;
   }

From 45f64739574aa4862f9cdda554fa98f3ba5661e9 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 13:33:55 -0700
Subject: [PATCH 1365/1827] Sundials nvecmanyvector may be missing

During configuration catch when `SUNDIALS::nvecmanyvector`
target is missing. If so, fall back to Sundials' nvector.
---
 cmake/SetupBOUTThirdParty.cmake    | 10 ++++-
 cmake_build_defines.hxx.in         |  1 +
 include/bout/build_config.hxx      |  1 +
 src/solver/impls/arkode/arkode.cxx | 63 +++++++++++++++++++++++++-----
 src/solver/impls/arkode/arkode.hxx | 14 ++++---
 5 files changed, 74 insertions(+), 15 deletions(-)

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 5cf418e83e..f0c98548ea 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -353,6 +353,7 @@ cmake_dependent_option(
   BOUT_USE_SUNDIALS "Enable support for SUNDIALS time solvers" OFF
   "NOT BOUT_DOWNLOAD_SUNDIALS" ON
 )
+set(BOUT_HAS_SUNDIALS_MANYVECTOR OFF)
 if(BOUT_USE_SUNDIALS)
   enable_language(C)
   if(BOUT_DOWNLOAD_SUNDIALS)
@@ -406,7 +407,14 @@ if(BOUT_USE_SUNDIALS)
     set(SUNDIALS_ROOT "${SUNDIALS_DIR}")
   endif()
   target_link_libraries(bout++ PUBLIC SUNDIALS::nvecparallel)
-  target_link_libraries(bout++ PUBLIC SUNDIALS::nvecmanyvector)
+  if(TARGET SUNDIALS::nvecmanyvector)
+    target_link_libraries(bout++ PUBLIC SUNDIALS::nvecmanyvector)
+    set(BOUT_HAS_SUNDIALS_MANYVECTOR ON)
+  else()
+    message(
+      STATUS "SUNDIALS ManyVector support not found; custom N_Vector disabled"
+    )
+  endif()
   target_link_libraries(bout++ PUBLIC SUNDIALS::cvode)
   target_link_libraries(bout++ PUBLIC SUNDIALS::ida)
   target_link_libraries(bout++ PUBLIC SUNDIALS::arkode)
diff --git a/cmake_build_defines.hxx.in b/cmake_build_defines.hxx.in
index 9c73679f29..7fd84c07d7 100644
--- a/cmake_build_defines.hxx.in
+++ b/cmake_build_defines.hxx.in
@@ -20,6 +20,7 @@
 #cmakedefine01 BOUT_HAS_SCOREP
 #cmakedefine01 BOUT_HAS_SLEPC
 #cmakedefine01 BOUT_HAS_SUNDIALS
+#cmakedefine01 BOUT_HAS_SUNDIALS_MANYVECTOR
 #cmakedefine01 BOUT_HAS_UUID_SYSTEM_GENERATOR
 #cmakedefine01 BOUT_USE_COLOR
 #cmakedefine01 BOUT_USE_OPENMP
diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx
index 08158d00e9..c10cd07746 100644
--- a/include/bout/build_config.hxx
+++ b/include/bout/build_config.hxx
@@ -30,6 +30,7 @@ constexpr auto has_uuid_system_generator =
     static_cast<bool>(BOUT_HAS_UUID_SYSTEM_GENERATOR);
 constexpr auto has_slepc = static_cast<bool>(BOUT_HAS_SLEPC);
 constexpr auto has_sundials = static_cast<bool>(BOUT_HAS_SUNDIALS);
+constexpr auto has_sundials_manyvector = static_cast<bool>(BOUT_HAS_SUNDIALS_MANYVECTOR);
 constexpr auto use_backtrace = static_cast<bool>(BOUT_USE_BACKTRACE);
 constexpr auto use_color = static_cast<bool>(BOUT_USE_COLOR);
 constexpr auto use_openmp = static_cast<bool>(BOUT_USE_OPENMP);
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 1c4f998a58..fb984def00 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -207,19 +207,20 @@ int ArkodeSolver::init() {
                n2Dvars(), neq, local_N);
 
   // Allocate memory
-  // uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
-  // if (uvec == nullptr) {
-  //   throw BoutException("SUNDIALS memory allocation failed\n");
-  // }
-
-  // uvec = N_VNew_Bout(suncontext, *f3d.back().var, false);
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   uvec = nvector_from_state(suncontext);
   if (uvec == nullptr) {
     throw BoutException("BOUT N_Vector failed\n");
   }
+#else
+  uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
+  if (uvec == nullptr) {
+    throw BoutException("SUNDIALS memory allocation failed\n");
+  }
 
   // Put the variables into uvec
-  // save_vars(N_VGetArrayPointer(uvec));
+  save_vars(N_VGetArrayPointer(uvec));
+#endif
 
   switch (treatment) {
   case Treatment::ImEx:
@@ -605,8 +606,11 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   }
 
   // Copy variables
-  // load_vars(N_VGetArrayPointer(uvec));
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_state(uvec);
+#else
+  load_vars(N_VGetArrayPointer(uvec));
+#endif
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
   // run_diffusive(simtime);
@@ -627,8 +631,12 @@ void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs_e({:e})", t);
 
   // Load state from udata
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_state(u);
   swap_deriv(du);
+#else
+  load_vars(N_VGetArrayPointer(u));
+#endif
 
   // Get the current timestep
   // Note: ARKodeGetCurrentStep updated too late in older versions
@@ -638,8 +646,12 @@ void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
   run_convective(t);
 
   // Save derivatives to dudata
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_state(u);
   swap_deriv(du);
+#else
+  save_derivs(N_VGetArrayPointer(du));
+#endif
 }
 
 /**************************************************************************
@@ -649,13 +661,21 @@ void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
 void ArkodeSolver::rhs_i(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs_i({:e})", t);
 
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_state(u);
   swap_deriv(du);
+#else
+  load_vars(N_VGetArrayPointer(u));
+#endif
   ARKodeGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_diffusive(t);
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_state(u);
   swap_deriv(du);
+#else
+  save_derivs(N_VGetArrayPointer(du));
+#endif
 }
 
 /**************************************************************************
@@ -664,13 +684,21 @@ void ArkodeSolver::rhs_i(BoutReal t, N_Vector u, N_Vector du) {
 void ArkodeSolver::rhs(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs({:e})", t);
 
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_state(u);
   swap_deriv(du);
+#else
+  load_vars(N_VGetArrayPointer(u));
+#endif
   ARKodeGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs(t);
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_state(u);
   swap_deriv(du);
+#else
+  save_derivs(N_VGetArrayPointer(du));
+#endif
 }
 
 /**************************************************************************
@@ -690,14 +718,22 @@ void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u,
   }
 
   // Load state from udata (as with res function)
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_state(u);
   swap_deriv(rvec);
+#else
+  load_vars(N_VGetArrayPointer(u));
+  load_derivs(N_VGetArrayPointer(rvec));
+#endif
 
   runPreconditioner(t, gamma, delta);
 
   // Save the solution from F_vars
-  // TODO: only need to swap zvec not u
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_deriv(zvec);
+#else
+  save_derivs(N_VGetArrayPointer(zvec));
+#endif
 
   pre_Wtime += bout::globals::mpi->MPI_Wtime() - tstart;
   pre_ncalls++;
@@ -715,14 +751,23 @@ void ArkodeSolver::jac(BoutReal t, N_Vector y, N_Vector v, N_Vector Jv) {
   }
 
   // Load state from ydate
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_state(y);
   swap_deriv(v);
+#else
+  load_vars(N_VGetArrayPointer(y));
+  load_derivs(N_VGetArrayPointer(v));
+#endif
 
   // Call function
   runJacobian(t);
 
   // Save Jv from vars
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   swap_deriv(Jv);
+#else
+  save_derivs(N_VGetArrayPointer(Jv));
+#endif
 }
 
 /**************************************************************************
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 57d386e821..830e9cc6f6 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -45,7 +45,9 @@ RegisterUnavailableSolver
 #include "bout/bout_types.hxx"
 #include "bout/region.hxx"
 #include "bout/sundials_backports.hxx"
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
 #include "../../nvector.hxx"
+#endif
 
 #include <nvector/nvector_parallel.h>
 #include <sundials/sundials_config.h>
@@ -201,12 +203,13 @@ private:
                              std::vector<BoutReal>& f2dtols,
                              std::vector<BoutReal>& f3dtols, bool bndry);
 
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
   N_Vector nvector_from_state(const sundials::Context& ctx) {
     std::vector<N_Vector> subvectors;
     subvectors.reserve(f2d.size() + f3d.size());
     const auto inserter = std::back_inserter(subvectors);
 
-    const auto var_str_to_nvector = [&ctx](auto &var_str) {
+    const auto var_str_to_nvector = [&ctx](auto& var_str) {
       return BoutNVector::create(ctx, *var_str.var, var_str.evolve_bndry);
     };
     std::transform(f2d.cbegin(), f2d.cend(), inserter, var_str_to_nvector);
@@ -216,12 +219,12 @@ private:
 
   void swap_state(const N_Vector u) {
     std::size_t i = 0;
-    for (auto &var_str : f2d) {
+    for (auto& var_str : f2d) {
       BoutNVector::swap(u, *var_str.var, i);
       i++;
     }
 
-    for (auto &var_str : f3d) {
+    for (auto& var_str : f3d) {
       BoutNVector::swap(u, *var_str.var, i);
       i++;
     }
@@ -229,16 +232,17 @@ private:
 
   void swap_deriv(const N_Vector du) {
     std::size_t i = 0;
-    for (auto &var_str : f2d) {
+    for (auto& var_str : f2d) {
       BoutNVector::swap(du, *var_str.F_var, i);
       i++;
     }
 
-    for (auto &var_str : f3d) {
+    for (auto& var_str : f3d) {
       BoutNVector::swap(du, *var_str.F_var, i);
       i++;
     }
   }
+#endif
 
   /// SPGMR solver structure
   SUNLinearSolver sun_solver{nullptr};

From b649511211398fb957afd844e8afd06752ccde68 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 13:56:26 -0700
Subject: [PATCH 1366/1827] ARKode: nvector option to select N_Vector

Defaults to using the Sundials parallel MPI implementation.
If Sundials many-vector is available then the custom N_Vector
is available.
---
 src/solver/impls/arkode/arkode.cxx | 190 +++++++++++++++++------------
 src/solver/impls/arkode/arkode.hxx |  12 ++
 2 files changed, 123 insertions(+), 79 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index fb984def00..48f3900f9c 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -152,6 +152,9 @@ ArkodeSolver::ArkodeSolver(Options* opts)
       use_jacobian((*options)["use_jacobian"]
                        .doc("Use user-supplied Jacobian function")
                        .withDefault(false)),
+      nvector_type((*options)["nvector"]
+                       .doc("N_Vector backend to use: sundials or manyvector")
+                       .withDefault(NVectorType::Sundials)),
 #if ARKODE_OPTIMAL_PARAMS_SUPPORT
       optimize(
           (*options)["optimize"].doc("Use ARKode optimal parameters").withDefault(false)),
@@ -183,6 +186,73 @@ ArkodeSolver::~ArkodeSolver() {
 #endif
 }
 
+/**************************************************************************
+ * N_Vector backend helpers
+ **************************************************************************/
+
+N_Vector ArkodeSolver::create_state_nvector(const int local_N, const int neq) {
+  if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+    auto* vec = nvector_from_state(suncontext);
+    if (vec == nullptr) {
+      throw BoutException("BOUT N_Vector failed\n");
+    }
+    return vec;
+#else
+    throw BoutException("ARKode option 'nvector = manyvector' requested, but BOUT++ "
+                        "was built without SUNDIALS ManyVector support");
+#endif
+  }
+
+  auto* vec =
+      callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
+  if (vec == nullptr) {
+    throw BoutException("SUNDIALS memory allocation failed\n");
+  }
+  save_vars(N_VGetArrayPointer(vec));
+  return vec;
+}
+
+void ArkodeSolver::load_state_from_nvector(N_Vector u) {
+  if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+    swap_state(u);
+    return;
+#endif
+  }
+  load_vars(N_VGetArrayPointer(u));
+}
+
+void ArkodeSolver::restore_state_nvector(N_Vector u) {
+  if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+    swap_state(u);
+    return;
+#endif
+  }
+  static_cast<void>(u);
+}
+
+void ArkodeSolver::load_deriv_from_nvector(N_Vector du) {
+  if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+    swap_deriv(du);
+    return;
+#endif
+  }
+  load_derivs(N_VGetArrayPointer(du));
+}
+
+void ArkodeSolver::restore_deriv_nvector(N_Vector du) {
+  if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+    swap_deriv(du);
+    return;
+#endif
+  }
+  save_derivs(N_VGetArrayPointer(du));
+}
+
 /**************************************************************************
  * Initialise
  **************************************************************************/
@@ -193,6 +263,11 @@ int ArkodeSolver::init() {
 
   output.write("Initialising SUNDIALS' ARKODE solver\n");
 
+  if (use_manyvector() and not BOUT_HAS_SUNDIALS_MANYVECTOR) {
+    throw BoutException("ARKode option 'nvector = manyvector' requested, but BOUT++ "
+                        "was built without SUNDIALS ManyVector support");
+  }
+
   // Calculate number of variables (in generic_solver)
   const int local_N = getLocalN();
 
@@ -206,21 +281,12 @@ int ArkodeSolver::init() {
   output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3Dvars(),
                n2Dvars(), neq, local_N);
 
-  // Allocate memory
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  uvec = nvector_from_state(suncontext);
-  if (uvec == nullptr) {
-    throw BoutException("BOUT N_Vector failed\n");
-  }
-#else
-  uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
-  if (uvec == nullptr) {
-    throw BoutException("SUNDIALS memory allocation failed\n");
-  }
+  output.write("\tUsing {} N_Vector backend\n", use_manyvector()
+                                                    ? "SUNDIALS ManyVector-backed custom"
+                                                    : "SUNDIALS parallel");
 
-  // Put the variables into uvec
-  save_vars(N_VGetArrayPointer(uvec));
-#endif
+  // Allocate memory
+  uvec = create_state_nvector(local_N, neq);
 
   switch (treatment) {
   case Treatment::ImEx:
@@ -606,11 +672,7 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   }
 
   // Copy variables
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_state(uvec);
-#else
-  load_vars(N_VGetArrayPointer(uvec));
-#endif
+  load_state_from_nvector(uvec);
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
   // run_diffusive(simtime);
@@ -631,12 +693,10 @@ void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs_e({:e})", t);
 
   // Load state from udata
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_state(u);
-  swap_deriv(du);
-#else
-  load_vars(N_VGetArrayPointer(u));
-#endif
+  load_state_from_nvector(u);
+  if (use_manyvector()) {
+    load_deriv_from_nvector(du);
+  }
 
   // Get the current timestep
   // Note: ARKodeGetCurrentStep updated too late in older versions
@@ -646,12 +706,8 @@ void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
   run_convective(t);
 
   // Save derivatives to dudata
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_state(u);
-  swap_deriv(du);
-#else
-  save_derivs(N_VGetArrayPointer(du));
-#endif
+  restore_state_nvector(u);
+  restore_deriv_nvector(du);
 }
 
 /**************************************************************************
@@ -661,21 +717,15 @@ void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
 void ArkodeSolver::rhs_i(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs_i({:e})", t);
 
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_state(u);
-  swap_deriv(du);
-#else
-  load_vars(N_VGetArrayPointer(u));
-#endif
+  load_state_from_nvector(u);
+  if (use_manyvector()) {
+    load_deriv_from_nvector(du);
+  }
   ARKodeGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_diffusive(t);
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_state(u);
-  swap_deriv(du);
-#else
-  save_derivs(N_VGetArrayPointer(du));
-#endif
+  restore_state_nvector(u);
+  restore_deriv_nvector(du);
 }
 
 /**************************************************************************
@@ -684,21 +734,15 @@ void ArkodeSolver::rhs_i(BoutReal t, N_Vector u, N_Vector du) {
 void ArkodeSolver::rhs(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs({:e})", t);
 
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_state(u);
-  swap_deriv(du);
-#else
-  load_vars(N_VGetArrayPointer(u));
-#endif
+  load_state_from_nvector(u);
+  if (use_manyvector()) {
+    load_deriv_from_nvector(du);
+  }
   ARKodeGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs(t);
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_state(u);
-  swap_deriv(du);
-#else
-  save_derivs(N_VGetArrayPointer(du));
-#endif
+  restore_state_nvector(u);
+  restore_deriv_nvector(du);
 }
 
 /**************************************************************************
@@ -718,22 +762,16 @@ void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u,
   }
 
   // Load state from udata (as with res function)
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_state(u);
-  swap_deriv(rvec);
-#else
-  load_vars(N_VGetArrayPointer(u));
-  load_derivs(N_VGetArrayPointer(rvec));
-#endif
+  load_state_from_nvector(u);
+  load_deriv_from_nvector(rvec);
 
   runPreconditioner(t, gamma, delta);
 
   // Save the solution from F_vars
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_deriv(zvec);
-#else
-  save_derivs(N_VGetArrayPointer(zvec));
-#endif
+  if (use_manyvector()) {
+    restore_state_nvector(u);
+  }
+  restore_deriv_nvector(zvec);
 
   pre_Wtime += bout::globals::mpi->MPI_Wtime() - tstart;
   pre_ncalls++;
@@ -751,23 +789,17 @@ void ArkodeSolver::jac(BoutReal t, N_Vector y, N_Vector v, N_Vector Jv) {
   }
 
   // Load state from ydate
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_state(y);
-  swap_deriv(v);
-#else
-  load_vars(N_VGetArrayPointer(y));
-  load_derivs(N_VGetArrayPointer(v));
-#endif
+  load_state_from_nvector(y);
+  load_deriv_from_nvector(v);
 
   // Call function
   runJacobian(t);
 
   // Save Jv from vars
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  swap_deriv(Jv);
-#else
-  save_derivs(N_VGetArrayPointer(Jv));
-#endif
+  if (use_manyvector()) {
+    restore_state_nvector(y);
+  }
+  restore_deriv_nvector(Jv);
 }
 
 /**************************************************************************
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 830e9cc6f6..ce1aa40026 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -79,6 +79,9 @@ BOUT_ENUM_CLASS(Treatment, ImEx, Implicit, Explicit);
 BOUT_ENUM_CLASS(AdapMethod, PID, PI, I, Explicit_Gustafsson, Implicit_Gustafsson,
                 ImEx_Gustafsson);
 
+// N_Vector backend
+BOUT_ENUM_CLASS(NVectorType, Sundials, ManyVector);
+
 // Shim for the ARKstep -> ARKode prefix change in SUNDIALS 7.1.0
 #if SUNDIALS_VERSION_LESS_THAN(7, 1, 0)
 #include <arkode/arkode_arkstep.h>
@@ -184,6 +187,8 @@ private:
   bool rightprec;
   /// Use user-supplied Jacobian function
   bool use_jacobian;
+  /// N_Vector backend to use
+  NVectorType nvector_type;
 #if ARKODE_OPTIMAL_PARAMS_SUPPORT
   /// Use ARKode optimal parameters
   bool optimize;
@@ -203,6 +208,13 @@ private:
                              std::vector<BoutReal>& f2dtols,
                              std::vector<BoutReal>& f3dtols, bool bndry);
 
+  bool use_manyvector() const { return nvector_type == NVectorType::ManyVector; }
+  N_Vector create_state_nvector(int local_N, int neq);
+  void load_state_from_nvector(N_Vector u);
+  void restore_state_nvector(N_Vector u);
+  void load_deriv_from_nvector(N_Vector du);
+  void restore_deriv_nvector(N_Vector du);
+
 #if BOUT_HAS_SUNDIALS_MANYVECTOR
   N_Vector nvector_from_state(const sundials::Context& ctx) {
     std::vector<N_Vector> subvectors;

From d894b63db150ff7b877a86702807a008b6b8bdb3 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 14:58:48 -0700
Subject: [PATCH 1367/1827] Sundials N_Vector backend for CVODE and IDA

Extends the Sundials ManyVector to Sundials and IDA interfaces.
To use, set
```
solver:nvector=manyvector
```

The default remains the MPI parallel N_Vector.
---
 include/bout/solver.hxx                   |   3 +
 src/solver/impls/arkode/arkode.cxx        | 138 +++-------
 src/solver/impls/arkode/arkode.hxx        |  59 +---
 src/solver/impls/cvode/cvode.cxx          | 144 +++-------
 src/solver/impls/cvode/cvode.hxx          |  19 +-
 src/solver/impls/ida/ida.cxx              |  76 ++----
 src/solver/impls/ida/ida.hxx              |  13 +-
 src/solver/nvector.hxx                    |  10 +
 src/solver/sundials_nvector_interface.hxx | 313 ++++++++++++++++++++++
 9 files changed, 451 insertions(+), 324 deletions(-)
 create mode 100644 src/solver/sundials_nvector_interface.hxx

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 446acefecb..0e1790d70f 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -50,6 +50,7 @@
 // C function pointer types
 
 class Solver;
+class SundialsNVectorInterface;
 
 /// RHS function pointer
 using rhsfunc = int (*)(BoutReal);
@@ -358,6 +359,8 @@ public:
   int getIterationOffset() const { return iteration_offset; }
 
 protected:
+  friend class SundialsNVectorInterface;
+
   /// Number of command-line arguments
   static int* pargc;
   /// Command-line arguments
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 48f3900f9c..4315202ced 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -186,73 +186,6 @@ ArkodeSolver::~ArkodeSolver() {
 #endif
 }
 
-/**************************************************************************
- * N_Vector backend helpers
- **************************************************************************/
-
-N_Vector ArkodeSolver::create_state_nvector(const int local_N, const int neq) {
-  if (use_manyvector()) {
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-    auto* vec = nvector_from_state(suncontext);
-    if (vec == nullptr) {
-      throw BoutException("BOUT N_Vector failed\n");
-    }
-    return vec;
-#else
-    throw BoutException("ARKode option 'nvector = manyvector' requested, but BOUT++ "
-                        "was built without SUNDIALS ManyVector support");
-#endif
-  }
-
-  auto* vec =
-      callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
-  if (vec == nullptr) {
-    throw BoutException("SUNDIALS memory allocation failed\n");
-  }
-  save_vars(N_VGetArrayPointer(vec));
-  return vec;
-}
-
-void ArkodeSolver::load_state_from_nvector(N_Vector u) {
-  if (use_manyvector()) {
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-    swap_state(u);
-    return;
-#endif
-  }
-  load_vars(N_VGetArrayPointer(u));
-}
-
-void ArkodeSolver::restore_state_nvector(N_Vector u) {
-  if (use_manyvector()) {
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-    swap_state(u);
-    return;
-#endif
-  }
-  static_cast<void>(u);
-}
-
-void ArkodeSolver::load_deriv_from_nvector(N_Vector du) {
-  if (use_manyvector()) {
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-    swap_deriv(du);
-    return;
-#endif
-  }
-  load_derivs(N_VGetArrayPointer(du));
-}
-
-void ArkodeSolver::restore_deriv_nvector(N_Vector du) {
-  if (use_manyvector()) {
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-    swap_deriv(du);
-    return;
-#endif
-  }
-  save_derivs(N_VGetArrayPointer(du));
-}
-
 /**************************************************************************
  * Initialise
  **************************************************************************/
@@ -260,13 +193,10 @@ void ArkodeSolver::restore_deriv_nvector(N_Vector du) {
 int ArkodeSolver::init() {
 
   Solver::init();
+  const auto backend = nvector_backend();
 
   output.write("Initialising SUNDIALS' ARKODE solver\n");
-
-  if (use_manyvector() and not BOUT_HAS_SUNDIALS_MANYVECTOR) {
-    throw BoutException("ARKode option 'nvector = manyvector' requested, but BOUT++ "
-                        "was built without SUNDIALS ManyVector support");
-  }
+  backend.ensure_manyvector_available();
 
   // Calculate number of variables (in generic_solver)
   const int local_N = getLocalN();
@@ -281,12 +211,10 @@ int ArkodeSolver::init() {
   output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3Dvars(),
                n2Dvars(), neq, local_N);
 
-  output.write("\tUsing {} N_Vector backend\n", use_manyvector()
-                                                    ? "SUNDIALS ManyVector-backed custom"
-                                                    : "SUNDIALS parallel");
+  output.write("\tUsing {} N_Vector backend\n", backend.backend_name());
 
   // Allocate memory
-  uvec = create_state_nvector(local_N, neq);
+  uvec = backend.create_state_vector(local_N, neq);
 
   switch (treatment) {
   case Treatment::ImEx:
@@ -638,6 +566,7 @@ int ArkodeSolver::run() {
 
 BoutReal ArkodeSolver::run(BoutReal tout) {
   TRACE("Running solver: solver::run({:e})", tout);
+  const auto backend = nvector_backend();
 
   bout::globals::mpi->MPI_Barrier(BoutComm::get());
 
@@ -672,7 +601,7 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   }
 
   // Copy variables
-  load_state_from_nvector(uvec);
+  backend.copy_state_from_vector(uvec);
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
   // run_diffusive(simtime);
@@ -691,12 +620,11 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
 
 void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs_e({:e})", t);
+  const auto backend = nvector_backend();
 
   // Load state from udata
-  load_state_from_nvector(u);
-  if (use_manyvector()) {
-    load_deriv_from_nvector(du);
-  }
+  backend.copy_state_from_vector(u);
+  backend.copy_deriv_from_vector(du);
 
   // Get the current timestep
   // Note: ARKodeGetCurrentStep updated too late in older versions
@@ -706,8 +634,8 @@ void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
   run_convective(t);
 
   // Save derivatives to dudata
-  restore_state_nvector(u);
-  restore_deriv_nvector(du);
+  backend.copy_state_to_vector(u);
+  backend.copy_deriv_to_vector(du);
 }
 
 /**************************************************************************
@@ -716,16 +644,15 @@ void ArkodeSolver::rhs_e(BoutReal t, N_Vector u, N_Vector du) {
 
 void ArkodeSolver::rhs_i(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs_i({:e})", t);
+  const auto backend = nvector_backend();
 
-  load_state_from_nvector(u);
-  if (use_manyvector()) {
-    load_deriv_from_nvector(du);
-  }
+  backend.copy_state_from_vector(u);
+  backend.copy_deriv_from_vector(du);
   ARKodeGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_diffusive(t);
-  restore_state_nvector(u);
-  restore_deriv_nvector(du);
+  backend.copy_state_to_vector(u);
+  backend.copy_deriv_to_vector(du);
 }
 
 /**************************************************************************
@@ -733,16 +660,15 @@ void ArkodeSolver::rhs_i(BoutReal t, N_Vector u, N_Vector du) {
  **************************************************************************/
 void ArkodeSolver::rhs(BoutReal t, N_Vector u, N_Vector du) {
   TRACE("Running RHS: ArkodeSolver::rhs({:e})", t);
+  const auto backend = nvector_backend();
 
-  load_state_from_nvector(u);
-  if (use_manyvector()) {
-    load_deriv_from_nvector(du);
-  }
+  backend.copy_state_from_vector(u);
+  backend.copy_deriv_from_vector(du);
   ARKodeGetLastStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs(t);
-  restore_state_nvector(u);
-  restore_deriv_nvector(du);
+  backend.copy_state_to_vector(u);
+  backend.copy_deriv_to_vector(du);
 }
 
 /**************************************************************************
@@ -752,6 +678,7 @@ void ArkodeSolver::rhs(BoutReal t, N_Vector u, N_Vector du) {
 void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u,
                        N_Vector rvec, N_Vector zvec) {
   TRACE("Running preconditioner: ArkodeSolver::pre({:e})", t);
+  const auto backend = nvector_backend();
 
   const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
 
@@ -762,16 +689,14 @@ void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u,
   }
 
   // Load state from udata (as with res function)
-  load_state_from_nvector(u);
-  load_deriv_from_nvector(rvec);
+  backend.copy_state_from_vector(u);
+  backend.copy_deriv_from_vector(rvec);
 
   runPreconditioner(t, gamma, delta);
 
   // Save the solution from F_vars
-  if (use_manyvector()) {
-    restore_state_nvector(u);
-  }
-  restore_deriv_nvector(zvec);
+  backend.copy_state_to_vector(u);
+  backend.copy_deriv_to_vector(zvec);
 
   pre_Wtime += bout::globals::mpi->MPI_Wtime() - tstart;
   pre_ncalls++;
@@ -783,23 +708,22 @@ void ArkodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u,
 
 void ArkodeSolver::jac(BoutReal t, N_Vector y, N_Vector v, N_Vector Jv) {
   TRACE("Running Jacobian: ArkodeSolver::jac({:e})", t);
+  const auto backend = nvector_backend();
 
   if (not hasJacobian()) {
     throw BoutException("No jacobian function supplied!\n");
   }
 
   // Load state from ydate
-  load_state_from_nvector(y);
-  load_deriv_from_nvector(v);
+  backend.copy_state_from_vector(y);
+  backend.copy_deriv_from_vector(v);
 
   // Call function
   runJacobian(t);
 
   // Save Jv from vars
-  if (use_manyvector()) {
-    restore_state_nvector(y);
-  }
-  restore_deriv_nvector(Jv);
+  backend.copy_state_to_vector(y);
+  backend.copy_deriv_to_vector(Jv);
 }
 
 /**************************************************************************
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index ce1aa40026..cc6b21c325 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -2,10 +2,8 @@
  * Interface to ARKODE solver
  * NOTE: ARKode is currently in beta testing so use with cautious optimism
  *
- * NOTE: Only one solver can currently be compiled in
- *
  **************************************************************************
- * Copyright 2010-2024 BOUT++ contributors
+ * Copyright 2010-2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -41,13 +39,11 @@ RegisterUnavailableSolver
 
 #else
 
+#include "../../sundials_nvector_interface.hxx"
 #include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/region.hxx"
 #include "bout/sundials_backports.hxx"
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-#include "../../nvector.hxx"
-#endif
 
 #include <nvector/nvector_parallel.h>
 #include <sundials/sundials_config.h>
@@ -79,9 +75,6 @@ BOUT_ENUM_CLASS(Treatment, ImEx, Implicit, Explicit);
 BOUT_ENUM_CLASS(AdapMethod, PID, PI, I, Explicit_Gustafsson, Implicit_Gustafsson,
                 ImEx_Gustafsson);
 
-// N_Vector backend
-BOUT_ENUM_CLASS(NVectorType, Sundials, ManyVector);
-
 // Shim for the ARKstep -> ARKode prefix change in SUNDIALS 7.1.0
 #if SUNDIALS_VERSION_LESS_THAN(7, 1, 0)
 #include <arkode/arkode_arkstep.h>
@@ -208,53 +201,9 @@ private:
                              std::vector<BoutReal>& f2dtols,
                              std::vector<BoutReal>& f3dtols, bool bndry);
 
-  bool use_manyvector() const { return nvector_type == NVectorType::ManyVector; }
-  N_Vector create_state_nvector(int local_N, int neq);
-  void load_state_from_nvector(N_Vector u);
-  void restore_state_nvector(N_Vector u);
-  void load_deriv_from_nvector(N_Vector du);
-  void restore_deriv_nvector(N_Vector du);
-
-#if BOUT_HAS_SUNDIALS_MANYVECTOR
-  N_Vector nvector_from_state(const sundials::Context& ctx) {
-    std::vector<N_Vector> subvectors;
-    subvectors.reserve(f2d.size() + f3d.size());
-    const auto inserter = std::back_inserter(subvectors);
-
-    const auto var_str_to_nvector = [&ctx](auto& var_str) {
-      return BoutNVector::create(ctx, *var_str.var, var_str.evolve_bndry);
-    };
-    std::transform(f2d.cbegin(), f2d.cend(), inserter, var_str_to_nvector);
-    std::transform(f3d.cbegin(), f3d.cend(), inserter, var_str_to_nvector);
-    return BoutNVector::create(ctx, subvectors);
-  }
-
-  void swap_state(const N_Vector u) {
-    std::size_t i = 0;
-    for (auto& var_str : f2d) {
-      BoutNVector::swap(u, *var_str.var, i);
-      i++;
-    }
-
-    for (auto& var_str : f3d) {
-      BoutNVector::swap(u, *var_str.var, i);
-      i++;
-    }
-  }
-
-  void swap_deriv(const N_Vector du) {
-    std::size_t i = 0;
-    for (auto& var_str : f2d) {
-      BoutNVector::swap(du, *var_str.F_var, i);
-      i++;
-    }
-
-    for (auto& var_str : f3d) {
-      BoutNVector::swap(du, *var_str.F_var, i);
-      i++;
-    }
+  SundialsNVectorInterface nvector_backend() {
+    return SundialsNVectorInterface(*this, suncontext, nvector_type);
   }
-#endif
 
   /// SPGMR solver structure
   SUNLinearSolver sun_solver{nullptr};
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 4f72e65933..6727dcb806 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -3,7 +3,7 @@
  *
  *
  **************************************************************************
- * Copyright 2010-2024 BOUT++ contributors
+ * Copyright 2010-2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -130,6 +130,9 @@ CvodeSolver::CvodeSolver(Options* opts)
                     .doc("Use right preconditioner? Otherwise use left.")
                     .withDefault(false)),
       use_jacobian((*options)["use_jacobian"].withDefault(false)),
+      nvector_type((*options)["nvector"]
+                       .doc("N_Vector backend to use: sundials or manyvector")
+                       .withDefault(NVectorType::Sundials)),
       cvode_nonlinear_convergence_coef(
           (*options)["cvode_nonlinear_convergence_coef"]
               .doc("Safety factor used in the nonlinear convergence test")
@@ -177,8 +180,10 @@ CvodeSolver::~CvodeSolver() {
  **************************************************************************/
 
 int CvodeSolver::init() {
+  const auto backend = nvector_backend();
 
   Solver::init();
+  backend.ensure_manyvector_available();
 
   output_progress.write("Initialising SUNDIALS' CVODE solver\n");
 
@@ -194,15 +199,10 @@ int CvodeSolver::init() {
 
   output_info.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n",
                     n3Dvars(), n2Dvars(), neq, local_N);
+  output_info.write("\tUsing {} N_Vector backend\n", backend.backend_name());
 
   // Allocate memory
-  uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
-  if (uvec == nullptr) {
-    throw BoutException("SUNDIALS memory allocation failed\n");
-  }
-
-  // Put the variables into uvec
-  save_vars(N_VGetArrayPointer(uvec));
+  uvec = backend.create_state_vector(local_N, neq);
 
   if (adams_moulton) {
     // By default use functional iteration for Adams-Moulton
@@ -274,12 +274,10 @@ int CvodeSolver::init() {
                      return Options::root()[f3.name]["atol"].withDefault(abstol);
                    });
 
-    N_Vector abstolvec = N_VClone(uvec);
-    if (abstolvec == nullptr) {
-      throw BoutException("SUNDIALS memory allocation (abstol vector) failed\n");
-    }
+    N_Vector abstolvec =
+        backend.clone_vector_like(uvec, "SUNDIALS memory allocation (abstol vector)");
 
-    set_vector_option_values(N_VGetArrayPointer(abstolvec), f2dtols, f3dtols);
+    backend.fill_vector_values(abstolvec, f2dtols, f3dtols);
 
     if (CVodeSVtolerances(cvode_mem, reltol, abstolvec) != CV_SUCCESS) {
       throw BoutException("CVodeSVtolerances failed\n");
@@ -316,14 +314,10 @@ int CvodeSolver::init() {
     auto f2d_constraints = create_constraints(f2d);
     auto f3d_constraints = create_constraints(f3d);
 
-    N_Vector constraints_vec = N_VClone(uvec);
-    if (constraints_vec == nullptr) {
-      throw BoutException("SUNDIALS memory allocation (positivity constraints vector) "
-                          "failed\n");
-    }
+    N_Vector constraints_vec = backend.clone_vector_like(
+        uvec, "SUNDIALS memory allocation (positivity constraints vector)");
 
-    set_vector_option_values(N_VGetArrayPointer(constraints_vec), f2d_constraints,
-                             f3d_constraints);
+    backend.fill_vector_values(constraints_vec, f2d_constraints, f3d_constraints);
 
     if (CVodeSetConstraints(cvode_mem, constraints_vec) != CV_SUCCESS) {
       throw BoutException("CVodeSetConstraints failed\n");
@@ -565,6 +559,7 @@ int CvodeSolver::run() {
 
 BoutReal CvodeSolver::run(BoutReal tout) {
   TRACE("Running solver: solver::run({})", tout);
+  const auto backend = nvector_backend();
 
   bout::globals::mpi->MPI_Barrier(BoutComm::get());
 
@@ -598,7 +593,7 @@ BoutReal CvodeSolver::run(BoutReal tout) {
   }
 
   // Copy variables
-  load_vars(N_VGetArrayPointer(uvec));
+  backend.copy_state_from_vector(uvec);
 
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
@@ -615,11 +610,12 @@ BoutReal CvodeSolver::run(BoutReal tout) {
  * RHS function du = F(t, u)
  **************************************************************************/
 
-void CvodeSolver::rhs(BoutReal t, BoutReal* udata, BoutReal* dudata, bool linear) {
+void CvodeSolver::rhs(BoutReal t, N_Vector u, N_Vector du, bool linear) {
   TRACE("Running RHS: CvodeSolver::res({})", t);
+  const auto backend = nvector_backend();
 
   // Load state from udata
-  load_vars(udata);
+  backend.copy_state_from_vector(u);
 
   // Get the current timestep
   // Note: CVodeGetCurrentStep updated too late in older versions
@@ -629,39 +625,38 @@ void CvodeSolver::rhs(BoutReal t, BoutReal* udata, BoutReal* dudata, bool linear
   run_rhs(t, linear);
 
   // Save derivatives to dudata
-  save_derivs(dudata);
+  backend.copy_state_to_vector(u);
+  backend.copy_deriv_to_vector(du);
 }
 
 /**************************************************************************
  * Preconditioner function
  **************************************************************************/
 
-void CvodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata,
-                      BoutReal* rvec, BoutReal* zvec) {
+void CvodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u,
+                      N_Vector rvec, N_Vector zvec) {
   TRACE("Running preconditioner: CvodeSolver::pre({})", t);
+  const auto backend = nvector_backend();
 
   BoutReal tstart = bout::globals::mpi->MPI_Wtime();
 
-  const auto length = N_VGetLocalLength_Parallel(uvec);
-
   if (!hasPreconditioner()) {
     // Identity (but should never happen)
-    for (int i = 0; i < length; i++) {
-      zvec[i] = rvec[i];
-    }
+    N_VScale(1.0, rvec, zvec);
     return;
   }
 
   // Load state from udata (as with res function)
-  load_vars(udata);
+  backend.copy_state_from_vector(u);
 
   // Load vector to be inverted into F_vars
-  load_derivs(rvec);
+  backend.copy_deriv_from_vector(rvec);
 
   runPreconditioner(t, gamma, delta);
 
   // Save the solution from F_vars
-  save_derivs(zvec);
+  backend.copy_state_to_vector(u);
+  backend.copy_deriv_to_vector(zvec);
 
   pre_Wtime += bout::globals::mpi->MPI_Wtime() - tstart;
   pre_ncalls++;
@@ -671,24 +666,26 @@ void CvodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udat
  * Jacobian-vector multiplication function
  **************************************************************************/
 
-void CvodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata) {
+void CvodeSolver::jac(BoutReal t, N_Vector y, N_Vector v, N_Vector Jv) {
   TRACE("Running Jacobian: CvodeSolver::jac({})", t);
+  const auto backend = nvector_backend();
 
   if (not hasJacobian()) {
     throw BoutException("No jacobian function supplied!\n");
   }
 
   // Load state from ydate
-  load_vars(ydata);
+  backend.copy_state_from_vector(y);
 
   // Load vector to be multiplied into F_vars
-  load_derivs(vdata);
+  backend.copy_deriv_from_vector(v);
 
   // Call function
   runJacobian(t);
 
   // Save Jv from vars
-  save_derivs(Jvdata);
+  backend.copy_state_to_vector(y);
+  backend.copy_deriv_to_vector(Jv);
 }
 
 /**************************************************************************
@@ -698,15 +695,11 @@ void CvodeSolver::jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jv
 // NOLINTBEGIN(readability-identifier-length)
 namespace {
 int cvode_linear_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
-
-  BoutReal* udata = N_VGetArrayPointer(u);
-  BoutReal* dudata = N_VGetArrayPointer(du);
-
   auto* s = static_cast<CvodeSolver*>(user_data);
 
   // Calculate RHS function
   try {
-    s->rhs(t, udata, dudata, true);
+    s->rhs(t, u, du, true);
   } catch (BoutRhsFail& error) {
     return 1;
   }
@@ -714,15 +707,11 @@ int cvode_linear_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
 }
 
 int cvode_nonlinear_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
-
-  BoutReal* udata = N_VGetArrayPointer(u);
-  BoutReal* dudata = N_VGetArrayPointer(du);
-
   auto* s = static_cast<CvodeSolver*>(user_data);
 
   // Calculate RHS function
   try {
-    s->rhs(t, udata, dudata, false);
+    s->rhs(t, u, du, false);
   } catch (BoutRhsFail& error) {
     return 1;
   }
@@ -738,14 +727,10 @@ int cvode_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector
 /// Preconditioner function
 int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec,
               BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) {
-  BoutReal* udata = N_VGetArrayPointer(yy);
-  BoutReal* rdata = N_VGetArrayPointer(rvec);
-  BoutReal* zdata = N_VGetArrayPointer(zvec);
-
   auto* s = static_cast<CvodeSolver*>(user_data);
 
   // Calculate residuals
-  s->pre(t, gamma, delta, udata, rdata, zdata);
+  s->pre(t, gamma, delta, yy, rvec, zvec);
 
   return 0;
 }
@@ -753,66 +738,19 @@ int cvode_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vec
 /// Jacobian-vector multiplication function
 int cvode_jac(N_Vector v, N_Vector Jv, BoutReal t, N_Vector y, N_Vector UNUSED(fy),
               void* user_data, N_Vector UNUSED(tmp)) {
-  BoutReal* ydata = N_VGetArrayPointer(y);   ///< System state
-  BoutReal* vdata = N_VGetArrayPointer(v);   ///< Input vector
-  BoutReal* Jvdata = N_VGetArrayPointer(Jv); ///< Jacobian*vector output
-
   auto* s = static_cast<CvodeSolver*>(user_data);
 
-  s->jac(t, ydata, vdata, Jvdata);
+  s->jac(t, y, v, Jv);
 
   return 0;
 }
 } // namespace
 // NOLINTEND(readability-identifier-length)
 
-/**************************************************************************
- * CVODE vector option functions
- **************************************************************************/
-
-void CvodeSolver::set_vector_option_values(BoutReal* option_data,
-                                           std::vector<BoutReal>& f2dtols,
-                                           std::vector<BoutReal>& f3dtols) {
-  int p = 0; // Counter for location in option_data array
-
-  // All boundaries
-  for (const auto& i2d : bout::globals::mesh->getRegion2D("RGN_BNDRY")) {
-    loop_vector_option_values_op(i2d, option_data, p, f2dtols, f3dtols, true);
-  }
-  // Bulk of points
-  for (const auto& i2d : bout::globals::mesh->getRegion2D("RGN_NOBNDRY")) {
-    loop_vector_option_values_op(i2d, option_data, p, f2dtols, f3dtols, false);
-  }
-}
-
-void CvodeSolver::loop_vector_option_values_op(Ind2D UNUSED(i2d), BoutReal* option_data,
-                                               int& p, std::vector<BoutReal>& f2dtols,
-                                               std::vector<BoutReal>& f3dtols,
-                                               bool bndry) {
-  // Loop over 2D variables
-  for (std::vector<BoutReal>::size_type i = 0; i < f2dtols.size(); i++) {
-    if (bndry && !f2d[i].evolve_bndry) {
-      continue;
-    }
-    option_data[p] = f2dtols[i];
-    p++;
-  }
-
-  for (int jz = 0; jz < bout::globals::mesh->LocalNz; jz++) {
-    // Loop over 3D variables
-    for (std::vector<BoutReal>::size_type i = 0; i < f3dtols.size(); i++) {
-      if (bndry && !f3d[i].evolve_bndry) {
-        continue;
-      }
-      option_data[p] = f3dtols[i];
-      p++;
-    }
-  }
-}
-
 void CvodeSolver::resetInternalFields() {
+  const auto backend = nvector_backend();
 
-  save_vars(N_VGetArrayPointer(uvec));
+  backend.copy_state_to_vector(uvec);
 
   if (CVodeReInit(cvode_mem, simtime, uvec) != CV_SUCCESS) {
     throw BoutException("CVodeReInit failed\n");
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index f0cc2eedf8..29ad4d40af 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -40,6 +40,7 @@ RegisterUnavailableSolver
 
 #else
 
+#include "../../sundials_nvector_interface.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/region.hxx"
 #include "bout/sundials_backports.hxx"
@@ -68,10 +69,10 @@ public:
   void resetInternalFields() override;
 
   // These functions are used internally (but need to be public)
-  void rhs(BoutReal t, BoutReal* udata, BoutReal* dudata, bool linear);
-  void pre(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec,
-           BoutReal* zvec);
-  void jac(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
+  void rhs(BoutReal t, N_Vector u, N_Vector du, bool linear);
+  void pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u, N_Vector rvec,
+           N_Vector zvec);
+  void jac(BoutReal t, N_Vector y, N_Vector v, N_Vector Jv);
 
 private:
   BoutReal hcur; //< Current internal timestep
@@ -122,6 +123,7 @@ private:
   /// Use right preconditioner? Otherwise use left.
   bool rightprec;
   bool use_jacobian;
+  NVectorType nvector_type;
   BoutReal cvode_nonlinear_convergence_coef;
   BoutReal cvode_linear_convergence_coef;
 
@@ -139,14 +141,13 @@ private:
 
   bool cvode_initialised{false};
 
-  void set_vector_option_values(BoutReal* option_data, std::vector<BoutReal>& f2dtols,
-                                std::vector<BoutReal>& f3dtols);
-  void loop_vector_option_values_op(Ind2D i2d, BoutReal* option_data, int& p,
-                                    std::vector<BoutReal>& f2dtols,
-                                    std::vector<BoutReal>& f3dtols, bool bndry);
   template <class FieldType>
   std::vector<BoutReal> create_constraints(const std::vector<VarStr<FieldType>>& fields);
 
+  SundialsNVectorInterface nvector_backend() {
+    return SundialsNVectorInterface(*this, suncontext, nvector_type);
+  }
+
   /// SPGMR solver structure
   SUNLinearSolver sun_solver{nullptr};
   /// Solver for functional iterations for Adams-Moulton
diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx
index 84a0bd4abd..61fece1b8b 100644
--- a/src/solver/impls/ida/ida.cxx
+++ b/src/solver/impls/ida/ida.cxx
@@ -80,6 +80,9 @@ IdaSolver::IdaSolver(Options* opts)
       correct_start((*options)["correct_start"]
                         .doc("Correct the initial values")
                         .withDefault(true)),
+      nvector_type((*options)["nvector"]
+                       .doc("N_Vector backend to use: sundials or manyvector")
+                       .withDefault(NVectorType::Sundials)),
       suncontext(createSUNContext(BoutComm::get())) {
   has_constraints = true; // This solver has constraints
 }
@@ -99,8 +102,10 @@ IdaSolver::~IdaSolver() {
  **************************************************************************/
 
 int IdaSolver::init() {
+  const auto backend = nvector_backend();
 
   Solver::init();
+  backend.ensure_manyvector_available();
 
   output.write("Initialising IDA solver\n");
 
@@ -119,32 +124,21 @@ int IdaSolver::init() {
 
   output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3d, n2d,
                neq, local_N);
+  output.write("\tUsing {} N_Vector backend\n", backend.backend_name());
 
   // Allocate memory
-  uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
-  if (uvec == nullptr) {
-    throw BoutException("SUNDIALS memory allocation failed\n");
-  }
-  duvec = N_VClone(uvec);
-  if (duvec == nullptr) {
-    throw BoutException("SUNDIALS memory allocation failed\n");
-  }
-  id = N_VClone(uvec);
-  if (id == nullptr) {
-    throw BoutException("SUNDIALS memory allocation failed\n");
-  }
-
-  // Put the variables into uvec
-  save_vars(N_VGetArrayPointer(uvec));
+  uvec = backend.create_state_vector(local_N, neq);
+  duvec = backend.clone_vector_like(uvec, "SUNDIALS memory allocation failed");
+  id = backend.clone_vector_like(uvec, "SUNDIALS memory allocation failed");
 
   // Get the starting time derivative
   run_rhs(simtime);
 
   // Put the time-derivatives into duvec
-  save_derivs(N_VGetArrayPointer(duvec));
+  backend.copy_deriv_to_vector(duvec);
 
   // Set the equation type in id(Differential or Algebraic. This is optional)
-  set_id(N_VGetArrayPointer(id));
+  backend.fill_id_vector(id);
 
   // Call IDACreate to initialise
   idamem = callWithSUNContext(IDACreate, suncontext);
@@ -258,6 +252,7 @@ int IdaSolver::run() {
 
 BoutReal IdaSolver::run(BoutReal tout) {
   TRACE("Running solver: solver::run({:e})", tout);
+  const auto backend = nvector_backend();
 
   if (!initialised) {
     throw BoutException("Running IDA solver without initialisation\n");
@@ -269,7 +264,7 @@ BoutReal IdaSolver::run(BoutReal tout) {
   const int flag = IDASolve(idamem, tout, &simtime, uvec, duvec, IDA_NORMAL);
 
   // Copy variables
-  load_vars(N_VGetArrayPointer(uvec));
+  backend.copy_state_from_vector(uvec);
 
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
@@ -287,55 +282,50 @@ BoutReal IdaSolver::run(BoutReal tout) {
  * Residual function F(t, u, du)
  **************************************************************************/
 
-void IdaSolver::res(BoutReal t, BoutReal* udata, BoutReal* dudata, BoutReal* rdata) {
+void IdaSolver::res(BoutReal t, N_Vector u, N_Vector du, N_Vector rr) {
   TRACE("Running RHS: IdaSolver::res({:e})", t);
+  const auto backend = nvector_backend();
 
   // Load state from udata
-  load_vars(udata);
+  backend.copy_state_from_vector(u);
 
   // Call RHS function
   run_rhs(t);
 
   // Save derivatives to rdata (residual)
-  save_derivs(rdata);
-
-  // If a differential equation, subtract dudata
-  const auto length = N_VGetLocalLength_Parallel(id);
-  const BoutReal* idd = N_VGetArrayPointer(id);
-  for (int i = 0; i < length; i++) {
-    if (idd[i] > 0.5) { // 1 -> differential, 0 -> algebraic
-      rdata[i] -= dudata[i];
-    }
-  }
+  backend.copy_state_to_vector(u);
+  backend.copy_deriv_to_vector(rr);
+  backend.subtract_differential_term(rr, du, id);
 }
 
 /**************************************************************************
  * Preconditioner function
  **************************************************************************/
 
-void IdaSolver::pre(BoutReal t, BoutReal cj, BoutReal delta, BoutReal* udata,
-                    BoutReal* rvec, BoutReal* zvec) {
+void IdaSolver::pre(BoutReal t, BoutReal cj, BoutReal delta, N_Vector u, N_Vector rvec,
+                    N_Vector zvec) {
   TRACE("Running preconditioner: IdaSolver::pre({:e})", t);
+  const auto backend = nvector_backend();
 
   const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
 
   if (!hasPreconditioner()) {
     // Identity (but should never happen)
-    const auto length = N_VGetLocalLength_Parallel(id);
-    std::copy(rvec, rvec + length, zvec);
+    N_VScale(1.0, rvec, zvec);
     return;
   }
 
   // Load state from udata (as with res function)
-  load_vars(udata);
+  backend.copy_state_from_vector(u);
 
   // Load vector to be inverted into F_vars
-  load_derivs(rvec);
+  backend.copy_deriv_from_vector(rvec);
 
   runPreconditioner(t, cj, delta);
 
   // Save the solution from F_vars
-  save_derivs(zvec);
+  backend.copy_state_to_vector(u);
+  backend.copy_deriv_to_vector(zvec);
 
   pre_Wtime += bout::globals::mpi->MPI_Wtime() - tstart;
   pre_ncalls++;
@@ -348,14 +338,10 @@ void IdaSolver::pre(BoutReal t, BoutReal cj, BoutReal delta, BoutReal* udata,
 // NOLINTBEGIN(readability-identifier-length)
 namespace {
 int idares(BoutReal t, N_Vector u, N_Vector du, N_Vector rr, void* user_data) {
-  BoutReal* udata = N_VGetArrayPointer(u);
-  BoutReal* dudata = N_VGetArrayPointer(du);
-  BoutReal* rdata = N_VGetArrayPointer(rr);
-
   auto* s = static_cast<IdaSolver*>(user_data);
 
   // Calculate residuals
-  s->res(t, udata, dudata, rdata);
+  s->res(t, u, du, rr);
 
   return 0;
 }
@@ -369,14 +355,10 @@ int ida_bbd_res(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du
 // Preconditioner function
 int ida_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector UNUSED(rr),
             N_Vector rvec, N_Vector zvec, BoutReal cj, BoutReal delta, void* user_data) {
-  BoutReal* udata = N_VGetArrayPointer(yy);
-  BoutReal* rdata = N_VGetArrayPointer(rvec);
-  BoutReal* zdata = N_VGetArrayPointer(zvec);
-
   auto* s = static_cast<IdaSolver*>(user_data);
 
   // Calculate residuals
-  s->pre(t, cj, delta, udata, rdata, zdata);
+  s->pre(t, cj, delta, yy, rvec, zvec);
 
   return 0;
 }
diff --git a/src/solver/impls/ida/ida.hxx b/src/solver/impls/ida/ida.hxx
index 199539f1d6..afce71401b 100644
--- a/src/solver/impls/ida/ida.hxx
+++ b/src/solver/impls/ida/ida.hxx
@@ -42,6 +42,7 @@ RegisterUnavailableSolver
 
 #else
 
+#include "../../sundials_nvector_interface.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/sundials_backports.hxx"
 
@@ -64,9 +65,9 @@ public:
   BoutReal run(BoutReal tout);
 
   // These functions used internally (but need to be public)
-  void res(BoutReal t, BoutReal* udata, BoutReal* dudata, BoutReal* rdata);
-  void pre(BoutReal t, BoutReal cj, BoutReal delta, BoutReal* udata, BoutReal* rvec,
-           BoutReal* zvec);
+  void res(BoutReal t, N_Vector u, N_Vector du, N_Vector rr);
+  void pre(BoutReal t, BoutReal cj, BoutReal delta, N_Vector u, N_Vector rvec,
+           N_Vector zvec);
 
 private:
   /// Absolute tolerance
@@ -79,6 +80,8 @@ private:
   bool use_precon;
   /// Correct the initial values
   bool correct_start;
+  /// N_Vector backend to use
+  NVectorType nvector_type;
 
   N_Vector uvec{nullptr};  // Values
   N_Vector duvec{nullptr}; // Time-derivatives
@@ -88,6 +91,10 @@ private:
   BoutReal pre_Wtime{0.0}; // Time in preconditioner
   int pre_ncalls{0};       // Number of calls to preconditioner
 
+  SundialsNVectorInterface nvector_backend() {
+    return SundialsNVectorInterface(*this, suncontext, nvector_type);
+  }
+
   /// SPGMR solver structure
   SUNLinearSolver sun_solver{nullptr};
   /// Context for SUNDIALS memory allocations
diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index bbbb420e9d..128c91a819 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -196,10 +196,20 @@ public:
     field.swapData(get_field<T>(v));
   }
 
+  template <typename T, typename = bout::utils::EnableIfField<T>>
+  static T& get(const N_Vector v) {
+    return get_field<T>(v);
+  }
+
   template <typename T, typename = bout::utils::EnableIfField<T>>
   static void swap(const N_Vector v, T& field, std::size_t subvector) {
     return BoutNVector::swap(N_VGetSubvector_ManyVector(v, subvector), field);
   }
+
+  template <typename T, typename = bout::utils::EnableIfField<T>>
+  static T& get(const N_Vector v, std::size_t subvector) {
+    return BoutNVector::get<T>(N_VGetSubvector_ManyVector(v, subvector));
+  }
 };
 
 #endif
diff --git a/src/solver/sundials_nvector_interface.hxx b/src/solver/sundials_nvector_interface.hxx
new file mode 100644
index 0000000000..100f140fb1
--- /dev/null
+++ b/src/solver/sundials_nvector_interface.hxx
@@ -0,0 +1,313 @@
+/**************************************************************************
+ * Shared helpers for SUNDIALS N_Vector backends used by BOUT++ solvers.
+ *
+ * Copyright 2010-2026 BOUT++ contributors
+ *
+ * Contact: Ben Dudson, dudson2@llnl.gov
+ *
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#ifndef BOUT_SUNDIALS_NVECTOR_INTERFACE_HXX
+#define BOUT_SUNDIALS_NVECTOR_INTERFACE_HXX
+
+#include "bout/bout_enum_class.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/solver.hxx"
+#include "bout/sundials_backports.hxx"
+
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+#include "nvector.hxx"
+#endif
+
+#include <algorithm>
+#include <iterator>
+#include <vector>
+
+BOUT_ENUM_CLASS(NVectorType, Sundials, ManyVector);
+
+class SundialsNVectorInterface {
+public:
+  SundialsNVectorInterface(Solver& solver_in, const sundials::Context& ctx_in,
+                           NVectorType nvector_type_in)
+      : solver(solver_in), ctx(ctx_in), nvector_type(nvector_type_in) {}
+
+  bool use_manyvector() const { return nvector_type == NVectorType::ManyVector; }
+
+  const char* backend_name() const {
+    return use_manyvector() ? "SUNDIALS ManyVector-backed custom" : "SUNDIALS parallel";
+  }
+
+  void ensure_manyvector_available() const {
+    if (use_manyvector() and not BOUT_HAS_SUNDIALS_MANYVECTOR) {
+      throw BoutException("SUNDIALS ManyVector backend requested, but BOUT++ was "
+                          "built without SUNDIALS ManyVector support");
+    }
+  }
+
+  N_Vector create_state_vector(int local_N, int neq) const {
+    ensure_manyvector_available();
+
+    if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+      auto* vec = nvector_from_state();
+      if (vec == nullptr) {
+        throw BoutException("BOUT N_Vector failed\n");
+      }
+      return vec;
+#endif
+    }
+
+    auto* vec = callWithSUNContext(N_VNew_Parallel, ctx, BoutComm::get(), local_N, neq);
+    if (vec == nullptr) {
+      throw BoutException("SUNDIALS memory allocation failed\n");
+    }
+    solver.save_vars(N_VGetArrayPointer(vec));
+    return vec;
+  }
+
+  N_Vector clone_vector_like(N_Vector source, const char* description) const {
+    auto* vec = N_VClone(source);
+    if (vec == nullptr) {
+      throw BoutException("{}\n", description);
+    }
+    return vec;
+  }
+
+  void copy_state_from_vector(N_Vector u) const {
+    ensure_manyvector_available();
+
+    if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+      swap_state(u);
+      return;
+#endif
+    }
+
+    solver.load_vars(N_VGetArrayPointer(u));
+  }
+
+  void copy_state_to_vector(N_Vector u) const {
+    ensure_manyvector_available();
+
+    if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+      swap_state(u);
+      return;
+#endif
+    }
+
+    solver.save_vars(N_VGetArrayPointer(u));
+  }
+
+  void copy_deriv_from_vector(N_Vector du) const {
+    ensure_manyvector_available();
+
+    if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+      swap_deriv(du);
+      return;
+#endif
+    }
+
+    solver.load_derivs(N_VGetArrayPointer(du));
+  }
+
+  void copy_deriv_to_vector(N_Vector du) const {
+    ensure_manyvector_available();
+
+    if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+      swap_deriv(du);
+      return;
+#endif
+    }
+
+    solver.save_derivs(N_VGetArrayPointer(du));
+  }
+
+  void fill_vector_values(N_Vector vec, const std::vector<BoutReal>& f2d_values,
+                          const std::vector<BoutReal>& f3d_values) const {
+    ensure_manyvector_available();
+
+    if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+      std::size_t i = 0;
+      for (std::size_t j = 0; j < f2d_values.size(); ++j, ++i) {
+        fill_field(BoutNVector::get<Field2D>(vec, i), f2d_values[j],
+                   solver.f2d[j].evolve_bndry);
+      }
+      for (std::size_t j = 0; j < f3d_values.size(); ++j, ++i) {
+        fill_field(BoutNVector::get<Field3D>(vec, i), f3d_values[j],
+                   solver.f3d[j].evolve_bndry);
+      }
+      return;
+#endif
+    }
+
+    BoutReal* option_data = N_VGetArrayPointer(vec);
+    int p = 0;
+    for (const auto& i2d : bout::globals::mesh->getRegion2D("RGN_BNDRY")) {
+      fill_vector_values_op(i2d, option_data, p, f2d_values, f3d_values, true);
+    }
+    for (const auto& i2d : bout::globals::mesh->getRegion2D("RGN_NOBNDRY")) {
+      fill_vector_values_op(i2d, option_data, p, f2d_values, f3d_values, false);
+    }
+  }
+
+  void fill_id_vector(N_Vector vec) const {
+    ensure_manyvector_available();
+
+    if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+      std::size_t i = 0;
+      for (const auto& field : solver.f2d) {
+        fill_field(BoutNVector::get<Field2D>(vec, i), field.constraint ? 0.0 : 1.0,
+                   field.evolve_bndry);
+        ++i;
+      }
+      for (const auto& field : solver.f3d) {
+        fill_field(BoutNVector::get<Field3D>(vec, i), field.constraint ? 0.0 : 1.0,
+                   field.evolve_bndry);
+        ++i;
+      }
+      return;
+#endif
+    }
+
+    solver.set_id(N_VGetArrayPointer(vec));
+  }
+
+  void subtract_differential_term(N_Vector residual, N_Vector du, N_Vector id) const {
+    ensure_manyvector_available();
+
+    if (use_manyvector()) {
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+      std::size_t i = 0;
+      for (const auto& field : solver.f2d) {
+        subtract_field(BoutNVector::get<Field2D>(residual, i),
+                       BoutNVector::get<Field2D>(du, i), BoutNVector::get<Field2D>(id, i),
+                       field.evolve_bndry);
+        ++i;
+      }
+      for (const auto& field : solver.f3d) {
+        subtract_field(BoutNVector::get<Field3D>(residual, i),
+                       BoutNVector::get<Field3D>(du, i), BoutNVector::get<Field3D>(id, i),
+                       field.evolve_bndry);
+        ++i;
+      }
+      return;
+#endif
+    }
+
+    const auto length = N_VGetLocalLength_Parallel(id);
+    const BoutReal* id_data = N_VGetArrayPointer(id);
+    BoutReal* residual_data = N_VGetArrayPointer(residual);
+    const BoutReal* du_data = N_VGetArrayPointer(du);
+    for (int i = 0; i < length; ++i) {
+      if (id_data[i] > 0.5) {
+        residual_data[i] -= du_data[i];
+      }
+    }
+  }
+
+private:
+  Solver& solver;
+  const sundials::Context& ctx;
+  NVectorType nvector_type;
+
+  void fill_vector_values_op(Ind2D UNUSED(i2d), BoutReal* option_data, int& p,
+                             const std::vector<BoutReal>& f2d_values,
+                             const std::vector<BoutReal>& f3d_values, bool bndry) const {
+    for (std::size_t i = 0; i < f2d_values.size(); ++i) {
+      if (bndry && !solver.f2d[i].evolve_bndry) {
+        continue;
+      }
+      option_data[p] = f2d_values[i];
+      ++p;
+    }
+
+    for (int jz = 0; jz < bout::globals::mesh->LocalNz; ++jz) {
+      for (std::size_t i = 0; i < f3d_values.size(); ++i) {
+        if (bndry && !solver.f3d[i].evolve_bndry) {
+          continue;
+        }
+        option_data[p] = f3d_values[i];
+        ++p;
+      }
+    }
+  }
+
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+  N_Vector nvector_from_state() const {
+    std::vector<N_Vector> subvectors;
+    subvectors.reserve(solver.f2d.size() + solver.f3d.size());
+    const auto inserter = std::back_inserter(subvectors);
+
+    const auto field_to_nvector = [this](const auto& var_str) {
+      return BoutNVector::create(ctx, *var_str.var, var_str.evolve_bndry);
+    };
+    std::transform(solver.f2d.cbegin(), solver.f2d.cend(), inserter, field_to_nvector);
+    std::transform(solver.f3d.cbegin(), solver.f3d.cend(), inserter, field_to_nvector);
+    return BoutNVector::create(ctx, subvectors);
+  }
+
+  void swap_state(const N_Vector u) const {
+    std::size_t i = 0;
+    for (auto& var_str : solver.f2d) {
+      BoutNVector::swap(u, *var_str.var, i);
+      ++i;
+    }
+    for (auto& var_str : solver.f3d) {
+      BoutNVector::swap(u, *var_str.var, i);
+      ++i;
+    }
+  }
+
+  void swap_deriv(const N_Vector du) const {
+    std::size_t i = 0;
+    for (auto& var_str : solver.f2d) {
+      BoutNVector::swap(du, *var_str.F_var, i);
+      ++i;
+    }
+    for (auto& var_str : solver.f3d) {
+      BoutNVector::swap(du, *var_str.F_var, i);
+      ++i;
+    }
+  }
+
+  template <typename FieldType>
+  static void fill_field(FieldType& field, BoutReal value, bool evolve_bndry) {
+    BOUT_FOR(i, field.getRegion(evolve_bndry ? RGN_ALL : RGN_NOBNDRY)) {
+      field[i] = value;
+    }
+  }
+
+  template <typename FieldType>
+  static void subtract_field(FieldType& residual, const FieldType& du,
+                             const FieldType& id, bool evolve_bndry) {
+    BOUT_FOR(i, residual.getRegion(evolve_bndry ? RGN_ALL : RGN_NOBNDRY)) {
+      if (id[i] > 0.5) {
+        residual[i] -= du[i];
+      }
+    }
+  }
+#endif
+};
+
+#endif

From ceeeb802034a7f7a80306974180c346e35d17cf7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 15:05:28 -0700
Subject: [PATCH 1368/1827] Document Sundials N_Vector options

Backend can select either the Sundials MPI parallel N_Vector,
or a ManyVector backed by BOUT++ fields.
---
 manual/sphinx/user_docs/time_integration.rst | 31 ++++++++++++++++++--
 src/solver/sundials_nvector_interface.hxx    | 22 ++++++++++++++
 2 files changed, 51 insertions(+), 2 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 37bf9a6abf..ee84d1010a 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -33,7 +33,7 @@ needed to make the solver available.
 
 .. _tab-solvers:
 .. table:: Available time integration solvers
-	   
+
    +---------------+-----------------------------------------+------------------------+
    | Name          | Description                             | Compile options        |
    +===============+=========================================+========================+
@@ -68,7 +68,7 @@ given in table :numref:`tab-solveropts`.
 
 .. _tab-solveropts:
 .. table:: Time integration solver options
-	   
+
    +--------------------------+--------------------------------------------+-------------------------------------+
    | Option                   | Description                                | Solvers used                        |
    +==========================+============================================+=====================================+
@@ -104,6 +104,9 @@ given in table :numref:`tab-solveropts`.
    +--------------------------+--------------------------------------------+-------------------------------------+
    | diagnose                 | Collect and print additional diagnostics   | cvode, imexbdf2, beuler             |
    +--------------------------+--------------------------------------------+-------------------------------------+
+   | nvector                  | ``N_Vector`` backend for SUNDIALS solvers: | cvode, ida, arkode                  |
+   |                          | ``sundials`` or ``manyvector``             |                                     |
+   +--------------------------+--------------------------------------------+-------------------------------------+
 
 |
 
@@ -111,6 +114,30 @@ The most commonly changed options are the absolute and relative solver
 tolerances, ``atol`` and ``rtol`` which should be varied to check
 convergence.
 
+SUNDIALS ``N_Vector`` backends
+------------------------------
+
+The SUNDIALS-based solvers ``cvode``, ``ida``, and ``arkode`` can select
+the ``N_Vector`` backend at runtime using ``solver:nvector``:
+
+.. code-block:: cfg
+
+    [solver]
+    type = cvode
+    nvector = sundials
+
+Valid values are:
+
+- ``sundials`` uses the standard SUNDIALS parallel ``N_Vector``. This is the
+  default.
+- ``manyvector`` uses the BOUT++ field-backed custom ``N_Vector`` built on top
+  of SUNDIALS ManyVector support.
+
+The ``manyvector`` option is only available when BOUT++ was built with SUNDIALS
+ManyVector support. If ``solver:nvector=manyvector`` is selected in a build
+that does not provide this support, solver initialisation will throw an
+exception.
+
 CVODE
 -----
 
diff --git a/src/solver/sundials_nvector_interface.hxx b/src/solver/sundials_nvector_interface.hxx
index 100f140fb1..1813d87860 100644
--- a/src/solver/sundials_nvector_interface.hxx
+++ b/src/solver/sundials_nvector_interface.hxx
@@ -39,20 +39,27 @@
 #include <iterator>
 #include <vector>
 
+/// Supported SUNDIALS ``N_Vector`` backends that can be selected at runtime.
 BOUT_ENUM_CLASS(NVectorType, Sundials, ManyVector);
 
+/// Helper for moving solver state between BOUT++ fields and a chosen ``N_Vector``
+/// backend without exposing backend-specific details in each solver wrapper.
 class SundialsNVectorInterface {
 public:
   SundialsNVectorInterface(Solver& solver_in, const sundials::Context& ctx_in,
                            NVectorType nvector_type_in)
       : solver(solver_in), ctx(ctx_in), nvector_type(nvector_type_in) {}
 
+  /// Return ``true`` when using the field-backed ManyVector implementation.
   bool use_manyvector() const { return nvector_type == NVectorType::ManyVector; }
 
+  /// Human-readable backend name for logs and error messages.
   const char* backend_name() const {
     return use_manyvector() ? "SUNDIALS ManyVector-backed custom" : "SUNDIALS parallel";
   }
 
+  /// Throw if the selected backend requires SUNDIALS ManyVector support that was
+  /// not enabled when BOUT++ was built.
   void ensure_manyvector_available() const {
     if (use_manyvector() and not BOUT_HAS_SUNDIALS_MANYVECTOR) {
       throw BoutException("SUNDIALS ManyVector backend requested, but BOUT++ was "
@@ -60,6 +67,7 @@ public:
     }
   }
 
+  /// Create the main solver state vector using the selected backend.
   N_Vector create_state_vector(int local_N, int neq) const {
     ensure_manyvector_available();
 
@@ -81,6 +89,7 @@ public:
     return vec;
   }
 
+  /// Clone a vector of the same backend/layout, with a descriptive error on failure.
   N_Vector clone_vector_like(N_Vector source, const char* description) const {
     auto* vec = N_VClone(source);
     if (vec == nullptr) {
@@ -89,6 +98,7 @@ public:
     return vec;
   }
 
+  /// Copy the current solution state from ``u`` into the solver fields.
   void copy_state_from_vector(N_Vector u) const {
     ensure_manyvector_available();
 
@@ -102,6 +112,7 @@ public:
     solver.load_vars(N_VGetArrayPointer(u));
   }
 
+  /// Copy the solver fields into the solution vector ``u``.
   void copy_state_to_vector(N_Vector u) const {
     ensure_manyvector_available();
 
@@ -115,6 +126,7 @@ public:
     solver.save_vars(N_VGetArrayPointer(u));
   }
 
+  /// Copy time-derivative values from ``du`` into the solver derivative fields.
   void copy_deriv_from_vector(N_Vector du) const {
     ensure_manyvector_available();
 
@@ -128,6 +140,7 @@ public:
     solver.load_derivs(N_VGetArrayPointer(du));
   }
 
+  /// Copy the solver derivative fields into ``du``.
   void copy_deriv_to_vector(N_Vector du) const {
     ensure_manyvector_available();
 
@@ -141,6 +154,8 @@ public:
     solver.save_derivs(N_VGetArrayPointer(du));
   }
 
+  /// Fill every evolved entry in ``vec`` with per-field constants, respecting
+  /// whether each field evolves boundary cells.
   void fill_vector_values(N_Vector vec, const std::vector<BoutReal>& f2d_values,
                           const std::vector<BoutReal>& f3d_values) const {
     ensure_manyvector_available();
@@ -170,6 +185,8 @@ public:
     }
   }
 
+  /// Fill the IDA ``id`` vector with ``1`` for differential variables and ``0``
+  /// for constrained algebraic variables.
   void fill_id_vector(N_Vector vec) const {
     ensure_manyvector_available();
 
@@ -193,6 +210,8 @@ public:
     solver.set_id(N_VGetArrayPointer(vec));
   }
 
+  /// Apply the IDA residual update ``residual -= du`` only on differential
+  /// components selected by ``id``.
   void subtract_differential_term(N_Vector residual, N_Vector du, N_Vector id) const {
     ensure_manyvector_available();
 
@@ -254,6 +273,7 @@ private:
   }
 
 #if BOUT_HAS_SUNDIALS_MANYVECTOR
+  /// Build a field-backed ManyVector that aliases the solver state variables.
   N_Vector nvector_from_state() const {
     std::vector<N_Vector> subvectors;
     subvectors.reserve(solver.f2d.size() + solver.f3d.size());
@@ -267,6 +287,7 @@ private:
     return BoutNVector::create(ctx, subvectors);
   }
 
+  /// Swap the active solver state fields with the subvectors contained in ``u``.
   void swap_state(const N_Vector u) const {
     std::size_t i = 0;
     for (auto& var_str : solver.f2d) {
@@ -279,6 +300,7 @@ private:
     }
   }
 
+  /// Swap the active solver derivative fields with the subvectors in ``du``.
   void swap_deriv(const N_Vector du) const {
     std::size_t i = 0;
     for (auto& var_str : solver.f2d) {

From d997e6c327d116579a00a6922a994f98da49efef Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 15:11:48 -0700
Subject: [PATCH 1369/1827] Formatting changes

---
 include/bout/sundials_backports.hxx | 9 +++++----
 tests/unit/solver/test_nvector.cxx  | 7 +++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/include/bout/sundials_backports.hxx b/include/bout/sundials_backports.hxx
index 3fcb87f6e2..bb17e593b2 100644
--- a/include/bout/sundials_backports.hxx
+++ b/include/bout/sundials_backports.hxx
@@ -32,10 +32,11 @@
 
 // NOLINTBEGIN(cppcoreguidelines-macro-usage)
 #define SUNDIALS_VERSION_AT_LEAST(major, minor, patch) \
-  ((major) < SUNDIALS_VERSION_MAJOR                      \
-   || ((major) == SUNDIALS_VERSION_MAJOR                 \
-       && ((minor) < SUNDIALS_VERSION_MINOR              \
-           || ((minor) == SUNDIALS_VERSION_MINOR && (patch) <= SUNDIALS_VERSION_PATCH))))
+  ((major) < SUNDIALS_VERSION_MAJOR                    \
+   || ((major) == SUNDIALS_VERSION_MAJOR               \
+       && ((minor) < SUNDIALS_VERSION_MINOR            \
+           || ((minor) == SUNDIALS_VERSION_MINOR       \
+               && (patch) <= SUNDIALS_VERSION_PATCH))))
 #define SUNDIALS_VERSION_LESS_THAN(major, minor, patch) \
   (!SUNDIALS_VERSION_AT_LEAST(major, minor, patch))
 // NOLINTEND(cppcoreguidelines-macro-usage)
diff --git a/tests/unit/solver/test_nvector.cxx b/tests/unit/solver/test_nvector.cxx
index 9aa5a15178..010977a51f 100644
--- a/tests/unit/solver/test_nvector.cxx
+++ b/tests/unit/solver/test_nvector.cxx
@@ -1,7 +1,7 @@
-#include "gtest/gtest.h"
-#include <bout/mesh.hxx>
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
+#include <bout/mesh.hxx>
+#include "gtest/gtest.h"
 
 class NVectorFixture : public ::testing::Test {
 public:
@@ -12,5 +12,4 @@ class NVectorFixture : public ::testing::Test {
 }
 
 TEST_F(NVectorFixture, Constructor) {
-
-}
\ No newline at end of file
+}

From c0abd209502203a20494e93409d340d5e92f3bce Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 15:42:05 -0700
Subject: [PATCH 1370/1827] Unit tests for custom N_Vector

Includes guards to handle when ManyVector is unavailable.
---
 tests/unit/CMakeLists.txt          |   1 +
 tests/unit/solver/test_nvector.cxx | 256 ++++++++++++++++++++++++++++-
 2 files changed, 251 insertions(+), 6 deletions(-)

diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 6c14b79fb0..4ba304b484 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -100,6 +100,7 @@ set(serial_tests_source
     ./mesh/test_paralleltransform.cxx
     ./solver/test_fakesolver.cxx
     ./solver/test_fakesolver.hxx
+    ./solver/test_nvector.cxx
     ./solver/test_solver.cxx
     ./solver/test_solverfactory.cxx
     ./sys/test_boutexception.cxx
diff --git a/tests/unit/solver/test_nvector.cxx b/tests/unit/solver/test_nvector.cxx
index 010977a51f..88aa03202b 100644
--- a/tests/unit/solver/test_nvector.cxx
+++ b/tests/unit/solver/test_nvector.cxx
@@ -1,15 +1,259 @@
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_SUNDIALS
+
+#include <cmath>
+#include <memory>
+#include <string>
+#include <type_traits>
+#include <vector>
+
+#include "fake_mesh_fixture.hxx"
+#include "test_extras.hxx"
+#include "bout/boutcomm.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
-#include <bout/mesh.hxx>
+#include "bout/sundials_backports.hxx"
 #include "gtest/gtest.h"
 
-class NVectorFixture : public ::testing::Test {
+#include "../../../src/solver/nvector.hxx"
+
+namespace {
+
+struct NVectorDestroy {
+  void operator()(N_Vector vec) const {
+    if (vec != nullptr) {
+      N_VDestroy(vec);
+    }
+  }
+};
+
+using UniqueNVector = std::unique_ptr<std::remove_pointer_t<N_Vector>, NVectorDestroy>;
+
+auto makeNVector(N_Vector vec) -> UniqueNVector { return UniqueNVector(vec); }
+
+template <typename FieldType>
+auto makePositiveField(BoutReal offset = 0.0) -> FieldType {
+  return makeField<FieldType>(
+      [offset](typename FieldType::ind_type& i) {
+        return offset + 1.0 + static_cast<BoutReal>((i.ind % 7) + 1);
+      },
+      bout::globals::mesh);
+}
+
+template <typename FieldType>
+auto makeSignedField() -> FieldType {
+  return makeField<FieldType>(
+      [](typename FieldType::ind_type& i) {
+        const auto magnitude = 1.0 + static_cast<BoutReal>(i.ind % 5);
+        return (i.ind % 2 == 0) ? magnitude : -magnitude;
+      },
+      bout::globals::mesh);
+}
+
+template <typename FieldType>
+auto regionSize(const FieldType& field, const std::string& region) -> sunindextype {
+  return static_cast<sunindextype>(field.getRegion(region).size());
+}
+
+template <typename FieldType, typename UnaryOp>
+auto sumField(const FieldType& field, const std::string& region, UnaryOp&& op)
+    -> BoutReal {
+  BoutReal result = 0.0;
+  for (const auto& i : field.getRegion(region)) {
+    result += op(field[i]);
+  }
+  return result;
+}
+
+template <typename FieldType, typename BinaryOp>
+auto sumFields(const FieldType& lhs, const FieldType& rhs, const std::string& region,
+               BinaryOp&& op) -> BoutReal {
+  BoutReal result = 0.0;
+  for (const auto& i : lhs.getRegion(region)) {
+    result += op(lhs[i], rhs[i]);
+  }
+  return result;
+}
+
+template <typename T>
+class BoutNVectorTest : public FakeMeshFixture {
 public:
-  Mesh mesh;
-  Field2D field1;
+  BoutNVectorTest() : sunctx(createSUNContext(BoutComm::get())) {}
+
+protected:
+  sundials::Context sunctx;
+};
+
+using FieldTypes = ::testing::Types<Field2D, Field3D>;
+TYPED_TEST_SUITE(BoutNVectorTest, FieldTypes);
 
-  NVectorFixture() : field1{0} {}
+TYPED_TEST(BoutNVectorTest, ConstructorAliasesFieldAndReportsLength) {
+  auto field = makePositiveField<TypeParam>();
+  auto vec = makeNVector(BoutNVector::create(this->sunctx, field, true));
+
+  ASSERT_NE(vec.get(), nullptr);
+  EXPECT_EQ(N_VGetVectorID(vec.get()), SUNDIALS_NVEC_CUSTOM);
+  EXPECT_EQ(N_VGetLength(vec.get()), regionSize(field, "RGN_ALL"));
+  EXPECT_EQ(&BoutNVector::get<TypeParam>(vec.get()), &field);
+
+  field = 3.25;
+  EXPECT_TRUE(IsFieldEqual(BoutNVector::get<TypeParam>(vec.get()), 3.25));
 }
 
-TEST_F(NVectorFixture, Constructor) {
+TYPED_TEST(BoutNVectorTest, ConstructorWithoutBoundaryUsesNoBoundaryLength) {
+  TypeParam field{bout::globals::mesh};
+  field.allocate();
+  field = 1.0;
+  for (const auto& i : field.getRegion("RGN_BNDRY")) {
+    field[i] = 100.0;
+  }
+
+  auto vec = makeNVector(BoutNVector::create(this->sunctx, field, false));
+
+  ASSERT_NE(vec.get(), nullptr);
+  EXPECT_EQ(N_VGetLength(vec.get()), regionSize(field, "RGN_NOBNDRY"));
+  EXPECT_DOUBLE_EQ(N_VL1Norm(vec.get()),
+                   static_cast<BoutReal>(regionSize(field, "RGN_NOBNDRY")));
 }
+
+TYPED_TEST(BoutNVectorTest, LinearAndPointwiseOperations) {
+  auto x = makePositiveField<TypeParam>(0.0);
+  auto y = makePositiveField<TypeParam>(20.0);
+  TypeParam z{bout::globals::mesh};
+  z.allocate();
+  z = 0.0;
+
+  auto vx = makeNVector(BoutNVector::create(this->sunctx, x, true));
+  auto vy = makeNVector(BoutNVector::create(this->sunctx, y, true));
+  auto vz = makeNVector(BoutNVector::create(this->sunctx, z, true));
+
+  N_VLinearSum(2.0, vx.get(), -1.0, vy.get(), vz.get());
+  auto expected = 2.0 * x - y;
+  EXPECT_TRUE(IsFieldEqual(z, expected));
+
+  N_VProd(vx.get(), vy.get(), vz.get());
+  expected = x * y;
+  EXPECT_TRUE(IsFieldEqual(z, expected));
+
+  N_VDiv(vy.get(), vx.get(), vz.get());
+  expected = y / x;
+  EXPECT_TRUE(IsFieldEqual(z, expected));
+
+  N_VScale(-0.5, vx.get(), vz.get());
+  expected = -0.5 * x;
+  EXPECT_TRUE(IsFieldEqual(z, expected));
+
+  auto signed_field = makeSignedField<TypeParam>();
+  auto vsigned = makeNVector(BoutNVector::create(this->sunctx, signed_field, true));
+
+  N_VAbs(vsigned.get(), vz.get());
+  expected = abs(signed_field);
+  EXPECT_TRUE(IsFieldEqual(z, expected));
+
+  N_VInv(vx.get(), vz.get());
+  expected = 1.0 / x;
+  EXPECT_TRUE(IsFieldEqual(z, expected));
+
+  N_VAddConst(vx.get(), 3.5, vz.get());
+  expected = 3.5 + x;
+  EXPECT_TRUE(IsFieldEqual(z, expected));
+
+  N_VConst(-2.0, vz.get());
+  EXPECT_TRUE(IsFieldEqual(z, -2.0));
+}
+
+TYPED_TEST(BoutNVectorTest, ReductionOperations) {
+  auto x = makeSignedField<TypeParam>();
+  auto weights = makePositiveField<TypeParam>(5.0);
+  auto vx = makeNVector(BoutNVector::create(this->sunctx, x, true));
+  auto vweights = makeNVector(BoutNVector::create(this->sunctx, weights, true));
+
+  const auto dot_expected = sumFields(
+      x, weights, "RGN_ALL", [](BoutReal lhs, BoutReal rhs) { return lhs * rhs; });
+  EXPECT_DOUBLE_EQ(N_VDotProd(vx.get(), vweights.get()), dot_expected);
+
+  const auto l1_expected =
+      sumField(x, "RGN_ALL", [](BoutReal value) { return std::abs(value); });
+  EXPECT_DOUBLE_EQ(N_VL1Norm(vx.get()), l1_expected);
+
+  const auto wl2_sq_expected =
+      sumFields(x, weights, "RGN_ALL",
+                [](BoutReal lhs, BoutReal rhs) { return std::pow(lhs * rhs, 2); });
+  const auto wl2_expected = std::sqrt(wl2_sq_expected);
+  EXPECT_NEAR(N_VWL2Norm(vx.get(), vweights.get()), wl2_expected, BoutRealTolerance);
+
+  const auto wrms_expected =
+      wl2_expected / std::sqrt(static_cast<BoutReal>(regionSize(x, "RGN_ALL")));
+  EXPECT_NEAR(N_VWrmsNorm(vx.get(), vweights.get()), wrms_expected, BoutRealTolerance);
+
+  EXPECT_DOUBLE_EQ(N_VMaxNorm(vx.get()), max(abs(x), true));
+  EXPECT_DOUBLE_EQ(N_VMin(vx.get()), min(x, true));
+}
+
+TYPED_TEST(BoutNVectorTest, CloneCreatesIndependentStorage) {
+  auto field = makePositiveField<TypeParam>();
+  auto vec = makeNVector(BoutNVector::create(this->sunctx, field, true));
+  auto clone = makeNVector(N_VClone(vec.get()));
+
+  ASSERT_NE(clone.get(), nullptr);
+  EXPECT_EQ(N_VGetVectorID(clone.get()), SUNDIALS_NVEC_CUSTOM);
+  EXPECT_EQ(N_VGetLength(clone.get()), N_VGetLength(vec.get()));
+  EXPECT_NE(&BoutNVector::get<TypeParam>(clone.get()),
+            &BoutNVector::get<TypeParam>(vec.get()));
+
+  N_VConst(42.0, clone.get());
+  EXPECT_TRUE(IsFieldEqual(BoutNVector::get<TypeParam>(clone.get()), 42.0));
+  EXPECT_FALSE(IsFieldEqual(field, 42.0));
+}
+
+TYPED_TEST(BoutNVectorTest, SwapExchangesFieldStorage) {
+  auto field = makePositiveField<TypeParam>(0.0);
+  auto other = makePositiveField<TypeParam>(100.0);
+  const auto original_field = field;
+  const auto original_other = other;
+
+  auto vec = makeNVector(BoutNVector::create(this->sunctx, field, true));
+
+  BoutNVector::swap(vec.get(), other);
+
+  EXPECT_TRUE(IsFieldEqual(field, original_other));
+  EXPECT_TRUE(IsFieldEqual(other, original_field));
+  EXPECT_TRUE(IsFieldEqual(BoutNVector::get<TypeParam>(vec.get()), original_other));
+}
+
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+TEST_F(FakeMeshFixture, ManyVectorGetAndSwapSubvectors) {
+  const auto sunctx = createSUNContext(BoutComm::get());
+  auto field2d = makePositiveField<Field2D>(0.0);
+  auto field3d = makePositiveField<Field3D>(50.0);
+  auto replacement2d = makePositiveField<Field2D>(100.0);
+  const auto original2d = field2d;
+  const auto original3d = field3d;
+  const auto original_replacement2d = replacement2d;
+
+  std::vector<N_Vector> subvectors;
+  subvectors.emplace_back(BoutNVector::create(sunctx, field2d, true));
+  subvectors.emplace_back(BoutNVector::create(sunctx, field3d, true));
+
+  auto manyvector = makeNVector(BoutNVector::create(sunctx, subvectors));
+
+  ASSERT_NE(manyvector.get(), nullptr);
+  EXPECT_EQ(&BoutNVector::get<Field2D>(manyvector.get(), 0), &field2d);
+  EXPECT_EQ(&BoutNVector::get<Field3D>(manyvector.get(), 1), &field3d);
+  EXPECT_EQ(N_VGetLength(manyvector.get()),
+            regionSize(field2d, "RGN_ALL") + regionSize(field3d, "RGN_ALL"));
+
+  BoutNVector::swap(manyvector.get(), replacement2d, 0);
+
+  EXPECT_TRUE(IsFieldEqual(field2d, original_replacement2d));
+  EXPECT_TRUE(IsFieldEqual(replacement2d, original2d));
+  EXPECT_TRUE(IsFieldEqual(BoutNVector::get<Field2D>(manyvector.get(), 0),
+                           original_replacement2d));
+  EXPECT_TRUE(IsFieldEqual(BoutNVector::get<Field3D>(manyvector.get(), 1), original3d));
+}
+#endif
+
+} // namespace
+
+#endif

From dfa59c771d6d0845eadf0d8eebfe86cba04714ee Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 16:18:52 -0700
Subject: [PATCH 1371/1827] NVector: Patch for MultiVector

Conditionally include `nvector/nvector_manyvector.h`
---
 src/solver/nvector.hxx | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/solver/nvector.hxx b/src/solver/nvector.hxx
index 128c91a819..39aa52d3ca 100644
--- a/src/solver/nvector.hxx
+++ b/src/solver/nvector.hxx
@@ -25,11 +25,14 @@
 
 #include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/build_defines.hxx>
 #include <bout/field.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <functional>
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
 #include <nvector/nvector_manyvector.h>
+#endif
 #include <sundials/sundials_nvector.h>
 #include <utility>
 
@@ -183,14 +186,6 @@ public:
     return v;
   }
 
-  template <typename V>
-  static N_Vector create(const sundials::Context& ctx, V& subvectors) {
-    const auto v = callWithSUNContext(N_VNew_ManyVector, ctx, std::size(subvectors),
-                                      std::data(subvectors));
-    ((N_VectorContent_ManyVector)v->content)->own_data = true;
-    return v;
-  }
-
   template <typename T, typename = bout::utils::EnableIfField<T>>
   static void swap(const N_Vector v, T& field) {
     field.swapData(get_field<T>(v));
@@ -201,6 +196,15 @@ public:
     return get_field<T>(v);
   }
 
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
+  template <typename V>
+  static N_Vector create(const sundials::Context& ctx, V& subvectors) {
+    const auto v = callWithSUNContext(N_VNew_ManyVector, ctx, std::size(subvectors),
+                                      std::data(subvectors));
+    ((N_VectorContent_ManyVector)v->content)->own_data = true;
+    return v;
+  }
+
   template <typename T, typename = bout::utils::EnableIfField<T>>
   static void swap(const N_Vector v, T& field, std::size_t subvector) {
     return BoutNVector::swap(N_VGetSubvector_ManyVector(v, subvector), field);
@@ -210,6 +214,7 @@ public:
   static T& get(const N_Vector v, std::size_t subvector) {
     return BoutNVector::get<T>(N_VGetSubvector_ManyVector(v, subvector));
   }
+#endif
 };
 
 #endif

From 307a8e0f23e7f44157f053760f2733b887f78730 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 16:31:49 -0700
Subject: [PATCH 1372/1827] Clang tidy

Missing includes and some `const` annotations.
---
 src/solver/impls/arkode/arkode.cxx        | 4 +++-
 src/solver/impls/cvode/cvode.cxx          | 9 ++++++---
 src/solver/impls/ida/ida.cxx              | 3 ++-
 src/solver/sundials_nvector_interface.hxx | 6 ++++++
 tests/unit/solver/test_nvector.cxx        | 1 +
 5 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 4315202ced..967790d21c 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -27,9 +27,9 @@
 
 #if BOUT_HAS_ARKODE
 
+#include "../../sundials_nvector_interface.hxx"
 #include "arkode.hxx"
 
-#include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
@@ -41,6 +41,7 @@
 #include "bout/msg_stack.hxx"
 #include "bout/options.hxx"
 #include "bout/output.hxx"
+#include "bout/region.hxx"
 #include "bout/solver.hxx"
 #include "bout/sundials_backports.hxx"
 #include "bout/unused.hxx"
@@ -57,6 +58,7 @@
 #include <algorithm>
 #include <iterator>
 #include <numeric>
+#include <string>
 #include <vector>
 
 // NOLINTBEGIN(readability-identifier-length)
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 6727dcb806..4e278dab98 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -30,6 +30,8 @@
 
 #if BOUT_HAS_CVODE
 
+#include "../../sundials_nvector_interface.hxx"
+
 #include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
@@ -59,6 +61,7 @@
 #include <iterator>
 #include <numeric>
 #include <string>
+#include <vector>
 
 BOUT_ENUM_CLASS(positivity_constraint, none, positive, non_negative, negative,
                 non_positive);
@@ -386,7 +389,7 @@ int CvodeSolver::init() {
         //   int band_width_default = n3Dvars()*(MXSUB+2);
         const int band_width_default = std::accumulate(
             begin(f3d), end(f3d), 0, [](int a, const VarStr<Field3D>& fvar) {
-              Mesh* localmesh = fvar.var->getMesh();
+              const Mesh* localmesh = fvar.var->getMesh();
               return a + localmesh->xend - localmesh->xstart + 3;
             });
 
@@ -576,7 +579,7 @@ BoutReal CvodeSolver::run(BoutReal tout) {
     CVodeGetCurrentTime(cvode_mem, &internal_time);
     while (internal_time < tout) {
       // Run another step
-      BoutReal last_time = internal_time;
+      const BoutReal last_time = internal_time;
       flag = CVode(cvode_mem, tout, uvec, &internal_time, CV_ONE_STEP);
 
       if (flag < 0) {
@@ -638,7 +641,7 @@ void CvodeSolver::pre(BoutReal t, BoutReal gamma, BoutReal delta, N_Vector u,
   TRACE("Running preconditioner: CvodeSolver::pre({})", t);
   const auto backend = nvector_backend();
 
-  BoutReal tstart = bout::globals::mpi->MPI_Wtime();
+  const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
 
   if (!hasPreconditioner()) {
     // Identity (but should never happen)
diff --git a/src/solver/impls/ida/ida.cxx b/src/solver/impls/ida/ida.cxx
index 61fece1b8b..191cdaf451 100644
--- a/src/solver/impls/ida/ida.cxx
+++ b/src/solver/impls/ida/ida.cxx
@@ -33,6 +33,8 @@
 
 #if BOUT_HAS_IDA
 
+#include "../../sundials_nvector_interface.hxx"
+
 #include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
@@ -51,7 +53,6 @@
 #include <ida/ida_bbdpre.h>
 #include <ida/ida_ls.h>
 
-#include <algorithm>
 #include <iterator>
 #include <numeric>
 #include <vector>
diff --git a/src/solver/sundials_nvector_interface.hxx b/src/solver/sundials_nvector_interface.hxx
index 1813d87860..d88221f259 100644
--- a/src/solver/sundials_nvector_interface.hxx
+++ b/src/solver/sundials_nvector_interface.hxx
@@ -27,9 +27,15 @@
 
 #include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
+#include "bout/field2d.hxx"
+#include "bout/globals.hxx"
+#include "bout/region.hxx"
 #include "bout/solver.hxx"
 #include "bout/sundials_backports.hxx"
+#include "bout/unused.hxx"
 
 #if BOUT_HAS_SUNDIALS_MANYVECTOR
 #include "nvector.hxx"
diff --git a/tests/unit/solver/test_nvector.cxx b/tests/unit/solver/test_nvector.cxx
index 88aa03202b..da3ae2199c 100644
--- a/tests/unit/solver/test_nvector.cxx
+++ b/tests/unit/solver/test_nvector.cxx
@@ -10,6 +10,7 @@
 
 #include "fake_mesh_fixture.hxx"
 #include "test_extras.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"

From 1968ac0e1f56f7da5f74a2c358d80282e76d3115 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 17 Jun 2026 16:58:21 -0700
Subject: [PATCH 1373/1827] Unit tests: Disable testing if missing ManyVector

---
 tests/unit/solver/test_nvector.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit/solver/test_nvector.cxx b/tests/unit/solver/test_nvector.cxx
index da3ae2199c..dc45008caa 100644
--- a/tests/unit/solver/test_nvector.cxx
+++ b/tests/unit/solver/test_nvector.cxx
@@ -1,6 +1,6 @@
 #include "bout/build_defines.hxx"
 
-#if BOUT_HAS_SUNDIALS
+#if BOUT_HAS_SUNDIALS_MANYVECTOR
 
 #include <cmath>
 #include <memory>

From 325d03b75efee9e386a71d2b6adff65939066881 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 17 Jun 2026 12:30:52 +0200
Subject: [PATCH 1374/1827] Apply clang-tidy improvements

---
 include/bout/petsc_operators.hxx                               | 2 +-
 src/mesh/petsc_operators.cxx                                   | 2 +-
 tests/integrated/test-petsc-operators/test_petsc_operators.cxx | 2 ++
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index 78196b2e29..c92a2b6d57 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -719,7 +719,7 @@ private:
   /// @param weights CSR nonzero-value array.
   void assembleFromCSR(const Array<int>& rows, const Array<int>& cols,
                        const Array<BoutReal>& weights) {
-    UniqueMat temp{new Mat{nullptr}};
+    const UniqueMat temp{new Mat{nullptr}};
     BOUT_DO_PETSC(MatCreate(BoutComm::get(), temp.get()));
     BOUT_DO_PETSC(MatSetType(*temp, MATMPIAIJ));
     BOUT_DO_PETSC(MatSetSizes(*temp, out_mapping->localSize(), PETSC_DECIDE,
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 0bec9053bb..54ec91c4df 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -1,4 +1,5 @@
 #include "bout/build_defines.hxx"
+#include "bout/field2d.hxx"
 #include "bout/petsc_interface.hxx"
 #include "bout/petsclib.hxx"
 #include <cmath>
@@ -9,7 +10,6 @@
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
-#include "bout/output.hxx"
 #include "bout/output_bout_types.hxx"
 #include "bout/petsc_operators.hxx"
 #include "bout/region.hxx"
diff --git a/tests/integrated/test-petsc-operators/test_petsc_operators.cxx b/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
index 31a17aa5d5..bd6166348c 100644
--- a/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
+++ b/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
@@ -5,7 +5,9 @@
 #include "bout/field_factory.hxx"
 #include "bout/globals.hxx"
 #include "bout/options.hxx"
+#include "bout/options_io.hxx"
 #include "bout/petsc_operators.hxx"
+#include "bout/region.hxx"
 
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);

From e9d56569bc7c67e2ada1c6f67f24498921ed32b5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 18 Jun 2026 10:59:09 +0200
Subject: [PATCH 1375/1827] FCI and 2D metrics don't mix well

---
 tests/integrated/test-petsc-operators/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/integrated/test-petsc-operators/CMakeLists.txt b/tests/integrated/test-petsc-operators/CMakeLists.txt
index 7191a39a30..6745344e34 100644
--- a/tests/integrated/test-petsc-operators/CMakeLists.txt
+++ b/tests/integrated/test-petsc-operators/CMakeLists.txt
@@ -3,5 +3,6 @@ bout_add_integrated_test(
   SOURCES test_petsc_operators.cxx
   USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_PETSC
+  REQUIRES BOUT_HAS_METRIC_3D
   EXTRA_FILES rotating-ellipse.py test_petsc_operators.py
 )

From c4a788d8003acfc22fcc3c0fa015de407478e573 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 18 Jun 2026 10:59:42 +0200
Subject: [PATCH 1376/1827] New zoidberg has a check for inner/outer convention

---
 tests/integrated/test-petsc-operators/rotating-ellipse.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-petsc-operators/rotating-ellipse.py b/tests/integrated/test-petsc-operators/rotating-ellipse.py
index 2482d580c9..bcaa456885 100755
--- a/tests/integrated/test-petsc-operators/rotating-ellipse.py
+++ b/tests/integrated/test-petsc-operators/rotating-ellipse.py
@@ -82,7 +82,7 @@
 # Generate a grid on each poloidal slice using the elliptic grid generator
 
 pol_grids = [
-    zoidberg.poloidal_grid.grid_elliptic(inner_line, outer_line, args.nx, args.nz)
+    zoidberg.poloidal_grid.grid_elliptic(outer_line, inner_line, args.nx, args.nz)
     for inner_line in inner_lines
 ]
 

From 51b848c2ac40586c21c498c19f90ad2914c0e2d5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 18 Jun 2026 14:34:08 +0200
Subject: [PATCH 1377/1827] Fixup formatting

---
 manual/sphinx/user_docs/time_integration.rst |  4 +--
 src/solver/impls/petsc/petsc.cxx             | 20 ++++++------
 src/solver/impls/pvode/pvode.cxx             |  8 ++---
 src/solver/impls/snes/snes.cxx               | 32 ++++++++++----------
 4 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 2e0d0f1b32..b12e497e02 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -33,7 +33,7 @@ needed to make the solver available.
 
 .. _tab-solvers:
 .. table:: Available time integration solvers
-	   
+
    +---------------+-----------------------------------------+------------------------+
    | Name          | Description                             | Compile options        |
    +===============+=========================================+========================+
@@ -68,7 +68,7 @@ given in table :numref:`tab-solveropts`.
 
 .. _tab-solveropts:
 .. table:: Time integration solver options
-	   
+
    +--------------------------+--------------------------------------------+-------------------------------------+
    | Option                   | Description                                | Solvers used                        |
    +==========================+============================================+=====================================+
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 0d5c16aebd..8e2ac92d88 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -64,10 +64,10 @@
 
 class ColoringStencil {
 private:
-  bool static isInSquare(int const i, int const j, int const n_square) {
+  bool static isInSquare(const int i, const int j, const int n_square) {
     return std::abs(i) <= n_square && std::abs(j) <= n_square;
   }
-  bool static isInCross(int const i, int const j, int const n_cross) {
+  bool static isInCross(const int i, const int j, const int n_cross) {
     if (i == 0) {
       return std::abs(j) <= n_cross;
     }
@@ -76,7 +76,7 @@ class ColoringStencil {
     }
     return false;
   }
-  bool static isInTaxi(int const i, int const j, int const n_taxi) {
+  bool static isInTaxi(const int i, const int j, const int n_taxi) {
     return std::abs(i) + std::abs(j) <= n_taxi;
   }
 
@@ -614,7 +614,7 @@ int PetscSolver::init() {
         n_taxi = 2;
       }
 
-      auto const xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
+      const auto xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
       {
         // This is ugly but can't think of a better and robust way to
         // count the non-zeros for some arbitrary stencil
@@ -734,7 +734,7 @@ int PetscSolver::init() {
       // Mark non-zero entries
 
       output_progress.write("Marking non-zero Jacobian entries\n");
-      PetscScalar const val = 1.0;
+      const PetscScalar val = 1.0;
       for (int x = mesh->xstart; x <= mesh->xend; x++) {
         for (int y = mesh->ystart; y <= mesh->yend; y++) {
 
@@ -753,21 +753,21 @@ int PetscSolver::init() {
                 continue;
               }
 
-              int const ind2 = ROUND(index(xi, yi, 0));
+              const int ind2 = ROUND(index(xi, yi, 0));
               if (ind2 < 0) {
                 continue; // A boundary point
               }
 
               // Depends on all variables on this cell
               for (int j = 0; j < n2d; j++) {
-                PetscInt const col = ind2 + j;
+                const PetscInt col = ind2 + j;
                 PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
               }
             }
           }
           // 3D fields
           for (int z = mesh->zstart; z <= mesh->zend; z++) {
-            int const ind = ROUND(index(x, y, z));
+            const int ind = ROUND(index(x, y, z));
 
             for (int i = 0; i < n3d; i++) {
               PetscInt row = ind + i;
@@ -777,7 +777,7 @@ int PetscSolver::init() {
 
               // Depends on 2D fields
               for (int j = 0; j < n2d; j++) {
-                PetscInt const col = ind0 + j;
+                const PetscInt col = ind0 + j;
                 PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
               }
 
@@ -802,7 +802,7 @@ int PetscSolver::init() {
 
                   // 3D fields on this cell
                   for (int j = 0; j < n3d; j++) {
-                    PetscInt const col = ind2 + j;
+                    const PetscInt col = ind2 + j;
                     int ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
 
                     if (ierr != 0) {
diff --git a/src/solver/impls/pvode/pvode.cxx b/src/solver/impls/pvode/pvode.cxx
index 0723faa99c..ba4dce5849 100644
--- a/src/solver/impls/pvode/pvode.cxx
+++ b/src/solver/impls/pvode/pvode.cxx
@@ -5,7 +5,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -20,7 +20,7 @@
  *
  * You should have received a copy of the GNU Lesser General Public License
  * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
- * 
+ *
  **************************************************************************/
 
 #include "bout/build_defines.hxx"
@@ -195,8 +195,8 @@ int PvodeSolver::init() {
   BoutReal* udata = N_VDATA(u);
   save_vars(udata);
 
-  /* Call CVodeMalloc to initialize CVODE: 
-     
+  /* Call CVodeMalloc to initialize CVODE:
+
      neq     is the problem size = number of equations
      f       is the user's right hand side function in y'=f(t,y)
      T0      is the initial time
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 2667ad55ff..1dd5e37c84 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -15,8 +15,8 @@
 #include <bout/output_bout_types.hxx>
 #include <bout/petsc_interface.hxx>
 #include <bout/solver.hxx>
-#include <bout/utils.hxx>
 #include <bout/unused.hxx>
+#include <bout/utils.hxx>
 
 #include <algorithm>
 #include <cmath>
@@ -35,10 +35,10 @@
 
 class ColoringStencil {
 private:
-  bool static isInSquare(int const i, int const j, int const n_square) {
+  bool static isInSquare(const int i, const int j, const int n_square) {
     return std::abs(i) <= n_square && std::abs(j) <= n_square;
   }
-  bool static isInCross(int const i, int const j, int const n_cross) {
+  bool static isInCross(const int i, const int j, const int n_cross) {
     if (i == 0) {
       return std::abs(j) <= n_cross;
     }
@@ -47,7 +47,7 @@ class ColoringStencil {
     }
     return false;
   }
-  bool static isInTaxi(int const i, int const j, int const n_taxi) {
+  bool static isInTaxi(const int i, const int j, const int n_taxi) {
     return std::abs(i) + std::abs(j) <= n_taxi;
   }
 
@@ -161,7 +161,7 @@ PetscErrorCode SNESSolver::FDJinitialise() {
                       .doc("Extent of stencil (taxi-cab norm)")
                       .withDefault<int>((n_square == 0 && n_cross == 0) ? 2 : 0);
 
-    auto const xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
+    const auto xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
     {
       // This is ugly but can't think of a better and robust way to
       // count the non-zeros for some arbitrary stencil
@@ -543,9 +543,9 @@ SNESSolver::SNESSolver(Options* opts)
       pseudo_alpha((*options)["pseudo_alpha"]
                        .doc("Sets timestep using dt = alpha / residual")
                        .withDefault(100. * atol * timestep)),
-      pseudo_alpha_minimum(
-          (*options)["pseudo_alpha_minimum"].doc("Minimum value of pseudo_alpha")
-          .withDefault(0.1 * pseudo_alpha)),
+      pseudo_alpha_minimum((*options)["pseudo_alpha_minimum"]
+                               .doc("Minimum value of pseudo_alpha")
+                               .withDefault(0.1 * pseudo_alpha)),
       pseudo_growth_factor((*options)["pseudo_growth_factor"]
                                .doc("PTC growth factor on success")
                                .withDefault(1.1)),
@@ -1191,10 +1191,10 @@ int SNESSolver::run() {
 
       if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Adjust pseudo_alpha to globally scale timesteps
-        pseudo_alpha = std::max({
-            updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate,
-                                 max_timestep * atol * 100),
-            pseudo_alpha_minimum});
+        pseudo_alpha =
+            std::max({updateGlobalTimestep(pseudo_alpha, nl_its, recent_failure_rate,
+                                           max_timestep * atol * 100),
+                      pseudo_alpha_minimum});
 
         // Adjust local timesteps
         PetscCall(updatePseudoTimestepping());
@@ -1541,10 +1541,10 @@ PetscErrorCode SNESSolver::updatePseudoTimestepping() {
 /// rapid changes in timestep.
 BoutReal SNESSolver::updatePseudoTimestep_inverse_residual(BoutReal previous_timestep,
                                                            BoutReal current_residual) {
-  return std::max({
-      std::min({std::max({pseudo_alpha / current_residual, previous_timestep / 1.5}),
-                1.5 * previous_timestep, max_timestep}),
-      dt_min_reset});
+  return std::max(
+      {std::min({std::max({pseudo_alpha / current_residual, previous_timestep / 1.5}),
+                 1.5 * previous_timestep, max_timestep}),
+       dt_min_reset});
 }
 
 // Strategy based on history of residuals

From 5704f8bbdd8b826e79b16317e570ad30d3c1f7e5 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 18 Jun 2026 12:10:13 +0100
Subject: [PATCH 1378/1827] Explicitly specify the required `inp` files

---
 tests/integrated/test-multigrid_laplace/CMakeLists.txt | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/tests/integrated/test-multigrid_laplace/CMakeLists.txt b/tests/integrated/test-multigrid_laplace/CMakeLists.txt
index b6bb16b8a8..a9af7d47c2 100644
--- a/tests/integrated/test-multigrid_laplace/CMakeLists.txt
+++ b/tests/integrated/test-multigrid_laplace/CMakeLists.txt
@@ -2,6 +2,12 @@ bout_add_integrated_test(
   test-multigrid-laplace
   SOURCES test_multigrid_laplace.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST USE_DATA_BOUT_INP
+  USE_RUNTEST
+  USE_DATA_BOUT_INP
   PROCESSORS 3
 )
+
+bout_copy_file(data/BOUT_jy4.inp)
+bout_copy_file(data/BOUT_jy63.inp)
+bout_copy_file(data/BOUT_jy127.inp)
+bout_copy_file(data/BOUT_unsheared.inp)
\ No newline at end of file

From 71234249f08a13af3bf186edc9393ddfb85bbce7 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 18 Jun 2026 16:55:15 +0100
Subject: [PATCH 1379/1827] Set `error_on_unused_options` option to false when
 running test_multigrid_laplace

to prevent spurious test failures due to unused options.
---
 .../integrated/test-multigrid_laplace/test_multigrid_laplace.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
index eb1c58d775..6f8c28b30e 100755
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
@@ -19,7 +19,7 @@ def test_multigrid_laplace():
     for nproc in [1, 2, 4]:
         for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]:
             # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
-            cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc}"
+            cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc} input:error_on_unused_options=false"
 
             shell(["rm data/BOUT.dmp.*.nc"])
 

From f38dbd145dd28c7bf1319e0ec2e2130626594f09 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 11:30:12 -0700
Subject: [PATCH 1380/1827] Fix non-CUDA builds

Use compatibility wrappers and include guards so that BOUT++ compiles
without CUDA.
---
 include/bout/bout_types.hxx     |  5 +-
 include/bout/build_config.hxx   |  2 +
 include/bout/field.hxx          |  4 +-
 include/bout/field2d.hxx        |  8 +--
 include/bout/field3d.hxx        |  4 +-
 include/bout/field_accessor.hxx |  5 +-
 include/bout/fieldops.hxx       | 97 +++++++++++++++++----------------
 include/bout/fieldperp.hxx      |  4 +-
 8 files changed, 66 insertions(+), 63 deletions(-)

diff --git a/include/bout/bout_types.hxx b/include/bout/bout_types.hxx
index db0698d83c..7747b937b3 100644
--- a/include/bout/bout_types.hxx
+++ b/include/bout/bout_types.hxx
@@ -22,6 +22,8 @@
 #ifndef BOUT_TYPES_H
 #define BOUT_TYPES_H
 
+#include "bout/build_config.hxx"
+
 #include <limits>
 #include <string>
 
@@ -145,9 +147,8 @@ struct Constant {
   T val;
   struct View {
     T v;
-    cudaStream_t stream = 0;
     View(T v) : v(v) {}
-    __host__ __device__ T operator()(int) const { return v; }
+    BOUT_HOST_DEVICE T operator()(int) const { return v; }
   };
   operator View() const { return {val}; }
 };
diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx
index c10cd07746..60c55abad7 100644
--- a/include/bout/build_config.hxx
+++ b/include/bout/build_config.hxx
@@ -52,10 +52,12 @@ constexpr auto use_msgstack = static_cast<bool>(BOUT_USE_MSGSTACK);
 #define BOUT_HOST_DEVICE __host__ __device__
 #define BOUT_HOST __host__
 #define BOUT_DEVICE __device__
+#define BOUT_FORCEINLINE __forceinline__
 #else
 #define BOUT_HOST_DEVICE
 #define BOUT_HOST
 #define BOUT_DEVICE
+#define BOUT_FORCEINLINE inline
 #endif
 
 #endif // BOUT_BUILD_OPTIONS_HXX
diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index cd1556c96b..c7f1d23fdd 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -547,8 +547,8 @@ class Field3DParallel;
   namespace bout::op {                                                             \
   struct name {                                                                    \
     template <typename LView, typename RView>                                      \
-    __host__ __device__ BoutReal operator()(int idx, const LView& L,               \
-                                            const RView& R) const {                \
+    BOUT_HOST_DEVICE BoutReal operator()(int idx, const LView& L,                  \
+                                         const RView& R) const {                   \
       return func(L(idx));                                                         \
     }                                                                              \
   };                                                                               \
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 7d79cd56d6..f3fd6ce4df 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -324,10 +324,10 @@ public:
     BoutReal* data;
     int mul = 1;
     int div = 1;
-    __host__ __device__ inline BoutReal operator()(int idx) const {
+    BOUT_HOST_DEVICE inline BoutReal operator()(int idx) const {
       return data[(idx * mul / div)];
     }
-    __host__ __device__ inline BoutReal& operator[](int idx) const {
+    BOUT_HOST_DEVICE inline BoutReal& operator[](int idx) const {
       return data[(idx * mul) / div];
     }
 
@@ -340,8 +340,8 @@ public:
   operator View() { return View{&data[0]}; }
   operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
 
-  __device__ inline BoutReal operator()(int i) { return View()(i); }
-  __device__ inline BoutReal operator()(int i) const { return View()(i); }
+  BOUT_DEVICE inline BoutReal operator()(int i) { return View()(i); }
+  BOUT_DEVICE inline BoutReal operator()(int i) const { return View()(i); }
 
 private:
   /// Internal data array. Handles allocation/freeing of memory
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 972322ec8b..e4c7b69ddc 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -460,10 +460,10 @@ public:
     BoutReal* data;
     int mul = 1;
     int div = 1;
-    __host__ __device__ inline BoutReal operator()(int idx) const {
+    BOUT_HOST_DEVICE inline BoutReal operator()(int idx) const {
       return data[(idx * mul) / div];
     }
-    __host__ __device__ inline BoutReal& operator[](int idx) const {
+    BOUT_HOST_DEVICE inline BoutReal& operator[](int idx) const {
       return data[(idx * mul) / div];
     }
 
diff --git a/include/bout/field_accessor.hxx b/include/bout/field_accessor.hxx
index a43420d6b3..7c0ba2eb7c 100644
--- a/include/bout/field_accessor.hxx
+++ b/include/bout/field_accessor.hxx
@@ -63,8 +63,7 @@ struct FieldAccessor {
 
     if (auto* Coords = f.getCoordinates()) {
       coords = CoordinatesAccessor{Coords};
-    }
-    else {
+    } else {
       coords = CoordinatesAccessor{};
     }
 
@@ -96,7 +95,7 @@ struct FieldAccessor {
   ///
   BOUT_HOST_DEVICE inline const BoutReal& operator[](int ind) const { return data[ind]; }
   BOUT_HOST_DEVICE inline BoutReal& operator[](int ind) { return data[ind]; }
-  __device__ inline BoutReal operator()(int i) const { return data[i]; }
+  BOUT_DEVICE inline BoutReal operator()(int i) const { return data[i]; }
 
   BOUT_HOST_DEVICE inline const BoutReal& operator[](const Ind3D& ind) const {
     return data[ind.ind];
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 114793ebc8..26e3b82cc5 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -5,10 +5,14 @@
 #include "bout/array.hxx"
 #include "bout/bout_types.hxx"
 
-#include <cuda_runtime.h>
 #include <optional>
 #include <type_traits>
 #include <unordered_map>
+#include <vector>
+
+#if BOUT_HAS_CUDA
+#include <cuda_runtime.h>
+#endif
 
 class Mesh;
 class Field3D;
@@ -51,57 +55,55 @@ struct Assign {
   int scale = 1;
   int offset = 0;
   template <typename Expr>
-  __host__ __device__ void operator()(int idx, BoutReal* out, const Expr& expr) const {
+  BOUT_HOST_DEVICE void operator()(int idx, BoutReal* out, const Expr& expr) const {
     out[(idx * scale) + offset] = expr.lhs(idx) + expr.rhs(idx);
   }
 };
 
 struct Add {
   template <typename LView, typename RView>
-  __host__ __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
-                                                          const RView& R) const {
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx, const LView& L,
+                                                        const RView& R) const {
     return L(idx) + R(idx);
   }
-  __host__ __device__ __forceinline__ BoutReal operator()(BoutReal a, BoutReal b) const {
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(BoutReal a, BoutReal b) const {
     return a + b;
   }
 };
-  struct Sub {
-    template <typename LView, typename RView>
-    __host__ __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
-                                                            const RView& R) const {
-      return L(idx) - R(idx);
-    }
-    __host__ __device__ __forceinline__ BoutReal operator()(BoutReal a,
-                                                            BoutReal b) const {
-      return a - b;
-    }
-  };
-  struct Mul {
-    template <typename LView, typename RView>
-    __host__ __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
-                                                            const RView& R) const {
-      return L(idx) * R(idx);
-    }
-    __host__ __device__ __forceinline__ BoutReal operator()(BoutReal a,
-                                                            BoutReal b) const {
-      return a * b;
-    }
-  };
-  struct Div {
-    template <typename LView, typename RView>
-    __host__ __device__ __forceinline__ BoutReal operator()(int idx, const LView& L,
-                                                            const RView& R) const {
-      return L(idx) / R(idx);
-    }
-    __host__ __device__ __forceinline__ BoutReal operator()(BoutReal a,
-                                                            BoutReal b) const {
-      return a / b;
-    }
-  };
+struct Sub {
+  template <typename LView, typename RView>
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx, const LView& L,
+                                                        const RView& R) const {
+    return L(idx) - R(idx);
+  }
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(BoutReal a, BoutReal b) const {
+    return a - b;
+  }
 };
+struct Mul {
+  template <typename LView, typename RView>
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx, const LView& L,
+                                                        const RView& R) const {
+    return L(idx) * R(idx);
+  }
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(BoutReal a, BoutReal b) const {
+    return a * b;
+  }
 };
+struct Div {
+  template <typename LView, typename RView>
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx, const LView& L,
+                                                        const RView& R) const {
+    return L(idx) / R(idx);
+  }
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(BoutReal a, BoutReal b) const {
+    return a / b;
+  }
+};
+}; // namespace op
+}; // namespace bout
 
+#if BOUT_HAS_CUDA && defined(__CUDACC__)
 template <typename Expr>
 __global__ void __launch_bounds__(THREADS) evaluatorExpr(BoutReal* out, const Expr expr) {
   int tid = threadIdx.x + blockIdx.x * blockDim.x;
@@ -127,9 +129,11 @@ __global__ void __launch_bounds__(THREADS) evaluatorExpr(BoutReal* out, const Ex
   //  out[idx] = expr(idx); // single‐pass fusion
   //}
 }
+#endif
 
 inline std::unordered_map<void*, Array<int>> regionIndicesCache;
 
+#if BOUT_HAS_CUDA && defined(__CUDACC__)
 struct StreamsRAII {
   std::vector<cudaStream_t> streams;
 
@@ -163,6 +167,7 @@ struct StreamsRAII {
   StreamsRAII& operator=(StreamsRAII&&) = delete;
 };
 inline struct StreamsRAII streams;
+#endif
 
 template <typename ResT, typename L, typename R, typename Func>
 struct BinaryExpr {
@@ -216,7 +221,7 @@ struct BinaryExpr {
     //}
   }
 
-  BinaryExpr& operator=(BinaryExpr const&) = delete;
+  BinaryExpr& operator=(const BinaryExpr&) = delete;
   BinaryExpr& operator=(BinaryExpr&&) = delete;
 
   inline int size() const { return indices.size(); }
@@ -240,11 +245,11 @@ struct BinaryExpr {
       this->div = div;
       return *this;
     }
-    __host__ __device__ __forceinline__ int size() const { return num_indices; }
-    __host__ __device__ __forceinline__ int regionIdx(int idx) const {
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE int size() const { return num_indices; }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE int regionIdx(int idx) const {
       return indices[idx];
     }
-    __host__ __device__ __forceinline__ BoutReal operator()(int idx) const {
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return f((idx * mul) / div, lhs, rhs); // single‐pass fusion
       //return f(lhs((idx * mul) / div), rhs((idx * mul) / div)); // single‐pass fusion
     }
@@ -254,18 +259,14 @@ struct BinaryExpr {
   operator View() const { return View{lhs, rhs, &indices[0], indices.size(), f}; }
 
   void evaluate(BoutReal* data) const {
-#if 1
+#if BOUT_HAS_CUDA && defined(__CUDACC__)
     cudaStream_t stream = streams.get();
     int blocks = (size() + THREADS - 1) / THREADS;
     evaluatorExpr<<<blocks, THREADS, 0, stream>>>(&data[0], static_cast<View>(*this));
     cudaStreamSynchronize(stream);
     streams.put(stream);
-#endif
-
-#if 0
-    // OpenMP impl.
+#else
     int e = size();
-    //#pragma omp parallel for
     for (int i = 0; i < e; ++i) {
       int idx = regionIdx(i);
       data[idx] = operator()(idx); // single‐pass fusion
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 98da0e4a94..b00ec1dcb4 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -324,10 +324,10 @@ public:
     BoutReal* data;
     int mul = 1;
     int div = 1;
-    __host__ __device__ inline BoutReal operator()(int idx) const {
+    BOUT_HOST_DEVICE inline BoutReal operator()(int idx) const {
       return data[(idx * mul) / div];
     }
-    __host__ __device__ inline BoutReal& operator[](int idx) const {
+    BOUT_HOST_DEVICE inline BoutReal& operator[](int idx) const {
       return data[(idx * mul) / div];
     }
 

From 98b9e5508d33fe0e5eea6105131162e99841ff7e Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 11:58:51 -0700
Subject: [PATCH 1381/1827] More fixes, remove duplications

---
 include/bout/field.hxx     |  80 +++++++++---------
 include/bout/field2d.hxx   |   2 -
 include/bout/field3d.hxx   | 167 +++----------------------------------
 include/bout/fieldperp.hxx |   5 +-
 include/bout/vector3d.hxx  |   6 +-
 5 files changed, 55 insertions(+), 205 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index c7f1d23fdd..e707b62816 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -543,47 +543,45 @@ class Field3DParallel;
 #ifdef FIELD_FUNC
 #error This macro has already been defined
 #else
-#define FIELD_FUNC(name, func)                                                     \
-  namespace bout::op {                                                             \
-  struct name {                                                                    \
-    template <typename LView, typename RView>                                      \
-    BOUT_HOST_DEVICE BoutReal operator()(int idx, const LView& L,                  \
-                                         const RView& R) const {                   \
-      return func(L(idx));                                                         \
-    }                                                                              \
-  };                                                                               \
-  };                                                                               \
-  template <typename T, typename = bout::utils::EnableIfField<T>>                  \
-  inline auto name(const T& f, const std::string& rgn = "RGN_ALL") {               \
-    if constexpr (std::is_same_v<T, Field3DParallel>) {                            \
-      /* Check if the input is allocated */                                        \
-      checkData(f);                                                                \
-      /* Define and allocate the output result */                                  \
-      T result{emptyFrom(f)};                                                      \
-      BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); }               \
-      for (int i = 0; i < f.numberParallelSlices(); ++i) {                         \
-        result.yup(i) = func(f.yup(i));                                            \
-        result.ydown(i) = func(f.ydown(i));                                        \
-      }                                                                            \
-      result.name = std::string(#name "(") + f.name + std::string(")");            \
-      checkData(result);                                                           \
-      return result;                                                               \
-    } else {                                                                       \
-      std::cout << "RUNNING " #name " with CUDA\n";                                \
-      return BinaryExpr<T, T, T, bout::op::name>{static_cast<typename T::View>(f), \
-                                                 static_cast<typename T::View>(f), \
-                                                 bout::op::name{},                 \
-                                                 f.getMesh(),                      \
-                                                 f.getLocation(),                  \
-                                                 f.getDirections(),                \
-                                                 std::nullopt,                     \
-                                                 f.getRegion(rgn)};                \
-    }                                                                              \
-  }                                                                                \
-  template <typename ResT, typename L, typename R, typename Func>                  \
-  inline auto name(const BinaryExpr<ResT, L, R, Func>& f,                          \
-                   const std::string& rgn = "RGN_ALL") {                           \
-    return name(ResT{f}, rgn);                                                     \
+#define FIELD_FUNC(name, func)                                                          \
+  namespace bout::op {                                                                  \
+  struct name {                                                                         \
+    template <typename LView, typename RView>                                           \
+    BOUT_HOST_DEVICE BoutReal operator()(int idx, const LView& L, const RView&) const { \
+      return func(L(idx));                                                              \
+    }                                                                                   \
+  };                                                                                    \
+  };                                                                                    \
+  template <typename T, typename = bout::utils::EnableIfField<T>>                       \
+  inline auto name(const T& f, const std::string& rgn = "RGN_ALL") {                    \
+    if constexpr (std::is_same_v<T, Field3DParallel>) {                                 \
+      /* Check if the input is allocated */                                             \
+      checkData(f);                                                                     \
+      /* Define and allocate the output result */                                       \
+      T result{emptyFrom(f)};                                                           \
+      BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); }                    \
+      for (int i = 0; i < f.numberParallelSlices(); ++i) {                              \
+        result.yup(i) = func(f.yup(i));                                                 \
+        result.ydown(i) = func(f.ydown(i));                                             \
+      }                                                                                 \
+      result.name = std::string(#name "(") + f.name + std::string(")");                 \
+      checkData(result);                                                                \
+      return result;                                                                    \
+    } else {                                                                            \
+      return BinaryExpr<T, T, T, bout::op::name>{static_cast<typename T::View>(f),      \
+                                                 static_cast<typename T::View>(f),      \
+                                                 bout::op::name{},                      \
+                                                 f.getMesh(),                           \
+                                                 f.getLocation(),                       \
+                                                 f.getDirections(),                     \
+                                                 std::nullopt,                          \
+                                                 f.getRegion(rgn)};                     \
+    }                                                                                   \
+  }                                                                                     \
+  template <typename ResT, typename L, typename R, typename Func>                       \
+  inline auto name(const BinaryExpr<ResT, L, R, Func>& f,                               \
+                   const std::string& rgn = "RGN_ALL") {                                \
+    return name(ResT{f}, rgn);                                                          \
   }
 #endif
 
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index f3fd6ce4df..7e3ca7506d 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -116,7 +116,6 @@ public:
                                   || (is_expr_constant_v<L> && is_expr_field2d_v<R>)
                                   || (is_expr_field2d_v<L> && is_expr_constant_v<R>)>>
   Field2D(const BinaryExpr<ResT, L, R, Func>& expr) {
-    std::cout << "RUNNING Field2D constructor with CUDA\n";
     Array<BoutReal> data{expr.size()};
     expr.evaluate(&data[0]);
     *this = std::move(Field2D{std::move(data), expr.getMesh(), expr.getLocation(),
@@ -193,7 +192,6 @@ public:
   template <typename ResT, typename L, typename R, typename Func>
   std::enable_if_t<is_expr_field2d_v<L>, Field2D&>
   operator=(const BinaryExpr<ResT, L, R, Func>& expr) {
-    std::cout << "RUNNING Field2D operator= with CUDA\n";
     if (isAllocated()) {
       expr.evaluate(&data[0]);
     } else {
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index e4c7b69ddc..2c5bc9d305 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -31,10 +31,12 @@ class Field3D;
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/build_config.hxx"
 #include "bout/field.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field_data.hxx"
 #include "bout/fieldperp.hxx"
+#include "bout/mesh.hxx"
 #include "bout/region.hxx"
 #include "bout/traits.hxx"
 
@@ -43,6 +45,7 @@ class Field3D;
 #include <optional>
 #include <ostream>
 #include <string>
+#include <type_traits>
 #include <utility>
 #include <vector>
 
@@ -200,7 +203,6 @@ public:
   template <typename L, typename R, typename Func,
             typename = std::enable_if_t<is_expr_field3d_v<L> || is_expr_field3d_v<R>>>
   Field3D(const BinaryExpr<Field3D, L, R, Func>& expr) {
-    //std::cout << "RUNNING constructor from BinaryExpr\n";
     Array<BoutReal> data{expr.size()};
     expr.evaluate(&data[0]);
     *this = std::move(Field3D{std::move(data), expr.getMesh(), expr.getLocation(),
@@ -491,7 +493,6 @@ public:
   template <typename ResT, typename L, typename R, typename Func>
   std::enable_if_t<is_expr_field3d_v<L>, Field3D&>
   operator=(BinaryExpr<ResT, L, R, Func>& expr) {
-    std::cout << "RUNNING operator= with CUDA\n";
     regionID = expr.getRegionID();
     if (isAllocated()) {
       expr.evaluate(&data[0]);
@@ -964,149 +965,17 @@ Field3DParallel Field3D::asField3DParallel() {
 }
 Field3DParallel Field3D::asField3DParallel() const { return Field3DParallel(*this); }
 
-inline Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-inline Field3D operator-(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-inline Field3D operator*(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-inline Field3D operator/(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-
-inline Field3D operator+(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() + rhs;
-}
-inline Field3D operator-(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() - rhs;
-}
-inline Field3D operator*(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() * rhs;
-}
-inline Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() / rhs;
-}
-
-inline Field3DParallel
-filledFrom(const Field3DParallel& f,
-           const std::function<BoutReal(int yoffset, Ind3D index)>& func) {
-  auto result{emptyFrom(f)};
-  if (f.isFci()) {
-    BOUT_FOR(i, result.getRegion("RGN_NOY")) { result[i] = func(0, i); }
-
-    for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
-      result.yup(i).allocate();
-      BOUT_FOR(d, result.yup(i).getValidRegionWithDefault("RGN_INVALID")) {
-        result.yup(i)[d] = func(i + 1, d);
-      }
-      result.ydown(i).allocate();
-      BOUT_FOR(d, result.ydown(i).getValidRegionWithDefault("RGN_INVALID")) {
-        result.ydown(i)[d] = func(-i - 1, d);
-      }
-    }
-  } else {
-    BOUT_FOR(i, result.getRegion("RGN_ALL")) { result[i] = func(0, i); }
-  }
-
-  return result;
-}
-
-inline Field3D copy(const Field3D& f) {
-  Field3D result{f};
-  result.allocate();
-  for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
-    result.yup(i).allocate();
-    result.ydown(i).allocate();
-  }
-  return result;
-}
-
-/// Field3DParallel is intended to behave like Field3D, but preserve parallel
-/// Fields.
-/// Operations on Field3D, like multiplication, exp and floor only work on the
-/// "main" field, Field3DParallel will retain the parallel slices.
-class Field3DParallel : public Field3D {
-public:
-  template <class... Types>
-  explicit Field3DParallel(Types... args) : Field3D(std::move(args)...) {
-    ensureFieldAligned();
-  }
-  Field3DParallel(const Field3D& f) : Field3D(f) { ensureFieldAligned(); }
-  Field3DParallel(const Field3D& f, bool isRef) : Field3D(f), isRef(isRef) {
-    ensureFieldAligned();
-  }
-  Field3DParallel(const Field2D& f) : Field3D(f) { ensureFieldAligned(); }
-  // Explicitly needed, as DirectionTypes is sometimes constructed from a
-  // brace enclosed list
-  explicit Field3DParallel(Mesh* localmesh = nullptr, CELL_LOC location_in = CELL_CENTRE,
-                           DirectionTypes directions_in = {YDirectionType::Standard,
-                                                           ZDirectionType::Standard},
-                           std::optional<size_t> regionID = {})
-      : Field3D(localmesh, location_in, directions_in, regionID) {
-    if (isFci()) {
-      splitParallelSlices();
-    }
-    ensureFieldAligned();
-  }
-  explicit Field3DParallel(Array<BoutReal> data, Mesh* localmesh,
-                           CELL_LOC location = CELL_CENTRE,
-                           DirectionTypes directions_in = {YDirectionType::Standard,
-                                                           ZDirectionType::Standard})
-      : Field3D(std::move(data), localmesh, location, directions_in) {
-    ensureFieldAligned();
-  }
-  explicit Field3DParallel(BoutReal, Mesh* mesh = nullptr);
-  Field3D& asField3D() { return *this; }
-  const Field3D& asField3D() const { return *this; }
-
-  Field3DParallel& operator*=(const Field3D&);
-  Field3DParallel& operator/=(const Field3D&);
-  Field3DParallel& operator+=(const Field3D&);
-  Field3DParallel& operator-=(const Field3D&);
-  Field3DParallel& operator*=(const Field3DParallel&);
-  Field3DParallel& operator/=(const Field3DParallel&);
-  Field3DParallel& operator+=(const Field3DParallel&);
-  Field3DParallel& operator-=(const Field3DParallel&);
-  Field3DParallel& operator*=(BoutReal);
-  Field3DParallel& operator/=(BoutReal);
-  Field3DParallel& operator+=(BoutReal);
-  Field3DParallel& operator-=(BoutReal);
-  Field3DParallel& operator=(const Field3D& rhs) {
-    Field3D::operator=(rhs);
-    ensureFieldAligned();
-    return *this;
-  }
-  Field3DParallel& operator=(Field3D&& rhs) {
-    Field3D::operator=(std::move(rhs));
-    ensureFieldAligned();
-    return *this;
-  }
-  Field3DParallel& operator=(BoutReal);
-  Field3DParallel& allocate();
+// A raw Field3D is an expression leaf
+template <>
+struct is_expr_field3d<Field3D> : std::true_type {};
 
-private:
-  void ensureFieldAligned();
-  bool isRef{false};
-};
+template <>
+struct is_expr_field2d<Field2D> : std::true_type {};
 
-Field3DParallel Field3D::asField3DParallel() {
-  if (isAllocated()) {
-    allocate();
-    for (size_t i = 0; i < numberParallelSlices(); ++i) {
-      if (yup(i).isAllocated()) {
-        yup(i).allocate();
-      }
-      if (ydown(i).isAllocated()) {
-        ydown(i).allocate();
-      }
-    }
-  }
-  return Field3DParallel(*this, true);
-}
-Field3DParallel Field3D::asField3DParallel() const { return Field3DParallel(*this); }
+template <typename ResT, typename L, typename R, typename Fun>
+struct is_expr_field3d<BinaryExpr<ResT, L, R, Fun>>
+    : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value
+                                       || is_expr_field3d_v<std::decay_t<R>>> {};
 
 inline Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs) {
   return lhs + rhs.asField3D();
@@ -1158,16 +1027,4 @@ filledFrom(const Field3DParallel& f,
   return result;
 }
 
-// A raw Field3D is an expression leaf
-template <>
-struct is_expr_field3d<Field3D> : std::true_type {};
-
-template <>
-struct is_expr_field2d<Field2D> : std::true_type {};
-
-template <typename ResT, typename L, typename R, typename Fun>
-struct is_expr_field3d<BinaryExpr<ResT, L, R, Fun>>
-    : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value
-                                       || is_expr_field3d_v<std::decay_t<R>>> {};
-
 #endif /* BOUT_FIELD3D_H */
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index b00ec1dcb4..c97028d913 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -2,9 +2,9 @@
  * Class for 2D X-Z slices
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -94,7 +94,6 @@ public:
       typename ResT, typename L, typename R, typename Func,
       typename = std::enable_if_t<(is_expr_fieldperp_v<L> && is_expr_fieldperp_v<R>)>>
   FieldPerp(const BinaryExpr<ResT, L, R, Func>& expr) {
-    std::cout << "RUNNING FieldPerp constructor with CUDA\n";
     Array<BoutReal> data{expr.size()};
     expr.evaluate(&data[0]);
     *this = std::move(FieldPerp{std::move(data), expr.getMesh(), expr.getLocation(),
diff --git a/include/bout/vector3d.hxx b/include/bout/vector3d.hxx
index 655a85ca73..73d3912838 100644
--- a/include/bout/vector3d.hxx
+++ b/include/bout/vector3d.hxx
@@ -3,12 +3,10 @@
  *
  * \brief Class for 3D vectors. Built on the Field3D class.
  *
- * \author B. Dudson, October 2007
- *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *

From b0fd981bc3a5a59bea82c333d7e1b819663414e0 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 12:23:37 -0700
Subject: [PATCH 1382/1827] More fixes

Defining missing operators and resolving include issues.
---
 include/bout/field2d.hxx |  9 ++++++
 include/bout/field3d.hxx | 66 +++++++++++++++++++++++++---------------
 src/field/field3d.cxx    | 33 ++++++++++++++++++++
 src/mesh/coordinates.cxx |  1 +
 src/mesh/difops.cxx      |  3 +-
 5 files changed, 86 insertions(+), 26 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 7e3ca7506d..b9c60aa02f 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -271,6 +271,15 @@ public:
     return operator()(jx, jy);
   }
 
+  Field2D& operator*=(const Field2D& rhs);
+  Field2D& operator/=(const Field2D& rhs);
+  Field2D& operator+=(const Field2D& rhs);
+  Field2D& operator-=(const Field2D& rhs);
+  Field2D& operator*=(BoutReal rhs);
+  Field2D& operator/=(BoutReal rhs);
+  Field2D& operator+=(BoutReal rhs);
+  Field2D& operator-=(BoutReal rhs);
+
 #define FIELD2D_OP_EQUALS(OP_SYM)                                           \
   template <typename R>                                                     \
   std::enable_if_t<is_expr_field2d_v<R> || is_expr_constant_v<R>, Field2D&> \
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 2c5bc9d305..81db064b41 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -36,7 +36,6 @@ class Field3D;
 #include "bout/field2d.hxx"
 #include "bout/field_data.hxx"
 #include "bout/fieldperp.hxx"
-#include "bout/mesh.hxx"
 #include "bout/region.hxx"
 #include "bout/traits.hxx"
 
@@ -526,6 +525,20 @@ public:
 
   ///@}
 
+  Field3D& operator*=(const Field3D& rhs);
+  Field3D& operator+=(const Field3D& rhs);
+  Field3D& operator-=(const Field3D& rhs);
+  Field3D& operator*=(const Field3DParallel& rhs);
+  Field3D& operator/=(const Field3DParallel& rhs);
+  Field3D& operator+=(const Field3DParallel& rhs);
+  Field3D& operator-=(const Field3DParallel& rhs);
+  Field3D& operator*=(const Field2D& rhs);
+  Field3D& operator+=(const Field2D& rhs);
+  Field3D& operator-=(const Field2D& rhs);
+  Field3D& operator*=(BoutReal rhs);
+  Field3D& operator+=(BoutReal rhs);
+  Field3D& operator-=(BoutReal rhs);
+
   /// Division operators
   ///@{
   Field3D& operator/=(const Field3D& rhs);
@@ -965,10 +978,29 @@ Field3DParallel Field3D::asField3DParallel() {
 }
 Field3DParallel Field3D::asField3DParallel() const { return Field3DParallel(*this); }
 
+inline Field3D& Field3D::operator*=(const Field3DParallel& rhs) {
+  return (*this) *= rhs.asField3D();
+}
+
+inline Field3D& Field3D::operator/=(const Field3DParallel& rhs) {
+  return (*this) /= rhs.asField3D();
+}
+
+inline Field3D& Field3D::operator+=(const Field3DParallel& rhs) {
+  return (*this) += rhs.asField3D();
+}
+
+inline Field3D& Field3D::operator-=(const Field3DParallel& rhs) {
+  return (*this) -= rhs.asField3D();
+}
+
 // A raw Field3D is an expression leaf
 template <>
 struct is_expr_field3d<Field3D> : std::true_type {};
 
+template <>
+struct is_expr_field3d<Field3DParallel> : std::true_type {};
+
 template <>
 struct is_expr_field2d<Field2D> : std::true_type {};
 
@@ -977,31 +1009,15 @@ struct is_expr_field3d<BinaryExpr<ResT, L, R, Fun>>
     : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value
                                        || is_expr_field3d_v<std::decay_t<R>>> {};
 
-inline Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-inline Field3D operator-(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-inline Field3D operator*(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
-inline Field3D operator/(const Field2D& lhs, const Field3DParallel& rhs) {
-  return lhs + rhs.asField3D();
-}
+Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs);
+Field3D operator-(const Field2D& lhs, const Field3DParallel& rhs);
+Field3D operator*(const Field2D& lhs, const Field3DParallel& rhs);
+Field3D operator/(const Field2D& lhs, const Field3DParallel& rhs);
 
-inline Field3D operator+(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() + rhs;
-}
-inline Field3D operator-(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() - rhs;
-}
-inline Field3D operator*(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() * rhs;
-}
-inline Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs) {
-  return lhs.asField3D() / rhs;
-}
+Field3D operator+(const Field3DParallel& lhs, const Field2D& rhs);
+Field3D operator-(const Field3DParallel& lhs, const Field2D& rhs);
+Field3D operator*(const Field3DParallel& lhs, const Field2D& rhs);
+Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs);
 
 inline Field3DParallel
 filledFrom(const Field3DParallel& f,
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index cc2a342f37..238bef1993 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -51,6 +51,7 @@
 #include <bout/fft.hxx>
 #include <bout/field3d.hxx>
 #include <bout/interpolation.hxx>
+#include <bout/mesh.hxx>
 #include <bout/output.hxx>
 #include <bout/utils.hxx>
 
@@ -84,6 +85,38 @@ Field3D::Field3D(const Field3D& f)
   }
 }
 
+Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs + rhs.asField3D();
+}
+
+Field3D operator-(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs - rhs.asField3D();
+}
+
+Field3D operator*(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs * rhs.asField3D();
+}
+
+Field3D operator/(const Field2D& lhs, const Field3DParallel& rhs) {
+  return lhs / rhs.asField3D();
+}
+
+Field3D operator+(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() + rhs;
+}
+
+Field3D operator-(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() - rhs;
+}
+
+Field3D operator*(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() * rhs;
+}
+
+Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs) {
+  return lhs.asField3D() / rhs;
+}
+
 Field3D::Field3D(const Field2D& f) : Field(f) {
 
   nx = fieldmesh->LocalNx;
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 6334054533..8980b00695 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -4,6 +4,7 @@
  * given the contravariant metric tensor terms
  **************************************************************************/
 
+#include "bout/coordinates_accessor.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_data.hxx"
 #include <bout/assert.hxx>
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 09433b0685..902ebfce93 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -284,7 +284,8 @@ Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
   auto Bxy_floc = f.getCoordinates()->Bxy;
 
   if (!f.hasParallelSlices()) {
-    return metric->Bxy * FDDY(v, f / Bxy_floc, outloc, method) / sqrt(metric->g_22);
+    Field3D f_B = f / Bxy_floc;
+    return metric->Bxy * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22);
   }
 
   // Need to modify yup and ydown fields

From bb5b495eb7199eee884eec001d36e9f57e86339c Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 12:51:16 -0700
Subject: [PATCH 1383/1827] Unit tests compiling again

---
 include/bout/fieldops.hxx                     | 29 +----------
 .../invert/laplace/test_laplace_cyclic.cxx    | 27 +++++-----
 tests/unit/test_extras.cxx                    | 11 ++++
 tests/unit/test_extras.hxx                    | 50 ++++++++++++++-----
 4 files changed, 62 insertions(+), 55 deletions(-)

diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 26e3b82cc5..302769ae70 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -187,38 +187,11 @@ struct BinaryExpr {
              const Region<IndType>& region)
       //: lhs(static_cast<typename L::View>(lhs)), rhs(static_cast<typename R::View>(rhs)),
       : lhs(lhs), rhs(rhs), f(f), mesh(mesh), location(location), directions(directions),
-        regionID(regionID), indices(region.getIndices().size()) {
+        indices(region.getIndices().size()), regionID(regionID) {
     // Copy the region indices into the managed array
     for (int i = 0; i < indices.size(); ++i) {
       indices[i] = region.getIndices()[i].ind;
     }
-    //std::cout << "===PRE-sorting indices\n";
-    //for (auto& ind : indices) {
-    //  std::cout << ind << " ";
-    //}
-    //std::cout << "===end PRE\n";
-    //std::sort(indices.begin(), indices.end(),
-    //          [](const auto& a, const auto& b) { return a < b; });
-    //std::cout << "===POST-sorting indices\n";
-    //for (auto& ind : indices) {
-    //  std::cout << ind << " ";
-    //}
-    //std::cout << "===end POST\n";
-    //if (regionIndicesCache.find(static_cast<void*>(const_cast<Region<IndType>*>(&region)))
-    //    != regionIndicesCache.end()) {
-    //  // If we have already computed the indices for this region, use them
-    //  indices =
-    //      regionIndicesCache[static_cast<void*>(const_cast<Region<IndType>*>(&region))];
-    //} else {
-    //  // Otherwise, compute the indices and store them in the cache
-    //  indices = Array<int>(region.getIndices().size());
-    //  // Copy the region indices into the managed array
-    //  for (int i = 0; i < indices.size(); ++i) {
-    //    indices[i] = region.getIndices()[i].ind;
-    //  }
-    //  regionIndicesCache[static_cast<void*>(const_cast<Region<IndType>*>(&region))] =
-    //      indices;
-    //}
   }
 
   BinaryExpr& operator=(const BinaryExpr&) = delete;
diff --git a/tests/unit/invert/laplace/test_laplace_cyclic.cxx b/tests/unit/invert/laplace/test_laplace_cyclic.cxx
index a0d99f66c9..586dd80adf 100644
--- a/tests/unit/invert/laplace/test_laplace_cyclic.cxx
+++ b/tests/unit/invert/laplace/test_laplace_cyclic.cxx
@@ -10,6 +10,7 @@
 #include "bout/invert_laplace.hxx"
 #include "gtest/gtest.h"
 
+#include "bout/bout_types.hxx"
 #include "bout/derivs.hxx"
 #include "bout/difops.hxx"
 #include "bout/field2d.hxx"
@@ -17,7 +18,6 @@
 #include "bout/griddata.hxx"
 #include "bout/mesh.hxx"
 #include "bout/options.hxx"
-#include "bout/vecops.hxx"
 
 #include "fake_mesh_fixture.hxx"
 
@@ -29,14 +29,13 @@ class CyclicForwardOperator {
   CyclicForwardOperator(bool xin_neumann, bool xout_neumann)
       : inner_x_neumann(xin_neumann), outer_x_neumann(xout_neumann),
 
-        a(0.0), c1(1.0), c2(1.0), d(1.0), ex(0.0), ez(0.0) {
-    coords = mesh->getCoordinates(CELL_CENTER);
-  }
+        a(0.0), c1(1.0), c2(1.0), d(1.0), ex(0.0), ez(0.0),
+        coords(mesh->getCoordinates(CELL_CENTER)) {}
 
-  const Field3D operator()(Field3D& f) {
-    auto result = d * Delp2(f)
-                  + (coords->g11 * DDX(f) + coords->g13 * DDZ(f)) * DDX(c2) / c1 + a * f
-                  + ex * DDX(f) + ez * DDZ(f);
+  Field3D operator()(Field3D& f) {
+    Field3D result = d * Delp2(f)
+                     + (coords->g11 * DDX(f) + coords->g13 * DDZ(f)) * DDX(c2) / c1
+                     + a * f + ex * DDX(f) + ez * DDZ(f);
     applyBoundaries(result, f);
     return result;
   }
@@ -45,7 +44,7 @@ class CyclicForwardOperator {
   CyclicForwardOperator();
   bool inner_x_neumann, outer_x_neumann; // If false then use Dirichlet conditions
 
-  void applyBoundaries(Field3D& newF, const Field3D& f) {
+  void applyBoundaries(Field3D& newF, const Field3D& f) const {
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) {
       if (inner_x_neumann) {
         newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]);
@@ -86,14 +85,14 @@ class CyclicTest : public FakeMeshFixture,
     coef3.allocate();
 
     BOUT_FOR(i, mesh->getRegion2D("RGN_ALL")) {
-      BoutReal x = i.x() / (BoutReal)nx - 0.5;
-      BoutReal y = i.y() / (BoutReal)ny - 0.5;
+      const BoutReal x = i.x() / (BoutReal)nx - 0.5;
+      const BoutReal y = i.y() / (BoutReal)ny - 0.5;
       coef2[i] = x + y;
     }
     BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) {
-      BoutReal x = i.x() / (BoutReal)nx - 0.5;
-      BoutReal y = i.y() / (BoutReal)ny - 0.5;
-      BoutReal z = i.z() / (BoutReal)nz - 0.5;
+      const BoutReal x = i.x() / (BoutReal)nx - 0.5;
+      const BoutReal y = i.y() / (BoutReal)ny - 0.5;
+      const BoutReal z = i.z() / (BoutReal)nz - 0.5;
       f3[i] = 1e3 * exp(-0.5 * sqrt(x * x + y * y + z * z) / sigmasq);
       coef3[i] = x + y + sin(2 * 3.14159265358979323846 * z);
     }
diff --git a/tests/unit/test_extras.cxx b/tests/unit/test_extras.cxx
index b1caf038d3..7cf7cc7c0d 100644
--- a/tests/unit/test_extras.cxx
+++ b/tests/unit/test_extras.cxx
@@ -1,4 +1,5 @@
 #include "test_extras.hxx"
+#include "fake_mesh_fixture.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
@@ -42,3 +43,13 @@ void fillField(Field2D& f, std::vector<std::vector<BoutReal>> values) {
     }
   }
 }
+
+using TestExtrasFieldExpr = FakeMeshFixture;
+
+TEST_F(TestExtrasFieldExpr, IsFieldEqualHandlesBinaryExprOnEitherSide) {
+  const Field2D field{1.0};
+  const Field2D expected{3.0};
+
+  EXPECT_TRUE(IsFieldEqual(field + 2.0, expected));
+  EXPECT_TRUE(IsFieldEqual(expected, field + 2.0));
+}
diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx
index dcc6cb3187..6038d981d4 100644
--- a/tests/unit/test_extras.hxx
+++ b/tests/unit/test_extras.hxx
@@ -7,15 +7,16 @@
 #include <iostream>
 #include <sstream>
 #include <string>
+#include <type_traits>
 #include <vector>
 
 #include "bout/bout_types.hxx"
 #include "bout/field.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/fieldperp.hxx"
 #include "bout/region.hxx"
 
-class Field2D;
-class Field3D;
-
 static constexpr BoutReal BoutRealTolerance{1e-15};
 // FFTs have a slightly looser tolerance than other functions
 static constexpr BoutReal FFTTolerance{1.e-12};
@@ -29,6 +30,23 @@ void fillField(Field2D& f, std::vector<std::vector<BoutReal>> values);
 
 using bout::utils::EnableIfField;
 
+template <typename T>
+inline constexpr bool isFieldOrFieldExpr_v =
+    bout::utils::is_Field_v<std::decay_t<T>> || is_expr_field2d_v<T>
+    || is_expr_field3d_v<T> || is_expr_fieldperp_v<T>;
+
+template <typename T,
+          typename = std::enable_if_t<bout::utils::is_Field_v<std::decay_t<T>>>>
+auto evaluateFieldExpr(const T& field) -> const T& {
+  return field;
+}
+
+template <typename ResT, typename L, typename R, typename Func,
+          typename = std::enable_if_t<bout::utils::is_Field_v<ResT>>>
+auto evaluateFieldExpr(const BinaryExpr<ResT, L, R, Func>& expr) -> ResT {
+  return ResT{expr};
+}
+
 /// Returns a field filled with the result of \p fill_function at each point
 /// Arbitrary arguments can be passed to the field constructor
 template <class T, class... Args, typename = EnableIfField<T>>
@@ -80,15 +98,19 @@ auto inline getIndexXYZ(const IndPerp& index) -> std::string {
 }
 
 /// Is \p field equal to \p reference, with a tolerance of \p tolerance?
-template <class T, class U, typename = EnableIfField<T, U>>
+template <class T, class U,
+          typename = std::enable_if_t<isFieldOrFieldExpr_v<T> && isFieldOrFieldExpr_v<U>>>
 auto IsFieldEqual(const T& field, const U& reference,
                   const std::string& region = "RGN_ALL",
                   BoutReal tolerance = BoutRealTolerance) -> ::testing::AssertionResult {
-  for (auto i : field.getRegion(region)) {
-    if (fabs(field[i] - reference[i]) > tolerance) {
+  const auto& evaluated_field = evaluateFieldExpr(field);
+  const auto& evaluated_reference = evaluateFieldExpr(reference);
+
+  for (auto i : evaluated_field.getRegion(region)) {
+    if (fabs(evaluated_field[i] - evaluated_reference[i]) > tolerance) {
       return ::testing::AssertionFailure()
-             << getFieldType(field) << "(" << getIndexXYZ(i) << ") == " << field[i]
-             << "; Expected: " << reference[i];
+             << getFieldType(evaluated_field) << "(" << getIndexXYZ(i)
+             << ") == " << evaluated_field[i] << "; Expected: " << evaluated_reference[i];
     }
   }
   return ::testing::AssertionSuccess();
@@ -96,15 +118,17 @@ auto IsFieldEqual(const T& field, const U& reference,
 
 /// Is \p field equal to \p reference, with a tolerance of \p tolerance?
 /// Overload for BoutReals
-template <class T, typename = EnableIfField<T>>
+template <class T, typename = std::enable_if_t<isFieldOrFieldExpr_v<T>>>
 auto IsFieldEqual(const T& field, BoutReal reference,
                   const std::string& region = "RGN_ALL",
                   BoutReal tolerance = BoutRealTolerance) -> ::testing::AssertionResult {
-  for (auto i : field.getRegion(region)) {
-    if (fabs(field[i] - reference) > tolerance) {
+  const auto& evaluated_field = evaluateFieldExpr(field);
+
+  for (auto i : evaluated_field.getRegion(region)) {
+    if (fabs(evaluated_field[i] - reference) > tolerance) {
       return ::testing::AssertionFailure()
-             << getFieldType(field) << "(" << getIndexXYZ(i) << ") == " << field[i]
-             << "; Expected: " << reference;
+             << getFieldType(evaluated_field) << "(" << getIndexXYZ(i)
+             << ") == " << evaluated_field[i] << "; Expected: " << reference;
     }
   }
   return ::testing::AssertionSuccess();

From a06e450975fadfc7777950400bffde0d767d3238 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 13:19:30 -0700
Subject: [PATCH 1384/1827] Fix warnings coming from Field constructors

---
 include/bout/field2d.hxx   | 16 ++++++++++------
 include/bout/field3d.hxx   | 15 ++++++++++-----
 include/bout/fieldops.hxx  |  5 ++---
 include/bout/fieldperp.hxx | 16 ++++++++++------
 4 files changed, 32 insertions(+), 20 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index b9c60aa02f..340b4b29fc 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -115,12 +115,9 @@ public:
       typename = std::enable_if_t<(is_expr_field2d_v<L> && is_expr_field2d_v<R>)
                                   || (is_expr_constant_v<L> && is_expr_field2d_v<R>)
                                   || (is_expr_field2d_v<L> && is_expr_constant_v<R>)>>
-  Field2D(const BinaryExpr<ResT, L, R, Func>& expr) {
-    Array<BoutReal> data{expr.size()};
-    expr.evaluate(&data[0]);
-    *this = std::move(Field2D{std::move(data), expr.getMesh(), expr.getLocation(),
-                              expr.getDirections()});
-  }
+  Field2D(const BinaryExpr<ResT, L, R, Func>& expr)
+      : Field2D(evaluateBinaryExpr(expr), expr.getMesh(), expr.getLocation(),
+                expr.getDirections()) {}
   /*!
    * Destructor
    */
@@ -351,6 +348,13 @@ public:
   BOUT_DEVICE inline BoutReal operator()(int i) const { return View()(i); }
 
 private:
+  template <typename ResT, typename L, typename R, typename Func>
+  static Array<BoutReal> evaluateBinaryExpr(const BinaryExpr<ResT, L, R, Func>& expr) {
+    Array<BoutReal> data{expr.size()};
+    expr.evaluate(&data[0]);
+    return data;
+  }
+
   /// Internal data array. Handles allocation/freeing of memory
   Array<BoutReal> data;
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 81db064b41..c2448e82fb 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -201,11 +201,9 @@ public:
                                           ZDirectionType::Standard});
   template <typename L, typename R, typename Func,
             typename = std::enable_if_t<is_expr_field3d_v<L> || is_expr_field3d_v<R>>>
-  Field3D(const BinaryExpr<Field3D, L, R, Func>& expr) {
-    Array<BoutReal> data{expr.size()};
-    expr.evaluate(&data[0]);
-    *this = std::move(Field3D{std::move(data), expr.getMesh(), expr.getLocation(),
-                              expr.getDirections()});
+  Field3D(const BinaryExpr<Field3D, L, R, Func>& expr)
+      : Field3D(evaluateBinaryExpr(expr), expr.getMesh(), expr.getLocation(),
+                expr.getDirections()) {
     setRegion(expr.getRegionID());
   }
   /// Destructor
@@ -643,6 +641,13 @@ protected:
   template <typename T, typename = bout::utils::EnableIfField<T>>
   void _track(const T& change, std::string operation);
   void _track(const BoutReal& change, std::string operation);
+
+  template <typename L, typename R, typename Func>
+  static Array<BoutReal> evaluateBinaryExpr(const BinaryExpr<Field3D, L, R, Func>& expr) {
+    Array<BoutReal> data{expr.size()};
+    expr.evaluate(&data[0]);
+    return data;
+  }
 };
 
 // Non-member overloaded operators
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 302769ae70..7cb5c67643 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -185,9 +185,8 @@ struct BinaryExpr {
   BinaryExpr(const typename L::View& lhs, const typename R::View& rhs, Func f, Mesh* mesh,
              CELL_LOC location, DirectionTypes directions, std::optional<size_t> regionID,
              const Region<IndType>& region)
-      //: lhs(static_cast<typename L::View>(lhs)), rhs(static_cast<typename R::View>(rhs)),
-      : lhs(lhs), rhs(rhs), f(f), mesh(mesh), location(location), directions(directions),
-        indices(region.getIndices().size()), regionID(regionID) {
+      : lhs(lhs), rhs(rhs), indices(region.getIndices().size()), f(f), mesh(mesh),
+        location(location), directions(directions), regionID(regionID) {
     // Copy the region indices into the managed array
     for (int i = 0; i < indices.size(); ++i) {
       indices[i] = region.getIndices()[i].ind;
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index c97028d913..74414d01d6 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -93,12 +93,9 @@ public:
   template <
       typename ResT, typename L, typename R, typename Func,
       typename = std::enable_if_t<(is_expr_fieldperp_v<L> && is_expr_fieldperp_v<R>)>>
-  FieldPerp(const BinaryExpr<ResT, L, R, Func>& expr) {
-    Array<BoutReal> data{expr.size()};
-    expr.evaluate(&data[0]);
-    *this = std::move(FieldPerp{std::move(data), expr.getMesh(), expr.getLocation(),
-                                /* yindex */ -1, expr.getDirections()});
-  }
+  FieldPerp(const BinaryExpr<ResT, L, R, Func>& expr)
+      : FieldPerp(evaluateBinaryExpr(expr), expr.getMesh(), expr.getLocation(),
+                  /* yindex */ -1, expr.getDirections()) {}
 
   ~FieldPerp() override = default;
 
@@ -340,6 +337,13 @@ public:
   operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
 
 private:
+  template <typename ResT, typename L, typename R, typename Func>
+  static Array<BoutReal> evaluateBinaryExpr(const BinaryExpr<ResT, L, R, Func>& expr) {
+    Array<BoutReal> data{expr.size()};
+    expr.evaluate(&data[0]);
+    return data;
+  }
+
   /// The Y index at which this FieldPerp is defined
   int yindex{-1};
 

From 801890652a437ebd36d45cd4078845b7b5150712 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 13:47:46 -0700
Subject: [PATCH 1385/1827] Fix unit tests

Expressions need to check the location of their arguments.
---
 include/bout/field.hxx   | 22 ++++++++++++++++++++++
 include/bout/field2d.hxx |  1 +
 include/bout/field3d.hxx |  2 ++
 3 files changed, 25 insertions(+)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index e707b62816..6b745747f8 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -183,8 +183,30 @@ inline bool areFieldsCompatible(const Field& field1, const Field& field2) {
                         #field2, toString((field2).getDirections()));                    \
   }
 
+#define ASSERT1_EXPR_COMPATIBLE(expr1, expr2)                                          \
+  if ((expr1).getLocation() != (expr2).getLocation()) {                                \
+    throw BoutException("Error in {:s}:{:d}\nFields at different position:"            \
+                        "`{:s}` at {:s}, `{:s}` at {:s}",                              \
+                        __FILE__, __LINE__, #expr1, toString((expr1).getLocation()),   \
+                        #expr2, toString((expr2).getLocation()));                      \
+  }                                                                                    \
+  if ((expr1).getMesh() != (expr2).getMesh()) {                                        \
+    throw BoutException("Error in {:s}:{:d}\nFields are on different Meshes:"          \
+                        "`{:s}` at {:p}, `{:s}` at {:p}",                              \
+                        __FILE__, __LINE__, #expr1,                                    \
+                        static_cast<void*>((expr1).getMesh()), #expr2,                 \
+                        static_cast<void*>((expr2).getMesh()));                        \
+  }                                                                                    \
+  if (!areDirectionsCompatible((expr1).getDirections(), (expr2).getDirections())) {    \
+    throw BoutException("Error in {:s}:{:d}\nFields at different directions:"          \
+                        "`{:s}` at {:s}, `{:s}` at {:s}",                              \
+                        __FILE__, __LINE__, #expr1, toString((expr1).getDirections()), \
+                        #expr2, toString((expr2).getDirections()));                    \
+  }
+
 #else
 #define ASSERT1_FIELDS_COMPATIBLE(field1, field2) ;
+#define ASSERT1_EXPR_COMPATIBLE(expr1, expr2) ;
 #endif
 
 /// Return an empty shell field of some type derived from Field, with metadata
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 340b4b29fc..c7d8252aaa 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -397,6 +397,7 @@ FIELD2D_FIELD2D_FIELD2D_OP(/, Div)
   std::enable_if_t<is_expr_field2d_v<L> && is_expr_field3d_v<R>, \
                    BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>> \
   operator OP_SYM(const L& lhs, const R& rhs) {                  \
+    ASSERT1_EXPR_COMPATIBLE(lhs, rhs);                           \
     auto regionID = rhs.getRegionID();                           \
     int mesh_nz = rhs.getMesh()->LocalNz;                        \
     return BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>{         \
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index c2448e82fb..e27a7600d2 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -666,6 +666,7 @@ FieldPerp operator/(const Field3D& lhs, const FieldPerp& rhs);
             typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>> \
   BinaryExpr<Field3D, L, R, bout::op::OP_TYPE> operator OP_SYM(const L& lhs,           \
                                                                const R& rhs) {         \
+    ASSERT1_EXPR_COMPATIBLE(lhs, rhs);                                                 \
     auto regionID =                                                                    \
         lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());          \
     return BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>{                               \
@@ -690,6 +691,7 @@ FIELD3D_FIELD3D_FIELD3D_OP(/, Div)
   std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>, \
                    BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>> \
   operator OP_SYM(const L& lhs, const R& rhs) {                  \
+    ASSERT1_EXPR_COMPATIBLE(lhs, rhs);                           \
     auto regionID = lhs.getRegionID();                           \
     int mesh_nz = lhs.getMesh()->LocalNz;                        \
     return BinaryExpr<Field3D, L, R, bout::op::OP_TYPE>{         \

From 6cab892e52f384a5507e9781d72b040947b7fac1 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 14:43:29 -0700
Subject: [PATCH 1386/1827] BinaryExpr::operator[](IndType) indexing

Allows evaluation of binary expressions at specific indices.

Fixed boundary implementation in Petsc3DAMG.
---
 include/bout/fieldops.hxx                     |  5 ++
 .../laplace/impls/petsc3damg/petsc3damg.cxx   | 73 +++++++++++++------
 tests/unit/test_extras.cxx                    | 16 ++++
 3 files changed, 70 insertions(+), 24 deletions(-)

diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 7cb5c67643..7475661376 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -200,6 +200,11 @@ struct BinaryExpr {
   inline BoutReal operator()(int idx) const {
     return f(idx, lhs, rhs); // single‐pass fusion
   }
+  template <typename IndType>
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE auto operator[](const IndType& d) const
+      -> decltype(d.ind, BoutReal{}) {
+    return operator()(d.ind);
+  }
   inline int regionIdx(int idx) const { return indices[idx]; }
 
   //operator ResT() { return ResT{*this}; }
diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
index 3be5e43e63..ddd0b15b7e 100644
--- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
+++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
@@ -120,39 +120,64 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes
 
   // Set up boundary conditions in operator
   const bool inner_X_neumann = isInnerBoundaryFlagSet(INVERT_AC_GRAD);
-  const auto inner_X_BC = inner_X_neumann ? -1. / coords->dx / sqrt(coords->g_11) : 0.5;
-  const auto inner_X_BC_plus = inner_X_neumann ? -inner_X_BC : 0.5;
-
-  BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
-    operator3D(i, i) = inner_X_BC[i];
-    operator3D(i, i.xp()) = inner_X_BC_plus[i];
+  if (inner_X_neumann) {
+    // This is a BinaryExpr that is only evaluated when needed
+    const auto inner_X_BC = -1. / coords->dx / sqrt(coords->g_11);
+    BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
+      const BoutReal bc = inner_X_BC[i];
+      operator3D(i, i) = bc;
+      operator3D(i, i.xp()) = -bc;
+    }
+  } else {
+    BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
+      operator3D(i, i) = 0.5;
+      operator3D(i, i.xp()) = 0.5;
+    }
   }
 
   const bool outer_X_neumann = isOuterBoundaryFlagSet(INVERT_AC_GRAD);
-  const auto outer_X_BC = outer_X_neumann ? 1. / coords->dx / sqrt(coords->g_11) : 0.5;
-  const auto outer_X_BC_minus = outer_X_neumann ? -outer_X_BC : 0.5;
-
-  BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
-    operator3D(i, i) = outer_X_BC[i];
-    operator3D(i, i.xm()) = outer_X_BC_minus[i];
+  if (outer_X_neumann) {
+    const auto outer_X_BC = 1. / coords->dx / sqrt(coords->g_11);
+    BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
+      const BoutReal bc = outer_X_BC[i];
+      operator3D(i, i) = bc;
+      operator3D(i, i.xm()) = -bc;
+    }
+  } else {
+    BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
+      operator3D(i, i) = 0.5;
+      operator3D(i, i.xm()) = 0.5;
+    }
   }
 
   const bool lower_Y_neumann = flagSet(lower_boundary_flags, INVERT_AC_GRAD);
-  const auto lower_Y_BC = lower_Y_neumann ? -1. / coords->dy / sqrt(coords->g_22) : 0.5;
-  const auto lower_Y_BC_plus = lower_Y_neumann ? -lower_Y_BC : 0.5;
-
-  BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) {
-    operator3D(i, i) = lower_Y_BC[i];
-    operator3D(i, i.yp()) = lower_Y_BC_plus[i];
+  if (lower_Y_neumann) {
+    const auto lower_Y_BC = -1. / coords->dy / sqrt(coords->g_22);
+    BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) {
+      const BoutReal bc = lower_Y_BC[i];
+      operator3D(i, i) = bc;
+      operator3D(i, i.yp()) = -bc;
+    }
+  } else {
+    BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) {
+      operator3D(i, i) = 0.5;
+      operator3D(i, i.yp()) = 0.5;
+    }
   }
 
   const bool upper_Y_neumann = flagSet(upper_boundary_flags, INVERT_AC_GRAD);
-  const auto upper_Y_BC = upper_Y_neumann ? 1. / coords->dy / sqrt(coords->g_22) : 0.5;
-  const auto upper_Y_BC_minus = upper_Y_neumann ? -upper_Y_BC : 0.5;
-
-  BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) {
-    operator3D(i, i) = upper_Y_BC[i];
-    operator3D(i, i.ym()) = upper_Y_BC_minus[i];
+  if (upper_Y_neumann) {
+    const auto upper_Y_BC = 1. / coords->dy / sqrt(coords->g_22);
+    BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) {
+      const BoutReal bc = upper_Y_BC[i];
+      operator3D(i, i) = bc;
+      operator3D(i, i.ym()) = -bc;
+    }
+  } else {
+    BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) {
+      operator3D(i, i) = 0.5;
+      operator3D(i, i.ym()) = 0.5;
+    }
   }
 }
 
diff --git a/tests/unit/test_extras.cxx b/tests/unit/test_extras.cxx
index 7cf7cc7c0d..f096292ed3 100644
--- a/tests/unit/test_extras.cxx
+++ b/tests/unit/test_extras.cxx
@@ -53,3 +53,19 @@ TEST_F(TestExtrasFieldExpr, IsFieldEqualHandlesBinaryExprOnEitherSide) {
   EXPECT_TRUE(IsFieldEqual(field + 2.0, expected));
   EXPECT_TRUE(IsFieldEqual(expected, field + 2.0));
 }
+
+TEST_F(TestExtrasFieldExpr, BinaryExprCanBeIndexedWithRegionIndex) {
+  const Field3D lhs{
+      makeField<Field3D>([](const Ind3D& i) { return static_cast<BoutReal>(i.x()); })};
+  const Field3D rhs{
+      makeField<Field3D>([](const Ind3D& i) { return static_cast<BoutReal>(i.y()); })};
+
+  const auto expr = lhs + 2.0 * rhs;
+  Field3D result{emptyFrom(lhs)};
+
+  BOUT_FOR_SERIAL(i, result.getRegion("RGN_ALL")) { result[i] = expr[i]; }
+
+  BOUT_FOR(i, result.getRegion("RGN_ALL")) {
+    EXPECT_DOUBLE_EQ(result[i], lhs[i] + 2.0 * rhs[i]);
+  }
+}

From 1caebb6874a6f85af3e2c359f9caed9ccdc9d1aa Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 15:25:20 -0700
Subject: [PATCH 1387/1827] SQ and mean for BinaryExpr

`SQ` ensures that its argument is only evaluated once.

`mean` is defined analogously to `min` and `max`: It evaluates
the expression and then calls the existing field operator.
---
 include/bout/field.hxx                        | 63 +++++++++++++++++++
 include/bout/fieldops.hxx                     |  6 ++
 include/bout/utils.hxx                        |  5 +-
 tests/unit/field/test_field2d.cxx             | 13 ++++
 tests/unit/field/test_field3d.cxx             | 30 +++++++++
 tests/unit/field/test_fieldperp.cxx           |  8 +++
 .../laplace/test_laplace_petsc3damg.cxx       |  6 +-
 7 files changed, 127 insertions(+), 4 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 6b745747f8..b0477d756e 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -496,6 +496,12 @@ inline BoutReal mean(const T& f, bool allpe = false,
   return result / static_cast<BoutReal>(count);
 }
 
+template <typename ResT, typename L, typename R, typename Func>
+inline BoutReal mean(const BinaryExpr<ResT, L, R, Func>& f, bool allpe = false,
+                     const std::string& rgn = "RGN_NOBNDRY") {
+  return mean(ResT{f}, allpe, rgn);
+}
+
 /// Exponent: pow(lhs, lhs) is \p lhs raised to the power of \p rhs
 ///
 /// This loops over the entire domain, including guard/boundary cells by
@@ -607,6 +613,63 @@ class Field3DParallel;
   }
 #endif
 
+namespace bout::op {
+struct Square {
+  template <typename LView, typename RView>
+  BOUT_HOST_DEVICE BoutReal operator()(int idx, const LView& L, const RView&) const {
+    const BoutReal value = L(idx);
+    return ::SQ(value);
+  }
+};
+}; // namespace bout::op
+
+template <typename T, typename = bout::utils::EnableIfField<T>>
+inline auto SQ(const T& f, const std::string& rgn = "RGN_ALL") {
+  if constexpr (std::is_same_v<T, Field3DParallel>) {
+    checkData(f);
+    T result{emptyFrom(f)};
+    if (f.hasParallelSlices() and !result.hasParallelSlices()) {
+      result.splitParallelSlices();
+    }
+    BOUT_FOR(d, result.getRegion(rgn)) { result[d] = ::SQ(f[d]); }
+    for (size_t i = 0; i < f.numberParallelSlices(); ++i) {
+      result.yup(i) = SQ(f.yup(i), rgn);
+      result.ydown(i) = SQ(f.ydown(i), rgn);
+    }
+    result.name = std::string("SQ(") + f.name + std::string(")");
+    checkData(result);
+    return result;
+  } else {
+    return BinaryExpr<T, T, T, bout::op::Square>{static_cast<typename T::View>(f),
+                                                 static_cast<typename T::View>(f),
+                                                 bout::op::Square{},
+                                                 f.getMesh(),
+                                                 f.getLocation(),
+                                                 f.getDirections(),
+                                                 std::nullopt,
+                                                 f.getRegion(rgn)};
+  }
+}
+
+template <typename ResT, typename L, typename R, typename Func>
+inline auto SQ(const BinaryExpr<ResT, L, R, Func>& f) {
+  return BinaryExpr<ResT, BinaryExpr<ResT, L, R, Func>, BinaryExpr<ResT, L, R, Func>,
+                    bout::op::Square>{
+      static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),
+      static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),
+      bout::op::Square{},
+      f.getMesh(),
+      f.getLocation(),
+      f.getDirections(),
+      f.getRegionID(),
+      f.indices};
+}
+
+template <typename ResT, typename L, typename R, typename Func>
+inline auto SQ(const BinaryExpr<ResT, L, R, Func>& f, const std::string& rgn) {
+  return SQ(ResT{f}, rgn);
+}
+
 /// Square root of \p f over region \p rgn
 ///
 /// This loops over the entire domain, including guard/boundary cells by
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 7475661376..5e662b24d4 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -193,6 +193,12 @@ struct BinaryExpr {
     }
   }
 
+  BinaryExpr(const typename L::View& lhs, const typename R::View& rhs, Func f, Mesh* mesh,
+             CELL_LOC location, DirectionTypes directions, std::optional<size_t> regionID,
+             const Array<int>& indices)
+      : lhs(lhs), rhs(rhs), indices(indices), f(f), mesh(mesh), location(location),
+        directions(directions), regionID(regionID) {}
+
   BinaryExpr& operator=(const BinaryExpr&) = delete;
   BinaryExpr& operator=(BinaryExpr&&) = delete;
 
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 9b24311c33..6fb7d38dc2 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -47,6 +47,8 @@
 #include <sstream>
 #include <string>
 
+class Field;
+
 #ifdef _MSC_VER
 // finite is not actually standard C++, it's a BSD extention for C
 inline auto finite(BoutReal x) -> bool { return std::isfinite(x); }
@@ -436,7 +438,8 @@ inline BoutReal randomu() {
  * Calculate the square of a variable \p t
  * i.e. t * t
  */
-template <typename T>
+template <typename T,
+          typename = std::enable_if_t<!std::is_base_of_v<Field, std::decay_t<T>>>>
 inline auto SQ(const T& t) {
   return t * t;
 }
diff --git a/tests/unit/field/test_field2d.cxx b/tests/unit/field/test_field2d.cxx
index cf9a0c1f25..67cf1d6c61 100644
--- a/tests/unit/field/test_field2d.cxx
+++ b/tests/unit/field/test_field2d.cxx
@@ -1175,6 +1175,19 @@ TEST_F(Field2DTest, Sqrt) {
   EXPECT_TRUE(IsFieldEqual(sqrt(field), 4.0));
 }
 
+TEST_F(Field2DTest, SQExpressionUsesSquareOp) {
+  Field2D field;
+
+  field = 2.0;
+  const auto expr = field + 1.0;
+
+  EXPECT_TRUE(
+      (std::is_same_v<std::decay_t<decltype(SQ(expr))>,
+                      BinaryExpr<Field2D, std::decay_t<decltype(expr)>,
+                                 std::decay_t<decltype(expr)>, bout::op::Square>>));
+  EXPECT_TRUE(IsFieldEqual(SQ(expr), 9.0));
+}
+
 TEST_F(Field2DTest, Abs) {
   Field2D field;
 
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 7672ec7dae..ba8f25ba30 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -1949,6 +1949,36 @@ TEST_F(Field3DTest, Sqrt) {
   EXPECT_TRUE(IsFieldEqual(sqrt(field), 4.0));
 }
 
+TEST_F(Field3DTest, SQExpressionUsesSquareOp) {
+  Field3D field;
+
+  field = 2.0;
+  const auto expr = field + 1.0;
+
+  EXPECT_TRUE(
+      (std::is_same_v<std::decay_t<decltype(SQ(expr))>,
+                      BinaryExpr<Field3D, std::decay_t<decltype(expr)>,
+                                 std::decay_t<decltype(expr)>, bout::op::Square>>));
+  EXPECT_TRUE(IsFieldEqual(SQ(expr), 9.0));
+}
+
+TEST_F(Field3DTest, SQField3DParallelPreservesParallelSlices) {
+  Field3DParallel field;
+
+  field = 2.0;
+  field.splitParallelSlices();
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+
+  const auto squared = SQ(field);
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(squared)>, Field3DParallel>));
+  EXPECT_TRUE(squared.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(squared, 4.0));
+  EXPECT_TRUE(IsFieldEqual(squared.yup(), 9.0));
+  EXPECT_TRUE(IsFieldEqual(squared.ydown(), 16.0));
+}
+
 TEST_F(Field3DTest, Abs) {
   Field3D field;
 
diff --git a/tests/unit/field/test_fieldperp.cxx b/tests/unit/field/test_fieldperp.cxx
index 8caafa96e4..82bf39f880 100644
--- a/tests/unit/field/test_fieldperp.cxx
+++ b/tests/unit/field/test_fieldperp.cxx
@@ -1577,6 +1577,14 @@ TEST_F(FieldPerpTest, Sqrt) {
   EXPECT_TRUE(IsFieldEqual(sqrt(field), 4.0));
 }
 
+TEST_F(FieldPerpTest, SQFieldPerp) {
+  FieldPerp field;
+  field.setIndex(0);
+
+  field = 3.0;
+  EXPECT_TRUE(IsFieldEqual(SQ(field), 9.0));
+}
+
 TEST_F(FieldPerpTest, Abs) {
   FieldPerp field;
   field.setIndex(0);
diff --git a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx
index 157ec22c84..846cb9107f 100644
--- a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx
+++ b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx
@@ -39,9 +39,9 @@ class ForwardOperator {
   }
 
   const Field3D operator()(Field3D& f) {
-    auto result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY")
-                  + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22) / c1 + a * f
-                  + ex * DDX(f) + ez * DDZ(f);
+    Field3D result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY")
+                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22) / c1 + a * f
+                     + ex * DDX(f) + ez * DDZ(f);
     applyBoundaries(result, f);
     return result;
   }

From 4e19f8e329426947e36293b212856e3936c2eb0a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 16:21:55 -0700
Subject: [PATCH 1388/1827] Region::getLinearIndices

Caches the Array<int> indices of the region. This will enable
kernels to avoid rebuilding the index array every time.
---
 include/bout/region.hxx                 | 36 ++++++++++++++------
 tests/unit/include/bout/test_region.cxx | 45 +++++++++++++++++++++++++
 2 files changed, 70 insertions(+), 11 deletions(-)

diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index e00ad6d41d..88829fc65e 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -49,6 +49,7 @@
 #include <utility>
 #include <vector>
 
+#include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
@@ -170,8 +171,8 @@ struct SpecificInd {
   int ny = -1, nz = -1; ///< Sizes of y and z dimensions
 
   SpecificInd() = default;
-  SpecificInd(int i, int ny, int nz) : ind(i), ny(ny), nz(nz){};
-  explicit SpecificInd(int i) : ind(i){};
+  SpecificInd(int i, int ny, int nz) : ind(i), ny(ny), nz(nz) {};
+  explicit SpecificInd(int i) : ind(i) {};
 
   /// Allow explicit conversion to an int
   explicit operator int() const { return ind; }
@@ -491,10 +492,9 @@ template <typename T = Ind3D>
 class Region {
   // Following prevents a Region being created with anything other
   // than Ind2D, Ind3D or IndPerp as template type
-  static_assert(
-      std::is_base_of_v<
-          Ind2D, T> || std::is_base_of_v<Ind3D, T> || std::is_base_of_v<IndPerp, T>,
-      "Region must be templated with one of IndPerp, Ind2D or Ind3D");
+  static_assert(std::is_base_of_v<Ind2D, T> || std::is_base_of_v<Ind3D, T>
+                    || std::is_base_of_v<IndPerp, T>,
+                "Region must be templated with one of IndPerp, Ind2D or Ind3D");
 
 public:
   using data_type = T;
@@ -570,7 +570,7 @@ public:
   };
 
   Region(RegionIndices& indices, int maxregionblocksize = MAXREGIONBLOCKSIZE)
-      : indices(indices), blocks(getContiguousBlocks(maxregionblocksize)){};
+      : indices(indices), blocks(getContiguousBlocks(maxregionblocksize)) {};
 
   // We need to first set the blocks, and only after that call getRegionIndices.
   // Do not put in the member initialisation
@@ -595,17 +595,28 @@ public:
 
   const ContiguousBlocks& getBlocks() const { return blocks; };
   const RegionIndices& getIndices() const { return indices; };
+  const Array<int>& getLinearIndices() const {
+    if (linearIndices.empty()) {
+      linearIndices = Array<int>(indices.size());
+      for (size_type i = 0; i < indices.size(); ++i) {
+        linearIndices[i] = indices[i].ind;
+      }
+    }
+    return linearIndices;
+  }
 
   /// Set the indices and ensure blocks updated
   void setIndices(RegionIndices& indicesIn, int maxregionblocksize = MAXREGIONBLOCKSIZE) {
     indices = indicesIn;
     blocks = getContiguousBlocks(maxregionblocksize);
+    invalidateLinearIndices();
   };
 
   /// Set the blocks and ensure indices updated
   void setBlocks(ContiguousBlocks& blocksIn) {
     blocks = blocksIn;
     indices = getRegionIndices();
+    invalidateLinearIndices();
   };
 
   /// Return a new Region that has the same indices as this one but
@@ -829,10 +840,13 @@ public:
   // sorted this would prevent this usage.
 
 private:
-  RegionIndices indices;   //< Flattened indices
-  ContiguousBlocks blocks; //< Contiguous sections of flattened indices
-  int ny = -1;             //< Size of y dimension
-  int nz = -1;             //< Size of z dimension
+  RegionIndices indices;            //< Flattened indices
+  ContiguousBlocks blocks;          //< Contiguous sections of flattened indices
+  int ny = -1;                      //< Size of y dimension
+  int nz = -1;                      //< Size of z dimension
+  mutable Array<int> linearIndices; //< Cached flattened integer indices
+
+  void invalidateLinearIndices() const { linearIndices.clear(); }
 
   /// Helper function to create a RegionIndices, given the start and end
   /// points in x, y, z, and the total y, z lengths
diff --git a/tests/unit/include/bout/test_region.cxx b/tests/unit/include/bout/test_region.cxx
index 00137c1ce7..fe66524735 100644
--- a/tests/unit/include/bout/test_region.cxx
+++ b/tests/unit/include/bout/test_region.cxx
@@ -111,6 +111,51 @@ TEST_F(RegionTest, regionFromIndices) {
   }
 }
 
+TEST_F(RegionTest, getLinearIndices) {
+  Region<Ind3D> region(0, mesh->LocalNx - 1, 0, mesh->LocalNy - 1, 0, mesh->LocalNz - 1,
+                       mesh->LocalNy, mesh->LocalNz);
+
+  const auto& indices = region.getIndices();
+  const auto& linearIndices = region.getLinearIndices();
+
+  ASSERT_EQ(linearIndices.size(), indices.size());
+  for (int i = 0; i < linearIndices.size(); ++i) {
+    EXPECT_EQ(linearIndices[i], indices[i].ind);
+  }
+}
+
+TEST_F(RegionTest, getLinearIndicesUpdatedAfterSetIndices) {
+  Region<Ind3D>::RegionIndices indicesIn{{0, 1, 1}, {2, 1, 1}, {4, 1, 1}};
+  Region<Ind3D> region(indicesIn);
+
+  const auto& initialLinearIndices = region.getLinearIndices();
+  ASSERT_EQ(initialLinearIndices.size(), 3);
+  EXPECT_EQ(initialLinearIndices[0], 0);
+  EXPECT_EQ(initialLinearIndices[1], 2);
+  EXPECT_EQ(initialLinearIndices[2], 4);
+
+  Region<Ind3D>::RegionIndices newIndices{{1, 1, 1}, {3, 1, 1}};
+  region.setIndices(newIndices);
+
+  const auto& updatedLinearIndices = region.getLinearIndices();
+  ASSERT_EQ(updatedLinearIndices.size(), 2);
+  EXPECT_EQ(updatedLinearIndices[0], 1);
+  EXPECT_EQ(updatedLinearIndices[1], 3);
+}
+
+TEST_F(RegionTest, getLinearIndicesUpdatedAfterSetBlocks) {
+  Region<Ind3D>::ContiguousBlocks blocks{{Ind3D{1, 1, 1}, Ind3D{3, 1, 1}},
+                                         {Ind3D{5, 1, 1}, Ind3D{6, 1, 1}}};
+  Region<Ind3D> region;
+  region.setBlocks(blocks);
+
+  const auto& linearIndices = region.getLinearIndices();
+  ASSERT_EQ(linearIndices.size(), 3);
+  EXPECT_EQ(linearIndices[0], 1);
+  EXPECT_EQ(linearIndices[1], 2);
+  EXPECT_EQ(linearIndices[2], 5);
+}
+
 TEST_F(RegionTest, regionFromBlocks) {
   Region<Ind3D> region(0, mesh->LocalNx - 1, 0, mesh->LocalNy - 1, 0, mesh->LocalNz - 1,
                        mesh->LocalNy, mesh->LocalNz);

From d67672618933adf3d4929d6c0b5e17aac95dfadf Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 17:10:06 -0700
Subject: [PATCH 1389/1827] Fix BinaryExpr::operator[] for Field2D expressions

Need to convert Ind3D linear indices into Ind2D indices.
---
 include/bout/fieldops.hxx                          | 6 +++++-
 src/invert/laplace/impls/petsc3damg/petsc3damg.cxx | 4 ++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 5e662b24d4..ad3faa2ff7 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -209,7 +209,11 @@ struct BinaryExpr {
   template <typename IndType>
   BOUT_HOST_DEVICE BOUT_FORCEINLINE auto operator[](const IndType& d) const
       -> decltype(d.ind, BoutReal{}) {
-    return operator()(d.ind);
+    if constexpr (std::is_same_v<ResT, Field2D>) {
+      return operator()(d.ind / d.nz);
+    } else {
+      return operator()(d.ind);
+    }
   }
   inline int regionIdx(int idx) const { return indices[idx]; }
 
diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
index ddd0b15b7e..76b9b94e9a 100644
--- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
+++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
@@ -4,9 +4,9 @@
  *                           Using PETSc Solvers
  *
  **************************************************************************
- * Copyright 2013 J. Buchanan, J.Omotani
+ * Copyright 2013 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *

From 0b9dbf681c4f628698e5acbd076530ae19cbaa54 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 17:12:17 -0700
Subject: [PATCH 1390/1827] Reductions on BinaryExpr: Min/Max/Mean

Perform reductions over binary expressions without having to allocate
an intermediate field.
---
 include/bout/field.hxx              |  43 +++++++-
 include/bout/fieldops.hxx           | 149 +++++++++++++++++++++++++++-
 tests/unit/field/test_field2d.cxx   |  30 ++++++
 tests/unit/field/test_field3d.cxx   |  48 +++++++++
 tests/unit/field/test_fieldperp.cxx |  16 +++
 tests/unit/test_extras.cxx          |  13 +++
 6 files changed, 293 insertions(+), 6 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index b0477d756e..ad365e8ec1 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -368,7 +368,19 @@ inline BoutReal min(const T& f, bool allpe = false,
 template <typename ResT, typename L, typename R, typename Func>
 inline BoutReal min(const BinaryExpr<ResT, L, R, Func>& f, bool allpe = false,
                     const std::string& rgn = "RGN_NOBNDRY") {
-  return min(ResT{f}, allpe, rgn);
+  const auto& region = f.getMesh()->template getRegion<ResT>(rgn);
+  const auto reduction_view =
+      makeReductionView(static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),
+                        region.getLinearIndices());
+  BoutReal result =
+      bout::reduce::Min::finalize(reduceExpr<bout::reduce::Min>(reduction_view));
+
+  if (allpe) {
+    BoutReal localresult = result;
+    MPI_Allreduce(&localresult, &result, 1, MPI_DOUBLE, MPI_MIN, BoutComm::get());
+  }
+
+  return result;
 }
 
 /// Returns true if all elements of \p f over \p region are equal. By
@@ -458,7 +470,19 @@ inline BoutReal max(const T& f, bool allpe = false,
 template <typename ResT, typename L, typename R, typename Func>
 inline BoutReal max(const BinaryExpr<ResT, L, R, Func>& f, bool allpe = false,
                     const std::string& rgn = "RGN_NOBNDRY") {
-  return max(ResT{f}, allpe, rgn);
+  const auto& region = f.getMesh()->template getRegion<ResT>(rgn);
+  const auto reduction_view =
+      makeReductionView(static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),
+                        region.getLinearIndices());
+  BoutReal result =
+      bout::reduce::Max::finalize(reduceExpr<bout::reduce::Max>(reduction_view));
+
+  if (allpe) {
+    BoutReal localresult = result;
+    MPI_Allreduce(&localresult, &result, 1, MPI_DOUBLE, MPI_MAX, BoutComm::get());
+  }
+
+  return result;
 }
 
 /// Mean of \p f, excluding the boundary/guard cells by default (can
@@ -499,7 +523,20 @@ inline BoutReal mean(const T& f, bool allpe = false,
 template <typename ResT, typename L, typename R, typename Func>
 inline BoutReal mean(const BinaryExpr<ResT, L, R, Func>& f, bool allpe = false,
                      const std::string& rgn = "RGN_NOBNDRY") {
-  return mean(ResT{f}, allpe, rgn);
+  const auto& region = f.getMesh()->template getRegion<ResT>(rgn);
+  const auto reduction_view =
+      makeReductionView(static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),
+                        region.getLinearIndices());
+  auto state = reduceExpr<bout::reduce::Mean>(reduction_view);
+
+  if (allpe) {
+    BoutReal localsum = state.sum;
+    int localcount = state.count;
+    MPI_Allreduce(&localsum, &state.sum, 1, MPI_DOUBLE, MPI_SUM, BoutComm::get());
+    MPI_Allreduce(&localcount, &state.count, 1, MPI_INT, MPI_SUM, BoutComm::get());
+  }
+
+  return bout::reduce::Mean::finalize(state);
 }
 
 /// Exponent: pow(lhs, lhs) is \p lhs raised to the power of \p rhs
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index ad3faa2ff7..4b5eab2f24 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -5,9 +5,9 @@
 #include "bout/array.hxx"
 #include "bout/bout_types.hxx"
 
+#include <limits>
 #include <optional>
 #include <type_traits>
-#include <unordered_map>
 #include <vector>
 
 #if BOUT_HAS_CUDA
@@ -101,8 +101,91 @@ struct Div {
   }
 };
 }; // namespace op
+
+namespace reduce {
+
+struct MinState {
+  BoutReal value;
+};
+
+struct MaxState {
+  BoutReal value;
+};
+
+struct MeanState {
+  BoutReal sum;
+  int count;
+};
+
+struct Min {
+  using State = MinState;
+
+  BOUT_HOST_DEVICE static State identity() {
+    return {std::numeric_limits<BoutReal>::infinity()};
+  }
+  BOUT_HOST_DEVICE static void accumulate(State& state, BoutReal value) {
+    state.value = value < state.value ? value : state.value;
+  }
+  BOUT_HOST_DEVICE static void combine(State& state, const State& other) {
+    state.value = other.value < state.value ? other.value : state.value;
+  }
+  static BoutReal finalize(const State& state) { return state.value; }
+};
+
+struct Max {
+  using State = MaxState;
+
+  BOUT_HOST_DEVICE static State identity() {
+    return {-std::numeric_limits<BoutReal>::infinity()};
+  }
+  BOUT_HOST_DEVICE static void accumulate(State& state, BoutReal value) {
+    state.value = value > state.value ? value : state.value;
+  }
+  BOUT_HOST_DEVICE static void combine(State& state, const State& other) {
+    state.value = other.value > state.value ? other.value : state.value;
+  }
+  static BoutReal finalize(const State& state) { return state.value; }
+};
+
+struct Mean {
+  using State = MeanState;
+
+  BOUT_HOST_DEVICE static State identity() { return {0.0, 0}; }
+  BOUT_HOST_DEVICE static void accumulate(State& state, BoutReal value) {
+    state.sum += value;
+    state.count += 1;
+  }
+  BOUT_HOST_DEVICE static void combine(State& state, const State& other) {
+    state.sum += other.sum;
+    state.count += other.count;
+  }
+  static BoutReal finalize(const State& state) {
+    return state.sum / static_cast<BoutReal>(state.count);
+  }
+};
+
+} // namespace reduce
 }; // namespace bout
 
+template <typename ExprView>
+struct ReductionView {
+  ExprView expr;
+  const int* indices;
+  int num_indices;
+
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE int size() const { return num_indices; }
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal valueAtRegionPos(int idx) const {
+    return expr(indices[idx]);
+  }
+};
+
+template <typename ExprView>
+ReductionView<ExprView> makeReductionView(const ExprView& expr,
+                                          const Array<int>& indices) {
+  return ReductionView<ExprView>{expr, indices.size() > 0 ? &indices[0] : nullptr,
+                                 indices.size()};
+}
+
 #if BOUT_HAS_CUDA && defined(__CUDACC__)
 template <typename Expr>
 __global__ void __launch_bounds__(THREADS) evaluatorExpr(BoutReal* out, const Expr expr) {
@@ -129,9 +212,39 @@ __global__ void __launch_bounds__(THREADS) evaluatorExpr(BoutReal* out, const Ex
   //  out[idx] = expr(idx); // single‐pass fusion
   //}
 }
-#endif
 
-inline std::unordered_map<void*, Array<int>> regionIndicesCache;
+template <typename Reducer, typename ExprView>
+__global__ void __launch_bounds__(THREADS)
+    reducerExpr(typename Reducer::State* partials, const ExprView expr) {
+  using State = typename Reducer::State;
+
+  __shared__ State shared[THREADS];
+
+  const int tid = threadIdx.x;
+  const int global = blockIdx.x * blockDim.x + tid;
+  const int stride = blockDim.x * gridDim.x;
+
+  State local = Reducer::identity();
+
+  for (int i = global; i < expr.size(); i += stride) {
+    Reducer::accumulate(local, expr.valueAtRegionPos(i));
+  }
+
+  shared[tid] = local;
+  __syncthreads();
+
+  for (int offset = blockDim.x / 2; offset > 0; offset /= 2) {
+    if (tid < offset) {
+      Reducer::combine(shared[tid], shared[tid + offset]);
+    }
+    __syncthreads();
+  }
+
+  if (tid == 0) {
+    partials[blockIdx.x] = shared[0];
+  }
+}
+#endif
 
 #if BOUT_HAS_CUDA && defined(__CUDACC__)
 struct StreamsRAII {
@@ -169,6 +282,36 @@ struct StreamsRAII {
 inline struct StreamsRAII streams;
 #endif
 
+template <typename Reducer, typename ExprView>
+auto reduceExpr(const ExprView& expr_view) -> typename Reducer::State {
+  using State = typename Reducer::State;
+
+  ASSERT1(expr_view.size() > 0);
+
+#if BOUT_HAS_CUDA && defined(__CUDACC__)
+  cudaStream_t stream = streams.get();
+  int blocks = (expr_view.size() + THREADS - 1) / THREADS;
+  blocks = blocks < 1024 ? blocks : 1024;
+  Array<State> partials(blocks);
+
+  reducerExpr<Reducer><<<blocks, THREADS, 0, stream>>>(&partials[0], expr_view);
+  cudaStreamSynchronize(stream);
+  streams.put(stream);
+
+  State result = Reducer::identity();
+  for (int i = 0; i < blocks; ++i) {
+    Reducer::combine(result, partials[i]);
+  }
+  return result;
+#else
+  State result = Reducer::identity();
+  for (int i = 0; i < expr_view.size(); ++i) {
+    Reducer::accumulate(result, expr_view.valueAtRegionPos(i));
+  }
+  return result;
+#endif
+}
+
 template <typename ResT, typename L, typename R, typename Func>
 struct BinaryExpr {
   typename L::View lhs;
diff --git a/tests/unit/field/test_field2d.cxx b/tests/unit/field/test_field2d.cxx
index 67cf1d6c61..9eebb276ba 100644
--- a/tests/unit/field/test_field2d.cxx
+++ b/tests/unit/field/test_field2d.cxx
@@ -1311,6 +1311,21 @@ TEST_F(Field2DTest, Min) {
   EXPECT_EQ(min(field, true, "RGN_ALL"), -99.0);
 }
 
+TEST_F(Field2DTest, MinBinaryExpr) {
+  Field2D field;
+
+  field = 50.0;
+  field(0, 0) = -99.0;
+  field(1, 1) = 60.0;
+  field(1, 2) = 40.0;
+  field(2, 4) = 99.0;
+
+  const auto expr = field / 2.0 - 5.0;
+
+  EXPECT_EQ(min(expr, false), 15.0);
+  EXPECT_EQ(min(expr, false, "RGN_ALL"), -54.5);
+}
+
 TEST_F(Field2DTest, Max) {
   Field2D field;
 
@@ -1328,6 +1343,21 @@ TEST_F(Field2DTest, Max) {
   EXPECT_EQ(max(field, true, "RGN_ALL"), 99.0);
 }
 
+TEST_F(Field2DTest, MaxBinaryExpr) {
+  Field2D field;
+
+  field = 50.0;
+  field(0, 0) = -99.0;
+  field(1, 1) = 40.0;
+  field(1, 2) = 60.0;
+  field(2, 4) = 99.0;
+
+  const auto expr = field / 2.0 - 5.0;
+
+  EXPECT_EQ(max(expr, false), 25.0);
+  EXPECT_EQ(max(expr, false, "RGN_ALL"), 44.5);
+}
+
 TEST_F(Field2DTest, Swap) {
   WithQuietOutput quiet{output_info};
 
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index ba8f25ba30..2941bf3d89 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -2102,6 +2102,21 @@ TEST_F(Field3DTest, Min) {
   EXPECT_EQ(min(field, true, "RGN_ALL"), -99.0);
 }
 
+TEST_F(Field3DTest, MinBinaryExpr) {
+  Field3D field;
+
+  field = 50.0;
+  field(0, 0, 0) = -99.0;
+  field(1, 1, 1) = 60.0;
+  field(1, 2, 2) = 40.0;
+  field(2, 4, 3) = 99.0;
+
+  const auto expr = field / 2.0 - 5.0;
+
+  EXPECT_EQ(min(expr, false), 15.0);
+  EXPECT_EQ(min(expr, false, "RGN_ALL"), -54.5);
+}
+
 TEST_F(Field3DTest, Max) {
   Field3D field;
 
@@ -2119,6 +2134,21 @@ TEST_F(Field3DTest, Max) {
   EXPECT_EQ(max(field, true, "RGN_ALL"), 99.0);
 }
 
+TEST_F(Field3DTest, MaxBinaryExpr) {
+  Field3D field;
+
+  field = 50.0;
+  field(0, 0, 0) = -99.0;
+  field(1, 1, 1) = 40.0;
+  field(1, 2, 2) = 60.0;
+  field(2, 4, 3) = 99.0;
+
+  const auto expr = field / 2.0 - 5.0;
+
+  EXPECT_EQ(max(expr, false), 25.0);
+  EXPECT_EQ(max(expr, false, "RGN_ALL"), 44.5);
+}
+
 TEST_F(Field3DTest, Mean) {
   Field3D field;
 
@@ -2138,6 +2168,24 @@ TEST_F(Field3DTest, Mean) {
   EXPECT_EQ(mean(field, true, "RGN_ALL"), mean_value_all);
 }
 
+TEST_F(Field3DTest, MeanBinaryExpr) {
+  Field3D field;
+
+  field = 50.0;
+  field(0, 0, 0) = 1.0;
+  field(1, 1, 1) = 40.0;
+  field(1, 2, 2) = 60.0;
+  field(2, 4, 3) = 109.0;
+
+  const int npoints_all = nx * ny * nz;
+  const BoutReal mean_value_nobndry = 103.0;
+  const BoutReal mean_value_all = 103.0 + 20.0 / npoints_all;
+  const auto expr = field * 2.0 + 3.0;
+
+  EXPECT_EQ(mean(expr, false), mean_value_nobndry);
+  EXPECT_EQ(mean(expr, false, "RGN_ALL"), mean_value_all);
+}
+
 TEST_F(Field3DTest, DC) {
   Field3D field;
 
diff --git a/tests/unit/field/test_fieldperp.cxx b/tests/unit/field/test_fieldperp.cxx
index 82bf39f880..4975a9e735 100644
--- a/tests/unit/field/test_fieldperp.cxx
+++ b/tests/unit/field/test_fieldperp.cxx
@@ -1738,6 +1738,22 @@ TEST_F(FieldPerpTest, Max) {
   EXPECT_EQ(max(field, true, "RGN_ALL"), 99.0);
 }
 
+TEST_F(FieldPerpTest, MaxBinaryExpr) {
+  FieldPerp field;
+  field.setIndex(0);
+
+  field = 50.0;
+  field(0, 0) = -99.0;
+  field(1, 1) = 40.0;
+  field(1, 2) = 60.0;
+  field(2, 4) = 99.0;
+
+  const auto expr = field / 2.0 - 5.0;
+
+  EXPECT_EQ(max(expr, false), 25.0);
+  EXPECT_EQ(max(expr, false, "RGN_ALL"), 44.5);
+}
+
 TEST_F(FieldPerpTest, OperatorEqualsFieldPerp) {
   FieldPerp field;
 
diff --git a/tests/unit/test_extras.cxx b/tests/unit/test_extras.cxx
index f096292ed3..30526f55c4 100644
--- a/tests/unit/test_extras.cxx
+++ b/tests/unit/test_extras.cxx
@@ -69,3 +69,16 @@ TEST_F(TestExtrasFieldExpr, BinaryExprCanBeIndexedWithRegionIndex) {
     EXPECT_DOUBLE_EQ(result[i], lhs[i] + 2.0 * rhs[i]);
   }
 }
+
+TEST_F(TestExtrasFieldExpr, Field2DBinaryExprCanBeIndexedWithInd3D) {
+  const Field2D lhs{
+      makeField<Field2D>([](const Ind2D& i) { return static_cast<BoutReal>(i.x()); })};
+  const Field2D rhs{
+      makeField<Field2D>([](const Ind2D& i) { return static_cast<BoutReal>(i.y()); })};
+
+  const auto expr = lhs + 2.0 * rhs;
+
+  BOUT_FOR(i, lhs.getMesh()->getRegion3D("RGN_ALL")) {
+    EXPECT_DOUBLE_EQ(expr[i], lhs[i] + 2.0 * rhs[i]);
+  }
+}

From 93507154f5ae15e7ecde376516430b7a4d68c07a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 17:25:33 -0700
Subject: [PATCH 1391/1827] Fieldops: Tidy Min,Max,Mean reductions

Move State types into their respective reduction classes.
---
 include/bout/fieldops.hxx | 26 ++++++++++----------------
 1 file changed, 10 insertions(+), 16 deletions(-)

diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 4b5eab2f24..8ae632c612 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -104,21 +104,10 @@ struct Div {
 
 namespace reduce {
 
-struct MinState {
-  BoutReal value;
-};
-
-struct MaxState {
-  BoutReal value;
-};
-
-struct MeanState {
-  BoutReal sum;
-  int count;
-};
-
 struct Min {
-  using State = MinState;
+  struct State {
+    BoutReal value;
+  };
 
   BOUT_HOST_DEVICE static State identity() {
     return {std::numeric_limits<BoutReal>::infinity()};
@@ -133,7 +122,9 @@ struct Min {
 };
 
 struct Max {
-  using State = MaxState;
+  struct State {
+    BoutReal value;
+  };
 
   BOUT_HOST_DEVICE static State identity() {
     return {-std::numeric_limits<BoutReal>::infinity()};
@@ -148,7 +139,10 @@ struct Max {
 };
 
 struct Mean {
-  using State = MeanState;
+  struct State {
+    BoutReal sum;
+    int count;
+  };
 
   BOUT_HOST_DEVICE static State identity() { return {0.0, 0}; }
   BOUT_HOST_DEVICE static void accumulate(State& state, BoutReal value) {

From 36c06ec62641d42ac9ba96b01f5ef007c952eac5 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 17:27:40 -0700
Subject: [PATCH 1392/1827] Formatting

---
 include/bout/assert.hxx  | 6 +++---
 include/bout/rajalib.hxx | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/bout/assert.hxx b/include/bout/assert.hxx
index 954ae8dba0..28bff1f2ec 100644
--- a/include/bout/assert.hxx
+++ b/include/bout/assert.hxx
@@ -2,16 +2,16 @@
  * Defines a macro ASSERT which throws a BoutException if a given
  * condition is false. Whether the assertion is tested depends on
  * the checking level, so assetions can be removed for optimised runs.
- * 
+ *
  * ASSERT<level> ( condition )
  *
  *   level     - An integer known at compile time.
  *               condition tested if level >= CHECK
  *
  *   condition - The expression to test
- * 
+ *
  * e.g. ASSERT2( condition ) will only test condition if CHECK >= 2
- * 
+ *
  */
 
 #ifndef BOUT_ASSERT_H
diff --git a/include/bout/rajalib.hxx b/include/bout/rajalib.hxx
index 20929304b5..29bab8f23b 100644
--- a/include/bout/rajalib.hxx
+++ b/include/bout/rajalib.hxx
@@ -137,7 +137,7 @@ private:
 /// to create variables which shadow the class members.
 ///
 #define BOUT_FOR_RAJA(index, region, ...) \
-RajaForAll(region) << [ =, ##__VA_ARGS__ ] RAJA_DEVICE(int index) mutable
+  RajaForAll(region) << [ =, ##__VA_ARGS__ ] RAJA_DEVICE(int index) mutable
 
 #else // BOUT_HAS_RAJA
 

From 09aaee6b28fc4aacb16e333d958fdb02b6ce2a9c Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 17:42:27 -0700
Subject: [PATCH 1393/1827] BinaryExpr: Use Region::getLinearIndices

Caches the indicex array rather than recreating it each time.
---
 include/bout/fieldops.hxx | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 8ae632c612..ee746f886d 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -322,13 +322,8 @@ struct BinaryExpr {
   BinaryExpr(const typename L::View& lhs, const typename R::View& rhs, Func f, Mesh* mesh,
              CELL_LOC location, DirectionTypes directions, std::optional<size_t> regionID,
              const Region<IndType>& region)
-      : lhs(lhs), rhs(rhs), indices(region.getIndices().size()), f(f), mesh(mesh),
-        location(location), directions(directions), regionID(regionID) {
-    // Copy the region indices into the managed array
-    for (int i = 0; i < indices.size(); ++i) {
-      indices[i] = region.getIndices()[i].ind;
-    }
-  }
+      : lhs(lhs), rhs(rhs), indices(region.getLinearIndices()), f(f), mesh(mesh),
+        location(location), directions(directions), regionID(regionID) {}
 
   BinaryExpr(const typename L::View& lhs, const typename R::View& rhs, Func f, Mesh* mesh,
              CELL_LOC location, DirectionTypes directions, std::optional<size_t> regionID,

From 94cf70fe73d75bf375a5b24afa71cc030efc43d3 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 17:59:28 -0700
Subject: [PATCH 1394/1827] Options: Assignment from BinaryExpr

Evaluates the expression to its result field type (ResT)
and stores that in the Option.
---
 include/bout/options.hxx               | 31 ++++++++++++++++----------
 tests/unit/sys/test_options_fields.cxx | 30 +++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 12 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 03e95488a8..87503b0a22 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -74,19 +74,19 @@ class Options;
  * which can be used as a map.
  *
  *     Options options;
- *     
+ *
  *     // Set values
  *     options["key"] = 1.0;
  *
  *     // Get values. Throws BoutException if not found
- *     int val = options["key"]; // Sets val to 1 
+ *     int val = options["key"]; // Sets val to 1
  *
  *     // Return as specified type. Throws BoutException if not found
  *     BoutReal var = options["key"].as<BoutReal>();
  *
  *     // A default value can be used if key is not found
  *     BoutReal value = options["pi"].withDefault(3.14);
- *    
+ *
  *     // Assign value with source label. Throws if already has a value from same source
  *     options["newkey"].assign(1.0, "some source");
  *
@@ -94,7 +94,7 @@ class Options;
  *     options["newkey"].force(2.0, "some source");
  *
  * A legacy interface is also supported:
- * 
+ *
  *     options.set("key", 1.0, "code"); // Sets a key from source "code"
  *
  *     int val;
@@ -119,9 +119,9 @@ class Options;
  *
  * Each Options object can also contain any number of sections, which are
  * themselves Options objects.
- * 
+ *
  *     Options &section = options["section"];
- * 
+ *
  * which can be nested:
  *
  *     options["section"]["subsection"]["value"] = 3;
@@ -134,13 +134,13 @@ class Options;
  *
  * e.g.
  *     options->getSection("section")->getSection("subsection")->set("value", 3);
- * 
+ *
  * Options also know about their parents:
  *
  *     Options &parent = section.parent();
- *     
+ *
  * or
- * 
+ *
  *     Options *parent = section->getParent();
  *
  * Root options object
@@ -150,8 +150,8 @@ class Options;
  * there is a global singleton Options object which can be accessed with a static function
  *
  *    Options &root = Options::root();
- * 
- * or 
+ *
+ * or
  *
  *    Options *root = Options::getRoot();
  *
@@ -193,7 +193,7 @@ public:
   /// @param[in] parent        Parent object
   /// @param[in] sectionName   Name of the section, including path from the root
   Options(Options* parent_instance, std::string full_name)
-      : parent_instance(parent_instance), full_name(std::move(full_name)){};
+      : parent_instance(parent_instance), full_name(std::move(full_name)) {};
 
   /// Initialise with a value
   /// These enable Options to be constructed using initializer lists
@@ -441,6 +441,13 @@ public:
     return inputvalue;
   }
 
+  template <typename ResT, typename L, typename R, typename Func>
+  ResT operator=(const BinaryExpr<ResT, L, R, Func>& expr) {
+    ResT value{expr};
+    assign<ResT>(value);
+    return value;
+  }
+
   /// Assign a value to the option.
   /// This will throw an exception if already has a value
   ///
diff --git a/tests/unit/sys/test_options_fields.cxx b/tests/unit/sys/test_options_fields.cxx
index 0c6ec953af..f94ed30386 100644
--- a/tests/unit/sys/test_options_fields.cxx
+++ b/tests/unit/sys/test_options_fields.cxx
@@ -36,6 +36,36 @@ TEST_F(OptionsFieldTest, StoreField2D) {
   EXPECT_TRUE(options.isValue());
 }
 
+TEST_F(OptionsFieldTest, StoreEvaluatedField3DExpression) {
+  Field3D lhs = 1.0;
+  Field3D rhs = 2.0;
+  lhs(0, 1, 1) = 3.0;
+  rhs(0, 1, 1) = 4.0;
+
+  Options options;
+  options = lhs + rhs;
+
+  Field3D stored = options;
+
+  EXPECT_DOUBLE_EQ(stored(0, 1, 0), 3.0);
+  EXPECT_DOUBLE_EQ(stored(0, 1, 1), 7.0);
+}
+
+TEST_F(OptionsFieldTest, StoreEvaluatedField2DExpression) {
+  Field2D lhs = 1.0;
+  Field2D rhs = 2.0;
+  lhs(0, 1) = 3.0;
+  rhs(0, 1) = 4.0;
+
+  Options options;
+  options = lhs + rhs;
+
+  Field2D stored = options;
+
+  EXPECT_DOUBLE_EQ(stored(0, 0), 3.0);
+  EXPECT_DOUBLE_EQ(stored(0, 1), 7.0);
+}
+
 TEST_F(OptionsFieldTest, RetrieveField3D) {
   Field3D field = 1.0;
   field(0, 1, 1) = 2.0;

From d3236d9ba3658b48bc62650f93fecddffb806933 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 21:36:19 -0700
Subject: [PATCH 1395/1827] BinaryExpr: if_else and if_else_zero conditionals

Binary expressions that take a boolean and branch
between two expressions.

`if_else_zero(bool, Expr)` evaluates an expression only if `bool` is
true, otherwise evaluates to zero.
---
 include/bout/field2d.hxx          | 69 +++++++++++++++++++++++++++++++
 include/bout/field3d.hxx          | 68 ++++++++++++++++++++++++++++++
 include/bout/fieldops.hxx         | 12 ++++++
 tests/unit/CMakeLists.txt         |  1 +
 tests/unit/field/test_if_else.cxx | 57 +++++++++++++++++++++++++
 5 files changed, 207 insertions(+)
 create mode 100644 tests/unit/field/test_if_else.cxx

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index c7d8252aaa..61cc4693a3 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -458,6 +458,75 @@ FIELD2D_BOUTREAL_FIELD2D_OP(-, Sub)
 FIELD2D_BOUTREAL_FIELD2D_OP(*, Mul)
 FIELD2D_BOUTREAL_FIELD2D_OP(/, Div)
 
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Field2D, L, R, bout::op::IfElse>>
+if_else(bool condition, const L& lhs, const R& rhs) {
+  return BinaryExpr<Field2D, L, R, bout::op::IfElse>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename R::View>(rhs),
+      bout::op::IfElse{condition},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      std::nullopt,
+      lhs.getMesh()->getRegion2D("RGN_ALL")};
+}
+
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Field3D, L, R, bout::op::IfElse>>
+if_else(bool condition, const L& lhs, const R& rhs) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  auto regionID = rhs.getRegionID();
+  int mesh_nz = rhs.getMesh()->LocalNz;
+  return BinaryExpr<Field3D, L, R, bout::op::IfElse>{
+      static_cast<typename L::View>(lhs).setScale(1, mesh_nz),
+      static_cast<typename R::View>(rhs),
+      bout::op::IfElse{condition},
+      rhs.getMesh(),
+      rhs.getLocation(),
+      rhs.getDirections(),
+      regionID,
+      rhs.getMesh()->getRegion("RGN_ALL")};
+}
+
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<Field2D, L, Constant<R>, bout::op::IfElse>>
+if_else(bool condition, const L& lhs, R rhs) {
+  return BinaryExpr<Field2D, L, Constant<R>, bout::op::IfElse>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename Constant<R>::View>(rhs),
+      bout::op::IfElse{condition},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      std::nullopt,
+      lhs.getMesh()->getRegion2D("RGN_ALL")};
+}
+
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Field2D, Constant<L>, R, bout::op::IfElse>>
+if_else(bool condition, L lhs, const R& rhs) {
+  return BinaryExpr<Field2D, Constant<L>, R, bout::op::IfElse>{
+      static_cast<typename Constant<L>::View>(lhs),
+      static_cast<typename R::View>(rhs),
+      bout::op::IfElse{condition},
+      rhs.getMesh(),
+      rhs.getLocation(),
+      rhs.getDirections(),
+      std::nullopt,
+      rhs.getMesh()->getRegion2D("RGN_ALL")};
+}
+
+template <typename L,
+          typename = std::enable_if_t<is_expr_field2d_v<L> || is_expr_field3d_v<L>>>
+auto if_else_zero(bool condition, const L& lhs) {
+  return if_else(condition, lhs, 0.0);
+}
+
 /*!
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index e27a7600d2..2c19c5e505 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -754,6 +754,74 @@ FIELD3D_BOUTREAL_FIELD3D_OP(-, Sub)
 FIELD3D_BOUTREAL_FIELD3D_OP(*, Mul)
 FIELD3D_BOUTREAL_FIELD3D_OP(/, Div)
 
+template <typename L, typename R,
+          typename = std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>>>
+BinaryExpr<Field3D, L, R, bout::op::IfElse> if_else(bool condition, const L& lhs,
+                                                    const R& rhs) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
+  return BinaryExpr<Field3D, L, R, bout::op::IfElse>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename R::View>(rhs),
+      bout::op::IfElse{condition},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      regionID,
+      (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
+                            : lhs.getMesh()->getRegion("RGN_ALL"))};
+}
+
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Field3D, L, R, bout::op::IfElse>>
+if_else(bool condition, const L& lhs, const R& rhs) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  auto regionID = lhs.getRegionID();
+  int mesh_nz = lhs.getMesh()->LocalNz;
+  return BinaryExpr<Field3D, L, R, bout::op::IfElse>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename R::View>(rhs).setScale(1, mesh_nz),
+      bout::op::IfElse{condition},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      regionID,
+      lhs.getMesh()->getRegion("RGN_ALL")};
+}
+
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<Field3D, L, Constant<R>, bout::op::IfElse>>
+if_else(bool condition, const L& lhs, R rhs) {
+  auto regionID = lhs.getRegionID();
+  return BinaryExpr<Field3D, L, Constant<R>, bout::op::IfElse>{
+      static_cast<typename L::View>(lhs),
+      static_cast<typename Constant<R>::View>(rhs),
+      bout::op::IfElse{condition},
+      lhs.getMesh(),
+      lhs.getLocation(),
+      lhs.getDirections(),
+      regionID,
+      lhs.getMesh()->getRegion("RGN_ALL")};
+}
+
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Field3D, Constant<L>, R, bout::op::IfElse>>
+if_else(bool condition, const L& lhs, const R& rhs) {
+  auto regionID = rhs.getRegionID();
+  return BinaryExpr<Field3D, Constant<L>, R, bout::op::IfElse>{
+      static_cast<typename Constant<L>::View>(lhs),
+      static_cast<typename R::View>(rhs),
+      bout::op::IfElse{condition},
+      rhs.getMesh(),
+      rhs.getLocation(),
+      rhs.getDirections(),
+      regionID,
+      rhs.getMesh()->getRegion("RGN_ALL")};
+}
+
 Field3DParallel operator+(const Field3D& lhs, const Field3DParallel& rhs);
 Field3DParallel operator-(const Field3D& lhs, const Field3DParallel& rhs);
 Field3DParallel operator*(const Field3D& lhs, const Field3DParallel& rhs);
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index ee746f886d..923c8078ef 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -100,6 +100,18 @@ struct Div {
     return a / b;
   }
 };
+struct IfElse {
+  bool condition;
+
+  template <typename LView, typename RView>
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx, const LView& L,
+                                                        const RView& R) const {
+    return condition ? L(idx) : R(idx);
+  }
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(BoutReal a, BoutReal b) const {
+    return condition ? a : b;
+  }
+};
 }; // namespace op
 
 namespace reduce {
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 4ba304b484..4963aaf1f0 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -60,6 +60,7 @@ set(serial_tests_source
     ./field/test_field3d.cxx
     ./field/test_field_factory.cxx
     ./field/test_fieldgroup.cxx
+    ./field/test_if_else.cxx
     ./field/test_fieldperp.cxx
     ./field/test_initialprofiles.cxx
     ./field/test_vector2d.cxx
diff --git a/tests/unit/field/test_if_else.cxx b/tests/unit/field/test_if_else.cxx
new file mode 100644
index 0000000000..c608aa79db
--- /dev/null
+++ b/tests/unit/field/test_if_else.cxx
@@ -0,0 +1,57 @@
+#include "gtest/gtest.h"
+
+#include "test_extras.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+
+#include "fake_mesh_fixture.hxx"
+
+#include <type_traits>
+
+using IfElseTest = FakeMeshFixture;
+
+TEST_F(IfElseTest, Field2DChoosesSelectedBranch) {
+  const Field2D lhs{makeField<Field2D>(
+      [](const Ind2D& i) { return static_cast<BoutReal>(i.x() + i.y()); })};
+  const Field2D rhs{makeField<Field2D>(
+      [](const Ind2D& i) { return static_cast<BoutReal>(10 + i.x() - i.y()); })};
+
+  const auto expr = if_else(true, lhs, rhs);
+
+  static_assert(std::is_same_v<std::decay_t<decltype(expr)>,
+                               BinaryExpr<Field2D, Field2D, Field2D, bout::op::IfElse>>);
+  EXPECT_TRUE(IsFieldEqual(expr, lhs));
+  EXPECT_TRUE(IsFieldEqual(if_else(false, lhs, rhs), rhs));
+}
+
+TEST_F(IfElseTest, Field3DMixesField2DAndField3D) {
+  const Field2D lhs{makeField<Field2D>(
+      [](const Ind2D& i) { return static_cast<BoutReal>(i.x() + 2 * i.y()); })};
+  const Field3D rhs{makeField<Field3D>(
+      [](const Ind3D& i) { return static_cast<BoutReal>(100 + i.x() + i.y() + i.z()); })};
+
+  const auto expr = if_else(true, lhs, rhs);
+  const Field3D expected{lhs};
+
+  static_assert(std::is_same_v<std::decay_t<decltype(expr)>,
+                               BinaryExpr<Field3D, Field2D, Field3D, bout::op::IfElse>>);
+  EXPECT_TRUE(IsFieldEqual(expr, expected));
+  EXPECT_TRUE(IsFieldEqual(if_else(false, lhs, rhs), rhs));
+}
+
+TEST_F(IfElseTest, IfElseZeroKeepsExpressionWhenConditionTrue) {
+  const Field3D field{makeField<Field3D>(
+      [](const Ind3D& i) { return static_cast<BoutReal>(1 + i.x() + i.y() + i.z()); })};
+  const auto source = 2.0 * field + 1.0;
+
+  EXPECT_TRUE(IsFieldEqual(if_else_zero(true, source), source));
+  EXPECT_TRUE(IsFieldEqual(if_else_zero(false, source), 0.0));
+}
+
+TEST_F(IfElseTest, InactiveBranchIsNotEvaluatedThroughMaskedArithmetic) {
+  const Field2D lhs{makeField<Field2D>(
+      [](const Ind2D& i) { return static_cast<BoutReal>(1 + i.x() + i.y()); })};
+  const Field2D rhs{filledFrom(lhs, BoutNaN)};
+
+  EXPECT_TRUE(IsFieldEqual(if_else(true, lhs, rhs), lhs));
+}

From f48cd517ed09b5fc458487f969b5587095fe2373 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 21:39:32 -0700
Subject: [PATCH 1396/1827] BinaryExpr: FIELD_FUNC fuse expressions

If operating on a BinaryExpr, lazily evaluate field functions like
`abs`, `sin`, `tanh`. This avoids allocating a field and evaluating
the expression.
---
 include/bout/field.hxx            | 16 ++++++++++++++--
 tests/unit/field/test_field2d.cxx | 13 +++++++++++++
 tests/unit/field/test_field3d.cxx | 13 +++++++++++++
 3 files changed, 40 insertions(+), 2 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index ad365e8ec1..6547c0a31d 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -644,8 +644,20 @@ class Field3DParallel;
     }                                                                                   \
   }                                                                                     \
   template <typename ResT, typename L, typename R, typename Func>                       \
-  inline auto name(const BinaryExpr<ResT, L, R, Func>& f,                               \
-                   const std::string& rgn = "RGN_ALL") {                                \
+  inline auto name(const BinaryExpr<ResT, L, R, Func>& f) {                             \
+    return BinaryExpr<ResT, BinaryExpr<ResT, L, R, Func>, BinaryExpr<ResT, L, R, Func>, \
+                      bout::op::name>{                                                  \
+        static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),                    \
+        static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),                    \
+        bout::op::name{},                                                               \
+        f.getMesh(),                                                                    \
+        f.getLocation(),                                                                \
+        f.getDirections(),                                                              \
+        f.getRegionID(),                                                                \
+        f.indices};                                                                     \
+  }                                                                                     \
+  template <typename ResT, typename L, typename R, typename Func>                       \
+  inline auto name(const BinaryExpr<ResT, L, R, Func>& f, const std::string& rgn) {     \
     return name(ResT{f}, rgn);                                                          \
   }
 #endif
diff --git a/tests/unit/field/test_field2d.cxx b/tests/unit/field/test_field2d.cxx
index 9eebb276ba..af98d50d34 100644
--- a/tests/unit/field/test_field2d.cxx
+++ b/tests/unit/field/test_field2d.cxx
@@ -1195,6 +1195,19 @@ TEST_F(Field2DTest, Abs) {
   EXPECT_TRUE(IsFieldEqual(abs(field), 31.0));
 }
 
+TEST_F(Field2DTest, AbsExpressionUsesAbsOp) {
+  Field2D field;
+
+  field = -2.0;
+  const auto expr = field + 1.0;
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(abs(expr))>,
+                              BinaryExpr<Field2D, std::decay_t<decltype(expr)>,
+                                         std::decay_t<decltype(expr)>, bout::op::abs>>));
+  EXPECT_TRUE(IsFieldEqual(abs(expr), 1.0));
+  EXPECT_TRUE(IsFieldEqual(abs(expr, "RGN_ALL"), 1.0));
+}
+
 TEST_F(Field2DTest, Exp) {
   Field2D field;
 
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 2941bf3d89..6e1bc8ba58 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -1986,6 +1986,19 @@ TEST_F(Field3DTest, Abs) {
   EXPECT_TRUE(IsFieldEqual(abs(field), 31.0));
 }
 
+TEST_F(Field3DTest, AbsExpressionUsesAbsOp) {
+  Field3D field;
+
+  field = -2.0;
+  const auto expr = field + 1.0;
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(abs(expr))>,
+                              BinaryExpr<Field3D, std::decay_t<decltype(expr)>,
+                                         std::decay_t<decltype(expr)>, bout::op::abs>>));
+  EXPECT_TRUE(IsFieldEqual(abs(expr), 1.0));
+  EXPECT_TRUE(IsFieldEqual(abs(expr, "RGN_ALL"), 1.0));
+}
+
 TEST_F(Field3DTest, Exp) {
   Field3D field;
 

From ac1836b30ab04c6f05ab5f9aa8d3767f31dd4cb9 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 18 Jun 2026 22:08:19 -0700
Subject: [PATCH 1397/1827] Fixes for 3D metrics and unit tests

Mostly specifying when to force evaluation of expressions (BinaryExpr
trees) into fields.
---
 src/field/vecops.cxx                          | 29 ++++++++++---------
 .../laplace/impls/petsc3damg/petsc3damg.cxx   |  6 ++--
 src/mesh/coordinates.cxx                      | 13 +++++----
 src/mesh/parallel/fci.cxx                     |  2 +-
 src/sys/derivs.cxx                            | 29 ++++++++++++-------
 tests/unit/solver/test_nvector.cxx            |  2 +-
 6 files changed, 45 insertions(+), 36 deletions(-)

diff --git a/src/field/vecops.cxx b/src/field/vecops.cxx
index 65a6b7e938..672e8f6c09 100644
--- a/src/field/vecops.cxx
+++ b/src/field/vecops.cxx
@@ -1,11 +1,10 @@
 /**************************************************************************
  * Operators on vector objects
- * B.Dudson, October 2007
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -161,8 +160,8 @@ Coordinates::FieldMetric Div(const Vector2D& v, CELL_LOC outloc,
   vcn.toContravariant();
 
   Coordinates::FieldMetric result = DDX(metric->J * vcn.x, outloc, method);
-  result += DDY(metric->J * vcn.y, outloc, method);
-  result += DDZ(metric->J * vcn.z, outloc, method);
+  result += DDY(Coordinates::FieldMetric{metric->J * vcn.y}, outloc, method);
+  result += DDZ(Coordinates::FieldMetric{metric->J * vcn.z}, outloc, method);
   result /= metric->J;
 
   return result;
@@ -195,8 +194,8 @@ Field3D Div(const Vector3D& v, CELL_LOC outloc, const std::string& method) {
   }
   auto result = DDY(vcnJy, outloc, method);
 
-  result += DDX(vcn.x.getCoordinates()->J * vcn.x, outloc, method);
-  result += DDZ(vcn.z.getCoordinates()->J * vcn.z, outloc, method);
+  result += DDX(Field3D{vcn.x.getCoordinates()->J * vcn.x}, outloc, method);
+  result += DDZ(Field3D{vcn.z.getCoordinates()->J * vcn.z}, outloc, method);
   result /= metric->J;
 
   return result;
@@ -224,10 +223,12 @@ Coordinates::FieldMetric Div(const Vector2D& v, const Field2D& f, CELL_LOC outlo
   Vector2D vcn = v;
   vcn.toContravariant();
 
-  Coordinates::FieldMetric result =
-      FDDX(vcn.x.getCoordinates()->J * vcn.x, f, outloc, method);
-  result += FDDY(vcn.y.getCoordinates()->J * vcn.y, f, outloc, method);
-  result += FDDZ(vcn.z.getCoordinates()->J * vcn.z, f, outloc, method);
+  Coordinates::FieldMetric result = FDDX(
+      Coordinates::FieldMetric{vcn.x.getCoordinates()->J * vcn.x}, f, outloc, method);
+  result += FDDY(Coordinates::FieldMetric{vcn.y.getCoordinates()->J * vcn.y}, f, outloc,
+                 method);
+  result += FDDZ(Coordinates::FieldMetric{vcn.z.getCoordinates()->J * vcn.z}, f, outloc,
+                 method);
   result /= metric->J;
 
   return result;
@@ -249,9 +250,9 @@ Field3D Div(const Vector3D& v, const Field3D& f, CELL_LOC outloc,
   Vector3D vcn = v;
   vcn.toContravariant();
 
-  Field3D result = FDDX(vcn.x.getCoordinates()->J * vcn.x, f, outloc, method);
-  result += FDDY(vcn.y.getCoordinates()->J * vcn.y, f, outloc, method);
-  result += FDDZ(vcn.z.getCoordinates()->J * vcn.z, f, outloc, method);
+  Field3D result = FDDX(Field3D{vcn.x.getCoordinates()->J * vcn.x}, f, outloc, method);
+  result += FDDY(Field3D{vcn.y.getCoordinates()->J * vcn.y}, f, outloc, method);
+  result += FDDZ(Field3D{vcn.z.getCoordinates()->J * vcn.z}, f, outloc, method);
   result /= metric->J;
 
   return result;
diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
index 76b9b94e9a..9966ad654d 100644
--- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
+++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
@@ -299,7 +299,7 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
   const Field3D dc_dx = issetC ? DDX(C2) : Field3D();
   const Field3D dc_dy = issetC ? DDY(C2) : Field3D();
   const Field3D dc_dz = issetC ? DDZ(C2) : Field3D();
-  const auto dJ_dy = DDY(coords->J / coords->g_22);
+  const auto dJ_dy = DDY(Coordinates::FieldMetric{coords->J / coords->g_22});
 
   // Set up the matrix for the internal points on the grid.
   // Boundary conditions were set in the constructor.
@@ -384,7 +384,7 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
   // Must add these (rather than assign) so that elements used in
   // interpolation don't overwrite each other.
   BOUT_FOR_SERIAL(l, indexer->getRegionNobndry()) {
-    BoutReal C_df_dy = (coords->G2[l] - dJ_dy[l] / coords->J[l]);
+    BoutReal C_df_dy = coords->G2[l] - (dJ_dy[l] / coords->J[l]);
     if (issetD) {
       C_df_dy *= D[l];
     }
@@ -395,7 +395,7 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
           / C1[l];
     }
 
-    BoutReal C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]);
+    BoutReal C_d2f_dy2 = coords->g22[l] - (1.0 / coords->g_22[l]);
     if (issetD) {
       C_d2f_dy2 *= D[l];
     }
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 8980b00695..0004e4673f 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -546,7 +546,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
                                   transform.get());
 
     // Compare calculated and loaded values
-    Field2D diff = J - Jcalc;
+    const auto diff = J - Jcalc;
     output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(diff)));
 
     mesh->communicate_no_slices(J);
@@ -1140,7 +1140,7 @@ int Coordinates::geometry(bool recalculate_staggered,
     if (localmesh->get(d2z, "d2z" + suffix, 0.0, false)) {
       output_warn.write(
           "\tWARNING: differencing quantity 'd2z' not found. Calculating from dz\n");
-      d1_dz = bout::derivatives::index::DDZ(1. / dz);
+      d1_dz = bout::derivatives::index::DDZ(FieldMetric{1. / dz});
       localmesh->communicate_no_slices(d1_dz);
       d1_dz =
           interpolateAndExtrapolate(d1_dz, location, true, true, true, transform.get());
@@ -1174,7 +1174,7 @@ int Coordinates::geometry(bool recalculate_staggered,
     if (localmesh->get(d2y, "d2y", 0.0, false)) {
       output_warn.write(
           "\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
-      d1_dy = DDY(1. / dy); // d/di(1/dy)
+      d1_dy = DDY(FieldMetric{1. / dy}); // d/di(1/dy)
 
       localmesh->communicate_no_slices(d1_dy);
       d1_dy =
@@ -1190,7 +1190,7 @@ int Coordinates::geometry(bool recalculate_staggered,
     if (localmesh->get(d2z, "d2z", 0.0, false)) {
       output_warn.write(
           "\tWARNING: differencing quantity 'd2z' not found. Calculating from dz\n");
-      d1_dz = bout::derivatives::index::DDZ(1. / dz);
+      d1_dz = bout::derivatives::index::DDZ(FieldMetric{1. / dz});
 
       localmesh->communicate_no_slices(d1_dz);
       d1_dz =
@@ -1578,7 +1578,7 @@ Coordinates::FieldMetric Coordinates::Div_par(const Field2D& f, CELL_LOC outloc,
   // Coordinates object
   auto Bxy_floc = f.getCoordinates()->Bxy;
 
-  return Bxy * Grad_par(f / Bxy_floc, outloc, method);
+  return Bxy * Grad_par(FieldMetric{f / Bxy_floc}, outloc, method);
 }
 
 Field3D Coordinates::Div_par(const Field3DParallel& f, CELL_LOC outloc,
@@ -1771,7 +1771,8 @@ FieldPerp Coordinates::Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
 
 Coordinates::FieldMetric Coordinates::Laplace_par(const Field2D& f, CELL_LOC outloc) {
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-  return D2DY2(f, outloc) / g_22 + DDY(J / g_22, outloc) * DDY(f, outloc) / J;
+  return D2DY2(f, outloc) / g_22
+         + DDY(FieldMetric{J / g_22}, outloc) * DDY(f, outloc) / J;
 }
 
 Field3D Coordinates::Laplace_par(const Field3DParallel& f, CELL_LOC outloc) {
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 0b4ea5f6d1..f498c60e0e 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -471,7 +471,7 @@ void FCITransform::outputVars(Options& output_options) {
 void FCITransform::loadParallelMetrics(Coordinates* coords) {
 #if BOUT_USE_METRIC_3D
   output_info.write("\tLoading parallel metrics\n");
-  const auto JB0 = coords->J * coords->Bxy;
+  const Coordinates::FieldMetric JB0 = coords->J * coords->Bxy;
   coords->J.splitParallelSlices();
   coords->J.disallowCalcParallelSlices();
   coords->J.resetRegionParallel(true);
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index aa42be66c2..e449dbcd30 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -17,9 +17,9 @@
  *    Div(v*f)
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -38,16 +38,23 @@
  *
  **************************************************************************/
 
+#include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
+#include <bout/coordinates.hxx>
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
 #include <bout/globals.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/output.hxx>
 #include <bout/unused.hxx>
 #include <bout/utils.hxx>
 
+#include <string>
+
 /*******************************************************************************
  * First central derivatives
  *******************************************************************************/
@@ -96,7 +103,7 @@ Coordinates::FieldMetric DDZ(const Field2D& f, CELL_LOC UNUSED(outloc),
 Vector3D DDZ(const Vector3D& v, CELL_LOC outloc, const std::string& method,
              const std::string& region) {
   Vector3D result(v.getMesh());
-  Coordinates* metric = v.x.getCoordinates(outloc);
+  const Coordinates* metric = v.x.getCoordinates(outloc);
 
   if (v.covariant) {
     // From equation (2.6.32) in D'Haeseleer
@@ -148,7 +155,7 @@ Vector2D DDZ(const Vector2D& v, CELL_LOC UNUSED(outloc),
 
 Field3D D2DX2(const Field3D& f, CELL_LOC outloc, const std::string& method,
               const std::string& region) {
-  Coordinates* coords = f.getCoordinates(outloc);
+  const Coordinates* coords = f.getCoordinates(outloc);
 
   Field3D result =
       bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx);
@@ -167,9 +174,9 @@ Field3D D2DX2(const Field3D& f, CELL_LOC outloc, const std::string& method,
 
 Coordinates::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc,
                                const std::string& method, const std::string& region) {
-  Coordinates* coords = f.getCoordinates(outloc);
+  const Coordinates* coords = f.getCoordinates(outloc);
 
-  Field2D result =
+  Coordinates::FieldMetric result =
       bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx);
 
   if (coords->non_uniform) {
@@ -185,7 +192,7 @@ Coordinates::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc,
 
 Field3D D2DY2(const Field3D& f, CELL_LOC outloc, const std::string& method,
               const std::string& region) {
-  Coordinates* coords = f.getCoordinates(outloc);
+  const Coordinates* coords = f.getCoordinates(outloc);
 
   Field3D result =
       bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy);
@@ -204,9 +211,9 @@ Field3D D2DY2(const Field3D& f, CELL_LOC outloc, const std::string& method,
 
 Coordinates::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc,
                                const std::string& method, const std::string& region) {
-  Coordinates* coords = f.getCoordinates(outloc);
+  const Coordinates* coords = f.getCoordinates(outloc);
 
-  Field2D result =
+  Coordinates::FieldMetric result =
       bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy);
   if (coords->non_uniform) {
     // Correction for non-uniform f.getMesh()
@@ -286,7 +293,7 @@ Coordinates::FieldMetric D2DXDY(const Field2D& f, CELL_LOC outloc,
                                 const std::string& method, const std::string& region,
                                 const std::string& dfdy_boundary_condition,
                                 const std::string& dfdy_region) {
-  std::string dy_region = dfdy_region.empty() ? region : dfdy_region;
+  const std::string dy_region = dfdy_region.empty() ? region : dfdy_region;
 
   // If staggering in x, take y-derivative at f's location.
   const auto y_location =
@@ -311,7 +318,7 @@ Coordinates::FieldMetric D2DXDY(const Field2D& f, CELL_LOC outloc,
 Field3D D2DXDY(const Field3D& f, CELL_LOC outloc, const std::string& method,
                const std::string& region, const std::string& dfdy_boundary_condition,
                const std::string& dfdy_region) {
-  std::string dy_region = dfdy_region.empty() ? region : dfdy_region;
+  const std::string dy_region = dfdy_region.empty() ? region : dfdy_region;
 
   // If staggering in x, take y-derivative at f's location.
   const auto y_location =
diff --git a/tests/unit/solver/test_nvector.cxx b/tests/unit/solver/test_nvector.cxx
index dc45008caa..18901b067f 100644
--- a/tests/unit/solver/test_nvector.cxx
+++ b/tests/unit/solver/test_nvector.cxx
@@ -130,7 +130,7 @@ TYPED_TEST(BoutNVectorTest, LinearAndPointwiseOperations) {
   auto vz = makeNVector(BoutNVector::create(this->sunctx, z, true));
 
   N_VLinearSum(2.0, vx.get(), -1.0, vy.get(), vz.get());
-  auto expected = 2.0 * x - y;
+  TypeParam expected = 2.0 * x - y;
   EXPECT_TRUE(IsFieldEqual(z, expected));
 
   N_VProd(vx.get(), vy.get(), vz.get());

From 1996d27e7ee28ea89fb71873b7d6fb9c99d26e27 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 19 Jun 2026 11:00:35 +0100
Subject: [PATCH 1398/1827] Use EXTRA_FILES multi-value argument for the extra
 input files

---
 tests/integrated/test-multigrid_laplace/CMakeLists.txt | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/integrated/test-multigrid_laplace/CMakeLists.txt b/tests/integrated/test-multigrid_laplace/CMakeLists.txt
index a9af7d47c2..b478a8a12a 100644
--- a/tests/integrated/test-multigrid_laplace/CMakeLists.txt
+++ b/tests/integrated/test-multigrid_laplace/CMakeLists.txt
@@ -4,10 +4,10 @@ bout_add_integrated_test(
   CONFLICTS BOUT_USE_METRIC_3D
   USE_RUNTEST
   USE_DATA_BOUT_INP
+  EXTRA_FILES
+    data/BOUT_jy4.inp
+    data/BOUT_jy63.inp
+    data/BOUT_jy127.inp
+    data/BOUT_unsheared.inp
   PROCESSORS 3
 )
-
-bout_copy_file(data/BOUT_jy4.inp)
-bout_copy_file(data/BOUT_jy63.inp)
-bout_copy_file(data/BOUT_jy127.inp)
-bout_copy_file(data/BOUT_unsheared.inp)
\ No newline at end of file

From fe0f15a6b3430a27ac8280e56a655e105dbb8ad6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 19 Jun 2026 12:06:25 +0200
Subject: [PATCH 1399/1827] Move also build containers to updated boutproject
 repo

---
 .docker/fedora/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.docker/fedora/Dockerfile b/.docker/fedora/Dockerfile
index 7d5c04418d..c6387df383 100644
--- a/.docker/fedora/Dockerfile
+++ b/.docker/fedora/Dockerfile
@@ -1,5 +1,5 @@
 ARG BASE
-FROM ghcr.io/dschwoerer/bout-container-base:$BASE
+FROM ghcr.io/boutproject/bout-container-base:$BASE
 
 # ----------------------------------------------------------------
 # Build and install BOUT++

From f7511ecb427c1769924102c5ed505929264317f5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 2 Dec 2025 13:28:32 +0100
Subject: [PATCH 1400/1827] Disable openmp for container and switch to CHECK=4
 for debugging

---
 .github/workflows/docker.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 809f59cf9c..cb11e55ec2 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -30,14 +30,14 @@ jobs:
             cmake: ON
             base_prefix: ""
             tag_prefix: "3d-"
-          - name: "Without 3D Metrics"
+          - name: "With 2D Metrics"
             cmake: OFF
             base_prefix: ""
             tag_prefix: ""
         config:
           - name: "Debug"
             tag_postfix: "debug"
-            options: "-DCHECK=3"
+            options: "-DCHECK=4"
             base_postfix: "mini"
 
           - name: "Optimised"
@@ -47,7 +47,7 @@ jobs:
 
           - name: "Full"
             tag_postfix: "full"
-            options: "-DCHECK=3"
+            options: "-DCHECK=4"
             base_postfix: "full"
 
     steps:

From ae139bdfe38874d6c36cf8c99040478244a7868f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 19 Jun 2026 12:15:10 +0200
Subject: [PATCH 1401/1827] Provide default argument for BASE

---
 .docker/fedora/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.docker/fedora/Dockerfile b/.docker/fedora/Dockerfile
index c6387df383..e0351bb605 100644
--- a/.docker/fedora/Dockerfile
+++ b/.docker/fedora/Dockerfile
@@ -1,4 +1,4 @@
-ARG BASE
+ARG BASE=mpich-full-main
 FROM ghcr.io/boutproject/bout-container-base:$BASE
 
 # ----------------------------------------------------------------

From 4c457551e857c65423d01623505dd896e7516566 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 11 May 2026 17:15:29 +0100
Subject: [PATCH 1402/1827] Reduce duplication in `Coordinates` ctors

---
 include/bout/coordinates.hxx |   3 +
 src/mesh/coordinates.cxx     | 562 ++++++++++-------------------------
 2 files changed, 168 insertions(+), 397 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 6d803ab28a..387c5ada25 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -44,6 +44,7 @@
 
 #include <array>
 #include <memory>
+#include <string>
 
 class Mesh;
 class YBoundary;
@@ -380,6 +381,8 @@ private:
   void checkContravariant();
 
   mutable std::array<std::shared_ptr<YBoundary>, 3> ybndrys;
+  /// Read quantities with given suffix from `Mesh`
+  void readFromMesh(Options* options, const std::string& suffix);
 };
 
 #endif // BOUT_COORDINATES_H
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 2e1c4ad389..623d250445 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -317,32 +317,12 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
 // also exist for consistency
 void checkStaggeredGet(Mesh* mesh, const std::string& name, const std::string& suffix) {
   if (mesh->sourceHasVar(name) != mesh->sourceHasVar(name + suffix)) {
-    throw BoutException("Attempting to read staggered fields from grid, but " + name
-                        + " is not present in both CELL_CENTRE and staggered versions.");
+    throw BoutException("Attempting to read staggered fields from grid, but '{}'"
+                        " is not present in both CELL_CENTRE and staggered versions.",
+                        name);
   }
 }
 
-// convenience function for repeated code
-int getAtLoc(Mesh* mesh, Coordinates::FieldMetric& var, const std::string& name,
-             const std::string& suffix, CELL_LOC location, BoutReal default_value = 0.) {
-
-  checkStaggeredGet(mesh, name, suffix);
-  int result = mesh->get(var, name + suffix, default_value, false, location);
-
-  return result;
-}
-
-int getAtLocAndFillGuards(Mesh* mesh, Coordinates::FieldMetric& var,
-                          const std::string& name, const std::string& suffix,
-                          CELL_LOC location, BoutReal default_value, bool extrapolate_x,
-                          bool extrapolate_y, bool no_extra_interpolate,
-                          ParallelTransform* pt) {
-  auto ret = getAtLoc(mesh, var, name, suffix, location, default_value);
-  var = interpolateAndExtrapolate(var, location, extrapolate_x, extrapolate_y,
-                                  no_extra_interpolate, pt);
-  return ret;
-}
-
 std::string getLocationSuffix(CELL_LOC location) {
   switch (location) {
   case CELL_CENTRE: {
@@ -392,9 +372,112 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
       G1_13(mesh), G1_23(mesh), G2_11(mesh), G2_22(mesh), G2_33(mesh), G2_12(mesh),
       G2_13(mesh), G2_23(mesh), G3_11(mesh), G3_22(mesh), G3_33(mesh), G3_12(mesh),
       G3_13(mesh), G3_23(mesh), G1(mesh), G2(mesh), G3(mesh), ShiftTorsion(mesh),
-      IntShiftTorsion(mesh), localmesh(mesh), localoptions(options),
+      IntShiftTorsion(mesh), nz(mesh->LocalNz), localmesh(mesh), localoptions(options),
       location(CELL_CENTRE) {
 
+  readFromMesh(options, "");
+  // Allow transform to fix things up
+  transform->loadParallelMetrics(this);
+}
+
+Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
+                         const Coordinates* coords_in, bool force_interpolate_from_centre)
+    : dx(1., mesh), dy(1., mesh), dz(1., mesh), d1_dx(mesh), d1_dy(mesh), d1_dz(mesh),
+      J(1., mesh), Bxy(1., mesh),
+      // Identity metric tensor
+      g11(1., mesh), g22(1., mesh), g33(1., mesh), g12(0, mesh), g13(0, mesh),
+      g23(0, mesh), g_11(1., mesh), g_22(1., mesh), g_33(1., mesh), g_12(0, mesh),
+      g_13(0, mesh), g_23(0, mesh), G1_11(mesh), G1_22(mesh), G1_33(mesh), G1_12(mesh),
+      G1_13(mesh), G1_23(mesh), G2_11(mesh), G2_22(mesh), G2_33(mesh), G2_12(mesh),
+      G2_13(mesh), G2_23(mesh), G3_11(mesh), G3_22(mesh), G3_33(mesh), G3_12(mesh),
+      G3_13(mesh), G3_23(mesh), G1(mesh), G2(mesh), G3(mesh), ShiftTorsion(mesh),
+      IntShiftTorsion(mesh), nz(mesh->LocalNz), localmesh(mesh), localoptions(options),
+      location(loc) {
+
+  const std::string suffix = getLocationSuffix(location);
+
+  if (not force_interpolate_from_centre and mesh->sourceHasVar("dx" + suffix)) {
+    readFromMesh(options, suffix);
+  } else {
+    // Interpolate fields from coords_in
+
+    if (isUniform(coords_in->dz)) {
+      dz = coords_in->dz;
+      dz.setLocation(location);
+    } else {
+      throw BoutException(
+          "We are asked to transform dz to get dz before we have a transform, which "
+          "might require dz!\nPlease provide a dz for the staggered quantity!");
+    }
+    setParallelTransform(options);
+    dx = interpolateAndExtrapolate(coords_in->dx, location, true, true, false,
+                                   transform.get());
+    dy = interpolateAndExtrapolate(coords_in->dy, location, true, true, false,
+                                   transform.get());
+    // not really needed - we have used dz already ...
+    dz = interpolateAndExtrapolate(coords_in->dz, location, true, true, false,
+                                   transform.get());
+
+    // Diagonal components of metric tensor g^{ij}
+    g11 = interpolateAndExtrapolate(coords_in->g11, location, true, true, false,
+                                    transform.get());
+    g22 = interpolateAndExtrapolate(coords_in->g22, location, true, true, false,
+                                    transform.get());
+    g33 = interpolateAndExtrapolate(coords_in->g33, location, true, true, false,
+                                    transform.get());
+
+    // Off-diagonal elements.
+    g12 = interpolateAndExtrapolate(coords_in->g12, location, true, true, false,
+                                    transform.get());
+    g13 = interpolateAndExtrapolate(coords_in->g13, location, true, true, false,
+                                    transform.get());
+    g23 = interpolateAndExtrapolate(coords_in->g23, location, true, true, false,
+                                    transform.get());
+
+    // 3x3 matrix inversion can exaggerate small interpolation errors, so it is
+    // more robust to interpolate and extrapolate derived quantities directly,
+    // rather than deriving from interpolated/extrapolated covariant metric
+    // components
+    g_11 = interpolateAndExtrapolate(coords_in->g_11, location, true, true, false,
+                                     transform.get());
+    g_22 = interpolateAndExtrapolate(coords_in->g_22, location, true, true, false,
+                                     transform.get());
+    g_33 = interpolateAndExtrapolate(coords_in->g_33, location, true, true, false,
+                                     transform.get());
+    g_12 = interpolateAndExtrapolate(coords_in->g_12, location, true, true, false,
+                                     transform.get());
+    g_13 = interpolateAndExtrapolate(coords_in->g_13, location, true, true, false,
+                                     transform.get());
+    g_23 = interpolateAndExtrapolate(coords_in->g_23, location, true, true, false,
+                                     transform.get());
+
+    // Check input metrics
+    checkContravariant();
+    checkCovariant();
+
+    J = interpolateAndExtrapolate(coords_in->J, location, true, true, false,
+                                  transform.get());
+    Bxy = interpolateAndExtrapolate(coords_in->Bxy, location, true, true, false,
+                                    transform.get());
+
+    bout::checkFinite(J, "The Jacobian", "RGN_NOCORNERS");
+    bout::checkPositive(J, "The Jacobian", "RGN_NOCORNERS");
+    bout::checkFinite(Bxy, "Bxy", "RGN_NOCORNERS");
+    bout::checkPositive(Bxy, "Bxy", "RGN_NOCORNERS");
+
+    ShiftTorsion = interpolateAndExtrapolate(coords_in->ShiftTorsion, location, true,
+                                             true, false, transform.get());
+
+    if (mesh->IncIntShear) {
+      IntShiftTorsion = interpolateAndExtrapolate(coords_in->IntShiftTorsion, location,
+                                                  true, true, false, transform.get());
+    }
+  }
+  // Allow transform to fix things up
+  transform->loadParallelMetrics(this);
+}
+
+void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   if (options == nullptr) {
     options = Options::getRoot()->getSection("mesh");
   }
@@ -404,9 +487,9 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
   // smooth at all the boundaries.
 
   const bool extrapolate_x =
-      (*options)["extrapolate_x"].withDefault(not mesh->sourceHasXBoundaryGuards());
+      (*options)["extrapolate_x"].withDefault(not localmesh->sourceHasXBoundaryGuards());
   const bool extrapolate_y =
-      (*options)["extrapolate_y"].withDefault(not mesh->sourceHasYBoundaryGuards());
+      (*options)["extrapolate_y"].withDefault(not localmesh->sourceHasYBoundaryGuards());
 
   if (extrapolate_x) {
     output_warn.write(_("WARNING: extrapolating input mesh quantities into x-boundary "
@@ -418,12 +501,25 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
                         "cells. Set option extrapolate_y=false to disable this.\n"));
   }
 
-  mesh->get(dx, "dx", 1.0, false);
-  mesh->get(dy, "dy", 1.0, false);
+  auto readField = [this, &suffix](const std::string& name, BoutReal def_value) {
+    checkStaggeredGet(localmesh, name, suffix);
 
-  nz = mesh->LocalNz;
+    FieldMetric field{localmesh};
+    localmesh->get(field, name + suffix, def_value, false, location);
+    if (field.getDirectionY() == YDirectionType::Aligned
+        and transform->canToFromFieldAligned()) {
+      return transform->fromFieldAligned(field);
+    }
+    return field.setDirectionY(YDirectionType::Standard);
+  };
+
+  auto fillGuards = [&, this](const auto& field) {
+    return interpolateAndExtrapolate(field, location, extrapolate_x, extrapolate_y, false,
+                                     transform.get());
+  };
 
   {
+    // dz
     auto& options = Options::root();
     const bool has_zperiod = options.isSet("zperiod");
     const auto zmin = has_zperiod ? 0.0 : options["ZMIN"].withDefault(0.0);
@@ -432,60 +528,37 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
 
     const auto default_dz = (zmax - zmin) * TWOPI / nz;
 
-    mesh->get(dz, "dz", default_dz, false);
+    dz = fillGuards(readField("dz", default_dz));
   }
 
   // required early for differentiation.
   setParallelTransform(options);
 
-  dz = interpolateAndExtrapolate(dz, location, extrapolate_x, extrapolate_y, false,
-                                 transform.get());
-  dx = interpolateAndExtrapolate(dx, location, extrapolate_x, extrapolate_y, false,
-                                 transform.get());
+  dx = fillGuards(readField("dx", 1.0));
 
-  if (mesh->periodicX) {
-    mesh->communicate_no_slices(dx);
+  if (localmesh->periodicX) {
+    localmesh->communicate_no_slices(dx);
   }
 
-  dy = interpolateAndExtrapolate(dy, location, extrapolate_x, extrapolate_y, false,
-                                 transform.get());
-
-  auto getUnaligned = [this](auto& field, const std::string& name,
-                             BoutReal default_value) {
-    localmesh->get(field, name, default_value, false);
-    if (field.getDirectionY() == YDirectionType::Aligned
-        and transform->canToFromFieldAligned()) {
-      return transform->fromFieldAligned(field);
-    } else {
-      return field.setDirectionY(YDirectionType::Standard);
-    }
-  };
-
-  auto getUnalignedAtLocation = [this, extrapolate_x, extrapolate_y,
-                                 getUnaligned](auto& field, const std::string& name,
-                                               BoutReal default_value) {
-    field = getUnaligned(field, name, default_value);
-    return interpolateAndExtrapolate(field, location, extrapolate_x, extrapolate_y, false,
-                                     transform.get());
-  };
+  dy = fillGuards(readField("dy", 1.0));
 
   // Diagonal components of metric tensor g^{ij} (default to 1)
-  g11 = getUnalignedAtLocation(g11, "g11", 1.0);
-  g22 = getUnalignedAtLocation(g22, "g22", 1.0);
-  g33 = getUnalignedAtLocation(g33, "g33", 1.0);
+  g11 = fillGuards(readField("g11", 1.0));
+  g22 = fillGuards(readField("g22", 1.0));
+  g33 = fillGuards(readField("g33", 1.0));
 
   // Off-diagonal elements. Default to 0
-  g12 = getUnalignedAtLocation(g12, "g12", 0.0);
-  g13 = getUnalignedAtLocation(g13, "g13", 0.0);
-  g23 = getUnalignedAtLocation(g23, "g23", 0.0);
+  g12 = fillGuards(readField("g12", 0.0));
+  g13 = fillGuards(readField("g13", 0.0));
+  g23 = fillGuards(readField("g23", 0.0));
 
   // Check input metrics
   checkContravariant();
 
-  /// Find covariant metric components
+  // Find covariant metric components
   auto covariant_component_names = {"g_11", "g_22", "g_33", "g_12", "g_13", "g_23"};
-  auto source_has_component = [&mesh](const std::string& name) {
-    return mesh->sourceHasVar(name);
+  auto source_has_component = [&suffix, this](const std::string& name) {
+    return localmesh->sourceHasVar(name + suffix);
   };
   // Check if any of the components are present
   if (std::any_of(begin(covariant_component_names), end(covariant_component_names),
@@ -493,12 +566,12 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
     // Check that all components are present
     if (std::all_of(begin(covariant_component_names), end(covariant_component_names),
                     source_has_component)) {
-      g_11 = getUnaligned(g_11, "g_11", 1.0);
-      g_22 = getUnaligned(g_22, "g_22", 1.0);
-      g_33 = getUnaligned(g_33, "g_33", 1.0);
-      g_12 = getUnaligned(g_12, "g_12", 0.0);
-      g_13 = getUnaligned(g_13, "g_13", 0.0);
-      g_23 = getUnaligned(g_23, "g_23", 0.0);
+      g_11 = readField("g_11", 1.0);
+      g_22 = readField("g_22", 1.0);
+      g_33 = readField("g_33", 1.0);
+      g_12 = readField("g_12", 0.0);
+      g_13 = readField("g_13", 0.0);
+      g_23 = readField("g_23", 0.0);
 
       output_warn.write("\tWARNING! Covariant components of metric tensor set manually. "
                         "Contravariant components NOT recalculated\n");
@@ -507,53 +580,44 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
       output_warn.write("Not all covariant components of metric tensor found. "
                         "Calculating all from the contravariant tensor\n");
       /// Calculate contravariant metric components if not found
-      if (calcCovariant("RGN_NOCORNERS") != 0) {
+      if (calcCovariant("RGN_NOCORNERS")) {
         throw BoutException("Error in calcCovariant call");
       }
     }
   } else {
     /// Calculate contravariant metric components if not found
-    if (calcCovariant("RGN_NOCORNERS") != 0) {
+    if (calcCovariant("RGN_NOCORNERS")) {
       throw BoutException("Error in calcCovariant call");
     }
   }
   // More robust to extrapolate derived quantities directly, rather than
   // deriving from extrapolated covariant metric components
-  g_11 = interpolateAndExtrapolate(g_11, location, extrapolate_x, extrapolate_y, false,
-                                   transform.get());
-  g_22 = interpolateAndExtrapolate(g_22, location, extrapolate_x, extrapolate_y, false,
-                                   transform.get());
-  g_33 = interpolateAndExtrapolate(g_33, location, extrapolate_x, extrapolate_y, false,
-                                   transform.get());
-  g_12 = interpolateAndExtrapolate(g_12, location, extrapolate_x, extrapolate_y, false,
-                                   transform.get());
-  g_13 = interpolateAndExtrapolate(g_13, location, extrapolate_x, extrapolate_y, false,
-                                   transform.get());
-  g_23 = interpolateAndExtrapolate(g_23, location, extrapolate_x, extrapolate_y, false,
-                                   transform.get());
+  g_11 = fillGuards(g_11);
+  g_22 = fillGuards(g_22);
+  g_33 = fillGuards(g_33);
+  g_12 = fillGuards(g_12);
+  g_13 = fillGuards(g_13);
+  g_23 = fillGuards(g_23);
 
   // Check covariant metrics
   checkCovariant();
 
-  /// Calculate Jacobian and Bxy
-  if (jacobian()) {
-    throw BoutException("Error in jacobian call");
-  }
+  // Calculate Jacobian and Bxy
+  jacobian();
 
   // Attempt to read J from the grid file
   auto Jcalc = J;
-  if (mesh->get(J, "J", 0.0, false)) {
+  if (localmesh->get(J, "J" + suffix, 0.0, false)) {
     output_warn.write(
         "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
     J = Jcalc;
   } else {
-    J = interpolateAndExtrapolate(J, location, extrapolate_x, extrapolate_y, false,
-                                  transform.get());
+    J = fillGuards(J);
 
     // Compare calculated and loaded values
     output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(J - Jcalc)));
 
-    mesh->communicate_no_slices(J);
+    localmesh->communicate_no_slices(J);
 
     // Re-evaluate Bxy using new J
     Bxy = sqrt(g_22) / J;
@@ -568,14 +632,13 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
 
   // Attempt to read Bxy from the grid file
   auto Bcalc = Bxy;
-  if (mesh->get(Bxy, "Bxy", 0.0, false)) {
+  if (localmesh->get(Bxy, "Bxy" + suffix, 0.0, false)) {
     output_warn.write("\tWARNING: Magnitude of B field 'Bxy' not found. Calculating from "
                       "metric tensor\n");
     Bxy = Bcalc;
   } else {
 
-    Bxy = interpolateAndExtrapolate(Bxy, location, extrapolate_x, extrapolate_y, false,
-                                    transform.get());
+    Bxy = fillGuards(Bxy);
     output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
   }
 
@@ -583,319 +646,24 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
   bout::checkFinite(Bxy, "Bxy", "RGN_NOCORNERS");
   bout::checkPositive(Bxy, "Bxy", "RGN_NOCORNERS");
 
-  if (mesh->get(ShiftTorsion, "ShiftTorsion", 0.0, false)) {
+  if (localmesh->get(ShiftTorsion, "ShiftTorsion" + suffix, 0.0, false)) {
     output_warn.write(
         "\tWARNING: No Torsion specified for zShift. Derivatives may not be correct\n");
     ShiftTorsion = 0.0;
   }
-  ShiftTorsion = interpolateAndExtrapolate(ShiftTorsion, location, extrapolate_x,
-                                           extrapolate_y, false, transform.get());
+  ShiftTorsion = fillGuards(ShiftTorsion);
 
   //////////////////////////////////////////////////////
 
-  if (mesh->IncIntShear) {
-    if (mesh->get(IntShiftTorsion, "IntShiftTorsion", 0.0, false)) {
+  if (localmesh->IncIntShear) {
+    if (localmesh->get(IntShiftTorsion, "IntShiftTorsion", 0.0, false)) {
       output_warn.write("\tWARNING: No Integrated torsion specified\n");
     }
-    IntShiftTorsion = interpolateAndExtrapolate(IntShiftTorsion, location, extrapolate_x,
-                                                extrapolate_y, false, transform.get());
+    IntShiftTorsion = fillGuards(IntShiftTorsion);
   } else {
     // IntShiftTorsion will not be used, but set to zero to avoid uninitialized field
     IntShiftTorsion = 0.;
   }
-
-  // Allow transform to fix things up
-  transform->loadParallelMetrics(this);
-}
-
-Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
-                         const Coordinates* coords_in, bool force_interpolate_from_centre)
-    : dx(1., mesh), dy(1., mesh), dz(1., mesh), d1_dx(mesh), d1_dy(mesh), d1_dz(mesh),
-      J(1., mesh), Bxy(1., mesh),
-      // Identity metric tensor
-      g11(1., mesh), g22(1., mesh), g33(1., mesh), g12(0, mesh), g13(0, mesh),
-      g23(0, mesh), g_11(1., mesh), g_22(1., mesh), g_33(1., mesh), g_12(0, mesh),
-      g_13(0, mesh), g_23(0, mesh), G1_11(mesh), G1_22(mesh), G1_33(mesh), G1_12(mesh),
-      G1_13(mesh), G1_23(mesh), G2_11(mesh), G2_22(mesh), G2_33(mesh), G2_12(mesh),
-      G2_13(mesh), G2_23(mesh), G3_11(mesh), G3_22(mesh), G3_33(mesh), G3_12(mesh),
-      G3_13(mesh), G3_23(mesh), G1(mesh), G2(mesh), G3(mesh), ShiftTorsion(mesh),
-      IntShiftTorsion(mesh), localmesh(mesh), localoptions(options), location(loc) {
-
-  std::string suffix = getLocationSuffix(location);
-
-  nz = mesh->LocalNz;
-
-  // Default to true in case staggered quantities are not read from file
-  bool extrapolate_x = true;
-  bool extrapolate_y = true;
-
-  if (!force_interpolate_from_centre && mesh->sourceHasVar("dx" + suffix)) {
-
-    extrapolate_x = not mesh->sourceHasXBoundaryGuards();
-    extrapolate_y = not mesh->sourceHasYBoundaryGuards();
-
-    if (extrapolate_x) {
-      output_warn.write(_("WARNING: extrapolating input mesh quantities into x-boundary "
-                          "cells\n"));
-    }
-
-    if (extrapolate_y) {
-      output_warn.write(_("WARNING: extrapolating input mesh quantities into y-boundary "
-                          "cells\n"));
-    }
-
-    {
-      auto& options = Options::root();
-      const bool has_zperiod = options.isSet("zperiod");
-      const auto zmin = has_zperiod ? 0.0 : options["ZMIN"].withDefault(0.0);
-      const auto zmax = has_zperiod ? 1.0 / options["zperiod"].withDefault(1.0)
-                                    : options["ZMAX"].withDefault(1.0);
-
-      const auto default_dz = (zmax - zmin) * TWOPI / nz;
-      getAtLoc(mesh, dz, "dz", suffix, location, default_dz);
-    }
-    setParallelTransform(options);
-
-    dz = interpolateAndExtrapolate(dz, location, extrapolate_x, extrapolate_y, false,
-                                   transform.get());
-
-    getAtLocAndFillGuards(mesh, dx, "dx", suffix, location, 1.0, extrapolate_x,
-                          extrapolate_y, false, transform.get());
-
-    if (mesh->periodicX) {
-      mesh->communicate_no_slices(dx);
-    }
-
-    getAtLocAndFillGuards(mesh, dy, "dy", suffix, location, 1.0, extrapolate_x,
-                          extrapolate_y, false, transform.get());
-
-    // grid data source has staggered fields, so read instead of interpolating
-    // Diagonal components of metric tensor g^{ij} (default to 1)
-    getAtLocAndFillGuards(mesh, g11, "g11", suffix, location, 1.0, extrapolate_x,
-                          extrapolate_y, false, transform.get());
-    getAtLocAndFillGuards(mesh, g22, "g22", suffix, location, 1.0, extrapolate_x,
-                          extrapolate_y, false, transform.get());
-    getAtLocAndFillGuards(mesh, g33, "g33", suffix, location, 1.0, extrapolate_x,
-                          extrapolate_y, false, transform.get());
-    getAtLocAndFillGuards(mesh, g12, "g12", suffix, location, 0.0, extrapolate_x,
-                          extrapolate_y, false, transform.get());
-    getAtLocAndFillGuards(mesh, g13, "g13", suffix, location, 0.0, extrapolate_x,
-                          extrapolate_y, false, transform.get());
-    getAtLocAndFillGuards(mesh, g23, "g23", suffix, location, 0.0, extrapolate_x,
-                          extrapolate_y, false, transform.get());
-
-    // Check input metrics
-    checkContravariant();
-
-    /// Find covariant metric components
-    auto covariant_component_names = {"g_11", "g_22", "g_33", "g_12", "g_13", "g_23"};
-    auto source_has_component = [&suffix, &mesh](const std::string& name) {
-      return mesh->sourceHasVar(name + suffix);
-    };
-    // Check if any of the components are present
-    if (std::any_of(begin(covariant_component_names), end(covariant_component_names),
-                    source_has_component)) {
-      // Check that all components are present
-      if (std::all_of(begin(covariant_component_names), end(covariant_component_names),
-                      source_has_component)) {
-
-        getAtLoc(mesh, g_11, "g_11", suffix, location);
-        getAtLoc(mesh, g_22, "g_22", suffix, location);
-        getAtLoc(mesh, g_33, "g_33", suffix, location);
-        getAtLoc(mesh, g_12, "g_12", suffix, location);
-        getAtLoc(mesh, g_13, "g_13", suffix, location);
-        getAtLoc(mesh, g_23, "g_23", suffix, location);
-
-        output_warn.write(
-            "\tWARNING! Staggered covariant components of metric tensor set manually. "
-            "Contravariant components NOT recalculated\n");
-
-      } else {
-        output_warn.write(
-            "Not all staggered covariant components of metric tensor found. "
-            "Calculating all from the contravariant tensor\n");
-        /// Calculate contravariant metric components if not found
-        if (calcCovariant("RGN_NOCORNERS")) {
-          throw BoutException("Error in staggered calcCovariant call");
-        }
-      }
-    } else {
-      /// Calculate contravariant metric components if not found
-      if (calcCovariant("RGN_NOCORNERS")) {
-        throw BoutException("Error in staggered calcCovariant call");
-      }
-    }
-    // More robust to extrapolate derived quantities directly, rather than
-    // deriving from extrapolated covariant metric components
-    g_11 = interpolateAndExtrapolate(g_11, location, extrapolate_x, extrapolate_y, false,
-                                     transform.get());
-    g_22 = interpolateAndExtrapolate(g_22, location, extrapolate_x, extrapolate_y, false,
-                                     transform.get());
-    g_33 = interpolateAndExtrapolate(g_33, location, extrapolate_x, extrapolate_y, false,
-                                     transform.get());
-    g_12 = interpolateAndExtrapolate(g_12, location, extrapolate_x, extrapolate_y, false,
-                                     transform.get());
-    g_13 = interpolateAndExtrapolate(g_13, location, extrapolate_x, extrapolate_y, false,
-                                     transform.get());
-    g_23 = interpolateAndExtrapolate(g_23, location, extrapolate_x, extrapolate_y, false,
-                                     transform.get());
-
-    // Check covariant metrics
-    checkCovariant();
-
-    /// Calculate Jacobian and Bxy
-    if (jacobian()) {
-      throw BoutException("Error in jacobian call while constructing staggered "
-                          "Coordinates");
-    }
-
-    // Attempt to read J from the grid file
-    auto Jcalc = J;
-    if (getAtLoc(mesh, J, "J", suffix, location)) {
-      output_warn.write(
-          "\tWARNING: Jacobian 'J_{:s}' not found. Calculating from metric tensor\n",
-          suffix);
-      J = Jcalc;
-    } else {
-      J = interpolateAndExtrapolate(J, location, extrapolate_x, extrapolate_y, false,
-                                    transform.get());
-
-      // Compare calculated and loaded values
-      output_warn.write("\tMaximum difference in J is %e\n", max(abs(J - Jcalc)));
-
-      // Re-evaluate Bxy using new J
-      Bxy = sqrt(g_22) / J;
-    }
-
-    // Check jacobian
-    bout::checkFinite(J, "J" + suffix, "RGN_NOCORNERS");
-    bout::checkPositive(J, "J" + suffix, "RGN_NOCORNERS");
-    if (min(abs(J)) < 1.0e-10) {
-      throw BoutException("\tERROR: Jacobian{:s} becomes very small\n", suffix);
-    }
-
-    // Attempt to read Bxy from the grid file
-    auto Bcalc = Bxy;
-    if (getAtLoc(mesh, Bxy, "Bxy", suffix, location)) {
-      output_warn.write(
-          "\tWARNING: Magnitude of B field 'Bxy_{:s}' not found. Calculating "
-          " from metric tensor\n",
-          suffix);
-      Bxy = Bcalc;
-    } else {
-      Bxy = interpolateAndExtrapolate(Bxy, location, extrapolate_x, extrapolate_y, false,
-                                      transform.get());
-
-      output_warn.write("\tMaximum difference in Bxy is %e\n", max(abs(Bxy - Bcalc)));
-    }
-
-    // Check Bxy
-    bout::checkFinite(Bxy, "Bxy" + suffix, "RGN_NOCORNERS");
-    bout::checkPositive(Bxy, "Bxy" + suffix, "RGN_NOCORNERS");
-
-    checkStaggeredGet(mesh, "ShiftTorsion", suffix);
-    if (mesh->get(ShiftTorsion, "ShiftTorsion" + suffix, 0.0, false)) {
-      output_warn.write(
-          "\tWARNING: No Torsion specified for zShift. Derivatives may not be correct\n");
-      ShiftTorsion = 0.0;
-    }
-    ShiftTorsion.setLocation(location);
-    ShiftTorsion = interpolateAndExtrapolate(ShiftTorsion, location, extrapolate_x,
-                                             extrapolate_y, false, transform.get());
-
-    //////////////////////////////////////////////////////
-
-    if (mesh->IncIntShear) {
-      checkStaggeredGet(mesh, "IntShiftTorsion", suffix);
-      if (mesh->get(IntShiftTorsion, "IntShiftTorsion" + suffix, 0.0, false)) {
-        output_warn.write("\tWARNING: No Integrated torsion specified\n");
-        IntShiftTorsion = 0.0;
-      }
-      IntShiftTorsion.setLocation(location);
-      IntShiftTorsion =
-          interpolateAndExtrapolate(IntShiftTorsion, location, extrapolate_x,
-                                    extrapolate_y, false, transform.get());
-    } else {
-      // IntShiftTorsion will not be used, but set to zero to avoid uninitialized field
-      IntShiftTorsion = 0.;
-    }
-  } else {
-    // Interpolate fields from coords_in
-
-    if (isUniform(coords_in->dz)) {
-      dz = coords_in->dz;
-      dz.setLocation(location);
-    } else {
-      throw BoutException(
-          "We are asked to transform dz to get dz before we have a transform, which "
-          "might require dz!\nPlease provide a dz for the staggered quantity!");
-    }
-    setParallelTransform(options);
-    dx = interpolateAndExtrapolate(coords_in->dx, location, true, true, false,
-                                   transform.get());
-    dy = interpolateAndExtrapolate(coords_in->dy, location, true, true, false,
-                                   transform.get());
-    // not really needed - we have used dz already ...
-    dz = interpolateAndExtrapolate(coords_in->dz, location, true, true, false,
-                                   transform.get());
-
-    // Diagonal components of metric tensor g^{ij}
-    g11 = interpolateAndExtrapolate(coords_in->g11, location, true, true, false,
-                                    transform.get());
-    g22 = interpolateAndExtrapolate(coords_in->g22, location, true, true, false,
-                                    transform.get());
-    g33 = interpolateAndExtrapolate(coords_in->g33, location, true, true, false,
-                                    transform.get());
-
-    // Off-diagonal elements.
-    g12 = interpolateAndExtrapolate(coords_in->g12, location, true, true, false,
-                                    transform.get());
-    g13 = interpolateAndExtrapolate(coords_in->g13, location, true, true, false,
-                                    transform.get());
-    g23 = interpolateAndExtrapolate(coords_in->g23, location, true, true, false,
-                                    transform.get());
-
-    // 3x3 matrix inversion can exaggerate small interpolation errors, so it is
-    // more robust to interpolate and extrapolate derived quantities directly,
-    // rather than deriving from interpolated/extrapolated covariant metric
-    // components
-    g_11 = interpolateAndExtrapolate(coords_in->g_11, location, true, true, false,
-                                     transform.get());
-    g_22 = interpolateAndExtrapolate(coords_in->g_22, location, true, true, false,
-                                     transform.get());
-    g_33 = interpolateAndExtrapolate(coords_in->g_33, location, true, true, false,
-                                     transform.get());
-    g_12 = interpolateAndExtrapolate(coords_in->g_12, location, true, true, false,
-                                     transform.get());
-    g_13 = interpolateAndExtrapolate(coords_in->g_13, location, true, true, false,
-                                     transform.get());
-    g_23 = interpolateAndExtrapolate(coords_in->g_23, location, true, true, false,
-                                     transform.get());
-
-    // Check input metrics
-    checkContravariant();
-    checkCovariant();
-
-    J = interpolateAndExtrapolate(coords_in->J, location, true, true, false,
-                                  transform.get());
-    Bxy = interpolateAndExtrapolate(coords_in->Bxy, location, true, true, false,
-                                    transform.get());
-
-    bout::checkFinite(J, "The Jacobian", "RGN_NOCORNERS");
-    bout::checkPositive(J, "The Jacobian", "RGN_NOCORNERS");
-    bout::checkFinite(Bxy, "Bxy", "RGN_NOCORNERS");
-    bout::checkPositive(Bxy, "Bxy", "RGN_NOCORNERS");
-
-    ShiftTorsion = interpolateAndExtrapolate(coords_in->ShiftTorsion, location, true,
-                                             true, false, transform.get());
-
-    if (mesh->IncIntShear) {
-      IntShiftTorsion = interpolateAndExtrapolate(coords_in->IntShiftTorsion, location,
-                                                  true, true, false, transform.get());
-    }
-  }
-  // Allow transform to fix things up
-  transform->loadParallelMetrics(this);
 }
 
 void Coordinates::outputVars(Options& output_options) {

From e85892234146adbe043b110e8731a7bb69a29f72 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 11 May 2026 18:20:26 +0100
Subject: [PATCH 1403/1827] Make `Mesh::getBoundaries{Par}` `const`

---
 include/bout/mesh.hxx            | 2 +-
 src/mesh/impls/bout/boutmesh.cxx | 2 +-
 src/mesh/impls/bout/boutmesh.hxx | 2 +-
 tests/unit/fake_mesh.hxx         | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 1453f51f5f..70d068ff37 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -482,7 +482,7 @@ public:
   // Boundary regions
 
   /// Return a vector containing all the boundary regions on this processor
-  virtual std::vector<BoundaryRegionBase*> getBoundaries() = 0;
+  virtual std::vector<BoundaryRegionBase*> getBoundaries() const = 0;
 
   /// Get the set of all possible boundaries in this configuration
   virtual std::set<std::string> getPossibleBoundaries() const {
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index f56979785c..2066523262 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -3242,7 +3242,7 @@ RangeIterator BoutMesh::iterateBndryUpperY() const {
   return RangeIterator(xs, xe);
 }
 
-std::vector<BoundaryRegionBase*> BoutMesh::getBoundaries() { return boundary; }
+std::vector<BoundaryRegionBase*> BoutMesh::getBoundaries() const { return boundary; }
 
 using bout::boundary::BoundaryRegionFCI;
 std::vector<std::shared_ptr<BoundaryRegionFCI>>
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index dfec3342ed..79121ede58 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -169,7 +169,7 @@ public:
   bool hasBndryUpperY() const override { return has_boundary_upper_y; }
 
   // Boundary regions
-  std::vector<BoundaryRegionBase*> getBoundaries() override;
+  std::vector<BoundaryRegionBase*> getBoundaries() const override;
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType type) const override;
   void addBoundaryPar(std::shared_ptr<bout::boundary::BoundaryRegionFCI> bndry,
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 4d4b985a22..aa08c2f043 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -176,7 +176,7 @@ public:
   bool hasBndryLowerY() const override { return false; }
   bool hasBndryUpperY() const override { return false; }
   void addBoundary(BoundaryRegionBase* region) override { boundaries.push_back(region); }
-  std::vector<BoundaryRegionBase*> getBoundaries() override { return boundaries; }
+  std::vector<BoundaryRegionBase*> getBoundaries() const override { return boundaries; }
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType UNUSED(type)) const override {
     return std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>();

From ad16bae0fc208eed81a738b40244be275afa2572 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 11 May 2026 18:21:00 +0100
Subject: [PATCH 1404/1827] Reduce duplication in `Coordinates` helper
 functions

---
 src/mesh/coordinates.cxx | 320 ++++++++++++++-------------------------
 1 file changed, 113 insertions(+), 207 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 623d250445..712c38e87b 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -34,47 +34,36 @@
 #include "parallel/shiftedmetricinterp.hxx"
 
 namespace {
-/// Interpolate a Field2D to a new CELL_LOC with interp_to.
-/// Communicates to set internal guard cells.
-/// Boundary guard cells are set by extrapolating from the grid, like
-/// 'free_o3' boundary conditions
-/// Corner guard cells are set to BoutNaN
-Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extrapolate_x,
-                                  bool extrapolate_y, bool no_extra_interpolate,
-                                  ParallelTransform* UNUSED(pt) = nullptr) {
-
-  Mesh* localmesh = f.getMesh();
-  Field2D result = interp_to(f, location, "RGN_NOBNDRY");
-  // Ensure result's data is unique. Otherwise result might be a duplicate of
-  // f (if no interpolation is needed, e.g. if interpolation is in the
-  // z-direction); then f would be communicated. Since this function is used
-  // on geometrical quantities that might not be periodic in y even on closed
-  // field lines (due to dependence on integrated shear), we don't want to
-  // communicate f. We will sort out result's boundary guard cells below, but
-  // not f's so we don't want to change f.
-  result.allocate();
-  localmesh->communicate_no_slices(result);
+// Extrapolate into boundaries (if requested) so that differential geometry
+// terms can be interpolated if necessary
+// Note: cannot use applyBoundary("free_o3") here because applyBoundary()
+// would try to create a new Coordinates object since we have not finished
+// initializing yet, leading to an infinite recursion.
+// Also, here we interpolate for the boundary points at xstart/ystart and
+// (xend+1)/(yend+1) instead of extrapolating.
+template <class T, typename = bout::utils::EnableIfField<T>>
+void fillGuards_impl(T& result, CELL_LOC location, const T& f, bool extrapolate_x,
+                     bool extrapolate_y, bool no_extra_interpolate = false) {
+  const auto* localmesh = result.getMesh();
+
+  const auto zstart = bout::build::use_metric_3d ? localmesh->zstart : 0;
+  const auto zend = bout::build::use_metric_3d ? localmesh->zend : 0;
 
-  // Extrapolate into boundaries (if requested) so that differential geometry
-  // terms can be interpolated if necessary
-  // Note: cannot use applyBoundary("free_o3") here because applyBoundary()
-  // would try to create a new Coordinates object since we have not finished
-  // initializing yet, leading to an infinite recursion.
-  // Also, here we interpolate for the boundary points at xstart/ystart and
-  // (xend+1)/(yend+1) instead of extrapolating.
   for (auto& newbndry : localmesh->getBoundaries()) {
     auto* bndry = newbndry->getLegacyPointer();
     if ((extrapolate_x and bndry->bx != 0) or (extrapolate_y and bndry->by != 0)) {
-      int extrap_start = 0;
-      if (not no_extra_interpolate) {
-        // Can use no_extra_interpolate argument to skip the extra interpolation when we
-        // want to extrapolate the Christoffel symbol terms which come from derivatives so
-        // don't have the extra point set already
-        if (((location == CELL_XLOW) && (bndry->bx > 0))
-            || ((location == CELL_YLOW) && (bndry->by > 0))) {
-          extrap_start = 1;
-        }
-      }
+      // Can use no_extra_interpolate argument to skip the extra interpolation when we
+      // want to extrapolate the Christoffel symbol terms which come from derivatives so
+      // don't have the extra point set already
+      const bool interpolating_into_x_boundary =
+          ((location == CELL_XLOW) and (bndry->bx > 0));
+      const bool interpolating_into_y_boundary =
+          ((location == CELL_YLOW) and (bndry->by > 0));
+      const int extrap_start =
+          (not no_extra_interpolate)
+                  and (interpolating_into_x_boundary or interpolating_into_y_boundary)
+              ? 1
+              : 0;
       for (bndry->first(); !bndry->isDone(); bndry->next1d()) {
         // interpolate extra boundary point that is missed by interp_to, if
         // necessary.
@@ -86,19 +75,21 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr
           ASSERT1(bndry->bx == 0 or localmesh->xstart > 1);
           ASSERT1(bndry->by == 0 or localmesh->ystart > 1);
           // note that either bx or by is >0 here
-          result(bndry->x, bndry->y) =
-              (9.
-                   * (f(bndry->x - bndry->bx, bndry->y - bndry->by)
-                      + f(bndry->x, bndry->y))
-               - f(bndry->x - (2 * bndry->bx), bndry->y - (2 * bndry->by))
-               - f(bndry->x + bndry->bx, bndry->y + bndry->by))
-              / 16.;
+          for (int zi = zstart; zi <= zend; ++zi) {
+            result(bndry->x, bndry->y, zi) =
+                (9.
+                     * (f(bndry->x - bndry->bx, bndry->y - bndry->by, zi)
+                        + f(bndry->x, bndry->y, zi))
+                 - f(bndry->x - (2 * bndry->bx), bndry->y - (2 * bndry->by), zi)
+                 - f(bndry->x + bndry->bx, bndry->y + bndry->by, zi))
+                / 16.;
+          }
         }
 
         // set boundary guard cells
-        if ((bndry->bx != 0 && localmesh->GlobalNx - 2 * bndry->width >= 3)
+        if ((bndry->bx != 0 && localmesh->GlobalNx - (2 * bndry->width) >= 3)
             || (bndry->by != 0
-                && localmesh->GlobalNy - localmesh->numberOfYBoundaries() * bndry->width
+                && localmesh->GlobalNy - (localmesh->numberOfYBoundaries() * bndry->width)
                        >= 3)) {
           if (bndry->bx != 0 && localmesh->LocalNx == 1 && bndry->width == 1) {
             throw BoutException(
@@ -118,15 +109,20 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr
           for (int i = extrap_start; i < bndry->width; i++) {
             const int xi = bndry->x + (i * bndry->bx);
             const int yi = bndry->y + (i * bndry->by);
-            result(xi, yi) = 3.0 * result(xi - bndry->bx, yi - bndry->by)
-                             - 3.0 * result(xi - 2 * bndry->bx, yi - 2 * bndry->by)
-                             + result(xi - 3 * bndry->bx, yi - 3 * bndry->by);
+            for (int zi = zstart; zi <= zend; ++zi) {
+              result(xi, yi, zi) =
+                  (3.0 * result(xi - bndry->bx, yi - bndry->by, zi))
+                  - (3.0 * result(xi - (2 * bndry->bx), yi - (2 * bndry->by), zi))
+                  + result(xi - (3 * bndry->bx), yi - (3 * bndry->by), zi);
+            }
           }
         } else {
           // not enough grid points to extrapolate, set equal to last grid point
           for (int i = extrap_start; i < bndry->width; i++) {
-            result(bndry->x + i * bndry->bx, bndry->y + i * bndry->by) =
-                result(bndry->x - bndry->bx, bndry->y - bndry->by);
+            for (int zi = zstart; zi <= zend; ++zi) {
+              result(bndry->x + (i * bndry->bx), bndry->y + (i * bndry->by), zi) =
+                  result(bndry->x - bndry->bx, bndry->y - bndry->by, zi);
+            }
           }
         }
       }
@@ -144,36 +140,40 @@ Field2D interpolateAndExtrapolate(const Field2D& f, CELL_LOC location, bool extr
     // Invalidate corner guard cells
     for (int i = 0; i < localmesh->xstart; i++) {
       for (int j = 0; j < localmesh->ystart; j++) {
-        result(i, j) = BoutNaN;
-        result(i, localmesh->LocalNy - 1 - j) = BoutNaN;
-        result(localmesh->LocalNx - 1 - i, j) = BoutNaN;
-        result(localmesh->LocalNx - 1 - i, localmesh->LocalNy - 1 - j) = BoutNaN;
+        for (int k = 0; k < f.getNz(); ++k) {
+          result(i, j, k) = BoutNaN;
+          result(i, localmesh->LocalNy - 1 - j, k) = BoutNaN;
+          result(localmesh->LocalNx - 1 - i, j, k) = BoutNaN;
+          result(localmesh->LocalNx - 1 - i, localmesh->LocalNy - 1 - j, k) = BoutNaN;
+        }
       }
     }
   }
 #endif
-
-  return result;
 }
 
-#if BOUT_USE_METRIC_3D
-Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
-                                  bool extrapolate_x, bool extrapolate_y,
-                                  bool no_extra_interpolate, ParallelTransform* pt_) {
+/// Interpolate a Field2D to a new CELL_LOC with interp_to.
+/// Communicates to set internal guard cells.
+/// Boundary guard cells are set by extrapolating from the grid, like
+/// 'free_o3' boundary conditions
+/// Corner guard cells are set to BoutNaN
+template <class T, typename = bout::utils::EnableIfField<T>>
+auto interpolateAndExtrapolate(const T& f_, CELL_LOC location, bool extrapolate_x,
+                               bool extrapolate_y, bool no_extra_interpolate,
+                               ParallelTransform* pt_ = nullptr) -> T {
 
   Mesh* localmesh = f_.getMesh();
-  Field3D result;
-  Field3D f = f_;
-  ParallelTransform* pt_f;
-  if (f.getCoordinates() == nullptr) {
-    // if input f is member of the Coordinates we are currently constructing, it will not
-    // have Coordinates and needs to use the passed-in ParallelTransform
-    pt_f = pt_;
-  } else {
-    // if input f is from Coordinates at a different location, it will have its own
-    // Coordinates, and we should use its ParallelTransform
-    pt_f = &f.getCoordinates()->getParallelTransform();
-  }
+  T f = f_;
+
+  // If input f is member of the Coordinates we are currently constructing, it will not
+  // have Coordinates and needs to use the passed-in ParallelTransform.
+  // Otherwise, if input f is from Coordinates at a different location, it will have its own
+  // Coordinates, and we should use its ParallelTransform
+  ParallelTransform* pt_f =
+      (not bout::build::use_metric_3d) or f.getCoordinates() == nullptr
+          ? pt_
+          : &f.getCoordinates()->getParallelTransform();
+
   if (f.getDirectionY() != YDirectionType::Standard) {
     if (pt_f->canToFromFieldAligned()) {
       f = pt_f->fromFieldAligned(f);
@@ -181,15 +181,15 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
       f.setDirectionY(YDirectionType::Standard);
     }
   }
+
+  T result;
   if (location == CELL_YLOW and f.getLocation() != CELL_YLOW) {
     auto f_aligned = pt_f->toFieldAligned(f, "RGN_NOX");
     result = interp_to(f_aligned, location, "RGN_NOBNDRY");
-    ParallelTransform* pt_result;
-    if (result.getCoordinates() == nullptr) {
-      pt_result = pt_;
-    } else {
-      pt_result = &result.getCoordinates()->getParallelTransform();
-    }
+    const auto* result_coords = result.getCoordinates();
+    ParallelTransform* pt_result =
+        result_coords == nullptr ? pt_ : &result_coords->getParallelTransform();
+
     result = pt_result->fromFieldAligned(result, "RGN_NOBNDRY");
   } else {
     result = interp_to(f, location, "RGN_NOBNDRY");
@@ -204,114 +204,11 @@ Field3D interpolateAndExtrapolate(const Field3D& f_, CELL_LOC location,
   result.allocate();
   localmesh->communicate_no_slices(result);
 
-  // Extrapolate into boundaries (if requested) so that differential geometry
-  // terms can be interpolated if necessary
-  // Note: cannot use applyBoundary("free_o3") here because applyBoundary()
-  // would try to create a new Coordinates object since we have not finished
-  // initializing yet, leading to an infinite recursion.
-  // Also, here we interpolate for the boundary points at xstart/ystart and
-  // (xend+1)/(yend+1) instead of extrapolating.
-  for (auto& newbndry : localmesh->getBoundaries()) {
-    auto bndry = newbndry->getLegacyPointer();
-    if ((extrapolate_x and bndry->bx != 0) or (extrapolate_y and bndry->by != 0)) {
-      int extrap_start = 0;
-      if (not no_extra_interpolate) {
-        // Can use no_extra_interpolate argument to skip the extra interpolation when we
-        // want to extrapolate the Christoffel symbol terms which come from derivatives so
-        // don't have the extra point set already
-        if ((location == CELL_XLOW) && (bndry->bx > 0)) {
-          extrap_start = 1;
-        } else if ((location == CELL_YLOW) && (bndry->by > 0)) {
-          extrap_start = 1;
-        }
-      }
-      for (bndry->first(); !bndry->isDone(); bndry->next1d()) {
-        // interpolate extra boundary point that is missed by interp_to, if
-        // necessary.
-        // Only interpolate this point if we are actually changing location. E.g.
-        // when we use this function to extrapolate J and Bxy on staggered grids,
-        // this point should already be set correctly because the metric
-        // components have been interpolated to here.
-        if (extrap_start > 0 and f.getLocation() != location) {
-          ASSERT1(bndry->bx == 0 or localmesh->xstart > 1);
-          ASSERT1(bndry->by == 0 or localmesh->ystart > 1);
-          // note that either bx or by is >0 here
-          for (int zi = localmesh->zstart; zi <= localmesh->zend; ++zi) {
-            result(bndry->x, bndry->y, zi) =
-                (9.
-                     * (f(bndry->x - bndry->bx, bndry->y - bndry->by, zi)
-                        + f(bndry->x, bndry->y, zi))
-                 - f(bndry->x - 2 * bndry->bx, bndry->y - 2 * bndry->by, zi)
-                 - f(bndry->x + bndry->bx, bndry->y + bndry->by, zi))
-                / 16.;
-          }
-        }
-        // set boundary guard cells
-        if ((bndry->bx != 0 && localmesh->GlobalNx - 2 * bndry->width >= 3)
-            || (bndry->by != 0 && localmesh->GlobalNy - 2 * bndry->width >= 3)) {
-          if (bndry->bx != 0 && localmesh->LocalNx == 1 && bndry->width == 1) {
-            throw BoutException(
-                "Not enough points in the x-direction on this "
-                "processor for extrapolation needed to use staggered grids. "
-                "Increase number of x-guard cells MXG or decrease number of "
-                "processors in the x-direction NXPE.");
-          }
-          if (bndry->by != 0 && localmesh->LocalNy == 1 && bndry->width == 1) {
-            throw BoutException(
-                "Not enough points in the y-direction on this "
-                "processor for extrapolation needed to use staggered grids. "
-                "Increase number of y-guard cells MYG or decrease number of "
-                "processors in the y-direction NYPE.");
-          }
-          // extrapolate into boundary guard cells if there are enough grid points
-          for (int i = extrap_start; i < bndry->width; i++) {
-            int xi = bndry->x + i * bndry->bx;
-            int yi = bndry->y + i * bndry->by;
-            for (int zi = localmesh->zstart; zi <= localmesh->zend; ++zi) {
-              result(xi, yi, zi) =
-                  3.0 * result(xi - bndry->bx, yi - bndry->by, zi)
-                  - 3.0 * result(xi - 2 * bndry->bx, yi - 2 * bndry->by, zi)
-                  + result(xi - 3 * bndry->bx, yi - 3 * bndry->by, zi);
-            }
-          }
-        } else {
-          // not enough grid points to extrapolate, set equal to last grid point
-          for (int i = extrap_start; i < bndry->width; i++) {
-            for (int zi = localmesh->zstart; zi <= localmesh->zend; ++zi) {
-              result(bndry->x + i * bndry->bx, bndry->y + i * bndry->by, zi) =
-                  result(bndry->x - bndry->bx, bndry->y - bndry->by, zi);
-            }
-          }
-        }
-      }
-    }
-  }
-#if CHECK > 0
-  if (not(
-          // if include_corner_cells=true, then we extrapolate valid data into the
-          // corner cells if they are not already filled
-          localmesh->include_corner_cells
-
-          // if we are not extrapolating at all, the corner cells should contain valid
-          // data
-          or (not extrapolate_x and not extrapolate_y))) {
-    // Invalidate corner guard cells
-    for (int i = 0; i < localmesh->xstart; i++) {
-      for (int j = 0; j < localmesh->ystart; j++) {
-        for (int k = 0; k < localmesh->LocalNz; ++k) {
-          result(i, j, k) = BoutNaN;
-          result(i, localmesh->LocalNy - 1 - j, k) = BoutNaN;
-          result(localmesh->LocalNx - 1 - i, j, k) = BoutNaN;
-          result(localmesh->LocalNx - 1 - i, localmesh->LocalNy - 1 - j, k) = BoutNaN;
-        }
-      }
-    }
-  }
-#endif // CHECK > 0
+  fillGuards_impl(result, location, f, extrapolate_x, extrapolate_y,
+                  no_extra_interpolate);
 
   return result;
 }
-#endif // BOUT_USE_METRIC_3D
 
 // If the CELL_CENTRE variable was read, the staggered version is required to
 // also exist for consistency
@@ -501,7 +398,8 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
                         "cells. Set option extrapolate_y=false to disable this.\n"));
   }
 
-  auto readField = [this, &suffix](const std::string& name, BoutReal def_value) {
+  auto readField = [this, &suffix](const std::string& name,
+                                   BoutReal def_value) -> FieldMetric {
     checkStaggeredGet(localmesh, name, suffix);
 
     FieldMetric field{localmesh};
@@ -513,9 +411,17 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
     return field.setDirectionY(YDirectionType::Standard);
   };
 
-  auto fillGuards = [&, this](const auto& field) {
-    return interpolateAndExtrapolate(field, location, extrapolate_x, extrapolate_y, false,
-                                     transform.get());
+  auto fillGuards = [&, this](FieldMetric& field) {
+    // Passing `field` in here twice is gross but ok because the second argument
+    // is only used when interpolating, and we're not interpolating here
+    fillGuards_impl(field, location, field, extrapolate_x, extrapolate_y);
+  };
+
+  auto readAndFillGuards = [&](const std::string& name,
+                               BoutReal def_value) -> FieldMetric {
+    auto field = readField(name, def_value);
+    fillGuards(field);
+    return field;
   };
 
   {
@@ -528,29 +434,29 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
 
     const auto default_dz = (zmax - zmin) * TWOPI / nz;
 
-    dz = fillGuards(readField("dz", default_dz));
+    dz = readAndFillGuards("dz", default_dz);
   }
 
   // required early for differentiation.
   setParallelTransform(options);
 
-  dx = fillGuards(readField("dx", 1.0));
+  dx = readAndFillGuards("dx", 1.0);
 
   if (localmesh->periodicX) {
     localmesh->communicate_no_slices(dx);
   }
 
-  dy = fillGuards(readField("dy", 1.0));
+  dy = readAndFillGuards("dy", 1.0);
 
   // Diagonal components of metric tensor g^{ij} (default to 1)
-  g11 = fillGuards(readField("g11", 1.0));
-  g22 = fillGuards(readField("g22", 1.0));
-  g33 = fillGuards(readField("g33", 1.0));
+  g11 = readAndFillGuards("g11", 1.0);
+  g22 = readAndFillGuards("g22", 1.0);
+  g33 = readAndFillGuards("g33", 1.0);
 
   // Off-diagonal elements. Default to 0
-  g12 = fillGuards(readField("g12", 0.0));
-  g13 = fillGuards(readField("g13", 0.0));
-  g23 = fillGuards(readField("g23", 0.0));
+  g12 = readAndFillGuards("g12", 0.0);
+  g13 = readAndFillGuards("g13", 0.0);
+  g23 = readAndFillGuards("g23", 0.0);
 
   // Check input metrics
   checkContravariant();
@@ -592,12 +498,12 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   }
   // More robust to extrapolate derived quantities directly, rather than
   // deriving from extrapolated covariant metric components
-  g_11 = fillGuards(g_11);
-  g_22 = fillGuards(g_22);
-  g_33 = fillGuards(g_33);
-  g_12 = fillGuards(g_12);
-  g_13 = fillGuards(g_13);
-  g_23 = fillGuards(g_23);
+  fillGuards(g_11);
+  fillGuards(g_22);
+  fillGuards(g_33);
+  fillGuards(g_12);
+  fillGuards(g_13);
+  fillGuards(g_23);
 
   // Check covariant metrics
   checkCovariant();
@@ -612,7 +518,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
         "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
     J = Jcalc;
   } else {
-    J = fillGuards(J);
+    fillGuards(J);
 
     // Compare calculated and loaded values
     output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(J - Jcalc)));
@@ -638,7 +544,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
     Bxy = Bcalc;
   } else {
 
-    Bxy = fillGuards(Bxy);
+    fillGuards(Bxy);
     output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
   }
 
@@ -651,7 +557,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
         "\tWARNING: No Torsion specified for zShift. Derivatives may not be correct\n");
     ShiftTorsion = 0.0;
   }
-  ShiftTorsion = fillGuards(ShiftTorsion);
+  fillGuards(ShiftTorsion);
 
   //////////////////////////////////////////////////////
 
@@ -659,7 +565,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
     if (localmesh->get(IntShiftTorsion, "IntShiftTorsion", 0.0, false)) {
       output_warn.write("\tWARNING: No Integrated torsion specified\n");
     }
-    IntShiftTorsion = fillGuards(IntShiftTorsion);
+    fillGuards(IntShiftTorsion);
   } else {
     // IntShiftTorsion will not be used, but set to zero to avoid uninitialized field
     IntShiftTorsion = 0.;

From d1a472dab05467be481de96e6111d6254eabcdf8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 11 May 2026 18:27:09 +0100
Subject: [PATCH 1405/1827] Add small helper in `Coordinates` interp ctor

---
 src/mesh/coordinates.cxx | 62 ++++++++++++++++------------------------
 1 file changed, 24 insertions(+), 38 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 712c38e87b..1e1112415c 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -307,67 +307,53 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
           "might require dz!\nPlease provide a dz for the staggered quantity!");
     }
     setParallelTransform(options);
-    dx = interpolateAndExtrapolate(coords_in->dx, location, true, true, false,
-                                   transform.get());
-    dy = interpolateAndExtrapolate(coords_in->dy, location, true, true, false,
-                                   transform.get());
+
+    auto interpField = [&, this](const FieldMetric& f) -> FieldMetric {
+      return interpolateAndExtrapolate(f, location, true, true, false, transform.get());
+    };
+
+    dx = interpField(coords_in->dx);
+    dy = interpField(coords_in->dy);
     // not really needed - we have used dz already ...
-    dz = interpolateAndExtrapolate(coords_in->dz, location, true, true, false,
-                                   transform.get());
+    dz = interpField(coords_in->dz);
 
     // Diagonal components of metric tensor g^{ij}
-    g11 = interpolateAndExtrapolate(coords_in->g11, location, true, true, false,
-                                    transform.get());
-    g22 = interpolateAndExtrapolate(coords_in->g22, location, true, true, false,
-                                    transform.get());
-    g33 = interpolateAndExtrapolate(coords_in->g33, location, true, true, false,
-                                    transform.get());
+    g11 = interpField(coords_in->g11);
+    g22 = interpField(coords_in->g22);
+    g33 = interpField(coords_in->g33);
 
     // Off-diagonal elements.
-    g12 = interpolateAndExtrapolate(coords_in->g12, location, true, true, false,
-                                    transform.get());
-    g13 = interpolateAndExtrapolate(coords_in->g13, location, true, true, false,
-                                    transform.get());
-    g23 = interpolateAndExtrapolate(coords_in->g23, location, true, true, false,
-                                    transform.get());
+    g12 = interpField(coords_in->g12);
+    g13 = interpField(coords_in->g13);
+    g23 = interpField(coords_in->g23);
 
     // 3x3 matrix inversion can exaggerate small interpolation errors, so it is
     // more robust to interpolate and extrapolate derived quantities directly,
     // rather than deriving from interpolated/extrapolated covariant metric
     // components
-    g_11 = interpolateAndExtrapolate(coords_in->g_11, location, true, true, false,
-                                     transform.get());
-    g_22 = interpolateAndExtrapolate(coords_in->g_22, location, true, true, false,
-                                     transform.get());
-    g_33 = interpolateAndExtrapolate(coords_in->g_33, location, true, true, false,
-                                     transform.get());
-    g_12 = interpolateAndExtrapolate(coords_in->g_12, location, true, true, false,
-                                     transform.get());
-    g_13 = interpolateAndExtrapolate(coords_in->g_13, location, true, true, false,
-                                     transform.get());
-    g_23 = interpolateAndExtrapolate(coords_in->g_23, location, true, true, false,
-                                     transform.get());
+    g_11 = interpField(coords_in->g_11);
+    g_22 = interpField(coords_in->g_22);
+    g_33 = interpField(coords_in->g_33);
+    g_12 = interpField(coords_in->g_12);
+    g_13 = interpField(coords_in->g_13);
+    g_23 = interpField(coords_in->g_23);
 
     // Check input metrics
     checkContravariant();
     checkCovariant();
 
-    J = interpolateAndExtrapolate(coords_in->J, location, true, true, false,
-                                  transform.get());
-    Bxy = interpolateAndExtrapolate(coords_in->Bxy, location, true, true, false,
-                                    transform.get());
+    J = interpField(coords_in->J);
+    Bxy = interpField(coords_in->Bxy);
 
     bout::checkFinite(J, "The Jacobian", "RGN_NOCORNERS");
     bout::checkPositive(J, "The Jacobian", "RGN_NOCORNERS");
     bout::checkFinite(Bxy, "Bxy", "RGN_NOCORNERS");
     bout::checkPositive(Bxy, "Bxy", "RGN_NOCORNERS");
 
-    ShiftTorsion = interpolateAndExtrapolate(coords_in->ShiftTorsion, location, true,
-                                             true, false, transform.get());
+    ShiftTorsion = interpField(coords_in->ShiftTorsion);
 
     if (mesh->IncIntShear) {
-      IntShiftTorsion = interpolateAndExtrapolate(coords_in->IntShiftTorsion, location,
-                                                  true, true, false, transform.get());
+      IntShiftTorsion = interpField(coords_in->IntShiftTorsion);
     }
   }
   // Allow transform to fix things up

From 3cb705d020ff4b0a30373907ed137fb25339cbfa Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 11 May 2026 18:30:44 +0100
Subject: [PATCH 1406/1827] Add missing headers

---
 src/mesh/coordinates.cxx | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 1e1112415c..1568688e76 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -9,25 +9,39 @@
 #include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/build_config.hxx>
 #include <bout/build_defines.hxx>
 #include <bout/constants.hxx>
 #include <bout/coordinates.hxx>
+#include <bout/dcomplex.hxx>
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
-#include <bout/field.hxx>
+#include <bout/field2d.hxx>
 #include <bout/globals.hxx>
+#include <bout/index_derivs_interface.hxx>
 #include <bout/interpolation.hxx>
+#include <bout/openmpwrap.hxx>
+#include <bout/options.hxx>
 #include <bout/output.hxx>
 #include <bout/output_bout_types.hxx>
 #include <bout/paralleltransform.hxx>
 #include <bout/region.hxx>
+#include <bout/sys/gettext.hxx>
 #include <bout/sys/timer.hxx>
+#include <bout/traits.hxx>
+#include <bout/unused.hxx>
 #include <bout/utils.hxx>
 #include <bout/yboundary_regions.hxx>
 
+#include <algorithm>
 #include <cmath>
+#include <cstdlib>
+#include <iterator>
 #include <memory>
 #include <string>
+#include <utility>
+
+#include <fmt/format.h>
 
 #include "invert3x3.hxx"
 #include "parallel/fci.hxx"

From 3a44769c894b60fa5580df1649af2d7ef2ae5e4a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 12 May 2026 17:03:56 +0100
Subject: [PATCH 1407/1827] Fix some clang-tidy warnings

---
 src/mesh/coordinates.cxx | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 1568688e76..ad5b1a1df2 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -486,13 +486,13 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
       output_warn.write("Not all covariant components of metric tensor found. "
                         "Calculating all from the contravariant tensor\n");
       /// Calculate contravariant metric components if not found
-      if (calcCovariant("RGN_NOCORNERS")) {
+      if (calcCovariant("RGN_NOCORNERS") != 0) {
         throw BoutException("Error in calcCovariant call");
       }
     }
   } else {
     /// Calculate contravariant metric components if not found
-    if (calcCovariant("RGN_NOCORNERS")) {
+    if (calcCovariant("RGN_NOCORNERS") != 0) {
       throw BoutException("Error in calcCovariant call");
     }
   }
@@ -513,7 +513,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
 
   // Attempt to read J from the grid file
   auto Jcalc = J;
-  if (localmesh->get(J, "J" + suffix, 0.0, false)) {
+  if (localmesh->get(J, "J" + suffix, 0.0, false) != 0) {
     output_warn.write(
         "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
     J = Jcalc;
@@ -538,7 +538,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
 
   // Attempt to read Bxy from the grid file
   auto Bcalc = Bxy;
-  if (localmesh->get(Bxy, "Bxy" + suffix, 0.0, false)) {
+  if (localmesh->get(Bxy, "Bxy" + suffix, 0.0, false) != 0) {
     output_warn.write("\tWARNING: Magnitude of B field 'Bxy' not found. Calculating from "
                       "metric tensor\n");
     Bxy = Bcalc;
@@ -552,7 +552,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   bout::checkFinite(Bxy, "Bxy", "RGN_NOCORNERS");
   bout::checkPositive(Bxy, "Bxy", "RGN_NOCORNERS");
 
-  if (localmesh->get(ShiftTorsion, "ShiftTorsion" + suffix, 0.0, false)) {
+  if (localmesh->get(ShiftTorsion, "ShiftTorsion" + suffix, 0.0, false) != 0) {
     output_warn.write(
         "\tWARNING: No Torsion specified for zShift. Derivatives may not be correct\n");
     ShiftTorsion = 0.0;
@@ -562,7 +562,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   //////////////////////////////////////////////////////
 
   if (localmesh->IncIntShear) {
-    if (localmesh->get(IntShiftTorsion, "IntShiftTorsion", 0.0, false)) {
+    if (localmesh->get(IntShiftTorsion, "IntShiftTorsion", 0.0, false) != 0) {
       output_warn.write("\tWARNING: No Integrated torsion specified\n");
     }
     fillGuards(IntShiftTorsion);
@@ -573,7 +573,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
 }
 
 void Coordinates::outputVars(Options& output_options) {
-  Timer time("io");
+  const Timer time("io");
   const std::string loc_string =
       (location == CELL_CENTRE) ? "" : "_" + toString(location);
 

From 61245ee1dca41239c2426108bd803f0c1825ec30 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 15 May 2026 14:28:56 +0100
Subject: [PATCH 1408/1827] Don't use helper functions to read `dz`

---
 src/mesh/coordinates.cxx | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index ad5b1a1df2..0803a61f04 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -398,6 +398,9 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
                         "cells. Set option extrapolate_y=false to disable this.\n"));
   }
 
+  // Some helper functions that let us avoid passing the same arguments every time
+
+  // Read from the mesh and transform from field aligned if required
   auto readField = [this, &suffix](const std::string& name,
                                    BoutReal def_value) -> FieldMetric {
     checkStaggeredGet(localmesh, name, suffix);
@@ -411,12 +414,14 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
     return field.setDirectionY(YDirectionType::Standard);
   };
 
+  // Just fill in the guard cells (via extrapolation) for an existing field
   auto fillGuards = [&, this](FieldMetric& field) {
     // Passing `field` in here twice is gross but ok because the second argument
     // is only used when interpolating, and we're not interpolating here
     fillGuards_impl(field, location, field, extrapolate_x, extrapolate_y);
   };
 
+  // Read the field, transform if required, and fill in the guards
   auto readAndFillGuards = [&](const std::string& name,
                                BoutReal def_value) -> FieldMetric {
     auto field = readField(name, def_value);
@@ -434,12 +439,20 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
 
     const auto default_dz = (zmax - zmin) * TWOPI / nz;
 
-    dz = readAndFillGuards("dz", default_dz);
+    // We can't use the helper functions here because in 3D we might (always?)
+    // need to transform from field aligned -- which requires dz! So we have to
+    // read it "plain" first...
+    localmesh->get(dz, "dz" + suffix, default_dz, false, location);
   }
 
-  // required early for differentiation.
+  // ...then we can set the transform (required early for differentiation)...
   setParallelTransform(options);
 
+  // ...and finally we can transform/interpolate/fill in guards
+  dz = interpolateAndExtrapolate(dz, location, extrapolate_x, extrapolate_y, false,
+                                 transform.get());
+
+  // everything else from this point on can use our helper functions
   dx = readAndFillGuards("dx", 1.0);
 
   if (localmesh->periodicX) {

From f5c5f6eb9f4bb2a9fd4824df67bd11422cbcbb0d Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 15 May 2026 15:07:37 +0100
Subject: [PATCH 1409/1827] Provide implementation oof
 `FakeGridDataSource::hasVar`

Also make virtual function `const`
---
 include/bout/griddata.hxx         | 21 ++++++++++++---------
 src/mesh/data/gridfromfile.cxx    |  2 +-
 src/mesh/data/gridfromoptions.cxx |  4 +++-
 tests/unit/fake_mesh.hxx          |  2 +-
 4 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/include/bout/griddata.hxx b/include/bout/griddata.hxx
index 29a32e5779..fd913a27f1 100644
--- a/include/bout/griddata.hxx
+++ b/include/bout/griddata.hxx
@@ -28,12 +28,15 @@ class GridDataSource;
 #ifndef BOUT_GRIDDATA_H
 #define BOUT_GRIDDATA_H
 
-#include "mesh.hxx"
-#include "bout/bout_types.hxx"
-#include "bout/options.hxx"
-
+#include <bout/bout_types.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
+#include <bout/mesh.hxx>
+#include <bout/options.hxx>
+#include <bout/unused.hxx>
+
+#include <string>
+#include <vector>
 
 /// Interface class to serve grid data
 /*!
@@ -46,8 +49,8 @@ public:
   GridDataSource(const bool source_is_file = false) : is_file(source_is_file) {}
   virtual ~GridDataSource() = default;
 
-  virtual bool
-  hasVar(const std::string& name) = 0; ///< Test if source can supply a variable
+  /// Test if source can supply a variable
+  virtual bool hasVar(const std::string& name) const = 0;
 
   /// Get a string
   virtual bool get(Mesh* m, std::string& sval, const std::string& name,
@@ -95,9 +98,9 @@ class GridFile : public GridDataSource {
 public:
   GridFile() = delete;
   GridFile(std::string gridfilename);
-  ~GridFile() = default;
+  ~GridFile() override = default;
 
-  bool hasVar(const std::string& name) override;
+  bool hasVar(const std::string& name) const override;
 
   /// Get a string
   bool get(Mesh* m, std::string& sval, const std::string& name,
@@ -178,7 +181,7 @@ public:
   /*!
    * Checks if the options has a given variable
    */
-  bool hasVar(const std::string& name) override;
+  bool hasVar(const std::string& name) const override;
 
   /*!
    * Reads strings from options. Uses Options::get to handle
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 27ad9411c2..56b4155e20 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -32,7 +32,7 @@ GridFile::GridFile(std::string gridfilename)
  * Tests whether a variable exists in the file
  *
  */
-bool GridFile::hasVar(const std::string& name) { return data.isSet(name); }
+bool GridFile::hasVar(const std::string& name) const { return data.isSet(name); }
 
 /*!
  * Read a string from file. If the string is not
diff --git a/src/mesh/data/gridfromoptions.cxx b/src/mesh/data/gridfromoptions.cxx
index 662329c526..7d21548340 100644
--- a/src/mesh/data/gridfromoptions.cxx
+++ b/src/mesh/data/gridfromoptions.cxx
@@ -7,7 +7,9 @@
 
 using bout::generator::Context;
 
-bool GridFromOptions::hasVar(const std::string& name) { return options->isSet(name); }
+bool GridFromOptions::hasVar(const std::string& name) const {
+  return options->isSet(name);
+}
 
 namespace {
 /// Return value of \p name in \p options, using \p def as a default
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index aa08c2f043..810e04cbb2 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -284,7 +284,7 @@ public:
   /// Take an rvalue (e.g. initializer list), convert to lvalue and delegate constructor
   FakeGridDataSource(Options&& values) : FakeGridDataSource(values) {}
 
-  bool hasVar(const std::string& UNUSED(name)) override { return false; }
+  bool hasVar(const std::string& name) const override { return values.isSet(name); }
 
   bool get([[maybe_unused]] Mesh* m, std::string& sval, const std::string& name,
            const std::string& def = "") override {

From 45c3ab1bd5db22cef26cb63363acca9728defdd3 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 15 May 2026 15:31:01 +0100
Subject: [PATCH 1410/1827] Small refactor to reading J/Bxy

---
 src/mesh/coordinates.cxx | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 0803a61f04..0572205e96 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -525,21 +525,21 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   jacobian();
 
   // Attempt to read J from the grid file
-  auto Jcalc = J;
-  if (localmesh->get(J, "J" + suffix, 0.0, false) != 0) {
-    output_warn.write(
-        "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
-    J = Jcalc;
-  } else {
-    fillGuards(J);
-
-    // Compare calculated and loaded values
+  if (localmesh->sourceHasVar("J" + suffix)) {
+    // Copy value previously calculated from metric components, use to check
+    // read in value
+    const auto Jcalc = J;
+    J = readAndFillGuards("J", 0.0);
     output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(J - Jcalc)));
 
     localmesh->communicate_no_slices(J);
 
     // Re-evaluate Bxy using new J
     Bxy = sqrt(g_22) / J;
+    fillGuards(Bxy);
+  } else {
+    output_warn.write(
+        "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
   }
 
   // Check jacobian
@@ -550,15 +550,15 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   }
 
   // Attempt to read Bxy from the grid file
-  auto Bcalc = Bxy;
-  if (localmesh->get(Bxy, "Bxy" + suffix, 0.0, false) != 0) {
+  if (localmesh->sourceHasVar("Bxy" + suffix)) {
+    // Copy value previously calculated from J, use to check read in value
+    const auto Bcalc = Bxy;
+    Bxy = readAndFillGuards("Bxy", 0.0);
+    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
+
+  } else {
     output_warn.write("\tWARNING: Magnitude of B field 'Bxy' not found. Calculating from "
                       "metric tensor\n");
-    Bxy = Bcalc;
-  } else {
-
-    fillGuards(Bxy);
-    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
   }
 
   // Check Bxy

From bf32c5bd30180d26191b7e459c9e061d131fec54 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 15 Jun 2026 14:23:15 +0100
Subject: [PATCH 1411/1827] Workaround `Mesh::sourceHasVar` not checking var
 dimensions

---
 src/mesh/coordinates.cxx | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 0572205e96..48dca145bc 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -524,8 +524,16 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   // Calculate Jacobian and Bxy
   jacobian();
 
+  // Mesh::sourceHasVar is (currently) insufficient to check whether we can
+  // actually read a variable because it might be present but have the wrong
+  // size, so we have to attempt to read it
+  auto source_has_var = [&suffix, this](const std::string& name) -> bool {
+    FieldMetric var{localmesh};
+    return localmesh->get(var, name + suffix, 0.0, false) == 0;
+  };
+
   // Attempt to read J from the grid file
-  if (localmesh->sourceHasVar("J" + suffix)) {
+  if (source_has_var("J")) {
     // Copy value previously calculated from metric components, use to check
     // read in value
     const auto Jcalc = J;
@@ -550,7 +558,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   }
 
   // Attempt to read Bxy from the grid file
-  if (localmesh->sourceHasVar("Bxy" + suffix)) {
+  if (source_has_var("Bxy")) {
     // Copy value previously calculated from J, use to check read in value
     const auto Bcalc = Bxy;
     Bxy = readAndFillGuards("Bxy", 0.0);

From 054aa9c8535a972938cde4c853fe993a44a9183a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 18 Jun 2026 14:49:37 +0100
Subject: [PATCH 1412/1827] Revert "Small refactor to reading J/Bxy"

This reverts commit 5c6c1c6903ffa45caafaec071ddbe28069ecffdb.
---
 src/mesh/coordinates.cxx | 40 ++++++++++++++++------------------------
 1 file changed, 16 insertions(+), 24 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 48dca145bc..0803a61f04 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -524,30 +524,22 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   // Calculate Jacobian and Bxy
   jacobian();
 
-  // Mesh::sourceHasVar is (currently) insufficient to check whether we can
-  // actually read a variable because it might be present but have the wrong
-  // size, so we have to attempt to read it
-  auto source_has_var = [&suffix, this](const std::string& name) -> bool {
-    FieldMetric var{localmesh};
-    return localmesh->get(var, name + suffix, 0.0, false) == 0;
-  };
-
   // Attempt to read J from the grid file
-  if (source_has_var("J")) {
-    // Copy value previously calculated from metric components, use to check
-    // read in value
-    const auto Jcalc = J;
-    J = readAndFillGuards("J", 0.0);
+  auto Jcalc = J;
+  if (localmesh->get(J, "J" + suffix, 0.0, false) != 0) {
+    output_warn.write(
+        "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
+    J = Jcalc;
+  } else {
+    fillGuards(J);
+
+    // Compare calculated and loaded values
     output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(J - Jcalc)));
 
     localmesh->communicate_no_slices(J);
 
     // Re-evaluate Bxy using new J
     Bxy = sqrt(g_22) / J;
-    fillGuards(Bxy);
-  } else {
-    output_warn.write(
-        "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
   }
 
   // Check jacobian
@@ -558,15 +550,15 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   }
 
   // Attempt to read Bxy from the grid file
-  if (source_has_var("Bxy")) {
-    // Copy value previously calculated from J, use to check read in value
-    const auto Bcalc = Bxy;
-    Bxy = readAndFillGuards("Bxy", 0.0);
-    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
-
-  } else {
+  auto Bcalc = Bxy;
+  if (localmesh->get(Bxy, "Bxy" + suffix, 0.0, false) != 0) {
     output_warn.write("\tWARNING: Magnitude of B field 'Bxy' not found. Calculating from "
                       "metric tensor\n");
+    Bxy = Bcalc;
+  } else {
+
+    fillGuards(Bxy);
+    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
   }
 
   // Check Bxy

From 91156953f26ba83a5572123b604327df0c6583ec Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 18 Jun 2026 14:51:20 +0100
Subject: [PATCH 1413/1827] Fix comment

[skip ci]
---
 src/mesh/coordinates.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 0803a61f04..ec4248c994 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -166,7 +166,7 @@ void fillGuards_impl(T& result, CELL_LOC location, const T& f, bool extrapolate_
 #endif
 }
 
-/// Interpolate a Field2D to a new CELL_LOC with interp_to.
+/// Interpolate a Field to a new CELL_LOC with interp_to.
 /// Communicates to set internal guard cells.
 /// Boundary guard cells are set by extrapolating from the grid, like
 /// 'free_o3' boundary conditions

From 78e8f0a3abf965bb575368a0a96b9ba627378693 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 18 Jun 2026 16:23:39 +0100
Subject: [PATCH 1414/1827] Ensure `J,Bxy` are unaligned when read from file

---
 src/mesh/coordinates.cxx | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index ec4248c994..613eab5866 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -400,13 +400,8 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
 
   // Some helper functions that let us avoid passing the same arguments every time
 
-  // Read from the mesh and transform from field aligned if required
-  auto readField = [this, &suffix](const std::string& name,
-                                   BoutReal def_value) -> FieldMetric {
-    checkStaggeredGet(localmesh, name, suffix);
-
-    FieldMetric field{localmesh};
-    localmesh->get(field, name + suffix, def_value, false, location);
+  // Ensure that we have an unaligned field, transforming if necessary
+  auto ensuredUnaligned = [this](FieldMetric& field) -> FieldMetric {
     if (field.getDirectionY() == YDirectionType::Aligned
         and transform->canToFromFieldAligned()) {
       return transform->fromFieldAligned(field);
@@ -414,6 +409,16 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
     return field.setDirectionY(YDirectionType::Standard);
   };
 
+  // Read from the mesh and transform from field aligned if required
+  auto readField = [this, &suffix, ensuredUnaligned](const std::string& name,
+                                                     BoutReal def_value) -> FieldMetric {
+    checkStaggeredGet(localmesh, name, suffix);
+
+    FieldMetric field{localmesh};
+    localmesh->get(field, name + suffix, def_value, false, location);
+    return ensuredUnaligned(field);
+  };
+
   // Just fill in the guard cells (via extrapolation) for an existing field
   auto fillGuards = [&, this](FieldMetric& field) {
     // Passing `field` in here twice is gross but ok because the second argument
@@ -531,6 +536,8 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
         "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
     J = Jcalc;
   } else {
+    checkStaggeredGet(localmesh, "J", suffix);
+    J = ensuredUnaligned(J);
     fillGuards(J);
 
     // Compare calculated and loaded values
@@ -556,7 +563,8 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
                       "metric tensor\n");
     Bxy = Bcalc;
   } else {
-
+    checkStaggeredGet(localmesh, "Bxy", suffix);
+    Bxy = ensuredUnaligned(Bxy);
     fillGuards(Bxy);
     output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
   }

From 0642f30b02878b937c90ec497f993375b32ded40 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 19 Jun 2026 12:01:29 +0100
Subject: [PATCH 1415/1827] Apply cmake-format formatting

---
 tests/integrated/test-multigrid_laplace/CMakeLists.txt | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/tests/integrated/test-multigrid_laplace/CMakeLists.txt b/tests/integrated/test-multigrid_laplace/CMakeLists.txt
index b478a8a12a..b64b0e166c 100644
--- a/tests/integrated/test-multigrid_laplace/CMakeLists.txt
+++ b/tests/integrated/test-multigrid_laplace/CMakeLists.txt
@@ -2,12 +2,8 @@ bout_add_integrated_test(
   test-multigrid-laplace
   SOURCES test_multigrid_laplace.cxx
   CONFLICTS BOUT_USE_METRIC_3D
-  USE_RUNTEST
-  USE_DATA_BOUT_INP
-  EXTRA_FILES
-    data/BOUT_jy4.inp
-    data/BOUT_jy63.inp
-    data/BOUT_jy127.inp
-    data/BOUT_unsheared.inp
+  USE_RUNTEST USE_DATA_BOUT_INP
+  EXTRA_FILES data/BOUT_jy4.inp data/BOUT_jy63.inp data/BOUT_jy127.inp
+              data/BOUT_unsheared.inp
   PROCESSORS 3
 )

From 58397e0a2af834afb2fbb200a23abb97ac40cd41 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 1 Dec 2025 15:00:20 +0000
Subject: [PATCH 1416/1827] Remove unused `Context` constructor

---
 include/bout/sys/generator_context.hxx | 3 ---
 src/sys/generator_context.cxx          | 3 ---
 2 files changed, 6 deletions(-)

diff --git a/include/bout/sys/generator_context.hxx b/include/bout/sys/generator_context.hxx
index bbe60fab65..528b96113d 100644
--- a/include/bout/sys/generator_context.hxx
+++ b/include/bout/sys/generator_context.hxx
@@ -27,9 +27,6 @@ public:
   ///
   Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t);
 
-  /// Specify the values directly
-  Context(BoutReal x, BoutReal y, BoutReal z, Mesh* msh, BoutReal t);
-
   /// If constructed without parameters, contains no values (null).
   /// Requesting x,y,z or t throws an exception
   Context() = default;
diff --git a/src/sys/generator_context.cxx b/src/sys/generator_context.cxx
index 31a5662378..6088f99fbd 100644
--- a/src/sys/generator_context.cxx
+++ b/src/sys/generator_context.cxx
@@ -45,8 +45,5 @@ Context::Context(const BoundaryRegion* bndry, int iz, CELL_LOC loc, BoutReal t,
   parameters["t"] = t;
 }
 
-Context::Context(BoutReal x, BoutReal y, BoutReal z, Mesh* msh, BoutReal t)
-    : localmesh(msh), parameters{{"x", x}, {"y", y}, {"z", z}, {"t", t}} {}
-
 } // namespace generator
 } // namespace bout

From ab96f260fde8fe6b958e8370349ad63687665037 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 2 Dec 2025 12:59:00 +0000
Subject: [PATCH 1417/1827] Add cell indices to `generator::Context`

---
 include/bout/sys/generator_context.hxx | 10 +++++++++-
 src/sys/generator_context.cxx          | 19 ++++++++-----------
 2 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/include/bout/sys/generator_context.hxx b/include/bout/sys/generator_context.hxx
index 528b96113d..a5dd9d236a 100644
--- a/include/bout/sys/generator_context.hxx
+++ b/include/bout/sys/generator_context.hxx
@@ -24,7 +24,6 @@ public:
       : Context(i.x(), i.y(), 0, (loc == CELL_ZLOW) ? CELL_CENTRE : loc, msh, t) {}
 
   /// Specify a cell index, together with the cell location, mesh and time
-  ///
   Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t);
 
   /// If constructed without parameters, contains no values (null).
@@ -41,6 +40,11 @@ public:
   BoutReal z() const { return get("z"); }
   BoutReal t() const { return get("t"); }
 
+  /// Cell indices
+  int ix() const { return ix_; }
+  int jy() const { return jy_; }
+  int kz() const { return kz_;}
+
   /// Set the value of a parameter with given name
   Context& set(const std::string& name, BoutReal value) {
     parameters[name] = value;
@@ -73,6 +77,10 @@ public:
   }
 
 private:
+  int ix_{0};
+  int jy_{0};
+  int kz_{0};
+
   Mesh* localmesh{nullptr}; ///< The mesh on which the position is defined
 
   /// Contains user-set values which can be set and retrieved
diff --git a/src/sys/generator_context.cxx b/src/sys/generator_context.cxx
index 6088f99fbd..01090daa51 100644
--- a/src/sys/generator_context.cxx
+++ b/src/sys/generator_context.cxx
@@ -9,7 +9,7 @@ namespace bout {
 namespace generator {
 
 Context::Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t)
-    : localmesh(msh) {
+    : ix_(ix), jy_(iy), kz_(iz), localmesh(msh) {
 
   parameters["x"] = (loc == CELL_XLOW) ? 0.5 * (msh->GlobalX(ix) + msh->GlobalX(ix - 1))
                                        : msh->GlobalX(ix);
@@ -24,20 +24,17 @@ Context::Context(int ix, int iy, int iz, CELL_LOC loc, Mesh* msh, BoutReal t)
 }
 
 Context::Context(const BoundaryRegion* bndry, int iz, CELL_LOC loc, BoutReal t, Mesh* msh)
-    : localmesh(msh) {
-
-  // Add one to X index if boundary is in -x direction, so that XLOW is on the boundary
-  const int ix = (bndry->bx < 0) ? bndry->x + 1 : bndry->x;
+    : // Add one to X index if boundary is in -x direction, so that XLOW is on the boundary
+      ix_((bndry->bx < 0) ? bndry->x + 1 : bndry->x),
+      jy_((bndry->by < 0) ? bndry->y + 1 : bndry->y), kz_(iz), localmesh(msh) {
 
   parameters["x"] = ((loc == CELL_XLOW) || (bndry->bx != 0))
-                        ? 0.5 * (msh->GlobalX(ix) + msh->GlobalX(ix - 1))
-                        : msh->GlobalX(ix);
-
-  const int iy = (bndry->by < 0) ? bndry->y + 1 : bndry->y;
+                        ? 0.5 * (msh->GlobalX(ix_) + msh->GlobalX(ix_ - 1))
+                        : msh->GlobalX(ix_);
 
   parameters["y"] = ((loc == CELL_YLOW) || (bndry->by != 0))
-                        ? PI * (msh->GlobalY(iy) + msh->GlobalY(iy - 1))
-                        : TWOPI * msh->GlobalY(iy);
+                        ? PI * (msh->GlobalY(jy_) + msh->GlobalY(jy_ - 1))
+                        : TWOPI * msh->GlobalY(jy_);
 
   parameters["z"] = (loc == CELL_ZLOW) ? PI * (msh->GlobalZ(iz) + msh->GlobalZ(iz - 1))
                                        : TWOPI * msh->GlobalZ(iz);

From c5ef3d1d40621a2278e294fba75b4594bd569d7a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 2 Dec 2025 13:28:48 +0000
Subject: [PATCH 1418/1827] Add ability to use variables from grid files in
 input expressions

---
 src/field/field_factory.cxx             | 48 ++++++++++++++++++++++---
 src/field/fieldgenerators.hxx           | 28 +++++++++++++++
 tests/unit/field/test_field_factory.cxx | 37 +++++++++++++++++++
 3 files changed, 108 insertions(+), 5 deletions(-)

diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index 188a64cf0c..3e671b5c93 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -19,20 +19,24 @@
  * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
  *
  **************************************************************************/
-#include <bout/globals.hxx>
 
 #include <bout/field_factory.hxx>
 
-#include <cmath>
-
+#include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
+#include <bout/globals.hxx>
 #include <bout/output.hxx>
 #include <bout/utils.hxx>
 
-#include "bout/constants.hxx"
-
 #include "fieldgenerators.hxx"
 
+#include <algorithm>
+#include <cmath>
+#include <iterator>
+#include <memory>
+#include <string>
+#include <vector>
+
 using bout::generator::Context;
 
 /// Helper function to create a FieldValue generator from a BoutReal
@@ -80,6 +84,16 @@ class FieldIndirect : public FieldGenerator {
 
   FieldGeneratorPtr target;
 };
+
+// Split a string on commas and trim whitespace from the results
+auto trimsplit(const std::string& str) -> std::vector<std::string> {
+  auto split = strsplit(str, ',');
+  std::vector<std::string> result{};
+  result.reserve(split.size());
+  std::transform(split.begin(), split.end(), std::back_inserter(result),
+                 [](const std::string& element) { return trim(element); });
+  return result;
+}
 } // namespace
 
 //////////////////////////////////////////////////////////
@@ -122,6 +136,30 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
         nonconst_options["input"]["max_recursion_depth"].as<std::string>());
   }
 
+  const auto field_variables =
+      nonconst_options["input"]["field_variables"]
+          .doc("Variables to read from the grid file and make available in expressions. "
+               "Comma-separated list of variable names")
+          .withDefault<std::string>("");
+
+  if (not field_variables.empty()) {
+    if (not localmesh->isDataSourceGridFile()) {
+      throw BoutException("A grid file ('mesh:file') is required for `field_variables`");
+    }
+
+    for (const auto& name : trimsplit(field_variables)) {
+      if (not localmesh->sourceHasVar(name)) {
+        const auto filename = Options::root()["mesh"]["file"].as<std::string>();
+        throw BoutException(
+            "Grid file '{}' missing `{}` specified in `input:field_variables`", filename,
+            name);
+      }
+      Field3D var;
+      localmesh->get(var, name);
+      addGenerator(name, std::make_shared<Field3DVariable>(var, name));
+    }
+  }
+
   // Useful values
   addGenerator("pi", std::make_shared<FieldValue>(PI));
   addGenerator("π", std::make_shared<FieldValue>(PI));
diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index 050e335448..9b46aea6d3 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -8,10 +8,14 @@
 #define BOUT_FIELDGENERATORS_H
 
 #include <bout/boutexception.hxx>
+#include <bout/field3d.hxx>
 #include <bout/field_factory.hxx>
+#include <bout/sys/expressionparser.hxx>
 #include <bout/unused.hxx>
 
 #include <cmath>
+#include <memory>
+#include <string>
 
 //////////////////////////////////////////////////////////
 // Generators from values
@@ -377,4 +381,28 @@ public:
   }
 };
 
+/// A `Field3D` that can be used in expressions
+class Field3DVariable : public FieldGenerator {
+public:
+  Field3DVariable(Field3D var, std::string name)
+      : variable(std::move(var)), name(std::move(name)) {}
+
+  double generate(const bout::generator::Context& ctx) override {
+    return variable(ctx.ix(), ctx.jy(), ctx.kz());
+  }
+
+  FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
+    if (args.size() != 0) {
+      throw ParseException("Variable '{}' takes no arguments but got {:d}", args.size());
+    }
+    return std::make_shared<Field3DVariable>(variable, name);
+  }
+
+  std::string str() const override { return name; }
+
+private:
+  Field3D variable;
+  std::string name;
+};
+
 #endif // BOUT_FIELDGENERATORS_H
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index b45206b979..8a02033f01 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -1,17 +1,21 @@
 #include "gtest/gtest.h"
 
+#include "fake_mesh.hxx"
 #include "test_extras.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/constants.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
+#include "bout/globals.hxx"
 #include "bout/mesh.hxx"
+#include "bout/options_io.hxx"
 #include "bout/output.hxx"
 #include "bout/paralleltransform.hxx"
 #include "bout/traits.hxx"
 
 #include "fake_mesh_fixture.hxx"
+#include "test_tmpfiles.hxx"
 
 // The unit tests use the global mesh
 using namespace bout::globals;
@@ -1027,3 +1031,36 @@ TYPED_TEST(FieldFactoryCreationTest, CreatePeriodicYacrossSeparatrix) {
 
   EXPECT_TRUE(IsFieldEqual(output, expected));
 }
+
+struct FieldFactoryFieldVariableTest : public FakeMeshFixture {
+  WithQuietOutput quiet{output_info};
+};
+
+TEST_F(FieldFactoryFieldVariableTest, CreateField3D) {
+  bout::testing::TempFile filename;
+
+  {
+    // Write some fields to a grid file
+    FieldFactory factory{mesh};
+    const auto rho = factory.create3D("sqrt(x^2 + y^2)");
+    const auto theta = factory.create3D("atan(y, x)");
+    Options grid{{"rho", rho},
+                 {"theta", theta},
+                 {"nx", mesh->LocalNx},
+                 {"ny", mesh->LocalNy},
+                 {"nz", mesh->LocalNz}};
+    bout::OptionsIO::create(filename)->write(grid);
+  }
+
+  {
+    Options options{{"mesh", {{"file", filename.string()}}},
+                    {"input", {{"field_variables", "rho, theta"}}}};
+
+    dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
+    auto factory = FieldFactory{mesh, &options};
+
+    const auto output = factory.create3D("rho * cos(theta)");
+    const auto x = factory.create3D("x");
+    EXPECT_TRUE(IsFieldEqual(output, x));
+  }
+}

From a843556c656e0a4f2ebe982ab995ecdfc8e4425c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 2 Dec 2025 13:29:18 +0000
Subject: [PATCH 1419/1827] tests: Only remove temp files if test passes

---
 tests/unit/test_tmpfiles.hxx | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/tests/unit/test_tmpfiles.hxx b/tests/unit/test_tmpfiles.hxx
index 6c37e7c792..db7387bb45 100644
--- a/tests/unit/test_tmpfiles.hxx
+++ b/tests/unit/test_tmpfiles.hxx
@@ -1,5 +1,6 @@
 #pragma once
 
+#include <exception>
 #include <filesystem>
 #include <fmt/core.h>
 #include <string>
@@ -30,7 +31,11 @@ public:
   TempFile& operator=(const TempFile&) = delete;
   TempFile& operator=(TempFile&&) = delete;
 
-  ~TempFile() { std::filesystem::remove_all(filename); }
+  ~TempFile() {
+    if (std::uncaught_exceptions() <= 0) {
+      std::filesystem::remove_all(filename);
+    }
+  }
 
   // Enable conversions to std::string / const char*
   operator std::string() const { return filename.string(); }

From 7c44c66752b32d4b8f9c9f87b434566a3b4c0284 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 2 Dec 2025 16:06:24 +0000
Subject: [PATCH 1420/1827] Enable reading `Field2D`s as well as `Field3D`s for
 expressions

---
 manual/sphinx/user_docs/input_grids.rst | 13 ++----
 src/field/field_factory.cxx             | 61 +++++++++++++++----------
 src/field/fieldgenerators.hxx           | 15 +++---
 tests/unit/field/test_field_factory.cxx | 60 +++++++++++++++++++++++-
 4 files changed, 109 insertions(+), 40 deletions(-)

diff --git a/manual/sphinx/user_docs/input_grids.rst b/manual/sphinx/user_docs/input_grids.rst
index 402fb30d06..2c17411141 100644
--- a/manual/sphinx/user_docs/input_grids.rst
+++ b/manual/sphinx/user_docs/input_grids.rst
@@ -156,19 +156,16 @@ these are the only quantities specified, then the coordinates revert to
 Cartesian.
 
 You can read additional quantities from the grid and make them available in
-expressions in the input file by listing them in the ``input:grid_variables``
-section, with the key being the name in the grid file (``mesh:file``) and the
-value being the type (one of ``field3d``, ``field2d``, ``boutreal``):
+expressions in the input file using ``input:read_Field3Ds`` and
+``input:read_Field2Ds``:
 
 .. code-block:: cfg
 
-   [input:grid_variables]
-   rho = field2d
-   theta = field2d
-   scale = boutreal
+   [input]
+   read_Field2Ds = rho, theta
 
    [mesh]
-   B = (scale / rho) * cos(theta)
+   B = (1 / rho) * cos(theta)
 
 This section describes how to generate inputs for tokamak equilibria. If
 you’re not interested in tokamaks then you can skip to the next section.
diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index 3e671b5c93..e9dbc0c804 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -24,8 +24,12 @@
 
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/fieldperp.hxx>
 #include <bout/globals.hxx>
 #include <bout/output.hxx>
+#include <bout/traits.hxx>
 #include <bout/utils.hxx>
 
 #include "fieldgenerators.hxx"
@@ -94,6 +98,35 @@ auto trimsplit(const std::string& str) -> std::vector<std::string> {
                  [](const std::string& element) { return trim(element); });
   return result;
 }
+
+// Read variables from the grid file and make them available in expressions
+template <class T>
+auto read_grid_variables(FieldFactory& factory, Mesh& mesh, Options& options,
+                         const std::string& option_name) {
+  const auto field_variables =
+      options["input"][option_name]
+          .doc("Variables to read from the grid file and make available in expressions. "
+               "Comma-separated list of variable names")
+          .withDefault<std::string>("");
+
+  if (not field_variables.empty()) {
+    if (not mesh.isDataSourceGridFile()) {
+      throw BoutException("A grid file ('mesh:file') is required for `input:{}`",
+                          option_name);
+    }
+
+    for (const auto& name : trimsplit(field_variables)) {
+      if (not mesh.sourceHasVar(name)) {
+        const auto filename = Options::root()["mesh"]["file"].as<std::string>();
+        throw BoutException("Grid file '{}' missing `{}` specified in `input:{}`",
+                            filename, name, option_name);
+      }
+      T var;
+      mesh.get(var, name);
+      factory.addGenerator(name, std::make_shared<GridVariable<T>>(var, name));
+    }
+  }
+}
 } // namespace
 
 //////////////////////////////////////////////////////////
@@ -136,30 +169,6 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
         nonconst_options["input"]["max_recursion_depth"].as<std::string>());
   }
 
-  const auto field_variables =
-      nonconst_options["input"]["field_variables"]
-          .doc("Variables to read from the grid file and make available in expressions. "
-               "Comma-separated list of variable names")
-          .withDefault<std::string>("");
-
-  if (not field_variables.empty()) {
-    if (not localmesh->isDataSourceGridFile()) {
-      throw BoutException("A grid file ('mesh:file') is required for `field_variables`");
-    }
-
-    for (const auto& name : trimsplit(field_variables)) {
-      if (not localmesh->sourceHasVar(name)) {
-        const auto filename = Options::root()["mesh"]["file"].as<std::string>();
-        throw BoutException(
-            "Grid file '{}' missing `{}` specified in `input:field_variables`", filename,
-            name);
-      }
-      Field3D var;
-      localmesh->get(var, name);
-      addGenerator(name, std::make_shared<Field3DVariable>(var, name));
-    }
-  }
-
   // Useful values
   addGenerator("pi", std::make_shared<FieldValue>(PI));
   addGenerator("π", std::make_shared<FieldValue>(PI));
@@ -217,6 +226,10 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
 
   // Periodic in the Y direction?
   addGenerator("is_periodic_y", std::make_shared<FieldPeriodicY>());
+
+  // Variables from the grid file
+  read_grid_variables<Field3D>(*this, *localmesh, nonconst_options, "read_Field3Ds");
+  read_grid_variables<Field2D>(*this, *localmesh, nonconst_options, "read_Field2Ds");
 }
 
 Field2D FieldFactory::create2D(const std::string& value, const Options* opt,
diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index 9b46aea6d3..49b2cb9690 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -8,9 +8,9 @@
 #define BOUT_FIELDGENERATORS_H
 
 #include <bout/boutexception.hxx>
-#include <bout/field3d.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/sys/expressionparser.hxx>
+#include <bout/traits.hxx>
 #include <bout/unused.hxx>
 
 #include <cmath>
@@ -311,7 +311,7 @@ public:
   // Constructor
   FieldTanhHat(FieldGeneratorPtr xin, FieldGeneratorPtr widthin,
                FieldGeneratorPtr centerin, FieldGeneratorPtr steepnessin)
-      : X(xin), width(widthin), center(centerin), steepness(steepnessin){};
+      : X(xin), width(widthin), center(centerin), steepness(steepnessin) {};
   // Clone containing the list of arguments
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override;
   BoutReal generate(const bout::generator::Context& pos) override;
@@ -326,7 +326,7 @@ private:
 class FieldWhere : public FieldGenerator {
 public:
   FieldWhere(FieldGeneratorPtr test, FieldGeneratorPtr gt0, FieldGeneratorPtr lt0)
-      : test(test), gt0(gt0), lt0(lt0){};
+      : test(test), gt0(gt0), lt0(lt0) {};
 
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 3) {
@@ -382,9 +382,10 @@ public:
 };
 
 /// A `Field3D` that can be used in expressions
-class Field3DVariable : public FieldGenerator {
+template <class T, typename = bout::utils::EnableIfField<T>>
+class GridVariable : public FieldGenerator {
 public:
-  Field3DVariable(Field3D var, std::string name)
+  GridVariable(T var, std::string name)
       : variable(std::move(var)), name(std::move(name)) {}
 
   double generate(const bout::generator::Context& ctx) override {
@@ -395,13 +396,13 @@ public:
     if (args.size() != 0) {
       throw ParseException("Variable '{}' takes no arguments but got {:d}", args.size());
     }
-    return std::make_shared<Field3DVariable>(variable, name);
+    return std::make_shared<GridVariable<T>>(variable, name);
   }
 
   std::string str() const override { return name; }
 
 private:
-  Field3D variable;
+  T variable;
   std::string name;
 };
 
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index 8a02033f01..1f88d9ce7e 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -1054,7 +1054,7 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField3D) {
 
   {
     Options options{{"mesh", {{"file", filename.string()}}},
-                    {"input", {{"field_variables", "rho, theta"}}}};
+                    {"input", {{"read_Field3Ds", "rho, theta"}}}};
 
     dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
     auto factory = FieldFactory{mesh, &options};
@@ -1064,3 +1064,61 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField3D) {
     EXPECT_TRUE(IsFieldEqual(output, x));
   }
 }
+
+TEST_F(FieldFactoryFieldVariableTest, CreateField2D) {
+  bout::testing::TempFile filename;
+
+  {
+    // Write some fields to a grid file
+    FieldFactory factory{mesh};
+    const auto rho = factory.create2D("sqrt(x^2 + y^2)");
+    const auto theta = factory.create2D("atan(y, x)");
+    Options grid{{"rho", rho},
+                 {"theta", theta},
+                 {"nx", mesh->LocalNx},
+                 {"ny", mesh->LocalNy},
+                 {"nz", mesh->LocalNz}};
+    bout::OptionsIO::create(filename)->write(grid);
+  }
+
+  {
+    Options options{{"mesh", {{"file", filename.string()}}},
+                    {"input", {{"read_Field2Ds", "rho, theta"}}}};
+
+    dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
+    auto factory = FieldFactory{mesh, &options};
+
+    const auto output = factory.create2D("rho * cos(theta)");
+    const auto x = factory.create2D("x");
+    EXPECT_TRUE(IsFieldEqual(output, x));
+  }
+}
+
+TEST_F(FieldFactoryFieldVariableTest, NoMeshFile) {
+  Options options{{"input", {{"read_Field2Ds", "rho, theta"}}}};
+
+  EXPECT_THROW((FieldFactory(mesh, &options)), BoutException);
+}
+
+TEST_F(FieldFactoryFieldVariableTest, MissingVariable) {
+  bout::testing::TempFile filename;
+
+  {
+    // Write some fields to a grid file
+    FieldFactory factory{mesh};
+    const auto rho = factory.create3D("sqrt(x^2 + y^2)");
+    Options grid{{"rho", rho},
+                 {"nx", mesh->LocalNx},
+                 {"ny", mesh->LocalNy},
+                 {"nz", mesh->LocalNz}};
+    bout::OptionsIO::create(filename)->write(grid);
+  }
+
+  {
+    Options options{{"mesh", {{"file", filename.string()}}},
+                    {"input", {{"read_Field3Ds", "rho, theta"}}}};
+
+    dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
+    EXPECT_THROW((FieldFactory{mesh, &options}), BoutException);
+  }
+}

From d3b1346c2d3fd573dbb0c172e9a3adf540fda5a8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 2 Dec 2025 16:49:00 +0000
Subject: [PATCH 1421/1827] Refactor reading grid variables for input
 expressions

---
 manual/sphinx/user_docs/input_grids.rst | 13 +++--
 src/field/field_factory.cxx             | 72 +++++++++++++------------
 tests/unit/field/test_field_factory.cxx | 42 ++++++++++++---
 3 files changed, 81 insertions(+), 46 deletions(-)

diff --git a/manual/sphinx/user_docs/input_grids.rst b/manual/sphinx/user_docs/input_grids.rst
index 2c17411141..402fb30d06 100644
--- a/manual/sphinx/user_docs/input_grids.rst
+++ b/manual/sphinx/user_docs/input_grids.rst
@@ -156,16 +156,19 @@ these are the only quantities specified, then the coordinates revert to
 Cartesian.
 
 You can read additional quantities from the grid and make them available in
-expressions in the input file using ``input:read_Field3Ds`` and
-``input:read_Field2Ds``:
+expressions in the input file by listing them in the ``input:grid_variables``
+section, with the key being the name in the grid file (``mesh:file``) and the
+value being the type (one of ``field3d``, ``field2d``, ``boutreal``):
 
 .. code-block:: cfg
 
-   [input]
-   read_Field2Ds = rho, theta
+   [input:grid_variables]
+   rho = field2d
+   theta = field2d
+   scale = boutreal
 
    [mesh]
-   B = (1 / rho) * cos(theta)
+   B = (scale / rho) * cos(theta)
 
 This section describes how to generate inputs for tokamak equilibria. If
 you’re not interested in tokamaks then you can skip to the next section.
diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index e9dbc0c804..19e6a2fd14 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -31,15 +31,15 @@
 #include <bout/output.hxx>
 #include <bout/traits.hxx>
 #include <bout/utils.hxx>
+#include <bout/bout_enum_class.hxx>
+#include <bout/bout_types.hxx>
+#include <bout/sys/expressionparser.hxx>
 
 #include "fieldgenerators.hxx"
 
-#include <algorithm>
 #include <cmath>
-#include <iterator>
 #include <memory>
 #include <string>
-#include <vector>
 
 using bout::generator::Context;
 
@@ -53,6 +53,8 @@ FieldGeneratorPtr generator(BoutReal* ptr) {
   return std::make_shared<FieldValuePtr>(ptr);
 }
 
+BOUT_ENUM_CLASS(GridVariableFunction, field3d, field2d, boutreal);
+
 namespace {
 /// Provides a placeholder whose target can be changed after creation.
 /// This enables recursive FieldGenerator expressions to be generated
@@ -89,41 +91,44 @@ class FieldIndirect : public FieldGenerator {
   FieldGeneratorPtr target;
 };
 
-// Split a string on commas and trim whitespace from the results
-auto trimsplit(const std::string& str) -> std::vector<std::string> {
-  auto split = strsplit(str, ',');
-  std::vector<std::string> result{};
-  result.reserve(split.size());
-  std::transform(split.begin(), split.end(), std::back_inserter(result),
-                 [](const std::string& element) { return trim(element); });
-  return result;
-}
-
 // Read variables from the grid file and make them available in expressions
 template <class T>
-auto read_grid_variables(FieldFactory& factory, Mesh& mesh, Options& options,
-                         const std::string& option_name) {
-  const auto field_variables =
-      options["input"][option_name]
-          .doc("Variables to read from the grid file and make available in expressions. "
-               "Comma-separated list of variable names")
-          .withDefault<std::string>("");
-
-  if (not field_variables.empty()) {
+auto add_grid_variable(FieldFactory& factory, Mesh& mesh, const std::string& name) {
+  T var;
+  mesh.get(var, name);
+  factory.addGenerator(name, std::make_shared<GridVariable<T>>(var, name));
+}
+
+auto read_grid_variables(FieldFactory& factory, Mesh& mesh, Options& options) {
+  auto& field_variables = options["input"]["grid_variables"].doc(
+      "Variables to read from the grid file and make available in expressions");
+
+  for (const auto& [name, value] : field_variables) {
     if (not mesh.isDataSourceGridFile()) {
-      throw BoutException("A grid file ('mesh:file') is required for `input:{}`",
-                          option_name);
+      throw BoutException(
+          "A grid file ('mesh:file') is required for `input:grid_variables`");
     }
 
-    for (const auto& name : trimsplit(field_variables)) {
-      if (not mesh.sourceHasVar(name)) {
-        const auto filename = Options::root()["mesh"]["file"].as<std::string>();
-        throw BoutException("Grid file '{}' missing `{}` specified in `input:{}`",
-                            filename, name, option_name);
-      }
-      T var;
+    if (not mesh.sourceHasVar(name)) {
+      const auto filename = Options::root()["mesh"]["file"].as<std::string>();
+      throw BoutException(
+          "Grid file '{}' missing `{}` specified in `input:grid_variables`", filename,
+          name);
+    }
+
+    const auto func = value.as<GridVariableFunction>();
+    switch (func) {
+    case GridVariableFunction::field3d:
+      add_grid_variable<Field3D>(factory, mesh, name);
+      break;
+    case GridVariableFunction::field2d:
+      add_grid_variable<Field2D>(factory, mesh, name);
+      break;
+    case GridVariableFunction::boutreal:
+      BoutReal var{};
       mesh.get(var, name);
-      factory.addGenerator(name, std::make_shared<GridVariable<T>>(var, name));
+      factory.addGenerator(name, std::make_shared<FieldValue>(var));
+      break;
     }
   }
 }
@@ -228,8 +233,7 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
   addGenerator("is_periodic_y", std::make_shared<FieldPeriodicY>());
 
   // Variables from the grid file
-  read_grid_variables<Field3D>(*this, *localmesh, nonconst_options, "read_Field3Ds");
-  read_grid_variables<Field2D>(*this, *localmesh, nonconst_options, "read_Field2Ds");
+  read_grid_variables(*this, *localmesh, nonconst_options);
 }
 
 Field2D FieldFactory::create2D(const std::string& value, const Options* opt,
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index 1f88d9ce7e..b6e916dc97 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -1053,8 +1053,9 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField3D) {
   }
 
   {
-    Options options{{"mesh", {{"file", filename.string()}}},
-                    {"input", {{"read_Field3Ds", "rho, theta"}}}};
+    Options options{
+        {"mesh", {{"file", filename.string()}}},
+        {"input", {{"grid_variables", {{"rho", "field3d"}, {"theta", "field3d"}}}}}};
 
     dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
     auto factory = FieldFactory{mesh, &options};
@@ -1082,8 +1083,9 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField2D) {
   }
 
   {
-    Options options{{"mesh", {{"file", filename.string()}}},
-                    {"input", {{"read_Field2Ds", "rho, theta"}}}};
+    Options options{
+        {"mesh", {{"file", filename.string()}}},
+        {"input", {{"grid_variables", {{"rho", "field2d"}, {"theta", "field2d"}}}}}};
 
     dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
     auto factory = FieldFactory{mesh, &options};
@@ -1094,8 +1096,33 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField2D) {
   }
 }
 
+TEST_F(FieldFactoryFieldVariableTest, ReadBoutReal) {
+  bout::testing::TempFile filename;
+
+  {
+    Options grid{{"rho", 4},
+                 {"theta", 5},
+                 {"nx", mesh->LocalNx},
+                 {"ny", mesh->LocalNy},
+                 {"nz", mesh->LocalNz}};
+    bout::OptionsIO::create(filename)->write(grid);
+  }
+
+  {
+    Options options{
+        {"mesh", {{"file", filename.string()}}},
+        {"input", {{"grid_variables", {{"rho", "boutreal"}, {"theta", "boutreal"}}}}}};
+
+    dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
+    auto factory = FieldFactory{mesh, &options};
+
+    const auto output = factory.create3D("rho * theta");
+    EXPECT_TRUE(IsFieldEqual(output, 4 * 5));
+  }
+}
+
 TEST_F(FieldFactoryFieldVariableTest, NoMeshFile) {
-  Options options{{"input", {{"read_Field2Ds", "rho, theta"}}}};
+  Options options{{"input", {{"grid_variables", {{"rho", "field3d"}}}}}};
 
   EXPECT_THROW((FieldFactory(mesh, &options)), BoutException);
 }
@@ -1115,8 +1142,9 @@ TEST_F(FieldFactoryFieldVariableTest, MissingVariable) {
   }
 
   {
-    Options options{{"mesh", {{"file", filename.string()}}},
-                    {"input", {{"read_Field3Ds", "rho, theta"}}}};
+    Options options{
+        {"mesh", {{"file", filename.string()}}},
+        {"input", {{"grid_variables", {{"rho", "field3d"}, {"theta", "field3d"}}}}}};
 
     dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
     EXPECT_THROW((FieldFactory{mesh, &options}), BoutException);

From 42b88b447af9d77dd752796ed010b907f36d5876 Mon Sep 17 00:00:00 2001
From: ZedThree <1486942+ZedThree@users.noreply.github.com>
Date: Tue, 2 Dec 2025 17:16:30 +0000
Subject: [PATCH 1422/1827] Apply clang-format changes

---
 include/bout/sys/generator_context.hxx | 2 +-
 src/field/field_factory.cxx            | 6 +++---
 src/field/fieldgenerators.hxx          | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/include/bout/sys/generator_context.hxx b/include/bout/sys/generator_context.hxx
index a5dd9d236a..e39eea1835 100644
--- a/include/bout/sys/generator_context.hxx
+++ b/include/bout/sys/generator_context.hxx
@@ -43,7 +43,7 @@ public:
   /// Cell indices
   int ix() const { return ix_; }
   int jy() const { return jy_; }
-  int kz() const { return kz_;}
+  int kz() const { return kz_; }
 
   /// Set the value of a parameter with given name
   Context& set(const std::string& name, BoutReal value) {
diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index 19e6a2fd14..fd06d90bd7 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -22,6 +22,8 @@
 
 #include <bout/field_factory.hxx>
 
+#include <bout/bout_enum_class.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/field2d.hxx>
@@ -29,11 +31,9 @@
 #include <bout/fieldperp.hxx>
 #include <bout/globals.hxx>
 #include <bout/output.hxx>
+#include <bout/sys/expressionparser.hxx>
 #include <bout/traits.hxx>
 #include <bout/utils.hxx>
-#include <bout/bout_enum_class.hxx>
-#include <bout/bout_types.hxx>
-#include <bout/sys/expressionparser.hxx>
 
 #include "fieldgenerators.hxx"
 
diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index 49b2cb9690..a777738d02 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -311,7 +311,7 @@ public:
   // Constructor
   FieldTanhHat(FieldGeneratorPtr xin, FieldGeneratorPtr widthin,
                FieldGeneratorPtr centerin, FieldGeneratorPtr steepnessin)
-      : X(xin), width(widthin), center(centerin), steepness(steepnessin) {};
+      : X(xin), width(widthin), center(centerin), steepness(steepnessin){};
   // Clone containing the list of arguments
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override;
   BoutReal generate(const bout::generator::Context& pos) override;
@@ -326,7 +326,7 @@ private:
 class FieldWhere : public FieldGenerator {
 public:
   FieldWhere(FieldGeneratorPtr test, FieldGeneratorPtr gt0, FieldGeneratorPtr lt0)
-      : test(test), gt0(gt0), lt0(lt0) {};
+      : test(test), gt0(gt0), lt0(lt0){};
 
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 3) {

From 5491001cc94efe60b1c155aea276eb8006c101cc Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 26 Mar 2026 15:39:37 -0700
Subject: [PATCH 1423/1827] FieldFactory: Use fieldmesh not localmesh

The constructor argument `localmesh` can be null but in that
case `fieldmesh` is set to `bout::globals::mesh`.
---
 src/field/field_factory.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index fd06d90bd7..3a396b29fd 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -233,7 +233,7 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
   addGenerator("is_periodic_y", std::make_shared<FieldPeriodicY>());
 
   // Variables from the grid file
-  read_grid_variables(*this, *localmesh, nonconst_options);
+  read_grid_variables(*this, *fieldmesh, nonconst_options);
 }
 
 Field2D FieldFactory::create2D(const std::string& value, const Options* opt,

From 7901046f56ab4329ecd356b416a37abd8afa6996 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 26 Mar 2026 15:41:13 -0700
Subject: [PATCH 1424/1827] GridVariable: Load grid variables lazily

`BoutMesh::load` creates a FieldFactory to read variables such as
mesh sizes. This then tries to load grid variables, which in turn
starts trying to create coordinates, use regions etc., none of which
has been constructed at that point.

This defers reading until it's needed, at which point it reads the
variable once and re-uses in subsequent calls.
---
 src/field/field_factory.cxx    |  6 ++----
 src/field/fieldgenerators.hxx  | 38 ++++++++++++++++++++++++++--------
 src/mesh/data/gridfromfile.cxx |  5 ++++-
 3 files changed, 35 insertions(+), 14 deletions(-)

diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index 3a396b29fd..793ea9f278 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -1,5 +1,5 @@
 /**************************************************************************
- * Copyright 2010-2025 BOUT++ contributors
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -94,9 +94,7 @@ class FieldIndirect : public FieldGenerator {
 // Read variables from the grid file and make them available in expressions
 template <class T>
 auto add_grid_variable(FieldFactory& factory, Mesh& mesh, const std::string& name) {
-  T var;
-  mesh.get(var, name);
-  factory.addGenerator(name, std::make_shared<GridVariable<T>>(var, name));
+  factory.addGenerator(name, std::make_shared<GridVariable<T>>(&mesh, name));
 }
 
 auto read_grid_variables(FieldFactory& factory, Mesh& mesh, Options& options) {
diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index a777738d02..9a2be94849 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -381,29 +381,49 @@ public:
   }
 };
 
-/// A `Field3D` that can be used in expressions
+/// A `Field3D` or `Field2D` that can be used in expressions
+///
+/// The variable is read from Mesh when first used and shared between
+/// clones. This is to avoid circular dependencies in construction.
 template <class T, typename = bout::utils::EnableIfField<T>>
 class GridVariable : public FieldGenerator {
+private:
+  struct LazyLoaded {
+    LazyLoaded(Mesh* mesh, std::string name) : mesh(mesh), name(std::move(name)) {}
+
+    Field3D get() {
+      if (!var.isAllocated()) {
+        this->mesh->get(this->var, this->name);
+      }
+      return this->var;
+    }
+
+    Mesh* mesh;
+    std::string name;
+    T var {};
+  };
+
+  std::shared_ptr<LazyLoaded> variable;
 public:
-  GridVariable(T var, std::string name)
-      : variable(std::move(var)), name(std::move(name)) {}
+  GridVariable(Mesh* mesh, std::string name)
+    : variable(std::make_shared<LazyLoaded>(mesh, std::move(name))) {}
+
+  GridVariable(std::shared_ptr<LazyLoaded> variable)
+    : variable(std::move(variable)) {}
 
   double generate(const bout::generator::Context& ctx) override {
-    return variable(ctx.ix(), ctx.jy(), ctx.kz());
+    return variable->get()(ctx.ix(), ctx.jy(), ctx.kz());
   }
 
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 0) {
       throw ParseException("Variable '{}' takes no arguments but got {:d}", args.size());
     }
-    return std::make_shared<GridVariable<T>>(variable, name);
+    return std::make_shared<GridVariable<T>>(variable);
   }
 
-  std::string str() const override { return name; }
+  std::string str() const override { return variable->name; }
 
-private:
-  T variable;
-  std::string name;
 };
 
 #endif // BOUT_FIELDGENERATORS_H
diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 27ad9411c2..35007bd1ff 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -197,7 +197,10 @@ bool GridFile::getField(Mesh* m, T& var, const std::string& name, BoutReal def,
   ///Ghost region widths.
   const int mxg = (m->LocalNx - (m->xend - m->xstart + 1)) / 2;
   const int myg = (m->LocalNy - (m->yend - m->ystart + 1)) / 2;
-  ///Check that ghost region widths are in fact integers
+  // Check grid has cells
+  ASSERT1(m->LocalNx > 0);
+  ASSERT1(m->LocalNy > 0);
+  // Check that ghost region widths are in fact integers
   ASSERT1((m->LocalNx - (m->xend - m->xstart + 1)) % 2 == 0);
   ASSERT1((m->LocalNy - (m->yend - m->ystart + 1)) % 2 == 0);
 

From e9475ff2038e14139186a29cb2b39e70ea91af23 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 26 Mar 2026 21:10:36 -0700
Subject: [PATCH 1425/1827] FieldData: Don't getCoordinates in constructor

No need to get coordinates before they are needed. Calling
this can result in problems if mesh is not fully constructed.
---
 src/field/field_data.cxx | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx
index b925cb1426..8f6a808482 100644
--- a/src/field/field_data.cxx
+++ b/src/field/field_data.cxx
@@ -53,11 +53,6 @@ FieldData::FieldData(Mesh* localmesh, CELL_LOC location_in)
           location_in, fieldmesh)) { // Need to check for nullptr again, because the
                                      // fieldmesh might still be
   // nullptr if the global mesh hasn't been initialized yet
-  if (fieldmesh != nullptr) {
-    // sets fieldCoordinates by getting Coordinates for our location from
-    // fieldmesh
-    getCoordinates();
-  }
 }
 
 FieldData::FieldData(const FieldData& other) {

From ab229707045de4fe736d3817b5d2d91c77d7260d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 26 Mar 2026 21:11:59 -0700
Subject: [PATCH 1426/1827] GridVariable: Check mesh->get return

Not strictly necessary because variables are checked
before creating a GridVariable, but doesn't hurt.
---
 src/field/fieldgenerators.hxx | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index 9a2be94849..e8d38b1573 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -311,7 +311,7 @@ public:
   // Constructor
   FieldTanhHat(FieldGeneratorPtr xin, FieldGeneratorPtr widthin,
                FieldGeneratorPtr centerin, FieldGeneratorPtr steepnessin)
-      : X(xin), width(widthin), center(centerin), steepness(steepnessin){};
+      : X(xin), width(widthin), center(centerin), steepness(steepnessin) {};
   // Clone containing the list of arguments
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override;
   BoutReal generate(const bout::generator::Context& pos) override;
@@ -326,7 +326,7 @@ private:
 class FieldWhere : public FieldGenerator {
 public:
   FieldWhere(FieldGeneratorPtr test, FieldGeneratorPtr gt0, FieldGeneratorPtr lt0)
-      : test(test), gt0(gt0), lt0(lt0){};
+      : test(test), gt0(gt0), lt0(lt0) {};
 
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 3) {
@@ -393,23 +393,26 @@ private:
 
     Field3D get() {
       if (!var.isAllocated()) {
-        this->mesh->get(this->var, this->name);
+        // Read variable from mesh
+        if (this->mesh->get(this->var, this->name) != 0) {
+          throw BoutException("Couldn't read GridVariable '{}'", this->name);
+        }
       }
       return this->var;
     }
 
     Mesh* mesh;
     std::string name;
-    T var {};
+    T var{};
   };
 
   std::shared_ptr<LazyLoaded> variable;
+
 public:
   GridVariable(Mesh* mesh, std::string name)
-    : variable(std::make_shared<LazyLoaded>(mesh, std::move(name))) {}
+      : variable(std::make_shared<LazyLoaded>(mesh, std::move(name))) {}
 
-  GridVariable(std::shared_ptr<LazyLoaded> variable)
-    : variable(std::move(variable)) {}
+  GridVariable(std::shared_ptr<LazyLoaded> variable) : variable(std::move(variable)) {}
 
   double generate(const bout::generator::Context& ctx) override {
     return variable->get()(ctx.ix(), ctx.jy(), ctx.kz());
@@ -423,7 +426,6 @@ public:
   }
 
   std::string str() const override { return variable->name; }
-
 };
 
 #endif // BOUT_FIELDGENERATORS_H

From d0726d99dfeac75e00006940330f05ce18e377ac Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 27 Mar 2026 16:57:30 -0700
Subject: [PATCH 1427/1827] FieldGenerators: Fixes and tidying

Missing argument to exception, misc. headers.
---
 src/field/fieldgenerators.hxx | 38 ++++++++++++++++++-----------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index e8d38b1573..c84a35109f 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -7,15 +7,20 @@
 #ifndef BOUT_FIELDGENERATORS_H
 #define BOUT_FIELDGENERATORS_H
 
+#include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/sys/expressionparser.hxx>
+#include <bout/sys/generator_context.hxx>
 #include <bout/traits.hxx>
 #include <bout/unused.hxx>
 
+#include <algorithm>
 #include <cmath>
+#include <list>
 #include <memory>
 #include <string>
+#include <utility>
 
 //////////////////////////////////////////////////////////
 // Generators from values
@@ -43,7 +48,7 @@ template <single_arg_op Op>
 class FieldGenOneArg : public FieldGenerator { ///< Template for single-argument function
 public:
   FieldGenOneArg(FieldGeneratorPtr g, const std::string& name = "function")
-      : gen(g), name(name) {}
+      : gen(std::move(g)), name(name) {}
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 1) {
       throw ParseException("Incorrect number of arguments to {:s}. Expecting 1, got {:d}",
@@ -70,7 +75,7 @@ class FieldGenTwoArg : public FieldGenerator { ///< Template for two-argument fu
 public:
   FieldGenTwoArg(FieldGeneratorPtr a, FieldGeneratorPtr b,
                  const std::string& name = "function")
-      : A(a), B(b), name(name) {}
+      : A(std::move(a)), B(std::move(b)), name(name) {}
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 2) {
       throw ParseException("Incorrect number of arguments to {:s}. Expecting 2, got {:d}",
@@ -93,11 +98,13 @@ private:
 /// Arc (Inverse) tangent. Either one or two argument versions
 class FieldATan : public FieldGenerator {
 public:
-  FieldATan(FieldGeneratorPtr a, FieldGeneratorPtr b = nullptr) : A(a), B(b) {}
+  FieldATan(FieldGeneratorPtr a, FieldGeneratorPtr b = nullptr)
+      : A(std::move(a)), B(std::move(b)) {}
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() == 1) {
       return std::make_shared<FieldATan>(args.front());
-    } else if (args.size() == 2) {
+    }
+    if (args.size() == 2) {
       return std::make_shared<FieldATan>(args.front(), args.back());
     }
     throw ParseException(
@@ -148,7 +155,7 @@ public:
   FieldMin() = default;
   FieldMin(const std::list<FieldGeneratorPtr> args) : input(args) {}
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
-    if (args.size() == 0) {
+    if (args.empty()) {
       throw ParseException("min function must have some inputs");
     }
     return std::make_shared<FieldMin>(args);
@@ -157,10 +164,7 @@ public:
     auto it = input.begin();
     BoutReal result = (*it)->generate(pos);
     for (; it != input.end(); it++) {
-      BoutReal val = (*it)->generate(pos);
-      if (val < result) {
-        result = val;
-      }
+      result = std::min(result, (*it)->generate(pos));
     }
     return result;
   }
@@ -175,7 +179,7 @@ public:
   FieldMax() = default;
   FieldMax(const std::list<FieldGeneratorPtr> args) : input(args) {}
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
-    if (args.size() == 0) {
+    if (args.empty()) {
       throw ParseException("max function must have some inputs");
     }
     return std::make_shared<FieldMax>(args);
@@ -184,10 +188,7 @@ public:
     auto it = input.begin();
     BoutReal result = (*it)->generate(pos);
     for (; it != input.end(); it++) {
-      BoutReal val = (*it)->generate(pos);
-      if (val > result) {
-        result = val;
-      }
+      result = std::max(result, (*it)->generate(pos));
     }
     return result;
   }
@@ -206,7 +207,7 @@ class FieldClamp : public FieldGenerator {
 public:
   FieldClamp() = default;
   FieldClamp(FieldGeneratorPtr value, FieldGeneratorPtr low, FieldGeneratorPtr high)
-      : value(value), low(low), high(high) {}
+      : value(std::move(value)), low(std::move(low)), high(std::move(high)) {}
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 3) {
       throw ParseException(
@@ -242,7 +243,7 @@ private:
 /// Generator to round to the nearest integer
 class FieldRound : public FieldGenerator {
 public:
-  FieldRound(FieldGeneratorPtr g) : gen(g) {}
+  FieldRound(FieldGeneratorPtr g) : gen(std::move(g)) {}
 
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
     if (args.size() != 1) {
@@ -419,8 +420,9 @@ public:
   }
 
   FieldGeneratorPtr clone(const std::list<FieldGeneratorPtr> args) override {
-    if (args.size() != 0) {
-      throw ParseException("Variable '{}' takes no arguments but got {:d}", args.size());
+    if (!args.empty()) {
+      throw ParseException("Variable '{}' takes no arguments but got {:d}",
+                           variable->name, args.size());
     }
     return std::make_shared<GridVariable<T>>(variable);
   }

From 2e967789c084339eebd4121926c62f3dd0fdb9d1 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 27 Mar 2026 21:53:47 -0700
Subject: [PATCH 1428/1827] GridVariable unit tests: Fix unit test

Unit tests now include Y guard cells.
---
 src/mesh/data/gridfromfile.cxx          |  1 +
 src/mesh/impls/bout/boutmesh.cxx        |  3 +-
 tests/unit/field/test_field_factory.cxx | 57 ++++++++++++-------------
 3 files changed, 30 insertions(+), 31 deletions(-)

diff --git a/src/mesh/data/gridfromfile.cxx b/src/mesh/data/gridfromfile.cxx
index 35007bd1ff..813ee1e3d8 100644
--- a/src/mesh/data/gridfromfile.cxx
+++ b/src/mesh/data/gridfromfile.cxx
@@ -3,6 +3,7 @@
 #include <bout/griddata.hxx>
 
 #include <bout/array.hxx>
+#include <bout/assert.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index f56979785c..3c05425241 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -2573,9 +2573,8 @@ bool BoutMesh::periodicY(int jx, BoutReal& ts) const {
 int BoutMesh::numberOfYBoundaries() const {
   if (jyseps2_1 != jyseps1_2) {
     return 2;
-  } else {
-    return 1;
   }
+  return 1;
 }
 
 std::pair<bool, BoutReal> BoutMesh::hasBranchCutLower(int jx) const {
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index b6e916dc97..c7b5bcd9ae 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -12,11 +12,14 @@
 #include "bout/options_io.hxx"
 #include "bout/output.hxx"
 #include "bout/paralleltransform.hxx"
+#include "bout/sys/generator_context.hxx"
 #include "bout/traits.hxx"
 
 #include "fake_mesh_fixture.hxx"
 #include "test_tmpfiles.hxx"
 
+#include <memory>
+
 // The unit tests use the global mesh
 using namespace bout::globals;
 using bout::generator::Context;
@@ -885,7 +888,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create2D) {
   mesh->getCoordinates()->setParallelTransform(
       bout::utils::make_unique<MockParallelTransform>(*mesh, true));
 
-  FieldFactory factory;
+  const FieldFactory factory;
 
   auto output = factory.create2D("x");
 
@@ -900,7 +903,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create3D) {
   mesh->getCoordinates()->setParallelTransform(
       bout::utils::make_unique<MockParallelTransform>(*mesh, true));
 
-  FieldFactory factory;
+  const FieldFactory factory;
 
   auto output = factory.create3D("x");
 
@@ -916,7 +919,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create2DNoTransform) {
 
   Options options;
   options["input"]["transform_from_field_aligned"] = false;
-  FieldFactory factory{mesh, &options};
+  const FieldFactory factory{mesh, &options};
 
   auto output = factory.create2D("x");
 
@@ -933,7 +936,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create3DNoTransform) {
 
   Options options;
   options["input"]["transform_from_field_aligned"] = false;
-  FieldFactory factory{mesh, &options};
+  const FieldFactory factory{mesh, &options};
 
   auto output = factory.create3D("x");
 
@@ -947,7 +950,7 @@ TEST_F(FieldFactoryCreateAndTransformTest, Create2DCantTransform) {
   mesh->getCoordinates()->setParallelTransform(
       bout::utils::make_unique<MockParallelTransform>(*mesh, false));
 
-  FieldFactory factory{mesh};
+  const FieldFactory factory{mesh};
 
   auto output = factory.create2D("x");
 
@@ -1041,14 +1044,12 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField3D) {
 
   {
     // Write some fields to a grid file
-    FieldFactory factory{mesh};
+    const FieldFactory factory{mesh};
     const auto rho = factory.create3D("sqrt(x^2 + y^2)");
     const auto theta = factory.create3D("atan(y, x)");
-    Options grid{{"rho", rho},
-                 {"theta", theta},
-                 {"nx", mesh->LocalNx},
-                 {"ny", mesh->LocalNy},
-                 {"nz", mesh->LocalNz}};
+    const Options grid{{"rho", rho},          {"theta", theta},
+                       {"nx", mesh->LocalNx}, {"ny", mesh->LocalNy - 2},
+                       {"nz", mesh->LocalNz}, {"y_boundary_guards", 1}};
     bout::OptionsIO::create(filename)->write(grid);
   }
 
@@ -1062,7 +1063,7 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField3D) {
 
     const auto output = factory.create3D("rho * cos(theta)");
     const auto x = factory.create3D("x");
-    EXPECT_TRUE(IsFieldEqual(output, x));
+    EXPECT_TRUE(IsFieldEqual(output, x, "RGN_ALL", 1e-14));
   }
 }
 
@@ -1071,14 +1072,12 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField2D) {
 
   {
     // Write some fields to a grid file
-    FieldFactory factory{mesh};
+    const FieldFactory factory{mesh};
     const auto rho = factory.create2D("sqrt(x^2 + y^2)");
     const auto theta = factory.create2D("atan(y, x)");
-    Options grid{{"rho", rho},
-                 {"theta", theta},
-                 {"nx", mesh->LocalNx},
-                 {"ny", mesh->LocalNy},
-                 {"nz", mesh->LocalNz}};
+    const Options grid{{"rho", rho},          {"theta", theta},
+                       {"nx", mesh->LocalNx}, {"ny", mesh->LocalNy - 2},
+                       {"nz", mesh->LocalNz}, {"y_boundary_guards", 1}};
     bout::OptionsIO::create(filename)->write(grid);
   }
 
@@ -1092,7 +1091,7 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField2D) {
 
     const auto output = factory.create2D("rho * cos(theta)");
     const auto x = factory.create2D("x");
-    EXPECT_TRUE(IsFieldEqual(output, x));
+    EXPECT_TRUE(IsFieldEqual(output, x, "RGN_ALL", 1e-14));
   }
 }
 
@@ -1100,11 +1099,11 @@ TEST_F(FieldFactoryFieldVariableTest, ReadBoutReal) {
   bout::testing::TempFile filename;
 
   {
-    Options grid{{"rho", 4},
-                 {"theta", 5},
-                 {"nx", mesh->LocalNx},
-                 {"ny", mesh->LocalNy},
-                 {"nz", mesh->LocalNz}};
+    const Options grid{{"rho", 4},
+                       {"theta", 5},
+                       {"nx", mesh->LocalNx},
+                       {"ny", mesh->LocalNy},
+                       {"nz", mesh->LocalNz}};
     bout::OptionsIO::create(filename)->write(grid);
   }
 
@@ -1132,12 +1131,12 @@ TEST_F(FieldFactoryFieldVariableTest, MissingVariable) {
 
   {
     // Write some fields to a grid file
-    FieldFactory factory{mesh};
+    const FieldFactory factory{mesh};
     const auto rho = factory.create3D("sqrt(x^2 + y^2)");
-    Options grid{{"rho", rho},
-                 {"nx", mesh->LocalNx},
-                 {"ny", mesh->LocalNy},
-                 {"nz", mesh->LocalNz}};
+    const Options grid{{"rho", rho},
+                       {"nx", mesh->LocalNx},
+                       {"ny", mesh->LocalNy},
+                       {"nz", mesh->LocalNz}};
     bout::OptionsIO::create(filename)->write(grid);
   }
 

From 5e18e164cb00d3a6f9a7f3f6e2c90a7fbc65c523 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 28 Mar 2026 09:12:18 -0700
Subject: [PATCH 1429/1827] Field2D/3D: Defer sizing until allocation

FieldFactory can create Fields when bout::mesh::global is non-null
but the size of the mesh (LocalNx etc.) is not set, because
FieldFactory is created inside BoutMesh::load() via Options.
---
 include/bout/field2d.hxx |  2 +-
 include/bout/field3d.hxx |  2 +-
 include/bout/mesh.hxx    |  2 +-
 src/field/field2d.cxx    | 24 +++++++++--------------
 src/field/field3d.cxx    | 41 ++++++++++++----------------------------
 5 files changed, 24 insertions(+), 47 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index efa878ef0a..374945d47e 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -289,7 +289,7 @@ private:
   Array<BoutReal> data;
 
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
-  int nx{-1}, ny{-1};
+  int nx{0}, ny{0};
 
   /// Time-derivative, can be nullptr
   Field2D* deriv{nullptr};
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index fabe2b646d..422523ed2e 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -551,7 +551,7 @@ public:
 
 protected:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
-  int nx{-1}, ny{-1}, nz{-1};
+  int nx{0}, ny{0}, nz{0};
 
   /// Internal data array. Handles allocation/freeing of memory
   Array<BoutReal> data;
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 1453f51f5f..ba2a1c640f 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -605,7 +605,7 @@ public:
   virtual int getLocalZIndexNoBoundaries(int zglobal) const = 0;
 
   /// Size of the mesh on this processor including guard/boundary cells
-  int LocalNx, LocalNy, LocalNz;
+  int LocalNx{0}, LocalNy{0}, LocalNz{0};
 
   /// Local ranges of data (inclusive), excluding guard cells
   int xstart, xend, ystart, yend, zstart, zend;
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index b363eeef07..e246ad4c63 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -46,12 +46,8 @@
 Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in,
                  [[maybe_unused]] std::optional<size_t> regionID)
     : Field(localmesh, location_in, directions_in) {
-
-  if (fieldmesh) {
-    nx = fieldmesh->LocalNx;
-    ny = fieldmesh->LocalNy;
-  }
-
+  // Note: Even if fieldmesh is not null, LocalNx and LocalNy may not
+  // be initialised.
 #if BOUT_USE_TRACK
   name = "<F2D>";
 #endif
@@ -62,11 +58,6 @@ Field2D::Field2D(const Field2D& f) : Field(f), data(f.data) {
 #if BOUT_USE_TRACK
   name = f.name;
 #endif
-
-  if (fieldmesh) {
-    nx = fieldmesh->LocalNx;
-    ny = fieldmesh->LocalNy;
-  }
 }
 
 Field2D::Field2D(BoutReal val, Mesh* localmesh) : Field2D(localmesh) { *this = val; }
@@ -89,13 +80,16 @@ Field2D::~Field2D() { delete deriv; }
 
 Field2D& Field2D::allocate() {
   if (data.empty()) {
-    if (!fieldmesh) {
+    if (fieldmesh == nullptr) {
       // fieldmesh was not initialized when this field was initialized, so use
-      // the global mesh and set some members to default values
+      // the global mesh
       fieldmesh = bout::globals::mesh;
-      nx = fieldmesh->LocalNx;
-      ny = fieldmesh->LocalNy;
     }
+    // Get size from the mesh.
+    nx = fieldmesh->LocalNx;
+    ny = fieldmesh->LocalNy;
+    ASSERT1(nx > 0);
+    ASSERT1(ny > 0);
     data.reallocate(nx * ny);
 #if CHECK > 2
     invalidateGuards(*this);
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 633eb42e9b..a449335f29 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -63,38 +63,21 @@ Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes direction
 #if BOUT_USE_TRACK
   name = "<F3D>";
 #endif
-
-  if (fieldmesh) {
-    nx = fieldmesh->LocalNx;
-    ny = fieldmesh->LocalNy;
-    nz = fieldmesh->LocalNz;
-  }
 }
 
 /// Doesn't copy any data, just create a new reference to the same data (copy on change
 /// later)
 Field3D::Field3D(const Field3D& f)
     : Field(f), data(f.data), yup_fields(f.yup_fields), ydown_fields(f.ydown_fields),
-      regionID(f.regionID) {
+      regionID(f.regionID) {}
 
-  if (fieldmesh) {
-    nx = fieldmesh->LocalNx;
-    ny = fieldmesh->LocalNy;
-    nz = fieldmesh->LocalNz;
-  }
-}
-
-Field3D::Field3D(const Field2D& f) : Field(f) {
-
-  nx = fieldmesh->LocalNx;
-  ny = fieldmesh->LocalNy;
-  nz = fieldmesh->LocalNz;
+Field3D::Field3D(const Field2D& f)
+    : Field(f), nx(fieldmesh->LocalNx), ny(fieldmesh->LocalNy), nz(fieldmesh->LocalNz) {
 
   *this = f;
 }
 
 Field3D::Field3D(const BoutReal val, Mesh* localmesh) : Field3D(localmesh) {
-
   *this = val;
 }
 
@@ -113,11 +96,8 @@ Field3DParallel::Field3DParallel(const BoutReal val, Mesh* localmesh)
 
 Field3D::Field3D(Array<BoutReal> data_in, Mesh* localmesh, CELL_LOC datalocation,
                  DirectionTypes directions_in)
-    : Field(localmesh, datalocation, directions_in), data(std::move(data_in)) {
-
-  nx = fieldmesh->LocalNx;
-  ny = fieldmesh->LocalNy;
-  nz = fieldmesh->LocalNz;
+    : Field(localmesh, datalocation, directions_in), nx(fieldmesh->LocalNx),
+      ny(fieldmesh->LocalNy), nz(fieldmesh->LocalNz), data(std::move(data_in)) {
 
   ASSERT1(data.size() == nx * ny * nz);
 }
@@ -126,14 +106,17 @@ Field3D::~Field3D() { delete deriv; }
 
 Field3D& Field3D::allocate() {
   if (data.empty()) {
-    if (!fieldmesh) {
+    if (fieldmesh == nullptr) {
       // fieldmesh was not initialized when this field was initialized, so use
       // the global mesh and set some members to default values
       fieldmesh = bout::globals::mesh;
-      nx = fieldmesh->LocalNx;
-      ny = fieldmesh->LocalNy;
-      nz = fieldmesh->LocalNz;
     }
+    nx = fieldmesh->LocalNx;
+    ny = fieldmesh->LocalNy;
+    nz = fieldmesh->LocalNz;
+    ASSERT1(nx > 0);
+    ASSERT1(ny > 0);
+    ASSERT1(nz > 0);
     data.reallocate(nx * ny * nz);
 #if CHECK > 2
     invalidateGuards(*this);

From 95b01d8bfca8ccbb9e140f18f44b68a55ae86a11 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 28 Mar 2026 09:15:05 -0700
Subject: [PATCH 1430/1827] Miscellaneous tidying

Addressing clang-tidy comments and Clang compiler warnings (sprintf use).
---
 include/bout/field2d.hxx                      |  1 +
 src/field/field2d.cxx                         |  1 +
 src/field/field3d.cxx                         |  2 +
 .../impls/multigrid/multigrid_laplace.cxx     | 29 +++++++-------
 .../impls/multigrid/multigrid_solver.cxx      | 38 ++++++++-----------
 src/invert/laplace/impls/pcr/pcr.cxx          | 23 ++++++-----
 6 files changed, 46 insertions(+), 48 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 374945d47e..5d07ea9aba 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -43,6 +43,7 @@ class Field2D;
 
 #include <cstddef>
 #include <ostream>
+#include <iostream>
 #include <string>
 
 #if BOUT_HAS_RAJA
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index e246ad4c63..a0b2b440e5 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -29,6 +29,7 @@
 #include "bout/build_defines.hxx"
 
 #include "bout/unused.hxx"
+#include <bout/array.hxx>
 #include <bout/assert.hxx>
 #include <bout/boundary_factory.hxx>
 #include <bout/boundary_op.hxx>
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index a449335f29..1241dee465 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -25,8 +25,10 @@
  *
  **************************************************************************/
 
+#include "bout/array.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/build_defines.hxx"
+#include "bout/field2d.hxx"
 
 #include "bout/index_derivs_interface.hxx"
 #include <bout/boutcomm.hxx>
diff --git a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
index 4be5bfbad3..c06a83585b 100644
--- a/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
+++ b/src/invert/laplace/impls/multigrid/multigrid_laplace.cxx
@@ -1,5 +1,5 @@
 /**************************************************************************
- * Perpendicular Laplacian inversion. 
+ * Perpendicular Laplacian inversion.
  *                           Using Geometrical Multigrid Solver
  *
  * Equation solved is:
@@ -9,7 +9,7 @@
  * Copyright 2016 K.S. Kang
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -32,8 +32,11 @@
 
 #if not BOUT_USE_METRIC_3D
 
+#include <bout/assert.hxx>
+#include <bout/boutexception.hxx>
 #include <bout/mesh.hxx>
 #include <bout/openmpwrap.hxx>
+#include <bout/output.hxx>
 
 #if BOUT_USE_OPENMP
 #include <omp.h>
@@ -107,11 +110,7 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_
   }
   Nz_global = localmesh->GlobalNz;
   Nz_local = Nz_global; // No parallelization in z-direction (for now)
-  //
-  //else {
-  //  Nz_local = localmesh->zend - localmesh->zstart + 1; // excluding guard cells
-  //  Nz_global = localmesh->GlobalNz - 2*localmesh->zstart; // excluding guard cells
-  // }
+
   if (mgcount == 0) {
     output << "Nz=" << Nz_global << "(" << Nz_local << ")" << endl;
   }
@@ -214,7 +213,9 @@ LaplaceMultigrid::LaplaceMultigrid(Options* opt, const CELL_LOC loc, Mesh* mesh_
     }
     BOUT_OMP_SAFE(parallel)
     BOUT_OMP_SAFE(master)
-    { output << "Num threads = " << omp_get_num_threads() << endl; }
+    {
+      output << "Num threads = " << omp_get_num_threads() << endl;
+    }
   }
 }
 
@@ -384,11 +385,9 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) {
   }
 
   if ((pcheck == 3) && (mgcount == 0)) {
-    FILE* outf;
-    char outfile[256];
-    sprintf(outfile, "test_matF_%d.mat", kMG->rProcI);
+    std::string outfile = fmt::format("test_matF_{:d}.mat", kMG->rProcI);
     output << "Out file= " << outfile << endl;
-    outf = fopen(outfile, "w");
+    FILE* outf = fopen(outfile.c_str(), "w");
     int dim = (lxx + 2) * (lzz + 2);
     fprintf(outf, "dim = %d (%d, %d)\n", dim, lxx, lzz);
 
@@ -411,11 +410,9 @@ FieldPerp LaplaceMultigrid::solve(const FieldPerp& b_in, const FieldPerp& x0) {
       output << i << "dimension= " << kMG->lnx[i - 1] << "(" << kMG->gnx[i - 1] << "),"
              << kMG->lnz[i - 1] << endl;
 
-      FILE* outf;
-      char outfile[256];
-      sprintf(outfile, "test_matC%1d_%d.mat", i, kMG->rProcI);
+      std::string outfile = fmt::format("test_matC{:1d}_{:d}.mat", i, kMG->rProcI);
       output << "Out file= " << outfile << endl;
-      outf = fopen(outfile, "w");
+      FILE* outf = fopen(outfile.c_str(), "w");
       int dim = (kMG->lnx[i - 1] + 2) * (kMG->lnz[i - 1] + 2);
       fprintf(outf, "dim = %d (%d,%d)\n", dim, kMG->lnx[i - 1], kMG->lnz[i - 1]);
 
diff --git a/src/invert/laplace/impls/multigrid/multigrid_solver.cxx b/src/invert/laplace/impls/multigrid/multigrid_solver.cxx
index 5ff616aa54..074e482320 100644
--- a/src/invert/laplace/impls/multigrid/multigrid_solver.cxx
+++ b/src/invert/laplace/impls/multigrid/multigrid_solver.cxx
@@ -1,5 +1,5 @@
 /**************************************************************************
- * Perpendicular Laplacian inversion. 
+ * Perpendicular Laplacian inversion.
  *                           Using Geometrical Multigrid Solver
  *
  * Equation solved is:
@@ -9,7 +9,7 @@
  * Copyright 2015 K.S. Kang
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -35,6 +35,9 @@
 #include "bout/unused.hxx"
 #include <bout/openmpwrap.hxx>
 
+#include <cstdio>
+#include <string>
+
 Multigrid1DP::Multigrid1DP(int level, int lx, int lz, int gx, int dl, int merge,
                            MPI_Comm comm, int check)
     : MultigridAlg(level, lx, lz, gx, lz, comm, check) {
@@ -195,11 +198,9 @@ void Multigrid1DP::setMultigridC(int UNUSED(plag)) {
 
     if (pcheck == 2) {
       for (int i = level; i >= 0; i--) {
-        FILE* outf;
-        char outfile[256];
-        sprintf(outfile, "2DP_matC%1d_%d.mat", i, rMG->rProcI);
+        std::string outfile = fmt::format("2DP_matC{:1d}_{:d}.mat", i, rMG->rProcI);
         output << "Out file= " << outfile << endl;
-        outf = fopen(outfile, "w");
+        FILE* outf = fopen(outfile.c_str(), "w");
         int dim = (rMG->lnx[i] + 2) * (rMG->lnz[i] + 2);
         fprintf(outf, "dim = %d (%d, %d)\n", dim, rMG->lnx[i], rMG->lnz[i]);
 
@@ -222,11 +223,9 @@ void Multigrid1DP::setMultigridC(int UNUSED(plag)) {
     }
     if (pcheck == 3) {
       for (int i = level; i >= 0; i--) {
-        FILE* outf;
-        char outfile[256];
-        sprintf(outfile, "S1D_matC%1d_%d.mat", i, sMG->rProcI);
+        std::string outfile = fmt::format("S1D_matC{:1d}_{:d}.mat", i, sMG->rProcI);
         output << "Out file= " << outfile << endl;
-        outf = fopen(outfile, "w");
+        FILE* outf = fopen(outfile.c_str(), "w");
         int dim = (sMG->lnx[i] + 2) * (sMG->lnz[i] + 2);
         fprintf(outf, "dim = %d\n", dim);
 
@@ -456,11 +455,9 @@ void Multigrid1DP::convertMatrixF2D(int level) {
     }
   }
   if (pcheck == 3) {
-    FILE* outf;
-    char outfile[256];
-    sprintf(outfile, "2DP_CP_%d.mat", rProcI);
+    std::string outfile = fmt::format("2DP_CP_{}.mat", rProcI);
     output << "Out file= " << outfile << endl;
-    outf = fopen(outfile, "w");
+    FILE* outf = fopen(outfile.c_str(), "w");
     fprintf(outf, "dim = (%d, %d)\n", ggx, gnz[0]);
 
     for (int ii = 0; ii < dim; ii++) {
@@ -476,11 +473,10 @@ void Multigrid1DP::convertMatrixF2D(int level) {
                                     MPI_SUM, comm2D);
 
   if (pcheck == 3) {
-    FILE* outf;
-    char outfile[256];
-    sprintf(outfile, "2DP_Conv_%d.mat", rProcI);
+
+    std::string outfile = fmt::format("2DP_Conv_{}.mat", rProcI);
     output << "Out file= " << outfile << endl;
-    outf = fopen(outfile, "w");
+    FILE* outf = fopen(outfile.c_str(), "w");
     fprintf(outf, "dim = (%d, %d)\n", ggx, gnz[0]);
 
     for (int ii = 0; ii < dim; ii++) {
@@ -625,10 +621,8 @@ void Multigrid2DPf1D::setMultigridC(int UNUSED(plag)) {
     }
     if (pcheck == 2) {
       for (int i = level; i >= 0; i--) {
-        FILE* outf;
-        char outfile[256];
-        sprintf(outfile, "S2D_matC%1d_%d.mat", i, sMG->rProcI);
-        outf = fopen(outfile, "w");
+        std::string outfile = fmt::format("S2D_matC{:1d}_{:d}.mat", i, sMG->rProcI);
+        FILE* outf = fopen(outfile.c_str(), "w");
         output << "Out file= " << outfile << endl;
         int dim = (sMG->lnx[i] + 2) * (sMG->lnz[i] + 2);
         fprintf(outf, "dim = %d\n", dim);
diff --git a/src/invert/laplace/impls/pcr/pcr.cxx b/src/invert/laplace/impls/pcr/pcr.cxx
index 93fbf09cdb..325242a3b2 100644
--- a/src/invert/laplace/impls/pcr/pcr.cxx
+++ b/src/invert/laplace/impls/pcr/pcr.cxx
@@ -45,11 +45,14 @@
 #include "../../common_transform.hxx"
 
 #include <bout/array.hxx>
+#include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
 #include <bout/dcomplex.hxx>
 #include <bout/fft.hxx>
+#include <bout/fieldperp.hxx>
 #include <bout/globals.hxx>
 #include <bout/lapack_routines.hxx>
 #include <bout/mesh.hxx>
@@ -124,8 +127,8 @@ LaplacePCR::LaplacePCR(Options* opt, CELL_LOC loc, Mesh* mesh_in, Solver* UNUSED
                                   // (unless periodic in x)
     xe = localmesh->LocalNx - 1;
   }
-  int n = xe - xs + 1; // Number of X points on this processor,
-                       // including boundaries but not guard cells
+  const int n = xe - xs + 1; // Number of X points on this processor,
+                             // including boundaries but not guard cells
 
   a.reallocate(nmode, n);
   b.reallocate(nmode, n);
@@ -148,7 +151,7 @@ FieldPerp LaplacePCR::solve(const FieldPerp& rhs, const FieldPerp& x0) {
 
   FieldPerp x{emptyFrom(rhs)}; // Result
 
-  int jy = rhs.getIndex(); // Get the Y index
+  const int jy = rhs.getIndex(); // Get the Y index
   x.setIndex(jy);
 
   // Get the width of the boundary
@@ -215,7 +218,7 @@ Field3D LaplacePCR::solve(const Field3D& rhs, const Field3D& x0) {
     outbndry = 1;
   }
 
-  int nx = xe - xs + 1; // Number of X points on this processor
+  const int nx = xe - xs + 1; // Number of X points on this processor
 
   // Get range of Y indices
   int ys = localmesh->ystart;
@@ -313,7 +316,7 @@ void LaplacePCR ::cr_pcr_solver(Matrix<dcomplex>& a_mpi, Matrix<dcomplex>& b_mpi
       // don't want to copy them.
       // xs = xstart if a proc has no boundary points
       // xs = 0 if a proc has boundary points
-      int offset = localmesh->xstart - xs;
+      const int offset = localmesh->xstart - xs;
       aa(kz, ix + 1) = a_mpi(kz, ix + offset);
       bb(kz, ix + 1) = b_mpi(kz, ix + offset);
       cc(kz, ix + 1) = c_mpi(kz, ix + offset);
@@ -400,7 +403,7 @@ void LaplacePCR ::apply_boundary_conditions(const Matrix<dcomplex>& a,
     }
   }
   if (localmesh->lastX()) {
-    int n = xe - xs + 1; // actual length of array
+    const int n = xe - xs + 1; // actual length of array
     for (int kz = 0; kz < nsys; kz++) {
       for (int ix = n - localmesh->xstart; ix < n; ix++) {
         x(kz, ix) = (r(kz, ix) - a(kz, ix) * x(kz, ix - 1)) / b(kz, ix);
@@ -419,7 +422,7 @@ void LaplacePCR ::cr_forward_multiple_row(Matrix<dcomplex>& a, Matrix<dcomplex>&
                                           Matrix<dcomplex>& r) const {
   const int nsys = std::get<0>(a.shape());
 
-  MPI_Comm comm = BoutComm::get();
+  const MPI_Comm comm = BoutComm::get();
   Array<dcomplex> alpha(nsys);
   Array<dcomplex> gamma(nsys);
   Array<dcomplex> sbuf(4 * nsys);
@@ -494,7 +497,7 @@ void LaplacePCR ::cr_backward_multiple_row(Matrix<dcomplex>& a, Matrix<dcomplex>
                                            Matrix<dcomplex>& x) const {
   const int nsys = std::get<0>(a.shape());
 
-  MPI_Comm comm = BoutComm::get();
+  const MPI_Comm comm = BoutComm::get();
 
   MPI_Status status;
   MPI_Request request[2];
@@ -533,7 +536,7 @@ void LaplacePCR ::cr_backward_multiple_row(Matrix<dcomplex>& a, Matrix<dcomplex>
     dist_row = dist_row / 2;
   }
   if (xproc < nprocs - 1) {
-    MPI_Wait(request + 1, &status);
+    MPI_Wait(&request[1], &status);
   }
 }
 
@@ -555,7 +558,7 @@ void LaplacePCR ::pcr_forward_single_row(Matrix<dcomplex>& a, Matrix<dcomplex>&
 
   MPI_Status status;
   Array<MPI_Request> request(4);
-  MPI_Comm comm = BoutComm::get();
+  const MPI_Comm comm = BoutComm::get();
 
   const int nlevel = log2(nprocs);
   const int nhprocs = nprocs / 2;

From fe00722b5bf016bb919b6cb3b929ccef93a4c245 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 28 Mar 2026 10:38:56 -0700
Subject: [PATCH 1431/1827] Field2D/3D: Partly revert 8ebc0a0

Set field sizes in the same way, but get and check sizes on allocation.
---
 include/bout/field2d.hxx |  2 +-
 include/bout/field3d.hxx |  2 +-
 src/field/field2d.cxx    | 15 +++++++++++----
 src/field/field3d.cxx    | 14 +++++++++++++-
 4 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 5d07ea9aba..0b437e1bd8 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -290,7 +290,7 @@ private:
   Array<BoutReal> data;
 
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
-  int nx{0}, ny{0};
+  int nx{-1}, ny{-1};
 
   /// Time-derivative, can be nullptr
   Field2D* deriv{nullptr};
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 422523ed2e..fabe2b646d 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -551,7 +551,7 @@ public:
 
 protected:
   /// Array sizes (from fieldmesh). These are valid only if fieldmesh is not null
-  int nx{0}, ny{0}, nz{0};
+  int nx{-1}, ny{-1}, nz{-1};
 
   /// Internal data array. Handles allocation/freeing of memory
   Array<BoutReal> data;
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index a0b2b440e5..9cad2652a0 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -4,7 +4,7 @@
  * Class for 2D X-Y profiles
  *
  **************************************************************************
- * Copyright 2010 - 2025 BOUT++ developers
+ * Copyright 2010 - 2026 BOUT++ developers
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -47,15 +47,22 @@
 Field2D::Field2D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes directions_in,
                  [[maybe_unused]] std::optional<size_t> regionID)
     : Field(localmesh, location_in, directions_in) {
-  // Note: Even if fieldmesh is not null, LocalNx and LocalNy may not
-  // be initialised.
+  if (fieldmesh != nullptr) {
+    // Note: Even if fieldmesh is not null, LocalNx and LocalNy may
+    // not be initialised.
+    nx = fieldmesh->LocalNx;
+    ny = fieldmesh->LocalNy;
+  }
 #if BOUT_USE_TRACK
   name = "<F2D>";
 #endif
 }
 
 Field2D::Field2D(const Field2D& f) : Field(f), data(f.data) {
-
+  if (fieldmesh != nullptr) {
+    nx = fieldmesh->LocalNx;
+    ny = fieldmesh->LocalNy;
+  }
 #if BOUT_USE_TRACK
   name = f.name;
 #endif
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 1241dee465..61bc9ce86a 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -65,13 +65,25 @@ Field3D::Field3D(Mesh* localmesh, CELL_LOC location_in, DirectionTypes direction
 #if BOUT_USE_TRACK
   name = "<F3D>";
 #endif
+
+  if (fieldmesh != nullptr) {
+    nx = fieldmesh->LocalNx;
+    ny = fieldmesh->LocalNy;
+    nz = fieldmesh->LocalNz;
+  }
 }
 
 /// Doesn't copy any data, just create a new reference to the same data (copy on change
 /// later)
 Field3D::Field3D(const Field3D& f)
     : Field(f), data(f.data), yup_fields(f.yup_fields), ydown_fields(f.ydown_fields),
-      regionID(f.regionID) {}
+      regionID(f.regionID) {
+  if (fieldmesh != nullptr) {
+    nx = fieldmesh->LocalNx;
+    ny = fieldmesh->LocalNy;
+    nz = fieldmesh->LocalNz;
+  }
+}
 
 Field3D::Field3D(const Field2D& f)
     : Field(f), nx(fieldmesh->LocalNx), ny(fieldmesh->LocalNy), nz(fieldmesh->LocalNz) {

From cd04c41650c3d5527cf1fbbb61adbb8756de4484 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 28 Mar 2026 11:22:00 -0700
Subject: [PATCH 1432/1827] FieldFactory: Don't test values in Y boundary

---
 tests/unit/field/test_field_factory.cxx | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index c7b5bcd9ae..7f31c83a3b 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -2,8 +2,10 @@
 
 #include "fake_mesh.hxx"
 #include "test_extras.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/constants.hxx"
+#include "bout/coordinates.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
@@ -12,13 +14,16 @@
 #include "bout/options_io.hxx"
 #include "bout/output.hxx"
 #include "bout/paralleltransform.hxx"
+#include "bout/sys/expressionparser.hxx"
 #include "bout/sys/generator_context.hxx"
 #include "bout/traits.hxx"
+#include "bout/utils.hxx"
 
 #include "fake_mesh_fixture.hxx"
 #include "test_tmpfiles.hxx"
 
 #include <memory>
+#include <string>
 
 // The unit tests use the global mesh
 using namespace bout::globals;
@@ -777,7 +782,7 @@ TEST_F(FieldFactoryTest, Recursion) {
   opt["input"]["max_recursion_depth"] = 4; // Should be sufficient for n=6
 
   // Create a factory with a max_recursion_depth != 0
-  FieldFactory factory_rec(nullptr, &opt);
+  const FieldFactory factory_rec(nullptr, &opt);
 
   // Fibonacci sequence: 1 1 2 3 5 8
   opt["fib"] = "where({n} - 2.5, [n={n}-1](fib) + [n={n}-2](fib), 1)";
@@ -809,7 +814,7 @@ TEST_F(FieldFactoryTest, ResolveLocalOptions) {
   options["f"] = "2 + 2";
   options["g"] = "f * f";
 
-  FieldFactoryExposer factory_local(mesh, &options);
+  const FieldFactoryExposer factory_local(mesh, &options);
   auto g = factory_local.resolve("g");
 
   EXPECT_EQ(g->generate({}), 16);
@@ -1040,7 +1045,7 @@ struct FieldFactoryFieldVariableTest : public FakeMeshFixture {
 };
 
 TEST_F(FieldFactoryFieldVariableTest, CreateField3D) {
-  bout::testing::TempFile filename;
+  const bout::testing::TempFile filename;
 
   {
     // Write some fields to a grid file
@@ -1063,12 +1068,12 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField3D) {
 
     const auto output = factory.create3D("rho * cos(theta)");
     const auto x = factory.create3D("x");
-    EXPECT_TRUE(IsFieldEqual(output, x, "RGN_ALL", 1e-14));
+    EXPECT_TRUE(IsFieldEqual(output, x, "RGN_NOBNDRY", 1e-14));
   }
 }
 
 TEST_F(FieldFactoryFieldVariableTest, CreateField2D) {
-  bout::testing::TempFile filename;
+  const bout::testing::TempFile filename;
 
   {
     // Write some fields to a grid file
@@ -1096,7 +1101,7 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField2D) {
 }
 
 TEST_F(FieldFactoryFieldVariableTest, ReadBoutReal) {
-  bout::testing::TempFile filename;
+  const bout::testing::TempFile filename;
 
   {
     const Options grid{{"rho", 4},
@@ -1127,7 +1132,7 @@ TEST_F(FieldFactoryFieldVariableTest, NoMeshFile) {
 }
 
 TEST_F(FieldFactoryFieldVariableTest, MissingVariable) {
-  bout::testing::TempFile filename;
+  const bout::testing::TempFile filename;
 
   {
     // Write some fields to a grid file

From 787538420396167dafd700b302a50899dc4f1274 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 28 Mar 2026 11:55:11 -0700
Subject: [PATCH 1433/1827] Clang formatting

---
 include/bout/field2d.hxx                      |  2 +-
 include/bout/invertable_operator.hxx          |  4 +-
 include/bout/options.hxx                      | 24 +++++-----
 include/bout/output.hxx                       |  8 ++--
 include/bout/physicsmodel.hxx                 | 47 +++++++++----------
 include/bout/sys/generator_context.hxx        |  2 +-
 include/bout/utils.hxx                        | 18 +++----
 src/invert/laplace/common_transform.cxx       | 24 +++++-----
 .../laplace/impls/serial_tri/serial_tri.hxx   |  2 +-
 src/invert/laplace/impls/spt/spt.hxx          | 14 +++---
 .../laplacexy/impls/hypre/laplacexy-hypre.cxx |  6 ++-
 src/mesh/coordinates_accessor.cxx             |  6 ++-
 src/mesh/parallel/fci_comm.hxx                |  4 +-
 src/mesh/parallel/shiftedmetric.cxx           |  4 +-
 src/solver/impls/petsc/petsc.cxx              | 20 ++++----
 src/solver/impls/snes/snes.hxx                |  6 +--
 src/sys/msg_stack.cxx                         |  8 +++-
 src/sys/options/options_netcdf.cxx            | 40 ++++++++--------
 18 files changed, 123 insertions(+), 116 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 0b437e1bd8..5143889d4c 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -42,8 +42,8 @@ class Field2D;
 #include "bout/region.hxx"
 
 #include <cstddef>
-#include <ostream>
 #include <iostream>
+#include <ostream>
 #include <string>
 
 #if BOUT_HAS_RAJA
diff --git a/include/bout/invertable_operator.hxx b/include/bout/invertable_operator.hxx
index d61c258654..6dcd92897a 100644
--- a/include/bout/invertable_operator.hxx
+++ b/include/bout/invertable_operator.hxx
@@ -135,9 +135,9 @@ public:
       : operatorFunction(func), preconditionerFunction(func),
         opt(optIn == nullptr ? Options::getRoot()->getSection("invertableOperator")
                              : optIn),
-        localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), lib(opt){
+        localmesh(localmeshIn == nullptr ? bout::globals::mesh : localmeshIn), lib(opt) {
 
-                                                                               };
+        };
 
   /// Destructor just has to cleanup the PETSc owned objects.
   ~InvertableOperator() {
diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 03e95488a8..48840a7b6f 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -74,19 +74,19 @@ class Options;
  * which can be used as a map.
  *
  *     Options options;
- *     
+ *
  *     // Set values
  *     options["key"] = 1.0;
  *
  *     // Get values. Throws BoutException if not found
- *     int val = options["key"]; // Sets val to 1 
+ *     int val = options["key"]; // Sets val to 1
  *
  *     // Return as specified type. Throws BoutException if not found
  *     BoutReal var = options["key"].as<BoutReal>();
  *
  *     // A default value can be used if key is not found
  *     BoutReal value = options["pi"].withDefault(3.14);
- *    
+ *
  *     // Assign value with source label. Throws if already has a value from same source
  *     options["newkey"].assign(1.0, "some source");
  *
@@ -94,7 +94,7 @@ class Options;
  *     options["newkey"].force(2.0, "some source");
  *
  * A legacy interface is also supported:
- * 
+ *
  *     options.set("key", 1.0, "code"); // Sets a key from source "code"
  *
  *     int val;
@@ -119,9 +119,9 @@ class Options;
  *
  * Each Options object can also contain any number of sections, which are
  * themselves Options objects.
- * 
+ *
  *     Options &section = options["section"];
- * 
+ *
  * which can be nested:
  *
  *     options["section"]["subsection"]["value"] = 3;
@@ -134,13 +134,13 @@ class Options;
  *
  * e.g.
  *     options->getSection("section")->getSection("subsection")->set("value", 3);
- * 
+ *
  * Options also know about their parents:
  *
  *     Options &parent = section.parent();
- *     
+ *
  * or
- * 
+ *
  *     Options *parent = section->getParent();
  *
  * Root options object
@@ -150,8 +150,8 @@ class Options;
  * there is a global singleton Options object which can be accessed with a static function
  *
  *    Options &root = Options::root();
- * 
- * or 
+ *
+ * or
  *
  *    Options *root = Options::getRoot();
  *
@@ -193,7 +193,7 @@ public:
   /// @param[in] parent        Parent object
   /// @param[in] sectionName   Name of the section, including path from the root
   Options(Options* parent_instance, std::string full_name)
-      : parent_instance(parent_instance), full_name(std::move(full_name)){};
+      : parent_instance(parent_instance), full_name(std::move(full_name)) {};
 
   /// Initialise with a value
   /// These enable Options to be constructed using initializer lists
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index 9416ab411b..43fc6c59bf 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -166,13 +166,13 @@ class ConditionalOutput : public Output {
 public:
   /// @param[in] base    The Output object which will be written to if enabled
   /// @param[in] enabled Should this be enabled by default?
-  ConditionalOutput(Output* base, bool enabled = true) : base(base), enabled(enabled){};
+  ConditionalOutput(Output* base, bool enabled = true) : base(base), enabled(enabled) {};
 
   /// Constuctor taking ConditionalOutput. This allows several layers of conditions
   ///
   /// @param[in] base    A ConditionalOutput which will be written to if enabled
   ///
-  ConditionalOutput(ConditionalOutput* base) : base(base), enabled(base->enabled){};
+  ConditionalOutput(ConditionalOutput* base) : base(base), enabled(base->enabled) {};
 
   /// If enabled, writes a string using fmt formatting
   /// by calling base->write
@@ -237,7 +237,7 @@ private:
 ///    output_debug << "debug message";
 /// compile but have no effect if BOUT_USE_OUTPUT_DEBUG is false
 template <typename T>
-DummyOutput& operator<<(DummyOutput& out, T const& UNUSED(t)) {
+DummyOutput& operator<<(DummyOutput& out, const T& UNUSED(t)) {
   return out;
 }
 
@@ -261,7 +261,7 @@ inline ConditionalOutput& operator<<(ConditionalOutput& out, stream_manipulator
 }
 
 template <typename T>
-ConditionalOutput& operator<<(ConditionalOutput& out, T const& t) {
+ConditionalOutput& operator<<(ConditionalOutput& out, const T& t) {
   if (out.isEnabled()) {
     *out.getBase() << t;
   }
diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index d653d96d68..8e8e3814cd 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -1,20 +1,20 @@
 /*!************************************************************************
  * \file physicsmodel.hxx
- * 
+ *
  * @brief Base class for Physics Models
- * 
- * 
+ *
+ *
  *
  * Changelog:
- * 
+ *
  * 2013-08 Ben Dudson <benjamin.dudson@york.ac.uk>
  *    * Initial version
- * 
+ *
  **************************************************************************
  * Copyright 2013 B.D.Dudson
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -167,9 +167,9 @@ public:
    *
    * Output
    * ------
-   * 
+   *
    * The time derivatives will be put in the ddt() variables
-   * 
+   *
    * Returns a flag: 0 indicates success, non-zero an error flag
    */
   int runRHS(BoutReal time, bool linear = false);
@@ -203,7 +203,7 @@ public:
   bool hasPrecon();
 
   /*!
-   * Run the preconditioner. The system state should be in the 
+   * Run the preconditioner. The system state should be in the
    * evolving variables, and the vector to be solved in the ddt() variables.
    * The result will be put in the ddt() variables.
    *
@@ -219,7 +219,7 @@ public:
 
   /*!
    * Run the Jacobian-vector multiplication function
-   * 
+   *
    * Note: this is usually only called by the Solver
    */
   int runJacobian(BoutReal t);
@@ -241,10 +241,10 @@ protected:
   // The init and rhs functions are implemented by user code to specify problem
   /*!
    * @brief This function is called once by the solver at the start of a simulation.
-   * 
+   *
    * A valid PhysicsModel must implement this function
-   * 
-   * Variables should be read from the inputs, and the variables to 
+   *
+   * Variables should be read from the inputs, and the variables to
    * be evolved should be specified.
    */
   virtual int init(bool restarting) = 0;
@@ -258,7 +258,7 @@ protected:
   /*!
    * @brief This function is called by the time integration solver
    * at least once per time step
-   * 
+   *
    * Variables being evolved will be set by the solver
    * before the call, and this function must calculate
    * and set the time-derivatives.
@@ -278,10 +278,10 @@ protected:
   /// Add additional variables other than the evolving variables to the restart files
   virtual void restartVars(Options& options);
 
-  /* 
+  /*
      If split operator is set to true, then
      convective() and diffusive() are called instead of rhs()
-     
+
      For implicit-explicit schemes, convective() will typically
      be treated explicitly, whilst diffusive() will be treated implicitly.
      For unsplit methods, both convective and diffusive will be called
@@ -334,7 +334,7 @@ protected:
    *
    * @param[in] var  The variable to evolve
    * @param[in] name The name to use for variable initialisation and output
-   * 
+   *
    * Note that the variable must not be destroyed (e.g. go out of scope)
    * after this call, since a pointer to \p var is stored in the solver.
    *
@@ -358,11 +358,11 @@ protected:
    * Specify a constrained variable \p var, which will be
    * adjusted to make \p F_var equal to zero.
    * If the solver does not support constraints then this will throw an exception
-   * 
+   *
    * @param[in] var  The variable the solver should modify
    * @param[in] F_var  The control variable, which the user will set
    * @param[in] name   The name to use for initialisation and output
-   * 
+   *
    */
   bool bout_constrain(Field3D& var, Field3D& F_var, const char* name);
 
@@ -491,8 +491,7 @@ private:
 
 /// Add fields to the solver.
 /// This should accept up to ten arguments
-#define SOLVE_FOR(...) \
-  { MACRO_FOR_EACH(SOLVE_FOR1, __VA_ARGS__) }
+#define SOLVE_FOR(...) {MACRO_FOR_EACH(SOLVE_FOR1, __VA_ARGS__)}
 
 /// Write this variable once to the grid file
 #define SAVE_ONCE1(var) dump.addOnce(var, #var);
@@ -532,8 +531,7 @@ private:
     dump.addOnce(var6, #var6);                         \
   }
 
-#define SAVE_ONCE(...) \
-  { MACRO_FOR_EACH(SAVE_ONCE1, __VA_ARGS__) }
+#define SAVE_ONCE(...) {MACRO_FOR_EACH(SAVE_ONCE1, __VA_ARGS__)}
 
 /// Write this variable every timestep
 #define SAVE_REPEAT1(var) dump.addRepeat(var, #var);
@@ -573,7 +571,6 @@ private:
     dump.addRepeat(var6, #var6);                         \
   }
 
-#define SAVE_REPEAT(...) \
-  { MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__) }
+#define SAVE_REPEAT(...) {MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__)}
 
 #endif // BOUT_PHYSICS_MODEL_H
diff --git a/include/bout/sys/generator_context.hxx b/include/bout/sys/generator_context.hxx
index e39eea1835..080b4d8ed7 100644
--- a/include/bout/sys/generator_context.hxx
+++ b/include/bout/sys/generator_context.hxx
@@ -33,7 +33,7 @@ public:
   /// The location on the boundary
   Context(const BoundaryRegion* bndry, int iz, CELL_LOC loc, BoutReal t, Mesh* msh);
   Context(const BoundaryRegion* bndry, CELL_LOC loc, BoutReal t, Mesh* msh)
-      : Context(bndry, 0, loc, t, msh){};
+      : Context(bndry, 0, loc, t, msh) {};
 
   BoutReal x() const { return get("x"); }
   BoutReal y() const { return get("y"); }
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 5088a025c1..eae3b27730 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -8,7 +8,7 @@
  * Copyright 2010 - 2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -484,7 +484,7 @@ inline bool is_pow2(int x) { return x && !((x - 1) & x); }
 
 /*!
  * Return the sign of a number \p a
- * by testing if a > 0 
+ * by testing if a > 0
  */
 template <typename T>
 T SIGN(T a) { // Return +1 or -1 (0 -> +1)
@@ -511,7 +511,7 @@ inline void checkData(BoutReal f) {
 }
 #else
 /// Ignored with disabled CHECK; Throw an exception if \p f is not finite
-inline void checkData(BoutReal UNUSED(f)){};
+inline void checkData(BoutReal UNUSED(f)) {};
 #endif
 
 /*!
@@ -587,7 +587,7 @@ BoutReal stringToReal(const std::string& s);
 
 /*!
  * Convert a string to an int
- * 
+ *
  * Throws BoutException if can't be done
  */
 int stringToInt(const std::string& s);
@@ -604,7 +604,7 @@ std::list<std::string>& strsplit(const std::string& s, char delim,
 
 /*!
  * Split a string on a given delimiter
- * 
+ *
  * @param[in] s     The string to split (not modified by call)
  * @param[in] delim The delimiter to split on (single char)
  */
@@ -612,7 +612,7 @@ std::list<std::string> strsplit(const std::string& s, char delim);
 
 /*!
  * Strips leading and trailing spaces from a string
- * 
+ *
  * @param[in] s   The string to trim (not modified)
  * @param[in] c   Collection of characters to remove
  */
@@ -620,7 +620,7 @@ std::string trim(const std::string& s, const std::string& c = " \t\r");
 
 /*!
  * Strips leading spaces from a string
- * 
+ *
  * @param[in] s   The string to trim (not modified)
  * @param[in] c   Collection of characters to remove
  */
@@ -628,7 +628,7 @@ std::string trimLeft(const std::string& s, const std::string& c = " \t");
 
 /*!
  * Strips leading spaces from a string
- * 
+ *
  * @param[in] s   The string to trim (not modified)
  * @param[in] c   Collection of characters to remove
  */
@@ -636,7 +636,7 @@ std::string trimRight(const std::string& s, const std::string& c = " \t\r");
 
 /*!
  * Strips the comments from a string
- * 
+ *
  * @param[in] s   The string to trim (not modified)
  * @param[in] c   Collection of characters to remove
  */
diff --git a/src/invert/laplace/common_transform.cxx b/src/invert/laplace/common_transform.cxx
index 847add4fea..98571624a1 100644
--- a/src/invert/laplace/common_transform.cxx
+++ b/src/invert/laplace/common_transform.cxx
@@ -28,8 +28,8 @@ FFTTransform::FFTTransform(const Mesh& mesh, int nmode, int xs, int xe, int ys,
 
 auto FFTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
                            const Field3D& x0, const Field2D& Acoef, const Field2D& C1coef,
-                           const Field2D& C2coef,
-                           const Field2D& Dcoef) const -> Matrices {
+                           const Field2D& C2coef, const Field2D& Dcoef) const
+    -> Matrices {
 
   Matrices result(nsys, nx);
 
@@ -79,8 +79,8 @@ auto FFTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
   return result;
 }
 
-auto FFTTransform::backward(const Field3D& rhs,
-                            const Matrix<dcomplex>& xcmplx3D) const -> Field3D {
+auto FFTTransform::backward(const Field3D& rhs, const Matrix<dcomplex>& xcmplx3D) const
+    -> Field3D {
   Field3D x{emptyFrom(rhs)};
 
   // FFT back to real space
@@ -162,8 +162,8 @@ auto FFTTransform::forward(const Laplacian& laplacian, const FieldPerp& rhs,
   return result;
 }
 
-auto FFTTransform::backward(const FieldPerp& rhs,
-                            const Matrix<dcomplex>& xcmplx) const -> FieldPerp {
+auto FFTTransform::backward(const FieldPerp& rhs, const Matrix<dcomplex>& xcmplx) const
+    -> FieldPerp {
   FieldPerp x{emptyFrom(rhs)};
 
   // FFT back to real space
@@ -209,8 +209,8 @@ DSTTransform::DSTTransform(const Mesh& mesh, int nmode, int xs, int xe, int ys,
 
 auto DSTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
                            const Field3D& x0, const Field2D& Acoef, const Field2D& C1coef,
-                           const Field2D& C2coef,
-                           const Field2D& Dcoef) const -> Matrices {
+                           const Field2D& C2coef, const Field2D& Dcoef) const
+    -> Matrices {
 
   Matrices result(nsys, nx);
 
@@ -260,8 +260,8 @@ auto DSTTransform::forward(const Laplacian& laplacian, const Field3D& rhs,
   return result;
 }
 
-auto DSTTransform::backward(const Field3D& rhs,
-                            const Matrix<dcomplex>& xcmplx3D) const -> Field3D {
+auto DSTTransform::backward(const Field3D& rhs, const Matrix<dcomplex>& xcmplx3D) const
+    -> Field3D {
   Field3D x{emptyFrom(rhs)};
 
   // DST back to real space
@@ -346,8 +346,8 @@ auto DSTTransform::forward(const Laplacian& laplacian, const FieldPerp& rhs,
   return result;
 }
 
-auto DSTTransform::backward(const FieldPerp& rhs,
-                            const Matrix<dcomplex>& xcmplx) const -> FieldPerp {
+auto DSTTransform::backward(const FieldPerp& rhs, const Matrix<dcomplex>& xcmplx) const
+    -> FieldPerp {
   FieldPerp x{emptyFrom(rhs)};
 
   // DST back to real space
diff --git a/src/invert/laplace/impls/serial_tri/serial_tri.hxx b/src/invert/laplace/impls/serial_tri/serial_tri.hxx
index 4aed777b7c..332c272f3f 100644
--- a/src/invert/laplace/impls/serial_tri/serial_tri.hxx
+++ b/src/invert/laplace/impls/serial_tri/serial_tri.hxx
@@ -52,7 +52,7 @@ class LaplaceSerialTri : public Laplacian {
 public:
   LaplaceSerialTri(Options* opt = nullptr, const CELL_LOC loc = CELL_CENTRE,
                    Mesh* mesh_in = nullptr, Solver* solver = nullptr);
-  ~LaplaceSerialTri(){};
+  ~LaplaceSerialTri() {};
 
   using Laplacian::setCoefA;
   void setCoefA(const Field2D& val) override {
diff --git a/src/invert/laplace/impls/spt/spt.hxx b/src/invert/laplace/impls/spt/spt.hxx
index a3b1acb7c3..e951f431e7 100644
--- a/src/invert/laplace/impls/spt/spt.hxx
+++ b/src/invert/laplace/impls/spt/spt.hxx
@@ -1,16 +1,16 @@
 /**************************************************************************
- * Perpendicular Laplacian inversion. 
+ * Perpendicular Laplacian inversion.
  *                           PARALLEL CODE - SIMPLE ALGORITHM
- * 
+ *
  * I'm just calling this Simple Parallel Tridag. Naive parallelisation of
  * the serial code. For use as a reference case.
- * 
+ *
  * Overlap calculation / communication of poloidal slices to achieve some
  * parallelism.
  *
  * Changelog
  * ---------
- * 
+ *
  * 2014-06  Ben Dudson <benjamin.dudson@york.ac.uk>
  *     * Removed static variables in functions, changing to class members.
  *
@@ -18,7 +18,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -142,8 +142,8 @@ private:
     Array<BoutReal> buffer;
   };
 
-  int ys, ye;         // Range of Y indices
-  SPT_data slicedata; // Used to solve for a single FieldPerp
+  int ys, ye;              // Range of Y indices
+  SPT_data slicedata;      // Used to solve for a single FieldPerp
   Array<SPT_data> alldata; // Used to solve a Field3D
 
   Array<dcomplex> dc1d; ///< 1D in Z for taking FFTs
diff --git a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
index 439d07a4e5..61632a332d 100644
--- a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
@@ -23,8 +23,10 @@
 #include <memory>
 
 #if BOUT_HAS_CUDA && defined(__CUDACC__)
-#define gpuErrchk(ans) \
-  { gpuAssert((ans), __FILE__, __LINE__); }
+#define gpuErrchk(ans)                    \
+  {                                       \
+    gpuAssert((ans), __FILE__, __LINE__); \
+  }
 inline void gpuAssert(cudaError_t code, const char* file, int line, bool abort = true) {
   if (code != cudaSuccess) {
     fprintf(stderr, "GPUassert: %s %s %d\n", cudaGetErrorString(code), file, line);
diff --git a/src/mesh/coordinates_accessor.cxx b/src/mesh/coordinates_accessor.cxx
index 0ce4b664b5..c874ea3ac2 100644
--- a/src/mesh/coordinates_accessor.cxx
+++ b/src/mesh/coordinates_accessor.cxx
@@ -45,8 +45,10 @@ CoordinatesAccessor::CoordinatesAccessor(const Coordinates* coords) {
   data[stripe_size * ind.ind + static_cast<int>(Offset::symbol)] = coords->symbol[ind];
 
   // Implement copy for each argument
-#define COPY_STRIPE(...) \
-  { MACRO_FOR_EACH(COPY_STRIPE1, __VA_ARGS__) }
+#define COPY_STRIPE(...)                      \
+  {                                           \
+    MACRO_FOR_EACH(COPY_STRIPE1, __VA_ARGS__) \
+  }
 
   // Iterate over all points in the field
   // Note this could be 2D or 3D, depending on FieldMetric type
diff --git a/src/mesh/parallel/fci_comm.hxx b/src/mesh/parallel/fci_comm.hxx
index 324cae8a22..34512b18c4 100644
--- a/src/mesh/parallel/fci_comm.hxx
+++ b/src/mesh/parallel/fci_comm.hxx
@@ -67,7 +67,7 @@ struct ProcLocal {
 struct GlobalToLocal1D {
   GlobalToLocal1D(int mg, int npe, int localwith, bool periodic)
       : mg(mg), npe(npe), localwith(localwith), local(localwith - (2 * mg)),
-        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic){};
+        global(local * npe), globalwith(global + (2 * mg)), periodic(periodic) {};
   ProcLocal convert(int id) const;
   int getLocalWith() const { return localwith; }
   int getGlobalWith() const { return globalwith; }
@@ -104,7 +104,7 @@ public:
   const BoutReal& operator[](IndG3D ind) const;
   GlobalField3DAccessInstance(const GlobalField3DAccess* gfa,
                               std::vector<BoutReal>&& data)
-      : gfa(gfa), data(std::move(data)){};
+      : gfa(gfa), data(std::move(data)) {};
 
 private:
   const GlobalField3DAccess* gfa;
diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 64c6d9a2ce..f167824541 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -39,8 +39,8 @@ void ShiftedMetric::checkInputGrid() {
                             "Should be 'shiftedmetric'.");
     }
   } // else: parallel_transform variable not found in grid input, indicates older input
-    //       file or grid from options so must rely on the user having ensured the type is
-    //       correct
+  //       file or grid from options so must rely on the user having ensured the type is
+  //       correct
 }
 
 void ShiftedMetric::outputVars(Options& output_options) {
diff --git a/src/solver/impls/petsc/petsc.cxx b/src/solver/impls/petsc/petsc.cxx
index 1e1e05596b..cc884c240c 100644
--- a/src/solver/impls/petsc/petsc.cxx
+++ b/src/solver/impls/petsc/petsc.cxx
@@ -64,10 +64,10 @@
 
 class ColoringStencil {
 private:
-  bool static isInSquare(int const i, int const j, int const n_square) {
+  bool static isInSquare(const int i, const int j, const int n_square) {
     return std::abs(i) <= n_square && std::abs(j) <= n_square;
   }
-  bool static isInCross(int const i, int const j, int const n_cross) {
+  bool static isInCross(const int i, const int j, const int n_cross) {
     if (i == 0) {
       return std::abs(j) <= n_cross;
     }
@@ -76,7 +76,7 @@ class ColoringStencil {
     }
     return false;
   }
-  bool static isInTaxi(int const i, int const j, int const n_taxi) {
+  bool static isInTaxi(const int i, const int j, const int n_taxi) {
     return std::abs(i) + std::abs(j) <= n_taxi;
   }
 
@@ -614,7 +614,7 @@ int PetscSolver::init() {
         n_taxi = 2;
       }
 
-      auto const xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
+      const auto xy_offsets = ColoringStencil::getOffsets(n_square, n_taxi, n_cross);
       {
         // This is ugly but can't think of a better and robust way to
         // count the non-zeros for some arbitrary stencil
@@ -734,7 +734,7 @@ int PetscSolver::init() {
       // Mark non-zero entries
 
       output_progress.write("Marking non-zero Jacobian entries\n");
-      PetscScalar const val = 1.0;
+      const PetscScalar val = 1.0;
       for (int x = mesh->xstart; x <= mesh->xend; x++) {
         for (int y = mesh->ystart; y <= mesh->yend; y++) {
 
@@ -753,21 +753,21 @@ int PetscSolver::init() {
                 continue;
               }
 
-              int const ind2 = ROUND(index(xi, yi, 0));
+              const int ind2 = ROUND(index(xi, yi, 0));
               if (ind2 < 0) {
                 continue; // A boundary point
               }
 
               // Depends on all variables on this cell
               for (int j = 0; j < n2d; j++) {
-                PetscInt const col = ind2 + j;
+                const PetscInt col = ind2 + j;
                 PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
               }
             }
           }
           // 3D fields
           for (int z = mesh->zstart; z <= mesh->zend; z++) {
-            int const ind = ROUND(index(x, y, z));
+            const int ind = ROUND(index(x, y, z));
 
             for (int i = 0; i < n3d; i++) {
               PetscInt row = ind + i;
@@ -777,7 +777,7 @@ int PetscSolver::init() {
 
               // Depends on 2D fields
               for (int j = 0; j < n2d; j++) {
-                PetscInt const col = ind0 + j;
+                const PetscInt col = ind0 + j;
                 PetscCall(MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES));
               }
 
@@ -802,7 +802,7 @@ int PetscSolver::init() {
 
                   // 3D fields on this cell
                   for (int j = 0; j < n3d; j++) {
-                    PetscInt const col = ind2 + j;
+                    const PetscInt col = ind2 + j;
                     int ierr = MatSetValues(Jfd, 1, &row, 1, &col, &val, INSERT_VALUES);
 
                     if (ierr != 0) {
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index fbcf3baddf..28f9881cab 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -202,8 +202,8 @@ private:
   BoutReal kI; ///< (0.2 - 0.4) Integral parameter (smooths history of changes)
   BoutReal kD; ///< (0.1 - 0.3) Derivative (dampens oscillation - optional)
   bool pid_consider_failures; ///< Reduce timestep increases if recent solves have failed
-  BoutReal recent_failure_rate;            ///< Rolling average of recent failure rate
-  BoutReal last_failure_weight;            ///< 1 / number of recent solves
+  BoutReal recent_failure_rate; ///< Rolling average of recent failure rate
+  BoutReal last_failure_weight; ///< 1 / number of recent solves
 
   BoutReal nl_its_prev;
   BoutReal nl_its_prev2;
@@ -245,7 +245,7 @@ private:
   bool matrix_free_operator; ///< Use matrix free Jacobian in the operator?
   int lag_jacobian;          ///< Re-use Jacobian
   bool jacobian_persists; ///< Re-use Jacobian and preconditioner across nonlinear solves
-  bool use_coloring;         ///< Use matrix coloring
+  bool use_coloring;      ///< Use matrix coloring
 
   bool jacobian_recalculated; ///< Flag set when Jacobian is recalculated
   bool prune_jacobian;        ///< Remove small elements in the Jacobian?
diff --git a/src/sys/msg_stack.cxx b/src/sys/msg_stack.cxx
index 3dbd7c2797..bd14a766ed 100644
--- a/src/sys/msg_stack.cxx
+++ b/src/sys/msg_stack.cxx
@@ -59,7 +59,9 @@ void MsgStack::pop() {
     return;
   }
   BOUT_OMP_SAFE(single)
-  { --position; }
+  {
+    --position;
+  }
 }
 
 void MsgStack::pop(int id) {
@@ -87,7 +89,9 @@ void MsgStack::clear() {
 
 void MsgStack::dump() {
   BOUT_OMP_SAFE(single)
-  { output << this->getDump(); }
+  {
+    output << this->getDump();
+  }
 }
 
 std::string MsgStack::getDump() {
diff --git a/src/sys/options/options_netcdf.cxx b/src/sys/options/options_netcdf.cxx
index f21f461c09..9170f7c284 100644
--- a/src/sys/options/options_netcdf.cxx
+++ b/src/sys/options/options_netcdf.cxx
@@ -132,25 +132,27 @@ void readGroup(const std::string& filename, const NcGroup& group, Options& resul
               {s2i(dims[0].getSize()), s2i(dims[1].getSize()), s2i(dims[2].getSize())});
           // We need to explicitly copy file, so that there is a pointer to the file, and
           // the file does not get closed, which would prevent us from reading.
-          result[var_name].setLazyLoad(std::make_unique<std::function<Tensor<double>(
-                                           int, int, int, int, int, int)>>(
-              [file, var](int xstart, int xend, int ystart, int yend, int zstart,
-                          int zend) {
-                const auto i2s = [](int i) {
-                  if (i < 0) {
-                    throw BoutException("BadCast {} < 0", i);
-                  }
-                  return static_cast<size_t>(i);
-                };
-                Tensor<double> value(xend - xstart + 1, yend - ystart + 1,
-                                     zend - zstart + 1);
-                const std::vector<size_t> index{i2s(xstart), i2s(ystart), i2s(zstart)};
-                const std::vector<size_t> count{i2s(xend - xstart + 1),
-                                                i2s(yend - ystart + 1),
-                                                i2s(zend - zstart + 1)};
-                var.getVar(index, count, value.begin());
-                return value;
-              }));
+          result[var_name].setLazyLoad(
+              std::make_unique<
+                  std::function<Tensor<double>(int, int, int, int, int, int)>>(
+                  [file, var](int xstart, int xend, int ystart, int yend, int zstart,
+                              int zend) {
+                    const auto i2s = [](int i) {
+                      if (i < 0) {
+                        throw BoutException("BadCast {} < 0", i);
+                      }
+                      return static_cast<size_t>(i);
+                    };
+                    Tensor<double> value(xend - xstart + 1, yend - ystart + 1,
+                                         zend - zstart + 1);
+                    const std::vector<size_t> index{i2s(xstart), i2s(ystart),
+                                                    i2s(zstart)};
+                    const std::vector<size_t> count{i2s(xend - xstart + 1),
+                                                    i2s(yend - ystart + 1),
+                                                    i2s(zend - zstart + 1)};
+                    var.getVar(index, count, value.begin());
+                    return value;
+                  }));
         } else {
           Tensor<double> value(static_cast<int>(dims[0].getSize()),
                                static_cast<int>(dims[1].getSize()),

From f94a1e12b5ef7daf3995828c07b1e15f5af0face Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 19 Jun 2026 14:22:11 +0100
Subject: [PATCH 1434/1827] Use `gridvar:` namespace for input variables read
 from grid

---
 manual/sphinx/user_docs/input_grids.rst | 82 +++++++++++++------------
 src/field/field_factory.cxx             |  4 +-
 tests/unit/field/test_field_factory.cxx |  4 +-
 3 files changed, 47 insertions(+), 43 deletions(-)

diff --git a/manual/sphinx/user_docs/input_grids.rst b/manual/sphinx/user_docs/input_grids.rst
index 402fb30d06..337fb16938 100644
--- a/manual/sphinx/user_docs/input_grids.rst
+++ b/manual/sphinx/user_docs/input_grids.rst
@@ -28,7 +28,7 @@ tensor is the identity matrix), but this can be changed by specifying
 the metric tensor components.
 
 Integer quantities such as ``nx`` can be numbers (like “260”), or
-expressions (like “256 + 2\*MXG”). 
+expressions (like “256 + 2\*MXG”).
 A common use is to make ``x`` and ``z`` dimensions have the same
 number of points, when ``x`` has ``mxg`` boundary cells on each
 boundary but ``z`` does not (since it is usually periodic):
@@ -37,14 +37,14 @@ boundary but ``z`` does not (since it is usually periodic):
 
     [mesh]
     nx = nz + 2*mxg  # X grid size
-    nz = 256         # Z grid size            
-    mxg = 2            
+    nz = 256         # Z grid size
+    mxg = 2
 
 
 Note that the order of the defintion within a section isn't important,
 variables can be used before they are defined. All variables are first
 read, and only processed if they are used.
-    
+
 Expressions are always calculated in floating point; When expressions
 are used to set integer quantities (such as the number of grid
 points), the expressions are calculated in floating point and then
@@ -60,7 +60,7 @@ the ``round`` function:
     nx = 256.4   # Error!
     nx = round(256.4) # ok
 
-    
+
 Real (floating-point) values can also be expressions, allowing quite
 complicated analytic inputs. For example in the example ``test-griddata``:
 
@@ -158,7 +158,9 @@ Cartesian.
 You can read additional quantities from the grid and make them available in
 expressions in the input file by listing them in the ``input:grid_variables``
 section, with the key being the name in the grid file (``mesh:file``) and the
-value being the type (one of ``field3d``, ``field2d``, ``boutreal``):
+value being the type (one of ``field3d``, ``field2d``, ``boutreal``). Variables
+read in this way are made available under a ``gridvar:`` namespace to avoid
+collisions with other input variables:
 
 .. code-block:: cfg
 
@@ -168,7 +170,7 @@ value being the type (one of ``field3d``, ``field2d``, ``boutreal``):
    scale = boutreal
 
    [mesh]
-   B = (scale / rho) * cos(theta)
+   B = (gridvar:scale / gridvar:rho) * cos(gridvar:theta)
 
 This section describes how to generate inputs for tokamak equilibria. If
 you’re not interested in tokamaks then you can skip to the next section.
@@ -219,7 +221,7 @@ From EFIT files
 A separate tool (in python) called `Hypnotoad <https://github.com/boutproject/hypnotoad>`_
 has been developed to create BOUT++ input files from R-Z equilibria. This can read EFIT ’g’
 (geqdsk) files, find flux surfaces, and calculate metric
-coefficients. 
+coefficients.
 
 From GRIDUE files
 --------------
@@ -281,7 +283,7 @@ As in the above code, creating an output file consists of the following steps:
 
 1. Define a magnetic field
 2. Define the grid points. This can be broken down into:
-   
+
    a) Define 2D "poloidal" grids
    b) Form a 3D grid by putting 2D grids together along the Y direction
 
@@ -307,9 +309,9 @@ In this case with 10 points in y (second argument to ``rectangular_grid(nx,ny,nz
 the y locations are :math:`\left(0.5, 1.5, 2.5, \ldots, 9.5\right)`.
 
 At each of these y locations ``rectangular_grid`` defines a rectangular 2D poloidal grid in
-the X-Z coordinates, by default with a length of 1 in each direction and centred on :math:`x=0,z=0`. 
+the X-Z coordinates, by default with a length of 1 in each direction and centred on :math:`x=0,z=0`.
 These 2D poloidal grids are then put together into a 3D ``Grid``. This process can be customised
-by separating step 2 (the ``rectangular_grid`` call) into stages 2a) and 2b). 
+by separating step 2 (the ``rectangular_grid`` call) into stages 2a) and 2b).
 For example, to create a periodic rectangular grid we could use the following::
 
    import numpy as np
@@ -333,7 +335,7 @@ input file (this is in ``examples/zoidberg/tokamak.py``)::
 
    import numpy as np
    import zoidberg
-   
+
    field = zoidberg.field.GEQDSK("g014220.00200") # Read magnetic field
 
    grid = zoidberg.grid.rectangular_grid(100, 10, 100,
@@ -345,13 +347,13 @@ input file (this is in ``examples/zoidberg/tokamak.py``)::
 
    # Create the forward and backward maps
    maps = zoidberg.make_maps(grid, field)
-   
+
    # Save to file
    zoidberg.write_maps(grid, field, maps, gridfile="grid.fci.nc")
 
    # Plot grid points and the points they map to in the forward direction
    zoidberg.plot.plot_forward_map(grid, maps)
-   
+
 In the last example only one poloidal grid was created (a ``RectangularPoloidalGrid``)
 and then re-used for each y slice. We can instead define a different grid for each y
 position. For example, to define a grid which expands along y (for some reason) we could do::
@@ -387,10 +389,10 @@ One way to create this grid is to define the grid points manually e.g.::
    r,theta = np.meshgrid(np.linspace(1,2,10),
                          np.linspace(0,2*np.pi, 10),
                          indexing="ij")
-   
+
    R = r * np.sin(theta)
    Z = r * np.cos(theta)
-  
+
    poloidal_grid = zoidberg.poloidal_grid.StructuredPoloidalGrid(R,Z)
 
 For more complicated shapes than circles, Zoidberg comes with an
@@ -402,11 +404,11 @@ outer boundaries::
    inner = zoidberg.rzline.shaped_line(R0=3.0, a=0.5,
                             elong=1.0, triang=0.0, indent=1.0,
                             n=50)
-   
+
    outer = zoidberg.rzline.shaped_line(R0=2.8, a=1.5,
                             elong=1.0, triang=0.0, indent=0.2,
                             n=50)
-   
+
    poloidal_grid = zoidberg.poloidal_grid.grid_elliptic(inner, outer,
                                                  100, 100, show=True)
 
@@ -414,9 +416,9 @@ which should produce the figure below:
 
 .. figure:: ../figs/zoidberg/elliptic_grid.png
    :name: elliptic
-   :alt: 
+   :alt:
    :scale: 50
-   
+
    A grid produced by ``grid_elliptic`` from shaped inner and outer lines
 
 
@@ -440,14 +442,14 @@ flux surface.
 At the moment this will not work correctly for slab geometries, but expects
 closed flux surfaces such as in a stellarator or tokamak. A simple test case
 is a straight stellarator::
-   
+
    import zoidberg
    field = zoidberg.field.StraightStellarator(I_coil=0.4, yperiod=10)
 
 By default ``StraightStellarator`` calculates the magnetic field due to four coils which spiral around
 the axis at a distance :math:`r=0.8` in a classical stellarator configuration. The ``yperiod``
 argument is the period in y after which the coils return to their starting locations.
-   
+
 To visualise the Poincare plot for this stellarator field, pass the ``MagneticField`` object
 to ``zoidberg.plot.plot_poincare``, together with start location(s) and periodicity information::
 
@@ -459,14 +461,14 @@ which should produce the following figure:
    :name: poincare
    :alt: Points on four oval shaped flux surfaces in x-z at three locations along the y direction
    :scale: 50
-   
+
    Poincare map of straight stellarator showing a single flux
    surface. Each colour corresponds to a different x-z plane
-   in the y direction. 
-           
+   in the y direction.
+
 The inputs here are the starting location :math:`\left(x,z\right) = \left(0.4, 0.0\right)`,
 and the periodicity in the y direction (10.0). By default this will
-integrate from this given starting location 40 times (``revs`` option) around the y domain (0 to 10). 
+integrate from this given starting location 40 times (``revs`` option) around the y domain (0 to 10).
 
 To create an ``RZline`` from these Poincare plots we need a
 list of points in order around the line. Since the points
@@ -476,14 +478,14 @@ this is a `known hard problem <https://en.wikipedia.org/wiki/Travelling_salesman
 but fortunately in this case the nearest neighbour algorithm seems to be quite robust provided there are enough points.
 
 An example of calculating a Poincare plot on a single y slice (y=0) and producing an ``RZline`` is::
-   
+
    from zoidberg.fieldtracer import trace_poincare
    rzcoord, ycoords = trace_poincare(field, 0.4, 0.0, 10.0,
                                      y_slices=[0])
-   
+
    R = rzcoord[:,0,0]
    Z = rzcoord[:,0,1]
-          
+
    line = zoidberg.rzline.line_from_points(R, Z)
 
    line.plot()
@@ -495,7 +497,7 @@ approximation to the flux surface, increase the number of points by setting the
 (y revolutions) in the ``trace_poincare`` call.
 
 In general the points along this line are not evenly
-distributed, but tend to cluster together in some regions and have large gaps in others. 
+distributed, but tend to cluster together in some regions and have large gaps in others.
 The elliptic grid generator places grid points on the boundaries
 which are uniform in the index of the ``RZline`` it is given.
 Passing a very uneven set of points will therefore result in
@@ -509,7 +511,7 @@ to create a grid file for a straight stellarator.
 
 Sections below now describe each part of Zoidberg in more detail. Further documentation
 of the API can be found in the docstrings and unit tests.
-   
+
 Magnetic fields
 ~~~~~~~~~~~~~~~
 
@@ -518,12 +520,12 @@ Magnetic fields can be defined in either cylindrical or Cartesian coordinates:
 
 * In Cartesian coordinates all (x,y,z) directions have the same units of length
 * In cylindrical coordinates the y coordinate is assumed to be an angle, so that
-  the distance in y is given by :math:`ds = R dy` where :math:`R` is the major radius.  
+  the distance in y is given by :math:`ds = R dy` where :math:`R` is the major radius.
 
 Which coordinate is used is controlled by the ``Rfunc`` method, which should return the
 major radius if using a cylindrical coordinate system.
-Should return ``None`` for a Cartesian coordinate system (the default). 
-  
+Should return ``None`` for a Cartesian coordinate system (the default).
+
 Several implementations inherit from ``MagneticField``, and provide:
 ``Bxfunc``, ``Byfunc``, ``Bzfunc`` which give the components of the magnetic field in
 the x,y and z directions respectively. These should be in the same units (e.g. Tesla) for
@@ -550,14 +552,14 @@ and has a given major radius (default 1)::
    field = zoidberg.field.CurvedSlab()
 
 Note that this uses a large aspect-ratio approximation, so the major radius
-is constant across the domain (independent of x). 
-    
+is constant across the domain (independent of x).
+
 Straight stellarator
 ++++++++++++++++++++
 
 This is generated by four coils with alternating currents arranged
 on the edge of a circle, which spiral around the axis::
-   
+
    import zoidberg
    field = zoidberg.field.StraightStellarator()
 
@@ -588,7 +590,7 @@ Plotting the magnetic field
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Routines to plot the magnetic field are in ``zoidberg.plot``. They include Poincare plots
-and 3D field line plots. 
+and 3D field line plots.
 
 For example, to make a Poincare plot from a MAST equilibrium::
 
@@ -634,7 +636,7 @@ To create a rectangular grid, pass the number of points and lengths in the x and
 to ``RectangularPoloidalGrid``::
 
    import zoidberg
-   
+
    rect = zoidberg.poloidal_grid.RectangularPoloidalGrid( nx, nz, Lx, Lz )
 
 By default the middle of the rectangle is at :math:`\left(R,Z\right) = \left(0,0\right)`
@@ -649,7 +651,7 @@ To create the structured curvilinear grids inner and outer lines are needed
 with the following formula:
 
 .. math::
-   
+
    R = R_0 - b + \left(a + b \cos\left(\theta\right)\cos\left(\theta + \delta\sin\left(\theta\right)\right)\right)
 
    Z = \left(1 + \epsilon\right)a\sin\left(\theta\right)
diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index 793ea9f278..8a8312d665 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -36,6 +36,7 @@
 #include <bout/utils.hxx>
 
 #include "fieldgenerators.hxx"
+#include "fmt/format.h"
 
 #include <cmath>
 #include <memory>
@@ -94,7 +95,8 @@ class FieldIndirect : public FieldGenerator {
 // Read variables from the grid file and make them available in expressions
 template <class T>
 auto add_grid_variable(FieldFactory& factory, Mesh& mesh, const std::string& name) {
-  factory.addGenerator(name, std::make_shared<GridVariable<T>>(&mesh, name));
+  factory.addGenerator(fmt::format("gridvar:{}", name),
+                       std::make_shared<GridVariable<T>>(&mesh, name));
 }
 
 auto read_grid_variables(FieldFactory& factory, Mesh& mesh, Options& options) {
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index 7f31c83a3b..25177c3169 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -1066,7 +1066,7 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField3D) {
     dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
     auto factory = FieldFactory{mesh, &options};
 
-    const auto output = factory.create3D("rho * cos(theta)");
+    const auto output = factory.create3D("gridvar:rho * cos(gridvar:theta)");
     const auto x = factory.create3D("x");
     EXPECT_TRUE(IsFieldEqual(output, x, "RGN_NOBNDRY", 1e-14));
   }
@@ -1094,7 +1094,7 @@ TEST_F(FieldFactoryFieldVariableTest, CreateField2D) {
     dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(new GridFile{filename});
     auto factory = FieldFactory{mesh, &options};
 
-    const auto output = factory.create2D("rho * cos(theta)");
+    const auto output = factory.create2D("gridvar:rho * cos(gridvar:theta)");
     const auto x = factory.create2D("x");
     EXPECT_TRUE(IsFieldEqual(output, x, "RGN_ALL", 1e-14));
   }

From 1c53604a06b600ac455460c111058f6aab9440d9 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 5 Jun 2026 19:15:12 +0100
Subject: [PATCH 1435/1827] Accumulated work trying to improve scaling for SNES

Has involved refactoring Solver to allow loading/saving from/to
arbitrary sets of fields. Have also changed how scale_vars works,
although I'll probably want to name a different setting for this. What
I've made it done doesn't appear to be what it was intended for
originally.
---
 include/bout/solver.hxx        | 213 ++++++++++++++++++++++++++++++++-
 src/solver/impls/snes/snes.cxx | 188 +++++++++++++++++++++--------
 src/solver/impls/snes/snes.hxx |  10 ++
 src/solver/solver.cxx          | 183 +---------------------------
 4 files changed, 365 insertions(+), 229 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 2e0da05224..90b2e5a59c 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -92,7 +92,8 @@ constexpr auto SOLVERIMEXBDF2 = "imexbdf2";
 constexpr auto SOLVERSNES = "snes";
 constexpr auto SOLVERRKGENERIC = "rkgeneric";
 
-enum class SOLVER_VAR_OP { LOAD_VARS, LOAD_DERIVS, SET_ID, SAVE_VARS, SAVE_DERIVS };
+enum class FieldCategories { VARS, DERIVS, MMS };
+enum class SOLVER_VAR_OP { LOAD, SET_ID, SAVE };
 
 /// A type to set where in the list monitors are added
 enum class MonitorPosition { BACK, FRONT };
@@ -391,6 +392,79 @@ protected:
     std::string description{""};         /// Description of what the variable is
   };
 
+  /// A structure for iterating over fields
+  template <FieldCategories C, class T>
+  struct VarIterator 
+  {
+    using iterator_category = std::random_access_iterator_tag;
+    using value_type = T;
+    using pointer = T*;
+    using reference = T&;
+    using underlying_iterator = std::vector<VarStr<T>>::iterator;
+    using difference_type = std::iterator_traits<underlying_iterator>::difference_type;
+
+    VarIterator(underlying_iterator _it) : it(std::move(_it)) {}
+
+    reference operator*() const {
+      switch (C) {
+      case(FieldCategories::VARS):
+        return *(it->var);
+      case(FieldCategories::DERIVS):
+        return *(it->F_var);
+      case(FieldCategories::MMS):
+        return *(it->MMS_err);
+      }
+    }
+    pointer operator->() const {
+      switch (C) {
+      case(FieldCategories::VARS):
+        return it->var;
+      case(FieldCategories::DERIVS):
+        return it->F_var;
+      case(FieldCategories::MMS):
+        return it->MMS_err.get();
+      }
+    }
+
+    VarIterator& operator++() { it++; return *this; }
+    VarIterator operator++(int) { VarIterator tmp = *this; ++(*this); return tmp; }
+    VarIterator& operator+=(difference_type n) { it += n; return *this; }
+    VarIterator operator+(difference_type n) const { return VarIterator(it + n); }
+    friend VarIterator operator+(difference_type n, const VarIterator& a) { return VarIterator(n + a.it); }
+
+    VarIterator& operator--() { it--; return *this; }
+    VarIterator operator--(int) { VarIterator tmp = *this; --(*this); return tmp; }
+    VarIterator& operator-=(difference_type n) { it -= n; return *this; }
+    VarIterator operator-(difference_type n) const { return VarIterator(it - n); }
+    friend VarIterator operator-(difference_type n, const VarIterator& a) { return VarIterator(n - a.it); }
+
+    difference_type operator-(const VarIterator& b) { return it - b.it; }
+    reference operator[](difference_type n) { return *VarIterator(it[n]); }
+    
+    friend bool operator== (const VarIterator& a, const VarIterator& b) { return a.it == b.it; }
+    friend bool operator!= (const VarIterator& a, const VarIterator& b) { return a.it != b.it; }
+    friend bool operator< (const VarIterator& a, const VarIterator& b) { return a.it < b.it; }
+    friend bool operator> (const VarIterator& a, const VarIterator& b) { return a.it > b.it; }
+    friend bool operator<= (const VarIterator& a, const VarIterator& b) { return a.it <= b.it; }
+    friend bool operator>= (const VarIterator& a, const VarIterator& b) { return a.it >= b.it; }
+
+  private:
+    underlying_iterator it;
+  };
+
+  template <FieldCategories C, class T>
+  struct VarRange {
+    using iterator = VarIterator<C, T>;
+
+    VarRange(std::vector<VarStr<T>>& vars) : _begin(vars.begin()), _end(vars.end()) {}
+
+    iterator begin() const { return _begin; }
+    iterator end() const {return _end; }
+  private:
+    iterator _begin, _end;
+  };
+
+  
   /// Does \p var represent field \p name?
   template <class T>
   friend bool operator==(const VarStr<T>& var, const std::string& name) {
@@ -519,6 +593,27 @@ protected:
   /// Get the currently set output timestep
   BoutReal getOutputTimestep() const { return output_timestep; }
 
+  /// Loop over variables (accessed by iterating the f2d_range and f3d_range
+  /// arguments) and domain. Used for all data operations for
+  /// consistency
+  template<class RangeF2D, class RangeF3D>
+  void loop_vars(RangeF2D f2d_range, RangeF3D f3d_range, BoutReal* udata, SOLVER_VAR_OP op) {
+    // Use global mesh: FIX THIS!
+    Mesh* mesh = bout::globals::mesh;
+
+    int p = 0; // Counter for location in udata array
+
+    // All boundaries
+    for (const auto& i2d : mesh->getRegion2D("RGN_BNDRY")) {
+      loop_vars_op(f2d_range, f3d_range, i2d, udata, p, op, true);
+    }
+
+    // Bulk of points
+    for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) {
+      loop_vars_op(f2d_range, f3d_range, i2d, udata, p, op, false);
+    }
+  }
+  
 private:
   /// Generate a random UUID (version 4) and broadcast it to all processors
   std::string createRunID() const;
@@ -573,9 +668,119 @@ private:
   /// Should be run after user RHS is called
   void post_rhs(BoutReal t);
 
-  /// Loading data from BOUT++ to/from solver
-  void loop_vars_op(Ind2D i2d, BoutReal* udata, int& p, SOLVER_VAR_OP op, bool bndry);
-  void loop_vars(BoutReal* udata, SOLVER_VAR_OP op);
+  /// Perform an operation at a given Ind2D (jx,jy) location, moving
+  /// data between BOUT++ and solver. This can be done on arbitrary
+  /// sets of fields (accessed using f2d_range and f3d_range), provided they
+  /// are the same number, shape, size, etc. as the fields being
+  /// solved for.
+  template<class RangeF2D, class RangeF3D>
+  void loop_vars_op(RangeF2D f2d_range, RangeF3D f3d_range, Ind2D i2d, BoutReal* udata, int& p, SOLVER_VAR_OP op, bool bndry) {
+/**************************************************************************
+ * Looping over variables
+ *
+ * NOTE: This part is very inefficient, and should be replaced ASAP
+ * Is the interleaving of variables needed or helpful to the solver?
+ **************************************************************************/
+  // Use global mesh: FIX THIS!
+  Mesh* mesh = bout::globals::mesh;
+
+  int nz = mesh->LocalNz;
+
+  switch (op) {
+  case SOLVER_VAR_OP::LOAD: {
+    /// Load variables from IDA into BOUT++
+
+    // Loop over 2D variables
+    auto metadata_it = f2d.begin();
+    for (auto& field : f2d_range) {
+      if (bndry && !metadata_it->evolve_bndry) {
+        continue;
+      }
+      field[i2d] = udata[p];
+      p++;
+      metadata_it++;
+    }
+
+    for (int jz = 0; jz < nz; jz++) {
+
+      auto metadata_it = f3d.begin();
+      // Loop over 3D variables
+      for (auto& field : f3d_range) {
+        if (bndry && !metadata_it->evolve_bndry) {
+          continue;
+        }
+        field[field.getMesh()->ind2Dto3D(i2d, jz)] = udata[p];
+        p++;
+        metadata_it++;
+      }
+    }
+    break;
+  }
+  case SOLVER_VAR_OP::SET_ID: {
+    /// Set the type of equation (Differential or Algebraic)
+
+    // Loop over 2D variables
+    for (const auto& metadata : f2d) {
+      if (bndry && !metadata.evolve_bndry) {
+        continue;
+      }
+      if (metadata.constraint) {
+        udata[p] = 0;
+      } else {
+        udata[p] = 1;
+      }
+      p++;
+    }
+
+    for (int jz = 0; jz < nz; jz++) {
+
+      // Loop over 3D variables
+      for (const auto& metadata : f3d) {
+        if (bndry && !metadata.evolve_bndry) {
+          continue;
+        }
+        if (metadata.constraint) {
+          udata[p] = 0;
+        } else {
+          udata[p] = 1;
+        }
+        p++;
+      }
+    }
+
+    break;
+  }
+  case SOLVER_VAR_OP::SAVE: {
+    /// Save variables from BOUT++ into IDA (only used at start of simulation)
+
+    // Loop over 2D variables
+    auto metadata_it = f2d.begin();
+    for (const auto& field : f2d_range) {
+      if (bndry && !metadata_it->evolve_bndry) {
+        continue;
+      }
+      udata[p] = field[i2d];
+      p++;
+      metadata_it++;
+    }
+
+    for (int jz = 0; jz < nz; jz++) {
+
+      auto metadata_it = f3d.begin();
+      // Loop over 3D variables
+      for (const auto& field : f3d_range) {
+        if (bndry && !metadata_it->evolve_bndry) {
+          continue;
+        }
+        udata[p] = field[field.getMesh()->ind2Dto3D(i2d, jz)];
+        p++;
+        metadata_it++;
+      }
+    }
+    break;
+  }
+  }
+}
 
   /// Check if a variable has already been added
   bool varAdded(const std::string& name);
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 1dd5e37c84..d0609b74cf 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -632,6 +632,9 @@ SNESSolver::SNESSolver(Options* opts)
       scale_vars((*options)["scale_vars"]
                      .doc("Scale variables (Jacobian column scaling)?")
                      .withDefault<bool>(false)),
+      rescale_period((*options)["rescale_period"]
+                         .doc("Number of timesteps before recalculating variabl secaling")
+                     .withDefault<int>(100)),
       asinh_vars((*options)["asinh_vars"]
                      .doc("Apply asinh() to all variables?")
                      .withDefault<bool>(false)) {}
@@ -655,6 +658,16 @@ int SNESSolver::init() {
   output_info.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n",
                     n3Dvars(), n2Dvars(), neq, nlocal);
 
+  // Initialise fields for storing residual of nonlinear solves
+  if (diagnose) {
+    for (const auto& f: f2d) {
+      resid_2d.emplace_back(emptyFrom(*f.var));
+    }
+    for (const auto& f: f3d) {
+      resid_3d.emplace_back(emptyFrom(*f.var));
+    }
+  }
+
   // Initialise PETSc components
 
   // Vectors
@@ -665,6 +678,9 @@ int SNESSolver::init() {
 
   PetscCall(VecDuplicate(snes_x, &snes_f));
   PetscCall(VecDuplicate(snes_x, &x0));
+  if (diagnose) {
+    PetscCall(VecDuplicate(snes_f, &f0));
+  }
 
   if ((equation_form == BoutSnesEquationForm::rearranged_backward_euler)
       || (equation_form == BoutSnesEquationForm::pseudo_transient)) {
@@ -755,6 +771,9 @@ int SNESSolver::init() {
     // Used so that the timestep does not have to be adjusted,
     // because that would require updating the preconditioner.
     PetscCall(VecDuplicate(snes_x, &output_x));
+    if (diagnose) {
+      PetscCall(VecDuplicate(snes_f, &output_f));
+    }
 
     // Initialize the Finite Difference Jacobian
     PetscCall(FDJinitialise());
@@ -856,6 +875,56 @@ int SNESSolver::init() {
   return 0;
 }
 
+PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
+        // Individual variable scaling
+        // Note: If variables are rescaled then the Jacobian columns
+        //       need to be scaled or recalculated
+          int istart, iend;
+          VecGetOwnershipRange(snes_x, &istart, &iend);
+
+          // Take ownership of snes_x and var_scaling_factors data
+          PetscScalar* snes_x_data = nullptr;
+          PetscCall(VecGetArray(snes_x, &snes_x_data));
+          PetscScalar* x1_data;
+          PetscCall(VecGetArray(x1, &x1_data));
+          PetscScalar* var_scaling_factors_data;
+          PetscCall(VecGetArray(var_scaling_factors, &var_scaling_factors_data));
+
+          // Normalise each value in the state
+          // Limit normalisation so scaling factor is never smaller than rtol
+          // NOTE: The normalisation value is being progressively updated, hence why we multiply var_scaling_scaling_factors by the new norm
+          for (int i = 0; i < iend - istart; ++i) {
+            // THIS LOOKS LIKE IT COULD INTRODUCE A SHARP DISCONTINUITY. COULD THAT BE A SOURCE OF NUMERICAL PROBLEMS? MAYBE, BUT NOTHING TOO SIGNIFICANT THOUGH
+            const PetscScalar norm =
+                BOUTMAX(std::abs(snes_x_data[i]), rtol / var_scaling_factors_data[i]);
+            snes_x_data[i] /= norm; // FIXME: Is this right? In most cases this means the variable is just 1. Yes, because this is just the guess for the next solution
+            x1_data[i] /= norm; // Update history for predictor
+            var_scaling_factors_data[i] *= norm;
+          }
+
+          // Restore vector underlying data
+          PetscCall(VecRestoreArray(var_scaling_factors, &var_scaling_factors_data));
+          PetscCall(VecRestoreArray(x1, &x1_data));
+          PetscCall(VecRestoreArray(snes_x, &snes_x_data));
+
+          if (diagnose) {
+            // Print maximum and minimum scaling factors
+            PetscReal max_scale, min_scale;
+            VecMax(var_scaling_factors, nullptr, &max_scale);
+            VecMin(var_scaling_factors, nullptr, &min_scale);
+            output.write("Var scaling: {} -> {}\n", min_scale, max_scale);
+          }
+          
+          // Force recalculation of the Jacobian
+          // TODO: Get my head around lagged jacobians so I can check if this is right
+          // SNESGetLagJacobianPersists(snes, saved_jacobian_persist);
+          // SNESSetLagJacobianPersists(snes, PETSC_FALSE);
+
+          SNESGetLagJacobian(snes, &saved_jacobian_lag);
+          SNESSetLagJacobian(snes, 1);
+          return PETSC_SUCCESS;
+}
+
 int SNESSolver::run() {
   // Set initial guess at the solution from variables
   {
@@ -875,6 +944,11 @@ int SNESSolver::run() {
     PetscCall(VecRestoreArray(snes_x, &xdata));
   }
 
+  if (scale_vars) {
+    int saved_jacobian_lag;
+    PetscCall(rescale(saved_jacobian_lag));
+  }
+
   // Initialise residuals
   local_residual = 0.0;
   local_residual_2d = 0.0;
@@ -884,6 +958,11 @@ int SNESSolver::run() {
     output.write("\n    Residual: {}\n", global_residual);
   }
 
+  // If saving solver residuals, need to get initial value.
+  if (diagnose) {
+    snes_function(snes_x, snes_f, false);
+  }    
+
   BoutReal target = simtime;
   recent_failure_rate = 0.0;
   for (int s = 1; s <= getNumberOutputSteps(); s++) {
@@ -892,6 +971,7 @@ int SNESSolver::run() {
     bool looping = true;
     int snes_failures = 0; // Count SNES convergence failures
     int saved_jacobian_lag = 0;
+    PetscBool saved_jacobian_persist = PETSC_FALSE;
     int loop_count = 0;
 
     const BoutReal start_global_residual = global_residual;
@@ -902,57 +982,16 @@ int SNESSolver::run() {
         break; // Could happen if step over multiple outputs
       }
 
-      if (scale_vars) {
-        // Individual variable scaling
-        // Note: If variables are rescaled then the Jacobian columns
-        //       need to be scaled or recalculated
-
-        if (loop_count % 100 == 0) {
-          // Rescale state (snes_x) so that all quantities are around 1
-          // If quantities are near zero then RTOL is used
-          int istart, iend;
-          VecGetOwnershipRange(snes_x, &istart, &iend);
-
-          // Take ownership of snes_x and var_scaling_factors data
-          PetscScalar* snes_x_data = nullptr;
-          PetscCall(VecGetArray(snes_x, &snes_x_data));
-          PetscScalar* x1_data;
-          PetscCall(VecGetArray(x1, &x1_data));
-          PetscScalar* var_scaling_factors_data;
-          PetscCall(VecGetArray(var_scaling_factors, &var_scaling_factors_data));
-
-          // Normalise each value in the state
-          // Limit normalisation so scaling factor is never smaller than rtol
-          for (int i = 0; i < iend - istart; ++i) {
-            const PetscScalar norm =
-                BOUTMAX(std::abs(snes_x_data[i]), rtol / var_scaling_factors_data[i]);
-            snes_x_data[i] /= norm;
-            x1_data[i] /= norm; // Update history for predictor
-            var_scaling_factors_data[i] *= norm;
-          }
-
-          // Restore vector underlying data
-          PetscCall(VecRestoreArray(var_scaling_factors, &var_scaling_factors_data));
-          PetscCall(VecRestoreArray(x1, &x1_data));
-          PetscCall(VecRestoreArray(snes_x, &snes_x_data));
-
-          if (diagnose) {
-            // Print maximum and minimum scaling factors
-            PetscReal max_scale, min_scale;
-            VecMax(var_scaling_factors, nullptr, &max_scale);
-            VecMin(var_scaling_factors, nullptr, &min_scale);
-            output.write("Var scaling: {} -> {}\n", min_scale, max_scale);
-          }
-
-          // Force recalculation of the Jacobian
-          SNESGetLagJacobian(snes, &saved_jacobian_lag);
-          SNESSetLagJacobian(snes, 1);
-        }
+      if (scale_vars and loop_count + 1 % rescale_period == 0) {
+        PetscCall(rescale(saved_jacobian_lag));
       }
       ++loop_count;
 
       // Copy the state (snes_x) into initial values (x0)
       VecCopy(snes_x, x0);
+      if (diagnose) {
+        VecCopy(snes_f, f0);
+      }
 
       if (equation_form == BoutSnesEquationForm::pseudo_transient) {
         // Pseudo-Transient Continuation
@@ -991,6 +1030,8 @@ int SNESSolver::run() {
           // Note: When the timestep is changed the preconditioner needs to be updated
           // => Step over the output time and interpolate if not matrix free
 
+          // FIXME: Is this the most appropriate thing to do when we're taking such massive timesteps?
+
           if (matrix_free) {
             // Ensure that the timestep goes to the next output time and then stops.
             // This avoids the need to interpolate
@@ -1077,6 +1118,9 @@ int SNESSolver::run() {
         }
         // Restore state
         VecCopy(x0, snes_x);
+        if (diagnose) {
+          VecCopy(f0, snes_f);
+        }
 
         // Recalculate the Jacobian
         if (jacobian_pruned and (snes_failures > 2) and (4 * lin_its > 3 * maxl)) {
@@ -1088,6 +1132,7 @@ int SNESSolver::run() {
           PetscCall(FDJrestoreFromPruning());
         }
 
+        // **** FIXME: Replace with booleans
         if (saved_jacobian_lag == 0) {
           // This triggers a Jacobian recalculation
           SNESGetLagJacobian(snes, &saved_jacobian_lag);
@@ -1108,6 +1153,7 @@ int SNESSolver::run() {
         continue; // Try again
       }
 
+        // **** FIXME: Replace with booleans
       if (saved_jacobian_lag != 0) {
         // Following successful step, reset Jacobian lag
         // to previous value
@@ -1232,11 +1278,19 @@ int SNESSolver::run() {
 
       // output_x <- alpha * x0 + (1 - alpha) * output_x
       VecAXPBY(output_x, alpha, 1. - alpha, x0);
-      output_time = target;
 
+      if (diagnose) {
+        VecCopy(snes_f, output_f);
+        VecAXPBY(output_f, alpha, 1 - alpha, f0);
+      }
+
+      output_time = target;
     } else {
       // Timestep was adjusted to hit target output time
       output_x = snes_x;
+      if (diagnose) {
+        output_f = snes_f;
+      }
     }
 
     // Put the result into variables
@@ -1244,6 +1298,7 @@ int SNESSolver::run() {
       // scaled_x <- output_x * var_scaling_factors
       PetscCall(VecPointwiseMult(scaled_x, output_x, var_scaling_factors));
     } else if (asinh_vars) {
+      // FIXME: scale_vars and asinh_vars aren't mutually exclusive, are they?
       PetscCall(VecCopy(output_x, scaled_x));
     } else {
       scaled_x = output_x;
@@ -1275,6 +1330,13 @@ int SNESSolver::run() {
       BoutComm::abort(1);
     }
 
+    if (diagnose) {
+      BoutReal* resid_data;
+      PetscCall(VecGetArray(output_f, &resid_data));
+      loop_vars(resid_2d, resid_3d, resid_data, SOLVER_VAR_OP::LOAD);
+      PetscCall(VecRestoreArray(output_f, &resid_data));
+    }
+
     if (call_monitors(output_time, s, getNumberOutputSteps()) != 0) {
       break; // User signalled to quit
     }
@@ -1672,6 +1734,10 @@ PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
   }
 
   PetscCall(VecRestoreArray(f, &fdata));
+
+  if (scale_vars) {
+    PetscCall(VecPointwiseDivide(f, f, var_scaling_factors));
+  }
   return PETSC_SUCCESS;
 }
 
@@ -1692,6 +1758,9 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
     // f = (x0 - x)/Δt + f
     // First calculate x - x0 to minimise floating point issues
     VecWAXPY(delta_x, -1.0, x0, x); // delta_x = x - x0
+    // if (scale_vars) {
+    //   VecPointwiseMult(delta_x, delta_x, var_scaling_factors);
+    // }
     VecAXPY(f, -1. / dt, delta_x);  // f <- f - delta_x / dt
     break;
   }
@@ -1700,6 +1769,9 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
     // except that Δt is a vector
     // f = (x0 - x)/Δt + f
     VecWAXPY(delta_x, -1.0, x0, x);
+    // if (scale_vars) {
+    //   VecPointwiseMult(delta_x, delta_x, var_scaling_factors);
+    // }
     VecPointwiseDivide(delta_x, delta_x, dt_vec); // delta_x /= dt
     VecAXPY(f, -1., delta_x);                     // f <- f - delta_x
     break;
@@ -1707,6 +1779,10 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
   case BoutSnesEquationForm::backward_euler: {
     // Backward Euler
     // Set f = x - x0 - Δt*f
+    // if (scale_vars) {
+    //   VecPointwiseMult(x, x, var_scaling_factors);
+    //   VecPointwiseMult(x0, x0, var_scaling_factors);
+    // }
     VecAYPX(f, -dt, x);   // f <- x - Δt*f
     VecAXPY(f, -1.0, x0); // f <- f - x0
     break;
@@ -1933,6 +2009,24 @@ void SNESSolver::outputVars(Options& output_options, bool save_repeat) {
     output_options["snes_pseudo_timestep"].assignRepeat(pseudo_timestep, "t", save_repeat,
                                                         "SNESSolver");
   }
+
+  if (diagnose) {
+    auto meta_2d_it = f2d.begin();
+    for (const auto& f : resid_2d) {
+      const std::string name = "resid_" + meta_2d_it->name;
+      output_options[name].assignRepeat(f, "t", save_repeat, "SNES");
+      output_options[name].attributes["description"] = meta_2d_it->description;
+      ++meta_2d_it;
+    }
+
+    auto meta_3d_it = f3d.begin();
+    for (const auto& f : resid_3d) {
+      const std::string name = "resid_" + meta_3d_it->name;
+      output_options[name].assignRepeat(f, "t", save_repeat, "SNES");
+      output_options[name].attributes["description"] = meta_3d_it->description;
+      ++meta_3d_it;
+    }
+  }
 }
 
 #endif // BOUT_HAS_PETSC
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index fbcf3baddf..2b5e0eb30d 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -115,6 +115,10 @@ private:
   PetscErrorCode FDJpruneJacobian();      ///< Remove small elements from the Jacobian
   PetscErrorCode FDJrestoreFromPruning(); ///< Restore Jacobian to original pattern
 
+  /// Rescale state (snes_x) so that all quantities are around 1. If
+  /// quantities are near zero then RTOL is used.
+  PetscErrorCode rescale(int& saved_jacobian_lag);
+
   /// Call the physics model RHS function
   ///
   /// @param[in] x       The state vector. Will be scaled if scale_vars=true
@@ -220,8 +224,10 @@ private:
   Vec snes_f;   ///< Used by SNES to store function
   Vec snes_x;   ///< Result of SNES
   Vec x0;       ///< Solution at start of current timestep
+  Vec f0;       ///< Residual at start of current timestep (only stored if diagnose = true)
   Vec delta_x;  ///< Change in solution
   Vec output_x; ///< Solution to output. Used if interpolating.
+  Vec output_f; ///< Residual to output, if diagnose == true. Used if interpolating.
 
   bool predictor;       ///< Use linear predictor?
   Vec x1;               ///< Previous solution
@@ -260,11 +266,15 @@ private:
   Vec jac_row_inv_norms;   ///< 1 / Norm of the rows of the Jacobian
 
   bool scale_vars;         ///< Scale individual variables?
+  int rescale_period;      ///< How many time-steps before rescaling variables
   Vec var_scaling_factors; ///< Factors to multiply variables when passing to user
   Vec scaled_x;            ///< The values passed to the user RHS
 
   bool asinh_vars; ///< Evolve asinh(vars) to compress magnitudes while preserving signs
   const BoutReal asinh_scale = 1e-5; // Scale below which asinh response becomes ~linear
+
+  std::vector<Field2D> resid_2d; ///< Storage for residuals of SNES solve, unpacked from snes_f
+  std::vector<Field3D> resid_3d; ///< Storage for residuals of SNES solve, unpacked from snes_f
 };
 
 #else
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index e105043c7c..0afb21f528 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1028,179 +1028,6 @@ std::unique_ptr<Solver> Solver::create(const SolverType& type, Options* opts) {
   return SolverFactory::getInstance().create(type, opts);
 }
 
-/**************************************************************************
- * Looping over variables
- *
- * NOTE: This part is very inefficient, and should be replaced ASAP
- * Is the interleaving of variables needed or helpful to the solver?
- **************************************************************************/
-
-/// Perform an operation at a given Ind2D (jx,jy) location, moving data between BOUT++ and CVODE
-void Solver::loop_vars_op(Ind2D i2d, BoutReal* udata, int& p, SOLVER_VAR_OP op,
-                          bool bndry) {
-  // Use global mesh: FIX THIS!
-  Mesh* mesh = bout::globals::mesh;
-
-  int nz = mesh->LocalNz;
-
-  switch (op) {
-  case SOLVER_VAR_OP::LOAD_VARS: {
-    /// Load variables from IDA into BOUT++
-
-    // Loop over 2D variables
-    for (const auto& f : f2d) {
-      if (bndry && !f.evolve_bndry) {
-        continue;
-      }
-      (*f.var)[i2d] = udata[p];
-      p++;
-    }
-
-    for (int jz = 0; jz < nz; jz++) {
-
-      // Loop over 3D variables
-      for (const auto& f : f3d) {
-        if (bndry && !f.evolve_bndry) {
-          continue;
-        }
-        (*f.var)[f.var->getMesh()->ind2Dto3D(i2d, jz)] = udata[p];
-        p++;
-      }
-    }
-    break;
-  }
-  case SOLVER_VAR_OP::LOAD_DERIVS: {
-    /// Load derivatives from IDA into BOUT++
-    /// Used for preconditioner
-
-    // Loop over 2D variables
-    for (const auto& f : f2d) {
-      if (bndry && !f.evolve_bndry) {
-        continue;
-      }
-      (*f.F_var)[i2d] = udata[p];
-      p++;
-    }
-
-    for (int jz = 0; jz < nz; jz++) {
-
-      // Loop over 3D variables
-      for (const auto& f : f3d) {
-        if (bndry && !f.evolve_bndry) {
-          continue;
-        }
-        (*f.F_var)[f.F_var->getMesh()->ind2Dto3D(i2d, jz)] = udata[p];
-        p++;
-      }
-    }
-
-    break;
-  }
-  case SOLVER_VAR_OP::SET_ID: {
-    /// Set the type of equation (Differential or Algebraic)
-
-    // Loop over 2D variables
-    for (const auto& f : f2d) {
-      if (bndry && !f.evolve_bndry) {
-        continue;
-      }
-      if (f.constraint) {
-        udata[p] = 0;
-      } else {
-        udata[p] = 1;
-      }
-      p++;
-    }
-
-    for (int jz = 0; jz < nz; jz++) {
-
-      // Loop over 3D variables
-      for (const auto& f : f3d) {
-        if (bndry && !f.evolve_bndry) {
-          continue;
-        }
-        if (f.constraint) {
-          udata[p] = 0;
-        } else {
-          udata[p] = 1;
-        }
-        p++;
-      }
-    }
-
-    break;
-  }
-  case SOLVER_VAR_OP::SAVE_VARS: {
-    /// Save variables from BOUT++ into IDA (only used at start of simulation)
-
-    // Loop over 2D variables
-    for (const auto& f : f2d) {
-      if (bndry && !f.evolve_bndry) {
-        continue;
-      }
-      udata[p] = (*f.var)[i2d];
-      p++;
-    }
-
-    for (int jz = 0; jz < nz; jz++) {
-
-      // Loop over 3D variables
-      for (const auto& f : f3d) {
-        if (bndry && !f.evolve_bndry) {
-          continue;
-        }
-        udata[p] = (*f.var)[f.var->getMesh()->ind2Dto3D(i2d, jz)];
-        p++;
-      }
-    }
-    break;
-  }
-    /// Save time-derivatives from BOUT++ into CVODE (returning RHS result)
-  case SOLVER_VAR_OP::SAVE_DERIVS: {
-
-    // Loop over 2D variables
-    for (const auto& f : f2d) {
-      if (bndry && !f.evolve_bndry) {
-        continue;
-      }
-      udata[p] = (*f.F_var)[i2d];
-      p++;
-    }
-
-    for (int jz = 0; jz < nz; jz++) {
-
-      // Loop over 3D variables
-      for (const auto& f : f3d) {
-        if (bndry && !f.evolve_bndry) {
-          continue;
-        }
-        udata[p] = (*f.F_var)[f.F_var->getMesh()->ind2Dto3D(i2d, jz)];
-        p++;
-      }
-    }
-    break;
-  }
-  }
-}
-
-/// Loop over variables and domain. Used for all data operations for consistency
-void Solver::loop_vars(BoutReal* udata, SOLVER_VAR_OP op) {
-  // Use global mesh: FIX THIS!
-  Mesh* mesh = bout::globals::mesh;
-
-  int p = 0; // Counter for location in udata array
-
-  // All boundaries
-  for (const auto& i2d : mesh->getRegion2D("RGN_BNDRY")) {
-    loop_vars_op(i2d, udata, p, op, true);
-  }
-
-  // Bulk of points
-  for (const auto& i2d : mesh->getRegion2D("RGN_NOBNDRY")) {
-    loop_vars_op(i2d, udata, p, op, false);
-  }
-}
-
 void Solver::load_vars(BoutReal* udata) {
   // Make sure data is allocated
   for (const auto& f : f2d) {
@@ -1211,7 +1038,7 @@ void Solver::load_vars(BoutReal* udata) {
     f.var->setLocation(f.location);
   }
 
-  loop_vars(udata, SOLVER_VAR_OP::LOAD_VARS);
+  loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d), VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::LOAD);
 
   // Mark each vector as either co- or contra-variant
 
@@ -1233,7 +1060,7 @@ void Solver::load_derivs(BoutReal* udata) {
     f.F_var->setLocation(f.location);
   }
 
-  loop_vars(udata, SOLVER_VAR_OP::LOAD_DERIVS);
+  loop_vars(VarRange<FieldCategories::DERIVS, Field2D>(f2d), VarRange<FieldCategories::DERIVS, Field3D>(f3d), udata, SOLVER_VAR_OP::LOAD);
 
   // Mark each vector as either co- or contra-variant
 
@@ -1275,7 +1102,7 @@ void Solver::save_vars(BoutReal* udata) {
     }
   }
 
-  loop_vars(udata, SOLVER_VAR_OP::SAVE_VARS);
+  loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d), VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::SAVE);
 }
 
 void Solver::save_derivs(BoutReal* dudata) {
@@ -1305,10 +1132,10 @@ void Solver::save_derivs(BoutReal* dudata) {
     }
   }
 
-  loop_vars(dudata, SOLVER_VAR_OP::SAVE_DERIVS);
+  loop_vars(VarRange<FieldCategories::DERIVS, Field2D>(f2d), VarRange<FieldCategories::DERIVS, Field3D>(f3d), dudata, SOLVER_VAR_OP::SAVE);
 }
 
-void Solver::set_id(BoutReal* udata) { loop_vars(udata, SOLVER_VAR_OP::SET_ID); }
+void Solver::set_id(BoutReal* udata) { loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d), VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::SET_ID); }
 
 Field3D Solver::globalIndex(int localStart) {
   // Use global mesh: FIX THIS!

From 769113792c4dd3ca047a1ba3cb77354f89587ca1 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 16 Jun 2026 15:25:58 +0100
Subject: [PATCH 1436/1827] Fix rescale period

---
 src/solver/impls/snes/snes.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index d0609b74cf..21b6ce2029 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -982,7 +982,7 @@ int SNESSolver::run() {
         break; // Could happen if step over multiple outputs
       }
 
-      if (scale_vars and loop_count + 1 % rescale_period == 0) {
+      if (scale_vars and (loop_count + 1) % rescale_period == 0) {
         PetscCall(rescale(saved_jacobian_lag));
       }
       ++loop_count;

From 13143335ab9c09d0f97ba52a2047f5efae67d4f1 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Wed, 17 Jun 2026 17:30:37 +0100
Subject: [PATCH 1437/1827] Make sure not to overwrite function eval with time
 deriv

---
 src/solver/impls/snes/snes.cxx | 44 +++++++++++++++++++++++++++++-----
 src/solver/impls/snes/snes.hxx |  1 +
 2 files changed, 39 insertions(+), 6 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 21b6ce2029..8b92712a0e 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -680,6 +680,7 @@ int SNESSolver::init() {
   PetscCall(VecDuplicate(snes_x, &x0));
   if (diagnose) {
     PetscCall(VecDuplicate(snes_f, &f0));
+    PetscCall(VecDuplicate(snes_f, &deriv));
   }
 
   if ((equation_form == BoutSnesEquationForm::rearranged_backward_euler)
@@ -982,7 +983,7 @@ int SNESSolver::run() {
         break; // Could happen if step over multiple outputs
       }
 
-      if (scale_vars and (loop_count + 1) % rescale_period == 0) {
+      if (scale_vars and loop_count % rescale_period == 0 and (s > 0 or loop_count > 0)) {
         PetscCall(rescale(saved_jacobian_lag));
       }
       ++loop_count;
@@ -1118,6 +1119,7 @@ int SNESSolver::run() {
         }
         // Restore state
         VecCopy(x0, snes_x);
+        // FIXME: Not sure I need this
         if (diagnose) {
           VecCopy(f0, snes_f);
         }
@@ -1198,20 +1200,37 @@ int SNESSolver::run() {
         }
 
         // Copy derivatives back
-        {
+        if (diagnose) {
+          BoutReal* fdata = nullptr;
+          PetscCall(VecGetArray(deriv, &fdata));
+          save_derivs(fdata);
+          PetscCall(VecRestoreArray(deriv, &fdata));
+          // Forward Euler
+          VecAXPY(snes_x, dt, deriv);
+        }
+        else {
           BoutReal* fdata = nullptr;
           PetscCall(VecGetArray(snes_f, &fdata));
           save_derivs(fdata);
           PetscCall(VecRestoreArray(snes_f, &fdata));
+          // Forward Euler
+          VecAXPY(snes_x, dt, snes_f);
         }
 
-        // Forward Euler
-        VecAXPY(snes_x, dt, snes_f);
       }
 
+        // int i;
+        // PetscReal norm, minval, maxval;
+        // PetscCall(VecNorm(snes_f, NORM_2, &norm));
+        // PetscCall(VecMin(snes_f, &i, &minval));
+        // PetscCall(VecMax(snes_f, &i, &maxval));
+        // output.write("Max, min, and norm of residual for SNES function: {}, {}, {}\n", maxval, minval, norm);
+
+
       simtime += dt;
 
       // Update local and global residuals
+      /// FIXME: This overwrites snes_f with the time derivs!
       PetscCall(updateResiduals(snes_x));
 
       if (diagnose) {
@@ -1280,6 +1299,7 @@ int SNESSolver::run() {
       VecAXPBY(output_x, alpha, 1. - alpha, x0);
 
       if (diagnose) {
+        // FIXME: Is this a good approach to take here? It's not the *actual* residual of a solve this way.
         VecCopy(snes_f, output_f);
         VecAXPBY(output_f, alpha, 1 - alpha, f0);
       }
@@ -1392,12 +1412,20 @@ PetscErrorCode SNESSolver::updateResiduals(Vec x) {
   local_residual_2d_prev = copy(local_residual_2d);
   global_residual_prev = global_residual;
 
+  const BoutReal* current_residual = nullptr;
+  if (diagnose) {
+  // Call RHS function to get time derivatives
+    PetscCall(rhs_function(x, deriv, false));
+
+  // Reading the residual vectors
+  PetscCall(VecGetArrayRead(deriv, &current_residual));
+  } else {
   // Call RHS function to get time derivatives
   PetscCall(rhs_function(x, snes_f, false));
 
   // Reading the residual vectors
-  const BoutReal* current_residual = nullptr;
   PetscCall(VecGetArrayRead(snes_f, &current_residual));
+  }
 
   // Note: The ordering of quantities in the PETSc vectors
   // depends on the Solver::loop_vars function
@@ -1465,8 +1493,12 @@ PetscErrorCode SNESSolver::updateResiduals(Vec x) {
     }
   }
 
+  if (diagnose) {
   // Restore Vec data arrays
-  PetscCall(VecRestoreArrayRead(snes_f, &current_residual));
+    PetscCall(VecRestoreArrayRead(deriv, &current_residual));
+  } else {
+    PetscCall(VecRestoreArrayRead(snes_f, &current_residual));
+  }
 
   // Global residual metric (RMS)
   global_residual = std::sqrt(mean(SQ(local_residual), true));
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 2b5e0eb30d..43e1783b07 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -222,6 +222,7 @@ private:
 
   PetscLib lib; ///< Handles initialising, finalising PETSc
   Vec snes_f;   ///< Used by SNES to store function
+  Vec deriv;    ///< Time derivative; only used if diagnose = true, otherwise will store in snes_f
   Vec snes_x;   ///< Result of SNES
   Vec x0;       ///< Solution at start of current timestep
   Vec f0;       ///< Residual at start of current timestep (only stored if diagnose = true)

From 227bba89301073a8d26a5065311e7bc3f395af34 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 19 Jun 2026 16:30:15 +0100
Subject: [PATCH 1438/1827] Add dynamic algorithm for rescaling variables in
 SNES

---
 src/solver/impls/snes/snes.cxx | 18 +++++++++++++-----
 src/solver/impls/snes/snes.hxx |  1 +
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 8b92712a0e..d36b0c13e6 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -633,8 +633,11 @@ SNESSolver::SNESSolver(Options* opts)
                      .doc("Scale variables (Jacobian column scaling)?")
                      .withDefault<bool>(false)),
       rescale_period((*options)["rescale_period"]
-                         .doc("Number of timesteps before recalculating variabl secaling")
-                     .withDefault<int>(100)),
+                         .doc("Number of iterations before recalculating variable scaling")
+                     .withDefault<int>(30)),
+      rescale_threshold((*options)["rescale_threshold"]
+                         .doc("How much change their should be in the norm of the state, before rescaling")
+                     .withDefault<BoutReal>(100.)),
       asinh_vars((*options)["asinh_vars"]
                      .doc("Apply asinh() to all variables?")
                      .withDefault<bool>(false)) {}
@@ -965,7 +968,9 @@ int SNESSolver::run() {
   }    
 
   BoutReal target = simtime;
+  BoutReal accumulated_change = 0.;
   recent_failure_rate = 0.0;
+  int loop_count = 0;
   for (int s = 1; s <= getNumberOutputSteps(); s++) {
     target += getOutputTimestep();
 
@@ -973,7 +978,6 @@ int SNESSolver::run() {
     int snes_failures = 0; // Count SNES convergence failures
     int saved_jacobian_lag = 0;
     PetscBool saved_jacobian_persist = PETSC_FALSE;
-    int loop_count = 0;
 
     const BoutReal start_global_residual = global_residual;
     do {
@@ -983,10 +987,12 @@ int SNESSolver::run() {
         break; // Could happen if step over multiple outputs
       }
 
-      if (scale_vars and loop_count % rescale_period == 0 and (s > 0 or loop_count > 0)) {
+      //output.write("Accumulated change to state is: {}", accumulated_change);
+      if (scale_vars and (accumulated_change > rescale_threshold or loop_count == rescale_period)) {
         PetscCall(rescale(saved_jacobian_lag));
+        accumulated_change = 0.;
+        loop_count = 0;
       }
-      ++loop_count;
 
       // Copy the state (snes_x) into initial values (x0)
       VecCopy(snes_x, x0);
@@ -1232,6 +1238,8 @@ int SNESSolver::run() {
       // Update local and global residuals
       /// FIXME: This overwrites snes_f with the time derivs!
       PetscCall(updateResiduals(snes_x));
+      accumulated_change += global_residual * dt;
+      ++loop_count;
 
       if (diagnose) {
         // Gather and print diagnostic information
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 43e1783b07..82f070805a 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -268,6 +268,7 @@ private:
 
   bool scale_vars;         ///< Scale individual variables?
   int rescale_period;      ///< How many time-steps before rescaling variables
+  BoutReal rescale_threshold; //< How much change in the state there should be before rescaling
   Vec var_scaling_factors; ///< Factors to multiply variables when passing to user
   Vec scaled_x;            ///< The values passed to the user RHS
 

From 9fa91a0c4528bde68f78a5a568e40fa85cca5bcc Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 19 Jun 2026 17:04:47 +0100
Subject: [PATCH 1439/1827] Tidying up (formatting, removing notes I left,
 etc.) for PR

---
 include/bout/solver.hxx        | 229 +++++++++++++++++++--------------
 src/solver/impls/snes/snes.cxx | 164 +++++++++++------------
 src/solver/impls/snes/snes.hxx |  17 ++-
 src/solver/solver.cxx          |  17 ++-
 4 files changed, 231 insertions(+), 196 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 90b2e5a59c..fa67ac1ca7 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -394,8 +394,7 @@ protected:
 
   /// A structure for iterating over fields
   template <FieldCategories C, class T>
-  struct VarIterator 
-  {
+  struct VarIterator {
     using iterator_category = std::random_access_iterator_tag;
     using value_type = T;
     using pointer = T*;
@@ -407,46 +406,82 @@ protected:
 
     reference operator*() const {
       switch (C) {
-      case(FieldCategories::VARS):
+      case (FieldCategories::VARS):
         return *(it->var);
-      case(FieldCategories::DERIVS):
+      case (FieldCategories::DERIVS):
         return *(it->F_var);
-      case(FieldCategories::MMS):
+      case (FieldCategories::MMS):
         return *(it->MMS_err);
       }
     }
     pointer operator->() const {
       switch (C) {
-      case(FieldCategories::VARS):
+      case (FieldCategories::VARS):
         return it->var;
-      case(FieldCategories::DERIVS):
+      case (FieldCategories::DERIVS):
         return it->F_var;
-      case(FieldCategories::MMS):
+      case (FieldCategories::MMS):
         return it->MMS_err.get();
       }
     }
 
-    VarIterator& operator++() { it++; return *this; }
-    VarIterator operator++(int) { VarIterator tmp = *this; ++(*this); return tmp; }
-    VarIterator& operator+=(difference_type n) { it += n; return *this; }
+    VarIterator& operator++() {
+      it++;
+      return *this;
+    }
+    VarIterator operator++(int) {
+      VarIterator tmp = *this;
+      ++(*this);
+      return tmp;
+    }
+    VarIterator& operator+=(difference_type n) {
+      it += n;
+      return *this;
+    }
     VarIterator operator+(difference_type n) const { return VarIterator(it + n); }
-    friend VarIterator operator+(difference_type n, const VarIterator& a) { return VarIterator(n + a.it); }
+    friend VarIterator operator+(difference_type n, const VarIterator& a) {
+      return VarIterator(n + a.it);
+    }
 
-    VarIterator& operator--() { it--; return *this; }
-    VarIterator operator--(int) { VarIterator tmp = *this; --(*this); return tmp; }
-    VarIterator& operator-=(difference_type n) { it -= n; return *this; }
+    VarIterator& operator--() {
+      it--;
+      return *this;
+    }
+    VarIterator operator--(int) {
+      VarIterator tmp = *this;
+      --(*this);
+      return tmp;
+    }
+    VarIterator& operator-=(difference_type n) {
+      it -= n;
+      return *this;
+    }
     VarIterator operator-(difference_type n) const { return VarIterator(it - n); }
-    friend VarIterator operator-(difference_type n, const VarIterator& a) { return VarIterator(n - a.it); }
+    friend VarIterator operator-(difference_type n, const VarIterator& a) {
+      return VarIterator(n - a.it);
+    }
 
     difference_type operator-(const VarIterator& b) { return it - b.it; }
     reference operator[](difference_type n) { return *VarIterator(it[n]); }
-    
-    friend bool operator== (const VarIterator& a, const VarIterator& b) { return a.it == b.it; }
-    friend bool operator!= (const VarIterator& a, const VarIterator& b) { return a.it != b.it; }
-    friend bool operator< (const VarIterator& a, const VarIterator& b) { return a.it < b.it; }
-    friend bool operator> (const VarIterator& a, const VarIterator& b) { return a.it > b.it; }
-    friend bool operator<= (const VarIterator& a, const VarIterator& b) { return a.it <= b.it; }
-    friend bool operator>= (const VarIterator& a, const VarIterator& b) { return a.it >= b.it; }
+
+    friend bool operator==(const VarIterator& a, const VarIterator& b) {
+      return a.it == b.it;
+    }
+    friend bool operator!=(const VarIterator& a, const VarIterator& b) {
+      return a.it != b.it;
+    }
+    friend bool operator<(const VarIterator& a, const VarIterator& b) {
+      return a.it < b.it;
+    }
+    friend bool operator>(const VarIterator& a, const VarIterator& b) {
+      return a.it > b.it;
+    }
+    friend bool operator<=(const VarIterator& a, const VarIterator& b) {
+      return a.it <= b.it;
+    }
+    friend bool operator>=(const VarIterator& a, const VarIterator& b) {
+      return a.it >= b.it;
+    }
 
   private:
     underlying_iterator it;
@@ -459,12 +494,12 @@ protected:
     VarRange(std::vector<VarStr<T>>& vars) : _begin(vars.begin()), _end(vars.end()) {}
 
     iterator begin() const { return _begin; }
-    iterator end() const {return _end; }
+    iterator end() const { return _end; }
+
   private:
     iterator _begin, _end;
   };
 
-  
   /// Does \p var represent field \p name?
   template <class T>
   friend bool operator==(const VarStr<T>& var, const std::string& name) {
@@ -596,8 +631,9 @@ protected:
   /// Loop over variables (accessed by iterating the f2d_range and f3d_range
   /// arguments) and domain. Used for all data operations for
   /// consistency
-  template<class RangeF2D, class RangeF3D>
-  void loop_vars(RangeF2D f2d_range, RangeF3D f3d_range, BoutReal* udata, SOLVER_VAR_OP op) {
+  template <class RangeF2D, class RangeF3D>
+  void loop_vars(RangeF2D f2d_range, RangeF3D f3d_range, BoutReal* udata,
+                 SOLVER_VAR_OP op) {
     // Use global mesh: FIX THIS!
     Mesh* mesh = bout::globals::mesh;
 
@@ -613,7 +649,7 @@ protected:
       loop_vars_op(f2d_range, f3d_range, i2d, udata, p, op, false);
     }
   }
-  
+
 private:
   /// Generate a random UUID (version 4) and broadcast it to all processors
   std::string createRunID() const;
@@ -673,69 +709,55 @@ private:
   /// sets of fields (accessed using f2d_range and f3d_range), provided they
   /// are the same number, shape, size, etc. as the fields being
   /// solved for.
-  template<class RangeF2D, class RangeF3D>
-  void loop_vars_op(RangeF2D f2d_range, RangeF3D f3d_range, Ind2D i2d, BoutReal* udata, int& p, SOLVER_VAR_OP op, bool bndry) {
-/**************************************************************************
+  template <class RangeF2D, class RangeF3D>
+  void loop_vars_op(RangeF2D f2d_range, RangeF3D f3d_range, Ind2D i2d, BoutReal* udata,
+                    int& p, SOLVER_VAR_OP op, bool bndry) {
+    /**************************************************************************
  * Looping over variables
  *
  * NOTE: This part is very inefficient, and should be replaced ASAP
  * Is the interleaving of variables needed or helpful to the solver?
  **************************************************************************/
-  // Use global mesh: FIX THIS!
-  Mesh* mesh = bout::globals::mesh;
-
-  int nz = mesh->LocalNz;
-
-  switch (op) {
-  case SOLVER_VAR_OP::LOAD: {
-    /// Load variables from IDA into BOUT++
+    // Use global mesh: FIX THIS!
+    Mesh* mesh = bout::globals::mesh;
 
-    // Loop over 2D variables
-    auto metadata_it = f2d.begin();
-    for (auto& field : f2d_range) {
-      if (bndry && !metadata_it->evolve_bndry) {
-        continue;
-      }
-      field[i2d] = udata[p];
-      p++;
-      metadata_it++;
-    }
+    int nz = mesh->LocalNz;
 
-    for (int jz = 0; jz < nz; jz++) {
+    switch (op) {
+    case SOLVER_VAR_OP::LOAD: {
+      /// Load variables from IDA into BOUT++
 
-      auto metadata_it = f3d.begin();
-      // Loop over 3D variables
-      for (auto& field : f3d_range) {
+      // Loop over 2D variables
+      auto metadata_it = f2d.begin();
+      for (auto& field : f2d_range) {
         if (bndry && !metadata_it->evolve_bndry) {
           continue;
         }
-        field[field.getMesh()->ind2Dto3D(i2d, jz)] = udata[p];
+        field[i2d] = udata[p];
         p++;
         metadata_it++;
       }
-    }
-    break;
-  }
-  case SOLVER_VAR_OP::SET_ID: {
-    /// Set the type of equation (Differential or Algebraic)
 
-    // Loop over 2D variables
-    for (const auto& metadata : f2d) {
-      if (bndry && !metadata.evolve_bndry) {
-        continue;
-      }
-      if (metadata.constraint) {
-        udata[p] = 0;
-      } else {
-        udata[p] = 1;
+      for (int jz = 0; jz < nz; jz++) {
+
+        auto metadata_it = f3d.begin();
+        // Loop over 3D variables
+        for (auto& field : f3d_range) {
+          if (bndry && !metadata_it->evolve_bndry) {
+            continue;
+          }
+          field[field.getMesh()->ind2Dto3D(i2d, jz)] = udata[p];
+          p++;
+          metadata_it++;
+        }
       }
-      p++;
+      break;
     }
+    case SOLVER_VAR_OP::SET_ID: {
+      /// Set the type of equation (Differential or Algebraic)
 
-    for (int jz = 0; jz < nz; jz++) {
-
-      // Loop over 3D variables
-      for (const auto& metadata : f3d) {
+      // Loop over 2D variables
+      for (const auto& metadata : f2d) {
         if (bndry && !metadata.evolve_bndry) {
           continue;
         }
@@ -746,41 +768,56 @@ private:
         }
         p++;
       }
-    }
 
-    break;
-  }
-  case SOLVER_VAR_OP::SAVE: {
-    /// Save variables from BOUT++ into IDA (only used at start of simulation)
-
-    // Loop over 2D variables
-    auto metadata_it = f2d.begin();
-    for (const auto& field : f2d_range) {
-      if (bndry && !metadata_it->evolve_bndry) {
-        continue;
+      for (int jz = 0; jz < nz; jz++) {
+
+        // Loop over 3D variables
+        for (const auto& metadata : f3d) {
+          if (bndry && !metadata.evolve_bndry) {
+            continue;
+          }
+          if (metadata.constraint) {
+            udata[p] = 0;
+          } else {
+            udata[p] = 1;
+          }
+          p++;
+        }
       }
-      udata[p] = field[i2d];
-      p++;
-      metadata_it++;
-    }
 
-    for (int jz = 0; jz < nz; jz++) {
+      break;
+    }
+    case SOLVER_VAR_OP::SAVE: {
+      /// Save variables from BOUT++ into IDA (only used at start of simulation)
 
-      auto metadata_it = f3d.begin();
-      // Loop over 3D variables
-      for (const auto& field : f3d_range) {
+      // Loop over 2D variables
+      auto metadata_it = f2d.begin();
+      for (const auto& field : f2d_range) {
         if (bndry && !metadata_it->evolve_bndry) {
           continue;
         }
-        udata[p] = field[field.getMesh()->ind2Dto3D(i2d, jz)];
+        udata[p] = field[i2d];
         p++;
         metadata_it++;
       }
+
+      for (int jz = 0; jz < nz; jz++) {
+
+        auto metadata_it = f3d.begin();
+        // Loop over 3D variables
+        for (const auto& field : f3d_range) {
+          if (bndry && !metadata_it->evolve_bndry) {
+            continue;
+          }
+          udata[p] = field[field.getMesh()->ind2Dto3D(i2d, jz)];
+          p++;
+          metadata_it++;
+        }
+      }
+      break;
+    }
     }
-    break;
-  }
   }
-}
 
   /// Check if a variable has already been added
   bool varAdded(const std::string& name);
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index d36b0c13e6..21757cda90 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -632,12 +632,14 @@ SNESSolver::SNESSolver(Options* opts)
       scale_vars((*options)["scale_vars"]
                      .doc("Scale variables (Jacobian column scaling)?")
                      .withDefault<bool>(false)),
-      rescale_period((*options)["rescale_period"]
-                         .doc("Number of iterations before recalculating variable scaling")
-                     .withDefault<int>(30)),
+      rescale_period(
+          (*options)["rescale_period"]
+              .doc("Number of iterations before recalculating variable scaling")
+              .withDefault<int>(30)),
       rescale_threshold((*options)["rescale_threshold"]
-                         .doc("How much change their should be in the norm of the state, before rescaling")
-                     .withDefault<BoutReal>(100.)),
+                            .doc("How much change their should be in the norm of the "
+                                 "state, before rescaling")
+                            .withDefault<BoutReal>(100.)),
       asinh_vars((*options)["asinh_vars"]
                      .doc("Apply asinh() to all variables?")
                      .withDefault<bool>(false)) {}
@@ -663,10 +665,10 @@ int SNESSolver::init() {
 
   // Initialise fields for storing residual of nonlinear solves
   if (diagnose) {
-    for (const auto& f: f2d) {
+    for (const auto& f : f2d) {
       resid_2d.emplace_back(emptyFrom(*f.var));
     }
-    for (const auto& f: f3d) {
+    for (const auto& f : f3d) {
       resid_3d.emplace_back(emptyFrom(*f.var));
     }
   }
@@ -880,53 +882,48 @@ int SNESSolver::init() {
 }
 
 PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
-        // Individual variable scaling
-        // Note: If variables are rescaled then the Jacobian columns
-        //       need to be scaled or recalculated
-          int istart, iend;
-          VecGetOwnershipRange(snes_x, &istart, &iend);
-
-          // Take ownership of snes_x and var_scaling_factors data
-          PetscScalar* snes_x_data = nullptr;
-          PetscCall(VecGetArray(snes_x, &snes_x_data));
-          PetscScalar* x1_data;
-          PetscCall(VecGetArray(x1, &x1_data));
-          PetscScalar* var_scaling_factors_data;
-          PetscCall(VecGetArray(var_scaling_factors, &var_scaling_factors_data));
-
-          // Normalise each value in the state
-          // Limit normalisation so scaling factor is never smaller than rtol
-          // NOTE: The normalisation value is being progressively updated, hence why we multiply var_scaling_scaling_factors by the new norm
-          for (int i = 0; i < iend - istart; ++i) {
-            // THIS LOOKS LIKE IT COULD INTRODUCE A SHARP DISCONTINUITY. COULD THAT BE A SOURCE OF NUMERICAL PROBLEMS? MAYBE, BUT NOTHING TOO SIGNIFICANT THOUGH
-            const PetscScalar norm =
-                BOUTMAX(std::abs(snes_x_data[i]), rtol / var_scaling_factors_data[i]);
-            snes_x_data[i] /= norm; // FIXME: Is this right? In most cases this means the variable is just 1. Yes, because this is just the guess for the next solution
-            x1_data[i] /= norm; // Update history for predictor
-            var_scaling_factors_data[i] *= norm;
-          }
+  // Individual variable scaling
+  // Note: If variables are rescaled then the Jacobian columns
+  //       need to be scaled or recalculated
+  int istart, iend;
+  VecGetOwnershipRange(snes_x, &istart, &iend);
+
+  // Take ownership of snes_x and var_scaling_factors data
+  PetscScalar* snes_x_data = nullptr;
+  PetscCall(VecGetArray(snes_x, &snes_x_data));
+  PetscScalar* x1_data;
+  PetscCall(VecGetArray(x1, &x1_data));
+  PetscScalar* var_scaling_factors_data;
+  PetscCall(VecGetArray(var_scaling_factors, &var_scaling_factors_data));
+
+  // Normalise each value in the state
+  // Limit normalisation so scaling factor is never smaller than rtol
+  for (int i = 0; i < iend - istart; ++i) {
+    const PetscScalar norm =
+        BOUTMAX(std::abs(snes_x_data[i]), rtol / var_scaling_factors_data[i]);
+    snes_x_data[i] /=
+        norm;
+    x1_data[i] /= norm; // Update history for predictor
+    var_scaling_factors_data[i] *= norm;
+  }
 
-          // Restore vector underlying data
-          PetscCall(VecRestoreArray(var_scaling_factors, &var_scaling_factors_data));
-          PetscCall(VecRestoreArray(x1, &x1_data));
-          PetscCall(VecRestoreArray(snes_x, &snes_x_data));
+  // Restore vector underlying data
+  PetscCall(VecRestoreArray(var_scaling_factors, &var_scaling_factors_data));
+  PetscCall(VecRestoreArray(x1, &x1_data));
+  PetscCall(VecRestoreArray(snes_x, &snes_x_data));
 
-          if (diagnose) {
-            // Print maximum and minimum scaling factors
-            PetscReal max_scale, min_scale;
-            VecMax(var_scaling_factors, nullptr, &max_scale);
-            VecMin(var_scaling_factors, nullptr, &min_scale);
-            output.write("Var scaling: {} -> {}\n", min_scale, max_scale);
-          }
-          
-          // Force recalculation of the Jacobian
-          // TODO: Get my head around lagged jacobians so I can check if this is right
-          // SNESGetLagJacobianPersists(snes, saved_jacobian_persist);
-          // SNESSetLagJacobianPersists(snes, PETSC_FALSE);
+  if (diagnose) {
+    // Print maximum and minimum scaling factors
+    PetscReal max_scale, min_scale;
+    VecMax(var_scaling_factors, nullptr, &max_scale);
+    VecMin(var_scaling_factors, nullptr, &min_scale);
+    output.write("Var scaling: {} -> {}\n", min_scale, max_scale);
+  }
 
-          SNESGetLagJacobian(snes, &saved_jacobian_lag);
-          SNESSetLagJacobian(snes, 1);
-          return PETSC_SUCCESS;
+  // Force recalculation of the Jacobian
+  SNESGetLagJacobian(snes, &saved_jacobian_lag);
+  SNESSetLagJacobian(snes, 1);
+  return PETSC_SUCCESS;
 }
 
 int SNESSolver::run() {
@@ -965,12 +962,12 @@ int SNESSolver::run() {
   // If saving solver residuals, need to get initial value.
   if (diagnose) {
     snes_function(snes_x, snes_f, false);
-  }    
+  }
 
   BoutReal target = simtime;
-  BoutReal accumulated_change = 0.;
   recent_failure_rate = 0.0;
-  int loop_count = 0;
+  int steps_since_rescale = 0;
+  BoutReal change_since_rescale = 0.;
   for (int s = 1; s <= getNumberOutputSteps(); s++) {
     target += getOutputTimestep();
 
@@ -987,11 +984,12 @@ int SNESSolver::run() {
         break; // Could happen if step over multiple outputs
       }
 
-      //output.write("Accumulated change to state is: {}", accumulated_change);
-      if (scale_vars and (accumulated_change > rescale_threshold or loop_count == rescale_period)) {
+      if (scale_vars
+          and (change_since_rescale > rescale_threshold
+               or steps_since_rescale == rescale_period)) {
         PetscCall(rescale(saved_jacobian_lag));
-        accumulated_change = 0.;
-        loop_count = 0;
+        change_since_rescale = 0.;
+        steps_since_rescale = 0;
       }
 
       // Copy the state (snes_x) into initial values (x0)
@@ -1037,8 +1035,6 @@ int SNESSolver::run() {
           // Note: When the timestep is changed the preconditioner needs to be updated
           // => Step over the output time and interpolate if not matrix free
 
-          // FIXME: Is this the most appropriate thing to do when we're taking such massive timesteps?
-
           if (matrix_free) {
             // Ensure that the timestep goes to the next output time and then stops.
             // This avoids the need to interpolate
@@ -1126,9 +1122,9 @@ int SNESSolver::run() {
         // Restore state
         VecCopy(x0, snes_x);
         // FIXME: Not sure I need this
-        if (diagnose) {
-          VecCopy(f0, snes_f);
-        }
+        // if (diagnose) {
+        //   VecCopy(f0, snes_f);
+        // }
 
         // Recalculate the Jacobian
         if (jacobian_pruned and (snes_failures > 2) and (4 * lin_its > 3 * maxl)) {
@@ -1140,7 +1136,6 @@ int SNESSolver::run() {
           PetscCall(FDJrestoreFromPruning());
         }
 
-        // **** FIXME: Replace with booleans
         if (saved_jacobian_lag == 0) {
           // This triggers a Jacobian recalculation
           SNESGetLagJacobian(snes, &saved_jacobian_lag);
@@ -1161,7 +1156,6 @@ int SNESSolver::run() {
         continue; // Try again
       }
 
-        // **** FIXME: Replace with booleans
       if (saved_jacobian_lag != 0) {
         // Following successful step, reset Jacobian lag
         // to previous value
@@ -1213,8 +1207,7 @@ int SNESSolver::run() {
           PetscCall(VecRestoreArray(deriv, &fdata));
           // Forward Euler
           VecAXPY(snes_x, dt, deriv);
-        }
-        else {
+        } else {
           BoutReal* fdata = nullptr;
           PetscCall(VecGetArray(snes_f, &fdata));
           save_derivs(fdata);
@@ -1222,24 +1215,21 @@ int SNESSolver::run() {
           // Forward Euler
           VecAXPY(snes_x, dt, snes_f);
         }
-
       }
 
-        // int i;
-        // PetscReal norm, minval, maxval;
-        // PetscCall(VecNorm(snes_f, NORM_2, &norm));
-        // PetscCall(VecMin(snes_f, &i, &minval));
-        // PetscCall(VecMax(snes_f, &i, &maxval));
-        // output.write("Max, min, and norm of residual for SNES function: {}, {}, {}\n", maxval, minval, norm);
-
+      // int i;
+      // PetscReal norm, minval, maxval;
+      // PetscCall(VecNorm(snes_f, NORM_2, &norm));
+      // PetscCall(VecMin(snes_f, &i, &minval));
+      // PetscCall(VecMax(snes_f, &i, &maxval));
+      // output.write("Max, min, and norm of residual for SNES function: {}, {}, {}\n", maxval, minval, norm);
 
       simtime += dt;
 
       // Update local and global residuals
-      /// FIXME: This overwrites snes_f with the time derivs!
       PetscCall(updateResiduals(snes_x));
-      accumulated_change += global_residual * dt;
-      ++loop_count;
+      change_since_rescale += global_residual * dt;
+      ++steps_since_rescale;
 
       if (diagnose) {
         // Gather and print diagnostic information
@@ -1307,7 +1297,6 @@ int SNESSolver::run() {
       VecAXPBY(output_x, alpha, 1. - alpha, x0);
 
       if (diagnose) {
-        // FIXME: Is this a good approach to take here? It's not the *actual* residual of a solve this way.
         VecCopy(snes_f, output_f);
         VecAXPBY(output_f, alpha, 1 - alpha, f0);
       }
@@ -1326,7 +1315,6 @@ int SNESSolver::run() {
       // scaled_x <- output_x * var_scaling_factors
       PetscCall(VecPointwiseMult(scaled_x, output_x, var_scaling_factors));
     } else if (asinh_vars) {
-      // FIXME: scale_vars and asinh_vars aren't mutually exclusive, are they?
       PetscCall(VecCopy(output_x, scaled_x));
     } else {
       scaled_x = output_x;
@@ -1422,17 +1410,17 @@ PetscErrorCode SNESSolver::updateResiduals(Vec x) {
 
   const BoutReal* current_residual = nullptr;
   if (diagnose) {
-  // Call RHS function to get time derivatives
+    // Call RHS function to get time derivatives
     PetscCall(rhs_function(x, deriv, false));
 
-  // Reading the residual vectors
-  PetscCall(VecGetArrayRead(deriv, &current_residual));
+    // Reading the residual vectors
+    PetscCall(VecGetArrayRead(deriv, &current_residual));
   } else {
-  // Call RHS function to get time derivatives
-  PetscCall(rhs_function(x, snes_f, false));
+    // Call RHS function to get time derivatives
+    PetscCall(rhs_function(x, snes_f, false));
 
-  // Reading the residual vectors
-  PetscCall(VecGetArrayRead(snes_f, &current_residual));
+    // Reading the residual vectors
+    PetscCall(VecGetArrayRead(snes_f, &current_residual));
   }
 
   // Note: The ordering of quantities in the PETSc vectors
@@ -1502,7 +1490,7 @@ PetscErrorCode SNESSolver::updateResiduals(Vec x) {
   }
 
   if (diagnose) {
-  // Restore Vec data arrays
+    // Restore Vec data arrays
     PetscCall(VecRestoreArrayRead(deriv, &current_residual));
   } else {
     PetscCall(VecRestoreArrayRead(snes_f, &current_residual));
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 82f070805a..9b5a6a6eeb 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -206,8 +206,8 @@ private:
   BoutReal kI; ///< (0.2 - 0.4) Integral parameter (smooths history of changes)
   BoutReal kD; ///< (0.1 - 0.3) Derivative (dampens oscillation - optional)
   bool pid_consider_failures; ///< Reduce timestep increases if recent solves have failed
-  BoutReal recent_failure_rate;            ///< Rolling average of recent failure rate
-  BoutReal last_failure_weight;            ///< 1 / number of recent solves
+  BoutReal recent_failure_rate; ///< Rolling average of recent failure rate
+  BoutReal last_failure_weight; ///< 1 / number of recent solves
 
   BoutReal nl_its_prev;
   BoutReal nl_its_prev2;
@@ -222,10 +222,10 @@ private:
 
   PetscLib lib; ///< Handles initialising, finalising PETSc
   Vec snes_f;   ///< Used by SNES to store function
-  Vec deriv;    ///< Time derivative; only used if diagnose = true, otherwise will store in snes_f
+  Vec deriv; ///< Time derivative; only used if diagnose = true, otherwise will store in snes_f
   Vec snes_x;   ///< Result of SNES
   Vec x0;       ///< Solution at start of current timestep
-  Vec f0;       ///< Residual at start of current timestep (only stored if diagnose = true)
+  Vec f0; ///< Residual at start of current timestep (only stored if diagnose = true)
   Vec delta_x;  ///< Change in solution
   Vec output_x; ///< Solution to output. Used if interpolating.
   Vec output_f; ///< Residual to output, if diagnose == true. Used if interpolating.
@@ -268,15 +268,18 @@ private:
 
   bool scale_vars;         ///< Scale individual variables?
   int rescale_period;      ///< How many time-steps before rescaling variables
-  BoutReal rescale_threshold; //< How much change in the state there should be before rescaling
+  BoutReal
+      rescale_threshold; //< How much change in the state there should be before rescaling
   Vec var_scaling_factors; ///< Factors to multiply variables when passing to user
   Vec scaled_x;            ///< The values passed to the user RHS
 
   bool asinh_vars; ///< Evolve asinh(vars) to compress magnitudes while preserving signs
   const BoutReal asinh_scale = 1e-5; // Scale below which asinh response becomes ~linear
 
-  std::vector<Field2D> resid_2d; ///< Storage for residuals of SNES solve, unpacked from snes_f
-  std::vector<Field3D> resid_3d; ///< Storage for residuals of SNES solve, unpacked from snes_f
+  std::vector<Field2D>
+      resid_2d; ///< Storage for residuals of SNES solve, unpacked from snes_f
+  std::vector<Field3D>
+      resid_3d; ///< Storage for residuals of SNES solve, unpacked from snes_f
 };
 
 #else
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 0afb21f528..b46b890574 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1038,7 +1038,8 @@ void Solver::load_vars(BoutReal* udata) {
     f.var->setLocation(f.location);
   }
 
-  loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d), VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::LOAD);
+  loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d),
+            VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::LOAD);
 
   // Mark each vector as either co- or contra-variant
 
@@ -1060,7 +1061,8 @@ void Solver::load_derivs(BoutReal* udata) {
     f.F_var->setLocation(f.location);
   }
 
-  loop_vars(VarRange<FieldCategories::DERIVS, Field2D>(f2d), VarRange<FieldCategories::DERIVS, Field3D>(f3d), udata, SOLVER_VAR_OP::LOAD);
+  loop_vars(VarRange<FieldCategories::DERIVS, Field2D>(f2d),
+            VarRange<FieldCategories::DERIVS, Field3D>(f3d), udata, SOLVER_VAR_OP::LOAD);
 
   // Mark each vector as either co- or contra-variant
 
@@ -1102,7 +1104,8 @@ void Solver::save_vars(BoutReal* udata) {
     }
   }
 
-  loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d), VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::SAVE);
+  loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d),
+            VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::SAVE);
 }
 
 void Solver::save_derivs(BoutReal* dudata) {
@@ -1132,10 +1135,14 @@ void Solver::save_derivs(BoutReal* dudata) {
     }
   }
 
-  loop_vars(VarRange<FieldCategories::DERIVS, Field2D>(f2d), VarRange<FieldCategories::DERIVS, Field3D>(f3d), dudata, SOLVER_VAR_OP::SAVE);
+  loop_vars(VarRange<FieldCategories::DERIVS, Field2D>(f2d),
+            VarRange<FieldCategories::DERIVS, Field3D>(f3d), dudata, SOLVER_VAR_OP::SAVE);
 }
 
-void Solver::set_id(BoutReal* udata) { loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d), VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::SET_ID); }
+void Solver::set_id(BoutReal* udata) {
+  loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d),
+            VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::SET_ID);
+}
 
 Field3D Solver::globalIndex(int localStart) {
   // Use global mesh: FIX THIS!

From 87d29ff2095874805b75d7c14375ecc25db3169c Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 19 Jun 2026 17:56:11 +0100
Subject: [PATCH 1440/1827] Add documentation for new approach to scaling in
 SNES

---
 manual/sphinx/user_docs/time_integration.rst | 32 ++++++++++++++++++++
 src/solver/impls/snes/snes.cxx               |  2 +-
 2 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index a2bd896f85..aae0d4fe9d 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -747,6 +747,34 @@ Setting ``solver:force_symmetric_coloring = true``, will make sure
 that the jacobian colouring matrix is symmetric.  This will often
 include a few extra non-zeros that the stencil will miss otherwise
 
+
+Variable Scaling
+~~~~~~~~~~~~~~~~
+
+There may be differences of many orders of magnitude between your
+variables or within variables across the domain. This can result in a
+particular area of the domain for a particular variable dominating the
+residual in the nonlinear solve because its residual has the largest
+absolute value, even if not the largest relative value. As a
+consequence, tighter tolerances will be needed to ensure other
+variables and parts of the domain are solved to sufficient
+accuracy. The ``scale_vars`` option can help address this by
+renormalising all variables to be of order unity across the entire
+domain.
+
+.. code-block:: ini
+
+   scale_vars = true
+   rescale_period = 30  # Maximum number of time-steps taken before rescaling the variables
+   rescale_threshold = 100.  # Approximate overall change to variables permitted before rescaling
+
+It has been found that scaling variables in this way allows
+simulations to run with much looser tolerances than would otherwise be
+possible (e.g., ``rtol = 1e-5`` and ``atol = 1e-3``). Four-times
+speedups have been observed by doing this. Once a steady-state has
+been reached the simulation can be run for a further few time-steps
+with tighter tolerances to improve the accuracy.
+
 Diagnostics and Monitoring
 ---------------------------
 
@@ -765,6 +793,10 @@ When ``equation_form = pseudo_transient``, the solver saves additional diagnosti
 These can be visualized to understand convergence behavior and identify
 problematic regions.
 
+The residuals from the last nonlinear solve are also saved with names
+``resid_<var name>``. Plotting these can help to understand which
+variables and parts of the domain are controlling convergence.
+
 Summary of solver options
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 21757cda90..571dc9504e 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -630,7 +630,7 @@ SNESSolver::SNESSolver(Options* opts)
                     .doc("Scale time derivatives (Jacobian row scaling)?")
                     .withDefault<bool>(false)),
       scale_vars((*options)["scale_vars"]
-                     .doc("Scale variables (Jacobian column scaling)?")
+                     .doc("Scale variables to be order unity?")
                      .withDefault<bool>(false)),
       rescale_period(
           (*options)["rescale_period"]

From b9de118a6d55e3333bcaf711604443bc70234e12 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 10:04:46 -0700
Subject: [PATCH 1441/1827] Fixes and tidying

- Replaced `auto` with `Field3D` in a couple of places, to force
  evaluation of a BinaryExpr.
- Removed some unnecessary intermediates, now that `abs` and `max`
  operate on BinaryExpr.
- Clang tidy changes to headers etc.

Integrated tests are now compiling locally for 2D and 3D metrics.
---
 include/bout/fieldops.hxx                     | 12 ++++------
 include/bout/fieldperp.hxx                    | 19 ++++++++-------
 include/bout/interpolation.hxx                | 24 +++++++++++++------
 include/bout/utils.hxx                        |  6 +++--
 .../laplace/impls/naulin/naulin_laplace.cxx   |  7 +++---
 src/mesh/coordinates.cxx                      | 13 ++++------
 .../test-petsc_laplace/test_petsc_laplace.cxx |  2 +-
 .../invert/laplace/test_laplace_hypre3d.cxx   | 10 ++++----
 8 files changed, 50 insertions(+), 43 deletions(-)

diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 923c8078ef..df513c0290 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -3,12 +3,16 @@
 #define BOUT_FIELDOPS_HXX
 
 #include "bout/array.hxx"
+#include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/build_config.hxx"
+#include "bout/build_defines.hxx"
+#include "bout/region.hxx"
 
+#include <cstddef>
 #include <limits>
 #include <optional>
 #include <type_traits>
-#include <vector>
 
 #if BOUT_HAS_CUDA
 #include <cuda_runtime.h>
@@ -198,12 +202,6 @@ __global__ void __launch_bounds__(THREADS) evaluatorExpr(BoutReal* out, const Ex
   int tid = threadIdx.x + blockIdx.x * blockDim.x;
   int e = expr.size();
 
-  // In-bounds version
-  //if (tid < e) {
-  //  int idx = expr.regionIdx(tid);
-  //  out[idx] = expr(idx); // single‐pass fusion
-  //}
-
   // Out-of-bounds version
   if (tid >= e) {
     return;
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 74414d01d6..9c4a957ee8 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -23,24 +23,27 @@
  *
  **************************************************************************/
 
-#include <cstddef>
-#include <optional>
-#include <vector>
 class FieldPerp;
 
 #ifndef BOUT_FIELDPERP_H
 #define BOUT_FIELDPERP_H
 
-#include "bout/field.hxx"
-
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/build_config.hxx"
+#include "bout/field.hxx"
+#include "bout/fieldops.hxx"
 #include "bout/region.hxx"
-
 #include "bout/unused.hxx"
+#include "bout/utils.hxx"
 
+#include <cstddef>
+#include <optional>
 #include <ostream>
 #include <string>
+#include <type_traits>
+#include <vector>
 
 class Field2D; // #include "bout/field2d.hxx"
 class Field3D; // #include "bout/field3d.hxx"
@@ -230,7 +233,7 @@ public:
                           jx, jz, nx, nz);
     }
 #endif
-    return data[jx * nz + jz];
+    return data[(jx * nz) + jz];
   }
 
   /*!
@@ -247,7 +250,7 @@ public:
                           jx, jz, nx, nz);
     }
 #endif
-    return data[jx * nz + jz];
+    return data[(jx * nz) + jz];
   }
 
   /*!
diff --git a/include/bout/interpolation.hxx b/include/bout/interpolation.hxx
index bf4ac5779b..40ff603712 100644
--- a/include/bout/interpolation.hxx
+++ b/include/bout/interpolation.hxx
@@ -26,9 +26,19 @@
 #ifndef BOUT_INTERP_H
 #define BOUT_INTERP_H
 
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
+#include "bout/msg_stack.hxx"
+#include "bout/region.hxx"
 #include "bout/stencils.hxx"
 
+#include <string>
+#include <type_traits>
+
 /// Perform interpolation between centre -> shifted or vice-versa
 /*!
   Interpolate using 4th-order staggered formula
@@ -56,14 +66,14 @@ inline BoutReal interp(const stencil& s) {
 */
 template <typename T>
 std::enable_if_t<bout::utils::is_Field2D_v<T> || bout::utils::is_Field3D_v<T>, const T>
-interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_ALL") {
+interp_to(const T& var, CELL_LOC loc, const std::string& region = "RGN_ALL") {
   static_assert(bout::utils::is_Field2D_v<T> || bout::utils::is_Field3D_v<T>,
                 "interp_to must be templated with one of Field2D or Field3D.");
   ASSERT1(loc != CELL_DEFAULT); // doesn't make sense to interplote to CELL_DEFAULT
 
   Mesh* fieldmesh = var.getMesh();
 
-  if ((loc != CELL_CENTRE) && (fieldmesh->StaggerGrids == false)) {
+  if ((loc != CELL_CENTRE) && !fieldmesh->StaggerGrids) {
     throw BoutException("Asked to interpolate, but StaggerGrids is disabled!");
   }
 
@@ -72,7 +82,7 @@ interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_ALL") {
     return var;
   }
 
-  // NOTE: invalidateGuards() is called in Field3D::alloctate() if the data
+  // NOTE: invalidateGuards() is called in Field3D::allocate() if the data
   // block is not already allocated, so will be called here if
   // region==RGN_NOBNDRY
   T result{emptyFrom(var).setLocation(loc)};
@@ -205,14 +215,14 @@ interp_to(const T& var, CELL_LOC loc, const std::string region = "RGN_ALL") {
 
 template <typename E>
 std::enable_if_t<is_expr_field3d_v<E> && !bout::utils::is_Field3D_v<E>, const Field3D>
-interp_to(const E& expr, CELL_LOC loc, const std::string rgn = "RGN_ALL") {
-  return interp_to(Field3D{expr}, loc, std::move(rgn));
+interp_to(const E& expr, CELL_LOC loc, const std::string& rgn = "RGN_ALL") {
+  return interp_to(Field3D{expr}, loc, rgn);
 }
 
 template <typename E>
 std::enable_if_t<is_expr_field2d_v<E> && !bout::utils::is_Field2D_v<E>, const Field2D>
-interp_to(const E& expr, CELL_LOC loc, const std::string rgn = "RGN_ALL") {
-  return interp_to(Field2D{expr}, loc, std::move(rgn));
+interp_to(const E& expr, CELL_LOC loc, const std::string& rgn = "RGN_ALL") {
+  return interp_to(Field2D{expr}, loc, rgn);
 }
 
 #endif // BOUT_INTERP_H
diff --git a/include/bout/utils.hxx b/include/bout/utils.hxx
index 6fb7d38dc2..3dbae60d74 100644
--- a/include/bout/utils.hxx
+++ b/include/bout/utils.hxx
@@ -29,12 +29,11 @@
 #ifndef BOUT_UTILS_H
 #define BOUT_UTILS_H
 
-#include "bout/build_config.hxx"
-
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_config.hxx"
 #include "bout/region.hxx"
 #include "bout/unused.hxx"
 
@@ -46,6 +45,9 @@
 #include <set>
 #include <sstream>
 #include <string>
+#include <tuple>
+#include <type_traits>
+#include <vector>
 
 class Field;
 
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index 647ed08bd9..ae8e78d1ff 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -18,9 +18,9 @@
  * =========
  *
  **************************************************************************
- * Copyright 2018 B.D.Dudson, M. Loiten, J. Omotani
+ * Copyright 2018 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, benjamin.dudson@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -274,9 +274,8 @@ Field3D LaplaceNaulin::solve(const Field3D& rhs, const Field3D& x0) {
   delp2solver->setCoefC2(C2coef_DC);
 
   // Use this below to normalize error for relative error estimate
-  Field3D SQField = SQ(rhsOverD);
   BoutReal RMS_rhsOverD = sqrt(mean(
-      SQField, true,
+      SQ(rhsOverD), true,
       "RGN_NOBNDRY")); // use sqrt(mean(SQ)) to make sure we do not divide by zero at a point
 
   BoutReal error_rel = 1e20, error_abs = 1e20, last_error = error_abs;
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 0004e4673f..a4602a5527 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -546,8 +546,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
                                   transform.get());
 
     // Compare calculated and loaded values
-    const auto diff = J - Jcalc;
-    output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(diff)));
+    output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(J - Jcalc)));
 
     mesh->communicate_no_slices(J);
 
@@ -572,8 +571,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options)
 
     Bxy = interpolateAndExtrapolate(Bxy, location, extrapolate_x, extrapolate_y, false,
                                     transform.get());
-    FieldMetric diff = Bxy - Bcalc;
-    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(diff)));
+    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
   }
 
   // Check Bxy
@@ -757,9 +755,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
       J = interpolateAndExtrapolate(J, location, extrapolate_x, extrapolate_y, false,
                                     transform.get());
 
-      FieldMetric diff = J - Jcalc;
       // Compare calculated and loaded values
-      output_warn.write("\tMaximum difference in J is %e\n", max(abs(diff)));
+      output_warn.write("\tMaximum difference in J is %e\n", max(abs(J - Jcalc)));
 
       // Re-evaluate Bxy using new J
       Bxy = sqrt(g_22) / J;
@@ -783,9 +780,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
     } else {
       Bxy = interpolateAndExtrapolate(Bxy, location, extrapolate_x, extrapolate_y, false,
                                       transform.get());
-
-      FieldMetric diff = Bxy - Bcalc;
-      output_warn.write("\tMaximum difference in Bxy is %e\n", max(abs(diff)));
+      output_warn.write("\tMaximum difference in Bxy is %e\n", max(abs(Bxy - Bcalc)));
     }
 
     // Check Bxy
diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
index 39b1918480..04182293e7 100644
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
@@ -99,7 +99,7 @@ void check_laplace(int test_num, std::string_view test_name, Laplacian& invert,
 template <class T>
 Field3D forward_laplace(const Field3D& field, const T& acoef, const T& ccoef,
                         const T& dcoef) {
-  auto bcoef =
+  Field3D bcoef =
       dcoef * Delp2(field) + Grad_perp(ccoef) * Grad_perp(field) / ccoef + acoef * field;
   apply_flat_boundary(bcoef);
   return bcoef;
diff --git a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
index 3b1bbc5d39..a721b96833 100644
--- a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
+++ b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
@@ -1,5 +1,7 @@
 #include "bout/build_defines.hxx"
 
+#if BOUT_HAS_HYPRE
+
 #include <math.h>
 #include <tuple>
 
@@ -18,8 +20,6 @@
 #include "bout/options.hxx"
 #include "bout/vecops.hxx"
 
-#if BOUT_HAS_HYPRE
-
 #include "fake_mesh_fixture.hxx"
 
 // The unit tests use the global mesh
@@ -39,9 +39,9 @@ class ForwardOperator {
   }
 
   const Field3D operator()(Field3D& f) {
-    auto result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY")
-                  + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22) / c1 + a * f
-                  + ex * DDX(f) + ez * DDZ(f);
+    Field3D result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY")
+                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22) / c1 + a * f
+                     + ex * DDX(f) + ez * DDZ(f);
     applyBoundaries(result, f);
     return result;
   }

From 0fdeedbb5225db95c8b11a8f7cba4dc4f027ea3a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 11:30:27 -0700
Subject: [PATCH 1442/1827] evaluateBinaryExpr: Allocate full size Arrays

The data arrays should be the full size of the field,
not the size of the expression domain.
---
 include/bout/field2d.hxx            |  5 ++++-
 include/bout/field3d.hxx            |  5 ++++-
 include/bout/fieldperp.hxx          |  5 ++++-
 tests/unit/field/test_field2d.cxx   | 10 ++++++++++
 tests/unit/field/test_field3d.cxx   | 10 ++++++++++
 tests/unit/field/test_fieldperp.cxx | 11 +++++++++++
 6 files changed, 43 insertions(+), 3 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 61cc4693a3..807b0ac1a3 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -350,7 +350,10 @@ public:
 private:
   template <typename ResT, typename L, typename R, typename Func>
   static Array<BoutReal> evaluateBinaryExpr(const BinaryExpr<ResT, L, R, Func>& expr) {
-    Array<BoutReal> data{expr.size()};
+    const auto* mesh = expr.getMesh();
+    ASSERT1(mesh != nullptr);
+
+    Array<BoutReal> data{mesh->LocalNx * mesh->LocalNy};
     expr.evaluate(&data[0]);
     return data;
   }
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 2c19c5e505..e3304bd791 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -644,7 +644,10 @@ protected:
 
   template <typename L, typename R, typename Func>
   static Array<BoutReal> evaluateBinaryExpr(const BinaryExpr<Field3D, L, R, Func>& expr) {
-    Array<BoutReal> data{expr.size()};
+    const auto* mesh = expr.getMesh();
+    ASSERT1(mesh != nullptr);
+
+    Array<BoutReal> data{mesh->LocalNx * mesh->LocalNy * mesh->LocalNz};
     expr.evaluate(&data[0]);
     return data;
   }
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 9c4a957ee8..9063b23890 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -342,7 +342,10 @@ public:
 private:
   template <typename ResT, typename L, typename R, typename Func>
   static Array<BoutReal> evaluateBinaryExpr(const BinaryExpr<ResT, L, R, Func>& expr) {
-    Array<BoutReal> data{expr.size()};
+    const auto* mesh = expr.getMesh();
+    ASSERT1(mesh != nullptr);
+
+    Array<BoutReal> data{mesh->LocalNx * mesh->LocalNz};
     expr.evaluate(&data[0]);
     return data;
   }
diff --git a/tests/unit/field/test_field2d.cxx b/tests/unit/field/test_field2d.cxx
index af98d50d34..23eddc15ef 100644
--- a/tests/unit/field/test_field2d.cxx
+++ b/tests/unit/field/test_field2d.cxx
@@ -1208,6 +1208,16 @@ TEST_F(Field2DTest, AbsExpressionUsesAbsOp) {
   EXPECT_TRUE(IsFieldEqual(abs(expr, "RGN_ALL"), 1.0));
 }
 
+TEST_F(Field2DTest, RegionLimitedExpressionConstructsField2D) {
+  Field2D field;
+
+  field = -31.0;
+
+  Field2D result = abs(field, "RGN_NOBNDRY");
+
+  EXPECT_TRUE(IsFieldEqual(result, 31.0, "RGN_NOBNDRY"));
+}
+
 TEST_F(Field2DTest, Exp) {
   Field2D field;
 
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 6e1bc8ba58..9feae8343b 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -1999,6 +1999,16 @@ TEST_F(Field3DTest, AbsExpressionUsesAbsOp) {
   EXPECT_TRUE(IsFieldEqual(abs(expr, "RGN_ALL"), 1.0));
 }
 
+TEST_F(Field3DTest, RegionLimitedExpressionConstructsField3D) {
+  Field3D field;
+
+  field = -31.0;
+
+  Field3D result = abs(field, "RGN_NOBNDRY");
+
+  EXPECT_TRUE(IsFieldEqual(result, 31.0, "RGN_NOBNDRY"));
+}
+
 TEST_F(Field3DTest, Exp) {
   Field3D field;
 
diff --git a/tests/unit/field/test_fieldperp.cxx b/tests/unit/field/test_fieldperp.cxx
index 4975a9e735..060355a7db 100644
--- a/tests/unit/field/test_fieldperp.cxx
+++ b/tests/unit/field/test_fieldperp.cxx
@@ -1593,6 +1593,17 @@ TEST_F(FieldPerpTest, Abs) {
   EXPECT_TRUE(IsFieldEqual(abs(field), 31.0));
 }
 
+TEST_F(FieldPerpTest, RegionLimitedExpressionConstructsFieldPerp) {
+  FieldPerp field;
+  field.setIndex(0);
+
+  field = -31.0;
+
+  FieldPerp result = abs(field, "RGN_NOX");
+
+  EXPECT_TRUE(IsFieldEqual(result, 31.0, "RGN_NOX"));
+}
+
 TEST_F(FieldPerpTest, Exp) {
   FieldPerp field;
   field.setIndex(0);

From 250a566064bb2a3641a017bf9fc8de90a8e6230a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 11:40:50 -0700
Subject: [PATCH 1443/1827] Coordinates: Evaluate to FieldMetric

Force evaluation of BinaryExpr by assigning to a FieldMetric.
---
 src/mesh/coordinates.cxx | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 1591cee27c..4f7a747a7b 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2036,7 +2036,6 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
     return *_g_22_yhigh;
   }
   _g_22_yhigh.emplace(emptyFrom(g_22));
-  //_g_22_yhigh->setLocation(CELL_YHIGH);
   auto* mesh = Bxy.getMesh();
   if (Bxy.isFci()) {
     if (mesh->get(_g_22_yhigh.value(), "g_22_cell_yhigh", 0.0, false) != 0) {
@@ -2052,7 +2051,7 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
 }
 
 void Coordinates::_compute_cell_area_x() const {
-  const auto area_centre = sqrt(g_22 * g_33 - SQ(g_23)) * dy * dz;
+  const FieldMetric area_centre = sqrt(g_22 * g_33 - SQ(g_23)) * dy * dz;
   _cell_area_xlow.emplace(emptyFrom(area_centre));
   _cell_area_xhigh.emplace(emptyFrom(area_centre));
   // We cannot setLocation, as that would trigger the computation of staggered
@@ -2068,7 +2067,7 @@ void Coordinates::_compute_cell_area_x() const {
 void Coordinates::_compute_cell_area_y() const {
   auto* mesh = Bxy.getMesh();
   if (g_11.isFci()) {
-    const auto jxz_centre = sqrt(g_11 * g_33 - SQ(g_13));
+    const FieldMetric jxz_centre = sqrt(g_11 * g_33 - SQ(g_13));
     auto jxz_ylow = emptyFrom(jxz_centre);
     auto jxz_yhigh = emptyFrom(jxz_centre);
 
@@ -2096,7 +2095,7 @@ void Coordinates::_compute_cell_area_y() const {
     _cell_area_yhigh.emplace(jxz_yhigh * dx * dz);
   } else {
     // Field aligned
-    const auto area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;
+    const FieldMetric area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;
     _cell_area_ylow.emplace(emptyFrom(area_centre));
     _cell_area_yhigh.emplace(emptyFrom(area_centre));
     // We cannot setLocation, as that would trigger the computation of staggered
@@ -2117,12 +2116,11 @@ void Coordinates::_compute_cell_area_y() const {
 }
 
 void Coordinates::_compute_cell_area_z() const {
-  const auto area_centre = sqrt(g_11 * g_22 - SQ(g_12)) * dx * dy;
+  const FieldMetric area_centre = sqrt(g_11 * g_22 - SQ(g_12)) * dx * dy;
   _cell_area_zlow.emplace(emptyFrom(area_centre));
   _cell_area_zhigh.emplace(emptyFrom(area_centre));
   // We cannot setLocation, as that would trigger the computation of staggered
   // metrics.
-  //ASSERT0(mesh->zstart > 0);
   BOUT_FOR(i, area_centre.getRegion("RGN_NOZ")) {
     (*_cell_area_zlow)[i] = 0.5 * (area_centre[i] + area_centre[i.zm()]);
     (*_cell_area_zhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.zp()]);

From 512e8535f82a38b155b678d47c9eed3d0ee3efea Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 11:41:27 -0700
Subject: [PATCH 1444/1827] Clang tidying

strLocation doesn't seem to be used and may return pointer
to temporary string.

Added missing headers.
---
 src/mesh/interpolation_xz.cxx | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/mesh/interpolation_xz.cxx b/src/mesh/interpolation_xz.cxx
index ec8bcc0502..04d20769e4 100644
--- a/src/mesh/interpolation_xz.cxx
+++ b/src/mesh/interpolation_xz.cxx
@@ -24,16 +24,20 @@
  **************************************************************************/
 
 #include "parallel/fci_comm.hxx"
+#include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
 #include <bout/globals.hxx>
 #include <bout/interpolation_xz.hxx>
+#include <bout/mesh.hxx>
 #include <bout/output.hxx>
 #include <bout/unused.hxx>
+#include <bout/utils.hxx>
 
 void printLocation(const Field3D& var) { output << toString(var.getLocation()); }
 void printLocation(const Field2D& var) { output << toString(var.getLocation()); }
 
-const char* strLocation(CELL_LOC loc) { return toString(loc).c_str(); }
-
 const Field3D interpolate(const Field3D& f, const Field3D& delta_x,
                           const Field3D& delta_z) {
   XZLagrange4pt interpolateMethod{f.getMesh()};
@@ -46,7 +50,7 @@ const Field3D interpolate(const Field2D& f, const Field3D& delta_x,
 }
 
 const Field3D interpolate(const Field2D& f, const Field3D& delta_x) {
-  Mesh* mesh = f.getMesh();
+  const Mesh* mesh = f.getMesh();
   ASSERT1(mesh == delta_x.getMesh());
   Field3D result{emptyFrom(delta_x)};
 

From 81fda045973e9e9877cbad8016ef52f68c1b3ac0 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 19 Jun 2026 20:02:34 +0100
Subject: [PATCH 1445/1827] Fixed linting complaints

---
 include/bout/solver.hxx        | 13 ++++++++-----
 src/solver/impls/snes/snes.cxx | 25 ++++++++++++++-----------
 src/solver/impls/snes/snes.hxx | 16 +++++++++-------
 src/solver/solver.cxx          |  2 +-
 4 files changed, 32 insertions(+), 24 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index fa67ac1ca7..eba8164419 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -40,10 +40,13 @@
 
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/globals.hxx"
 #include "bout/monitor.hxx"
 #include "bout/options.hxx"
+#include "bout/regions.hxx"
 #include "bout/unused.hxx"
 
+#include <iterator>
 #include <memory>
 
 ///////////////////////////////////////////////////////////////////
@@ -92,8 +95,8 @@ constexpr auto SOLVERIMEXBDF2 = "imexbdf2";
 constexpr auto SOLVERSNES = "snes";
 constexpr auto SOLVERRKGENERIC = "rkgeneric";
 
-enum class FieldCategories { VARS, DERIVS, MMS };
-enum class SOLVER_VAR_OP { LOAD, SET_ID, SAVE };
+enum class FieldCategories : std::uint8_t { VARS, DERIVS, MMS };
+enum class SOLVER_VAR_OP : std::uint8_t { LOAD, SET_ID, SAVE };
 
 /// A type to set where in the list monitors are added
 enum class MonitorPosition { BACK, FRONT };
@@ -635,7 +638,7 @@ protected:
   void loop_vars(RangeF2D f2d_range, RangeF3D f3d_range, BoutReal* udata,
                  SOLVER_VAR_OP op) {
     // Use global mesh: FIX THIS!
-    Mesh* mesh = bout::globals::mesh;
+    const Mesh* mesh = bout::globals::mesh;
 
     int p = 0; // Counter for location in udata array
 
@@ -719,9 +722,9 @@ private:
  * Is the interleaving of variables needed or helpful to the solver?
  **************************************************************************/
     // Use global mesh: FIX THIS!
-    Mesh* mesh = bout::globals::mesh;
+    const Mesh* mesh = bout::globals::mesh;
 
-    int nz = mesh->LocalNz;
+    const int nz = mesh->LocalNz;
 
     switch (op) {
     case SOLVER_VAR_OP::LOAD: {
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 571dc9504e..3c26db4d5b 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -885,15 +885,16 @@ PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
   // Individual variable scaling
   // Note: If variables are rescaled then the Jacobian columns
   //       need to be scaled or recalculated
-  int istart, iend;
+  int istart = 0;
+  int iend = 0;
   VecGetOwnershipRange(snes_x, &istart, &iend);
 
   // Take ownership of snes_x and var_scaling_factors data
   PetscScalar* snes_x_data = nullptr;
   PetscCall(VecGetArray(snes_x, &snes_x_data));
-  PetscScalar* x1_data;
+  PetscScalar* x1_data = nullptr;
   PetscCall(VecGetArray(x1, &x1_data));
-  PetscScalar* var_scaling_factors_data;
+  PetscScalar* var_scaling_factors_data = nullptr;
   PetscCall(VecGetArray(var_scaling_factors, &var_scaling_factors_data));
 
   // Normalise each value in the state
@@ -901,8 +902,7 @@ PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
   for (int i = 0; i < iend - istart; ++i) {
     const PetscScalar norm =
         BOUTMAX(std::abs(snes_x_data[i]), rtol / var_scaling_factors_data[i]);
-    snes_x_data[i] /=
-        norm;
+    snes_x_data[i] /= norm;
     x1_data[i] /= norm; // Update history for predictor
     var_scaling_factors_data[i] *= norm;
   }
@@ -914,7 +914,8 @@ PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
 
   if (diagnose) {
     // Print maximum and minimum scaling factors
-    PetscReal max_scale, min_scale;
+    PetscReal max_scale = 0.;
+    PetscReal min_scale = 0.;
     VecMax(var_scaling_factors, nullptr, &max_scale);
     VecMin(var_scaling_factors, nullptr, &min_scale);
     output.write("Var scaling: {} -> {}\n", min_scale, max_scale);
@@ -922,6 +923,10 @@ PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
 
   // Force recalculation of the Jacobian
   SNESGetLagJacobian(snes, &saved_jacobian_lag);
+  // FIXME: This isn't actually what we want to happen. The lag should
+  // stay as before, we just want to make sure the Jacobian gets
+  // re-evaluated at the start of the solve. We need to use
+  // SNESSetJacobianPersist for that.
   SNESSetLagJacobian(snes, 1);
   return PETSC_SUCCESS;
 }
@@ -945,8 +950,8 @@ int SNESSolver::run() {
     PetscCall(VecRestoreArray(snes_x, &xdata));
   }
 
+  int saved_jacobian_lag = 0;
   if (scale_vars) {
-    int saved_jacobian_lag;
     PetscCall(rescale(saved_jacobian_lag));
   }
 
@@ -973,8 +978,6 @@ int SNESSolver::run() {
 
     bool looping = true;
     int snes_failures = 0; // Count SNES convergence failures
-    int saved_jacobian_lag = 0;
-    PetscBool saved_jacobian_persist = PETSC_FALSE;
 
     const BoutReal start_global_residual = global_residual;
     do {
@@ -1347,7 +1350,7 @@ int SNESSolver::run() {
     }
 
     if (diagnose) {
-      BoutReal* resid_data;
+      BoutReal* resid_data = nullptr;
       PetscCall(VecGetArray(output_f, &resid_data));
       loop_vars(resid_2d, resid_3d, resid_data, SOLVER_VAR_OP::LOAD);
       PetscCall(VecRestoreArray(output_f, &resid_data));
@@ -1789,7 +1792,7 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
     // if (scale_vars) {
     //   VecPointwiseMult(delta_x, delta_x, var_scaling_factors);
     // }
-    VecAXPY(f, -1. / dt, delta_x);  // f <- f - delta_x / dt
+    VecAXPY(f, -1. / dt, delta_x); // f <- f - delta_x / dt
     break;
   }
   case BoutSnesEquationForm::pseudo_transient: {
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 9b5a6a6eeb..3b1ffe99f0 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -35,6 +35,8 @@
 
 class SNESSolver;
 
+#include <vector>
+
 #include "mpi.h"
 
 #include <bout/bout_enum_class.hxx>
@@ -223,10 +225,10 @@ private:
   PetscLib lib; ///< Handles initialising, finalising PETSc
   Vec snes_f;   ///< Used by SNES to store function
   Vec deriv; ///< Time derivative; only used if diagnose = true, otherwise will store in snes_f
-  Vec snes_x;   ///< Result of SNES
-  Vec x0;       ///< Solution at start of current timestep
-  Vec f0; ///< Residual at start of current timestep (only stored if diagnose = true)
-  Vec delta_x;  ///< Change in solution
+  Vec snes_x;  ///< Result of SNES
+  Vec x0;      ///< Solution at start of current timestep
+  Vec f0;      ///< Residual at start of current timestep (only stored if diagnose = true)
+  Vec delta_x; ///< Change in solution
   Vec output_x; ///< Solution to output. Used if interpolating.
   Vec output_f; ///< Residual to output, if diagnose == true. Used if interpolating.
 
@@ -252,7 +254,7 @@ private:
   bool matrix_free_operator; ///< Use matrix free Jacobian in the operator?
   int lag_jacobian;          ///< Re-use Jacobian
   bool jacobian_persists; ///< Re-use Jacobian and preconditioner across nonlinear solves
-  bool use_coloring;         ///< Use matrix coloring
+  bool use_coloring;      ///< Use matrix coloring
 
   bool jacobian_recalculated; ///< Flag set when Jacobian is recalculated
   bool prune_jacobian;        ///< Remove small elements in the Jacobian?
@@ -266,8 +268,8 @@ private:
   Vec rhs_scaling_factors; ///< Factors to multiply RHS function
   Vec jac_row_inv_norms;   ///< 1 / Norm of the rows of the Jacobian
 
-  bool scale_vars;         ///< Scale individual variables?
-  int rescale_period;      ///< How many time-steps before rescaling variables
+  bool scale_vars;    ///< Scale individual variables?
+  int rescale_period; ///< How many time-steps before rescaling variables
   BoutReal
       rescale_threshold; //< How much change in the state there should be before rescaling
   Vec var_scaling_factors; ///< Factors to multiply variables when passing to user
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index b46b890574..1f7b654427 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -2,7 +2,7 @@
  * Copyright 2010 - 2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify

From 19b82e19a61c7f50a4dc880d6ab82c86c0c02ea7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 19 Jun 2026 19:32:37 +0000
Subject: [PATCH 1446/1827] Bump externalpackages/googletest from `8736d2c` to
 `0b1e895`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `8736d2c` to `0b1e895`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/8736d2cd5c1dcba41170ed2fddca14021d4916c3...0b1e895ba4226c2fda5ee0178c9b5b1195a741aa)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: 0b1e895ba4226c2fda5ee0178c9b5b1195a741aa
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 8736d2cd5c..0b1e895ba4 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 8736d2cd5c1dcba41170ed2fddca14021d4916c3
+Subproject commit 0b1e895ba4226c2fda5ee0178c9b5b1195a741aa

From c7a8b1e6cde242ef9e48beb1b41eb87e36a7dca4 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 19 Jun 2026 19:32:38 +0000
Subject: [PATCH 1447/1827] Bump actions/checkout from 6 to 7

Bumps [actions/checkout](https://github.com/actions/checkout) from 6 to 7.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v6...v7)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/auto-formatting.yml   | 2 +-
 .github/workflows/clang-tidy-review.yml | 2 +-
 .github/workflows/docker.yml            | 2 +-
 .github/workflows/python-package.yml    | 6 +++---
 .github/workflows/tests.yml             | 4 ++--
 5 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/auto-formatting.yml b/.github/workflows/auto-formatting.yml
index 8c4c34320f..518cfd3898 100644
--- a/.github/workflows/auto-formatting.yml
+++ b/.github/workflows/auto-formatting.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0
diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
index 360a162456..0573addd9c 100644
--- a/.github/workflows/clang-tidy-review.yml
+++ b/.github/workflows/clang-tidy-review.yml
@@ -16,7 +16,7 @@ jobs:
     if: ${{ !endsWith(github.head_ref, '-rc') }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           submodules: true
 
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 809f59cf9c..ba4e1937ae 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -52,7 +52,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@master
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 915265e850..e2023fa5c8 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -17,7 +17,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 0
         submodules: true
@@ -57,7 +57,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 0
         submodules: true
@@ -106,7 +106,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 0
         submodules: true
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ff11a2a4c9..76c627b9b4 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -153,7 +153,7 @@ jobs:
                  libparpack2-dev
                  libhypre-dev
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           submodules: true
 
@@ -200,7 +200,7 @@ jobs:
     env:
       BOUT_TEST_DOWNLOAD_FLAGS: --retry-on-http-error=502,503,504 --tries 3
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           submodules: true
 

From 70d54848cc92d04cfb2a18d989522602836edc28 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Fri, 19 Jun 2026 20:46:58 +0100
Subject: [PATCH 1448/1827] Fixed a few bugs and clang-tidy issues

---
 include/bout/solver.hxx        | 6 ++++--
 src/solver/impls/snes/snes.cxx | 8 ++++----
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index eba8164419..1a3d475edf 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -41,11 +41,13 @@
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/globals.hxx"
+#include "bout/mesh.hxx"
 #include "bout/monitor.hxx"
 #include "bout/options.hxx"
-#include "bout/regions.hxx"
+#include "bout/region.hxx"
 #include "bout/unused.hxx"
 
+#include <cstdint>
 #include <iterator>
 #include <memory>
 
@@ -487,7 +489,7 @@ protected:
     }
 
   private:
-    underlying_iterator it;
+    underlying_iterator it{};
   };
 
   template <FieldCategories C, class T>
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 3c26db4d5b..5003117e3f 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -1204,10 +1204,10 @@ int SNESSolver::run() {
 
         // Copy derivatives back
         if (diagnose) {
-          BoutReal* fdata = nullptr;
-          PetscCall(VecGetArray(deriv, &fdata));
-          save_derivs(fdata);
-          PetscCall(VecRestoreArray(deriv, &fdata));
+          BoutReal* ddata = nullptr;
+          PetscCall(VecGetArray(deriv, &ddata));
+          save_derivs(ddata);
+          PetscCall(VecRestoreArray(deriv, &ddata));
           // Forward Euler
           VecAXPY(snes_x, dt, deriv);
         } else {

From 7cb424fb0b5dc09497259bb9c8fb2c896f9492bd Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 14:35:07 -0700
Subject: [PATCH 1449/1827] BinaryExpr: Assignment operators propagate metadata

Assigning an expression to a field should update the field
metadata (location, Y slice for FieldPerp) to the value
from the BinaryExpr.

Unit tests now pass locally with CHECK=4.
---
 include/bout/field.hxx              | 34 +++++++++++++++++++++++---
 include/bout/field2d.hxx            | 10 +++++---
 include/bout/field3d.hxx            | 15 ++++++++----
 include/bout/fieldops.hxx           | 11 ++++++---
 include/bout/fieldperp.hxx          | 17 ++++++++++++-
 include/bout/petsc_interface.hxx    | 10 ++++----
 src/field/fieldperp.cxx             |  2 +-
 src/mesh/coordinates.cxx            |  4 +--
 tests/unit/field/test_field2d.cxx   | 19 ++++++++++++++-
 tests/unit/field/test_field3d.cxx   | 21 +++++++++++++++-
 tests/unit/field/test_fieldperp.cxx | 38 ++++++++++++++++++++++++++++-
 11 files changed, 153 insertions(+), 28 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 6547c0a31d..a8e1952546 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -605,6 +605,28 @@ T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
  *
  */
 class Field3DParallel;
+class FieldPerp;
+
+namespace bout::detail {
+template <typename T>
+std::optional<int> getPerpYIndex(const T& value) {
+  if constexpr (std::is_same_v<std::decay_t<T>, ::FieldPerp>) {
+    return value.getIndex();
+  } else {
+    return std::nullopt;
+  }
+}
+
+template <typename ResT, typename L, typename R, typename Func>
+std::optional<int> getPerpYIndex(const BinaryExpr<ResT, L, R, Func>& expr) {
+  if constexpr (std::is_same_v<ResT, ::FieldPerp>) {
+    return expr.getIndex();
+  } else {
+    return std::nullopt;
+  }
+}
+} // namespace bout::detail
+
 #ifdef FIELD_FUNC
 #error This macro has already been defined
 #else
@@ -640,7 +662,8 @@ class Field3DParallel;
                                                  f.getLocation(),                       \
                                                  f.getDirections(),                     \
                                                  std::nullopt,                          \
-                                                 f.getRegion(rgn)};                     \
+                                                 f.getRegion(rgn),                      \
+                                                 bout::detail::getPerpYIndex(f)};       \
     }                                                                                   \
   }                                                                                     \
   template <typename ResT, typename L, typename R, typename Func>                       \
@@ -654,7 +677,8 @@ class Field3DParallel;
         f.getLocation(),                                                                \
         f.getDirections(),                                                              \
         f.getRegionID(),                                                                \
-        f.indices};                                                                     \
+        f.indices,                                                                      \
+        bout::detail::getPerpYIndex(f)};                                                \
   }                                                                                     \
   template <typename ResT, typename L, typename R, typename Func>                       \
   inline auto name(const BinaryExpr<ResT, L, R, Func>& f, const std::string& rgn) {     \
@@ -696,7 +720,8 @@ inline auto SQ(const T& f, const std::string& rgn = "RGN_ALL") {
                                                  f.getLocation(),
                                                  f.getDirections(),
                                                  std::nullopt,
-                                                 f.getRegion(rgn)};
+                                                 f.getRegion(rgn),
+                                                 bout::detail::getPerpYIndex(f)};
   }
 }
 
@@ -711,7 +736,8 @@ inline auto SQ(const BinaryExpr<ResT, L, R, Func>& f) {
       f.getLocation(),
       f.getDirections(),
       f.getRegionID(),
-      f.indices};
+      f.indices,
+      bout::detail::getPerpYIndex(f)};
 }
 
 template <typename ResT, typename L, typename R, typename Func>
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 807b0ac1a3..7ab8bdfb25 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -189,11 +189,15 @@ public:
   template <typename ResT, typename L, typename R, typename Func>
   std::enable_if_t<is_expr_field2d_v<L>, Field2D&>
   operator=(const BinaryExpr<ResT, L, R, Func>& expr) {
-    if (isAllocated()) {
-      expr.evaluate(&data[0]);
-    } else {
+    if (!isAllocated() || getMesh() != expr.getMesh()) {
       *this = Field2D{expr};
+      return *this;
     }
+
+    setLocation(expr.getLocation());
+    setDirections(expr.getDirections());
+    allocate();
+    expr.evaluate(&data[0]);
     return *this;
   }
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index e3304bd791..112e73219e 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -489,13 +489,18 @@ public:
   Field3D& operator=(BoutReal val);
   template <typename ResT, typename L, typename R, typename Func>
   std::enable_if_t<is_expr_field3d_v<L>, Field3D&>
-  operator=(BinaryExpr<ResT, L, R, Func>& expr) {
-    regionID = expr.getRegionID();
-    if (isAllocated()) {
-      expr.evaluate(&data[0]);
-    } else {
+  operator=(const BinaryExpr<ResT, L, R, Func>& expr) {
+    if (!isAllocated() || getMesh() != expr.getMesh()) {
       *this = Field3D{expr};
+      return *this;
     }
+
+    clearParallelSlices();
+    setRegion(expr.getRegionID());
+    setLocation(expr.getLocation());
+    setDirections(expr.getDirections());
+    allocate();
+    expr.evaluate(&data[0]);
     return *this;
   }
 
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index df513c0290..25765e6f6b 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -21,6 +21,7 @@
 class Mesh;
 class Field3D;
 class Field2D;
+class FieldPerp;
 
 template <typename T>
 struct is_expr_field2d : std::false_type {};
@@ -327,19 +328,20 @@ struct BinaryExpr {
   CELL_LOC location = CELL_CENTRE;
   DirectionTypes directions;
   std::optional<size_t> regionID;
+  std::optional<int> yindex;
 
   template <typename IndType>
   BinaryExpr(const typename L::View& lhs, const typename R::View& rhs, Func f, Mesh* mesh,
              CELL_LOC location, DirectionTypes directions, std::optional<size_t> regionID,
-             const Region<IndType>& region)
+             const Region<IndType>& region, std::optional<int> yindex = std::nullopt)
       : lhs(lhs), rhs(rhs), indices(region.getLinearIndices()), f(f), mesh(mesh),
-        location(location), directions(directions), regionID(regionID) {}
+        location(location), directions(directions), regionID(regionID), yindex(yindex) {}
 
   BinaryExpr(const typename L::View& lhs, const typename R::View& rhs, Func f, Mesh* mesh,
              CELL_LOC location, DirectionTypes directions, std::optional<size_t> regionID,
-             const Array<int>& indices)
+             const Array<int>& indices, std::optional<int> yindex = std::nullopt)
       : lhs(lhs), rhs(rhs), indices(indices), f(f), mesh(mesh), location(location),
-        directions(directions), regionID(regionID) {}
+        directions(directions), regionID(regionID), yindex(yindex) {}
 
   BinaryExpr& operator=(const BinaryExpr&) = delete;
   BinaryExpr& operator=(BinaryExpr&&) = delete;
@@ -407,6 +409,7 @@ struct BinaryExpr {
   CELL_LOC getLocation() const { return location; }
   DirectionTypes getDirections() const { return directions; }
   std::optional<size_t> getRegionID() const { return regionID; };
+  int getIndex() const { return yindex.value_or(-1); }
 };
 
 #endif // BOUT_FIELDSOPS_HXX
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 9063b23890..b16bc562bb 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -98,7 +98,7 @@ public:
       typename = std::enable_if_t<(is_expr_fieldperp_v<L> && is_expr_fieldperp_v<R>)>>
   FieldPerp(const BinaryExpr<ResT, L, R, Func>& expr)
       : FieldPerp(evaluateBinaryExpr(expr), expr.getMesh(), expr.getLocation(),
-                  /* yindex */ -1, expr.getDirections()) {}
+                  expr.getIndex(), expr.getDirections()) {}
 
   ~FieldPerp() override = default;
 
@@ -108,6 +108,21 @@ public:
   FieldPerp& operator=(const FieldPerp& rhs);
   FieldPerp& operator=(FieldPerp&& rhs) = default;
   FieldPerp& operator=(BoutReal rhs);
+  template <typename ResT, typename L, typename R, typename Func>
+  std::enable_if_t<is_expr_fieldperp_v<L>, FieldPerp&>
+  operator=(const BinaryExpr<ResT, L, R, Func>& expr) {
+    if (!isAllocated() || getMesh() != expr.getMesh()) {
+      *this = FieldPerp{expr};
+      return *this;
+    }
+
+    setLocation(expr.getLocation());
+    setDirections(expr.getDirections());
+    setIndex(expr.getIndex());
+    allocate();
+    expr.evaluate(&data[0]);
+    return *this;
+  }
 
   /// Return a Region<IndPerp> reference to use to iterate over this field
   const Region<IndPerp>& getRegion(REGION region) const;
diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 2ce71d0549..830a7f4122 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -355,7 +355,7 @@ public:
       ASSERT2(positions.size() == weights.size());
 #if CHECK > 2
       for (const auto val : weights) {
-        ASSERT3(finite(val));
+        ASSERT3(std::isfinite(val));
       }
 #endif
       if (positions.empty()) {
@@ -376,25 +376,25 @@ public:
       if (this == &other) {
         return *this;
       }
-      ASSERT3(finite(static_cast<BoutReal>(other)));
+      ASSERT3(std::isfinite(static_cast<BoutReal>(other)));
       *this = static_cast<BoutReal>(other);
       return *this;
     }
     Element& operator=(BoutReal val) {
 
-      ASSERT3(finite(val));
+      ASSERT3(std::isfinite(val));
       value = val;
       setValues(val, INSERT_VALUES);
       return *this;
     }
     Element& operator+=(BoutReal val) {
 
-      ASSERT3(finite(val));
+      ASSERT3(std::isfinite(val));
       auto columnPosition = std::find(positions.begin(), positions.end(), petscCol);
       if (columnPosition != positions.end()) {
         const int index = std::distance(positions.begin(), columnPosition);
         value += weights[index] * val;
-        ASSERT3(finite(value));
+        ASSERT3(std::isfinite(value));
       }
       setValues(val, ADD_VALUES);
       return *this;
diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index bf9e6b348d..72976704f2 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -2,7 +2,7 @@
  * Class for 2D X-Z slices
  *
  **************************************************************************
- * Copyright 2010 - 2025 BOUT++ developers
+ * Copyright 2010 - 2026 BOUT++ developers
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 4f7a747a7b..f10f903d19 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1345,8 +1345,8 @@ int Coordinates::jacobian() {
   const bool extrapolate_x = not localmesh->sourceHasXBoundaryGuards();
   const bool extrapolate_y = not localmesh->sourceHasYBoundaryGuards();
 
-  auto g = FieldMetric{g11 * g22 * g33 + 2.0 * g12 * g13 * g23 - g11 * g23 * g23
-                       - g22 * g13 * g13 - g33 * g12 * g12};
+  FieldMetric g = g11 * g22 * g33 + 2.0 * g12 * g13 * g23 - g11 * g23 * g23
+                  - g22 * g13 * g13 - g33 * g12 * g12;
 
   // Check that g is positive
   bout::checkPositive(g, "The determinant of g^ij", "RGN_NOBNDRY");
diff --git a/tests/unit/field/test_field2d.cxx b/tests/unit/field/test_field2d.cxx
index 23eddc15ef..a91acd4a40 100644
--- a/tests/unit/field/test_field2d.cxx
+++ b/tests/unit/field/test_field2d.cxx
@@ -853,7 +853,7 @@ TEST_F(Field2DTest, InvalidateGuards) {
 
   sum = 0;
   for (const auto& i : field) {
-    if (!finite(field[i])) {
+    if (!std::isfinite(field[i])) {
       sum++;
     }
   }
@@ -1502,6 +1502,23 @@ TEST_F(Field2DTest, OperatorEqualsField2D) {
   EXPECT_EQ(field.getDirectionZ(), field2.getDirectionZ());
 }
 
+TEST_F(Field2DTest, OperatorEqualsBinaryExprCopiesMetadata) {
+  Field2D source{
+      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+  source = 4.;
+
+  Field2D target(mesh_staggered);
+  target = 0.;
+
+  target = sqrt(source);
+
+  EXPECT_EQ(target.getMesh(), source.getMesh());
+  EXPECT_EQ(target.getLocation(), source.getLocation());
+  EXPECT_EQ(target.getDirectionY(), source.getDirectionY());
+  EXPECT_EQ(target.getDirectionZ(), source.getDirectionZ());
+  EXPECT_TRUE(IsFieldEqual(target, 2.));
+}
+
 TEST_F(Field2DTest, EmptyFrom) {
   // Create field with non-default arguments so we can check they get copied
   // to 'field2'.
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 9feae8343b..905b182018 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -1211,7 +1211,7 @@ TEST_F(Field3DTest, InvalidateGuards) {
 
   sum = 0;
   for (const auto& i : field) {
-    if (!finite(field[i])) {
+    if (!std::isfinite(field[i])) {
       sum++;
     }
   }
@@ -2517,6 +2517,25 @@ TEST_F(Field3DTest, OperatorEqualsField3D) {
   EXPECT_EQ(field.getDirectionZ(), field2.getDirectionZ());
 }
 
+TEST_F(Field3DTest, OperatorEqualsBinaryExprCopiesMetadata) {
+  Field3D source{
+      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+  source = 9.;
+
+  Field3D target(mesh_staggered);
+  target = 0.;
+  target.splitParallelSlices();
+
+  target = sqrt(source);
+
+  EXPECT_EQ(target.getMesh(), source.getMesh());
+  EXPECT_EQ(target.getLocation(), source.getLocation());
+  EXPECT_EQ(target.getDirectionY(), source.getDirectionY());
+  EXPECT_EQ(target.getDirectionZ(), source.getDirectionZ());
+  EXPECT_FALSE(target.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(target, 3.));
+}
+
 TEST_F(Field3DTest, EmptyFrom) {
   // Create field with non-default arguments so we can check they get copied
   // to 'field2'.
diff --git a/tests/unit/field/test_fieldperp.cxx b/tests/unit/field/test_fieldperp.cxx
index 060355a7db..46f07d589f 100644
--- a/tests/unit/field/test_fieldperp.cxx
+++ b/tests/unit/field/test_fieldperp.cxx
@@ -849,7 +849,7 @@ TEST_F(FieldPerpTest, InvalidateGuards) {
 
   sum = 0;
   for (const auto& i : field) {
-    if (!finite(field[i])) {
+    if (!std::isfinite(field[i])) {
       sum++;
     }
   }
@@ -1784,6 +1784,42 @@ TEST_F(FieldPerpTest, OperatorEqualsFieldPerp) {
   EXPECT_EQ(field.getDirectionZ(), field2.getDirectionZ());
 }
 
+TEST_F(FieldPerpTest, ConstructFromBinaryExprCopiesMetadata) {
+  FieldPerp source{
+      mesh_staggered, CELL_XLOW, 3, {YDirectionType::Aligned, ZDirectionType::Average}};
+  source = 4.;
+
+  FieldPerp result{sqrt(source)};
+
+  EXPECT_EQ(result.getMesh(), source.getMesh());
+  EXPECT_EQ(result.getLocation(), source.getLocation());
+  EXPECT_EQ(result.getIndex(), source.getIndex());
+  EXPECT_EQ(result.getDirectionY(), source.getDirectionY());
+  EXPECT_EQ(result.getDirectionZ(), source.getDirectionZ());
+  EXPECT_TRUE(IsFieldEqual(result, 2.));
+}
+
+TEST_F(FieldPerpTest, OperatorEqualsBinaryExprCopiesMetadata) {
+  FieldPerp source{
+      mesh_staggered, CELL_XLOW, 3, {YDirectionType::Aligned, ZDirectionType::Average}};
+  source = 4.;
+
+  FieldPerp target{mesh_staggered,
+                   CELL_CENTRE,
+                   1,
+                   {YDirectionType::Standard, ZDirectionType::Standard}};
+  target = 0.;
+
+  target = sqrt(source);
+
+  EXPECT_EQ(target.getMesh(), source.getMesh());
+  EXPECT_EQ(target.getLocation(), source.getLocation());
+  EXPECT_EQ(target.getIndex(), source.getIndex());
+  EXPECT_EQ(target.getDirectionY(), source.getDirectionY());
+  EXPECT_EQ(target.getDirectionZ(), source.getDirectionZ());
+  EXPECT_TRUE(IsFieldEqual(target, 2.));
+}
+
 TEST_F(FieldPerpTest, EmptyFrom) {
   // Create field with non-default arguments so we can check they get copied
   // to 'field2'.

From b0ff0c6d90675b03483da2f81b3f2c843be7dddc Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 15:36:39 -0700
Subject: [PATCH 1450/1827] examples/elm-pb: Tidying and fix for BoutExpr

Argument to `where` needs to be converted to a Field
from a BinaryExpr.
---
 examples/elm-pb/elm_pb.cxx | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx
index 9eb7396987..62cc970869 100644
--- a/examples/elm-pb/elm_pb.cxx
+++ b/examples/elm-pb/elm_pb.cxx
@@ -6,9 +6,14 @@
  *******************************************************************************/
 
 #include <bout/bout.hxx>
+#include <bout/bout_types.hxx>
+#include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
+#include <bout/coordinates.hxx>
 #include <bout/derivs.hxx>
 #include <bout/difops.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/fv_ops.hxx>
 #include <bout/initialprofiles.hxx>
@@ -16,6 +21,7 @@
 #include <bout/invert/laplacexy.hxx>
 #include <bout/invert_laplace.hxx>
 #include <bout/invert_parderiv.hxx>
+#include <bout/output.hxx>
 #include <bout/sourcex.hxx>
 #include <bout/tokamak_coordinates.hxx>
 #include <bout/utils.hxx>
@@ -246,8 +252,8 @@ class ELMpb : public PhysicsModel {
   std::unique_ptr<Laplacian> phiSolver{nullptr};
   std::unique_ptr<Laplacian> aparSolver{nullptr};
 
-  const Field2D N0tanh(BoutReal n0_height, BoutReal n0_ave, BoutReal n0_width,
-                       BoutReal n0_center, BoutReal n0_bottom_x) {
+  Field2D N0tanh(BoutReal n0_height, BoutReal n0_ave, BoutReal n0_width,
+                 BoutReal n0_center, BoutReal n0_bottom_x) {
     Field2D result;
     result.allocate();
 
@@ -1138,7 +1144,7 @@ class ELMpb : public PhysicsModel {
       // Only if not restarting: Check initial perturbation
 
       // Set U to zero where P0 < vacuum_pressure
-      U = where(P0 - vacuum_pressure, U, 0.0);
+      U = where(Field2D{P0 - vacuum_pressure}, U, 0.0);
 
       if (constn0) {
         ubyn = U;
@@ -1202,7 +1208,7 @@ class ELMpb : public PhysicsModel {
     // Perform communications
     mesh->communicate(comms);
 
-    Coordinates* metric = mesh->getCoordinates();
+    const Coordinates* metric = mesh->getCoordinates();
 
     ////////////////////////////////////////////
     // Transitions from 0 in core to 1 in vacuum
@@ -1698,10 +1704,10 @@ class ELMpb : public PhysicsModel {
       // Vacuum solution
       if (relax_j_vac) {
         // Calculate the J and Psi profile we're aiming for
-        Field3D Jtarget = Jpar * (1.0 - vac_mask); // Zero in vacuum
+        const Field3D Jtarget = Jpar * (1.0 - vac_mask); // Zero in vacuum
 
         // Invert laplacian for Psi
-        Field3D Psitarget = aparSolver->solve(Jtarget);
+        const Field3D Psitarget = aparSolver->solve(Jtarget);
 
         // Add a relaxation term in the vacuum
         ddt(Psi) =
@@ -1832,7 +1838,7 @@ class ELMpb : public PhysicsModel {
       ddt(U) -= 0.5 * Upara2 * bracket(Pi0, Dperp2Phi, bm_exb) / B0;
       Field3D B0phi = B0 * phi;
       mesh->communicate(B0phi);
-      Field3D B0phi0 = B0 * phi0;
+      Field2D B0phi0 = B0 * phi0;
       mesh->communicate(B0phi0);
       ddt(U) += 0.5 * Upara2 * bracket(B0phi, Dperp2Pi0, bm_exb) / B0;
       ddt(U) += 0.5 * Upara2 * bracket(B0phi0, Dperp2Pi, bm_exb) / B0;

From 404e063674e8e95ffb71e08d6b336176a4e7f776 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 15:41:07 -0700
Subject: [PATCH 1451/1827] Updating documentation

Document field expressions and GPU support changes.
---
 manual/sphinx/developer_docs/data_types.rst   | 129 +++++++++-----
 manual/sphinx/index.rst                       |  29 ++--
 .../sphinx/user_docs/algebraic_operators.rst  |  74 ++++++---
 manual/sphinx/user_docs/field_expressions.rst | 151 +++++++++++++++++
 manual/sphinx/user_docs/gpu_support.rst       | 157 ++++++++++++------
 .../sphinx/user_docs/parallel-transforms.rst  |  15 ++
 6 files changed, 432 insertions(+), 123 deletions(-)
 create mode 100644 manual/sphinx/user_docs/field_expressions.rst

diff --git a/manual/sphinx/developer_docs/data_types.rst b/manual/sphinx/developer_docs/data_types.rst
index f9411dcb39..7feb3945aa 100644
--- a/manual/sphinx/developer_docs/data_types.rst
+++ b/manual/sphinx/developer_docs/data_types.rst
@@ -280,7 +280,7 @@ The region to iterate over can be over ``Field2D``, ``Field3D``, or
 -  `RGN_NOY`, which skips the y boundaries and guard cells
 
 New regions can be created and modified, see section below.
-   
+
 A standard C++ range for loop can also be used, but this is unlikely
 to OpenMP parallelise or vectorise::
 
@@ -306,7 +306,7 @@ For loops inside parallel regions, there is ``BOUT_FOR_INNER``::
       }
       ...
     }
-    
+
 If a more general OpenMP directive is needed, there is
 ``BOUT_FOR_OMP``::
 
@@ -314,7 +314,7 @@ If a more general OpenMP directive is needed, there is
     BOUT_FOR_OMP(i, region, parallel for reduction(max:result)) {
       result = f[i] > result ? f[i] : result;
     }
-  
+
 The iterator provides access to the x, y, z indices::
 
     Field3D f(0.0);
@@ -385,14 +385,14 @@ good performance on typical x86_64 hardware. Some simple diagnostics
 are printed at the start of the BOUT++ output which may help. For
 example the ``blob2d`` example prints::
 
-  Registered region 3D RGN_ALL: 
-	Total blocks : 1040, min(count)/max(count) : 64 (1040)/ 64 (1040), Max imbalance : 1, Small block count : 0
+  Registered region 3D RGN_ALL:
+    Total blocks : 1040, min(count)/max(count) : 64 (1040)/ 64 (1040), Max imbalance : 1, Small block count : 0
 
 In this case all blocks are the same size, so the ``Max imbalance``
 (ratio of maximum to minimum block size) is 1. The ``Small block
 count`` is currently defined as the number of blocks with a size less
 than half the maximum block size. Ideally all blocks should be a
-similar size, so that work is evenly balanced between threads. 
+similar size, so that work is evenly balanced between threads.
 
 Creating new regions
 ~~~~~~~~~~~~~~~~~~~~
@@ -422,7 +422,7 @@ in the mask (i.e. set subtraction)::
 or::
 
   auto region = mask(mesh->getRegion2D("RGN_ALL"), mesh->getRegion2D("RGN_GUARDS"));
-  
+
 The above example would produce a region containing all the indices in
 ``RGN_ALL`` which are not in ``RGN_GUARDS``.
 
@@ -444,7 +444,7 @@ In the current implementation overwriting a region, by attempting to
 add a region which already exists, is not allowed, and will result in
 a ``BoutException`` being thrown. This restriction may be removed in
 future.
-  
+
 .. _sec-rangeiterator:
 
 Iterating over ranges
@@ -493,33 +493,73 @@ initialised in the constructor.
 
 .. _sec-fieldops:
 
-Field2D/Field3D Arithmetic Operators
-------------------------------------
-
-The arithmetic operators (``+``, ``-``, ``/``, ``*``) for `Field2D`
-and `Field3D` are generated automatically using the `Jinja`_
-templating system. This requires Python 3 (2.7 may work, but only 3 is
-supported).
-
-Because this is fairly low-level code, and we don't expect it to
-change very much, the generated code is kept in the git
-repository. This has the benefit that Python and Jinja are not needed
-to build BOUT++, only to change the ``Field`` operator code.
-
-.. warning:: You should not modify the generated code
-             directly. Instead, modify the template and re-generate
-             the code. If you commit changes to the template and/or
-             driver, make sure to re-generate the code and commit it
-             as well
-
-The Jinja template is in ``src/field/gen_fieldops.jinja``, and the
-driver is ``src/field/gen_fieldops.py``. The driver loops over every
-combination of `BoutReal`, `Field2D`, `Field3D` (collectively just
-"fields" here) with the arithmetic operators, and uses the template to
-generate the appropriate code. There is some logic in the template to
-handle certain combinations of the input fields: for example, for the
-binary infix operators, only check the two arguments are on identical
-meshes if neither is `BoutReal`.
+Field expressions and generated operators
+-----------------------------------------
+
+At user level, field algebra now looks more uniform than it used to:
+ordinary arithmetic and many unary algebraic operators can be combined
+into lazy expressions and only materialized when a concrete field or
+scalar result is needed.
+
+This implementation is split into two layers.
+
+``BinaryExpr`` and views
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+The lazy-expression layer lives in ``include/bout/fieldops.hxx``. The
+central type is ``BinaryExpr``, which stores:
+
+- views of the left and right expression operands
+- the operation functor
+- mesh and metadata needed to check compatibility and materialize the
+  result
+- a cached list of linear region indices describing where the
+  expression is valid
+
+`Field2D`, `Field3D`, and `FieldPerp` act as expression leaves by
+providing lightweight ``View`` types. Those views are the device- and
+backend-friendly objects used by the expression evaluator.
+
+Materialization happens when a field is constructed or assigned from an
+expression, when an expression is stored in `Options`, or when a scalar
+reduction such as ``min`` or ``mean`` is requested. The same mechanism
+is also used to propagate metadata such as mesh, staggered location,
+directions, and `FieldPerp` y-index.
+
+The unary algebraic helpers in ``include/bout/field.hxx`` build on the
+same mechanism. Functions such as ``sqrt``, ``abs``, ``SQ``,
+``if_else``, ``if_else_zero``, ``min``, ``max``, and ``mean`` can all
+operate directly on lazy expressions.
+
+Generated eager operators
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The eager arithmetic operators and in-place update paths are still
+generated automatically using the `Jinja`_ templating system. The main
+files are:
+
+- ``src/field/gen_fieldops.jinja``
+- ``src/field/gen_fieldops.py``
+- ``src/field/generated_fieldops.cxx``
+
+The generated code handles the broad matrix of combinations between
+`BoutReal`, `Field2D`, `Field3D`, `Field3DParallel`, and `FieldPerp`,
+including several mixed-rank and in-place cases where hand-maintaining
+all overloads would be error-prone.
+
+The generated loops now also depend on the configured execution backend.
+At configure time, the generator is told whether to emit RAJA-based,
+OpenMP-based, or serial loop bodies for the eager paths.
+
+Because this is low-level code, the generated source is kept in the git
+repository. Python and Jinja are therefore only needed when changing the
+operator generator itself, not for an ordinary build.
+
+.. warning::
+
+   Do not edit ``generated_fieldops.cxx`` directly. Instead, modify the
+   template or generator, then regenerate the file and commit both the
+   source change and the regenerated output.
 
 To install Jinja:
 
@@ -527,16 +567,17 @@ To install Jinja:
 
    $ pip3 install --user Jinja2
 
-To re-generate the code, there is a ``make`` target for
-``gen_fieldops.cxx`` in ``src/field/makefile``. This also tries to
-apply ``clang-format`` in order to keep to a consistent code style.
+To regenerate the code, use the target for ``gen_fieldops.cxx`` in
+``src/field/makefile`` or the corresponding CMake-driven generation
+path. This also applies ``clang-format`` to keep the output consistent.
 
-.. note:: ``clang-format`` is bundled with ``clang``. This should be
-          available through your system package manager. If you do not
-          have sufficient privileges on your system, you can install
-          it from the source `clang`_. One of the BOUT++ maintainers
-          can help apply it for you too.
+.. note::
+
+   ``clang-format`` is bundled with ``clang``. This should be available
+   through your system package manager. If you do not have sufficient
+   privileges on your system, you can install it from the source
+   `clang`_. One of the BOUT++ maintainers can also help apply it for
+   you.
 
 .. _Jinja: http://jinja.pocoo.org/
 .. _clang: https://clang.llvm.org/
-
diff --git a/manual/sphinx/index.rst b/manual/sphinx/index.rst
index 9408d05057..6a5a48ba34 100644
--- a/manual/sphinx/index.rst
+++ b/manual/sphinx/index.rst
@@ -15,10 +15,12 @@ The documentation is divided into the following sections:
   * :ref:`model-outputs`
 
   * :ref:`bout-interfaces`
-  
+
+  * :ref:`performance-and-accelerators`
+
 * :ref:`developer-docs`
 
-     
+
 .. toctree::
    :maxdepth: 2
    :caption: Getting started
@@ -30,25 +32,24 @@ The documentation is divided into the following sections:
    user_docs/advanced_install
    user_docs/running_bout
    user_docs/new_in_v5
-   
+
 .. toctree::
    :maxdepth: 2
    :caption: BOUT++ models
    :name: bout-models
-      
+
    user_docs/physics_models
    user_docs/makefiles
    user_docs/variable_init
    user_docs/boundary_options
    user_docs/testing
-   user_docs/gpu_support
    user_docs/adios2
-   
+
 .. toctree::
    :maxdepth: 2
    :caption: Model inputs
    :name: model-inputs
-   
+
    user_docs/bout_options
    user_docs/input_grids
 
@@ -56,19 +57,20 @@ The documentation is divided into the following sections:
    :maxdepth: 2
    :caption: Model outputs
    :name: model-outputs
-   
+
    user_docs/output_and_post
    user_docs/python_boutpp
-   
+
 .. toctree::
    :maxdepth: 2
    :caption: BOUT++ interfaces
    :name: bout-interfaces
-   
+
    user_docs/time_integration
    user_docs/parallel-transforms
    user_docs/laplacian
    user_docs/differential_operators
+   user_docs/field_expressions
    user_docs/algebraic_operators
    user_docs/staggered_grids
    user_docs/eigenvalue_solver
@@ -76,6 +78,13 @@ The documentation is divided into the following sections:
    user_docs/invertable_operator
    user_docs/petsc
 
+.. toctree::
+   :maxdepth: 2
+   :caption: Performance and accelerators
+   :name: performance-and-accelerators
+
+   user_docs/gpu_support
+
 .. toctree::
    :maxdepth: 1
    :caption: Field-aligned coordinate systems
diff --git a/manual/sphinx/user_docs/algebraic_operators.rst b/manual/sphinx/user_docs/algebraic_operators.rst
index b2089f9ec3..b8c40d4dc5 100644
--- a/manual/sphinx/user_docs/algebraic_operators.rst
+++ b/manual/sphinx/user_docs/algebraic_operators.rst
@@ -1,28 +1,39 @@
 .. _sec-algebraic-ops:
 
 Algebraic operators
-=========================
+===================
 
 BOUT++ provides a wide variety of algebraic operators acting on fields.
 
-The algebraic operators are listed in :numref:`tab-algebraic-ops`.
-For a completely up-to-date list, see the ``Non-member functions``
-part of :doc:`field2d.hxx<../_breathe_autogen/file/field2d_8hxx>`,
-:doc:`field3d.hxx<../_breathe_autogen/file/field3d_8hxx>`,
+Most of these operators can participate in the lazy field-expression
+system described in :ref:`sec-field-expressions`. In practice this means
+you can usually write ordinary algebraic code and let BOUT++ delay
+evaluation until assignment or reduction.
+
+For a completely up-to-date list, see the ``Non-member functions`` part
+of :doc:`field2d.hxx<../_breathe_autogen/file/field2d_8hxx>`,
+:doc:`field3d.hxx<../_breathe_autogen/file/field3d_8hxx>`, and
 :doc:`fieldperp.hxx<../_breathe_autogen/file/fieldperp_8hxx>`.
 
+Common operators
+----------------
+
 .. _tab-algebraic-ops:
 .. table:: Algebraic operators
 
-   +------------------------------------------+------------------------------------------------------+ 
-   |  Name                                    | Description                                          |
+   +------------------------------------------+------------------------------------------------------+
+   | Name                                     | Description                                          |
    +==========================================+======================================================+
-   | ``min(f, allpe=true, region)``           | Minimum (optionally over all processes)              | 
+   | ``min(f, allpe=true, region)``           | Minimum (optionally over all processes)              |
    +------------------------------------------+------------------------------------------------------+
    | ``max(f, allpe=true, region)``           | Maximum (optionally over all processes)              |
    +------------------------------------------+------------------------------------------------------+
+   | ``mean(f, allpe=true, region)``          | Mean (optionally over all processes)                 |
+   +------------------------------------------+------------------------------------------------------+
    | ``pow(lhs, rhs, region)``                | :math:`\mathtt{lhs}^\mathtt{rhs}`                    |
    +------------------------------------------+------------------------------------------------------+
+   | ``SQ(f, region)``                        | Square of ``f``                                      |
+   +------------------------------------------+------------------------------------------------------+
    | ``sqrt(f, region)``                      | :math:`\sqrt{(f)}`                                   |
    +------------------------------------------+------------------------------------------------------+
    | ``abs(f, region)``                       | :math:`|f|`                                          |
@@ -65,24 +76,43 @@ part of :doc:`field2d.hxx<../_breathe_autogen/file/field2d_8hxx>`,
    |                                          | of `f` as opposed to the AC, alternating current, or |
    |                                          | fluctuating part)                                    |
    +------------------------------------------+------------------------------------------------------+
+   | ``if_else(cond, lhs, rhs)``              | Select between two algebraic branches                |
+   +------------------------------------------+------------------------------------------------------+
+   | ``if_else_zero(cond, expr)``             | Select either ``expr`` or zero                       |
+   +------------------------------------------+------------------------------------------------------+
+
+These operators can usually be combined directly in expressions::
+
+  Field3D rhs = sqrt(SQ(n) + SQ(T));
+  Field3D masked = if_else(use_drive, source * profile, sink * profile);
+  BoutReal max_error = max(abs(lhs - rhs), true);
+
+Reductions such as ``min``, ``max``, and ``mean`` can operate directly
+on an expression, so an intermediate field is often unnecessary.
+
+Region arguments
+----------------
 
-These operators take a ``region`` argument, whose values can be [#]_ (see
-:ref:`sec-iterating`)
+These operators take a ``region`` argument. Common values are [#]_ (see
+:ref:`sec-iterating`):
 
--  `RGN_ALL`, which is the whole mesh;
+- ``RGN_ALL``, which is the whole mesh
+- ``RGN_NOBNDRY``, which skips all boundaries
+- ``RGN_NOX``, which skips the x boundaries
+- ``RGN_NOY``, which skips the y boundaries
 
--  `RGN_NOBNDRY`, which skips all boundaries;
+The default is usually ``RGN_ALL``. Restricting the region can improve
+performance when guard-cell values will not be used.
 
--  `RGN_NOX`, which skips the x boundaries
+When a region-limited expression is materialized into a field, only the
+selected region is guaranteed to contain valid values. This is the same
+performance-oriented convention used by other field operators.
 
--  `RGN_NOY`, which skips the y boundaries
+Further reading
+---------------
 
-The default value for the region argument is `RGN_ALL` which should work in all
-cases.  However, the region argument can be used for optimization, to skip
-calculations in guard cells if it is known that those results will not be
-needed (for example, if no derivatives of the result will be calculated). Since
-these operators can be relatively expensive compared to addition, subtraction,
-multiplication this can be a useful performance improvement.
+- :ref:`sec-field-expressions`
+- :ref:`sec-gpusupport`
 
-.. [#] More regions may be added in future, for example to act on only subsets of the
-       physical domain.
+.. [#] More regions may be added in future, for example to act on only
+       subsets of the physical domain.
diff --git a/manual/sphinx/user_docs/field_expressions.rst b/manual/sphinx/user_docs/field_expressions.rst
new file mode 100644
index 0000000000..62a50988d6
--- /dev/null
+++ b/manual/sphinx/user_docs/field_expressions.rst
@@ -0,0 +1,151 @@
+.. _sec-field-expressions:
+
+Field Expressions
+=================
+
+BOUT++ field algebra now supports *lazy expressions* for many common
+operations. Instead of creating a temporary field for every ``+``,
+``-``, ``*``, ``/``, ``sqrt`` or ``abs``, BOUT++ can keep the expression
+symbolic and evaluate it only when a concrete field or scalar result is
+needed.
+
+This keeps ordinary model code readable while reducing temporary
+allocations and extra loops over the mesh. It is especially helpful for
+accelerator backends, where launching fewer kernels matters.
+
+What stays lazy
+---------------
+
+The following operations can form lazy expressions over `Field2D`,
+`Field3D`, `Field3DParallel`, and `FieldPerp` where the combination makes
+sense:
+
+- Arithmetic operators: ``+``, ``-``, ``*``, ``/``
+- Unary algebraic operators such as ``sqrt``, ``abs``, ``exp``, ``log``,
+  ``sin``, ``cos``, ``tan``, ``sinh``, ``cosh``, ``tanh``, ``floor``,
+  and ``SQ``
+- Simple conditionals with ``if_else`` and ``if_else_zero``
+- Reductions such as ``min``, ``max``, and ``mean``
+
+For example::
+
+  Field3D n, T;
+  Field3D result;
+
+  result = sqrt(SQ(n) + SQ(T));
+
+The right-hand side can stay lazy until the assignment to ``result``.
+
+When evaluation happens
+-----------------------
+
+An expression is evaluated when BOUT++ needs actual storage or a scalar
+answer. Common triggers are:
+
+- assigning to a field
+- constructing a field from an expression
+- assigning a field expression into an `Options` object
+- calling scalar reductions such as ``min``, ``max``, or ``mean``
+
+Examples::
+
+  Field3D result = n + T;
+  options["rhs"] = n + T;
+  BoutReal max_value = max(abs(n + T), true);
+
+Region-limited expressions
+--------------------------
+
+Many algebraic operators take a ``region`` argument, usually defaulting
+to ``RGN_ALL``. A lazy expression keeps track of that region.
+
+Only values inside the requested region are guaranteed to be valid after
+materialization. This is useful for skipping guard-cell work when the
+result will only be used in a smaller region::
+
+  Field3D interior = abs(n, "RGN_NOBNDRY");
+
+As with other region-limited field operations in BOUT++, code that later
+uses guard cells should communicate or otherwise fill those cells before
+relying on them.
+
+Metadata propagation
+--------------------
+
+When an expression is materialized into a field, BOUT++ propagates the
+field metadata carried by the expression:
+
+- mesh pointer
+- cell location
+- field directions
+- for `FieldPerp`, the y-index
+
+This means expressions are intended to behave like ordinary field
+operations in user code. Compatibility checks still apply: combining
+fields on different meshes or incompatible staggered locations is an
+error.
+
+Mixed field types
+-----------------
+
+Several mixed-type combinations are supported directly:
+
+- `Field2D` with `Field3D`: the 2D quantity is broadcast in ``z``
+- `FieldPerp` with matching perpendicular data: the operation uses the
+  `FieldPerp` y-index
+- expressions involving metric components may return
+  `Coordinates::FieldMetric`, which is `Field2D` or `Field3D` depending
+  on how BOUT++ was built
+
+In practice, this means code such as::
+
+  Coordinates::FieldMetric grad = coords->J / coords->g_22;
+  Field3D rhs = density * temperature + background_2d;
+
+can use the same algebraic style even when metric dimensionality or
+field rank differs.
+
+Conditionals
+------------
+
+``if_else`` selects between two algebraic branches without forcing the
+branches to be precomputed::
+
+  Field3D rhs = if_else(use_source, source * density, sink * density);
+
+``if_else_zero(condition, expr)`` is a shorthand for selecting either an
+expression or zero::
+
+  Field3D rhs = if_else_zero(include_drive, drive * profile);
+
+This is particularly convenient when optional source terms are enabled
+or disabled by compile-time or run-time logic.
+
+Reductions on expressions
+-------------------------
+
+Reductions can operate directly on expressions instead of requiring an
+intermediate field::
+
+  BoutReal rms = sqrt(mean(SQ(n - n0), true, "RGN_NOBNDRY"));
+  BoutReal max_error = max(abs(lhs - rhs), true);
+
+This is often clearer than explicitly constructing a temporary field,
+and it avoids extra storage.
+
+Relation to GPU execution
+-------------------------
+
+Lazy field expressions are the high-level path to reducing temporary
+work. They are a good default when ordinary field algebra expresses the
+operation clearly.
+
+For more control, especially when you want to fuse derivative operators
+into a single explicit loop, see :ref:`sec-gpusupport`.
+
+See also
+--------
+
+- :doc:`algebraic_operators`
+- :doc:`gpu_support`
+- :doc:`differential_operators`
diff --git a/manual/sphinx/user_docs/gpu_support.rst b/manual/sphinx/user_docs/gpu_support.rst
index cc0cba8def..670c1a9b32 100644
--- a/manual/sphinx/user_docs/gpu_support.rst
+++ b/manual/sphinx/user_docs/gpu_support.rst
@@ -3,68 +3,92 @@
 GPU support
 ===========
 
-This section describes work in progress to develop GPU support in
-BOUT++ models.  It includes both configuration and compilation on GPU
-systems, but also ways to write physics models which are designed to
-give higher performance. These methods may also be beneficial for CPU
-architectures, but have fewer safety checks, less functionality and
-run-time flexibility than the field operators.
+This section describes the main ways to run BOUT++ work efficiently on
+GPUs or other accelerator-style backends.
 
-To use the single index operators and the ``BOUT_FOR_RAJA`` loop macro::
+There are now two complementary levels of optimization:
+
+1. Write ordinary field algebra and let BOUT++ keep many algebraic
+   expressions lazy until assignment or reduction.
+2. Drop down to explicit `RAJA` loops and single-index operators when
+   you want complete control over loop fusion and kernel structure.
+
+The first approach is usually the best starting point. The second is for
+hot loops where you want to manually combine derivative operators,
+accessors, and run-time captures in one kernel.
+
+Automatic fusion with field expressions
+---------------------------------------
+
+Many algebraic operations on fields can now be represented as lazy
+expressions. This keeps user code close to the familiar field-based
+style while reducing temporary fields and extra passes over memory.
+
+Typical examples are:
+
+.. code-block:: cpp
+
+   Field3D rhs = sqrt(SQ(n) + SQ(T));
+   ddt(n) = source * profile - sink * n;
+   BoutReal max_error = max(abs(lhs - rhs), true);
+
+This is the highest-level route to better execution behavior, and it is
+usually the most maintainable. See :ref:`sec-field-expressions` for the
+details of what stays lazy and when evaluation happens.
+
+Lazy expressions mainly help with *algebraic* fusion. If your hot path
+is dominated by differential operators and you need to fuse those
+operators into a single explicit loop, use the lower-level approach
+described below.
+
+Manual fusion with RAJA loops
+-----------------------------
+
+To use the single-index operators and the ``BOUT_FOR_RAJA`` loop macro::
 
   #include "bout/single_index_ops.hxx"
   #include "bout/rajalib.hxx"
 
-To run parts of a physics model RHS function on a GPU, the basic
-outline of the code is to (optionally) first copy any class member
-variables which will be used in the loop into local variables
-(see below for an alternative method)::
+To run part of a physics-model RHS on a GPU, start by copying any class
+member variables needed inside the loop into local variables, or capture
+them explicitly::
 
-  auto _setting = setting; // Create a local variable to capture
+  auto _setting = setting;
 
-Then create a `FieldAccessor` to efficiently access field and
-coordinate system data inside the loop::
+Then create `FieldAccessor` objects to read and write field data inside
+the loop::
 
   auto n_acc = FieldAccessor<>(n);
   auto phi_acc = FieldAccessor<>(phi);
 
-There are also ``Field2DAccessor``s for accessing ``Field2D``
-types. If fields are staggered, then the expected location should be
-passed as a template parameter::
+There are also ``Field2DAccessor`` objects for `Field2D`. If fields are
+staggered, the expected location can be supplied as a template
+parameter::
 
   auto Jpar_acc = FieldAccessor<CELL_YLOW>(Jpar);
 
-which enables the cell location to be checked in the operators at
-compile time rather than run time.
+Finally the loop itself can be written as::
 
-Finally the loop itself can be written something like::
+  Field3D result;
+  auto result_acc = FieldAccessor<>(result);
 
   BOUT_FOR_RAJA(i, region) {
-    ddt(n_acc)[i] = -bracket(phi_acc, n_acc, i) - 2 * DDZ(n_acc, i);
-    /* ... */
+    result_acc[i] = -bracket(phi_acc, n_acc, i) - 2.0 * DDZ(n_acc, i);
   };
 
 Note the semicolon after the closing brace, which is needed because
-this is the body of a lambda function. Inside the body of the loop,
-the operators like ``bracket`` and ``DDZ`` calculate the derivatives
-at a single index ``i``. These are "single index operators` and are
-defined in ``bout/single_index_ops.hxx``.
-
-Any class member variables which are used inside the loop must be captured
-as a local variable. If this is not done, then the code will probably compile,
-but may produce an illegal memory access error at runtime on the GPU. To
-capture the class member, you can copy any class member variables which
-will be used in the loop into local variables::
+this is the body of a lambda function. Inside the loop, operators such
+as ``bracket`` and ``DDZ`` act at a single index ``i``. These are the
+single-index operators defined in ``bout/single_index_ops.hxx``.
 
-  auto _setting = setting; // Create a local variable to capture
-
-and then use ``_setting`` rather than ``setting`` inside the loop.
-Alternatively, add variables to be captured to a CAPTURE argument to
-the ``BOUT_FOR_RAJA`` loop::
+Any class member variables used inside the loop must be captured
+carefully. Otherwise the code may compile but fail at run time on the
+GPU. Instead of using ``this`` implicitly, either shadow members with
+local variables or add them to the capture list::
 
   BOUT_FOR_RAJA(i, region, CAPTURE(setting)) {
     ddt(n_acc)[i] = -bracket(phi_acc, n_acc, i) - 2 * DDZ(n_acc, i);
-    /* ... code which uses `setting` ... */
+    /* ... code that uses `setting` ... */
   };
 
 If RAJA is not available, the ``BOUT_FOR_RAJA`` macro will revert to
@@ -75,10 +99,26 @@ Note: An important difference between ``BOUT_FOR`` and
 ``BOUT_FOR_RAJA`` (apart from the closing semicolon) is that the type
 of the index ``i`` is different inside the loop: ``BOUT_FOR`` uses
 ``SpecificInd`` types (typically ``Ind3D``), but ``BOUT_FOR_RAJA``
-uses ``int``.  ``SpecificInd`` can be explicitly cast to ``int`` so
+uses ``int``. ``SpecificInd`` can be explicitly cast to ``int`` so
 use ``static_cast<int>(i)`` to ensure that it's an integer both with
 and without RAJA. This might (hopefully) change in future versions.
 
+Choosing between the two approaches
+-----------------------------------
+
+Use lazy field expressions when:
+
+- the code is mostly algebraic combinations of existing fields
+- readability matters more than extracting the last bit of performance
+- you want a clear default path that still maps well to accelerator
+  backends
+
+Use explicit RAJA loops and single-index operators when:
+
+- a hot loop is dominated by derivatives
+- you want to combine many operations into one kernel manually
+- you need direct control over captures, data access, or loop structure
+
 Examples
 --------
 
@@ -115,8 +155,12 @@ Notes:
 CMake configuration
 -------------------
 
-To compile BOUT++ components into GPU kernels a few different pieces need to be configured to work together:
-RAJA, Umpire, and a CUDA compiler.
+To compile BOUT++ components into GPU kernels, a few different pieces
+need to work together: RAJA, Umpire, and a CUDA-capable compiler.
+
+The generated eager field-operator code also selects a loop backend at
+configure time. If RAJA is enabled it uses RAJA loops, otherwise it
+falls back to OpenMP or serial loops depending on the build.
 
 
 .. _tab-gpusupport-cmake:
@@ -136,6 +180,25 @@ RAJA, Umpire, and a CUDA compiler.
    | BOUT_ENABLE_WARNINGS | nvcc has incompatible warning flags     | On (turn Off for CUDA) |
    +----------------------+-----------------------------------------+------------------------+
 
+Shifted metric on GPUs
+----------------------
+
+When BOUT++ is built with CUDA, the shifted-metric parallel transform
+has a CUDA implementation of its toroidal ``shiftZ`` work used while
+calculating parallel slices during communication.
+
+This is most relevant when using:
+
+.. code-block:: cfg
+
+   [mesh:paralleltransform]
+   type = shifted
+   calcParallelSlices_on_communicate = true
+
+The current implementation is specialized for supported power-of-two
+``LocalNz`` values. If parallel slices are disabled on communicate, as in
+the aligned-transform workflow, this precomputed-slice path is not used.
+
 Single index operators
 ----------------------
 
@@ -263,7 +326,7 @@ likely that the results might be architecture dependent.
 
 To minimise the number of times this data needs to be copied from
 individual fields into the single array, and then copied from CPU to
-GPU, ``CoordinatesAccessor``s are cached. A map (``coords_store``
+GPU, ``CoordinatesAccessor``\ s are cached. A map (``coords_store``
 defined in ``coordinates_accessor.cxx``) associates
 ``Array<BoutReal>`` objects (containing the array of data) to
 ``Coordinates`` pointers. If a ``CoordinatesAccessor`` is constructed
@@ -314,10 +377,10 @@ This is a `good talk by John Lakos [ACCU 2017] on memory allocators
 Future work
 -----------
 
-Indices
-~~~~~~~
-
-Setting up a RAJA loop to run on a GPU is still cumbersome and inefficient
+The GPU path is still evolving. The main long-term direction is to let
+more of ordinary field code map efficiently onto accelerator backends,
+so that manual kernel construction is only needed for the most
+performance-critical cases.
 due to the need to transform CPU data structures into a form which can
 be passed to and used on the GPU. In the ``bout/rajalib.hxx`` header there
 is code like::
@@ -332,7 +395,7 @@ is code like::
      auto _ob_i_ind_raw = &_ob_i_ind[0];
 
 which is creating a raw pointer (``_ob_i_ind_raw``) to an array of
-``int``s which are allocated using Umpire. The original ``indices``
+``int``\ s which are allocated using Umpire. The original ``indices``
 are allocated using ``new`` and are inside a C++ ``std::vector``.  The
 RAJA loop then uses this array like this::
 
diff --git a/manual/sphinx/user_docs/parallel-transforms.rst b/manual/sphinx/user_docs/parallel-transforms.rst
index 3ee3eccfb8..9d9b94af9e 100644
--- a/manual/sphinx/user_docs/parallel-transforms.rst
+++ b/manual/sphinx/user_docs/parallel-transforms.rst
@@ -120,6 +120,21 @@ Note that here :math:`\theta_0` does not need to be constant in X
 (radius), since it is only the relative shifts between Y locations
 which matters.
 
+When BOUT++ is built with CUDA, the shifted-metric implementation also
+has a GPU path for the ``shiftZ`` work used to calculate parallel
+slices during communication. This is most useful in the standard
+shifted-metric workflow with
+
+.. code-block:: cfg
+
+   [mesh:paralleltransform]
+   type = shifted
+   calcParallelSlices_on_communicate = true
+
+If ``calcParallelSlices_on_communicate = false`` is used, BOUT++ is in
+the aligned-transform mode described below, so those precomputed
+parallel slices are not generated on communicate.
+
 Special handling is needed for parallel boundary conditions, see
 :ref:`sec-parallel-bc-shifted-metric`.
 

From c88908b2bfad108656b3d139435b705219adface Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 15:55:45 -0700
Subject: [PATCH 1452/1827] Remove unneeded BinaryExpr evaluations

max(abs(BinaryExpr)) will now perform the reduction without allocating
and filling a field.
---
 src/field/fieldperp.cxx           |  2 +-
 src/mesh/coordinates.cxx          | 28 ++++++++++++++--------------
 src/mesh/coordinates_accessor.cxx |  4 ++--
 tests/unit/test_extras.hxx        |  1 +
 4 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index 72976704f2..5176a79c64 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -209,7 +209,7 @@ bool operator==(const FieldPerp& a, const FieldPerp& b) {
   if (!a.isAllocated() || !b.isAllocated()) {
     return false;
   }
-  return (a.getIndex() == b.getIndex()) and (min(FieldPerp{abs(a - b)}) < 1e-10);
+  return (a.getIndex() == b.getIndex()) and (min(abs(a - b)) < 1e-10);
 }
 
 std::ostream& operator<<(std::ostream& out, const FieldPerp& value) {
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index f10f903d19..057ffa65b5 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1269,15 +1269,15 @@ int Coordinates::calcCovariant(const std::string& region) {
   }
 
   BoutReal maxerr;
-  maxerr = BOUTMAX(max(abs(FieldMetric{(g_11 * g11 + g_12 * g12 + g_13 * g13) - 1})),
-                   max(abs(FieldMetric{(g_12 * g12 + g_22 * g22 + g_23 * g23) - 1})),
-                   max(abs(FieldMetric{(g_13 * g13 + g_23 * g23 + g_33 * g33) - 1})));
+  maxerr = BOUTMAX(max(abs((g_11 * g11 + g_12 * g12 + g_13 * g13) - 1)),
+                   max(abs((g_12 * g12 + g_22 * g22 + g_23 * g23) - 1)),
+                   max(abs((g_13 * g13 + g_23 * g23 + g_33 * g33) - 1)));
 
   output_info.write("\tLocal maximum error in diagonal inversion is {:e}\n", maxerr);
 
-  maxerr = BOUTMAX(max(abs(FieldMetric{g_11 * g12 + g_12 * g22 + g_13 * g23})),
-                   max(abs(FieldMetric{g_11 * g13 + g_12 * g23 + g_13 * g33})),
-                   max(abs(FieldMetric{g_12 * g13 + g_22 * g23 + g_23 * g33})));
+  maxerr = BOUTMAX(max(abs(g_11 * g12 + g_12 * g22 + g_13 * g23)),
+                   max(abs(g_11 * g13 + g_12 * g23 + g_13 * g33)),
+                   max(abs(g_12 * g13 + g_22 * g23 + g_23 * g33)));
 
   output_info.write("\tLocal maximum error in off-diagonal inversion is {:e}\n", maxerr);
 
@@ -1324,15 +1324,15 @@ int Coordinates::calcContravariant(const std::string& region) {
   }
 
   BoutReal maxerr;
-  maxerr = BOUTMAX(max(abs(FieldMetric{(g_11 * g11 + g_12 * g12 + g_13 * g13) - 1})),
-                   max(abs(FieldMetric{(g_12 * g12 + g_22 * g22 + g_23 * g23) - 1})),
-                   max(abs(FieldMetric{(g_13 * g13 + g_23 * g23 + g_33 * g33) - 1})));
+  maxerr = BOUTMAX(max(abs((g_11 * g11 + g_12 * g12 + g_13 * g13) - 1)),
+                   max(abs((g_12 * g12 + g_22 * g22 + g_23 * g23) - 1)),
+                   max(abs((g_13 * g13 + g_23 * g23 + g_33 * g33) - 1)));
 
   output_info.write("\tMaximum error in diagonal inversion is {:e}\n", maxerr);
 
-  maxerr = BOUTMAX(max(abs(FieldMetric{g_11 * g12 + g_12 * g22 + g_13 * g23})),
-                   max(abs(FieldMetric{g_11 * g13 + g_12 * g23 + g_13 * g33})),
-                   max(abs(FieldMetric{g_12 * g13 + g_22 * g23 + g_23 * g33})));
+  maxerr = BOUTMAX(max(abs(g_11 * g12 + g_12 * g22 + g_13 * g23)),
+                   max(abs(g_11 * g13 + g_12 * g23 + g_13 * g33)),
+                   max(abs(g_12 * g13 + g_22 * g23 + g_23 * g33)));
 
   output_info.write("\tMaximum error in off-diagonal inversion is {:e}\n", maxerr);
   return 0;
@@ -1345,8 +1345,8 @@ int Coordinates::jacobian() {
   const bool extrapolate_x = not localmesh->sourceHasXBoundaryGuards();
   const bool extrapolate_y = not localmesh->sourceHasYBoundaryGuards();
 
-  FieldMetric g = g11 * g22 * g33 + 2.0 * g12 * g13 * g23 - g11 * g23 * g23
-                  - g22 * g13 * g13 - g33 * g12 * g12;
+  const FieldMetric g = g11 * g22 * g33 + 2.0 * g12 * g13 * g23 - g11 * g23 * g23
+                        - g22 * g13 * g13 - g33 * g12 * g12;
 
   // Check that g is positive
   bout::checkPositive(g, "The determinant of g^ij", "RGN_NOBNDRY");
diff --git a/src/mesh/coordinates_accessor.cxx b/src/mesh/coordinates_accessor.cxx
index d28b0db1c4..efc27e9715 100644
--- a/src/mesh/coordinates_accessor.cxx
+++ b/src/mesh/coordinates_accessor.cxx
@@ -1,6 +1,6 @@
 #include "bout/coordinates_accessor.hxx"
-#include <bout/build_defines.hxx>
-
+#include "bout/build_defines.hxx"
+#include "bout/macro_for_each.hxx"
 #include "bout/mesh.hxx"
 
 #include <map>
diff --git a/tests/unit/test_extras.hxx b/tests/unit/test_extras.hxx
index 6038d981d4..4b2226a54c 100644
--- a/tests/unit/test_extras.hxx
+++ b/tests/unit/test_extras.hxx
@@ -14,6 +14,7 @@
 #include "bout/field.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
+#include "bout/fieldops.hxx"
 #include "bout/fieldperp.hxx"
 #include "bout/region.hxx"
 

From ca94ba5144a307e29fb7638761c1e5f1076633bf Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 21:50:15 -0700
Subject: [PATCH 1453/1827] Fields: Move unary minus to headers

Enables inlining, and should now return a lazy BinaryExpr
rather than eagerly evaluating.
---
 include/bout/field2d.hxx   | 2 +-
 include/bout/field3d.hxx   | 2 +-
 include/bout/fieldperp.hxx | 2 +-
 src/field/field2d.cxx      | 3 ---
 src/field/field3d.cxx      | 2 --
 src/field/fieldperp.cxx    | 3 ---
 6 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 7ab8bdfb25..8ac33e3d9d 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -538,7 +538,7 @@ auto if_else_zero(bool condition, const L& lhs) {
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
  */
-Field2D operator-(const Field2D& f);
+inline auto operator-(const Field2D& f) { return -1.0 * f; }
 
 // Non-member functions
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 112e73219e..632b114273 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -859,7 +859,7 @@ Field3DParallel operator/(const Field3DParallel& lhs, BoutReal rhs);
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
  */
-Field3D operator-(const Field3D& f);
+inline auto operator-(const Field3D& f) { return -1.0 * f; }
 
 // Non-member functions
 
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index b16bc562bb..aba78359e0 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -407,7 +407,7 @@ FieldPerp operator/(BoutReal lhs, const FieldPerp& rhs);
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
  */
-FieldPerp operator-(const FieldPerp& f);
+inline auto operator-(const FieldPerp& f) { return -1.0 * f; }
 
 /// Create a FieldPerp by slicing a 3D field at a given y
 const FieldPerp sliceXZ(const Field3D& f, int y);
diff --git a/src/field/field2d.cxx b/src/field/field2d.cxx
index b363eeef07..61799e3444 100644
--- a/src/field/field2d.cxx
+++ b/src/field/field2d.cxx
@@ -331,9 +331,6 @@ void Field2D::swapData(Field2D& other) { std::swap(data, other.data); }
 
 ////////////// NON-MEMBER OVERLOADED OPERATORS //////////////
 
-// Unary minus
-Field2D operator-(const Field2D& f) { return -1.0 * f; }
-
 //////////////// NON-MEMBER FUNCTIONS //////////////////
 
 namespace {
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 238bef1993..6db47bddfc 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -709,8 +709,6 @@ void Field3D::swapData(Field3D& other) { std::swap(data, other.data); }
  *               NON-MEMBER OVERLOADED OPERATORS
  ***************************************************************/
 
-Field3D operator-(const Field3D& f) { return -1.0 * f; }
-
 //////////////// NON-MEMBER FUNCTIONS //////////////////
 
 Field3D pow(const Field3D& lhs, const Field2D& rhs, const std::string& rgn) {
diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index 5176a79c64..b7b2d9d731 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -150,9 +150,6 @@ FieldPerp fromFieldAligned(const FieldPerp& f, const std::string& region) {
 
 ////////////// NON-MEMBER OVERLOADED OPERATORS //////////////
 
-// Unary minus
-FieldPerp operator-(const FieldPerp& f) { return -1.0 * f; }
-
 /////////////////////////////////////////////////
 // functions
 

From 43c50503373785ca889494729c8b174792935c8a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 22:02:51 -0700
Subject: [PATCH 1454/1827] BOUT_FORCEINLINE: Strengthen for CPU case

If using Clang or GCC set the always_inline attribute
---
 include/bout/build_config.hxx | 10 ++++++++++
 include/bout/field2d.hxx      |  4 ++--
 include/bout/field3d.hxx      | 14 ++------------
 include/bout/fieldops.hxx     | 19 ++++++++++++++++---
 include/bout/fieldperp.hxx    |  7 ++-----
 5 files changed, 32 insertions(+), 22 deletions(-)

diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx
index 60c55abad7..abc78e2cf0 100644
--- a/include/bout/build_config.hxx
+++ b/include/bout/build_config.hxx
@@ -53,6 +53,16 @@ constexpr auto use_msgstack = static_cast<bool>(BOUT_USE_MSGSTACK);
 #define BOUT_HOST __host__
 #define BOUT_DEVICE __device__
 #define BOUT_FORCEINLINE __forceinline__
+#elif defined(_MSC_VER)
+#define BOUT_HOST_DEVICE
+#define BOUT_HOST
+#define BOUT_DEVICE
+#define BOUT_FORCEINLINE __forceinline
+#elif defined(__clang__) || defined(__GNUC__)
+#define BOUT_HOST_DEVICE
+#define BOUT_HOST
+#define BOUT_DEVICE
+#define BOUT_FORCEINLINE inline __attribute__((always_inline))
 #else
 #define BOUT_HOST_DEVICE
 #define BOUT_HOST
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 8ac33e3d9d..cc6482edcc 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -332,10 +332,10 @@ public:
     BoutReal* data;
     int mul = 1;
     int div = 1;
-    BOUT_HOST_DEVICE inline BoutReal operator()(int idx) const {
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return data[(idx * mul / div)];
     }
-    BOUT_HOST_DEVICE inline BoutReal& operator[](int idx) const {
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal& operator[](int idx) const {
       return data[(idx * mul) / div];
     }
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 632b114273..4524573bee 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -459,10 +459,10 @@ public:
     BoutReal* data;
     int mul = 1;
     int div = 1;
-    BOUT_HOST_DEVICE inline BoutReal operator()(int idx) const {
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return data[(idx * mul) / div];
     }
-    BOUT_HOST_DEVICE inline BoutReal& operator[](int idx) const {
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal& operator[](int idx) const {
       return data[(idx * mul) / div];
     }
 
@@ -1077,16 +1077,6 @@ inline Field3D& Field3D::operator-=(const Field3DParallel& rhs) {
   return (*this) -= rhs.asField3D();
 }
 
-// A raw Field3D is an expression leaf
-template <>
-struct is_expr_field3d<Field3D> : std::true_type {};
-
-template <>
-struct is_expr_field3d<Field3DParallel> : std::true_type {};
-
-template <>
-struct is_expr_field2d<Field2D> : std::true_type {};
-
 template <typename ResT, typename L, typename R, typename Fun>
 struct is_expr_field3d<BinaryExpr<ResT, L, R, Fun>>
     : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 25765e6f6b..53e28042c9 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -20,12 +20,16 @@
 
 class Mesh;
 class Field3D;
+class Field3DParallel;
 class Field2D;
 class FieldPerp;
 
 template <typename T>
 struct is_expr_field2d : std::false_type {};
 
+template <>
+struct is_expr_field2d<Field2D> : std::true_type {};
+
 template <typename T>
 inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::value;
 
@@ -33,9 +37,18 @@ inline constexpr bool is_expr_field2d_v = is_expr_field2d<std::decay_t<T>>::valu
 template <typename T>
 struct is_expr_field3d : std::false_type {};
 
+template <>
+struct is_expr_field3d<Field3D> : std::true_type {};
+
+template <>
+struct is_expr_field3d<Field3DParallel> : std::true_type {};
+
 template <typename T>
 struct is_expr_fieldperp : std::false_type {};
 
+template <>
+struct is_expr_fieldperp<FieldPerp> : std::true_type {};
+
 template <typename T>
 inline constexpr bool is_expr_fieldperp_v = is_expr_fieldperp<std::decay_t<T>>::value;
 
@@ -346,8 +359,8 @@ struct BinaryExpr {
   BinaryExpr& operator=(const BinaryExpr&) = delete;
   BinaryExpr& operator=(BinaryExpr&&) = delete;
 
-  inline int size() const { return indices.size(); }
-  inline BoutReal operator()(int idx) const {
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE int size() const { return indices.size(); }
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
     return f(idx, lhs, rhs); // single‐pass fusion
   }
   template <typename IndType>
@@ -359,7 +372,7 @@ struct BinaryExpr {
       return operator()(d.ind);
     }
   }
-  inline int regionIdx(int idx) const { return indices[idx]; }
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE int regionIdx(int idx) const { return indices[idx]; }
 
   //operator ResT() { return ResT{*this}; }
   struct View {
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index aba78359e0..fc45102b89 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -338,10 +338,10 @@ public:
     BoutReal* data;
     int mul = 1;
     int div = 1;
-    BOUT_HOST_DEVICE inline BoutReal operator()(int idx) const {
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return data[(idx * mul) / div];
     }
-    BOUT_HOST_DEVICE inline BoutReal& operator[](int idx) const {
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal& operator[](int idx) const {
       return data[(idx * mul) / div];
     }
 
@@ -451,9 +451,6 @@ bool operator==(const FieldPerp& a, const FieldPerp& b);
 /// Output a string describing a FieldPerp to a stream
 std::ostream& operator<<(std::ostream& out, const FieldPerp& value);
 
-template <>
-struct is_expr_fieldperp<FieldPerp> : std::true_type {};
-
 template <typename ResT, typename L, typename R, typename Fun>
 struct is_expr_fieldperp<BinaryExpr<ResT, L, R, Fun>>
     : std::integral_constant<bool, is_expr_fieldperp_v<std::decay_t<L>>

From 50839f16a3421d85aec0651632eaf22b788f6da0 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 19 Jun 2026 22:40:02 -0700
Subject: [PATCH 1455/1827] Fields: Move move-assignment to headers

Fix unitary minus so that it avoids dependency loop with Mesh.
---
 include/bout/field2d.hxx   | 12 +++++++++++-
 include/bout/field3d.hxx   | 36 +++++++++++++++++++++++++++++++++---
 include/bout/fieldperp.hxx | 27 ++++++++++++++++++++++-----
 src/field/field3d.cxx      | 23 -----------------------
 src/mesh/difops.cxx        | 12 +++++++++---
 5 files changed, 75 insertions(+), 35 deletions(-)

diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index cc6482edcc..0a670fa0d0 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -538,7 +538,17 @@ auto if_else_zero(bool condition, const L& lhs) {
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
  */
-inline auto operator-(const Field2D& f) { return -1.0 * f; }
+inline auto operator-(const Field2D& f) {
+  return BinaryExpr<Field2D, Constant<BoutReal>, Field2D, bout::op::Mul>{
+      static_cast<typename Constant<BoutReal>::View>(-1.0),
+      static_cast<Field2D::View>(f),
+      bout::op::Mul{},
+      f.getMesh(),
+      f.getLocation(),
+      f.getDirections(),
+      std::nullopt,
+      f.getRegion("RGN_ALL")};
+}
 
 // Non-member functions
 
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 4524573bee..09c7f1ce55 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -207,7 +207,7 @@ public:
     setRegion(expr.getRegionID());
   }
   /// Destructor
-  ~Field3D() override;
+  ~Field3D() override { delete deriv; }
 
   /// Data type stored in this field
   using value_type = BoutReal;
@@ -482,7 +482,26 @@ public:
   /// Assignment operators
   ///@{
   Field3D& operator=(const Field3D& rhs);
-  Field3D& operator=(Field3D&& rhs) noexcept;
+  Field3D& operator=(Field3D&& rhs) noexcept {
+    track(rhs, "operator=");
+
+    // Move parallel slices or delete existing ones.
+    yup_fields = std::move(rhs.yup_fields);
+    ydown_fields = std::move(rhs.ydown_fields);
+
+    // Move the data and data sizes
+    nx = rhs.nx;
+    ny = rhs.ny;
+    nz = rhs.nz;
+    regionID = rhs.regionID;
+
+    data = std::move(rhs.data);
+
+    // Move base slice last
+    Field::operator=(std::move(rhs));
+
+    return *this;
+  }
   Field3D& operator=(const Field2D& rhs);
   /// return void, as only part initialised
   void operator=(const FieldPerp& rhs);
@@ -859,7 +878,18 @@ Field3DParallel operator/(const Field3DParallel& lhs, BoutReal rhs);
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
  */
-inline auto operator-(const Field3D& f) { return -1.0 * f; }
+inline auto operator-(const Field3D& f) {
+  auto regionID = f.getRegionID();
+  return BinaryExpr<Field3D, Constant<BoutReal>, Field3D, bout::op::Mul>{
+      static_cast<typename Constant<BoutReal>::View>(-1.0),
+      static_cast<Field3D::View>(f),
+      bout::op::Mul{},
+      f.getMesh(),
+      f.getLocation(),
+      f.getDirections(),
+      regionID,
+      f.getRegion("RGN_ALL")};
+}
 
 // Non-member functions
 
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index fc45102b89..36a116e1b5 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -95,7 +95,9 @@ public:
 
   template <
       typename ResT, typename L, typename R, typename Func,
-      typename = std::enable_if_t<(is_expr_fieldperp_v<L> && is_expr_fieldperp_v<R>)>>
+      typename = std::enable_if_t<(is_expr_fieldperp_v<L> && is_expr_fieldperp_v<R>)
+                                  || (is_expr_constant_v<L> && is_expr_fieldperp_v<R>)
+                                  || (is_expr_fieldperp_v<L> && is_expr_constant_v<R>)>>
   FieldPerp(const BinaryExpr<ResT, L, R, Func>& expr)
       : FieldPerp(evaluateBinaryExpr(expr), expr.getMesh(), expr.getLocation(),
                   expr.getIndex(), expr.getDirections()) {}
@@ -109,7 +111,7 @@ public:
   FieldPerp& operator=(FieldPerp&& rhs) = default;
   FieldPerp& operator=(BoutReal rhs);
   template <typename ResT, typename L, typename R, typename Func>
-  std::enable_if_t<is_expr_fieldperp_v<L>, FieldPerp&>
+  std::enable_if_t<is_expr_fieldperp_v<L> || is_expr_constant_v<L>, FieldPerp&>
   operator=(const BinaryExpr<ResT, L, R, Func>& expr) {
     if (!isAllocated() || getMesh() != expr.getMesh()) {
       *this = FieldPerp{expr};
@@ -407,7 +409,18 @@ FieldPerp operator/(BoutReal lhs, const FieldPerp& rhs);
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
  */
-inline auto operator-(const FieldPerp& f) { return -1.0 * f; }
+inline auto operator-(const FieldPerp& f) {
+  return BinaryExpr<FieldPerp, Constant<BoutReal>, FieldPerp, bout::op::Mul>{
+      static_cast<typename Constant<BoutReal>::View>(-1.0),
+      static_cast<FieldPerp::View>(f),
+      bout::op::Mul{},
+      f.getMesh(),
+      f.getLocation(),
+      f.getDirections(),
+      std::nullopt,
+      f.getRegion("RGN_ALL"),
+      f.getIndex()};
+}
 
 /// Create a FieldPerp by slicing a 3D field at a given y
 const FieldPerp sliceXZ(const Field3D& f, int y);
@@ -453,7 +466,11 @@ std::ostream& operator<<(std::ostream& out, const FieldPerp& value);
 
 template <typename ResT, typename L, typename R, typename Fun>
 struct is_expr_fieldperp<BinaryExpr<ResT, L, R, Fun>>
-    : std::integral_constant<bool, is_expr_fieldperp_v<std::decay_t<L>>
-                                       && is_expr_fieldperp_v<std::decay_t<R>>> {};
+    : std::integral_constant<bool, (is_expr_fieldperp_v<std::decay_t<L>>
+                                    && is_expr_fieldperp_v<std::decay_t<R>>)
+                                       || (is_expr_constant_v<std::decay_t<L>>
+                                           && is_expr_fieldperp_v<std::decay_t<R>>)
+                                       || (is_expr_fieldperp_v<std::decay_t<L>>
+                                           && is_expr_constant_v<std::decay_t<R>>)> {};
 
 #endif
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 6db47bddfc..7915579440 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -155,8 +155,6 @@ Field3D::Field3D(Array<BoutReal> data_in, Mesh* localmesh, CELL_LOC datalocation
   ASSERT1(data.size() == nx * ny * nz);
 }
 
-Field3D::~Field3D() { delete deriv; }
-
 Field3D& Field3D::allocate() {
   if (data.empty()) {
     if (!fieldmesh) {
@@ -313,27 +311,6 @@ Field3D& Field3D::operator=(const Field3D& rhs) {
   return *this;
 }
 
-Field3D& Field3D::operator=(Field3D&& rhs) noexcept {
-  track(rhs, "operator=");
-
-  // Move parallel slices or delete existing ones.
-  yup_fields = std::move(rhs.yup_fields);
-  ydown_fields = std::move(rhs.ydown_fields);
-
-  // Move the data and data sizes
-  nx = rhs.nx;
-  ny = rhs.ny;
-  nz = rhs.nz;
-  regionID = rhs.regionID;
-
-  data = std::move(rhs.data);
-
-  // Move base slice last
-  Field::operator=(std::move(rhs));
-
-  return *this;
-}
-
 Field3D& Field3D::operator=(const Field2D& rhs) {
   track(rhs, "operator=");
 
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 902ebfce93..3f7aec08bf 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -2,9 +2,9 @@
  * Various differential operators defined on BOUT grid
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -26,10 +26,16 @@
 #include "bout/build_defines.hxx"
 
 #include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
+#include <bout/boutexception.hxx>
+#include <bout/coordinates.hxx>
 #include <bout/derivs.hxx>
 #include <bout/difops.hxx>
 #include <bout/fft.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
 #include <bout/globals.hxx>
+#include <bout/mesh.hxx>
 #include <bout/solver.hxx>
 #include <bout/utils.hxx>
 #include <bout/vecops.hxx>
@@ -800,7 +806,7 @@ Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method,
     break;
   case BRACKET_SIMPLE: {
     // Use a subset of terms for comparison to BOUT-06
-    result = VDDZ(-DDX(f, outloc), g, outloc);
+    result = VDDZ(Field3D{-DDX(f, outloc)}, g, outloc);
     break;
   }
   default: {

From 1a66918f5caf48b838e78d058d6c694378792273 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 20 Jun 2026 13:14:42 -0700
Subject: [PATCH 1456/1827] Solver::VarIterator: Replace switch with if
 constexpr

C is a template parameter so can be determined at compile time.
---
 include/bout/solver.hxx | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 1a3d475edf..24398c8fd2 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -410,22 +410,22 @@ protected:
     VarIterator(underlying_iterator _it) : it(std::move(_it)) {}
 
     reference operator*() const {
-      switch (C) {
-      case (FieldCategories::VARS):
+      if constexpr (C == FieldCategories::VARS) {
         return *(it->var);
-      case (FieldCategories::DERIVS):
+      } else if constexpr (C == FieldCategories::DERIVS) {
         return *(it->F_var);
-      case (FieldCategories::MMS):
+      } else {
+        static_assert(C == FieldCategories::MMS);
         return *(it->MMS_err);
       }
     }
     pointer operator->() const {
-      switch (C) {
-      case (FieldCategories::VARS):
+      if constexpr (C == FieldCategories::VARS) {
         return it->var;
-      case (FieldCategories::DERIVS):
+      } else if constexpr (C == FieldCategories::DERIVS) {
         return it->F_var;
-      case (FieldCategories::MMS):
+      } else {
+        static_assert(C == FieldCategories::MMS);
         return it->MMS_err.get();
       }
     }

From af78c6f293100b7f71cb8916eb6688826662e4d2 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 20 Jun 2026 13:19:56 -0700
Subject: [PATCH 1457/1827] SNESSolver::rescale: Handle predictor=false case

The x1 vector is only allocated if predictor is enabled.
---
 src/solver/impls/snes/snes.cxx | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 5003117e3f..db34eb43f7 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -893,7 +893,10 @@ PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
   PetscScalar* snes_x_data = nullptr;
   PetscCall(VecGetArray(snes_x, &snes_x_data));
   PetscScalar* x1_data = nullptr;
-  PetscCall(VecGetArray(x1, &x1_data));
+  if (predictor) {
+    // x1 is only allocated if predictor is enabled
+    PetscCall(VecGetArray(x1, &x1_data));
+  }
   PetscScalar* var_scaling_factors_data = nullptr;
   PetscCall(VecGetArray(var_scaling_factors, &var_scaling_factors_data));
 
@@ -903,13 +906,17 @@ PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
     const PetscScalar norm =
         BOUTMAX(std::abs(snes_x_data[i]), rtol / var_scaling_factors_data[i]);
     snes_x_data[i] /= norm;
-    x1_data[i] /= norm; // Update history for predictor
+    if (predictor) {
+      x1_data[i] /= norm; // Update history for predictor
+    }
     var_scaling_factors_data[i] *= norm;
   }
 
   // Restore vector underlying data
   PetscCall(VecRestoreArray(var_scaling_factors, &var_scaling_factors_data));
-  PetscCall(VecRestoreArray(x1, &x1_data));
+  if (predictor) {
+    PetscCall(VecRestoreArray(x1, &x1_data));
+  }
   PetscCall(VecRestoreArray(snes_x, &snes_x_data));
 
   if (diagnose) {

From 2cfb90a582646d9acb9a275ef332a4645fc6cbb6 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 20 Jun 2026 13:26:32 -0700
Subject: [PATCH 1458/1827] Solver::loop_vars_op: Increment metadata
 unconditionally

Previously metadata_it only advanced on the non-continue path. If one
field had evolve_bndry == false, every later field in that boundary
loop would be checked against the same stale metadata entry and
skipped too.
---
 include/bout/solver.hxx | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 24398c8fd2..7030559cd9 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -735,12 +735,13 @@ private:
       // Loop over 2D variables
       auto metadata_it = f2d.begin();
       for (auto& field : f2d_range) {
-        if (bndry && !metadata_it->evolve_bndry) {
+        const auto& metadata = *metadata_it;
+        ++metadata_it;
+        if (bndry && !metadata.evolve_bndry) {
           continue;
         }
         field[i2d] = udata[p];
         p++;
-        metadata_it++;
       }
 
       for (int jz = 0; jz < nz; jz++) {
@@ -748,12 +749,13 @@ private:
         auto metadata_it = f3d.begin();
         // Loop over 3D variables
         for (auto& field : f3d_range) {
-          if (bndry && !metadata_it->evolve_bndry) {
+          const auto& metadata = *metadata_it;
+          ++metadata_it;
+          if (bndry && !metadata.evolve_bndry) {
             continue;
           }
           field[field.getMesh()->ind2Dto3D(i2d, jz)] = udata[p];
           p++;
-          metadata_it++;
         }
       }
       break;
@@ -798,12 +800,13 @@ private:
       // Loop over 2D variables
       auto metadata_it = f2d.begin();
       for (const auto& field : f2d_range) {
-        if (bndry && !metadata_it->evolve_bndry) {
+        const auto& metadata = *metadata_it;
+        ++metadata_it;
+        if (bndry && !metadata.evolve_bndry) {
           continue;
         }
         udata[p] = field[i2d];
         p++;
-        metadata_it++;
       }
 
       for (int jz = 0; jz < nz; jz++) {
@@ -811,12 +814,13 @@ private:
         auto metadata_it = f3d.begin();
         // Loop over 3D variables
         for (const auto& field : f3d_range) {
-          if (bndry && !metadata_it->evolve_bndry) {
+          const auto& metadata = *metadata_it;
+          ++metadata_it;
+          if (bndry && !metadata.evolve_bndry) {
             continue;
           }
           udata[p] = field[field.getMesh()->ind2Dto3D(i2d, jz)];
           p++;
-          metadata_it++;
         }
       }
       break;

From 013aef48f8e1f464686f265ae9c9c2a701b25345 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 20 Jun 2026 13:30:07 -0700
Subject: [PATCH 1459/1827] SNESSolver: scale_vars in zero iteration case

When SNES takes zero iterations (nl_its == 0) a simple Euler
step is taken. If scale_vars is true then the derivatives
should be scaled to be consistent with rhs_function.
---
 src/solver/impls/snes/snes.cxx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index db34eb43f7..5f3896a5c9 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -1215,6 +1215,9 @@ int SNESSolver::run() {
           PetscCall(VecGetArray(deriv, &ddata));
           save_derivs(ddata);
           PetscCall(VecRestoreArray(deriv, &ddata));
+          if (scale_vars) {
+            PetscCall(VecPointwiseDivide(deriv, deriv, var_scaling_factors));
+          }
           // Forward Euler
           VecAXPY(snes_x, dt, deriv);
         } else {
@@ -1222,6 +1225,9 @@ int SNESSolver::run() {
           PetscCall(VecGetArray(snes_f, &fdata));
           save_derivs(fdata);
           PetscCall(VecRestoreArray(snes_f, &fdata));
+          if (scale_vars) {
+            PetscCall(VecPointwiseDivide(snes_f, snes_f, var_scaling_factors));
+          }
           // Forward Euler
           VecAXPY(snes_x, dt, snes_f);
         }

From e0ca819e2fd5d0b7c17110826c011392b6d095a2 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 20 Jun 2026 14:02:43 -0700
Subject: [PATCH 1460/1827] Delete commented-out code

---
 include/bout/solver.hxx        | 10 +++++-----
 src/solver/impls/snes/snes.cxx | 23 +----------------------
 2 files changed, 6 insertions(+), 27 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 7030559cd9..09ede6a32b 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -718,11 +718,11 @@ private:
   void loop_vars_op(RangeF2D f2d_range, RangeF3D f3d_range, Ind2D i2d, BoutReal* udata,
                     int& p, SOLVER_VAR_OP op, bool bndry) {
     /**************************************************************************
- * Looping over variables
- *
- * NOTE: This part is very inefficient, and should be replaced ASAP
- * Is the interleaving of variables needed or helpful to the solver?
- **************************************************************************/
+     * Looping over variables
+     *
+     * NOTE: This part is very inefficient, and should be replaced ASAP
+     * Is the interleaving of variables needed or helpful to the solver?
+     **************************************************************************/
     // Use global mesh: FIX THIS!
     const Mesh* mesh = bout::globals::mesh;
 
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 5f3896a5c9..b703ab1c90 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -1131,10 +1131,6 @@ int SNESSolver::run() {
         }
         // Restore state
         VecCopy(x0, snes_x);
-        // FIXME: Not sure I need this
-        // if (diagnose) {
-        //   VecCopy(f0, snes_f);
-        // }
 
         // Recalculate the Jacobian
         if (jacobian_pruned and (snes_failures > 2) and (4 * lin_its > 3 * maxl)) {
@@ -1233,13 +1229,6 @@ int SNESSolver::run() {
         }
       }
 
-      // int i;
-      // PetscReal norm, minval, maxval;
-      // PetscCall(VecNorm(snes_f, NORM_2, &norm));
-      // PetscCall(VecMin(snes_f, &i, &minval));
-      // PetscCall(VecMax(snes_f, &i, &maxval));
-      // output.write("Max, min, and norm of residual for SNES function: {}, {}, {}\n", maxval, minval, norm);
-
       simtime += dt;
 
       // Update local and global residuals
@@ -1802,10 +1791,7 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
     // f = (x0 - x)/Δt + f
     // First calculate x - x0 to minimise floating point issues
     VecWAXPY(delta_x, -1.0, x0, x); // delta_x = x - x0
-    // if (scale_vars) {
-    //   VecPointwiseMult(delta_x, delta_x, var_scaling_factors);
-    // }
-    VecAXPY(f, -1. / dt, delta_x); // f <- f - delta_x / dt
+    VecAXPY(f, -1. / dt, delta_x);  // f <- f - delta_x / dt
     break;
   }
   case BoutSnesEquationForm::pseudo_transient: {
@@ -1813,9 +1799,6 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
     // except that Δt is a vector
     // f = (x0 - x)/Δt + f
     VecWAXPY(delta_x, -1.0, x0, x);
-    // if (scale_vars) {
-    //   VecPointwiseMult(delta_x, delta_x, var_scaling_factors);
-    // }
     VecPointwiseDivide(delta_x, delta_x, dt_vec); // delta_x /= dt
     VecAXPY(f, -1., delta_x);                     // f <- f - delta_x
     break;
@@ -1823,10 +1806,6 @@ PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
   case BoutSnesEquationForm::backward_euler: {
     // Backward Euler
     // Set f = x - x0 - Δt*f
-    // if (scale_vars) {
-    //   VecPointwiseMult(x, x, var_scaling_factors);
-    //   VecPointwiseMult(x0, x0, var_scaling_factors);
-    // }
     VecAYPX(f, -dt, x);   // f <- x - Δt*f
     VecAXPY(f, -1.0, x0); // f <- f - x0
     break;

From 333af2a506366c67e9e557b29f46d6837a9cc994 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 20 Jun 2026 15:08:36 -0700
Subject: [PATCH 1461/1827] Tidy some translations, fill in missing

---
 locale/ka/libbout.po | 72 ++++++++++++++++++++++++++++++++++++++------
 1 file changed, 63 insertions(+), 9 deletions(-)

diff --git a/locale/ka/libbout.po b/locale/ka/libbout.po
index a5bc263f9e..70ed52aafb 100644
--- a/locale/ka/libbout.po
+++ b/locale/ka/libbout.po
@@ -52,7 +52,7 @@ msgstr "\t -> კარგი მნიშვნელობა\n"
 #, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
-msgstr ""
+msgstr "\t -> რეგიონი Leg jyseps1_1+1 ({:d}) MYSUB-ის ({:d}) ნამრავლი უნდა იყოს\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, c++-format
@@ -60,6 +60,8 @@ msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> რეგიონი leg jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) MYSUB-ის ({:d}) "
+"ნამრავლი უნდა იყოს\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, c++-format
@@ -67,6 +69,8 @@ msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
+"\t -> რეგიონი leg ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) MYSUB-ის ({:d}) "
+"ნამრავლი უნდა იყოს\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, c++-format
@@ -74,6 +78,8 @@ msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> რეგიონი leg ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) MYSUB-ის ({:d}) "
+"ნამრავლი უნდა იყოს\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, c++-format
@@ -121,6 +127,8 @@ msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
 msgstr ""
+"\tდომენი დაყოფილია (NXPE={:d}, NYPE={:d}) დომენებად (localNx={:d}, "
+"localNy={:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, c++-format
@@ -268,7 +276,7 @@ msgstr "\tnz წაკითხულია შეყვანილი ბა
 
 #: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
-msgstr "\tკოვარიანტული ვექტორის წაკითხვა "
+msgstr "\tკონტრავარიანტული ვექტორის წაკითხვა "
 
 #: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
@@ -397,6 +405,34 @@ msgid ""
 "\n"
 "{}"
 msgstr ""
+"\n"
+"აღმოჩენილია გამოუყენებელი შეყვანის პარამეტრები:\n"
+"-----\n"
+"{:i}\n"
+"-----\n"
+"შესაძლებელია, ზოგიერთი პარამეტრი შეცდომით გაქვთ აკრეფილი. BOUT++-ის "
+"შეყვანის არგუმენტები\n"
+"ახლა დიდ და პატარა ასოებს არჩევს და ზოგიერთ მათგანს სახელიც შეეცვალა. "
+"შეგიძლიათ გაუშვათ\n"
+"\n"
+"    <BOUT++ directory>/bin/bout-v5-input-file-upgrader.py {}/{}\n"
+"\n"
+"რათა ყველაზე გავრცელებული პრობლემები ავტომატურად გასწორდეს. თუ ზემოთ მოცემული "
+"პარამეტრები\n"
+"ზოგჯერ სხვა პარამეტრებზეა დამოკიდებული, შეგიძლიათ გამოიძახოთ\n"
+"`Options::setConditionallyUsed()`, მაგალითად:\n"
+"\n"
+"    Options::root()[\"{}\"].setConditionallyUsed();\n"
+"\n"
+"რათა მონაკვეთი ან მნიშვნელობა სხვა მნიშვნელობებზე დამოკიდებულად მონიშნოთ და ამ "
+"შემოწმებაში\n"
+"მისი იგნორირება მოხდეს. თუ დარწმუნებული ხართ, რომ ზემოთ მითითებული შეყვანები\n"
+"შეცდომა არაა, შეგიძლიათ დააყენოთ 'input:error_on_unused_options=false', რათა\n"
+"გამოუყენებელი პარამეტრების ეს შემოწმება გამოირთოს. ასევე ყოველთვის შეგიძლიათ\n"
+"'input:validate=true' დააყენოთ, რათა შეყვანები სრული სიმულაციის გაშვების "
+"გარეშე გადაამოწმოთ.\n"
+"\n"
+"{}"
 
 #: ../src/bout++.cxx:389
 #, c++-format
@@ -486,7 +522,7 @@ msgstr "ყველა გამოყენებული პარამე
 #: ../src/bout++.cxx:535
 #, c++-format
 msgid "BOUT++ version {:s}\n"
-msgstr "BOUT++-ის მხარდაჭერა {:s}\n"
+msgstr "BOUT++ ვერსია {:s}\n"
 
 #: ../src/bout++.cxx:147
 msgid "Bad command line arguments:\n"
@@ -566,8 +602,7 @@ msgstr "წაკითხვის შეცდომა მთელი რი
 #. Failed . Probably not important enough to stop the simulation
 #: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
-msgstr ""
-"bout-log-color-ის გაშვება შეუძლებელია. დარწმუნდით, რომ ის თქვენს PATH-შია\n"
+msgstr "bout-log-color-ის გაშვება შეუძლებელია. დარწმუნდით, რომ ის თქვენს PATH-შია\n"
 
 #: ../src/solver/solver.cxx:772
 #, c++-format
@@ -804,6 +839,8 @@ msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
+"სიმ. დრო | RHS გამოთვ. | კედლ. დრო | გამოთვ. ინვ. კავშ. I/O  ამომხს.\n"
+"\n"
 
 #: ../src/bout++.cxx:879
 msgid ""
@@ -811,6 +848,9 @@ msgid ""
 "Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
+"სიმ. დრო | RHS_e გამოთვ. | RHS_I გამოთვ. | კედლ. დრო | გამოთვ. ინვ. კავშ. "
+"I/O  ამომხს.\n"
+"\n"
 
 #: ../src/solver/solver.cxx:514
 #, c++-format
@@ -839,6 +879,8 @@ msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
+"დროითი წარმოებული არასწორ მდებარეობაზეა - ველი არის {:s}-ზე, წარმოებული კი "
+"{:s}-ზე ველისთვის '{:s}'\n"
 
 #: ../src/solver/solver.cxx:1494
 #, c++-format
@@ -868,16 +910,22 @@ msgid ""
 "This is likely the result of clashing input options, and you may have to "
 "rename one of them.\n"
 msgstr ""
+"მიმდინარეობს პარამეტრის '{0}' ინდექსაცია '{1}'-ით, მაგრამ '{0}' მნიშვნელობაა "
+"და არა სექცია.\n"
+"ეს, სავარაუდოდ, კონფლიქტური შეყვანის პარამეტრების შედეგია და შეიძლება ერთ-"
+"ერთის სახელის გადარქმევა დაგჭირდეთ.\n"
 
 #: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
 msgstr ""
+"უცნობი პარამეტრია paralleltransform.\n"
+"დასაშვები მნიშვნელობებია 'identity', 'shifted', 'fci'"
 
 #: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
-msgstr "გამოიყენებელი პარამეტრები:\n"
+msgstr "გამოუყენებელი პარამეტრები:\n"
 
 #: ../src/bout++.cxx:446
 #, c++-format
@@ -994,30 +1042,36 @@ msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
+"გაფრთხილება: FFT-ის ეფექტური წარმადობისთვის ტოროიდული წერტილების რაოდენობა "
+"უნდა იყოს 2^n -- თუ FFT-ებს იყენებთ, განიხილეთ MZ-ის ({:d}) შეცვლა\n"
 
 #: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
-msgstr ""
+msgstr "გაფრთხილება: შეყვანილი ბადის სიდიდეები ექსტრაპოლირდება x-სასაზღვრო უჯრედებში\n"
 
 #: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
+"გაფრთხილება: შეყვანილი ბადის სიდიდეები ექსტრაპოლირდება x-სასაზღვრო უჯრედებში. "
+"ამის გასათიშად დააყენეთ პარამეტრი extrapolate_x=false.\n"
 
 #: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
-msgstr ""
+msgstr "გაფრთხილება: შეყვანილი ბადის სიდიდეები ექსტრაპოლირდება y-სასაზღვრო უჯრედებში\n"
 
 #: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
+"გაფრთხილება: შეყვანილი ბადის სიდიდეები ექსტრაპოლირდება y-სასაზღვრო უჯრედებში. "
+"ამის გასათიშად დააყენეთ პარამეტრი extrapolate_y=false.\n"
 
 #: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
-msgstr ""
+msgstr "კედლის დროის ზღვარი საათებში. ნაგულისხმევად (< 0) ზღვარი არ არსებობს"
 
 #: ../src/sys/optionsreader.cxx:42
 #, c++-format

From cfb0f1260a6e3b58ce3d19a788dc750006fa689b Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 20 Jun 2026 15:28:28 -0700
Subject: [PATCH 1462/1827] Update de,es,fr,zh_CN and zh_TW locales

---
 locale/de/libbout.po    | 514 +++++++++++++++++++++++-----------------
 locale/es/libbout.po    | 511 ++++++++++++++++++++++-----------------
 locale/fr/libbout.po    | 319 ++++++++++++++++++-------
 locale/zh_CN/libbout.po | 311 ++++++++++++++++++------
 locale/zh_TW/libbout.po | 371 ++++++++++++++++++++---------
 5 files changed, 1325 insertions(+), 701 deletions(-)

diff --git a/locale/de/libbout.po b/locale/de/libbout.po
index 242beb45ca..38d9f62a3e 100644
--- a/locale/de/libbout.po
+++ b/locale/de/libbout.po
@@ -19,99 +19,98 @@ msgstr ""
 "X-Generator: Poedit 2.2.1\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:182
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
-"\t -> `Core` Region iyseps2_1-iyseps1_1 ({:d}-{:d} = {:d}) muss ein "
-"Vielfaches von MYSUB ({:d}) sein\n"
+"\t -> `Core` Region iyseps2_1-iyseps1_1 ({:d}-{:d} = {:d}) muss ein Vielfaches von MYSUB ({:d}) sein\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:215
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
-"\t -> `Core` Region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) muss ein "
-"Vielfaches von MYSUB ({:d}) sein\n"
+"\t -> `Core` Region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) muss ein Vielfaches von MYSUB ({:d}) sein\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:190
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
-"\t -> `Core` Region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) muss ein "
-"Vielfaches von MYSUB ({:d}) sein\n"
+"\t -> `Core` Region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) muss ein Vielfaches von MYSUB ({:d}) sein\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
-msgstr "\t -> Wert OK\n"
+msgstr ""
+"\t -> Wert OK\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:171
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
 msgstr ""
-"\t -> `Leg` Region jyseps1_1+1 ({:d}) muss ein Vielfaches von MYSUB ({:d}) "
-"sein\n"
+"\t -> `Leg` Region jyseps1_1+1 ({:d}) muss ein Vielfaches von MYSUB ({:d}) sein\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:206
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
-"\t -> `Leg` Region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) muss ein "
-"Vielfaches von MYSUB ({:d}) sein\n"
+"\t -> `Leg` Region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) muss ein Vielfaches von MYSUB ({:d}) sein\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:223
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
-"\t -> `Leg` Region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) muss ein Vielfaches "
-"von MYSUB ({:d}) sein\n"
+"\t -> `Leg` Region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) muss ein Vielfaches von MYSUB ({:d}) sein\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:199
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
-"\t -> `Leg` Region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) muss ein "
-"Vielfaches von MYSUB ({:d}) sein\n"
+"\t -> `Leg` Region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) muss ein Vielfaches von MYSUB ({:d}) sein\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:166
-#, fuzzy, c++-format
+#, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
-msgstr "\t -> ny/NYPE ({:d}/{:d} = {:d}) muss >= MYG ({:d}) sein\n"
+msgstr ""
+"\t -> ny/NYPE ({:d}/{:d} = {:d}) muss >= MYG ({:d}) sein\n"
 
 #: ../src/bout++.cxx:575
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tADIOS2 support {}\n"
-msgstr "\tNetCDF Unterstützung ist aktiviert\n"
+msgstr ""
+"\tUnterstützung für ADIOS2 {}\n"
 
 #: ../src/bout++.cxx:583
 #, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
+"\tBacktrace in Ausnahmen {}\n"
 
 #. Loop over all possibilities
 #. Processors divide equally
 #. Mesh in X divides equally
 #. Mesh in Y divides equally
 #: ../src/mesh/impls/bout/boutmesh.cxx:288
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tCandidate value: {:d}\n"
-msgstr "\tzu überprüfender Wert: {:d}\n"
+msgstr ""
+"\tzu überprüfender Wert: {:d}\n"
 
 #: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
+"\tFarben in Protokollen {}\n"
 
 #: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
@@ -120,35 +119,33 @@ msgstr "\tKommandozeilenoptionen für diese Ausführung: "
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
 #: ../src/bout++.cxx:595
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tCompiled with flags : {:s}\n"
-msgstr "\tWurde kompiliert mit den Optionen : {:s}\n"
+msgstr ""
+"\tWurde kompiliert mit den Optionen : {:s}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:315
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
 msgstr ""
-"\tDas Gebiet wird in NXPE={:d} mal NYPE={:d} Gebiete der Größe localNx={:d} "
-"mal localNy={:d} aufgeteilt\n"
+"\tDas Gebiet wird in NXPE={:d} mal NYPE={:d} Gebiete der Größe localNx={:d} mal localNy={:d} aufgeteilt\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:357
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
-"\tFEHLER: {:d} Punkte in der Y-Richtung können nicht gleichmässig zwischen "
-"{:d} Prozessen verteilt werden\n"
+"\tFEHLER: {:d} Punkte in der Y-Richtung können nicht gleichmässig zwischen {:d} Prozessen verteilt werden\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:365
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
-"\tFEHLER: {:d} Punkte in der Y-Richtung können nicht gleichmässig zwischen "
-"{:d} Prozessen verteilt werden\n"
+"\tFEHLER: {:d} Punkte in der Y-Richtung können nicht gleichmässig zwischen {:d} Prozessen verteilt werden\n"
 
 #: ../src/sys/options/options_ini.cxx:200
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\tEmpty key\n"
 "\tLine: {:s}"
@@ -157,41 +154,45 @@ msgstr ""
 "\tZeile: {:s}"
 
 #: ../src/sys/optionsreader.cxx:127
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tEmpty key or value in command line '{:s}'\n"
-msgstr "\tSchlüssel (Key) oder Wert nicht gesetzt in der Befehlszeile '{:s}'\n"
+msgstr ""
+"\tSchlüssel (Key) oder Wert nicht gesetzt in der Befehlszeile '{:s}'\n"
 
 #: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
+"\tZusätzliche Debug-Ausgabe {}\n"
 
 #: ../src/bout++.cxx:568
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tFFT support {}\n"
-msgstr "\tNetCDF Unterstützung ist aktiviert\n"
+msgstr ""
+"\tUnterstützung für FFT {}\n"
 
 #: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
+"\tVerfolgung von Feldnamen {}\n"
 
 #: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
+"\tGleitkomma-Ausnahmen {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
 msgstr "\tGittergröße: "
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:499
-#, fuzzy
 msgid "\tGuard cells (x,y,z): "
-msgstr "\tGuardzellen (x,y): "
+msgstr "\tGuard-Zellen (x,y,z): "
 
 #: ../src/sys/options/options_ini.cxx:204
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\tKey must not contain ':' character\n"
 "\tLine: {:s}"
@@ -203,36 +204,43 @@ msgstr ""
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
+"\tUnterstützung für LAPACK {}\n"
 
 #: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
+"\tNachrichten-Stack {}\n"
 
 #: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
+"\tMetrikmodus ist {}\n"
 
 #: ../src/sys/optionsreader.cxx:111
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
-msgstr "\t'=' darf nicht mehrfach vorkommen: '{:s}'\n"
+msgstr ""
+"\t'=' darf nicht mehrfach vorkommen: '{:s}'\n"
 
 #: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
+"\tUnterstützung für natürliche Sprache {}\n"
 
 #: ../src/bout++.cxx:574
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tNetCDF support {}{}\n"
-msgstr "\tNetCDF Unterstützung ist aktiviert\n"
+msgstr ""
+"\tUnterstützung für NetCDF {}{}\n"
 
 #: ../src/bout++.cxx:585
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOpenMP parallelisation {}, using {} threads\n"
-msgstr "\tOpenMP Parallelisierung mit {:d} Threads ist aktiviert\n"
+msgstr ""
+"\tOpenMP-Parallelisierung {}, mit {} Threads\n"
 
 #. Mark the option as used
 #. Option not found
@@ -242,41 +250,48 @@ msgid "\tOption "
 msgstr "\tOption "
 
 #: ../src/sys/options.cxx:369
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOption {} = {}"
-msgstr "\tOption "
+msgstr "\tOption {} = {}"
 
 #: ../src/sys/options/options_ini.cxx:70
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOptions file '{:s}' not found\n"
-msgstr "\tDie Optionendatei '{:s}' konnte nicht gefunden werden\n"
+msgstr ""
+"\tDie Optionendatei '{:s}' konnte nicht gefunden werden\n"
 
 #: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
+"\tUnterstützung für PETSc {}\n"
 
 #: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
+"\tUnterstützung für PVODE {}\n"
 
 #: ../src/bout++.cxx:564
 msgid "\tParallel NetCDF support disabled\n"
-msgstr "\tParallele-NetCDF Unterstützung ist deaktiviert\n"
+msgstr ""
+"\tParallele-NetCDF Unterstützung ist deaktiviert\n"
 
 #: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
-msgstr "\tParllele-NetCDF Unterstützung ist aktiviert\n"
+msgstr ""
+"\tParllele-NetCDF Unterstützung ist aktiviert\n"
 
 #: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
+"\tUnterstützung für schönere Funktionsnamen {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
-msgstr "\tnz wird von der Griddatei gelesen\n"
+msgstr ""
+"\tnz wird von der Griddatei gelesen\n"
 
 #: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
@@ -289,45 +304,52 @@ msgstr "\tKovariantevektoren werden gelesen "
 #: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
-msgstr ""
+msgstr "\tPrüfung auf Laufzeitfehler {}"
 
 #: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
+"\tUnterstützung für SLEPc {}\n"
 
 #: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
+"\tUnterstützung für SUNDIALS {}\n"
 
 #: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
+"\tUnterstützung für Score-P {}\n"
 
 #: ../src/bout++.cxx:589
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tSignal handling support {}\n"
-msgstr "\tSignalverarbeitung ist deaktiviert\n"
+msgstr ""
+"\tUnterstützung für Signalbehandlung {}\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:76
 #, c++-format
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
+"\tVerwende einen Zeitschritt von {:e}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
-msgstr "\tfertig\n"
+msgstr ""
+"\tfertig\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:41
 msgid ""
 "\n"
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
+"\n"
+"\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 
 #: ../src/bout++.cxx:378
-#, fuzzy
 msgid ""
 "\n"
 "  -d <data directory>\t\tLook in <data directory> for input/output files\n"
@@ -340,8 +362,7 @@ msgstr ""
 "\n"
 "  -d <Datenordner>\tEin- und Ausgabedateien sind im <Datenordner>\n"
 "  -f <Optionendatei>\tOptinen werden aus der <Optionendatei> gelesen\n"
-"  -o <Einstellungsdatei>\tGenutzte Optionen werden in der "
-"<Einstellungsdatei> gespeichert\n"
+"  -o <Einstellungsdatei>\tGenutzte Optionen werden in der <Einstellungsdatei> gespeichert\n"
 "  -l, --log <Logdatei>\tSchreibe das Log in die <Logdatei>\n"
 "  -v, --verbose\t\tWortreicherer Ausgabe\n"
 "  -q, --quiet\t\tNur wichtigere Ausgaben anzeigen\n"
@@ -353,9 +374,12 @@ msgid ""
 "  {1: ^{2}}{0}\n"
 "  Did you mean '{0}'?"
 msgstr ""
+"\n"
+"  {1: ^{2}}{0}\n"
+"  Meinten Sie '{0}'?"
 
 #: ../src/solver/solver.cxx:586
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run finished at  : {:s}\n"
@@ -364,7 +388,7 @@ msgstr ""
 "Simulation beendet um {:s}\n"
 
 #: ../src/solver/solver.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run started at  : {:s}\n"
@@ -402,6 +426,30 @@ msgid ""
 "\n"
 "{}"
 msgstr ""
+"\n"
+"There were unused input options:\n"
+"-----\n"
+"{:i}\n"
+"-----\n"
+"It's possible you've mistyped some options. BOUT++ input arguments are\n"
+"now case-sensitive, and some have changed name. You can try running\n"
+"\n"
+"    <BOUT++ directory>/bin/bout-v5-input-file-upgrader.py {}/{}\n"
+"\n"
+"to automatically fix the most common issues. If these options above\n"
+"are sometimes used depending on other options, you can call\n"
+"`Options::setConditionallyUsed()`, for example:\n"
+"\n"
+"    Options::root()[\"{}\"].setConditionallyUsed();\n"
+"\n"
+"to mark a section or value as depending on other values, and so ignore\n"
+"it in this check. Alternatively, if you're sure the above inputs are\n"
+"not a mistake, you can set 'input:error_on_unused_options=false' to\n"
+"turn off this check for unused options. You can always set\n"
+"'input:validate=true' to check inputs without running the full\n"
+"simulation.\n"
+"\n"
+"{}"
 
 #: ../src/bout++.cxx:389
 #, c++-format
@@ -435,62 +483,84 @@ msgid ""
 "For all possible input parameters, see the user manual and/or the physics "
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
+"  --print-config\t\tPrint the compile-time configuration\n"
+"  --list-solvers\t\tList the available time solvers\n"
+"  --help-solver <solver>\tPrint help for the given time solver\n"
+"  --list-laplacians\t\tList the available Laplacian inversion solvers\n"
+"  --help-laplacian <laplacian>\tPrint help for the given Laplacian inversion solver\n"
+"  --list-laplacexz\t\tList the available LaplaceXZ inversion solvers\n"
+"  --help-laplacexz <laplacexz>\tPrint help for the given LaplaceXZ inversion solver\n"
+"  --list-invertpars\t\tList the available InvertPar solvers\n"
+"  --help-invertpar <invertpar>\tPrint help for the given InvertPar solver\n"
+"  --list-rkschemes\t\tList the available Runge-Kutta schemes\n"
+"  --help-rkscheme <rkscheme>\tPrint help for the given Runge-Kutta scheme\n"
+"  --list-meshes\t\t\tList the available Meshes\n"
+"  --help-mesh <mesh>\t\tPrint help for the given Mesh\n"
+"  --list-xzinterpolations\tList the available XZInterpolations\n"
+"  --help-xzinterpolation <xzinterpolation>\tPrint help for the given XZInterpolation\n"
+"  --list-zinterpolations\tList the available ZInterpolations\n"
+"  --help-zinterpolation <zinterpolation>\tPrint help for the given ZInterpolation\n"
+"  -h, --help\t\t\tThis message\n"
+"  restart [append]\t\tRestart the simulation. If append is specified, append to the existing output files, otherwise overwrite them\n"
+"  VAR=VALUE\t\t\tSpecify a VALUE for input parameter VAR\n"
+"\n"
+"For all possible input parameters, see the user manual and/or the physics model source (e.g. {:s}.cxx)\n"
 
 #: ../src/bout++.cxx:386
-#, fuzzy
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
-msgstr "  -c, --color\t\tFarbliche Ausgabe mit bout-log-color\n"
+msgstr ""
+"  -c, --color\t\tFarbliche Ausgabe mit bout-log-color\n"
 
 #: ../include/bout/options.hxx:899
-#, fuzzy
 msgid ") overwritten with:"
-msgstr ") überschrieben mit {:s}"
+msgstr ") überschrieben mit:"
 
 #: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
-msgstr ""
+msgstr ", level {}"
 
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
-msgstr ""
+msgstr "4 of 8"
 
 #: ../src/sys/options.cxx:895
 msgid "All options used\n"
-msgstr "Alle genutzten Optionen\n"
+msgstr ""
+"Alle genutzten Optionen\n"
 
 #: ../src/bout++.cxx:535
-#, fuzzy, c++-format
+#, c++-format
 msgid "BOUT++ version {:s}\n"
-msgstr "BOUT++ Version {:s}\n"
+msgstr ""
+"BOUT++ Version {:s}\n"
 
 #: ../src/bout++.cxx:147
-#, fuzzy
 msgid "Bad command line arguments:\n"
-msgstr "\t'=' darf nicht mehrfach vorkommen: '{:s}'\n"
+msgstr ""
+"Bad command line arguments:\n"
 
 #: ../src/sys/expressionparser.cxx:192
 #, c++-format
 msgid "Boolean operator argument {:e} is not a bool"
-msgstr ""
+msgstr "Boolean operator argument {:e} is not a bool"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
 msgstr "Randgebiete auf diesem Prozessor: "
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:348
-#, fuzzy, c++-format
+#, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr ""
-"{:d} Punkte in der X-Richtung können nicht gleichmässig zwischen {:d} "
-"Prozessen verteilt werden\n"
+"{:d} Punkte in der X-Richtung können nicht gleichmässig zwischen {:d} Prozessen verteilt werden\n"
 
 #: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
-msgstr ""
+msgstr "Check if a file exists, and exit if it does."
 
 #: ../src/bout++.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
 "\n"
@@ -504,58 +574,55 @@ msgstr "Befehlszeile"
 
 #: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
-msgstr "Kompiliert mit:\n"
+msgstr ""
+"Kompiliert mit:\n"
 
 #: ../tests/unit/src/test_bout++.cxx:362
-#, fuzzy
 msgid "Compiled with flags"
-msgstr "\tWurde kompiliert mit den Optionen : {:s}\n"
+msgstr "Compiled with flags"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
 msgstr "Standardregionen werden erstellt"
 
 #: ../src/bout++.cxx:527
-#, fuzzy, c++-format
+#, c++-format
 msgid "Could not create PID file {:s}"
-msgstr "Die Ausgabedatei '{:s}' konnte nicht geöffnet werden\n"
+msgstr "PID-Datei {:s} konnte nicht erstellt werden"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
-msgstr ""
-"Es konnte keine gültige Anzahl an Prozessoren in X Richtung gefunden werden "
-"(NXPE). Versuche es mit einer anderen Zahl an Prozessoren."
+msgstr "Es konnte keine gültige Anzahl an Prozessoren in X Richtung gefunden werden (NXPE). Versuche es mit einer anderen Zahl an Prozessoren."
 
 #: ../src/sys/options/options_ini.cxx:160
-#, fuzzy, c++-format
+#, c++-format
 msgid "Could not open output file '{:s}'\n"
-msgstr "Die Ausgabedatei '{:s}' konnte nicht geöffnet werden\n"
+msgstr ""
+"Die Ausgabedatei '{:s}' konnte nicht geöffnet werden\n"
 
 #: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
-msgstr ""
+msgstr "Konnte {:s}/{:s}.{:d} nicht zum Schreiben öffnen"
 
 #. Error reading
 #: ../src/mesh/mesh.cxx:543
-#, fuzzy, c++-format
+#, c++-format
 msgid "Could not read integer array '{:s}'\n"
-msgstr "Der Ganzzahlen-Array '{:s}' konnte nicht gelesen werden\n"
+msgstr ""
+"Der Ganzzahlen-Array '{:s}' konnte nicht gelesen werden\n"
 
 #. Failed . Probably not important enough to stop the simulation
 #: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
-"Der Befehl 'bout-log-color' konnte nicht ausgeführt werden. Stellen Sie "
-"sicher, dass er sich in $PATH befindet.\n"
+"Der Befehl 'bout-log-color' konnte nicht ausgeführt werden. Stellen Sie sicher, dass er sich in $PATH befindet.\n"
 
 #: ../src/solver/solver.cxx:772
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
-msgstr ""
-"'Monitor' konnte nicht hinzugefügt werden: {:g} ist nicht ein Vielfaches von "
-"{:g}!"
+msgstr "'Monitor' konnte nicht hinzugefügt werden: {:g} ist nicht ein Vielfaches von {:g}!"
 
 #: ../src/sys/expressionparser.cxx:312
 #, c++-format
@@ -565,85 +632,90 @@ msgid ""
 "may need to change your input file.\n"
 "{}"
 msgstr ""
+"Generator '{}' konnte nicht gefunden werden. BOUT++-Ausdrücke unterscheiden nun zwischen Groß- und Kleinschreibung, daher\n"
+"müssen Sie möglicherweise Ihre Eingabedatei ändern.\n"
+"{}"
 
 #: ../src/mesh/mesh.cxx:587
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
 msgstr "Die Region '{:s}' ist nicht in regionMap2D"
 
 #: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
 msgstr "Die Region '{:s}' ist nicht in regionMap3D"
 
 #: ../src/mesh/mesh.cxx:595
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
 msgstr "Die Region '{:s}' ist nicht in regionMapPerp"
 
 #. Convert any exceptions to something a bit more useful
 #: ../src/sys/options.cxx:361
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
-msgstr ""
-"Die Option {:s} = '{:s}' konnte nicht als ganze Zahl interpretiert werden."
+msgstr "{} konnte nicht aus der Option {:s} = '{:s}' gelesen werden: {}"
 
 #: ../src/bout++.cxx:515
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
-msgstr "Der Datenordner \"{:s}\" existiert nicht oder ist nicht lesbar\n"
+msgstr ""
+"Der Datenordner \"{:s}\" existiert nicht oder ist nicht lesbar\n"
 
 #: ../src/bout++.cxx:512
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
 msgstr ""
 "\"{:s}\" soll als Datenordner verwendet werden, ist jedoch kein Ordner\n"
 
 #: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
-msgstr "FEHLER: Der Integrator ist bereits initialisiert.\n"
+msgstr ""
+"FEHLER: Der Integrator ist bereits initialisiert.\n"
 
 #: ../src/bout++.cxx:216
-#, fuzzy, c++-format
+#, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
-msgstr "Es wurde ein Fehler während der Initialisierung gefunden: {:s}\n"
+msgstr ""
+"Es wurde ein Fehler während der Initialisierung gefunden: {:s}\n"
 
 #: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
 msgstr "Es wurde ein Fehler beim Schreiben der Einstellungsdatei gefunden"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:323
-#, fuzzy, c++-format
+#, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
 msgstr "Fehler: nx muss größer als 2 mal MXG sein (2 * {:d})"
 
 #: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
 msgstr ""
-"Der Integrator konnte nicht initialisiert werden. Der Prozess wird "
-"abgebrochen\n"
+"Der Integrator konnte nicht initialisiert werden. Der Prozess wird abgebrochen\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:281
-#, fuzzy, c++-format
+#, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
-msgstr "Suche NXPE Wert (optimal = {:f})\n"
+msgstr ""
+"Suche NXPE Wert (optimal = {:f})\n"
 
 #: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
-msgstr "initialisiere den Integrator\n"
+msgstr ""
+"initialisiere den Integrator\n"
 
 #: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
 msgstr ""
-"Optionendatei (Eingabe) und Einstellungsdatei (Ausgabe) müssen verschieden "
-"sein.\n"
+"Optionendatei (Eingabe) und Einstellungsdatei (Ausgabe) müssen verschieden sein.\n"
 "Verwende -o <Einstellungsdatei>.\n"
 
 #: ../src/sys/optionsreader.cxx:76
 msgid "Invalid command line option '-' found - maybe check whitespace?"
-msgstr ""
+msgstr "Invalid command line option '-' found - maybe check whitespace?"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
@@ -659,85 +731,83 @@ msgstr "Das Gitter muss ny enthalten"
 
 #. Not found
 #: ../src/mesh/mesh.cxx:547
-#, fuzzy, c++-format
+#, c++-format
 msgid "Missing integer array {:s}\n"
-msgstr "Ganzzahlen-Array '{:s}' nicht gesetzt\n"
+msgstr ""
+"Ganzzahlen-Array '{:s}' nicht gesetzt\n"
 
 #: ../src/solver/solver.cxx:911
-#, fuzzy, c++-format
+#, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
-msgstr "Beendigung durch Monitor\n"
+msgstr ""
+"Monitor signalisierte Beenden (Ausnahme {})\n"
 
 #: ../src/solver/solver.cxx:889
-#, fuzzy, c++-format
+#, c++-format
 msgid "Monitor signalled to quit (return code {})"
-msgstr "Der Monitor signaliserte die Beendigung"
+msgstr "Monitor signalisierte Beenden (Rückgabecode {})"
 
 #: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
-msgstr ""
+msgstr "Name of file whose existence triggers a stop"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
 msgstr "Keine Randregionen auf diesem Prozessor"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:586
-#, fuzzy
 msgid "No boundary regions; domain is periodic\n"
-msgstr "Keine Randregionen auf diesem Prozessor"
+msgstr ""
+"Keine Randregionen; Domäne ist periodisch\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:245
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
 msgstr ""
-"Anzahl an Prozessoren ({:d}) nicht teilbar durch Anzahl in x Richtung "
-"({:d})\n"
+"Anzahl an Prozessoren ({:d}) nicht teilbar durch Anzahl in x Richtung ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:258
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
 msgstr ""
-"Anzahl an Prozessoren ({:d}) nicht teilbar durch Anzahl in x Richtung "
-"({:d})\n"
+"Anzahl an Prozessoren ({:d}) nicht teilbar durch Anzahl in x Richtung ({:d})\n"
 
 #. Less than 2 time-steps left
 #: ../src/bout++.cxx:908
-#, fuzzy, c++-format
+#, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
-msgstr "Nur noch {:e} Sekunden verfügbar. Abbruch\n"
+msgstr ""
+"Nur noch {:e} Sekunden ({:.2f} Schritte) übrig. Beende\n"
 
 #: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
 #: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
 #: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
 #: ../src/sys/options.cxx:789
-#, fuzzy, c++-format
+#, c++-format
 msgid "Option {:s} has no value"
 msgstr "Der Option '{:s}' wurde kein Wert zugewiesen"
 
 #. Doesn't exist
 #: ../src/sys/options.cxx:172
-#, fuzzy, c++-format
+#, c++-format
 msgid "Option {:s}:{:s} does not exist"
 msgstr "Die Option {:s}:{:s} exisitiert nicht"
 
 #: ../include/bout/options.hxx:904
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
 "value was '{:s}'."
-msgstr ""
-"Optionen: Der Wert {2:s} wird mit dem Wert {1:s} gleichen Ursprungs ({0:s}) "
-"überschrieben."
+msgstr "Optionen: Setze einen Wert aus derselben Quelle ({:s}) auf den neuen Wert '{:s}' - der alte Wert war '{:s}'."
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:588
-#, fuzzy
 msgid "Possible boundary regions are: "
 msgstr "Keine Randregionen auf diesem Prozessor"
 
 #: ../src/bout++.cxx:545
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Processor number: {:d} of {:d}\n"
 "\n"
@@ -746,24 +816,25 @@ msgstr ""
 "\n"
 
 #: ../src/mesh/mesh.cxx:642
-#, fuzzy, c++-format
+#, c++-format
 msgid "Registered region 2D {:s}"
 msgstr "2D Region '{:s}' hinzugefügt"
 
 #: ../src/mesh/mesh.cxx:632
-#, fuzzy, c++-format
+#, c++-format
 msgid "Registered region 3D {:s}"
 msgstr "3D Region '{:s}' hinzugefügt"
 
 #: ../src/mesh/mesh.cxx:652
-#, fuzzy, c++-format
+#, c++-format
 msgid "Registered region Perp {:s}"
 msgstr "Perp Region '{:s}' hinzugefügt"
 
 #: ../src/bout++.cxx:536
-#, fuzzy, c++-format
+#, c++-format
 msgid "Revision: {:s}\n"
-msgstr "Revision: {:s}\n"
+msgstr ""
+"Revision: {:s}\n"
 
 #: ../src/solver/solver.cxx:587
 msgid "Run time : "
@@ -780,15 +851,14 @@ msgstr ""
 
 #: ../tests/unit/src/test_bout++.cxx:359
 msgid "Signal"
-msgstr ""
+msgstr "Signal"
 
 #: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
-"Simu Zeit | RHS Berech. | Echtdauer |  Rechnen Inver Komm    I/O   "
-"Integrator\n"
+"Simu Zeit | RHS Berech. | Echtdauer |  Rechnen Inver Komm    I/O   Integrator\n"
 "\n"
 
 #: ../src/bout++.cxx:879
@@ -797,56 +867,53 @@ msgid ""
 "Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
-"Simu Zeit |  #expl RHS    | #impl RHS    | Echtdauer |  Rechnen Inv   "
-"Komm    I/O   Integrator\n"
+"Simu Zeit |  #expl RHS    | #impl RHS    | Echtdauer |  Rechnen Inv   Komm    I/O   Integrator\n"
 "\n"
 
 #: ../src/solver/solver.cxx:514
-#, fuzzy, c++-format
+#, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
-"Integriere mit einem `Monitor`-Zeitschritt von {1:e} für {0:d} Aufrufe.\n"
+"Solver läuft für {:d} Ausgaben mit einem Monitor-Zeitschritt von {:e}\n"
 
 #: ../src/solver/solver.cxx:510
-#, fuzzy, c++-format
+#, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
-msgstr "Integriere {:d} Zeitschritte von je {:e}\n"
+msgstr ""
+"Integriere {:d} Zeitschritte von je {:e}\n"
 
 #: ../src/solver/solver.cxx:788
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
 "called!"
-msgstr ""
-"Der Integrator kann den Zeitschritt nicht von {:g} auf {:g} reduzieren, "
-"nachdem er initialisiert wurde!"
+msgstr "Der Integrator kann den Zeitschritt nicht von {:g} auf {:g} reduzieren, nachdem er initialisiert wurde!"
 
 #: ../src/solver/solver.cxx:1289
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
-"Die zeitliche Ableitung ist an der falschen Stelle. Das Feld '{2:s}' ist an "
-"Position {0:s}, während die Ableitung an Position {1:s} ist.\n"
+"Zeitliche Ableitung an falscher Stelle - Feld ist bei {:s}, Ableitung ist bei {:s} für Feld '{:s}'\n"
 
 #: ../src/solver/solver.cxx:1494
-#, fuzzy, c++-format
+#, c++-format
 msgid "Time derivative for variable '{:s}' not set"
 msgstr "Zeitliche Ableitung für Variable '{:s}' nicht gesetzt"
 
 #: ../src/mesh/mesh.cxx:638
-#, fuzzy, c++-format
+#, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
 msgstr "Die Region '{:s}' ist bereits vorhanden in der regionMap2D"
 
 #: ../src/mesh/mesh.cxx:614
-#, fuzzy, c++-format
+#, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
 msgstr "Die Region '{:s}' ist bereits vorhanden in der regionMap3D"
 
 #: ../src/mesh/mesh.cxx:649
-#, fuzzy, c++-format
+#, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
 msgstr "Die Region '{:s}' ist bereits vorhanden in der regionMapPerp"
 
@@ -858,6 +925,8 @@ msgid ""
 "This is likely the result of clashing input options, and you may have to "
 "rename one of them.\n"
 msgstr ""
+"Es wird versucht, Option '{0}' mit '{1}' zu indizieren, aber '{0}' ist ein Wert und kein Abschnitt.\n"
+"Dies ist wahrscheinlich das Ergebnis kollidierender Eingabeoptionen, und Sie müssen möglicherweise eine davon umbenennen.\n"
 
 #: ../src/mesh/coordinates.cxx:1464
 msgid ""
@@ -869,152 +938,161 @@ msgstr ""
 
 #: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
-msgstr "Ungenutzte Optionen:\n"
+msgstr ""
+"Ungenutzte Optionen:\n"
 
 #: ../src/bout++.cxx:446
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
-msgstr "Benutzung: {:s} -d <Datenordner>\n"
+msgstr ""
+"Benutzung: {:s} -d <Datenordner>\n"
 
 #: ../src/bout++.cxx:455
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
-msgstr "Benutzung: {:s} -f <Optionendatei>\n"
+msgstr ""
+"Benutzung: {:s} -f <Optionendatei>\n"
 
 #: ../src/bout++.cxx:473
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
-msgstr "Benutzung: {:s} -f <Logdatei>\n"
+msgstr ""
+"Benutzung: {:s} -f <Logdatei>\n"
 
 #: ../src/bout++.cxx:464
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
-msgstr "Benutzung: {:s} -f <Einstellungsdatei>\n"
+msgstr ""
+"Benutzung: {:s} -f <Einstellungsdatei>\n"
 
 #: ../src/bout++.cxx:360
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {} {} <name>\n"
-msgstr "Benutzung: {:s} -f <Logdatei>\n"
+msgstr ""
+"Verwendung: {} {} <Name>\n"
 
 #: ../tests/unit/src/test_bout++.cxx:32 ../tests/unit/src/test_bout++.cxx:46
 msgid "Usage:"
-msgstr ""
+msgstr "Usage:"
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
 #: ../src/bout++.cxx:374
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
 "[VAR=VALUE]\n"
 msgstr ""
-"Benutzung: {:s} [-d <Datenordner>] [-f <Optionendatei>] [restart [append]] "
-"[VAR=WERT]\n"
+"Benutzung: {:s} [-d <Datenordner>] [-f <Optionendatei>] [restart [append]] [VAR=WERT]\n"
 
 #. restart file should be written by physics model
 #: ../src/solver/solver.cxx:927
-#, fuzzy
 msgid "User signalled to quit. Returning\n"
-msgstr "Beendigung durch Monitor\n"
+msgstr ""
+"Beendigung durch Monitor\n"
 
 #: ../src/sys/options.cxx:486
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} = {:e} is not a bool"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
 #: ../src/sys/options.cxx:426
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
 msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
 
 #: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
-msgstr ""
+msgstr "Wert für Option {:s} kann nicht in ein BoutReal umgewandelt werden"
 
 #: ../src/sys/options.cxx:623
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
-msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
+msgstr "Wert für Option {:s} kann nicht in ein Field2D umgewandelt werden"
 
 #: ../src/sys/options.cxx:571
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
-msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
+msgstr "Wert für Option {:s} kann nicht in ein Field3D umgewandelt werden"
 
 #: ../src/sys/options.cxx:705
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
-msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
+msgstr "Wert für Option {:s} kann nicht in ein FieldPerp umgewandelt werden"
 
 #: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
-msgstr ""
+msgstr "Wert für Option {:s} kann nicht in ein bool umgewandelt werden"
 
 #: ../src/sys/options.cxx:751
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
-msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
+msgstr "Wert für Option {:s} kann nicht in ein Array<BoutReal> umgewandelt werden"
 
 #: ../src/sys/options.cxx:773
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
-msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
+msgstr "Wert für Option {:s} kann nicht in eine Matrix<BoutReal> umgewandelt werden"
 
 #: ../src/sys/options.cxx:795
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
-msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
+msgstr "Wert für Option {:s} kann nicht in einen Tensor<BoutReal> umgewandelt werden"
 
 #. Another type which can't be converted
 #: ../src/sys/options.cxx:418
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} is not an integer"
-msgstr "Wert der Option {:s} = {:e} ist keine Ganzzahl"
+msgstr "Wert für Option {:s} ist keine Ganzzahl"
 
 #: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
-#, fuzzy, c++-format
+#, c++-format
 msgid "Variable '{:s}' not initialised"
 msgstr "Variable '{:s}' ist nicht initialisiert"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:467
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
-"WARNUNG: Anzahl der toroidalen Punkte sollte 2^n für effiziente FFTs sein. "
-"Ändere MZ falls FFTs verwendet werden\n"
+"WARNUNG: Die Anzahl toroidaler Punkte sollte für effiziente FFT-Leistung 2^n sein -- ziehen Sie eine Änderung von MZ ({:d}) in Betracht, wenn Sie FFTs verwenden\n"
 
 #: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
+"WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 
 #: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
+"WARNING: extrapolating input mesh quantities into x-boundary cells. Set option extrapolate_x=false to disable this.\n"
 
 #: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
+"WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 
 #: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
+"WARNING: extrapolating input mesh quantities into y-boundary cells. Set option extrapolate_y=false to disable this.\n"
 
 #: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
-msgstr ""
+msgstr "Wall time limit in hours. By default (< 0), no limit"
 
 #: ../src/sys/optionsreader.cxx:42
-#, fuzzy, c++-format
+#, c++-format
 msgid "Writing options to file {:s}\n"
-msgstr "Optionen werden in {:s} gespeichert\n"
+msgstr ""
+"Optionen werden in {:s} gespeichert\n"
 
 #. / The source label given to default values
 #: ../src/sys/options.cxx:34
diff --git a/locale/es/libbout.po b/locale/es/libbout.po
index 68db78ada9..3346bd882e 100644
--- a/locale/es/libbout.po
+++ b/locale/es/libbout.po
@@ -17,99 +17,98 @@ msgstr ""
 "Content-Transfer-Encoding: 8bit\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:182
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
-"\t -> La región `Core` jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) debe ser un "
-"múltiplo de MYSUB ({:d})\n"
+"\t -> La región `Core` jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) debe ser un múltiplo de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:215
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
-"\t -> La región `Core` jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) debe ser un "
-"múltiplo de MYSUB ({:d})\n"
+"\t -> La región `Core` jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) debe ser un múltiplo de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:190
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
-"\t -> La región `Core` jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) debe ser un "
-"múltiplo de MYSUB ({:d})\n"
+"\t -> La región `Core` jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) debe ser un múltiplo de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
-msgstr "\t -> El valor es bueno\n"
+msgstr ""
+"\t -> El valor es bueno\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:171
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
 msgstr ""
-"\t -> La región `Leg` jyseps1_1+1 ({:d}) debe ser un múltiplo de MYSUB "
-"({:d})\n"
+"\t -> La región `Leg` jyseps1_1+1 ({:d}) debe ser un múltiplo de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:206
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
-"\t -> La región `Leg` jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) debe ser un "
-"múltiplo de MYSUB ({:d})\n"
+"\t -> La región `Leg` jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) debe ser un múltiplo de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:223
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
-"\t -> La región `Leg` ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) debe ser un "
-"múltiplo de MYSUB ({:d})\n"
+"\t -> La región `Leg` ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) debe ser un múltiplo de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:199
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
-"\t -> La región `Leg` ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) debe ser un "
-"múltiplo de MYSUB ({:d})\n"
+"\t -> La región `Leg` ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) debe ser un múltiplo de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:166
-#, fuzzy, c++-format
+#, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
-msgstr "\t -> ny/NYPE ({:d}/{:d} = {:d}) debe ser >= MYG ({:d})\n"
+msgstr ""
+"\t -> ny/NYPE ({:d}/{:d} = {:d}) debe ser >= MYG ({:d})\n"
 
 #: ../src/bout++.cxx:575
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tADIOS2 support {}\n"
-msgstr "\tSoporte netCDF activado\n"
+msgstr ""
+"\tCompatibilidad con ADIOS2 {}\n"
 
 #: ../src/bout++.cxx:583
 #, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
+"\tTraza inversa en excepciones {}\n"
 
 #. Loop over all possibilities
 #. Processors divide equally
 #. Mesh in X divides equally
 #. Mesh in Y divides equally
 #: ../src/mesh/impls/bout/boutmesh.cxx:288
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tCandidate value: {:d}\n"
-msgstr "\tValor candidato: {:d}\n"
+msgstr ""
+"\tValor candidato: {:d}\n"
 
 #: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
+"\tColor en los registros {}\n"
 
 #: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
@@ -118,35 +117,33 @@ msgstr "\tParámetros de línea de comandos para esta ejecución :"
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
 #: ../src/bout++.cxx:595
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tCompiled with flags : {:s}\n"
-msgstr "\tCompilado con las opciones `flags` : {:s}\n"
+msgstr ""
+"\tCompilado con las opciones `flags` : {:s}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:315
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
 msgstr ""
-"\tDominio separado (NXPE={:d}, NYPE={:d}) en los dominios (localNx={:d}, "
-"localNy={:d})\n"
+"\tDominio separado (NXPE={:d}, NYPE={:d}) en los dominios (localNx={:d}, localNy={:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:357
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
-"\tERROR: No se pueden separar {:d} Y puntos entre {:d} procesadores por "
-"igual\n"
+"\tERROR: No se pueden separar {:d} Y puntos entre {:d} procesadores por igual\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:365
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
-"\tERROR: No se pueden separar {:d} Y puntos entre {:d} procesadores por "
-"igual\n"
+"\tERROR: No se pueden separar {:d} Y puntos entre {:d} procesadores por igual\n"
 
 #: ../src/sys/options/options_ini.cxx:200
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\tEmpty key\n"
 "\tLine: {:s}"
@@ -155,41 +152,45 @@ msgstr ""
 "\tLínea: {:s}"
 
 #: ../src/sys/optionsreader.cxx:127
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tEmpty key or value in command line '{:s}'\n"
-msgstr "\tEntrada o valor vacío en la línea de comandos '{:s}'\n"
+msgstr ""
+"\tEntrada o valor vacío en la línea de comandos '{:s}'\n"
 
 #: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
+"\tSalida adicional de depuración {}\n"
 
 #: ../src/bout++.cxx:568
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tFFT support {}\n"
-msgstr "\tSoporte netCDF activado\n"
+msgstr ""
+"\tCompatibilidad con FFT {}\n"
 
 #: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
+"\tSeguimiento del nombre de campo {}\n"
 
 #: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
+"\tExcepciones de punto flotante {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
 msgstr "\tTamaño de la malla (`grid`): "
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:499
-#, fuzzy
 msgid "\tGuard cells (x,y,z): "
-msgstr "\tProteger celdas (x,y): "
+msgstr "\tCeldas de guarda (x,y,z): "
 
 #: ../src/sys/options/options_ini.cxx:204
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\tKey must not contain ':' character\n"
 "\tLine: {:s}"
@@ -201,37 +202,43 @@ msgstr ""
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
+"\tCompatibilidad con LAPACK {}\n"
 
 #: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
+"\tPila de mensajes {}\n"
 
 #: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
+"\tEl modo de métricas es {}\n"
 
 #: ../src/sys/optionsreader.cxx:111
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
-msgstr "\tMutilples '=' en el argumento de la línea de comandos '{:s}'\n"
+msgstr ""
+"\tMutilples '=' en el argumento de la línea de comandos '{:s}'\n"
 
 #: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
+"\tCompatibilidad con lenguaje natural {}\n"
 
 #: ../src/bout++.cxx:574
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tNetCDF support {}{}\n"
-msgstr "\tSoporte netCDF activado\n"
+msgstr ""
+"\tCompatibilidad con NetCDF {}{}\n"
 
 #: ../src/bout++.cxx:585
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOpenMP parallelisation {}, using {} threads\n"
 msgstr ""
-"\tParalelización en OpenMP activada, usando {:d} procesos (`threads`)\n"
+"\tParalelización con OpenMP {}, usando {} hilos\n"
 
 #. Mark the option as used
 #. Option not found
@@ -241,41 +248,48 @@ msgid "\tOption "
 msgstr "\tOpción "
 
 #: ../src/sys/options.cxx:369
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOption {} = {}"
-msgstr "\tOpción "
+msgstr "\tOpción {} = {}"
 
 #: ../src/sys/options/options_ini.cxx:70
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOptions file '{:s}' not found\n"
-msgstr "\tOpciones de archivo '{:s}' no encontrados\n"
+msgstr ""
+"\tOpciones de archivo '{:s}' no encontrados\n"
 
 #: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
+"\tCompatibilidad con PETSc {}\n"
 
 #: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
+"\tCompatibilidad con PVODE {}\n"
 
 #: ../src/bout++.cxx:564
 msgid "\tParallel NetCDF support disabled\n"
-msgstr "\tSoporte para NetCDF paralelo desactivado\n"
+msgstr ""
+"\tSoporte para NetCDF paralelo desactivado\n"
 
 #: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
-msgstr "\tSoporte para NetCDF paralelo activado\n"
+msgstr ""
+"\tSoporte para NetCDF paralelo activado\n"
 
 #: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
+"\tCompatibilidad con nombres de función detallados {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
-msgstr "\tLeer nz del archivo input de la malla `grid`\n"
+msgstr ""
+"\tLeer nz del archivo input de la malla `grid`\n"
 
 #: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
@@ -288,45 +302,52 @@ msgstr "\tLeyendo vector covariante "
 #: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
-msgstr ""
+msgstr "\tComprobación de errores en tiempo de ejecución {}"
 
 #: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
+"\tCompatibilidad con SLEPc {}\n"
 
 #: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
+"\tCompatibilidad con SUNDIALS {}\n"
 
 #: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
+"\tCompatibilidad con Score-P {}\n"
 
 #: ../src/bout++.cxx:589
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tSignal handling support {}\n"
-msgstr "\tGestión de señal desactivada\n"
+msgstr ""
+"\tCompatibilidad con manejo de señales {}\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:76
 #, c++-format
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
+"\tUsando un paso de tiempo {:e}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
-msgstr "\tlisto\n"
+msgstr ""
+"\tlisto\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:41
 msgid ""
 "\n"
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
+"\n"
+"\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 
 #: ../src/bout++.cxx:378
-#, fuzzy
 msgid ""
 "\n"
 "  -d <data directory>\t\tLook in <data directory> for input/output files\n"
@@ -339,8 +360,7 @@ msgstr ""
 "\n"
 "  -d <data directory>\tBuscar en <data directory> los archivos input/output\n"
 "  -f <options filename>\tUsar OPCIONES descritas en <options filename>\n"
-"  -o <settings filename>\tGuardar OPCIONES usadas descritas en <options "
-"filename>\n"
+"  -o <settings filename>\tGuardar OPCIONES usadas descritas en <options filename>\n"
 "  -l, --log <log filename>\tImprimir registro `log` en <log filename>\n"
 "  -v, --verbose\t\tAumentar verbosidad\n"
 "  -q, --quiet\t\tDisminuir verbosidad\n"
@@ -352,9 +372,12 @@ msgid ""
 "  {1: ^{2}}{0}\n"
 "  Did you mean '{0}'?"
 msgstr ""
+"\n"
+"  {1: ^{2}}{0}\n"
+"  ¿Quiso decir '{0}'?"
 
 #: ../src/solver/solver.cxx:586
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run finished at  : {:s}\n"
@@ -363,7 +386,7 @@ msgstr ""
 "Ejecución finalizada en  : {:s}\n"
 
 #: ../src/solver/solver.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run started at  : {:s}\n"
@@ -401,6 +424,30 @@ msgid ""
 "\n"
 "{}"
 msgstr ""
+"\n"
+"There were unused input options:\n"
+"-----\n"
+"{:i}\n"
+"-----\n"
+"It's possible you've mistyped some options. BOUT++ input arguments are\n"
+"now case-sensitive, and some have changed name. You can try running\n"
+"\n"
+"    <BOUT++ directory>/bin/bout-v5-input-file-upgrader.py {}/{}\n"
+"\n"
+"to automatically fix the most common issues. If these options above\n"
+"are sometimes used depending on other options, you can call\n"
+"`Options::setConditionallyUsed()`, for example:\n"
+"\n"
+"    Options::root()[\"{}\"].setConditionallyUsed();\n"
+"\n"
+"to mark a section or value as depending on other values, and so ignore\n"
+"it in this check. Alternatively, if you're sure the above inputs are\n"
+"not a mistake, you can set 'input:error_on_unused_options=false' to\n"
+"turn off this check for unused options. You can always set\n"
+"'input:validate=true' to check inputs without running the full\n"
+"simulation.\n"
+"\n"
+"{}"
 
 #: ../src/bout++.cxx:389
 #, c++-format
@@ -434,59 +481,84 @@ msgid ""
 "For all possible input parameters, see the user manual and/or the physics "
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
+"  --print-config\t\tPrint the compile-time configuration\n"
+"  --list-solvers\t\tList the available time solvers\n"
+"  --help-solver <solver>\tPrint help for the given time solver\n"
+"  --list-laplacians\t\tList the available Laplacian inversion solvers\n"
+"  --help-laplacian <laplacian>\tPrint help for the given Laplacian inversion solver\n"
+"  --list-laplacexz\t\tList the available LaplaceXZ inversion solvers\n"
+"  --help-laplacexz <laplacexz>\tPrint help for the given LaplaceXZ inversion solver\n"
+"  --list-invertpars\t\tList the available InvertPar solvers\n"
+"  --help-invertpar <invertpar>\tPrint help for the given InvertPar solver\n"
+"  --list-rkschemes\t\tList the available Runge-Kutta schemes\n"
+"  --help-rkscheme <rkscheme>\tPrint help for the given Runge-Kutta scheme\n"
+"  --list-meshes\t\t\tList the available Meshes\n"
+"  --help-mesh <mesh>\t\tPrint help for the given Mesh\n"
+"  --list-xzinterpolations\tList the available XZInterpolations\n"
+"  --help-xzinterpolation <xzinterpolation>\tPrint help for the given XZInterpolation\n"
+"  --list-zinterpolations\tList the available ZInterpolations\n"
+"  --help-zinterpolation <zinterpolation>\tPrint help for the given ZInterpolation\n"
+"  -h, --help\t\t\tThis message\n"
+"  restart [append]\t\tRestart the simulation. If append is specified, append to the existing output files, otherwise overwrite them\n"
+"  VAR=VALUE\t\t\tSpecify a VALUE for input parameter VAR\n"
+"\n"
+"For all possible input parameters, see the user manual and/or the physics model source (e.g. {:s}.cxx)\n"
 
 #: ../src/bout++.cxx:386
-#, fuzzy
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
-msgstr "  -c, --color\t\tSalida de color usando bout-log-color\n"
+msgstr ""
+"  -c, --color\t\tSalida de color usando bout-log-color\n"
 
 #: ../include/bout/options.hxx:899
 msgid ") overwritten with:"
-msgstr ""
+msgstr ") sobrescrito con:"
 
 #: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
-msgstr ""
+msgstr ", level {}"
 
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
-msgstr ""
+msgstr "4 of 8"
 
 #: ../src/sys/options.cxx:895
 msgid "All options used\n"
-msgstr "Usando todas las opciones\n"
+msgstr ""
+"Usando todas las opciones\n"
 
 #: ../src/bout++.cxx:535
-#, fuzzy, c++-format
+#, c++-format
 msgid "BOUT++ version {:s}\n"
-msgstr "Versión de BOUT++ {:s}\n"
+msgstr ""
+"Versión de BOUT++ {:s}\n"
 
 #: ../src/bout++.cxx:147
-#, fuzzy
 msgid "Bad command line arguments:\n"
-msgstr "\tMutilples '=' en el argumento de la línea de comandos '{:s}'\n"
+msgstr ""
+"Bad command line arguments:\n"
 
 #: ../src/sys/expressionparser.cxx:192
 #, c++-format
 msgid "Boolean operator argument {:e} is not a bool"
-msgstr ""
+msgstr "Boolean operator argument {:e} is not a bool"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
 msgstr "Regiones frontera en este procesador: "
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:348
-#, fuzzy, c++-format
+#, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
-msgstr "No se pueden dividir {:d} X points entre {:d} procesadores por igual\n"
+msgstr ""
+"No se pueden dividir {:d} X points entre {:d} procesadores por igual\n"
 
 #: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
-msgstr ""
+msgstr "Check if a file exists, and exit if it does."
 
 #: ../src/bout++.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
 "\n"
@@ -500,54 +572,53 @@ msgstr "Línea de comandos"
 
 #: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
-msgstr "Opciones de tiempo de compilación:\n"
+msgstr ""
+"Opciones de tiempo de compilación:\n"
 
 #: ../tests/unit/src/test_bout++.cxx:362
-#, fuzzy
 msgid "Compiled with flags"
-msgstr "\tCompilado con las opciones `flags` : {:s}\n"
+msgstr "Compiled with flags"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
 msgstr "Construyendo regiones por defecto"
 
 #: ../src/bout++.cxx:527
-#, fuzzy, c++-format
+#, c++-format
 msgid "Could not create PID file {:s}"
-msgstr "No se pudo abrir el archivo de salida `output` '{:s}'\n"
+msgstr "No se pudo crear el archivo PID {:s}"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
-msgstr ""
-"No se pudo encontrar un valor válido para NXPE. Intente usar un número "
-"diferente de procesadores."
+msgstr "No se pudo encontrar un valor válido para NXPE. Intente usar un número diferente de procesadores."
 
 #: ../src/sys/options/options_ini.cxx:160
-#, fuzzy, c++-format
+#, c++-format
 msgid "Could not open output file '{:s}'\n"
-msgstr "No se pudo abrir el archivo de salida `output` '{:s}'\n"
+msgstr ""
+"No se pudo abrir el archivo de salida `output` '{:s}'\n"
 
 #: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
-msgstr ""
+msgstr "No se pudo abrir {:s}/{:s}.{:d} para escritura"
 
 #. Error reading
 #: ../src/mesh/mesh.cxx:543
-#, fuzzy, c++-format
+#, c++-format
 msgid "Could not read integer array '{:s}'\n"
-msgstr "No se pudo leer la matriz de enteros '{:s}'\n"
+msgstr ""
+"No se pudo leer la matriz de enteros '{:s}'\n"
 
 #. Failed . Probably not important enough to stop the simulation
 #: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
-"No se pudo ejecutar bout-log-color. Asegúrese de que se encuentre en su "
-"PATH\n"
+"No se pudo ejecutar bout-log-color. Asegúrese de que se encuentre en su PATH\n"
 
 #: ../src/solver/solver.cxx:772
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
 msgstr "No se pudo añadir el Monitor: {:g} no és multiplo de {:g}!"
 
@@ -559,81 +630,90 @@ msgid ""
 "may need to change your input file.\n"
 "{}"
 msgstr ""
+"No se pudo encontrar el generador '{}'. Las expresiones de BOUT++ ahora distinguen entre mayúsculas y minúsculas, por lo que\n"
+"puede que tenga que cambiar su archivo de entrada.\n"
+"{}"
 
 #: ../src/mesh/mesh.cxx:587
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
 msgstr "No se pudo encontrar la región {:s} en regionMap2D"
 
 #: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
 msgstr "No se pudo encontrar la región {:s} en regionMap2D"
 
 #: ../src/mesh/mesh.cxx:595
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
 msgstr "No se pudo encontrar la región {:s} en regionMapPerp"
 
 #. Convert any exceptions to something a bit more useful
 #: ../src/sys/options.cxx:361
-#, fuzzy, c++-format
+#, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
-msgstr "No se pudo recuperar el entero de la opción {:s} = '{:s}'"
+msgstr "No se pudo obtener {} de la opción {:s} = '{:s}': {}"
 
 #: ../src/bout++.cxx:515
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
-msgstr "DataDir \"{:s}\" no existe o no es accessible\n"
+msgstr ""
+"DataDir \"{:s}\" no existe o no es accessible\n"
 
 #: ../src/bout++.cxx:512
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
-msgstr "DataDir \"{:s}\" no es un directorio\n"
+msgstr ""
+"DataDir \"{:s}\" no es un directorio\n"
 
 #: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
-msgstr "ERROR: el Solver ya se encuentra inicializado\n"
+msgstr ""
+"ERROR: el Solver ya se encuentra inicializado\n"
 
 #: ../src/bout++.cxx:216
-#, fuzzy, c++-format
+#, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
-msgstr "Error encontrado durante la inicialización:{:s}\n"
+msgstr ""
+"Error encontrado durante la inicialización:{:s}\n"
 
 #: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
 msgstr "Error durante el paso de opciones"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:323
-#, fuzzy, c++-format
+#, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
 msgstr "Error: nx debe ser mayor que 2 veces MXG (2 * {:d})"
 
 #: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
-msgstr "Fallo en inicializar el solver-> Abortando\n"
+msgstr ""
+"Fallo en inicializar el solver-> Abortando\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:281
-#, fuzzy, c++-format
+#, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
-msgstr "Encontrando valor para NXPE (ideal = {:f})\n"
+msgstr ""
+"Encontrando valor para NXPE (ideal = {:f})\n"
 
 #: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
-msgstr "Initializando el solver\n"
+msgstr ""
+"Initializando el solver\n"
 
 #: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
 msgstr ""
-"Archivos de entrada y salida (`input/output`) para las opciones deben ser "
-"diferentes.\n"
+"Archivos de entrada y salida (`input/output`) para las opciones deben ser diferentes.\n"
 "Añada -o <settings file> para evitar este problema.\n"
 
 #: ../src/sys/optionsreader.cxx:76
 msgid "Invalid command line option '-' found - maybe check whitespace?"
-msgstr ""
+msgstr "Invalid command line option '-' found - maybe check whitespace?"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
@@ -649,85 +729,83 @@ msgstr "La malla `mesh` debe contener ny"
 
 #. Not found
 #: ../src/mesh/mesh.cxx:547
-#, fuzzy, c++-format
+#, c++-format
 msgid "Missing integer array {:s}\n"
-msgstr "Fala la matriz entera {:s}\n"
+msgstr ""
+"Fala la matriz entera {:s}\n"
 
 #: ../src/solver/solver.cxx:911
-#, fuzzy, c++-format
+#, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
-msgstr "Monitor indicó salir\n"
+msgstr ""
+"El monitor indicó salir (excepción {})\n"
 
 #: ../src/solver/solver.cxx:889
-#, fuzzy, c++-format
+#, c++-format
 msgid "Monitor signalled to quit (return code {})"
-msgstr "Monitor indicó salir"
+msgstr "El monitor indicó salir (código de retorno {})"
 
 #: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
-msgstr ""
+msgstr "Name of file whose existence triggers a stop"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
 msgstr "Sin regiones de frontera en este procesador"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:586
-#, fuzzy
 msgid "No boundary regions; domain is periodic\n"
-msgstr "Sin regiones de frontera en este procesador"
+msgstr ""
+"No hay regiones de frontera; el dominio es periódico\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:245
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
 msgstr ""
-"Número de procesadores ({:d}) no divisible para NPs en la dirección x "
-"({:d})\n"
+"Número de procesadores ({:d}) no divisible para NPs en la dirección x ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:258
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
 msgstr ""
-"Número de procesadores ({:d}) no divisible para NPs en la dirección x "
-"({:d})\n"
+"Número de procesadores ({:d}) no divisible para NPs en la dirección x ({:d})\n"
 
 #. Less than 2 time-steps left
 #: ../src/bout++.cxx:908
-#, fuzzy, c++-format
+#, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
-msgstr "Solo faltan {:e} segundos. Saliendo\n"
+msgstr ""
+"Solo quedan {:e} segundos ({:.2f} pasos). Saliendo\n"
 
 #: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
 #: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
 #: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
 #: ../src/sys/options.cxx:789
-#, fuzzy, c++-format
+#, c++-format
 msgid "Option {:s} has no value"
 msgstr "Opción {:s} sin valor"
 
 #. Doesn't exist
 #: ../src/sys/options.cxx:172
-#, fuzzy, c++-format
+#, c++-format
 msgid "Option {:s}:{:s} does not exist"
 msgstr "Opción {:s}:{:s} no existe"
 
 #: ../include/bout/options.hxx:904
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
 "value was '{:s}'."
-msgstr ""
-"Opciones: Cambiando valor de la misma fuente ({:s}) al valor nuevo '{:s}' - "
-"valor anterior era '{:s}'."
+msgstr "Opciones: estableciendo un valor desde la misma fuente ({:s}) al nuevo valor '{:s}' - el valor anterior era '{:s}'."
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:588
-#, fuzzy
 msgid "Possible boundary regions are: "
 msgstr "Sin regiones de frontera en este procesador"
 
 #: ../src/bout++.cxx:545
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Processor number: {:d} of {:d}\n"
 "\n"
@@ -736,24 +814,25 @@ msgstr ""
 "\n"
 
 #: ../src/mesh/mesh.cxx:642
-#, fuzzy, c++-format
+#, c++-format
 msgid "Registered region 2D {:s}"
 msgstr "Región 2D registrada {:s}"
 
 #: ../src/mesh/mesh.cxx:632
-#, fuzzy, c++-format
+#, c++-format
 msgid "Registered region 3D {:s}"
 msgstr "Región 3D registrada {:s}"
 
 #: ../src/mesh/mesh.cxx:652
-#, fuzzy, c++-format
+#, c++-format
 msgid "Registered region Perp {:s}"
 msgstr "Región Perp registrada {:s}"
 
 #: ../src/bout++.cxx:536
-#, fuzzy, c++-format
+#, c++-format
 msgid "Revision: {:s}\n"
-msgstr "Revisión: {:s}\n"
+msgstr ""
+"Revisión: {:s}\n"
 
 #: ../src/solver/solver.cxx:587
 msgid "Run time : "
@@ -770,15 +849,14 @@ msgstr ""
 
 #: ../tests/unit/src/test_bout++.cxx:359
 msgid "Signal"
-msgstr ""
+msgstr "Signal"
 
 #: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
-"Tiempo Sim  |  RHS eval.  | Tiempo Wall |  Calc    Inv   Com    I/O   "
-"SOLVER\n"
+"Tiempo Sim  |  RHS eval.  | Tiempo Wall |  Calc    Inv   Com    I/O   SOLVER\n"
 "\n"
 
 #: ../src/bout++.cxx:879
@@ -787,59 +865,53 @@ msgid ""
 "Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
-"Tiempo Sim  |  RHS_e eval.  | RHS_I eval.  | Tiempo Wall |  Calc    Inv   "
-"Com    I/O   SOLVER\n"
+"Tiempo Sim  |  RHS_e eval.  | RHS_I eval.  | Tiempo Wall |  Calc    Inv   Com    I/O   SOLVER\n"
 "\n"
 
 #: ../src/solver/solver.cxx:514
-#, fuzzy, c++-format
+#, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
-"Solver corriendo para {:d} outputs con intervalos de tiempo de monitor de "
-"{:e}\n"
+"El solucionador se ejecuta para {:d} salidas con un paso de tiempo de monitor de {:e}\n"
 
 #: ../src/solver/solver.cxx:510
-#, fuzzy, c++-format
+#, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr ""
-"Solver corriendo para {:d} outputs con intervalos de tiempo de output de "
-"{:e}\n"
+"Solver corriendo para {:d} outputs con intervalos de tiempo de output de {:e}\n"
 
 #: ../src/solver/solver.cxx:788
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
 "called!"
-msgstr ""
-"Solver::addMonitor: No se puedo reducir el intervalo de tiempo (de {:g} a "
-"{:g}) después de que init fuera llamado!"
+msgstr "Solver::addMonitor: No se puedo reducir el intervalo de tiempo (de {:g} a {:g}) después de que init fuera llamado!"
 
 #: ../src/solver/solver.cxx:1289
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
-"Derivada del tiempo en lugar erróneo - El field se encuentra en  {:s}, la "
-"derivada se encuentra en {:s} para el field '{:s}'\n"
+"Derivada temporal en ubicación incorrecta: el campo está en {:s}, la derivada está en {:s} para el campo '{:s}'\n"
 
 #: ../src/solver/solver.cxx:1494
-#, fuzzy, c++-format
+#, c++-format
 msgid "Time derivative for variable '{:s}' not set"
 msgstr "Derivada del tiempo para la variable '{:s}' no fijada"
 
 #: ../src/mesh/mesh.cxx:638
-#, fuzzy, c++-format
+#, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
 msgstr "Intentando añadir una región ya existente {:s} a regionMap2D"
 
 #: ../src/mesh/mesh.cxx:614
-#, fuzzy, c++-format
+#, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
 msgstr "Intentando añadir una región ya existente {:s} a regionMap3D"
 
 #: ../src/mesh/mesh.cxx:649
-#, fuzzy, c++-format
+#, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
 msgstr "Intentando añadir una región ya existente {:s} a regionMapPerp"
 
@@ -851,6 +923,8 @@ msgid ""
 "This is likely the result of clashing input options, and you may have to "
 "rename one of them.\n"
 msgstr ""
+"Se está intentando indexar la opción '{0}' con '{1}', pero '{0}' es un valor, no una sección.\n"
+"Es probable que esto sea el resultado de opciones de entrada en conflicto, y puede que tenga que cambiar el nombre de una de ellas.\n"
 
 #: ../src/mesh/coordinates.cxx:1464
 msgid ""
@@ -862,152 +936,161 @@ msgstr ""
 
 #: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
-msgstr "Opciones sin usar:\n"
+msgstr ""
+"Opciones sin usar:\n"
 
 #: ../src/bout++.cxx:446
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
-msgstr "Correcto uso es {:s} -d <data directory>\n"
+msgstr ""
+"Correcto uso es {:s} -d <data directory>\n"
 
 #: ../src/bout++.cxx:455
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
-msgstr "Correcto uso es {:s} -f <options filename>\n"
+msgstr ""
+"Correcto uso es {:s} -f <options filename>\n"
 
 #: ../src/bout++.cxx:473
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
-msgstr "Correcto uso es {:s} -l <log filename>\n"
+msgstr ""
+"Correcto uso es {:s} -l <log filename>\n"
 
 #: ../src/bout++.cxx:464
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
-msgstr "Correcto uso es {:s} -o <settings filename>\n"
+msgstr ""
+"Correcto uso es {:s} -o <settings filename>\n"
 
 #: ../src/bout++.cxx:360
-#, fuzzy, c++-format
+#, c++-format
 msgid "Usage is {} {} <name>\n"
-msgstr "Correcto uso es {:s} -l <log filename>\n"
+msgstr ""
+"Uso: {} {} <nombre>\n"
 
 #: ../tests/unit/src/test_bout++.cxx:32 ../tests/unit/src/test_bout++.cxx:46
 msgid "Usage:"
-msgstr ""
+msgstr "Usage:"
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
 #: ../src/bout++.cxx:374
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
 "[VAR=VALUE]\n"
 msgstr ""
-"Uso: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
-"[VAR=VALUE]\n"
+"Uso: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] [VAR=VALUE]\n"
 
 #. restart file should be written by physics model
 #: ../src/solver/solver.cxx:927
-#, fuzzy
 msgid "User signalled to quit. Returning\n"
-msgstr "Monitor indicó salir\n"
+msgstr ""
+"Monitor indicó salir\n"
 
 #: ../src/sys/options.cxx:486
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} = {:e} is not a bool"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
 #: ../src/sys/options.cxx:426
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
 msgstr "Valor para la opción {:s} = {:e} no es un entero"
 
 #: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
-msgstr ""
+msgstr "El valor de la opción {:s} no se puede convertir a un BoutReal"
 
 #: ../src/sys/options.cxx:623
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
-msgstr "Valor para la opción {:s} = {:e} no es un entero"
+msgstr "El valor de la opción {:s} no se puede convertir a un Field2D"
 
 #: ../src/sys/options.cxx:571
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
-msgstr "Valor para la opción {:s} = {:e} no es un entero"
+msgstr "El valor de la opción {:s} no se puede convertir a un Field3D"
 
 #: ../src/sys/options.cxx:705
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
-msgstr "Valor para la opción {:s} = {:e} no es un entero"
+msgstr "El valor de la opción {:s} no se puede convertir a un FieldPerp"
 
 #: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
-msgstr ""
+msgstr "El valor de la opción {:s} no se puede convertir a un bool"
 
 #: ../src/sys/options.cxx:751
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
-msgstr "Valor para la opción {:s} = {:e} no es un entero"
+msgstr "El valor de la opción {:s} no se puede convertir a un Array<BoutReal>"
 
 #: ../src/sys/options.cxx:773
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
-msgstr "Valor para la opción {:s} = {:e} no es un entero"
+msgstr "El valor de la opción {:s} no se puede convertir a una Matrix<BoutReal>"
 
 #: ../src/sys/options.cxx:795
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
-msgstr "Valor para la opción {:s} = {:e} no es un entero"
+msgstr "El valor de la opción {:s} no se puede convertir a un Tensor<BoutReal>"
 
 #. Another type which can't be converted
 #: ../src/sys/options.cxx:418
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} is not an integer"
-msgstr "Valor para la opción {:s} = {:e} no es un entero"
+msgstr "El valor de la opción {:s} no es un entero"
 
 #: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
-#, fuzzy, c++-format
+#, c++-format
 msgid "Variable '{:s}' not initialised"
 msgstr "Variable '{:s}' sin inicializar"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:467
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
-"WARNING: el número de puntos toroidales debería ser 2^n para una FFT "
-"eficiente -- considere cambiar MZ si se usan FFTs\n"
+"ADVERTENCIA: el número de puntos toroidales debe ser 2^n para un rendimiento eficiente de FFT; considere cambiar MZ ({:d}) si usa FFT\n"
 
 #: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
+"WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 
 #: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
+"WARNING: extrapolating input mesh quantities into x-boundary cells. Set option extrapolate_x=false to disable this.\n"
 
 #: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
+"WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 
 #: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
+"WARNING: extrapolating input mesh quantities into y-boundary cells. Set option extrapolate_y=false to disable this.\n"
 
 #: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
-msgstr ""
+msgstr "Wall time limit in hours. By default (< 0), no limit"
 
 #: ../src/sys/optionsreader.cxx:42
-#, fuzzy, c++-format
+#, c++-format
 msgid "Writing options to file {:s}\n"
-msgstr "Escribiendo opciones a archivo {:s}\n"
+msgstr ""
+"Escribiendo opciones a archivo {:s}\n"
 
 #. / The source label given to default values
 #: ../src/sys/options.cxx:34
diff --git a/locale/fr/libbout.po b/locale/fr/libbout.po
index e9b5476696..8b8ca69328 100644
--- a/locale/fr/libbout.po
+++ b/locale/fr/libbout.po
@@ -23,6 +23,7 @@ msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
+"\t -> région Core jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) doit être un multiple de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:215
 #, c++-format
@@ -30,6 +31,7 @@ msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
+"\t -> région Core jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) doit être un multiple de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:190
 #, c++-format
@@ -37,16 +39,19 @@ msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
+"\t -> région Core jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) doit être un multiple de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
 msgstr ""
+"\t -> Valeur correcte\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:171
 #, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> région Leg jyseps1_1+1 ({:d}) doit être un multiple de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, c++-format
@@ -54,6 +59,7 @@ msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> région leg jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) doit être un multiple de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, c++-format
@@ -61,6 +67,7 @@ msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
+"\t -> région leg ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) doit être un multiple de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, c++-format
@@ -68,21 +75,25 @@ msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> région leg ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) doit être un multiple de MYSUB ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
 msgstr ""
+"\t -> ny/NYPE ({:d}/{:d} = {:d}) doit être >= MYG ({:d})\n"
 
 #: ../src/bout++.cxx:575
 #, c++-format
 msgid "\tADIOS2 support {}\n"
 msgstr ""
+"\tPrise en charge de ADIOS2 {}\n"
 
 #: ../src/bout++.cxx:583
 #, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
+"\tTrace d'appel dans les exceptions {}\n"
 
 #. Loop over all possibilities
 #. Processors divide equally
@@ -92,15 +103,17 @@ msgstr ""
 #, c++-format
 msgid "\tCandidate value: {:d}\n"
 msgstr ""
+"\tValeur candidate : {:d}\n"
 
 #: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
+"\tCouleur dans les journaux {}\n"
 
 #: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
-msgstr ""
+msgstr "\tOptions de ligne de commande pour cette exécution : "
 
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
@@ -108,6 +121,7 @@ msgstr ""
 #, c++-format
 msgid "\tCompiled with flags : {:s}\n"
 msgstr ""
+"\tCompilé avec les options : {:s}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:315
 #, c++-format
@@ -115,16 +129,19 @@ msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
 msgstr ""
+"\tDomaine découpé (NXPE={:d}, NYPE={:d}) en sous-domaines (localNx={:d}, localNy={:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
+"\tERREUR : impossible de répartir {:d} points Y équitablement entre {:d} processeurs\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:365
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
+"\tERREUR : impossible de répartir {:d} points Z équitablement entre {:d} processeurs\n"
 
 #: ../src/sys/options/options_ini.cxx:200
 #, c++-format
@@ -132,39 +149,46 @@ msgid ""
 "\tEmpty key\n"
 "\tLine: {:s}"
 msgstr ""
+"\tClé vide\n"
+"\tLigne : {:s}"
 
 #: ../src/sys/optionsreader.cxx:127
 #, c++-format
 msgid "\tEmpty key or value in command line '{:s}'\n"
 msgstr ""
+"\tClé ou valeur vide dans la ligne de commande '{:s}'\n"
 
 #: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
+"\tSortie de débogage supplémentaire {}\n"
 
 #: ../src/bout++.cxx:568
 #, c++-format
 msgid "\tFFT support {}\n"
 msgstr ""
+"\tPrise en charge de FFT {}\n"
 
 #: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
+"\tSuivi des noms de champ {}\n"
 
 #: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
+"\tExceptions en virgule flottante {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
-msgstr ""
+msgstr "\tTaille de la grille : "
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:499
 msgid "\tGuard cells (x,y,z): "
-msgstr ""
+msgstr "\tCellules de garde (x,y,z) : "
 
 #: ../src/sys/options/options_ini.cxx:204
 #, c++-format
@@ -172,133 +196,157 @@ msgid ""
 "\tKey must not contain ':' character\n"
 "\tLine: {:s}"
 msgstr ""
+"\tLa clé ne doit pas contenir le caractère ':'\n"
+"\tLigne : {:s}"
 
 #: ../src/bout++.cxx:570
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
+"\tPrise en charge de LAPACK {}\n"
 
 #: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
+"\tPile de messages {}\n"
 
 #: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
+"\tLe mode de métriques est {}\n"
 
 #: ../src/sys/optionsreader.cxx:111
 #, c++-format
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
 msgstr ""
+"\tPlusieurs '=' dans l'argument de ligne de commande '{:s}'\n"
 
 #: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
+"\tPrise en charge des langues naturelles {}\n"
 
 #: ../src/bout++.cxx:574
 #, c++-format
 msgid "\tNetCDF support {}{}\n"
 msgstr ""
+"\tPrise en charge de NetCDF {}{}\n"
 
 #: ../src/bout++.cxx:585
 #, c++-format
 msgid "\tOpenMP parallelisation {}, using {} threads\n"
 msgstr ""
+"\tParallélisation OpenMP {}, avec {} threads\n"
 
 #. Mark the option as used
 #. Option not found
 #: ../include/bout/options.hxx:586 ../include/bout/options.hxx:619
 #: ../include/bout/options.hxx:643 ../include/bout/options.hxx:896
 msgid "\tOption "
-msgstr ""
+msgstr "\tOption "
 
 #: ../src/sys/options.cxx:369
 #, c++-format
 msgid "\tOption {} = {}"
-msgstr ""
+msgstr "\tOption {} = {}"
 
 #: ../src/sys/options/options_ini.cxx:70
 #, c++-format
 msgid "\tOptions file '{:s}' not found\n"
 msgstr ""
+"\tFichier d'options '{:s}' introuvable\n"
 
 #: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
+"\tPrise en charge de PETSc {}\n"
 
 #: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
+"\tPrise en charge de PVODE {}\n"
 
 #: ../src/bout++.cxx:564
 msgid "\tParallel NetCDF support disabled\n"
 msgstr ""
+"\tPrise en charge de NetCDF parallèle désactivée\n"
 
 #: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
 msgstr ""
+"\tPrise en charge de NetCDF parallèle activée\n"
 
 #: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
+"\tPrise en charge des noms de fonctions détaillés {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
 msgstr ""
+"\tnz lu depuis le fichier de grille d'entrée\n"
 
 #: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
-msgstr ""
+msgstr "\tLecture du vecteur contravariant "
 
 #: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
-msgstr ""
+msgstr "\tLecture du vecteur covariant "
 
 #: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
-msgstr ""
+msgstr "\tVérification des erreurs à l'exécution {}"
 
 #: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
+"\tPrise en charge de SLEPc {}\n"
 
 #: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
+"\tPrise en charge de SUNDIALS {}\n"
 
 #: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
+"\tPrise en charge de Score-P {}\n"
 
 #: ../src/bout++.cxx:589
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tSignal handling support {}\n"
-msgstr "\tTraitement du signal désactivé\n"
+msgstr ""
+"\tPrise en charge de la gestion des signaux {}\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:76
 #, c++-format
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
+"\tUtilisation d'un pas de temps {:e}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
 msgstr ""
+"\tterminé\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:41
 msgid ""
 "\n"
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
+"\n"
+"\tSolveur fractionné Runge-Kutta-Legendre et SSP-RK3\n"
 
 #: ../src/bout++.cxx:378
 msgid ""
@@ -310,6 +358,13 @@ msgid ""
 "  -v, --verbose\t\t\tIncrease verbosity\n"
 "  -q, --quiet\t\t\tDecrease verbosity\n"
 msgstr ""
+"\n"
+"  -d <répertoire des données>\t\tChercher les fichiers d'entrée/sortie dans <répertoire des données>\n"
+"  -f <nom du fichier d'options>\t\tUtiliser les OPTIONS indiquées dans <nom du fichier d'options>\n"
+"  -o <nom du fichier de paramètres>\tEnregistrer les OPTIONS utilisées dans <nom du fichier d'options>\n"
+"  -l, --log <nom du fichier journal>\tÉcrire le journal dans <nom du fichier journal>\n"
+"  -v, --verbose\t\t\tAugmenter la verbosité\n"
+"  -q, --quiet\t\t\tRéduire la verbosité\n"
 
 #: ../src/sys/expressionparser.cxx:341
 #, c++-format
@@ -318,24 +373,27 @@ msgid ""
 "  {1: ^{2}}{0}\n"
 "  Did you mean '{0}'?"
 msgstr ""
+"\n"
+"  {1: ^{2}}{0}\n"
+"  Vouliez-vous dire '{0}' ?"
 
 #: ../src/solver/solver.cxx:586
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run finished at  : {:s}\n"
 msgstr ""
 "\n"
-"L'exécution se termine à {:s}\n"
+"Exécution terminée à : {:s}\n"
 
 #: ../src/solver/solver.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run started at  : {:s}\n"
 msgstr ""
 "\n"
-"L'exécution se termine à {:s}\n"
+"Exécution démarrée à : {:s}\n"
 
 #. Raw string to help with the formatting of the message, and a
 #. separate variable so clang-format doesn't barf on the
@@ -367,6 +425,31 @@ msgid ""
 "\n"
 "{}"
 msgstr ""
+"\n"
+"Des options d'entrée inutilisées ont été trouvées :\n"
+"-----\n"
+"{:i}\n"
+"-----\n"
+"Il est possible que certaines options aient été mal saisies. Les arguments\n"
+"d'entrée de BOUT++ distinguent désormais les majuscules et les minuscules,\n"
+"et certains ont changé de nom. Vous pouvez essayer d'exécuter\n"
+"\n"
+"    <BOUT++ directory>/bin/bout-v5-input-file-upgrader.py {}/{}\n"
+"\n"
+"afin de corriger automatiquement les problèmes les plus courants. Si les\n"
+"options ci-dessus ne sont utilisées que dans certains cas selon d'autres\n"
+"options, vous pouvez appeler `Options::setConditionallyUsed()`, par exemple :\n"
+"\n"
+"    Options::root()[\"{}\"].setConditionallyUsed();\n"
+"\n"
+"afin de marquer une section ou une valeur comme dépendant d'autres valeurs\n"
+"et de l'ignorer lors de cette vérification. Sinon, si vous êtes certain que\n"
+"les entrées ci-dessus ne sont pas une erreur, vous pouvez définir\n"
+"'input:error_on_unused_options=false' pour désactiver cette vérification des\n"
+"options inutilisées. Vous pouvez également définir 'input:validate=true'\n"
+"pour vérifier les entrées sans lancer la simulation complète.\n"
+"\n"
+"{}"
 
 #: ../src/bout++.cxx:389
 #, c++-format
@@ -400,115 +483,146 @@ msgid ""
 "For all possible input parameters, see the user manual and/or the physics "
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
+"  --print-config\t\tAfficher la configuration de compilation\n"
+"  --list-solvers\t\tLister les solveurs temporels disponibles\n"
+"  --help-solver <solver>\tAfficher l'aide du solveur temporel indiqué\n"
+"  --list-laplacians\t\tLister les solveurs d'inversion laplacienne disponibles\n"
+"  --help-laplacian <laplacian>\tAfficher l'aide du solveur d'inversion laplacienne indiqué\n"
+"  --list-laplacexz\t\tLister les solveurs d'inversion LaplaceXZ disponibles\n"
+"  --help-laplacexz <laplacexz>\tAfficher l'aide du solveur d'inversion LaplaceXZ indiqué\n"
+"  --list-invertpars\t\tLister les solveurs InvertPar disponibles\n"
+"  --help-invertpar <invertpar>\tAfficher l'aide du solveur InvertPar indiqué\n"
+"  --list-rkschemes\t\tLister les schémas de Runge-Kutta disponibles\n"
+"  --help-rkscheme <rkscheme>\tAfficher l'aide du schéma de Runge-Kutta indiqué\n"
+"  --list-meshes\t\t\tLister les maillages disponibles\n"
+"  --help-mesh <mesh>\t\tAfficher l'aide du maillage indiqué\n"
+"  --list-xzinterpolations\tLister les interpolations XZ disponibles\n"
+"  --help-xzinterpolation <xzinterpolation>\tAfficher l'aide de l'interpolation XZ indiquée\n"
+"  --list-zinterpolations\tLister les interpolations Z disponibles\n"
+"  --help-zinterpolation <zinterpolation>\tAfficher l'aide de l'interpolation Z indiquée\n"
+"  -h, --help\t\t\tCe message\n"
+"  restart [append]\t\tRedémarrer la simulation. Si append est indiqué, les données sont ajoutées aux fichiers de sortie existants ; sinon, ils sont écrasés\n"
+"  VAR=VALUE\t\t\tDéfinir VALUE pour le paramètre d'entrée VAR\n"
+"\n"
+"Pour la liste complète des paramètres d'entrée, consultez le manuel utilisateur et/ou la source du modèle physique (p. ex. {:s}.cxx)\n"
 
 #: ../src/bout++.cxx:386
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
 msgstr ""
+"  -c, --color\t\t\tSortie colorée avec bout-log-color\n"
 
 #: ../include/bout/options.hxx:899
 msgid ") overwritten with:"
-msgstr ""
+msgstr ") écrasée par :"
 
 #: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
-msgstr ""
+msgstr ", niveau {}"
 
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
-msgstr ""
+msgstr "4 sur 8"
 
 #: ../src/sys/options.cxx:895
 msgid "All options used\n"
 msgstr ""
+"Toutes les options ont été utilisées\n"
 
 #: ../src/bout++.cxx:535
 #, c++-format
 msgid "BOUT++ version {:s}\n"
 msgstr ""
+"Version de BOUT++ {:s}\n"
 
 #: ../src/bout++.cxx:147
 msgid "Bad command line arguments:\n"
 msgstr ""
+"Arguments de ligne de commande incorrects :\n"
 
 #: ../src/sys/expressionparser.cxx:192
 #, c++-format
 msgid "Boolean operator argument {:e} is not a bool"
-msgstr ""
+msgstr "L'argument {:e} de l'opérateur booléen n'est pas un booléen"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
-msgstr ""
+msgstr "Régions de bord dans ce processeur : "
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:348
 #, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr ""
+"Impossible de répartir {:d} points X équitablement entre {:d} processeurs\n"
 
 #: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
-msgstr ""
+msgstr "Vérifier si un fichier existe, et quitter si c'est le cas."
 
 #: ../src/bout++.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
 "\n"
 msgstr ""
-"Code compilé le {:s} à {:s}\n"
+"Code compilé sur {:s} à {:s}\n"
 "\n"
 
 #: ../src/sys/optionsreader.cxx:130
 msgid "Command line"
-msgstr ""
+msgstr "Ligne de commande"
 
 #: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
 msgstr ""
+"Options de compilation :\n"
 
 #: ../tests/unit/src/test_bout++.cxx:362
 msgid "Compiled with flags"
-msgstr ""
+msgstr "Compilé avec les options"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
-msgstr ""
+msgstr "Construction des régions par défaut"
 
 #: ../src/bout++.cxx:527
 #, c++-format
 msgid "Could not create PID file {:s}"
-msgstr ""
+msgstr "Impossible de créer le fichier PID {:s}"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
-msgstr ""
+msgstr "Impossible de trouver une valeur valide pour NXPE. Essayez un autre nombre de processeurs."
 
 #: ../src/sys/options/options_ini.cxx:160
 #, c++-format
 msgid "Could not open output file '{:s}'\n"
 msgstr ""
+"Impossible d'ouvrir le fichier de sortie '{:s}'\n"
 
 #: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
-msgstr ""
+msgstr "Impossible d'ouvrir {:s}/{:s}.{:d} en écriture"
 
 #. Error reading
 #: ../src/mesh/mesh.cxx:543
 #, c++-format
 msgid "Could not read integer array '{:s}'\n"
 msgstr ""
+"Impossible de lire le tableau d'entiers '{:s}'\n"
 
 #. Failed . Probably not important enough to stop the simulation
 #: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
+"Impossible d'exécuter bout-log-color. Assurez-vous qu'il se trouve dans votre PATH\n"
 
 #: ../src/solver/solver.cxx:772
 #, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
-msgstr ""
+msgstr "Impossible d'ajouter le moniteur : {:g} n'est pas un multiple de {:g} !"
 
 #: ../src/sys/expressionparser.cxx:312
 #, c++-format
@@ -518,137 +632,154 @@ msgid ""
 "may need to change your input file.\n"
 "{}"
 msgstr ""
+"Impossible de trouver le générateur '{}'. Les expressions BOUT++ distinguent désormais les majuscules et les minuscules ;\n"
+"vous devrez peut-être modifier votre fichier d'entrée.\n"
+"{}"
 
 #: ../src/mesh/mesh.cxx:587
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
-msgstr ""
+msgstr "Impossible de trouver la région {:s} dans regionMap2D"
 
 #: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
-msgstr ""
+msgstr "Impossible de trouver la région {:s} dans regionMap3D"
 
 #: ../src/mesh/mesh.cxx:595
 #, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
-msgstr ""
+msgstr "Impossible de trouver la région {:s} dans regionMapPerp"
 
 #. Convert any exceptions to something a bit more useful
 #: ../src/sys/options.cxx:361
 #, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
-msgstr ""
+msgstr "Impossible d'obtenir {} à partir de l'option {:s} = '{:s}' : {}"
 
 #: ../src/bout++.cxx:515
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
 msgstr ""
 "Le répertoire de données \"{:s}\" n'existe pas ou n'est pas accessible\n"
 
 #: ../src/bout++.cxx:512
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
-msgstr "\"{:s}\" n'est pas un répertoire\n"
+msgstr ""
+"Le répertoire de données \"{:s}\" n'est pas un répertoire\n"
 
 #: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
 msgstr ""
+"ERREUR : le solveur est déjà initialisé\n"
 
 #: ../src/bout++.cxx:216
-#, fuzzy, c++-format
+#, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
-msgstr "Erreur rencontrée lors de l'initialisation : {:s}\n"
+msgstr ""
+"Erreur lors de l'initialisation : {:s}\n"
 
 #: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
-msgstr ""
+msgstr "Erreur lors de l'écriture des paramètres"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:323
 #, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
-msgstr ""
+msgstr "Erreur : nx doit être supérieur à 2 fois MXG (2 * {:d})"
 
 #: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
-msgstr "Échec d'initialisation du solutionneur -> Abandonner\n"
+msgstr ""
+"Échec d'initialisation du solutionneur -> Abandonner\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:281
 #, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
 msgstr ""
+"Recherche d'une valeur pour NXPE (idéal = {:f})\n"
 
 #: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
 msgstr ""
+"Initialisation du solveur\n"
 
 #: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
 msgstr ""
+"Les fichiers d'entrée et de sortie des paramètres doivent être différents.\n"
+"Fournissez -o <settings file> pour éviter ce problème.\n"
 
 #: ../src/sys/optionsreader.cxx:76
 msgid "Invalid command line option '-' found - maybe check whitespace?"
-msgstr ""
+msgstr "Option de ligne de commande '-' invalide trouvée ; vérifiez peut-être les espaces"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
-msgstr ""
+msgstr "Chargement de la grille"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:451
 msgid "Mesh must contain nx"
-msgstr ""
+msgstr "La grille doit contenir nx"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:455
 msgid "Mesh must contain ny"
-msgstr ""
+msgstr "La grille doit contenir ny"
 
 #. Not found
 #: ../src/mesh/mesh.cxx:547
 #, c++-format
 msgid "Missing integer array {:s}\n"
 msgstr ""
+"Tableau d'entiers manquant {:s}\n"
 
 #: ../src/solver/solver.cxx:911
 #, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
 msgstr ""
+"Le moniteur a signalé l'arrêt (exception {})\n"
 
 #: ../src/solver/solver.cxx:889
 #, c++-format
 msgid "Monitor signalled to quit (return code {})"
-msgstr ""
+msgstr "Le moniteur a signalé l'arrêt (code de retour {})"
 
 #: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
-msgstr ""
+msgstr "Nom du fichier dont l'existence déclenche un arrêt"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
-msgstr ""
+msgstr "Aucune région de bord dans ce processeur"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:586
 msgid "No boundary regions; domain is periodic\n"
 msgstr ""
+"Aucune région de bord ; le domaine est périodique\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:245
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
 msgstr ""
+"Le nombre de processeurs ({:d}) n'est pas divisible par les NP dans la direction x ({:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:258
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
 msgstr ""
+"Le nombre de processeurs ({:d}) n'est pas divisible par les NP dans la direction y ({:d})\n"
 
 #. Less than 2 time-steps left
 #: ../src/bout++.cxx:908
 #, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
 msgstr ""
+"Il ne reste que {:e} secondes ({:.2f} pas). Arrêt\n"
 
 #: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
 #: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
@@ -656,24 +787,24 @@ msgstr ""
 #: ../src/sys/options.cxx:789
 #, c++-format
 msgid "Option {:s} has no value"
-msgstr ""
+msgstr "L'option {:s} n'a pas de valeur"
 
 #. Doesn't exist
 #: ../src/sys/options.cxx:172
 #, c++-format
 msgid "Option {:s}:{:s} does not exist"
-msgstr ""
+msgstr "L'option {:s}:{:s} n'existe pas"
 
 #: ../include/bout/options.hxx:904
 #, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
 "value was '{:s}'."
-msgstr ""
+msgstr "Options : définition d'une valeur depuis la même source ({:s}) vers la nouvelle valeur '{:s}' - l'ancienne valeur était '{:s}'."
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:588
 msgid "Possible boundary regions are: "
-msgstr ""
+msgstr "Les régions de bord possibles sont : "
 
 #: ../src/bout++.cxx:545
 #, c++-format
@@ -681,26 +812,29 @@ msgid ""
 "Processor number: {:d} of {:d}\n"
 "\n"
 msgstr ""
+"Processeur numéro {:d} sur {:d}\n"
+"\n"
 
 #: ../src/mesh/mesh.cxx:642
 #, c++-format
 msgid "Registered region 2D {:s}"
-msgstr ""
+msgstr "Région 2D enregistrée {:s}"
 
 #: ../src/mesh/mesh.cxx:632
 #, c++-format
 msgid "Registered region 3D {:s}"
-msgstr ""
+msgstr "Région 3D enregistrée {:s}"
 
 #: ../src/mesh/mesh.cxx:652
 #, c++-format
 msgid "Registered region Perp {:s}"
-msgstr ""
+msgstr "Région Perp enregistrée {:s}"
 
 #: ../src/bout++.cxx:536
 #, c++-format
 msgid "Revision: {:s}\n"
 msgstr ""
+"Révision : {:s}\n"
 
 #: ../src/solver/solver.cxx:587
 msgid "Run time : "
@@ -717,13 +851,15 @@ msgstr ""
 
 #: ../tests/unit/src/test_bout++.cxx:359
 msgid "Signal"
-msgstr ""
+msgstr "Signal"
 
 #: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
+"Temps sim. | Eval. RHS  | Temps mur |  Calc  Inv  Comm   E/S  SOLVEUR\n"
+"\n"
 
 #: ../src/bout++.cxx:879
 msgid ""
@@ -731,25 +867,27 @@ msgid ""
 "Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
+"Temps sim. | Eval. RHS_e | Eval. RHS_I | Temps mur |  Calc  Inv  Comm   E/S  SOLVEUR\n"
+"\n"
 
 #: ../src/solver/solver.cxx:514
-#, fuzzy, c++-format
+#, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
-"Le solveur fonctionne pour {:d} sorties avec un temps de moniteur de {:e}\n"
+"Le solveur s'exécute pour {:d} sorties avec un pas de temps de moniteur de {:e}\n"
 
 #: ../src/solver/solver.cxx:510
-#, fuzzy, c++-format
+#, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr ""
-"Le solveur fonctionne pour {:d} sorties avec un pas de sortie de {:e}\n"
+"Le solveur s'exécute pour {:d} sorties avec un pas de temps de sortie de {:e}\n"
 
 #: ../src/solver/solver.cxx:788
 #, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
 "called!"
-msgstr ""
+msgstr "Solver::addMonitor : impossible de réduire le pas de temps (de {:g} à {:g}) après l'appel à init !"
 
 #: ../src/solver/solver.cxx:1289
 #, c++-format
@@ -757,26 +895,27 @@ msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
+"Dérivée temporelle au mauvais emplacement - le champ est à {:s}, la dérivée est à {:s} pour le champ '{:s}'\n"
 
 #: ../src/solver/solver.cxx:1494
 #, c++-format
 msgid "Time derivative for variable '{:s}' not set"
-msgstr ""
+msgstr "La dérivée temporelle de la variable '{:s}' n'est pas définie"
 
 #: ../src/mesh/mesh.cxx:638
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
-msgstr ""
+msgstr "Tentative d'ajout d'une région déjà existante {:s} à regionMap2D"
 
 #: ../src/mesh/mesh.cxx:614
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
-msgstr ""
+msgstr "Tentative d'ajout d'une région déjà existante {:s} à regionMap3D"
 
 #: ../src/mesh/mesh.cxx:649
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
-msgstr ""
+msgstr "Tentative d'ajout d'une région déjà existante {:s} à regionMapPerp"
 
 #: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
 #, c++-format
@@ -786,45 +925,55 @@ msgid ""
 "This is likely the result of clashing input options, and you may have to "
 "rename one of them.\n"
 msgstr ""
+"Tentative d'indexer l'option '{0}' avec '{1}', mais '{0}' est une valeur, pas une section.\n"
+"Ceci est probablement dû à des options d'entrée en conflit, et vous devrez peut-être renommer l'une d'elles.\n"
 
 #: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
 msgstr ""
+"Option paralleltransform non reconnue.\n"
+"Les choix valides sont 'identity', 'shifted', 'fci'"
 
 #: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
 msgstr ""
+"Options inutilisées :\n"
 
 #: ../src/bout++.cxx:446
 #, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
 msgstr ""
+"Utilisation : {:s} -d <répertoire des données>\n"
 
 #: ../src/bout++.cxx:455
 #, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
 msgstr ""
+"Utilisation : {:s} -f <nom du fichier d'options>\n"
 
 #: ../src/bout++.cxx:473
 #, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
 msgstr ""
+"Utilisation : {:s} -l <nom du fichier journal>\n"
 
 #: ../src/bout++.cxx:464
 #, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
 msgstr ""
+"Utilisation : {:s} -o <nom du fichier de paramètres>\n"
 
 #: ../src/bout++.cxx:360
 #, c++-format
 msgid "Usage is {} {} <name>\n"
 msgstr ""
+"Utilisation : {} {} <nom>\n"
 
 #: ../tests/unit/src/test_bout++.cxx:32 ../tests/unit/src/test_bout++.cxx:46
 msgid "Usage:"
-msgstr ""
+msgstr "Utilisation :"
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
@@ -834,72 +983,74 @@ msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
 "[VAR=VALUE]\n"
 msgstr ""
+"Utilisation : {:s} [-d <répertoire des données>] [-f <nom du fichier d'options>] [restart [append]] [VAR=VALUE]\n"
 
 #. restart file should be written by physics model
 #: ../src/solver/solver.cxx:927
 msgid "User signalled to quit. Returning\n"
 msgstr ""
+"L'utilisateur a demandé l'arrêt. Retour\n"
 
 #: ../src/sys/options.cxx:486
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} = {:e} is not a bool"
-msgstr "\"{:s}\" n'est pas un répertoire\n"
+msgstr "La valeur de l'option {:s} = {:e} n'est pas un booléen"
 
 #: ../src/sys/options.cxx:426
 #, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
-msgstr ""
+msgstr "La valeur de l'option {:s} = {:e} n'est pas un entier"
 
 #: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
-msgstr ""
+msgstr "La valeur de l'option {:s} ne peut pas être convertie en BoutReal"
 
 #: ../src/sys/options.cxx:623
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
-msgstr ""
+msgstr "La valeur de l'option {:s} ne peut pas être convertie en Field2D"
 
 #: ../src/sys/options.cxx:571
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
-msgstr ""
+msgstr "La valeur de l'option {:s} ne peut pas être convertie en Field3D"
 
 #: ../src/sys/options.cxx:705
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
-msgstr ""
+msgstr "La valeur de l'option {:s} ne peut pas être convertie en FieldPerp"
 
 #: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
-msgstr ""
+msgstr "La valeur de l'option {:s} ne peut pas être convertie en bool"
 
 #: ../src/sys/options.cxx:751
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
-msgstr ""
+msgstr "La valeur de l'option {:s} ne peut pas être convertie en Array<BoutReal>"
 
 #: ../src/sys/options.cxx:773
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
-msgstr ""
+msgstr "La valeur de l'option {:s} ne peut pas être convertie en Matrix<BoutReal>"
 
 #: ../src/sys/options.cxx:795
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
-msgstr ""
+msgstr "La valeur de l'option {:s} ne peut pas être convertie en Tensor<BoutReal>"
 
 #. Another type which can't be converted
 #: ../src/sys/options.cxx:418
 #, c++-format
 msgid "Value for option {:s} is not an integer"
-msgstr ""
+msgstr "La valeur de l'option {:s} n'est pas un entier"
 
 #: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
 #, c++-format
 msgid "Variable '{:s}' not initialised"
-msgstr ""
+msgstr "La variable '{:s}' n'est pas initialisée"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:467
 #, c++-format
@@ -907,40 +1058,46 @@ msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
+"AVERTISSEMENT : le nombre de points toroïdaux devrait être 2^n pour de bonnes performances FFT ; envisagez de modifier MZ ({:d}) si vous utilisez des FFT\n"
 
 #: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
+"AVERTISSEMENT : extrapolation des quantités de la grille d'entrée dans les cellules de bord x\n"
 
 #: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
+"AVERTISSEMENT : extrapolation des quantités de la grille d'entrée dans les cellules de bord x. Définissez l'option extrapolate_x=false pour désactiver cela.\n"
 
 #: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
+"AVERTISSEMENT : extrapolation des quantités de la grille d'entrée dans les cellules de bord y\n"
 
 #: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
+"AVERTISSEMENT : extrapolation des quantités de la grille d'entrée dans les cellules de bord y. Définissez l'option extrapolate_y=false pour désactiver cela.\n"
 
 #: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
-msgstr ""
+msgstr "Limite de temps mur en heures. Par défaut (< 0), aucune limite"
 
 #: ../src/sys/optionsreader.cxx:42
 #, c++-format
 msgid "Writing options to file {:s}\n"
 msgstr ""
+"Écriture des options dans le fichier {:s}\n"
 
 #. / The source label given to default values
 #: ../src/sys/options.cxx:34
 msgid "default"
-msgstr ""
+msgstr "par défaut"
 
 #~ msgid "\tChecking disabled\n"
 #~ msgstr "\tVérification désactivée\n"
diff --git a/locale/zh_CN/libbout.po b/locale/zh_CN/libbout.po
index ecf8517d62..f735dd1727 100644
--- a/locale/zh_CN/libbout.po
+++ b/locale/zh_CN/libbout.po
@@ -22,6 +22,7 @@ msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
+"\t -> Core 区域 jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) 必须是 MYSUB ({:d}) 的整数倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:215
 #, c++-format
@@ -29,6 +30,7 @@ msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
+"\t -> Core 区域 jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) 必须是 MYSUB ({:d}) 的整数倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:190
 #, c++-format
@@ -36,16 +38,19 @@ msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
+"\t -> Core 区域 jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) 必须是 MYSUB ({:d}) 的整数倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
 msgstr ""
+"\t -> 有效值\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:171
 #, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> Leg 区域 jyseps1_1+1 ({:d}) 必须是 MYSUB ({:d}) 的整数倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, c++-format
@@ -53,6 +58,7 @@ msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> leg 区域 jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) 必须是 MYSUB ({:d}) 的整数倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, c++-format
@@ -60,6 +66,7 @@ msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
+"\t -> leg 区域 ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) 必须是 MYSUB ({:d}) 的整数倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, c++-format
@@ -67,21 +74,25 @@ msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> leg 区域 ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) 必须是 MYSUB ({:d}) 的整数倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
 msgstr ""
+"\t -> ny/NYPE ({:d}/{:d} = {:d}) 必须 >= MYG ({:d})\n"
 
 #: ../src/bout++.cxx:575
 #, c++-format
 msgid "\tADIOS2 support {}\n"
 msgstr ""
+"\tADIOS2 支持 {}\n"
 
 #: ../src/bout++.cxx:583
 #, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
+"\t异常中的回溯 {}\n"
 
 #. Loop over all possibilities
 #. Processors divide equally
@@ -91,15 +102,17 @@ msgstr ""
 #, c++-format
 msgid "\tCandidate value: {:d}\n"
 msgstr ""
+"\t候选值：{:d}\n"
 
 #: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
+"\t日志着色 {}\n"
 
 #: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
-msgstr ""
+msgstr "\t本次运行的命令行选项："
 
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
@@ -107,6 +120,7 @@ msgstr ""
 #, c++-format
 msgid "\tCompiled with flags : {:s}\n"
 msgstr ""
+"\t编译标志：{:s}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:315
 #, c++-format
@@ -114,16 +128,19 @@ msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
 msgstr ""
+"\t域已拆分为 (NXPE={:d}, NYPE={:d})，局部域为 (localNx={:d}, localNy={:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
+"\t错误：无法将 {:d} 个 Y 点平均分给 {:d} 个处理器\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:365
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
+"\t错误：无法将 {:d} 个 Z 点平均分给 {:d} 个处理器\n"
 
 #: ../src/sys/options/options_ini.cxx:200
 #, c++-format
@@ -131,39 +148,46 @@ msgid ""
 "\tEmpty key\n"
 "\tLine: {:s}"
 msgstr ""
+"\t空键\n"
+"\t行：{:s}"
 
 #: ../src/sys/optionsreader.cxx:127
 #, c++-format
 msgid "\tEmpty key or value in command line '{:s}'\n"
 msgstr ""
+"\t命令行中存在空键或空值 '{:s}'\n"
 
 #: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
+"\t额外调试输出 {}\n"
 
 #: ../src/bout++.cxx:568
 #, c++-format
 msgid "\tFFT support {}\n"
 msgstr ""
+"\tFFT 支持 {}\n"
 
 #: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
+"\t字段名跟踪 {}\n"
 
 #: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
+"\t浮点异常 {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
-msgstr ""
+msgstr "\t网格大小："
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:499
 msgid "\tGuard cells (x,y,z): "
-msgstr ""
+msgstr "\t保护单元 (x,y,z)："
 
 #: ../src/sys/options/options_ini.cxx:204
 #, c++-format
@@ -171,41 +195,50 @@ msgid ""
 "\tKey must not contain ':' character\n"
 "\tLine: {:s}"
 msgstr ""
+"\t键中不能包含字符 ':'\n"
+"\t行：{:s}"
 
 #: ../src/bout++.cxx:570
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
+"\tLAPACK 支持 {}\n"
 
 #: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
+"\t消息栈 {}\n"
 
 #: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
+"\t度量模式为 {}\n"
 
 #: ../src/sys/optionsreader.cxx:111
 #, c++-format
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
 msgstr ""
+"\t命令行参数 '{:s}' 中包含多个 '='\n"
 
 #: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
+"\t自然语言支持 {}\n"
 
 #: ../src/bout++.cxx:574
 #, c++-format
 msgid "\tNetCDF support {}{}\n"
 msgstr ""
+"\tNetCDF 支持 {}{}\n"
 
 #: ../src/bout++.cxx:585
 #, c++-format
 msgid "\tOpenMP parallelisation {}, using {} threads\n"
 msgstr ""
+"\tOpenMP 并行化 {}，使用 {} 个线程\n"
 
 #. Mark the option as used
 #. Option not found
@@ -215,89 +248,104 @@ msgid "\tOption "
 msgstr "\t选项 "
 
 #: ../src/sys/options.cxx:369
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOption {} = {}"
-msgstr "\t选项 "
+msgstr "\t选项 {} = {}"
 
 #: ../src/sys/options/options_ini.cxx:70
 #, c++-format
 msgid "\tOptions file '{:s}' not found\n"
 msgstr ""
+"\t未找到选项文件 '{:s}'\n"
 
 #: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
+"\tPETSc 支持 {}\n"
 
 #: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
+"\tPVODE 支持 {}\n"
 
 #: ../src/bout++.cxx:564
 msgid "\tParallel NetCDF support disabled\n"
 msgstr ""
+"\t并行 NetCDF 支持已禁用\n"
 
 #: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
 msgstr ""
+"\t并行 NetCDF 支持已启用\n"
 
 #: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
+"\t详细函数名支持 {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
 msgstr ""
+"\t已从输入网格文件读取 nz\n"
 
 #: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
-msgstr ""
+msgstr "\t正在读取逆变向量 "
 
 #: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
-msgstr ""
+msgstr "\t正在读取协变向量 "
 
 #: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
-msgstr ""
+msgstr "\t运行时错误检查 {}"
 
 #: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
+"\tSLEPc 支持 {}\n"
 
 #: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
+"\tSUNDIALS 支持 {}\n"
 
 #: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
+"\tScore-P 支持 {}\n"
 
 #: ../src/bout++.cxx:589
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tSignal handling support {}\n"
-msgstr "\t测试关掉\n"
+msgstr ""
+"\t信号处理支持 {}\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:76
 #, c++-format
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
+"\t使用时间步长 {:e}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
 msgstr ""
+"\t完成\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:41
 msgid ""
 "\n"
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
+"\n"
+"\tSplit Runge-Kutta-Legendre 与 SSP-RK3 求解器\n"
 
 #: ../src/bout++.cxx:378
 msgid ""
@@ -309,6 +357,13 @@ msgid ""
 "  -v, --verbose\t\t\tIncrease verbosity\n"
 "  -q, --quiet\t\t\tDecrease verbosity\n"
 msgstr ""
+"\n"
+"  -d <数据目录>\t\t在 <数据目录> 中查找输入/输出文件\n"
+"  -f <选项文件名>\t\t使用 <选项文件名> 中给出的 OPTIONS\n"
+"  -o <设置文件名>\t将已使用的 OPTIONS 保存到 <选项文件名>\n"
+"  -l, --log <日志文件名>\t将日志输出到 <日志文件名>\n"
+"  -v, --verbose\t\t\t提高详细程度\n"
+"  -q, --quiet\t\t\t降低详细程度\n"
 
 #: ../src/sys/expressionparser.cxx:341
 #, c++-format
@@ -317,24 +372,27 @@ msgid ""
 "  {1: ^{2}}{0}\n"
 "  Did you mean '{0}'?"
 msgstr ""
+"\n"
+"  {1: ^{2}}{0}\n"
+"  您是不是想写 '{0}'？"
 
 #: ../src/solver/solver.cxx:586
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run finished at  : {:s}\n"
 msgstr ""
 "\n"
-"计算结束于 {:s}\n"
+"运行结束时间：{:s}\n"
 
 #: ../src/solver/solver.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run started at  : {:s}\n"
 msgstr ""
 "\n"
-"计算从 {:s} 开始\n"
+"运行开始时间：{:s}\n"
 
 #. Raw string to help with the formatting of the message, and a
 #. separate variable so clang-format doesn't barf on the
@@ -366,6 +424,28 @@ msgid ""
 "\n"
 "{}"
 msgstr ""
+"\n"
+"发现未使用的输入选项：\n"
+"-----\n"
+"{:i}\n"
+"-----\n"
+"有些选项可能被误拼写了。BOUT++ 的输入参数现在区分大小写，\n"
+"并且其中一些名称已经改变。您可以尝试运行\n"
+"\n"
+"    <BOUT++ directory>/bin/bout-v5-input-file-upgrader.py {}/{}\n"
+"\n"
+"以自动修复最常见的问题。如果上面的这些选项有时会根据其他\n"
+"选项而被使用，您可以调用 `Options::setConditionallyUsed()`，例如：\n"
+"\n"
+"    Options::root()[\"{}\"].setConditionallyUsed();\n"
+"\n"
+"将某个节或值标记为依赖于其他值，从而在这项检查中忽略它。或者，\n"
+"如果您确信以上输入并非错误，可以设置\n"
+"'input:error_on_unused_options=false' 来关闭这项未使用选项检查。\n"
+"您也始终可以设置 'input:validate=true'，在不运行完整模拟的情况下\n"
+"检查输入。\n"
+"\n"
+"{}"
 
 #: ../src/bout++.cxx:389
 #, c++-format
@@ -399,115 +479,146 @@ msgid ""
 "For all possible input parameters, see the user manual and/or the physics "
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
+"  --print-config\t\t显示编译时配置\n"
+"  --list-solvers\t\t列出可用的时间求解器\n"
+"  --help-solver <solver>\t显示指定时间求解器的帮助\n"
+"  --list-laplacians\t\t列出可用的拉普拉斯反演求解器\n"
+"  --help-laplacian <laplacian>\t显示指定拉普拉斯反演求解器的帮助\n"
+"  --list-laplacexz\t\t列出可用的 LaplaceXZ 反演求解器\n"
+"  --help-laplacexz <laplacexz>\t显示指定 LaplaceXZ 反演求解器的帮助\n"
+"  --list-invertpars\t\t列出可用的 InvertPar 求解器\n"
+"  --help-invertpar <invertpar>\t显示指定 InvertPar 求解器的帮助\n"
+"  --list-rkschemes\t\t列出可用的 Runge-Kutta 格式\n"
+"  --help-rkscheme <rkscheme>\t显示指定 Runge-Kutta 格式的帮助\n"
+"  --list-meshes\t\t\t列出可用的 Mesh\n"
+"  --help-mesh <mesh>\t\t显示指定 Mesh 的帮助\n"
+"  --list-xzinterpolations\t列出可用的 XZInterpolation\n"
+"  --help-xzinterpolation <xzinterpolation>\t显示指定 XZInterpolation 的帮助\n"
+"  --list-zinterpolations\t列出可用的 ZInterpolation\n"
+"  --help-zinterpolation <zinterpolation>\t显示指定 ZInterpolation 的帮助\n"
+"  -h, --help\t\t\t此消息\n"
+"  restart [append]\t\t重新启动模拟。若指定 append，则追加到现有输出文件，否则覆盖它们\n"
+"  VAR=VALUE\t\t\t为输入参数 VAR 指定一个 VALUE\n"
+"\n"
+"有关所有可能的输入参数，请参阅用户手册和/或物理模型源码（例如 {:s}.cxx）\n"
 
 #: ../src/bout++.cxx:386
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
 msgstr ""
+"  -c, --color\t\t\t使用 bout-log-color 输出彩色日志\n"
 
 #: ../include/bout/options.hxx:899
 msgid ") overwritten with:"
-msgstr ""
+msgstr ") 被覆盖为："
 
 #: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
-msgstr ""
+msgstr ", 级别 {}"
 
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
-msgstr ""
+msgstr "4 / 8"
 
 #: ../src/sys/options.cxx:895
 msgid "All options used\n"
 msgstr ""
+"所有选项均已使用\n"
 
 #: ../src/bout++.cxx:535
 #, c++-format
 msgid "BOUT++ version {:s}\n"
 msgstr ""
+"BOUT++ 版本 {:s}\n"
 
 #: ../src/bout++.cxx:147
 msgid "Bad command line arguments:\n"
 msgstr ""
+"错误的命令行参数：\n"
 
 #: ../src/sys/expressionparser.cxx:192
 #, c++-format
 msgid "Boolean operator argument {:e} is not a bool"
-msgstr ""
+msgstr "布尔运算符参数 {:e} 不是布尔值"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
-msgstr ""
+msgstr "该处理器中的边界区域："
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:348
 #, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr ""
+"无法将 {:d} 个 X 点平均分配给 {:d} 个处理器\n"
 
 #: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
-msgstr ""
+msgstr "检查文件是否存在，若存在则退出。"
 
 #: ../src/bout++.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
 "\n"
 msgstr ""
-"代码于 {:s} {:s} 编译\n"
+"代码编译于 {:s}，时间 {:s}\n"
 "\n"
 
 #: ../src/sys/optionsreader.cxx:130
 msgid "Command line"
-msgstr ""
+msgstr "命令行"
 
 #: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
 msgstr ""
+"编译时选项：\n"
 
 #: ../tests/unit/src/test_bout++.cxx:362
 msgid "Compiled with flags"
-msgstr ""
+msgstr "编译标志"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
-msgstr ""
+msgstr "正在构建默认区域"
 
 #: ../src/bout++.cxx:527
 #, c++-format
 msgid "Could not create PID file {:s}"
-msgstr ""
+msgstr "无法创建 PID 文件 {:s}"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
 "Could not find a valid value for NXPE. Try a different number of processors."
-msgstr ""
+msgstr "无法为 NXPE 找到有效值。请尝试使用不同数量的处理器。"
 
 #: ../src/sys/options/options_ini.cxx:160
 #, c++-format
 msgid "Could not open output file '{:s}'\n"
 msgstr ""
+"无法打开输出文件 '{:s}'\n"
 
 #: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
-msgstr ""
+msgstr "无法打开 {:s}/{:s}.{:d} 进行写入"
 
 #. Error reading
 #: ../src/mesh/mesh.cxx:543
 #, c++-format
 msgid "Could not read integer array '{:s}'\n"
 msgstr ""
+"无法读取整数数组 '{:s}'\n"
 
 #. Failed . Probably not important enough to stop the simulation
 #: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
+"无法运行 bout-log-color。请确认它在您的 PATH 中\n"
 
 #: ../src/solver/solver.cxx:772
 #, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
-msgstr ""
+msgstr "无法添加监视器：{:g} 不是 {:g} 的整数倍！"
 
 #: ../src/sys/expressionparser.cxx:312
 #, c++-format
@@ -517,136 +628,154 @@ msgid ""
 "may need to change your input file.\n"
 "{}"
 msgstr ""
+"无法找到生成器 '{}'。BOUT++ 表达式现在区分大小写，因此\n"
+"您可能需要修改输入文件。\n"
+"{}"
 
 #: ../src/mesh/mesh.cxx:587
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
-msgstr ""
+msgstr "无法在 regionMap2D 中找到区域 {:s}"
 
 #: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
-msgstr ""
+msgstr "无法在 regionMap3D 中找到区域 {:s}"
 
 #: ../src/mesh/mesh.cxx:595
 #, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
-msgstr ""
+msgstr "无法在 regionMapPerp 中找到区域 {:s}"
 
 #. Convert any exceptions to something a bit more useful
 #: ../src/sys/options.cxx:361
 #, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
-msgstr ""
+msgstr "无法从选项 {1:s} = '{2:s}' 获取 {0}：{3}"
 
 #: ../src/bout++.cxx:515
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
-msgstr "\"{:s}\" 不存在或不可访问\n"
+msgstr ""
+"数据目录 \"{:s}\" 不存在或不可访问\n"
 
 #: ../src/bout++.cxx:512
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
-msgstr "\"{:s}\" 不是目录\n"
+msgstr ""
+"数据目录 \"{:s}\" 不是目录\n"
 
 #: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
 msgstr ""
+"错误：求解器已经初始化\n"
 
 #: ../src/bout++.cxx:216
-#, fuzzy, c++-format
+#, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
-msgstr "启动时遇到错误 : {:s}\n"
+msgstr ""
+"初始化期间发生错误：{:s}\n"
 
 #: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
-msgstr ""
+msgstr "写入设置时发生错误"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:323
 #, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
-msgstr ""
+msgstr "错误：nx 必须大于 2 倍 MXG（2 * {:d}）"
 
 #: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
 msgstr ""
+"求解器初始化失败 -> 中止\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:281
 #, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
 msgstr ""
+"正在查找 NXPE 的值（理想值 = {:f}）\n"
 
 #: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
 msgstr ""
+"正在初始化求解器\n"
 
 #: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
 msgstr ""
+"设置的输入文件和输出文件必须不同。\n"
+"请提供 -o <settings file> 以避免此问题。\n"
 
 #: ../src/sys/optionsreader.cxx:76
 msgid "Invalid command line option '-' found - maybe check whitespace?"
-msgstr ""
+msgstr "发现无效的命令行选项 '-'，也许应检查空白字符？"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
-msgstr ""
+msgstr "正在加载网格"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:451
 msgid "Mesh must contain nx"
-msgstr ""
+msgstr "网格必须包含 nx"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:455
 msgid "Mesh must contain ny"
-msgstr ""
+msgstr "网格必须包含 ny"
 
 #. Not found
 #: ../src/mesh/mesh.cxx:547
 #, c++-format
 msgid "Missing integer array {:s}\n"
 msgstr ""
+"缺少整数数组 {:s}\n"
 
 #: ../src/solver/solver.cxx:911
 #, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
 msgstr ""
+"监视器发出退出信号（异常 {}）\n"
 
 #: ../src/solver/solver.cxx:889
 #, c++-format
 msgid "Monitor signalled to quit (return code {})"
-msgstr ""
+msgstr "监视器发出退出信号（返回码 {}）"
 
 #: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
-msgstr ""
+msgstr "触发停止的文件名"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
-msgstr ""
+msgstr "该处理器中没有边界区域"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:586
 msgid "No boundary regions; domain is periodic\n"
 msgstr ""
+"没有边界区域；区域是周期性的\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:245
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
 msgstr ""
+"处理器数量 ({:d}) 不能被 x 方向上的 NP 数 ({:d}) 整除\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:258
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
 msgstr ""
+"处理器数量 ({:d}) 不能被 y 方向上的 NP 数 ({:d}) 整除\n"
 
 #. Less than 2 time-steps left
 #: ../src/bout++.cxx:908
 #, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
 msgstr ""
+"只剩 {:e} 秒（{:.2f} 步）。正在退出\n"
 
 #: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
 #: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
@@ -654,24 +783,24 @@ msgstr ""
 #: ../src/sys/options.cxx:789
 #, c++-format
 msgid "Option {:s} has no value"
-msgstr ""
+msgstr "选项 {:s} 没有值"
 
 #. Doesn't exist
 #: ../src/sys/options.cxx:172
 #, c++-format
 msgid "Option {:s}:{:s} does not exist"
-msgstr ""
+msgstr "选项 {:s}:{:s} 不存在"
 
 #: ../include/bout/options.hxx:904
 #, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
 "value was '{:s}'."
-msgstr ""
+msgstr "选项：正在将来自同一来源 ({:s}) 的值设置为新值 '{:s}'，旧值为 '{:s}'。"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:588
 msgid "Possible boundary regions are: "
-msgstr ""
+msgstr "可能的边界区域有："
 
 #: ../src/bout++.cxx:545
 #, c++-format
@@ -679,26 +808,29 @@ msgid ""
 "Processor number: {:d} of {:d}\n"
 "\n"
 msgstr ""
+"处理器编号：{:d} / {:d}\n"
+"\n"
 
 #: ../src/mesh/mesh.cxx:642
 #, c++-format
 msgid "Registered region 2D {:s}"
-msgstr ""
+msgstr "已注册 2D 区域 {:s}"
 
 #: ../src/mesh/mesh.cxx:632
 #, c++-format
 msgid "Registered region 3D {:s}"
-msgstr ""
+msgstr "已注册 3D 区域 {:s}"
 
 #: ../src/mesh/mesh.cxx:652
 #, c++-format
 msgid "Registered region Perp {:s}"
-msgstr ""
+msgstr "已注册 Perp 区域 {:s}"
 
 #: ../src/bout++.cxx:536
 #, c++-format
 msgid "Revision: {:s}\n"
 msgstr ""
+"修订版本：{:s}\n"
 
 #: ../src/solver/solver.cxx:587
 msgid "Run time : "
@@ -715,13 +847,15 @@ msgstr ""
 
 #: ../tests/unit/src/test_bout++.cxx:359
 msgid "Signal"
-msgstr ""
+msgstr "信号"
 
 #: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
+"模拟时间 | RHS 次数 | 墙钟时间 | 计算 反演 通信 I/O 求解器\n"
+"\n"
 
 #: ../src/bout++.cxx:879
 msgid ""
@@ -729,23 +863,27 @@ msgid ""
 "Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
+"模拟时间 | RHS_e 次数 | RHS_I 次数 | 墙钟时间 | 计算 反演 通信 I/O 求解器\n"
+"\n"
 
 #: ../src/solver/solver.cxx:514
 #, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
+"求解器正在运行 {:d} 个输出，监视步长为 {:e}\n"
 
 #: ../src/solver/solver.cxx:510
 #, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr ""
+"求解器正在运行 {:d} 个输出，输出步长为 {:e}\n"
 
 #: ../src/solver/solver.cxx:788
 #, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
 "called!"
-msgstr ""
+msgstr "Solver::addMonitor：在调用 init 之后无法将时间步长从 {:g} 减少到 {:g}！"
 
 #: ../src/solver/solver.cxx:1289
 #, c++-format
@@ -753,26 +891,27 @@ msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
+"时间导数位于错误位置 - 字段位于 {:s}，导数位于 {:s}，对应字段 '{:s}'\n"
 
 #: ../src/solver/solver.cxx:1494
 #, c++-format
 msgid "Time derivative for variable '{:s}' not set"
-msgstr ""
+msgstr "变量 '{:s}' 的时间导数尚未设置"
 
 #: ../src/mesh/mesh.cxx:638
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
-msgstr ""
+msgstr "试图将已存在的区域 {:s} 添加到 regionMap2D"
 
 #: ../src/mesh/mesh.cxx:614
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
-msgstr ""
+msgstr "试图将已存在的区域 {:s} 添加到 regionMap3D"
 
 #: ../src/mesh/mesh.cxx:649
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
-msgstr ""
+msgstr "试图将已存在的区域 {:s} 添加到 regionMapPerp"
 
 #: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
 #, c++-format
@@ -782,45 +921,55 @@ msgid ""
 "This is likely the result of clashing input options, and you may have to "
 "rename one of them.\n"
 msgstr ""
+"正在尝试用 '{1}' 索引选项 '{0}'，但 '{0}' 是一个值，而不是一个节。\n"
+"这很可能是输入选项冲突导致的，您可能需要重命名其中之一。\n"
 
 #: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
 msgstr ""
+"无法识别的 paralleltransform 选项。\n"
+"有效选项为 'identity'、'shifted'、'fci'"
 
 #: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
 msgstr ""
+"未使用的选项：\n"
 
 #: ../src/bout++.cxx:446
 #, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
 msgstr ""
+"用法：{:s} -d <数据目录>\n"
 
 #: ../src/bout++.cxx:455
 #, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
 msgstr ""
+"用法：{:s} -f <选项文件名>\n"
 
 #: ../src/bout++.cxx:473
 #, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
 msgstr ""
+"用法：{:s} -l <日志文件名>\n"
 
 #: ../src/bout++.cxx:464
 #, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
 msgstr ""
+"用法：{:s} -o <设置文件名>\n"
 
 #: ../src/bout++.cxx:360
 #, c++-format
 msgid "Usage is {} {} <name>\n"
 msgstr ""
+"用法：{} {} <名称>\n"
 
 #: ../tests/unit/src/test_bout++.cxx:32 ../tests/unit/src/test_bout++.cxx:46
 msgid "Usage:"
-msgstr ""
+msgstr "用法："
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
@@ -830,72 +979,74 @@ msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
 "[VAR=VALUE]\n"
 msgstr ""
+"用法：{:s} [-d <数据目录>] [-f <选项文件名>] [restart [append]] [VAR=VALUE]\n"
 
 #. restart file should be written by physics model
 #: ../src/solver/solver.cxx:927
 msgid "User signalled to quit. Returning\n"
 msgstr ""
+"用户发出退出信号。正在返回\n"
 
 #: ../src/sys/options.cxx:486
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} = {:e} is not a bool"
-msgstr "\"{:s}\" 不是目录\n"
+msgstr "选项 {:s} = {:e} 的值不是布尔值"
 
 #: ../src/sys/options.cxx:426
 #, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
-msgstr ""
+msgstr "选项 {:s} = {:e} 的值不是整数"
 
 #: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
-msgstr ""
+msgstr "选项 {:s} 的值无法转换为 BoutReal"
 
 #: ../src/sys/options.cxx:623
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
-msgstr ""
+msgstr "选项 {:s} 的值无法转换为 Field2D"
 
 #: ../src/sys/options.cxx:571
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
-msgstr ""
+msgstr "选项 {:s} 的值无法转换为 Field3D"
 
 #: ../src/sys/options.cxx:705
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
-msgstr ""
+msgstr "选项 {:s} 的值无法转换为 FieldPerp"
 
 #: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
-msgstr ""
+msgstr "选项 {:s} 的值无法转换为 bool"
 
 #: ../src/sys/options.cxx:751
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
-msgstr ""
+msgstr "选项 {:s} 的值无法转换为 Array<BoutReal>"
 
 #: ../src/sys/options.cxx:773
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
-msgstr ""
+msgstr "选项 {:s} 的值无法转换为 Matrix<BoutReal>"
 
 #: ../src/sys/options.cxx:795
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
-msgstr ""
+msgstr "选项 {:s} 的值无法转换为 Tensor<BoutReal>"
 
 #. Another type which can't be converted
 #: ../src/sys/options.cxx:418
 #, c++-format
 msgid "Value for option {:s} is not an integer"
-msgstr ""
+msgstr "选项 {:s} 的值不是整数"
 
 #: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
 #, c++-format
 msgid "Variable '{:s}' not initialised"
-msgstr ""
+msgstr "变量 '{:s}' 尚未初始化"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:467
 #, c++-format
@@ -903,40 +1054,46 @@ msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
+"警告：为了获得高效的 FFT 性能，环向点数应为 2^n；如果使用 FFT，请考虑修改 MZ ({:d})\n"
 
 #: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
+"警告：正在将输入网格量外推到 x 边界单元\n"
 
 #: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
+"警告：正在将输入网格量外推到 x 边界单元。设置选项 extrapolate_x=false 可禁用此行为。\n"
 
 #: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
+"警告：正在将输入网格量外推到 y 边界单元\n"
 
 #: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
+"警告：正在将输入网格量外推到 y 边界单元。设置选项 extrapolate_y=false 可禁用此行为。\n"
 
 #: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
-msgstr ""
+msgstr "墙钟时间限制（小时）。默认值（< 0）表示不限制"
 
 #: ../src/sys/optionsreader.cxx:42
 #, c++-format
 msgid "Writing options to file {:s}\n"
 msgstr ""
+"正在将选项写入文件 {:s}\n"
 
 #. / The source label given to default values
 #: ../src/sys/options.cxx:34
 msgid "default"
-msgstr ""
+msgstr "默认"
 
 #~ msgid "\tChecking disabled\n"
 #~ msgstr "\t测试关掉\n"
diff --git a/locale/zh_TW/libbout.po b/locale/zh_TW/libbout.po
index abf44db51f..8b79978d95 100644
--- a/locale/zh_TW/libbout.po
+++ b/locale/zh_TW/libbout.po
@@ -22,6 +22,7 @@ msgid ""
 "\t -> Core region jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
+"\t -> Core 區域 jyseps2_1-jyseps1_1 ({:d}-{:d} = {:d}) 必須是 MYSUB ({:d}) 的整數倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:215
 #, c++-format
@@ -29,6 +30,7 @@ msgid ""
 "\t -> Core region jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
+"\t -> Core 區域 jyseps2_2-jyseps1_1 ({:d}-{:d} = {:d}) 必須是 MYSUB ({:d}) 的整數倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:190
 #, c++-format
@@ -36,16 +38,19 @@ msgid ""
 "\t -> Core region jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) must be a multiple "
 "of MYSUB ({:d})\n"
 msgstr ""
+"\t -> Core 區域 jyseps2_2-jyseps1_2 ({:d}-{:d} = {:d}) 必須是 MYSUB ({:d}) 的整數倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:300
 msgid "\t -> Good value\n"
-msgstr "\t -> 好的號碼\n"
+msgstr ""
+"\t -> 好的號碼\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:171
 #, c++-format
 msgid ""
 "\t -> Leg region jyseps1_1+1 ({:d}) must be a multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> Leg 區域 jyseps1_1+1 ({:d}) 必須是 MYSUB ({:d}) 的整數倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:206
 #, c++-format
@@ -53,6 +58,7 @@ msgid ""
 "\t -> leg region jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> leg 區域 jyseps1_2-ny_inner+1 ({:d}-{:d}+1 = {:d}) 必須是 MYSUB ({:d}) 的整數倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:223
 #, c++-format
@@ -60,6 +66,7 @@ msgid ""
 "\t -> leg region ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) must be a multiple of "
 "MYSUB ({:d})\n"
 msgstr ""
+"\t -> leg 區域 ny-jyseps2_2-1 ({:d}-{:d}-1 = {:d}) 必須是 MYSUB ({:d}) 的整數倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:199
 #, c++-format
@@ -67,63 +74,73 @@ msgid ""
 "\t -> leg region ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) must be a "
 "multiple of MYSUB ({:d})\n"
 msgstr ""
+"\t -> leg 區域 ny_inner-jyseps2_1-1 ({:d}-{:d}-1 = {:d}) 必須是 MYSUB ({:d}) 的整數倍\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:166
 #, c++-format
 msgid "\t -> ny/NYPE ({:d}/{:d} = {:d}) must be >= MYG ({:d})\n"
 msgstr ""
+"\t -> ny/NYPE ({:d}/{:d} = {:d}) 必須 >= MYG ({:d})\n"
 
 #: ../src/bout++.cxx:575
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tADIOS2 support {}\n"
-msgstr "\tOpenMP並行化已禁用\n"
+msgstr ""
+"\tADIOS2 支援 {}\n"
 
 #: ../src/bout++.cxx:583
 #, c++-format
 msgid "\tBacktrace in exceptions {}\n"
 msgstr ""
+"\t例外中的回溯 {}\n"
 
 #. Loop over all possibilities
 #. Processors divide equally
 #. Mesh in X divides equally
 #. Mesh in Y divides equally
 #: ../src/mesh/impls/bout/boutmesh.cxx:288
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tCandidate value: {:d}\n"
-msgstr "\t候選人數目 {:d}\n"
+msgstr ""
+"\t候選值：{:d}\n"
 
 #: ../src/bout++.cxx:584
 #, c++-format
 msgid "\tColour in logs {}\n"
 msgstr ""
+"\t日誌著色 {}\n"
 
 #: ../src/bout++.cxx:599
 msgid "\tCommand line options for this run : "
-msgstr ""
+msgstr "\t本次執行的命令列選項："
 
 #. The stringify is needed here as BOUT_FLAGS_STRING may already contain quoted strings
 #. which could cause problems (e.g. terminate strings).
 #: ../src/bout++.cxx:595
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tCompiled with flags : {:s}\n"
-msgstr "\t用設置編譯: {:s}\n"
+msgstr ""
+"\t編譯旗標：{:s}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:315
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\tDomain split (NXPE={:d}, NYPE={:d}) into domains (localNx={:d}, "
 "localNy={:d})\n"
-msgstr "\t域 (NXPE={:d}, NYPE={:d}) 分裂成域 (localNx={:d}, localNy={:d})\n"
+msgstr ""
+"\t網域已拆分為 (NXPE={:d}, NYPE={:d})，局部網域為 (localNx={:d}, localNy={:d})\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:357
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Y points equally between {:d} processors\n"
 msgstr ""
+"\t錯誤：無法將 {:d} 個 Y 點平均分配給 {:d} 個處理器\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:365
 #, c++-format
 msgid "\tERROR: Cannot split {:d} Z points equally between {:d} processors\n"
 msgstr ""
+"\t錯誤：無法將 {:d} 個 Z 點平均分配給 {:d} 個處理器\n"
 
 #: ../src/sys/options/options_ini.cxx:200
 #, c++-format
@@ -131,31 +148,38 @@ msgid ""
 "\tEmpty key\n"
 "\tLine: {:s}"
 msgstr ""
+"\t空鍵\n"
+"\t行：{:s}"
 
 #: ../src/sys/optionsreader.cxx:127
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tEmpty key or value in command line '{:s}'\n"
-msgstr "\t命令行中的空鍵或值 '{:s}'\n"
+msgstr ""
+"\t命令列中存在空鍵或空值 '{:s}'\n"
 
 #: ../src/bout++.cxx:587
 #, c++-format
 msgid "\tExtra debug output {}\n"
 msgstr ""
+"\t額外除錯輸出 {}\n"
 
 #: ../src/bout++.cxx:568
 #, c++-format
 msgid "\tFFT support {}\n"
 msgstr ""
+"\tFFT 支援 {}\n"
 
 #: ../src/bout++.cxx:590
 #, c++-format
 msgid "\tField name tracking {}\n"
 msgstr ""
+"\t欄位名稱追蹤 {}\n"
 
 #: ../src/bout++.cxx:588
 #, c++-format
 msgid "\tFloating-point exceptions {}\n"
 msgstr ""
+"\t浮點例外 {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:476
 msgid "\tGrid size: "
@@ -163,7 +187,7 @@ msgstr "\t網格大小: "
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:499
 msgid "\tGuard cells (x,y,z): "
-msgstr ""
+msgstr "\t保護單元 (x,y,z)："
 
 #: ../src/sys/options/options_ini.cxx:204
 #, c++-format
@@ -171,41 +195,50 @@ msgid ""
 "\tKey must not contain ':' character\n"
 "\tLine: {:s}"
 msgstr ""
+"\t鍵中不可包含字元 ':'\n"
+"\t行：{:s}"
 
 #: ../src/bout++.cxx:570
 #, c++-format
 msgid "\tLAPACK support {}\n"
 msgstr ""
+"\tLAPACK 支援 {}\n"
 
 #: ../src/bout++.cxx:591
 #, c++-format
 msgid "\tMessage stack {}\n"
 msgstr ""
+"\t訊息堆疊 {}\n"
 
 #: ../src/bout++.cxx:567
 #, c++-format
 msgid "\tMetrics mode is {}\n"
 msgstr ""
+"\t度量模式為 {}\n"
 
 #: ../src/sys/optionsreader.cxx:111
 #, c++-format
 msgid "\tMultiple '=' in command-line argument '{:s}'\n"
 msgstr ""
+"\t命令列參數 '{:s}' 中包含多個 '='\n"
 
 #: ../src/bout++.cxx:569
 #, c++-format
 msgid "\tNatural language support {}\n"
 msgstr ""
+"\t自然語言支援 {}\n"
 
 #: ../src/bout++.cxx:574
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tNetCDF support {}{}\n"
-msgstr "\tOpenMP並行化已禁用\n"
+msgstr ""
+"\tNetCDF 支援 {}{}\n"
 
 #: ../src/bout++.cxx:585
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOpenMP parallelisation {}, using {} threads\n"
-msgstr "\t啟用OpenMP並行化。 使用{:d}個線程\n"
+msgstr ""
+"\tOpenMP 平行化 {}，使用 {} 個執行緒\n"
 
 #. Mark the option as used
 #. Option not found
@@ -215,90 +248,104 @@ msgid "\tOption "
 msgstr "\t選項 "
 
 #: ../src/sys/options.cxx:369
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOption {} = {}"
-msgstr "\t選項 "
+msgstr "\t選項 {} = {}"
 
 #: ../src/sys/options/options_ini.cxx:70
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tOptions file '{:s}' not found\n"
-msgstr "\t找不到選項文件 '{:s}'\n"
+msgstr ""
+"\t找不到選項檔案 '{:s}'\n"
 
 #: ../src/bout++.cxx:576
 #, c++-format
 msgid "\tPETSc support {}\n"
 msgstr ""
+"\tPETSc 支援 {}\n"
 
 #: ../src/bout++.cxx:579
 #, c++-format
 msgid "\tPVODE support {}\n"
 msgstr ""
+"\tPVODE 支援 {}\n"
 
 #: ../src/bout++.cxx:564
-#, fuzzy
 msgid "\tParallel NetCDF support disabled\n"
-msgstr "\tOpenMP並行化已禁用\n"
+msgstr ""
+"\t平行 NetCDF 支援已停用\n"
 
 #: ../src/bout++.cxx:562
 msgid "\tParallel NetCDF support enabled\n"
 msgstr ""
+"\t平行 NetCDF 支援已啟用\n"
 
 #: ../src/bout++.cxx:577
 #, c++-format
 msgid "\tPretty function name support {}\n"
 msgstr ""
+"\t詳細函式名稱支援 {}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:473
 msgid "\tRead nz from input grid file\n"
 msgstr ""
+"\t已從輸入網格檔案讀取 nz\n"
 
 #: ../src/mesh/mesh.cxx:249
 msgid "\tReading contravariant vector "
-msgstr ""
+msgstr "\t正在讀取逆變向量 "
 
 #: ../src/mesh/mesh.cxx:242 ../src/mesh/mesh.cxx:263
 msgid "\tReading covariant vector "
-msgstr ""
+msgstr "\t正在讀取協變向量 "
 
 #: ../src/bout++.cxx:555
 #, c++-format
 msgid "\tRuntime error checking {}"
-msgstr ""
+msgstr "\t執行期錯誤檢查 {}"
 
 #: ../src/bout++.cxx:581
 #, c++-format
 msgid "\tSLEPc support {}\n"
 msgstr ""
+"\tSLEPc 支援 {}\n"
 
 #: ../src/bout++.cxx:582
 #, c++-format
 msgid "\tSUNDIALS support {}\n"
 msgstr ""
+"\tSUNDIALS 支援 {}\n"
 
 #: ../src/bout++.cxx:580
 #, c++-format
 msgid "\tScore-P support {}\n"
 msgstr ""
+"\tScore-P 支援 {}\n"
 
 #: ../src/bout++.cxx:589
-#, fuzzy, c++-format
+#, c++-format
 msgid "\tSignal handling support {}\n"
-msgstr "\t測試關掉\n"
+msgstr ""
+"\t訊號處理支援 {}\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:76
 #, c++-format
 msgid "\tUsing a timestep {:e}\n"
 msgstr ""
+"\t使用時間步長 {:e}\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:613
 msgid "\tdone\n"
-msgstr "\t完\n"
+msgstr ""
+"\t完\n"
 
 #: ../src/solver/impls/split-rk/split-rk.cxx:41
 msgid ""
 "\n"
 "\tSplit Runge-Kutta-Legendre and SSP-RK3 solver\n"
 msgstr ""
+"\n"
+"\tSplit Runge-Kutta-Legendre 與 SSP-RK3 求解器\n"
 
 #: ../src/bout++.cxx:378
 msgid ""
@@ -310,6 +357,13 @@ msgid ""
 "  -v, --verbose\t\t\tIncrease verbosity\n"
 "  -q, --quiet\t\t\tDecrease verbosity\n"
 msgstr ""
+"\n"
+"  -d <資料目錄>\t\t在 <資料目錄> 中尋找輸入/輸出檔案\n"
+"  -f <選項檔名>\t\t使用 <選項檔名> 中給出的 OPTIONS\n"
+"  -o <設定檔名>\t將已使用的 OPTIONS 儲存到 <選項檔名>\n"
+"  -l, --log <日誌檔名>\t將日誌輸出到 <日誌檔名>\n"
+"  -v, --verbose\t\t\t提高詳細程度\n"
+"  -q, --quiet\t\t\t降低詳細程度\n"
 
 #: ../src/sys/expressionparser.cxx:341
 #, c++-format
@@ -318,24 +372,27 @@ msgid ""
 "  {1: ^{2}}{0}\n"
 "  Did you mean '{0}'?"
 msgstr ""
+"\n"
+"  {1: ^{2}}{0}\n"
+"  您是不是想寫 '{0}'？"
 
 #: ../src/solver/solver.cxx:586
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run finished at  : {:s}\n"
 msgstr ""
 "\n"
-"计算结束于 {:s}\n"
+"執行結束時間：{:s}\n"
 
 #: ../src/solver/solver.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "\n"
 "Run started at  : {:s}\n"
 msgstr ""
 "\n"
-"计算从 {:s} 开始\n"
+"執行開始時間：{:s}\n"
 
 #. Raw string to help with the formatting of the message, and a
 #. separate variable so clang-format doesn't barf on the
@@ -367,6 +424,28 @@ msgid ""
 "\n"
 "{}"
 msgstr ""
+"\n"
+"發現未使用的輸入選項：\n"
+"-----\n"
+"{:i}\n"
+"-----\n"
+"有些選項可能被拼錯了。BOUT++ 的輸入參數現在區分大小寫，\n"
+"而且其中有些名稱已經改變。您可以嘗試執行\n"
+"\n"
+"    <BOUT++ directory>/bin/bout-v5-input-file-upgrader.py {}/{}\n"
+"\n"
+"來自動修正常見問題。如果上面的這些選項有時會依賴其他選項\n"
+"才被使用，您可以呼叫 `Options::setConditionallyUsed()`，例如：\n"
+"\n"
+"    Options::root()[\"{}\"].setConditionallyUsed();\n"
+"\n"
+"將某個區段或值標記為依賴其他值，從而在這項檢查中忽略它。或者，\n"
+"如果您確定以上輸入不是錯誤，可以設定\n"
+"'input:error_on_unused_options=false' 來關閉這項未使用選項檢查。\n"
+"您也隨時可以設定 'input:validate=true'，在不執行完整模擬的情況下\n"
+"檢查輸入。\n"
+"\n"
+"{}"
 
 #: ../src/bout++.cxx:389
 #, c++-format
@@ -400,85 +479,112 @@ msgid ""
 "For all possible input parameters, see the user manual and/or the physics "
 "model source (e.g. {:s}.cxx)\n"
 msgstr ""
+"  --print-config\t\t顯示編譯時設定\n"
+"  --list-solvers\t\t列出可用的時間求解器\n"
+"  --help-solver <solver>\t顯示指定時間求解器的說明\n"
+"  --list-laplacians\t\t列出可用的拉普拉斯反演求解器\n"
+"  --help-laplacian <laplacian>\t顯示指定拉普拉斯反演求解器的說明\n"
+"  --list-laplacexz\t\t列出可用的 LaplaceXZ 反演求解器\n"
+"  --help-laplacexz <laplacexz>\t顯示指定 LaplaceXZ 反演求解器的說明\n"
+"  --list-invertpars\t\t列出可用的 InvertPar 求解器\n"
+"  --help-invertpar <invertpar>\t顯示指定 InvertPar 求解器的說明\n"
+"  --list-rkschemes\t\t列出可用的 Runge-Kutta 格式\n"
+"  --help-rkscheme <rkscheme>\t顯示指定 Runge-Kutta 格式的說明\n"
+"  --list-meshes\t\t\t列出可用的 Mesh\n"
+"  --help-mesh <mesh>\t\t顯示指定 Mesh 的說明\n"
+"  --list-xzinterpolations\t列出可用的 XZInterpolation\n"
+"  --help-xzinterpolation <xzinterpolation>\t顯示指定 XZInterpolation 的說明\n"
+"  --list-zinterpolations\t列出可用的 ZInterpolation\n"
+"  --help-zinterpolation <zinterpolation>\t顯示指定 ZInterpolation 的說明\n"
+"  -h, --help\t\t\t此訊息\n"
+"  restart [append]\t\t重新啟動模擬。若指定 append，則附加到現有輸出檔案，否則覆寫它們\n"
+"  VAR=VALUE\t\t\t為輸入參數 VAR 指定一個 VALUE\n"
+"\n"
+"有關所有可能的輸入參數，請參閱使用者手冊和/或物理模型原始碼（例如 {:s}.cxx）\n"
 
 #: ../src/bout++.cxx:386
 msgid "  -c, --color\t\t\tColor output using bout-log-color\n"
 msgstr ""
+"  -c, --color\t\t\t使用 bout-log-color 輸出彩色日誌\n"
 
 #: ../include/bout/options.hxx:899
 msgid ") overwritten with:"
-msgstr ""
+msgstr ") 被覆寫為："
 
 #: ../src/bout++.cxx:557
 #, c++-format
 msgid ", level {}"
-msgstr ""
+msgstr ", 等級 {}"
 
 #: ../tests/unit/src/test_bout++.cxx:352
 msgid "4 of 8"
-msgstr ""
+msgstr "4 / 8"
 
 #: ../src/sys/options.cxx:895
 msgid "All options used\n"
 msgstr ""
+"所有選項皆已使用\n"
 
 #: ../src/bout++.cxx:535
-#, fuzzy, c++-format
+#, c++-format
 msgid "BOUT++ version {:s}\n"
-msgstr "BOUT++ 版 {:s}\n"
+msgstr ""
+"BOUT++ 版本 {:s}\n"
 
 #: ../src/bout++.cxx:147
 msgid "Bad command line arguments:\n"
 msgstr ""
+"錯誤的命令列參數：\n"
 
 #: ../src/sys/expressionparser.cxx:192
 #, c++-format
 msgid "Boolean operator argument {:e} is not a bool"
-msgstr ""
+msgstr "布林運算子參數 {:e} 不是布林值"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:595
 msgid "Boundary regions in this processor: "
-msgstr ""
+msgstr "此處理器中的邊界區域："
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:348
 #, c++-format
 msgid "Cannot split {:d} X points equally between {:d} processors\n"
 msgstr ""
+"無法將 {:d} 個 X 點平均分配給 {:d} 個處理器\n"
 
 #: ../src/bout++.cxx:829
 msgid "Check if a file exists, and exit if it does."
-msgstr ""
+msgstr "檢查檔案是否存在，若存在則結束。"
 
 #: ../src/bout++.cxx:540
-#, fuzzy, c++-format
+#, c++-format
 msgid ""
 "Code compiled on {:s} at {:s}\n"
 "\n"
 msgstr ""
-"代碼於 {:s} {:s} 编译\n"
+"程式碼編譯於 {:s}，時間 {:s}\n"
 "\n"
 
 #: ../src/sys/optionsreader.cxx:130
 msgid "Command line"
-msgstr ""
+msgstr "命令列"
 
 #: ../src/bout++.cxx:551 ../tests/unit/src/test_bout++.cxx:358
 msgid "Compile-time options:\n"
-msgstr "編譯選項:\n"
+msgstr ""
+"編譯選項:\n"
 
 #: ../tests/unit/src/test_bout++.cxx:362
-#, fuzzy
 msgid "Compiled with flags"
-msgstr "\t用設置編譯: {:s}\n"
+msgstr "編譯旗標"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:604
 msgid "Constructing default regions"
-msgstr ""
+msgstr "正在建立預設區域"
 
 #: ../src/bout++.cxx:527
-#, fuzzy, c++-format
+#, c++-format
 msgid "Could not create PID file {:s}"
-msgstr "無法打開輸出文件 '{:s}'\n"
+msgstr "無法建立 PID 檔案 {:s}"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:309
 msgid ""
@@ -486,30 +592,33 @@ msgid ""
 msgstr "無法找到NXPE的有效值。 嘗試不同數量的處理器。"
 
 #: ../src/sys/options/options_ini.cxx:160
-#, fuzzy, c++-format
+#, c++-format
 msgid "Could not open output file '{:s}'\n"
-msgstr "無法打開輸出文件 '{:s}'\n"
+msgstr ""
+"無法開啟輸出檔案 '{:s}'\n"
 
 #: ../src/bout++.cxx:657
 #, c++-format
 msgid "Could not open {:s}/{:s}.{:d} for writing"
-msgstr ""
+msgstr "無法開啟 {:s}/{:s}.{:d} 以供寫入"
 
 #. Error reading
 #: ../src/mesh/mesh.cxx:543
 #, c++-format
 msgid "Could not read integer array '{:s}'\n"
 msgstr ""
+"無法讀取整數陣列 '{:s}'\n"
 
 #. Failed . Probably not important enough to stop the simulation
 #: ../src/bout++.cxx:637
 msgid "Could not run bout-log-color. Make sure it is in your PATH\n"
 msgstr ""
+"無法執行 bout-log-color。請確認它在您的 PATH 中\n"
 
 #: ../src/solver/solver.cxx:772
 #, c++-format
 msgid "Couldn't add Monitor: {:g} is not a multiple of {:g}!"
-msgstr ""
+msgstr "無法加入監視器：{:g} 不是 {:g} 的整數倍！"
 
 #: ../src/sys/expressionparser.cxx:312
 #, c++-format
@@ -519,78 +628,90 @@ msgid ""
 "may need to change your input file.\n"
 "{}"
 msgstr ""
+"找不到產生器 '{}'。BOUT++ 表達式現在區分大小寫，因此\n"
+"您可能需要修改輸入檔案。\n"
+"{}"
 
 #: ../src/mesh/mesh.cxx:587
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap2D"
-msgstr ""
+msgstr "無法在 regionMap2D 中找到區域 {:s}"
 
 #: ../src/mesh/mesh.cxx:571 ../src/mesh/mesh.cxx:579
 #, c++-format
 msgid "Couldn't find region {:s} in regionMap3D"
-msgstr ""
+msgstr "無法在 regionMap3D 中找到區域 {:s}"
 
 #: ../src/mesh/mesh.cxx:595
 #, c++-format
 msgid "Couldn't find region {:s} in regionMapPerp"
-msgstr ""
+msgstr "無法在 regionMapPerp 中找到區域 {:s}"
 
 #. Convert any exceptions to something a bit more useful
 #: ../src/sys/options.cxx:361
 #, c++-format
 msgid "Couldn't get {} from option {:s} = '{:s}': {}"
-msgstr ""
+msgstr "無法從選項 {1:s} = '{2:s}' 取得 {0}：{3}"
 
 #: ../src/bout++.cxx:515
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" does not exist or is not accessible\n"
-msgstr "\"{:s}\" 不存在或不可訪問\n"
+msgstr ""
+"資料目錄 \"{:s}\" 不存在或無法存取\n"
 
 #: ../src/bout++.cxx:512
-#, fuzzy, c++-format
+#, c++-format
 msgid "DataDir \"{:s}\" is not a directory\n"
-msgstr "\"{:s}\" 不是目錄\n"
+msgstr ""
+"資料目錄 \"{:s}\" 不是目錄\n"
 
 #: ../src/solver/solver.cxx:671
 msgid "ERROR: Solver is already initialised\n"
 msgstr ""
+"錯誤：求解器已初始化\n"
 
 #: ../src/bout++.cxx:216
-#, fuzzy, c++-format
+#, c++-format
 msgid "Error encountered during initialisation: {:s}\n"
-msgstr "啟動時遇到錯誤 : {:s}\n"
+msgstr ""
+"初始化期間發生錯誤：{:s}\n"
 
 #: ../src/bout++.cxx:751
 msgid "Error whilst writing settings"
-msgstr ""
+msgstr "寫入設定時發生錯誤"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:323
 #, c++-format
 msgid "Error: nx must be greater than 2 times MXG (2 * {:d})"
-msgstr ""
+msgstr "錯誤：nx 必須大於 2 倍 MXG（2 * {:d}）"
 
 #: ../src/solver/solver.cxx:520
 msgid "Failed to initialise solver-> Aborting\n"
 msgstr ""
+"初始化求解器失敗 -> 中止\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:281
 #, c++-format
 msgid "Finding value for NXPE (ideal = {:f})\n"
 msgstr ""
+"正在尋找 NXPE 的值（理想值 = {:f}）\n"
 
 #: ../src/solver/solver.cxx:674
 msgid "Initialising solver\n"
-msgstr "初始化求解器\n"
+msgstr ""
+"初始化求解器\n"
 
 #: ../src/bout++.cxx:501
 msgid ""
 "Input and output file for settings must be different.\n"
 "Provide -o <settings file> to avoid this issue.\n"
 msgstr ""
+"設定的輸入檔與輸出檔必須不同。\n"
+"請提供 -o <settings file> 以避免此問題。\n"
 
 #: ../src/sys/optionsreader.cxx:76
 msgid "Invalid command line option '-' found - maybe check whitespace?"
-msgstr ""
+msgstr "找到無效的命令列選項 '-'，也許應檢查空白字元？"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:436
 msgid "Loading mesh"
@@ -598,82 +719,88 @@ msgstr "加載網格"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:451
 msgid "Mesh must contain nx"
-msgstr ""
+msgstr "網格必須包含 nx"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:455
 msgid "Mesh must contain ny"
-msgstr ""
+msgstr "網格必須包含 ny"
 
 #. Not found
 #: ../src/mesh/mesh.cxx:547
 #, c++-format
 msgid "Missing integer array {:s}\n"
 msgstr ""
+"缺少整數陣列 {:s}\n"
 
 #: ../src/solver/solver.cxx:911
 #, c++-format
 msgid "Monitor signalled to quit (exception {})\n"
 msgstr ""
+"監視器發出離開訊號（例外 {}）\n"
 
 #: ../src/solver/solver.cxx:889
 #, c++-format
 msgid "Monitor signalled to quit (return code {})"
-msgstr ""
+msgstr "監視器發出離開訊號（回傳碼 {}）"
 
 #: ../src/bout++.cxx:834
 msgid "Name of file whose existence triggers a stop"
-msgstr ""
+msgstr "其存在會觸發停止的檔案名稱"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:601
 msgid "No boundary regions in this processor"
-msgstr ""
+msgstr "此處理器中沒有邊界區域"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:586
 msgid "No boundary regions; domain is periodic\n"
 msgstr ""
+"沒有邊界區域；區域是週期性的\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:245
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in x direction ({:d})\n"
 msgstr ""
+"處理器數量 ({:d}) 無法被 x 方向上的 NP 數 ({:d}) 整除\n"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:258
 #, c++-format
 msgid ""
 "Number of processors ({:d}) not divisible by NPs in y direction ({:d})\n"
 msgstr ""
+"處理器數量 ({:d}) 無法被 y 方向上的 NP 數 ({:d}) 整除\n"
 
 #. Less than 2 time-steps left
 #: ../src/bout++.cxx:908
 #, c++-format
 msgid "Only {:e} seconds ({:.2f} steps) left. Quitting\n"
 msgstr ""
+"只剩下 {:e} 秒（{:.2f} 步）。正在結束\n"
 
 #: ../src/sys/options.cxx:382 ../src/sys/options.cxx:398
 #: ../src/sys/options.cxx:441 ../src/sys/options.cxx:471
 #: ../src/sys/options.cxx:745 ../src/sys/options.cxx:767
 #: ../src/sys/options.cxx:789
-#, fuzzy, c++-format
+#, c++-format
 msgid "Option {:s} has no value"
-msgstr "\"{:s}\" 不是目錄\n"
+msgstr "選項 {:s} 沒有值"
 
 #. Doesn't exist
 #: ../src/sys/options.cxx:172
-#, fuzzy, c++-format
+#, c++-format
 msgid "Option {:s}:{:s} does not exist"
-msgstr "選項{:s}:{:s}不存在"
+msgstr "選項 {:s}:{:s} 不存在"
 
 #: ../include/bout/options.hxx:904
 #, c++-format
 msgid ""
 "Options: Setting a value from same source ({:s}) to new value '{:s}' - old "
 "value was '{:s}'."
-msgstr ""
+msgstr "選項：正在將來自相同來源 ({:s}) 的值設定為新值 '{:s}'，舊值為 '{:s}'。"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:588
 msgid "Possible boundary regions are: "
-msgstr ""
+msgstr "可能的邊界區域有："
 
 #: ../src/bout++.cxx:545
 #, c++-format
@@ -681,26 +808,29 @@ msgid ""
 "Processor number: {:d} of {:d}\n"
 "\n"
 msgstr ""
+"處理器編號：{:d} / {:d}\n"
+"\n"
 
 #: ../src/mesh/mesh.cxx:642
 #, c++-format
 msgid "Registered region 2D {:s}"
-msgstr ""
+msgstr "已註冊 2D 區域 {:s}"
 
 #: ../src/mesh/mesh.cxx:632
 #, c++-format
 msgid "Registered region 3D {:s}"
-msgstr ""
+msgstr "已註冊 3D 區域 {:s}"
 
 #: ../src/mesh/mesh.cxx:652
 #, c++-format
 msgid "Registered region Perp {:s}"
-msgstr ""
+msgstr "已註冊 Perp 區域 {:s}"
 
 #: ../src/bout++.cxx:536
-#, fuzzy, c++-format
+#, c++-format
 msgid "Revision: {:s}\n"
-msgstr "版: {:s}\n"
+msgstr ""
+"修訂版：{:s}\n"
 
 #: ../src/solver/solver.cxx:587
 msgid "Run time : "
@@ -717,15 +847,14 @@ msgstr ""
 
 #: ../tests/unit/src/test_bout++.cxx:359
 msgid "Signal"
-msgstr ""
+msgstr "訊號"
 
 #: ../src/bout++.cxx:876
 msgid ""
 "Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
-"模擬時間   |   評估數量   |  時鐘時間   |  計算    逆溫   通訊   輸入輸出  時"
-"間整合\n"
+"模擬時間   |   評估數量   |  時鐘時間   |  計算    逆溫   通訊   輸入輸出  時間整合\n"
 "\n"
 
 #: ../src/bout++.cxx:879
@@ -734,26 +863,27 @@ msgid ""
 "Comm    I/O   SOLVER\n"
 "\n"
 msgstr ""
-"模擬時間   |   評估數量(e)  | 評估數量(I)    |  時鐘時間   |  計算    逆溫   "
-"通訊   輸入輸出  時間整合\n"
+"模擬時間   |   評估數量(e)  | 評估數量(I)    |  時鐘時間   |  計算    逆溫   通訊   輸入輸出  時間整合\n"
 "\n"
 
 #: ../src/solver/solver.cxx:514
 #, c++-format
 msgid "Solver running for {:d} outputs with monitor timestep of {:e}\n"
 msgstr ""
+"求解器正在執行 {:d} 個輸出，監視步長為 {:e}\n"
 
 #: ../src/solver/solver.cxx:510
 #, c++-format
 msgid "Solver running for {:d} outputs with output timestep of {:e}\n"
 msgstr ""
+"求解器正在執行 {:d} 個輸出，輸出步長為 {:e}\n"
 
 #: ../src/solver/solver.cxx:788
 #, c++-format
 msgid ""
 "Solver::addMonitor: Cannot reduce timestep (from {:g} to {:g}) after init is "
 "called!"
-msgstr ""
+msgstr "Solver::addMonitor：在呼叫 init 之後無法將時間步長從 {:g} 降低到 {:g}！"
 
 #: ../src/solver/solver.cxx:1289
 #, c++-format
@@ -761,26 +891,27 @@ msgid ""
 "Time derivative at wrong location - Field is at {:s}, derivative is at {:s} "
 "for field '{:s}'\n"
 msgstr ""
+"時間導數位於錯誤位置 - 欄位位於 {:s}，導數位於 {:s}，對應欄位 '{:s}'\n"
 
 #: ../src/solver/solver.cxx:1494
 #, c++-format
 msgid "Time derivative for variable '{:s}' not set"
-msgstr ""
+msgstr "變數 '{:s}' 的時間導數尚未設定"
 
 #: ../src/mesh/mesh.cxx:638
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap2D"
-msgstr ""
+msgstr "嘗試將已存在的區域 {:s} 加入 regionMap2D"
 
 #: ../src/mesh/mesh.cxx:614
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMap3D"
-msgstr ""
+msgstr "嘗試將已存在的區域 {:s} 加入 regionMap3D"
 
 #: ../src/mesh/mesh.cxx:649
 #, c++-format
 msgid "Trying to add an already existing region {:s} to regionMapPerp"
-msgstr ""
+msgstr "嘗試將已存在的區域 {:s} 加入 regionMapPerp"
 
 #: ../src/sys/options.cxx:112 ../src/sys/options.cxx:151
 #, c++-format
@@ -790,45 +921,55 @@ msgid ""
 "This is likely the result of clashing input options, and you may have to "
 "rename one of them.\n"
 msgstr ""
+"正在嘗試以 '{1}' 索引選項 '{0}'，但 '{0}' 是一個值，而不是一個區段。\n"
+"這很可能是輸入選項互相衝突的結果，您可能需要重新命名其中之一。\n"
 
 #: ../src/mesh/coordinates.cxx:1464
 msgid ""
 "Unrecognised paralleltransform option.\n"
 "Valid choices are 'identity', 'shifted', 'fci'"
 msgstr ""
+"無法辨識的 paralleltransform 選項。\n"
+"有效選項為 'identity'、'shifted'、'fci'"
 
 #: ../src/sys/options.cxx:899
 msgid "Unused options:\n"
 msgstr ""
+"未使用的選項：\n"
 
 #: ../src/bout++.cxx:446
 #, c++-format
 msgid "Usage is {:s} -d <data directory>\n"
 msgstr ""
+"用法：{:s} -d <資料目錄>\n"
 
 #: ../src/bout++.cxx:455
 #, c++-format
 msgid "Usage is {:s} -f <options filename>\n"
 msgstr ""
+"用法：{:s} -f <選項檔名>\n"
 
 #: ../src/bout++.cxx:473
 #, c++-format
 msgid "Usage is {:s} -l <log filename>\n"
 msgstr ""
+"用法：{:s} -l <日誌檔名>\n"
 
 #: ../src/bout++.cxx:464
 #, c++-format
 msgid "Usage is {:s} -o <settings filename>\n"
 msgstr ""
+"用法：{:s} -o <設定檔名>\n"
 
 #: ../src/bout++.cxx:360
 #, c++-format
 msgid "Usage is {} {} <name>\n"
 msgstr ""
+"用法：{} {} <名稱>\n"
 
 #: ../tests/unit/src/test_bout++.cxx:32 ../tests/unit/src/test_bout++.cxx:46
 msgid "Usage:"
-msgstr ""
+msgstr "用法："
 
 #. Print help message -- note this will be displayed once per processor as we've not
 #. started MPI yet.
@@ -838,72 +979,74 @@ msgid ""
 "Usage: {:s} [-d <data directory>] [-f <options filename>] [restart [append]] "
 "[VAR=VALUE]\n"
 msgstr ""
+"用法：{:s} [-d <資料目錄>] [-f <選項檔名>] [restart [append]] [VAR=VALUE]\n"
 
 #. restart file should be written by physics model
 #: ../src/solver/solver.cxx:927
 msgid "User signalled to quit. Returning\n"
 msgstr ""
+"使用者發出離開訊號。正在返回\n"
 
 #: ../src/sys/options.cxx:486
-#, fuzzy, c++-format
+#, c++-format
 msgid "Value for option {:s} = {:e} is not a bool"
-msgstr "\"{:s}\" 不是目錄\n"
+msgstr "選項 {:s} = {:e} 的值不是布林值"
 
 #: ../src/sys/options.cxx:426
 #, c++-format
 msgid "Value for option {:s} = {:e} is not an integer"
-msgstr ""
+msgstr "選項 {:s} = {:e} 的值不是整數"
 
 #: ../src/sys/options.cxx:456
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a BoutReal"
-msgstr ""
+msgstr "選項 {:s} 的值無法轉換為 BoutReal"
 
 #: ../src/sys/options.cxx:623
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field2D"
-msgstr ""
+msgstr "選項 {:s} 的值無法轉換為 Field2D"
 
 #: ../src/sys/options.cxx:571
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a Field3D"
-msgstr ""
+msgstr "選項 {:s} 的值無法轉換為 Field3D"
 
 #: ../src/sys/options.cxx:705
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a FieldPerp"
-msgstr ""
+msgstr "選項 {:s} 的值無法轉換為 FieldPerp"
 
 #: ../src/sys/options.cxx:491
 #, c++-format
 msgid "Value for option {:s} cannot be converted to a bool"
-msgstr ""
+msgstr "選項 {:s} 的值無法轉換為 bool"
 
 #: ../src/sys/options.cxx:751
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Array<BoutReal>"
-msgstr ""
+msgstr "選項 {:s} 的值無法轉換為 Array<BoutReal>"
 
 #: ../src/sys/options.cxx:773
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Matrix<BoutReal>"
-msgstr ""
+msgstr "選項 {:s} 的值無法轉換為 Matrix<BoutReal>"
 
 #: ../src/sys/options.cxx:795
 #, c++-format
 msgid "Value for option {:s} cannot be converted to an Tensor<BoutReal>"
-msgstr ""
+msgstr "選項 {:s} 的值無法轉換為 Tensor<BoutReal>"
 
 #. Another type which can't be converted
 #: ../src/sys/options.cxx:418
 #, c++-format
 msgid "Value for option {:s} is not an integer"
-msgstr ""
+msgstr "選項 {:s} 的值不是整數"
 
 #: ../src/solver/solver.cxx:1240 ../src/solver/solver.cxx:1246
 #, c++-format
 msgid "Variable '{:s}' not initialised"
-msgstr ""
+msgstr "變數 '{:s}' 尚未初始化"
 
 #: ../src/mesh/impls/bout/boutmesh.cxx:467
 #, c++-format
@@ -911,35 +1054,41 @@ msgid ""
 "WARNING: Number of toroidal points should be 2^n for efficient FFT "
 "performance -- consider changing MZ ({:d}) if using FFTs\n"
 msgstr ""
+"警告：為了獲得高效的 FFT 效能，環向點數應為 2^n；若使用 FFT，請考慮修改 MZ ({:d})\n"
 
 #: ../src/mesh/coordinates.cxx:635
 msgid "WARNING: extrapolating input mesh quantities into x-boundary cells\n"
 msgstr ""
+"警告：正在將輸入網格量外推到 x 邊界單元\n"
 
 #: ../src/mesh/coordinates.cxx:412
 msgid ""
 "WARNING: extrapolating input mesh quantities into x-boundary cells. Set "
 "option extrapolate_x=false to disable this.\n"
 msgstr ""
+"警告：正在將輸入網格量外推到 x 邊界單元。設定選項 extrapolate_x=false 可停用此行為。\n"
 
 #: ../src/mesh/coordinates.cxx:640
 msgid "WARNING: extrapolating input mesh quantities into y-boundary cells\n"
 msgstr ""
+"警告：正在將輸入網格量外推到 y 邊界單元\n"
 
 #: ../src/mesh/coordinates.cxx:417
 msgid ""
 "WARNING: extrapolating input mesh quantities into y-boundary cells. Set "
 "option extrapolate_y=false to disable this.\n"
 msgstr ""
+"警告：正在將輸入網格量外推到 y 邊界單元。設定選項 extrapolate_y=false 可停用此行為。\n"
 
 #: ../src/bout++.cxx:825
 msgid "Wall time limit in hours. By default (< 0), no limit"
-msgstr ""
+msgstr "牆鐘時間限制（小時）。預設值（< 0）表示不限制"
 
 #: ../src/sys/optionsreader.cxx:42
-#, fuzzy, c++-format
+#, c++-format
 msgid "Writing options to file {:s}\n"
-msgstr "寫選項到文件 "
+msgstr ""
+"正在將選項寫入檔案 {:s}\n"
 
 #. / The source label given to default values
 #: ../src/sys/options.cxx:34

From 8deac5b50f7e19c3f90890b21b67238aa8a4f19f Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 22 Jun 2026 12:42:51 +0100
Subject: [PATCH 1463/1827] Refactor test_datafile_facade for pytest

---
 .../test_datafile_facade.py                   | 61 ++++++++-----------
 1 file changed, 24 insertions(+), 37 deletions(-)

diff --git a/tests/integrated/test-datafilefacade/test_datafile_facade.py b/tests/integrated/test-datafilefacade/test_datafile_facade.py
index 7a4d947f27..ae1cb9ef3c 100755
--- a/tests/integrated/test-datafilefacade/test_datafile_facade.py
+++ b/tests/integrated/test-datafilefacade/test_datafile_facade.py
@@ -5,9 +5,10 @@
 # requires: netcdf
 # cores: 2
 
+import pytest
+import numpy
 from boutdata.collect import collect
 from boututils.run_wrapper import shell, launch_safe
-import numpy
 
 
 testvars = {
@@ -33,44 +34,30 @@
 }
 
 
-def test_datafile_facade():
-
-    success = True
-
-    for nproc in [1, 2]:
-        # delete any existing output
-        shell(["rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc"])
-
-        print(f"   {nproc} processor....")
+@pytest.mark.parametrize("nproc", [1, 2])
+def test_datafile_facade(nproc):
 
-        # run the test executable
-        s, out = launch_safe("./test-datafile-facade", nproc=nproc, pipe=True)
-        with open(f"run.log.{nproc}", "w") as f:
-            f.write(out)
+    # delete any existing output
+    shell(["rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc"])
 
-        # check the results
-        for name, expected in testvars.items():
-            # check non-evolving version
-            result = collect(name, path="data", info=False)
+    print(f"   {nproc} processor(s)....")
 
-            if result.dtype.kind in ("S", "U"):
-                if str(result) != expected:
-                    success = False
-                    print(
-                        f"{name} is different: got '{str(result)}', expected '{expected}'"
-                    )
-                continue
+    # run the test executable
+    s, out = launch_safe("./test-datafile-facade", nproc=nproc, pipe=True)
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
 
-            if not numpy.allclose(expected, result):
-                success = False
-                print(f"{name} is different: {numpy.max(numpy.abs(expected - result))}")
+    # Check the results
+    for name, expected in testvars.items():
+        # Check non-evolving version
+        result = collect(name, path="data", info=False)
 
-    if success:
-        print("=> All DataFileFacade tests passed")
-        # clean up binary files
-        shell(
-            [
-                "rm -f data/BOUT.dmp.*.nc data/BOUT.restart.*.nc data/restart/BOUT.restart.0.nc"
-            ]
-        )
-    assert success, "=> Some failed tests"
+        if result.dtype.kind in ("S", "U"):
+            assert str(result) == expected, (
+                f"{name} is different: got '{str(result)}', expected '{expected}'"
+            )
+        else:
+            diff = numpy.max(numpy.abs(expected - result))
+            assert numpy.allclose(expected, result), (
+                f"{name} is different: max diff is {diff}"
+            )

From 4e7cb9d9b788bc7bcbcb37374b1ea866b67840ad Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 22 Jun 2026 12:59:16 +0100
Subject: [PATCH 1464/1827] Refactor test_initial for pytest

---
 tests/integrated/test-initial/test_initial.py | 123 ++++++++----------
 1 file changed, 56 insertions(+), 67 deletions(-)

diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index cf61514fac..55bc162a4b 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -5,11 +5,13 @@
 import pytest
 import configparser
 import itertools
+import platform
+import warnings
 import numpy as np
 from scipy.special import erf
 from pathlib import Path
 
-from boututils.run_wrapper import launch_safe
+from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
 # requires not make
@@ -154,20 +156,19 @@ def fmod(x, denominator=1.0):
 erf = erf
 
 
-def test_initial():
-    # Running the test
-
-    # Some parameters
-    success = True
+@pytest.mark.parametrize("nproc", [1, 2, 3, 4])
+def test_initial(nproc):
     tolerance = 1e-13
     cmd = "./test_initial"
     datadir = Path("data")
     inputfile = datadir / "BOUT.inp"
 
+    shell(["rm -f data/BOUT.dmp.*.nc"])
+
     # Read the input file
     config = configparser.ConfigParser()
     with open(inputfile, "r") as f:
-        config.read_file(itertools.chain(["[global]"], f), source=inputfile)
+        config.read_file(itertools.chain(["[global]"], f), source=str(inputfile))
 
     # Find the variables that have a "function" option
     varlist = [key for key, values in config.items() if "function" in values]
@@ -176,67 +177,55 @@ def test_initial():
     for coord in ["var_x", "var_y", "var_z"]:
         varlist.remove(coord)
 
-    nprocs = [1, 2, 3, 4]
-    for nproc in nprocs:
-        status, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
-        with open("run.log.{}".format(nproc), "w") as f:
-            f.write(out)
-
-        if status != 0:
-            print(status)
-            pytest.fail("=> Could not run test")
-
-        # Collect the coordinate arrays separately
-        x = collect("var_x", xguards=True, yguards=True, path=datadir, info=False)
-        y = collect("var_y", xguards=True, yguards=True, path=datadir, info=False)
-        z = collect("var_z", xguards=True, yguards=True, path=datadir, info=False)
-
-        # Evaluate the functions
-        for var in varlist:
-            function = config[var]["function"]
-            function = function.replace("^", "**")
-            if ":" in function:
-                print(
-                    "{} contains reference to variable - not possible to resolve at this time".format(
-                        var
+    status, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
+
+    # Collect the coordinate arrays separately
+    x = collect("var_x", xguards=True, yguards=True, path=str(datadir), info=False)
+    y = collect("var_y", xguards=True, yguards=True, path=str(datadir), info=False)
+    z = collect("var_z", xguards=True, yguards=True, path=str(datadir), info=False)
+
+    failures = []
+
+    # Evaluate the functions
+    for var in varlist:
+        function = config[var]["function"]
+        function = function.replace("^", "**")
+
+        if ":" in function:
+            print(
+                f"{var} contains reference to variable - not possible to resolve at this time"
+            )
+            continue
+
+        context = {"x": x, "y": y, "z": z}
+
+        try:
+            analytic = eval(function, globals(), context)
+        except NotImplementedError as err:
+            print(f"{err.args[0]} not implemented, skipping")
+            continue
+
+        data = collect(var, xguards=True, yguards=True, path=str(datadir), info=False)
+        E2 = np.sqrt(np.mean((analytic - data) ** 2))
+        if E2 >= tolerance:
+            if var in ("mixmode", "mixmode_seed") and E2 < 1e-3:
+                arch = platform.machine()
+                if arch == "i686":
+                    # This can happen due tue excess precision e.g. on X87 architecture
+                    warnings.warn(
+                        f"WARNING: Excess precision detected on i686 architecture for {var} (E2={E2:.4e})"
                     )
-                )
-                continue
-
-            context = {"x": x, "y": y, "z": z}
-            try:
-                analytic = eval(function, globals(), context)
-            except NotImplementedError as err:
-                print("{} not implemented, skipping".format(err.args[0]))
-            else:
-                data = collect(
-                    var, xguards=True, yguards=True, path=datadir, info=False
-                )
-                E2 = np.sqrt(np.mean((analytic - data) ** 2))
-                if E2 < tolerance:
-                    success_string = "PASS"
+                    continue
                 else:
-                    if (var == "mixmode" or var == "mixmode_seed") and E2 < 1e-3:
-                        import platform
-
-                        arch = platform.machine()
-                        if arch == "i686":
-                            # This can happen due tue excess precision e.g. on X87 architecture
-                            success_string = "WARNING"
-                        else:
-                            print(
-                                "This should only happen in i686 with an x87 math architecture."
-                            )
-                            print("We detected however an %s architecture." % arch)
-                            success_string = "FAIL"
-                            success = False
-                    else:
-                        success_string = "FAIL"
-                        success = False
-                print(
-                    "\tChecking {var:<12}: l-2: {err:.4e} ... {success}".format(
-                        var=var, err=E2, success=success_string
+                    failures.append(
+                        f"{var} (arch: {arch}): l-2 error {E2:.4e} >= {tolerance}"
                     )
-                )
+            else:
+                failures.append(f"{var}: l-2 error {E2:.4e} >= {tolerance}")
 
-    assert success, " => Some failed tests"
+    # Assert that the failures list is empty, otherwise print all collected failures
+    assert not failures, (
+        "The following variables failed tolerance checks:\n" + "\n".join(failures)
+    )

From 2c384efdac095934b67497b104ce359594952198 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 22 Jun 2026 14:43:08 +0100
Subject: [PATCH 1465/1827] Refactor test_multigrid_laplace for pytest

---
 .../test_multigrid_laplace.py                 | 69 ++++++++++---------
 1 file changed, 36 insertions(+), 33 deletions(-)

diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
index 6f8c28b30e..d29a7596f3 100755
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.py
@@ -4,6 +4,7 @@
 # Run the test, check the error
 #
 
+import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
@@ -11,38 +12,40 @@
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
 
-def test_multigrid_laplace():
+@pytest.mark.parametrize("nproc", [1, 2, 4])
+@pytest.mark.parametrize(
+    "inputfile", ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]
+)
+def test_multigrid_laplace(nproc, inputfile):
+    # set nxpe on the command line as we only use solution from one point in y,
+    # so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
+    cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc} input:error_on_unused_options=false"
+
+    shell(["rm -f data/BOUT.dmp.*.nc"])
 
     print("Running multigrid Laplacian inversion test")
-    success = True
-
-    for nproc in [1, 2, 4]:
-        for inputfile in ["BOUT_jy4.inp", "BOUT_jy63.inp", "BOUT_jy127.inp"]:
-            # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
-            cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc} input:error_on_unused_options=false"
-
-            shell(["rm data/BOUT.dmp.*.nc"])
-
-            print("   %d processors, input file is %s" % (nproc, inputfile))
-            s, out = launch_safe(cmd, nproc=nproc, pipe=True)
-            with open("run.log." + str(nproc), "w") as f:
-                f.write(out)
-
-            # Collect errors
-            errors = [
-                collect("max_error" + str(i), path="data")
-                for i in range(1, numTests + 1)
-            ]
-
-            for i, e in enumerate(errors):
-                print("Checking test " + str(i))
-                if e < 0.0:
-                    print("Fail, solver did not converge")
-                    success = False
-                if e > tol:
-                    print("Fail, maximum absolute error = " + str(e))
-                    success = False
-                else:
-                    print("Pass")
-
-    assert success, " => Some failed tests"
+    print(f"{nproc} processors, input file is: {inputfile}")
+
+    s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+
+    # Save a log file uniquely named for this specific combination
+    input_file_name = inputfile.replace(".inp", "")
+    with open(f"run.log.{nproc}.{input_file_name}", "w") as f:
+        f.write(out)
+
+    # Collect errors
+    failures = []
+    for i in range(1, numTests + 1):
+        var_name = f"max_error{i}"
+        e = collect(var_name, path="data", info=False)
+
+        if e < 0.0:
+            failures.append(
+                f"Sub-test {i} ({var_name}): Solver did not converge (error = {e})"
+            )
+        elif e > tol:
+            failures.append(
+                f"Sub-test {i} ({var_name}): Absolute error {e} exceeds tolerance {tol}"
+            )
+
+    assert not failures, "Some failed tests:\n" + "\n".join(failures)

From 70e341d33f81a5acff5baa9feb6d2201c06c9692 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 22 Jun 2026 14:57:13 +0100
Subject: [PATCH 1466/1827] Refactor test_fieldgroupComm for pytest

---
 .../test_fieldgroupComm.py                    | 67 ++++++++-----------
 1 file changed, 29 insertions(+), 38 deletions(-)

diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
index 917fdc0754..a88cc182e0 100755
--- a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
+++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
@@ -9,52 +9,43 @@
 # Requires: not metric_3d
 # Cores: 4
 
-
+import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 from numpy import abs, seterr
 
 
-def test_fieldgroupcomm():
-
+@pytest.mark.parametrize("nproc", [1, 2, 4])
+def test_fieldgroupcomm(nproc):
     # Good chance we'll do 0.0/0.0, which generates a warning
     # Ignore this warning
     seterr(divide="ignore", invalid="ignore")
 
-    varCorrect = "fld1"
-    varsComp = ["fld2", "fld3"]
-    name = "FieldGroup comm"
-    exeName = "test_fieldgroupcomm"
+    var_correct = "fld1"
+    vars_comp = ["fld2", "fld3"]
+    exe_name = "test_fieldgroupcomm"
     tol = 1e-10  # Relative tolerance
 
-    print("Running {nm} test".format(nm=name))
-    success = True
-
-    for nproc in [1, 2, 4]:
-        cmd = "./{exe} ".format(exe=exeName)
-
-        shell("rm data/BOUT.dmp.*.nc")
-
-        print("   %d processors ...." % (nproc))
-        s, out = launch_safe(cmd, nproc=nproc, pipe=True)
-        with open("run.log." + str(nproc), "w") as f:
-            f.write(out)
-
-        # Analyse result
-        # /"Correct" answer
-        f1 = collect(varCorrect, path="data", info=False)
-        f1max = abs(f1).max()
-        # /Two different fields which should be identical to correct
-        err = []
-        for v in varsComp:
-            tmp = collect(v, path="data", info=False)
-            err.append(abs((f1 - tmp)).max() / f1max)
-
-        for i, e in enumerate(err):
-            if e > tol:
-                print(
-                    "Fail, in {i}th comparison relative error is {re}".format(i=i, re=e)
-                )
-                success = False
-
-    assert success, " => Some failed tests"
+    cmd = f"./{exe_name}"
+
+    shell(["rm -f data/BOUT.dmp.*.nc"])
+
+    print(f"Running FieldGroup comm test on {nproc} processor(s)...")
+    s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
+
+    # Analyse result
+    # /"Correct" answer
+    f1 = collect(var_correct, path="data", info=False)
+    f1max = abs(f1).max()
+    # /Two different fields which should be identical to correct
+    err = []
+    for v in vars_comp:
+        tmp = collect(v, path="data", info=False)
+        relative_error = abs(f1 - tmp).max() / f1max
+
+        if relative_error > tol:
+            err.append(f"Field '{v}' mismatch: relative error is {relative_error:.4e})")
+
+    assert not err, f"Failures encountered on {nproc} processor(s):\n" + "\n".join(err)

From 9577bbdd3cf72d40547bbc76a3d46c2347c46986 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 22 Jun 2026 15:06:03 +0100
Subject: [PATCH 1467/1827] Refactor test_griddata_yboundary_guards for pytest

---
 .../test_griddata_yboundary_guards.py         | 245 +++++++-----------
 1 file changed, 91 insertions(+), 154 deletions(-)

diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
index 9666a2f762..ad738830e2 100755
--- a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
+++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
@@ -1,57 +1,65 @@
 #!/usr/bin/env python3
 
-from boututils.run_wrapper import shell, launch_safe
-from boutdata.collect import collect
-from netCDF4 import Dataset
-import numpy
-from pathlib import Path
-from sys import stdout
-
 # Cores: 6
 # Requires: netcdf
 
+import pytest
+import numpy
+from pathlib import Path
+from netCDF4 import Dataset
+from boututils.run_wrapper import shell, launch_safe
+from boutdata.collect import collect
 
-def test_griddata_yboundary_guards():
 
+@pytest.mark.parametrize("topology", ["doublenull", "singlenull"])
+@pytest.mark.parametrize("n_yguards", [0, 1, 2])
+def test_griddata_yboundary_guards(topology, n_yguards):
     nx = 4
     ny = 24
-    blocksize = ny / 6
+    blocksize = ny // 6
+    nproc = 6
+
+
+    datadir = Path(f"data-{topology}-{n_yguards}")
+    datadir.mkdir(parents=True, exist_ok=True)
+
+    gridname = f"grid-{topology}-{n_yguards}.nc"
+    file_path = datadir / gridname
 
-    # first generate some grid files to test
-    # double null case:
-    for n_yguards in [0, 1, 2]:
-        datadir = Path("data-doublenull-" + str(n_yguards))
-        gridname = "grid-doublenull-" + str(n_yguards) + ".nc"
-        file_path = datadir / gridname
+    # first generate grid file to test
+    with Dataset(file_path, "w") as gridfile:
+        gridfile.createDimension("x", nx)
 
-        with Dataset(file_path, "w") as gridfile:
-            gridfile.createDimension("x", nx)
+        if topology == "doublenull":
             gridfile.createDimension("y", ny + 4 * n_yguards)
+        else:
+            gridfile.createDimension("y", ny + 2 * n_yguards)
 
-            gridfile.createVariable("nx", numpy.int32)
-            gridfile["nx"][...] = nx
+        gridfile.createVariable("nx", numpy.int32)
+        gridfile["nx"][...] = nx
 
-            gridfile.createVariable("ny", numpy.int32)
-            gridfile["ny"][...] = ny
+        gridfile.createVariable("ny", numpy.int32)
+        gridfile["ny"][...] = ny
 
-            gridfile.createVariable("y_boundary_guards", numpy.int32)
-            gridfile["y_boundary_guards"][...] = n_yguards
+        gridfile.createVariable("y_boundary_guards", numpy.int32)
+        gridfile["y_boundary_guards"][...] = n_yguards
 
-            gridfile.createVariable("MXG", numpy.int32)
-            gridfile["MXG"][...] = 1
+        gridfile.createVariable("MXG", numpy.int32)
+        gridfile["MXG"][...] = 1
 
-            gridfile.createVariable("MYG", numpy.int32)
-            gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards
+        gridfile.createVariable("MYG", numpy.int32)
+        gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards
 
-            gridfile.createVariable("ixseps1", numpy.int32)
-            gridfile["ixseps1"][...] = nx // 2 - 1
+        gridfile.createVariable("ixseps1", numpy.int32)
+        gridfile["ixseps1"][...] = nx // 2 - 1
 
-            gridfile.createVariable("ixseps2", numpy.int32)
-            gridfile["ixseps2"][...] = nx // 2 - 1
+        gridfile.createVariable("ixseps2", numpy.int32)
+        gridfile["ixseps2"][...] = nx // 2 - 1
 
-            gridfile.createVariable("jyseps1_1", numpy.int32)
-            gridfile["jyseps1_1"][...] = blocksize - 1
+        gridfile.createVariable("jyseps1_1", numpy.int32)
+        gridfile["jyseps1_1"][...] = blocksize - 1
 
+        if topology == "doublenull":
             gridfile.createVariable("jyseps2_1", numpy.int32)
             gridfile["jyseps2_1"][...] = 2 * blocksize - 1
 
@@ -60,49 +68,7 @@ def test_griddata_yboundary_guards():
 
             gridfile.createVariable("jyseps1_2", numpy.int32)
             gridfile["jyseps1_2"][...] = 4 * blocksize - 1
-
-            gridfile.createVariable("jyseps2_2", numpy.int32)
-            gridfile["jyseps2_2"][...] = 5 * blocksize - 1
-
-            testdata = numpy.zeros([nx, ny + 4 * n_yguards])
-            testdata[:, :] = numpy.arange(ny + 4 * n_yguards)[numpy.newaxis, :]
-            gridfile.createVariable("test", float, ("x", "y"))
-            gridfile["test"][...] = testdata
-
-    # grid files for single-null:
-    for n_yguards in [0, 1, 2]:
-        datadir = Path("data-singlenull-" + str(n_yguards))
-        gridname = "grid-singlenull-" + str(n_yguards) + ".nc"
-        file_path = datadir / gridname
-
-        with Dataset(file_path, "w") as gridfile:
-            gridfile.createDimension("x", nx)
-            gridfile.createDimension("y", ny + 2 * n_yguards)
-
-            gridfile.createVariable("nx", numpy.int32)
-            gridfile["nx"][...] = nx
-
-            gridfile.createVariable("ny", numpy.int32)
-            gridfile["ny"][...] = ny
-
-            gridfile.createVariable("y_boundary_guards", numpy.int32)
-            gridfile["y_boundary_guards"][...] = n_yguards
-
-            gridfile.createVariable("MXG", numpy.int32)
-            gridfile["MXG"][...] = 1
-
-            gridfile.createVariable("MYG", numpy.int32)
-            gridfile["MYG"][...] = 2 if n_yguards == 0 else n_yguards
-
-            gridfile.createVariable("ixseps1", numpy.int32)
-            gridfile["ixseps1"][...] = nx // 2 - 1
-
-            gridfile.createVariable("ixseps2", numpy.int32)
-            gridfile["ixseps2"][...] = nx // 2 - 1
-
-            gridfile.createVariable("jyseps1_1", numpy.int32)
-            gridfile["jyseps1_1"][...] = blocksize - 1
-
+        else:  # singlenull
             gridfile.createVariable("jyseps2_1", numpy.int32)
             gridfile["jyseps2_1"][...] = ny // 2
 
@@ -112,91 +78,62 @@ def test_griddata_yboundary_guards():
             gridfile.createVariable("jyseps1_2", numpy.int32)
             gridfile["jyseps1_2"][...] = ny // 2
 
-            gridfile.createVariable("jyseps2_2", numpy.int32)
-            gridfile["jyseps2_2"][...] = 5 * blocksize - 1
-
-            testdata = numpy.zeros([nx, ny + 2 * n_yguards])
-            testdata[:, :] = numpy.arange(ny + 2 * n_yguards)[numpy.newaxis, :]
-            gridfile.createVariable("test", float, ("x", "y"))
-            gridfile["test"][...] = testdata
-
-    for nproc in [6]:
-        stdout.write("Checking %d processors ... " % (nproc))
+        gridfile.createVariable("jyseps2_2", numpy.int32)
+        gridfile["jyseps2_2"][...] = 5 * blocksize - 1
 
-        shell(["rm ./data*/BOUT.dmp.*.nc run.log.*"])
+        y_dim = ny + (4 * n_yguards if topology == "doublenull" else 2 * n_yguards)
+        testdata = numpy.zeros([nx, y_dim])
+        testdata[:, :] = numpy.arange(y_dim)[numpy.newaxis, :]
+        gridfile.createVariable("test", float, ("x", "y"))
+        gridfile["test"][...] = testdata
 
-        success = True
+    shell([f"rm -f {datadir}/BOUT.dmp.*.nc run.log.*"])
 
-        # double null tests
-        for n_yguards in [0, 1, 2]:
-            datadir = "data-doublenull-" + str(n_yguards)
+    print(
+        f"Running {topology} test with n_yguards={n_yguards} on {nproc} processors..."
+    )
 
-            s, out = launch_safe(
-                "./test_griddata -d " + datadir, nproc=nproc, pipe=True
-            )
+    s, out = launch_safe(f"./test_griddata -d {datadir}", nproc=nproc, pipe=True)
 
-            with open("run.log.doublenull." + str(nproc), "a") as f:
-                f.write(out)
+    with open(f"run.log.{topology}.{n_yguards}.{nproc}", "w") as f:
+        f.write(out)
 
-            testfield = collect("test", path=datadir, info=False, yguards=True)
+    testfield = collect("test", path=str(datadir), info=False, yguards=True)
 
-            if n_yguards == 0:
+    if topology == "doublenull":
+        if n_yguards == 0:
                 # output has 2 y-guard cells, but grid file did not
-                myg = 2
-                checkfield = list(numpy.zeros(myg))
-                checkfield += list(numpy.arange(ny // 2))
-                checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1)
-                checkfield += list(numpy.zeros(myg) + checkfield[-1])
-            else:
-                checkfield = []
-                checkfield += list(numpy.arange(n_yguards))
-                checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1)
-                checkfield += list(
-                    numpy.arange(ny // 2) + checkfield[-1] + 1 + 2 * n_yguards
-                )
-                checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
-            checkfield = numpy.array(checkfield)
-
-            # Test value of testfield
-            if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13:
-                print(
-                    "Failed: testfield does not match in doublenull case for n_yguards="
-                    + str(n_yguards)
-                )
-                success = False
-
-        # single null tests
-        for n_yguards in [0, 1, 2]:
-            datadir = "data-singlenull-" + str(n_yguards)
-
-            s, out = launch_safe(
-                "./test_griddata -d " + datadir, nproc=nproc, pipe=True
+            myg = 2
+            checkfield = list(numpy.zeros(myg))
+            checkfield += list(numpy.arange(ny // 2))
+            checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1)
+            checkfield += list(numpy.zeros(myg) + checkfield[-1])
+        else:
+            checkfield = []
+            checkfield += list(numpy.arange(n_yguards))
+            checkfield += list(numpy.arange(ny // 2) + checkfield[-1] + 1)
+            checkfield += list(
+                numpy.arange(ny // 2) + checkfield[-1] + 1 + 2 * n_yguards
             )
-
-            with open("run.log.singlenull." + str(nproc), "a") as f:
-                f.write(out)
-
-            testfield = collect("test", path=datadir, info=False, yguards=True)
-
-            if n_yguards == 0:
+            checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
+    else:  # singlenull
+        if n_yguards == 0:
                 # output has 2 y-guard cells, but grid file did not
-                myg = 2
-                checkfield = list(numpy.zeros(myg))
-                checkfield += list(numpy.arange(ny))
-                checkfield += list(numpy.zeros(myg) + checkfield[-1])
-            else:
-                checkfield = []
-                checkfield += list(numpy.arange(n_yguards))
-                checkfield += list(numpy.arange(ny) + checkfield[-1] + 1)
-                checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
-            checkfield = numpy.array(checkfield)
-
-            # Test value of testfield
-            if numpy.max(numpy.abs(testfield - checkfield)) > 1e-13:
-                print(
-                    "Failed: testfield does not match in doublenull case for n_yguards="
-                    + str(n_yguards)
-                )
-                success = False
-
-        assert success
+            myg = 2
+            checkfield = list(numpy.zeros(myg))
+            checkfield += list(numpy.arange(ny))
+            checkfield += list(numpy.zeros(myg) + checkfield[-1])
+        else:
+            checkfield = []
+            checkfield += list(numpy.arange(n_yguards))
+            checkfield += list(numpy.arange(ny) + checkfield[-1] + 1)
+            checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
+
+    checkfield = numpy.array(checkfield)
+
+    # Test value of testfield
+    max_diff = numpy.max(numpy.abs(testfield - checkfield))
+    assert max_diff <= 1e-13, (
+        f"testfield mismatch in {topology} configuration for n_yguards={n_yguards}. "
+        f"Maximum difference encountered: {max_diff:.4e}"
+    )

From 883083a2eef5f966ed937d153c3b7d8f21595b47 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 22 Jun 2026 16:29:03 +0100
Subject: [PATCH 1468/1827] Refactor test_laplacexy for pytest

---
 .../test-laplacexy/test_laplacexy.py          | 83 +++++++++----------
 1 file changed, 38 insertions(+), 45 deletions(-)

diff --git a/tests/integrated/test-laplacexy/test_laplacexy.py b/tests/integrated/test-laplacexy/test_laplacexy.py
index 750600a6cb..1976e851f3 100755
--- a/tests/integrated/test-laplacexy/test_laplacexy.py
+++ b/tests/integrated/test-laplacexy/test_laplacexy.py
@@ -9,6 +9,7 @@
 # requires: all_tests
 # cores: 8
 
+import pytest
 from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
 
@@ -52,48 +53,40 @@
 ]
 
 
-def test_laplacexy():
-
-    print("Running LaplaceXY inversion test")
-    success = True
-
-    for nproc in [8]:
-        print("   %d processors...." % nproc)
-        for nonorth, tol in [(False, tol_orth), (True, tol_nonorth)]:
-            for args in argslist:
-                if not nonorth:
-                    args += " mesh:g12=0."
-
-                cmd = "./test-laplacexy " + args
-
-                shell(["rm data/BOUT.dmp.*.nc > /dev/null 2>&1"])
-
-                if "hypre" in args:
-                    s, out = launch(cmd, nproc=nproc, pipe=True, verbose=True)
-                    if s == 134:
-                        # PETSc did not recognise pctype option, probably means it
-                        # was not compiled with hypre, so skip tests that need
-                        # hypre to converge
-                        print(
-                            "hypre not available as pre-conditioner in PETSc. Skipping..."
-                        )
-                        continue
-                else:
-                    s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
-
-                f = open("run.log." + str(nproc), "w")
-                f.write(out)
-                f.close()
-
-                # Collect output data
-                error = collect("max_error", path="data", info=False)
-                if error <= 0:
-                    print("Convergence error")
-                    success = False
-                elif error > tol:
-                    print("Fail, maximum error is = " + str(error))
-                    success = False
-                else:
-                    print("Pass")
-
-    assert success, " => Some failed tests"
+@pytest.mark.parametrize(
+    "is_nonorth, tol",
+    [(False, tol_orth), (True, tol_nonorth)],
+    ids=["orthogonal", "non_orthogonal"],
+)
+@pytest.mark.parametrize("case_idx, base_args", enumerate(argslist))
+def test_laplacexy(is_nonorth, tol, case_idx, base_args):
+    nproc = 8
+
+    args = base_args if is_nonorth else f"{base_args} mesh:g12=0."
+    cmd = f"./test-laplacexy {args}"
+
+    shell(["rm -f data/BOUT.dmp.*.nc"])
+
+    if "hypre" in args:
+        s, out = launch(cmd, nproc=nproc, pipe=True, verbose=True)
+        if s == 134:
+            # PETSc did not recognise pctype option, probably means it
+            # was not compiled with hypre, so skip tests that need
+            # hypre to converge
+            pytest.skip("hypre not available as pre-conditioner in PETSc. Skipping...")
+    else:
+        s, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+
+    label = "nonorth" if is_nonorth else "orth"
+    log_filename = f"run.log.{nproc}.{label}.case_{case_idx}"
+    with open(log_filename, "w") as f:
+        f.write(out)
+
+    # Collect output data
+    error = collect("max_error", path="data", info=False)
+
+    assert error > 0, "Convergence error"
+    assert error <= tol, (
+        f"Validation failure on case {case_idx} ({label}). "
+        f"Maximum absolute error {error:.4e} exceeds defined tolerance threshold {tol:.4e}"
+    )

From ec7fdd61ddce2708244805ca6beca15759f8cae4 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 22 Jun 2026 16:39:18 +0100
Subject: [PATCH 1469/1827] Refactor test_multigrid_laplace_unsheared for
 pytest

---
 .../test_multigrid_laplace_unsheared.py       | 64 +++++++++----------
 1 file changed, 31 insertions(+), 33 deletions(-)

diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py
index 3be9bf1bbc..627db84371 100755
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace_unsheared.py
@@ -4,6 +4,7 @@
 # Run the test, check the error
 #
 
+import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
@@ -11,44 +12,41 @@
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
 
-def test_multigrid_laplace_unsheared():
+@pytest.mark.parametrize("nproc", [1, 3])
+def test_multigrid_laplace_unsheared(nproc):
+    # Make sure we don't use too many cores:
+    # Reduce number of OpenMP threads when using multiple MPI processes
+    mthread = 1 if nproc > 1 else 2
 
-    print("Running multigrid Laplacian inversion test (unsheared)")
-    success = True
+    # set nxpe on the command line as we only use solution from one point in y,
+    # so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
+    inputfile = "BOUT_unsheared.inp"
+    cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc}"
 
-    for nproc in [1, 3]:
-        # Make sure we don't use too many cores:
-        # Reduce number of OpenMP threads when using multiple MPI processes
-        mthread = 2
-        if nproc > 1:
-            mthread = 1
+    shell(["rm -f data/BOUT.dmp.*.nc"])
 
-        # set nxpe on the command line as we only use solution from one point in y,
-        # so splitting in y-direction is redundant (and also doesn't help test the multigrid solver)
-        inputfile = "BOUT_unsheared.inp"
-        cmd = f"./test_multigrid_laplace -f {inputfile} NXPE={nproc}"
+    print(
+        f"Running unsheared multigrid Laplacian test: {nproc} procs, {mthread} thread(s)"
+    )
 
-        shell(["rm data/BOUT.dmp.*.nc"])
+    s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
 
-        print("   %d processors..." % nproc)
-        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-        with open("run.log." + str(nproc), "w") as f:
-            f.write(out)
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
 
-        # Collect errors
-        errors = [
-            collect("max_error" + str(i), path="data") for i in range(1, numTests + 1)
-        ]
+    # Collect errors
+    failures = []
+    for i in range(1, numTests + 1):
+        var_name = f"max_error{i}"
+        e = collect(var_name, path="data", info=False)
 
-        for i, e in enumerate(errors):
-            print("Checking test " + str(i))
-            if e < 0.0:
-                print("Fail, solver did not converge")
-                success = False
-            if e > tol:
-                print("Fail, maximum absolute error = " + str(e))
-                success = False
-            else:
-                print("Pass")
+        if e < 0.0:
+            failures.append(
+                f"Sub-test {i} ({var_name}): Solver did not converge (error = {e})"
+            )
+        elif e > tol:
+            failures.append(
+                f"Sub-test {i} ({var_name}): Absolute error {e:.4e} exceeds tolerance {tol:.4e}"
+            )
 
-    assert success, " => Some failed tests"
+    assert not failures, "Some failed tests:\n" + "\n".join(failures)

From 66a2c5c05adf366351c6ef69fee21b1f8db41ded Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 22 Jun 2026 16:48:47 +0100
Subject: [PATCH 1470/1827] Refactor test_naulin_laplace for pytest

---
 .../test_naulin_laplace.py                    | 66 ++++++++-----------
 1 file changed, 28 insertions(+), 38 deletions(-)

diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
index 52c2e5144d..e252cfed54 100755
--- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
+++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
@@ -1,56 +1,46 @@
 #!/usr/bin/env python3
 
 # requires: not metric_3d
+# Cores: 3
 
-#
-# Run the test, check the error
-#
-
+import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
-# Cores: 3
-
 tol = 2e-7  # Absolute tolerance
 numTests = 4  # We test 4 different boundary conditions (with slightly different inputs for each)
 
 
-def test_naulin_laplace():
-
-    print("Running LaplaceNaulin inversion test")
-    success = True
+@pytest.mark.parametrize("nproc", [1, 3])
+def test_naulin_laplace(nproc):
+    # Make sure we don't use too many cores:
+    # Reduce number of OpenMP threads when using multiple MPI processes
+    mthread = 1 if nproc > 1 else 2
 
-    for nproc in [1, 3]:
-        # Make sure we don't use too many cores:
-        # Reduce number of OpenMP threads when using multiple MPI processes
-        mthread = 2
-        if nproc > 1:
-            mthread = 1
+    # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver)
+    cmd = f"./test_naulin_laplace NXPE={nproc}"
 
-        # set nxpe on the command line as we only use solution from one point in y, so splitting in y-direction is redundant (and also doesn't help test the solver)
-        cmd = "./test_naulin_laplace NXPE=" + str(nproc)
+    shell(["rm -f data/BOUT.dmp.*.nc"])
 
-        shell(["rm data/BOUT.dmp.*.nc"])
+    print(f"Running LaplaceNaulin inversion test: {nproc} procs, {mthread} thread(s)")
+    s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
 
-        print("   %d processors..." % nproc)
-        s, out = launch_safe(cmd, nproc=nproc, mthread=mthread, pipe=True)
-        with open("run.log." + str(nproc), "w") as f:
-            f.write(out)
+    with open(f"run.log.{nproc}", "w") as f:
+        f.write(out)
 
-        # Collect errors
-        errors = [
-            collect("max_error" + str(i), path="data") for i in range(1, numTests + 1)
-        ]
+    # Collect errors
+    failures = []
+    for i in range(1, numTests + 1):
+        var_name = f"max_error{i}"
+        e = collect(var_name, path="data", info=False)
 
-        for i, e in enumerate(errors):
-            print("Checking test " + str(i))
-            if e < 0.0:
-                print("Fail, solver did not converge")
-                success = False
-            if e > tol:
-                print("Fail, maximum absolute error = " + str(e))
-                success = False
-            else:
-                print("Pass")
+        if e < 0.0:
+            failures.append(
+                f"Sub-test {i} ({var_name}): Solver did not converge (error = {e})"
+            )
+        elif e > tol:
+            failures.append(
+                f"Sub-test {i} ({var_name}): Absolute error {e:.4e} exceeds tolerance threshold {tol:.4e}"
+            )
 
-    assert success, " => Some failed tests"
+    assert not failures, "Some failed tests:\n" + "\n".join(failures)

From a085053f7da1ff35644bffe18c43cafd5feee683 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 22 Jun 2026 22:57:50 -0700
Subject: [PATCH 1471/1827] Field3D::View remove mul,div index scaling

Not needed in current use, and may prevent vectorization.
---
 include/bout/field3d.hxx | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 09c7f1ce55..3cde85f3be 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -457,18 +457,17 @@ public:
 
   struct View {
     BoutReal* data;
-    int mul = 1;
-    int div = 1;
     BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
-      return data[(idx * mul) / div];
+      return data[idx];
     }
     BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal& operator[](int idx) const {
-      return data[(idx * mul) / div];
+      return data[idx];
     }
 
-    View& setScale(int mul, int div) {
-      this->mul = mul;
-      this->div = div;
+    template <typename Mul, typename Div>
+    View& setScale(Mul, Div) {
+      static_assert(!std::is_same_v<Mul, Mul>,
+                    "Field3D::View does not support setScale()");
       return *this;
     }
   };

From c63a090e7826444f9359244cdc796c745bab59b4 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 22 Jun 2026 23:01:06 -0700
Subject: [PATCH 1472/1827] BinaryExpr::evaluate optimize Field3D case

If iterating over Field3D, the RegionID can be used to get the
Region and so the blocks. This avoids lookup of array indices
and helps vectorize simple loops.
---
 include/bout/build_config.hxx | 19 +++++++++++++++++++
 include/bout/field3d.hxx      |  4 ++++
 include/bout/fieldops.hxx     | 28 ++++++++++++++++++++++++----
 src/field/field3d.cxx         | 13 +++++++++++++
 4 files changed, 60 insertions(+), 4 deletions(-)

diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx
index abc78e2cf0..9a160161d4 100644
--- a/include/bout/build_config.hxx
+++ b/include/bout/build_config.hxx
@@ -70,4 +70,23 @@ constexpr auto use_msgstack = static_cast<bool>(BOUT_USE_MSGSTACK);
 #define BOUT_FORCEINLINE inline
 #endif
 
+#if defined(_MSC_VER)
+#define BOUT_ASSUME(condition) __assume(condition)
+#elif defined(__clang__)
+#if __has_builtin(__builtin_assume)
+#define BOUT_ASSUME(condition) __builtin_assume(condition)
+#else
+#define BOUT_ASSUME(condition) ((void)0)
+#endif
+#elif defined(__GNUC__)
+#define BOUT_ASSUME(condition) \
+  do {                         \
+    if (!(condition)) {        \
+      __builtin_unreachable(); \
+    }                          \
+  } while (false)
+#else
+#define BOUT_ASSUME(condition) ((void)0)
+#endif
+
 #endif // BOUT_BUILD_OPTIONS_HXX
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 3cde85f3be..6ce9fd3397 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -52,6 +52,10 @@ class Mesh;
 class Options;
 class Field3DParallel;
 
+namespace bout::detail {
+const Region<Ind3D>& getField3DRegion(const Mesh* mesh, std::optional<size_t> regionID);
+}
+
 #include "bout/fieldops.hxx"
 
 /// Class for 3D X-Y-Z scalar fields
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 53e28042c9..219c9150f3 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -24,6 +24,10 @@ class Field3DParallel;
 class Field2D;
 class FieldPerp;
 
+namespace bout::detail {
+const Region<Ind3D>& getField3DRegion(const Mesh* mesh, std::optional<size_t> regionID);
+}
+
 template <typename T>
 struct is_expr_field2d : std::false_type {};
 
@@ -410,10 +414,26 @@ struct BinaryExpr {
     cudaStreamSynchronize(stream);
     streams.put(stream);
 #else
-    int e = size();
-    for (int i = 0; i < e; ++i) {
-      int idx = regionIdx(i);
-      data[idx] = operator()(idx); // single‐pass fusion
+    if constexpr (std::is_same_v<ResT, Field3D>) {
+      const auto& region = bout::detail::getField3DRegion(mesh, regionID);
+      for (auto block = region.getBlocks().cbegin(), end = region.getBlocks().cend();
+           block < end; ++block) {
+        const int block_begin = block->first.ind;
+        const int block_end = block->second.ind;
+
+        BOUT_ASSUME(block_begin >= 0);
+        BOUT_ASSUME(block_begin <= block_end);
+
+        for (int idx = block_begin; idx < block_end; ++idx) {
+          data[idx] = operator()(idx);
+        }
+      }
+    } else {
+      int e = size();
+      for (int i = 0; i < e; ++i) {
+        int idx = regionIdx(i);
+        data[idx] = operator()(idx); // single‐pass fusion
+      }
     }
 #endif
   }
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 7915579440..9e459cc97d 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -927,6 +927,19 @@ std::ostream& operator<<(std::ostream& out, const Field3D& value) {
   return out;
 }
 
+namespace bout::detail {
+
+const Region<Ind3D>& getField3DRegion(const Mesh* mesh, std::optional<size_t> regionID) {
+  ASSERT1(mesh != nullptr);
+
+  if (regionID.has_value()) {
+    return mesh->getRegion(regionID.value());
+  }
+  return mesh->getRegion("RGN_ALL");
+}
+
+} // namespace bout::detail
+
 void swap(Field3D& first, Field3D& second) noexcept {
   using std::swap;
 

From 62379c7c1264106cdb074974e1fab612bdae8fa2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 17 Jun 2026 11:31:28 +0200
Subject: [PATCH 1473/1827] Fix off by one error

---
 include/bout/boundary_region_iter.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 296d1c8e53..d7cdff268d 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -540,7 +540,7 @@ public:
   signed char _valid() const { return region->bndry_points[pos].valid; }
   Ind3D _ind() const { return region->bndry_points[pos].index; }
   signed char _boundary_width() const {
-    return region->localmesh->ystart - region->bndry_points[pos].abs_offset;
+    return region->localmesh->ystart - region->bndry_points[pos].abs_offset + 1;
   }
   BoutReal _length([[maybe_unused]] CELL_LOC loc) const {
     ASSERT3(loc == CELL_CENTRE);

From c65424b4707ab2957326788b276e9fc75a02fcbc Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 23 Jun 2026 10:32:16 +0100
Subject: [PATCH 1474/1827] Refactor test_petsc_laplace_MAST_grid for pytest

---
 .../test_petsc_laplace_MAST_grid.py           | 69 ++++++++-----------
 1 file changed, 30 insertions(+), 39 deletions(-)

diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
index 9c67f4bc80..5489a47736 100755
--- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
@@ -8,59 +8,50 @@
 # requires: petsc
 # cores: 4
 
+import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
-from sys import stdout
 
 # Variables to compare
 vars = [
-    ["max_error1", 2.0e-4],
-    ["max_error2", 1.0e-4],
-    ["max_error3", 1.0e-4],
-    ["max_error4", 1.0e-4],
-    ["max_error5", 2.0e-3],
-    ["max_error6", 3.0e-4],
-    ["max_error7", 2.0e-4],
-    ["max_error8", 1.0e-4],
+    ("max_error1", 2.0e-4),
+    ("max_error2", 1.0e-4),
+    ("max_error3", 1.0e-4),
+    ("max_error4", 1.0e-4),
+    ("max_error5", 2.0e-3),
+    ("max_error6", 3.0e-4),
+    ("max_error7", 2.0e-4),
+    ("max_error8", 1.0e-4),
 ]
 # tol = 1e-4                  # Absolute (?) tolerance
 
 
-def test_petsc_laplace_MAST_grid():
-
+@pytest.mark.parametrize("nproc", [1, 2, 4])
+@pytest.mark.parametrize("jy", [2, 34, 65, 81, 113])
+def test_petsc_laplace_MAST_grid(nproc, jy):
     print(
         "Running PETSc Laplacian inversion test with non-identity metric (taken from grid for MAST SOL)"
     )
-    success = True
 
-    for nproc in [1, 2, 4]:
-        #  nxpe = 1
-        #  if nproc > 2:
-        #    nxpe = 2
-        for jy in [2, 34, 65, 81, 113]:
-            cmd = "./test_petsc_laplace_MAST_grid mesh:file=grids/grid_MAST_SOL_jyis{}.nc".format(
-                jy
-            )
+    cmd = f"./test_petsc_laplace_MAST_grid mesh:file=grids/grid_MAST_SOL_jyis{jy}.nc"
+
+    shell(["rm -f data/BOUT.dmp.*.nc"])
 
-            shell(["rm data/BOUT.dmp.*.nc"])
+    s, out = launch_safe(cmd, nproc=nproc, pipe=True)
 
-            print("   {} processors, grid_MAST_SOL_jyis{}".format(nproc, jy))
-            s, out = launch_safe(cmd, nproc=nproc, pipe=True)
-            f = open("run.log." + str(nproc), "w")
-            f.write(out)
-            f.close()
+    with open(f"run.log.{nproc}.jy_{jy}", "w") as f:
+        f.write(out)
 
-            # Collect output data
-            for v in vars:
-                stdout.write("      Checking " + v[0] + " ... ")
-                error = collect(v[0], path="data", info=False)
-                if error <= 0:
-                    print("Convergence error")
-                    success = False
-                elif error > v[1]:
-                    print("Fail, maximum error is = " + str(error))
-                    success = False
-                else:
-                    print("Pass")
+    # Collect output data
+    failures = []
+    for var_name, tolerance in vars:
+        error = collect(var_name, path="data", info=False)
+
+        if error <= 0:
+            failures.append(f"{var_name}: Solver did not converge (error = {error})")
+        elif error > tolerance:
+            failures.append(
+                f"{var_name}: Absolute error {error:.4e} exceeds tolerance {tolerance:.4e}"
+            )
 
-    assert success, " => Some failed tests"
+    assert not failures, "Some failed tests:\n" + "\n".join(failures)

From 1f4c9e1523fc7f166c475b0d214296c8ff4af280 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 23 Jun 2026 11:29:47 +0100
Subject: [PATCH 1475/1827] Apply ruff formatting

---
 .../test_griddata_yboundary_guards.py                        | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
index ad738830e2..6faf020dbc 100755
--- a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
+++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
@@ -19,7 +19,6 @@ def test_griddata_yboundary_guards(topology, n_yguards):
     blocksize = ny // 6
     nproc = 6
 
-
     datadir = Path(f"data-{topology}-{n_yguards}")
     datadir.mkdir(parents=True, exist_ok=True)
 
@@ -102,7 +101,7 @@ def test_griddata_yboundary_guards(topology, n_yguards):
 
     if topology == "doublenull":
         if n_yguards == 0:
-                # output has 2 y-guard cells, but grid file did not
+            # output has 2 y-guard cells, but grid file did not
             myg = 2
             checkfield = list(numpy.zeros(myg))
             checkfield += list(numpy.arange(ny // 2))
@@ -118,7 +117,7 @@ def test_griddata_yboundary_guards(topology, n_yguards):
             checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
     else:  # singlenull
         if n_yguards == 0:
-                # output has 2 y-guard cells, but grid file did not
+            # output has 2 y-guard cells, but grid file did not
             myg = 2
             checkfield = list(numpy.zeros(myg))
             checkfield += list(numpy.arange(ny))

From d0072e83aeb1866f26612749ae37854a93d43fee Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 23 Jun 2026 11:39:13 +0100
Subject: [PATCH 1476/1827] Refactor test_twistshift for pytest

---
 .../test-twistshift/test_twistshift.py        | 75 ++++++++-----------
 1 file changed, 32 insertions(+), 43 deletions(-)

diff --git a/tests/integrated/test-twistshift/test_twistshift.py b/tests/integrated/test-twistshift/test_twistshift.py
index d586244bb4..712d777b70 100755
--- a/tests/integrated/test-twistshift/test_twistshift.py
+++ b/tests/integrated/test-twistshift/test_twistshift.py
@@ -1,18 +1,24 @@
 #!/usr/bin/env python3
 
+import numpy as np
 from boutdata import collect
 from boututils.run_wrapper import launch_safe
-import numpy
 
 datapath = "data"
 nproc = 1
 tol = 1.0e-13
+non_periodic_tol = 1.0e-6
+
+GUARD_PAIRS = [(0, -4), (1, -3), (2, -2), (3, -1)]
 
 
 def test_twistshift():
 
-    s, out = launch_safe("./test-twistshift", nproc=nproc, pipe=True)
-    with open("run.log." + str(nproc), "w") as f:
+    cmd = "./test-twistshift"
+
+    s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+
+    with open(f"run.log.{nproc}", "w") as f:
         f.write(out)
 
     test = collect("test", path=datapath, yguards=True, info=False)
@@ -22,52 +28,35 @@ def test_twistshift():
     # from boututils.showdata import showdata
     # showdata([test, test_aligned, result], titles=['test', 'test_aligned', 'result'])
 
-    success = True
-
     # Check test_aligned is *not* periodic in y
-    def test1(ylower, yupper):
-        global success
-        if numpy.any(
-            numpy.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :]) < 1.0e-6
-        ):
-            success = False
-            print(
-                "Fail - test_aligned should not be periodic jy=%i and jy=%i should be "
-                "different",
-                yupper,
-                ylower,
+    failures = []
+    for ylower, yupper in GUARD_PAIRS:
+        diff = np.abs(test_aligned[:, yupper, :] - test_aligned[:, ylower, :])
+        if np.any(diff < non_periodic_tol):
+            failures.append(
+                f"Alignment Check: 'test_aligned' should not be periodic. "
+                f"Slices at jy={yupper} and jy={ylower} are identical within {non_periodic_tol}."
             )
 
-    test1(0, -4)
-    test1(1, -3)
-    test1(2, -2)
-    test1(3, -1)
-
     # Check test and result are the same
-    if numpy.any(numpy.abs(result - test) > tol):
-        print(
-            "Fail - result has not been communicated correctly - is different from input"
+    diff_result_test = np.abs(result - test)
+    if np.any(diff_result_test > tol):
+        max_diff = np.max(diff_result_test)
+        failures.append(
+            f"Fail - result has not been communicated correctly - is different from input. "
+            f"Maximum divergence is {max_diff:.4e} (exceeds {tol:.4e} tolerance)."
         )
-        success = False
 
     # Check result is periodic in y
-    def test2(ylower, yupper):
-        global success
-        if numpy.any(numpy.abs(result[:, yupper, :] - result[:, ylower, :]) > tol):
-            success = False
-            print(
-                "Fail - result should be periodic jy=%i and jy=%i should not be "
-                "different",
-                yupper,
-                ylower,
+    for ylower, yupper in GUARD_PAIRS:
+        diff = np.abs(result[:, yupper, :] - result[:, ylower, :])
+        if np.any(diff > tol):
+            max_diff = np.max(diff)
+            failures.append(
+                f"Fail - result should be periodic  jy={yupper} and jy={ylower} should not be different. "
+                f"Maximum difference is {max_diff:.4e}."
             )
-            print(ylower, result[:, ylower, :])
-            print(yupper, result[:, yupper, :])
-            print(result[:, ylower, :] - result[:, yupper, :])
-
-    test2(0, -4)
-    test2(1, -3)
-    test2(2, -2)
-    test2(3, -1)
 
-    assert success
+    assert not failures, "TwistShift validation encountered failures:\n" + "\n".join(
+        failures
+    )

From 2e5367a60f20d820b5b758854a03cea28168feb4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 23 Jun 2026 14:30:10 +0200
Subject: [PATCH 1477/1827] Move implementations to different file

---
 include/bout/fv_ops.hxx                 | 971 +-----------------------
 src/mesh/fv_ops.cxx                     |  69 ++
 tests/unit/include/bout/test_fv_ops.cxx |   2 +-
 3 files changed, 84 insertions(+), 958 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 3a1a4eaee8..d256bad32a 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -77,245 +77,14 @@ Field3D D4DY4(const Field3D& d, const Field3D& f);
    */
 Field3D D4DY4_Index(const Field3D& f, bool bndry_flux = true);
 
-/*!
-   * Stencil used for Finite Volume calculations
-   * which includes cell face values L and R
-   */
-struct Stencil1D {
-  /// Cell centre values
-  BoutReal c;
-  BoutReal m;
-  BoutReal p;
-  BoutReal mm = BoutNaN;
-  BoutReal pp = BoutNaN;
-
-  /// Left cell face value
-  BoutReal L = BoutNaN;
-  /// Right cell face value
-  BoutReal R = BoutNaN;
-};
-
-/*!
-   * First order upwind for testing
-   */
-struct Upwind {
-  void operator()(Stencil1D& n) { n.L = n.R = n.c; }
-};
-
-/*!
-   * Fromm method
-   */
-struct Fromm {
-  void operator()(Stencil1D& n) {
-    n.L = n.c - (0.25 * (n.p - n.m));
-    n.R = n.c + (0.25 * (n.p - n.m));
-  }
-};
-
-/*!
-   * Second order slope limiter method
-   *
-   * Limits slope to minimum absolute value
-   * of left and right gradients. If at a maximum
-   * or minimum slope set to zero, i.e. reverts
-   * to first order upwinding
-   */
-struct MinMod {
-  void operator()(Stencil1D& n) {
-    // Choose the gradient within the cell
-    // as the minimum (smoothest) solution
-    const BoutReal slope = _minmod(n.p - n.c, n.c - n.m);
-    n.L = n.c - (0.5 * slope);
-    n.R = n.c + (0.5 * slope);
-  }
-
-private:
-  /*!
-     * Internal helper function for minmod slope limiter
-     *
-     * If the inputs have different signs then
-     * returns zero, otherwise chooses the value
-     * with the minimum magnitude.
-     */
-  static BoutReal _minmod(BoutReal a, BoutReal b) {
-    if (a * b <= 0.0) {
-      return 0.0;
-    }
-
-    if (fabs(a) < fabs(b)) {
-      return a;
-    }
-    return b;
-  }
-};
-
-/*!
-   * Monotonised Central (MC) second order slope limiter (Van Leer)
-   *
-   * Limits the slope based on taking the slope with
-   * the minimum absolute value from central, 2*left and
-   * 2*right. If any of these slopes have different signs
-   * then the slope reverts to zero (i.e. 1st-order upwinding).
-   */
-struct MC {
-  void operator()(Stencil1D& n) {
-    const BoutReal slope = minmod(2. * (n.p - n.c),  // 2*right difference
-                                  0.5 * (n.p - n.m), // Central difference
-                                  2. * (n.c - n.m)); // 2*left difference
-    n.L = n.c - (0.5 * slope);
-    n.R = n.c + (0.5 * slope);
-  }
-
-private:
-  // Return zero if any signs are different
-  // otherwise return the value with the minimum magnitude
-  static BoutReal minmod(BoutReal a, BoutReal b, BoutReal c) {
-    // if any of the signs are different, return zero gradient
-    if ((a * b <= 0.0) || (a * c <= 0.0)) {
-      return 0.0;
-    }
-
-    // Return the minimum absolute value
-    return SIGN(a) * BOUTMIN(fabs(a), fabs(b), fabs(c));
-  }
-};
-
-/// Superbee limiter
-///
-/// This corresponds to the limiter function
-///    φ(r) = max(0, min(2r, 1), min(r,2)
-///
-/// The value at cell right (i.e. i + 1/2) is:
-///
-///   n.R = n.c - φ(r) (n.c - (n.p + n.c)/2)
-///       = n.c + φ(r) (n.p - n.c)/2
-///
-/// Four regimes:
-///  a) r < 1/2 -> φ(r) = 2r
-///     n.R = n.c + gL
-///  b) 1/2 < r < 1 -> φ(r) = 1
-///     n.R = n.c + gR/2
-///  c) 1 < r < 2 -> φ(r) = r
-///     n.R = n.c + gL/2
-///  d) 2 < r  -> φ(r) = 2
-///     n.R = n.c + gR
-///
-///  where the left and right gradients are:
-///   gL = n.c - n.m
-///   gR = n.p - n.c
-///
-struct Superbee {
-  void operator()(Stencil1D& n) {
-    const BoutReal gL = n.c - n.m;
-    const BoutReal gR = n.p - n.c;
-
-    // r = gL / gR
-    // Limiter is φ(r)
-    if (gL * gR < 0) {
-      // Different signs => Zero gradient
-      n.L = n.R = n.c;
-    } else {
-      const BoutReal sign = SIGN(gL);
-      const BoutReal abs_gL = fabs(gL);
-      const BoutReal abs_gR = fabs(gR);
-      const BoutReal half_slope =
-          sign * BOUTMAX(BOUTMIN(abs_gL, 0.5 * abs_gR), BOUTMIN(abs_gR, 0.5 * abs_gL));
-      n.L = n.c - half_slope;
-      n.R = n.c + half_slope;
-    }
-  }
-};
-
-/*!
-   * Symmetric Van Albada second order slope limiter
-   *
-   * Uses a smooth (differentiable) approximation to `max(a*b, 0)` to avoid
-   * introducing a kink at extrema, which can be helpful for nonlinear solvers
-   * and finite-difference Jacobian calculations.
-   *
-   * The limited slope is calculated from the left and right differences
-   * `dl = c - m` and `dr = p - c` as
-   *
-   *   slope = (pos(dl*dr) * (dl + dr)) / (dl^2 + dr^2)
-   *
-   * where `pos(x)` is a smooth approximation to `max(x, 0)`.
-   */
-struct VanAlbada {
-  void operator()(Stencil1D& n) {
-    const BoutReal dl = n.c - n.m;
-    const BoutReal dr = n.p - n.c;
-
-    const BoutReal denom = dl * dl + dr * dr;
-
-    // Smoothness parameters:
-    // - keep division well-defined when dl=dr=0
-    // - provide a differentiable approximation to max(dl*dr, 0)
-    const BoutReal eps = 1e-12 * denom + 1e-30;
-
-    const BoutReal ab = dl * dr;
-    const BoutReal ab_pos = 0.5 * (ab + sqrt(ab * ab + eps * eps));
-
-    const BoutReal slope = (ab_pos * (dl + dr)) / (denom + eps);
-
-    n.L = n.c - 0.5 * slope;
-    n.R = n.c + 0.5 * slope;
-  }
-};
-
-/*!
-   * WENO3-JS (Jiang-Shu) reconstruction to cell faces
-   *
-   * This is a third-order essentially non-oscillatory reconstruction using two
-   * candidate second-order polynomials and smoothness-weighted blending.
-   *
-   * Unlike TVD slope limiters (e.g. ``MC``), WENO reconstruction is generally
-   * smooth (differentiable) for all inputs, but it does not enforce strict
-   * monotonicity.
-   *
-   * Uses only the three-point stencil (`m`, `c`, `p`), so it is a drop-in
-   * replacement anywhere `Stencil1D` is populated with those values.
-   */
-struct WENO3 {
-  void operator()(Stencil1D& n) {
-    // Right face (between c and p): value from cell c (left state at i+1/2)
-    const BoutReal p0_r = 0.5 * (-n.m + 3.0 * n.c);
-    const BoutReal p1_r = 0.5 * (n.c + n.p);
-
-    const BoutReal beta0_r = SQ(n.c - n.m);
-    const BoutReal beta1_r = SQ(n.p - n.c);
-
-    // Left face (between m and c): value from cell c (right state at i-1/2)
-    const BoutReal p0_l = 0.5 * (-n.p + 3.0 * n.c);
-    const BoutReal p1_l = 0.5 * (n.m + n.c);
-
-    const BoutReal beta0_l = beta1_r;
-    const BoutReal beta1_l = beta0_r;
-
-    // Smoothness parameter (scaled to local variation)
-    const BoutReal eps = 1e-12 * (beta0_r + beta1_r) + 1e-30;
-
-    // Linear weights for WENO3-JS
-    constexpr BoutReal d0 = 1.0 / 3.0;
-    constexpr BoutReal d1 = 2.0 / 3.0;
-
-    // Right face weights
-    const BoutReal a0_r = d0 / SQ(eps + beta0_r);
-    const BoutReal a1_r = d1 / SQ(eps + beta1_r);
-    const BoutReal wsum_r = a0_r + a1_r;
-    const BoutReal w0_r = a0_r / wsum_r;
-    const BoutReal w1_r = a1_r / wsum_r;
-
-    // Left face weights (mirrored)
-    const BoutReal a0_l = d0 / SQ(eps + beta0_l);
-    const BoutReal a1_l = d1 / SQ(eps + beta1_l);
-    const BoutReal wsum_l = a0_l + a1_l;
-    const BoutReal w0_l = a0_l / wsum_l;
-    const BoutReal w1_l = a1_l / wsum_l;
-
-    n.R = w0_r * p0_r + w1_r * p1_r;
-    n.L = w0_l * p0_l + w1_l * p1_l;
-  }
-};
+// FluxLimiter
+class Upwind;
+class Fromm;
+class MinMod;
+class MC;
+class Superbee;
+class VanAlbada;
+class WENO3;
 
 /*!
    * Communicate fluxes between processors
@@ -341,173 +110,7 @@ void communicateFluxes(Field3D& f);
 /// NB: Uses to/from FieldAligned coordinates
 template <typename CellEdges = MC>
 Field3D Div_par(const Field3D& f_in, const Field3D& v_in, const Field3D& wave_speed_in,
-                bool fixflux = true) {
-
-  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
-  ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
-
-  const Mesh* mesh = f_in.getMesh();
-
-  CellEdges cellboundary;
-
-  ASSERT2(f_in.getDirectionY() == v_in.getDirectionY());
-  ASSERT2(f_in.getDirectionY() == wave_speed_in.getDirectionY());
-  const bool are_unaligned =
-      ((f_in.getDirectionY() == YDirectionType::Standard)
-       and (v_in.getDirectionY() == YDirectionType::Standard)
-       and (wave_speed_in.getDirectionY() == YDirectionType::Standard));
-
-  Field3D f = are_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in;
-  Field3D v = are_unaligned ? toFieldAligned(v_in, "RGN_NOX") : v_in;
-  Field3D wave_speed =
-      are_unaligned ? toFieldAligned(wave_speed_in, "RGN_NOX") : wave_speed_in;
-
-  Coordinates* coord = f_in.getCoordinates();
-
-  Field3D result{zeroFrom(f)};
-
-  for (int i = mesh->xstart; i <= mesh->xend; i++) {
-    const bool is_periodic_y = mesh->periodicY(i);
-    const bool is_first_y = mesh->firstY(i);
-    const bool is_last_y = mesh->lastY(i);
-
-    // Only need one guard cell, so no need to communicate fluxes Instead
-    // calculate in guard cells to get fluxes consistent between processors, but
-    // don't include the boundary cell. Note that this implies special handling
-    // of boundaries later
-    const int ys = (!is_first_y || is_periodic_y) ? mesh->ystart - 1 : mesh->ystart;
-    const int ye = (!is_last_y || is_periodic_y) ? mesh->yend + 1 : mesh->yend;
-
-    for (int j = ys; j <= ye; j++) {
-      // Pre-calculate factors which multiply fluxes
-#if not(BOUT_USE_METRIC_3D)
-      // For right cell boundaries
-      BoutReal common_factor = (coord->J(i, j) + coord->J(i, j + 1))
-                               / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1)));
-
-      const BoutReal flux_factor_rc = common_factor / (coord->dy(i, j) * coord->J(i, j));
-      const BoutReal flux_factor_rp =
-          common_factor / (coord->dy(i, j + 1) * coord->J(i, j + 1));
-
-      // For left cell boundaries
-      common_factor = (coord->J(i, j) + coord->J(i, j - 1))
-                      / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1)));
-
-      const BoutReal flux_factor_lc = common_factor / (coord->dy(i, j) * coord->J(i, j));
-      const BoutReal flux_factor_lm =
-          common_factor / (coord->dy(i, j - 1) * coord->J(i, j - 1));
-#endif
-      for (int k = mesh->zstart; k <= mesh->zend; k++) {
-#if BOUT_USE_METRIC_3D
-        // For right cell boundaries
-        BoutReal common_factor =
-            (coord->J(i, j, k) + coord->J(i, j + 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
-
-        BoutReal flux_factor_rc =
-            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
-        BoutReal flux_factor_rp =
-            common_factor / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
-
-        // For left cell boundaries
-        common_factor = (coord->J(i, j, k) + coord->J(i, j - 1, k))
-                        / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
-
-        BoutReal flux_factor_lc =
-            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
-        BoutReal flux_factor_lm =
-            common_factor / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
-#endif
-
-        ////////////////////////////////////////////
-        // Reconstruct f at the cell faces
-        // This calculates s.R and s.L for the Right and Left
-        // face values on this cell
-
-        // Reconstruct f at the cell faces
-        Stencil1D s;
-        s.c = f(i, j, k);
-        s.m = f(i, j - 1, k);
-        s.p = f(i, j + 1, k);
-
-        cellboundary(s); // Calculate s.R and s.L
-
-        ////////////////////////////////////////////
-        // Right boundary
-
-        // Calculate velocity at right boundary (y+1/2)
-        BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j + 1, k));
-        BoutReal flux = NAN;
-
-        if (is_last_y && (j == mesh->yend) && !is_periodic_y) {
-          // Last point in domain
-
-          const BoutReal bndryval = 0.5 * (s.c + s.p);
-          if (fixflux) {
-            // Use mid-point to be consistent with boundary conditions
-            flux = bndryval * vpar;
-          } else {
-            // Add flux due to difference in boundary values
-            flux = (s.R * vpar) + (wave_speed(i, j, k) * (s.R - bndryval));
-          }
-        } else {
-
-          // Maximum wave speed in the two cells
-          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k));
-
-          if (vpar > amax) {
-            // Supersonic flow out of this cell
-            flux = s.R * vpar;
-          } else if (vpar < -amax) {
-            // Supersonic flow into this cell
-            flux = 0.0;
-          } else {
-            // Subsonic flow, so a mix of right and left fluxes
-            flux = s.R * 0.5 * (vpar + amax);
-          }
-        }
-
-        result(i, j, k) += flux * flux_factor_rc;
-        result(i, j + 1, k) -= flux * flux_factor_rp;
-
-        ////////////////////////////////////////////
-        // Calculate at left boundary
-
-        vpar = 0.5 * (v(i, j, k) + v(i, j - 1, k));
-
-        if (is_first_y && (j == mesh->ystart) && !is_periodic_y) {
-          // First point in domain
-          const BoutReal bndryval = 0.5 * (s.c + s.m);
-          if (fixflux) {
-            // Use mid-point to be consistent with boundary conditions
-            flux = bndryval * vpar;
-          } else {
-            // Add flux due to difference in boundary values
-            flux = (s.L * vpar) - (wave_speed(i, j, k) * (s.L - bndryval));
-          }
-        } else {
-
-          // Maximum wave speed in the two cells
-          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k));
-
-          if (vpar < -amax) {
-            // Supersonic out of this cell
-            flux = s.L * vpar;
-          } else if (vpar > amax) {
-            // Supersonic into this cell
-            flux = 0.0;
-          } else {
-            flux = s.L * 0.5 * (vpar - amax);
-          }
-        }
-
-        result(i, j, k) -= flux * flux_factor_lc;
-        result(i, j - 1, k) += flux * flux_factor_lm;
-      }
-    }
-  }
-  return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result;
-}
+                bool fixflux = true);
 
 /*!
    * Div ( n * v )  -- Magnetic drifts
@@ -522,142 +125,7 @@ Field3D Div_par(const Field3D& f_in, const Field3D& v_in, const Field3D& wave_sp
    *
    */
 template <typename CellEdges = MC>
-Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
-  ASSERT1(n_in.getLocation() == v.getLocation());
-  ASSERT1_FIELDS_COMPATIBLE(n_in, v.x);
-
-  const Mesh* mesh = n_in.getMesh();
-
-  CellEdges cellboundary;
-
-  Coordinates* coord = n_in.getCoordinates();
-
-  if (v.covariant) {
-    // Got a covariant vector instead
-    throw BoutException("Div_f_v passed a covariant v");
-  }
-
-  Field3D result{zeroFrom(n_in)};
-
-  Field3D vx = v.x;
-  Field3D vz = v.z;
-  Field3D n = n_in;
-
-  BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
-    // Calculate velocities
-    const BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]);
-    const BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]);
-    const BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J[i.xm()] + coord->J[i]);
-    const BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J[i.xp()] + coord->J[i]);
-
-    // X direction
-    Stencil1D s;
-    s.c = n[i];
-    s.m = n[i.xm()];
-    s.mm = n[i.xmm()];
-    s.p = n[i.xp()];
-    s.pp = n[i.xpp()];
-
-    cellboundary(s);
-
-    if ((i.x() == mesh->xend) && (mesh->lastX())) {
-      // At right boundary in X
-      if (bndry_flux) {
-        BoutReal flux = NAN;
-        if (vR > 0.0) {
-          // Flux to boundary
-          flux = vR * s.R;
-        } else {
-          // Flux in from boundary
-          flux = vR * 0.5 * (n[i.xp()] + n[i]);
-        }
-        result[i] += flux / (coord->dx[i] * coord->J[i]);
-        result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]);
-      }
-    } else {
-      // Not at a boundary
-      if (vR > 0.0) {
-        // Flux out into next cell
-        const BoutReal flux = vR * s.R;
-        result[i] += flux / (coord->dx[i] * coord->J[i]);
-        result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]);
-      }
-    }
-
-    // Left side
-
-    if ((i.x() == mesh->xstart) && (mesh->firstX())) {
-      // At left boundary in X
-
-      if (bndry_flux) {
-        BoutReal flux = NAN;
-        if (vL < 0.0) {
-          // Flux to boundary
-          flux = vL * s.L;
-        } else {
-          // Flux in from boundary
-          flux = vL * 0.5 * (n[i.xm()] + n[i]);
-        }
-        result[i] -= flux / (coord->dx[i] * coord->J[i]);
-        result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]);
-      }
-    } else {
-      // Not at a boundary
-      if (vL < 0.0) {
-        const BoutReal flux = vL * s.L;
-        result[i] -= flux / (coord->dx[i] * coord->J[i]);
-        result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]);
-      }
-    }
-
-    /// NOTE: Need to communicate fluxes
-
-    // Z direction
-    s.m = n[i.zm()];
-    s.mm = n[i.zmm()];
-    s.p = n[i.zp()];
-    s.pp = n[i.zpp()];
-
-    cellboundary(s);
-
-    if (vU > 0.0) {
-      const BoutReal flux = vU * s.R;
-      result[i] += flux / (coord->J[i] * coord->dz[i]);
-      result[i.zp()] -= flux / (coord->J[i.zp()] * coord->dz[i.zp()]);
-    }
-    if (vD < 0.0) {
-      const BoutReal flux = vD * s.L;
-      result[i] -= flux / (coord->J[i] * coord->dz[i]);
-      result[i.zm()] += flux / (coord->J[i.zm()] * coord->dz[i.zm()]);
-    }
-  }
-
-  communicateFluxes(result);
-
-  // Y advection
-  // Currently just using simple centered differences
-  // so no fluxes need to be exchanged
-
-  n = toFieldAligned(n_in, "RGN_NOX");
-  Field3D vy = toFieldAligned(v.y, "RGN_NOX");
-
-  Field3D yresult = 0.0;
-  yresult.setDirectionY(YDirectionType::Aligned);
-
-  BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
-    // Y velocities on y boundaries
-    const BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]);
-    const BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]);
-
-    // n (advected quantity) on y boundaries
-    // Note: Use unshifted n_in variable
-    const BoutReal nU = 0.5 * (n[i] + n[i.yp()]);
-    const BoutReal nD = 0.5 * (n[i] + n[i.ym()]);
-
-    yresult[i] = (nU * vU - nD * vD) / (coord->J[i] * coord->dy[i]);
-  }
-  return result + fromFieldAligned(yresult, "RGN_NOBNDRY");
-}
+Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 
 /*!
    * X-Z Finite Volume diffusion operator
@@ -687,222 +155,7 @@ Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc = CELL_
 template <typename CellEdges = MC>
 Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
                     const Field3D& wave_speed_in, Field3D& flow_ylow,
-                    bool fixflux = true) {
-
-  Coordinates* coord = f_in.getCoordinates();
-  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
-
-  if (f_in.isFci()) {
-    // Use mid-point (cell boundary) averages
-
-    ASSERT1(f_in.hasParallelSlices());
-    ASSERT1(v_in.hasParallelSlices());
-
-    const auto& f_up = f_in.yup();
-    const auto& f_down = f_in.ydown();
-
-    const auto& v_up = v_in.yup();
-    const auto& v_down = v_in.ydown();
-
-    Field3D result{emptyFrom(f_in)};
-    BOUT_FOR(i, f_in.getRegion("RGN_NOBNDRY")) {
-      const auto iyp = i.yp();
-      const auto iym = i.ym();
-
-      result[i] = (0.25 * (f_in[i] + f_up[iyp]) * (v_in[i] + v_up[iyp])
-                       * (coord->J[i] + coord->J.yup()[iyp])
-                       / (sqrt(coord->g_22[i]) + sqrt(coord->g_22.yup()[iyp]))
-                   - 0.25 * (f_in[i] + f_down[iym]) * (v_in[i] + v_down[iym])
-                         * (coord->J[i] + coord->J.ydown()[iym])
-                         / (sqrt(coord->g_22[i]) + sqrt(coord->g_22.ydown()[iym])))
-                  / (coord->dy[i] * coord->J[i]);
-    }
-    return result;
-  }
-  ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
-
-  const Mesh* mesh = f_in.getMesh();
-
-  CellEdges cellboundary;
-
-  ASSERT2(f_in.getDirectionY() == v_in.getDirectionY());
-  ASSERT2(f_in.getDirectionY() == wave_speed_in.getDirectionY());
-  const bool are_unaligned =
-      ((f_in.getDirectionY() == YDirectionType::Standard)
-       and (v_in.getDirectionY() == YDirectionType::Standard)
-       and (wave_speed_in.getDirectionY() == YDirectionType::Standard));
-
-  const Field3D f = are_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in;
-  const Field3D v = are_unaligned ? toFieldAligned(v_in, "RGN_NOX") : v_in;
-  const Field3D wave_speed =
-      are_unaligned ? toFieldAligned(wave_speed_in, "RGN_NOX") : wave_speed_in;
-
-  Field3D result{zeroFrom(f)};
-  flow_ylow = zeroFrom(f);
-
-  for (int i = mesh->xstart; i <= mesh->xend; i++) {
-    const bool is_periodic_y = mesh->periodicY(i);
-    const bool is_first_y = mesh->firstY(i);
-    const bool is_last_y = mesh->lastY(i);
-
-    // Only need one guard cell, so no need to communicate fluxes Instead
-    // calculate in guard cells to get fluxes consistent between processors, but
-    // don't include the boundary cell. Note that this implies special handling
-    // of boundaries later
-    const int ys = (!is_first_y || is_periodic_y) ? mesh->ystart - 1 : mesh->ystart;
-    const int ye = (!is_last_y || is_periodic_y) ? mesh->yend + 1 : mesh->yend;
-
-    for (int j = ys; j <= ye; j++) {
-      // Pre-calculate factors which multiply fluxes
-#if not(BOUT_USE_METRIC_3D)
-      // For right cell boundaries
-      const BoutReal common_factor_r =
-          (coord->J(i, j) + coord->J(i, j + 1))
-          / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1)));
-
-      const BoutReal flux_factor_rc =
-          common_factor_r / (coord->dy(i, j) * coord->J(i, j));
-      const BoutReal flux_factor_rp =
-          common_factor_r / (coord->dy(i, j + 1) * coord->J(i, j + 1));
-
-      const BoutReal area_rp =
-          common_factor_r * coord->dx(i, j + 1) * coord->dz(i, j + 1);
-
-      // For left cell boundaries
-      const BoutReal common_factor_l =
-          (coord->J(i, j) + coord->J(i, j - 1))
-          / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1)));
-
-      const BoutReal flux_factor_lc =
-          common_factor_l / (coord->dy(i, j) * coord->J(i, j));
-      const BoutReal flux_factor_lm =
-          common_factor_l / (coord->dy(i, j - 1) * coord->J(i, j - 1));
-
-      const BoutReal area_lc = common_factor_l * coord->dx(i, j) * coord->dz(i, j);
-#endif
-      for (int k = 0; k < mesh->LocalNz; k++) {
-#if BOUT_USE_METRIC_3D
-        // For right cell boundaries
-        const BoutReal common_factor_r =
-            (coord->J(i, j, k) + coord->J(i, j + 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
-
-        const BoutReal flux_factor_rc =
-            common_factor_r / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal flux_factor_rp =
-            common_factor_r / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
-
-        const BoutReal area_rp =
-            common_factor_r * coord->dx(i, j + 1, k) * coord->dz(i, j + 1, k);
-
-        // For left cell boundaries
-        const BoutReal common_factor_l =
-            (coord->J(i, j, k) + coord->J(i, j - 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
-
-        const BoutReal flux_factor_lc =
-            common_factor_l / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal flux_factor_lm =
-            common_factor_l / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
-
-        const BoutReal area_lc =
-            common_factor_l * coord->dx(i, j, k) * coord->dz(i, j, k);
-#endif
-
-        ////////////////////////////////////////////
-        // Reconstruct f at the cell faces
-        // This calculates s.R and s.L for the Right and Left
-        // face values on this cell
-
-        // Reconstruct f at the cell faces
-        // TODO(peter): We can remove this #ifdef guard after switching to C++20
-#if __cpp_designated_initializers >= 201707L
-        Stencil1D s{.c = f(i, j, k), .m = f(i, j - 1, k), .p = f(i, j + 1, k)};
-#else
-        Stencil1D s{f(i, j, k), f(i, j - 1, k), f(i, j + 1, k), BoutNaN,
-                    BoutNaN,    BoutNaN,        BoutNaN};
-#endif
-        cellboundary(s); // Calculate s.R and s.L
-
-        ////////////////////////////////////////////
-        // Reconstruct v at the cell faces
-        // TODO(peter): We can remove this #ifdef guard after switching to C++20
-#if __cpp_designated_initializers >= 201707L
-        Stencil1D sv{.c = v(i, j, k), .m = v(i, j - 1, k), .p = v(i, j + 1, k)};
-#else
-        Stencil1D sv{v(i, j, k), v(i, j - 1, k), v(i, j + 1, k), BoutNaN,
-                     BoutNaN,    BoutNaN,        BoutNaN};
-#endif
-        cellboundary(sv); // Calculate sv.R and sv.L
-
-        ////////////////////////////////////////////
-        // Right boundary
-
-        BoutReal flux = BoutNaN;
-
-        if (is_last_y && (j == mesh->yend) && !is_periodic_y) {
-          // Last point in domain
-
-          // Calculate velocity at right boundary (y+1/2)
-          const BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j + 1, k));
-
-          const BoutReal bndryval = 0.5 * (s.c + s.p);
-          if (fixflux) {
-            // Use mid-point to be consistent with boundary conditions
-            flux = bndryval * vpar;
-          } else {
-            // Add flux due to difference in boundary values
-            flux = (s.R * vpar) + (wave_speed(i, j, k) * (s.R - bndryval));
-          }
-
-        } else {
-          // Maximum wave speed in the two cells
-          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
-                                        fabs(v(i, j, k)), fabs(v(i, j + 1, k)));
-
-          flux = s.R * 0.5 * (sv.R + amax);
-        }
-
-        result(i, j, k) += flux * flux_factor_rc;
-        result(i, j + 1, k) -= flux * flux_factor_rp;
-
-        flow_ylow(i, j + 1, k) += flux * area_rp;
-
-        ////////////////////////////////////////////
-        // Calculate at left boundary
-
-        if (is_first_y && (j == mesh->ystart) && !is_periodic_y) {
-          // First point in domain
-          const BoutReal bndryval = 0.5 * (s.c + s.m);
-          const BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j - 1, k));
-          if (fixflux) {
-            // Use mid-point to be consistent with boundary conditions
-            flux = bndryval * vpar;
-          } else {
-            // Add flux due to difference in boundary values
-            flux = (s.L * vpar) - (wave_speed(i, j, k) * (s.L - bndryval));
-          }
-        } else {
-
-          // Maximum wave speed in the two cells
-          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
-                                        fabs(v(i, j, k)), fabs(v(i, j - 1, k)));
-
-          flux = s.L * 0.5 * (sv.L - amax);
-        }
-
-        result(i, j, k) -= flux * flux_factor_lc;
-        result(i, j - 1, k) += flux * flux_factor_lm;
-
-        flow_ylow(i, j, k) += flux * area_lc;
-      }
-    }
-  }
-  if (are_unaligned) {
-    flow_ylow = fromFieldAligned(flow_ylow, "RGN_NOBNDRY");
-  }
-  return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result;
-}
+                    bool fixflux = true);
 
 /// This operator calculates Div_par(f v v)
 /// It is used primarily (only?) in the parallel momentum equation.
@@ -912,204 +165,8 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
 /// fv is not interpolated to cell boundaries.
 template <typename CellEdges = MC>
 Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
-                    const Field3D& wave_speed_in, bool fixflux = true) {
-  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
-  const Mesh* mesh = f_in.getMesh();
-  const Coordinates* coord = f_in.getCoordinates();
-  CellEdges cellboundary;
-
-  if (f_in.isFci()) {
-    // FCI version, using yup/down fields
-    ASSERT1(f_in.hasParallelSlices());
-    ASSERT1(v_in.hasParallelSlices());
-
-    const auto& B = coord->Bxy;
-    const auto& B_up = coord->Bxy.yup();
-    const auto& B_down = coord->Bxy.ydown();
-
-    const auto& f_up = f_in.yup();
-    const auto& f_down = f_in.ydown();
-
-    const auto& v_up = v_in.yup();
-    const auto& v_down = v_in.ydown();
-
-    const auto& g_22 = coord->g_22;
-    const auto& dy = coord->dy;
-
-    Field3D result{emptyFrom(f_in)};
-    BOUT_FOR(i, f_in.getRegion("RGN_NOBNDRY")) {
-      const auto iyp = i.yp();
-      const auto iym = i.ym();
-
-      // Maximum local wave speed
-      const BoutReal amax =
-          BOUTMAX(wave_speed_in[i], fabs(v_in[i]), fabs(v_up[iyp]), fabs(v_down[iym]));
-
-      const BoutReal term = (f_up[iyp] * v_up[iyp] * v_up[iyp] / B_up[iyp])
-                            - (f_down[iym] * v_down[iym] * v_down[iym] / B_down[iym]);
-
-      // Penalty terms. This implementation is very dissipative.
-      BoutReal penalty =
-          (amax * (f_in[i] * v_in[i] - f_up[iyp] * v_up[iyp]) / (B[i] + B_up[iyp]))
-          + (amax * (f_in[i] * v_in[i] - f_down[iym] * v_down[iym])
-             / (B[i] + B_down[iym]));
-
-      if (fabs(penalty) > fabs(term) and penalty * v_in[i] > 0) {
-        if (term * penalty > 0) {
-          penalty = term;
-        } else {
-          penalty = -term;
-        }
-      }
-
-      result[i] = B[i] * (term + penalty) / (2 * dy[i] * sqrt(g_22[i]));
-
-#if CHECK > 0
-      if (!std::isfinite(result[i])) {
-        throw BoutException("Non-finite value in Div_par_fvv at {}\n"
-                            "fup {} vup {} fdown {} vdown {} amax {}\n",
-                            "B {} Bup {} Bdown {} dy {} sqrt(g_22} {}", i, f_up[i],
-                            v_up[i], f_down[i], v_down[i], amax, B[i], B_up[i], B_down[i],
-                            dy[i], sqrt(g_22[i]));
-      }
-#endif
-    }
-    return result;
-  }
-
-  ASSERT1(areFieldsCompatible(f_in, wave_speed_in));
-
-  /// Ensure that f, v and wave_speed are field aligned
-  Field3D f = toFieldAligned(f_in, "RGN_NOX");
-  Field3D v = toFieldAligned(v_in, "RGN_NOX");
-  Field3D wave_speed = toFieldAligned(wave_speed_in, "RGN_NOX");
-
-  Field3D result{zeroFrom(f)};
-
-  for (int i = mesh->xstart; i <= mesh->xend; i++) {
-    const bool is_periodic_y = mesh->periodicY(i);
-    const bool is_first_y = mesh->firstY(i);
-    const bool is_last_y = mesh->lastY(i);
-
-    // Only need one guard cell, so no need to communicate fluxes Instead
-    // calculate in guard cells to get fluxes consistent between processors, but
-    // don't include the boundary cell. Note that this implies special handling
-    // of boundaries later
-    const int ys = (!is_first_y || is_periodic_y) ? mesh->ystart - 1 : mesh->ystart;
-    const int ye = (!is_last_y || is_periodic_y) ? mesh->yend + 1 : mesh->yend;
-
-    for (int j = ys; j <= ye; j++) {
-      // Pre-calculate factors which multiply fluxes
-
-      for (int k = 0; k < mesh->LocalNz; k++) {
-        // For right cell boundaries
-        const BoutReal common_factor_r =
-            (coord->J(i, j, k) + coord->J(i, j + 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
-
-        const BoutReal flux_factor_rc =
-            common_factor_r / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal flux_factor_rp =
-            common_factor_r / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
-
-        // For left cell boundaries
-        const BoutReal common_factor_l =
-            (coord->J(i, j, k) + coord->J(i, j - 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
-
-        const BoutReal flux_factor_lc =
-            common_factor_l / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal flux_factor_lm =
-            common_factor_l / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
-
-        ////////////////////////////////////////////
-        // Reconstruct f at the cell faces
-        // This calculates s.R and s.L for the Right and Left
-        // face values on this cell
-
-        // Reconstruct f at the cell faces
-#if __cpp_designated_initializers >= 201707L
-        Stencil1D s{.c = f(i, j, k), .m = f(i, j - 1, k), .p = f(i, j + 1, k)};
-#else
-        Stencil1D s{f(i, j, k), f(i, j - 1, k), f(i, j + 1, k), BoutNaN,
-                    BoutNaN,    BoutNaN,        BoutNaN};
-#endif
-        cellboundary(s); // Calculate s.R and s.L
-
-        ////////////////////////////////////////////
-        // Reconstruct v at the cell faces
-        // TODO(peter): We can remove this #ifdef guard after switching to C++20
-#if __cpp_designated_initializers >= 201707L
-        Stencil1D sv{.c = v(i, j, k), .m = v(i, j - 1, k), .p = v(i, j + 1, k)};
-#else
-        Stencil1D sv{v(i, j, k), v(i, j - 1, k), v(i, j + 1, k), BoutNaN,
-                     BoutNaN,    BoutNaN,        BoutNaN};
-#endif
-        cellboundary(sv);
-
-        ////////////////////////////////////////////
-        // Right boundary
-
-        // Calculate velocity at right boundary (y+1/2)
-        const BoutReal v_mid_r = 0.5 * (sv.c + sv.p);
-        // And mid-point density at right boundary
-        const BoutReal n_mid_r = 0.5 * (s.c + s.p);
-        BoutReal flux = NAN;
-
-        if (mesh->lastY(i) && (j == mesh->yend) && !mesh->periodicY(i)) {
-          // Last point in domain
-
-          if (fixflux) {
-            // Use mid-point to be consistent with boundary conditions
-            flux = n_mid_r * v_mid_r * v_mid_r;
-          } else {
-            // Add flux due to difference in boundary values
-            flux = (s.R * sv.R * sv.R) // Use right cell edge values
-                   + (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.p)) * n_mid_r
-                      * (sv.R - v_mid_r)); // Damp differences in velocity, not flux
-          }
-        } else {
-          // Maximum wave speed in the two cells
-          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
-                                        fabs(sv.c), fabs(sv.p));
-
-          flux = s.R * 0.5 * (sv.R + amax) * sv.R;
-        }
-
-        result(i, j, k) += flux * flux_factor_rc;
-        result(i, j + 1, k) -= flux * flux_factor_rp;
-
-        ////////////////////////////////////////////
-        // Calculate at left boundary
-
-        const BoutReal v_mid_l = 0.5 * (sv.c + sv.m);
-        const BoutReal n_mid_l = 0.5 * (s.c + s.m);
-
-        if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) {
-          // First point in domain
-          if (fixflux) {
-            // Use mid-point to be consistent with boundary conditions
-            flux = n_mid_l * v_mid_l * v_mid_l;
-          } else {
-            // Add flux due to difference in boundary values
-            flux = (s.L * sv.L * sv.L)
-                   - (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.m)) * n_mid_l
-                      * (sv.L - v_mid_l));
-          }
-        } else {
-          // Maximum wave speed in the two cells
-          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
-                                        fabs(sv.c), fabs(sv.m));
-
-          flux = s.L * 0.5 * (sv.L - amax) * sv.L;
-        }
-
-        result(i, j, k) -= flux * flux_factor_lc;
-        result(i, j - 1, k) += flux * flux_factor_lm;
-      }
-    }
-  }
-  return fromFieldAligned(result, "RGN_NOBNDRY");
-}
+                    const Field3D& wave_speed_in, bool fixflux = true);
+// extern template Field3D Div_par_fvv<MC>(const Field3D& f_in, const Field3D& v_in,
+// 				const Field3D& wave_speed_in, bool fixflux = true);
 } // namespace FV
 #endif // BOUT_FV_OPS_H
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index 6b8d8a6f21..a1333b1406 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -1,4 +1,5 @@
 #include "bout/fv_ops.hxx"
+#include "bout/fv_ops_impl.hxx"
 
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
@@ -563,4 +564,72 @@ Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc) {
   return result;
 }
 
+//  BOUT_ENUM_CLASS(FluxLimiter, Upwind, Fromm, MinMod, MC, Superbee, VanAlbada, WENO3);
+
+template Field3D Div_par_fvv<Upwind>(const Field3D& f_in, const Field3D& v_in,
+                                     const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_par<Upwind>(const Field3D& f_in, const Field3D& v_in,
+                                 const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_f_v<Upwind>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
+template Field3D Div_par_mod<Upwind>(const Field3D& f_in, const Field3D& v_in,
+                                     const Field3D& wave_speed_in, Field3D& flow_ylow,
+                                     bool fixflux = true);
+
+template Field3D Div_par_fvv<Fromm>(const Field3D& f_in, const Field3D& v_in,
+                                    const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_par<Fromm>(const Field3D& f_in, const Field3D& v_in,
+                                const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_f_v<Fromm>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
+template Field3D Div_par_mod<Fromm>(const Field3D& f_in, const Field3D& v_in,
+                                    const Field3D& wave_speed_in, Field3D& flow_ylow,
+                                    bool fixflux = true);
+
+template Field3D Div_par_fvv<MinMod>(const Field3D& f_in, const Field3D& v_in,
+                                     const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_par<MinMod>(const Field3D& f_in, const Field3D& v_in,
+                                 const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_f_v<MinMod>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
+template Field3D Div_par_mod<MinMod>(const Field3D& f_in, const Field3D& v_in,
+                                     const Field3D& wave_speed_in, Field3D& flow_ylow,
+                                     bool fixflux = true);
+
+template Field3D Div_par_fvv<MC>(const Field3D& f_in, const Field3D& v_in,
+                                 const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_par<MC>(const Field3D& f_in, const Field3D& v_in,
+                             const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_f_v<MC>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
+template Field3D Div_par_mod<MC>(const Field3D& f_in, const Field3D& v_in,
+                                 const Field3D& wave_speed_in, Field3D& flow_ylow,
+                                 bool fixflux = true);
+
+template Field3D Div_par_fvv<Superbee>(const Field3D& f_in, const Field3D& v_in,
+                                       const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_par<Superbee>(const Field3D& f_in, const Field3D& v_in,
+                                   const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_f_v<Superbee>(const Field3D& n_in, const Vector3D& v,
+                                   bool bndry_flux);
+template Field3D Div_par_mod<Superbee>(const Field3D& f_in, const Field3D& v_in,
+                                       const Field3D& wave_speed_in, Field3D& flow_ylow,
+                                       bool fixflux = true);
+
+template Field3D Div_par_fvv<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
+                                        const Field3D& wave_speed_in,
+                                        bool fixflux = true);
+template Field3D Div_par<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
+                                    const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_f_v<VanAlbada>(const Field3D& n_in, const Vector3D& v,
+                                    bool bndry_flux);
+template Field3D Div_par_mod<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
+                                        const Field3D& wave_speed_in, Field3D& flow_ylow,
+                                        bool fixflux = true);
+
+template Field3D Div_par_fvv<WENO3>(const Field3D& f_in, const Field3D& v_in,
+                                    const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_par<WENO3>(const Field3D& f_in, const Field3D& v_in,
+                                const Field3D& wave_speed_in, bool fixflux = true);
+template Field3D Div_f_v<WENO3>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
+template Field3D Div_par_mod<WENO3>(const Field3D& f_in, const Field3D& v_in,
+                                    const Field3D& wave_speed_in, Field3D& flow_ylow,
+                                    bool fixflux = true);
+
 } // Namespace FV
diff --git a/tests/unit/include/bout/test_fv_ops.cxx b/tests/unit/include/bout/test_fv_ops.cxx
index e78c0cca41..5064b076b9 100644
--- a/tests/unit/include/bout/test_fv_ops.cxx
+++ b/tests/unit/include/bout/test_fv_ops.cxx
@@ -1,6 +1,6 @@
 #include "gtest/gtest.h"
 
-#include <bout/fv_ops.hxx>
+#include <bout/fv_ops_impl.hxx>
 
 TEST(FVOpsLimiterTest, VanAlbadaConstant) {
   FV::Stencil1D s{};

From 7a1a902ce46b4d119e673c9cd41e247c07859cf4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 23 Jun 2026 14:30:42 +0200
Subject: [PATCH 1478/1827] Add to cmake file

---
 CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0c42fbdeb2..239274c453 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -140,6 +140,7 @@ set(BOUT_SOURCES
     ./include/bout/fieldgroup.hxx
     ./include/bout/fieldperp.hxx
     ./include/bout/fv_ops.hxx
+    ./include/bout/fv_ops_impl.hxx
     ./include/bout/generic_factory.hxx
     ./include/bout/globalfield.hxx
     ./include/bout/globalindexer.hxx

From 392f84217ec9dceb75ff4f72319fe19d09f3f075 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 23 Jun 2026 14:37:31 +0200
Subject: [PATCH 1479/1827] Add implementation file

---
 include/bout/fv_ops_impl.hxx | 1054 ++++++++++++++++++++++++++++++++++
 1 file changed, 1054 insertions(+)
 create mode 100644 include/bout/fv_ops_impl.hxx

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
new file mode 100644
index 0000000000..8326f73d28
--- /dev/null
+++ b/include/bout/fv_ops_impl.hxx
@@ -0,0 +1,1054 @@
+/*
+  Finite-volume discretisation methods. Flux-conservative form
+ */
+
+#ifndef BOUT_FV_OPS_IMPL_H
+#define BOUT_FV_OPS_IMPL_H
+
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/build_defines.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/field.hxx"
+#include "bout/field3d.hxx"
+#include "bout/globals.hxx"
+#include "bout/mesh.hxx"
+#include "bout/output_bout_types.hxx" // NOLINT(unused-includes, misc-include-cleaner)
+#include "bout/region.hxx"
+#include "bout/utils.hxx"
+#include "bout/vector2d.hxx"
+
+#include <cmath>
+
+namespace FV {
+/*!
+   * Stencil used for Finite Volume calculations
+   * which includes cell face values L and R
+   */
+struct Stencil1D {
+  /// Cell centre values
+  BoutReal c;
+  BoutReal m;
+  BoutReal p;
+  BoutReal mm = BoutNaN;
+  BoutReal pp = BoutNaN;
+
+  /// Left cell face value
+  BoutReal L = BoutNaN;
+  /// Right cell face value
+  BoutReal R = BoutNaN;
+};
+
+/*!
+   * First order upwind for testing
+   */
+struct Upwind {
+  void operator()(Stencil1D& n) { n.L = n.R = n.c; }
+};
+
+/*!
+   * Fromm method
+   */
+struct Fromm {
+  void operator()(Stencil1D& n) {
+    n.L = n.c - (0.25 * (n.p - n.m));
+    n.R = n.c + (0.25 * (n.p - n.m));
+  }
+};
+
+/*!
+   * Second order slope limiter method
+   *
+   * Limits slope to minimum absolute value
+   * of left and right gradients. If at a maximum
+   * or minimum slope set to zero, i.e. reverts
+   * to first order upwinding
+   */
+struct MinMod {
+  void operator()(Stencil1D& n) {
+    // Choose the gradient within the cell
+    // as the minimum (smoothest) solution
+    const BoutReal slope = _minmod(n.p - n.c, n.c - n.m);
+    n.L = n.c - (0.5 * slope);
+    n.R = n.c + (0.5 * slope);
+  }
+
+private:
+  /*!
+     * Internal helper function for minmod slope limiter
+     *
+     * If the inputs have different signs then
+     * returns zero, otherwise chooses the value
+     * with the minimum magnitude.
+     */
+  static BoutReal _minmod(BoutReal a, BoutReal b) {
+    if (a * b <= 0.0) {
+      return 0.0;
+    }
+
+    if (fabs(a) < fabs(b)) {
+      return a;
+    }
+    return b;
+  }
+};
+
+/*!
+   * Monotonised Central (MC) second order slope limiter (Van Leer)
+   *
+   * Limits the slope based on taking the slope with
+   * the minimum absolute value from central, 2*left and
+   * 2*right. If any of these slopes have different signs
+   * then the slope reverts to zero (i.e. 1st-order upwinding).
+   */
+struct MC {
+  void operator()(Stencil1D& n) {
+    const BoutReal slope = minmod(2. * (n.p - n.c),  // 2*right difference
+                                  0.5 * (n.p - n.m), // Central difference
+                                  2. * (n.c - n.m)); // 2*left difference
+    n.L = n.c - (0.5 * slope);
+    n.R = n.c + (0.5 * slope);
+  }
+
+private:
+  // Return zero if any signs are different
+  // otherwise return the value with the minimum magnitude
+  static BoutReal minmod(BoutReal a, BoutReal b, BoutReal c) {
+    // if any of the signs are different, return zero gradient
+    if ((a * b <= 0.0) || (a * c <= 0.0)) {
+      return 0.0;
+    }
+
+    // Return the minimum absolute value
+    return SIGN(a) * BOUTMIN(fabs(a), fabs(b), fabs(c));
+  }
+};
+
+/// Superbee limiter
+///
+/// This corresponds to the limiter function
+///    φ(r) = max(0, min(2r, 1), min(r,2)
+///
+/// The value at cell right (i.e. i + 1/2) is:
+///
+///   n.R = n.c - φ(r) (n.c - (n.p + n.c)/2)
+///       = n.c + φ(r) (n.p - n.c)/2
+///
+/// Four regimes:
+///  a) r < 1/2 -> φ(r) = 2r
+///     n.R = n.c + gL
+///  b) 1/2 < r < 1 -> φ(r) = 1
+///     n.R = n.c + gR/2
+///  c) 1 < r < 2 -> φ(r) = r
+///     n.R = n.c + gL/2
+///  d) 2 < r  -> φ(r) = 2
+///     n.R = n.c + gR
+///
+///  where the left and right gradients are:
+///   gL = n.c - n.m
+///   gR = n.p - n.c
+///
+struct Superbee {
+  void operator()(Stencil1D& n) {
+    const BoutReal gL = n.c - n.m;
+    const BoutReal gR = n.p - n.c;
+
+    // r = gL / gR
+    // Limiter is φ(r)
+    if (gL * gR < 0) {
+      // Different signs => Zero gradient
+      n.L = n.R = n.c;
+    } else {
+      const BoutReal sign = SIGN(gL);
+      const BoutReal abs_gL = fabs(gL);
+      const BoutReal abs_gR = fabs(gR);
+      const BoutReal half_slope =
+          sign * BOUTMAX(BOUTMIN(abs_gL, 0.5 * abs_gR), BOUTMIN(abs_gR, 0.5 * abs_gL));
+      n.L = n.c - half_slope;
+      n.R = n.c + half_slope;
+    }
+  }
+};
+
+/*!
+   * Symmetric Van Albada second order slope limiter
+   *
+   * Uses a smooth (differentiable) approximation to `max(a*b, 0)` to avoid
+   * introducing a kink at extrema, which can be helpful for nonlinear solvers
+   * and finite-difference Jacobian calculations.
+   *
+   * The limited slope is calculated from the left and right differences
+   * `dl = c - m` and `dr = p - c` as
+   *
+   *   slope = (pos(dl*dr) * (dl + dr)) / (dl^2 + dr^2)
+   *
+   * where `pos(x)` is a smooth approximation to `max(x, 0)`.
+   */
+struct VanAlbada {
+  void operator()(Stencil1D& n) {
+    const BoutReal dl = n.c - n.m;
+    const BoutReal dr = n.p - n.c;
+
+    const BoutReal denom = dl * dl + dr * dr;
+
+    // Smoothness parameters:
+    // - keep division well-defined when dl=dr=0
+    // - provide a differentiable approximation to max(dl*dr, 0)
+    const BoutReal eps = 1e-12 * denom + 1e-30;
+
+    const BoutReal ab = dl * dr;
+    const BoutReal ab_pos = 0.5 * (ab + sqrt(ab * ab + eps * eps));
+
+    const BoutReal slope = (ab_pos * (dl + dr)) / (denom + eps);
+
+    n.L = n.c - 0.5 * slope;
+    n.R = n.c + 0.5 * slope;
+  }
+};
+
+/*!
+   * WENO3-JS (Jiang-Shu) reconstruction to cell faces
+   *
+   * This is a third-order essentially non-oscillatory reconstruction using two
+   * candidate second-order polynomials and smoothness-weighted blending.
+   *
+   * Unlike TVD slope limiters (e.g. ``MC``), WENO reconstruction is generally
+   * smooth (differentiable) for all inputs, but it does not enforce strict
+   * monotonicity.
+   *
+   * Uses only the three-point stencil (`m`, `c`, `p`), so it is a drop-in
+   * replacement anywhere `Stencil1D` is populated with those values.
+   */
+struct WENO3 {
+  void operator()(Stencil1D& n) {
+    // Right face (between c and p): value from cell c (left state at i+1/2)
+    const BoutReal p0_r = 0.5 * (-n.m + 3.0 * n.c);
+    const BoutReal p1_r = 0.5 * (n.c + n.p);
+
+    const BoutReal beta0_r = SQ(n.c - n.m);
+    const BoutReal beta1_r = SQ(n.p - n.c);
+
+    // Left face (between m and c): value from cell c (right state at i-1/2)
+    const BoutReal p0_l = 0.5 * (-n.p + 3.0 * n.c);
+    const BoutReal p1_l = 0.5 * (n.m + n.c);
+
+    const BoutReal beta0_l = beta1_r;
+    const BoutReal beta1_l = beta0_r;
+
+    // Smoothness parameter (scaled to local variation)
+    const BoutReal eps = 1e-12 * (beta0_r + beta1_r) + 1e-30;
+
+    // Linear weights for WENO3-JS
+    constexpr BoutReal d0 = 1.0 / 3.0;
+    constexpr BoutReal d1 = 2.0 / 3.0;
+
+    // Right face weights
+    const BoutReal a0_r = d0 / SQ(eps + beta0_r);
+    const BoutReal a1_r = d1 / SQ(eps + beta1_r);
+    const BoutReal wsum_r = a0_r + a1_r;
+    const BoutReal w0_r = a0_r / wsum_r;
+    const BoutReal w1_r = a1_r / wsum_r;
+
+    // Left face weights (mirrored)
+    const BoutReal a0_l = d0 / SQ(eps + beta0_l);
+    const BoutReal a1_l = d1 / SQ(eps + beta1_l);
+    const BoutReal wsum_l = a0_l + a1_l;
+    const BoutReal w0_l = a0_l / wsum_l;
+    const BoutReal w1_l = a1_l / wsum_l;
+
+    n.R = w0_r * p0_r + w1_r * p1_r;
+    n.L = w0_l * p0_l + w1_l * p1_l;
+  }
+};
+
+/*!
+   * Communicate fluxes between processors
+   * Takes values in guard cells, and adds them to cells
+   */
+void communicateFluxes(Field3D& f);
+
+/// Finite volume parallel divergence
+///
+/// Preserves the sum of f*J*dx*dy*dz over the domain
+///
+/// @param[in] f_in   The field being advected.
+///                   This will be reconstructed at cell faces
+///                   using the given CellEdges method
+/// @param[in] v_in   The advection velocity.
+///                   This will be interpolated to cell boundaries
+///                   using linear interpolation
+/// @param[in] wave_speed_in  Local maximum speed of all waves in the system at each
+//                            point in space
+/// @param[in] fixflux     Fix the flux at the boundary to be the value at the
+///                        midpoint (for boundary conditions)
+///
+/// NB: Uses to/from FieldAligned coordinates
+template <typename CellEdges>
+Field3D Div_par(const Field3D& f_in, const Field3D& v_in, const Field3D& wave_speed_in,
+                bool fixflux) {
+
+  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
+  ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
+
+  const Mesh* mesh = f_in.getMesh();
+
+  CellEdges cellboundary;
+
+  ASSERT2(f_in.getDirectionY() == v_in.getDirectionY());
+  ASSERT2(f_in.getDirectionY() == wave_speed_in.getDirectionY());
+  const bool are_unaligned =
+      ((f_in.getDirectionY() == YDirectionType::Standard)
+       and (v_in.getDirectionY() == YDirectionType::Standard)
+       and (wave_speed_in.getDirectionY() == YDirectionType::Standard));
+
+  Field3D f = are_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in;
+  Field3D v = are_unaligned ? toFieldAligned(v_in, "RGN_NOX") : v_in;
+  Field3D wave_speed =
+      are_unaligned ? toFieldAligned(wave_speed_in, "RGN_NOX") : wave_speed_in;
+
+  Coordinates* coord = f_in.getCoordinates();
+
+  Field3D result{zeroFrom(f)};
+
+  for (int i = mesh->xstart; i <= mesh->xend; i++) {
+    const bool is_periodic_y = mesh->periodicY(i);
+    const bool is_first_y = mesh->firstY(i);
+    const bool is_last_y = mesh->lastY(i);
+
+    // Only need one guard cell, so no need to communicate fluxes Instead
+    // calculate in guard cells to get fluxes consistent between processors, but
+    // don't include the boundary cell. Note that this implies special handling
+    // of boundaries later
+    const int ys = (!is_first_y || is_periodic_y) ? mesh->ystart - 1 : mesh->ystart;
+    const int ye = (!is_last_y || is_periodic_y) ? mesh->yend + 1 : mesh->yend;
+
+    for (int j = ys; j <= ye; j++) {
+      // Pre-calculate factors which multiply fluxes
+#if not(BOUT_USE_METRIC_3D)
+      // For right cell boundaries
+      BoutReal common_factor = (coord->J(i, j) + coord->J(i, j + 1))
+                               / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1)));
+
+      const BoutReal flux_factor_rc = common_factor / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_rp =
+          common_factor / (coord->dy(i, j + 1) * coord->J(i, j + 1));
+
+      // For left cell boundaries
+      common_factor = (coord->J(i, j) + coord->J(i, j - 1))
+                      / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1)));
+
+      const BoutReal flux_factor_lc = common_factor / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_lm =
+          common_factor / (coord->dy(i, j - 1) * coord->J(i, j - 1));
+#endif
+      for (int k = mesh->zstart; k <= mesh->zend; k++) {
+#if BOUT_USE_METRIC_3D
+        // For right cell boundaries
+        BoutReal common_factor =
+            (coord->J(i, j, k) + coord->J(i, j + 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
+
+        BoutReal flux_factor_rc =
+            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
+        BoutReal flux_factor_rp =
+            common_factor / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
+
+        // For left cell boundaries
+        common_factor = (coord->J(i, j, k) + coord->J(i, j - 1, k))
+                        / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
+
+        BoutReal flux_factor_lc =
+            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
+        BoutReal flux_factor_lm =
+            common_factor / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
+#endif
+
+        ////////////////////////////////////////////
+        // Reconstruct f at the cell faces
+        // This calculates s.R and s.L for the Right and Left
+        // face values on this cell
+
+        // Reconstruct f at the cell faces
+        Stencil1D s;
+        s.c = f(i, j, k);
+        s.m = f(i, j - 1, k);
+        s.p = f(i, j + 1, k);
+
+        cellboundary(s); // Calculate s.R and s.L
+
+        ////////////////////////////////////////////
+        // Right boundary
+
+        // Calculate velocity at right boundary (y+1/2)
+        BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j + 1, k));
+        BoutReal flux = NAN;
+
+        if (is_last_y && (j == mesh->yend) && !is_periodic_y) {
+          // Last point in domain
+
+          const BoutReal bndryval = 0.5 * (s.c + s.p);
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = bndryval * vpar;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.R * vpar) + (wave_speed(i, j, k) * (s.R - bndryval));
+          }
+        } else {
+
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k));
+
+          if (vpar > amax) {
+            // Supersonic flow out of this cell
+            flux = s.R * vpar;
+          } else if (vpar < -amax) {
+            // Supersonic flow into this cell
+            flux = 0.0;
+          } else {
+            // Subsonic flow, so a mix of right and left fluxes
+            flux = s.R * 0.5 * (vpar + amax);
+          }
+        }
+
+        result(i, j, k) += flux * flux_factor_rc;
+        result(i, j + 1, k) -= flux * flux_factor_rp;
+
+        ////////////////////////////////////////////
+        // Calculate at left boundary
+
+        vpar = 0.5 * (v(i, j, k) + v(i, j - 1, k));
+
+        if (is_first_y && (j == mesh->ystart) && !is_periodic_y) {
+          // First point in domain
+          const BoutReal bndryval = 0.5 * (s.c + s.m);
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = bndryval * vpar;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.L * vpar) - (wave_speed(i, j, k) * (s.L - bndryval));
+          }
+        } else {
+
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k));
+
+          if (vpar < -amax) {
+            // Supersonic out of this cell
+            flux = s.L * vpar;
+          } else if (vpar > amax) {
+            // Supersonic into this cell
+            flux = 0.0;
+          } else {
+            flux = s.L * 0.5 * (vpar - amax);
+          }
+        }
+
+        result(i, j, k) -= flux * flux_factor_lc;
+        result(i, j - 1, k) += flux * flux_factor_lm;
+      }
+    }
+  }
+  return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result;
+}
+
+/*!
+   * Div ( n * v )  -- Magnetic drifts
+   *
+   * This uses the expression
+   *
+   * Div( A ) = 1/J * d/di ( J * A^i )
+   *
+   * Hence the input vector should be contravariant
+   *
+   * Note: Uses to/from FieldAligned
+   *
+   */
+template <typename CellEdges>
+Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
+  ASSERT1(n_in.getLocation() == v.getLocation());
+  ASSERT1_FIELDS_COMPATIBLE(n_in, v.x);
+
+  const Mesh* mesh = n_in.getMesh();
+
+  CellEdges cellboundary;
+
+  Coordinates* coord = n_in.getCoordinates();
+
+  if (v.covariant) {
+    // Got a covariant vector instead
+    throw BoutException("Div_f_v passed a covariant v");
+  }
+
+  Field3D result{zeroFrom(n_in)};
+
+  Field3D vx = v.x;
+  Field3D vz = v.z;
+  Field3D n = n_in;
+
+  BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
+    // Calculate velocities
+    const BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]);
+    const BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]);
+    const BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J[i.xm()] + coord->J[i]);
+    const BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J[i.xp()] + coord->J[i]);
+
+    // X direction
+    Stencil1D s;
+    s.c = n[i];
+    s.m = n[i.xm()];
+    s.mm = n[i.xmm()];
+    s.p = n[i.xp()];
+    s.pp = n[i.xpp()];
+
+    cellboundary(s);
+
+    if ((i.x() == mesh->xend) && (mesh->lastX())) {
+      // At right boundary in X
+      if (bndry_flux) {
+        BoutReal flux = NAN;
+        if (vR > 0.0) {
+          // Flux to boundary
+          flux = vR * s.R;
+        } else {
+          // Flux in from boundary
+          flux = vR * 0.5 * (n[i.xp()] + n[i]);
+        }
+        result[i] += flux / (coord->dx[i] * coord->J[i]);
+        result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]);
+      }
+    } else {
+      // Not at a boundary
+      if (vR > 0.0) {
+        // Flux out into next cell
+        const BoutReal flux = vR * s.R;
+        result[i] += flux / (coord->dx[i] * coord->J[i]);
+        result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]);
+      }
+    }
+
+    // Left side
+
+    if ((i.x() == mesh->xstart) && (mesh->firstX())) {
+      // At left boundary in X
+
+      if (bndry_flux) {
+        BoutReal flux = NAN;
+        if (vL < 0.0) {
+          // Flux to boundary
+          flux = vL * s.L;
+        } else {
+          // Flux in from boundary
+          flux = vL * 0.5 * (n[i.xm()] + n[i]);
+        }
+        result[i] -= flux / (coord->dx[i] * coord->J[i]);
+        result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]);
+      }
+    } else {
+      // Not at a boundary
+      if (vL < 0.0) {
+        const BoutReal flux = vL * s.L;
+        result[i] -= flux / (coord->dx[i] * coord->J[i]);
+        result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]);
+      }
+    }
+
+    /// NOTE: Need to communicate fluxes
+
+    // Z direction
+    s.m = n[i.zm()];
+    s.mm = n[i.zmm()];
+    s.p = n[i.zp()];
+    s.pp = n[i.zpp()];
+
+    cellboundary(s);
+
+    if (vU > 0.0) {
+      const BoutReal flux = vU * s.R;
+      result[i] += flux / (coord->J[i] * coord->dz[i]);
+      result[i.zp()] -= flux / (coord->J[i.zp()] * coord->dz[i.zp()]);
+    }
+    if (vD < 0.0) {
+      const BoutReal flux = vD * s.L;
+      result[i] -= flux / (coord->J[i] * coord->dz[i]);
+      result[i.zm()] += flux / (coord->J[i.zm()] * coord->dz[i.zm()]);
+    }
+  }
+
+  communicateFluxes(result);
+
+  // Y advection
+  // Currently just using simple centered differences
+  // so no fluxes need to be exchanged
+
+  n = toFieldAligned(n_in, "RGN_NOX");
+  Field3D vy = toFieldAligned(v.y, "RGN_NOX");
+
+  Field3D yresult = 0.0;
+  yresult.setDirectionY(YDirectionType::Aligned);
+
+  BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
+    // Y velocities on y boundaries
+    const BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]);
+    const BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]);
+
+    // n (advected quantity) on y boundaries
+    // Note: Use unshifted n_in variable
+    const BoutReal nU = 0.5 * (n[i] + n[i.yp()]);
+    const BoutReal nD = 0.5 * (n[i] + n[i.ym()]);
+
+    yresult[i] = (nU * vU - nD * vD) / (coord->J[i] * coord->dy[i]);
+  }
+  return result + fromFieldAligned(yresult, "RGN_NOBNDRY");
+}
+
+/// Finite volume parallel divergence
+///
+/// NOTE: Modified version, applies limiter to velocity and field
+///       Performs better (smaller overshoots) than Div_par
+///
+/// Preserves the sum of f*J*dx*dy*dz over the domain
+///
+/// @param[in] f_in   The field being advected.
+///                   This will be reconstructed at cell faces
+///                   using the given CellEdges method
+/// @param[in] v_in   The advection velocity.
+///                   This will be interpolated to cell boundaries
+///                   using linear interpolation
+/// @param[in] wave_speed_in  Local maximum speed of all waves in the system at each
+//                            point in space
+/// @param[in] fixflux     Fix the flux at the boundary to be the value at the
+///                        midpoint (for boundary conditions)
+///
+/// @param[out] flow_ylow    Flow at the lower Y cell boundary
+///                          Already includes area factor * flux
+template <typename CellEdges>
+Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
+                    const Field3D& wave_speed_in, Field3D& flow_ylow, bool fixflux) {
+
+  Coordinates* coord = f_in.getCoordinates();
+  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
+
+  if (f_in.isFci()) {
+    // Use mid-point (cell boundary) averages
+
+    ASSERT1(f_in.hasParallelSlices());
+    ASSERT1(v_in.hasParallelSlices());
+
+    const auto& f_up = f_in.yup();
+    const auto& f_down = f_in.ydown();
+
+    const auto& v_up = v_in.yup();
+    const auto& v_down = v_in.ydown();
+
+    Field3D result{emptyFrom(f_in)};
+    BOUT_FOR(i, f_in.getRegion("RGN_NOBNDRY")) {
+      const auto iyp = i.yp();
+      const auto iym = i.ym();
+
+      result[i] = (0.25 * (f_in[i] + f_up[iyp]) * (v_in[i] + v_up[iyp])
+                       * (coord->J[i] + coord->J.yup()[iyp])
+                       / (sqrt(coord->g_22[i]) + sqrt(coord->g_22.yup()[iyp]))
+                   - 0.25 * (f_in[i] + f_down[iym]) * (v_in[i] + v_down[iym])
+                         * (coord->J[i] + coord->J.ydown()[iym])
+                         / (sqrt(coord->g_22[i]) + sqrt(coord->g_22.ydown()[iym])))
+                  / (coord->dy[i] * coord->J[i]);
+    }
+    return result;
+  }
+  ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
+
+  const Mesh* mesh = f_in.getMesh();
+
+  CellEdges cellboundary;
+
+  ASSERT2(f_in.getDirectionY() == v_in.getDirectionY());
+  ASSERT2(f_in.getDirectionY() == wave_speed_in.getDirectionY());
+  const bool are_unaligned =
+      ((f_in.getDirectionY() == YDirectionType::Standard)
+       and (v_in.getDirectionY() == YDirectionType::Standard)
+       and (wave_speed_in.getDirectionY() == YDirectionType::Standard));
+
+  const Field3D f = are_unaligned ? toFieldAligned(f_in, "RGN_NOX") : f_in;
+  const Field3D v = are_unaligned ? toFieldAligned(v_in, "RGN_NOX") : v_in;
+  const Field3D wave_speed =
+      are_unaligned ? toFieldAligned(wave_speed_in, "RGN_NOX") : wave_speed_in;
+
+  Field3D result{zeroFrom(f)};
+  flow_ylow = zeroFrom(f);
+
+  for (int i = mesh->xstart; i <= mesh->xend; i++) {
+    const bool is_periodic_y = mesh->periodicY(i);
+    const bool is_first_y = mesh->firstY(i);
+    const bool is_last_y = mesh->lastY(i);
+
+    // Only need one guard cell, so no need to communicate fluxes Instead
+    // calculate in guard cells to get fluxes consistent between processors, but
+    // don't include the boundary cell. Note that this implies special handling
+    // of boundaries later
+    const int ys = (!is_first_y || is_periodic_y) ? mesh->ystart - 1 : mesh->ystart;
+    const int ye = (!is_last_y || is_periodic_y) ? mesh->yend + 1 : mesh->yend;
+
+    for (int j = ys; j <= ye; j++) {
+      // Pre-calculate factors which multiply fluxes
+#if not(BOUT_USE_METRIC_3D)
+      // For right cell boundaries
+      const BoutReal common_factor_r =
+          (coord->J(i, j) + coord->J(i, j + 1))
+          / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j + 1)));
+
+      const BoutReal flux_factor_rc =
+          common_factor_r / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_rp =
+          common_factor_r / (coord->dy(i, j + 1) * coord->J(i, j + 1));
+
+      const BoutReal area_rp =
+          common_factor_r * coord->dx(i, j + 1) * coord->dz(i, j + 1);
+
+      // For left cell boundaries
+      const BoutReal common_factor_l =
+          (coord->J(i, j) + coord->J(i, j - 1))
+          / (sqrt(coord->g_22(i, j)) + sqrt(coord->g_22(i, j - 1)));
+
+      const BoutReal flux_factor_lc =
+          common_factor_l / (coord->dy(i, j) * coord->J(i, j));
+      const BoutReal flux_factor_lm =
+          common_factor_l / (coord->dy(i, j - 1) * coord->J(i, j - 1));
+
+      const BoutReal area_lc = common_factor_l * coord->dx(i, j) * coord->dz(i, j);
+#endif
+      for (int k = 0; k < mesh->LocalNz; k++) {
+#if BOUT_USE_METRIC_3D
+        // For right cell boundaries
+        const BoutReal common_factor_r =
+            (coord->J(i, j, k) + coord->J(i, j + 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
+
+        const BoutReal flux_factor_rc =
+            common_factor_r / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal flux_factor_rp =
+            common_factor_r / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
+
+        const BoutReal area_rp =
+            common_factor_r * coord->dx(i, j + 1, k) * coord->dz(i, j + 1, k);
+
+        // For left cell boundaries
+        const BoutReal common_factor_l =
+            (coord->J(i, j, k) + coord->J(i, j - 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
+
+        const BoutReal flux_factor_lc =
+            common_factor_l / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal flux_factor_lm =
+            common_factor_l / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
+
+        const BoutReal area_lc =
+            common_factor_l * coord->dx(i, j, k) * coord->dz(i, j, k);
+#endif
+
+        ////////////////////////////////////////////
+        // Reconstruct f at the cell faces
+        // This calculates s.R and s.L for the Right and Left
+        // face values on this cell
+
+        // Reconstruct f at the cell faces
+        // TODO(peter): We can remove this #ifdef guard after switching to C++20
+#if __cpp_designated_initializers >= 201707L
+        Stencil1D s{.c = f(i, j, k), .m = f(i, j - 1, k), .p = f(i, j + 1, k)};
+#else
+        Stencil1D s{f(i, j, k), f(i, j - 1, k), f(i, j + 1, k), BoutNaN,
+                    BoutNaN,    BoutNaN,        BoutNaN};
+#endif
+        cellboundary(s); // Calculate s.R and s.L
+
+        ////////////////////////////////////////////
+        // Reconstruct v at the cell faces
+        // TODO(peter): We can remove this #ifdef guard after switching to C++20
+#if __cpp_designated_initializers >= 201707L
+        Stencil1D sv{.c = v(i, j, k), .m = v(i, j - 1, k), .p = v(i, j + 1, k)};
+#else
+        Stencil1D sv{v(i, j, k), v(i, j - 1, k), v(i, j + 1, k), BoutNaN,
+                     BoutNaN,    BoutNaN,        BoutNaN};
+#endif
+        cellboundary(sv); // Calculate sv.R and sv.L
+
+        ////////////////////////////////////////////
+        // Right boundary
+
+        BoutReal flux = BoutNaN;
+
+        if (is_last_y && (j == mesh->yend) && !is_periodic_y) {
+          // Last point in domain
+
+          // Calculate velocity at right boundary (y+1/2)
+          const BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j + 1, k));
+
+          const BoutReal bndryval = 0.5 * (s.c + s.p);
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = bndryval * vpar;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.R * vpar) + (wave_speed(i, j, k) * (s.R - bndryval));
+          }
+
+        } else {
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
+                                        fabs(v(i, j, k)), fabs(v(i, j + 1, k)));
+
+          flux = s.R * 0.5 * (sv.R + amax);
+        }
+
+        result(i, j, k) += flux * flux_factor_rc;
+        result(i, j + 1, k) -= flux * flux_factor_rp;
+
+        flow_ylow(i, j + 1, k) += flux * area_rp;
+
+        ////////////////////////////////////////////
+        // Calculate at left boundary
+
+        if (is_first_y && (j == mesh->ystart) && !is_periodic_y) {
+          // First point in domain
+          const BoutReal bndryval = 0.5 * (s.c + s.m);
+          const BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j - 1, k));
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = bndryval * vpar;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.L * vpar) - (wave_speed(i, j, k) * (s.L - bndryval));
+          }
+        } else {
+
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
+                                        fabs(v(i, j, k)), fabs(v(i, j - 1, k)));
+
+          flux = s.L * 0.5 * (sv.L - amax);
+        }
+
+        result(i, j, k) -= flux * flux_factor_lc;
+        result(i, j - 1, k) += flux * flux_factor_lm;
+
+        flow_ylow(i, j, k) += flux * area_lc;
+      }
+    }
+  }
+  if (are_unaligned) {
+    flow_ylow = fromFieldAligned(flow_ylow, "RGN_NOBNDRY");
+  }
+  return are_unaligned ? fromFieldAligned(result, "RGN_NOBNDRY") : result;
+}
+
+/// This operator calculates Div_par(f v v)
+/// It is used primarily (only?) in the parallel momentum equation.
+///
+/// This operator is used rather than Div(f fv) so that the values of
+/// f and v are consistent with other advection equations: The product
+/// fv is not interpolated to cell boundaries.
+template <typename CellEdges>
+Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
+                    const Field3D& wave_speed_in, bool fixflux) {
+  ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
+  const Mesh* mesh = f_in.getMesh();
+  const Coordinates* coord = f_in.getCoordinates();
+  CellEdges cellboundary;
+
+  if (f_in.isFci()) {
+    // FCI version, using yup/down fields
+    ASSERT1(f_in.hasParallelSlices());
+    ASSERT1(v_in.hasParallelSlices());
+
+    const auto& B = coord->Bxy;
+    const auto& B_up = coord->Bxy.yup();
+    const auto& B_down = coord->Bxy.ydown();
+
+    const auto& f_up = f_in.yup();
+    const auto& f_down = f_in.ydown();
+
+    const auto& v_up = v_in.yup();
+    const auto& v_down = v_in.ydown();
+
+    const auto& g_22 = coord->g_22;
+    const auto& dy = coord->dy;
+
+    Field3D result{emptyFrom(f_in)};
+    BOUT_FOR(i, f_in.getRegion("RGN_NOBNDRY")) {
+      const auto iyp = i.yp();
+      const auto iym = i.ym();
+
+      // Maximum local wave speed
+      const BoutReal amax =
+          BOUTMAX(wave_speed_in[i], fabs(v_in[i]), fabs(v_up[iyp]), fabs(v_down[iym]));
+
+      const BoutReal term = (f_up[iyp] * v_up[iyp] * v_up[iyp] / B_up[iyp])
+                            - (f_down[iym] * v_down[iym] * v_down[iym] / B_down[iym]);
+
+      // Penalty terms. This implementation is very dissipative.
+      BoutReal penalty =
+          (amax * (f_in[i] * v_in[i] - f_up[iyp] * v_up[iyp]) / (B[i] + B_up[iyp]))
+          + (amax * (f_in[i] * v_in[i] - f_down[iym] * v_down[iym])
+             / (B[i] + B_down[iym]));
+
+      if (fabs(penalty) > fabs(term) and penalty * v_in[i] > 0) {
+        if (term * penalty > 0) {
+          penalty = term;
+        } else {
+          penalty = -term;
+        }
+      }
+
+      result[i] = B[i] * (term + penalty) / (2 * dy[i] * sqrt(g_22[i]));
+
+#if CHECK > 0
+      if (!std::isfinite(result[i])) {
+        throw BoutException("Non-finite value in Div_par_fvv at {}\n"
+                            "fup {} vup {} fdown {} vdown {} amax {}\n",
+                            "B {} Bup {} Bdown {} dy {} sqrt(g_22} {}", i, f_up[i],
+                            v_up[i], f_down[i], v_down[i], amax, B[i], B_up[i], B_down[i],
+                            dy[i], sqrt(g_22[i]));
+      }
+#endif
+    }
+    return result;
+  }
+
+  ASSERT1(areFieldsCompatible(f_in, wave_speed_in));
+
+  /// Ensure that f, v and wave_speed are field aligned
+  Field3D f = toFieldAligned(f_in, "RGN_NOX");
+  Field3D v = toFieldAligned(v_in, "RGN_NOX");
+  Field3D wave_speed = toFieldAligned(wave_speed_in, "RGN_NOX");
+
+  Field3D result{zeroFrom(f)};
+
+  for (int i = mesh->xstart; i <= mesh->xend; i++) {
+    const bool is_periodic_y = mesh->periodicY(i);
+    const bool is_first_y = mesh->firstY(i);
+    const bool is_last_y = mesh->lastY(i);
+
+    // Only need one guard cell, so no need to communicate fluxes Instead
+    // calculate in guard cells to get fluxes consistent between processors, but
+    // don't include the boundary cell. Note that this implies special handling
+    // of boundaries later
+    const int ys = (!is_first_y || is_periodic_y) ? mesh->ystart - 1 : mesh->ystart;
+    const int ye = (!is_last_y || is_periodic_y) ? mesh->yend + 1 : mesh->yend;
+
+    for (int j = ys; j <= ye; j++) {
+      // Pre-calculate factors which multiply fluxes
+
+      for (int k = 0; k < mesh->LocalNz; k++) {
+        // For right cell boundaries
+        const BoutReal common_factor_r =
+            (coord->J(i, j, k) + coord->J(i, j + 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
+
+        const BoutReal flux_factor_rc =
+            common_factor_r / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal flux_factor_rp =
+            common_factor_r / (coord->dy(i, j + 1, k) * coord->J(i, j + 1, k));
+
+        // For left cell boundaries
+        const BoutReal common_factor_l =
+            (coord->J(i, j, k) + coord->J(i, j - 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
+
+        const BoutReal flux_factor_lc =
+            common_factor_l / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal flux_factor_lm =
+            common_factor_l / (coord->dy(i, j - 1, k) * coord->J(i, j - 1, k));
+
+        ////////////////////////////////////////////
+        // Reconstruct f at the cell faces
+        // This calculates s.R and s.L for the Right and Left
+        // face values on this cell
+
+        // Reconstruct f at the cell faces
+#if __cpp_designated_initializers >= 201707L
+        Stencil1D s{.c = f(i, j, k), .m = f(i, j - 1, k), .p = f(i, j + 1, k)};
+#else
+        Stencil1D s{f(i, j, k), f(i, j - 1, k), f(i, j + 1, k), BoutNaN,
+                    BoutNaN,    BoutNaN,        BoutNaN};
+#endif
+        cellboundary(s); // Calculate s.R and s.L
+
+        ////////////////////////////////////////////
+        // Reconstruct v at the cell faces
+        // TODO(peter): We can remove this #ifdef guard after switching to C++20
+#if __cpp_designated_initializers >= 201707L
+        Stencil1D sv{.c = v(i, j, k), .m = v(i, j - 1, k), .p = v(i, j + 1, k)};
+#else
+        Stencil1D sv{v(i, j, k), v(i, j - 1, k), v(i, j + 1, k), BoutNaN,
+                     BoutNaN,    BoutNaN,        BoutNaN};
+#endif
+        cellboundary(sv);
+
+        ////////////////////////////////////////////
+        // Right boundary
+
+        // Calculate velocity at right boundary (y+1/2)
+        const BoutReal v_mid_r = 0.5 * (sv.c + sv.p);
+        // And mid-point density at right boundary
+        const BoutReal n_mid_r = 0.5 * (s.c + s.p);
+        BoutReal flux = NAN;
+
+        if (mesh->lastY(i) && (j == mesh->yend) && !mesh->periodicY(i)) {
+          // Last point in domain
+
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = n_mid_r * v_mid_r * v_mid_r;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.R * sv.R * sv.R) // Use right cell edge values
+                   + (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.p)) * n_mid_r
+                      * (sv.R - v_mid_r)); // Damp differences in velocity, not flux
+          }
+        } else {
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
+                                        fabs(sv.c), fabs(sv.p));
+
+          flux = s.R * 0.5 * (sv.R + amax) * sv.R;
+        }
+
+        result(i, j, k) += flux * flux_factor_rc;
+        result(i, j + 1, k) -= flux * flux_factor_rp;
+
+        ////////////////////////////////////////////
+        // Calculate at left boundary
+
+        const BoutReal v_mid_l = 0.5 * (sv.c + sv.m);
+        const BoutReal n_mid_l = 0.5 * (s.c + s.m);
+
+        if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) {
+          // First point in domain
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux = n_mid_l * v_mid_l * v_mid_l;
+          } else {
+            // Add flux due to difference in boundary values
+            flux = (s.L * sv.L * sv.L)
+                   - (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.m)) * n_mid_l
+                      * (sv.L - v_mid_l));
+          }
+        } else {
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
+                                        fabs(sv.c), fabs(sv.m));
+
+          flux = s.L * 0.5 * (sv.L - amax) * sv.L;
+        }
+
+        result(i, j, k) -= flux * flux_factor_lc;
+        result(i, j - 1, k) += flux * flux_factor_lm;
+      }
+    }
+  }
+  return fromFieldAligned(result, "RGN_NOBNDRY");
+}
+} // namespace FV
+#endif // BOUT_FV_OPS_H

From 81e7772f944ed4d4ca4748461f4b4ffbb8f1b93e Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 23 Jun 2026 15:43:23 +0100
Subject: [PATCH 1480/1827] Use SNESSetLagJacobianPersists to force
 recalculating Jacobian

Previously when something happened that would require the Jacobian to
be recalculated (instead of lagged), SNESSetLagJacobian() would be
used to set the lag to 1 for the next time-step. However, this would
turn off lagging altogether for that time-step. What we actually want
to do is use SNESSetLagJacobianPersists() so that the Jacobian is
recalculated at the start of the time-step and then is lagged as
usual. This commit changes to doing that.

Note that, in practice, the lag wasn't actually being forced to 1 in
most cases, because previously there was a line that would set it
back to the value from the configurations. As far as I can tell this
line shouldn't have been there.
---
 src/solver/impls/snes/snes.cxx | 52 ++++++++++++++--------------------
 src/solver/impls/snes/snes.hxx |  2 +-
 2 files changed, 22 insertions(+), 32 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index b703ab1c90..fce7cadcf5 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -881,7 +881,7 @@ int SNESSolver::init() {
   return 0;
 }
 
-PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
+PetscErrorCode SNESSolver::rescale() {
   // Individual variable scaling
   // Note: If variables are rescaled then the Jacobian columns
   //       need to be scaled or recalculated
@@ -929,12 +929,8 @@ PetscErrorCode SNESSolver::rescale(int& saved_jacobian_lag) {
   }
 
   // Force recalculation of the Jacobian
-  SNESGetLagJacobian(snes, &saved_jacobian_lag);
-  // FIXME: This isn't actually what we want to happen. The lag should
-  // stay as before, we just want to make sure the Jacobian gets
-  // re-evaluated at the start of the solve. We need to use
-  // SNESSetJacobianPersist for that.
-  SNESSetLagJacobian(snes, 1);
+  PetscCall(SNESSetLagJacobianPersists(snes, PETSC_FALSE));
+
   return PETSC_SUCCESS;
 }
 
@@ -957,9 +953,8 @@ int SNESSolver::run() {
     PetscCall(VecRestoreArray(snes_x, &xdata));
   }
 
-  int saved_jacobian_lag = 0;
   if (scale_vars) {
-    PetscCall(rescale(saved_jacobian_lag));
+    PetscCall(rescale());
   }
 
   // Initialise residuals
@@ -980,6 +975,8 @@ int SNESSolver::run() {
   recent_failure_rate = 0.0;
   int steps_since_rescale = 0;
   BoutReal change_since_rescale = 0.;
+  // Tracks whether we force persisting of lagged Jacobian to be turned off for the next time-step
+  bool persist_jac_lag_off = false;
   for (int s = 1; s <= getNumberOutputSteps(); s++) {
     target += getOutputTimestep();
 
@@ -994,10 +991,17 @@ int SNESSolver::run() {
         break; // Could happen if step over multiple outputs
       }
 
+      if (persist_jac_lag_off) {
+        persist_jac_lag_off = false;
+      } else {
+        PetscCall(
+            SNESSetLagJacobianPersists(snes, static_cast<PetscBool>(jacobian_persists)));
+      }
+
       if (scale_vars
           and (change_since_rescale > rescale_threshold
                or steps_since_rescale == rescale_period)) {
-        PetscCall(rescale(saved_jacobian_lag));
+        PetscCall(rescale());
         change_since_rescale = 0.;
         steps_since_rescale = 0;
       }
@@ -1026,14 +1030,14 @@ int SNESSolver::run() {
         if (timestep < dt_min_reset) {
           // Hit the minimum timestep, probably through repeated failures
 
-          if (saved_jacobian_lag != 0) {
+          if (persist_jac_lag_off) {
             // Already tried this and it didn't work
             throw BoutException("Solver failed after many attempts");
           }
 
           // Try resetting the preconditioner, turn off predictor, and use a large timestep
-          SNESGetLagJacobian(snes, &saved_jacobian_lag);
-          SNESSetLagJacobian(snes, 1);
+          PetscCall(SNESSetLagJacobianPersists(snes, PETSC_FALSE));
+          persist_jac_lag_off = true;
           timestep = getOutputTimestep();
           predictor = false; // Predictor can cause problems in near steady-state.
         }
@@ -1060,8 +1064,6 @@ int SNESSolver::run() {
           const BoutReal beta = dt / (simtime - time1);
           VecAXPBY(snes_x, -beta, (1. + beta), x1);
         }
-
-        SNESSetLagJacobian(snes, lag_jacobian);
       }
 
       // Run the solver
@@ -1142,11 +1144,8 @@ int SNESSolver::run() {
           PetscCall(FDJrestoreFromPruning());
         }
 
-        if (saved_jacobian_lag == 0) {
-          // This triggers a Jacobian recalculation
-          SNESGetLagJacobian(snes, &saved_jacobian_lag);
-          SNESSetLagJacobian(snes, 1);
-        }
+        PetscCall(SNESSetLagJacobianPersists(snes, PETSC_FALSE));
+        persist_jac_lag_off = true;
 
         // Check lock state
         PetscInt lock_state;
@@ -1162,13 +1161,6 @@ int SNESSolver::run() {
         continue; // Try again
       }
 
-      if (saved_jacobian_lag != 0) {
-        // Following successful step, reset Jacobian lag
-        // to previous value
-        SNESSetLagJacobian(snes, saved_jacobian_lag);
-        saved_jacobian_lag = 0;
-      }
-
       if (predictor) {
         // Save previous values: x1 <- x0
         VecCopy(x0, x1);
@@ -1275,10 +1267,8 @@ int SNESSolver::run() {
 
       if (static_cast<BoutReal>(lin_its) / nl_its > 0.5 * maxl) {
         // Recompute Jacobian if number of linear iterations is too high
-        if (saved_jacobian_lag == 0) {
-          SNESGetLagJacobian(snes, &saved_jacobian_lag);
-          SNESSetLagJacobian(snes, 1);
-        }
+        PetscCall(SNESSetLagJacobianPersists(snes, PETSC_FALSE));
+        persist_jac_lag_off = true;
       }
 
       snes_failures = 0;
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 3b1ffe99f0..ce0edc0b47 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -119,7 +119,7 @@ private:
 
   /// Rescale state (snes_x) so that all quantities are around 1. If
   /// quantities are near zero then RTOL is used.
-  PetscErrorCode rescale(int& saved_jacobian_lag);
+  PetscErrorCode rescale();
 
   /// Call the physics model RHS function
   ///

From 563df79c8b729e193aae6e24cfa4a9e790a125c4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 11:26:01 +0200
Subject: [PATCH 1481/1827] Return int

---
 include/bout/boundary_region_iter.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index d7cdff268d..242306c04f 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -539,7 +539,7 @@ public:
   signed char _offset() const { return region->bndry_points[pos].offset; }
   signed char _valid() const { return region->bndry_points[pos].valid; }
   Ind3D _ind() const { return region->bndry_points[pos].index; }
-  signed char _boundary_width() const {
+  int _boundary_width() const {
     return region->localmesh->ystart - region->bndry_points[pos].abs_offset + 1;
   }
   BoutReal _length([[maybe_unused]] CELL_LOC loc) const {
@@ -663,7 +663,7 @@ public:
   signed char _offset() const { return region->_dir; }
   signed char _valid() const { return region->valid; }
   Ind3D _ind() const { return region->rgn[pos]; }
-  signed char _boundary_width() const {
+  int _boundary_width() const {
     if constexpr (isX) {
       return region->localmesh->xstart;
     }

From e5ba73d8a978308d9934a36efba4cfab2e2fde68 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 11:32:51 +0200
Subject: [PATCH 1482/1827] Improve code comments

Co-authored-by: Peter Hill <zed.three@gmail.com>
---
 include/bout/fv_ops.hxx | 4 +---
 src/mesh/fv_ops.cxx     | 3 +--
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index d256bad32a..89caaadf97 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -77,7 +77,7 @@ Field3D D4DY4(const Field3D& d, const Field3D& f);
    */
 Field3D D4DY4_Index(const Field3D& f, bool bndry_flux = true);
 
-// FluxLimiter
+// Forward declarations of flux limiters
 class Upwind;
 class Fromm;
 class MinMod;
@@ -166,7 +166,5 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
 template <typename CellEdges = MC>
 Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
                     const Field3D& wave_speed_in, bool fixflux = true);
-// extern template Field3D Div_par_fvv<MC>(const Field3D& f_in, const Field3D& v_in,
-// 				const Field3D& wave_speed_in, bool fixflux = true);
 } // namespace FV
 #endif // BOUT_FV_OPS_H
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index a1333b1406..1bd00d34a9 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -564,8 +564,7 @@ Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc) {
   return result;
 }
 
-//  BOUT_ENUM_CLASS(FluxLimiter, Upwind, Fromm, MinMod, MC, Superbee, VanAlbada, WENO3);
-
+// Explicit instantiations of flux-limited finite volume methods
 template Field3D Div_par_fvv<Upwind>(const Field3D& f_in, const Field3D& v_in,
                                      const Field3D& wave_speed_in, bool fixflux = true);
 template Field3D Div_par<Upwind>(const Field3D& f_in, const Field3D& v_in,

From f8a246996d733c52e6183797b02123e20f14b5e4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 11:35:51 +0200
Subject: [PATCH 1483/1827] Remove pre-C++20 fall back path

---
 include/bout/fv_ops_impl.hxx | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 8326f73d28..e27fd32828 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -754,24 +754,12 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
         // face values on this cell
 
         // Reconstruct f at the cell faces
-        // TODO(peter): We can remove this #ifdef guard after switching to C++20
-#if __cpp_designated_initializers >= 201707L
         Stencil1D s{.c = f(i, j, k), .m = f(i, j - 1, k), .p = f(i, j + 1, k)};
-#else
-        Stencil1D s{f(i, j, k), f(i, j - 1, k), f(i, j + 1, k), BoutNaN,
-                    BoutNaN,    BoutNaN,        BoutNaN};
-#endif
         cellboundary(s); // Calculate s.R and s.L
 
         ////////////////////////////////////////////
         // Reconstruct v at the cell faces
-        // TODO(peter): We can remove this #ifdef guard after switching to C++20
-#if __cpp_designated_initializers >= 201707L
         Stencil1D sv{.c = v(i, j, k), .m = v(i, j - 1, k), .p = v(i, j + 1, k)};
-#else
-        Stencil1D sv{v(i, j, k), v(i, j - 1, k), v(i, j + 1, k), BoutNaN,
-                     BoutNaN,    BoutNaN,        BoutNaN};
-#endif
         cellboundary(sv); // Calculate sv.R and sv.L
 
         ////////////////////////////////////////////
@@ -967,23 +955,12 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
         // face values on this cell
 
         // Reconstruct f at the cell faces
-#if __cpp_designated_initializers >= 201707L
         Stencil1D s{.c = f(i, j, k), .m = f(i, j - 1, k), .p = f(i, j + 1, k)};
-#else
-        Stencil1D s{f(i, j, k), f(i, j - 1, k), f(i, j + 1, k), BoutNaN,
-                    BoutNaN,    BoutNaN,        BoutNaN};
-#endif
         cellboundary(s); // Calculate s.R and s.L
 
         ////////////////////////////////////////////
         // Reconstruct v at the cell faces
-        // TODO(peter): We can remove this #ifdef guard after switching to C++20
-#if __cpp_designated_initializers >= 201707L
         Stencil1D sv{.c = v(i, j, k), .m = v(i, j - 1, k), .p = v(i, j + 1, k)};
-#else
-        Stencil1D sv{v(i, j, k), v(i, j - 1, k), v(i, j + 1, k), BoutNaN,
-                     BoutNaN,    BoutNaN,        BoutNaN};
-#endif
         cellboundary(sv);
 
         ////////////////////////////////////////////

From 8f8e0359bcd2285dae281a3051caad334ef470ed Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 11:45:56 +0200
Subject: [PATCH 1484/1827] Apply clang-tidy fixes

---
 include/bout/fv_ops_impl.hxx | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index e27fd32828..91117a6961 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -28,9 +28,9 @@ namespace FV {
    */
 struct Stencil1D {
   /// Cell centre values
-  BoutReal c;
-  BoutReal m;
-  BoutReal p;
+  BoutReal c{};
+  BoutReal m{};
+  BoutReal p{};
   BoutReal mm = BoutNaN;
   BoutReal pp = BoutNaN;
 
@@ -190,20 +190,20 @@ struct VanAlbada {
     const BoutReal dl = n.c - n.m;
     const BoutReal dr = n.p - n.c;
 
-    const BoutReal denom = dl * dl + dr * dr;
+    const BoutReal denom = (dl * dl) + (dr * dr);
 
     // Smoothness parameters:
     // - keep division well-defined when dl=dr=0
     // - provide a differentiable approximation to max(dl*dr, 0)
-    const BoutReal eps = 1e-12 * denom + 1e-30;
+    const BoutReal eps = (1e-12 * denom) + 1e-30;
 
     const BoutReal ab = dl * dr;
-    const BoutReal ab_pos = 0.5 * (ab + sqrt(ab * ab + eps * eps));
+    const BoutReal ab_pos = 0.5 * (ab + sqrt((ab * ab) + (eps * eps)));
 
     const BoutReal slope = (ab_pos * (dl + dr)) / (denom + eps);
 
-    n.L = n.c - 0.5 * slope;
-    n.R = n.c + 0.5 * slope;
+    n.L = n.c - (0.5 * slope);
+    n.R = n.c + (0.5 * slope);
   }
 };
 
@@ -237,7 +237,7 @@ struct WENO3 {
     const BoutReal beta1_l = beta0_r;
 
     // Smoothness parameter (scaled to local variation)
-    const BoutReal eps = 1e-12 * (beta0_r + beta1_r) + 1e-30;
+    const BoutReal eps = (1e-12 * (beta0_r + beta1_r)) + 1e-30;
 
     // Linear weights for WENO3-JS
     constexpr BoutReal d0 = 1.0 / 3.0;
@@ -257,8 +257,8 @@ struct WENO3 {
     const BoutReal w0_l = a0_l / wsum_l;
     const BoutReal w1_l = a1_l / wsum_l;
 
-    n.R = w0_r * p0_r + w1_r * p1_r;
-    n.L = w0_l * p0_l + w1_l * p1_l;
+    n.R = (w0_r * p0_r) + (w1_r * p1_r);
+    n.L = (w0_l * p0_l) + (w1_l * p1_l);
   }
 };
 

From bc980b1366fc6d3feec0c033e21f0c9464de6334 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 12:07:02 +0200
Subject: [PATCH 1485/1827] Ensure calls to _compute_... are guarded

---
 include/bout/coordinates.hxx | 140 ++++++++++++++++++++++++-----------
 1 file changed, 98 insertions(+), 42 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 6d803ab28a..a8f4c09c5c 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -116,103 +116,159 @@ public:
   FieldMetric& g_22_yhigh();
   // Cell Areas
   const FieldMetric& cell_area_xlow() const {
-    if (!_cell_area_xlow.has_value()) {
+    if (_cell_area_xlow.has_value()) {
+      return *_cell_area_xlow;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_x();
+      ASSERT2(_cell_area_xlow.has_value());
+      return *_cell_area_xlow;
     }
-    ASSERT2(_cell_area_xlow.has_value());
-    return *_cell_area_xlow;
   }
   const FieldMetric& cell_area_xhigh() const {
-    if (!_cell_area_xhigh.has_value()) {
+    if (_cell_area_xhigh.has_value()) {
+      return *_cell_area_xhigh;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_x();
+      ASSERT2(_cell_area_xhigh.has_value());
+      return *_cell_area_xhigh;
     }
-    ASSERT2(_cell_area_xhigh.has_value());
-    return *_cell_area_xhigh;
   }
   const FieldMetric& cell_area_ylow() const {
-    if (!_cell_area_ylow.has_value()) {
+    if (_cell_area_ylow.has_value()) {
+      return *_cell_area_ylow;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_y();
+      ASSERT2(_cell_area_ylow.has_value());
+      return *_cell_area_ylow;
     }
-    ASSERT2(_cell_area_ylow.has_value());
-    return *_cell_area_ylow;
   }
   const FieldMetric& cell_area_yhigh() const {
-    if (!_cell_area_yhigh.has_value()) {
+    if (_cell_area_yhigh.has_value()) {
+      return *_cell_area_yhigh;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_y();
+      ASSERT2(_cell_area_yhigh.has_value());
+      return *_cell_area_yhigh;
     }
-    ASSERT2(_cell_area_yhigh.has_value());
-    return *_cell_area_yhigh;
   }
   const FieldMetric& cell_area_zlow() const {
-    if (!_cell_area_zlow.has_value()) {
+    if (_cell_area_zlow.has_value()) {
+      return *_cell_area_zlow;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_z();
+      ASSERT2(_cell_area_zlow.has_value());
+      return *_cell_area_zlow;
     }
-    ASSERT2(_cell_area_zlow.has_value());
-    return *_cell_area_zlow;
   }
   const FieldMetric& cell_area_zhigh() const {
-    if (!_cell_area_zhigh.has_value()) {
+    if (_cell_area_zhigh.has_value()) {
+      return *_cell_area_zhigh;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_z();
+      ASSERT2(_cell_area_zhigh.has_value());
+      return *_cell_area_zhigh;
     }
-    ASSERT2(_cell_area_zhigh.has_value());
-    return *_cell_area_zhigh;
   }
   FieldMetric& cell_area_xlow() {
-    if (!_cell_area_xlow.has_value()) {
+    if (_cell_area_xlow.has_value()) {
+      return *_cell_area_xlow;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_x();
+      ASSERT2(_cell_area_xlow.has_value());
+      return *_cell_area_xlow;
     }
-    ASSERT2(_cell_area_xlow.has_value());
-    return *_cell_area_xlow;
   }
   FieldMetric& cell_area_xhigh() {
-    if (!_cell_area_xhigh.has_value()) {
+    if (_cell_area_xhigh.has_value()) {
+      return *_cell_area_xhigh;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_x();
+      ASSERT2(_cell_area_xhigh.has_value());
+      return *_cell_area_xhigh;
     }
-    ASSERT2(_cell_area_xhigh.has_value());
-    return *_cell_area_xhigh;
   }
   FieldMetric& cell_area_ylow() {
-    if (!_cell_area_ylow.has_value()) {
+    if (_cell_area_ylow.has_value()) {
+      return *_cell_area_ylow;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_y();
+      ASSERT2(_cell_area_ylow.has_value());
+      return *_cell_area_ylow;
     }
-    ASSERT2(_cell_area_ylow.has_value());
-    return *_cell_area_ylow;
   }
   FieldMetric& cell_area_yhigh() {
-    if (!_cell_area_yhigh.has_value()) {
+    if (_cell_area_yhigh.has_value()) {
+      return *_cell_area_yhigh;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_y();
+      ASSERT2(_cell_area_yhigh.has_value());
+      return *_cell_area_yhigh;
     }
-    ASSERT2(_cell_area_yhigh.has_value());
-    return *_cell_area_yhigh;
   }
   FieldMetric& cell_area_zlow() {
-    if (!_cell_area_zlow.has_value()) {
+    if (_cell_area_zlow.has_value()) {
+      return *_cell_area_zlow;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_z();
+      ASSERT2(_cell_area_zlow.has_value());
+      return *_cell_area_zlow;
     }
-    ASSERT2(_cell_area_zlow.has_value());
-    return *_cell_area_zlow;
   }
   FieldMetric& cell_area_zhigh() {
-    if (!_cell_area_zhigh.has_value()) {
+    if (_cell_area_zhigh.has_value()) {
+      return *_cell_area_zhigh;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_area_z();
+      ASSERT2(_cell_area_zhigh.has_value());
+      return *_cell_area_zhigh;
     }
-    ASSERT2(_cell_area_zhigh.has_value());
-    return *_cell_area_zhigh;
   }
   // Cell Volume
   const FieldMetric& cell_volume() const {
-    if (!_cell_volume.has_value()) {
+    if (_cell_volume.has_value()) {
+      return *_cell_volume;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_volume();
+      ASSERT2(_cell_volume.has_value());
+      return *_cell_volume;
     }
-    ASSERT2(_cell_volume.has_value());
-    return *_cell_volume;
   }
   FieldMetric& cell_volume() {
-    if (!_cell_volume.has_value()) {
+    if (_cell_volume.has_value()) {
+      return *_cell_volume;
+    }
+    BOUT_OMP_SAFE(critical)
+    {
       _compute_cell_volume();
+      ASSERT2(_cell_volume.has_value());
+      return *_cell_volume;
     }
-    ASSERT2(_cell_volume.has_value());
-    return *_cell_volume;
   }
 
 private:

From 9ff3c73ee5ab0f61d9a493b3513558834cce9ab7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 12:46:20 +0200
Subject: [PATCH 1486/1827] Add comment about impl header

---
 include/bout/fv_ops.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 89caaadf97..ab791efb41 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -78,6 +78,8 @@ Field3D D4DY4(const Field3D& d, const Field3D& f);
 Field3D D4DY4_Index(const Field3D& f, bool bndry_flux = true);
 
 // Forward declarations of flux limiters
+// If you want to use your own flux limiter, you need to
+// #include <bout/fv_ops_impl.hxx> to instantiate the templates.
 class Upwind;
 class Fromm;
 class MinMod;

From b98954f95021b9ad5bbd60795eaab84e571ee2f5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 12:46:36 +0200
Subject: [PATCH 1487/1827] Add comments about explicit instantiation

---
 include/bout/fv_ops_impl.hxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 91117a6961..81d4c67c25 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -43,6 +43,7 @@ struct Stencil1D {
 /*!
    * First order upwind for testing
    */
+// NB: The templates need to be explicitly instantiated in fv_ops.cxx
 struct Upwind {
   void operator()(Stencil1D& n) { n.L = n.R = n.c; }
 };
@@ -50,6 +51,7 @@ struct Upwind {
 /*!
    * Fromm method
    */
+// NB: The templates need to be explicitly instantiated in fv_ops.cxx
 struct Fromm {
   void operator()(Stencil1D& n) {
     n.L = n.c - (0.25 * (n.p - n.m));
@@ -65,6 +67,7 @@ struct Fromm {
    * or minimum slope set to zero, i.e. reverts
    * to first order upwinding
    */
+// NB: The templates need to be explicitly instantiated in fv_ops.cxx
 struct MinMod {
   void operator()(Stencil1D& n) {
     // Choose the gradient within the cell
@@ -102,6 +105,7 @@ private:
    * 2*right. If any of these slopes have different signs
    * then the slope reverts to zero (i.e. 1st-order upwinding).
    */
+// NB: The templates need to be explicitly instantiated in fv_ops.cxx
 struct MC {
   void operator()(Stencil1D& n) {
     const BoutReal slope = minmod(2. * (n.p - n.c),  // 2*right difference
@@ -149,6 +153,7 @@ private:
 ///   gL = n.c - n.m
 ///   gR = n.p - n.c
 ///
+// NB: The templates need to be explicitly instantiated in fv_ops.cxx
 struct Superbee {
   void operator()(Stencil1D& n) {
     const BoutReal gL = n.c - n.m;
@@ -185,6 +190,7 @@ struct Superbee {
    *
    * where `pos(x)` is a smooth approximation to `max(x, 0)`.
    */
+// NB: The templates need to be explicitly instantiated in fv_ops.cxx
 struct VanAlbada {
   void operator()(Stencil1D& n) {
     const BoutReal dl = n.c - n.m;
@@ -220,6 +226,7 @@ struct VanAlbada {
    * Uses only the three-point stencil (`m`, `c`, `p`), so it is a drop-in
    * replacement anywhere `Stencil1D` is populated with those values.
    */
+// NB: The templates need to be explicitly instantiated in fv_ops.cxx
 struct WENO3 {
   void operator()(Stencil1D& n) {
     // Right face (between c and p): value from cell c (left state at i+1/2)

From e68d1659aca232c6e01278325817dd9c01dff56a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 12:53:49 +0200
Subject: [PATCH 1488/1827] Do not return from critical areas

---
 include/bout/coordinates.hxx | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index a8f4c09c5c..2917e39388 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -123,8 +123,8 @@ public:
     {
       _compute_cell_area_x();
       ASSERT2(_cell_area_xlow.has_value());
-      return *_cell_area_xlow;
     }
+    return *_cell_area_xlow;
   }
   const FieldMetric& cell_area_xhigh() const {
     if (_cell_area_xhigh.has_value()) {
@@ -134,8 +134,8 @@ public:
     {
       _compute_cell_area_x();
       ASSERT2(_cell_area_xhigh.has_value());
-      return *_cell_area_xhigh;
     }
+    return *_cell_area_xhigh;
   }
   const FieldMetric& cell_area_ylow() const {
     if (_cell_area_ylow.has_value()) {
@@ -145,8 +145,8 @@ public:
     {
       _compute_cell_area_y();
       ASSERT2(_cell_area_ylow.has_value());
-      return *_cell_area_ylow;
     }
+    return *_cell_area_ylow;
   }
   const FieldMetric& cell_area_yhigh() const {
     if (_cell_area_yhigh.has_value()) {
@@ -156,8 +156,8 @@ public:
     {
       _compute_cell_area_y();
       ASSERT2(_cell_area_yhigh.has_value());
-      return *_cell_area_yhigh;
     }
+    return *_cell_area_yhigh;
   }
   const FieldMetric& cell_area_zlow() const {
     if (_cell_area_zlow.has_value()) {
@@ -167,8 +167,8 @@ public:
     {
       _compute_cell_area_z();
       ASSERT2(_cell_area_zlow.has_value());
-      return *_cell_area_zlow;
     }
+    return *_cell_area_zlow;
   }
   const FieldMetric& cell_area_zhigh() const {
     if (_cell_area_zhigh.has_value()) {
@@ -178,8 +178,8 @@ public:
     {
       _compute_cell_area_z();
       ASSERT2(_cell_area_zhigh.has_value());
-      return *_cell_area_zhigh;
     }
+    return *_cell_area_zhigh;
   }
   FieldMetric& cell_area_xlow() {
     if (_cell_area_xlow.has_value()) {
@@ -189,8 +189,8 @@ public:
     {
       _compute_cell_area_x();
       ASSERT2(_cell_area_xlow.has_value());
-      return *_cell_area_xlow;
     }
+    return *_cell_area_xlow;
   }
   FieldMetric& cell_area_xhigh() {
     if (_cell_area_xhigh.has_value()) {
@@ -200,8 +200,8 @@ public:
     {
       _compute_cell_area_x();
       ASSERT2(_cell_area_xhigh.has_value());
-      return *_cell_area_xhigh;
     }
+    return *_cell_area_xhigh;
   }
   FieldMetric& cell_area_ylow() {
     if (_cell_area_ylow.has_value()) {
@@ -211,8 +211,8 @@ public:
     {
       _compute_cell_area_y();
       ASSERT2(_cell_area_ylow.has_value());
-      return *_cell_area_ylow;
     }
+    return *_cell_area_ylow;
   }
   FieldMetric& cell_area_yhigh() {
     if (_cell_area_yhigh.has_value()) {
@@ -222,8 +222,8 @@ public:
     {
       _compute_cell_area_y();
       ASSERT2(_cell_area_yhigh.has_value());
-      return *_cell_area_yhigh;
     }
+    return *_cell_area_yhigh;
   }
   FieldMetric& cell_area_zlow() {
     if (_cell_area_zlow.has_value()) {
@@ -233,8 +233,8 @@ public:
     {
       _compute_cell_area_z();
       ASSERT2(_cell_area_zlow.has_value());
-      return *_cell_area_zlow;
     }
+    return *_cell_area_zlow;
   }
   FieldMetric& cell_area_zhigh() {
     if (_cell_area_zhigh.has_value()) {
@@ -244,8 +244,8 @@ public:
     {
       _compute_cell_area_z();
       ASSERT2(_cell_area_zhigh.has_value());
-      return *_cell_area_zhigh;
     }
+    return *_cell_area_zhigh;
   }
   // Cell Volume
   const FieldMetric& cell_volume() const {
@@ -256,8 +256,8 @@ public:
     {
       _compute_cell_volume();
       ASSERT2(_cell_volume.has_value());
-      return *_cell_volume;
     }
+    return *_cell_volume;
   }
   FieldMetric& cell_volume() {
     if (_cell_volume.has_value()) {
@@ -267,8 +267,8 @@ public:
     {
       _compute_cell_volume();
       ASSERT2(_cell_volume.has_value());
-      return *_cell_volume;
     }
+    return *_cell_volume;
   }
 
 private:

From a99536026e6683285a2f1dd3c78029cf18fb1243 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 13:01:08 +0200
Subject: [PATCH 1489/1827] Add missing header

---
 src/mesh/difops.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 1eef4d7524..79ffbcc44b 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -35,7 +35,9 @@
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/globals.hxx>
+#include <bout/index_derivs_interface.hxx>
 #include <bout/mesh.hxx>
+#include <bout/region.hxx>
 #include <bout/solver.hxx>
 #include <bout/utils.hxx>
 #include <bout/vecops.hxx>

From 5284cc185075cda283c2424d82e9649a633d9e2d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 13:12:22 +0200
Subject: [PATCH 1490/1827] Remove TRACE

---
 src/mesh/difops.cxx | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 79ffbcc44b..8ecd9d64ff 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -35,7 +35,6 @@
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/globals.hxx>
-#include <bout/index_derivs_interface.hxx>
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 #include <bout/solver.hxx>
@@ -377,8 +376,6 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc)
 
 Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D& flow_ylow,
                                bool bndry_flux) {
-  TRACE("FV::Div_par_K_Grad_par_mod");
-
   ASSERT2(Kin.getLocation() == fin.getLocation());
 
   const Mesh* mesh = Kin.getMesh();

From 1672208242c2bf2c6428129c6945efa49cb24f3d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 14:10:57 +0200
Subject: [PATCH 1491/1827] Move critical section to compute functions

---
 include/bout/coordinates.hxx |  98 +++++------------
 src/mesh/coordinates.cxx     | 202 ++++++++++++++++++++---------------
 2 files changed, 146 insertions(+), 154 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 2917e39388..a21f62cd4d 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -119,132 +119,96 @@ public:
     if (_cell_area_xlow.has_value()) {
       return *_cell_area_xlow;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_x();
-      ASSERT2(_cell_area_xlow.has_value());
-    }
+    _compute_cell_area_x();
+    ASSERT2(_cell_area_xlow.has_value());
     return *_cell_area_xlow;
   }
   const FieldMetric& cell_area_xhigh() const {
     if (_cell_area_xhigh.has_value()) {
       return *_cell_area_xhigh;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_x();
-      ASSERT2(_cell_area_xhigh.has_value());
-    }
+    _compute_cell_area_x();
+    ASSERT2(_cell_area_xhigh.has_value());
     return *_cell_area_xhigh;
   }
   const FieldMetric& cell_area_ylow() const {
     if (_cell_area_ylow.has_value()) {
       return *_cell_area_ylow;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_y();
-      ASSERT2(_cell_area_ylow.has_value());
-    }
+    _compute_cell_area_y();
+    ASSERT2(_cell_area_ylow.has_value());
     return *_cell_area_ylow;
   }
   const FieldMetric& cell_area_yhigh() const {
     if (_cell_area_yhigh.has_value()) {
       return *_cell_area_yhigh;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_y();
-      ASSERT2(_cell_area_yhigh.has_value());
-    }
+    _compute_cell_area_y();
+    ASSERT2(_cell_area_yhigh.has_value());
     return *_cell_area_yhigh;
   }
   const FieldMetric& cell_area_zlow() const {
     if (_cell_area_zlow.has_value()) {
       return *_cell_area_zlow;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_z();
-      ASSERT2(_cell_area_zlow.has_value());
-    }
+    _compute_cell_area_z();
+    ASSERT2(_cell_area_zlow.has_value());
     return *_cell_area_zlow;
   }
   const FieldMetric& cell_area_zhigh() const {
     if (_cell_area_zhigh.has_value()) {
       return *_cell_area_zhigh;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_z();
-      ASSERT2(_cell_area_zhigh.has_value());
-    }
+    _compute_cell_area_z();
+    ASSERT2(_cell_area_zhigh.has_value());
     return *_cell_area_zhigh;
   }
   FieldMetric& cell_area_xlow() {
     if (_cell_area_xlow.has_value()) {
       return *_cell_area_xlow;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_x();
-      ASSERT2(_cell_area_xlow.has_value());
-    }
+    _compute_cell_area_x();
+    ASSERT2(_cell_area_xlow.has_value());
     return *_cell_area_xlow;
   }
   FieldMetric& cell_area_xhigh() {
     if (_cell_area_xhigh.has_value()) {
       return *_cell_area_xhigh;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_x();
-      ASSERT2(_cell_area_xhigh.has_value());
-    }
+    _compute_cell_area_x();
+    ASSERT2(_cell_area_xhigh.has_value());
     return *_cell_area_xhigh;
   }
   FieldMetric& cell_area_ylow() {
     if (_cell_area_ylow.has_value()) {
       return *_cell_area_ylow;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_y();
-      ASSERT2(_cell_area_ylow.has_value());
-    }
+    _compute_cell_area_y();
+    ASSERT2(_cell_area_ylow.has_value());
     return *_cell_area_ylow;
   }
   FieldMetric& cell_area_yhigh() {
     if (_cell_area_yhigh.has_value()) {
       return *_cell_area_yhigh;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_y();
-      ASSERT2(_cell_area_yhigh.has_value());
-    }
+    _compute_cell_area_y();
+    ASSERT2(_cell_area_yhigh.has_value());
     return *_cell_area_yhigh;
   }
   FieldMetric& cell_area_zlow() {
     if (_cell_area_zlow.has_value()) {
       return *_cell_area_zlow;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_z();
-      ASSERT2(_cell_area_zlow.has_value());
-    }
+    _compute_cell_area_z();
+    ASSERT2(_cell_area_zlow.has_value());
     return *_cell_area_zlow;
   }
   FieldMetric& cell_area_zhigh() {
     if (_cell_area_zhigh.has_value()) {
       return *_cell_area_zhigh;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_area_z();
-      ASSERT2(_cell_area_zhigh.has_value());
-    }
+    _compute_cell_area_z();
+    ASSERT2(_cell_area_zhigh.has_value());
     return *_cell_area_zhigh;
   }
   // Cell Volume
@@ -252,22 +216,16 @@ public:
     if (_cell_volume.has_value()) {
       return *_cell_volume;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_volume();
-      ASSERT2(_cell_volume.has_value());
-    }
+    _compute_cell_volume();
+    ASSERT2(_cell_volume.has_value());
     return *_cell_volume;
   }
   FieldMetric& cell_volume() {
     if (_cell_volume.has_value()) {
       return *_cell_volume;
     }
-    BOUT_OMP_SAFE(critical)
-    {
-      _compute_cell_volume();
-      ASSERT2(_cell_volume.has_value());
-    }
+    _compute_cell_volume();
+    ASSERT2(_cell_volume.has_value());
     return *_cell_volume;
   }
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 057ffa65b5..afb63f981d 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2015,17 +2015,23 @@ const Coordinates::FieldMetric& Coordinates::g_22_ylow() const {
   if (_g_22_ylow.has_value()) {
     return *_g_22_ylow;
   }
-  _g_22_ylow.emplace(emptyFrom(g_22));
-  //_g_22_ylow->setLocation(CELL_YLOW);
-  auto* mesh = Bxy.getMesh();
-  if (Bxy.isFci()) {
-    if (mesh->get(_g_22_ylow.value(), "g_22_cell_ylow", 0.0, false) != 0) {
-      throw BoutException("The grid file does not contain `g_22_cell_ylow`.");
-    }
-  } else {
-    ASSERT0(mesh->ystart > 0);
-    BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
-      _g_22_ylow.value()[i] = SQ(0.5 * (std::sqrt(g_22[i]) + std::sqrt(g_22[i.ym()])));
+  BOUT_OMP_SAFE(critical)
+  {
+    if (!_g_22_ylow.has_value()) {
+      _g_22_ylow.emplace(emptyFrom(g_22));
+      //_g_22_ylow->setLocation(CELL_YLOW);
+      auto* mesh = Bxy.getMesh();
+      if (Bxy.isFci()) {
+        if (mesh->get(_g_22_ylow.value(), "g_22_cell_ylow", 0.0, false) != 0) {
+          throw BoutException("The grid file does not contain `g_22_cell_ylow`.");
+        }
+      } else {
+        ASSERT0(mesh->ystart > 0);
+        BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
+          _g_22_ylow.value()[i] =
+              SQ(0.5 * (std::sqrt(g_22[i]) + std::sqrt(g_22[i.ym()])));
+        }
+      }
     }
   }
   return g_22_ylow();
@@ -2035,99 +2041,127 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
   if (_g_22_yhigh.has_value()) {
     return *_g_22_yhigh;
   }
-  _g_22_yhigh.emplace(emptyFrom(g_22));
-  auto* mesh = Bxy.getMesh();
-  if (Bxy.isFci()) {
-    if (mesh->get(_g_22_yhigh.value(), "g_22_cell_yhigh", 0.0, false) != 0) {
-      throw BoutException("The grid file does not contain `g_22_cell_yhigh`.");
-    }
-  } else {
-    ASSERT0(mesh->ystart > 0);
-    BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
-      _g_22_yhigh.value()[i] = SQ(0.5 * (std::sqrt(g_22[i]) + std::sqrt(g_22[i.yp()])));
+  BOUT_OMP_SAFE(critical)
+  {
+    if (!_g_22_yhigh.has_value()) {
+      _g_22_yhigh.emplace(emptyFrom(g_22));
+      auto* mesh = Bxy.getMesh();
+      if (Bxy.isFci()) {
+        if (mesh->get(_g_22_yhigh.value(), "g_22_cell_yhigh", 0.0, false) != 0) {
+          throw BoutException("The grid file does not contain `g_22_cell_yhigh`.");
+        }
+      } else {
+        ASSERT0(mesh->ystart > 0);
+        BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
+          _g_22_yhigh.value()[i] =
+              SQ(0.5 * (std::sqrt(g_22[i]) + std::sqrt(g_22[i.yp()])));
+        }
+      }
     }
   }
   return g_22_yhigh();
 }
 
 void Coordinates::_compute_cell_area_x() const {
-  const FieldMetric area_centre = sqrt(g_22 * g_33 - SQ(g_23)) * dy * dz;
-  _cell_area_xlow.emplace(emptyFrom(area_centre));
-  _cell_area_xhigh.emplace(emptyFrom(area_centre));
-  // We cannot setLocation, as that would trigger the computation of staggered
-  // metrics.
-  auto* mesh = Bxy.getMesh();
-  ASSERT0(mesh->xstart > 0);
-  BOUT_FOR(i, area_centre.getRegion("RGN_NOX")) {
-    (*_cell_area_xlow)[i] = 0.5 * (area_centre[i] + area_centre[i.xm()]);
-    (*_cell_area_xhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.xp()]);
+  BOUT_OMP_SAFE(critical)
+  {
+    if (!_cell_area_xlow.has_value()) {
+      const FieldMetric area_centre = sqrt(g_22 * g_33 - SQ(g_23)) * dy * dz;
+      _cell_area_xlow.emplace(emptyFrom(area_centre));
+      _cell_area_xhigh.emplace(emptyFrom(area_centre));
+      // We cannot setLocation, as that would trigger the computation of staggered
+      // metrics.
+      auto* mesh = Bxy.getMesh();
+      ASSERT0(mesh->xstart > 0);
+      BOUT_FOR(i, area_centre.getRegion("RGN_NOX")) {
+        (*_cell_area_xlow)[i] = 0.5 * (area_centre[i] + area_centre[i.xm()]);
+        (*_cell_area_xhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.xp()]);
+      }
+    }
   }
 }
 
 void Coordinates::_compute_cell_area_y() const {
-  auto* mesh = Bxy.getMesh();
-  if (g_11.isFci()) {
-    const FieldMetric jxz_centre = sqrt(g_11 * g_33 - SQ(g_13));
-    auto jxz_ylow = emptyFrom(jxz_centre);
-    auto jxz_yhigh = emptyFrom(jxz_centre);
-
-    auto By_c = emptyFrom(jxz_centre);
-    auto By_h = emptyFrom(jxz_yhigh);
-    auto By_l = emptyFrom(jxz_ylow);
-    if (mesh->get(By_c, "By", 0.0, false, CELL_CENTRE) != 0) {
-      throw BoutException("The grid file does not contain `By`.");
-    }
-    if (mesh->get(By_l, "By_cell_ylow", 0.0, false) != 0) {
-      throw BoutException("The grid file does not contain `By_cell_ylow`.");
-    }
-    if (mesh->get(By_h, "By_cell_yhigh", 0.0, false) != 0) {
-      throw BoutException("The grid file does not contain `By_cell_yhigh`.");
-    }
-    BOUT_FOR(i, By_c.getRegion("RGN_NOY")) {
-      jxz_ylow[i] = By_c[i] / By_l[i] * jxz_centre[i];
-      jxz_yhigh[i] = By_c[i] / By_h[i] * jxz_centre[i];
-    }
-    ASSERT3(isUniform(dx, true, "RGN_ALL"));
-    ASSERT2(isUniform(dx, false, "RGN_ALL"));
-    ASSERT3(isUniform(dz, true, "RGN_ALL"));
-    ASSERT2(isUniform(dz, false, "RGN_ALL"));
-    _cell_area_ylow.emplace(jxz_ylow * dx * dz);
-    _cell_area_yhigh.emplace(jxz_yhigh * dx * dz);
-  } else {
-    // Field aligned
-    const FieldMetric area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;
-    _cell_area_ylow.emplace(emptyFrom(area_centre));
-    _cell_area_yhigh.emplace(emptyFrom(area_centre));
-    // We cannot setLocation, as that would trigger the computation of staggered
-    // metrics.
-    BOUT_FOR(i, mesh->getRegion("RGN_ALL")) {
-      if (i.y() > 0) {
-        (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
-      } else {
-        (*_cell_area_ylow)[i] = BoutNaN;
-      }
-      if (i.y() < mesh->LocalNy - 1) {
-        (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
+  BOUT_OMP_SAFE(critical)
+  {
+    if (!_cell_area_ylow.has_value()) {
+      auto* mesh = Bxy.getMesh();
+      if (g_11.isFci()) {
+        const FieldMetric jxz_centre = sqrt(g_11 * g_33 - SQ(g_13));
+        auto jxz_ylow = emptyFrom(jxz_centre);
+        auto jxz_yhigh = emptyFrom(jxz_centre);
+
+        auto By_c = emptyFrom(jxz_centre);
+        auto By_h = emptyFrom(jxz_yhigh);
+        auto By_l = emptyFrom(jxz_ylow);
+        if (mesh->get(By_c, "By", 0.0, false, CELL_CENTRE) != 0) {
+          throw BoutException("The grid file does not contain `By`.");
+        }
+        if (mesh->get(By_l, "By_cell_ylow", 0.0, false) != 0) {
+          throw BoutException("The grid file does not contain `By_cell_ylow`.");
+        }
+        if (mesh->get(By_h, "By_cell_yhigh", 0.0, false) != 0) {
+          throw BoutException("The grid file does not contain `By_cell_yhigh`.");
+        }
+        BOUT_FOR(i, By_c.getRegion("RGN_NOY")) {
+          jxz_ylow[i] = By_c[i] / By_l[i] * jxz_centre[i];
+          jxz_yhigh[i] = By_c[i] / By_h[i] * jxz_centre[i];
+        }
+        ASSERT3(isUniform(dx, true, "RGN_ALL"));
+        ASSERT2(isUniform(dx, false, "RGN_ALL"));
+        ASSERT3(isUniform(dz, true, "RGN_ALL"));
+        ASSERT2(isUniform(dz, false, "RGN_ALL"));
+        _cell_area_ylow.emplace(jxz_ylow * dx * dz);
+        _cell_area_yhigh.emplace(jxz_yhigh * dx * dz);
       } else {
-        (*_cell_area_yhigh)[i] = BoutNaN;
+        // Field aligned
+        const FieldMetric area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;
+        _cell_area_ylow.emplace(emptyFrom(area_centre));
+        _cell_area_yhigh.emplace(emptyFrom(area_centre));
+        // We cannot setLocation, as that would trigger the computation of staggered
+        // metrics.
+        BOUT_FOR(i, mesh->getRegion("RGN_ALL")) {
+          if (i.y() > 0) {
+            (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
+          } else {
+            (*_cell_area_ylow)[i] = BoutNaN;
+          }
+          if (i.y() < mesh->LocalNy - 1) {
+            (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
+          } else {
+            (*_cell_area_yhigh)[i] = BoutNaN;
+          }
+        }
       }
     }
   }
 }
 
 void Coordinates::_compute_cell_area_z() const {
-  const FieldMetric area_centre = sqrt(g_11 * g_22 - SQ(g_12)) * dx * dy;
-  _cell_area_zlow.emplace(emptyFrom(area_centre));
-  _cell_area_zhigh.emplace(emptyFrom(area_centre));
-  // We cannot setLocation, as that would trigger the computation of staggered
-  // metrics.
-  BOUT_FOR(i, area_centre.getRegion("RGN_NOZ")) {
-    (*_cell_area_zlow)[i] = 0.5 * (area_centre[i] + area_centre[i.zm()]);
-    (*_cell_area_zhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.zp()]);
+  BOUT_OMP_SAFE(critical)
+  {
+    if (!_cell_volume.has_value()) {
+      const FieldMetric area_centre = sqrt(g_11 * g_22 - SQ(g_12)) * dx * dy;
+      _cell_area_zlow.emplace(emptyFrom(area_centre));
+      _cell_area_zhigh.emplace(emptyFrom(area_centre));
+      // We cannot setLocation, as that would trigger the computation of staggered
+      // metrics.
+      BOUT_FOR(i, area_centre.getRegion("RGN_NOZ")) {
+        (*_cell_area_zlow)[i] = 0.5 * (area_centre[i] + area_centre[i.zm()]);
+        (*_cell_area_zhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.zp()]);
+      }
+    }
   }
 }
 
-void Coordinates::_compute_cell_volume() const { _cell_volume.emplace(J * dx * dy * dz); }
+void Coordinates::_compute_cell_volume() const {
+  BOUT_OMP_SAFE(critical)
+  {
+    if (!_cell_volume.has_value()) {
+      _cell_volume.emplace(J * dx * dy * dz);
+    }
+  }
+}
 
 std::shared_ptr<YBoundary> Coordinates::makeYBoundary(YBndryType type) const {
   return std::make_shared<YBoundary>(type, localoptions, *localmesh);

From b89867dd3a54d17d1c7b4174a79baabebec44c54 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 24 Jun 2026 14:11:38 +0200
Subject: [PATCH 1492/1827] Add DDY template for expression

---
 include/bout/derivs.hxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/include/bout/derivs.hxx b/include/bout/derivs.hxx
index a8d9279378..92f094f550 100644
--- a/include/bout/derivs.hxx
+++ b/include/bout/derivs.hxx
@@ -86,6 +86,13 @@ Field3D DDY(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
             const std::string& method = "DEFAULT",
             const std::string& region = "RGN_NOBNDRY");
 
+template <typename E>
+std::enable_if_t<is_expr_field3d_v<E> && !bout::utils::is_Field3D_v<E>, const Field3D>
+DDY(const E& expr, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
+    const std::string& region = "RGN_NOBNDRY") {
+  return DDY(Field3D{expr}, outloc, method, region);
+}
+
 /// Calculate first partial derivative in Y
 ///
 ///   \f$\partial / \partial y\f$

From 0b35178f1fb36e90fb3cc1a0b65d57af79f2569d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 24 Jun 2026 15:41:54 -0700
Subject: [PATCH 1493/1827] Apply suggestions from code review

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Peter Hill <zed.three@gmail.com>
---
 include/bout/build_config.hxx | 8 +++++++-
 include/bout/field3d.hxx      | 3 +--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx
index 9a160161d4..e2e047812a 100644
--- a/include/bout/build_config.hxx
+++ b/include/bout/build_config.hxx
@@ -70,7 +70,13 @@ constexpr auto use_msgstack = static_cast<bool>(BOUT_USE_MSGSTACK);
 #define BOUT_FORCEINLINE inline
 #endif
 
-#if defined(_MSC_VER)
+#ifdef __has_cpp_attribute
+#if __has_cpp_attribute(assume) >= 202207L
+#define BOUT_ASSUME(condition) [[assume(condition)]]
+#endif
+#endif
+#else
+#ifdef _MSC_VER
 #define BOUT_ASSUME(condition) __assume(condition)
 #elif defined(__clang__)
 #if __has_builtin(__builtin_assume)
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 6ce9fd3397..47a35323ff 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -53,7 +53,6 @@ class Options;
 class Field3DParallel;
 
 namespace bout::detail {
-const Region<Ind3D>& getField3DRegion(const Mesh* mesh, std::optional<size_t> regionID);
 }
 
 #include "bout/fieldops.hxx"
@@ -469,7 +468,7 @@ public:
     }
 
     template <typename Mul, typename Div>
-    View& setScale(Mul, Div) {
+    View& setScale(Mul /*unused*/, Div /*unused*/) {
       static_assert(!std::is_same_v<Mul, Mul>,
                     "Field3D::View does not support setScale()");
       return *this;

From 1f7e6ceabd3abfb2723a64df2c4578538c76f50f Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 24 Jun 2026 16:21:33 -0700
Subject: [PATCH 1494/1827] Tidying up a bit

---
 include/bout/build_config.hxx | 11 +++++------
 include/bout/field3d.hxx      |  3 ---
 include/bout/fieldops.hxx     |  8 +++++++-
 3 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx
index e2e047812a..aa7f257ca5 100644
--- a/include/bout/build_config.hxx
+++ b/include/bout/build_config.hxx
@@ -48,6 +48,8 @@ constexpr auto use_msgstack = static_cast<bool>(BOUT_USE_MSGSTACK);
 #undef STRINGIFY1
 #undef STRINGIFY
 
+// NOLINTBEGIN(cppcoreguidelines-macro-usage)
+// These defines are used to provide compiler-specific flags
 #if BOUT_HAS_CUDA && defined(__CUDACC__)
 #define BOUT_HOST_DEVICE __host__ __device__
 #define BOUT_HOST __host__
@@ -70,13 +72,9 @@ constexpr auto use_msgstack = static_cast<bool>(BOUT_USE_MSGSTACK);
 #define BOUT_FORCEINLINE inline
 #endif
 
-#ifdef __has_cpp_attribute
-#if __has_cpp_attribute(assume) >= 202207L
+#if defined(__has_cpp_attribute) && __has_cpp_attribute(assume) >= 202207L
 #define BOUT_ASSUME(condition) [[assume(condition)]]
-#endif
-#endif
-#else
-#ifdef _MSC_VER
+#elif defined(_MSC_VER)
 #define BOUT_ASSUME(condition) __assume(condition)
 #elif defined(__clang__)
 #if __has_builtin(__builtin_assume)
@@ -94,5 +92,6 @@ constexpr auto use_msgstack = static_cast<bool>(BOUT_USE_MSGSTACK);
 #else
 #define BOUT_ASSUME(condition) ((void)0)
 #endif
+// NOLINTEND(cppcoreguidelines-macro-usage)
 
 #endif // BOUT_BUILD_OPTIONS_HXX
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 47a35323ff..6901b34087 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -52,9 +52,6 @@ class Mesh;
 class Options;
 class Field3DParallel;
 
-namespace bout::detail {
-}
-
 #include "bout/fieldops.hxx"
 
 /// Class for 3D X-Y-Z scalar fields
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 219c9150f3..f36061ceaa 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -25,8 +25,11 @@ class Field2D;
 class FieldPerp;
 
 namespace bout::detail {
+// This is defined in field3d.cxx
+// It is used because Mesh is an incomplete type so methods cannot be called
+// in the template functions in this header file.
 const Region<Ind3D>& getField3DRegion(const Mesh* mesh, std::optional<size_t> regionID);
-}
+} // namespace bout::detail
 
 template <typename T>
 struct is_expr_field2d : std::false_type {};
@@ -415,12 +418,15 @@ struct BinaryExpr {
     streams.put(stream);
 #else
     if constexpr (std::is_same_v<ResT, Field3D>) {
+      // Optimize common case of Field3D on CPUs.
+      // Get the Region without directly using incomplete Mesh type
       const auto& region = bout::detail::getField3DRegion(mesh, regionID);
       for (auto block = region.getBlocks().cbegin(), end = region.getBlocks().cend();
            block < end; ++block) {
         const int block_begin = block->first.ind;
         const int block_end = block->second.ind;
 
+        // Help optimizer establish loop bounds
         BOUT_ASSUME(block_begin >= 0);
         BOUT_ASSUME(block_begin <= block_end);
 

From 88408fe3d88d631bc7f7fac5fb878d20d46b262d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 24 Jun 2026 21:01:58 -0700
Subject: [PATCH 1495/1827] Addressing review comments

- Throw exception if `use_precon` is used. Added to `boutupgrader`.
- Remove temporary workaround for Hermes-3 braginskii_conduction
- Prefer `if` to `#if`
---
 src/solver/impls/cvode/cvode.cxx | 22 +++++-----------------
 1 file changed, 5 insertions(+), 17 deletions(-)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 21244055bc..dcb8e9fe71 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -171,21 +171,11 @@ CvodeSolver::CvodeSolver(Options* opts)
   canReset = true;
 
   if ((*options)["use_precon"].isSet()) {
-    output_warn << "WARNING: solver:use_precon is deprecated for CVODE and is now "
-                   "ignored. Use solver:cvode_precon_method=none to disable "
-                   "preconditioning.\n";
+    throw BoutException("solver:use_precon is deprecated for CVODE and is now "
+                        "ignored. Use solver:cvode_precon_method=none to disable "
+                        "preconditioning.\n");
   }
 
-#if BOUT_HAS_PETSC
-  // This is a temporary fix to initialise PetscLib early, working
-  // around a bug in Hermes-3 braginskii_conduction that creates a
-  // "petsc:type" subsection.
-  if (precon_method == CvodePreconMethod::petsc
-      || ((precon_method == CvodePreconMethod::Auto) && !this->hasPreconditioner())) {
-    petsc_lib = std::make_unique<PetscLib>();
-  }
-#endif
-
   // Add diagnostics to output
   // Needs to be in constructor not init() because init() is called after
   // Solver::outputVars()
@@ -408,12 +398,10 @@ int CvodeSolver::init() {
     if (selected_precon == CvodePreconMethod::Auto) {
       if (hasPreconditioner()) {
         selected_precon = CvodePreconMethod::user;
-      } else {
-#if BOUT_HAS_PETSC
+      } else if (bout::build::has_petsc) {
         selected_precon = CvodePreconMethod::petsc;
-#else
+      } else {
         selected_precon = CvodePreconMethod::bbd;
-#endif
       }
     }
 

From 5ddf056c198d1dd6de3c2ab8a2d9a79b2caf1835 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 24 Jun 2026 21:32:10 -0700
Subject: [PATCH 1496/1827] cvode: Guard against manyvector + petsc

PETSc preconditioning requires converting between BOUT++ state
vectors and PETSc vectors.
---
 src/solver/impls/cvode/cvode.cxx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index dcb8e9fe71..2cdeeed9c3 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -928,6 +928,11 @@ int CvodeSolver::petscPSetup(BoutReal t, N_Vector yy, N_Vector UNUSED(yp),
   s->petsc_t = t;
   s->petsc_gamma = gamma;
 
+  if (s->nvector_type == NVectorType::ManyVector) {
+    throw BoutException("solver:cvode_precon_method=petsc is not supported with "
+                        "solver:nvector=manyvector");
+  }
+
   auto* ydata = N_VGetArrayPointer(yy);
 
   PetscErrorCode ierr = VecPlaceArray(s->petsc_x, ydata);

From d392578a615e2ffcd00bce32174d7d74dc3e17bd Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 24 Jun 2026 21:34:39 -0700
Subject: [PATCH 1497/1827] Update examples and docs

Trying to catch examples of `use_precon` with CVODE solver.
---
 examples/6field-simple/data/BOUT.inp           | 2 +-
 examples/IMEX/diffusion-nl/README.md           | 3 +--
 examples/constraints/laplace-dae/data/BOUT.inp | 2 +-
 examples/dalf3/data/BOUT.inp                   | 2 +-
 examples/elm-pb-outerloop/data/BOUT.inp        | 2 +-
 examples/elm-pb/Python/data/BOUT.inp           | 2 +-
 examples/elm-pb/Python/data0/BOUT.inp          | 2 +-
 examples/elm-pb/data-hypre/BOUT.inp            | 3 +--
 examples/elm-pb/data-nonlinear/BOUT.inp        | 2 +-
 examples/elm-pb/data/BOUT.inp                  | 2 +-
 examples/elm-pb/relaxing/BOUT.inp              | 3 +--
 examples/elm-pb/test/BOUT.inp                  | 2 +-
 examples/preconditioning/wave/data/BOUT.inp    | 2 +-
 manual/sphinx/user_docs/time_integration.rst   | 7 +++++--
 tests/MMS/elm-pb/data/BOUT.inp                 | 2 +-
 15 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/examples/6field-simple/data/BOUT.inp b/examples/6field-simple/data/BOUT.inp
index 1e1bacfe6f..951182af06 100644
--- a/examples/6field-simple/data/BOUT.inp
+++ b/examples/6field-simple/data/BOUT.inp
@@ -61,7 +61,7 @@ fft_measurement_flag = measure  # If using FFTW, perform tests to determine fast
 atol = 1e-08 # absolute tolerance
 rtol = 1e-05  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 
 mxstep = 10000   # Number of internal steps between outputs
 output_step = 1.0       # time between outputs
diff --git a/examples/IMEX/diffusion-nl/README.md b/examples/IMEX/diffusion-nl/README.md
index 3654d484ee..8356955b95 100644
--- a/examples/IMEX/diffusion-nl/README.md
+++ b/examples/IMEX/diffusion-nl/README.md
@@ -32,7 +32,7 @@ Preconditioning
 
 The preconditioner can be enabled by adding another flag (or setting in BOUT.inp)
 
-    $ ./diffusion-nl solver:use_precon=true
+    $ ./diffusion-nl solver:cvode_precon_method=user
 
 which then greatly reduces the number of iterations needed by CVODE:
 
@@ -59,4 +59,3 @@ can be calculated using finite differences. This uses coloring to improve effici
     1.000e+00          2               26       3.10e-03    31.9    0.0    5.9    7.8   54.4
     2.000e+00          2               23       2.24e-03    35.7    0.0    7.0    7.9   49.4
     3.000e+00          2               18       2.04e-03    35.0    0.0    6.2    8.5   50.4
-
diff --git a/examples/constraints/laplace-dae/data/BOUT.inp b/examples/constraints/laplace-dae/data/BOUT.inp
index ea7c8d1765..ccc9a647ee 100644
--- a/examples/constraints/laplace-dae/data/BOUT.inp
+++ b/examples/constraints/laplace-dae/data/BOUT.inp
@@ -54,7 +54,7 @@ mxstep = 50000
 
 #type=splitrk
 #timestep=1e-4
-use_precon = true
+cvode_precon_method = user
 output_step = 0.01   # time between outputs
 # Settings for split operator test case
 
diff --git a/examples/dalf3/data/BOUT.inp b/examples/dalf3/data/BOUT.inp
index cd6070a1dd..53fa675f83 100644
--- a/examples/dalf3/data/BOUT.inp
+++ b/examples/dalf3/data/BOUT.inp
@@ -58,7 +58,7 @@ group_nonblock = false  # Use non-blocking group operations?
 atol = 1e-08 # absolute tolerance
 rtol = 1e-05  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 use_jacobian = false  # Use user-supplied Jacobian
 
 mxstep = 5000   # Number of internal steps between outputs
diff --git a/examples/elm-pb-outerloop/data/BOUT.inp b/examples/elm-pb-outerloop/data/BOUT.inp
index 797ad91125..560da2999f 100644
--- a/examples/elm-pb-outerloop/data/BOUT.inp
+++ b/examples/elm-pb-outerloop/data/BOUT.inp
@@ -49,7 +49,7 @@ fft_measurement_flag = measure  # If using FFTW, perform tests to determine fast
 atol = 1e-08 # absolute tolerance
 rtol = 1e-05  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 
 mxstep = 5000   # Number of internal steps between outputs
 output_step = 1       # time between outputs
diff --git a/examples/elm-pb/Python/data/BOUT.inp b/examples/elm-pb/Python/data/BOUT.inp
index f0970f22bd..73020e34d4 100644
--- a/examples/elm-pb/Python/data/BOUT.inp
+++ b/examples/elm-pb/Python/data/BOUT.inp
@@ -67,7 +67,7 @@ upwind = W3
 atol = 1e-08 # absolute tolerance
 rtol = 1e-05  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 use_jacobian = false  # Use user-supplied Jacobian
 
 mxstep = 5000   # Number of internal steps between outputs
diff --git a/examples/elm-pb/Python/data0/BOUT.inp b/examples/elm-pb/Python/data0/BOUT.inp
index 918530981c..330ee8bc06 100644
--- a/examples/elm-pb/Python/data0/BOUT.inp
+++ b/examples/elm-pb/Python/data0/BOUT.inp
@@ -68,7 +68,7 @@ upwind = W3
 atol = 1e-08 # absolute tolerance
 rtol = 1e-05  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 use_jacobian = false  # Use user-supplied Jacobian
 
 mxstep = 5000   # Number of internal steps between outputs
diff --git a/examples/elm-pb/data-hypre/BOUT.inp b/examples/elm-pb/data-hypre/BOUT.inp
index 45dd59b536..93088f3d48 100644
--- a/examples/elm-pb/data-hypre/BOUT.inp
+++ b/examples/elm-pb/data-hypre/BOUT.inp
@@ -44,7 +44,7 @@ fft_measurement_flag = measure  # If using FFTW, perform tests to determine fast
 atol = 1.0e-8 # absolute tolerance
 rtol = 1.0e-5  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 
 mxstep = 5000   # Number of internal steps between outputs
 
@@ -240,4 +240,3 @@ bndry_core = neumann
 bndry_xin = none
 bndry_xout = none
 #bndry_target = neumann
-
diff --git a/examples/elm-pb/data-nonlinear/BOUT.inp b/examples/elm-pb/data-nonlinear/BOUT.inp
index b61829c709..e13228ebdf 100644
--- a/examples/elm-pb/data-nonlinear/BOUT.inp
+++ b/examples/elm-pb/data-nonlinear/BOUT.inp
@@ -66,7 +66,7 @@ fft_measurement_flag = measure  # If using FFTW, perform tests to determine fast
 atol = 1e-08 # absolute tolerance
 rtol = 1e-05  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 use_jacobian = false  # Use user-supplied Jacobian
 
 mxstep = 5000   # Number of internal steps between outputs
diff --git a/examples/elm-pb/data/BOUT.inp b/examples/elm-pb/data/BOUT.inp
index a37d69a43a..43b1b6f4b0 100644
--- a/examples/elm-pb/data/BOUT.inp
+++ b/examples/elm-pb/data/BOUT.inp
@@ -47,7 +47,7 @@ fft_measurement_flag = measure  # If using FFTW, perform tests to determine fast
 atol = 1e-08 # absolute tolerance
 rtol = 1e-05  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 
 mxstep = 5000   # Number of internal steps between outputs
 output_step = 1       # time between outputs
diff --git a/examples/elm-pb/relaxing/BOUT.inp b/examples/elm-pb/relaxing/BOUT.inp
index d9489611e6..cd911417b2 100644
--- a/examples/elm-pb/relaxing/BOUT.inp
+++ b/examples/elm-pb/relaxing/BOUT.inp
@@ -75,7 +75,7 @@ fft_measurement_flag = measure  # If using FFTW, perform tests to determine fast
 atol = 1.0e-8 # absolute tolerance
 rtol = 1.0e-5  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 
 mxstep = 50000   # Number of internal steps between outputs
 
@@ -296,4 +296,3 @@ bndry_core = neumann
 bndry_xin = none
 bndry_xout = none
 #bndry_target = neumann
-
diff --git a/examples/elm-pb/test/BOUT.inp b/examples/elm-pb/test/BOUT.inp
index 63f3d96f2b..76ccf14888 100644
--- a/examples/elm-pb/test/BOUT.inp
+++ b/examples/elm-pb/test/BOUT.inp
@@ -79,7 +79,7 @@ upwind = W3
 atol = 1e-08 # absolute tolerance
 rtol = 1e-05  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 use_jacobian = false  # Use user-supplied Jacobian
 
 mxstep = 5000   # Number of internal steps between outputs
diff --git a/examples/preconditioning/wave/data/BOUT.inp b/examples/preconditioning/wave/data/BOUT.inp
index b7a2e816c3..ca2f31c741 100644
--- a/examples/preconditioning/wave/data/BOUT.inp
+++ b/examples/preconditioning/wave/data/BOUT.inp
@@ -12,7 +12,7 @@ first = c2
 
 [solver]
 type = cvode          # Need CVODE or PETSc
-use_precon = true     # Use preconditioner
+cvode_precon_method = user  # Use user-supplied preconditioner
 use_jacobian = false  # Use user-supplied preconditioner?
 rightprec = false     # Use Right preconditioner (default left)
 diagnose = true       # Print additional diagnostics
diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 8a2c0b0101..097b62eeda 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -87,7 +87,10 @@ given in table :numref:`tab-solveropts`.
    +--------------------------+--------------------------------------------+-------------------------------------+
    | adaptive                 | Adapt timestep? (Y/N)                      | rk4, imexbdf2                       |
    +--------------------------+--------------------------------------------+-------------------------------------+
-   | use\_precon              | Use a preconditioner? (Y/N)                | pvode, cvode, ida, imexbdf2         |
+   | use\_precon              | Use a preconditioner? (Y/N)                | pvode, ida, imexbdf2                |
+   +--------------------------+--------------------------------------------+-------------------------------------+
+   | cvode\_precon\_method    | CVODE preconditioner: none, auto, user,   | cvode                               |
+   |                          | petsc, or bbd                              |                                     |
    +--------------------------+--------------------------------------------+-------------------------------------+
    | mudq, mldq               | BBD preconditioner settings                | pvode, cvode, ida                   |
    +--------------------------+--------------------------------------------+-------------------------------------+
@@ -1246,7 +1249,7 @@ then in the ``BOUT.inp`` settings file switch on the preconditioner
 
     [solver]
     type = cvode          # Need CVODE or PETSc
-    use_precon = true     # Use preconditioner
+    cvode_precon_method = user   # Use user-supplied preconditioner
     rightprec = false     # Use Right preconditioner (default left)
 
 Jacobian function
diff --git a/tests/MMS/elm-pb/data/BOUT.inp b/tests/MMS/elm-pb/data/BOUT.inp
index abfcf09d1d..6b939bef78 100644
--- a/tests/MMS/elm-pb/data/BOUT.inp
+++ b/tests/MMS/elm-pb/data/BOUT.inp
@@ -59,7 +59,7 @@ mms = true
 atol = 1e-12 # absolute tolerance
 rtol = 1e-08  # relative tolerance
 
-use_precon = false    # Use preconditioner: User-supplied or BBD
+cvode_precon_method = none  # Disable CVODE preconditioning
 use_jacobian = false  # Use user-supplied Jacobian
 
 mxstep = 5000   # Number of internal steps between outputs

From 35ed0c4393faf84c188d994200455f0954650518 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 25 Jun 2026 13:10:02 -0700
Subject: [PATCH 1498/1827] snes: Initialise dt

Fixes a bug due to uninitialised dt. The residuals calculation calls
the RHS function with time `simtime + dt`, so occasionally the time
would be large values (e.g. 1e200). This would crash `hermes-3` if
`upstream_density_feedback` was being used, because the integration of
the error would blow up.
---
 src/solver/impls/snes/snes.hxx | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 521b65cd6d..6cdaac082c 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -134,7 +134,7 @@ private:
   BoutReal output_residual_ratio; ///< Trigger an output when residual falls by this ratio
 
   BoutReal timestep;     ///< Internal timestep
-  BoutReal dt;           ///< Current timestep used in snes_function.
+  BoutReal dt{0.0};      ///< Current timestep used in snes_function.
   BoutReal dt_min_reset; ///< If dt falls below this, reset solve
   BoutReal max_timestep; ///< Maximum timestep
 
@@ -173,12 +173,12 @@ private:
   /// Calculate per-cell and global residuals
   /// given an input system state `x`
   PetscErrorCode updateResiduals(Vec x);
-  Field3D local_residual;         ///< Residual of Field3D quantities in each cell
-  Field2D local_residual_2d;      ///< Residual of Field2D quantities in each cell
-  BoutReal global_residual;       ///< Global residual measure
-  Field3D local_residual_prev;    ///< Previous Field3D local residuals
-  Field2D local_residual_2d_prev; ///< Previous Field2D local residuals
-  BoutReal global_residual_prev;  ///< Previous global residual
+  Field3D local_residual{0.0};         ///< Residual of Field3D quantities in each cell
+  Field2D local_residual_2d{0.0};      ///< Residual of Field2D quantities in each cell
+  BoutReal global_residual{0.0};       ///< Global residual measure
+  Field3D local_residual_prev{0.0};    ///< Previous Field3D local residuals
+  Field2D local_residual_2d_prev{0.0}; ///< Previous Field2D local residuals
+  BoutReal global_residual_prev{0.0};  ///< Previous global residual
 
   /// Initialize the Pseudo-Transient Continuation method
   PetscErrorCode initPseudoTimestepping();

From 26876b7d6bf786b6c47dcc9ebd06b009939db8fc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 26 Jun 2026 14:09:49 +0200
Subject: [PATCH 1499/1827] Add missing used header

---
 include/bout/derivs.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/derivs.hxx b/include/bout/derivs.hxx
index 92f094f550..14bc5c2824 100644
--- a/include/bout/derivs.hxx
+++ b/include/bout/derivs.hxx
@@ -35,6 +35,7 @@
 #include "bout/vector3d.hxx"
 
 #include "bout/bout_types.hxx"
+#include <type_traits>
 
 ////////// FIRST DERIVATIVES //////////
 

From d26d00e2cf21f9a421e97250ad542bcec932d9ae Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 26 Jun 2026 15:05:12 +0200
Subject: [PATCH 1500/1827] Only retain `iter` as public API

Also add some documentation. Thanks @ZedThree for the comment!
---
 include/bout/yboundary_regions.hxx           | 31 ++++++++++----------
 manual/sphinx/user_docs/boundary_options.rst |  2 +-
 2 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index b1aec6bc2e..f5fbf5ce1f 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -24,17 +24,12 @@
 
 class YBoundary {
 public:
+  /// Iterate over the boundary.
+  /// This function takes a lamda / templated function, that applies the boundary on the given point.
+  /// The function must take a `auto& point` as argument.
+  /// See also the documentation at ../../manual/sphinx/user_docs/boundary_options.rst
   template <class Func>
-  void iter_regions(const Func& func) {
-    for (auto& region : boundary_regions) {
-      func(*region);
-    }
-    for (auto& region : boundary_regions_par) {
-      func(*region);
-    }
-  }
-  template <class Func>
-  void iter_points(const Func& func) {
+  void iter(const Func& func) {
     iter_regions([&](auto& region) {
       for (auto& point : region) {
         func(point);
@@ -42,11 +37,6 @@ public:
     });
   }
 
-  template <class Func>
-  void iter(const Func& func) {
-    return iter_points(func);
-  }
-
   YBoundary(YBndryType type, Options* options_ptr, const Mesh& mesh) {
     bool lower_y = true;
     bool upper_y = true;
@@ -106,7 +96,7 @@ public:
     // Cache boundary regions
     _contains.emplace_back(&mesh, false);
     _contains.emplace_back(&mesh, false);
-    iter_points([&](const auto& point) {
+    iter([&](const auto& point) {
       if (point.dir() == 1) {
         _contains[1][point.ind()] = true;
       } else if (point.dir() == -1) {
@@ -138,6 +128,15 @@ public:
   }
 
 private:
+  template <class Func>
+  void iter_regions(const Func& func) {
+    for (auto& region : boundary_regions) {
+      func(*region);
+    }
+    for (auto& region : boundary_regions_par) {
+      func(*region);
+    }
+  }
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>> boundary_regions_par;
   std::vector<std::shared_ptr<NewBoundaryRegionY>> boundary_regions;
 
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 1aba0321d2..cecbf07b45 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -500,7 +500,7 @@ geometries, as flux coordinate independent (FCI) method::
 
       void rhs() {
         BoutReal totalFlux = 0;
-        mesh->getCoordinates()->getYBoundary()->iter_points([&](auto& point) {
+        mesh->getCoordinates()->getYBoundary()->iter([&](auto& point) {
           BoutReal flux = point.interpolate_sheath_o2(N) * point.interpolate_sheath_o2(V);
           totalFlux += flux;
         });

From d42c8ab8a01c0701c630c45a857480e1ad08f296 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 26 Jun 2026 15:42:47 +0200
Subject: [PATCH 1501/1827] Add dirichlet_o2 yboundary unit test

---
 tests/unit/CMakeLists.txt                  |  1 +
 tests/unit/include/bout/test_yboundary.cxx | 26 ++++++++++++++++++++++
 2 files changed, 27 insertions(+)
 create mode 100644 tests/unit/include/bout/test_yboundary.cxx

diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 4963aaf1f0..ae4435a6f9 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -83,6 +83,7 @@ set(serial_tests_source
     ./include/bout/test_stencil.cxx
     ./include/bout/test_template_combinations.cxx
     ./include/bout/test_traits.cxx
+    ./include/bout/test_yboundary.cxx
     ./include/test_cyclic_reduction.cxx
     ./include/test_derivs.cxx
     ./include/test_mask.cxx
diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
new file mode 100644
index 0000000000..6b732e5af5
--- /dev/null
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -0,0 +1,26 @@
+#include "gtest/gtest.h"
+
+#include "bout/boutexception.hxx"
+//#include "bout/boundary_region_iter.hxx"
+#include "bout/yboundary_regions.hxx"
+
+#include "fake_mesh_fixture.hxx"
+
+using YBTest = FakeMeshFixture;
+
+using bout::globals::mesh;
+
+TEST_F(YBTest, dirichlet_o2) {
+
+  Field3D test = 0.0;
+
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+
+  sheath.iter([&](auto& point) { point.dirichlet_o2(test, 1); });
+  for (int x = mesh->xstart; x <= mesh->xend; ++x) {
+    for (int z = mesh->zstart; z <= mesh->zend; ++z) {
+      EXPECT_DOUBLE_EQ(test(x, 0, z), 2.0);
+      EXPECT_DOUBLE_EQ(test(x, mesh->yend + 1, z), 2.0);
+    }
+  }
+}

From 71e6c823a99b15e0abb1f737c62c45587ff8e642 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 26 Jun 2026 16:06:15 +0200
Subject: [PATCH 1502/1827] Improve dirichlet_o2 unit test

Thanks @ZedThree for the feedback!
---
 tests/unit/include/bout/test_yboundary.cxx | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index 6b732e5af5..baeeb41abc 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -5,22 +5,15 @@
 #include "bout/yboundary_regions.hxx"
 
 #include "fake_mesh_fixture.hxx"
+#include "test_extras.hxx"
 
 using YBTest = FakeMeshFixture;
 
 using bout::globals::mesh;
 
 TEST_F(YBTest, dirichlet_o2) {
-
-  Field3D test = 0.0;
-
+  Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-
-  sheath.iter([&](auto& point) { point.dirichlet_o2(test, 1); });
-  for (int x = mesh->xstart; x <= mesh->xend; ++x) {
-    for (int z = mesh->zstart; z <= mesh->zend; ++z) {
-      EXPECT_DOUBLE_EQ(test(x, 0, z), 2.0);
-      EXPECT_DOUBLE_EQ(test(x, mesh->yend + 1, z), 2.0);
-    }
-  }
+  sheath.iter([&](auto& point) { point.dirichlet_o2(test, 2); });
+  EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }

From c47e72c76736c18e7499dc0166c6b21279438fcc Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 26 Jun 2026 16:07:30 +0200
Subject: [PATCH 1503/1827] Add interpolate_boundary_o2 test

---
 tests/unit/include/bout/test_yboundary.cxx | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index baeeb41abc..583b0e04ae 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -17,3 +17,18 @@ TEST_F(YBTest, dirichlet_o2) {
   sheath.iter([&](auto& point) { point.dirichlet_o2(test, 2); });
   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }
+
+// Not yet implemented for FA
+// TEST_F(YBTest, dirichlet_o3) {
+//   Field3D test = 1.0;
+//   YBoundary sheath(YBndryType::all, nullptr, *mesh);
+//   sheath.iter([&](auto& point) { point.dirichlet_o3(test, 2); });
+//   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
+// }
+
+TEST_F(YBTest, interpolate_boundary_o2) {
+  Field3D test = 1.0;
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter(
+      [&](auto& point) { EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0); });
+}

From 16b293562f2a8c0b2ac99a798f923b6c474ec049 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 26 Jun 2026 16:29:11 +0200
Subject: [PATCH 1504/1827] Rename to interpolate_boundary_o?

---
 include/bout/boundary_iterator.hxx           | 14 +++++------
 include/bout/parallel_boundary_region.hxx    | 26 +++++++++++---------
 manual/sphinx/user_docs/boundary_options.rst |  8 +++---
 3 files changed, 25 insertions(+), 23 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index bf03e15636..0c3c05b474 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -44,7 +44,7 @@ public:
 
   BoutReal extrapolate_grad_o2(const Field3D& f) const { return f[ind()] - yprev(f); }
 
-  BoutReal extrapolate_sheath_o2(const Field3D& f) const {
+  BoutReal extrapolate_boundary_o2(const Field3D& f) const {
     return (f[ind()] * 3 - yprev(f)) * 0.5;
   }
 
@@ -57,21 +57,21 @@ public:
     return (2 * f(0, ind())) - f(0, ind().yp(-_by).xp(-_bx));
   }
 
-  BoutReal interpolate_sheath_o2(const Field3D& f) const {
+  BoutReal interpolate_boundary_o2(const Field3D& f) const {
     return (f[ind()] + ynext(f)) * 0.5;
   }
 
-  BoutReal
-  interpolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+  BoutReal interpolate_boundary_o2(
+      const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return (f(0, ind()) + f(0, ind().yp(-_by).xp(-_bx))) * 0.5;
   }
 
-  BoutReal
-  extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+  BoutReal extrapolate_boundary_o2(
+      const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return 0.5 * (3 * f(0, ind()) - f(0, ind().yp(-_by).xp(-_bx)));
   }
 
-  BoutReal extrapolate_sheath_free(const Field3D& f, SheathLimitMode mode) const {
+  BoutReal extrapolate_boundary_free(const Field3D& f, SheathLimitMode mode) const {
     const BoutReal fac =
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
     const BoutReal val = ythis(f);
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 48668a5908..0de6ed19ec 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -143,32 +143,34 @@ public:
   void setValid(signed char valid) { bndry_position->valid = valid; }
 
   // extrapolate a given point to the boundary
-  BoutReal extrapolate_sheath_o1(const Field3D& f) const { return ythis(f); }
-  BoutReal extrapolate_sheath_o2(const Field3D& f) const {
+  BoutReal extrapolate_boundary_o1(const Field3D& f) const { return ythis(f); }
+  BoutReal extrapolate_boundary_o2(const Field3D& f) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
-      return extrapolate_sheath_o1(f);
+      return extrapolate_boundary_o1(f);
     }
     return ythis(f) * (1 + length(f.getLocation())) - yprev(f) * length(f.getLocation());
   }
-  BoutReal
-  extrapolate_sheath_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
+  BoutReal extrapolate_boundary_o1(
+      const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
     return ythis(f);
   }
-  BoutReal extrapolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
-                                 CELL_LOC loc = CELL_CENTRE) const {
+  BoutReal
+  extrapolate_boundary_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
+                          CELL_LOC loc = CELL_CENTRE) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
-      return extrapolate_sheath_o1(f);
+      return extrapolate_boundary_o1(f);
     }
     return ythis(f) * (1 + length(loc)) - yprev(f) * length(loc);
   }
 
-  BoutReal interpolate_sheath_o2(const Field3D& f) const {
+  BoutReal interpolate_boundary_o2(const Field3D& f) const {
     return ythis(f) * (1 - length(f.getLocation())) + ynext(f) * length(f.getLocation());
   }
-  BoutReal interpolate_sheath_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
-                                 CELL_LOC loc = CELL_CENTRE) const {
+  BoutReal
+  interpolate_boundary_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
+                          CELL_LOC loc = CELL_CENTRE) const {
     return ythis(f) * (1 - length(loc)) + ynext(f) * length(loc);
   }
 
@@ -298,7 +300,7 @@ public:
     }
   }
 
-  BoutReal extrapolate_sheath_free(const Field3D& f, SheathLimitMode mode) const {
+  BoutReal extrapolate_boundary_free(const Field3D& f, SheathLimitMode mode) const {
     const auto fac = valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
                                  : (mode == SheathLimitMode::linear_free ? 0 : 1);
     auto val = ythis(f);
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index cecbf07b45..9718be8c5d 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -501,7 +501,7 @@ geometries, as flux coordinate independent (FCI) method::
       void rhs() {
         BoutReal totalFlux = 0;
         mesh->getCoordinates()->getYBoundary()->iter([&](auto& point) {
-          BoutReal flux = point.interpolate_sheath_o2(N) * point.interpolate_sheath_o2(V);
+          BoutReal flux = point.interpolate_boundary_o2(N) * point.interpolate_boundary_o2(V);
           totalFlux += flux;
         });
       }
@@ -535,11 +535,11 @@ Here is a short summary of some members of ``point``, where ``f`` is a :
    * - ``point.yprev(f)``
      - Returns the value at the second to last point in the domain, if it is
        valid. NB: this point may not be valid.
-   * - ``point.interpolate_sheath_o2(f)``
+   * - ``point.interpolate_boundary_o2(f)``
      - Returns the value at the boundary, assuming the bounday value has been set
-   * - ``point.extrapolate_sheath_o1(f)``
+   * - ``point.extrapolate_boundary_o1(f)``
      - Returns the value at the boundary, extrapolating from the bulk, first order
-   * - ``point.extrapolate_sheath_o2(f)``
+   * - ``point.extrapolate_boundary_o2(f)``
      - Returns the value at the boundary, extrapolating from the bulk, second order
    * - ``point.extrapolate_next_o{1,2}(f)``
      - Extrapolate into the boundary from the bulk, first or second order

From 3303846ade388d1cabfaa2817beafaf1f0e90d9e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 26 Jun 2026 16:30:59 +0200
Subject: [PATCH 1505/1827] Rename to BoundaryLimitMode

---
 include/bout/boundary_iterator.hxx        |  8 ++++----
 include/bout/parallel_boundary_region.hxx | 24 +++++++++++------------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 0c3c05b474..85917f0295 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -71,19 +71,19 @@ public:
     return 0.5 * (3 * f(0, ind()) - f(0, ind().yp(-_by).xp(-_bx)));
   }
 
-  BoutReal extrapolate_boundary_free(const Field3D& f, SheathLimitMode mode) const {
+  BoutReal extrapolate_boundary_free(const Field3D& f, BoundaryLimitMode mode) const {
     const BoutReal fac =
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
     const BoutReal val = ythis(f);
-    const BoutReal next = mode == SheathLimitMode::linear_free ? val + fac : val * fac;
+    const BoutReal next = mode == BoundaryLimitMode::linear_free ? val + fac : val * fac;
     return 0.5 * (val + next);
   }
 
-  void set_free(Field3D& f, SheathLimitMode mode) const {
+  void set_free(Field3D& f, BoundaryLimitMode mode) const {
     const BoutReal fac =
         bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
     BoutReal val = ythis(f);
-    if (mode == SheathLimitMode::linear_free) {
+    if (mode == BoundaryLimitMode::linear_free) {
       for (int i = 1; i <= localmesh->ystart; ++i) {
         val += fac;
         f[ind().yp(_by * i).xp(_bx * i)] = val;
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 0de6ed19ec..3e3b1238a0 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -26,7 +26,7 @@
  *
  */
 
-BOUT_ENUM_CLASS(SheathLimitMode, limit_free, exponential_free, linear_free);
+BOUT_ENUM_CLASS(BoundaryLimitMode, limit_free, exponential_free, linear_free);
 
 namespace bout {
 namespace parallel_boundary_region {
@@ -73,8 +73,8 @@ using IndicesIterConst = IndicesVec::const_iterator;
 ///         ^ boundary
 ///
 /// exp( 2*log(fc) - log(fm) )
-inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, SheathLimitMode mode) {
-  if ((fm < fc) && (mode == SheathLimitMode::limit_free)) {
+inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, BoundaryLimitMode mode) {
+  if ((fm < fc) && (mode == BoundaryLimitMode::limit_free)) {
     return fc; // Neumann rather than increasing into boundary
   }
   if (fm < 1e-10) {
@@ -83,11 +83,11 @@ inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, SheathLimitMode mode) {
 
   BoutReal fp = 0;
   switch (mode) {
-  case SheathLimitMode::limit_free:
-  case SheathLimitMode::exponential_free:
+  case BoundaryLimitMode::limit_free:
+  case BoundaryLimitMode::exponential_free:
     fp = SQ(fc) / fm; // Exponential
     break;
-  case SheathLimitMode::linear_free:
+  case BoundaryLimitMode::linear_free:
     fp = (2.0 * fc) - fm; // Linear
     break;
   }
@@ -300,19 +300,19 @@ public:
     }
   }
 
-  BoutReal extrapolate_boundary_free(const Field3D& f, SheathLimitMode mode) const {
+  BoutReal extrapolate_boundary_free(const Field3D& f, BoundaryLimitMode mode) const {
     const auto fac = valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
-                                 : (mode == SheathLimitMode::linear_free ? 0 : 1);
+                                 : (mode == BoundaryLimitMode::linear_free ? 0 : 1);
     auto val = ythis(f);
-    BoutReal next = mode == SheathLimitMode::linear_free ? val + fac : val * fac;
+    BoutReal next = mode == BoundaryLimitMode::linear_free ? val + fac : val * fac;
     return val * length(f.getLocation()) + next * (1 - length(f.getLocation()));
   }
 
-  void set_free(Field3D& f, SheathLimitMode mode) const {
+  void set_free(Field3D& f, BoundaryLimitMode mode) const {
     const auto fac = valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
-                                 : (mode == SheathLimitMode::linear_free ? 0 : 1);
+                                 : (mode == BoundaryLimitMode::linear_free ? 0 : 1);
     auto val = ythis(f);
-    if (mode == SheathLimitMode::linear_free) {
+    if (mode == BoundaryLimitMode::linear_free) {
       ITER() {
         val += fac;
         getAt(f, i) = val;

From b0f322fc92b9f9e0c29491ef9a4586bb7a4d3408 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 26 Jun 2026 19:32:36 +0000
Subject: [PATCH 1506/1827] Bump actions/cache from 5 to 6

Bumps [actions/cache](https://github.com/actions/cache) from 5 to 6.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](https://github.com/actions/cache/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 76c627b9b4..d9cbc07574 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -168,14 +168,14 @@ jobs:
           python -m pip install -r requirements.txt
 
       - name: Cache Zenodo test data
-        uses: actions/cache@v5
+        uses: actions/cache@v6
         with:
           path: build/tests/integrated/test-fci-mpi/grid.fci.nc
           # If we update the test, invalidate the cache
           key: zenodo-data-${{ hashFiles('tests/integrated/test-fci-mpi/CMakeLists.txt') }}
 
       - name: Cache SUNDIALS build
-        uses: actions/cache@v5
+        uses: actions/cache@v6
         with:
           path: /home/runner/local
           key: bout-sundials-${{ matrix.config.os }}${{ matrix.config.build_petsc }}
@@ -205,7 +205,7 @@ jobs:
           submodules: true
 
       - name: Cache Zenodo test data
-        uses: actions/cache@v5
+        uses: actions/cache@v6
         with:
           path: build/tests/integrated/test-fci-mpi/grid.fci.nc
           # If we update the test, invalidate the cache

From 3dfefc99930db321e2242a63bd49935fcf0bd939 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 26 Jun 2026 19:32:36 +0000
Subject: [PATCH 1507/1827] Bump externalpackages/googletest from `0b1e895` to
 `8b53336`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `0b1e895` to `8b53336`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/0b1e895ba4226c2fda5ee0178c9b5b1195a741aa...8b53336594cc52213c6c2c7a0b29194fa896d039)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: 8b53336594cc52213c6c2c7a0b29194fa896d039
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 0b1e895ba4..8b53336594 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 0b1e895ba4226c2fda5ee0178c9b5b1195a741aa
+Subproject commit 8b53336594cc52213c6c2c7a0b29194fa896d039

From bf5f01df35c6c57b4af507d1b22b8e0a9b7a5da6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 09:07:12 +0200
Subject: [PATCH 1508/1827] Remove unused headers

---
 include/bout/fv_ops.hxx                    | 3 ---
 tests/MMS/spatial/finite-volume/fv_mms.cxx | 1 -
 2 files changed, 4 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index ab791efb41..b2b0e49120 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -7,7 +7,6 @@
 
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
-#include "bout/boutexception.hxx"
 #include "bout/build_defines.hxx"
 #include "bout/coordinates.hxx"
 #include "bout/field.hxx"
@@ -19,8 +18,6 @@
 #include "bout/utils.hxx"
 #include "bout/vector2d.hxx"
 
-#include <cmath>
-
 namespace FV {
 /*!
  * Div ( a Grad_perp(f) ) -- ∇⊥ ( a ⋅ ∇⊥ f) -- Vorticity
diff --git a/tests/MMS/spatial/finite-volume/fv_mms.cxx b/tests/MMS/spatial/finite-volume/fv_mms.cxx
index 19f3f14610..1de6052e89 100644
--- a/tests/MMS/spatial/finite-volume/fv_mms.cxx
+++ b/tests/MMS/spatial/finite-volume/fv_mms.cxx
@@ -7,7 +7,6 @@
 #include "bout/globals.hxx"
 #include "bout/options.hxx"
 #include "bout/options_io.hxx"
-#include "bout/utils.hxx"
 
 #include <fmt/format.h>
 

From 3e1c2cbff404cc75e50d454c89868dc4715ceb35 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 09:13:31 +0200
Subject: [PATCH 1509/1827] Fix formatting

---
 include/bout/difops.hxx                       | 28 +++++------
 include/bout/invert_laplace.hxx               |  4 +-
 include/bout/optionsreader.hxx                |  4 +-
 include/bout/output.hxx                       |  8 ++--
 include/bout/physicsmodel.hxx                 | 47 +++++++++----------
 manual/sphinx/user_docs/bout_options.rst      | 24 +++++-----
 manual/sphinx/user_docs/installing.rst        |  2 +-
 manual/sphinx/user_docs/variable_init.rst     | 26 +++++-----
 .../laplace/impls/naulin/naulin_laplace.hxx   |  4 +-
 9 files changed, 72 insertions(+), 75 deletions(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index dba81ed043..f16f5acc93 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -1,11 +1,11 @@
 /*!******************************************************************************
  * \file difops.hxx
- * 
+ *
  * Differential operators
  *
  * Changelog:
  *
- * 2009-01 Ben Dudson <bd512@york.ac.uk> 
+ * 2009-01 Ben Dudson <bd512@york.ac.uk>
  *    * Added two optional parameters which can be put in any order
  *      These determine the method to use (DIFF_METHOD)
  *      and CELL_LOC location of the result.
@@ -15,7 +15,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -30,7 +30,7 @@
  *
  * You should have received a copy of the GNU Lesser General Public License
  * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
- * 
+ *
  *******************************************************************************/
 
 #ifndef BOUT_DIFOPS_H
@@ -81,7 +81,7 @@ Field3D Grad_parP(const Field3D& apar, const Field3D& f);
  * \f[
  *    v\mathbf{b}_0 \cdot \nabla f
  * \f]
- * 
+ *
  *
  * @param[in] v  The velocity in y direction
  * @param[in] f  The scalar field to be differentiated
@@ -175,7 +175,7 @@ inline Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc, DIFF_METHOD method)
 
 /*!
  * Parallel divergence of diffusive flux, K*Grad_par
- * 
+ *
  * \f[
  *    \nabla \cdot ( \mathbf{b}_0 kY (\mathbf{b}_0 \cdot \nabla) f )
  * \f]
@@ -199,8 +199,8 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f,
  * Perpendicular Laplacian operator
  *
  * This version only includes terms in X and Z, dropping
- * derivatives in Y. This is the inverse operation to 
- * the Laplacian inversion class. 
+ * derivatives in Y. This is the inverse operation to
+ * the Laplacian inversion class.
  *
  * For the full perpendicular Laplacian, use Laplace_perp
  */
@@ -212,7 +212,7 @@ FieldPerp Delp2(const FieldPerp& f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT
 /*!
  * Perpendicular Laplacian, keeping y derivatives
  *
- * 
+ *
  */
 Coordinates::FieldMetric
 Laplace_perp(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
@@ -246,18 +246,18 @@ Field2D Laplace_perpXY(const Field2D& A, const Field2D& f);
 
 /*!
  * Terms of form b0 x Grad(phi) dot Grad(A)
- * 
+ *
  */
 Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
                                           CELL_LOC outloc = CELL_DEFAULT);
 
 /*!
- * Terms of form 
+ * Terms of form
  *
  * \f[
  *   \mathbf{b}_0 \times \nabla \phi \cdot \nabla A
  * \f]
- * 
+ *
  * @param[in] phi The scalar potential
  * @param[in] A   The field being advected
  * @param[in] outloc  The cell location where the result is defined. By default the same as A.
@@ -291,13 +291,13 @@ constexpr BRACKET_METHOD BRACKET_CTU = BRACKET_METHOD::ctu;
  * \f[
  *   [f, g] = (1/B) \mathbf{b}_0 \times \nabla f  \cdot \nabla g
  * \f]
- * 
+ *
  * @param[in] f  The potential
  * @param[in] g  The field being advected
  * @param[in] method   The method to use
  * @param[in] outloc   The cell location where the result is defined. Default is the same as g
  * @param[in] solver   Pointer to the time integration solver
- * 
+ *
  */
 Coordinates::FieldMetric bracket(const Field2D& f, const Field2D& g,
                                  BRACKET_METHOD method = BRACKET_STD,
diff --git a/include/bout/invert_laplace.hxx b/include/bout/invert_laplace.hxx
index 846c05557d..76212dcd76 100644
--- a/include/bout/invert_laplace.hxx
+++ b/include/bout/invert_laplace.hxx
@@ -7,14 +7,14 @@
  * \f[
  *   d \nabla^2_\perp x + (1/c)\nabla_\perp c\cdot\nabla_\perp x + a x = b
  * \f]
- * 
+ *
  * Where a, c and d are functions of x and y only (not z)
  */
 /**************************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
diff --git a/include/bout/optionsreader.hxx b/include/bout/optionsreader.hxx
index 20bd0f680b..ca9778b3c4 100644
--- a/include/bout/optionsreader.hxx
+++ b/include/bout/optionsreader.hxx
@@ -5,13 +5,13 @@
 * different file formats
 *
 * Handles the command-line parsing
-* 
+*
 */
 /*************************************************************************
 * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
 *
 * Contact: Ben Dudson, bd512@york.ac.uk
-* 
+*
 * This file is part of BOUT++.
 *
 * BOUT++ is free software: you can redistribute it and/or modify
diff --git a/include/bout/output.hxx b/include/bout/output.hxx
index a0bb92cef7..1399f2cbd7 100644
--- a/include/bout/output.hxx
+++ b/include/bout/output.hxx
@@ -165,13 +165,13 @@ class ConditionalOutput : public Output {
 public:
   /// @param[in] base    The Output object which will be written to if enabled
   /// @param[in] enabled Should this be enabled by default?
-  ConditionalOutput(Output* base, bool enabled = true) : base(base), enabled(enabled){};
+  ConditionalOutput(Output* base, bool enabled = true) : base(base), enabled(enabled) {};
 
   /// Constuctor taking ConditionalOutput. This allows several layers of conditions
   ///
   /// @param[in] base    A ConditionalOutput which will be written to if enabled
   ///
-  ConditionalOutput(ConditionalOutput* base) : base(base), enabled(base->enabled){};
+  ConditionalOutput(ConditionalOutput* base) : base(base), enabled(base->enabled) {};
 
   /// If enabled, writes a string using fmt formatting
   /// by calling base->write
@@ -236,7 +236,7 @@ private:
 ///    output_debug << "debug message";
 /// compile but have no effect if BOUT_USE_OUTPUT_DEBUG is false
 template <typename T>
-DummyOutput& operator<<(DummyOutput& out, T const& UNUSED(t)) {
+DummyOutput& operator<<(DummyOutput& out, const T& UNUSED(t)) {
   return out;
 }
 
@@ -260,7 +260,7 @@ inline ConditionalOutput& operator<<(ConditionalOutput& out, stream_manipulator
 }
 
 template <typename T>
-ConditionalOutput& operator<<(ConditionalOutput& out, T const& t) {
+ConditionalOutput& operator<<(ConditionalOutput& out, const T& t) {
   if (out.isEnabled()) {
     *out.getBase() << t;
   }
diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index 8de726930e..f9160f5709 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -1,20 +1,20 @@
 /*!************************************************************************
  * \file physicsmodel.hxx
- * 
+ *
  * @brief Base class for Physics Models
- * 
- * 
+ *
+ *
  *
  * Changelog:
- * 
+ *
  * 2013-08 Ben Dudson <benjamin.dudson@york.ac.uk>
  *    * Initial version
- * 
+ *
  **************************************************************************
  * Copyright 2013 B.D.Dudson
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -167,9 +167,9 @@ public:
    *
    * Output
    * ------
-   * 
+   *
    * The time derivatives will be put in the ddt() variables
-   * 
+   *
    * Returns a flag: 0 indicates success, non-zero an error flag
    */
   int runRHS(BoutReal time, bool linear = false);
@@ -203,7 +203,7 @@ public:
   bool hasPrecon();
 
   /*!
-   * Run the preconditioner. The system state should be in the 
+   * Run the preconditioner. The system state should be in the
    * evolving variables, and the vector to be solved in the ddt() variables.
    * The result will be put in the ddt() variables.
    *
@@ -219,7 +219,7 @@ public:
 
   /*!
    * Run the Jacobian-vector multiplication function
-   * 
+   *
    * Note: this is usually only called by the Solver
    */
   int runJacobian(BoutReal t);
@@ -241,10 +241,10 @@ protected:
   // The init and rhs functions are implemented by user code to specify problem
   /*!
    * @brief This function is called once by the solver at the start of a simulation.
-   * 
+   *
    * A valid PhysicsModel must implement this function
-   * 
-   * Variables should be read from the inputs, and the variables to 
+   *
+   * Variables should be read from the inputs, and the variables to
    * be evolved should be specified.
    */
   virtual int init(bool restarting) = 0;
@@ -258,7 +258,7 @@ protected:
   /*!
    * @brief This function is called by the time integration solver
    * at least once per time step
-   * 
+   *
    * Variables being evolved will be set by the solver
    * before the call, and this function must calculate
    * and set the time-derivatives.
@@ -278,10 +278,10 @@ protected:
   /// Add additional variables other than the evolving variables to the restart files
   virtual void restartVars(Options& options);
 
-  /* 
+  /*
      If split operator is set to true, then
      convective() and diffusive() are called instead of rhs()
-     
+
      For implicit-explicit schemes, convective() will typically
      be treated explicitly, whilst diffusive() will be treated implicitly.
      For unsplit methods, both convective and diffusive will be called
@@ -334,7 +334,7 @@ protected:
    *
    * @param[in] var  The variable to evolve
    * @param[in] name The name to use for variable initialisation and output
-   * 
+   *
    * Note that the variable must not be destroyed (e.g. go out of scope)
    * after this call, since a pointer to \p var is stored in the solver.
    *
@@ -358,11 +358,11 @@ protected:
    * Specify a constrained variable \p var, which will be
    * adjusted to make \p F_var equal to zero.
    * If the solver does not support constraints then this will throw an exception
-   * 
+   *
    * @param[in] var  The variable the solver should modify
    * @param[in] F_var  The control variable, which the user will set
    * @param[in] name   The name to use for initialisation and output
-   * 
+   *
    */
   bool bout_constrain(Field3D& var, Field3D& F_var, const char* name);
 
@@ -490,8 +490,7 @@ private:
 
 /// Add fields to the solver.
 /// This should accept up to ten arguments
-#define SOLVE_FOR(...) \
-  { MACRO_FOR_EACH(SOLVE_FOR1, __VA_ARGS__) }
+#define SOLVE_FOR(...) {MACRO_FOR_EACH(SOLVE_FOR1, __VA_ARGS__)}
 
 /// Write this variable once to the grid file
 #define SAVE_ONCE1(var) dump.addOnce(var, #var);
@@ -531,8 +530,7 @@ private:
     dump.addOnce(var6, #var6);                         \
   }
 
-#define SAVE_ONCE(...) \
-  { MACRO_FOR_EACH(SAVE_ONCE1, __VA_ARGS__) }
+#define SAVE_ONCE(...) {MACRO_FOR_EACH(SAVE_ONCE1, __VA_ARGS__)}
 
 /// Write this variable every timestep
 #define SAVE_REPEAT1(var) dump.addRepeat(var, #var);
@@ -572,7 +570,6 @@ private:
     dump.addRepeat(var6, #var6);                         \
   }
 
-#define SAVE_REPEAT(...) \
-  { MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__) }
+#define SAVE_REPEAT(...) {MACRO_FOR_EACH(SAVE_REPEAT1, __VA_ARGS__)}
 
 #endif // BOUT_PHYSICS_MODEL_H
diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst
index 45f82ea61d..bc0aee552e 100644
--- a/manual/sphinx/user_docs/bout_options.rst
+++ b/manual/sphinx/user_docs/bout_options.rst
@@ -100,7 +100,7 @@ A number of functions are defined, listed in table
 is that if a number comes before a symbol or an opening bracket (``(``)
 then a multiplication is assumed: ``2x+3y^2`` is the same as
 ``2*x + 3*y^2``, which with the usual precedence rules is the same as
-``(2*x) + (3*(y^2))``. 
+``(2*x) + (3*(y^2))``.
 
 Expressions can span more than one line, which can make long expressions
 easier to read:
@@ -176,7 +176,7 @@ Special symbols in Option names
 If option names start with numbers or ``.`` or contain symbols such as
 ``+`` and ``-`` then these symbols need to be escaped in expressions
 or they will be treated as arithmetic operators like addition or
-subtraction. To escape a single character 
+subtraction. To escape a single character
 ``\`` (backslash) can be used, for example ``plasma\-density * 10``
 would read the option ``plasma-density`` and multiply it
 by 10 e.g
@@ -561,7 +561,7 @@ in table :numref:`tab-outputopts`.
 
 .. _tab-outputopts:
 .. table:: Output file options
-	   
+
    +----------------------+-----------------------------------------+----------------+
    | Option               | Description                             | Default value  |
    +======================+=========================================+================+
@@ -597,7 +597,7 @@ Implementation
 To control the behaviour of BOUT++ a set of options is used, with
 options organised into sections which can be nested. To represent this
 tree structure there is the `Options` class defined in
-``bout++/include/options.hxx``. 
+``bout++/include/options.hxx``.
 
 To access the options, there is a static function (singleton)::
 
@@ -610,7 +610,7 @@ assigning, treating options as a map or dictionary::
 
     options["nout"] = 10;    // Integer
     options["restart"] = true;  // bool
-    
+
 Internally these values are stored in a variant type, which supports commonly
 used types including strings, integers, real numbers and fields (2D and
 3D). Since strings can be stored, any type can be assigned, so long as it can be
@@ -783,7 +783,7 @@ currently supported, but use of the newer interface above is
 encouraged.
 
 To access the options, there is a static function (singleton)::
-  
+
     Options *options = Options::getRoot();
 
 which gives the top-level (root) options class. Setting options is done
@@ -909,10 +909,10 @@ Note that by default reading as ``Field2D`` or ``Field3D`` will use the global
 pass a field which the result should be similar to::
 
   Field3D example = ... // Some existing field
-  
+
   Field3D f3d = fields_in["f3d"].as<Field3D>(example);
 
-Meta data like ``Mesh`` pointer, will be taken from ``example``. 
+Meta data like ``Mesh`` pointer, will be taken from ``example``.
 
 Currently converting from ``Matrix`` or ``Tensor`` types only works if
 the data in the ``Matrix`` or ``Tensor`` is the same size as the
@@ -938,17 +938,17 @@ automatically set the ``"time_dimension"`` attribute::
   data["scalar"] = 1.0;
   // You can set the attribute manually like so:
   data["scalar"].attributes["time_dimension"] = "t";
-  
+
   // Or use `assignRepeat` to do it automatically:
   data["field"].assignRepeat(Field3D(2.0));
-  
+
   bout::OptionsIO::create("time.nc")->write(data);
-  
+
   // Update time-dependent values. This can be done without `force` if the time_dimension
   // attribute is set
   data["scalar"] = 2.0;
   data["field"] = Field3D(3.0);
-  
+
   // Append data to file
   bout::OptionsIO::create({{"file", "time.nc"}, {"append", true}})->write(data);
 
diff --git a/manual/sphinx/user_docs/installing.rst b/manual/sphinx/user_docs/installing.rst
index 2abbf29fd6..ead172a442 100644
--- a/manual/sphinx/user_docs/installing.rst
+++ b/manual/sphinx/user_docs/installing.rst
@@ -501,7 +501,7 @@ or conda::
 
     $ conda install numpy scipy matplotlib sympy netcdf4 future importlib-metadata
 
-They may also be available from your Linux system's package manager. 
+They may also be available from your Linux system's package manager.
 
 For example on Fedora::
 
diff --git a/manual/sphinx/user_docs/variable_init.rst b/manual/sphinx/user_docs/variable_init.rst
index 5079e237d9..9009ece180 100644
--- a/manual/sphinx/user_docs/variable_init.rst
+++ b/manual/sphinx/user_docs/variable_init.rst
@@ -174,7 +174,7 @@ expressions.
 .. _tab-initexprfunc:
 .. table:: Initialisation expression functions
 
-   +------------------------------------------+------------------------------------------------------+ 
+   +------------------------------------------+------------------------------------------------------+
    |  Name                                    | Description                                          |
    +==========================================+======================================================+
    | ``abs(x)``                               | Absolute value :math:`|x|`                           |
@@ -240,8 +240,8 @@ In addition there are some special functions which enable control flow
 
 .. _tab-exprcontrol:
 .. table:: Control flow and special functions
-           
-   +------------------------------------------+------------------------------------------------------+ 
+
+   +------------------------------------------+------------------------------------------------------+
    |  Name                                    | Description                                          |
    +==========================================+======================================================+
    | ``where(expr, gt0, lt0)``                | If the first ``expr`` evaluates to a value greater   |
@@ -260,8 +260,8 @@ In addition there are some special functions which enable control flow
    |                                          | is evaluated before the ``expr`` expression.         |
    |                                          | Example: ``[n=2]( {n}^{n} )`` is ``2^2``.            |
    +------------------------------------------+------------------------------------------------------+
-   
-   
+
+
 For field-aligned tokamak simulations, the Y direction is along the
 field and in the core this will have a discontinuity at the twist-shift
 location where field-lines are matched onto each other. To handle this,
@@ -331,13 +331,13 @@ to ``generate`` in the ``Context`` object.
 ::
 
   Field3D shear = ...; // Value calculated in BOUT++
-  
+
   FieldFactory factory(mesh);
   auto gen = factory->parse("model:viscosity");
 
   Field3D viscosity;
   viscosity.allocate();
-  
+
   BOUT_FOR(i, viscosity.region("RGN_ALL")) {
     viscosity[i] = gen->generate(bout::generator::Context(i, CELL_CENTRE, mesh, 0.0)
                                    .set("shear", shear[i]));
@@ -368,7 +368,7 @@ call functions, as in the above example ``viscosity`` is a function of
 which uses ``{arg}`` as the input value. We could then call this function:
 
 .. code-block:: cfg
-                
+
     result = [arg = x*2](mycosh)
 
 
@@ -383,7 +383,7 @@ occur. Recursive functions can however be enabled by setting
 ``input:max_recursion_depth != 0`` e.g.:
 
 .. code-block:: cfg
-                
+
     [input]
     max_recursion_depth = 10  # 0 = none, -1 = unlimited
 
@@ -410,7 +410,7 @@ recursion is used.
 Note: Use of this facility in general is not encouraged, as it can
 easily lead to very inefficient and hard to understand code. It is
 here because occasionally it might be necessary, and because making
-the input language Turing complete was irresistible. 
+the input language Turing complete was irresistible.
 
 Initalising variables with the ``FieldFactory`` class
 -----------------------------------------------------
@@ -459,7 +459,7 @@ containing values which can be used in expressions, in particular `x`,
 `Context` object, allowing data from BOUT++ to be used in expressions.
 There are also ways to manipulate `Context` objects for more complex
 expressions and functions, see below for details.
-    
+
 All classes inheriting from `FieldGenerator` must implement
 a `FieldGenerator::generate` function, which returns the
 value at the given ``(x,y,z,t)`` position. Classes should also implement
@@ -587,9 +587,9 @@ the same value. This can be one of:
 -  -2 for a symbol (e.g. “sinh”, “x” or “pi”). This includes anything
    which starts with a letter, and contains only letters, numbers, and
    underscores. The string is stored in the variable ``string curident``
-  
+
 -  -3 for a ``Context`` parameter which appeared surrounded by braces ``{}``.
-   
+
 -  0 to mean end of input
 
 -  The character if none of the above. Since letters and numbers are
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.hxx b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
index 8aa4f8b23f..edcc562c99 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.hxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
@@ -124,7 +124,7 @@
  * Copyright 2018 B.D.Dudson, M. Loiten, J. Omotani
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -167,7 +167,7 @@ const RegisterLaplace<LaplaceNaulin> registerlaplacenaulin(LAPLACE_NAULIN);
 
 /// Solves the 2D Laplacian equation
 /*!
- * 
+ *
  */
 class LaplaceNaulin : public Laplacian {
 public:

From 71b4525b0a32c20412f2b7bca4bfe9c4ebf4213e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 09:14:31 +0200
Subject: [PATCH 1510/1827] Remove tabs from rst

---
 manual/sphinx/user_docs/bout_options.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst
index bc0aee552e..eb71de26e3 100644
--- a/manual/sphinx/user_docs/bout_options.rst
+++ b/manual/sphinx/user_docs/bout_options.rst
@@ -247,13 +247,13 @@ combinations of the format codes::
 
   // [section1]
   // value1 = 42
-  // value2 = hello		# doc: This says hello
+  // value2 = hello            # doc: This says hello
   //
   // [section2]
   // value5 = 3
   //
   // [section2:subsection1]
-  // value3 = true		# type: bool, doc: This is a bool
+  // value3 = true             # type: bool, doc: This is a bool
   // value4 = 3.2
 
   // Only keys, inline sections, and 'doc', 'type', and 'source' attributes.
@@ -261,9 +261,9 @@ combinations of the format codes::
   output.write("{:kids}", options);
 
   // section1:value1
-  // section1:value2		# doc: This says hello
+  // section1:value2           # doc: This says hello
   // section2:value5
-  // section2:subsection1:value3		# type: bool, doc: This is a bool, source: a test
+  // section2:subsection1:value3       # type: bool, doc: This is a bool, source: a test
   // section2:subsection1:value4
 
 

From 47a4c13c3ede5de94574093e13ec1b80fa3759e2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 09:15:44 +0200
Subject: [PATCH 1511/1827] Fir formatting and whitespace

---
 include/bout/dcomplex.hxx                     |  6 +--
 include/bout/gyro_average.hxx                 |  6 +--
 include/bout/openmpwrap.hxx                   |  2 +-
 manual/sphinx/developer_docs/code_layout.rst  |  1 -
 .../developer_docs/performance_profiling.rst  | 38 +++++++++----------
 manual/sphinx/user_docs/laplacian.rst         |  2 +-
 manual/sphinx/user_docs/physics_models.rst    |  6 +--
 manual/sphinx/user_docs/running_bout.rst      |  1 -
 src/invert/lapack_routines.cxx                |  8 ++--
 .../laplace/impls/cyclic/cyclic_laplace.hxx   |  4 +-
 10 files changed, 36 insertions(+), 38 deletions(-)

diff --git a/include/bout/dcomplex.hxx b/include/bout/dcomplex.hxx
index 556f1e72bb..2d3e0c5ca7 100644
--- a/include/bout/dcomplex.hxx
+++ b/include/bout/dcomplex.hxx
@@ -7,12 +7,12 @@
  *
  * 2015-03-09 Ben Dudson <bd512@york.ac.uk>
  *    o Removed, redefined in terms of std::complex
- * 
+ *
  **************************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -27,7 +27,7 @@
  *
  * You should have received a copy of the GNU Lesser General Public License
  * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
- * 
+ *
  */
 #ifndef BOUT_DCOMPLEX_H
 #define BOUT_DCOMPLEX_H
diff --git a/include/bout/gyro_average.hxx b/include/bout/gyro_average.hxx
index 665024797d..9ce68871cc 100644
--- a/include/bout/gyro_average.hxx
+++ b/include/bout/gyro_average.hxx
@@ -1,17 +1,17 @@
 /*!************************************************************
  * \file gyro_average.hxx
- * 
+ *
  * Gyro-averaging operators
  *
  *
  * 2010-09-03 Ben Dudson <bd512@york.ac.uk>
  *    * Initial version, simple averaging operator
- * 
+ *
  **************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
diff --git a/include/bout/openmpwrap.hxx b/include/bout/openmpwrap.hxx
index 00d0b1e5b7..19cc181787 100644
--- a/include/bout/openmpwrap.hxx
+++ b/include/bout/openmpwrap.hxx
@@ -4,7 +4,7 @@
  * Copyright 2017
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
diff --git a/manual/sphinx/developer_docs/code_layout.rst b/manual/sphinx/developer_docs/code_layout.rst
index 833b763ce9..3c02602b44 100644
--- a/manual/sphinx/developer_docs/code_layout.rst
+++ b/manual/sphinx/developer_docs/code_layout.rst
@@ -131,4 +131,3 @@ The layout of the ``src/`` directory is as follows:
   - General purpose utilities used throughout the library, such as
     `BoutException`, wrappers for C libraries like ``PETSc`` and
     ``HYPRE``, screen and file input and output.
-
diff --git a/manual/sphinx/developer_docs/performance_profiling.rst b/manual/sphinx/developer_docs/performance_profiling.rst
index de14d695da..d171f403a4 100644
--- a/manual/sphinx/developer_docs/performance_profiling.rst
+++ b/manual/sphinx/developer_docs/performance_profiling.rst
@@ -7,13 +7,13 @@ Performance profiling
 =====================
 
 Analyzing code behaviour is vital for getting the best performance from BOUT++.
-This is done by profiling the code, that is, building and running the code 
+This is done by profiling the code, that is, building and running the code
 using tools that report the amount of time each processor spends in functions,
 on communications, etc.
 
-This section describes how to compile and run BOUT++ using the 
+This section describes how to compile and run BOUT++ using the
 `Scorep <http://www.vi-hps.org/projects/score-p/>`_/`Scalasca <http://www.scalasca.org/>`_
-and 
+and
 `Extrae <https://tools.bsc.es/extrae/>`_/`Paraver <https://tools.bsc.es/paraver/>`_
 tool chains.
 Both are suitable for analyzing code parallelized with MPI and/or OpenMP.
@@ -29,10 +29,10 @@ Instrumentation
 
 Scorep automatically reports the time spent in MPI communications and OpenMP
 loops. However, to obtain information on the time spent in specific functions,
-it is necessary to instrument the source code. The macros to do this are 
+it is necessary to instrument the source code. The macros to do this are
 provided in ``scorepwrapper.hxx``.
 
-To include a function in Scorep's timing, include the scorep wrapper in the 
+To include a function in Scorep's timing, include the scorep wrapper in the
 source code
 
 .. code-block:: c++
@@ -72,8 +72,8 @@ inside ``applyBoundary`` with the name "display name". Any number of Scorep user
 can be used in a function; user regions can also be nested.
 
 **Caution** Instrumenting a function makes it execute more slowly. This can
-result in misleading profiling information, particularly if 
-fast-but-frequently-called functions are instrumented. Try to instrument 
+result in misleading profiling information, particularly if
+fast-but-frequently-called functions are instrumented. Try to instrument
 significant functions only.
 
 The profiling overhead in sensibly-instrumented code should be only a few
@@ -111,14 +111,14 @@ When running the code, prepend the run command with ``scalasca -analyze``, e.g.
     $ scalasca -analyze mpirun -np 2 elm_pb
 
 The run then produces an "archive" containing profiling data in a directory
-called ``scorep_<exec_name>_<proc_info>_sum``.  To view the profiling 
+called ``scorep_<exec_name>_<proc_info>_sum``.  To view the profiling
 information with the cube viewer, do
 
 .. code-block:: bash
 
     $ cube scorep_<exec_name>_<proc_info>_sum/profile.cubex
 
-Note that Scorep does not run if doing so would produce an archive with the 
+Note that Scorep does not run if doing so would produce an archive with the
 same name as an existing archive. Therefore to rerun an executable on the same
 number of processors, it is necessary to move or delete the first archive.
 
@@ -140,19 +140,19 @@ As of 23rd January 2019, the following configuration should work
     $ module load archer-netcdf/4.1.3
     $ module load scalasca
 
-Note that due to a bug in the ``CC`` compiler, it is necessary to modify 
+Note that due to a bug in the ``CC`` compiler, it is necessary to modify
 ``make.config`` after configuration if profiling OpenMP-parallelized code:
 
 * add the flag ``-fopenmp`` to ``BOUT_FLAGS``
-* add the flag ``--thread=omp:ancestry`` as an argument to ``scorep`` in ``CXX`` 
+* add the flag ``--thread=omp:ancestry`` as an argument to ``scorep`` in ``CXX``
 
 
 Extrae/Paraver profiling
 ------------------------
 
 `Extrae <https://tools.bsc.es/extrae/>`_ is a powerful tool allowing visualization
-of commumication and computation in parallel codes. It requires minimal 
-instrumentation; however the trace files produced can be extremely large. 
+of commumication and computation in parallel codes. It requires minimal
+instrumentation; however the trace files produced can be extremely large.
 
 Instrumentation, configure and build
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -218,7 +218,7 @@ Reducing trace file size
 
 When trace files are very large, Paraver will prompt the user to filter or cut
 the file to reduce its size.
-Filtering removes some information from the trace, making it small enough to 
+Filtering removes some information from the trace, making it small enough to
 open and allow the user to select a region of interest.
 Cutting crops the trace to a region of interest.
 Both operations create new trace files, and never overwrite the original trace.
@@ -233,15 +233,15 @@ The following prescription should work for manipulating large trace files:
         c) in 'Keep States' select box for 'Running'
         d) in 'Keep States' select box for 'IO'
         e) select a min duration of 1000
-        f) click 'Apply' 
+        f) click 'Apply'
 4. View 'useful duration' configuration and locate the region of interest
 5. Zoom into the region of interest, and start and end the zoom on equivalent
-   large sections of computation (blue/green) 
+   large sections of computation (blue/green)
 6. Right click -> Run -> Cutter
 7. Change the 'Input' trace file to cut from the filtered to the original one.
 8. Click cut.
 
-This produces a trace file which has all the original profiling information, 
+This produces a trace file which has all the original profiling information,
 but is much smaller as it is limited in time to a region of interest.
 
 Machine-specific installation
@@ -265,6 +265,6 @@ As of 1st February 2019, the following configuration should work
     $
     $ export CRAYPE_LINK_TYPE=dynamic
 
-Note that due to a bug in the ``CC`` compiler, it is necessary to modify 
-``make.config`` after configuration to add the flag  ``-fopenmp`` to 
+Note that due to a bug in the ``CC`` compiler, it is necessary to modify
+``make.config`` after configuration to add the flag  ``-fopenmp`` to
 ``BOUT_FLAGS``, when profiling OpenMP-parallelized code.
diff --git a/manual/sphinx/user_docs/laplacian.rst b/manual/sphinx/user_docs/laplacian.rst
index 1529149726..ade760d5c5 100644
--- a/manual/sphinx/user_docs/laplacian.rst
+++ b/manual/sphinx/user_docs/laplacian.rst
@@ -847,7 +847,7 @@ subdomain using the Thomas algorithm.
 
 **Constraints.** This method requires that:
 
-* ``NXPE`` is a power of 2. 
+* ``NXPE`` is a power of 2.
 * ``NXPE > 2^(max_levels+1)``
 
 .. _sec-LaplaceXY:
diff --git a/manual/sphinx/user_docs/physics_models.rst b/manual/sphinx/user_docs/physics_models.rst
index d9a45f4014..25aefdddd3 100644
--- a/manual/sphinx/user_docs/physics_models.rst
+++ b/manual/sphinx/user_docs/physics_models.rst
@@ -528,7 +528,7 @@ is the macro::
     OPTION(options, g, 5.0/3.0);
 
 which is equivalent to::
-  
+
     g = options["g"].withDefault( 5.0/3.0 );
 
 See :ref:`sec-options` for more details of how to use the input
@@ -734,14 +734,14 @@ and ``a(1,y,z)`` is in the domain, then the boundary would be set so that::
 rearranged as::
 
     a(0,y,z) = - a(1,y,z) + b(0,y,z) + b(1,y,z)
-    
+
 To copy the boundary cells (and communication guard cells), iterate
 over them::
 
     BOUT_FOR(i, a.getRegion("RGN_GUARDS")) {
       a[i] = b[i];
     }
-    
+
 See :ref:`sec-iterating` for more details on iterating over custom regions.
 
 .. _sec-custom-bc:
diff --git a/manual/sphinx/user_docs/running_bout.rst b/manual/sphinx/user_docs/running_bout.rst
index 5ee7a9bfb3..f0c53fc74e 100644
--- a/manual/sphinx/user_docs/running_bout.rst
+++ b/manual/sphinx/user_docs/running_bout.rst
@@ -673,4 +673,3 @@ then the BOUT++ restart will fail.
 **Note** It is a good idea to set ``nxpe`` in the ``BOUT.inp`` file to be consistent with
 what you set here. If it is inconsistent then the restart will fail, but the error message may
 not be particularly enlightening.
-
diff --git a/src/invert/lapack_routines.cxx b/src/invert/lapack_routines.cxx
index 638385dfe8..1ccb021abb 100644
--- a/src/invert/lapack_routines.cxx
+++ b/src/invert/lapack_routines.cxx
@@ -2,7 +2,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -97,7 +97,7 @@ int tridag(const dcomplex* a, const dcomplex* b, const dcomplex* c, const dcompl
 }
 
 /* Real tridiagonal solver
- * 
+ *
  * Returns true on success
  */
 bool tridag(const BoutReal* a, const BoutReal* b, const BoutReal* c, const BoutReal* r,
@@ -148,7 +148,7 @@ bool tridag(const BoutReal* a, const BoutReal* b, const BoutReal* c, const BoutR
 }
 
 /* Real cyclic tridiagonal solver
- * 
+ *
  * Uses Sherman-Morrison formula
  */
 void cyclic_tridag(BoutReal* a, BoutReal* b, BoutReal* c, BoutReal* r, BoutReal* x,
@@ -198,7 +198,7 @@ void cyclic_tridag(BoutReal* a, BoutReal* b, BoutReal* c, BoutReal* r, BoutReal*
 }
 
 /*! Complex band solver using ZGBSV
- * 
+ *
  * n      Size of the matrix (number of equations)
  * kl     Number of subdiagonals
  * ku     Number of superdiagonals
diff --git a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
index 6aa9a4eb19..00b9ad01af 100644
--- a/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
+++ b/src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
@@ -1,6 +1,6 @@
 /*!\file
  * Perpendicular Laplacian inversion in serial or parallel
- * 
+ *
  * Simplified version of serial_tri and spt algorithms. Uses FFTs and
  * the cyclic reduction class to solve tridiagonal systems.
  */
@@ -8,7 +8,7 @@
  * Copyright 2013 B.D.Dudson
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify

From 6d08e297c5a0a8ba34b57c3ef3e6246acc4cde4e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 09:16:55 +0200
Subject: [PATCH 1512/1827] Revert googletest changes

---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 0b1e895ba4..8b53336594 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 0b1e895ba4226c2fda5ee0178c9b5b1195a741aa
+Subproject commit 8b53336594cc52213c6c2c7a0b29194fa896d039

From c1dddecd8918d01a1b877bf49b219f5518f7437b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 10:45:55 +0200
Subject: [PATCH 1513/1827] CI: run tests with ctest on fedora

---
 .ci_fedora.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index c865e8a0aa..6199e8b6c1 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -58,4 +58,4 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
 	 -DBOUT_USE_SYSTEM_CPPTRACE=ON
 
     time make -C build build-check -j 2
-    time make -C build check
+    cd build && time ctest --output-on-failure --timeout 300

From 7de0aab8b1be7bd0c24cf83e677581fa49433e81 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 11:49:27 +0200
Subject: [PATCH 1514/1827] Be explicit about grid size

---
 tests/unit/include/bout/test_yboundary.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index 583b0e04ae..fae1a2a59a 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -7,11 +7,11 @@
 #include "fake_mesh_fixture.hxx"
 #include "test_extras.hxx"
 
-using YBTest = FakeMeshFixture;
+using YBTest = FakeMeshFixture_tmpl<3, 5, 7>;
 
 using bout::globals::mesh;
 
-TEST_F(YBTest, dirichlet_o2) {
+TEST_F(YBTest, dirichlet_o2_rgn) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](auto& point) { point.dirichlet_o2(test, 2); });

From 152c639fbe0d7c7990b2171db77250a7ac619889 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 11:49:46 +0200
Subject: [PATCH 1515/1827] Add test for extrapolate_boundary_o2

---
 tests/unit/include/bout/test_yboundary.cxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index fae1a2a59a..c68708e5b6 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -32,3 +32,10 @@ TEST_F(YBTest, interpolate_boundary_o2) {
   sheath.iter(
       [&](auto& point) { EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0); });
 }
+
+TEST_F(YBTest, extrapolate_boundary_o2) {
+  Field3D test = 1.0;
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter(
+      [&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_boundary_o2(test), 1.0); });
+}

From 4845503ab87704cecf624c95a39ebe78e0efce1a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 11:51:10 +0200
Subject: [PATCH 1516/1827] Add dirichlet_o1 and dirichlet_o3 for FA

---
 include/bout/boundary_iterator.hxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 85917f0295..2ee68e2b18 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -38,9 +38,13 @@ protected:
 public:
   BoundaryRegionIter& operator*() { return *this; }
 
+  void dirichlet_o1(Field3D& f, BoutReal value) const { ynext(f) = value; }
   void dirichlet_o2(Field3D& f, BoutReal value) const {
     ynext(f) = bout::parallel_stencil::dirichlet_o2(1, f[ind()], 0.5, value);
   }
+  void dirichlet_o3(Field3D& f, BoutReal value) const {
+    ynext(f) = bout::parallel_stencil::dirichlet_o3(2, yprev(f), 1, f[ind()], 0.5, value);
+  }
 
   BoutReal extrapolate_grad_o2(const Field3D& f) const { return f[ind()] - yprev(f); }
 

From dfe11f163c07a90d9d38473b23add78cd15d2f44 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 11:51:40 +0200
Subject: [PATCH 1517/1827] Add tests for dirichlet_o1 and dirichlet_o3 for FA

---
 tests/unit/include/bout/test_yboundary.cxx | 27 ++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index c68708e5b6..f20e97573b 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -39,3 +39,30 @@ TEST_F(YBTest, extrapolate_boundary_o2) {
   sheath.iter(
       [&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_boundary_o2(test), 1.0); });
 }
+
+TEST_F(YBTest, dirichlet_o1) {
+  Field3D test = 1.0;
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) {
+    point.dirichlet_o1(test, 2.0);
+    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.5);
+  });
+}
+
+TEST_F(YBTest, dirichlet_o2) {
+  Field3D test = 1.0;
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) {
+    point.dirichlet_o2(test, 2.0);
+    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 2.0);
+  });
+}
+
+TEST_F(YBTest, dirichlet_o3) {
+  Field3D test = 1.0;
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) {
+    point.dirichlet_o3(test, 2.0);
+    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 7. / 3.);
+  });
+}

From 3f5c6a6ce1f22b8e68468ba843444a688857fbeb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 11:52:30 +0200
Subject: [PATCH 1518/1827] Add tests for interpolate/extrapolate for FA

---
 tests/unit/include/bout/test_yboundary.cxx | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index f20e97573b..d9118ea6b2 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -66,3 +66,17 @@ TEST_F(YBTest, dirichlet_o3) {
     EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 7. / 3.);
   });
 }
+
+TEST_F(YBTest, interpolate_boundary_o2_square) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter(
+      [&](auto& point) { EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 2.5); });
+}
+
+TEST_F(YBTest, extrapolate_boundary_o2_square) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter(
+      [&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_boundary_o2(test), 1.5); });
+}

From 04fa6c91ae766c1fa3f602403facb0520b7d0109 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 11:54:11 +0200
Subject: [PATCH 1519/1827] Remove commented out code

---
 tests/unit/include/bout/test_yboundary.cxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index d9118ea6b2..db222337dc 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -1,7 +1,6 @@
 #include "gtest/gtest.h"
 
 #include "bout/boutexception.hxx"
-//#include "bout/boundary_region_iter.hxx"
 #include "bout/yboundary_regions.hxx"
 
 #include "fake_mesh_fixture.hxx"

From 41df0a7a25faf6cf1f2999a5abd35b50c28be05e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 13:35:10 +0200
Subject: [PATCH 1520/1827] Fixup boundary_free functions

* Ensure both implementations provide same API
* Ensure they use the same implementation
---
 include/bout/boundary_iterator.hxx        | 22 ++++---
 include/bout/boundary_region_iter.hxx     | 12 +---
 include/bout/parallel_boundary_region.hxx | 76 +++++------------------
 include/bout/yboundary_regions.hxx        |  5 +-
 4 files changed, 30 insertions(+), 85 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 2ee68e2b18..840a73f106 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -1,6 +1,7 @@
 #pragma once
 
 #include "bout/assert.hxx"
+#include "bout/boundary_common.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
@@ -75,19 +76,20 @@ public:
     return 0.5 * (3 * f(0, ind()) - f(0, ind().yp(-_by).xp(-_bx)));
   }
 
-  BoutReal extrapolate_boundary_free(const Field3D& f, BoundaryLimitMode mode) const {
-    const BoutReal fac =
-        bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
+  BoutReal
+  extrapolate_boundary_free(const Field3D& f,
+                            bout::boundary::BoundaryFreeExtrapolation mode) const {
+    const BoutReal fac = bout::boundary::limitFreeScale(yprev(f), ythis(f), mode);
     const BoutReal val = ythis(f);
-    const BoutReal next = mode == BoundaryLimitMode::linear_free ? val + fac : val * fac;
+    const BoutReal next =
+        mode == bout::boundary::BoundaryFreeExtrapolation::linear ? val + fac : val * fac;
     return 0.5 * (val + next);
   }
 
-  void set_free(Field3D& f, BoundaryLimitMode mode) const {
-    const BoutReal fac =
-        bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f), mode);
+  void set_free(Field3D& f, bout::boundary::BoundaryFreeExtrapolation mode) const {
+    const BoutReal fac = bout::boundary::limitFreeScale(yprev(f), ythis(f), mode);
     BoutReal val = ythis(f);
-    if (mode == BoundaryLimitMode::linear_free) {
+    if (mode == bout::boundary::BoundaryFreeExtrapolation::linear) {
       for (int i = 1; i <= localmesh->ystart; ++i) {
         val += fac;
         f[ind().yp(_by * i).xp(_bx * i)] = val;
@@ -101,8 +103,8 @@ public:
   }
 
   void limitFree(Field3D& f) const {
-    const BoutReal fac =
-        bout::parallel_boundary_region::limitFreeScale(yprev(f), ythis(f));
+    const BoutReal fac = bout::boundary::limitFreeScale(
+        yprev(f), ythis(f), bout::boundary::BoundaryFreeExtrapolation::limited);
     BoutReal val = ythis(f);
     for (int i = 1; i <= localmesh->ystart; ++i) {
       val *= fac;
diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 242306c04f..b1e95ff044 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -10,6 +10,7 @@
 #include <vector>
 
 #include "bout/assert.hxx"
+#include "bout/boundary_common.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/field_data.hxx"
 #include "bout/utils.hxx"
@@ -34,17 +35,6 @@ enum class BndryType : std::int8_t {
   num
 };
 
-/// Types of free boundary condition
-/// ================== ===================================================
-/// Name               Description
-/// ================== ===================================================
-/// ``limited``        use exponential if decreasing, otherwise Neumanm
-/// ``exponential``    use exponential extrapolation
-/// ``linear``         use linear extrapolation
-/// ================== ===================================================
-enum class BoundaryFreeExtrapolation : std::int8_t { limited, exponential, linear };
-//BOUT_ENUM_CLASS(BoundaryFreeExtrapolation, limited, exponential, linear);
-
 template <typename impl>
 class BoundaryRegionIterBase {
   BoundaryRegionIterBase() = default;
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 3e3b1238a0..40c3474ffe 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -12,6 +12,7 @@
 #include <string>
 #include <vector>
 
+#include "bout/boundary_common.hxx"
 #include "bout/build_defines.hxx"
 #include "bout/field2d.hxx"
 #include "bout/region.hxx"
@@ -26,8 +27,6 @@
  *
  */
 
-BOUT_ENUM_CLASS(BoundaryLimitMode, limit_free, exponential_free, linear_free);
-
 namespace bout {
 namespace parallel_boundary_region {
 
@@ -65,58 +64,6 @@ using IndicesVec = std::vector<Indices>;
 using IndicesIter = IndicesVec::iterator;
 using IndicesIterConst = IndicesVec::const_iterator;
 
-/// Limited free gradient of log of a quantity
-/// This ensures that the guard cell values remain positive
-/// while also ensuring that the quantity never increases
-///
-///  fm  fc | fp
-///         ^ boundary
-///
-/// exp( 2*log(fc) - log(fm) )
-inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, BoundaryLimitMode mode) {
-  if ((fm < fc) && (mode == BoundaryLimitMode::limit_free)) {
-    return fc; // Neumann rather than increasing into boundary
-  }
-  if (fm < 1e-10) {
-    return fc; // Low / no density condition
-  }
-
-  BoutReal fp = 0;
-  switch (mode) {
-  case BoundaryLimitMode::limit_free:
-  case BoundaryLimitMode::exponential_free:
-    fp = SQ(fc) / fm; // Exponential
-    break;
-  case BoundaryLimitMode::linear_free:
-    fp = (2.0 * fc) - fm; // Linear
-    break;
-  }
-
-#if CHECKLEVEL >= 2
-  if (!std::isfinite(fp)) {
-    throw BoutException("SheathBoundary limitFree: {}, {} -> {}", fm, fc, fp);
-  }
-#endif
-
-  return fp;
-}
-
-inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc) {
-  if (fm < fc) {
-    return 1; // Neumann rather than increasing into boundary
-  }
-  if (fm < 1e-10) {
-    return 1; // Low / no density condition
-  }
-  BoutReal fp = fc / fm;
-#if CHECKLEVEL >= 2
-  if (!std::isfinite(fp)) {
-    throw BoutException("SheathBoundaryParallel limitFree: {}, {} -> {}", fm, fc, fp);
-  }
-#endif
-  return fp;
-}
-
 template <class IndicesVec, class IndicesIter>
 class BoundaryRegionParIterBase {
 
@@ -300,19 +247,24 @@ public:
     }
   }
 
-  BoutReal extrapolate_boundary_free(const Field3D& f, BoundaryLimitMode mode) const {
-    const auto fac = valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
-                                 : (mode == BoundaryLimitMode::linear_free ? 0 : 1);
+  BoutReal
+  extrapolate_boundary_free(const Field3D& f,
+                            bout::boundary::BoundaryFreeExtrapolation mode) const {
+    const auto fac =
+        valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
+                    : (mode == bout::boundary::BoundaryFreeExtrapolation::linear ? 0 : 1);
     auto val = ythis(f);
-    BoutReal next = mode == BoundaryLimitMode::linear_free ? val + fac : val * fac;
+    BoutReal next =
+        mode == bout::boundary::BoundaryFreeExtrapolation::linear ? val + fac : val * fac;
     return val * length(f.getLocation()) + next * (1 - length(f.getLocation()));
   }
 
-  void set_free(Field3D& f, BoundaryLimitMode mode) const {
-    const auto fac = valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
-                                 : (mode == BoundaryLimitMode::linear_free ? 0 : 1);
+  void set_free(Field3D& f, bout::boundary::BoundaryFreeExtrapolation mode) const {
+    const auto fac =
+        valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
+                    : (mode == bout::boundary::BoundaryFreeExtrapolation::linear ? 0 : 1);
     auto val = ythis(f);
-    if (mode == BoundaryLimitMode::linear_free) {
+    if (mode == bout::boundary::BoundaryFreeExtrapolation::linear) {
       ITER() {
         val += fac;
         getAt(f, i) = val;
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index f5fbf5ce1f..6bce1119db 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -1,9 +1,10 @@
 #pragma once
 
-#include <bout/boundary_region_iter.hxx>
+#include "bout/boundary_common.hxx"
+#include "bout/boundary_region_iter.hxx"
 
-#include "./boundary_iterator.hxx"
 #include "bout/assert.hxx"
+#include "bout/boundary_iterator.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field_data.hxx"
 #include "bout/globals.hxx"

From 59660e9ace5b3bf9607352e1b7d5f5a6c3db3949 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 13:35:36 +0200
Subject: [PATCH 1521/1827] Add tests for extrapolate_boundary_free and
 set_free

---
 tests/unit/include/bout/test_yboundary.cxx | 25 ++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index db222337dc..c55d31eda5 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -66,6 +66,31 @@ TEST_F(YBTest, dirichlet_o3) {
   });
 }
 
+TEST_F(YBTest, extrapolate_boundary_free) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2) + 1; }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) {
+    EXPECT_DOUBLE_EQ(point.extrapolate_boundary_free(
+                         test, bout::boundary::BoundaryFreeExtrapolation::limited),
+                     3);
+    EXPECT_DOUBLE_EQ(point.extrapolate_boundary_free(
+                         test, bout::boundary::BoundaryFreeExtrapolation::linear),
+                     3.5);
+    EXPECT_DOUBLE_EQ(point.extrapolate_boundary_free(
+                         test, bout::boundary::BoundaryFreeExtrapolation::exponential),
+                     5);
+  });
+}
+
+TEST_F(YBTest, set_free) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2) + 1; }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) {
+    point.set_free(test, bout::boundary::BoundaryFreeExtrapolation::limited);
+    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 3);
+  });
+}
+
 TEST_F(YBTest, interpolate_boundary_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);

From a5566a3ed995a949b23a8915b71349ebd1d4eee1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 13:38:58 +0200
Subject: [PATCH 1522/1827] Add unit test for grad_o2

---
 tests/unit/include/bout/test_yboundary.cxx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index c55d31eda5..383fc68349 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -104,3 +104,9 @@ TEST_F(YBTest, extrapolate_boundary_o2_square) {
   sheath.iter(
       [&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_boundary_o2(test), 1.5); });
 }
+
+TEST_F(YBTest, extrapolate_grad_o2_square) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_grad_o2(test), 1); });
+}

From 63a88b56429c4b7cd6456c0d9954e40d16051fd1 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Mon, 29 Jun 2026 12:41:47 +0100
Subject: [PATCH 1523/1827] Fix test_yupdown (test all combinations of
 `shift_types` and `variables`)

---
 tests/integrated/test-yupdown/test_yupdown.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py
index b2569f4d60..e5b4b162cf 100755
--- a/tests/integrated/test-yupdown/test_yupdown.py
+++ b/tests/integrated/test-yupdown/test_yupdown.py
@@ -33,10 +33,11 @@ def run_case(shift_type, variable):
     return False
 
 
-@pytest.mark.parametrize("shift_type, variable", list(zip(shift_types, variables)))
+@pytest.mark.parametrize("shift_type", shift_types)
+@pytest.mark.parametrize("variable", variables)
 def test_case(shift_type, variable):
     # MPI oversubscribe
     os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
 
     success = run_case(shift_type, variable)
-    assert success, f"Test failed for shift_type={shift_type}: , variable={variable}"
+    assert success, f"Test failed for shift_type={shift_type}, variable={variable}"

From b5beb22e5d03584a21c2091b70b41f15ad5373db Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 13:54:58 +0200
Subject: [PATCH 1524/1827] add test for next_o2

---
 tests/unit/include/bout/test_yboundary.cxx | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index 383fc68349..1ae242da65 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -110,3 +110,9 @@ TEST_F(YBTest, extrapolate_grad_o2_square) {
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_grad_o2(test), 1); });
 }
+
+TEST_F(YBTest, extrapolate_next_o2_square) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_next_o2(test), 2); });
+}

From 27ec4038ee572db08f2bc0a6e8314f0fd6412b08 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 15:34:33 +0200
Subject: [PATCH 1525/1827] Implementations have to start with _

---
 include/bout/boundary_region_iter.hxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index b1e95ff044..aaf7ac37c9 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -518,8 +518,8 @@ public:
     return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
-  BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
-                 int off) const {
+  BoutReal _getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
+                  int off) const {
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }
@@ -638,8 +638,8 @@ public:
     }
   }
   template <bool check = true>
-  BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
-                 int off) const {
+  BoutReal _getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
+                  int off) const {
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }

From 09fa911b8b5234848292cc56927621d3de8bbcb5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 29 Jun 2026 15:40:33 +0200
Subject: [PATCH 1526/1827] getBoundaries can be const

---
 include/bout/mesh.hxx            | 2 +-
 src/mesh/impls/bout/boutmesh.cxx | 2 +-
 src/mesh/impls/bout/boutmesh.hxx | 2 +-
 tests/unit/fake_mesh.hxx         | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 929e9d5aa7..abead4968e 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -482,7 +482,7 @@ public:
   // Boundary regions
 
   /// Return a vector containing all the boundary regions on this processor
-  virtual std::vector<BoundaryRegionBase*> getBoundaries() = 0;
+  virtual std::vector<BoundaryRegionBase*> getBoundaries() const = 0;
 
   /// Get the set of all possible boundaries in this configuration
   virtual std::set<std::string> getPossibleBoundaries() const {
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 7ab45c327a..e1d2cbfc70 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -3250,7 +3250,7 @@ RangeIterator BoutMesh::iterateBndryUpperY() const {
   return RangeIterator(xs, xe);
 }
 
-std::vector<BoundaryRegionBase*> BoutMesh::getBoundaries() { return boundary; }
+std::vector<BoundaryRegionBase*> BoutMesh::getBoundaries() const { return boundary; }
 
 using bout::boundary::BoundaryRegionFCI;
 std::vector<std::shared_ptr<BoundaryRegionFCI>>
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index dfec3342ed..79121ede58 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -169,7 +169,7 @@ public:
   bool hasBndryUpperY() const override { return has_boundary_upper_y; }
 
   // Boundary regions
-  std::vector<BoundaryRegionBase*> getBoundaries() override;
+  std::vector<BoundaryRegionBase*> getBoundaries() const override;
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType type) const override;
   void addBoundaryPar(std::shared_ptr<bout::boundary::BoundaryRegionFCI> bndry,
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 4d4b985a22..aa08c2f043 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -176,7 +176,7 @@ public:
   bool hasBndryLowerY() const override { return false; }
   bool hasBndryUpperY() const override { return false; }
   void addBoundary(BoundaryRegionBase* region) override { boundaries.push_back(region); }
-  std::vector<BoundaryRegionBase*> getBoundaries() override { return boundaries; }
+  std::vector<BoundaryRegionBase*> getBoundaries() const override { return boundaries; }
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType UNUSED(type)) const override {
     return std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>();

From 5ccd8d7f590524fd20d6873c4c48321e784fea69 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 29 Jun 2026 11:42:15 -0700
Subject: [PATCH 1527/1827] FieldFactory::read_grid_variables Catch null mesh

FieldFactory can be called early in startup, potentially before
the global Mesh has been set. This guards against that by checking
for null mesh passed to `read_grid_variables`.
---
 src/field/field_factory.cxx             | 25 +++++++++++++++----------
 tests/unit/field/test_field_factory.cxx | 11 +++++++++++
 2 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index 8a8312d665..1f5984ba48 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -93,23 +93,30 @@ class FieldIndirect : public FieldGenerator {
 };
 
 // Read variables from the grid file and make them available in expressions
-template <class T>
 auto add_grid_variable(FieldFactory& factory, Mesh& mesh, const std::string& name) {
   factory.addGenerator(fmt::format("gridvar:{}", name),
-                       std::make_shared<GridVariable<T>>(&mesh, name));
+                       std::make_shared<GridVariable>(&mesh, name));
 }
 
-auto read_grid_variables(FieldFactory& factory, Mesh& mesh, Options& options) {
+auto read_grid_variables(FieldFactory& factory, Mesh* mesh, Options& options) {
   auto& field_variables = options["input"]["grid_variables"].doc(
       "Variables to read from the grid file and make available in expressions");
 
+  if (field_variables.cbegin() == field_variables.cend()) {
+    return;
+  }
+
+  if (mesh == nullptr) {
+    throw BoutException("A mesh is required for `input:grid_variables`");
+  }
+
   for (const auto& [name, value] : field_variables) {
-    if (not mesh.isDataSourceGridFile()) {
+    if (not mesh->isDataSourceGridFile()) {
       throw BoutException(
           "A grid file ('mesh:file') is required for `input:grid_variables`");
     }
 
-    if (not mesh.sourceHasVar(name)) {
+    if (not mesh->sourceHasVar(name)) {
       const auto filename = Options::root()["mesh"]["file"].as<std::string>();
       throw BoutException(
           "Grid file '{}' missing `{}` specified in `input:grid_variables`", filename,
@@ -119,14 +126,12 @@ auto read_grid_variables(FieldFactory& factory, Mesh& mesh, Options& options) {
     const auto func = value.as<GridVariableFunction>();
     switch (func) {
     case GridVariableFunction::field3d:
-      add_grid_variable<Field3D>(factory, mesh, name);
-      break;
     case GridVariableFunction::field2d:
-      add_grid_variable<Field2D>(factory, mesh, name);
+      add_grid_variable(factory, *mesh, name);
       break;
     case GridVariableFunction::boutreal:
       BoutReal var{};
-      mesh.get(var, name);
+      mesh->get(var, name);
       factory.addGenerator(name, std::make_shared<FieldValue>(var));
       break;
     }
@@ -233,7 +238,7 @@ FieldFactory::FieldFactory(Mesh* localmesh, Options* opt)
   addGenerator("is_periodic_y", std::make_shared<FieldPeriodicY>());
 
   // Variables from the grid file
-  read_grid_variables(*this, *fieldmesh, nonconst_options);
+  read_grid_variables(*this, fieldmesh, nonconst_options);
 }
 
 Field2D FieldFactory::create2D(const std::string& value, const Options* opt,
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index 25177c3169..9db9fcef10 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -1131,6 +1131,17 @@ TEST_F(FieldFactoryFieldVariableTest, NoMeshFile) {
   EXPECT_THROW((FieldFactory(mesh, &options)), BoutException);
 }
 
+TEST_F(FieldFactoryFieldVariableTest, NoMeshAvailable) {
+  auto* old_mesh = bout::globals::mesh;
+  bout::globals::mesh = nullptr;
+
+  Options options{{"input", {{"grid_variables", {{"rho", "field3d"}}}}}};
+
+  EXPECT_THROW((FieldFactory(nullptr, &options)), BoutException);
+
+  bout::globals::mesh = old_mesh;
+}
+
 TEST_F(FieldFactoryFieldVariableTest, MissingVariable) {
   const bout::testing::TempFile filename;
 

From 74310f6a9d6e93eade873eae332b3d10d934b185 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 29 Jun 2026 11:44:29 -0700
Subject: [PATCH 1528/1827] GridVariable::LazyLoad thread safety and
 performance

LazyLoad::get() always returned a Field3D, so BoutReal or Field2D
grid variables would be converted to Field3D on every call to
generate(). Now converting once to Field3D and storing that.

GridVariable::generate() is called in a BOUT_FOR loop so should
be thread-safe. Adds locks around the `mesh->get` call.
---
 src/field/fieldgenerators.hxx | 32 ++++++++++++++++++++------------
 1 file changed, 20 insertions(+), 12 deletions(-)

diff --git a/src/field/fieldgenerators.hxx b/src/field/fieldgenerators.hxx
index c84a35109f..80d97b1a68 100644
--- a/src/field/fieldgenerators.hxx
+++ b/src/field/fieldgenerators.hxx
@@ -16,9 +16,11 @@
 #include <bout/unused.hxx>
 
 #include <algorithm>
+#include <atomic>
 #include <cmath>
 #include <list>
 #include <memory>
+#include <mutex>
 #include <string>
 #include <utility>
 
@@ -382,29 +384,35 @@ public:
   }
 };
 
-/// A `Field3D` or `Field2D` that can be used in expressions
+/// A grid file variable that can be used in expressions
 ///
 /// The variable is read from Mesh when first used and shared between
 /// clones. This is to avoid circular dependencies in construction.
-template <class T, typename = bout::utils::EnableIfField<T>>
 class GridVariable : public FieldGenerator {
 private:
   struct LazyLoaded {
-    LazyLoaded(Mesh* mesh, std::string name) : mesh(mesh), name(std::move(name)) {}
-
-    Field3D get() {
-      if (!var.isAllocated()) {
-        // Read variable from mesh
-        if (this->mesh->get(this->var, this->name) != 0) {
-          throw BoutException("Couldn't read GridVariable '{}'", this->name);
+    LazyLoaded(Mesh* mesh, std::string name)
+        : mesh(mesh), name(std::move(name)), var(mesh) {}
+
+    const Field3D& get() {
+      if (!is_loaded.load(std::memory_order_acquire)) {
+        std::lock_guard<std::mutex> guard(load_mutex);
+        if (!is_loaded.load(std::memory_order_relaxed)) {
+          // Read and convert the variable once, then share it between all clones.
+          if (mesh->get(var, name) != 0) {
+            throw BoutException("Couldn't read GridVariable '{}'", name);
+          }
+          is_loaded.store(true, std::memory_order_release);
         }
       }
-      return this->var;
+      return var;
     }
 
     Mesh* mesh;
     std::string name;
-    T var{};
+    Field3D var;
+    std::atomic<bool> is_loaded{false};
+    std::mutex load_mutex;
   };
 
   std::shared_ptr<LazyLoaded> variable;
@@ -424,7 +432,7 @@ public:
       throw ParseException("Variable '{}' takes no arguments but got {:d}",
                            variable->name, args.size());
     }
-    return std::make_shared<GridVariable<T>>(variable);
+    return std::make_shared<GridVariable>(variable);
   }
 
   std::string str() const override { return variable->name; }

From 83f1a567c614e879a88e4b478303f620dc2811fc Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 29 Jun 2026 13:39:00 -0700
Subject: [PATCH 1529/1827] Fixes and tidying

- Arithmetic expression on FieldMetrics
- Check for null source in Mesh::get
- Use BOUT_USE_METRIC_3D rather than BOUT_HAS_METRIC_3D
---
 src/mesh/mesh.cxx                                   |  6 ++++++
 src/mesh/petsc_operators.cxx                        | 13 +++++++------
 .../integrated/test-petsc-operators/CMakeLists.txt  |  2 +-
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index c44a62aa7e..33368e6d6a 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -189,10 +189,16 @@ int Mesh::get(bool& bval, const std::string& name, bool def) {
 }
 
 int Mesh::get(Array<int>& var, const std::string& name) {
+  if (source == nullptr) {
+    return 1;
+  }
   return source->get(var, name) ? 0 : 1;
 }
 
 int Mesh::get(Array<BoutReal>& var, const std::string& name) {
+  if (source == nullptr) {
+    return 1;
+  }
   return source->get(var, name) ? 0 : 1;
 }
 
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 54ec91c4df..573044a0a1 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -1,21 +1,22 @@
 #include "bout/build_defines.hxx"
-#include "bout/field2d.hxx"
-#include "bout/petsc_interface.hxx"
-#include "bout/petsclib.hxx"
-#include <cmath>
 
 #if BOUT_HAS_PETSC
 
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/output_bout_types.hxx"
+#include "bout/petsc_interface.hxx"
 #include "bout/petsc_operators.hxx"
+#include "bout/petsclib.hxx"
 #include "bout/region.hxx"
 #include "bout/utils.hxx"
 
 #include <algorithm>
+#include <cmath>
 #include <memory>
 #include <string>
 #include <utility>
@@ -332,14 +333,14 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   auto* coords = mesh->getCoordinates();
 
   // Parallel spacing in cell space
-  Field3D dl = coords->dy * sqrt(coords->g_22);
+  Field3D dl = Coordinates::FieldMetric{coords->dy * sqrt(coords->g_22)};
   dl.splitParallelSlices();
   dl.yup() = 0.0;
   dl.ydown() = 0.0;
   dl.applyParallelBoundary("parallel_neumann_o1");
 
   // Cell volume
-  Field3D dV = coords->J * coords->dx * coords->dy * coords->dz;
+  Field3D dV = Coordinates::FieldMetric{coords->J * coords->dx * coords->dy * coords->dz};
   dV.splitParallelSlices();
   dV.yup() = 0.0;
   dV.ydown() = 0.0;
diff --git a/tests/integrated/test-petsc-operators/CMakeLists.txt b/tests/integrated/test-petsc-operators/CMakeLists.txt
index 6745344e34..d0860a88e7 100644
--- a/tests/integrated/test-petsc-operators/CMakeLists.txt
+++ b/tests/integrated/test-petsc-operators/CMakeLists.txt
@@ -3,6 +3,6 @@ bout_add_integrated_test(
   SOURCES test_petsc_operators.cxx
   USE_RUNTEST USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_PETSC
-  REQUIRES BOUT_HAS_METRIC_3D
+  REQUIRES BOUT_USE_METRIC_3D
   EXTRA_FILES rotating-ellipse.py test_petsc_operators.py
 )

From ca092e8b787c2d925e5be9365b3fcd5c9afb2757 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 29 Jun 2026 13:47:51 -0700
Subject: [PATCH 1530/1827] PetscOperator::assembleFromCSR preallocate

Iterate over elements to preallocate the PETSc matrix
before setting element values.
---
 include/bout/petsc_operators.hxx | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/include/bout/petsc_operators.hxx b/include/bout/petsc_operators.hxx
index c92a2b6d57..5a7df5b088 100644
--- a/include/bout/petsc_operators.hxx
+++ b/include/bout/petsc_operators.hxx
@@ -725,7 +725,34 @@ private:
     BOUT_DO_PETSC(MatSetSizes(*temp, out_mapping->localSize(), PETSC_DECIDE,
                               out_mapping->globalSize(), in_mapping->globalSize()));
 
+    PetscInt col_start{0};
+    PetscInt col_end{0};
+    BOUT_DO_PETSC(MatGetOwnershipRangeColumn(*temp, &col_start, &col_end));
+
     const auto& local_rows = out_mapping->localStoredIndices();
+    std::vector<PetscInt> d_nnz(local_rows.size(), 0);
+    std::vector<PetscInt> o_nnz(local_rows.size(), 0);
+    for (PetscInt local_row = 0; local_row < static_cast<PetscInt>(local_rows.size());
+         ++local_row) {
+      const int stored_row = local_rows[local_row];
+      if (stored_row < 0 || stored_row + 1 >= static_cast<int>(rows.size())) {
+        continue;
+      }
+      const int start = rows[stored_row];
+      const int end = rows[stored_row + 1];
+      for (int index = start; index < end; ++index) {
+        const PetscInt stored_col = cols[index];
+        if (col_start <= stored_col && stored_col < col_end) {
+          ++d_nnz[local_row];
+        } else {
+          ++o_nnz[local_row];
+        }
+      }
+    }
+    BOUT_DO_PETSC(MatMPIAIJSetPreallocation(*temp, 0,
+                                            d_nnz.empty() ? nullptr : d_nnz.data(), 0,
+                                            o_nnz.empty() ? nullptr : o_nnz.data()));
+
     for (PetscInt local_row = 0; local_row < static_cast<PetscInt>(local_rows.size());
          ++local_row) {
       const int stored_row = local_rows[local_row];

From b5dc10b4eb5c40f6df1bf2fd3c630899a1600c3f Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 29 Jun 2026 17:43:13 -0700
Subject: [PATCH 1531/1827] test-petsc-operators: Fixes

Changes in `next` mean communicating Bxy throws exception
(disabled calc parallel slices).
---
 tests/integrated/test-petsc-operators/rotating-ellipse.py      | 2 +-
 tests/integrated/test-petsc-operators/test_petsc_operators.cxx | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/integrated/test-petsc-operators/rotating-ellipse.py b/tests/integrated/test-petsc-operators/rotating-ellipse.py
index bcaa456885..2482d580c9 100755
--- a/tests/integrated/test-petsc-operators/rotating-ellipse.py
+++ b/tests/integrated/test-petsc-operators/rotating-ellipse.py
@@ -82,7 +82,7 @@
 # Generate a grid on each poloidal slice using the elliptic grid generator
 
 pol_grids = [
-    zoidberg.poloidal_grid.grid_elliptic(outer_line, inner_line, args.nx, args.nz)
+    zoidberg.poloidal_grid.grid_elliptic(inner_line, outer_line, args.nx, args.nz)
     for inner_line in inner_lines
 ]
 
diff --git a/tests/integrated/test-petsc-operators/test_petsc_operators.cxx b/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
index bd6166348c..6c70c65f39 100644
--- a/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
+++ b/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
@@ -50,7 +50,6 @@ int main(int argc, char** argv) {
     dump["div_par_op"] = parallel.Div_par(f);
 
     auto* coords = bout::globals::mesh->getCoordinates();
-    bout::globals::mesh->communicate(coords->Bxy);
     coords->Bxy.applyParallelBoundary("parallel_neumann_o1");
     dump["div_par_yud"] = Div_par(f);
 

From 9c53d77d42c58536a25518f27e78301185ab1778 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 29 Jun 2026 21:36:55 -0700
Subject: [PATCH 1532/1827] Manual page on PetscOperator

---
 manual/sphinx/index.rst                       |   9 +-
 manual/sphinx/user_docs/boundary_options.rst  |   3 +
 .../user_docs/differential_operators.rst      |   4 +
 .../sphinx/user_docs/parallel-transforms.rst  |   3 +
 .../sphinx/user_docs/parallel_operators.rst   | 302 ++++++++++++++++++
 5 files changed, 317 insertions(+), 4 deletions(-)
 create mode 100644 manual/sphinx/user_docs/parallel_operators.rst

diff --git a/manual/sphinx/index.rst b/manual/sphinx/index.rst
index 6a5a48ba34..1d4aaeab10 100644
--- a/manual/sphinx/index.rst
+++ b/manual/sphinx/index.rst
@@ -68,15 +68,16 @@ The documentation is divided into the following sections:
 
    user_docs/time_integration
    user_docs/parallel-transforms
-   user_docs/laplacian
    user_docs/differential_operators
-   user_docs/field_expressions
+   user_docs/parallel_operators
    user_docs/algebraic_operators
+   user_docs/field_expressions
    user_docs/staggered_grids
-   user_docs/eigenvalue_solver
-   user_docs/nonlocal
+   user_docs/laplacian
    user_docs/invertable_operator
    user_docs/petsc
+   user_docs/eigenvalue_solver
+   user_docs/nonlocal
 
 .. toctree::
    :maxdepth: 2
diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 1aba0321d2..7ca782fc44 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -275,6 +275,9 @@ and ``bndry_down = none`` to skip unnecessary operations on y-boundary
 cells of the base variable. For example, for an evolving variable
 ``f``, put a section in the ``BOUT.inp`` input file like
 
+The PETSc FCI operators described in :ref:`sec-parallel-operators-petsc-fci`
+use the same parallel boundary data and application order.
+
 .. code-block:: cfg
 
     [f]
diff --git a/manual/sphinx/user_docs/differential_operators.rst b/manual/sphinx/user_docs/differential_operators.rst
index 71dbeb4f9e..54a99faa71 100644
--- a/manual/sphinx/user_docs/differential_operators.rst
+++ b/manual/sphinx/user_docs/differential_operators.rst
@@ -619,6 +619,10 @@ The parallel diffusion operator calculates :math:`\nabla_{||}\left[k\partial_||\
 This is done by calculating the flux :math:`k\partial_{||}\left(f\right)` on cell boundaries
 using central differencing.
 
+For FCI meshes there is also a PETSc-based support-operator implementation
+which constructs sparse matrix parallel operators from grid metadata. That
+interface is documented separately in :ref:`sec-parallel-operators-petsc-fci`.
+
 
 Advection in 3D
 ~~~~~~~~~~~~~~~
diff --git a/manual/sphinx/user_docs/parallel-transforms.rst b/manual/sphinx/user_docs/parallel-transforms.rst
index 9d9b94af9e..3d8c117a36 100644
--- a/manual/sphinx/user_docs/parallel-transforms.rst
+++ b/manual/sphinx/user_docs/parallel-transforms.rst
@@ -209,5 +209,8 @@ backward_zt_prime(x,y,z).
 Tools for calculating these mappings include Zoidberg, a Python tool
 which carries out field-line tracing and generates FCI inputs.
 
+For PETSc-based support-operator discretisations built from these FCI mappings,
+see :ref:`sec-parallel-operators-petsc-fci`.
+
 Special handling is needed for parallel boundary conditions, see
 :ref:`sec-parallel-bc-fci`.
diff --git a/manual/sphinx/user_docs/parallel_operators.rst b/manual/sphinx/user_docs/parallel_operators.rst
new file mode 100644
index 0000000000..b44e60ad70
--- /dev/null
+++ b/manual/sphinx/user_docs/parallel_operators.rst
@@ -0,0 +1,302 @@
+.. _sec-parallel-operators-petsc-fci:
+
+Parallel operators with PETSc (FCI)
+===================================
+
+BOUT++ provides a PETSc-based interface for constructing parallel operators on
+FCI grids from mesh metadata. These operators are intended for cases where the
+standard field-based parallel operators described in :ref:`sec-diffops` are not
+the best fit, for example when using FCI and wanting a conservative
+support-operator discretisation built from the traced field-line geometry.
+
+This interface constructs sparse matrix PETSc operators that act on ``Field3D``
+data and the associated FCI parallel-boundary values. The main entry point is the
+``PetscOperators`` class in ``bout/petsc_operators.hxx``.
+
+
+When to use these operators
+---------------------------
+
+Use the PETSc FCI operators when all of the following are true:
+
+- The mesh uses the FCI parallel transform, ``mesh:paralleltransform:type = fci``
+- BOUT++ is built with PETSc support
+- BOUT++ is built with 3D metrics enabled
+- The grid file includes the FCI operator weights generated during grid
+  construction.
+
+If you are using the identity or shifted-metric parallel transforms, or if you
+simply need the standard field operators such as ``Grad_par`` or
+``Div_par_K_Grad_par``, use the routines documented in
+:ref:`sec-diffops` instead.
+
+
+Requirements
+------------
+
+Build requirements
+~~~~~~~~~~~~~~~~~~
+
+This feature requires:
+
+- PETSc support in BOUT++
+- 3D metrics enabled in BOUT++
+
+See :ref:`sec-PETSc-install` for PETSc installation and configuration details.
+
+Mesh and grid requirements
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+These operators are designed for the FCI transform described in :ref:`sec-fci`.
+The grid file must contain the additional numbering, interpolation, and weight
+arrays needed to construct the PETSc matrices. These are typically generated by
+the Zoidberg-based FCI grid tooling.
+
+To construct ``PetscOperators``, the mesh metadata currently required are:
+
+- Cell-space numbering fields:
+
+  - ``cell_number``
+  - ``forward_cell_number``
+  - ``backward_cell_number``
+
+- Cell-space size information:
+
+  - ``total_cells``
+
+- Leg-numbering fields:
+
+  - ``forward_leg_interior_number``
+  - ``forward_leg_boundary_number``
+  - ``backward_leg_interior_number``
+  - ``backward_leg_boundary_number``
+
+- Leg-space size information:
+
+  - ``n_forward_legs``
+  - ``n_backward_legs``
+
+- CSR data for the forward and backward interpolation operators:
+
+  - ``forward_rows``
+  - ``forward_columns``
+  - ``forward_weights``
+  - ``backward_rows``
+  - ``backward_columns``
+  - ``backward_weights``
+
+- Leg-weight arrays:
+
+  - ``forward_leg_weights``
+  - ``backward_leg_weights``
+
+If these metadata arrays are not present, constructing ``PetscOperators`` will
+fail during setup.
+
+
+Boundary conditions and communication
+-------------------------------------
+
+The PETSc FCI operators use the same parallel boundary data as the rest of the
+FCI workflow. In particular, parallel boundary conditions must be applied to the
+parallel slices after communication, as described in
+:ref:`sec-parallel-bc-fci`.
+
+A typical sequence is:
+
+.. code-block:: C++
+
+   f.applyBoundary();
+   mesh->communicate(f);
+   f.applyParallelBoundary("parallel_neumann_o1");
+
+The exact boundary operator should match the operator you are constructing or
+comparing against. For example, diffusion operators usually use Neumann
+parallel-boundary values, while other comparisons may use Dirichlet values.
+
+
+Constructing the operators
+--------------------------
+
+Include the header:
+
+.. code-block:: C++
+
+   #include <bout/petsc_operators.hxx>
+
+Construct the operator factory from the mesh, then build the grouped parallel
+operators:
+
+.. code-block:: C++
+
+   PetscOperators ops(mesh);
+   auto parallel = ops.getParallel();
+
+The returned ``parallel`` object contains:
+
+- Cell-to-cell operators such as ``Grad_par``, ``Div_par``, and
+  ``Div_par_Grad_par``
+- Half-step operators on the forward and backward FCI legs
+- Interpolation, injection, and restriction operators between cell space and
+  leg space
+- The cell volume field ``dV`` used in the support-operator construction
+
+These operators can then be applied directly to ``Field3D`` values.
+
+
+The ``PetscOperator`` class
+---------------------------
+
+The sparse operator type is a templated ``PetscOperator`` class.
+Operators map between a row space and a column space, which are tracked in the
+type system. In practice, the most common custom operator is likely to be a
+``PetscCellOperator``, which maps from cell space to cell space.
+
+Available aliases include:
+
+- ``PetscCellOperator`` for cell-to-cell operators
+- ``PetscForwardOperator`` and ``PetscBackwardOperator`` for cell-to-leg operators
+- ``PetscForwardToCellOperator`` and ``PetscBackwardToCellOperator`` for leg-to-cell operators
+
+Creating a ``PetscOperator``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+There are two main ways to create a ``PetscOperator``:
+
+- From CSR arrays stored in the mesh file
+- From an already-assembled PETSc ``Mat``
+
+The CSR constructor takes:
+
+- An output-space mapping
+- An input-space mapping
+- A CSR row-pointer array ``rows``
+- A CSR column-index array ``cols``
+- A CSR weight array ``weights``
+
+This is how the built-in forward and backward FCI interpolation operators are
+constructed:
+
+.. code-block:: C++
+
+   PetscForwardOperator forward(
+       forward_leg_mapping, cell_mapping,
+       meshGetArray<int>("forward_rows"),
+       meshGetArray<int>("forward_columns"),
+       meshGetArray<BoutReal>("forward_weights"));
+
+   PetscBackwardOperator backward(
+       backward_leg_mapping, cell_mapping,
+       meshGetArray<int>("backward_rows"),
+       meshGetArray<int>("backward_columns"),
+       meshGetArray<BoutReal>("backward_weights"));
+
+To implement a new operator, one straightforward route is:
+
+1. Generate the CSR arrays for the operator you want
+2. Write those arrays into the mesh or grid metadata
+3. Read them back with ``meshGetArray<int>()`` / ``meshGetArray<BoutReal>()``
+4. Construct the corresponding ``PetscOperator``
+
+For many custom differential operators, ``PetscCellOperator`` is the natural
+starting point because both the input and output live in the cell space.
+
+Operator application and algebra
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Once constructed, ``PetscOperator`` supports:
+
+- Application to compatible PETSc vectors
+- Application to ``Field3D`` when the input space is cell space
+- ``transpose()`` to swap input and output spaces
+- Operator addition: ``A + B``
+- Operator subtraction: ``A - B``
+- Scalar multiplication: ``A * alpha``
+- Operator composition: ``A * B`` when the inner and outer spaces match
+- Diagonal operator construction with ``PetscOperator::diagonal(...)`` for
+  same-space operators
+
+For example:
+
+.. code-block:: C++
+
+   auto Grad_plus = Inv_dl_plus * (Forward - Inject_plus);
+   auto Div_minus = Neg_inv_dV * Grad_plus.transpose() * DV_leg_plus;
+   auto Grad_par = ((Restrict_minus * Grad_plus)
+                    + (Restrict_plus * Grad_minus)) * 0.5;
+
+This operator algebra is one of the main advantages of the PETSc-based
+representation: once the primitive interpolation and injection operators exist,
+new support-operator constructions can be built by combining them directly.
+
+
+Example
+-------
+
+The basic usage pattern is:
+
+.. code-block:: C++
+
+   PetscOperators ops(mesh);
+   auto parallel = ops.getParallel();
+
+   Field3D f = ...;
+   mesh->communicate(f);
+   f.applyParallelBoundary("parallel_neumann_o1");
+
+   Field3D grad_f = parallel.Grad_par(f);
+   Field3D div_grad_f = parallel.Div_par_Grad_par(f);
+
+   Field3D K = 1.0;
+   mesh->communicate(K);
+   K.applyParallelBoundary("parallel_neumann_o1");
+
+   Field3D diffusive = parallel.Div_par_K_Grad_par(K, f);
+
+The integrated test in ``tests/integrated/test-petsc-operators`` provides a
+more complete example comparing these PETSc operators with the existing
+field-based parallel operators on an FCI grid.
+
+
+Relation to the standard parallel operators
+-------------------------------------------
+
+The standard routines in :ref:`sec-diffops` operate directly on fields and are
+the default choice in most models. The PETSc FCI operators documented here are
+an additional interface for constructing sparse matrix operators from FCI geometry.
+The main advantage is that sparse matrices can be manipulated to e.g. calculate
+divergence operators from gradient operators (the Support Operator Method).
+
+In practice:
+
+- Use :ref:`sec-diffops` for the usual BOUT++ differential-operator workflow
+- Use this page when you need the PETSc/FCI operator construction explicitly
+
+
+Performance and limitations
+---------------------------
+
+Operator setup is substantially more expensive than applying an already-built
+operator, because the PETSc matrices must be assembled from the FCI metadata.
+Construct the operators once, then reuse them.
+
+These operators also require additional memory for the PETSc matrices and
+vectors, so they are best suited to cases where that setup cost is justified by
+repeated operator application or by the need for the support-operator
+construction.
+
+Current limitations include:
+
+- The interface is intended for FCI grids, not the identity or shifted-metric
+  transforms
+- PETSc and 3D metrics are required
+- The grid metadata must be generated ahead of time
+
+
+See also
+--------
+
+- :ref:`sec-diffops`
+- :ref:`sec-fci`
+- :ref:`sec-parallel-bc-fci`
+- :ref:`sec-petsc`

From 421ab80d9f866d9aac55ad28d1eeef3cc30cdeb4 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 30 Jun 2026 11:39:43 +0100
Subject: [PATCH 1533/1827] Fedora CI: Run integrated tests via cmake rather
 than ctest

---
 .ci_fedora.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci_fedora.sh b/.ci_fedora.sh
index 5021df22c6..a29a146d58 100755
--- a/.ci_fedora.sh
+++ b/.ci_fedora.sh
@@ -64,4 +64,4 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
 	 -DBOUT_USE_SYSTEM_CPPTRACE=ON
 
     time make -C build build-check -j 2
-    cd build && time ctest --output-on-failure --timeout 300
+    cd build && time cmake --build . --target check

From 38bd12b379e591a76c89d4fc632414cb3e58c4d3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:13:25 +0200
Subject: [PATCH 1534/1827] Cleanup: run test_snb directly

---
 tests/integrated/test-snb/runtest     | 6 ------
 tests/integrated/test-snb/test_snb.py | 2 +-
 2 files changed, 1 insertion(+), 7 deletions(-)
 delete mode 100755 tests/integrated/test-snb/runtest

diff --git a/tests/integrated/test-snb/runtest b/tests/integrated/test-snb/runtest
deleted file mode 100755
index 6aaee40a22..0000000000
--- a/tests/integrated/test-snb/runtest
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-
-#requires: not metric_3d
-
-make
-./test_snb
diff --git a/tests/integrated/test-snb/test_snb.py b/tests/integrated/test-snb/test_snb.py
index 1095b40a70..925db99092 100644
--- a/tests/integrated/test-snb/test_snb.py
+++ b/tests/integrated/test-snb/test_snb.py
@@ -1,2 +1,2 @@
 def test_runtest(assert_success_in_shell):
-    assert_success_in_shell("./runtest")
+    assert_success_in_shell("./test_snb")

From 50bb963b5304e88a79ec32966bd2089d0384c923 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:14:24 +0200
Subject: [PATCH 1535/1827] Cleanup: remove magic comments

---
 tests/integrated/test-backtrace/test_backtrace.py            | 2 --
 tests/integrated/test-cyclic/test_cyclic.py                  | 3 ---
 .../test-drift-instability/test_drift_instability.py         | 2 --
 tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py  | 5 -----
 tests/integrated/test-gyro/test_gyro.py                      | 5 -----
 .../test_interchange_instability.py                          | 5 -----
 .../integrated/test-laplacexy-short/test_laplacexy_short.py  | 3 ---
 .../test-laplacexy2-hypre/test_laplacexy2_hypre.py           | 3 ---
 tests/integrated/test-naulin-laplace/test_naulin_laplace.py  | 3 ---
 .../test_petsc_laplace_MAST_grid.py                          | 4 ----
 tests/integrated/test-slepc-solver/test_slepc_solver.py      | 2 --
 tests/integrated/test-vec/test_vec.py                        | 2 --
 12 files changed, 39 deletions(-)

diff --git a/tests/integrated/test-backtrace/test_backtrace.py b/tests/integrated/test-backtrace/test_backtrace.py
index 4572010c62..e93d5e13d2 100755
--- a/tests/integrated/test-backtrace/test_backtrace.py
+++ b/tests/integrated/test-backtrace/test_backtrace.py
@@ -2,8 +2,6 @@
 
 # Test enabling/disabling exception backtrace from environment variable
 
-# requires all_tests
-
 from boututils.run_wrapper import shell
 import os
 
diff --git a/tests/integrated/test-cyclic/test_cyclic.py b/tests/integrated/test-cyclic/test_cyclic.py
index 38a2d70012..19f78a48d9 100755
--- a/tests/integrated/test-cyclic/test_cyclic.py
+++ b/tests/integrated/test-cyclic/test_cyclic.py
@@ -4,9 +4,6 @@
 # Run the test, check it completed successfully
 #
 
-# Requires: netcdf
-# Cores: 4
-
 from boututils.run_wrapper import shell, launch
 from sys import stdout
 
diff --git a/tests/integrated/test-drift-instability/test_drift_instability.py b/tests/integrated/test-drift-instability/test_drift_instability.py
index e8db2d9798..45b927fc59 100644
--- a/tests/integrated/test-drift-instability/test_drift_instability.py
+++ b/tests/integrated/test-drift-instability/test_drift_instability.py
@@ -4,8 +4,6 @@
 # Run the test, compare results against the benchmark
 #
 
-# Requires: not metric_3d
-
 import pytest
 import numpy as np
 
diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
index a88cc182e0..499db2c030 100755
--- a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
+++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
@@ -4,11 +4,6 @@
 # Run the test, compare results
 #
 
-# Requires: all_tests
-# Requires: netcdf
-# Requires: not metric_3d
-# Cores: 4
-
 import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
diff --git a/tests/integrated/test-gyro/test_gyro.py b/tests/integrated/test-gyro/test_gyro.py
index 5f2f984ea0..d8a8978263 100755
--- a/tests/integrated/test-gyro/test_gyro.py
+++ b/tests/integrated/test-gyro/test_gyro.py
@@ -4,11 +4,6 @@
 #
 # Run the test, compare results against the benchmark
 #
-
-# requires: not metric_3d
-# Requires: netcdf
-# Cores: 4
-
 import pytest
 import numpy as np
 from sys import stdout
diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index 2bc9b1c461..1442fc898f 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -3,11 +3,6 @@
 #
 # Run the test, compare results against the benchmark
 #
-
-# requires: not metric_3d
-# requires: netcdf
-# cores: 2
-
 import numpy as np
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
diff --git a/tests/integrated/test-laplacexy-short/test_laplacexy_short.py b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
index 135c04141b..d24ad14efd 100755
--- a/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
+++ b/tests/integrated/test-laplacexy-short/test_laplacexy_short.py
@@ -4,9 +4,6 @@
 # Run the test, compare results against the benchmark
 #
 
-# requires: not metric_3d
-# requires: petsc
-# cores: 8
 
 import pytest
 from boututils.run_wrapper import shell, launch, launch_safe
diff --git a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
index 8b1a75942d..189d364650 100755
--- a/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
+++ b/tests/integrated/test-laplacexy2-hypre/test_laplacexy2_hypre.py
@@ -4,9 +4,6 @@
 # Run the test, compare results against the benchmark
 #
 
-# requires: hypre
-# cores: 8
-
 import pytest
 from boutdata.collect import collect
 from boututils.run_wrapper import launch_safe, shell
diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
index e252cfed54..32958c58de 100755
--- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
+++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.py
@@ -1,8 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: not metric_3d
-# Cores: 3
-
 import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
diff --git a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
index 5489a47736..1ecdc5a99a 100755
--- a/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
+++ b/tests/integrated/test-petsc_laplace_MAST-grid/test_petsc_laplace_MAST_grid.py
@@ -4,10 +4,6 @@
 # Run the test, compare results against the benchmark
 #
 
-# requires: all_tests
-# requires: petsc
-# cores: 4
-
 import pytest
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
diff --git a/tests/integrated/test-slepc-solver/test_slepc_solver.py b/tests/integrated/test-slepc-solver/test_slepc_solver.py
index 2df73df018..dd09216739 100755
--- a/tests/integrated/test-slepc-solver/test_slepc_solver.py
+++ b/tests/integrated/test-slepc-solver/test_slepc_solver.py
@@ -1,7 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: slepc
-
 from boutdata.collect import collect
 from boututils.run_wrapper import launch_safe
 import numpy.testing as npt
diff --git a/tests/integrated/test-vec/test_vec.py b/tests/integrated/test-vec/test_vec.py
index ff2e14d608..2fa84e8686 100755
--- a/tests/integrated/test-vec/test_vec.py
+++ b/tests/integrated/test-vec/test_vec.py
@@ -1,7 +1,5 @@
 #!/usr/bin/env python3
 
-# Cores: 4
-
 from boututils.run_wrapper import launch_safe
 
 

From c1e2216588d4a60180b3ecf38e892854ee85430e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:14:42 +0200
Subject: [PATCH 1536/1827] Remove copy-pasted comment

---
 tests/integrated/test-yupdown/test_yupdown.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py
index e5b4b162cf..452170910b 100755
--- a/tests/integrated/test-yupdown/test_yupdown.py
+++ b/tests/integrated/test-yupdown/test_yupdown.py
@@ -37,7 +37,7 @@ def run_case(shift_type, variable):
 @pytest.mark.parametrize("variable", variables)
 def test_case(shift_type, variable):
     # MPI oversubscribe
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"
 
     success = run_case(shift_type, variable)
     assert success, f"Test failed for shift_type={shift_type}, variable={variable}"

From b7dc440e85f945919ea6c42d318e2928b534e2cb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:17:18 +0200
Subject: [PATCH 1537/1827] Do not duplicate runs for different variables

---
 tests/integrated/test-yupdown/test_yupdown.py | 25 ++++++++++---------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py
index 452170910b..566ede706a 100755
--- a/tests/integrated/test-yupdown/test_yupdown.py
+++ b/tests/integrated/test-yupdown/test_yupdown.py
@@ -6,7 +6,6 @@
 from numpy import max, abs
 
 shift_types = ["shifted", "shiftedinterp"]
-variables = [("ddy", "ddy_check"), ("ddy2", "ddy_check")]
 
 
 def run_case(shift_type, variable):
@@ -20,24 +19,26 @@ def run_case(shift_type, variable):
     with open("run.log", "w") as f:
         f.write(out)
 
-    v, v_check = variable
-    print("Testing %s and %s ... " % (v, v_check))
-    ddy = collect(v, path="data", xguards=False, yguards=False, info=False)
-    ddy_check = collect(v_check, path="data", xguards=False, yguards=False, info=False)
+    ret = True
+    for v, v_check in [("ddy", "ddy_check"), ("ddy2", "ddy_check")]:
+        print("Testing %s and %s ... " % (v, v_check))
+        ddy = collect(v, path="data", xguards=False, yguards=False, info=False)
+        ddy_check = collect(
+            v_check, path="data", xguards=False, yguards=False, info=False
+        )
 
-    diff = max(abs(ddy - ddy_check))
+        diff = max(abs(ddy - ddy_check))
 
-    print(f"shifttype: {shift_type} Max difference {diff}")
-    if diff < 2e-5:
-        return True
-    return False
+        print(f"shifttype: {shift_type} Max difference {diff}")
+        if diff >= 2e-5:
+            ret = False
+    return ret
 
 
 @pytest.mark.parametrize("shift_type", shift_types)
-@pytest.mark.parametrize("variable", variables)
 def test_case(shift_type, variable):
     # MPI oversubscribe
     os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"
 
     success = run_case(shift_type, variable)
-    assert success, f"Test failed for shift_type={shift_type}, variable={variable}"
+    assert success, f"Test failed for shift_type={shift_type}"

From 3e91960bc8849c9dcec64fdde1d102fe4ee2e8ed Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:19:08 +0200
Subject: [PATCH 1538/1827] prefer launch for MPI aware jobs

---
 tests/integrated/test-beuler/test_beuler.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/integrated/test-beuler/test_beuler.py b/tests/integrated/test-beuler/test_beuler.py
index ab028a9c2e..9ed8fc7327 100755
--- a/tests/integrated/test-beuler/test_beuler.py
+++ b/tests/integrated/test-beuler/test_beuler.py
@@ -1,13 +1,11 @@
 #!/usr/bin/env python3
 
-# requires: petsc
-
-from boututils.run_wrapper import shell_safe
+from boututils.run_wrapper import launch_safe
 
 
 def test_beuler():
     print("Running solver test")
-    status, out = shell_safe("./test_beuler", pipe=True)
+    status, out = launch_safe("./test_beuler", nproc=1, mthread=1, pipe=True)
     with open("run.log", "w") as f:
         f.write(out)
 

From 6e0c09a97805e9fbc280286f2f0b44eb13f8eb49 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:19:26 +0200
Subject: [PATCH 1539/1827] Remove print statement

---
 tests/integrated/test-boutpp/print/test_boutpp_print.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/integrated/test-boutpp/print/test_boutpp_print.py b/tests/integrated/test-boutpp/print/test_boutpp_print.py
index 26934a0080..4305f65d42 100644
--- a/tests/integrated/test-boutpp/print/test_boutpp_print.py
+++ b/tests/integrated/test-boutpp/print/test_boutpp_print.py
@@ -9,7 +9,6 @@ def test_boutpp_print(run_isolated):
     msg = "Can we print to the log from python? 🎉 __does_it_still__work {} {:s}"
     cmd = ["python3", "test.py", msg]
 
-    print(f"+ python3 test.py {msg} > out.log")
     with open("out.log", "w") as f:
         subprocess.run(cmd, stdout=f, check=True)
 

From f7b6510ab3c2f61e054d4dee5cf8ac7b0b8d4e30 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:19:45 +0200
Subject: [PATCH 1540/1827] Ensure we always have a Path object

---
 tests/integrated/test-command-args/test_command_args.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/integrated/test-command-args/test_command_args.py b/tests/integrated/test-command-args/test_command_args.py
index c8f786ef4f..8dc66ef7af 100755
--- a/tests/integrated/test-command-args/test_command_args.py
+++ b/tests/integrated/test-command-args/test_command_args.py
@@ -8,7 +8,9 @@
 import platform
 
 
-OUTPUT_FILE = Path("stdout.log") if platform.system() == "FreeBSD" else "stderr.log"
+OUTPUT_FILE = (
+    Path("stdout.log") if platform.system() == "FreeBSD" else Path("stderr.log")
+)
 
 
 class TestCommandLineArgs(unittest.TestCase):

From 264e6997501f343ae28a74cdf6146e3d903b4249 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:23:04 +0200
Subject: [PATCH 1541/1827] output errors

---
 tests/integrated/test-fci-mpi/test_fci_mpi.py | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/tests/integrated/test-fci-mpi/test_fci_mpi.py b/tests/integrated/test-fci-mpi/test_fci_mpi.py
index 51d5795d3f..05df0bf974 100755
--- a/tests/integrated/test-fci-mpi/test_fci_mpi.py
+++ b/tests/integrated/test-fci-mpi/test_fci_mpi.py
@@ -32,17 +32,17 @@ def run_case(nxpe: int, nype: int, mthread: int):
     def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
         run_case(nxpe, nype, mthread)
 
-        failures = []
+        failures = ""
 
         for name, val in ref.items():
             try:
                 npt.assert_allclose(val, collect(name, **COLLECT_KW))
             except AssertionError as e:
-                failures.append((nxpe, nype, name, e))
+                failures += f"\ncase {nxpe=} {nype=} {name=}\n{e}"
 
         return failures
 
-    failures = []
+    failures = ""
 
     for implementation in ["hermitespline", "monotonichermitespline"]:
         for nslice in NSLICES:
@@ -66,13 +66,7 @@ def test_case(nxpe: int, nype: int, mthread: int, ref: dict) -> bool:
 
                 mthread = MAXCORES // (nxpe * nype)
                 failures_ = test_case(nxpe, nype, mthread, ref)
-                failures.extend(failures_)
+                failures += failures_
 
         success = len(failures) == 0
-
-        assert success, "\nSome tests failed:"
-
-        if not success:
-            for nxpe, nype, name, error in failures:
-                print("----------")
-                print(f"case {nxpe=} {nype=} {name=}\n{error}")
+        assert success, "\nSome tests failed:\n" + failures

From 421765592d88c22f7b89a7ce1b97cc70928459ac Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:23:20 +0200
Subject: [PATCH 1542/1827] Turn comment into assert

---
 .../test_griddata_yboundary_guards.py                          | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
index 6faf020dbc..f426767855 100755
--- a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
+++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
@@ -115,7 +115,8 @@ def test_griddata_yboundary_guards(topology, n_yguards):
                 numpy.arange(ny // 2) + checkfield[-1] + 1 + 2 * n_yguards
             )
             checkfield += list(numpy.arange(n_yguards) + checkfield[-1] + 1)
-    else:  # singlenull
+    else:
+        assert topology == "singlenull"
         if n_yguards == 0:
             # output has 2 y-guard cells, but grid file did not
             myg = 2

From 875711eece5e8ab844ea941d35dbf7463cec3a00 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:23:31 +0200
Subject: [PATCH 1543/1827] simplify code

---
 .../test_interchange_instability.py                           | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index 1442fc898f..c06ec98a0c 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -20,9 +20,7 @@ def test_interchange_instability():
     shell("rm data_10/BOUT.dmp.*")
 
     def growth_rate(path, nproc, log=False):
-        pipe = False
-        if log:
-            pipe = True
+        pipe = bool(log)
         s, out = launch_safe(
             "./2fluid -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe
         )

From 9b44341a91e4370a1139f480ea19e426a5f01c15 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:23:39 +0200
Subject: [PATCH 1544/1827] use context manager

---
 .../test_interchange_instability.py                          | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/integrated/test-interchange-instability/test_interchange_instability.py b/tests/integrated/test-interchange-instability/test_interchange_instability.py
index c06ec98a0c..af0006c930 100755
--- a/tests/integrated/test-interchange-instability/test_interchange_instability.py
+++ b/tests/integrated/test-interchange-instability/test_interchange_instability.py
@@ -25,9 +25,8 @@ def growth_rate(path, nproc, log=False):
             "./2fluid -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe
         )
         if pipe:
-            f = open(log, "w")
-            f.write(out)
-            f.close()
+            with open(log, "w") as f:
+                f.write(out)
         # Get time base
         tarr = collect("t_array", path=path)
         nt = len(tarr)

From 18194b8739bcf2b847ef03290f84fa86cdc7b1d0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:23:57 +0200
Subject: [PATCH 1545/1827] use f-string

---
 tests/integrated/test-interpolate-z/test_interpolate_z.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-interpolate-z/test_interpolate_z.py b/tests/integrated/test-interpolate-z/test_interpolate_z.py
index 7fdc02ea1b..7c2052fc21 100755
--- a/tests/integrated/test-interpolate-z/test_interpolate_z.py
+++ b/tests/integrated/test-interpolate-z/test_interpolate_z.py
@@ -46,8 +46,8 @@ def test_interpolate_z():
         for nx in nxlist:
             dx = 1.0 / (nx)
 
-            args = " mesh:nx={nx4} mesh:dx={dx} MZ={nx} zinterpolation:type={method}".format(
-                nx4=nx + 4, dx=dx, nx=nx, method=method
+            args = (
+                f" mesh:nx={nx + 4} mesh:dx={dx} MZ={nx} zinterpolation:type={method}"
             )
 
             cmd = "./test_interpolate" + args

From 176552dc94f388defc22ba61661208bb709e923f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:26:27 +0200
Subject: [PATCH 1546/1827] Run all tests

---
 tests/integrated/test-invpar/test_invpar.py | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/tests/integrated/test-invpar/test_invpar.py b/tests/integrated/test-invpar/test_invpar.py
index c7fd0fc565..74a09897c5 100755
--- a/tests/integrated/test-invpar/test_invpar.py
+++ b/tests/integrated/test-invpar/test_invpar.py
@@ -49,14 +49,7 @@ def test_invpar():
             s, _ = launch(cmd + " -q -q -q " + f, nproc=nproc, mthread=1)
 
             code += s
-
-            if s == 0:
-                print("PASSED")
-            else:
-                print("FAILED")
-            assert s == 0, f"Test failed for flag={f}"
-
-    if code == 0:
-        print(" => All inversion tests passed")
-    else:
-        print(" => Some failed tests")
+            print(
+                "Run with flags {f} and {nproc} cores {'PASSED' if s == 0 else 'FAILED'}"
+            )
+    assert code == 0, "Some tests failed"

From e1e9f4417c0ef3892b46f1a09fc10007c9070ea1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:27:50 +0200
Subject: [PATCH 1547/1827] Remove stale code

This is only useful if run independently, which is not possible anymore
---
 tests/integrated/test-squash/test_squash.py | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/tests/integrated/test-squash/test_squash.py b/tests/integrated/test-squash/test_squash.py
index ab13380811..dc570a5455 100755
--- a/tests/integrated/test-squash/test_squash.py
+++ b/tests/integrated/test-squash/test_squash.py
@@ -3,7 +3,6 @@
 import itertools
 import time
 import numpy as np
-import argparse
 import re
 from boututils.datafile import DataFile
 from boututils.run_wrapper import launch_safe, shell_safe
@@ -80,16 +79,7 @@ def verify(f1, f2):
 
 
 def test_squash():
-    parser = argparse.ArgumentParser(description="Test the bout-squashoutput wrapper")
-    parser.add_argument(
-        "executable",
-        help="Path to bout-squashoutput",
-        default="../../../bin",
-        nargs="?",
-    )
-    args = parser.parse_args()
-
-    bout_squashoutput = Path(args.executable + "/bout-squashoutput")
+    bout_squashoutput = Path("../../../bin/bout-squashoutput")
 
     if not Path.exists(bout_squashoutput):
         bout_squashoutput = "bout-squashoutput"

From 454b53f968355f068a9fad3bdc07a1d83af7481f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:28:17 +0200
Subject: [PATCH 1548/1827] Simplify expression

---
 .../test-invertable-operator/test_invertable_operator.py      | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/integrated/test-invertable-operator/test_invertable_operator.py b/tests/integrated/test-invertable-operator/test_invertable_operator.py
index 3a8379f323..dad2cba758 100755
--- a/tests/integrated/test-invertable-operator/test_invertable_operator.py
+++ b/tests/integrated/test-invertable-operator/test_invertable_operator.py
@@ -22,9 +22,7 @@
 
 
 def run(path, nproc, log=False):
-    pipe = False
-    if log:
-        pipe = True
+    pipe = bool(log)
     s, out = launch_safe(
         "./invertable_operator -d " + path, nproc=nproc, mthread=nthreads, pipe=pipe
     )

From a7e16c28389d6976ccd8c66e4c730023f3a652d0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:28:29 +0200
Subject: [PATCH 1549/1827] Remove commented out code

---
 .../test-twistshift-staggered/test_twistshift_staggered.py     | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
index 19eca67f68..af11015c58 100755
--- a/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
+++ b/tests/integrated/test-twistshift-staggered/test_twistshift_staggered.py
@@ -18,9 +18,6 @@ def test_twistshift_staggered():
     test_aligned = collect("test_aligned", path=datapath, yguards=True, info=False)
     check = collect("check", path=datapath, yguards=True, info=False)
 
-    # from boututils.showdata import showdata
-    # showdata([test, test_aligned, check], titles=['test', 'test_aligned', 'check'])
-
     success = True
 
     # Check test_aligned is *not* periodic in y

From 44700a2a41802ebab9304952e5cbf0db66e0c826 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:28:45 +0200
Subject: [PATCH 1550/1827] status is always true

---
 tests/integrated/test-vec/test_vec.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/integrated/test-vec/test_vec.py b/tests/integrated/test-vec/test_vec.py
index 2fa84e8686..3c232e1f17 100755
--- a/tests/integrated/test-vec/test_vec.py
+++ b/tests/integrated/test-vec/test_vec.py
@@ -5,9 +5,7 @@
 
 def test_vec():
 
-    status, out = launch_safe("./testVec", nproc=4, pipe=True)
+    _, out = launch_safe("./testVec", nproc=4, pipe=True)
 
     with open("run.log.4", "w") as f:
         f.write(out)
-
-    assert not status, " => Test failed"

From 1b8826f212b93a06dc1292c3fcf483dfb173d586 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:29:07 +0200
Subject: [PATCH 1551/1827] status is always true

---
 tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py | 2 +-
 tests/integrated/test-initial/test_initial.py               | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
index 499db2c030..7cf1347329 100755
--- a/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
+++ b/tests/integrated/test-fieldgroupComm/test_fieldgroupComm.py
@@ -26,7 +26,7 @@ def test_fieldgroupcomm(nproc):
     shell(["rm -f data/BOUT.dmp.*.nc"])
 
     print(f"Running FieldGroup comm test on {nproc} processor(s)...")
-    s, out = launch_safe(cmd, nproc=nproc, pipe=True)
+    _, out = launch_safe(cmd, nproc=nproc, pipe=True)
     with open(f"run.log.{nproc}", "w") as f:
         f.write(out)
 
diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index 55bc162a4b..d3b10b1dbd 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -177,7 +177,7 @@ def test_initial(nproc):
     for coord in ["var_x", "var_y", "var_z"]:
         varlist.remove(coord)
 
-    status, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
+    _, out = launch_safe(cmd, nproc=nproc, pipe=True, verbose=True)
     with open(f"run.log.{nproc}", "w") as f:
         f.write(out)
 

From ca1ca0e2943355f3ec5d261fb8ca9361b8dc982b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:47:03 +0200
Subject: [PATCH 1552/1827] Remove legacy magic comments

---
 tests/MMS/GBS/runtest.broken                       |  2 --
 tests/MMS/advection/arakawa/runtest                |  3 ---
 tests/MMS/advection/central/runtest                |  3 ---
 tests/MMS/advection/upwind/runtest                 |  3 ---
 tests/MMS/advection/weno3/runtest                  |  3 ---
 tests/MMS/bracket/runtest                          |  3 ---
 tests/MMS/derivatives3/runtest                     |  3 ---
 tests/MMS/shiftedmetricinterp/runtest              |  3 ---
 tests/MMS/spatial/fci/runtest                      |  3 ---
 tests/MMS/time-petsc/runtest                       |  6 +-----
 tests/MMS/upwinding3/runtest                       |  3 ---
 tests/README.md                                    | 14 ++------------
 .../test_boutpp_collect_staggered.py               |  3 ---
 .../test-boutpp/collect/test_boutpp_collect.py     |  3 ---
 .../legacy-model/test_boutpp_legacy_model.py       |  3 ---
 .../test-boutpp/mms-ddz/test_boutpp_mms_ddz.py     |  3 ---
 .../simple-model/test_boutpp_simple_model.py       |  3 ---
 .../integrated/test-boutpp/slicing/test_slicing.py |  2 --
 tests/integrated/test-collect/test_collect.py      |  2 --
 .../test-communications/test_communications.py     |  3 ---
 .../test-coordinates-initialization/runtest        |  2 --
 .../test-datafilefacade/test_datafile_facade.py    |  2 --
 tests/integrated/test-delp2/test_delp2.py          |  2 --
 .../test_griddata_yboundary_guards.py              |  3 ---
 tests/integrated/test-initial/test_initial.py      |  4 ----
 .../test_invertable_operator.py                    |  5 -----
 tests/integrated/test-invpar/test_invpar.py        |  4 ----
 .../test-laplace-hypre3d/test_laplace_hypre3d.py   |  2 --
 .../test-laplace-petsc3d/test_laplace_petsc3d.py   |  2 --
 tests/integrated/test-laplace/test_laplace.py      |  4 ----
 .../test-laplacexy-fv/test_laplacexy_fv.py         |  4 ----
 tests/integrated/test-laplacexy/test_laplacexy.py  |  5 -----
 tests/integrated/test-laplacexz/test_laplacexz.py  |  3 ---
 .../test-options-netcdf/test_options_netcdf.py     |  2 --
 .../test-petsc_laplace/test_petsc_laplace.py       |  4 ----
 .../test-region-iterator/test_region_iterator.py   |  3 ---
 .../integrated/test-restart-io/test_restart_io.py  |  2 --
 tests/integrated/test-smooth/test_smooth.py        |  3 ---
 tests/integrated/test-squash/test_squash.py        |  4 ----
 39 files changed, 3 insertions(+), 128 deletions(-)

diff --git a/tests/MMS/GBS/runtest.broken b/tests/MMS/GBS/runtest.broken
index b30eb8b2bc..a653b8ef7c 100755
--- a/tests/MMS/GBS/runtest.broken
+++ b/tests/MMS/GBS/runtest.broken
@@ -1,7 +1,5 @@
 #!/bin/bash
 
-#requires: all_tests
-
 for test in slab2d slab3d
 do
     if ! ./runtest-$test
diff --git a/tests/MMS/advection/arakawa/runtest b/tests/MMS/advection/arakawa/runtest
index 44a07c8f56..f099331b6f 100755
--- a/tests/MMS/advection/arakawa/runtest
+++ b/tests/MMS/advection/arakawa/runtest
@@ -1,8 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: all_tests
-# Requires: not make
-
 import parent
 
 parent.make_parent()
diff --git a/tests/MMS/advection/central/runtest b/tests/MMS/advection/central/runtest
index 66e9450160..ffc4d621bf 100755
--- a/tests/MMS/advection/central/runtest
+++ b/tests/MMS/advection/central/runtest
@@ -1,8 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: all_tests
-# Requires: not make
-
 import parent
 
 parent.make_parent()
diff --git a/tests/MMS/advection/upwind/runtest b/tests/MMS/advection/upwind/runtest
index a0fed59ee9..dbc351a97c 100755
--- a/tests/MMS/advection/upwind/runtest
+++ b/tests/MMS/advection/upwind/runtest
@@ -1,8 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: all_tests
-# Requires: not make
-
 import parent
 
 parent.make_parent()
diff --git a/tests/MMS/advection/weno3/runtest b/tests/MMS/advection/weno3/runtest
index 773e3f044c..d923c2717d 100755
--- a/tests/MMS/advection/weno3/runtest
+++ b/tests/MMS/advection/weno3/runtest
@@ -1,8 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: all_tests
-# Requires: not make
-
 import parent
 
 parent.make_parent()
diff --git a/tests/MMS/bracket/runtest b/tests/MMS/bracket/runtest
index 19c2add599..907ec2d694 100755
--- a/tests/MMS/bracket/runtest
+++ b/tests/MMS/bracket/runtest
@@ -11,9 +11,6 @@ from builtins import str
 
 import numpy as np
 
-# Requires: boutpp
-# requires: not make
-
 import boutpp as bc
 
 bc.init("-q -q -q")
diff --git a/tests/MMS/derivatives3/runtest b/tests/MMS/derivatives3/runtest
index 9064bd93dc..7d88f92572 100755
--- a/tests/MMS/derivatives3/runtest
+++ b/tests/MMS/derivatives3/runtest
@@ -2,9 +2,6 @@
 
 import boutpp
 
-# requires boutpp
-# requires not make
-
 import numpy as np
 import itertools
 from sys import exit
diff --git a/tests/MMS/shiftedmetricinterp/runtest b/tests/MMS/shiftedmetricinterp/runtest
index 6accc4b181..bba9f1ab06 100755
--- a/tests/MMS/shiftedmetricinterp/runtest
+++ b/tests/MMS/shiftedmetricinterp/runtest
@@ -2,9 +2,6 @@
 
 import boutpp
 
-# requires boutpp
-# requires not make
-
 from boutdata.data import BoutOptionsFile
 import numpy as np
 import itertools
diff --git a/tests/MMS/spatial/fci/runtest b/tests/MMS/spatial/fci/runtest
index 9dd4d1817f..cd2104aa3e 100755
--- a/tests/MMS/spatial/fci/runtest
+++ b/tests/MMS/spatial/fci/runtest
@@ -3,9 +3,6 @@
 # Python script to run and analyse MMS test
 #
 
-# Cores: 2
-# requires: zoidberg
-
 import argparse
 import json
 import pathlib
diff --git a/tests/MMS/time-petsc/runtest b/tests/MMS/time-petsc/runtest
index 0ceac22bc3..832a086e68 100755
--- a/tests/MMS/time-petsc/runtest
+++ b/tests/MMS/time-petsc/runtest
@@ -1,7 +1,3 @@
 #!/usr/bin/env sh
 
-#requires: petsc
-#requires: not make
-#requires: all_tests
-
-(cd ../time && ./runtest only_petsc )
\ No newline at end of file
+(cd ../time && ./runtest only_petsc )
diff --git a/tests/MMS/upwinding3/runtest b/tests/MMS/upwinding3/runtest
index 15ab296cad..01bc83fea3 100755
--- a/tests/MMS/upwinding3/runtest
+++ b/tests/MMS/upwinding3/runtest
@@ -2,9 +2,6 @@
 
 import boutpp
 
-# requires boutpp
-# requires not make
-
 import numpy as np
 import itertools
 from sys import exit
diff --git a/tests/README.md b/tests/README.md
index 3725a1b985..1defe24de5 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -38,15 +38,5 @@ them to be run for every commit or pull request.
 ## Test requirements
 
 Some tests require a particular library to be available, or are known
-to not work or take too long in a particular environment (looking
-at you Travis). The integrated and MMS test scripts (called "runtest")
-can contain lines starting with "#requires", which specify what that
-test requires. If a requirement is not met, then the test is skipped.
-
-The "requirements" subdirectory contains python code to handle these
-requirements (in "__init__.py"), and some scripts which are used to
-test for some requirements.
-
-
-
-
+to not work or take too long in a particular environment. They must be
+declared in the CMakeLists.txt
diff --git a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
index d88595e434..254245396a 100755
--- a/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
+++ b/tests/integrated/test-boutpp/collect-staggered/test_boutpp_collect_staggered.py
@@ -2,9 +2,6 @@
 
 import boutpp as bc
 
-# requires boutpp
-# requires not make
-
 
 def test_boutpp_collect_staggered(run_isolated):
 
diff --git a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
index 89ad9d6b5b..2596a79263 100755
--- a/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
+++ b/tests/integrated/test-boutpp/collect/test_boutpp_collect.py
@@ -3,9 +3,6 @@
 import numpy as np
 from boutdata import collect
 
-# requires boutpp
-# requires not make
-
 
 def test_boutpp_collect(run_isolated):
 
diff --git a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
index d1f6ea736a..938487fc8f 100755
--- a/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
+++ b/tests/integrated/test-boutpp/legacy-model/test_boutpp_legacy_model.py
@@ -1,9 +1,6 @@
 #!/usr/bin/env python3
 import boutpp
 
-# requires boutpp
-# requires not make
-
 
 def test_boutpp_legacy_model(run_isolated):
 
diff --git a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
index 1e2421e59b..87c69d414c 100755
--- a/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
+++ b/tests/integrated/test-boutpp/mms-ddz/test_boutpp_mms_ddz.py
@@ -2,9 +2,6 @@
 import boutpp
 import numpy as np
 
-# requires boutpp
-# requires not make
-
 
 def test_boutpp_mms_ddz(run_isolated):
 
diff --git a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
index a443f22cd8..56ef07f152 100755
--- a/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
+++ b/tests/integrated/test-boutpp/simple-model/test_boutpp_simple_model.py
@@ -1,8 +1,5 @@
 #!/usr/bin/env python3
 
-# requires boutpp
-# requires not make
-
 import boutpp
 
 
diff --git a/tests/integrated/test-boutpp/slicing/test_slicing.py b/tests/integrated/test-boutpp/slicing/test_slicing.py
index cffc767bf8..166825adf8 100755
--- a/tests/integrated/test-boutpp/slicing/test_slicing.py
+++ b/tests/integrated/test-boutpp/slicing/test_slicing.py
@@ -1,6 +1,4 @@
 #!/usr/bin/env python3
-# requires boutpp
-# requires not make
 import numpy as np
 import numpy.testing as npt
 import boutpp as bc
diff --git a/tests/integrated/test-collect/test_collect.py b/tests/integrated/test-collect/test_collect.py
index eade57557a..c8204b1ca9 100755
--- a/tests/integrated/test-collect/test_collect.py
+++ b/tests/integrated/test-collect/test_collect.py
@@ -1,7 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: all_tests
-
 from boututils.run_wrapper import shell_safe
 
 from boutdata import collect
diff --git a/tests/integrated/test-communications/test_communications.py b/tests/integrated/test-communications/test_communications.py
index 75150ccde1..51beb1f537 100755
--- a/tests/integrated/test-communications/test_communications.py
+++ b/tests/integrated/test-communications/test_communications.py
@@ -5,9 +5,6 @@
 from boututils.datafile import DataFile
 from boututils.run_wrapper import shell, launch_safe
 
-# Cores: 18
-# Requires: netcdf
-
 # Note, the expected values for the communicated cells, which are used to test the
 # results, are shown in corner_communication_diagram.ods
 
diff --git a/tests/integrated/test-coordinates-initialization/runtest b/tests/integrated/test-coordinates-initialization/runtest
index 60c3e3c980..3d73c8fdef 100755
--- a/tests/integrated/test-coordinates-initialization/runtest
+++ b/tests/integrated/test-coordinates-initialization/runtest
@@ -1,7 +1,5 @@
 #!/usr/bin/env bash
 
-# Cores: 3
-
 make || exit
 
 test -z $MPIRUN  && MPIRUN='mpirun -np'
diff --git a/tests/integrated/test-datafilefacade/test_datafile_facade.py b/tests/integrated/test-datafilefacade/test_datafile_facade.py
index ae1cb9ef3c..2f1e3a5187 100755
--- a/tests/integrated/test-datafilefacade/test_datafile_facade.py
+++ b/tests/integrated/test-datafilefacade/test_datafile_facade.py
@@ -2,8 +2,6 @@
 #
 # Test the DataFileFacade interface by writing to dump files using the SAVE_ONCE macro
 #
-# requires: netcdf
-# cores: 2
 
 import pytest
 import numpy
diff --git a/tests/integrated/test-delp2/test_delp2.py b/tests/integrated/test-delp2/test_delp2.py
index b3a16eded9..4f48974537 100755
--- a/tests/integrated/test-delp2/test_delp2.py
+++ b/tests/integrated/test-delp2/test_delp2.py
@@ -1,6 +1,4 @@
 #!/usr/bin/env python3
-# requires: fftw
-# cores: 4
 
 import pytest
 import numpy as np
diff --git a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
index f426767855..6f96acd8e2 100755
--- a/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
+++ b/tests/integrated/test-griddata-yboundary-guards/test_griddata_yboundary_guards.py
@@ -1,8 +1,5 @@
 #!/usr/bin/env python3
 
-# Cores: 6
-# Requires: netcdf
-
 import pytest
 import numpy
 from pathlib import Path
diff --git a/tests/integrated/test-initial/test_initial.py b/tests/integrated/test-initial/test_initial.py
index d3b10b1dbd..3a803cc163 100755
--- a/tests/integrated/test-initial/test_initial.py
+++ b/tests/integrated/test-initial/test_initial.py
@@ -14,10 +14,6 @@
 from boututils.run_wrapper import shell, launch_safe
 from boutdata.collect import collect
 
-# requires not make
-# requires scipy
-# cores: 4
-
 ########################################
 # Implementations of BOUT++ functions
 
diff --git a/tests/integrated/test-invertable-operator/test_invertable_operator.py b/tests/integrated/test-invertable-operator/test_invertable_operator.py
index dad2cba758..f7b40e4204 100755
--- a/tests/integrated/test-invertable-operator/test_invertable_operator.py
+++ b/tests/integrated/test-invertable-operator/test_invertable_operator.py
@@ -1,9 +1,4 @@
 #!/usr/bin/env python3
-
-# requires: petsc
-# requires: not metric_3d
-# cores: 2
-
 #
 # Run the test, compare results against expected value
 #
diff --git a/tests/integrated/test-invpar/test_invpar.py b/tests/integrated/test-invpar/test_invpar.py
index 74a09897c5..6a911821be 100755
--- a/tests/integrated/test-invpar/test_invpar.py
+++ b/tests/integrated/test-invpar/test_invpar.py
@@ -4,10 +4,6 @@
 # Run the test, check it completed successfully
 #
 
-# requires: not metric_3d
-# Requires: netcdf
-# Cores: 4
-
 from boututils.run_wrapper import shell, launch
 
 
diff --git a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
index 6c5f87dc24..e2fa11c13a 100755
--- a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
+++ b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
@@ -1,7 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: hypre
-
 from boutdata import collect
 from boututils.run_wrapper import launch_safe
 
diff --git a/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
index 3a255d48a7..02ab98b23c 100755
--- a/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
+++ b/tests/integrated/test-laplace-petsc3d/test_laplace_petsc3d.py
@@ -1,7 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: petsc
-
 from boutdata import collect
 from boututils.run_wrapper import launch
 
diff --git a/tests/integrated/test-laplace/test_laplace.py b/tests/integrated/test-laplace/test_laplace.py
index 254485a6a0..b2460c5d3a 100755
--- a/tests/integrated/test-laplace/test_laplace.py
+++ b/tests/integrated/test-laplace/test_laplace.py
@@ -5,10 +5,6 @@
 # Run the test, compare results against the benchmark
 #
 
-# requires: not metric_3d
-# Requires: netcdf
-# Cores: 4
-
 import pytest
 import numpy.testing as npt
 from boututils.run_wrapper import shell, launch_safe
diff --git a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
index 03f12c04b7..0e11b7be45 100755
--- a/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
+++ b/tests/integrated/test-laplacexy-fv/test_laplacexy_fv.py
@@ -4,10 +4,6 @@
 # Run the test, compare results against the benchmark
 #
 
-# requires: not metric_3d
-# requires: petsc
-# cores: 8
-
 import pytest
 from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
diff --git a/tests/integrated/test-laplacexy/test_laplacexy.py b/tests/integrated/test-laplacexy/test_laplacexy.py
index 1976e851f3..fd32b9b223 100755
--- a/tests/integrated/test-laplacexy/test_laplacexy.py
+++ b/tests/integrated/test-laplacexy/test_laplacexy.py
@@ -4,11 +4,6 @@
 # Run the test, compare results against the benchmark
 #
 
-# requires: not metric_3d
-# requires: petsc
-# requires: all_tests
-# cores: 8
-
 import pytest
 from boututils.run_wrapper import shell, launch, launch_safe
 from boutdata.collect import collect
diff --git a/tests/integrated/test-laplacexz/test_laplacexz.py b/tests/integrated/test-laplacexz/test_laplacexz.py
index 02a7239285..4262aa0ada 100755
--- a/tests/integrated/test-laplacexz/test_laplacexz.py
+++ b/tests/integrated/test-laplacexz/test_laplacexz.py
@@ -1,8 +1,5 @@
 #!/usr/bin/env python3
 
-# requires: not metric_3d
-# requires: petsc
-
 #
 # Run the test, compare results against the benchmark
 #
diff --git a/tests/integrated/test-options-netcdf/test_options_netcdf.py b/tests/integrated/test-options-netcdf/test_options_netcdf.py
index f8a4a92b01..1147249b99 100755
--- a/tests/integrated/test-options-netcdf/test_options_netcdf.py
+++ b/tests/integrated/test-options-netcdf/test_options_netcdf.py
@@ -1,8 +1,6 @@
 #!/usr/bin/env python3
 
 # Note: This test requires NCDF4, whereas on Travis NCDF is used
-# requires: netcdf
-# requires: not legacy_netcdf
 
 from boututils.datafile import DataFile
 from boututils.run_wrapper import shell, launch_safe as launch
diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
index 3ac9a802f1..3a977d4f98 100755
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.py
@@ -4,10 +4,6 @@
 # Run the test, compare results against the benchmark
 #
 
-# requires: petsc
-# requires: all_tests
-# cores: 4
-
 import pathlib
 import pytest
 from boututils.run_wrapper import shell, launch_safe
diff --git a/tests/integrated/test-region-iterator/test_region_iterator.py b/tests/integrated/test-region-iterator/test_region_iterator.py
index 7b5f25599d..c7f84de6a4 100755
--- a/tests/integrated/test-region-iterator/test_region_iterator.py
+++ b/tests/integrated/test-region-iterator/test_region_iterator.py
@@ -4,9 +4,6 @@
 # Run the test, check it completed successfully
 #
 
-# requires: netcdf
-# cores: 2
-
 from boututils.run_wrapper import launch_safe
 
 
diff --git a/tests/integrated/test-restart-io/test_restart_io.py b/tests/integrated/test-restart-io/test_restart_io.py
index f37e56f5c1..2d5cb373c9 100755
--- a/tests/integrated/test-restart-io/test_restart_io.py
+++ b/tests/integrated/test-restart-io/test_restart_io.py
@@ -2,8 +2,6 @@
 #
 # Test file I/O by loading from restart files and writing to dump files
 #
-# requires: netcdf
-# cores: 4
 
 from boutdata import restart
 from boutdata.collect import collect
diff --git a/tests/integrated/test-smooth/test_smooth.py b/tests/integrated/test-smooth/test_smooth.py
index 40858eb15e..6c4fecc712 100755
--- a/tests/integrated/test-smooth/test_smooth.py
+++ b/tests/integrated/test-smooth/test_smooth.py
@@ -4,9 +4,6 @@
 # Run the test, compare results against the benchmark
 #
 
-# Requires: netcdf
-# Cores: 4
-
 import pytest
 import numpy as np
 import itertools
diff --git a/tests/integrated/test-squash/test_squash.py b/tests/integrated/test-squash/test_squash.py
index dc570a5455..58501be718 100755
--- a/tests/integrated/test-squash/test_squash.py
+++ b/tests/integrated/test-squash/test_squash.py
@@ -8,10 +8,6 @@
 from boututils.run_wrapper import launch_safe, shell_safe
 from pathlib import Path
 
-# requires: all_tests
-# requires: netcdf
-# cores: 4
-
 IGNORED_VARS_PATTERN = re.compile(
     "(wtime|ncalls|arkode|cvode|run_id|run_restart_from|M.?SUB|N.?PE|iteration|wall_time|has_legacy_netcdf|hist_hi|openmp_threads).*"
 )

From 8aa63cb5e436f834c47359e3a4e28c7997db6ce2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 14:48:38 +0200
Subject: [PATCH 1553/1827] Fixup test_yupdown

---
 tests/integrated/test-yupdown/test_yupdown.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py
index 566ede706a..ec7df3bbef 100755
--- a/tests/integrated/test-yupdown/test_yupdown.py
+++ b/tests/integrated/test-yupdown/test_yupdown.py
@@ -8,7 +8,7 @@
 shift_types = ["shifted", "shiftedinterp"]
 
 
-def run_case(shift_type, variable):
+def run_case(shift_type):
     s, out = launch_safe(
         "./test_yupdown mesh:paralleltransform:type=" + shift_type,
         nproc=1,
@@ -36,9 +36,9 @@ def run_case(shift_type, variable):
 
 
 @pytest.mark.parametrize("shift_type", shift_types)
-def test_case(shift_type, variable):
+def test_case(shift_type):
     # MPI oversubscribe
     os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"
 
-    success = run_case(shift_type, variable)
+    success = run_case(shift_type)
     assert success, f"Test failed for shift_type={shift_type}"

From 88af6c53288a7ab3cb69029129a4a243609ef922 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 15:29:02 +0200
Subject: [PATCH 1554/1827] Revert "prefer launch for MPI aware jobs"

This reverts commit 3e91960bc8849c9dcec64fdde1d102fe4ee2e8ed.

We do not call MPI_finalize.
This make mpirun unhappy.
---
 tests/integrated/test-beuler/test_beuler.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/integrated/test-beuler/test_beuler.py b/tests/integrated/test-beuler/test_beuler.py
index 9ed8fc7327..ab028a9c2e 100755
--- a/tests/integrated/test-beuler/test_beuler.py
+++ b/tests/integrated/test-beuler/test_beuler.py
@@ -1,11 +1,13 @@
 #!/usr/bin/env python3
 
-from boututils.run_wrapper import launch_safe
+# requires: petsc
+
+from boututils.run_wrapper import shell_safe
 
 
 def test_beuler():
     print("Running solver test")
-    status, out = launch_safe("./test_beuler", nproc=1, mthread=1, pipe=True)
+    status, out = shell_safe("./test_beuler", pipe=True)
     with open("run.log", "w") as f:
         f.write(out)
 

From 1608fe4ab0f51c2bcbb77d759da67c980aa79b90 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 15:31:25 +0200
Subject: [PATCH 1555/1827] Return BoutReal for computed values

---
 include/bout/boundary_region_iter.hxx | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index aaf7ac37c9..2e08e4366f 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -146,23 +146,20 @@ public:
   /// off = 1 is the last point in the domain
   /// off = 2 is the second to last point in the domain
   template <bool check = true>
-  BoutReal& getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
-                  int off) const {
+  BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
+                 int off) const {
     return static_cast<const impl*>(this)->template _getAt<check>(func, off);
   }
   /// Get the first point in the boundary
-  const BoutReal&
-  next(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+  BoutReal next(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
     return static_cast<const impl*>(this)->_getAt(func, 0);
   }
   /// Get the last point in the domain
-  const BoutReal&
-  current(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+  BoutReal current(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
     return static_cast<const impl*>(this)->_getAt(func, 1);
   }
   /// Get the second to last point in the domain - this may not be valid and thus throw
-  const BoutReal&
-  prev(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+  BoutReal prev(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
     return static_cast<const impl*>(this)->_getAt(func, 2);
   }
 

From 2819acf0c5a0e8a06188d670d38c6796429c59b9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 15:32:44 +0200
Subject: [PATCH 1556/1827] Fix sign error

---
 include/bout/boundary_region_iter.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 2e08e4366f..fd8012802c 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -704,7 +704,7 @@ inline BoundaryRegionX* NewBoundaryRegionXOut(const std::string& name, int ymin,
 inline BoundaryRegionY* NewBoundaryRegionYUp(const std::string& name, int xmin, int xmax,
                                              Mesh* mesh) {
   auto* pointer = new BoundaryRegionY(
-      name, -1, mesh,
+      name, 1, mesh,
       Region<Ind3D>(xmin, xmax, mesh->yend, mesh->yend, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
   pointer->legacy = new ::BoundaryRegionYUp(name, xmin, xmax, mesh);
@@ -714,7 +714,7 @@ inline BoundaryRegionY* NewBoundaryRegionYUp(const std::string& name, int xmin,
 inline BoundaryRegionY* NewBoundaryRegionYDown(const std::string& name, int xmin,
                                                int xmax, Mesh* mesh) {
   auto* pointer = new BoundaryRegionY(
-      name, 1, mesh,
+      name, -1, mesh,
       Region<Ind3D>(xmin, xmax, mesh->ystart, mesh->ystart, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
   pointer->legacy = new ::BoundaryRegionYDown(name, xmin, xmax, mesh);

From 2ad43242f332cd4f70197db25a8f146be954c1f0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 30 Jun 2026 15:33:52 +0200
Subject: [PATCH 1557/1827] Switch to bout::boundary::BoundaryRegionY*

---
 include/bout/yboundary_regions.hxx | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 6bce1119db..cbb2ab59fa 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -85,13 +85,12 @@ public:
         }
       }
     } else {
-      if (lower_y) {
-        boundary_regions.push_back(
-            std::make_shared<NewBoundaryRegionY>(mesh, true, mesh.iterateBndryLowerY()));
-      }
-      if (upper_y) {
-        boundary_regions.push_back(
-            std::make_shared<NewBoundaryRegionY>(mesh, false, mesh.iterateBndryUpperY()));
+      for (auto* bndry : mesh.getBoundaries()) {
+        if ((lower_y && bndry->location == BndryLoc::ydown)
+            or (upper_y && bndry->location == BndryLoc::yup)) {
+          boundary_regions.push_back(
+              dynamic_cast<bout::boundary::BoundaryRegionY*>(bndry));
+        }
       }
     }
     // Cache boundary regions
@@ -139,7 +138,7 @@ private:
     }
   }
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>> boundary_regions_par;
-  std::vector<std::shared_ptr<NewBoundaryRegionY>> boundary_regions;
+  std::vector<bout::boundary::BoundaryRegionY*> boundary_regions;
 
   std::vector<BoutMask> _contains;
 };

From 82035472d481fc69842a3bbec13626be2811cc15 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 30 Jun 2026 15:25:10 +0100
Subject: [PATCH 1558/1827] Collect all errors and assert at the end

---
 tests/integrated/test-yupdown/test_yupdown.py | 22 ++++++++-----------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/tests/integrated/test-yupdown/test_yupdown.py b/tests/integrated/test-yupdown/test_yupdown.py
index ec7df3bbef..6d9f5de9e4 100755
--- a/tests/integrated/test-yupdown/test_yupdown.py
+++ b/tests/integrated/test-yupdown/test_yupdown.py
@@ -8,7 +8,11 @@
 shift_types = ["shifted", "shiftedinterp"]
 
 
-def run_case(shift_type):
+@pytest.mark.parametrize("shift_type", shift_types)
+def test_case(shift_type):
+
+    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # MPI oversubscribe
+
     s, out = launch_safe(
         "./test_yupdown mesh:paralleltransform:type=" + shift_type,
         nproc=1,
@@ -19,7 +23,7 @@ def run_case(shift_type):
     with open("run.log", "w") as f:
         f.write(out)
 
-    ret = True
+    errors = []
     for v, v_check in [("ddy", "ddy_check"), ("ddy2", "ddy_check")]:
         print("Testing %s and %s ... " % (v, v_check))
         ddy = collect(v, path="data", xguards=False, yguards=False, info=False)
@@ -29,16 +33,8 @@ def run_case(shift_type):
 
         diff = max(abs(ddy - ddy_check))
 
-        print(f"shifttype: {shift_type} Max difference {diff}")
+        print(f"shifttype: {shift_type} | {v} Max difference {diff}")
         if diff >= 2e-5:
-            ret = False
-    return ret
-
-
-@pytest.mark.parametrize("shift_type", shift_types)
-def test_case(shift_type):
-    # MPI oversubscribe
-    os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"
+            errors.append(f"{v} exceeded tolerance (diff: {diff})")
 
-    success = run_case(shift_type)
-    assert success, f"Test failed for shift_type={shift_type}"
+    assert not errors, f"Failures for {shift_type}:\n" + "\n".join(errors)

From fc2d560c9e71ec1ff9b7172677294649bcde1804 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 30 Jun 2026 14:22:55 -0700
Subject: [PATCH 1559/1827] Capture git diff when building

- Generates a git diff on build, so the diff used when compiling
  is stored, not the diff when configuring. Handles out-of-source
  builds and cases where the source is not under git e.g. release
  tarballs.

- Stores the diff as a string in a compilation unit git_metadata.cxx

- Saves to output, along with flags indicating whether the diff
  was available, and whether the build had uncommitted changes.
---
 CMakeLists.txt                              |  22 +++-
 cmake/GenerateGitMetadata.cmake             | 126 ++++++++++++++++++++
 include/bout/git_metadata.hxx               |  21 ++++
 manual/sphinx/user_docs/output_and_post.rst |  28 ++++-
 manual/sphinx/user_docs/running_bout.rst    |  12 +-
 src/bout++.cxx                              |  15 +++
 6 files changed, 213 insertions(+), 11 deletions(-)
 create mode 100644 cmake/GenerateGitMetadata.cmake
 create mode 100644 include/bout/git_metadata.hxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3caf4d8caf..c594e47c03 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -389,6 +389,7 @@ set(BOUT_SOURCES
     ./src/sys/timer.cxx
     ./src/sys/type_name.cxx
     ./src/sys/utils.cxx
+    ./include/bout/git_metadata.hxx
     ${CMAKE_CURRENT_BINARY_DIR}/include/bout/revision.hxx
     ${CMAKE_CURRENT_BINARY_DIR}/include/bout/version.hxx
 )
@@ -520,8 +521,26 @@ add_custom_command(
   MAIN_DEPENDENCY "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateDateTimeFile.cmake"
 )
 
-add_library(bout++ ${BOUT_SOURCES} ${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx)
+set(BOUT_GIT_METADATA_SOURCE ${CMAKE_CURRENT_BINARY_DIR}/git_metadata.cxx)
+set_source_files_properties(
+  ${BOUT_GIT_METADATA_SOURCE} PROPERTIES GENERATED TRUE
+)
+add_custom_target(
+  bout++-git-metadata
+  COMMAND
+    ${CMAKE_COMMAND} -DOUTPUT_FILE=${BOUT_GIT_METADATA_SOURCE}
+    -DSOURCE_DIR=${PROJECT_SOURCE_DIR} -DGIT_EXECUTABLE=${GIT_EXECUTABLE} -P
+    "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateGitMetadata.cmake"
+  BYPRODUCTS ${BOUT_GIT_METADATA_SOURCE}
+  COMMENT "Generating git metadata source"
+)
+
+add_library(
+  bout++ ${BOUT_SOURCES} ${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx
+         ${BOUT_GIT_METADATA_SOURCE}
+)
 add_library(bout++::bout++ ALIAS bout++)
+add_dependencies(bout++ bout++-git-metadata)
 target_link_libraries(bout++ PUBLIC MPI::MPI_CXX)
 target_include_directories(
   bout++
@@ -566,6 +585,7 @@ set(BOUT_VERSION_MINOR ${PROJECT_VERSION_MINOR})
 set(BOUT_VERSION_PATCH ${PROJECT_VERSION_PATCH})
 
 # Get the git commit
+find_package(Git QUIET)
 include(GetGitRevisionDescription)
 get_git_head_revision(GIT_REFSPEC BOUT_REVISION)
 if(BOUT_REVISION STREQUAL "GITDIR-NOTFOUND")
diff --git a/cmake/GenerateGitMetadata.cmake b/cmake/GenerateGitMetadata.cmake
new file mode 100644
index 0000000000..65451d0a39
--- /dev/null
+++ b/cmake/GenerateGitMetadata.cmake
@@ -0,0 +1,126 @@
+function(escape_cxx_string input output)
+  set(value "${input}")
+  string(REPLACE "\\" "\\\\" value "${value}")
+  string(REPLACE "\"" "\\\"" value "${value}")
+  string(REPLACE "\r" "" value "${value}")
+  string(REPLACE "\n" "\\n\"\n\"" value "${value}")
+  set(${output}
+      "${value}"
+      PARENT_SCOPE
+  )
+endfunction()
+
+set(git_metadata_available false)
+set(git_dirty false)
+set(git_diff "")
+
+if(NOT DEFINED OUTPUT_FILE)
+  message(FATAL_ERROR "OUTPUT_FILE must be set")
+endif()
+if(NOT DEFINED SOURCE_DIR)
+  message(FATAL_ERROR "SOURCE_DIR must be set")
+endif()
+
+if(NOT DEFINED GIT_EXECUTABLE OR GIT_EXECUTABLE STREQUAL "")
+  find_program(GIT_EXECUTABLE git)
+endif()
+
+if(GIT_EXECUTABLE)
+  execute_process(
+    COMMAND "${GIT_EXECUTABLE}" rev-parse --is-inside-work-tree
+    WORKING_DIRECTORY "${SOURCE_DIR}"
+    RESULT_VARIABLE git_repo_result
+    OUTPUT_VARIABLE git_repo_output
+    ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+
+  if(git_repo_result EQUAL 0 AND git_repo_output STREQUAL "true")
+    set(git_metadata_available true)
+
+    execute_process(
+      COMMAND "${GIT_EXECUTABLE}" rev-parse --verify HEAD
+      WORKING_DIRECTORY "${SOURCE_DIR}"
+      RESULT_VARIABLE git_head_result
+      OUTPUT_QUIET ERROR_QUIET
+    )
+
+    if(git_head_result EQUAL 0)
+      execute_process(
+        COMMAND "${GIT_EXECUTABLE}" diff --no-ext-diff --binary HEAD --
+        WORKING_DIRECTORY "${SOURCE_DIR}"
+        RESULT_VARIABLE git_diff_result
+        OUTPUT_VARIABLE git_diff
+        ERROR_QUIET
+      )
+      if(NOT git_diff_result EQUAL 0)
+        set(git_diff "")
+      endif()
+    else()
+      execute_process(
+        COMMAND "${GIT_EXECUTABLE}" diff --no-ext-diff --binary --cached --
+        WORKING_DIRECTORY "${SOURCE_DIR}"
+        RESULT_VARIABLE git_cached_diff_result
+        OUTPUT_VARIABLE git_cached_diff
+        ERROR_QUIET
+      )
+      if(NOT git_cached_diff_result EQUAL 0)
+        set(git_cached_diff "")
+      endif()
+
+      execute_process(
+        COMMAND "${GIT_EXECUTABLE}" diff --no-ext-diff --binary --
+        WORKING_DIRECTORY "${SOURCE_DIR}"
+        RESULT_VARIABLE git_worktree_diff_result
+        OUTPUT_VARIABLE git_worktree_diff
+        ERROR_QUIET
+      )
+      if(NOT git_worktree_diff_result EQUAL 0)
+        set(git_worktree_diff "")
+      endif()
+
+      set(git_diff "${git_cached_diff}")
+      if(NOT git_cached_diff STREQUAL "" AND NOT git_worktree_diff STREQUAL "")
+        string(APPEND git_diff "\n")
+      endif()
+      string(APPEND git_diff "${git_worktree_diff}")
+    endif()
+
+    if(NOT git_diff STREQUAL "")
+      set(git_dirty true)
+    endif()
+  endif()
+endif()
+
+escape_cxx_string("${git_diff}" git_diff_escaped)
+
+set(output_tmp "${OUTPUT_FILE}.tmp")
+file(WRITE "${output_tmp}" "#include \"bout/git_metadata.hxx\"\n\n")
+file(APPEND "${output_tmp}" "namespace bout {\n")
+file(APPEND "${output_tmp}" "namespace version {\n")
+file(APPEND "${output_tmp}" "namespace {\n")
+file(
+  APPEND "${output_tmp}"
+  "constexpr bool git_metadata_available_value = ${git_metadata_available};\n"
+)
+file(APPEND "${output_tmp}" "constexpr bool git_dirty_value = ${git_dirty};\n")
+file(APPEND "${output_tmp}" "constexpr char git_diff_value[] =\n")
+file(APPEND "${output_tmp}" "\"${git_diff_escaped}\";\n")
+file(APPEND "${output_tmp}" "} // namespace\n\n")
+file(
+  APPEND "${output_tmp}"
+  "auto git_metadata_available() -> bool { return git_metadata_available_value; }\n"
+)
+file(APPEND "${output_tmp}"
+     "auto git_dirty() -> bool { return git_dirty_value; }\n"
+)
+file(APPEND "${output_tmp}"
+     "auto git_diff() -> std::string_view { return git_diff_value; }\n"
+)
+file(APPEND "${output_tmp}" "} // namespace version\n")
+file(APPEND "${output_tmp}" "} // namespace bout\n")
+
+execute_process(
+  COMMAND "${CMAKE_COMMAND}" -E copy_if_different "${output_tmp}"
+          "${OUTPUT_FILE}"
+)
+execute_process(COMMAND "${CMAKE_COMMAND}" -E rm -f "${output_tmp}")
diff --git a/include/bout/git_metadata.hxx b/include/bout/git_metadata.hxx
new file mode 100644
index 0000000000..0fc1018cdb
--- /dev/null
+++ b/include/bout/git_metadata.hxx
@@ -0,0 +1,21 @@
+#ifndef BOUT_GIT_METADATA_H
+#define BOUT_GIT_METADATA_H
+
+#include <string_view>
+
+namespace bout {
+namespace version {
+
+/// True if git metadata could be collected for this build.
+auto git_metadata_available() -> bool;
+
+/// True if the source tree had tracked uncommitted changes at build time.
+auto git_dirty() -> bool;
+
+/// Diff of tracked changes in the source tree at build time.
+auto git_diff() -> std::string_view;
+
+} // namespace version
+} // namespace bout
+
+#endif // BOUT_GIT_METADATA_H
diff --git a/manual/sphinx/user_docs/output_and_post.rst b/manual/sphinx/user_docs/output_and_post.rst
index 71f4098113..33ad5e2498 100644
--- a/manual/sphinx/user_docs/output_and_post.rst
+++ b/manual/sphinx/user_docs/output_and_post.rst
@@ -135,7 +135,7 @@ is the ``BoutData`` class.
     >>> from boutdata.data import BoutData
     >>> d = BoutData(path=".")
 
-where the path is optional, and should point to the directory containing the BOUT.inp 
+where the path is optional, and should point to the directory containing the BOUT.inp
 (input) and BOUT.dmp.* (output) files. This will return a dictionary with keys
 "path" (the given path to the data), "options" (the input options) and "outputs" (the output data).
 The tree of options can be printed:
@@ -152,7 +152,7 @@ The tree of options can be printed:
        |   |- bndry_all = neumann
        |   |- scale = 0.0
        |- phisolver
-       |   |- fourth_order = true        
+       |   |- fourth_order = true
        ...
 
 and accessed as a tree of dictionaries:
@@ -177,7 +177,7 @@ In a similar way the outputs are available as dictionary keys:
     ...
     >>> d["outputs"]["rho_s"]
     0.00092165524660235405
-    
+
 There are several modules available for reading NetCDF files, so to
 provide a consistent interface, file access is wrapped into a class
 DataFile. This provides a simple interface for reading and writing files
@@ -257,7 +257,7 @@ To plot data, a convenient wrapper around matplotlib is ``plotdata``
 
     from boutdata import collect
     n = collect("n") # Read data as NumPy array [t,x,y,z]
-    
+
     from boututils.plotdata import plotdata
     plotdata(n[-1,:,0,:])
 
@@ -272,7 +272,7 @@ It is sometimes useful to see an animation of a simulation. To do this there is
 
     from boutdata import collect
     n = collect("n") # Read data as NumPy array [t,x,y,z]
-    
+
     from boututils.showdata import showdata
     showdata(n[:,:,0,:])
 
@@ -642,6 +642,24 @@ data, BOUT++ saves some metadata into output files.
    +---------------------------------------------------------------------------+
    | Variables                                                                 |
    +=============================+=============================================+
+   | `BOUT_VERSION`              | BOUT++ version as a double.                 |
+   +-----------------------------+---------------------------------------------+
+   | `bout_git_hash`             | Git hash of the BOUT++ version that the     |
+   |                             | code was compiled with.                     |
+   +-----------------------------+---------------------------------------------+
+   | `bout_git_diff`             | Git diff of tracked changes in the BOUT++   |
+   |                             | source tree when the code was built. Empty  |
+   |                             | for a clean tree or when git metadata is    |
+   |                             | unavailable.                                |
+   +-----------------------------+---------------------------------------------+
+   | `bout_git_diff_available`   | True if BOUT++ could inspect the source     |
+   |                             | tree with git at build time. False for      |
+   |                             | release tarballs or builds without git.     |
+   +-----------------------------+---------------------------------------------+
+   | `bout_git_dirty`            | True if the source tree had tracked         |
+   |                             | uncommitted changes when the code was       |
+   |                             | built.                                      |
+   +-----------------------------+---------------------------------------------+
    | `run_id`                    | Unique identifier (UUID) for a run          |
    +-----------------------------+---------------------------------------------+
    | `run_restart_from`          | If the run was restarted, the `run_id` of   |
diff --git a/manual/sphinx/user_docs/running_bout.rst b/manual/sphinx/user_docs/running_bout.rst
index 59c5b53828..9d49a010f6 100644
--- a/manual/sphinx/user_docs/running_bout.rst
+++ b/manual/sphinx/user_docs/running_bout.rst
@@ -269,6 +269,7 @@ First comes the introductory blurb::
 
     BOUT++ version 4.4.0
     Revision: 7cfbc6890a82cb6b3b6c81870d8a8fca723de542
+    Git tree: clean
     Code compiled on Dec  7 2021 at 15:14:05
 
     B.Dudson (University of York), M.Umansky (LLNL) 2007
@@ -276,10 +277,12 @@ First comes the introductory blurb::
 
 The version number (4.4.0 here) gets increased occasionally after some
 major feature has been added. To help match simulations to code
-versions, the Git revision of the core BOUT++ code and the date and
-time it was compiled is recorded. This information makes it possible
-to verify precisely which version of the code was used for any given
-run.
+versions, the Git revision of the core BOUT++ code, whether the source
+tree was clean when it was built, and the date and time it was compiled
+is recorded. If BOUT++ is built from a git checkout with uncommitted
+tracked changes, the corresponding git diff is also saved in the output
+metadata. This information makes it possible to verify precisely which
+version of the code was used for any given run.
 
 The processor number comes next::
 
@@ -673,4 +676,3 @@ then the BOUT++ restart will fail.
 **Note** It is a good idea to set ``nxpe`` in the ``BOUT.inp`` file to be consistent with
 what you set here. If it is inconsistent then the restart will fail, but the error message may
 not be particularly enlightening.
-
diff --git a/src/bout++.cxx b/src/bout++.cxx
index cad3edf6c3..c6b39fc702 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -40,6 +40,7 @@ static constexpr auto DEFAULT_DIR = "data";
 #include "bout/build_defines.hxx"
 #include "bout/coordinates_accessor.hxx"
 #include "bout/dcomplex.hxx"
+#include "bout/git_metadata.hxx"
 #include "bout/globals.hxx"
 #include "bout/hyprelib.hxx"
 #include "bout/interpolation_xz.hxx"
@@ -541,6 +542,12 @@ void savePIDtoFile(const std::string& data_dir, int MYPE) {
 void printStartupHeader(int MYPE, int NPES) {
   output_progress.write(_f("BOUT++ version {:s}\n"), bout::version::full);
   output_progress.write(_f("Revision: {:s}\n"), bout::version::revision);
+  if (bout::version::git_metadata_available()) {
+    output_progress.write("Git tree: {}\n",
+                          bout::version::git_dirty() ? "dirty" : "clean");
+  } else {
+    output_progress.write("Git tree: unavailable\n");
+  }
 #ifdef MD5SUM
   output_progress.write("MD5 checksum: {:s}\n", BUILDFLAG(MD5SUM));
 #endif
@@ -682,6 +689,9 @@ void setRunStartInfo(Options& options) {
   // output BOUT.settings file was used as input
   runinfo["version"].force(bout::version::full, "Output");
   runinfo["revision"].force(bout::version::revision, "Output");
+  runinfo["git_diff"].force(std::string{bout::version::git_diff()}, "Output");
+  runinfo["git_diff_available"].force(bout::version::git_metadata_available(), "Output");
+  runinfo["git_dirty"].force(bout::version::git_dirty(), "Output");
 
   time_t start_time = time(nullptr);
   runinfo["started"].force(ctime(&start_time), "Output");
@@ -723,6 +733,11 @@ void addBuildFlagsToOptions(Options& options) {
   options["has_cuda"].force(bout::build::has_cuda);
   options["use_metric_3d"].force(bout::build::use_metric_3d);
   options["use_msgstack"].force(bout::build::use_msgstack);
+  options["bout_git_hash"].force(bout::version::revision, "Output");
+  options["bout_git_diff"].force(std::string{bout::version::git_diff()}, "Output");
+  options["bout_git_diff_available"].force(bout::version::git_metadata_available(),
+                                           "Output");
+  options["bout_git_dirty"].force(bout::version::git_dirty(), "Output");
 }
 
 void writeSettingsFile(Options& options, const std::string& data_dir,

From 00c9b40984920e80f9630be758c25fad22cc879e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 09:47:53 +0200
Subject: [PATCH 1560/1827] Remove legacy implementation for FA

---
 include/bout/boundary_iterator.hxx | 121 -----------------------------
 1 file changed, 121 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 840a73f106..8d13a7c897 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -39,127 +39,6 @@ protected:
 public:
   BoundaryRegionIter& operator*() { return *this; }
 
-  void dirichlet_o1(Field3D& f, BoutReal value) const { ynext(f) = value; }
-  void dirichlet_o2(Field3D& f, BoutReal value) const {
-    ynext(f) = bout::parallel_stencil::dirichlet_o2(1, f[ind()], 0.5, value);
-  }
-  void dirichlet_o3(Field3D& f, BoutReal value) const {
-    ynext(f) = bout::parallel_stencil::dirichlet_o3(2, yprev(f), 1, f[ind()], 0.5, value);
-  }
-
-  BoutReal extrapolate_grad_o2(const Field3D& f) const { return f[ind()] - yprev(f); }
-
-  BoutReal extrapolate_boundary_o2(const Field3D& f) const {
-    return (f[ind()] * 3 - yprev(f)) * 0.5;
-  }
-
-  BoutReal extrapolate_next_o2(const Field3D& f) const {
-    return (2 * f[ind()]) - yprev(f);
-  }
-
-  BoutReal
-  extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return (2 * f(0, ind())) - f(0, ind().yp(-_by).xp(-_bx));
-  }
-
-  BoutReal interpolate_boundary_o2(const Field3D& f) const {
-    return (f[ind()] + ynext(f)) * 0.5;
-  }
-
-  BoutReal interpolate_boundary_o2(
-      const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return (f(0, ind()) + f(0, ind().yp(-_by).xp(-_bx))) * 0.5;
-  }
-
-  BoutReal extrapolate_boundary_o2(
-      const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return 0.5 * (3 * f(0, ind()) - f(0, ind().yp(-_by).xp(-_bx)));
-  }
-
-  BoutReal
-  extrapolate_boundary_free(const Field3D& f,
-                            bout::boundary::BoundaryFreeExtrapolation mode) const {
-    const BoutReal fac = bout::boundary::limitFreeScale(yprev(f), ythis(f), mode);
-    const BoutReal val = ythis(f);
-    const BoutReal next =
-        mode == bout::boundary::BoundaryFreeExtrapolation::linear ? val + fac : val * fac;
-    return 0.5 * (val + next);
-  }
-
-  void set_free(Field3D& f, bout::boundary::BoundaryFreeExtrapolation mode) const {
-    const BoutReal fac = bout::boundary::limitFreeScale(yprev(f), ythis(f), mode);
-    BoutReal val = ythis(f);
-    if (mode == bout::boundary::BoundaryFreeExtrapolation::linear) {
-      for (int i = 1; i <= localmesh->ystart; ++i) {
-        val += fac;
-        f[ind().yp(_by * i).xp(_bx * i)] = val;
-      }
-    } else {
-      for (int i = 1; i <= localmesh->ystart; ++i) {
-        val *= fac;
-        f[ind().yp(_by * i).xp(_bx * i)] = val;
-      }
-    }
-  }
-
-  void limitFree(Field3D& f) const {
-    const BoutReal fac = bout::boundary::limitFreeScale(
-        yprev(f), ythis(f), bout::boundary::BoundaryFreeExtrapolation::limited);
-    BoutReal val = ythis(f);
-    for (int i = 1; i <= localmesh->ystart; ++i) {
-      val *= fac;
-      f[ind().yp(_by * i).xp(_bx * i)] = val;
-    }
-  }
-
-  bool is_lower() const {
-    ASSERT2(_bx == 0);
-    return _by == -1;
-  }
-
-  void neumann_o1(Field3D& f, BoutReal grad) const {
-    BoutReal val = ythis(f);
-    for (int i = 1; i <= localmesh->ystart; ++i) {
-      val += grad;
-      f[ind().yp(_by * i).xp(_bx * i)] = val;
-    }
-  }
-
-  void neumann_o2(Field3D& f, BoutReal grad) const {
-    BoutReal val = yprev(f) + grad;
-    for (int i = 1; i <= localmesh->ystart; ++i) {
-      val += grad;
-      f[ind().yp(_by * i).xp(_bx * i)] = val;
-    }
-  }
-
-  void limit_at_least(Field3D& f, BoutReal value) const {
-    ynext(f) = std::max(ynext(f), value);
-  }
-
-  BoutReal& ynext(Field3D& f) const { return f[ind().yp(_by).xp(_bx)]; }
-  const BoutReal& ynext(const Field3D& f) const { return f[ind().yp(_by).xp(_bx)]; }
-  BoutReal& yprev(Field3D& f) const { return f[ind().yp(-_by).xp(-_bx)]; }
-  const BoutReal& yprev(const Field3D& f) const { return f[ind().yp(-_by).xp(-_bx)]; }
-  BoutReal& ythis(Field3D& f) const { return f[ind()]; }
-  const BoutReal& ythis(const Field3D& f) const { return f[ind()]; }
-
-  void setYPrevIfValid(Field3D& f, BoutReal val) const { yprev(f) = val; }
-  void setAll(Field3D& f, const BoutReal val) const {
-    for (int i = -localmesh->ystart; i <= localmesh->ystart; ++i) {
-      f[ind().yp(_by * i).xp(_bx * i)] = val;
-    }
-  }
-
-  static int abs_offset() { return 1; }
-
-  BoutReal& ynext(Field2D& f) const { return f[ind().yp(_by).xp(_bx)]; }
-  const BoutReal& ynext(const Field2D& f) const { return f[ind().yp(_by).xp(_bx)]; }
-  BoutReal& yprev(Field2D& f) const { return f[ind().yp(-_by).xp(-_bx)]; }
-  const BoutReal& yprev(const Field2D& f) const { return f[ind().yp(-_by).xp(-_bx)]; }
-
-  int dir() const { return _dir; }
-
 protected:
   int x() const { return _x; }
   int y() const { return _y; }

From 2adbad5f96ce17de9cc8f92033e638a002ae6ff7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 09:57:26 +0200
Subject: [PATCH 1561/1827] Remove legacy implementation for FCI

---
 include/bout/parallel_boundary_region.hxx | 259 ----------------------
 1 file changed, 259 deletions(-)

diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 40c3474ffe..e6489acb53 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -89,265 +89,6 @@ public:
   // setter
   void setValid(signed char valid) { bndry_position->valid = valid; }
 
-  // extrapolate a given point to the boundary
-  BoutReal extrapolate_boundary_o1(const Field3D& f) const { return ythis(f); }
-  BoutReal extrapolate_boundary_o2(const Field3D& f) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_boundary_o1(f);
-    }
-    return ythis(f) * (1 + length(f.getLocation())) - yprev(f) * length(f.getLocation());
-  }
-  BoutReal extrapolate_boundary_o1(
-      const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return ythis(f);
-  }
-  BoutReal
-  extrapolate_boundary_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
-                          CELL_LOC loc = CELL_CENTRE) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_boundary_o1(f);
-    }
-    return ythis(f) * (1 + length(loc)) - yprev(f) * length(loc);
-  }
-
-  BoutReal interpolate_boundary_o2(const Field3D& f) const {
-    return ythis(f) * (1 - length(f.getLocation())) + ynext(f) * length(f.getLocation());
-  }
-  BoutReal
-  interpolate_boundary_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
-                          CELL_LOC loc = CELL_CENTRE) const {
-    return ythis(f) * (1 - length(loc)) + ynext(f) * length(loc);
-  }
-
-  BoutReal extrapolate_next_o1(const Field3D& f) const { return ythis(f); }
-  BoutReal extrapolate_next_o2(const Field3D& f) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_next_o1(f);
-    }
-    return ythis(f) * 2 - yprev(f);
-  }
-
-  BoutReal
-  extrapolate_next_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return ythis(f);
-  }
-  BoutReal
-  extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_next_o1(f);
-    }
-    return ythis(f) * 2 - yprev(f);
-  }
-
-  // extrapolate the gradient into the boundary
-  BoutReal extrapolate_grad_o1([[maybe_unused]] const Field3D& f) const { return 0; }
-  BoutReal extrapolate_grad_o2(const Field3D& f) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_grad_o1(f);
-    }
-    return ythis(f) - ynext(f);
-  }
-
-  BoundaryRegionParIterBase& operator*() { return *this; }
-
-  BoundaryRegionParIterBase& operator++() {
-    ++bndry_position;
-    return *this;
-  }
-
-  bool operator!=(const BoundaryRegionParIterBase& rhs) {
-    return bndry_position != rhs.bndry_position;
-  }
-
-#define ITER() for (int i = 0; i < localmesh->ystart - abs_offset(); ++i)
-  // dirichlet boundary code
-  void dirichlet_o1(Field3D& f, BoutReal value) const {
-    ITER() { getAt(f, i) = value; }
-  }
-
-  void dirichlet_o2(Field3D& f, BoutReal value) const {
-    if (length(f.getLocation()) < small_value) {
-      return dirichlet_o1(f, value);
-    }
-    ITER() {
-      getAt(f, i) = parallel_stencil::dirichlet_o2(
-          i + 1, ythis(f), i + 1 - length(f.getLocation()), value);
-    }
-  }
-
-  void dirichlet_o3(Field3D& f, BoutReal value) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return dirichlet_o2(f, value);
-    }
-    if (length(f.getLocation()) < small_value) {
-      ITER() {
-        getAt(f, i) = parallel_stencil::dirichlet_o2(
-            i + 2, yprev(f), i + 1 - length(f.getLocation()), value);
-      }
-    } else {
-      ITER() {
-        getAt(f, i) = parallel_stencil::dirichlet_o3(
-            i + 2, yprev(f), i + 1, ythis(f), i + 1 - length(f.getLocation()), value);
-      }
-    }
-  }
-
-  void limit_at_least(Field3D& f, BoutReal value) const {
-    ITER() {
-      if (getAt(f, i) < value) {
-        getAt(f, i) = value;
-      }
-    }
-  }
-
-  bool is_lower() const { return _dir == -1; }
-
-  // NB: value needs to be scaled by dy
-  // neumann_o1 is actually o2 if we would use an appropriate one-sided stencil.
-  // But in general we do not, and thus for normal C2 stencils, this is 1st order.
-  void neumann_o1(Field3D& f, BoutReal value) const {
-    ITER() { getAt(f, i) = ythis(f) + value * (i + 1); }
-  }
-
-  // NB: value needs to be scaled by dy
-  void neumann_o2(Field3D& f, BoutReal value) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return neumann_o1(f, value);
-    }
-    ITER() { getAt(f, i) = yprev(f) + (2 + i) * value; }
-  }
-
-  // NB: value needs to be scaled by dy
-  void neumann_o3(Field3D& f, BoutReal value) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return neumann_o2(f, value);
-    }
-    ITER() {
-      getAt(f, i) = parallel_stencil::neumann_o3(i + 1 - length(f.getLocation()), value,
-                                                 i + 1, ythis(f), 2, yprev(f));
-    }
-  }
-
-  // extrapolate into the boundary using only monotonic decreasing values.
-  // f needs to be positive
-  void limitFree(Field3D& f) const {
-    const auto fac = valid() > 0 ? limitFreeScale(yprev(f), ythis(f)) : 1;
-    auto val = ythis(f);
-    ITER() {
-      val *= fac;
-      getAt(f, i) = val;
-    }
-  }
-
-  BoutReal
-  extrapolate_boundary_free(const Field3D& f,
-                            bout::boundary::BoundaryFreeExtrapolation mode) const {
-    const auto fac =
-        valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
-                    : (mode == bout::boundary::BoundaryFreeExtrapolation::linear ? 0 : 1);
-    auto val = ythis(f);
-    BoutReal next =
-        mode == bout::boundary::BoundaryFreeExtrapolation::linear ? val + fac : val * fac;
-    return val * length(f.getLocation()) + next * (1 - length(f.getLocation()));
-  }
-
-  void set_free(Field3D& f, bout::boundary::BoundaryFreeExtrapolation mode) const {
-    const auto fac =
-        valid() > 0 ? limitFreeScale(yprev(f), ythis(f), mode)
-                    : (mode == bout::boundary::BoundaryFreeExtrapolation::linear ? 0 : 1);
-    auto val = ythis(f);
-    if (mode == bout::boundary::BoundaryFreeExtrapolation::linear) {
-      ITER() {
-        val += fac;
-        getAt(f, i) = val;
-      }
-    } else {
-      ITER() {
-        val *= fac;
-        getAt(f, i) = val;
-      }
-    }
-  }
-
-  void setAll(Field3D& f, const BoutReal val) const {
-    for (int i = -localmesh->ystart; i <= localmesh->ystart; ++i) {
-      f.ynext(i)[ind().yp(i)] = val;
-    }
-  }
-
-  template <bool check = true>
-  BoutReal& getAt(Field3D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
-    if constexpr (check) {
-      ASSERT3(valid() > -off - 2);
-    }
-    auto _off = offset() + off * _dir;
-    return f.ynext(_off)[ind().yp(_off)];
-  }
-  template <bool check = true>
-  const BoutReal& getAt(const Field3D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
-    if constexpr (check) {
-      ASSERT3(valid() > -off - 2);
-    }
-    auto _off = offset() + off * _dir;
-    return f.ynext(_off)[ind().yp(_off)];
-  }
-
-  const BoutReal& ynext(const Field3D& f) const { return getAt(f, 0); }
-  BoutReal& ynext(Field3D& f) const { return getAt(f, 0); }
-  const BoutReal& ythis(const Field3D& f) const { return getAt(f, -1); }
-  BoutReal& ythis(Field3D& f) const { return getAt(f, -1); }
-  const BoutReal& yprev(const Field3D& f) const { return getAt(f, -2); }
-  BoutReal& yprev(Field3D& f) const { return getAt(f, -2); }
-
-  template <bool check = true>
-  BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
-                 int off) const {
-    if constexpr (check) {
-      ASSERT3(valid() > -off - 2);
-    }
-    auto _off = offset() + off * _dir;
-    return f(_off, ind().yp(_off));
-  }
-  BoutReal ynext(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return getAt(f, 0);
-  }
-  BoutReal ythis(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return getAt(f, -1);
-  }
-  BoutReal yprev(const std::function<BoutReal(int yoffset, Ind3D ind)>& f) const {
-    return getAt(f, -2);
-  }
-
-  void setYPrevIfValid(Field3D& f, BoutReal val) const {
-    if (valid() > 0) {
-      yprev(f) = val;
-    }
-  }
-
-#if not(BOUT_USE_METRIC_3D)
-  const BoutReal& ynext(const Field2D& f) const { return f.ynext(_dir)[ind().yp(_dir)]; }
-  BoutReal& ynext(Field2D& f) const { return f.ynext(_dir)[ind().yp(_dir)]; }
-
-  const BoutReal& yprev(const Field2D& f) const {
-    ASSERT3(valid() > 0);
-    return f.ynext(-_dir)[ind().yp(-_dir)];
-  }
-  BoutReal& yprev(Field2D& f) const {
-    ASSERT3(valid() > 0);
-    return f.ynext(-_dir)[ind().yp(-_dir)];
-  }
-#endif
-
 private:
   const IndicesVec& bndry_points;
   IndicesIter bndry_position;

From b413c14f7a949b7e4d8237ca07a4eb5fa8ea8ab5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 09:57:46 +0200
Subject: [PATCH 1562/1827] Update documentation

---
 manual/sphinx/user_docs/boundary_options.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/manual/sphinx/user_docs/boundary_options.rst b/manual/sphinx/user_docs/boundary_options.rst
index 9718be8c5d..ec6e25202b 100644
--- a/manual/sphinx/user_docs/boundary_options.rst
+++ b/manual/sphinx/user_docs/boundary_options.rst
@@ -528,11 +528,11 @@ Here is a short summary of some members of ``point``, where ``f`` is a :
 
    * - Function
      - Description
-   * - ``point.ythis(f)``
+   * - ``point.current(f)``
      - Returns the value at the last point in the domain
-   * - ``point.ynext(f)``
+   * - ``point.next(f)``
      - Returns the value at the first point in the boundary, i.e. one beyond the domain.
-   * - ``point.yprev(f)``
+   * - ``point.prev(f)``
      - Returns the value at the second to last point in the domain, if it is
        valid. NB: this point may not be valid.
    * - ``point.interpolate_boundary_o2(f)``

From 69dc6b0d45f7a37355d7bf865fe61980af33a8d0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 09:58:13 +0200
Subject: [PATCH 1563/1827] Add more unit tests

---
 tests/unit/include/bout/test_yboundary.cxx | 63 +++++++++++++++++++---
 1 file changed, 55 insertions(+), 8 deletions(-)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index 1ae242da65..dc9da34a01 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -1,29 +1,31 @@
 #include "gtest/gtest.h"
 
 #include "bout/boutexception.hxx"
+#include "bout/output_bout_types.hxx"
 #include "bout/yboundary_regions.hxx"
 
 #include "fake_mesh_fixture.hxx"
 #include "test_extras.hxx"
 
-using YBTest = FakeMeshFixture_tmpl<3, 5, 7>;
+using YBTest = FakeMeshFixture_tmpl<4, 5, 7>;
 
 using bout::globals::mesh;
 
 TEST_F(YBTest, dirichlet_o2_rgn) {
+  dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](auto& point) { point.dirichlet_o2(test, 2); });
   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }
 
-// Not yet implemented for FA
-// TEST_F(YBTest, dirichlet_o3) {
-//   Field3D test = 1.0;
-//   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-//   sheath.iter([&](auto& point) { point.dirichlet_o3(test, 2); });
-//   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
-// }
+TEST_F(YBTest, bndry_size) {
+  dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  int sum = 0;
+  sheath.iter([&](auto& point) { sum++; });
+  EXPECT_EQ(sum, 28);
+}
 
 TEST_F(YBTest, interpolate_boundary_o2) {
   Field3D test = 1.0;
@@ -111,8 +113,53 @@ TEST_F(YBTest, extrapolate_grad_o2_square) {
   sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_grad_o2(test), 1); });
 }
 
+TEST_F(YBTest, extrapolate_next_o1_square) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_next_o1(test), 1); });
+}
+
 TEST_F(YBTest, extrapolate_next_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_next_o2(test), 2); });
 }
+
+TEST_F(YBTest, next_square) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
+}
+
+TEST_F(YBTest, current_square) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.current(test), 1); });
+}
+
+TEST_F(YBTest, prev_square) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
+}
+
+TEST_F(YBTest, getAt_square) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) {
+    EXPECT_DOUBLE_EQ(point.getAt(test, 0), 4);
+    EXPECT_DOUBLE_EQ(point.getAt(test, 1), 1);
+    EXPECT_DOUBLE_EQ(point.getAt(test, 2), 0);
+  });
+}
+
+TEST_F(YBTest, getAt_func) {
+  Field3D test = makeField<Field3D>([&](auto& i) { return i.y() - 2; }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  auto square = [&](int yo, Ind3D ind) -> double { return SQ(test[ind]); };
+  sheath.iter([&](auto& point) {
+    EXPECT_DOUBLE_EQ(point.getAt(square, 0), 4);
+    EXPECT_DOUBLE_EQ(point.getAt(square, 1), 1);
+    EXPECT_DOUBLE_EQ(point.getAt(square, 2), 0);
+  });
+}

From cc4a312833188ad7ac5acb32c24f20b9d9ce6db4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 10:30:51 +0200
Subject: [PATCH 1564/1827] Switch to shared_ptr for getBoundaries

---
 include/bout/boundary_factory.hxx         | 29 +++++++++++---------
 include/bout/boundary_region_iter.hxx     | 33 ++++++++++++-----------
 include/bout/mesh.hxx                     |  4 +--
 include/bout/yboundary_regions.hxx        |  6 ++---
 src/field/field3d.cxx                     |  6 ++---
 src/field/field_data.cxx                  |  2 +-
 src/mesh/boundary_factory.cxx             | 32 ++++++++++++----------
 src/mesh/impls/bout/boutmesh.cxx          | 16 +++++------
 src/mesh/impls/bout/boutmesh.hxx          |  4 +--
 tests/unit/fake_mesh.hxx                  | 10 ++++---
 tests/unit/field/test_vector3d.cxx        | 11 --------
 tests/unit/mesh/test_boundary_factory.cxx |  5 ++--
 12 files changed, 78 insertions(+), 80 deletions(-)

diff --git a/include/bout/boundary_factory.hxx b/include/bout/boundary_factory.hxx
index 5f1f6e06a6..46a6c04b01 100644
--- a/include/bout/boundary_factory.hxx
+++ b/include/bout/boundary_factory.hxx
@@ -13,17 +13,18 @@ class BoundaryRegion;
 class BoundaryModifier;
 
 #include <map>
+#include <memory>
 #include <string>
 
 /// Create BoundaryOp objects on demand
 /*!
  * This implements a simple string parser, used to match boundary condition
  * names like "dirichlet" with a BoundaryOp object.
- * 
+ *
  * Modifiers: Simple modifications of boundary conditions can be performed,
  * for example transforming the coordinate system
- * 
- * This is a singleton, so only one instance can exist. This is 
+ *
+ * This is a singleton, so only one instance can exist. This is
  * enforced by making the constructor private, and having a getInstance() method
  * to return a pointer to the only instance.
  *
@@ -33,7 +34,7 @@ class BoundaryModifier;
  * Boundaries are defined as classes which inherit from BoundaryOp
  * These define a clone() function which creates a new BoundaryOp,
  * given a list of arguments. See boundary_standard.hxx for examples.
- * 
+ *
  *     class MyBoundary : public BoundaryOp {
  *      public:
  *       BoundaryOp* clone(BoundaryRegion *region, const list<string> &args) {
@@ -43,23 +44,23 @@ class BoundaryModifier;
  *       void apply(Field2D &f);
  *       void apply(Field3D &f);
  *     };
- * 
+ *
  * The singleton instance of BoundaryFactory from getInstance():
- * 
+ *
  *     BoundaryFactory* bf = BoundaryFactory::getInstance();
  *
  * New boundary types can be added to the BoundaryFactory
  *
  *     bf->add(new MyBoundary, "myboundary");
- * 
+ *
  *
  * Subsequent calls to create() or createFromOptions() can make use
  * of the boundary type "myboundary".
  *
  * BoundaryOpBase *bndry = bf->create("myboundary()", new BoundaryRegionXOut("xout", 0, 10, localmesh));
- * 
+ *
  * where the region is defined in boundary_region.hxx
- * 
+ *
  */
 class BoundaryFactory {
 public:
@@ -70,13 +71,15 @@ public:
   static void cleanup(); ///< Frees all memory
 
   /// Create a boundary operation object
-  BoundaryOpBase* create(const std::string& name, BoundaryRegionBase* region);
-  BoundaryOpBase* create(const char* name, BoundaryRegionBase* region);
+  BoundaryOpBase* create(const std::string& name,
+                         std::shared_ptr<BoundaryRegionBase> region);
+  BoundaryOpBase* create(const char* name, std::shared_ptr<BoundaryRegionBase> region);
 
   /// Create a boundary object using the options file
   BoundaryOpBase* createFromOptions(const std::string& varname,
-                                    BoundaryRegionBase* region);
-  BoundaryOpBase* createFromOptions(const char* varname, BoundaryRegionBase* region);
+                                    std::shared_ptr<BoundaryRegionBase> region);
+  BoundaryOpBase* createFromOptions(const char* varname,
+                                    std::shared_ptr<BoundaryRegionBase> region);
 
   /*!
    * Add available boundary conditions and modifiers
diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index fd8012802c..3ead105153 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -681,9 +681,9 @@ using BoundaryRegionY = BoundaryRegionXY<false>;
 using BoundaryRegionIterX = BoundaryRegionIterXY<true>;
 using BoundaryRegionIterY = BoundaryRegionIterXY<false>;
 
-inline BoundaryRegionX* NewBoundaryRegionXIn(const std::string& name, int ymin, int ymax,
-                                             Mesh* mesh) {
-  auto* pointer = new BoundaryRegionX(
+inline std::shared_ptr<BoundaryRegionX>
+NewBoundaryRegionXIn(const std::string& name, int ymin, int ymax, Mesh* mesh) {
+  auto pointer = std::make_shared<BoundaryRegionX>(
       name, -1, mesh,
       Region<Ind3D>(mesh->xstart, mesh->xstart, ymin, ymax, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
@@ -691,9 +691,9 @@ inline BoundaryRegionX* NewBoundaryRegionXIn(const std::string& name, int ymin,
   return pointer;
 }
 
-inline BoundaryRegionX* NewBoundaryRegionXOut(const std::string& name, int ymin, int ymax,
-                                              Mesh* mesh) {
-  auto* pointer = new BoundaryRegionX(
+inline std::shared_ptr<BoundaryRegionX>
+NewBoundaryRegionXOut(const std::string& name, int ymin, int ymax, Mesh* mesh) {
+  auto pointer = std::make_shared<BoundaryRegionX>(
       name, 1, mesh,
       Region<Ind3D>(mesh->xend, mesh->xend, ymin, ymax, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
@@ -701,9 +701,9 @@ inline BoundaryRegionX* NewBoundaryRegionXOut(const std::string& name, int ymin,
   return pointer;
 }
 
-inline BoundaryRegionY* NewBoundaryRegionYUp(const std::string& name, int xmin, int xmax,
-                                             Mesh* mesh) {
-  auto* pointer = new BoundaryRegionY(
+inline std::shared_ptr<BoundaryRegionY>
+NewBoundaryRegionYUp(const std::string& name, int xmin, int xmax, Mesh* mesh) {
+  auto pointer = std::make_shared<BoundaryRegionY>(
       name, 1, mesh,
       Region<Ind3D>(xmin, xmax, mesh->yend, mesh->yend, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
@@ -711,9 +711,9 @@ inline BoundaryRegionY* NewBoundaryRegionYUp(const std::string& name, int xmin,
   return pointer;
 }
 
-inline BoundaryRegionY* NewBoundaryRegionYDown(const std::string& name, int xmin,
-                                               int xmax, Mesh* mesh) {
-  auto* pointer = new BoundaryRegionY(
+inline std::shared_ptr<BoundaryRegionY>
+NewBoundaryRegionYDown(const std::string& name, int xmin, int xmax, Mesh* mesh) {
+  auto pointer = std::make_shared<BoundaryRegionY>(
       name, -1, mesh,
       Region<Ind3D>(xmin, xmax, mesh->ystart, mesh->ystart, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
@@ -722,17 +722,18 @@ inline BoundaryRegionY* NewBoundaryRegionYDown(const std::string& name, int xmin
 }
 
 template <class Func>
-void iter_boundary(const BoundaryRegionBase* bndrybase, const Func& func) {
+void iter_boundary(std::shared_ptr<const BoundaryRegionBase> bndrybase,
+                   const Func& func) {
   if (bndrybase->isX) {
-    const auto* const bndry = dynamic_cast<const BoundaryRegionX*>(bndrybase);
+    const auto* const bndry = dynamic_cast<const BoundaryRegionX*>(bndrybase.get());
     return iter_boundary(*bndry, func);
   }
   if (bndrybase->isY) {
-    const auto* const bndry = dynamic_cast<const BoundaryRegionY*>(bndrybase);
+    const auto* const bndry = dynamic_cast<const BoundaryRegionY*>(bndrybase.get());
     return iter_boundary(*bndry, func);
   }
   if (bndrybase->isParallel) {
-    const auto* const bndry = dynamic_cast<const BoundaryRegionFCI*>(bndrybase);
+    const auto* const bndry = dynamic_cast<const BoundaryRegionFCI*>(bndrybase.get());
     return iter_boundary(*bndry, func);
   }
   throw BoutException("{} is of unknown type - probably a legacy iterator",
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index abead4968e..1e729997aa 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -482,7 +482,7 @@ public:
   // Boundary regions
 
   /// Return a vector containing all the boundary regions on this processor
-  virtual std::vector<BoundaryRegionBase*> getBoundaries() const = 0;
+  virtual std::vector<std::shared_ptr<BoundaryRegionBase>> getBoundaries() const = 0;
 
   /// Get the set of all possible boundaries in this configuration
   virtual std::set<std::string> getPossibleBoundaries() const {
@@ -490,7 +490,7 @@ public:
   };
 
   /// Add a boundary region to this processor
-  virtual void addBoundary(BoundaryRegionBase* UNUSED(bndry)) {
+  virtual void addBoundary(std::shared_ptr<BoundaryRegionBase> UNUSED(bndry)) {
     throw BoutException("This has never been implemented");
   };
 
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index cbb2ab59fa..ca70c2eb11 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -85,11 +85,11 @@ public:
         }
       }
     } else {
-      for (auto* bndry : mesh.getBoundaries()) {
+      for (auto& bndry : mesh.getBoundaries()) {
         if ((lower_y && bndry->location == BndryLoc::ydown)
             or (upper_y && bndry->location == BndryLoc::yup)) {
           boundary_regions.push_back(
-              dynamic_cast<bout::boundary::BoundaryRegionY*>(bndry));
+              std::dynamic_pointer_cast<bout::boundary::BoundaryRegionY>(bndry));
         }
       }
     }
@@ -138,7 +138,7 @@ private:
     }
   }
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>> boundary_regions_par;
-  std::vector<bout::boundary::BoundaryRegionY*> boundary_regions;
+  std::vector<std::shared_ptr<bout::boundary::BoundaryRegionY>> boundary_regions;
 
   std::vector<BoutMask> _contains;
 };
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 9e459cc97d..42fc0c4199 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -621,7 +621,7 @@ void Field3D::applyParallelBoundary(const std::string& condition) {
   /// Loop over the mesh boundary regions
   for (const auto& reg : fieldmesh->getBoundariesPar()) {
     auto op = std::unique_ptr<BoundaryOpPar>{
-        dynamic_cast<BoundaryOpPar*>(bfact->create(condition, reg.get()))};
+        dynamic_cast<BoundaryOpPar*>(bfact->create(condition, reg))};
     op->apply(*this);
   }
 }
@@ -644,7 +644,7 @@ void Field3D::applyParallelBoundary(const std::string& region,
   for (const auto& reg : fieldmesh->getBoundariesPar()) {
     if (reg->label == region) {
       auto op = std::unique_ptr<BoundaryOpPar>{
-          dynamic_cast<BoundaryOpPar*>(bfact->create(condition, reg.get()))};
+          dynamic_cast<BoundaryOpPar*>(bfact->create(condition, reg))};
       op->apply(*this);
       break;
     }
@@ -671,7 +671,7 @@ void Field3D::applyParallelBoundary(const std::string& region,
       // BoundaryFactory can't create boundaries using Field3Ds, so get temporary
       // boundary of the right type
       auto tmp = std::unique_ptr<BoundaryOpPar>{
-          dynamic_cast<BoundaryOpPar*>(bfact->create(condition, reg.get()))};
+          dynamic_cast<BoundaryOpPar*>(bfact->create(condition, reg))};
       // then clone that with the actual argument
       auto op = std::unique_ptr<BoundaryOpPar>{tmp->clone(reg.get(), f)};
       op->apply(*this);
diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx
index b925cb1426..65d02b83a8 100644
--- a/src/field/field_data.cxx
+++ b/src/field/field_data.cxx
@@ -154,7 +154,7 @@ void FieldData::setBoundary(const std::string& name) {
   /// Get the mesh boundary regions
   /// Loop over the mesh parallel boundary regions
   for (const auto& reg : mesh->getBoundariesPar()) {
-    auto* op = dynamic_cast<BoundaryOpPar*>(bfact->createFromOptions(name, reg.get()));
+    auto* op = dynamic_cast<BoundaryOpPar*>(bfact->createFromOptions(name, reg));
     if (op != nullptr) {
       bndry_op_par.push_back(op);
     }
diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index 988fcfce9b..c2316afb72 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -85,7 +85,8 @@ void BoundaryFactory::cleanup() {
   instance = nullptr;
 }
 
-BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase* region) {
+BoundaryOpBase* BoundaryFactory::create(const string& name,
+                                        std::shared_ptr<BoundaryRegionBase> region) {
 
   // Search for a string of the form: modifier(operation)
   auto pos = name.find('(');
@@ -107,8 +108,8 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
       // Clone the boundary operation, passing the region to operate over,
       // an empty args list and empty keyword map
       list<string> args;
-      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionFCI*>(region), args,
-                        {});
+      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionFCI*>(region.get()),
+                        args, {});
     } else {
       // Perpendicular boundary
       BoundaryOp* op = findBoundaryOp(trim(name));
@@ -199,16 +200,16 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
   if (pop != nullptr) {
     // An operation with arguments
     if (region->isParallel) {
-      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionFCI*>(region), arglist,
-                        keywords);
+      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionFCI*>(region.get()),
+                        arglist, keywords);
     }
     if (region->isX) {
-      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionX*>(region), arglist,
-                        keywords);
+      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionX*>(region.get()),
+                        arglist, keywords);
     }
     if (region->isY) {
-      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionY*>(region), arglist,
-                        keywords);
+      return pop->clone(dynamic_cast<bout::boundary::BoundaryRegionY*>(region.get()),
+                        arglist, keywords);
     }
   }
   if (!region->isParallel) {
@@ -227,12 +228,14 @@ BoundaryOpBase* BoundaryFactory::create(const string& name, BoundaryRegionBase*
   return nullptr;
 }
 
-BoundaryOpBase* BoundaryFactory::create(const char* name, BoundaryRegionBase* region) {
+BoundaryOpBase* BoundaryFactory::create(const char* name,
+                                        std::shared_ptr<BoundaryRegionBase> region) {
   return create(string(name), region);
 }
 
-BoundaryOpBase* BoundaryFactory::createFromOptions(const string& varname,
-                                                   BoundaryRegionBase* region) {
+BoundaryOpBase*
+BoundaryFactory::createFromOptions(const string& varname,
+                                   std::shared_ptr<BoundaryRegionBase> region) {
   if (region == nullptr) {
     return nullptr;
   }
@@ -357,8 +360,9 @@ BoundaryOpBase* BoundaryFactory::createFromOptions(const string& varname,
   // values. If a user want to override, specify "none" or "null"
 }
 
-BoundaryOpBase* BoundaryFactory::createFromOptions(const char* varname,
-                                                   BoundaryRegionBase* region) {
+BoundaryOpBase*
+BoundaryFactory::createFromOptions(const char* varname,
+                                   std::shared_ptr<BoundaryRegionBase> region) {
   return createFromOptions(string(varname), region);
 }
 
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index e1d2cbfc70..e7c7b9ebd8 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -94,11 +94,6 @@ BoutMesh::~BoutMesh() {
   // Delete the communication handles
   clear_handles();
 
-  // Delete the boundary regions
-  for (const auto& bndry : boundary) {
-    delete bndry;
-  }
-
   if (comm_x != MPI_COMM_NULL) {
     MPI_Comm_free(&comm_x);
   }
@@ -1175,9 +1170,10 @@ std::set<std::string> BoutMesh::getPossibleBoundaries() const {
 
         // Get the boundaries and shove their names into the set
         auto boundaries = mesh_copy.getBoundaries();
-        std::transform(boundaries.begin(), boundaries.end(),
-                       std::inserter(all_boundaries, all_boundaries.begin()),
-                       [](BoundaryRegionBase* boundary) { return boundary->label; });
+        std::transform(
+            boundaries.begin(), boundaries.end(),
+            std::inserter(all_boundaries, all_boundaries.begin()),
+            [](std::shared_ptr<BoundaryRegionBase> boundary) { return boundary->label; });
       };
 
   // This is sufficient to get the SOL boundary, if it exists
@@ -3250,7 +3246,9 @@ RangeIterator BoutMesh::iterateBndryUpperY() const {
   return RangeIterator(xs, xe);
 }
 
-std::vector<BoundaryRegionBase*> BoutMesh::getBoundaries() const { return boundary; }
+std::vector<std::shared_ptr<BoundaryRegionBase>> BoutMesh::getBoundaries() const {
+  return boundary;
+}
 
 using bout::boundary::BoundaryRegionFCI;
 std::vector<std::shared_ptr<BoundaryRegionFCI>>
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index 79121ede58..a6d97a8944 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -169,7 +169,7 @@ public:
   bool hasBndryUpperY() const override { return has_boundary_upper_y; }
 
   // Boundary regions
-  std::vector<BoundaryRegionBase*> getBoundaries() const override;
+  std::vector<std::shared_ptr<BoundaryRegionBase>> getBoundaries() const override;
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType type) const override;
   void addBoundaryPar(std::shared_ptr<bout::boundary::BoundaryRegionFCI> bndry,
@@ -416,7 +416,7 @@ protected:
   void addBoundaryRegions();
 
 private:
-  std::vector<BoundaryRegionBase*> boundary; // Vector of boundary regions
+  std::vector<std::shared_ptr<BoundaryRegionBase>> boundary; // Vector of boundary regions
   std::array<std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>,
              static_cast<int>(BoundaryParType::SIZE)>
       par_boundary; // Vector of parallel boundary regions
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index aa08c2f043..9353e8da38 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -175,8 +175,12 @@ public:
   RangeIterator iterateBndryUpperInnerY() const override { return RangeIterator(); }
   bool hasBndryLowerY() const override { return false; }
   bool hasBndryUpperY() const override { return false; }
-  void addBoundary(BoundaryRegionBase* region) override { boundaries.push_back(region); }
-  std::vector<BoundaryRegionBase*> getBoundaries() const override { return boundaries; }
+  void addBoundary(std::shared_ptr<BoundaryRegionBase> region) override {
+    boundaries.push_back(region);
+  }
+  std::vector<std::shared_ptr<BoundaryRegionBase>> getBoundaries() const override {
+    return boundaries;
+  }
   std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>
   getBoundariesPar(BoundaryParType UNUSED(type)) const override {
     return std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>>();
@@ -268,7 +272,7 @@ public:
   using Mesh::msg_len;
 
 private:
-  std::vector<BoundaryRegionBase*> boundaries;
+  std::vector<std::shared_ptr<BoundaryRegionBase>> boundaries;
 };
 
 /// FakeGridDataSource provides a non-null GridDataSource* source to use with FakeMesh, to
diff --git a/tests/unit/field/test_vector3d.cxx b/tests/unit/field/test_vector3d.cxx
index d87d4c4bed..5b197d5cdf 100644
--- a/tests/unit/field/test_vector3d.cxx
+++ b/tests/unit/field/test_vector3d.cxx
@@ -21,11 +21,6 @@ class Vector3DTest : public ::testing::Test {
     WithQuietOutput quiet{output_info};
     // Delete any existing mesh
     if (mesh != nullptr) {
-      // Delete boundary regions
-      for (auto& r : mesh->getBoundaries()) {
-        delete r;
-      }
-
       delete mesh;
       mesh = nullptr;
     }
@@ -57,12 +52,6 @@ class Vector3DTest : public ::testing::Test {
   }
 
   ~Vector3DTest() override {
-    if (mesh != nullptr) {
-      // Delete boundary regions
-      for (auto& r : mesh->getBoundaries()) {
-        delete r;
-      }
-    }
     delete mesh;
     mesh = nullptr;
     delete mesh_staggered;
diff --git a/tests/unit/mesh/test_boundary_factory.cxx b/tests/unit/mesh/test_boundary_factory.cxx
index fd0100b755..fc9a6e95b0 100644
--- a/tests/unit/mesh/test_boundary_factory.cxx
+++ b/tests/unit/mesh/test_boundary_factory.cxx
@@ -39,21 +39,20 @@ class BoundaryFactoryTest : public ::testing::Test {
 
     fac->add(new TestBoundary(), "testboundary");
 
-    region = new BoundaryRegionXIn{"test_region", 0, 1, mesh};
+    region = std::make_shared<BoundaryRegionXIn>("test_region", 0, 1, mesh);
   }
 
   virtual ~BoundaryFactoryTest() {
     delete mesh;
     mesh = nullptr;
 
-    delete region;
     BoundaryFactory::cleanup();
 
     delete boundary;
   }
 
   BoundaryFactory* fac{BoundaryFactory::getInstance()};
-  BoundaryRegionXIn* region{nullptr};
+  std::shared_ptr<BoundaryRegionXIn> region;
   BoundaryOpBase* boundary{nullptr};
 };
 

From 6408fa44c611e7148746c35e94eff4c2b32311e0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 11:14:33 +0200
Subject: [PATCH 1565/1827] Add even more unit tests

---
 tests/unit/include/bout/test_yboundary.cxx | 59 ++++++++++++++++++++--
 1 file changed, 55 insertions(+), 4 deletions(-)

diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index dc9da34a01..ce531c27f8 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -19,6 +19,30 @@ TEST_F(YBTest, dirichlet_o2_rgn) {
   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }
 
+TEST_F(YBTest, neumann_o1_rgn) {
+  dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
+  Field3D test = 1.0;
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { point.neumann_o1(test, 1); });
+  EXPECT_TRUE(IsFieldEqual(test, 2.0, "RGN_YGUARDS"));
+}
+
+TEST_F(YBTest, neumann_o2_rgn) {
+  dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
+  Field3D test = 1.0;
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { point.neumann_o2(test, 1); });
+  EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
+}
+
+TEST_F(YBTest, neumann_o3_rgn) {
+  dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
+  Field3D test = 1.0;
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { point.neumann_o3(test, 1); });
+  EXPECT_TRUE(IsFieldEqual(test, 0.0, "RGN_YGUARDS"));
+}
+
 TEST_F(YBTest, bndry_size) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
@@ -34,6 +58,13 @@ TEST_F(YBTest, interpolate_boundary_o2) {
       [&](auto& point) { EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0); });
 }
 
+TEST_F(YBTest, interpolate_boundary_o2_const) {
+  const Field3D test = 1.0;
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter(
+      [&](auto& point) { EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0); });
+}
+
 TEST_F(YBTest, extrapolate_boundary_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
@@ -100,11 +131,13 @@ TEST_F(YBTest, interpolate_boundary_o2_square) {
       [&](auto& point) { EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 2.5); });
 }
 
-TEST_F(YBTest, extrapolate_boundary_o2_square) {
-  Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+TEST_F(YBTest, limit_at_least) {
+  Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter(
-      [&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_boundary_o2(test), 1.5); });
+  sheath.iter([&](auto& point) {
+    point.limit_at_least(test, 2.0);
+    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.5);
+  });
 }
 
 TEST_F(YBTest, extrapolate_grad_o2_square) {
@@ -143,6 +176,24 @@ TEST_F(YBTest, prev_square) {
   sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
 }
 
+TEST_F(YBTest, next_const) {
+  const Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
+}
+
+TEST_F(YBTest, current_const) {
+  const Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.current(test), 1); });
+}
+
+TEST_F(YBTest, prev_const) {
+  const Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
+  YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
+}
+
 TEST_F(YBTest, getAt_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);

From 2f0db3910a9953a6b454de6773c168e895a4e0ad Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 11:21:12 +0200
Subject: [PATCH 1566/1827] Add missing file

---
 include/bout/boundary_common.hxx | 56 ++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 include/bout/boundary_common.hxx

diff --git a/include/bout/boundary_common.hxx b/include/bout/boundary_common.hxx
new file mode 100644
index 0000000000..3a8c128b55
--- /dev/null
+++ b/include/bout/boundary_common.hxx
@@ -0,0 +1,56 @@
+#pragma once
+
+#include <bout/bout_types.hxx>
+#include <bout/build_config.hxx>
+
+namespace bout {
+namespace boundary {
+/// Types of free boundary condition
+/// ================== ===================================================
+/// Name               Description
+/// ================== ===================================================
+/// ``limited``        use exponential if decreasing, otherwise Neumanm
+/// ``exponential``    use exponential extrapolation
+/// ``linear``         use linear extrapolation
+/// ================== ===================================================
+enum class BoundaryFreeExtrapolation : std::int8_t { limited, exponential, linear };
+
+// Limited free gradient of log of a quantity
+// This ensures that the guard cell values remain positive
+// while also ensuring that the quantity never increases
+//
+//  fm  fc | fp
+//         ^ boundary
+//
+// exp( 2*log(fc) - log(fm) )
+inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc,
+                               bout::boundary::BoundaryFreeExtrapolation mode) {
+  if ((fm < fc) && (mode == bout::boundary::BoundaryFreeExtrapolation::limited)) {
+    return fc; // Neumann rather than increasing into boundary
+  }
+  if (fm < 1e-10) {
+    return fc; // Low / no density condition
+  }
+
+  BoutReal fp = 0;
+  switch (mode) {
+  case bout::boundary::BoundaryFreeExtrapolation::limited:
+  case bout::boundary::BoundaryFreeExtrapolation::exponential:
+    fp = fc * fc / fm; // Exponential
+    break;
+  case bout::boundary::BoundaryFreeExtrapolation::linear:
+    fp = (2.0 * fc) - fm; // Linear
+    break;
+  }
+
+#if CHECKLEVEL >= 2
+  if (!std::isfinite(fp)) {
+    throw BoutException("SheathBoundary limitFree: {}, {} -> {}", fm, fc, fp);
+  }
+#endif
+
+  return fp;
+}
+
+} // namespace boundary
+} // namespace bout

From 402c44b8105e4deda4640b86880433f0e42052f7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 11:34:03 +0200
Subject: [PATCH 1567/1827] Apply clang-tidy fixes

---
 include/bout/boundary_common.hxx      | 1 -
 include/bout/boundary_factory.hxx     | 4 ++--
 include/bout/boundary_region_iter.hxx | 3 ++-
 src/mesh/boundary_factory.cxx         | 8 +++++---
 src/mesh/impls/bout/boutmesh.cxx      | 9 +++++----
 5 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/include/bout/boundary_common.hxx b/include/bout/boundary_common.hxx
index 3a8c128b55..a88c9dcc1f 100644
--- a/include/bout/boundary_common.hxx
+++ b/include/bout/boundary_common.hxx
@@ -1,7 +1,6 @@
 #pragma once
 
 #include <bout/bout_types.hxx>
-#include <bout/build_config.hxx>
 
 namespace bout {
 namespace boundary {
diff --git a/include/bout/boundary_factory.hxx b/include/bout/boundary_factory.hxx
index 46a6c04b01..3a6b44352e 100644
--- a/include/bout/boundary_factory.hxx
+++ b/include/bout/boundary_factory.hxx
@@ -72,12 +72,12 @@ public:
 
   /// Create a boundary operation object
   BoundaryOpBase* create(const std::string& name,
-                         std::shared_ptr<BoundaryRegionBase> region);
+                         const std::shared_ptr<BoundaryRegionBase>& region);
   BoundaryOpBase* create(const char* name, std::shared_ptr<BoundaryRegionBase> region);
 
   /// Create a boundary object using the options file
   BoundaryOpBase* createFromOptions(const std::string& varname,
-                                    std::shared_ptr<BoundaryRegionBase> region);
+                                    const std::shared_ptr<BoundaryRegionBase>& region);
   BoundaryOpBase* createFromOptions(const char* varname,
                                     std::shared_ptr<BoundaryRegionBase> region);
 
diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 3ead105153..db650a7510 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -5,6 +5,7 @@
 #include <cstddef>
 #include <cstdint>
 #include <functional>
+#include <memory>
 #include <string>
 #include <type_traits>
 #include <vector>
@@ -722,7 +723,7 @@ NewBoundaryRegionYDown(const std::string& name, int xmin, int xmax, Mesh* mesh)
 }
 
 template <class Func>
-void iter_boundary(std::shared_ptr<const BoundaryRegionBase> bndrybase,
+void iter_boundary(const std::shared_ptr<const BoundaryRegionBase>& bndrybase,
                    const Func& func) {
   if (bndrybase->isX) {
     const auto* const bndry = dynamic_cast<const BoundaryRegionX*>(bndrybase.get());
diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index c2316afb72..cb1ecd8904 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -11,6 +11,7 @@
 #include <array>
 #include <list>
 #include <map>
+#include <memory>
 #include <string>
 using std::list;
 using std::string;
@@ -85,8 +86,9 @@ void BoundaryFactory::cleanup() {
   instance = nullptr;
 }
 
-BoundaryOpBase* BoundaryFactory::create(const string& name,
-                                        std::shared_ptr<BoundaryRegionBase> region) {
+BoundaryOpBase*
+BoundaryFactory::create(const string& name,
+                        const std::shared_ptr<BoundaryRegionBase>& region) {
 
   // Search for a string of the form: modifier(operation)
   auto pos = name.find('(');
@@ -235,7 +237,7 @@ BoundaryOpBase* BoundaryFactory::create(const char* name,
 
 BoundaryOpBase*
 BoundaryFactory::createFromOptions(const string& varname,
-                                   std::shared_ptr<BoundaryRegionBase> region) {
+                                   const std::shared_ptr<BoundaryRegionBase>& region) {
   if (region == nullptr) {
     return nullptr;
   }
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 913d42a129..0e3c8bdcf3 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -1170,10 +1170,11 @@ std::set<std::string> BoutMesh::getPossibleBoundaries() const {
 
         // Get the boundaries and shove their names into the set
         auto boundaries = mesh_copy.getBoundaries();
-        std::transform(
-            boundaries.begin(), boundaries.end(),
-            std::inserter(all_boundaries, all_boundaries.begin()),
-            [](std::shared_ptr<BoundaryRegionBase> boundary) { return boundary->label; });
+        std::transform(boundaries.begin(), boundaries.end(),
+                       std::inserter(all_boundaries, all_boundaries.begin()),
+                       [](const std::shared_ptr<BoundaryRegionBase>& boundary) {
+                         return boundary->label;
+                       });
       };
 
   // This is sufficient to get the SOL boundary, if it exists

From e9ac3b91cc30f3bf0eaf4c69e435a790ec88002e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 11:34:59 +0200
Subject: [PATCH 1568/1827] Use unsigned for enum

---
 include/bout/boundary_common.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/boundary_common.hxx b/include/bout/boundary_common.hxx
index a88c9dcc1f..b3b1bd7dcd 100644
--- a/include/bout/boundary_common.hxx
+++ b/include/bout/boundary_common.hxx
@@ -12,7 +12,7 @@ namespace boundary {
 /// ``exponential``    use exponential extrapolation
 /// ``linear``         use linear extrapolation
 /// ================== ===================================================
-enum class BoundaryFreeExtrapolation : std::int8_t { limited, exponential, linear };
+enum class BoundaryFreeExtrapolation : std::uint8_t { limited, exponential, linear };
 
 // Limited free gradient of log of a quantity
 // This ensures that the guard cell values remain positive

From 83501853d5a93cf692cfd7b525d0d2daaffbc82b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 11:36:53 +0200
Subject: [PATCH 1569/1827] Do not try to delete shared_ptr

---
 tests/unit/field/test_vector2d.cxx | 21 ++++-----------------
 1 file changed, 4 insertions(+), 17 deletions(-)

diff --git a/tests/unit/field/test_vector2d.cxx b/tests/unit/field/test_vector2d.cxx
index ded551084e..d99d2ed179 100644
--- a/tests/unit/field/test_vector2d.cxx
+++ b/tests/unit/field/test_vector2d.cxx
@@ -23,15 +23,8 @@ class Vector2DTest : public ::testing::Test {
 protected:
   Vector2DTest() {
     // Delete any existing mesh
-    if (mesh != nullptr) {
-      // Delete boundary regions
-      for (auto& r : mesh->getBoundaries()) {
-        delete r;
-      }
-
-      delete mesh;
-      mesh = nullptr;
-    }
+    delete mesh;
+    mesh = nullptr;
     bout::globals::mpi = new MpiWrapper();
     mesh = new FakeMesh(nx, ny, nz);
     static_cast<FakeMesh*>(mesh)->setCoordinates(nullptr);
@@ -60,14 +53,8 @@ class Vector2DTest : public ::testing::Test {
   }
 
   virtual ~Vector2DTest() {
-    if (mesh != nullptr) {
-      // Delete boundary regions
-      for (auto& r : mesh->getBoundaries()) {
-        delete r;
-      }
-      delete mesh;
-      mesh = nullptr;
-    }
+    delete mesh;
+    mesh = nullptr;
     delete mesh_staggered;
     mesh_staggered = nullptr;
     delete bout::globals::mpi;

From 8e35339472f01ed36c5f1e3769ebef163364b7b9 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 11:37:07 +0200
Subject: [PATCH 1570/1827] Remove unused header

---
 include/bout/boundary_iterator.hxx        | 1 -
 include/bout/parallel_boundary_region.hxx | 1 -
 include/bout/yboundary_regions.hxx        | 1 -
 3 files changed, 3 deletions(-)

diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index 8d13a7c897..b2d2b9fb99 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -1,7 +1,6 @@
 #pragma once
 
 #include "bout/assert.hxx"
-#include "bout/boundary_common.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 5e08f55897..2d17288a3d 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -12,7 +12,6 @@
 #include <string>
 #include <vector>
 
-#include "bout/boundary_common.hxx"
 #include "bout/build_defines.hxx"
 #include "bout/field2d.hxx"
 #include "bout/region.hxx"
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index ca70c2eb11..bb9f52bbda 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -1,6 +1,5 @@
 #pragma once
 
-#include "bout/boundary_common.hxx"
 #include "bout/boundary_region_iter.hxx"
 
 #include "bout/assert.hxx"

From 177796122aa552e92c13b2b5dcffb048a3a2fc11 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 11:51:35 +0200
Subject: [PATCH 1571/1827] Apply clang-tidy fixes

---
 include/bout/boundary_common.hxx  | 2 ++
 include/bout/boundary_factory.hxx | 5 +++--
 src/mesh/boundary_factory.cxx     | 7 ++++---
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/include/bout/boundary_common.hxx b/include/bout/boundary_common.hxx
index b3b1bd7dcd..6d08f2c9c0 100644
--- a/include/bout/boundary_common.hxx
+++ b/include/bout/boundary_common.hxx
@@ -2,6 +2,8 @@
 
 #include <bout/bout_types.hxx>
 
+#include <cstdint>
+
 namespace bout {
 namespace boundary {
 /// Types of free boundary condition
diff --git a/include/bout/boundary_factory.hxx b/include/bout/boundary_factory.hxx
index 3a6b44352e..17807138be 100644
--- a/include/bout/boundary_factory.hxx
+++ b/include/bout/boundary_factory.hxx
@@ -73,13 +73,14 @@ public:
   /// Create a boundary operation object
   BoundaryOpBase* create(const std::string& name,
                          const std::shared_ptr<BoundaryRegionBase>& region);
-  BoundaryOpBase* create(const char* name, std::shared_ptr<BoundaryRegionBase> region);
+  BoundaryOpBase* create(const char* name,
+                         const std::shared_ptr<BoundaryRegionBase>& region);
 
   /// Create a boundary object using the options file
   BoundaryOpBase* createFromOptions(const std::string& varname,
                                     const std::shared_ptr<BoundaryRegionBase>& region);
   BoundaryOpBase* createFromOptions(const char* varname,
-                                    std::shared_ptr<BoundaryRegionBase> region);
+                                    const std::shared_ptr<BoundaryRegionBase>& region);
 
   /*!
    * Add available boundary conditions and modifiers
diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index cb1ecd8904..f0c41cf8a1 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -230,8 +230,9 @@ BoundaryFactory::create(const string& name,
   return nullptr;
 }
 
-BoundaryOpBase* BoundaryFactory::create(const char* name,
-                                        std::shared_ptr<BoundaryRegionBase> region) {
+BoundaryOpBase*
+BoundaryFactory::create(const char* name,
+                        const std::shared_ptr<BoundaryRegionBase>& region) {
   return create(string(name), region);
 }
 
@@ -364,7 +365,7 @@ BoundaryFactory::createFromOptions(const string& varname,
 
 BoundaryOpBase*
 BoundaryFactory::createFromOptions(const char* varname,
-                                   std::shared_ptr<BoundaryRegionBase> region) {
+                                   const std::shared_ptr<BoundaryRegionBase>& region) {
   return createFromOptions(string(varname), region);
 }
 

From f9549c2667825e812ac47f03783bb1b7848f0318 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 1 Jul 2026 13:36:55 +0200
Subject: [PATCH 1572/1827] Fix y location

---
 include/bout/boundary_region_iter.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index db650a7510..6b6cd5b6ff 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -559,7 +559,7 @@ public:
       location = dir == 1 ? BNDRY_XOUT : BNDRY_XIN;
     } else {
       this->isY = true;
-      location = dir == 1 ? BNDRY_YDOWN : BNDRY_YUP;
+      location = dir == 1 ? BNDRY_YUP : BNDRY_YDOWN;
     }
   }
   int dir() { return _dir; }

From f893f3da21bbe19bdaba4f5bb17b547d8b2dd326 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Jul 2026 11:18:56 +0200
Subject: [PATCH 1573/1827] Fix nonorthogonal MMS test for hermes-3

---
 src/mesh/coordinates.cxx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index afb63f981d..10b560f71c 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2066,7 +2066,7 @@ void Coordinates::_compute_cell_area_x() const {
   BOUT_OMP_SAFE(critical)
   {
     if (!_cell_area_xlow.has_value()) {
-      const FieldMetric area_centre = sqrt(g_22 * g_33 - SQ(g_23)) * dy * dz;
+      const FieldMetric area_centre = J / sqrt(g_11) * dy * dz;
       _cell_area_xlow.emplace(emptyFrom(area_centre));
       _cell_area_xhigh.emplace(emptyFrom(area_centre));
       // We cannot setLocation, as that would trigger the computation of staggered
@@ -2087,7 +2087,7 @@ void Coordinates::_compute_cell_area_y() const {
     if (!_cell_area_ylow.has_value()) {
       auto* mesh = Bxy.getMesh();
       if (g_11.isFci()) {
-        const FieldMetric jxz_centre = sqrt(g_11 * g_33 - SQ(g_13));
+        const FieldMetric jxz_centre = J / sqrt(g_22);
         auto jxz_ylow = emptyFrom(jxz_centre);
         auto jxz_yhigh = emptyFrom(jxz_centre);
 
@@ -2115,7 +2115,7 @@ void Coordinates::_compute_cell_area_y() const {
         _cell_area_yhigh.emplace(jxz_yhigh * dx * dz);
       } else {
         // Field aligned
-        const FieldMetric area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;
+        const FieldMetric area_centre = J / sqrt(g_22) * dx * dz;
         _cell_area_ylow.emplace(emptyFrom(area_centre));
         _cell_area_yhigh.emplace(emptyFrom(area_centre));
         // We cannot setLocation, as that would trigger the computation of staggered
@@ -2141,7 +2141,7 @@ void Coordinates::_compute_cell_area_z() const {
   BOUT_OMP_SAFE(critical)
   {
     if (!_cell_volume.has_value()) {
-      const FieldMetric area_centre = sqrt(g_11 * g_22 - SQ(g_12)) * dx * dy;
+      const FieldMetric area_centre = J / sqrt(g_33) * dx * dy;
       _cell_area_zlow.emplace(emptyFrom(area_centre));
       _cell_area_zhigh.emplace(emptyFrom(area_centre));
       // We cannot setLocation, as that would trigger the computation of staggered

From 6a0e276028fbdd2e817f5a67813e64c9a1417850 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Jul 2026 11:52:10 +0200
Subject: [PATCH 1574/1827] Ensure fv_ops.hxx is parsed before fv_ops_impl.hxx

We need to ensure that fv_ops_impl.hxx is never parsed before
fv_ops.hxx, as fv_ops.hxx provides default arguments, which is
forbiddef for a redeclaration. To ensure this, fv_ops.hxx is included
in fv_ops_impl.hxx, so that fv_ops_impl.hxx can be included and
fv_ops.hxx can appear afterwards without causing an error.
---
 include/bout/fv_ops_impl.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 67efdd6476..3755467027 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -12,6 +12,7 @@
 #include "bout/coordinates.hxx"
 #include "bout/field.hxx"
 #include "bout/field3d.hxx"
+#include "bout/fv_ops.hxx" // NOLINT(unused-includes, misc-include-cleaner)
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
 #include "bout/output_bout_types.hxx" // NOLINT(unused-includes, misc-include-cleaner)

From a333188125e25094e00f9f11dc8377d862c56340 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Jul 2026 12:55:06 +0200
Subject: [PATCH 1575/1827] Port Div_par_fvv_heating from hermes-3

---
 include/bout/fv_ops_impl.hxx | 261 +++++++++++++++++++++++++++++++++++
 1 file changed, 261 insertions(+)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 3755467027..f99ec961e3 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -981,5 +981,266 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
   }
   return fromFieldAligned(result, "RGN_NOBNDRY");
 }
+
+// Calculates viscous heating due to numerical momentum fluxes
+// and flow of kinetic energy (in flow_ylow)
+template <typename CellEdges = MC>
+Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
+                            const Field3D& wave_speed_in, Field3D& flow_ylow,
+                            bool fixflux = true) {
+
+  ASSERT1(areFieldsCompatible(f_in, v_in));
+  ASSERT1(areFieldsCompatible(f_in, wave_speed_in));
+
+  Mesh* mesh = f_in.getMesh();
+  Coordinates* coord = f_in.getCoordinates();
+  CellEdges cellboundary;
+
+  if (f_in.isFci()) {
+    // FCI version, using yup/down fields
+    ASSERT1(f_in.hasParallelSlices());
+    ASSERT1(v_in.hasParallelSlices());
+
+    const auto B = coord->Bxy;
+    const auto B_up = coord->Bxy.yup();
+    const auto B_down = coord->Bxy.ydown();
+
+    const auto& f_up = f_in.yup();
+    const auto& f_down = f_in.ydown();
+
+    const auto& v_up = v_in.yup();
+    const auto& v_down = v_in.ydown();
+
+    const auto g_22 = coord->g_22;
+    const auto dy = coord->dy;
+
+    Field3D result{emptyFrom(f_in)};
+    flow_ylow = zeroFrom(f_in);
+
+    BOUT_FOR(i, f_in.getRegion("RGN_NOBNDRY")) {
+      const auto iyp = i.yp();
+      const auto iym = i.ym();
+
+      //Maximum local wave speed
+      const BoutReal amax =
+          BOUTMAX(wave_speed_in[i], fabs(v_in[i]), fabs(v_up[iyp]), fabs(v_down[iym]));
+
+      result[i] =
+          B[i]
+          * ((f_up[iyp] * v_up[iyp] * v_up[iyp] / B_up[iyp])
+             - (f_down[iym] * v_down[iym] * v_down[iym] / B_down[iym])
+             // Penalty terms. This implementation is very dissipative.
+             // Note: This version adds a viscosity that damps gradients of velocity
+             + amax * (f_in[i] + f_up[iyp]) * (v_in[i] - v_up[iyp]) / (B[i] + B_up[iyp])
+             + amax * (f_in[i] + f_down[iym]) * (v_in[i] - v_down[iym])
+                   / (B[i] + B_down[iym]))
+          / (2 * dy[i] * sqrt(g_22[i]));
+
+#if CHECK > 0
+      if (!std::isfinite(result[i])) {
+        throw BoutException("Non-finite value in Div_par_fvv at {}\n"
+                            "fup {} vup {} fdown {} vdown {} amax {}\n",
+                            "B {} Bup {} Bdown {} dy {} sqrt(g_22} {}", i, f_up[i],
+                            v_up[i], f_down[i], v_down[i], amax, B[i], B_up[i], B_down[i],
+                            dy[i], sqrt(g_22[i]));
+      }
+#endif
+    }
+    return result;
+  }
+
+  /// Ensure that f, v and wave_speed are field aligned
+  Field3D f = toFieldAligned(f_in, "RGN_NOX");
+  Field3D v = toFieldAligned(v_in, "RGN_NOX");
+  Field3D wave_speed = toFieldAligned(wave_speed_in, "RGN_NOX");
+
+  // result and flow_ylow are field-aligned.
+  // Will be converted to non-aligned before return.
+  Field3D result{zeroFrom(f)};
+  flow_ylow = zeroFrom(f);
+
+  // Only need one guard cell, so no need to communicate fluxes
+  // Instead calculate in guard cells to preserve fluxes
+  int ys = mesh->ystart - 1;
+  int ye = mesh->yend + 1;
+
+  for (int i = mesh->xstart; i <= mesh->xend; i++) {
+
+    if (!mesh->firstY(i) || mesh->periodicY(i)) {
+      // Calculate in guard cell to get fluxes consistent between processors
+      ys = mesh->ystart - 1;
+    } else {
+      // Don't include the boundary cell. Note that this implies special
+      // handling of boundaries later
+      ys = mesh->ystart;
+    }
+
+    if (!mesh->lastY(i) || mesh->periodicY(i)) {
+      // Calculate in guard cells
+      ye = mesh->yend + 1;
+    } else {
+      // Not in boundary cells
+      ye = mesh->yend;
+    }
+
+    for (int j = ys; j <= ye; j++) {
+      for (int k = 0; k < mesh->LocalNz; k++) {
+        // Pre-calculate factors which multiply fluxes
+        // Note: In 3D metric geometries these quantities can depend on (i,j,k),
+        // so calculate inside the k loop.
+
+        // For right cell boundaries
+        BoutReal common_factor =
+            (coord->J(i, j, k) + coord->J(i, j + 1, k))
+            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
+
+        const BoutReal flux_factor_rc =
+            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal area_rp =
+            common_factor * coord->dx(i, j + 1, k) * coord->dz(i, j + 1, k);
+
+        // For left cell boundaries
+        common_factor = (coord->J(i, j, k) + coord->J(i, j - 1, k))
+                        / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
+
+        const BoutReal flux_factor_lc =
+            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
+        const BoutReal area_lc = common_factor * coord->dx(i, j, k) * coord->dz(i, j, k);
+
+        ////////////////////////////////////////////
+        // Reconstruct f at the cell faces
+        // This calculates s.R and s.L for the Right and Left
+        // face values on this cell
+
+        // Reconstruct f at the cell faces
+        Stencil1D s;
+        s.c = f(i, j, k);
+        s.m = f(i, j - 1, k);
+        s.p = f(i, j + 1, k);
+
+        cellboundary(s); // Calculate s.R and s.L
+
+        // Reconstruct v at the cell faces
+        Stencil1D sv;
+        sv.c = v(i, j, k);
+        sv.m = v(i, j - 1, k);
+        sv.p = v(i, j + 1, k);
+
+        cellboundary(sv);
+
+        ////////////////////////////////////////////
+        // Right boundary
+
+        // Calculate velocity at right boundary (y+1/2)
+        BoutReal v_mid = 0.5 * (sv.c + sv.p);
+        // And mid-point density at right boundary
+        BoutReal n_mid = 0.5 * (s.c + s.p);
+
+        if (mesh->lastY(i) && (j == mesh->yend) && !mesh->periodicY(i)) {
+          // Last point in domain
+
+          // Expected loss of kinetic energy into boundary
+          // This is used in the sheath boundary condition to calculate
+          // energy losses.
+          const BoutReal expected_ke = 0.5 * n_mid * v_mid * v_mid * v_mid;
+
+          BoutReal flux_mom;
+          if (fixflux) {
+            // Mid-point consistent with boundary conditions
+            // but kinetic energy loss will not match expected
+            // -> Adjust energy balance in pressure equation
+            flux_mom = n_mid * v_mid * v_mid;
+          } else {
+            flux_mom = s.R * sv.R * sv.R
+                       + BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.p))
+                             * (s.R * sv.R - n_mid * v_mid);
+          }
+
+          // Assume that particle flux is fixed to boundary value
+          const BoutReal flux_part = n_mid * v_mid;
+
+          // d/dt(1/2 m n v^2) = v * d/dt(mnv) - 1/2 m v^2 * dn/dt
+          const BoutReal actual_ke = sv.c * flux_mom - 0.5 * sv.c * sv.c * flux_part;
+
+          // Note: If the actual loss was higher than expected, then
+          //       plasma heating is needed to compensate
+          result(i, j, k) += (actual_ke - expected_ke) * flux_factor_rc;
+
+          // Final flow through boundary is the expected value
+          flow_ylow(i, j + 1, k) += expected_ke * area_rp; //expected_ke * area_rp;
+
+        } else {
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
+                                        fabs(sv.c), fabs(sv.p));
+
+          // Viscous heating due to relaxation of velocity towards midpoint
+          result(i, j, k) +=
+              (amax + 0.5 * sv.R) * s.R * (sv.c - sv.p) * (sv.R - v_mid) * flux_factor_rc;
+
+          // Kinetic energy flow into next cell.
+          // Note: Different from flow out of this cell; the difference
+          //       is in the viscous heating.
+          const BoutReal flux_part = s.R * 0.5 * (sv.R + amax);
+          const BoutReal flux_mom = flux_part * sv.R;
+
+          flow_ylow(i, j + 1, k) +=
+              (sv.p * flux_mom - 0.5 * SQ(sv.p) * flux_part) * area_rp;
+        }
+
+        ////////////////////////////////////////////
+        // Calculate at left boundary
+
+        v_mid = 0.5 * (sv.c + sv.m);
+        n_mid = 0.5 * (s.c + s.m);
+
+        // Expected KE loss. Note minus sign because negative v into boundary
+        const BoutReal expected_ke = -0.5 * n_mid * v_mid * v_mid * v_mid;
+
+        if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) {
+          // First point in domain
+          BoutReal flux_mom;
+          if (fixflux) {
+            // Use mid-point to be consistent with boundary conditions
+            flux_mom = n_mid * v_mid * v_mid;
+          } else {
+            // Add flux due to difference in boundary values
+            flux_mom = s.L * sv.L * sv.L
+                       - BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.m))
+                             * (s.L * sv.L - n_mid * v_mid);
+          }
+
+          // Assume that density flux is fixed to boundary value
+          const BoutReal flux_part = n_mid * v_mid;
+
+          // d/dt(1/2 m n v^2) = v * d/dt(mnv) - 1/2 m v^2 * dn/dt
+          const BoutReal actual_ke = -sv.c * flux_mom + 0.5 * sv.c * sv.c * flux_part;
+
+          result(i, j, k) += (actual_ke - expected_ke) * flux_factor_lc;
+
+          flow_ylow(i, j, k) -= expected_ke * area_lc;
+        } else {
+          // Maximum wave speed in the two cells
+          const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
+                                        fabs(sv.c), fabs(sv.m));
+
+          // Viscous heating due to relaxation
+          result(i, j, k) +=
+              (amax - 0.5 * sv.L) * s.L * (sv.c - sv.m) * (sv.L - v_mid) * flux_factor_lc;
+
+          // Kinetic energy flow into this cell.
+          // Note: Different from flow out of left cell; the difference
+          //       is in the viscous heating.
+          const BoutReal flux_part = s.L * 0.5 * (sv.L - amax);
+          const BoutReal flux_mom = flux_part * sv.L;
+
+          flow_ylow(i, j, k) += (sv.c * flux_mom - 0.5 * SQ(sv.c) * flux_part) * area_lc;
+        }
+      }
+    }
+  }
+  flow_ylow = fromFieldAligned(flow_ylow, "RGN_NOBNDRY");
+  return fromFieldAligned(result, "RGN_NOBNDRY");
+}
 } // namespace FV
 #endif // BOUT_FV_OPS_H

From 4b8f73fb0e871a2e897cc59ba384511ee8ac307c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Jul 2026 12:56:02 +0200
Subject: [PATCH 1576/1827] Port Div_a_Grad_perp_limit from hermes-3

---
 include/bout/fv_ops_impl.hxx | 252 +++++++++++++++++++++++++++++++++++
 1 file changed, 252 insertions(+)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index f99ec961e3..ac9041a19b 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -1242,5 +1242,257 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
   flow_ylow = fromFieldAligned(flow_ylow, "RGN_NOBNDRY");
   return fromFieldAligned(result, "RGN_NOBNDRY");
 }
+
+/// Div ( a g Grad_perp(f) )  -- Perpendicular gradient-driven advection
+///
+/// This version uses a slope limiter to calculate cell edge values of g in X,
+/// the advects the upwind cell edge.
+///
+/// 1st order upwinding is used in Y.
+template <typename CellEdges = MC>
+const Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g,
+                                    const Field3D& f) {
+  ASSERT2(a.getLocation() == f.getLocation());
+
+  Mesh* mesh = a.getMesh();
+
+  // Requires at least 2 communication guard cells in X, 1 in Y
+  ASSERT1(mesh->xstart >= 2);
+  ASSERT1(mesh->ystart >= 1);
+
+  CellEdges cellboundary;
+
+  Field3D result{zeroFrom(f)};
+
+  Coordinates* coord = f.getCoordinates();
+
+  // Flux in x
+
+  for (int i = mesh->xstart - 1; i <= mesh->xend; i++) {
+    for (int j = mesh->ystart; j <= mesh->yend; j++) {
+      for (int k = 0; k < mesh->LocalNz; k++) {
+        // Calculate flux from i to i+1
+
+        const BoutReal gradient = f(i + 1, j, k) - f(i, j, k);
+
+        // Mid-point average boundary value of 'a'
+        const BoutReal aedge = 0.5 * (a(i + 1, j, k) + a(i, j, k));
+        BoutReal gedge;
+        if (((i == mesh->xstart - 1) and mesh->firstX())
+            or ((i == mesh->xend) and mesh->lastX())) {
+          // Mid-point average boundary value of 'g'
+          gedge = 0.5 * (g(i + 1, j, k) + g(i, j, k));
+        } else if (gradient > 0) {
+          // Flux is from (i+1) to (i)
+          // Reconstruct `g` at left of (i+1, j, k)
+
+          Stencil1D sg;
+          sg.m = g(i, j, k);
+          sg.c = g(i + 1, j, k);
+          sg.p = g(i + 2, j, k);
+          cellboundary(sg); // Calculate sg.R and sg.L
+
+          gedge = sg.L;
+        } else {
+          // Flux is from (i) to (i+1)
+          // Reconstruct `g` at right of (i, j, k)
+
+          Stencil1D sg;
+          sg.m = g(i - 1, j, k);
+          sg.c = g(i, j, k);
+          sg.p = g(i + 1, j, k);
+          cellboundary(sg); // Calculate sg.R and sg.L
+
+          gedge = sg.R;
+        }
+
+        // Flux across cell edge
+        const BoutReal fout = gradient * aedge * gedge
+                              * (coord->J(i, j, k) * coord->g11(i, j, k)
+                                 + coord->J(i + 1, j, k) * coord->g11(i + 1, j, k))
+                              / (coord->dx(i, j, k) + coord->dx(i + 1, j, k));
+
+        result(i, j, k) += fout / (coord->dx(i, j, k) * coord->J(i, j, k));
+        result(i + 1, j, k) -= fout / (coord->dx(i + 1, j, k) * coord->J(i + 1, j, k));
+      }
+    }
+  }
+
+  // Y and Z fluxes require Y derivatives
+
+  // Fields containing values along the magnetic field
+  Field3D fup(mesh), fdown(mesh);
+  Field3D aup(mesh), adown(mesh);
+  Field3D gup(mesh), gdown(mesh);
+
+  // Values on this y slice (centre).
+  // This is needed because toFieldAligned may modify the field
+  Field3D ac = a;
+  Field3D gc = g;
+  Field3D fc = f;
+
+  // Result of the Y and Z fluxes
+  Field3D yzresult(mesh);
+  yzresult.allocate();
+
+  if (f.hasParallelSlices() && a.hasParallelSlices() && g.hasParallelSlices()) {
+    // All inputs have yup and ydown
+
+    fup = f.yup();
+    fdown = f.ydown();
+
+    aup = a.yup();
+    adown = a.ydown();
+
+    gup = g.yup();
+    gdown = g.ydown();
+  } else {
+    // At least one input doesn't have yup/ydown fields.
+    // Need to shift to/from field aligned coordinates
+
+    fup = fdown = fc = toFieldAligned(f);
+    aup = adown = ac = toFieldAligned(a);
+    gup = gdown = gc = toFieldAligned(g);
+    yzresult.setDirectionY(YDirectionType::Aligned);
+  }
+
+  // Y flux
+
+  for (int i = mesh->xstart; i <= mesh->xend; i++) {
+    for (int j = mesh->ystart; j <= mesh->yend; j++) {
+#if BOUT_USE_METRIC_3D
+      for (int k = 0; k < mesh->LocalNz; k++)
+#else
+      int k = 0;
+#endif
+      {
+        BoutReal coef_u =
+            0.5
+            * (coord->g_23(i, j, k) / SQ(coord->J(i, j, k) * coord->Bxy(i, j, k))
+               + coord->g_23(i, j + 1, k)
+                     / SQ(coord->J(i, j + 1, k) * coord->Bxy(i, j + 1, k)));
+
+        BoutReal coef_d =
+            0.5
+            * (coord->g_23(i, j, k) / SQ(coord->J(i, j, k) * coord->Bxy(i, j, k))
+               + coord->g_23(i, j - 1, k)
+                     / SQ(coord->J(i, j - 1, k) * coord->Bxy(i, j - 1, k)));
+
+#if not BOUT_USE_METRIC_3D
+        for (int k = 0; k < mesh->LocalNz; k++)
+#endif
+        {
+          // Calculate flux between j and j+1
+          int kp = (k + 1) % mesh->LocalNz;
+          int km = (k - 1 + mesh->LocalNz) % mesh->LocalNz;
+
+          // Calculate Z derivative at y boundary
+          BoutReal dfdz =
+              0.25 * (fc(i, j, kp) - fc(i, j, km) + fup(i, j + 1, kp) - fup(i, j + 1, km))
+              / coord->dz(i, j, k);
+
+          // Y derivative
+          BoutReal dfdy = 2. * (fup(i, j + 1, k) - fc(i, j, k))
+                          / (coord->dy(i, j + 1, k) + coord->dy(i, j, k));
+
+          BoutReal aedge = 0.5 * (ac(i, j, k) + aup(i, j + 1, k));
+          BoutReal gedge;
+          if ((j == mesh->yend) and mesh->lastY(i)) {
+            // Midpoint boundary value
+            gedge = 0.5 * (gc(i, j, k) + gup(i, j + 1, k));
+          } else if (dfdy > 0) {
+            // Flux from (j+1) to (j)
+            gedge = gup(i, j + 1, k);
+          } else {
+            // Flux from (j) to (j+1)
+            gedge = gc(i, j, k);
+          }
+
+          BoutReal fout = aedge * gedge * 0.5
+                          * (coord->J(i, j, k) * coord->g23(i, j, k)
+                             + coord->J(i, j + 1, k) * coord->g23(i, j + 1, k))
+                          * (dfdz - coef_u * dfdy);
+
+          yzresult(i, j, k) = fout / (coord->dy(i, j, k) * coord->J(i, j, k));
+
+          // Calculate flux between j and j-1
+          dfdz =
+              0.25
+              * (fc(i, j, kp) - fc(i, j, km) + fdown(i, j - 1, kp) - fdown(i, j - 1, km))
+              / coord->dz(i, j, k);
+
+          dfdy = 2. * (fc(i, j, k) - fdown(i, j - 1, k))
+                 / (coord->dy(i, j, k) + coord->dy(i, j - 1, k));
+
+          aedge = 0.5 * (ac(i, j, k) + adown(i, j - 1, k));
+          if ((j == mesh->ystart) and mesh->firstY(i)) {
+            gedge = 0.5 * (gc(i, j, k) + gdown(i, j - 1, k));
+          } else if (dfdy > 0) {
+            gedge = gc(i, j, k);
+          } else {
+            gedge = gdown(i, j - 1, k);
+          }
+
+          fout = aedge * gedge * 0.5
+                 * (coord->J(i, j, k) * coord->g23(i, j, k)
+                    + coord->J(i, j - 1, k) * coord->g23(i, j - 1, k))
+                 * (dfdz - coef_d * dfdy);
+
+          yzresult(i, j, k) -= fout / (coord->dy(i, j, k) * coord->J(i, j, k));
+        }
+      }
+    }
+  }
+
+  // Z flux
+  // Easier since all metrics constant in Z
+
+  for (int i = mesh->xstart; i <= mesh->xend; i++) {
+    for (int j = mesh->ystart; j <= mesh->yend; j++) {
+#if BOUT_USE_METRIC_3D
+      for (int k = 0; k < mesh->LocalNz; k++)
+#else
+      int k = 0;
+#endif
+      {
+        // Coefficient in front of df/dy term
+        BoutReal coef =
+            coord->g_23(i, j, k)
+            / (coord->dy(i, j + 1, k) + 2. * coord->dy(i, j, k) + coord->dy(i, j - 1, k))
+            / SQ(coord->J(i, j, k) * coord->Bxy(i, j, k));
+#if not BOUT_USE_METRIC_3D
+        for (int k = 0; k < mesh->LocalNz; k++)
+#endif
+        {
+          // Calculate flux between k and k+1
+          int kp = (k + 1) % mesh->LocalNz;
+
+          BoutReal gradient =
+              // df/dz
+              (fc(i, j, kp) - fc(i, j, k)) / coord->dz(i, j, k)
+
+              // - g_yz * df/dy / SQ(J*B)
+              - coef
+                    * (fup(i, j + 1, k) + fup(i, j + 1, kp) - fdown(i, j - 1, k)
+                       - fdown(i, j - 1, kp));
+
+          BoutReal fout = gradient * 0.5 * (ac(i, j, kp) + ac(i, j, k))
+                          * ((gradient > 0) ? gc(i, j, kp) : gc(i, j, k));
+
+          yzresult(i, j, k) += fout / coord->dz(i, j, k);
+          yzresult(i, j, kp) -= fout / coord->dz(i, j, kp);
+        }
+      }
+    }
+  }
+  // Check if we need to transform back
+  if (f.hasParallelSlices() && a.hasParallelSlices()) {
+    result += yzresult;
+  } else {
+    result += fromFieldAligned(yzresult);
+  }
+  return result;
+}
+
 } // namespace FV
 #endif // BOUT_FV_OPS_H

From d42c5f5f9bc9c2f06f4b8f1874bb7b4259e52349 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Jul 2026 12:58:49 +0200
Subject: [PATCH 1577/1827] Declare communicateFluxes only once

---
 include/bout/fv_ops.hxx      | 17 +++++++++++++++++
 include/bout/fv_ops_impl.hxx | 12 +++---------
 2 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index b2b0e49120..c7a6f6774c 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -165,5 +165,22 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
 template <typename CellEdges = MC>
 Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
                     const Field3D& wave_speed_in, bool fixflux = true);
+
+/// Calculates viscous heating due to numerical momentum fluxes
+/// and flow of kinetic energy (in flow_ylow)
+template <typename CellEdges = MC>
+Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
+                            const Field3D& wave_speed_in, Field3D& flow_ylow,
+                            bool fixflux = true);
+
+/// Div ( a g Grad_perp(f) )  -- Perpendicular gradient-driven advection
+///
+/// This version uses a slope limiter to calculate cell edge values of g in X,
+/// the advects the upwind cell edge.
+///
+/// 1st order upwinding is used in Y.
+template <typename CellEdges = MC>
+const Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D& f);
+
 } // namespace FV
 #endif // BOUT_FV_OPS_H
diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index ac9041a19b..ecbfe4add4 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -270,12 +270,6 @@ struct WENO3 {
   }
 };
 
-/*!
-   * Communicate fluxes between processors
-   * Takes values in guard cells, and adds them to cells
-   */
-void communicateFluxes(Field3D& f);
-
 /// Finite volume parallel divergence
 ///
 /// Preserves the sum of f*J*dx*dy*dz over the domain
@@ -984,10 +978,10 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
 
 // Calculates viscous heating due to numerical momentum fluxes
 // and flow of kinetic energy (in flow_ylow)
-template <typename CellEdges = MC>
+template <typename CellEdges>
 Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
                             const Field3D& wave_speed_in, Field3D& flow_ylow,
-                            bool fixflux = true) {
+                            bool fixflux) {
 
   ASSERT1(areFieldsCompatible(f_in, v_in));
   ASSERT1(areFieldsCompatible(f_in, wave_speed_in));
@@ -1249,7 +1243,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
 /// the advects the upwind cell edge.
 ///
 /// 1st order upwinding is used in Y.
-template <typename CellEdges = MC>
+template <typename CellEdges>
 const Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g,
                                     const Field3D& f) {
   ASSERT2(a.getLocation() == f.getLocation());

From d9277946570e15bc6dff8125924fa3daa40a2acf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Jul 2026 13:09:41 +0200
Subject: [PATCH 1578/1827] Add explicit instantiations for moved functions

---
 src/mesh/fv_ops.cxx | 36 +++++++++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index 1bd00d34a9..01c7ca8352 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -573,6 +573,11 @@ template Field3D Div_f_v<Upwind>(const Field3D& n_in, const Vector3D& v, bool bn
 template Field3D Div_par_mod<Upwind>(const Field3D& f_in, const Field3D& v_in,
                                      const Field3D& wave_speed_in, Field3D& flow_ylow,
                                      bool fixflux = true);
+template Field3D Div_par_fvv_heating<Upwind>(const Field3D& f_in, const Field3D& v_in,
+                                             const Field3D& wave_speed_in,
+                                             Field3D& flow_ylow, bool fixflux = true);
+template Field3D Div_a_Grad_perp_limit<Upwind>(const Field3D& a, const Field3D& g,
+                                               const Field3D& f);
 
 template Field3D Div_par_fvv<Fromm>(const Field3D& f_in, const Field3D& v_in,
                                     const Field3D& wave_speed_in, bool fixflux = true);
@@ -582,6 +587,11 @@ template Field3D Div_f_v<Fromm>(const Field3D& n_in, const Vector3D& v, bool bnd
 template Field3D Div_par_mod<Fromm>(const Field3D& f_in, const Field3D& v_in,
                                     const Field3D& wave_speed_in, Field3D& flow_ylow,
                                     bool fixflux = true);
+template Field3D Div_par_fvv_heating<Fromm>(const Field3D& f_in, const Field3D& v_in,
+                                            const Field3D& wave_speed_in,
+                                            Field3D& flow_ylow, bool fixflux = true);
+template Field3D Div_a_Grad_perp_limit<Fromm>(const Field3D& a, const Field3D& g,
+                                              const Field3D& f);
 
 template Field3D Div_par_fvv<MinMod>(const Field3D& f_in, const Field3D& v_in,
                                      const Field3D& wave_speed_in, bool fixflux = true);
@@ -591,6 +601,11 @@ template Field3D Div_f_v<MinMod>(const Field3D& n_in, const Vector3D& v, bool bn
 template Field3D Div_par_mod<MinMod>(const Field3D& f_in, const Field3D& v_in,
                                      const Field3D& wave_speed_in, Field3D& flow_ylow,
                                      bool fixflux = true);
+template Field3D Div_par_fvv_heating<MinMod>(const Field3D& f_in, const Field3D& v_in,
+                                             const Field3D& wave_speed_in,
+                                             Field3D& flow_ylow, bool fixflux = true);
+template Field3D Div_a_Grad_perp_limit<MinMod>(const Field3D& a, const Field3D& g,
+                                               const Field3D& f);
 
 template Field3D Div_par_fvv<MC>(const Field3D& f_in, const Field3D& v_in,
                                  const Field3D& wave_speed_in, bool fixflux = true);
@@ -600,6 +615,11 @@ template Field3D Div_f_v<MC>(const Field3D& n_in, const Vector3D& v, bool bndry_
 template Field3D Div_par_mod<MC>(const Field3D& f_in, const Field3D& v_in,
                                  const Field3D& wave_speed_in, Field3D& flow_ylow,
                                  bool fixflux = true);
+template Field3D Div_par_fvv_heating<MC>(const Field3D& f_in, const Field3D& v_in,
+                                         const Field3D& wave_speed_in, Field3D& flow_ylow,
+                                         bool fixflux = true);
+template Field3D Div_a_Grad_perp_limit<MC>(const Field3D& a, const Field3D& g,
+                                           const Field3D& f);
 
 template Field3D Div_par_fvv<Superbee>(const Field3D& f_in, const Field3D& v_in,
                                        const Field3D& wave_speed_in, bool fixflux = true);
@@ -610,6 +630,11 @@ template Field3D Div_f_v<Superbee>(const Field3D& n_in, const Vector3D& v,
 template Field3D Div_par_mod<Superbee>(const Field3D& f_in, const Field3D& v_in,
                                        const Field3D& wave_speed_in, Field3D& flow_ylow,
                                        bool fixflux = true);
+template Field3D Div_par_fvv_heating<Superbee>(const Field3D& f_in, const Field3D& v_in,
+                                               const Field3D& wave_speed_in,
+                                               Field3D& flow_ylow, bool fixflux = true);
+template Field3D Div_a_Grad_perp_limit<Superbee>(const Field3D& a, const Field3D& g,
+                                                 const Field3D& f);
 
 template Field3D Div_par_fvv<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
                                         const Field3D& wave_speed_in,
@@ -621,6 +646,11 @@ template Field3D Div_f_v<VanAlbada>(const Field3D& n_in, const Vector3D& v,
 template Field3D Div_par_mod<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
                                         const Field3D& wave_speed_in, Field3D& flow_ylow,
                                         bool fixflux = true);
+template Field3D Div_par_fvv_heating<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
+                                                const Field3D& wave_speed_in,
+                                                Field3D& flow_ylow, bool fixflux = true);
+template Field3D Div_a_Grad_perp_limit<VanAlbada>(const Field3D& a, const Field3D& g,
+                                                  const Field3D& f);
 
 template Field3D Div_par_fvv<WENO3>(const Field3D& f_in, const Field3D& v_in,
                                     const Field3D& wave_speed_in, bool fixflux = true);
@@ -630,5 +660,9 @@ template Field3D Div_f_v<WENO3>(const Field3D& n_in, const Vector3D& v, bool bnd
 template Field3D Div_par_mod<WENO3>(const Field3D& f_in, const Field3D& v_in,
                                     const Field3D& wave_speed_in, Field3D& flow_ylow,
                                     bool fixflux = true);
-
+template Field3D Div_par_fvv_heating<WENO3>(const Field3D& f_in, const Field3D& v_in,
+                                            const Field3D& wave_speed_in,
+                                            Field3D& flow_ylow, bool fixflux = true);
+template Field3D Div_a_Grad_perp_limit<WENO3>(const Field3D& a, const Field3D& g,
+                                              const Field3D& f);
 } // Namespace FV

From 3c4383d12ec98ede8b6154c427ae0a4c00604e77 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 2 Jul 2026 13:12:13 +0200
Subject: [PATCH 1579/1827] Return should be non-const

---
 include/bout/fv_ops.hxx      | 2 +-
 include/bout/fv_ops_impl.hxx | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index c7a6f6774c..98dc689bfd 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -180,7 +180,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
 ///
 /// 1st order upwinding is used in Y.
 template <typename CellEdges = MC>
-const Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D& f);
+Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D& f);
 
 } // namespace FV
 #endif // BOUT_FV_OPS_H
diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index ecbfe4add4..9e436ad95d 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -1244,8 +1244,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
 ///
 /// 1st order upwinding is used in Y.
 template <typename CellEdges>
-const Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g,
-                                    const Field3D& f) {
+Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D& f) {
   ASSERT2(a.getLocation() == f.getLocation());
 
   Mesh* mesh = a.getMesh();

From 0b187d94572086b6fae3a376e43e375a72f1ecdc Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 4 Jul 2026 08:54:01 -0700
Subject: [PATCH 1580/1827] Coordinates::_compute_cell_area_z check
 _compute_cell_area_z

Was testing _cell_volume.has_value() rather than
_cell_area_zlow.has_value().

Added regression test.
---
 src/mesh/coordinates.cxx             |  2 +-
 tests/unit/mesh/test_coordinates.cxx | 27 +++++++++++++++++++++++++++
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 10b560f71c..e7a7579d45 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -2140,7 +2140,7 @@ void Coordinates::_compute_cell_area_y() const {
 void Coordinates::_compute_cell_area_z() const {
   BOUT_OMP_SAFE(critical)
   {
-    if (!_cell_volume.has_value()) {
+    if (!_cell_area_zlow.has_value()) {
       const FieldMetric area_centre = J / sqrt(g_33) * dx * dy;
       _cell_area_zlow.emplace(emptyFrom(area_centre));
       _cell_area_zhigh.emplace(emptyFrom(area_centre));
diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx
index ea233cd9ca..8e1aa2e13f 100644
--- a/tests/unit/mesh/test_coordinates.cxx
+++ b/tests/unit/mesh/test_coordinates.cxx
@@ -374,3 +374,30 @@ TEST_F(CoordinatesTest, CellAreasUpdate) {
 
   EXPECT_TRUE(IsFieldEqual(coords.cell_volume(), 8.0));
 }
+
+TEST_F(CoordinatesTest, CellAreaZComputedAfterCellVolume) {
+  Coordinates coords{mesh,
+                     FieldMetric{1.0},  // dx
+                     FieldMetric{1.0},  // dy
+                     FieldMetric{1.0},  // dz
+                     FieldMetric{6.0},  // J
+                     FieldMetric{1.0},  // Bxy
+                     FieldMetric{1.0},  // g11
+                     FieldMetric{1.0},  // g22
+                     FieldMetric{9.0},  // g33
+                     FieldMetric{0.0},  // g12
+                     FieldMetric{0.0},  // g13
+                     FieldMetric{0.0},  // g23
+                     FieldMetric{4.0},  // g_11
+                     FieldMetric{1.0},  // g_22
+                     FieldMetric{9.0},  // g_33
+                     FieldMetric{0.0},  // g_12
+                     FieldMetric{0.0},  // g_13
+                     FieldMetric{0.0},  // g_23
+                     FieldMetric{0.0},  // ShiftTorsion
+                     FieldMetric{0.0}}; // IntShiftTorsion
+
+  EXPECT_TRUE(IsFieldEqual(coords.cell_volume(), 6.0));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zlow(), 2.0, "RGN_NOZ"));
+  EXPECT_TRUE(IsFieldEqual(coords.cell_area_zhigh(), 2.0, "RGN_NOZ"));
+}

From 2c41fcabfcffe7e5197f2609aaa2bba2dcb9823d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 4 Jul 2026 08:55:48 -0700
Subject: [PATCH 1581/1827] FV ops: Document diagnostics for FCI args

Field-aligned operation returns a flow diagnostic, but this is
not currently done for FCI. Set to zero and document behavior.
---
 include/bout/coordinates.hxx             | 9 +--------
 include/bout/difops.hxx                  | 1 +
 include/bout/fv_ops.hxx                  | 1 +
 include/bout/fv_ops_impl.hxx             | 1 +
 tests/MMS/spatial/finite-volume/makefile | 2 +-
 5 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index a21f62cd4d..14019728d0 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -1,15 +1,8 @@
 /**************************************************************************
  * Describes coordinate systems
  *
- * ChangeLog
- * =========
- *
- * 2014-11-10 Ben Dudson <bd512@york.ac.uk>
- *    * Created by separating metric from Mesh
- *
- *
  **************************************************************************
- * Copyright 2014-2025 BOUT++ contributors
+ * Copyright 2014-2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 2070cc30d3..0754c1feb6 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -196,6 +196,7 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f,
                            CELL_LOC outloc = CELL_DEFAULT);
 
 /// Version with energy flow diagnostic
+/// For FCI fields, `flow_ylow` is currently returned as zero.
 Field3D Div_par_K_Grad_par_mod(const Field3D& k, const Field3D& f, Field3D& flow_ylow,
                                bool bndry_flux = true);
 
diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index b2b0e49120..94c599c58c 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -151,6 +151,7 @@ Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc = CELL_
 ///
 /// @param[out] flow_ylow    Flow at the lower Y cell boundary
 ///                          Already includes area factor * flux
+///                          For FCI fields this diagnostic is currently set to zero.
 template <typename CellEdges = MC>
 Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
                     const Field3D& wave_speed_in, Field3D& flow_ylow,
diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 3755467027..7da980e584 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -635,6 +635,7 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
     const auto& v_down = v_in.ydown();
 
     Field3D result{emptyFrom(f_in)};
+    flow_ylow = zeroFrom(f_in);
     BOUT_FOR(i, f_in.getRegion("RGN_NOBNDRY")) {
       const auto iyp = i.yp();
       const auto iym = i.ym();
diff --git a/tests/MMS/spatial/finite-volume/makefile b/tests/MMS/spatial/finite-volume/makefile
index 88ba6c77e7..7111f5ed8e 100644
--- a/tests/MMS/spatial/finite-volume/makefile
+++ b/tests/MMS/spatial/finite-volume/makefile
@@ -1,6 +1,6 @@
 
 BOUT_TOP	= ../../../..
 
-SOURCEC		= fci_mms.cxx
+SOURCEC		= fv_mms.cxx
 
 include $(BOUT_TOP)/make.config

From 8fb81ad62617baeb304b2a6478d277d2717f4e81 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 4 Jul 2026 10:29:14 -0700
Subject: [PATCH 1582/1827] Documentation of FV operators and metric caching

Short descriptions of the ported operators, SuperBee slope limiter,
and metric derived quantity caching.
---
 manual/sphinx/developer_docs/mesh.rst         | 23 +++++++
 .../user_docs/differential_operators.rst      | 65 +++++++++++++++++++
 2 files changed, 88 insertions(+)

diff --git a/manual/sphinx/developer_docs/mesh.rst b/manual/sphinx/developer_docs/mesh.rst
index ff3e40d4b0..b1861fc416 100644
--- a/manual/sphinx/developer_docs/mesh.rst
+++ b/manual/sphinx/developer_docs/mesh.rst
@@ -307,3 +307,26 @@ because they are needed in a lot of the code. They shouldn’t change
 after initialisation, unless the physics model starts doing fancy
 things with deforming meshes. In that case it is up to the user to
 ensure they are updated.
+
+.. _sec-derived-geometric-quantities:
+
+Derived geometric quantities
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+`Coordinates` also provides several quantities derived from the metric tensor
+and Jacobian, rather than requiring each operator to reconstruct them locally.
+Examples include:
+
+* `g_22` evaluated at the lower and upper `y` cell faces
+* cell-face areas in the `x`, `y`, and `z` directions
+* cell volumes
+
+These are used by conservative operators, especially the finite-volume
+operators documented in :ref:`sec-finite-volume-operators`, where fluxes are
+naturally expressed as a face area multiplied by a face flux and divided by a
+cell volume.
+
+In the current implementation these quantities are computed lazily from the
+current metric data and then cached for reuse. This keeps the operator code
+closer to the discrete flux expressions while centralising the geometry
+construction in `Coordinates`.
diff --git a/manual/sphinx/user_docs/differential_operators.rst b/manual/sphinx/user_docs/differential_operators.rst
index 71dbeb4f9e..3de13001ab 100644
--- a/manual/sphinx/user_docs/differential_operators.rst
+++ b/manual/sphinx/user_docs/differential_operators.rst
@@ -503,6 +503,8 @@ neglected if :math:`g_{xy}` and :math:`g_{yz}` are non-zero. An
 example of usage of the brackets can be found in for example
 ``examples/MMS/advection`` or ``examples/blob2d``.
 
+.. _sec-finite-volume-operators:
+
 Finite volume, conservative finite difference methods
 -----------------------------------------------------
 
@@ -537,6 +539,8 @@ The methods can be used by including the
 
 Some methods (those with templates) are defined in the header, but others
 are defined in :doc:`src/mesh/fv_ops.cxx<../_breathe_autogen/file/fv__ops_8cxx>`.
+These operators use derived geometric quantities such as cell-face areas and
+cell volumes; see :ref:`sec-derived-geometric-quantities`.
 
 
 Parallel divergence ``Div_par``
@@ -570,6 +574,45 @@ be changed at compile time e.g::
 A list of available limiters is given in section :ref:`sec-slope-limiters` below.
 
 
+Modified parallel divergence ``Div_par_mod``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is a modified version of ``FV::Div_par`` which applies the limiter to both
+the advected field and the velocity. This typically gives smaller overshoots
+than ``FV::Div_par`` for the same limiter choice.
+
+::
+
+   template<typename CellEdges = MC>
+   Field3D Div_par_mod(const Field3D &f_in, const Field3D &v_in,
+                       const Field3D &a, Field3D &flow_ylow,
+                       bool fixflux=true);
+
+
+The extra output argument ``flow_ylow`` stores the flow through the lower
+:math:`y` cell boundary, including the area factor. This can be useful as a
+diagnostic in energy or flux budgets. For FCI fields this diagnostic is
+currently returned as zero.
+
+
+Parallel momentum flux ``Div_par_fvv``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This operator calculates the divergence of :math:`f v v`, and is mainly useful
+for the parallel momentum equation:
+
+::
+
+   template<typename CellEdges = MC>
+   Field3D Div_par_fvv(const Field3D &f_in, const Field3D &v_in,
+                       const Field3D &a, bool fixflux=true);
+
+
+This is provided separately rather than forming :math:`fv` first, so that the
+reconstructed values of :math:`f` and :math:`v` remain consistent with the
+other finite-volume advection operators.
+
+
 Example and convergence test
 ++++++++++++++++++++++++++++
 
@@ -620,6 +663,24 @@ This is done by calculating the flux :math:`k\partial_{||}\left(f\right)` on cel
 using central differencing.
 
 
+Parallel diffusion with flow diagnostic ``Div_par_K_Grad_par_mod``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This variant of the parallel diffusion operator also returns a lower-face flow
+diagnostic:
+
+::
+
+   Field3D Div_par_K_Grad_par_mod(const Field3D &k, const Field3D &f,
+                                  Field3D &flow_ylow,
+                                  bool bndry_flux=true);
+
+
+As for ``Div_par_mod``, ``flow_ylow`` stores the lower :math:`y` boundary flow
+including the area factor. For FCI fields this diagnostic is currently returned
+as zero.
+
+
 Advection in 3D
 ~~~~~~~~~~~~~~~
 
@@ -667,6 +728,10 @@ values. Several slope limiters are defined in ``fv_ops.hxx``:
   to ``MinMod``. It has smaller dissipation than ``MinMod`` so is the
   default.
 
+* ``Superbee`` - A more compressive TVD limiter than ``MC`` or ``MinMod``.
+  It tends to sharpen steep gradients and contacts more aggressively, at the
+  cost of being less smooth.
+
 * ``VanAlbada`` - A smooth (differentiable) symmetric slope limiter which
   avoids piecewise branches at extrema. This can be useful for nonlinear
   solvers and finite-difference Jacobian calculations.

From 743b042bdb770939e90e507233c1d97f43426b56 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 4 Jul 2026 15:08:24 -0700
Subject: [PATCH 1583/1827] Apply suggestions from code review

Co-authored-by: David Bold <dave@ipp.mpg.de>
---
 cmake/GenerateGitMetadata.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/GenerateGitMetadata.cmake b/cmake/GenerateGitMetadata.cmake
index 65451d0a39..b21d7c58e0 100644
--- a/cmake/GenerateGitMetadata.cmake
+++ b/cmake/GenerateGitMetadata.cmake
@@ -64,7 +64,7 @@ if(GIT_EXECUTABLE)
         ERROR_QUIET
       )
       if(NOT git_cached_diff_result EQUAL 0)
-        set(git_cached_diff "")
+        set(git_cached_diff "git diff unavailable")
       endif()
 
       execute_process(

From 1925059551e1884e981bc5d2777424a9594d28a7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sat, 4 Jul 2026 15:37:30 -0700
Subject: [PATCH 1584/1827] Git metadata: Configure git_metadata.cxx.in file

Configures a .in file, rather than emitting all lines of the file.
Easier to read and maintain (hopefully).
---
 cmake/GenerateGitMetadata.cmake | 26 +++-----------------------
 cmake/git_metadata.cxx.in       | 16 ++++++++++++++++
 2 files changed, 19 insertions(+), 23 deletions(-)
 create mode 100644 cmake/git_metadata.cxx.in

diff --git a/cmake/GenerateGitMetadata.cmake b/cmake/GenerateGitMetadata.cmake
index b21d7c58e0..f38bde80ae 100644
--- a/cmake/GenerateGitMetadata.cmake
+++ b/cmake/GenerateGitMetadata.cmake
@@ -94,30 +94,10 @@ endif()
 escape_cxx_string("${git_diff}" git_diff_escaped)
 
 set(output_tmp "${OUTPUT_FILE}.tmp")
-file(WRITE "${output_tmp}" "#include \"bout/git_metadata.hxx\"\n\n")
-file(APPEND "${output_tmp}" "namespace bout {\n")
-file(APPEND "${output_tmp}" "namespace version {\n")
-file(APPEND "${output_tmp}" "namespace {\n")
-file(
-  APPEND "${output_tmp}"
-  "constexpr bool git_metadata_available_value = ${git_metadata_available};\n"
-)
-file(APPEND "${output_tmp}" "constexpr bool git_dirty_value = ${git_dirty};\n")
-file(APPEND "${output_tmp}" "constexpr char git_diff_value[] =\n")
-file(APPEND "${output_tmp}" "\"${git_diff_escaped}\";\n")
-file(APPEND "${output_tmp}" "} // namespace\n\n")
-file(
-  APPEND "${output_tmp}"
-  "auto git_metadata_available() -> bool { return git_metadata_available_value; }\n"
-)
-file(APPEND "${output_tmp}"
-     "auto git_dirty() -> bool { return git_dirty_value; }\n"
-)
-file(APPEND "${output_tmp}"
-     "auto git_diff() -> std::string_view { return git_diff_value; }\n"
+
+configure_file(
+  "${CMAKE_CURRENT_LIST_DIR}/git_metadata.cxx.in" "${output_tmp}" @ONLY
 )
-file(APPEND "${output_tmp}" "} // namespace version\n")
-file(APPEND "${output_tmp}" "} // namespace bout\n")
 
 execute_process(
   COMMAND "${CMAKE_COMMAND}" -E copy_if_different "${output_tmp}"
diff --git a/cmake/git_metadata.cxx.in b/cmake/git_metadata.cxx.in
new file mode 100644
index 0000000000..fc8a5b1a2f
--- /dev/null
+++ b/cmake/git_metadata.cxx.in
@@ -0,0 +1,16 @@
+#include "bout/git_metadata.hxx"
+
+namespace bout {
+namespace version {
+namespace {
+constexpr bool git_metadata_available_value = @git_metadata_available@;
+constexpr bool git_dirty_value = @git_dirty@;
+constexpr char git_diff_value[] =
+"@git_diff_escaped@";
+} // namespace
+
+auto git_metadata_available() -> bool { return git_metadata_available_value; }
+auto git_dirty() -> bool { return git_dirty_value; }
+auto git_diff() -> std::string_view { return git_diff_value; }
+} // namespace version
+} // namespace bout

From 25e2acdce3fdfcfbcef796b5696f73de7d314063 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 6 Jul 2026 13:13:06 +0200
Subject: [PATCH 1585/1827] Regenerate time also for updated, untracked files

---
 CMakeLists.txt | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c594e47c03..9ecc645a7c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -512,15 +512,6 @@ else()
 endif()
 set(BOUT_USE_PYTHON ${BOUT_ENABLE_PYTHON})
 
-# Ensure that the compile date/time is up-to-date when any of the sources change
-add_custom_command(
-  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx
-  COMMAND ${CMAKE_COMMAND} -P
-          "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateDateTimeFile.cmake"
-  DEPENDS ${BOUT_SOURCES}
-  MAIN_DEPENDENCY "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateDateTimeFile.cmake"
-)
-
 set(BOUT_GIT_METADATA_SOURCE ${CMAKE_CURRENT_BINARY_DIR}/git_metadata.cxx)
 set_source_files_properties(
   ${BOUT_GIT_METADATA_SOURCE} PROPERTIES GENERATED TRUE
@@ -535,6 +526,15 @@ add_custom_target(
   COMMENT "Generating git metadata source"
 )
 
+# Ensure that the compile date/time is up-to-date when any of the sources change
+add_custom_command(
+  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx
+  COMMAND ${CMAKE_COMMAND} -P
+          "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateDateTimeFile.cmake"
+  DEPENDS ${BOUT_SOURCES} ${CMAKE_CURRENT_BINARY_DIR}/git_metadata.cxx
+  MAIN_DEPENDENCY "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateDateTimeFile.cmake"
+)
+
 add_library(
   bout++ ${BOUT_SOURCES} ${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx
          ${BOUT_GIT_METADATA_SOURCE}

From 7dbeb5122d93fdcb4fd4a1f4141053ca5779649d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 6 Jul 2026 13:14:42 +0200
Subject: [PATCH 1586/1827] Use filename directly

This makes it easier to understand the code, as we do not need to check
the definition to understand it.
---
 CMakeLists.txt | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9ecc645a7c..c091aec2f5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -512,17 +512,16 @@ else()
 endif()
 set(BOUT_USE_PYTHON ${BOUT_ENABLE_PYTHON})
 
-set(BOUT_GIT_METADATA_SOURCE ${CMAKE_CURRENT_BINARY_DIR}/git_metadata.cxx)
 set_source_files_properties(
-  ${BOUT_GIT_METADATA_SOURCE} PROPERTIES GENERATED TRUE
+  ${CMAKE_CURRENT_BINARY_DIR}/git_metadata.cxx PROPERTIES GENERATED TRUE
 )
 add_custom_target(
   bout++-git-metadata
   COMMAND
-    ${CMAKE_COMMAND} -DOUTPUT_FILE=${BOUT_GIT_METADATA_SOURCE}
+    ${CMAKE_COMMAND} -DOUTPUT_FILE=${CMAKE_CURRENT_BINARY_DIR}/git_metadata.cxx
     -DSOURCE_DIR=${PROJECT_SOURCE_DIR} -DGIT_EXECUTABLE=${GIT_EXECUTABLE} -P
     "${CMAKE_CURRENT_LIST_DIR}/cmake/GenerateGitMetadata.cmake"
-  BYPRODUCTS ${BOUT_GIT_METADATA_SOURCE}
+  BYPRODUCTS ${CMAKE_CURRENT_BINARY_DIR}/git_metadata.cxx
   COMMENT "Generating git metadata source"
 )
 
@@ -537,7 +536,7 @@ add_custom_command(
 
 add_library(
   bout++ ${BOUT_SOURCES} ${CMAKE_CURRENT_BINARY_DIR}/bout++-time.cxx
-         ${BOUT_GIT_METADATA_SOURCE}
+         ${CMAKE_CURRENT_BINARY_DIR}/git_metadata.cxx
 )
 add_library(bout++::bout++ ALIAS bout++)
 add_dependencies(bout++ bout++-git-metadata)

From 0091b66e4bfe296903d34d05cf5049aa6deffa50 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 6 Jul 2026 13:22:45 +0200
Subject: [PATCH 1587/1827] Next version for next will be 5.3.0

---
 CMakeLists.txt                       |  2 +-
 tools/pylib/_boutpp_build/backend.py | 16 ++++++----------
 2 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3caf4d8caf..ac9b32a127 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -31,7 +31,7 @@ endif()
 # Set the version here, strip any extra tags to use in `project`
 # We try to use git to get a full description, inspired by setuptools_scm
 set(_bout_previous_version "5.2.0")
-set(_bout_next_version "5.2.1")
+set(_bout_next_version "5.3.0")
 execute_process(
   COMMAND "git" describe --tags --match=v${_bout_previous_version}
   COMMAND sed -e s/${_bout_previous_version}-/${_bout_next_version}.dev/ -e
diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 922ef1c48c..824e7552ad 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -12,7 +12,7 @@
 
 try:
     import packaging.tags  # packaging
-except:
+except ImportError:
     packaging = None
 
 
@@ -36,7 +36,7 @@ def getversion():
             return version.lstrip("v")
 
         _bout_previous_version = "v5.2.0"
-        _bout_next_version = "v5.2.1"
+        _bout_next_version = "v5.3.0"
 
         try:
             try:
@@ -161,7 +161,6 @@ def build_wheel(wheel_directory, config_settings=None, metadata_directory=None):
     )
     run(f"cmake --build  _wheel_build/ -j {os.cpu_count()}")
     run("cmake --install _wheel_build/")
-    distinfo = f"_wheel_install"
     prepare_metadata_for_build_wheel("_wheel_install", record=True)
 
     # Do not add --symlink as python's does not extract that as symlinks
@@ -220,8 +219,8 @@ def build_sdist(sdist_directory, config_settings=None):
         )
         with open("LICENSE") as src:
             pre = "License: "
-            for l in src:
-                f.write(f"{pre}{l}")
+            for line in src:
+                f.write(f"{pre}{line}")
                 pre = "         "
         f.write("Description-Content-Type: text/markdown\n\n")
         with open("README.md") as src:
@@ -344,11 +343,8 @@ def help():
     """
     table = []
     for k, v in todos.items():
-        try:
-            doc = v.__doc__.strip()
-            doc = " : " + doc
-        except:
-            doc = ""
+        doc = v.__doc__.strip()
+        doc = " : " + doc
         table.append((k, doc))
     maxkey = max([len(k) for k, _ in table])
     fmt = f"   %-{maxkey}s%s"

From 665798b525bf49d3f728dee14c9db7408edd515e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 6 Jul 2026 15:25:17 +0200
Subject: [PATCH 1588/1827] Apply clang-tidy fixes

---
 include/bout/fv_ops_impl.hxx | 65 +++++++++++++++++++-----------------
 1 file changed, 34 insertions(+), 31 deletions(-)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 9e436ad95d..9400f5deb1 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -986,7 +986,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
   ASSERT1(areFieldsCompatible(f_in, v_in));
   ASSERT1(areFieldsCompatible(f_in, wave_speed_in));
 
-  Mesh* mesh = f_in.getMesh();
+  const Mesh* mesh = f_in.getMesh();
   Coordinates* coord = f_in.getCoordinates();
   CellEdges cellboundary;
 
@@ -1138,23 +1138,23 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
           // energy losses.
           const BoutReal expected_ke = 0.5 * n_mid * v_mid * v_mid * v_mid;
 
-          BoutReal flux_mom;
+          BoutReal flux_mom = NAN;
           if (fixflux) {
             // Mid-point consistent with boundary conditions
             // but kinetic energy loss will not match expected
             // -> Adjust energy balance in pressure equation
             flux_mom = n_mid * v_mid * v_mid;
           } else {
-            flux_mom = s.R * sv.R * sv.R
-                       + BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.p))
-                             * (s.R * sv.R - n_mid * v_mid);
+            flux_mom = (s.R * sv.R * sv.R)
+                       + (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.p))
+                          * (s.R * sv.R - n_mid * v_mid));
           }
 
           // Assume that particle flux is fixed to boundary value
           const BoutReal flux_part = n_mid * v_mid;
 
           // d/dt(1/2 m n v^2) = v * d/dt(mnv) - 1/2 m v^2 * dn/dt
-          const BoutReal actual_ke = sv.c * flux_mom - 0.5 * sv.c * sv.c * flux_part;
+          const BoutReal actual_ke = (sv.c * flux_mom) - (0.5 * sv.c * sv.c * flux_part);
 
           // Note: If the actual loss was higher than expected, then
           //       plasma heating is needed to compensate
@@ -1193,22 +1193,22 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
 
         if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) {
           // First point in domain
-          BoutReal flux_mom;
+          BoutReal flux_mom = NAN;
           if (fixflux) {
             // Use mid-point to be consistent with boundary conditions
             flux_mom = n_mid * v_mid * v_mid;
           } else {
             // Add flux due to difference in boundary values
-            flux_mom = s.L * sv.L * sv.L
-                       - BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.m))
-                             * (s.L * sv.L - n_mid * v_mid);
+            flux_mom = (s.L * sv.L * sv.L)
+                       - (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.m))
+                          * (s.L * sv.L - n_mid * v_mid));
           }
 
           // Assume that density flux is fixed to boundary value
           const BoutReal flux_part = n_mid * v_mid;
 
           // d/dt(1/2 m n v^2) = v * d/dt(mnv) - 1/2 m v^2 * dn/dt
-          const BoutReal actual_ke = -sv.c * flux_mom + 0.5 * sv.c * sv.c * flux_part;
+          const BoutReal actual_ke = (-sv.c * flux_mom) + (0.5 * sv.c * sv.c * flux_part);
 
           result(i, j, k) += (actual_ke - expected_ke) * flux_factor_lc;
 
@@ -1270,7 +1270,7 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
 
         // Mid-point average boundary value of 'a'
         const BoutReal aedge = 0.5 * (a(i + 1, j, k) + a(i, j, k));
-        BoutReal gedge;
+        BoutReal gedge = NAN;
         if (((i == mesh->xstart - 1) and mesh->firstX())
             or ((i == mesh->xend) and mesh->lastX())) {
           // Mid-point average boundary value of 'g'
@@ -1314,9 +1314,12 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
   // Y and Z fluxes require Y derivatives
 
   // Fields containing values along the magnetic field
-  Field3D fup(mesh), fdown(mesh);
-  Field3D aup(mesh), adown(mesh);
-  Field3D gup(mesh), gdown(mesh);
+  Field3D fup(mesh);
+  Field3D fdown(mesh);
+  Field3D aup(mesh);
+  Field3D adown(mesh);
+  Field3D gup(mesh);
+  Field3D gdown(mesh);
 
   // Values on this y slice (centre).
   // This is needed because toFieldAligned may modify the field
@@ -1356,16 +1359,16 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
 #if BOUT_USE_METRIC_3D
       for (int k = 0; k < mesh->LocalNz; k++)
 #else
-      int k = 0;
+      const int k = 0;
 #endif
       {
-        BoutReal coef_u =
+        const BoutReal coef_u =
             0.5
             * (coord->g_23(i, j, k) / SQ(coord->J(i, j, k) * coord->Bxy(i, j, k))
                + coord->g_23(i, j + 1, k)
                      / SQ(coord->J(i, j + 1, k) * coord->Bxy(i, j + 1, k)));
 
-        BoutReal coef_d =
+        const BoutReal coef_d =
             0.5
             * (coord->g_23(i, j, k) / SQ(coord->J(i, j, k) * coord->Bxy(i, j, k))
                + coord->g_23(i, j - 1, k)
@@ -1376,8 +1379,8 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
 #endif
         {
           // Calculate flux between j and j+1
-          int kp = (k + 1) % mesh->LocalNz;
-          int km = (k - 1 + mesh->LocalNz) % mesh->LocalNz;
+          const int kp = (k + 1) % mesh->LocalNz;
+          const int km = (k - 1 + mesh->LocalNz) % mesh->LocalNz;
 
           // Calculate Z derivative at y boundary
           BoutReal dfdz =
@@ -1389,7 +1392,7 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
                           / (coord->dy(i, j + 1, k) + coord->dy(i, j, k));
 
           BoutReal aedge = 0.5 * (ac(i, j, k) + aup(i, j + 1, k));
-          BoutReal gedge;
+          BoutReal gedge = NAN;
           if ((j == mesh->yend) and mesh->lastY(i)) {
             // Midpoint boundary value
             gedge = 0.5 * (gc(i, j, k) + gup(i, j + 1, k));
@@ -1445,11 +1448,11 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
 #if BOUT_USE_METRIC_3D
       for (int k = 0; k < mesh->LocalNz; k++)
 #else
-      int k = 0;
+      const int k = 0;
 #endif
       {
         // Coefficient in front of df/dy term
-        BoutReal coef =
+        const BoutReal coef =
             coord->g_23(i, j, k)
             / (coord->dy(i, j + 1, k) + 2. * coord->dy(i, j, k) + coord->dy(i, j - 1, k))
             / SQ(coord->J(i, j, k) * coord->Bxy(i, j, k));
@@ -1458,19 +1461,19 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
 #endif
         {
           // Calculate flux between k and k+1
-          int kp = (k + 1) % mesh->LocalNz;
+          const int kp = (k + 1) % mesh->LocalNz;
 
-          BoutReal gradient =
+          const BoutReal gradient =
               // df/dz
-              (fc(i, j, kp) - fc(i, j, k)) / coord->dz(i, j, k)
+              ((fc(i, j, kp) - fc(i, j, k)) / coord->dz(i, j, k))
 
               // - g_yz * df/dy / SQ(J*B)
-              - coef
-                    * (fup(i, j + 1, k) + fup(i, j + 1, kp) - fdown(i, j - 1, k)
-                       - fdown(i, j - 1, kp));
+              - (coef
+                 * (fup(i, j + 1, k) + fup(i, j + 1, kp) - fdown(i, j - 1, k)
+                    - fdown(i, j - 1, kp)));
 
-          BoutReal fout = gradient * 0.5 * (ac(i, j, kp) + ac(i, j, k))
-                          * ((gradient > 0) ? gc(i, j, kp) : gc(i, j, k));
+          const BoutReal fout = gradient * 0.5 * (ac(i, j, kp) + ac(i, j, k))
+                                * ((gradient > 0) ? gc(i, j, kp) : gc(i, j, k));
 
           yzresult(i, j, k) += fout / coord->dz(i, j, k);
           yzresult(i, j, kp) -= fout / coord->dz(i, j, kp);

From 6eeaacb1d4404b2f3cdf0c7dfe72ba68c5c34915 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 6 Jul 2026 15:27:31 +0200
Subject: [PATCH 1589/1827] Prefer std::abs

This is a template that always uses the correct datatype, so we do not
implicitly cast as double.
---
 include/bout/fv_ops_impl.hxx | 45 ++++++++++++++++++------------------
 1 file changed, 23 insertions(+), 22 deletions(-)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 9400f5deb1..09b4a2f87f 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -91,7 +91,7 @@ private:
       return 0.0;
     }
 
-    if (fabs(a) < fabs(b)) {
+    if (std::abs(a) < std::abs(b)) {
       return a;
     }
     return b;
@@ -126,7 +126,7 @@ private:
     }
 
     // Return the minimum absolute value
-    return SIGN(a) * BOUTMIN(fabs(a), fabs(b), fabs(c));
+    return SIGN(a) * BOUTMIN(std::abs(a), std::abs(b), std::abs(c));
   }
 };
 
@@ -167,8 +167,8 @@ struct Superbee {
       n.L = n.R = n.c;
     } else {
       const BoutReal sign = SIGN(gL);
-      const BoutReal abs_gL = fabs(gL);
-      const BoutReal abs_gR = fabs(gR);
+      const BoutReal abs_gL = std::abs(gL);
+      const BoutReal abs_gR = std::abs(gR);
       const BoutReal half_slope =
           sign * BOUTMAX(BOUTMIN(abs_gL, 0.5 * abs_gR), BOUTMIN(abs_gR, 0.5 * abs_gL));
       n.L = n.c - half_slope;
@@ -741,7 +741,7 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
         } else {
           // Maximum wave speed in the two cells
           const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
-                                        fabs(v(i, j, k)), fabs(v(i, j + 1, k)));
+                                        std::abs(v(i, j, k)), std::abs(v(i, j + 1, k)));
 
           flux = s.R * 0.5 * (sv.R + amax);
         }
@@ -769,7 +769,7 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
 
           // Maximum wave speed in the two cells
           const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
-                                        fabs(v(i, j, k)), fabs(v(i, j - 1, k)));
+                                        std::abs(v(i, j, k)), std::abs(v(i, j - 1, k)));
 
           flux = s.L * 0.5 * (sv.L - amax);
         }
@@ -825,8 +825,8 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
       const auto iym = i.ym();
 
       // Maximum local wave speed
-      const BoutReal amax =
-          BOUTMAX(wave_speed_in[i], fabs(v_in[i]), fabs(v_up[iyp]), fabs(v_down[iym]));
+      const BoutReal amax = BOUTMAX(wave_speed_in[i], std::abs(v_in[i]),
+                                    std::abs(v_up[iyp]), std::abs(v_down[iym]));
 
       const BoutReal term = (f_up[iyp] * v_up[iyp] * v_up[iyp] / B_up[iyp])
                             - (f_down[iym] * v_down[iym] * v_down[iym] / B_down[iym]);
@@ -837,7 +837,7 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
           + (amax * (f_in[i] * v_in[i] - f_down[iym] * v_down[iym])
              / (B[i] + B_down[iym]));
 
-      if (fabs(penalty) > fabs(term) and penalty * v_in[i] > 0) {
+      if (std::abs(penalty) > std::abs(term) and penalty * v_in[i] > 0) {
         if (term * penalty > 0) {
           penalty = term;
         } else {
@@ -928,14 +928,15 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
             flux = n_mid_r * v_mid_r * v_mid_r;
           } else {
             // Add flux due to difference in boundary values
-            flux = (s.R * sv.R * sv.R) // Use right cell edge values
-                   + (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.p)) * n_mid_r
-                      * (sv.R - v_mid_r)); // Damp differences in velocity, not flux
+            flux =
+                (s.R * sv.R * sv.R) // Use right cell edge values
+                + (BOUTMAX(wave_speed(i, j, k), std::abs(sv.c), std::abs(sv.p)) * n_mid_r
+                   * (sv.R - v_mid_r)); // Damp differences in velocity, not flux
           }
         } else {
           // Maximum wave speed in the two cells
           const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
-                                        fabs(sv.c), fabs(sv.p));
+                                        std::abs(sv.c), std::abs(sv.p));
 
           flux = s.R * 0.5 * (sv.R + amax) * sv.R;
         }
@@ -957,13 +958,13 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
           } else {
             // Add flux due to difference in boundary values
             flux = (s.L * sv.L * sv.L)
-                   - (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.m)) * n_mid_l
-                      * (sv.L - v_mid_l));
+                   - (BOUTMAX(wave_speed(i, j, k), std::abs(sv.c), std::abs(sv.m))
+                      * n_mid_l * (sv.L - v_mid_l));
           }
         } else {
           // Maximum wave speed in the two cells
           const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
-                                        fabs(sv.c), fabs(sv.m));
+                                        std::abs(sv.c), std::abs(sv.m));
 
           flux = s.L * 0.5 * (sv.L - amax) * sv.L;
         }
@@ -1016,8 +1017,8 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
       const auto iym = i.ym();
 
       //Maximum local wave speed
-      const BoutReal amax =
-          BOUTMAX(wave_speed_in[i], fabs(v_in[i]), fabs(v_up[iyp]), fabs(v_down[iym]));
+      const BoutReal amax = BOUTMAX(wave_speed_in[i], std::abs(v_in[i]),
+                                    std::abs(v_up[iyp]), std::abs(v_down[iym]));
 
       result[i] =
           B[i]
@@ -1146,7 +1147,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
             flux_mom = n_mid * v_mid * v_mid;
           } else {
             flux_mom = (s.R * sv.R * sv.R)
-                       + (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.p))
+                       + (BOUTMAX(wave_speed(i, j, k), std::abs(sv.c), std::abs(sv.p))
                           * (s.R * sv.R - n_mid * v_mid));
           }
 
@@ -1166,7 +1167,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
         } else {
           // Maximum wave speed in the two cells
           const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j + 1, k),
-                                        fabs(sv.c), fabs(sv.p));
+                                        std::abs(sv.c), std::abs(sv.p));
 
           // Viscous heating due to relaxation of velocity towards midpoint
           result(i, j, k) +=
@@ -1200,7 +1201,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
           } else {
             // Add flux due to difference in boundary values
             flux_mom = (s.L * sv.L * sv.L)
-                       - (BOUTMAX(wave_speed(i, j, k), fabs(sv.c), fabs(sv.m))
+                       - (BOUTMAX(wave_speed(i, j, k), std::abs(sv.c), std::abs(sv.m))
                           * (s.L * sv.L - n_mid * v_mid));
           }
 
@@ -1216,7 +1217,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
         } else {
           // Maximum wave speed in the two cells
           const BoutReal amax = BOUTMAX(wave_speed(i, j, k), wave_speed(i, j - 1, k),
-                                        fabs(sv.c), fabs(sv.m));
+                                        std::abs(sv.c), std::abs(sv.m));
 
           // Viscous heating due to relaxation
           result(i, j, k) +=

From 091d45f72848ca86162355d2caa1710a232c11c8 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Tue, 7 Jul 2026 14:57:07 +0100
Subject: [PATCH 1590/1827] Remove `runtest` file for test-petsc-operators

Not needed in new framework.
---
 tests/integrated/test-petsc-operators/runtest | 5 -----
 1 file changed, 5 deletions(-)
 delete mode 100755 tests/integrated/test-petsc-operators/runtest

diff --git a/tests/integrated/test-petsc-operators/runtest b/tests/integrated/test-petsc-operators/runtest
deleted file mode 100755
index 63d8b931e3..0000000000
--- a/tests/integrated/test-petsc-operators/runtest
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/env bash
-#
-# requires: petsc
-
-python3 -m pytest .

From fcd84b3b1625330d3391a7a2536f3bb59a287e58 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 7 Jul 2026 14:54:23 -0700
Subject: [PATCH 1591/1827] Div_a_Grad_perp_limit: Use slices like
 Div_a_Grad_perp

Functions both now use `makeslices` to handle field-aligned
or FCI metrics.
---
 include/bout/fv_ops_impl.hxx | 169 +++++++++++++++++++----------------
 1 file changed, 93 insertions(+), 76 deletions(-)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 9d169223b6..7ab4c2a042 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -270,6 +270,22 @@ struct WENO3 {
   }
 };
 
+template <class T>
+struct Slices {
+  T c;
+  T up;
+  T down;
+
+  Slices(bool use_slices, const T& field)
+      : c(use_slices ? field : toFieldAligned(field)), up(use_slices ? field.yup() : c),
+        down(use_slices ? field.ydown() : c) {}
+};
+
+template <class T>
+Slices<T> makeslices(bool use_slices, const T& field) {
+  return Slices<T>(use_slices, field);
+}
+
 /// Finite volume parallel divergence
 ///
 /// Preserves the sum of f*J*dx*dy*dz over the domain
@@ -1313,44 +1329,44 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
     }
   }
 
-  // Y and Z fluxes require Y derivatives
+  const bool fci =
+      f.hasParallelSlices() && a.hasParallelSlices() && g.hasParallelSlices();
 
-  // Fields containing values along the magnetic field
-  Field3D fup(mesh);
-  Field3D fdown(mesh);
-  Field3D aup(mesh);
-  Field3D adown(mesh);
-  Field3D gup(mesh);
-  Field3D gdown(mesh);
+#if BOUT_USE_METRIC_3D
+  if (fci) {
+    // 3D Metric, need yup/ydown fields.
+    // Requires previous communication of metrics.
+    if (!coord->g23.hasParallelSlices() || !coord->g_23.hasParallelSlices()
+        || !coord->dy.hasParallelSlices() || !coord->dz.hasParallelSlices()
+        || !coord->Bxy.hasParallelSlices() || !coord->J.hasParallelSlices()) {
+      throw BoutException("metrics have no yup/down: Maybe communicate in init?");
+    }
+  }
+#endif
+
+  // Y and Z fluxes require Y derivatives
 
   // Values on this y slice (centre).
   // This is needed because toFieldAligned may modify the field
-  Field3D ac = a;
-  Field3D gc = g;
-  Field3D fc = f;
+  const auto f_slice = makeslices(fci, f);
+  const auto a_slice = makeslices(fci, a);
+  const auto g_slice = makeslices(fci, g);
 
-  // Result of the Y and Z fluxes
-  Field3D yzresult(mesh);
-  yzresult.allocate();
-
-  if (f.hasParallelSlices() && a.hasParallelSlices() && g.hasParallelSlices()) {
-    // All inputs have yup and ydown
-
-    fup = f.yup();
-    fdown = f.ydown();
-
-    aup = a.yup();
-    adown = a.ydown();
-
-    gup = g.yup();
-    gdown = g.ydown();
-  } else {
-    // At least one input doesn't have yup/ydown fields.
-    // Need to shift to/from field aligned coordinates
+#if BOUT_USE_METRIC_3D
+  const bool metric_fci = fci;
+#else
+  constexpr bool metric_fci = false;
+#endif
+  const auto g23 = makeslices(metric_fci, coord->g23);
+  const auto g_23 = makeslices(metric_fci, coord->g_23);
+  const auto J = makeslices(metric_fci, coord->J);
+  const auto dy = makeslices(metric_fci, coord->dy);
+  const auto dz = makeslices(metric_fci, coord->dz);
+  const auto Bxy = makeslices(metric_fci, coord->Bxy);
 
-    fup = fdown = fc = toFieldAligned(f);
-    aup = adown = ac = toFieldAligned(a);
-    gup = gdown = gc = toFieldAligned(g);
+  // Result of the Y and Z fluxes
+  Field3D yzresult(0.0, mesh);
+  if (!fci) {
     yzresult.setDirectionY(YDirectionType::Aligned);
   }
 
@@ -1366,15 +1382,14 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
       {
         const BoutReal coef_u =
             0.5
-            * (coord->g_23(i, j, k) / SQ(coord->J(i, j, k) * coord->Bxy(i, j, k))
-               + coord->g_23(i, j + 1, k)
-                     / SQ(coord->J(i, j + 1, k) * coord->Bxy(i, j + 1, k)));
+            * (g_23.c(i, j, k) / SQ(J.c(i, j, k) * Bxy.c(i, j, k))
+               + g_23.up(i, j + 1, k) / SQ(J.up(i, j + 1, k) * Bxy.up(i, j + 1, k)));
 
         const BoutReal coef_d =
             0.5
-            * (coord->g_23(i, j, k) / SQ(coord->J(i, j, k) * coord->Bxy(i, j, k))
-               + coord->g_23(i, j - 1, k)
-                     / SQ(coord->J(i, j - 1, k) * coord->Bxy(i, j - 1, k)));
+            * (g_23.c(i, j, k) / SQ(J.c(i, j, k) * Bxy.c(i, j, k))
+               + g_23.down(i, j - 1, k)
+                     / SQ(J.down(i, j - 1, k) * Bxy.down(i, j - 1, k)));
 
 #if not BOUT_USE_METRIC_3D
         for (int k = 0; k < mesh->LocalNz; k++)
@@ -1385,58 +1400,59 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
           const int km = (k - 1 + mesh->LocalNz) % mesh->LocalNz;
 
           // Calculate Z derivative at y boundary
-          BoutReal dfdz =
-              0.25 * (fc(i, j, kp) - fc(i, j, km) + fup(i, j + 1, kp) - fup(i, j + 1, km))
-              / coord->dz(i, j, k);
+          BoutReal dfdz = 0.5
+                          * (f_slice.c(i, j, kp) - f_slice.c(i, j, km)
+                             + f_slice.up(i, j + 1, kp) - f_slice.up(i, j + 1, km))
+                          / (dz.c(i, j, k) + dz.up(i, j + 1, k));
 
           // Y derivative
-          BoutReal dfdy = 2. * (fup(i, j + 1, k) - fc(i, j, k))
-                          / (coord->dy(i, j + 1, k) + coord->dy(i, j, k));
+          BoutReal dfdy = 2. * (f_slice.up(i, j + 1, k) - f_slice.c(i, j, k))
+                          / (dy.up(i, j + 1, k) + dy.c(i, j, k));
 
-          BoutReal aedge = 0.5 * (ac(i, j, k) + aup(i, j + 1, k));
+          BoutReal aedge = 0.5 * (a_slice.c(i, j, k) + a_slice.up(i, j + 1, k));
           BoutReal gedge = NAN;
           if ((j == mesh->yend) and mesh->lastY(i)) {
             // Midpoint boundary value
-            gedge = 0.5 * (gc(i, j, k) + gup(i, j + 1, k));
+            gedge = 0.5 * (g_slice.c(i, j, k) + g_slice.up(i, j + 1, k));
           } else if (dfdy > 0) {
             // Flux from (j+1) to (j)
-            gedge = gup(i, j + 1, k);
+            gedge = g_slice.up(i, j + 1, k);
           } else {
             // Flux from (j) to (j+1)
-            gedge = gc(i, j, k);
+            gedge = g_slice.c(i, j, k);
           }
 
-          BoutReal fout = aedge * gedge * 0.5
-                          * (coord->J(i, j, k) * coord->g23(i, j, k)
-                             + coord->J(i, j + 1, k) * coord->g23(i, j + 1, k))
-                          * (dfdz - coef_u * dfdy);
+          BoutReal fout =
+              aedge * gedge * 0.5
+              * (J.c(i, j, k) * g23.c(i, j, k) + J.up(i, j + 1, k) * g23.up(i, j + 1, k))
+              * (dfdz - coef_u * dfdy);
 
-          yzresult(i, j, k) = fout / (coord->dy(i, j, k) * coord->J(i, j, k));
+          yzresult(i, j, k) += fout / (dy.c(i, j, k) * J.c(i, j, k));
 
           // Calculate flux between j and j-1
-          dfdz =
-              0.25
-              * (fc(i, j, kp) - fc(i, j, km) + fdown(i, j - 1, kp) - fdown(i, j - 1, km))
-              / coord->dz(i, j, k);
+          dfdz = 0.5
+                 * (f_slice.c(i, j, kp) - f_slice.c(i, j, km) + f_slice.down(i, j - 1, kp)
+                    - f_slice.down(i, j - 1, km))
+                 / (dz.c(i, j, k) + dz.down(i, j - 1, k));
 
-          dfdy = 2. * (fc(i, j, k) - fdown(i, j - 1, k))
-                 / (coord->dy(i, j, k) + coord->dy(i, j - 1, k));
+          dfdy = 2. * (f_slice.c(i, j, k) - f_slice.down(i, j - 1, k))
+                 / (dy.c(i, j, k) + dy.down(i, j - 1, k));
 
-          aedge = 0.5 * (ac(i, j, k) + adown(i, j - 1, k));
+          aedge = 0.5 * (a_slice.c(i, j, k) + a_slice.down(i, j - 1, k));
           if ((j == mesh->ystart) and mesh->firstY(i)) {
-            gedge = 0.5 * (gc(i, j, k) + gdown(i, j - 1, k));
+            gedge = 0.5 * (g_slice.c(i, j, k) + g_slice.down(i, j - 1, k));
           } else if (dfdy > 0) {
-            gedge = gc(i, j, k);
+            gedge = g_slice.c(i, j, k);
           } else {
-            gedge = gdown(i, j - 1, k);
+            gedge = g_slice.down(i, j - 1, k);
           }
 
           fout = aedge * gedge * 0.5
-                 * (coord->J(i, j, k) * coord->g23(i, j, k)
-                    + coord->J(i, j - 1, k) * coord->g23(i, j - 1, k))
+                 * (J.c(i, j, k) * g23.c(i, j, k)
+                    + J.down(i, j - 1, k) * g23.down(i, j - 1, k))
                  * (dfdz - coef_d * dfdy);
 
-          yzresult(i, j, k) -= fout / (coord->dy(i, j, k) * coord->J(i, j, k));
+          yzresult(i, j, k) -= fout / (dy.c(i, j, k) * J.c(i, j, k));
         }
       }
     }
@@ -1455,9 +1471,9 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
       {
         // Coefficient in front of df/dy term
         const BoutReal coef =
-            coord->g_23(i, j, k)
-            / (coord->dy(i, j + 1, k) + 2. * coord->dy(i, j, k) + coord->dy(i, j - 1, k))
-            / SQ(coord->J(i, j, k) * coord->Bxy(i, j, k));
+            g_23.c(i, j, k)
+            / (dy.up(i, j + 1, k) + 2. * dy.c(i, j, k) + dy.down(i, j - 1, k))
+            / SQ(J.c(i, j, k) * Bxy.c(i, j, k));
 #if not BOUT_USE_METRIC_3D
         for (int k = 0; k < mesh->LocalNz; k++)
 #endif
@@ -1467,24 +1483,25 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
 
           const BoutReal gradient =
               // df/dz
-              ((fc(i, j, kp) - fc(i, j, k)) / coord->dz(i, j, k))
+              ((f_slice.c(i, j, kp) - f_slice.c(i, j, k)) / dz.c(i, j, k))
 
               // - g_yz * df/dy / SQ(J*B)
               - (coef
-                 * (fup(i, j + 1, k) + fup(i, j + 1, kp) - fdown(i, j - 1, k)
-                    - fdown(i, j - 1, kp)));
+                 * (f_slice.up(i, j + 1, k) + f_slice.up(i, j + 1, kp)
+                    - f_slice.down(i, j - 1, k) - f_slice.down(i, j - 1, kp)));
 
-          const BoutReal fout = gradient * 0.5 * (ac(i, j, kp) + ac(i, j, k))
-                                * ((gradient > 0) ? gc(i, j, kp) : gc(i, j, k));
+          const BoutReal fout =
+              gradient * 0.5 * (a_slice.c(i, j, kp) + a_slice.c(i, j, k))
+              * ((gradient > 0) ? g_slice.c(i, j, kp) : g_slice.c(i, j, k));
 
-          yzresult(i, j, k) += fout / coord->dz(i, j, k);
-          yzresult(i, j, kp) -= fout / coord->dz(i, j, kp);
+          yzresult(i, j, k) += fout / dz.c(i, j, k);
+          yzresult(i, j, kp) -= fout / dz.c(i, j, kp);
         }
       }
     }
   }
   // Check if we need to transform back
-  if (f.hasParallelSlices() && a.hasParallelSlices()) {
+  if (fci) {
     result += yzresult;
   } else {
     result += fromFieldAligned(yzresult);

From 06d7ff52389746f9596a617a1bcda88f8287c05a Mon Sep 17 00:00:00 2001
From: malamast <malamas.tsagkaridis@gmail.com>
Date: Tue, 7 Jul 2026 16:39:07 -0700
Subject: [PATCH 1592/1827] boundary_standard: Added a legacy implementation of
 1st order Dirichlet and Neumann BCs.

- This is what we used to do in Bout++ version 3.

- Higher order extrapolation can be unstable sometimes so I added back the 1st order BC. You can use thm in the input file by setting e.g. dirichlet_o1.

- Implementation for staggered grids is not done.
---
 include/bout/boundary_standard.hxx |  48 ++++++
 src/mesh/boundary_factory.cxx      |  11 +-
 src/mesh/boundary_standard.cxx     | 261 +++++++++++++++++++++++++++++
 3 files changed, 316 insertions(+), 4 deletions(-)

diff --git a/include/bout/boundary_standard.hxx b/include/bout/boundary_standard.hxx
index b1116e159f..3cb4b23803 100644
--- a/include/bout/boundary_standard.hxx
+++ b/include/bout/boundary_standard.hxx
@@ -33,6 +33,30 @@ private:
   BoutReal val;
 };
 
+/// Dirichlet (set to zero) boundary condition
+class BoundaryDirichlet_O1 : public BoundaryOp {
+public:
+  BoundaryDirichlet_O1() : gen(nullptr) {}
+  BoundaryDirichlet_O1(BoundaryRegion* region, std::shared_ptr<FieldGenerator> g)
+      : BoundaryOp(region), gen(std::move(g)) {}
+
+  using BoundaryOp::clone;
+  BoundaryOp* clone(BoundaryRegion* region, const std::list<std::string>& args) override;
+
+  using BoundaryOp::apply;
+  void apply(Field2D& f) override;
+  void apply(Field2D& f, BoutReal t) override;
+  void apply(Field3D& f) override;
+  void apply(Field3D& f, BoutReal t) override;
+
+  using BoundaryOp::apply_ddt;
+  void apply_ddt(Field2D& f) override;
+  void apply_ddt(Field3D& f) override;
+
+private:
+  std::shared_ptr<FieldGenerator> gen; // Generator
+};
+
 /// Dirichlet (set to zero) boundary condition
 class BoundaryDirichlet : public BoundaryOp {
 public:
@@ -163,6 +187,30 @@ public:
   void apply(Field3D& f) override;
 };
 
+/// Neumann (zero-gradient) boundary condition, using 1st order on boundary
+class BoundaryNeumann_O1 : public BoundaryOp {
+public:
+  BoundaryNeumann_O1() : gen(nullptr) {}
+  BoundaryNeumann_O1(BoundaryRegion* region, std::shared_ptr<FieldGenerator> g)
+      : BoundaryOp(region), gen(std::move(g)) {}
+
+  using BoundaryOp::clone;
+  BoundaryOp* clone(BoundaryRegion* region, const std::list<std::string>& args) override;
+
+  using BoundaryOp::apply;
+  void apply(Field2D& f) override;
+  void apply(Field2D& f, BoutReal t) override;
+  void apply(Field3D& f) override;
+  void apply(Field3D& f, BoutReal t) override;
+
+  using BoundaryOp::apply_ddt;
+  void apply_ddt(Field2D& f) override;
+  void apply_ddt(Field3D& f) override;
+
+private:
+  std::shared_ptr<FieldGenerator> gen;
+};
+
 /// Neumann boundary condition set half way between guard cell and grid cell at 2nd order accuracy
 class BoundaryNeumann_2ndOrder : public BoundaryOp {
 public:
diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index 988fcfce9b..db1189900c 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -20,15 +20,18 @@ using std::string;
 BoundaryFactory* BoundaryFactory::instance = nullptr;
 
 BoundaryFactory::BoundaryFactory() {
-  add(new BoundaryDirichlet(), "dirichlet");
+  add(new BoundaryDirichlet(), "dirichlet"); // Default
+  add(new BoundaryDirichlet_O1(), "dirichlet_o1"); // Old implementation in v3
   add(new BoundaryDirichlet(), "dirichlet_o2"); // Synonym for "dirichlet"
   add(new BoundaryDirichlet_O3(), "dirichlet_o3");
   add(new BoundaryDirichlet_O4(), "dirichlet_o4");
   add(new BoundaryDirichlet_4thOrder(), "dirichlet_4thorder");
-  add(new BoundaryNeumann(), "neumann");
-  add(new BoundaryNeumann(), "neumann_O2"); // Synonym for "neumann"
+
+  add(new BoundaryNeumann(), "neumann"); // Default
+  add(new BoundaryNeumann_O1(), "neumann_o1"); // Old implementation in v3
+  add(new BoundaryNeumann(), "neumann_o2"); // Synonym for "neumann"
   add(new BoundaryNeumann_4thOrder(), "neumann_4thorder");
-  add(new BoundaryNeumann_O4(), "neumann_O4");
+  add(new BoundaryNeumann_O4(), "neumann_o4");
   add(new BoundaryNeumannPar(), "neumannpar");
   add(new BoundaryNeumann_NonOrthogonal(), "neumann_nonorthogonal");
   add(new BoundaryRobin(), "robin");
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 141cab0a43..ba0eea658e 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -115,6 +115,135 @@ void verifyNumPoints(BoundaryRegion* region, int ptsRequired) {
 void verifyNumPoints(BoundaryRegion*, int) {}
 #endif
 
+
+///////////////////////////////////////////////////////////////
+
+BoundaryOp* BoundaryDirichlet_O1::clone(BoundaryRegion* region,
+                                     const std::list<std::string>& args) {
+  verifyNumPoints(region, 1);
+
+  std::shared_ptr<FieldGenerator> newgen;
+  if (!args.empty()) {
+    // First argument should be an expression
+    newgen = FieldFactory::get()->parse(args.front());
+  }
+  return new BoundaryDirichlet_O1(region, newgen);
+}
+
+void BoundaryDirichlet_O1::apply(Field2D& f) { BoundaryDirichlet_O1::apply(f, 0.); }
+
+void BoundaryDirichlet_O1::apply(Field2D& f, BoutReal t) {
+  // Set (at 1st order) the value at the grid cell to the guard cells.
+
+  Mesh* mesh = bndry->localmesh;
+  ASSERT1(mesh == f.getMesh());
+  bndry->first();
+
+  // Decide which generator to use
+  std::shared_ptr<FieldGenerator> fg = gen;
+  if (!fg) {
+    fg = f.getBndryGenerator(bndry->location);
+  }
+
+  BoutReal val = 0.0;
+
+  // Check for staggered grids
+
+  CELL_LOC loc = f.getLocation();
+  if (mesh->StaggerGrids) {
+    // Staggered
+    throw BoutException("dirichlet_o1 BC is not implementated for staggered grids.");
+
+  } else {
+    // Non-staggered, standard case
+    for (; !bndry->isDone(); bndry->next1d()) {
+
+      if (fg) {
+        val = fg->generate(Context(bndry, loc, t, mesh));
+      }
+      f(bndry->x, bndry->y) = val;
+
+      // Need to set second guard cell, as may be used for interpolation or upwinding derivatives
+      // This is not very efficient. Both boundary cells can be treated in one loop.
+      for (int i = 1; i < bndry->width; i++) {
+        int xi = bndry->x + i * bndry->bx;
+        int yi = bndry->y + i * bndry->by;
+        f(xi, yi) =  val;                    
+      }   
+      
+    }
+  }
+}
+
+void BoundaryDirichlet_O1::apply(Field3D& f) { BoundaryDirichlet_O1::apply(f, 0.); }
+
+void BoundaryDirichlet_O1::apply(Field3D& f, BoutReal t) {
+  // Set (at 1st order) the value at the grid cell to the guard cells.
+
+  Mesh* mesh = bndry->localmesh;
+  ASSERT1(mesh == f.getMesh());
+  bndry->first();
+
+  // Decide which generator to use
+  std::shared_ptr<FieldGenerator> fg = gen;
+  if (!fg) {
+    fg = f.getBndryGenerator(bndry->location);
+  }
+
+  BoutReal val = 0.0;
+
+  // Check for staggered grids
+
+  CELL_LOC loc = f.getLocation();
+  if (mesh->StaggerGrids) {
+    // Staggered.
+    throw BoutException("dirichlet_o1 BC is not implementated for staggered grids.");
+
+  } else {
+    // Standard (non-staggered) case
+    for (; !bndry->isDone(); bndry->next1d()) {
+      for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        if (fg) {
+          val = fg->generate(Context(bndry, zk, loc, t, mesh));
+        }
+        f(bndry->x, bndry->y, zk) = val;
+      }
+
+      // This is not very efficient. Both boundary cells can be treated in one loop.
+      for (int i = 1; i < bndry->width; i++) {
+        // Set any other guard cells using the values on the cells
+        int xi = bndry->x + i * bndry->bx;
+        int yi = bndry->y + i * bndry->by;
+        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          if (fg) {
+            val = fg->generate(Context(bndry, zk, loc, t, mesh));
+          }
+          f(xi, yi, zk) = val;
+        }
+      }
+    }
+  }
+}
+
+void BoundaryDirichlet_O1::apply_ddt(Field2D& f) {
+  Field2D* dt = f.timeDeriv();
+  for (bndry->first(); !bndry->isDone(); bndry->next()) {
+    (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero
+  }
+}
+
+void BoundaryDirichlet_O1::apply_ddt(Field3D& f) {
+  Mesh* mesh = bndry->localmesh;
+  ASSERT1(mesh == f.getMesh());
+  Field3D* dt = f.timeDeriv();
+
+  for (bndry->first(); !bndry->isDone(); bndry->next()) {
+    for (int z = 0; z < mesh->LocalNz; z++) {
+      (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
+    }
+  }
+}
+
 ///////////////////////////////////////////////////////////////
 
 BoundaryOp* BoundaryDirichlet::clone(BoundaryRegion* region,
@@ -1714,6 +1843,138 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
   ///////////////////////////////////////////////////////////////
 
+  BoundaryOp* BoundaryNeumann_O1::clone(BoundaryRegion * region,
+                                     const std::list<std::string>& args) {
+    verifyNumPoints(region, 1);
+    std::shared_ptr<FieldGenerator> newgen = nullptr;
+    if (!args.empty()) {
+      // First argument should be an expression
+      newgen = FieldFactory::get()->parse(args.front());
+    }
+    return new BoundaryNeumann_O1(region, newgen);
+  }
+
+  void BoundaryNeumann_O1::apply(Field2D & f) { BoundaryNeumann_O1::apply(f, 0.); }
+
+  void BoundaryNeumann_O1::apply(Field2D & f, BoutReal t) {
+  // Set (at 1st order) the gradient/value at the grid cell to the guard cells.
+
+
+#if not(BOUT_USE_METRIC_3D)
+    Mesh* mesh = bndry->localmesh;
+    ASSERT1(mesh == f.getMesh());
+    Coordinates* metric = f.getCoordinates();
+
+    bndry->first();
+
+    // Decide which generator to use
+    std::shared_ptr<FieldGenerator> fg = gen;
+    if (!fg) {
+      fg = f.getBndryGenerator(bndry->location);
+    }
+
+    BoutReal val = 0.0;
+
+    // Check for staggered grids
+
+    CELL_LOC loc = f.getLocation();
+    if (mesh->StaggerGrids) {
+      // Staggered. 
+      throw BoutException("neumann_o1 BC is not implementated for staggered grids.");
+
+    } else {
+      // Non-staggered, standard case
+
+      for (bndry->first(); !bndry->isDone(); bndry->next1d()) {
+        BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
+                         + bndry->by * metric->dy(bndry->x, bndry->y);
+
+        if (fg) {
+          val = fg->generate(Context(bndry, loc, t, mesh));
+        }
+
+        f(bndry->x, bndry->y) =
+            f(bndry->x - bndry->bx, bndry->y - bndry->by) + delta * val;
+        if (bndry->width == 2) {
+          f(bndry->x + bndry->bx, bndry->y + bndry->by) = f(bndry->x, bndry->y) + delta * val;              
+        }
+      }
+    }
+#else
+  throw BoutException("Applying boundary condition 'neumann' to Field2D "
+                      "not compatible with 3D metrics in all cases.");
+#endif
+  }
+
+  void BoundaryNeumann_O1::apply(Field3D & f) { BoundaryNeumann_O1::apply(f, 0.); }
+
+  void BoundaryNeumann_O1::apply(Field3D & f, BoutReal t) {
+    Mesh* mesh = bndry->localmesh;
+    ASSERT1(mesh == f.getMesh());
+    Coordinates* metric = f.getCoordinates();
+
+    bndry->first();
+
+    // Decide which generator to use
+    std::shared_ptr<FieldGenerator> fg = gen;
+    if (!fg) {
+      fg = f.getBndryGenerator(bndry->location);
+    }
+
+    BoutReal val = 0.0;
+
+    // Check for staggered grids
+
+    CELL_LOC loc = f.getLocation();
+    if (mesh->StaggerGrids) {
+      // Staggered. 
+      throw BoutException("neumann_o1 BC is not implementated for staggered grids.");
+
+    } else {
+      for (; !bndry->isDone(); bndry->next1d()) {
+#if BOUT_USE_METRIC_3D
+        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+          BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
+                           + bndry->by * metric->dy(bndry->x, bndry->y, zk);
+#else
+      BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
+                       + bndry->by * metric->dy(bndry->x, bndry->y);
+      for (int zk = 0; zk < mesh->LocalNz; zk++) {
+#endif
+          if (fg) {
+            val = fg->generate(Context(bndry, zk, loc, t, mesh));
+          }
+          f(bndry->x, bndry->y, zk) =
+              f(bndry->x - bndry->bx, bndry->y - bndry->by, zk) + delta * val;
+          if (bndry->width == 2) {
+            f(bndry->x + bndry->bx, bndry->y + bndry->by, zk) =
+                f(bndry->x, bndry->y, zk) + delta * val;                
+          }
+        }
+      }
+    }
+  }
+
+  void BoundaryNeumann_O1::apply_ddt(Field2D & f) {
+    Field2D* dt = f.timeDeriv();
+    for (bndry->first(); !bndry->isDone(); bndry->next()) {
+      (*dt)(bndry->x, bndry->y) = 0.; // Set time derivative to zero
+    }
+  }
+
+  void BoundaryNeumann_O1::apply_ddt(Field3D & f) {
+    Mesh* mesh = bndry->localmesh;
+    ASSERT1(mesh == f.getMesh());
+    Field3D* dt = f.timeDeriv();
+    for (bndry->first(); !bndry->isDone(); bndry->next()) {
+      for (int z = 0; z < mesh->LocalNz; z++) {
+        (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
+      }
+    }
+  }
+
+  ///////////////////////////////////////////////////////////////
+
   BoundaryOp* BoundaryNeumann::clone(BoundaryRegion * region,
                                      const std::list<std::string>& args) {
     verifyNumPoints(region, 1);

From a9a5f418f8d75243c87e922c4e4923feb3c833e5 Mon Sep 17 00:00:00 2001
From: malamast <malamas.tsagkaridis@gmail.com>
Date: Tue, 7 Jul 2026 16:59:42 -0700
Subject: [PATCH 1593/1827] boundary_standard: changed LocalNz to zend to make
 it compatible with the rest of the BC code.

-This was a later change to the BCs
---
 src/mesh/boundary_standard.cxx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index ba0eea658e..f12d079d01 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -202,7 +202,7 @@ void BoundaryDirichlet_O1::apply(Field3D& f, BoutReal t) {
   } else {
     // Standard (non-staggered) case
     for (; !bndry->isDone(); bndry->next1d()) {
-      for (int zk = 0; zk < mesh->LocalNz; zk++) {
+      for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
         if (fg) {
           val = fg->generate(Context(bndry, zk, loc, t, mesh));
         }
@@ -214,7 +214,7 @@ void BoundaryDirichlet_O1::apply(Field3D& f, BoutReal t) {
         // Set any other guard cells using the values on the cells
         int xi = bndry->x + i * bndry->bx;
         int yi = bndry->y + i * bndry->by;
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           if (fg) {
             val = fg->generate(Context(bndry, zk, loc, t, mesh));
           }
@@ -238,7 +238,7 @@ void BoundaryDirichlet_O1::apply_ddt(Field3D& f) {
   Field3D* dt = f.timeDeriv();
 
   for (bndry->first(); !bndry->isDone(); bndry->next()) {
-    for (int z = 0; z < mesh->LocalNz; z++) {
+    for (int z = mesh->zstart; z <= mesh->zend; z++) {
       (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
     }
   }
@@ -1933,13 +1933,13 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     } else {
       for (; !bndry->isDone(); bndry->next1d()) {
 #if BOUT_USE_METRIC_3D
-        for (int zk = 0; zk < mesh->LocalNz; zk++) {
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
           BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                            + bndry->by * metric->dy(bndry->x, bndry->y, zk);
 #else
       BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
                        + bndry->by * metric->dy(bndry->x, bndry->y);
-      for (int zk = 0; zk < mesh->LocalNz; zk++) {
+      for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
 #endif
           if (fg) {
             val = fg->generate(Context(bndry, zk, loc, t, mesh));
@@ -1967,7 +1967,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     ASSERT1(mesh == f.getMesh());
     Field3D* dt = f.timeDeriv();
     for (bndry->first(); !bndry->isDone(); bndry->next()) {
-      for (int z = 0; z < mesh->LocalNz; z++) {
+      for (int z = mesh->zstart; z <= mesh->zend; z++) {
         (*dt)(bndry->x, bndry->y, z) = 0.; // Set time derivative to zero
       }
     }

From a96044748c6464b5fc297460476a306c7719905d Mon Sep 17 00:00:00 2001
From: malamast <malamas.tsagkaridis@gmail.com>
Date: Tue, 7 Jul 2026 17:23:00 -0700
Subject: [PATCH 1594/1827] Apply clang-format

---
 src/mesh/boundary_factory.cxx  |  6 +++---
 src/mesh/boundary_standard.cxx | 32 +++++++++++++++-----------------
 2 files changed, 18 insertions(+), 20 deletions(-)

diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index db1189900c..58e37ed53f 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -20,16 +20,16 @@ using std::string;
 BoundaryFactory* BoundaryFactory::instance = nullptr;
 
 BoundaryFactory::BoundaryFactory() {
-  add(new BoundaryDirichlet(), "dirichlet"); // Default
+  add(new BoundaryDirichlet(), "dirichlet");       // Default
   add(new BoundaryDirichlet_O1(), "dirichlet_o1"); // Old implementation in v3
   add(new BoundaryDirichlet(), "dirichlet_o2"); // Synonym for "dirichlet"
   add(new BoundaryDirichlet_O3(), "dirichlet_o3");
   add(new BoundaryDirichlet_O4(), "dirichlet_o4");
   add(new BoundaryDirichlet_4thOrder(), "dirichlet_4thorder");
 
-  add(new BoundaryNeumann(), "neumann"); // Default
+  add(new BoundaryNeumann(), "neumann");       // Default
   add(new BoundaryNeumann_O1(), "neumann_o1"); // Old implementation in v3
-  add(new BoundaryNeumann(), "neumann_o2"); // Synonym for "neumann"
+  add(new BoundaryNeumann(), "neumann_o2");    // Synonym for "neumann"
   add(new BoundaryNeumann_4thOrder(), "neumann_4thorder");
   add(new BoundaryNeumann_O4(), "neumann_o4");
   add(new BoundaryNeumannPar(), "neumannpar");
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index f12d079d01..8917011a93 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -115,11 +115,10 @@ void verifyNumPoints(BoundaryRegion* region, int ptsRequired) {
 void verifyNumPoints(BoundaryRegion*, int) {}
 #endif
 
-
 ///////////////////////////////////////////////////////////////
 
 BoundaryOp* BoundaryDirichlet_O1::clone(BoundaryRegion* region,
-                                     const std::list<std::string>& args) {
+                                        const std::list<std::string>& args) {
   verifyNumPoints(region, 1);
 
   std::shared_ptr<FieldGenerator> newgen;
@@ -168,9 +167,8 @@ void BoundaryDirichlet_O1::apply(Field2D& f, BoutReal t) {
       for (int i = 1; i < bndry->width; i++) {
         int xi = bndry->x + i * bndry->bx;
         int yi = bndry->y + i * bndry->by;
-        f(xi, yi) =  val;                    
-      }   
-      
+        f(xi, yi) = val;
+      }
     }
   }
 }
@@ -1844,7 +1842,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
   ///////////////////////////////////////////////////////////////
 
   BoundaryOp* BoundaryNeumann_O1::clone(BoundaryRegion * region,
-                                     const std::list<std::string>& args) {
+                                        const std::list<std::string>& args) {
     verifyNumPoints(region, 1);
     std::shared_ptr<FieldGenerator> newgen = nullptr;
     if (!args.empty()) {
@@ -1857,8 +1855,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
   void BoundaryNeumann_O1::apply(Field2D & f) { BoundaryNeumann_O1::apply(f, 0.); }
 
   void BoundaryNeumann_O1::apply(Field2D & f, BoutReal t) {
-  // Set (at 1st order) the gradient/value at the grid cell to the guard cells.
-
+    // Set (at 1st order) the gradient/value at the grid cell to the guard cells.
 
 #if not(BOUT_USE_METRIC_3D)
     Mesh* mesh = bndry->localmesh;
@@ -1879,7 +1876,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
     CELL_LOC loc = f.getLocation();
     if (mesh->StaggerGrids) {
-      // Staggered. 
+      // Staggered.
       throw BoutException("neumann_o1 BC is not implementated for staggered grids.");
 
     } else {
@@ -1896,13 +1893,14 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         f(bndry->x, bndry->y) =
             f(bndry->x - bndry->bx, bndry->y - bndry->by) + delta * val;
         if (bndry->width == 2) {
-          f(bndry->x + bndry->bx, bndry->y + bndry->by) = f(bndry->x, bndry->y) + delta * val;              
+          f(bndry->x + bndry->bx, bndry->y + bndry->by) =
+              f(bndry->x, bndry->y) + delta * val;
         }
       }
     }
 #else
-  throw BoutException("Applying boundary condition 'neumann' to Field2D "
-                      "not compatible with 3D metrics in all cases.");
+    throw BoutException("Applying boundary condition 'neumann' to Field2D "
+                        "not compatible with 3D metrics in all cases.");
 #endif
   }
 
@@ -1927,7 +1925,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
     CELL_LOC loc = f.getLocation();
     if (mesh->StaggerGrids) {
-      // Staggered. 
+      // Staggered.
       throw BoutException("neumann_o1 BC is not implementated for staggered grids.");
 
     } else {
@@ -1937,9 +1935,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                            + bndry->by * metric->dy(bndry->x, bndry->y, zk);
 #else
-      BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
-                       + bndry->by * metric->dy(bndry->x, bndry->y);
-      for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
+        BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
+                         + bndry->by * metric->dy(bndry->x, bndry->y);
+        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
 #endif
           if (fg) {
             val = fg->generate(Context(bndry, zk, loc, t, mesh));
@@ -1948,7 +1946,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
               f(bndry->x - bndry->bx, bndry->y - bndry->by, zk) + delta * val;
           if (bndry->width == 2) {
             f(bndry->x + bndry->bx, bndry->y + bndry->by, zk) =
-                f(bndry->x, bndry->y, zk) + delta * val;                
+                f(bndry->x, bndry->y, zk) + delta * val;
           }
         }
       }

From 5bc750a13e47225bcba91eeb74d9f8fdee6b9bf6 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 7 Jul 2026 21:59:32 -0700
Subject: [PATCH 1595/1827] Document new FV ops

---
 manual/sphinx/user_docs/coordinates.rst       | 35 +++++------
 .../user_docs/differential_operators.rst      | 59 +++++++++++++++++++
 2 files changed, 77 insertions(+), 17 deletions(-)

diff --git a/manual/sphinx/user_docs/coordinates.rst b/manual/sphinx/user_docs/coordinates.rst
index 2ac086e05e..d270dda468 100644
--- a/manual/sphinx/user_docs/coordinates.rst
+++ b/manual/sphinx/user_docs/coordinates.rst
@@ -77,7 +77,7 @@ The cross products are:
 .. math::
    :label: eq:psithetazetacrossproducts
 
-   \boldsymbol{e}_\psi\times\boldsymbol{e}_\theta = J_{\psi\theta\zeta} \nabla\zeta \qquad 
+   \boldsymbol{e}_\psi\times\boldsymbol{e}_\theta = J_{\psi\theta\zeta} \nabla\zeta \qquad
    \boldsymbol{e}_\psi\times\boldsymbol{e}_\zeta = -J_{\psi\theta\zeta} \nabla\theta \qquad
    \boldsymbol{e}_\theta\times\boldsymbol{e}_\zeta = J_{\psi\theta\zeta} \nabla\psi
 
@@ -122,7 +122,7 @@ To align to the magnetic field we define a local field line pitch `\nu`:
    \frac{{B_{\text{tor}}}{h_\theta}}{{B_{\text{pol}}}R}
    \end{aligned}
 
-The sign of the poloidal field `{B_{\text{pol}}}` and toroidal field 
+The sign of the poloidal field `{B_{\text{pol}}}` and toroidal field
 `{B_{\text{tor}}}` can be either + or -.
 
 The field-aligned coordinates `\left(x,y,z\right)` are defined by:
@@ -158,7 +158,7 @@ The reciprocal basis vectors are
    \nabla z = \nabla\zeta - \sigma_{B\text{pol}}\left[\int_{\theta_0}^\theta{\frac{\partial \nu\left(\psi,\theta\right)}{\partial \psi}} d\theta\right] \nabla\psi
    - \sigma_{B\text{pol}}\nu\left(\psi, \theta\right)\nabla\theta
    \end{aligned}
-  
+
 The term in square brackets is the integrated local shear:
 
 .. math::
@@ -167,18 +167,18 @@ The term in square brackets is the integrated local shear:
    \begin{aligned}
    I = \int_{y_0}^y\frac{\partial\nu\left(x, y\right)}{\partial\psi}dy\end{aligned}
 
-  
+
 The basis vectors are:
 
 .. math::
    :label: eq:basisvectors
-   
+
    \begin{aligned}
    \boldsymbol{e}_x =& J_{xyz}\left(\nabla y \times \nabla z\right) = {\sigma_{B\text{pol}}} {\boldsymbol{e}}_\psi + I{\boldsymbol{e}}_\zeta \\
    \boldsymbol{e}_y =& J_{xyz}\left(\nabla z \times \nabla x\right) = {\boldsymbol{e}}_\theta + \nu{\boldsymbol{e}}_\phi \\
    \boldsymbol{e}_z =& J_{xyz}\left(\nabla x \times \nabla y\right) = {\boldsymbol{e}}_\zeta
    \end{aligned}
- 
+
 where `{\boldsymbol{e}}_\phi =
 {\sigma_{B\text{pol}}}{\boldsymbol{e}}_\zeta` is always anticlockwise when
 seen from above the tokamak looking down. The direction of
@@ -458,7 +458,7 @@ The reciprocal basis vectors are
 
 .. math::
    :label: eq:reciprocalbasisvectorsrighthanded
-   
+
    \begin{aligned}
    \nabla x =& {\sigma_{B\text{pol}}} \nabla \psi \\
    \nabla \eta =& {\sigma_{B\text{pol}}} \nabla \theta \\
@@ -469,7 +469,7 @@ and basis vectors
 
 .. math::
    :label: eq:basisvectorsrighthanded
-   
+
    \begin{aligned}
    \boldsymbol{e}_x =& J_{x\eta z}\left(\nabla y \times \nabla z\right) = {\sigma_{B\text{pol}}} {\boldsymbol{e}}_\psi + I{\boldsymbol{e}}_\zeta \\
    \boldsymbol{e}_\eta =& J_{x\eta z}\left(\nabla z \times \nabla x\right) = {\sigma_{B\text{pol}}} {\boldsymbol{e}}_\theta + \nu{\boldsymbol{e}}_\zeta \\
@@ -853,7 +853,7 @@ Components of `\nabla\times{\boldsymbol{b}}` are [#curvature]_:
 
    \begin{aligned}
    \left(\nabla\times{\boldsymbol{b}}\right)^x =& {\sigma_y}\frac{{B_{\text{pol}}}}{{h_\theta}}{\frac{\partial }{\partial y}}\left(\frac{{B_{\text{tor}}}
-   R}{B}\right) \\ 
+   R}{B}\right) \\
    \left(\nabla\times{\boldsymbol{b}}\right)^y =& -{\sigma_y}\frac{{B_{\text{pol}}}}{{h_\theta}}{\frac{\partial }{\partial x}}\left(\frac{{B_{\text{tor}}}R}{B}\right) \\
    \left(\nabla\times{\boldsymbol{b}}\right)^z =& \frac{{B_{\text{pol}}}}{{h_\theta}}{\frac{\partial }{\partial x}}\left(\frac{B{h_\theta}}{{B_{\text{pol}}}}\right) - \frac{{B_{\text{pol}}}{B_{\text{tor}}} R}{{h_\theta}B}{\frac{\partial \nu}{\partial x}} - {\sigma_y}I\frac{{|B_{\text{pol}}|}}{{h_\theta}}{\frac{\partial }{\partial y}}\left(\frac{{B_{\text{tor}}} R}{B}\right) \\
    \end{aligned}
@@ -919,7 +919,7 @@ we can re-write the above components as:
                 flip, the `x`-coordinate stays the same and the
                 `z`-coordinate flips sign. The `y`-coordinate stays
                 the same, or the `\eta`-coordinate flips sign.
-                Therefore the x-component of `\nabla\times\boldsymbol{b}` 
+                Therefore the x-component of `\nabla\times\boldsymbol{b}`
                 should flip sign, the `z`-component should not flip
                 sign (product of two sign flips), and the
                 `y`-component should flip sign if '`y`' is `y` and not
@@ -1383,7 +1383,7 @@ and
            \frac{{B_{\text{pol}}}}{B{h_\theta}}{\frac{\partial }{\partial y}}\left(\frac{{B_{\text{tor}}}R}{B}\right)\end{aligned}
 
 The second and third terms partly cancel, and using
-`\sigma_y\sigma_{B\text{pol}}{\frac{\partial I}{\partial y}} = 
+`\sigma_y\sigma_{B\text{pol}}{\frac{\partial I}{\partial y}} =
 {\frac{\partial \nu}{\partial x}}`
 
 .. math::
@@ -1750,10 +1750,10 @@ Differential geometry
 =====================
 
 .. warning:: The following are notes from [haeseleer]_. If you are new to this
-	     topic it is strongly suggested to read [haeseleer]_ chapter 2
-	     instead, as here not all terms are defined, and the discussion of
-	     co- and contra variant components is incomplete. Similiarly, the
-	     notation is based on [haeseleer]_ and not explained in detail.
+             topic it is strongly suggested to read [haeseleer]_ chapter 2
+             instead, as here not all terms are defined, and the discussion of
+             co- and contra variant components is incomplete. Similiarly, the
+             notation is based on [haeseleer]_ and not explained in detail.
 
 Sets of vectors `\left\{\mathbf{A, B, C}\right\}` and
 `\left\{\mathbf{a, b, c}\right\}` are reciprocal if
@@ -2229,8 +2229,9 @@ The perpendicular Laplacian can therefore be written in divergence form as:
    +& \frac{1}{J}\frac{\partial}{\partial z}\left[Jg^{xz}\left(\frac{\partial}{\partial x} - \frac{g_{xy}}{g_{yy}}\frac{\partial}{\partial y}\right) + Jg^{zz}\left(\frac{\partial}{\partial z} - \frac{g_{yz}}{g_{yy}}\frac{\partial}{\partial y}\right)\right]
    \end{aligned}
 
-This form is currently implemented in ``FV::Div_a_Grad_perp``
-(``bout/fv_ops.hxx``) but that operator currently assumes that the
+This form is currently implemented in ``FV::Div_a_Grad_perp`` and the
+limited variant ``FV::Div_a_Grad_perp_limit`` (both in
+``bout/fv_ops.hxx``), but these operators currently assume that the
 off-diagonal terms `g^{xz}` and `g^{xy}` are zero, which is the case
 for orthogonal grids with shifted metrics but not in general.
 
diff --git a/manual/sphinx/user_docs/differential_operators.rst b/manual/sphinx/user_docs/differential_operators.rst
index bcc04dcc29..e3a2d03d79 100644
--- a/manual/sphinx/user_docs/differential_operators.rst
+++ b/manual/sphinx/user_docs/differential_operators.rst
@@ -613,6 +613,65 @@ reconstructed values of :math:`f` and :math:`v` remain consistent with the
 other finite-volume advection operators.
 
 
+Parallel momentum-flux heating ``Div_par_fvv_heating``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This operator is a companion to ``FV::Div_par_fvv``. It calculates the heating
+associated with the numerical momentum-flux discretisation, and returns a
+diagnostic for the kinetic-energy flow through the lower :math:`y` cell face:
+
+::
+
+   template<typename CellEdges = MC>
+   Field3D Div_par_fvv_heating(const Field3D &f_in, const Field3D &v_in,
+                               const Field3D &a, Field3D &flow_ylow,
+                               bool fixflux=true);
+
+
+The returned field is intended for use in parallel momentum and energy systems
+where ``FV::Div_par_fvv`` is used in the momentum equation. The extra output
+argument ``flow_ylow`` stores the lower-face kinetic-energy flow, including the
+area factor. For FCI fields this diagnostic is currently returned as zero.
+
+As with the other finite-volume parallel operators, ``fixflux=true`` adjusts
+boundary fluxes to remain consistent with the imposed boundary values.
+
+
+Perpendicular finite-volume operators
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The finite-volume operators in ``bout/fv_ops.hxx`` also include conservative
+perpendicular operators. The baseline operator
+``FV::Div_a_Grad_perp(a, f)`` calculates
+:math:`\nabla \cdot \left( a \nabla_\perp f \right)` in flux-conservative form:
+
+::
+
+   Field3D Div_a_Grad_perp(const Field3D &a, const Field3D &f);
+
+
+There is also a limited variant:
+
+::
+
+   template<typename CellEdges = MC>
+   Field3D Div_a_Grad_perp_limit(const Field3D &a, const Field3D &g,
+                                 const Field3D &f);
+
+
+This calculates :math:`\nabla \cdot \left( a g \nabla_\perp f \right)` using a
+limited reconstruction of :math:`g` on cell faces. The arguments are:
+
+* ``a`` - the transport coefficient
+* ``g`` - the factor reconstructed and upwinded at cell faces
+* ``f`` - the field whose perpendicular gradient is used
+
+In the :math:`x` direction, the chosen ``CellEdges`` limiter is used to
+reconstruct cell-edge values of :math:`g`. In the :math:`y` direction,
+first-order upwinding is used. As with ``FV::Div_par``, the template parameter
+selects the limiter family described in :ref:`sec-slope-limiters`.
+
+
 Example and convergence test
 ++++++++++++++++++++++++++++
 

From 0f34609247361f6857fda40fdd68ea5dd309792d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 6 Jul 2026 15:29:33 +0200
Subject: [PATCH 1596/1827] Prefer BoutNaN

---
 include/bout/fv_ops_impl.hxx | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 7ab4c2a042..1b7a36f874 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -383,7 +383,7 @@ Field3D Div_par(const Field3D& f_in, const Field3D& v_in, const Field3D& wave_sp
 
         // Calculate velocity at right boundary (y+1/2)
         BoutReal vpar = 0.5 * (v(i, j, k) + v(i, j + 1, k));
-        BoutReal flux = NAN;
+        BoutReal flux = BoutNaN;
 
         if (is_last_y && (j == mesh->yend) && !is_periodic_y) {
           // Last point in domain
@@ -509,7 +509,7 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
     if ((i.x() == mesh->xend) && (mesh->lastX())) {
       // At right boundary in X
       if (bndry_flux) {
-        BoutReal flux = NAN;
+        BoutReal flux = BoutNaN;
         if (vR > 0.0) {
           // Flux to boundary
           flux = vR * s.R;
@@ -536,7 +536,7 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
       // At left boundary in X
 
       if (bndry_flux) {
-        BoutReal flux = NAN;
+        BoutReal flux = BoutNaN;
         if (vL < 0.0) {
           // Flux to boundary
           flux = vL * s.L;
@@ -935,7 +935,7 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
         const BoutReal v_mid_r = 0.5 * (sv.c + sv.p);
         // And mid-point density at right boundary
         const BoutReal n_mid_r = 0.5 * (s.c + s.p);
-        BoutReal flux = NAN;
+        BoutReal flux = BoutNaN;
 
         if (mesh->lastY(i) && (j == mesh->yend) && !mesh->periodicY(i)) {
           // Last point in domain
@@ -1156,7 +1156,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
           // energy losses.
           const BoutReal expected_ke = 0.5 * n_mid * v_mid * v_mid * v_mid;
 
-          BoutReal flux_mom = NAN;
+          BoutReal flux_mom = BoutNaN;
           if (fixflux) {
             // Mid-point consistent with boundary conditions
             // but kinetic energy loss will not match expected
@@ -1211,7 +1211,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
 
         if (mesh->firstY(i) && (j == mesh->ystart) && !mesh->periodicY(i)) {
           // First point in domain
-          BoutReal flux_mom = NAN;
+          BoutReal flux_mom = BoutNaN;
           if (fixflux) {
             // Use mid-point to be consistent with boundary conditions
             flux_mom = n_mid * v_mid * v_mid;
@@ -1288,7 +1288,7 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
 
         // Mid-point average boundary value of 'a'
         const BoutReal aedge = 0.5 * (a(i + 1, j, k) + a(i, j, k));
-        BoutReal gedge = NAN;
+        BoutReal gedge = BoutNaN;
         if (((i == mesh->xstart - 1) and mesh->firstX())
             or ((i == mesh->xend) and mesh->lastX())) {
           // Mid-point average boundary value of 'g'
@@ -1410,7 +1410,7 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
                           / (dy.up(i, j + 1, k) + dy.c(i, j, k));
 
           BoutReal aedge = 0.5 * (a_slice.c(i, j, k) + a_slice.up(i, j + 1, k));
-          BoutReal gedge = NAN;
+          BoutReal gedge = BoutNaN;
           if ((j == mesh->yend) and mesh->lastY(i)) {
             // Midpoint boundary value
             gedge = 0.5 * (g_slice.c(i, j, k) + g_slice.up(i, j + 1, k));

From d70505f34d1fdd8ba2db6b6e97d845eb53b72fe4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 8 Jul 2026 09:06:02 +0200
Subject: [PATCH 1597/1827] Clear more cached data

---
 src/mesh/coordinates.cxx | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 8a416a5acb..3543995702 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -917,6 +917,16 @@ int Coordinates::geometry(bool recalculate_staggered,
   invSgCache.reset();
   CoordinatesAccessor::clear(this);
 
+  _g_22_ylow.reset();
+  _g_22_yhigh.reset();
+  _cell_area_xlow.reset();
+  _cell_area_xhigh.reset();
+  _cell_area_ylow.reset();
+  _cell_area_yhigh.reset();
+  _cell_area_zlow.reset();
+  _cell_area_zhigh.reset();
+  _cell_volume.reset();
+
   return 0;
 }
 

From b47246a1afaf9e40b2cf57b6e10d05ec5d86b990 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 8 Jul 2026 10:38:22 +0200
Subject: [PATCH 1598/1827] Fixup merge

---
 include/bout/fv_ops.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 1cc96341f0..0504281102 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -19,6 +19,7 @@
 #include "bout/vector2d.hxx"
 
 namespace FV {
+/// Vorticity:
 /// \f[
 ///   \nabla (a \cdot \nabla_\perp(f))
 /// \f]

From 7f8adf5b3f461aba2903590669349a283b8246e7 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 8 Jul 2026 10:56:05 +0200
Subject: [PATCH 1599/1827] Remove unused headers

---
 include/bout/fv_ops.hxx | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 17b4748ae4..2ae0d3d547 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -5,17 +5,11 @@
 #ifndef BOUT_FV_OPS_H
 #define BOUT_FV_OPS_H
 
-#include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
-#include "bout/build_defines.hxx"
-#include "bout/coordinates.hxx"
 #include "bout/field.hxx"
 #include "bout/field3d.hxx"
-#include "bout/globals.hxx"
 #include "bout/mesh.hxx"
 #include "bout/output_bout_types.hxx" // NOLINT(unused-includes, misc-include-cleaner)
-#include "bout/region.hxx"
-#include "bout/utils.hxx"
 #include "bout/vector2d.hxx"
 
 namespace FV {

From 370aa694a359156cc27d2aa171abf1fca6a982a2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 8 Jul 2026 11:09:05 +0200
Subject: [PATCH 1600/1827] Next version for next will be 6.0.0

---
 CMakeLists.txt                       | 2 +-
 tools/pylib/_boutpp_build/backend.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ac9b32a127..a397c3e979 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -31,7 +31,7 @@ endif()
 # Set the version here, strip any extra tags to use in `project`
 # We try to use git to get a full description, inspired by setuptools_scm
 set(_bout_previous_version "5.2.0")
-set(_bout_next_version "5.3.0")
+set(_bout_next_version "6.0.0")
 execute_process(
   COMMAND "git" describe --tags --match=v${_bout_previous_version}
   COMMAND sed -e s/${_bout_previous_version}-/${_bout_next_version}.dev/ -e
diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
index 824e7552ad..7037c6b07e 100755
--- a/tools/pylib/_boutpp_build/backend.py
+++ b/tools/pylib/_boutpp_build/backend.py
@@ -36,7 +36,7 @@ def getversion():
             return version.lstrip("v")
 
         _bout_previous_version = "v5.2.0"
-        _bout_next_version = "v5.3.0"
+        _bout_next_version = "v6.0.0"
 
         try:
             try:

From 77c9c26508b75c50af8db4490f03ce6d8521190b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 9 Jul 2026 12:05:15 +0200
Subject: [PATCH 1601/1827] Add guards to handle case with only 1 point in x/y
 direction

---
 src/mesh/fv_ops.cxx | 166 +++++++++++++++++++++++---------------------
 1 file changed, 86 insertions(+), 80 deletions(-)

diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index 1bd00d34a9..51834073ae 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -45,22 +45,25 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
 
   const int xs = mesh->xstart - 1;
   const int xe = mesh->xend;
-
-  for (int i = xs; i <= xe; i++) {
-    for (int j = mesh->ystart; j <= mesh->yend; j++) {
-      for (int k = mesh->zstart; k <= mesh->zend; k++) {
-        // Calculate flux from i to i+1
-
-        const BoutReal fout = 0.5 * (a(i, j, k) + a(i + 1, j, k))
-                              * (coord->J(i, j, k) * coord->g11(i, j, k)
-                                 + coord->J(i + 1, j, k) * coord->g11(i + 1, j, k))
-                              * (f(i + 1, j, k) - f(i, j, k))
-                              / (coord->dx(i, j, k) + coord->dx(i + 1, j, k));
-
-        result(i, j, k) += fout / (coord->dx(i, j, k) * coord->J(i, j, k));
-        result(i + 1, j, k) -= fout / (coord->dx(i + 1, j, k) * coord->J(i + 1, j, k));
+  if (xs >= 0) {
+    for (int i = xs; i <= xe; i++) {
+      for (int j = mesh->ystart; j <= mesh->yend; j++) {
+        for (int k = mesh->zstart; k <= mesh->zend; k++) {
+          // Calculate flux from i to i+1
+
+          const BoutReal fout = 0.5 * (a(i, j, k) + a(i + 1, j, k))
+                                * (coord->J(i, j, k) * coord->g11(i, j, k)
+                                   + coord->J(i + 1, j, k) * coord->g11(i + 1, j, k))
+                                * (f(i + 1, j, k) - f(i, j, k))
+                                / (coord->dx(i, j, k) + coord->dx(i + 1, j, k));
+
+          result(i, j, k) += fout / (coord->dx(i, j, k) * coord->J(i, j, k));
+          result(i + 1, j, k) -= fout / (coord->dx(i + 1, j, k) * coord->J(i + 1, j, k));
+        }
       }
     }
+  } else {
+    ASSERT1(mesh->xend == 0);
   }
 
   const bool fci = f.hasParallelSlices() && a.hasParallelSlices();
@@ -72,7 +75,7 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
     if (!coord->g23.hasParallelSlices() || !coord->g_23.hasParallelSlices()
         || !coord->dy.hasParallelSlices() || !coord->dz.hasParallelSlices()
         || !coord->Bxy.hasParallelSlices() || !coord->J.hasParallelSlices()) {
-      throw BoutException("metrics have no yup/down: Maybe communicate in init?");
+      throw BoutException("metrics have no yup/down!");
     }
   }
 
@@ -101,72 +104,75 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
   }
 
   // Y flux
-
-  BOUT_FOR(i, yzresult.getRegion("RGN_NOBNDRY")) {
-    auto ikp = i.zp();
-    auto ikm = i.zm();
-    {
-      const BoutReal coef = 0.5
-                            * (g_23.c[i] / SQ(J.c[i] * Bxy.c[i])
-                               + g_23.up[i.yp()] / SQ(J.up[i.yp()] * Bxy.up[i.yp()]));
-
-      // Calculate Z derivative at y boundary
-      const BoutReal dfdz = 0.5
-                            * (f_slice.c[ikp] - f_slice.c[ikm] + f_slice.up[ikp.yp()]
-                               - f_slice.up[ikm.yp()])
-                            / (dz.c[i] + dz.up[i.yp()]);
-
-      // Y derivative
-      const BoutReal dfdy =
-          2. * (f_slice.up[i.yp()] - f_slice.c[i]) / (dy.up[i.yp()] + dy.c[i]);
-
-      const BoutReal fout = 0.25 * (a_slice.c[i] + a_slice.up[i.yp()])
-                            * (J.c[i] * g23.c[i] + J.up[i.yp()] * g23.up[i.yp()])
-                            * (dfdz - coef * dfdy);
-
-      yzresult[i] += fout / (dy.c[i] * J.c[i]);
-    }
-    {
-      // Calculate flux between j and j-1
-      const BoutReal coef =
-          0.5
-          * (g_23.c[i] / SQ(J.c[i] * Bxy.c[i])
-             + g_23.down[i.ym()] / SQ(J.down[i.ym()] * Bxy.down[i.ym()]));
-
-      const BoutReal dfdz = 0.5
-                            * (f_slice.c[ikp] - f_slice.c[ikm] + f_slice.down[ikp.ym()]
-                               - f_slice.down[ikm.ym()])
-                            / (dz.c[i] + dz.down[i.ym()]);
-
-      const BoutReal dfdy =
-          2. * (f_slice.c[i] - f_slice.down[i.ym()]) / (dy.c[i] + dy.down[i.ym()]);
-
-      const BoutReal fout = 0.25 * (a_slice.c[i] + a_slice.down[i.ym()])
-                            * (J.c[i] * g23.c[i] + J.down[i.ym()] * g23.down[i.ym()])
-                            * (dfdz - coef * dfdy);
-
-      yzresult[i] -= fout / (dy.c[i] * J.c[i]);
-    }
-    // Z flux
-    {
-
-      // Coefficient in front of df/dy term
-      const BoutReal coef = g_23.c[i] / (dy.up[i.yp()] + 2. * dy.c[i] + dy.down[i.ym()])
-                            / SQ(J.c[i] * Bxy.c[i]);
-
-      const BoutReal fout =
-          0.25 * (a_slice.c[i] + a_slice.c[ikp])
-          * (J.c[i] * coord->g33[i] + J.c[ikp] * coord->g33[ikp])
-          * ( // df/dz
-              (f_slice.c[ikp] - f_slice.c[i]) / dz.c[i]
-              // - g_yz * df/dy / SQ(J*B)
-              - coef
-                    * (f_slice.up[i.yp()] + f_slice.up[ikp.yp()] - f_slice.down[i.ym()]
-                       - f_slice.down[ikp.ym()]));
-
-      yzresult[i] += fout / (J.c[i] * dz.c[i]);
-      yzresult[ikp] -= fout / (J.c[ikp] * dz.c[ikp]);
+  if (mesh->ystart > 0) {
+    BOUT_FOR(i, yzresult.getRegion("RGN_NOBNDRY")) {
+      auto ikp = i.zp();
+      auto ikm = i.zm();
+      {
+        const BoutReal coef = 0.5
+                              * (g_23.c[i] / SQ(J.c[i] * Bxy.c[i])
+                                 + g_23.up[i.yp()] / SQ(J.up[i.yp()] * Bxy.up[i.yp()]));
+
+        // Calculate Z derivative at y boundary
+        const BoutReal dfdz = 0.5
+                              * (f_slice.c[ikp] - f_slice.c[ikm] + f_slice.up[ikp.yp()]
+                                 - f_slice.up[ikm.yp()])
+                              / (dz.c[i] + dz.up[i.yp()]);
+
+        // Y derivative
+        const BoutReal dfdy =
+            2. * (f_slice.up[i.yp()] - f_slice.c[i]) / (dy.up[i.yp()] + dy.c[i]);
+
+        const BoutReal fout = 0.25 * (a_slice.c[i] + a_slice.up[i.yp()])
+                              * (J.c[i] * g23.c[i] + J.up[i.yp()] * g23.up[i.yp()])
+                              * (dfdz - coef * dfdy);
+
+        yzresult[i] += fout / (dy.c[i] * J.c[i]);
+      }
+      {
+        // Calculate flux between j and j-1
+        const BoutReal coef =
+            0.5
+            * (g_23.c[i] / SQ(J.c[i] * Bxy.c[i])
+               + g_23.down[i.ym()] / SQ(J.down[i.ym()] * Bxy.down[i.ym()]));
+
+        const BoutReal dfdz = 0.5
+                              * (f_slice.c[ikp] - f_slice.c[ikm] + f_slice.down[ikp.ym()]
+                                 - f_slice.down[ikm.ym()])
+                              / (dz.c[i] + dz.down[i.ym()]);
+
+        const BoutReal dfdy =
+            2. * (f_slice.c[i] - f_slice.down[i.ym()]) / (dy.c[i] + dy.down[i.ym()]);
+
+        const BoutReal fout = 0.25 * (a_slice.c[i] + a_slice.down[i.ym()])
+                              * (J.c[i] * g23.c[i] + J.down[i.ym()] * g23.down[i.ym()])
+                              * (dfdz - coef * dfdy);
+
+        yzresult[i] -= fout / (dy.c[i] * J.c[i]);
+      }
+      // Z flux
+      {
+
+        // Coefficient in front of df/dy term
+        const BoutReal coef = g_23.c[i] / (dy.up[i.yp()] + 2. * dy.c[i] + dy.down[i.ym()])
+                              / SQ(J.c[i] * Bxy.c[i]);
+
+        const BoutReal fout =
+            0.25 * (a_slice.c[i] + a_slice.c[ikp])
+            * (J.c[i] * coord->g33[i] + J.c[ikp] * coord->g33[ikp])
+            * ( // df/dz
+                (f_slice.c[ikp] - f_slice.c[i]) / dz.c[i]
+                // - g_yz * df/dy / SQ(J*B)
+                - coef
+                      * (f_slice.up[i.yp()] + f_slice.up[ikp.yp()] - f_slice.down[i.ym()]
+                         - f_slice.down[ikp.ym()]));
+
+        yzresult[i] += fout / (J.c[i] * dz.c[i]);
+        yzresult[ikp] -= fout / (J.c[ikp] * dz.c[ikp]);
+      }
     }
+  } else {
+    ASSERT1(mesh->yend == 0);
   }
 
   // Check if we need to transform back

From 427aa210ce30fe54b39d8ce830b30d378b0d6314 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 9 Jul 2026 14:25:24 +0200
Subject: [PATCH 1602/1827] Remove \\ at end of comments

This was partially broken by clang-format.
It also make the compiler unhappy, that warns about that.
---
 src/invert/laplace/impls/naulin/naulin_laplace.hxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.hxx b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
index edcc562c99..a94d855034 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.hxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
@@ -5,7 +5,7 @@
 /// \f{eqnarray}
 ///   \nabla^2(\phi[i+1])
 ///      + 1/DC(C_1 D)\nabla_\perp(DC(C_2))\nabla_\perp(\phi[i+1])
-///      + DC(A/D)\phi[i+1] \\
+///      + DC(A/D)\phi[i+1]
 ///   = rhs(\phi[i])
 ///        + 1/DC(C_1 D)\nabla_\perp(DC(C_2))\nabla_\perp(\phi[i])
 ///        + DC(A/D)\phi[i]
@@ -28,16 +28,16 @@
 /// In an orthogonal system, we have that:
 ///
 /// \f{eqnarray}{
-/// \Omega^D &=& \nabla\cdot(n\nabla_\perp \phi)\                    \
-///       &=& n \nabla_\perp^2 \phi + \nabla n\cdot\nabla_\perp \phi\\
-///       &=& n \Omega + \nabla n\cdot\nabla_\perp \phi\\
+/// \Omega^D &=& \nabla\cdot(n\nabla_\perp \phi)
+///       &=& n \nabla_\perp^2 \phi + \nabla n\cdot\nabla_\perp \phi
+///       &=& n \Omega + \nabla n\cdot\nabla_\perp \phi
 ///       &=& n \Omega + \nabla_\perp n\cdot\nabla_\perp \phi
 /// \f}
 ///
 /// Rearranging gives
 ///
 /// \f{eqnarray}{
-/// \Omega  &=& \frac{\Omega^D}{n} - \nabla_\perp \ln(n)\cdot\nabla_\perp \phi\ \
+/// \Omega  &=& \frac{\Omega^D}{n} - \nabla_\perp \ln(n)\cdot\nabla_\perp \phi
 /// \nabla_\perp^2 \phi
 /// &=& \frac{\Omega^D}{n} - \nabla_\perp \ln(n)\cdot\nabla_\perp \phi
 /// \f}

From 9df3238af83907d72d9a87278f566a3e517e9989 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 11 May 2026 13:53:01 +0100
Subject: [PATCH 1603/1827] Major `Coordinates` refactor

Refactor `Coordinates` with a more encapsulated interface. Derived quantities
are now automatically updated when the metric components are changed.

The most impactful change is the conversion of the metric components and grid
sizes to `const&` methods:

```diff
- coords.dx
+ coords.dx()
```

Among other things, this change allows us to defer computation of many of the
derived quantities (such as Christoffel symbols) and remove the
`Coordinates::geometry` method.
---
 CHANGELOG.md                                  |   16 +
 CMakeLists.txt                                |   26 +-
 examples/6field-simple/elm_6f.cxx             |   10 +-
 .../IMEX/drift-wave-constraint/test-drift.cxx |    6 +-
 examples/conducting-wall-mode/cwm.cxx         |    6 +-
 .../elm-pb-outerloop/elm_pb_outerloop.cxx     |   10 +-
 examples/elm-pb/elm_pb.cxx                    |   10 +-
 examples/fci-wave/fci-wave.cxx                |    2 +-
 examples/gyro-gem/gem.cxx                     |   10 +-
 examples/laplace-petsc3d/test-laplace3d.cxx   |   14 +-
 include/bout/christoffel_symbols.hxx          |   63 +
 include/bout/coordinates.hxx                  |  326 ++++-
 include/bout/field.hxx                        |    3 +
 include/bout/field3d.hxx                      |    7 +-
 include/bout/fv_ops_impl.hxx                  |   78 +-
 include/bout/g_values.hxx                     |   28 +
 include/bout/mesh.hxx                         |   20 +-
 include/bout/metric_tensor.hxx                |  104 ++
 include/bout/parallel_boundary_op.hxx         |    6 +-
 include/bout/paralleltransform.hxx            |    4 -
 include/bout/tokamak_coordinates.hxx          |   17 +-
 src/field/vecops.cxx                          |  128 +-
 src/field/vector2d.cxx                        |   70 +-
 src/field/vector3d.cxx                        |   94 +-
 .../laplace/impls/hypre3d/hypre3d_laplace.cxx |   90 +-
 .../laplace/impls/naulin/naulin_laplace.cxx   |    4 +-
 .../laplace/impls/petsc/petsc_laplace.cxx     |   51 +-
 .../laplace/impls/petsc3damg/petsc3damg.cxx   |   82 +-
 src/invert/laplace/invert_laplace.cxx         |    2 +-
 .../laplacexy/impls/hypre/laplacexy-hypre.cxx |   44 +-
 .../laplacexy/impls/petsc/laplacexy-petsc.cxx |   36 +-
 .../impls/petsc2/laplacexy-petsc2.cxx         |   44 +-
 .../impls/cyclic/laplacexz-cyclic.cxx         |    2 +-
 src/invert/parderiv/impls/cyclic/cyclic.cxx   |   14 +-
 .../pardiv/impls/cyclic/pardiv_cyclic.cxx     |    6 +-
 src/mesh/boundary_standard.cxx                |   10 +-
 src/mesh/christoffel_symbols.cxx              |  116 ++
 src/mesh/coordinates.cxx                      | 1243 +++++++----------
 src/mesh/coordinates_accessor.cxx             |   24 +-
 src/mesh/difops.cxx                           |   82 +-
 src/mesh/fv_ops.cxx                           |   36 +-
 src/mesh/g_values.cxx                         |   34 +
 src/mesh/mesh.cxx                             |   48 +-
 src/mesh/metric_tensor.cxx                    |  154 ++
 src/mesh/parallel/fci.cxx                     |   94 +-
 src/mesh/parallel/fci.hxx                     |    2 -
 src/mesh/petsc_operators.cxx                  |    4 +-
 src/mesh/tokamak_coordinates.cxx              |   55 +-
 src/physics/smoothing.cxx                     |   18 +-
 src/sys/derivs.cxx                            |  106 +-
 tests/MMS/GBS/gbs.cxx                         |   27 +-
 tests/MMS/advection/advection.cxx             |    4 +-
 tests/MMS/diffusion/diffusion.cxx             |   20 +-
 tests/MMS/diffusion2/diffusion.cxx            |   21 +-
 tests/MMS/elm-pb/elm_pb.cxx                   |    8 +-
 tests/MMS/fieldalign/fieldalign.cxx           |   14 +-
 tests/MMS/hw/hw.cxx                           |    4 +-
 tests/MMS/laplace/laplace.cxx                 |    4 +-
 tests/MMS/spatial/diffusion/diffusion.cxx     |   21 +-
 tests/MMS/tokamak/tokamak.cxx                 |    4 +-
 tests/MMS/wave-1d/wave.cxx                    |   25 +-
 .../test-drift-instability/2fluid.cxx         |    4 +-
 .../test-interchange-instability/2fluid.cxx   |    4 +-
 .../test-laplacexy-short/test-laplacexy.cxx   |    6 +-
 .../test-laplacexy/test-laplacexy.cxx         |    4 +-
 .../test-laplacexz/test-laplacexz.cxx         |   31 +-
 .../test_multigrid_laplace.cxx                |    6 +-
 .../test_naulin_laplace.cxx                   |    5 +-
 .../test_petsc_operators.cxx                  |    1 -
 tests/integrated/test-snb/test_snb.cxx        |   16 +-
 tests/unit/fake_mesh_fixture.hxx              |   62 +-
 tests/unit/fake_parallel_mesh.hxx             |    1 -
 tests/unit/field/test_field_factory.cxx       |    2 -
 tests/unit/field/test_vector2d.cxx            |    1 -
 tests/unit/field/test_vector3d.cxx            |    1 -
 .../unit/include/bout/test_petsc_indexer.cxx  |    1 -
 .../invert/laplace/test_laplace_cyclic.cxx    |    7 +-
 .../invert/laplace/test_laplace_hypre3d.cxx   |   11 +-
 .../laplace/test_laplace_petsc3damg.cxx       |   11 +-
 tests/unit/mesh/data/test_gridfromoptions.cxx |  120 +-
 .../unit/mesh/parallel/test_shiftedmetric.cxx |    1 -
 tests/unit/mesh/test_coordinates.cxx          |  451 ++++--
 tests/unit/mesh/test_coordinates_accessor.cxx |  185 +--
 tests/unit/mesh/test_interpolation.cxx        |    1 -
 tools/pylib/_boutpp_build/boutcpp.pxd.jinja   |   55 +-
 tools/pylib/_boutpp_build/boutpp.pyx.jinja    |    2 +-
 tools/pylib/_boutpp_build/helper.cxx.jinja    |    7 +-
 87 files changed, 2664 insertions(+), 1943 deletions(-)
 create mode 100644 include/bout/christoffel_symbols.hxx
 create mode 100644 include/bout/g_values.hxx
 create mode 100644 include/bout/metric_tensor.hxx
 create mode 100644 src/mesh/christoffel_symbols.cxx
 create mode 100644 src/mesh/g_values.cxx
 create mode 100644 src/mesh/metric_tensor.cxx

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 41e3e2c47b..a0cbfd5915 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,21 @@
 # Changelog
 
+## [v6.0.0](https://github.com/boutproject/BOUT-dev/tree/v6.0.0
+
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.2.0...)
+
+### Breaking changes
+
+- `Coordinates` has been refactored to with a more encapsulated interface. This
+  allows us to ensure that derived quantities are correctly updated when the
+  metric components are changed, as well as defer creation of the Christoffel
+  symbols, and other derivatives of the metric components. This change will
+  require most physics models to be updated. You can do this with the
+  `bout-upgrader` from `boutdata`:
+  ```console
+  $ bout-upgrader v6 v6_upgrader file/to/update.cxx
+  ````
+
 ## [v5.2.0](https://github.com/boutproject/BOUT-dev/tree/v5.2.0
 
 [Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.1...v5.2.0)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index e6e424b55c..689c668264 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -116,10 +116,11 @@ set(BOUT_SOURCES
     ./include/bout/bout.hxx
     ./include/bout/bout_enum_class.hxx
     ./include/bout/bout_types.hxx
-    ./include/bout/build_config.hxx
     ./include/bout/boutcomm.hxx
     ./include/bout/boutexception.hxx
+    ./include/bout/build_config.hxx
     ./include/bout/caliper_wrapper.hxx
+    ./include/bout/christoffel_symbols.hxx
     ./include/bout/constants.hxx
     ./include/bout/coordinates.hxx
     ./include/bout/coordinates_accessor.hxx
@@ -136,18 +137,21 @@ set(BOUT_SOURCES
     ./include/bout/field_accessor.hxx
     ./include/bout/field_data.hxx
     ./include/bout/field_factory.hxx
-    ./include/bout/fieldops.hxx
     ./include/bout/fieldgroup.hxx
+    ./include/bout/fieldops.hxx
     ./include/bout/fieldperp.hxx
     ./include/bout/fv_ops.hxx
     ./include/bout/fv_ops_impl.hxx
+    ./include/bout/g_values.hxx
     ./include/bout/generic_factory.hxx
+    ./include/bout/git_metadata.hxx
     ./include/bout/globalfield.hxx
     ./include/bout/globalindexer.hxx
     ./include/bout/globals.hxx
     ./include/bout/griddata.hxx
     ./include/bout/gyro_average.hxx
     ./include/bout/hypre_interface.hxx
+    ./include/bout/hyprelib.hxx
     ./include/bout/index_derivs.hxx
     ./include/bout/index_derivs_interface.hxx
     ./include/bout/initialprofiles.hxx
@@ -164,6 +168,7 @@ set(BOUT_SOURCES
     ./include/bout/macro_for_each.hxx
     ./include/bout/mask.hxx
     ./include/bout/mesh.hxx
+    ./include/bout/metric_tensor.hxx
     ./include/bout/monitor.hxx
     ./include/bout/mpi_wrapper.hxx
     ./include/bout/msg_stack.hxx
@@ -216,8 +221,8 @@ set(BOUT_SOURCES
     ./include/bout/vector2d.hxx
     ./include/bout/vector3d.hxx
     ./include/bout/where.hxx
-    ./src/bout++.cxx
     ./src/bout++-time.hxx
+    ./src/bout++.cxx
     ./src/field/field.cxx
     ./src/field/field2d.cxx
     ./src/field/field3d.cxx
@@ -240,6 +245,8 @@ set(BOUT_SOURCES
     ./src/invert/laplace/common_transform.hxx
     ./src/invert/laplace/impls/cyclic/cyclic_laplace.cxx
     ./src/invert/laplace/impls/cyclic/cyclic_laplace.hxx
+    ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
+    ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx
     ./src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.cxx
     ./src/invert/laplace/impls/iterative_parallel_tri/iterative_parallel_tri.hxx
     ./src/invert/laplace/impls/multigrid/multigrid_alg.cxx
@@ -262,8 +269,6 @@ set(BOUT_SOURCES
     ./src/invert/laplace/impls/serial_tri/serial_tri.hxx
     ./src/invert/laplace/impls/spt/spt.cxx
     ./src/invert/laplace/impls/spt/spt.hxx
-    ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
-    ./src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx
     ./src/invert/laplace/invert_laplace.cxx
     ./src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
     ./src/invert/laplacexy/impls/hypre/laplacexy-hypre.hxx
@@ -286,23 +291,26 @@ set(BOUT_SOURCES
     ./src/mesh/boundary_factory.cxx
     ./src/mesh/boundary_region.cxx
     ./src/mesh/boundary_standard.cxx
+    ./src/mesh/christoffel_symbols.cxx
     ./src/mesh/coordinates.cxx
     ./src/mesh/coordinates_accessor.cxx
     ./src/mesh/data/gridfromfile.cxx
     ./src/mesh/data/gridfromoptions.cxx
     ./src/mesh/difops.cxx
     ./src/mesh/fv_ops.cxx
+    ./src/mesh/g_values.cxx
     ./src/mesh/impls/bout/boutmesh.cxx
     ./src/mesh/impls/bout/boutmesh.hxx
     ./src/mesh/index_derivs.cxx
-    ./src/mesh/interpolation_xz.cxx
     ./src/mesh/interpolation/bilinear_xz.cxx
     ./src/mesh/interpolation/hermite_spline_xz.cxx
     ./src/mesh/interpolation/hermite_spline_z.cxx
     ./src/mesh/interpolation/interpolation_z.cxx
     ./src/mesh/interpolation/lagrange_4pt_xz.cxx
+    ./src/mesh/interpolation_xz.cxx
     ./src/mesh/invert3x3.hxx
     ./src/mesh/mesh.cxx
+    ./src/mesh/metric_tensor.cxx
     ./src/mesh/parallel/fci.cxx
     ./src/mesh/parallel/fci.hxx
     ./src/mesh/parallel/fci_comm.cxx
@@ -369,18 +377,17 @@ set(BOUT_SOURCES
     ./src/sys/derivs.cxx
     ./src/sys/expressionparser.cxx
     ./src/sys/generator_context.cxx
-    ./include/bout/hyprelib.hxx
     ./src/sys/hyprelib.cxx
     ./src/sys/msg_stack.cxx
     ./src/sys/options.cxx
     ./src/sys/options/optionparser.hxx
+    ./src/sys/options/options_adios.cxx
+    ./src/sys/options/options_adios.hxx
     ./src/sys/options/options_ini.cxx
     ./src/sys/options/options_ini.hxx
     ./src/sys/options/options_io.cxx
     ./src/sys/options/options_netcdf.cxx
     ./src/sys/options/options_netcdf.hxx
-    ./src/sys/options/options_adios.cxx
-    ./src/sys/options/options_adios.hxx
     ./src/sys/optionsreader.cxx
     ./src/sys/output.cxx
     ./src/sys/output_bout_types.cxx
@@ -390,7 +397,6 @@ set(BOUT_SOURCES
     ./src/sys/timer.cxx
     ./src/sys/type_name.cxx
     ./src/sys/utils.cxx
-    ./include/bout/git_metadata.hxx
     ${CMAKE_CURRENT_BINARY_DIR}/include/bout/revision.hxx
     ${CMAKE_CURRENT_BINARY_DIR}/include/bout/version.hxx
 )
diff --git a/examples/6field-simple/elm_6f.cxx b/examples/6field-simple/elm_6f.cxx
index 7208d89ddf..61b98c2836 100644
--- a/examples/6field-simple/elm_6f.cxx
+++ b/examples/6field-simple/elm_6f.cxx
@@ -356,7 +356,7 @@ class Elm_6f : public PhysicsModel {
       result.allocate();
       for (auto i : result) {
         result[i] =
-            (fp[i.yp()] - fm[i.ym()]) / (2. * coord->dy[i] * sqrt(coord->g_22[i]));
+            (fp[i.yp()] - fm[i.ym()]) / (2. * coord->dy()[i] * sqrt(coord->g_22()[i]));
       }
     } else {
       result = Grad_par(f, loc);
@@ -696,7 +696,7 @@ class Elm_6f : public PhysicsModel {
 
     if (mesh->IncIntShear) {
       // BOUT-06 style, using d/dx = d/dpsi + I * d/dz
-      mesh->getCoordinates()->IntShiftTorsion = I;
+      mesh->getCoordinates()->setIntShiftTorsion(I);
     } else {
       // Dimits style, using local coordinate system
       if (include_curvature) {
@@ -1399,11 +1399,11 @@ class Elm_6f : public PhysicsModel {
       if (hyperviscos > 0.0) {
         // Calculate coefficient.
 
-        hyper_mu_x = hyperviscos * coord->g_11 * SQ(coord->dx)
-                     * abs(coord->g11 * D2DX2(U)) / (abs(U) + 1e-3);
+        hyper_mu_x = hyperviscos * coord->g_11() * SQ(coord->dx())
+                     * abs(coord->g11() * D2DX2(U)) / (abs(U) + 1e-3);
         hyper_mu_x.applyBoundary("dirichlet"); // Set to zero on all boundaries
 
-        ddt(U) += hyper_mu_x * coord->g11 * D2DX2(U);
+        ddt(U) += hyper_mu_x * coord->g11() * D2DX2(U);
 
         if (first_run) {
           // Print out maximum values of viscosity used on this processor
diff --git a/examples/IMEX/drift-wave-constraint/test-drift.cxx b/examples/IMEX/drift-wave-constraint/test-drift.cxx
index e3bf88acfc..ddeb5ef9d4 100644
--- a/examples/IMEX/drift-wave-constraint/test-drift.cxx
+++ b/examples/IMEX/drift-wave-constraint/test-drift.cxx
@@ -61,10 +61,10 @@ class DriftWave : public PhysicsModel {
       // This code results in ddt(Ne) depending on y+2, y-2
       // which are not (currently) included in the coloring
       // The result is that IMEX-BDF2 with coloring doesn't converge
-      
+
     Ve = ( Grad_par(phi) - Grad_par(Ne) ) / nu;
     mesh->communicate(Ve);
-    
+
     ddt(Ne) = -Div_par(Ve);
     ddt(Vort) = -Div_par(Ve);
     */
@@ -82,7 +82,7 @@ class DriftWave : public PhysicsModel {
     // ddt(phi) = Delp2(phi) - Vort;
 
     // This version uses central differencing for Delp2
-    ddt(phi) = (coord->g11 * D2DX2(phi) + coord->g33 * D2DZ2(phi)) - Vort;
+    ddt(phi) = (coord->g11() * D2DX2(phi) + coord->g33() * D2DZ2(phi)) - Vort;
 
     return 0;
   }
diff --git a/examples/conducting-wall-mode/cwm.cxx b/examples/conducting-wall-mode/cwm.cxx
index b302b5dfb3..1eda76c493 100644
--- a/examples/conducting-wall-mode/cwm.cxx
+++ b/examples/conducting-wall-mode/cwm.cxx
@@ -319,7 +319,7 @@ class CWM : public PhysicsModel {
       result = VDDX(DDZ(p), f);
     } else {
       // Use full expression with all terms
-      result = b0xGrad_dot_Grad(p, f) / coord->Bxy;
+      result = b0xGrad_dot_Grad(p, f) / coord->Bxy();
     }
     return result;
   }
@@ -331,7 +331,7 @@ class CWM : public PhysicsModel {
       result = VDDZ(-DDX(p), f);
     } else {
       // Use full expression with all terms
-      result = b0xGrad_dot_Grad(p, f) / coord->Bxy;
+      result = b0xGrad_dot_Grad(p, f) / coord->Bxy();
     }
     return result;
   }
@@ -343,7 +343,7 @@ class CWM : public PhysicsModel {
       result = VDDX(DDZ(p), f) + VDDZ(-DDX(p), f);
     } else {
       // Use full expression with all terms
-      result = b0xGrad_dot_Grad(p, f) / coord->Bxy;
+      result = b0xGrad_dot_Grad(p, f) / coord->Bxy();
     }
     return result;
   }
diff --git a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
index dbad416281..54c3faf3e0 100644
--- a/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
+++ b/examples/elm-pb-outerloop/elm_pb_outerloop.cxx
@@ -819,7 +819,7 @@ class ELMpb : public PhysicsModel {
 
     if (mesh->IncIntShear) {
       // BOUT-06 style, using d/dx = d/dpsi + I * d/dz
-      mesh->getCoordinates()->IntShiftTorsion = I;
+      mesh->getCoordinates()->setIntShiftTorsion(I);
     } else {
       // Dimits style, using local coordinate system
       if (include_curvature) {
@@ -1749,11 +1749,11 @@ class ELMpb : public PhysicsModel {
     if (hyperviscos > 0.0) {
       // Calculate coefficient.
 
-      hyper_mu_x = hyperviscos * metric->g_11 * SQ(metric->dx)
-                   * abs(metric->g11 * D2DX2(U)) / (abs(U) + 1e-3);
+      hyper_mu_x = hyperviscos * metric->g_11() * SQ(metric->dx())
+                   * abs(metric->g11() * D2DX2(U)) / (abs(U) + 1e-3);
       hyper_mu_x.applyBoundary("dirichlet"); // Set to zero on all boundaries
 
-      ddt(U) += hyper_mu_x * metric->g11 * D2DX2(U);
+      ddt(U) += hyper_mu_x * metric->g11() * D2DX2(U);
 
       if (first_run) { // Print out maximum values of viscosity used on this processor
         output.write("   Hyper-viscosity values:\n");
@@ -1865,7 +1865,7 @@ class ELMpb : public PhysicsModel {
         BoutReal pnorm = P0(0, 0);
         ddt(P) += heating_P * source_expx2(P0, 2. * hp_width, 0.5 * hp_length)
                   * (Tbar / pnorm); // heat source
-        ddt(P) += (100. * source_tanhx(P0, hp_width, hp_length) + 0.01) * metric->g11
+        ddt(P) += (100. * source_tanhx(P0, hp_width, hp_length) + 0.01) * metric->g11()
                   * D2DX2(P) * (Tbar / Lbar / Lbar); // radial diffusion
       }
 
diff --git a/examples/elm-pb/elm_pb.cxx b/examples/elm-pb/elm_pb.cxx
index 62cc970869..e4bd1bbee3 100644
--- a/examples/elm-pb/elm_pb.cxx
+++ b/examples/elm-pb/elm_pb.cxx
@@ -775,7 +775,7 @@ class ELMpb : public PhysicsModel {
 
     if (mesh->IncIntShear) {
       // BOUT-06 style, using d/dx = d/dpsi + I * d/dz
-      mesh->getCoordinates()->IntShiftTorsion = I;
+      mesh->getCoordinates()->setIntShiftTorsion(I);
     } else {
       // Dimits style, using local coordinate system
       if (include_curvature) {
@@ -1772,11 +1772,11 @@ class ELMpb : public PhysicsModel {
     if (hyperviscos > 0.0) {
       // Calculate coefficient.
 
-      hyper_mu_x = hyperviscos * metric->g_11 * SQ(metric->dx)
-                   * abs(metric->g11 * D2DX2(U)) / (abs(U) + 1e-3);
+      hyper_mu_x = hyperviscos * metric->g_11() * SQ(metric->dx())
+                   * abs(metric->g11() * D2DX2(U)) / (abs(U) + 1e-3);
       hyper_mu_x.applyBoundary("dirichlet"); // Set to zero on all boundaries
 
-      ddt(U) += hyper_mu_x * metric->g11 * D2DX2(U);
+      ddt(U) += hyper_mu_x * metric->g11() * D2DX2(U);
 
       if (first_run) { // Print out maximum values of viscosity used on this processor
         output.write("   Hyper-viscosity values:\n");
@@ -1914,7 +1914,7 @@ class ELMpb : public PhysicsModel {
       BoutReal pnorm = P0(0, 0);
       ddt(P) += heating_P * source_expx2(P0, 2. * hp_width, 0.5 * hp_length)
                 * (Tbar / pnorm); // heat source
-      ddt(P) += (100. * source_tanhx(P0, hp_width, hp_length) + 0.01) * metric->g11
+      ddt(P) += (100. * source_tanhx(P0, hp_width, hp_length) + 0.01) * metric->g11()
                 * D2DX2(P) * (Tbar / Lbar / Lbar); // radial diffusion
     }
 
diff --git a/examples/fci-wave/fci-wave.cxx b/examples/fci-wave/fci-wave.cxx
index 9f8bb18b8f..0ea61f3e8d 100644
--- a/examples/fci-wave/fci-wave.cxx
+++ b/examples/fci-wave/fci-wave.cxx
@@ -45,7 +45,7 @@ class FCIwave : public PhysicsModel {
 
     for (auto i : result.getRegion(RGN_NOBNDRY)) {
       result[i] = Bxyz[i] * (f_B.yup()[i.yp()] - f_B.ydown()[i.ym()])
-                  / (2. * coord->dy[i] * sqrt(coord->g_22[i]));
+                  / (2. * coord->dy()[i] * sqrt(coord->g_22()[i]));
 
       if (!finite(result[i])) {
         output.write("[{:d},{:d},{:d}]: {:e}, {:e} -> {:e}\n", i.x(), i.y(), i.z(),
diff --git a/examples/gyro-gem/gem.cxx b/examples/gyro-gem/gem.cxx
index f4347ca2b3..4e5e8538c3 100644
--- a/examples/gyro-gem/gem.cxx
+++ b/examples/gyro-gem/gem.cxx
@@ -363,7 +363,7 @@ class GEM : public PhysicsModel {
       if (curv_logB) {
         Grad_par_logB = Grad_par(logB);
       } else {
-        Grad_par_logB = Grad_par(log(coord->Bxy));
+        Grad_par_logB = Grad_par(log(coord->Bxy()));
       }
     } else {
       Grad_par_logB = 0.;
@@ -1116,7 +1116,7 @@ class GEM : public PhysicsModel {
     if (curv_logB) {
       return -bracket(2. * logB, f, BRACKET_ARAKAWA);
     }
-    return -bracket(2. * log(coord->Bxy), f, BRACKET_ARAKAWA);
+    return -bracket(2. * log(coord->Bxy()), f, BRACKET_ARAKAWA);
   }
 
   ////////////////////////////////////////////////////////////////////////
@@ -1131,7 +1131,7 @@ class GEM : public PhysicsModel {
     delp2.applyBoundary("neumann");
     mesh->communicate(delp2);
 
-    return nu_perp * Delp2(delp2 * SQ(SQ(1. / coord->Bxy)))
+    return nu_perp * Delp2(delp2 * SQ(SQ(1. / coord->Bxy())))
            - nu_par * Grad2_par2(f) // NB: This should be changed for variable B
         ;
   }
@@ -1147,8 +1147,8 @@ class GEM : public PhysicsModel {
   }
 
   const Field3D Div_parP(const Field3D& f, CELL_LOC loc = CELL_DEFAULT) {
-    return interp_to(coord->Bxy, loc)
-           * Grad_parP(f / interp_to(coord->Bxy, f.getLocation()), loc);
+    return interp_to(coord->Bxy(), loc)
+           * Grad_parP(f / interp_to(coord->Bxy(), f.getLocation()), loc);
   }
 };
 
diff --git a/examples/laplace-petsc3d/test-laplace3d.cxx b/examples/laplace-petsc3d/test-laplace3d.cxx
index 46bfce7859..9f21a69be1 100644
--- a/examples/laplace-petsc3d/test-laplace3d.cxx
+++ b/examples/laplace-petsc3d/test-laplace3d.cxx
@@ -36,13 +36,13 @@ Field3D this_Laplace_perp(const Field3D& f) {
   // dfdy not divided by dy yet
   auto dfdy = bout::derivatives::index::DDY(f, CELL_DEFAULT, "DEFAULT", "RGN_NOY");
 
-  return coords->G1 * DDX(f)
-         + (coords->G2 - DDY(coords->J / coords->g_22) / coords->J) * DDY(f)
-         + coords->G3 * DDZ(f) + coords->g11 * D2DX2(f)
-         + (coords->g22 - 1. / coords->g_22) * D2DY2(f) + coords->g33 * D2DZ2(f)
+  return coords->G1() * DDX(f)
+         + (coords->G2() - DDY(coords->J() / coords->g_22()) / coords->J()) * DDY(f)
+         + coords->G3() * DDZ(f) + coords->g11() * D2DX2(f)
+         + (coords->g22() - 1. / coords->g_22()) * D2DY2(f) + coords->g33() * D2DZ2(f)
          + 2.
-               * (coords->g12 * DDX(dfdy) / coords->dy + coords->g13 * D2DXDZ(f)
-                  + coords->g23 * D2DYDZ(f));
+               * (coords->g12() * DDX(dfdy) / coords->dy() + coords->g13() * D2DXDZ(f)
+                  + coords->g23() * D2DYDZ(f));
 }
 
 int main(int argc, char** argv) {
@@ -136,7 +136,7 @@ int main(int argc, char** argv) {
   ///////////////////////////////////////////////////////////////////////////////////////
   // Calculate error
   ///////////////////////////////////////////////////////////////////////////////////////
-  auto& g_22 = mesh->getCoordinates()->g_22;
+  auto& g_22 = mesh->getCoordinates()->g_22();
   Field3D rhs_check = D * this_Laplace_perp(f)
                       + (Grad(f) * Grad(C2) - DDY(C2) * DDY(f) / g_22) / C1 + A * f;
   // The usual way to do this would be
diff --git a/include/bout/christoffel_symbols.hxx b/include/bout/christoffel_symbols.hxx
new file mode 100644
index 0000000000..db88b8688e
--- /dev/null
+++ b/include/bout/christoffel_symbols.hxx
@@ -0,0 +1,63 @@
+#ifndef BOUT_CHRISTOFFELSYMBOLS_HXX
+#define BOUT_CHRISTOFFELSYMBOLS_HXX
+
+#include <bout/metric_tensor.hxx>
+
+class Coordinates;
+
+class ChristoffelSymbols {
+
+public:
+  explicit ChristoffelSymbols(const Coordinates& coordinates);
+
+  const bout::FieldMetric& G1_11() const { return G1_11_m; }
+  const bout::FieldMetric& G1_22() const { return G1_22_m; }
+  const bout::FieldMetric& G1_33() const { return G1_33_m; }
+  const bout::FieldMetric& G1_12() const { return G1_12_m; }
+  const bout::FieldMetric& G1_13() const { return G1_13_m; }
+  const bout::FieldMetric& G1_23() const { return G1_23_m; }
+
+  const bout::FieldMetric& G2_11() const { return G2_11_m; }
+  const bout::FieldMetric& G2_22() const { return G2_22_m; }
+  const bout::FieldMetric& G2_33() const { return G2_33_m; }
+  const bout::FieldMetric& G2_12() const { return G2_12_m; }
+  const bout::FieldMetric& G2_13() const { return G2_13_m; }
+  const bout::FieldMetric& G2_23() const { return G2_23_m; }
+
+  const bout::FieldMetric& G3_11() const { return G3_11_m; }
+  const bout::FieldMetric& G3_22() const { return G3_22_m; }
+  const bout::FieldMetric& G3_33() const { return G3_33_m; }
+  const bout::FieldMetric& G3_12() const { return G3_12_m; }
+  const bout::FieldMetric& G3_13() const { return G3_13_m; }
+  const bout::FieldMetric& G3_23() const { return G3_23_m; }
+
+  // Transforms the ChristoffelSymbols by applying the given function to every element
+  template <class F>
+  void map(F function) {
+    G1_11_m = function(G1_11_m);
+    G1_22_m = function(G1_22_m);
+    G1_33_m = function(G1_33_m);
+    G1_12_m = function(G1_12_m);
+    G1_13_m = function(G1_13_m);
+    G1_23_m = function(G1_23_m);
+    G2_11_m = function(G2_11_m);
+    G2_22_m = function(G2_22_m);
+    G2_33_m = function(G2_33_m);
+    G2_12_m = function(G2_12_m);
+    G2_13_m = function(G2_13_m);
+    G2_23_m = function(G2_23_m);
+    G3_11_m = function(G3_11_m);
+    G3_22_m = function(G3_22_m);
+    G3_33_m = function(G3_33_m);
+    G3_12_m = function(G3_12_m);
+    G3_13_m = function(G3_13_m);
+    G3_23_m = function(G3_23_m);
+  }
+
+private:
+  bout::FieldMetric G1_11_m, G1_22_m, G1_33_m, G1_12_m, G1_13_m, G1_23_m;
+  bout::FieldMetric G2_11_m, G2_22_m, G2_33_m, G2_12_m, G2_13_m, G2_23_m;
+  bout::FieldMetric G3_11_m, G3_22_m, G3_33_m, G3_12_m, G3_13_m, G3_23_m;
+};
+
+#endif //BOUT_CHRISTOFFELSYMBOLS_HXX
diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 2c33701762..2c73828060 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -30,30 +30,29 @@
 #include "bout/field_data.hxx"
 #include <bout/bout_types.hxx>
 #include <bout/build_defines.hxx>
+#include <bout/christoffel_symbols.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
+#include <bout/g_values.hxx>
+#include <bout/metric_tensor.hxx>
 #include <bout/paralleltransform.hxx>
 #include <optional>
 
 #include <array>
 #include <memory>
 #include <string>
+#include <string_view>
+#include <utility>
 
 class Mesh;
 class YBoundary;
 
 /*!
  * Represents a coordinate system, and associated operators
- *
- * This is a container for a collection of metric tensor components
  */
 class Coordinates {
 public:
-#if BOUT_USE_METRIC_3D
-  using FieldMetric = Field3D;
-#else
-  using FieldMetric = Field2D;
-#endif
+  using FieldMetric = bout::FieldMetric;
 
   /// Standard constructor from input
   Coordinates(Mesh* mesh, Options* options = nullptr);
@@ -64,8 +63,8 @@ public:
   /// force_interpolate_from_centre argument to true to always interpolate
   /// (useful if CELL_CENTRE Coordinates have been changed, so reading from file
   /// would not be correct).
-  Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
-              const Coordinates* coords_in, bool force_interpolate_from_centre = false);
+  Coordinates(Mesh* mesh, Options* options, CELL_LOC loc, const Coordinates* coords_in,
+              bool force_interpolate_from_centre = false);
 
   /// A constructor useful for testing purposes. To use it, inherit
   /// from Coordinates. If \p calculate_geometry is true (default),
@@ -76,32 +75,81 @@ public:
               FieldMetric g_22, FieldMetric g_33, FieldMetric g_12, FieldMetric g_13,
               FieldMetric g_23, FieldMetric ShiftTorsion, FieldMetric IntShiftTorsion);
 
-  Coordinates& operator=(Coordinates&&) = default;
-
-  ~Coordinates() = default;
-
   /// Add variables to \p output_options, for post-processing
   void outputVars(Options& output_options);
 
-  FieldMetric dx, dy, dz; ///< Mesh spacing in x, y and z
+  ///< Mesh spacing in x, y and z
+  const FieldMetric& dx() const { return dx_; }
+  const FieldMetric& dy() const { return dy_; }
+  const FieldMetric& dz() const { return dz_; }
+
+  const BoutReal& dx(int x, int y, int z) const { return dx_(x, y, z); }
+  const BoutReal& dy(int x, int y, int z) const { return dy_(x, y, z); }
+  const BoutReal& dz(int x, int y, int z) const { return dz_(x, y, z); }
+
+#if BOUT_USE_METRIC_3D
+  const BoutReal* dx(int x, int y) const { return dx_(x, y); }
+  const BoutReal* dy(int x, int y) const { return dy_(x, y); }
+  const BoutReal* dz(int x, int y) const { return dz_(x, y); }
+#else
+  const BoutReal& dx(int x, int y) const { return dx_(x, y); }
+  const BoutReal& dy(int x, int y) const { return dy_(x, y); }
+  const BoutReal& dz(int x, int y) const { return dz_(x, y); }
+#endif
+
+  const BoutReal& IntShiftTorsion(int x, int y, int z) const {
+    return IntShiftTorsion_(x, y, z);
+  }
+
+#if not(BOUT_USE_METRIC_3D)
+  const BoutReal& IntShiftTorsion(int x, int y) const { return IntShiftTorsion_(x, y); }
+#endif
+
+  const BoutReal& J(int x, int y, int z) const { return J()(x, y, z); }
+
+#if not(BOUT_USE_METRIC_3D)
+  const BoutReal& J(int x, int y) const { return J()(x, y); }
+#endif
+
+  void setDx(FieldMetric dx, bool communicate = true);
+  void setDy(FieldMetric dy, bool communicate = true);
+  void setDz(FieldMetric dz, bool communicate = true);
+
+  void setD1_dx(FieldMetric d1_dx) { d1_dx_ = std::move(d1_dx); }
+  void setD1_dy(FieldMetric d1_dy) { d1_dy_ = std::move(d1_dy); }
+  void setD1_dz(FieldMetric d1_dz) { d1_dz_ = std::move(d1_dz); }
 
   /// Length of the Z domain. Used for FFTs
   const Field2D& zlength() const;
 
-  /// True if corrections for non-uniform mesh spacing should be included in operators
-  bool non_uniform;
-  /// 2nd-order correction for non-uniform meshes d/di(1/dx), d/di(1/dy) and d/di(1/dz)
-  FieldMetric d1_dx, d1_dy, d1_dz;
+  const BoutReal& zlength(int x, int y) const { return zlength()(x, y); }
 
-  FieldMetric J; ///< Coordinate system Jacobian, so volume of cell is J*dx*dy*dz
+  /// True if corrections for non-uniform mesh spacing should be included in operators
+  bool non_uniform() const { return non_uniform_; }
+  void setNon_uniform(bool non_uniform) { non_uniform_ = non_uniform; }
 
-  FieldMetric Bxy; ///< Magnitude of B = nabla z times nabla x
+  /// 2nd-order correction for non-uniform meshes d/di(1/dx), d/di(1/dy) and d/di(1/dz)
+  const FieldMetric& d1_dx() const { return d1_dx_; }
+  const FieldMetric& d1_dy() const { return d1_dy_; }
+  const FieldMetric& d1_dz() const { return d1_dz_; }
 
-  /// Contravariant metric tensor (g^{ij})
-  FieldMetric g11, g22, g33, g12, g13, g23;
+#if BOUT_USE_METRIC_3D
+  const BoutReal& d1_dx(int x, int y, int z) const { return d1_dx_(x, y, z); }
+  const BoutReal& d1_dy(int x, int y, int z) const { return d1_dy_(x, y, z); }
+  const BoutReal& d1_dz(int x, int y, int z) const { return d1_dz_(x, y, z); }
+#else
+  const BoutReal& d1_dx(int x, int y) const { return d1_dx_(x, y); }
+  const BoutReal& d1_dy(int x, int y) const { return d1_dy_(x, y); }
+  const BoutReal& d1_dz(int x, int y) const { return d1_dz_(x, y); }
+#endif
 
   /// Covariant metric tensor
-  FieldMetric g_11, g_22, g_33, g_12, g_13, g_23;
+  const FieldMetric& g_11() const { return covariantMetricTensor.g11(); }
+  const FieldMetric& g_22() const { return covariantMetricTensor.g22(); }
+  const FieldMetric& g_33() const { return covariantMetricTensor.g33(); }
+  const FieldMetric& g_12() const { return covariantMetricTensor.g12(); }
+  const FieldMetric& g_13() const { return covariantMetricTensor.g13(); }
+  const FieldMetric& g_23() const { return covariantMetricTensor.g23(); }
 
   /// get g_22 at the cell faces;
   const FieldMetric& g_22_ylow() const;
@@ -235,26 +283,116 @@ private:
   void _compute_cell_volume() const;
 
 public:
-  /// Christoffel symbol of the second kind (connection coefficients)
-  FieldMetric G1_11, G1_22, G1_33, G1_12, G1_13, G1_23;
-  FieldMetric G2_11, G2_22, G2_33, G2_12, G2_13, G2_23;
-  FieldMetric G3_11, G3_22, G3_33, G3_12, G3_13, G3_23;
+  /// Contravariant metric tensor (g^{ij})
+  const FieldMetric& g11() const { return contravariantMetricTensor.g11(); }
+  const FieldMetric& g22() const { return contravariantMetricTensor.g22(); }
+  const FieldMetric& g33() const { return contravariantMetricTensor.g33(); }
+  const FieldMetric& g12() const { return contravariantMetricTensor.g12(); }
+  const FieldMetric& g13() const { return contravariantMetricTensor.g13(); }
+  const FieldMetric& g23() const { return contravariantMetricTensor.g23(); }
+
+  /// Covariant metric tensor
+  const BoutReal& g_11(int x, int y, int z) const {
+    return covariantMetricTensor.g11(x, y, z);
+  }
+  const BoutReal& g_22(int x, int y, int z) const {
+    return covariantMetricTensor.g22(x, y, z);
+  }
+  const BoutReal& g_33(int x, int y, int z) const {
+    return covariantMetricTensor.g33(x, y, z);
+  }
+  const BoutReal& g_12(int x, int y, int z) const {
+    return covariantMetricTensor.g12(x, y, z);
+  }
+  const BoutReal& g_13(int x, int y, int z) const {
+    return covariantMetricTensor.g13(x, y, z);
+  }
+  const BoutReal& g_23(int x, int y, int z) const {
+    return covariantMetricTensor.g23(x, y, z);
+  }
+
+#if not(BOUT_USE_METRIC_3D)
+  const BoutReal& g_11(int x, int y) const { return covariantMetricTensor.g11(x, y); }
+  const BoutReal& g_22(int x, int y) const { return covariantMetricTensor.g22(x, y); }
+  const BoutReal& g_33(int x, int y) const { return covariantMetricTensor.g33(x, y); }
+  const BoutReal& g_12(int x, int y) const { return covariantMetricTensor.g12(x, y); }
+  const BoutReal& g_13(int x, int y) const { return covariantMetricTensor.g13(x, y); }
+  const BoutReal& g_23(int x, int y) const { return covariantMetricTensor.g23(x, y); }
+#endif
+
+  /// Contravariant metric tensor (g^{ij})
+  const BoutReal& g11(int x, int y, int z) const {
+    return contravariantMetricTensor.g11(x, y, z);
+  }
+  const BoutReal& g22(int x, int y, int z) const {
+    return contravariantMetricTensor.g22(x, y, z);
+  }
+  const BoutReal& g33(int x, int y, int z) const {
+    return contravariantMetricTensor.g33(x, y, z);
+  }
+  const BoutReal& g12(int x, int y, int z) const {
+    return contravariantMetricTensor.g12(x, y, z);
+  }
+  const BoutReal& g13(int x, int y, int z) const {
+    return contravariantMetricTensor.g13(x, y, z);
+  }
+  const BoutReal& g23(int x, int y, int z) const {
+    return contravariantMetricTensor.g23(x, y, z);
+  }
+
+#if not(BOUT_USE_METRIC_3D)
+  const BoutReal& g11(int x, int y) const { return contravariantMetricTensor.g11(x, y); }
+  const BoutReal& g22(int x, int y) const { return contravariantMetricTensor.g22(x, y); }
+  const BoutReal& g33(int x, int y) const { return contravariantMetricTensor.g33(x, y); }
+  const BoutReal& g12(int x, int y) const { return contravariantMetricTensor.g12(x, y); }
+  const BoutReal& g13(int x, int y) const { return contravariantMetricTensor.g13(x, y); }
+  const BoutReal& g23(int x, int y) const { return contravariantMetricTensor.g23(x, y); }
+#endif
+
+  const ContravariantMetricTensor& getContravariantMetricTensor() const {
+    return contravariantMetricTensor;
+  }
 
-  FieldMetric G1, G2, G3;
+  const CovariantMetricTensor& getCovariantMetricTensor() const {
+    return covariantMetricTensor;
+  }
+
+  void setContravariantMetricTensor(const ContravariantMetricTensor& metric_tensor,
+                                    const std::string& region = "RGN_ALL",
+                                    bool recalculate_staggered = true,
+                                    bool force_interpolate_from_centre = false);
+
+  void setCovariantMetricTensor(const CovariantMetricTensor& metric_tensor,
+                                const std::string& region = "RGN_ALL",
+                                bool recalculate_staggered = true,
+                                bool force_interpolate_from_centre = false);
+
+  void setMetricTensor(const ContravariantMetricTensor& contravariant_metric_tensor,
+                       const CovariantMetricTensor& covariant_metric_tensor);
+
+  void communicateMetricTensor();
+
+  void communicateDz();
+
+  ///< Coordinate system Jacobian, so volume of cell is J*dx*dy*dz
+  const FieldMetric& J() const;
+
+  ///< Magnitude of B = nabla z times nabla x
+  const FieldMetric& Bxy() const { return Bxy_; }
+
+  void setJ(const FieldMetric& J, bool communicate = true);
+
+  void setBxy(FieldMetric Bxy, bool communicate = true);
 
   /// d pitch angle / dx. Needed for vector differentials (Curl)
-  FieldMetric ShiftTorsion;
+  const FieldMetric& ShiftTorsion() const { return ShiftTorsion_; }
 
-  FieldMetric IntShiftTorsion; ///< Integrated shear (I in BOUT notation)
+  ///< Integrated shear (I in BOUT notation)
+  const FieldMetric& IntShiftTorsion() const { return IntShiftTorsion_; }
 
-  /// Calculate differential geometry quantities from the metric tensor
-  int geometry(bool recalculate_staggered = true,
-               bool force_interpolate_from_centre = false);
-  /// Invert contravatiant metric to get covariant components
-  int calcCovariant(const std::string& region = "RGN_ALL");
-  /// Invert covariant metric to get contravariant components
-  int calcContravariant(const std::string& region = "RGN_ALL");
-  int jacobian(); ///< Calculate J and Bxy
+  void setIntShiftTorsion(FieldMetric IntShiftTorsion) {
+    IntShiftTorsion_ = std::move(IntShiftTorsion);
+  }
 
   ///////////////////////////////////////////////////////////
   // Parallel transforms
@@ -279,7 +417,7 @@ public:
 
   FieldMetric DDX(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
                   const std::string& method = "DEFAULT",
-                  const std::string& region = "RGN_NOBNDRY");
+                  const std::string& region = "RGN_NOBNDRY") const;
 
   FieldMetric DDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
                   const std::string& method = "DEFAULT",
@@ -287,11 +425,11 @@ public:
 
   FieldMetric DDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
                   const std::string& method = "DEFAULT",
-                  const std::string& region = "RGN_NOBNDRY");
+                  const std::string& region = "RGN_NOBNDRY") const;
 
   Field3D DDX(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
               const std::string& method = "DEFAULT",
-              const std::string& region = "RGN_NOBNDRY");
+              const std::string& region = "RGN_NOBNDRY") const;
 
   Field3D DDY(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
               const std::string& method = "DEFAULT",
@@ -299,7 +437,7 @@ public:
 
   Field3D DDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
               const std::string& method = "DEFAULT",
-              const std::string& region = "RGN_NOBNDRY");
+              const std::string& region = "RGN_NOBNDRY") const;
 
   /// Gradient along magnetic field  b.Grad(f)
   FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc = CELL_DEFAULT,
@@ -352,7 +490,55 @@ public:
 
   // Full perpendicular Laplacian, in form of inverse of Laplacian operator in LaplaceXY
   // solver
-  Field2D Laplace_perpXY(const Field2D& A, const Field2D& f);
+  Field2D Laplace_perpXY(const Field2D& A, const Field2D& f) const;
+
+  /// Christoffel symbol of the second kind (connection coefficients)
+  const FieldMetric& G1_11() const { return christoffel_symbols().G1_11(); }
+  const FieldMetric& G1_22() const { return christoffel_symbols().G1_22(); }
+  const FieldMetric& G1_33() const { return christoffel_symbols().G1_33(); }
+  const FieldMetric& G1_12() const { return christoffel_symbols().G1_12(); }
+  const FieldMetric& G1_13() const { return christoffel_symbols().G1_13(); }
+  const FieldMetric& G1_23() const { return christoffel_symbols().G1_23(); }
+  const FieldMetric& G2_11() const { return christoffel_symbols().G2_11(); }
+  const FieldMetric& G2_22() const { return christoffel_symbols().G2_22(); }
+  const FieldMetric& G2_33() const { return christoffel_symbols().G2_33(); }
+  const FieldMetric& G2_12() const { return christoffel_symbols().G2_12(); }
+  const FieldMetric& G2_13() const { return christoffel_symbols().G2_13(); }
+  const FieldMetric& G2_23() const { return christoffel_symbols().G2_23(); }
+  const FieldMetric& G3_11() const { return christoffel_symbols().G3_11(); }
+  const FieldMetric& G3_22() const { return christoffel_symbols().G3_22(); }
+  const FieldMetric& G3_33() const { return christoffel_symbols().G3_33(); }
+  const FieldMetric& G3_12() const { return christoffel_symbols().G3_12(); }
+  const FieldMetric& G3_13() const { return christoffel_symbols().G3_13(); }
+  const FieldMetric& G3_23() const { return christoffel_symbols().G3_23(); }
+
+  const FieldMetric& G1() const { return g_values().G1(); }
+  const FieldMetric& G2() const { return g_values().G2(); }
+  const FieldMetric& G3() const { return g_values().G3(); }
+
+  const BoutReal& G1(int x, int y, int z) const { return G1()(x, y, z); }
+  const BoutReal& G2(int x, int y, int z) const { return G2()(x, y, z); }
+  const BoutReal& G3(int x, int y, int z) const { return G3()(x, y, z); }
+
+#if not(BOUT_USE_METRIC_3D)
+  const BoutReal& G1(int x, int y) const { return G1()(x, y); }
+  const BoutReal& G2(int x, int y) const { return G2()(x, y); }
+  const BoutReal& G3(int x, int y) const { return G3()(x, y); }
+#endif
+
+  const FieldMetric& Grad2_par2_DDY_invSg(CELL_LOC outloc,
+                                          const std::string& method) const;
+
+  const FieldMetric& invSg() const;
+
+  const ChristoffelSymbols& christoffel_symbols() const;
+
+  GValues& g_values() const;
+
+  void recalculateAndReset(bool recalculate_staggered,
+                           bool force_interpolate_from_centre);
+
+  FieldMetric recalculateJacobian() const;
 
   friend std::shared_ptr<YBoundary> getYBoundary(Coordinates* coords, YBndryType type);
 
@@ -360,36 +546,78 @@ private:
   std::shared_ptr<YBoundary> makeYBoundary(YBndryType type) const;
   int nz; // Size of mesh in Z. This is mesh->ngz-1
   Mesh* localmesh;
-  Options* localoptions;
+  Options* localoptions{nullptr};
   CELL_LOC location;
 
+  /// True if corrections for non-uniform mesh spacing should be included in operators
+  bool non_uniform_{};
+
+  FieldMetric dx_, dy_, dz_; ///< Mesh spacing in x, y and z
+
+  /// 2nd-order correction for non-uniform meshes d/di(1/dx), d/di(1/dy) and d/di(1/dz)
+  FieldMetric d1_dx_, d1_dy_, d1_dz_;
+
+  /// d pitch angle / dx. Needed for vector differentials (Curl)
+  FieldMetric ShiftTorsion_;
+
+  ///< Integrated shear (I in BOUT notation)
+  FieldMetric IntShiftTorsion_;
+
   /// Handles calculation of yup and ydown
   std::unique_ptr<ParallelTransform> transform{nullptr};
 
   /// Cache variable for `zlength`. Invalidated when
-  /// `Coordinates::geometry` is called
+  /// `Coordinates::recalculateAndReset` is called
   mutable std::unique_ptr<Field2D> zlength_cache{nullptr};
 
   /// Cache variable for Grad2_par2
   mutable std::map<std::string, std::unique_ptr<FieldMetric>> Grad2_par2_DDY_invSgCache;
   mutable std::unique_ptr<FieldMetric> invSgCache{nullptr};
 
+  ContravariantMetricTensor contravariantMetricTensor;
+  CovariantMetricTensor covariantMetricTensor;
+
+  /// Christoffel symbol of the second kind (connection coefficients)
+  mutable std::unique_ptr<ChristoffelSymbols> christoffel_symbols_cache{nullptr};
+
+  /// `g_values` needs renaming, when we know what the name should be
+  mutable std::unique_ptr<GValues> g_values_cache{nullptr};
+
+  mutable std::unique_ptr<FieldMetric> jacobian_cache{nullptr};
+
+  FieldMetric Bxy_; ///< Magnitude of B = nabla z times nabla x
+
   /// Set the parallel (y) transform from the options file.
   /// Used in the constructor to create the transform object.
   void setParallelTransform(Options* options);
 
-  const FieldMetric& invSg() const;
-  const FieldMetric& Grad2_par2_DDY_invSg(CELL_LOC outloc,
-                                          const std::string& method) const;
-
   // check that covariant tensors are positive (if expected) and finite (always)
   void checkCovariant();
   // check that contravariant tensors are positive (if expected) and finite (always)
   void checkContravariant();
 
   mutable std::array<std::shared_ptr<YBoundary>, 3> ybndrys;
+
+  FieldMetric recalculateBxy() const;
+
+  /// Non-uniform meshes. Need to use DDX, DDY
+  void correctionForNonUniformMeshes(bool force_interpolate_from_centre);
+
+  void interpolateFromCoordinates(Options* options, const Coordinates* coords_in);
+
   /// Read quantities with given suffix from `Mesh`
   void readFromMesh(Options* options, const std::string& suffix);
+
+  /// Read parallel slices of metric components from `Mesh`
+  void readParallelMetricComponents();
+
+protected:
+  /// For testing purposes only; inherit and make this public
+  void splitBxyParallelSlices();
 };
 
+namespace bout {
+std::string parallelSliceFieldName(std::string_view field, int offset);
+}
+
 #endif // BOUT_COORDINATES_H
diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index b39a82eb0b..96c17a1193 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -134,12 +134,15 @@ public:
   virtual void setRegion([[maybe_unused]] std::optional<size_t> regionID) {}
   virtual void setRegion([[maybe_unused]] const std::string& region_name) {}
   virtual void resetRegion() {}
+  virtual void resetRegionParallel([[maybe_unused]] bool force) {};
   virtual std::optional<size_t> getRegionID() const { return {}; }
   virtual bool hasParallelSlices() const { return true; }
   virtual void calcParallelSlices() {}
   virtual void splitParallelSlices() {}
   virtual void clearParallelSlices() {}
   virtual size_t numberParallelSlices() const { return 0; }
+  virtual bool areCalcParallelSlicesAllowed() const { return false; }
+  virtual void disallowCalcParallelSlices() {}
 
 private:
   /// Labels for the type of coordinate system this field is defined over
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 905e736999..d60ba4b281 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -355,7 +355,7 @@ public:
   const Region<Ind3D>& getValidRegionWithDefault(const std::string& region_name) const;
   void setRegion(const std::string& region_name) override;
   void resetRegion() override { regionID.reset(); };
-  void resetRegionParallel(bool force = false);
+  void resetRegionParallel(bool force = false) override;
   void setRegion(size_t id) override { regionID = id; };
   void setRegion(std::optional<size_t> id) override { regionID = id; };
   std::optional<size_t> getRegionID() const override { return regionID; };
@@ -601,6 +601,8 @@ public:
   friend class Vector2D;
 
   void calcParallelSlices() override;
+  bool areCalcParallelSlicesAllowed() const override { return _allowCalcParallelSlices; };
+  void disallowCalcParallelSlices() override { _allowCalcParallelSlices = false; };
 
   void applyBoundary(bool init = false) override;
   void applyBoundary(BoutReal t);
@@ -633,9 +635,6 @@ public:
 
   std::weak_ptr<Options> getTracking() { return tracking; };
 
-  bool areCalcParallelSlicesAllowed() const { return _allowCalcParallelSlices; };
-  void disallowCalcParallelSlices() { _allowCalcParallelSlices = false; };
-
   inline Field3DParallel asField3DParallel();
   inline Field3DParallel asField3DParallel() const;
 
diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 1b7a36f874..c86a376bc0 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -491,10 +491,10 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Calculate velocities
-    const BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J[i.zp()] + coord->J[i]);
-    const BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J[i.zm()] + coord->J[i]);
-    const BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J[i.xm()] + coord->J[i]);
-    const BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J[i.xp()] + coord->J[i]);
+    const BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J()[i.zp()] + coord->J()[i]);
+    const BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J()[i.zm()] + coord->J()[i]);
+    const BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J()[i.xm()] + coord->J()[i]);
+    const BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J()[i.xp()] + coord->J()[i]);
 
     // X direction
     Stencil1D s;
@@ -517,16 +517,16 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
           // Flux in from boundary
           flux = vR * 0.5 * (n[i.xp()] + n[i]);
         }
-        result[i] += flux / (coord->dx[i] * coord->J[i]);
-        result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]);
+        result[i] += flux / (coord->dx()[i] * coord->J()[i]);
+        result[i.xp()] -= flux / (coord->dx()[i.xp()] * coord->J()[i.xp()]);
       }
     } else {
       // Not at a boundary
       if (vR > 0.0) {
         // Flux out into next cell
         const BoutReal flux = vR * s.R;
-        result[i] += flux / (coord->dx[i] * coord->J[i]);
-        result[i.xp()] -= flux / (coord->dx[i.xp()] * coord->J[i.xp()]);
+        result[i] += flux / (coord->dx()[i] * coord->J()[i]);
+        result[i.xp()] -= flux / (coord->dx()[i.xp()] * coord->J()[i.xp()]);
       }
     }
 
@@ -544,15 +544,15 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
           // Flux in from boundary
           flux = vL * 0.5 * (n[i.xm()] + n[i]);
         }
-        result[i] -= flux / (coord->dx[i] * coord->J[i]);
-        result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]);
+        result[i] -= flux / (coord->dx()[i] * coord->J()[i]);
+        result[i.xm()] += flux / (coord->dx()[i.xm()] * coord->J()[i.xm()]);
       }
     } else {
       // Not at a boundary
       if (vL < 0.0) {
         const BoutReal flux = vL * s.L;
-        result[i] -= flux / (coord->dx[i] * coord->J[i]);
-        result[i.xm()] += flux / (coord->dx[i.xm()] * coord->J[i.xm()]);
+        result[i] -= flux / (coord->dx()[i] * coord->J()[i]);
+        result[i.xm()] += flux / (coord->dx()[i.xm()] * coord->J()[i.xm()]);
       }
     }
 
@@ -568,13 +568,13 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 
     if (vU > 0.0) {
       const BoutReal flux = vU * s.R;
-      result[i] += flux / (coord->J[i] * coord->dz[i]);
-      result[i.zp()] -= flux / (coord->J[i.zp()] * coord->dz[i.zp()]);
+      result[i] += flux / (coord->J()[i] * coord->dz()[i]);
+      result[i.zp()] -= flux / (coord->J()[i.zp()] * coord->dz()[i.zp()]);
     }
     if (vD < 0.0) {
       const BoutReal flux = vD * s.L;
-      result[i] -= flux / (coord->J[i] * coord->dz[i]);
-      result[i.zm()] += flux / (coord->J[i.zm()] * coord->dz[i.zm()]);
+      result[i] -= flux / (coord->J()[i] * coord->dz()[i]);
+      result[i.zm()] += flux / (coord->J()[i.zm()] * coord->dz()[i.zm()]);
     }
   }
 
@@ -592,15 +592,15 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Y velocities on y boundaries
-    const BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J[i] + coord->J[i.yp()]);
-    const BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J[i] + coord->J[i.ym()]);
+    const BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J()[i] + coord->J()[i.yp()]);
+    const BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J()[i] + coord->J()[i.ym()]);
 
     // n (advected quantity) on y boundaries
     // Note: Use unshifted n_in variable
     const BoutReal nU = 0.5 * (n[i] + n[i.yp()]);
     const BoutReal nD = 0.5 * (n[i] + n[i.ym()]);
 
-    yresult[i] = (nU * vU - nD * vD) / (coord->J[i] * coord->dy[i]);
+    yresult[i] = (nU * vU - nD * vD) / (coord->J()[i] * coord->dy()[i]);
   }
   return result + fromFieldAligned(yresult, "RGN_NOBNDRY");
 }
@@ -823,9 +823,9 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
     ASSERT1(f_in.hasParallelSlices());
     ASSERT1(v_in.hasParallelSlices());
 
-    const auto& B = coord->Bxy;
-    const auto& B_up = coord->Bxy.yup();
-    const auto& B_down = coord->Bxy.ydown();
+    const auto& B = coord->Bxy();
+    const auto& B_up = coord->Bxy().yup();
+    const auto& B_down = coord->Bxy().ydown();
 
     const auto& f_up = f_in.yup();
     const auto& f_down = f_in.ydown();
@@ -833,8 +833,8 @@ Field3D Div_par_fvv(const Field3D& f_in, const Field3D& v_in,
     const auto& v_up = v_in.yup();
     const auto& v_down = v_in.ydown();
 
-    const auto& g_22 = coord->g_22;
-    const auto& dy = coord->dy;
+    const auto& g_22 = coord->g_22();
+    const auto& dy = coord->dy();
 
     Field3D result{emptyFrom(f_in)};
     BOUT_FOR(i, f_in.getRegion("RGN_NOBNDRY")) {
@@ -1013,9 +1013,9 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
     ASSERT1(f_in.hasParallelSlices());
     ASSERT1(v_in.hasParallelSlices());
 
-    const auto B = coord->Bxy;
-    const auto B_up = coord->Bxy.yup();
-    const auto B_down = coord->Bxy.ydown();
+    const auto B = coord->Bxy();
+    const auto B_up = coord->Bxy().yup();
+    const auto B_down = coord->Bxy().ydown();
 
     const auto& f_up = f_in.yup();
     const auto& f_down = f_in.ydown();
@@ -1023,8 +1023,8 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
     const auto& v_up = v_in.yup();
     const auto& v_down = v_in.ydown();
 
-    const auto g_22 = coord->g_22;
-    const auto dy = coord->dy;
+    const auto g_22 = coord->g_22();
+    const auto dy = coord->dy();
 
     Field3D result{emptyFrom(f_in)};
     flow_ylow = zeroFrom(f_in);
@@ -1336,10 +1336,10 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
   if (fci) {
     // 3D Metric, need yup/ydown fields.
     // Requires previous communication of metrics.
-    if (!coord->g23.hasParallelSlices() || !coord->g_23.hasParallelSlices()
-        || !coord->dy.hasParallelSlices() || !coord->dz.hasParallelSlices()
-        || !coord->Bxy.hasParallelSlices() || !coord->J.hasParallelSlices()) {
-      throw BoutException("metrics have no yup/down: Maybe communicate in init?");
+    if (!coord->g23().hasParallelSlices() || !coord->g_23().hasParallelSlices()
+        || !coord->dy().hasParallelSlices() || !coord->dz().hasParallelSlices()
+        || !coord->Bxy().hasParallelSlices() || !coord->J().hasParallelSlices()) {
+      throw BoutException("metrics have no yup/down!");
     }
   }
 #endif
@@ -1357,12 +1357,12 @@ Field3D Div_a_Grad_perp_limit(const Field3D& a, const Field3D& g, const Field3D&
 #else
   constexpr bool metric_fci = false;
 #endif
-  const auto g23 = makeslices(metric_fci, coord->g23);
-  const auto g_23 = makeslices(metric_fci, coord->g_23);
-  const auto J = makeslices(metric_fci, coord->J);
-  const auto dy = makeslices(metric_fci, coord->dy);
-  const auto dz = makeslices(metric_fci, coord->dz);
-  const auto Bxy = makeslices(metric_fci, coord->Bxy);
+  const auto g23 = makeslices(metric_fci, coord->g23());
+  const auto g_23 = makeslices(metric_fci, coord->g_23());
+  const auto J = makeslices(metric_fci, coord->J());
+  const auto dy = makeslices(metric_fci, coord->dy());
+  const auto dz = makeslices(metric_fci, coord->dz());
+  const auto Bxy = makeslices(metric_fci, coord->Bxy());
 
   // Result of the Y and Z fluxes
   Field3D yzresult(0.0, mesh);
diff --git a/include/bout/g_values.hxx b/include/bout/g_values.hxx
new file mode 100644
index 0000000000..cbbd6d24ff
--- /dev/null
+++ b/include/bout/g_values.hxx
@@ -0,0 +1,28 @@
+#ifndef BOUT_GVALUES_HXX
+#define BOUT_GVALUES_HXX
+
+#include <bout/metric_tensor.hxx>
+
+class Coordinates;
+
+/// `GValues` needs renaming, when we know what the name should be
+class GValues {
+public:
+  explicit GValues(const Coordinates& coordinates);
+
+  const bout::FieldMetric& G1() const { return G1_m; }
+  const bout::FieldMetric& G2() const { return G2_m; }
+  const bout::FieldMetric& G3() const { return G3_m; }
+
+  template <class F>
+  void map(F function) {
+    G1_m = function(G1_m);
+    G2_m = function(G2_m);
+    G3_m = function(G3_m);
+  }
+
+private:
+  bout::FieldMetric G1_m, G2_m, G3_m;
+};
+
+#endif //BOUT_GVALUES_HXX
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 84f9ec36c6..833d23c419 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -624,25 +624,7 @@ public:
     return getCoordinatesSmart(location).get();
   };
 
-  std::shared_ptr<Coordinates>
-  getCoordinatesSmart(const CELL_LOC location = CELL_CENTRE) {
-    ASSERT1(location != CELL_DEFAULT);
-    ASSERT1(location != CELL_VSHIFT);
-
-    auto found = coords_map.find(location);
-    if (found != coords_map.end()) {
-      // True branch most common, returns immediately
-      return found->second;
-    }
-
-    // No coordinate system set. Create default
-    // Note that this can't be allocated here due to incomplete type
-    // (circular dependency between Mesh and Coordinates)
-    auto inserted = coords_map.emplace(location, nullptr);
-    inserted.first->second = createDefaultCoordinates(location);
-    inserted.first->second->geometry(false);
-    return inserted.first->second;
-  }
+  std::shared_ptr<Coordinates> getCoordinatesSmart(const CELL_LOC location = CELL_CENTRE);
 
   std::shared_ptr<Coordinates>
   getCoordinatesConst(const CELL_LOC location = CELL_CENTRE) const {
diff --git a/include/bout/metric_tensor.hxx b/include/bout/metric_tensor.hxx
new file mode 100644
index 0000000000..bef5bc3079
--- /dev/null
+++ b/include/bout/metric_tensor.hxx
@@ -0,0 +1,104 @@
+#ifndef BOUT_METRIC_TENSOR_HXX
+#define BOUT_METRIC_TENSOR_HXX
+
+#include <bout/bout_types.hxx>
+#include <bout/build_defines.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+
+#include <string>
+#include <string_view>
+
+namespace bout {
+#if BOUT_USE_METRIC_3D
+using FieldMetric = Field3D;
+#else
+using FieldMetric = Field2D;
+#endif
+} // namespace bout
+
+class Coordinates;
+
+class MetricTensor {
+public:
+  friend class Coordinates;
+
+#if BOUT_USE_METRIC_3D
+  using Metric2DSlice = const BoutReal*;
+#else
+  using Metric2DSlice = const BoutReal&;
+#endif
+  using FieldMetric = bout::FieldMetric;
+
+  MetricTensor(const MetricTensor&) = default;
+  MetricTensor(MetricTensor&&) = default;
+  MetricTensor& operator=(const MetricTensor&) = default;
+  MetricTensor& operator=(MetricTensor&&) = default;
+  MetricTensor(FieldMetric g11, FieldMetric g22, FieldMetric g33, FieldMetric g12,
+               FieldMetric g13, FieldMetric g23);
+
+  MetricTensor(BoutReal g11, BoutReal g22, BoutReal g33, BoutReal g12, BoutReal g13,
+               BoutReal g23, Mesh* mesh);
+  virtual ~MetricTensor() = default;
+
+  /// Check that tensors are positive (if expected) and finite (always)
+  void check(int ystart);
+
+  const FieldMetric& g11() const { return g11_m; }
+  const FieldMetric& g22() const { return g22_m; }
+  const FieldMetric& g33() const { return g33_m; }
+  const FieldMetric& g12() const { return g12_m; }
+  const FieldMetric& g13() const { return g13_m; }
+  const FieldMetric& g23() const { return g23_m; }
+
+  const BoutReal& g11(int x, int y, int z) const { return g11_m(x, y, z); }
+  const BoutReal& g22(int x, int y, int z) const { return g22_m(x, y, z); }
+  const BoutReal& g33(int x, int y, int z) const { return g33_m(x, y, z); }
+  const BoutReal& g12(int x, int y, int z) const { return g12_m(x, y, z); }
+  const BoutReal& g13(int x, int y, int z) const { return g13_m(x, y, z); }
+  const BoutReal& g23(int x, int y, int z) const { return g23_m(x, y, z); }
+
+  Metric2DSlice g11(int x, int y) const { return g11_m(x, y); }
+  Metric2DSlice g22(int x, int y) const { return g22_m(x, y); }
+  Metric2DSlice g33(int x, int y) const { return g33_m(x, y); }
+  Metric2DSlice g12(int x, int y) const { return g12_m(x, y); }
+  Metric2DSlice g13(int x, int y) const { return g13_m(x, y); }
+  Metric2DSlice g23(int x, int y) const { return g23_m(x, y); }
+
+  /// Transforms the MetricTensor by applying the given function to every component
+  template <class F>
+  void map(F function) {
+    g11_m = function(g11_m);
+    g22_m = function(g22_m);
+    g33_m = function(g33_m);
+    g12_m = function(g12_m);
+    g13_m = function(g13_m);
+    g23_m = function(g23_m);
+  }
+
+  void communicate();
+
+private:
+  FieldMetric g11_m, g22_m, g33_m, g12_m, g13_m, g23_m;
+};
+
+class CovariantMetricTensor;
+class ContravariantMetricTensor;
+
+class CovariantMetricTensor : public MetricTensor {
+public:
+  using MetricTensor::MetricTensor;
+
+  auto inverse(const std::string& region = "RGN_ALL", bool communicate = true)
+      -> ContravariantMetricTensor;
+};
+
+class ContravariantMetricTensor : public MetricTensor {
+public:
+  using MetricTensor::MetricTensor;
+
+  auto inverse(const std::string& region = "RGN_ALL", bool communicate = true)
+      -> CovariantMetricTensor;
+};
+
+#endif //BOUT_METRIC_TENSOR_HXX
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index 5139cd5090..d98aa7d4e8 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -211,7 +211,7 @@ public:
   void apply(Field3D& f, BoutReal t) override {
     if (bndry != nullptr) {
       f.ynext(bndry->dir()).allocate(); // Ensure unique before modifying
-      auto dy = f.getCoordinates()->dy;
+      auto dy = f.getCoordinates()->dy();
       for (auto pnt : *bndry) {
         BoutReal value = getValue(pnt, t);
         if (isNeumann) {
@@ -222,7 +222,7 @@ public:
     }
     if (bndryX != nullptr) {
       f.allocate();
-      auto dy = f.getCoordinates()->dx;
+      auto dy = f.getCoordinates()->dx();
       for (auto pnt : *bndryX) {
         BoutReal value = getValue(pnt, t);
         if (isNeumann) {
@@ -233,7 +233,7 @@ public:
     }
     if (bndryY != nullptr) {
       f.allocate();
-      auto dy = f.getCoordinates()->dy;
+      auto dy = f.getCoordinates()->dy();
       for (auto pnt : *bndryY) {
         BoutReal value = getValue(pnt, t);
         if (isNeumann) {
diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx
index d9ed397bb5..6952069251 100644
--- a/include/bout/paralleltransform.hxx
+++ b/include/bout/paralleltransform.hxx
@@ -91,10 +91,6 @@ public:
   /// require a twist-shift at branch cuts on closed field lines?
   virtual bool requiresTwistShift(bool twist_shift_enabled, YDirectionType ytype) = 0;
 
-  /// Can be implemented to load parallel metrics
-  /// Needed by FCI
-  virtual void loadParallelMetrics([[maybe_unused]] Coordinates* coords) {}
-
 protected:
   /// This method should be called in the constructor to check that if the grid
   /// has a 'parallel_transform' variable, it has the correct value
diff --git a/include/bout/tokamak_coordinates.hxx b/include/bout/tokamak_coordinates.hxx
index f056033bb9..295d0bf9d1 100644
--- a/include/bout/tokamak_coordinates.hxx
+++ b/include/bout/tokamak_coordinates.hxx
@@ -4,6 +4,7 @@
 #include <bout/bout_types.hxx>
 #include <bout/coordinates.hxx>
 #include <bout/field2d.hxx>
+#include <bout/metric_tensor.hxx>
 
 class Mesh;
 
@@ -14,21 +15,21 @@ namespace bout {
 /// `I_unnormalised` are normalised.
 struct TokamakCoordinates {
   /// Major radius
-  Field2D Rxy;
+  FieldMetric Rxy;
   /// Vertical height
-  Field2D Zxy;
+  FieldMetric Zxy;
   /// Poloidal magnetic field
-  Field2D Bpxy;
+  FieldMetric Bpxy;
   /// Toroidal magnetic field
-  Field2D Btxy;
+  FieldMetric Btxy;
   /// Total magnetic field
-  Field2D Bxy;
+  FieldMetric Bxy;
   /// Poloidal arc length
-  Field2D hthe;
+  FieldMetric hthe;
   /// Integrated shear (normalised)
-  Coordinates::FieldMetric I;
+  FieldMetric I;
   /// Unnormalised integrated shear
-  Coordinates::FieldMetric I_unnormalised;
+  FieldMetric I_unnormalised;
 };
 
 /// Read, normalise, calculate, and set the metric components for a BOUT++
diff --git a/src/field/vecops.cxx b/src/field/vecops.cxx
index 672e8f6c09..1bb3d991f4 100644
--- a/src/field/vecops.cxx
+++ b/src/field/vecops.cxx
@@ -104,10 +104,10 @@ Vector3D Grad_perp(const Field3D& f, CELL_LOC outloc, const std::string& method)
   Vector3D result(f.getMesh());
 
   result.x = DDX(f, outloc, method)
-             - metric->g_12 * DDY(f, outloc, method) / SQ(metric->J * metric->Bxy);
+             - metric->g_12() * DDY(f, outloc, method) / SQ(metric->J() * metric->Bxy());
   result.y = 0.0;
   result.z = DDZ(f, outloc, method)
-             - metric->g_23 * DDY(f, outloc, method) / SQ(metric->J * metric->Bxy);
+             - metric->g_23() * DDY(f, outloc, method) / SQ(metric->J() * metric->Bxy());
 
   result.setLocation(result.x.getLocation());
 
@@ -126,9 +126,9 @@ Vector2D Grad_perp(const Field2D& f, CELL_LOC outloc, const std::string& method)
   Vector2D result(f.getMesh());
 
   result.x = DDX(f, outloc, method)
-             - metric->g_12 * DDY(f, outloc, method) / SQ(metric->J * metric->Bxy);
+             - metric->g_12() * DDY(f, outloc, method) / SQ(metric->J() * metric->Bxy());
   result.y = 0.0;
-  result.z = -metric->g_23 * DDY(f, outloc, method) / SQ(metric->J * metric->Bxy);
+  result.z = -metric->g_23() * DDY(f, outloc, method) / SQ(metric->J() * metric->Bxy());
 
   result.setLocation(result.x.getLocation());
 
@@ -159,10 +159,10 @@ Coordinates::FieldMetric Div(const Vector2D& v, CELL_LOC outloc,
   Vector2D vcn = v;
   vcn.toContravariant();
 
-  Coordinates::FieldMetric result = DDX(metric->J * vcn.x, outloc, method);
-  result += DDY(Coordinates::FieldMetric{metric->J * vcn.y}, outloc, method);
-  result += DDZ(Coordinates::FieldMetric{metric->J * vcn.z}, outloc, method);
-  result /= metric->J;
+  Coordinates::FieldMetric result = DDX(metric->J() * vcn.x, outloc, method);
+  result += DDY(Coordinates::FieldMetric{metric->J() * vcn.y}, outloc, method);
+  result += DDZ(Coordinates::FieldMetric{metric->J() * vcn.z}, outloc, method);
+  result /= metric->J();
 
   return result;
 }
@@ -185,7 +185,7 @@ Field3D Div(const Vector3D& v, CELL_LOC outloc, const std::string& method) {
   Vector3D vcn = v;
   vcn.toContravariant();
 
-  Field3D vcnJy = vcn.y.getCoordinates()->J * vcn.y;
+  Field3D vcnJy = vcn.y.getCoordinates()->J() * vcn.y;
   if (v.y.hasParallelSlices()) {
     // If v.y has parallel slices then we are using ShiftedMetric (with
     // mesh:calcParallelSlices_on_communicate=true) or FCI, so we should calculate
@@ -194,9 +194,9 @@ Field3D Div(const Vector3D& v, CELL_LOC outloc, const std::string& method) {
   }
   auto result = DDY(vcnJy, outloc, method);
 
-  result += DDX(Field3D{vcn.x.getCoordinates()->J * vcn.x}, outloc, method);
-  result += DDZ(Field3D{vcn.z.getCoordinates()->J * vcn.z}, outloc, method);
-  result /= metric->J;
+  result += DDX(Field3D{vcn.x.getCoordinates()->J() * vcn.x}, outloc, method);
+  result += DDZ(Field3D{vcn.z.getCoordinates()->J() * vcn.z}, outloc, method);
+  result /= metric->J();
 
   return result;
 }
@@ -224,12 +224,12 @@ Coordinates::FieldMetric Div(const Vector2D& v, const Field2D& f, CELL_LOC outlo
   vcn.toContravariant();
 
   Coordinates::FieldMetric result = FDDX(
-      Coordinates::FieldMetric{vcn.x.getCoordinates()->J * vcn.x}, f, outloc, method);
-  result += FDDY(Coordinates::FieldMetric{vcn.y.getCoordinates()->J * vcn.y}, f, outloc,
+      Coordinates::FieldMetric{vcn.x.getCoordinates()->J() * vcn.x}, f, outloc, method);
+  result += FDDY(Coordinates::FieldMetric{vcn.y.getCoordinates()->J() * vcn.y}, f, outloc,
                  method);
-  result += FDDZ(Coordinates::FieldMetric{vcn.z.getCoordinates()->J * vcn.z}, f, outloc,
+  result += FDDZ(Coordinates::FieldMetric{vcn.z.getCoordinates()->J() * vcn.z}, f, outloc,
                  method);
-  result /= metric->J;
+  result /= metric->J();
 
   return result;
 }
@@ -250,10 +250,10 @@ Field3D Div(const Vector3D& v, const Field3D& f, CELL_LOC outloc,
   Vector3D vcn = v;
   vcn.toContravariant();
 
-  Field3D result = FDDX(Field3D{vcn.x.getCoordinates()->J * vcn.x}, f, outloc, method);
-  result += FDDY(Field3D{vcn.y.getCoordinates()->J * vcn.y}, f, outloc, method);
-  result += FDDZ(Field3D{vcn.z.getCoordinates()->J * vcn.z}, f, outloc, method);
-  result /= metric->J;
+  Field3D result = FDDX(Field3D{vcn.x.getCoordinates()->J() * vcn.x}, f, outloc, method);
+  result += FDDY(Field3D{vcn.y.getCoordinates()->J() * vcn.y}, f, outloc, method);
+  result += FDDZ(Field3D{vcn.z.getCoordinates()->J() * vcn.z}, f, outloc, method);
+  result /= metric->J();
 
   return result;
 }
@@ -274,12 +274,12 @@ Vector2D Curl(const Vector2D& v) {
 
   // get components (curl(v))^j
   Vector2D result(localmesh);
-  result.x = (DDY(vco.z) - DDZ(vco.y)) / metric->J;
-  result.y = (DDZ(vco.x) - DDX(vco.z)) / metric->J;
-  result.z = (DDX(vco.y) - DDY(vco.x)) / metric->J;
+  result.x = (DDY(vco.z) - DDZ(vco.y)) / metric->J();
+  result.y = (DDZ(vco.x) - DDX(vco.z)) / metric->J();
+  result.z = (DDX(vco.y) - DDY(vco.x)) / metric->J();
 
   /// Coordinate torsion
-  result.z -= metric->ShiftTorsion * vco.z / metric->J;
+  result.z -= metric->ShiftTorsion() * vco.z / metric->J();
 
   result.setLocation(v.getLocation());
 
@@ -302,12 +302,12 @@ Vector3D Curl(const Vector3D& v) {
 
   // get components (curl(v))^j
   Vector3D result(localmesh);
-  result.x = (DDY(vco.z) - DDZ(vco.y)) / metric->J;
-  result.y = (DDZ(vco.x) - DDX(vco.z)) / metric->J;
-  result.z = (DDX(vco.y) - DDY(vco.x)) / metric->J;
+  result.x = (DDY(vco.z) - DDZ(vco.y)) / metric->J();
+  result.y = (DDZ(vco.x) - DDX(vco.z)) / metric->J();
+  result.z = (DDX(vco.y) - DDY(vco.x)) / metric->J();
 
   // Coordinate torsion
-  result.z -= metric->ShiftTorsion * vco.z / metric->J;
+  result.z -= metric->ShiftTorsion() * vco.z / metric->J();
 
   result.setLocation(v.getLocation());
 
@@ -387,80 +387,80 @@ R V_dot_Grad(const T& v, const F& a) {
     result.x = VDDX(vcn.x, a.x) + VDDY(vcn.y, a.x) + VDDZ(vcn.z, a.x);
     BOUT_FOR(i, result.x.getRegion("RGN_ALL")) {
       result.x[i] -= vcn.x[i]
-                     * (metric->G1_11[i] * a.x[i] + metric->G2_11[i] * a.y[i]
-                        + metric->G3_11[i] * a.z[i]);
+                     * (metric->G1_11()[i] * a.x[i] + metric->G2_11()[i] * a.y[i]
+                        + metric->G3_11()[i] * a.z[i]);
       result.x[i] -= vcn.y[i]
-                     * (metric->G1_12[i] * a.x[i] + metric->G2_12[i] * a.y[i]
-                        + metric->G3_12[i] * a.z[i]);
+                     * (metric->G1_12()[i] * a.x[i] + metric->G2_12()[i] * a.y[i]
+                        + metric->G3_12()[i] * a.z[i]);
       result.x[i] -= vcn.z[i]
-                     * (metric->G1_13[i] * a.x[i] + metric->G2_13[i] * a.y[i]
-                        + metric->G3_13[i] * a.z[i]);
+                     * (metric->G1_13()[i] * a.x[i] + metric->G2_13()[i] * a.y[i]
+                        + metric->G3_13()[i] * a.z[i]);
     }
 
     result.y = VDDX(vcn.x, a.y) + VDDY(vcn.y, a.y) + VDDZ(vcn.z, a.y);
     BOUT_FOR(i, result.y.getRegion("RGN_ALL")) {
       result.y[i] -= vcn.x[i]
-                     * (metric->G1_12[i] * a.x[i] + metric->G2_12[i] * a.y[i]
-                        + metric->G3_12[i] * a.z[i]);
+                     * (metric->G1_12()[i] * a.x[i] + metric->G2_12()[i] * a.y[i]
+                        + metric->G3_12()[i] * a.z[i]);
       result.y[i] -= vcn.y[i]
-                     * (metric->G1_22[i] * a.x[i] + metric->G2_22[i] * a.y[i]
-                        + metric->G3_22[i] * a.z[i]);
+                     * (metric->G1_22()[i] * a.x[i] + metric->G2_22()[i] * a.y[i]
+                        + metric->G3_22()[i] * a.z[i]);
       result.y[i] -= vcn.z[i]
-                     * (metric->G1_23[i] * a.x[i] + metric->G2_23[i] * a.y[i]
-                        + metric->G3_23[i] * a.z[i]);
+                     * (metric->G1_23()[i] * a.x[i] + metric->G2_23()[i] * a.y[i]
+                        + metric->G3_23()[i] * a.z[i]);
     }
 
     result.z = VDDX(vcn.x, a.z) + VDDY(vcn.y, a.z) + VDDZ(vcn.z, a.z);
     BOUT_FOR(i, result.z.getRegion("RGN_ALL")) {
       result.z[i] -= vcn.x[i]
-                     * (metric->G1_13[i] * a.x[i] + metric->G2_13[i] * a.y[i]
-                        + metric->G3_13[i] * a.z[i]);
+                     * (metric->G1_13()[i] * a.x[i] + metric->G2_13()[i] * a.y[i]
+                        + metric->G3_13()[i] * a.z[i]);
       result.z[i] -= vcn.y[i]
-                     * (metric->G1_23[i] * a.x[i] + metric->G2_23[i] * a.y[i]
-                        + metric->G3_23[i] * a.z[i]);
+                     * (metric->G1_23()[i] * a.x[i] + metric->G2_23()[i] * a.y[i]
+                        + metric->G3_23()[i] * a.z[i]);
       result.z[i] -= vcn.z[i]
-                     * (metric->G1_33[i] * a.x[i] + metric->G2_33[i] * a.y[i]
-                        + metric->G3_33[i] * a.z[i]);
+                     * (metric->G1_33()[i] * a.x[i] + metric->G2_33()[i] * a.y[i]
+                        + metric->G3_33()[i] * a.z[i]);
     }
     result.covariant = true;
   } else {
     result.x = VDDX(vcn.x, a.x) + VDDY(vcn.y, a.x) + VDDZ(vcn.z, a.x);
     BOUT_FOR(i, result.x.getRegion("RGN_ALL")) {
       result.x[i] += vcn.x[i]
-                     * (metric->G1_11[i] * a.x[i] + metric->G1_12[i] * a.y[i]
-                        + metric->G1_13[i] * a.z[i]);
+                     * (metric->G1_11()[i] * a.x[i] + metric->G1_12()[i] * a.y[i]
+                        + metric->G1_13()[i] * a.z[i]);
       result.x[i] += vcn.y[i]
-                     * (metric->G1_12[i] * a.x[i] + metric->G1_22[i] * a.y[i]
-                        + metric->G1_23[i] * a.z[i]);
+                     * (metric->G1_12()[i] * a.x[i] + metric->G1_22()[i] * a.y[i]
+                        + metric->G1_23()[i] * a.z[i]);
       result.x[i] += vcn.z[i]
-                     * (metric->G1_13[i] * a.x[i] + metric->G1_23[i] * a.y[i]
-                        + metric->G1_33[i] * a.z[i]);
+                     * (metric->G1_13()[i] * a.x[i] + metric->G1_23()[i] * a.y[i]
+                        + metric->G1_33()[i] * a.z[i]);
     }
 
     result.y = VDDX(vcn.x, a.y) + VDDY(vcn.y, a.y) + VDDZ(vcn.z, a.y);
     BOUT_FOR(i, result.y.getRegion("RGN_ALL")) {
       result.y[i] += vcn.x[i]
-                     * (metric->G2_11[i] * a.x[i] + metric->G2_12[i] * a.y[i]
-                        + metric->G2_13[i] * a.z[i]);
+                     * (metric->G2_11()[i] * a.x[i] + metric->G2_12()[i] * a.y[i]
+                        + metric->G2_13()[i] * a.z[i]);
       result.y[i] += vcn.y[i]
-                     * (metric->G2_12[i] * a.x[i] + metric->G2_22[i] * a.y[i]
-                        + metric->G2_23[i] * a.z[i]);
+                     * (metric->G2_12()[i] * a.x[i] + metric->G2_22()[i] * a.y[i]
+                        + metric->G2_23()[i] * a.z[i]);
       result.y[i] += vcn.z[i]
-                     * (metric->G2_13[i] * a.x[i] + metric->G2_23[i] * a.y[i]
-                        + metric->G2_33[i] * a.z[i]);
+                     * (metric->G2_13()[i] * a.x[i] + metric->G2_23()[i] * a.y[i]
+                        + metric->G2_33()[i] * a.z[i]);
     }
 
     result.z = VDDX(vcn.x, a.z) + VDDY(vcn.y, a.z) + VDDZ(vcn.z, a.z);
     BOUT_FOR(i, result.z.getRegion("RGN_ALL")) {
       result.z[i] += vcn.x[i]
-                     * (metric->G3_11[i] * a.x[i] + metric->G3_12[i] * a.y[i]
-                        + metric->G3_13[i] * a.z[i]);
+                     * (metric->G3_11()[i] * a.x[i] + metric->G3_12()[i] * a.y[i]
+                        + metric->G3_13()[i] * a.z[i]);
       result.z[i] += vcn.y[i]
-                     * (metric->G3_12[i] * a.x[i] + metric->G3_22[i] * a.y[i]
-                        + metric->G3_23[i] * a.z[i]);
+                     * (metric->G3_12()[i] * a.x[i] + metric->G3_22()[i] * a.y[i]
+                        + metric->G3_23()[i] * a.z[i]);
       result.z[i] += vcn.z[i]
-                     * (metric->G3_13[i] * a.x[i] + metric->G3_23[i] * a.y[i]
-                        + metric->G3_33[i] * a.z[i]);
+                     * (metric->G3_13()[i] * a.x[i] + metric->G3_23()[i] * a.y[i]
+                        + metric->G3_33()[i] * a.z[i]);
     }
 
     result.covariant = false;
diff --git a/src/field/vector2d.cxx b/src/field/vector2d.cxx
index ab2d993549..bf20b130f5 100644
--- a/src/field/vector2d.cxx
+++ b/src/field/vector2d.cxx
@@ -2,7 +2,7 @@
  * Class for 2D vectors. Built on the Field2D class,
  * all operators relating to vectors are here (none in Field classes)
  *
- * As with Field2D, Vector2D are constant in z (toroidal angle) 
+ * As with Field2D, Vector2D are constant in z (toroidal angle)
  *
  * B.Dudson, October 2007
  *
@@ -10,7 +10,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -86,12 +86,12 @@ void Vector2D::toCovariant() {
 
       // multiply by g_{ij}
       BOUT_FOR(i, x.getRegion("RGN_ALL")) {
-        x[i] = metric_x->g_11[i] * x[i] + metric_x->g_12[i] * y_at_x[i]
-               + metric_x->g_13[i] * z_at_x[i];
-        y[i] = metric_y->g_22[i] * y[i] + metric_y->g_12[i] * x_at_y[i]
-               + metric_y->g_23[i] * z_at_y[i];
-        z[i] = metric_z->g_33[i] * z[i] + metric_z->g_13[i] * x_at_z[i]
-               + metric_z->g_23[i] * y_at_z[i];
+        x[i] = metric_x->g_11()[i] * x[i] + metric_x->g_12()[i] * y_at_x[i]
+               + metric_x->g_13()[i] * z_at_x[i];
+        y[i] = metric_y->g_22()[i] * y[i] + metric_y->g_12()[i] * x_at_y[i]
+               + metric_y->g_23()[i] * z_at_y[i];
+        z[i] = metric_z->g_33()[i] * z[i] + metric_z->g_13()[i] * x_at_z[i]
+               + metric_z->g_23()[i] * y_at_z[i];
       };
     } else {
       const auto metric = localmesh->getCoordinates(location);
@@ -100,9 +100,12 @@ void Vector2D::toCovariant() {
       Coordinates::FieldMetric gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)};
 
       BOUT_FOR(i, x.getRegion("RGN_ALL")) {
-        gx[i] = metric->g_11[i] * x[i] + metric->g_12[i] * y[i] + metric->g_13[i] * z[i];
-        gy[i] = metric->g_22[i] * y[i] + metric->g_12[i] * x[i] + metric->g_23[i] * z[i];
-        gz[i] = metric->g_33[i] * z[i] + metric->g_13[i] * x[i] + metric->g_23[i] * y[i];
+        gx[i] = metric->g_11()[i] * x[i] + metric->g_12()[i] * y[i]
+                + metric->g_13()[i] * z[i];
+        gy[i] = metric->g_22()[i] * y[i] + metric->g_12()[i] * x[i]
+                + metric->g_23()[i] * z[i];
+        gz[i] = metric->g_33()[i] * z[i] + metric->g_13()[i] * x[i]
+                + metric->g_23()[i] * y[i];
       };
 
       x = gx;
@@ -140,12 +143,12 @@ void Vector2D::toContravariant() {
 
       // multiply by g_{ij}
       BOUT_FOR(i, x.getRegion("RGN_ALL")) {
-        x[i] = metric_x->g11[i] * x[i] + metric_x->g12[i] * y_at_x[i]
-               + metric_x->g13[i] * z_at_x[i];
-        y[i] = metric_y->g22[i] * y[i] + metric_y->g12[i] * x_at_y[i]
-               + metric_y->g23[i] * z_at_y[i];
-        z[i] = metric_z->g33[i] * z[i] + metric_z->g13[i] * x_at_z[i]
-               + metric_z->g23[i] * y_at_z[i];
+        x[i] = metric_x->g11()[i] * x[i] + metric_x->g12()[i] * y_at_x[i]
+               + metric_x->g13()[i] * z_at_x[i];
+        y[i] = metric_y->g22()[i] * y[i] + metric_y->g12()[i] * x_at_y[i]
+               + metric_y->g23()[i] * z_at_y[i];
+        z[i] = metric_z->g33()[i] * z[i] + metric_z->g13()[i] * x_at_z[i]
+               + metric_z->g23()[i] * y_at_z[i];
       };
 
     } else {
@@ -155,9 +158,12 @@ void Vector2D::toContravariant() {
       Coordinates::FieldMetric gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)};
 
       BOUT_FOR(i, x.getRegion("RGN_ALL")) {
-        gx[i] = metric->g11[i] * x[i] + metric->g12[i] * y[i] + metric->g13[i] * z[i];
-        gy[i] = metric->g22[i] * y[i] + metric->g12[i] * x[i] + metric->g23[i] * z[i];
-        gz[i] = metric->g33[i] * z[i] + metric->g13[i] * x[i] + metric->g23[i] * y[i];
+        gx[i] =
+            metric->g11()[i] * x[i] + metric->g12()[i] * y[i] + metric->g13()[i] * z[i];
+        gy[i] =
+            metric->g22()[i] * y[i] + metric->g12()[i] * x[i] + metric->g23()[i] * z[i];
+        gz[i] =
+            metric->g33()[i] * z[i] + metric->g13()[i] * x[i] + metric->g23()[i] * y[i];
       };
 
       x = gx;
@@ -197,7 +203,7 @@ Vector2D* Vector2D::timeDeriv() {
 }
 
 /***************************************************************
- *                         OPERATORS 
+ *                         OPERATORS
  ***************************************************************/
 
 /////////////////// ASSIGNMENT ////////////////////
@@ -303,7 +309,7 @@ Vector2D& Vector2D::operator/=(const Field2D& rhs) {
 }
 
 /***************************************************************
- *                      BINARY OPERATORS 
+ *                      BINARY OPERATORS
  ***************************************************************/
 
 ////////////////// ADDITION //////////////////////
@@ -390,18 +396,18 @@ const Coordinates::FieldMetric Vector2D::operator*(const Vector2D& rhs) const {
 
     if (covariant) {
       // Both covariant
-      result =
-          x * rhs.x * metric->g11 + y * rhs.y * metric->g22 + z * rhs.z * metric->g33;
-      result += (x * rhs.y + y * rhs.x) * metric->g12
-                + (x * rhs.z + z * rhs.x) * metric->g13
-                + (y * rhs.z + z * rhs.y) * metric->g23;
+      result = x * rhs.x * metric->g11() + y * rhs.y * metric->g22()
+               + z * rhs.z * metric->g33();
+      result += (x * rhs.y + y * rhs.x) * metric->g12()
+                + (x * rhs.z + z * rhs.x) * metric->g13()
+                + (y * rhs.z + z * rhs.y) * metric->g23();
     } else {
       // Both contravariant
-      result =
-          x * rhs.x * metric->g_11 + y * rhs.y * metric->g_22 + z * rhs.z * metric->g_33;
-      result += (x * rhs.y + y * rhs.x) * metric->g_12
-                + (x * rhs.z + z * rhs.x) * metric->g_13
-                + (y * rhs.z + z * rhs.y) * metric->g_23;
+      result = x * rhs.x * metric->g_11() + y * rhs.y * metric->g_22()
+               + z * rhs.z * metric->g_33();
+      result += (x * rhs.y + y * rhs.x) * metric->g_12()
+                + (x * rhs.z + z * rhs.x) * metric->g_13()
+                + (y * rhs.z + z * rhs.y) * metric->g_23();
     }
   }
 
diff --git a/src/field/vector3d.cxx b/src/field/vector3d.cxx
index 7fb4a88918..7c5a5e3d67 100644
--- a/src/field/vector3d.cxx
+++ b/src/field/vector3d.cxx
@@ -10,7 +10,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -87,12 +87,12 @@ void Vector3D::toCovariant() {
 
       // multiply by g_{ij}
       BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) {
-        x[i] = metric_x->g_11[i] * x[i] + metric_x->g_12[i] * y_at_x[i]
-               + metric_x->g_13[i] * z_at_x[i];
-        y[i] = metric_y->g_22[i] * y[i] + metric_y->g_12[i] * x_at_y[i]
-               + metric_y->g_23[i] * z_at_y[i];
-        z[i] = metric_z->g_33[i] * z[i] + metric_z->g_13[i] * x_at_z[i]
-               + metric_z->g_23[i] * y_at_z[i];
+        x[i] = metric_x->g_11()[i] * x[i] + metric_x->g_12()[i] * y_at_x[i]
+               + metric_x->g_13()[i] * z_at_x[i];
+        y[i] = metric_y->g_22()[i] * y[i] + metric_y->g_12()[i] * x_at_y[i]
+               + metric_y->g_23()[i] * z_at_y[i];
+        z[i] = metric_z->g_33()[i] * z[i] + metric_z->g_13()[i] * x_at_z[i]
+               + metric_z->g_23()[i] * y_at_z[i];
       };
     } else {
       const auto metric = localmesh->getCoordinates(location);
@@ -101,9 +101,12 @@ void Vector3D::toCovariant() {
       Field3D gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)};
 
       BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) {
-        gx[i] = metric->g_11[i] * x[i] + metric->g_12[i] * y[i] + metric->g_13[i] * z[i];
-        gy[i] = metric->g_22[i] * y[i] + metric->g_12[i] * x[i] + metric->g_23[i] * z[i];
-        gz[i] = metric->g_33[i] * z[i] + metric->g_13[i] * x[i] + metric->g_23[i] * y[i];
+        gx[i] = metric->g_11()[i] * x[i] + metric->g_12()[i] * y[i]
+                + metric->g_13()[i] * z[i];
+        gy[i] = metric->g_22()[i] * y[i] + metric->g_12()[i] * x[i]
+                + metric->g_23()[i] * z[i];
+        gz[i] = metric->g_33()[i] * z[i] + metric->g_13()[i] * x[i]
+                + metric->g_23()[i] * y[i];
       };
 
       x = gx;
@@ -141,12 +144,12 @@ void Vector3D::toContravariant() {
 
       // multiply by g_{ij}
       BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) {
-        x[i] = metric_x->g11[i] * x[i] + metric_x->g12[i] * y_at_x[i]
-               + metric_x->g13[i] * z_at_x[i];
-        y[i] = metric_y->g22[i] * y[i] + metric_y->g12[i] * x_at_y[i]
-               + metric_y->g23[i] * z_at_y[i];
-        z[i] = metric_z->g33[i] * z[i] + metric_z->g13[i] * x_at_z[i]
-               + metric_z->g23[i] * y_at_z[i];
+        x[i] = metric_x->g11()[i] * x[i] + metric_x->g12()[i] * y_at_x[i]
+               + metric_x->g13()[i] * z_at_x[i];
+        y[i] = metric_y->g22()[i] * y[i] + metric_y->g12()[i] * x_at_y[i]
+               + metric_y->g23()[i] * z_at_y[i];
+        z[i] = metric_z->g33()[i] * z[i] + metric_z->g13()[i] * x_at_z[i]
+               + metric_z->g23()[i] * y_at_z[i];
       };
 
     } else {
@@ -156,9 +159,12 @@ void Vector3D::toContravariant() {
       Field3D gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)};
 
       BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) {
-        gx[i] = metric->g11[i] * x[i] + metric->g12[i] * y[i] + metric->g13[i] * z[i];
-        gy[i] = metric->g22[i] * y[i] + metric->g12[i] * x[i] + metric->g23[i] * z[i];
-        gz[i] = metric->g33[i] * z[i] + metric->g13[i] * x[i] + metric->g23[i] * y[i];
+        gx[i] =
+            metric->g11()[i] * x[i] + metric->g12()[i] * y[i] + metric->g13()[i] * z[i];
+        gy[i] =
+            metric->g22()[i] * y[i] + metric->g12()[i] * x[i] + metric->g23()[i] * z[i];
+        gz[i] =
+            metric->g33()[i] * z[i] + metric->g13()[i] * x[i] + metric->g23()[i] * y[i];
       };
 
       x = gx;
@@ -199,7 +205,7 @@ Vector3D* Vector3D::timeDeriv() {
 }
 
 /***************************************************************
- *                         OPERATORS 
+ *                         OPERATORS
  ***************************************************************/
 
 /////////////////// ASSIGNMENT ////////////////////
@@ -379,9 +385,9 @@ Vector3D& Vector3D::operator/=(const Field3D& rhs) {
     Coordinates* metric = localmesh->getCoordinates(lhs.getLocation()); \
                                                                         \
     /* calculate contravariant components of cross-product */           \
-    result.x = (lco.y * rco.z - lco.z * rco.y) / metric->J;             \
-    result.y = (lco.z * rco.x - lco.x * rco.z) / metric->J;             \
-    result.z = (lco.x * rco.y - lco.y * rco.x) / metric->J;             \
+    result.x = (lco.y * rco.z - lco.z * rco.y) / metric->J();           \
+    result.y = (lco.z * rco.x - lco.x * rco.z) / metric->J();           \
+    result.z = (lco.x * rco.y - lco.y * rco.x) / metric->J();           \
     result.covariant = false;                                           \
                                                                         \
     return result;                                                      \
@@ -393,7 +399,7 @@ CROSS(Vector3D, Vector2D, Vector3D)
 CROSS(Vector2D, Vector2D, Vector2D)
 
 /***************************************************************
- *                      BINARY OPERATORS 
+ *                      BINARY OPERATORS
  ***************************************************************/
 
 ////////////////// ADDITION //////////////////////
@@ -482,18 +488,18 @@ const Field3D Vector3D::operator*(const Vector3D& rhs) const {
 
     if (covariant) {
       // Both covariant
-      result =
-          x * rhs.x * metric->g11 + y * rhs.y * metric->g22 + z * rhs.z * metric->g33;
-      result += (x * rhs.y + y * rhs.x) * metric->g12
-                + (x * rhs.z + z * rhs.x) * metric->g13
-                + (y * rhs.z + z * rhs.y) * metric->g23;
+      result = x * rhs.x * metric->g11() + y * rhs.y * metric->g22()
+               + z * rhs.z * metric->g33();
+      result += (x * rhs.y + y * rhs.x) * metric->g12()
+                + (x * rhs.z + z * rhs.x) * metric->g13()
+                + (y * rhs.z + z * rhs.y) * metric->g23();
     } else {
       // Both contravariant
-      result =
-          x * rhs.x * metric->g_11 + y * rhs.y * metric->g_22 + z * rhs.z * metric->g_33;
-      result += (x * rhs.y + y * rhs.x) * metric->g_12
-                + (x * rhs.z + z * rhs.x) * metric->g_13
-                + (y * rhs.z + z * rhs.y) * metric->g_23;
+      result = x * rhs.x * metric->g_11() + y * rhs.y * metric->g_22()
+               + z * rhs.z * metric->g_33();
+      result += (x * rhs.y + y * rhs.x) * metric->g_12()
+                + (x * rhs.z + z * rhs.x) * metric->g_13()
+                + (y * rhs.z + z * rhs.y) * metric->g_23();
     }
   }
 
@@ -514,18 +520,18 @@ const Field3D Vector3D::operator*(const Vector2D& rhs) const {
     Coordinates* metric = x.getCoordinates(location);
     if (covariant) {
       // Both covariant
-      result =
-          x * rhs.x * metric->g11 + y * rhs.y * metric->g22 + z * rhs.z * metric->g33;
-      result += (x * rhs.y + y * rhs.x) * metric->g12
-                + (x * rhs.z + z * rhs.x) * metric->g13
-                + (y * rhs.z + z * rhs.y) * metric->g23;
+      result = x * rhs.x * metric->g11() + y * rhs.y * metric->g22()
+               + z * rhs.z * metric->g33();
+      result += (x * rhs.y + y * rhs.x) * metric->g12()
+                + (x * rhs.z + z * rhs.x) * metric->g13()
+                + (y * rhs.z + z * rhs.y) * metric->g23();
     } else {
       // Both contravariant
-      result =
-          x * rhs.x * metric->g_11 + y * rhs.y * metric->g_22 + z * rhs.z * metric->g_33;
-      result += (x * rhs.y + y * rhs.x) * metric->g_12
-                + (x * rhs.z + z * rhs.x) * metric->g_13
-                + (y * rhs.z + z * rhs.y) * metric->g_23;
+      result = x * rhs.x * metric->g_11() + y * rhs.y * metric->g_22()
+               + z * rhs.z * metric->g_33();
+      result += (x * rhs.y + y * rhs.x) * metric->g_12()
+                + (x * rhs.z + z * rhs.x) * metric->g_13()
+                + (y * rhs.z + z * rhs.y) * metric->g_23();
     }
   }
 
diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
index c50be1db85..6a321b0adf 100644
--- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
+++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
@@ -106,8 +106,8 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
     if (isInnerBoundaryFlagSet(INVERT_AC_GRAD)) {
       // Neumann on inner X boundary
-      operator3D(i, i) = -1. / coords->dx[i] / sqrt(coords->g_11[i]);
-      operator3D(i, i.xp()) = 1. / coords->dx[i] / sqrt(coords->g_11[i]);
+      operator3D(i, i) = -1. / coords->dx()[i] / sqrt(coords->g_11()[i]);
+      operator3D(i, i.xp()) = 1. / coords->dx()[i] / sqrt(coords->g_11()[i]);
     } else {
       // Dirichlet on inner X boundary
       operator3D(i, i) = 0.5;
@@ -118,8 +118,8 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
     if (isOuterBoundaryFlagSet(INVERT_AC_GRAD)) {
       // Neumann on outer X boundary
-      operator3D(i, i) = 1. / coords->dx[i] / sqrt(coords->g_11[i]);
-      operator3D(i, i.xm()) = -1. / coords->dx[i] / sqrt(coords->g_11[i]);
+      operator3D(i, i) = 1. / coords->dx()[i] / sqrt(coords->g_11()[i]);
+      operator3D(i, i.xm()) = -1. / coords->dx()[i] / sqrt(coords->g_11()[i]);
     } else {
       // Dirichlet on outer X boundary
       operator3D(i, i) = 0.5;
@@ -130,8 +130,8 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) {
     if ((lower_boundary_flags & INVERT_AC_GRAD) != 0) {
       // Neumann on lower Y boundary
-      operator3D(i, i) = -1. / coords->dy[i] / sqrt(coords->g_22[i]);
-      operator3D(i, i.yp()) = 1. / coords->dy[i] / sqrt(coords->g_22[i]);
+      operator3D(i, i) = -1. / coords->dy()[i] / sqrt(coords->g_22()[i]);
+      operator3D(i, i.yp()) = 1. / coords->dy()[i] / sqrt(coords->g_22()[i]);
     } else {
       // Dirichlet on lower Y boundary
       operator3D(i, i) = 0.5;
@@ -142,8 +142,8 @@ LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
   BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) {
     if ((upper_boundary_flags & INVERT_AC_GRAD) != 0) {
       // Neumann on upper Y boundary
-      operator3D(i, i) = 1. / coords->dy[i] / sqrt(coords->g_22[i]);
-      operator3D(i, i.ym()) = -1. / coords->dy[i] / sqrt(coords->g_22[i]);
+      operator3D(i, i) = 1. / coords->dy()[i] / sqrt(coords->g_22()[i]);
+      operator3D(i, i.ym()) = -1. / coords->dy()[i] / sqrt(coords->g_22()[i]);
     } else {
       // Dirichlet on upper Y boundary
       operator3D(i, i) = 0.5;
@@ -276,7 +276,7 @@ void LaplaceHypre3d::updateMatrix3D() {
   const Field3D dc_dx = issetC ? DDX(C2) : Field3D();
   const Field3D dc_dy = issetC ? DDY(C2) : Field3D();
   const Field3D dc_dz = issetC ? DDZ(C2) : Field3D();
-  const auto dJ_dy = DDY(coords->J / coords->g_22);
+  const auto dJ_dy = DDY(coords->J() / coords->g_22());
 
   // Set up the matrix for the internal points on the grid.
   // Boundary conditions were set in the constructor.
@@ -285,18 +285,18 @@ void LaplaceHypre3d::updateMatrix3D() {
     // avoid confusing it with the x-index.
 
     // Calculate coefficients for the terms in the differential operator
-    BoutReal C_df_dx = coords->G1[l];
-    BoutReal C_df_dz = coords->G3[l];
+    BoutReal C_df_dx = coords->G1()[l];
+    BoutReal C_df_dz = coords->G3()[l];
     if (issetD) {
       C_df_dx *= D[l];
       C_df_dz *= D[l];
     }
     if (issetC) {
-      C_df_dx += (coords->g11[l] * dc_dx[l] + coords->g12[l] * dc_dy[l]
-                  + coords->g13[l] * dc_dz[l])
+      C_df_dx += (coords->g11()[l] * dc_dx[l] + coords->g12()[l] * dc_dy[l]
+                  + coords->g13()[l] * dc_dz[l])
                  / C1[l];
-      C_df_dz += (coords->g13[l] * dc_dx[l] + coords->g23[l] * dc_dy[l]
-                  + coords->g33[l] * dc_dz[l])
+      C_df_dz += (coords->g13()[l] * dc_dx[l] + coords->g23()[l] * dc_dy[l]
+                  + coords->g33()[l] * dc_dz[l])
                  / C1[l];
     }
     if (issetE) {
@@ -304,32 +304,32 @@ void LaplaceHypre3d::updateMatrix3D() {
       C_df_dz += Ez[l];
     }
 
-    BoutReal C_d2f_dx2 = coords->g11[l];
-    BoutReal C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]);
-    BoutReal C_d2f_dz2 = coords->g33[l];
+    BoutReal C_d2f_dx2 = coords->g11()[l];
+    BoutReal C_d2f_dy2 = (coords->g22()[l] - 1.0 / coords->g_22()[l]);
+    BoutReal C_d2f_dz2 = coords->g33()[l];
     if (issetD) {
       C_d2f_dx2 *= D[l];
       C_d2f_dy2 *= D[l];
       C_d2f_dz2 *= D[l];
     }
 
-    BoutReal C_d2f_dxdz = 2 * coords->g13[l];
+    BoutReal C_d2f_dxdz = 2 * coords->g13()[l];
     if (issetD) {
       C_d2f_dxdz *= D[l];
     }
 
     // Adjust the coefficients to include finite-difference factors
     if (nonuniform) {
-      C_df_dx += C_d2f_dx2 * coords->d1_dx[l];
+      C_df_dx += C_d2f_dx2 * coords->d1_dx()[l];
     }
-    C_df_dx /= 2 * coords->dx[l];
-    C_df_dz /= 2 * coords->dz[l];
+    C_df_dx /= 2 * coords->dx()[l];
+    C_df_dz /= 2 * coords->dz()[l];
 
-    C_d2f_dx2 /= SQ(coords->dx[l]);
-    C_d2f_dy2 /= SQ(coords->dy[l]);
-    C_d2f_dz2 /= SQ(coords->dz[l]);
+    C_d2f_dx2 /= SQ(coords->dx()[l]);
+    C_d2f_dy2 /= SQ(coords->dy()[l]);
+    C_d2f_dz2 /= SQ(coords->dz()[l]);
 
-    C_d2f_dxdz /= 4 * coords->dx[l] * coords->dz[l];
+    C_d2f_dxdz /= 4 * coords->dx()[l] * coords->dz()[l];
 
     operator3D(l, l) = -2 * (C_d2f_dx2 + C_d2f_dy2 + C_d2f_dz2) + A[l];
     operator3D(l, l.xp()) = C_df_dx + C_d2f_dx2;
@@ -360,24 +360,24 @@ void LaplaceHypre3d::updateMatrix3D() {
   // Must add these (rather than assign) so that elements used in
   // interpolation don't overwrite each other.
   BOUT_FOR_SERIAL(l, indexer->getRegionNobndry()) {
-    BoutReal C_df_dy = (coords->G2[l] - dJ_dy[l] / coords->J[l]);
+    BoutReal C_df_dy = (coords->G2()[l] - dJ_dy[l] / coords->J()[l]);
     if (issetD) {
       C_df_dy *= D[l];
     }
     if (issetC) {
-      C_df_dy +=
-          (coords->g12[l] * dc_dx[l] + (coords->g22[l] - 1. / coords->g_22[l]) * dc_dy[l]
-           + coords->g23[l] * dc_dz[l])
-          / C1[l];
+      C_df_dy += (coords->g12()[l] * dc_dx[l]
+                  + (coords->g22()[l] - 1. / coords->g_22()[l]) * dc_dy[l]
+                  + coords->g23()[l] * dc_dz[l])
+                 / C1[l];
     }
 
-    BoutReal C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]);
+    BoutReal C_d2f_dy2 = (coords->g22()[l] - 1.0 / coords->g_22()[l]);
     if (issetD) {
       C_d2f_dy2 *= D[l];
     }
 
-    BoutReal C_d2f_dxdy = 2 * coords->g12[l];
-    BoutReal C_d2f_dydz = 2 * coords->g23[l];
+    BoutReal C_d2f_dxdy = 2 * coords->g12()[l];
+    BoutReal C_d2f_dydz = 2 * coords->g23()[l];
     if (issetD) {
       C_d2f_dxdy *= D[l];
       C_d2f_dydz *= D[l];
@@ -385,14 +385,14 @@ void LaplaceHypre3d::updateMatrix3D() {
 
     // Adjust the coefficients to include finite-difference factors
     if (nonuniform) {
-      C_df_dy += C_d2f_dy2 * coords->d1_dy[l];
+      C_df_dy += C_d2f_dy2 * coords->d1_dy()[l];
     }
-    C_df_dy /= 2 * coords->dy[l];
-    C_d2f_dy2 /= SQ(coords->dy[l]);
-    C_d2f_dxdy /= 4 * coords->dx[l]; // NOTE: This value is not completed here. It needs
-                                     // to be divide by dx(i +/- 1, j, k) when using to
-                                     // set a matrix element
-    C_d2f_dydz /= 4 * coords->dy[l] * coords->dz[l];
+    C_df_dy /= 2 * coords->dy()[l];
+    C_d2f_dy2 /= SQ(coords->dy()[l]);
+    C_d2f_dxdy /= 4 * coords->dx()[l]; // NOTE: This value is not completed here. It needs
+                                       // to be divide by dx(i +/- 1, j, k) when using to
+                                       // set a matrix element
+    C_d2f_dydz /= 4 * coords->dy()[l] * coords->dz()[l];
 
     // The values stored in the y-boundary are already interpolated
     // up/down, so we don't want the matrix to do any such
@@ -402,10 +402,10 @@ void LaplaceHypre3d::updateMatrix3D() {
 
     operator3D.yup(yup)(l, l.yp()) += C_df_dy + C_d2f_dy2;
     operator3D.ydown(ydown)(l, l.ym()) += -C_df_dy + C_d2f_dy2;
-    operator3D.yup(yup)(l, l.xp().yp()) += C_d2f_dxdy / coords->dy[l.xp()];
-    operator3D.ydown(ydown)(l, l.xp().ym()) += -C_d2f_dxdy / coords->dy[l.xp()];
-    operator3D.yup(yup)(l, l.xm().yp()) += -C_d2f_dxdy / coords->dy[l.xm()];
-    operator3D.ydown(ydown)(l, l.xm().ym()) += C_d2f_dxdy / coords->dy[l.xm()];
+    operator3D.yup(yup)(l, l.xp().yp()) += C_d2f_dxdy / coords->dy()[l.xp()];
+    operator3D.ydown(ydown)(l, l.xp().ym()) += -C_d2f_dxdy / coords->dy()[l.xp()];
+    operator3D.yup(yup)(l, l.xm().yp()) += -C_d2f_dxdy / coords->dy()[l.xm()];
+    operator3D.ydown(ydown)(l, l.xm().ym()) += C_d2f_dxdy / coords->dy()[l.xm()];
     operator3D.yup(yup)(l, l.yp().zp()) += C_d2f_dydz;
     operator3D.yup(yup)(l, l.yp().zm()) += -C_d2f_dydz;
     operator3D.ydown(ydown)(l, l.ym().zp()) += -C_d2f_dydz;
diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.cxx b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
index 3faba2f0ea..c5c2a19915 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.cxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.cxx
@@ -189,8 +189,8 @@ Field3D LaplaceNaulin::solve(const Field3D& rhs, const Field3D& x0) {
     Field3D ddx_x = DDX(x_in, location, "C2");
     Field3D ddz_x = DDZ(x_in, location, "FFT");
     return rhsOverD
-           - (coords->g11 * coef_x_AC * ddx_x + coords->g33 * coef_z * ddz_x
-              + coords->g13 * (coef_x_AC * ddz_x + coef_z * ddx_x))
+           - (coords->g11() * coef_x_AC * ddx_x + coords->g33() * coef_z * ddz_x
+              + coords->g13() * (coef_x_AC * ddz_x + coef_z * ddx_x))
            - AOverD_AC * x_in;
   };
 
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 89ba25405b..880471f7b3 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -403,16 +403,16 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
 LaplacePetsc::CoeffsA LaplacePetsc::Coeffs(Ind3D i) {
   const auto x = i.x();
 
-  BoutReal coef1 = coords->g11[i];      // X 2nd derivative coefficient
-  BoutReal coef2 = coords->g33[i];      // Z 2nd derivative coefficient
-  BoutReal coef3 = 2. * coords->g13[i]; // X-Z mixed derivative coefficient
+  BoutReal coef1 = coords->g11()[i];      // X 2nd derivative coefficient
+  BoutReal coef2 = coords->g33()[i];      // Z 2nd derivative coefficient
+  BoutReal coef3 = 2. * coords->g13()[i]; // X-Z mixed derivative coefficient
 
   BoutReal coef4 = 0.0;
   BoutReal coef5 = 0.0;
   // If global flag all_terms are set (true by default)
   if (all_terms) {
-    coef4 = coords->G1[i]; // X 1st derivative
-    coef5 = coords->G3[i]; // Z 1st derivative
+    coef4 = coords->G1()[i]; // X 1st derivative
+    coef5 = coords->G3()[i]; // Z 1st derivative
 
     ASSERT3(std::isfinite(coef4));
     ASSERT3(std::isfinite(coef5));
@@ -421,14 +421,15 @@ LaplacePetsc::CoeffsA LaplacePetsc::Coeffs(Ind3D i) {
   if (nonuniform) {
     // non-uniform mesh correction
     if ((x != 0) && (x != (localmesh->LocalNx - 1))) {
-      coef4 -= 0.5 * ((coords->dx[i.xp()] - coords->dx[i.xm()]) / SQ(coords->dx[i]))
+      coef4 -= 0.5 * ((coords->dx()[i.xp()] - coords->dx()[i.xm()]) / SQ(coords->dx()[i]))
                * coef1; // BOUT-06 term
     }
   }
 
   if (localmesh->IncIntShear) {
     // d2dz2 term
-    coef2 += coords->g11[i] * coords->IntShiftTorsion[i] * coords->IntShiftTorsion[i];
+    coef2 +=
+        coords->g11()[i] * coords->IntShiftTorsion()[i] * coords->IntShiftTorsion()[i];
     // Mixed derivative
     coef3 = 0.0; // This cancels out
   }
@@ -450,19 +451,19 @@ LaplacePetsc::CoeffsA LaplacePetsc::Coeffs(Ind3D i) {
       if (fourth_order) {
         // Fourth order discretization of C in x
         ddx_C = (-C2[i.xpp()] + (8. * C2[i.xp()]) - (8. * C2[i.xm()]) + C2[i.xmm()])
-                / (12. * coords->dx[i] * (C1[i]));
+                / (12. * coords->dx()[i] * (C1[i]));
         // Fourth order discretization of C in z
         ddz_C = (-C2[i.zpp()] + (8. * C2[i.zp()]) - (8. * C2[i.zm()]) + C2[i.zmm()])
-                / (12. * coords->dz[i] * (C1[i]));
+                / (12. * coords->dz()[i] * (C1[i]));
       } else {
         // Second order discretization of C in x
-        ddx_C = (C2[i.xp()] - C2[i.xm()]) / (2. * coords->dx[i] * (C1[i]));
+        ddx_C = (C2[i.xp()] - C2[i.xm()]) / (2. * coords->dx()[i] * (C1[i]));
         // Second order discretization of C in z
-        ddz_C = (C2[i.zp()] - C2[i.zm()]) / (2. * coords->dz[i] * (C1[i]));
+        ddz_C = (C2[i.zp()] - C2[i.zm()]) / (2. * coords->dz()[i] * (C1[i]));
       }
 
-      coef4 += (coords->g11[i] * ddx_C) + (coords->g13[i] * ddz_C);
-      coef5 += (coords->g13[i] * ddx_C) + (coords->g33[i] * ddz_C);
+      coef4 += (coords->g11()[i] * ddx_C) + (coords->g13()[i] * ddz_C);
+      coef5 += (coords->g13()[i] * ddx_C) + (coords->g33()[i] * ddz_C);
     }
   }
 
@@ -487,8 +488,8 @@ void LaplacePetsc::setSecondOrderMatrix(int y, bool inner_X_neumann,
                                         bool outer_X_neumann) {
   // Set the boundaries
   if (inner_X_neumann) {
-    const auto dx = sliceXZ(coords->dx, y);
-    const auto g11 = sliceXZ(coords->g11, y);
+    const auto dx = sliceXZ(coords->dx(), y);
+    const auto g11 = sliceXZ(coords->g11(), y);
 
     BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
       const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
@@ -502,8 +503,8 @@ void LaplacePetsc::setSecondOrderMatrix(int y, bool inner_X_neumann,
     }
   }
   if (outer_X_neumann) {
-    const auto dx = sliceXZ(coords->dx, y);
-    const auto g11 = sliceXZ(coords->g11, y);
+    const auto dx = sliceXZ(coords->dx(), y);
+    const auto g11 = sliceXZ(coords->g11(), y);
 
     BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
       const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
@@ -535,9 +536,9 @@ void LaplacePetsc::setSecondOrderMatrix(int y, bool inner_X_neumann,
     ASSERT3(std::isfinite(A4));
     ASSERT3(std::isfinite(A5));
 
-    const BoutReal dx = coords->dx[i];
+    const BoutReal dx = coords->dx()[i];
     const BoutReal dx2 = SQ(dx);
-    const BoutReal dz = coords->dz[i];
+    const BoutReal dz = coords->dz()[i];
     const BoutReal dz2 = SQ(dz);
     const BoutReal dxdz = dx * dz;
     operator2D(l, l) = A0 - (2.0 * ((A1 / dx2) + (A2 / dz2)));
@@ -557,8 +558,8 @@ void LaplacePetsc::setFourthOrderMatrix(int y, bool inner_X_neumann,
 
   // Set boundaries
   if (inner_X_neumann) {
-    const auto dx = sliceXZ(coords->dx, y);
-    const auto g11 = sliceXZ(coords->g11, y);
+    const auto dx = sliceXZ(coords->dx(), y);
+    const auto g11 = sliceXZ(coords->g11(), y);
 
     BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
       const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
@@ -579,8 +580,8 @@ void LaplacePetsc::setFourthOrderMatrix(int y, bool inner_X_neumann,
   }
 
   if (outer_X_neumann) {
-    const auto dx = sliceXZ(coords->dx, y);
-    const auto g11 = sliceXZ(coords->g11, y);
+    const auto dx = sliceXZ(coords->dx(), y);
+    const auto g11 = sliceXZ(coords->g11(), y);
 
     BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
       const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
@@ -618,9 +619,9 @@ void LaplacePetsc::setFourthOrderMatrix(int y, bool inner_X_neumann,
     ASSERT3(std::isfinite(A4));
     ASSERT3(std::isfinite(A5));
 
-    const BoutReal dx = coords->dx[i];
+    const BoutReal dx = coords->dx()[i];
     const BoutReal dx2 = SQ(dx);
-    const BoutReal dz = coords->dz[i];
+    const BoutReal dz = coords->dz()[i];
     const BoutReal dz2 = SQ(dz);
     const BoutReal dxdz = dx * dz;
 
diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
index 9966ad654d..fa73016db0 100644
--- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
+++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
@@ -122,7 +122,7 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes
   const bool inner_X_neumann = isInnerBoundaryFlagSet(INVERT_AC_GRAD);
   if (inner_X_neumann) {
     // This is a BinaryExpr that is only evaluated when needed
-    const auto inner_X_BC = -1. / coords->dx / sqrt(coords->g_11);
+    const auto inner_X_BC = -1. / coords->dx() / sqrt(coords->g_11());
     BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
       const BoutReal bc = inner_X_BC[i];
       operator3D(i, i) = bc;
@@ -137,7 +137,7 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes
 
   const bool outer_X_neumann = isOuterBoundaryFlagSet(INVERT_AC_GRAD);
   if (outer_X_neumann) {
-    const auto outer_X_BC = 1. / coords->dx / sqrt(coords->g_11);
+    const auto outer_X_BC = 1. / coords->dx() / sqrt(coords->g_11());
     BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
       const BoutReal bc = outer_X_BC[i];
       operator3D(i, i) = bc;
@@ -152,7 +152,7 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes
 
   const bool lower_Y_neumann = flagSet(lower_boundary_flags, INVERT_AC_GRAD);
   if (lower_Y_neumann) {
-    const auto lower_Y_BC = -1. / coords->dy / sqrt(coords->g_22);
+    const auto lower_Y_BC = -1. / coords->dy() / sqrt(coords->g_22());
     BOUT_FOR_SERIAL(i, indexer->getRegionLowerY()) {
       const BoutReal bc = lower_Y_BC[i];
       operator3D(i, i) = bc;
@@ -167,7 +167,7 @@ LaplacePetsc3dAmg::LaplacePetsc3dAmg(Options* opt, const CELL_LOC loc, Mesh* mes
 
   const bool upper_Y_neumann = flagSet(upper_boundary_flags, INVERT_AC_GRAD);
   if (upper_Y_neumann) {
-    const auto upper_Y_BC = 1. / coords->dy / sqrt(coords->g_22);
+    const auto upper_Y_BC = 1. / coords->dy() / sqrt(coords->g_22());
     BOUT_FOR_SERIAL(i, indexer->getRegionUpperY()) {
       const BoutReal bc = upper_Y_BC[i];
       operator3D(i, i) = bc;
@@ -299,7 +299,7 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
   const Field3D dc_dx = issetC ? DDX(C2) : Field3D();
   const Field3D dc_dy = issetC ? DDY(C2) : Field3D();
   const Field3D dc_dz = issetC ? DDZ(C2) : Field3D();
-  const auto dJ_dy = DDY(Coordinates::FieldMetric{coords->J / coords->g_22});
+  const auto dJ_dy = DDY(Coordinates::FieldMetric{coords->J() / coords->g_22()});
 
   // Set up the matrix for the internal points on the grid.
   // Boundary conditions were set in the constructor.
@@ -308,18 +308,18 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
     // avoid confusing it with the x-index.
 
     // Calculate coefficients for the terms in the differential operator
-    BoutReal C_df_dx = coords->G1[l];
-    BoutReal C_df_dz = coords->G3[l];
+    BoutReal C_df_dx = coords->G1()[l];
+    BoutReal C_df_dz = coords->G3()[l];
     if (issetD) {
       C_df_dx *= D[l];
       C_df_dz *= D[l];
     }
     if (issetC) {
-      C_df_dx += (coords->g11[l] * dc_dx[l] + coords->g12[l] * dc_dy[l]
-                  + coords->g13[l] * dc_dz[l])
+      C_df_dx += (coords->g11()[l] * dc_dx[l] + coords->g12()[l] * dc_dy[l]
+                  + coords->g13()[l] * dc_dz[l])
                  / C1[l];
-      C_df_dz += (coords->g13[l] * dc_dx[l] + coords->g23[l] * dc_dy[l]
-                  + coords->g33[l] * dc_dz[l])
+      C_df_dz += (coords->g13()[l] * dc_dx[l] + coords->g23()[l] * dc_dy[l]
+                  + coords->g33()[l] * dc_dz[l])
                  / C1[l];
     }
     if (issetE) {
@@ -327,32 +327,32 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
       C_df_dz += Ez[l];
     }
 
-    BoutReal C_d2f_dx2 = coords->g11[l];
-    BoutReal C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]);
-    BoutReal C_d2f_dz2 = coords->g33[l];
+    BoutReal C_d2f_dx2 = coords->g11()[l];
+    BoutReal C_d2f_dy2 = (coords->g22()[l] - 1.0 / coords->g_22()[l]);
+    BoutReal C_d2f_dz2 = coords->g33()[l];
     if (issetD) {
       C_d2f_dx2 *= D[l];
       C_d2f_dy2 *= D[l];
       C_d2f_dz2 *= D[l];
     }
 
-    BoutReal C_d2f_dxdz = 2 * coords->g13[l];
+    BoutReal C_d2f_dxdz = 2 * coords->g13()[l];
     if (issetD) {
       C_d2f_dxdz *= D[l];
     }
 
     // Adjust the coefficients to include finite-difference factors
     if (nonuniform) {
-      C_df_dx += C_d2f_dx2 * coords->d1_dx[l];
+      C_df_dx += C_d2f_dx2 * coords->d1_dx()[l];
     }
-    C_df_dx /= 2 * coords->dx[l];
-    C_df_dz /= 2 * coords->dz[l];
+    C_df_dx /= 2 * coords->dx()[l];
+    C_df_dz /= 2 * coords->dz()[l];
 
-    C_d2f_dx2 /= SQ(coords->dx[l]);
-    C_d2f_dy2 /= SQ(coords->dy[l]);
-    C_d2f_dz2 /= SQ(coords->dz[l]);
+    C_d2f_dx2 /= SQ(coords->dx()[l]);
+    C_d2f_dy2 /= SQ(coords->dy()[l]);
+    C_d2f_dz2 /= SQ(coords->dz()[l]);
 
-    C_d2f_dxdz /= 4 * coords->dx[l] * coords->dz[l];
+    C_d2f_dxdz /= 4 * coords->dx()[l] * coords->dz()[l];
 
     operator3D(l, l) = -2 * (C_d2f_dx2 + C_d2f_dy2 + C_d2f_dz2) + A[l];
     operator3D(l, l.xp()) = C_df_dx + C_d2f_dx2;
@@ -384,24 +384,24 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
   // Must add these (rather than assign) so that elements used in
   // interpolation don't overwrite each other.
   BOUT_FOR_SERIAL(l, indexer->getRegionNobndry()) {
-    BoutReal C_df_dy = coords->G2[l] - (dJ_dy[l] / coords->J[l]);
+    BoutReal C_df_dy = coords->G2()[l] - (dJ_dy[l] / coords->J()[l]);
     if (issetD) {
       C_df_dy *= D[l];
     }
     if (issetC) {
-      C_df_dy +=
-          (coords->g12[l] * dc_dx[l] + (coords->g22[l] - 1. / coords->g_22[l]) * dc_dy[l]
-           + coords->g23[l] * dc_dz[l])
-          / C1[l];
+      C_df_dy += (coords->g12()[l] * dc_dx[l]
+                  + (coords->g22()[l] - 1. / coords->g_22()[l]) * dc_dy[l]
+                  + coords->g23()[l] * dc_dz[l])
+                 / C1[l];
     }
 
-    BoutReal C_d2f_dy2 = coords->g22[l] - (1.0 / coords->g_22[l]);
+    BoutReal C_d2f_dy2 = coords->g22()[l] - (1.0 / coords->g_22()[l]);
     if (issetD) {
       C_d2f_dy2 *= D[l];
     }
 
-    BoutReal C_d2f_dxdy = 2 * coords->g12[l];
-    BoutReal C_d2f_dydz = 2 * coords->g23[l];
+    BoutReal C_d2f_dxdy = 2 * coords->g12()[l];
+    BoutReal C_d2f_dydz = 2 * coords->g23()[l];
     if (issetD) {
       C_d2f_dxdy *= D[l];
       C_d2f_dydz *= D[l];
@@ -409,15 +409,15 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
 
     // Adjust the coefficients to include finite-difference factors
     if (nonuniform) {
-      C_df_dy += C_d2f_dy2 * coords->d1_dy[l];
+      C_df_dy += C_d2f_dy2 * coords->d1_dy()[l];
     }
-    C_df_dy /= 2 * coords->dy[l];
-    C_d2f_dy2 /= SQ(coords->dy[l]);
+    C_df_dy /= 2 * coords->dy()[l];
+    C_d2f_dy2 /= SQ(coords->dy()[l]);
     C_d2f_dxdy /=
-        4 * coords->dx[l]; // NOTE: This value is not completed here. It needs to
-                           // be divide by dx(i +/- 1, j, k) when using to set a
-                           // matrix element
-    C_d2f_dydz /= 4 * coords->dy[l] * coords->dz[l];
+        4 * coords->dx()[l]; // NOTE: This value is not completed here. It needs to
+                             // be divide by dx(i +/- 1, j, k) when using to set a
+                             // matrix element
+    C_d2f_dydz /= 4 * coords->dy()[l] * coords->dz()[l];
 
     // The values stored in the y-boundary are already interpolated
     // up/down, so we don't want the matrix to do any such
@@ -427,10 +427,10 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
 
     operator3D.yup(yup)(l, l.yp()) += C_df_dy + C_d2f_dy2;
     operator3D.ydown(ydown)(l, l.ym()) += -C_df_dy + C_d2f_dy2;
-    operator3D.yup(yup)(l, l.xp().yp()) += C_d2f_dxdy / coords->dy[l.xp()];
-    operator3D.ydown(ydown)(l, l.xp().ym()) += -C_d2f_dxdy / coords->dy[l.xp()];
-    operator3D.yup(yup)(l, l.xm().yp()) += -C_d2f_dxdy / coords->dy[l.xm()];
-    operator3D.ydown(ydown)(l, l.xm().ym()) += C_d2f_dxdy / coords->dy[l.xm()];
+    operator3D.yup(yup)(l, l.xp().yp()) += C_d2f_dxdy / coords->dy()[l.xp()];
+    operator3D.ydown(ydown)(l, l.xp().ym()) += -C_d2f_dxdy / coords->dy()[l.xp()];
+    operator3D.yup(yup)(l, l.xm().yp()) += -C_d2f_dxdy / coords->dy()[l.xm()];
+    operator3D.ydown(ydown)(l, l.xm().ym()) += C_d2f_dxdy / coords->dy()[l.xm()];
     operator3D.yup(yup)(l, l.yp().zp()) += C_d2f_dydz;
     operator3D.yup(yup)(l, l.yp().zm()) += -C_d2f_dydz;
     operator3D.ydown(ydown)(l, l.ym().zp()) += -C_d2f_dydz;
diff --git a/src/invert/laplace/invert_laplace.cxx b/src/invert/laplace/invert_laplace.cxx
index 9af6fd20f9..0ec5f471da 100644
--- a/src/invert/laplace/invert_laplace.cxx
+++ b/src/invert/laplace/invert_laplace.cxx
@@ -104,7 +104,7 @@ Laplacian::Laplacian(Options* options, const CELL_LOC loc, Mesh* mesh_in,
 
   nonuniform = (*options)["nonuniform"]
                    .doc("Use non-uniform grid corrections? Default is the mesh setting.")
-                   .withDefault(coords->non_uniform);
+                   .withDefault(coords->non_uniform());
 
   all_terms =
       (*options)["all_terms"].doc("Include first derivative terms?").withDefault(true);
diff --git a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
index 61632a332d..fbba16673c 100644
--- a/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
+++ b/src/invert/laplacexy/impls/hypre/laplacexy-hypre.cxx
@@ -113,20 +113,20 @@ void LaplaceXY2Hypre::setCoefs(const Field2D& A, const Field2D& B) {
     // XX component
 
     // Metrics on x+1/2 boundary
-    BoutReal J = 0.5 * (coords->J[index] + coords->J[ind_xp]);
-    BoutReal g11 = 0.5 * (coords->g11[index] + coords->g11[ind_xp]);
-    BoutReal dx = 0.5 * (coords->dx[index] + coords->dx[ind_xp]);
+    BoutReal J = 0.5 * (coords->J()[index] + coords->J()[ind_xp]);
+    BoutReal g11 = 0.5 * (coords->g11()[index] + coords->g11()[ind_xp]);
+    BoutReal dx = 0.5 * (coords->dx()[index] + coords->dx()[ind_xp]);
     BoutReal Acoef = 0.5 * (A[index] + A[ind_xp]);
 
-    BoutReal xp = Acoef * J * g11 / (coords->J[index] * dx * coords->dx[index]);
+    BoutReal xp = Acoef * J * g11 / (coords->J()[index] * dx * coords->dx()[index]);
 
     // Metrics on x-1/2 boundary
-    J = 0.5 * (coords->J[index] + coords->J[ind_xm]);
-    g11 = 0.5 * (coords->g11[index] + coords->g11[ind_xm]);
-    dx = 0.5 * (coords->dx[index] + coords->dx[ind_xm]);
+    J = 0.5 * (coords->J()[index] + coords->J()[ind_xm]);
+    g11 = 0.5 * (coords->g11()[index] + coords->g11()[ind_xm]);
+    dx = 0.5 * (coords->dx()[index] + coords->dx()[ind_xm]);
     Acoef = 0.5 * (A[index] + A[ind_xm]);
 
-    BoutReal xm = Acoef * J * g11 / (coords->J[index] * dx * coords->dx[index]);
+    BoutReal xm = Acoef * J * g11 / (coords->J()[index] * dx * coords->dx()[index]);
 
     BoutReal c = B[index] - xp - xm; // Central coefficient
 
@@ -139,27 +139,27 @@ void LaplaceXY2Hypre::setCoefs(const Field2D& A, const Field2D& B) {
 
       // YY component
       // Metrics at y+1/2
-      J = 0.5 * (coords->J[index] + coords->J[ind_yp]);
-      BoutReal g_22 = 0.5 * (coords->g_22[index] + coords->g_22[ind_yp]);
-      BoutReal g23 = 0.5 * (coords->g23[index] + coords->g23[ind_yp]);
-      BoutReal g_23 = 0.5 * (coords->g_23[index] + coords->g_23[ind_yp]);
-      BoutReal dy = 0.5 * (coords->dy[index] + coords->dy[ind_yp]);
+      J = 0.5 * (coords->J()[index] + coords->J()[ind_yp]);
+      BoutReal g_22 = 0.5 * (coords->g_22()[index] + coords->g_22()[ind_yp]);
+      BoutReal g23 = 0.5 * (coords->g23()[index] + coords->g23()[ind_yp]);
+      BoutReal g_23 = 0.5 * (coords->g_23()[index] + coords->g_23()[ind_yp]);
+      BoutReal dy = 0.5 * (coords->dy()[index] + coords->dy()[ind_yp]);
       Acoef = 0.5 * (A[ind_yp] + A[index]);
 
-      BoutReal yp =
-          -Acoef * J * g23 * g_23 / (g_22 * coords->J[index] * dy * coords->dy[index]);
+      BoutReal yp = -Acoef * J * g23 * g_23
+                    / (g_22 * coords->J()[index] * dy * coords->dy()[index]);
       c -= yp;
 
       // Metrics at y-1/2
-      J = 0.5 * (coords->J[index] + coords->J[ind_ym]);
-      g_22 = 0.5 * (coords->g_22[index] + coords->g_22[ind_ym]);
-      g23 = 0.5 * (coords->g23[index] + coords->g23[ind_ym]);
-      g_23 = 0.5 * (coords->g_23[index] + coords->g_23[ind_ym]);
-      dy = 0.5 * (coords->dy[index] + coords->dy[ind_ym]);
+      J = 0.5 * (coords->J()[index] + coords->J()[ind_ym]);
+      g_22 = 0.5 * (coords->g_22()[index] + coords->g_22()[ind_ym]);
+      g23 = 0.5 * (coords->g23()[index] + coords->g23()[ind_ym]);
+      g_23 = 0.5 * (coords->g_23()[index] + coords->g_23()[ind_ym]);
+      dy = 0.5 * (coords->dy()[index] + coords->dy()[ind_ym]);
       Acoef = 0.5 * (A[ind_ym] + A[index]);
 
-      BoutReal ym =
-          -Acoef * J * g23 * g_23 / (g_22 * coords->J[index] * dy * coords->dy[index]);
+      BoutReal ym = -Acoef * J * g23 * g_23
+                    / (g_22 * coords->J()[index] * dy * coords->dy()[index]);
       c -= ym;
       M(index, ind_yp) = yp;
       M(index, ind_ym) = ym;
diff --git a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
index 04abecfe05..881a0b7fc0 100644
--- a/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
+++ b/src/invert/laplacexy/impls/petsc/laplacexy-petsc.cxx
@@ -906,13 +906,13 @@ void LaplaceXYpetsc::setMatrixElementsFiniteVolume(const Field2D& A, const Field
   // (1/J) d/dx ( J * g11 d/dx ) + (1/J) d/dy ( J * g22 d/dy )
 
   auto coords = localmesh->getCoordinates(location);
-  const Field2D J_DC = DC(coords->J);
-  const Field2D g11_DC = DC(coords->g11);
-  const Field2D dx_DC = DC(coords->dx);
-  const Field2D dy_DC = DC(coords->dy);
-  const Field2D g_22_DC = DC(coords->g_22);
-  const Field2D g_23_DC = DC(coords->g_23);
-  const Field2D g23_DC = DC(coords->g23);
+  const Field2D J_DC = DC(coords->J());
+  const Field2D g11_DC = DC(coords->g11());
+  const Field2D dx_DC = DC(coords->dx());
+  const Field2D dy_DC = DC(coords->dy());
+  const Field2D g_22_DC = DC(coords->g_22());
+  const Field2D g_23_DC = DC(coords->g_23());
+  const Field2D g23_DC = DC(coords->g23());
 
   for (int x = localmesh->xstart; x <= localmesh->xend; x++) {
     for (int y = localmesh->ystart; y <= localmesh->yend; y++) {
@@ -1017,17 +1017,17 @@ void LaplaceXYpetsc::setMatrixElementsFiniteDifference(const Field2D& A,
   //   + B*f
 
   auto coords = localmesh->getCoordinates(location);
-  const Field2D G1_2D = DC(coords->G1);
-  const Field2D G2_2D = DC(coords->G2);
-  const Field2D J_2D = DC(coords->J);
-  const Field2D g11_2D = DC(coords->g11);
-  const Field2D g_22_2D = DC(coords->g_22);
-  const Field2D g22_2D = DC(coords->g22);
-  const Field2D g12_2D = DC(coords->g12);
-  const Field2D d1_dx_2D = DC(coords->d1_dx);
-  const Field2D d1_dy_2D = DC(coords->d1_dy);
-  const Field2D dx_2D = DC(coords->dx);
-  const Field2D dy_2D = DC(coords->dy);
+  const Field2D G1_2D = DC(coords->G1());
+  const Field2D G2_2D = DC(coords->G2());
+  const Field2D J_2D = DC(coords->J());
+  const Field2D g11_2D = DC(coords->g11());
+  const Field2D g_22_2D = DC(coords->g_22());
+  const Field2D g22_2D = DC(coords->g22());
+  const Field2D g12_2D = DC(coords->g12());
+  const Field2D d1_dx_2D = DC(coords->d1_dx());
+  const Field2D d1_dy_2D = DC(coords->d1_dy());
+  const Field2D dx_2D = DC(coords->dx());
+  const Field2D dy_2D = DC(coords->dy());
 
   const Field2D coef_dfdy = G2_2D - DC(DDY(J_2D / g_22_2D) / J_2D);
 
diff --git a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
index 01019466a8..bdfc3bb5ff 100644
--- a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
+++ b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
@@ -157,20 +157,20 @@ void LaplaceXYpetsc2::setCoefs(const Field2D& A, const Field2D& B) {
     // XX component
 
     // Metrics on x+1/2 boundary
-    BoutReal J = 0.5 * (coords->J[index] + coords->J[ind_xp]);
-    BoutReal g11 = 0.5 * (coords->g11[index] + coords->g11[ind_xp]);
-    BoutReal dx = 0.5 * (coords->dx[index] + coords->dx[ind_xp]);
+    BoutReal J = 0.5 * (coords->J()[index] + coords->J()[ind_xp]);
+    BoutReal g11 = 0.5 * (coords->g11()[index] + coords->g11()[ind_xp]);
+    BoutReal dx = 0.5 * (coords->dx()[index] + coords->dx()[ind_xp]);
     BoutReal Acoef = 0.5 * (A[index] + A[ind_xp]);
 
-    BoutReal xp = Acoef * J * g11 / (coords->J[index] * dx * coords->dx[index]);
+    BoutReal xp = Acoef * J * g11 / (coords->J()[index] * dx * coords->dx()[index]);
 
     // Metrics on x-1/2 boundary
-    J = 0.5 * (coords->J[index] + coords->J[ind_xm]);
-    g11 = 0.5 * (coords->g11[index] + coords->g11[ind_xm]);
-    dx = 0.5 * (coords->dx[index] + coords->dx[ind_xm]);
+    J = 0.5 * (coords->J()[index] + coords->J()[ind_xm]);
+    g11 = 0.5 * (coords->g11()[index] + coords->g11()[ind_xm]);
+    dx = 0.5 * (coords->dx()[index] + coords->dx()[ind_xm]);
     Acoef = 0.5 * (A[index] + A[ind_xm]);
 
-    BoutReal xm = Acoef * J * g11 / (coords->J[index] * dx * coords->dx[index]);
+    BoutReal xm = Acoef * J * g11 / (coords->J()[index] * dx * coords->dx()[index]);
 
     BoutReal c = B[index] - xp - xm; // Central coefficient
 
@@ -183,28 +183,28 @@ void LaplaceXYpetsc2::setCoefs(const Field2D& A, const Field2D& B) {
 
       // YY component
       // Metrics at y+1/2
-      J = 0.5 * (coords->J[index] + coords->J[ind_yp]);
-      BoutReal g_22 = 0.5 * (coords->g_22[index] + coords->g_22[ind_yp]);
-      BoutReal g23 = 0.5 * (coords->g23[index] + coords->g23[ind_yp]);
-      BoutReal g_23 = 0.5 * (coords->g_23[index] + coords->g_23[ind_yp]);
-      BoutReal dy = 0.5 * (coords->dy[index] + coords->dy[ind_yp]);
+      J = 0.5 * (coords->J()[index] + coords->J()[ind_yp]);
+      BoutReal g_22 = 0.5 * (coords->g_22()[index] + coords->g_22()[ind_yp]);
+      BoutReal g23 = 0.5 * (coords->g23()[index] + coords->g23()[ind_yp]);
+      BoutReal g_23 = 0.5 * (coords->g_23()[index] + coords->g_23()[ind_yp]);
+      BoutReal dy = 0.5 * (coords->dy()[index] + coords->dy()[ind_yp]);
       Acoef = 0.5 * (A[ind_yp] + A[index]);
 
-      BoutReal yp =
-          -Acoef * J * g23 * g_23 / (g_22 * coords->J[index] * dy * coords->dy[index]);
+      BoutReal yp = -Acoef * J * g23 * g_23
+                    / (g_22 * coords->J()[index] * dy * coords->dy()[index]);
       c -= yp;
       matrix(index, ind_yp) = yp;
 
       // Metrics at y-1/2
-      J = 0.5 * (coords->J[index] + coords->J[ind_ym]);
-      g_22 = 0.5 * (coords->g_22[index] + coords->g_22[ind_ym]);
-      g23 = 0.5 * (coords->g23[index] + coords->g23[ind_ym]);
-      g_23 = 0.5 * (coords->g_23[index] + coords->g_23[ind_ym]);
-      dy = 0.5 * (coords->dy[index] + coords->dy[ind_ym]);
+      J = 0.5 * (coords->J()[index] + coords->J()[ind_ym]);
+      g_22 = 0.5 * (coords->g_22()[index] + coords->g_22()[ind_ym]);
+      g23 = 0.5 * (coords->g23()[index] + coords->g23()[ind_ym]);
+      g_23 = 0.5 * (coords->g_23()[index] + coords->g_23()[ind_ym]);
+      dy = 0.5 * (coords->dy()[index] + coords->dy()[ind_ym]);
       Acoef = 0.5 * (A[ind_ym] + A[index]);
 
-      BoutReal ym =
-          -Acoef * J * g23 * g_23 / (g_22 * coords->J[index] * dy * coords->dy[index]);
+      BoutReal ym = -Acoef * J * g23 * g_23
+                    / (g_22 * coords->J()[index] * dy * coords->dy()[index]);
       c -= ym;
       matrix(index, ind_ym) = ym;
     }
diff --git a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
index b3e619df0c..0a7030dec9 100644
--- a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
+++ b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
@@ -74,7 +74,7 @@ void LaplaceXZcyclic::setCoefs(const Field2D& A2D, const Field2D& B2D) {
   Coordinates* coord = localmesh->getCoordinates(location);
 
   // NOTE: For now the X-Z terms are omitted, so check that they are small
-  ASSERT2(max(abs(coord->g13)) < 1e-5);
+  ASSERT2(max(abs(coord->g13())) < 1e-5);
 
   int ind = 0;
   const BoutReal zlength = getUniform(coord->zlength());
diff --git a/src/invert/parderiv/impls/cyclic/cyclic.cxx b/src/invert/parderiv/impls/cyclic/cyclic.cxx
index c32c3d4b2d..6f432e3bcc 100644
--- a/src/invert/parderiv/impls/cyclic/cyclic.cxx
+++ b/src/invert/parderiv/impls/cyclic/cyclic.cxx
@@ -1,14 +1,14 @@
 /************************************************************************
  * Inversion of parallel derivatives
- * 
- * Inverts a matrix of the form 
+ *
+ * Inverts a matrix of the form
  *
  * A + B * Grad2_par2 + C*D2DYDZ + + D*D2DZ2 + E*DDY
- * 
+ *
  * Parallel algorithm, using Cyclic Reduction
  *
  * Author: Ben Dudson, University of York, Oct 2011
- * 
+ *
  * Known issues:
  * ------------
  *
@@ -17,7 +17,7 @@
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -58,7 +58,7 @@ InvertParCR::InvertParCR(Options* opt, CELL_LOC location, Mesh* mesh_in)
   // Number of k equations to solve for each x location
   nsys = 1 + (localmesh->LocalNz) / 2;
 
-  sg = sqrt(localmesh->getCoordinates(location)->g_22);
+  sg = sqrt(localmesh->getCoordinates(location)->g_22());
   sg = DDY(1. / sg) / sg;
 }
 
@@ -160,7 +160,7 @@ const Field3D InvertParCR::solve(const Field3D& f) {
         BoutReal ecoef = E(x, y + local_ystart)
                          + sg(x, y + local_ystart) * B(x, y + local_ystart); // ddy
 
-        if (coord->non_uniform) {
+        if (coord->non_uniform()) {
           ecoef += bcoef * coord->d1_dy(x, y + local_ystart);
         }
 
diff --git a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
index aad01c5f2f..b5aee9d0a1 100644
--- a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
+++ b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
@@ -104,9 +104,9 @@ Field3D InvertParDivCR::solve(const Field3D& f) {
   auto b = Matrix<dcomplex>(nsys, size);
   auto c = Matrix<dcomplex>(nsys, size);
 
-  const Field2D dy = coord->dy;
-  const Field2D J = coord->J;
-  const Field2D g_22 = coord->g_22;
+  const Field2D dy = coord->dy();
+  const Field2D J = coord->J();
+  const Field2D g_22 = coord->g_22();
 
   const auto zlength = getUniform(coord->zlength());
   // Loop over flux-surfaces
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 141cab0a43..56eec912b5 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -2661,8 +2661,8 @@ void BoundaryNeumann::apply([[maybe_unused]] Field2D& f, [[maybe_unused]] BoutRe
       rfft(f(x - 2 * bx, y), mesh->LocalNz, c1.begin());
       c1[0] = c0[0] - c1[0]; // Only need gradient
 
-      // Solve  metric->g11*d2f/dx2 - metric->g33*kz^2f = 0
-      // Assume metric->g11, metric->g33 constant -> exponential growth or decay
+      // Solve  metric->g11()*d2f/dx2 - metric->g33()*kz^2f = 0
+      // Assume metric->g11(), metric->g33() constant -> exponential growth or decay
 
       // Loop in X towards edge of domain
       do {
@@ -2878,8 +2878,8 @@ void BoundaryNeumann::apply([[maybe_unused]] Field2D& f, [[maybe_unused]] BoutRe
           c1[jz] = la * c2[jz] + lb * c1[jz] + lc * c0[jz];
         }
       }
-      // Solve  metric->g11*d2f/dx2 - metric->g33*kz^2f = 0
-      // Assume metric->g11, metric->g33 constant -> exponential growth or decay
+      // Solve  metric->g11()*d2f/dx2 - metric->g33()*kz^2f = 0
+      // Assume metric->g11(), metric->g33() constant -> exponential growth or decay
       BoutReal xpos = 0.0;
       // Loop in X towards edge of domain
       do {
@@ -2976,7 +2976,7 @@ void BoundaryNeumann::apply([[maybe_unused]] Field2D& f, [[maybe_unused]] BoutRe
           var.z(jx + 1, jy, jz) = var.z(jx - 3, jy, jz) + 4. * metric->dx(jx, jy) * tmp;
         }
 
-        // d/dx( Jmetric->g11 B_x ) = - d/dx( Jmetric->g12 B_y + Jmetric->g13 B_z)
+        // d/dx( Jmetric->g11() B_x ) = - d/dx( Jmetric->g12() B_y + Jmetric->g13() B_z)
         //                    - d/dy( JB^y ) - d/dz( JB^z )
 
         tmp =
diff --git a/src/mesh/christoffel_symbols.cxx b/src/mesh/christoffel_symbols.cxx
new file mode 100644
index 0000000000..943f020f36
--- /dev/null
+++ b/src/mesh/christoffel_symbols.cxx
@@ -0,0 +1,116 @@
+#include "bout/christoffel_symbols.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/mesh.hxx"
+#include "bout/output.hxx"
+
+ChristoffelSymbols::ChristoffelSymbols(const Coordinates& coordinates) {
+  // Calculate Christoffel symbol terms (18 independent values)
+  // Note: This calculation is completely general: metric
+  // tensor can be 2D or 3D. For 2D, all DDZ terms are zero
+
+  const auto& contravariantMetricTensor = coordinates.getContravariantMetricTensor();
+  const auto& covariantMetricTensor = coordinates.getCovariantMetricTensor();
+
+  const auto& g11 = contravariantMetricTensor.g11();
+  const auto& g22 = contravariantMetricTensor.g22();
+  const auto& g33 = contravariantMetricTensor.g33();
+  const auto& g12 = contravariantMetricTensor.g12();
+  const auto& g13 = contravariantMetricTensor.g13();
+  const auto& g23 = contravariantMetricTensor.g23();
+
+  const auto& g_11 = covariantMetricTensor.g11();
+  const auto& g_22 = covariantMetricTensor.g22();
+  const auto& g_33 = covariantMetricTensor.g33();
+  const auto& g_12 = covariantMetricTensor.g12();
+  const auto& g_13 = covariantMetricTensor.g13();
+  const auto& g_23 = covariantMetricTensor.g23();
+
+  G1_11_m = 0.5 * g11 * coordinates.DDX(g_11)
+            + g12 * (coordinates.DDX(g_12) - 0.5 * coordinates.DDY(g_11))
+            + g13 * (coordinates.DDX(g_13) - 0.5 * coordinates.DDZ(g_11));
+  G1_22_m = g11 * (coordinates.DDY(g_12) - 0.5 * coordinates.DDX(g_22))
+            + 0.5 * g12 * coordinates.DDY(g_22)
+            + g13 * (coordinates.DDY(g_23) - 0.5 * coordinates.DDZ(g_22));
+  G1_33_m = g11 * (coordinates.DDZ(g_13) - 0.5 * coordinates.DDX(g_33))
+            + g12 * (coordinates.DDZ(g_23) - 0.5 * coordinates.DDY(g_33))
+            + 0.5 * g13 * coordinates.DDZ(g_33);
+  G1_12_m =
+      0.5 * g11 * coordinates.DDY(g_11) + 0.5 * g12 * coordinates.DDX(g_22)
+      + 0.5 * g13
+            * (coordinates.DDY(g_13) + coordinates.DDX(g_23) - coordinates.DDZ(g_12));
+  G1_13_m =
+      0.5 * g11 * coordinates.DDZ(g_11)
+      + 0.5 * g12
+            * (coordinates.DDZ(g_12) + coordinates.DDX(g_23) - coordinates.DDY(g_13))
+      + 0.5 * g13 * coordinates.DDX(g_33);
+  G1_23_m =
+      0.5 * g11 * (coordinates.DDZ(g_12) + coordinates.DDY(g_13) - coordinates.DDX(g_23))
+      + 0.5 * g12
+            * (coordinates.DDZ(g_22) + coordinates.DDY(g_23) - coordinates.DDY(g_23))
+      // + 0.5 *g13*(coordinates.DDZ(g_32) + coordinates.DDY(g_33) - coordinates.DDZ(g_23));
+      // which equals
+      + 0.5 * g13 * coordinates.DDY(g_33);
+
+  G2_11_m = 0.5 * g12 * coordinates.DDX(g_11)
+            + g22 * (coordinates.DDX(g_12) - 0.5 * coordinates.DDY(g_11))
+            + g23 * (coordinates.DDX(g_13) - 0.5 * coordinates.DDZ(g_11));
+  G2_22_m = g12 * (coordinates.DDY(g_12) - 0.5 * coordinates.DDX(g_22))
+            + 0.5 * g22 * coordinates.DDY(g_22)
+            + g23 * (coordinates.DDY(g23) - 0.5 * coordinates.DDZ(g_22));
+  G2_33_m = g12 * (coordinates.DDZ(g_13) - 0.5 * coordinates.DDX(g_33))
+            + g22 * (coordinates.DDZ(g_23) - 0.5 * coordinates.DDY(g_33))
+            + 0.5 * g23 * coordinates.DDZ(g_33);
+  G2_12_m =
+      0.5 * g12 * coordinates.DDY(g_11) + 0.5 * g22 * coordinates.DDX(g_22)
+      + 0.5 * g23
+            * (coordinates.DDY(g_13) + coordinates.DDX(g_23) - coordinates.DDZ(g_12));
+  G2_13_m =
+      // 0.5 *g21*(coordinates.DDZ(g_11) + coordinates.DDX(covariantMetricTensor.Getg13()) - coordinates.DDX(g_13))
+      // which equals
+      0.5 * g12 * (coordinates.DDZ(g_11) + coordinates.DDX(g_13) - coordinates.DDX(g_13))
+      // + 0.5 *g22*(coordinates.DDZ(covariantMetricTensor.Getg21()) + coordinates.DDX(g_23) - coordinates.DDY(g_13))
+      // which equals
+      + 0.5 * g22
+            * (coordinates.DDZ(g_12) + coordinates.DDX(g_23) - coordinates.DDY(g_13))
+      // + 0.5 *g23*(coordinates.DDZ(covariantMetricTensor.Getg31()) + coordinates.DDX(g_33) - coordinates.DDZ(g_13));
+      // which equals
+      + 0.5 * g23 * coordinates.DDX(g_33);
+  G2_23_m =
+      0.5 * g12 * (coordinates.DDZ(g_12) + coordinates.DDY(g_13) - coordinates.DDX(g_23))
+      + 0.5 * g22 * coordinates.DDZ(g_22) + 0.5 * g23 * coordinates.DDY(g_33);
+
+  G3_11_m = 0.5 * g13 * coordinates.DDX(g_11)
+            + g23 * (coordinates.DDX(g_12) - 0.5 * coordinates.DDY(g_11))
+            + g33 * (coordinates.DDX(g_13) - 0.5 * coordinates.DDZ(g_11));
+  G3_22_m = g13 * (coordinates.DDY(g_12) - 0.5 * coordinates.DDX(g_22))
+            + 0.5 * g23 * coordinates.DDY(g_22)
+            + g33 * (coordinates.DDY(g_23) - 0.5 * coordinates.DDZ(g_22));
+  G3_33_m = g13 * (coordinates.DDZ(g_13) - 0.5 * coordinates.DDX(g_33))
+            + g23 * (coordinates.DDZ(g_23) - 0.5 * coordinates.DDY(g_33))
+            + 0.5 * g33 * coordinates.DDZ(g_33);
+  G3_12_m =
+      // 0.5 *g31*(coordinates.DDY(g_11) + coordinates.DDX(covariantMetricTensor.Getg12()) - coordinates.DDX(g_12))
+      // which equals to
+      0.5 * g13 * coordinates.DDY(g_11)
+      // + 0.5 *g32*(coordinates.DDY(covariantMetricTensor.Getg21()) + coordinates.DDX(g_22) - coordinates.DDY(g_12))
+      // which equals to
+      + 0.5 * g23 * coordinates.DDX(g_22)
+      //+ 0.5 *g33*(coordinates.DDY(covariantMetricTensor.Getg31()) + coordinates.DDX(covariantMetricTensor.Getg32()) - coordinates.DDZ(g_12));
+      // which equals to
+      + 0.5 * g33 * (coordinates.DDY(g_13)) + coordinates.DDX(g_23)
+      - coordinates.DDZ(g_12);
+  G3_13_m =
+      0.5 * g13 * coordinates.DDZ(g_11)
+      + 0.5 * g23
+            * (coordinates.DDZ(g_12) + coordinates.DDX(g_23) - coordinates.DDY(g_13))
+      + 0.5 * g33 * coordinates.DDX(g_33);
+  G3_23_m = 0.5 * g13 * (coordinates.DDZ(g_12) + coordinates.DDY(g_13))
+            - coordinates.DDX(g_23) + 0.5 * g23 * coordinates.DDZ(g_22)
+            + 0.5 * g33 * coordinates.DDY(g_33);
+
+  output_progress.write("\tCommunicating connection terms\n");
+
+  G1_11_m.getMesh()->communicate(G1_11_m, G1_22_m, G1_33_m, G1_12_m, G1_13_m, G1_23_m,
+                                 G2_11_m, G2_22_m, G2_33_m, G2_12_m, G2_13_m, G2_23_m,
+                                 G3_11_m, G3_22_m, G3_33_m, G3_12_m, G3_13_m, G3_23_m);
+}
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 3543995702..22b43a9f8e 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -4,9 +4,11 @@
  * given the contravariant metric tensor terms
  **************************************************************************/
 
+#include "bout/christoffel_symbols.hxx"
 #include "bout/coordinates_accessor.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_data.hxx"
+#include "bout/g_values.hxx"
 #include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
@@ -21,6 +23,7 @@
 #include <bout/globals.hxx>
 #include <bout/index_derivs_interface.hxx>
 #include <bout/interpolation.hxx>
+#include <bout/metric_tensor.hxx>
 #include <bout/openmpwrap.hxx>
 #include <bout/options.hxx>
 #include <bout/output.hxx>
@@ -37,14 +40,13 @@
 #include <algorithm>
 #include <cmath>
 #include <cstdlib>
-#include <iterator>
 #include <memory>
 #include <string>
+#include <string_view>
 #include <utility>
 
 #include <fmt/format.h>
 
-#include "invert3x3.hxx"
 #include "parallel/fci.hxx"
 #include "parallel/shiftedmetricinterp.hxx"
 
@@ -266,45 +268,38 @@ Coordinates::Coordinates(Mesh* mesh, FieldMetric dx, FieldMetric dy, FieldMetric
                          FieldMetric g_33, FieldMetric g_12, FieldMetric g_13,
                          FieldMetric g_23, FieldMetric ShiftTorsion,
                          FieldMetric IntShiftTorsion)
-    : dx(std::move(dx)), dy(std::move(dy)), dz(dz), J(std::move(J)), Bxy(std::move(Bxy)),
-      g11(std::move(g11)), g22(std::move(g22)), g33(std::move(g33)), g12(std::move(g12)),
-      g13(std::move(g13)), g23(std::move(g23)), g_11(std::move(g_11)),
-      g_22(std::move(g_22)), g_33(std::move(g_33)), g_12(std::move(g_12)),
-      g_13(std::move(g_13)), g_23(std::move(g_23)), ShiftTorsion(std::move(ShiftTorsion)),
-      IntShiftTorsion(std::move(IntShiftTorsion)), nz(mesh->LocalNz), localmesh(mesh),
-      localoptions(nullptr), location(CELL_CENTRE) {}
+    : nz(mesh->LocalNz), localmesh(mesh), location(CELL_CENTRE), dx_(std::move(dx)),
+      dy_(std::move(dy)), dz_(std::move(dz)), ShiftTorsion_(std::move(ShiftTorsion)),
+      IntShiftTorsion_(std::move(IntShiftTorsion)),
+      transform(bout::utils::make_unique<ParallelTransformIdentity>(*localmesh)),
+      contravariantMetricTensor(std::move(g11), std::move(g22), std::move(g33),
+                                std::move(g12), std::move(g13), std::move(g23)),
+      covariantMetricTensor(std::move(g_11), std::move(g_22), std::move(g_33),
+                            std::move(g_12), std::move(g_13), std::move(g_23)),
+      jacobian_cache(std::make_unique<FieldMetric>(std::move(J))), Bxy_(std::move(Bxy)) {}
 
 Coordinates::Coordinates(Mesh* mesh, Options* options)
-    : dx(1., mesh), dy(1., mesh), dz(1., mesh), d1_dx(mesh), d1_dy(mesh), d1_dz(mesh),
-      J(1., mesh), Bxy(1., mesh),
-      // Identity metric tensor
-      g11(1., mesh), g22(1., mesh), g33(1., mesh), g12(0, mesh), g13(0, mesh),
-      g23(0, mesh), g_11(1., mesh), g_22(1., mesh), g_33(1., mesh), g_12(0, mesh),
-      g_13(0, mesh), g_23(0, mesh), G1_11(mesh), G1_22(mesh), G1_33(mesh), G1_12(mesh),
-      G1_13(mesh), G1_23(mesh), G2_11(mesh), G2_22(mesh), G2_33(mesh), G2_12(mesh),
-      G2_13(mesh), G2_23(mesh), G3_11(mesh), G3_22(mesh), G3_33(mesh), G3_12(mesh),
-      G3_13(mesh), G3_23(mesh), G1(mesh), G2(mesh), G3(mesh), ShiftTorsion(mesh),
-      IntShiftTorsion(mesh), nz(mesh->LocalNz), localmesh(mesh), localoptions(options),
-      location(CELL_CENTRE) {
+    : nz(mesh->LocalNz), localmesh(mesh), localoptions(options), location(CELL_CENTRE),
+      dx_(1., mesh), dy_(1., mesh), dz_(1., mesh), d1_dx_(mesh), d1_dy_(mesh),
+      d1_dz_(mesh), ShiftTorsion_(0.0, mesh), IntShiftTorsion_(0.0, mesh),
+      contravariantMetricTensor(1., 1., 1., 0, 0, 0, mesh),
+      covariantMetricTensor(1., 1., 1., 0, 0, 0, mesh), Bxy_(1., mesh) {
 
   readFromMesh(options, "");
-  // Allow transform to fix things up
-  transform->loadParallelMetrics(this);
+
+  if (transform != nullptr and not transform->canToFromFieldAligned()) {
+    // Read parallel metrics from gridfile for FCI
+    readParallelMetricComponents();
+  }
 }
 
 Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
                          const Coordinates* coords_in, bool force_interpolate_from_centre)
-    : dx(1., mesh), dy(1., mesh), dz(1., mesh), d1_dx(mesh), d1_dy(mesh), d1_dz(mesh),
-      J(1., mesh), Bxy(1., mesh),
-      // Identity metric tensor
-      g11(1., mesh), g22(1., mesh), g33(1., mesh), g12(0, mesh), g13(0, mesh),
-      g23(0, mesh), g_11(1., mesh), g_22(1., mesh), g_33(1., mesh), g_12(0, mesh),
-      g_13(0, mesh), g_23(0, mesh), G1_11(mesh), G1_22(mesh), G1_33(mesh), G1_12(mesh),
-      G1_13(mesh), G1_23(mesh), G2_11(mesh), G2_22(mesh), G2_33(mesh), G2_12(mesh),
-      G2_13(mesh), G2_23(mesh), G3_11(mesh), G3_22(mesh), G3_33(mesh), G3_12(mesh),
-      G3_13(mesh), G3_23(mesh), G1(mesh), G2(mesh), G3(mesh), ShiftTorsion(mesh),
-      IntShiftTorsion(mesh), nz(mesh->LocalNz), localmesh(mesh), localoptions(options),
-      location(loc) {
+    : nz(mesh->LocalNz), localmesh(mesh), localoptions(options), location(loc),
+      dx_(1., mesh), dy_(1., mesh), dz_(1., mesh), d1_dx_(mesh), d1_dy_(mesh),
+      d1_dz_(mesh), ShiftTorsion_(0.0, mesh), IntShiftTorsion_(0.0, mesh),
+      contravariantMetricTensor(1., 1., 1., 0, 0, 0, mesh),
+      covariantMetricTensor(1., 1., 1., 0, 0, 0, mesh), Bxy_(1., mesh) {
 
   const std::string suffix = getLocationSuffix(location);
 
@@ -313,9 +308,9 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
   } else {
     // Interpolate fields from coords_in
 
-    if (isUniform(coords_in->dz)) {
-      dz = coords_in->dz;
-      dz.setLocation(location);
+    if (isUniform(coords_in->dz_)) {
+      dz_ = coords_in->dz_;
+      dz_.setLocation(location);
     } else {
       throw BoutException(
           "We are asked to transform dz to get dz before we have a transform, which "
@@ -327,52 +322,39 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
       return interpolateAndExtrapolate(f, location, true, true, false, transform.get());
     };
 
-    dx = interpField(coords_in->dx);
-    dy = interpField(coords_in->dy);
+    dx_ = interpField(coords_in->dx_);
+    dy_ = interpField(coords_in->dy_);
     // not really needed - we have used dz already ...
-    dz = interpField(coords_in->dz);
-
-    // Diagonal components of metric tensor g^{ij}
-    g11 = interpField(coords_in->g11);
-    g22 = interpField(coords_in->g22);
-    g33 = interpField(coords_in->g33);
-
-    // Off-diagonal elements.
-    g12 = interpField(coords_in->g12);
-    g13 = interpField(coords_in->g13);
-    g23 = interpField(coords_in->g23);
-
-    // 3x3 matrix inversion can exaggerate small interpolation errors, so it is
-    // more robust to interpolate and extrapolate derived quantities directly,
-    // rather than deriving from interpolated/extrapolated covariant metric
-    // components
-    g_11 = interpField(coords_in->g_11);
-    g_22 = interpField(coords_in->g_22);
-    g_33 = interpField(coords_in->g_33);
-    g_12 = interpField(coords_in->g_12);
-    g_13 = interpField(coords_in->g_13);
-    g_23 = interpField(coords_in->g_23);
+    dz_ = interpField(coords_in->dz_);
+
+    setMetricTensor(coords_in->getContravariantMetricTensor(),
+                    coords_in->getCovariantMetricTensor());
+
+    contravariantMetricTensor.map(interpField);
+    covariantMetricTensor.map(interpField);
 
     // Check input metrics
     checkContravariant();
     checkCovariant();
 
-    J = interpField(coords_in->J);
-    Bxy = interpField(coords_in->Bxy);
+    setJ(interpField(coords_in->J()));
+    setBxy(interpField(coords_in->Bxy()));
 
-    bout::checkFinite(J, "The Jacobian", "RGN_NOCORNERS");
-    bout::checkPositive(J, "The Jacobian", "RGN_NOCORNERS");
-    bout::checkFinite(Bxy, "Bxy", "RGN_NOCORNERS");
-    bout::checkPositive(Bxy, "Bxy", "RGN_NOCORNERS");
+    bout::checkFinite(J(), "The Jacobian", "RGN_NOCORNERS");
+    bout::checkPositive(J(), "The Jacobian", "RGN_NOCORNERS");
+    bout::checkFinite(Bxy(), "Bxy", "RGN_NOCORNERS");
+    bout::checkPositive(Bxy(), "Bxy", "RGN_NOCORNERS");
 
-    ShiftTorsion = interpField(coords_in->ShiftTorsion);
+    ShiftTorsion_ = interpField(coords_in->ShiftTorsion_);
 
     if (mesh->IncIntShear) {
-      IntShiftTorsion = interpField(coords_in->IntShiftTorsion);
+      IntShiftTorsion_ = interpField(coords_in->IntShiftTorsion_);
+    }
+    if (not transform->canToFromFieldAligned()) {
+      // Read parallel metrics from gridfile for FCI
+      readParallelMetricComponents();
     }
   }
-  // Allow transform to fix things up
-  transform->loadParallelMetrics(this);
 }
 
 void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
@@ -425,6 +407,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
     // Passing `field` in here twice is gross but ok because the second argument
     // is only used when interpolating, and we're not interpolating here
     fillGuards_impl(field, location, field, extrapolate_x, extrapolate_y);
+    return field;
   };
 
   // Read the field, transform if required, and fill in the guards
@@ -448,34 +431,27 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
     // We can't use the helper functions here because in 3D we might (always?)
     // need to transform from field aligned -- which requires dz! So we have to
     // read it "plain" first...
-    localmesh->get(dz, "dz" + suffix, default_dz, false, location);
+    localmesh->get(dz_, "dz" + suffix, default_dz, false, location);
   }
 
   // ...then we can set the transform (required early for differentiation)...
   setParallelTransform(options);
 
   // ...and finally we can transform/interpolate/fill in guards
-  dz = interpolateAndExtrapolate(dz, location, extrapolate_x, extrapolate_y, false,
-                                 transform.get());
+  setDz(interpolateAndExtrapolate(dz_, location, extrapolate_x, extrapolate_y, false,
+                                  transform.get()));
 
   // everything else from this point on can use our helper functions
-  dx = readAndFillGuards("dx", 1.0);
-
-  if (localmesh->periodicX) {
-    localmesh->communicate_no_slices(dx);
-  }
+  setDx(readAndFillGuards("dx", 1.0), localmesh->periodicX);
 
-  dy = readAndFillGuards("dy", 1.0);
+  setDy(readAndFillGuards("dy", 1.0));
 
   // Diagonal components of metric tensor g^{ij} (default to 1)
-  g11 = readAndFillGuards("g11", 1.0);
-  g22 = readAndFillGuards("g22", 1.0);
-  g33 = readAndFillGuards("g33", 1.0);
-
-  // Off-diagonal elements. Default to 0
-  g12 = readAndFillGuards("g12", 0.0);
-  g13 = readAndFillGuards("g13", 0.0);
-  g23 = readAndFillGuards("g23", 0.0);
+  contravariantMetricTensor = ContravariantMetricTensor{
+      readAndFillGuards("g11", 1.0), readAndFillGuards("g22", 1.0),
+      readAndFillGuards("g33", 1.0), readAndFillGuards("g12", 0.0),
+      readAndFillGuards("g13", 0.0), readAndFillGuards("g23", 0.0),
+  };
 
   // Check input metrics
   checkContravariant();
@@ -485,115 +461,161 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   auto source_has_component = [&suffix, this](const std::string& name) {
     return localmesh->sourceHasVar(name + suffix);
   };
-  // Check if any of the components are present
-  if (std::any_of(begin(covariant_component_names), end(covariant_component_names),
-                  source_has_component)) {
-    // Check that all components are present
-    if (std::all_of(begin(covariant_component_names), end(covariant_component_names),
-                    source_has_component)) {
-      g_11 = readField("g_11", 1.0);
-      g_22 = readField("g_22", 1.0);
-      g_33 = readField("g_33", 1.0);
-      g_12 = readField("g_12", 0.0);
-      g_13 = readField("g_13", 0.0);
-      g_23 = readField("g_23", 0.0);
-
-      output_warn.write("\tWARNING! Covariant components of metric tensor set manually. "
-                        "Contravariant components NOT recalculated\n");
 
-    } else {
+  // Check if any of the components are present, all of them are present
+  if (const bool all_present =
+          std::ranges::all_of(covariant_component_names, source_has_component);
+      std::ranges::any_of(covariant_component_names, source_has_component)
+      and all_present) {
+    covariantMetricTensor = CovariantMetricTensor{
+        readAndFillGuards("g_11", 1.0), readAndFillGuards("g_22", 1.0),
+        readAndFillGuards("g_33", 1.0), readAndFillGuards("g_12", 0.0),
+        readAndFillGuards("g_13", 0.0), readAndFillGuards("g_23", 0.0),
+    };
+
+    output_warn.write("\tWARNING! Covariant components of metric tensor set manually. "
+                      "Contravariant components NOT recalculated\n");
+  } else {
+    if (not all_present) {
       output_warn.write("Not all covariant components of metric tensor found. "
                         "Calculating all from the contravariant tensor\n");
-      /// Calculate contravariant metric components if not found
-      if (calcCovariant("RGN_NOCORNERS") != 0) {
-        throw BoutException("Error in calcCovariant call");
-      }
-    }
-  } else {
-    /// Calculate contravariant metric components if not found
-    if (calcCovariant("RGN_NOCORNERS") != 0) {
-      throw BoutException("Error in calcCovariant call");
     }
+    covariantMetricTensor = contravariantMetricTensor.inverse("RGN_NOCORNERS", false);
+
+    // More robust to extrapolate derived quantities directly, rather than
+    // deriving from extrapolated covariant metric components
+    covariantMetricTensor.map(fillGuards);
   }
-  // More robust to extrapolate derived quantities directly, rather than
-  // deriving from extrapolated covariant metric components
-  fillGuards(g_11);
-  fillGuards(g_22);
-  fillGuards(g_33);
-  fillGuards(g_12);
-  fillGuards(g_13);
-  fillGuards(g_23);
 
   // Check covariant metrics
   checkCovariant();
 
-  // Calculate Jacobian and Bxy
-  jacobian();
-
   // Attempt to read J from the grid file
-  auto Jcalc = J;
-  if (localmesh->get(J, "J" + suffix, 0.0, false) != 0) {
+  auto Jcalc = J();
+  FieldMetric J_temp{localmesh};
+  if (localmesh->get(J_temp, "J" + suffix, 0.0, false) != 0) {
     output_warn.write(
         "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
-    J = Jcalc;
   } else {
     checkStaggeredGet(localmesh, "J", suffix);
-    J = ensuredUnaligned(J);
-    fillGuards(J);
+    *jacobian_cache = ensuredUnaligned(J_temp);
+    fillGuards(*jacobian_cache);
 
     // Compare calculated and loaded values
-    output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(J - Jcalc)));
-
-    localmesh->communicate_no_slices(J);
+    output_warn.write("\tMaximum difference in J is {:e}\n", max(abs(J() - Jcalc)));
 
-    // Re-evaluate Bxy using new J
-    Bxy = sqrt(g_22) / J;
+    localmesh->communicate_no_slices(*jacobian_cache);
   }
 
   // Check jacobian
-  bout::checkFinite(J, "J", "RGN_NOCORNERS");
-  bout::checkPositive(J, "J", "RGN_NOCORNERS");
-  if (min(abs(J)) < 1.0e-10) {
-    throw BoutException("\tERROR: Jacobian becomes very small\n");
+  bout::checkFinite(J(), "J" + suffix, "RGN_NOCORNERS");
+  bout::checkPositive(J(), "J" + suffix, "RGN_NOCORNERS");
+  if (min(abs(J())) < 1.0e-10) {
+    throw BoutException("\tERROR: Jacobian{:s} becomes very small\n", suffix);
   }
 
   // Attempt to read Bxy from the grid file
-  auto Bcalc = Bxy;
-  if (localmesh->get(Bxy, "Bxy" + suffix, 0.0, false) != 0) {
+  const FieldMetric Bcalc = sqrt(g_22()) / J();
+  if (localmesh->get(Bxy_, "Bxy" + suffix, 0.0, false) != 0) {
     output_warn.write("\tWARNING: Magnitude of B field 'Bxy' not found. Calculating from "
                       "metric tensor\n");
-    Bxy = Bcalc;
+    Bxy_ = interpolateAndExtrapolate(Bcalc, location, extrapolate_x, extrapolate_y, false,
+                                     transform.get());
   } else {
     checkStaggeredGet(localmesh, "Bxy", suffix);
-    Bxy = ensuredUnaligned(Bxy);
-    fillGuards(Bxy);
-    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy - Bcalc)));
+    Bxy_ = ensuredUnaligned(Bxy_);
+    fillGuards(Bxy_);
+    output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy_ - Bcalc)));
   }
 
   // Check Bxy
-  bout::checkFinite(Bxy, "Bxy", "RGN_NOCORNERS");
-  bout::checkPositive(Bxy, "Bxy", "RGN_NOCORNERS");
+  bout::checkFinite(Bxy(), "Bxy" + suffix, "RGN_NOCORNERS");
+  bout::checkPositive(Bxy(), "Bxy" + suffix, "RGN_NOCORNERS");
 
-  if (localmesh->get(ShiftTorsion, "ShiftTorsion" + suffix, 0.0, false) != 0) {
-    output_warn.write(
-        "\tWARNING: No Torsion specified for zShift. Derivatives may not be correct\n");
-    ShiftTorsion = 0.0;
+  if (not localmesh->sourceHasVar("ShiftTorsion" + suffix)) {
+    output_warn.write("\tWARNING: No Torsion specified for zShift. "
+                      "Derivatives may not be correct\n");
+  } else {
+    ShiftTorsion_ = readAndFillGuards("ShiftTorsion", 0.0);
   }
-  fillGuards(ShiftTorsion);
-
-  //////////////////////////////////////////////////////
 
   if (localmesh->IncIntShear) {
-    if (localmesh->get(IntShiftTorsion, "IntShiftTorsion", 0.0, false) != 0) {
+    if (not localmesh->sourceHasVar("IntShiftTorsion" + suffix)) {
       output_warn.write("\tWARNING: No Integrated torsion specified\n");
+    } else {
+      IntShiftTorsion_ = readAndFillGuards("IntShiftTorsion", 0.0);
+    }
+  }
+}
+
+namespace bout {
+// Get a unique name for a field based on the sign/magnitude of the offset
+std::string parallelSliceFieldName(std::string_view field, int offset) {
+  using namespace std::string_view_literals;
+  const std::string_view direction = (offset > 0) ? "forward"sv : "backward"sv;
+  // We only have a suffix for parallel slices beyond the first
+  // This is for backwards compatibility
+  const std::string slice_suffix =
+      (std::abs(offset) > 1) ? fmt::format("_{}", std::abs(offset)) : "";
+  return fmt::format("{}_{}{}", direction, field, slice_suffix);
+};
+} // namespace bout
+
+namespace {
+void load_parallel_metric_component(std::string_view name, bout::FieldMetric& component,
+                                    int offset) {
+  Mesh* mesh = component.getMesh();
+  bout::FieldMetric tmp{mesh};
+  const auto pname = bout::parallelSliceFieldName(name, offset);
+  if (mesh->get(tmp, pname, 0.0, false) != 0) {
+    throw BoutException("Could not read {:s} from grid file!\n"
+                        "  Fix it up with `zoidberg-update-parallel-metrics <grid>`",
+                        pname);
+  }
+  if (!component.hasParallelSlices()) {
+    component.splitParallelSlices();
+    component.disallowCalcParallelSlices();
+    component.resetRegionParallel(true);
+  }
+  auto& pcom = component.ynext(offset);
+  pcom.allocate();
+  BOUT_FOR(i, component.getRegion("RGN_NOBNDRY")) { pcom[i.yp(offset)] = tmp[i]; }
+}
+} // namespace
+
+void Coordinates::readParallelMetricComponents() {
+  if (not bout::build::use_metric_3d) {
+    return;
+  }
+  output_info.write("\tLoading parallel metrics\n");
+  const FieldMetric JB0 = J() * Bxy();
+  jacobian_cache->splitParallelSlices();
+  jacobian_cache->disallowCalcParallelSlices();
+  jacobian_cache->resetRegionParallel(true);
+  for (int i = 1; i <= localmesh->ystart; ++i) {
+    auto read_offset = [i](std::string_view name, FieldMetric& component) {
+      load_parallel_metric_component(name, component, -i);
+      load_parallel_metric_component(name, component, i);
+    };
+
+    read_offset("g11", covariantMetricTensor.g11_m);
+    read_offset("g22", covariantMetricTensor.g22_m);
+    read_offset("g33", covariantMetricTensor.g33_m);
+    read_offset("g13", covariantMetricTensor.g13_m);
+    read_offset("g_11", contravariantMetricTensor.g11_m);
+    read_offset("g_22", contravariantMetricTensor.g22_m);
+    read_offset("g_33", contravariantMetricTensor.g33_m);
+    read_offset("g_13", contravariantMetricTensor.g13_m);
+    read_offset("dy", dy_);
+    read_offset("Bxy", Bxy_);
+
+    jacobian_cache->ynext(i).allocate();
+    jacobian_cache->ynext(-i).allocate();
+    BOUT_FOR(j, JB0.getRegion("RGN_NOBNDRY")) {
+      jacobian_cache->ynext(i)[j.yp(i)] = JB0[j] / Bxy_.ynext(i)[j.yp(i)];
+      jacobian_cache->ynext(-i)[j.yp(-i)] = JB0[j] / Bxy_.ynext(-i)[j.yp(-i)];
     }
-    fillGuards(IntShiftTorsion);
-  } else {
-    // IntShiftTorsion will not be used, but set to zero to avoid uninitialized field
-    IntShiftTorsion = 0.;
   }
-  // Allow transform to fix things up
-  transform->loadParallelMetrics(this);
 }
 
 void Coordinates::outputVars(Options& output_options) {
@@ -601,317 +623,96 @@ void Coordinates::outputVars(Options& output_options) {
   const std::string loc_string =
       (location == CELL_CENTRE) ? "" : "_" + toString(location);
 
-  output_options["dx" + loc_string].force(dx, "Coordinates");
-  output_options["dy" + loc_string].force(dy, "Coordinates");
-  output_options["dz" + loc_string].force(dz, "Coordinates");
+  output_options["dx" + loc_string].force(dx(), "Coordinates");
+  output_options["dy" + loc_string].force(dy(), "Coordinates");
+  output_options["dz" + loc_string].force(dz(), "Coordinates");
 
-  output_options["g11" + loc_string].force(g11, "Coordinates");
-  output_options["g22" + loc_string].force(g22, "Coordinates");
-  output_options["g33" + loc_string].force(g33, "Coordinates");
-  output_options["g12" + loc_string].force(g12, "Coordinates");
-  output_options["g13" + loc_string].force(g13, "Coordinates");
-  output_options["g23" + loc_string].force(g23, "Coordinates");
+  output_options["g11" + loc_string].force(g11(), "Coordinates");
+  output_options["g22" + loc_string].force(g22(), "Coordinates");
+  output_options["g33" + loc_string].force(g33(), "Coordinates");
+  output_options["g12" + loc_string].force(g12(), "Coordinates");
+  output_options["g13" + loc_string].force(g13(), "Coordinates");
+  output_options["g23" + loc_string].force(g23(), "Coordinates");
 
-  output_options["g_11" + loc_string].force(g_11, "Coordinates");
-  output_options["g_22" + loc_string].force(g_22, "Coordinates");
-  output_options["g_33" + loc_string].force(g_33, "Coordinates");
-  output_options["g_12" + loc_string].force(g_12, "Coordinates");
-  output_options["g_13" + loc_string].force(g_13, "Coordinates");
-  output_options["g_23" + loc_string].force(g_23, "Coordinates");
+  output_options["g_11" + loc_string].force(g_11(), "Coordinates");
+  output_options["g_22" + loc_string].force(g_22(), "Coordinates");
+  output_options["g_33" + loc_string].force(g_33(), "Coordinates");
+  output_options["g_12" + loc_string].force(g_12(), "Coordinates");
+  output_options["g_13" + loc_string].force(g_13(), "Coordinates");
+  output_options["g_23" + loc_string].force(g_23(), "Coordinates");
 
-  output_options["J" + loc_string].force(J, "Coordinates");
-  output_options["Bxy" + loc_string].force(Bxy, "Coordinates");
+  output_options["J" + loc_string].force(J(), "Coordinates");
+  output_options["Bxy" + loc_string].force(Bxy(), "Coordinates");
 
-  output_options["G1" + loc_string].force(G1, "Coordinates");
-  output_options["G2" + loc_string].force(G2, "Coordinates");
-  output_options["G3" + loc_string].force(G3, "Coordinates");
+  output_options["G1" + loc_string].force(G1(), "Coordinates");
+  output_options["G2" + loc_string].force(G2(), "Coordinates");
+  output_options["G3" + loc_string].force(G3(), "Coordinates");
 
   getParallelTransform().outputVars(output_options);
 }
 
 const Field2D& Coordinates::zlength() const {
-  BOUT_OMP_SAFE(critical)
+  BOUT_OMP(critical)
   if (not zlength_cache) {
     zlength_cache = std::make_unique<Field2D>(0., localmesh);
 
 #if BOUT_USE_METRIC_3D
-    BOUT_FOR_SERIAL(i, dz.getRegion("RGN_ALL")) { (*zlength_cache)[i] += dz[i]; }
+    BOUT_FOR_SERIAL(i, dz().getRegion("RGN_ALL")) { (*zlength_cache)[i] += dz()[i]; }
 #else
-    (*zlength_cache) = dz * nz;
+    (*zlength_cache) = dz_ * nz;
 #endif
   }
 
   return *zlength_cache;
 }
 
-int Coordinates::geometry(bool recalculate_staggered,
-                          bool force_interpolate_from_centre) {
-
-  localmesh->communicate_no_slices(dx, dy, dz, g11, g22, g33, g12, g13, g23, g_11, g_22,
-                                   g_33, g_12, g_13, g_23, J, Bxy);
-
-  output_progress.write("Calculating differential geometry terms\n");
-
+void Coordinates::setDx(FieldMetric dx, const bool communicate) {
   if (min(abs(dx)) < 1e-8) {
     throw BoutException("dx magnitude less than 1e-8");
   }
+  dx_ = std::move(dx);
+  if (communicate) {
+    localmesh->communicate_no_slices(dx_);
+  }
+}
 
+void Coordinates::setDy(FieldMetric dy, const bool communicate) {
   if (min(abs(dy)) < 1e-8) {
     throw BoutException("dy magnitude less than 1e-8");
   }
+  dy_ = std::move(dy);
+  if (communicate) {
+    localmesh->communicate_no_slices(dy_);
+  }
+}
 
+void Coordinates::setDz(FieldMetric dz, const bool communicate) {
   if (min(abs(dz)) < 1e-8) {
     throw BoutException("dz magnitude less than 1e-8");
   }
+  dz_ = std::move(dz);
+  if (communicate) {
+    localmesh->communicate_no_slices(dz_);
+  }
+}
+
+void Coordinates::recalculateAndReset(bool recalculate_staggered,
+                                      bool force_interpolate_from_centre) {
 
   // Check input metrics
   checkContravariant();
   checkCovariant();
 
-  // Calculate Christoffel symbol terms (18 independent values)
-  // Note: This calculation is completely general: metric
-  // tensor can be 2D or 3D. For 2D, all DDZ terms are zero
-
-  if (!g11.isFci()) {
-    G1_11 = 0.5 * g11 * DDX(g_11) + g12 * (DDX(g_12) - 0.5 * DDY(g_11))
-            + g13 * (DDX(g_13) - 0.5 * DDZ(g_11));
-    G1_22 = g11 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g12 * DDY(g_22)
-            + g13 * (DDY(g_23) - 0.5 * DDZ(g_22));
-    G1_33 = g11 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g12 * (DDZ(g_23) - 0.5 * DDY(g_33))
-            + 0.5 * g13 * DDZ(g_33);
-    G1_12 = 0.5 * g11 * DDY(g_11) + 0.5 * g12 * DDX(g_22)
-            + 0.5 * g13 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
-    G1_13 = 0.5 * g11 * DDZ(g_11) + 0.5 * g12 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
-            + 0.5 * g13 * DDX(g_33);
-    G1_23 = 0.5 * g11 * (DDZ(g_12) + DDY(g_13) - DDX(g_23))
-            + 0.5 * g12 * (DDZ(g_22) + DDY(g_23) - DDY(g_23))
-            // + 0.5 *g13*(DDZ(g_32) + DDY(g_33) - DDZ(g_23));
-            // which equals
-            + 0.5 * g13 * DDY(g_33);
-
-    G2_11 = 0.5 * g12 * DDX(g_11) + g22 * (DDX(g_12) - 0.5 * DDY(g_11))
-            + g23 * (DDX(g_13) - 0.5 * DDZ(g_11));
-    G2_22 = g12 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g22 * DDY(g_22)
-            + g23 * (DDY(g23) - 0.5 * DDZ(g_22));
-    G2_33 = g12 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g22 * (DDZ(g_23) - 0.5 * DDY(g_33))
-            + 0.5 * g23 * DDZ(g_33);
-    G2_12 = 0.5 * g12 * DDY(g_11) + 0.5 * g22 * DDX(g_22)
-            + 0.5 * g23 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
-    G2_13 =
-        // 0.5 *g21*(DDZ(g_11) + DDX(g_13) - DDX(g_13))
-        // which equals
-        0.5 * g12 * (DDZ(g_11) + DDX(g_13) - DDX(g_13))
-        // + 0.5 *g22*(DDZ(g_21) + DDX(g_23) - DDY(g_13))
-        // which equals
-        + 0.5 * g22 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
-        // + 0.5 *g23*(DDZ(g_31) + DDX(g_33) - DDZ(g_13));
-        // which equals
-        + 0.5 * g23 * DDX(g_33);
-    G2_23 = 0.5 * g12 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g22 * DDZ(g_22)
-            + 0.5 * g23 * DDY(g_33);
-
-    G3_11 = 0.5 * g13 * DDX(g_11) + g23 * (DDX(g_12) - 0.5 * DDY(g_11))
-            + g33 * (DDX(g_13) - 0.5 * DDZ(g_11));
-    G3_22 = g13 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g23 * DDY(g_22)
-            + g33 * (DDY(g_23) - 0.5 * DDZ(g_22));
-    G3_33 = g13 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g23 * (DDZ(g_23) - 0.5 * DDY(g_33))
-            + 0.5 * g33 * DDZ(g_33);
-    G3_12 =
-        // 0.5 *g31*(DDY(g_11) + DDX(g_12) - DDX(g_12))
-        // which equals to
-        0.5 * g13 * DDY(g_11)
-        // + 0.5 *g32*(DDY(g_21) + DDX(g_22) - DDY(g_12))
-        // which equals to
-        + 0.5 * g23 * DDX(g_22)
-        //+ 0.5 *g33*(DDY(g_31) + DDX(g_32) - DDZ(g_12));
-        // which equals to
-        + 0.5 * g33 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
-    G3_13 = 0.5 * g13 * DDZ(g_11) + 0.5 * g23 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
-            + 0.5 * g33 * DDX(g_33);
-    G3_23 = 0.5 * g13 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g23 * DDZ(g_22)
-            + 0.5 * g33 * DDY(g_33);
-
-    G1 = (DDX(J * g11) + DDY(J.asField3DParallel() * g12) + DDZ(J * g13)) / J;
-    G2 = (DDX(J * g12) + DDY(J.asField3DParallel() * g22) + DDZ(J * g23)) / J;
-    G3 = (DDX(J * g13) + DDY(J.asField3DParallel() * g23) + DDZ(J * g33)) / J;
-
-    // Communicate christoffel symbol terms
-    output_progress.write("\tCommunicating connection terms\n");
-
-    localmesh->communicate_no_slices(G1_11, G1_22, G1_33, G1_12, G1_13, G1_23, G2_11,
-                                     G2_22, G2_33, G2_12, G2_13, G2_23, G3_11, G3_22,
-                                     G3_33, G3_12, G3_13, G3_23, G1, G2, G3);
-
-    // Set boundary guard cells of Christoffel symbol terms
-    // Ideally, when location is staggered, we would set the upper/outer boundary point
-    // correctly rather than by extrapolating here: e.g. if location==CELL_YLOW and we are
-    // at the upper y-boundary the x- and z-derivatives at yend+1 at the boundary can be
-    // calculated because the guard cells are available, while the y-derivative could be
-    // calculated from the CELL_CENTRE metric components (which have guard cells available
-    // past the boundary location). This would avoid the problem that the y-boundary on the
-    // CELL_YLOW grid is at a 'guard cell' location (yend+1).
-    // However, the above would require lots of special handling, so just extrapolate for
-    // now.
-    G1_11 = interpolateAndExtrapolate(G1_11, location, true, true, true, transform.get());
-    G1_22 = interpolateAndExtrapolate(G1_22, location, true, true, true, transform.get());
-    G1_33 = interpolateAndExtrapolate(G1_33, location, true, true, true, transform.get());
-    G1_12 = interpolateAndExtrapolate(G1_12, location, true, true, true, transform.get());
-    G1_13 = interpolateAndExtrapolate(G1_13, location, true, true, true, transform.get());
-    G1_23 = interpolateAndExtrapolate(G1_23, location, true, true, true, transform.get());
-
-    G2_11 = interpolateAndExtrapolate(G2_11, location, true, true, true, transform.get());
-    G2_22 = interpolateAndExtrapolate(G2_22, location, true, true, true, transform.get());
-    G2_33 = interpolateAndExtrapolate(G2_33, location, true, true, true, transform.get());
-    G2_12 = interpolateAndExtrapolate(G2_12, location, true, true, true, transform.get());
-    G2_13 = interpolateAndExtrapolate(G2_13, location, true, true, true, transform.get());
-    G2_23 = interpolateAndExtrapolate(G2_23, location, true, true, true, transform.get());
-
-    G3_11 = interpolateAndExtrapolate(G3_11, location, true, true, true, transform.get());
-    G3_22 = interpolateAndExtrapolate(G3_22, location, true, true, true, transform.get());
-    G3_33 = interpolateAndExtrapolate(G3_33, location, true, true, true, transform.get());
-    G3_12 = interpolateAndExtrapolate(G3_12, location, true, true, true, transform.get());
-    G3_13 = interpolateAndExtrapolate(G3_13, location, true, true, true, transform.get());
-    G3_23 = interpolateAndExtrapolate(G3_23, location, true, true, true, transform.get());
-
-    G1 = interpolateAndExtrapolate(G1, location, true, true, true, transform.get());
-    G2 = interpolateAndExtrapolate(G2, location, true, true, true, transform.get());
-    G3 = interpolateAndExtrapolate(G3, location, true, true, true, transform.get());
-  } else {
-    G1_11 = G1_22 = G1_33 = G1_12 = G1_13 = G1_23 =
-
-        G2_11 = G2_22 = G2_33 = G2_12 = G2_13 = G2_23 =
-
-            G3_11 = G3_22 = G3_33 = G3_12 = G3_13 = G3_23 =
-
-                G1 = G2 = G3 = BoutNaN;
-  }
-
-  //////////////////////////////////////////////////////
-  /// Non-uniform meshes. Need to use DDX, DDY
-
-  OPTION(Options::getRoot(), non_uniform, true);
-
-  Coordinates::FieldMetric d2x(localmesh), d2y(localmesh),
-      d2z(localmesh); // d^2 x / d i^2
-
-  // Read correction for non-uniform meshes
-  std::string suffix = getLocationSuffix(location);
-  if (location == CELL_CENTRE
-      or (!force_interpolate_from_centre and localmesh->sourceHasVar("dx" + suffix))) {
-    bool extrapolate_x = not localmesh->sourceHasXBoundaryGuards();
-    bool extrapolate_y = not localmesh->sourceHasYBoundaryGuards();
-
-    if (localmesh->get(d2x, "d2x" + suffix, 0.0, false, location)) {
-      output_warn.write(
-          "\tWARNING: differencing quantity 'd2x' not found. Calculating from dx\n");
-      d1_dx = bout::derivatives::index::DDX(FieldMetric{1. / dx}); // d/di(1/dx)
-
-      localmesh->communicate_no_slices(d1_dx);
-      d1_dx =
-          interpolateAndExtrapolate(d1_dx, location, true, true, true, transform.get());
-    } else {
-      d2x.setLocation(location);
-      // set boundary cells if necessary
-      d2x = interpolateAndExtrapolate(d2x, location, extrapolate_x, extrapolate_y, false,
-                                      transform.get());
-
-      d1_dx = -d2x / (dx * dx);
-    }
+  christoffel_symbols_cache.reset();
+  g_values_cache.reset();
 
-    if (localmesh->get(d2y, "d2y" + suffix, 0.0, false, location)) {
-      output_warn.write(
-          "\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
-      d1_dy = DDY(1. / dy.asField3DParallel()); // d/di(1/dy)
-
-      localmesh->communicate_no_slices(d1_dy);
-      d1_dy =
-          interpolateAndExtrapolate(d1_dy, location, true, true, true, transform.get());
-    } else {
-      d2y.setLocation(location);
-      // set boundary cells if necessary
-      d2y = interpolateAndExtrapolate(d2y, location, extrapolate_x, extrapolate_y, false,
-                                      transform.get());
-
-      d1_dy = -d2y / (dy * dy);
-    }
-
-#if BOUT_USE_METRIC_3D
-    if (localmesh->get(d2z, "d2z" + suffix, 0.0, false)) {
-      output_warn.write(
-          "\tWARNING: differencing quantity 'd2z' not found. Calculating from dz\n");
-      d1_dz = bout::derivatives::index::DDZ(FieldMetric{1. / dz});
-      localmesh->communicate_no_slices(d1_dz);
-      d1_dz =
-          interpolateAndExtrapolate(d1_dz, location, true, true, true, transform.get());
-    } else {
-      d2z.setLocation(location);
-      // set boundary cells if necessary
-      d2z = interpolateAndExtrapolate(d2z, location, extrapolate_x, extrapolate_y, false,
-                                      transform.get());
-
-      d1_dz = -d2z / (dz * dz);
-    }
-#else
-    d1_dz = 0;
-#endif
-  } else {
-    if (localmesh->get(d2x, "d2x", 0.0, false)) {
-      output_warn.write(
-          "\tWARNING: differencing quantity 'd2x' not found. Calculating from dx\n");
-      d1_dx = bout::derivatives::index::DDX(FieldMetric{1. / dx}); // d/di(1/dx)
-
-      localmesh->communicate_no_slices(d1_dx);
-      d1_dx =
-          interpolateAndExtrapolate(d1_dx, location, true, true, true, transform.get());
-    } else {
-      // Shift d2x to our location
-      d2x = interpolateAndExtrapolate(d2x, location, true, true, false, transform.get());
-
-      d1_dx = -d2x / (dx * dx);
-    }
-
-    if (localmesh->get(d2y, "d2y", 0.0, false)) {
-      output_warn.write(
-          "\tWARNING: differencing quantity 'd2y' not found. Calculating from dy\n");
-      d1_dy = DDY(FieldMetric{1. / dy}); // d/di(1/dy)
-
-      localmesh->communicate_no_slices(d1_dy);
-      d1_dy =
-          interpolateAndExtrapolate(d1_dy, location, true, true, true, transform.get());
-    } else {
-      // Shift d2y to our location
-      d2y = interpolateAndExtrapolate(d2y, location, true, true, false, transform.get());
-
-      d1_dy = -d2y / (dy * dy);
-    }
-
-#if BOUT_USE_METRIC_3D
-    if (localmesh->get(d2z, "d2z", 0.0, false)) {
-      output_warn.write(
-          "\tWARNING: differencing quantity 'd2z' not found. Calculating from dz\n");
-      d1_dz = bout::derivatives::index::DDZ(FieldMetric{1. / dz});
-
-      localmesh->communicate_no_slices(d1_dz);
-      d1_dz =
-          interpolateAndExtrapolate(d1_dz, location, true, true, true, transform.get());
-    } else {
-      // Shift d2z to our location
-      d2z = interpolateAndExtrapolate(d2z, location, true, true, false, transform.get());
-
-      d1_dz = -d2z / (dz * dz);
-    }
-#else
-    d1_dz = 0;
-#endif
-  }
-  localmesh->communicate_no_slices(d1_dx, d1_dy, d1_dz);
+  correctionForNonUniformMeshes(force_interpolate_from_centre);
 
   if (location == CELL_CENTRE && recalculate_staggered) {
     // Re-calculate interpolated Coordinates at staggered locations
     localmesh->recalculateStaggeredCoordinates();
   }
 
-  // Invalidate and recalculate cached variables and any accessor
   zlength_cache.reset();
   Grad2_par2_DDY_invSgCache.clear();
   invSgCache.reset();
@@ -926,156 +727,102 @@ int Coordinates::geometry(bool recalculate_staggered,
   _cell_area_zlow.reset();
   _cell_area_zhigh.reset();
   _cell_volume.reset();
-
-  return 0;
 }
 
-int Coordinates::calcCovariant(const std::string& region) {
-
-  // Make sure metric elements are allocated
-  g_11.allocate();
-  g_22.allocate();
-  g_33.allocate();
-  g_12.allocate();
-  g_13.allocate();
-  g_23.allocate();
-
-  g_11.setLocation(location);
-  g_22.setLocation(location);
-  g_33.setLocation(location);
-  g_12.setLocation(location);
-  g_13.setLocation(location);
-  g_23.setLocation(location);
-
-  // Perform inversion of g^{ij} to get g_{ij}
-  // NOTE: Currently this bit assumes that metric terms are Field2D objects
-
-  auto a = Matrix<BoutReal>(3, 3);
-
-  BOUT_FOR_SERIAL(i, g11.getRegion(region)) {
-    a(0, 0) = g11[i];
-    a(1, 1) = g22[i];
-    a(2, 2) = g33[i];
-
-    a(0, 1) = a(1, 0) = g12[i];
-    a(1, 2) = a(2, 1) = g23[i];
-    a(0, 2) = a(2, 0) = g13[i];
-
-    if (const auto det = bout::invert3x3(a); det.has_value()) {
-      output_error.write("\tERROR: metric tensor is singular at {}, determinant: {:e}\n",
-                         i, det.value());
-      return 1;
-    }
-
-    g_11[i] = a(0, 0);
-    g_22[i] = a(1, 1);
-    g_33[i] = a(2, 2);
+void Coordinates::correctionForNonUniformMeshes(bool force_interpolate_from_centre) {
+  OPTION(Options::getRoot(), non_uniform_, true);
 
-    g_12[i] = a(0, 1);
-    g_13[i] = a(0, 2);
-    g_23[i] = a(1, 2);
-  }
+  FieldMetric d2x(localmesh);
+  FieldMetric d2y(localmesh);
 
-  BoutReal maxerr;
-  maxerr = BOUTMAX(max(abs((g_11 * g11 + g_12 * g12 + g_13 * g13) - 1)),
-                   max(abs((g_12 * g12 + g_22 * g22 + g_23 * g23) - 1)),
-                   max(abs((g_13 * g13 + g_23 * g23 + g_33 * g33) - 1)));
-
-  output_info.write("\tLocal maximum error in diagonal inversion is {:e}\n", maxerr);
-
-  maxerr = BOUTMAX(max(abs(g_11 * g12 + g_12 * g22 + g_13 * g23)),
-                   max(abs(g_11 * g13 + g_12 * g23 + g_13 * g33)),
-                   max(abs(g_12 * g13 + g_22 * g23 + g_23 * g33)));
+  // Read correction for non-uniform meshes
+  const std::string suffix = getLocationSuffix(location);
 
-  output_info.write("\tLocal maximum error in off-diagonal inversion is {:e}\n", maxerr);
+  auto extrapolate_x = true;
+  auto extrapolate_y = true;
+  if (location == CELL_CENTRE
+      or (!force_interpolate_from_centre and localmesh->sourceHasVar("dx" + suffix))) {
+    extrapolate_x = not localmesh->sourceHasXBoundaryGuards();
+    extrapolate_y = not localmesh->sourceHasYBoundaryGuards();
+  }
 
-  return 0;
-}
+  if (localmesh->get(d2x, "d2x" + suffix, 0.0, false, location) != 0) {
+    output_warn.write("\tWARNING: differencing quantity 'd2x' not found. "
+                      "Calculating from dx\n");
+    d1_dx_ = bout::derivatives::index::DDX(FieldMetric{1. / dx()}); // d/di(1/dx)
 
-int Coordinates::calcContravariant(const std::string& region) {
+    localmesh->communicate_no_slices(d1_dx_);
+    d1_dx_ =
+        interpolateAndExtrapolate(d1_dx_, location, true, true, true, transform.get());
+  } else {
+    d2x.setLocation(location);
+    // set boundary cells if necessary
+    d2x = interpolateAndExtrapolate(d2x, location, extrapolate_x, extrapolate_y, false,
+                                    transform.get());
 
-  // Make sure metric elements are allocated
-  g11.allocate();
-  g22.allocate();
-  g33.allocate();
-  g12.allocate();
-  g13.allocate();
-  g23.allocate();
+    d1_dx_ = -d2x / (dx() * dx());
+  }
 
-  // Perform inversion of g_{ij} to get g^{ij}
-  // NOTE: Currently this bit assumes that metric terms are Field2D objects
+  if (localmesh->get(d2y, "d2y" + suffix, 0.0, false, location) != 0) {
+    output_warn.write("\tWARNING: differencing quantity 'd2y' not found. "
+                      "Calculating from dy\n");
+    d1_dy_ = DDY(1. / dy().asField3DParallel()); // d/di(1/dy)
 
-  auto a = Matrix<BoutReal>(3, 3);
+    localmesh->communicate_no_slices(d1_dy_);
+    d1_dy_ =
+        interpolateAndExtrapolate(d1_dy_, location, true, true, true, transform.get());
+  } else {
+    d2y.setLocation(location);
+    // set boundary cells if necessary
+    d2y = interpolateAndExtrapolate(d2y, location, extrapolate_x, extrapolate_y, false,
+                                    transform.get());
 
-  BOUT_FOR_SERIAL(i, g_11.getRegion(region)) {
-    a(0, 0) = g_11[i];
-    a(1, 1) = g_22[i];
-    a(2, 2) = g_33[i];
+    d1_dy_ = -d2y / (dy() * dy());
+  }
 
-    a(0, 1) = a(1, 0) = g_12[i];
-    a(1, 2) = a(2, 1) = g_23[i];
-    a(0, 2) = a(2, 0) = g_13[i];
+  if (bout::build::use_metric_3d) {
+    FieldMetric d2z(localmesh); // d^2 x / d i^2
+    if (localmesh->get(d2z, "d2z" + suffix, 0.0, false, location) != 0) {
+      output_warn.write("\tWARNING: differencing quantity 'd2z' not found. "
+                        "Calculating from dz\n");
+      d1_dz_ = bout::derivatives::index::DDZ(FieldMetric{1. / dz()});
+      localmesh->communicate(d1_dz_);
+      d1_dz_ =
+          interpolateAndExtrapolate(d1_dz_, location, true, true, true, transform.get());
+    } else {
+      d2z.setLocation(location);
+      // set boundary cells if necessary
+      d2z = interpolateAndExtrapolate(d2z, location, extrapolate_x, extrapolate_y, false,
+                                      transform.get());
 
-    if (const auto det = bout::invert3x3(a); det.has_value()) {
-      output_error.write("\tERROR: metric tensor is singular at {}, determinant: {:e}\n",
-                         i, det.value());
-      return 1;
+      d1_dz_ = -d2z / (dz() * dz());
     }
-
-    g11[i] = a(0, 0);
-    g22[i] = a(1, 1);
-    g33[i] = a(2, 2);
-
-    g12[i] = a(0, 1);
-    g13[i] = a(0, 2);
-    g23[i] = a(1, 2);
+  } else {
+    d1_dz_ = 0;
   }
 
-  BoutReal maxerr;
-  maxerr = BOUTMAX(max(abs((g_11 * g11 + g_12 * g12 + g_13 * g13) - 1)),
-                   max(abs((g_12 * g12 + g_22 * g22 + g_23 * g23) - 1)),
-                   max(abs((g_13 * g13 + g_23 * g23 + g_33 * g33) - 1)));
-
-  output_info.write("\tMaximum error in diagonal inversion is {:e}\n", maxerr);
-
-  maxerr = BOUTMAX(max(abs(g_11 * g12 + g_12 * g22 + g_13 * g23)),
-                   max(abs(g_11 * g13 + g_12 * g23 + g_13 * g33)),
-                   max(abs(g_12 * g13 + g_22 * g23 + g_23 * g33)));
-
-  output_info.write("\tMaximum error in off-diagonal inversion is {:e}\n", maxerr);
-  return 0;
+  localmesh->communicate(d1_dx_, d1_dy_, d1_dz_);
 }
 
-int Coordinates::jacobian() {
-
+Coordinates::FieldMetric Coordinates::recalculateJacobian() const {
   // calculate Jacobian using g^-1 = det[g^ij], J = sqrt(g)
+  const FieldMetric g_matrix = g11() * g22() * g33() + 2.0 * g12() * g13() * g23()
+                               - g11() * g23() * g23() - g22() * g13() * g13()
+                               - g33() * g12() * g12();
 
-  const bool extrapolate_x = not localmesh->sourceHasXBoundaryGuards();
-  const bool extrapolate_y = not localmesh->sourceHasYBoundaryGuards();
+  bout::checkPositive(g_matrix, "The determinant of g^ij", "RGN_NOBNDRY");
 
-  const FieldMetric g = g11 * g22 * g33 + 2.0 * g12 * g13 * g23 - g11 * g23 * g23
-                        - g22 * g13 * g13 - g33 * g12 * g12;
-
-  // Check that g is positive
-  bout::checkPositive(g, "The determinant of g^ij", "RGN_NOBNDRY");
-
-  J = 1. / sqrt(g);
-  // More robust to extrapolate derived quantities directly, rather than
-  // deriving from extrapolated covariant metric components
-  J = interpolateAndExtrapolate(J, location, extrapolate_x, extrapolate_y, false,
-                                transform.get());
-
-  Bxy = sqrt(g_22) / J;
-  Bxy = interpolateAndExtrapolate(Bxy, location, extrapolate_x, extrapolate_y, false,
-                                  transform.get());
+  return 1. / sqrt(g_matrix);
+}
 
-  return 0;
+Coordinates::FieldMetric Coordinates::recalculateBxy() const {
+  return sqrt(g_22()) / J();
 }
 
 namespace {
 // Utility function for fixing up guard cells of zShift
 void fixZShiftGuards(Field2D& zShift) {
-  auto localmesh = zShift.getMesh();
+  auto* localmesh = zShift.getMesh();
 
   // extrapolate into boundary guard cells if necessary
   zShift = interpolateAndExtrapolate(zShift, zShift.getLocation(),
@@ -1174,12 +921,12 @@ void Coordinates::setParallelTransform(Options* options) {
 
     // Flux Coordinate Independent method
     const bool fci_zperiodic = (*ptoptions)["z_periodic"].withDefault(true);
-    transform =
-        bout::utils::make_unique<FCITransform>(*localmesh, dy, fci_zperiodic, ptoptions);
-
+    transform = bout::utils::make_unique<FCITransform>(*localmesh, dy(), fci_zperiodic,
+                                                       ptoptions);
   } else {
-    throw BoutException(_("Unrecognised paralleltransform option.\n"
-                          "Valid choices are 'identity', 'shifted', 'fci'"));
+    throw BoutException(_f("Unrecognised paralleltransform option '{}'.\n"
+                           "Valid choices are 'identity', 'shifted', 'fci'"),
+                        ptstr);
   }
 }
 
@@ -1190,19 +937,19 @@ void Coordinates::setParallelTransform(Options* options) {
 
 Coordinates::FieldMetric Coordinates::DDX(const Field2D& f, CELL_LOC loc,
                                           const std::string& method,
-                                          const std::string& region) {
+                                          const std::string& region) const {
   ASSERT1(location == loc || loc == CELL_DEFAULT);
-  return bout::derivatives::index::DDX(f, loc, method, region) / dx;
+  return bout::derivatives::index::DDX(f, loc, method, region) / dx();
 }
 Field3D Coordinates::DDX(const Field3D& f, CELL_LOC outloc, const std::string& method,
-                         const std::string& region) {
+                         const std::string& region) const {
 
   auto result = bout::derivatives::index::DDX(f, outloc, method, region);
-  result /= dx;
+  result /= dx();
 
   if (f.getMesh()->IncIntShear) {
     // Using BOUT-06 style shifting
-    result += IntShiftTorsion * DDZ(f, outloc, method, region);
+    result += IntShiftTorsion() * DDZ(f, outloc, method, region);
   }
 
   return result;
@@ -1212,17 +959,17 @@ Coordinates::FieldMetric Coordinates::DDY(const Field2D& f, CELL_LOC loc,
                                           const std::string& method,
                                           const std::string& region) const {
   ASSERT1(location == loc || loc == CELL_DEFAULT);
-  return bout::derivatives::index::DDY(f, loc, method, region) / dy;
+  return bout::derivatives::index::DDY(f, loc, method, region) / dy();
 }
 
 Field3D Coordinates::DDY(const Field3DParallel& f, CELL_LOC outloc,
                          const std::string& method, const std::string& region) const {
-  return bout::derivatives::index::DDY(f, outloc, method, region) / dy;
+  return bout::derivatives::index::DDY(f, outloc, method, region) / dy();
 };
 
 Coordinates::FieldMetric Coordinates::DDZ(const Field2D& f, CELL_LOC loc,
                                           const std::string& UNUSED(method),
-                                          const std::string& UNUSED(region)) {
+                                          const std::string& UNUSED(region)) const {
   ASSERT1(location == loc || loc == CELL_DEFAULT);
   ASSERT1(f.getMesh() == localmesh);
   if (loc == CELL_DEFAULT) {
@@ -1231,8 +978,8 @@ Coordinates::FieldMetric Coordinates::DDZ(const Field2D& f, CELL_LOC loc,
   return zeroFrom(f).setLocation(loc);
 }
 Field3D Coordinates::DDZ(const Field3D& f, CELL_LOC outloc, const std::string& method,
-                         const std::string& region) {
-  return bout::derivatives::index::DDZ(f, outloc, method, region) / dz;
+                         const std::string& region) const {
+  return bout::derivatives::index::DDZ(f, outloc, method, region) / dz();
 };
 
 /////////////////////////////////////////////////////////
@@ -1241,7 +988,6 @@ Field3D Coordinates::DDZ(const Field3D& f, CELL_LOC outloc, const std::string& m
 Coordinates::FieldMetric Coordinates::Grad_par(const Field2D& var,
                                                [[maybe_unused]] CELL_LOC outloc,
                                                const std::string& UNUSED(method)) {
-
   ASSERT1(location == outloc
           || (outloc == CELL_DEFAULT && location == var.getLocation()));
 
@@ -1285,9 +1031,9 @@ Coordinates::FieldMetric Coordinates::Div_par(const Field2D& f, CELL_LOC outloc,
 
   // Need Bxy at location of f, which might be different from location of this
   // Coordinates object
-  auto Bxy_floc = f.getCoordinates()->Bxy;
+  auto Bxy_floc = f.getCoordinates()->Bxy();
 
-  return Bxy * Grad_par(FieldMetric{f / Bxy_floc}, outloc, method);
+  return Bxy_ * Grad_par(FieldMetric{f / Bxy_floc}, outloc, method);
 }
 
 Field3D Coordinates::Div_par(const Field3DParallel& f, CELL_LOC outloc,
@@ -1297,9 +1043,9 @@ Field3D Coordinates::Div_par(const Field3DParallel& f, CELL_LOC outloc,
 
   // Need Bxy at location of f, which might be different from location of this
   // Coordinates object
-  const auto& Bxy_floc = f.getCoordinates()->Bxy;
+  const auto& Bxy_floc = f.getCoordinates()->Bxy();
 
-  return Bxy * Grad_par(f / Bxy_floc, outloc, method);
+  return Bxy() * Grad_par(f / Bxy_floc, outloc, method);
 }
 
 /////////////////////////////////////////////////////////
@@ -1312,7 +1058,7 @@ Coordinates::FieldMetric Coordinates::Grad2_par2(const Field2D& f, CELL_LOC outl
   ASSERT1(location == outloc || (outloc == CELL_DEFAULT && location == f.getLocation()));
 
   auto result = Grad2_par2_DDY_invSg(outloc, method) * DDY(f, outloc, method)
-                + D2DY2(f, outloc, method) / g_22;
+                + D2DY2(f, outloc, method) / g_22();
 
   return result;
 }
@@ -1327,7 +1073,7 @@ Field3D Coordinates::Grad2_par2(const Field3DParallel& f, CELL_LOC outloc,
 
   Field3D result = ::DDY(f, outloc, method);
 
-  Field3D r2 = D2DY2(f, outloc, method) / g_22;
+  Field3D r2 = D2DY2(f, outloc, method) / g_22();
 
   result = Grad2_par2_DDY_invSg(outloc, method) * result + r2;
 
@@ -1346,9 +1092,7 @@ Coordinates::FieldMetric Coordinates::Delp2(const Field2D& f, CELL_LOC outloc,
 
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
-  auto result = G1 * DDX(f, outloc) + g11 * D2DX2(f, outloc);
-
-  return result;
+  return G1() * DDX(f, outloc) + g11() * D2DX2(f, outloc);
 }
 
 Field3D Coordinates::Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
@@ -1364,7 +1108,7 @@ Field3D Coordinates::Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
     // copy mesh, location, etc
     return f * 0;
   }
-  ASSERT2(localmesh->xstart > 0); // Need at least one guard cell
+  ASSERT2(localmesh->xstart > 0); // Need at least one guard cell;
 
   Field3D result{emptyFrom(f).setLocation(outloc)};
 
@@ -1407,9 +1151,10 @@ Field3D Coordinates::Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
       }
     }
   } else {
-    result = G1 * ::DDX(f, outloc) + G3 * ::DDZ(f, outloc) + g11 * ::D2DX2(f, outloc)
-             + g33 * ::D2DZ2(f, outloc) + 2 * g13 * ::D2DXDZ(f, outloc);
-  };
+    result = G1() * ::DDX(f, outloc) + G3() * ::DDZ(f, outloc)
+             + g11() * ::D2DX2(f, outloc) + g33() * ::D2DZ2(f, outloc)
+             + 2 * g13() * ::D2DXDZ(f, outloc);
+  }
 
   ASSERT2(result.getLocation() == outloc);
 
@@ -1433,7 +1178,7 @@ FieldPerp Coordinates::Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
 
   FieldPerp result{emptyFrom(f).setLocation(outloc)};
 
-  int jy = f.getIndex();
+  const int jy = f.getIndex();
   result.setIndex(jy);
 
   if (useFFT and localmesh->getNZPE() == 1) {
@@ -1480,14 +1225,14 @@ FieldPerp Coordinates::Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
 
 Coordinates::FieldMetric Coordinates::Laplace_par(const Field2D& f, CELL_LOC outloc) {
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-  return D2DY2(f, outloc) / g_22
-         + DDY(FieldMetric{J / g_22}, outloc) * DDY(f, outloc) / J;
+  return D2DY2(f, outloc) / g_22()
+         + DDY(FieldMetric{J() / g_22()}, outloc) * DDY(f, outloc) / J();
 }
 
 Field3D Coordinates::Laplace_par(const Field3DParallel& f, CELL_LOC outloc) {
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-  return D2DY2(f, outloc) / g_22
-         + DDY(J.asField3DParallel() / g_22, outloc) * ::DDY(f, outloc) / J;
+  return D2DY2(f, outloc) / g_22()
+         + DDY(J().asField3DParallel() / g_22(), outloc) * ::DDY(f, outloc) / J();
 }
 
 // Full Laplacian operator on scalar field
@@ -1498,13 +1243,11 @@ Coordinates::FieldMetric Coordinates::Laplace(const Field2D& f, CELL_LOC outloc,
 
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
-  auto result = G1 * DDX(f, outloc) + G2 * DDY(f, outloc) + g11 * D2DX2(f, outloc)
-                + g22 * D2DY2(f, outloc)
-                + 2.0 * g12
-                      * D2DXDY(f, outloc, "DEFAULT", "RGN_NOBNDRY",
-                               dfdy_boundary_conditions, dfdy_dy_region);
-
-  return result;
+  return G1() * DDX(f, outloc) + G2() * DDY(f, outloc) + g11() * D2DX2(f, outloc)
+         + g22() * D2DY2(f, outloc)
+         + 2.0 * g12()
+               * ::D2DXDY(f, outloc, "DEFAULT", "RGN_NOBNDRY", dfdy_boundary_conditions,
+                          dfdy_dy_region);
 }
 
 Field3D Coordinates::Laplace(const Field3DParallel& f, CELL_LOC outloc,
@@ -1513,23 +1256,20 @@ Field3D Coordinates::Laplace(const Field3DParallel& f, CELL_LOC outloc,
 
   ASSERT1(location == outloc || outloc == CELL_DEFAULT);
 
-  Field3D result = G1 * ::DDX(f, outloc) + G2 * ::DDY(f, outloc) + G3 * ::DDZ(f, outloc)
-                   + g11 * D2DX2(f, outloc) + g22 * D2DY2(f, outloc)
-                   + g33 * D2DZ2(f, outloc)
-                   + 2.0
-                         * (g12
-                                * D2DXDY(f, outloc, "DEFAULT", "RGN_NOBNDRY",
-                                         dfdy_boundary_conditions, dfdy_dy_region)
-                            + g13 * D2DXDZ(f, outloc) + g23 * D2DYDZ(f, outloc));
-
-  return result;
+  return G1() * ::DDX(f, outloc) + G2() * ::DDY(f, outloc) + G3() * ::DDZ(f, outloc)
+         + g11() * ::D2DX2(f, outloc) + g22() * ::D2DY2(f, outloc)
+         + g33() * ::D2DZ2(f, outloc)
+         + 2.0
+               * (g12()
+                      * D2DXDY(f, outloc, "DEFAULT", "RGN_NOBNDRY",
+                               dfdy_boundary_conditions, dfdy_dy_region)
+                  + g13() * ::D2DXDZ(f, outloc) + g23() * ::D2DYDZ(f, outloc));
 }
 
 // Full perpendicular Laplacian, in form of inverse of Laplacian operator in LaplaceXY
 // solver
 Field2D Coordinates::Laplace_perpXY([[maybe_unused]] const Field2D& A,
-                                    [[maybe_unused]] const Field2D& f) {
-
+                                    [[maybe_unused]] const Field2D& f) const {
 #if not(BOUT_USE_METRIC_3D)
   Field2D result;
   result.allocate();
@@ -1539,45 +1279,45 @@ Field2D Coordinates::Laplace_perpXY([[maybe_unused]] const Field2D& A,
     // outer x boundary
     const auto outer_x_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.xp()]); };
     const BoutReal outer_x_A = outer_x_avg(A);
-    const BoutReal outer_x_J = outer_x_avg(J);
-    const BoutReal outer_x_g11 = outer_x_avg(g11);
-    const BoutReal outer_x_dx = outer_x_avg(dx);
+    const BoutReal outer_x_J = outer_x_avg(J());
+    const BoutReal outer_x_g11 = outer_x_avg(g11());
+    const BoutReal outer_x_dx = outer_x_avg(dx());
     const BoutReal outer_x_value =
-        outer_x_A * outer_x_J * outer_x_g11 / (J[i] * outer_x_dx * dx[i]);
+        outer_x_A * outer_x_J * outer_x_g11 / (J()[i] * outer_x_dx * dx()[i]);
     result[i] += outer_x_value * (f[i.xp()] - f[i]);
 
     // inner x boundary
     const auto inner_x_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.xm()]); };
     const BoutReal inner_x_A = inner_x_avg(A);
-    const BoutReal inner_x_J = inner_x_avg(J);
-    const BoutReal inner_x_g11 = inner_x_avg(g11);
-    const BoutReal inner_x_dx = inner_x_avg(dx);
+    const BoutReal inner_x_J = inner_x_avg(J());
+    const BoutReal inner_x_g11 = inner_x_avg(g11());
+    const BoutReal inner_x_dx = inner_x_avg(dx());
     const BoutReal inner_x_value =
-        inner_x_A * inner_x_J * inner_x_g11 / (J[i] * inner_x_dx * dx[i]);
+        inner_x_A * inner_x_J * inner_x_g11 / (J()[i] * inner_x_dx * dx()[i]);
     result[i] += inner_x_value * (f[i.xm()] - f[i]);
 
     // upper y boundary
     const auto upper_y_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.yp()]); };
     const BoutReal upper_y_A = upper_y_avg(A);
-    const BoutReal upper_y_J = upper_y_avg(J);
-    const BoutReal upper_y_g_22 = upper_y_avg(g_22);
-    const BoutReal upper_y_g23 = upper_y_avg(g23);
-    const BoutReal upper_y_g_23 = upper_y_avg(g_23);
-    const BoutReal upper_y_dy = upper_y_avg(dy);
+    const BoutReal upper_y_J = upper_y_avg(J());
+    const BoutReal upper_y_g_22 = upper_y_avg(g_22());
+    const BoutReal upper_y_g23 = upper_y_avg(g23());
+    const BoutReal upper_y_g_23 = upper_y_avg(g_23());
+    const BoutReal upper_y_dy = upper_y_avg(dy());
     const BoutReal upper_y_value = -upper_y_A * upper_y_J * upper_y_g23 * upper_y_g_23
-                                   / (upper_y_g_22 * J[i] * upper_y_dy * dy[i]);
+                                   / (upper_y_g_22 * J()[i] * upper_y_dy * dy()[i]);
     result[i] += upper_y_value * (f[i.yp()] - f[i]);
 
     // lower y boundary
     const auto lower_y_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.ym()]); };
     const BoutReal lower_y_A = lower_y_avg(A);
-    const BoutReal lower_y_J = lower_y_avg(J);
-    const BoutReal lower_y_g_22 = lower_y_avg(g_22);
-    const BoutReal lower_y_g23 = lower_y_avg(g23);
-    const BoutReal lower_y_g_23 = lower_y_avg(g_23);
-    const BoutReal lower_y_dy = lower_y_avg(dy);
+    const BoutReal lower_y_J = lower_y_avg(J());
+    const BoutReal lower_y_g_22 = lower_y_avg(g_22());
+    const BoutReal lower_y_g23 = lower_y_avg(g23());
+    const BoutReal lower_y_g_23 = lower_y_avg(g_23());
+    const BoutReal lower_y_dy = lower_y_avg(dy());
     const BoutReal lower_y_value = -lower_y_A * lower_y_J * lower_y_g23 * lower_y_g_23
-                                   / (lower_y_g_22 * J[i] * lower_y_dy * dy[i]);
+                                   / (lower_y_g_22 * J()[i] * lower_y_dy * dy()[i]);
     result[i] += lower_y_value * (f[i.ym()] - f[i]);
   }
 
@@ -1587,10 +1327,43 @@ Field2D Coordinates::Laplace_perpXY([[maybe_unused]] const Field2D& A,
 #endif
 }
 
+const ChristoffelSymbols& Coordinates::christoffel_symbols() const {
+  if (christoffel_symbols_cache == nullptr) {
+    christoffel_symbols_cache = std::make_unique<ChristoffelSymbols>(*this);
+    // Set boundary guard cells of Christoffel symbol terms
+    // Ideally, when location is staggered, we would set the upper/outer boundary point
+    // correctly rather than by extrapolating here: e.g. if location==CELL_YLOW and we are
+    // at the upper y-boundary the x- and z-derivatives at yend+1 at the boundary can be
+    // calculated because the guard cells are available, while the y-derivative could be
+    // calculated from the CELL_CENTRE metric components (which have guard cells available
+    // past the boundary location). This would avoid the problem that the y-boundary on the
+    // CELL_YLOW grid is at a 'guard cell' location (yend+1).
+    // However, the above would require lots of special handling, so just extrapolate for
+    // now.
+
+    christoffel_symbols_cache->map([this](const FieldMetric& component) {
+      return interpolateAndExtrapolate(component, location, true, true, false,
+                                       transform.get());
+    });
+  }
+  return *christoffel_symbols_cache;
+}
+
+GValues& Coordinates::g_values() const {
+  if (g_values_cache == nullptr) {
+    g_values_cache = std::make_unique<GValues>(*this);
+    g_values_cache->map([this](const FieldMetric& component) {
+      return interpolateAndExtrapolate(component, location, true, true, true,
+                                       transform.get());
+    });
+  }
+  return *g_values_cache;
+}
+
 const Coordinates::FieldMetric& Coordinates::invSg() const {
   if (invSgCache == nullptr) {
     auto ptr = std::make_unique<Coordinates::FieldMetric>();
-    (*ptr) = 1.0 / sqrt(g_22);
+    (*ptr) = 1.0 / sqrt(g_22());
     invSgCache = std::move(ptr);
   }
   return *invSgCache;
@@ -1598,6 +1371,7 @@ const Coordinates::FieldMetric& Coordinates::invSg() const {
 
 const Coordinates::FieldMetric&
 Coordinates::Grad2_par2_DDY_invSg(CELL_LOC outloc, const std::string& method) const {
+
   if (auto search = Grad2_par2_DDY_invSgCache.find(method);
       search != Grad2_par2_DDY_invSgCache.end()) {
     return *search->second;
@@ -1615,107 +1389,27 @@ Coordinates::Grad2_par2_DDY_invSg(CELL_LOC outloc, const std::string& method) co
   return *Grad2_par2_DDY_invSgCache[method];
 }
 
-void Coordinates::checkCovariant() {
-  // Diagonal metric components should be finite
-  bout::checkFinite(g_11, "g_11", "RGN_NOCORNERS");
-  bout::checkFinite(g_22, "g_22", "RGN_NOCORNERS");
-  bout::checkFinite(g_33, "g_33", "RGN_NOCORNERS");
-  if (g_11.hasParallelSlices() && &g_11.ynext(1) != &g_11) {
-    for (int dy = 1; dy <= localmesh->ystart; ++dy) {
-      for (const auto sign : {1, -1}) {
-        bout::checkFinite(g_11.ynext(sign * dy), "g_11.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkFinite(g_22.ynext(sign * dy), "g_22.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkFinite(g_33.ynext(sign * dy), "g_33.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-      }
-    }
-  }
-  // Diagonal metric components should be positive
-  bout::checkPositive(g_11, "g_11", "RGN_NOCORNERS");
-  bout::checkPositive(g_22, "g_22", "RGN_NOCORNERS");
-  bout::checkPositive(g_33, "g_33", "RGN_NOCORNERS");
-  if (g_11.hasParallelSlices() && &g_11.ynext(1) != &g_11) {
-    for (int dy = 1; dy <= localmesh->ystart; ++dy) {
-      for (const auto sign : {1, -1}) {
-        bout::checkPositive(g_11.ynext(sign * dy), "g_11.ynext",
-                            fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkPositive(g_22.ynext(sign * dy), "g_22.ynext",
-                            fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkPositive(g_33.ynext(sign * dy), "g_33.ynext",
-                            fmt::format("RGN_YPAR_{:+d}", sign * dy));
-      }
-    }
-  }
+void Coordinates::checkCovariant() { covariantMetricTensor.check(localmesh->ystart); }
 
-  // Off-diagonal metric components should be finite
-  bout::checkFinite(g_12, "g_12", "RGN_NOCORNERS");
-  bout::checkFinite(g_13, "g_13", "RGN_NOCORNERS");
-  bout::checkFinite(g_23, "g_23", "RGN_NOCORNERS");
-  if (g_23.hasParallelSlices() && &g_23.ynext(1) != &g_23) {
-    for (int dy = 1; dy <= localmesh->ystart; ++dy) {
-      for (const auto sign : {1, -1}) {
-        bout::checkFinite(g_12.ynext(sign * dy), "g_12.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkFinite(g_13.ynext(sign * dy), "g_13.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkFinite(g_23.ynext(sign * dy), "g_23.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-      }
-    }
-  }
+void Coordinates::checkContravariant() {
+  contravariantMetricTensor.check(localmesh->ystart);
 }
 
-void Coordinates::checkContravariant() {
-  // Diagonal metric components should be finite
-  bout::checkFinite(g11, "g11", "RGN_NOCORNERS");
-  bout::checkFinite(g22, "g22", "RGN_NOCORNERS");
-  bout::checkFinite(g33, "g33", "RGN_NOCORNERS");
-  if (g11.hasParallelSlices() && &g11.ynext(1) != &g11) {
-    for (int dy = 1; dy <= localmesh->ystart; ++dy) {
-      for (const auto sign : {1, -1}) {
-        bout::checkFinite(g11.ynext(sign * dy), "g11.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkFinite(g22.ynext(sign * dy), "g22.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkFinite(g33.ynext(sign * dy), "g33.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-      }
-    }
-  }
-  // Diagonal metric components should be positive
-  bout::checkPositive(g11, "g11", "RGN_NOCORNERS");
-  bout::checkPositive(g22, "g22", "RGN_NOCORNERS");
-  bout::checkPositive(g33, "g33", "RGN_NOCORNERS");
-  if (g11.hasParallelSlices() && &g11.ynext(1) != &g11) {
-    for (int dy = 1; dy <= localmesh->ystart; ++dy) {
-      for (const auto sign : {1, -1}) {
-        bout::checkPositive(g11.ynext(sign * dy), "g11.ynext",
-                            fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkPositive(g22.ynext(sign * dy), "g22.ynext",
-                            fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkPositive(g33.ynext(sign * dy), "g33.ynext",
-                            fmt::format("RGN_YPAR_{:+d}", sign * dy));
-      }
-    }
+const Coordinates::FieldMetric& Coordinates::J() const {
+  if (jacobian_cache == nullptr) {
+    jacobian_cache = std::make_unique<FieldMetric>(recalculateJacobian());
   }
+  return *jacobian_cache;
+}
 
-  // Off-diagonal metric components should be finite
-  bout::checkFinite(g12, "g12", "RGN_NOCORNERS");
-  bout::checkFinite(g13, "g13", "RGN_NOCORNERS");
-  bout::checkFinite(g23, "g23", "RGN_NOCORNERS");
-  if (g23.hasParallelSlices() && &g23.ynext(1) != &g23) {
-    for (int dy = 1; dy <= localmesh->ystart; ++dy) {
-      for (const auto sign : {1, -1}) {
-        bout::checkFinite(g12.ynext(sign * dy), "g12.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkFinite(g13.ynext(sign * dy), "g13.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-        bout::checkFinite(g23.ynext(sign * dy), "g23.ynext",
-                          fmt::format("RGN_YPAR_{:+d}", sign * dy));
-      }
-    }
+void Coordinates::setJ(const FieldMetric& J, const bool communicate) {
+  bout::checkFinite(J, "J", "RGN_NOCORNERS");
+  bout::checkPositive(J, "J", "RGN_NOCORNERS");
+
+  //TODO: Calculate J and check value is close
+  jacobian_cache = std::make_unique<FieldMetric>(J);
+  if (communicate) {
+    localmesh->communicate_no_slices(*jacobian_cache);
   }
 }
 
@@ -1726,18 +1420,16 @@ const Coordinates::FieldMetric& Coordinates::g_22_ylow() const {
   BOUT_OMP_SAFE(critical)
   {
     if (!_g_22_ylow.has_value()) {
-      _g_22_ylow.emplace(emptyFrom(g_22));
-      //_g_22_ylow->setLocation(CELL_YLOW);
-      auto* mesh = Bxy.getMesh();
-      if (Bxy.isFci()) {
-        if (mesh->get(_g_22_ylow.value(), "g_22_cell_ylow", 0.0, false) != 0) {
+      _g_22_ylow.emplace(emptyFrom(g_22()));
+      if (Bxy().isFci()) {
+        if (localmesh->get(_g_22_ylow.value(), "g_22_cell_ylow", 0.0, false) != 0) {
           throw BoutException("The grid file does not contain `g_22_cell_ylow`.");
         }
       } else {
-        ASSERT0(mesh->ystart > 0);
-        BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
+        ASSERT0(localmesh->ystart > 0);
+        BOUT_FOR(i, g_22().getRegion("RGN_NOY")) {
           _g_22_ylow.value()[i] =
-              SQ(0.5 * (std::sqrt(g_22[i]) + std::sqrt(g_22[i.ym()])));
+              SQ(0.5 * (std::sqrt(g_22()[i]) + std::sqrt(g_22()[i.ym()])));
         }
       }
     }
@@ -1752,17 +1444,16 @@ const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
   BOUT_OMP_SAFE(critical)
   {
     if (!_g_22_yhigh.has_value()) {
-      _g_22_yhigh.emplace(emptyFrom(g_22));
-      auto* mesh = Bxy.getMesh();
-      if (Bxy.isFci()) {
-        if (mesh->get(_g_22_yhigh.value(), "g_22_cell_yhigh", 0.0, false) != 0) {
+      _g_22_yhigh.emplace(emptyFrom(g_22()));
+      if (Bxy().isFci()) {
+        if (localmesh->get(_g_22_yhigh.value(), "g_22_cell_yhigh", 0.0, false) != 0) {
           throw BoutException("The grid file does not contain `g_22_cell_yhigh`.");
         }
       } else {
-        ASSERT0(mesh->ystart > 0);
-        BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
+        ASSERT0(localmesh->ystart > 0);
+        BOUT_FOR(i, g_22().getRegion("RGN_NOY")) {
           _g_22_yhigh.value()[i] =
-              SQ(0.5 * (std::sqrt(g_22[i]) + std::sqrt(g_22[i.yp()])));
+              SQ(0.5 * (std::sqrt(g_22()[i]) + std::sqrt(g_22()[i.yp()])));
         }
       }
     }
@@ -1774,13 +1465,12 @@ void Coordinates::_compute_cell_area_x() const {
   BOUT_OMP_SAFE(critical)
   {
     if (!_cell_area_xlow.has_value()) {
-      const FieldMetric area_centre = J / sqrt(g_11) * dy * dz;
+      const FieldMetric area_centre = J() / sqrt(g_11()) * dy_ * dz_;
       _cell_area_xlow.emplace(emptyFrom(area_centre));
       _cell_area_xhigh.emplace(emptyFrom(area_centre));
       // We cannot setLocation, as that would trigger the computation of staggered
       // metrics.
-      auto* mesh = Bxy.getMesh();
-      ASSERT0(mesh->xstart > 0);
+      ASSERT0(localmesh->xstart > 0);
       BOUT_FOR(i, area_centre.getRegion("RGN_NOX")) {
         (*_cell_area_xlow)[i] = 0.5 * (area_centre[i] + area_centre[i.xm()]);
         (*_cell_area_xhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.xp()]);
@@ -1793,48 +1483,47 @@ void Coordinates::_compute_cell_area_y() const {
   BOUT_OMP_SAFE(critical)
   {
     if (!_cell_area_ylow.has_value()) {
-      auto* mesh = Bxy.getMesh();
-      if (g_11.isFci()) {
-        const FieldMetric jxz_centre = J / sqrt(g_22);
+      if (g_11().isFci()) {
+        const FieldMetric jxz_centre = J() / sqrt(g_22());
         auto jxz_ylow = emptyFrom(jxz_centre);
         auto jxz_yhigh = emptyFrom(jxz_centre);
 
         auto By_c = emptyFrom(jxz_centre);
         auto By_h = emptyFrom(jxz_yhigh);
         auto By_l = emptyFrom(jxz_ylow);
-        if (mesh->get(By_c, "By", 0.0, false, CELL_CENTRE) != 0) {
+        if (localmesh->get(By_c, "By", 0.0, false, CELL_CENTRE) != 0) {
           throw BoutException("The grid file does not contain `By`.");
         }
-        if (mesh->get(By_l, "By_cell_ylow", 0.0, false) != 0) {
+        if (localmesh->get(By_l, "By_cell_ylow", 0.0, false) != 0) {
           throw BoutException("The grid file does not contain `By_cell_ylow`.");
         }
-        if (mesh->get(By_h, "By_cell_yhigh", 0.0, false) != 0) {
+        if (localmesh->get(By_h, "By_cell_yhigh", 0.0, false) != 0) {
           throw BoutException("The grid file does not contain `By_cell_yhigh`.");
         }
         BOUT_FOR(i, By_c.getRegion("RGN_NOY")) {
           jxz_ylow[i] = By_c[i] / By_l[i] * jxz_centre[i];
           jxz_yhigh[i] = By_c[i] / By_h[i] * jxz_centre[i];
         }
-        ASSERT3(isUniform(dx, true, "RGN_ALL"));
-        ASSERT2(isUniform(dx, false, "RGN_ALL"));
-        ASSERT3(isUniform(dz, true, "RGN_ALL"));
-        ASSERT2(isUniform(dz, false, "RGN_ALL"));
-        _cell_area_ylow.emplace(jxz_ylow * dx * dz);
-        _cell_area_yhigh.emplace(jxz_yhigh * dx * dz);
+        ASSERT3(isUniform(dx_, true, "RGN_ALL"));
+        ASSERT2(isUniform(dx_, false, "RGN_ALL"));
+        ASSERT3(isUniform(dz_, true, "RGN_ALL"));
+        ASSERT2(isUniform(dz_, false, "RGN_ALL"));
+        _cell_area_ylow.emplace(jxz_ylow * dx_ * dz_);
+        _cell_area_yhigh.emplace(jxz_yhigh * dx_ * dz_);
       } else {
         // Field aligned
-        const FieldMetric area_centre = J / sqrt(g_22) * dx * dz;
+        const FieldMetric area_centre = J() / sqrt(g_22()) * dx_ * dz_;
         _cell_area_ylow.emplace(emptyFrom(area_centre));
         _cell_area_yhigh.emplace(emptyFrom(area_centre));
         // We cannot setLocation, as that would trigger the computation of staggered
         // metrics.
-        BOUT_FOR(i, mesh->getRegion("RGN_ALL")) {
+        BOUT_FOR(i, localmesh->getRegion("RGN_ALL")) {
           if (i.y() > 0) {
             (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
           } else {
             (*_cell_area_ylow)[i] = BoutNaN;
           }
-          if (i.y() < mesh->LocalNy - 1) {
+          if (i.y() < localmesh->LocalNy - 1) {
             (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
           } else {
             (*_cell_area_yhigh)[i] = BoutNaN;
@@ -1849,7 +1538,7 @@ void Coordinates::_compute_cell_area_z() const {
   BOUT_OMP_SAFE(critical)
   {
     if (!_cell_area_zlow.has_value()) {
-      const FieldMetric area_centre = J / sqrt(g_33) * dx * dy;
+      const FieldMetric area_centre = J() / sqrt(g_33()) * dx_ * dy_;
       _cell_area_zlow.emplace(emptyFrom(area_centre));
       _cell_area_zhigh.emplace(emptyFrom(area_centre));
       // We cannot setLocation, as that would trigger the computation of staggered
@@ -1866,7 +1555,7 @@ void Coordinates::_compute_cell_volume() const {
   BOUT_OMP_SAFE(critical)
   {
     if (!_cell_volume.has_value()) {
-      _cell_volume.emplace(J * dx * dy * dz);
+      _cell_volume.emplace(*jacobian_cache * dx_ * dy_ * dz_);
     }
   }
 }
@@ -1874,3 +1563,47 @@ void Coordinates::_compute_cell_volume() const {
 std::shared_ptr<YBoundary> Coordinates::makeYBoundary(YBndryType type) const {
   return std::make_shared<YBoundary>(type, localoptions, *localmesh);
 }
+
+void Coordinates::setBxy(FieldMetric Bxy, const bool communicate) {
+  //TODO: Calculate Bxy and check value is close
+  Bxy_ = std::move(Bxy);
+  if (communicate) {
+    localmesh->communicate_no_slices(Bxy_);
+  }
+}
+
+void Coordinates::setContravariantMetricTensor(
+    const ContravariantMetricTensor& metric_tensor, const std::string& region,
+    bool recalculate_staggered, bool force_interpolate_from_centre) {
+  contravariantMetricTensor = metric_tensor;
+  covariantMetricTensor = contravariantMetricTensor.inverse(region);
+  recalculateAndReset(recalculate_staggered, force_interpolate_from_centre);
+}
+
+void Coordinates::setCovariantMetricTensor(const CovariantMetricTensor& metric_tensor,
+                                           const std::string& region,
+                                           bool recalculate_staggered,
+                                           bool force_interpolate_from_centre) {
+  covariantMetricTensor = metric_tensor;
+  contravariantMetricTensor = covariantMetricTensor.inverse(region);
+  recalculateAndReset(recalculate_staggered, force_interpolate_from_centre);
+}
+
+void Coordinates::setMetricTensor(
+    const ContravariantMetricTensor& contravariant_metric_tensor,
+    const CovariantMetricTensor& covariant_metric_tensor) {
+  contravariantMetricTensor = contravariant_metric_tensor;
+  covariantMetricTensor = covariant_metric_tensor;
+}
+
+void Coordinates::communicateMetricTensor() {
+  contravariantMetricTensor.communicate();
+  covariantMetricTensor.communicate();
+}
+
+void Coordinates::communicateDz() { localmesh->communicate(dz_); }
+
+void Coordinates::splitBxyParallelSlices() {
+  Bxy_.splitParallelSlices();
+  Bxy_.yup() = Bxy_.ydown() = Bxy_;
+}
diff --git a/src/mesh/coordinates_accessor.cxx b/src/mesh/coordinates_accessor.cxx
index efc27e9715..0f11906c21 100644
--- a/src/mesh/coordinates_accessor.cxx
+++ b/src/mesh/coordinates_accessor.cxx
@@ -18,7 +18,7 @@ CoordinatesAccessor::CoordinatesAccessor(const Coordinates* coords) {
   ASSERT0(coords != nullptr);
 
   // Size of the mesh in Z. Used to convert 3D -> 2D index
-  Mesh* mesh = coords->dx.getMesh();
+  Mesh* mesh = coords->dx().getMesh();
   mesh_nz = mesh->LocalNz;
 
   auto search = coords_store.find(coords);
@@ -41,9 +41,11 @@ CoordinatesAccessor::CoordinatesAccessor(const Coordinates* coords) {
 
   // Copy data from Coordinates variable into data array
   // Uses the symbol to look up the corresponding Offset
-#define COPY_STRIPE1(symbol)        \
-  if (coords->symbol.isAllocated()) \
-    data[stripe_size * ind.ind + static_cast<int>(Offset::symbol)] = coords->symbol[ind];
+#define COPY_STRIPE1(symbol)                                         \
+  if (coords->symbol().isAllocated()) {                              \
+    data[stripe_size * ind.ind + static_cast<int>(Offset::symbol)] = \
+        coords->symbol()[ind];                                       \
+  }
 
   // Implement copy for each argument
 #define COPY_STRIPE(...)                      \
@@ -53,19 +55,19 @@ CoordinatesAccessor::CoordinatesAccessor(const Coordinates* coords) {
 
   // Iterate over all points in the field
   // Note this could be 2D or 3D, depending on FieldMetric type
-  for (const auto& ind : coords->dx.getRegion("RGN_ALL")) {
+  for (const auto& ind : coords->dx().getRegion("RGN_ALL")) {
     COPY_STRIPE(dx, dy, dz);
     COPY_STRIPE(d1_dx, d1_dy, d1_dz);
     COPY_STRIPE(J);
 
-    if (coords->Bxy.isAllocated()) {
-      data[stripe_size * ind.ind + static_cast<int>(Offset::B)] = coords->Bxy[ind];
-      if (coords->Bxy.yup().isAllocated())
+    if (coords->Bxy().isAllocated()) {
+      data[stripe_size * ind.ind + static_cast<int>(Offset::B)] = coords->Bxy()[ind];
+      if (coords->Bxy().yup().isAllocated())
         data[stripe_size * ind.ind + static_cast<int>(Offset::Byup)] =
-            coords->Bxy.yup()[ind];
-      if (coords->Bxy.ydown().isAllocated())
+            coords->Bxy().yup()[ind];
+      if (coords->Bxy().ydown().isAllocated())
         data[stripe_size * ind.ind + static_cast<int>(Offset::Bydown)] =
-            coords->Bxy.ydown()[ind];
+            coords->Bxy().ydown()[ind];
     }
 
     COPY_STRIPE(G1, G3);
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 8ecd9d64ff..1b9a993e1a 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -288,11 +288,11 @@ Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
                      const std::string& method) {
   Coordinates* metric = f.getCoordinates(outloc);
 
-  auto Bxy_floc = f.getCoordinates()->Bxy;
+  auto Bxy_floc = f.getCoordinates()->Bxy();
 
   if (!f.hasParallelSlices()) {
     Field3D f_B = f / Bxy_floc;
-    return metric->Bxy * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22);
+    return metric->Bxy() * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22());
   }
 
   // Need to modify yup and ydown fields
@@ -301,7 +301,7 @@ Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
   f_B.splitParallelSlices();
   f_B.yup() = f.yup() / Bxy_floc;
   f_B.ydown() = f.ydown() / Bxy_floc;
-  return metric->Bxy * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22);
+  return metric->Bxy() * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22());
 }
 
 Field3D Div_par_flux(const Field3D& v, const Field3D& f, const std::string& method,
@@ -405,24 +405,24 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D&
       // Upper cell edge
       const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]); // K at the upper boundary
       const BoutReal J_up =
-          0.5 * (coord->J[i] + coord->J.yup()[iyp]); // Jacobian at boundary
-      const BoutReal g_22_up = 0.5 * (coord->g_22[i] + coord->g_22.yup()[iyp]);
+          0.5 * (coord->J()[i] + coord->J().yup()[iyp]); // Jacobian at boundary
+      const BoutReal g_22_up = 0.5 * (coord->g_22()[i] + coord->g_22().yup()[iyp]);
       const BoutReal gradient_up =
-          2. * (f_up[iyp] - fin[i]) / (coord->dy[i] + coord->dy.yup()[iyp]);
+          2. * (f_up[iyp] - fin[i]) / (coord->dy()[i] + coord->dy().yup()[iyp]);
 
       const BoutReal flux_up = c_up * J_up * gradient_up / g_22_up;
 
       // Lower cell edge
       const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]); // K at the lower boundary
       const BoutReal J_down =
-          0.5 * (coord->J[i] + coord->J.ydown()[iym]); // Jacobian at boundary
-      const BoutReal g_22_down = 0.5 * (coord->g_22[i] + coord->g_22.ydown()[iym]);
+          0.5 * (coord->J()[i] + coord->J().ydown()[iym]); // Jacobian at boundary
+      const BoutReal g_22_down = 0.5 * (coord->g_22()[i] + coord->g_22().ydown()[iym]);
       const BoutReal gradient_down =
-          2. * (fin[i] - f_down[iym]) / (coord->dy[i] + coord->dy.ydown()[iym]);
+          2. * (fin[i] - f_down[iym]) / (coord->dy()[i] + coord->dy().ydown()[iym]);
 
       const BoutReal flux_down = c_down * J_down * gradient_down / g_22_down;
 
-      result[i] = (flux_up - flux_down) / (coord->dy[i] * coord->J[i]);
+      result[i] = (flux_up - flux_down) / (coord->dy()[i] * coord->J()[i]);
     }
 
     return result;
@@ -446,26 +446,26 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D&
 
     if (bndry_flux || is_periodic_y || !mesh->lastY(ix) || (iy != mesh->yend)) {
       const BoutReal c = 0.5 * (K[i] + K[iyp]);               // K at the upper boundary
-      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary
-      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
-      const BoutReal gradient = 2. * (f[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
+      const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iyp]); // Jacobian at boundary
+      const BoutReal g_22 = 0.5 * (coord->g_22()[i] + coord->g_22()[iyp]);
+      const BoutReal gradient = 2. * (f[iyp] - f[i]) / (coord->dy()[i] + coord->dy()[iyp]);
 
       const BoutReal flux = c * J * gradient / g_22;
 
-      result[i] += flux / (coord->dy[i] * coord->J[i]);
+      result[i] += flux / (coord->dy()[i] * coord->J()[i]);
     }
 
     // Calculate flux at lower surface
     if (bndry_flux || is_periodic_y || !mesh->firstY(ix) || (iy != mesh->ystart)) {
       const BoutReal c = 0.5 * (K[i] + K[iym]);               // K at the lower boundary
-      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary
-      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
-      const BoutReal gradient = 2. * (f[i] - f[iym]) / (coord->dy[i] + coord->dy[iym]);
+      const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iym]); // Jacobian at boundary
+      const BoutReal g_22 = 0.5 * (coord->g_22()[i] + coord->g_22()[iym]);
+      const BoutReal gradient = 2. * (f[i] - f[iym]) / (coord->dy()[i] + coord->dy()[iym]);
 
       const BoutReal flux = c * J * gradient / g_22;
 
-      result[i] -= flux / (coord->dy[i] * coord->J[i]);
-      flow_ylow[i] = -flux * coord->dx[i] * coord->dz[i];
+      result[i] -= flux / (coord->dy()[i] * coord->J()[i]);
+      flow_ylow[i] = -flux * coord->dx()[i] * coord->dz()[i];
     }
   }
 
@@ -580,12 +580,12 @@ Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
   Coordinates::FieldMetric dpdy = DDY(phi, outloc);
 
   // Calculate advection velocity
-  Coordinates::FieldMetric vx = -metric->g_23 * dpdy;
-  Coordinates::FieldMetric vy = metric->g_23 * dpdx;
+  Coordinates::FieldMetric vx = -metric->g_23() * dpdy;
+  Coordinates::FieldMetric vy = metric->g_23() * dpdx;
 
   // Upwind A using these velocities
   Coordinates::FieldMetric result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc);
-  result /= metric->J * sqrt(metric->g_22);
+  result /= metric->J() * sqrt(metric->g_22());
 
   ASSERT1(result.getLocation() == outloc);
 
@@ -612,20 +612,20 @@ Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc)
   Coordinates::FieldMetric dpdy = DDY(phi, outloc);
 
   // Calculate advection velocity
-  Coordinates::FieldMetric vx = -metric->g_23 * dpdy;
-  Coordinates::FieldMetric vy = metric->g_23 * dpdx;
-  Coordinates::FieldMetric vz = metric->g_12 * dpdy - metric->g_22 * dpdx;
+  Coordinates::FieldMetric vx = -metric->g_23() * dpdy;
+  Coordinates::FieldMetric vy = metric->g_23() * dpdx;
+  Coordinates::FieldMetric vz = metric->g_12() * dpdy - metric->g_22() * dpdx;
 
   if (mesh->IncIntShear) {
     // BOUT-06 style differencing
-    vz += metric->IntShiftTorsion * vx;
+    vz += metric->IntShiftTorsion() * vx;
   }
 
   // Upwind A using these velocities
 
   Field3D result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc) + VDDZ(vz, A, outloc);
 
-  result /= (metric->J * sqrt(metric->g_22));
+  result /= (metric->J() * sqrt(metric->g_22()));
 
 #if BOUT_USE_TRACK
   result.name = "b0xGrad_dot_Grad(" + phi.name + "," + A.name + ")";
@@ -652,14 +652,14 @@ Field3D b0xGrad_dot_Grad(const Field3D& p, const Field2D& A, CELL_LOC outloc) {
   Field3D dpdz = DDZ(p, outloc);
 
   // Calculate advection velocity
-  Field3D vx = metric->g_22 * dpdz - metric->g_23 * dpdy;
-  Field3D vy = metric->g_23 * dpdx - metric->g_12 * dpdz;
+  Field3D vx = metric->g_22() * dpdz - metric->g_23() * dpdy;
+  Field3D vy = metric->g_23() * dpdx - metric->g_12() * dpdz;
 
   // Upwind A using these velocities
 
   Field3D result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc);
 
-  result /= (metric->J * sqrt(metric->g_22));
+  result /= (metric->J() * sqrt(metric->g_22()));
 
 #if BOUT_USE_TRACK
   result.name = "b0xGrad_dot_Grad(" + p.name + "," + A.name + ")";
@@ -688,18 +688,18 @@ Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A, CELL_LOC outloc)
   Field3D dpdz = DDZ(phi, outloc);
 
   // Calculate advection velocity
-  Field3D vx = metric->g_22 * dpdz - metric->g_23 * dpdy;
-  Field3D vy = metric->g_23 * dpdx - metric->g_12 * dpdz;
-  Field3D vz = metric->g_12 * dpdy - metric->g_22 * dpdx;
+  Field3D vx = metric->g_22() * dpdz - metric->g_23() * dpdy;
+  Field3D vy = metric->g_23() * dpdx - metric->g_12() * dpdz;
+  Field3D vz = metric->g_12() * dpdy - metric->g_22() * dpdx;
 
   if (mesh->IncIntShear) {
     // BOUT-06 style differencing
-    vz += metric->IntShiftTorsion * vx;
+    vz += metric->IntShiftTorsion() * vx;
   }
 
   Field3D result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc) + VDDZ(vz, A, outloc);
 
-  result /= (metric->J * sqrt(metric->g_22));
+  result /= (metric->J() * sqrt(metric->g_22()));
 
 #if BOUT_USE_TRACK
   result.name = "b0xGrad_dot_Grad(" + phi.name + "," + A.name + ")";
@@ -733,7 +733,7 @@ Coordinates::FieldMetric bracket(const Field2D& f, const Field2D& g,
     result.setLocation(outloc);
   } else {
     // Use full expression with all terms
-    result = b0xGrad_dot_Grad(f, g, outloc) / f.getCoordinates(outloc)->Bxy;
+    result = b0xGrad_dot_Grad(f, g, outloc) / f.getCoordinates(outloc)->Bxy();
   }
   return result;
 }
@@ -808,7 +808,7 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
 
     BOUT_FOR(j2D, result.getRegion2D("RGN_NOBNDRY")) {
       // Get constants for this iteration
-      const BoutReal spacingFactor = 1.0 / (12 * metric->dz[j2D] * metric->dx[j2D]);
+      const BoutReal spacingFactor = 1.0 / (12 * metric->dz()[j2D] * metric->dx()[j2D]);
       const int jy = j2D.y(), jx = j2D.x();
       const int xm = jx - 1, xp = jx + 1;
 
@@ -880,7 +880,7 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
   }
   default: {
     // Use full expression with all terms
-    result = b0xGrad_dot_Grad(f, g, outloc) / metric->Bxy;
+    result = b0xGrad_dot_Grad(f, g, outloc) / metric->Bxy();
   }
   }
   return result;
@@ -915,7 +915,7 @@ Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method,
   default: {
     // Use full expression with all terms
     Coordinates* metric = f.getCoordinates(outloc);
-    result = b0xGrad_dot_Grad(f, g, outloc) / metric->Bxy;
+    result = b0xGrad_dot_Grad(f, g, outloc) / metric->Bxy();
   }
   }
 
@@ -1058,7 +1058,7 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
 
     BOUT_FOR(j2D, result.getRegion2D("RGN_NOBNDRY")) {
 #if not(BOUT_USE_METRIC_3D)
-      const BoutReal spacingFactor = 1.0 / (12 * metric->dz[j2D] * metric->dx[j2D]);
+      const BoutReal spacingFactor = 1.0 / (12 * metric->dz()[j2D] * metric->dx()[j2D]);
 #endif
       const int jy = j2D.y(), jx = j2D.x();
       const int xm = jx - 1, xp = jx + 1;
@@ -1156,7 +1156,7 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
   }
   default: {
     // Use full expression with all terms
-    result = b0xGrad_dot_Grad(f, g, outloc) / metric->Bxy;
+    result = b0xGrad_dot_Grad(f, g, outloc) / metric->Bxy();
   }
   }
 
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index 660fc51abc..e8958e128d 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -71,9 +71,9 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
     // 3D Metric, need yup/ydown fields.
     // Requires previous communication of metrics
     // -- should insert communication here?
-    if (!coord->g23.hasParallelSlices() || !coord->g_23.hasParallelSlices()
-        || !coord->dy.hasParallelSlices() || !coord->dz.hasParallelSlices()
-        || !coord->Bxy.hasParallelSlices() || !coord->J.hasParallelSlices()) {
+    if (!coord->g23().hasParallelSlices() || !coord->g_23().hasParallelSlices()
+        || !coord->dy().hasParallelSlices() || !coord->dz().hasParallelSlices()
+        || !coord->Bxy().hasParallelSlices() || !coord->J().hasParallelSlices()) {
       throw BoutException("metrics have no yup/down!");
     }
   }
@@ -89,12 +89,12 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
 
   // Only in 3D case with FCI do the metrics have parallel slices
   const bool metric_fci = fci and bout::build::use_metric_3d;
-  const auto g23 = makeslices(metric_fci, coord->g23);
-  const auto g_23 = makeslices(metric_fci, coord->g_23);
-  const auto J = makeslices(metric_fci, coord->J);
-  const auto dy = makeslices(metric_fci, coord->dy);
-  const auto dz = makeslices(metric_fci, coord->dz);
-  const auto Bxy = makeslices(metric_fci, coord->Bxy);
+  const auto g23 = makeslices(metric_fci, coord->g23());
+  const auto g_23 = makeslices(metric_fci, coord->g_23());
+  const auto J = makeslices(metric_fci, coord->J());
+  const auto dy = makeslices(metric_fci, coord->dy());
+  const auto dz = makeslices(metric_fci, coord->dz());
+  const auto Bxy = makeslices(metric_fci, coord->Bxy());
 
   // Result of the Y and Z fluxes
   Field3D yzresult(0.0, mesh);
@@ -158,7 +158,7 @@ Field3D Div_a_Grad_perp(const Field3D& a, const Field3D& f) {
 
         const BoutReal fout =
             0.25 * (a_slice.c[i] + a_slice.c[ikp])
-            * (J.c[i] * coord->g33[i] + J.c[ikp] * coord->g33[ikp])
+            * (J.c[i] * coord->g33()[i] + J.c[ikp] * coord->g33()[ikp])
             * ( // df/dz
                 (f_slice.c[ikp] - f_slice.c[i]) / dz.c[i]
                 // - g_yz * df/dy / SQ(J*B)
@@ -215,30 +215,30 @@ Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin, bool bndry_fl
         || (i.y() != mesh->yend)) {
 
       const BoutReal c = 0.5 * (K[i] + Kup[iyp]);             // K at the upper boundary
-      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary
-      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
+      const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iyp]); // Jacobian at boundary
+      const BoutReal g_22 = 0.5 * (coord->g_22()[i] + coord->g_22()[iyp]);
 
-      const BoutReal gradient = 2. * (fup[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
+      const BoutReal gradient = 2. * (fup[iyp] - f[i]) / (coord->dy()[i] + coord->dy()[iyp]);
 
       const BoutReal flux = c * J * gradient / g_22;
 
-      result[i] += flux / (coord->dy[i] * coord->J[i]);
+      result[i] += flux / (coord->dy()[i] * coord->J()[i]);
     }
 
     // Calculate flux at lower surface
     if (bndry_flux || mesh->periodicY(i.x()) || !mesh->firstY(i.x())
         || (i.y() != mesh->ystart)) {
       const BoutReal c = 0.5 * (K[i] + Kdown[iym]);           // K at the lower boundary
-      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary
+      const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iym]); // Jacobian at boundary
 
-      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
+      const BoutReal g_22 = 0.5 * (coord->g_22()[i] + coord->g_22()[iym]);
 
       const BoutReal gradient =
-          2. * (f[i] - fdown[iym]) / (coord->dy[i] + coord->dy[iym]);
+          2. * (f[i] - fdown[iym]) / (coord->dy()[i] + coord->dy()[iym]);
 
       const BoutReal flux = c * J * gradient / g_22;
 
-      result[i] -= flux / (coord->dy[i] * coord->J[i]);
+      result[i] -= flux / (coord->dy()[i] * coord->J()[i]);
     }
   }
 
diff --git a/src/mesh/g_values.cxx b/src/mesh/g_values.cxx
new file mode 100644
index 0000000000..31a794fe22
--- /dev/null
+++ b/src/mesh/g_values.cxx
@@ -0,0 +1,34 @@
+#include "bout/g_values.hxx"
+#include "bout/coordinates.hxx"
+#include "bout/mesh.hxx"
+#include "bout/metric_tensor.hxx"
+
+GValues::GValues(const Coordinates& coordinates) {
+
+  const auto& contravariantMetricTensor = coordinates.getContravariantMetricTensor();
+  const auto& J = coordinates.J();
+
+  const auto& g11 = contravariantMetricTensor.g11();
+  const auto& g22 = contravariantMetricTensor.g22();
+  const auto& g33 = contravariantMetricTensor.g33();
+  const auto& g12 = contravariantMetricTensor.g12();
+  const auto& g13 = contravariantMetricTensor.g13();
+  const auto& g23 = contravariantMetricTensor.g23();
+
+  auto* mesh = J.getMesh();
+
+  bout::FieldMetric Jg12 = J * g12;
+  mesh->communicate(Jg12);
+  G1_m =
+      (coordinates.DDX(J * g11) + coordinates.DDY(Jg12) + coordinates.DDZ(J * g13)) / J;
+  bout::FieldMetric Jg22 = J * g22;
+  mesh->communicate(Jg22);
+  G2_m =
+      (coordinates.DDX(J * g12) + coordinates.DDY(Jg22) + coordinates.DDZ(J * g23)) / J;
+  bout::FieldMetric Jg23 = J * g23;
+  mesh->communicate(Jg23);
+  G3_m =
+      (coordinates.DDX(J * g13) + coordinates.DDY(Jg23) + coordinates.DDZ(J * g33)) / J;
+
+  mesh->communicate(G1_m, G2_m, G3_m);
+}
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 33368e6d6a..00bd0b5bc4 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -1,3 +1,4 @@
+#include "bout/assert.hxx"
 #include <bout/array.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
@@ -554,12 +555,39 @@ Mesh::createDefaultCoordinates(const CELL_LOC location,
   if (location == CELL_CENTRE || location == CELL_DEFAULT) {
     // Initialize coordinates from input
     return std::make_shared<Coordinates>(this, options);
-  } else {
-    // Interpolate coordinates from CELL_CENTRE version
-    return std::make_shared<Coordinates>(this, options, location,
-                                         getCoordinates(CELL_CENTRE),
-                                         force_interpolate_from_centre);
   }
+  // Interpolate coordinates from CELL_CENTRE version
+  return std::make_shared<Coordinates>(this, options, location,
+                                       getCoordinates(CELL_CENTRE),
+                                       force_interpolate_from_centre);
+}
+
+std::shared_ptr<Coordinates> Mesh::getCoordinatesSmart(CELL_LOC location) {
+  ASSERT1(location != CELL_DEFAULT);
+  ASSERT1(location != CELL_VSHIFT);
+
+  auto found = coords_map.find(location);
+  if (found != coords_map.end()) {
+    // True branch most common, returns immediately
+    return found->second;
+  }
+
+  // No coordinate system set. Create default
+  // Note that this can't be allocated here due to incomplete type
+  // (circular dependency between Mesh and Coordinates)
+  auto inserted = coords_map.emplace(location, nullptr);
+  auto force_interpolate_from_centre = false;
+  inserted.first->second =
+      createDefaultCoordinates(location, force_interpolate_from_centre);
+
+  auto recalculate_staggered = false;
+  inserted.first->second->recalculateAndReset(recalculate_staggered,
+                                              force_interpolate_from_centre);
+
+  inserted.first->second->communicateMetricTensor();
+  inserted.first->second->communicateDz();
+
+  return inserted.first->second;
 }
 
 const Region<>& Mesh::getRegion3D(const std::string& region_name) const {
@@ -772,8 +800,14 @@ void Mesh::recalculateStaggeredCoordinates() {
       continue;
     }
 
-    *coords_map[location] = std::move(*createDefaultCoordinates(location, true));
-    coords_map[location]->geometry(false, true);
+    auto force_interpolate_from_centre = true;
+    Coordinates& new_coordinates =
+        *createDefaultCoordinates(location, force_interpolate_from_centre);
+    *coords_map[location] = std::move(new_coordinates);
+
+    auto recalculate_staggered = false;
+    new_coordinates.recalculateAndReset(recalculate_staggered,
+                                        force_interpolate_from_centre);
   }
 }
 
diff --git a/src/mesh/metric_tensor.cxx b/src/mesh/metric_tensor.cxx
new file mode 100644
index 0000000000..5444f538d3
--- /dev/null
+++ b/src/mesh/metric_tensor.cxx
@@ -0,0 +1,154 @@
+#include "bout/metric_tensor.hxx"
+#include "invert3x3.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/field2d.hxx"
+#include "bout/mesh.hxx"
+#include "bout/output.hxx"
+#include "bout/region.hxx"
+#include "bout/utils.hxx"
+
+#include <fmt/format.h>
+
+#include <cstdlib>
+#include <string>
+#include <utility>
+
+MetricTensor::MetricTensor(FieldMetric g11, FieldMetric g22, FieldMetric g33,
+                           FieldMetric g12, FieldMetric g13, FieldMetric g23)
+    : g11_m(std::move(g11)), g22_m(std::move(g22)), g33_m(std::move(g33)),
+      g12_m(std::move(g12)), g13_m(std::move(g13)), g23_m(std::move(g23)) {}
+
+MetricTensor::MetricTensor(const BoutReal g11, const BoutReal g22, const BoutReal g33,
+                           const BoutReal g12, const BoutReal g13, const BoutReal g23,
+                           Mesh* mesh)
+    : g11_m(g11, mesh), g22_m(g22, mesh), g33_m(g33, mesh), g12_m(g12, mesh),
+      g13_m(g13, mesh), g23_m(g23, mesh) {}
+
+void MetricTensor::check(int ystart) {
+  const bool non_identity_parallel_transform =
+      g11_m.hasParallelSlices() && &g11_m.ynext(1) != &g11_m;
+
+  // Diagonal metric components should be finite
+  bout::checkFinite(g11_m, "g11", "RGN_NOCORNERS");
+  bout::checkFinite(g22_m, "g22", "RGN_NOCORNERS");
+  bout::checkFinite(g33_m, "g33", "RGN_NOCORNERS");
+  if (non_identity_parallel_transform) {
+    for (int dy = 1; dy <= ystart; ++dy) {
+      for (const auto sign : {1, -1}) {
+        const auto region = fmt::format("RGN_YPAR_{:+d}", sign * dy);
+        bout::checkFinite(g11_m.ynext(sign * dy), "g11.ynext", region);
+        bout::checkFinite(g22_m.ynext(sign * dy), "g22.ynext", region);
+        bout::checkFinite(g33_m.ynext(sign * dy), "g33.ynext", region);
+      }
+    }
+  }
+
+  // Diagonal metric components should be positive
+  bout::checkPositive(g11_m, "g11", "RGN_NOCORNERS");
+  bout::checkPositive(g22_m, "g22", "RGN_NOCORNERS");
+  bout::checkPositive(g33_m, "g33", "RGN_NOCORNERS");
+  if (non_identity_parallel_transform) {
+    for (int dy = 1; dy <= ystart; ++dy) {
+      for (const auto sign : {1, -1}) {
+        const auto region = fmt::format("RGN_YPAR_{:+d}", sign * dy);
+        bout::checkPositive(g11_m.ynext(sign * dy), "g11.ynext", region);
+        bout::checkPositive(g22_m.ynext(sign * dy), "g22.ynext", region);
+        bout::checkPositive(g33_m.ynext(sign * dy), "g33.ynext", region);
+      }
+    }
+  }
+
+  // Off-diagonal metric components should be finite
+  bout::checkFinite(g12_m, "g12", "RGN_NOCORNERS");
+  bout::checkFinite(g13_m, "g13", "RGN_NOCORNERS");
+  bout::checkFinite(g23_m, "g23", "RGN_NOCORNERS");
+  // Check off-diagonal separately, might not have them even if we have parallel
+  // slices for the diagonal components
+  if (g23_m.hasParallelSlices() && &g23_m.ynext(1) != &g23_m) {
+    for (int dy = 1; dy <= ystart; ++dy) {
+      for (const auto sign : {1, -1}) {
+        const auto region = fmt::format("RGN_YPAR_{:+d}", sign * dy);
+        bout::checkFinite(g12_m.ynext(sign * dy), "g12.ynext", region);
+        bout::checkFinite(g13_m.ynext(sign * dy), "g13.ynext", region);
+        bout::checkFinite(g23_m.ynext(sign * dy), "g23.ynext", region);
+      }
+    }
+  }
+}
+
+namespace {
+template <class InverseMetric>
+auto inverse_impl(const MetricTensor& metric, const std::string& region)
+    -> InverseMetric {
+  // Perform inversion of g{ij} to get g^{ij}, or vice versa
+  auto matrix = Matrix<BoutReal>(3, 3);
+
+  bout::FieldMetric g_11 = emptyFrom(metric.g11());
+  bout::FieldMetric g_22 = emptyFrom(metric.g22());
+  bout::FieldMetric g_33 = emptyFrom(metric.g33());
+  bout::FieldMetric g_12 = emptyFrom(metric.g12());
+  bout::FieldMetric g_13 = emptyFrom(metric.g13());
+  bout::FieldMetric g_23 = emptyFrom(metric.g23());
+
+  BOUT_FOR_SERIAL(i, metric.g11().getRegion(region)) {
+    matrix(0, 0) = metric.g11()[i];
+    matrix(1, 1) = metric.g22()[i];
+    matrix(2, 2) = metric.g33()[i];
+
+    matrix(0, 1) = matrix(1, 0) = metric.g12()[i];
+    matrix(1, 2) = matrix(2, 1) = metric.g23()[i];
+    matrix(0, 2) = matrix(2, 0) = metric.g13()[i];
+
+    if (const auto det = bout::invert3x3(matrix); det.has_value()) {
+      throw BoutException("ERROR: metric tensor is singular at ({}, {}), determinant: {}",
+                          i.x(), i.y(), det.value());
+    }
+
+    g_11[i] = matrix(0, 0);
+    g_22[i] = matrix(1, 1);
+    g_33[i] = matrix(2, 2);
+    g_12[i] = matrix(0, 1);
+    g_13[i] = matrix(0, 2);
+    g_23[i] = matrix(1, 2);
+  }
+
+  const BoutReal diagonal_maxerr =
+      BOUTMAX(max(abs((g_11 * g_11 + g_12 * g_12 + g_13 * g_13) - 1)),
+              max(abs((g_12 * g_12 + g_22 * g_22 + g_23 * g_23) - 1)),
+              max(abs((g_13 * g_13 + g_23 * g_23 + g_33 * g_33) - 1)));
+
+  output_info.write("\tMaximum error in diagonal inversion is {:e}\n", diagonal_maxerr);
+
+  const BoutReal off_diagonal_maxerr =
+      BOUTMAX(max(abs(g_11 * g_12 + g_12 * g_22 + g_13 * g_23)),
+              max(abs(g_11 * g_13 + g_12 * g_23 + g_13 * g_33)),
+              max(abs(g_12 * g_13 + g_22 * g_23 + g_23 * g_33)));
+
+  output_info.write("\tMaximum error in off-diagonal inversion is {:e}\n",
+                    off_diagonal_maxerr);
+  return InverseMetric(g_11, g_22, g_33, g_12, g_13, g_23);
+}
+} // namespace
+
+auto CovariantMetricTensor::inverse(const std::string& region, bool communicate)
+    -> ContravariantMetricTensor {
+  auto result = inverse_impl<ContravariantMetricTensor>(*this, region);
+  if (communicate) {
+    result.communicate();
+  }
+  return result;
+}
+
+auto ContravariantMetricTensor::inverse(const std::string& region, bool communicate)
+    -> CovariantMetricTensor {
+  auto result = inverse_impl<CovariantMetricTensor>(*this, region);
+  if (communicate) {
+    result.communicate();
+  }
+  return result;
+}
+
+void MetricTensor::communicate() {
+  g11_m.getMesh()->communicate_no_slices(g11_m, g22_m, g33_m, g12_m, g13_m, g23_m);
+}
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index aebfeb654c..72861eb68f 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -42,10 +42,11 @@
 #include "bout/boundary_region_iter.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
-#include "bout/build_defines.hxx"
+#include "bout/coordinates.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_data.hxx"
+#include "bout/interpolation_xz.hxx"
 #include "bout/mesh.hxx"
 #include "bout/msg_stack.hxx"
 #include "bout/options.hxx"
@@ -62,61 +63,9 @@
 #include <cstdlib>
 #include <memory>
 #include <string>
-#include <string_view>
 
-using namespace std::string_view_literals;
 using bout::boundary::BoundaryRegionFCI;
 
-namespace {
-// Get a unique name for a field based on the sign/magnitude of the offset
-std::string parallel_slice_field_name(const std::string& field, int offset) {
-  const std::string direction = (offset > 0) ? "forward" : "backward";
-  // We only have a suffix for parallel slices beyond the first
-  // This is for backwards compatibility
-  const std::string slice_suffix =
-      (std::abs(offset) > 1) ? "_" + std::to_string(std::abs(offset)) : "";
-  return direction + "_" + field + slice_suffix;
-};
-
-#if BOUT_USE_METRIC_3D
-void load_parallel_metric_component(std::string name, Field3D& component, int offset) {
-  Mesh* mesh = component.getMesh();
-  Field3D tmp{mesh};
-  const auto pname = parallel_slice_field_name(name, offset);
-  if (mesh->get(tmp, pname, 0.0, false) != 0) {
-    throw BoutException("Could not read {:s} from grid file!\n"
-                        "  Fix it up with `zoidberg-update-parallel-metrics <grid>`",
-                        pname);
-  }
-  if (!component.hasParallelSlices()) {
-    component.splitParallelSlices();
-    component.disallowCalcParallelSlices();
-    component.resetRegionParallel(true);
-  }
-  auto& pcom = component.ynext(offset);
-  pcom.allocate();
-  BOUT_FOR(i, component.getRegion("RGN_NOBNDRY")) { pcom[i.yp(offset)] = tmp[i]; }
-}
-
-void load_parallel_metric_components(Coordinates* coords, int offset) {
-#define LOAD_PAR(var) load_parallel_metric_component(#var, coords->var, offset)
-  LOAD_PAR(g11);
-  LOAD_PAR(g22);
-  LOAD_PAR(g33);
-  LOAD_PAR(g13);
-  LOAD_PAR(g_11);
-  LOAD_PAR(g_22);
-  LOAD_PAR(g_33);
-  LOAD_PAR(g_13);
-  LOAD_PAR(dy);
-  LOAD_PAR(Bxy);
-
-#undef LOAD_PAR
-}
-#endif
-
-} // namespace
-
 FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
                Options& options, int offset,
                const std::shared_ptr<BoundaryRegionFCI>& inner_boundary,
@@ -155,29 +104,31 @@ FCIMap::FCIMap(Mesh& mesh, [[maybe_unused]] const Coordinates::FieldMetric& dy,
   map_mesh->get(R, "R", 0.0, false);
   map_mesh->get(Z, "Z", 0.0, false);
 
+  using bout::parallelSliceFieldName;
+
   // If we can't read in any of these fields, things will silently not
   // work, so best throw
-  if (map_mesh->get(xt_prime, parallel_slice_field_name("xt_prime", offset), 0.0, false)
+  if (map_mesh->get(xt_prime, parallelSliceFieldName("xt_prime", offset), 0.0, false)
       != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
-                        parallel_slice_field_name("xt_prime", offset));
+                        parallelSliceFieldName("xt_prime", offset));
   }
-  if (map_mesh->get(zt_prime, parallel_slice_field_name("zt_prime", offset), 0.0, false)
+  if (map_mesh->get(zt_prime, parallelSliceFieldName("zt_prime", offset), 0.0, false)
       != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
-                        parallel_slice_field_name("zt_prime", offset));
+                        parallelSliceFieldName("zt_prime", offset));
   }
-  if (map_mesh->get(R_prime, parallel_slice_field_name("R", offset), 0.0, false) != 0) {
+  if (map_mesh->get(R_prime, parallelSliceFieldName("R", offset), 0.0, false) != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
-                        parallel_slice_field_name("R", offset));
+                        parallelSliceFieldName("R", offset));
   }
-  if (map_mesh->get(Z_prime, parallel_slice_field_name("Z", offset), 0.0, false) != 0) {
+  if (map_mesh->get(Z_prime, parallelSliceFieldName("Z", offset), 0.0, false) != 0) {
     throw BoutException("Could not read {:s} from grid file!\n"
                         "  Either add it to the grid file, or reduce MYG",
-                        parallel_slice_field_name("Z", offset));
+                        parallelSliceFieldName("Z", offset));
   }
 
   // Cell corners
@@ -467,24 +418,3 @@ void FCITransform::outputVars(Options& output_options) {
   output_options["R"].force(R, "FCI");
   output_options["Z"].force(Z, "FCI");
 }
-
-void FCITransform::loadParallelMetrics([[maybe_unused]] Coordinates* coords) {
-#if BOUT_USE_METRIC_3D
-  output_info.write("\tLoading parallel metrics\n");
-  const Coordinates::FieldMetric JB0 = coords->J * coords->Bxy;
-  coords->J.splitParallelSlices();
-  coords->J.disallowCalcParallelSlices();
-  coords->J.resetRegionParallel(true);
-  for (int i = 1; i <= mesh.ystart; ++i) {
-    load_parallel_metric_components(coords, -i);
-    load_parallel_metric_components(coords, i);
-
-    coords->J.ynext(i).allocate();
-    coords->J.ynext(-i).allocate();
-    BOUT_FOR(j, JB0.getRegion("RGN_NOBNDRY")) {
-      coords->J.ynext(i)[j.yp(i)] = JB0[j] / coords->Bxy.ynext(i)[j.yp(i)];
-      coords->J.ynext(-i)[j.yp(-i)] = JB0[j] / coords->Bxy.ynext(-i)[j.yp(-i)];
-    }
-  }
-#endif
-}
diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx
index a90e3e98dd..f5d0642675 100644
--- a/src/mesh/parallel/fci.hxx
+++ b/src/mesh/parallel/fci.hxx
@@ -126,8 +126,6 @@ public:
     return false;
   }
 
-  void loadParallelMetrics(Coordinates* coords) override;
-
 protected:
   void checkInputGrid() override;
 
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 573044a0a1..6b4de3fe22 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -333,14 +333,14 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   auto* coords = mesh->getCoordinates();
 
   // Parallel spacing in cell space
-  Field3D dl = Coordinates::FieldMetric{coords->dy * sqrt(coords->g_22)};
+  Field3D dl = Coordinates::FieldMetric{coords->dy() * sqrt(coords->g_22())};
   dl.splitParallelSlices();
   dl.yup() = 0.0;
   dl.ydown() = 0.0;
   dl.applyParallelBoundary("parallel_neumann_o1");
 
   // Cell volume
-  Field3D dV = Coordinates::FieldMetric{coords->J * coords->dx * coords->dy * coords->dz};
+  Field3D dV = Coordinates::FieldMetric{coords->J() * coords->dx() * coords->dy() * coords->dz()};
   dV.splitParallelSlices();
   dV.yup() = 0.0;
   dV.ydown() = 0.0;
diff --git a/src/mesh/tokamak_coordinates.cxx b/src/mesh/tokamak_coordinates.cxx
index af8b6335bf..06e38155f0 100644
--- a/src/mesh/tokamak_coordinates.cxx
+++ b/src/mesh/tokamak_coordinates.cxx
@@ -2,37 +2,38 @@
 #include <bout/coordinates.hxx>
 #include <bout/field2d.hxx>
 #include <bout/mesh.hxx>
+#include <bout/metric_tensor.hxx>
 #include <bout/tokamak_coordinates.hxx>
 #include <bout/utils.hxx>
 
 namespace bout {
 TokamakCoordinates set_tokamak_coordinates(Mesh& mesh, BoutReal Lbar, BoutReal Bbar,
                                            bool no_shear, BoutReal shear_factor) {
-  Field2D Rxy;
+  FieldMetric Rxy;
   mesh.get(Rxy, "Rxy"); // [m]
   Rxy /= Lbar;
 
-  Field2D Zxy;
+  FieldMetric Zxy;
   mesh.get(Zxy, "Zxy"); // [m]
   Zxy /= Lbar;
 
-  Field2D Bpxy;
+  FieldMetric Bpxy;
   mesh.get(Bpxy, "Bpxy"); // [T]
   Bpxy /= Bbar;
 
-  Field2D Btxy;
+  FieldMetric Btxy;
   mesh.get(Btxy, "Btxy"); // [T]
   Btxy /= Bbar;
 
-  Field2D Bxy;
+  FieldMetric Bxy;
   mesh.get(Bxy, "Bxy"); // [T]
   Bxy /= Bbar;
 
-  Field2D hthe;
+  FieldMetric hthe;
   mesh.get(hthe, "hthe"); // [m / radian]
   hthe /= Lbar;
 
-  Coordinates::FieldMetric I;
+  bout::FieldMetric I;
   if (no_shear) {
     I = 0.0;
   } else {
@@ -41,36 +42,36 @@ TokamakCoordinates set_tokamak_coordinates(Mesh& mesh, BoutReal Lbar, BoutReal B
   const auto I_unnormalised = I;
   I *= Lbar * Lbar * Bbar * shear_factor;
 
-  Coordinates::FieldMetric dx;
+  bout::FieldMetric dx;
   if (mesh.get(dx, "dpsi") != 0) {
-    dx = mesh.getCoordinates()->dx;
+    dx = mesh.getCoordinates()->dx();
   }
   dx /= Lbar * Lbar * Bbar;
 
   const BoutReal sign_of_bp = min(Bpxy, true) < 0.0 ? -1.0 : 1.0;
 
-  auto* coords = mesh.getCoordinates();
+  auto* coord = mesh.getCoordinates();
 
-  coords->Bxy = Bxy;
-  coords->dx = dx;
+  const FieldMetric g11 = SQ(Rxy * Bpxy);
+  const FieldMetric g22 = 1.0 / SQ(hthe);
+  const FieldMetric g33 = SQ(I) * g11 + SQ(Bxy) / g11;
+  const FieldMetric g12 = 0.0;
+  const FieldMetric g13 = -I * g11;
+  const FieldMetric g23 = -sign_of_bp * Btxy / (hthe * Bpxy * Rxy);
 
-  coords->g11 = SQ(Rxy * Bpxy);
-  coords->g22 = 1.0 / SQ(hthe);
-  coords->g33 = SQ(I) * coords->g11 + SQ(Bxy) / coords->g11;
-  coords->g12 = 0.0;
-  coords->g13 = -I * coords->g11;
-  coords->g23 = -sign_of_bp * Btxy / (hthe * Bpxy * Rxy);
+  const FieldMetric g_11 = 1.0 / g11 + SQ(I * Rxy);
+  const FieldMetric g_22 = SQ(Bxy * hthe / Bpxy);
+  const FieldMetric g_33 = Rxy * Rxy;
+  const FieldMetric g_12 = sign_of_bp * Btxy * hthe * I * Rxy / Bpxy;
+  const FieldMetric g_13 = I * Rxy * Rxy;
+  const FieldMetric g_23 = sign_of_bp * Btxy * hthe * Rxy / Bpxy;
 
-  coords->J = hthe / Bpxy;
+  coord->setMetricTensor(ContravariantMetricTensor(g11, g22, g33, g12, g13, g23),
+                         CovariantMetricTensor(g_11, g_22, g_33, g_12, g_13, g_23));
 
-  coords->g_11 = 1.0 / coords->g11 + SQ(I * Rxy);
-  coords->g_22 = SQ(Bxy * hthe / Bpxy);
-  coords->g_33 = Rxy * Rxy;
-  coords->g_12 = sign_of_bp * Btxy * hthe * I * Rxy / Bpxy;
-  coords->g_13 = I * Rxy * Rxy;
-  coords->g_23 = sign_of_bp * Btxy * hthe * Rxy / Bpxy;
-
-  coords->geometry();
+  coord->setJ(FieldMetric{hthe / Bpxy});
+  coord->setBxy(Bxy);
+  coord->setDx(dx);
 
   return {Rxy, Zxy, Bpxy, Btxy, Bxy, hthe, I, I_unnormalised};
 }
diff --git a/src/physics/smoothing.cxx b/src/physics/smoothing.cxx
index 1b437b4352..b643a016c8 100644
--- a/src/physics/smoothing.cxx
+++ b/src/physics/smoothing.cxx
@@ -4,15 +4,15 @@
  *
  * 2014-10-29 Ben Dudson <bd512@york.ac.uk>
  *    * Moving averaging routines here from Mesh
- * 
+ *
  * 2010-05-17 Ben Dudson <bd512@york.ac.uk>
  *    * Added nonlinear filter
- * 
+ *
  **************************************************************
  * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -107,7 +107,7 @@ const Field3D smooth_y(const Field3D& f) {
 
   Issues
   ======
-  
+
   Assumes every processor has the same domain shape
 
   Will only work if X communicator is constant in Y
@@ -162,14 +162,14 @@ const Field2D averageX(const Field2D& f) {
   ======
 
   Creates static arrays
-  
+
   Not thread safe
-  
+
   Assumes every processor has the same domain shape
-  
+
   Will only work if X communicator is constant in Y
   so no processor/branch cuts in X
-  
+
  */
 const Field3D averageX(const Field3D& f) {
   Mesh* mesh = f.getMesh();
@@ -349,7 +349,7 @@ BoutReal Vol_Integral([[maybe_unused]] const Field2D& var) {
   BoutReal Int_Glb;
   Coordinates* metric = var.getCoordinates();
 
-  auto result = metric->J * var * metric->dx * metric->dy;
+  auto result = metric->J() * var * metric->dx() * metric->dy();
 
   Int_Glb = Average_XY(result);
   Int_Glb *= static_cast<BoutReal>(
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index e449dbcd30..db44b388f1 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -76,7 +76,7 @@ Coordinates::FieldMetric DDX(const Field2D& f, CELL_LOC outloc, const std::strin
 Field3D DDY(const Field3DParallel& f, CELL_LOC outloc, const std::string& method,
             const std::string& region) {
   return bout::derivatives::index::DDY(f, outloc, method, region)
-         / f.getCoordinates(outloc)->dy;
+         / f.getCoordinates(outloc)->dy();
 }
 
 Coordinates::FieldMetric DDY(const Field2D& f, CELL_LOC outloc, const std::string& method,
@@ -89,7 +89,7 @@ Coordinates::FieldMetric DDY(const Field2D& f, CELL_LOC outloc, const std::strin
 Field3D DDZ(const Field3D& f, CELL_LOC outloc, const std::string& method,
             const std::string& region) {
   return bout::derivatives::index::DDZ(f, outloc, method, region)
-         / f.getCoordinates(outloc)->dz;
+         / f.getCoordinates(outloc)->dz();
 }
 
 Coordinates::FieldMetric DDZ(const Field2D& f, CELL_LOC UNUSED(outloc),
@@ -107,21 +107,21 @@ Vector3D DDZ(const Vector3D& v, CELL_LOC outloc, const std::string& method,
 
   if (v.covariant) {
     // From equation (2.6.32) in D'Haeseleer
-    result.x = DDZ(v.x, outloc, method, region) - v.x * metric->G1_13
-               - v.y * metric->G2_13 - v.z * metric->G3_13;
-    result.y = DDZ(v.y, outloc, method, region) - v.x * metric->G1_23
-               - v.y * metric->G2_23 - v.z * metric->G3_23;
-    result.z = DDZ(v.z, outloc, method, region) - v.x * metric->G1_33
-               - v.y * metric->G2_33 - v.z * metric->G3_33;
+    result.x = DDZ(v.x, outloc, method, region) - v.x * metric->G1_13()
+               - v.y * metric->G2_13() - v.z * metric->G3_13();
+    result.y = DDZ(v.y, outloc, method, region) - v.x * metric->G1_23()
+               - v.y * metric->G2_23() - v.z * metric->G3_23();
+    result.z = DDZ(v.z, outloc, method, region) - v.x * metric->G1_33()
+               - v.y * metric->G2_33() - v.z * metric->G3_33();
     result.covariant = true;
   } else {
     // From equation (2.6.31) in D'Haeseleer
-    result.x = DDZ(v.x, outloc, method, region) + v.x * metric->G1_13
-               + v.y * metric->G1_23 + v.z * metric->G1_33;
-    result.y = DDZ(v.y, outloc, method, region) + v.x * metric->G2_13
-               + v.y * metric->G2_23 + v.z * metric->G2_33;
-    result.z = DDZ(v.z, outloc, method, region) + v.x * metric->G3_13
-               + v.y * metric->G3_23 + v.z * metric->G3_33;
+    result.x = DDZ(v.x, outloc, method, region) + v.x * metric->G1_13()
+               + v.y * metric->G1_23() + v.z * metric->G1_33();
+    result.y = DDZ(v.y, outloc, method, region) + v.x * metric->G2_13()
+               + v.y * metric->G2_23() + v.z * metric->G2_33();
+    result.z = DDZ(v.z, outloc, method, region) + v.x * metric->G3_13()
+               + v.y * metric->G3_23() + v.z * metric->G3_33();
     result.covariant = false;
   }
 
@@ -158,12 +158,13 @@ Field3D D2DX2(const Field3D& f, CELL_LOC outloc, const std::string& method,
   const Coordinates* coords = f.getCoordinates(outloc);
 
   Field3D result =
-      bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx);
+      bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx());
 
-  if (coords->non_uniform) {
+  if (coords->non_uniform()) {
     // Correction for non-uniform f.getMesh()
-    result += coords->d1_dx * bout::derivatives::index::DDX(f, outloc, "DEFAULT", region)
-              / coords->dx;
+    result += coords->d1_dx()
+              * bout::derivatives::index::DDX(f, outloc, "DEFAULT", region)
+              / coords->dx();
   }
 
   ASSERT2(((outloc == CELL_DEFAULT) && (result.getLocation() == f.getLocation()))
@@ -177,12 +178,13 @@ Coordinates::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc,
   const Coordinates* coords = f.getCoordinates(outloc);
 
   Coordinates::FieldMetric result =
-      bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx);
+      bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx());
 
-  if (coords->non_uniform) {
+  if (coords->non_uniform()) {
     // Correction for non-uniform f.getMesh()
-    result += coords->d1_dx * bout::derivatives::index::DDX(f, outloc, "DEFAULT", region)
-              / coords->dx;
+    result += coords->d1_dx()
+              * bout::derivatives::index::DDX(f, outloc, "DEFAULT", region)
+              / coords->dx();
   }
 
   return result;
@@ -195,12 +197,13 @@ Field3D D2DY2(const Field3D& f, CELL_LOC outloc, const std::string& method,
   const Coordinates* coords = f.getCoordinates(outloc);
 
   Field3D result =
-      bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy);
+      bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy());
 
-  if (coords->non_uniform) {
+  if (coords->non_uniform()) {
     // Correction for non-uniform f.getMesh()
-    result += coords->d1_dy * bout::derivatives::index::DDY(f, outloc, "DEFAULT", region)
-              / coords->dy;
+    result += coords->d1_dy()
+              * bout::derivatives::index::DDY(f, outloc, "DEFAULT", region)
+              / coords->dy();
   }
 
   ASSERT2(((outloc == CELL_DEFAULT) && (result.getLocation() == f.getLocation()))
@@ -214,11 +217,12 @@ Coordinates::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc,
   const Coordinates* coords = f.getCoordinates(outloc);
 
   Coordinates::FieldMetric result =
-      bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy);
-  if (coords->non_uniform) {
+      bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy());
+  if (coords->non_uniform()) {
     // Correction for non-uniform f.getMesh()
-    result += coords->d1_dy * bout::derivatives::index::DDY(f, outloc, "DEFAULT", region)
-              / coords->dy;
+    result += coords->d1_dy()
+              * bout::derivatives::index::DDY(f, outloc, "DEFAULT", region)
+              / coords->dy();
   }
 
   return result;
@@ -229,13 +233,13 @@ Coordinates::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc,
 Field3D D2DZ2(const Field3D& f, CELL_LOC outloc, const std::string& method,
               const std::string& region) {
   return bout::derivatives::index::D2DZ2(f, outloc, method, region)
-         / SQ(f.getCoordinates(outloc)->dz);
+         / SQ(f.getCoordinates(outloc)->dz());
 }
 
 Coordinates::FieldMetric D2DZ2(const Field2D& f, CELL_LOC outloc,
                                const std::string& method, const std::string& region) {
   return bout::derivatives::index::D2DZ2(f, outloc, method, region)
-         / SQ(f.getCoordinates(outloc)->dz);
+         / SQ(f.getCoordinates(outloc)->dz());
 }
 
 /*******************************************************************************
@@ -245,37 +249,37 @@ Coordinates::FieldMetric D2DZ2(const Field2D& f, CELL_LOC outloc,
 Field3D D4DX4(const Field3D& f, CELL_LOC outloc, const std::string& method,
               const std::string& region) {
   return bout::derivatives::index::D4DX4(f, outloc, method, region)
-         / SQ(SQ(f.getCoordinates(outloc)->dx));
+         / SQ(SQ(f.getCoordinates(outloc)->dx()));
 }
 
 Coordinates::FieldMetric D4DX4(const Field2D& f, CELL_LOC outloc,
                                const std::string& method, const std::string& region) {
   return bout::derivatives::index::D4DX4(f, outloc, method, region)
-         / SQ(SQ(f.getCoordinates(outloc)->dx));
+         / SQ(SQ(f.getCoordinates(outloc)->dx()));
 }
 
 Field3D D4DY4(const Field3D& f, CELL_LOC outloc, const std::string& method,
               const std::string& region) {
   return bout::derivatives::index::D4DY4(f, outloc, method, region)
-         / SQ(SQ(f.getCoordinates(outloc)->dy));
+         / SQ(SQ(f.getCoordinates(outloc)->dy()));
 }
 
 Coordinates::FieldMetric D4DY4(const Field2D& f, CELL_LOC outloc,
                                const std::string& method, const std::string& region) {
   return bout::derivatives::index::D4DY4(f, outloc, method, region)
-         / SQ(SQ(f.getCoordinates(outloc)->dy));
+         / SQ(SQ(f.getCoordinates(outloc)->dy()));
 }
 
 Field3D D4DZ4(const Field3D& f, CELL_LOC outloc, const std::string& method,
               const std::string& region) {
   return bout::derivatives::index::D4DZ4(f, outloc, method, region)
-         / SQ(SQ(f.getCoordinates(outloc)->dz));
+         / SQ(SQ(f.getCoordinates(outloc)->dz()));
 }
 
 Coordinates::FieldMetric D4DZ4(const Field2D& f, CELL_LOC outloc,
                                const std::string& method, const std::string& region) {
   return bout::derivatives::index::D4DZ4(f, outloc, method, region)
-         / SQ(SQ(f.getCoordinates(outloc)->dz));
+         / SQ(SQ(f.getCoordinates(outloc)->dz()));
 }
 
 /*******************************************************************************
@@ -393,14 +397,14 @@ Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc,
 Coordinates::FieldMetric VDDX(const Field2D& v, const Field2D& f, CELL_LOC outloc,
                               const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDX(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dx;
+         / f.getCoordinates(outloc)->dx();
 }
 
 /// General version for 2 or 3-D objects
 Field3D VDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc,
              const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDX(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dx;
+         / f.getCoordinates(outloc)->dx();
 }
 
 ////////////// Y DERIVATIVE /////////////////
@@ -409,14 +413,14 @@ Field3D VDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc,
 Coordinates::FieldMetric VDDY(const Field2D& v, const Field2D& f, CELL_LOC outloc,
                               const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDY(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dy;
+         / f.getCoordinates(outloc)->dy();
 }
 
 // general case
 Field3D VDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc,
              const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDY(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dy;
+         / f.getCoordinates(outloc)->dy();
 }
 
 ////////////// Z DERIVATIVE /////////////////
@@ -425,7 +429,7 @@ Field3D VDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc,
 Coordinates::FieldMetric VDDZ(const Field2D& v, const Field2D& f, CELL_LOC outloc,
                               const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDZ(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dz;
+         / f.getCoordinates(outloc)->dz();
 }
 
 // Note that this is zero because no compression is included
@@ -435,7 +439,7 @@ Coordinates::FieldMetric VDDZ([[maybe_unused]] const Field3D& v, const Field2D&
 #if BOUT_USE_METRIC_3D
   Field3D tmp{f};
   return bout::derivatives::index::VDDZ(v, tmp, outloc, method, region)
-         / f.getCoordinates(outloc)->dz;
+         / f.getCoordinates(outloc)->dz();
 #else
   if (outloc == CELL_DEFAULT) {
     outloc = f.getLocation();
@@ -448,7 +452,7 @@ Coordinates::FieldMetric VDDZ([[maybe_unused]] const Field3D& v, const Field2D&
 Field3D VDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc,
              const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDZ(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dz;
+         / f.getCoordinates(outloc)->dz();
 }
 
 /*******************************************************************************
@@ -457,13 +461,13 @@ Field3D VDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc,
 Coordinates::FieldMetric FDDX(const Field2D& v, const Field2D& f, CELL_LOC outloc,
                               const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDX(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dx;
+         / f.getCoordinates(outloc)->dx();
 }
 
 Field3D FDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc,
              const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDX(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dx;
+         / f.getCoordinates(outloc)->dx();
 }
 
 /////////////////////////////////////////////////////////////////////////
@@ -471,13 +475,13 @@ Field3D FDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc,
 Coordinates::FieldMetric FDDY(const Field2D& v, const Field2D& f, CELL_LOC outloc,
                               const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDY(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dy;
+         / f.getCoordinates(outloc)->dy();
 }
 
 Field3D FDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc,
              const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDY(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dy;
+         / f.getCoordinates(outloc)->dy();
 }
 
 /////////////////////////////////////////////////////////////////////////
@@ -485,11 +489,11 @@ Field3D FDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc,
 Coordinates::FieldMetric FDDZ(const Field2D& v, const Field2D& f, CELL_LOC outloc,
                               const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDZ(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dz;
+         / f.getCoordinates(outloc)->dz();
 }
 
 Field3D FDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc,
              const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDZ(v, f, outloc, method, region)
-         / f.getCoordinates(outloc)->dz;
+         / f.getCoordinates(outloc)->dz();
 }
diff --git a/tests/MMS/GBS/gbs.cxx b/tests/MMS/GBS/gbs.cxx
index 6d7fbcafd2..ab23efbd6c 100644
--- a/tests/MMS/GBS/gbs.cxx
+++ b/tests/MMS/GBS/gbs.cxx
@@ -281,7 +281,7 @@ int GBS::init(bool restarting) {
     break;
   }
   case 3: { // logB, taken from mesh
-    logB = log(coords->Bxy);
+    logB = log(coords->Bxy());
     break;
   }
   default:
@@ -292,14 +292,14 @@ int GBS::init(bool restarting) {
   phiSolver = Laplacian::create(opt->getSection("phiSolver"));
   aparSolver = Laplacian::create(opt->getSection("aparSolver"));
 
-  dx4 = SQ(SQ(coords->dx));
-  dy4 = SQ(SQ(coords->dy));
-  dz4 = SQ(SQ(coords->dz));
+  dx4 = SQ(SQ(coords->dx()));
+  dy4 = SQ(SQ(coords->dy()));
+  dz4 = SQ(SQ(coords->dz()));
 
   SAVE_REPEAT(Ve);
 
   output.write("dx = {:e}, dy = {:e}, dz = {:e}\n", coords->dx(2, 2), coords->dy(2, 2),
-               coords->dz);
+               coords->dz());
   output.write("g11 = {:e}, g22 = {:e}, g33 = {:e}\n", coords->g11(2, 2),
                coords->g22(2, 2), coords->g33(2, 2));
   output.write("g12 = {:e}, g23 = {:e}\n", coords->g12(2, 2), coords->g23(2, 2));
@@ -369,7 +369,7 @@ int GBS::rhs(BoutReal t) {
   Gi = 0.0;
   if (ionvis) {
     Field3D tau_i = Omega_ci * tau_i0 * pow(Ti, 1.5) / Ne;
-    Gi = -(0.96 * Ti * Ne * tau_i) * (2. * Grad_par(Vi) + C(phi) / coords->Bxy);
+    Gi = -(0.96 * Ti * Ne * tau_i) * (2. * Grad_par(Vi) + C(phi) / coords->Bxy());
     mesh->communicate(Gi);
     Gi.applyBoundary("neumann");
   } else {
@@ -382,7 +382,8 @@ int GBS::rhs(BoutReal t) {
   Ge = 0.0;
   if (elecvis) {
     Ge = -(0.73 * Te * Ne * tau_e)
-         * (2. * Grad_par(Ve) + (5. * C(Te) + 5. * Te * C(logNe) + C(phi)) / coords->Bxy);
+         * (2. * Grad_par(Ve)
+            + (5. * C(Te) + 5. * Te * C(logNe) + C(phi)) / coords->Bxy());
     mesh->communicate(Ge);
     Ge.applyBoundary("neumann");
   } else {
@@ -396,8 +397,8 @@ int GBS::rhs(BoutReal t) {
 
   if (evolve_Ne) {
     // Density
-    ddt(Ne) = -vE_Grad(Ne, phi)                            // ExB term
-              + (2. / coords->Bxy) * (C(Pe) - Ne * C(phi)) // Perpendicular compression
+    ddt(Ne) = -vE_Grad(Ne, phi)                              // ExB term
+              + (2. / coords->Bxy()) * (C(Pe) - Ne * C(phi)) // Perpendicular compression
               + D(Ne, Dn) + H(Ne, Hn);
 
     if (parallel) {
@@ -414,7 +415,7 @@ int GBS::rhs(BoutReal t) {
   if (evolve_Te) {
     // Electron temperature
     ddt(Te) = -vE_Grad(Te, phi)
-              + (4. / 3.) * (Te / coords->Bxy)
+              + (4. / 3.) * (Te / coords->Bxy())
                     * ((7. / 2.) * C(Te) + (Te / Ne) * C(Ne) - C(phi))
               + D(Te, Dte) + H(Te, Hte);
 
@@ -438,14 +439,14 @@ int GBS::rhs(BoutReal t) {
   if (evolve_Vort) {
     // Vorticity
     ddt(Vort) = -vE_Grad(Vort, phi) // ExB term
-                + 2. * coords->Bxy * C(Pe) / Ne + coords->Bxy * C(Gi) / (3. * Ne)
+                + 2. * coords->Bxy() * C(Pe) / Ne + coords->Bxy() * C(Gi) / (3. * Ne)
                 + D(Vort, Dvort) + H(Vort, Hvort);
 
     if (parallel) {
       Field3D delV = Vi - Ve;
       mesh->communicate(delV);
       ddt(Vort) -= Vpar_Grad_par(Vi, Vort); // Parallel advection
-      ddt(Vort) += SQ(coords->Bxy) * (Grad_par(delV) + (Vi - Ve) * Grad_par(logNe));
+      ddt(Vort) += SQ(coords->Bxy()) * (Grad_par(delV) + (Vi - Ve) * Grad_par(logNe));
     }
   }
 
@@ -481,7 +482,7 @@ const Field3D GBS::C(const Field3D& f) { // Curvature operator
     mesh->communicate(g);
     return bxcv * Grad(g);
   }
-  return coords->Bxy * bracket(logB, f, BRACKET_ARAKAWA);
+  return coords->Bxy() * bracket(logB, f, BRACKET_ARAKAWA);
 }
 
 const Field3D GBS::D(const Field3D& f, BoutReal d) { // Diffusion operator
diff --git a/tests/MMS/advection/advection.cxx b/tests/MMS/advection/advection.cxx
index 1201fbc3ac..6b8510ec83 100644
--- a/tests/MMS/advection/advection.cxx
+++ b/tests/MMS/advection/advection.cxx
@@ -18,8 +18,8 @@ class AdvectMMS : public PhysicsModel {
 
     Coordinates* coords = mesh->getCoordinates();
 
-    dx_sq_sq = SQ(SQ(coords->dx));
-    dz_sq_sq = SQ(SQ(coords->dz));
+    dx_sq_sq = SQ(SQ(coords->dx()));
+    dz_sq_sq = SQ(SQ(coords->dz()));
 
     return 0;
   }
diff --git a/tests/MMS/diffusion/diffusion.cxx b/tests/MMS/diffusion/diffusion.cxx
index bd969d4d86..3353767e35 100644
--- a/tests/MMS/diffusion/diffusion.cxx
+++ b/tests/MMS/diffusion/diffusion.cxx
@@ -32,8 +32,8 @@ int Diffusion::init(bool UNUSED(restarting)) {
 
   /*this assumes equidistant grid*/
   int nguard = mesh->xstart;
-  coord->dx = Lx / (mesh->GlobalNx - 2 * nguard);
-  coord->dy = Ly / (mesh->GlobalNy - 2 * nguard);
+  coord->setDx(Lx / (mesh->GlobalNx - 2 * nguard));
+  coord->setDy(Ly / (mesh->GlobalNy - 2 * nguard));
 
   SAVE_ONCE2(Lx, Ly);
 
@@ -43,20 +43,8 @@ int Diffusion::init(bool UNUSED(restarting)) {
   SAVE_ONCE(mu_N);
 
   //set mesh
-  coord->g11 = 1.0;
-  coord->g22 = 1.0;
-  coord->g33 = 1.0;
-  coord->g12 = 0.0;
-  coord->g13 = 0.0;
-  coord->g23 = 0.0;
-
-  coord->g_11 = 1.0;
-  coord->g_22 = 1.0;
-  coord->g_33 = 1.0;
-  coord->g_12 = 0.0;
-  coord->g_13 = 0.0;
-  coord->g_23 = 0.0;
-  coord->geometry();
+  coord->setMetricTensor(ContravariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0),
+                         CovariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0));
 
   // Tell BOUT++ to solve N
   SOLVE_FOR(N);
diff --git a/tests/MMS/diffusion2/diffusion.cxx b/tests/MMS/diffusion2/diffusion.cxx
index bd2cd72a08..50313fcd2a 100644
--- a/tests/MMS/diffusion2/diffusion.cxx
+++ b/tests/MMS/diffusion2/diffusion.cxx
@@ -2,6 +2,7 @@
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
 #include <bout/initialprofiles.hxx>
+#include <bout/metric_tensor.hxx>
 #include <bout/physicsmodel.hxx>
 #include <math.h>
 
@@ -21,9 +22,9 @@ class Diffusion : public PhysicsModel {
     meshoptions->get("Ly", Ly, 1.0);
 
     /*this assumes equidistant grid*/
-    coords->dx = Lx / (mesh->GlobalNx - 2 * mesh->xstart);
+    coords->setDx(Lx / (mesh->GlobalNx - 2 * mesh->xstart));
 
-    coords->dy = Ly / (mesh->GlobalNy - 2 * mesh->ystart);
+    coords->setDy(Ly / (mesh->GlobalNy - 2 * mesh->ystart));
 
     output.write("SIZES: {:d}, {:d}, {:e}\n", mesh->GlobalNy,
                  (mesh->GlobalNy - 2 * mesh->ystart), coords->dy(0, 0, 0));
@@ -38,20 +39,8 @@ class Diffusion : public PhysicsModel {
     SAVE_ONCE3(Dx, Dy, Dz);
 
     // set mesh
-    coords->g11 = 1.0;
-    coords->g22 = 1.0;
-    coords->g33 = 1.0;
-    coords->g12 = 0.0;
-    coords->g13 = 0.0;
-    coords->g23 = 0.0;
-
-    coords->g_11 = 1.0;
-    coords->g_22 = 1.0;
-    coords->g_33 = 1.0;
-    coords->g_12 = 0.0;
-    coords->g_13 = 0.0;
-    coords->g_23 = 0.0;
-    coords->geometry();
+    coords->setMetricTensor(ContravariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0),
+                            CovariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0));
 
     // Tell BOUT++ to solve N
     SOLVE_FOR(N);
diff --git a/tests/MMS/elm-pb/elm_pb.cxx b/tests/MMS/elm-pb/elm_pb.cxx
index 8fb2a58cbf..f678f89aac 100644
--- a/tests/MMS/elm-pb/elm_pb.cxx
+++ b/tests/MMS/elm-pb/elm_pb.cxx
@@ -292,7 +292,7 @@ class ELMpb : public PhysicsModel {
     const auto& hthe = tokamak_coords.hthe;
     const auto& I = tokamak_coords.I_unnormalised;
 
-    B0 = tokamak_coords.Bxy;
+    B0 = tokamak_coords.Bxy();
 
     if (include_curvature) {
       // Load curvature term
@@ -315,7 +315,7 @@ class ELMpb : public PhysicsModel {
     if (ShiftXderivs) {
       if (mesh->IncIntShear) {
         // BOUT-06 style, using d/dx = d/dpsi + I * d/dz
-        mesh->getCoordinates()->IntShiftTorsion = I;
+        mesh->getCoordinates()->setIntShiftTorsion(I);
       } else {
         // Dimits style, using local coordinate system
         if (include_curvature) {
@@ -596,7 +596,7 @@ class ELMpb : public PhysicsModel {
       ddt(U) += viscos_perp * Delp2(U); // Perpendicular viscosity
     }
 
-    ddt(U) -= 10 * (SQ(SQ(coords->dx)) * D4DX4(U) + SQ(SQ(coords->dz)) * D4DZ4(U));
+    ddt(U) -= 10 * (SQ(SQ(coords->dx())) * D4DX4(U) + SQ(SQ(coords->dz())) * D4DZ4(U));
 
     ////////////////////////////////////////////////////
     // Pressure equation
@@ -616,7 +616,7 @@ class ELMpb : public PhysicsModel {
       ddt(P) += diffusion_par * Grad2_par2(P); // Parallel diffusion
     }
 
-    ddt(P) -= 10 * (SQ(SQ(coords->dx)) * D4DX4(P) + SQ(SQ(coords->dz)) * D4DZ4(P));
+    ddt(P) -= 10 * (SQ(SQ(coords->dx())) * D4DX4(P) + SQ(SQ(coords->dz())) * D4DZ4(P));
 
     ////////////////////////////////////////////////////
     // Compressional effects
diff --git a/tests/MMS/fieldalign/fieldalign.cxx b/tests/MMS/fieldalign/fieldalign.cxx
index 75481dee9a..16e9c50bc8 100644
--- a/tests/MMS/fieldalign/fieldalign.cxx
+++ b/tests/MMS/fieldalign/fieldalign.cxx
@@ -20,14 +20,16 @@ class FieldAlign : public PhysicsModel {
     // df/dt = df/dtheta + df/dphi
 
     ddt(f) =
-        vx / G * (metric->g11 * DDX(f) + metric->g12 * DDY(f) + metric->g13 * DDZ(f))
-        + vy / G * (metric->g12 * DDX(f) + metric->g22 * DDY(f) + metric->g23 * DDZ(f))
+        vx / G
+            * (metric->g11() * DDX(f) + metric->g12() * DDY(f) + metric->g13() * DDZ(f))
+        + vy / G
+              * (metric->g12() * DDX(f) + metric->g22() * DDY(f) + metric->g23() * DDZ(f))
         + // Upwinding with second-order central differencing
         vz / G
-            * (metric->g13 * DDX(f) + metric->g23 * DDY(f)
-               + metric->g33 * DDZ(f));  // (unstable without additional dissipation)
-    -SQ(SQ(metric->dx)) * D4DX4(f)       /*- SQ(SQ(metric->dy))*D4DY4(f)*/
-        - SQ(SQ(metric->dz)) * D4DZ4(f); // Numerical dissipation terms
+            * (metric->g13() * DDX(f) + metric->g23() * DDY(f)
+               + metric->g33() * DDZ(f));  // (unstable without additional dissipation)
+    -SQ(SQ(metric->dx())) * D4DX4(f)       /*- SQ(SQ(metric->dy()))*D4DY4(f)*/
+        - SQ(SQ(metric->dz())) * D4DZ4(f); // Numerical dissipation terms
 
     return 0;
   }
diff --git a/tests/MMS/hw/hw.cxx b/tests/MMS/hw/hw.cxx
index c5dd25773f..c51e17ab14 100644
--- a/tests/MMS/hw/hw.cxx
+++ b/tests/MMS/hw/hw.cxx
@@ -39,8 +39,8 @@ class Hw : public PhysicsModel {
 
     /*this assumes equidistant grid*/
     int nguard = mesh->xstart;
-    mesh->getCoordinates()->dx = Lx / (mesh->GlobalNx - 2 * nguard);
-    mesh->getCoordinates()->dz = TWOPI * Lx / (mesh->LocalNz);
+    mesh->getCoordinates()->setDx(Lx / (mesh->GlobalNx - 2 * nguard));
+    mesh->getCoordinates()->setDz(TWOPI * Lx / (mesh->LocalNz));
     /////
 
     SOLVE_FOR2(n, vort);
diff --git a/tests/MMS/laplace/laplace.cxx b/tests/MMS/laplace/laplace.cxx
index 214c022cd5..5bb87231e8 100644
--- a/tests/MMS/laplace/laplace.cxx
+++ b/tests/MMS/laplace/laplace.cxx
@@ -26,8 +26,8 @@ int main(int argc, char** argv) {
   meshoptions->get("Lx", Lx, 1.0);
 
   /*this assumes equidistant grid*/
-  mesh->getCoordinates()->dx = Lx / (mesh->GlobalNx - 2 * mesh->xstart);
-  mesh->getCoordinates()->dz = TWOPI * Lx / (mesh->GlobalNz - 2 * mesh->zstart);
+  mesh->getCoordinates()->setDx(Lx / (mesh->GlobalNx - 2 * mesh->xstart));
+  mesh->getCoordinates()->setDz(TWOPI * Lx / (mesh->GlobalNz - 2 * mesh->zstart));
   /////
 
   // Create a Laplacian inversion solver
diff --git a/tests/MMS/spatial/diffusion/diffusion.cxx b/tests/MMS/spatial/diffusion/diffusion.cxx
index 45e516751a..0050cd2bcf 100644
--- a/tests/MMS/spatial/diffusion/diffusion.cxx
+++ b/tests/MMS/spatial/diffusion/diffusion.cxx
@@ -2,6 +2,7 @@
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
 #include <bout/initialprofiles.hxx>
+#include <bout/metric_tensor.hxx>
 #include <bout/physicsmodel.hxx>
 #include <math.h>
 
@@ -22,9 +23,9 @@ class Diffusion : public PhysicsModel {
     meshoptions->get("Ly", Ly, 1.0);
 
     /*this assumes equidistant grid*/
-    coords->dx = Lx / (mesh->GlobalNx - 2 * mesh->xstart);
+    coords->setDx(Lx / (mesh->GlobalNx - 2 * mesh->xstart));
 
-    coords->dy = Ly / (mesh->GlobalNy - 2 * mesh->ystart);
+    coords->setDy(Ly / (mesh->GlobalNy - 2 * mesh->ystart));
 
     output.write("SIZES: {:d}, {:d}, {:e}\n", mesh->GlobalNy,
                  (mesh->GlobalNy - 2 * mesh->ystart), coords->dy(0, 0, 0));
@@ -39,20 +40,8 @@ class Diffusion : public PhysicsModel {
     SAVE_ONCE3(Dx, Dy, Dz);
 
     // set mesh
-    coords->g11 = 1.0;
-    coords->g22 = 1.0;
-    coords->g33 = 1.0;
-    coords->g12 = 0.0;
-    coords->g13 = 0.0;
-    coords->g23 = 0.0;
-
-    coords->g_11 = 1.0;
-    coords->g_22 = 1.0;
-    coords->g_33 = 1.0;
-    coords->g_12 = 0.0;
-    coords->g_13 = 0.0;
-    coords->g_23 = 0.0;
-    coords->geometry();
+    coords->setMetricTensor(ContravariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0),
+                            CovariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0));
 
     // Tell BOUT++ to solve N
     SOLVE_FOR(N);
diff --git a/tests/MMS/tokamak/tokamak.cxx b/tests/MMS/tokamak/tokamak.cxx
index 8b6baab950..fa89c9eb36 100644
--- a/tests/MMS/tokamak/tokamak.cxx
+++ b/tests/MMS/tokamak/tokamak.cxx
@@ -34,8 +34,8 @@ class TokamakMMS : public PhysicsModel {
     // Test bracket advection operator
     ddt(advect) = -1e-3 * bracket(drive, advect, BRACKET_ARAKAWA)
                   - 10.
-                        * (SQ(SQ(mesh->getCoordinates()->dx)) * D4DX4(advect)
-                           + SQ(SQ(mesh->getCoordinates()->dz)) * D4DZ4(advect));
+                        * (SQ(SQ(mesh->getCoordinates()->dx())) * D4DX4(advect)
+                           + SQ(SQ(mesh->getCoordinates()->dz())) * D4DZ4(advect));
 
     // Test perpendicular diffusion operator
     ddt(delp2) = 1e-5 * Delp2(delp2);
diff --git a/tests/MMS/wave-1d/wave.cxx b/tests/MMS/wave-1d/wave.cxx
index 4f53d098c6..7c2506f3d8 100644
--- a/tests/MMS/wave-1d/wave.cxx
+++ b/tests/MMS/wave-1d/wave.cxx
@@ -1,6 +1,7 @@
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
 #include <bout/initialprofiles.hxx>
+#include <bout/metric_tensor.hxx>
 #include <bout/physicsmodel.hxx>
 #include <bout/unused.hxx>
 #include <cmath>
@@ -26,26 +27,14 @@ class Wave1D : public PhysicsModel {
 
     // this assumes equidistant grid
     int nguard = mesh->xstart;
-    coord->dx = Lx / (mesh->GlobalNx - 2 * nguard);
-    coord->dy = Ly / (mesh->GlobalNy - 2 * nguard);
+    coord->setDx(Lx / (mesh->GlobalNx - 2 * nguard));
+    coord->setDy(Ly / (mesh->GlobalNy - 2 * nguard));
 
     SAVE_ONCE(Lx, Ly);
 
     //set mesh
-    coord->g11 = 1.0;
-    coord->g22 = 1.0;
-    coord->g33 = 1.0;
-    coord->g12 = 0.0;
-    coord->g13 = 0.0;
-    coord->g23 = 0.0;
-
-    coord->g_11 = 1.0;
-    coord->g_22 = 1.0;
-    coord->g_33 = 1.0;
-    coord->g_12 = 0.0;
-    coord->g_13 = 0.0;
-    coord->g_23 = 0.0;
-    coord->geometry();
+    coord->setMetricTensor(ContravariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0),
+                           CovariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0));
 
     g.setLocation(CELL_XLOW); // g staggered to the left of f
 
@@ -63,8 +52,8 @@ class Wave1D : public PhysicsModel {
     g.applyBoundary(t);
 
     // Central differencing
-    ddt(f) = DDX(g, CELL_CENTRE); // + 20*SQ(coord->dx)*D2DX2(f);
-    ddt(g) = DDX(f, CELL_XLOW);   // + 20*SQ(coord->dx)*D2DX2(g);
+    ddt(f) = DDX(g, CELL_CENTRE); // + 20*SQ(coord->dx())*D2DX2(f);
+    ddt(g) = DDX(f, CELL_XLOW);   // + 20*SQ(coord->dx())*D2DX2(g);
 
     return 0;
   }
diff --git a/tests/integrated/test-drift-instability/2fluid.cxx b/tests/integrated/test-drift-instability/2fluid.cxx
index dca5a69e3b..59f3b22342 100644
--- a/tests/integrated/test-drift-instability/2fluid.cxx
+++ b/tests/integrated/test-drift-instability/2fluid.cxx
@@ -14,7 +14,7 @@
 #include <cmath>
 
 // just define a macro for V_E dot Grad
-#define vE_Grad(f, p) (b0xGrad_dot_Grad(p, f) / coord->Bxy)
+#define vE_Grad(f, p) (b0xGrad_dot_Grad(p, f) / coord->Bxy())
 
 class TwoFluid : public PhysicsModel {
   // 2D initial profiles
@@ -368,7 +368,7 @@ class TwoFluid : public PhysicsModel {
     if (evolve_rho) {
       auto divPar_jpar_ylow = Div_par(jpar);
       mesh->communicate(divPar_jpar_ylow);
-      ddt(rho) += SQ(coord->Bxy) * interp_to(divPar_jpar_ylow, CELL_CENTRE);
+      ddt(rho) += SQ(coord->Bxy()) * interp_to(divPar_jpar_ylow, CELL_CENTRE);
     }
 
     // AJPAR
diff --git a/tests/integrated/test-interchange-instability/2fluid.cxx b/tests/integrated/test-interchange-instability/2fluid.cxx
index db0fef2fbf..3909093007 100644
--- a/tests/integrated/test-interchange-instability/2fluid.cxx
+++ b/tests/integrated/test-interchange-instability/2fluid.cxx
@@ -142,10 +142,10 @@ class Interchange : public PhysicsModel {
     Field3D pei = (Te0 + Ti0) * Ni;
 
     // DENSITY EQUATION
-    ddt(Ni) = -b0xGrad_dot_Grad(phi, Ni0) / coord->Bxy;
+    ddt(Ni) = -b0xGrad_dot_Grad(phi, Ni0) / coord->Bxy();
 
     // VORTICITY
-    ddt(rho) = 2.0 * coord->Bxy * b0xcv * Grad(pei);
+    ddt(rho) = 2.0 * coord->Bxy() * b0xcv * Grad(pei);
 
     return (0);
   }
diff --git a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx
index 7c284290b3..1ae5ded0da 100644
--- a/tests/integrated/test-laplacexy-short/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy-short/test-laplacexy.cxx
@@ -74,8 +74,8 @@ int main(int argc, char** argv) {
   if (include_y_derivs) {
     rhs = a * DC(Laplace_perp(f)) + DC(Grad_perp(a) * Grad_perp(f)) + b * f;
   } else {
-    rhs =
-        a * DC(Delp2(f, CELL_DEFAULT, false)) + DC(coords->g11 * DDX(a) * DDX(f)) + b * f;
+    rhs = a * DC(Delp2(f, CELL_DEFAULT, false)) + DC(coords->g11() * DDX(a) * DDX(f))
+          + b * f;
   }
 
   laplacexy->setCoefs(a, b);
@@ -92,7 +92,7 @@ int main(int argc, char** argv) {
     rhs_check = a * DC(Laplace_perp(sol)) + DC(Grad_perp(a) * Grad_perp(sol)) + b * sol;
   } else {
     rhs_check = a * DC(Delp2(sol, CELL_DEFAULT, false))
-                + DC(coords->g11 * DDX(a) * DDX(sol)) + b * sol;
+                + DC(coords->g11() * DDX(a) * DDX(sol)) + b * sol;
   }
 
   Options dump;
diff --git a/tests/integrated/test-laplacexy/test-laplacexy.cxx b/tests/integrated/test-laplacexy/test-laplacexy.cxx
index 543274d37d..3e215def58 100644
--- a/tests/integrated/test-laplacexy/test-laplacexy.cxx
+++ b/tests/integrated/test-laplacexy/test-laplacexy.cxx
@@ -69,7 +69,7 @@ int main(int argc, char** argv) {
   if (include_y_derivs) {
     rhs = a * Laplace_perp(f) + Grad_perp(a) * Grad_perp(f) + b * f;
   } else {
-    rhs = a * Delp2(f, CELL_DEFAULT, false) + coords->g11 * DDX(a) * DDX(f) + b * f;
+    rhs = a * Delp2(f, CELL_DEFAULT, false) + coords->g11() * DDX(a) * DDX(f) + b * f;
   }
 
   auto laplacexy = LaplaceXY::create();
@@ -89,7 +89,7 @@ int main(int argc, char** argv) {
         a * Laplace_perp(solution) + Grad_perp(a) * Grad_perp(solution) + b * solution;
   } else {
     rhs_check = a * Delp2(solution, CELL_DEFAULT, false)
-                + coords->g11 * DDX(a) * DDX(solution) + b * solution;
+                + coords->g11() * DDX(a) * DDX(solution) + b * solution;
   }
 
   Options dump;
diff --git a/tests/integrated/test-laplacexz/test-laplacexz.cxx b/tests/integrated/test-laplacexz/test-laplacexz.cxx
index 6e43d2f3f7..81688eb135 100644
--- a/tests/integrated/test-laplacexz/test-laplacexz.cxx
+++ b/tests/integrated/test-laplacexz/test-laplacexz.cxx
@@ -9,30 +9,39 @@
  * -mat_superlu_dist_statprint
  */
 #include <bout/bout.hxx>
-
 #include <bout/derivs.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
 #include <bout/field_factory.hxx>
+#include <bout/globals.hxx>
 #include <bout/invert/laplacexz.hxx>
+#include <bout/options.hxx>
+#include <bout/options_io.hxx>
+#include <bout/output.hxx>
 
 int main(int argc, char** argv) {
   BoutInitialise(argc, argv);
 
   auto inv = LaplaceXZ::create(bout::globals::mesh);
 
-  auto coord = bout::globals::mesh->getCoordinates();
-  coord->g13 = 1.8; // test off-diagonal components with nonzero value
+  auto* coord = bout::globals::mesh->getCoordinates();
+  // test off-diagonal components with nonzero value
+  coord->setContravariantMetricTensor({1.0, 1.0, 1.0, 0.1, 0.8, 0.1});
 
   // create some input field
-  Field3D f = FieldFactory::get()->create3D("f", Options::getRoot(), bout::globals::mesh);
+  const Field3D f =
+      FieldFactory::get()->create3D("f", Options::getRoot(), bout::globals::mesh);
 
   // Calculate the Laplacian with non-zero g13
-  Field3D g = coord->g11 * D2DX2(f) + coord->g13 * D2DXDZ(f) + coord->g33 * D2DZ2(f);
+  const Field3D g =
+      coord->g11() * D2DX2(f) + coord->g13() * D2DXDZ(f) + coord->g33() * D2DZ2(f);
 
   inv->setCoefs(Field2D(1.0), Field2D(0.0));
 
-  Field3D f2 = inv->solve(g, 0.0); // Invert the Laplacian.
+  const Field3D f2 = inv->solve(g, 0.0); // Invert the Laplacian.
 
-  coord->g13 = 0.0; // reset to 0.0 for original laplacexz test
+  // reset to 0.0 for original laplacexz test
+  coord->setContravariantMetricTensor({1.0, 1.0, 1.0, 0.0, 0.0, 0.0});
 
   // Now the normal test.
   output.write("Setting coefficients\n");
@@ -41,17 +50,17 @@ int main(int argc, char** argv) {
 
   output.write("First solve\n");
 
-  Field3D rhs =
+  const Field3D rhs =
       FieldFactory::get()->create3D("rhs", Options::getRoot(), bout::globals::mesh);
-  Field3D x = inv->solve(rhs, 0.0);
+  const Field3D x = inv->solve(rhs, 0.0);
 
   output.write("Second solve\n");
 
   inv->setCoefs(Field3D(2.0), Field3D(0.1));
 
-  Field3D rhs2 =
+  const Field3D rhs2 =
       FieldFactory::get()->create3D("rhs", Options::getRoot(), bout::globals::mesh);
-  Field3D x2 = inv->solve(rhs2, 0.0);
+  const Field3D x2 = inv->solve(rhs2, 0.0);
 
   Options dump;
 
diff --git a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx
index a3e128bfdc..b9f80a6ae0 100644
--- a/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx
+++ b/tests/integrated/test-multigrid_laplace/test_multigrid_laplace.cxx
@@ -298,9 +298,9 @@ int main(int argc, char** argv) {
 Field3D this_Grad_perp_dot_Grad_perp(const Field3D& f, const Field3D& g) {
   auto* mesh = f.getMesh();
 
-  Field3D result = mesh->getCoordinates()->g11 * ::DDX(f) * ::DDX(g)
-                   + mesh->getCoordinates()->g33 * ::DDZ(f) * ::DDZ(g)
-                   + mesh->getCoordinates()->g13 * (DDX(f) * DDZ(g) + DDZ(f) * DDX(g));
+  Field3D result = mesh->getCoordinates()->g11() * ::DDX(f) * ::DDX(g)
+                   + mesh->getCoordinates()->g33() * ::DDZ(f) * ::DDZ(g)
+                   + mesh->getCoordinates()->g13() * (DDX(f) * DDZ(g) + DDZ(f) * DDX(g));
 
   return result;
 }
diff --git a/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx b/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx
index e9af4e5b36..a4af049d14 100644
--- a/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx
+++ b/tests/integrated/test-naulin-laplace/test_naulin_laplace.cxx
@@ -304,8 +304,9 @@ int main(int argc, char** argv) {
 
 Field3D this_Grad_perp_dot_Grad_perp(const Field3D& f, const Field3D& g) {
   const auto* coords = f.getCoordinates();
-  Field3D result = coords->g11 * ::DDX(f) * ::DDX(g) + coords->g33 * ::DDZ(f) * ::DDZ(g)
-                   + coords->g13 * (DDX(f) * DDZ(g) + DDZ(f) * DDX(g));
+  Field3D result = coords->g11() * ::DDX(f) * ::DDX(g)
+                   + coords->g33() * ::DDZ(f) * ::DDZ(g)
+                   + coords->g13() * (DDX(f) * DDZ(g) + DDZ(f) * DDX(g));
 
   return result;
 }
diff --git a/tests/integrated/test-petsc-operators/test_petsc_operators.cxx b/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
index 6c70c65f39..2d41d0ae0a 100644
--- a/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
+++ b/tests/integrated/test-petsc-operators/test_petsc_operators.cxx
@@ -50,7 +50,6 @@ int main(int argc, char** argv) {
     dump["div_par_op"] = parallel.Div_par(f);
 
     auto* coords = bout::globals::mesh->getCoordinates();
-    coords->Bxy.applyParallelBoundary("parallel_neumann_o1");
     dump["div_par_yud"] = Div_par(f);
 
     dump["div_par_grad_par_op"] = parallel.Div_par_Grad_par(f_neumann);
diff --git a/tests/integrated/test-snb/test_snb.cxx b/tests/integrated/test-snb/test_snb.cxx
index 1b96bfc8b1..68a2884a1e 100644
--- a/tests/integrated/test-snb/test_snb.cxx
+++ b/tests/integrated/test-snb/test_snb.cxx
@@ -1,6 +1,8 @@
 #include <bout/bout.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
+#include <bout/coordinates.hxx>
+#include <bout/field2d.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/output.hxx>
 #include <bout/snb.hxx>
@@ -207,14 +209,18 @@ int main(int argc, char** argv) {
     // Change the mesh spacing and cell volume (Jdy)
     Coordinates* coord = Te.getCoordinates();
 
+    auto dy_copy = coord->dy();
+    auto J_copy = coord->J();
     for (int x = mesh->xstart; x <= mesh->xend; x++) {
       for (int y = mesh->ystart; y <= mesh->yend; y++) {
-        double yn = (double(y) + 0.5) / double(mesh->yend + 1);
+        const double y_n = (double(y) + 0.5) / double(mesh->yend + 1);
 
-        coord->dy(x, y) = 1. - 0.9 * yn;
-        coord->J(x, y) = (1. + yn * yn);
+        dy_copy(x, y) = 1. - 0.9 * y_n;
+        J_copy(x, y) = 1. + y_n * y_n;
       }
     }
+    coord->setDy(dy_copy);
+    coord->setJ(J_copy);
 
     HeatFluxSNB snb;
 
@@ -228,8 +234,8 @@ int main(int argc, char** argv) {
     // Check that fluxes are not equal
     EXPECT_FALSE(IsFieldClose(Div_q, Div_q_SH, "RGN_NOBNDRY"));
 
-    const Field2D dy = coord->dy;
-    const Field2D J = coord->J;
+    const Field2D dy = coord->dy();
+    const Field2D J = coord->J();
 
     // Integrate Div(q) over domain
     BoutReal q_sh = 0.0;
diff --git a/tests/unit/fake_mesh_fixture.hxx b/tests/unit/fake_mesh_fixture.hxx
index 2758dbe416..da1b65cb87 100644
--- a/tests/unit/fake_mesh_fixture.hxx
+++ b/tests/unit/fake_mesh_fixture.hxx
@@ -3,11 +3,14 @@
 #include <gtest/gtest.h>
 #include <memory>
 
+#include "bout/build_config.hxx"
+#include "bout/metric_tensor.hxx"
 #include <bout/boundary_region.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/build_defines.hxx>
 #include <bout/coordinates.hxx>
+#include <bout/field2d.hxx>
 #include <bout/globals.hxx>
 #include <bout/griddata.hxx>
 #include <bout/mesh.hxx>
@@ -47,22 +50,22 @@ public:
         Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0},
         Field2D{0.0}, Field2D{0.0}, Field2D{1.0}, Field2D{1.0}, Field2D{1.0},
         Field2D{0.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0});
-
-    // Set some auxilliary variables
-    // Usually set in geometry()
-    // Note: For testing these are set to non-zero values
-    test_coords->G1 = test_coords->G2 = test_coords->G3 = 0.1;
+    mesh_m.setCoordinates(test_coords);
 
     // Set nonuniform corrections
-    test_coords->non_uniform = true;
-    test_coords->d1_dx = test_coords->d1_dy = 0.2;
-    test_coords->d1_dz = 0.0;
-#if BOUT_USE_METRIC_3D
-    test_coords->Bxy.splitParallelSlices();
-    test_coords->Bxy.yup() = test_coords->Bxy.ydown() = test_coords->Bxy;
-#endif
-
-    // No call to Coordinates::geometry() needed here
+    test_coords->setNon_uniform(true);
+    test_coords->setD1_dx(0.2);
+    test_coords->setD1_dy(0.2);
+    test_coords->setD1_dz(0.0);
+
+    if (bout::build::use_metric_3d) {
+      bout::FieldMetric mutable_Bxy = test_coords->Bxy();
+      mutable_Bxy.splitParallelSlices();
+      mutable_Bxy.yup() = test_coords->Bxy();
+      mutable_Bxy.ydown() = test_coords->Bxy();
+      test_coords->setBxy(mutable_Bxy);
+    }
+
     mesh_m.setCoordinates(test_coords);
     mesh_m.setGridDataSource(new FakeGridDataSource());
     // May need a ParallelTransform to create fields, because create3D calls
@@ -89,22 +92,25 @@ public:
         Field2D{1.0, &mesh_staggered_m}, Field2D{0.0, &mesh_staggered_m},
         Field2D{0.0, &mesh_staggered_m}, Field2D{0.0, &mesh_staggered_m},
         Field2D{0.0, &mesh_staggered_m}, Field2D{0.0, &mesh_staggered_m});
-
-    // Set some auxilliary variables
-    test_coords_staggered->G1 = test_coords_staggered->G2 = test_coords_staggered->G3 =
-        0.1;
+    mesh_staggered_m.setCoordinates(test_coords_staggered);
 
     // Set nonuniform corrections
-    test_coords_staggered->non_uniform = true;
-    test_coords_staggered->d1_dx = test_coords_staggered->d1_dy = 0.2;
-    test_coords_staggered->d1_dz = 0.0;
-#if BOUT_USE_METRIC_3D
-    test_coords_staggered->Bxy.splitParallelSlices();
-    test_coords_staggered->Bxy.yup() = test_coords_staggered->Bxy.ydown() =
-        test_coords_staggered->Bxy;
-#endif
-
-    // No call to Coordinates::geometry() needed here
+    test_coords_staggered->setNon_uniform(true);
+    test_coords_staggered->setD1_dx(0.2);
+    test_coords_staggered->setD1_dy(0.2);
+    test_coords_staggered->setD1_dz(0.0);
+
+    if (bout::build::use_metric_3d) {
+      bout::FieldMetric mutable_Bxy = test_coords_staggered->Bxy();
+      mutable_Bxy.splitParallelSlices();
+      test_coords_staggered->setBxy(mutable_Bxy);
+
+      mutable_Bxy = test_coords_staggered->Bxy();
+      mutable_Bxy.yup() = test_coords_staggered->Bxy();
+      mutable_Bxy.ydown() = test_coords_staggered->Bxy();
+      test_coords_staggered->setBxy(mutable_Bxy);
+    }
+
     test_coords_staggered->setParallelTransform(
         bout::utils::make_unique<ParallelTransformIdentity>(mesh_staggered_m));
 
diff --git a/tests/unit/fake_parallel_mesh.hxx b/tests/unit/fake_parallel_mesh.hxx
index f679963064..bc2892db53 100644
--- a/tests/unit/fake_parallel_mesh.hxx
+++ b/tests/unit/fake_parallel_mesh.hxx
@@ -265,7 +265,6 @@ std::vector<FakeParallelMesh> createFakeProcessors(int nx, int ny, int nz, int n
           Field2D{0.0}, Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0},
           Field2D{0.0}, Field2D{0.0}, Field2D{1.0}, Field2D{1.0}, Field2D{1.0},
           Field2D{0.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0});
-      // No call to Coordinates::geometry() needed here
       static_cast<FakeParallelMesh*>(&meshes[j + i * nype])->setCoordinates(test_coords);
       test_coords->setParallelTransform(
           bout::utils::make_unique<ParallelTransformIdentity>(*bout::globals::mesh));
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index 9db9fcef10..38ca612521 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -565,8 +565,6 @@ TYPED_TEST(FieldFactoryCreationTest, CreateOnMesh) {
       Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0},
       Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0},
       Field2D{0.0}, Field2D{0.0}));
-  // No call to Coordinates::geometry() needed here
-
   localmesh.getCoordinates()->setParallelTransform(
       bout::utils::make_unique<ParallelTransformIdentity>(localmesh));
 
diff --git a/tests/unit/field/test_vector2d.cxx b/tests/unit/field/test_vector2d.cxx
index d99d2ed179..354b6b85ad 100644
--- a/tests/unit/field/test_vector2d.cxx
+++ b/tests/unit/field/test_vector2d.cxx
@@ -42,7 +42,6 @@ class Vector2DTest : public ::testing::Test {
         Field2D{1.0}, Field2D{2.0}, Field2D{3.0}, Field2D{4.0}, Field2D{5.0},
         Field2D{6.0}, Field2D{1.0}, Field2D{2.0}, Field2D{3.0}, Field2D{4.0},
         Field2D{5.0}, Field2D{6.0}, Field2D{0.0}, Field2D{0.0}));
-    // No call to Coordinates::geometry() needed here
 
     delete mesh_staggered;
     mesh_staggered = new FakeMesh(nx, ny, nz);
diff --git a/tests/unit/field/test_vector3d.cxx b/tests/unit/field/test_vector3d.cxx
index 5b197d5cdf..68977e2228 100644
--- a/tests/unit/field/test_vector3d.cxx
+++ b/tests/unit/field/test_vector3d.cxx
@@ -41,7 +41,6 @@ class Vector3DTest : public ::testing::Test {
         Field2D{1.0}, Field2D{2.0}, Field2D{3.0}, Field2D{4.0}, Field2D{5.0},
         Field2D{6.0}, Field2D{1.0}, Field2D{2.0}, Field2D{3.0}, Field2D{4.0},
         Field2D{5.0}, Field2D{6.0}, Field2D{0.0}, Field2D{0.0}));
-    // No call to Coordinates::geometry() needed here
 
     delete mesh_staggered;
     mesh_staggered = new FakeMesh(nx, ny, nz);
diff --git a/tests/unit/include/bout/test_petsc_indexer.cxx b/tests/unit/include/bout/test_petsc_indexer.cxx
index 0e9f597eae..9b1d0a15f8 100644
--- a/tests/unit/include/bout/test_petsc_indexer.cxx
+++ b/tests/unit/include/bout/test_petsc_indexer.cxx
@@ -45,7 +45,6 @@ class IndexerTest : public FakeMeshFixture {
         Field2D{0.0}, Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0},
         Field2D{0.0}, Field2D{0.0}, Field2D{1.0}, Field2D{1.0}, Field2D{1.0},
         Field2D{0.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0});
-    // No call to Coordinates::geometry() needed here
     mesh2.setCoordinates(test_coords);
     // May need a ParallelTransform to create fields, because create3D calls
     // fromFieldAligned
diff --git a/tests/unit/invert/laplace/test_laplace_cyclic.cxx b/tests/unit/invert/laplace/test_laplace_cyclic.cxx
index 586dd80adf..c01488a320 100644
--- a/tests/unit/invert/laplace/test_laplace_cyclic.cxx
+++ b/tests/unit/invert/laplace/test_laplace_cyclic.cxx
@@ -34,7 +34,7 @@ class CyclicForwardOperator {
 
   Field3D operator()(Field3D& f) {
     Field3D result = d * Delp2(f)
-                     + (coords->g11 * DDX(f) + coords->g13 * DDZ(f)) * DDX(c2) / c1
+                     + (coords->g11() * DDX(f) + coords->g13() * DDZ(f)) * DDX(c2) / c1
                      + a * f + ex * DDX(f) + ez * DDZ(f);
     applyBoundaries(result, f);
     return result;
@@ -47,7 +47,7 @@ class CyclicForwardOperator {
   void applyBoundaries(Field3D& newF, const Field3D& f) const {
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) {
       if (inner_x_neumann) {
-        newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i.xp()] - f[i]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i] + f[i.xp()]);
       }
@@ -55,7 +55,7 @@ class CyclicForwardOperator {
 
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_OUTER_X")) {
       if (outer_x_neumann) {
-        newF[i] = (f[i] - f[i.xm()]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i] - f[i.xm()]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i.xm()] + f[i]);
       }
@@ -79,7 +79,6 @@ class CyclicTest : public FakeMeshFixture,
 
     static_cast<FakeMesh*>(bout::globals::mesh)
         ->setGridDataSource(new GridFromOptions(Options::getRoot()));
-    bout::globals::mesh->getCoordinates()->geometry();
     f3.allocate();
     coef2.allocate();
     coef3.allocate();
diff --git a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
index a721b96833..3a9c332480 100644
--- a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
+++ b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
@@ -40,7 +40,7 @@ class ForwardOperator {
 
   const Field3D operator()(Field3D& f) {
     Field3D result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY")
-                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22) / c1 + a * f
+                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22()) / c1 + a * f
                      + ex * DDX(f) + ez * DDZ(f);
     applyBoundaries(result, f);
     return result;
@@ -56,7 +56,7 @@ class ForwardOperator {
   void applyBoundaries(Field3D& newF, Field3D& f) {
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) {
       if (inner_x_neumann) {
-        newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i.xp()] - f[i]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i] + f[i.xp()]);
       }
@@ -64,7 +64,7 @@ class ForwardOperator {
 
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_OUTER_X")) {
       if (outer_x_neumann) {
-        newF[i] = (f[i] - f[i.xm()]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i] - f[i.xm()]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i.xm()] + f[i]);
       }
@@ -72,7 +72,7 @@ class ForwardOperator {
 
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) {
       if (lower_y_neumann) {
-        newF[i] = (f[i.yp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i.yp()] - f[i]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i] + f[i.yp()]);
       }
@@ -80,7 +80,7 @@ class ForwardOperator {
 
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) {
       if (upper_y_neumann) {
-        newF[i] = (f[i] - f[i.ym()]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i] - f[i.ym()]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i.ym()] + f[i]);
       }
@@ -98,7 +98,6 @@ class LaplaceHypre3dTest
     int nx = mesh->GlobalNx, ny = mesh->GlobalNy, nz = mesh->GlobalNz;
     static_cast<FakeMesh*>(bout::globals::mesh)
         ->setGridDataSource(new GridFromOptions(Options::getRoot()));
-    bout::globals::mesh->getCoordinates()->geometry();
     f3.allocate();
     coef2.allocate();
     coef3.allocate();
diff --git a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx
index 846cb9107f..2b856871bc 100644
--- a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx
+++ b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx
@@ -40,7 +40,7 @@ class ForwardOperator {
 
   const Field3D operator()(Field3D& f) {
     Field3D result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY")
-                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22) / c1 + a * f
+                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22()) / c1 + a * f
                      + ex * DDX(f) + ez * DDZ(f);
     applyBoundaries(result, f);
     return result;
@@ -56,7 +56,7 @@ class ForwardOperator {
   void applyBoundaries(Field3D& newF, Field3D& f) {
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) {
       if (inner_x_neumann) {
-        newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i.xp()] - f[i]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i] + f[i.xp()]);
       }
@@ -64,7 +64,7 @@ class ForwardOperator {
 
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_OUTER_X")) {
       if (outer_x_neumann) {
-        newF[i] = (f[i] - f[i.xm()]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i] - f[i.xm()]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i.xm()] + f[i]);
       }
@@ -72,7 +72,7 @@ class ForwardOperator {
 
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_LOWER_Y")) {
       if (lower_y_neumann) {
-        newF[i] = (f[i.yp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i.yp()] - f[i]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i] + f[i.yp()]);
       }
@@ -80,7 +80,7 @@ class ForwardOperator {
 
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_UPPER_Y")) {
       if (upper_y_neumann) {
-        newF[i] = (f[i] - f[i.ym()]) / coords->dx[i] / sqrt(coords->g_11[i]);
+        newF[i] = (f[i] - f[i.ym()]) / coords->dx()[i] / sqrt(coords->g_11()[i]);
       } else {
         newF[i] = 0.5 * (f[i.ym()] + f[i]);
       }
@@ -99,7 +99,6 @@ class Petsc3dAmgTest
     int nx = mesh->GlobalNx, ny = mesh->GlobalNy, nz = mesh->GlobalNz;
     static_cast<FakeMesh*>(bout::globals::mesh)
         ->setGridDataSource(new GridFromOptions(Options::getRoot()));
-    bout::globals::mesh->getCoordinates()->geometry();
     f3.allocate();
     coef2.allocate();
     coef3.allocate();
diff --git a/tests/unit/mesh/data/test_gridfromoptions.cxx b/tests/unit/mesh/data/test_gridfromoptions.cxx
index 41dd40fcc3..9b1fb9410b 100644
--- a/tests/unit/mesh/data/test_gridfromoptions.cxx
+++ b/tests/unit/mesh/data/test_gridfromoptions.cxx
@@ -360,12 +360,12 @@ TEST_F(GridFromOptionsTest, CoordinatesCentre) {
 
   mesh_from_options.communicate(expected_2d);
 
-  EXPECT_TRUE(IsFieldEqual(coords->g11, expected_metric + 5.));
-  EXPECT_TRUE(IsFieldEqual(coords->g22, expected_metric + 4.));
-  EXPECT_TRUE(IsFieldEqual(coords->g33, expected_metric + 3.));
-  EXPECT_TRUE(IsFieldEqual(coords->g12, expected_metric + 2.));
-  EXPECT_TRUE(IsFieldEqual(coords->g13, expected_metric + 1.));
-  EXPECT_TRUE(IsFieldEqual(coords->g23, expected_metric));
+  EXPECT_TRUE(IsFieldEqual(coords->g11(), expected_metric + 5.));
+  EXPECT_TRUE(IsFieldEqual(coords->g22(), expected_metric + 4.));
+  EXPECT_TRUE(IsFieldEqual(coords->g33(), expected_metric + 3.));
+  EXPECT_TRUE(IsFieldEqual(coords->g12(), expected_metric + 2.));
+  EXPECT_TRUE(IsFieldEqual(coords->g13(), expected_metric + 1.));
+  EXPECT_TRUE(IsFieldEqual(coords->g23(), expected_metric));
 }
 
 #if not(BOUT_USE_METRIC_3D)
@@ -374,12 +374,12 @@ TEST_F(GridFromOptionsTest, CoordinatesZlow) {
 
   mesh_from_options.communicate(expected_2d);
 
-  EXPECT_TRUE(IsFieldEqual(coords->g11, expected_metric + 5.));
-  EXPECT_TRUE(IsFieldEqual(coords->g22, expected_metric + 4.));
-  EXPECT_TRUE(IsFieldEqual(coords->g33, expected_metric + 3.));
-  EXPECT_TRUE(IsFieldEqual(coords->g12, expected_metric + 2.));
-  EXPECT_TRUE(IsFieldEqual(coords->g13, expected_metric + 1.));
-  EXPECT_TRUE(IsFieldEqual(coords->g23, expected_metric));
+  EXPECT_TRUE(IsFieldEqual(coords->g11(), expected_metric + 5.));
+  EXPECT_TRUE(IsFieldEqual(coords->g22(), expected_metric + 4.));
+  EXPECT_TRUE(IsFieldEqual(coords->g33(), expected_metric + 3.));
+  EXPECT_TRUE(IsFieldEqual(coords->g12(), expected_metric + 2.));
+  EXPECT_TRUE(IsFieldEqual(coords->g13(), expected_metric + 1.));
+  EXPECT_TRUE(IsFieldEqual(coords->g23(), expected_metric));
 }
 #else
 // Maybe replace by MMS test, because we need a periodic function in z.
@@ -403,16 +403,16 @@ TEST_F(GridFromOptionsTest, CoordinatesXlowInterp) {
   mesh_from_options.communicate(expected_xlow);
 
   EXPECT_TRUE(
-      IsFieldEqual(coords->g11, expected_xlow + 5., "RGN_NOBNDRY", this_tolerance));
+      IsFieldEqual(coords->g11(), expected_xlow + 5., "RGN_NOBNDRY", this_tolerance));
   EXPECT_TRUE(
-      IsFieldEqual(coords->g22, expected_xlow + 4., "RGN_NOBNDRY", this_tolerance));
+      IsFieldEqual(coords->g22(), expected_xlow + 4., "RGN_NOBNDRY", this_tolerance));
   EXPECT_TRUE(
-      IsFieldEqual(coords->g33, expected_xlow + 3., "RGN_NOBNDRY", this_tolerance));
+      IsFieldEqual(coords->g33(), expected_xlow + 3., "RGN_NOBNDRY", this_tolerance));
   EXPECT_TRUE(
-      IsFieldEqual(coords->g12, expected_xlow + 2., "RGN_NOBNDRY", this_tolerance));
+      IsFieldEqual(coords->g12(), expected_xlow + 2., "RGN_NOBNDRY", this_tolerance));
   EXPECT_TRUE(
-      IsFieldEqual(coords->g13, expected_xlow + 1., "RGN_NOBNDRY", this_tolerance));
-  EXPECT_TRUE(IsFieldEqual(coords->g23, expected_xlow, "RGN_NOBNDRY", this_tolerance));
+      IsFieldEqual(coords->g13(), expected_xlow + 1., "RGN_NOBNDRY", this_tolerance));
+  EXPECT_TRUE(IsFieldEqual(coords->g23(), expected_xlow, "RGN_NOBNDRY", this_tolerance));
 }
 
 TEST_F(GridFromOptionsTest, CoordinatesXlowRead) {
@@ -443,18 +443,18 @@ TEST_F(GridFromOptionsTest, CoordinatesXlowRead) {
 
   mesh_from_options.communicate(expected_xlow);
 
-  EXPECT_TRUE(IsFieldEqual(coords->g11, expected_xlow + 5.));
-  EXPECT_TRUE(coords->g11.getLocation() == CELL_XLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g22, expected_xlow + 4.));
-  EXPECT_TRUE(coords->g22.getLocation() == CELL_XLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g33, expected_xlow + 3.));
-  EXPECT_TRUE(coords->g33.getLocation() == CELL_XLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g12, expected_xlow + 2.));
-  EXPECT_TRUE(coords->g12.getLocation() == CELL_XLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g13, expected_xlow + 1.));
-  EXPECT_TRUE(coords->g13.getLocation() == CELL_XLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g23, expected_xlow));
-  EXPECT_TRUE(coords->g23.getLocation() == CELL_XLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g11(), expected_xlow + 5.));
+  EXPECT_TRUE(coords->g11().getLocation() == CELL_XLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g22(), expected_xlow + 4.));
+  EXPECT_TRUE(coords->g22().getLocation() == CELL_XLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g33(), expected_xlow + 3.));
+  EXPECT_TRUE(coords->g33().getLocation() == CELL_XLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g12(), expected_xlow + 2.));
+  EXPECT_TRUE(coords->g12().getLocation() == CELL_XLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g13(), expected_xlow + 1.));
+  EXPECT_TRUE(coords->g13().getLocation() == CELL_XLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g23(), expected_xlow));
+  EXPECT_TRUE(coords->g23().getLocation() == CELL_XLOW);
 }
 
 TEST_F(GridFromOptionsTest, CoordinatesYlowInterp) {
@@ -476,22 +476,22 @@ TEST_F(GridFromOptionsTest, CoordinatesYlowInterp) {
   mesh_from_options.communicate(expected_ylow);
 
   EXPECT_TRUE(
-      IsFieldEqual(coords->g11, expected_ylow + 5., "RGN_NOBNDRY", this_tolerance));
-  EXPECT_TRUE(coords->g11.getLocation() == CELL_YLOW);
+      IsFieldEqual(coords->g11(), expected_ylow + 5., "RGN_NOBNDRY", this_tolerance));
+  EXPECT_TRUE(coords->g11().getLocation() == CELL_YLOW);
   EXPECT_TRUE(
-      IsFieldEqual(coords->g22, expected_ylow + 4., "RGN_NOBNDRY", this_tolerance));
-  EXPECT_TRUE(coords->g22.getLocation() == CELL_YLOW);
+      IsFieldEqual(coords->g22(), expected_ylow + 4., "RGN_NOBNDRY", this_tolerance));
+  EXPECT_TRUE(coords->g22().getLocation() == CELL_YLOW);
   EXPECT_TRUE(
-      IsFieldEqual(coords->g33, expected_ylow + 3., "RGN_NOBNDRY", this_tolerance));
-  EXPECT_TRUE(coords->g33.getLocation() == CELL_YLOW);
+      IsFieldEqual(coords->g33(), expected_ylow + 3., "RGN_NOBNDRY", this_tolerance));
+  EXPECT_TRUE(coords->g33().getLocation() == CELL_YLOW);
   EXPECT_TRUE(
-      IsFieldEqual(coords->g12, expected_ylow + 2., "RGN_NOBNDRY", this_tolerance));
-  EXPECT_TRUE(coords->g12.getLocation() == CELL_YLOW);
+      IsFieldEqual(coords->g12(), expected_ylow + 2., "RGN_NOBNDRY", this_tolerance));
+  EXPECT_TRUE(coords->g12().getLocation() == CELL_YLOW);
   EXPECT_TRUE(
-      IsFieldEqual(coords->g13, expected_ylow + 1., "RGN_NOBNDRY", this_tolerance));
-  EXPECT_TRUE(coords->g13.getLocation() == CELL_YLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g23, expected_ylow, "RGN_NOBNDRY", this_tolerance));
-  EXPECT_TRUE(coords->g23.getLocation() == CELL_YLOW);
+      IsFieldEqual(coords->g13(), expected_ylow + 1., "RGN_NOBNDRY", this_tolerance));
+  EXPECT_TRUE(coords->g13().getLocation() == CELL_YLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g23(), expected_ylow, "RGN_NOBNDRY", this_tolerance));
+  EXPECT_TRUE(coords->g23().getLocation() == CELL_YLOW);
 #endif
 }
 
@@ -525,18 +525,18 @@ TEST_F(GridFromOptionsTest, CoordinatesYlowRead) {
 
   mesh_from_options.communicate(expected_ylow);
 
-  EXPECT_TRUE(IsFieldEqual(coords->g11, expected_ylow + 5., "RGN_ALL", this_tolerance));
-  EXPECT_TRUE(coords->g11.getLocation() == CELL_YLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g22, expected_ylow + 4., "RGN_ALL", this_tolerance));
-  EXPECT_TRUE(coords->g22.getLocation() == CELL_YLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g33, expected_ylow + 3., "RGN_ALL", this_tolerance));
-  EXPECT_TRUE(coords->g33.getLocation() == CELL_YLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g12, expected_ylow + 2., "RGN_ALL", this_tolerance));
-  EXPECT_TRUE(coords->g12.getLocation() == CELL_YLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g13, expected_ylow + 1., "RGN_ALL", this_tolerance));
-  EXPECT_TRUE(coords->g13.getLocation() == CELL_YLOW);
-  EXPECT_TRUE(IsFieldEqual(coords->g23, expected_ylow, "RGN_ALL", this_tolerance));
-  EXPECT_TRUE(coords->g23.getLocation() == CELL_YLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g11(), expected_ylow + 5., "RGN_ALL", this_tolerance));
+  EXPECT_TRUE(coords->g11().getLocation() == CELL_YLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g22(), expected_ylow + 4., "RGN_ALL", this_tolerance));
+  EXPECT_TRUE(coords->g22().getLocation() == CELL_YLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g33(), expected_ylow + 3., "RGN_ALL", this_tolerance));
+  EXPECT_TRUE(coords->g33().getLocation() == CELL_YLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g12(), expected_ylow + 2., "RGN_ALL", this_tolerance));
+  EXPECT_TRUE(coords->g12().getLocation() == CELL_YLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g13(), expected_ylow + 1., "RGN_ALL", this_tolerance));
+  EXPECT_TRUE(coords->g13().getLocation() == CELL_YLOW);
+  EXPECT_TRUE(IsFieldEqual(coords->g23(), expected_ylow, "RGN_ALL", this_tolerance));
+  EXPECT_TRUE(coords->g23().getLocation() == CELL_YLOW);
 #endif
 }
 
@@ -547,11 +547,11 @@ TEST_F(GridFromOptionsTest, CoordinatesZlowRead) {
 
   auto coords = mesh_from_options.getCoordinates(CELL_ZLOW);
 
-  EXPECT_TRUE(IsFieldEqual(coords->g11, expected_2d + 5.));
-  EXPECT_TRUE(IsFieldEqual(coords->g22, expected_2d + 4.));
-  EXPECT_TRUE(IsFieldEqual(coords->g33, expected_2d + 3.));
-  EXPECT_TRUE(IsFieldEqual(coords->g12, expected_2d + 2.));
-  EXPECT_TRUE(IsFieldEqual(coords->g13, expected_2d + 1.));
-  EXPECT_TRUE(IsFieldEqual(coords->g23, expected_2d));
+  EXPECT_TRUE(IsFieldEqual(coords->g11(), expected_2d + 5.));
+  EXPECT_TRUE(IsFieldEqual(coords->g22(), expected_2d + 4.));
+  EXPECT_TRUE(IsFieldEqual(coords->g33(), expected_2d + 3.));
+  EXPECT_TRUE(IsFieldEqual(coords->g12(), expected_2d + 2.));
+  EXPECT_TRUE(IsFieldEqual(coords->g13(), expected_2d + 1.));
+  EXPECT_TRUE(IsFieldEqual(coords->g23(), expected_2d));
 #endif
 }
diff --git a/tests/unit/mesh/parallel/test_shiftedmetric.cxx b/tests/unit/mesh/parallel/test_shiftedmetric.cxx
index 579e6fdd7b..30839bf393 100644
--- a/tests/unit/mesh/parallel/test_shiftedmetric.cxx
+++ b/tests/unit/mesh/parallel/test_shiftedmetric.cxx
@@ -44,7 +44,6 @@ class ShiftedMetricTest : public ::testing::Test {
         Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0}, Field2D{0.0},
         Field2D{0.0}, Field2D{1.0}, Field2D{1.0}, Field2D{1.0}, Field2D{0.0},
         Field2D{0.0}, Field2D{0.0}, Field2D{0.0}, Field2D{0.0}));
-    // No call to Coordinates::geometry() needed here
 
     auto coords = mesh->getCoordinates();
     coords->setParallelTransform(bout::utils::make_unique<Transform>(
diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx
index 8e1aa2e13f..532ccff6db 100644
--- a/tests/unit/mesh/test_coordinates.cxx
+++ b/tests/unit/mesh/test_coordinates.cxx
@@ -1,4 +1,5 @@
 #include "gtest/gtest.h"
+#include <cmath>
 
 #include "bout/build_defines.hxx"
 #include "bout/constants.hxx"
@@ -6,6 +7,7 @@
 #include "bout/mesh.hxx"
 #include "bout/output.hxx"
 
+#include "fake_mesh.hxx"
 #include "fake_mesh_fixture.hxx"
 #include "test_extras.hxx"
 
@@ -42,7 +44,6 @@ TEST_F(CoordinatesTest, ZLength) {
                      FieldMetric{0.0},  // g_23
                      FieldMetric{0.0},  // ShiftTorsion
                      FieldMetric{0.0}}; // IntShiftTorsion
-  // No call to Coordinates::geometry() needed here
 
   EXPECT_TRUE(IsFieldEqual(coords.zlength(), 7.0));
 }
@@ -75,7 +76,6 @@ TEST_F(CoordinatesTest, ZLength3D) {
                      FieldMetric{0.0},  // g_23
                      FieldMetric{0.0},  // ShiftTorsion
                      FieldMetric{0.0}}; // IntShiftTorsion
-  // No call to Coordinates::geometry() needed here
 
   EXPECT_TRUE(IsFieldEqual(coords.zlength(), expected));
 }
@@ -102,12 +102,11 @@ TEST_F(CoordinatesTest, Jacobian) {
                      FieldMetric{0.0},  // g_23
                      FieldMetric{0.0},  // ShiftTorsion
                      FieldMetric{0.0}}; // IntShiftTorsion
-  // No call to Coordinates::geometry() needed here
 
-  EXPECT_NO_THROW(coords.jacobian());
+  EXPECT_NO_THROW(coords.recalculateJacobian());
 
-  EXPECT_TRUE(IsFieldEqual(coords.J, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.J(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.Bxy(), 1.0));
 }
 
 /// To do generalise these tests
@@ -133,16 +132,16 @@ TEST_F(CoordinatesTest, CalcContravariant) {
                      FieldMetric{0.0},  // g_23
                      FieldMetric{0.0},  // ShiftTorsion
                      FieldMetric{0.0}}; // IntShiftTorsion
-  // No call to Coordinates::geometry() needed here
 
-  coords.calcCovariant();
+  coords.setContravariantMetricTensor(
+      ContravariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.g_11, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_22, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_33, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_12, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_13, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_23, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_11(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_22(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_33(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_12(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_13(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_23(), 0.0));
 }
 
 TEST_F(CoordinatesTest, CalcCovariant) {
@@ -166,35 +165,34 @@ TEST_F(CoordinatesTest, CalcCovariant) {
                      FieldMetric{0.0},  // g_23
                      FieldMetric{0.0},  // ShiftTorsion
                      FieldMetric{0.0}}; // IntShiftTorsion
-  // No call to Coordinates::geometry() needed here
 
-  coords.calcContravariant();
+  coords.setCovariantMetricTensor(CovariantMetricTensor(1.0, 1.0, 1.0, 0.0, 0.0, 0.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.g11, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g22, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g33, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g12, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g13, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g23, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g11(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g22(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g33(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g12(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g13(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g23(), 0.0));
 }
 // #endif
 
 TEST_F(CoordinatesTest, DefaultConstructor) {
   Coordinates coords(mesh);
 
-  EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dz, default_dz));
+  EXPECT_TRUE(IsFieldEqual(coords.dx(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dy(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dz(), default_dz));
 
-  EXPECT_TRUE(IsFieldEqual(coords.g11, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g22, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g33, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g12, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g13, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g23, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g11(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g22(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g33(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g12(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g13(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g23(), 0.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.J, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.J(), 1.0, "RGN_NOCORNERS"));
+  EXPECT_TRUE(IsFieldEqual(coords.Bxy(), 1.0, "RGN_NOCORNERS"));
 }
 
 TEST_F(CoordinatesTest, ConstructWithMeshSpacing) {
@@ -204,58 +202,58 @@ TEST_F(CoordinatesTest, ConstructWithMeshSpacing) {
 
   Coordinates coords(mesh);
 
-  EXPECT_TRUE(IsFieldEqual(coords.dx, 2.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dy, 3.2));
-  EXPECT_TRUE(IsFieldEqual(coords.dz, 42.));
+  EXPECT_TRUE(IsFieldEqual(coords.dx(), 2.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dy(), 3.2));
+  EXPECT_TRUE(IsFieldEqual(coords.dz(), 42.));
 
-  EXPECT_TRUE(IsFieldEqual(coords.g11, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g22, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g33, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g12, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g13, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g23, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g11(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g22(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g33(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g12(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g13(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g23(), 0.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.J, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.J(), 1.0, "RGN_NOCORNERS"));
+  EXPECT_TRUE(IsFieldEqual(coords.Bxy(), 1.0, "RGN_NOCORNERS"));
 }
 
 TEST_F(CoordinatesTest, SmallMeshSpacing) {
   static_cast<FakeMesh*>(bout::globals::mesh)
       ->setGridDataSource(new FakeGridDataSource({{"dx", 1e-9}}));
 
-  Coordinates coords(mesh);
-  EXPECT_THROW(coords.geometry(), BoutException);
+  WithQuietOutput quiet_info{output_info};
+  WithQuietOutput quiet_warn{output_warn};
+  EXPECT_THROW(Coordinates{mesh}, BoutException);
 }
 
 TEST_F(CoordinatesTest, ConstructWithDiagonalContravariantMetric) {
 
-  static_cast<FakeMesh*>(bout::globals::mesh)
-      ->setGridDataSource(
-          new FakeGridDataSource({{"g11", 2.0}, {"g22", 3.2}, {"g33", 42}}));
+  dynamic_cast<FakeMesh*>(mesh)->setGridDataSource(
+      new FakeGridDataSource({{"g11", 2.0}, {"g22", 3.2}, {"g33", 42}}));
 
-  Coordinates coords(mesh);
+  const Coordinates coords(mesh);
 
   // Didn't specify grid spacing, so default to 1
-  EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dz, default_dz));
+  EXPECT_TRUE(IsFieldEqual(coords.dx(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dy(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dz(), default_dz));
 
   // Diagonal contravariant metric
-  EXPECT_TRUE(IsFieldEqual(coords.g11, 2.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g22, 3.2));
-  EXPECT_TRUE(IsFieldEqual(coords.g33, 42));
-  EXPECT_TRUE(IsFieldEqual(coords.g12, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g13, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g23, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g11(), 2.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g22(), 3.2));
+  EXPECT_TRUE(IsFieldEqual(coords.g33(), 42));
+  EXPECT_TRUE(IsFieldEqual(coords.g12(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g13(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g23(), 0.0));
 
   // Covariant metric should be inverse
   // Note: Not calculated in corners
-  EXPECT_TRUE(IsFieldEqual(coords.g_11, 1. / 2.0, "RGN_NOCORNERS"));
-  EXPECT_TRUE(IsFieldEqual(coords.g_22, 1. / 3.2, "RGN_NOCORNERS"));
-  EXPECT_TRUE(IsFieldEqual(coords.g_33, 1. / 42, "RGN_NOCORNERS"));
+  EXPECT_TRUE(IsFieldEqual(coords.g_11(), 1. / 2.0, "RGN_NOCORNERS"));
+  EXPECT_TRUE(IsFieldEqual(coords.g_22(), 1. / 3.2, "RGN_NOCORNERS"));
+  EXPECT_TRUE(IsFieldEqual(coords.g_33(), 1. / 42, "RGN_NOCORNERS"));
 
-  EXPECT_TRUE(IsFieldEqual(coords.J, 1. / sqrt(2.0 * 3.2 * 42), "RGN_NOCORNERS"));
-  EXPECT_TRUE(IsFieldEqual(coords.Bxy, sqrt(2.0 * 42), "RGN_NOCORNERS", 1e-10));
+  EXPECT_TRUE(IsFieldEqual(coords.J(), 1. / sqrt(2.0 * 3.2 * 42), "RGN_NOCORNERS"));
+  EXPECT_TRUE(IsFieldEqual(coords.Bxy(), sqrt(2.0 * 42), "RGN_NOCORNERS", 1e-10));
 }
 
 TEST_F(CoordinatesTest, NegativeJacobian) {
@@ -294,21 +292,19 @@ TEST_F(CoordinatesTest, CellAreas) {
                      FieldMetric{0.0},  // g_23
                      FieldMetric{0.0},  // ShiftTorsion
                      FieldMetric{0.0}}; // IntShiftTorsion
-  // No call to Coordinates::geometry() needed here
-
-  EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dz, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dx(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dy(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dz(), 1.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.g_11, 4.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_22, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_33, 9.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_12, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_13, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_23, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_11(), 4.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_22(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_33(), 9.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_12(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_13(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_23(), 0.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.J, 6.0));
-  EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.J(), 6.0));
+  EXPECT_TRUE(IsFieldEqual(coords.Bxy(), 1.0));
 
   EXPECT_TRUE(IsFieldEqual(coords.cell_area_xlow(), 3.0, "RGN_NOX"));
   EXPECT_TRUE(IsFieldEqual(coords.cell_area_xhigh(), 3.0, "RGN_NOX"));
@@ -343,19 +339,19 @@ TEST_F(CoordinatesTest, CellAreasUpdate) {
                      FieldMetric{0.0}}; // IntShiftTorsion
   // No call to Coordinates::geometry() needed here
 
-  EXPECT_TRUE(IsFieldEqual(coords.dx, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dy, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.dz, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dx(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dy(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.dz(), 1.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.g_11, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_22, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_33, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_12, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_13, 0.0));
-  EXPECT_TRUE(IsFieldEqual(coords.g_23, 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_11(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_22(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_33(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_12(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_13(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g_23(), 0.0));
 
-  EXPECT_TRUE(IsFieldEqual(coords.J, 1.0));
-  EXPECT_TRUE(IsFieldEqual(coords.Bxy, 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.J(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.Bxy(), 1.0));
 
   coords.cell_area_xlow() *= 2;
   coords.cell_area_xhigh() *= 3;
@@ -401,3 +397,282 @@ TEST_F(CoordinatesTest, CellAreaZComputedAfterCellVolume) {
   EXPECT_TRUE(IsFieldEqual(coords.cell_area_zlow(), 2.0, "RGN_NOZ"));
   EXPECT_TRUE(IsFieldEqual(coords.cell_area_zhigh(), 2.0, "RGN_NOZ"));
 }
+
+TEST_F(CoordinatesTest, GetContravariantMetricTensor) {
+  Coordinates coords{mesh,
+                     FieldMetric{1.0},  // dx
+                     FieldMetric{1.0},  // dy
+                     FieldMetric{1.0},  // dz
+                     FieldMetric{0.0},  // J
+                     FieldMetric{0.0},  // Bxy
+                     FieldMetric{1.2},  // g11
+                     FieldMetric{2.3},  // g22
+                     FieldMetric{3.4},  // g33
+                     FieldMetric{4.5},  // g12
+                     FieldMetric{5.6},  // g13
+                     FieldMetric{6.7},  // g23
+                     FieldMetric{1.0},  // g_11
+                     FieldMetric{1.0},  // g_22
+                     FieldMetric{1.0},  // g_23
+                     FieldMetric{0.0},  // g_12
+                     FieldMetric{0.0},  // g_13
+                     FieldMetric{0.0},  // g_23
+                     FieldMetric{0.0},  // ShiftTorsion
+                     FieldMetric{0.0}}; // IntShiftTorsion
+
+  EXPECT_TRUE(IsFieldEqual(coords.g11(), 1.2));
+  EXPECT_TRUE(IsFieldEqual(coords.g22(), 2.3));
+  EXPECT_TRUE(IsFieldEqual(coords.g33(), 3.4));
+  EXPECT_TRUE(IsFieldEqual(coords.g12(), 4.5));
+  EXPECT_TRUE(IsFieldEqual(coords.g13(), 5.6));
+  EXPECT_TRUE(IsFieldEqual(coords.g23(), 6.7));
+}
+
+TEST_F(CoordinatesTest, SetContravariantMetricTensor) {
+  // Set initial values for the metric tensor in the Coordinates constructor
+  Coordinates coords{mesh,
+                     FieldMetric{1.0},  // dx
+                     FieldMetric{1.0},  // dy
+                     FieldMetric{1.0},  // dz
+                     FieldMetric{0.0},  // J
+                     FieldMetric{0.0},  // Bxy
+                     FieldMetric{0.0},  // g11
+                     FieldMetric{0.0},  // g22
+                     FieldMetric{0.0},  // g33
+                     FieldMetric{0.0},  // g12
+                     FieldMetric{0.0},  // g13
+                     FieldMetric{0.0},  // g23
+                     FieldMetric{1.0},  // g_11
+                     FieldMetric{1.0},  // g_22
+                     FieldMetric{1.0},  // g_23
+                     FieldMetric{0.0},  // g_12
+                     FieldMetric{0.0},  // g_13
+                     FieldMetric{0.0},  // g_23
+                     FieldMetric{0.0},  // ShiftTorsion
+                     FieldMetric{0.0}}; // IntShiftTorsion
+
+  //  Modify with setter
+  auto updated_metric_tensor = ContravariantMetricTensor(1.0, 2.0, 0.4, 1.0, 0.0, 0.2);
+  coords.setContravariantMetricTensor(updated_metric_tensor);
+
+  //  Get values with getter and check they have been modified as expected
+  EXPECT_TRUE(IsFieldEqual(coords.g11(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g22(), 2.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g33(), 0.4));
+  EXPECT_TRUE(IsFieldEqual(coords.g12(), 1.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g13(), 0.0));
+  EXPECT_TRUE(IsFieldEqual(coords.g23(), 0.2));
+}
+
+TEST_F(CoordinatesTest, CheckCovariantCalculatedFromContravariant) {
+
+  // Set initial values for the metric tensor in the Coordinates constructor
+  Coordinates coords{mesh,
+                     FieldMetric{1.0},  // dx
+                     FieldMetric{1.0},  // dy
+                     FieldMetric{1.0},  // dz
+                     FieldMetric{0.0},  // J
+                     FieldMetric{0.0},  // Bxy
+                     FieldMetric{0.0},  // g11
+                     FieldMetric{0.0},  // g22
+                     FieldMetric{0.0},  // g33
+                     FieldMetric{0.0},  // g12
+                     FieldMetric{0.0},  // g13
+                     FieldMetric{0.0},  // g23
+                     FieldMetric{1.0},  // g_11
+                     FieldMetric{1.0},  // g_22
+                     FieldMetric{1.0},  // g_23
+                     FieldMetric{0.0},  // g_12
+                     FieldMetric{0.0},  // g_13
+                     FieldMetric{0.0},  // g_23
+                     FieldMetric{0.0},  // ShiftTorsion
+                     FieldMetric{0.0}}; // IntShiftTorsion
+
+  //  Modify contravariant components
+  constexpr double g11 = 1.0;
+  constexpr double g22 = 1.0;
+  constexpr double g33 = 1.0;
+  const double g12 = sqrt(3.0) / 4.0; // (std::sqrt only constexpr since C++26)
+  constexpr double g13 = 0.5;
+  const double g23 = sqrt(3.0) / 4.0; // (std::sqrt only constexpr since C++26)
+  auto updated_metric_tensor = ContravariantMetricTensor(g11, g22, g33, g12, g13, g23);
+  coords.setContravariantMetricTensor(updated_metric_tensor);
+
+  //  Check that the covariant components have been calculated corrected
+  constexpr double expected_g_11 = 13.0 / 9.0;
+  constexpr double expected_g_22 = 4.0 / 3.0;
+  constexpr double expected_g_33 = 13.0 / 9.0;
+  const double expected_g_12 = -2.0 * sqrt(3.0) / 9.0;
+  constexpr double expected_g_13 = -5.0 / 9.0;
+  const double expected_g_23 = -2.0 * sqrt(3.0) / 9.0;
+
+  EXPECT_TRUE(IsFieldEqual(coords.g_11(), expected_g_11));
+  EXPECT_TRUE(IsFieldEqual(coords.g_22(), expected_g_22));
+  EXPECT_TRUE(IsFieldEqual(coords.g_33(), expected_g_33));
+  EXPECT_TRUE(IsFieldEqual(coords.g_12(), expected_g_12));
+  EXPECT_TRUE(IsFieldEqual(coords.g_13(), expected_g_13));
+  EXPECT_TRUE(IsFieldEqual(coords.g_23(), expected_g_23));
+}
+
+TEST_F(CoordinatesTest, CheckContravariantCalculatedFromCovariant) {
+
+  // Set initial values for the metric tensor in the Coordinates constructor
+  Coordinates coords{mesh,
+                     FieldMetric{1.0},  // dx
+                     FieldMetric{1.0},  // dy
+                     FieldMetric{1.0},  // dz
+                     FieldMetric{0.0},  // J
+                     FieldMetric{0.0},  // Bxy
+                     FieldMetric{0.0},  // g11
+                     FieldMetric{0.0},  // g22
+                     FieldMetric{0.0},  // g33
+                     FieldMetric{0.0},  // g12
+                     FieldMetric{0.0},  // g13
+                     FieldMetric{0.0},  // g23
+                     FieldMetric{1.0},  // g_11
+                     FieldMetric{1.0},  // g_22
+                     FieldMetric{1.0},  // g_23
+                     FieldMetric{0.0},  // g_12
+                     FieldMetric{0.0},  // g_13
+                     FieldMetric{0.0},  // g_23
+                     FieldMetric{0.0},  // ShiftTorsion
+                     FieldMetric{0.0}}; // IntShiftTorsion
+
+  //  Modify covariant components
+  constexpr double g_11 = 1.0;
+  constexpr double g_22 = 1.0;
+  constexpr double g_33 = 1.0;
+  const double g_12 = sqrt(3.0) / 4.0; // (std::sqrt only constexpr since C++26)
+  constexpr double g_13 = 0.5;
+  const double g_23 = sqrt(3.0) / 4.0; // (std::sqrt only constexpr since C++26)
+  auto updated_metric_tensor = CovariantMetricTensor(g_11, g_22, g_33, g_12, g_13, g_23);
+  coords.setCovariantMetricTensor(updated_metric_tensor);
+
+  //  Check that the contravariant components have been calculated corrected
+  constexpr double expected_g11 = 13.0 / 9.0;
+  constexpr double expected_g22 = 4.0 / 3.0;
+  constexpr double expected_g33 = 13.0 / 9.0;
+  const double expected_g12 = -2.0 * sqrt(3.0) / 9.0;
+  constexpr double expected_g13 = -5.0 / 9.0;
+  const double expected_g23 = -2.0 * sqrt(3.0) / 9.0;
+
+  EXPECT_TRUE(IsFieldEqual(coords.g11(), expected_g11));
+  EXPECT_TRUE(IsFieldEqual(coords.g22(), expected_g22));
+  EXPECT_TRUE(IsFieldEqual(coords.g33(), expected_g33));
+  EXPECT_TRUE(IsFieldEqual(coords.g12(), expected_g12));
+  EXPECT_TRUE(IsFieldEqual(coords.g13(), expected_g13));
+  EXPECT_TRUE(IsFieldEqual(coords.g23(), expected_g23));
+}
+
+TEST_F(CoordinatesTest, GetCovariantMetricTensor) {
+  Coordinates coords{mesh,
+                     FieldMetric{1.0},  // dx
+                     FieldMetric{1.0},  // dy
+                     FieldMetric{1.0},  // dz
+                     FieldMetric{0.0},  // J
+                     FieldMetric{0.0},  // Bxy
+                     FieldMetric{1.2},  // g11
+                     FieldMetric{2.3},  // g22
+                     FieldMetric{3.4},  // g33
+                     FieldMetric{4.5},  // g12
+                     FieldMetric{5.6},  // g13
+                     FieldMetric{6.7},  // g23
+                     FieldMetric{9.7},  // g_11
+                     FieldMetric{7.5},  // g_22
+                     FieldMetric{4.7},  // g_23
+                     FieldMetric{3.9},  // g_12
+                     FieldMetric{1.7},  // g_13
+                     FieldMetric{5.3},  // g_23
+                     FieldMetric{0.0},  // ShiftTorsion
+                     FieldMetric{0.0}}; // IntShiftTorsion
+
+  EXPECT_TRUE(IsFieldEqual(coords.g_11(), 9.7));
+  EXPECT_TRUE(IsFieldEqual(coords.g_22(), 7.5));
+  EXPECT_TRUE(IsFieldEqual(coords.g_33(), 4.7));
+  EXPECT_TRUE(IsFieldEqual(coords.g_12(), 3.9));
+  EXPECT_TRUE(IsFieldEqual(coords.g_13(), 1.7));
+  EXPECT_TRUE(IsFieldEqual(coords.g_23(), 5.3));
+}
+
+TEST_F(CoordinatesTest, SetCovariantMetricTensor) {
+  {
+    // Set initial values for the metric tensor in the Coordinates constructor
+    Coordinates coords{mesh,
+                       FieldMetric{1.0},  // dx
+                       FieldMetric{1.0},  // dy
+                       FieldMetric{1.0},  // dz
+                       FieldMetric{0.0},  // J
+                       FieldMetric{0.0},  // Bxy
+                       FieldMetric{0.0},  // g11
+                       FieldMetric{0.0},  // g22
+                       FieldMetric{0.0},  // g33
+                       FieldMetric{0.0},  // g12
+                       FieldMetric{0.0},  // g13
+                       FieldMetric{0.0},  // g23
+                       FieldMetric{1.0},  // g_11
+                       FieldMetric{1.0},  // g_22
+                       FieldMetric{1.0},  // g_23
+                       FieldMetric{0.0},  // g_12
+                       FieldMetric{0.0},  // g_13
+                       FieldMetric{0.0},  // g_23
+                       FieldMetric{0.0},  // ShiftTorsion
+                       FieldMetric{0.0}}; // IntShiftTorsion
+
+    //  Modify with setter
+    auto updated_metric_tensor = CovariantMetricTensor(1.0, 2.0, 0.4, 1.0, 0.0, 0.2);
+    coords.setCovariantMetricTensor(updated_metric_tensor);
+
+    //  Get values with getter and check they have been modified as expected
+    EXPECT_TRUE(IsFieldEqual(coords.g_11(), 1.0));
+    EXPECT_TRUE(IsFieldEqual(coords.g_22(), 2.0));
+    EXPECT_TRUE(IsFieldEqual(coords.g_33(), 0.4));
+    EXPECT_TRUE(IsFieldEqual(coords.g_12(), 1.0));
+    EXPECT_TRUE(IsFieldEqual(coords.g_13(), 0.0));
+    EXPECT_TRUE(IsFieldEqual(coords.g_23(), 0.2));
+  }
+}
+
+TEST_F(CoordinatesTest, IndexedAccessors) {
+
+  int x = mesh->xstart;
+  int y = mesh->ystart;
+#if BOUT_USE_METRIC_3D
+  int z = mesh->LocalNz;
+#endif
+
+  output_info.disable();
+  output_warn.disable();
+  Coordinates coords(mesh);
+  output_warn.enable();
+  output_info.enable();
+
+  const auto& dx = coords.dx();
+  const auto& dy = coords.dy();
+#if BOUT_USE_METRIC_3D
+  const auto& dz = coords.dz();
+#endif
+
+#if not(BOUT_USE_METRIC_3D)
+  const BoutReal expected_dx = dx(x, y);
+  const BoutReal expected_dy = dy(x, y);
+#else
+  const BoutReal expected_dx = dx(x, y, z);
+  const BoutReal expected_dy = dy(x, y, z);
+  const BoutReal expected_dz = dz(x, y, z);
+#endif
+
+#if not(BOUT_USE_METRIC_3D)
+  const FieldMetric& actual_dx = coords.dx(x, y);
+  const FieldMetric& actual_dy = coords.dy(x, y);
+#else
+  const Field3D& actual_dx = coords.dx(x, y, z);
+  const Field3D& actual_dy = coords.dy(x, y, z);
+  const Field3D& actual_dz = coords.dz(x, y, z);
+#endif
+
+  EXPECT_EQ(actual_dx, expected_dx);
+  EXPECT_EQ(actual_dy, expected_dy);
+#if BOUT_USE_METRIC_3D
+  EXPECT_EQ(actual_dz, expected_dz);
+#endif
+}
diff --git a/tests/unit/mesh/test_coordinates_accessor.cxx b/tests/unit/mesh/test_coordinates_accessor.cxx
index 16985981bb..47fde99d17 100644
--- a/tests/unit/mesh/test_coordinates_accessor.cxx
+++ b/tests/unit/mesh/test_coordinates_accessor.cxx
@@ -1,6 +1,8 @@
 #include "gtest/gtest.h"
 
+#include "bout/build_config.hxx"
 #include "bout/build_defines.hxx"
+#include "bout/coordinates.hxx"
 #include "bout/coordinates_accessor.hxx"
 
 #include "fake_mesh_fixture.hxx"
@@ -52,41 +54,48 @@ TEST_F(CoordinatesAccessorTest, ClearOneReused) {
   EXPECT_EQ(CoordinatesAccessor::clear(), 1);
 }
 
+namespace {
+struct TestCoordinates : public Coordinates {
+  using Coordinates::Coordinates;
+  using Coordinates::splitBxyParallelSlices;
+};
+} // namespace
+
 TEST_F(CoordinatesAccessorTest, ClearBoth) {
   CoordinatesAccessor::clear(); // Should clear any left over
 
   // Make a new Coordinates object to access
-  Coordinates coords{mesh,
-                     FieldMetric{1.0},  // dx
-                     FieldMetric{1.0},  // dy
-                     FieldMetric{1.0},  // dz
-                     FieldMetric{1.0},  // J
-                     FieldMetric{1.0},  // Bxy
-                     FieldMetric{1.0},  // g11
-                     FieldMetric{1.0},  // g22
-                     FieldMetric{1.0},  // g33
-                     FieldMetric{0.0},  // g12
-                     FieldMetric{0.0},  // g13
-                     FieldMetric{0.0},  // g23
-                     FieldMetric{1.0},  // g_11
-                     FieldMetric{1.0},  // g_22
-                     FieldMetric{1.0},  // g_23
-                     FieldMetric{0.0},  // g_12
-                     FieldMetric{0.0},  // g_13
-                     FieldMetric{0.0},  // g_23
-                     FieldMetric{0.0},  // ShiftTorsion
-                     FieldMetric{0.0}}; // IntShiftTorsion
+  TestCoordinates coords{mesh,
+                         FieldMetric{1.0},  // dx
+                         FieldMetric{1.0},  // dy
+                         FieldMetric{1.0},  // dz
+                         FieldMetric{1.0},  // J
+                         FieldMetric{1.0},  // Bxy
+                         FieldMetric{1.0},  // g11
+                         FieldMetric{1.0},  // g22
+                         FieldMetric{1.0},  // g33
+                         FieldMetric{0.0},  // g12
+                         FieldMetric{0.0},  // g13
+                         FieldMetric{0.0},  // g23
+                         FieldMetric{1.0},  // g_11
+                         FieldMetric{1.0},  // g_22
+                         FieldMetric{1.0},  // g_23
+                         FieldMetric{0.0},  // g_12
+                         FieldMetric{0.0},  // g_13
+                         FieldMetric{0.0},  // g_23
+                         FieldMetric{0.0},  // ShiftTorsion
+                         FieldMetric{0.0}}; // IntShiftTorsion
   // Need to set geometry information
-  coords.G1 = coords.G2 = coords.G3 = 0.2;
-  coords.non_uniform = true;
-  coords.d1_dx = coords.d1_dy = coords.d1_dz = 0.1;
-#if BOUT_USE_METRIC_3D
-  coords.Bxy.splitParallelSlices();
-  coords.Bxy.yup() = coords.Bxy.ydown() = coords.Bxy;
-#endif
+  coords.setNon_uniform(true);
+  coords.setD1_dx(0.1);
+  coords.setD1_dy(0.1);
+  coords.setD1_dz(0.1);
+  if (bout::build::use_metric_3d) {
+    coords.splitBxyParallelSlices();
+  }
 
-  CoordinatesAccessor acc(mesh->getCoordinates());
-  CoordinatesAccessor acc2(&coords); // Different from previous Coordinates
+  const CoordinatesAccessor acc(mesh->getCoordinates());
+  const CoordinatesAccessor acc2(&coords); // Different from previous Coordinates
 
   // Clear both
   EXPECT_EQ(CoordinatesAccessor::clear(), 2);
@@ -96,37 +105,37 @@ TEST_F(CoordinatesAccessorTest, ClearOneTwo) {
   CoordinatesAccessor::clear(); // Should clear any left over
 
   // Make a new Coordinates object to access
-  Coordinates coords{mesh,
-                     FieldMetric{1.0},  // dx
-                     FieldMetric{1.0},  // dy
-                     FieldMetric{1.0},  // dz
-                     FieldMetric{1.0},  // J
-                     FieldMetric{1.0},  // Bxy
-                     FieldMetric{1.0},  // g11
-                     FieldMetric{1.0},  // g22
-                     FieldMetric{1.0},  // g33
-                     FieldMetric{0.0},  // g12
-                     FieldMetric{0.0},  // g13
-                     FieldMetric{0.0},  // g23
-                     FieldMetric{1.0},  // g_11
-                     FieldMetric{1.0},  // g_22
-                     FieldMetric{1.0},  // g_23
-                     FieldMetric{0.0},  // g_12
-                     FieldMetric{0.0},  // g_13
-                     FieldMetric{0.0},  // g_23
-                     FieldMetric{0.0},  // ShiftTorsion
-                     FieldMetric{0.0}}; // IntShiftTorsion
+  TestCoordinates coords{mesh,
+                         FieldMetric{1.0},  // dx
+                         FieldMetric{1.0},  // dy
+                         FieldMetric{1.0},  // dz
+                         FieldMetric{1.0},  // J
+                         FieldMetric{1.0},  // Bxy
+                         FieldMetric{1.0},  // g11
+                         FieldMetric{1.0},  // g22
+                         FieldMetric{1.0},  // g33
+                         FieldMetric{0.0},  // g12
+                         FieldMetric{0.0},  // g13
+                         FieldMetric{0.0},  // g23
+                         FieldMetric{1.0},  // g_11
+                         FieldMetric{1.0},  // g_22
+                         FieldMetric{1.0},  // g_23
+                         FieldMetric{0.0},  // g_12
+                         FieldMetric{0.0},  // g_13
+                         FieldMetric{0.0},  // g_23
+                         FieldMetric{0.0},  // ShiftTorsion
+                         FieldMetric{0.0}}; // IntShiftTorsion
   // Need to set geometry information
-  coords.G1 = coords.G2 = coords.G3 = 0.2;
-  coords.non_uniform = true;
-  coords.d1_dx = coords.d1_dy = coords.d1_dz = 0.1;
-#if BOUT_USE_METRIC_3D
-  coords.Bxy.splitParallelSlices();
-  coords.Bxy.yup() = coords.Bxy.ydown() = coords.Bxy;
-#endif
+  coords.setNon_uniform(true);
+  coords.setD1_dx(0.1);
+  coords.setD1_dy(0.1);
+  coords.setD1_dz(0.1);
+  if (bout::build::use_metric_3d) {
+    coords.splitBxyParallelSlices();
+  }
 
-  CoordinatesAccessor acc(mesh->getCoordinates());
-  CoordinatesAccessor acc2(&coords); // Different from previous Coordinates
+  const CoordinatesAccessor acc(mesh->getCoordinates());
+  const CoordinatesAccessor acc2(&coords); // Different from previous Coordinates
 
   // clear first one
   EXPECT_EQ(CoordinatesAccessor::clear(mesh->getCoordinates()), 1);
@@ -138,37 +147,37 @@ TEST_F(CoordinatesAccessorTest, ClearTwoOneNone) {
   CoordinatesAccessor::clear(); // Should clear any left over
 
   // Make a new Coordinates object to access
-  Coordinates coords{mesh,
-                     FieldMetric{1.0},  // dx
-                     FieldMetric{1.0},  // dy
-                     FieldMetric{1.0},  // dz
-                     FieldMetric{1.0},  // J
-                     FieldMetric{1.0},  // Bxy
-                     FieldMetric{1.0},  // g11
-                     FieldMetric{1.0},  // g22
-                     FieldMetric{1.0},  // g33
-                     FieldMetric{0.0},  // g12
-                     FieldMetric{0.0},  // g13
-                     FieldMetric{0.0},  // g23
-                     FieldMetric{1.0},  // g_11
-                     FieldMetric{1.0},  // g_22
-                     FieldMetric{1.0},  // g_23
-                     FieldMetric{0.0},  // g_12
-                     FieldMetric{0.0},  // g_13
-                     FieldMetric{0.0},  // g_23
-                     FieldMetric{0.0},  // ShiftTorsion
-                     FieldMetric{0.0}}; // IntShiftTorsion
+  TestCoordinates coords{mesh,
+                         FieldMetric{1.0},  // dx
+                         FieldMetric{1.0},  // dy
+                         FieldMetric{1.0},  // dz
+                         FieldMetric{1.0},  // J
+                         FieldMetric{1.0},  // Bxy
+                         FieldMetric{1.0},  // g11
+                         FieldMetric{1.0},  // g22
+                         FieldMetric{1.0},  // g33
+                         FieldMetric{0.0},  // g12
+                         FieldMetric{0.0},  // g13
+                         FieldMetric{0.0},  // g23
+                         FieldMetric{1.0},  // g_11
+                         FieldMetric{1.0},  // g_22
+                         FieldMetric{1.0},  // g_23
+                         FieldMetric{0.0},  // g_12
+                         FieldMetric{0.0},  // g_13
+                         FieldMetric{0.0},  // g_23
+                         FieldMetric{0.0},  // ShiftTorsion
+                         FieldMetric{0.0}}; // IntShiftTorsion
   // Need to set geometry information
-  coords.G1 = coords.G2 = coords.G3 = 0.2;
-  coords.non_uniform = true;
-  coords.d1_dx = coords.d1_dy = coords.d1_dz = 0.1;
-#if BOUT_USE_METRIC_3D
-  coords.Bxy.splitParallelSlices();
-  coords.Bxy.yup() = coords.Bxy.ydown() = coords.Bxy;
-#endif
-
-  CoordinatesAccessor acc(mesh->getCoordinates());
-  CoordinatesAccessor acc2(&coords); // Different from previous Coordinates
+  coords.setNon_uniform(true);
+  coords.setD1_dx(0.1);
+  coords.setD1_dy(0.1);
+  coords.setD1_dz(0.1);
+  if (bout::build::use_metric_3d) {
+    coords.splitBxyParallelSlices();
+  }
+
+  const CoordinatesAccessor acc(mesh->getCoordinates());
+  const CoordinatesAccessor acc2(&coords); // Different from previous Coordinates
 
   // clear second one
   EXPECT_EQ(CoordinatesAccessor::clear(&coords), 1);
diff --git a/tests/unit/mesh/test_interpolation.cxx b/tests/unit/mesh/test_interpolation.cxx
index d14d54964e..55a385133e 100644
--- a/tests/unit/mesh/test_interpolation.cxx
+++ b/tests/unit/mesh/test_interpolation.cxx
@@ -70,7 +70,6 @@ class Field3DInterpToTest : public ::testing::Test {
               Field2D{0.0, mesh}, Field2D{0.0, mesh}, Field2D{0.0, mesh},
               Field2D{0.0, mesh}),
           location);
-      // No call to Coordinates::geometry() needed here
       mesh->getCoordinates(location)->setParallelTransform(
           bout::utils::make_unique<ParallelTransformIdentity>(*mesh));
     }
diff --git a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
index 9de826384b..acb749f9df 100644
--- a/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
+++ b/tools/pylib/_boutpp_build/boutcpp.pxd.jinja
@@ -68,21 +68,46 @@ cdef extern from "bout/mesh.hxx":
 cdef extern from "bout/coordinates.hxx":
     cppclass Coordinates:
         Coordinates()
-        {{ metric_field }} dx, dy, dz
-        {{ metric_field }} J
-        {{ metric_field }} Bxy
-        {{ metric_field }} g11, g22, g33, g12, g13, g23
-        {{ metric_field }} g_11, g_22, g_33, g_12, g_13, g_23
-        {{ metric_field }} G1_11, G1_22, G1_33, G1_12, G1_13, G1_23
-        {{ metric_field }} G2_11, G2_22, G2_33, G2_12, G2_13, G2_23
-        {{ metric_field }} G3_11, G3_22, G3_33, G3_12, G3_13, G3_23
-        {{ metric_field }} G1, G2, G3
-        {{ metric_field }} ShiftTorsion
-        {{ metric_field }} IntShiftTorsion
-        int geometry() except +raise_bout_py_error
-        int calcCovariant() except +raise_bout_py_error
-        int calcContravariant() except +raise_bout_py_error
-        int jacobian() except +raise_bout_py_error
+        {{ metric_field }} dx()
+        {{ metric_field }} dy()
+        {{ metric_field }} dz()
+        {{ metric_field }} J()
+        {{ metric_field }} Bxy()
+        {{ metric_field }} g11()
+        {{ metric_field }} g22()
+        {{ metric_field }} g33()
+        {{ metric_field }} g12()
+        {{ metric_field }} g13()
+        {{ metric_field }} g23()
+        {{ metric_field }} g_11()
+        {{ metric_field }} g_22()
+        {{ metric_field }} g_33()
+        {{ metric_field }} g_12()
+        {{ metric_field }} g_13()
+        {{ metric_field }} g_23()
+        {{ metric_field }} G1_11()
+        {{ metric_field }} G1_22()
+        {{ metric_field }} G1_33()
+        {{ metric_field }} G1_12()
+        {{ metric_field }} G1_13()
+        {{ metric_field }} G1_23()
+        {{ metric_field }} G2_11()
+        {{ metric_field }} G2_22()
+        {{ metric_field }} G2_33()
+        {{ metric_field }} G2_12()
+        {{ metric_field }} G2_13()
+        {{ metric_field }} G2_23()
+        {{ metric_field }} G3_11()
+        {{ metric_field }} G3_22()
+        {{ metric_field }} G3_33()
+        {{ metric_field }} G3_12()
+        {{ metric_field }} G3_13()
+        {{ metric_field }} G3_23()
+        {{ metric_field }} G1()
+        {{ metric_field }} G2()
+        {{ metric_field }} G3()
+        {{ metric_field }} ShiftTorsion()
+        {{ metric_field }} IntShiftTorsion()
 
 cdef extern from "bout/fieldgroup.hxx":
     cppclass FieldGroup:
diff --git a/tools/pylib/_boutpp_build/boutpp.pyx.jinja b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
index 587aa7d6a5..f72f6ee95a 100644
--- a/tools/pylib/_boutpp_build/boutpp.pyx.jinja
+++ b/tools/pylib/_boutpp_build/boutpp.pyx.jinja
@@ -876,7 +876,7 @@ cdef public {{ metric_field }} IntShiftTorsion
 
     def _setmembers(self):
 {% for f in "dx", "dy", "dz", "J", "Bxy", "g11", "g22", "g33", "g12", "g13", "g23", "g_11", "g_22", "g_33", "g_12", "g_13", "g_23", "G1_11", "G1_22", "G1_33", "G1_12", "G1_13", "G1_23", "G2_11", "G2_22", "G2_33", "G2_12", "G2_13", "G2_23", "G3_11", "G3_22", "G3_33", "G3_12", "G3_13", "G3_23", "G1", "G2", "G3", "ShiftTorsion", "IntShiftTorsion" %}
-        self.{{f}} = {{ metric_field.fdd }}FromPtr(&self.cobj.{{f}})
+        self.{{f}} = {{ metric_field.fdd }}FromObj(self.cobj.{{f}}())
 {% endfor %}
 
 {{ class("Laplacian", comment="""
diff --git a/tools/pylib/_boutpp_build/helper.cxx.jinja b/tools/pylib/_boutpp_build/helper.cxx.jinja
index fdaa944f3e..a611bc813d 100644
--- a/tools/pylib/_boutpp_build/helper.cxx.jinja
+++ b/tools/pylib/_boutpp_build/helper.cxx.jinja
@@ -170,8 +170,7 @@ Mesh * c_get_global_mesh(){
 void c_mesh_normalise(Mesh * msh, double norm){
   //printf("%g\n",norm);
   auto coord = msh->getCoordinates();
-  coord->dx /= norm;
-  coord->dy /= norm;
-  coord->dz /= norm;
-  coord->geometry();
+  coord->setDx(coord->dx() / norm);
+  coord->setDy(coord->dy() / norm);
+  coord->setDz(coord->dz() / norm);
 }

From c761c016f4ec686618da5fb9de24e1302d1427a3 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 8 Jul 2026 17:58:10 +0100
Subject: [PATCH 1604/1827] Move derivative operators out of `Coordinates`

---
 include/bout/coordinates.hxx     |  81 -------
 include/bout/derivs.hxx          | 129 +++++-----
 include/bout/difops.hxx          |  76 +++---
 src/mesh/christoffel_symbols.cxx | 120 ++++------
 src/mesh/coordinates.cxx         | 397 -------------------------------
 src/mesh/difops.cxx              | 367 +++++++++++++++++++++-------
 src/mesh/g_values.cxx            |  10 +-
 src/sys/derivs.cxx               | 113 +++++----
 8 files changed, 492 insertions(+), 801 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 2c73828060..d2019ed31f 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -411,87 +411,6 @@ public:
     return *transform;
   }
 
-  ///////////////////////////////////////////////////////////
-  // Operators
-  ///////////////////////////////////////////////////////////
-
-  FieldMetric DDX(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                  const std::string& method = "DEFAULT",
-                  const std::string& region = "RGN_NOBNDRY") const;
-
-  FieldMetric DDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                  const std::string& method = "DEFAULT",
-                  const std::string& region = "RGN_NOBNDRY") const;
-
-  FieldMetric DDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                  const std::string& method = "DEFAULT",
-                  const std::string& region = "RGN_NOBNDRY") const;
-
-  Field3D DDX(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
-              const std::string& method = "DEFAULT",
-              const std::string& region = "RGN_NOBNDRY") const;
-
-  Field3D DDY(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
-              const std::string& method = "DEFAULT",
-              const std::string& region = "RGN_NOBNDRY") const;
-
-  Field3D DDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
-              const std::string& method = "DEFAULT",
-              const std::string& region = "RGN_NOBNDRY") const;
-
-  /// Gradient along magnetic field  b.Grad(f)
-  FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc = CELL_DEFAULT,
-                       const std::string& method = "DEFAULT");
-
-  Field3D Grad_par(const Field3DParallel& var, CELL_LOC outloc = CELL_DEFAULT,
-                   const std::string& method = "DEFAULT");
-
-  /// Advection along magnetic field V*b.Grad(f)
-  FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f,
-                            CELL_LOC outloc = CELL_DEFAULT,
-                            const std::string& method = "DEFAULT");
-
-  Field3D Vpar_Grad_par(const Field3D& v, const Field3DParallel& f,
-                        CELL_LOC outloc = CELL_DEFAULT,
-                        const std::string& method = "DEFAULT");
-
-  /// Divergence along magnetic field  Div(b*f) = B.Grad(f/B)
-  FieldMetric Div_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                      const std::string& method = "DEFAULT");
-
-  Field3D Div_par(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
-                  const std::string& method = "DEFAULT");
-
-  // Second derivative along magnetic field
-  FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                         const std::string& method = "DEFAULT");
-
-  Field3D Grad2_par2(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
-                     const std::string& method = "DEFAULT");
-  // Perpendicular Laplacian operator, using only X-Z derivatives
-  // NOTE: This might be better bundled with the Laplacian inversion code
-  // since it makes use of the same coefficients and FFT routines
-  FieldMetric Delp2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT = true);
-  Field3D Delp2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT = true);
-  FieldPerp Delp2(const FieldPerp& f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT = true);
-
-  // Full parallel Laplacian operator on scalar field
-  // Laplace_par(f) = Div( b (b dot Grad(f)) )
-  FieldMetric Laplace_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT);
-  Field3D Laplace_par(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT);
-
-  // Full Laplacian operator on scalar field
-  FieldMetric Laplace(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                      const std::string& dfdy_boundary_conditions = "free_o3",
-                      const std::string& dfdy_dy_region = "");
-  Field3D Laplace(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
-                  const std::string& dfdy_boundary_conditions = "free_o3",
-                  const std::string& dfdy_dy_region = "");
-
-  // Full perpendicular Laplacian, in form of inverse of Laplacian operator in LaplaceXY
-  // solver
-  Field2D Laplace_perpXY(const Field2D& A, const Field2D& f) const;
-
   /// Christoffel symbol of the second kind (connection coefficients)
   const FieldMetric& G1_11() const { return christoffel_symbols().G1_11(); }
   const FieldMetric& G1_22() const { return christoffel_symbols().G1_22(); }
diff --git a/include/bout/derivs.hxx b/include/bout/derivs.hxx
index 14bc5c2824..be9f2f4111 100644
--- a/include/bout/derivs.hxx
+++ b/include/bout/derivs.hxx
@@ -29,12 +29,14 @@
 #ifndef BOUT_DERIVS_H
 #define BOUT_DERIVS_H
 
+#include "bout/bout_types.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
+#include "bout/metric_tensor.hxx"
 #include "bout/vector2d.hxx"
 #include "bout/vector3d.hxx"
 
-#include "bout/bout_types.hxx"
+#include <string>
 #include <type_traits>
 
 ////////// FIRST DERIVATIVES //////////
@@ -67,9 +69,9 @@ Field3D DDX(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric DDX(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                             const std::string& method = "DEFAULT",
-                             const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric DDX(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                      const std::string& method = "DEFAULT",
+                      const std::string& region = "RGN_NOBNDRY");
 
 /// Calculate first partial derivative in Y
 ///
@@ -106,9 +108,9 @@ DDY(const E& expr, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric DDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                             const std::string& method = "DEFAULT",
-                             const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric DDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                      const std::string& method = "DEFAULT",
+                      const std::string& region = "RGN_NOBNDRY");
 
 /// Calculate first partial derivative in Z
 ///
@@ -138,9 +140,9 @@ Field3D DDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric DDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                             const std::string& method = "DEFAULT",
-                             const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric DDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                      const std::string& method = "DEFAULT",
+                      const std::string& region = "RGN_NOBNDRY");
 
 /// Calculate first partial derivative in Z
 ///
@@ -204,9 +206,9 @@ Field3D D2DX2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                               const std::string& method = "DEFAULT",
-                               const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                        const std::string& method = "DEFAULT",
+                        const std::string& region = "RGN_NOBNDRY");
 
 /// Calculate second partial derivative in Y
 ///
@@ -236,9 +238,9 @@ Field3D D2DY2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                               const std::string& method = "DEFAULT",
-                               const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                        const std::string& method = "DEFAULT",
+                        const std::string& region = "RGN_NOBNDRY");
 
 /// Calculate second partial derivative in Z
 ///
@@ -268,9 +270,9 @@ Field3D D2DZ2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric D2DZ2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                               const std::string& method = "DEFAULT",
-                               const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric D2DZ2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                        const std::string& method = "DEFAULT",
+                        const std::string& region = "RGN_NOBNDRY");
 
 ////////// FOURTH DERIVATIVES //////////
 
@@ -302,9 +304,9 @@ Field3D D4DX4(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric D4DX4(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                               const std::string& method = "DEFAULT",
-                               const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric D4DX4(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                        const std::string& method = "DEFAULT",
+                        const std::string& region = "RGN_NOBNDRY");
 
 /// Calculate forth partial derivative in Y
 ///
@@ -334,9 +336,9 @@ Field3D D4DY4(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric D4DY4(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                               const std::string& method = "DEFAULT",
-                               const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric D4DY4(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                        const std::string& method = "DEFAULT",
+                        const std::string& region = "RGN_NOBNDRY");
 
 /// Calculate forth partial derivative in Z
 ///
@@ -366,9 +368,9 @@ Field3D D4DZ4(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric D4DZ4(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                               const std::string& method = "DEFAULT",
-                               const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric D4DZ4(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                        const std::string& method = "DEFAULT",
+                        const std::string& region = "RGN_NOBNDRY");
 
 /// For terms of form v * grad(f)
 ///
@@ -400,10 +402,9 @@ Field3D VDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric VDDX(const Field2D& v, const Field2D& f,
-                              CELL_LOC outloc = CELL_DEFAULT,
-                              const std::string& method = "DEFAULT",
-                              const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric VDDX(const Field2D& v, const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                       const std::string& method = "DEFAULT",
+                       const std::string& region = "RGN_NOBNDRY");
 
 /// For terms of form v * grad(f)
 ///
@@ -435,10 +436,9 @@ Field3D VDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc = CELL_
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric VDDY(const Field2D& v, const Field2D& f,
-                              CELL_LOC outloc = CELL_DEFAULT,
-                              const std::string& method = "DEFAULT",
-                              const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric VDDY(const Field2D& v, const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                       const std::string& method = "DEFAULT",
+                       const std::string& region = "RGN_NOBNDRY");
 
 /// For terms of form v * grad(f)
 ///
@@ -470,10 +470,9 @@ Field3D VDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric VDDZ(const Field2D& v, const Field2D& f,
-                              CELL_LOC outloc = CELL_DEFAULT,
-                              const std::string& method = "DEFAULT",
-                              const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric VDDZ(const Field2D& v, const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                       const std::string& method = "DEFAULT",
+                       const std::string& region = "RGN_NOBNDRY");
 
 /// For terms of form v * grad(f)
 ///
@@ -488,10 +487,9 @@ Coordinates::FieldMetric VDDZ(const Field2D& v, const Field2D& f,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric VDDZ(const Field3D& v, const Field2D& f,
-                              CELL_LOC outloc = CELL_DEFAULT,
-                              const std::string& method = "DEFAULT",
-                              const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric VDDZ(const Field3D& v, const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                       const std::string& method = "DEFAULT",
+                       const std::string& region = "RGN_NOBNDRY");
 
 /// for terms of form div(v * f)
 ///
@@ -523,10 +521,9 @@ Field3D FDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric FDDX(const Field2D& v, const Field2D& f,
-                              CELL_LOC outloc = CELL_DEFAULT,
-                              const std::string& method = "DEFAULT",
-                              const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric FDDX(const Field2D& v, const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                       const std::string& method = "DEFAULT",
+                       const std::string& region = "RGN_NOBNDRY");
 
 /// for terms of form div(v * f)
 ///
@@ -558,10 +555,9 @@ Field3D FDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc = CELL_
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric FDDY(const Field2D& v, const Field2D& f,
-                              CELL_LOC outloc = CELL_DEFAULT,
-                              const std::string& method = "DEFAULT",
-                              const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric FDDY(const Field2D& v, const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                       const std::string& method = "DEFAULT",
+                       const std::string& region = "RGN_NOBNDRY");
 
 /// for terms of form div(v * f)
 ///
@@ -593,10 +589,9 @@ Field3D FDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric FDDZ(const Field2D& v, const Field2D& f,
-                              CELL_LOC outloc = CELL_DEFAULT,
-                              const std::string& method = "DEFAULT",
-                              const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric FDDZ(const Field2D& v, const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                       const std::string& method = "DEFAULT",
+                       const std::string& region = "RGN_NOBNDRY");
 
 /// Calculate mixed partial derivative in x and y
 ///
@@ -639,11 +634,11 @@ Field3D D2DXDY(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                        (default) then the same as the region for the calculation as a
 ///                        whole. If dfdy_region < region in size then this will cause
 ///                        errors.
-Coordinates::FieldMetric D2DXDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                                const std::string& method = "DEFAULT",
-                                const std::string& region = "RGN_NOBNDRY",
-                                const std::string& dfdy_boundary_condition = "free_o3",
-                                const std::string& dfdy_region = "");
+bout::FieldMetric D2DXDY(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                         const std::string& method = "DEFAULT",
+                         const std::string& region = "RGN_NOBNDRY",
+                         const std::string& dfdy_boundary_condition = "free_o3",
+                         const std::string& dfdy_region = "");
 
 /// Calculate mixed partial derivative in x and z
 ///
@@ -673,9 +668,9 @@ Field3D D2DXDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric D2DXDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                                const std::string& method = "DEFAULT",
-                                const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric D2DXDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                         const std::string& method = "DEFAULT",
+                         const std::string& region = "RGN_NOBNDRY");
 
 /// Calculate mixed partial derivative in y and z
 ///
@@ -705,8 +700,8 @@ Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Coordinates::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                                const std::string& method = "DEFAULT",
-                                const std::string& region = "RGN_NOBNDRY");
+bout::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                         const std::string& method = "DEFAULT",
+                         const std::string& region = "RGN_NOBNDRY");
 
 #endif // BOUT_DERIVS_H
diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 28a4da9f51..fcde8a9b7c 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -36,11 +36,12 @@
 #ifndef BOUT_DIFOPS_H
 #define BOUT_DIFOPS_H
 
+#include "bout/bout_types.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
+#include "bout/metric_tensor.hxx"
 
-#include "bout/bout_types.hxx"
-#include "bout/coordinates.hxx"
+#include <string>
 
 class Solver;
 
@@ -53,10 +54,10 @@ class Solver;
  * enabled)
  * @param[in] method  The method to use. The default is set in the options.
  */
-Coordinates::FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc = CELL_DEFAULT,
-                                  const std::string& method = "DEFAULT");
-inline Coordinates::FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc,
-                                         DIFF_METHOD method) {
+bout::FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc = CELL_DEFAULT,
+                           const std::string& method = "DEFAULT");
+inline bout::FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc,
+                                  DIFF_METHOD method) {
   return Grad_par(var, outloc, toString(method));
 }
 
@@ -89,12 +90,12 @@ Field3D Grad_parP(const Field3D& apar, const Field3D& f);
  * @param[in] method  The numerical method to use. The default is set in the options
  *
  */
-Coordinates::FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f,
-                                       CELL_LOC outloc = CELL_DEFAULT,
-                                       const std::string& method = "DEFAULT");
+bout::FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f,
+                                CELL_LOC outloc = CELL_DEFAULT,
+                                const std::string& method = "DEFAULT");
 
-inline Coordinates::FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f,
-                                              CELL_LOC outloc, DIFF_METHOD method) {
+inline bout::FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f,
+                                       CELL_LOC outloc, DIFF_METHOD method) {
   return Vpar_Grad_par(v, f, outloc, toString(method));
 }
 
@@ -118,11 +119,10 @@ inline Field3D Vpar_Grad_par(const Field3D& v, const Field3D& f, CELL_LOC outloc
  * @param[in] method  The numerical method to use
  *
  */
-Coordinates::FieldMetric Div_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                                 const std::string& method = "DEFAULT");
+bout::FieldMetric Div_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                          const std::string& method = "DEFAULT");
 
-inline Coordinates::FieldMetric Div_par(const Field2D& f, CELL_LOC outloc,
-                                        DIFF_METHOD method) {
+inline bout::FieldMetric Div_par(const Field2D& f, CELL_LOC outloc, DIFF_METHOD method) {
   return Div_par(f, outloc, toString(method));
 }
 
@@ -160,10 +160,10 @@ inline Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
  * @param[in] f The field to be differentiated
  * @param[in] outloc The cell location of the result
  */
-Coordinates::FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                                    const std::string& method = "DEFAULT");
-inline Coordinates::FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc,
-                                           DIFF_METHOD method) {
+bout::FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                             const std::string& method = "DEFAULT");
+inline bout::FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc,
+                                    DIFF_METHOD method) {
   return Grad2_par2(f, outloc, toString(method));
 }
 
@@ -183,11 +183,11 @@ inline Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc, DIFF_METHOD method)
  * @param[in] kY  The diffusion coefficient
  * @param[in] f   The field whose gradient drives a flux
  */
-Coordinates::FieldMetric Div_par_K_Grad_par(BoutReal kY, const Field2D& f,
-                                            CELL_LOC outloc = CELL_DEFAULT);
+bout::FieldMetric Div_par_K_Grad_par(BoutReal kY, const Field2D& f,
+                                     CELL_LOC outloc = CELL_DEFAULT);
 Field3D Div_par_K_Grad_par(BoutReal kY, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT);
-Coordinates::FieldMetric Div_par_K_Grad_par(const Field2D& kY, const Field2D& f,
-                                            CELL_LOC outloc = CELL_DEFAULT);
+bout::FieldMetric Div_par_K_Grad_par(const Field2D& kY, const Field2D& f,
+                                     CELL_LOC outloc = CELL_DEFAULT);
 Field3D Div_par_K_Grad_par(const Field2D& kY, const Field3D& f,
                            CELL_LOC outloc = CELL_DEFAULT);
 Field3D Div_par_K_Grad_par(const Field3D& kY, const Field2D& f,
@@ -209,8 +209,8 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& k, const Field3D& f, Field3D& flow
  *
  * For the full perpendicular Laplacian, use Laplace_perp
  */
-Coordinates::FieldMetric Delp2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                               bool useFFT = true);
+bout::FieldMetric Delp2(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                        bool useFFT = true);
 Field3D Delp2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT = true);
 FieldPerp Delp2(const FieldPerp& f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT = true);
 
@@ -219,10 +219,9 @@ FieldPerp Delp2(const FieldPerp& f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT
  *
  *
  */
-Coordinates::FieldMetric
-Laplace_perp(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-             const std::string& dfdy_boundary_condition = "free_o3",
-             const std::string& dfdy_region = "");
+bout::FieldMetric Laplace_perp(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                               const std::string& dfdy_boundary_condition = "free_o3",
+                               const std::string& dfdy_region = "");
 Field3D Laplace_perp(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
                      const std::string& dfdy_boundary_condition = "free_o3",
                      const std::string& dfdy_region = "");
@@ -231,15 +230,15 @@ Field3D Laplace_perp(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
  * Parallel Laplacian operator
  *
  */
-Coordinates::FieldMetric Laplace_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT);
+bout::FieldMetric Laplace_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT);
 Field3D Laplace_par(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT);
 
 /*!
  * Full Laplacian operator (par + perp)
  */
-Coordinates::FieldMetric Laplace(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
-                                 const std::string& dfdy_boundary_condition = "free_o3",
-                                 const std::string& dfdy_region = "");
+bout::FieldMetric Laplace(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
+                          const std::string& dfdy_boundary_condition = "free_o3",
+                          const std::string& dfdy_region = "");
 Field3D Laplace(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
                 const std::string& dfdy_boundary_condition = "free_o3",
                 const std::string& dfdy_region = "");
@@ -253,8 +252,8 @@ Field2D Laplace_perpXY(const Field2D& A, const Field2D& f);
  * Terms of form b0 x Grad(phi) dot Grad(A)
  *
  */
-Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
-                                          CELL_LOC outloc = CELL_DEFAULT);
+bout::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
+                                   CELL_LOC outloc = CELL_DEFAULT);
 
 /*!
  * Terms of form
@@ -304,10 +303,9 @@ constexpr BRACKET_METHOD BRACKET_CTU = BRACKET_METHOD::ctu;
  * @param[in] solver   Pointer to the time integration solver
  *
  */
-Coordinates::FieldMetric bracket(const Field2D& f, const Field2D& g,
-                                 BRACKET_METHOD method = BRACKET_STD,
-                                 CELL_LOC outloc = CELL_DEFAULT,
-                                 Solver* solver = nullptr);
+bout::FieldMetric bracket(const Field2D& f, const Field2D& g,
+                          BRACKET_METHOD method = BRACKET_STD,
+                          CELL_LOC outloc = CELL_DEFAULT, Solver* solver = nullptr);
 Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method = BRACKET_STD,
                 CELL_LOC outloc = CELL_DEFAULT, Solver* solver = nullptr);
 Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method = BRACKET_STD,
diff --git a/src/mesh/christoffel_symbols.cxx b/src/mesh/christoffel_symbols.cxx
index 943f020f36..c90d7c6d58 100644
--- a/src/mesh/christoffel_symbols.cxx
+++ b/src/mesh/christoffel_symbols.cxx
@@ -1,5 +1,6 @@
 #include "bout/christoffel_symbols.hxx"
 #include "bout/coordinates.hxx"
+#include "bout/derivs.hxx"
 #include "bout/mesh.hxx"
 #include "bout/output.hxx"
 
@@ -25,88 +26,63 @@ ChristoffelSymbols::ChristoffelSymbols(const Coordinates& coordinates) {
   const auto& g_13 = covariantMetricTensor.g13();
   const auto& g_23 = covariantMetricTensor.g23();
 
-  G1_11_m = 0.5 * g11 * coordinates.DDX(g_11)
-            + g12 * (coordinates.DDX(g_12) - 0.5 * coordinates.DDY(g_11))
-            + g13 * (coordinates.DDX(g_13) - 0.5 * coordinates.DDZ(g_11));
-  G1_22_m = g11 * (coordinates.DDY(g_12) - 0.5 * coordinates.DDX(g_22))
-            + 0.5 * g12 * coordinates.DDY(g_22)
-            + g13 * (coordinates.DDY(g_23) - 0.5 * coordinates.DDZ(g_22));
-  G1_33_m = g11 * (coordinates.DDZ(g_13) - 0.5 * coordinates.DDX(g_33))
-            + g12 * (coordinates.DDZ(g_23) - 0.5 * coordinates.DDY(g_33))
-            + 0.5 * g13 * coordinates.DDZ(g_33);
-  G1_12_m =
-      0.5 * g11 * coordinates.DDY(g_11) + 0.5 * g12 * coordinates.DDX(g_22)
-      + 0.5 * g13
-            * (coordinates.DDY(g_13) + coordinates.DDX(g_23) - coordinates.DDZ(g_12));
-  G1_13_m =
-      0.5 * g11 * coordinates.DDZ(g_11)
-      + 0.5 * g12
-            * (coordinates.DDZ(g_12) + coordinates.DDX(g_23) - coordinates.DDY(g_13))
-      + 0.5 * g13 * coordinates.DDX(g_33);
-  G1_23_m =
-      0.5 * g11 * (coordinates.DDZ(g_12) + coordinates.DDY(g_13) - coordinates.DDX(g_23))
-      + 0.5 * g12
-            * (coordinates.DDZ(g_22) + coordinates.DDY(g_23) - coordinates.DDY(g_23))
-      // + 0.5 *g13*(coordinates.DDZ(g_32) + coordinates.DDY(g_33) - coordinates.DDZ(g_23));
-      // which equals
-      + 0.5 * g13 * coordinates.DDY(g_33);
+  G1_11_m = 0.5 * g11 * DDX(g_11) + g12 * (DDX(g_12) - 0.5 * DDY(g_11))
+            + g13 * (DDX(g_13) - 0.5 * DDZ(g_11));
+  G1_22_m = g11 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g12 * DDY(g_22)
+            + g13 * (DDY(g_23) - 0.5 * DDZ(g_22));
+  G1_33_m = g11 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g12 * (DDZ(g_23) - 0.5 * DDY(g_33))
+            + 0.5 * g13 * DDZ(g_33);
+  G1_12_m = 0.5 * g11 * DDY(g_11) + 0.5 * g12 * DDX(g_22)
+            + 0.5 * g13 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
+  G1_13_m = 0.5 * g11 * DDZ(g_11) + 0.5 * g12 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
+            + 0.5 * g13 * DDX(g_33);
+  G1_23_m = 0.5 * g11 * (DDZ(g_12) + DDY(g_13) - DDX(g_23))
+            + 0.5 * g12 * (DDZ(g_22) + DDY(g_23) - DDY(g_23))
+            // + 0.5 *g13*(DDZ(g_32) + DDY(g_33) - DDZ(g_23));
+            // which equals
+            + 0.5 * g13 * DDY(g_33);
 
-  G2_11_m = 0.5 * g12 * coordinates.DDX(g_11)
-            + g22 * (coordinates.DDX(g_12) - 0.5 * coordinates.DDY(g_11))
-            + g23 * (coordinates.DDX(g_13) - 0.5 * coordinates.DDZ(g_11));
-  G2_22_m = g12 * (coordinates.DDY(g_12) - 0.5 * coordinates.DDX(g_22))
-            + 0.5 * g22 * coordinates.DDY(g_22)
-            + g23 * (coordinates.DDY(g23) - 0.5 * coordinates.DDZ(g_22));
-  G2_33_m = g12 * (coordinates.DDZ(g_13) - 0.5 * coordinates.DDX(g_33))
-            + g22 * (coordinates.DDZ(g_23) - 0.5 * coordinates.DDY(g_33))
-            + 0.5 * g23 * coordinates.DDZ(g_33);
-  G2_12_m =
-      0.5 * g12 * coordinates.DDY(g_11) + 0.5 * g22 * coordinates.DDX(g_22)
-      + 0.5 * g23
-            * (coordinates.DDY(g_13) + coordinates.DDX(g_23) - coordinates.DDZ(g_12));
+  G2_11_m = 0.5 * g12 * DDX(g_11) + g22 * (DDX(g_12) - 0.5 * DDY(g_11))
+            + g23 * (DDX(g_13) - 0.5 * DDZ(g_11));
+  G2_22_m = g12 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g22 * DDY(g_22)
+            + g23 * (DDY(g23) - 0.5 * DDZ(g_22));
+  G2_33_m = g12 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g22 * (DDZ(g_23) - 0.5 * DDY(g_33))
+            + 0.5 * g23 * DDZ(g_33);
+  G2_12_m = 0.5 * g12 * DDY(g_11) + 0.5 * g22 * DDX(g_22)
+            + 0.5 * g23 * (DDY(g_13) + DDX(g_23) - DDZ(g_12));
   G2_13_m =
-      // 0.5 *g21*(coordinates.DDZ(g_11) + coordinates.DDX(covariantMetricTensor.Getg13()) - coordinates.DDX(g_13))
+      // 0.5 *g21*(DDZ(g_11) + DDX(covariantMetricTensor.Getg13()) - DDX(g_13))
       // which equals
-      0.5 * g12 * (coordinates.DDZ(g_11) + coordinates.DDX(g_13) - coordinates.DDX(g_13))
-      // + 0.5 *g22*(coordinates.DDZ(covariantMetricTensor.Getg21()) + coordinates.DDX(g_23) - coordinates.DDY(g_13))
+      0.5 * g12 * (DDZ(g_11) + DDX(g_13) - DDX(g_13))
+      // + 0.5 *g22*(DDZ(covariantMetricTensor.Getg21()) + DDX(g_23) - DDY(g_13))
       // which equals
-      + 0.5 * g22
-            * (coordinates.DDZ(g_12) + coordinates.DDX(g_23) - coordinates.DDY(g_13))
-      // + 0.5 *g23*(coordinates.DDZ(covariantMetricTensor.Getg31()) + coordinates.DDX(g_33) - coordinates.DDZ(g_13));
+      + 0.5 * g22 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
+      // + 0.5 *g23*(DDZ(covariantMetricTensor.Getg31()) + DDX(g_33) - DDZ(g_13));
       // which equals
-      + 0.5 * g23 * coordinates.DDX(g_33);
-  G2_23_m =
-      0.5 * g12 * (coordinates.DDZ(g_12) + coordinates.DDY(g_13) - coordinates.DDX(g_23))
-      + 0.5 * g22 * coordinates.DDZ(g_22) + 0.5 * g23 * coordinates.DDY(g_33);
+      + 0.5 * g23 * DDX(g_33);
+  G2_23_m = 0.5 * g12 * (DDZ(g_12) + DDY(g_13) - DDX(g_23)) + 0.5 * g22 * DDZ(g_22)
+            + 0.5 * g23 * DDY(g_33);
 
-  G3_11_m = 0.5 * g13 * coordinates.DDX(g_11)
-            + g23 * (coordinates.DDX(g_12) - 0.5 * coordinates.DDY(g_11))
-            + g33 * (coordinates.DDX(g_13) - 0.5 * coordinates.DDZ(g_11));
-  G3_22_m = g13 * (coordinates.DDY(g_12) - 0.5 * coordinates.DDX(g_22))
-            + 0.5 * g23 * coordinates.DDY(g_22)
-            + g33 * (coordinates.DDY(g_23) - 0.5 * coordinates.DDZ(g_22));
-  G3_33_m = g13 * (coordinates.DDZ(g_13) - 0.5 * coordinates.DDX(g_33))
-            + g23 * (coordinates.DDZ(g_23) - 0.5 * coordinates.DDY(g_33))
-            + 0.5 * g33 * coordinates.DDZ(g_33);
+  G3_11_m = 0.5 * g13 * DDX(g_11) + g23 * (DDX(g_12) - 0.5 * DDY(g_11))
+            + g33 * (DDX(g_13) - 0.5 * DDZ(g_11));
+  G3_22_m = g13 * (DDY(g_12) - 0.5 * DDX(g_22)) + 0.5 * g23 * DDY(g_22)
+            + g33 * (DDY(g_23) - 0.5 * DDZ(g_22));
+  G3_33_m = g13 * (DDZ(g_13) - 0.5 * DDX(g_33)) + g23 * (DDZ(g_23) - 0.5 * DDY(g_33))
+            + 0.5 * g33 * DDZ(g_33);
   G3_12_m =
-      // 0.5 *g31*(coordinates.DDY(g_11) + coordinates.DDX(covariantMetricTensor.Getg12()) - coordinates.DDX(g_12))
+      // 0.5 *g31*(DDY(g_11) + DDX(covariantMetricTensor.Getg12()) - DDX(g_12))
       // which equals to
-      0.5 * g13 * coordinates.DDY(g_11)
-      // + 0.5 *g32*(coordinates.DDY(covariantMetricTensor.Getg21()) + coordinates.DDX(g_22) - coordinates.DDY(g_12))
+      0.5 * g13 * DDY(g_11)
+      // + 0.5 *g32*(DDY(covariantMetricTensor.Getg21()) + DDX(g_22) - DDY(g_12))
       // which equals to
-      + 0.5 * g23 * coordinates.DDX(g_22)
-      //+ 0.5 *g33*(coordinates.DDY(covariantMetricTensor.Getg31()) + coordinates.DDX(covariantMetricTensor.Getg32()) - coordinates.DDZ(g_12));
+      + 0.5 * g23 * DDX(g_22)
+      //+ 0.5 *g33*(DDY(covariantMetricTensor.Getg31()) + DDX(covariantMetricTensor.Getg32()) - DDZ(g_12));
       // which equals to
-      + 0.5 * g33 * (coordinates.DDY(g_13)) + coordinates.DDX(g_23)
-      - coordinates.DDZ(g_12);
-  G3_13_m =
-      0.5 * g13 * coordinates.DDZ(g_11)
-      + 0.5 * g23
-            * (coordinates.DDZ(g_12) + coordinates.DDX(g_23) - coordinates.DDY(g_13))
-      + 0.5 * g33 * coordinates.DDX(g_33);
-  G3_23_m = 0.5 * g13 * (coordinates.DDZ(g_12) + coordinates.DDY(g_13))
-            - coordinates.DDX(g_23) + 0.5 * g23 * coordinates.DDZ(g_22)
-            + 0.5 * g33 * coordinates.DDY(g_33);
+      + 0.5 * g33 * (DDY(g_13)) + DDX(g_23) - DDZ(g_12);
+  G3_13_m = 0.5 * g13 * DDZ(g_11) + 0.5 * g23 * (DDZ(g_12) + DDX(g_23) - DDY(g_13))
+            + 0.5 * g33 * DDX(g_33);
+  G3_23_m = 0.5 * g13 * (DDZ(g_12) + DDY(g_13)) - DDX(g_23) + 0.5 * g23 * DDZ(g_22)
+            + 0.5 * g33 * DDY(g_33);
 
   output_progress.write("\tCommunicating connection terms\n");
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 22b43a9f8e..b07b9b1995 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -930,403 +930,6 @@ void Coordinates::setParallelTransform(Options* options) {
   }
 }
 
-/*******************************************************************************
- * Operators
- *
- *******************************************************************************/
-
-Coordinates::FieldMetric Coordinates::DDX(const Field2D& f, CELL_LOC loc,
-                                          const std::string& method,
-                                          const std::string& region) const {
-  ASSERT1(location == loc || loc == CELL_DEFAULT);
-  return bout::derivatives::index::DDX(f, loc, method, region) / dx();
-}
-Field3D Coordinates::DDX(const Field3D& f, CELL_LOC outloc, const std::string& method,
-                         const std::string& region) const {
-
-  auto result = bout::derivatives::index::DDX(f, outloc, method, region);
-  result /= dx();
-
-  if (f.getMesh()->IncIntShear) {
-    // Using BOUT-06 style shifting
-    result += IntShiftTorsion() * DDZ(f, outloc, method, region);
-  }
-
-  return result;
-};
-
-Coordinates::FieldMetric Coordinates::DDY(const Field2D& f, CELL_LOC loc,
-                                          const std::string& method,
-                                          const std::string& region) const {
-  ASSERT1(location == loc || loc == CELL_DEFAULT);
-  return bout::derivatives::index::DDY(f, loc, method, region) / dy();
-}
-
-Field3D Coordinates::DDY(const Field3DParallel& f, CELL_LOC outloc,
-                         const std::string& method, const std::string& region) const {
-  return bout::derivatives::index::DDY(f, outloc, method, region) / dy();
-};
-
-Coordinates::FieldMetric Coordinates::DDZ(const Field2D& f, CELL_LOC loc,
-                                          const std::string& UNUSED(method),
-                                          const std::string& UNUSED(region)) const {
-  ASSERT1(location == loc || loc == CELL_DEFAULT);
-  ASSERT1(f.getMesh() == localmesh);
-  if (loc == CELL_DEFAULT) {
-    loc = f.getLocation();
-  }
-  return zeroFrom(f).setLocation(loc);
-}
-Field3D Coordinates::DDZ(const Field3D& f, CELL_LOC outloc, const std::string& method,
-                         const std::string& region) const {
-  return bout::derivatives::index::DDZ(f, outloc, method, region) / dz();
-};
-
-/////////////////////////////////////////////////////////
-// Parallel gradient
-
-Coordinates::FieldMetric Coordinates::Grad_par(const Field2D& var,
-                                               [[maybe_unused]] CELL_LOC outloc,
-                                               const std::string& UNUSED(method)) {
-  ASSERT1(location == outloc
-          || (outloc == CELL_DEFAULT && location == var.getLocation()));
-
-  return DDY(var) * invSg();
-}
-
-Field3D Coordinates::Grad_par(const Field3DParallel& var, CELL_LOC outloc,
-                              const std::string& method) {
-
-  ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-
-  return ::DDY(var, outloc, method) * invSg();
-}
-
-/////////////////////////////////////////////////////////
-// Vpar_Grad_par
-// vparallel times the parallel derivative along unperturbed B-field
-
-Coordinates::FieldMetric Coordinates::Vpar_Grad_par(const Field2D& v, const Field2D& f,
-                                                    [[maybe_unused]] CELL_LOC outloc,
-                                                    const std::string& UNUSED(method)) {
-  ASSERT1(location == outloc || (outloc == CELL_DEFAULT && location == f.getLocation()));
-
-  return VDDY(v, f) * invSg();
-}
-
-Field3D Coordinates::Vpar_Grad_par(const Field3D& v, const Field3DParallel& f,
-                                   CELL_LOC outloc, const std::string& method) {
-  ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-
-  return VDDY(v, f, outloc, method) * invSg();
-}
-
-/////////////////////////////////////////////////////////
-// Parallel divergence
-
-Coordinates::FieldMetric Coordinates::Div_par(const Field2D& f, CELL_LOC outloc,
-                                              const std::string& method) {
-
-  ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-
-  // Need Bxy at location of f, which might be different from location of this
-  // Coordinates object
-  auto Bxy_floc = f.getCoordinates()->Bxy();
-
-  return Bxy_ * Grad_par(FieldMetric{f / Bxy_floc}, outloc, method);
-}
-
-Field3D Coordinates::Div_par(const Field3DParallel& f, CELL_LOC outloc,
-                             const std::string& method) {
-
-  ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-
-  // Need Bxy at location of f, which might be different from location of this
-  // Coordinates object
-  const auto& Bxy_floc = f.getCoordinates()->Bxy();
-
-  return Bxy() * Grad_par(f / Bxy_floc, outloc, method);
-}
-
-/////////////////////////////////////////////////////////
-// second parallel derivative (b dot Grad)(b dot Grad)
-// Note: For parallel Laplacian use Laplace_par
-
-Coordinates::FieldMetric Coordinates::Grad2_par2(const Field2D& f, CELL_LOC outloc,
-                                                 const std::string& method) {
-
-  ASSERT1(location == outloc || (outloc == CELL_DEFAULT && location == f.getLocation()));
-
-  auto result = Grad2_par2_DDY_invSg(outloc, method) * DDY(f, outloc, method)
-                + D2DY2(f, outloc, method) / g_22();
-
-  return result;
-}
-
-Field3D Coordinates::Grad2_par2(const Field3DParallel& f, CELL_LOC outloc,
-                                const std::string& method) {
-
-  if (outloc == CELL_DEFAULT) {
-    outloc = f.getLocation();
-  }
-  ASSERT1(location == outloc);
-
-  Field3D result = ::DDY(f, outloc, method);
-
-  Field3D r2 = D2DY2(f, outloc, method) / g_22();
-
-  result = Grad2_par2_DDY_invSg(outloc, method) * result + r2;
-
-  ASSERT2(result.getLocation() == outloc);
-
-  return result;
-}
-
-/////////////////////////////////////////////////////////
-// perpendicular Laplacian operator
-
-#include <bout/invert_laplace.hxx> // Delp2 uses same coefficients as inversion code
-
-Coordinates::FieldMetric Coordinates::Delp2(const Field2D& f, CELL_LOC outloc,
-                                            bool UNUSED(useFFT)) {
-
-  ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-
-  return G1() * DDX(f, outloc) + g11() * D2DX2(f, outloc);
-}
-
-Field3D Coordinates::Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
-
-  if (outloc == CELL_DEFAULT) {
-    outloc = f.getLocation();
-  }
-
-  ASSERT1(location == outloc);
-  ASSERT1(f.getLocation() == outloc);
-
-  if (localmesh->GlobalNx == 1 && localmesh->GlobalNz == 1) {
-    // copy mesh, location, etc
-    return f * 0;
-  }
-  ASSERT2(localmesh->xstart > 0); // Need at least one guard cell;
-
-  Field3D result{emptyFrom(f).setLocation(outloc)};
-
-  if (useFFT and not bout::build::use_metric_3d and localmesh->getNZPE() == 1) {
-    int ncz = localmesh->LocalNz;
-
-    // Allocate memory
-    auto ft = Matrix<dcomplex>(localmesh->LocalNx, ncz / 2 + 1);
-    auto delft = Matrix<dcomplex>(localmesh->LocalNx, ncz / 2 + 1);
-
-    // Loop over y indices
-    // Note: should not include y-guard or y-boundary points here as that would
-    // use values from corner cells in dx, which may not be initialised.
-    for (int jy = localmesh->ystart; jy <= localmesh->yend; jy++) {
-
-      // Take forward FFT
-
-      for (int jx = 0; jx < localmesh->LocalNx; jx++) {
-        rfft(&f(jx, jy, 0), ncz, &ft(jx, 0));
-      }
-
-      // Loop over kz
-      for (int jz = 0; jz <= ncz / 2; jz++) {
-
-        // No smoothing in the x direction
-        for (int jx = localmesh->xstart; jx <= localmesh->xend; jx++) {
-          // Perform x derivative
-
-          dcomplex a, b, c;
-          laplace_tridag_coefs(jx, jy, jz, a, b, c, nullptr, nullptr, outloc);
-
-          delft(jx, jz) = a * ft(jx - 1, jz) + b * ft(jx, jz) + c * ft(jx + 1, jz);
-        }
-      }
-
-      // Reverse FFT
-      for (int jx = localmesh->xstart; jx <= localmesh->xend; jx++) {
-
-        irfft(&delft(jx, 0), ncz, &result(jx, jy, 0));
-      }
-    }
-  } else {
-    result = G1() * ::DDX(f, outloc) + G3() * ::DDZ(f, outloc)
-             + g11() * ::D2DX2(f, outloc) + g33() * ::D2DZ2(f, outloc)
-             + 2 * g13() * ::D2DXDZ(f, outloc);
-  }
-
-  ASSERT2(result.getLocation() == outloc);
-
-  return result;
-}
-
-FieldPerp Coordinates::Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
-
-  if (outloc == CELL_DEFAULT) {
-    outloc = f.getLocation();
-  }
-
-  ASSERT1(location == outloc);
-  ASSERT1(f.getLocation() == outloc);
-
-  if (localmesh->GlobalNx == 1 && localmesh->GlobalNz == 1) {
-    // copy mesh, location, etc
-    return f * 0;
-  }
-  ASSERT2(localmesh->xstart > 0); // Need at least one guard cell
-
-  FieldPerp result{emptyFrom(f).setLocation(outloc)};
-
-  const int jy = f.getIndex();
-  result.setIndex(jy);
-
-  if (useFFT and localmesh->getNZPE() == 1) {
-    int ncz = localmesh->LocalNz;
-
-    // Allocate memory
-    auto ft = Matrix<dcomplex>(localmesh->LocalNx, ncz / 2 + 1);
-    auto delft = Matrix<dcomplex>(localmesh->LocalNx, ncz / 2 + 1);
-
-    // Take forward FFT
-    for (int jx = 0; jx < localmesh->LocalNx; jx++) {
-      rfft(&f(jx, 0), ncz, &ft(jx, 0));
-    }
-
-    // Loop over kz
-    for (int jz = 0; jz <= ncz / 2; jz++) {
-
-      // No smoothing in the x direction
-      for (int jx = localmesh->xstart; jx <= localmesh->xend; jx++) {
-        // Perform x derivative
-
-        dcomplex a, b, c;
-        laplace_tridag_coefs(jx, jy, jz, a, b, c);
-
-        delft(jx, jz) = a * ft(jx - 1, jz) + b * ft(jx, jz) + c * ft(jx + 1, jz);
-      }
-    }
-
-    // Reverse FFT
-    for (int jx = localmesh->xstart; jx <= localmesh->xend; jx++) {
-      irfft(&delft(jx, 0), ncz, &result(jx, 0));
-    }
-
-  } else {
-    throw BoutException("Non-fourier Delp2 not currently implented for FieldPerp.");
-    // Would be the following but don't have standard derivative operators for FieldPerps
-    // yet
-    // result = G1 * ::DDX(f, outloc) + G3 * ::DDZ(f, outloc) + g11 * ::D2DX2(f, outloc)
-    //          + g33 * ::D2DZ2(f, outloc) + 2 * g13 * ::D2DXDZ(f, outloc);
-  };
-
-  return result;
-}
-
-Coordinates::FieldMetric Coordinates::Laplace_par(const Field2D& f, CELL_LOC outloc) {
-  ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-  return D2DY2(f, outloc) / g_22()
-         + DDY(FieldMetric{J() / g_22()}, outloc) * DDY(f, outloc) / J();
-}
-
-Field3D Coordinates::Laplace_par(const Field3DParallel& f, CELL_LOC outloc) {
-  ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-  return D2DY2(f, outloc) / g_22()
-         + DDY(J().asField3DParallel() / g_22(), outloc) * ::DDY(f, outloc) / J();
-}
-
-// Full Laplacian operator on scalar field
-
-Coordinates::FieldMetric Coordinates::Laplace(const Field2D& f, CELL_LOC outloc,
-                                              const std::string& dfdy_boundary_conditions,
-                                              const std::string& dfdy_dy_region) {
-
-  ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-
-  return G1() * DDX(f, outloc) + G2() * DDY(f, outloc) + g11() * D2DX2(f, outloc)
-         + g22() * D2DY2(f, outloc)
-         + 2.0 * g12()
-               * ::D2DXDY(f, outloc, "DEFAULT", "RGN_NOBNDRY", dfdy_boundary_conditions,
-                          dfdy_dy_region);
-}
-
-Field3D Coordinates::Laplace(const Field3DParallel& f, CELL_LOC outloc,
-                             const std::string& dfdy_boundary_conditions,
-                             const std::string& dfdy_dy_region) {
-
-  ASSERT1(location == outloc || outloc == CELL_DEFAULT);
-
-  return G1() * ::DDX(f, outloc) + G2() * ::DDY(f, outloc) + G3() * ::DDZ(f, outloc)
-         + g11() * ::D2DX2(f, outloc) + g22() * ::D2DY2(f, outloc)
-         + g33() * ::D2DZ2(f, outloc)
-         + 2.0
-               * (g12()
-                      * D2DXDY(f, outloc, "DEFAULT", "RGN_NOBNDRY",
-                               dfdy_boundary_conditions, dfdy_dy_region)
-                  + g13() * ::D2DXDZ(f, outloc) + g23() * ::D2DYDZ(f, outloc));
-}
-
-// Full perpendicular Laplacian, in form of inverse of Laplacian operator in LaplaceXY
-// solver
-Field2D Coordinates::Laplace_perpXY([[maybe_unused]] const Field2D& A,
-                                    [[maybe_unused]] const Field2D& f) const {
-#if not(BOUT_USE_METRIC_3D)
-  Field2D result;
-  result.allocate();
-  for (auto i : result.getRegion(RGN_NOBNDRY)) {
-    result[i] = 0.;
-
-    // outer x boundary
-    const auto outer_x_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.xp()]); };
-    const BoutReal outer_x_A = outer_x_avg(A);
-    const BoutReal outer_x_J = outer_x_avg(J());
-    const BoutReal outer_x_g11 = outer_x_avg(g11());
-    const BoutReal outer_x_dx = outer_x_avg(dx());
-    const BoutReal outer_x_value =
-        outer_x_A * outer_x_J * outer_x_g11 / (J()[i] * outer_x_dx * dx()[i]);
-    result[i] += outer_x_value * (f[i.xp()] - f[i]);
-
-    // inner x boundary
-    const auto inner_x_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.xm()]); };
-    const BoutReal inner_x_A = inner_x_avg(A);
-    const BoutReal inner_x_J = inner_x_avg(J());
-    const BoutReal inner_x_g11 = inner_x_avg(g11());
-    const BoutReal inner_x_dx = inner_x_avg(dx());
-    const BoutReal inner_x_value =
-        inner_x_A * inner_x_J * inner_x_g11 / (J()[i] * inner_x_dx * dx()[i]);
-    result[i] += inner_x_value * (f[i.xm()] - f[i]);
-
-    // upper y boundary
-    const auto upper_y_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.yp()]); };
-    const BoutReal upper_y_A = upper_y_avg(A);
-    const BoutReal upper_y_J = upper_y_avg(J());
-    const BoutReal upper_y_g_22 = upper_y_avg(g_22());
-    const BoutReal upper_y_g23 = upper_y_avg(g23());
-    const BoutReal upper_y_g_23 = upper_y_avg(g_23());
-    const BoutReal upper_y_dy = upper_y_avg(dy());
-    const BoutReal upper_y_value = -upper_y_A * upper_y_J * upper_y_g23 * upper_y_g_23
-                                   / (upper_y_g_22 * J()[i] * upper_y_dy * dy()[i]);
-    result[i] += upper_y_value * (f[i.yp()] - f[i]);
-
-    // lower y boundary
-    const auto lower_y_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.ym()]); };
-    const BoutReal lower_y_A = lower_y_avg(A);
-    const BoutReal lower_y_J = lower_y_avg(J());
-    const BoutReal lower_y_g_22 = lower_y_avg(g_22());
-    const BoutReal lower_y_g23 = lower_y_avg(g23());
-    const BoutReal lower_y_g_23 = lower_y_avg(g_23());
-    const BoutReal lower_y_dy = lower_y_avg(dy());
-    const BoutReal lower_y_value = -lower_y_A * lower_y_J * lower_y_g23 * lower_y_g_23
-                                   / (lower_y_g_22 * J()[i] * lower_y_dy * dy()[i]);
-    result[i] += lower_y_value * (f[i.ym()] - f[i]);
-  }
-
-  return result;
-#else
-  throw BoutException("Coordinates::Laplace_perpXY for 3D metric not implemented");
-#endif
-}
-
 const ChristoffelSymbols& Coordinates::christoffel_symbols() const {
   if (christoffel_symbols_cache == nullptr) {
     christoffel_symbols_cache = std::make_unique<ChristoffelSymbols>(*this);
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 1b9a993e1a..7e2c313b53 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -23,8 +23,10 @@
  *
  **************************************************************************/
 
+#include "bout/build_config.hxx"
 #include "bout/build_defines.hxx"
-
+#include "bout/dcomplex.hxx"
+#include "bout/metric_tensor.hxx"
 #include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
@@ -35,40 +37,30 @@
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/globals.hxx>
+#include <bout/interpolation.hxx>
+#include <bout/invert_laplace.hxx> // Delp2 uses same coefficients as inversion code
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 #include <bout/solver.hxx>
+#include <bout/unused.hxx>
 #include <bout/utils.hxx>
 #include <bout/vecops.hxx>
 
-#include <bout/invert_laplace.hxx> // Delp2 uses same coefficients as inversion code
-
-#include <bout/interpolation.hxx>
-#include <bout/unused.hxx>
-
 #include <cmath>
+#include <string>
 
 /*******************************************************************************
 * Grad_par
 * The parallel derivative along unperturbed B-field
 *******************************************************************************/
 
-Coordinates::FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc,
-                                  const std::string& method) {
-  return var.getCoordinates(outloc)->Grad_par(var, outloc, method);
-}
-
-Coordinates::FieldMetric Grad_par(const Field2D& var, const std::string& method,
-                                  CELL_LOC outloc) {
-  return var.getCoordinates(outloc)->Grad_par(var, outloc, method);
+bout::FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc,
+                           const std::string& method) {
+  return DDY(var, outloc, method) * var.getCoordinates(outloc)->invSg();
 }
 
 Field3D Grad_par(const Field3D& var, CELL_LOC outloc, const std::string& method) {
-  return var.getCoordinates(outloc)->Grad_par(var, outloc, method);
-}
-
-Field3D Grad_par(const Field3D& var, const std::string& method, CELL_LOC outloc) {
-  return var.getCoordinates(outloc)->Grad_par(var, outloc, method);
+  return DDY(var, outloc, method) * var.getCoordinates(outloc)->invSg();
 }
 
 /*******************************************************************************
@@ -198,46 +190,34 @@ Field3D Grad_parP(const Field3D& apar, const Field3D& f) {
 * vparallel times the parallel derivative along unperturbed B-field
 *******************************************************************************/
 
-Coordinates::FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f,
-                                       CELL_LOC outloc, const std::string& method) {
-  return f.getCoordinates(outloc)->Vpar_Grad_par(v, f, outloc, method);
-}
-
-Coordinates::FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f,
-                                       const std::string& method, CELL_LOC outloc) {
-  return f.getCoordinates(outloc)->Vpar_Grad_par(v, f, outloc, method);
+bout::FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f, CELL_LOC outloc,
+                                const std::string& method) {
+  return VDDY(v, f, outloc, method) * f.getCoordinates(outloc)->invSg();
 }
 
 Field3D Vpar_Grad_par(const Field3D& v, const Field3D& f, CELL_LOC outloc,
                       const std::string& method) {
-  return f.getCoordinates(outloc)->Vpar_Grad_par(v, f, outloc, method);
-}
-
-Field3D Vpar_Grad_par(const Field3D& v, const Field3D& f, const std::string& method,
-                      CELL_LOC outloc) {
-  return f.getCoordinates(outloc)->Vpar_Grad_par(v, f, outloc, method);
+  return VDDY(v, f, outloc, method) * f.getCoordinates(outloc)->invSg();
 }
 
 /*******************************************************************************
 * Div_par
 * parallel divergence operator B \partial_{||} (F/B)
 *******************************************************************************/
-Coordinates::FieldMetric Div_par(const Field2D& f, CELL_LOC outloc,
-                                 const std::string& method) {
-  return f.getCoordinates(outloc)->Div_par(f, outloc, method);
-}
+bout::FieldMetric Div_par(const Field2D& f, CELL_LOC outloc, const std::string& method) {
+  const auto& Bxy_outloc = f.getCoordinates(outloc)->Bxy();
+  // Need Bxy at location of f, which might be different from outloc
+  const auto& Bxy_floc = f.getCoordinates()->Bxy();
 
-Coordinates::FieldMetric Div_par(const Field2D& f, const std::string& method,
-                                 CELL_LOC outloc) {
-  return f.getCoordinates(outloc)->Div_par(f, outloc, method);
+  return Bxy_outloc * Grad_par(bout::FieldMetric{f / Bxy_floc}, outloc, method);
 }
 
 Field3D Div_par(const Field3D& f, CELL_LOC outloc, const std::string& method) {
-  return f.getCoordinates(outloc)->Div_par(f, outloc, method);
-}
+  const auto& Bxy_outloc = f.getCoordinates(outloc)->Bxy();
+  // Need Bxy at location of f, which might be different from outloc
+  const auto& Bxy_floc = f.getCoordinates()->Bxy();
 
-Field3D Div_par(const Field3D& f, const std::string& method, CELL_LOC outloc) {
-  return f.getCoordinates(outloc)->Div_par(f, outloc, method);
+  return Bxy_outloc * Grad_par(Field3D{f / Bxy_floc}, outloc, method);
 }
 
 Field3D Div_par(const Field3D& f, const Field3D& v) {
@@ -318,13 +298,23 @@ Field3D Div_par_flux(const Field3D& v, const Field3D& f, const std::string& meth
 * Note: For parallel Laplacian use LaplacePar
 *******************************************************************************/
 
-Coordinates::FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc,
-                                    const std::string& method) {
-  return f.getCoordinates(outloc)->Grad2_par2(f, outloc, method);
+bout::FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc,
+                             const std::string& method) {
+  const auto& coords = *f.getCoordinates(outloc);
+
+  return coords.Grad2_par2_DDY_invSg(outloc, method) * DDY(f, outloc, method)
+         + D2DY2(f, outloc, method) / coords.g_22();
 }
 
 Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc, const std::string& method) {
-  return f.getCoordinates(outloc)->Grad2_par2(f, outloc, method);
+  if (outloc == CELL_DEFAULT) {
+    outloc = f.getLocation();
+  }
+
+  const auto& coords = *f.getCoordinates(outloc);
+
+  return coords.Grad2_par2_DDY_invSg(outloc, method) * DDY(f, outloc, method)
+         + D2DY2(f, outloc, method) / coords.g_22();
 }
 
 /*******************************************************************************
@@ -332,8 +322,7 @@ Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc, const std::string& method)
 * Parallel divergence of diffusive flux, K*Grad_par
 *******************************************************************************/
 
-Coordinates::FieldMetric Div_par_K_Grad_par(BoutReal kY, const Field2D& f,
-                                            CELL_LOC outloc) {
+bout::FieldMetric Div_par_K_Grad_par(BoutReal kY, const Field2D& f, CELL_LOC outloc) {
   return kY * Grad2_par2(f, outloc);
 }
 
@@ -341,8 +330,8 @@ Field3D Div_par_K_Grad_par(BoutReal kY, const Field3D& f, CELL_LOC outloc) {
   return kY * Grad2_par2(f, outloc);
 }
 
-Coordinates::FieldMetric Div_par_K_Grad_par(const Field2D& kY, const Field2D& f,
-                                            CELL_LOC outloc) {
+bout::FieldMetric Div_par_K_Grad_par(const Field2D& kY, const Field2D& f,
+                                     CELL_LOC outloc) {
   if (outloc == CELL_DEFAULT) {
     outloc = f.getLocation();
   }
@@ -445,10 +434,11 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D&
     const bool is_periodic_y = mesh->periodicY(ix);
 
     if (bndry_flux || is_periodic_y || !mesh->lastY(ix) || (iy != mesh->yend)) {
-      const BoutReal c = 0.5 * (K[i] + K[iyp]);               // K at the upper boundary
+      const BoutReal c = 0.5 * (K[i] + K[iyp]); // K at the upper boundary
       const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iyp]); // Jacobian at boundary
       const BoutReal g_22 = 0.5 * (coord->g_22()[i] + coord->g_22()[iyp]);
-      const BoutReal gradient = 2. * (f[iyp] - f[i]) / (coord->dy()[i] + coord->dy()[iyp]);
+      const BoutReal gradient =
+          2. * (f[iyp] - f[i]) / (coord->dy()[i] + coord->dy()[iyp]);
 
       const BoutReal flux = c * J * gradient / g_22;
 
@@ -457,10 +447,11 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D&
 
     // Calculate flux at lower surface
     if (bndry_flux || is_periodic_y || !mesh->firstY(ix) || (iy != mesh->ystart)) {
-      const BoutReal c = 0.5 * (K[i] + K[iym]);               // K at the lower boundary
+      const BoutReal c = 0.5 * (K[i] + K[iym]); // K at the lower boundary
       const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iym]); // Jacobian at boundary
       const BoutReal g_22 = 0.5 * (coord->g_22()[i] + coord->g_22()[iym]);
-      const BoutReal gradient = 2. * (f[i] - f[iym]) / (coord->dy()[i] + coord->dy()[iym]);
+      const BoutReal gradient =
+          2. * (f[i] - f[iym]) / (coord->dy()[i] + coord->dy()[iym]);
 
       const BoutReal flux = c * J * gradient / g_22;
 
@@ -481,16 +472,136 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D&
 * perpendicular Laplacian operator
 *******************************************************************************/
 
-Coordinates::FieldMetric Delp2(const Field2D& f, CELL_LOC outloc, bool useFFT) {
-  return f.getCoordinates(outloc)->Delp2(f, outloc, useFFT);
+bout::FieldMetric Delp2(const Field2D& f, CELL_LOC outloc, [[maybe_unused]] bool useFFT) {
+  const auto& coords = *f.getCoordinates(outloc);
+  return coords.G1() * DDX(f, outloc) + coords.g11() * D2DX2(f, outloc);
 }
 
 Field3D Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
-  return f.getCoordinates(outloc)->Delp2(f, outloc, useFFT);
+  if (outloc == CELL_DEFAULT) {
+    outloc = f.getLocation();
+  }
+
+  ASSERT1(f.getLocation() == outloc);
+  const auto* mesh = f.getMesh();
+
+  if (mesh->GlobalNx == 1 && mesh->GlobalNz == 1) {
+    // copy mesh, location, etc
+    return f * 0;
+  }
+  ASSERT2(mesh->xstart > 0); // Need at least one guard cell;
+
+  Field3D result{emptyFrom(f).setLocation(outloc)};
+
+  if (useFFT and not bout::build::use_metric_3d and mesh->getNZPE() == 1) {
+    const int ncz = mesh->LocalNz;
+
+    // Allocate memory
+    auto ft = Matrix<dcomplex>(mesh->LocalNx, (ncz / 2) + 1);
+    auto delft = Matrix<dcomplex>(mesh->LocalNx, ncz / 2 + 1);
+
+    // Loop over y indices
+    // Note: should not include y-guard or y-boundary points here as that would
+    // use values from corner cells in dx, which may not be initialised.
+    for (int jy = mesh->ystart; jy <= mesh->yend; jy++) {
+
+      // Take forward FFT
+
+      for (int jx = 0; jx < mesh->LocalNx; jx++) {
+        rfft(&f(jx, jy, 0), ncz, &ft(jx, 0));
+      }
+
+      // Loop over kz
+      for (int jz = 0; jz <= ncz / 2; jz++) {
+
+        // No smoothing in the x direction
+        for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
+          // Perform x derivative
+
+          dcomplex a, b, c;
+          laplace_tridag_coefs(jx, jy, jz, a, b, c, nullptr, nullptr, outloc);
+
+          delft(jx, jz) = a * ft(jx - 1, jz) + b * ft(jx, jz) + c * ft(jx + 1, jz);
+        }
+      }
+
+      // Reverse FFT
+      for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
+
+        irfft(&delft(jx, 0), ncz, &result(jx, jy, 0));
+      }
+    }
+  } else {
+    const auto& coords = *f.getCoordinates(outloc);
+    result = coords.G1() * DDX(f, outloc) + coords.G3() * DDZ(f, outloc)
+             + coords.g11() * D2DX2(f, outloc) + coords.g33() * D2DZ2(f, outloc)
+             + 2 * coords.g13() * D2DXDZ(f, outloc);
+  }
+
+  ASSERT2(result.getLocation() == outloc);
+
+  return result;
 }
 
 FieldPerp Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
-  return f.getCoordinates(outloc)->Delp2(f, outloc, useFFT);
+  if (outloc == CELL_DEFAULT) {
+    outloc = f.getLocation();
+  }
+
+  ASSERT1(f.getLocation() == outloc);
+  const auto* mesh = f.getMesh();
+
+  if (mesh->GlobalNx == 1 && mesh->GlobalNz == 1) {
+    // copy mesh, location, etc
+    return f * 0;
+  }
+  ASSERT2(mesh->xstart > 0); // Need at least one guard cell
+
+  FieldPerp result{emptyFrom(f).setLocation(outloc)};
+
+  const int jy = f.getIndex();
+  result.setIndex(jy);
+
+  if (useFFT and mesh->getNZPE() == 1) {
+    int ncz = mesh->LocalNz;
+
+    // Allocate memory
+    auto ft = Matrix<dcomplex>(mesh->LocalNx, ncz / 2 + 1);
+    auto delft = Matrix<dcomplex>(mesh->LocalNx, ncz / 2 + 1);
+
+    // Take forward FFT
+    for (int jx = 0; jx < mesh->LocalNx; jx++) {
+      rfft(&f(jx, 0), ncz, &ft(jx, 0));
+    }
+
+    // Loop over kz
+    for (int jz = 0; jz <= ncz / 2; jz++) {
+
+      // No smoothing in the x direction
+      for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
+        // Perform x derivative
+
+        dcomplex a, b, c;
+        laplace_tridag_coefs(jx, jy, jz, a, b, c);
+
+        delft(jx, jz) = a * ft(jx - 1, jz) + b * ft(jx, jz) + c * ft(jx + 1, jz);
+      }
+    }
+
+    // Reverse FFT
+    for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
+      irfft(&delft(jx, 0), ncz, &result(jx, 0));
+    }
+
+  } else {
+    throw BoutException("Non-fourier Delp2 not currently implented for FieldPerp.");
+    // Would be the following but don't have standard derivative operators for FieldPerps
+    // yet
+    // result = G1 * ::DDX(f, outloc) + G3 * ::DDZ(f, outloc) + g11 * ::D2DX2(f, outloc)
+    //          + g33 * ::D2DZ2(f, outloc) + 2 * g13 * ::D2DXDZ(f, outloc);
+  };
+
+  return result;
 }
 
 /*******************************************************************************
@@ -500,9 +611,9 @@ FieldPerp Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
 * Laplace_perp = Laplace - Laplace_par
 *******************************************************************************/
 
-Coordinates::FieldMetric Laplace_perp(const Field2D& f, CELL_LOC outloc,
-                                      const std::string& dfdy_boundary_condition,
-                                      const std::string& dfdy_region) {
+bout::FieldMetric Laplace_perp(const Field2D& f, CELL_LOC outloc,
+                               const std::string& dfdy_boundary_condition,
+                               const std::string& dfdy_region) {
   return Laplace(f, outloc, dfdy_boundary_condition, dfdy_region)
          - Laplace_par(f, outloc);
 }
@@ -522,12 +633,18 @@ Field3D Laplace_perp(const Field3D& f, CELL_LOC outloc,
  *
  *******************************************************************************/
 
-Coordinates::FieldMetric Laplace_par(const Field2D& f, CELL_LOC outloc) {
-  return f.getCoordinates(outloc)->Laplace_par(f, outloc);
+bout::FieldMetric Laplace_par(const Field2D& f, CELL_LOC outloc) {
+  const auto& coords = *f.getCoordinates(outloc);
+  return D2DY2(f, outloc) / coords.g_22()
+         + DDY(bout::FieldMetric{coords.J() / coords.g_22()}, outloc) * DDY(f, outloc)
+               / coords.J();
 }
 
 Field3D Laplace_par(const Field3D& f, CELL_LOC outloc) {
-  return f.getCoordinates(outloc)->Laplace_par(f, outloc);
+  const auto& coords = *f.getCoordinates(outloc);
+  return D2DY2(f, outloc) / coords.g_22()
+         + DDY(coords.J().asField3DParallel() / coords.g_22(), outloc) * DDY(f, outloc)
+               / coords.J();
 }
 
 /*******************************************************************************
@@ -535,18 +652,31 @@ Field3D Laplace_par(const Field3D& f, CELL_LOC outloc) {
 * Full Laplacian operator on scalar field
 *******************************************************************************/
 
-Coordinates::FieldMetric Laplace(const Field2D& f, CELL_LOC outloc,
-                                 const std::string& dfdy_boundary_condition,
-                                 const std::string& dfdy_region) {
-  return f.getCoordinates(outloc)->Laplace(f, outloc, dfdy_boundary_condition,
-                                           dfdy_region);
+bout::FieldMetric Laplace(const Field2D& f, CELL_LOC outloc,
+                          const std::string& dfdy_boundary_condition,
+                          const std::string& dfdy_region) {
+  const auto& coords = *f.getCoordinates(outloc);
+
+  return coords.G1() * DDX(f, outloc) + coords.G2() * DDY(f, outloc)
+         + coords.g11() * D2DX2(f, outloc) + coords.g22() * D2DY2(f, outloc)
+         + 2.0 * coords.g12()
+               * D2DXDY(f, outloc, "DEFAULT", "RGN_NOBNDRY", dfdy_boundary_condition,
+                        dfdy_region);
 }
 
 Field3D Laplace(const Field3D& f, CELL_LOC outloc,
                 const std::string& dfdy_boundary_condition,
                 const std::string& dfdy_region) {
-  return f.getCoordinates(outloc)->Laplace(f, outloc, dfdy_boundary_condition,
-                                           dfdy_region);
+  const auto& coords = *f.getCoordinates(outloc);
+
+  return coords.G1() * DDX(f, outloc) + coords.G2() * DDY(f, outloc)
+         + coords.G3() * DDZ(f, outloc) + coords.g11() * D2DX2(f, outloc)
+         + coords.g22() * D2DY2(f, outloc) + coords.g33() * D2DZ2(f, outloc)
+         + 2.0
+               * (coords.g12()
+                      * D2DXDY(f, outloc, "DEFAULT", "RGN_NOBNDRY",
+                               dfdy_boundary_condition, dfdy_region)
+                  + coords.g13() * D2DXDZ(f, outloc) + coords.g23() * D2DYDZ(f, outloc));
 }
 
 /*******************************************************************************
@@ -555,7 +685,65 @@ Field3D Laplace(const Field3D& f, CELL_LOC outloc,
  *******************************************************************************/
 
 Field2D Laplace_perpXY(const Field2D& A, const Field2D& f) {
-  return f.getCoordinates()->Laplace_perpXY(A, f);
+#if BOUT_USE_METRIC_3D
+  throw BoutException("Coordinates::Laplace_perpXY for 3D metric not implemented");
+#else
+  const auto& coords = *f.getCoordinates();
+
+  Field2D result;
+  result.allocate();
+  for (auto i : result.getRegion(RGN_NOBNDRY)) {
+    result[i] = 0.;
+
+    // outer x boundary
+    const auto outer_x_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.xp()]); };
+    const BoutReal outer_x_A = outer_x_avg(A);
+    const BoutReal outer_x_J = outer_x_avg(coords.J());
+    const BoutReal outer_x_g11 = outer_x_avg(coords.g11());
+    const BoutReal outer_x_dx = outer_x_avg(coords.dx());
+    const BoutReal outer_x_value = outer_x_A * outer_x_J * outer_x_g11
+                                   / (coords.J()[i] * outer_x_dx * coords.dx()[i]);
+    result[i] += outer_x_value * (f[i.xp()] - f[i]);
+
+    // inner x boundary
+    const auto inner_x_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.xm()]); };
+    const BoutReal inner_x_A = inner_x_avg(A);
+    const BoutReal inner_x_J = inner_x_avg(coords.J());
+    const BoutReal inner_x_g11 = inner_x_avg(coords.g11());
+    const BoutReal inner_x_dx = inner_x_avg(coords.dx());
+    const BoutReal inner_x_value = inner_x_A * inner_x_J * inner_x_g11
+                                   / (coords.J()[i] * inner_x_dx * coords.dx()[i]);
+    result[i] += inner_x_value * (f[i.xm()] - f[i]);
+
+    // upper y boundary
+    const auto upper_y_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.yp()]); };
+    const BoutReal upper_y_A = upper_y_avg(A);
+    const BoutReal upper_y_J = upper_y_avg(coords.J());
+    const BoutReal upper_y_g_22 = upper_y_avg(coords.g_22());
+    const BoutReal upper_y_g23 = upper_y_avg(coords.g23());
+    const BoutReal upper_y_g_23 = upper_y_avg(coords.g_23());
+    const BoutReal upper_y_dy = upper_y_avg(coords.dy());
+    const BoutReal upper_y_value =
+        -upper_y_A * upper_y_J * upper_y_g23 * upper_y_g_23
+        / (upper_y_g_22 * coords.J()[i] * upper_y_dy * coords.dy()[i]);
+    result[i] += upper_y_value * (f[i.yp()] - f[i]);
+
+    // lower y boundary
+    const auto lower_y_avg = [&i](const auto& f) { return 0.5 * (f[i] + f[i.ym()]); };
+    const BoutReal lower_y_A = lower_y_avg(A);
+    const BoutReal lower_y_J = lower_y_avg(coords.J());
+    const BoutReal lower_y_g_22 = lower_y_avg(coords.g_22());
+    const BoutReal lower_y_g23 = lower_y_avg(coords.g23());
+    const BoutReal lower_y_g_23 = lower_y_avg(coords.g_23());
+    const BoutReal lower_y_dy = lower_y_avg(coords.dy());
+    const BoutReal lower_y_value =
+        -lower_y_A * lower_y_J * lower_y_g23 * lower_y_g_23
+        / (lower_y_g_22 * coords.J()[i] * lower_y_dy * coords.dy()[i]);
+    result[i] += lower_y_value * (f[i.ym()] - f[i]);
+  }
+
+  return result;
+#endif
 }
 
 /*******************************************************************************
@@ -564,8 +752,8 @@ Field2D Laplace_perpXY(const Field2D& A, const Field2D& f) {
 * Used for ExB terms and perturbed B field using A_||
 *******************************************************************************/
 
-Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
-                                          CELL_LOC outloc) {
+bout::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
+                                   CELL_LOC outloc) {
 
   if (outloc == CELL_DEFAULT) {
     outloc = A.getLocation();
@@ -576,15 +764,15 @@ Coordinates::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
   Coordinates* metric = phi.getCoordinates(outloc);
 
   // Calculate phi derivatives
-  Coordinates::FieldMetric dpdx = DDX(phi, outloc);
-  Coordinates::FieldMetric dpdy = DDY(phi, outloc);
+  bout::FieldMetric dpdx = DDX(phi, outloc);
+  bout::FieldMetric dpdy = DDY(phi, outloc);
 
   // Calculate advection velocity
-  Coordinates::FieldMetric vx = -metric->g_23() * dpdy;
-  Coordinates::FieldMetric vy = metric->g_23() * dpdx;
+  bout::FieldMetric vx = -metric->g_23() * dpdy;
+  bout::FieldMetric vy = metric->g_23() * dpdx;
 
   // Upwind A using these velocities
-  Coordinates::FieldMetric result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc);
+  bout::FieldMetric result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc);
   result /= metric->J() * sqrt(metric->g_22());
 
   ASSERT1(result.getLocation() == outloc);
@@ -608,13 +796,13 @@ Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc)
   Coordinates* metric = phi.getCoordinates(outloc);
 
   // Calculate phi derivatives
-  Coordinates::FieldMetric dpdx = DDX(phi, outloc);
-  Coordinates::FieldMetric dpdy = DDY(phi, outloc);
+  bout::FieldMetric dpdx = DDX(phi, outloc);
+  bout::FieldMetric dpdy = DDY(phi, outloc);
 
   // Calculate advection velocity
-  Coordinates::FieldMetric vx = -metric->g_23() * dpdy;
-  Coordinates::FieldMetric vy = metric->g_23() * dpdx;
-  Coordinates::FieldMetric vz = metric->g_12() * dpdy - metric->g_22() * dpdx;
+  bout::FieldMetric vx = -metric->g_23() * dpdy;
+  bout::FieldMetric vy = metric->g_23() * dpdx;
+  bout::FieldMetric vz = metric->g_12() * dpdy - metric->g_22() * dpdx;
 
   if (mesh->IncIntShear) {
     // BOUT-06 style differencing
@@ -715,9 +903,8 @@ Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A, CELL_LOC outloc)
  * Terms of form b0 x Grad(f) dot Grad(g) / B = [f, g]
  *******************************************************************************/
 
-Coordinates::FieldMetric bracket(const Field2D& f, const Field2D& g,
-                                 BRACKET_METHOD method, CELL_LOC outloc,
-                                 Solver* UNUSED(solver)) {
+bout::FieldMetric bracket(const Field2D& f, const Field2D& g, BRACKET_METHOD method,
+                          CELL_LOC outloc, Solver* UNUSED(solver)) {
 
   ASSERT1_FIELDS_COMPATIBLE(f, g);
   if (outloc == CELL_DEFAULT) {
@@ -725,7 +912,7 @@ Coordinates::FieldMetric bracket(const Field2D& f, const Field2D& g,
   }
   ASSERT1(outloc == g.getLocation());
 
-  Coordinates::FieldMetric result{emptyFrom(f)};
+  bout::FieldMetric result{emptyFrom(f)};
 
   if ((method == BRACKET_SIMPLE) || (method == BRACKET_ARAKAWA)) {
     // Use a subset of terms for comparison to BOUT-06
diff --git a/src/mesh/g_values.cxx b/src/mesh/g_values.cxx
index 31a794fe22..644f58d52b 100644
--- a/src/mesh/g_values.cxx
+++ b/src/mesh/g_values.cxx
@@ -1,5 +1,6 @@
 #include "bout/g_values.hxx"
 #include "bout/coordinates.hxx"
+#include "bout/derivs.hxx"
 #include "bout/mesh.hxx"
 #include "bout/metric_tensor.hxx"
 
@@ -19,16 +20,13 @@ GValues::GValues(const Coordinates& coordinates) {
 
   bout::FieldMetric Jg12 = J * g12;
   mesh->communicate(Jg12);
-  G1_m =
-      (coordinates.DDX(J * g11) + coordinates.DDY(Jg12) + coordinates.DDZ(J * g13)) / J;
+  G1_m = (DDX(J * g11) + DDY(Jg12) + DDZ(J * g13)) / J;
   bout::FieldMetric Jg22 = J * g22;
   mesh->communicate(Jg22);
-  G2_m =
-      (coordinates.DDX(J * g12) + coordinates.DDY(Jg22) + coordinates.DDZ(J * g23)) / J;
+  G2_m = (DDX(J * g12) + DDY(Jg22) + DDZ(J * g23)) / J;
   bout::FieldMetric Jg23 = J * g23;
   mesh->communicate(Jg23);
-  G3_m =
-      (coordinates.DDX(J * g13) + coordinates.DDY(Jg23) + coordinates.DDZ(J * g33)) / J;
+  G3_m = (DDX(J * g13) + DDY(Jg23) + DDZ(J * g33)) / J;
 
   mesh->communicate(G1_m, G2_m, G3_m);
 }
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index db44b388f1..444135a88d 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -48,7 +48,9 @@
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/globals.hxx>
+#include <bout/index_derivs_interface.hxx>
 #include <bout/interpolation.hxx>
+#include <bout/metric_tensor.hxx>
 #include <bout/output.hxx>
 #include <bout/unused.hxx>
 #include <bout/utils.hxx>
@@ -63,12 +65,23 @@
 
 Field3D DDX(const Field3D& f, CELL_LOC outloc, const std::string& method,
             const std::string& region) {
-  return f.getCoordinates(outloc)->DDX(f, outloc, method, region);
+  const auto& coords = *f.getCoordinates();
+
+  Field3D result = bout::derivatives::index::DDX(f, outloc, method, region) / coords.dx();
+
+  if (f.getMesh()->IncIntShear) {
+    // Using BOUT-06 style shifting
+    result += coords.IntShiftTorsion() * DDZ(f, outloc, method, region);
+  }
+
+  return result;
 }
 
-Coordinates::FieldMetric DDX(const Field2D& f, CELL_LOC outloc, const std::string& method,
-                             const std::string& region) {
-  return f.getCoordinates(outloc)->DDX(f, outloc, method, region);
+bout::FieldMetric DDX(const Field2D& f, CELL_LOC outloc, const std::string& method,
+                      const std::string& region) {
+  ASSERT1(f.getLocation() == outloc || outloc == CELL_DEFAULT);
+  return bout::derivatives::index::DDX(f, outloc, method, region)
+         / f.getCoordinates()->dx();
 }
 
 ////////////// Y DERIVATIVE /////////////////
@@ -79,9 +92,11 @@ Field3D DDY(const Field3DParallel& f, CELL_LOC outloc, const std::string& method
          / f.getCoordinates(outloc)->dy();
 }
 
-Coordinates::FieldMetric DDY(const Field2D& f, CELL_LOC outloc, const std::string& method,
-                             const std::string& region) {
-  return f.getCoordinates(outloc)->DDY(f, outloc, method, region);
+bout::FieldMetric DDY(const Field2D& f, CELL_LOC outloc, const std::string& method,
+                      const std::string& region) {
+  ASSERT1(f.getLocation() == outloc || outloc == CELL_DEFAULT);
+  return bout::derivatives::index::DDY(f, outloc, method, region)
+         / f.getCoordinates()->dy();
 }
 
 ////////////// Z DERIVATIVE /////////////////
@@ -92,9 +107,9 @@ Field3D DDZ(const Field3D& f, CELL_LOC outloc, const std::string& method,
          / f.getCoordinates(outloc)->dz();
 }
 
-Coordinates::FieldMetric DDZ(const Field2D& f, CELL_LOC UNUSED(outloc),
-                             const std::string& UNUSED(method),
-                             const std::string& UNUSED(region)) {
+bout::FieldMetric DDZ(const Field2D& f, CELL_LOC UNUSED(outloc),
+                      const std::string& UNUSED(method),
+                      const std::string& UNUSED(region)) {
   auto tmp = Field2D(0., f.getMesh());
   tmp.setLocation(f.getLocation());
   return tmp;
@@ -173,11 +188,11 @@ Field3D D2DX2(const Field3D& f, CELL_LOC outloc, const std::string& method,
   return result;
 }
 
-Coordinates::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc,
-                               const std::string& method, const std::string& region) {
+bout::FieldMetric D2DX2(const Field2D& f, CELL_LOC outloc, const std::string& method,
+                        const std::string& region) {
   const Coordinates* coords = f.getCoordinates(outloc);
 
-  Coordinates::FieldMetric result =
+  bout::FieldMetric result =
       bout::derivatives::index::D2DX2(f, outloc, method, region) / SQ(coords->dx());
 
   if (coords->non_uniform()) {
@@ -212,11 +227,11 @@ Field3D D2DY2(const Field3D& f, CELL_LOC outloc, const std::string& method,
   return result;
 }
 
-Coordinates::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc,
-                               const std::string& method, const std::string& region) {
+bout::FieldMetric D2DY2(const Field2D& f, CELL_LOC outloc, const std::string& method,
+                        const std::string& region) {
   const Coordinates* coords = f.getCoordinates(outloc);
 
-  Coordinates::FieldMetric result =
+  bout::FieldMetric result =
       bout::derivatives::index::D2DY2(f, outloc, method, region) / SQ(coords->dy());
   if (coords->non_uniform()) {
     // Correction for non-uniform f.getMesh()
@@ -236,8 +251,8 @@ Field3D D2DZ2(const Field3D& f, CELL_LOC outloc, const std::string& method,
          / SQ(f.getCoordinates(outloc)->dz());
 }
 
-Coordinates::FieldMetric D2DZ2(const Field2D& f, CELL_LOC outloc,
-                               const std::string& method, const std::string& region) {
+bout::FieldMetric D2DZ2(const Field2D& f, CELL_LOC outloc, const std::string& method,
+                        const std::string& region) {
   return bout::derivatives::index::D2DZ2(f, outloc, method, region)
          / SQ(f.getCoordinates(outloc)->dz());
 }
@@ -252,8 +267,8 @@ Field3D D4DX4(const Field3D& f, CELL_LOC outloc, const std::string& method,
          / SQ(SQ(f.getCoordinates(outloc)->dx()));
 }
 
-Coordinates::FieldMetric D4DX4(const Field2D& f, CELL_LOC outloc,
-                               const std::string& method, const std::string& region) {
+bout::FieldMetric D4DX4(const Field2D& f, CELL_LOC outloc, const std::string& method,
+                        const std::string& region) {
   return bout::derivatives::index::D4DX4(f, outloc, method, region)
          / SQ(SQ(f.getCoordinates(outloc)->dx()));
 }
@@ -264,8 +279,8 @@ Field3D D4DY4(const Field3D& f, CELL_LOC outloc, const std::string& method,
          / SQ(SQ(f.getCoordinates(outloc)->dy()));
 }
 
-Coordinates::FieldMetric D4DY4(const Field2D& f, CELL_LOC outloc,
-                               const std::string& method, const std::string& region) {
+bout::FieldMetric D4DY4(const Field2D& f, CELL_LOC outloc, const std::string& method,
+                        const std::string& region) {
   return bout::derivatives::index::D4DY4(f, outloc, method, region)
          / SQ(SQ(f.getCoordinates(outloc)->dy()));
 }
@@ -276,8 +291,8 @@ Field3D D4DZ4(const Field3D& f, CELL_LOC outloc, const std::string& method,
          / SQ(SQ(f.getCoordinates(outloc)->dz()));
 }
 
-Coordinates::FieldMetric D4DZ4(const Field2D& f, CELL_LOC outloc,
-                               const std::string& method, const std::string& region) {
+bout::FieldMetric D4DZ4(const Field2D& f, CELL_LOC outloc, const std::string& method,
+                        const std::string& region) {
   return bout::derivatives::index::D4DZ4(f, outloc, method, region)
          / SQ(SQ(f.getCoordinates(outloc)->dz()));
 }
@@ -293,10 +308,10 @@ Coordinates::FieldMetric D4DZ4(const Field2D& f, CELL_LOC outloc,
  *
  * ** Communicates and applies boundary in X.
  */
-Coordinates::FieldMetric D2DXDY(const Field2D& f, CELL_LOC outloc,
-                                const std::string& method, const std::string& region,
-                                const std::string& dfdy_boundary_condition,
-                                const std::string& dfdy_region) {
+bout::FieldMetric D2DXDY(const Field2D& f, CELL_LOC outloc, const std::string& method,
+                         const std::string& region,
+                         const std::string& dfdy_boundary_condition,
+                         const std::string& dfdy_region) {
   const std::string dy_region = dfdy_region.empty() ? region : dfdy_region;
 
   // If staggering in x, take y-derivative at f's location.
@@ -337,9 +352,9 @@ Field3D D2DXDY(const Field3D& f, CELL_LOC outloc, const std::string& method,
   return DDX(dfdy, outloc, method, region);
 }
 
-Coordinates::FieldMetric D2DXDZ(const Field2D& f, CELL_LOC outloc,
-                                [[maybe_unused]] const std::string& method,
-                                [[maybe_unused]] const std::string& region) {
+bout::FieldMetric D2DXDZ(const Field2D& f, CELL_LOC outloc,
+                         [[maybe_unused]] const std::string& method,
+                         [[maybe_unused]] const std::string& region) {
 #if BOUT_USE_METRIC_3D
   Field3D tmp{f};
   return D2DXDZ(tmp, outloc, method, region);
@@ -362,9 +377,9 @@ Field3D D2DXDZ(const Field3D& f, CELL_LOC outloc, const std::string& method,
   return DDZ(DDX(f, x_location, method, region), outloc, method, region);
 }
 
-Coordinates::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc,
-                                [[maybe_unused]] const std::string& method,
-                                [[maybe_unused]] const std::string& region) {
+bout::FieldMetric D2DYDZ(const Field2D& f, CELL_LOC outloc,
+                         [[maybe_unused]] const std::string& method,
+                         [[maybe_unused]] const std::string& region) {
 #if BOUT_USE_METRIC_3D
   Field3D tmp{f};
   return D2DYDZ(tmp, outloc, method, region);
@@ -394,8 +409,8 @@ Field3D D2DYDZ(const Field3D& f, CELL_LOC outloc,
 ////////////// X DERIVATIVE /////////////////
 
 /// Special case where both arguments are 2D.
-Coordinates::FieldMetric VDDX(const Field2D& v, const Field2D& f, CELL_LOC outloc,
-                              const std::string& method, const std::string& region) {
+bout::FieldMetric VDDX(const Field2D& v, const Field2D& f, CELL_LOC outloc,
+                       const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDX(v, f, outloc, method, region)
          / f.getCoordinates(outloc)->dx();
 }
@@ -410,8 +425,8 @@ Field3D VDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc,
 ////////////// Y DERIVATIVE /////////////////
 
 // special case where both are 2D
-Coordinates::FieldMetric VDDY(const Field2D& v, const Field2D& f, CELL_LOC outloc,
-                              const std::string& method, const std::string& region) {
+bout::FieldMetric VDDY(const Field2D& v, const Field2D& f, CELL_LOC outloc,
+                       const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDY(v, f, outloc, method, region)
          / f.getCoordinates(outloc)->dy();
 }
@@ -426,16 +441,16 @@ Field3D VDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc,
 ////////////// Z DERIVATIVE /////////////////
 
 // special case where both are 2D
-Coordinates::FieldMetric VDDZ(const Field2D& v, const Field2D& f, CELL_LOC outloc,
-                              const std::string& method, const std::string& region) {
+bout::FieldMetric VDDZ(const Field2D& v, const Field2D& f, CELL_LOC outloc,
+                       const std::string& method, const std::string& region) {
   return bout::derivatives::index::VDDZ(v, f, outloc, method, region)
          / f.getCoordinates(outloc)->dz();
 }
 
 // Note that this is zero because no compression is included
-Coordinates::FieldMetric VDDZ([[maybe_unused]] const Field3D& v, const Field2D& f,
-                              CELL_LOC outloc, [[maybe_unused]] const std::string& method,
-                              [[maybe_unused]] const std::string& region) {
+bout::FieldMetric VDDZ([[maybe_unused]] const Field3D& v, const Field2D& f,
+                       CELL_LOC outloc, [[maybe_unused]] const std::string& method,
+                       [[maybe_unused]] const std::string& region) {
 #if BOUT_USE_METRIC_3D
   Field3D tmp{f};
   return bout::derivatives::index::VDDZ(v, tmp, outloc, method, region)
@@ -458,8 +473,8 @@ Field3D VDDZ(const Field3D& v, const Field3D& f, CELL_LOC outloc,
 /*******************************************************************************
  * Flux conserving schemes
  *******************************************************************************/
-Coordinates::FieldMetric FDDX(const Field2D& v, const Field2D& f, CELL_LOC outloc,
-                              const std::string& method, const std::string& region) {
+bout::FieldMetric FDDX(const Field2D& v, const Field2D& f, CELL_LOC outloc,
+                       const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDX(v, f, outloc, method, region)
          / f.getCoordinates(outloc)->dx();
 }
@@ -472,8 +487,8 @@ Field3D FDDX(const Field3D& v, const Field3D& f, CELL_LOC outloc,
 
 /////////////////////////////////////////////////////////////////////////
 
-Coordinates::FieldMetric FDDY(const Field2D& v, const Field2D& f, CELL_LOC outloc,
-                              const std::string& method, const std::string& region) {
+bout::FieldMetric FDDY(const Field2D& v, const Field2D& f, CELL_LOC outloc,
+                       const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDY(v, f, outloc, method, region)
          / f.getCoordinates(outloc)->dy();
 }
@@ -486,8 +501,8 @@ Field3D FDDY(const Field3D& v, const Field3DParallel& f, CELL_LOC outloc,
 
 /////////////////////////////////////////////////////////////////////////
 
-Coordinates::FieldMetric FDDZ(const Field2D& v, const Field2D& f, CELL_LOC outloc,
-                              const std::string& method, const std::string& region) {
+bout::FieldMetric FDDZ(const Field2D& v, const Field2D& f, CELL_LOC outloc,
+                       const std::string& method, const std::string& region) {
   return bout::derivatives::index::FDDZ(v, f, outloc, method, region)
          / f.getCoordinates(outloc)->dz();
 }

From adec652faf1b16a2bb21988d8878656b882458b3 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 8 Jul 2026 18:04:38 +0100
Subject: [PATCH 1605/1827] Clang tidy+format

---
 include/bout/derivs.hxx                       |   4 +-
 include/bout/fv_ops_impl.hxx                  |  18 +-
 src/mesh/difops.cxx                           | 286 ++++++++++--------
 src/mesh/fv_ops.cxx                           |   7 +-
 src/mesh/petsc_operators.cxx                  |   3 +-
 src/sys/derivs.cxx                            |   3 -
 .../invert/laplace/test_laplace_hypre3d.cxx   |   4 +-
 .../laplace/test_laplace_petsc3damg.cxx       |   4 +-
 8 files changed, 176 insertions(+), 153 deletions(-)

diff --git a/include/bout/derivs.hxx b/include/bout/derivs.hxx
index be9f2f4111..8ee3b872a1 100644
--- a/include/bout/derivs.hxx
+++ b/include/bout/derivs.hxx
@@ -156,7 +156,7 @@ bout::FieldMetric DDZ(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Vector3D DDZ(const Vector3D& f, CELL_LOC outloc = CELL_DEFAULT,
+Vector3D DDZ(const Vector3D& v, CELL_LOC outloc = CELL_DEFAULT,
              const std::string& method = "DEFAULT",
              const std::string& region = "RGN_NOBNDRY");
 
@@ -172,7 +172,7 @@ Vector3D DDZ(const Vector3D& f, CELL_LOC outloc = CELL_DEFAULT,
 ///                    If not given, defaults to DIFF_DEFAULT
 /// @param[in] region  What region is expected to be calculated
 ///                    If not given, defaults to RGN_NOBNDRY
-Vector2D DDZ(const Vector2D& f, CELL_LOC outloc = CELL_DEFAULT,
+Vector2D DDZ(const Vector2D& v, CELL_LOC outloc = CELL_DEFAULT,
              const std::string& method = "DEFAULT",
              const std::string& region = "RGN_NOBNDRY");
 
diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index c86a376bc0..a4e8f908bf 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -491,10 +491,14 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Calculate velocities
-    const BoutReal vU = 0.25 * (vz[i.zp()] + vz[i]) * (coord->J()[i.zp()] + coord->J()[i]);
-    const BoutReal vD = 0.25 * (vz[i.zm()] + vz[i]) * (coord->J()[i.zm()] + coord->J()[i]);
-    const BoutReal vL = 0.25 * (vx[i.xm()] + vx[i]) * (coord->J()[i.xm()] + coord->J()[i]);
-    const BoutReal vR = 0.25 * (vx[i.xp()] + vx[i]) * (coord->J()[i.xp()] + coord->J()[i]);
+    const BoutReal vU =
+        0.25 * (vz[i.zp()] + vz[i]) * (coord->J()[i.zp()] + coord->J()[i]);
+    const BoutReal vD =
+        0.25 * (vz[i.zm()] + vz[i]) * (coord->J()[i.zm()] + coord->J()[i]);
+    const BoutReal vL =
+        0.25 * (vx[i.xm()] + vx[i]) * (coord->J()[i.xm()] + coord->J()[i]);
+    const BoutReal vR =
+        0.25 * (vx[i.xp()] + vx[i]) * (coord->J()[i.xp()] + coord->J()[i]);
 
     // X direction
     Stencil1D s;
@@ -592,8 +596,10 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Y velocities on y boundaries
-    const BoutReal vU = 0.25 * (vy[i] + vy[i.yp()]) * (coord->J()[i] + coord->J()[i.yp()]);
-    const BoutReal vD = 0.25 * (vy[i] + vy[i.ym()]) * (coord->J()[i] + coord->J()[i.ym()]);
+    const BoutReal vU =
+        0.25 * (vy[i] + vy[i.yp()]) * (coord->J()[i] + coord->J()[i.yp()]);
+    const BoutReal vD =
+        0.25 * (vy[i] + vy[i.ym()]) * (coord->J()[i] + coord->J()[i.ym()]);
 
     // n (advected quantity) on y boundaries
     // Note: Use unshifted n_in variable
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 7e2c313b53..9a22efa67f 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -44,7 +44,6 @@
 #include <bout/solver.hxx>
 #include <bout/unused.hxx>
 #include <bout/utils.hxx>
-#include <bout/vecops.hxx>
 
 #include <cmath>
 #include <string>
@@ -78,13 +77,13 @@ Field3D Grad_parP(const Field3D& apar, const Field3D& f) {
   ASSERT1_FIELDS_COMPATIBLE(apar, f);
   ASSERT1(f.hasParallelSlices());
 
-  Mesh* mesh = apar.getMesh();
+  const Mesh* mesh = apar.getMesh();
 
   Field3D result{emptyFrom(f)};
 
-  int ncz = mesh->LocalNz;
+  const int ncz = mesh->LocalNz;
 
-  Coordinates* metric = apar.getCoordinates();
+  const Coordinates* metric = apar.getCoordinates();
 
   Field3D gys{emptyFrom(f)};
 
@@ -93,8 +92,8 @@ Field3D Grad_parP(const Field3D& apar, const Field3D& f) {
     for (int y = 1; y <= mesh->LocalNy - 2; y++) {
       for (int z = 0; z < ncz; z++) {
         gys(x, y, z) = (f.yup()(x, y + 1, z) - f.ydown()(x, y - 1, z))
-                       / (0.5 * metric->dy(x, y + 1, z) + metric->dy(x, y, z)
-                          + 0.5 * metric->dy(x, y - 1, z));
+                       / ((0.5 * metric->dy(x, y + 1, z)) + metric->dy(x, y, z)
+                          + (0.5 * metric->dy(x, y - 1, z)));
       }
     }
   }
@@ -102,19 +101,19 @@ Field3D Grad_parP(const Field3D& apar, const Field3D& f) {
   for (int x = 1; x <= mesh->LocalNx - 2; x++) {
     for (int y = mesh->ystart; y <= mesh->yend; y++) {
       for (int z = 0; z < ncz; z++) {
-        BoutReal by = 1. / sqrt(metric->g_22(x, y, z));
+        const BoutReal by = 1. / sqrt(metric->g_22(x, y, z));
         // Z indices zm and zp
-        int zm = (z - 1 + ncz) % ncz;
-        int zp = (z + 1) % ncz;
+        const int zm = (z - 1 + ncz) % ncz;
+        const int zp = (z + 1) % ncz;
 
         // bx = -DDZ(apar)
-        BoutReal bx = (apar(x, y, zm) - apar(x, y, zp))
-                      / (0.5 * metric->dz(x, y, zm) + metric->dz(x, y, z)
-                         + 0.5 * metric->dz(x, y, zp));
+        const BoutReal bx = (apar(x, y, zm) - apar(x, y, zp))
+                            / ((0.5 * metric->dz(x, y, zm)) + metric->dz(x, y, z)
+                               + (0.5 * metric->dz(x, y, zp)));
         // bz = DDX(f)
-        BoutReal bz = (apar(x + 1, y, z) - apar(x - 1, y, z))
-                      / (0.5 * metric->dx(x - 1, y, z) + metric->dx(x, y, z)
-                         + 0.5 * metric->dx(x + 1, y, z));
+        const BoutReal bz = (apar(x + 1, y, z) - apar(x - 1, y, z))
+                            / ((0.5 * metric->dx(x - 1, y, z)) + metric->dx(x, y, z)
+                               + (0.5 * metric->dx(x + 1, y, z)));
 
         // Now calculate (bx*d/dx + by*d/dy + bz*d/dz) f
 
@@ -227,29 +226,29 @@ Field3D Div_par(const Field3D& f, const Field3D& v) {
 
   // Parallel divergence, using velocities at cell boundaries
   // Note: Not guaranteed to be flux conservative
-  Mesh* mesh = f.getMesh();
+  const Mesh* mesh = f.getMesh();
 
   Field3D result{emptyFrom(f)};
 
-  Coordinates* coord = f.getCoordinates();
+  const Coordinates* coord = f.getCoordinates();
 
   for (int i = mesh->xstart; i <= mesh->xend; i++) {
     for (int j = mesh->ystart; j <= mesh->yend; j++) {
       for (int k = mesh->zstart; k <= mesh->zend; k++) {
         // Value of f and v at left cell face
-        BoutReal fL = 0.5 * (f(i, j, k) + f.ydown()(i, j - 1, k));
-        BoutReal vL = 0.5 * (v(i, j, k) + v.ydown()(i, j - 1, k));
+        const BoutReal fL = 0.5 * (f(i, j, k) + f.ydown()(i, j - 1, k));
+        const BoutReal vL = 0.5 * (v(i, j, k) + v.ydown()(i, j - 1, k));
 
-        BoutReal fR = 0.5 * (f(i, j, k) + f.yup()(i, j + 1, k));
-        BoutReal vR = 0.5 * (v(i, j, k) + v.yup()(i, j + 1, k));
+        const BoutReal fR = 0.5 * (f(i, j, k) + f.yup()(i, j + 1, k));
+        const BoutReal vR = 0.5 * (v(i, j, k) + v.yup()(i, j + 1, k));
 
         // Calculate flux at right boundary (y+1/2)
-        BoutReal fluxRight =
+        const BoutReal fluxRight =
             fR * vR * (coord->J(i, j, k) + coord->J(i, j + 1, k))
             / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
 
         // Calculate at left boundary (y-1/2)
-        BoutReal fluxLeft =
+        const BoutReal fluxLeft =
             fL * vL * (coord->J(i, j, k) + coord->J(i, j - 1, k))
             / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
 
@@ -266,12 +265,12 @@ Field3D Div_par(const Field3D& f, const Field3D& v) {
 
 Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
                      const std::string& method) {
-  Coordinates* metric = f.getCoordinates(outloc);
+  const Coordinates* metric = f.getCoordinates(outloc);
 
   auto Bxy_floc = f.getCoordinates()->Bxy();
 
   if (!f.hasParallelSlices()) {
-    Field3D f_B = f / Bxy_floc;
+    const Field3D f_B = f / Bxy_floc;
     return metric->Bxy() * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22());
   }
 
@@ -284,8 +283,8 @@ Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
   return metric->Bxy() * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22());
 }
 
-Field3D Div_par_flux(const Field3D& v, const Field3D& f, const std::string& method,
-                     CELL_LOC outloc) {
+static Field3D Div_par_flux(const Field3D& v, const Field3D& f, const std::string& method,
+                            CELL_LOC outloc) {
   return Div_par_flux(v, f, outloc, method);
 }
 
@@ -498,7 +497,7 @@ Field3D Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
 
     // Allocate memory
     auto ft = Matrix<dcomplex>(mesh->LocalNx, (ncz / 2) + 1);
-    auto delft = Matrix<dcomplex>(mesh->LocalNx, ncz / 2 + 1);
+    auto delft = Matrix<dcomplex>(mesh->LocalNx, (ncz / 2) + 1);
 
     // Loop over y indices
     // Note: should not include y-guard or y-boundary points here as that would
@@ -518,7 +517,9 @@ Field3D Delp2(const Field3D& f, CELL_LOC outloc, bool useFFT) {
         for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
           // Perform x derivative
 
-          dcomplex a, b, c;
+          dcomplex a;
+          dcomplex b;
+          dcomplex c;
           laplace_tridag_coefs(jx, jy, jz, a, b, c, nullptr, nullptr, outloc);
 
           delft(jx, jz) = a * ft(jx - 1, jz) + b * ft(jx, jz) + c * ft(jx + 1, jz);
@@ -563,11 +564,11 @@ FieldPerp Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
   result.setIndex(jy);
 
   if (useFFT and mesh->getNZPE() == 1) {
-    int ncz = mesh->LocalNz;
+    const int ncz = mesh->LocalNz;
 
     // Allocate memory
-    auto ft = Matrix<dcomplex>(mesh->LocalNx, ncz / 2 + 1);
-    auto delft = Matrix<dcomplex>(mesh->LocalNx, ncz / 2 + 1);
+    auto ft = Matrix<dcomplex>(mesh->LocalNx, (ncz / 2) + 1);
+    auto delft = Matrix<dcomplex>(mesh->LocalNx, (ncz / 2) + 1);
 
     // Take forward FFT
     for (int jx = 0; jx < mesh->LocalNx; jx++) {
@@ -581,7 +582,9 @@ FieldPerp Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {
       for (int jx = mesh->xstart; jx <= mesh->xend; jx++) {
         // Perform x derivative
 
-        dcomplex a, b, c;
+        dcomplex a;
+        dcomplex b;
+        dcomplex c;
         laplace_tridag_coefs(jx, jy, jz, a, b, c);
 
         delft(jx, jz) = a * ft(jx - 1, jz) + b * ft(jx, jz) + c * ft(jx + 1, jz);
@@ -761,15 +764,15 @@ bout::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
 
   ASSERT1(phi.getMesh() == A.getMesh());
 
-  Coordinates* metric = phi.getCoordinates(outloc);
+  const Coordinates* metric = phi.getCoordinates(outloc);
 
   // Calculate phi derivatives
-  bout::FieldMetric dpdx = DDX(phi, outloc);
-  bout::FieldMetric dpdy = DDY(phi, outloc);
+  const bout::FieldMetric dpdx = DDX(phi, outloc);
+  const bout::FieldMetric dpdy = DDY(phi, outloc);
 
   // Calculate advection velocity
-  bout::FieldMetric vx = -metric->g_23() * dpdy;
-  bout::FieldMetric vy = metric->g_23() * dpdx;
+  const bout::FieldMetric vx = -metric->g_23() * dpdy;
+  const bout::FieldMetric vy = metric->g_23() * dpdx;
 
   // Upwind A using these velocities
   bout::FieldMetric result = VDDX(vx, A, outloc) + VDDY(vy, A, outloc);
@@ -791,17 +794,17 @@ Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc)
 
   ASSERT1(phi.getMesh() == A.getMesh());
 
-  Mesh* mesh = phi.getMesh();
+  const Mesh* mesh = phi.getMesh();
 
-  Coordinates* metric = phi.getCoordinates(outloc);
+  const Coordinates* metric = phi.getCoordinates(outloc);
 
   // Calculate phi derivatives
-  bout::FieldMetric dpdx = DDX(phi, outloc);
-  bout::FieldMetric dpdy = DDY(phi, outloc);
+  const bout::FieldMetric dpdx = DDX(phi, outloc);
+  const bout::FieldMetric dpdy = DDY(phi, outloc);
 
   // Calculate advection velocity
-  bout::FieldMetric vx = -metric->g_23() * dpdy;
-  bout::FieldMetric vy = metric->g_23() * dpdx;
+  const bout::FieldMetric vx = -metric->g_23() * dpdy;
+  const bout::FieldMetric vy = metric->g_23() * dpdx;
   bout::FieldMetric vz = metric->g_12() * dpdy - metric->g_22() * dpdx;
 
   if (mesh->IncIntShear) {
@@ -832,16 +835,16 @@ Field3D b0xGrad_dot_Grad(const Field3D& p, const Field2D& A, CELL_LOC outloc) {
 
   ASSERT1(p.getMesh() == A.getMesh());
 
-  Coordinates* metric = p.getCoordinates(outloc);
+  const Coordinates* metric = p.getCoordinates(outloc);
 
   // Calculate phi derivatives
-  Field3D dpdx = DDX(p, outloc);
-  Field3D dpdy = DDY(p, outloc);
-  Field3D dpdz = DDZ(p, outloc);
+  const Field3D dpdx = DDX(p, outloc);
+  const Field3D dpdy = DDY(p, outloc);
+  const Field3D dpdz = DDZ(p, outloc);
 
   // Calculate advection velocity
-  Field3D vx = metric->g_22() * dpdz - metric->g_23() * dpdy;
-  Field3D vy = metric->g_23() * dpdx - metric->g_12() * dpdz;
+  const Field3D vx = metric->g_22() * dpdz - metric->g_23() * dpdy;
+  const Field3D vy = metric->g_23() * dpdx - metric->g_12() * dpdz;
 
   // Upwind A using these velocities
 
@@ -866,18 +869,18 @@ Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A, CELL_LOC outloc)
 
   ASSERT1(phi.getMesh() == A.getMesh());
 
-  Mesh* mesh = phi.getMesh();
+  const Mesh* mesh = phi.getMesh();
 
-  Coordinates* metric = phi.getCoordinates(outloc);
+  const Coordinates* metric = phi.getCoordinates(outloc);
 
   // Calculate phi derivatives
-  Field3D dpdx = DDX(phi, outloc);
-  Field3D dpdy = DDY(phi, outloc);
-  Field3D dpdz = DDZ(phi, outloc);
+  const Field3D dpdx = DDX(phi, outloc);
+  const Field3D dpdy = DDY(phi, outloc);
+  const Field3D dpdz = DDZ(phi, outloc);
 
   // Calculate advection velocity
-  Field3D vx = metric->g_22() * dpdz - metric->g_23() * dpdy;
-  Field3D vy = metric->g_23() * dpdx - metric->g_12() * dpdz;
+  const Field3D vx = metric->g_22() * dpdz - metric->g_23() * dpdy;
+  const Field3D vy = metric->g_23() * dpdx - metric->g_12() * dpdz;
   Field3D vz = metric->g_12() * dpdy - metric->g_22() * dpdx;
 
   if (mesh->IncIntShear) {
@@ -934,18 +937,18 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
   }
   ASSERT1(outloc == g.getLocation());
 
-  [[maybe_unused]] Mesh* mesh = f.getMesh();
+  [[maybe_unused]] const Mesh* mesh = f.getMesh();
 
   Field3D result{emptyFrom(f).setLocation(outloc)};
 
-  Coordinates* metric = f.getCoordinates(outloc);
+  const Coordinates* metric = f.getCoordinates(outloc);
 
   switch (method) {
   case BRACKET_CTU: {
     // First order Corner Transport Upwind method
     // P.Collela JCP 87, 171-200 (1990)
 
-    if (!solver) {
+    if (solver == nullptr) {
       throw BoutException("CTU method requires access to the solver");
     }
 
@@ -955,13 +958,14 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
     for (int x = mesh->xstart; x <= mesh->xend; x++) {
       for (int y = mesh->ystart; y <= mesh->yend; y++) {
         for (int z = 0; z < ncz; z++) {
-          int zm = (z - 1 + ncz) % ncz;
-          int zp = (z + 1) % ncz;
+          const int zm = (z - 1 + ncz) % ncz;
+          const int zp = (z + 1) % ncz;
 
-          BoutReal gp, gm;
+          BoutReal gp;
+          BoutReal gm;
 
           // Vx = DDZ(f)
-          BoutReal vx = (f(x, y, zp) - f(x, y, zm)) / (2. * metric->dz(x, y, z));
+          const BoutReal vx = (f(x, y, zp) - f(x, y, zm)) / (2. * metric->dz(x, y, z));
 
           // Set stability condition
           solver->setMaxTimestep(metric->dx(x, y, z) / (fabs(vx) + 1e-16));
@@ -996,14 +1000,20 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
     BOUT_FOR(j2D, result.getRegion2D("RGN_NOBNDRY")) {
       // Get constants for this iteration
       const BoutReal spacingFactor = 1.0 / (12 * metric->dz()[j2D] * metric->dx()[j2D]);
-      const int jy = j2D.y(), jx = j2D.x();
-      const int xm = jx - 1, xp = jx + 1;
+      const int jy = j2D.y();
+      const int jx = j2D.x();
+      const int xm = jx - 1;
+      const int xp = jx + 1;
 
       // Extract relevant Field2D values
-      const BoutReal gxm = g(xm, jy), gc = g(jx, jy), gxp = g(xp, jy);
+      const BoutReal gxm = g(xm, jy);
+      const BoutReal gc = g(jx, jy);
+      const BoutReal gxp = g(xp, jy);
 
       // Index Field3D as 2D to get start of z data block
-      const auto fxm = f(xm, jy), fc = f(jx, jy), fxp = f(xp, jy);
+      const auto fxm = f(xm, jy);
+      const auto fc = f(jx, jy);
+      const auto fxp = f(xp, jy);
 
       // Here we split the loop over z into three parts; the first value, the middle block
       // and the last value
@@ -1018,8 +1028,8 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
         const BoutReal Jpp = 2 * (fc[jzp] - fc[jzm]) * (gxp - gxm);
 
         // J+x
-        const BoutReal Jpx = gxp * (fxp[jzp] - fxp[jzm]) - gxm * (fxm[jzp] - fxm[jzm])
-                             + gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]);
+        const BoutReal Jpx = (gxp * (fxp[jzp] - fxp[jzm])) - (gxm * (fxm[jzp] - fxm[jzm]))
+                             + (gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]));
 
         result(jx, jy, 0) = (Jpp + Jpx) * spacingFactor;
       }
@@ -1033,8 +1043,8 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
         const BoutReal Jpp = 2 * (fc[jzp] - fc[jzm]) * (gxp - gxm);
 
         // J+x
-        const BoutReal Jpx = gxp * (fxp[jzp] - fxp[jzm]) - gxm * (fxm[jzp] - fxm[jzm])
-                             + gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]);
+        const BoutReal Jpx = (gxp * (fxp[jzp] - fxp[jzm])) - (gxm * (fxm[jzp] - fxm[jzm]))
+                             + (gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]));
 
         result(jx, jy, jz) = (Jpp + Jpx) * spacingFactor;
       }
@@ -1048,8 +1058,8 @@ Field3D bracket(const Field3D& f, const Field2D& g, BRACKET_METHOD method,
         const BoutReal Jpp = 2 * (fc[jzp] - fc[jzm]) * (gxp - gxm);
 
         // J+x
-        const BoutReal Jpx = gxp * (fxp[jzp] - fxp[jzm]) - gxm * (fxm[jzp] - fxm[jzm])
-                             + gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]);
+        const BoutReal Jpx = (gxp * (fxp[jzp] - fxp[jzm])) - (gxm * (fxm[jzp] - fxm[jzm]))
+                             + (gc * (fxp[jzm] - fxp[jzp] - fxm[jzm] + fxm[jzp]));
 
         result(jx, jy, ncz - 1) = (Jpp + Jpx) * spacingFactor;
       }
@@ -1101,7 +1111,7 @@ Field3D bracket(const Field2D& f, const Field3D& g, BRACKET_METHOD method,
   }
   default: {
     // Use full expression with all terms
-    Coordinates* metric = f.getCoordinates(outloc);
+    const Coordinates* metric = f.getCoordinates(outloc);
     result = b0xGrad_dot_Grad(f, g, outloc) / metric->Bxy();
   }
   }
@@ -1121,7 +1131,7 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
 
   Field3D result{emptyFrom(f).setLocation(outloc)};
 
-  Coordinates* metric = f.getCoordinates(outloc);
+  const Coordinates* metric = f.getCoordinates(outloc);
 
   if (mesh->GlobalNx == 1 || mesh->GlobalNz == 1) {
     result = 0;
@@ -1134,32 +1144,33 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
     // First order Corner Transport Upwind method
     // P.Collela JCP 87, 171-200 (1990)
 #if not(BOUT_USE_METRIC_3D)
-    if (!solver) {
+    if (solver == nullptr) {
       throw BoutException("CTU method requires access to the solver");
     }
 
     // Get current timestep
-    BoutReal dt = solver->getCurrentTimestep();
+    const BoutReal dt = solver->getCurrentTimestep();
 
-    FieldPerp vx(mesh), vz(mesh);
+    FieldPerp vx(mesh);
+    FieldPerp vz(mesh);
     vx.allocate();
     vx.setLocation(outloc);
     vz.allocate();
     vz.setLocation(outloc);
 
-    int ncz = mesh->LocalNz;
+    const int ncz = mesh->LocalNz;
     for (int y = mesh->ystart; y <= mesh->yend; y++) {
       for (int x = 1; x <= mesh->LocalNx - 2; x++) {
         for (int z = mesh->zstart; z <= mesh->zend; z++) {
-          int zm = (z - 1 + ncz) % ncz;
-          int zp = (z + 1) % ncz;
+          const int zm = (z - 1 + ncz) % ncz;
+          const int zp = (z + 1) % ncz;
 
           // Vx = DDZ(f)
           vx(x, z) = (f(x, y, zp) - f(x, y, zm)) / (2. * metric->dz(x, y, z));
           // Vz = -DDX(f)
           vz(x, z) = (f(x - 1, y, z) - f(x + 1, y, z))
-                     / (0.5 * metric->dx(x - 1, y) + metric->dx(x, y)
-                        + 0.5 * metric->dx(x + 1, y));
+                     / ((0.5 * metric->dx(x - 1, y)) + metric->dx(x, y)
+                        + (0.5 * metric->dx(x + 1, y)));
 
           // Set stability condition
           solver->setMaxTimestep(fabs(metric->dx(x, y)) / (fabs(vx(x, z)) + 1e-16));
@@ -1171,33 +1182,34 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
 
       for (int x = mesh->xstart; x <= mesh->xend; x++) {
         for (int z = 0; z < ncz; z++) {
-          int zm = (z - 1 + ncz) % ncz;
-          int zp = (z + 1) % ncz;
+          const int zm = (z - 1 + ncz) % ncz;
+          const int zp = (z + 1) % ncz;
 
-          BoutReal gp, gm;
+          BoutReal gp;
+          BoutReal gm;
 
           // X differencing
           if (vx(x, z) > 0.0) {
             gp = g(x, y, z)
-                 + (0.5 * dt / metric->dz(x, y))
-                       * ((vz(x, z) > 0) ? vz(x, z) * (g(x, y, zm) - g(x, y, z))
-                                         : vz(x, z) * (g(x, y, z) - g(x, y, zp)));
+                 + ((0.5 * dt / metric->dz(x, y))
+                    * ((vz(x, z) > 0) ? vz(x, z) * (g(x, y, zm) - g(x, y, z))
+                                      : vz(x, z) * (g(x, y, z) - g(x, y, zp))));
 
             gm = g(x - 1, y, z)
-                 + (0.5 * dt / metric->dz(x, y))
-                       * ((vz(x, z) > 0) ? vz(x, z) * (g(x - 1, y, zm) - g(x - 1, y, z))
-                                         : vz(x, z) * (g(x - 1, y, z) - g(x - 1, y, zp)));
+                 + ((0.5 * dt / metric->dz(x, y))
+                    * ((vz(x, z) > 0) ? vz(x, z) * (g(x - 1, y, zm) - g(x - 1, y, z))
+                                      : vz(x, z) * (g(x - 1, y, z) - g(x - 1, y, zp))));
 
           } else {
             gp = g(x + 1, y, z)
-                 + (0.5 * dt / metric->dz(x, y))
-                       * ((vz(x, z) > 0) ? vz(x, z) * (g(x + 1, y, zm) - g(x + 1, y, z))
-                                         : vz[x][z] * (g(x + 1, y, z) - g(x + 1, y, zp)));
+                 + ((0.5 * dt / metric->dz(x, y))
+                    * ((vz(x, z) > 0) ? vz(x, z) * (g(x + 1, y, zm) - g(x + 1, y, z))
+                                      : vz[x][z] * (g(x + 1, y, z) - g(x + 1, y, zp))));
 
             gm = g(x, y, z)
-                 + (0.5 * dt / metric->dz(x, y))
-                       * ((vz(x, z) > 0) ? vz(x, z) * (g(x, y, zm) - g(x, y, z))
-                                         : vz(x, z) * (g(x, y, z) - g(x, y, zp)));
+                 + ((0.5 * dt / metric->dz(x, y))
+                    * ((vz(x, z) > 0) ? vz(x, z) * (g(x, y, zm) - g(x, y, z))
+                                      : vz(x, z) * (g(x, y, z) - g(x, y, zp))));
           }
 
           result(x, y, z) = vx(x, z) * (gp - gm) / metric->dx(x, y);
@@ -1205,24 +1217,24 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
           // Z differencing
           if (vz(x, z) > 0.0) {
             gp = g(x, y, z)
-                 + (0.5 * dt / metric->dx(x, y))
-                       * ((vx[x][z] > 0) ? vx[x][z] * (g(x - 1, y, z) - g(x, y, z))
-                                         : vx[x][z] * (g(x, y, z) - g(x + 1, y, z)));
+                 + ((0.5 * dt / metric->dx(x, y))
+                    * ((vx[x][z] > 0) ? vx[x][z] * (g(x - 1, y, z) - g(x, y, z))
+                                      : vx[x][z] * (g(x, y, z) - g(x + 1, y, z))));
 
             gm = g(x, y, zm)
-                 + (0.5 * dt / metric->dx(x, y))
-                       * ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, zm) - g(x, y, zm))
-                                         : vx(x, z) * (g(x, y, zm) - g(x + 1, y, zm)));
+                 + ((0.5 * dt / metric->dx(x, y))
+                    * ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, zm) - g(x, y, zm))
+                                      : vx(x, z) * (g(x, y, zm) - g(x + 1, y, zm))));
           } else {
             gp = g(x, y, zp)
-                 + (0.5 * dt / metric->dx(x, y))
-                       * ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, zp) - g(x, y, zp))
-                                         : vx(x, z) * (g(x, y, zp) - g(x + 1, y, zp)));
+                 + ((0.5 * dt / metric->dx(x, y))
+                    * ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, zp) - g(x, y, zp))
+                                      : vx(x, z) * (g(x, y, zp) - g(x + 1, y, zp))));
 
             gm = g(x, y, z)
-                 + (0.5 * dt / metric->dx(x, y))
-                       * ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, z) - g(x, y, z))
-                                         : vx(x, z) * (g(x, y, z) - g(x + 1, y, z)));
+                 + ((0.5 * dt / metric->dx(x, y))
+                    * ((vx(x, z) > 0) ? vx(x, z) * (g(x - 1, y, z) - g(x, y, z))
+                                      : vx(x, z) * (g(x, y, z) - g(x + 1, y, z))));
           }
 
           result(x, y, z) += vz(x, z) * (gp - gm) / metric->dz(x, y);
@@ -1247,11 +1259,17 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
 #if not(BOUT_USE_METRIC_3D)
       const BoutReal spacingFactor = 1.0 / (12 * metric->dz()[j2D] * metric->dx()[j2D]);
 #endif
-      const int jy = j2D.y(), jx = j2D.x();
-      const int xm = jx - 1, xp = jx + 1;
-
-      const auto Fxm = f_temp(xm, jy), Fx = f_temp(jx, jy), Fxp = f_temp(xp, jy);
-      const auto Gxm = g_temp(xm, jy), Gx = g_temp(jx, jy), Gxp = g_temp(xp, jy);
+      const int jy = j2D.y();
+      const int jx = j2D.x();
+      const int xm = jx - 1;
+      const int xp = jx + 1;
+
+      const auto Fxm = f_temp(xm, jy);
+      const auto Fx = f_temp(jx, jy);
+      const auto Fxp = f_temp(xp, jy);
+      const auto Gxm = g_temp(xm, jy);
+      const auto Gx = g_temp(jx, jy);
+      const auto Gxp = g_temp(xp, jy);
 
       // Here we split the loop over z into three parts; the first value, the middle block
       // and the last value
@@ -1267,18 +1285,18 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
 #endif
 
         // J++ = DDZ(f)*DDX(g) - DDX(f)*DDZ(g)
-        const BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz])
-                              - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm]));
+        const BoutReal Jpp = (((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz]))
+                              - ((Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm])));
 
         // J+x
         const BoutReal Jpx =
-            (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm])
-             - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm]));
+            ((Gxp[jz] * (Fxp[jzp] - Fxp[jzm])) - (Gxm[jz] * (Fxm[jzp] - Fxm[jzm]))
+             - (Gx[jzp] * (Fxp[jzp] - Fxm[jzp])) + (Gx[jzm] * (Fxp[jzm] - Fxm[jzm])));
 
         // Jx+
         const BoutReal Jxp =
-            (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm])
-             - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm]));
+            ((Gxp[jzp] * (Fx[jzp] - Fxp[jz])) - (Gxm[jzm] * (Fxm[jz] - Fx[jzm]))
+             - (Gxm[jzp] * (Fx[jzp] - Fxm[jz])) + (Gxp[jzm] * (Fxp[jz] - Fx[jzm])));
 
         result(jx, jy, jz) = (Jpp + Jpx + Jxp) * spacingFactor;
       }
@@ -1292,18 +1310,18 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
         const int jzm = jz - 1;
 
         // J++ = DDZ(f)*DDX(g) - DDX(f)*DDZ(g)
-        const BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz])
-                              - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm]));
+        const BoutReal Jpp = (((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz]))
+                              - ((Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm])));
 
         // J+x
         const BoutReal Jpx =
-            (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm])
-             - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm]));
+            ((Gxp[jz] * (Fxp[jzp] - Fxp[jzm])) - (Gxm[jz] * (Fxm[jzp] - Fxm[jzm]))
+             - (Gx[jzp] * (Fxp[jzp] - Fxm[jzp])) + (Gx[jzm] * (Fxp[jzm] - Fxm[jzm])));
 
         // Jx+
         const BoutReal Jxp =
-            (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm])
-             - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm]));
+            ((Gxp[jzp] * (Fx[jzp] - Fxp[jz])) - (Gxm[jzm] * (Fxm[jz] - Fx[jzm]))
+             - (Gxm[jzp] * (Fx[jzp] - Fxm[jz])) + (Gxp[jzm] * (Fxp[jz] - Fx[jzm])));
 
         result(jx, jy, jz) = (Jpp + Jpx + Jxp) * spacingFactor;
       }
@@ -1318,18 +1336,18 @@ Field3D bracket(const Field3D& f, const Field3D& g, BRACKET_METHOD method,
 #endif
 
         // J++ = DDZ(f)*DDX(g) - DDX(f)*DDZ(g)
-        const BoutReal Jpp = ((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz])
-                              - (Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm]));
+        const BoutReal Jpp = (((Fx[jzp] - Fx[jzm]) * (Gxp[jz] - Gxm[jz]))
+                              - ((Fxp[jz] - Fxm[jz]) * (Gx[jzp] - Gx[jzm])));
 
         // J+x
         const BoutReal Jpx =
-            (Gxp[jz] * (Fxp[jzp] - Fxp[jzm]) - Gxm[jz] * (Fxm[jzp] - Fxm[jzm])
-             - Gx[jzp] * (Fxp[jzp] - Fxm[jzp]) + Gx[jzm] * (Fxp[jzm] - Fxm[jzm]));
+            ((Gxp[jz] * (Fxp[jzp] - Fxp[jzm])) - (Gxm[jz] * (Fxm[jzp] - Fxm[jzm]))
+             - (Gx[jzp] * (Fxp[jzp] - Fxm[jzp])) + (Gx[jzm] * (Fxp[jzm] - Fxm[jzm])));
 
         // Jx+
         const BoutReal Jxp =
-            (Gxp[jzp] * (Fx[jzp] - Fxp[jz]) - Gxm[jzm] * (Fxm[jz] - Fx[jzm])
-             - Gxm[jzp] * (Fx[jzp] - Fxm[jz]) + Gxp[jzm] * (Fxp[jz] - Fx[jzm]));
+            ((Gxp[jzp] * (Fx[jzp] - Fxp[jz])) - (Gxm[jzm] * (Fxm[jz] - Fx[jzm]))
+             - (Gxm[jzp] * (Fx[jzp] - Fxm[jz])) + (Gxp[jzm] * (Fxp[jz] - Fx[jzm])));
 
         result(jx, jy, jz) = (Jpp + Jpx + Jxp) * spacingFactor;
       }
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index e8958e128d..a400028256 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -214,11 +214,12 @@ Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin, bool bndry_fl
     if (bndry_flux || mesh->periodicY(i.x()) || !mesh->lastY(i.x())
         || (i.y() != mesh->yend)) {
 
-      const BoutReal c = 0.5 * (K[i] + Kup[iyp]);             // K at the upper boundary
+      const BoutReal c = 0.5 * (K[i] + Kup[iyp]); // K at the upper boundary
       const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iyp]); // Jacobian at boundary
       const BoutReal g_22 = 0.5 * (coord->g_22()[i] + coord->g_22()[iyp]);
 
-      const BoutReal gradient = 2. * (fup[iyp] - f[i]) / (coord->dy()[i] + coord->dy()[iyp]);
+      const BoutReal gradient =
+          2. * (fup[iyp] - f[i]) / (coord->dy()[i] + coord->dy()[iyp]);
 
       const BoutReal flux = c * J * gradient / g_22;
 
@@ -228,7 +229,7 @@ Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin, bool bndry_fl
     // Calculate flux at lower surface
     if (bndry_flux || mesh->periodicY(i.x()) || !mesh->firstY(i.x())
         || (i.y() != mesh->ystart)) {
-      const BoutReal c = 0.5 * (K[i] + Kdown[iym]);           // K at the lower boundary
+      const BoutReal c = 0.5 * (K[i] + Kdown[iym]); // K at the lower boundary
       const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iym]); // Jacobian at boundary
 
       const BoutReal g_22 = 0.5 * (coord->g_22()[i] + coord->g_22()[iym]);
diff --git a/src/mesh/petsc_operators.cxx b/src/mesh/petsc_operators.cxx
index 6b4de3fe22..42a35fbf5d 100644
--- a/src/mesh/petsc_operators.cxx
+++ b/src/mesh/petsc_operators.cxx
@@ -340,7 +340,8 @@ PetscOperators::Parallel PetscOperators::getParallel() const {
   dl.applyParallelBoundary("parallel_neumann_o1");
 
   // Cell volume
-  Field3D dV = Coordinates::FieldMetric{coords->J() * coords->dx() * coords->dy() * coords->dz()};
+  Field3D dV =
+      Coordinates::FieldMetric{coords->J() * coords->dx() * coords->dy() * coords->dz()};
   dV.splitParallelSlices();
   dV.yup() = 0.0;
   dV.ydown() = 0.0;
diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index 444135a88d..4cc18d1ae9 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -41,7 +41,6 @@
 #include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/build_defines.hxx>
-#include <bout/constants.hxx>
 #include <bout/coordinates.hxx>
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
@@ -51,9 +50,7 @@
 #include <bout/index_derivs_interface.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/metric_tensor.hxx>
-#include <bout/output.hxx>
 #include <bout/unused.hxx>
-#include <bout/utils.hxx>
 
 #include <string>
 
diff --git a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
index 3a9c332480..e0febdbb22 100644
--- a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
+++ b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
@@ -40,8 +40,8 @@ class ForwardOperator {
 
   const Field3D operator()(Field3D& f) {
     Field3D result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY")
-                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22()) / c1 + a * f
-                     + ex * DDX(f) + ez * DDZ(f);
+                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22()) / c1
+                     + a * f + ex * DDX(f) + ez * DDZ(f);
     applyBoundaries(result, f);
     return result;
   }
diff --git a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx
index 2b856871bc..dcb5e74b31 100644
--- a/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx
+++ b/tests/unit/invert/laplace/test_laplace_petsc3damg.cxx
@@ -40,8 +40,8 @@ class ForwardOperator {
 
   const Field3D operator()(Field3D& f) {
     Field3D result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY")
-                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22()) / c1 + a * f
-                     + ex * DDX(f) + ez * DDZ(f);
+                     + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22()) / c1
+                     + a * f + ex * DDX(f) + ez * DDZ(f);
     applyBoundaries(result, f);
     return result;
   }

From 448fadb1719e601363efab9d50a69e818623e742 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 8 Jul 2026 16:45:49 -0700
Subject: [PATCH 1606/1827] Coordinates::readParallelMetricComponents swap
 co/contra-variant

Covariant metrics have `_`. The new code is consistent with
e.g. metric reads around line 450.
---
 src/mesh/coordinates.cxx | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index b07b9b1995..6359dbe13e 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -598,14 +598,14 @@ void Coordinates::readParallelMetricComponents() {
       load_parallel_metric_component(name, component, i);
     };
 
-    read_offset("g11", covariantMetricTensor.g11_m);
-    read_offset("g22", covariantMetricTensor.g22_m);
-    read_offset("g33", covariantMetricTensor.g33_m);
-    read_offset("g13", covariantMetricTensor.g13_m);
-    read_offset("g_11", contravariantMetricTensor.g11_m);
-    read_offset("g_22", contravariantMetricTensor.g22_m);
-    read_offset("g_33", contravariantMetricTensor.g33_m);
-    read_offset("g_13", contravariantMetricTensor.g13_m);
+    read_offset("g_11", covariantMetricTensor.g11_m);
+    read_offset("g_22", covariantMetricTensor.g22_m);
+    read_offset("g_33", covariantMetricTensor.g33_m);
+    read_offset("g_13", covariantMetricTensor.g13_m);
+    read_offset("g11", contravariantMetricTensor.g11_m);
+    read_offset("g22", contravariantMetricTensor.g22_m);
+    read_offset("g33", contravariantMetricTensor.g33_m);
+    read_offset("g13", contravariantMetricTensor.g13_m);
     read_offset("dy", dy_);
     read_offset("Bxy", Bxy_);
 

From b7b7f125b30ad79c06e7923ec05dab06a6d96dfe Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 8 Jul 2026 17:20:23 -0700
Subject: [PATCH 1607/1827] Mesh::recalculateStaggeredCoordinates move after
 reset

`new_coordinates` should be moved into `coords_map` after it has
been recalculated, not before.
---
 src/mesh/mesh.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 00bd0b5bc4..c8367f3541 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -803,11 +803,11 @@ void Mesh::recalculateStaggeredCoordinates() {
     auto force_interpolate_from_centre = true;
     Coordinates& new_coordinates =
         *createDefaultCoordinates(location, force_interpolate_from_centre);
-    *coords_map[location] = std::move(new_coordinates);
 
     auto recalculate_staggered = false;
     new_coordinates.recalculateAndReset(recalculate_staggered,
                                         force_interpolate_from_centre);
+    *coords_map[location] = std::move(new_coordinates);
   }
 }
 

From 3580dc581cca7426a747b0996ff07ec381b85080 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 8 Jul 2026 17:23:28 -0700
Subject: [PATCH 1608/1827] Coordinates: Invalidate caches when cell spacing
 set

`CoordinatesAccessor` and non-uniform geometry quantities
depend on cell spacing. Reset cache so they are updated when needed.

Bxy is not calculated on demand, so is calculated in
`set*MetricTensor` methods.
---
 include/bout/coordinates.hxx |  4 +++
 src/mesh/coordinates.cxx     | 63 +++++++++++++++++++++++++++++-------
 2 files changed, 56 insertions(+), 11 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index d2019ed31f..f5d528b689 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -514,6 +514,10 @@ private:
   void checkCovariant();
   // check that contravariant tensors are positive (if expected) and finite (always)
   void checkContravariant();
+  void invalidateMetricCaches();
+  void invalidateJacobianCaches();
+  void invalidateCellGeometryCaches();
+  void invalidateAccessorCache();
 
   mutable std::array<std::shared_ptr<YBoundary>, 3> ybndrys;
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 6359dbe13e..05cc515c9a 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -671,6 +671,8 @@ void Coordinates::setDx(FieldMetric dx, const bool communicate) {
     throw BoutException("dx magnitude less than 1e-8");
   }
   dx_ = std::move(dx);
+  invalidateCellGeometryCaches();
+  invalidateAccessorCache();
   if (communicate) {
     localmesh->communicate_no_slices(dx_);
   }
@@ -681,6 +683,8 @@ void Coordinates::setDy(FieldMetric dy, const bool communicate) {
     throw BoutException("dy magnitude less than 1e-8");
   }
   dy_ = std::move(dy);
+  invalidateCellGeometryCaches();
+  invalidateAccessorCache();
   if (communicate) {
     localmesh->communicate_no_slices(dy_);
   }
@@ -691,6 +695,9 @@ void Coordinates::setDz(FieldMetric dz, const bool communicate) {
     throw BoutException("dz magnitude less than 1e-8");
   }
   dz_ = std::move(dz);
+  zlength_cache.reset();
+  invalidateCellGeometryCaches();
+  invalidateAccessorCache();
   if (communicate) {
     localmesh->communicate_no_slices(dz_);
   }
@@ -716,17 +723,8 @@ void Coordinates::recalculateAndReset(bool recalculate_staggered,
   zlength_cache.reset();
   Grad2_par2_DDY_invSgCache.clear();
   invSgCache.reset();
-  CoordinatesAccessor::clear(this);
-
-  _g_22_ylow.reset();
-  _g_22_yhigh.reset();
-  _cell_area_xlow.reset();
-  _cell_area_xhigh.reset();
-  _cell_area_ylow.reset();
-  _cell_area_yhigh.reset();
-  _cell_area_zlow.reset();
-  _cell_area_zhigh.reset();
-  _cell_volume.reset();
+  invalidateCellGeometryCaches();
+  invalidateAccessorCache();
 }
 
 void Coordinates::correctionForNonUniformMeshes(bool force_interpolate_from_centre) {
@@ -998,6 +996,36 @@ void Coordinates::checkContravariant() {
   contravariantMetricTensor.check(localmesh->ystart);
 }
 
+void Coordinates::invalidateCellGeometryCaches() {
+  _g_22_ylow.reset();
+  _g_22_yhigh.reset();
+  _cell_area_xlow.reset();
+  _cell_area_xhigh.reset();
+  _cell_area_ylow.reset();
+  _cell_area_yhigh.reset();
+  _cell_area_zlow.reset();
+  _cell_area_zhigh.reset();
+  _cell_volume.reset();
+}
+
+void Coordinates::invalidateAccessorCache() { CoordinatesAccessor::clear(this); }
+
+void Coordinates::invalidateJacobianCaches() {
+  g_values_cache.reset();
+  invalidateCellGeometryCaches();
+  invalidateAccessorCache();
+}
+
+void Coordinates::invalidateMetricCaches() {
+  christoffel_symbols_cache.reset();
+  g_values_cache.reset();
+  Grad2_par2_DDY_invSgCache.clear();
+  invSgCache.reset();
+  jacobian_cache.reset();
+  invalidateCellGeometryCaches();
+  invalidateAccessorCache();
+}
+
 const Coordinates::FieldMetric& Coordinates::J() const {
   if (jacobian_cache == nullptr) {
     jacobian_cache = std::make_unique<FieldMetric>(recalculateJacobian());
@@ -1010,6 +1038,7 @@ void Coordinates::setJ(const FieldMetric& J, const bool communicate) {
   bout::checkPositive(J, "J", "RGN_NOCORNERS");
 
   //TODO: Calculate J and check value is close
+  invalidateJacobianCaches();
   jacobian_cache = std::make_unique<FieldMetric>(J);
   if (communicate) {
     localmesh->communicate_no_slices(*jacobian_cache);
@@ -1170,6 +1199,9 @@ std::shared_ptr<YBoundary> Coordinates::makeYBoundary(YBndryType type) const {
 void Coordinates::setBxy(FieldMetric Bxy, const bool communicate) {
   //TODO: Calculate Bxy and check value is close
   Bxy_ = std::move(Bxy);
+  _g_22_ylow.reset();
+  _g_22_yhigh.reset();
+  invalidateAccessorCache();
   if (communicate) {
     localmesh->communicate_no_slices(Bxy_);
   }
@@ -1180,6 +1212,9 @@ void Coordinates::setContravariantMetricTensor(
     bool recalculate_staggered, bool force_interpolate_from_centre) {
   contravariantMetricTensor = metric_tensor;
   covariantMetricTensor = contravariantMetricTensor.inverse(region);
+  invalidateMetricCaches();
+  setJ(recalculateJacobian());
+  setBxy(recalculateBxy());
   recalculateAndReset(recalculate_staggered, force_interpolate_from_centre);
 }
 
@@ -1189,6 +1224,9 @@ void Coordinates::setCovariantMetricTensor(const CovariantMetricTensor& metric_t
                                            bool force_interpolate_from_centre) {
   covariantMetricTensor = metric_tensor;
   contravariantMetricTensor = covariantMetricTensor.inverse(region);
+  invalidateMetricCaches();
+  setJ(recalculateJacobian());
+  setBxy(recalculateBxy());
   recalculateAndReset(recalculate_staggered, force_interpolate_from_centre);
 }
 
@@ -1197,6 +1235,9 @@ void Coordinates::setMetricTensor(
     const CovariantMetricTensor& covariant_metric_tensor) {
   contravariantMetricTensor = contravariant_metric_tensor;
   covariantMetricTensor = covariant_metric_tensor;
+  invalidateMetricCaches();
+  setJ(recalculateJacobian());
+  setBxy(recalculateBxy());
 }
 
 void Coordinates::communicateMetricTensor() {

From 74147965700c58243e6532384baf038a8909e228 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 8 Jul 2026 17:26:03 -0700
Subject: [PATCH 1609/1827] test_coordinates: Fix IndexedAccessors

z index should be in range.

Indexed accessors return BoutReal, not reference to field.
---
 tests/unit/mesh/test_coordinates.cxx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/unit/mesh/test_coordinates.cxx b/tests/unit/mesh/test_coordinates.cxx
index 532ccff6db..05f77d0c98 100644
--- a/tests/unit/mesh/test_coordinates.cxx
+++ b/tests/unit/mesh/test_coordinates.cxx
@@ -637,7 +637,7 @@ TEST_F(CoordinatesTest, IndexedAccessors) {
   int x = mesh->xstart;
   int y = mesh->ystart;
 #if BOUT_USE_METRIC_3D
-  int z = mesh->LocalNz;
+  int z = mesh->zstart;
 #endif
 
   output_info.disable();
@@ -662,12 +662,12 @@ TEST_F(CoordinatesTest, IndexedAccessors) {
 #endif
 
 #if not(BOUT_USE_METRIC_3D)
-  const FieldMetric& actual_dx = coords.dx(x, y);
-  const FieldMetric& actual_dy = coords.dy(x, y);
+  const BoutReal actual_dx = coords.dx(x, y);
+  const BoutReal actual_dy = coords.dy(x, y);
 #else
-  const Field3D& actual_dx = coords.dx(x, y, z);
-  const Field3D& actual_dy = coords.dy(x, y, z);
-  const Field3D& actual_dz = coords.dz(x, y, z);
+  const BoutReal actual_dx = coords.dx(x, y, z);
+  const BoutReal actual_dy = coords.dy(x, y, z);
+  const BoutReal actual_dz = coords.dz(x, y, z);
 #endif
 
   EXPECT_EQ(actual_dx, expected_dx);

From 740f40f3eed0302988c51aa1fe4c3a38f56f1919 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 9 Jul 2026 14:27:04 +0100
Subject: [PATCH 1610/1827] Fix setting location of derivatives

---
 src/sys/derivs.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/sys/derivs.cxx b/src/sys/derivs.cxx
index 4cc18d1ae9..b41b83900a 100644
--- a/src/sys/derivs.cxx
+++ b/src/sys/derivs.cxx
@@ -62,7 +62,7 @@
 
 Field3D DDX(const Field3D& f, CELL_LOC outloc, const std::string& method,
             const std::string& region) {
-  const auto& coords = *f.getCoordinates();
+  const auto& coords = *f.getCoordinates(outloc);
 
   Field3D result = bout::derivatives::index::DDX(f, outloc, method, region) / coords.dx();
 
@@ -78,7 +78,7 @@ bout::FieldMetric DDX(const Field2D& f, CELL_LOC outloc, const std::string& meth
                       const std::string& region) {
   ASSERT1(f.getLocation() == outloc || outloc == CELL_DEFAULT);
   return bout::derivatives::index::DDX(f, outloc, method, region)
-         / f.getCoordinates()->dx();
+         / f.getCoordinates(outloc)->dx();
 }
 
 ////////////// Y DERIVATIVE /////////////////
@@ -93,7 +93,7 @@ bout::FieldMetric DDY(const Field2D& f, CELL_LOC outloc, const std::string& meth
                       const std::string& region) {
   ASSERT1(f.getLocation() == outloc || outloc == CELL_DEFAULT);
   return bout::derivatives::index::DDY(f, outloc, method, region)
-         / f.getCoordinates()->dy();
+         / f.getCoordinates(outloc)->dy();
 }
 
 ////////////// Z DERIVATIVE /////////////////

From 69950d18d9ca1638c733d76c5e3e5d1987e8dc35 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 9 Jul 2026 14:44:17 +0100
Subject: [PATCH 1611/1827] Fix broken examples

---
 examples/6field-simple/elm_6f.cxx     | 40 +++++++++++++++++++--------
 examples/conducting-wall-mode/cwm.cxx | 14 +++++++++-
 2 files changed, 41 insertions(+), 13 deletions(-)

diff --git a/examples/6field-simple/elm_6f.cxx b/examples/6field-simple/elm_6f.cxx
index 61b98c2836..1ffa925580 100644
--- a/examples/6field-simple/elm_6f.cxx
+++ b/examples/6field-simple/elm_6f.cxx
@@ -6,19 +6,32 @@
  * T. Xia
  *******************************************************************************/
 
+#include "bout/assert.hxx"
 #include "bout/bout.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/constants.hxx"
+#include "bout/coordinates.hxx"
 #include "bout/derivs.hxx"
+#include "bout/difops.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/fieldgroup.hxx"
 #include "bout/initialprofiles.hxx"
 #include "bout/interpolation_xz.hxx"
 #include "bout/invert_laplace.hxx"
-#include "bout/invert_parderiv.hxx"
 #include "bout/msg_stack.hxx"
+#include "bout/output.hxx"
 #include "bout/physicsmodel.hxx"
+#include "bout/smoothing.hxx"
 #include "bout/sourcex.hxx"
 #include "bout/tokamak_coordinates.hxx"
+#include "bout/unused.hxx"
+#include "bout/vecops.hxx"
+#include "bout/where.hxx"
 
 #include <cmath>
+#include <memory>
 
 constexpr BoutReal eV_K = 11605.0; // 1eV = 11605K
 
@@ -929,7 +942,7 @@ class Elm_6f : public PhysicsModel {
     output.write("\tlog Lambda: {:e}\n", LnLambda);
 
     nu_e = 2.91e-6 * LnLambda * ((N0)*Nbar * density / 1.e6)
-           * pow(Te0 * Tebar, -1.5); // nu_e in 1/S.
+           * pow(Field2D{Te0 * Tebar}, -1.5); // nu_e in 1/S.
     output.write("\telectron collision rate: {:e} -> {:e} [1/s]\n", min(nu_e), max(nu_e));
     // nu_e.applyBoundary();
     // mesh->communicate(nu_e);
@@ -941,7 +954,8 @@ class Elm_6f : public PhysicsModel {
       // xqx addition, begin
       // Use Spitzer thermal conductivities
       nu_i = 4.80e-8 * (Zi * Zi * Zi * Zi / sqrt(AA)) * LnLambda
-             * ((N0)*Nbar * density / 1.e6) * pow(Ti0 * Tibar, -1.5); // nu_i in 1/S.
+             * ((N0)*Nbar * density / 1.e6)
+             * pow(Field2D{Ti0 * Tibar}, -1.5); // nu_i in 1/S.
       // output.write("\tCoulomb Logarithm: {:e} \n", max(LnLambda));
       output.write("\tion collision rate: {:e} -> {:e} [1/s]\n", min(nu_i), max(nu_i));
 
@@ -1006,8 +1020,9 @@ class Elm_6f : public PhysicsModel {
       // Use Spitzer resistivity
       output.write("\n\tSpizter parameters");
       // output.write("\tTemperature: {:e} -> {:e} [eV]\n", min(Te), max(Te));
-      eta_spitzer = 0.51 * 1.03e-4 * Zi * LnLambda
-                    * pow(Te0 * Tebar, -1.5); // eta in Ohm-m. NOTE: ln(Lambda) = 20
+      eta_spitzer =
+          0.51 * 1.03e-4 * Zi * LnLambda
+          * pow(Field2D{Te0 * Tebar}, -1.5); // eta in Ohm-m. NOTE: ln(Lambda) = 20
       output.write("\tSpitzer resistivity: {:e} -> {:e} [Ohm m]\n", min(eta_spitzer),
                    max(eta_spitzer));
       eta_spitzer /= SI::mu0 * Va * Lbar;
@@ -1114,7 +1129,7 @@ class Elm_6f : public PhysicsModel {
       // Only if not restarting: Check initial perturbation
 
       // Set U to zero where P0 < vacuum_pressure
-      U = where(P0 - vacuum_pressure, U, 0.0);
+      U = where(Field2D{P0 - vacuum_pressure}, U, 0.0);
 
       //    Field2D lap_temp = 0.0;
       Field2D logn0 = laplace_alpha * N0;
@@ -1241,24 +1256,25 @@ class Elm_6f : public PhysicsModel {
       // Update resistivity
       if (spitzer_resist) {
         // Use Spitzer formula
-        eta_spitzer = 0.51 * 1.03e-4 * Zi * LnLambda
-                      * pow(Te_tmp * Tebar, -1.5); // eta in Ohm-m. ln(Lambda) = 20
+        eta_spitzer =
+            0.51 * 1.03e-4 * Zi * LnLambda
+            * pow(Field3D{Te_tmp * Tebar}, -1.5); // eta in Ohm-m. ln(Lambda) = 20
         eta_spitzer /= SI::mu0 * Va * Lbar;
       } else {
         eta = core_resist + (vac_resist - core_resist) * vac_mask;
       }
 
       nu_e = 2.91e-6 * LnLambda * (N_tmp * Nbar * density / 1.e6)
-             * pow(Te_tmp * Tebar, -1.5); // nu_e in 1/S.
+             * pow(Field3D{Te_tmp * Tebar}, -1.5); // nu_e in 1/S.
 
       if (diffusion_par > 0.0) {
         // Use Spitzer thermal conductivities
 
         nu_i = 4.80e-8 * (Zi * Zi * Zi * Zi / sqrt(AA)) * LnLambda
                * (N_tmp * Nbar * density / 1.e6)
-               * pow(Ti_tmp * Tibar, -1.5);         // nu_i in 1/S.
-        vth_i = 9.79e3 * sqrt(Ti_tmp * Tibar / AA); // vth_i in m/S.
-        vth_e = 4.19e5 * sqrt(Te_tmp * Tebar);      // vth_e in m/S.
+               * pow(Field3D{Ti_tmp * Tibar}, -1.5); // nu_i in 1/S.
+        vth_i = 9.79e3 * sqrt(Ti_tmp * Tibar / AA);  // vth_i in m/S.
+        vth_e = 4.19e5 * sqrt(Te_tmp * Tebar);       // vth_e in m/S.
       }
 
       if (diffusion_par > 0.0) {
diff --git a/examples/conducting-wall-mode/cwm.cxx b/examples/conducting-wall-mode/cwm.cxx
index 1eda76c493..c3cd40630c 100644
--- a/examples/conducting-wall-mode/cwm.cxx
+++ b/examples/conducting-wall-mode/cwm.cxx
@@ -5,14 +5,26 @@
  * Model version in the code created by M. Umansky and J. Myra.
  *******************************************************************************/
 
+#include <bout/bout_types.hxx>
+#include <bout/coordinates.hxx>
 #include <bout/derivs.hxx>
+#include <bout/difops.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/globals.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert_laplace.hxx>
+#include <bout/output.hxx>
 #include <bout/physicsmodel.hxx>
+#include <bout/sys/range.hxx>
 #include <bout/tokamak_coordinates.hxx>
+#include <bout/unused.hxx>
 #include <bout/utils.hxx>
 
+#include <cmath>
+#include <memory>
+
 class CWM : public PhysicsModel {
 private:
   // 2D initial profiles
@@ -328,7 +340,7 @@ class CWM : public PhysicsModel {
     Field3D result;
     if (bout_exb) {
       // Use a subset of terms for comparison to BOUT-06
-      result = VDDZ(-DDX(p), f);
+      result = VDDZ(Field2D{-DDX(p)}, f);
     } else {
       // Use full expression with all terms
       result = b0xGrad_dot_Grad(p, f) / coord->Bxy();

From 7da06afb392e6fc19ebe614b37d483326cee5fd4 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 9 Jul 2026 14:44:34 +0100
Subject: [PATCH 1612/1827] Fix some clang-tidy warnings

---
 examples/fci-wave/fci-wave.cxx                |  3 +-
 examples/laplace-petsc3d/test-laplace3d.cxx   |  2 +-
 include/bout/coordinates.hxx                  |  2 +-
 include/bout/mesh.hxx                         |  2 +-
 include/bout/metric_tensor.hxx                |  1 -
 src/field/vector2d.cxx                        | 93 +++++++++++--------
 src/field/vector3d.cxx                        | 88 ++++++++++--------
 .../laplace/impls/petsc3damg/petsc3damg.cxx   |  9 +-
 .../impls/petsc2/laplacexy-petsc2.cxx         | 12 +--
 .../impls/cyclic/laplacexz-cyclic.cxx         |  4 +-
 src/mesh/coordinates.cxx                      |  2 +-
 src/mesh/coordinates_accessor.cxx             | 10 +-
 src/mesh/difops.cxx                           |  5 -
 tests/MMS/GBS/gbs.cxx                         |  1 +
 tests/MMS/advection/advection.cxx             |  1 +
 tests/MMS/fieldalign/fieldalign.cxx           |  1 +
 tests/MMS/tokamak/tokamak.cxx                 |  1 +
 tests/MMS/wave-1d/wave.cxx                    |  1 +
 .../test-drift-instability/2fluid.cxx         |  1 +
 tests/integrated/test-snb/test_snb.cxx        |  4 +-
 20 files changed, 134 insertions(+), 109 deletions(-)

diff --git a/examples/fci-wave/fci-wave.cxx b/examples/fci-wave/fci-wave.cxx
index 0ea61f3e8d..fd3adbe2ab 100644
--- a/examples/fci-wave/fci-wave.cxx
+++ b/examples/fci-wave/fci-wave.cxx
@@ -1,7 +1,8 @@
-
 #include "bout/parallel_boundary_region.hxx"
 #include "bout/physicsmodel.hxx"
 
+#include <cmath>
+
 class FCIwave : public PhysicsModel {
 private:
   Field3D n, nv; //< Evolving density, momentum
diff --git a/examples/laplace-petsc3d/test-laplace3d.cxx b/examples/laplace-petsc3d/test-laplace3d.cxx
index 9f21a69be1..5e40b42495 100644
--- a/examples/laplace-petsc3d/test-laplace3d.cxx
+++ b/examples/laplace-petsc3d/test-laplace3d.cxx
@@ -136,7 +136,7 @@ int main(int argc, char** argv) {
   ///////////////////////////////////////////////////////////////////////////////////////
   // Calculate error
   ///////////////////////////////////////////////////////////////////////////////////////
-  auto& g_22 = mesh->getCoordinates()->g_22();
+  const auto& g_22 = mesh->getCoordinates()->g_22();
   Field3D rhs_check = D * this_Laplace_perp(f)
                       + (Grad(f) * Grad(C2) - DDY(C2) * DDY(f) / g_22) / C1 + A * f;
   // The usual way to do this would be
diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index f5d528b689..f01e3883e0 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -517,7 +517,7 @@ private:
   void invalidateMetricCaches();
   void invalidateJacobianCaches();
   void invalidateCellGeometryCaches();
-  void invalidateAccessorCache();
+  void invalidateAccessorCache() const;
 
   mutable std::array<std::shared_ptr<YBoundary>, 3> ybndrys;
 
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 833d23c419..ed1dff68b7 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -624,7 +624,7 @@ public:
     return getCoordinatesSmart(location).get();
   };
 
-  std::shared_ptr<Coordinates> getCoordinatesSmart(const CELL_LOC location = CELL_CENTRE);
+  std::shared_ptr<Coordinates> getCoordinatesSmart(CELL_LOC location = CELL_CENTRE);
 
   std::shared_ptr<Coordinates>
   getCoordinatesConst(const CELL_LOC location = CELL_CENTRE) const {
diff --git a/include/bout/metric_tensor.hxx b/include/bout/metric_tensor.hxx
index bef5bc3079..9e510f2bb9 100644
--- a/include/bout/metric_tensor.hxx
+++ b/include/bout/metric_tensor.hxx
@@ -7,7 +7,6 @@
 #include <bout/field3d.hxx>
 
 #include <string>
-#include <string_view>
 
 namespace bout {
 #if BOUT_USE_METRIC_3D
diff --git a/src/field/vector2d.cxx b/src/field/vector2d.cxx
index bf20b130f5..d6182117ff 100644
--- a/src/field/vector2d.cxx
+++ b/src/field/vector2d.cxx
@@ -28,16 +28,26 @@
  *
  **************************************************************************/
 
-#include <bout/globals.hxx>
-
+#include <bout/assert.hxx>
 #include <bout/boundary_op.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/coordinates.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field_data.hxx>
+#include <bout/globals.hxx>
 #include <bout/interpolation.hxx>
+#include <bout/metric_tensor.hxx>
+#include <bout/region.hxx>
 #include <bout/scorepwrapper.hxx>
 #include <bout/vector2d.hxx>
 
+#include <cmath>
+#include <cstdlib>
+#include <string>
+
 Vector2D::Vector2D(const Vector2D& f)
-    : FieldData(f), x(f.x), y(f.y), z(f.z), covariant(f.covariant), deriv(nullptr),
+    : FieldData(f), x(f.x), y(f.y), z(f.z), covariant(f.covariant),
       location(f.getLocation()) {}
 
 Vector2D::Vector2D(Mesh* localmesh, bool covariant, CELL_LOC location)
@@ -67,10 +77,9 @@ void Vector2D::toCovariant() {
     Mesh* localmesh = getMesh();
 
     if (location == CELL_VSHIFT) {
-      Coordinates *metric_x, *metric_y, *metric_z;
-      metric_x = localmesh->getCoordinates(CELL_XLOW);
-      metric_y = localmesh->getCoordinates(CELL_YLOW);
-      metric_z = localmesh->getCoordinates(CELL_ZLOW);
+      const auto* metric_x = localmesh->getCoordinates(CELL_XLOW);
+      const auto* metric_y = localmesh->getCoordinates(CELL_YLOW);
+      const auto* metric_z = localmesh->getCoordinates(CELL_ZLOW);
 
       // Fields at different locations so we need to interpolate
       // Note : Could reduce peak memory requirement here by just
@@ -86,26 +95,28 @@ void Vector2D::toCovariant() {
 
       // multiply by g_{ij}
       BOUT_FOR(i, x.getRegion("RGN_ALL")) {
-        x[i] = metric_x->g_11()[i] * x[i] + metric_x->g_12()[i] * y_at_x[i]
-               + metric_x->g_13()[i] * z_at_x[i];
-        y[i] = metric_y->g_22()[i] * y[i] + metric_y->g_12()[i] * x_at_y[i]
-               + metric_y->g_23()[i] * z_at_y[i];
-        z[i] = metric_z->g_33()[i] * z[i] + metric_z->g_13()[i] * x_at_z[i]
-               + metric_z->g_23()[i] * y_at_z[i];
+        x[i] = (metric_x->g_11()[i] * x[i]) + (metric_x->g_12()[i] * y_at_x[i])
+               + (metric_x->g_13()[i] * z_at_x[i]);
+        y[i] = (metric_y->g_22()[i] * y[i]) + (metric_y->g_12()[i] * x_at_y[i])
+               + (metric_y->g_23()[i] * z_at_y[i]);
+        z[i] = (metric_z->g_33()[i] * z[i]) + (metric_z->g_13()[i] * x_at_z[i])
+               + (metric_z->g_23()[i] * y_at_z[i]);
       };
     } else {
-      const auto metric = localmesh->getCoordinates(location);
+      auto* const metric = localmesh->getCoordinates(location);
 
       // Need to use temporary arrays to store result
-      Coordinates::FieldMetric gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)};
+      bout::FieldMetric gx{emptyFrom(x)};
+      bout::FieldMetric gy{emptyFrom(y)};
+      bout::FieldMetric gz{emptyFrom(z)};
 
       BOUT_FOR(i, x.getRegion("RGN_ALL")) {
-        gx[i] = metric->g_11()[i] * x[i] + metric->g_12()[i] * y[i]
-                + metric->g_13()[i] * z[i];
-        gy[i] = metric->g_22()[i] * y[i] + metric->g_12()[i] * x[i]
-                + metric->g_23()[i] * z[i];
-        gz[i] = metric->g_33()[i] * z[i] + metric->g_13()[i] * x[i]
-                + metric->g_23()[i] * y[i];
+        gx[i] = (metric->g_11()[i] * x[i]) + (metric->g_12()[i] * y[i])
+                + (metric->g_13()[i] * z[i]);
+        gy[i] = (metric->g_22()[i] * y[i]) + (metric->g_12()[i] * x[i])
+                + (metric->g_23()[i] * z[i]);
+        gz[i] = (metric->g_33()[i] * z[i]) + (metric->g_13()[i] * x[i])
+                + (metric->g_23()[i] * y[i]);
       };
 
       x = gx;
@@ -123,11 +134,9 @@ void Vector2D::toContravariant() {
     Mesh* localmesh = getMesh();
 
     if (location == CELL_VSHIFT) {
-      Coordinates *metric_x, *metric_y, *metric_z;
-
-      metric_x = localmesh->getCoordinates(CELL_XLOW);
-      metric_y = localmesh->getCoordinates(CELL_YLOW);
-      metric_z = localmesh->getCoordinates(CELL_ZLOW);
+      const auto* metric_x = localmesh->getCoordinates(CELL_XLOW);
+      const auto* metric_y = localmesh->getCoordinates(CELL_YLOW);
+      const auto* metric_z = localmesh->getCoordinates(CELL_ZLOW);
 
       // Fields at different locations so we need to interpolate
       // Note : Could reduce peak memory requirement here by just
@@ -143,27 +152,29 @@ void Vector2D::toContravariant() {
 
       // multiply by g_{ij}
       BOUT_FOR(i, x.getRegion("RGN_ALL")) {
-        x[i] = metric_x->g11()[i] * x[i] + metric_x->g12()[i] * y_at_x[i]
-               + metric_x->g13()[i] * z_at_x[i];
-        y[i] = metric_y->g22()[i] * y[i] + metric_y->g12()[i] * x_at_y[i]
-               + metric_y->g23()[i] * z_at_y[i];
-        z[i] = metric_z->g33()[i] * z[i] + metric_z->g13()[i] * x_at_z[i]
-               + metric_z->g23()[i] * y_at_z[i];
+        x[i] = (metric_x->g11()[i] * x[i]) + (metric_x->g12()[i] * y_at_x[i])
+               + (metric_x->g13()[i] * z_at_x[i]);
+        y[i] = (metric_y->g22()[i] * y[i]) + (metric_y->g12()[i] * x_at_y[i])
+               + (metric_y->g23()[i] * z_at_y[i]);
+        z[i] = (metric_z->g33()[i] * z[i]) + (metric_z->g13()[i] * x_at_z[i])
+               + (metric_z->g23()[i] * y_at_z[i]);
       };
 
     } else {
-      const auto metric = localmesh->getCoordinates(location);
+      auto* const metric = localmesh->getCoordinates(location);
 
       // Need to use temporary arrays to store result
-      Coordinates::FieldMetric gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)};
+      bout::FieldMetric gx{emptyFrom(x)};
+      bout::FieldMetric gy{emptyFrom(y)};
+      bout::FieldMetric gz{emptyFrom(z)};
 
       BOUT_FOR(i, x.getRegion("RGN_ALL")) {
-        gx[i] =
-            metric->g11()[i] * x[i] + metric->g12()[i] * y[i] + metric->g13()[i] * z[i];
-        gy[i] =
-            metric->g22()[i] * y[i] + metric->g12()[i] * x[i] + metric->g23()[i] * z[i];
-        gz[i] =
-            metric->g33()[i] * z[i] + metric->g13()[i] * x[i] + metric->g23()[i] * y[i];
+        gx[i] = (metric->g11()[i] * x[i]) + (metric->g12()[i] * y[i])
+                + (metric->g13()[i] * z[i]);
+        gy[i] = (metric->g22()[i] * y[i]) + (metric->g12()[i] * x[i])
+                + (metric->g23()[i] * z[i]);
+        gz[i] = (metric->g33()[i] * z[i]) + (metric->g13()[i] * x[i])
+                + (metric->g23()[i] * y[i]);
       };
 
       x = gx;
@@ -392,7 +403,7 @@ const Coordinates::FieldMetric Vector2D::operator*(const Vector2D& rhs) const {
     result = x * rhs.x + y * rhs.y + z * rhs.z;
   } else {
     // Both are covariant or contravariant
-    Coordinates* metric = localmesh->getCoordinates(location);
+    const Coordinates* metric = localmesh->getCoordinates(location);
 
     if (covariant) {
       // Both covariant
diff --git a/src/field/vector3d.cxx b/src/field/vector3d.cxx
index 7c5a5e3d67..fc61ab2a24 100644
--- a/src/field/vector3d.cxx
+++ b/src/field/vector3d.cxx
@@ -28,17 +28,24 @@
  *
  **************************************************************************/
 
-#include <bout/globals.hxx>
-
 #include <bout/assert.hxx>
 #include <bout/boundary_op.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
+#include <bout/coordinates.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field_data.hxx>
+#include <bout/globals.hxx>
 #include <bout/interpolation.hxx>
+#include <bout/region.hxx>
 #include <bout/scorepwrapper.hxx>
 #include <bout/vector3d.hxx>
 
+#include <cmath>
+#include <cstdlib>
+
 Vector3D::Vector3D(const Vector3D& f)
-    : FieldData(f), x(f.x), y(f.y), z(f.z), covariant(f.covariant), deriv(nullptr),
+    : FieldData(f), x(f.x), y(f.y), z(f.z), covariant(f.covariant),
       location(f.getLocation()) {}
 
 Vector3D::Vector3D(Mesh* localmesh, bool covariant, CELL_LOC location)
@@ -68,10 +75,9 @@ void Vector3D::toCovariant() {
     Mesh* localmesh = getMesh();
 
     if (location == CELL_VSHIFT) {
-      Coordinates *metric_x, *metric_y, *metric_z;
-      metric_x = localmesh->getCoordinates(CELL_XLOW);
-      metric_y = localmesh->getCoordinates(CELL_YLOW);
-      metric_z = localmesh->getCoordinates(CELL_ZLOW);
+      const auto* metric_x = localmesh->getCoordinates(CELL_XLOW);
+      const auto* metric_y = localmesh->getCoordinates(CELL_YLOW);
+      const auto* metric_z = localmesh->getCoordinates(CELL_ZLOW);
 
       // Fields at different locations so we need to interpolate
       // Note : Could reduce peak memory requirement here by just
@@ -87,26 +93,28 @@ void Vector3D::toCovariant() {
 
       // multiply by g_{ij}
       BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) {
-        x[i] = metric_x->g_11()[i] * x[i] + metric_x->g_12()[i] * y_at_x[i]
-               + metric_x->g_13()[i] * z_at_x[i];
-        y[i] = metric_y->g_22()[i] * y[i] + metric_y->g_12()[i] * x_at_y[i]
-               + metric_y->g_23()[i] * z_at_y[i];
-        z[i] = metric_z->g_33()[i] * z[i] + metric_z->g_13()[i] * x_at_z[i]
-               + metric_z->g_23()[i] * y_at_z[i];
+        x[i] = (metric_x->g_11()[i] * x[i]) + (metric_x->g_12()[i] * y_at_x[i])
+               + (metric_x->g_13()[i] * z_at_x[i]);
+        y[i] = (metric_y->g_22()[i] * y[i]) + (metric_y->g_12()[i] * x_at_y[i])
+               + (metric_y->g_23()[i] * z_at_y[i]);
+        z[i] = (metric_z->g_33()[i] * z[i]) + (metric_z->g_13()[i] * x_at_z[i])
+               + (metric_z->g_23()[i] * y_at_z[i]);
       };
     } else {
-      const auto metric = localmesh->getCoordinates(location);
+      auto* const metric = localmesh->getCoordinates(location);
 
       // Need to use temporary arrays to store result
-      Field3D gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)};
+      Field3D gx{emptyFrom(x)};
+      Field3D gy{emptyFrom(y)};
+      Field3D gz{emptyFrom(z)};
 
       BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) {
-        gx[i] = metric->g_11()[i] * x[i] + metric->g_12()[i] * y[i]
-                + metric->g_13()[i] * z[i];
-        gy[i] = metric->g_22()[i] * y[i] + metric->g_12()[i] * x[i]
-                + metric->g_23()[i] * z[i];
-        gz[i] = metric->g_33()[i] * z[i] + metric->g_13()[i] * x[i]
-                + metric->g_23()[i] * y[i];
+        gx[i] = (metric->g_11()[i] * x[i]) + (metric->g_12()[i] * y[i])
+                + (metric->g_13()[i] * z[i]);
+        gy[i] = (metric->g_22()[i] * y[i]) + (metric->g_12()[i] * x[i])
+                + (metric->g_23()[i] * z[i]);
+        gz[i] = (metric->g_33()[i] * z[i]) + (metric->g_13()[i] * x[i])
+                + (metric->g_23()[i] * y[i]);
       };
 
       x = gx;
@@ -124,11 +132,9 @@ void Vector3D::toContravariant() {
     Mesh* localmesh = getMesh();
 
     if (location == CELL_VSHIFT) {
-      Coordinates *metric_x, *metric_y, *metric_z;
-
-      metric_x = localmesh->getCoordinates(CELL_XLOW);
-      metric_y = localmesh->getCoordinates(CELL_YLOW);
-      metric_z = localmesh->getCoordinates(CELL_ZLOW);
+      const auto* metric_x = localmesh->getCoordinates(CELL_XLOW);
+      const auto* metric_y = localmesh->getCoordinates(CELL_YLOW);
+      const auto* metric_z = localmesh->getCoordinates(CELL_ZLOW);
 
       // Fields at different locations so we need to interpolate
       // Note : Could reduce peak memory requirement here by just
@@ -144,27 +150,29 @@ void Vector3D::toContravariant() {
 
       // multiply by g_{ij}
       BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) {
-        x[i] = metric_x->g11()[i] * x[i] + metric_x->g12()[i] * y_at_x[i]
-               + metric_x->g13()[i] * z_at_x[i];
-        y[i] = metric_y->g22()[i] * y[i] + metric_y->g12()[i] * x_at_y[i]
-               + metric_y->g23()[i] * z_at_y[i];
-        z[i] = metric_z->g33()[i] * z[i] + metric_z->g13()[i] * x_at_z[i]
-               + metric_z->g23()[i] * y_at_z[i];
+        x[i] = (metric_x->g11()[i] * x[i]) + (metric_x->g12()[i] * y_at_x[i])
+               + (metric_x->g13()[i] * z_at_x[i]);
+        y[i] = (metric_y->g22()[i] * y[i]) + (metric_y->g12()[i] * x_at_y[i])
+               + (metric_y->g23()[i] * z_at_y[i]);
+        z[i] = (metric_z->g33()[i] * z[i]) + (metric_z->g13()[i] * x_at_z[i])
+               + (metric_z->g23()[i] * y_at_z[i]);
       };
 
     } else {
-      const auto metric = localmesh->getCoordinates(location);
+      auto* const metric = localmesh->getCoordinates(location);
 
       // Need to use temporary arrays to store result
-      Field3D gx{emptyFrom(x)}, gy{emptyFrom(y)}, gz{emptyFrom(z)};
+      Field3D gx{emptyFrom(x)};
+      Field3D gy{emptyFrom(y)};
+      Field3D gz{emptyFrom(z)};
 
       BOUT_FOR(i, localmesh->getRegion3D("RGN_ALL")) {
-        gx[i] =
-            metric->g11()[i] * x[i] + metric->g12()[i] * y[i] + metric->g13()[i] * z[i];
-        gy[i] =
-            metric->g22()[i] * y[i] + metric->g12()[i] * x[i] + metric->g23()[i] * z[i];
-        gz[i] =
-            metric->g33()[i] * z[i] + metric->g13()[i] * x[i] + metric->g23()[i] * y[i];
+        gx[i] = (metric->g11()[i] * x[i]) + (metric->g12()[i] * y[i])
+                + (metric->g13()[i] * z[i]);
+        gy[i] = (metric->g22()[i] * y[i]) + (metric->g12()[i] * x[i])
+                + (metric->g23()[i] * z[i]);
+        gz[i] = (metric->g33()[i] * z[i]) + (metric->g13()[i] * x[i])
+                + (metric->g23()[i] * y[i]);
       };
 
       x = gx;
diff --git a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
index fa73016db0..d254ea4a68 100644
--- a/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
+++ b/src/invert/laplace/impls/petsc3damg/petsc3damg.cxx
@@ -24,14 +24,15 @@
  * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
  *
  **************************************************************************/
-#include "bout/bout_types.hxx"
-#include "bout/build_defines.hxx"
+
+#include <bout/build_defines.hxx>
 
 #if BOUT_HAS_PETSC
 
 #include "petsc3damg.hxx"
 
 #include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/derivs.hxx>
 #include <bout/mesh.hxx>
@@ -40,6 +41,8 @@
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 
+#include <cmath>
+
 using bout::utils::flagSet;
 
 #ifdef PETSC_HAVE_HYPRE
@@ -328,7 +331,7 @@ void LaplacePetsc3dAmg::updateMatrix3D() {
     }
 
     BoutReal C_d2f_dx2 = coords->g11()[l];
-    BoutReal C_d2f_dy2 = (coords->g22()[l] - 1.0 / coords->g_22()[l]);
+    BoutReal C_d2f_dy2 = (coords->g22()[l] - (1.0 / coords->g_22()[l]));
     BoutReal C_d2f_dz2 = coords->g33()[l];
     if (issetD) {
       C_d2f_dx2 *= D[l];
diff --git a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
index bdfc3bb5ff..916dc0c6af 100644
--- a/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
+++ b/src/invert/laplacexy/impls/petsc2/laplacexy-petsc2.cxx
@@ -162,7 +162,7 @@ void LaplaceXYpetsc2::setCoefs(const Field2D& A, const Field2D& B) {
     BoutReal dx = 0.5 * (coords->dx()[index] + coords->dx()[ind_xp]);
     BoutReal Acoef = 0.5 * (A[index] + A[ind_xp]);
 
-    BoutReal xp = Acoef * J * g11 / (coords->J()[index] * dx * coords->dx()[index]);
+    const BoutReal xp = Acoef * J * g11 / (coords->J()[index] * dx * coords->dx()[index]);
 
     // Metrics on x-1/2 boundary
     J = 0.5 * (coords->J()[index] + coords->J()[ind_xm]);
@@ -170,7 +170,7 @@ void LaplaceXYpetsc2::setCoefs(const Field2D& A, const Field2D& B) {
     dx = 0.5 * (coords->dx()[index] + coords->dx()[ind_xm]);
     Acoef = 0.5 * (A[index] + A[ind_xm]);
 
-    BoutReal xm = Acoef * J * g11 / (coords->J()[index] * dx * coords->dx()[index]);
+    const BoutReal xm = Acoef * J * g11 / (coords->J()[index] * dx * coords->dx()[index]);
 
     BoutReal c = B[index] - xp - xm; // Central coefficient
 
@@ -190,8 +190,8 @@ void LaplaceXYpetsc2::setCoefs(const Field2D& A, const Field2D& B) {
       BoutReal dy = 0.5 * (coords->dy()[index] + coords->dy()[ind_yp]);
       Acoef = 0.5 * (A[ind_yp] + A[index]);
 
-      BoutReal yp = -Acoef * J * g23 * g_23
-                    / (g_22 * coords->J()[index] * dy * coords->dy()[index]);
+      const BoutReal yp = -Acoef * J * g23 * g_23
+                          / (g_22 * coords->J()[index] * dy * coords->dy()[index]);
       c -= yp;
       matrix(index, ind_yp) = yp;
 
@@ -203,8 +203,8 @@ void LaplaceXYpetsc2::setCoefs(const Field2D& A, const Field2D& B) {
       dy = 0.5 * (coords->dy()[index] + coords->dy()[ind_ym]);
       Acoef = 0.5 * (A[ind_ym] + A[index]);
 
-      BoutReal ym = -Acoef * J * g23 * g_23
-                    / (g_22 * coords->J()[index] * dy * coords->dy()[index]);
+      const BoutReal ym = -Acoef * J * g23 * g_23
+                          / (g_22 * coords->J()[index] * dy * coords->dy()[index]);
       c -= ym;
       matrix(index, ind_ym) = ym;
     }
diff --git a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
index 0a7030dec9..2048bb587f 100644
--- a/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
+++ b/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx
@@ -5,11 +5,11 @@
 
 #include <bout/constants.hxx>
 #include <bout/fft.hxx>
+#include <bout/field3d.hxx>
+#include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 
-#include <bout/output.hxx>
-
 LaplaceXZcyclic::LaplaceXZcyclic(Mesh* m, Options* options, const CELL_LOC loc)
     : LaplaceXZ(m, options, loc) {
   // Note: `m` may be nullptr, but localmesh is set in LaplaceXZ base constructor
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 05cc515c9a..4ae9fcf1b4 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1008,7 +1008,7 @@ void Coordinates::invalidateCellGeometryCaches() {
   _cell_volume.reset();
 }
 
-void Coordinates::invalidateAccessorCache() { CoordinatesAccessor::clear(this); }
+void Coordinates::invalidateAccessorCache() const { CoordinatesAccessor::clear(this); }
 
 void Coordinates::invalidateJacobianCaches() {
   g_values_cache.reset();
diff --git a/src/mesh/coordinates_accessor.cxx b/src/mesh/coordinates_accessor.cxx
index 0f11906c21..2c9eaf6de9 100644
--- a/src/mesh/coordinates_accessor.cxx
+++ b/src/mesh/coordinates_accessor.cxx
@@ -18,7 +18,7 @@ CoordinatesAccessor::CoordinatesAccessor(const Coordinates* coords) {
   ASSERT0(coords != nullptr);
 
   // Size of the mesh in Z. Used to convert 3D -> 2D index
-  Mesh* mesh = coords->dx().getMesh();
+  const Mesh* mesh = coords->dx().getMesh();
   mesh_nz = mesh->LocalNz;
 
   auto search = coords_store.find(coords);
@@ -61,13 +61,15 @@ CoordinatesAccessor::CoordinatesAccessor(const Coordinates* coords) {
     COPY_STRIPE(J);
 
     if (coords->Bxy().isAllocated()) {
-      data[stripe_size * ind.ind + static_cast<int>(Offset::B)] = coords->Bxy()[ind];
-      if (coords->Bxy().yup().isAllocated())
+      data[(stripe_size * ind.ind) + static_cast<int>(Offset::B)] = coords->Bxy()[ind];
+      if (coords->Bxy().yup().isAllocated()) {
         data[stripe_size * ind.ind + static_cast<int>(Offset::Byup)] =
             coords->Bxy().yup()[ind];
-      if (coords->Bxy().ydown().isAllocated())
+      }
+      if (coords->Bxy().ydown().isAllocated()) {
         data[stripe_size * ind.ind + static_cast<int>(Offset::Bydown)] =
             coords->Bxy().ydown()[ind];
+      }
     }
 
     COPY_STRIPE(G1, G3);
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 9a22efa67f..96793e2d7d 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -283,11 +283,6 @@ Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
   return metric->Bxy() * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22());
 }
 
-static Field3D Div_par_flux(const Field3D& v, const Field3D& f, const std::string& method,
-                            CELL_LOC outloc) {
-  return Div_par_flux(v, f, outloc, method);
-}
-
 /*******************************************************************************
 * Grad2_par2
 * second parallel derivative
diff --git a/tests/MMS/GBS/gbs.cxx b/tests/MMS/GBS/gbs.cxx
index ab23efbd6c..e2c42ead65 100644
--- a/tests/MMS/GBS/gbs.cxx
+++ b/tests/MMS/GBS/gbs.cxx
@@ -16,6 +16,7 @@
 
 #include <bout/bout_types.hxx>
 #include <bout/derivs.hxx>
+#include <bout/field3d.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/tokamak_coordinates.hxx>
diff --git a/tests/MMS/advection/advection.cxx b/tests/MMS/advection/advection.cxx
index 6b8510ec83..2480fdb8c6 100644
--- a/tests/MMS/advection/advection.cxx
+++ b/tests/MMS/advection/advection.cxx
@@ -4,6 +4,7 @@
  */
 
 #include <bout/derivs.hxx>
+#include <bout/field2d.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/physicsmodel.hxx>
 
diff --git a/tests/MMS/fieldalign/fieldalign.cxx b/tests/MMS/fieldalign/fieldalign.cxx
index 16e9c50bc8..c5574f26b0 100644
--- a/tests/MMS/fieldalign/fieldalign.cxx
+++ b/tests/MMS/fieldalign/fieldalign.cxx
@@ -1,4 +1,5 @@
 #include <bout/derivs.hxx>
+#include <bout/field2d.hxx>
 #include <bout/physicsmodel.hxx>
 
 class FieldAlign : public PhysicsModel {
diff --git a/tests/MMS/tokamak/tokamak.cxx b/tests/MMS/tokamak/tokamak.cxx
index fa89c9eb36..9648ddf7f5 100644
--- a/tests/MMS/tokamak/tokamak.cxx
+++ b/tests/MMS/tokamak/tokamak.cxx
@@ -8,6 +8,7 @@
 
 #include <bout/bout_types.hxx>
 #include <bout/derivs.hxx>
+#include <bout/field2d.hxx>
 #include <bout/field_factory.hxx>
 #include <bout/options.hxx>
 #include <bout/physicsmodel.hxx>
diff --git a/tests/MMS/wave-1d/wave.cxx b/tests/MMS/wave-1d/wave.cxx
index 7c2506f3d8..b5cc343297 100644
--- a/tests/MMS/wave-1d/wave.cxx
+++ b/tests/MMS/wave-1d/wave.cxx
@@ -1,5 +1,6 @@
 #include <bout/constants.hxx>
 #include <bout/derivs.hxx>
+#include <bout/field3d.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/metric_tensor.hxx>
 #include <bout/physicsmodel.hxx>
diff --git a/tests/integrated/test-drift-instability/2fluid.cxx b/tests/integrated/test-drift-instability/2fluid.cxx
index 59f3b22342..7af5834e8c 100644
--- a/tests/integrated/test-drift-instability/2fluid.cxx
+++ b/tests/integrated/test-drift-instability/2fluid.cxx
@@ -5,6 +5,7 @@
 
 #include <bout/bout.hxx>
 #include <bout/derivs.hxx>
+#include <bout/field2d.hxx>
 #include <bout/initialprofiles.hxx>
 #include <bout/interpolation.hxx>
 #include <bout/invert_laplace.hxx>
diff --git a/tests/integrated/test-snb/test_snb.cxx b/tests/integrated/test-snb/test_snb.cxx
index 68a2884a1e..40dfd4880d 100644
--- a/tests/integrated/test-snb/test_snb.cxx
+++ b/tests/integrated/test-snb/test_snb.cxx
@@ -215,8 +215,8 @@ int main(int argc, char** argv) {
       for (int y = mesh->ystart; y <= mesh->yend; y++) {
         const double y_n = (double(y) + 0.5) / double(mesh->yend + 1);
 
-        dy_copy(x, y) = 1. - 0.9 * y_n;
-        J_copy(x, y) = 1. + y_n * y_n;
+        dy_copy(x, y) = 1. - (0.9 * y_n);
+        J_copy(x, y) = 1. + (y_n * y_n);
       }
     }
     coord->setDy(dy_copy);

From d546becb906d49d5fd50488c55c87fc25aff8bf9 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 9 Jul 2026 11:57:33 -0700
Subject: [PATCH 1613/1827] Div_par: Use Field3DParallel

Convert input to Field3DParallel before dividing by Bxy,
to ensure that yup/ydown fields are retained.
---
 src/mesh/difops.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 96793e2d7d..433316a793 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -216,7 +216,7 @@ Field3D Div_par(const Field3D& f, CELL_LOC outloc, const std::string& method) {
   // Need Bxy at location of f, which might be different from outloc
   const auto& Bxy_floc = f.getCoordinates()->Bxy();
 
-  return Bxy_outloc * Grad_par(Field3D{f / Bxy_floc}, outloc, method);
+  return Bxy_outloc * Grad_par(Field3DParallel{f} / Bxy_floc, outloc, method);
 }
 
 Field3D Div_par(const Field3D& f, const Field3D& v) {

From 0870329749ea1d59a211d1dae7a868df67fecd56 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 9 Jul 2026 13:25:34 -0700
Subject: [PATCH 1614/1827] Coordinates: Use communicate_no_slices

Should now be consistent with `next` branch. Avoids
calculation of parallel slices for derived metric quantities.
---
 src/mesh/coordinates.cxx | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 4ae9fcf1b4..01dbbb1ce1 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -496,6 +496,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
   if (localmesh->get(J_temp, "J" + suffix, 0.0, false) != 0) {
     output_warn.write(
         "\tWARNING: Jacobian 'J' not found. Calculating from metric tensor\n");
+    localmesh->communicate_no_slices(*jacobian_cache);
   } else {
     checkStaggeredGet(localmesh, "J", suffix);
     *jacobian_cache = ensuredUnaligned(J_temp);
@@ -521,6 +522,7 @@ void Coordinates::readFromMesh(Options* options, const std::string& suffix) {
                       "metric tensor\n");
     Bxy_ = interpolateAndExtrapolate(Bcalc, location, extrapolate_x, extrapolate_y, false,
                                      transform.get());
+    localmesh->communicate_no_slices(Bxy_);
   } else {
     checkStaggeredGet(localmesh, "Bxy", suffix);
     Bxy_ = ensuredUnaligned(Bxy_);
@@ -784,7 +786,7 @@ void Coordinates::correctionForNonUniformMeshes(bool force_interpolate_from_cent
       output_warn.write("\tWARNING: differencing quantity 'd2z' not found. "
                         "Calculating from dz\n");
       d1_dz_ = bout::derivatives::index::DDZ(FieldMetric{1. / dz()});
-      localmesh->communicate(d1_dz_);
+      localmesh->communicate_no_slices(d1_dz_);
       d1_dz_ =
           interpolateAndExtrapolate(d1_dz_, location, true, true, true, transform.get());
     } else {
@@ -799,7 +801,7 @@ void Coordinates::correctionForNonUniformMeshes(bool force_interpolate_from_cent
     d1_dz_ = 0;
   }
 
-  localmesh->communicate(d1_dx_, d1_dy_, d1_dz_);
+  localmesh->communicate_no_slices(d1_dx_, d1_dy_, d1_dz_);
 }
 
 Coordinates::FieldMetric Coordinates::recalculateJacobian() const {

From 312bfc35e04be1407215200b7729124305a34861 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 9 Jul 2026 13:26:33 -0700
Subject: [PATCH 1615/1827] Coordinates: Getters use BOUT_OMP_SAFE

Makes lazy getters thread-safe by adding named critical sections.
Named so that nested sections (code in critical section calling
a function that also contains a critical section) doesn't lead to
deadlock.
---
 src/mesh/coordinates.cxx | 106 +++++++++++++++++++++++----------------
 1 file changed, 63 insertions(+), 43 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 01dbbb1ce1..80329536c7 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -931,65 +931,82 @@ void Coordinates::setParallelTransform(Options* options) {
 }
 
 const ChristoffelSymbols& Coordinates::christoffel_symbols() const {
-  if (christoffel_symbols_cache == nullptr) {
-    christoffel_symbols_cache = std::make_unique<ChristoffelSymbols>(*this);
-    // Set boundary guard cells of Christoffel symbol terms
-    // Ideally, when location is staggered, we would set the upper/outer boundary point
-    // correctly rather than by extrapolating here: e.g. if location==CELL_YLOW and we are
-    // at the upper y-boundary the x- and z-derivatives at yend+1 at the boundary can be
-    // calculated because the guard cells are available, while the y-derivative could be
-    // calculated from the CELL_CENTRE metric components (which have guard cells available
-    // past the boundary location). This would avoid the problem that the y-boundary on the
-    // CELL_YLOW grid is at a 'guard cell' location (yend+1).
-    // However, the above would require lots of special handling, so just extrapolate for
-    // now.
-
-    christoffel_symbols_cache->map([this](const FieldMetric& component) {
-      return interpolateAndExtrapolate(component, location, true, true, false,
-                                       transform.get());
-    });
+  BOUT_OMP_SAFE(critical(christoffel_symbols_cache))
+  {
+    if (christoffel_symbols_cache == nullptr) {
+      christoffel_symbols_cache = std::make_unique<ChristoffelSymbols>(*this);
+      // Set boundary guard cells of Christoffel symbol terms
+      // Ideally, when location is staggered, we would set the upper/outer boundary point
+      // correctly rather than by extrapolating here: e.g. if location==CELL_YLOW and we are
+      // at the upper y-boundary the x- and z-derivatives at yend+1 at the boundary can be
+      // calculated because the guard cells are available, while the y-derivative could be
+      // calculated from the CELL_CENTRE metric components (which have guard cells available
+      // past the boundary location). This would avoid the problem that the y-boundary on the
+      // CELL_YLOW grid is at a 'guard cell' location (yend+1).
+      // However, the above would require lots of special handling, so just extrapolate for
+      // now.
+
+      christoffel_symbols_cache->map([this](const FieldMetric& component) {
+        return interpolateAndExtrapolate(component, location, true, true, false,
+                                         transform.get());
+      });
+    }
   }
   return *christoffel_symbols_cache;
 }
 
 GValues& Coordinates::g_values() const {
-  if (g_values_cache == nullptr) {
-    g_values_cache = std::make_unique<GValues>(*this);
-    g_values_cache->map([this](const FieldMetric& component) {
-      return interpolateAndExtrapolate(component, location, true, true, true,
-                                       transform.get());
-    });
+  BOUT_OMP_SAFE(critical(g_values_cache))
+  {
+    if (g_values_cache == nullptr) {
+      g_values_cache = std::make_unique<GValues>(*this);
+      g_values_cache->map([this](const FieldMetric& component) {
+        return interpolateAndExtrapolate(component, location, true, true, true,
+                                         transform.get());
+      });
+    }
   }
   return *g_values_cache;
 }
 
 const Coordinates::FieldMetric& Coordinates::invSg() const {
-  if (invSgCache == nullptr) {
-    auto ptr = std::make_unique<Coordinates::FieldMetric>();
-    (*ptr) = 1.0 / sqrt(g_22());
-    invSgCache = std::move(ptr);
+  BOUT_OMP_SAFE(critical(invSg_cache))
+  {
+    if (invSgCache == nullptr) {
+      auto ptr = std::make_unique<Coordinates::FieldMetric>();
+      (*ptr) = 1.0 / sqrt(g_22());
+      invSgCache = std::move(ptr);
+    }
   }
   return *invSgCache;
 }
 
 const Coordinates::FieldMetric&
 Coordinates::Grad2_par2_DDY_invSg(CELL_LOC outloc, const std::string& method) const {
+  const FieldMetric* result{nullptr};
+  BOUT_OMP_SAFE(critical(Grad2_par2_DDY_invSg_cache))
+  {
+    if (auto search = Grad2_par2_DDY_invSgCache.find(method);
+        search != Grad2_par2_DDY_invSgCache.end()) {
+      result = search->second.get();
+    } else {
+      if (invSgCache == nullptr) {
+        auto ptr = std::make_unique<Coordinates::FieldMetric>();
+        (*ptr) = 1.0 / sqrt(g_22());
+        invSgCache = std::move(ptr);
+      }
 
-  if (auto search = Grad2_par2_DDY_invSgCache.find(method);
-      search != Grad2_par2_DDY_invSgCache.end()) {
-    return *search->second;
-  }
-  invSg();
-
-  // Communicate to get parallel slices
-  localmesh->communicate(*invSgCache);
-  invSgCache->applyParallelBoundary("parallel_neumann_o2");
+      // Communicate to get parallel slices
+      localmesh->communicate(*invSgCache);
+      invSgCache->applyParallelBoundary("parallel_neumann_o2");
 
-  // cache
-  auto ptr = std::make_unique<Coordinates::FieldMetric>();
-  *ptr = DDY(*invSgCache, outloc, method) * invSg();
-  Grad2_par2_DDY_invSgCache[method] = std::move(ptr);
-  return *Grad2_par2_DDY_invSgCache[method];
+      auto ptr = std::make_unique<Coordinates::FieldMetric>();
+      *ptr = DDY(*invSgCache, outloc, method) * (*invSgCache);
+      result = ptr.get();
+      Grad2_par2_DDY_invSgCache[method] = std::move(ptr);
+    }
+  }
+  return *result;
 }
 
 void Coordinates::checkCovariant() { covariantMetricTensor.check(localmesh->ystart); }
@@ -1029,8 +1046,11 @@ void Coordinates::invalidateMetricCaches() {
 }
 
 const Coordinates::FieldMetric& Coordinates::J() const {
-  if (jacobian_cache == nullptr) {
-    jacobian_cache = std::make_unique<FieldMetric>(recalculateJacobian());
+  BOUT_OMP_SAFE(critical(jacobian_cache))
+  {
+    if (jacobian_cache == nullptr) {
+      jacobian_cache = std::make_unique<FieldMetric>(recalculateJacobian());
+    }
   }
   return *jacobian_cache;
 }

From 23ddf98e76471e9b28be2be94ae4367c57d039c6 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 9 Jul 2026 13:48:40 -0700
Subject: [PATCH 1616/1827] Delete unneededed expr.hxx

This was an experiment in expression templates, that has now
been replaced by the BinaryExpr machinery.
---
 CMakeLists.txt                                |   1 -
 examples/performance/arithmetic/.gitignore    |   1 -
 .../performance/arithmetic/arithmetic.cxx     | 106 ---------
 examples/performance/arithmetic/data/BOUT.inp |   5 -
 examples/performance/arithmetic/run.sh        |   5 -
 .../performance/arithmetic_3d2d/.gitignore    |   1 -
 .../arithmetic_3d2d/arithmetic_3d2d.cxx       | 116 ----------
 .../performance/arithmetic_3d2d/data/BOUT.inp |   5 -
 examples/performance/arithmetic_3d2d/run.sh   |   5 -
 include/bout/expr.hxx                         | 208 ------------------
 10 files changed, 453 deletions(-)
 delete mode 100644 examples/performance/arithmetic/.gitignore
 delete mode 100644 examples/performance/arithmetic/arithmetic.cxx
 delete mode 100644 examples/performance/arithmetic/data/BOUT.inp
 delete mode 100755 examples/performance/arithmetic/run.sh
 delete mode 100644 examples/performance/arithmetic_3d2d/.gitignore
 delete mode 100644 examples/performance/arithmetic_3d2d/arithmetic_3d2d.cxx
 delete mode 100644 examples/performance/arithmetic_3d2d/data/BOUT.inp
 delete mode 100644 examples/performance/arithmetic_3d2d/run.sh
 delete mode 100644 include/bout/expr.hxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e6e424b55c..23919726cc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -128,7 +128,6 @@ set(BOUT_SOURCES
     ./include/bout/deriv_store.hxx
     ./include/bout/derivs.hxx
     ./include/bout/difops.hxx
-    ./include/bout/expr.hxx
     ./include/bout/fft.hxx
     ./include/bout/field.hxx
     ./include/bout/field2d.hxx
diff --git a/examples/performance/arithmetic/.gitignore b/examples/performance/arithmetic/.gitignore
deleted file mode 100644
index 077be4cbd0..0000000000
--- a/examples/performance/arithmetic/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-arithmetic
\ No newline at end of file
diff --git a/examples/performance/arithmetic/arithmetic.cxx b/examples/performance/arithmetic/arithmetic.cxx
deleted file mode 100644
index fc2357978a..0000000000
--- a/examples/performance/arithmetic/arithmetic.cxx
+++ /dev/null
@@ -1,106 +0,0 @@
-/*
- * Timing of arithmetic operations
- *
- */
-
-#include <bout/physicsmodel.hxx>
-
-#include <bout/expr.hxx>
-
-#include <chrono>
-
-using SteadyClock = std::chrono::time_point<std::chrono::steady_clock>;
-using Duration = std::chrono::duration<double>;
-using namespace std::chrono;
-
-#define TIMEIT(elapsed, ...)                                                     \
-  {                                                                              \
-    SteadyClock start = steady_clock::now();                                     \
-    { __VA_ARGS__; }                                                             \
-    Duration diff = steady_clock::now() - start;                                 \
-    diff *= 1000 * 1000;                                                         \
-    elapsed.min = diff > elapsed.min ? elapsed.min : diff;                       \
-    elapsed.max = diff < elapsed.max ? elapsed.max : diff;                       \
-    elapsed.count++;                                                             \
-    elapsed.avg = elapsed.avg * (1 - 1. / elapsed.count) + diff / elapsed.count; \
-  }
-
-struct Durations {
-  Duration max;
-  Duration min;
-  Duration avg;
-  int count;
-};
-
-class Arithmetic : public PhysicsModel {
-protected:
-  int init(bool) {
-
-    Field3D a = 1.0;
-    Field3D b = 2.0;
-    Field3D c = 3.0;
-    a.setRegion("RGN_ALL");
-    b.setRegion("RGN_NOBNDRY");
-
-    Field3D result1, result2, result3, result4;
-
-    // Using Field methods (classic operator overloading)
-
-    result1 = 2. * a + b * c;
-#define dur_init {Duration::min(), Duration::max(), Duration::zero(), 0}
-    Durations elapsed1 = dur_init, elapsed2 = dur_init, elapsed3 = dur_init,
-              elapsed4 = dur_init;
-
-    for (int ik = 0; ik < 1e3; ++ik) {
-      TIMEIT(elapsed1, result1 = 2. * a + b * c;);
-
-      // Using C loops
-      result2.allocate();
-      BoutReal* rd = &result2(0, 0, 0);
-      BoutReal* ad = &a(0, 0, 0);
-      BoutReal* bd = &b(0, 0, 0);
-      BoutReal* cd = &c(0, 0, 0);
-      TIMEIT(
-          elapsed2,
-          for (int i = 0, iend = (mesh->LocalNx * mesh->LocalNy * mesh->LocalNz) - 1;
-               i != iend; i++) {
-            *rd = 2. * (*ad) + (*bd) * (*cd);
-            rd++;
-            ad++;
-            bd++;
-            cd++;
-          });
-
-      // Template expressions
-      TIMEIT(elapsed3, result3 = eval3D(add(mul(2, a), mul(b, c))););
-
-      // Range iterator
-      result4.allocate();
-      TIMEIT(elapsed4, for (auto i : result4) result4[i] = 2. * a[i] + b[i] * c[i];);
-    }
-
-    output.enable();
-    output << "TIMING      |    minimum |       mean |    maximum\n"
-           << "----------- | ---------- | ---------- | ----------\n";
-    //#define PRINT(str,elapsed)   output << str << elapsed.min.count()<<
-    //elapsed.avg.count()<< elapsed.max.count() << endl;
-#define PRINT(str, elapsed)                                          \
-  output.write("{:s} | {:7.3f} us | {:7.3f} us | {:7.3f} us\n", str, \
-               elapsed.min.count(), elapsed.avg.count(), elapsed.max.count())
-    PRINT("Fields:    ", elapsed1);
-    PRINT("C loop:    ", elapsed2);
-    PRINT("Templates: ", elapsed3);
-    PRINT("Range For: ", elapsed4);
-    output.disable();
-    SOLVE_FOR(n);
-    return 0;
-  }
-
-  int rhs(BoutReal) {
-    ddt(n) = 0;
-    return 0;
-  }
-  Field3D n;
-};
-
-BOUTMAIN(Arithmetic);
diff --git a/examples/performance/arithmetic/data/BOUT.inp b/examples/performance/arithmetic/data/BOUT.inp
deleted file mode 100644
index 0deb623c4b..0000000000
--- a/examples/performance/arithmetic/data/BOUT.inp
+++ /dev/null
@@ -1,5 +0,0 @@
-MZ = 1024
-
-[mesh]
-nx = 50
-ny = 2
diff --git a/examples/performance/arithmetic/run.sh b/examples/performance/arithmetic/run.sh
deleted file mode 100755
index 3a1cc844a6..0000000000
--- a/examples/performance/arithmetic/run.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/env bash
-
-make || exit
-
-./arithmetic  -q -q -q
diff --git a/examples/performance/arithmetic_3d2d/.gitignore b/examples/performance/arithmetic_3d2d/.gitignore
deleted file mode 100644
index 14968af063..0000000000
--- a/examples/performance/arithmetic_3d2d/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-arithmetic_3d2d
\ No newline at end of file
diff --git a/examples/performance/arithmetic_3d2d/arithmetic_3d2d.cxx b/examples/performance/arithmetic_3d2d/arithmetic_3d2d.cxx
deleted file mode 100644
index 83167a5b42..0000000000
--- a/examples/performance/arithmetic_3d2d/arithmetic_3d2d.cxx
+++ /dev/null
@@ -1,116 +0,0 @@
-/*
- * Timing of arithmetic operations (Field3D/Field2D mixed)
- *
- */
-
-#include <bout/physicsmodel.hxx>
-
-#include <bout/expr.hxx>
-
-#include <algorithm>
-#include <chrono>
-#include <iomanip>
-
-using SteadyClock = std::chrono::time_point<std::chrono::steady_clock>;
-using Duration = std::chrono::duration<double>;
-using namespace std::chrono;
-
-#define TIMEIT(NAME, ...)                                                        \
-  {                                                                              \
-    SteadyClock start = steady_clock::now();                                     \
-    __VA_ARGS__                                                                  \
-    Duration diff = steady_clock::now() - start;                                 \
-    auto elapsed = elapsedMap[NAME];                                             \
-    elapsed.min = std::min(diff, elapsed.min);                                   \
-    elapsed.max = std::max(diff, elapsed.max);                                   \
-    elapsed.count++;                                                             \
-    elapsed.avg = elapsed.avg * (1 - 1. / elapsed.count) + diff / elapsed.count; \
-    elapsedMap[NAME] = elapsed;                                                  \
-  }
-
-struct Durations {
-  Duration max;
-  Duration min;
-  Duration avg;
-  int count;
-  Durations()
-      : max(Duration::min()), min(Duration::max()), avg(Duration::zero()), count(0){};
-};
-
-class Arithmetic : public PhysicsModel {
-protected:
-  std::map<std::string, Durations> elapsedMap;
-
-  int init(bool) {
-    Field3D a = 1.0;
-    Field3D b = 2.0;
-    Field2D c = 3.0;
-
-    Field3D result1, result2, result3, result4;
-
-    // Using Field methods (classic operator overloading)
-    result1 = 2. * a + b * c;
-
-    for (int ik = 0; ik < 1e2; ++ik) {
-      result1.allocate();
-      TIMEIT("Fields", result1 = 2. * a + b * c;);
-
-      // Using C loops
-      result2.allocate();
-      BoutReal* rd = &result2(0, 0, 0);
-      BoutReal* ad = &a(0, 0, 0);
-      BoutReal* bd = &b(0, 0, 0);
-      BoutReal* cd = &c(0, 0, 0);
-      TIMEIT(
-          "C loop",
-          for (int i = 0, iend = (mesh->LocalNx * mesh->LocalNy) - 1; i != iend; i++) {
-            for (int j = 0, jend = mesh->LocalNz - 1; j != jend; j++) {
-              *rd = 2. * (*ad) + (*bd) * (*cd);
-              rd++;
-              ad++;
-              bd++;
-            }
-            cd++;
-          });
-
-      // Template expressions
-      result3.allocate();
-      TIMEIT("Templates", result3 = eval3D(add(mul(2, a), mul(b, c))););
-
-      // Range iterator
-      result4.allocate();
-      TIMEIT("Range For", for (auto i : result4) result4[i] = 2. * a[i] + b[i] * c[i];);
-    }
-
-    output.enable();
-    constexpr int width = 15;
-    output << std::setw(width) << "TIMING";
-    output << std::setw(width) << "min";
-    output << std::setw(width) << "avg";
-    output << std::setw(width) << "max";
-    output << "\n======";
-    for (int i = 0; i < 4 * width; ++i) {
-      output << "=";
-    };
-    output << "\n";
-
-    for (const auto& approach : elapsedMap) {
-      output << std::setw(width) << approach.first;
-      output << std::setw(width) << approach.second.min.count();
-      output << std::setw(width) << approach.second.avg.count();
-      output << std::setw(width) << approach.second.max.count();
-      output << "\n";
-    }
-    output.disable();
-    SOLVE_FOR(n);
-    return 0;
-  }
-
-  int rhs(BoutReal) {
-    ddt(n) = 0;
-    return 0;
-  }
-  Field3D n;
-};
-
-BOUTMAIN(Arithmetic);
diff --git a/examples/performance/arithmetic_3d2d/data/BOUT.inp b/examples/performance/arithmetic_3d2d/data/BOUT.inp
deleted file mode 100644
index 0deb623c4b..0000000000
--- a/examples/performance/arithmetic_3d2d/data/BOUT.inp
+++ /dev/null
@@ -1,5 +0,0 @@
-MZ = 1024
-
-[mesh]
-nx = 50
-ny = 2
diff --git a/examples/performance/arithmetic_3d2d/run.sh b/examples/performance/arithmetic_3d2d/run.sh
deleted file mode 100644
index ee36808c21..0000000000
--- a/examples/performance/arithmetic_3d2d/run.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/env bash
-
-make || exit
-
-./arithmetic_3d2d  -q -q -q
diff --git a/include/bout/expr.hxx b/include/bout/expr.hxx
deleted file mode 100644
index 267af202ed..0000000000
--- a/include/bout/expr.hxx
+++ /dev/null
@@ -1,208 +0,0 @@
-/**************************************************************************
- *
- * Operators, and support for template expressions
- * 
- * Originally based on article by Klaus Kreft & Angelika Langer
- * http://www.angelikalanger.com/Articles/Cuj/ExpressionTemplates/ExpressionTemplates.htm
- * 
- * Parts adapted from Blitz++ library
- *
- **************************************************************************/
-
-#ifndef BOUT_EXPR_H
-#define BOUT_EXPR_H
-
-#warning expr.hxx is deprecated. Do not use!
-
-#include <bout/field2d.hxx>
-#include <bout/field3d.hxx>
-#include <bout/mesh.hxx>
-
-/// Literal class to capture BoutReal values in expressions
-class Literal {
-public:
-  /// Type of this expression
-  using type = Literal;
-
-  Literal(BoutReal v) : val(v) {}
-  ~Literal() {}
-  BoutReal operator()(int x, int y, int z) const { return val; }
-
-private:
-  const BoutReal val;
-};
-
-class Field3DExpr {
-public:
-  using type = Field3D;
-
-  Field3DExpr(const Field3D& f) : data(&f(0, 0, 0)) {}
-  const BoutReal& operator()(int x, int y, int z) const {
-    return data[(x * bout::globals::mesh->LocalNy + y) * bout::globals::mesh->LocalNz
-                + z];
-  }
-
-private:
-  const BoutReal* data;
-};
-
-class Field2DExpr {
-public:
-  using type = Field2D;
-
-  Field2DExpr(const Field2D& f) : data(&f(0, 0)) {}
-  const BoutReal& operator()(int x, int y, int z) const {
-    return data[x * bout::globals::mesh->LocalNy + y];
-  }
-
-private:
-  const BoutReal* data;
-};
-
-/// Expression traits, to convert doubles etc. to Literal
-
-template <class ExprT>
-struct exprTraits {
-  using expr_type = ExprT;
-};
-
-template <>
-struct exprTraits<double> {
-  using expr_type = Literal;
-};
-
-template <>
-struct exprTraits<float> {
-  using expr_type = Literal;
-};
-
-template <>
-struct exprTraits<int> {
-  using expr_type = Literal;
-};
-
-///////////////////////////////////////////////
-// asExpr: convert objects to expressions
-
-template <typename T>
-struct asExpr {
-  using type = T;
-  static const T& getExpr(const T& x) { return x; }
-};
-
-template <>
-struct asExpr<int> {
-  using type = Literal;
-  static const Literal getExpr(const int& x) { return Literal(x); }
-};
-
-template <>
-struct asExpr<double> {
-  using type = Literal;
-  static const Literal getExpr(const double& x) { return Literal(x); }
-};
-
-template <>
-struct asExpr<float> {
-  using type = Literal;
-  static const Literal getExpr(const float& x) { return Literal(x); }
-};
-
-template <>
-struct asExpr<Field3D> {
-  using type = Field3DExpr;
-  static const Field3DExpr getExpr(const Field3D& x) { return Field3DExpr(x); }
-};
-
-/////////////////////////////////////////////////////////////
-// Type promotion. Work out the type of a calculation,
-// based on the type of the arguments
-
-template <typename Lhs, typename Rhs> // If in doubt, convert to Field3D
-struct PromoteType {
-  using type = Field3D;
-};
-
-/////////////////////////////////////////////////////////////
-// Binary expressions
-
-template <class ExprT1, class ExprT2, class BinOp>
-class BinaryExpr {
-public:
-  BinaryExpr(const ExprT1& e1, const ExprT2& e2) : _expr1(e1), _expr2(e2) {}
-
-  // Work out the type of the inputs
-  using ltype = typename exprTraits<ExprT1>::expr_type;
-  using rtype = typename exprTraits<ExprT2>::expr_type;
-
-  /// Type of the resulting expression
-  using type = typename PromoteType<ltype, rtype>::type;
-
-  BoutReal operator()(int x, int y, int z) const {
-    return BinOp::apply((_expr1)(x, y, z), (_expr2)(x, y, z));
-  }
-
-private:
-  ltype const _expr1;
-  rtype const _expr2;
-};
-
-template <typename ExprT1, typename ExprT2, class name>
-struct BinaryResult {
-  using arg1 = typename asExpr<ExprT1>::type;
-  using arg2 = typename asExpr<ExprT2>::type;
-  using type = BinaryExpr<arg1, arg2, name>;
-};
-
-/// Binary operator classes
-
-#define DEFINE_BINARY_OP(name, op)    \
-  struct name {                       \
-    template <typename T>             \
-    static inline T apply(T a, T b) { \
-      return a op b;                  \
-    }                                 \
-  };
-
-DEFINE_BINARY_OP(Add, +)
-DEFINE_BINARY_OP(Subtract, -)
-DEFINE_BINARY_OP(Multiply, *)
-DEFINE_BINARY_OP(Divide, /)
-
-struct Power {
-  template <typename T>
-  static inline T apply(T a, T b) {
-    return pow(a, b);
-  }
-};
-
-/// Define functions add, mul which use operator structs
-#define DEFINE_OVERLOAD_FUNC(name, func)                                     \
-  template <typename ExprT1, typename ExprT2>                                \
-  typename BinaryResult<ExprT1, ExprT2, name>::type func(const ExprT1& e1,   \
-                                                         const ExprT2& e2) { \
-    using type = typename BinaryResult<ExprT1, ExprT2, name>::type;          \
-    return type(asExpr<ExprT1>::getExpr(e1), asExpr<ExprT2>::getExpr(e2));   \
-  }
-
-/// Addition of two Expressions
-DEFINE_OVERLOAD_FUNC(Add, add);
-/// Multiplication of two Expressions
-DEFINE_OVERLOAD_FUNC(Multiply, mul);
-
-/// A function to evaluate expressions
-template <typename Expr>
-const Field3D eval3D(Expr e) {
-  Field3D result;
-  result.allocate();
-  for (int i = 0; i < bout::globals::mesh->LocalNx; i++) {
-    for (int j = 0; j < bout::globals::mesh->LocalNy; j++) {
-      for (int k = 0; k < bout::globals::mesh->LocalNz; k++) {
-        result(i, j, k) = e(i, j, k);
-      }
-    }
-  }
-  return result;
-}
-
-#endif // BOUT_EXPR_H

From 49774de6ffb6701bd26e8ef67434e7cb25435b1a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 9 Jul 2026 20:47:10 -0700
Subject: [PATCH 1617/1827] Field3DParallel BinaryExpr templates

Views handle yup/ydown slices, evaluating lazy expressions in parallel
slices if assigned to a Field3DParallel.
---
 include/bout/bout_types.hxx       |   4 +
 include/bout/field2d.hxx          |   4 +
 include/bout/field3d.hxx          | 147 ++++++++++++++++++++++------
 include/bout/fieldops.hxx         |  76 ++++++++++++++-
 include/bout/fieldperp.hxx        |   4 +
 tests/unit/field/test_field3d.cxx | 155 ++++++++++++++++++++++++++++++
 6 files changed, 362 insertions(+), 28 deletions(-)

diff --git a/include/bout/bout_types.hxx b/include/bout/bout_types.hxx
index 7747b937b3..dee2ea22e7 100644
--- a/include/bout/bout_types.hxx
+++ b/include/bout/bout_types.hxx
@@ -149,6 +149,10 @@ struct Constant {
     T v;
     View(T v) : v(v) {}
     BOUT_HOST_DEVICE T operator()(int) const { return v; }
+    BOUT_HOST_DEVICE bool hasParallelSlices() const { return false; }
+    BOUT_HOST_DEVICE int numberParallelSlices() const { return 0; }
+    BOUT_HOST_DEVICE View yup(int = 0) const { return *this; }
+    BOUT_HOST_DEVICE View ydown(int = 0) const { return *this; }
   };
   operator View() const { return {val}; }
 };
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index 540680bb73..ce3009f4ad 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -345,6 +345,10 @@ public:
       this->div = div;
       return *this;
     }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE bool hasParallelSlices() const { return false; }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE int numberParallelSlices() const { return 0; }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE View yup(int = 0) const { return *this; }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE View ydown(int = 0) const { return *this; }
   };
   operator View() { return View{&data[0]}; }
   operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 905e736999..02e582c20a 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -465,6 +465,10 @@ public:
 
   struct View {
     BoutReal* data;
+    const Field3D* yup_fields{nullptr};
+    const Field3D* ydown_fields{nullptr};
+    int num_parallel_slices{0};
+
     BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return data[idx];
     }
@@ -478,9 +482,34 @@ public:
                     "Field3D::View does not support setScale()");
       return *this;
     }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE bool hasParallelSlices() const {
+      return num_parallel_slices > 0;
+    }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE int numberParallelSlices() const {
+      return num_parallel_slices;
+    }
+    BOUT_FORCEINLINE View yup(int slice = 0) const {
+      ASSERT2(slice < num_parallel_slices);
+      ASSERT2(yup_fields[slice].isAllocated());
+      return static_cast<Field3D::View>(yup_fields[slice]);
+    }
+    BOUT_FORCEINLINE View ydown(int slice = 0) const {
+      ASSERT2(slice < num_parallel_slices);
+      ASSERT2(ydown_fields[slice].isAllocated());
+      return static_cast<Field3D::View>(ydown_fields[slice]);
+    }
   };
-  operator View() { return View{&data[0]}; }
-  operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
+  operator View() {
+    return View{&data[0], hasParallelSlices() ? yup_fields.data() : nullptr,
+                hasParallelSlices() ? ydown_fields.data() : nullptr,
+                static_cast<int>(numberParallelSlices())};
+  }
+  operator View() const {
+    return View{const_cast<BoutReal*>(&data[0]),
+                hasParallelSlices() ? yup_fields.data() : nullptr,
+                hasParallelSlices() ? ydown_fields.data() : nullptr,
+                static_cast<int>(numberParallelSlices())};
+  }
   //operator View() const { return View{&data[0]}; }
 
   /////////////////////////////////////////////////////////
@@ -856,31 +885,6 @@ if_else(bool condition, const L& lhs, const R& rhs) {
       rhs.getMesh()->getRegion("RGN_ALL")};
 }
 
-Field3DParallel operator+(const Field3D& lhs, const Field3DParallel& rhs);
-Field3DParallel operator-(const Field3D& lhs, const Field3DParallel& rhs);
-Field3DParallel operator*(const Field3D& lhs, const Field3DParallel& rhs);
-Field3DParallel operator/(const Field3D& lhs, const Field3DParallel& rhs);
-
-Field3DParallel operator+(const Field3DParallel& lhs, const Field3D& rhs);
-Field3DParallel operator-(const Field3DParallel& lhs, const Field3D& rhs);
-Field3DParallel operator*(const Field3DParallel& lhs, const Field3D& rhs);
-Field3DParallel operator/(const Field3DParallel& lhs, const Field3D& rhs);
-
-Field3DParallel operator+(const Field3DParallel& lhs, const Field3DParallel& rhs);
-Field3DParallel operator-(const Field3DParallel& lhs, const Field3DParallel& rhs);
-Field3DParallel operator*(const Field3DParallel& lhs, const Field3DParallel& rhs);
-Field3DParallel operator/(const Field3DParallel& lhs, const Field3DParallel& rhs);
-
-Field3DParallel operator+(BoutReal lhs, const Field3DParallel& rhs);
-Field3DParallel operator-(BoutReal lhs, const Field3DParallel& rhs);
-Field3DParallel operator*(BoutReal lhs, const Field3DParallel& rhs);
-Field3DParallel operator/(BoutReal lhs, const Field3DParallel& rhs);
-
-Field3DParallel operator+(const Field3DParallel& lhs, BoutReal rhs);
-Field3DParallel operator-(const Field3DParallel& lhs, BoutReal rhs);
-Field3DParallel operator*(const Field3DParallel& lhs, BoutReal rhs);
-Field3DParallel operator/(const Field3DParallel& lhs, BoutReal rhs);
-
 /*!
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
@@ -1024,6 +1028,13 @@ public:
   explicit Field3DParallel(Types... args) : Field3D(std::move(args)...) {
     ensureFieldAligned();
   }
+  template <typename L, typename R, typename Func,
+            typename = std::enable_if_t<is_expr_field3d_v<L> || is_expr_field3d_v<R>>>
+  Field3DParallel(const BinaryExpr<Field3D, L, R, Func>& expr)
+      : Field3DParallel(expr.getMesh(), expr.getLocation(), expr.getDirections(),
+                        expr.getRegionID()) {
+    *this = expr;
+  }
   Field3DParallel(const Field3D& f) : Field3D(f) { ensureFieldAligned(); }
   Field3DParallel(const Field3D& f, bool isRef) : Field3D(f), isRef(isRef) {
     ensureFieldAligned();
@@ -1052,6 +1063,53 @@ public:
   Field3D& asField3D() { return *this; }
   const Field3D& asField3D() const { return *this; }
 
+  struct View {
+    Field3D::View base;
+    const Field3D* yup_fields{nullptr};
+    const Field3D* ydown_fields{nullptr};
+    int num_parallel_slices{0};
+
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
+      return base(idx);
+    }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal& operator[](int idx) const {
+      return base[idx];
+    }
+
+    template <typename Mul, typename Div>
+    View& setScale(Mul /*unused*/, Div /*unused*/) {
+      static_assert(!std::is_same_v<Mul, Mul>,
+                    "Field3DParallel::View does not support setScale()");
+      return *this;
+    }
+
+    BOUT_FORCEINLINE bool hasParallelSlices() const { return num_parallel_slices > 0; }
+    BOUT_FORCEINLINE int numberParallelSlices() const { return num_parallel_slices; }
+    BOUT_FORCEINLINE View yup(int slice = 0) const {
+      ASSERT2(slice < num_parallel_slices);
+      ASSERT2(yup_fields[slice].isAllocated());
+      return View{static_cast<Field3D::View>(yup_fields[slice]), nullptr, nullptr, 0};
+    }
+    BOUT_FORCEINLINE View ydown(int slice = 0) const {
+      ASSERT2(slice < num_parallel_slices);
+      ASSERT2(ydown_fields[slice].isAllocated());
+      return View{static_cast<Field3D::View>(ydown_fields[slice]), nullptr, nullptr, 0};
+    }
+  };
+
+  operator View() {
+    return View{static_cast<Field3D::View>(*this),
+                hasParallelSlices() ? yup_fields.data() : nullptr,
+                hasParallelSlices() ? ydown_fields.data() : nullptr,
+                static_cast<int>(numberParallelSlices())};
+  }
+  operator View() const {
+    return View{static_cast<Field3D::View>(*this),
+                hasParallelSlices() ? yup_fields.data() : nullptr,
+                hasParallelSlices() ? ydown_fields.data() : nullptr,
+                static_cast<int>(numberParallelSlices())};
+  }
+
   Field3DParallel& operator*=(const Field3D&);
   Field3DParallel& operator/=(const Field3D&);
   Field3DParallel& operator+=(const Field3D&);
@@ -1074,6 +1132,41 @@ public:
     ensureFieldAligned();
     return *this;
   }
+  template <typename ResT, typename L, typename R, typename Func>
+  std::enable_if_t<is_expr_field3d_v<L> || is_expr_field3d_v<R>, Field3DParallel&>
+  operator=(const BinaryExpr<ResT, L, R, Func>& expr) {
+    if (getMesh() != expr.getMesh()) {
+      clearParallelSlices();
+      fieldmesh = expr.getMesh();
+      data = Array<BoutReal>{};
+    }
+    if (isFci()) {
+      if (!hasParallelSlices()) {
+        splitParallelSlices();
+      }
+    } else if (hasParallelSlices()) {
+      clearParallelSlices();
+    }
+
+    setRegion(expr.getRegionID());
+    setLocation(expr.getLocation());
+    setDirections(expr.getDirections());
+    allocate();
+    expr.evaluate(static_cast<Field3D::View>(*this).data);
+
+    if (isFci()) {
+      ASSERT2(expr.hasParallelSlices());
+      ASSERT2(expr.numberParallelSlices() == static_cast<int>(numberParallelSlices()));
+      for (int i = 0; i < expr.numberParallelSlices(); ++i) {
+        yup(i).allocate();
+        ydown(i).allocate();
+        expr.yup(i).evaluate(static_cast<Field3D::View>(yup(i)).data);
+        expr.ydown(i).evaluate(static_cast<Field3D::View>(ydown(i)).data);
+      }
+    }
+
+    return *this;
+  }
   Field3DParallel& operator=(BoutReal);
   Field3DParallel& allocate();
 
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index f36061ceaa..a09734ad21 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -381,6 +381,43 @@ struct BinaryExpr {
   }
   BOUT_HOST_DEVICE BOUT_FORCEINLINE int regionIdx(int idx) const { return indices[idx]; }
 
+  bool hasParallelSlices() const {
+    if constexpr (is_expr_constant_v<L> && is_expr_constant_v<R>) {
+      return false;
+    } else if constexpr (is_expr_constant_v<L>) {
+      return rhs.hasParallelSlices();
+    } else if constexpr (is_expr_constant_v<R>) {
+      return lhs.hasParallelSlices();
+    } else {
+      return lhs.hasParallelSlices() && rhs.hasParallelSlices();
+    }
+  }
+  int numberParallelSlices() const {
+    if (!hasParallelSlices()) {
+      return 0;
+    }
+    if constexpr (is_expr_constant_v<L> && is_expr_constant_v<R>) {
+      return 0;
+    } else if constexpr (is_expr_constant_v<L>) {
+      return rhs.numberParallelSlices();
+    } else if constexpr (is_expr_constant_v<R>) {
+      return lhs.numberParallelSlices();
+    } else {
+      ASSERT2(lhs.numberParallelSlices() == rhs.numberParallelSlices());
+      return lhs.numberParallelSlices();
+    }
+  }
+  auto yup(int slice = 0) const {
+    return BinaryExpr<ResT, L, R, Func>{lhs.yup(slice), rhs.yup(slice), f,
+                                        mesh,           location,       directions,
+                                        regionID,       indices,        yindex};
+  }
+  auto ydown(int slice = 0) const {
+    return BinaryExpr<ResT, L, R, Func>{
+        lhs.ydown(slice), rhs.ydown(slice), f,       mesh,  location,
+        directions,       regionID,         indices, yindex};
+  }
+
   //operator ResT() { return ResT{*this}; }
   struct View {
     typename L::View lhs;
@@ -396,13 +433,50 @@ struct BinaryExpr {
       this->div = div;
       return *this;
     }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE bool hasParallelSlices() const {
+      if constexpr (is_expr_constant_v<L> && is_expr_constant_v<R>) {
+        return false;
+      } else if constexpr (is_expr_constant_v<L>) {
+        return rhs.hasParallelSlices();
+      } else if constexpr (is_expr_constant_v<R>) {
+        return lhs.hasParallelSlices();
+      } else {
+        return lhs.hasParallelSlices() && rhs.hasParallelSlices();
+      }
+    }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE int numberParallelSlices() const {
+      if (!hasParallelSlices()) {
+        return 0;
+      }
+      if constexpr (is_expr_constant_v<L> && is_expr_constant_v<R>) {
+        return 0;
+      } else if constexpr (is_expr_constant_v<L>) {
+        return rhs.numberParallelSlices();
+      } else if constexpr (is_expr_constant_v<R>) {
+        return lhs.numberParallelSlices();
+      } else {
+        ASSERT2(lhs.numberParallelSlices() == rhs.numberParallelSlices());
+        return lhs.numberParallelSlices();
+      }
+    }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE auto yup(int slice = 0) const {
+      auto result = *this;
+      result.lhs = lhs.yup(slice);
+      result.rhs = rhs.yup(slice);
+      return result;
+    }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE auto ydown(int slice = 0) const {
+      auto result = *this;
+      result.lhs = lhs.ydown(slice);
+      result.rhs = rhs.ydown(slice);
+      return result;
+    }
     BOUT_HOST_DEVICE BOUT_FORCEINLINE int size() const { return num_indices; }
     BOUT_HOST_DEVICE BOUT_FORCEINLINE int regionIdx(int idx) const {
       return indices[idx];
     }
     BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return f((idx * mul) / div, lhs, rhs); // single‐pass fusion
-      //return f(lhs((idx * mul) / div), rhs((idx * mul) / div)); // single‐pass fusion
     }
   };
 
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 36a116e1b5..83bb3b79b0 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -352,6 +352,10 @@ public:
       this->div = div;
       return *this;
     }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE bool hasParallelSlices() const { return false; }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE int numberParallelSlices() const { return 0; }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE View yup(int = 0) const { return *this; }
+    BOUT_HOST_DEVICE BOUT_FORCEINLINE View ydown(int = 0) const { return *this; }
   };
   operator View() { return View{&data[0]}; }
   operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 905b182018..f0b672f324 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -12,6 +12,7 @@
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
 #include "bout/output.hxx"
+#include "bout/paralleltransform.hxx"
 #include "bout/unused.hxx"
 #include "bout/utils.hxx"
 
@@ -27,6 +28,34 @@ using namespace bout::globals;
 // Reuse the "standard" fixture for FakeMesh
 using Field3DTest = FakeMeshFixture;
 
+class MockFciParallelTransform : public ParallelTransform {
+public:
+  explicit MockFciParallelTransform(Mesh& mesh_in) : ParallelTransform(mesh_in) {}
+
+  void calcParallelSlices(Field3D& f) override {
+    if (!f.hasParallelSlices()) {
+      f.splitParallelSlices();
+    }
+    for (size_t i = 0; i < f.numberParallelSlices(); ++i) {
+      f.yup(i) = f;
+      f.ydown(i) = f;
+    }
+  }
+
+  Field3D toFieldAligned(const Field3D& f, const std::string&) override { return f; }
+  FieldPerp toFieldAligned(const FieldPerp& f, const std::string&) override { return f; }
+  Field3D fromFieldAligned(const Field3D& f, const std::string&) override { return f; }
+  FieldPerp fromFieldAligned(const FieldPerp& f, const std::string&) override {
+    return f;
+  }
+
+  bool canToFromFieldAligned() const override { return false; }
+  bool requiresTwistShift(bool, YDirectionType) override { return false; }
+
+protected:
+  void checkInputGrid() override {}
+};
+
 TEST_F(Field3DTest, Is3D) {
   Field3D field;
 
@@ -1979,6 +2008,132 @@ TEST_F(Field3DTest, SQField3DParallelPreservesParallelSlices) {
   EXPECT_TRUE(IsFieldEqual(squared.ydown(), 16.0));
 }
 
+TEST_F(Field3DTest, Field3DParallelArithmeticReturnsLazyExpr) {
+  Field3DParallel parallel;
+  Field3D field;
+
+  parallel = 2.0;
+  parallel.splitParallelSlices();
+  parallel.yup() = 3.0;
+  parallel.ydown() = 4.0;
+  field = 5.0;
+
+  const auto expr = parallel + field;
+
+  EXPECT_TRUE(
+      (std::is_same_v<std::decay_t<decltype(expr)>,
+                      BinaryExpr<Field3D, Field3DParallel, Field3D, bout::op::Add>>));
+
+  Field3DParallel result{expr};
+
+  EXPECT_FALSE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 7.0));
+}
+
+TEST_F(Field3DTest, Field3DParallelAssignmentFromLazyExprDiscardsSlicesWhenNotFci) {
+  Field3DParallel parallel;
+  Field3DParallel result;
+
+  parallel = 2.0;
+  parallel.splitParallelSlices();
+  parallel.yup() = 3.0;
+  parallel.ydown() = 4.0;
+
+  const auto expr = 10.0 - parallel;
+
+  EXPECT_TRUE((std::is_same_v<
+               std::decay_t<decltype(expr)>,
+               BinaryExpr<Field3D, Constant<BoutReal>, Field3DParallel, bout::op::Sub>>));
+
+  result = expr;
+
+  EXPECT_FALSE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 8.0));
+}
+
+#if CHECK >= 2
+TEST_F(Field3DTest, Field3DParallelAssignmentFromLazyExprRequiresField3DSlicesInFci) {
+  mesh->getCoordinates()->setParallelTransform(
+      bout::utils::make_unique<MockFciParallelTransform>(*mesh));
+
+  Field3DParallel parallel;
+  Field3D field;
+
+  parallel = 2.0;
+  parallel.yup() = 3.0;
+  parallel.ydown() = 4.0;
+  field = 5.0;
+
+  EXPECT_THROW(Field3DParallel result{parallel + field}, BoutException);
+}
+#endif
+
+TEST_F(Field3DTest, Field3DParallelAssignmentFromLazyExprUsesField3DSlicesInFci) {
+  mesh->getCoordinates()->setParallelTransform(
+      bout::utils::make_unique<MockFciParallelTransform>(*mesh));
+
+  Field3DParallel parallel;
+  Field3D field;
+
+  parallel = 2.0;
+  parallel.yup() = 3.0;
+  parallel.ydown() = 4.0;
+
+  field = 5.0;
+  field.splitParallelSlices();
+  field.yup() = 7.0;
+  field.ydown() = 11.0;
+
+  Field3DParallel result{parallel + field};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 7.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 10.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 15.0));
+}
+
+TEST_F(Field3DTest, Field3DParallelAssignmentFromField3DExprUsesSlicesInFci) {
+  mesh->getCoordinates()->setParallelTransform(
+      bout::utils::make_unique<MockFciParallelTransform>(*mesh));
+
+  Field3D lhs;
+  Field3D rhs;
+
+  lhs = 2.0;
+  lhs.splitParallelSlices();
+  lhs.yup() = 3.0;
+  lhs.ydown() = 4.0;
+
+  rhs = 5.0;
+  rhs.splitParallelSlices();
+  rhs.yup() = 7.0;
+  rhs.ydown() = 11.0;
+
+  Field3DParallel result{lhs * rhs};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 10.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 21.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 44.0));
+}
+
+TEST_F(Field3DTest, Field3DParallelAssignmentFromScalarExprUsesSlicesInFci) {
+  mesh->getCoordinates()->setParallelTransform(
+      bout::utils::make_unique<MockFciParallelTransform>(*mesh));
+
+  Field3DParallel parallel;
+  parallel = 2.0;
+  parallel.yup() = 3.0;
+  parallel.ydown() = 4.0;
+
+  Field3DParallel result{parallel + 1.0};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 3.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 4.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 5.0));
+}
+
 TEST_F(Field3DTest, Abs) {
   Field3D field;
 

From 470abe40140ca1e1a65634676fabfc6e8fdd27f6 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 8 Jul 2026 14:21:53 +0200
Subject: [PATCH 1618/1827] Add unit test to ensure Field3DParallel works for
 products with FCI

---
 tests/unit/field/test_field3d.cxx | 936 +++++++++++++++---------------
 1 file changed, 484 insertions(+), 452 deletions(-)

diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index f0b672f324..89286a8f80 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -27,6 +27,7 @@ using namespace bout::globals;
 
 // Reuse the "standard" fixture for FakeMesh
 using Field3DTest = FakeMeshFixture;
+using Field3DTestFCI = FakeMeshFixture_tmpl<3, 5, 7, true>;
 
 class MockFciParallelTransform : public ParallelTransform {
 public:
@@ -2132,618 +2133,649 @@ TEST_F(Field3DTest, Field3DParallelAssignmentFromScalarExprUsesSlicesInFci) {
   EXPECT_TRUE(IsFieldEqual(result, 3.0));
   EXPECT_TRUE(IsFieldEqual(result.yup(), 4.0));
   EXPECT_TRUE(IsFieldEqual(result.ydown(), 5.0));
-}
 
-TEST_F(Field3DTest, Abs) {
-  Field3D field;
+  TEST_F(Field3DTestFCI, MulField3DParallelPreservesParallelSlices) {
+    Field3D field;
+    EXPECT_TRUE(field.isFci());
+
+    field = 2.0;
+    field.splitParallelSlices();
+    field.yup() = 3.0;
+    field.ydown() = 4.0;
+    field.resetRegionParallel();
+
+    Field3D rhs;
+    EXPECT_TRUE(rhs.isFci());
+    rhs = 3.0;
+    rhs.splitParallelSlices();
+    rhs.yup() = 4.0;
+    rhs.ydown() = 5.0;
+    rhs.resetRegionParallel();
+
+    const Field3D prod = field * rhs;
+
+    EXPECT_FALSE(prod.hasParallelSlices());
+    EXPECT_TRUE(IsFieldEqual(prod, 6.0));
+
+    const Field3DParallel prodpar = field.asField3DParallel() * rhs;
+    EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(prodpar)>, Field3DParallel>));
+    EXPECT_TRUE(prodpar.hasParallelSlices());
+    EXPECT_TRUE(IsFieldEqual(prodpar, 6.0));
+    EXPECT_TRUE(IsFieldEqual(prodpar.yup(), 12.0, "RGN_YPAR_+1"));
+    EXPECT_TRUE(IsFieldEqual(prodpar.ydown(), 20.0, "RGN_YPAR_-1"));
+  }
 
-  field = -31.0;
-  EXPECT_TRUE(IsFieldEqual(abs(field), 31.0));
-}
+  TEST_F(Field3DTest, Abs) {
+    Field3D field;
 
-TEST_F(Field3DTest, AbsExpressionUsesAbsOp) {
-  Field3D field;
+    field = -31.0;
+    EXPECT_TRUE(IsFieldEqual(abs(field), 31.0));
+  }
 
-  field = -2.0;
-  const auto expr = field + 1.0;
+  TEST_F(Field3DTest, AbsExpressionUsesAbsOp) {
+    Field3D field;
 
-  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(abs(expr))>,
-                              BinaryExpr<Field3D, std::decay_t<decltype(expr)>,
-                                         std::decay_t<decltype(expr)>, bout::op::abs>>));
-  EXPECT_TRUE(IsFieldEqual(abs(expr), 1.0));
-  EXPECT_TRUE(IsFieldEqual(abs(expr, "RGN_ALL"), 1.0));
-}
+    field = -2.0;
+    const auto expr = field + 1.0;
 
-TEST_F(Field3DTest, RegionLimitedExpressionConstructsField3D) {
-  Field3D field;
+    EXPECT_TRUE(
+        (std::is_same_v<std::decay_t<decltype(abs(expr))>,
+                        BinaryExpr<Field3D, std::decay_t<decltype(expr)>,
+                                   std::decay_t<decltype(expr)>, bout::op::abs>>));
+    EXPECT_TRUE(IsFieldEqual(abs(expr), 1.0));
+    EXPECT_TRUE(IsFieldEqual(abs(expr, "RGN_ALL"), 1.0));
+  }
 
-  field = -31.0;
+  TEST_F(Field3DTest, RegionLimitedExpressionConstructsField3D) {
+    Field3D field;
 
-  Field3D result = abs(field, "RGN_NOBNDRY");
+    field = -31.0;
 
-  EXPECT_TRUE(IsFieldEqual(result, 31.0, "RGN_NOBNDRY"));
-}
+    Field3D result = abs(field, "RGN_NOBNDRY");
 
-TEST_F(Field3DTest, Exp) {
-  Field3D field;
+    EXPECT_TRUE(IsFieldEqual(result, 31.0, "RGN_NOBNDRY"));
+  }
 
-  field = 2.5;
-  const BoutReal expected = 12.182493960703473;
-  EXPECT_TRUE(IsFieldEqual(exp(field), expected));
-}
+  TEST_F(Field3DTest, Exp) {
+    Field3D field;
 
-TEST_F(Field3DTest, Log) {
-  Field3D field;
+    field = 2.5;
+    const BoutReal expected = 12.182493960703473;
+    EXPECT_TRUE(IsFieldEqual(exp(field), expected));
+  }
 
-  field = 12.182493960703473;
-  const BoutReal expected = 2.5;
-  EXPECT_TRUE(IsFieldEqual(log(field), expected));
-}
+  TEST_F(Field3DTest, Log) {
+    Field3D field;
 
-TEST_F(Field3DTest, LogExp) {
-  Field3D field;
+    field = 12.182493960703473;
+    const BoutReal expected = 2.5;
+    EXPECT_TRUE(IsFieldEqual(log(field), expected));
+  }
 
-  field = 2.5;
-  const BoutReal expected = 2.5;
-  EXPECT_TRUE(IsFieldEqual(log(exp(field)), expected));
-}
+  TEST_F(Field3DTest, LogExp) {
+    Field3D field;
 
-TEST_F(Field3DTest, Sin) {
-  Field3D field;
+    field = 2.5;
+    const BoutReal expected = 2.5;
+    EXPECT_TRUE(IsFieldEqual(log(exp(field)), expected));
+  }
 
-  field = PI / 2.0;
-  EXPECT_TRUE(IsFieldEqual(sin(field), 1.0));
+  TEST_F(Field3DTest, Sin) {
+    Field3D field;
 
-  field = PI;
-  EXPECT_TRUE(IsFieldEqual(sin(field), 0.0));
-}
+    field = PI / 2.0;
+    EXPECT_TRUE(IsFieldEqual(sin(field), 1.0));
 
-TEST_F(Field3DTest, Cos) {
-  Field3D field;
+    field = PI;
+    EXPECT_TRUE(IsFieldEqual(sin(field), 0.0));
+  }
 
-  field = PI / 2.0;
-  EXPECT_TRUE(IsFieldEqual(cos(field), 0.0));
+  TEST_F(Field3DTest, Cos) {
+    Field3D field;
 
-  field = PI;
-  EXPECT_TRUE(IsFieldEqual(cos(field), -1.0));
-}
+    field = PI / 2.0;
+    EXPECT_TRUE(IsFieldEqual(cos(field), 0.0));
 
-TEST_F(Field3DTest, Tan) {
-  Field3D field;
+    field = PI;
+    EXPECT_TRUE(IsFieldEqual(cos(field), -1.0));
+  }
 
-  field = PI / 4.0;
-  EXPECT_TRUE(IsFieldEqual(tan(field), 1.0));
+  TEST_F(Field3DTest, Tan) {
+    Field3D field;
 
-  field = PI;
-  EXPECT_TRUE(IsFieldEqual(tan(field), 0.0));
-}
+    field = PI / 4.0;
+    EXPECT_TRUE(IsFieldEqual(tan(field), 1.0));
 
-TEST_F(Field3DTest, Sinh) {
-  Field3D field;
+    field = PI;
+    EXPECT_TRUE(IsFieldEqual(tan(field), 0.0));
+  }
 
-  field = 1.0;
-  const BoutReal expected = 1.1752011936438014;
-  EXPECT_TRUE(IsFieldEqual(sinh(field), expected));
+  TEST_F(Field3DTest, Sinh) {
+    Field3D field;
 
-  field = -1.0;
-  EXPECT_TRUE(IsFieldEqual(sinh(field), -expected));
-}
+    field = 1.0;
+    const BoutReal expected = 1.1752011936438014;
+    EXPECT_TRUE(IsFieldEqual(sinh(field), expected));
 
-TEST_F(Field3DTest, Cosh) {
-  Field3D field;
+    field = -1.0;
+    EXPECT_TRUE(IsFieldEqual(sinh(field), -expected));
+  }
 
-  field = 1.0;
-  const BoutReal expected = 1.5430806348152437;
-  EXPECT_TRUE(IsFieldEqual(cosh(field), expected));
+  TEST_F(Field3DTest, Cosh) {
+    Field3D field;
 
-  field = -1.0;
-  EXPECT_TRUE(IsFieldEqual(cosh(field), expected));
-}
+    field = 1.0;
+    const BoutReal expected = 1.5430806348152437;
+    EXPECT_TRUE(IsFieldEqual(cosh(field), expected));
 
-TEST_F(Field3DTest, Tanh) {
-  Field3D field;
+    field = -1.0;
+    EXPECT_TRUE(IsFieldEqual(cosh(field), expected));
+  }
 
-  field = 1.0;
-  const BoutReal expected = 0.761594155955764;
-  EXPECT_TRUE(IsFieldEqual(tanh(field), expected));
+  TEST_F(Field3DTest, Tanh) {
+    Field3D field;
 
-  field = -1.0;
-  EXPECT_TRUE(IsFieldEqual(tanh(field), -expected));
-}
+    field = 1.0;
+    const BoutReal expected = 0.761594155955764;
+    EXPECT_TRUE(IsFieldEqual(tanh(field), expected));
 
-TEST_F(Field3DTest, Floor) {
-  Field3D field;
+    field = -1.0;
+    EXPECT_TRUE(IsFieldEqual(tanh(field), -expected));
+  }
 
-  field = 50.0;
-  field(1, 1, 1) = 49.9;
-  field(2, 3, 4) = -20;
+  TEST_F(Field3DTest, Floor) {
+    Field3D field;
 
-  const BoutReal floor_value = 50.0;
+    field = 50.0;
+    field(1, 1, 1) = 49.9;
+    field(2, 3, 4) = -20;
 
-  EXPECT_TRUE(IsFieldEqual(floor(field, floor_value), floor_value));
-}
+    const BoutReal floor_value = 50.0;
 
-TEST_F(Field3DTest, Min) {
-  Field3D field;
+    EXPECT_TRUE(IsFieldEqual(floor(field, floor_value), floor_value));
+  }
 
-  field = 50.0;
-  field(0, 0, 0) = -99.0;
-  field(1, 1, 1) = 60.0;
-  field(1, 2, 2) = 40.0;
-  field(2, 4, 3) = 99.0;
+  TEST_F(Field3DTest, Min) {
+    Field3D field;
 
-  // min doesn't include guard cells
-  const BoutReal min_value = 40.0;
+    field = 50.0;
+    field(0, 0, 0) = -99.0;
+    field(1, 1, 1) = 60.0;
+    field(1, 2, 2) = 40.0;
+    field(2, 4, 3) = 99.0;
 
-  EXPECT_EQ(min(field, false), min_value);
-  EXPECT_EQ(min(field, false, "RGN_ALL"), -99.0);
-  EXPECT_EQ(min(field, true, "RGN_ALL"), -99.0);
-}
+    // min doesn't include guard cells
+    const BoutReal min_value = 40.0;
 
-TEST_F(Field3DTest, MinBinaryExpr) {
-  Field3D field;
+    EXPECT_EQ(min(field, false), min_value);
+    EXPECT_EQ(min(field, false, "RGN_ALL"), -99.0);
+    EXPECT_EQ(min(field, true, "RGN_ALL"), -99.0);
+  }
 
-  field = 50.0;
-  field(0, 0, 0) = -99.0;
-  field(1, 1, 1) = 60.0;
-  field(1, 2, 2) = 40.0;
-  field(2, 4, 3) = 99.0;
+  TEST_F(Field3DTest, MinBinaryExpr) {
+    Field3D field;
 
-  const auto expr = field / 2.0 - 5.0;
+    field = 50.0;
+    field(0, 0, 0) = -99.0;
+    field(1, 1, 1) = 60.0;
+    field(1, 2, 2) = 40.0;
+    field(2, 4, 3) = 99.0;
 
-  EXPECT_EQ(min(expr, false), 15.0);
-  EXPECT_EQ(min(expr, false, "RGN_ALL"), -54.5);
-}
+    const auto expr = field / 2.0 - 5.0;
 
-TEST_F(Field3DTest, Max) {
-  Field3D field;
+    EXPECT_EQ(min(expr, false), 15.0);
+    EXPECT_EQ(min(expr, false, "RGN_ALL"), -54.5);
+  }
 
-  field = 50.0;
-  field(0, 0, 0) = -99.0;
-  field(1, 1, 1) = 40.0;
-  field(1, 2, 2) = 60.0;
-  field(2, 4, 3) = 99.0;
+  TEST_F(Field3DTest, Max) {
+    Field3D field;
 
-  // max doesn't include guard cells
-  const BoutReal max_value = 60.0;
+    field = 50.0;
+    field(0, 0, 0) = -99.0;
+    field(1, 1, 1) = 40.0;
+    field(1, 2, 2) = 60.0;
+    field(2, 4, 3) = 99.0;
 
-  EXPECT_EQ(max(field, false), max_value);
-  EXPECT_EQ(max(field, false, "RGN_ALL"), 99.0);
-  EXPECT_EQ(max(field, true, "RGN_ALL"), 99.0);
-}
+    // max doesn't include guard cells
+    const BoutReal max_value = 60.0;
 
-TEST_F(Field3DTest, MaxBinaryExpr) {
-  Field3D field;
+    EXPECT_EQ(max(field, false), max_value);
+    EXPECT_EQ(max(field, false, "RGN_ALL"), 99.0);
+    EXPECT_EQ(max(field, true, "RGN_ALL"), 99.0);
+  }
 
-  field = 50.0;
-  field(0, 0, 0) = -99.0;
-  field(1, 1, 1) = 40.0;
-  field(1, 2, 2) = 60.0;
-  field(2, 4, 3) = 99.0;
+  TEST_F(Field3DTest, MaxBinaryExpr) {
+    Field3D field;
 
-  const auto expr = field / 2.0 - 5.0;
+    field = 50.0;
+    field(0, 0, 0) = -99.0;
+    field(1, 1, 1) = 40.0;
+    field(1, 2, 2) = 60.0;
+    field(2, 4, 3) = 99.0;
 
-  EXPECT_EQ(max(expr, false), 25.0);
-  EXPECT_EQ(max(expr, false, "RGN_ALL"), 44.5);
-}
+    const auto expr = field / 2.0 - 5.0;
 
-TEST_F(Field3DTest, Mean) {
-  Field3D field;
+    EXPECT_EQ(max(expr, false), 25.0);
+    EXPECT_EQ(max(expr, false, "RGN_ALL"), 44.5);
+  }
 
-  field = 50.0;
-  field(0, 0, 0) = 1.0;
-  field(1, 1, 1) = 40.0;
-  field(1, 2, 2) = 60.0;
-  field(2, 4, 3) = 109.0;
+  TEST_F(Field3DTest, Mean) {
+    Field3D field;
 
-  // mean doesn't include guard cells by default
-  const int npoints_all = nx * ny * nz;
-  const BoutReal mean_value_nobndry = 50.0;
-  const BoutReal mean_value_all = 50.0 + 10.0 / npoints_all;
+    field = 50.0;
+    field(0, 0, 0) = 1.0;
+    field(1, 1, 1) = 40.0;
+    field(1, 2, 2) = 60.0;
+    field(2, 4, 3) = 109.0;
 
-  EXPECT_EQ(mean(field, false), mean_value_nobndry);
-  EXPECT_EQ(mean(field, false, "RGN_ALL"), mean_value_all);
-  EXPECT_EQ(mean(field, true, "RGN_ALL"), mean_value_all);
-}
+    // mean doesn't include guard cells by default
+    const int npoints_all = nx * ny * nz;
+    const BoutReal mean_value_nobndry = 50.0;
+    const BoutReal mean_value_all = 50.0 + 10.0 / npoints_all;
 
-TEST_F(Field3DTest, MeanBinaryExpr) {
-  Field3D field;
-
-  field = 50.0;
-  field(0, 0, 0) = 1.0;
-  field(1, 1, 1) = 40.0;
-  field(1, 2, 2) = 60.0;
-  field(2, 4, 3) = 109.0;
+    EXPECT_EQ(mean(field, false), mean_value_nobndry);
+    EXPECT_EQ(mean(field, false, "RGN_ALL"), mean_value_all);
+    EXPECT_EQ(mean(field, true, "RGN_ALL"), mean_value_all);
+  }
 
-  const int npoints_all = nx * ny * nz;
-  const BoutReal mean_value_nobndry = 103.0;
-  const BoutReal mean_value_all = 103.0 + 20.0 / npoints_all;
-  const auto expr = field * 2.0 + 3.0;
+  TEST_F(Field3DTest, MeanBinaryExpr) {
+    Field3D field;
 
-  EXPECT_EQ(mean(expr, false), mean_value_nobndry);
-  EXPECT_EQ(mean(expr, false, "RGN_ALL"), mean_value_all);
-}
+    field = 50.0;
+    field(0, 0, 0) = 1.0;
+    field(1, 1, 1) = 40.0;
+    field(1, 2, 2) = 60.0;
+    field(2, 4, 3) = 109.0;
 
-TEST_F(Field3DTest, DC) {
-  Field3D field;
+    const int npoints_all = nx * ny * nz;
+    const BoutReal mean_value_nobndry = 103.0;
+    const BoutReal mean_value_all = 103.0 + 20.0 / npoints_all;
+    const auto expr = field * 2.0 + 3.0;
 
-  field = 1.0;
-  for (const auto& i : field) {
-    field[i] = i.z();
+    EXPECT_EQ(mean(expr, false), mean_value_nobndry);
+    EXPECT_EQ(mean(expr, false, "RGN_ALL"), mean_value_all);
   }
 
-  EXPECT_TRUE(IsFieldEqual(DC(field), 3.0));
-}
+  TEST_F(Field3DTest, DC) {
+    Field3D field;
 
-TEST_F(Field3DTest, Swap) {
-  WithQuietOutput quiet{output_info};
+    field = 1.0;
+    for (const auto& i : field) {
+      field[i] = i.z();
+    }
 
-  // First field
-  Field3D first(1., mesh_staggered);
+    EXPECT_TRUE(IsFieldEqual(DC(field), 3.0));
+  }
 
-  first.setLocation(CELL_XLOW);
+  TEST_F(Field3DTest, Swap) {
+    WithQuietOutput quiet{output_info};
 
-  first.splitParallelSlices();
-  first.yup() = 1.5;
-  first.ydown() = 0.5;
+    // First field
+    Field3D first(1., mesh_staggered);
 
-  ddt(first) = 1.1;
+    first.setLocation(CELL_XLOW);
 
-  // Mesh for second field
-  constexpr int second_nx = Field3DTest::nx + 2;
-  constexpr int second_ny = Field3DTest::ny + 2;
-  constexpr int second_nz = Field3DTest::nz + 2;
+    first.splitParallelSlices();
+    first.yup() = 1.5;
+    first.ydown() = 0.5;
 
-  FakeMesh second_mesh{second_nx, second_ny, second_nz};
-  second_mesh.setCoordinates(nullptr);
-  second_mesh.StaggerGrids = false;
-  second_mesh.createDefaultRegions();
+    ddt(first) = 1.1;
 
-  // Second field
-  Field3D second(2., &second_mesh);
+    // Mesh for second field
+    constexpr int second_nx = Field3DTest::nx + 2;
+    constexpr int second_ny = Field3DTest::ny + 2;
+    constexpr int second_nz = Field3DTest::nz + 2;
 
-  second.splitParallelSlices();
-  second.yup() = 2.2;
-  second.ydown() = 1.2;
+    FakeMesh second_mesh{second_nx, second_ny, second_nz};
+    second_mesh.setCoordinates(nullptr);
+    second_mesh.StaggerGrids = false;
+    second_mesh.createDefaultRegions();
 
-  ddt(second) = 2.4;
+    // Second field
+    Field3D second(2., &second_mesh);
 
-  // Basic sanity check
-  EXPECT_TRUE(IsFieldEqual(first, 1.0));
-  EXPECT_TRUE(IsFieldEqual(second, 2.0));
+    second.splitParallelSlices();
+    second.yup() = 2.2;
+    second.ydown() = 1.2;
 
-  // swap is marked noexcept, so absolutely should not throw!
-  ASSERT_NO_THROW(swap(first, second));
+    ddt(second) = 2.4;
 
-  // Values
-  EXPECT_TRUE(IsFieldEqual(first, 2.0));
-  EXPECT_TRUE(IsFieldEqual(second, 1.0));
+    // Basic sanity check
+    EXPECT_TRUE(IsFieldEqual(first, 1.0));
+    EXPECT_TRUE(IsFieldEqual(second, 2.0));
 
-  EXPECT_TRUE(IsFieldEqual(first.yup(), 2.2));
-  EXPECT_TRUE(IsFieldEqual(first.ydown(), 1.2));
+    // swap is marked noexcept, so absolutely should not throw!
+    ASSERT_NO_THROW(swap(first, second));
 
-  EXPECT_TRUE(IsFieldEqual(second.yup(), 1.5));
-  EXPECT_TRUE(IsFieldEqual(second.ydown(), 0.5));
+    // Values
+    EXPECT_TRUE(IsFieldEqual(first, 2.0));
+    EXPECT_TRUE(IsFieldEqual(second, 1.0));
 
-  EXPECT_TRUE(IsFieldEqual(ddt(first), 2.4));
-  EXPECT_TRUE(IsFieldEqual(ddt(second), 1.1));
+    EXPECT_TRUE(IsFieldEqual(first.yup(), 2.2));
+    EXPECT_TRUE(IsFieldEqual(first.ydown(), 1.2));
 
-  // Mesh properties
-  EXPECT_EQ(first.getMesh(), &second_mesh);
-  EXPECT_EQ(second.getMesh(), mesh_staggered);
+    EXPECT_TRUE(IsFieldEqual(second.yup(), 1.5));
+    EXPECT_TRUE(IsFieldEqual(second.ydown(), 0.5));
 
-  EXPECT_EQ(first.getNx(), second_nx);
-  EXPECT_EQ(first.getNy(), second_ny);
-  EXPECT_EQ(first.getNz(), second_nz);
+    EXPECT_TRUE(IsFieldEqual(ddt(first), 2.4));
+    EXPECT_TRUE(IsFieldEqual(ddt(second), 1.1));
 
-  EXPECT_EQ(second.getNx(), Field3DTest::nx);
-  EXPECT_EQ(second.getNy(), Field3DTest::ny);
-  EXPECT_EQ(second.getNz(), Field3DTest::nz);
+    // Mesh properties
+    EXPECT_EQ(first.getMesh(), &second_mesh);
+    EXPECT_EQ(second.getMesh(), mesh_staggered);
 
-  EXPECT_EQ(first.getLocation(), CELL_CENTRE);
-  EXPECT_EQ(second.getLocation(), CELL_XLOW);
+    EXPECT_EQ(first.getNx(), second_nx);
+    EXPECT_EQ(first.getNy(), second_ny);
+    EXPECT_EQ(first.getNz(), second_nz);
 
-  // We don't check the boundaries, but the data is protected and
-  // there are no inquiry functions
-}
+    EXPECT_EQ(second.getNx(), Field3DTest::nx);
+    EXPECT_EQ(second.getNy(), Field3DTest::ny);
+    EXPECT_EQ(second.getNz(), Field3DTest::nz);
 
-TEST_F(Field3DTest, MoveCtor) {
-  // First field
-  Field3D first(1., mesh_staggered);
+    EXPECT_EQ(first.getLocation(), CELL_CENTRE);
+    EXPECT_EQ(second.getLocation(), CELL_XLOW);
 
-  first.setLocation(CELL_XLOW);
+    // We don't check the boundaries, but the data is protected and
+    // there are no inquiry functions
+  }
 
-  first.splitParallelSlices();
-  first.yup() = 1.5;
-  first.ydown() = 0.5;
+  TEST_F(Field3DTest, MoveCtor) {
+    // First field
+    Field3D first(1., mesh_staggered);
 
-  ddt(first) = 1.1;
+    first.setLocation(CELL_XLOW);
 
-  // Second field
-  Field3D second{std::move(first)};
+    first.splitParallelSlices();
+    first.yup() = 1.5;
+    first.ydown() = 0.5;
 
-  // Values
-  EXPECT_TRUE(IsFieldEqual(second, 1.0));
+    ddt(first) = 1.1;
 
-  EXPECT_TRUE(IsFieldEqual(second.yup(), 1.5));
-  EXPECT_TRUE(IsFieldEqual(second.ydown(), 0.5));
+    // Second field
+    Field3D second{std::move(first)};
 
-  EXPECT_TRUE(IsFieldEqual(ddt(second), 1.1));
+    // Values
+    EXPECT_TRUE(IsFieldEqual(second, 1.0));
 
-  // Mesh properties
-  EXPECT_EQ(second.getMesh(), mesh_staggered);
+    EXPECT_TRUE(IsFieldEqual(second.yup(), 1.5));
+    EXPECT_TRUE(IsFieldEqual(second.ydown(), 0.5));
 
-  EXPECT_EQ(second.getNx(), Field3DTest::nx);
-  EXPECT_EQ(second.getNy(), Field3DTest::ny);
-  EXPECT_EQ(second.getNz(), Field3DTest::nz);
+    EXPECT_TRUE(IsFieldEqual(ddt(second), 1.1));
 
-  EXPECT_EQ(second.getLocation(), CELL_XLOW);
+    // Mesh properties
+    EXPECT_EQ(second.getMesh(), mesh_staggered);
 
-  // We don't check the boundaries, but the data is protected and
-  // there are no inquiry functions
-}
+    EXPECT_EQ(second.getNx(), Field3DTest::nx);
+    EXPECT_EQ(second.getNy(), Field3DTest::ny);
+    EXPECT_EQ(second.getNz(), Field3DTest::nz);
 
-TEST_F(Field3DTest, FillField) {
-  Field3D f{mesh};
+    EXPECT_EQ(second.getLocation(), CELL_XLOW);
 
-  fillField(f, {{{1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.}},
+    // We don't check the boundaries, but the data is protected and
+    // there are no inquiry functions
+  }
 
-                {{1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.}},
+  TEST_F(Field3DTest, FillField) {
+    Field3D f{mesh};
+
+    fillField(f, {{{1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.}},
+
+                  {{1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.}},
+
+                  {{1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.},
+                   {1., 1., 1., 1., 1., 1., 1.}}});
+
+    EXPECT_TRUE(IsFieldEqual(f, 1.));
+
+    fillField(f, {{{0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.}},
+
+                  {{0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.}},
+
+                  {{0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.},
+                   {0., 1., 2., 3., 4., 5., 6.}}});
+
+    Field3D g{mesh};
+    g.allocate();
+    BOUT_FOR_SERIAL(i, g.getRegion("RGN_ALL")) { g[i] = i.z(); }
+
+    EXPECT_TRUE(IsFieldEqual(f, g));
+  }
 
-                {{1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.},
-                 {1., 1., 1., 1., 1., 1., 1.}}});
+#if BOUT_HAS_FFTW
+  namespace bout {
+  namespace testing {
 
-  EXPECT_TRUE(IsFieldEqual(f, 1.));
+  // Amplitudes for the nth wavenumber
+  constexpr int k0{1};
+  constexpr int k1{2};
+  constexpr int k2{3};
 
-  fillField(f, {{{0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.}},
+  const BoutReal box_size{TWOPI / Field3DTest::nz};
 
-                {{0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.}},
+  // Helper function for the filter and lowpass tests
+  BoutReal zWaves(Field3D::ind_type& i) {
+    return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size)
+           + std::sin(k2 * i.z() * box_size);
+  }
+  } // namespace testing
+  } // namespace bout
 
-                {{0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.},
-                 {0., 1., 2., 3., 4., 5., 6.}}});
+  TEST_F(Field3DTest, Filter) {
 
-  Field3D g{mesh};
-  g.allocate();
-  BOUT_FOR_SERIAL(i, g.getRegion("RGN_ALL")) { g[i] = i.z(); }
+    using namespace bout::testing;
 
-  EXPECT_TRUE(IsFieldEqual(f, g));
-}
+    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-#if BOUT_HAS_FFTW
-namespace bout {
-namespace testing {
+    auto expected = makeField<Field3D>(
+        [&](Field3D::ind_type& i) { return std::cos(k1 * i.z() * box_size); },
+        bout::globals::mesh);
 
-// Amplitudes for the nth wavenumber
-constexpr int k0{1};
-constexpr int k1{2};
-constexpr int k2{3};
+    auto output = filter(input, 2);
 
-const BoutReal box_size{TWOPI / Field3DTest::nz};
+    EXPECT_TRUE(IsFieldEqual(output, expected));
+  }
 
-// Helper function for the filter and lowpass tests
-BoutReal zWaves(Field3D::ind_type& i) {
-  return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size)
-         + std::sin(k2 * i.z() * box_size);
-}
-} // namespace testing
-} // namespace bout
+  TEST_F(Field3DTest, LowPassOneArg) {
 
-TEST_F(Field3DTest, Filter) {
+    using namespace bout::testing;
 
-  using namespace bout::testing;
+    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+    auto expected = makeField<Field3D>(
+        [&](Field3D::ind_type& i) {
+          return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
+        },
+        bout::globals::mesh);
 
-  auto expected = makeField<Field3D>(
-      [&](Field3D::ind_type& i) { return std::cos(k1 * i.z() * box_size); },
-      bout::globals::mesh);
+    auto output = lowPass(input, 2);
 
-  auto output = filter(input, 2);
+    EXPECT_TRUE(IsFieldEqual(output, expected));
+  }
 
-  EXPECT_TRUE(IsFieldEqual(output, expected));
-}
+  TEST_F(Field3DTest, LowPassOneArgNothing) {
 
-TEST_F(Field3DTest, LowPassOneArg) {
+    using namespace bout::testing;
 
-  using namespace bout::testing;
+    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+    auto output = lowPass(input, 20);
 
-  auto expected = makeField<Field3D>(
-      [&](Field3D::ind_type& i) {
-        return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
-      },
-      bout::globals::mesh);
+    EXPECT_TRUE(IsFieldEqual(output, input));
+  }
 
-  auto output = lowPass(input, 2);
+  TEST_F(Field3DTest, LowPassTwoArg) {
 
-  EXPECT_TRUE(IsFieldEqual(output, expected));
-}
+    using namespace bout::testing;
 
-TEST_F(Field3DTest, LowPassOneArgNothing) {
+    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-  using namespace bout::testing;
+    auto expected = makeField<Field3D>(
+        [&](Field3D::ind_type& i) {
+          return std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
+        },
+        bout::globals::mesh);
 
-  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+    auto output = lowPass(input, 2, false);
 
-  auto output = lowPass(input, 20);
+    EXPECT_TRUE(IsFieldEqual(output, expected));
 
-  EXPECT_TRUE(IsFieldEqual(output, input));
-}
+    // Check passing int still works
+    auto output2 = lowPass(input, 2, 0);
 
-TEST_F(Field3DTest, LowPassTwoArg) {
+    EXPECT_TRUE(IsFieldEqual(output2, expected));
 
-  using namespace bout::testing;
+    // Calling lowPass with an int that is not 0 or 1 is an error
+    EXPECT_THROW(lowPass(input, 2, -1), BoutException);
+    EXPECT_THROW(lowPass(input, 2, 2), BoutException);
+  }
 
-  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+  TEST_F(Field3DTest, LowPassTwoArgKeepZonal) {
 
-  auto expected = makeField<Field3D>(
-      [&](Field3D::ind_type& i) {
-        return std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
-      },
-      bout::globals::mesh);
+    using namespace bout::testing;
 
-  auto output = lowPass(input, 2, false);
+    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-  EXPECT_TRUE(IsFieldEqual(output, expected));
+    auto expected = makeField<Field3D>(
+        [&](Field3D::ind_type& i) {
+          return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
+        },
+        bout::globals::mesh);
 
-  // Check passing int still works
-  auto output2 = lowPass(input, 2, 0);
+    auto output = lowPass(input, 2, true);
 
-  EXPECT_TRUE(IsFieldEqual(output2, expected));
+    EXPECT_TRUE(IsFieldEqual(output, expected));
 
-  // Calling lowPass with an int that is not 0 or 1 is an error
-  EXPECT_THROW(lowPass(input, 2, -1), BoutException);
-  EXPECT_THROW(lowPass(input, 2, 2), BoutException);
-}
+    // Check passing int still works
+    auto output2 = lowPass(input, 2, 1);
 
-TEST_F(Field3DTest, LowPassTwoArgKeepZonal) {
+    EXPECT_TRUE(IsFieldEqual(output2, expected));
+  }
 
-  using namespace bout::testing;
+  TEST_F(Field3DTest, LowPassTwoArgNothing) {
 
-  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+    using namespace bout::testing;
 
-  auto expected = makeField<Field3D>(
-      [&](Field3D::ind_type& i) {
-        return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
-      },
-      bout::globals::mesh);
+    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-  auto output = lowPass(input, 2, true);
+    auto output = lowPass(input, 20, true);
 
-  EXPECT_TRUE(IsFieldEqual(output, expected));
+    EXPECT_TRUE(IsFieldEqual(output, input));
+  }
+#endif
 
-  // Check passing int still works
-  auto output2 = lowPass(input, 2, 1);
+  TEST_F(Field3DTest, OperatorEqualsField3D) {
+    Field3D field;
 
-  EXPECT_TRUE(IsFieldEqual(output2, expected));
-}
+    // Create field with non-default arguments so we can check they get copied
+    // to 'field'.
+    // Note that Average z-direction type is not really allowed for Field3D, but
+    // we don't check anywhere at the moment.
+    Field3D field2{
+        mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
 
-TEST_F(Field3DTest, LowPassTwoArgNothing) {
+    field = field2;
 
-  using namespace bout::testing;
+    EXPECT_TRUE(areFieldsCompatible(field, field2));
+    EXPECT_EQ(field.getMesh(), field2.getMesh());
+    EXPECT_EQ(field.getLocation(), field2.getLocation());
+    EXPECT_EQ(field.getDirectionY(), field2.getDirectionY());
+    EXPECT_EQ(field.getDirectionZ(), field2.getDirectionZ());
+  }
 
-  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+  TEST_F(Field3DTest, OperatorEqualsBinaryExprCopiesMetadata) {
+    Field3D source{
+        mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+    source = 9.;
 
-  auto output = lowPass(input, 20, true);
+    Field3D target(mesh_staggered);
+    target = 0.;
+    target.splitParallelSlices();
 
-  EXPECT_TRUE(IsFieldEqual(output, input));
-}
-#endif
+    target = sqrt(source);
 
-TEST_F(Field3DTest, OperatorEqualsField3D) {
-  Field3D field;
+    EXPECT_EQ(target.getMesh(), source.getMesh());
+    EXPECT_EQ(target.getLocation(), source.getLocation());
+    EXPECT_EQ(target.getDirectionY(), source.getDirectionY());
+    EXPECT_EQ(target.getDirectionZ(), source.getDirectionZ());
+    EXPECT_FALSE(target.hasParallelSlices());
+    EXPECT_TRUE(IsFieldEqual(target, 3.));
+  }
 
-  // Create field with non-default arguments so we can check they get copied
-  // to 'field'.
-  // Note that Average z-direction type is not really allowed for Field3D, but
-  // we don't check anywhere at the moment.
-  Field3D field2{
-      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+  TEST_F(Field3DTest, EmptyFrom) {
+    // Create field with non-default arguments so we can check they get copied
+    // to 'field2'.
+    // Note that Average z-direction type is not really allowed for Field3D, but
+    // we don't check anywhere at the moment.
+    Field3D field{
+        mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+    field = 5.;
+
+    Field3D field2{emptyFrom(field)};
+    EXPECT_EQ(field2.getMesh(), mesh_staggered);
+    EXPECT_EQ(field2.getLocation(), CELL_XLOW);
+    EXPECT_EQ(field2.getDirectionY(), YDirectionType::Aligned);
+    EXPECT_EQ(field2.getDirectionZ(), ZDirectionType::Average);
+    EXPECT_TRUE(field2.isAllocated());
+  }
 
-  field = field2;
+  TEST_F(Field3DTest, ZeroFrom) {
+    // Create field with non-default arguments so we can check they get copied
+    // to 'field2'.
+    // Note that Average z-direction type is not really allowed for Field3D, but
+    // we don't check anywhere at the moment.
+    Field3D field{
+        mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+    field = 5.;
+
+    Field3D field2{zeroFrom(field)};
+    EXPECT_EQ(field2.getMesh(), mesh_staggered);
+    EXPECT_EQ(field2.getLocation(), CELL_XLOW);
+    EXPECT_EQ(field2.getDirectionY(), YDirectionType::Aligned);
+    EXPECT_EQ(field2.getDirectionZ(), ZDirectionType::Average);
+    EXPECT_TRUE(field2.isAllocated());
+    EXPECT_TRUE(IsFieldEqual(field2, 0.));
+  }
 
-  EXPECT_TRUE(areFieldsCompatible(field, field2));
-  EXPECT_EQ(field.getMesh(), field2.getMesh());
-  EXPECT_EQ(field.getLocation(), field2.getLocation());
-  EXPECT_EQ(field.getDirectionY(), field2.getDirectionY());
-  EXPECT_EQ(field.getDirectionZ(), field2.getDirectionZ());
-}
-
-TEST_F(Field3DTest, OperatorEqualsBinaryExprCopiesMetadata) {
-  Field3D source{
-      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
-  source = 9.;
-
-  Field3D target(mesh_staggered);
-  target = 0.;
-  target.splitParallelSlices();
-
-  target = sqrt(source);
-
-  EXPECT_EQ(target.getMesh(), source.getMesh());
-  EXPECT_EQ(target.getLocation(), source.getLocation());
-  EXPECT_EQ(target.getDirectionY(), source.getDirectionY());
-  EXPECT_EQ(target.getDirectionZ(), source.getDirectionZ());
-  EXPECT_FALSE(target.hasParallelSlices());
-  EXPECT_TRUE(IsFieldEqual(target, 3.));
-}
-
-TEST_F(Field3DTest, EmptyFrom) {
-  // Create field with non-default arguments so we can check they get copied
-  // to 'field2'.
-  // Note that Average z-direction type is not really allowed for Field3D, but
-  // we don't check anywhere at the moment.
-  Field3D field{
-      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
-  field = 5.;
-
-  Field3D field2{emptyFrom(field)};
-  EXPECT_EQ(field2.getMesh(), mesh_staggered);
-  EXPECT_EQ(field2.getLocation(), CELL_XLOW);
-  EXPECT_EQ(field2.getDirectionY(), YDirectionType::Aligned);
-  EXPECT_EQ(field2.getDirectionZ(), ZDirectionType::Average);
-  EXPECT_TRUE(field2.isAllocated());
-}
-
-TEST_F(Field3DTest, ZeroFrom) {
-  // Create field with non-default arguments so we can check they get copied
-  // to 'field2'.
-  // Note that Average z-direction type is not really allowed for Field3D, but
-  // we don't check anywhere at the moment.
-  Field3D field{
-      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
-  field = 5.;
-
-  Field3D field2{zeroFrom(field)};
-  EXPECT_EQ(field2.getMesh(), mesh_staggered);
-  EXPECT_EQ(field2.getLocation(), CELL_XLOW);
-  EXPECT_EQ(field2.getDirectionY(), YDirectionType::Aligned);
-  EXPECT_EQ(field2.getDirectionZ(), ZDirectionType::Average);
-  EXPECT_TRUE(field2.isAllocated());
-  EXPECT_TRUE(IsFieldEqual(field2, 0.));
-}
-
-TEST_F(Field3DTest, Field3DParallel) {
-  Field3DParallel field(1.0);
-  field = 1.0;
+  TEST_F(Field3DTest, Field3DParallel) {
+    Field3DParallel field(1.0);
+    field = 1.0;
 
-  Field3D field2 = field;
+    Field3D field2 = field;
 
-  auto& field3 = field.asField3D();
+    auto& field3 = field.asField3D();
 
-  field *= 2;
+    field *= 2;
 
-  EXPECT_TRUE(IsFieldEqual(field, 2.0));
-  EXPECT_TRUE(IsFieldEqual(field2, 1.0));
-  EXPECT_TRUE(IsFieldEqual(field3, 2.0));
+    EXPECT_TRUE(IsFieldEqual(field, 2.0));
+    EXPECT_TRUE(IsFieldEqual(field2, 1.0));
+    EXPECT_TRUE(IsFieldEqual(field3, 2.0));
 
-  field3.asField3DParallel() *= 3;
+    field3.asField3DParallel() *= 3;
 
-  EXPECT_TRUE(IsFieldEqual(field3, 6.0));
-}
+    EXPECT_TRUE(IsFieldEqual(field3, 6.0));
+  }
 
 // Restore compiler warnings
 #pragma GCC diagnostic pop

From c23f2d532b8093beab2fc37868ae420f1b7ac124 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 9 Jul 2026 11:44:46 +0200
Subject: [PATCH 1619/1827] Allow FCI fixture

---
 tests/unit/fake_mesh_fixture.hxx | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/tests/unit/fake_mesh_fixture.hxx b/tests/unit/fake_mesh_fixture.hxx
index 2758dbe416..3c261a6121 100644
--- a/tests/unit/fake_mesh_fixture.hxx
+++ b/tests/unit/fake_mesh_fixture.hxx
@@ -31,7 +31,7 @@
 /// Use this template class directly to use different sized grid:
 ///
 ///     using MyTest = FakeMeshFixture_tmpl<7, 9, 11>;
-template <int NX, int NY, int NZ>
+template <int NX, int NY, int NZ, bool FCI = false>
 class FakeMeshFixture_tmpl : public ::testing::Test {
 public:
   FakeMeshFixture_tmpl()
@@ -113,6 +113,11 @@ public:
     mesh_staggered_m.setCoordinates(test_coords_staggered, CELL_XLOW);
     mesh_staggered_m.setCoordinates(test_coords_staggered, CELL_YLOW);
     mesh_staggered_m.setCoordinates(test_coords_staggered, CELL_ZLOW);
+
+    if constexpr (FCI) {
+      mesh_m.getCoordinates()->setParallelTransform(
+          bout::utils::make_unique<MockParallelTransform>(mesh_m, false));
+    }
   }
 
   FakeMeshFixture_tmpl(const FakeMeshFixture_tmpl&) = delete;

From 356fd0c3e48c6a5b905e9565576bea11378cfed8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 9 Jul 2026 11:44:33 +0200
Subject: [PATCH 1620/1827] Move MockParallelTransform

To make it reusable
---
 tests/unit/fake_mesh.hxx                | 51 +++++++++++++++++++++++++
 tests/unit/field/test_field_factory.cxx | 51 -------------------------
 2 files changed, 51 insertions(+), 51 deletions(-)

diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index f957652a62..6559e554f2 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -366,3 +366,54 @@ public:
 private:
   Options values; ///< Store values to be returned by get()
 };
+
+// A mock ParallelTransform to test transform_from_field_aligned
+// property of FieldFactory. For now, the transform just returns the
+// negative of the input. Ideally, this will get moved to GoogleMock
+// when we start using it.
+//
+// Can turn off the ability to do the transform. Should still be valid
+class MockParallelTransform : public ParallelTransform {
+public:
+  MockParallelTransform(Mesh& mesh, bool allow_transform_)
+      : ParallelTransform(mesh), allow_transform(allow_transform_) {}
+  ~MockParallelTransform() = default;
+
+  void calcParallelSlices(Field3D&) override {}
+
+  bool canToFromFieldAligned() const override { return allow_transform; }
+
+  bool requiresTwistShift(bool, YDirectionType) override { return false; }
+
+  void checkInputGrid() override {}
+
+  Field3D fromFieldAligned(const Field3D& f, const std::string&) override {
+    if (f.getDirectionY() != YDirectionType::Aligned) {
+      throw BoutException("Unaligned field passed to fromFieldAligned");
+    }
+    return -f;
+  }
+
+  FieldPerp fromFieldAligned(const FieldPerp& f, const std::string&) override {
+    if (f.getDirectionY() != YDirectionType::Aligned) {
+      throw BoutException("Unaligned field passed to fromFieldAligned");
+    }
+    return -f;
+  }
+
+  Field3D toFieldAligned(const Field3D& f, const std::string&) override {
+    if (f.getDirectionY() != YDirectionType::Standard) {
+      throw BoutException("Aligned field passed to toFieldAligned");
+    }
+    return -f;
+  }
+  FieldPerp toFieldAligned(const FieldPerp& f, const std::string&) override {
+    if (f.getDirectionY() != YDirectionType::Standard) {
+      throw BoutException("Aligned field passed to toFieldAligned");
+    }
+    return -f;
+  }
+
+private:
+  const bool allow_transform;
+};
diff --git a/tests/unit/field/test_field_factory.cxx b/tests/unit/field/test_field_factory.cxx
index 9db9fcef10..8cb08ed230 100644
--- a/tests/unit/field/test_field_factory.cxx
+++ b/tests/unit/field/test_field_factory.cxx
@@ -832,57 +832,6 @@ TEST_F(FieldFactoryTest, FuzzyFind) {
   EXPECT_EQ(CAPS_matches.size(), 1);
 }
 
-// A mock ParallelTransform to test transform_from_field_aligned
-// property of FieldFactory. For now, the transform just returns the
-// negative of the input. Ideally, this will get moved to GoogleMock
-// when we start using it.
-//
-// Can turn off the ability to do the transform. Should still be valid
-class MockParallelTransform : public ParallelTransform {
-public:
-  MockParallelTransform(Mesh& mesh, bool allow_transform_)
-      : ParallelTransform(mesh), allow_transform(allow_transform_) {}
-  ~MockParallelTransform() = default;
-
-  void calcParallelSlices(Field3D&) override {}
-
-  bool canToFromFieldAligned() const override { return allow_transform; }
-
-  bool requiresTwistShift(bool, YDirectionType) override { return false; }
-
-  void checkInputGrid() override {}
-
-  Field3D fromFieldAligned(const Field3D& f, const std::string&) override {
-    if (f.getDirectionY() != YDirectionType::Aligned) {
-      throw BoutException("Unaligned field passed to fromFieldAligned");
-    }
-    return -f;
-  }
-
-  FieldPerp fromFieldAligned(const FieldPerp& f, const std::string&) override {
-    if (f.getDirectionY() != YDirectionType::Aligned) {
-      throw BoutException("Unaligned field passed to fromFieldAligned");
-    }
-    return -f;
-  }
-
-  Field3D toFieldAligned(const Field3D& f, const std::string&) override {
-    if (f.getDirectionY() != YDirectionType::Standard) {
-      throw BoutException("Aligned field passed to toFieldAligned");
-    }
-    return -f;
-  }
-  FieldPerp toFieldAligned(const FieldPerp& f, const std::string&) override {
-    if (f.getDirectionY() != YDirectionType::Standard) {
-      throw BoutException("Aligned field passed to toFieldAligned");
-    }
-    return -f;
-  }
-
-private:
-  const bool allow_transform;
-};
-
 class FieldFactoryCreateAndTransformTest : public FakeMeshFixture {
 public:
   WithQuietOutput quiet_info{output_info};

From 8f66c008d013104f684a2c4bf7dd9f404e5e73a1 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 9 Jul 2026 22:12:40 -0700
Subject: [PATCH 1621/1827] test_field3d: Tidying, define FakeMeshFixtureFCI

Implement some clang-tidy suggestions, use FakeMeshFixtureFCI for
tests with FCI parallel transform.
---
 tests/unit/fake_mesh_fixture.hxx  |    1 +
 tests/unit/field/test_field3d.cxx | 1091 ++++++++++++++---------------
 2 files changed, 528 insertions(+), 564 deletions(-)

diff --git a/tests/unit/fake_mesh_fixture.hxx b/tests/unit/fake_mesh_fixture.hxx
index 3c261a6121..92d8ee2a13 100644
--- a/tests/unit/fake_mesh_fixture.hxx
+++ b/tests/unit/fake_mesh_fixture.hxx
@@ -153,3 +153,4 @@ public:
 };
 
 using FakeMeshFixture = FakeMeshFixture_tmpl<3, 5, 7>;
+using FakeMeshFixtureFCI = FakeMeshFixture_tmpl<3, 5, 7, true>;
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 89286a8f80..173991a31d 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -7,14 +7,16 @@
 #include "gtest/gtest.h"
 
 #include "test_extras.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/constants.hxx"
+#include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
 #include "bout/output.hxx"
 #include "bout/paralleltransform.hxx"
+#include "bout/region.hxx"
 #include "bout/unused.hxx"
-#include "bout/utils.hxx"
 
 #include <cmath>
 #include <set>
@@ -27,35 +29,7 @@ using namespace bout::globals;
 
 // Reuse the "standard" fixture for FakeMesh
 using Field3DTest = FakeMeshFixture;
-using Field3DTestFCI = FakeMeshFixture_tmpl<3, 5, 7, true>;
-
-class MockFciParallelTransform : public ParallelTransform {
-public:
-  explicit MockFciParallelTransform(Mesh& mesh_in) : ParallelTransform(mesh_in) {}
-
-  void calcParallelSlices(Field3D& f) override {
-    if (!f.hasParallelSlices()) {
-      f.splitParallelSlices();
-    }
-    for (size_t i = 0; i < f.numberParallelSlices(); ++i) {
-      f.yup(i) = f;
-      f.ydown(i) = f;
-    }
-  }
-
-  Field3D toFieldAligned(const Field3D& f, const std::string&) override { return f; }
-  FieldPerp toFieldAligned(const FieldPerp& f, const std::string&) override { return f; }
-  Field3D fromFieldAligned(const Field3D& f, const std::string&) override { return f; }
-  FieldPerp fromFieldAligned(const FieldPerp& f, const std::string&) override {
-    return f;
-  }
-
-  bool canToFromFieldAligned() const override { return false; }
-  bool requiresTwistShift(bool, YDirectionType) override { return false; }
-
-protected:
-  void checkInputGrid() override {}
-};
+using Field3DTestFCI = FakeMeshFixtureFCI;
 
 TEST_F(Field3DTest, Is3D) {
   Field3D field;
@@ -104,14 +78,14 @@ TEST_F(Field3DTest, GetGridSizes) {
 }
 
 TEST_F(Field3DTest, CreateOnGivenMesh) {
-  int test_nx = Field3DTest::nx + 2;
-  int test_ny = Field3DTest::ny + 2;
-  int test_nz = Field3DTest::nz + 2;
+  const int test_nx = Field3DTest::nx + 2;
+  const int test_ny = Field3DTest::ny + 2;
+  const int test_nz = Field3DTest::nz + 2;
 
   FakeMesh fieldmesh{test_nx, test_ny, test_nz};
   fieldmesh.setCoordinates(nullptr);
 
-  Field3D field{&fieldmesh};
+  const Field3D field{&fieldmesh};
 
   EXPECT_EQ(field.getNx(), test_nx);
   EXPECT_EQ(field.getNy(), test_ny);
@@ -121,17 +95,17 @@ TEST_F(Field3DTest, CreateOnGivenMesh) {
 TEST_F(Field3DTest, CopyCheckFieldmesh) {
   WithQuietOutput quiet{output_info};
 
-  int test_nx = Field3DTest::nx + 2;
-  int test_ny = Field3DTest::ny + 2;
-  int test_nz = Field3DTest::nz + 2;
+  const int test_nx = Field3DTest::nx + 2;
+  const int test_ny = Field3DTest::ny + 2;
+  const int test_nz = Field3DTest::nz + 2;
 
   FakeMesh fieldmesh{test_nx, test_ny, test_nz};
   fieldmesh.setCoordinates(nullptr);
   fieldmesh.createDefaultRegions();
 
-  Field3D field{0.0, &fieldmesh};
+  const Field3D field{0.0, &fieldmesh};
 
-  Field3D field2{field};
+  const Field3D field2{field};
 
   EXPECT_EQ(field2.getNx(), test_nx);
   EXPECT_EQ(field2.getNy(), test_ny);
@@ -196,10 +170,10 @@ TEST_F(Field3DTest, CreateCopyOnNullMesh) {
 TEST_F(Field3DTest, TimeDeriv) {
   Field3D field;
 
-  auto deriv = field.timeDeriv();
+  auto* deriv = field.timeDeriv();
   EXPECT_NE(&field, deriv);
 
-  auto deriv2 = field.timeDeriv();
+  auto* deriv2 = field.timeDeriv();
   EXPECT_EQ(deriv, deriv2);
 
   EXPECT_EQ(&(ddt(field)), deriv);
@@ -323,9 +297,9 @@ TEST_F(Field3DTest, ConstYnext) {
 
   const Field3D& field2 = field;
 
-  auto& yup = field2.ynext(1);
+  const auto& yup = field2.ynext(1);
   EXPECT_NE(&field2, &yup);
-  auto& ydown = field2.ynext(-1);
+  const auto& ydown = field2.ynext(-1);
   EXPECT_NE(&field2, &ydown);
   EXPECT_NE(&yup, &ydown);
 
@@ -335,9 +309,9 @@ TEST_F(Field3DTest, ConstYnext) {
 }
 
 TEST_F(Field3DTest, GetGlobalMesh) {
-  Field3D field;
+  const Field3D field;
 
-  auto localmesh = field.getMesh();
+  auto* localmesh = field.getMesh();
 
   EXPECT_EQ(localmesh, mesh);
 }
@@ -346,9 +320,9 @@ TEST_F(Field3DTest, GetLocalMesh) {
   FakeMesh myMesh{nx + 1, ny + 2, nz + 3};
   myMesh.setCoordinates(nullptr);
 
-  Field3D field(&myMesh);
+  const Field3D field(&myMesh);
 
-  auto localmesh = field.getMesh();
+  auto* localmesh = field.getMesh();
 
   EXPECT_EQ(localmesh, &myMesh);
 }
@@ -463,8 +437,9 @@ TEST_F(Field3DTest, IterateOverRegionInd3D_RGN_ALL) {
 
   // We use a set in case for some reason the iterator doesn't visit
   // each point in the order we expect
-  std::set<std::vector<int>> test_indices{{0, 0, 0}, {0, 0, 1}, {0, 1, 0}, {1, 0, 0},
-                                          {0, 1, 1}, {1, 0, 1}, {1, 1, 0}, {1, 1, 1}};
+  const std::set<std::vector<int>> test_indices{{0, 0, 0}, {0, 0, 1}, {0, 1, 0},
+                                                {1, 0, 0}, {0, 1, 1}, {1, 0, 1},
+                                                {1, 1, 0}, {1, 1, 1}};
   const int num_sentinels = test_indices.size();
 
   // Assign sentinel value to watch out for to our chosen points
@@ -802,7 +777,7 @@ TEST_F(Field3DTest, IterateOverRGN_ZGUARDS) {
   test_indices.insert({1, 1, 1});
 
   // This is the set of indices actually inside the region we want
-  std::set<std::vector<int>> region_indices;
+  const std::set<std::vector<int>> region_indices;
 
   const int num_sentinels = region_indices.size();
 
@@ -913,7 +888,7 @@ TEST_F(Field3DTest, IterateOver2DRGN_NOBNDRY) {
     EXPECT_EQ(i.z(), 0);
   }
 
-  EXPECT_EQ(sum, nx * ny - 2 * nx - 2 * (ny - 2));
+  EXPECT_EQ(sum, (nx * ny) - (2 * nx) - (2 * (ny - 2)));
 }
 
 TEST_F(Field3DTest, IterateOver2DRGN_NOX) {
@@ -931,7 +906,7 @@ TEST_F(Field3DTest, IterateOver2DRGN_NOX) {
     EXPECT_EQ(i.z(), 0);
   }
 
-  EXPECT_EQ(sum, nx * ny - 2 * ny);
+  EXPECT_EQ(sum, (nx * ny) - (2 * ny));
 }
 
 TEST_F(Field3DTest, IterateOver2DRGN_NOY) {
@@ -949,7 +924,7 @@ TEST_F(Field3DTest, IterateOver2DRGN_NOY) {
     EXPECT_EQ(i.z(), 0);
   }
 
-  EXPECT_EQ(sum, nx * ny - 2 * nx);
+  EXPECT_EQ(sum, (nx * ny) - (2 * nx));
 }
 
 TEST_F(Field3DTest, Indexing) {
@@ -981,7 +956,7 @@ TEST_F(Field3DTest, IndexingInd3D) {
     }
   }
 
-  Ind3D ind{(2 * ny + 2) * nz + 2};
+  const Ind3D ind{(((2 * ny) + 2) * nz) + 2};
 
   EXPECT_DOUBLE_EQ(field[ind], 6);
 }
@@ -1001,7 +976,7 @@ TEST_F(Field3DTest, ConstIndexingInd3D) {
 
   const Field3D field2{field1};
 
-  Ind3D ind{(2 * ny + 2) * nz + 2};
+  const Ind3D ind{(((2 * ny) + 2) * nz) + 2};
 
   EXPECT_DOUBLE_EQ(field2[ind], 6);
 }
@@ -1012,7 +987,7 @@ TEST_F(Field3DTest, IndexingInd2D) {
   int ix = 1, iy = 2, iz = 3;
   field(ix, iy, iz) = sentinel;
 
-  Ind2D ind{iy + ny * ix, ny, 1};
+  const Ind2D ind{iy + (ny * ix), ny, 1};
   EXPECT_DOUBLE_EQ(field(ind, iz), sentinel);
   field(ind, iz) = -sentinel;
   EXPECT_DOUBLE_EQ(field(ix, iy, iz), -sentinel);
@@ -1024,7 +999,7 @@ TEST_F(Field3DTest, ConstIndexingInd2D) {
   int ix = 1, iy = 2, iz = 3;
   field(ix, iy, iz) = sentinel;
 
-  Ind2D ind{iy + ny * ix, ny, 1};
+  const Ind2D ind{iy + (ny * ix), ny, 1};
   const Field3D field2{field};
 
   EXPECT_DOUBLE_EQ(field2(ind, iz), sentinel);
@@ -1036,7 +1011,7 @@ TEST_F(Field3DTest, IndexingIndPerp) {
   int ix = 1, iy = 2, iz = 3;
   field(ix, iy, iz) = sentinel;
 
-  IndPerp ind{iz + nz * ix, 1, nz};
+  const IndPerp ind{iz + (nz * ix), 1, nz};
   EXPECT_DOUBLE_EQ(field(ind, iy), sentinel);
   field(ind, iy) = -sentinel;
   EXPECT_DOUBLE_EQ(field(ix, iy, iz), -sentinel);
@@ -1057,7 +1032,7 @@ TEST_F(Field3DTest, IndexingToZPointer) {
 
   for (int i = 0; i < nx; ++i) {
     for (int j = 0; j < ny; ++j) {
-      auto tmp = field(i, j);
+      auto* tmp = field(i, j);
       for (int k = 0; k < nz; ++k) {
         EXPECT_EQ(tmp[k], i + j + k);
         tmp[k] = -1.0;
@@ -1086,7 +1061,7 @@ TEST_F(Field3DTest, ConstIndexingToZPointer) {
 
   for (int i = 0; i < nx; ++i) {
     for (int j = 0; j < ny; ++j) {
-      auto tmp = field(i, j);
+      const auto* tmp = field(i, j);
       for (int k = 0; k < nz; ++k) {
         EXPECT_EQ(tmp[k], 1.0);
         field2(i, j, k) = tmp[k];
@@ -1259,15 +1234,15 @@ TEST_F(Field3DTest, CreateFromBoutReal) {
 }
 
 TEST_F(Field3DTest, CreateFromField3D) {
-  Field3D field(99.0);
-  Field3D result(field);
+  const Field3D field(99.0);
+  const Field3D result(field);
 
   EXPECT_TRUE(IsFieldEqual(result, 99.0));
 }
 
 TEST_F(Field3DTest, CreateFromField2D) {
-  Field2D field(99.0);
-  Field3D result(field);
+  const Field2D field(99.0);
+  const Field3D result(field);
 
   EXPECT_TRUE(IsFieldEqual(result, 99.0));
 }
@@ -1289,7 +1264,7 @@ TEST_F(Field3DTest, AssignFromInvalid) {
 
 TEST_F(Field3DTest, AssignFromField2D) {
   Field3D field;
-  Field2D field2(2.0);
+  const Field2D field2(2.0);
 
   field = field2;
 
@@ -2053,10 +2028,7 @@ TEST_F(Field3DTest, Field3DParallelAssignmentFromLazyExprDiscardsSlicesWhenNotFc
 }
 
 #if CHECK >= 2
-TEST_F(Field3DTest, Field3DParallelAssignmentFromLazyExprRequiresField3DSlicesInFci) {
-  mesh->getCoordinates()->setParallelTransform(
-      bout::utils::make_unique<MockFciParallelTransform>(*mesh));
-
+TEST_F(Field3DTestFCI, Field3DParallelAssignmentFromLazyExprRequiresField3DSlicesInFci) {
   Field3DParallel parallel;
   Field3D field;
 
@@ -2069,10 +2041,7 @@ TEST_F(Field3DTest, Field3DParallelAssignmentFromLazyExprRequiresField3DSlicesIn
 }
 #endif
 
-TEST_F(Field3DTest, Field3DParallelAssignmentFromLazyExprUsesField3DSlicesInFci) {
-  mesh->getCoordinates()->setParallelTransform(
-      bout::utils::make_unique<MockFciParallelTransform>(*mesh));
-
+TEST_F(Field3DTestFCI, Field3DParallelAssignmentFromLazyExprUsesField3DSlicesInFci) {
   Field3DParallel parallel;
   Field3D field;
 
@@ -2093,10 +2062,7 @@ TEST_F(Field3DTest, Field3DParallelAssignmentFromLazyExprUsesField3DSlicesInFci)
   EXPECT_TRUE(IsFieldEqual(result.ydown(), 15.0));
 }
 
-TEST_F(Field3DTest, Field3DParallelAssignmentFromField3DExprUsesSlicesInFci) {
-  mesh->getCoordinates()->setParallelTransform(
-      bout::utils::make_unique<MockFciParallelTransform>(*mesh));
-
+TEST_F(Field3DTestFCI, Field3DParallelAssignmentFromField3DExprUsesSlicesInFci) {
   Field3D lhs;
   Field3D rhs;
 
@@ -2118,10 +2084,7 @@ TEST_F(Field3DTest, Field3DParallelAssignmentFromField3DExprUsesSlicesInFci) {
   EXPECT_TRUE(IsFieldEqual(result.ydown(), 44.0));
 }
 
-TEST_F(Field3DTest, Field3DParallelAssignmentFromScalarExprUsesSlicesInFci) {
-  mesh->getCoordinates()->setParallelTransform(
-      bout::utils::make_unique<MockFciParallelTransform>(*mesh));
-
+TEST_F(Field3DTestFCI, Field3DParallelAssignmentFromScalarExprUsesSlicesInFci) {
   Field3DParallel parallel;
   parallel = 2.0;
   parallel.yup() = 3.0;
@@ -2133,649 +2096,649 @@ TEST_F(Field3DTest, Field3DParallelAssignmentFromScalarExprUsesSlicesInFci) {
   EXPECT_TRUE(IsFieldEqual(result, 3.0));
   EXPECT_TRUE(IsFieldEqual(result.yup(), 4.0));
   EXPECT_TRUE(IsFieldEqual(result.ydown(), 5.0));
+}
 
-  TEST_F(Field3DTestFCI, MulField3DParallelPreservesParallelSlices) {
-    Field3D field;
-    EXPECT_TRUE(field.isFci());
-
-    field = 2.0;
-    field.splitParallelSlices();
-    field.yup() = 3.0;
-    field.ydown() = 4.0;
-    field.resetRegionParallel();
-
-    Field3D rhs;
-    EXPECT_TRUE(rhs.isFci());
-    rhs = 3.0;
-    rhs.splitParallelSlices();
-    rhs.yup() = 4.0;
-    rhs.ydown() = 5.0;
-    rhs.resetRegionParallel();
-
-    const Field3D prod = field * rhs;
-
-    EXPECT_FALSE(prod.hasParallelSlices());
-    EXPECT_TRUE(IsFieldEqual(prod, 6.0));
-
-    const Field3DParallel prodpar = field.asField3DParallel() * rhs;
-    EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(prodpar)>, Field3DParallel>));
-    EXPECT_TRUE(prodpar.hasParallelSlices());
-    EXPECT_TRUE(IsFieldEqual(prodpar, 6.0));
-    EXPECT_TRUE(IsFieldEqual(prodpar.yup(), 12.0, "RGN_YPAR_+1"));
-    EXPECT_TRUE(IsFieldEqual(prodpar.ydown(), 20.0, "RGN_YPAR_-1"));
-  }
+TEST_F(Field3DTestFCI, MulField3DParallelPreservesParallelSlices) {
+  Field3D field;
+  EXPECT_TRUE(field.isFci());
 
-  TEST_F(Field3DTest, Abs) {
-    Field3D field;
+  field = 2.0;
+  field.splitParallelSlices();
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+  field.resetRegionParallel();
 
-    field = -31.0;
-    EXPECT_TRUE(IsFieldEqual(abs(field), 31.0));
-  }
+  Field3D rhs;
+  EXPECT_TRUE(rhs.isFci());
+  rhs = 3.0;
+  rhs.splitParallelSlices();
+  rhs.yup() = 4.0;
+  rhs.ydown() = 5.0;
+  rhs.resetRegionParallel();
 
-  TEST_F(Field3DTest, AbsExpressionUsesAbsOp) {
-    Field3D field;
+  const Field3D prod = field * rhs;
 
-    field = -2.0;
-    const auto expr = field + 1.0;
+  EXPECT_FALSE(prod.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(prod, 6.0));
 
-    EXPECT_TRUE(
-        (std::is_same_v<std::decay_t<decltype(abs(expr))>,
-                        BinaryExpr<Field3D, std::decay_t<decltype(expr)>,
-                                   std::decay_t<decltype(expr)>, bout::op::abs>>));
-    EXPECT_TRUE(IsFieldEqual(abs(expr), 1.0));
-    EXPECT_TRUE(IsFieldEqual(abs(expr, "RGN_ALL"), 1.0));
-  }
+  const Field3DParallel prodpar = field.asField3DParallel() * rhs;
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(prodpar)>, Field3DParallel>));
+  EXPECT_TRUE(prodpar.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(prodpar, 6.0));
+  EXPECT_TRUE(IsFieldEqual(prodpar.yup(), 12.0, "RGN_YPAR_+1"));
+  EXPECT_TRUE(IsFieldEqual(prodpar.ydown(), 20.0, "RGN_YPAR_-1"));
+}
 
-  TEST_F(Field3DTest, RegionLimitedExpressionConstructsField3D) {
-    Field3D field;
+TEST_F(Field3DTest, Abs) {
+  Field3D field;
 
-    field = -31.0;
+  field = -31.0;
+  EXPECT_TRUE(IsFieldEqual(abs(field), 31.0));
+}
 
-    Field3D result = abs(field, "RGN_NOBNDRY");
+TEST_F(Field3DTest, AbsExpressionUsesAbsOp) {
+  Field3D field;
 
-    EXPECT_TRUE(IsFieldEqual(result, 31.0, "RGN_NOBNDRY"));
-  }
+  field = -2.0;
+  const auto expr = field + 1.0;
 
-  TEST_F(Field3DTest, Exp) {
-    Field3D field;
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(abs(expr))>,
+                              BinaryExpr<Field3D, std::decay_t<decltype(expr)>,
+                                         std::decay_t<decltype(expr)>, bout::op::abs>>));
+  EXPECT_TRUE(IsFieldEqual(abs(expr), 1.0));
+  EXPECT_TRUE(IsFieldEqual(abs(expr, "RGN_ALL"), 1.0));
+}
 
-    field = 2.5;
-    const BoutReal expected = 12.182493960703473;
-    EXPECT_TRUE(IsFieldEqual(exp(field), expected));
-  }
+TEST_F(Field3DTest, RegionLimitedExpressionConstructsField3D) {
+  Field3D field;
 
-  TEST_F(Field3DTest, Log) {
-    Field3D field;
+  field = -31.0;
 
-    field = 12.182493960703473;
-    const BoutReal expected = 2.5;
-    EXPECT_TRUE(IsFieldEqual(log(field), expected));
-  }
+  Field3D result = abs(field, "RGN_NOBNDRY");
 
-  TEST_F(Field3DTest, LogExp) {
-    Field3D field;
+  EXPECT_TRUE(IsFieldEqual(result, 31.0, "RGN_NOBNDRY"));
+}
 
-    field = 2.5;
-    const BoutReal expected = 2.5;
-    EXPECT_TRUE(IsFieldEqual(log(exp(field)), expected));
-  }
+TEST_F(Field3DTest, Exp) {
+  Field3D field;
 
-  TEST_F(Field3DTest, Sin) {
-    Field3D field;
+  field = 2.5;
+  const BoutReal expected = 12.182493960703473;
+  EXPECT_TRUE(IsFieldEqual(exp(field), expected));
+}
 
-    field = PI / 2.0;
-    EXPECT_TRUE(IsFieldEqual(sin(field), 1.0));
+TEST_F(Field3DTest, Log) {
+  Field3D field;
 
-    field = PI;
-    EXPECT_TRUE(IsFieldEqual(sin(field), 0.0));
-  }
+  field = 12.182493960703473;
+  const BoutReal expected = 2.5;
+  EXPECT_TRUE(IsFieldEqual(log(field), expected));
+}
 
-  TEST_F(Field3DTest, Cos) {
-    Field3D field;
+TEST_F(Field3DTest, LogExp) {
+  Field3D field;
 
-    field = PI / 2.0;
-    EXPECT_TRUE(IsFieldEqual(cos(field), 0.0));
+  field = 2.5;
+  const BoutReal expected = 2.5;
+  EXPECT_TRUE(IsFieldEqual(log(exp(field)), expected));
+}
 
-    field = PI;
-    EXPECT_TRUE(IsFieldEqual(cos(field), -1.0));
-  }
+TEST_F(Field3DTest, Sin) {
+  Field3D field;
 
-  TEST_F(Field3DTest, Tan) {
-    Field3D field;
+  field = PI / 2.0;
+  EXPECT_TRUE(IsFieldEqual(sin(field), 1.0));
 
-    field = PI / 4.0;
-    EXPECT_TRUE(IsFieldEqual(tan(field), 1.0));
+  field = PI;
+  EXPECT_TRUE(IsFieldEqual(sin(field), 0.0));
+}
 
-    field = PI;
-    EXPECT_TRUE(IsFieldEqual(tan(field), 0.0));
-  }
+TEST_F(Field3DTest, Cos) {
+  Field3D field;
 
-  TEST_F(Field3DTest, Sinh) {
-    Field3D field;
+  field = PI / 2.0;
+  EXPECT_TRUE(IsFieldEqual(cos(field), 0.0));
 
-    field = 1.0;
-    const BoutReal expected = 1.1752011936438014;
-    EXPECT_TRUE(IsFieldEqual(sinh(field), expected));
+  field = PI;
+  EXPECT_TRUE(IsFieldEqual(cos(field), -1.0));
+}
 
-    field = -1.0;
-    EXPECT_TRUE(IsFieldEqual(sinh(field), -expected));
-  }
+TEST_F(Field3DTest, Tan) {
+  Field3D field;
 
-  TEST_F(Field3DTest, Cosh) {
-    Field3D field;
+  field = PI / 4.0;
+  EXPECT_TRUE(IsFieldEqual(tan(field), 1.0));
 
-    field = 1.0;
-    const BoutReal expected = 1.5430806348152437;
-    EXPECT_TRUE(IsFieldEqual(cosh(field), expected));
+  field = PI;
+  EXPECT_TRUE(IsFieldEqual(tan(field), 0.0));
+}
 
-    field = -1.0;
-    EXPECT_TRUE(IsFieldEqual(cosh(field), expected));
-  }
+TEST_F(Field3DTest, Sinh) {
+  Field3D field;
 
-  TEST_F(Field3DTest, Tanh) {
-    Field3D field;
+  field = 1.0;
+  const BoutReal expected = 1.1752011936438014;
+  EXPECT_TRUE(IsFieldEqual(sinh(field), expected));
 
-    field = 1.0;
-    const BoutReal expected = 0.761594155955764;
-    EXPECT_TRUE(IsFieldEqual(tanh(field), expected));
+  field = -1.0;
+  EXPECT_TRUE(IsFieldEqual(sinh(field), -expected));
+}
 
-    field = -1.0;
-    EXPECT_TRUE(IsFieldEqual(tanh(field), -expected));
-  }
+TEST_F(Field3DTest, Cosh) {
+  Field3D field;
 
-  TEST_F(Field3DTest, Floor) {
-    Field3D field;
+  field = 1.0;
+  const BoutReal expected = 1.5430806348152437;
+  EXPECT_TRUE(IsFieldEqual(cosh(field), expected));
 
-    field = 50.0;
-    field(1, 1, 1) = 49.9;
-    field(2, 3, 4) = -20;
+  field = -1.0;
+  EXPECT_TRUE(IsFieldEqual(cosh(field), expected));
+}
 
-    const BoutReal floor_value = 50.0;
+TEST_F(Field3DTest, Tanh) {
+  Field3D field;
 
-    EXPECT_TRUE(IsFieldEqual(floor(field, floor_value), floor_value));
-  }
+  field = 1.0;
+  const BoutReal expected = 0.761594155955764;
+  EXPECT_TRUE(IsFieldEqual(tanh(field), expected));
 
-  TEST_F(Field3DTest, Min) {
-    Field3D field;
+  field = -1.0;
+  EXPECT_TRUE(IsFieldEqual(tanh(field), -expected));
+}
 
-    field = 50.0;
-    field(0, 0, 0) = -99.0;
-    field(1, 1, 1) = 60.0;
-    field(1, 2, 2) = 40.0;
-    field(2, 4, 3) = 99.0;
+TEST_F(Field3DTest, Floor) {
+  Field3D field;
 
-    // min doesn't include guard cells
-    const BoutReal min_value = 40.0;
+  field = 50.0;
+  field(1, 1, 1) = 49.9;
+  field(2, 3, 4) = -20;
 
-    EXPECT_EQ(min(field, false), min_value);
-    EXPECT_EQ(min(field, false, "RGN_ALL"), -99.0);
-    EXPECT_EQ(min(field, true, "RGN_ALL"), -99.0);
-  }
+  const BoutReal floor_value = 50.0;
 
-  TEST_F(Field3DTest, MinBinaryExpr) {
-    Field3D field;
+  EXPECT_TRUE(IsFieldEqual(floor(field, floor_value), floor_value));
+}
 
-    field = 50.0;
-    field(0, 0, 0) = -99.0;
-    field(1, 1, 1) = 60.0;
-    field(1, 2, 2) = 40.0;
-    field(2, 4, 3) = 99.0;
+TEST_F(Field3DTest, Min) {
+  Field3D field;
 
-    const auto expr = field / 2.0 - 5.0;
+  field = 50.0;
+  field(0, 0, 0) = -99.0;
+  field(1, 1, 1) = 60.0;
+  field(1, 2, 2) = 40.0;
+  field(2, 4, 3) = 99.0;
 
-    EXPECT_EQ(min(expr, false), 15.0);
-    EXPECT_EQ(min(expr, false, "RGN_ALL"), -54.5);
-  }
+  // min doesn't include guard cells
+  const BoutReal min_value = 40.0;
 
-  TEST_F(Field3DTest, Max) {
-    Field3D field;
+  EXPECT_EQ(min(field, false), min_value);
+  EXPECT_EQ(min(field, false, "RGN_ALL"), -99.0);
+  EXPECT_EQ(min(field, true, "RGN_ALL"), -99.0);
+}
 
-    field = 50.0;
-    field(0, 0, 0) = -99.0;
-    field(1, 1, 1) = 40.0;
-    field(1, 2, 2) = 60.0;
-    field(2, 4, 3) = 99.0;
+TEST_F(Field3DTest, MinBinaryExpr) {
+  Field3D field;
 
-    // max doesn't include guard cells
-    const BoutReal max_value = 60.0;
+  field = 50.0;
+  field(0, 0, 0) = -99.0;
+  field(1, 1, 1) = 60.0;
+  field(1, 2, 2) = 40.0;
+  field(2, 4, 3) = 99.0;
 
-    EXPECT_EQ(max(field, false), max_value);
-    EXPECT_EQ(max(field, false, "RGN_ALL"), 99.0);
-    EXPECT_EQ(max(field, true, "RGN_ALL"), 99.0);
-  }
+  const auto expr = field / 2.0 - 5.0;
 
-  TEST_F(Field3DTest, MaxBinaryExpr) {
-    Field3D field;
+  EXPECT_EQ(min(expr, false), 15.0);
+  EXPECT_EQ(min(expr, false, "RGN_ALL"), -54.5);
+}
 
-    field = 50.0;
-    field(0, 0, 0) = -99.0;
-    field(1, 1, 1) = 40.0;
-    field(1, 2, 2) = 60.0;
-    field(2, 4, 3) = 99.0;
+TEST_F(Field3DTest, Max) {
+  Field3D field;
 
-    const auto expr = field / 2.0 - 5.0;
+  field = 50.0;
+  field(0, 0, 0) = -99.0;
+  field(1, 1, 1) = 40.0;
+  field(1, 2, 2) = 60.0;
+  field(2, 4, 3) = 99.0;
 
-    EXPECT_EQ(max(expr, false), 25.0);
-    EXPECT_EQ(max(expr, false, "RGN_ALL"), 44.5);
-  }
+  // max doesn't include guard cells
+  const BoutReal max_value = 60.0;
 
-  TEST_F(Field3DTest, Mean) {
-    Field3D field;
+  EXPECT_EQ(max(field, false), max_value);
+  EXPECT_EQ(max(field, false, "RGN_ALL"), 99.0);
+  EXPECT_EQ(max(field, true, "RGN_ALL"), 99.0);
+}
 
-    field = 50.0;
-    field(0, 0, 0) = 1.0;
-    field(1, 1, 1) = 40.0;
-    field(1, 2, 2) = 60.0;
-    field(2, 4, 3) = 109.0;
+TEST_F(Field3DTest, MaxBinaryExpr) {
+  Field3D field;
 
-    // mean doesn't include guard cells by default
-    const int npoints_all = nx * ny * nz;
-    const BoutReal mean_value_nobndry = 50.0;
-    const BoutReal mean_value_all = 50.0 + 10.0 / npoints_all;
+  field = 50.0;
+  field(0, 0, 0) = -99.0;
+  field(1, 1, 1) = 40.0;
+  field(1, 2, 2) = 60.0;
+  field(2, 4, 3) = 99.0;
 
-    EXPECT_EQ(mean(field, false), mean_value_nobndry);
-    EXPECT_EQ(mean(field, false, "RGN_ALL"), mean_value_all);
-    EXPECT_EQ(mean(field, true, "RGN_ALL"), mean_value_all);
-  }
+  const auto expr = field / 2.0 - 5.0;
 
-  TEST_F(Field3DTest, MeanBinaryExpr) {
-    Field3D field;
+  EXPECT_EQ(max(expr, false), 25.0);
+  EXPECT_EQ(max(expr, false, "RGN_ALL"), 44.5);
+}
 
-    field = 50.0;
-    field(0, 0, 0) = 1.0;
-    field(1, 1, 1) = 40.0;
-    field(1, 2, 2) = 60.0;
-    field(2, 4, 3) = 109.0;
+TEST_F(Field3DTest, Mean) {
+  Field3D field;
 
-    const int npoints_all = nx * ny * nz;
-    const BoutReal mean_value_nobndry = 103.0;
-    const BoutReal mean_value_all = 103.0 + 20.0 / npoints_all;
-    const auto expr = field * 2.0 + 3.0;
+  field = 50.0;
+  field(0, 0, 0) = 1.0;
+  field(1, 1, 1) = 40.0;
+  field(1, 2, 2) = 60.0;
+  field(2, 4, 3) = 109.0;
 
-    EXPECT_EQ(mean(expr, false), mean_value_nobndry);
-    EXPECT_EQ(mean(expr, false, "RGN_ALL"), mean_value_all);
-  }
+  // mean doesn't include guard cells by default
+  const int npoints_all = nx * ny * nz;
+  const BoutReal mean_value_nobndry = 50.0;
+  const BoutReal mean_value_all = 50.0 + 10.0 / npoints_all;
 
-  TEST_F(Field3DTest, DC) {
-    Field3D field;
+  EXPECT_EQ(mean(field, false), mean_value_nobndry);
+  EXPECT_EQ(mean(field, false, "RGN_ALL"), mean_value_all);
+  EXPECT_EQ(mean(field, true, "RGN_ALL"), mean_value_all);
+}
 
-    field = 1.0;
-    for (const auto& i : field) {
-      field[i] = i.z();
-    }
+TEST_F(Field3DTest, MeanBinaryExpr) {
+  Field3D field;
+
+  field = 50.0;
+  field(0, 0, 0) = 1.0;
+  field(1, 1, 1) = 40.0;
+  field(1, 2, 2) = 60.0;
+  field(2, 4, 3) = 109.0;
+
+  const int npoints_all = nx * ny * nz;
+  const BoutReal mean_value_nobndry = 103.0;
+  const BoutReal mean_value_all = 103.0 + 20.0 / npoints_all;
+  const auto expr = field * 2.0 + 3.0;
+
+  EXPECT_EQ(mean(expr, false), mean_value_nobndry);
+  EXPECT_EQ(mean(expr, false, "RGN_ALL"), mean_value_all);
+}
+
+TEST_F(Field3DTest, DC) {
+  Field3D field;
 
-    EXPECT_TRUE(IsFieldEqual(DC(field), 3.0));
+  field = 1.0;
+  for (const auto& i : field) {
+    field[i] = i.z();
   }
 
-  TEST_F(Field3DTest, Swap) {
-    WithQuietOutput quiet{output_info};
+  EXPECT_TRUE(IsFieldEqual(DC(field), 3.0));
+}
 
-    // First field
-    Field3D first(1., mesh_staggered);
+TEST_F(Field3DTest, Swap) {
+  WithQuietOutput quiet{output_info};
 
-    first.setLocation(CELL_XLOW);
+  // First field
+  Field3D first(1., mesh_staggered);
 
-    first.splitParallelSlices();
-    first.yup() = 1.5;
-    first.ydown() = 0.5;
+  first.setLocation(CELL_XLOW);
 
-    ddt(first) = 1.1;
+  first.splitParallelSlices();
+  first.yup() = 1.5;
+  first.ydown() = 0.5;
 
-    // Mesh for second field
-    constexpr int second_nx = Field3DTest::nx + 2;
-    constexpr int second_ny = Field3DTest::ny + 2;
-    constexpr int second_nz = Field3DTest::nz + 2;
+  ddt(first) = 1.1;
 
-    FakeMesh second_mesh{second_nx, second_ny, second_nz};
-    second_mesh.setCoordinates(nullptr);
-    second_mesh.StaggerGrids = false;
-    second_mesh.createDefaultRegions();
+  // Mesh for second field
+  constexpr int second_nx = Field3DTest::nx + 2;
+  constexpr int second_ny = Field3DTest::ny + 2;
+  constexpr int second_nz = Field3DTest::nz + 2;
 
-    // Second field
-    Field3D second(2., &second_mesh);
+  FakeMesh second_mesh{second_nx, second_ny, second_nz};
+  second_mesh.setCoordinates(nullptr);
+  second_mesh.StaggerGrids = false;
+  second_mesh.createDefaultRegions();
 
-    second.splitParallelSlices();
-    second.yup() = 2.2;
-    second.ydown() = 1.2;
+  // Second field
+  Field3D second(2., &second_mesh);
 
-    ddt(second) = 2.4;
+  second.splitParallelSlices();
+  second.yup() = 2.2;
+  second.ydown() = 1.2;
 
-    // Basic sanity check
-    EXPECT_TRUE(IsFieldEqual(first, 1.0));
-    EXPECT_TRUE(IsFieldEqual(second, 2.0));
+  ddt(second) = 2.4;
 
-    // swap is marked noexcept, so absolutely should not throw!
-    ASSERT_NO_THROW(swap(first, second));
+  // Basic sanity check
+  EXPECT_TRUE(IsFieldEqual(first, 1.0));
+  EXPECT_TRUE(IsFieldEqual(second, 2.0));
 
-    // Values
-    EXPECT_TRUE(IsFieldEqual(first, 2.0));
-    EXPECT_TRUE(IsFieldEqual(second, 1.0));
+  // swap is marked noexcept, so absolutely should not throw!
+  ASSERT_NO_THROW(swap(first, second));
 
-    EXPECT_TRUE(IsFieldEqual(first.yup(), 2.2));
-    EXPECT_TRUE(IsFieldEqual(first.ydown(), 1.2));
+  // Values
+  EXPECT_TRUE(IsFieldEqual(first, 2.0));
+  EXPECT_TRUE(IsFieldEqual(second, 1.0));
 
-    EXPECT_TRUE(IsFieldEqual(second.yup(), 1.5));
-    EXPECT_TRUE(IsFieldEqual(second.ydown(), 0.5));
+  EXPECT_TRUE(IsFieldEqual(first.yup(), 2.2));
+  EXPECT_TRUE(IsFieldEqual(first.ydown(), 1.2));
 
-    EXPECT_TRUE(IsFieldEqual(ddt(first), 2.4));
-    EXPECT_TRUE(IsFieldEqual(ddt(second), 1.1));
+  EXPECT_TRUE(IsFieldEqual(second.yup(), 1.5));
+  EXPECT_TRUE(IsFieldEqual(second.ydown(), 0.5));
 
-    // Mesh properties
-    EXPECT_EQ(first.getMesh(), &second_mesh);
-    EXPECT_EQ(second.getMesh(), mesh_staggered);
+  EXPECT_TRUE(IsFieldEqual(ddt(first), 2.4));
+  EXPECT_TRUE(IsFieldEqual(ddt(second), 1.1));
 
-    EXPECT_EQ(first.getNx(), second_nx);
-    EXPECT_EQ(first.getNy(), second_ny);
-    EXPECT_EQ(first.getNz(), second_nz);
+  // Mesh properties
+  EXPECT_EQ(first.getMesh(), &second_mesh);
+  EXPECT_EQ(second.getMesh(), mesh_staggered);
 
-    EXPECT_EQ(second.getNx(), Field3DTest::nx);
-    EXPECT_EQ(second.getNy(), Field3DTest::ny);
-    EXPECT_EQ(second.getNz(), Field3DTest::nz);
+  EXPECT_EQ(first.getNx(), second_nx);
+  EXPECT_EQ(first.getNy(), second_ny);
+  EXPECT_EQ(first.getNz(), second_nz);
 
-    EXPECT_EQ(first.getLocation(), CELL_CENTRE);
-    EXPECT_EQ(second.getLocation(), CELL_XLOW);
+  EXPECT_EQ(second.getNx(), Field3DTest::nx);
+  EXPECT_EQ(second.getNy(), Field3DTest::ny);
+  EXPECT_EQ(second.getNz(), Field3DTest::nz);
 
-    // We don't check the boundaries, but the data is protected and
-    // there are no inquiry functions
-  }
+  EXPECT_EQ(first.getLocation(), CELL_CENTRE);
+  EXPECT_EQ(second.getLocation(), CELL_XLOW);
 
-  TEST_F(Field3DTest, MoveCtor) {
-    // First field
-    Field3D first(1., mesh_staggered);
+  // We don't check the boundaries, but the data is protected and
+  // there are no inquiry functions
+}
 
-    first.setLocation(CELL_XLOW);
+TEST_F(Field3DTest, MoveCtor) {
+  // First field
+  Field3D first(1., mesh_staggered);
 
-    first.splitParallelSlices();
-    first.yup() = 1.5;
-    first.ydown() = 0.5;
+  first.setLocation(CELL_XLOW);
 
-    ddt(first) = 1.1;
+  first.splitParallelSlices();
+  first.yup() = 1.5;
+  first.ydown() = 0.5;
 
-    // Second field
-    Field3D second{std::move(first)};
+  ddt(first) = 1.1;
 
-    // Values
-    EXPECT_TRUE(IsFieldEqual(second, 1.0));
+  // Second field
+  Field3D second{std::move(first)};
 
-    EXPECT_TRUE(IsFieldEqual(second.yup(), 1.5));
-    EXPECT_TRUE(IsFieldEqual(second.ydown(), 0.5));
+  // Values
+  EXPECT_TRUE(IsFieldEqual(second, 1.0));
 
-    EXPECT_TRUE(IsFieldEqual(ddt(second), 1.1));
+  EXPECT_TRUE(IsFieldEqual(second.yup(), 1.5));
+  EXPECT_TRUE(IsFieldEqual(second.ydown(), 0.5));
 
-    // Mesh properties
-    EXPECT_EQ(second.getMesh(), mesh_staggered);
+  EXPECT_TRUE(IsFieldEqual(ddt(second), 1.1));
 
-    EXPECT_EQ(second.getNx(), Field3DTest::nx);
-    EXPECT_EQ(second.getNy(), Field3DTest::ny);
-    EXPECT_EQ(second.getNz(), Field3DTest::nz);
+  // Mesh properties
+  EXPECT_EQ(second.getMesh(), mesh_staggered);
 
-    EXPECT_EQ(second.getLocation(), CELL_XLOW);
+  EXPECT_EQ(second.getNx(), Field3DTest::nx);
+  EXPECT_EQ(second.getNy(), Field3DTest::ny);
+  EXPECT_EQ(second.getNz(), Field3DTest::nz);
 
-    // We don't check the boundaries, but the data is protected and
-    // there are no inquiry functions
-  }
+  EXPECT_EQ(second.getLocation(), CELL_XLOW);
 
-  TEST_F(Field3DTest, FillField) {
-    Field3D f{mesh};
-
-    fillField(f, {{{1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.}},
-
-                  {{1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.}},
-
-                  {{1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.},
-                   {1., 1., 1., 1., 1., 1., 1.}}});
-
-    EXPECT_TRUE(IsFieldEqual(f, 1.));
-
-    fillField(f, {{{0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.}},
-
-                  {{0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.}},
-
-                  {{0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.},
-                   {0., 1., 2., 3., 4., 5., 6.}}});
-
-    Field3D g{mesh};
-    g.allocate();
-    BOUT_FOR_SERIAL(i, g.getRegion("RGN_ALL")) { g[i] = i.z(); }
-
-    EXPECT_TRUE(IsFieldEqual(f, g));
-  }
+  // We don't check the boundaries, but the data is protected and
+  // there are no inquiry functions
+}
 
-#if BOUT_HAS_FFTW
-  namespace bout {
-  namespace testing {
+TEST_F(Field3DTest, FillField) {
+  Field3D f{mesh};
 
-  // Amplitudes for the nth wavenumber
-  constexpr int k0{1};
-  constexpr int k1{2};
-  constexpr int k2{3};
+  fillField(f, {{{1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.}},
 
-  const BoutReal box_size{TWOPI / Field3DTest::nz};
+                {{1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.}},
 
-  // Helper function for the filter and lowpass tests
-  BoutReal zWaves(Field3D::ind_type& i) {
-    return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size)
-           + std::sin(k2 * i.z() * box_size);
-  }
-  } // namespace testing
-  } // namespace bout
+                {{1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.},
+                 {1., 1., 1., 1., 1., 1., 1.}}});
 
-  TEST_F(Field3DTest, Filter) {
+  EXPECT_TRUE(IsFieldEqual(f, 1.));
 
-    using namespace bout::testing;
+  fillField(f, {{{0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.}},
 
-    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+                {{0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.}},
 
-    auto expected = makeField<Field3D>(
-        [&](Field3D::ind_type& i) { return std::cos(k1 * i.z() * box_size); },
-        bout::globals::mesh);
+                {{0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.},
+                 {0., 1., 2., 3., 4., 5., 6.}}});
 
-    auto output = filter(input, 2);
+  Field3D g{mesh};
+  g.allocate();
+  BOUT_FOR_SERIAL(i, g.getRegion("RGN_ALL")) { g[i] = i.z(); }
 
-    EXPECT_TRUE(IsFieldEqual(output, expected));
-  }
+  EXPECT_TRUE(IsFieldEqual(f, g));
+}
 
-  TEST_F(Field3DTest, LowPassOneArg) {
+#if BOUT_HAS_FFTW
+namespace bout {
+namespace testing {
 
-    using namespace bout::testing;
+// Amplitudes for the nth wavenumber
+constexpr int k0{1};
+constexpr int k1{2};
+constexpr int k2{3};
 
-    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+const BoutReal box_size{TWOPI / Field3DTest::nz};
 
-    auto expected = makeField<Field3D>(
-        [&](Field3D::ind_type& i) {
-          return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
-        },
-        bout::globals::mesh);
+// Helper function for the filter and lowpass tests
+BoutReal zWaves(Field3D::ind_type& i) {
+  return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size)
+         + std::sin(k2 * i.z() * box_size);
+}
+} // namespace testing
+} // namespace bout
 
-    auto output = lowPass(input, 2);
+TEST_F(Field3DTest, Filter) {
 
-    EXPECT_TRUE(IsFieldEqual(output, expected));
-  }
+  using namespace bout::testing;
 
-  TEST_F(Field3DTest, LowPassOneArgNothing) {
+  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-    using namespace bout::testing;
+  auto expected = makeField<Field3D>(
+      [&](Field3D::ind_type& i) { return std::cos(k1 * i.z() * box_size); },
+      bout::globals::mesh);
 
-    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+  auto output = filter(input, 2);
 
-    auto output = lowPass(input, 20);
+  EXPECT_TRUE(IsFieldEqual(output, expected));
+}
 
-    EXPECT_TRUE(IsFieldEqual(output, input));
-  }
+TEST_F(Field3DTest, LowPassOneArg) {
 
-  TEST_F(Field3DTest, LowPassTwoArg) {
+  using namespace bout::testing;
 
-    using namespace bout::testing;
+  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+  auto expected = makeField<Field3D>(
+      [&](Field3D::ind_type& i) {
+        return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
+      },
+      bout::globals::mesh);
 
-    auto expected = makeField<Field3D>(
-        [&](Field3D::ind_type& i) {
-          return std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
-        },
-        bout::globals::mesh);
+  auto output = lowPass(input, 2);
 
-    auto output = lowPass(input, 2, false);
+  EXPECT_TRUE(IsFieldEqual(output, expected));
+}
 
-    EXPECT_TRUE(IsFieldEqual(output, expected));
+TEST_F(Field3DTest, LowPassOneArgNothing) {
 
-    // Check passing int still works
-    auto output2 = lowPass(input, 2, 0);
+  using namespace bout::testing;
 
-    EXPECT_TRUE(IsFieldEqual(output2, expected));
+  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-    // Calling lowPass with an int that is not 0 or 1 is an error
-    EXPECT_THROW(lowPass(input, 2, -1), BoutException);
-    EXPECT_THROW(lowPass(input, 2, 2), BoutException);
-  }
+  auto output = lowPass(input, 20);
 
-  TEST_F(Field3DTest, LowPassTwoArgKeepZonal) {
+  EXPECT_TRUE(IsFieldEqual(output, input));
+}
 
-    using namespace bout::testing;
+TEST_F(Field3DTest, LowPassTwoArg) {
 
-    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+  using namespace bout::testing;
 
-    auto expected = makeField<Field3D>(
-        [&](Field3D::ind_type& i) {
-          return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
-        },
-        bout::globals::mesh);
+  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-    auto output = lowPass(input, 2, true);
+  auto expected = makeField<Field3D>(
+      [&](Field3D::ind_type& i) {
+        return std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
+      },
+      bout::globals::mesh);
 
-    EXPECT_TRUE(IsFieldEqual(output, expected));
+  auto output = lowPass(input, 2, false);
 
-    // Check passing int still works
-    auto output2 = lowPass(input, 2, 1);
+  EXPECT_TRUE(IsFieldEqual(output, expected));
 
-    EXPECT_TRUE(IsFieldEqual(output2, expected));
-  }
+  // Check passing int still works
+  auto output2 = lowPass(input, 2, 0);
 
-  TEST_F(Field3DTest, LowPassTwoArgNothing) {
+  EXPECT_TRUE(IsFieldEqual(output2, expected));
 
-    using namespace bout::testing;
+  // Calling lowPass with an int that is not 0 or 1 is an error
+  EXPECT_THROW(lowPass(input, 2, -1), BoutException);
+  EXPECT_THROW(lowPass(input, 2, 2), BoutException);
+}
 
-    auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
+TEST_F(Field3DTest, LowPassTwoArgKeepZonal) {
 
-    auto output = lowPass(input, 20, true);
+  using namespace bout::testing;
 
-    EXPECT_TRUE(IsFieldEqual(output, input));
-  }
-#endif
+  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-  TEST_F(Field3DTest, OperatorEqualsField3D) {
-    Field3D field;
+  auto expected = makeField<Field3D>(
+      [&](Field3D::ind_type& i) {
+        return 1.0 + std::sin(k0 * i.z() * box_size) + std::cos(k1 * i.z() * box_size);
+      },
+      bout::globals::mesh);
 
-    // Create field with non-default arguments so we can check they get copied
-    // to 'field'.
-    // Note that Average z-direction type is not really allowed for Field3D, but
-    // we don't check anywhere at the moment.
-    Field3D field2{
-        mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+  auto output = lowPass(input, 2, true);
 
-    field = field2;
+  EXPECT_TRUE(IsFieldEqual(output, expected));
 
-    EXPECT_TRUE(areFieldsCompatible(field, field2));
-    EXPECT_EQ(field.getMesh(), field2.getMesh());
-    EXPECT_EQ(field.getLocation(), field2.getLocation());
-    EXPECT_EQ(field.getDirectionY(), field2.getDirectionY());
-    EXPECT_EQ(field.getDirectionZ(), field2.getDirectionZ());
-  }
+  // Check passing int still works
+  auto output2 = lowPass(input, 2, 1);
 
-  TEST_F(Field3DTest, OperatorEqualsBinaryExprCopiesMetadata) {
-    Field3D source{
-        mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
-    source = 9.;
+  EXPECT_TRUE(IsFieldEqual(output2, expected));
+}
 
-    Field3D target(mesh_staggered);
-    target = 0.;
-    target.splitParallelSlices();
+TEST_F(Field3DTest, LowPassTwoArgNothing) {
 
-    target = sqrt(source);
+  using namespace bout::testing;
 
-    EXPECT_EQ(target.getMesh(), source.getMesh());
-    EXPECT_EQ(target.getLocation(), source.getLocation());
-    EXPECT_EQ(target.getDirectionY(), source.getDirectionY());
-    EXPECT_EQ(target.getDirectionZ(), source.getDirectionZ());
-    EXPECT_FALSE(target.hasParallelSlices());
-    EXPECT_TRUE(IsFieldEqual(target, 3.));
-  }
+  auto input = makeField<Field3D>(zWaves, bout::globals::mesh);
 
-  TEST_F(Field3DTest, EmptyFrom) {
-    // Create field with non-default arguments so we can check they get copied
-    // to 'field2'.
-    // Note that Average z-direction type is not really allowed for Field3D, but
-    // we don't check anywhere at the moment.
-    Field3D field{
-        mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
-    field = 5.;
-
-    Field3D field2{emptyFrom(field)};
-    EXPECT_EQ(field2.getMesh(), mesh_staggered);
-    EXPECT_EQ(field2.getLocation(), CELL_XLOW);
-    EXPECT_EQ(field2.getDirectionY(), YDirectionType::Aligned);
-    EXPECT_EQ(field2.getDirectionZ(), ZDirectionType::Average);
-    EXPECT_TRUE(field2.isAllocated());
-  }
+  auto output = lowPass(input, 20, true);
 
-  TEST_F(Field3DTest, ZeroFrom) {
-    // Create field with non-default arguments so we can check they get copied
-    // to 'field2'.
-    // Note that Average z-direction type is not really allowed for Field3D, but
-    // we don't check anywhere at the moment.
-    Field3D field{
-        mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
-    field = 5.;
-
-    Field3D field2{zeroFrom(field)};
-    EXPECT_EQ(field2.getMesh(), mesh_staggered);
-    EXPECT_EQ(field2.getLocation(), CELL_XLOW);
-    EXPECT_EQ(field2.getDirectionY(), YDirectionType::Aligned);
-    EXPECT_EQ(field2.getDirectionZ(), ZDirectionType::Average);
-    EXPECT_TRUE(field2.isAllocated());
-    EXPECT_TRUE(IsFieldEqual(field2, 0.));
-  }
+  EXPECT_TRUE(IsFieldEqual(output, input));
+}
+#endif
 
-  TEST_F(Field3DTest, Field3DParallel) {
-    Field3DParallel field(1.0);
-    field = 1.0;
+TEST_F(Field3DTest, OperatorEqualsField3D) {
+  Field3D field;
 
-    Field3D field2 = field;
+  // Create field with non-default arguments so we can check they get copied
+  // to 'field'.
+  // Note that Average z-direction type is not really allowed for Field3D, but
+  // we don't check anywhere at the moment.
+  Field3D field2{
+      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
 
-    auto& field3 = field.asField3D();
+  field = field2;
 
-    field *= 2;
+  EXPECT_TRUE(areFieldsCompatible(field, field2));
+  EXPECT_EQ(field.getMesh(), field2.getMesh());
+  EXPECT_EQ(field.getLocation(), field2.getLocation());
+  EXPECT_EQ(field.getDirectionY(), field2.getDirectionY());
+  EXPECT_EQ(field.getDirectionZ(), field2.getDirectionZ());
+}
+
+TEST_F(Field3DTest, OperatorEqualsBinaryExprCopiesMetadata) {
+  Field3D source{
+      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+  source = 9.;
+
+  Field3D target(mesh_staggered);
+  target = 0.;
+  target.splitParallelSlices();
+
+  target = sqrt(source);
+
+  EXPECT_EQ(target.getMesh(), source.getMesh());
+  EXPECT_EQ(target.getLocation(), source.getLocation());
+  EXPECT_EQ(target.getDirectionY(), source.getDirectionY());
+  EXPECT_EQ(target.getDirectionZ(), source.getDirectionZ());
+  EXPECT_FALSE(target.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(target, 3.));
+}
+
+TEST_F(Field3DTest, EmptyFrom) {
+  // Create field with non-default arguments so we can check they get copied
+  // to 'field2'.
+  // Note that Average z-direction type is not really allowed for Field3D, but
+  // we don't check anywhere at the moment.
+  Field3D field{
+      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+  field = 5.;
+
+  Field3D field2{emptyFrom(field)};
+  EXPECT_EQ(field2.getMesh(), mesh_staggered);
+  EXPECT_EQ(field2.getLocation(), CELL_XLOW);
+  EXPECT_EQ(field2.getDirectionY(), YDirectionType::Aligned);
+  EXPECT_EQ(field2.getDirectionZ(), ZDirectionType::Average);
+  EXPECT_TRUE(field2.isAllocated());
+}
+
+TEST_F(Field3DTest, ZeroFrom) {
+  // Create field with non-default arguments so we can check they get copied
+  // to 'field2'.
+  // Note that Average z-direction type is not really allowed for Field3D, but
+  // we don't check anywhere at the moment.
+  Field3D field{
+      mesh_staggered, CELL_XLOW, {YDirectionType::Aligned, ZDirectionType::Average}};
+  field = 5.;
+
+  Field3D field2{zeroFrom(field)};
+  EXPECT_EQ(field2.getMesh(), mesh_staggered);
+  EXPECT_EQ(field2.getLocation(), CELL_XLOW);
+  EXPECT_EQ(field2.getDirectionY(), YDirectionType::Aligned);
+  EXPECT_EQ(field2.getDirectionZ(), ZDirectionType::Average);
+  EXPECT_TRUE(field2.isAllocated());
+  EXPECT_TRUE(IsFieldEqual(field2, 0.));
+}
+
+TEST_F(Field3DTest, Field3DParallel) {
+  Field3DParallel field(1.0);
+  field = 1.0;
 
-    EXPECT_TRUE(IsFieldEqual(field, 2.0));
-    EXPECT_TRUE(IsFieldEqual(field2, 1.0));
-    EXPECT_TRUE(IsFieldEqual(field3, 2.0));
+  Field3D field2 = field;
 
-    field3.asField3DParallel() *= 3;
+  auto& field3 = field.asField3D();
 
-    EXPECT_TRUE(IsFieldEqual(field3, 6.0));
-  }
+  field *= 2;
+
+  EXPECT_TRUE(IsFieldEqual(field, 2.0));
+  EXPECT_TRUE(IsFieldEqual(field2, 1.0));
+  EXPECT_TRUE(IsFieldEqual(field3, 2.0));
+
+  field3.asField3DParallel() *= 3;
+
+  EXPECT_TRUE(IsFieldEqual(field3, 6.0));
+}
 
 // Restore compiler warnings
 #pragma GCC diagnostic pop

From ceaaf980e6079f0370924c3ea91769b45df3c97d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 9 Jul 2026 11:54:06 +0200
Subject: [PATCH 1622/1827] Functions of Field3DParallel preserve slices

More unit tests
---
 include/bout/field.hxx            | 119 ++++++++--------
 include/bout/fieldops.hxx         |   2 +
 src/field/field3d.cxx             |   5 +
 tests/unit/field/test_field3d.cxx | 222 +++++++++++++++++++++++++++++-
 4 files changed, 289 insertions(+), 59 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index b39a82eb0b..b20e8915e9 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -608,6 +608,20 @@ class Field3DParallel;
 class FieldPerp;
 
 namespace bout::detail {
+template <typename T>
+using UnaryFieldResult_t =
+    std::conditional_t<std::is_same_v<std::decay_t<T>, ::Field3DParallel>, ::Field3D,
+                       std::decay_t<T>>;
+
+template <typename T>
+std::optional<size_t> getUnaryRegionID(const Mesh* mesh, const std::string& region_name) {
+  if constexpr (std::is_same_v<UnaryFieldResult_t<T>, ::Field3D>) {
+    return bout::detail::getField3DRegionID(mesh, region_name);
+  } else {
+    return std::nullopt;
+  }
+}
+
 template <typename T>
 std::optional<int> getPerpYIndex(const T& value) {
   if constexpr (std::is_same_v<std::decay_t<T>, ::FieldPerp>) {
@@ -641,35 +655,23 @@ std::optional<int> getPerpYIndex(const BinaryExpr<ResT, L, R, Func>& expr) {
   };                                                                                    \
   template <typename T, typename = bout::utils::EnableIfField<T>>                       \
   inline auto name(const T& f, const std::string& rgn = "RGN_ALL") {                    \
-    if constexpr (std::is_same_v<T, Field3DParallel>) {                                 \
-      /* Check if the input is allocated */                                             \
-      checkData(f);                                                                     \
-      /* Define and allocate the output result */                                       \
-      T result{emptyFrom(f)};                                                           \
-      BOUT_FOR(d, result.getRegion(rgn)) { result[d] = func(f[d]); }                    \
-      for (int i = 0; i < f.numberParallelSlices(); ++i) {                              \
-        result.yup(i) = func(f.yup(i));                                                 \
-        result.ydown(i) = func(f.ydown(i));                                             \
-      }                                                                                 \
-      result.name = std::string(#name "(") + f.name + std::string(")");                 \
-      checkData(result);                                                                \
-      return result;                                                                    \
-    } else {                                                                            \
-      return BinaryExpr<T, T, T, bout::op::name>{static_cast<typename T::View>(f),      \
-                                                 static_cast<typename T::View>(f),      \
-                                                 bout::op::name{},                      \
-                                                 f.getMesh(),                           \
-                                                 f.getLocation(),                       \
-                                                 f.getDirections(),                     \
-                                                 std::nullopt,                          \
-                                                 f.getRegion(rgn),                      \
-                                                 bout::detail::getPerpYIndex(f)};       \
-    }                                                                                   \
+    using ResT = bout::detail::UnaryFieldResult_t<T>;                                   \
+    return BinaryExpr<ResT, T, T, bout::op::name>{                                      \
+        static_cast<typename T::View>(f),                                               \
+        static_cast<typename T::View>(f),                                               \
+        bout::op::name{},                                                               \
+        f.getMesh(),                                                                    \
+        f.getLocation(),                                                                \
+        f.getDirections(),                                                              \
+        bout::detail::getUnaryRegionID<T>(f.getMesh(), rgn),                            \
+        f.getMesh()->template getRegion<ResT>(rgn),                                     \
+        bout::detail::getPerpYIndex(f)};                                                \
   }                                                                                     \
   template <typename ResT, typename L, typename R, typename Func>                       \
   inline auto name(const BinaryExpr<ResT, L, R, Func>& f) {                             \
-    return BinaryExpr<ResT, BinaryExpr<ResT, L, R, Func>, BinaryExpr<ResT, L, R, Func>, \
-                      bout::op::name>{                                                  \
+    using UnaryResT = bout::detail::UnaryFieldResult_t<ResT>;                           \
+    return BinaryExpr<UnaryResT, BinaryExpr<ResT, L, R, Func>,                          \
+                      BinaryExpr<ResT, L, R, Func>, bout::op::name>{                    \
         static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),                    \
         static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),                    \
         bout::op::name{},                                                               \
@@ -682,7 +684,18 @@ std::optional<int> getPerpYIndex(const BinaryExpr<ResT, L, R, Func>& expr) {
   }                                                                                     \
   template <typename ResT, typename L, typename R, typename Func>                       \
   inline auto name(const BinaryExpr<ResT, L, R, Func>& f, const std::string& rgn) {     \
-    return name(ResT{f}, rgn);                                                          \
+    using UnaryResT = bout::detail::UnaryFieldResult_t<ResT>;                           \
+    return BinaryExpr<UnaryResT, BinaryExpr<ResT, L, R, Func>,                          \
+                      BinaryExpr<ResT, L, R, Func>, bout::op::name>{                    \
+        static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),                    \
+        static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),                    \
+        bout::op::name{},                                                               \
+        f.getMesh(),                                                                    \
+        f.getLocation(),                                                                \
+        f.getDirections(),                                                              \
+        bout::detail::getUnaryRegionID<UnaryResT>(f.getMesh(), rgn),                    \
+        f.getMesh()->template getRegion<UnaryResT>(rgn),                                \
+        bout::detail::getPerpYIndex(f)};                                                \
   }
 #endif
 
@@ -698,36 +711,23 @@ struct Square {
 
 template <typename T, typename = bout::utils::EnableIfField<T>>
 inline auto SQ(const T& f, const std::string& rgn = "RGN_ALL") {
-  if constexpr (std::is_same_v<T, Field3DParallel>) {
-    checkData(f);
-    T result{emptyFrom(f)};
-    if (f.hasParallelSlices() and !result.hasParallelSlices()) {
-      result.splitParallelSlices();
-    }
-    BOUT_FOR(d, result.getRegion(rgn)) { result[d] = ::SQ(f[d]); }
-    for (size_t i = 0; i < f.numberParallelSlices(); ++i) {
-      result.yup(i) = SQ(f.yup(i), rgn);
-      result.ydown(i) = SQ(f.ydown(i), rgn);
-    }
-    result.name = std::string("SQ(") + f.name + std::string(")");
-    checkData(result);
-    return result;
-  } else {
-    return BinaryExpr<T, T, T, bout::op::Square>{static_cast<typename T::View>(f),
-                                                 static_cast<typename T::View>(f),
-                                                 bout::op::Square{},
-                                                 f.getMesh(),
-                                                 f.getLocation(),
-                                                 f.getDirections(),
-                                                 std::nullopt,
-                                                 f.getRegion(rgn),
-                                                 bout::detail::getPerpYIndex(f)};
-  }
+  using ResT = bout::detail::UnaryFieldResult_t<T>;
+  return BinaryExpr<ResT, T, T, bout::op::Square>{
+      static_cast<typename T::View>(f),
+      static_cast<typename T::View>(f),
+      bout::op::Square{},
+      f.getMesh(),
+      f.getLocation(),
+      f.getDirections(),
+      bout::detail::getUnaryRegionID<T>(f.getMesh(), rgn),
+      f.getMesh()->template getRegion<ResT>(rgn),
+      bout::detail::getPerpYIndex(f)};
 }
 
 template <typename ResT, typename L, typename R, typename Func>
 inline auto SQ(const BinaryExpr<ResT, L, R, Func>& f) {
-  return BinaryExpr<ResT, BinaryExpr<ResT, L, R, Func>, BinaryExpr<ResT, L, R, Func>,
+  using UnaryResT = bout::detail::UnaryFieldResult_t<ResT>;
+  return BinaryExpr<UnaryResT, BinaryExpr<ResT, L, R, Func>, BinaryExpr<ResT, L, R, Func>,
                     bout::op::Square>{
       static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),
       static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),
@@ -742,7 +742,18 @@ inline auto SQ(const BinaryExpr<ResT, L, R, Func>& f) {
 
 template <typename ResT, typename L, typename R, typename Func>
 inline auto SQ(const BinaryExpr<ResT, L, R, Func>& f, const std::string& rgn) {
-  return SQ(ResT{f}, rgn);
+  using UnaryResT = bout::detail::UnaryFieldResult_t<ResT>;
+  return BinaryExpr<UnaryResT, BinaryExpr<ResT, L, R, Func>, BinaryExpr<ResT, L, R, Func>,
+                    bout::op::Square>{
+      static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),
+      static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(f),
+      bout::op::Square{},
+      f.getMesh(),
+      f.getLocation(),
+      f.getDirections(),
+      bout::detail::getUnaryRegionID<UnaryResT>(f.getMesh(), rgn),
+      f.getMesh()->template getRegion<UnaryResT>(rgn),
+      bout::detail::getPerpYIndex(f)};
 }
 
 /// Square root of \p f over region \p rgn
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index a09734ad21..52d2c82a13 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -12,6 +12,7 @@
 #include <cstddef>
 #include <limits>
 #include <optional>
+#include <string>
 #include <type_traits>
 
 #if BOUT_HAS_CUDA
@@ -29,6 +30,7 @@ namespace bout::detail {
 // It is used because Mesh is an incomplete type so methods cannot be called
 // in the template functions in this header file.
 const Region<Ind3D>& getField3DRegion(const Mesh* mesh, std::optional<size_t> regionID);
+size_t getField3DRegionID(const Mesh* mesh, const std::string& region_name);
 } // namespace bout::detail
 
 template <typename T>
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 8700096e24..5da438dcdf 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -936,6 +936,11 @@ const Region<Ind3D>& getField3DRegion(const Mesh* mesh, std::optional<size_t> re
   return mesh->getRegion("RGN_ALL");
 }
 
+size_t getField3DRegionID(const Mesh* mesh, const std::string& region_name) {
+  ASSERT1(mesh != nullptr);
+  return mesh->getRegionID(region_name);
+}
+
 } // namespace bout::detail
 
 void swap(Field3D& first, Field3D& second) noexcept {
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 173991a31d..38f51a8164 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -1977,11 +1977,16 @@ TEST_F(Field3DTest, SQField3DParallelPreservesParallelSlices) {
 
   const auto squared = SQ(field);
 
-  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(squared)>, Field3DParallel>));
-  EXPECT_TRUE(squared.hasParallelSlices());
-  EXPECT_TRUE(IsFieldEqual(squared, 4.0));
-  EXPECT_TRUE(IsFieldEqual(squared.yup(), 9.0));
-  EXPECT_TRUE(IsFieldEqual(squared.ydown(), 16.0));
+  EXPECT_TRUE((std::is_same_v<
+               std::decay_t<decltype(squared)>,
+               BinaryExpr<Field3D, Field3DParallel, Field3DParallel, bout::op::Square>>));
+
+  Field3DParallel result{squared};
+
+  EXPECT_FALSE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 4.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 9.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 16.0));
 }
 
 TEST_F(Field3DTest, Field3DParallelArithmeticReturnsLazyExpr) {
@@ -2098,6 +2103,127 @@ TEST_F(Field3DTestFCI, Field3DParallelAssignmentFromScalarExprUsesSlicesInFci) {
   EXPECT_TRUE(IsFieldEqual(result.ydown(), 5.0));
 }
 
+TEST_F(Field3DTestFCI, SqrtField3DParallelPreservesParallelSlices) {
+  Field3DParallel field;
+
+  field = 4.0;
+  field.splitParallelSlices();
+  field.yup() = 9.0;
+  field.ydown() = 16.0;
+  field.resetRegionParallel();
+
+  {
+    const auto expr = sqrt(field);
+
+    EXPECT_TRUE((std::is_same_v<
+                 std::decay_t<decltype(expr)>,
+                 BinaryExpr<Field3D, Field3DParallel, Field3DParallel, bout::op::sqrt>>));
+
+    const Field3DParallel res{expr};
+
+    EXPECT_TRUE(res.hasParallelSlices());
+    EXPECT_TRUE(IsFieldEqual(res, 2.0));
+    EXPECT_TRUE(IsFieldEqual(res.yup(), 3.0));
+    EXPECT_TRUE(IsFieldEqual(res.ydown(), 4.0));
+  }
+  {
+    const Field3D res = sqrt(field.asField3D());
+
+    EXPECT_FALSE(res.hasParallelSlices());
+  }
+}
+
+TEST_F(Field3DTestFCI, SqrtField3DParallelExprPreservesParallelSlices) {
+  Field3DParallel lhs;
+  Field3D rhs;
+
+  lhs = 3.0;
+  lhs.yup() = 8.0;
+  lhs.ydown() = 15.0;
+
+  rhs = 1.0;
+  rhs.splitParallelSlices();
+  rhs.yup() = 1.0;
+  rhs.ydown() = 1.0;
+
+  Field3DParallel result{sqrt(lhs + rhs)};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 2.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 3.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 4.0));
+}
+
+TEST_F(Field3DTestFCI, SqrtField3DParallelRegionExprPreservesParallelSlices) {
+  Field3DParallel lhs;
+  Field3D rhs;
+
+  lhs = 3.0;
+  lhs.yup() = 8.0;
+  lhs.ydown() = 15.0;
+
+  rhs = 1.0;
+  rhs.splitParallelSlices();
+  rhs.yup() = 1.0;
+  rhs.ydown() = 1.0;
+
+  const auto base = lhs + rhs;
+  const auto expr = sqrt(base, "RGN_ALL");
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(expr)>,
+                              BinaryExpr<Field3D, std::decay_t<decltype(base)>,
+                                         std::decay_t<decltype(base)>, bout::op::sqrt>>));
+
+  Field3DParallel result{expr};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 2.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 3.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 4.0));
+}
+
+TEST_F(Field3DTestFCI, SQField3DParallelPreservesParallelSlices) {
+  Field3DParallel field;
+
+  field = 2.0;
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+
+  const auto expr = SQ(field);
+
+  EXPECT_TRUE((std::is_same_v<
+               std::decay_t<decltype(expr)>,
+               BinaryExpr<Field3D, Field3DParallel, Field3DParallel, bout::op::Square>>));
+
+  Field3DParallel result{expr};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 4.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 9.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 16.0));
+}
+
+TEST_F(Field3DTestFCI, SQField3DParallelExprPreservesParallelSlices) {
+  Field3DParallel lhs;
+  Field3D rhs;
+
+  lhs = 2.0;
+  lhs.yup() = 3.0;
+  lhs.ydown() = 4.0;
+
+  rhs = 1.0;
+  rhs.splitParallelSlices();
+  rhs.yup() = 2.0;
+  rhs.ydown() = 3.0;
+
+  Field3DParallel result{SQ(lhs + rhs)};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 9.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 25.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 49.0));
+}
+
 TEST_F(Field3DTestFCI, MulField3DParallelPreservesParallelSlices) {
   Field3D field;
   EXPECT_TRUE(field.isFci());
@@ -2129,6 +2255,92 @@ TEST_F(Field3DTestFCI, MulField3DParallelPreservesParallelSlices) {
   EXPECT_TRUE(IsFieldEqual(prodpar.ydown(), 20.0, "RGN_YPAR_-1"));
 }
 
+TEST_F(Field3DTestFCI, DivField3DParallelPreservesParallelSlices) {
+  Field3D field;
+
+  field = 2.0;
+  field.splitParallelSlices();
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+  field.resetRegionParallel();
+
+  Field3DParallel rhs{1.0};
+  EXPECT_TRUE(IsFieldEqual(rhs.ydown(), 1, "RGN_YPAR_-1"));
+  rhs *= 3.0;
+  EXPECT_TRUE(IsFieldEqual(rhs.ydown(), 3, "RGN_YPAR_-1"));
+  rhs.yup() *= 4;
+  EXPECT_TRUE(IsFieldEqual(rhs.ydown(), 3, "RGN_YPAR_-1"));
+  rhs.ydown() *= 20. / 3;
+  EXPECT_TRUE(IsFieldEqual(rhs.ydown(), 20, "RGN_YPAR_-1"));
+
+  const Field3D prod = field / rhs.asField3D();
+
+  EXPECT_FALSE(prod.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(prod, 2. / 3));
+
+  const Field3DParallel prodpar = field / rhs;
+  EXPECT_TRUE(prodpar.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(prodpar, 2. / 3));
+  EXPECT_TRUE(IsFieldEqual(prodpar.yup(), .25, "RGN_YPAR_+1"));
+  EXPECT_TRUE(IsFieldEqual(prodpar.ydown(), 4. / 20, "RGN_YPAR_-1"));
+}
+
+TEST_F(Field3DTestFCI, AddField3DParallelPreservesParallelSlices) {
+  Field3D field;
+  field = 2.0;
+  field.splitParallelSlices();
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+  field.resetRegionParallel();
+
+  Field3D rhs;
+  rhs = 3.0;
+  rhs.splitParallelSlices();
+  rhs.yup() = 4.0;
+  rhs.ydown() = 5.0;
+  rhs.resetRegionParallel();
+
+  const Field3D res = field + rhs;
+
+  EXPECT_FALSE(res.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(res, 5.0));
+
+  const Field3DParallel respar = field.asField3DParallel() + rhs;
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(respar)>, Field3DParallel>));
+  EXPECT_TRUE(respar.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(respar, 5.0));
+  EXPECT_TRUE(IsFieldEqual(respar.yup(), 7.0, "RGN_YPAR_+1"));
+  EXPECT_TRUE(IsFieldEqual(respar.ydown(), 9.0, "RGN_YPAR_-1"));
+}
+
+TEST_F(Field3DTestFCI, SubField3DParallelPreservesParallelSlices) {
+  Field3D field;
+  field = 2.0;
+  field.splitParallelSlices();
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+  field.resetRegionParallel();
+
+  Field3D rhs;
+  rhs = 3.0;
+  rhs.splitParallelSlices();
+  rhs.yup() = 5.0;
+  rhs.ydown() = 7.0;
+  rhs.resetRegionParallel();
+
+  const Field3D res = field - rhs;
+
+  EXPECT_FALSE(res.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(res, -1.0));
+
+  const Field3DParallel respar = field.asField3DParallel() - rhs;
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(respar)>, Field3DParallel>));
+  EXPECT_TRUE(respar.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(respar, -1.0));
+  EXPECT_TRUE(IsFieldEqual(respar.yup(), -2.0, "RGN_YPAR_+1"));
+  EXPECT_TRUE(IsFieldEqual(respar.ydown(), -3.0, "RGN_YPAR_-1"));
+}
+
 TEST_F(Field3DTest, Abs) {
   Field3D field;
 

From 16a66f0b596923ba81d54e214ba0250e1c084c68 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 8 Jul 2026 13:52:19 +0100
Subject: [PATCH 1623/1827] Clang-Tidy: Use 'contains' to check for membership

---
 include/bout/options.hxx | 6 +++---
 src/sys/options.cxx      | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 87503b0a22..b68364c60c 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -355,7 +355,7 @@ public:
 
   /// Return true if this value has attribute \p key
   bool hasAttribute(const std::string& key) const {
-    return attributes.find(key) != attributes.end();
+    return attributes.contains(key);
   }
 
   /// Set attributes, overwriting any already set
@@ -579,7 +579,7 @@ public:
     value_used = true; // Note this is mutable
 
     output_info << "\tOption " << full_name << " = " << val;
-    if (attributes.count("source")) {
+    if (attributes.contains("source")) {
       // Specify the source of the setting
       output_info << " (" << bout::utils::variantToString(attributes.at("source")) << ")";
     }
@@ -907,7 +907,7 @@ private:
     // If already set, and not time evolving then check for changing values
     // If a variable has a "time_dimension" attribute then it is assumed
     // that updates to the value is ok and don't need to be forced.
-    if (isSet() && (attributes.find("time_dimension") == attributes.end())) {
+    if (isSet() && (!attributes.contains("time_dimension"))) {
       // Check if current value the same as new value
       if (!bout::utils::variantEqualTo(value, val)) {
         if (force or !bout::utils::variantEqualTo(attributes["source"], source)) {
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 85cfa7a49a..dbbe372298 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -1053,9 +1053,9 @@ bout::details::OptionsFormatterBase::format(const Options& options,
       fmt::format_to(ctx.out(), " = {}", as_str);
     }
 
-    const bool has_doc = options.attributes.count("doc") != 0U;
-    const bool has_source = options.attributes.count("source") != 0U;
-    const bool has_type = options.attributes.count("type") != 0U;
+    const bool has_doc = options.attributes.contains("doc");
+    const bool has_source = options.attributes.contains("source");
+    const bool has_type = options.attributes.contains("type");
 
     std::vector<std::string> comments;
 

From 252067479a736291497f4be95221ac69f645b671 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 8 Jul 2026 14:58:32 +0100
Subject: [PATCH 1624/1827] Refactor map::find expression: lookup and retrieval
 in a single step with C++17 initializer syntax

---
 src/field/field_data.cxx | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx
index 8f6a808482..b54f95ba64 100644
--- a/src/field/field_data.cxx
+++ b/src/field/field_data.cxx
@@ -189,12 +189,11 @@ void FieldData::addBndryGenerator(FieldGeneratorPtr gen, BndryLoc location) {
 }
 
 FieldGeneratorPtr FieldData::getBndryGenerator(BndryLoc location) {
-  auto it = bndry_generator.find(location);
-  if (it == bndry_generator.end()) {
-    return nullptr;
+  if (const auto it = bndry_generator.find(location); it != bndry_generator.end()) {
+    return it->second;
   }
 
-  return it->second;
+  return nullptr;
 }
 
 Mesh* FieldData::getMesh() const {

From 28542c95c77314ba4ceca1e839a84f41dc700d4e Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 8 Jul 2026 15:17:19 +0100
Subject: [PATCH 1625/1827] Lookup and retrieval in a single step with C++17
 initializer syntax

---
 src/field/field_factory.cxx | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/src/field/field_factory.cxx b/src/field/field_factory.cxx
index 1f5984ba48..220597a215 100644
--- a/src/field/field_factory.cxx
+++ b/src/field/field_factory.cxx
@@ -301,8 +301,7 @@ Field3D FieldFactory::create3D(FieldGeneratorPtr gen, Mesh* localmesh, CELL_LOC
   };
 
   if (transform_from_field_aligned) {
-    auto coords = result.getCoordinates();
-    if (coords == nullptr) {
+    if (auto coords = result.getCoordinates(); coords == nullptr) {
       // Should not lead to issues. If called from the coordinates
       // constructor, then this is expected, and the result will be
       // transformed. Otherwise, if the field is used untransformed,
@@ -352,8 +351,7 @@ FieldPerp FieldFactory::createPerp(FieldGeneratorPtr gen, Mesh* localmesh, CELL_
   };
 
   if (transform_from_field_aligned) {
-    auto coords = result.getCoordinates();
-    if (coords == nullptr) {
+    if (auto coords = result.getCoordinates(); coords == nullptr) {
       // Should not lead to issues. If called from the coordinates
       // constructor, then this is expected, and the result will be
       // transformed. Otherwise, if the field is used untransformed,
@@ -376,8 +374,7 @@ const Options* FieldFactory::findOption(const Options* opt, const std::string& n
   const Options* result = opt;
 
   // Check if name contains a section separator ':'
-  size_t pos = name.find(':');
-  if (pos == std::string::npos) {
+  if (auto pos = name.find(':'); pos == std::string::npos) {
     // No separator. Try this section, and then go through parents
 
     while (!result->isSet(name)) {
@@ -517,8 +514,7 @@ FieldGeneratorPtr FieldFactory::parse(const std::string& input,
     key = opt->str() + key; // Include options context in key
   }
 
-  auto it = cache.find(key);
-  if (it != cache.end()) {
+  if (auto it = cache.find(key); it != cache.end()) {
     return it->second;
   }
 

From a56a9960117e0bc1d06cdcee748e100446611b04 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 8 Jul 2026 13:27:25 +0100
Subject: [PATCH 1626/1827] Move variable 'search' to if-init-statement

---
 src/mesh/coordinates_accessor.cxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/mesh/coordinates_accessor.cxx b/src/mesh/coordinates_accessor.cxx
index efc27e9715..6967087a0e 100644
--- a/src/mesh/coordinates_accessor.cxx
+++ b/src/mesh/coordinates_accessor.cxx
@@ -21,8 +21,7 @@ CoordinatesAccessor::CoordinatesAccessor(const Coordinates* coords) {
   Mesh* mesh = coords->dx.getMesh();
   mesh_nz = mesh->LocalNz;
 
-  auto search = coords_store.find(coords);
-  if (search != coords_store.end()) {
+  if (const auto search = coords_store.find(coords); search != coords_store.end()) {
     // Found, so get the pointer to the data
     data = search->second.begin();
     return;

From 6ca5bbdbd8df5424526d67002846dfb076ae7708 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 10 Jul 2026 14:37:23 +0100
Subject: [PATCH 1627/1827] Ensure `PetscMatrix` destroys owned `Mat` object

---
 include/bout/petsc_interface.hxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 3ef3a2a49a..7b911e8755 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -292,8 +292,8 @@ public:
 
   /// Copy constructor
   PetscMatrix(const PetscMatrix<T>& mat)
-      : matrix(new Mat()), indexConverter(mat.indexConverter), pt(mat.pt),
-        yoffset(mat.yoffset), initialised(mat.initialised) {
+      : matrix(new Mat(), bout::petsc::MatDeleter{}), indexConverter(mat.indexConverter),
+        pt(mat.pt), yoffset(mat.yoffset), initialised(mat.initialised) {
     MatDuplicate(*mat.matrix, MAT_COPY_VALUES, matrix.get());
   }
 
@@ -307,7 +307,7 @@ public:
   // Construct a matrix capable of operating on the specified field,
   // preallocating memory if requested and possible.
   PetscMatrix(IndexerPtr<T> indConverter, bool preallocate = true)
-      : matrix(new Mat()), indexConverter(indConverter),
+      : matrix(new Mat(), bout::petsc::MatDeleter{}), indexConverter(indConverter),
         pt(&indConverter->getMesh()->getCoordinates()->getParallelTransform()) {
     MPI_Comm comm = std::is_same_v<T, FieldPerp> ? indConverter->getMesh()->getXZcomm()
                                                  : BoutComm::get();

From 67382589ef3cb1705de2549fe2361426ae028ad8 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 10 Jul 2026 14:40:35 +0100
Subject: [PATCH 1628/1827] Ensure `ksp` gets cleaned up in `LaplacePetsc`
 destructor

---
 src/invert/laplace/impls/petsc/petsc_laplace.cxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 89ba25405b..faac0e8feb 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -259,6 +259,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
       KSPDestroy(&ksp);
     }
     KSPCreate(comm, &ksp);
+    ksp_initialised = true;
 
     // Configure Linear Solver
 #if PETSC_VERSION_GE(3, 5, 0)

From 61b01d5b910e625e06c8ea78aa1b2b1ced7774de Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 10 Jul 2026 14:41:12 +0100
Subject: [PATCH 1629/1827] Remove unnecessary `MPI_Comm` member

---
 src/invert/laplace/impls/petsc/petsc_laplace.cxx | 5 ++---
 src/invert/laplace/impls/petsc/petsc_laplace.hxx | 1 -
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index faac0e8feb..33481f9bde 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -140,8 +140,7 @@ LaplacePetsc::LaplacePetsc(Options* opt, const CELL_LOC loc, Mesh* mesh_in,
                            [[maybe_unused]] Solver* solver)
     : Laplacian(opt, loc, mesh_in), A(0.0, mesh_in), C1(1.0, mesh_in), C2(1.0, mesh_in),
       D(1.0, mesh_in), Ex(0.0, mesh_in), Ez(0.0, mesh_in), issetD(false), issetC(false),
-      issetE(false), comm(localmesh->getXZcomm()),
-      opts(opt == nullptr ? &(Options::root()["laplace"]) : opt),
+      issetE(false), opts(opt == nullptr ? &(Options::root()["laplace"]) : opt),
       // WARNING: only a few of these options actually make sense: see the
       // PETSc documentation to work out which they are (possibly
       // pbjacobi, sor might be useful choices?)
@@ -258,7 +257,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
     if (ksp_initialised) {
       KSPDestroy(&ksp);
     }
-    KSPCreate(comm, &ksp);
+    KSPCreate(localmesh->getXZcomm(), &ksp);
     ksp_initialised = true;
 
     // Configure Linear Solver
diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.hxx b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
index cfd47702c9..557207f142 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.hxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.hxx
@@ -233,7 +233,6 @@ private:
   /// Y-index of solution field.
   int yindex = -1;
 
-  MPI_Comm comm;
   KSP ksp = nullptr; ///< PETSc solver
   bool ksp_initialised = false;
 

From a0341279241c8cbbe0f1bd7e0e68f352f5f54f3c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 10 Jul 2026 14:44:49 +0100
Subject: [PATCH 1630/1827] Remove unnecessary local `PetscLib` from test

---
 tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
index 04182293e7..01e9d3f51e 100644
--- a/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
+++ b/tests/integrated/test-petsc_laplace/test_petsc_laplace.cxx
@@ -37,7 +37,6 @@
 #include "bout/options.hxx"
 #include "bout/options_io.hxx"
 #include "bout/output.hxx"
-#include "bout/petsclib.hxx"
 #include "bout/traits.hxx"
 #include "bout/vecops.hxx"
 
@@ -174,9 +173,6 @@ int main(int argc, char** argv) {
 
   BoutInitialise(argc, argv);
 
-  // Need this here to ensure PETSc isn't finalised until after the global mesh,
-  // otherwise we get problems from `MPI_Comm_free` on the X communicator
-  PetscLib lib{};
   {
     // Not be used for 3D metrics
     Options::root()["laplace"].setConditionallyUsed();

From b2f52cde587b5322e38213285ccefa88e9ea150e Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 10 Jul 2026 08:24:28 -0700
Subject: [PATCH 1631/1827] Field3DParallel unit test

If the parallel transform is not FCI then parallel slices are not
calculated on assignment to Field3DParallel.
---
 tests/unit/field/test_field3d.cxx | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 38f51a8164..eee92c806e 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -1967,7 +1967,7 @@ TEST_F(Field3DTest, SQExpressionUsesSquareOp) {
   EXPECT_TRUE(IsFieldEqual(SQ(expr), 9.0));
 }
 
-TEST_F(Field3DTest, SQField3DParallelPreservesParallelSlices) {
+TEST_F(Field3DTest, SQField3DParallelNoFCIDropsParallelSlices) {
   Field3DParallel field;
 
   field = 2.0;
@@ -1983,10 +1983,9 @@ TEST_F(Field3DTest, SQField3DParallelPreservesParallelSlices) {
 
   Field3DParallel result{squared};
 
+  // Not FCI so parallel slices are not calculated
   EXPECT_FALSE(result.hasParallelSlices());
   EXPECT_TRUE(IsFieldEqual(result, 4.0));
-  EXPECT_TRUE(IsFieldEqual(result.yup(), 9.0));
-  EXPECT_TRUE(IsFieldEqual(result.ydown(), 16.0));
 }
 
 TEST_F(Field3DTest, Field3DParallelArithmeticReturnsLazyExpr) {

From 858c5c1961a8970c1b3a4e8443ddc693b1d82084 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 10 Jul 2026 09:59:49 -0700
Subject: [PATCH 1632/1827] Lazy pow function on fields

---
 include/bout/field.hxx            | 232 ++++++++++++++++++++++++++----
 include/bout/field3d.hxx          |   1 -
 include/bout/fieldperp.hxx        |   5 +
 include/bout/fv_ops.hxx           |  14 +-
 src/field/field3d.cxx             |  16 ---
 src/field/fieldperp.cxx           |  35 +++++
 tests/unit/field/test_field2d.cxx |  13 ++
 tests/unit/field/test_field3d.cxx |  74 ++++++++++
 8 files changed, 340 insertions(+), 50 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index b20e8915e9..05bccf250c 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -539,53 +539,233 @@ inline BoutReal mean(const BinaryExpr<ResT, L, R, Func>& f, bool allpe = false,
   return bout::reduce::Mean::finalize(state);
 }
 
+namespace bout::op {
+struct Pow {
+  template <typename LView, typename RView>
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx, const LView& L,
+                                                        const RView& R) const {
+    return ::pow(L(idx), R(idx));
+  }
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(BoutReal a, BoutReal b) const {
+    return ::pow(a, b);
+  }
+};
+}; // namespace bout::op
+
+namespace bout::detail {
+template <typename T>
+std::optional<int> getPerpYIndex(const T& value);
+
+template <typename ResT, typename L, typename R, typename Func>
+std::optional<int> getPerpYIndex(const BinaryExpr<ResT, L, R, Func>& expr);
+
+template <typename ResT>
+std::optional<size_t> getPowRegionID(const Mesh* mesh, const std::string& region_name) {
+  if constexpr (std::is_same_v<ResT, Field3D>) {
+    return bout::detail::getField3DRegionID(mesh, region_name);
+  } else {
+    return std::nullopt;
+  }
+}
+
+template <typename ResT, typename L, typename R, typename LView, typename RView,
+          typename IndType>
+auto makePowExpr(const LView& lhs_view, const RView& rhs_view, Mesh* mesh,
+                 CELL_LOC location, DirectionTypes directions,
+                 std::optional<size_t> regionID, const Region<IndType>& region,
+                 std::optional<int> yindex = std::nullopt) {
+  return BinaryExpr<ResT, L, R, bout::op::Pow>{lhs_view, rhs_view, bout::op::Pow{},
+                                               mesh,     location, directions,
+                                               regionID, region,   yindex};
+}
+} // namespace bout::detail
+
 /// Exponent: pow(lhs, lhs) is \p lhs raised to the power of \p rhs
 ///
 /// This loops over the entire domain, including guard/boundary cells by
 /// default (can be changed using the \p rgn argument)
 /// If CHECK >= 3 then the result will be checked for non-finite numbers
-template <typename T, typename = bout::utils::EnableIfField<T>>
-T pow(const T& lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Field2D, L, R, bout::op::Pow>>
+pow(const L& lhs, const R& rhs) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  return bout::detail::makePowExpr<Field2D, L, R>(
+      static_cast<typename L::View>(lhs), static_cast<typename R::View>(rhs),
+      lhs.getMesh(), lhs.getLocation(), lhs.getDirections(), std::nullopt,
+      lhs.getMesh()->getRegion2D("RGN_ALL"));
+}
 
-  ASSERT1(areFieldsCompatible(lhs, rhs));
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Field2D, L, R, bout::op::Pow>>
+pow(const L& lhs, const R& rhs, const std::string& rgn) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  return bout::detail::makePowExpr<Field2D, L, R>(
+      static_cast<typename L::View>(lhs), static_cast<typename R::View>(rhs),
+      lhs.getMesh(), lhs.getLocation(), lhs.getDirections(), std::nullopt,
+      lhs.getMesh()->getRegion2D(rgn));
+}
+
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Field3D, L, R, bout::op::Pow>>
+pow(const L& lhs, const R& rhs) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  auto regionID = lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID());
+  return bout::detail::makePowExpr<Field3D, L, R>(
+      static_cast<typename L::View>(lhs), static_cast<typename R::View>(rhs),
+      lhs.getMesh(), lhs.getLocation(), lhs.getDirections(), regionID,
+      (regionID.has_value() ? lhs.getMesh()->getRegion(regionID.value())
+                            : lhs.getMesh()->getRegion("RGN_ALL")),
+      bout::detail::getPerpYIndex(lhs));
+}
 
-  T result{emptyFrom(lhs)};
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Field3D, L, R, bout::op::Pow>>
+pow(const L& lhs, const R& rhs, const std::string& rgn) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  return bout::detail::makePowExpr<Field3D, L, R>(
+      static_cast<typename L::View>(lhs), static_cast<typename R::View>(rhs),
+      lhs.getMesh(), lhs.getLocation(), lhs.getDirections(),
+      bout::detail::getPowRegionID<Field3D>(lhs.getMesh(), rgn),
+      lhs.getMesh()->getRegion(rgn), bout::detail::getPerpYIndex(lhs));
+}
 
-  BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs[i]); }
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Field3D, L, R, bout::op::Pow>>
+pow(const L& lhs, const R& rhs) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  int mesh_nz = lhs.getMesh()->LocalNz;
+  return bout::detail::makePowExpr<Field3D, L, R>(
+      static_cast<typename L::View>(lhs),
+      static_cast<typename R::View>(rhs).setScale(1, mesh_nz), lhs.getMesh(),
+      lhs.getLocation(), lhs.getDirections(), lhs.getRegionID(),
+      lhs.getMesh()->getRegion("RGN_ALL"), bout::detail::getPerpYIndex(lhs));
+}
 
-  checkData(result);
-  return result;
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Field3D, L, R, bout::op::Pow>>
+pow(const L& lhs, const R& rhs, const std::string& rgn) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  int mesh_nz = lhs.getMesh()->LocalNz;
+  return bout::detail::makePowExpr<Field3D, L, R>(
+      static_cast<typename L::View>(lhs),
+      static_cast<typename R::View>(rhs).setScale(1, mesh_nz), lhs.getMesh(),
+      lhs.getLocation(), lhs.getDirections(),
+      bout::detail::getPowRegionID<Field3D>(lhs.getMesh(), rgn),
+      lhs.getMesh()->getRegion(rgn), bout::detail::getPerpYIndex(lhs));
 }
 
-template <typename T, typename = bout::utils::EnableIfField<T>>
-T pow(const T& lhs, BoutReal rhs, const std::string& rgn = "RGN_ALL") {
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Field3D, L, R, bout::op::Pow>>
+pow(const L& lhs, const R& rhs) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  int mesh_nz = rhs.getMesh()->LocalNz;
+  return bout::detail::makePowExpr<Field3D, L, R>(
+      static_cast<typename L::View>(lhs).setScale(1, mesh_nz),
+      static_cast<typename R::View>(rhs), rhs.getMesh(), rhs.getLocation(),
+      rhs.getDirections(), rhs.getRegionID(), rhs.getMesh()->getRegion("RGN_ALL"),
+      bout::detail::getPerpYIndex(rhs));
+}
 
-  // Check if the inputs are allocated
-  checkData(lhs);
-  checkData(rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Field3D, L, R, bout::op::Pow>>
+pow(const L& lhs, const R& rhs, const std::string& rgn) {
+  ASSERT1_EXPR_COMPATIBLE(lhs, rhs);
+  int mesh_nz = rhs.getMesh()->LocalNz;
+  return bout::detail::makePowExpr<Field3D, L, R>(
+      static_cast<typename L::View>(lhs).setScale(1, mesh_nz),
+      static_cast<typename R::View>(rhs), rhs.getMesh(), rhs.getLocation(),
+      rhs.getDirections(), bout::detail::getPowRegionID<Field3D>(rhs.getMesh(), rgn),
+      rhs.getMesh()->getRegion(rgn), bout::detail::getPerpYIndex(rhs));
+}
 
-  T result{emptyFrom(lhs)};
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<Field2D, L, Constant<R>, bout::op::Pow>>
+pow(const L& lhs, R rhs) {
+  return bout::detail::makePowExpr<Field2D, L, Constant<R>>(
+      static_cast<typename L::View>(lhs), static_cast<typename Constant<R>::View>(rhs),
+      lhs.getMesh(), lhs.getLocation(), lhs.getDirections(), std::nullopt,
+      lhs.getMesh()->getRegion2D("RGN_ALL"));
+}
 
-  BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs); }
+template <typename L, typename R>
+std::enable_if_t<is_expr_field2d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<Field2D, L, Constant<R>, bout::op::Pow>>
+pow(const L& lhs, R rhs, const std::string& rgn) {
+  return bout::detail::makePowExpr<Field2D, L, Constant<R>>(
+      static_cast<typename L::View>(lhs), static_cast<typename Constant<R>::View>(rhs),
+      lhs.getMesh(), lhs.getLocation(), lhs.getDirections(), std::nullopt,
+      lhs.getMesh()->getRegion2D(rgn));
+}
 
-  checkData(result);
-  return result;
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Field2D, Constant<L>, R, bout::op::Pow>>
+pow(L lhs, const R& rhs) {
+  return bout::detail::makePowExpr<Field2D, Constant<L>, R>(
+      static_cast<typename Constant<L>::View>(lhs), static_cast<typename R::View>(rhs),
+      rhs.getMesh(), rhs.getLocation(), rhs.getDirections(), std::nullopt,
+      rhs.getMesh()->getRegion2D("RGN_ALL"));
 }
 
-template <typename T, typename = bout::utils::EnableIfField<T>>
-T pow(BoutReal lhs, const T& rhs, const std::string& rgn = "RGN_ALL") {
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field2d_v<R>,
+                 BinaryExpr<Field2D, Constant<L>, R, bout::op::Pow>>
+pow(L lhs, const R& rhs, const std::string& rgn) {
+  return bout::detail::makePowExpr<Field2D, Constant<L>, R>(
+      static_cast<typename Constant<L>::View>(lhs), static_cast<typename R::View>(rhs),
+      rhs.getMesh(), rhs.getLocation(), rhs.getDirections(), std::nullopt,
+      rhs.getMesh()->getRegion2D(rgn));
+}
 
-  // Check if the inputs are allocated
-  checkData(lhs);
-  checkData(rhs);
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<Field3D, L, Constant<R>, bout::op::Pow>>
+pow(const L& lhs, R rhs) {
+  return bout::detail::makePowExpr<Field3D, L, Constant<R>>(
+      static_cast<typename L::View>(lhs), static_cast<typename Constant<R>::View>(rhs),
+      lhs.getMesh(), lhs.getLocation(), lhs.getDirections(), lhs.getRegionID(),
+      lhs.getMesh()->getRegion("RGN_ALL"), bout::detail::getPerpYIndex(lhs));
+}
 
-  // Define and allocate the output result
-  T result{emptyFrom(rhs)};
+template <typename L, typename R>
+std::enable_if_t<is_expr_field3d_v<L> && is_expr_constant_v<R>,
+                 BinaryExpr<Field3D, L, Constant<R>, bout::op::Pow>>
+pow(const L& lhs, R rhs, const std::string& rgn) {
+  return bout::detail::makePowExpr<Field3D, L, Constant<R>>(
+      static_cast<typename L::View>(lhs), static_cast<typename Constant<R>::View>(rhs),
+      lhs.getMesh(), lhs.getLocation(), lhs.getDirections(),
+      bout::detail::getPowRegionID<Field3D>(lhs.getMesh(), rgn),
+      lhs.getMesh()->getRegion(rgn), bout::detail::getPerpYIndex(lhs));
+}
 
-  BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs, rhs[i]); }
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Field3D, Constant<L>, R, bout::op::Pow>>
+pow(L lhs, const R& rhs) {
+  return bout::detail::makePowExpr<Field3D, Constant<L>, R>(
+      static_cast<typename Constant<L>::View>(lhs), static_cast<typename R::View>(rhs),
+      rhs.getMesh(), rhs.getLocation(), rhs.getDirections(), rhs.getRegionID(),
+      rhs.getMesh()->getRegion("RGN_ALL"), bout::detail::getPerpYIndex(rhs));
+}
 
-  checkData(result);
-  return result;
+template <typename L, typename R>
+std::enable_if_t<is_expr_constant_v<L> && is_expr_field3d_v<R>,
+                 BinaryExpr<Field3D, Constant<L>, R, bout::op::Pow>>
+pow(L lhs, const R& rhs, const std::string& rgn) {
+  return bout::detail::makePowExpr<Field3D, Constant<L>, R>(
+      static_cast<typename Constant<L>::View>(lhs), static_cast<typename R::View>(rhs),
+      rhs.getMesh(), rhs.getLocation(), rhs.getDirections(),
+      bout::detail::getPowRegionID<Field3D>(rhs.getMesh(), rgn),
+      rhs.getMesh()->getRegion(rgn), bout::detail::getPerpYIndex(rhs));
 }
 
 /*!
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 02e582c20a..63e20c349e 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -911,7 +911,6 @@ inline auto operator-(const Field3D& f) {
 /// This loops over the entire domain, including guard/boundary cells by
 /// default (can be changed using the \p rgn argument).
 /// If CHECK >= 3 then the result will be checked for non-finite numbers
-Field3D pow(const Field3D& lhs, const Field2D& rhs, const std::string& rgn = "RGN_ALL");
 FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs,
               const std::string& rgn = "RGN_ALL");
 
diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 83bb3b79b0..834c82be4d 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -409,6 +409,11 @@ FieldPerp operator/(const FieldPerp& lhs, const Field2D& rhs);
 FieldPerp operator/(const FieldPerp& lhs, BoutReal rhs);
 FieldPerp operator/(BoutReal lhs, const FieldPerp& rhs);
 
+FieldPerp pow(const FieldPerp& lhs, const FieldPerp& rhs,
+              const std::string& rgn = "RGN_ALL");
+FieldPerp pow(const FieldPerp& lhs, BoutReal rhs, const std::string& rgn = "RGN_ALL");
+FieldPerp pow(BoutReal lhs, const FieldPerp& rhs, const std::string& rgn = "RGN_ALL");
+
 /*!
  * Unary minus. Returns the negative of given field,
  * iterates over whole domain including guard/boundary cells.
diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 306ff3301f..67db42cf0b 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -79,13 +79,13 @@ Field3D D4DY4_Index(const Field3D& f, bool bndry_flux = true);
 // Forward declarations of flux limiters
 // If you want to use your own flux limiter, you need to
 // #include <bout/fv_ops_impl.hxx> to instantiate the templates.
-class Upwind;
-class Fromm;
-class MinMod;
-class MC;
-class Superbee;
-class VanAlbada;
-class WENO3;
+struct Upwind;
+struct Fromm;
+struct MinMod;
+struct MC;
+struct Superbee;
+struct VanAlbada;
+struct WENO3;
 
 /*!
    * Communicate fluxes between processors
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 5da438dcdf..95ea1de05a 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -686,22 +686,6 @@ void Field3D::swapData(Field3D& other) { std::swap(data, other.data); }
 
 //////////////// NON-MEMBER FUNCTIONS //////////////////
 
-Field3D pow(const Field3D& lhs, const Field2D& rhs, const std::string& rgn) {
-
-  // Check if the inputs are allocated
-  checkData(lhs);
-  checkData(rhs);
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  // Define and allocate the output result
-  Field3D result{emptyFrom(lhs)};
-
-  BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs[i]); }
-
-  checkData(result);
-  return result;
-}
-
 FieldPerp pow(const Field3D& lhs, const FieldPerp& rhs, const std::string& rgn) {
 
   checkData(lhs);
diff --git a/src/field/fieldperp.cxx b/src/field/fieldperp.cxx
index b7b2d9d731..bca551c29d 100644
--- a/src/field/fieldperp.cxx
+++ b/src/field/fieldperp.cxx
@@ -153,6 +153,41 @@ FieldPerp fromFieldAligned(const FieldPerp& f, const std::string& region) {
 /////////////////////////////////////////////////
 // functions
 
+FieldPerp pow(const FieldPerp& lhs, const FieldPerp& rhs, const std::string& rgn) {
+  checkData(lhs);
+  checkData(rhs);
+  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
+
+  FieldPerp result{emptyFrom(lhs)};
+
+  BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs[i]); }
+
+  checkData(result);
+  return result;
+}
+
+FieldPerp pow(const FieldPerp& lhs, BoutReal rhs, const std::string& rgn) {
+  checkData(lhs);
+
+  FieldPerp result{emptyFrom(lhs)};
+
+  BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs[i], rhs); }
+
+  checkData(result);
+  return result;
+}
+
+FieldPerp pow(BoutReal lhs, const FieldPerp& rhs, const std::string& rgn) {
+  checkData(rhs);
+
+  FieldPerp result{emptyFrom(rhs)};
+
+  BOUT_FOR(i, result.getRegion(rgn)) { result[i] = ::pow(lhs, rhs[i]); }
+
+  checkData(result);
+  return result;
+}
+
 const FieldPerp sliceXZ(const Field3D& f, int y) {
   // Source field should be valid
   checkData(f);
diff --git a/tests/unit/field/test_field2d.cxx b/tests/unit/field/test_field2d.cxx
index a91acd4a40..1420c79bc2 100644
--- a/tests/unit/field/test_field2d.cxx
+++ b/tests/unit/field/test_field2d.cxx
@@ -1168,6 +1168,19 @@ TEST_F(Field2DTest, PowField2DField2D) {
   EXPECT_TRUE(IsFieldEqual(c, 64.0));
 }
 
+TEST_F(Field2DTest, PowExpressionUsesPowOp) {
+  Field2D field;
+
+  field = 2.0;
+  const auto expr = field + 1.0;
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(pow(expr, 2.0))>,
+                              BinaryExpr<Field2D, std::decay_t<decltype(expr)>,
+                                         Constant<double>, bout::op::Pow>>));
+  EXPECT_TRUE(IsFieldEqual(pow(expr, 2.0), 9.0));
+  EXPECT_TRUE(IsFieldEqual(pow(expr, 2.0, "RGN_ALL"), 9.0));
+}
+
 TEST_F(Field2DTest, Sqrt) {
   Field2D field;
 
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index eee92c806e..4ddc7dde5c 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -1947,6 +1947,37 @@ TEST_F(Field3DTest, PowField3DField3D) {
   EXPECT_TRUE(IsFieldEqual(c, 64.0));
 }
 
+TEST_F(Field3DTest, PowExpressionUsesPowOp) {
+  Field3D field;
+
+  field = 2.0;
+  const auto expr = field + 1.0;
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(pow(expr, 2.0))>,
+                              BinaryExpr<Field3D, std::decay_t<decltype(expr)>,
+                                         Constant<double>, bout::op::Pow>>));
+  EXPECT_TRUE(IsFieldEqual(pow(expr, 2.0), 9.0));
+}
+
+TEST_F(Field3DTest, PowMixedField2DField3DExpressionUsesPowOp) {
+  Field2D lhs;
+  Field3D rhs;
+
+  lhs = 2.0;
+  rhs = 3.0;
+
+  const auto lhs_expr = lhs + 1.0;
+  const auto rhs_expr = rhs + 1.0;
+  const auto expr = pow(lhs_expr, rhs_expr);
+
+  EXPECT_TRUE(
+      (std::is_same_v<std::decay_t<decltype(expr)>,
+                      BinaryExpr<Field3D, std::decay_t<decltype(lhs_expr)>,
+                                 std::decay_t<decltype(rhs_expr)>, bout::op::Pow>>));
+  EXPECT_TRUE(IsFieldEqual(expr, 81.0));
+  EXPECT_TRUE(IsFieldEqual(pow(lhs_expr, rhs_expr, "RGN_ALL"), 81.0));
+}
+
 TEST_F(Field3DTest, Sqrt) {
   Field3D field;
 
@@ -2132,6 +2163,49 @@ TEST_F(Field3DTestFCI, SqrtField3DParallelPreservesParallelSlices) {
   }
 }
 
+TEST_F(Field3DTestFCI, PowField3DParallelExprPreservesParallelSlices) {
+  Field3DParallel field;
+
+  field = 2.0;
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+
+  const auto expr = pow(field + 1.0, 2.0);
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(expr)>,
+                              BinaryExpr<Field3D, std::decay_t<decltype(field + 1.0)>,
+                                         Constant<double>, bout::op::Pow>>));
+
+  Field3DParallel result{expr};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 9.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 16.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 25.0));
+}
+
+TEST_F(Field3DTestFCI, PowField3DParallelRegionExprPreservesParallelSlices) {
+  Field3DParallel field;
+
+  field = 2.0;
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+
+  const auto base = field + 1.0;
+  const auto expr = pow(base, 2.0, "RGN_ALL");
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(expr)>,
+                              BinaryExpr<Field3D, std::decay_t<decltype(base)>,
+                                         Constant<double>, bout::op::Pow>>));
+
+  Field3DParallel result{expr};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 9.0));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 16.0));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 25.0));
+}
+
 TEST_F(Field3DTestFCI, SqrtField3DParallelExprPreservesParallelSlices) {
   Field3DParallel lhs;
   Field3D rhs;

From c808fa7bf87d5f2be63d790058efa4ae1939e05b Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 10 Jul 2026 10:26:40 -0700
Subject: [PATCH 1633/1827] floor: Return BinaryExpr

Makes the `floor` function lazy, so it can be inlined into template
expressions.
---
 include/bout/field.hxx              | 99 +++++++++++++++++------------
 tests/unit/field/test_field2d.cxx   | 13 ++++
 tests/unit/field/test_field3d.cxx   | 55 ++++++++++++++++
 tests/unit/field/test_fieldperp.cxx | 14 ++++
 4 files changed, 142 insertions(+), 39 deletions(-)

diff --git a/include/bout/field.hxx b/include/bout/field.hxx
index 05bccf250c..67ce45dc4b 100644
--- a/include/bout/field.hxx
+++ b/include/bout/field.hxx
@@ -33,10 +33,12 @@ class Field;
 #include <cstdio>
 #include <optional>
 #include <string>
+#include <type_traits>
 
 #include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_config.hxx"
 #include "bout/field_data.hxx"
 #include "bout/region.hxx"
 #include "bout/traits.hxx"
@@ -887,6 +889,20 @@ struct Square {
     return ::SQ(value);
   }
 };
+
+struct Floor {
+  template <typename LView, typename RView>
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx, const LView& L,
+                                                        const RView& R) const {
+    const BoutReal value = L(idx);
+    const BoutReal floor_value = R(idx);
+    return value < floor_value ? floor_value : value;
+  }
+  BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(BoutReal value,
+                                                        BoutReal floor_value) const {
+    return value < floor_value ? floor_value : value;
+  }
+};
 }; // namespace bout::op
 
 template <typename T, typename = bout::utils::EnableIfField<T>>
@@ -1065,46 +1081,51 @@ class Field3DParallel;
 /// @param[in] f    The floor value
 /// @param[in] rgn  The region to calculate the result over
 template <typename T, typename = bout::utils::EnableIfField<T>>
-inline T floor(const T& var, BoutReal f, const std::string& rgn = "RGN_ALL") {
-  checkData(var);
-  T result = copy(var);
+inline auto floor(const T& var, BoutReal f, const std::string& rgn = "RGN_ALL") {
+  using ResT = bout::detail::UnaryFieldResult_t<T>;
+  return BinaryExpr<ResT, T, Constant<BoutReal>, bout::op::Floor>{
+      static_cast<typename T::View>(var),
+      static_cast<typename Constant<BoutReal>::View>(f),
+      bout::op::Floor{},
+      var.getMesh(),
+      var.getLocation(),
+      var.getDirections(),
+      bout::detail::getUnaryRegionID<T>(var.getMesh(), rgn),
+      var.getMesh()->template getRegion<ResT>(rgn),
+      bout::detail::getPerpYIndex(var)};
+}
 
-  BOUT_FOR(d, var.getRegion(rgn)) {
-    if (result[d] < f) {
-      result[d] = f;
-    }
-  }
-  if constexpr (std::is_same_v<T, Field3DParallel>) {
-    if (var.hasParallelSlices()) {
-      for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
-        if (result.yup(i).isAllocated()) {
-          BOUT_FOR(d, result.yup(i).getRegion(rgn)) {
-            if (result.yup(i)[d] < f) {
-              result.yup(i)[d] = f;
-            }
-          }
-        } else {
-          if (result.isFci()) {
-            throw BoutException("Expected parallel slice to be allocated");
-          }
-        }
-        if (result.ydown(i).isAllocated()) {
-          BOUT_FOR(d, result.ydown(i).getRegion(rgn)) {
-            if (result.ydown(i)[d] < f) {
-              result.ydown(i)[d] = f;
-            }
-          }
-        } else {
-          if (result.isFci()) {
-            throw BoutException("Expected parallel slice to be allocated");
-          }
-        }
-      }
-    }
-  } else {
-    result.clearParallelSlices();
-  }
-  return result;
+template <typename ResT, typename L, typename R, typename Func>
+inline auto floor(const BinaryExpr<ResT, L, R, Func>& var, BoutReal f) {
+  using UnaryResT = bout::detail::UnaryFieldResult_t<ResT>;
+  return BinaryExpr<UnaryResT, BinaryExpr<ResT, L, R, Func>, Constant<BoutReal>,
+                    bout::op::Floor>{
+      static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(var),
+      static_cast<typename Constant<BoutReal>::View>(f),
+      bout::op::Floor{},
+      var.getMesh(),
+      var.getLocation(),
+      var.getDirections(),
+      var.getRegionID(),
+      var.indices,
+      bout::detail::getPerpYIndex(var)};
+}
+
+template <typename ResT, typename L, typename R, typename Func>
+inline auto floor(const BinaryExpr<ResT, L, R, Func>& var, BoutReal f,
+                  const std::string& rgn) {
+  using UnaryResT = bout::detail::UnaryFieldResult_t<ResT>;
+  return BinaryExpr<UnaryResT, BinaryExpr<ResT, L, R, Func>, Constant<BoutReal>,
+                    bout::op::Floor>{
+      static_cast<typename BinaryExpr<ResT, L, R, Func>::View>(var),
+      static_cast<typename Constant<BoutReal>::View>(f),
+      bout::op::Floor{},
+      var.getMesh(),
+      var.getLocation(),
+      var.getDirections(),
+      bout::detail::getUnaryRegionID<UnaryResT>(var.getMesh(), rgn),
+      var.getMesh()->template getRegion<UnaryResT>(rgn),
+      bout::detail::getPerpYIndex(var)};
 }
 
 #undef FIELD_FUNC
diff --git a/tests/unit/field/test_field2d.cxx b/tests/unit/field/test_field2d.cxx
index 1420c79bc2..91721714ec 100644
--- a/tests/unit/field/test_field2d.cxx
+++ b/tests/unit/field/test_field2d.cxx
@@ -1330,6 +1330,19 @@ TEST_F(Field2DTest, Floor) {
   EXPECT_TRUE(IsFieldEqual(floor(field, floor_value), floor_value));
 }
 
+TEST_F(Field2DTest, FloorExpressionUsesFloorOp) {
+  Field2D field;
+
+  field = 2.0;
+  const auto expr = field + 1.0;
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(floor(expr, 5.0))>,
+                              BinaryExpr<Field2D, std::decay_t<decltype(expr)>,
+                                         Constant<BoutReal>, bout::op::Floor>>));
+  EXPECT_TRUE(IsFieldEqual(floor(expr, 5.0), 5.0));
+  EXPECT_TRUE(IsFieldEqual(floor(expr, 5.0, "RGN_ALL"), 5.0));
+}
+
 TEST_F(Field2DTest, Min) {
   Field2D field;
 
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 4ddc7dde5c..6a6ecb9aea 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -2543,6 +2543,61 @@ TEST_F(Field3DTest, Floor) {
   EXPECT_TRUE(IsFieldEqual(floor(field, floor_value), floor_value));
 }
 
+TEST_F(Field3DTest, FloorExpressionUsesFloorOp) {
+  Field3D field;
+
+  field = 2.0;
+  const auto expr = field + 1.0;
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(floor(expr, 5.0))>,
+                              BinaryExpr<Field3D, std::decay_t<decltype(expr)>,
+                                         Constant<BoutReal>, bout::op::Floor>>));
+  EXPECT_TRUE(IsFieldEqual(floor(expr, 5.0), 5.0));
+}
+
+TEST_F(Field3DTestFCI, FloorField3DParallelExprPreservesParallelSlices) {
+  Field3DParallel field;
+
+  field = 2.0;
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+
+  const auto expr = floor(field + 1.0, 4.5);
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(expr)>,
+                              BinaryExpr<Field3D, std::decay_t<decltype(field + 1.0)>,
+                                         Constant<BoutReal>, bout::op::Floor>>));
+
+  Field3DParallel result{expr};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 4.5));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 4.5));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 5.0));
+}
+
+TEST_F(Field3DTestFCI, FloorField3DParallelRegionExprPreservesParallelSlices) {
+  Field3DParallel field;
+
+  field = 2.0;
+  field.yup() = 3.0;
+  field.ydown() = 4.0;
+
+  const auto base = field + 1.0;
+  const auto expr = floor(base, 4.5, "RGN_ALL");
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(expr)>,
+                              BinaryExpr<Field3D, std::decay_t<decltype(base)>,
+                                         Constant<BoutReal>, bout::op::Floor>>));
+
+  Field3DParallel result{expr};
+
+  EXPECT_TRUE(result.hasParallelSlices());
+  EXPECT_TRUE(IsFieldEqual(result, 4.5));
+  EXPECT_TRUE(IsFieldEqual(result.yup(), 4.5));
+  EXPECT_TRUE(IsFieldEqual(result.ydown(), 5.0));
+}
+
 TEST_F(Field3DTest, Min) {
   Field3D field;
 
diff --git a/tests/unit/field/test_fieldperp.cxx b/tests/unit/field/test_fieldperp.cxx
index 46f07d589f..754316e077 100644
--- a/tests/unit/field/test_fieldperp.cxx
+++ b/tests/unit/field/test_fieldperp.cxx
@@ -1713,6 +1713,20 @@ TEST_F(FieldPerpTest, Floor) {
   EXPECT_TRUE(IsFieldEqual(floor(field, floor_value), floor_value));
 }
 
+TEST_F(FieldPerpTest, FloorExpressionUsesFloorOp) {
+  FieldPerp field;
+  field.setIndex(0);
+
+  field = 2.0;
+  const auto expr = field + 1.0;
+
+  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(floor(expr, 5.0))>,
+                              BinaryExpr<FieldPerp, std::decay_t<decltype(expr)>,
+                                         Constant<BoutReal>, bout::op::Floor>>));
+  EXPECT_TRUE(IsFieldEqual(floor(expr, 5.0), 5.0));
+  EXPECT_TRUE(IsFieldEqual(floor(expr, 5.0, "RGN_ALL"), 5.0));
+}
+
 TEST_F(FieldPerpTest, Min) {
   FieldPerp field;
   field.setIndex(0);

From b9d13fd154a1f5ef7fcf522d39212a4a3e48cdce Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 10 Jul 2026 19:32:48 +0000
Subject: [PATCH 1634/1827] Bump astral-sh/setup-uv from 5 to 7

Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 5 to 7.
- [Release notes](https://github.com/astral-sh/setup-uv/releases)
- [Commits](https://github.com/astral-sh/setup-uv/compare/v5...v7)

---
updated-dependencies:
- dependency-name: astral-sh/setup-uv
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 06294e6091..7ad1f6e70b 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -158,7 +158,7 @@ jobs:
           submodules: true
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           enable-cache: true
 

From c7493e49edb7d6300e2cd0d13fac677b3b4e93bc Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 10 Jul 2026 13:07:07 -0700
Subject: [PATCH 1635/1827] generated_fieldops: Remove eager functions

Arithmetic operators now use the lazy `BinaryExpr` expressions.
---
 include/bout/field3d.hxx         |   10 -
 src/field/gen_fieldops.jinja     |    6 +-
 src/field/gen_fieldops.py        |   18 +
 src/field/generated_fieldops.cxx | 1336 ------------------------------
 tests/unit/fake_mesh.hxx         |    3 +-
 5 files changed, 24 insertions(+), 1349 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 63e20c349e..ade329bb6c 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -1211,16 +1211,6 @@ struct is_expr_field3d<BinaryExpr<ResT, L, R, Fun>>
     : std::integral_constant<bool, is_expr_field3d<std::decay_t<L>>::value
                                        || is_expr_field3d_v<std::decay_t<R>>> {};
 
-Field3D operator+(const Field2D& lhs, const Field3DParallel& rhs);
-Field3D operator-(const Field2D& lhs, const Field3DParallel& rhs);
-Field3D operator*(const Field2D& lhs, const Field3DParallel& rhs);
-Field3D operator/(const Field2D& lhs, const Field3DParallel& rhs);
-
-Field3D operator+(const Field3DParallel& lhs, const Field2D& rhs);
-Field3D operator-(const Field3DParallel& lhs, const Field2D& rhs);
-Field3D operator*(const Field3DParallel& lhs, const Field2D& rhs);
-Field3D operator/(const Field3DParallel& lhs, const Field2D& rhs);
-
 inline Field3DParallel
 filledFrom(const Field3DParallel& f,
            const std::function<BoutReal(int yoffset, Ind3D index)>& func) {
diff --git a/src/field/gen_fieldops.jinja b/src/field/gen_fieldops.jinja
index 913acadf7b..89f46469bd 100644
--- a/src/field/gen_fieldops.jinja
+++ b/src/field/gen_fieldops.jinja
@@ -1,6 +1,7 @@
 {% set use_parallel_arg = lhs.field_type == "Field3DParallel" or rhs.field_type == "Field3DParallel" %}
 {% set use_raja_path = region_loop == "BOUT_FOR_RAJA" and not use_parallel_arg %}
 
+{% if emit_free_binary %}
 // Provide the C++ wrapper for {{operator_name}} of {{lhs}} and {{rhs}}
 {{out}} operator{{operator}}(const {{lhs.passByReference}}, const {{rhs.passByReference}}) {
   {% if lhs != "BoutReal" and rhs != "BoutReal" %}
@@ -140,8 +141,9 @@
   checkData({{out.name}});
   return {{out.name}};
 }
+{% endif %}
 
-{% if out.field_type == lhs.field_type and lhs == "Field3D" %}
+{% if emit_update_inplace %}
 // Provide the C++ operator to update {{lhs}} by {{operator_name}} with {{rhs}}
 {{lhs}} &{{lhs}}::update_{{operator_name}}_inplace(const {{rhs.passByReference}}) {
   // only if data is unique we update the field
@@ -234,7 +236,7 @@
 {% endif %}
 
 
-{% if out.field_type == lhs.field_type %}
+{% if emit_member_op_equals %}
 // Provide the C++ operator to update {{lhs}} by {{operator_name}} with {{rhs}}
 {{lhs}} &{{lhs}}::operator{{operator}}=(const {{rhs.passByReference}}) {
   // only if data is unique we update the field
diff --git a/src/field/gen_fieldops.py b/src/field/gen_fieldops.py
index 6610286af5..e77530ff97 100755
--- a/src/field/gen_fieldops.py
+++ b/src/field/gen_fieldops.py
@@ -254,6 +254,21 @@ def returnType(f1, f2):
         return copy(field3D)
 
 
+def emit_free_binary_wrapper(out):
+    """Return True if this operator still needs an eager non-member wrapper."""
+    return out.field_type == "FieldPerp"
+
+
+def emit_update_inplace(lhs, out):
+    """Return True if this operator needs a Field3D update_*_inplace definition."""
+    return out.field_type == lhs.field_type and lhs.field_type == "Field3D"
+
+
+def emit_member_operator_equals(lhs, out):
+    """Return True if this operator needs an in-place operator definition."""
+    return out.field_type == lhs.field_type
+
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         description="Generate code for the Field arithmetic operators"
@@ -365,6 +380,9 @@ def returnType(f1, f2):
                 "out": out,
                 "lhs": lhs,
                 "rhs": rhs,
+                "emit_free_binary": emit_free_binary_wrapper(out),
+                "emit_update_inplace": emit_update_inplace(lhs, out),
+                "emit_member_op_equals": emit_member_operator_equals(lhs, out),
                 #
                 "region_loop": region_loop,
                 "region_name": region_name,
diff --git a/src/field/generated_fieldops.cxx b/src/field/generated_fieldops.cxx
index d47b2a7a89..1e9ade4ba4 100644
--- a/src/field/generated_fieldops.cxx
+++ b/src/field/generated_fieldops.cxx
@@ -9,23 +9,6 @@
 #include <bout/mesh.hxx>
 #include <bout/region.hxx>
 
-// Provide the C++ wrapper for multiplication of Field3D and Field3D
-Field3D operator*(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by multiplication with Field3D
 Field3D& Field3D::update_multiplication_inplace(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -78,23 +61,6 @@ Field3D& Field3D::operator*=(const Field3D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for division of Field3D and Field3D
-Field3D operator/(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] / rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by division with Field3D
 Field3D& Field3D::update_division_inplace(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -147,23 +113,6 @@ Field3D& Field3D::operator/=(const Field3D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for addition of Field3D and Field3D
-Field3D operator+(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by addition with Field3D
 Field3D& Field3D::update_addition_inplace(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -216,23 +165,6 @@ Field3D& Field3D::operator+=(const Field3D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for subtraction of Field3D and Field3D
-Field3D operator-(const Field3D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by subtraction with Field3D
 Field3D& Field3D::update_subtraction_inplace(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -285,28 +217,6 @@ Field3D& Field3D::operator-=(const Field3D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for multiplication of Field3D and Field2D
-Field3D operator*(const Field3D& lhs, const Field2D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR_SERIAL(index, rhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[base_ind + jz] * rhs[index];
-    }
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by multiplication with Field2D
 Field3D& Field3D::update_multiplication_inplace(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -365,29 +275,6 @@ Field3D& Field3D::operator*=(const Field2D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for division of Field3D and Field2D
-Field3D operator/(const Field3D& lhs, const Field2D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR_SERIAL(index, rhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    const auto tmp = 1.0 / rhs[index];
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[base_ind + jz] * tmp;
-    }
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by division with Field2D
 Field3D& Field3D::update_division_inplace(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -448,28 +335,6 @@ Field3D& Field3D::operator/=(const Field2D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for addition of Field3D and Field2D
-Field3D operator+(const Field3D& lhs, const Field2D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR_SERIAL(index, rhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[base_ind + jz] + rhs[index];
-    }
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by addition with Field2D
 Field3D& Field3D::update_addition_inplace(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -528,28 +393,6 @@ Field3D& Field3D::operator+=(const Field2D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for subtraction of Field3D and Field2D
-Field3D operator-(const Field3D& lhs, const Field2D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR_SERIAL(index, rhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[base_ind + jz] - rhs[index];
-    }
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by subtraction with Field2D
 Field3D& Field3D::update_subtraction_inplace(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -684,22 +527,6 @@ FieldPerp operator-(const Field3D& lhs, const FieldPerp& rhs) {
   return result;
 }
 
-// Provide the C++ wrapper for multiplication of Field3D and BoutReal
-Field3D operator*(const Field3D& lhs, const BoutReal rhs) {
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by multiplication with BoutReal
 Field3D& Field3D::update_multiplication_inplace(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -746,23 +573,6 @@ Field3D& Field3D::operator*=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for division of Field3D and BoutReal
-Field3D operator/(const Field3D& lhs, const BoutReal rhs) {
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  const auto tmp = 1.0 / rhs;
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * tmp;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by division with BoutReal
 Field3D& Field3D::update_division_inplace(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -811,22 +621,6 @@ Field3D& Field3D::operator/=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for addition of Field3D and BoutReal
-Field3D operator+(const Field3D& lhs, const BoutReal rhs) {
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by addition with BoutReal
 Field3D& Field3D::update_addition_inplace(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -873,22 +667,6 @@ Field3D& Field3D::operator+=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for subtraction of Field3D and BoutReal
-Field3D operator-(const Field3D& lhs, const BoutReal rhs) {
-
-  Field3D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3D by subtraction with BoutReal
 Field3D& Field3D::update_subtraction_inplace(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -935,109 +713,6 @@ Field3D& Field3D::operator-=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for multiplication of Field2D and Field3D
-Field3D operator*(const Field2D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR_SERIAL(index, lhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[index] * rhs[base_ind + jz];
-    }
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for division of Field2D and Field3D
-Field3D operator/(const Field2D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR_SERIAL(index, lhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[index] / rhs[base_ind + jz];
-    }
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for addition of Field2D and Field3D
-Field3D operator+(const Field2D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR_SERIAL(index, lhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[index] + rhs[base_ind + jz];
-    }
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for subtraction of Field2D and Field3D
-Field3D operator-(const Field2D& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  Mesh* localmesh = lhs.getMesh();
-
-  BOUT_FOR_SERIAL(index, lhs.getRegion("RGN_ALL")) {
-    const auto base_ind = localmesh->ind2Dto3D(index);
-    for (int jz = 0; jz < localmesh->LocalNz; ++jz) {
-      result[base_ind + jz] = lhs[index] - rhs[base_ind + jz];
-    }
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for multiplication of Field2D and Field2D
-Field2D operator*(const Field2D& lhs, const Field2D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field2D by multiplication with Field2D
 Field2D& Field2D::operator*=(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -1058,21 +733,6 @@ Field2D& Field2D::operator*=(const Field2D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for division of Field2D and Field2D
-Field2D operator/(const Field2D& lhs, const Field2D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] / rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field2D by division with Field2D
 Field2D& Field2D::operator/=(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -1093,21 +753,6 @@ Field2D& Field2D::operator/=(const Field2D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for addition of Field2D and Field2D
-Field2D operator+(const Field2D& lhs, const Field2D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field2D by addition with Field2D
 Field2D& Field2D::operator+=(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -1128,21 +773,6 @@ Field2D& Field2D::operator+=(const Field2D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for subtraction of Field2D and Field2D
-Field2D operator-(const Field2D& lhs, const Field2D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field2D by subtraction with Field2D
 Field2D& Field2D::operator-=(const Field2D& rhs) {
   // only if data is unique we update the field
@@ -1239,20 +869,6 @@ FieldPerp operator-(const Field2D& lhs, const FieldPerp& rhs) {
   return result;
 }
 
-// Provide the C++ wrapper for multiplication of Field2D and BoutReal
-Field2D operator*(const Field2D& lhs, const BoutReal rhs) {
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field2D by multiplication with BoutReal
 Field2D& Field2D::operator*=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -1272,21 +888,6 @@ Field2D& Field2D::operator*=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for division of Field2D and BoutReal
-Field2D operator/(const Field2D& lhs, const BoutReal rhs) {
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  const auto tmp = 1.0 / rhs;
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * tmp;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field2D by division with BoutReal
 Field2D& Field2D::operator/=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -1307,20 +908,6 @@ Field2D& Field2D::operator/=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for addition of Field2D and BoutReal
-Field2D operator+(const Field2D& lhs, const BoutReal rhs) {
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field2D by addition with BoutReal
 Field2D& Field2D::operator+=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -1340,20 +927,6 @@ Field2D& Field2D::operator+=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for subtraction of Field2D and BoutReal
-Field2D operator-(const Field2D& lhs, const BoutReal rhs) {
-
-  Field2D result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field2D by subtraction with BoutReal
 Field2D& Field2D::operator-=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -2006,126 +1579,6 @@ FieldPerp& FieldPerp::operator-=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for multiplication of BoutReal and Field3D
-Field3D operator*(const BoutReal lhs, const Field3D& rhs) {
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs * rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for division of BoutReal and Field3D
-Field3D operator/(const BoutReal lhs, const Field3D& rhs) {
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs / rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for addition of BoutReal and Field3D
-Field3D operator+(const BoutReal lhs, const Field3D& rhs) {
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs + rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for subtraction of BoutReal and Field3D
-Field3D operator-(const BoutReal lhs, const Field3D& rhs) {
-
-  Field3D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs - rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for multiplication of BoutReal and Field2D
-Field2D operator*(const BoutReal lhs, const Field2D& rhs) {
-
-  Field2D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs * rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for division of BoutReal and Field2D
-Field2D operator/(const BoutReal lhs, const Field2D& rhs) {
-
-  Field2D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs / rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for addition of BoutReal and Field2D
-Field2D operator+(const BoutReal lhs, const Field2D& rhs) {
-
-  Field2D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs + rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for subtraction of BoutReal and Field2D
-Field2D operator-(const BoutReal lhs, const Field2D& rhs) {
-
-  Field2D result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs - rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ wrapper for multiplication of BoutReal and FieldPerp
 FieldPerp operator*(const BoutReal lhs, const FieldPerp& rhs) {
 
@@ -2182,216 +1635,6 @@ FieldPerp operator-(const BoutReal lhs, const FieldPerp& rhs) {
   return result;
 }
 
-// Provide the C++ wrapper for multiplication of Field3D and Field3DParallel
-Field3DParallel operator*(const Field3D& lhs, const Field3DParallel& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) * rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for division of Field3D and Field3DParallel
-Field3DParallel operator/(const Field3D& lhs, const Field3DParallel& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) / rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] / rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for addition of Field3D and Field3DParallel
-Field3DParallel operator+(const Field3D& lhs, const Field3DParallel& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) + rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for subtraction of Field3D and Field3DParallel
-Field3DParallel operator-(const Field3D& lhs, const Field3DParallel& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) - rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for multiplication of Field3DParallel and Field3D
-Field3DParallel operator*(const Field3DParallel& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) * rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by multiplication with Field3D
 Field3DParallel& Field3DParallel::operator*=(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -2431,48 +1674,6 @@ Field3DParallel& Field3DParallel::operator*=(const Field3D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for division of Field3DParallel and Field3D
-Field3DParallel operator/(const Field3DParallel& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) / rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] / rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by division with Field3D
 Field3DParallel& Field3DParallel::operator/=(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -2512,48 +1713,6 @@ Field3DParallel& Field3DParallel::operator/=(const Field3D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for addition of Field3DParallel and Field3D
-Field3DParallel operator+(const Field3DParallel& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) + rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by addition with Field3D
 Field3DParallel& Field3DParallel::operator+=(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -2593,48 +1752,6 @@ Field3DParallel& Field3DParallel::operator+=(const Field3D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for subtraction of Field3DParallel and Field3D
-Field3DParallel operator-(const Field3DParallel& lhs, const Field3D& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) - rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by subtraction with Field3D
 Field3DParallel& Field3DParallel::operator-=(const Field3D& rhs) {
   // only if data is unique we update the field
@@ -2674,48 +1791,6 @@ Field3DParallel& Field3DParallel::operator-=(const Field3D& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for multiplication of Field3DParallel and Field3DParallel
-Field3DParallel operator*(const Field3DParallel& lhs, const Field3DParallel& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) * rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) * rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by multiplication with Field3DParallel
 Field3DParallel& Field3DParallel::operator*=(const Field3DParallel& rhs) {
   // only if data is unique we update the field
@@ -2755,48 +1830,6 @@ Field3DParallel& Field3DParallel::operator*=(const Field3DParallel& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for division of Field3DParallel and Field3DParallel
-Field3DParallel operator/(const Field3DParallel& lhs, const Field3DParallel& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) / rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) / rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] / rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by division with Field3DParallel
 Field3DParallel& Field3DParallel::operator/=(const Field3DParallel& rhs) {
   // only if data is unique we update the field
@@ -2836,48 +1869,6 @@ Field3DParallel& Field3DParallel::operator/=(const Field3DParallel& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for addition of Field3DParallel and Field3DParallel
-Field3DParallel operator+(const Field3DParallel& lhs, const Field3DParallel& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) + rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) + rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by addition with Field3DParallel
 Field3DParallel& Field3DParallel::operator+=(const Field3DParallel& rhs) {
   // only if data is unique we update the field
@@ -2917,48 +1908,6 @@ Field3DParallel& Field3DParallel::operator+=(const Field3DParallel& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for subtraction of Field3DParallel and Field3DParallel
-Field3DParallel operator-(const Field3DParallel& lhs, const Field3DParallel& rhs) {
-  ASSERT1_FIELDS_COMPATIBLE(lhs, rhs);
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getMesh()->getCommonRegion(lhs.getRegionID(), rhs.getRegionID()));
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) - rhs.yup(i);
-      result.ydown(i) = lhs.ydown(i) - rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by subtraction with Field3DParallel
 Field3DParallel& Field3DParallel::operator-=(const Field3DParallel& rhs) {
   // only if data is unique we update the field
@@ -2998,42 +1947,6 @@ Field3DParallel& Field3DParallel::operator-=(const Field3DParallel& rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for multiplication of Field3DParallel and BoutReal
-Field3DParallel operator*(const Field3DParallel& lhs, const BoutReal rhs) {
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) * rhs;
-      result.ydown(i) = lhs.ydown(i) * rhs;
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * rhs;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by multiplication with BoutReal
 Field3DParallel& Field3DParallel::operator*=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -3070,43 +1983,6 @@ Field3DParallel& Field3DParallel::operator*=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for division of Field3DParallel and BoutReal
-Field3DParallel operator/(const Field3DParallel& lhs, const BoutReal rhs) {
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) / rhs;
-      result.ydown(i) = lhs.ydown(i) / rhs;
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  const auto tmp = 1.0 / rhs;
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] * tmp;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by division with BoutReal
 Field3DParallel& Field3DParallel::operator/=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -3143,42 +2019,6 @@ Field3DParallel& Field3DParallel::operator/=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for addition of Field3DParallel and BoutReal
-Field3DParallel operator+(const Field3DParallel& lhs, const BoutReal rhs) {
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) + rhs;
-      result.ydown(i) = lhs.ydown(i) + rhs;
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] + rhs;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by addition with BoutReal
 Field3DParallel& Field3DParallel::operator+=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -3215,42 +2055,6 @@ Field3DParallel& Field3DParallel::operator+=(const BoutReal rhs) {
   return *this;
 }
 
-// Provide the C++ wrapper for subtraction of Field3DParallel and BoutReal
-Field3DParallel operator-(const Field3DParallel& lhs, const BoutReal rhs) {
-
-  Field3DParallel result{emptyFrom(lhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(lhs.getRegionID());
-  if (result.isFci()) {
-
-    ASSERT2(lhs.hasParallelSlices());
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      ASSERT2(lhs.ydown(i).isAllocated());
-      ASSERT2(lhs.yup(i).isAllocated());
-    }
-
-    result.splitParallelSlices();
-    for (size_t i{0}; i < lhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs.yup(i) - rhs;
-      result.ydown(i) = lhs.ydown(i) - rhs;
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs[index] - rhs;
-  }
-  checkData(result);
-  return result;
-}
-
 // Provide the C++ operator to update Field3DParallel by subtraction with BoutReal
 Field3DParallel& Field3DParallel::operator-=(const BoutReal rhs) {
   // only if data is unique we update the field
@@ -3286,143 +2090,3 @@ Field3DParallel& Field3DParallel::operator-=(const BoutReal rhs) {
   }
   return *this;
 }
-
-// Provide the C++ wrapper for multiplication of BoutReal and Field3DParallel
-Field3DParallel operator*(const BoutReal lhs, const Field3DParallel& rhs) {
-
-  Field3DParallel result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-  if (result.isFci()) {
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs * rhs.yup(i);
-      result.ydown(i) = lhs * rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs * rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for division of BoutReal and Field3DParallel
-Field3DParallel operator/(const BoutReal lhs, const Field3DParallel& rhs) {
-
-  Field3DParallel result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-  if (result.isFci()) {
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs / rhs.yup(i);
-      result.ydown(i) = lhs / rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs / rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for addition of BoutReal and Field3DParallel
-Field3DParallel operator+(const BoutReal lhs, const Field3DParallel& rhs) {
-
-  Field3DParallel result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-  if (result.isFci()) {
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs + rhs.yup(i);
-      result.ydown(i) = lhs + rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs + rhs[index];
-  }
-  checkData(result);
-  return result;
-}
-
-// Provide the C++ wrapper for subtraction of BoutReal and Field3DParallel
-Field3DParallel operator-(const BoutReal lhs, const Field3DParallel& rhs) {
-
-  Field3DParallel result{emptyFrom(rhs)};
-  checkData(lhs);
-  checkData(rhs);
-
-  result.setRegion(rhs.getRegionID());
-  if (result.isFci()) {
-
-    ASSERT2(rhs.hasParallelSlices());
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      ASSERT2(rhs.ydown(i).isAllocated());
-      ASSERT2(rhs.yup(i).isAllocated());
-    }
-    result.splitParallelSlices();
-    for (size_t i{0}; i < rhs.numberParallelSlices(); ++i) {
-      result.yup(i) = lhs - rhs.yup(i);
-      result.ydown(i) = lhs - rhs.ydown(i);
-    }
-
-    ASSERT2(result.hasParallelSlices());
-    for (size_t i{0}; i < result.numberParallelSlices(); ++i) {
-      ASSERT2(result.ydown(i).isAllocated());
-      ASSERT2(result.yup(i).isAllocated());
-    }
-  }
-
-  BOUT_FOR_SERIAL(index, result.getValidRegionWithDefault("RGN_ALL")) {
-    result[index] = lhs - rhs[index];
-  }
-  checkData(result);
-  return result;
-}
diff --git a/tests/unit/fake_mesh.hxx b/tests/unit/fake_mesh.hxx
index 6559e554f2..216d04e18a 100644
--- a/tests/unit/fake_mesh.hxx
+++ b/tests/unit/fake_mesh.hxx
@@ -13,6 +13,7 @@
 #include <bout/griddata.hxx>
 #include <bout/mesh.hxx>
 #include <bout/mpi_wrapper.hxx>
+#include <bout/paralleltransform.hxx>
 #include <bout/region.hxx>
 #include <bout/sys/range.hxx>
 #include <bout/unused.hxx>
@@ -90,7 +91,7 @@ public:
 
   void setCoordinates(std::shared_ptr<Coordinates> coords,
                       CELL_LOC location = CELL_CENTRE) {
-    coords_map[location] = coords;
+    coords_map[location] = std::move(coords);
   }
 
   void setGridDataSource(GridDataSource* source_in) { source = source_in; }

From d41d93c85d37993a5109815c66d714728a9c4f95 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 10 Jul 2026 16:30:57 -0700
Subject: [PATCH 1636/1827] Field3DParallel::View simplify

Remove unnecessary data members that dublicate the Field3D::View base.
---
 include/bout/field3d.hxx | 46 ++++++++++++++++------------------------
 1 file changed, 18 insertions(+), 28 deletions(-)

diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index ade329bb6c..5562c58b49 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -488,11 +488,13 @@ public:
     BOUT_HOST_DEVICE BOUT_FORCEINLINE int numberParallelSlices() const {
       return num_parallel_slices;
     }
+    /// Not a DEVICE function because it dereferences a Field3D pointer
     BOUT_FORCEINLINE View yup(int slice = 0) const {
       ASSERT2(slice < num_parallel_slices);
       ASSERT2(yup_fields[slice].isAllocated());
       return static_cast<Field3D::View>(yup_fields[slice]);
     }
+    /// Not a DEVICE function because it dereferences a Field3D pointer
     BOUT_FORCEINLINE View ydown(int slice = 0) const {
       ASSERT2(slice < num_parallel_slices);
       ASSERT2(ydown_fields[slice].isAllocated());
@@ -500,14 +502,11 @@ public:
     }
   };
   operator View() {
-    return View{&data[0], hasParallelSlices() ? yup_fields.data() : nullptr,
-                hasParallelSlices() ? ydown_fields.data() : nullptr,
+    return View{&data[0], yup_fields.data(), ydown_fields.data(),
                 static_cast<int>(numberParallelSlices())};
   }
   operator View() const {
-    return View{const_cast<BoutReal*>(&data[0]),
-                hasParallelSlices() ? yup_fields.data() : nullptr,
-                hasParallelSlices() ? ydown_fields.data() : nullptr,
+    return View{const_cast<BoutReal*>(&data[0]), yup_fields.data(), ydown_fields.data(),
                 static_cast<int>(numberParallelSlices())};
   }
   //operator View() const { return View{&data[0]}; }
@@ -1064,9 +1063,6 @@ public:
 
   struct View {
     Field3D::View base;
-    const Field3D* yup_fields{nullptr};
-    const Field3D* ydown_fields{nullptr};
-    int num_parallel_slices{0};
 
     BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return base(idx);
@@ -1082,32 +1078,26 @@ public:
       return *this;
     }
 
-    BOUT_FORCEINLINE bool hasParallelSlices() const { return num_parallel_slices > 0; }
-    BOUT_FORCEINLINE int numberParallelSlices() const { return num_parallel_slices; }
+    BOUT_FORCEINLINE bool hasParallelSlices() const { return base.hasParallelSlices(); }
+    BOUT_FORCEINLINE int numberParallelSlices() const {
+      return base.numberParallelSlices();
+    }
+    /// Not a DEVICE function because it dereferences a Field3D pointer
     BOUT_FORCEINLINE View yup(int slice = 0) const {
-      ASSERT2(slice < num_parallel_slices);
-      ASSERT2(yup_fields[slice].isAllocated());
-      return View{static_cast<Field3D::View>(yup_fields[slice]), nullptr, nullptr, 0};
+      ASSERT2(slice < base.num_parallel_slices);
+      ASSERT2(base.yup_fields[slice].isAllocated());
+      return View{static_cast<Field3D::View>(base.yup_fields[slice])};
     }
+    /// Not a DEVICE function because it dereferences a Field3D pointer
     BOUT_FORCEINLINE View ydown(int slice = 0) const {
-      ASSERT2(slice < num_parallel_slices);
-      ASSERT2(ydown_fields[slice].isAllocated());
-      return View{static_cast<Field3D::View>(ydown_fields[slice]), nullptr, nullptr, 0};
+      ASSERT2(slice < base.num_parallel_slices);
+      ASSERT2(base.ydown_fields[slice].isAllocated());
+      return View{static_cast<Field3D::View>(base.ydown_fields[slice])};
     }
   };
 
-  operator View() {
-    return View{static_cast<Field3D::View>(*this),
-                hasParallelSlices() ? yup_fields.data() : nullptr,
-                hasParallelSlices() ? ydown_fields.data() : nullptr,
-                static_cast<int>(numberParallelSlices())};
-  }
-  operator View() const {
-    return View{static_cast<Field3D::View>(*this),
-                hasParallelSlices() ? yup_fields.data() : nullptr,
-                hasParallelSlices() ? ydown_fields.data() : nullptr,
-                static_cast<int>(numberParallelSlices())};
-  }
+  operator View() { return View{static_cast<Field3D::View>(*this)}; }
+  operator View() const { return View{static_cast<Field3D::View>(*this)}; }
 
   Field3DParallel& operator*=(const Field3D&);
   Field3DParallel& operator/=(const Field3D&);

From 3c6565df8e66cfeb7c70ea1ccaad90001c7da664 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 10 Jul 2026 16:49:40 -0700
Subject: [PATCH 1637/1827] manual: Updates for Field3DParallel expressions

---
 manual/sphinx/developer_docs/data_types.rst   | 33 ++++++++++-------
 .../sphinx/user_docs/algebraic_operators.rst  | 17 +++++++--
 manual/sphinx/user_docs/field_expressions.rst | 35 +++++++++++++++----
 3 files changed, 64 insertions(+), 21 deletions(-)

diff --git a/manual/sphinx/developer_docs/data_types.rst b/manual/sphinx/developer_docs/data_types.rst
index 7feb3945aa..ba4faa6e42 100644
--- a/manual/sphinx/developer_docs/data_types.rst
+++ b/manual/sphinx/developer_docs/data_types.rst
@@ -515,37 +515,44 @@ central type is ``BinaryExpr``, which stores:
   result
 - a cached list of linear region indices describing where the
   expression is valid
+- for 3D expressions, any parallel-slice structure needed to evaluate
+  matching ``yup`` and ``ydown`` expressions
 
-`Field2D`, `Field3D`, and `FieldPerp` act as expression leaves by
-providing lightweight ``View`` types. Those views are the device- and
-backend-friendly objects used by the expression evaluator.
+`Field2D`, `Field3D`, `Field3DParallel`, and `FieldPerp` act as
+expression leaves by providing lightweight ``View`` types. Constants are
+also wrapped in small view objects so they can participate in the same
+expression machinery. These views are the device- and backend-friendly
+objects used by the expression evaluator.
 
 Materialization happens when a field is constructed or assigned from an
 expression, when an expression is stored in `Options`, or when a scalar
 reduction such as ``min`` or ``mean`` is requested. The same mechanism
 is also used to propagate metadata such as mesh, staggered location,
-directions, and `FieldPerp` y-index.
+directions, `FieldPerp` y-index, and for `Field3DParallel` the
+forward/backward parallel slices on FCI meshes.
 
 The unary algebraic helpers in ``include/bout/field.hxx`` build on the
 same mechanism. Functions such as ``sqrt``, ``abs``, ``SQ``,
-``if_else``, ``if_else_zero``, ``min``, ``max``, and ``mean`` can all
-operate directly on lazy expressions.
+``pow``, ``floor``, ``if_else``, ``if_else_zero``, ``min``, ``max``,
+and ``mean`` can all operate directly on lazy expressions.
 
 Generated eager operators
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The eager arithmetic operators and in-place update paths are still
-generated automatically using the `Jinja`_ templating system. The main
-files are:
+The remaining eager arithmetic operators and in-place update paths are
+still generated automatically using the `Jinja`_ templating system. The
+main files are:
 
 - ``src/field/gen_fieldops.jinja``
 - ``src/field/gen_fieldops.py``
 - ``src/field/generated_fieldops.cxx``
 
-The generated code handles the broad matrix of combinations between
-`BoutReal`, `Field2D`, `Field3D`, `Field3DParallel`, and `FieldPerp`,
-including several mixed-rank and in-place cases where hand-maintaining
-all overloads would be error-prone.
+The generated code still handles combinations between `BoutReal`,
+`Field2D`, `Field3D`, `Field3DParallel`, and `FieldPerp`, especially the
+eager `FieldPerp` wrappers and in-place update operators where
+hand-maintaining all overloads would be error-prone. More free
+non-member arithmetic now lives in the header-defined lazy-expression
+path, so the generator covers a smaller subset than it used to.
 
 The generated loops now also depend on the configured execution backend.
 At configure time, the generator is told whether to emit RAJA-based,
diff --git a/manual/sphinx/user_docs/algebraic_operators.rst b/manual/sphinx/user_docs/algebraic_operators.rst
index b8c40d4dc5..6955ab5580 100644
--- a/manual/sphinx/user_docs/algebraic_operators.rst
+++ b/manual/sphinx/user_docs/algebraic_operators.rst
@@ -30,7 +30,7 @@ Common operators
    +------------------------------------------+------------------------------------------------------+
    | ``mean(f, allpe=true, region)``          | Mean (optionally over all processes)                 |
    +------------------------------------------+------------------------------------------------------+
-   | ``pow(lhs, rhs, region)``                | :math:`\mathtt{lhs}^\mathtt{rhs}`                    |
+   | ``pow(lhs, rhs[, region])``              | :math:`\mathtt{lhs}^\mathtt{rhs}`                    |
    +------------------------------------------+------------------------------------------------------+
    | ``SQ(f, region)``                        | Square of ``f``                                      |
    +------------------------------------------+------------------------------------------------------+
@@ -54,7 +54,8 @@ Common operators
    +------------------------------------------+------------------------------------------------------+
    | ``tanh(f, region)``                      | :math:`\tanh(f)`                                     |
    +------------------------------------------+------------------------------------------------------+
-   | ``floor(f, region)``                     | Returns a field with the floor of `f` at each point  |
+   | ``floor(f, floor_value[, region])``      | Returns a field where values below ``floor_value``   |
+   |                                          | are replaced by ``floor_value``                      |
    +------------------------------------------+------------------------------------------------------+
    | ``filter(f, n, region)``                 | Calculate the amplitude of the Fourier mode in the   |
    |                                          | z-direction with mode number `n`                     |
@@ -84,12 +85,18 @@ Common operators
 These operators can usually be combined directly in expressions::
 
   Field3D rhs = sqrt(SQ(n) + SQ(T));
+  Field3D profile = pow(n + n0, 1.5);
   Field3D masked = if_else(use_drive, source * profile, sink * profile);
   BoutReal max_error = max(abs(lhs - rhs), true);
 
 Reductions such as ``min``, ``max``, and ``mean`` can operate directly
 on an expression, so an intermediate field is often unnecessary.
 
+``pow`` also participates in lazy field expressions, including mixed
+`Field2D`/`Field3D` cases where the `Field2D` operand is broadcast in
+``z``. `FieldPerp` also has ``pow`` overloads for `FieldPerp` with
+`FieldPerp` or a scalar.
+
 Region arguments
 ----------------
 
@@ -108,6 +115,12 @@ When a region-limited expression is materialized into a field, only the
 selected region is guaranteed to contain valid values. This is the same
 performance-oriented convention used by other field operators.
 
+`Field3DParallel` follows the same rule for the main field data. On FCI
+meshes, materializing a lazy expression into `Field3DParallel` also
+preserves the forward and backward parallel slices when those slices are
+available on the expression operands. Materializing the same expression
+into plain `Field3D` does not preserve those slices.
+
 Further reading
 ---------------
 
diff --git a/manual/sphinx/user_docs/field_expressions.rst b/manual/sphinx/user_docs/field_expressions.rst
index 62a50988d6..7c82d48884 100644
--- a/manual/sphinx/user_docs/field_expressions.rst
+++ b/manual/sphinx/user_docs/field_expressions.rst
@@ -5,9 +5,9 @@ Field Expressions
 
 BOUT++ field algebra now supports *lazy expressions* for many common
 operations. Instead of creating a temporary field for every ``+``,
-``-``, ``*``, ``/``, ``sqrt`` or ``abs``, BOUT++ can keep the expression
-symbolic and evaluate it only when a concrete field or scalar result is
-needed.
+``-``, ``*``, ``/``, ``pow``, ``sqrt`` or ``abs``, BOUT++ can keep the
+expression symbolic and evaluate it only when a concrete field or scalar
+result is needed.
 
 This keeps ordinary model code readable while reducing temporary
 allocations and extra loops over the mesh. It is especially helpful for
@@ -21,9 +21,9 @@ The following operations can form lazy expressions over `Field2D`,
 sense:
 
 - Arithmetic operators: ``+``, ``-``, ``*``, ``/``
+- Binary algebraic helpers such as ``pow`` and ``floor``
 - Unary algebraic operators such as ``sqrt``, ``abs``, ``exp``, ``log``,
-  ``sin``, ``cos``, ``tan``, ``sinh``, ``cosh``, ``tanh``, ``floor``,
-  and ``SQ``
+  ``sin``, ``cos``, ``tan``, ``sinh``, ``cosh``, ``tanh``, and ``SQ``
 - Simple conditionals with ``if_else`` and ``if_else_zero``
 - Reductions such as ``min``, ``max``, and ``mean``
 
@@ -32,7 +32,7 @@ For example::
   Field3D n, T;
   Field3D result;
 
-  result = sqrt(SQ(n) + SQ(T));
+  result = sqrt(SQ(n) + pow(T + 1.0, 2.0));
 
 The right-hand side can stay lazy until the assignment to ``result``.
 
@@ -93,6 +93,8 @@ Several mixed-type combinations are supported directly:
 - `Field2D` with `Field3D`: the 2D quantity is broadcast in ``z``
 - `FieldPerp` with matching perpendicular data: the operation uses the
   `FieldPerp` y-index
+- `pow` follows the same mixed-rank pattern, so either operand can be
+  `Field2D` or `Field3D` and the result is a `Field3D`
 - expressions involving metric components may return
   `Coordinates::FieldMetric`, which is `Field2D` or `Field3D` depending
   on how BOUT++ was built
@@ -121,6 +123,27 @@ expression or zero::
 This is particularly convenient when optional source terms are enabled
 or disabled by compile-time or run-time logic.
 
+`Field3DParallel` and FCI
+-------------------------
+
+Lazy expressions can also carry parallel-slice information. This matters
+when working with `Field3DParallel` on FCI meshes:
+
+- materializing into `Field3DParallel` preserves ``yup`` and ``ydown``
+  slices
+- materializing the same expression into plain `Field3D` keeps only the
+  main field values
+- on FCI meshes, operands contributing to a `Field3DParallel`
+  expression must have compatible parallel slices available
+
+For example::
+
+  Field3DParallel f_par, g_par;
+  Field3DParallel result = sqrt(f_par + g_par);
+
+On a non-FCI mesh, assigning a lazy expression to `Field3DParallel`
+still evaluates the main field, but no parallel slices are retained.
+
 Reductions on expressions
 -------------------------
 

From 87f6feb331adeed9fcc171a295ee363a509e52d9 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 16 Jul 2026 12:03:17 -0700
Subject: [PATCH 1638/1827] Reapply "Merge pull request #3082 from
 boutproject/next-elimBE"

This reverts commit 81befc23a51139f22c8b2835cacebd16dfdd5457.
---
 CMakeLists.txt                                |   1 +
 include/bout/hypre_interface.hxx              | 185 +++++++++++++++++-
 .../laplace/impls/hypre3d/hypre3d_laplace.cxx |   5 +
 src/sys/hypre_interface.cxx                   | 131 +++++++++++++
 4 files changed, 320 insertions(+), 2 deletions(-)
 create mode 100644 src/sys/hypre_interface.cxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e6e424b55c..6b1c4290db 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -371,6 +371,7 @@ set(BOUT_SOURCES
     ./src/sys/generator_context.cxx
     ./include/bout/hyprelib.hxx
     ./src/sys/hyprelib.cxx
+    ./src/sys/hypre_interface.cxx
     ./src/sys/msg_stack.cxx
     ./src/sys/options.cxx
     ./src/sys/options/optionparser.hxx
diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index 189e91d159..f9f97b5bb3 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -58,6 +58,110 @@ int checkHypreError(int error) {
 // TODO: set sizes
 // TODO: set contiguous blocks at once
 
+/// Wrapper around HYPRE_Complex, that calls HypreFree when destroyed.
+struct HypreComplexArray {
+  HYPRE_Complex* data;
+
+  HypreComplexArray(int n) { HypreMalloc(data, sizeof(HYPRE_Complex) * n); }
+
+  ~HypreComplexArray() { HypreFree(data); }
+};
+
+/// Shared pointter to a HypreComplexArray. When the last copy is destroyed
+/// the HYPRE_Complex array inside will be free'd.
+using BCValuesPtr = std::shared_ptr<HypreComplexArray>;
+
+/*!
+ * This function modifies the input for the HYPRE_IJMatrixSetValues() routine to
+ * eliminate the boundary condition equations (see below for details on how the
+ * equations are adjusted).  It modifies the arrays ncols, rows, cols, and
+ * values.  It also returns a row_indexes array.  This can then be passed to the
+ * HYPRE_IJMatrixSetValues2() routine to set up the matrix in hypre.
+ *
+ * The arguments nb and bi_array indicate the boundary equations.  The routine
+ * returns info needed to adjust the right-hand-side and solution vector through
+ * the functions AdjustRightHandSideEquations and AdjustSolutionEquations.
+ *
+ * NOTE: It may make sense from an organizational standpoint to collect many of
+ * these arguments in a structure of some sort.
+ *
+ * Notation, assumptions, and other details:
+ *
+ * - Boundary equation i is assumed to have two coefficients
+ *
+ *      b_ii * u_i + b_ij * u_j = rhs_i
+ *
+ * - We also assume that each boundary equation has only one interior equation k
+ *   coupled to it (such that k = j) with coupling coefficient a_ki
+ *
+ *      a_ki * u_i + a_kj * u_j + ... = rhs_k
+ *
+ * - Each equation k is adjusted as follows:
+ *
+ *      a_kj = a_kj - a_ki * b_ij / b_ii
+ *      a_ki = 0
+ *
+ * - Boundary equations are adjusted to be identity equations in the matrix, but
+ *   the boundary coefficients (b_ii, b_ij) are returned for use later
+ *
+ * - Right-hand-side equations are adjusted in AdjustRightHandSideEquations() as
+ *   follows: rhs_k = rhs_k - a_ki * rhs_i / b_ii
+ *
+ * - Solution unknowns are adjusted at boundaries in AdjustSolutionEquations as
+ *   follows: u_i = (rhs_i - b_ij * u_j) / b_ii
+ *
+ * - Naming conventions: Arrays starting with 'b' are boundary equation arrays
+ *   indexed by 'bnum', and arrays starting with 'a' are non-boundary arrays
+ *   (interior matrix equations) indexed by 'anum'.  When 'num' is prefixed with
+ *   a row or column number 'i', 'j', or 'k', the array holds the corresponding
+ *   local data index for that row or column (e.g., an index into the local
+ *   solution vector).  Matrix coefficients are named as above, e.g., 'bij' is
+ *   the coefficient for b_ij.
+ *
+ *   NOTE: Implementation in src/sys/hypre_interface.cxx
+ */
+struct BCMatrixEquations {
+  HYPRE_Int nb;
+  HYPRE_Int* binum_array;
+  HYPRE_Int* bjnum_array;
+  HYPRE_Complex* bii_array;
+  HYPRE_Complex* bij_array;
+  HYPRE_Int na;
+  HYPRE_Int* aknum_array;
+  HYPRE_Complex* aki_array;
+
+  BCMatrixEquations() = delete;
+
+  BCMatrixEquations(HYPRE_Int nrows, HYPRE_Int* ncols, HYPRE_BigInt* rows,
+                    HYPRE_Int** row_indexes_ptr, HYPRE_BigInt* cols,
+                    HYPRE_Complex* values,
+                    HYPRE_Int nb,         // number of boundary equations
+                    HYPRE_Int* bi_array); // row i for each boundary equation
+
+  ~BCMatrixEquations() {
+    // Free arrays
+    HypreFree(binum_array);
+    HypreFree(bjnum_array);
+    HypreFree(bii_array);
+    HypreFree(bij_array);
+    HypreFree(aknum_array);
+    HypreFree(aki_array);
+  }
+
+  /// Applies in-place modification of the rhs array.
+  ///
+  /// Returns an array of boundary values that can be used to apply
+  /// boundary conditions to a solution vector.
+  BCValuesPtr adjustBCRightHandSideEquations(HYPRE_Complex* rhs);
+
+  /// Apply boundary conditions to the solution.
+  /// Uses the BCValuesPtr returned from adjustBCRightHandSideEquations()
+  void adjustBCSolutionEquations(BCValuesPtr brhs, HYPRE_Complex* solution);
+};
+
+/// A shared pointer to a BCMatrixEquations object
+using BCMatrixPtr = std::shared_ptr<BCMatrixEquations>;
+
 template <class T>
 class HypreVector {
   MPI_Comm comm;
@@ -174,6 +278,14 @@ public:
     HypreMalloc(V, vsize * sizeof(HYPRE_Complex));
   }
 
+  // Data for eliminating boundary equation
+  bool elimBErhs = false;
+  bool elimBEsol = false;
+  BCMatrixPtr bcmatrix;
+  BCValuesPtr bcvalues; /// Stores rhs values of BC rows
+
+  void syncElimBErhs(HypreVector<T>& rhs) { bcvalues = rhs.bcvalues; }
+
   void assemble() {
     CALI_CXX_MARK_FUNCTION;
     writeCacheToHypre();
@@ -183,11 +295,17 @@ public:
   }
 
   void writeCacheToHypre() {
+    if (elimBErhs) {
+      bcvalues = bcmatrix->adjustBCRightHandSideEquations(V);
+    }
     checkHypreError(HYPRE_IJVectorSetValues(hypre_vector, vsize, I, V));
   }
 
   void readCacheFromHypre() {
     checkHypreError(HYPRE_IJVectorGetValues(hypre_vector, vsize, I, V));
+    if (elimBEsol) {
+      bcmatrix->adjustBCSolutionEquations(bcvalues, V);
+    }
   }
 
   T toField() {
@@ -667,6 +785,20 @@ public:
     return Element(*this, global_row, global_column, positions, weights);
   }
 
+  // Data for eliminating boundary equations
+  bool elimBE = false;
+  BCMatrixPtr bcmatrix; // Shared pointer
+
+  void setElimBE() { elimBE = true; }
+
+  void setElimBEVectors(HypreVector<T>& sol, HypreVector<T>& rhs) {
+    sol.elimBEsol = elimBE;
+    sol.bcmatrix = bcmatrix;
+
+    rhs.elimBErhs = elimBE;
+    rhs.bcmatrix = bcmatrix;
+  }
+
   void assemble() {
     CALI_CXX_MARK_FUNCTION;
 
@@ -695,8 +827,32 @@ public:
         entry++;
       }
     }
-    checkHypreError(
-        HYPRE_IJMatrixSetValues(*hypre_matrix, num_rows, num_cols, rawI, cols, vals));
+
+    // Eliminate boundary condition equations in hypre SetValues input arguments
+    if (elimBE) {
+      HYPRE_Int* bi_array;
+      HYPRE_Int* row_indexes;
+      // There must be an easier way to get nb
+      int nb = 0;
+      BOUT_FOR_SERIAL(i, index_converter->getRegionBndry()) { nb++; }
+      HypreMalloc(bi_array, nb * sizeof(HYPRE_Int));
+      nb = 0;
+      BOUT_FOR_SERIAL(i, index_converter->getRegionBndry()) {
+        bi_array[nb] = index_converter->getGlobal(i);
+        nb++;
+      }
+
+      bcmatrix = std::make_shared<BCMatrixEquations>(
+          num_rows, num_cols, rawI, &row_indexes, cols, vals, nb, bi_array);
+      HypreFree(bi_array);
+
+      checkHypreError(HYPRE_IJMatrixSetValues2(*hypre_matrix, num_rows, num_cols, rawI,
+                                               row_indexes, cols, vals));
+      HypreFree(row_indexes);
+    } else {
+      checkHypreError(
+          HYPRE_IJMatrixSetValues(*hypre_matrix, num_rows, num_cols, rawI, cols, vals));
+    }
     checkHypreError(HYPRE_IJMatrixAssemble(*hypre_matrix));
     checkHypreError(HYPRE_IJMatrixGetObject(*hypre_matrix,
                                             reinterpret_cast<void**>(&parallel_matrix)));
@@ -876,6 +1032,31 @@ public:
     setMaxIter(
         options["maxits"].doc("Maximum iterations for Hypre solver").withDefault(10000));
 
+    switch (solver_type) {
+    case HYPRE_SOLVER_TYPE::gmres: {
+      HYPRE_ParCSRGMRESSetKDim(solver,
+                               options["kdim"]
+                                   .doc("Set the maximum size of the Krylov space")
+                                   .withDefault(30));
+
+      if (options["skip_real_residual_check"]
+              .doc("Skip the evaluation and the check of the actual residual?")
+              .withDefault<bool>(false)) {
+        HYPRE_GMRESSetSkipRealResidualCheck(solver, 1);
+      }
+      break;
+    }
+    case HYPRE_SOLVER_TYPE::bicgstab: {
+      break;
+    }
+    case HYPRE_SOLVER_TYPE::pcg: {
+      break;
+    }
+    default: {
+      throw BoutException("Unsupported hypre_solver_type {}", toString(solver_type));
+    }
+    }
+
     HYPRE_BoomerAMGCreate(&precon);
     HYPRE_BoomerAMGSetOldDefault(precon);
 #if BOUT_HAS_CUDA
diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
index c50be1db85..beb83a216d 100644
--- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
+++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
@@ -218,11 +218,15 @@ Field3D LaplaceHypre3d::solve(const Field3D& b_in, const Field3D& x0) {
 
   CALI_MARK_BEGIN("LaplaceHypre3d_solve:vectorAssemble");
 
+  operator3D.setElimBEVectors(solution, rhs);
+
   rhs.importValuesFromField(b);
   solution.importValuesFromField(x0);
   rhs.assemble();
   solution.assemble();
 
+  solution.syncElimBErhs(rhs);
+
   CALI_MARK_END("LaplaceHypre3d_solve:vectorAssemble");
 
   CALI_MARK_BEGIN("LaplaceHypre3d_solve:solve");
@@ -411,6 +415,7 @@ void LaplaceHypre3d::updateMatrix3D() {
     operator3D.ydown(ydown)(l, l.ym().zp()) += -C_d2f_dydz;
     operator3D.ydown(ydown)(l, l.ym().zm()) += C_d2f_dydz;
   }
+  operator3D.setElimBE();
   operator3D.assemble();
 
   if (print_matrix) {
diff --git a/src/sys/hypre_interface.cxx b/src/sys/hypre_interface.cxx
new file mode 100644
index 0000000000..1838bd5158
--- /dev/null
+++ b/src/sys/hypre_interface.cxx
@@ -0,0 +1,131 @@
+
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_HYPRE
+
+#include "bout/hypre_interface.hxx"
+
+namespace bout {
+
+BCMatrixEquations::BCMatrixEquations(HYPRE_Int nrows, HYPRE_Int* ncols,
+                                     HYPRE_BigInt* rows, HYPRE_Int** row_indexes_ptr,
+                                     HYPRE_BigInt* cols, HYPRE_Complex* values,
+                                     HYPRE_Int nb, HYPRE_Int* bi_array)
+    : nb(nb) {
+  HYPRE_Int* row_indexes;
+
+  // Create the row_indexes array
+  row_indexes = (HYPRE_Int*)malloc(sizeof(HYPRE_Int) * nrows);
+  row_indexes[0] = 0;
+  for (HYPRE_Int i = 1; i < nrows; i++) {
+    row_indexes[i] = row_indexes[i - 1] + ncols[i - 1];
+  }
+
+  // Assume just one interior equation coupled to each boundary equation
+  na = nb;
+
+  // Allocate arrays
+  HypreMalloc(binum_array, sizeof(HYPRE_Int) * nb);
+  HypreMalloc(bjnum_array, sizeof(HYPRE_Int) * nb);
+  HypreMalloc(bii_array, sizeof(HYPRE_Complex) * nb);
+  HypreMalloc(bij_array, sizeof(HYPRE_Complex) * nb);
+  HypreMalloc(aknum_array, sizeof(HYPRE_Int) * na);
+  HypreMalloc(aki_array, sizeof(HYPRE_Complex) * na);
+
+  HYPRE_Int binum = 0;
+  HYPRE_Int aknum = 0;
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    // Get boundary equation information and adjust boundary equations
+    // Find row i in rows array (assume i increases and rows is sorted)
+    HYPRE_Int i = bi_array[bnum];
+    for (; binum < nrows; binum++) {
+      if (i == rows[binum]) {
+        break; // Found row i in rows array
+      }
+    }
+    HYPRE_Int bcoeffnum = row_indexes[binum];
+    HYPRE_Complex bii{0.0}, bij{0.0};
+    HYPRE_Int j = 0;
+
+    for (HYPRE_Int m = 0; m < 2; m++) { // Assume only two boundary equation coefficients
+      if (cols[bcoeffnum + m] == i) {
+        bii = values[bcoeffnum + m];
+        values[bcoeffnum + m] = -1.0; // Identity equation (negative definite matrix)
+      } else {
+        j = cols[bcoeffnum + m];
+        bij = values[bcoeffnum + m];
+        values[bcoeffnum + m] = 0.0; // Identity equation
+      }
+    }
+    ncols[binum] = 1; // Identity equation
+
+    /* Get interior equation information and adjust interior equations */
+    /* Find row k in rows array (assume k increases and rows is sorted) */
+    HYPRE_Int k = j; // Assume equation k = j
+    for (; aknum < nrows; aknum++) {
+      if (k == rows[aknum]) {
+        break; // Found row k in rows array
+      }
+    }
+    HYPRE_Int acoeffnum = row_indexes[aknum];
+
+    HYPRE_Int mkj = 0;
+    HYPRE_Complex aki{0.0};
+    for (HYPRE_Int m = 0; m < ncols[aknum]; m++) {
+      if (cols[acoeffnum + m] == j) {
+        mkj = m; // Save for update of akj value below
+      }
+      if (cols[acoeffnum + m] == i) {
+        aki = values[acoeffnum + m];
+        values[acoeffnum + m] = 0.0; // Eliminate coupling to boundary equation
+      }
+    }
+    values[acoeffnum + mkj] -= aki * bij / bii; // Update akj value
+
+    // Update arrays
+    HYPRE_Int anum = bnum; // Assume only one interior equation k
+    binum_array[bnum] = binum;
+    bjnum_array[bnum] = aknum; // Assume only one interior equation k
+    bii_array[bnum] = bii;
+    bij_array[bnum] = bij;
+    aknum_array[anum] = aknum;
+    aki_array[anum] = aki;
+  }
+
+  // Set return arguments
+  *row_indexes_ptr = row_indexes;
+}
+
+BCValuesPtr BCMatrixEquations::adjustBCRightHandSideEquations(HYPRE_Complex* rhs) {
+
+  // Allocate array to store boundary row values
+  BCValuesPtr brhs = std::make_shared<HypreComplexArray>(nb);
+
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    HYPRE_Int binum = binum_array[bnum];
+    brhs->data[bnum] = rhs[binum];
+  }
+
+  for (HYPRE_Int anum = 0; anum < na; anum++) {
+    HYPRE_Int bnum = anum; // Assume only one interior equation per boundary equation
+    HYPRE_Int aknum = aknum_array[anum];
+    rhs[aknum] -= aki_array[anum] * brhs->data[bnum] / bii_array[bnum];
+  }
+
+  return brhs;
+}
+
+void BCMatrixEquations::adjustBCSolutionEquations(BCValuesPtr brhs,
+                                                  HYPRE_Complex* solution) {
+
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    HYPRE_Int binum = binum_array[bnum];
+    HYPRE_Int bjnum = bjnum_array[bnum];
+    solution[binum] =
+        (brhs->data[bnum] - bij_array[bnum] * solution[bjnum]) / bii_array[bnum];
+  }
+}
+
+} // namespace bout
+
+#endif // BOUT_HAS_HYPRE

From 4ed7b90933732f679a473fc1d31b7588fd00b752 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 16 Jul 2026 13:49:59 -0700
Subject: [PATCH 1639/1827] hypre_interface: Use std::isfinite

---
 include/bout/hypre_interface.hxx | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index f9f97b5bb3..f016ee96d8 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -5,8 +5,11 @@
 
 #if BOUT_HAS_HYPRE
 
+#include "bout/assert.hxx"
 #include "bout/bout_enum_class.hxx"
+#include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
+#include "bout/boutexception.hxx"
 #include "bout/caliper_wrapper.hxx"
 #include "bout/field.hxx"
 #include "bout/globalindexer.hxx"
@@ -383,19 +386,19 @@ public:
     }
 
     Element& operator=(const Element& other) {
-      ASSERT3(finite(static_cast<BoutReal>(other)));
+      ASSERT3(std::isfinite(static_cast<BoutReal>(other)));
       return *this = static_cast<BoutReal>(other);
     }
     Element& operator=(BoutReal value_) {
-      ASSERT3(finite(value_));
+      ASSERT3(std::isfinite(value_));
       value = value_;
       vector->V[vec_i] = value_;
       return *this;
     }
     Element& operator+=(BoutReal value_) {
-      ASSERT3(finite(value_));
+      ASSERT3(std::isfinite(value_));
       value += value_;
-      ASSERT3(finite(value));
+      ASSERT3(std::isfinite(value));
       vector->V[vec_i] += value_;
       return *this;
     }
@@ -550,7 +553,7 @@ public:
           weights(weights_) {
 #if CHECK > 2
       for (const auto val : weights) {
-        ASSERT3(finite(val));
+        ASSERT3(std::isfinite(val));
       }
 #endif
       ASSERT2(positions.size() == weights.size());
@@ -563,19 +566,19 @@ public:
     }
     Element& operator=(const Element& other) {
 
-      ASSERT3(finite(static_cast<BoutReal>(other)));
+      ASSERT3(std::isfinite(static_cast<BoutReal>(other)));
       return *this = static_cast<BoutReal>(other);
     }
     Element& operator=(BoutReal value_) {
 
-      ASSERT3(finite(value_));
+      ASSERT3(std::isfinite(value_));
       value = value_;
       setValues(value);
       return *this;
     }
     Element& operator+=(BoutReal value_) {
 
-      ASSERT3(finite(value_));
+      ASSERT3(std::isfinite(value_));
       auto column_position = std::find(cbegin(positions), cend(positions), column);
       if (column_position != cend(positions)) {
         const auto i = std::distance(cbegin(positions), column_position);

From f6cbdb02a2b03053419e3861cc4f3704ddb964e5 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 16 Jul 2026 16:09:15 -0700
Subject: [PATCH 1640/1827] HypreVector::importValuesFromField don't call
 assemble

The vector should be assembled once after importing values.
Assembling twice with elimBE over-corrects the RHS.
---
 include/bout/hypre_interface.hxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index f016ee96d8..c595d4cca8 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -331,6 +331,7 @@ public:
     return result;
   }
 
+  // Loads values into I and V arrays but does not assemble
   void importValuesFromField(const T& f) {
     CALI_CXX_MARK_FUNCTION;
 
@@ -345,8 +346,6 @@ public:
     }
 
     ASSERT2(vec_i == vsize);
-    // writeCacheToHypre(); // redundant assemble already performs writeCacheToHypre
-    assemble();
     have_indices = true;
   }
 

From 9aae2b7d969f0e9e0f076a16217de36ef4951de7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 16 Jul 2026 16:19:41 -0700
Subject: [PATCH 1641/1827] Hypre BCMatrixEquations: Use HypreMalloc

row_indexes is free'd using HypreFree, so should be allocated using
HypreMalloc.
---
 src/sys/hypre_interface.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sys/hypre_interface.cxx b/src/sys/hypre_interface.cxx
index 1838bd5158..d90392cf1e 100644
--- a/src/sys/hypre_interface.cxx
+++ b/src/sys/hypre_interface.cxx
@@ -15,7 +15,7 @@ BCMatrixEquations::BCMatrixEquations(HYPRE_Int nrows, HYPRE_Int* ncols,
   HYPRE_Int* row_indexes;
 
   // Create the row_indexes array
-  row_indexes = (HYPRE_Int*)malloc(sizeof(HYPRE_Int) * nrows);
+  HypreMalloc(row_indexes, sizeof(HYPRE_Int) * nrows);
   row_indexes[0] = 0;
   for (HYPRE_Int i = 1; i < nrows; i++) {
     row_indexes[i] = row_indexes[i - 1] + ncols[i - 1];

From d8e5419794a30546b73a3842d54610d45f12f9ee Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 17 Jul 2026 17:11:14 -0700
Subject: [PATCH 1642/1827] Options: ConvertContainer for Array/Matrix/Tensor

NVCC doesn't accept `Array<int, ArrayData<int>>` as `C<scalar>`
so treats ConvertContainer<Array...> as partially specialized.

This explicitly writes convertors for Array, Matrix and Tensor
containers.
---
 src/sys/options.cxx | 87 ++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 74 insertions(+), 13 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 85cfa7a49a..5f1f2fe91b 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -749,13 +749,11 @@ namespace {
 template <class Container>
 struct ConvertContainer;
 
-/// Visitor to convert an int, BoutReal or Array/Matrix/Tensor to the
-/// appropriate container. Templated on both the container class C
-/// and scalar type Scalar.
-template <template <class> class C, class Scalar>
-struct ConvertContainer<C<Scalar>> {
-  using Container = C<Scalar>;
-  ConvertContainer(std::string error, Container similar_to_)
+template <class Container>
+struct ConvertContainerBase {
+  using Scalar = typename Container::data_type;
+
+  ConvertContainerBase(std::string error, Container similar_to_)
       : error_message(std::move(error)), similar_to(std::move(similar_to_)) {}
 
   Container operator()(int value) {
@@ -772,20 +770,19 @@ struct ConvertContainer<C<Scalar>> {
 
   Container operator()(const Container& value) { return value; }
 
-  // Convert between scalar types: C<OtherScalar> -> C<Scalar>
-  // The size of the returned result will be the same as the input value
-  template <class OtherScalar>
-  Container operator()(const C<OtherScalar>& value) {
+  // Convert between scalar types while preserving the shape of the input.
+  template <class OtherContainer>
+  Container convert(const OtherContainer& value) {
     Container result(similar_to);
     result.reshape(value.shape()); // Resize to shape of input
 
     std::transform(std::begin(value), std::end(value), std::begin(result),
-                   [](const OtherScalar& x) { return static_cast<Scalar>(x); });
+                   [](const auto& x) { return static_cast<Scalar>(x); });
     return result;
   }
 
   template <class Other>
-  Container operator()([[maybe_unused]] const Other& value) {
+  Container incompatible([[maybe_unused]] const Other& value) {
     throw BoutException(error_message);
   }
 
@@ -793,6 +790,70 @@ struct ConvertContainer<C<Scalar>> {
   std::string error_message;
   Container similar_to;
 };
+
+/// Visitor to convert an int, BoutReal or Array to the appropriate Array type.
+template <class Scalar, class Backing>
+struct ConvertContainer<Array<Scalar, Backing>>
+    : ConvertContainerBase<Array<Scalar, Backing>> {
+  using Container = Array<Scalar, Backing>;
+  using Base = ConvertContainerBase<Container>;
+
+  using Base::Base;
+  using Base::operator();
+
+  // The size of the returned result will be the same as the input value
+  template <class OtherScalar, class OtherBacking>
+  Container operator()(const Array<OtherScalar, OtherBacking>& value) {
+    return this->convert(value);
+  }
+
+  template <class Other>
+  Container operator()([[maybe_unused]] const Other& value) {
+    return this->incompatible(value);
+  }
+};
+
+/// Visitor to convert an int, BoutReal or Matrix to the appropriate Matrix type.
+template <class Scalar>
+struct ConvertContainer<Matrix<Scalar>> : ConvertContainerBase<Matrix<Scalar>> {
+  using Container = Matrix<Scalar>;
+  using Base = ConvertContainerBase<Container>;
+
+  using Base::Base;
+  using Base::operator();
+
+  // The size of the returned result will be the same as the input value
+  template <class OtherScalar>
+  Container operator()(const Matrix<OtherScalar>& value) {
+    return this->convert(value);
+  }
+
+  template <class Other>
+  Container operator()([[maybe_unused]] const Other& value) {
+    return this->incompatible(value);
+  }
+};
+
+/// Visitor to convert an int, BoutReal or Tensor to the appropriate Tensor type.
+template <class Scalar>
+struct ConvertContainer<Tensor<Scalar>> : ConvertContainerBase<Tensor<Scalar>> {
+  using Container = Tensor<Scalar>;
+  using Base = ConvertContainerBase<Container>;
+
+  using Base::Base;
+  using Base::operator();
+
+  // The size of the returned result will be the same as the input value
+  template <class OtherScalar>
+  Container operator()(const Tensor<OtherScalar>& value) {
+    return this->convert(value);
+  }
+
+  template <class Other>
+  Container operator()([[maybe_unused]] const Other& value) {
+    return this->incompatible(value);
+  }
+};
 } // namespace
 
 namespace {

From 403f1c878ae2efa99b581d3bc3fa2468faacb359 Mon Sep 17 00:00:00 2001
From: Ben Dudson <bd512@york.ac.uk>
Date: Fri, 17 Jul 2026 17:32:02 -0700
Subject: [PATCH 1643/1827] ASSERT: Wrap string literals in string_view

fmt uses `begin` rather than `std::begin` so that NVCC
fails to find an overload for `char[]` literals.
---
 include/bout/assert.hxx | 40 +++++++++++++++++++++++-----------------
 1 file changed, 23 insertions(+), 17 deletions(-)

diff --git a/include/bout/assert.hxx b/include/bout/assert.hxx
index 63bed2407b..bebd7e4372 100644
--- a/include/bout/assert.hxx
+++ b/include/bout/assert.hxx
@@ -19,6 +19,8 @@
 
 #include "bout/boutexception.hxx"
 
+#include <string_view>
+
 #ifndef CHECK
 #define CHECKLEVEL 0
 #else
@@ -26,41 +28,45 @@
 #endif
 
 #if CHECKLEVEL >= 0
-#define ASSERT0(condition)                                                               \
-  if (!(condition)) {                                                                    \
-    throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \
-                        #condition);                                                     \
+#define ASSERT0(condition)                                           \
+  if (!(condition)) {                                                \
+    throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", \
+                        std::string_view(__FILE__), __LINE__,        \
+                        std::string_view(#condition));               \
   }
 #else // CHECKLEVEL >= 0
 #define ASSERT0(condition)
 #endif
 
 #if CHECKLEVEL >= 1
-#define ASSERT1(condition)                                                               \
-  if (!(condition)) {                                                                    \
-    throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \
-                        #condition);                                                     \
-    abort();                                                                             \
+#define ASSERT1(condition)                                           \
+  if (!(condition)) {                                                \
+    throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", \
+                        std::string_view(__FILE__), __LINE__,        \
+                        std::string_view(#condition));               \
+    abort();                                                         \
   }
 #else // CHECKLEVEL >= 1
 #define ASSERT1(condition)
 #endif
 
 #if CHECKLEVEL >= 2
-#define ASSERT2(condition)                                                               \
-  if (!(condition)) {                                                                    \
-    throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \
-                        #condition);                                                     \
+#define ASSERT2(condition)                                           \
+  if (!(condition)) {                                                \
+    throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", \
+                        std::string_view(__FILE__), __LINE__,        \
+                        std::string_view(#condition));               \
   }
 #else // CHECKLEVEL >= 2
 #define ASSERT2(condition)
 #endif
 
 #if CHECKLEVEL >= 3
-#define ASSERT3(condition)                                                               \
-  if (!(condition)) {                                                                    \
-    throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", __FILE__, __LINE__, \
-                        #condition);                                                     \
+#define ASSERT3(condition)                                           \
+  if (!(condition)) {                                                \
+    throw BoutException("Assertion failed in {:s}, line {:d}: {:s}", \
+                        std::string_view(__FILE__), __LINE__,        \
+                        std::string_view(#condition));               \
   }
 #else // CHECKLEVEL >= 3
 #define ASSERT3(condition)

From 0934c93416a83ab99223649f02de64e41caafc18 Mon Sep 17 00:00:00 2001
From: Ben Dudson <bd512@york.ac.uk>
Date: Fri, 17 Jul 2026 17:34:20 -0700
Subject: [PATCH 1644/1827] BinaryExpr: size() can't be a DEVICE function

Calls `Array::size()` that accesses a shared pointer to `ArrayData`.
Doesn't need to be a device function since called outside kernel.
---
 include/bout/array.hxx       | 3 ++-
 include/bout/boundary_op.hxx | 2 ++
 include/bout/fieldops.hxx    | 3 ++-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/include/bout/array.hxx b/include/bout/array.hxx
index 0a0034b8fa..9e1437eb9c 100644
--- a/include/bout/array.hxx
+++ b/include/bout/array.hxx
@@ -37,6 +37,7 @@
 #include <omp.h>
 #endif
 
+#include "bout/build_config.hxx"
 #include "bout/build_defines.hxx"
 
 #if BOUT_HAS_UMPIRE
@@ -98,7 +99,7 @@ struct ArrayData {
   }
   iterator<T> begin() const { return data; }
   iterator<T> end() const { return data + len; }
-  int size() const { return len; }
+  BOUT_FORCEINLINE int size() const { return len; }
 
   /// Copy assignment
   /// Copy the underlying data from one array to the other
diff --git a/include/bout/boundary_op.hxx b/include/bout/boundary_op.hxx
index e4d2c459bf..dedc56d0e8 100644
--- a/include/bout/boundary_op.hxx
+++ b/include/bout/boundary_op.hxx
@@ -86,6 +86,8 @@ public:
   BoundaryModifier() = default;
   BoundaryModifier(BoundaryOp* operation) : BoundaryOp(operation->bndry), op(operation) {}
   virtual BoundaryOp* cloneMod(BoundaryOp* op, const std::list<std::string>& args) = 0;
+
+  using BoundaryOp::clone;
   BoundaryOp* clone(BoundaryRegion* UNUSED(region),
                     const std::list<std::string>& UNUSED(args)) override {
     throw BoutException("This must not be used!");
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index f36061ceaa..46bcaf77ec 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -7,6 +7,7 @@
 #include "bout/bout_types.hxx"
 #include "bout/build_config.hxx"
 #include "bout/build_defines.hxx"
+#include "bout/build_config.hxx"
 #include "bout/region.hxx"
 
 #include <cstddef>
@@ -366,7 +367,7 @@ struct BinaryExpr {
   BinaryExpr& operator=(const BinaryExpr&) = delete;
   BinaryExpr& operator=(BinaryExpr&&) = delete;
 
-  BOUT_HOST_DEVICE BOUT_FORCEINLINE int size() const { return indices.size(); }
+  BOUT_FORCEINLINE int size() const { return indices.size(); }
   BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
     return f(idx, lhs, rhs); // single‐pass fusion
   }

From b5a058769ffaba6f95d5bceee9e2ebb9573deb7d Mon Sep 17 00:00:00 2001
From: Ben Dudson <bd512@york.ac.uk>
Date: Fri, 17 Jul 2026 17:36:59 -0700
Subject: [PATCH 1645/1827] Fix warnings for NVCC

- Remove default arguments for fv_ops specializations
- Use base class functions rather than partial overload
---
 include/bout/fieldperp.hxx         |  6 ++--
 include/bout/griddata.hxx          |  2 ++
 include/bout/paralleltransform.hxx |  8 +++++
 include/bout/region.hxx            |  2 ++
 src/mesh/fv_ops.cxx                | 57 +++++++++++++++---------------
 5 files changed, 43 insertions(+), 32 deletions(-)

diff --git a/include/bout/fieldperp.hxx b/include/bout/fieldperp.hxx
index 36a116e1b5..4814be1d90 100644
--- a/include/bout/fieldperp.hxx
+++ b/include/bout/fieldperp.hxx
@@ -438,8 +438,8 @@ inline FieldPerp emptyFrom<FieldPerp>(const FieldPerp& f) {
 #if CHECK > 0
 void checkData(const FieldPerp& f, const std::string& region = "RGN_NOX");
 #else
-inline void checkData(const FieldPerp& UNUSED(f),
-                      const std::string& UNUSED(region) = "RGN_NOX") {}
+inline void checkData([[maybe_unused]] const FieldPerp& f,
+                      [[maybe_unused]] const std::string& region = "RGN_NOX") {}
 #endif
 
 /// Force guard cells of passed field \p var to NaN
@@ -452,7 +452,7 @@ inline void invalidateGuards(FieldPerp& UNUSED(var)) {}
 /// toString template specialisation
 /// Defined in utils.hxx
 template <>
-inline std::string toString<>(const FieldPerp& UNUSED(val)) {
+inline std::string toString<>([[maybe_unused]] const FieldPerp& val) {
   return "<FieldPerp>";
 }
 
diff --git a/include/bout/griddata.hxx b/include/bout/griddata.hxx
index d5aff04b4d..61a8a2b40b 100644
--- a/include/bout/griddata.hxx
+++ b/include/bout/griddata.hxx
@@ -196,6 +196,8 @@ public:
    */
   bool hasVar(const std::string& name) const override;
 
+  using GridDataSource::get;
+
   /*!
    * Reads strings from options. Uses Options::get to handle
    * expressions
diff --git a/include/bout/paralleltransform.hxx b/include/bout/paralleltransform.hxx
index d9ed397bb5..2b578c2900 100644
--- a/include/bout/paralleltransform.hxx
+++ b/include/bout/paralleltransform.hxx
@@ -124,6 +124,8 @@ public:
    */
   void calcParallelSlices(Field3D& f) override;
 
+  using ParallelTransform::toFieldAligned;
+
   /*!
    * The field is already aligned in Y, so this
    * does nothing
@@ -141,6 +143,8 @@ public:
     return result.setDirectionY(YDirectionType::Aligned);
   }
 
+  using ParallelTransform::fromFieldAligned;
+
   /*!
    * The field is already aligned in Y, so this
    * does nothing
@@ -196,6 +200,8 @@ public:
    */
   void calcParallelSlices(Field3D& f) override;
 
+  using ParallelTransform::toFieldAligned;
+
   /*!
    * Uses FFTs and a phase shift to align the grid points
    * with the y coordinate (along magnetic field usually).
@@ -209,6 +215,8 @@ public:
   FieldPerp toFieldAligned(const FieldPerp& f,
                            const std::string& region = "RGN_ALL") override;
 
+  using ParallelTransform::fromFieldAligned;
+
   /*!
    * Converts a field back to X-Z orthogonal coordinates
    * from field aligned coordinates.
diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index df6769eda4..b4922bae00 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -254,6 +254,7 @@ struct SpecificInd {
     case (DIRECTION::Z):
       return zp(dd);
     }
+    return *this;
   }
 
   /// Templated routine to return index.?m(offset), where `?` is one of {x,y,z}
@@ -274,6 +275,7 @@ struct SpecificInd {
     case (DIRECTION::Z):
       return zm(dd);
     }
+    return *this;
   }
 
   inline SpecificInd xp(int dx = 1) const { return {ind + (dx * ny * nz), ny, nz}; }
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index 660fc51abc..d8c6eaaa01 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -571,103 +571,102 @@ Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc) {
 
 // Explicit instantiations of flux-limited finite volume methods
 template Field3D Div_par_fvv<Upwind>(const Field3D& f_in, const Field3D& v_in,
-                                     const Field3D& wave_speed_in, bool fixflux = true);
+                                     const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_par<Upwind>(const Field3D& f_in, const Field3D& v_in,
-                                 const Field3D& wave_speed_in, bool fixflux = true);
+                                 const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_f_v<Upwind>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<Upwind>(const Field3D& f_in, const Field3D& v_in,
                                      const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                     bool fixflux = true);
+                                     bool fixflux);
 template Field3D Div_par_fvv_heating<Upwind>(const Field3D& f_in, const Field3D& v_in,
                                              const Field3D& wave_speed_in,
-                                             Field3D& flow_ylow, bool fixflux = true);
+                                             Field3D& flow_ylow, bool fixflux);
 template Field3D Div_a_Grad_perp_limit<Upwind>(const Field3D& a, const Field3D& g,
                                                const Field3D& f);
 
 template Field3D Div_par_fvv<Fromm>(const Field3D& f_in, const Field3D& v_in,
-                                    const Field3D& wave_speed_in, bool fixflux = true);
+                                    const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_par<Fromm>(const Field3D& f_in, const Field3D& v_in,
-                                const Field3D& wave_speed_in, bool fixflux = true);
+                                const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_f_v<Fromm>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<Fromm>(const Field3D& f_in, const Field3D& v_in,
                                     const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                    bool fixflux = true);
+                                    bool fixflux);
 template Field3D Div_par_fvv_heating<Fromm>(const Field3D& f_in, const Field3D& v_in,
                                             const Field3D& wave_speed_in,
-                                            Field3D& flow_ylow, bool fixflux = true);
+                                            Field3D& flow_ylow, bool fixflux);
 template Field3D Div_a_Grad_perp_limit<Fromm>(const Field3D& a, const Field3D& g,
                                               const Field3D& f);
 
 template Field3D Div_par_fvv<MinMod>(const Field3D& f_in, const Field3D& v_in,
-                                     const Field3D& wave_speed_in, bool fixflux = true);
+                                     const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_par<MinMod>(const Field3D& f_in, const Field3D& v_in,
-                                 const Field3D& wave_speed_in, bool fixflux = true);
+                                 const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_f_v<MinMod>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<MinMod>(const Field3D& f_in, const Field3D& v_in,
                                      const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                     bool fixflux = true);
+                                     bool fixflux);
 template Field3D Div_par_fvv_heating<MinMod>(const Field3D& f_in, const Field3D& v_in,
                                              const Field3D& wave_speed_in,
-                                             Field3D& flow_ylow, bool fixflux = true);
+                                             Field3D& flow_ylow, bool fixflux);
 template Field3D Div_a_Grad_perp_limit<MinMod>(const Field3D& a, const Field3D& g,
                                                const Field3D& f);
 
 template Field3D Div_par_fvv<MC>(const Field3D& f_in, const Field3D& v_in,
-                                 const Field3D& wave_speed_in, bool fixflux = true);
+                                 const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_par<MC>(const Field3D& f_in, const Field3D& v_in,
-                             const Field3D& wave_speed_in, bool fixflux = true);
+                             const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_f_v<MC>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<MC>(const Field3D& f_in, const Field3D& v_in,
                                  const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                 bool fixflux = true);
+                                 bool fixflux);
 template Field3D Div_par_fvv_heating<MC>(const Field3D& f_in, const Field3D& v_in,
                                          const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                         bool fixflux = true);
+                                         bool fixflux);
 template Field3D Div_a_Grad_perp_limit<MC>(const Field3D& a, const Field3D& g,
                                            const Field3D& f);
 
 template Field3D Div_par_fvv<Superbee>(const Field3D& f_in, const Field3D& v_in,
-                                       const Field3D& wave_speed_in, bool fixflux = true);
+                                       const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_par<Superbee>(const Field3D& f_in, const Field3D& v_in,
-                                   const Field3D& wave_speed_in, bool fixflux = true);
+                                   const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_f_v<Superbee>(const Field3D& n_in, const Vector3D& v,
                                    bool bndry_flux);
 template Field3D Div_par_mod<Superbee>(const Field3D& f_in, const Field3D& v_in,
                                        const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                       bool fixflux = true);
+                                       bool fixflux);
 template Field3D Div_par_fvv_heating<Superbee>(const Field3D& f_in, const Field3D& v_in,
                                                const Field3D& wave_speed_in,
-                                               Field3D& flow_ylow, bool fixflux = true);
+                                               Field3D& flow_ylow, bool fixflux);
 template Field3D Div_a_Grad_perp_limit<Superbee>(const Field3D& a, const Field3D& g,
                                                  const Field3D& f);
 
 template Field3D Div_par_fvv<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
-                                        const Field3D& wave_speed_in,
-                                        bool fixflux = true);
+                                        const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_par<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
-                                    const Field3D& wave_speed_in, bool fixflux = true);
+                                    const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_f_v<VanAlbada>(const Field3D& n_in, const Vector3D& v,
                                     bool bndry_flux);
 template Field3D Div_par_mod<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
                                         const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                        bool fixflux = true);
+                                        bool fixflux);
 template Field3D Div_par_fvv_heating<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
                                                 const Field3D& wave_speed_in,
-                                                Field3D& flow_ylow, bool fixflux = true);
+                                                Field3D& flow_ylow, bool fixflux);
 template Field3D Div_a_Grad_perp_limit<VanAlbada>(const Field3D& a, const Field3D& g,
                                                   const Field3D& f);
 
 template Field3D Div_par_fvv<WENO3>(const Field3D& f_in, const Field3D& v_in,
-                                    const Field3D& wave_speed_in, bool fixflux = true);
+                                    const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_par<WENO3>(const Field3D& f_in, const Field3D& v_in,
-                                const Field3D& wave_speed_in, bool fixflux = true);
+                                const Field3D& wave_speed_in, bool fixflux);
 template Field3D Div_f_v<WENO3>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<WENO3>(const Field3D& f_in, const Field3D& v_in,
                                     const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                    bool fixflux = true);
+                                    bool fixflux);
 template Field3D Div_par_fvv_heating<WENO3>(const Field3D& f_in, const Field3D& v_in,
                                             const Field3D& wave_speed_in,
-                                            Field3D& flow_ylow, bool fixflux = true);
+                                            Field3D& flow_ylow, bool fixflux);
 template Field3D Div_a_Grad_perp_limit<WENO3>(const Field3D& a, const Field3D& g,
                                               const Field3D& f);
 } // Namespace FV

From 112e722e8517fc06e15355bb2610fc98df56dc01 Mon Sep 17 00:00:00 2001
From: Mike Kryjak <mikekryjak@gmail.com>
Date: Mon, 20 Jul 2026 11:13:25 +0100
Subject: [PATCH 1646/1827] Improve cvode use_precon exception

---
 src/solver/impls/cvode/cvode.cxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 2cdeeed9c3..d3441ad959 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -172,8 +172,9 @@ CvodeSolver::CvodeSolver(Options* opts)
 
   if ((*options)["use_precon"].isSet()) {
     throw BoutException("solver:use_precon is deprecated for CVODE and is now "
-                        "ignored. Use solver:cvode_precon_method=none to disable "
-                        "preconditioning.\n");
+                        "ignored. To reproduce behaviour of use_precon=true, "
+                        "set cvode_precon_method=user. This enables the Hermes-3 "
+                        "physical preconditioners.\n");
   }
 
   // Add diagnostics to output

From 4244d606620f2896a81179e630e747ea2c01a0c8 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 22 Jul 2026 00:48:33 +0200
Subject: [PATCH 1647/1827] Fix comments by ensuring \\ is not at end of line

---
 src/invert/laplace/impls/naulin/naulin_laplace.hxx | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/invert/laplace/impls/naulin/naulin_laplace.hxx b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
index a94d855034..f857ca8356 100644
--- a/src/invert/laplace/impls/naulin/naulin_laplace.hxx
+++ b/src/invert/laplace/impls/naulin/naulin_laplace.hxx
@@ -6,7 +6,7 @@
 ///   \nabla^2(\phi[i+1])
 ///      + 1/DC(C_1 D)\nabla_\perp(DC(C_2))\nabla_\perp(\phi[i+1])
 ///      + DC(A/D)\phi[i+1]
-///   = rhs(\phi[i])
+///      \\ = rhs(\phi[i])
 ///        + 1/DC(C_1 D)\nabla_\perp(DC(C_2))\nabla_\perp(\phi[i])
 ///        + DC(A/D)\phi[i]
 /// \f}
@@ -29,16 +29,16 @@
 ///
 /// \f{eqnarray}{
 /// \Omega^D &=& \nabla\cdot(n\nabla_\perp \phi)
-///       &=& n \nabla_\perp^2 \phi + \nabla n\cdot\nabla_\perp \phi
-///       &=& n \Omega + \nabla n\cdot\nabla_\perp \phi
-///       &=& n \Omega + \nabla_\perp n\cdot\nabla_\perp \phi
+///     \\ &=&n \nabla_\perp^2 \phi + \nabla n\cdot\nabla_\perp \phi
+///     \\ &=&n \Omega + \nabla n\cdot\nabla_\perp \phi
+///     \\ &=&n \Omega + \nabla_\perp n\cdot\nabla_\perp \phi
 /// \f}
 ///
 /// Rearranging gives
 ///
 /// \f{eqnarray}{
 /// \Omega  &=& \frac{\Omega^D}{n} - \nabla_\perp \ln(n)\cdot\nabla_\perp \phi
-/// \nabla_\perp^2 \phi
+/// \\ \nabla_\perp^2 \phi
 /// &=& \frac{\Omega^D}{n} - \nabla_\perp \ln(n)\cdot\nabla_\perp \phi
 /// \f}
 ///

From 4687df8e99028f7cc90f87360b74398f5855e83b Mon Sep 17 00:00:00 2001
From: malamast <malamas.tsagkaridis@gmail.com>
Date: Wed, 22 Jul 2026 17:22:28 -0700
Subject: [PATCH 1648/1827] Apply perk-formatting

---
 src/mesh/boundary_factory.cxx  |  2 +-
 src/mesh/boundary_standard.cxx | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index 627297eeed..3841a95b11 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -23,7 +23,7 @@ BoundaryFactory* BoundaryFactory::instance = nullptr;
 BoundaryFactory::BoundaryFactory() {
   add(new BoundaryDirichlet(), "dirichlet");       // Default
   add(new BoundaryDirichlet_O1(), "dirichlet_o1"); // Old implementation in v3
-  add(new BoundaryDirichlet(), "dirichlet_o2"); // Synonym for "dirichlet"
+  add(new BoundaryDirichlet(), "dirichlet_o2");    // Synonym for "dirichlet"
   add(new BoundaryDirichlet_O3(), "dirichlet_o3");
   add(new BoundaryDirichlet_O4(), "dirichlet_o4");
   add(new BoundaryDirichlet_4thOrder(), "dirichlet_4thorder");
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 8917011a93..491b4a5b71 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -1899,8 +1899,8 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
       }
     }
 #else
-    throw BoutException("Applying boundary condition 'neumann' to Field2D "
-                        "not compatible with 3D metrics in all cases.");
+  throw BoutException("Applying boundary condition 'neumann' to Field2D "
+                      "not compatible with 3D metrics in all cases.");
 #endif
   }
 
@@ -1935,9 +1935,9 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
           BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                            + bndry->by * metric->dy(bndry->x, bndry->y, zk);
 #else
-        BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
-                         + bndry->by * metric->dy(bndry->x, bndry->y);
-        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
+      BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
+                       + bndry->by * metric->dy(bndry->x, bndry->y);
+      for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
 #endif
           if (fg) {
             val = fg->generate(Context(bndry, zk, loc, t, mesh));

From dcffc23600002c74455ca1e94bfdf0e43612b345 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 24 Jul 2026 20:18:50 +0000
Subject: [PATCH 1649/1827] Bump actions/setup-python from 6 to 7

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6 to 7.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v6...v7)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/auto-formatting.yml | 2 +-
 .github/workflows/python-package.yml  | 6 +++---
 .github/workflows/tests.yml           | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/auto-formatting.yml b/.github/workflows/auto-formatting.yml
index 518cfd3898..7274f34038 100644
--- a/.github/workflows/auto-formatting.yml
+++ b/.github/workflows/auto-formatting.yml
@@ -16,7 +16,7 @@ jobs:
           fetch-depth: 0
 
       - name: "Set up Python"
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
 
       - name: Install uv
         uses: astral-sh/setup-uv@v7
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index e2023fa5c8..53561934e2 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -22,7 +22,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -62,7 +62,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -111,7 +111,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 7ad1f6e70b..16218f39be 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -162,7 +162,7 @@ jobs:
         with:
           enable-cache: true
 
-      - uses: actions/setup-python@v6
+      - uses: actions/setup-python@v7
         with:
           python-version: '3.x'
 

From e4b126dd9f68ababe8419de3310d6d6ea5a0f63b Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 27 Jul 2026 15:28:51 +0100
Subject: [PATCH 1650/1827] Don't compute G-values unnecessarily or when using
 FCI

Also make G-value computation more like main branch
---
 src/mesh/coordinates.cxx | 13 ++++++++++---
 src/mesh/g_values.cxx    | 14 ++++----------
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 80329536c7..5a6c484856 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -646,9 +646,16 @@ void Coordinates::outputVars(Options& output_options) {
   output_options["J" + loc_string].force(J(), "Coordinates");
   output_options["Bxy" + loc_string].force(Bxy(), "Coordinates");
 
-  output_options["G1" + loc_string].force(G1(), "Coordinates");
-  output_options["G2" + loc_string].force(G2(), "Coordinates");
-  output_options["G3" + loc_string].force(G3(), "Coordinates");
+  if (g_values_cache != nullptr) {
+    // If we haven't used them yet, then presumably we don't actually need them,
+    // so let's not compute them now.
+    // Also, previously, we were explicitly setting the G-values to NaN for FCI
+    // instead of computing them (presumably because these are both difficult to
+    // compute accurately for FCI and unneeded in FCI models in practice).
+    output_options["G1" + loc_string].force(G1(), "Coordinates");
+    output_options["G2" + loc_string].force(G2(), "Coordinates");
+    output_options["G3" + loc_string].force(G3(), "Coordinates");
+  }
 
   getParallelTransform().outputVars(output_options);
 }
diff --git a/src/mesh/g_values.cxx b/src/mesh/g_values.cxx
index 644f58d52b..cf4713464e 100644
--- a/src/mesh/g_values.cxx
+++ b/src/mesh/g_values.cxx
@@ -18,15 +18,9 @@ GValues::GValues(const Coordinates& coordinates) {
 
   auto* mesh = J.getMesh();
 
-  bout::FieldMetric Jg12 = J * g12;
-  mesh->communicate(Jg12);
-  G1_m = (DDX(J * g11) + DDY(Jg12) + DDZ(J * g13)) / J;
-  bout::FieldMetric Jg22 = J * g22;
-  mesh->communicate(Jg22);
-  G2_m = (DDX(J * g12) + DDY(Jg22) + DDZ(J * g23)) / J;
-  bout::FieldMetric Jg23 = J * g23;
-  mesh->communicate(Jg23);
-  G3_m = (DDX(J * g13) + DDY(Jg23) + DDZ(J * g33)) / J;
+  G1_m = (DDX(J * g11) + DDY(J.asField3DParallel() * g12) + DDZ(J * g13)) / J;
+  G2_m = (DDX(J * g12) + DDY(J.asField3DParallel() * g22) + DDZ(J * g23)) / J;
+  G3_m = (DDX(J * g13) + DDY(J.asField3DParallel() * g23) + DDZ(J * g33)) / J;
 
-  mesh->communicate(G1_m, G2_m, G3_m);
+  mesh->communicate_no_slices(G1_m, G2_m, G3_m);
 }

From 99eaae12812827bcdfab3519574af0673dc3d8bb Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 28 Jul 2026 17:42:10 +0100
Subject: [PATCH 1651/1827] Ensure option names updated to match path

---
 include/bout/options.hxx        |  3 +++
 src/sys/options.cxx             | 12 +++++++++++-
 tests/unit/sys/test_options.cxx | 25 +++++++++++++++++++++++++
 3 files changed, 39 insertions(+), 1 deletion(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 87503b0a22..b030f0c29c 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -934,6 +934,9 @@ private:
   bool similar(T lhs, T rhs) const {
     return lhs == rhs;
   }
+
+  /// Replaces the start of the name of an Option and any children
+  void recursively_update_names(size_t len, const std::string& new_prefix);
 };
 
 // Specialised assign methods for types stored in ValueType
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 85cfa7a49a..d1249b7c74 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -258,16 +258,19 @@ Options& Options::operator=(Options&& other) noexcept {
 
   value = std::move(other.value);
   attributes = std::move(other.attributes);
-  full_name = std::move(other.full_name);
   is_section = other.is_section;
   children = std::move(other.children);
   value_used = other.value_used;
 
   // Ensure that this is the parent of all children,
   // otherwise will point to the original Options instance
+  const auto len = other.full_name.size();
+  const std::string new_prefix = len == 0 ? full_name + ":" : full_name;
   for (auto& child : children) {
     child.second.parent_instance = this;
+    child.second.recursively_update_names(len, new_prefix);
   }
+
   return *this;
 }
 
@@ -1028,6 +1031,13 @@ std::vector<int> Options::getShape() const {
   return lazy_shape;
 }
 
+void Options::recursively_update_names(size_t len, const std::string& new_prefix) {
+  full_name.replace(0, len, new_prefix);
+  for (auto& [_, child] : children) {
+    child.recursively_update_names(len, new_prefix);
+  }
+}
+
 fmt::format_context::iterator
 bout::details::OptionsFormatterBase::format(const Options& options,
                                             fmt::format_context& ctx) const {
diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx
index d4d803d685..110943e71a 100644
--- a/tests/unit/sys/test_options.cxx
+++ b/tests/unit/sys/test_options.cxx
@@ -671,6 +671,16 @@ TEST_F(OptionsTest, AssignSection) {
   EXPECT_TRUE(option2["key"].isValue());
 }
 
+TEST_F(OptionsTest, AssignSectionName) {
+  Options option1, option2;
+
+  option1["key"] = 42;
+
+  option2 = option1["key"].copy();
+
+  EXPECT_EQ(option2.str(), "");
+}
+
 TEST_F(OptionsTest, AssignSectionReplace) {
   Options option1, option2;
 
@@ -702,6 +712,21 @@ TEST_F(OptionsTest, AssignSubSection) {
   EXPECT_EQ(option2["key2"]["key1"].as<int>(), 42);
 }
 
+TEST_F(OptionsTest, AssignSubSectionName) {
+  Options option1, option2, option3;
+
+  option1["key1"] = 42;
+
+  option2["key2"] = option1.copy();
+
+  option3["key3"] = option2["key2"].copy();
+
+  EXPECT_EQ(option2["key2"].str(), "key2");
+  EXPECT_EQ(option2["key2"]["key1"].str(), "key2:key1");
+  EXPECT_EQ(option2["key3"]["key2"].str(), "key3:key2");
+  EXPECT_EQ(option2["key3"]["key2"]["key1"].str(), "key3:key2:key1");
+}
+
 TEST_F(OptionsTest, AssignSubSectionParent) {
   Options option1, option2;
 

From 6607c3afa6ec0990248291988a1e6df97b68cf49 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 28 Jul 2026 18:19:38 +0100
Subject: [PATCH 1652/1827] Include header with size_t

---
 include/bout/options.hxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index b030f0c29c..b1235741c3 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -55,6 +55,7 @@ class Options;
 #include <fmt/format.h>
 
 #include <cmath>
+#include <cstddef>
 #include <functional>
 #include <map>
 #include <ostream>

From 1b5149b5a0c3661ce0b535acfbc15217f24fdb44 Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Wed, 29 Jul 2026 11:07:38 +0100
Subject: [PATCH 1653/1827] Cover corner-cases when updating option names

---
 src/sys/options.cxx             | 15 +++++++++++++--
 tests/unit/sys/test_options.cxx | 31 ++++++++++++++++++++++++-------
 2 files changed, 37 insertions(+), 9 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index d1249b7c74..62a17270fb 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -262,10 +262,21 @@ Options& Options::operator=(Options&& other) noexcept {
   children = std::move(other.children);
   value_used = other.value_used;
 
+  size_t len = other.full_name.size();
+  std::string new_prefix;
+  if (len == 0) {
+    new_prefix = full_name.empty() ? full_name : full_name + ":";
+  } else {
+    new_prefix = full_name;
+    // If new_prefix is empty but the old name is not then we also
+    // need to remove a colon when updating names
+    if (full_name.empty()) {
+      len += 1;
+    }
+  }
+
   // Ensure that this is the parent of all children,
   // otherwise will point to the original Options instance
-  const auto len = other.full_name.size();
-  const std::string new_prefix = len == 0 ? full_name + ":" : full_name;
   for (auto& child : children) {
     child.second.parent_instance = this;
     child.second.recursively_update_names(len, new_prefix);
diff --git a/tests/unit/sys/test_options.cxx b/tests/unit/sys/test_options.cxx
index 110943e71a..4dcb858863 100644
--- a/tests/unit/sys/test_options.cxx
+++ b/tests/unit/sys/test_options.cxx
@@ -660,6 +660,19 @@ TEST_F(OptionsTest, AssignOption) {
   EXPECT_EQ(option2.as<int>(), 42);
 }
 
+TEST_F(OptionsTest, AssignOptionName) {
+  Options option1, option2, option3;
+
+  option1 = 42;
+
+  option2 = option1.copy();
+  option3["key"] = option1.copy();
+
+  EXPECT_EQ(option2.str(), "");
+  EXPECT_EQ(option3.str(), "");
+  EXPECT_EQ(option3["key"].str(), "key");
+}
+
 TEST_F(OptionsTest, AssignSection) {
   Options option1, option2;
 
@@ -672,13 +685,16 @@ TEST_F(OptionsTest, AssignSection) {
 }
 
 TEST_F(OptionsTest, AssignSectionName) {
-  Options option1, option2;
+  Options option1, option2, option3;
 
   option1["key"] = 42;
 
-  option2 = option1["key"].copy();
+  option2 = option1.copy();
+  option3 = option1["key"].copy();
 
   EXPECT_EQ(option2.str(), "");
+  EXPECT_EQ(option2["key"].str(), "key");
+  EXPECT_EQ(option3.str(), "");
 }
 
 TEST_F(OptionsTest, AssignSectionReplace) {
@@ -713,18 +729,19 @@ TEST_F(OptionsTest, AssignSubSection) {
 }
 
 TEST_F(OptionsTest, AssignSubSectionName) {
-  Options option1, option2, option3;
+  Options option1, option2, option3, option4;
 
   option1["key1"] = 42;
-
   option2["key2"] = option1.copy();
-
   option3["key3"] = option2["key2"].copy();
+  option4 = option2["key2"].copy();
 
   EXPECT_EQ(option2["key2"].str(), "key2");
   EXPECT_EQ(option2["key2"]["key1"].str(), "key2:key1");
-  EXPECT_EQ(option2["key3"]["key2"].str(), "key3:key2");
-  EXPECT_EQ(option2["key3"]["key2"]["key1"].str(), "key3:key2:key1");
+  EXPECT_EQ(option3["key3"]["key2"].str(), "key3:key2");
+  EXPECT_EQ(option3["key3"]["key2"]["key1"].str(), "key3:key2:key1");
+  EXPECT_EQ(option4.str(), "");
+  EXPECT_EQ(option4["key1"].str(), "key1");
 }
 
 TEST_F(OptionsTest, AssignSubSectionParent) {

From a972f3f349e1a0e5f7075fca45078c8c10eff6b2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 30 Jul 2026 07:21:41 +0200
Subject: [PATCH 1654/1827] Use regionID of parallel slices for parallel slices

---
 include/bout/fieldops.hxx | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 52d2c82a13..6a809b7893 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -410,14 +410,29 @@ struct BinaryExpr {
     }
   }
   auto yup(int slice = 0) const {
-    return BinaryExpr<ResT, L, R, Func>{lhs.yup(slice), rhs.yup(slice), f,
-                                        mesh,           location,       directions,
-                                        regionID,       indices,        yindex};
+    return BinaryExpr<ResT, L, R, Func>{
+        lhs.yup(slice),
+        rhs.yup(slice),
+        f,
+        mesh,
+        location,
+        directions,
+        mesh->getCommonRegion(lhs.yup(slice).getRegionID(), rhs.yup(slice).getRegionID()),
+        indices,
+        yindex};
   }
   auto ydown(int slice = 0) const {
     return BinaryExpr<ResT, L, R, Func>{
-        lhs.ydown(slice), rhs.ydown(slice), f,       mesh,  location,
-        directions,       regionID,         indices, yindex};
+        lhs.ydown(slice),
+        rhs.ydown(slice),
+        f,
+        mesh,
+        location,
+        directions,
+        mesh->getCommonRegion(lhs.ydown(slice).getRegionID(),
+                              rhs.ydown(slice).getRegionID()),
+        indices,
+        yindex};
   }
 
   //operator ResT() { return ResT{*this}; }

From 3e2b57c676680bbf299cb7bef4dd2eab49148905 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Thu, 30 Jul 2026 17:22:51 +0100
Subject: [PATCH 1655/1827] Fix typos in `LaplacePetsc` after conversion

Fixes #3442
---
 .../laplace/impls/petsc/petsc_laplace.cxx      | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/invert/laplace/impls/petsc/petsc_laplace.cxx b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
index 33481f9bde..bc1cd91d51 100644
--- a/src/invert/laplace/impls/petsc/petsc_laplace.cxx
+++ b/src/invert/laplace/impls/petsc/petsc_laplace.cxx
@@ -336,7 +336,7 @@ FieldPerp LaplacePetsc::solve(const FieldPerp& b, const FieldPerp& x0) {
   }
   if (!isOuterBoundaryFlagSet(INVERT_RHS)) {
     BOUT_FOR_SERIAL(index, indexer->getRegionOuterX()) {
-      rhs(index) = isInnerBoundaryFlagSet(INVERT_SET) ? x0[index] : 0.0;
+      rhs(index) = isOuterBoundaryFlagSet(INVERT_SET) ? x0[index] : 0.0;
     }
   }
 
@@ -488,10 +488,10 @@ void LaplacePetsc::setSecondOrderMatrix(int y, bool inner_X_neumann,
   // Set the boundaries
   if (inner_X_neumann) {
     const auto dx = sliceXZ(coords->dx, y);
-    const auto g11 = sliceXZ(coords->g11, y);
+    const auto g_11 = sliceXZ(coords->g_11, y);
 
     BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
-      const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
+      const auto factor = 1. / dx[i] / std::sqrt(g_11[i]);
       operator2D(i, i) = -factor;
       operator2D(i, i.xp()) = factor;
     }
@@ -503,10 +503,10 @@ void LaplacePetsc::setSecondOrderMatrix(int y, bool inner_X_neumann,
   }
   if (outer_X_neumann) {
     const auto dx = sliceXZ(coords->dx, y);
-    const auto g11 = sliceXZ(coords->g11, y);
+    const auto g_11 = sliceXZ(coords->g_11, y);
 
     BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
-      const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
+      const auto factor = 1. / dx[i] / std::sqrt(g_11[i]);
       operator2D(i, i) = factor;
       operator2D(i, i.xm()) = -factor;
     }
@@ -558,10 +558,10 @@ void LaplacePetsc::setFourthOrderMatrix(int y, bool inner_X_neumann,
   // Set boundaries
   if (inner_X_neumann) {
     const auto dx = sliceXZ(coords->dx, y);
-    const auto g11 = sliceXZ(coords->g11, y);
+    const auto g_11 = sliceXZ(coords->g_11, y);
 
     BOUT_FOR_SERIAL(i, indexer->getRegionInnerX()) {
-      const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
+      const auto factor = 1. / dx[i] / std::sqrt(g_11[i]);
       operator2D(i, i) = (-25.0 / 12.0) * factor;
       operator2D(i, i.xp(1)) = 4.0 * factor;
       operator2D(i, i.xp(2)) = -3.0 * factor;
@@ -580,10 +580,10 @@ void LaplacePetsc::setFourthOrderMatrix(int y, bool inner_X_neumann,
 
   if (outer_X_neumann) {
     const auto dx = sliceXZ(coords->dx, y);
-    const auto g11 = sliceXZ(coords->g11, y);
+    const auto g_11 = sliceXZ(coords->g_11, y);
 
     BOUT_FOR_SERIAL(i, indexer->getRegionOuterX()) {
-      const auto factor = 1. / dx[i] / std::sqrt(g11[i]);
+      const auto factor = 1. / dx[i] / std::sqrt(g_11[i]);
       operator2D(i, i) = (25.0 / 12.0) * factor;
       operator2D(i, i.xm(1)) = -4.0 * factor;
       operator2D(i, i.xm(2)) = 3.0 * factor;

From d911d51c457e745af4839134c4aa3e904205c16b Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 30 Jul 2026 16:43:44 -0700
Subject: [PATCH 1656/1827] Extend ADIOSStream to read modes

---
 include/bout/adios_object.hxx     | 25 ++++++++++---------------
 src/sys/adios_object.cxx          | 21 +++++++++++++++++++--
 src/sys/options/options_adios.cxx | 23 ++++++++---------------
 3 files changed, 37 insertions(+), 32 deletions(-)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 63a2d4f85f..901857e7d4 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -21,6 +21,7 @@
 #include <adios2.h>
 #include <memory>
 #include <mpi.h>
+#include <string>
 
 namespace bout {
 
@@ -43,7 +44,8 @@ public:
   int adiosStep = 0;
 
   /** create or return the ADIOSStream based on the target file name */
-  static ADIOSStream& ADIOSGetStream(const std::string& fname, adios2::Mode mode);
+  static ADIOSStream& ADIOSGetStream(const std::string& fname, adios2::Mode mode,
+                                     const std::string& engineType = "BP5");
 
   ~ADIOSStream();
 
@@ -78,7 +80,7 @@ public:
     if (not engine_) {
       engine_ = io.Open(fname, file_mode);
       if (not engine_) {
-        throw BoutException("Could not open ADIOS file '{:s}' for writing", fname);
+        throw BoutException("Could not open ADIOS file '{:s}'", fname);
       }
     }
     return engine_;
@@ -101,24 +103,17 @@ public:
 
   void finish() {
     if (engine_) {
-      engine().EndStep();
+      if (isInStep) {
+        engine().EndStep();
+        isInStep = false;
+      }
       engine().Close();
+      engine_ = adios2::Engine();
     }
   }
 
 private:
-  ADIOSStream(const std::string& fname, adios2::Mode mode)
-      : fname(fname), file_mode(mode) {
-
-    ADIOSPtr adiosp = GetADIOSPtr();
-    std::string ioname = "write_" + fname;
-    try {
-      io = adiosp->AtIO(ioname);
-    } catch (const std::invalid_argument& e) {
-      io = adiosp->DeclareIO(ioname);
-      io.SetEngine("BP5");
-    }
-  };
+  ADIOSStream(const std::string& fname, adios2::Mode mode, const std::string& engineType);
 
   std::string fname;
   adios2::Mode file_mode;
diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx
index 1b3e0a12e2..d6aa862493 100644
--- a/src/sys/adios_object.cxx
+++ b/src/sys/adios_object.cxx
@@ -7,6 +7,7 @@
 
 #include <adios2.h>
 
+#include <string>
 #include <unordered_map>
 
 namespace bout {
@@ -57,10 +58,26 @@ ADIOSStream::~ADIOSStream() {
   }
 }
 
-ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname, adios2::Mode mode) {
+ADIOSStream::ADIOSStream(const std::string& fname, adios2::Mode mode,
+                         const std::string& engineType)
+    : fname(fname), file_mode(mode) {
+
+  ADIOSPtr adiosp = GetADIOSPtr();
+  try {
+    io = adiosp->AtIO(fname);
+  } catch (const std::invalid_argument& e) {
+    io = adiosp->DeclareIO(fname);
+    if (!engineType.empty()) {
+      io.SetEngine(engineType);
+    }
+  }
+}
+
+ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname, adios2::Mode mode,
+                                         const std::string& engineType) {
   auto it = adiosStreams.find(fname);
   if (it == adiosStreams.end()) {
-    it = adiosStreams.emplace(fname, ADIOSStream(fname, mode)).first;
+    it = adiosStreams.emplace(fname, ADIOSStream(fname, mode, engineType)).first;
   }
   return it->second;
 }
diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 844284a400..6e0227d7b9 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -356,16 +356,9 @@ Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
   const Timer timer("io");
 
   // Open file
-  const ADIOSPtr adiosp = GetADIOSPtr();
-  adios2::IO io;
-  const std::string ioname = "read_" + filename;
-  try {
-    io = adiosp->AtIO(ioname);
-  } catch (const std::invalid_argument& e) {
-    io = adiosp->DeclareIO(ioname);
-  }
-
-  adios2::Engine reader = io.Open(filename, adios2::Mode::ReadRandomAccess);
+  ADIOSStream& stream =
+      ADIOSStream::ADIOSGetStream(filename, adios2::Mode::ReadRandomAccess);
+  adios2::Engine& reader = stream.engine();
   if (!reader) {
     throw BoutException("Could not open ADIOS file '{:s}' for reading\n", filename);
   }
@@ -373,7 +366,7 @@ Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
   Options result;
 
   // Iterate over all variables
-  for (const auto& varpair : io.AvailableVariables()) {
+  for (const auto& varpair : stream.io.AvailableVariables()) {
     const auto& var_name = varpair.first; // Name of the variable
 
     auto it = varpair.second.find("Type");
@@ -388,21 +381,21 @@ Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
     // Note: Copying the value rather than simple assignment is used
     // because the Options assignment operator overwrites full_name.
     var = 0; // Setting is_section to false
-    var.value = readVariable(reader, io, var_name, var_type).value;
+    var.value = readVariable(reader, stream.io, var_name, var_type).value;
     var.attributes["source"] = filename;
 
     // Get variable attributes
-    for (const auto& attpair : io.AvailableAttributes(var_name, "/", true)) {
+    for (const auto& attpair : stream.io.AvailableAttributes(var_name, "/", true)) {
       const auto& att_name = attpair.first; // Attribute name
       const auto& att = attpair.second;     // attribute params
 
       auto it = att.find("Type");
       const std::string& att_type = it->second;
-      readAttribute(io, att_name, att_type, var);
+      readAttribute(stream.io, att_name, att_type, var);
     }
   }
 
-  reader.Close();
+  stream.finish();
 
   return result;
 }

From 86e6ba88dbc08a94f59edc949a36def650ca1232 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 30 Jul 2026 17:27:11 -0700
Subject: [PATCH 1657/1827] Add simple Get/Put

---
 include/bout/adios_object.hxx | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 901857e7d4..a52703c08a 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -16,6 +16,8 @@
 
 #if BOUT_HAS_ADIOS2
 
+#include "bout/assert.hxx"
+#include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
 
 #include <adios2.h>
@@ -58,6 +60,21 @@ public:
     return v;
   }
 
+  template <class T>
+  void Get(const std::string& varname, T& value, adios2::Mode mode = adios2::Mode::Sync) {
+    auto variable = GetValueVariable<T>(varname);
+    ASSERT1(variable.ShapeID() == adios2::ShapeID::GlobalValue);
+    engine().Get(variable, &value, mode);
+  }
+
+  template <class T>
+  void Put(const std::string& varname, T value) {
+    if (BoutComm::rank() != 0) {
+      return;
+    }
+    engine().Put(GetValueVariable<T>(varname), value);
+  }
+
   template <class T>
   adios2::Variable<T>
   GetArrayVariable(const std::string& varname, const adios2::Dims& shape,

From dcf3091d8d86ff5cbe3b461f67b3eac5f00f41d6 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 30 Jul 2026 17:52:12 -0700
Subject: [PATCH 1658/1827] Add get for Array/Matrix/Tensor

---
 include/bout/adios_object.hxx | 67 ++++++++++++++++++++++++++++++++++-
 1 file changed, 66 insertions(+), 1 deletion(-)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index a52703c08a..80d055aa67 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -19,11 +19,14 @@
 #include "bout/assert.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/utils.hxx"
 
 #include <adios2.h>
 #include <memory>
 #include <mpi.h>
 #include <string>
+#include <tuple>
+#include <utility>
 
 namespace bout {
 
@@ -62,11 +65,30 @@ public:
 
   template <class T>
   void Get(const std::string& varname, T& value, adios2::Mode mode = adios2::Mode::Sync) {
-    auto variable = GetValueVariable<T>(varname);
+    auto variable = io.InquireVariable<T>(varname);
+    ASSERT1(variable);
     ASSERT1(variable.ShapeID() == adios2::ShapeID::GlobalValue);
     engine().Get(variable, &value, mode);
   }
 
+  template <class T>
+  void Get(const std::string& varname, Array<T>& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    GetArrayLike(varname, value, mode);
+  }
+
+  template <class T>
+  void Get(const std::string& varname, Matrix<T>& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    GetArrayLike(varname, value, mode);
+  }
+
+  template <class T>
+  void Get(const std::string& varname, Tensor<T>& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    GetArrayLike(varname, value, mode);
+  }
+
   template <class T>
   void Put(const std::string& varname, T value) {
     if (BoutComm::rank() != 0) {
@@ -132,6 +154,49 @@ public:
 private:
   ADIOSStream(const std::string& fname, adios2::Mode mode, const std::string& engineType);
 
+  template <class Container>
+  void GetArrayLike(const std::string& varname, Container& value, adios2::Mode mode) {
+    using T = typename Container::data_type;
+    auto variable = io.InquireVariable<T>(varname);
+    ASSERT1(variable);
+    ASSERT1(variable.ShapeID() == adios2::ShapeID::GlobalArray);
+
+    const auto shape = variable.Shape();
+    auto dims_attr = io.InquireAttribute<std::string>(varname + "/__xarray_dimensions__");
+    std::size_t offset = 0;
+
+    if (dims_attr) {
+      const auto dim_names = dims_attr.Data();
+      if (!dim_names.empty() && dim_names[0] == "rank") {
+        ASSERT1(!shape.empty());
+        ASSERT1(static_cast<std::size_t>(BoutComm::rank()) < shape[0]);
+
+        adios2::Dims start{static_cast<std::size_t>(BoutComm::rank())};
+        adios2::Dims count{1};
+        for (std::size_t i = 1; i < shape.size(); i++) {
+          start.push_back(0);
+          count.push_back(shape[i]);
+        }
+
+        variable.SetSelection(adios2::Box<adios2::Dims>{start, count});
+        variable.SetMemorySelection(adios2::Box<adios2::Dims>{start, count});
+        offset = 1;
+      }
+    }
+
+    constexpr auto ndims = std::tuple_size_v<decltype(value.shape())>;
+    ASSERT1(shape.size() == ndims + offset);
+
+    resizeForShape(value, shape, offset, std::make_index_sequence<ndims>{});
+    engine().Get(variable, value.begin(), mode);
+  }
+
+  template <class Container, std::size_t... I>
+  void resizeForShape(Container& value, const adios2::Dims& shape, std::size_t offset,
+                      std::index_sequence<I...> /*indices*/) {
+    value.reallocate(static_cast<typename Container::size_type>(shape[offset + I])...);
+  }
+
   std::string fname;
   adios2::Mode file_mode;
   adios2::Engine engine_;

From 50465fefedb3662653148a05ec7ceb717d997493 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 30 Jul 2026 18:11:52 -0700
Subject: [PATCH 1659/1827] Add put for Array/Matrix/Tensor

---
 include/bout/adios_object.hxx | 53 +++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 80d055aa67..4d3efcf620 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -27,6 +27,7 @@
 #include <string>
 #include <tuple>
 #include <utility>
+#include <vector>
 
 namespace bout {
 
@@ -97,6 +98,21 @@ public:
     engine().Put(GetValueVariable<T>(varname), value);
   }
 
+  template <class T>
+  void Put(const std::string& varname, const Array<T>& value) {
+    PutArrayLike(varname, value);
+  }
+
+  template <class T>
+  void Put(const std::string& varname, const Matrix<T>& value) {
+    PutArrayLike(varname, value);
+  }
+
+  template <class T>
+  void Put(const std::string& varname, const Tensor<T>& value) {
+    PutArrayLike(varname, value);
+  }
+
   template <class T>
   adios2::Variable<T>
   GetArrayVariable(const std::string& varname, const adios2::Dims& shape,
@@ -191,6 +207,43 @@ private:
     engine().Get(variable, value.begin(), mode);
   }
 
+  template <class Container>
+  void PutArrayLike(const std::string& varname, const Container& value) {
+    using T = typename Container::data_type;
+    auto var = GetArrayVariable<T>(varname, makeShape(BoutComm::size(), value),
+                                   makeDimNames(value), BoutComm::rank());
+    var.SetSelection(adios2::Box<adios2::Dims>{makeStart(value), makeShape(1, value)});
+    engine().Put<T>(var, value.begin());
+  }
+
+  template <class Container>
+  adios2::Dims makeShape(std::size_t first, const Container& value) const {
+    return std::apply(
+        [first](auto... sizes) {
+          return adios2::Dims{first, static_cast<std::size_t>(sizes)...};
+        },
+        value.shape());
+  }
+
+  template <class Container>
+  adios2::Dims makeStart(const Container& value) const {
+    constexpr auto ndims = std::tuple_size_v<decltype(value.shape())>;
+    adios2::Dims start(ndims + 1, 0);
+    start[0] = static_cast<std::size_t>(BoutComm::rank());
+    return start;
+  }
+
+  template <class Container>
+  std::vector<std::string> makeDimNames(const Container& value) const {
+    constexpr auto ndims = std::tuple_size_v<decltype(value.shape())>;
+    std::vector<std::string> dim_names{"rank"};
+    dim_names.reserve(ndims + 1);
+    for (std::size_t i = 0; i < ndims; i++) {
+      dim_names.push_back("dim_" + std::to_string(i));
+    }
+    return dim_names;
+  }
+
   template <class Container, std::size_t... I>
   void resizeForShape(Container& value, const adios2::Dims& shape, std::size_t offset,
                       std::index_sequence<I...> /*indices*/) {

From d2ad823e1bef7729953da3610c59b1481354611b Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 30 Jul 2026 18:16:25 -0700
Subject: [PATCH 1660/1827] Add get for Fields

---
 include/bout/adios_object.hxx | 85 +++++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 4d3efcf620..0330e2e97e 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -19,6 +19,10 @@
 #include "bout/assert.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/fieldperp.hxx"
+#include "bout/mesh.hxx"
 #include "bout/utils.hxx"
 
 #include <adios2.h>
@@ -90,6 +94,24 @@ public:
     GetArrayLike(varname, value, mode);
   }
 
+  void Get(const std::string& varname, Field2D& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    value.allocate();
+    GetField(varname, {"x", "y"}, *value.getMesh(), &value(0, 0), mode);
+  }
+
+  void Get(const std::string& varname, Field3D& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    value.allocate();
+    GetField(varname, {"x", "y", "z"}, *value.getMesh(), &value(0, 0, 0), mode);
+  }
+
+  void Get(const std::string& varname, FieldPerp& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    value.allocate();
+    GetField(varname, {"x", "z"}, *value.getMesh(), &value(0, 0), mode);
+  }
+
   template <class T>
   void Put(const std::string& varname, T value) {
     if (BoutComm::rank() != 0) {
@@ -170,6 +192,69 @@ public:
 private:
   ADIOSStream(const std::string& fname, adios2::Mode mode, const std::string& engineType);
 
+  struct FieldSelection {
+    adios2::Dims start;
+    adios2::Dims count;
+    adios2::Dims mem_start;
+    adios2::Dims mem_count;
+
+    auto selection() const { return adios2::Box<adios2::Dims>{start, count}; }
+    auto memorySelection() const {
+      return adios2::Box<adios2::Dims>{mem_start, mem_count};
+    }
+  };
+
+  void GetField(const std::string& varname, const std::vector<std::string>& dim_names,
+                const Mesh& mesh, BoutReal* data, adios2::Mode mode) {
+    auto variable = io.InquireVariable<BoutReal>(varname);
+    ASSERT1(variable);
+    ASSERT1(variable.ShapeID() == adios2::ShapeID::GlobalArray);
+
+    auto selection = makeFieldSelection(dim_names, mesh);
+    variable.SetSelection(selection.selection());
+    variable.SetMemorySelection(selection.memorySelection());
+    engine().Get(variable, data, mode);
+  }
+
+  FieldSelection makeFieldSelection(const std::vector<std::string>& dim_names,
+                                    const Mesh& mesh) const {
+    ASSERT1(!dim_names.empty());
+    ASSERT1(dim_names.size() <= 3);
+    ASSERT1(dim_names[0] == "x");
+
+    FieldSelection selection;
+    selection.start.push_back(static_cast<std::size_t>(mesh.MapGlobalX));
+    selection.count.push_back(static_cast<std::size_t>(mesh.MapCountX));
+    selection.mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalX));
+    selection.mem_count.push_back(static_cast<std::size_t>(mesh.LocalNx));
+
+    if (dim_names.size() > 1) {
+      if (dim_names[1] == "y") {
+        selection.start.push_back(static_cast<std::size_t>(mesh.MapGlobalY));
+        selection.count.push_back(static_cast<std::size_t>(mesh.MapCountY));
+        selection.mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalY));
+        selection.mem_count.push_back(static_cast<std::size_t>(mesh.LocalNy));
+      } else if (dim_names[1] == "z") {
+        selection.start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
+        selection.count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
+        selection.mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));
+        selection.mem_count.push_back(static_cast<std::size_t>(mesh.LocalNz));
+      } else {
+        ASSERT1(false);
+      }
+    }
+
+    if (dim_names.size() > 2) {
+      ASSERT1(dim_names[2] == "z");
+      selection.start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
+      selection.count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
+      selection.mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));
+      selection.mem_count.push_back(static_cast<std::size_t>(mesh.LocalNz));
+    }
+
+    return selection;
+  }
+
   template <class Container>
   void GetArrayLike(const std::string& varname, Container& value, adios2::Mode mode) {
     using T = typename Container::data_type;

From 357ec23a67cbdb0832d9fa37c647e21f37102ac5 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 30 Jul 2026 18:18:18 -0700
Subject: [PATCH 1661/1827] Add put for Fields

---
 include/bout/adios_object.hxx | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 0330e2e97e..25924346d6 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -135,6 +135,18 @@ public:
     PutArrayLike(varname, value);
   }
 
+  void Put(const std::string& varname, const Field2D& value) {
+    PutField(varname, {"x", "y"}, *value.getMesh(), &value(0, 0));
+  }
+
+  void Put(const std::string& varname, const Field3D& value) {
+    PutField(varname, {"x", "y", "z"}, *value.getMesh(), &value(0, 0, 0));
+  }
+
+  void Put(const std::string& varname, const FieldPerp& value) {
+    PutField(varname, {"x", "z"}, *value.getMesh(), &value(0, 0));
+  }
+
   template <class T>
   adios2::Variable<T>
   GetArrayVariable(const std::string& varname, const adios2::Dims& shape,
@@ -193,6 +205,7 @@ private:
   ADIOSStream(const std::string& fname, adios2::Mode mode, const std::string& engineType);
 
   struct FieldSelection {
+    adios2::Dims shape;
     adios2::Dims start;
     adios2::Dims count;
     adios2::Dims mem_start;
@@ -216,6 +229,16 @@ private:
     engine().Get(variable, data, mode);
   }
 
+  void PutField(const std::string& varname, const std::vector<std::string>& dim_names,
+                const Mesh& mesh, const BoutReal* data) {
+    auto selection = makeFieldSelection(dim_names, mesh);
+    auto variable =
+        GetArrayVariable<BoutReal>(varname, selection.shape, dim_names, BoutComm::rank());
+    variable.SetSelection(selection.selection());
+    variable.SetMemorySelection(selection.memorySelection());
+    engine().Put(variable, data);
+  }
+
   FieldSelection makeFieldSelection(const std::vector<std::string>& dim_names,
                                     const Mesh& mesh) const {
     ASSERT1(!dim_names.empty());
@@ -223,6 +246,7 @@ private:
     ASSERT1(dim_names[0] == "x");
 
     FieldSelection selection;
+    selection.shape.push_back(static_cast<std::size_t>(mesh.GlobalNx));
     selection.start.push_back(static_cast<std::size_t>(mesh.MapGlobalX));
     selection.count.push_back(static_cast<std::size_t>(mesh.MapCountX));
     selection.mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalX));
@@ -230,11 +254,13 @@ private:
 
     if (dim_names.size() > 1) {
       if (dim_names[1] == "y") {
+        selection.shape.push_back(static_cast<std::size_t>(mesh.GlobalNy));
         selection.start.push_back(static_cast<std::size_t>(mesh.MapGlobalY));
         selection.count.push_back(static_cast<std::size_t>(mesh.MapCountY));
         selection.mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalY));
         selection.mem_count.push_back(static_cast<std::size_t>(mesh.LocalNy));
       } else if (dim_names[1] == "z") {
+        selection.shape.push_back(static_cast<std::size_t>(mesh.GlobalNz));
         selection.start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
         selection.count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
         selection.mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));
@@ -245,7 +271,9 @@ private:
     }
 
     if (dim_names.size() > 2) {
+      ASSERT1(dim_names[1] == "y");
       ASSERT1(dim_names[2] == "z");
+      selection.shape.push_back(static_cast<std::size_t>(mesh.GlobalNz));
       selection.start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
       selection.count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
       selection.mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));

From 84d0788f9842048d9cd68adbe1aa52de685074ae Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 30 Jul 2026 18:45:42 -0700
Subject: [PATCH 1662/1827] Use new adios_object functionality in options_adios

---
 include/bout/adios_object.hxx     |  15 +-
 src/sys/options/options_adios.cxx | 349 +++++-------------------------
 2 files changed, 64 insertions(+), 300 deletions(-)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 25924346d6..62a05e00f2 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -22,6 +22,7 @@
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/fieldperp.hxx"
+#include "bout/globals.hxx"
 #include "bout/mesh.hxx"
 #include "bout/utils.hxx"
 
@@ -292,7 +293,7 @@ private:
 
     const auto shape = variable.Shape();
     auto dims_attr = io.InquireAttribute<std::string>(varname + "/__xarray_dimensions__");
-    std::size_t offset = 0;
+    auto read_shape = shape;
 
     if (dims_attr) {
       const auto dim_names = dims_attr.Data();
@@ -309,14 +310,20 @@ private:
 
         variable.SetSelection(adios2::Box<adios2::Dims>{start, count});
         variable.SetMemorySelection(adios2::Box<adios2::Dims>{start, count});
-        offset = 1;
+        read_shape = adios2::Dims(shape.begin() + 1, shape.end());
+      } else if (!dim_names.empty() && dim_names[0] == "x") {
+        ASSERT1(globals::mesh);
+        auto selection = makeFieldSelection(dim_names, *globals::mesh);
+        variable.SetSelection(selection.selection());
+        variable.SetMemorySelection(selection.memorySelection());
+        read_shape = selection.mem_count;
       }
     }
 
     constexpr auto ndims = std::tuple_size_v<decltype(value.shape())>;
-    ASSERT1(shape.size() == ndims + offset);
+    ASSERT1(read_shape.size() == ndims);
 
-    resizeForShape(value, shape, offset, std::make_index_sequence<ndims>{});
+    resizeForShape(value, read_shape, 0, std::make_index_sequence<ndims>{});
     engine().Get(variable, value.begin(), mode);
   }
 
diff --git a/src/sys/options/options_adios.cxx b/src/sys/options/options_adios.cxx
index 6e0227d7b9..4abf55bcd5 100644
--- a/src/sys/options/options_adios.cxx
+++ b/src/sys/options/options_adios.cxx
@@ -10,157 +10,41 @@
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field2d.hxx"
-#include "bout/globals.hxx"
-#include "bout/mesh.hxx"
 #include "bout/options.hxx"
 #include "bout/options_io.hxx"
 #include "bout/output.hxx"
 #include "bout/sys/timer.hxx"
 #include "bout/sys/variant.hxx"
-#include "bout/traits.hxx"
 #include "bout/utils.hxx"
 
 #include <adios2.h> // IWYU pragma: keep
 #include <fmt/format.h>
 #include <fmt/ranges.h>
 
-#include <algorithm>
 #include <cstddef>
 #include <cstdint>
 #include <exception>
-#include <iterator>
 #include <stdexcept>
 #include <string>
-#include <utility>
-#include <vector>
 
 namespace {
-auto to_int_dims(const adios2::Dims& dims) {
-  std::vector<int> int_dims;
-  int_dims.reserve(dims.size());
-  std::transform(dims.begin(), dims.end(), std::back_inserter(int_dims),
-                 [](auto dim) { return static_cast<int>(dim); });
-  return int_dims;
-}
-
-// Helper class to construct Adios hyperslices
-struct Selection {
-  // Offset of this processor's data into the global array
-  adios2::Dims start;
-  // The size of the mapped region
-  adios2::Dims count;
-  // Where the actual data starts in data pointer (to exclude ghost cells)
-  adios2::Dims mem_start;
-  // The actual size of data pointer in memory (including ghost cells)
-  adios2::Dims mem_count;
-  // Global shape, including boundaries but not guard cells
-  adios2::Dims shape;
-  // Shape of the local variable to read into
-  std::vector<int> dims;
-
-  // Distributed Field/Array/Matrix/Tensor
-  bool should_set_selection{false};
-
-  Selection(const std::vector<std::string>& dim_names, const std::vector<int>& dim_sizes,
-            const Mesh& mesh) {
-    const auto ndims = dim_names.size();
-    const bool dim0_is_rank = ndims > 0 ? (dim_names[0] == "rank") : false;
-    const bool dim0_is_x = ndims > 0 ? (dim_names[0] == "x") : false;
-    const bool dim1_is_y = ndims > 1 ? (dim_names[1] == "y") : false;
-    const bool dim1_is_z = ndims > 1 ? (dim_names[1] == "z") : false;
-    const bool dim2_is_z = ndims > 2 ? (dim_names[2] == "z") : false;
-
-    should_set_selection = dim0_is_rank or (ndims == 2 and dim0_is_x and dim1_is_y)
-                           or (ndims == 2 and dim0_is_x and dim1_is_z)
-                           or (ndims == 3 and dim0_is_x and dim1_is_y and dim2_is_z);
-
-    if (dim0_is_rank) {
-      const auto ndim_sizes = dim_sizes.size();
-      ASSERT3(ndim_sizes > 1);
-
-      // This is a distributed array, so the local variable is going
-      // to be shape (dim_sizes[1]...) (that is, drop the rank)
-      dims.push_back(dim_sizes[1]);
-      // but we tell adios to read our rank's bit with the full ndims
-      start = {static_cast<std::size_t>(BoutComm::rank()), 0};
-      count = {std::size_t{1}, static_cast<std::size_t>(dim_sizes[0])};
-
-      if (ndim_sizes > 2) {
-        dims.push_back(dim_sizes[2]);
-        start.push_back(0);
-        count.push_back(dim_sizes[1]);
-      }
-      if (ndim_sizes > 3) {
-        dims.push_back(dim_sizes[3]);
-        start.push_back(0);
-        count.push_back(dim_sizes[2]);
-      }
-      mem_count = count;
-      mem_start = start;
-      return;
-    }
-
-    if (ndims > 0) {
-      dims.push_back(dim0_is_x ? mesh.LocalNx : dim_sizes[0]);
-    }
-    if (ndims > 1) {
-      if (dim1_is_y) {
-        dims.push_back(mesh.LocalNy);
-      } else if (dim1_is_z) {
-        dims.push_back(mesh.LocalNz);
-      } else {
-        dims.push_back(dim_sizes[1]);
-      }
-    }
-    if (ndims > 2) {
-      dims.push_back(dim2_is_z ? mesh.LocalNz : dim_sizes[2]);
-    }
-
-    shape.push_back(static_cast<std::size_t>(mesh.GlobalNx));
-    start.push_back(static_cast<std::size_t>(mesh.MapGlobalX));
-    count.push_back(static_cast<std::size_t>(mesh.MapCountX));
-    mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalX));
-    mem_count.push_back(static_cast<std::size_t>(mesh.LocalNx));
-
-    if (dim1_is_y) {
-      shape.push_back(static_cast<std::size_t>(mesh.GlobalNy));
-      start.push_back(static_cast<std::size_t>(mesh.MapGlobalY));
-      count.push_back(static_cast<std::size_t>(mesh.MapCountY));
-      mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalY));
-      mem_count.push_back(static_cast<std::size_t>(mesh.LocalNy));
-    } else if (dim1_is_z) {
-      shape.push_back(static_cast<std::size_t>(mesh.GlobalNz));
-      start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
-      count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
-      mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));
-      mem_count.push_back(static_cast<std::size_t>(mesh.LocalNz));
-    }
-
-    if (dim2_is_z) {
-      shape.push_back(static_cast<std::size_t>(mesh.GlobalNz));
-      start.push_back(static_cast<std::size_t>(mesh.MapGlobalZ));
-      count.push_back(static_cast<std::size_t>(mesh.MapCountZ));
-      mem_start.push_back(static_cast<std::size_t>(mesh.MapLocalZ));
-      mem_count.push_back(static_cast<std::size_t>(mesh.LocalNz));
+std::size_t getLocalNDims(adios2::IO& io, const std::string& name,
+                          const adios2::Dims& shape) {
+  auto dims_attr = io.InquireAttribute<std::string>(name + "/__xarray_dimensions__");
+  if (dims_attr) {
+    const auto dim_names = dims_attr.Data();
+    if (!dim_names.empty() && dim_names[0] == "rank") {
+      ASSERT1(!shape.empty());
+      return shape.size() - 1;
     }
   }
+  return shape.size();
+}
 
-  auto selection() const { return adios2::Box<adios2::Dims>{start, count}; }
-  auto memorySelection() const { return adios2::Box<adios2::Dims>{mem_start, mem_count}; }
-};
-
-template <template <class> class T, class U>
-auto read_variable(adios2::IO& io, adios2::Engine& reader, const std::string& name,
-                   const Selection& selection, T<U>& value) {
-  auto variable = io.InquireVariable<U>(name);
-
-  if (selection.should_set_selection) {
-    variable.SetSelection(selection.selection());
-    variable.SetMemorySelection(selection.memorySelection());
-  }
-
+template <class T>
+Options readArrayVariable(bout::ADIOSStream& stream, const std::string& name, T& value) {
   try {
-    reader.Get<U>(variable, value.begin(), adios2::Mode::Sync);
+    stream.Get(name, value);
   } catch (const std::exception& e) {
     output_warn.write("ADIOS exception while reading '{}': {}\n", name, e.what());
     return Options{};
@@ -169,84 +53,77 @@ auto read_variable(adios2::IO& io, adios2::Engine& reader, const std::string& na
 }
 
 template <class T>
-Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name,
+Options readVariable(bout::ADIOSStream& stream, const std::string& name,
                      const std::string& type) {
-  auto variable = io.InquireVariable<T>(name);
-
-  using bout::globals::mesh;
+  auto variable = stream.io.InquireVariable<T>(name);
 
   if (variable.ShapeID() == adios2::ShapeID::GlobalValue) {
     T value;
-    reader.Get<T>(variable, &value, adios2::Mode::Sync);
+    stream.Get(name, value);
     return Options(value);
   }
 
   if (variable.ShapeID() == adios2::ShapeID::LocalArray) {
     throw BoutException("ADIOS reader did not implement reading local arrays like `{}` "
                         "'{}' in file '{}'\n",
-                        type, name, reader.Name());
+                        type, name, stream.engine().Name());
   }
 
   if (type != "double" && type != "float" && type != "int32_t" && type != "int64_t") {
     throw BoutException("ADIOS reader did not implement reading arrays that are not "
                         "`double`/`float`/`int32_t`/`int64_t` type. "
                         "Found `{}` '{}' in file '{}'\n",
-                        type, name, reader.Name());
+                        type, name, stream.engine().Name());
   }
 
   if (type == "double" && sizeof(BoutReal) != sizeof(double)) {
     throw BoutException(
         "ADIOS does not allow for implicit type conversions. BoutReal type is "
         "float but found `{}` '{}' in file '{}'\n",
-        type, name, reader.Name());
+        type, name, stream.engine().Name());
   }
 
   if (type == "float" && sizeof(BoutReal) != sizeof(float)) {
     throw BoutException(
         "ADIOS reader does not allow for implicit type conversions. BoutReal type is "
         "double but found `{}` '{}' in file '{}'",
-        type, name, reader.Name());
+        type, name, stream.engine().Name());
   }
 
-  const auto dims = to_int_dims(variable.Shape());
-  auto dims_attr =
-      io.InquireAttribute<std::string>(fmt::format("{}/__xarray_dimensions__", name))
-          .Data();
-
-  const auto selection = Selection(dims_attr, dims, *mesh);
-  const auto ndims = selection.dims.size();
+  const auto shape = variable.Shape();
+  const auto ndims = getLocalNDims(stream.io, name, shape);
 
   switch (ndims) {
   case 1: {
     if (type == "float" or type == "double") {
-      Array<BoutReal> value(dims[0]);
-      return read_variable(io, reader, name, selection, value);
+      Array<BoutReal> value;
+      return readArrayVariable(stream, name, value);
     }
     if (type == "int32_t" or type == "int64_t") {
-      Array<int> value(dims[0]);
-      return read_variable(io, reader, name, selection, value);
+      Array<int> value;
+      return readArrayVariable(stream, name, value);
     }
     break;
   }
   case 2: {
     if (type == "float" or type == "double") {
-      Matrix<BoutReal> value(selection.dims[0], selection.dims[1]);
-      return read_variable(io, reader, name, selection, value);
+      Matrix<BoutReal> value;
+      return readArrayVariable(stream, name, value);
     }
     if (type == "int32_t" or type == "int64_t") {
-      Matrix<int> value(selection.dims[0], selection.dims[1]);
-      return read_variable(io, reader, name, selection, value);
+      Matrix<int> value;
+      return readArrayVariable(stream, name, value);
     }
     break;
   }
   case 3: {
     if (type == "float" or type == "double") {
-      Tensor<BoutReal> value(selection.dims[0], selection.dims[1], selection.dims[2]);
-      return read_variable(io, reader, name, selection, value);
+      Tensor<BoutReal> value;
+      return readArrayVariable(stream, name, value);
     }
     if (type == "int32_t" or type == "int64_t") {
-      Tensor<int> value(selection.dims[0], selection.dims[1], selection.dims[2]);
-      return read_variable(io, reader, name, selection, value);
+      Tensor<int> value;
+      return readArrayVariable(stream, name, value);
     }
     break;
   }
@@ -254,52 +131,52 @@ Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string&
   default:
     break;
   }
-  auto dims_str = fmt::format("[{}]", fmt::join(dims, ", "));
+  auto dims_str = fmt::format("[{}]", fmt::join(shape, ", "));
   throw BoutException(
       "ADIOS reader failed to read '{}' (shape: {}, type: '{}') in file '{}'\n", name,
-      dims_str, type, reader.Name());
+      dims_str, type, stream.engine().Name());
 }
 
-Options readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name,
+Options readVariable(bout::ADIOSStream& stream, const std::string& name,
                      const std::string& type) {
   if (type == adios2::GetType<std::string>()) {
-    return readVariable<std::string>(reader, io, name, type);
+    return readVariable<std::string>(stream, name, type);
   }
   if (type == adios2::GetType<char>()) {
-    return readVariable<char>(reader, io, name, type);
+    return readVariable<char>(stream, name, type);
   }
   if (type == adios2::GetType<int8_t>()) {
-    return readVariable<int8_t>(reader, io, name, type);
+    return readVariable<int8_t>(stream, name, type);
   }
   if (type == adios2::GetType<int16_t>()) {
-    return readVariable<int16_t>(reader, io, name, type);
+    return readVariable<int16_t>(stream, name, type);
   }
   if (type == adios2::GetType<int32_t>()) {
-    return readVariable<int32_t>(reader, io, name, type);
+    return readVariable<int32_t>(stream, name, type);
   }
   if (type == adios2::GetType<int64_t>()) {
-    return readVariable<int64_t>(reader, io, name, type);
+    return readVariable<int64_t>(stream, name, type);
   }
   if (type == adios2::GetType<uint8_t>()) {
-    return readVariable<uint8_t>(reader, io, name, type);
+    return readVariable<uint8_t>(stream, name, type);
   }
   if (type == adios2::GetType<uint16_t>()) {
-    return readVariable<uint16_t>(reader, io, name, type);
+    return readVariable<uint16_t>(stream, name, type);
   }
   if (type == adios2::GetType<uint32_t>()) {
-    return readVariable<uint32_t>(reader, io, name, type);
+    return readVariable<uint32_t>(stream, name, type);
   }
   if (type == adios2::GetType<uint64_t>()) {
-    return readVariable<uint64_t>(reader, io, name, type);
+    return readVariable<uint64_t>(stream, name, type);
   }
   if (type == adios2::GetType<float>()) {
-    return readVariable<float>(reader, io, name, type);
+    return readVariable<float>(stream, name, type);
   }
   if (type == adios2::GetType<double>()) {
-    return readVariable<double>(reader, io, name, type);
+    return readVariable<double>(stream, name, type);
   }
   if (type == adios2::GetType<long double>()) {
-    return readVariable<long double>(reader, io, name, type);
+    return readVariable<long double>(stream, name, type);
   }
 
   output_warn.write("ADIOS readVariable can't read type '{}' (variable '{}')\n", type,
@@ -381,7 +258,7 @@ Options OptionsADIOS::read([[maybe_unused]] bool lazy) {
     // Note: Copying the value rather than simple assignment is used
     // because the Options assignment operator overwrites full_name.
     var = 0; // Setting is_section to false
-    var.value = readVariable(reader, stream.io, var_name, var_type).value;
+    var.value = readVariable(stream, var_name, var_type).value;
     var.attributes["source"] = filename;
 
     // Get variable attributes
@@ -414,142 +291,22 @@ void OptionsADIOS::verifyTimesteps() const {
 }
 } // namespace bout
 
-const std::vector<std::string> DIMS_X = {"x"};
-const std::vector<std::string> DIMS_XY = {"x", "y"};
-const std::vector<std::string> DIMS_XZ = {"x", "z"};
-const std::vector<std::string> DIMS_XYZ = {"x", "y", "z"};
-
 namespace {
-using bout::utils::tuple_index_sequence;
-
-template <class Tuple, std::size_t... I>
-auto make_shape_impl(std::size_t first, const Tuple& t,
-                     std::index_sequence<I...> /* index */) {
-  return adios2::Dims{first, static_cast<std::size_t>(std::get<I>(t))...};
-}
-// Return an `adios2::Dims` with value ``{first, value.shape()[0]...}``
-template <class T>
-auto make_shape(std::size_t first, const T& value) {
-  const auto shape = value.shape();
-  return make_shape_impl(first, shape, tuple_index_sequence<decltype(shape)>{});
-}
-
-template <class Tuple, std::size_t... I>
-auto make_start_impl(const Tuple& t, std::index_sequence<I...> /* index */) {
-  // Hey look, a legitimate use of the comma operator to get a bunch
-  // of zeros the length of the index_sequence!
-  return adios2::Dims{static_cast<std::size_t>(BoutComm::rank()),
-                      (std::get<I>(t), std::size_t{0})...};
-}
-// Return an `adios2::Dims` with value ``{rank, 0...}``, with as many zeros as the dimension of ``T``
-template <class T>
-auto make_start(const T& value) {
-  const auto shape = value.shape();
-  return make_start_impl(shape, tuple_index_sequence<decltype(shape)>{});
-}
-
-template <std::size_t... I>
-auto make_dims_impl(std::index_sequence<I...> /*index*/) {
-  using namespace std::string_literals;
-  return std::vector{"rank"s, (fmt::format("dim_{}", I))...};
-}
-// Return vector of dimension names: `{"rank", "dim_0", ...}`
-template <class T>
-auto make_dims(const T& value) {
-  return make_dims_impl(tuple_index_sequence<decltype(value.shape())>{});
-}
-
 /// Visit a variant type, and put the data into a NcVar
 struct ADIOSPutVarVisitor {
   ADIOSPutVarVisitor(const std::string& name, bout::ADIOSStream& stream)
       : varname(name), stream(stream) {}
   template <typename T>
   void operator()(const T& value) {
-    adios2::Variable<T> var = stream.GetValueVariable<T>(varname);
-    stream.engine().Put(var, value);
+    stream.Put(varname, value);
   }
 
-  void operator()(const Array<int>& value) { amt_put_helper(value); }
-  void operator()(const Array<BoutReal>& value) { amt_put_helper(value); }
-  void operator()(const Matrix<int>& value) { amt_put_helper(value); }
-  void operator()(const Matrix<BoutReal>& value) { amt_put_helper(value); }
-  void operator()(const Tensor<int>& value) { amt_put_helper(value); }
-  void operator()(const Tensor<BoutReal>& value) { amt_put_helper(value); }
-  void operator()(bool value) {
-    // Scalars are only written from processor 0
-    if (BoutComm::rank() != 0) {
-      return;
-    }
-    stream.engine().Put(stream.GetValueVariable<int>(varname), static_cast<int>(value));
-  }
-  void operator()(int value) {
-    // Scalars are only written from processor 0
-    if (BoutComm::rank() != 0) {
-      return;
-    }
-    stream.engine().Put(stream.GetValueVariable<int>(varname), value);
-  }
-  void operator()(BoutReal value) {
-    // Scalars are only written from processor 0
-    if (BoutComm::rank() != 0) {
-      return;
-    }
-    stream.engine().Put(stream.GetValueVariable<BoutReal>(varname), value);
-  }
-
-  void operator()(const std::string& value) {
-    // Scalars are only written from processor 0
-    if (BoutComm::rank() != 0) {
-      return;
-    }
-    stream.engine().Put<std::string>(stream.GetValueVariable<std::string>(varname), value,
-                                     adios2::Mode::Sync);
-  }
-
-  void operator()(const Field2D& value) {
-    // Empty dim_sizes is fine because we provide full list of dim_names
-    auto selection = Selection(DIMS_XY, {}, *value.getMesh());
-    auto var = stream.GetArrayVariable<BoutReal>(varname, selection.shape, DIMS_XY,
-                                                 BoutComm::rank());
-    var.SetSelection(selection.selection());
-    var.SetMemorySelection(selection.memorySelection());
-    stream.engine().Put(var, &value(0, 0));
-  }
-
-  void operator()(const Field3D& value) {
-    // Empty dim_sizes is fine because we provide full list of dim_names
-    auto selection = Selection(DIMS_XYZ, {}, *value.getMesh());
-    auto var = stream.GetArrayVariable<BoutReal>(varname, selection.shape, DIMS_XYZ,
-                                                 BoutComm::rank());
-    var.SetSelection(selection.selection());
-    var.SetMemorySelection(selection.memorySelection());
-    stream.engine().Put(var, &value(0, 0, 0));
-  }
-
-  void operator()(const FieldPerp& value) {
-    // Empty dim_sizes is fine because we provide full list of dim_names
-    auto selection = Selection(DIMS_XZ, {}, *value.getMesh());
-    auto var = stream.GetArrayVariable<BoutReal>(varname, selection.shape, DIMS_XZ,
-                                                 BoutComm::rank());
-    var.SetSelection(selection.selection());
-    var.SetMemorySelection(selection.memorySelection());
-    stream.engine().Put<BoutReal>(var, &value(0, 0));
-  }
+  void operator()(bool value) { stream.Put(varname, static_cast<int>(value)); }
 
 private:
   // Ok to keep const/refs here as visitor is only a temporary
   const std::string& varname; // NOLINT(*-avoid-const-or-ref-data-members)
   bout::ADIOSStream& stream;  // NOLINT(*-avoid-const-or-ref-data-members)
-
-  // helper for `Array`, `Matrix`, `Tensor`
-  template <template <class> class T, class U>
-  void amt_put_helper(const T<U>& value) {
-    const auto shape = make_shape(static_cast<std::size_t>(BoutComm::size()), value);
-    auto var =
-        stream.GetArrayVariable<U>(varname, shape, make_dims(value), BoutComm::rank());
-    var.SetSelection({make_start(value), make_shape(1, value)});
-    stream.engine().Put<U>(var, value.begin());
-  }
 };
 
 /// Visit a variant type, and put the data into a NcVar

From 5a8ff7880b0ed7eec0f8bf74df0bcd7f6a157e35 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 4 Aug 2026 06:34:57 -0700
Subject: [PATCH 1663/1827] Apply suggestions from code review

Co-authored-by: Peter Hill <zed.three@gmail.com>
---
 include/bout/assert.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/assert.hxx b/include/bout/assert.hxx
index bebd7e4372..e243a8c829 100644
--- a/include/bout/assert.hxx
+++ b/include/bout/assert.hxx
@@ -19,7 +19,7 @@
 
 #include "bout/boutexception.hxx"
 
-#include <string_view>
+#include <string_view>  // IWYU pragma: export
 
 #ifndef CHECK
 #define CHECKLEVEL 0

From 184c3989eaf217ba781c782a8b0e5fe12af5c7c8 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 4 Aug 2026 06:37:50 -0700
Subject: [PATCH 1664/1827] BOUT_UNREACHABLE macro

Rather than returning incorrect values, mark code as unreachable.
When C++23 is used, this can be replaced with std::unreachable.
---
 include/bout/build_config.hxx | 9 +++++++++
 include/bout/fieldops.hxx     | 1 -
 include/bout/region.hxx       | 5 +++--
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/include/bout/build_config.hxx b/include/bout/build_config.hxx
index aa7f257ca5..0fed934af0 100644
--- a/include/bout/build_config.hxx
+++ b/include/bout/build_config.hxx
@@ -92,6 +92,15 @@ constexpr auto use_msgstack = static_cast<bool>(BOUT_USE_MSGSTACK);
 #else
 #define BOUT_ASSUME(condition) ((void)0)
 #endif
+
+#if defined(__GNUC__) || defined(__clang__)
+#define BOUT_UNREACHABLE() __builtin_unreachable()
+#elif defined(_MSC_VER)
+#define BOUT_UNREACHABLE() __assume(false)
+#else
+// Cannot call std::abort in device code
+#define BOUT_UNREACHABLE()
+#endif
 // NOLINTEND(cppcoreguidelines-macro-usage)
 
 #endif // BOUT_BUILD_OPTIONS_HXX
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 46bcaf77ec..e75c889bb3 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -7,7 +7,6 @@
 #include "bout/bout_types.hxx"
 #include "bout/build_config.hxx"
 #include "bout/build_defines.hxx"
-#include "bout/build_config.hxx"
 #include "bout/region.hxx"
 
 #include <cstddef>
diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index b4922bae00..a8a9ab2d1d 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -53,6 +53,7 @@
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_config.hxx"
 #include "bout/build_defines.hxx"
 #include "bout/openmpwrap.hxx" // IWYU pragma: keep
 
@@ -254,7 +255,7 @@ struct SpecificInd {
     case (DIRECTION::Z):
       return zp(dd);
     }
-    return *this;
+    BOUT_UNREACHABLE();
   }
 
   /// Templated routine to return index.?m(offset), where `?` is one of {x,y,z}
@@ -275,7 +276,7 @@ struct SpecificInd {
     case (DIRECTION::Z):
       return zm(dd);
     }
-    return *this;
+    BOUT_UNREACHABLE();
   }
 
   inline SpecificInd xp(int dx = 1) const { return {ind + (dx * ny * nz), ny, nz}; }

From 6e45535ca714225dfdc5631f3e424c9fdf5b0cff Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 4 Aug 2026 06:44:28 -0700
Subject: [PATCH 1665/1827] Formatting

---
 include/bout/assert.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/assert.hxx b/include/bout/assert.hxx
index e243a8c829..9de22f958b 100644
--- a/include/bout/assert.hxx
+++ b/include/bout/assert.hxx
@@ -19,7 +19,7 @@
 
 #include "bout/boutexception.hxx"
 
-#include <string_view>  // IWYU pragma: export
+#include <string_view> // IWYU pragma: export
 
 #ifndef CHECK
 #define CHECKLEVEL 0

From 36a4b891acee4d05575cf38fe37a38db03cb85dc Mon Sep 17 00:00:00 2001
From: Chris MacMackin <chris.macmackin@ukaea.uk>
Date: Tue, 4 Aug 2026 14:52:44 +0100
Subject: [PATCH 1666/1827] Simplify name updating logic

Co-authored-by: Peter Hill <peter.hill@york.ac.uk>
---
 src/sys/options.cxx | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 62a17270fb..a13277a1b3 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -263,16 +263,13 @@ Options& Options::operator=(Options&& other) noexcept {
   value_used = other.value_used;
 
   size_t len = other.full_name.size();
-  std::string new_prefix;
-  if (len == 0) {
-    new_prefix = full_name.empty() ? full_name : full_name + ":";
-  } else {
-    new_prefix = full_name;
-    // If new_prefix is empty but the old name is not then we also
-    // need to remove a colon when updating names
-    if (full_name.empty()) {
-      len += 1;
-    }
+  std::string new_prefix = full_name;
+  if (len == 0 and not full_name.empty()) {
+    // Append section delimiter to new name
+    new_prefix += ":";
+  } else if (len != 0 and full_name.empty()) {
+    // Remove extraneous section delimiter from old name
+    len += 1;
   }
 
   // Ensure that this is the parent of all children,

From 45d6b9e0062aea724c8814a3d0133577d4021241 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 5 Aug 2026 10:49:43 +0200
Subject: [PATCH 1667/1827] Use regionID directly on view and add wrapper for
 getCommonRegionID

---
 include/bout/fieldops.hxx | 7 ++++---
 src/mesh/mesh.cxx         | 7 +++++++
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 6a809b7893..49097779f9 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -31,6 +31,8 @@ namespace bout::detail {
 // in the template functions in this header file.
 const Region<Ind3D>& getField3DRegion(const Mesh* mesh, std::optional<size_t> regionID);
 size_t getField3DRegionID(const Mesh* mesh, const std::string& region_name);
+std::optional<size_t> meshGetCommenRegionID(Mesh* mesh, std::optional<size_t> regionID1,
+                                            std::optional<size_t> regionID2);
 } // namespace bout::detail
 
 template <typename T>
@@ -417,7 +419,7 @@ struct BinaryExpr {
         mesh,
         location,
         directions,
-        mesh->getCommonRegion(lhs.yup(slice).getRegionID(), rhs.yup(slice).getRegionID()),
+        meshGetCommonRegion(mesh, lhs.yup(slice).regionID, rhs.yup(slice).regionID),
         indices,
         yindex};
   }
@@ -429,8 +431,7 @@ struct BinaryExpr {
         mesh,
         location,
         directions,
-        mesh->getCommonRegion(lhs.ydown(slice).getRegionID(),
-                              rhs.ydown(slice).getRegionID()),
+        meshGetCommonRegion(mesh, lhs.ydown(slice).regionID, rhs.ydown(slice).regionID),
         indices,
         yindex};
   }
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 33368e6d6a..d58c9605be 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -863,3 +863,10 @@ std::optional<size_t> Mesh::getCommonRegion(std::optional<size_t> lhs,
   }
   return region3Dintersect[pos];
 }
+
+namespace bout::detail {
+std::optional<size_t> meshGetCommenRegionID(Mesh* mesh, std::optional<size_t> regionID1,
+                                            std::optional<size_t> regionID2) {
+  return mesh->getCommenRegionID(regionID1, regionID2);
+}
+} // namespace bout::detail

From 24d1742f1466922a082afa8a5596a6ff127638af Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 5 Aug 2026 06:14:44 -0700
Subject: [PATCH 1668/1827] Clang tidy fixes

---
 include/bout/hypre_interface.hxx              | 26 ++++++++++++++++---
 .../laplace/impls/hypre3d/hypre3d_laplace.cxx | 18 +++++++++----
 .../invert/laplace/test_laplace_hypre3d.cxx   | 18 ++++++++-----
 3 files changed, 46 insertions(+), 16 deletions(-)

diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index c595d4cca8..a118ff4787 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -12,8 +12,13 @@
 #include "bout/boutexception.hxx"
 #include "bout/caliper_wrapper.hxx"
 #include "bout/field.hxx"
+#include "bout/field2d.hxx"
 #include "bout/globalindexer.hxx"
 #include "bout/hyprelib.hxx"
+#include "bout/options.hxx"
+#include "bout/output.hxx"
+#include "bout/paralleltransform.hxx"
+#include "bout/region.hxx"
 #include "bout/utils.hxx"
 
 #include "HYPRE.h"
@@ -23,7 +28,10 @@
 #include "HYPRE_utilities.h"
 #include "_hypre_utilities.h"
 
+#include <cmath>
+#include <iterator>
 #include <memory>
+#include <vector>
 
 // BOUT_ENUM_CLASS does not work inside namespaces
 BOUT_ENUM_CLASS(HYPRE_SOLVER_TYPE, gmres, bicgstab, pcg);
@@ -213,7 +221,7 @@ public:
     other.V = nullptr;
   }
 
-  HypreVector<T>& operator=(HypreVector<T>&& other) {
+  HypreVector<T>& operator=(HypreVector<T>&& other) noexcept {
     comm = other.comm;
     jlower = other.jlower;
     jupper = other.jupper;
@@ -291,6 +299,10 @@ public:
 
   void assemble() {
     CALI_CXX_MARK_FUNCTION;
+
+    // Should not already be assembled
+    ASSERT1(parallel_vector == nullptr);
+
     writeCacheToHypre();
     checkHypreError(HYPRE_IJVectorAssemble(hypre_vector));
     checkHypreError(HYPRE_IJVectorGetObject(hypre_vector,
@@ -352,8 +364,14 @@ public:
   HYPRE_IJVector get() { return hypre_vector; }
   const HYPRE_IJVector& get() const { return hypre_vector; }
 
-  HYPRE_ParVector getParallel() { return parallel_vector; }
-  const HYPRE_ParVector& getParallel() const { return parallel_vector; }
+  HYPRE_ParVector getParallel() {
+    ASSERT1(parallel_vector != nullptr);
+    return parallel_vector;
+  }
+  const HYPRE_ParVector& getParallel() const {
+    ASSERT1(parallel_vector != nullptr);
+    return parallel_vector;
+  }
 
   class Element {
     HypreVector<T>* vector;
@@ -777,7 +795,7 @@ public:
           pw.begin(), pw.end(), std::back_inserter(positions),
           [this, ny, nz](ParallelTransform::PositionsAndWeights p) -> HYPRE_Int {
             return this->index_converter->getGlobal(
-                ind_type(p.i * ny * nz + p.j * nz + p.k, ny, nz));
+                ind_type((((p.i * ny) + p.j) * nz) + p.k, ny, nz));
           });
       std::transform(pw.begin(), pw.end(), std::back_inserter(weights),
                      [](ParallelTransform::PositionsAndWeights p) -> HYPRE_Complex {
diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
index beb83a216d..05e2ddd83f 100644
--- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
+++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
@@ -3,7 +3,7 @@
  *                           Using Hypre Solvers
  *
  **************************************************************************
- * Copyright 2021 - 2025 BOUT++ contributors
+ * Copyright 2021 - 2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -30,17 +30,25 @@
 #include "hypre3d_laplace.hxx"
 
 #include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
+#include <bout/boutexception.hxx>
 #include <bout/caliper_wrapper.hxx>
 #include <bout/derivs.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/globalindexer.hxx>
 #include <bout/hypre_interface.hxx>
 #include <bout/mesh.hxx>
 #include <bout/operatorstencil.hxx>
+#include <bout/region.hxx>
 #include <bout/solver.hxx>
 #include <bout/sys/timer.hxx>
 #include <bout/utils.hxx>
 
 #include <cmath>
+#include <memory>
+#include <vector>
 
 LaplaceHypre3d::LaplaceHypre3d(Options* opt, const CELL_LOC loc, Mesh* mesh_in, Solver*)
     : Laplacian(opt, loc, mesh_in), A(0.0), C1(1.0), C2(1.0), D(1.0), Ex(0.0), Ez(0.0),
@@ -232,7 +240,7 @@ Field3D LaplaceHypre3d::solve(const Field3D& b_in, const Field3D& x0) {
   CALI_MARK_BEGIN("LaplaceHypre3d_solve:solve");
   // Invoke solver
   {
-    Timer timer("hypresolve");
+    const Timer timer("hypresolve");
     linearSystem.solve();
   }
 
@@ -309,7 +317,7 @@ void LaplaceHypre3d::updateMatrix3D() {
     }
 
     BoutReal C_d2f_dx2 = coords->g11[l];
-    BoutReal C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]);
+    BoutReal C_d2f_dy2 = (coords->g22[l] - (1.0 / coords->g_22[l]));
     BoutReal C_d2f_dz2 = coords->g33[l];
     if (issetD) {
       C_d2f_dx2 *= D[l];
@@ -364,7 +372,7 @@ void LaplaceHypre3d::updateMatrix3D() {
   // Must add these (rather than assign) so that elements used in
   // interpolation don't overwrite each other.
   BOUT_FOR_SERIAL(l, indexer->getRegionNobndry()) {
-    BoutReal C_df_dy = (coords->G2[l] - dJ_dy[l] / coords->J[l]);
+    BoutReal C_df_dy = (coords->G2[l] - (dJ_dy[l] / coords->J[l]));
     if (issetD) {
       C_df_dy *= D[l];
     }
@@ -375,7 +383,7 @@ void LaplaceHypre3d::updateMatrix3D() {
           / C1[l];
     }
 
-    BoutReal C_d2f_dy2 = (coords->g22[l] - 1.0 / coords->g_22[l]);
+    BoutReal C_d2f_dy2 = (coords->g22[l] - (1.0 / coords->g_22[l]));
     if (issetD) {
       C_d2f_dy2 *= D[l];
     }
diff --git a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
index a721b96833..92d7b3194b 100644
--- a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
+++ b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
@@ -10,14 +10,18 @@
 #include "bout/invert_laplace.hxx"
 #include "gtest/gtest.h"
 
+#include "bout/bout_types.hxx"
+#include "bout/coordinates.hxx"
 #include "bout/derivs.hxx"
 #include "bout/difops.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
+#include "bout/globals.hxx"
 #include "bout/griddata.hxx"
 #include "bout/hypre_interface.hxx"
 #include "bout/mesh.hxx"
 #include "bout/options.hxx"
+#include "bout/region.hxx"
 #include "bout/vecops.hxx"
 
 #include "fake_mesh_fixture.hxx"
@@ -38,7 +42,7 @@ class ForwardOperator {
     upper_y_neumann = yup_neumann;
   }
 
-  const Field3D operator()(Field3D& f) {
+  Field3D operator()(Field3D& f) {
     Field3D result = d * Laplace_perp(f, CELL_DEFAULT, "free", "RGN_NOY")
                      + (Grad(f) * Grad(c2) - DDY(c2) * DDY(f) / coords->g_22) / c1 + a * f
                      + ex * DDX(f) + ez * DDZ(f);
@@ -53,7 +57,7 @@ class ForwardOperator {
   bool inner_x_neumann, outer_x_neumann, // If false then use Dirichlet conditions
       lower_y_neumann, upper_y_neumann;
 
-  void applyBoundaries(Field3D& newF, Field3D& f) {
+  void applyBoundaries(Field3D& newF, Field3D& f) const {
     BOUT_FOR(i, f.getMesh()->getRegion3D("RGN_INNER_X")) {
       if (inner_x_neumann) {
         newF[i] = (f[i.xp()] - f[i]) / coords->dx[i] / sqrt(coords->g_11[i]);
@@ -104,14 +108,14 @@ class LaplaceHypre3dTest
     coef3.allocate();
 
     BOUT_FOR(i, mesh->getRegion2D("RGN_ALL")) {
-      BoutReal x = i.x() / (BoutReal)nx - 0.5;
-      BoutReal y = i.y() / (BoutReal)ny - 0.5;
+      const BoutReal x = i.x() / (BoutReal)nx - 0.5;
+      const BoutReal y = i.y() / (BoutReal)ny - 0.5;
       coef2[i] = x + y;
     }
     BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) {
-      BoutReal x = i.x() / (BoutReal)nx - 0.5;
-      BoutReal y = i.y() / (BoutReal)ny - 0.5;
-      BoutReal z = i.z() / (BoutReal)nz - 0.5;
+      const BoutReal x = i.x() / (BoutReal)nx - 0.5;
+      const BoutReal y = i.y() / (BoutReal)ny - 0.5;
+      const BoutReal z = i.z() / (BoutReal)nz - 0.5;
       f3[i] = 1e3 * exp(-0.5 * sqrt(x * x + y * y + z * z) / sigmasq);
       coef3[i] = x + y + sin(2 * 3.14159265358979323846 * z);
     }

From d887f78c3b7de474c15b4663f46fbeae0623a1b8 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 5 Aug 2026 09:35:13 -0700
Subject: [PATCH 1669/1827] BinaryExpr: Track valid regionID of expressions

Add `getRegionID()` function to expression nodes, because some
e.g. `Constant` can return an empty regionID (meaning all regions).
---
 include/bout/bout_types.hxx       |  3 +++
 include/bout/field2d.hxx          |  6 ++++++
 include/bout/field3d.hxx          | 18 ++++++++++++++----
 include/bout/fieldops.hxx         | 18 ++++++++++++------
 include/bout/hypre_interface.hxx  | 18 ++++++++++--------
 include/bout/mesh.hxx             |  3 ++-
 src/field/field.cxx               |  8 +++++---
 src/mesh/mesh.cxx                 |  4 ++--
 tests/unit/field/test_field3d.cxx | 12 ++++++++++--
 9 files changed, 64 insertions(+), 26 deletions(-)

diff --git a/include/bout/bout_types.hxx b/include/bout/bout_types.hxx
index dee2ea22e7..1d8b459c0c 100644
--- a/include/bout/bout_types.hxx
+++ b/include/bout/bout_types.hxx
@@ -25,6 +25,7 @@
 #include "bout/build_config.hxx"
 
 #include <limits>
+#include <optional>
 #include <string>
 
 /// Size of real numbers
@@ -153,6 +154,8 @@ struct Constant {
     BOUT_HOST_DEVICE int numberParallelSlices() const { return 0; }
     BOUT_HOST_DEVICE View yup(int = 0) const { return *this; }
     BOUT_HOST_DEVICE View ydown(int = 0) const { return *this; }
+
+    std::optional<size_t> getRegionID() const { return {}; }
   };
   operator View() const { return {val}; }
 };
diff --git a/include/bout/field2d.hxx b/include/bout/field2d.hxx
index ce3009f4ad..13a26faa38 100644
--- a/include/bout/field2d.hxx
+++ b/include/bout/field2d.hxx
@@ -35,6 +35,8 @@ class Field2D;
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/build_config.hxx"
 #include "bout/build_defines.hxx"
 #include "bout/field.hxx"
 #include "bout/field_data.hxx"
@@ -45,6 +47,7 @@ class Field2D;
 #include <iostream>
 #include <ostream>
 #include <string>
+#include <type_traits>
 
 #include "bout/fieldops.hxx"
 
@@ -333,6 +336,7 @@ public:
     BoutReal* data;
     int mul = 1;
     int div = 1;
+
     BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return data[(idx * mul / div)];
     }
@@ -349,6 +353,8 @@ public:
     BOUT_HOST_DEVICE BOUT_FORCEINLINE int numberParallelSlices() const { return 0; }
     BOUT_HOST_DEVICE BOUT_FORCEINLINE View yup(int = 0) const { return *this; }
     BOUT_HOST_DEVICE BOUT_FORCEINLINE View ydown(int = 0) const { return *this; }
+
+    std::optional<size_t> getRegionID() const { return {}; }
   };
   operator View() { return View{&data[0]}; }
   operator View() const { return View{const_cast<BoutReal*>(&data[0])}; }
diff --git a/include/bout/field3d.hxx b/include/bout/field3d.hxx
index 5562c58b49..239597625c 100644
--- a/include/bout/field3d.hxx
+++ b/include/bout/field3d.hxx
@@ -31,6 +31,7 @@ class Field3D;
 #include "bout/array.hxx"
 #include "bout/assert.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/boutexception.hxx"
 #include "bout/build_config.hxx"
 #include "bout/field.hxx"
 #include "bout/field2d.hxx"
@@ -468,6 +469,7 @@ public:
     const Field3D* yup_fields{nullptr};
     const Field3D* ydown_fields{nullptr};
     int num_parallel_slices{0};
+    std::optional<size_t> regionID;
 
     BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return data[idx];
@@ -500,14 +502,16 @@ public:
       ASSERT2(ydown_fields[slice].isAllocated());
       return static_cast<Field3D::View>(ydown_fields[slice]);
     }
+
+    std::optional<size_t> getRegionID() const { return regionID; }
   };
   operator View() {
     return View{&data[0], yup_fields.data(), ydown_fields.data(),
-                static_cast<int>(numberParallelSlices())};
+                static_cast<int>(numberParallelSlices()), regionID};
   }
   operator View() const {
     return View{const_cast<BoutReal*>(&data[0]), yup_fields.data(), ydown_fields.data(),
-                static_cast<int>(numberParallelSlices())};
+                static_cast<int>(numberParallelSlices()), regionID};
   }
   //operator View() const { return View{&data[0]}; }
 
@@ -1094,6 +1098,8 @@ public:
       ASSERT2(base.ydown_fields[slice].isAllocated());
       return View{static_cast<Field3D::View>(base.ydown_fields[slice])};
     }
+
+    std::optional<size_t> getRegionID() const { return base.regionID; }
   };
 
   operator View() { return View{static_cast<Field3D::View>(*this)}; }
@@ -1149,8 +1155,12 @@ public:
       for (int i = 0; i < expr.numberParallelSlices(); ++i) {
         yup(i).allocate();
         ydown(i).allocate();
-        expr.yup(i).evaluate(static_cast<Field3D::View>(yup(i)).data);
-        expr.ydown(i).evaluate(static_cast<Field3D::View>(ydown(i)).data);
+        auto expr_yup = expr.yup(i);
+        auto expr_ydown = expr.ydown(i);
+        yup(i).setRegion(expr_yup.getRegionID());
+        ydown(i).setRegion(expr_ydown.getRegionID());
+        expr_yup.evaluate(static_cast<Field3D::View>(yup(i)).data);
+        expr_ydown.evaluate(static_cast<Field3D::View>(ydown(i)).data);
       }
     }
 
diff --git a/include/bout/fieldops.hxx b/include/bout/fieldops.hxx
index 49097779f9..2faeb39263 100644
--- a/include/bout/fieldops.hxx
+++ b/include/bout/fieldops.hxx
@@ -31,7 +31,7 @@ namespace bout::detail {
 // in the template functions in this header file.
 const Region<Ind3D>& getField3DRegion(const Mesh* mesh, std::optional<size_t> regionID);
 size_t getField3DRegionID(const Mesh* mesh, const std::string& region_name);
-std::optional<size_t> meshGetCommenRegionID(Mesh* mesh, std::optional<size_t> regionID1,
+std::optional<size_t> meshGetCommonRegionID(Mesh* mesh, std::optional<size_t> regionID1,
                                             std::optional<size_t> regionID2);
 } // namespace bout::detail
 
@@ -419,7 +419,8 @@ struct BinaryExpr {
         mesh,
         location,
         directions,
-        meshGetCommonRegion(mesh, lhs.yup(slice).regionID, rhs.yup(slice).regionID),
+        bout::detail::meshGetCommonRegionID(mesh, lhs.yup(slice).getRegionID(),
+                                            rhs.yup(slice).getRegionID()),
         indices,
         yindex};
   }
@@ -431,18 +432,19 @@ struct BinaryExpr {
         mesh,
         location,
         directions,
-        meshGetCommonRegion(mesh, lhs.ydown(slice).regionID, rhs.ydown(slice).regionID),
+        bout::detail::meshGetCommonRegionID(mesh, lhs.ydown(slice).getRegionID(),
+                                            rhs.ydown(slice).getRegionID()),
         indices,
         yindex};
   }
 
-  //operator ResT() { return ResT{*this}; }
   struct View {
     typename L::View lhs;
     typename R::View rhs;
     const int* indices;
     int num_indices;
     Func f;
+    std::optional<size_t> regionID;
     int mul = 1;
     int div = 1;
 
@@ -496,10 +498,14 @@ struct BinaryExpr {
     BOUT_HOST_DEVICE BOUT_FORCEINLINE BoutReal operator()(int idx) const {
       return f((idx * mul) / div, lhs, rhs); // single‐pass fusion
     }
+
+    std::optional<size_t> getRegionID() const { return regionID; }
   };
 
-  operator View() { return View{lhs, rhs, &indices[0], indices.size(), f}; }
-  operator View() const { return View{lhs, rhs, &indices[0], indices.size(), f}; }
+  operator View() { return View{lhs, rhs, &indices[0], indices.size(), f, regionID}; }
+  operator View() const {
+    return View{lhs, rhs, &indices[0], indices.size(), f, regionID};
+  }
 
   void evaluate(BoutReal* data) const {
 #if BOUT_HAS_CUDA && defined(__CUDACC__)
diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index 189e91d159..d718a2b01a 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -5,6 +5,7 @@
 
 #if BOUT_HAS_HYPRE
 
+#include "bout/assert.hxx"
 #include "bout/bout_enum_class.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/caliper_wrapper.hxx"
@@ -20,6 +21,7 @@
 #include "HYPRE_utilities.h"
 #include "_hypre_utilities.h"
 
+#include <cmath>
 #include <memory>
 
 // BOUT_ENUM_CLASS does not work inside namespaces
@@ -265,19 +267,19 @@ public:
     }
 
     Element& operator=(const Element& other) {
-      ASSERT3(finite(static_cast<BoutReal>(other)));
+      ASSERT3(std::isfinite(static_cast<BoutReal>(other)));
       return *this = static_cast<BoutReal>(other);
     }
     Element& operator=(BoutReal value_) {
-      ASSERT3(finite(value_));
+      ASSERT3(std::isfinite(value_));
       value = value_;
       vector->V[vec_i] = value_;
       return *this;
     }
     Element& operator+=(BoutReal value_) {
-      ASSERT3(finite(value_));
+      ASSERT3(std::isfinite(value_));
       value += value_;
-      ASSERT3(finite(value));
+      ASSERT3(std::isfinite(value));
       vector->V[vec_i] += value_;
       return *this;
     }
@@ -432,7 +434,7 @@ public:
           weights(weights_) {
 #if CHECK > 2
       for (const auto val : weights) {
-        ASSERT3(finite(val));
+        ASSERT3(std::isfinite(val));
       }
 #endif
       ASSERT2(positions.size() == weights.size());
@@ -445,19 +447,19 @@ public:
     }
     Element& operator=(const Element& other) {
 
-      ASSERT3(finite(static_cast<BoutReal>(other)));
+      ASSERT3(std::isfinite(static_cast<BoutReal>(other)));
       return *this = static_cast<BoutReal>(other);
     }
     Element& operator=(BoutReal value_) {
 
-      ASSERT3(finite(value_));
+      ASSERT3(std::isfinite(value_));
       value = value_;
       setValues(value);
       return *this;
     }
     Element& operator+=(BoutReal value_) {
 
-      ASSERT3(finite(value_));
+      ASSERT3(std::isfinite(value_));
       auto column_position = std::find(cbegin(positions), cend(positions), column);
       if (column_position != cend(positions)) {
         const auto i = std::distance(cbegin(positions), column_position);
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index 84f9ec36c6..923019db15 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -850,7 +850,8 @@ public:
   // Switch for communication of corner guard and boundary cells
   const bool include_corner_cells;
 
-  std::optional<size_t> getCommonRegion(std::optional<size_t>, std::optional<size_t>);
+  std::optional<size_t> getCommonRegion(std::optional<size_t> lhs,
+                                        std::optional<size_t> rhs);
   size_t getRegionID(const std::string& region) const;
   const Region<Ind3D>& getRegion(size_t RegionID) const { return region3D[RegionID]; }
   const Region<Ind3D>& getRegion(std::optional<size_t> RegionID) const {
diff --git a/src/field/field.cxx b/src/field/field.cxx
index e9b01f0bcb..8c7e8bbfee 100644
--- a/src/field/field.cxx
+++ b/src/field/field.cxx
@@ -2,10 +2,10 @@
  * Base class for fields
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
+ *
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
- * 
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -23,9 +23,11 @@
  *
  **************************************************************************/
 
+#include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/coordinates.hxx>
 #include <bout/field.hxx>
+#include <bout/field_data.hxx>
 #include <bout/mesh.hxx>
 #include <bout/output.hxx>
 #include <bout/utils.hxx>
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index d58c9605be..0b74c44364 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -865,8 +865,8 @@ std::optional<size_t> Mesh::getCommonRegion(std::optional<size_t> lhs,
 }
 
 namespace bout::detail {
-std::optional<size_t> meshGetCommenRegionID(Mesh* mesh, std::optional<size_t> regionID1,
+std::optional<size_t> meshGetCommonRegionID(Mesh* mesh, std::optional<size_t> regionID1,
                                             std::optional<size_t> regionID2) {
-  return mesh->getCommenRegionID(regionID1, regionID2);
+  return mesh->getCommonRegion(regionID1, regionID2);
 }
 } // namespace bout::detail
diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 6a6ecb9aea..2be751a7c4 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -12,14 +12,18 @@
 #include "bout/constants.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
+#include "bout/fieldops.hxx"
+#include "bout/globals.hxx"
 #include "bout/mesh.hxx"
 #include "bout/output.hxx"
+#include "bout/output_bout_types.hxx"
 #include "bout/paralleltransform.hxx"
 #include "bout/region.hxx"
 #include "bout/unused.hxx"
 
 #include <cmath>
 #include <set>
+#include <type_traits>
 #include <vector>
 
 #include "fake_mesh_fixture.hxx"
@@ -2152,9 +2156,13 @@ TEST_F(Field3DTestFCI, SqrtField3DParallelPreservesParallelSlices) {
     const Field3DParallel res{expr};
 
     EXPECT_TRUE(res.hasParallelSlices());
+    // Input yup/ydown fields are only valid over limited regions, so
+    // calculations are only performed over those regions.
+    EXPECT_EQ(res.yup().getRegionID(), field.yup().getRegionID());
+    EXPECT_EQ(res.ydown().getRegionID(), field.ydown().getRegionID());
     EXPECT_TRUE(IsFieldEqual(res, 2.0));
-    EXPECT_TRUE(IsFieldEqual(res.yup(), 3.0));
-    EXPECT_TRUE(IsFieldEqual(res.ydown(), 4.0));
+    EXPECT_TRUE(IsFieldEqual(res.yup(), 3.0, "RGN_YPAR_+1"));
+    EXPECT_TRUE(IsFieldEqual(res.ydown(), 4.0, "RGN_YPAR_-1"));
   }
   {
     const Field3D res = sqrt(field.asField3D());

From df638bf7abb616384648e0a915838536ecae3e5e Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 6 Aug 2026 14:11:56 -0700
Subject: [PATCH 1670/1827] Get ADIOS tests passing

---
 include/bout/adios_object.hxx          | 44 ++++++++++++----------
 src/sys/adios_object.cxx               | 52 ++++++++++++++------------
 tests/unit/sys/test_options_adios2.cxx |  3 +-
 3 files changed, 55 insertions(+), 44 deletions(-)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 62a05e00f2..79ea4a1f1a 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -45,7 +45,6 @@ using EnginePtr = std::shared_ptr<adios2::Engine>;
 using IOPtr = std::shared_ptr<adios2::IO>;
 
 ADIOSPtr GetADIOSPtr();
-IOPtr GetIOPtr(const std::string IOName);
 
 class ADIOSStream {
 public:
@@ -114,38 +113,44 @@ public:
   }
 
   template <class T>
-  void Put(const std::string& varname, T value) {
+  void Put(const std::string& varname, T value, adios2::Mode mode = adios2::Mode::Sync) {
     if (BoutComm::rank() != 0) {
       return;
     }
-    engine().Put(GetValueVariable<T>(varname), value);
+    engine().Put(GetValueVariable<T>(varname), value, mode);
   }
 
   template <class T>
-  void Put(const std::string& varname, const Array<T>& value) {
-    PutArrayLike(varname, value);
+  void Put(const std::string& varname, const Array<T>& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    PutArrayLike(varname, value, mode);
   }
 
   template <class T>
-  void Put(const std::string& varname, const Matrix<T>& value) {
-    PutArrayLike(varname, value);
+  void Put(const std::string& varname, const Matrix<T>& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    PutArrayLike(varname, value, mode);
   }
 
   template <class T>
-  void Put(const std::string& varname, const Tensor<T>& value) {
-    PutArrayLike(varname, value);
+  void Put(const std::string& varname, const Tensor<T>& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    PutArrayLike(varname, value, mode);
   }
 
-  void Put(const std::string& varname, const Field2D& value) {
-    PutField(varname, {"x", "y"}, *value.getMesh(), &value(0, 0));
+  void Put(const std::string& varname, const Field2D& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    PutField(varname, {"x", "y"}, *value.getMesh(), &value(0, 0), mode);
   }
 
-  void Put(const std::string& varname, const Field3D& value) {
-    PutField(varname, {"x", "y", "z"}, *value.getMesh(), &value(0, 0, 0));
+  void Put(const std::string& varname, const Field3D& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    PutField(varname, {"x", "y", "z"}, *value.getMesh(), &value(0, 0, 0), mode);
   }
 
-  void Put(const std::string& varname, const FieldPerp& value) {
-    PutField(varname, {"x", "z"}, *value.getMesh(), &value(0, 0));
+  void Put(const std::string& varname, const FieldPerp& value,
+           adios2::Mode mode = adios2::Mode::Sync) {
+    PutField(varname, {"x", "z"}, *value.getMesh(), &value(0, 0), mode);
   }
 
   template <class T>
@@ -231,13 +236,13 @@ private:
   }
 
   void PutField(const std::string& varname, const std::vector<std::string>& dim_names,
-                const Mesh& mesh, const BoutReal* data) {
+                const Mesh& mesh, const BoutReal* data, adios2::Mode mode) {
     auto selection = makeFieldSelection(dim_names, mesh);
     auto variable =
         GetArrayVariable<BoutReal>(varname, selection.shape, dim_names, BoutComm::rank());
     variable.SetSelection(selection.selection());
     variable.SetMemorySelection(selection.memorySelection());
-    engine().Put(variable, data);
+    engine().Put(variable, data, mode);
   }
 
   FieldSelection makeFieldSelection(const std::vector<std::string>& dim_names,
@@ -328,12 +333,13 @@ private:
   }
 
   template <class Container>
-  void PutArrayLike(const std::string& varname, const Container& value) {
+  void PutArrayLike(const std::string& varname, const Container& value,
+                    adios2::Mode mode) {
     using T = typename Container::data_type;
     auto var = GetArrayVariable<T>(varname, makeShape(BoutComm::size(), value),
                                    makeDimNames(value), BoutComm::rank());
     var.SetSelection(adios2::Box<adios2::Dims>{makeStart(value), makeShape(1, value)});
-    engine().Put<T>(var, value.begin());
+    engine().Put<T>(var, value.begin(), mode);
   }
 
   template <class Container>
diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx
index d6aa862493..b6a7953385 100644
--- a/src/sys/adios_object.cxx
+++ b/src/sys/adios_object.cxx
@@ -15,6 +15,30 @@ namespace bout {
 static ADIOSPtr adios = nullptr;
 static std::unordered_map<std::string, ADIOSStream> adiosStreams;
 
+namespace {
+std::string GetIOName(const std::string& fname, adios2::Mode mode) {
+  switch (mode) {
+  case adios2::Mode::Read:
+    return "read_" + fname;
+  case adios2::Mode::ReadRandomAccess:
+    return "read_random_access_" + fname;
+  case adios2::Mode::Append:
+    return "append_" + fname;
+  case adios2::Mode::Write:
+    return "write_" + fname;
+  default:
+    return fname;
+  }
+}
+
+adios2::IO GetIO(const std::string& fname, adios2::Mode mode,
+                 const std::string& engineType) {
+  auto io = GetADIOSPtr()->DeclareIO(GetIOName(fname, mode));
+  io.SetEngine(engineType);
+  return io;
+}
+} // namespace
+
 void ADIOSInit(MPI_Comm comm) { adios = std::make_shared<adios2::ADIOS>(comm); }
 
 void ADIOSInit(const std::string configFile, MPI_Comm comm) {
@@ -38,16 +62,6 @@ ADIOSPtr GetADIOSPtr() {
   return adios;
 }
 
-IOPtr GetIOPtr(const std::string IOName) {
-  auto adios = GetADIOSPtr();
-  IOPtr io = nullptr;
-  try {
-    io = std::make_shared<adios2::IO>(adios->AtIO(IOName));
-  } catch (std::invalid_argument& e) {
-  }
-  return io;
-}
-
 ADIOSStream::~ADIOSStream() {
   if (engine_) {
     if (isInStep) {
@@ -60,24 +74,14 @@ ADIOSStream::~ADIOSStream() {
 
 ADIOSStream::ADIOSStream(const std::string& fname, adios2::Mode mode,
                          const std::string& engineType)
-    : fname(fname), file_mode(mode) {
-
-  ADIOSPtr adiosp = GetADIOSPtr();
-  try {
-    io = adiosp->AtIO(fname);
-  } catch (const std::invalid_argument& e) {
-    io = adiosp->DeclareIO(fname);
-    if (!engineType.empty()) {
-      io.SetEngine(engineType);
-    }
-  }
-}
+    : io(GetIO(fname, mode, engineType)), fname(fname), file_mode(mode) {}
 
 ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname, adios2::Mode mode,
                                          const std::string& engineType) {
-  auto it = adiosStreams.find(fname);
+  const auto key = GetIOName(fname, mode);
+  auto it = adiosStreams.find(key);
   if (it == adiosStreams.end()) {
-    it = adiosStreams.emplace(fname, ADIOSStream(fname, mode, engineType)).first;
+    it = adiosStreams.emplace(key, ADIOSStream(fname, mode, engineType)).first;
   }
   return it->second;
 }
diff --git a/tests/unit/sys/test_options_adios2.cxx b/tests/unit/sys/test_options_adios2.cxx
index 13bbe3db54..a0fcf20b2e 100644
--- a/tests/unit/sys/test_options_adios2.cxx
+++ b/tests/unit/sys/test_options_adios2.cxx
@@ -27,7 +27,8 @@ class OptionsAdios2Test : public FakeMeshFixture {
   static void TearDownTestSuite() { bout::ADIOSFinalize(); }
 
   ~OptionsAdios2Test() override {
-    bout::ADIOSStream::ADIOSGetStream(filename, adios2::Mode::Deferred).engine().Close();
+    bout::ADIOSStream::ADIOSGetStream(filename, adios2::Mode::Write).finish();
+    bout::ADIOSStream::ADIOSGetStream(filename, adios2::Mode::Append).finish();
   }
 
   // A temporary filename

From b5b946e7a041f5841303a485cb113709765ece64 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Thu, 6 Aug 2026 16:59:42 -0700
Subject: [PATCH 1671/1827] Remove unused code

---
 include/bout/adios_object.hxx |  8 --------
 src/sys/adios_object.cxx      | 29 -----------------------------
 2 files changed, 37 deletions(-)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index 79ea4a1f1a..fafeb77a0d 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -41,16 +41,12 @@ void ADIOSInit(const std::string configFile, MPI_Comm comm);
 void ADIOSFinalize();
 
 using ADIOSPtr = std::shared_ptr<adios2::ADIOS>;
-using EnginePtr = std::shared_ptr<adios2::Engine>;
-using IOPtr = std::shared_ptr<adios2::IO>;
 
 ADIOSPtr GetADIOSPtr();
 
 class ADIOSStream {
 public:
   adios2::IO io;
-  adios2::Variable<double> vTime;
-  adios2::Variable<int> vStep;
   int adiosStep = 0;
 
   /** create or return the ADIOSStream based on the target file name */
@@ -384,10 +380,6 @@ private:
   bool isInStep = false;
 };
 
-/** Set user parameters for an IO group */
-void ADIOSSetParameters(const std::string& input, char delimKeyValue, char delimItem,
-                        adios2::IO& io);
-
 } // namespace bout
 
 #endif //BOUT_HAS_ADIOS2
diff --git a/src/sys/adios_object.cxx b/src/sys/adios_object.cxx
index b6a7953385..596be66b93 100644
--- a/src/sys/adios_object.cxx
+++ b/src/sys/adios_object.cxx
@@ -86,34 +86,5 @@ ADIOSStream& ADIOSStream::ADIOSGetStream(const std::string& fname, adios2::Mode
   return it->second;
 }
 
-void ADIOSSetParameters(const std::string& input, char delimKeyValue, char delimItem,
-                        adios2::IO& io) {
-  auto lf_Trim = [](std::string& input) {
-    input.erase(0, input.find_first_not_of(" \n\r\t")); // prefixing spaces
-    input.erase(input.find_last_not_of(" \n\r\t") + 1); // suffixing spaces
-  };
-
-  std::istringstream inputSS(input);
-  std::string parameter;
-  while (std::getline(inputSS, parameter, delimItem)) {
-    const size_t position = parameter.find(delimKeyValue);
-    if (position == std::string::npos) {
-      throw BoutException("ADIOSSetParameters(): wrong format for IO parameter "
-                          + parameter + ", format must be key" + delimKeyValue
-                          + "value for each entry");
-    }
-
-    std::string key = parameter.substr(0, position);
-    lf_Trim(key);
-    std::string value = parameter.substr(position + 1);
-    lf_Trim(value);
-    if (value.length() == 0) {
-      throw BoutException("ADIOS2SetParameters: empty value in IO parameter " + parameter
-                          + ", format must be key" + delimKeyValue + "value");
-    }
-    io.SetParameter(key, value);
-  }
-}
-
 } // namespace bout
 #endif //BOUT_HAS_ADIOS2

From 0103177af854175e9cafdae4d88545dc4ce29ca0 Mon Sep 17 00:00:00 2001
From: Steven Roberts <roberts115@llnl.gov>
Date: Fri, 7 Aug 2026 10:12:22 -0700
Subject: [PATCH 1672/1827] Remove unnecessary arg

---
 include/bout/adios_object.hxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/bout/adios_object.hxx b/include/bout/adios_object.hxx
index fafeb77a0d..ee7e82e45a 100755
--- a/include/bout/adios_object.hxx
+++ b/include/bout/adios_object.hxx
@@ -324,7 +324,7 @@ private:
     constexpr auto ndims = std::tuple_size_v<decltype(value.shape())>;
     ASSERT1(read_shape.size() == ndims);
 
-    resizeForShape(value, read_shape, 0, std::make_index_sequence<ndims>{});
+    resizeForShape(value, read_shape, std::make_index_sequence<ndims>{});
     engine().Get(variable, value.begin(), mode);
   }
 
@@ -367,9 +367,9 @@ private:
   }
 
   template <class Container, std::size_t... I>
-  void resizeForShape(Container& value, const adios2::Dims& shape, std::size_t offset,
+  void resizeForShape(Container& value, const adios2::Dims& shape,
                       std::index_sequence<I...> /*indices*/) {
-    value.reallocate(static_cast<typename Container::size_type>(shape[offset + I])...);
+    value.reallocate(static_cast<typename Container::size_type>(shape[I])...);
   }
 
   std::string fname;

From a511a6632640ebfe2df2f1fd483dcd72c6702319 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 10 Aug 2026 15:42:01 +0200
Subject: [PATCH 1673/1827] Add Conduction_Methods to Div_par_K_Grad_par_mod

Copied from Hermes-3

Co-authored-by: Ben Dudson <dudson2@llnl.gov>
---
 include/bout/difops.hxx |   3 +-
 src/mesh/difops.cxx     | 115 ++++++++++++++++++++++++++++++++--------
 2 files changed, 96 insertions(+), 22 deletions(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 28a4da9f51..bd97971553 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -198,7 +198,8 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f,
 /// Version with energy flow diagnostic
 /// For FCI fields, `flow_ylow` is currently returned as zero.
 Field3D Div_par_K_Grad_par_mod(const Field3D& k, const Field3D& f, Field3D& flow_ylow,
-                               bool bndry_flux = true);
+                               bool bndry_flux = true,
+                               const std::string& method = "orginal");
 
 /*!
  * Perpendicular Laplacian operator
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 8ecd9d64ff..7dc114b33a 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -374,8 +374,13 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc)
          + Div_par(kY, outloc) * Grad_par(f, outloc);
 }
 
-Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D& flow_ylow,
-                               bool bndry_flux) {
+namespace bout {
+enum ConductionMethod : uint8_t { Original, ProductJK, Harmonic };
+}
+
+template <bout::ConductionMethod conduction_method>
+Field3D Div_par_K_Grad_par_mod_impl(const Field3D& Kin, const Field3D& fin,
+                                    Field3D& flow_ylow, bool bndry_flux) {
   ASSERT2(Kin.getLocation() == fin.getLocation());
 
   const Mesh* mesh = Kin.getMesh();
@@ -437,32 +442,83 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D&
 
   BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
     // Calculate flux at upper surface
-    const auto ix = i.x();
-    const auto iy = i.y();
+
     const auto iyp = i.yp();
     const auto iym = i.ym();
 
-    const bool is_periodic_y = mesh->periodicY(ix);
-
-    if (bndry_flux || is_periodic_y || !mesh->lastY(ix) || (iy != mesh->yend)) {
-      const BoutReal c = 0.5 * (K[i] + K[iyp]);               // K at the upper boundary
-      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary
-      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
-      const BoutReal gradient = 2. * (f[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
-
-      const BoutReal flux = c * J * gradient / g_22;
-
+    if (bndry_flux || mesh->periodicY(i.x()) || !mesh->lastY(i.x())
+        || (i.y() != mesh->yend)) {
+      BoutReal flux = 0.0;
+
+      if constexpr (conduction_method == bout::ConductionMethod::Original) {
+        const BoutReal c = 0.5 * (K[i] + K[iyp]);               // K at the upper boundary
+        const BoutReal J = 0.5 * (coord->J[i] + coord->J[iyp]); // Jacobian at boundary
+        const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
+
+        const BoutReal gradient = 2. * (f[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
+
+        flux = c * J * gradient / g_22;
+      } else if constexpr (conduction_method == bout::ConductionMethod::ProductJK) {
+        // Intended to reduce sensitivity of result to K in small cells
+        const BoutReal cJ =
+            0.5 * (K[i] * coord->J[i] + K[iyp] * coord->J[iyp]); // K * J at boundary
+        const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iyp]);
+
+        const BoutReal gradient = 2. * (f[iyp] - f[i]) / (coord->dy[i] + coord->dy[iyp]);
+
+        flux = cJ * gradient / g_22;
+      } else if constexpr (conduction_method == bout::ConductionMethod::Harmonic) {
+        // Harmonic average (serial resistance)
+        const BoutReal cond_i = K[i] * coord->J[i] / (coord->g_22[i] * coord->dy[i]);
+        const BoutReal cond_iyp =
+            K[iyp] * coord->J[iyp] / (coord->g_22[iyp] * coord->dy[iyp]);
+        const BoutReal denom = cond_i + cond_iyp;
+
+        // Harmonic mean: series resistance of two half-cells
+        const BoutReal C_edge =
+            (std::abs(denom) > std::numeric_limits<BoutReal>::epsilon())
+                ? 2.0 * cond_i * cond_iyp / denom
+                : 0.0;
+
+        flux = C_edge * (f[iyp] - f[i]);
+      }
       result[i] += flux / (coord->dy[i] * coord->J[i]);
     }
 
     // Calculate flux at lower surface
-    if (bndry_flux || is_periodic_y || !mesh->firstY(ix) || (iy != mesh->ystart)) {
-      const BoutReal c = 0.5 * (K[i] + K[iym]);               // K at the lower boundary
-      const BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary
-      const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
-      const BoutReal gradient = 2. * (f[i] - f[iym]) / (coord->dy[i] + coord->dy[iym]);
-
-      const BoutReal flux = c * J * gradient / g_22;
+    if (bndry_flux || mesh->periodicY(i.x()) || !mesh->firstY(i.x())
+        || (i.y() != mesh->ystart)) {
+      BoutReal flux = 0.0;
+
+      if constexpr (conduction_method == bout::ConductionMethod::Original) {
+        const BoutReal c = 0.5 * (K[i] + K[iym]);               // K at the lower boundary
+        const BoutReal J = 0.5 * (coord->J[i] + coord->J[iym]); // Jacobian at boundary
+        const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
+
+        const BoutReal gradient = 2. * (f[i] - f[iym]) / (coord->dy[i] + coord->dy[iym]);
+
+        flux = c * J * gradient / g_22;
+      } else if constexpr (conduction_method == bout::ConductionMethod::ProductJK) {
+        const BoutReal cJ =
+            0.5 * (K[i] * coord->J[i] + K[iym] * coord->J[iym]); // K * J at boundary
+        const BoutReal g_22 = 0.5 * (coord->g_22[i] + coord->g_22[iym]);
+
+        const BoutReal gradient = 2. * (f[i] - f[iym]) / (coord->dy[i] + coord->dy[iym]);
+
+        flux = cJ * gradient / g_22;
+      } else if constexpr (conduction_method == bout::ConductionMethod::Harmonic) {
+        const BoutReal cond_i = K[i] * coord->J[i] / (coord->g_22[i] * coord->dy[i]);
+        const BoutReal cond_iym =
+            K[iym] * coord->J[iym] / (coord->g_22[iym] * coord->dy[iym]);
+        const BoutReal denom = cond_i + cond_iym;
+
+        const BoutReal C_edge =
+            (std::abs(denom) > std::numeric_limits<BoutReal>::epsilon())
+                ? 2.0 * cond_i * cond_iym / denom
+                : 0.0;
+
+        flux = C_edge * (f[i] - f[iym]);
+      }
 
       result[i] -= flux / (coord->dy[i] * coord->J[i]);
       flow_ylow[i] = -flux * coord->dx[i] * coord->dz[i];
@@ -476,6 +532,23 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D&
   return result;
 }
 
+Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D& flow_ylow,
+                               bool bndry_flux, const std::string& method) {
+  if (method == "orginal") {
+    return Div_par_K_Grad_par_mod_impl<bout::ConductionMethod::Original>(
+        Kin, fin, flow_ylow, bndry_flux);
+  }
+  if (method == "productJK") {
+    return Div_par_K_Grad_par_mod_impl<bout::ConductionMethod::ProductJK>(
+        Kin, fin, flow_ylow, bndry_flux);
+  }
+  if (method == "harmonic") {
+    return Div_par_K_Grad_par_mod_impl<bout::ConductionMethod::Harmonic>(
+        Kin, fin, flow_ylow, bndry_flux);
+  }
+  throw BoutException(
+      "Unknown method `{}` - choose from `orginal`, `productJK` or `harmonic`.", method);
+}
 /*******************************************************************************
 * Delp2
 * perpendicular Laplacian operator

From 4cc1b15aad1f003230fc809a16e2f078cb73d34c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 10 Aug 2026 16:22:46 +0200
Subject: [PATCH 1674/1827] Add missing headers

---
 src/mesh/difops.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 7dc114b33a..fdaa7536f9 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -47,6 +47,8 @@
 #include <bout/unused.hxx>
 
 #include <cmath>
+#include <cstdint>
+#include <limits>
 
 /*******************************************************************************
 * Grad_par

From aee181f57c7efbf17bb67bbcf62f2feccceb11b3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 10 Aug 2026 16:23:12 +0200
Subject: [PATCH 1675/1827] Use internal implementation to private namespace

---
 src/mesh/difops.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index fdaa7536f9..4b3eabd5cb 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -380,6 +380,7 @@ namespace bout {
 enum ConductionMethod : uint8_t { Original, ProductJK, Harmonic };
 }
 
+namespace {
 template <bout::ConductionMethod conduction_method>
 Field3D Div_par_K_Grad_par_mod_impl(const Field3D& Kin, const Field3D& fin,
                                     Field3D& flow_ylow, bool bndry_flux) {
@@ -533,6 +534,7 @@ Field3D Div_par_K_Grad_par_mod_impl(const Field3D& Kin, const Field3D& fin,
 
   return result;
 }
+} // namespace
 
 Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D& flow_ylow,
                                bool bndry_flux, const std::string& method) {

From 6341c8e0ec49cdd4a9a8d7fc148a576a817a0996 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 11 Aug 2026 12:00:53 +0200
Subject: [PATCH 1676/1827] Prefere enum class

---
 src/mesh/difops.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 4b3eabd5cb..b30047a505 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -377,7 +377,7 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc)
 }
 
 namespace bout {
-enum ConductionMethod : uint8_t { Original, ProductJK, Harmonic };
+enum class ConductionMethod : uint8_t { Original, ProductJK, Harmonic };
 }
 
 namespace {

From a012a67f02175f6b9a658c0dee48d9a871561784 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 11 Aug 2026 11:59:52 +0200
Subject: [PATCH 1677/1827] Use Field3DParallel if we need parallel fields

---
 include/bout/difops.hxx | 13 +++++++------
 src/mesh/difops.cxx     | 12 ++++++------
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 28a4da9f51..d442109356 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -126,10 +126,10 @@ inline Coordinates::FieldMetric Div_par(const Field2D& f, CELL_LOC outloc,
   return Div_par(f, outloc, toString(method));
 }
 
-Field3D Div_par(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+Field3D Div_par(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                 const std::string& method = "DEFAULT");
 
-inline Field3D Div_par(const Field3D& f, CELL_LOC outloc, DIFF_METHOD method) {
+inline Field3D Div_par(const Field3DParallel& f, CELL_LOC outloc, DIFF_METHOD method) {
   return Div_par(f, outloc, toString(method));
 }
 
@@ -137,15 +137,16 @@ inline Field3D Div_par(const Field3D& f, CELL_LOC outloc, DIFF_METHOD method) {
 // Both f and v are interpolated onto cell boundaries
 // using 2nd order central difference, then multiplied together
 // to get the flux at the boundary.
-Field3D Div_par(const Field3D& f, const Field3D& v);
+Field3D Div_par(const Field3DParallel& f, const Field3D& v);
 
 // Flux methods. Model divergence of flux: df/dt =  Div(v * f)
 // TODO : Should we add Field2D versions?
-Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+Field3D Div_par_flux(const Field3DParallel& v, const Field3DParallel& f,
+                     CELL_LOC outloc = CELL_DEFAULT,
                      const std::string& method = "DEFAULT");
 
-inline Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
-                            DIFF_METHOD method) {
+inline Field3D Div_par_flux(const Field3DParallel& v, const Field3DParallel& f,
+                            CELL_LOC outloc, DIFF_METHOD method) {
   return Div_par_flux(v, f, outloc, toString(method));
 }
 
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 8ecd9d64ff..9d14e9c367 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -232,15 +232,15 @@ Coordinates::FieldMetric Div_par(const Field2D& f, const std::string& method,
   return f.getCoordinates(outloc)->Div_par(f, outloc, method);
 }
 
-Field3D Div_par(const Field3D& f, CELL_LOC outloc, const std::string& method) {
+Field3D Div_par(const Field3DParallel& f, CELL_LOC outloc, const std::string& method) {
   return f.getCoordinates(outloc)->Div_par(f, outloc, method);
 }
 
-Field3D Div_par(const Field3D& f, const std::string& method, CELL_LOC outloc) {
+Field3D Div_par(const Field3DParallel& f, const std::string& method, CELL_LOC outloc) {
   return f.getCoordinates(outloc)->Div_par(f, outloc, method);
 }
 
-Field3D Div_par(const Field3D& f, const Field3D& v) {
+Field3D Div_par(const Field3DParallel& f, const Field3DParallel& v) {
   ASSERT1_FIELDS_COMPATIBLE(f, v);
   ASSERT1(f.hasParallelSlices());
   ASSERT1(v.hasParallelSlices());
@@ -284,7 +284,7 @@ Field3D Div_par(const Field3D& f, const Field3D& v) {
 
 //////// Flux methods
 
-Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
+Field3D Div_par_flux(const Field3DParallel& v, const Field3DParallel& f, CELL_LOC outloc,
                      const std::string& method) {
   Coordinates* metric = f.getCoordinates(outloc);
 
@@ -304,8 +304,8 @@ Field3D Div_par_flux(const Field3D& v, const Field3D& f, CELL_LOC outloc,
   return metric->Bxy * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22);
 }
 
-Field3D Div_par_flux(const Field3D& v, const Field3D& f, const std::string& method,
-                     CELL_LOC outloc) {
+Field3D Div_par_flux(const Field3DParallel& v, const Field3DParallel& f,
+                     const std::string& method, CELL_LOC outloc) {
   return Div_par_flux(v, f, outloc, method);
 }
 

From 2f228e278a8669b79bc53e22f66e5ac41260560b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 11 Aug 2026 12:24:54 +0200
Subject: [PATCH 1678/1827] Remove not used legacy wrappers

---
 src/mesh/difops.cxx | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 9d14e9c367..98e3c0c8ac 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -236,10 +236,6 @@ Field3D Div_par(const Field3DParallel& f, CELL_LOC outloc, const std::string& me
   return f.getCoordinates(outloc)->Div_par(f, outloc, method);
 }
 
-Field3D Div_par(const Field3DParallel& f, const std::string& method, CELL_LOC outloc) {
-  return f.getCoordinates(outloc)->Div_par(f, outloc, method);
-}
-
 Field3D Div_par(const Field3DParallel& f, const Field3DParallel& v) {
   ASSERT1_FIELDS_COMPATIBLE(f, v);
   ASSERT1(f.hasParallelSlices());
@@ -304,11 +300,6 @@ Field3D Div_par_flux(const Field3DParallel& v, const Field3DParallel& f, CELL_LO
   return metric->Bxy * FDDY(v, f_B, outloc, method) / sqrt(metric->g_22);
 }
 
-Field3D Div_par_flux(const Field3DParallel& v, const Field3DParallel& f,
-                     const std::string& method, CELL_LOC outloc) {
-  return Div_par_flux(v, f, outloc, method);
-}
-
 /*******************************************************************************
 * Grad2_par2
 * second parallel derivative

From 7fc1c2dc9e800ee009f67dc1521186e1c990391b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 12 Aug 2026 09:03:47 +0200
Subject: [PATCH 1679/1827] Fix signature in header for Div_par taking two
 fields

---
 include/bout/difops.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index d442109356..7baf6b2463 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -137,7 +137,7 @@ inline Field3D Div_par(const Field3DParallel& f, CELL_LOC outloc, DIFF_METHOD me
 // Both f and v are interpolated onto cell boundaries
 // using 2nd order central difference, then multiplied together
 // to get the flux at the boundary.
-Field3D Div_par(const Field3DParallel& f, const Field3D& v);
+Field3D Div_par(const Field3DParallel& f, const Field3DParallel& v);
 
 // Flux methods. Model divergence of flux: df/dt =  Div(v * f)
 // TODO : Should we add Field2D versions?

From dfaab1b507ee19568896e608b582cde492c6d1ad Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 12 Aug 2026 09:12:36 +0200
Subject: [PATCH 1680/1827] Use enum in API and add docs

Co-authored-by: Ben Dudson <dudson2@llnl.gov>
---
 include/bout/difops.hxx | 22 +++++++++++++++++++---
 src/mesh/difops.cxx     | 14 +++++---------
 2 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index bd97971553..d3ad9ae4e8 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -195,11 +195,27 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field2D& f,
 Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f,
                            CELL_LOC outloc = CELL_DEFAULT);
 
+namespace bout {
+enum class ConductionMethod : uint8_t {
+  /// Separately averages :math:`K`, :math:`J`, :math:`g_{22}`, and
+  /// :math:`dy` at the face and then multiplies them together.
+  Original,
+  /// Uses the same stencil as ``Original`` but averages :math:`J K`
+  /// together before applying the face gradient.
+  ProductJK,
+  ///  Uses a harmonic average of the half-cell conductances
+  /// :math:`K J / (g_{22} dy)`. This better matches a series-resistance
+  /// interpretation of two adjacent half-cells and can give noticeably
+  /// different results when coefficients or cell sizes vary strongly.
+  Harmonic
+};
+}
 /// Version with energy flow diagnostic
 /// For FCI fields, `flow_ylow` is currently returned as zero.
-Field3D Div_par_K_Grad_par_mod(const Field3D& k, const Field3D& f, Field3D& flow_ylow,
-                               bool bndry_flux = true,
-                               const std::string& method = "orginal");
+Field3D
+Div_par_K_Grad_par_mod(const Field3D& k, const Field3D& f, Field3D& flow_ylow,
+                       bool bndry_flux = true,
+                       bout::ConductionMethod method = bout::ConductionMethod::Original);
 
 /*!
  * Perpendicular Laplacian operator
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index b30047a505..18d3eec131 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -376,10 +376,6 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc)
          + Div_par(kY, outloc) * Grad_par(f, outloc);
 }
 
-namespace bout {
-enum class ConductionMethod : uint8_t { Original, ProductJK, Harmonic };
-}
-
 namespace {
 template <bout::ConductionMethod conduction_method>
 Field3D Div_par_K_Grad_par_mod_impl(const Field3D& Kin, const Field3D& fin,
@@ -537,21 +533,21 @@ Field3D Div_par_K_Grad_par_mod_impl(const Field3D& Kin, const Field3D& fin,
 } // namespace
 
 Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D& flow_ylow,
-                               bool bndry_flux, const std::string& method) {
-  if (method == "orginal") {
+                               bool bndry_flux, bout::ConductionMethod method) {
+  if (method == bout::ConductionMethod::Original) {
     return Div_par_K_Grad_par_mod_impl<bout::ConductionMethod::Original>(
         Kin, fin, flow_ylow, bndry_flux);
   }
-  if (method == "productJK") {
+  if (method == bout::ConductionMethod::ProductJK) {
     return Div_par_K_Grad_par_mod_impl<bout::ConductionMethod::ProductJK>(
         Kin, fin, flow_ylow, bndry_flux);
   }
-  if (method == "harmonic") {
+  if (method == bout::ConductionMethod::Harmonic) {
     return Div_par_K_Grad_par_mod_impl<bout::ConductionMethod::Harmonic>(
         Kin, fin, flow_ylow, bndry_flux);
   }
   throw BoutException(
-      "Unknown method `{}` - choose from `orginal`, `productJK` or `harmonic`.", method);
+      "Unknown method `{}` - choose from `Original`, `ProductJK` or `Harmonic`.", method);
 }
 /*******************************************************************************
 * Delp2

From ad9fe7297253e66f9fff2e0a40be459084cfd26a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 12 Aug 2026 09:23:22 +0200
Subject: [PATCH 1681/1827] Cast to int

If we get there, it is either because a new enum has been added, but
not updated here. In this case we could try to print the enum. The
other, potentially more likely cause is, that the user casted an int
that was out of range. In which case we can only print the integer
value.
---
 src/mesh/difops.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 18d3eec131..d09760972f 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -547,7 +547,8 @@ Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D&
         Kin, fin, flow_ylow, bndry_flux);
   }
   throw BoutException(
-      "Unknown method `{}` - choose from `Original`, `ProductJK` or `Harmonic`.", method);
+      "Unknown method `{}` - choose from `Original`, `ProductJK` or `Harmonic`.",
+      static_cast<int>(method));
 }
 /*******************************************************************************
 * Delp2

From b213a15c74b1be8cd80ba5b1d23ed4fa998c1941 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 12 Aug 2026 11:20:27 +0200
Subject: [PATCH 1682/1827] Move header to enum definition

---
 include/bout/difops.hxx | 2 ++
 src/mesh/difops.cxx     | 1 -
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index d3ad9ae4e8..317fc17152 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -42,6 +42,8 @@
 #include "bout/bout_types.hxx"
 #include "bout/coordinates.hxx"
 
+#include <cstdint>
+
 class Solver;
 
 /*!
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index d09760972f..c748c92915 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -47,7 +47,6 @@
 #include <bout/unused.hxx>
 
 #include <cmath>
-#include <cstdint>
 #include <limits>
 
 /*******************************************************************************

From 359f187267c3c4ddfda9b2683554450864fa788e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 12 Aug 2026 12:05:18 +0200
Subject: [PATCH 1683/1827] First cast to f3dp to compute parallel slices for
 FCI

---
 include/bout/derivs.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/derivs.hxx b/include/bout/derivs.hxx
index 8ee3b872a1..37cb6e1911 100644
--- a/include/bout/derivs.hxx
+++ b/include/bout/derivs.hxx
@@ -93,7 +93,7 @@ template <typename E>
 std::enable_if_t<is_expr_field3d_v<E> && !bout::utils::is_Field3D_v<E>, const Field3D>
 DDY(const E& expr, CELL_LOC outloc = CELL_DEFAULT, const std::string& method = "DEFAULT",
     const std::string& region = "RGN_NOBNDRY") {
-  return DDY(Field3D{expr}, outloc, method, region);
+  return DDY(Field3D{Field3DParallel{expr}}, outloc, method, region);
 }
 
 /// Calculate first partial derivative in Y

From 33f791e78c42a145da8fca7bab57432df66d5c7c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 12 Aug 2026 12:07:59 +0200
Subject: [PATCH 1684/1827] Remove not-needed .asField3DParallel()

The computation of the parallel slices depends on the target type
---
 src/mesh/coordinates.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 5a6c484856..5e461602d0 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -773,7 +773,7 @@ void Coordinates::correctionForNonUniformMeshes(bool force_interpolate_from_cent
   if (localmesh->get(d2y, "d2y" + suffix, 0.0, false, location) != 0) {
     output_warn.write("\tWARNING: differencing quantity 'd2y' not found. "
                       "Calculating from dy\n");
-    d1_dy_ = DDY(1. / dy().asField3DParallel()); // d/di(1/dy)
+    d1_dy_ = DDY(1. / dy()); // d/di(1/dy)
 
     localmesh->communicate_no_slices(d1_dy_);
     d1_dy_ =

From 6ee7369cc7403a089d5361b5f038fe6a1bcafc50 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 12 Aug 2026 12:12:55 +0200
Subject: [PATCH 1685/1827] Grad_par: take Field3DParallel as parallel slices
 are needed for FCI

---
 include/bout/difops.hxx | 22 ++++++++++++----------
 src/mesh/difops.cxx     | 17 +++++++++--------
 2 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 2e9e924139..ec7d59364e 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -61,7 +61,7 @@ inline bout::FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc,
   return Grad_par(var, outloc, toString(method));
 }
 
-Field3D Grad_par(const Field3D& var, CELL_LOC outloc = CELL_DEFAULT,
+Field3D Grad_par(const Field3DParallel& var, CELL_LOC outloc = CELL_DEFAULT,
                  const std::string& method = "DEFAULT");
 
 /*!
@@ -99,11 +99,12 @@ inline bout::FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f,
   return Vpar_Grad_par(v, f, outloc, toString(method));
 }
 
-Field3D Vpar_Grad_par(const Field3D& v, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+Field3D Vpar_Grad_par(const Field3DParallel& v, const Field3DParallel& f,
+                      CELL_LOC outloc = CELL_DEFAULT,
                       const std::string& method = "DEFAULT");
 
-inline Field3D Vpar_Grad_par(const Field3D& v, const Field3D& f, CELL_LOC outloc,
-                             DIFF_METHOD method) {
+inline Field3D Vpar_Grad_par(const Field3DParallel& v, const Field3DParallel& f,
+                             CELL_LOC outloc, DIFF_METHOD method) {
   return Vpar_Grad_par(v, f, outloc, toString(method));
 }
 
@@ -186,20 +187,21 @@ inline Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc, DIFF_METHOD method)
  */
 bout::FieldMetric Div_par_K_Grad_par(BoutReal kY, const Field2D& f,
                                      CELL_LOC outloc = CELL_DEFAULT);
-Field3D Div_par_K_Grad_par(BoutReal kY, const Field3D& f, CELL_LOC outloc = CELL_DEFAULT);
+Field3D Div_par_K_Grad_par(BoutReal kY, const Field3DParallel& f,
+                           CELL_LOC outloc = CELL_DEFAULT);
 bout::FieldMetric Div_par_K_Grad_par(const Field2D& kY, const Field2D& f,
                                      CELL_LOC outloc = CELL_DEFAULT);
-Field3D Div_par_K_Grad_par(const Field2D& kY, const Field3D& f,
+Field3D Div_par_K_Grad_par(const Field2D& kY, const Field3DParallel& f,
                            CELL_LOC outloc = CELL_DEFAULT);
-Field3D Div_par_K_Grad_par(const Field3D& kY, const Field2D& f,
+Field3D Div_par_K_Grad_par(const Field3DParallel& kY, const Field2D& f,
                            CELL_LOC outloc = CELL_DEFAULT);
-Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f,
+Field3D Div_par_K_Grad_par(const Field3DParallel& kY, const Field3DParallel& f,
                            CELL_LOC outloc = CELL_DEFAULT);
 
 /// Version with energy flow diagnostic
 /// For FCI fields, `flow_ylow` is currently returned as zero.
-Field3D Div_par_K_Grad_par_mod(const Field3D& k, const Field3D& f, Field3D& flow_ylow,
-                               bool bndry_flux = true);
+Field3D Div_par_K_Grad_par_mod(const Field3DParallel& k, const Field3DParallel& f,
+                               Field3D& flow_ylow, bool bndry_flux = true);
 
 /*!
  * Perpendicular Laplacian operator
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 10acde73f0..a434322e2c 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -58,7 +58,7 @@ bout::FieldMetric Grad_par(const Field2D& var, CELL_LOC outloc,
   return DDY(var, outloc, method) * var.getCoordinates(outloc)->invSg();
 }
 
-Field3D Grad_par(const Field3D& var, CELL_LOC outloc, const std::string& method) {
+Field3D Grad_par(const Field3DParallel& var, CELL_LOC outloc, const std::string& method) {
   return DDY(var, outloc, method) * var.getCoordinates(outloc)->invSg();
 }
 
@@ -194,7 +194,7 @@ bout::FieldMetric Vpar_Grad_par(const Field2D& v, const Field2D& f, CELL_LOC out
   return VDDY(v, f, outloc, method) * f.getCoordinates(outloc)->invSg();
 }
 
-Field3D Vpar_Grad_par(const Field3D& v, const Field3D& f, CELL_LOC outloc,
+Field3D Vpar_Grad_par(const Field3DParallel& v, const Field3DParallel& f, CELL_LOC outloc,
                       const std::string& method) {
   return VDDY(v, f, outloc, method) * f.getCoordinates(outloc)->invSg();
 }
@@ -320,7 +320,7 @@ bout::FieldMetric Div_par_K_Grad_par(BoutReal kY, const Field2D& f, CELL_LOC out
   return kY * Grad2_par2(f, outloc);
 }
 
-Field3D Div_par_K_Grad_par(BoutReal kY, const Field3D& f, CELL_LOC outloc) {
+Field3D Div_par_K_Grad_par(BoutReal kY, const Field3DParallel& f, CELL_LOC outloc) {
   return kY * Grad2_par2(f, outloc);
 }
 
@@ -333,7 +333,7 @@ bout::FieldMetric Div_par_K_Grad_par(const Field2D& kY, const Field2D& f,
          + Div_par(kY, outloc) * Grad_par(f, outloc);
 }
 
-Field3D Div_par_K_Grad_par(const Field2D& kY, const Field3D& f, CELL_LOC outloc) {
+Field3D Div_par_K_Grad_par(const Field2D& kY, const Field3DParallel& f, CELL_LOC outloc) {
   if (outloc == CELL_DEFAULT) {
     outloc = f.getLocation();
   }
@@ -341,7 +341,7 @@ Field3D Div_par_K_Grad_par(const Field2D& kY, const Field3D& f, CELL_LOC outloc)
          + Div_par(kY, outloc) * Grad_par(f, outloc);
 }
 
-Field3D Div_par_K_Grad_par(const Field3D& kY, const Field2D& f, CELL_LOC outloc) {
+Field3D Div_par_K_Grad_par(const Field3DParallel& kY, const Field2D& f, CELL_LOC outloc) {
   if (outloc == CELL_DEFAULT) {
     outloc = f.getLocation();
   }
@@ -349,7 +349,8 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field2D& f, CELL_LOC outloc)
          + Div_par(kY, outloc) * Grad_par(f, outloc);
 }
 
-Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc) {
+Field3D Div_par_K_Grad_par(const Field3DParallel& kY, const Field3DParallel& f,
+                           CELL_LOC outloc) {
   if (outloc == CELL_DEFAULT) {
     outloc = f.getLocation();
   }
@@ -357,8 +358,8 @@ Field3D Div_par_K_Grad_par(const Field3D& kY, const Field3D& f, CELL_LOC outloc)
          + Div_par(kY, outloc) * Grad_par(f, outloc);
 }
 
-Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D& flow_ylow,
-                               bool bndry_flux) {
+Field3D Div_par_K_Grad_par_mod(const Field3DParallel& Kin, const Field3DParallel& fin,
+                               Field3D& flow_ylow, bool bndry_flux) {
   ASSERT2(Kin.getLocation() == fin.getLocation());
 
   const Mesh* mesh = Kin.getMesh();

From 99c365ec57a9c18da35d54f43eb5c844ae765ebf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 12 Aug 2026 12:40:38 +0200
Subject: [PATCH 1686/1827] Use switch to iterate through options

---
 src/mesh/difops.cxx | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index c748c92915..a51383482c 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -533,17 +533,15 @@ Field3D Div_par_K_Grad_par_mod_impl(const Field3D& Kin, const Field3D& fin,
 
 Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D& flow_ylow,
                                bool bndry_flux, bout::ConductionMethod method) {
-  if (method == bout::ConductionMethod::Original) {
-    return Div_par_K_Grad_par_mod_impl<bout::ConductionMethod::Original>(
-        Kin, fin, flow_ylow, bndry_flux);
-  }
-  if (method == bout::ConductionMethod::ProductJK) {
-    return Div_par_K_Grad_par_mod_impl<bout::ConductionMethod::ProductJK>(
-        Kin, fin, flow_ylow, bndry_flux);
-  }
-  if (method == bout::ConductionMethod::Harmonic) {
-    return Div_par_K_Grad_par_mod_impl<bout::ConductionMethod::Harmonic>(
-        Kin, fin, flow_ylow, bndry_flux);
+  using enum bout::ConductionMethod;
+
+  switch (method) {
+  case Original:
+    return Div_par_K_Grad_par_mod_impl<Original>(Kin, fin, flow_ylow, bndry_flux);
+  case ProductJK:
+    return Div_par_K_Grad_par_mod_impl<ProductJK>(Kin, fin, flow_ylow, bndry_flux);
+  case Harmonic:
+    return Div_par_K_Grad_par_mod_impl<Harmonic>(Kin, fin, flow_ylow, bndry_flux);
   }
   throw BoutException(
       "Unknown method `{}` - choose from `Original`, `ProductJK` or `Harmonic`.",

From c5b5e2edf2f7fe8a346cab8140ad1bb0d4d20b42 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 12 Aug 2026 13:01:13 +0100
Subject: [PATCH 1687/1827] Apply formatting

---
 include/bout/options.hxx | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index b68364c60c..abfef745e9 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -354,9 +354,7 @@ public:
   std::map<std::string, AttributeType> attributes;
 
   /// Return true if this value has attribute \p key
-  bool hasAttribute(const std::string& key) const {
-    return attributes.contains(key);
-  }
+  bool hasAttribute(const std::string& key) const { return attributes.contains(key); }
 
   /// Set attributes, overwriting any already set
   ///

From 7fe3fecb3d8602a65fbe65bc9bacfd66488ce444 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 3 Jul 2026 13:15:15 +0100
Subject: [PATCH 1688/1827] Use std::ranges::find instead of std::find

---
 include/bout/hypre_interface.hxx         | 4 ++--
 include/bout/multiostream.hxx            | 8 ++++----
 include/bout/petsc_interface.hxx         | 2 +-
 include/bout/solver.hxx                  | 2 +-
 src/sys/options.cxx                      | 3 +--
 tests/unit/solver/test_solverfactory.cxx | 2 +-
 6 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index d718a2b01a..832c3fbcc0 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -460,9 +460,9 @@ public:
     Element& operator+=(BoutReal value_) {
 
       ASSERT3(std::isfinite(value_));
-      auto column_position = std::find(cbegin(positions), cend(positions), column);
+      auto column_position = std::ranges::find(positions, column);
       if (column_position != cend(positions)) {
-        const auto i = std::distance(cbegin(positions), column_position);
+        const auto i = std::distance(begin(positions), column_position);
         value += weights[i] * value_;
       }
       addValues(value_);
diff --git a/include/bout/multiostream.hxx b/include/bout/multiostream.hxx
index ca3cc2d0c7..d038c8f659 100644
--- a/include/bout/multiostream.hxx
+++ b/include/bout/multiostream.hxx
@@ -17,7 +17,7 @@ private:
 
 public:
   void add(std::basic_ostream<char_type, traits>& str) {
-    auto pos = std::find(streams_.begin(), streams_.end(), &str);
+    auto pos = std::ranges::find(streams_, &str);
 
     // Already been added
     if (pos != streams_.end()) {
@@ -28,7 +28,7 @@ public:
   }
 
   void remove(std::basic_ostream<char_type, traits>& str) {
-    auto pos = std::find(streams_.begin(), streams_.end(), &str);
+    auto pos = std::ranges::find(streams_, &str);
 
     if (pos != streams_.end()) {
       streams_.erase(pos);
@@ -74,8 +74,8 @@ private:
 
 public:
   multiostream()
-      : multioutbuf_init(), std::basic_ostream<char_type, traits>(
-                                multioutbuf_init::buf()) {}
+      : multioutbuf_init(),
+        std::basic_ostream<char_type, traits>(multioutbuf_init::buf()) {}
 
   void add(std::basic_ostream<char_type, traits>& str) {
     multioutbuf_init::buf()->add(str);
diff --git a/include/bout/petsc_interface.hxx b/include/bout/petsc_interface.hxx
index 7b911e8755..c81ce5947e 100644
--- a/include/bout/petsc_interface.hxx
+++ b/include/bout/petsc_interface.hxx
@@ -406,7 +406,7 @@ public:
     Element& operator+=(BoutReal val) {
 
       ASSERT3(std::isfinite(val));
-      auto columnPosition = std::find(positions.begin(), positions.end(), petscCol);
+      auto columnPosition = std::ranges::find(positions, petscCol);
       if (columnPosition != positions.end()) {
         const int index = std::distance(positions.begin(), columnPosition);
         value += weights[index] * val;
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 09ede6a32b..18e1a6de59 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -514,7 +514,7 @@ protected:
   /// Does \p vars contain a field with \p name?
   template <class T>
   bool contains(const std::vector<VarStr<T>>& vars, const std::string& name) {
-    const auto in_vars = std::find(begin(vars), end(vars), name);
+    const auto in_vars = std::ranges::find(vars, name);
     return in_vars != end(vars);
   }
 
diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index d7bdeeadff..0e0241e9f9 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -949,8 +949,7 @@ Options Options::getUnused(const std::vector<std::string>& exclude_sources) cons
       return false;
     }
     const auto source = option.attributes.at("source").as<std::string>();
-    return std::find(exclude_sources.begin(), exclude_sources.end(), source)
-           != exclude_sources.end();
+    return std::ranges::find(exclude_sources, source) != std::ranges::end(exclude_sources);
   };
 
   const auto conditionally_used = [](const Options& option) -> bool {
diff --git a/tests/unit/solver/test_solverfactory.cxx b/tests/unit/solver/test_solverfactory.cxx
index 577c2986fe..2168aebc4c 100644
--- a/tests/unit/solver/test_solverfactory.cxx
+++ b/tests/unit/solver/test_solverfactory.cxx
@@ -17,7 +17,7 @@ TEST(SolverFactoryTest, GetDefaultSolverType) {
 TEST(SolverFactoryTest, RegisterSolver) {
   auto available = SolverFactory::getInstance().listAvailable();
 
-  auto found_fake = std::find(begin(available), end(available), "fake_solver");
+  auto found_fake = std::ranges::find(available, "fake_solver");
 
   EXPECT_NE(found_fake, end(available));
 }

From 1e45173534e033fb5856d7f2afac83d1dce1ba9c Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 2 Jul 2026 12:21:38 +0100
Subject: [PATCH 1689/1827] Fix ranges::find with projection

Extract `VarStr::name` to compare to `name`
---
 include/bout/solver.hxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 18e1a6de59..97e07ee5ff 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -514,7 +514,7 @@ protected:
   /// Does \p vars contain a field with \p name?
   template <class T>
   bool contains(const std::vector<VarStr<T>>& vars, const std::string& name) {
-    const auto in_vars = std::ranges::find(vars, name);
+    const auto in_vars = std::ranges::find(vars, name, &VarStr<T>::name);
     return in_vars != end(vars);
   }
 

From bd048758892614e170265cb6c1fb305824e6a264 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Thu, 2 Jul 2026 12:33:39 +0100
Subject: [PATCH 1690/1827] Use std::ranges::end for consistency (and slightly
 safer)

---
 include/bout/solver.hxx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 97e07ee5ff..b081b8bfd0 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -514,8 +514,7 @@ protected:
   /// Does \p vars contain a field with \p name?
   template <class T>
   bool contains(const std::vector<VarStr<T>>& vars, const std::string& name) {
-    const auto in_vars = std::ranges::find(vars, name, &VarStr<T>::name);
-    return in_vars != end(vars);
+    return std::ranges::find(vars, name, &VarStr<T>::name) != std::ranges::end(vars);
   }
 
   /// Vectors of variables to evolve

From 04bd654450de81ed1a2c83dd430898b14f9e443c Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Fri, 3 Jul 2026 13:47:07 +0100
Subject: [PATCH 1691/1827] Use std::ranges library for std::fill and
 std::transform

---
 src/sys/options.cxx | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/sys/options.cxx b/src/sys/options.cxx
index 0e0241e9f9..efd88474fc 100644
--- a/src/sys/options.cxx
+++ b/src/sys/options.cxx
@@ -769,13 +769,13 @@ struct ConvertContainerBase {
 
   Container operator()(int value) {
     Container result(similar_to);
-    std::fill(std::begin(result), std::end(result), static_cast<Scalar>(value));
+    std::ranges::fill(result, static_cast<Scalar>(value));
     return result;
   }
 
   Container operator()(BoutReal value) {
     Container result(similar_to);
-    std::fill(std::begin(result), std::end(result), static_cast<Scalar>(value));
+    std::ranges::fill(result, static_cast<Scalar>(value));
     return result;
   }
 
@@ -787,8 +787,8 @@ struct ConvertContainerBase {
     Container result(similar_to);
     result.reshape(value.shape()); // Resize to shape of input
 
-    std::transform(std::begin(value), std::end(value), std::begin(result),
-                   [](const auto& x) { return static_cast<Scalar>(x); });
+    std::ranges::transform(value, std::begin(result),
+                           [](const auto& x) { return static_cast<Scalar>(x); });
     return result;
   }
 
@@ -949,7 +949,8 @@ Options Options::getUnused(const std::vector<std::string>& exclude_sources) cons
       return false;
     }
     const auto source = option.attributes.at("source").as<std::string>();
-    return std::ranges::find(exclude_sources, source) != std::ranges::end(exclude_sources);
+    return std::ranges::find(exclude_sources, source)
+           != std::ranges::end(exclude_sources);
   };
 
   const auto conditionally_used = [](const Options& option) -> bool {

From fe342f99a769c28ff84fb3dc68225b8aa4418d34 Mon Sep 17 00:00:00 2001
From: tomc271 <tomc271@gmail.com>
Date: Wed, 8 Jul 2026 10:46:51 +0100
Subject: [PATCH 1692/1827] Use `std::ranges::sort` and `std::ranges::unique`
 to avoid the verbose iterator pairs `begin(), end()` in `makeUnique()`.

---
 src/field/fieldgroup.cxx | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/field/fieldgroup.cxx b/src/field/fieldgroup.cxx
index f85cbb6843..f9f166fa32 100644
--- a/src/field/fieldgroup.cxx
+++ b/src/field/fieldgroup.cxx
@@ -1,5 +1,5 @@
-
 #include <bout/fieldgroup.hxx>
+#include <algorithm>
 
 FieldGroup operator+(const FieldGroup& lhs, const FieldGroup& rhs) {
   return FieldGroup(lhs) += rhs;
@@ -7,16 +7,16 @@ FieldGroup operator+(const FieldGroup& lhs, const FieldGroup& rhs) {
 
 void FieldGroup::makeUnique() {
   // Need to sort vector before making unique
-  std::sort(fvec.begin(), fvec.end());
+  std::ranges::sort(fvec);
 
   // Remove duplicate entries (doesn't resize vector though)
-  auto last = std::unique(fvec.begin(), fvec.end());
+  auto fvec_dupes = std::ranges::unique(fvec);
 
   // Resizes vector to remove memory no longer required
-  fvec.erase(last, fvec.end());
+  fvec.erase(fvec_dupes.begin(), fvec_dupes.end());
 
   // Now do the same for the vector of Field3Ds
-  std::sort(f3vec.begin(), f3vec.end());
-  auto last_f3 = std::unique(f3vec.begin(), f3vec.end());
-  f3vec.erase(last_f3, f3vec.end());
+  std::ranges::sort(f3vec);
+  auto f3vec_dupes = std::ranges::unique(f3vec);
+  f3vec.erase(f3vec_dupes.begin(), f3vec_dupes.end());
 }

From aa7e4e93d62496f9a90a5625062f48439fd83757 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 12 Aug 2026 15:23:17 +0100
Subject: [PATCH 1693/1827] Fix clang-tidy warnings

---
 include/bout/solver.hxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index b081b8bfd0..0d4b330ec6 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -45,11 +45,12 @@
 #include "bout/monitor.hxx"
 #include "bout/options.hxx"
 #include "bout/region.hxx"
-#include "bout/unused.hxx"
 
+#include <algorithm>
 #include <cstdint>
 #include <iterator>
 #include <memory>
+#include <vector>
 
 ///////////////////////////////////////////////////////////////////
 // C function pointer types

From 12351b9cb1c7c97b25e524175d1c031f0d7023ca Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 10:45:45 +0200
Subject: [PATCH 1694/1827] Fix signature in cxx

---
 src/mesh/difops.cxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 7111725bdb..3c2a15b184 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -524,8 +524,9 @@ Field3D Div_par_K_Grad_par_mod_impl(const Field3DParallel& Kin,
 }
 } // namespace
 
-Field3D Div_par_K_Grad_par_mod(const Field3D& Kin, const Field3D& fin, Field3D& flow_ylow,
-                               bool bndry_flux, bout::ConductionMethod method) {
+Field3D Div_par_K_Grad_par_mod(const Field3DParallel& Kin, const Field3DParallel& fin,
+                               Field3D& flow_ylow, bool bndry_flux,
+                               bout::ConductionMethod method) {
   using enum bout::ConductionMethod;
 
   switch (method) {

From 0213d07380eeb8276e46d0ebdc697e06e147fc78 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 12:10:38 +0200
Subject: [PATCH 1695/1827] Add BOUT_ENUM_CLASS_NS

A version of BOUT_ENUM_CLASS that can create namespaced enums
---
 include/bout/bout_enum_class.hxx | 43 ++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index 334fa657da..58f444a34e 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -105,4 +105,47 @@
     return out << toString(e);                                                 \
   }
 
+/// Create an enum class with toString and <enum name>FromString functions, and an
+/// Options::as<enum> overload to read the enum
+#define BOUT_ENUM_CLASS_NS(ns, enumname, ...)                                      \
+  namespace ns {                                                                   \
+  enum class enumname : std::int8_t { __VA_ARGS__ };                               \
+  }                                                                                \
+                                                                                   \
+  inline std::string toString(ns::enumname e) {                                    \
+                                                                                   \
+    const static std::map<ns::enumname, std::string> toString_map = {              \
+        BOUT_ENUM_CLASS_MAP_ARGS(BOUT_ENUM_CLASS_STR, ns::enumname, __VA_ARGS__)}; \
+    auto found = toString_map.find(e);                                             \
+    if (found == toString_map.end()) {                                             \
+      throw BoutException("Did not find enum {:d}", static_cast<int>(e));          \
+    }                                                                              \
+    return found->second;                                                          \
+  }                                                                                \
+  namespace ns {                                                                   \
+  inline enumname BOUT_MAKE_FROMSTRING_NAME(enumname)(const std::string& s) {      \
+    const static std::map<std::string, enumname> fromString_map = {                \
+        BOUT_ENUM_CLASS_MAP_ARGS(BOUT_STR_ENUM_CLASS, enumname, __VA_ARGS__)};     \
+    auto found = fromString_map.find(s);                                           \
+    if (found == fromString_map.end()) {                                           \
+      std::string valid_values{};                                                  \
+      for (auto const& entry : fromString_map) {                                   \
+        valid_values += std::string(" ") + entry.first;                            \
+      }                                                                            \
+      throw BoutException("Did not find enum {:s}. Valid values: {:s}", s,         \
+                          valid_values);                                           \
+    }                                                                              \
+    return found->second;                                                          \
+  }                                                                                \
+  }                                                                                \
+                                                                                   \
+  template <>                                                                      \
+  inline ns::enumname Options::as<ns::enumname>(const ns::enumname&) const {       \
+    return BOUT_MAKE_FROMSTRING_NAME(ns::enumname)(this->as<std::string>());       \
+  }                                                                                \
+                                                                                   \
+  inline std::ostream& operator<<(std::ostream& out, const ns::enumname& e) {      \
+    return out << toString(e);                                                     \
+  }
+
 #endif // BOUT_ENUM_CLASS_H

From efd6a661267acfad64531d067ebad10f6edd497d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 12:13:13 +0200
Subject: [PATCH 1696/1827] Switch bout::ConductionMethod to BOUT_ENUM_CLASS_NS

---
 include/bout/difops.hxx | 38 +++++++++++++++++++++-----------------
 1 file changed, 21 insertions(+), 17 deletions(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 336050feaf..951ff5612f 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -36,14 +36,15 @@
 #ifndef BOUT_DIFOPS_H
 #define BOUT_DIFOPS_H
 
+#include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/coordinates.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/metric_tensor.hxx"
 
-#include <string>
-
 #include <cstdint>
+#include <string>
 
 class Solver;
 
@@ -200,21 +201,24 @@ Field3D Div_par_K_Grad_par(const Field3DParallel& kY, const Field2D& f,
 Field3D Div_par_K_Grad_par(const Field3DParallel& kY, const Field3DParallel& f,
                            CELL_LOC outloc = CELL_DEFAULT);
 
-namespace bout {
-enum class ConductionMethod : uint8_t {
-  /// Separately averages :math:`K`, :math:`J`, :math:`g_{22}`, and
-  /// :math:`dy` at the face and then multiplies them together.
-  Original,
-  /// Uses the same stencil as ``Original`` but averages :math:`J K`
-  /// together before applying the face gradient.
-  ProductJK,
-  ///  Uses a harmonic average of the half-cell conductances
-  /// :math:`K J / (g_{22} dy)`. This better matches a series-resistance
-  /// interpretation of two adjacent half-cells and can give noticeably
-  /// different results when coefficients or cell sizes vary strongly.
-  Harmonic
-};
-}
+/// enum class bout::ConductionMethod
+/// ---------------------------------
+///
+/// Original:
+/// Separately averages :math:`K`, :math:`J`, :math:`g_{22}`, and
+/// :math:`dy` at the face and then multiplies them together.
+///
+/// ProductJK:
+/// Uses the same stencil as ``Original`` but averages :math:`J K`
+/// together before applying the face gradient.
+///
+/// Harmonic:
+///  Uses a harmonic average of the half-cell conductances
+/// :math:`K J / (g_{22} dy)`. This better matches a series-resistance
+/// interpretation of two adjacent half-cells and can give noticeably
+/// different results when coefficients or cell sizes vary strongly.
+BOUT_ENUM_CLASS_NS(bout, ConductionMethod, Original, ProductJK, Harmonic);
+
 /// Version with energy flow diagnostic
 /// For FCI fields, `flow_ylow` is currently returned as zero.
 Field3D

From 615254cfd2121c19fd5efefc817e48d192d66c80 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 13:18:42 +0200
Subject: [PATCH 1697/1827] Fix BOUT_ENUM_CLASS_NS

---
 include/bout/bout_enum_class.hxx | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index 58f444a34e..aa427b1830 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -141,11 +141,12 @@
                                                                                    \
   template <>                                                                      \
   inline ns::enumname Options::as<ns::enumname>(const ns::enumname&) const {       \
-    return BOUT_MAKE_FROMSTRING_NAME(ns::enumname)(this->as<std::string>());       \
+    return ns::BOUT_MAKE_FROMSTRING_NAME(enumname)(this->as<std::string>());       \
   }                                                                                \
-                                                                                   \
-  inline std::ostream& operator<<(std::ostream& out, const ns::enumname& e) {      \
+  namespace ns {                                                                   \
+  inline std::ostream& operator<<(std::ostream& out, const enumname& e) {          \
     return out << toString(e);                                                     \
+  }                                                                                \
   }
 
 #endif // BOUT_ENUM_CLASS_H

From 45fd7a369eb0ce909cb6b7368b3a070a412df75d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 13:19:44 +0200
Subject: [PATCH 1698/1827] Add unit tests for namespaced enum class

---
 .../include/bout/test_bout_enum_class.cxx     | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/tests/unit/include/bout/test_bout_enum_class.cxx b/tests/unit/include/bout/test_bout_enum_class.cxx
index 4811c76be8..87b775cea5 100644
--- a/tests/unit/include/bout/test_bout_enum_class.cxx
+++ b/tests/unit/include/bout/test_bout_enum_class.cxx
@@ -6,12 +6,24 @@
 #include "bout/output.hxx"
 
 BOUT_ENUM_CLASS(TestEnum, foo, bar);
+BOUT_ENUM_CLASS_NS(bout, TestEnum, foo, bar);
+
+TEST(BoutEnumClassNS, toString) {
+  EXPECT_EQ(toString(bout::TestEnum::foo), "foo");
+  EXPECT_EQ(toString(bout::TestEnum::bar), "bar");
+}
 
 TEST(BoutEnumClass, toString) {
   EXPECT_EQ(toString(TestEnum::foo), "foo");
   EXPECT_EQ(toString(TestEnum::bar), "bar");
 }
 
+TEST(BoutEnumClassNS, fromString) {
+  EXPECT_EQ(bout::TestEnumFromString("foo"), bout::TestEnum::foo);
+  EXPECT_EQ(bout::TestEnumFromString("bar"), bout::TestEnum::bar);
+  EXPECT_THROW(bout::TestEnumFromString("expect_fail"), BoutException);
+}
+
 TEST(BoutEnumClass, fromString) {
   EXPECT_EQ(TestEnumFromString("foo"), TestEnum::foo);
   EXPECT_EQ(TestEnumFromString("bar"), TestEnum::bar);
@@ -38,6 +50,26 @@ TEST(BoutEnumClass, options) {
   EXPECT_THROW(options["optfail"].as<TestEnum>(), BoutException);
 }
 
+TEST(BoutEnumClassNS, options) {
+  WithQuietOutput quiet_info{output_info};
+
+  Options options;
+
+  auto opt1 = options["opt"].withDefault(bout::TestEnum::foo);
+  EXPECT_EQ(opt1, bout::TestEnum::foo);
+  EXPECT_NE(opt1, bout::TestEnum::bar);
+
+  options["opt"] = "bar";
+
+  auto opt2 = options["opt"].as<bout::TestEnum>();
+  EXPECT_EQ(opt2, bout::TestEnum::bar);
+  EXPECT_NE(opt2, bout::TestEnum::foo);
+
+  options["optfail"] = "expect_fail";
+
+  EXPECT_THROW(options["optfail"].as<bout::TestEnum>(), BoutException);
+}
+
 TEST(BoutEnumClass, ostream) {
   auto sstream = std::stringstream();
 
@@ -45,3 +77,11 @@ TEST(BoutEnumClass, ostream) {
 
   EXPECT_EQ(sstream.str(), "foobar");
 }
+
+TEST(BoutEnumClassNS, ostream) {
+  auto sstream = std::stringstream();
+
+  sstream << bout::TestEnum::foo << bout::TestEnum::bar;
+
+  EXPECT_EQ(sstream.str(), "foobar");
+}

From cc0ab454e4f328f92037052e33afcd9c4681eae0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 13:22:39 +0200
Subject: [PATCH 1699/1827] Add unit test for nested namespaces

---
 .../include/bout/test_bout_enum_class.cxx     | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/tests/unit/include/bout/test_bout_enum_class.cxx b/tests/unit/include/bout/test_bout_enum_class.cxx
index 87b775cea5..83508a522e 100644
--- a/tests/unit/include/bout/test_bout_enum_class.cxx
+++ b/tests/unit/include/bout/test_bout_enum_class.cxx
@@ -7,6 +7,7 @@
 
 BOUT_ENUM_CLASS(TestEnum, foo, bar);
 BOUT_ENUM_CLASS_NS(bout, TestEnum, foo, bar);
+BOUT_ENUM_CLASS_NS(bout::test, TestEnum, foo, bar);
 
 TEST(BoutEnumClassNS, toString) {
   EXPECT_EQ(toString(bout::TestEnum::foo), "foo");
@@ -70,6 +71,26 @@ TEST(BoutEnumClassNS, options) {
   EXPECT_THROW(options["optfail"].as<bout::TestEnum>(), BoutException);
 }
 
+TEST(BoutEnumClassNS2, options) {
+  WithQuietOutput quiet_info{output_info};
+
+  Options options;
+
+  auto opt1 = options["opt"].withDefault(bout::test::TestEnum::foo);
+  EXPECT_EQ(opt1, bout::test::TestEnum::foo);
+  EXPECT_NE(opt1, bout::test::TestEnum::bar);
+
+  options["opt"] = "bar";
+
+  auto opt2 = options["opt"].as<bout::test::TestEnum>();
+  EXPECT_EQ(opt2, bout::test::TestEnum::bar);
+  EXPECT_NE(opt2, bout::test::TestEnum::foo);
+
+  options["optfail"] = "expect_fail";
+
+  EXPECT_THROW(options["optfail"].as<bout::test::TestEnum>(), BoutException);
+}
+
 TEST(BoutEnumClass, ostream) {
   auto sstream = std::stringstream();
 

From f32587acf9c6c2a540c481c86d135926cdbca29d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 14:01:35 +0200
Subject: [PATCH 1700/1827] Ensure we do not break B for FCI

---
 src/mesh/coordinates.cxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 5e461602d0..34a9dbc993 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -823,6 +823,7 @@ Coordinates::FieldMetric Coordinates::recalculateJacobian() const {
 }
 
 Coordinates::FieldMetric Coordinates::recalculateBxy() const {
+  ASSERT2(not J().isFci());
   return sqrt(g_22()) / J();
 }
 

From 25b79ade8a145a59ec79e2235a69bdda3c41bab4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 14:06:22 +0200
Subject: [PATCH 1701/1827] Do not add parallel slices to parallel slices

---
 src/mesh/coordinates.cxx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 34a9dbc993..fca933621e 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1278,6 +1278,9 @@ void Coordinates::communicateMetricTensor() {
 void Coordinates::communicateDz() { localmesh->communicate(dz_); }
 
 void Coordinates::splitBxyParallelSlices() {
-  Bxy_.splitParallelSlices();
-  Bxy_.yup() = Bxy_.ydown() = Bxy_;
+  if (not Bxy_.hasParallelSlices()) {
+    auto copy = Bxy_;
+    Bxy_.splitParallelSlices();
+    Bxy_.yup() = Bxy_.ydown() = copy;
+  }
 }

From d1d09e8672b7a80a1beb1eeb2403156e98c6a3e2 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 14:29:36 +0200
Subject: [PATCH 1702/1827] Add normalisation for metrics

---
 include/bout/coordinates.hxx |  7 +++++
 src/mesh/coordinates.cxx     | 55 ++++++++++++++++++++++++++++++++++++
 2 files changed, 62 insertions(+)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index f01e3883e0..dc88d20b3c 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -372,6 +372,13 @@ public:
 
   void communicateMetricTensor();
 
+private:
+  void normaliseMetricTokamak(BoutReal rho_s0, BoutReal Bnorm);
+  void normaliseMetricFCI(BoutReal rho_s0, BoutReal Bnorm);
+
+public:
+  void normaliseMetric(BoutReal rho_s0, BoutReal Bnorm);
+
   void communicateDz();
 
   ///< Coordinate system Jacobian, so volume of cell is J*dx*dy*dz
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index fca933621e..df9daea0d0 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1284,3 +1284,58 @@ void Coordinates::splitBxyParallelSlices() {
     Bxy_.yup() = Bxy_.ydown() = copy;
   }
 }
+
+void Coordinates::normaliseMetricTokamak(const BoutReal rho_s0, const BoutReal Bnorm) {
+  contravariantMetricTensor = ContravariantMetricTensor(
+      contravariantMetricTensor.g11() / SQ(Bnorm * rho_s0),
+      contravariantMetricTensor.g22() * SQ(rho_s0),
+      contravariantMetricTensor.g33() * SQ(rho_s0),
+      contravariantMetricTensor.g12() / Bnorm, contravariantMetricTensor.g13() / Bnorm,
+      contravariantMetricTensor.g23() * SQ(rho_s0));
+
+  covariantMetricTensor = CovariantMetricTensor(
+      covariantMetricTensor.g11() * SQ(Bnorm * rho_s0),
+      covariantMetricTensor.g22() / SQ(rho_s0), covariantMetricTensor.g33() / SQ(rho_s0),
+      covariantMetricTensor.g12() * Bnorm, covariantMetricTensor.g13() * Bnorm,
+      covariantMetricTensor.g23() / SQ(rho_s0));
+
+  setBxy(Bxy() / Bnorm);
+  setJ(J() * Bnorm / rho_s0);
+  invalidateMetricCaches();
+}
+
+void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm) {
+  BoutReal rhoSQ = SQ(rho_s0);
+
+  // coord->g11.asField3DParallel() *= rhoSQ;
+  contravariantMetricTensor.map([&](auto f) -> FieldMetric {
+    if (f.hasParallelSlices()) {
+      return f.asField3DParallel() * rhoSQ;
+    };
+    return f * rhoSQ;
+  });
+
+  //coord->g_11.asField3DParallel() /= rhoSQ;
+  covariantMetricTensor.map([&](auto f) -> FieldMetric {
+    if (f.hasParallelSlices()) {
+      return f.asField3DParallel() / rhoSQ;
+    };
+    return f / rhoSQ;
+  });
+  // coord->J.asField3DParallel() /= rho_s0 * rho_s0 * rho_s0;
+  if (J().hasParallelSlices()) {
+    setJ(Field3DParallel{J() * (rho_s0 * rho_s0 * rho_s0)});
+  } else {
+    setJ(J() * (rho_s0 * rho_s0 * rho_s0));
+  }
+  setBxy(Field3DParallel(Bxy() / Bnorm));
+  invalidateMetricCaches();
+}
+
+void Coordinates::normaliseMetric(const BoutReal rho_s0, const BoutReal Bnorm) {
+  ASSERT2(hasParallelTransform());
+  if (Bxy().isFci()) {
+    return normaliseMetricFCI(rho_s0, Bnorm);
+  }
+  return normaliseMetricTokamak(rho_s0, Bnorm);
+}

From 1dd158300224c8509da5f31f7b1ca1cdb7b30018 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 14:57:26 +0200
Subject: [PATCH 1703/1827] Fix compilation for 2D metrics

---
 src/mesh/coordinates.cxx | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index df9daea0d0..7f34758107 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1323,12 +1323,17 @@ void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm
     return f / rhoSQ;
   });
   // coord->J.asField3DParallel() /= rho_s0 * rho_s0 * rho_s0;
-  if (J().hasParallelSlices()) {
-    setJ(Field3DParallel{J() * (rho_s0 * rho_s0 * rho_s0)});
+  if constexpr (bout::build::use_metric_3d) {
+    if (J().hasParallelSlices()) {
+      setJ(Field3DParallel{J() * (rho_s0 * rho_s0 * rho_s0)});
+    } else {
+      setJ(J() * (rho_s0 * rho_s0 * rho_s0));
+    }
+    setBxy(Field3DParallel(Bxy() / Bnorm));
   } else {
     setJ(J() * (rho_s0 * rho_s0 * rho_s0));
+    setBxy(Bxy() / Bnorm);
   }
-  setBxy(Field3DParallel(Bxy() / Bnorm));
   invalidateMetricCaches();
 }
 

From 2735dcb4a1f6547e720f9cf5c30ba4cacc7ea45b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 14:57:47 +0200
Subject: [PATCH 1704/1827] Suppress unused var warnings

---
 src/mesh/difops.cxx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 3c2a15b184..3d72763bef 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -762,10 +762,13 @@ Field3D Laplace(const Field3D& f, CELL_LOC outloc,
  * Inverse of Laplacian operator in LaplaceXY solver
  *******************************************************************************/
 
-Field2D Laplace_perpXY(const Field2D& A, const Field2D& f) {
 #if BOUT_USE_METRIC_3D
+Field2D Laplace_perpXY([[maybe_unused]] const Field2D& A,
+                       [[maybe_unused]] const Field2D& f) {
   throw BoutException("Coordinates::Laplace_perpXY for 3D metric not implemented");
+}
 #else
+Field2D Laplace_perpXY(const Field2D& A, const Field2D& f) {
   const auto& coords = *f.getCoordinates();
 
   Field2D result;
@@ -821,8 +824,8 @@ Field2D Laplace_perpXY(const Field2D& A, const Field2D& f) {
   }
 
   return result;
-#endif
 }
+#endif
 
 /*******************************************************************************
 * b0xGrad_dot_Grad

From 6fb9096882660427e805da6ed0de9f734904ebfd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 15:24:57 +0200
Subject: [PATCH 1705/1827] Use unsigned int for enum

---
 include/bout/bout_enum_class.hxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/bout_enum_class.hxx b/include/bout/bout_enum_class.hxx
index aa427b1830..ce088a4628 100644
--- a/include/bout/bout_enum_class.hxx
+++ b/include/bout/bout_enum_class.hxx
@@ -67,7 +67,7 @@
 /// Create an enum class with toString and <enum name>FromString functions, and an
 /// Options::as<enum> overload to read the enum
 #define BOUT_ENUM_CLASS(enumname, ...)                                         \
-  enum class enumname : std::int8_t { __VA_ARGS__ };                           \
+  enum class enumname : std::uint8_t { __VA_ARGS__ };                          \
                                                                                \
   inline std::string toString(enumname e) {                                    \
                                                                                \
@@ -109,7 +109,7 @@
 /// Options::as<enum> overload to read the enum
 #define BOUT_ENUM_CLASS_NS(ns, enumname, ...)                                      \
   namespace ns {                                                                   \
-  enum class enumname : std::int8_t { __VA_ARGS__ };                               \
+  enum class enumname : std::uint8_t { __VA_ARGS__ };                              \
   }                                                                                \
                                                                                    \
   inline std::string toString(ns::enumname e) {                                    \

From 6282f56f7d35b091f65ff211893411d8fb825cfb Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 15:35:52 +0200
Subject: [PATCH 1706/1827] Switch to preprocessor #if

---
 src/mesh/coordinates.cxx | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 7f34758107..b4e937f559 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1323,17 +1323,17 @@ void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm
     return f / rhoSQ;
   });
   // coord->J.asField3DParallel() /= rho_s0 * rho_s0 * rho_s0;
-  if constexpr (bout::build::use_metric_3d) {
-    if (J().hasParallelSlices()) {
-      setJ(Field3DParallel{J() * (rho_s0 * rho_s0 * rho_s0)});
-    } else {
-      setJ(J() * (rho_s0 * rho_s0 * rho_s0));
-    }
-    setBxy(Field3DParallel(Bxy() / Bnorm));
+#if BOUT_USE_METRIC_3D
+  if (J().hasParallelSlices()) {
+    setJ(Field3DParallel{J() * (rho_s0 * rho_s0 * rho_s0)});
   } else {
     setJ(J() * (rho_s0 * rho_s0 * rho_s0));
-    setBxy(Bxy() / Bnorm);
   }
+  setBxy(Field3DParallel(Bxy() / Bnorm));
+#else
+  setJ(J() * (rho_s0 * rho_s0 * rho_s0));
+  setBxy(Bxy() / Bnorm);
+#endif
   invalidateMetricCaches();
 }
 

From 40ac19eb883ed62760223774383c8011b05d028b Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 13 Aug 2026 08:30:09 -0700
Subject: [PATCH 1707/1827] Div_par_K_Grad_par_mod: Error with ConductionMethod
 string

Use `toString` to convert an unhandled ConductionMethod into a string.
Should be easier for a user to understand than an integer.
---
 src/mesh/difops.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 3c2a15b184..e6913a67eb 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -539,7 +539,7 @@ Field3D Div_par_K_Grad_par_mod(const Field3DParallel& Kin, const Field3DParallel
   }
   throw BoutException(
       "Unknown method `{}` - choose from `Original`, `ProductJK` or `Harmonic`.",
-      static_cast<int>(method));
+      toString(method));
 }
 /*******************************************************************************
 * Delp2

From be2ff917fe276ccbd74f1f0d7768629218275168 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 11:40:40 +0200
Subject: [PATCH 1708/1827] Use pre-computed cell areas for Div_par_fvv_heating

Div_par_fvv has been changed to use pre-computed cell areas.  As
Div_par_fvv_heating is used to compute the numerical heating of
Div_par_fvv, it is imporent that the numerical details, like how the
cell face areas are computed, so that they give matching results.

Thanks to Mike Kryjak, who noticed this issue while reviewing a
Hermes-3 PR.
---
 include/bout/fv_ops_impl.hxx | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index a4e8f908bf..1b1379d5ad 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -1108,22 +1108,14 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
         // so calculate inside the k loop.
 
         // For right cell boundaries
-        BoutReal common_factor =
-            (coord->J(i, j, k) + coord->J(i, j + 1, k))
-            / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j + 1, k)));
+        const BoutReal area_rp = coord->cell_area_yhigh()(i, j, k);
 
-        const BoutReal flux_factor_rc =
-            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal area_rp =
-            common_factor * coord->dx(i, j + 1, k) * coord->dz(i, j + 1, k);
+        const BoutReal flux_factor_rc = area_rp / coord->cell_volume()(i, j, k);
 
         // For left cell boundaries
-        common_factor = (coord->J(i, j, k) + coord->J(i, j - 1, k))
-                        / (sqrt(coord->g_22(i, j, k)) + sqrt(coord->g_22(i, j - 1, k)));
+        const BoutReal area_lc = coord->cell_area_ylow()(i, j, k);
 
-        const BoutReal flux_factor_lc =
-            common_factor / (coord->dy(i, j, k) * coord->J(i, j, k));
-        const BoutReal area_lc = common_factor * coord->dx(i, j, k) * coord->dz(i, j, k);
+        const BoutReal flux_factor_lc = area_lc / coord->cell_volume()(i, j, k);
 
         ////////////////////////////////////////////
         // Reconstruct f at the cell faces
@@ -1185,7 +1177,7 @@ Field3D Div_par_fvv_heating(const Field3D& f_in, const Field3D& v_in,
           result(i, j, k) += (actual_ke - expected_ke) * flux_factor_rc;
 
           // Final flow through boundary is the expected value
-          flow_ylow(i, j + 1, k) += expected_ke * area_rp; //expected_ke * area_rp;
+          flow_ylow(i, j + 1, k) += expected_ke * area_rp;
 
         } else {
           // Maximum wave speed in the two cells

From 75d4fb9fa4e14682cd88d978be04c134f0689184 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 14 Aug 2026 10:43:19 +0200
Subject: [PATCH 1709/1827] Add dx normalisation for Tokamak geometry

---
 src/mesh/coordinates.cxx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index b4e937f559..a54fbaa5aa 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1299,6 +1299,7 @@ void Coordinates::normaliseMetricTokamak(const BoutReal rho_s0, const BoutReal B
       covariantMetricTensor.g12() * Bnorm, covariantMetricTensor.g13() * Bnorm,
       covariantMetricTensor.g23() / SQ(rho_s0));
 
+  setDx(dx() / (rho_s0 * rho_s0 * Bnorm));
   setBxy(Bxy() / Bnorm);
   setJ(J() * Bnorm / rho_s0);
   invalidateMetricCaches();

From 993e633f9a4ebf20d1d145bc73fedd80bd75200b Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 14 Aug 2026 10:45:18 +0200
Subject: [PATCH 1710/1827] Improve comments

---
 src/mesh/coordinates.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index a54fbaa5aa..c8abceaa16 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1308,7 +1308,7 @@ void Coordinates::normaliseMetricTokamak(const BoutReal rho_s0, const BoutReal B
 void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm) {
   BoutReal rhoSQ = SQ(rho_s0);
 
-  // coord->g11.asField3DParallel() *= rhoSQ;
+  // g??.asField3DParallel() *= rhoSQ;
   contravariantMetricTensor.map([&](auto f) -> FieldMetric {
     if (f.hasParallelSlices()) {
       return f.asField3DParallel() * rhoSQ;
@@ -1316,14 +1316,14 @@ void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm
     return f * rhoSQ;
   });
 
-  //coord->g_11.asField3DParallel() /= rhoSQ;
+  // g_??.asField3DParallel() /= rhoSQ;
   covariantMetricTensor.map([&](auto f) -> FieldMetric {
     if (f.hasParallelSlices()) {
       return f.asField3DParallel() / rhoSQ;
     };
     return f / rhoSQ;
   });
-  // coord->J.asField3DParallel() /= rho_s0 * rho_s0 * rho_s0;
+  // J.asField3DParallel() /= rho_s0 * rho_s0 * rho_s0;
 #if BOUT_USE_METRIC_3D
   if (J().hasParallelSlices()) {
     setJ(Field3DParallel{J() * (rho_s0 * rho_s0 * rho_s0)});

From bb4964e993659960848117f308346767c7f3a57f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 14 Aug 2026 10:45:31 +0200
Subject: [PATCH 1711/1827] Fix J normalisation

---
 src/mesh/coordinates.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index c8abceaa16..ee80827094 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1326,13 +1326,13 @@ void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm
   // J.asField3DParallel() /= rho_s0 * rho_s0 * rho_s0;
 #if BOUT_USE_METRIC_3D
   if (J().hasParallelSlices()) {
-    setJ(Field3DParallel{J() * (rho_s0 * rho_s0 * rho_s0)});
+    setJ(Field3DParallel{J() / (rho_s0 * rho_s0 * rho_s0)});
   } else {
-    setJ(J() * (rho_s0 * rho_s0 * rho_s0));
+    setJ(J() / (rho_s0 * rho_s0 * rho_s0));
   }
   setBxy(Field3DParallel(Bxy() / Bnorm));
 #else
-  setJ(J() * (rho_s0 * rho_s0 * rho_s0));
+  setJ(J() / (rho_s0 * rho_s0 * rho_s0));
   setBxy(Bxy() / Bnorm);
 #endif
   invalidateMetricCaches();

From 524ceab35d9a90739f3a3942622f665ecaa954b9 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 14 Aug 2026 10:07:52 -0700
Subject: [PATCH 1712/1827] Refactored Hypre boundary row elimination

The row elimination is now an implementation detail that doesn't
require changes to the HypreMatrix and HypreVector interface.

The elimination is applied to temporary working vectors when
assembling the HypreVector, so the input values are not mutated.

New tests check the boundary elimination.
---
 include/bout/hypre_interface.hxx              | 230 +++++++++++++-----
 .../laplace/impls/hypre3d/hypre3d_laplace.cxx |   6 -
 .../laplace/impls/hypre3d/hypre3d_laplace.hxx |   2 +-
 src/sys/hypre_interface.cxx                   | 128 +++++++---
 .../include/bout/test_hypre_interface.cxx     | 229 +++++++++++++++--
 .../invert/laplace/test_laplace_hypre3d.cxx   |  11 +
 6 files changed, 489 insertions(+), 117 deletions(-)

diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index a118ff4787..d71659ca3a 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -28,6 +28,7 @@
 #include "HYPRE_utilities.h"
 #include "_hypre_utilities.h"
 
+#include <algorithm>
 #include <cmath>
 #include <iterator>
 #include <memory>
@@ -131,47 +132,70 @@ using BCValuesPtr = std::shared_ptr<HypreComplexArray>;
  *
  *   NOTE: Implementation in src/sys/hypre_interface.cxx
  */
-struct BCMatrixEquations {
+struct BoundaryElimination {
   HYPRE_Int nb;
   HYPRE_Int* binum_array;
   HYPRE_Int* bjnum_array;
+  HYPRE_Int* bdep_array;
   HYPRE_Complex* bii_array;
   HYPRE_Complex* bij_array;
   HYPRE_Int na;
   HYPRE_Int* aknum_array;
   HYPRE_Complex* aki_array;
+  std::vector<HYPRE_Int> reduction_order;
+  std::vector<HYPRE_Int> expansion_order;
 
-  BCMatrixEquations() = delete;
+  BoundaryElimination() = delete;
 
-  BCMatrixEquations(HYPRE_Int nrows, HYPRE_Int* ncols, HYPRE_BigInt* rows,
-                    HYPRE_Int** row_indexes_ptr, HYPRE_BigInt* cols,
-                    HYPRE_Complex* values,
-                    HYPRE_Int nb,         // number of boundary equations
-                    HYPRE_Int* bi_array); // row i for each boundary equation
+  BoundaryElimination(HYPRE_Int nrows, HYPRE_Int* ncols, HYPRE_BigInt* rows,
+                      HYPRE_Int** row_indexes_ptr, HYPRE_BigInt* cols,
+                      HYPRE_Complex* values,
+                      HYPRE_Int nb,         // number of boundary equations
+                      HYPRE_Int* bi_array); // row i for each boundary equation
 
-  ~BCMatrixEquations() {
+  ~BoundaryElimination() {
     // Free arrays
     HypreFree(binum_array);
     HypreFree(bjnum_array);
+    HypreFree(bdep_array);
     HypreFree(bii_array);
     HypreFree(bij_array);
     HypreFree(aknum_array);
     HypreFree(aki_array);
   }
 
+  HYPRE_Int size() const { return nb; }
+
+  /// Copy boundary-row entries from an existing full-space vector.
+  BCValuesPtr copyBoundaryRowValues(const HYPRE_Complex* values) const;
+
+  /// Evaluate the original boundary equations using the supplied full-space vector.
+  BCValuesPtr evaluateBoundaryEquations(const HYPRE_Complex* values) const;
+
   /// Applies in-place modification of the rhs array.
   ///
-  /// Returns an array of boundary values that can be used to apply
-  /// boundary conditions to a solution vector.
-  BCValuesPtr adjustBCRightHandSideEquations(HYPRE_Complex* rhs);
+  /// Returns boundary values needed to reconstruct the full-space solution.
+  BCValuesPtr reduceRightHandSideInPlace(HYPRE_Complex* rhs) const;
 
   /// Apply boundary conditions to the solution.
-  /// Uses the BCValuesPtr returned from adjustBCRightHandSideEquations()
-  void adjustBCSolutionEquations(BCValuesPtr brhs, HYPRE_Complex* solution);
+  /// Uses the BCValuesPtr returned from reduceRightHandSideInPlace()
+  void expandSolutionInPlace(BCValuesPtr brhs, HYPRE_Complex* solution) const;
+
+  /// Reconstruct the action of the full operator from the reduced matrix-vector product.
+  void expandMatvecResultInPlace(BCValuesPtr boundary_operator_values,
+                                 BCValuesPtr full_boundary_values,
+                                 HYPRE_Complex* result) const;
+};
+
+/// A shared pointer to a BoundaryElimination object
+using BoundaryEliminationPtr = std::shared_ptr<BoundaryElimination>;
+
+struct BoundaryEliminationState {
+  BCValuesPtr interior_values;
+  BCValuesPtr boundary_values;
 };
 
-/// A shared pointer to a BCMatrixEquations object
-using BCMatrixPtr = std::shared_ptr<BCMatrixEquations>;
+enum class HypreVectorReadMode { standard, solution, matvec };
 
 template <class T>
 class HypreVector {
@@ -185,6 +209,8 @@ class HypreVector {
   bool have_indices{false};
   HYPRE_BigInt* I{nullptr};
   HYPRE_Complex* V{nullptr};
+  HYPRE_Complex* workV{nullptr};
+  bool cache_current{false};
   HypreLib hyprelib{};
 
 public:
@@ -201,6 +227,7 @@ public:
     checkHypreError(HYPRE_IJVectorDestroy(hypre_vector));
     HypreFree(I);
     HypreFree(V);
+    HypreFree(workV);
   }
 
   // Disable copy, at least for now: not clear that HYPRE_IJVector is
@@ -212,13 +239,15 @@ public:
       : comm(other.comm), jlower(other.jlower), jupper(other.jupper), vsize(other.vsize),
         indexConverter(other.indexConverter), location(other.location),
         initialised(other.initialised), have_indices(other.have_indices), I(other.I),
-        V(other.V) {
+        V(other.V), workV(other.workV), cache_current(other.cache_current) {
     std::swap(hypre_vector, other.hypre_vector);
     std::swap(parallel_vector, other.parallel_vector);
     other.initialised = false;
     other.have_indices = false;
     other.I = nullptr;
     other.V = nullptr;
+    other.workV = nullptr;
+    other.cache_current = false;
   }
 
   HypreVector<T>& operator=(HypreVector<T>&& other) noexcept {
@@ -236,8 +265,12 @@ public:
     other.have_indices = false;
     I = other.I;
     V = other.V;
+    workV = other.workV;
+    cache_current = other.cache_current;
     other.I = nullptr;
     other.V = nullptr;
+    other.workV = nullptr;
+    other.cache_current = false;
     return *this;
   }
 
@@ -267,7 +300,9 @@ public:
     initialised = true;
     HypreMalloc(I, vsize * sizeof(HYPRE_BigInt));
     HypreMalloc(V, vsize * sizeof(HYPRE_Complex));
+    HypreMalloc(workV, vsize * sizeof(HYPRE_Complex));
     importValuesFromField(f);
+    assemble();
   }
 
   /// Construct a vector with given index set, but don't set any values
@@ -287,40 +322,70 @@ public:
     location = CELL_LOC::centre;
     HypreMalloc(I, vsize * sizeof(HYPRE_BigInt));
     HypreMalloc(V, vsize * sizeof(HYPRE_Complex));
+    HypreMalloc(workV, vsize * sizeof(HYPRE_Complex));
   }
 
-  // Data for eliminating boundary equation
-  bool elimBErhs = false;
-  bool elimBEsol = false;
-  BCMatrixPtr bcmatrix;
-  BCValuesPtr bcvalues; /// Stores rhs values of BC rows
-
-  void syncElimBErhs(HypreVector<T>& rhs) { bcvalues = rhs.bcvalues; }
-
-  void assemble() {
+  void assemble(const BoundaryElimination* boundary_elimination = nullptr,
+                BoundaryEliminationState* elimination_state = nullptr) {
     CALI_CXX_MARK_FUNCTION;
 
-    // Should not already be assembled
-    ASSERT1(parallel_vector == nullptr);
-
-    writeCacheToHypre();
+    parallel_vector = nullptr;
+    checkHypreError(HYPRE_IJVectorInitialize(hypre_vector));
+    writeCacheToHypre(boundary_elimination, elimination_state);
     checkHypreError(HYPRE_IJVectorAssemble(hypre_vector));
     checkHypreError(HYPRE_IJVectorGetObject(hypre_vector,
                                             reinterpret_cast<void**>(&parallel_vector)));
+    cache_current = true;
   }
 
-  void writeCacheToHypre() {
-    if (elimBErhs) {
-      bcvalues = bcmatrix->adjustBCRightHandSideEquations(V);
+  void writeCacheToHypre(const BoundaryElimination* boundary_elimination = nullptr,
+                         BoundaryEliminationState* elimination_state = nullptr) {
+    HYPRE_Complex* values = V;
+    if (boundary_elimination != nullptr) {
+      ASSERT1(elimination_state != nullptr);
+      std::copy(V, V + vsize, workV);
+      values = workV;
+      elimination_state->interior_values =
+          boundary_elimination->reduceRightHandSideInPlace(values);
+      elimination_state->boundary_values = elimination_state->interior_values;
+    } else if (elimination_state != nullptr) {
+      elimination_state->interior_values = nullptr;
+      elimination_state->boundary_values = nullptr;
     }
-    checkHypreError(HYPRE_IJVectorSetValues(hypre_vector, vsize, I, V));
+    checkHypreError(HYPRE_IJVectorSetValues(hypre_vector, vsize, I, values));
   }
 
-  void readCacheFromHypre() {
-    checkHypreError(HYPRE_IJVectorGetValues(hypre_vector, vsize, I, V));
-    if (elimBEsol) {
-      bcmatrix->adjustBCSolutionEquations(bcvalues, V);
+  void readCacheFromHypre(const BoundaryElimination* boundary_elimination = nullptr,
+                          const BoundaryEliminationState* elimination_state = nullptr,
+                          HypreVectorReadMode mode = HypreVectorReadMode::standard) {
+    HYPRE_Complex* values = V;
+    if ((boundary_elimination != nullptr) and (mode != HypreVectorReadMode::standard)) {
+      values = workV;
+    }
+    checkHypreError(HYPRE_IJVectorGetValues(hypre_vector, vsize, I, values));
+    if (boundary_elimination != nullptr) {
+      switch (mode) {
+      case HypreVectorReadMode::standard:
+        break;
+      case HypreVectorReadMode::solution:
+        ASSERT1(elimination_state != nullptr);
+        ASSERT1(elimination_state->interior_values != nullptr);
+        boundary_elimination->expandSolutionInPlace(elimination_state->interior_values,
+                                                    values);
+        std::copy(values, values + vsize, V);
+        break;
+      case HypreVectorReadMode::matvec:
+        ASSERT1(elimination_state != nullptr);
+        ASSERT1(elimination_state->interior_values != nullptr);
+        ASSERT1(elimination_state->boundary_values != nullptr);
+        boundary_elimination->expandMatvecResultInPlace(
+            elimination_state->interior_values, elimination_state->boundary_values,
+            values);
+        std::copy(values, values + vsize, V);
+        break;
+      }
     }
+    cache_current = true;
   }
 
   T toField() {
@@ -329,7 +394,9 @@ public:
     T result(indexConverter->getMesh());
     result.allocate().setLocation(location);
 
-    readCacheFromHypre();
+    if ((!cache_current) and (parallel_vector != nullptr)) {
+      readCacheFromHypre();
+    }
     // Note that this only populates boundaries to a depth of 1
     int count = 0;
     BOUT_FOR_SERIAL(i, indexConverter->getRegionAll()) {
@@ -359,10 +426,12 @@ public:
 
     ASSERT2(vec_i == vsize);
     have_indices = true;
+    cache_current = true;
   }
 
   HYPRE_IJVector get() { return hypre_vector; }
   const HYPRE_IJVector& get() const { return hypre_vector; }
+  const HYPRE_Complex* getValues() const { return V; }
 
   HYPRE_ParVector getParallel() {
     ASSERT1(parallel_vector != nullptr);
@@ -410,6 +479,7 @@ public:
       ASSERT3(std::isfinite(value_));
       value = value_;
       vector->V[vec_i] = value_;
+      vector->cache_current = true;
       return *this;
     }
     Element& operator+=(BoutReal value_) {
@@ -417,6 +487,7 @@ public:
       value += value_;
       ASSERT3(std::isfinite(value));
       vector->V[vec_i] += value_;
+      vector->cache_current = true;
       return *this;
     }
     operator BoutReal() const { return value; }
@@ -439,11 +510,20 @@ public:
 
   friend void swap(HypreVector<T>& lhs, HypreVector<T>& rhs) {
     using std::swap;
+    swap(lhs.comm, rhs.comm);
+    swap(lhs.jlower, rhs.jlower);
+    swap(lhs.jupper, rhs.jupper);
+    swap(lhs.vsize, rhs.vsize);
     swap(lhs.hypre_vector, rhs.hypre_vector);
     swap(lhs.parallel_vector, rhs.parallel_vector);
     swap(lhs.indexConverter, rhs.indexConverter);
     swap(lhs.location, rhs.location);
     swap(lhs.initialised, rhs.initialised);
+    swap(lhs.have_indices, rhs.have_indices);
+    swap(lhs.I, rhs.I);
+    swap(lhs.V, rhs.V);
+    swap(lhs.workV, rhs.workV);
+    swap(lhs.cache_current, rhs.cache_current);
   }
 };
 
@@ -463,6 +543,8 @@ class HypreMatrix {
   std::vector<HYPRE_BigInt>* I;
   std::vector<std::vector<HYPRE_BigInt>>* J;
   std::vector<std::vector<HYPRE_Complex>>* V;
+  bool elimBE{false};
+  BoundaryEliminationPtr boundary_elimination;
   HypreLib hyprelib{};
 
   // todo also take care of I,J,V
@@ -486,7 +568,8 @@ public:
         index_converter(other.index_converter), location(other.location),
         initialised(other.initialised), yoffset(other.yoffset),
         parallel_transform(other.parallel_transform), assembled(other.assembled),
-        num_rows(other.num_rows), I(other.I), J(other.J), V(other.V) {
+        num_rows(other.num_rows), I(other.I), J(other.J), V(other.V),
+        elimBE(other.elimBE), boundary_elimination(other.boundary_elimination) {
     std::swap(hypre_matrix, other.hypre_matrix);
     std::swap(parallel_matrix, other.parallel_matrix);
   }
@@ -507,6 +590,8 @@ public:
     I = other.I;
     J = other.J;
     V = other.V;
+    elimBE = other.elimBE;
+    boundary_elimination = other.boundary_elimination;
     return *this;
   }
 
@@ -805,33 +890,21 @@ public:
     return Element(*this, global_row, global_column, positions, weights);
   }
 
-  // Data for eliminating boundary equations
-  bool elimBE = false;
-  BCMatrixPtr bcmatrix; // Shared pointer
-
   void setElimBE() { elimBE = true; }
 
-  void setElimBEVectors(HypreVector<T>& sol, HypreVector<T>& rhs) {
-    sol.elimBEsol = elimBE;
-    sol.bcmatrix = bcmatrix;
-
-    rhs.elimBErhs = elimBE;
-    rhs.bcmatrix = bcmatrix;
-  }
-
   void assemble() {
     CALI_CXX_MARK_FUNCTION;
 
     HYPRE_BigInt num_entries = 0;
-    HYPRE_BigInt* num_cols;
+    HYPRE_Int* num_cols;
     HYPRE_BigInt* cols;
     HYPRE_BigInt* rawI;
     HYPRE_Complex* vals;
 
-    HypreMalloc(num_cols, num_rows * sizeof(HYPRE_BigInt));
+    HypreMalloc(num_cols, num_rows * sizeof(HYPRE_Int));
     for (HYPRE_BigInt i = 0; i < num_rows; ++i) {
-      num_cols[i] = (*J)[i].size();
-      num_entries += (*J)[i].size();
+      num_cols[i] = static_cast<HYPRE_Int>((*J)[i].size());
+      num_entries += num_cols[i];
     }
 
     HypreMalloc(rawI, num_rows * sizeof(HYPRE_BigInt));
@@ -862,7 +935,7 @@ public:
         nb++;
       }
 
-      bcmatrix = std::make_shared<BCMatrixEquations>(
+      boundary_elimination = std::make_shared<BoundaryElimination>(
           num_rows, num_cols, rawI, &row_indexes, cols, vals, nb, bi_array);
       HypreFree(bi_array);
 
@@ -870,6 +943,7 @@ public:
                                                row_indexes, cols, vals));
       HypreFree(row_indexes);
     } else {
+      boundary_elimination = nullptr;
       checkHypreError(
           HYPRE_IJMatrixSetValues(*hypre_matrix, num_rows, num_cols, rawI, cols, vals));
     }
@@ -917,12 +991,17 @@ public:
     result.I = I; // We want the pointer to transfer so this works like a view
     result.J = J;
     result.V = V;
+    result.elimBE = elimBE;
+    result.boundary_elimination = boundary_elimination;
 
     return result;
   }
 
   HYPRE_IJMatrix get() { return *hypre_matrix; }
   const HYPRE_IJMatrix& get() const { return *hypre_matrix; }
+  const BoundaryElimination* getBoundaryElimination() const {
+    return boundary_elimination.get();
+  }
 
   HYPRE_ParCSRMatrix getParallel() { return parallel_matrix; }
   const HYPRE_ParCSRMatrix& getParallel() const { return parallel_matrix; }
@@ -932,8 +1011,33 @@ public:
   void computeAxpby(double alpha, HypreVector<T>& x, double beta, HypreVector<T>& y) {
     CALI_CXX_MARK_FUNCTION;
 
+    BoundaryEliminationState elimination_state;
+    if (boundary_elimination != nullptr) {
+      elimination_state.interior_values =
+          boundary_elimination->evaluateBoundaryEquations(x.getValues());
+      elimination_state.boundary_values =
+          std::make_shared<HypreComplexArray>(boundary_elimination->size());
+      BCValuesPtr y_boundary_values;
+      if (beta != 0.0) {
+        y_boundary_values = boundary_elimination->copyBoundaryRowValues(y.getValues());
+      }
+      for (HYPRE_Int i = 0; i < boundary_elimination->size(); ++i) {
+        const HYPRE_Complex operator_value = elimination_state.interior_values->data[i];
+        elimination_state.interior_values->data[i] = alpha * operator_value;
+        elimination_state.boundary_values->data[i] =
+            alpha * operator_value
+            + (y_boundary_values != nullptr ? beta * y_boundary_values->data[i] : 0.0);
+      }
+    }
+
+    x.assemble();
+    y.assemble();
     checkHypreError(HYPRE_ParCSRMatrixMatvec(alpha, parallel_matrix, x.getParallel(),
                                              beta, y.getParallel()));
+    y.readCacheFromHypre(boundary_elimination.get(),
+                         boundary_elimination != nullptr ? &elimination_state : nullptr,
+                         boundary_elimination != nullptr ? HypreVectorReadMode::matvec
+                                                         : HypreVectorReadMode::standard);
   }
 
   // y = A*x
@@ -941,8 +1045,7 @@ public:
   void computeAx(HypreVector<T>& x, HypreVector<T>& y) {
     CALI_CXX_MARK_FUNCTION;
 
-    checkHypreError(HYPRE_ParCSRMatrixMatvec(1.0, parallel_matrix, x.getParallel(), 0.0,
-                                             y.getParallel()));
+    computeAxpby(1.0, x, 0.0, y);
   }
 };
 
@@ -1161,6 +1264,11 @@ public:
     ASSERT2(A != nullptr);
     ASSERT2(x != nullptr);
     ASSERT2(b != nullptr);
+    BoundaryEliminationState elimination_state;
+    const auto* boundary_elimination = A->getBoundaryElimination();
+    b->assemble(boundary_elimination,
+                boundary_elimination != nullptr ? &elimination_state : nullptr);
+    x->assemble();
     if (not solver_setup) {
       checkHypreError(
           solverSetup(solver, A->getParallel(), b->getParallel(), x->getParallel()));
@@ -1170,6 +1278,12 @@ public:
     solve_err = checkHypreError(
         solverSolve(solver, A->getParallel(), b->getParallel(), x->getParallel()));
 
+    x->readCacheFromHypre(boundary_elimination,
+                          boundary_elimination != nullptr ? &elimination_state : nullptr,
+                          boundary_elimination != nullptr
+                              ? HypreVectorReadMode::solution
+                              : HypreVectorReadMode::standard);
+
     return solve_err;
   }
 }; // class HypreSystem
diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
index 05e2ddd83f..f7ae40ed39 100644
--- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
+++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
@@ -226,14 +226,8 @@ Field3D LaplaceHypre3d::solve(const Field3D& b_in, const Field3D& x0) {
 
   CALI_MARK_BEGIN("LaplaceHypre3d_solve:vectorAssemble");
 
-  operator3D.setElimBEVectors(solution, rhs);
-
   rhs.importValuesFromField(b);
   solution.importValuesFromField(x0);
-  rhs.assemble();
-  solution.assemble();
-
-  solution.syncElimBErhs(rhs);
 
   CALI_MARK_END("LaplaceHypre3d_solve:vectorAssemble");
 
diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx
index d58ef6f688..a5ecaab45e 100644
--- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx
+++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.hxx
@@ -145,7 +145,7 @@ public:
   }
 
   // Return a reference to the matrix objects representing the Laplace
-  // operator. These will be (re)construct if necessary.
+  // operator. These will be (re)constructed if necessary.
   bout::HypreMatrix<Field3D>& getMatrix3D();
   IndexerPtr<Field3D> getIndexer() { return indexer; }
 
diff --git a/src/sys/hypre_interface.cxx b/src/sys/hypre_interface.cxx
index d90392cf1e..a70848f56a 100644
--- a/src/sys/hypre_interface.cxx
+++ b/src/sys/hypre_interface.cxx
@@ -5,14 +5,25 @@
 
 #include "bout/hypre_interface.hxx"
 
+#include <numeric>
+
 namespace bout {
 
-BCMatrixEquations::BCMatrixEquations(HYPRE_Int nrows, HYPRE_Int* ncols,
-                                     HYPRE_BigInt* rows, HYPRE_Int** row_indexes_ptr,
-                                     HYPRE_BigInt* cols, HYPRE_Complex* values,
-                                     HYPRE_Int nb, HYPRE_Int* bi_array)
+BoundaryElimination::BoundaryElimination(HYPRE_Int nrows, HYPRE_Int* ncols,
+                                         HYPRE_BigInt* rows, HYPRE_Int** row_indexes_ptr,
+                                         HYPRE_BigInt* cols, HYPRE_Complex* values,
+                                         HYPRE_Int nb, HYPRE_Int* bi_array)
     : nb(nb) {
   HYPRE_Int* row_indexes;
+  const auto find_local_row = [nrows, rows](HYPRE_BigInt row) -> HYPRE_Int {
+    auto row_position = std::lower_bound(rows, rows + nrows, row);
+    if ((row_position == rows + nrows) || (*row_position != row)) {
+      throw BoutException("Could not find local row {} while constructing boundary "
+                          "elimination data",
+                          row);
+    }
+    return static_cast<HYPRE_Int>(std::distance(rows, row_position));
+  };
 
   // Create the row_indexes array
   HypreMalloc(row_indexes, sizeof(HYPRE_Int) * nrows);
@@ -27,22 +38,21 @@ BCMatrixEquations::BCMatrixEquations(HYPRE_Int nrows, HYPRE_Int* ncols,
   // Allocate arrays
   HypreMalloc(binum_array, sizeof(HYPRE_Int) * nb);
   HypreMalloc(bjnum_array, sizeof(HYPRE_Int) * nb);
+  HypreMalloc(bdep_array, sizeof(HYPRE_Int) * nb);
   HypreMalloc(bii_array, sizeof(HYPRE_Complex) * nb);
   HypreMalloc(bij_array, sizeof(HYPRE_Complex) * nb);
   HypreMalloc(aknum_array, sizeof(HYPRE_Int) * na);
   HypreMalloc(aki_array, sizeof(HYPRE_Complex) * na);
 
-  HYPRE_Int binum = 0;
-  HYPRE_Int aknum = 0;
+  std::vector<HYPRE_Int> boundary_at_row(nrows, -1);
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    boundary_at_row[find_local_row(bi_array[bnum])] = bnum;
+  }
+
   for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
     // Get boundary equation information and adjust boundary equations
-    // Find row i in rows array (assume i increases and rows is sorted)
     HYPRE_Int i = bi_array[bnum];
-    for (; binum < nrows; binum++) {
-      if (i == rows[binum]) {
-        break; // Found row i in rows array
-      }
-    }
+    const HYPRE_Int binum = find_local_row(i);
     HYPRE_Int bcoeffnum = row_indexes[binum];
     HYPRE_Complex bii{0.0}, bij{0.0};
     HYPRE_Int j = 0;
@@ -60,13 +70,8 @@ BCMatrixEquations::BCMatrixEquations(HYPRE_Int nrows, HYPRE_Int* ncols,
     ncols[binum] = 1; // Identity equation
 
     /* Get interior equation information and adjust interior equations */
-    /* Find row k in rows array (assume k increases and rows is sorted) */
     HYPRE_Int k = j; // Assume equation k = j
-    for (; aknum < nrows; aknum++) {
-      if (k == rows[aknum]) {
-        break; // Found row k in rows array
-      }
-    }
+    const HYPRE_Int aknum = find_local_row(k);
     HYPRE_Int acoeffnum = row_indexes[aknum];
 
     HYPRE_Int mkj = 0;
@@ -86,39 +91,91 @@ BCMatrixEquations::BCMatrixEquations(HYPRE_Int nrows, HYPRE_Int* ncols,
     HYPRE_Int anum = bnum; // Assume only one interior equation k
     binum_array[bnum] = binum;
     bjnum_array[bnum] = aknum; // Assume only one interior equation k
+    bdep_array[bnum] = boundary_at_row[aknum];
     bii_array[bnum] = bii;
     bij_array[bnum] = bij;
     aknum_array[anum] = aknum;
     aki_array[anum] = aki;
   }
 
+  std::vector<HYPRE_Int> dependency_depth(nb, -1);
+  const auto get_depth = [&dependency_depth, this](const auto& self,
+                                                   HYPRE_Int bnum) -> HYPRE_Int {
+    if (dependency_depth[bnum] >= 0) {
+      return dependency_depth[bnum];
+    }
+    const HYPRE_Int dep = bdep_array[bnum];
+    if (dep < 0) {
+      dependency_depth[bnum] = 0;
+    } else {
+      dependency_depth[bnum] = 1 + self(self, dep);
+    }
+    return dependency_depth[bnum];
+  };
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    get_depth(get_depth, bnum);
+  }
+
+  expansion_order.resize(nb);
+  std::iota(expansion_order.begin(), expansion_order.end(), 0);
+  std::sort(expansion_order.begin(), expansion_order.end(),
+            [&dependency_depth](HYPRE_Int lhs, HYPRE_Int rhs) {
+              if (dependency_depth[lhs] != dependency_depth[rhs]) {
+                return dependency_depth[lhs] < dependency_depth[rhs];
+              }
+              return lhs < rhs;
+            });
+  reduction_order = expansion_order;
+  std::reverse(reduction_order.begin(), reduction_order.end());
+
   // Set return arguments
   *row_indexes_ptr = row_indexes;
 }
 
-BCValuesPtr BCMatrixEquations::adjustBCRightHandSideEquations(HYPRE_Complex* rhs) {
+BCValuesPtr
+BoundaryElimination::copyBoundaryRowValues(const HYPRE_Complex* values) const {
+  BCValuesPtr boundary_values = std::make_shared<HypreComplexArray>(nb);
 
-  // Allocate array to store boundary row values
-  BCValuesPtr brhs = std::make_shared<HypreComplexArray>(nb);
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    boundary_values->data[bnum] = values[binum_array[bnum]];
+  }
+
+  return boundary_values;
+}
+
+BCValuesPtr
+BoundaryElimination::evaluateBoundaryEquations(const HYPRE_Complex* values) const {
+  BCValuesPtr boundary_values = std::make_shared<HypreComplexArray>(nb);
 
   for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
-    HYPRE_Int binum = binum_array[bnum];
-    brhs->data[bnum] = rhs[binum];
+    boundary_values->data[bnum] = (bii_array[bnum] * values[binum_array[bnum]])
+                                  + (bij_array[bnum] * values[bjnum_array[bnum]]);
   }
 
-  for (HYPRE_Int anum = 0; anum < na; anum++) {
-    HYPRE_Int bnum = anum; // Assume only one interior equation per boundary equation
+  return boundary_values;
+}
+
+BCValuesPtr BoundaryElimination::reduceRightHandSideInPlace(HYPRE_Complex* rhs) const {
+
+  // Allocate array to store boundary row values
+  BCValuesPtr brhs = copyBoundaryRowValues(rhs);
+
+  for (HYPRE_Int bnum : reduction_order) {
+    HYPRE_Int anum = bnum; // Assume only one interior equation per boundary equation
     HYPRE_Int aknum = aknum_array[anum];
     rhs[aknum] -= aki_array[anum] * brhs->data[bnum] / bii_array[bnum];
+    if (bdep_array[bnum] >= 0) {
+      brhs->data[bdep_array[bnum]] = rhs[aknum];
+    }
   }
 
   return brhs;
 }
 
-void BCMatrixEquations::adjustBCSolutionEquations(BCValuesPtr brhs,
-                                                  HYPRE_Complex* solution) {
+void BoundaryElimination::expandSolutionInPlace(BCValuesPtr brhs,
+                                                HYPRE_Complex* solution) const {
 
-  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+  for (HYPRE_Int bnum : expansion_order) {
     HYPRE_Int binum = binum_array[bnum];
     HYPRE_Int bjnum = bjnum_array[bnum];
     solution[binum] =
@@ -126,6 +183,21 @@ void BCMatrixEquations::adjustBCSolutionEquations(BCValuesPtr brhs,
   }
 }
 
+void BoundaryElimination::expandMatvecResultInPlace(BCValuesPtr boundary_operator_values,
+                                                    BCValuesPtr full_boundary_values,
+                                                    HYPRE_Complex* result) const {
+  for (HYPRE_Int anum = 0; anum < na; anum++) {
+    HYPRE_Int bnum = anum; // Assume only one interior equation per boundary equation
+    HYPRE_Int aknum = aknum_array[anum];
+    result[aknum] +=
+        aki_array[anum] * boundary_operator_values->data[bnum] / bii_array[bnum];
+  }
+
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    result[binum_array[bnum]] = full_boundary_values->data[bnum];
+  }
+}
+
 } // namespace bout
 
 #endif // BOUT_HAS_HYPRE
diff --git a/tests/unit/include/bout/test_hypre_interface.cxx b/tests/unit/include/bout/test_hypre_interface.cxx
index ec22140647..1d83ae2734 100644
--- a/tests/unit/include/bout/test_hypre_interface.cxx
+++ b/tests/unit/include/bout/test_hypre_interface.cxx
@@ -1,15 +1,19 @@
+#include "bout/build_defines.hxx"
+
 #if BOUT_HAS_HYPRE
 
 #include "HYPRE.h"
 #include "HYPRE_IJ_mv.h"
 #include "HYPRE_parcsr_ls.h"
 
+#include <array>
 #include <cmath>
+#include <set>
+#include <vector>
 
 #include "fake_mesh_fixture.hxx"
 #include "test_extras.hxx"
 
-#include "gmock/gmock.h"
 #include "gtest/gtest.h"
 
 #include "bout/field3d.hxx"
@@ -154,13 +158,30 @@ TYPED_TEST(HypreVectorTest, Swap) {
 //////////////////////////////////////////////////
 // HypreMatrix tests
 
-class MockTransform : public ParallelTransformIdentity {
+class TestParallelTransform : public ParallelTransformIdentity {
 public:
-  explicit MockTransform(Mesh& mesh_in) : ParallelTransformIdentity(mesh_in){};
-  MOCK_METHOD(std::vector<PositionsAndWeights>, getWeightsForYUpApproximation,
-              (int i, int j, int k), (override));
-  MOCK_METHOD(std::vector<PositionsAndWeights>, getWeightsForYDownApproximation,
-              (int i, int j, int k), (override));
+  explicit TestParallelTransform(Mesh& mesh_in) : ParallelTransformIdentity(mesh_in) {}
+
+  std::vector<PositionsAndWeights> getWeightsForYUpApproximation(int i, int j,
+                                                                 int k) override {
+    last_up = {i, j, k};
+    up_calls += 1;
+    return y_up_weights;
+  }
+
+  std::vector<PositionsAndWeights> getWeightsForYDownApproximation(int i, int j,
+                                                                   int k) override {
+    last_down = {i, j, k};
+    down_calls += 1;
+    return y_down_weights;
+  }
+
+  std::vector<PositionsAndWeights> y_up_weights;
+  std::vector<PositionsAndWeights> y_down_weights;
+  std::array<int, 3> last_up{-1, -1, -1};
+  std::array<int, 3> last_down{-1, -1, -1};
+  int up_calls{0};
+  int down_calls{0};
 };
 
 template <class T>
@@ -169,7 +190,7 @@ class HypreMatrixTest : public FakeMeshFixture {
   WithQuietOutput all{output};
   T field;
   IndexerPtr<T> indexer;
-  MockTransform* pt{nullptr};
+  TestParallelTransform* pt{nullptr};
   std::vector<ParallelTransform::PositionsAndWeights> yUpWeights, yDownWeights;
   using ind_type = typename T::ind_type;
   ind_type indexA, indexB, iWU0, iWU1, iWU2, iWD0, iWD1, iWD2;
@@ -199,7 +220,8 @@ class HypreMatrixTest : public FakeMeshFixture {
     iWU1 = indexB;
     iWU2 = indexB.xp();
 
-    auto transform = bout::utils::make_unique<MockTransform>(*bout::globals::mesh);
+    auto transform =
+        bout::utils::make_unique<TestParallelTransform>(*bout::globals::mesh);
     ParallelTransform::PositionsAndWeights wUp0 = {iWU0.x(), iWU0.y(), iWU0.z(), 0.5},
                                            wUp1 = {iWU1.x(), iWU1.y(), iWU1.z(), 1.0},
                                            wUp2 = {iWU2.x(), iWU2.y(), iWU2.z(), 0.5},
@@ -208,8 +230,14 @@ class HypreMatrixTest : public FakeMeshFixture {
                                            wDown2 = {iWD2.x(), iWD2.y(), iWD2.z(), 0.5};
     yUpWeights = {wUp0, wUp1, wUp2};
     yDownWeights = {wDown0, wDown1, wDown2};
-    pt = transform.get();
-    field.getCoordinates()->setParallelTransform(std::move(transform));
+    transform->y_up_weights = yUpWeights;
+    transform->y_down_weights = yDownWeights;
+    bout::globals::mesh->getCoordinates()->setParallelTransform(std::move(transform));
+    pt = dynamic_cast<TestParallelTransform*>(
+        &bout::globals::mesh->getCoordinates()->getParallelTransform());
+    if (pt == nullptr) {
+      throw BoutException("Failed to install TestParallelTransform in HypreMatrixTest");
+    }
   }
   virtual ~HypreMatrixTest() = default;
 };
@@ -307,7 +335,9 @@ TYPED_TEST(HypreMatrixTest, SetElements) {
       HYPRE_Int ncolumns{1};
       HYPRE_Complex value;
       BOUT_OMP_SAFE(critical)
-      { HYPRE_IJMatrixGetValues(raw_matrix, 1, &ncolumns, &i_index, &j_index, &value); }
+      {
+        HYPRE_IJMatrixGetValues(raw_matrix, 1, &ncolumns, &i_index, &j_index, &value);
+      }
       if (i == j) {
         EXPECT_EQ(static_cast<BoutReal>(value),
                   static_cast<BoutReal>(this->indexer->getGlobal(i)));
@@ -382,8 +412,6 @@ auto IsHypreMatrixEqual(const HypreMatrix<T>& matrix, const HypreMatrix<T>& refe
 }
 
 TYPED_TEST(HypreMatrixTest, YUp) {
-  using namespace ::testing;
-
   HypreMatrix<TypeParam> matrix(this->indexer);
 
   if constexpr (std::is_same_v<TypeParam, FieldPerp>) {
@@ -392,15 +420,11 @@ TYPED_TEST(HypreMatrixTest, YUp) {
   }
 
   HypreMatrix<TypeParam> expected(this->indexer);
-  MockTransform* transform = this->pt;
   const BoutReal value = 42.0;
 
   if constexpr (std::is_same_v<TypeParam, Field2D>) {
     expected(this->indexA, this->indexB) = value;
   } else {
-    EXPECT_CALL(*transform, getWeightsForYUpApproximation(
-                                this->indexB.x(), this->indexA.y(), this->indexB.z()))
-        .WillOnce(Return(this->yUpWeights));
     expected(this->indexA, this->iWU0) = this->yUpWeights[0].weight * value;
     expected(this->indexA, this->iWU1) = this->yUpWeights[1].weight * value;
     expected(this->indexA, this->iWU2) = this->yUpWeights[2].weight * value;
@@ -408,6 +432,13 @@ TYPED_TEST(HypreMatrixTest, YUp) {
 
   matrix.yup()(this->indexA, this->indexB) = value;
 
+  if constexpr (std::is_same_v<TypeParam, Field3D>) {
+    EXPECT_EQ(this->pt->up_calls, 1);
+    EXPECT_EQ(this->pt->last_up[0], this->indexB.x());
+    EXPECT_EQ(this->pt->last_up[1], this->indexA.y());
+    EXPECT_EQ(this->pt->last_up[2], this->indexB.z());
+  }
+
   expected.assemble();
   matrix.assemble();
 
@@ -415,8 +446,6 @@ TYPED_TEST(HypreMatrixTest, YUp) {
 }
 
 TYPED_TEST(HypreMatrixTest, YDown) {
-  using namespace ::testing;
-
   HypreMatrix<TypeParam> matrix(this->indexer);
 
   if constexpr (std::is_same_v<TypeParam, FieldPerp>) {
@@ -425,15 +454,11 @@ TYPED_TEST(HypreMatrixTest, YDown) {
   }
 
   HypreMatrix<TypeParam> expected(this->indexer);
-  MockTransform* transform = this->pt;
   const BoutReal value = 42.0;
 
   if constexpr (std::is_same_v<TypeParam, Field2D>) {
     expected(this->indexB, this->indexA) = value;
   } else {
-    EXPECT_CALL(*transform, getWeightsForYDownApproximation(
-                                this->indexA.x(), this->indexB.y(), this->indexA.z()))
-        .WillOnce(Return(this->yDownWeights));
     expected(this->indexB, this->iWD0) = this->yDownWeights[0].weight * value;
     expected(this->indexB, this->iWD1) = this->yDownWeights[1].weight * value;
     expected(this->indexB, this->iWD2) = this->yDownWeights[2].weight * value;
@@ -441,6 +466,13 @@ TYPED_TEST(HypreMatrixTest, YDown) {
 
   matrix.ydown()(this->indexB, this->indexA) = value;
 
+  if constexpr (std::is_same_v<TypeParam, Field3D>) {
+    EXPECT_EQ(this->pt->down_calls, 1);
+    EXPECT_EQ(this->pt->last_down[0], this->indexA.x());
+    EXPECT_EQ(this->pt->last_down[1], this->indexB.y());
+    EXPECT_EQ(this->pt->last_down[2], this->indexA.z());
+  }
+
   expected.assemble();
   matrix.assemble();
 
@@ -462,4 +494,153 @@ TYPED_TEST(HypreMatrixTest, YNext0) {
   EXPECT_TRUE(IsHypreMatrixEqual(matrix, expected));
 }
 
+namespace {
+
+struct RawBoundaryEliminationSystem {
+  std::vector<HYPRE_Int> ncols;
+  std::vector<HYPRE_BigInt> rows;
+  std::vector<HYPRE_BigInt> cols;
+  std::vector<HYPRE_Complex> values;
+  std::vector<HYPRE_Int> boundary_rows;
+  HYPRE_Int* row_indexes{nullptr};
+  std::unique_ptr<bout::BoundaryElimination> elimination;
+
+  RawBoundaryEliminationSystem(std::initializer_list<HYPRE_Int> ncols_in,
+                               std::initializer_list<HYPRE_BigInt> rows_in,
+                               std::initializer_list<HYPRE_BigInt> cols_in,
+                               std::initializer_list<HYPRE_Complex> values_in,
+                               std::initializer_list<HYPRE_Int> boundary_rows_in)
+      : ncols(ncols_in), rows(rows_in), cols(cols_in), values(values_in),
+        boundary_rows(boundary_rows_in) {
+    elimination = std::make_unique<bout::BoundaryElimination>(
+        static_cast<HYPRE_Int>(rows.size()), ncols.data(), rows.data(), &row_indexes,
+        cols.data(), values.data(), static_cast<HYPRE_Int>(boundary_rows.size()),
+        boundary_rows.data());
+  }
+
+  ~RawBoundaryEliminationSystem() {
+    if (row_indexes != nullptr) {
+      HypreFree(row_indexes);
+    }
+  }
+};
+
+RawBoundaryEliminationSystem makeSingleBoundarySystem() {
+  return {{2, 3, 2},
+          {0, 1, 2},
+          {0, 1, 0, 1, 2, 1, 2},
+          {2.0, 3.0, 5.0, 7.0, 11.0, 13.0, 17.0},
+          {0}};
+}
+
+RawBoundaryEliminationSystem makeBackwardCoupledRowSystem() {
+  return {{2, 3, 3, 2},
+          {0, 1, 2, 3},
+          {0, 2, 1, 2, 3, 0, 2, 3, 1, 3},
+          {2.0, 3.0, 31.0, 37.0, 29.0, 5.0, 7.0, 11.0, 23.0, 19.0},
+          {0, 3}};
+}
+
+} // namespace
+
+TEST(BoundaryEliminationTest, TransformsSingleBoundarySystem) {
+  auto system = makeSingleBoundarySystem();
+
+  EXPECT_EQ(system.ncols[0], 1);
+  EXPECT_EQ(system.values[0], -1.0);
+  EXPECT_EQ(system.values[1], 0.0);
+  EXPECT_EQ(system.values[2], 0.0);
+  EXPECT_DOUBLE_EQ(system.values[3], -0.5);
+  EXPECT_EQ(system.values[4], 11.0);
+  EXPECT_EQ(system.values[5], 13.0);
+  EXPECT_EQ(system.values[6], 17.0);
+
+  ASSERT_NE(system.elimination, nullptr);
+  EXPECT_EQ(system.elimination->binum_array[0], 0);
+  EXPECT_EQ(system.elimination->bjnum_array[0], 1);
+  EXPECT_EQ(system.elimination->bdep_array[0], -1);
+  EXPECT_EQ(system.elimination->bii_array[0], 2.0);
+  EXPECT_EQ(system.elimination->bij_array[0], 3.0);
+  EXPECT_EQ(system.elimination->aknum_array[0], 1);
+  EXPECT_EQ(system.elimination->aki_array[0], 5.0);
+}
+
+TEST(BoundaryEliminationTest, ReducesRightHandSideForSingleBoundarySystem) {
+  auto system = makeSingleBoundarySystem();
+  std::array<HYPRE_Complex, 3> rhs{{19.0, 23.0, 29.0}};
+
+  auto brhs = system.elimination->reduceRightHandSideInPlace(rhs.data());
+
+  ASSERT_NE(brhs, nullptr);
+  EXPECT_EQ(brhs->data[0], 19.0);
+  EXPECT_EQ(rhs[0], 19.0);
+  EXPECT_DOUBLE_EQ(rhs[1], -24.5);
+  EXPECT_EQ(rhs[2], 29.0);
+}
+
+TEST(BoundaryEliminationTest, ExpandsSolutionForSingleBoundarySystem) {
+  auto system = makeSingleBoundarySystem();
+  auto brhs = std::make_shared<bout::HypreComplexArray>(1);
+  brhs->data[0] = 19.0;
+  std::array<HYPRE_Complex, 3> solution{{0.0, 2.0, 3.0}};
+
+  system.elimination->expandSolutionInPlace(brhs, solution.data());
+
+  EXPECT_DOUBLE_EQ(solution[0], 6.5);
+  EXPECT_EQ(solution[1], 2.0);
+  EXPECT_EQ(solution[2], 3.0);
+}
+
+TEST(BoundaryEliminationTest, ReconstructsMatvecForSingleBoundarySystem) {
+  auto system = makeSingleBoundarySystem();
+  std::array<HYPRE_Complex, 3> x{{1.0, 2.0, 3.0}};
+  std::array<HYPRE_Complex, 3> reduced_result{{-1.0, 32.0, 77.0}};
+  auto boundary_values = system.elimination->evaluateBoundaryEquations(x.data());
+
+  system.elimination->expandMatvecResultInPlace(boundary_values, boundary_values,
+                                                reduced_result.data());
+
+  EXPECT_EQ(reduced_result[0], 8.0);
+  EXPECT_EQ(reduced_result[1], 52.0);
+  EXPECT_EQ(reduced_result[2], 77.0);
+}
+
+TEST(BoundaryEliminationTest, HandlesBackwardCoupledRows) {
+  auto system = makeBackwardCoupledRowSystem();
+
+  EXPECT_EQ(system.ncols[0], 1);
+  EXPECT_EQ(system.ncols[3], 1);
+  EXPECT_EQ(system.values[0], -1.0);
+  EXPECT_EQ(system.values[1], 0.0);
+  EXPECT_DOUBLE_EQ(system.values[2], 31.0 - (29.0 * 23.0 / 19.0));
+  EXPECT_EQ(system.values[4], 0.0);
+  EXPECT_EQ(system.values[5], 0.0);
+  EXPECT_DOUBLE_EQ(system.values[6], -0.5);
+  EXPECT_EQ(system.values[8], 0.0);
+  EXPECT_EQ(system.values[9], -1.0);
+
+  EXPECT_EQ(system.elimination->aknum_array[0], 2);
+  EXPECT_EQ(system.elimination->aknum_array[1], 1);
+}
+
+TEST(BoundaryEliminationTest, DifferentEliminationObjectsProduceDifferentReducedSystems) {
+  auto system_a = makeSingleBoundarySystem();
+  RawBoundaryEliminationSystem system_b{{2, 3, 2},
+                                        {0, 1, 2},
+                                        {0, 1, 0, 1, 2, 1, 2},
+                                        {4.0, -1.0, 6.0, 9.0, 10.0, 13.0, 17.0},
+                                        {0}};
+  std::array<HYPRE_Complex, 3> rhs_a{{19.0, 23.0, 29.0}};
+  std::array<HYPRE_Complex, 3> rhs_b = rhs_a;
+
+  auto brhs_a = system_a.elimination->reduceRightHandSideInPlace(rhs_a.data());
+  auto brhs_b = system_b.elimination->reduceRightHandSideInPlace(rhs_b.data());
+
+  EXPECT_EQ(brhs_a->data[0], 19.0);
+  EXPECT_EQ(brhs_b->data[0], 19.0);
+  EXPECT_DOUBLE_EQ(rhs_a[1], -24.5);
+  EXPECT_DOUBLE_EQ(rhs_b[1], -5.5);
+  EXPECT_NE(rhs_a[1], rhs_b[1]);
+}
+
 #endif // BOUT_HAS_HYPRE
diff --git a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
index 92d7b3194b..3924245bad 100644
--- a/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
+++ b/tests/unit/invert/laplace/test_laplace_hypre3d.cxx
@@ -351,6 +351,17 @@ TEST_P(LaplaceHypre3dTest, TestSolve3DGuess) {
   BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) { EXPECT_NEAR(expected[i], actual[i], tol); }
 }
 
+TEST_P(LaplaceHypre3dTest, TestSolve3DRepeated) {
+  const Field3D rhs = forward(f3);
+  const Field3D first = solver.solve(rhs);
+  const Field3D second = solver.solve(rhs);
+
+  BOUT_FOR(i, mesh->getRegion3D("RGN_ALL")) {
+    EXPECT_NEAR(f3[i], first[i], tol);
+    EXPECT_NEAR(f3[i], second[i], tol);
+  }
+}
+
 TEST_P(LaplaceHypre3dTest, TestSolvePerp) {
   FieldPerp f(1.0);
   EXPECT_THROW(solver.solve(f), BoutException);

From 4100f8828b990ace616793559d2cc97ff808031b Mon Sep 17 00:00:00 2001
From: totork <ttork96@gmail.com>
Date: Mon, 17 Aug 2026 09:31:03 +0200
Subject: [PATCH 1713/1827] Adjust parallel diffusion operator for fci

---
 src/mesh/difops.cxx | 21 +++++++--------------
 1 file changed, 7 insertions(+), 14 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index e6913a67eb..c1c89628b9 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -385,32 +385,25 @@ Field3D Div_par_K_Grad_par_mod_impl(const Field3DParallel& Kin,
 
     Field3D result{zeroFrom(fin)};
     flow_ylow = zeroFrom(fin);
-
+    
     BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
       const auto iyp = i.yp();
       const auto iym = i.ym();
 
       // Upper cell edge
       const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]); // K at the upper boundary
-      const BoutReal J_up =
-          0.5 * (coord->J()[i] + coord->J().yup()[iyp]); // Jacobian at boundary
-      const BoutReal g_22_up = 0.5 * (coord->g_22()[i] + coord->g_22().yup()[iyp]);
-      const BoutReal gradient_up =
-          2. * (f_up[iyp] - fin[i]) / (coord->dy()[i] + coord->dy().yup()[iyp]);
+      const BoutReal gradient_up = (f_up[iyp] - fin[i]) / (coord->dy()[i] * sqrt(g_22_yhigh()[i]));
 
-      const BoutReal flux_up = c_up * J_up * gradient_up / g_22_up;
+      const BoutReal flux_up = c_up * gradient_up * coord->cell_area_yhigh()[i];
 
       // Lower cell edge
       const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]); // K at the lower boundary
-      const BoutReal J_down =
-          0.5 * (coord->J()[i] + coord->J().ydown()[iym]); // Jacobian at boundary
-      const BoutReal g_22_down = 0.5 * (coord->g_22()[i] + coord->g_22().ydown()[iym]);
-      const BoutReal gradient_down =
-          2. * (fin[i] - f_down[iym]) / (coord->dy()[i] + coord->dy().ydown()[iym]);
+      const BoutReal gradient_down = (fin[i] - f_down[iym]) / (coord->dy()[i] * sqrt(g_22_ylow()[i]));
 
-      const BoutReal flux_down = c_down * J_down * gradient_down / g_22_down;
+      const BoutReal flux_down = c_down * gradient_down * coord->cell_area_ylow()[i];
 
-      result[i] = (flux_up - flux_down) / (coord->dy()[i] * coord->J()[i]);
+      // Add the fluxes
+      result[i] = (flux_up - flux_down) / (coord->cell_volume()[i]);
     }
 
     return result;

From 6ba4f1d5a6816870a999e4439a9b5f80f056b66a Mon Sep 17 00:00:00 2001
From: totork <ttork96@gmail.com>
Date: Mon, 17 Aug 2026 09:38:18 +0200
Subject: [PATCH 1714/1827] Add missing class

---
 src/mesh/difops.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index c1c89628b9..66f388c805 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -392,13 +392,13 @@ Field3D Div_par_K_Grad_par_mod_impl(const Field3DParallel& Kin,
 
       // Upper cell edge
       const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]); // K at the upper boundary
-      const BoutReal gradient_up = (f_up[iyp] - fin[i]) / (coord->dy()[i] * sqrt(g_22_yhigh()[i]));
+      const BoutReal gradient_up = (f_up[iyp] - fin[i]) / (coord->dy()[i] * sqrt(coord->g_22_yhigh()[i]));
 
       const BoutReal flux_up = c_up * gradient_up * coord->cell_area_yhigh()[i];
 
       // Lower cell edge
       const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]); // K at the lower boundary
-      const BoutReal gradient_down = (fin[i] - f_down[iym]) / (coord->dy()[i] * sqrt(g_22_ylow()[i]));
+      const BoutReal gradient_down = (fin[i] - f_down[iym]) / (coord->dy()[i] * sqrt(coord->g_22_ylow()[i]));
 
       const BoutReal flux_down = c_down * gradient_down * coord->cell_area_ylow()[i];
 

From 3f35c51e4ff2ce79dff0280faaca96dc76ef846e Mon Sep 17 00:00:00 2001
From: totork <ttork96@gmail.com>
Date: Mon, 17 Aug 2026 09:52:55 +0200
Subject: [PATCH 1715/1827] Delete brackets

---
 src/mesh/difops.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 66f388c805..4def0328e3 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -392,13 +392,13 @@ Field3D Div_par_K_Grad_par_mod_impl(const Field3DParallel& Kin,
 
       // Upper cell edge
       const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]); // K at the upper boundary
-      const BoutReal gradient_up = (f_up[iyp] - fin[i]) / (coord->dy()[i] * sqrt(coord->g_22_yhigh()[i]));
+      const BoutReal gradient_up = (f_up[iyp] - fin[i]) / (coord->dy[i] * sqrt(coord->g_22_yhigh()[i]));
 
       const BoutReal flux_up = c_up * gradient_up * coord->cell_area_yhigh()[i];
 
       // Lower cell edge
       const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]); // K at the lower boundary
-      const BoutReal gradient_down = (fin[i] - f_down[iym]) / (coord->dy()[i] * sqrt(coord->g_22_ylow()[i]));
+      const BoutReal gradient_down = (fin[i] - f_down[iym]) / (coord->dy[i] * sqrt(coord->g_22_ylow()[i]));
 
       const BoutReal flux_down = c_down * gradient_down * coord->cell_area_ylow()[i];
 

From 2111e68726f6dbe3c937aaf5a71a006d75c0b608 Mon Sep 17 00:00:00 2001
From: totork <ttork96@gmail.com>
Date: Mon, 17 Aug 2026 10:02:20 +0200
Subject: [PATCH 1716/1827] Add missing () for dy

---
 src/mesh/difops.cxx | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 4def0328e3..bcd74a622b 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -385,20 +385,22 @@ Field3D Div_par_K_Grad_par_mod_impl(const Field3DParallel& Kin,
 
     Field3D result{zeroFrom(fin)};
     flow_ylow = zeroFrom(fin);
-    
+
     BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
       const auto iyp = i.yp();
       const auto iym = i.ym();
 
       // Upper cell edge
       const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]); // K at the upper boundary
-      const BoutReal gradient_up = (f_up[iyp] - fin[i]) / (coord->dy[i] * sqrt(coord->g_22_yhigh()[i]));
+      const BoutReal gradient_up =
+          (f_up[iyp] - fin[i]) / (coord->dy()[i] * sqrt(coord->g_22_yhigh()[i]));
 
       const BoutReal flux_up = c_up * gradient_up * coord->cell_area_yhigh()[i];
 
       // Lower cell edge
       const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]); // K at the lower boundary
-      const BoutReal gradient_down = (fin[i] - f_down[iym]) / (coord->dy[i] * sqrt(coord->g_22_ylow()[i]));
+      const BoutReal gradient_down =
+          (fin[i] - f_down[iym]) / (coord->dy()[i] * sqrt(coord->g_22_ylow()[i]));
 
       const BoutReal flux_down = c_down * gradient_down * coord->cell_area_ylow()[i];
 

From eddc7e1d36ac7c7e4e71a9ab39e8235e1079bf6a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 17 Aug 2026 12:43:17 +0200
Subject: [PATCH 1717/1827] Avoid returning void from function call

---
 src/mesh/coordinates.cxx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index ee80827094..bacbbe81c4 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1341,7 +1341,8 @@ void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm
 void Coordinates::normaliseMetric(const BoutReal rho_s0, const BoutReal Bnorm) {
   ASSERT2(hasParallelTransform());
   if (Bxy().isFci()) {
-    return normaliseMetricFCI(rho_s0, Bnorm);
+    normaliseMetricFCI(rho_s0, Bnorm);
+    return;
   }
-  return normaliseMetricTokamak(rho_s0, Bnorm);
+  normaliseMetricTokamak(rho_s0, Bnorm);
 }

From 7913512c4959115fd4c509cab4101e104e51a2a6 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 17 Aug 2026 15:36:59 -0700
Subject: [PATCH 1718/1827] Generalize boundary elimination code

Fixes the integrated Laplace-Hypre3D tests.

GPT says: The boundary-elimination logic in [src/sys/hypre_interface.cxx (line
48)](/Users/dudson2/code/BOUT-next/src/sys/hypre_interface.cxx:48) was
only removing each boundary variable from one coupled row; in the
hypre3d stencil, the same Y-boundary value can appear in multiple
nearby rows, especially in the SOL case. I changed BoundaryElimination
to collect all representable row couplings for each boundary equation,
store them with per-boundary offsets, and apply them during matrix
reduction, RHS reduction, and matvec reconstruction. The interface
metadata was updated in [include/bout/hypre_interface.hxx (line
103)](/Users/dudson2/code/BOUT-next/include/bout/hypre_interface.hxx:103),
and I added multi-coupling unit coverage in
[tests/unit/include/bout/test_hypre_interface.cxx (line
618)](/Users/dudson2/code/BOUT-next/tests/unit/include/bout/test_hypre_interface.cxx:618).
---
 include/bout/hypre_interface.hxx              |  12 +-
 src/sys/hypre_interface.cxx                   | 136 +++++++++++++-----
 .../test_laplace_hypre3d.py                   |   2 +-
 .../include/bout/test_hypre_interface.cxx     |  66 +++++++++
 4 files changed, 173 insertions(+), 43 deletions(-)

diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index d71659ca3a..6a53c27f0c 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -103,12 +103,16 @@ using BCValuesPtr = std::shared_ptr<HypreComplexArray>;
  *
  *      b_ii * u_i + b_ij * u_j = rhs_i
  *
- * - We also assume that each boundary equation has only one interior equation k
- *   coupled to it (such that k = j) with coupling coefficient a_ki
+ * - We also assume that each boundary equation has only one retained unknown j
+ *   on the boundary row
+ *
+ *      b_ii * u_i + b_ij * u_j = rhs_i
+ *
+ * - Any number of other equations k may couple to u_i with coefficient a_ki
  *
  *      a_ki * u_i + a_kj * u_j + ... = rhs_k
  *
- * - Each equation k is adjusted as follows:
+ * - Each such equation k is adjusted as follows:
  *
  *      a_kj = a_kj - a_ki * b_ij / b_ii
  *      a_ki = 0
@@ -140,6 +144,7 @@ struct BoundaryElimination {
   HYPRE_Complex* bii_array;
   HYPRE_Complex* bij_array;
   HYPRE_Int na;
+  HYPRE_Int* aoffset_array;
   HYPRE_Int* aknum_array;
   HYPRE_Complex* aki_array;
   std::vector<HYPRE_Int> reduction_order;
@@ -160,6 +165,7 @@ struct BoundaryElimination {
     HypreFree(bdep_array);
     HypreFree(bii_array);
     HypreFree(bij_array);
+    HypreFree(aoffset_array);
     HypreFree(aknum_array);
     HypreFree(aki_array);
   }
diff --git a/src/sys/hypre_interface.cxx b/src/sys/hypre_interface.cxx
index a70848f56a..101484913a 100644
--- a/src/sys/hypre_interface.cxx
+++ b/src/sys/hypre_interface.cxx
@@ -6,6 +6,7 @@
 #include "bout/hypre_interface.hxx"
 
 #include <numeric>
+#include <unordered_map>
 
 namespace bout {
 
@@ -32,32 +33,49 @@ BoundaryElimination::BoundaryElimination(HYPRE_Int nrows, HYPRE_Int* ncols,
     row_indexes[i] = row_indexes[i - 1] + ncols[i - 1];
   }
 
-  // Assume just one interior equation coupled to each boundary equation
-  na = nb;
-
   // Allocate arrays
   HypreMalloc(binum_array, sizeof(HYPRE_Int) * nb);
   HypreMalloc(bjnum_array, sizeof(HYPRE_Int) * nb);
   HypreMalloc(bdep_array, sizeof(HYPRE_Int) * nb);
   HypreMalloc(bii_array, sizeof(HYPRE_Complex) * nb);
   HypreMalloc(bij_array, sizeof(HYPRE_Complex) * nb);
-  HypreMalloc(aknum_array, sizeof(HYPRE_Int) * na);
-  HypreMalloc(aki_array, sizeof(HYPRE_Complex) * na);
 
   std::vector<HYPRE_Int> boundary_at_row(nrows, -1);
   for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
     boundary_at_row[find_local_row(bi_array[bnum])] = bnum;
   }
 
+  struct BoundaryOccurrence {
+    HYPRE_Int rownum;
+    HYPRE_Int row_offset;
+  };
+  std::unordered_map<HYPRE_BigInt, HYPRE_Int> boundary_number_for_row;
+  boundary_number_for_row.reserve(nb);
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    boundary_number_for_row.emplace(bi_array[bnum], bnum);
+  }
+
+  std::vector<std::vector<BoundaryOccurrence>> occurrences_by_boundary(nb);
+  for (HYPRE_Int rownum = 0; rownum < nrows; rownum++) {
+    const HYPRE_Int row_start = row_indexes[rownum];
+    for (HYPRE_Int m = 0; m < ncols[rownum]; m++) {
+      const auto boundary_position = boundary_number_for_row.find(cols[row_start + m]);
+      if (boundary_position != boundary_number_for_row.end()) {
+        occurrences_by_boundary[boundary_position->second].push_back({rownum, m});
+      }
+    }
+  }
+
+  std::vector<HYPRE_BigInt> bjrow_array(nb, -1);
   for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
     // Get boundary equation information and adjust boundary equations
     HYPRE_Int i = bi_array[bnum];
     const HYPRE_Int binum = find_local_row(i);
     HYPRE_Int bcoeffnum = row_indexes[binum];
     HYPRE_Complex bii{0.0}, bij{0.0};
-    HYPRE_Int j = 0;
+    HYPRE_BigInt j = -1;
 
-    for (HYPRE_Int m = 0; m < 2; m++) { // Assume only two boundary equation coefficients
+    for (HYPRE_Int m = 0; m < ncols[binum]; m++) {
       if (cols[bcoeffnum + m] == i) {
         bii = values[bcoeffnum + m];
         values[bcoeffnum + m] = -1.0; // Identity equation (negative definite matrix)
@@ -67,37 +85,75 @@ BoundaryElimination::BoundaryElimination(HYPRE_Int nrows, HYPRE_Int* ncols,
         values[bcoeffnum + m] = 0.0; // Identity equation
       }
     }
-    ncols[binum] = 1; // Identity equation
-
-    /* Get interior equation information and adjust interior equations */
-    HYPRE_Int k = j; // Assume equation k = j
-    const HYPRE_Int aknum = find_local_row(k);
-    HYPRE_Int acoeffnum = row_indexes[aknum];
-
-    HYPRE_Int mkj = 0;
-    HYPRE_Complex aki{0.0};
-    for (HYPRE_Int m = 0; m < ncols[aknum]; m++) {
-      if (cols[acoeffnum + m] == j) {
-        mkj = m; // Save for update of akj value below
-      }
-      if (cols[acoeffnum + m] == i) {
-        aki = values[acoeffnum + m];
-        values[acoeffnum + m] = 0.0; // Eliminate coupling to boundary equation
-      }
+    if (j < 0) {
+      throw BoutException("Boundary row {} does not contain a retained neighbour", i);
+    }
+    if (bii == 0.0) {
+      throw BoutException("Boundary row {} has zero diagonal coefficient", i);
     }
-    values[acoeffnum + mkj] -= aki * bij / bii; // Update akj value
+    ncols[binum] = 1; // Identity equation
 
     // Update arrays
-    HYPRE_Int anum = bnum; // Assume only one interior equation k
     binum_array[bnum] = binum;
-    bjnum_array[bnum] = aknum; // Assume only one interior equation k
-    bdep_array[bnum] = boundary_at_row[aknum];
+    bjnum_array[bnum] = find_local_row(j);
+    bdep_array[bnum] = boundary_at_row[bjnum_array[bnum]];
     bii_array[bnum] = bii;
     bij_array[bnum] = bij;
-    aknum_array[anum] = aknum;
-    aki_array[anum] = aki;
+    bjrow_array[bnum] = j;
   }
 
+  std::vector<HYPRE_Int> aoffsets(nb + 1, 0);
+  std::vector<HYPRE_Int> aknums;
+  std::vector<HYPRE_Complex> akis;
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    const HYPRE_Int binum = binum_array[bnum];
+    const HYPRE_Int bjnum = bjnum_array[bnum];
+    const HYPRE_BigInt j = bjrow_array[bnum];
+
+    for (const auto& occurrence : occurrences_by_boundary[bnum]) {
+      const HYPRE_Int aknum = occurrence.rownum;
+      if (aknum == binum) {
+        continue;
+      }
+      if ((boundary_at_row[aknum] >= 0) && (aknum != bjnum)) {
+        continue;
+      }
+
+      const HYPRE_Int acoeffnum = row_indexes[aknum];
+      const HYPRE_Int aki_position = acoeffnum + occurrence.row_offset;
+      const HYPRE_Complex aki = values[aki_position];
+      if (aki == 0.0) {
+        continue;
+      }
+
+      HYPRE_Int j_position = -1;
+      for (HYPRE_Int m = 0; m < ncols[aknum]; m++) {
+        if (cols[acoeffnum + m] == j) {
+          j_position = acoeffnum + m;
+          break;
+        }
+      }
+      if (j_position < 0) {
+        continue;
+      }
+
+      values[aki_position] = 0.0; // Eliminate coupling to boundary equation
+      values[j_position] -= aki * bij_array[bnum] / bii_array[bnum];
+
+      aknums.push_back(aknum);
+      akis.push_back(aki);
+    }
+    aoffsets[bnum + 1] = static_cast<HYPRE_Int>(aknums.size());
+  }
+
+  na = static_cast<HYPRE_Int>(aknums.size());
+  HypreMalloc(aoffset_array, sizeof(HYPRE_Int) * (nb + 1));
+  std::copy(aoffsets.begin(), aoffsets.end(), aoffset_array);
+  HypreMalloc(aknum_array, sizeof(HYPRE_Int) * na);
+  std::copy(aknums.begin(), aknums.end(), aknum_array);
+  HypreMalloc(aki_array, sizeof(HYPRE_Complex) * na);
+  std::copy(akis.begin(), akis.end(), aki_array);
+
   std::vector<HYPRE_Int> dependency_depth(nb, -1);
   const auto get_depth = [&dependency_depth, this](const auto& self,
                                                    HYPRE_Int bnum) -> HYPRE_Int {
@@ -161,11 +217,12 @@ BCValuesPtr BoundaryElimination::reduceRightHandSideInPlace(HYPRE_Complex* rhs)
   BCValuesPtr brhs = copyBoundaryRowValues(rhs);
 
   for (HYPRE_Int bnum : reduction_order) {
-    HYPRE_Int anum = bnum; // Assume only one interior equation per boundary equation
-    HYPRE_Int aknum = aknum_array[anum];
-    rhs[aknum] -= aki_array[anum] * brhs->data[bnum] / bii_array[bnum];
+    for (HYPRE_Int anum = aoffset_array[bnum]; anum < aoffset_array[bnum + 1]; anum++) {
+      HYPRE_Int aknum = aknum_array[anum];
+      rhs[aknum] -= aki_array[anum] * brhs->data[bnum] / bii_array[bnum];
+    }
     if (bdep_array[bnum] >= 0) {
-      brhs->data[bdep_array[bnum]] = rhs[aknum];
+      brhs->data[bdep_array[bnum]] = rhs[bjnum_array[bnum]];
     }
   }
 
@@ -186,11 +243,12 @@ void BoundaryElimination::expandSolutionInPlace(BCValuesPtr brhs,
 void BoundaryElimination::expandMatvecResultInPlace(BCValuesPtr boundary_operator_values,
                                                     BCValuesPtr full_boundary_values,
                                                     HYPRE_Complex* result) const {
-  for (HYPRE_Int anum = 0; anum < na; anum++) {
-    HYPRE_Int bnum = anum; // Assume only one interior equation per boundary equation
-    HYPRE_Int aknum = aknum_array[anum];
-    result[aknum] +=
-        aki_array[anum] * boundary_operator_values->data[bnum] / bii_array[bnum];
+  for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
+    for (HYPRE_Int anum = aoffset_array[bnum]; anum < aoffset_array[bnum + 1]; anum++) {
+      HYPRE_Int aknum = aknum_array[anum];
+      result[aknum] +=
+          aki_array[anum] * boundary_operator_values->data[bnum] / bii_array[bnum];
+    }
   }
 
   for (HYPRE_Int bnum = 0; bnum < nb; bnum++) {
diff --git a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
index e2fa11c13a..014b91ef00 100755
--- a/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
+++ b/tests/integrated/test-laplace-hypre3d/test_laplace_hypre3d.py
@@ -17,7 +17,7 @@ def test_laplace_hypre3d():
 
     success = True
     for directory, nproc in test_directories:
-        command = "test-laplace3d -d " + directory
+        command = "./test-laplace3d -d " + directory
         print("running on", nproc, "processors:", command)
         launch_safe(command, nproc=nproc)
 
diff --git a/tests/unit/include/bout/test_hypre_interface.cxx b/tests/unit/include/bout/test_hypre_interface.cxx
index 1d83ae2734..2be393f1b6 100644
--- a/tests/unit/include/bout/test_hypre_interface.cxx
+++ b/tests/unit/include/bout/test_hypre_interface.cxx
@@ -533,6 +533,14 @@ RawBoundaryEliminationSystem makeSingleBoundarySystem() {
           {0}};
 }
 
+RawBoundaryEliminationSystem makeMultiCoupledBoundarySystem() {
+  return {{2, 3, 3, 2},
+          {0, 1, 2, 3},
+          {0, 1, 0, 1, 3, 0, 1, 2, 2, 3},
+          {2.0, 3.0, 5.0, 7.0, 11.0, 13.0, 17.0, 19.0, 23.0, 29.0},
+          {0}};
+}
+
 RawBoundaryEliminationSystem makeBackwardCoupledRowSystem() {
   return {{2, 3, 3, 2},
           {0, 1, 2, 3},
@@ -561,6 +569,8 @@ TEST(BoundaryEliminationTest, TransformsSingleBoundarySystem) {
   EXPECT_EQ(system.elimination->bdep_array[0], -1);
   EXPECT_EQ(system.elimination->bii_array[0], 2.0);
   EXPECT_EQ(system.elimination->bij_array[0], 3.0);
+  EXPECT_EQ(system.elimination->aoffset_array[0], 0);
+  EXPECT_EQ(system.elimination->aoffset_array[1], 1);
   EXPECT_EQ(system.elimination->aknum_array[0], 1);
   EXPECT_EQ(system.elimination->aki_array[0], 5.0);
 }
@@ -605,6 +615,59 @@ TEST(BoundaryEliminationTest, ReconstructsMatvecForSingleBoundarySystem) {
   EXPECT_EQ(reduced_result[2], 77.0);
 }
 
+TEST(BoundaryEliminationTest, EliminatesBoundaryCouplingsFromAllAffectedRows) {
+  auto system = makeMultiCoupledBoundarySystem();
+
+  EXPECT_EQ(system.ncols[0], 1);
+  EXPECT_EQ(system.values[0], -1.0);
+  EXPECT_EQ(system.values[1], 0.0);
+  EXPECT_EQ(system.values[2], 0.0);
+  EXPECT_DOUBLE_EQ(system.values[3], -0.5);
+  EXPECT_EQ(system.values[4], 11.0);
+  EXPECT_EQ(system.values[5], 0.0);
+  EXPECT_DOUBLE_EQ(system.values[6], -2.5);
+  EXPECT_EQ(system.values[7], 19.0);
+  EXPECT_EQ(system.values[8], 23.0);
+  EXPECT_EQ(system.values[9], 29.0);
+
+  EXPECT_EQ(system.elimination->na, 2);
+  EXPECT_EQ(system.elimination->aoffset_array[0], 0);
+  EXPECT_EQ(system.elimination->aoffset_array[1], 2);
+  EXPECT_EQ(system.elimination->aknum_array[0], 1);
+  EXPECT_EQ(system.elimination->aknum_array[1], 2);
+  EXPECT_EQ(system.elimination->aki_array[0], 5.0);
+  EXPECT_EQ(system.elimination->aki_array[1], 13.0);
+}
+
+TEST(BoundaryEliminationTest, ReducesRightHandSideForMultipleAffectedRows) {
+  auto system = makeMultiCoupledBoundarySystem();
+  std::array<HYPRE_Complex, 4> rhs{{19.0, 23.0, 31.0, 37.0}};
+
+  auto brhs = system.elimination->reduceRightHandSideInPlace(rhs.data());
+
+  ASSERT_NE(brhs, nullptr);
+  EXPECT_EQ(brhs->data[0], 19.0);
+  EXPECT_EQ(rhs[0], 19.0);
+  EXPECT_DOUBLE_EQ(rhs[1], -24.5);
+  EXPECT_DOUBLE_EQ(rhs[2], -92.5);
+  EXPECT_EQ(rhs[3], 37.0);
+}
+
+TEST(BoundaryEliminationTest, ReconstructsMatvecForMultipleAffectedRows) {
+  auto system = makeMultiCoupledBoundarySystem();
+  std::array<HYPRE_Complex, 4> x{{1.0, 2.0, 3.0, 4.0}};
+  std::array<HYPRE_Complex, 4> reduced_result{{-1.0, 32.0, 52.0, 185.0}};
+  auto boundary_values = system.elimination->evaluateBoundaryEquations(x.data());
+
+  system.elimination->expandMatvecResultInPlace(boundary_values, boundary_values,
+                                                reduced_result.data());
+
+  EXPECT_EQ(reduced_result[0], 8.0);
+  EXPECT_EQ(reduced_result[1], 52.0);
+  EXPECT_EQ(reduced_result[2], 104.0);
+  EXPECT_EQ(reduced_result[3], 185.0);
+}
+
 TEST(BoundaryEliminationTest, HandlesBackwardCoupledRows) {
   auto system = makeBackwardCoupledRowSystem();
 
@@ -619,6 +682,9 @@ TEST(BoundaryEliminationTest, HandlesBackwardCoupledRows) {
   EXPECT_EQ(system.values[8], 0.0);
   EXPECT_EQ(system.values[9], -1.0);
 
+  EXPECT_EQ(system.elimination->aoffset_array[0], 0);
+  EXPECT_EQ(system.elimination->aoffset_array[1], 1);
+  EXPECT_EQ(system.elimination->aoffset_array[2], 2);
   EXPECT_EQ(system.elimination->aknum_array[0], 2);
   EXPECT_EQ(system.elimination->aknum_array[1], 1);
 }

From 1a60d3fcba9e048b9a44662405fb010c36feeaef Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Mon, 17 Aug 2026 22:24:01 -0700
Subject: [PATCH 1719/1827] SNES solver: Save Jacobian to file

- PetscPreconditioner saves Jacobian using PETSc binary or ASCII
  format.
- Solver saves metadata: A Jacobian global index offset field to
  the dmp files, and a JSON file with the variable information.
- SNES solver outputs Jacobian if `save_jacobian = true`.  An option
  `jacobian_export_kind` select whether the Jacobian is calculated using
  the nonlinear system being solved (that depends on timestep and
  scaling), the scaled RHS function (that depends on variable scaling),
  or the raw `rhs` function is saved.
---
 include/bout/petsc_preconditioner.hxx |  15 +++
 include/bout/solver.hxx               |  29 +++++
 src/solver/impls/snes/snes.cxx        | 176 ++++++++++++++++++++++----
 src/solver/impls/snes/snes.hxx        |  31 ++++-
 src/solver/petsc_preconditioner.cxx   |  27 ++++
 src/solver/solver.cxx                 | 133 +++++++++++++++++++
 6 files changed, 381 insertions(+), 30 deletions(-)

diff --git a/include/bout/petsc_preconditioner.hxx b/include/bout/petsc_preconditioner.hxx
index be283413fc..9fe33f7330 100644
--- a/include/bout/petsc_preconditioner.hxx
+++ b/include/bout/petsc_preconditioner.hxx
@@ -10,8 +10,11 @@
 #ifndef BOUT_PETSC_PRECONDITIONER_H
 #define BOUT_PETSC_PRECONDITIONER_H
 
+#include "bout/bout_enum_class.hxx"
 #include "bout/build_defines.hxx"
 
+BOUT_ENUM_CLASS(PetscMatrixExportFormat, binary, ascii);
+
 #if BOUT_HAS_PETSC
 
 #include "bout/petsc_interface.hxx"
@@ -22,6 +25,8 @@
 #include <petscmat.h>
 #include <petscvec.h>
 
+#include <string>
+
 class Options;
 class Field3D;
 
@@ -73,6 +78,13 @@ public:
   Mat jacobian() const { return Jfd; }
   MatFDColoring coloring() const { return fdcoloring; }
 
+  static PetscErrorCode
+  saveMatrix(Mat matrix, const std::string& filename,
+             PetscMatrixExportFormat format = PetscMatrixExportFormat::binary);
+  PetscErrorCode
+  saveMatrix(const std::string& filename,
+             PetscMatrixExportFormat format = PetscMatrixExportFormat::binary) const;
+
   void reset();
 
 private:
@@ -86,6 +98,9 @@ private:
 // unconditionally in PETSc-enabled compilation units.
 class PetscPreconditioner {
 public:
+  void saveMatrix(
+      const std::string& UNUSED(filename),
+      PetscMatrixExportFormat UNUSED(format) = PetscMatrixExportFormat::binary) const {}
   void reset() {}
 };
 
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 0d4b330ec6..10a3d294f1 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -38,6 +38,7 @@
 
 #include "bout/build_defines.hxx"
 
+#include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/globals.hxx"
@@ -101,6 +102,8 @@ constexpr auto SOLVERRKGENERIC = "rkgeneric";
 enum class FieldCategories : std::uint8_t { VARS, DERIVS, MMS };
 enum class SOLVER_VAR_OP : std::uint8_t { LOAD, SET_ID, SAVE };
 
+BOUT_ENUM_CLASS(JacobianExportKind, system, scaled, rhs);
+
 /// A type to set where in the list monitors are added
 enum class MonitorPosition { BACK, FRONT };
 
@@ -368,6 +371,25 @@ public:
 protected:
   friend class SundialsNVectorInterface;
 
+  struct JacobianVariableMetadata {
+    int offset{0};
+    std::string name;
+    std::string location;
+    bool evolve_bndry{false};
+    bool constraint{false};
+    std::string description;
+  };
+
+  struct JacobianMetadata {
+    int format_version{1};
+    std::string solver_name;
+    int n2d{0};
+    int n3d{0};
+    std::vector<JacobianVariableMetadata> variables_2d;
+    std::vector<JacobianVariableMetadata> variables_3d;
+    std::string ordering;
+  };
+
   /// Number of command-line arguments
   static int* pargc;
   /// Command-line arguments
@@ -606,6 +628,12 @@ protected:
 
   /// Returns a Field3D containing the global indices
   Field3D globalIndex(int localStart);
+  Field3D jacobianIndexBase(int localStart = 0);
+  std::vector<JacobianVariableMetadata> getJacobianMetadata2D() const;
+  std::vector<JacobianVariableMetadata> getJacobianMetadata3D() const;
+  JacobianMetadata getJacobianMetadata(const std::string& solver_name) const;
+  void writeJacobianMetadataJson(const std::string& filename,
+                                 const std::string& solver_name) const;
 
   /// Maximum internal timestep
   BoutReal max_dt{-1.0};
@@ -670,6 +698,7 @@ private:
   std::string run_restart_from = "yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy";
   /// Save `run_id` and `run_restart_from` every output
   bool save_repeat_run_id{false};
+  bool save_jacobian_index_base{false};
 
   /// Current iteration (output time-step) number
   int iteration{0};
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index e7d367331a..8c40cf5722 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -21,6 +21,7 @@
 #include <algorithm>
 #include <cmath>
 #include <cstddef>
+#include <fmt/format.h>
 #include <vector>
 
 #include "petscerror.h"
@@ -61,6 +62,15 @@ PetscErrorCode FormFunctionForColoring(void* UNUSED(snes), Vec x, Vec f, void* c
   return static_cast<SNESSolver*>(ctx)->snes_function(x, f, true);
 }
 
+PetscErrorCode FormRawFunctionForColoring(void* UNUSED(snes), Vec x, Vec f, void* ctx) {
+  return static_cast<SNESSolver*>(ctx)->raw_rhs_function(x, f, true);
+}
+
+PetscErrorCode FormScaledFunctionForColoring(void* UNUSED(snes), Vec x, Vec f,
+                                             void* ctx) {
+  return static_cast<SNESSolver*>(ctx)->scaled_rhs_function(x, f, true);
+}
+
 PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
   // Get the context
   SNESSolver* s;
@@ -71,6 +81,8 @@ PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
 
 PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
                                           void* ctx);
+PetscErrorCode ComputeJacobianDefaultMaybeExport(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
+                                                 void* ctx);
 } // namespace
 
 PetscErrorCode SNESSolver::FDJinitialise() {
@@ -111,9 +123,9 @@ PetscErrorCode SNESSolver::FDJinitialise() {
         nullptr, &Jfd);
 
     if (matrix_free_operator) {
-      SNESSetJacobian(snes, Jmf, Jfd, SNESComputeJacobianDefault, this);
+      SNESSetJacobian(snes, Jmf, Jfd, ComputeJacobianDefaultMaybeExport, this);
     } else {
-      SNESSetJacobian(snes, Jfd, Jfd, SNESComputeJacobianDefault, this);
+      SNESSetJacobian(snes, Jfd, Jfd, ComputeJacobianDefaultMaybeExport, this);
     }
 
     MatSetOption(Jfd, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
@@ -364,7 +376,99 @@ SNESSolver::SNESSolver(Options* opts)
                             .withDefault<BoutReal>(100.)),
       asinh_vars((*options)["asinh_vars"]
                      .doc("Apply asinh() to all variables?")
-                     .withDefault<bool>(false)) {}
+                     .withDefault<bool>(false)),
+      save_jacobian((*options)["save_jacobian"]
+                        .doc("Save Jacobian matrices for diagnostics?")
+                        .withDefault<bool>(false)),
+      jacobian_export_kind((*options)["jacobian_export_kind"]
+                               .doc("Which Jacobian to save: system, scaled, rhs")
+                               .withDefault(JacobianExportKind::system)),
+      jacobian_export_prefix(
+          (*options)["jacobian_export_prefix"]
+              .doc("Prefix for saved Jacobian matrix and metadata files")
+              .withDefault("jacobian")),
+      jacobian_export_format((*options)["jacobian_export_format"]
+                                 .doc("Format for saved Jacobian matrices: binary, ascii")
+                                 .withDefault(PetscMatrixExportFormat::binary)) {}
+
+std::string SNESSolver::getJacobianExportStem(JacobianExportKind kind) {
+  return fmt::format("{}_{}_{:06d}", jacobian_export_prefix, toString(kind),
+                     jacobian_export_counter++);
+}
+
+std::string SNESSolver::getJacobianMatrixFilename(const std::string& stem) const {
+  return stem
+         + (jacobian_export_format == PetscMatrixExportFormat::binary ? ".dat" : ".txt");
+}
+
+PetscErrorCode
+SNESSolver::exportMatrixAndMetadata(const PetscPreconditioner& preconditioner,
+                                    const std::string& stem) {
+  if (!jacobian_metadata_written) {
+    writeJacobianMetadataJson(jacobian_export_prefix + "_metadata.json", "snes");
+    jacobian_metadata_written = true;
+  }
+
+  PetscCall(
+      preconditioner.saveMatrix(getJacobianMatrixFilename(stem), jacobian_export_format));
+  PetscFunctionReturn(PETSC_SUCCESS);
+}
+
+PetscErrorCode SNESSolver::saveDiagnosticJacobian(JacobianExportKind kind, Vec x_solver) {
+  PetscPreconditioner diagnostic_preconditioner;
+  Field3D index = globalIndex(0);
+  PetscCall(diagnostic_preconditioner.createJacobianPattern(
+      index, *options, nlocal, n2Dvars(), n3Dvars(), BoutComm::get()));
+
+  if (kind == JacobianExportKind::rhs) {
+    PetscCall(diagnostic_preconditioner.updateColoring(FormRawFunctionForColoring, this));
+  } else {
+    PetscCall(
+        diagnostic_preconditioner.updateColoring(FormScaledFunctionForColoring, this));
+  }
+
+  Vec x_evaluate = x_solver;
+  Vec physical_x{nullptr};
+  if (kind == JacobianExportKind::rhs) {
+    PetscCall(VecDuplicate(x_solver, &physical_x));
+    PetscCall(toPhysicalState(x_solver, physical_x));
+    x_evaluate = physical_x;
+  }
+
+  Mat diagnostic_jacobian = diagnostic_preconditioner.jacobian();
+  PetscCall(MatZeroEntries(diagnostic_jacobian));
+  PetscCall(SNESComputeJacobianDefaultColor(snes, x_evaluate, diagnostic_jacobian,
+                                            diagnostic_jacobian,
+                                            diagnostic_preconditioner.coloring()));
+  PetscCall(
+      exportMatrixAndMetadata(diagnostic_preconditioner, getJacobianExportStem(kind)));
+
+  if (physical_x != nullptr) {
+    PetscCall(VecDestroy(&physical_x));
+  }
+
+  PetscFunctionReturn(PETSC_SUCCESS);
+}
+
+PetscErrorCode SNESSolver::maybeExportJacobian(Mat system_jacobian, Vec x_solver) {
+  if (!save_jacobian) {
+    PetscFunctionReturn(PETSC_SUCCESS);
+  }
+
+  if (jacobian_export_kind == JacobianExportKind::system) {
+    if (!jacobian_metadata_written) {
+      writeJacobianMetadataJson(jacobian_export_prefix + "_metadata.json", "snes");
+      jacobian_metadata_written = true;
+    }
+    PetscCall(PetscPreconditioner::saveMatrix(
+        system_jacobian,
+        getJacobianMatrixFilename(getJacobianExportStem(jacobian_export_kind)),
+        jacobian_export_format));
+    PetscFunctionReturn(PETSC_SUCCESS);
+  }
+
+  PetscFunctionReturn(saveDiagnosticJacobian(jacobian_export_kind, x_solver));
+}
 
 int SNESSolver::init() {
   Solver::init();
@@ -1128,13 +1232,13 @@ PetscErrorCode SNESSolver::updateResiduals(Vec x) {
   const BoutReal* current_residual = nullptr;
   if (diagnose) {
     // Call RHS function to get time derivatives
-    PetscCall(rhs_function(x, deriv, false));
+    PetscCall(scaled_rhs_function(x, deriv, false));
 
     // Reading the residual vectors
     PetscCall(VecGetArrayRead(deriv, &current_residual));
   } else {
     // Call RHS function to get time derivatives
-    PetscCall(rhs_function(x, snes_f, false));
+    PetscCall(scaled_rhs_function(x, snes_f, false));
 
     // Reading the residual vectors
     PetscCall(VecGetArrayRead(snes_f, &current_residual));
@@ -1415,34 +1519,34 @@ BoutReal SNESSolver::updatePseudoTimestep(BoutReal previous_timestep,
   throw BoutException("SNESSolver::updatePseudoTimestep invalid BoutPTCStrategy");
 }
 
-PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
-  // Get data from PETSc into BOUT++ fields
+PetscErrorCode SNESSolver::toPhysicalState(Vec x, Vec physical_x) {
   if (scale_vars) {
-    // scaled_x <- x * var_scaling_factors
-    PetscCall(VecPointwiseMult(scaled_x, x, var_scaling_factors));
-  } else if (asinh_vars) {
-    PetscCall(VecCopy(x, scaled_x));
+    PetscCall(VecPointwiseMult(physical_x, x, var_scaling_factors));
   } else {
-    scaled_x = x;
+    PetscCall(VecCopy(x, physical_x));
   }
 
   if (asinh_vars) {
     PetscInt size;
-    PetscCall(VecGetLocalSize(scaled_x, &size));
+    PetscCall(VecGetLocalSize(physical_x, &size));
 
-    BoutReal* scaled_data = nullptr;
-    PetscCall(VecGetArray(scaled_x, &scaled_data));
+    BoutReal* physical_data = nullptr;
+    PetscCall(VecGetArray(physical_x, &physical_data));
     for (PetscInt i = 0; i != size; ++i) {
-      scaled_data[i] = asinh_scale * std::sinh(scaled_data[i]);
+      physical_data[i] = asinh_scale * std::sinh(physical_data[i]);
     }
-    PetscCall(VecRestoreArray(scaled_x, &scaled_data));
+    PetscCall(VecRestoreArray(physical_x, &physical_data));
   }
 
+  return PETSC_SUCCESS;
+}
+
+PetscErrorCode SNESSolver::raw_rhs_function(Vec x, Vec f, bool linear) {
   const BoutReal* xdata = nullptr;
-  PetscCall(VecGetArrayRead(scaled_x, &xdata));
+  PetscCall(VecGetArrayRead(x, &xdata));
   // const_cast needed due to load_vars API. Not writing to xdata.
   load_vars(const_cast<BoutReal*>(xdata));
-  PetscCall(VecRestoreArrayRead(scaled_x, &xdata));
+  PetscCall(VecRestoreArrayRead(x, &xdata));
 
   try {
     // Call RHS function
@@ -1460,6 +1564,18 @@ PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
   BoutReal* fdata = nullptr;
   PetscCall(VecGetArray(f, &fdata));
   save_derivs(fdata);
+  PetscCall(VecRestoreArray(f, &fdata));
+
+  return PETSC_SUCCESS;
+}
+
+PetscErrorCode SNESSolver::scaled_rhs_function(Vec x, Vec f, bool linear) {
+  if (!scale_vars && !asinh_vars) {
+    return raw_rhs_function(x, f, linear);
+  }
+
+  PetscCall(toPhysicalState(x, scaled_x));
+  PetscCall(raw_rhs_function(scaled_x, f, linear));
 
   if (asinh_vars) {
     // Modify time-derivatives for asinh(var) using chain rule
@@ -1472,14 +1588,15 @@ PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
     PetscCall(VecGetLocalSize(f, &size));
     const BoutReal* scaled_data = nullptr;
     PetscCall(VecGetArrayRead(scaled_x, &scaled_data));
+    BoutReal* fdata = nullptr;
+    PetscCall(VecGetArray(f, &fdata));
     for (PetscInt i = 0; i != size; ++i) {
       fdata[i] /= std::sqrt(SQ(scaled_data[i]) + SQ(asinh_scale));
     }
+    PetscCall(VecRestoreArray(f, &fdata));
     PetscCall(VecRestoreArrayRead(scaled_x, &scaled_data));
   }
 
-  PetscCall(VecRestoreArray(f, &fdata));
-
   if (scale_vars) {
     PetscCall(VecPointwiseDivide(f, f, var_scaling_factors));
   }
@@ -1490,7 +1607,7 @@ PetscErrorCode SNESSolver::rhs_function(Vec x, Vec f, bool linear) {
 PetscErrorCode SNESSolver::snes_function(Vec x, Vec f, bool linear) {
 
   // Call the RHS function
-  if (rhs_function(x, f, linear) != PETSC_SUCCESS) {
+  if (scaled_rhs_function(x, f, linear) != PETSC_SUCCESS) {
     // Tell SNES that the input was out of domain
     SNESSetFunctionDomainError(snes);
     // Note: Returning non-zero error here leaves vectors in locked state
@@ -1664,7 +1781,20 @@ PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat Jac_ne
   CHKERRQ(err);
 
   // Call the SNESSolver function
-  return fctx->scaleJacobian(Jac_new);
+  PetscCall(fctx->scaleJacobian(Jac_new));
+  PetscFunctionReturn(fctx->maybeExportJacobian(Jac_new, x1));
+}
+
+PetscErrorCode ComputeJacobianDefaultMaybeExport(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
+                                                 void* ctx) {
+  PetscErrorCode err = SNESComputeJacobianDefault(snes, x1, Jac, Jac_new, ctx);
+  CHKERRQ(err);
+
+  if ((err != 0) or (ctx == nullptr)) {
+    return err;
+  }
+
+  PetscFunctionReturn(static_cast<SNESSolver*>(ctx)->maybeExportJacobian(Jac_new, x1));
 }
 } // namespace
 
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index c8042cf2dc..d45ab1cdaf 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -110,6 +110,18 @@ public:
   /// finite difference approximated Jacobian.
   PetscErrorCode scaleJacobian(Mat Jac_new);
 
+  /// Convert solver coordinates into the physical variables used by the model.
+  PetscErrorCode toPhysicalState(Vec x, Vec physical_x);
+
+  /// Call the physics model RHS function on a vector of physical variables.
+  PetscErrorCode raw_rhs_function(Vec x, Vec f, bool linear);
+
+  /// Apply solver-coordinate transforms, call the raw RHS, and transform the
+  /// resulting derivatives back into solver coordinates.
+  PetscErrorCode scaled_rhs_function(Vec x, Vec f, bool linear);
+
+  PetscErrorCode maybeExportJacobian(Mat system_jacobian, Vec x_solver);
+
   /// Save diagnostics to output
   void outputVars(Options& output_options, bool save_repeat = true) override;
 
@@ -121,13 +133,11 @@ private:
   /// Rescale state (snes_x) so that all quantities are around 1. If
   /// quantities are near zero then RTOL is used.
   PetscErrorCode rescale();
-
-  /// Call the physics model RHS function
-  ///
-  /// @param[in] x       The state vector. Will be scaled if scale_vars=true
-  /// @param[out] f      The vector for the result f(x)
-  /// @param[in] linear  Specifies that the SNES solver is in a linear (KSP) inner loop
-  PetscErrorCode rhs_function(Vec x, Vec f, bool linear);
+  PetscErrorCode saveDiagnosticJacobian(JacobianExportKind kind, Vec x_solver);
+  std::string getJacobianExportStem(JacobianExportKind kind);
+  std::string getJacobianMatrixFilename(const std::string& stem) const;
+  PetscErrorCode exportMatrixAndMetadata(const PetscPreconditioner& preconditioner,
+                                         const std::string& stem);
 
   BoutSnesOutput output_trigger; ///< Sets when outputs are written
 
@@ -278,6 +288,13 @@ private:
   bool asinh_vars; ///< Evolve asinh(vars) to compress magnitudes while preserving signs
   const BoutReal asinh_scale = 1e-5; // Scale below which asinh response becomes ~linear
 
+  bool save_jacobian;                      ///< Save Jacobian matrices for diagnostics
+  JacobianExportKind jacobian_export_kind; ///< Which Jacobian to save
+  std::string jacobian_export_prefix; ///< Prefix for Jacobian matrix/metadata outputs
+  PetscMatrixExportFormat jacobian_export_format; ///< Output format for matrix save
+  int jacobian_export_counter{0};                 ///< Running counter for saved Jacobians
+  bool jacobian_metadata_written{false}; ///< Has the shared JSON metadata been written?
+
   std::vector<Field2D>
       resid_2d; ///< Storage for residuals of SNES solve, unpacked from snes_f
   std::vector<Field3D>
diff --git a/src/solver/petsc_preconditioner.cxx b/src/solver/petsc_preconditioner.cxx
index 508d001fd3..063d85812e 100644
--- a/src/solver/petsc_preconditioner.cxx
+++ b/src/solver/petsc_preconditioner.cxx
@@ -6,6 +6,7 @@
 
 #include "bout/assert.hxx"
 #include "bout/boutcomm.hxx"
+#include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
@@ -16,6 +17,7 @@
 #include <algorithm>
 #include <cmath>
 #include <set>
+#include <string>
 #include <utility>
 #include <vector>
 
@@ -71,6 +73,31 @@ void PetscPreconditioner::reset() {
   }
 }
 
+PetscErrorCode PetscPreconditioner::saveMatrix(Mat matrix, const std::string& filename,
+                                               PetscMatrixExportFormat format) {
+  if (matrix == nullptr) {
+    throw BoutException("Cannot save Jacobian matrix: matrix has not been created yet");
+  }
+
+  PetscViewer viewer{nullptr};
+  if (format == PetscMatrixExportFormat::binary) {
+    PetscCall(PetscViewerBinaryOpen(BoutComm::get(), filename.c_str(), FILE_MODE_WRITE,
+                                    &viewer));
+  } else {
+    PetscCall(PetscViewerASCIIOpen(BoutComm::get(), filename.c_str(), &viewer));
+  }
+
+  PetscCall(MatView(matrix, viewer));
+  PetscCall(PetscViewerDestroy(&viewer));
+
+  PetscFunctionReturn(PETSC_SUCCESS);
+}
+
+PetscErrorCode PetscPreconditioner::saveMatrix(const std::string& filename,
+                                               PetscMatrixExportFormat format) const {
+  return saveMatrix(Jfd, filename, format);
+}
+
 PetscErrorCode PetscPreconditioner::createJacobianPattern(Field3D& index,
                                                           Options& options,
                                                           PetscInt nlocal, int n2d,
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 1f7b654427..133451c9e7 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -51,6 +51,7 @@
 
 #include <cmath>
 #include <ctime>
+#include <fstream>
 #include <memory>
 #include <numeric>
 #include <set>
@@ -79,6 +80,44 @@
 int* Solver::pargc = nullptr;
 char*** Solver::pargv = nullptr;
 
+namespace {
+std::string jsonEscape(const std::string& input) {
+  std::string escaped;
+  escaped.reserve(input.size());
+
+  for (const char ch : input) {
+    switch (ch) {
+    case '\\':
+      escaped += "\\\\";
+      break;
+    case '"':
+      escaped += "\\\"";
+      break;
+    case '\b':
+      escaped += "\\b";
+      break;
+    case '\f':
+      escaped += "\\f";
+      break;
+    case '\n':
+      escaped += "\\n";
+      break;
+    case '\r':
+      escaped += "\\r";
+      break;
+    case '\t':
+      escaped += "\\t";
+      break;
+    default:
+      escaped += ch;
+      break;
+    }
+  }
+
+  return escaped;
+}
+} // namespace
+
 /**************************************************************************
  * Constructor
  **************************************************************************/
@@ -94,6 +133,10 @@ Solver::Solver(Options* opts)
                                   "timestep, to make it easier to concatenate output "
                                   "data sets in time")
                              .withDefault(false)),
+      save_jacobian_index_base(
+          (*options)["save_jacobian_index_base"]
+              .doc("Write the base global index field used for Jacobian diagnostics")
+              .withDefault(false)),
       is_nonsplit_model_diffusive(
           (*options)["is_nonsplit_model_diffusive"]
               .doc("If not a split operator, treat RHS as diffusive?")
@@ -705,6 +748,11 @@ void Solver::outputVars(Options& output_options, bool save_repeat) {
            "or the previous run did not have a run_id.")
       .assignRepeat(run_restart_from, "t", save_repeat and save_repeat_run_id, "Solver");
 
+  if (save_jacobian_index_base) {
+    output_options["jacobian_index_base"].assignRepeat(jacobianIndexBase(), "t",
+                                                       save_repeat, "Solver");
+  }
+
   // Add 2D and 3D evolving fields to output file
   for (const auto& f : f2d) {
     // Add to dump file (appending)
@@ -1207,6 +1255,91 @@ Field3D Solver::globalIndex(int localStart) {
   return index;
 }
 
+Field3D Solver::jacobianIndexBase(int localStart) { return globalIndex(localStart); }
+
+std::vector<Solver::JacobianVariableMetadata> Solver::getJacobianMetadata2D() const {
+  std::vector<JacobianVariableMetadata> metadata;
+  metadata.reserve(f2d.size());
+
+  for (int i = 0; i < static_cast<int>(f2d.size()); ++i) {
+    metadata.push_back(JacobianVariableMetadata{i, f2d[i].name, toString(f2d[i].location),
+                                                f2d[i].evolve_bndry, f2d[i].constraint,
+                                                f2d[i].description});
+  }
+
+  return metadata;
+}
+
+std::vector<Solver::JacobianVariableMetadata> Solver::getJacobianMetadata3D() const {
+  std::vector<JacobianVariableMetadata> metadata;
+  metadata.reserve(f3d.size());
+
+  for (int i = 0; i < static_cast<int>(f3d.size()); ++i) {
+    metadata.push_back(JacobianVariableMetadata{i, f3d[i].name, toString(f3d[i].location),
+                                                f3d[i].evolve_bndry, f3d[i].constraint,
+                                                f3d[i].description});
+  }
+
+  return metadata;
+}
+
+Solver::JacobianMetadata
+Solver::getJacobianMetadata(const std::string& solver_name) const {
+  return JacobianMetadata{1,
+                          solver_name,
+                          n2Dvars(),
+                          n3Dvars(),
+                          getJacobianMetadata2D(),
+                          getJacobianMetadata3D(),
+                          "For each (x,y): 2D variables at z=0, then 3D variables for "
+                          "z=0..Nz-1; evolved boundary points precede RGN_NOBNDRY"};
+}
+
+void Solver::writeJacobianMetadataJson(const std::string& filename,
+                                       const std::string& solver_name) const {
+  if (MYPE != 0) {
+    return;
+  }
+
+  const auto metadata = getJacobianMetadata(solver_name);
+  std::ofstream json_file(filename);
+  if (!json_file.is_open()) {
+    throw BoutException("Failed to open Jacobian metadata file '{}'", filename);
+  }
+
+  auto write_variables = [&](const std::vector<JacobianVariableMetadata>& variables,
+                             const char* name) {
+    json_file << "  \"" << name << "\": [\n";
+    for (std::size_t i = 0; i < variables.size(); ++i) {
+      const auto& variable = variables[i];
+      json_file << "    {\"offset\": " << variable.offset << ", "
+                << "\"name\": \"" << jsonEscape(variable.name) << "\", "
+                << "\"location\": \"" << jsonEscape(variable.location) << "\", "
+                << "\"evolve_bndry\": " << (variable.evolve_bndry ? "true" : "false")
+                << ", "
+                << "\"constraint\": " << (variable.constraint ? "true" : "false") << ", "
+                << "\"description\": \"" << jsonEscape(variable.description) << "\"}";
+      if (i + 1 != variables.size()) {
+        json_file << ",";
+      }
+      json_file << "\n";
+    }
+    json_file << "  ]";
+  };
+
+  json_file << "{\n"
+            << "  \"format_version\": " << metadata.format_version << ",\n"
+            << "  \"solver\": \"" << jsonEscape(metadata.solver_name) << "\",\n"
+            << "  \"n2d\": " << metadata.n2d << ",\n"
+            << "  \"n3d\": " << metadata.n3d << ",\n";
+  write_variables(metadata.variables_2d, "variables_2d");
+  json_file << ",\n";
+  write_variables(metadata.variables_3d, "variables_3d");
+  json_file << ",\n"
+            << "  \"ordering\": \"" << jsonEscape(metadata.ordering) << "\"\n"
+            << "}\n";
+}
+
 /**************************************************************************
  * Running user-supplied functions
  **************************************************************************/

From bb0ca6266a2d78245105137c825d225efd0167b7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 18 Aug 2026 21:28:11 -0700
Subject: [PATCH 1720/1827] SNES solver: Save Jacobian to data directory

Saves to same directory as the dmp file outputs,
using `Options::root()["datadir"]`
---
 src/solver/impls/snes/snes.cxx | 35 +++++++++++++++++-----------------
 src/solver/impls/snes/snes.hxx |  3 +--
 src/solver/solver.cxx          | 10 +++++++---
 3 files changed, 25 insertions(+), 23 deletions(-)

diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 8c40cf5722..b756463358 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -14,6 +14,7 @@
 #include <bout/output.hxx>
 #include <bout/output_bout_types.hxx>
 #include <bout/petsc_interface.hxx>
+#include <bout/petsc_preconditioner.hxx>
 #include <bout/solver.hxx>
 #include <bout/unused.hxx>
 #include <bout/utils.hxx>
@@ -392,7 +393,9 @@ SNESSolver::SNESSolver(Options* opts)
                                  .withDefault(PetscMatrixExportFormat::binary)) {}
 
 std::string SNESSolver::getJacobianExportStem(JacobianExportKind kind) {
-  return fmt::format("{}_{}_{:06d}", jacobian_export_prefix, toString(kind),
+  // The directory the output data is stored in
+  const std::string datadir = Options::root()["datadir"];
+  return fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix, toString(kind),
                      jacobian_export_counter++);
 }
 
@@ -401,16 +404,19 @@ std::string SNESSolver::getJacobianMatrixFilename(const std::string& stem) const
          + (jacobian_export_format == PetscMatrixExportFormat::binary ? ".dat" : ".txt");
 }
 
-PetscErrorCode
-SNESSolver::exportMatrixAndMetadata(const PetscPreconditioner& preconditioner,
-                                    const std::string& stem) {
+PetscErrorCode SNESSolver::exportMatrixAndMetadata(Mat jacobian,
+                                                   const std::string& stem) {
   if (!jacobian_metadata_written) {
-    writeJacobianMetadataJson(jacobian_export_prefix + "_metadata.json", "snes");
+    const std::string datadir = Options::root()["datadir"];
+    const std::string metadata_filename =
+        datadir + "/" + jacobian_export_prefix + "_metadata.json";
+    output.write("Jacobian metadata written to {}\n", metadata_filename);
+    writeJacobianMetadataJson(metadata_filename, "snes");
     jacobian_metadata_written = true;
   }
 
-  PetscCall(
-      preconditioner.saveMatrix(getJacobianMatrixFilename(stem), jacobian_export_format));
+  PetscCall(PetscPreconditioner::saveMatrix(jacobian, getJacobianMatrixFilename(stem),
+                                            jacobian_export_format));
   PetscFunctionReturn(PETSC_SUCCESS);
 }
 
@@ -440,8 +446,7 @@ PetscErrorCode SNESSolver::saveDiagnosticJacobian(JacobianExportKind kind, Vec x
   PetscCall(SNESComputeJacobianDefaultColor(snes, x_evaluate, diagnostic_jacobian,
                                             diagnostic_jacobian,
                                             diagnostic_preconditioner.coloring()));
-  PetscCall(
-      exportMatrixAndMetadata(diagnostic_preconditioner, getJacobianExportStem(kind)));
+  PetscCall(exportMatrixAndMetadata(diagnostic_jacobian, getJacobianExportStem(kind)));
 
   if (physical_x != nullptr) {
     PetscCall(VecDestroy(&physical_x));
@@ -456,14 +461,8 @@ PetscErrorCode SNESSolver::maybeExportJacobian(Mat system_jacobian, Vec x_solver
   }
 
   if (jacobian_export_kind == JacobianExportKind::system) {
-    if (!jacobian_metadata_written) {
-      writeJacobianMetadataJson(jacobian_export_prefix + "_metadata.json", "snes");
-      jacobian_metadata_written = true;
-    }
-    PetscCall(PetscPreconditioner::saveMatrix(
-        system_jacobian,
-        getJacobianMatrixFilename(getJacobianExportStem(jacobian_export_kind)),
-        jacobian_export_format));
+    PetscCall(exportMatrixAndMetadata(system_jacobian,
+                                      getJacobianExportStem(jacobian_export_kind)));
     PetscFunctionReturn(PETSC_SUCCESS);
   }
 
@@ -1787,7 +1786,7 @@ PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat Jac_ne
 
 PetscErrorCode ComputeJacobianDefaultMaybeExport(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
                                                  void* ctx) {
-  PetscErrorCode err = SNESComputeJacobianDefault(snes, x1, Jac, Jac_new, ctx);
+  const PetscErrorCode err = SNESComputeJacobianDefault(snes, x1, Jac, Jac_new, ctx);
   CHKERRQ(err);
 
   if ((err != 0) or (ctx == nullptr)) {
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index d45ab1cdaf..5c866c2f3a 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -136,8 +136,7 @@ private:
   PetscErrorCode saveDiagnosticJacobian(JacobianExportKind kind, Vec x_solver);
   std::string getJacobianExportStem(JacobianExportKind kind);
   std::string getJacobianMatrixFilename(const std::string& stem) const;
-  PetscErrorCode exportMatrixAndMetadata(const PetscPreconditioner& preconditioner,
-                                         const std::string& stem);
+  PetscErrorCode exportMatrixAndMetadata(Mat jacobian, const std::string& stem);
 
   BoutSnesOutput output_trigger; ///< Sets when outputs are written
 
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 133451c9e7..340680f498 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -57,6 +57,7 @@
 #include <set>
 #include <string>
 #include <utility>
+#include <vector>
 
 // Implementations:
 #include "impls/adams_bashforth/adams_bashforth.hxx"
@@ -748,9 +749,12 @@ void Solver::outputVars(Options& output_options, bool save_repeat) {
            "or the previous run did not have a run_id.")
       .assignRepeat(run_restart_from, "t", save_repeat and save_repeat_run_id, "Solver");
 
-  if (save_jacobian_index_base) {
-    output_options["jacobian_index_base"].assignRepeat(jacobianIndexBase(), "t",
-                                                       save_repeat, "Solver");
+  if (initialised and save_jacobian_index_base) {
+    // The Jacobian index base offsets are not time-dependent
+    // Only need to calculate once, but can only be calculated
+    // once the solver has been initialised. This outputVars
+    // is called once at the start before Solver is initialised.
+    output_options["jacobian_index_base"].force(jacobianIndexBase(), "Solver");
   }
 
   // Add 2D and 3D evolving fields to output file

From e932d239a3fbdb95f3ad254bfe5c2c9b6093a6fe Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 18 Aug 2026 21:30:05 -0700
Subject: [PATCH 1721/1827] integrated test test-snes-save-jacobian

Started a test to check the output Jacobian
---
 tests/integrated/CMakeLists.txt               |  1 +
 .../test-snes-save-jacobian/CMakeLists.txt    |  7 +++++
 .../test-snes-save-jacobian/data/BOUT.inp     | 12 +++++++++
 .../test_snes_save_jacobian.cxx               | 27 +++++++++++++++++++
 .../test_snes_save_jacobian.py                |  2 ++
 5 files changed, 49 insertions(+)
 create mode 100644 tests/integrated/test-snes-save-jacobian/CMakeLists.txt
 create mode 100644 tests/integrated/test-snes-save-jacobian/data/BOUT.inp
 create mode 100644 tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.cxx
 create mode 100644 tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py

diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt
index d87bd329f0..41a21deac0 100644
--- a/tests/integrated/CMakeLists.txt
+++ b/tests/integrated/CMakeLists.txt
@@ -40,6 +40,7 @@ add_subdirectory(test-restarting)
 add_subdirectory(test-slepc-solver)
 add_subdirectory(test-smooth)
 add_subdirectory(test-snb)
+add_subdirectory(test-snes-save-jacobian)
 add_subdirectory(test-solver)
 add_subdirectory(test-squash)
 add_subdirectory(test-stopCheck)
diff --git a/tests/integrated/test-snes-save-jacobian/CMakeLists.txt b/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
new file mode 100644
index 0000000000..115ed8b250
--- /dev/null
+++ b/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
@@ -0,0 +1,7 @@
+bout_add_integrated_test(
+  test-snes-save-jacobian
+  SOURCES test_snes_save_jacobian.cxx
+  CONFLICTS BOUT_USE_METRIC_3D
+  USE_DATA_BOUT_INP
+  REQUIRES BOUT_HAS_FFTW
+)
diff --git a/tests/integrated/test-snes-save-jacobian/data/BOUT.inp b/tests/integrated/test-snes-save-jacobian/data/BOUT.inp
new file mode 100644
index 0000000000..03fc71159b
--- /dev/null
+++ b/tests/integrated/test-snes-save-jacobian/data/BOUT.inp
@@ -0,0 +1,12 @@
+MXG = 0
+
+[mesh]
+nx = 1
+ny = 16
+nz = 1
+
+[solver]
+type = snes
+snes_type = newtonls
+save_jacobian_index_base = true
+save_jacobian = true
diff --git a/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.cxx b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.cxx
new file mode 100644
index 0000000000..7d35b949be
--- /dev/null
+++ b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.cxx
@@ -0,0 +1,27 @@
+#include <bout/bout_types.hxx>
+#include <bout/field3d.hxx>
+#include <bout/physicsmodel.hxx>
+#include <bout/unused.hxx>
+
+class TestSolver : public PhysicsModel {
+public:
+  Field3D f, g;
+
+  int init(bool UNUSED(restarting)) override {
+    solver->add(f, "f");
+    solver->add(g, "g");
+
+    f = 1.0;
+    g = 0.0;
+
+    return 0;
+  }
+
+  int rhs(BoutReal UNUSED(time)) override {
+    ddt(f) = -0.1 * f;
+    ddt(g) = 0.5 * f - g;
+    return 0;
+  }
+};
+
+BOUTMAIN(TestSolver);
diff --git a/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
new file mode 100644
index 0000000000..3b6973745c
--- /dev/null
+++ b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
@@ -0,0 +1,2 @@
+def test_runtest(assert_success_in_shell):
+    assert_success_in_shell("./test_snes_save_jacobian")

From 70a6e70d07946e0cbce626698611995168d8862f Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 18 Aug 2026 23:01:10 -0700
Subject: [PATCH 1722/1827] Add PetscBinaryIO and Jacobian reader

---
 .../test-snes-save-jacobian/CMakeLists.txt    |   3 +
 .../test-snes-save-jacobian/PetscBinaryIO.py  | 588 ++++++++++++++++++
 .../test-snes-save-jacobian/read_jacobian.py  | 309 +++++++++
 3 files changed, 900 insertions(+)
 create mode 100755 tests/integrated/test-snes-save-jacobian/PetscBinaryIO.py
 create mode 100644 tests/integrated/test-snes-save-jacobian/read_jacobian.py

diff --git a/tests/integrated/test-snes-save-jacobian/CMakeLists.txt b/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
index 115ed8b250..f75c1d7c96 100644
--- a/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
+++ b/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
@@ -5,3 +5,6 @@ bout_add_integrated_test(
   USE_DATA_BOUT_INP
   REQUIRES BOUT_HAS_FFTW
 )
+
+configure_file(read_jacobian.py read_jacobian.py COPYONLY)
+configure_file(PetscBinaryIO.py PetscBinaryIO.py COPYONLY)
diff --git a/tests/integrated/test-snes-save-jacobian/PetscBinaryIO.py b/tests/integrated/test-snes-save-jacobian/PetscBinaryIO.py
new file mode 100755
index 0000000000..e3b329c11a
--- /dev/null
+++ b/tests/integrated/test-snes-save-jacobian/PetscBinaryIO.py
@@ -0,0 +1,588 @@
+"""PetscBinaryIO
+===============
+
+Provides
+  1. PETSc-named objects Vec, Mat, and IS that inherit numpy.ndarray
+  2. A class to read and write these objects from PETSc binary files.
+
+The standard usage of this module should look like:
+
+  >>> import PetscBinaryIO
+  >>> io = PetscBinaryIO.PetscBinaryIO()
+  >>> objects = io.readBinaryFile('file.dat')
+
+or
+
+  >>> import PetscBinaryIO
+  >>> import numpy
+  >>> vec = numpy.array([1., 2., 3.]).view(PetscBinaryIO.Vec)
+  >>> io = PetscBinaryIO.PetscBinaryIO()
+  >>> io.writeBinaryFile('file.dat', [vec,])
+
+to read in objects one at a time use such as
+
+  >>> import PetscBinaryIO
+  >>> io = PetscBinaryIO.PetscBinaryIO()
+  >>> fh = open('file.dat')
+  >>> objecttype = io.readObjectType(fh)
+  >>> if objecttype == 'Vec':
+  >>>   v = io.readVec(fh)
+
+   Note that one must read in the object type first and then call readVec(), readMat() etc.
+
+
+See also PetscBinaryIO.__doc__ and methods therein.
+
+This module can also be used as a command line tool for converting matrices.
+Run with --help to see options.
+"""
+
+import numpy as np
+import functools
+
+try:
+    basestring  # Python-2 has basestring as a common parent of unicode and str
+except NameError:
+    basestring = str  # Python-3 is unicode through and through
+
+
+def update_wrapper_with_doc(wrapper, wrapped):
+    """Similar to functools.update_wrapper, but also gets the wrapper's __doc__ string"""
+    wdoc = wrapper.__doc__
+
+    functools.update_wrapper(wrapper, wrapped)
+    if wdoc is not None:
+        if wrapper.__doc__ is None:
+            wrapper.__doc__ = wdoc
+        else:
+            wrapper.__doc__ = wrapper.__doc__ + wdoc
+    return wrapper
+
+
+def wraps_with_doc(wrapped):
+    """Similar to functools.wraps, but also gets the wrapper's __doc__ string"""
+    return functools.partial(update_wrapper_with_doc, wrapped=wrapped)
+
+
+def decorate_with_conf(f):
+    """Decorates methods to take kwargs for precisions."""
+
+    @wraps_with_doc(f)
+    def decorated_f(self, *args, **kwargs):
+        """
+        Additional kwargs:
+          precision: 'single', 'double', '__float128' for scalars
+          indices: '32bit', '64-bit' integer size
+          complexscalars: True/False
+
+          Note these are set in order of preference:
+            1. kwargs if given here
+            2. PetscBinaryIO class __init__ arguments
+            3. PETSC_DIR/PETSC_ARCH defaults
+        """
+
+        changed = False
+        old_precision = self.precision
+        old_indices = self.indices
+        old_complexscalars = self.complexscalars
+
+        try:
+            self.precision = kwargs.pop("precision")
+        except KeyError:
+            pass
+        else:
+            changed = True
+
+        try:
+            self.indices = kwargs.pop("indices")
+        except KeyError:
+            pass
+        else:
+            changed = True
+
+        try:
+            self.complexscalars = kwargs.pop("complexscalars")
+        except KeyError:
+            pass
+        else:
+            changed = True
+
+        if changed:
+            self._update_dtypes()
+
+        result = f(self, *args, **kwargs)
+
+        if changed:
+            self.precision = old_precision
+            self.indices = old_indices
+            self.complexscalars = old_complexscalars
+            self._update_dtypes()
+
+        return result
+
+    return decorated_f
+
+
+class DoneWithFile(Exception):
+    pass
+
+
+class Vec(np.ndarray):
+    """Vec represented as 1D numpy array
+
+    The best way to instantiate this class for use with writeBinaryFile()
+    is through the numpy view method:
+
+    vec = numpy.array([1,2,3]).view(Vec)
+    """
+
+    _classid = 1211214
+
+
+class MatDense(np.matrix):
+    """Mat represented as 2D numpy array
+
+    The best way to instantiate this class for use with writeBinaryFile()
+    is through the numpy view method:
+
+    mat = numpy.array([[1,0],[0,1]]).view(Mat)
+    """
+
+    _classid = 1211216
+
+
+class MatSparse(tuple):
+    """Mat represented as CSR tuple ((M, N), (rowindices, col, val))
+
+    This should be instantiated from a tuple:
+
+    mat = MatSparse( ((M,N), (rowindices,col,val)) )
+    """
+
+    _classid = 1211216
+
+    def __repr__(self):
+        return "MatSparse: %s" % super(MatSparse, self).__repr__()
+
+
+class IS(np.ndarray):
+    """IS represented as 1D numpy array
+
+    The best way to instantiate this class for use with writeBinaryFile()
+    is through the numpy "view" method:
+
+    an_is = numpy.array([3,4,5]).view(IS)
+    """
+
+    _classid = 1211218
+
+
+class PetscBinaryIO(object):
+    """Reader/Writer class for PETSc binary files.
+
+    Note that by default, precisions for both scalars and indices, as well as
+    complex scalars, are picked up from the PETSC_DIR/PETSC_ARCH configuration
+    as set by environmental variables.
+
+    Alternatively, defaults can be overridden at class instantiation, or for
+    a given method call.
+    """
+
+    _classid = {
+        1211216: "Mat",
+        1211214: "Vec",
+        1211218: "IS",
+        1211219: "Bag",
+        1211213: "Real",
+    }
+
+    def __init__(self, precision=None, indices=None, complexscalars=None):
+        if (precision is None) or (indices is None) or (complexscalars is None):
+            import petsc_conf
+
+            defaultprecision, defaultindices, defaultcomplexscalars = (
+                petsc_conf.get_conf()
+            )
+            if precision is None:
+                if defaultprecision is None:
+                    precision = "double"
+                else:
+                    precision = defaultprecision
+
+            if indices is None:
+                if defaultindices is None:
+                    indices = "32bit"
+                else:
+                    indices = defaultindices
+
+            if complexscalars is None:
+                if defaultcomplexscalars is None:
+                    complexscalars = False
+                else:
+                    complexscalars = defaultcomplexscalars
+
+        self.precision = precision
+        if self.precision == "__float128":
+            raise RuntimeError(
+                "__float128 (quadruple) precision is not properly supported. One may use double precision by using -binary_write_double in PETSc and precision='double' here"
+            )
+        self.indices = indices
+        self.complexscalars = complexscalars
+        self._update_dtypes()
+
+    def _update_dtypes(self):
+        if self.indices == "64bit":
+            self._inttype = np.dtype(">i8")
+        else:
+            self._inttype = np.dtype(">i4")
+
+        if self.precision == "__float128":
+            nbyte = 16
+        elif self.precision == "single":
+            nbyte = 4
+        else:
+            nbyte = 8
+
+        if self.complexscalars:
+            name = "c"
+            nbyte = nbyte * 2  # complex scalar takes twice as many bytes
+        else:
+            name = "f"
+
+        self._scalartype = ">{0}{1}".format(name, nbyte)
+
+    @decorate_with_conf
+    def readReal(self, fh):
+        """Reads a single real from a binary file handle, must be called after readObjectType()."""
+
+        try:
+            vals = np.fromfile(fh, dtype=self._scalartype, count=1)
+        except MemoryError:
+            raise IOError("Inconsistent or invalid real data in file")
+        if not len(vals) == 1:
+            raise IOError("Inconsistent or invalid real data in file")
+        return vals
+
+    @decorate_with_conf
+    def readVec(self, fh):
+        """Reads a PETSc Vec from a binary file handle, must be called after readObjectType()."""
+
+        nz = np.fromfile(fh, dtype=self._inttype, count=1)[0]
+        try:
+            vals = np.fromfile(fh, dtype=self._scalartype, count=nz)
+        except MemoryError:
+            raise IOError("Inconsistent or invalid Vec data in file")
+        if not len(vals) == nz:
+            raise IOError("Inconsistent or invalid Vec data in file")
+        return vals.view(Vec)
+
+    @decorate_with_conf
+    def writeVec(self, fh, vec):
+        """Writes a PETSc Vec to a binary file handle."""
+
+        metadata = np.array([Vec._classid, len(vec)], dtype=self._inttype)
+        metadata.tofile(fh)
+        vec.astype(self._scalartype).tofile(fh)
+        return
+
+    @decorate_with_conf
+    def readMatSparse(self, fh):
+        """Reads a PETSc Mat, returning a sparse representation of the data. Must be called after readObjectType()
+
+        (M,N), (I,J,V) = readMatSparse(fid)
+
+        Input:
+          fid : file handle to open binary file.
+        Output:
+          M,N : matrix size
+          I,J : arrays of row and column for each nonzero
+          V: nonzero value
+        """
+
+        try:
+            M, N, nz = np.fromfile(fh, dtype=self._inttype, count=3)
+            I = np.empty(M + 1, dtype=self._inttype)
+            I[0] = 0
+            rownz = np.fromfile(fh, dtype=self._inttype, count=M)
+            np.cumsum(rownz, out=I[1:])
+            assert I[-1] == nz
+
+            J = np.fromfile(fh, dtype=self._inttype, count=nz)
+            assert len(J) == nz
+            V = np.fromfile(fh, dtype=self._scalartype, count=nz)
+            assert len(V) == nz
+        except (AssertionError, MemoryError, IndexError):
+            raise IOError("Inconsistent or invalid Mat data in file")
+
+        return MatSparse(((M, N), (I, J, V)))
+
+    @decorate_with_conf
+    def writeMatSparse(self, fh, mat):
+        """Writes a Mat into a PETSc binary file handle"""
+
+        ((M, N), (I, J, V)) = mat
+        metadata = np.array([MatSparse._classid, M, N, I[-1]], dtype=self._inttype)
+        rownz = I[1:] - I[:-1]
+
+        assert len(J.shape) == len(V.shape) == len(I.shape) == 1
+        assert len(J) == len(V) == I[-1] == rownz.sum()
+        assert (rownz > -1).all()
+
+        metadata.tofile(fh)
+        rownz.astype(self._inttype).tofile(fh)
+        J.astype(self._inttype).tofile(fh)
+        V.astype(self._scalartype).tofile(fh)
+        return
+
+    @decorate_with_conf
+    def readMatDense(self, fh):
+        """Reads a PETSc Mat, returning a dense representation of the data, must be called after readObjectType()"""
+
+        try:
+            M, N, nz = np.fromfile(fh, dtype=self._inttype, count=3)
+            I = np.empty(M + 1, dtype=self._inttype)
+            I[0] = 0
+            rownz = np.fromfile(fh, dtype=self._inttype, count=M)
+            np.cumsum(rownz, out=I[1:])
+            assert I[-1] == nz
+
+            J = np.fromfile(fh, dtype=self._inttype, count=nz)
+            assert len(J) == nz
+            V = np.fromfile(fh, dtype=self._scalartype, count=nz)
+            assert len(V) == nz
+
+        except (AssertionError, MemoryError, IndexError):
+            raise IOError("Inconsistent or invalid Mat data in file")
+
+        mat = np.zeros((M, N), dtype=self._scalartype)
+        for row in range(M):
+            rstart, rend = I[row : row + 2]
+            mat[row, J[rstart:rend]] = V[rstart:rend]
+        return mat.view(MatDense)
+
+    @decorate_with_conf
+    def readMatSciPy(self, fh):
+        from scipy.sparse import csr_matrix
+
+        (M, N), (I, J, V) = self.readMatSparse(fh)
+        return csr_matrix((V, J, I), shape=(M, N))
+
+    @decorate_with_conf
+    def writeMatSciPy(self, fh, mat):
+        from scipy.sparse import csr_matrix
+
+        if hasattr(mat, "tocsr"):
+            mat = mat.tocsr()
+        assert isinstance(mat, csr_matrix)
+        V = mat.data
+        M, N = mat.shape
+        J = mat.indices
+        I = mat.indptr
+        return self.writeMatSparse(fh, (mat.shape, (mat.indptr, mat.indices, mat.data)))
+
+    @decorate_with_conf
+    def readMat(self, fh, mattype="sparse"):
+        """Reads a PETSc Mat from binary file handle, must be called after readObjectType()
+
+        optional mattype: 'sparse" or 'dense'
+
+        See also: readMatSparse, readMatDense
+        """
+
+        if mattype == "sparse":
+            return self.readMatSparse(fh)
+        elif mattype == "dense":
+            return self.readMatDense(fh)
+        elif mattype == "scipy.sparse":
+            return self.readMatSciPy(fh)
+        else:
+            raise RuntimeError(
+                "Invalid matrix type requested: choose sparse/dense/scipy.sparse"
+            )
+
+    @decorate_with_conf
+    def readIS(self, fh):
+        """Reads a PETSc Index Set from binary file handle, must be called after readObjectType()"""
+
+        try:
+            nz = np.fromfile(fh, dtype=self._inttype, count=1)[0]
+            v = np.fromfile(fh, dtype=self._inttype, count=nz)
+            assert len(v) == nz
+        except (MemoryError, IndexError):
+            raise IOError("Inconsistent or invalid IS data in file")
+        return v.view(IS)
+
+    @decorate_with_conf
+    def writeIS(self, fh, anis):
+        """Writes a PETSc IS to binary file handle."""
+
+        metadata = np.array([IS._classid, len(anis)], dtype=self._inttype)
+        metadata.tofile(fh)
+        anis.astype(self._inttype).tofile(fh)
+        return
+
+    @decorate_with_conf
+    def readObjectType(self, fid):
+        """Returns the next object type as a string in the file"""
+        try:
+            header = np.fromfile(fid, dtype=self._inttype, count=1)[0]
+        except (MemoryError, IndexError):
+            raise DoneWithFile
+        try:
+            objecttype = self._classid[header]
+        except KeyError:
+            raise IOError(
+                "Invalid PetscObject CLASSID or object not implemented for python"
+            )
+        return objecttype
+
+    @decorate_with_conf
+    def readBinaryFile(self, fid, mattype="sparse"):
+        """Reads a PETSc binary file, returning a tuple of the contained objects.
+
+        objects = self.readBinaryFile(fid, **kwargs)
+
+        Input:
+          fid : either file name or handle to an open binary file.
+
+        Output:
+          objects : tuple of objects representing the data in numpy arrays.
+
+        Optional:
+          mattype :
+            'sparse': Return matrices as raw CSR: (M, N), (row, col, val).
+            'dense': Return matrices as MxN numpy arrays.
+            'scipy.sparse': Return matrices as scipy.sparse objects.
+        """
+
+        close = False
+
+        if isinstance(fid, basestring):
+            fid = open(fid, "rb")
+            close = True
+
+        objects = []
+        try:
+            while True:
+                objecttype = self.readObjectType(fid)
+
+                if objecttype == "Vec":
+                    objects.append(self.readVec(fid))
+                elif objecttype == "IS":
+                    objects.append(self.readIS(fid))
+                elif objecttype == "Mat":
+                    objects.append(self.readMat(fid, mattype))
+                elif objecttype == "Real":
+                    objects.append(self.readReal(fid))
+                elif objecttype == "Bag":
+                    raise NotImplementedError("Bag Reader not yet implemented")
+        except DoneWithFile:
+            pass
+        finally:
+            if close:
+                fid.close()
+
+        return tuple(objects)
+
+    @decorate_with_conf
+    def writeBinaryFile(self, fid, objects):
+        """Writes a PETSc binary file containing the objects given.
+
+        readBinaryFile(fid, objects)
+
+        Input:
+          fid : either file handle to an open binary file, or filename.
+          objects : list of objects representing the data in numpy arrays,
+                    which must be of type Vec, IS, MatSparse, or MatSciPy.
+        """
+        close = False
+        if isinstance(fid, basestring):
+            fid = open(fid, "wb")
+            close = True
+
+        for petscobj in objects:
+            if isinstance(petscobj, Vec):
+                self.writeVec(fid, petscobj)
+            elif isinstance(petscobj, IS):
+                self.writeIS(fid, petscobj)
+            elif isinstance(petscobj, MatSparse):
+                self.writeMatSparse(fid, petscobj)
+            elif isinstance(petscobj, MatDense):
+                if close:
+                    fid.close()
+                raise NotImplementedError("Writing a dense matrix is not yet supported")
+            else:
+                try:
+                    self.writeMatSciPy(fid, petscobj)
+                except AssertionError:
+                    if close:
+                        fid.close()
+                    raise TypeError(
+                        "Object %s is not a valid PETSc object" % (petscobj.__repr__())
+                    )
+        if close:
+            fid.close()
+        return
+
+
+def _convert(infile, outfile, args):
+    ext = os.path.splitext(infile)[1]
+    if ext in (".mtx", ".npz"):
+        if ext == ".mtx":
+            import scipy.io
+
+            mat = scipy.io.mmread(infile)
+        else:
+            import scipy.sparse
+
+            mat = scipy.sparse.load_npz(infile)
+        if args.symmetrize:
+            mat = (mat + mat.T) / 2
+        with open(outfile, "wb") as fd:
+            PetscBinaryIO().writeMatSciPy(
+                fd,
+                mat,
+                precision=args.precision,
+                complexscalars=args.complex,
+                indices=args.indices,
+            )
+    else:
+        print("Unknown format: {}".format(infile))
+        exit(1)
+
+
+if __name__ == "__main__":
+    import argparse
+    import os
+
+    parser = argparse.ArgumentParser("PetscBinaryIO")
+    subparsers = parser.add_subparsers(title="commands")
+    convert = subparsers.add_parser(
+        "convert", help="convert matrices to/from PETSc format"
+    )
+    convert.add_argument("infile", help="file to convert")
+    convert.add_argument(
+        "-o", "--outfile", help="name of output file (defaults to {infile}.petsc)"
+    )
+    convert.add_argument(
+        "--symmetrize",
+        help="Symmetrize (A+A^T)/2 during conversion",
+        action="store_true",
+    )
+    convert.add_argument(
+        "--precision",
+        help="Precision of scalar values",
+        choices=["single", "double", "__float128"],
+        default="double",
+    )
+    convert.add_argument("--complex", help="Use complex scalars", action="store_true")
+    convert.add_argument(
+        "--indices",
+        help="Integer size for indices",
+        choices=["32bit", "64bit"],
+        default="32bit",
+    )
+    args = parser.parse_args()
+    if args.outfile is None:
+        args.outfile = os.path.splitext(args.infile)[0] + ".petsc"
+    _convert(args.infile, args.outfile, args)
diff --git a/tests/integrated/test-snes-save-jacobian/read_jacobian.py b/tests/integrated/test-snes-save-jacobian/read_jacobian.py
new file mode 100644
index 0000000000..be3e6fc514
--- /dev/null
+++ b/tests/integrated/test-snes-save-jacobian/read_jacobian.py
@@ -0,0 +1,309 @@
+#!/usr/bin/env python3
+
+"""Read Jacobian diagnostics written by the SNES save-jacobian test.
+
+This helper is intentionally lightweight:
+
+- PETSc binary matrices are read using the bundled ``PetscBinaryIO.py``
+- ``jacobian_index_base`` is read with ``boutdata.collect`` so MPI-written dump
+  files can be reconstructed in serial
+- NumPy is the only required array dependency
+- Pandas and SciPy are optional convenience layers
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import sys
+from pathlib import Path
+from typing import Any
+
+import numpy as np
+
+
+SCRIPT_DIR = Path(__file__).resolve().parent
+REPO_ROOT = SCRIPT_DIR.parents[2]
+
+# Allow this script to run directly from the test directory or build directory.
+for extra_path in (
+    SCRIPT_DIR,
+    REPO_ROOT / "tools" / "pylib",
+    REPO_ROOT / "build" / "tools" / "pylib",
+):
+    if extra_path.exists():
+        sys.path.insert(0, str(extra_path))
+
+import PetscBinaryIO  # noqa: E402
+
+
+RawPetscSparse = tuple[tuple[int, int], tuple[np.ndarray, np.ndarray, np.ndarray]]
+
+
+def load_metadata(path: str | Path) -> dict[str, Any]:
+    """Load Jacobian variable metadata from JSON."""
+
+    with Path(path).open("r", encoding="utf-8") as handle:
+        return json.load(handle)
+
+
+def load_index_base(data_dir: str | Path) -> np.ndarray:
+    """Load ``jacobian_index_base`` from BOUT++ dump files using ``boutdata``."""
+
+    try:
+        from boutdata.collect import collect
+    except ImportError as exc:
+        raise ImportError(
+            "Could not import boutdata.collect. Make sure tools/pylib and "
+            "build/tools/pylib are on PYTHONPATH, and that the Python "
+            "NetCDF dependencies required by boutdata (for example "
+            "'netCDF4') are installed."
+        ) from exc
+
+    index_base = np.asarray(
+        collect("jacobian_index_base", path=str(data_dir), info=False, xguards=True)
+    )
+
+    if index_base.ndim == 2:
+        return index_base[:, :, np.newaxis]
+    if index_base.ndim != 3:
+        raise ValueError(
+            f"Expected jacobian_index_base to have 2 or 3 dimensions, got {index_base.ndim}"
+        )
+    return index_base
+
+
+def _find_matrix_file(data_dir: Path) -> Path:
+    matrix_files = sorted(data_dir.glob("jacobian_*.dat"))
+    if not matrix_files:
+        raise FileNotFoundError(f"No PETSc binary matrix files found in {data_dir}")
+    if len(matrix_files) > 1:
+        raise ValueError(
+            f"Found multiple Jacobian matrix files in {data_dir}; specify one explicitly"
+        )
+    return matrix_files[0]
+
+
+def load_petsc_matrix(
+    path: str | Path, matrix_format: str = "dense"
+) -> np.ndarray | RawPetscSparse:
+    """Load a PETSc binary matrix using the bundled ``PetscBinaryIO`` helper.
+
+    Parameters
+    ----------
+    path:
+        Path to a PETSc binary matrix file.
+    matrix_format:
+        Either ``'dense'`` or ``'sparse'``.
+    """
+
+    if matrix_format not in {"dense", "sparse"}:
+        raise ValueError(
+            f"matrix_format must be 'dense' or 'sparse', got {matrix_format!r}"
+        )
+
+    io = PetscBinaryIO.PetscBinaryIO(
+        precision="double", indices="32bit", complexscalars=False
+    )
+    objects = io.readBinaryFile(str(path), mattype=matrix_format)
+    if not objects:
+        raise ValueError(f"No PETSc objects found in {path}")
+
+    matrix = objects[0]
+    if matrix_format == "dense":
+        return np.asarray(matrix)
+    return matrix
+
+
+def sparse_to_dense(matrix: RawPetscSparse) -> np.ndarray:
+    """Convert a raw PETSc CSR tuple into a dense NumPy array."""
+
+    (nrows, ncols), (indptr, indices, values) = matrix
+    dense = np.zeros((nrows, ncols), dtype=np.asarray(values).dtype)
+    for row in range(nrows):
+        start = int(indptr[row])
+        end = int(indptr[row + 1])
+        dense[row, np.asarray(indices[start:end], dtype=int)] = values[start:end]
+    return dense
+
+
+def to_numpy_dense(matrix: np.ndarray | RawPetscSparse) -> np.ndarray:
+    """Return a dense NumPy matrix regardless of the original representation."""
+
+    if isinstance(matrix, np.ndarray):
+        return np.asarray(matrix)
+    return sparse_to_dense(matrix)
+
+
+def to_scipy_csr(matrix: np.ndarray | RawPetscSparse):
+    """Convert a PETSc sparse matrix representation to ``scipy.sparse.csr_matrix``."""
+
+    try:
+        from scipy.sparse import csr_matrix
+    except ImportError as exc:
+        raise ImportError("SciPy is required for CSR conversion") from exc
+
+    if isinstance(matrix, np.ndarray):
+        return csr_matrix(matrix)
+
+    (nrows, ncols), (indptr, indices, values) = matrix
+    return csr_matrix((values, indices, indptr), shape=(nrows, ncols))
+
+
+def _make_label(name: str, x: int, y: int, z: int) -> str:
+    return f"{name}[x={x},y={y},z={z}]"
+
+
+def build_dof_table(
+    index_base: np.ndarray, metadata: dict[str, Any]
+) -> list[dict[str, Any]]:
+    """Expand ``jacobian_index_base`` plus variable metadata into one record per DOF."""
+
+    records: list[dict[str, Any]] = []
+    variables_2d = metadata.get("variables_2d", [])
+    variables_3d = metadata.get("variables_3d", [])
+    n2d = int(metadata.get("n2d", len(variables_2d)))
+
+    nx, ny, nz = index_base.shape
+    for x in range(nx):
+        for y in range(ny):
+            for z in range(nz):
+                base = int(round(float(index_base[x, y, z])))
+                if base < 0:
+                    continue
+
+                if z == 0:
+                    for variable in variables_2d:
+                        global_index = base + int(variable["offset"])
+                        records.append(
+                            {
+                                "global_index": global_index,
+                                "name": variable["name"],
+                                "field_rank": "2d",
+                                "offset": int(variable["offset"]),
+                                "x": x,
+                                "y": y,
+                                "z": 0,
+                                "label": _make_label(variable["name"], x, y, 0),
+                            }
+                        )
+                    base_3d = base + n2d
+                else:
+                    base_3d = base
+
+                for variable in variables_3d:
+                    global_index = base_3d + int(variable["offset"])
+                    records.append(
+                        {
+                            "global_index": global_index,
+                            "name": variable["name"],
+                            "field_rank": "3d",
+                            "offset": int(variable["offset"]),
+                            "x": x,
+                            "y": y,
+                            "z": z,
+                            "label": _make_label(variable["name"], x, y, z),
+                        }
+                    )
+
+    records.sort(key=lambda record: record["global_index"])
+    return records
+
+
+def load_jacobian(
+    data_dir: str | Path = "data",
+    matrix_filename: str | Path | None = None,
+    matrix_format: str = "dense",
+) -> tuple[np.ndarray | RawPetscSparse, list[dict[str, Any]], list[str]]:
+    """Load the Jacobian matrix and its expanded row/column metadata.
+
+    Returns
+    -------
+    matrix
+        Dense ``np.ndarray`` if ``matrix_format='dense'``, otherwise the raw PETSc CSR
+        tuple ``((M, N), (indptr, indices, values))``.
+    dofs
+        One dict per matrix row/column, sorted by ``global_index``.
+    labels
+        Convenience list of labels, ordered to match rows and columns of ``matrix``.
+    """
+
+    data_path = Path(data_dir)
+    metadata = load_metadata(data_path / "jacobian_metadata.json")
+    index_base = load_index_base(data_path)
+
+    matrix_path = (
+        Path(matrix_filename)
+        if matrix_filename is not None
+        else _find_matrix_file(data_path)
+    )
+    matrix = load_petsc_matrix(matrix_path, matrix_format=matrix_format)
+    dofs = build_dof_table(index_base, metadata)
+    labels = [record["label"] for record in dofs]
+    return matrix, dofs, labels
+
+
+def to_pandas(matrix: np.ndarray | RawPetscSparse, dofs: list[dict[str, Any]]):
+    """Return ``(matrix_df, dof_df)`` using Pandas.
+
+    Pandas is imported lazily so the core reader still works when Pandas is not installed.
+    """
+
+    try:
+        import pandas as pd
+    except ImportError as exc:
+        raise ImportError("Pandas is required for the DataFrame adapter") from exc
+
+    dense_matrix = to_numpy_dense(matrix)
+    labels = [record["label"] for record in dofs]
+    matrix_df = pd.DataFrame(dense_matrix, index=labels, columns=labels)
+    dof_df = pd.DataFrame(dofs)
+    return matrix_df, dof_df
+
+
+def _main() -> None:
+    parser = argparse.ArgumentParser(description="Read SNES Jacobian test output")
+    parser.add_argument(
+        "--data-dir", default="data", help="Directory containing Jacobian outputs"
+    )
+    parser.add_argument(
+        "--matrix-format",
+        choices=("dense", "sparse"),
+        default="dense",
+        help="Read the PETSc matrix as a dense NumPy array or raw sparse CSR tuple",
+    )
+    parser.add_argument(
+        "--matrix-file",
+        default=None,
+        help="Explicit path to the PETSc binary matrix file. Defaults to the only jacobian_*.dat file",
+    )
+    parser.add_argument(
+        "--print-matrix",
+        action="store_true",
+        help="Print the dense Jacobian matrix after loading",
+    )
+    args = parser.parse_args()
+
+    matrix, dofs, labels = load_jacobian(
+        data_dir=args.data_dir,
+        matrix_filename=args.matrix_file,
+        matrix_format=args.matrix_format,
+    )
+
+    if isinstance(matrix, np.ndarray):
+        shape = matrix.shape
+    else:
+        shape = matrix[0]
+
+    print(f"Loaded Jacobian with shape {shape}")
+    print(f"Loaded {len(dofs)} row/column labels")
+    print("First few DOFs:")
+    for record in dofs[: min(10, len(dofs))]:
+        print(f"  {record['global_index']:>4}: {record['label']}")
+
+    if args.print_matrix:
+        print(to_numpy_dense(matrix))
+
+
+if __name__ == "__main__":
+    _main()

From fa34beb970ffa8e543bddbf73b3fcfdb16700ae3 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 19 Aug 2026 10:10:23 +0200
Subject: [PATCH 1723/1827] Add normalisation of g_22_y*

---
 src/mesh/coordinates.cxx | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index bacbbe81c4..25f5f73ed3 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1336,6 +1336,14 @@ void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm
   setBxy(Bxy() / Bnorm);
 #endif
   invalidateMetricCaches();
+  // No we compute g_22_* - they must not be cleared. If they get
+  // cleared, they will be recomputed, but not normalised!
+  g_22_ylow();
+  g_22_yhigh();
+  ASSERT2(_g_22_ylow.has_value());
+  (*_g_22_ylow) /= rhoSQ;
+  ASSERT2(_g_22_yhigh.has_value());
+  (*_g_22_yhigh) /= rhoSQ;
 }
 
 void Coordinates::normaliseMetric(const BoutReal rho_s0, const BoutReal Bnorm) {

From adce6ca5f183b6916c7a19e59a1df9dadf05806e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 19 Aug 2026 10:12:53 +0200
Subject: [PATCH 1724/1827] Handle non-FCI case in normaliseMetricFCI

---
 src/mesh/coordinates.cxx | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 25f5f73ed3..679587e347 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1338,12 +1338,14 @@ void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm
   invalidateMetricCaches();
   // No we compute g_22_* - they must not be cleared. If they get
   // cleared, they will be recomputed, but not normalised!
-  g_22_ylow();
-  g_22_yhigh();
-  ASSERT2(_g_22_ylow.has_value());
-  (*_g_22_ylow) /= rhoSQ;
-  ASSERT2(_g_22_yhigh.has_value());
-  (*_g_22_yhigh) /= rhoSQ;
+  if (Bxy().isFci()) {
+    g_22_ylow();
+    g_22_yhigh();
+    ASSERT2(_g_22_ylow.has_value());
+    (*_g_22_ylow) /= rhoSQ;
+    ASSERT2(_g_22_yhigh.has_value());
+    (*_g_22_yhigh) /= rhoSQ;
+  }
 }
 
 void Coordinates::normaliseMetric(const BoutReal rho_s0, const BoutReal Bnorm) {

From cf90f2590aea0578903fd4e4612ae85d20ef6149 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 19 Aug 2026 10:26:01 +0200
Subject: [PATCH 1725/1827] Remove non-const version from header

It has never been implemented
---
 include/bout/coordinates.hxx | 2 --
 1 file changed, 2 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index dc88d20b3c..479f08156c 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -154,8 +154,6 @@ public:
   /// get g_22 at the cell faces;
   const FieldMetric& g_22_ylow() const;
   const FieldMetric& g_22_yhigh() const;
-  FieldMetric& g_22_ylow();
-  FieldMetric& g_22_yhigh();
   // Cell Areas
   const FieldMetric& cell_area_xlow() const {
     if (_cell_area_xlow.has_value()) {

From 2e951d6a6229bbf2c565eb35cde69b782d9f3a8a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 19 Aug 2026 14:44:23 -0700
Subject: [PATCH 1726/1827] test-snes-save-jacobian: Test outputs

Checks that the Jacobian can be read in either sparse or dense format,
and that the values are as expected.
---
 .../test-snes-save-jacobian/CMakeLists.txt    |  3 +-
 .../test-snes-save-jacobian/read_jacobian.py  | 24 ++++++++++---
 .../test_snes_save_jacobian.py                | 36 +++++++++++++++++++
 3 files changed, 57 insertions(+), 6 deletions(-)

diff --git a/tests/integrated/test-snes-save-jacobian/CMakeLists.txt b/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
index f75c1d7c96..7d043e793e 100644
--- a/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
+++ b/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
@@ -1,9 +1,8 @@
 bout_add_integrated_test(
   test-snes-save-jacobian
   SOURCES test_snes_save_jacobian.cxx
-  CONFLICTS BOUT_USE_METRIC_3D
+  REQUIRES BOUT_HAS_PETSC
   USE_DATA_BOUT_INP
-  REQUIRES BOUT_HAS_FFTW
 )
 
 configure_file(read_jacobian.py read_jacobian.py COPYONLY)
diff --git a/tests/integrated/test-snes-save-jacobian/read_jacobian.py b/tests/integrated/test-snes-save-jacobian/read_jacobian.py
index be3e6fc514..c7dd830169 100644
--- a/tests/integrated/test-snes-save-jacobian/read_jacobian.py
+++ b/tests/integrated/test-snes-save-jacobian/read_jacobian.py
@@ -23,15 +23,31 @@
 
 
 SCRIPT_DIR = Path(__file__).resolve().parent
-REPO_ROOT = SCRIPT_DIR.parents[2]
+
+
+def _discover_repo_root() -> Path | None:
+    """Find the source-tree root from either the source or copied build script."""
+
+    for candidate in (SCRIPT_DIR, *SCRIPT_DIR.parents):
+        if (candidate / "tools" / "pylib").exists():
+            return candidate
+        if (
+            candidate.name == "build"
+            and (candidate.parent / "tools" / "pylib").exists()
+        ):
+            return candidate.parent
+    return None
+
+
+REPO_ROOT = _discover_repo_root()
 
 # Allow this script to run directly from the test directory or build directory.
 for extra_path in (
     SCRIPT_DIR,
-    REPO_ROOT / "tools" / "pylib",
-    REPO_ROOT / "build" / "tools" / "pylib",
+    None if REPO_ROOT is None else REPO_ROOT / "tools" / "pylib",
+    None if REPO_ROOT is None else REPO_ROOT / "build" / "tools" / "pylib",
 ):
-    if extra_path.exists():
+    if extra_path is not None and extra_path.exists():
         sys.path.insert(0, str(extra_path))
 
 import PetscBinaryIO  # noqa: E402
diff --git a/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
index 3b6973745c..4ce492b1ac 100644
--- a/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
+++ b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
@@ -1,2 +1,38 @@
+from pathlib import Path
+import numpy as np
+from read_jacobian import load_jacobian, to_numpy_dense
+
+TEST_DIR = Path(".")
+
+
 def test_runtest(assert_success_in_shell):
     assert_success_in_shell("./test_snes_save_jacobian")
+
+    data_dir = TEST_DIR / "data"
+    metadata_file = data_dir / "jacobian_metadata.json"
+    matrix_files = sorted(data_dir.glob("jacobian_*.dat"))
+
+    assert metadata_file.exists()
+    assert len(matrix_files) == 1
+
+    dense_matrix, dofs, labels = load_jacobian(data_dir=data_dir, matrix_format="dense")
+    sparse_matrix, sparse_dofs, sparse_labels = load_jacobian(
+        data_dir=data_dir, matrix_format="sparse"
+    )
+
+    np.testing.assert_allclose(to_numpy_dense(sparse_matrix), dense_matrix)
+    assert sparse_dofs == dofs
+    assert sparse_labels == labels
+
+    assert dense_matrix.shape == (32, 32)
+    assert len(dofs) == 32
+    assert labels[:4] == [
+        "f[x=0,y=0,z=0]",
+        "g[x=0,y=0,z=0]",
+        "f[x=0,y=1,z=0]",
+        "g[x=0,y=1,z=0]",
+    ]
+
+    expected_block = np.array([[-1.1, 0.0], [0.5, -2.0]])
+    expected_matrix = np.kron(np.eye(16), expected_block)
+    np.testing.assert_allclose(dense_matrix, expected_matrix)

From d6a66f177017d09ac8a773d3347742cc65d0a6e0 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 19 Aug 2026 16:19:39 -0700
Subject: [PATCH 1727/1827] read_jacobian: extract_block and tests

Utility that extracts the block of the Jacobian corresponding
to rows of variable A and columns of variable B.
---
 .../test-snes-save-jacobian/read_jacobian.py  | 110 +++++++++++++++++-
 .../test_snes_save_jacobian.py                |  86 +++++++++++++-
 2 files changed, 193 insertions(+), 3 deletions(-)

diff --git a/tests/integrated/test-snes-save-jacobian/read_jacobian.py b/tests/integrated/test-snes-save-jacobian/read_jacobian.py
index c7dd830169..c778cc707d 100644
--- a/tests/integrated/test-snes-save-jacobian/read_jacobian.py
+++ b/tests/integrated/test-snes-save-jacobian/read_jacobian.py
@@ -56,6 +56,15 @@ def _discover_repo_root() -> Path | None:
 RawPetscSparse = tuple[tuple[int, int], tuple[np.ndarray, np.ndarray, np.ndarray]]
 
 
+def _to_native_endian(array: np.ndarray) -> np.ndarray:
+    """Return an array with native byte order for downstream Python libraries."""
+
+    result = np.asarray(array)
+    if result.dtype.byteorder in {"=", "|"}:
+        return result
+    return result.byteswap().view(result.dtype.newbyteorder("="))
+
+
 def load_metadata(path: str | Path) -> dict[str, Any]:
     """Load Jacobian variable metadata from JSON."""
 
@@ -127,7 +136,7 @@ def load_petsc_matrix(
 
     matrix = objects[0]
     if matrix_format == "dense":
-        return np.asarray(matrix)
+        return _to_native_endian(np.asarray(matrix))
     return matrix
 
 
@@ -140,7 +149,7 @@ def sparse_to_dense(matrix: RawPetscSparse) -> np.ndarray:
         start = int(indptr[row])
         end = int(indptr[row + 1])
         dense[row, np.asarray(indices[start:end], dtype=int)] = values[start:end]
-    return dense
+    return _to_native_endian(dense)
 
 
 def to_numpy_dense(matrix: np.ndarray | RawPetscSparse) -> np.ndarray:
@@ -166,6 +175,103 @@ def to_scipy_csr(matrix: np.ndarray | RawPetscSparse):
     return csr_matrix((values, indices, indptr), shape=(nrows, ncols))
 
 
+def _normalise_dofs(dofs: Any) -> list[dict[str, Any]]:
+    """Return DOF records as a plain list of dicts.
+
+    This accepts either the native ``list[dict]`` returned by ``load_jacobian()``
+    or a Pandas DataFrame created by ``to_pandas()``.
+    """
+
+    if hasattr(dofs, "to_dict"):
+        return list(dofs.to_dict(orient="records"))
+    return list(dofs)
+
+
+def variable_indices(dofs: Any, variable_name: str) -> list[int]:
+    """Return matrix row/column positions corresponding to one variable."""
+
+    records = _normalise_dofs(dofs)
+    positions = [
+        position
+        for position, record in enumerate(records)
+        if record["name"] == variable_name
+    ]
+    if not positions:
+        raise KeyError(f"Variable {variable_name!r} was not found in the DOF metadata")
+    return positions
+
+
+def _slice_raw_petsc_sparse(
+    matrix: RawPetscSparse, row_indices: list[int], col_indices: list[int]
+) -> RawPetscSparse:
+    """Slice a raw PETSc CSR tuple and return the same sparse representation."""
+
+    (_, _), (indptr, indices, values) = matrix
+    col_lookup = {old_col: new_col for new_col, old_col in enumerate(col_indices)}
+    sliced_indptr = np.zeros(len(row_indices) + 1, dtype=np.asarray(indptr).dtype)
+    sliced_indices: list[int] = []
+    sliced_values: list[Any] = []
+
+    nnz = 0
+    for new_row, old_row in enumerate(row_indices):
+        start = int(indptr[old_row])
+        end = int(indptr[old_row + 1])
+        for entry_index in range(start, end):
+            old_col = int(indices[entry_index])
+            new_col = col_lookup.get(old_col)
+            if new_col is None:
+                continue
+            sliced_indices.append(new_col)
+            sliced_values.append(values[entry_index])
+            nnz += 1
+        sliced_indptr[new_row + 1] = nnz
+
+    return (
+        (len(row_indices), len(col_indices)),
+        (
+            sliced_indptr,
+            np.asarray(sliced_indices, dtype=np.asarray(indices).dtype),
+            np.asarray(sliced_values, dtype=np.asarray(values).dtype),
+        ),
+    )
+
+
+def extract_block(matrix: Any, dofs: Any, row_variable: str, col_variable: str) -> Any:
+    """Extract a variable-to-variable Jacobian block.
+
+    Parameters
+    ----------
+    matrix:
+        A dense NumPy array, raw PETSc CSR tuple, or Pandas DataFrame.
+    dofs:
+        DOF metadata as returned by ``load_jacobian()`` or the DataFrame returned
+        by ``to_pandas()``.
+    row_variable, col_variable:
+        Variable names to select from the row and column spaces respectively.
+
+    Returns
+    -------
+    A sliced object in the same representation family as the input ``matrix``.
+    """
+
+    row_indices = variable_indices(dofs, row_variable)
+    col_indices = variable_indices(dofs, col_variable)
+
+    if isinstance(matrix, np.ndarray):
+        return matrix[np.ix_(row_indices, col_indices)]
+
+    if isinstance(matrix, tuple) and len(matrix) == 2:
+        return _slice_raw_petsc_sparse(matrix, row_indices, col_indices)
+
+    if hasattr(matrix, "iloc"):
+        return matrix.iloc[row_indices, col_indices]
+
+    raise TypeError(
+        "extract_block() supports NumPy dense arrays, raw PETSc CSR tuples, "
+        "and Pandas DataFrames"
+    )
+
+
 def _make_label(name: str, x: int, y: int, z: int) -> str:
     return f"{name}[x={x},y={y},z={z}]"
 
diff --git a/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
index 4ce492b1ac..43ce0ee4ac 100644
--- a/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
+++ b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
@@ -1,6 +1,7 @@
 from pathlib import Path
 import numpy as np
-from read_jacobian import load_jacobian, to_numpy_dense
+
+from read_jacobian import extract_block, load_jacobian, to_numpy_dense, to_pandas
 
 TEST_DIR = Path(".")
 
@@ -36,3 +37,86 @@ def test_runtest(assert_success_in_shell):
     expected_block = np.array([[-1.1, 0.0], [0.5, -2.0]])
     expected_matrix = np.kron(np.eye(16), expected_block)
     np.testing.assert_allclose(dense_matrix, expected_matrix)
+
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "f", "f"), -1.1 * np.eye(16)
+    )
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "f", "g"), np.zeros((16, 16))
+    )
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "g", "f"), 0.5 * np.eye(16)
+    )
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "g", "g"), -2.0 * np.eye(16)
+    )
+
+    sparse_ff = extract_block(sparse_matrix, dofs, "f", "f")
+    sparse_gf = extract_block(sparse_matrix, dofs, "g", "f")
+    np.testing.assert_allclose(to_numpy_dense(sparse_ff), -1.1 * np.eye(16))
+    np.testing.assert_allclose(to_numpy_dense(sparse_gf), 0.5 * np.eye(16))
+
+    try:
+        import pandas as pd
+    except ImportError:
+        pd = None
+
+    if pd is not None:
+        matrix_df, dof_df = to_pandas(dense_matrix, dofs)
+        ff_df = extract_block(matrix_df, dof_df, "f", "f")
+        assert isinstance(ff_df, pd.DataFrame)
+        assert list(ff_df.index[:2]) == ["f[x=0,y=0,z=0]", "f[x=0,y=1,z=0]"]
+        assert list(ff_df.columns[:2]) == ["f[x=0,y=0,z=0]", "f[x=0,y=1,z=0]"]
+        np.testing.assert_allclose(ff_df.to_numpy(), -1.1 * np.eye(16))
+
+
+def test_rhs_jacobian(assert_success_in_shell):
+    assert_success_in_shell(
+        "./test_snes_save_jacobian "
+        "solver:jacobian_export_kind=rhs "
+        "solver:jacobian_export_prefix=jacobian_rhs_test"
+    )
+
+    data_dir = TEST_DIR / "data"
+    metadata_file = data_dir / "jacobian_metadata.json"
+    matrix_file = data_dir / "jacobian_rhs_test_rhs_000000.dat"
+
+    assert metadata_file.exists()
+    assert matrix_file.exists()
+
+    dense_matrix, dofs, labels = load_jacobian(
+        data_dir=data_dir, matrix_filename=matrix_file, matrix_format="dense"
+    )
+    sparse_matrix, sparse_dofs, sparse_labels = load_jacobian(
+        data_dir=data_dir, matrix_filename=matrix_file, matrix_format="sparse"
+    )
+
+    np.testing.assert_allclose(to_numpy_dense(sparse_matrix), dense_matrix)
+    assert sparse_dofs == dofs
+    assert sparse_labels == labels
+
+    assert dense_matrix.shape == (32, 32)
+    assert len(dofs) == 32
+    assert labels[:4] == [
+        "f[x=0,y=0,z=0]",
+        "g[x=0,y=0,z=0]",
+        "f[x=0,y=1,z=0]",
+        "g[x=0,y=1,z=0]",
+    ]
+
+    expected_block = np.array([[-0.1, 0.0], [0.5, -1.0]])
+    expected_matrix = np.kron(np.eye(16), expected_block)
+    np.testing.assert_allclose(dense_matrix, expected_matrix)
+
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "f", "f"), -0.1 * np.eye(16)
+    )
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "g", "f"), 0.5 * np.eye(16)
+    )
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "g", "g"), -1.0 * np.eye(16)
+    )
+
+    sparse_gf = extract_block(sparse_matrix, dofs, "g", "f")
+    np.testing.assert_allclose(to_numpy_dense(sparse_gf), 0.5 * np.eye(16))

From 7b9434698c31f5b8f5cb75c8c072483f1b88ae42 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 19 Aug 2026 16:40:58 -0700
Subject: [PATCH 1728/1827] Document Jacobian save methods and API

Adds docstrings and user manual on writing the Jacobian from
SNES and read it into Python.
---
 include/bout/petsc_preconditioner.hxx        |  7 ++
 include/bout/solver.hxx                      | 33 +++++++-
 manual/sphinx/user_docs/time_integration.rst | 80 ++++++++++++++++++++
 src/solver/impls/snes/snes.cxx               | 13 ++--
 src/solver/impls/snes/snes.hxx               | 40 +++++++---
 src/solver/solver.cxx                        |  3 +-
 6 files changed, 158 insertions(+), 18 deletions(-)

diff --git a/include/bout/petsc_preconditioner.hxx b/include/bout/petsc_preconditioner.hxx
index 9fe33f7330..877c52358d 100644
--- a/include/bout/petsc_preconditioner.hxx
+++ b/include/bout/petsc_preconditioner.hxx
@@ -78,9 +78,16 @@ public:
   Mat jacobian() const { return Jfd; }
   MatFDColoring coloring() const { return fdcoloring; }
 
+  /// Save an arbitrary PETSc matrix to disk using ``MatView``.
+  ///
+  /// This is a low-level utility used by solver-specific diagnostic code. It only
+  /// writes the matrix itself in PETSc binary or ASCII format; companion metadata
+  /// such as variable names and index mapping must be written separately by the
+  /// calling solver.
   static PetscErrorCode
   saveMatrix(Mat matrix, const std::string& filename,
              PetscMatrixExportFormat format = PetscMatrixExportFormat::binary);
+  /// Save the internally owned coloring Jacobian matrix ``Jfd``.
   PetscErrorCode
   saveMatrix(const std::string& filename,
              PetscMatrixExportFormat format = PetscMatrixExportFormat::binary) const;
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 10a3d294f1..ade7475206 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -102,7 +102,12 @@ constexpr auto SOLVERRKGENERIC = "rkgeneric";
 enum class FieldCategories : std::uint8_t { VARS, DERIVS, MMS };
 enum class SOLVER_VAR_OP : std::uint8_t { LOAD, SET_ID, SAVE };
 
-BOUT_ENUM_CLASS(JacobianExportKind, system, scaled, rhs);
+BOUT_ENUM_CLASS(
+    JacobianExportKind,
+    system, ///< Jacobian of the full nonlinear system solved by the solver
+    scaled, ///< Jacobian after solver-coordinate transforms such as variable scaling
+    rhs     ///< Jacobian of the raw model RHS in physical variables
+);
 
 /// A type to set where in the list monitors are added
 enum class MonitorPosition { BACK, FRONT };
@@ -371,6 +376,11 @@ public:
 protected:
   friend class SundialsNVectorInterface;
 
+  /// Per-variable metadata written alongside Jacobian diagnostics.
+  ///
+  /// ``offset`` gives the variable position within the per-cell ordering used by
+  /// the PETSc matrix. The full row/column mapping is reconstructed by combining
+  /// these records with ``jacobian_index_base`` from the dump files.
   struct JacobianVariableMetadata {
     int offset{0};
     std::string name;
@@ -380,6 +390,11 @@ protected:
     std::string description;
   };
 
+  /// Top-level JSON description of a saved Jacobian.
+  ///
+  /// This metadata is intentionally compact: per-variable properties are stored
+  /// once here, while per-cell offsets are reconstructed from
+  /// ``jacobian_index_base`` in the output data files.
   struct JacobianMetadata {
     int format_version{1};
     std::string solver_name;
@@ -626,12 +641,25 @@ protected:
   void save_derivs(BoutReal* dudata);
   void set_id(BoutReal* udata);
 
-  /// Returns a Field3D containing the global indices
+  /// Returns a Field3D containing the global indices for each locally-owned DOF.
   Field3D globalIndex(int localStart);
+  /// Returns the base global index for the Jacobian ordering in each cell.
+  ///
+  /// Combined with the variable metadata JSON written by
+  /// ``writeJacobianMetadataJson()``, this allows PETSc matrix rows/columns to be
+  /// mapped back to variable names and ``(x, y, z)`` coordinates in Python.
   Field3D jacobianIndexBase(int localStart = 0);
+  /// Return compact metadata for all evolved ``Field2D`` variables.
   std::vector<JacobianVariableMetadata> getJacobianMetadata2D() const;
+  /// Return compact metadata for all evolved ``Field3D`` variables.
   std::vector<JacobianVariableMetadata> getJacobianMetadata3D() const;
+  /// Build the complete Jacobian metadata record for JSON export.
   JacobianMetadata getJacobianMetadata(const std::string& solver_name) const;
+  /// Write Jacobian metadata as JSON on rank 0.
+  ///
+  /// The JSON file is solver-independent; solver-specific matrix files and the
+  /// ``jacobian_index_base`` output together provide the remaining information
+  /// needed to reconstruct a labeled Jacobian in post-processing.
   void writeJacobianMetadataJson(const std::string& filename,
                                  const std::string& solver_name) const;
 
@@ -698,6 +726,7 @@ private:
   std::string run_restart_from = "yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy";
   /// Save `run_id` and `run_restart_from` every output
   bool save_repeat_run_id{false};
+  /// Write ``jacobian_index_base`` to the dump files for Jacobian diagnostics.
   bool save_jacobian_index_base{false};
 
   /// Current iteration (output time-step) number
diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index f05c11a9ae..e981270c26 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -107,6 +107,9 @@ given in table :numref:`tab-solveropts`.
    +--------------------------+--------------------------------------------+-------------------------------------+
    | diagnose                 | Collect and print additional diagnostics   | cvode, imexbdf2, beuler             |
    +--------------------------+--------------------------------------------+-------------------------------------+
+   | save\_jacobian\_index\_base | Write the per-cell Jacobian base index  | beuler / snes                       |
+   |                          | field used to reconstruct saved Jacobians  |                                     |
+   +--------------------------+--------------------------------------------+-------------------------------------+
    | nvector                  | ``N_Vector`` backend for SUNDIALS solvers: | cvode, ida, arkode                  |
    |                          | ``sundials`` or ``manyvector``             |                                     |
    +--------------------------+--------------------------------------------+-------------------------------------+
@@ -775,6 +778,71 @@ Setting ``solver:force_symmetric_coloring = true``, will make sure
 that the jacobian colouring matrix is symmetric.  This will often
 include a few extra non-zeros that the stencil will miss otherwise
 
+Saving Jacobians for diagnostics
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The SNES solver can save PETSc Jacobian matrices for post-processing.
+This is useful for checking sparsity structure, understanding variable
+coupling, and diagnosing whether solver scaling is helping.
+
+Enable this with:
+
+.. code-block:: ini
+
+   [solver]
+   type = snes
+   save_jacobian = true
+   save_jacobian_index_base = true
+
+By default this writes the Jacobian of the nonlinear system actually
+solved by SNES. Three Jacobian definitions are available:
+
+- ``system``: the Jacobian of the full nonlinear system solved by SNES,
+  including timestep terms and any solver-specific rearrangement.
+- ``scaled``: the Jacobian after solver-coordinate transforms such as
+  variable scaling or ``asinh`` variables.
+- ``rhs``: the Jacobian of the bare model ``rhs()`` in physical variables.
+
+For example, to save the raw RHS Jacobian instead of the system Jacobian:
+
+.. code-block:: bash
+
+   ./your_model solver:save_jacobian=true \
+                solver:save_jacobian_index_base=true \
+                solver:jacobian_export_kind=rhs
+
+To save an ASCII matrix with a custom filename prefix:
+
+.. code-block:: ini
+
+   [solver]
+   save_jacobian = true
+   save_jacobian_index_base = true
+   jacobian_export_kind = scaled
+   jacobian_export_format = ascii
+   jacobian_export_prefix = jacobian_scaled_debug
+
+The Jacobian files are written into ``datadir``:
+
+- ``<prefix>_<kind>_<counter>.dat`` or ``.txt``: PETSc matrix written by
+  ``MatView``.
+- ``<prefix>_metadata.json``: compact JSON metadata describing the ordering
+  of 2D and 3D evolved variables.
+- ``jacobian_index_base`` in the normal BOUT++ dump files: the per-cell base
+  global index needed to expand the compact JSON metadata into one row/column
+  label per degree of freedom.
+
+The JSON metadata stores per-variable information once, including name,
+location, ``evolve_bndry``, and ``constraint`` flags. Row and column labels
+for individual matrix entries are reconstructed by combining this JSON with
+``jacobian_index_base`` and the mesh shape.
+
+For now, an example Python reader is provided in
+``tests/integrated/test-snes-save-jacobian/read_jacobian.py``. It can load
+the PETSc matrix into dense NumPy form, keep it sparse, optionally create
+Pandas views, and extract variable-to-variable blocks such as ``df/dg``.
+This helper is intended to move into a Python package later, likely xBOUT.
+
 
 Variable Scaling
 ~~~~~~~~~~~~~~~~
@@ -878,12 +946,24 @@ Summary of solver options
 +---------------------------+---------------+----------------------------------------------------+
 | diagnose                  | false         | Print diagnostic information every iteration       |
 +---------------------------+---------------+----------------------------------------------------+
+| save_jacobian             | false         | Save Jacobian matrices for diagnostics             |
++---------------------------+---------------+----------------------------------------------------+
+| jacobian_export_kind      | system        | Which Jacobian to save: ``system``, ``scaled``,    |
+|                           |               | or ``rhs``                                         |
++---------------------------+---------------+----------------------------------------------------+
+| jacobian_export_prefix    | jacobian      | Prefix for Jacobian matrix files and metadata JSON |
++---------------------------+---------------+----------------------------------------------------+
+| jacobian_export_format    | binary        | Matrix file format written by PETSc ``MatView``    |
++---------------------------+---------------+----------------------------------------------------+
 | stencil:cross             | 0             | If ``matrix_free=false`` and ``use_coloring=true`` |
 | stencil:square            | 0             | Set the size and shape of the Jacobian coloring    |
 | stencil:taxi              | 2             | stencil.                                           |
 +---------------------------+---------------+----------------------------------------------------+
 | force_symmetric_coloring  | false         | Ensure that the Jacobian coloring is symmetric     |
 +---------------------------+---------------+----------------------------------------------------+
+| save_jacobian_index_base  | false         | Write ``jacobian_index_base`` to the dump files    |
+|                           |               | so saved Jacobians can be reconstructed            |
++---------------------------+---------------+----------------------------------------------------+
 
 The predictor is linear extrapolation from the last two timesteps. It seems to be
 effective, but can be disabled by setting ``predictor = false``.
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index b756463358..9310dccf46 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -379,18 +379,19 @@ SNESSolver::SNESSolver(Options* opts)
                      .doc("Apply asinh() to all variables?")
                      .withDefault<bool>(false)),
       save_jacobian((*options)["save_jacobian"]
-                        .doc("Save Jacobian matrices for diagnostics?")
+                        .doc("Save PETSc Jacobian diagnostics to datadir")
                         .withDefault<bool>(false)),
       jacobian_export_kind((*options)["jacobian_export_kind"]
-                               .doc("Which Jacobian to save: system, scaled, rhs")
+                               .doc("Which Jacobian to save: system, scaled, or rhs")
                                .withDefault(JacobianExportKind::system)),
       jacobian_export_prefix(
           (*options)["jacobian_export_prefix"]
-              .doc("Prefix for saved Jacobian matrix and metadata files")
+              .doc("Prefix for saved Jacobian matrix files and shared metadata JSON")
               .withDefault("jacobian")),
-      jacobian_export_format((*options)["jacobian_export_format"]
-                                 .doc("Format for saved Jacobian matrices: binary, ascii")
-                                 .withDefault(PetscMatrixExportFormat::binary)) {}
+      jacobian_export_format(
+          (*options)["jacobian_export_format"]
+              .doc("PETSc MatView format for saved Jacobians: binary or ascii")
+              .withDefault(PetscMatrixExportFormat::binary)) {}
 
 std::string SNESSolver::getJacobianExportStem(JacobianExportKind kind) {
   // The directory the output data is stored in
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 5c866c2f3a..130d561116 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -111,15 +111,29 @@ public:
   PetscErrorCode scaleJacobian(Mat Jac_new);
 
   /// Convert solver coordinates into the physical variables used by the model.
+  ///
+  /// This applies any active solver-space transforms, for example variable
+  /// scaling or ``asinh`` variables, before the model RHS is evaluated.
   PetscErrorCode toPhysicalState(Vec x, Vec physical_x);
 
-  /// Call the physics model RHS function on a vector of physical variables.
+  /// Evaluate the bare model RHS in physical variables.
+  ///
+  /// This loads ``x`` into the BOUT++ evolving fields, calls ``run_rhs()``, and
+  /// stores the resulting derivatives in ``f`` without applying solver-space
+  /// transforms.
   PetscErrorCode raw_rhs_function(Vec x, Vec f, bool linear);
 
-  /// Apply solver-coordinate transforms, call the raw RHS, and transform the
-  /// resulting derivatives back into solver coordinates.
+  /// Evaluate the RHS in solver coordinates.
+  ///
+  /// This maps ``x`` into physical variables, calls ``raw_rhs_function()``, then
+  /// transforms the derivatives back into the coordinate system used internally by
+  /// SNES.
   PetscErrorCode scaled_rhs_function(Vec x, Vec f, bool linear);
 
+  /// Save a diagnostic Jacobian if enabled by ``solver:save_jacobian``.
+  ///
+  /// ``system`` exports the Jacobian used directly by SNES. ``scaled`` and ``rhs``
+  /// build throwaway coloring Jacobians for diagnostics only.
   PetscErrorCode maybeExportJacobian(Mat system_jacobian, Vec x_solver);
 
   /// Save diagnostics to output
@@ -133,9 +147,13 @@ private:
   /// Rescale state (snes_x) so that all quantities are around 1. If
   /// quantities are near zero then RTOL is used.
   PetscErrorCode rescale();
+  /// Build and save a diagnostic Jacobian of the requested kind.
   PetscErrorCode saveDiagnosticJacobian(JacobianExportKind kind, Vec x_solver);
+  /// Construct the basename used for Jacobian outputs in ``datadir``.
   std::string getJacobianExportStem(JacobianExportKind kind);
+  /// Return the matrix filename including the extension for the selected format.
   std::string getJacobianMatrixFilename(const std::string& stem) const;
+  /// Write the matrix and shared JSON metadata for one diagnostic Jacobian.
   PetscErrorCode exportMatrixAndMetadata(Mat jacobian, const std::string& stem);
 
   BoutSnesOutput output_trigger; ///< Sets when outputs are written
@@ -287,12 +305,16 @@ private:
   bool asinh_vars; ///< Evolve asinh(vars) to compress magnitudes while preserving signs
   const BoutReal asinh_scale = 1e-5; // Scale below which asinh response becomes ~linear
 
-  bool save_jacobian;                      ///< Save Jacobian matrices for diagnostics
-  JacobianExportKind jacobian_export_kind; ///< Which Jacobian to save
-  std::string jacobian_export_prefix; ///< Prefix for Jacobian matrix/metadata outputs
-  PetscMatrixExportFormat jacobian_export_format; ///< Output format for matrix save
-  int jacobian_export_counter{0};                 ///< Running counter for saved Jacobians
-  bool jacobian_metadata_written{false}; ///< Has the shared JSON metadata been written?
+  bool save_jacobian; ///< Save Jacobian diagnostics to ``datadir``?
+  JacobianExportKind
+      jacobian_export_kind; ///< Export ``system``, ``scaled``, or ``rhs`` Jacobian
+  std::string jacobian_export_prefix; ///< Prefix for matrix files and ``*_metadata.json``
+  PetscMatrixExportFormat
+      jacobian_export_format; ///< PETSc ``MatView`` format: binary or ascii
+  int jacobian_export_counter{
+      0}; ///< Running counter appended to successive Jacobian saves
+  bool jacobian_metadata_written{
+      false}; ///< Has the shared metadata JSON already been written?
 
   std::vector<Field2D>
       resid_2d; ///< Storage for residuals of SNES solve, unpacked from snes_f
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 340680f498..21943a14e5 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -136,7 +136,8 @@ Solver::Solver(Options* opts)
                              .withDefault(false)),
       save_jacobian_index_base(
           (*options)["save_jacobian_index_base"]
-              .doc("Write the base global index field used for Jacobian diagnostics")
+              .doc("Write jacobian_index_base so saved PETSc Jacobians can be mapped "
+                   "back to variables and cell indices in post-processing")
               .withDefault(false)),
       is_nonsplit_model_diffusive(
           (*options)["is_nonsplit_model_diffusive"]

From 9de4335dcdd1d735d333df1d31d938d67ed238f4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 20 Aug 2026 10:07:15 +0200
Subject: [PATCH 1729/1827] Add missing headers

---
 src/mesh/boundary_standard.cxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 491b4a5b71..dac6822c43 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -1,3 +1,8 @@
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/sys/expressionparser.hxx"
 #include <bout/boundary_standard.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/build_defines.hxx>
@@ -10,6 +15,8 @@
 #include <bout/output.hxx>
 #include <bout/sys/generator_context.hxx>
 #include <bout/utils.hxx>
+#include <list>
+#include <memory>
 
 using bout::generator::Context;
 

From 7ec4b68a459c74fbb0126b09fbaa3ec165db8376 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 20 Aug 2026 10:13:20 +0200
Subject: [PATCH 1730/1827] apply clang-tidy fixes

---
 include/bout/boundary_standard.hxx |   2 +
 src/mesh/boundary_standard.cxx     | 134 ++++++++++++++---------------
 2 files changed, 65 insertions(+), 71 deletions(-)

diff --git a/include/bout/boundary_standard.hxx b/include/bout/boundary_standard.hxx
index 3cb4b23803..b7848dcf64 100644
--- a/include/bout/boundary_standard.hxx
+++ b/include/bout/boundary_standard.hxx
@@ -5,9 +5,11 @@
 
 #include "bout/boundary_op.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/sys/expressionparser.hxx"
 #include "bout/unused.hxx"
 #include <bout/field_factory.hxx>
 
+#include <memory>
 #include <utility>
 
 /// Dirichlet boundary condition set half way between guard cell and grid cell at 2nd order accuracy
diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index dac6822c43..9a6038eaf5 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -155,27 +155,25 @@ void BoundaryDirichlet_O1::apply(Field2D& f, BoutReal t) {
 
   // Check for staggered grids
 
-  CELL_LOC loc = f.getLocation();
+  CELL_LOC const loc = f.getLocation();
   if (mesh->StaggerGrids) {
     // Staggered
     throw BoutException("dirichlet_o1 BC is not implementated for staggered grids.");
 
-  } else {
-    // Non-staggered, standard case
-    for (; !bndry->isDone(); bndry->next1d()) {
+  } // Non-staggered, standard case
+  for (; !bndry->isDone(); bndry->next1d()) {
 
-      if (fg) {
-        val = fg->generate(Context(bndry, loc, t, mesh));
-      }
-      f(bndry->x, bndry->y) = val;
+    if (fg) {
+      val = fg->generate(Context(bndry, loc, t, mesh));
+    }
+    f(bndry->x, bndry->y) = val;
 
-      // Need to set second guard cell, as may be used for interpolation or upwinding derivatives
-      // This is not very efficient. Both boundary cells can be treated in one loop.
-      for (int i = 1; i < bndry->width; i++) {
-        int xi = bndry->x + i * bndry->bx;
-        int yi = bndry->y + i * bndry->by;
-        f(xi, yi) = val;
-      }
+    // Need to set second guard cell, as may be used for interpolation or upwinding derivatives
+    // This is not very efficient. Both boundary cells can be treated in one loop.
+    for (int i = 1; i < bndry->width; i++) {
+      int xi = bndry->x + i * bndry->bx;
+      int yi = bndry->y + i * bndry->by;
+      f(xi, yi) = val;
     }
   }
 }
@@ -199,32 +197,30 @@ void BoundaryDirichlet_O1::apply(Field3D& f, BoutReal t) {
 
   // Check for staggered grids
 
-  CELL_LOC loc = f.getLocation();
+  CELL_LOC const loc = f.getLocation();
   if (mesh->StaggerGrids) {
     // Staggered.
     throw BoutException("dirichlet_o1 BC is not implementated for staggered grids.");
 
-  } else {
-    // Standard (non-staggered) case
-    for (; !bndry->isDone(); bndry->next1d()) {
+  } // Standard (non-staggered) case
+  for (; !bndry->isDone(); bndry->next1d()) {
+    for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
+      if (fg) {
+        val = fg->generate(Context(bndry, zk, loc, t, mesh));
+      }
+      f(bndry->x, bndry->y, zk) = val;
+    }
+
+    // This is not very efficient. Both boundary cells can be treated in one loop.
+    for (int i = 1; i < bndry->width; i++) {
+      // Set any other guard cells using the values on the cells
+      int xi = bndry->x + i * bndry->bx;
+      int yi = bndry->y + i * bndry->by;
       for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
         if (fg) {
           val = fg->generate(Context(bndry, zk, loc, t, mesh));
         }
-        f(bndry->x, bndry->y, zk) = val;
-      }
-
-      // This is not very efficient. Both boundary cells can be treated in one loop.
-      for (int i = 1; i < bndry->width; i++) {
-        // Set any other guard cells using the values on the cells
-        int xi = bndry->x + i * bndry->bx;
-        int yi = bndry->y + i * bndry->by;
-        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
-          if (fg) {
-            val = fg->generate(Context(bndry, zk, loc, t, mesh));
-          }
-          f(xi, yi, zk) = val;
-        }
+        f(xi, yi, zk) = val;
       }
     }
   }
@@ -238,7 +234,7 @@ void BoundaryDirichlet_O1::apply_ddt(Field2D& f) {
 }
 
 void BoundaryDirichlet_O1::apply_ddt(Field3D& f) {
-  Mesh* mesh = bndry->localmesh;
+  const Mesh* mesh = bndry->localmesh;
   ASSERT1(mesh == f.getMesh());
   Field3D* dt = f.timeDeriv();
 
@@ -1867,7 +1863,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 #if not(BOUT_USE_METRIC_3D)
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
-    Coordinates* metric = f.getCoordinates();
+    const Coordinates* metric = f.getCoordinates();
 
     bndry->first();
 
@@ -1881,30 +1877,28 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
     // Check for staggered grids
 
-    CELL_LOC loc = f.getLocation();
+    CELL_LOC const loc = f.getLocation();
     if (mesh->StaggerGrids) {
       // Staggered.
       throw BoutException("neumann_o1 BC is not implementated for staggered grids.");
 
-    } else {
-      // Non-staggered, standard case
+    } // Non-staggered, standard case
 
-      for (bndry->first(); !bndry->isDone(); bndry->next1d()) {
-        BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
-                         + bndry->by * metric->dy(bndry->x, bndry->y);
+    for (bndry->first(); !bndry->isDone(); bndry->next1d()) {
+      BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
+                       + bndry->by * metric->dy(bndry->x, bndry->y);
 
-        if (fg) {
-          val = fg->generate(Context(bndry, loc, t, mesh));
-        }
+      if (fg) {
+        val = fg->generate(Context(bndry, loc, t, mesh));
+      }
 
-        f(bndry->x, bndry->y) =
-            f(bndry->x - bndry->bx, bndry->y - bndry->by) + delta * val;
-        if (bndry->width == 2) {
-          f(bndry->x + bndry->bx, bndry->y + bndry->by) =
-              f(bndry->x, bndry->y) + delta * val;
-        }
+      f(bndry->x, bndry->y) = f(bndry->x - bndry->bx, bndry->y - bndry->by) + delta * val;
+      if (bndry->width == 2) {
+        f(bndry->x + bndry->bx, bndry->y + bndry->by) =
+            f(bndry->x, bndry->y) + delta * val;
       }
     }
+
 #else
   throw BoutException("Applying boundary condition 'neumann' to Field2D "
                       "not compatible with 3D metrics in all cases.");
@@ -1916,7 +1910,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
   void BoundaryNeumann_O1::apply(Field3D & f, BoutReal t) {
     Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
-    Coordinates* metric = f.getCoordinates();
+    const Coordinates* metric = f.getCoordinates();
 
     bndry->first();
 
@@ -1930,31 +1924,29 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
 
     // Check for staggered grids
 
-    CELL_LOC loc = f.getLocation();
+    CELL_LOC const loc = f.getLocation();
     if (mesh->StaggerGrids) {
       // Staggered.
       throw BoutException("neumann_o1 BC is not implementated for staggered grids.");
-
-    } else {
-      for (; !bndry->isDone(); bndry->next1d()) {
+    }
+    for (; !bndry->isDone(); bndry->next1d()) {
 #if BOUT_USE_METRIC_3D
-        for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
-          BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
-                           + bndry->by * metric->dy(bndry->x, bndry->y, zk);
-#else
-      BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
-                       + bndry->by * metric->dy(bndry->x, bndry->y);
       for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
+        BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
+                         + bndry->by * metric->dy(bndry->x, bndry->y, zk);
+#else
+    BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
+                     + bndry->by * metric->dy(bndry->x, bndry->y);
+    for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
 #endif
-          if (fg) {
-            val = fg->generate(Context(bndry, zk, loc, t, mesh));
-          }
-          f(bndry->x, bndry->y, zk) =
-              f(bndry->x - bndry->bx, bndry->y - bndry->by, zk) + delta * val;
-          if (bndry->width == 2) {
-            f(bndry->x + bndry->bx, bndry->y + bndry->by, zk) =
-                f(bndry->x, bndry->y, zk) + delta * val;
-          }
+        if (fg) {
+          val = fg->generate(Context(bndry, zk, loc, t, mesh));
+        }
+        f(bndry->x, bndry->y, zk) =
+            f(bndry->x - bndry->bx, bndry->y - bndry->by, zk) + delta * val;
+        if (bndry->width == 2) {
+          f(bndry->x + bndry->bx, bndry->y + bndry->by, zk) =
+              f(bndry->x, bndry->y, zk) + delta * val;
         }
       }
     }
@@ -1968,7 +1960,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
   }
 
   void BoundaryNeumann_O1::apply_ddt(Field3D & f) {
-    Mesh* mesh = bndry->localmesh;
+    const Mesh* mesh = bndry->localmesh;
     ASSERT1(mesh == f.getMesh());
     Field3D* dt = f.timeDeriv();
     for (bndry->first(); !bndry->isDone(); bndry->next()) {

From 767436baf4202cda3949b0814301635214ccec94 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 20 Aug 2026 10:17:03 +0200
Subject: [PATCH 1731/1827] Check for only for fields location

Whether staggering is enabled or not does not really matter.
---
 src/mesh/boundary_standard.cxx | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 9a6038eaf5..4fca0b4f17 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -156,7 +156,7 @@ void BoundaryDirichlet_O1::apply(Field2D& f, BoutReal t) {
   // Check for staggered grids
 
   CELL_LOC const loc = f.getLocation();
-  if (mesh->StaggerGrids) {
+  if (loc != CELL_CENTRE) {
     // Staggered
     throw BoutException("dirichlet_o1 BC is not implementated for staggered grids.");
 
@@ -198,7 +198,7 @@ void BoundaryDirichlet_O1::apply(Field3D& f, BoutReal t) {
   // Check for staggered grids
 
   CELL_LOC const loc = f.getLocation();
-  if (mesh->StaggerGrids) {
+  if (loc != CELL_CENTRE) {
     // Staggered.
     throw BoutException("dirichlet_o1 BC is not implementated for staggered grids.");
 
@@ -443,7 +443,7 @@ void BoundaryDirichlet::apply(Field3D& f, BoutReal t) {
   // Check for staggered grids
 
   CELL_LOC loc = f.getLocation();
-  if (mesh->StaggerGrids && loc != CELL_CENTRE) {
+  if (loc != CELL_CENTRE) {
     // Staggered. Need to apply slightly differently
 
     if (loc == CELL_XLOW) {
@@ -945,7 +945,7 @@ void BoundaryDirichlet_O3::apply(Field3D& f, BoutReal t) {
   // Check for staggered grids
 
   CELL_LOC loc = f.getLocation();
-  if (mesh->StaggerGrids && loc != CELL_CENTRE) {
+  if (loc != CELL_CENTRE) {
     // Staggered. Need to apply slightly differently
 
     if (loc == CELL_XLOW) {
@@ -1402,7 +1402,7 @@ void BoundaryDirichlet_O4::apply(Field3D& f, BoutReal t) {
   // Check for staggered grids
 
   CELL_LOC loc = f.getLocation();
-  if (mesh->StaggerGrids && loc != CELL_CENTRE) {
+  if (loc != CELL_CENTRE) {
     // Staggered. Need to apply slightly differently
 
     if (loc == CELL_XLOW) {
@@ -1878,7 +1878,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     // Check for staggered grids
 
     CELL_LOC const loc = f.getLocation();
-    if (mesh->StaggerGrids) {
+    if (loc != CELL_CENTRE) {
       // Staggered.
       throw BoutException("neumann_o1 BC is not implementated for staggered grids.");
 
@@ -1925,7 +1925,7 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     // Check for staggered grids
 
     CELL_LOC const loc = f.getLocation();
-    if (mesh->StaggerGrids) {
+    if (loc != CELL_CENTRE) {
       // Staggered.
       throw BoutException("neumann_o1 BC is not implementated for staggered grids.");
     }
@@ -2215,7 +2215,7 @@ void BoundaryNeumann::apply([[maybe_unused]] Field2D& f, [[maybe_unused]] BoutRe
     // Check for staggered grids
 
     CELL_LOC loc = f.getLocation();
-    if (mesh->StaggerGrids && loc != CELL_CENTRE) {
+    if (loc != CELL_CENTRE) {
       // Staggered. Need to apply slightly differently
       // Use one-sided differencing. Cell is now on
       // the boundary, so use one-sided differencing
@@ -2504,7 +2504,7 @@ void BoundaryNeumann::apply([[maybe_unused]] Field2D& f, [[maybe_unused]] BoutRe
 
     // Check for staggered grids
     CELL_LOC loc = f.getLocation();
-    if (mesh->StaggerGrids && loc != CELL_CENTRE) {
+    if (loc != CELL_CENTRE) {
       throw BoutException("neumann_o4 not implemented with staggered grid yet");
     } else {
       // Non-staggered, standard case
@@ -2556,7 +2556,7 @@ void BoundaryNeumann::apply([[maybe_unused]] Field2D& f, [[maybe_unused]] BoutRe
 
     // Check for staggered grids
     CELL_LOC loc = f.getLocation();
-    if (mesh->StaggerGrids && loc != CELL_CENTRE) {
+    if (loc != CELL_CENTRE) {
       throw BoutException("neumann_o4 not implemented with staggered grid yet");
     } else {
       Coordinates* coords = f.getCoordinates();

From d418f681a211254e1866ffeda5e4d88d1717858a Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 20 Aug 2026 10:21:36 +0200
Subject: [PATCH 1732/1827] Apply some clang-tidy fixes

---
 src/mesh/boundary_standard.cxx | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/mesh/boundary_standard.cxx b/src/mesh/boundary_standard.cxx
index 4fca0b4f17..1e496b4414 100644
--- a/src/mesh/boundary_standard.cxx
+++ b/src/mesh/boundary_standard.cxx
@@ -171,8 +171,8 @@ void BoundaryDirichlet_O1::apply(Field2D& f, BoutReal t) {
     // Need to set second guard cell, as may be used for interpolation or upwinding derivatives
     // This is not very efficient. Both boundary cells can be treated in one loop.
     for (int i = 1; i < bndry->width; i++) {
-      int xi = bndry->x + i * bndry->bx;
-      int yi = bndry->y + i * bndry->by;
+      const int xi = bndry->x + (i * bndry->bx);
+      const int yi = bndry->y + (i * bndry->by);
       f(xi, yi) = val;
     }
   }
@@ -214,8 +214,8 @@ void BoundaryDirichlet_O1::apply(Field3D& f, BoutReal t) {
     // This is not very efficient. Both boundary cells can be treated in one loop.
     for (int i = 1; i < bndry->width; i++) {
       // Set any other guard cells using the values on the cells
-      int xi = bndry->x + i * bndry->bx;
-      int yi = bndry->y + i * bndry->by;
+      const int xi = bndry->x + (i * bndry->bx);
+      const int yi = bndry->y + (i * bndry->by);
       for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
         if (fg) {
           val = fg->generate(Context(bndry, zk, loc, t, mesh));
@@ -1885,17 +1885,18 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
     } // Non-staggered, standard case
 
     for (bndry->first(); !bndry->isDone(); bndry->next1d()) {
-      BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
-                       + bndry->by * metric->dy(bndry->x, bndry->y);
+      const BoutReal delta = (bndry->bx * metric->dx(bndry->x, bndry->y))
+                             + (bndry->by * metric->dy(bndry->x, bndry->y));
 
       if (fg) {
         val = fg->generate(Context(bndry, loc, t, mesh));
       }
 
-      f(bndry->x, bndry->y) = f(bndry->x - bndry->bx, bndry->y - bndry->by) + delta * val;
+      f(bndry->x, bndry->y) =
+          f(bndry->x - bndry->bx, bndry->y - bndry->by) + (delta * val);
       if (bndry->width == 2) {
         f(bndry->x + bndry->bx, bndry->y + bndry->by) =
-            f(bndry->x, bndry->y) + delta * val;
+            f(bndry->x, bndry->y) + (delta * val);
       }
     }
 
@@ -1935,18 +1936,18 @@ void BoundaryNeumann_NonOrthogonal::apply(Field3D& f) {
         BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y, zk)
                          + bndry->by * metric->dy(bndry->x, bndry->y, zk);
 #else
-    BoutReal delta = bndry->bx * metric->dx(bndry->x, bndry->y)
-                     + bndry->by * metric->dy(bndry->x, bndry->y);
+    const BoutReal delta = (bndry->bx * metric->dx(bndry->x, bndry->y))
+                           + (bndry->by * metric->dy(bndry->x, bndry->y));
     for (int zk = mesh->zstart; zk <= mesh->zend; zk++) {
 #endif
         if (fg) {
           val = fg->generate(Context(bndry, zk, loc, t, mesh));
         }
         f(bndry->x, bndry->y, zk) =
-            f(bndry->x - bndry->bx, bndry->y - bndry->by, zk) + delta * val;
+            f(bndry->x - bndry->bx, bndry->y - bndry->by, zk) + (delta * val);
         if (bndry->width == 2) {
           f(bndry->x + bndry->bx, bndry->y + bndry->by, zk) =
-              f(bndry->x, bndry->y, zk) + delta * val;
+              f(bndry->x, bndry->y, zk) + (delta * val);
         }
       }
     }

From bb63ea48df85124e6420ef4331fad752166e7ca5 Mon Sep 17 00:00:00 2001
From: totork <ttork96@gmail.com>
Date: Fri, 21 Aug 2026 11:59:16 +0200
Subject: [PATCH 1733/1827] Added dissipative flag to Div_par_mod in Fci

---
 include/bout/fv_ops.hxx                            |  2 +-
 include/bout/fv_ops_impl.hxx                       | 14 +++++++++++++-
 manual/sphinx/user_docs/differential_operators.rst |  5 +++--
 src/mesh/fv_ops.cxx                                | 14 +++++++-------
 4 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index 67db42cf0b..fea31ef431 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -157,7 +157,7 @@ Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc = CELL_
 template <typename CellEdges = MC>
 Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
                     const Field3D& wave_speed_in, Field3D& flow_ylow,
-                    bool fixflux = true);
+                    bool fixflux = true, bool dissipative = false);
 
 /// This operator calculates Div_par(f v v)
 /// It is used primarily (only?) in the parallel momentum equation.
diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 1b1379d5ad..161e188ca3 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -633,11 +633,15 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 ///                          Already includes area factor * flux
 template <typename CellEdges>
 Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
-                    const Field3D& wave_speed_in, Field3D& flow_ylow, bool fixflux) {
+                    const Field3D& wave_speed_in, Field3D& flow_ylow, bool fixflux, bool dissipative) {
 
   Coordinates* coord = f_in.getCoordinates();
   ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
 
+  if (!f_in.isFci() && dissipative) {
+    throw BoutException("Using dissipative flag in Div_par_mod but no Fci parallel transform. This flag will have no impact on the simulation");
+  }
+  
   if (f_in.isFci()) {
     // Use mid-point (cell boundary) averages
 
@@ -661,6 +665,14 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
                    - 0.25 * (f_in[i] + f_down[iym]) * (v_in[i] + v_down[iym])
                          * coord->cell_area_ylow()[i])
                   / coord->cell_volume()[i];
+
+      if (dissipative) {
+        const BoutReal amax = BOUTMAX(fabs(wave_speed_in[i]), fabs(v_in[i]), fabs(v_up[iyp]), fabs(v_down[iym]));       
+        result[i] += (0.5 * amax * (f_in[i] - f_up[iyp]) * coord->cell_area_yhigh()[i]
+                      + 0.5 * amax * (f_in[i] - f_down[iym]) * coord->cell_area_ylow()[i])
+                     / coord->cell_volume()[i];
+      }
+      
     }
     return result;
   }
diff --git a/manual/sphinx/user_docs/differential_operators.rst b/manual/sphinx/user_docs/differential_operators.rst
index 529037eb8b..de1d370f81 100644
--- a/manual/sphinx/user_docs/differential_operators.rst
+++ b/manual/sphinx/user_docs/differential_operators.rst
@@ -586,13 +586,14 @@ than ``FV::Div_par`` for the same limiter choice.
    template<typename CellEdges = MC>
    Field3D Div_par_mod(const Field3D &f_in, const Field3D &v_in,
                        const Field3D &a, Field3D &flow_ylow,
-                       bool fixflux=true);
+                       bool fixflux=true, bool dissipative=false);
 
 
 The extra output argument ``flow_ylow`` stores the flow through the lower
 :math:`y` cell boundary, including the area factor. This can be useful as a
 diagnostic in energy or flux budgets. For FCI fields this diagnostic is
-currently returned as zero.
+currently returned as zero. The flag ``dissipative`` activates a local
+Rusanov-flux if used in Fci.
 
 
 Parallel momentum flux ``Div_par_fvv``
diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index fb67883c50..d00187fedc 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -578,7 +578,7 @@ template Field3D Div_par<Upwind>(const Field3D& f_in, const Field3D& v_in,
 template Field3D Div_f_v<Upwind>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<Upwind>(const Field3D& f_in, const Field3D& v_in,
                                      const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                     bool fixflux);
+                                     bool fixflux, bool dissipative);
 template Field3D Div_par_fvv_heating<Upwind>(const Field3D& f_in, const Field3D& v_in,
                                              const Field3D& wave_speed_in,
                                              Field3D& flow_ylow, bool fixflux);
@@ -592,7 +592,7 @@ template Field3D Div_par<Fromm>(const Field3D& f_in, const Field3D& v_in,
 template Field3D Div_f_v<Fromm>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<Fromm>(const Field3D& f_in, const Field3D& v_in,
                                     const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                    bool fixflux);
+                                    bool fixflux, bool dissipative);
 template Field3D Div_par_fvv_heating<Fromm>(const Field3D& f_in, const Field3D& v_in,
                                             const Field3D& wave_speed_in,
                                             Field3D& flow_ylow, bool fixflux);
@@ -606,7 +606,7 @@ template Field3D Div_par<MinMod>(const Field3D& f_in, const Field3D& v_in,
 template Field3D Div_f_v<MinMod>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<MinMod>(const Field3D& f_in, const Field3D& v_in,
                                      const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                     bool fixflux);
+                                     bool fixflux, bool dissipative);
 template Field3D Div_par_fvv_heating<MinMod>(const Field3D& f_in, const Field3D& v_in,
                                              const Field3D& wave_speed_in,
                                              Field3D& flow_ylow, bool fixflux);
@@ -620,7 +620,7 @@ template Field3D Div_par<MC>(const Field3D& f_in, const Field3D& v_in,
 template Field3D Div_f_v<MC>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<MC>(const Field3D& f_in, const Field3D& v_in,
                                  const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                 bool fixflux);
+                                 bool fixflux, bool dissipative);
 template Field3D Div_par_fvv_heating<MC>(const Field3D& f_in, const Field3D& v_in,
                                          const Field3D& wave_speed_in, Field3D& flow_ylow,
                                          bool fixflux);
@@ -635,7 +635,7 @@ template Field3D Div_f_v<Superbee>(const Field3D& n_in, const Vector3D& v,
                                    bool bndry_flux);
 template Field3D Div_par_mod<Superbee>(const Field3D& f_in, const Field3D& v_in,
                                        const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                       bool fixflux);
+                                       bool fixflux, bool dissipative);
 template Field3D Div_par_fvv_heating<Superbee>(const Field3D& f_in, const Field3D& v_in,
                                                const Field3D& wave_speed_in,
                                                Field3D& flow_ylow, bool fixflux);
@@ -650,7 +650,7 @@ template Field3D Div_f_v<VanAlbada>(const Field3D& n_in, const Vector3D& v,
                                     bool bndry_flux);
 template Field3D Div_par_mod<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
                                         const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                        bool fixflux);
+                                        bool fixflux, bool dissipative);
 template Field3D Div_par_fvv_heating<VanAlbada>(const Field3D& f_in, const Field3D& v_in,
                                                 const Field3D& wave_speed_in,
                                                 Field3D& flow_ylow, bool fixflux);
@@ -664,7 +664,7 @@ template Field3D Div_par<WENO3>(const Field3D& f_in, const Field3D& v_in,
 template Field3D Div_f_v<WENO3>(const Field3D& n_in, const Vector3D& v, bool bndry_flux);
 template Field3D Div_par_mod<WENO3>(const Field3D& f_in, const Field3D& v_in,
                                     const Field3D& wave_speed_in, Field3D& flow_ylow,
-                                    bool fixflux);
+                                    bool fixflux, bool dissipative);
 template Field3D Div_par_fvv_heating<WENO3>(const Field3D& f_in, const Field3D& v_in,
                                             const Field3D& wave_speed_in,
                                             Field3D& flow_ylow, bool fixflux);

From d204053e05fa61445616486998d68d30ce8d6963 Mon Sep 17 00:00:00 2001
From: totork <ttork96@gmail.com>
Date: Fri, 21 Aug 2026 12:14:50 +0200
Subject: [PATCH 1734/1827] Formatting

---
 include/bout/fv_ops.hxx      |  4 ++--
 include/bout/fv_ops_impl.hxx | 12 +++++++-----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/include/bout/fv_ops.hxx b/include/bout/fv_ops.hxx
index fea31ef431..cdb0a067ed 100644
--- a/include/bout/fv_ops.hxx
+++ b/include/bout/fv_ops.hxx
@@ -156,8 +156,8 @@ Field3D Div_Perp_Lap(const Field3D& a, const Field3D& f, CELL_LOC outloc = CELL_
 ///                          For FCI fields this diagnostic is currently set to zero.
 template <typename CellEdges = MC>
 Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
-                    const Field3D& wave_speed_in, Field3D& flow_ylow,
-                    bool fixflux = true, bool dissipative = false);
+                    const Field3D& wave_speed_in, Field3D& flow_ylow, bool fixflux = true,
+                    bool dissipative = false);
 
 /// This operator calculates Div_par(f v v)
 /// It is used primarily (only?) in the parallel momentum equation.
diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 161e188ca3..548f6bfc3a 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -633,15 +633,17 @@ Field3D Div_f_v(const Field3D& n_in, const Vector3D& v, bool bndry_flux) {
 ///                          Already includes area factor * flux
 template <typename CellEdges>
 Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
-                    const Field3D& wave_speed_in, Field3D& flow_ylow, bool fixflux, bool dissipative) {
+                    const Field3D& wave_speed_in, Field3D& flow_ylow, bool fixflux,
+                    bool dissipative) {
 
   Coordinates* coord = f_in.getCoordinates();
   ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
 
   if (!f_in.isFci() && dissipative) {
-    throw BoutException("Using dissipative flag in Div_par_mod but no Fci parallel transform. This flag will have no impact on the simulation");
+    throw BoutException("Using dissipative flag in Div_par_mod but no Fci parallel "
+                        "transform. This flag will have no impact on the simulation");
   }
-  
+
   if (f_in.isFci()) {
     // Use mid-point (cell boundary) averages
 
@@ -667,12 +669,12 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
                   / coord->cell_volume()[i];
 
       if (dissipative) {
-        const BoutReal amax = BOUTMAX(fabs(wave_speed_in[i]), fabs(v_in[i]), fabs(v_up[iyp]), fabs(v_down[iym]));       
+        const BoutReal amax = BOUTMAX(fabs(wave_speed_in[i]), fabs(v_in[i]),
+                                      fabs(v_up[iyp]), fabs(v_down[iym]));
         result[i] += (0.5 * amax * (f_in[i] - f_up[iyp]) * coord->cell_area_yhigh()[i]
                       + 0.5 * amax * (f_in[i] - f_down[iym]) * coord->cell_area_ylow()[i])
                      / coord->cell_volume()[i];
       }
-      
     }
     return result;
   }

From d5f4814fa8901e9cee021379678fd4a7313f4141 Mon Sep 17 00:00:00 2001
From: totork <ttork96@gmail.com>
Date: Fri, 21 Aug 2026 12:16:40 +0200
Subject: [PATCH 1735/1827] Only check if dissipative is used in Div_par_mod in
 the non-Fci part

---
 include/bout/fv_ops_impl.hxx | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/include/bout/fv_ops_impl.hxx b/include/bout/fv_ops_impl.hxx
index 548f6bfc3a..8f76dae6a3 100644
--- a/include/bout/fv_ops_impl.hxx
+++ b/include/bout/fv_ops_impl.hxx
@@ -639,11 +639,6 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
   Coordinates* coord = f_in.getCoordinates();
   ASSERT1_FIELDS_COMPATIBLE(f_in, v_in);
 
-  if (!f_in.isFci() && dissipative) {
-    throw BoutException("Using dissipative flag in Div_par_mod but no Fci parallel "
-                        "transform. This flag will have no impact on the simulation");
-  }
-
   if (f_in.isFci()) {
     // Use mid-point (cell boundary) averages
 
@@ -680,6 +675,12 @@ Field3D Div_par_mod(const Field3D& f_in, const Field3D& v_in,
   }
   ASSERT1_FIELDS_COMPATIBLE(f_in, wave_speed_in);
 
+  // Throw error when not Fci
+  if (dissipative) {
+    throw BoutException("Using dissipative flag in Div_par_mod but no Fci parallel "
+                        "transform. This flag will have no impact on the simulation");
+  }
+
   const Mesh* mesh = f_in.getMesh();
 
   CellEdges cellboundary;

From d13ac5e983fe766a8b5037d600e8015e13ac5340 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 21 Aug 2026 14:02:07 +0200
Subject: [PATCH 1736/1827] Add wrapper for Bxy

---
 include/bout/coordinates.hxx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index f01e3883e0..2ef6cfb113 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -111,6 +111,11 @@ public:
   const BoutReal& J(int x, int y) const { return J()(x, y); }
 #endif
 
+  const BoutReal& Bxy(int x, int y, int z) const { return Bxy()(x, y, z); }
+#if not(BOUT_USE_METRIC_3D)
+  const BoutReal& Bxy(int x, int y) const { return Bxy()(x, y); }
+#endif
+
   void setDx(FieldMetric dx, bool communicate = true);
   void setDy(FieldMetric dy, bool communicate = true);
   void setDz(FieldMetric dz, bool communicate = true);

From d6e66f58990d155aecff796375f22d75c29bec61 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 21 Aug 2026 08:49:26 -0700
Subject: [PATCH 1737/1827] CVODE solver save jacobian

---
 manual/sphinx/user_docs/time_integration.rst  |   2 +-
 src/solver/impls/cvode/cvode.cxx              | 245 +++++++++++++++++-
 src/solver/impls/cvode/cvode.hxx              |  19 +-
 tests/integrated/CMakeLists.txt               |   1 +
 .../PetscBinaryIO.py                          |   0
 .../read_jacobian.py                          |   4 +-
 .../test-cvode-save-jacobian/CMakeLists.txt   |   9 +
 .../test-cvode-save-jacobian/data/BOUT.inp    |  29 +++
 .../test_cvode_save_jacobian.cxx              |  27 ++
 .../test_cvode_save_jacobian.py               |  95 +++++++
 .../test-snes-save-jacobian/CMakeLists.txt    |   4 +-
 11 files changed, 415 insertions(+), 20 deletions(-)
 rename tests/integrated/{test-snes-save-jacobian => jacobian_tools}/PetscBinaryIO.py (100%)
 rename tests/integrated/{test-snes-save-jacobian => jacobian_tools}/read_jacobian.py (98%)
 create mode 100644 tests/integrated/test-cvode-save-jacobian/CMakeLists.txt
 create mode 100644 tests/integrated/test-cvode-save-jacobian/data/BOUT.inp
 create mode 100644 tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.cxx
 create mode 100644 tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.py

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index e981270c26..150bb43c87 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -838,7 +838,7 @@ for individual matrix entries are reconstructed by combining this JSON with
 ``jacobian_index_base`` and the mesh shape.
 
 For now, an example Python reader is provided in
-``tests/integrated/test-snes-save-jacobian/read_jacobian.py``. It can load
+``tests/integrated/jacobian_tools/read_jacobian.py``. It can load
 the PETSc matrix into dense NumPy form, keep it sparse, optionally create
 Pandas views, and extract variable-to-variable blocks such as ``df/dg``.
 This helper is intended to move into a Python package later, likely xBOUT.
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index d3441ad959..8394702a5f 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -166,6 +166,23 @@ CvodeSolver::CvodeSolver(Options* opts)
               .doc("Factor by which the Krylov linear solver’s convergence test constant "
                    "is reduced from the nonlinear solver test constant.")
               .withDefault(0.05)),
+      save_jacobian((*options)["save_jacobian"]
+                        .doc("Save PETSc Jacobian diagnostics to datadir")
+                        .withDefault(false)),
+      jacobian_export_kind((*options)["jacobian_export_kind"]
+                               .doc("Which Jacobian to save: system, scaled, or rhs")
+                               .withDefault(JacobianExportKind::system)),
+      jacobian_export_trigger((*options)["jacobian_export_trigger"]
+                                  .doc("When to save Jacobians: output or linear_setup")
+                                  .withDefault(CvodeJacobianExportTrigger::linear_setup)),
+      jacobian_export_prefix(
+          (*options)["jacobian_export_prefix"]
+              .doc("Prefix for saved Jacobian matrix files and shared metadata JSON")
+              .withDefault("jacobian")),
+      jacobian_export_format(
+          (*options)["jacobian_export_format"]
+              .doc("PETSc MatView format for saved Jacobians: binary or ascii")
+              .withDefault(PetscMatrixExportFormat::binary)),
       suncontext(createSUNContext(BoutComm::get())) {
   has_constraints = false; // This solver doesn't have constraints
   canReset = true;
@@ -223,6 +240,115 @@ CvodeSolver::~CvodeSolver() {
   }
 }
 
+#if BOUT_HAS_PETSC
+std::string CvodeSolver::getJacobianExportStem(JacobianExportKind kind) {
+  const std::string datadir = Options::root()["datadir"];
+  return fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix, toString(kind),
+                     jacobian_export_counter++);
+}
+
+std::string CvodeSolver::getJacobianMatrixFilename(const std::string& stem) const {
+  return stem
+         + (jacobian_export_format == PetscMatrixExportFormat::binary ? ".dat" : ".txt");
+}
+
+PetscErrorCode CvodeSolver::exportMatrixAndMetadata(Mat jacobian,
+                                                    const std::string& stem) {
+  if (!jacobian_metadata_written) {
+    const std::string datadir = Options::root()["datadir"];
+    const std::string metadata_filename =
+        datadir + "/" + jacobian_export_prefix + "_metadata.json";
+    output.write("Jacobian metadata written to {}\n", metadata_filename);
+    writeJacobianMetadataJson(metadata_filename, "cvode");
+    jacobian_metadata_written = true;
+  }
+
+  PetscCall(PetscPreconditioner::saveMatrix(jacobian, getJacobianMatrixFilename(stem),
+                                            jacobian_export_format));
+  PetscFunctionReturn(PETSC_SUCCESS);
+}
+
+PetscErrorCode CvodeSolver::saveDiagnosticJacobian(JacobianExportKind kind, Vec x,
+                                                   BoutReal t, BoutReal gamma) {
+  if (kind == JacobianExportKind::scaled) {
+    throw BoutException("solver:jacobian_export_kind=scaled is not supported for CVODE");
+  }
+
+  petsc_t = t;
+  petsc_gamma = gamma;
+
+  PetscPreconditioner diagnostic_preconditioner;
+  Field3D index = globalIndex(0);
+  PetscCall(diagnostic_preconditioner.createJacobianPattern(
+      index, *options, getLocalN(), n2Dvars(), n3Dvars(), BoutComm::get()));
+
+  if (kind == JacobianExportKind::rhs) {
+    PetscCall(diagnostic_preconditioner.updateColoring(CvodeSolver::petscFormRhsFunction,
+                                                       this));
+  } else {
+    PetscCall(
+        diagnostic_preconditioner.updateColoring(CvodeSolver::petscFormFunction, this));
+  }
+
+  Vec diagnostic_f{nullptr};
+  PetscCall(VecDuplicate(x, &diagnostic_f));
+  if (kind == JacobianExportKind::rhs) {
+    PetscCall(CvodeSolver::petscFormRhsFunction(nullptr, x, diagnostic_f, this));
+  } else {
+    PetscCall(CvodeSolver::petscFormFunction(nullptr, x, diagnostic_f, this));
+  }
+  PetscCall(MatFDColoringSetF(diagnostic_preconditioner.coloring(), diagnostic_f));
+
+  Mat diagnostic_jacobian = diagnostic_preconditioner.jacobian();
+  PetscCall(MatZeroEntries(diagnostic_jacobian));
+  PetscCall(MatFDColoringApply(diagnostic_jacobian, diagnostic_preconditioner.coloring(),
+                               x, nullptr));
+  PetscCall(MatAssemblyBegin(diagnostic_jacobian, MAT_FINAL_ASSEMBLY));
+  PetscCall(MatAssemblyEnd(diagnostic_jacobian, MAT_FINAL_ASSEMBLY));
+  PetscCall(exportMatrixAndMetadata(diagnostic_jacobian, getJacobianExportStem(kind)));
+  PetscCall(VecDestroy(&diagnostic_f));
+
+  PetscFunctionReturn(PETSC_SUCCESS);
+}
+
+PetscErrorCode CvodeSolver::maybeExportJacobian(Mat system_jacobian, Vec x, BoutReal t,
+                                                BoutReal gamma) {
+  if (!save_jacobian
+      or jacobian_export_trigger != CvodeJacobianExportTrigger::linear_setup) {
+    PetscFunctionReturn(PETSC_SUCCESS);
+  }
+
+  if (jacobian_export_kind == JacobianExportKind::system) {
+    PetscCall(exportMatrixAndMetadata(system_jacobian,
+                                      getJacobianExportStem(jacobian_export_kind)));
+    PetscFunctionReturn(PETSC_SUCCESS);
+  }
+
+  PetscFunctionReturn(saveDiagnosticJacobian(jacobian_export_kind, x, t, gamma));
+}
+
+PetscErrorCode CvodeSolver::maybeExportOutputJacobian(BoutReal t) {
+  if (!save_jacobian or jacobian_export_trigger != CvodeJacobianExportTrigger::output) {
+    PetscFunctionReturn(PETSC_SUCCESS);
+  }
+
+  Vec x{nullptr};
+  PetscCall(VecCreate(BoutComm::get(), &x));
+  PetscCall(VecSetSizes(x, getLocalN(), PETSC_DETERMINE));
+  PetscCall(VecSetType(x, VECMPI));
+  PetscCall(VecSetUp(x));
+
+  BoutReal* xdata = nullptr;
+  PetscCall(VecGetArray(x, &xdata));
+  save_vars(xdata);
+  PetscCall(VecRestoreArray(x, &xdata));
+
+  PetscErrorCode ierr = saveDiagnosticJacobian(JacobianExportKind::rhs, x, t, 0.0);
+  PetscCall(VecDestroy(&x));
+  PetscFunctionReturn(ierr);
+}
+#endif
+
 /**************************************************************************
  * Initialise
  **************************************************************************/
@@ -381,6 +507,57 @@ int CvodeSolver::init() {
     N_VDestroy(constraints_vec);
   }
 
+  CvodePreconMethod selected_precon = precon_method;
+  if (selected_precon == CvodePreconMethod::Auto) {
+    if (hasPreconditioner()) {
+      selected_precon = CvodePreconMethod::user;
+    } else if (bout::build::has_petsc) {
+      selected_precon = CvodePreconMethod::petsc;
+    } else {
+      selected_precon = CvodePreconMethod::bbd;
+    }
+  }
+
+  if (save_jacobian) {
+#if !BOUT_HAS_PETSC
+    throw BoutException("solver:save_jacobian for CVODE requires PETSc support.");
+#else
+    if (jacobian_export_kind == JacobianExportKind::scaled) {
+      throw BoutException(
+          "solver:jacobian_export_kind=scaled is not supported for CVODE because "
+          "CVODE does not currently apply solver-coordinate scaling.");
+    }
+    if (jacobian_export_kind == JacobianExportKind::system
+        and jacobian_export_trigger != CvodeJacobianExportTrigger::linear_setup) {
+      throw BoutException("solver:jacobian_export_kind=system for CVODE requires "
+                          "solver:jacobian_export_trigger=linear_setup.");
+    }
+    if (jacobian_export_trigger == CvodeJacobianExportTrigger::output
+        and jacobian_export_kind != JacobianExportKind::rhs) {
+      throw BoutException("solver:jacobian_export_trigger=output for CVODE currently "
+                          "supports only solver:jacobian_export_kind=rhs.");
+    }
+    if (jacobian_export_trigger == CvodeJacobianExportTrigger::linear_setup) {
+      if (func_iter) {
+        throw BoutException("solver:jacobian_export_trigger=linear_setup for CVODE "
+                            "requires Newton iteration (set solver:func_iter=false).");
+      }
+      if (nvector_type == NVectorType::ManyVector) {
+        throw BoutException("solver:jacobian_export_trigger=linear_setup for CVODE is "
+                            "not supported with solver:nvector=manyvector.");
+      }
+      if (selected_precon != CvodePreconMethod::petsc) {
+        throw BoutException("solver:jacobian_export_trigger=linear_setup for CVODE "
+                            "currently requires solver:cvode_precon_method=petsc "
+                            "(or auto resolving to petsc).");
+      }
+    }
+    if (!petsc_lib) {
+      petsc_lib = std::make_unique<PetscLib>();
+    }
+#endif
+  }
+
   /// Newton method can include Preconditioners and Jacobian function
   if (func_iter) {
     output_info.write("\tUsing Functional iteration\n");
@@ -395,17 +572,6 @@ int CvodeSolver::init() {
   } else {
     output_info.write("\tUsing Newton iteration\n");
 
-    CvodePreconMethod selected_precon = precon_method;
-    if (selected_precon == CvodePreconMethod::Auto) {
-      if (hasPreconditioner()) {
-        selected_precon = CvodePreconMethod::user;
-      } else if (bout::build::has_petsc) {
-        selected_precon = CvodePreconMethod::petsc;
-      } else {
-        selected_precon = CvodePreconMethod::bbd;
-      }
-    }
-
     auto prectype = SUN_PREC_NONE;
     if (selected_precon != CvodePreconMethod::none) {
       if (rightprec) {
@@ -719,14 +885,21 @@ BoutReal CvodeSolver::run(BoutReal tout) {
   // Copy variables
   backend.copy_state_from_vector(uvec);
 
-  // Call rhs function to get extra variables at this time
-  run_rhs(simtime);
-
   if (flag < 0) {
     throw BoutException("ERROR CVODE solve failed at t = {:e}, flag = {:d}\n", simtime,
                         flag);
   }
 
+#if BOUT_HAS_PETSC
+  const PetscErrorCode jacobian_export_error = maybeExportOutputJacobian(simtime);
+  if (jacobian_export_error != PETSC_SUCCESS) {
+    throw BoutException("Failed to export CVODE Jacobian diagnostics");
+  }
+#endif
+
+  // Call rhs function to get extra variables at this time
+  run_rhs(simtime);
+
   return simtime;
 }
 
@@ -921,6 +1094,38 @@ PetscErrorCode CvodeSolver::petscFormFunction(void* UNUSED(dummy), Vec x, Vec f,
   return PETSC_SUCCESS;
 }
 
+PetscErrorCode CvodeSolver::petscFormRhsFunction(void* UNUSED(dummy), Vec x, Vec f,
+                                                 void* ctx) {
+  auto* s = static_cast<CvodeSolver*>(ctx);
+
+  PetscInt length = 0;
+  PetscCall(VecGetLocalSize(x, &length));
+  s->petsc_rhs_tmp.resize(static_cast<std::size_t>(length));
+
+  const BoutReal* xdata = nullptr;
+  PetscCall(VecGetArrayRead(x, &xdata));
+
+  BoutReal* fdata = nullptr;
+  PetscCall(VecGetArray(f, &fdata));
+
+  try {
+    s->rhs(s->petsc_t, const_cast<BoutReal*>(xdata), s->petsc_rhs_tmp.data(), true);
+  } catch (BoutRhsFail&) {
+    PetscCall(VecRestoreArrayRead(x, &xdata));
+    PetscCall(VecRestoreArray(f, &fdata));
+    return 1;
+  }
+
+  for (PetscInt i = 0; i < length; ++i) {
+    fdata[i] = s->petsc_rhs_tmp[i];
+  }
+
+  PetscCall(VecRestoreArrayRead(x, &xdata));
+  PetscCall(VecRestoreArray(f, &fdata));
+
+  return PETSC_SUCCESS;
+}
+
 int CvodeSolver::petscPSetup(BoutReal t, N_Vector yy, N_Vector UNUSED(yp),
                              CvodeBool UNUSED(jok), CvodeBool* jcurPtr, BoutReal gamma,
                              void* user_data) {
@@ -947,6 +1152,12 @@ int CvodeSolver::petscPSetup(BoutReal t, N_Vector yy, N_Vector UNUSED(yp),
     return 1;
   }
 
+  ierr = MatFDColoringSetF(s->petsc_preconditioner.coloring(), s->petsc_f);
+  if (ierr != 0) {
+    VecResetArray(s->petsc_x);
+    return 1;
+  }
+
   Mat J = s->petsc_preconditioner.jacobian();
   ierr = MatZeroEntries(J);
   if (ierr != 0) {
@@ -969,6 +1180,12 @@ int CvodeSolver::petscPSetup(BoutReal t, N_Vector yy, N_Vector UNUSED(yp),
     return 1;
   }
 
+  ierr = s->maybeExportJacobian(J, s->petsc_x, t, gamma);
+  if (ierr != 0) {
+    VecResetArray(s->petsc_x);
+    return 1;
+  }
+
   ierr = KSPSetOperators(s->petsc_ksp, J, J);
   if (ierr == 0) {
     ierr = KSPSetUp(s->petsc_ksp);
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index c242e4128a..51332260d6 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -44,11 +44,11 @@ RegisterUnavailableSolver
 
 #include "../../sundials_nvector_interface.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/petsc_preconditioner.hxx"
 #include "bout/region.hxx"
 #include "bout/sundials_backports.hxx"
 
 #if BOUT_HAS_PETSC
-#include "bout/petsc_preconditioner.hxx"
 #include "bout/petsclib.hxx"
 
 #include <petscksp.h>
@@ -68,6 +68,7 @@ RegisterSolver<CvodeSolver> registersolvercvode("cvode");
 // Preconditioner selection for CVODE.
 // Note: String comparisons are case-insensitive so "Auto" avoids conflict with keyword
 BOUT_ENUM_CLASS(CvodePreconMethod, none, Auto, user, petsc, bbd);
+BOUT_ENUM_CLASS(CvodeJacobianExportTrigger, output, linear_setup);
 
 #if SUNDIALS_VERSION_AT_LEAST(6, 0, 0)
 using CvodeBool = sunbooleantype;
@@ -99,11 +100,20 @@ public:
 private:
 #if BOUT_HAS_PETSC
   static PetscErrorCode petscFormFunction(void* dummy, Vec x, Vec f, void* ctx);
+  static PetscErrorCode petscFormRhsFunction(void* dummy, Vec x, Vec f, void* ctx);
   static int petscPSetup(BoutReal t, N_Vector yy, N_Vector yp, CvodeBool jok,
                          CvodeBool* jcurPtr, BoutReal gamma, void* user_data);
   static int petscPSolve(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec,
                          N_Vector zvec, BoutReal gamma, BoutReal delta, int lr,
                          void* user_data);
+  std::string getJacobianExportStem(JacobianExportKind kind);
+  std::string getJacobianMatrixFilename(const std::string& stem) const;
+  PetscErrorCode exportMatrixAndMetadata(Mat jacobian, const std::string& stem);
+  PetscErrorCode saveDiagnosticJacobian(JacobianExportKind kind, Vec x, BoutReal t,
+                                        BoutReal gamma);
+  PetscErrorCode maybeExportJacobian(Mat system_jacobian, Vec x, BoutReal t,
+                                     BoutReal gamma);
+  PetscErrorCode maybeExportOutputJacobian(BoutReal t);
 #endif
 
   BoutReal hcur; //< Current internal timestep
@@ -160,6 +170,13 @@ private:
   NVectorType nvector_type;
   BoutReal cvode_nonlinear_convergence_coef;
   BoutReal cvode_linear_convergence_coef;
+  bool save_jacobian;
+  JacobianExportKind jacobian_export_kind;
+  CvodeJacobianExportTrigger jacobian_export_trigger;
+  std::string jacobian_export_prefix;
+  PetscMatrixExportFormat jacobian_export_format;
+  int jacobian_export_counter{0};
+  bool jacobian_metadata_written{false};
 
   // Diagnostics from CVODE
   int nsteps{0};
diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt
index 41a21deac0..7a8ac9ab89 100644
--- a/tests/integrated/CMakeLists.txt
+++ b/tests/integrated/CMakeLists.txt
@@ -6,6 +6,7 @@ add_subdirectory(test-command-args)
 add_subdirectory(test-communications)
 add_subdirectory(test-coordinates-initialization)
 add_subdirectory(test-cyclic)
+add_subdirectory(test-cvode-save-jacobian)
 add_subdirectory(test-delp2)
 add_subdirectory(test-datafilefacade)
 add_subdirectory(test-drift-instability)
diff --git a/tests/integrated/test-snes-save-jacobian/PetscBinaryIO.py b/tests/integrated/jacobian_tools/PetscBinaryIO.py
similarity index 100%
rename from tests/integrated/test-snes-save-jacobian/PetscBinaryIO.py
rename to tests/integrated/jacobian_tools/PetscBinaryIO.py
diff --git a/tests/integrated/test-snes-save-jacobian/read_jacobian.py b/tests/integrated/jacobian_tools/read_jacobian.py
similarity index 98%
rename from tests/integrated/test-snes-save-jacobian/read_jacobian.py
rename to tests/integrated/jacobian_tools/read_jacobian.py
index c778cc707d..2af8462646 100644
--- a/tests/integrated/test-snes-save-jacobian/read_jacobian.py
+++ b/tests/integrated/jacobian_tools/read_jacobian.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""Read Jacobian diagnostics written by the SNES save-jacobian test.
+"""Read Jacobian diagnostics written by integrated Jacobian export tests.
 
 This helper is intentionally lightweight:
 
@@ -384,7 +384,7 @@ def to_pandas(matrix: np.ndarray | RawPetscSparse, dofs: list[dict[str, Any]]):
 
 
 def _main() -> None:
-    parser = argparse.ArgumentParser(description="Read SNES Jacobian test output")
+    parser = argparse.ArgumentParser(description="Read integrated-test Jacobian output")
     parser.add_argument(
         "--data-dir", default="data", help="Directory containing Jacobian outputs"
     )
diff --git a/tests/integrated/test-cvode-save-jacobian/CMakeLists.txt b/tests/integrated/test-cvode-save-jacobian/CMakeLists.txt
new file mode 100644
index 0000000000..8a7d70af96
--- /dev/null
+++ b/tests/integrated/test-cvode-save-jacobian/CMakeLists.txt
@@ -0,0 +1,9 @@
+bout_add_integrated_test(
+  test-cvode-save-jacobian
+  SOURCES test_cvode_save_jacobian.cxx
+  REQUIRES BOUT_HAS_PETSC BOUT_HAS_CVODE
+  USE_DATA_BOUT_INP
+)
+
+configure_file(../jacobian_tools/read_jacobian.py read_jacobian.py COPYONLY)
+configure_file(../jacobian_tools/PetscBinaryIO.py PetscBinaryIO.py COPYONLY)
diff --git a/tests/integrated/test-cvode-save-jacobian/data/BOUT.inp b/tests/integrated/test-cvode-save-jacobian/data/BOUT.inp
new file mode 100644
index 0000000000..b8b6c72f33
--- /dev/null
+++ b/tests/integrated/test-cvode-save-jacobian/data/BOUT.inp
@@ -0,0 +1,29 @@
+MXG = 0
+
+[mesh]
+nx = 1
+ny = 16
+nz = 1
+
+[solver]
+type = cvode
+nout = 1
+
+# Force the timestep and order so the gamma factor is known
+output_step = 0.1
+start_timestep = 0.1
+min_timestep = 0.1
+max_timestep = 0.1
+
+cvode_max_order = 1
+
+# Loose tolerances so the step is accepted
+atol = 1
+rtol = 1
+
+save_jacobian_index_base = true
+save_jacobian = true
+jacobian_export_kind = rhs
+jacobian_export_trigger = output
+
+cvode_precon_method = none
diff --git a/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.cxx b/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.cxx
new file mode 100644
index 0000000000..7d35b949be
--- /dev/null
+++ b/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.cxx
@@ -0,0 +1,27 @@
+#include <bout/bout_types.hxx>
+#include <bout/field3d.hxx>
+#include <bout/physicsmodel.hxx>
+#include <bout/unused.hxx>
+
+class TestSolver : public PhysicsModel {
+public:
+  Field3D f, g;
+
+  int init(bool UNUSED(restarting)) override {
+    solver->add(f, "f");
+    solver->add(g, "g");
+
+    f = 1.0;
+    g = 0.0;
+
+    return 0;
+  }
+
+  int rhs(BoutReal UNUSED(time)) override {
+    ddt(f) = -0.1 * f;
+    ddt(g) = 0.5 * f - g;
+    return 0;
+  }
+};
+
+BOUTMAIN(TestSolver);
diff --git a/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.py b/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.py
new file mode 100644
index 0000000000..ebf658c692
--- /dev/null
+++ b/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.py
@@ -0,0 +1,95 @@
+from pathlib import Path
+import numpy as np
+from boutdata.collect import collect
+
+from read_jacobian import extract_block, load_jacobian, to_numpy_dense
+
+TEST_DIR = Path(".")
+
+
+def test_rhs_jacobian_output_trigger(assert_success_in_shell):
+    assert_success_in_shell("./test_cvode_save_jacobian")
+
+    data_dir = TEST_DIR / "data"
+    metadata_file = data_dir / "jacobian_metadata.json"
+    matrix_file = data_dir / "jacobian_rhs_000000.dat"
+
+    assert metadata_file.exists()
+    assert matrix_file.exists()
+
+    dense_matrix, dofs, labels = load_jacobian(
+        data_dir=data_dir, matrix_filename=matrix_file, matrix_format="dense"
+    )
+    sparse_matrix, sparse_dofs, sparse_labels = load_jacobian(
+        data_dir=data_dir, matrix_filename=matrix_file, matrix_format="sparse"
+    )
+
+    np.testing.assert_allclose(to_numpy_dense(sparse_matrix), dense_matrix)
+    assert sparse_dofs == dofs
+    assert sparse_labels == labels
+
+    expected_block = np.array([[-0.1, 0.0], [0.5, -1.0]])
+    expected_matrix = np.kron(np.eye(16), expected_block)
+    np.testing.assert_allclose(dense_matrix, expected_matrix)
+
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "f", "f"), -0.1 * np.eye(16)
+    )
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "g", "f"), 0.5 * np.eye(16)
+    )
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "g", "g"), -1.0 * np.eye(16)
+    )
+
+
+def test_system_jacobian_linear_setup_trigger(assert_success_in_shell):
+    assert_success_in_shell(
+        "./test_cvode_save_jacobian "
+        "solver:cvode_precon_method=petsc "
+        "solver:jacobian_export_kind=system "
+        "solver:jacobian_export_trigger=linear_setup "
+        "solver:jacobian_export_prefix=jacobian_system_test"
+    )
+
+    data_dir = TEST_DIR / "data"
+    metadata_file = data_dir / "jacobian_system_test_metadata.json"
+    matrix_file = data_dir / "jacobian_system_test_system_000000.dat"
+
+    assert metadata_file.exists()
+    assert matrix_file.exists()
+
+    dense_matrix, dofs, labels = load_jacobian(
+        data_dir=data_dir, matrix_filename=matrix_file, matrix_format="dense"
+    )
+    sparse_matrix, sparse_dofs, sparse_labels = load_jacobian(
+        data_dir=data_dir, matrix_filename=matrix_file, matrix_format="sparse"
+    )
+
+    np.testing.assert_allclose(to_numpy_dense(sparse_matrix), dense_matrix)
+    assert sparse_dofs == dofs
+    assert sparse_labels == labels
+
+    last_step = float(
+        np.ravel(
+            np.asarray(collect("cvode_last_step", path=str(data_dir), info=False))
+        )[-1]
+    )
+    expected_block = np.array(
+        [[1.0 + 0.1 * last_step, 0.0], [-0.5 * last_step, 1.0 + last_step]]
+    )
+    expected_matrix = np.kron(np.eye(16), expected_block)
+    np.testing.assert_allclose(dense_matrix, expected_matrix)
+
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "f", "f"),
+        (1.0 + 0.1 * last_step) * np.eye(16),
+    )
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "g", "f"),
+        (-0.5 * last_step) * np.eye(16),
+    )
+    np.testing.assert_allclose(
+        extract_block(dense_matrix, dofs, "g", "g"),
+        (1.0 + last_step) * np.eye(16),
+    )
diff --git a/tests/integrated/test-snes-save-jacobian/CMakeLists.txt b/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
index 7d043e793e..3dbc63f76e 100644
--- a/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
+++ b/tests/integrated/test-snes-save-jacobian/CMakeLists.txt
@@ -5,5 +5,5 @@ bout_add_integrated_test(
   USE_DATA_BOUT_INP
 )
 
-configure_file(read_jacobian.py read_jacobian.py COPYONLY)
-configure_file(PetscBinaryIO.py PetscBinaryIO.py COPYONLY)
+configure_file(../jacobian_tools/read_jacobian.py read_jacobian.py COPYONLY)
+configure_file(../jacobian_tools/PetscBinaryIO.py PetscBinaryIO.py COPYONLY)

From edaf4f7c318850d90d960eaef5368098eb8839a6 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 21 Aug 2026 08:58:21 -0700
Subject: [PATCH 1738/1827] Document cvode jacobian output

Documentation includes a table of settings, and examples.
---
 manual/sphinx/user_docs/time_integration.rst | 74 +++++++++++++++++++-
 src/solver/impls/cvode/cvode.cxx             | 10 +--
 src/solver/impls/cvode/cvode.hxx             | 33 ++++++---
 3 files changed, 103 insertions(+), 14 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 150bb43c87..171400f0b3 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -107,7 +107,17 @@ given in table :numref:`tab-solveropts`.
    +--------------------------+--------------------------------------------+-------------------------------------+
    | diagnose                 | Collect and print additional diagnostics   | cvode, imexbdf2, beuler             |
    +--------------------------+--------------------------------------------+-------------------------------------+
-   | save\_jacobian\_index\_base | Write the per-cell Jacobian base index  | beuler / snes                       |
+   | save\_jacobian           | Save PETSc Jacobian diagnostics            | cvode, beuler / snes                |
+   +--------------------------+--------------------------------------------+-------------------------------------+
+   | jacobian\_export\_kind   | Which Jacobian to save                     | cvode, beuler / snes                |
+   +--------------------------+--------------------------------------------+-------------------------------------+
+   | jacobian\_export\_trigger | When to save Jacobians                    | cvode                               |
+   +--------------------------+--------------------------------------------+-------------------------------------+
+   | jacobian\_export\_prefix | Prefix for Jacobian matrix/metadata files  | cvode, beuler / snes                |
+   +--------------------------+--------------------------------------------+-------------------------------------+
+   | jacobian\_export\_format | PETSc output format for Jacobians          | cvode, beuler / snes                |
+   +--------------------------+--------------------------------------------+-------------------------------------+
+   | save\_jacobian\_index\_base | Write the per-cell Jacobian base index  | cvode, beuler / snes                |
    |                          | field used to reconstruct saved Jacobians  |                                     |
    +--------------------------+--------------------------------------------+-------------------------------------+
    | nvector                  | ``N_Vector`` backend for SUNDIALS solvers: | cvode, ida, arkode                  |
@@ -226,6 +236,68 @@ nonlinear solvers:
 The linear solver type can be set using the ``linear_solver`` option.
 Valid choices include ``gmres`` (the default), ``fgmres``, ``tfqmr``, ``bcgs``.
 
+CVODE Jacobian diagnostics
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+CVODE can also save PETSc finite-difference Jacobians for post-processing,
+using the same metadata format as the SNES Jacobian diagnostics.
+
+The shared options are:
+
+- ``save_jacobian = true`` to enable exports
+- ``jacobian_export_kind = system`` or ``rhs``
+- ``jacobian_export_prefix`` to choose the output filename prefix
+- ``jacobian_export_format = binary`` or ``ascii``
+- ``save_jacobian_index_base = true`` to save the per-cell index-base field
+
+CVODE adds one extra option:
+
+- ``jacobian_export_trigger = linear_setup`` exports whenever CVODE rebuilds
+  linear solver data.
+- ``jacobian_export_trigger = output`` exports once per solver output timestep.
+
+The supported combinations are:
+
+- ``jacobian_export_kind = system`` requires
+  ``jacobian_export_trigger = linear_setup`` and
+  ``cvode_precon_method = petsc``.
+- ``jacobian_export_kind = rhs`` with
+  ``jacobian_export_trigger = output`` works without PETSc preconditioning and is
+  the easiest way to inspect the model Jacobian.
+- ``jacobian_export_kind = rhs`` with
+  ``jacobian_export_trigger = linear_setup`` is also supported on the PETSc
+  preconditioner path.
+- ``jacobian_export_kind = scaled`` is not currently supported in CVODE because
+  the solver does not yet apply a separate scaling transform.
+
+For example, to save the raw RHS Jacobian once per output timestep:
+
+.. code-block:: ini
+
+   [solver]
+   type = cvode
+   save_jacobian = true
+   save_jacobian_index_base = true
+   jacobian_export_kind = rhs
+   jacobian_export_trigger = output
+
+To save the linearised CVODE system Jacobian whenever the PETSc
+preconditioner is rebuilt:
+
+.. code-block:: ini
+
+   [solver]
+   type = cvode
+   cvode_precon_method = petsc
+   save_jacobian = true
+   save_jacobian_index_base = true
+   jacobian_export_kind = system
+   jacobian_export_trigger = linear_setup
+
+As with the SNES Jacobian export, the output files are written into
+``datadir`` and can be inspected using
+``tests/integrated/jacobian_tools/read_jacobian.py``.
+
 IMEX-BDF2
 ---------
 
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 8394702a5f..645307da4e 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -170,11 +170,13 @@ CvodeSolver::CvodeSolver(Options* opts)
                         .doc("Save PETSc Jacobian diagnostics to datadir")
                         .withDefault(false)),
       jacobian_export_kind((*options)["jacobian_export_kind"]
-                               .doc("Which Jacobian to save: system, scaled, or rhs")
+                               .doc("Which Jacobian to save for CVODE: system or rhs "
+                                    "(scaled is not supported)")
                                .withDefault(JacobianExportKind::system)),
-      jacobian_export_trigger((*options)["jacobian_export_trigger"]
-                                  .doc("When to save Jacobians: output or linear_setup")
-                                  .withDefault(CvodeJacobianExportTrigger::linear_setup)),
+      jacobian_export_trigger(
+          (*options)["jacobian_export_trigger"]
+              .doc("When to save CVODE Jacobians: output or linear_setup")
+              .withDefault(CvodeJacobianExportTrigger::linear_setup)),
       jacobian_export_prefix(
           (*options)["jacobian_export_prefix"]
               .doc("Prefix for saved Jacobian matrix files and shared metadata JSON")
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index 51332260d6..e17cda4624 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -68,7 +68,10 @@ RegisterSolver<CvodeSolver> registersolvercvode("cvode");
 // Preconditioner selection for CVODE.
 // Note: String comparisons are case-insensitive so "Auto" avoids conflict with keyword
 BOUT_ENUM_CLASS(CvodePreconMethod, none, Auto, user, petsc, bbd);
-BOUT_ENUM_CLASS(CvodeJacobianExportTrigger, output, linear_setup);
+BOUT_ENUM_CLASS(CvodeJacobianExportTrigger,
+                output,      ///< Export once per solver output timestep
+                linear_setup ///< Export whenever CVODE rebuilds linear solver data
+);
 
 #if SUNDIALS_VERSION_AT_LEAST(6, 0, 0)
 using CvodeBool = sunbooleantype;
@@ -99,20 +102,28 @@ public:
 
 private:
 #if BOUT_HAS_PETSC
+  /// PETSc callback for the CVODE system function ``x - gamma * rhs(t, x)``.
   static PetscErrorCode petscFormFunction(void* dummy, Vec x, Vec f, void* ctx);
+  /// PETSc callback for the raw CVODE RHS ``rhs(t, x)`` with ``linear=true``.
   static PetscErrorCode petscFormRhsFunction(void* dummy, Vec x, Vec f, void* ctx);
   static int petscPSetup(BoutReal t, N_Vector yy, N_Vector yp, CvodeBool jok,
                          CvodeBool* jcurPtr, BoutReal gamma, void* user_data);
   static int petscPSolve(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec,
                          N_Vector zvec, BoutReal gamma, BoutReal delta, int lr,
                          void* user_data);
+  /// Construct the basename used for Jacobian outputs in ``datadir``.
   std::string getJacobianExportStem(JacobianExportKind kind);
+  /// Return the matrix filename including the extension for the selected format.
   std::string getJacobianMatrixFilename(const std::string& stem) const;
+  /// Write one Jacobian matrix and the shared metadata JSON.
   PetscErrorCode exportMatrixAndMetadata(Mat jacobian, const std::string& stem);
+  /// Build and save a diagnostic Jacobian of the requested kind.
   PetscErrorCode saveDiagnosticJacobian(JacobianExportKind kind, Vec x, BoutReal t,
                                         BoutReal gamma);
+  /// Save Jacobians during CVODE linear solver setup callbacks.
   PetscErrorCode maybeExportJacobian(Mat system_jacobian, Vec x, BoutReal t,
                                      BoutReal gamma);
+  /// Save Jacobians once per solver output timestep.
   PetscErrorCode maybeExportOutputJacobian(BoutReal t);
 #endif
 
@@ -170,13 +181,17 @@ private:
   NVectorType nvector_type;
   BoutReal cvode_nonlinear_convergence_coef;
   BoutReal cvode_linear_convergence_coef;
-  bool save_jacobian;
-  JacobianExportKind jacobian_export_kind;
-  CvodeJacobianExportTrigger jacobian_export_trigger;
-  std::string jacobian_export_prefix;
-  PetscMatrixExportFormat jacobian_export_format;
-  int jacobian_export_counter{0};
-  bool jacobian_metadata_written{false};
+  bool save_jacobian; ///< Save PETSc Jacobian diagnostics to ``datadir``?
+  JacobianExportKind jacobian_export_kind; ///< Export ``system`` or ``rhs`` Jacobian
+  CvodeJacobianExportTrigger
+      jacobian_export_trigger;        ///< Export on ``output`` or ``linear_setup``
+  std::string jacobian_export_prefix; ///< Prefix for matrix files and ``*_metadata.json``
+  PetscMatrixExportFormat
+      jacobian_export_format; ///< PETSc ``MatView`` format: binary or ascii
+  int jacobian_export_counter{
+      0}; ///< Running counter appended to successive Jacobian saves
+  bool jacobian_metadata_written{
+      false}; ///< Has the shared metadata JSON already been written?
 
   // Diagnostics from CVODE
   int nsteps{0};
@@ -207,7 +222,7 @@ private:
   sundials::Context suncontext;
 
 #if BOUT_HAS_PETSC
-  // PETSc-coloring-based preconditioning for CVODE
+  // PETSc-coloring-based preconditioning and Jacobian diagnostics for CVODE
   std::unique_ptr<PetscLib> petsc_lib;
   PetscPreconditioner petsc_preconditioner;
   KSP petsc_ksp{nullptr};

From d8e866013098e11c51f02a30ffe288e8d8887db6 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Aug 2026 15:47:13 +0100
Subject: [PATCH 1739/1827] Use spaceship operator for comparison operators
 where possible

---
 .clang-format                             |  2 +-
 include/bout/boundary_region_iter.hxx     | 24 +++++++--
 include/bout/operatorstencil.hxx          | 59 +++++++----------------
 include/bout/options.hxx                  |  5 +-
 include/bout/parallel_boundary_region.hxx |  8 ++-
 include/bout/region.hxx                   | 35 ++------------
 include/bout/solver.hxx                   | 19 +-------
 include/bout/sys/expressionparser.hxx     |  4 +-
 src/mesh/impls/bout/boutmesh.hxx          |  4 ++
 tests/unit/mesh/test_boutmesh.cxx         | 21 --------
 10 files changed, 53 insertions(+), 128 deletions(-)

diff --git a/.clang-format b/.clang-format
index 51cf39683a..9f7c5d763e 100644
--- a/.clang-format
+++ b/.clang-format
@@ -112,6 +112,6 @@ StatementMacros:
   - BOUT_OMP
   - BOUT_OMP_PERF
   - BOUT_OMP_SAFE
-Standard:        c++14
+Standard:        c++20
 TabWidth:        8
 UseTab:          Never
diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 6b6cd5b6ff..6de145b7d3 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -534,10 +534,17 @@ public:
     ASSERT3(loc == CELL_CENTRE);
     return region->bndry_points[pos].length;
   }
-  bool operator!=(BoundaryRegionIterFCI lhs) const {
+
+  auto operator<=>(const BoundaryRegionIterFCI& rhs) const {
+    ASSERT3(region == rhs.region);
+    return pos <=> rhs.pos;
+  }
+
+  bool operator==(BoundaryRegionIterFCI lhs) const {
     ASSERT3(region == lhs.region);
-    return pos != lhs.pos;
+    return pos == lhs.pos;
   }
+
   BoundaryRegionIterFCI& operator++() {
     ++pos;
     return *this;
@@ -666,10 +673,17 @@ public:
     }
     return 0.5;
   }
-  bool operator!=(BoundaryRegionIterXY<isX> lhs) {
-    ASSERT3(region == lhs.region);
-    return pos != lhs.pos;
+
+  auto operator<=>(const BoundaryRegionIterXY<isX>& rhs) const {
+    ASSERT3(region == rhs.region);
+    return pos <=> rhs.pos;
+  }
+
+  bool operator==(BoundaryRegionIterXY<isX> rhs) const {
+    ASSERT3(region == rhs.region);
+    return pos == rhs.pos;
   }
+
   BoundaryRegionIterXY& operator++() {
     ++pos;
     return *this;
diff --git a/include/bout/operatorstencil.hxx b/include/bout/operatorstencil.hxx
index 118dc7a068..1823548ce9 100644
--- a/include/bout/operatorstencil.hxx
+++ b/include/bout/operatorstencil.hxx
@@ -45,9 +45,9 @@
 /// subtracted from them.
 template <class T>
 struct IndexOffset {
-  static_assert(
-      std::is_same_v<T, Ind3D> || std::is_same_v<T, Ind2D> || std::is_same_v<T, IndPerp>,
-      "IndexOffset only works with SpecificInd types");
+  static_assert(std::is_same_v<T, Ind3D> || std::is_same_v<T, Ind2D>
+                    || std::is_same_v<T, IndPerp>,
+                "IndexOffset only works with SpecificInd types");
   int dx = 0, dy = 0, dz = 0;
 
   const inline IndexOffset xp(int delta_x = 1) const { return {dx + delta_x, dy, dz}; }
@@ -69,26 +69,9 @@ struct IndexOffset {
     dz -= n.dz;
     return *this;
   }
-};
 
-template <class T>
-inline bool operator==(const IndexOffset<T>& lhs, const IndexOffset<T>& rhs) {
-  return lhs.dx == rhs.dx && lhs.dy == rhs.dy && lhs.dz == rhs.dz;
-}
-template <class T>
-inline bool operator!=(const IndexOffset<T>& lhs, const IndexOffset<T>& rhs) {
-  return !operator==(lhs, rhs);
-}
-template <class T>
-inline bool operator<(const IndexOffset<T>& lhs, const IndexOffset<T>& rhs) {
-  if (lhs.dx != rhs.dx) {
-    return lhs.dx < rhs.dx;
-  } else if (lhs.dy != rhs.dy) {
-    return lhs.dy < rhs.dy;
-  } else {
-    return lhs.dz < rhs.dz;
-  }
-}
+  auto operator<=>(const IndexOffset<T>&) const = default;
+};
 
 template <class T>
 const inline IndexOffset<T> operator+(IndexOffset<T> lhs, const IndexOffset<T>& rhs) {
@@ -133,9 +116,9 @@ using OffsetIndPerp = IndexOffset<IndPerp>;
 template <class T>
 class OperatorStencil {
 public:
-  static_assert(
-      std::is_same_v<T, Ind3D> || std::is_same_v<T, Ind2D> || std::is_same_v<T, IndPerp>,
-      "OperatorStencil only works with SpecificInd types");
+  static_assert(std::is_same_v<T, Ind3D> || std::is_same_v<T, Ind2D>
+                    || std::is_same_v<T, IndPerp>,
+                "OperatorStencil only works with SpecificInd types");
   using offset = IndexOffset<T>;
   using stencil_part = std::vector<offset>;
   using stencil_test = std::function<bool(T)>;
@@ -271,14 +254,11 @@ OperatorStencil<T> squareStencil(Mesh* localmesh) {
   std::vector<IndexOffset<T>> offsetsVec(offsets.begin(), offsets.end());
   stencil.add(
       [localmesh](T ind) -> bool {
-        return (
-            localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend
-            && (std::is_same_v<
-                    T,
-                    IndPerp> || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend))
-            && (std::is_same_v<
-                    T,
-                    Ind2D> || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend)));
+        return (localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend
+                && (std::is_same_v<T, IndPerp>
+                    || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend))
+                && (std::is_same_v<T, Ind2D>
+                    || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend)));
       },
       offsetsVec);
   stencil.add([](T UNUSED(ind)) -> bool { return true; }, {zero});
@@ -308,14 +288,11 @@ OperatorStencil<T> starStencil(Mesh* localmesh) {
   std::vector<IndexOffset<T>> offsetsVec(offsets.begin(), offsets.end());
   stencil.add(
       [localmesh](T ind) -> bool {
-        return (
-            localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend
-            && (std::is_same_v<
-                    T,
-                    IndPerp> || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend))
-            && (std::is_same_v<
-                    T,
-                    Ind2D> || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend)));
+        return (localmesh->xstart <= ind.x() && ind.x() <= localmesh->xend
+                && (std::is_same_v<T, IndPerp>
+                    || (localmesh->ystart <= ind.y() && ind.y() <= localmesh->yend))
+                && (std::is_same_v<T, Ind2D>
+                    || (localmesh->zstart <= ind.z() && ind.z() <= localmesh->zend)));
       },
       offsetsVec);
   stencil.add([](T UNUSED(ind)) -> bool { return true; }, {zero});
diff --git a/include/bout/options.hxx b/include/bout/options.hxx
index 0ff81822b6..b7eb9eb29c 100644
--- a/include/bout/options.hxx
+++ b/include/bout/options.hxx
@@ -410,9 +410,8 @@ public:
     /// Edit distance from original search term
     std::string::size_type distance;
     /// Comparison operator so this works in a std::multiset
-    friend bool operator<(const FuzzyMatch& lhs, const FuzzyMatch& rhs) {
-      return lhs.distance < rhs.distance;
-    }
+    auto operator<=>(const FuzzyMatch& rhs) const { return distance <=> rhs.distance; }
+    bool operator==(const FuzzyMatch& rhs) const { return distance == rhs.distance; }
   };
 
   /// Find approximate matches for \p name throughout the whole
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 2d17288a3d..30c51c6c86 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -52,12 +52,10 @@ struct Indices {
           signed char offset, unsigned char abs_offset)
       : index(index), intersection(intersection), length(length), valid(valid),
         offset(offset), abs_offset(abs_offset) {};
-};
 
-inline bool operator<(const Indices& lhs, const Indices& rhs) {
-  return lhs.index < rhs.index;
-}
-inline bool operator<(const Indices& lhs, const Ind3D& rhs) { return lhs.index < rhs; }
+  auto operator<=>(const Indices& rhs) const { return index <=> rhs.index; }
+  auto operator<=>(const Ind3D& rhs) const { return index <=> rhs; }
+};
 
 using IndicesVec = std::vector<Indices>;
 using IndicesIter = IndicesVec::iterator;
diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index a8a9ab2d1d..6901f346e7 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -327,38 +327,11 @@ struct SpecificInd {
   inline SpecificInd offset(int dx, int dy, int dz) const {
     return zpm(dz).yp(dy).xp(dx);
   }
-};
-
-/// Relational operators
-template <IND_TYPE N>
-inline bool operator==(const SpecificInd<N>& lhs, const SpecificInd<N>& rhs) {
-  return lhs.ind == rhs.ind;
-}
-
-template <IND_TYPE N>
-inline bool operator!=(const SpecificInd<N>& lhs, const SpecificInd<N>& rhs) {
-  return !operator==(lhs, rhs);
-}
-
-template <IND_TYPE N>
-inline bool operator<(const SpecificInd<N>& lhs, const SpecificInd<N>& rhs) {
-  return lhs.ind < rhs.ind;
-}
 
-template <IND_TYPE N>
-inline bool operator>(const SpecificInd<N>& lhs, const SpecificInd<N>& rhs) {
-  return operator<(rhs, lhs);
-}
-
-template <IND_TYPE N>
-inline bool operator>=(const SpecificInd<N>& lhs, const SpecificInd<N>& rhs) {
-  return !operator<(lhs, rhs);
-}
-
-template <IND_TYPE N>
-inline bool operator<=(const SpecificInd<N>& lhs, const SpecificInd<N>& rhs) {
-  return !operator>(lhs, rhs);
-}
+  /// Relational operator
+  auto operator<=>(const SpecificInd<N>& rhs) const { return ind <=> rhs.ind; }
+  bool operator==(const SpecificInd<N>& rhs) const { return ind == rhs.ind; }
+};
 
 /// Arithmetic operators with integers
 template <IND_TYPE N>
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 0d4b330ec6..d28a7c8b54 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -470,24 +470,7 @@ protected:
     difference_type operator-(const VarIterator& b) { return it - b.it; }
     reference operator[](difference_type n) { return *VarIterator(it[n]); }
 
-    friend bool operator==(const VarIterator& a, const VarIterator& b) {
-      return a.it == b.it;
-    }
-    friend bool operator!=(const VarIterator& a, const VarIterator& b) {
-      return a.it != b.it;
-    }
-    friend bool operator<(const VarIterator& a, const VarIterator& b) {
-      return a.it < b.it;
-    }
-    friend bool operator>(const VarIterator& a, const VarIterator& b) {
-      return a.it > b.it;
-    }
-    friend bool operator<=(const VarIterator& a, const VarIterator& b) {
-      return a.it <= b.it;
-    }
-    friend bool operator>=(const VarIterator& a, const VarIterator& b) {
-      return a.it >= b.it;
-    }
+    auto operator<=>(const VarIterator& rhs) const = default;
 
   private:
     underlying_iterator it{};
diff --git a/include/bout/sys/expressionparser.hxx b/include/bout/sys/expressionparser.hxx
index 8b2442e843..f87ee2adbc 100644
--- a/include/bout/sys/expressionparser.hxx
+++ b/include/bout/sys/expressionparser.hxx
@@ -131,9 +131,7 @@ protected:
     /// Edit distance from original search term
     std::string::size_type distance;
     /// Comparison operator so this works in a std::multiset
-    friend bool operator<(const FuzzyMatch& lhs, const FuzzyMatch& rhs) {
-      return (lhs.distance < rhs.distance) and (lhs.name < rhs.name);
-    }
+    auto operator<=>(const FuzzyMatch&) const = default;
   };
 
   /// Find approximate matches for \p name in the known generators. \p
diff --git a/src/mesh/impls/bout/boutmesh.hxx b/src/mesh/impls/bout/boutmesh.hxx
index a6d97a8944..abe7be9809 100644
--- a/src/mesh/impls/bout/boutmesh.hxx
+++ b/src/mesh/impls/bout/boutmesh.hxx
@@ -255,6 +255,8 @@ protected:
     int jyseps1_2;
     int jyseps2_2;
     int ny_inner;
+
+    auto operator<=>(const YDecompositionIndices&) const = default;
   };
 
   /// Version of `setYDecompositionindices` that returns the values
@@ -353,6 +355,8 @@ protected:
     int UDATA_INDEST, UDATA_OUTDEST, UDATA_XSPLIT;
     int DDATA_INDEST, DDATA_OUTDEST, DDATA_XSPLIT;
     int IDATA_DEST, ODATA_DEST; // X inner and outer destinations
+
+    auto operator<=>(const ConnectionInfo&) const = default;
   };
 
   /// Return the communication parameters as calculated by `topology`
diff --git a/tests/unit/mesh/test_boutmesh.cxx b/tests/unit/mesh/test_boutmesh.cxx
index d803a98155..172677b980 100644
--- a/tests/unit/mesh/test_boutmesh.cxx
+++ b/tests/unit/mesh/test_boutmesh.cxx
@@ -93,27 +93,6 @@ BoutMeshExposer::BoutMeshExposer(const BoutMeshParameters& inputs, bool periodic
                inputs.y_indices.jyseps2_1, inputs.y_indices.jyseps1_2,
                inputs.y_indices.jyseps2_2, inputs.y_indices.ny_inner) {}
 
-/// Equality operator to help testing
-bool operator==(const BoutMeshExposer::YDecompositionIndices& lhs,
-                const BoutMeshExposer::YDecompositionIndices& rhs) {
-  return (lhs.jyseps1_1 == rhs.jyseps1_1) and (lhs.jyseps2_1 == rhs.jyseps2_1)
-         and (lhs.jyseps1_2 == rhs.jyseps1_2) and (lhs.jyseps2_2 == rhs.jyseps2_2)
-         and (lhs.ny_inner == rhs.ny_inner);
-}
-
-bool operator==(const BoutMeshExposer::ConnectionInfo& lhs,
-                const BoutMeshExposer::ConnectionInfo& rhs) {
-  return (lhs.TS_up_in == rhs.TS_up_in) and (lhs.TS_up_out == rhs.TS_up_out)
-         and (lhs.TS_down_in == rhs.TS_down_in) and (lhs.TS_down_out == rhs.TS_down_out)
-         and (lhs.UDATA_INDEST == rhs.UDATA_INDEST)
-         and (lhs.UDATA_OUTDEST == rhs.UDATA_OUTDEST)
-         and (lhs.UDATA_XSPLIT == rhs.UDATA_XSPLIT)
-         and (lhs.DDATA_INDEST == rhs.DDATA_INDEST)
-         and (lhs.DDATA_OUTDEST == rhs.DDATA_OUTDEST)
-         and (lhs.DDATA_XSPLIT == rhs.DDATA_XSPLIT) and (lhs.IDATA_DEST == rhs.IDATA_DEST)
-         and (lhs.ODATA_DEST == rhs.ODATA_DEST);
-}
-
 /// Stream operator to print a nice message instead of bytes if a test fails
 std::ostream& operator<<(std::ostream& out,
                          const BoutMeshExposer::YDecompositionIndices& value) {

From 93d9fa26f8ae98ff01738ad6cfa61039318690b2 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Aug 2026 15:53:50 +0100
Subject: [PATCH 1740/1827] Fix some clang-tidy issues

---
 include/bout/operatorstencil.hxx | 24 +++++++-------
 include/bout/region.hxx          | 54 +++++++++++++++-----------------
 2 files changed, 37 insertions(+), 41 deletions(-)

diff --git a/include/bout/operatorstencil.hxx b/include/bout/operatorstencil.hxx
index 1823548ce9..1135a79fc7 100644
--- a/include/bout/operatorstencil.hxx
+++ b/include/bout/operatorstencil.hxx
@@ -33,9 +33,7 @@
 #include <algorithm>
 #include <functional>
 #include <iterator>
-#include <tuple>
 #include <type_traits>
-#include <utility>
 #include <vector>
 
 #include <bout/mesh.hxx>
@@ -50,12 +48,12 @@ struct IndexOffset {
                 "IndexOffset only works with SpecificInd types");
   int dx = 0, dy = 0, dz = 0;
 
-  const inline IndexOffset xp(int delta_x = 1) const { return {dx + delta_x, dy, dz}; }
-  const inline IndexOffset xm(int delta_x = 1) const { return xp(-delta_x); }
-  const inline IndexOffset yp(int delta_y = 1) const { return {dx, dy + delta_y, dz}; }
-  const inline IndexOffset ym(int delta_y = 1) const { return yp(-delta_y); }
-  const inline IndexOffset zp(int delta_z = 1) const { return {dx, dy, dz + delta_z}; }
-  const inline IndexOffset zm(int delta_z = 1) const { return zp(-delta_z); }
+  IndexOffset xp(int delta_x = 1) const { return {dx + delta_x, dy, dz}; }
+  IndexOffset xm(int delta_x = 1) const { return xp(-delta_x); }
+  IndexOffset yp(int delta_y = 1) const { return {dx, dy + delta_y, dz}; }
+  IndexOffset ym(int delta_y = 1) const { return yp(-delta_y); }
+  IndexOffset zp(int delta_z = 1) const { return {dx, dy, dz + delta_z}; }
+  IndexOffset zm(int delta_z = 1) const { return zp(-delta_z); }
 
   IndexOffset& operator+=(const IndexOffset& n) {
     dx += n.dx;
@@ -74,24 +72,24 @@ struct IndexOffset {
 };
 
 template <class T>
-const inline IndexOffset<T> operator+(IndexOffset<T> lhs, const IndexOffset<T>& rhs) {
+inline IndexOffset<T> operator+(IndexOffset<T> lhs, const IndexOffset<T>& rhs) {
   return lhs += rhs;
 }
 template <class T>
-const inline IndexOffset<T> operator-(IndexOffset<T> lhs, const IndexOffset<T>& rhs) {
+inline IndexOffset<T> operator-(IndexOffset<T> lhs, const IndexOffset<T>& rhs) {
   return lhs -= rhs;
 }
 
 template <class T>
-const inline T operator+(const T& lhs, const IndexOffset<T>& rhs) {
+inline T operator+(const T& lhs, const IndexOffset<T>& rhs) {
   return lhs.offset(rhs.dx, rhs.dy, rhs.dz);
 }
 template <class T>
-const inline T operator+(const IndexOffset<T>& lhs, const T& rhs) {
+inline T operator+(const IndexOffset<T>& lhs, const T& rhs) {
   return operator+(rhs, lhs);
 }
 template <class T>
-const inline T operator-(const T& lhs, const IndexOffset<T>& rhs) {
+inline T operator-(const T& lhs, const IndexOffset<T>& rhs) {
   // If CHECKLEVEL >= 3 then SpecificInd<N>.zm() complains about
   // negative values.
   return lhs.offset(-rhs.dx, -rhs.dy, -rhs.dz);
diff --git a/include/bout/region.hxx b/include/bout/region.hxx
index 6901f346e7..e47be5a551 100644
--- a/include/bout/region.hxx
+++ b/include/bout/region.hxx
@@ -241,18 +241,18 @@ struct SpecificInd {
   /// and is determined by the `dir` template argument. The offset corresponds
   /// to the `dd` template argument.
   template <int dd, DIRECTION dir>
-  inline SpecificInd plus() const {
+  SpecificInd plus() const {
     static_assert(dir == DIRECTION::X || dir == DIRECTION::Y || dir == DIRECTION::Z
                       || dir == DIRECTION::YAligned || dir == DIRECTION::YOrthogonal,
                   "Unhandled DIRECTION in SpecificInd::plus");
     switch (dir) {
-    case (DIRECTION::X):
+    case DIRECTION::X:
       return xp(dd);
-    case (DIRECTION::Y):
-    case (DIRECTION::YAligned):
-    case (DIRECTION::YOrthogonal):
+    case DIRECTION::Y:
+    case DIRECTION::YAligned:
+    case DIRECTION::YOrthogonal:
       return yp(dd);
-    case (DIRECTION::Z):
+    case DIRECTION::Z:
       return zp(dd);
     }
     BOUT_UNREACHABLE();
@@ -262,28 +262,28 @@ struct SpecificInd {
   /// and is determined by the `dir` template argument. The offset corresponds
   /// to the `dd` template argument.
   template <int dd, DIRECTION dir>
-  inline SpecificInd minus() const {
+  SpecificInd minus() const {
     static_assert(dir == DIRECTION::X || dir == DIRECTION::Y || dir == DIRECTION::Z
                       || dir == DIRECTION::YAligned || dir == DIRECTION::YOrthogonal,
                   "Unhandled DIRECTION in SpecificInd::minus");
     switch (dir) {
-    case (DIRECTION::X):
+    case DIRECTION::X:
       return xm(dd);
-    case (DIRECTION::Y):
-    case (DIRECTION::YAligned):
-    case (DIRECTION::YOrthogonal):
+    case DIRECTION::Y:
+    case DIRECTION::YAligned:
+    case DIRECTION::YOrthogonal:
       return ym(dd);
-    case (DIRECTION::Z):
+    case DIRECTION::Z:
       return zm(dd);
     }
     BOUT_UNREACHABLE();
   }
 
-  inline SpecificInd xp(int dx = 1) const { return {ind + (dx * ny * nz), ny, nz}; }
+  SpecificInd xp(int dx = 1) const { return {ind + (dx * ny * nz), ny, nz}; }
   /// The index one point -1 in x
-  inline SpecificInd xm(int dx = 1) const { return xp(-dx); }
+  SpecificInd xm(int dx = 1) const { return xp(-dx); }
   /// The index one point +1 in y
-  inline SpecificInd yp(int dy = 1) const {
+  SpecificInd yp(int dy = 1) const {
 #if CHECK >= 4
     if (y() + dy < 0 or y() + dy >= ny) {
       throw BoutException("Offset in y ({:d}) would go out of bounds at {:d}", dy, ind);
@@ -293,12 +293,12 @@ struct SpecificInd {
     return {ind + (dy * nz), ny, nz};
   }
   /// The index one point -1 in y
-  inline SpecificInd ym(int dy = 1) const { return yp(-dy); }
+  SpecificInd ym(int dy = 1) const { return yp(-dy); }
   /// The index one point +1 in z. Wraps around zend to zstart
   /// An alternative, non-branching calculation is :
   /// ind + dz - nz * ((ind + dz) / nz  - ind / nz)
   /// but this appears no faster (and perhaps slower).
-  inline SpecificInd zp(int dz = 1) const {
+  SpecificInd zp(int dz = 1) const {
     ASSERT3(dz >= 0);
     dz = dz <= nz ? dz : dz % nz; //Fix in case dz > nz, if not force it to be in range
     return {(ind + dz) % nz < dz ? ind - nz + dz : ind + dz, ny, nz};
@@ -307,26 +307,24 @@ struct SpecificInd {
   /// An alternative, non-branching calculation is :
   /// ind - dz + nz * ( (nz + ind) / nz - (nz + ind - dz) / nz)
   /// but this appears no faster (and perhaps slower).
-  inline SpecificInd zm(int dz = 1) const {
+  SpecificInd zm(int dz = 1) const {
     dz = dz <= nz ? dz : dz % nz; //Fix in case dz > nz, if not force it to be in range
     ASSERT3(dz >= 0);
     return {(ind) % nz < dz ? ind + nz - dz : ind - dz, ny, nz};
   }
   /// Automatically select zm or zp depending on sign
-  inline SpecificInd zpm(int dz) const { return dz > 0 ? zp(dz) : zm(-dz); }
+  SpecificInd zpm(int dz) const { return dz > 0 ? zp(dz) : zm(-dz); }
 
   // and for 2 cells
-  inline SpecificInd xpp() const { return xp(2); }
-  inline SpecificInd xmm() const { return xm(2); }
-  inline SpecificInd ypp() const { return yp(2); }
-  inline SpecificInd ymm() const { return ym(2); }
-  inline SpecificInd zpp() const { return zp(2); }
-  inline SpecificInd zmm() const { return zm(2); }
+  SpecificInd xpp() const { return xp(2); }
+  SpecificInd xmm() const { return xm(2); }
+  SpecificInd ypp() const { return yp(2); }
+  SpecificInd ymm() const { return ym(2); }
+  SpecificInd zpp() const { return zp(2); }
+  SpecificInd zmm() const { return zm(2); }
 
   /// Generic offset of \p index in multiple directions simultaneously
-  inline SpecificInd offset(int dx, int dy, int dz) const {
-    return zpm(dz).yp(dy).xp(dx);
-  }
+  SpecificInd offset(int dx, int dy, int dz) const { return zpm(dz).yp(dy).xp(dx); }
 
   /// Relational operator
   auto operator<=>(const SpecificInd<N>& rhs) const { return ind <=> rhs.ind; }

From 28a75eb8177b3ff243f8bfabcbf3d9ad1c19fb85 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 21 Aug 2026 19:33:44 +0000
Subject: [PATCH 1741/1827] Bump externalpackages/googletest from `8b53336` to
 `91c99b6`

Bumps [externalpackages/googletest](https://github.com/google/googletest) from `8b53336` to `91c99b6`.
- [Release notes](https://github.com/google/googletest/releases)
- [Commits](https://github.com/google/googletest/compare/8b53336594cc52213c6c2c7a0b29194fa896d039...91c99b6ffecb6f37ca11c25a0db84007c263c1f2)

---
updated-dependencies:
- dependency-name: externalpackages/googletest
  dependency-version: 91c99b6ffecb6f37ca11c25a0db84007c263c1f2
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 externalpackages/googletest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/externalpackages/googletest b/externalpackages/googletest
index 8b53336594..91c99b6ffe 160000
--- a/externalpackages/googletest
+++ b/externalpackages/googletest
@@ -1 +1 @@
-Subproject commit 8b53336594cc52213c6c2c7a0b29194fa896d039
+Subproject commit 91c99b6ffecb6f37ca11c25a0db84007c263c1f2

From ce102be15cfab561840a39721a9f4f4fe60d8938 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Sun, 23 Aug 2026 11:39:33 -0700
Subject: [PATCH 1742/1827] Jacobian metadata always jacobian_metadata.json

Use of prefix for the metadata file was inconsistent. Since it's
always the same, always use the same name.
---
 manual/sphinx/user_docs/time_integration.rst                | 6 +++---
 src/solver/impls/cvode/cvode.cxx                            | 3 +--
 src/solver/impls/snes/snes.cxx                              | 3 +--
 .../test-cvode-save-jacobian/test_cvode_save_jacobian.py    | 4 ++--
 .../test-snes-save-jacobian/test_snes_save_jacobian.py      | 2 +-
 5 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/manual/sphinx/user_docs/time_integration.rst b/manual/sphinx/user_docs/time_integration.rst
index 171400f0b3..cf0d08112c 100644
--- a/manual/sphinx/user_docs/time_integration.rst
+++ b/manual/sphinx/user_docs/time_integration.rst
@@ -113,7 +113,7 @@ given in table :numref:`tab-solveropts`.
    +--------------------------+--------------------------------------------+-------------------------------------+
    | jacobian\_export\_trigger | When to save Jacobians                    | cvode                               |
    +--------------------------+--------------------------------------------+-------------------------------------+
-   | jacobian\_export\_prefix | Prefix for Jacobian matrix/metadata files  | cvode, beuler / snes                |
+   | jacobian\_export\_prefix | Prefix for Jacobian matrix files           | cvode, beuler / snes                |
    +--------------------------+--------------------------------------------+-------------------------------------+
    | jacobian\_export\_format | PETSc output format for Jacobians          | cvode, beuler / snes                |
    +--------------------------+--------------------------------------------+-------------------------------------+
@@ -898,7 +898,7 @@ The Jacobian files are written into ``datadir``:
 
 - ``<prefix>_<kind>_<counter>.dat`` or ``.txt``: PETSc matrix written by
   ``MatView``.
-- ``<prefix>_metadata.json``: compact JSON metadata describing the ordering
+- ``jacobian_metadata.json``: compact JSON metadata describing the ordering
   of 2D and 3D evolved variables.
 - ``jacobian_index_base`` in the normal BOUT++ dump files: the per-cell base
   global index needed to expand the compact JSON metadata into one row/column
@@ -1023,7 +1023,7 @@ Summary of solver options
 | jacobian_export_kind      | system        | Which Jacobian to save: ``system``, ``scaled``,    |
 |                           |               | or ``rhs``                                         |
 +---------------------------+---------------+----------------------------------------------------+
-| jacobian_export_prefix    | jacobian      | Prefix for Jacobian matrix files and metadata JSON |
+| jacobian_export_prefix    | jacobian      | Prefix for Jacobian matrix files                   |
 +---------------------------+---------------+----------------------------------------------------+
 | jacobian_export_format    | binary        | Matrix file format written by PETSc ``MatView``    |
 +---------------------------+---------------+----------------------------------------------------+
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 645307da4e..d96be8df02 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -258,8 +258,7 @@ PetscErrorCode CvodeSolver::exportMatrixAndMetadata(Mat jacobian,
                                                     const std::string& stem) {
   if (!jacobian_metadata_written) {
     const std::string datadir = Options::root()["datadir"];
-    const std::string metadata_filename =
-        datadir + "/" + jacobian_export_prefix + "_metadata.json";
+    const std::string metadata_filename = datadir + "/jacobian_metadata.json";
     output.write("Jacobian metadata written to {}\n", metadata_filename);
     writeJacobianMetadataJson(metadata_filename, "cvode");
     jacobian_metadata_written = true;
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 9310dccf46..275b1023da 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -409,8 +409,7 @@ PetscErrorCode SNESSolver::exportMatrixAndMetadata(Mat jacobian,
                                                    const std::string& stem) {
   if (!jacobian_metadata_written) {
     const std::string datadir = Options::root()["datadir"];
-    const std::string metadata_filename =
-        datadir + "/" + jacobian_export_prefix + "_metadata.json";
+    const std::string metadata_filename = datadir + "/jacobian_metadata.json";
     output.write("Jacobian metadata written to {}\n", metadata_filename);
     writeJacobianMetadataJson(metadata_filename, "snes");
     jacobian_metadata_written = true;
diff --git a/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.py b/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.py
index ebf658c692..0e1bed10d5 100644
--- a/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.py
+++ b/tests/integrated/test-cvode-save-jacobian/test_cvode_save_jacobian.py
@@ -1,7 +1,7 @@
 from pathlib import Path
+
 import numpy as np
 from boutdata.collect import collect
-
 from read_jacobian import extract_block, load_jacobian, to_numpy_dense
 
 TEST_DIR = Path(".")
@@ -53,7 +53,7 @@ def test_system_jacobian_linear_setup_trigger(assert_success_in_shell):
     )
 
     data_dir = TEST_DIR / "data"
-    metadata_file = data_dir / "jacobian_system_test_metadata.json"
+    metadata_file = data_dir / "jacobian_metadata.json"
     matrix_file = data_dir / "jacobian_system_test_system_000000.dat"
 
     assert metadata_file.exists()
diff --git a/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
index 43ce0ee4ac..c524e791e5 100644
--- a/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
+++ b/tests/integrated/test-snes-save-jacobian/test_snes_save_jacobian.py
@@ -1,6 +1,6 @@
 from pathlib import Path
-import numpy as np
 
+import numpy as np
 from read_jacobian import extract_block, load_jacobian, to_numpy_dense, to_pandas
 
 TEST_DIR = Path(".")

From 50f4b02e06314e8e45ffcc14414f1527181da459 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 21 Aug 2026 13:59:41 +0200
Subject: [PATCH 1743/1827] Add API to set metric tensors and J and B

---
 include/bout/coordinates.hxx |  4 ++++
 src/mesh/coordinates.cxx     | 10 ++++++++++
 2 files changed, 14 insertions(+)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 479f08156c..4de7a7e911 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -368,6 +368,10 @@ public:
   void setMetricTensor(const ContravariantMetricTensor& contravariant_metric_tensor,
                        const CovariantMetricTensor& covariant_metric_tensor);
 
+  void setMetricTensorJB(const ContravariantMetricTensor& contravariant_metric_tensor,
+                         const CovariantMetricTensor& covariant_metric_tensor,
+                         const FieldMetric& J, const FieldMetric& Bxy);
+
   void communicateMetricTensor();
 
 private:
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 679587e347..d7e8ec5f89 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1269,6 +1269,16 @@ void Coordinates::setMetricTensor(
   setJ(recalculateJacobian());
   setBxy(recalculateBxy());
 }
+void Coordinates::setMetricTensorJB(
+    const ContravariantMetricTensor& contravariant_metric_tensor,
+    const CovariantMetricTensor& covariant_metric_tensor, const FieldMetric& J,
+    const FieldMetric& Bxy) {
+  contravariantMetricTensor = contravariant_metric_tensor;
+  covariantMetricTensor = covariant_metric_tensor;
+  setJ(J);
+  setBxy(Bxy);
+  invalidateMetricCaches();
+}
 
 void Coordinates::communicateMetricTensor() {
   contravariantMetricTensor.communicate();

From 8ca53f02ecd2e91fecda2e66ce7c49f79572a823 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 12:09:33 +0200
Subject: [PATCH 1744/1827] Add MetricNormaliser class

---
 include/bout/coordinates.hxx | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 4de7a7e911..54c2230cbb 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -46,6 +46,7 @@
 
 class Mesh;
 class YBoundary;
+class MetricNormaliser;
 
 /*!
  * Represents a coordinate system, and associated operators
@@ -551,5 +552,24 @@ protected:
 namespace bout {
 std::string parallelSliceFieldName(std::string_view field, int offset);
 }
+/// Represents a way to normalise the coordinate system
+/// If a component returns nothing, no normalisation is performed.
+/// Coordinate values are divided by the respective component from
+/// MetricNormaliser, with the exception of the contravariant metric
+/// tensor, which is multiplied by the normalisation factor.
+struct MetricNormaliser {
+  std::optional<BoutReal> g() const { return {}; };
+  std::optional<BoutReal> g11() const { return {}; };
+  std::optional<BoutReal> g22() const { return {}; };
+  std::optional<BoutReal> g33() const { return {}; };
+  std::optional<BoutReal> g12() const { return {}; };
+  std::optional<BoutReal> g13() const { return {}; };
+  std::optional<BoutReal> g23() const { return {}; };
+  std::optional<BoutReal> dx() const { return {}; };
+  std::optional<BoutReal> dy() const { return {}; };
+  std::optional<BoutReal> dz() const { return {}; };
+  std::optional<BoutReal> J() const { return {}; };
+  std::optional<BoutReal> Bxy() const { return {}; };
+};
 
 #endif // BOUT_COORDINATES_H

From cd182518eff2a92867758f39414f3dd84b47f9c1 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 12:10:12 +0200
Subject: [PATCH 1745/1827] Add normalisation to MetricTensors

---
 include/bout/metric_tensor.hxx |  8 +++++++
 src/mesh/metric_tensor.cxx     | 42 ++++++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+)

diff --git a/include/bout/metric_tensor.hxx b/include/bout/metric_tensor.hxx
index 9e510f2bb9..5f253d7e1c 100644
--- a/include/bout/metric_tensor.hxx
+++ b/include/bout/metric_tensor.hxx
@@ -17,6 +17,7 @@ using FieldMetric = Field2D;
 } // namespace bout
 
 class Coordinates;
+class MetricNormaliser;
 
 class MetricTensor {
 public:
@@ -77,6 +78,9 @@ public:
 
   void communicate();
 
+  template <class F>
+  void normaliseMetric(const MetricNormaliser& norm, F&& op);
+
 private:
   FieldMetric g11_m, g22_m, g33_m, g12_m, g13_m, g23_m;
 };
@@ -90,6 +94,8 @@ public:
 
   auto inverse(const std::string& region = "RGN_ALL", bool communicate = true)
       -> ContravariantMetricTensor;
+
+  void normaliseMetric(const MetricNormaliser& norm);
 };
 
 class ContravariantMetricTensor : public MetricTensor {
@@ -98,6 +104,8 @@ public:
 
   auto inverse(const std::string& region = "RGN_ALL", bool communicate = true)
       -> CovariantMetricTensor;
+
+  void normaliseMetric(const MetricNormaliser& norm);
 };
 
 #endif //BOUT_METRIC_TENSOR_HXX
diff --git a/src/mesh/metric_tensor.cxx b/src/mesh/metric_tensor.cxx
index 5444f538d3..16f44d6b05 100644
--- a/src/mesh/metric_tensor.cxx
+++ b/src/mesh/metric_tensor.cxx
@@ -149,6 +149,48 @@ auto ContravariantMetricTensor::inverse(const std::string& region, bool communic
   return result;
 }
 
+template <class F>
+void MetricTensor::normaliseMetric(const MetricNormaliser& norm, F&& op) {
+  if (norm.g().has_value()) {
+    op(g11_m, norm.g());
+    op(g22_m, norm.g());
+    op(g33_m, norm.g());
+    op(g12_m, norm.g());
+    op(g13_m, norm.g());
+    op(g23_m, norm.g());
+  } else {
+    op(g11_m, norm.g11());
+    op(g22_m, norm.g22());
+    op(g33_m, norm.g33());
+    op(g12_m, norm.g12());
+    op(g13_m, norm.g13());
+    op(g23_m, norm.g23());
+  }
+}
+
+void ContravariantMetricTensor::normaliseMetric(const MetricNormaliser& norm) {
+  MetricTensor::normaliseMetric(norm, [](FieldMetric& f, auto fac) {
+    if (fac.has_value()) {
+      if (f.hasParallelSlices()) {
+        f.asField3DParallel() *= fac.value();
+      } else {
+        f *= fac.value();
+      }
+    }
+  });
+}
+void CovariantMetricTensor::normaliseMetric(const MetricNormaliser& norm) {
+  MetricTensor::normaliseMetric(norm, [](FieldMetric& f, auto fac) {
+    if (fac.has_value()) {
+      if (f.hasParallelSlices()) {
+        f.asField3DParallel() /= fac.value();
+      } else {
+        f /= fac.value();
+      }
+    }
+  });
+}
+
 void MetricTensor::communicate() {
   g11_m.getMesh()->communicate_no_slices(g11_m, g22_m, g33_m, g12_m, g13_m, g23_m);
 }

From f9210bc57b115a287622d21ede8033ce6e5ae690 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 12:14:00 +0200
Subject: [PATCH 1746/1827] Add generic normalisation to coordinates

---
 include/bout/coordinates.hxx |  2 ++
 src/mesh/coordinates.cxx     | 53 ++++++++++++++++++++++++++++++++++++
 2 files changed, 55 insertions(+)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 54c2230cbb..65ff0fd8f9 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -384,6 +384,8 @@ public:
 
   void communicateDz();
 
+  void normaliseMetric(const MetricNormaliser& norm);
+
   ///< Coordinate system Jacobian, so volume of cell is J*dx*dy*dz
   const FieldMetric& J() const;
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index d7e8ec5f89..22a2112486 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1366,3 +1366,56 @@ void Coordinates::normaliseMetric(const BoutReal rho_s0, const BoutReal Bnorm) {
   }
   normaliseMetricTokamak(rho_s0, Bnorm);
 }
+
+void Coordinates::normaliseMetric(const MetricNormaliser& norm) {
+  covariantMetricTensor.normaliseMetric(norm);
+  contravariantMetricTensor.normaliseMetric(norm);
+
+#if BOUT_USE_METRIC_3D
+  using FieldMetricParallel = Field3DParallel;
+#else
+  using FieldMetricParallel = Field2D;
+#endif
+
+  if (norm.J().has_value()) {
+    if (J().hasParallelSlices()) {
+      setJ(FieldMetricParallel{J() / *norm.J()});
+    } else {
+      setJ(J() / *norm.J());
+    }
+  }
+  if (norm.Bxy().has_value()) {
+    if (Bxy().hasParallelSlices()) {
+      setBxy(FieldMetricParallel{Bxy() / *norm.Bxy()});
+    } else {
+      setBxy(Bxy() / *norm.Bxy());
+    }
+  }
+  if (norm.dx().has_value()) {
+    setDx(dx() / *norm.dx());
+  }
+  if (norm.dy().has_value()) {
+    setDy(dy() / *norm.dy());
+  }
+  if (norm.dz().has_value()) {
+    setDz(dz() / *norm.dz());
+  }
+  invalidateMetricCaches();
+  if (norm.g().has_value() or norm.g22().has_value()) {
+    if (Bxy().isFci()) {
+      // No we compute g_22_* - they must not be cleared. If they get
+      // cleared, they will be recomputed, but not normalised!
+#if __cpp_lib_optional >= 202110L
+      auto g22 = norm.g().or_else(norm.g22).value();
+#else
+      auto g22 = norm.g().has_value() ? norm.g().value() : norm.g22().value();
+#endif
+      g_22_ylow();
+      g_22_yhigh();
+      ASSERT2(_g_22_ylow.has_value());
+      (*_g_22_ylow) /= g22;
+      ASSERT2(_g_22_yhigh.has_value());
+      (*_g_22_yhigh) /= g22;
+    }
+  }
+}

From 30e762411538c470d071195fb5852eebd8d69ae4 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 12:15:01 +0200
Subject: [PATCH 1747/1827] Remove specific normalisation

---
 include/bout/coordinates.hxx |  7 ----
 src/mesh/coordinates.cxx     | 72 ------------------------------------
 2 files changed, 79 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 65ff0fd8f9..74056776c3 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -375,13 +375,6 @@ public:
 
   void communicateMetricTensor();
 
-private:
-  void normaliseMetricTokamak(BoutReal rho_s0, BoutReal Bnorm);
-  void normaliseMetricFCI(BoutReal rho_s0, BoutReal Bnorm);
-
-public:
-  void normaliseMetric(BoutReal rho_s0, BoutReal Bnorm);
-
   void communicateDz();
 
   void normaliseMetric(const MetricNormaliser& norm);
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 22a2112486..89eaf6707c 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1295,78 +1295,6 @@ void Coordinates::splitBxyParallelSlices() {
   }
 }
 
-void Coordinates::normaliseMetricTokamak(const BoutReal rho_s0, const BoutReal Bnorm) {
-  contravariantMetricTensor = ContravariantMetricTensor(
-      contravariantMetricTensor.g11() / SQ(Bnorm * rho_s0),
-      contravariantMetricTensor.g22() * SQ(rho_s0),
-      contravariantMetricTensor.g33() * SQ(rho_s0),
-      contravariantMetricTensor.g12() / Bnorm, contravariantMetricTensor.g13() / Bnorm,
-      contravariantMetricTensor.g23() * SQ(rho_s0));
-
-  covariantMetricTensor = CovariantMetricTensor(
-      covariantMetricTensor.g11() * SQ(Bnorm * rho_s0),
-      covariantMetricTensor.g22() / SQ(rho_s0), covariantMetricTensor.g33() / SQ(rho_s0),
-      covariantMetricTensor.g12() * Bnorm, covariantMetricTensor.g13() * Bnorm,
-      covariantMetricTensor.g23() / SQ(rho_s0));
-
-  setDx(dx() / (rho_s0 * rho_s0 * Bnorm));
-  setBxy(Bxy() / Bnorm);
-  setJ(J() * Bnorm / rho_s0);
-  invalidateMetricCaches();
-}
-
-void Coordinates::normaliseMetricFCI(const BoutReal rho_s0, const BoutReal Bnorm) {
-  BoutReal rhoSQ = SQ(rho_s0);
-
-  // g??.asField3DParallel() *= rhoSQ;
-  contravariantMetricTensor.map([&](auto f) -> FieldMetric {
-    if (f.hasParallelSlices()) {
-      return f.asField3DParallel() * rhoSQ;
-    };
-    return f * rhoSQ;
-  });
-
-  // g_??.asField3DParallel() /= rhoSQ;
-  covariantMetricTensor.map([&](auto f) -> FieldMetric {
-    if (f.hasParallelSlices()) {
-      return f.asField3DParallel() / rhoSQ;
-    };
-    return f / rhoSQ;
-  });
-  // J.asField3DParallel() /= rho_s0 * rho_s0 * rho_s0;
-#if BOUT_USE_METRIC_3D
-  if (J().hasParallelSlices()) {
-    setJ(Field3DParallel{J() / (rho_s0 * rho_s0 * rho_s0)});
-  } else {
-    setJ(J() / (rho_s0 * rho_s0 * rho_s0));
-  }
-  setBxy(Field3DParallel(Bxy() / Bnorm));
-#else
-  setJ(J() / (rho_s0 * rho_s0 * rho_s0));
-  setBxy(Bxy() / Bnorm);
-#endif
-  invalidateMetricCaches();
-  // No we compute g_22_* - they must not be cleared. If they get
-  // cleared, they will be recomputed, but not normalised!
-  if (Bxy().isFci()) {
-    g_22_ylow();
-    g_22_yhigh();
-    ASSERT2(_g_22_ylow.has_value());
-    (*_g_22_ylow) /= rhoSQ;
-    ASSERT2(_g_22_yhigh.has_value());
-    (*_g_22_yhigh) /= rhoSQ;
-  }
-}
-
-void Coordinates::normaliseMetric(const BoutReal rho_s0, const BoutReal Bnorm) {
-  ASSERT2(hasParallelTransform());
-  if (Bxy().isFci()) {
-    normaliseMetricFCI(rho_s0, Bnorm);
-    return;
-  }
-  normaliseMetricTokamak(rho_s0, Bnorm);
-}
-
 void Coordinates::normaliseMetric(const MetricNormaliser& norm) {
   covariantMetricTensor.normaliseMetric(norm);
   contravariantMetricTensor.normaliseMetric(norm);

From da0c682c5d2caa8190005d40357baac53199ca8d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 12:15:43 +0200
Subject: [PATCH 1748/1827] Add normalisations to tokamak_coordinates

---
 include/bout/tokamak_coordinates.hxx | 34 ++++++++++++++++++++++++++++
 src/mesh/tokamak_coordinates.cxx     | 23 +++++++++++++++++++
 2 files changed, 57 insertions(+)

diff --git a/include/bout/tokamak_coordinates.hxx b/include/bout/tokamak_coordinates.hxx
index 295d0bf9d1..5a78a60573 100644
--- a/include/bout/tokamak_coordinates.hxx
+++ b/include/bout/tokamak_coordinates.hxx
@@ -45,6 +45,40 @@ TokamakCoordinates set_tokamak_coordinates(Mesh& mesh, BoutReal Lbar = 1.0,
                                            BoutReal Bbar = 1.0, bool no_shear = false,
                                            BoutReal shear_factor = 1.0);
 
+class TokamakMetricNormaliser : public MetricNormaliser {
+public:
+  TokamakMetricNormaliser(BoutReal Bnorm, BoutReal rho_s0)
+      : Bnorm(Bnorm), rho_s0(rho_s0) {};
+  std::optional<BoutReal> g11();
+  std::optional<BoutReal> g22();
+  std::optional<BoutReal> g33();
+  std::optional<BoutReal> g12();
+  std::optional<BoutReal> g13();
+  std::optional<BoutReal> g23();
+  std::optional<BoutReal> dx();
+  std::optional<BoutReal> J();
+  std::optional<BoutReal> Bxy();
+
+private:
+  BoutReal Bnorm;
+  BoutReal rho_s0;
+};
+
+class FCIMetricNormaliser : public MetricNormaliser {
+public:
+  FCIMetricNormaliser(BoutReal Bnorm, BoutReal rho_s0) : Bnorm(Bnorm), rho_s0(rho_s0) {};
+  std::optional<BoutReal> g();
+  std::optional<BoutReal> J();
+  std::optional<BoutReal> Bxy();
+
+private:
+  BoutReal Bnorm;
+  BoutReal rho_s0;
+};
+
+std::unique_ptr<MetricNormaliser>
+TokamakOrFCIMetricNormaliser(const Mesh* mesh, BoutReal Bnorm, BoutReal rho_s0);
+
 } // namespace bout
 
 #endif //BOUT_TOKAMAK_COORDINATES_HXX
diff --git a/src/mesh/tokamak_coordinates.cxx b/src/mesh/tokamak_coordinates.cxx
index 06e38155f0..efb97f4b6b 100644
--- a/src/mesh/tokamak_coordinates.cxx
+++ b/src/mesh/tokamak_coordinates.cxx
@@ -75,4 +75,27 @@ TokamakCoordinates set_tokamak_coordinates(Mesh& mesh, BoutReal Lbar, BoutReal B
 
   return {Rxy, Zxy, Bpxy, Btxy, Bxy, hthe, I, I_unnormalised};
 }
+
+std::optional<BoutReal> TokamakMetricNormaliser::g11() { return 1 / SQ(Bnorm * rho_s0); }
+std::optional<BoutReal> TokamakMetricNormaliser::g22() { return SQ(rho_s0); }
+std::optional<BoutReal> TokamakMetricNormaliser::g33() { return SQ(rho_s0); }
+std::optional<BoutReal> TokamakMetricNormaliser::g12() { return 1 / Bnorm; }
+std::optional<BoutReal> TokamakMetricNormaliser::g13() { return 1 / Bnorm; }
+std::optional<BoutReal> TokamakMetricNormaliser::g23() { return SQ(rho_s0); }
+std::optional<BoutReal> TokamakMetricNormaliser::dx() { return rho_s0 * rho_s0 * Bnorm; }
+std::optional<BoutReal> TokamakMetricNormaliser::J() { return rho_s0 / Bnorm; }
+std::optional<BoutReal> TokamakMetricNormaliser::Bxy() { return Bnorm; }
+
+std::optional<BoutReal> FCIMetricNormaliser::g() { return SQ(rho_s0); }
+std::optional<BoutReal> FCIMetricNormaliser::J() { return SQ(rho_s0) * rho_s0; }
+std::optional<BoutReal> FCIMetricNormaliser::Bxy() { return Bnorm; }
+
+std::unique_ptr<MetricNormaliser>
+TokamakOrFCIMetricNormaliser(const Mesh* mesh, BoutReal Bnorm, BoutReal rho_s0) {
+  if (mesh->isFci()) {
+    return std::make_unique<FCIMetricNormaliser>(Bnorm, rho_s0);
+  }
+  return std::make_unique<TokamakMetricNormaliser>(Bnorm, rho_s0);
+}
+
 } // namespace bout

From d49fbec64f1c2d2a22e452452abfc6778896898e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 12:31:08 +0200
Subject: [PATCH 1749/1827] Add missing virtual/override

---
 include/bout/coordinates.hxx         | 24 +++++++++++-----------
 include/bout/tokamak_coordinates.hxx | 24 +++++++++++-----------
 src/mesh/tokamak_coordinates.cxx     | 30 ++++++++++++++++------------
 3 files changed, 41 insertions(+), 37 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 74056776c3..8818d4c4a8 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -553,18 +553,18 @@ std::string parallelSliceFieldName(std::string_view field, int offset);
 /// MetricNormaliser, with the exception of the contravariant metric
 /// tensor, which is multiplied by the normalisation factor.
 struct MetricNormaliser {
-  std::optional<BoutReal> g() const { return {}; };
-  std::optional<BoutReal> g11() const { return {}; };
-  std::optional<BoutReal> g22() const { return {}; };
-  std::optional<BoutReal> g33() const { return {}; };
-  std::optional<BoutReal> g12() const { return {}; };
-  std::optional<BoutReal> g13() const { return {}; };
-  std::optional<BoutReal> g23() const { return {}; };
-  std::optional<BoutReal> dx() const { return {}; };
-  std::optional<BoutReal> dy() const { return {}; };
-  std::optional<BoutReal> dz() const { return {}; };
-  std::optional<BoutReal> J() const { return {}; };
-  std::optional<BoutReal> Bxy() const { return {}; };
+  virtual std::optional<BoutReal> g() const { return {}; };
+  virtual std::optional<BoutReal> g11() const { return {}; };
+  virtual std::optional<BoutReal> g22() const { return {}; };
+  virtual std::optional<BoutReal> g33() const { return {}; };
+  virtual std::optional<BoutReal> g12() const { return {}; };
+  virtual std::optional<BoutReal> g13() const { return {}; };
+  virtual std::optional<BoutReal> g23() const { return {}; };
+  virtual std::optional<BoutReal> dx() const { return {}; };
+  virtual std::optional<BoutReal> dy() const { return {}; };
+  virtual std::optional<BoutReal> dz() const { return {}; };
+  virtual std::optional<BoutReal> J() const { return {}; };
+  virtual std::optional<BoutReal> Bxy() const { return {}; };
 };
 
 #endif // BOUT_COORDINATES_H
diff --git a/include/bout/tokamak_coordinates.hxx b/include/bout/tokamak_coordinates.hxx
index 5a78a60573..fd0b51bdc2 100644
--- a/include/bout/tokamak_coordinates.hxx
+++ b/include/bout/tokamak_coordinates.hxx
@@ -49,15 +49,15 @@ class TokamakMetricNormaliser : public MetricNormaliser {
 public:
   TokamakMetricNormaliser(BoutReal Bnorm, BoutReal rho_s0)
       : Bnorm(Bnorm), rho_s0(rho_s0) {};
-  std::optional<BoutReal> g11();
-  std::optional<BoutReal> g22();
-  std::optional<BoutReal> g33();
-  std::optional<BoutReal> g12();
-  std::optional<BoutReal> g13();
-  std::optional<BoutReal> g23();
-  std::optional<BoutReal> dx();
-  std::optional<BoutReal> J();
-  std::optional<BoutReal> Bxy();
+  std::optional<BoutReal> g11() const override;
+  std::optional<BoutReal> g22() const override;
+  std::optional<BoutReal> g33() const override;
+  std::optional<BoutReal> g12() const override;
+  std::optional<BoutReal> g13() const override;
+  std::optional<BoutReal> g23() const override;
+  std::optional<BoutReal> dx() const override;
+  std::optional<BoutReal> J() const override;
+  std::optional<BoutReal> Bxy() const override;
 
 private:
   BoutReal Bnorm;
@@ -67,9 +67,9 @@ private:
 class FCIMetricNormaliser : public MetricNormaliser {
 public:
   FCIMetricNormaliser(BoutReal Bnorm, BoutReal rho_s0) : Bnorm(Bnorm), rho_s0(rho_s0) {};
-  std::optional<BoutReal> g();
-  std::optional<BoutReal> J();
-  std::optional<BoutReal> Bxy();
+  std::optional<BoutReal> g() const override;
+  std::optional<BoutReal> J() const override;
+  std::optional<BoutReal> Bxy() const override;
 
 private:
   BoutReal Bnorm;
diff --git a/src/mesh/tokamak_coordinates.cxx b/src/mesh/tokamak_coordinates.cxx
index efb97f4b6b..c0644ec4cb 100644
--- a/src/mesh/tokamak_coordinates.cxx
+++ b/src/mesh/tokamak_coordinates.cxx
@@ -76,19 +76,23 @@ TokamakCoordinates set_tokamak_coordinates(Mesh& mesh, BoutReal Lbar, BoutReal B
   return {Rxy, Zxy, Bpxy, Btxy, Bxy, hthe, I, I_unnormalised};
 }
 
-std::optional<BoutReal> TokamakMetricNormaliser::g11() { return 1 / SQ(Bnorm * rho_s0); }
-std::optional<BoutReal> TokamakMetricNormaliser::g22() { return SQ(rho_s0); }
-std::optional<BoutReal> TokamakMetricNormaliser::g33() { return SQ(rho_s0); }
-std::optional<BoutReal> TokamakMetricNormaliser::g12() { return 1 / Bnorm; }
-std::optional<BoutReal> TokamakMetricNormaliser::g13() { return 1 / Bnorm; }
-std::optional<BoutReal> TokamakMetricNormaliser::g23() { return SQ(rho_s0); }
-std::optional<BoutReal> TokamakMetricNormaliser::dx() { return rho_s0 * rho_s0 * Bnorm; }
-std::optional<BoutReal> TokamakMetricNormaliser::J() { return rho_s0 / Bnorm; }
-std::optional<BoutReal> TokamakMetricNormaliser::Bxy() { return Bnorm; }
-
-std::optional<BoutReal> FCIMetricNormaliser::g() { return SQ(rho_s0); }
-std::optional<BoutReal> FCIMetricNormaliser::J() { return SQ(rho_s0) * rho_s0; }
-std::optional<BoutReal> FCIMetricNormaliser::Bxy() { return Bnorm; }
+std::optional<BoutReal> TokamakMetricNormaliser::g11() const {
+  return 1 / SQ(Bnorm * rho_s0);
+}
+std::optional<BoutReal> TokamakMetricNormaliser::g22() const { return SQ(rho_s0); }
+std::optional<BoutReal> TokamakMetricNormaliser::g33() const { return SQ(rho_s0); }
+std::optional<BoutReal> TokamakMetricNormaliser::g12() const { return 1 / Bnorm; }
+std::optional<BoutReal> TokamakMetricNormaliser::g13() const { return 1 / Bnorm; }
+std::optional<BoutReal> TokamakMetricNormaliser::g23() const { return SQ(rho_s0); }
+std::optional<BoutReal> TokamakMetricNormaliser::dx() const {
+  return rho_s0 * rho_s0 * Bnorm;
+}
+std::optional<BoutReal> TokamakMetricNormaliser::J() const { return rho_s0 / Bnorm; }
+std::optional<BoutReal> TokamakMetricNormaliser::Bxy() const { return Bnorm; }
+
+std::optional<BoutReal> FCIMetricNormaliser::g() const { return SQ(rho_s0); }
+std::optional<BoutReal> FCIMetricNormaliser::J() const { return SQ(rho_s0) * rho_s0; }
+std::optional<BoutReal> FCIMetricNormaliser::Bxy() const { return Bnorm; }
 
 std::unique_ptr<MetricNormaliser>
 TokamakOrFCIMetricNormaliser(const Mesh* mesh, BoutReal Bnorm, BoutReal rho_s0) {

From a220081612c6f0d1e558f05bc9d63dd83c8f6fdd Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 12:57:24 +0200
Subject: [PATCH 1750/1827] Turn MetricNormaliser into a plain struct

---
 include/bout/coordinates.hxx         | 27 ++++++++++-----------
 include/bout/metric_tensor.hxx       |  2 +-
 include/bout/tokamak_coordinates.hxx | 35 ++--------------------------
 src/mesh/coordinates.cxx             | 32 +++++++++++--------------
 src/mesh/metric_tensor.cxx           | 26 ++++++++++-----------
 src/mesh/tokamak_coordinates.cxx     | 34 ++++++++++-----------------
 6 files changed, 56 insertions(+), 100 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 8818d4c4a8..492428ac74 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -46,7 +46,7 @@
 
 class Mesh;
 class YBoundary;
-class MetricNormaliser;
+struct MetricNormaliser;
 
 /*!
  * Represents a coordinate system, and associated operators
@@ -547,24 +547,25 @@ protected:
 namespace bout {
 std::string parallelSliceFieldName(std::string_view field, int offset);
 }
+
 /// Represents a way to normalise the coordinate system
 /// If a component returns nothing, no normalisation is performed.
 /// Coordinate values are divided by the respective component from
 /// MetricNormaliser, with the exception of the contravariant metric
 /// tensor, which is multiplied by the normalisation factor.
 struct MetricNormaliser {
-  virtual std::optional<BoutReal> g() const { return {}; };
-  virtual std::optional<BoutReal> g11() const { return {}; };
-  virtual std::optional<BoutReal> g22() const { return {}; };
-  virtual std::optional<BoutReal> g33() const { return {}; };
-  virtual std::optional<BoutReal> g12() const { return {}; };
-  virtual std::optional<BoutReal> g13() const { return {}; };
-  virtual std::optional<BoutReal> g23() const { return {}; };
-  virtual std::optional<BoutReal> dx() const { return {}; };
-  virtual std::optional<BoutReal> dy() const { return {}; };
-  virtual std::optional<BoutReal> dz() const { return {}; };
-  virtual std::optional<BoutReal> J() const { return {}; };
-  virtual std::optional<BoutReal> Bxy() const { return {}; };
+  std::optional<BoutReal> g{};
+  std::optional<BoutReal> g11{};
+  std::optional<BoutReal> g22{};
+  std::optional<BoutReal> g33{};
+  std::optional<BoutReal> g12{};
+  std::optional<BoutReal> g13{};
+  std::optional<BoutReal> g23{};
+  std::optional<BoutReal> dx{};
+  std::optional<BoutReal> dy{};
+  std::optional<BoutReal> dz{};
+  std::optional<BoutReal> J{};
+  std::optional<BoutReal> Bxy{};
 };
 
 #endif // BOUT_COORDINATES_H
diff --git a/include/bout/metric_tensor.hxx b/include/bout/metric_tensor.hxx
index 5f253d7e1c..3d645bdf23 100644
--- a/include/bout/metric_tensor.hxx
+++ b/include/bout/metric_tensor.hxx
@@ -17,7 +17,7 @@ using FieldMetric = Field2D;
 } // namespace bout
 
 class Coordinates;
-class MetricNormaliser;
+struct MetricNormaliser;
 
 class MetricTensor {
 public:
diff --git a/include/bout/tokamak_coordinates.hxx b/include/bout/tokamak_coordinates.hxx
index fd0b51bdc2..4bde1a9a97 100644
--- a/include/bout/tokamak_coordinates.hxx
+++ b/include/bout/tokamak_coordinates.hxx
@@ -45,39 +45,8 @@ TokamakCoordinates set_tokamak_coordinates(Mesh& mesh, BoutReal Lbar = 1.0,
                                            BoutReal Bbar = 1.0, bool no_shear = false,
                                            BoutReal shear_factor = 1.0);
 
-class TokamakMetricNormaliser : public MetricNormaliser {
-public:
-  TokamakMetricNormaliser(BoutReal Bnorm, BoutReal rho_s0)
-      : Bnorm(Bnorm), rho_s0(rho_s0) {};
-  std::optional<BoutReal> g11() const override;
-  std::optional<BoutReal> g22() const override;
-  std::optional<BoutReal> g33() const override;
-  std::optional<BoutReal> g12() const override;
-  std::optional<BoutReal> g13() const override;
-  std::optional<BoutReal> g23() const override;
-  std::optional<BoutReal> dx() const override;
-  std::optional<BoutReal> J() const override;
-  std::optional<BoutReal> Bxy() const override;
-
-private:
-  BoutReal Bnorm;
-  BoutReal rho_s0;
-};
-
-class FCIMetricNormaliser : public MetricNormaliser {
-public:
-  FCIMetricNormaliser(BoutReal Bnorm, BoutReal rho_s0) : Bnorm(Bnorm), rho_s0(rho_s0) {};
-  std::optional<BoutReal> g() const override;
-  std::optional<BoutReal> J() const override;
-  std::optional<BoutReal> Bxy() const override;
-
-private:
-  BoutReal Bnorm;
-  BoutReal rho_s0;
-};
-
-std::unique_ptr<MetricNormaliser>
-TokamakOrFCIMetricNormaliser(const Mesh* mesh, BoutReal Bnorm, BoutReal rho_s0);
+MetricNormaliser TokamakOrFCIMetricNormaliser(const Mesh* mesh, BoutReal Bnorm,
+                                              BoutReal rho_s0);
 
 } // namespace bout
 
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 89eaf6707c..85d28e89fc 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1305,39 +1305,35 @@ void Coordinates::normaliseMetric(const MetricNormaliser& norm) {
   using FieldMetricParallel = Field2D;
 #endif
 
-  if (norm.J().has_value()) {
+  if (norm.J.has_value()) {
     if (J().hasParallelSlices()) {
-      setJ(FieldMetricParallel{J() / *norm.J()});
+      setJ(FieldMetricParallel{J() / *norm.J});
     } else {
-      setJ(J() / *norm.J());
+      setJ(J() / *norm.J);
     }
   }
-  if (norm.Bxy().has_value()) {
+  if (norm.Bxy.has_value()) {
     if (Bxy().hasParallelSlices()) {
-      setBxy(FieldMetricParallel{Bxy() / *norm.Bxy()});
+      setBxy(FieldMetricParallel{Bxy() / *norm.Bxy});
     } else {
-      setBxy(Bxy() / *norm.Bxy());
+      setBxy(Bxy() / *norm.Bxy);
     }
   }
-  if (norm.dx().has_value()) {
-    setDx(dx() / *norm.dx());
+  if (norm.dx.has_value()) {
+    setDx(dx() / *norm.dx);
   }
-  if (norm.dy().has_value()) {
-    setDy(dy() / *norm.dy());
+  if (norm.dy.has_value()) {
+    setDy(dy() / *norm.dy);
   }
-  if (norm.dz().has_value()) {
-    setDz(dz() / *norm.dz());
+  if (norm.dz.has_value()) {
+    setDz(dz() / *norm.dz);
   }
   invalidateMetricCaches();
-  if (norm.g().has_value() or norm.g22().has_value()) {
+  if (norm.g.has_value() or norm.g22.has_value()) {
     if (Bxy().isFci()) {
       // No we compute g_22_* - they must not be cleared. If they get
       // cleared, they will be recomputed, but not normalised!
-#if __cpp_lib_optional >= 202110L
-      auto g22 = norm.g().or_else(norm.g22).value();
-#else
-      auto g22 = norm.g().has_value() ? norm.g().value() : norm.g22().value();
-#endif
+      auto g22 = norm.g.has_value() ? norm.g.value() : norm.g22.value();
       g_22_ylow();
       g_22_yhigh();
       ASSERT2(_g_22_ylow.has_value());
diff --git a/src/mesh/metric_tensor.cxx b/src/mesh/metric_tensor.cxx
index 16f44d6b05..f8e84278a6 100644
--- a/src/mesh/metric_tensor.cxx
+++ b/src/mesh/metric_tensor.cxx
@@ -151,20 +151,20 @@ auto ContravariantMetricTensor::inverse(const std::string& region, bool communic
 
 template <class F>
 void MetricTensor::normaliseMetric(const MetricNormaliser& norm, F&& op) {
-  if (norm.g().has_value()) {
-    op(g11_m, norm.g());
-    op(g22_m, norm.g());
-    op(g33_m, norm.g());
-    op(g12_m, norm.g());
-    op(g13_m, norm.g());
-    op(g23_m, norm.g());
+  if (norm.g.has_value()) {
+    op(g11_m, norm.g);
+    op(g22_m, norm.g);
+    op(g33_m, norm.g);
+    op(g12_m, norm.g);
+    op(g13_m, norm.g);
+    op(g23_m, norm.g);
   } else {
-    op(g11_m, norm.g11());
-    op(g22_m, norm.g22());
-    op(g33_m, norm.g33());
-    op(g12_m, norm.g12());
-    op(g13_m, norm.g13());
-    op(g23_m, norm.g23());
+    op(g11_m, norm.g11);
+    op(g22_m, norm.g22);
+    op(g33_m, norm.g33);
+    op(g12_m, norm.g12);
+    op(g13_m, norm.g13);
+    op(g23_m, norm.g23);
   }
 }
 
diff --git a/src/mesh/tokamak_coordinates.cxx b/src/mesh/tokamak_coordinates.cxx
index c0644ec4cb..8f651eec23 100644
--- a/src/mesh/tokamak_coordinates.cxx
+++ b/src/mesh/tokamak_coordinates.cxx
@@ -76,30 +76,20 @@ TokamakCoordinates set_tokamak_coordinates(Mesh& mesh, BoutReal Lbar, BoutReal B
   return {Rxy, Zxy, Bpxy, Btxy, Bxy, hthe, I, I_unnormalised};
 }
 
-std::optional<BoutReal> TokamakMetricNormaliser::g11() const {
-  return 1 / SQ(Bnorm * rho_s0);
-}
-std::optional<BoutReal> TokamakMetricNormaliser::g22() const { return SQ(rho_s0); }
-std::optional<BoutReal> TokamakMetricNormaliser::g33() const { return SQ(rho_s0); }
-std::optional<BoutReal> TokamakMetricNormaliser::g12() const { return 1 / Bnorm; }
-std::optional<BoutReal> TokamakMetricNormaliser::g13() const { return 1 / Bnorm; }
-std::optional<BoutReal> TokamakMetricNormaliser::g23() const { return SQ(rho_s0); }
-std::optional<BoutReal> TokamakMetricNormaliser::dx() const {
-  return rho_s0 * rho_s0 * Bnorm;
-}
-std::optional<BoutReal> TokamakMetricNormaliser::J() const { return rho_s0 / Bnorm; }
-std::optional<BoutReal> TokamakMetricNormaliser::Bxy() const { return Bnorm; }
-
-std::optional<BoutReal> FCIMetricNormaliser::g() const { return SQ(rho_s0); }
-std::optional<BoutReal> FCIMetricNormaliser::J() const { return SQ(rho_s0) * rho_s0; }
-std::optional<BoutReal> FCIMetricNormaliser::Bxy() const { return Bnorm; }
-
-std::unique_ptr<MetricNormaliser>
-TokamakOrFCIMetricNormaliser(const Mesh* mesh, BoutReal Bnorm, BoutReal rho_s0) {
+MetricNormaliser TokamakOrFCIMetricNormaliser(const Mesh* mesh, BoutReal Bnorm,
+                                              BoutReal rho_s0) {
   if (mesh->isFci()) {
-    return std::make_unique<FCIMetricNormaliser>(Bnorm, rho_s0);
+    return {.g{SQ(rho_s0)}, .J{rho_s0 * rho_s0 * rho_s0}, .Bxy{Bnorm}};
   }
-  return std::make_unique<TokamakMetricNormaliser>(Bnorm, rho_s0);
+  return {.g11{1 / SQ(Bnorm * rho_s0)},
+          .g22{SQ(rho_s0)},
+          .g33{SQ(rho_s0)},
+          .g12{1 / Bnorm},
+          .g13{1 / Bnorm},
+          .g23{SQ(rho_s0)},
+          .dx{rho_s0 * rho_s0 * Bnorm},
+          .J{rho_s0 / Bnorm},
+          .Bxy{Bnorm}};
 }
 
 } // namespace bout

From 01621b99ecd5614ea817cb71a9cb7338ebda1066 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 13:05:28 +0200
Subject: [PATCH 1751/1827] Use const ref

---
 include/bout/metric_tensor.hxx | 2 +-
 src/mesh/metric_tensor.cxx     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/bout/metric_tensor.hxx b/include/bout/metric_tensor.hxx
index 3d645bdf23..8ccaf23395 100644
--- a/include/bout/metric_tensor.hxx
+++ b/include/bout/metric_tensor.hxx
@@ -79,7 +79,7 @@ public:
   void communicate();
 
   template <class F>
-  void normaliseMetric(const MetricNormaliser& norm, F&& op);
+  void normaliseMetric(const MetricNormaliser& norm, const F& op);
 
 private:
   FieldMetric g11_m, g22_m, g33_m, g12_m, g13_m, g23_m;
diff --git a/src/mesh/metric_tensor.cxx b/src/mesh/metric_tensor.cxx
index f8e84278a6..1347f88a7e 100644
--- a/src/mesh/metric_tensor.cxx
+++ b/src/mesh/metric_tensor.cxx
@@ -150,7 +150,7 @@ auto ContravariantMetricTensor::inverse(const std::string& region, bool communic
 }
 
 template <class F>
-void MetricTensor::normaliseMetric(const MetricNormaliser& norm, F&& op) {
+void MetricTensor::normaliseMetric(const MetricNormaliser& norm, const F& op) {
   if (norm.g.has_value()) {
     op(g11_m, norm.g);
     op(g22_m, norm.g);

From ae9b5e78ed21a8d028c89c48368c47e862bbcfa0 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 13:06:22 +0200
Subject: [PATCH 1752/1827] Remove redundant initialisation

---
 include/bout/coordinates.hxx | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 492428ac74..56af8ff7d8 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -554,18 +554,18 @@ std::string parallelSliceFieldName(std::string_view field, int offset);
 /// MetricNormaliser, with the exception of the contravariant metric
 /// tensor, which is multiplied by the normalisation factor.
 struct MetricNormaliser {
-  std::optional<BoutReal> g{};
-  std::optional<BoutReal> g11{};
-  std::optional<BoutReal> g22{};
-  std::optional<BoutReal> g33{};
-  std::optional<BoutReal> g12{};
-  std::optional<BoutReal> g13{};
-  std::optional<BoutReal> g23{};
-  std::optional<BoutReal> dx{};
-  std::optional<BoutReal> dy{};
-  std::optional<BoutReal> dz{};
-  std::optional<BoutReal> J{};
-  std::optional<BoutReal> Bxy{};
+  std::optional<BoutReal> g;
+  std::optional<BoutReal> g11;
+  std::optional<BoutReal> g22;
+  std::optional<BoutReal> g33;
+  std::optional<BoutReal> g12;
+  std::optional<BoutReal> g13;
+  std::optional<BoutReal> g23;
+  std::optional<BoutReal> dx;
+  std::optional<BoutReal> dy;
+  std::optional<BoutReal> dz;
+  std::optional<BoutReal> J;
+  std::optional<BoutReal> Bxy;
 };
 
 #endif // BOUT_COORDINATES_H

From 41171122711968097fb38c69d1c8e79aa6c2f17e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 13 Aug 2026 11:22:25 +0200
Subject: [PATCH 1753/1827] Update prek tools to work with python3.15

---
 .pre-commit-config.yaml |   4 +-
 uv.lock                 | 746 ++++++++++++++++++++++++----------------
 2 files changed, 443 insertions(+), 307 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 84a440847b..31369b738b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -24,14 +24,14 @@ repos:
 
 # C++ formatting
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v22.1.1
+  rev: v22.1.8
   hooks:
   - id: clang-format
     types_or: [c++, c, cuda]
 
 # Python linting and formatting
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.6
+  rev: v0.16.2
   hooks:
     # Run the linter.
     - id: ruff-check
diff --git a/uv.lock b/uv.lock
index b75bf34bea..ac72aed7bd 100644
--- a/uv.lock
+++ b/uv.lock
@@ -23,14 +23,18 @@ maint = [
     { name = "ruamel-yaml", specifier = "~=0.19" },
     { name = "unidecode", specifier = "~=1.3" },
 ]
+pytest = [
+    { name = "pytest", specifier = "~=8.4" },
+    { name = "pytest-xdist", specifier = "~=3.8" },
+]
 
 [[package]]
 name = "attrs"
-version = "25.4.0"
+version = "26.1.0"
 source = { registry = "https://pypi.org/simple" }
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+    { url = "https://files.pythonhosted.org/packages/64/b4/17d4b0b2a2dc85a6df63d1157e028ed19f90d4cd97c36717afef2bc2f395/attrs-26.1.0-py3-none-any.whl", hash = "sha256:c647aa4a12dfbad9333ca4e71fe62ddc36f4e63b2d260a37a8b83d2f043ac309", size = 67548, upload-time = "2026-03-19T14:22:23.645Z" },
 ]
 
 [[package]]
@@ -48,129 +52,208 @@ wheels = [
 
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 name = "typing-extensions"
-version = "4.15.0"
+version = "4.16.0"
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@@ -706,9 +842,9 @@ wheels = [
 
 [[package]]
 name = "urllib3"
-version = "2.6.3"
+version = "2.7.0"
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From e4e2d6ae4001715fefdf02a4ae579076a087ce8e Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Mon, 24 Aug 2026 13:37:43 +0200
Subject: [PATCH 1754/1827] Update pyproject.toml and uv.lock

---
 pyproject.toml | 18 +++++++++---------
 uv.lock        | 36 ++++++++++++++++++------------------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4a76c03fd2..9e61e655f5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,26 +10,26 @@ console_output_style = "plain"
 
 [dependency-groups]
 dev = [
-     "cmake~=4.2",
-     "clang-format~=22.0",
-     "clang-tidy~=22.0",
-     "clangd~=22.0",
+     "cmake~=4.4",
+     "clang-format~=22.1",
+     "clang-tidy~=22.1",
+     "clangd~=22.1",
      "clangd-tidy~=1.1",
      "cmakelang~=0.6",
      "prek>=0.3.10",
      "pyyaml~=6.0",
-     "ruff~=0.15",
+     "ruff~=0.16",
      "sphinx-lint~=1.0",
-     "sync-with-uv~=0.5.0",
+     "sync-with-uv~=0.6.0",
 ]
 pytest = [
-     "pytest~=8.4",
+     "pytest~=9.1",
      "pytest-xdist~=3.8",
 ]
 maint = [
-      "pygithub~=2.8",
+      "pygithub~=2.10",
       "ruamel-yaml~=0.19",
-      "Unidecode~=1.3",
+      "Unidecode~=1.4",
 ]
 
 [tool.uv.workspace]
diff --git a/uv.lock b/uv.lock
index ac72aed7bd..48166cce48 100644
--- a/uv.lock
+++ b/uv.lock
@@ -6,25 +6,25 @@ requires-python = ">=3.14"
 
 [manifest.dependency-groups]
 dev = [
-    { name = "clang-format", specifier = "~=22.0" },
-    { name = "clang-tidy", specifier = "~=22.0" },
-    { name = "clangd", specifier = "~=22.0" },
+    { name = "clang-format", specifier = "~=22.1" },
+    { name = "clang-tidy", specifier = "~=22.1" },
+    { name = "clangd", specifier = "~=22.1" },
     { name = "clangd-tidy", specifier = "~=1.1" },
-    { name = "cmake", specifier = "~=4.2" },
+    { name = "cmake", specifier = "~=4.4" },
     { name = "cmakelang", specifier = "~=0.6" },
     { name = "prek", specifier = ">=0.3.10" },
     { name = "pyyaml", specifier = "~=6.0" },
-    { name = "ruff", specifier = "~=0.15" },
+    { name = "ruff", specifier = "~=0.16" },
     { name = "sphinx-lint", specifier = "~=1.0" },
-    { name = "sync-with-uv", specifier = "~=0.5.0" },
+    { name = "sync-with-uv", specifier = "~=0.6.0" },
 ]
 maint = [
-    { name = "pygithub", specifier = "~=2.8" },
+    { name = "pygithub", specifier = "~=2.10" },
     { name = "ruamel-yaml", specifier = "~=0.19" },
-    { name = "unidecode", specifier = "~=1.3" },
+    { name = "unidecode", specifier = "~=1.4" },
 ]
 pytest = [
-    { name = "pytest", specifier = "~=8.4" },
+    { name = "pytest", specifier = "~=9.1" },
     { name = "pytest-xdist", specifier = "~=3.8" },
 ]
 
@@ -517,7 +517,7 @@ wheels = [
 
 [[package]]
 name = "pygithub"
-version = "2.9.1"
+version = "2.10.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "pyjwt", extra = ["crypto"] },
@@ -526,9 +526,9 @@ dependencies = [
     { name = "typing-extensions" },
     { name = "urllib3" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/ab/c3/8465a311197e16cf5ab68789fe689535e90f6b61ab524cc32a39e67237ae/pygithub-2.9.1.tar.gz", hash = "sha256:59771d7ff63d54d427be2e7d0dad2208dfffc2b0a045fec959263787739b611c", size = 2594989, upload-time = "2026-04-14T07:26:13.622Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/e1/9b/195603d5371861005a3467c5e4afd02fd0698795a2aa36dc41498b9d879d/pygithub-2.10.0.tar.gz", hash = "sha256:90ff24ef1cd1bd57124c2a3869cafee9d7b066909129ecdaba2c2d1903bc118d", size = 2750952, upload-time = "2026-08-20T10:05:08.327Z" }
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+    { url = "https://files.pythonhosted.org/packages/91/71/f314841697a1d52af3e1ea7c5e1c3f09685b64ae4c58ff16b605a866255d/pygithub-2.10.0-py3-none-any.whl", hash = "sha256:192ada2a76e4afc7d6b37e500c9bfeba1731e6506697445a5ba1c4af8bf0b924", size = 455554, upload-time = "2026-08-20T10:05:06.991Z" },
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 [[package]]
@@ -591,7 +591,7 @@ wheels = [
 
 [[package]]
 name = "pytest"
-version = "8.4.2"
+version = "9.1.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "colorama", marker = "sys_platform == 'win32'" },
@@ -600,9 +600,9 @@ dependencies = [
     { name = "pluggy" },
     { name = "pygments" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/a3/5c/00a0e072241553e1a7496d638deababa67c5058571567b92a7eaa258397c/pytest-8.4.2.tar.gz", hash = "sha256:86c0d0b93306b961d58d62a4db4879f27fe25513d4b969df351abdddb3c30e01", size = 1519618, upload-time = "2025-09-04T14:34:22.711Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/e4/47/b9efed96c114afcfa3c9d3fe98a76a1d14c74a9e266d397cf6eb64be5e01/pytest-9.1.1.tar.gz", hash = "sha256:1088fbde8f2b49d95a549a195707afa7a76a3ce9bcadc26b6d71f0ffda5fe313", size = 1636369, upload-time = "2026-06-19T10:58:32.857Z" }
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+    { url = "https://files.pythonhosted.org/packages/24/25/1de2678b631f5a49215c6c96fff41ba892b0a34df68d6d80292b1b48aa7f/pytest-9.1.1-py3-none-any.whl", hash = "sha256:37a86b45efb9a47a61a36449063e8e18d0cab3161329fc099eb21783169c4f0c", size = 386536, upload-time = "2026-06-19T10:58:31.347Z" },
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 [[package]]
@@ -783,16 +783,16 @@ wheels = [
 
 [[package]]
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-version = "0.5.0"
+version = "0.6.0"
 source = { registry = "https://pypi.org/simple" }
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     { name = "cyclopts" },
     { name = "tomli" },
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+    { url = "https://files.pythonhosted.org/packages/8c/c3/353b684b02ab653fbbd60172fac7a715b0d49d03a7c7da51db2a364dc061/sync_with_uv-0.6.0-py3-none-any.whl", hash = "sha256:acb634a3ddc406f0d713b9263106f52b7d4a7ee791d2105efe8d4a6f6abc42dd", size = 14456, upload-time = "2026-07-14T11:36:36.452Z" },
 ]
 
 [[package]]

From ef2fda3f593731392e3a94a5e137c3742b65541c Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 25 Aug 2026 08:47:56 +0200
Subject: [PATCH 1755/1827] Be explit about it being not set

---
 include/bout/coordinates.hxx | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 56af8ff7d8..8173fd05c5 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -554,18 +554,18 @@ std::string parallelSliceFieldName(std::string_view field, int offset);
 /// MetricNormaliser, with the exception of the contravariant metric
 /// tensor, which is multiplied by the normalisation factor.
 struct MetricNormaliser {
-  std::optional<BoutReal> g;
-  std::optional<BoutReal> g11;
-  std::optional<BoutReal> g22;
-  std::optional<BoutReal> g33;
-  std::optional<BoutReal> g12;
-  std::optional<BoutReal> g13;
-  std::optional<BoutReal> g23;
-  std::optional<BoutReal> dx;
-  std::optional<BoutReal> dy;
-  std::optional<BoutReal> dz;
-  std::optional<BoutReal> J;
-  std::optional<BoutReal> Bxy;
+  std::optional<BoutReal> g = std::nullopt;
+  std::optional<BoutReal> g11 = std::nullopt;
+  std::optional<BoutReal> g22 = std::nullopt;
+  std::optional<BoutReal> g33 = std::nullopt;
+  std::optional<BoutReal> g12 = std::nullopt;
+  std::optional<BoutReal> g13 = std::nullopt;
+  std::optional<BoutReal> g23 = std::nullopt;
+  std::optional<BoutReal> dx = std::nullopt;
+  std::optional<BoutReal> dy = std::nullopt;
+  std::optional<BoutReal> dz = std::nullopt;
+  std::optional<BoutReal> J = std::nullopt;
+  std::optional<BoutReal> Bxy = std::nullopt;
 };
 
 #endif // BOUT_COORDINATES_H

From 5ca22b6232d524b00ca0aa447fd26ad1761a2ca2 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 18 Aug 2026 16:19:10 +0100
Subject: [PATCH 1756/1827] Remove unused enum

---
 include/bout/boundary_region_iter.hxx | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 6de145b7d3..e960f63bb9 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -3,7 +3,6 @@
 #include <algorithm>
 #include <cmath>
 #include <cstddef>
-#include <cstdint>
 #include <functional>
 #include <memory>
 #include <string>
@@ -24,18 +23,6 @@
 namespace bout {
 namespace boundary {
 
-/// Physical type of y boundary
-enum class BndryType : std::int8_t {
-  sheath,
-  not_sheath_par,
-  core,
-  sol,
-  sol_perp,
-  sol_par,
-  all,
-  num
-};
-
 template <typename impl>
 class BoundaryRegionIterBase {
   BoundaryRegionIterBase() = default;

From 9d6b9ca0aa35d7104c1dcbb81b88bb34dd8a7047 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 18 Aug 2026 17:03:43 +0100
Subject: [PATCH 1757/1827] Move `YBoundary` into `bout::boundary` namespace
 for consistency

Also move the free friend function `getYBoundary` into `Coordinates`
---
 include/bout/boundary_region_iter.hxx         | 25 ++++++++-----------
 include/bout/coordinates.hxx                  | 11 +++++---
 include/bout/yboundary_regions.hxx            | 16 +++++-------
 src/mesh/coordinates.cxx                      |  9 +++++--
 .../test-fci-boundary/get_par_bndry.cxx       |  5 ++--
 tests/unit/include/bout/test_yboundary.cxx    |  2 ++
 6 files changed, 35 insertions(+), 33 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index e960f63bb9..16f892b299 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -752,24 +752,21 @@ void iter_boundary(const Bndry& bndry, const Func& func) {
   }
 }
 
-} // namespace boundary
-} // namespace bout
-inline bout::boundary::BoundaryRegionIterFCI
-begin(const bout::boundary::BoundaryRegionFCI& reg) {
-  return bout::boundary::BoundaryRegionIterFCI(&reg, true);
+inline auto begin(const BoundaryRegionFCI& reg) {
+  return BoundaryRegionIterFCI(&reg, true);
 }
-inline bout::boundary::BoundaryRegionIterFCI
-end(const bout::boundary::BoundaryRegionFCI& reg) {
-  return bout::boundary::BoundaryRegionIterFCI(&reg, false);
+inline auto end(const BoundaryRegionFCI& reg) {
+  return BoundaryRegionIterFCI(&reg, false);
 }
 
 template <bool isX>
-inline bout::boundary::BoundaryRegionIterXY<isX>
-begin(const bout::boundary::BoundaryRegionXY<isX>& reg) {
-  return bout::boundary::BoundaryRegionIterXY<isX>(&reg, true);
+inline auto begin(const BoundaryRegionXY<isX>& reg) {
+  return BoundaryRegionIterXY<isX>(&reg, true);
 }
 template <bool isX>
-inline bout::boundary::BoundaryRegionIterXY<isX>
-end(const bout::boundary::BoundaryRegionXY<isX>& reg) {
-  return bout::boundary::BoundaryRegionIterXY<isX>(&reg, false);
+inline auto end(const BoundaryRegionXY<isX>& reg) {
+  return BoundaryRegionIterXY<isX>(&reg, false);
 }
+
+} // namespace boundary
+} // namespace bout
diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index 9bf8cd7513..d7526f9023 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -45,9 +45,12 @@
 #include <utility>
 
 class Mesh;
-class YBoundary;
 struct MetricNormaliser;
 
+namespace bout::boundary {
+class YBoundary;
+}
+
 /*!
  * Represents a coordinate system, and associated operators
  */
@@ -469,10 +472,10 @@ public:
 
   FieldMetric recalculateJacobian() const;
 
-  friend std::shared_ptr<YBoundary> getYBoundary(Coordinates* coords, YBndryType type);
+  const bout::boundary::YBoundary&
+  getYBoundary(YBndryType type = YBndryType::sheath) const;
 
 private:
-  std::shared_ptr<YBoundary> makeYBoundary(YBndryType type) const;
   int nz; // Size of mesh in Z. This is mesh->ngz-1
   Mesh* localmesh;
   Options* localoptions{nullptr};
@@ -529,7 +532,7 @@ private:
   void invalidateCellGeometryCaches();
   void invalidateAccessorCache() const;
 
-  mutable std::array<std::shared_ptr<YBoundary>, 3> ybndrys;
+  mutable std::array<std::shared_ptr<bout::boundary::YBoundary>, 3> ybndrys;
 
   FieldMetric recalculateBxy() const;
 
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index bb9f52bbda..26905615a0 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -14,6 +14,8 @@
 #include <memory>
 #include <vector>
 
+namespace bout {
+namespace boundary {
 /// This class allows to simplify iterating over y-boundaries.
 ///
 /// It makes it easier to write code for FieldAligned boundaries, but if a bit
@@ -136,17 +138,11 @@ private:
       func(*region);
     }
   }
-  std::vector<std::shared_ptr<bout::boundary::BoundaryRegionFCI>> boundary_regions_par;
-  std::vector<std::shared_ptr<bout::boundary::BoundaryRegionY>> boundary_regions;
+  std::vector<std::shared_ptr<BoundaryRegionFCI>> boundary_regions_par;
+  std::vector<std::shared_ptr<BoundaryRegionY>> boundary_regions;
 
   std::vector<BoutMask> _contains;
 };
 
-inline std::shared_ptr<YBoundary> getYBoundary(Coordinates* coords,
-                                               YBndryType type = YBndryType::sheath) {
-  auto itype = static_cast<int>(type);
-  if (coords->ybndrys[itype] == nullptr) {
-    coords->ybndrys[itype] = coords->makeYBoundary(type);
-  }
-  return coords->ybndrys[itype];
-}
+} // namespace boundary
+} // namespace bout
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 85d28e89fc..4e61276457 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -1222,8 +1222,13 @@ void Coordinates::_compute_cell_volume() const {
   }
 }
 
-std::shared_ptr<YBoundary> Coordinates::makeYBoundary(YBndryType type) const {
-  return std::make_shared<YBoundary>(type, localoptions, *localmesh);
+const bout::boundary::YBoundary& Coordinates::getYBoundary(YBndryType type) const {
+  using bout::boundary::YBoundary;
+  const auto itype = static_cast<int>(type);
+  if (ybndrys.at(itype) == nullptr) {
+    ybndrys.at(itype) = std::make_shared<YBoundary>(type, localoptions, *localmesh);
+  }
+  return *ybndrys.at(itype);
 }
 
 void Coordinates::setBxy(FieldMetric Bxy, const bool communicate) {
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 1d5b9a5d63..098ec2ea4a 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -43,14 +43,13 @@ int main(int argc, char** argv) {
   }
 
   {
-    const Options dummy;
-    auto ybndry = getYBoundary(mesh->getCoordinates());
+    const auto& ybndry = mesh->getCoordinates()->getYBoundary();
 
     std::vector<Field3D> fields((mesh->ystart * 2) + 1, Field3D{0.0});
     for (auto& field : fields) {
       field.allocate();
     }
-    ybndry->iter(
+    ybndry.iter(
         [&](const auto& pnt) { fields[pnt.dir() + mesh->ystart][pnt.ind()] += 1; });
 
     for (int i = -mesh->ystart; i <= mesh->ystart; ++i) {
diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index ce531c27f8..f78fcff382 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -9,6 +9,8 @@
 
 using YBTest = FakeMeshFixture_tmpl<4, 5, 7>;
 
+using bout::boundary::YBoundary;
+using bout::boundary::YBoundaryPoint;
 using bout::globals::mesh;
 
 TEST_F(YBTest, dirichlet_o2_rgn) {

From 3e726651c0dc73769f436e7c2bb129d288c9c674 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 18 Aug 2026 17:49:23 +0100
Subject: [PATCH 1758/1827] Add some helper concepts for `YBoundary` functions

Also remove indirection through `iter_regions`
---
 include/bout/yboundary_regions.hxx         | 42 +++++++-----
 tests/unit/include/bout/test_yboundary.cxx | 78 +++++++++++++---------
 2 files changed, 73 insertions(+), 47 deletions(-)

diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 26905615a0..ba44ea2e43 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -2,7 +2,6 @@
 
 #include "bout/boundary_region_iter.hxx"
 
-#include "bout/assert.hxx"
 #include "bout/boundary_iterator.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field_data.hxx"
@@ -11,11 +10,22 @@
 #include "bout/options.hxx"
 #include "bout/parallel_boundary_region.hxx"
 #include "bout/region.hxx"
+
+#include <concepts>
 #include <memory>
 #include <vector>
 
 namespace bout {
 namespace boundary {
+/// Helper concept for functions to pass into `YBoundary::iter`
+///
+/// The function passed into `YBoundary::iter` operates over elements of types
+/// derived from `BoundaryRegionIterBase`, but because this uses CRTP they can
+/// be a bit difficult to name. Instead use `YBoundaryPoint auto` as the
+/// parameter type.
+template <class T>
+concept YBoundaryPoint = std::derived_from<T, BoundaryRegionIterBase<T>>;
+
 /// This class allows to simplify iterating over y-boundaries.
 ///
 /// It makes it easier to write code for FieldAligned boundaries, but if a bit
@@ -28,15 +38,22 @@ class YBoundary {
 public:
   /// Iterate over the boundary.
   /// This function takes a lamda / templated function, that applies the boundary on the given point.
-  /// The function must take a `auto& point` as argument.
+  /// The function must take a `const YBoundaryPoint auto& point` as its only argument.
   /// See also the documentation at ../../manual/sphinx/user_docs/boundary_options.rst
-  template <class Func>
-  void iter(const Func& func) {
-    iter_regions([&](auto& region) {
-      for (auto& point : region) {
+  template <class F>
+    requires std::regular_invocable<F&, const BoundaryRegionIterY&>
+             || std::regular_invocable<F&, const BoundaryRegionIterFCI&>
+  void iter(F func) {
+    for (auto& region : boundary_regions) {
+      for (auto& point : *region) {
         func(point);
       }
-    });
+    }
+    for (auto& region : boundary_regions_par) {
+      for (auto& point : *region) {
+        func(point);
+      }
+    }
   }
 
   YBoundary(YBndryType type, Options* options_ptr, const Mesh& mesh) {
@@ -97,7 +114,7 @@ public:
     // Cache boundary regions
     _contains.emplace_back(&mesh, false);
     _contains.emplace_back(&mesh, false);
-    iter([&](const auto& point) {
+    iter([&](const YBoundaryPoint auto& point) {
       if (point.dir() == 1) {
         _contains[1][point.ind()] = true;
       } else if (point.dir() == -1) {
@@ -129,15 +146,6 @@ public:
   }
 
 private:
-  template <class Func>
-  void iter_regions(const Func& func) {
-    for (auto& region : boundary_regions) {
-      func(*region);
-    }
-    for (auto& region : boundary_regions_par) {
-      func(*region);
-    }
-  }
   std::vector<std::shared_ptr<BoundaryRegionFCI>> boundary_regions_par;
   std::vector<std::shared_ptr<BoundaryRegionY>> boundary_regions;
 
diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index f78fcff382..0255dd6de2 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -17,7 +17,7 @@ TEST_F(YBTest, dirichlet_o2_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { point.dirichlet_o2(test, 2); });
+  sheath.iter([&](const YBoundaryPoint auto& point) { point.dirichlet_o2(test, 2); });
   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }
 
@@ -25,7 +25,7 @@ TEST_F(YBTest, neumann_o1_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { point.neumann_o1(test, 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) { point.neumann_o1(test, 1); });
   EXPECT_TRUE(IsFieldEqual(test, 2.0, "RGN_YGUARDS"));
 }
 
@@ -33,7 +33,7 @@ TEST_F(YBTest, neumann_o2_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { point.neumann_o2(test, 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) { point.neumann_o2(test, 1); });
   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }
 
@@ -41,7 +41,7 @@ TEST_F(YBTest, neumann_o3_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { point.neumann_o3(test, 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) { point.neumann_o3(test, 1); });
   EXPECT_TRUE(IsFieldEqual(test, 0.0, "RGN_YGUARDS"));
 }
 
@@ -49,35 +49,38 @@ TEST_F(YBTest, bndry_size) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   int sum = 0;
-  sheath.iter([&](auto& point) { sum++; });
+  sheath.iter([&](const YBoundaryPoint auto& point) { sum++; });
   EXPECT_EQ(sum, 28);
 }
 
 TEST_F(YBTest, interpolate_boundary_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter(
-      [&](auto& point) { EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0); });
+  sheath.iter([&](const YBoundaryPoint auto& point) {
+    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0);
+  });
 }
 
 TEST_F(YBTest, interpolate_boundary_o2_const) {
   const Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter(
-      [&](auto& point) { EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0); });
+  sheath.iter([&](const YBoundaryPoint auto& point) {
+    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0);
+  });
 }
 
 TEST_F(YBTest, extrapolate_boundary_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter(
-      [&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_boundary_o2(test), 1.0); });
+  sheath.iter([&](const YBoundaryPoint auto& point) {
+    EXPECT_DOUBLE_EQ(point.extrapolate_boundary_o2(test), 1.0);
+  });
 }
 
 TEST_F(YBTest, dirichlet_o1) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) {
+  sheath.iter([&](const YBoundaryPoint auto& point) {
     point.dirichlet_o1(test, 2.0);
     EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.5);
   });
@@ -86,7 +89,7 @@ TEST_F(YBTest, dirichlet_o1) {
 TEST_F(YBTest, dirichlet_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) {
+  sheath.iter([&](const YBoundaryPoint auto& point) {
     point.dirichlet_o2(test, 2.0);
     EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 2.0);
   });
@@ -95,7 +98,7 @@ TEST_F(YBTest, dirichlet_o2) {
 TEST_F(YBTest, dirichlet_o3) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) {
+  sheath.iter([&](const YBoundaryPoint auto& point) {
     point.dirichlet_o3(test, 2.0);
     EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 7. / 3.);
   });
@@ -104,7 +107,7 @@ TEST_F(YBTest, dirichlet_o3) {
 TEST_F(YBTest, extrapolate_boundary_free) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2) + 1; }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) {
+  sheath.iter([&](const YBoundaryPoint auto& point) {
     EXPECT_DOUBLE_EQ(point.extrapolate_boundary_free(
                          test, bout::boundary::BoundaryFreeExtrapolation::limited),
                      3);
@@ -120,7 +123,7 @@ TEST_F(YBTest, extrapolate_boundary_free) {
 TEST_F(YBTest, set_free) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2) + 1; }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) {
+  sheath.iter([&](const YBoundaryPoint auto& point) {
     point.set_free(test, bout::boundary::BoundaryFreeExtrapolation::limited);
     EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 3);
   });
@@ -129,14 +132,15 @@ TEST_F(YBTest, set_free) {
 TEST_F(YBTest, interpolate_boundary_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter(
-      [&](auto& point) { EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 2.5); });
+  sheath.iter([&](const YBoundaryPoint auto& point) {
+    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 2.5);
+  });
 }
 
 TEST_F(YBTest, limit_at_least) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) {
+  sheath.iter([&](const YBoundaryPoint auto& point) {
     point.limit_at_least(test, 2.0);
     EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.5);
   });
@@ -145,61 +149,75 @@ TEST_F(YBTest, limit_at_least) {
 TEST_F(YBTest, extrapolate_grad_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_grad_o2(test), 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) {
+    EXPECT_DOUBLE_EQ(point.extrapolate_grad_o2(test), 1);
+  });
 }
 
 TEST_F(YBTest, extrapolate_next_o1_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_next_o1(test), 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) {
+    EXPECT_DOUBLE_EQ(point.extrapolate_next_o1(test), 1);
+  });
 }
 
 TEST_F(YBTest, extrapolate_next_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.extrapolate_next_o2(test), 2); });
+  sheath.iter([&](const YBoundaryPoint auto& point) {
+    EXPECT_DOUBLE_EQ(point.extrapolate_next_o2(test), 2);
+  });
 }
 
 TEST_F(YBTest, next_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
+  sheath.iter(
+      [&](const YBoundaryPoint auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
 }
 
 TEST_F(YBTest, current_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.current(test), 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) {
+    EXPECT_DOUBLE_EQ(point.current(test), 1);
+  });
 }
 
 TEST_F(YBTest, prev_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
+  sheath.iter(
+      [&](const YBoundaryPoint auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
 }
 
 TEST_F(YBTest, next_const) {
   const Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
+  sheath.iter(
+      [&](const YBoundaryPoint auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
 }
 
 TEST_F(YBTest, current_const) {
   const Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.current(test), 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) {
+    EXPECT_DOUBLE_EQ(point.current(test), 1);
+  });
 }
 
 TEST_F(YBTest, prev_const) {
   const Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
+  sheath.iter(
+      [&](const YBoundaryPoint auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
 }
 
 TEST_F(YBTest, getAt_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](auto& point) {
+  sheath.iter([&](const YBoundaryPoint auto& point) {
     EXPECT_DOUBLE_EQ(point.getAt(test, 0), 4);
     EXPECT_DOUBLE_EQ(point.getAt(test, 1), 1);
     EXPECT_DOUBLE_EQ(point.getAt(test, 2), 0);
@@ -210,7 +228,7 @@ TEST_F(YBTest, getAt_func) {
   Field3D test = makeField<Field3D>([&](auto& i) { return i.y() - 2; }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   auto square = [&](int yo, Ind3D ind) -> double { return SQ(test[ind]); };
-  sheath.iter([&](auto& point) {
+  sheath.iter([&](const YBoundaryPoint auto& point) {
     EXPECT_DOUBLE_EQ(point.getAt(square, 0), 4);
     EXPECT_DOUBLE_EQ(point.getAt(square, 1), 1);
     EXPECT_DOUBLE_EQ(point.getAt(square, 2), 0);

From bb1d5c9b33a2678d8ccf1a9333d7cf295d295f69 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 18 Aug 2026 18:06:25 +0100
Subject: [PATCH 1759/1827] Small refactor of `YBoundary`

- Move body of ctor to .cxx file
- Inline two-element vector
---
 CMakeLists.txt                     |  2 +
 include/bout/yboundary_regions.hxx | 94 ++++++------------------------
 src/mesh/yboundary_regions.cxx     | 72 +++++++++++++++++++++++
 3 files changed, 91 insertions(+), 77 deletions(-)
 create mode 100644 src/mesh/yboundary_regions.cxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 359e33e1c8..c08b651317 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -220,6 +220,7 @@ set(BOUT_SOURCES
     ./include/bout/vector2d.hxx
     ./include/bout/vector3d.hxx
     ./include/bout/where.hxx
+    ./include/bout/yboundary_regions.hxx
     ./src/bout++-time.hxx
     ./src/bout++.cxx
     ./src/field/field.cxx
@@ -323,6 +324,7 @@ set(BOUT_SOURCES
     ./src/mesh/petsc_operators.cxx
     ./src/mesh/surfaceiter.cxx
     ./src/mesh/tokamak_coordinates.cxx
+    ./src/mesh/yboundary_regions.cxx
     ./src/physics/gyro_average.cxx
     ./src/physics/physicsmodel.cxx
     ./src/physics/smoothing.cxx
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index ba44ea2e43..afb1266cde 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -2,19 +2,17 @@
 
 #include "bout/boundary_region_iter.hxx"
 
-#include "bout/boundary_iterator.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field_data.hxx"
-#include "bout/globals.hxx"
 #include "bout/mask.hxx"
-#include "bout/options.hxx"
-#include "bout/parallel_boundary_region.hxx"
 #include "bout/region.hxx"
 
 #include <concepts>
 #include <memory>
 #include <vector>
 
+class Options;
+
 namespace bout {
 namespace boundary {
 /// Helper concept for functions to pass into `YBoundary::iter`
@@ -36,6 +34,8 @@ concept YBoundaryPoint = std::derived_from<T, BoundaryRegionIterBase<T>>;
 
 class YBoundary {
 public:
+  YBoundary(YBndryType type, Options* options_ptr, const Mesh& mesh);
+
   /// Iterate over the boundary.
   /// This function takes a lamda / templated function, that applies the boundary on the given point.
   /// The function must take a `const YBoundaryPoint auto& point` as its only argument.
@@ -56,86 +56,25 @@ public:
     }
   }
 
-  YBoundary(YBndryType type, Options* options_ptr, const Mesh& mesh) {
-    bool lower_y = true;
-    bool upper_y = true;
-    bool outer_x = true;
-    bool inner_x = false;
-    if (options_ptr != nullptr) {
-      auto& options = *options_ptr;
-      if (!mesh.isFci()) {
-        lower_y =
-            options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
-        upper_y =
-            options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(upper_y);
-      } else {
-        outer_x =
-            options["outer_x"].doc("Boundary on outer x?").withDefault<bool>(outer_x);
-        inner_x =
-            options["inner_x"].doc("Boundary on inner x?").withDefault<bool>(inner_x);
-      }
-    }
-    switch (type) {
-    case YBndryType::sheath:
-      break;
-    case YBndryType::not_sheath:
-      lower_y = !lower_y;
-      upper_y = !upper_y;
-      outer_x = !outer_x;
-      inner_x = !inner_x;
-      break;
-    case YBndryType::all:
-      lower_y = true;
-      upper_y = true;
-      outer_x = true;
-      inner_x = true;
-    }
+  /// Return true if this boundary in the lower direction contains point \p ind
+  bool contains_low(const Ind3D& ind) const { return _contains_low[ind]; }
+  /// Return true if this boundary in the upper direction contains point \p ind
+  bool contains_high(const Ind3D& ind) const { return _contains_high[ind]; }
 
-    if (mesh.isFci()) {
-      if (outer_x) {
-        for (auto& bndry : mesh.getBoundariesPar(BoundaryParType::xout)) {
-          boundary_regions_par.push_back(bndry);
-        }
-      }
-      if (inner_x) {
-        for (auto& bndry : mesh.getBoundariesPar(BoundaryParType::xin)) {
-          boundary_regions_par.push_back(bndry);
-        }
-      }
-    } else {
-      for (auto& bndry : mesh.getBoundaries()) {
-        if ((lower_y && bndry->location == BndryLoc::ydown)
-            or (upper_y && bndry->location == BndryLoc::yup)) {
-          boundary_regions.push_back(
-              std::dynamic_pointer_cast<bout::boundary::BoundaryRegionY>(bndry));
-        }
-      }
-    }
-    // Cache boundary regions
-    _contains.emplace_back(&mesh, false);
-    _contains.emplace_back(&mesh, false);
-    iter([&](const YBoundaryPoint auto& point) {
-      if (point.dir() == 1) {
-        _contains[1][point.ind()] = true;
-      } else if (point.dir() == -1) {
-        _contains[0][point.ind()] = true;
-      }
-    });
-  }
-
-  bool contains_low(Ind3D ind) const { return _contains[0][ind]; }
-  bool contains_high(Ind3D ind) const { return _contains[1][ind]; }
+  /// Return true if this boundary in direction \p dir contains point \p ind
   template <int dir>
-  bool contains(Ind3D ind) const {
+  bool contains(const Ind3D& ind) const {
     static_assert(dir == 1 || dir == -1);
     if constexpr (dir == 1) {
-      return _contains[1][ind];
+      return _contains_high[ind];
     }
     if constexpr (dir == -1) {
-      return _contains[0][ind];
+      return _contains_low[ind];
     }
   }
-  bool contains(int dir, Ind3D ind) const {
+
+  /// Return true if this boundary in direction \p dir contains point \p ind
+  bool contains(int dir, const Ind3D& ind) const {
     if (dir == 1) {
       return contains<+1>(ind);
     }
@@ -149,7 +88,8 @@ private:
   std::vector<std::shared_ptr<BoundaryRegionFCI>> boundary_regions_par;
   std::vector<std::shared_ptr<BoundaryRegionY>> boundary_regions;
 
-  std::vector<BoutMask> _contains;
+  BoutMask _contains_low;
+  BoutMask _contains_high;
 };
 
 } // namespace boundary
diff --git a/src/mesh/yboundary_regions.cxx b/src/mesh/yboundary_regions.cxx
new file mode 100644
index 0000000000..2e1f9ab734
--- /dev/null
+++ b/src/mesh/yboundary_regions.cxx
@@ -0,0 +1,72 @@
+#include "bout/yboundary_regions.hxx"
+
+#include "bout/boundary_region_iter.hxx"
+#include "bout/field_data.hxx"
+#include "bout/options.hxx"
+#include "bout/parallel_boundary_region.hxx"
+
+#include <memory>
+
+namespace bout::boundary {
+YBoundary::YBoundary(YBndryType type, Options* options_ptr, const Mesh& mesh)
+    : _contains_low(&mesh, false), _contains_high(&mesh, false) {
+  bool lower_y = true;
+  bool upper_y = true;
+  bool outer_x = true;
+  bool inner_x = false;
+  if (options_ptr != nullptr) {
+    auto& options = *options_ptr;
+    if (!mesh.isFci()) {
+      lower_y = options["lower_y"].doc("Boundary on lower y?").withDefault<bool>(lower_y);
+      upper_y = options["upper_y"].doc("Boundary on upper y?").withDefault<bool>(upper_y);
+    } else {
+      outer_x = options["outer_x"].doc("Boundary on outer x?").withDefault<bool>(outer_x);
+      inner_x = options["inner_x"].doc("Boundary on inner x?").withDefault<bool>(inner_x);
+    }
+  }
+  switch (type) {
+  case YBndryType::sheath:
+    break;
+  case YBndryType::not_sheath:
+    lower_y = !lower_y;
+    upper_y = !upper_y;
+    outer_x = !outer_x;
+    inner_x = !inner_x;
+    break;
+  case YBndryType::all:
+    lower_y = true;
+    upper_y = true;
+    outer_x = true;
+    inner_x = true;
+  }
+
+  if (mesh.isFci()) {
+    if (outer_x) {
+      for (auto& bndry : mesh.getBoundariesPar(BoundaryParType::xout)) {
+        boundary_regions_par.push_back(bndry);
+      }
+    }
+    if (inner_x) {
+      for (auto& bndry : mesh.getBoundariesPar(BoundaryParType::xin)) {
+        boundary_regions_par.push_back(bndry);
+      }
+    }
+  } else {
+    for (auto& bndry : mesh.getBoundaries()) {
+      if ((lower_y && bndry->location == BndryLoc::ydown)
+          or (upper_y && bndry->location == BndryLoc::yup)) {
+        boundary_regions.push_back(
+            std::dynamic_pointer_cast<bout::boundary::BoundaryRegionY>(bndry));
+      }
+    }
+  }
+  // Cache boundary regions
+  iter([&](const YBoundaryPoint auto& point) {
+    if (point.dir() == 1) {
+      _contains_high[point.ind()] = true;
+    } else if (point.dir() == -1) {
+      _contains_low[point.ind()] = true;
+    }
+  });
+}
+} // namespace bout::boundary

From b3c5ab18e3a641ccdab8c1875d754fe6bb843ec9 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 19 Aug 2026 16:57:31 +0100
Subject: [PATCH 1760/1827] Add helper function for CRTP in boundary region
 iterator

---
 include/bout/boundary_region_iter.hxx | 80 +++++++++++----------------
 1 file changed, 31 insertions(+), 49 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 16f892b299..45afecda4a 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -23,24 +23,26 @@
 namespace bout {
 namespace boundary {
 
-template <typename impl>
+template <typename Impl>
 class BoundaryRegionIterBase {
   BoundaryRegionIterBase() = default;
-  /// get the index at the last point in domain
+
+  /// Get a reference to the derived/implementation class
+  const Impl& impl() const { return *static_cast<const Impl*>(this); }
+
 public:
-  Ind3D ind() const { return static_cast<const impl*>(this)->_ind(); }
+  /// Get the index at the last point in domain
+  Ind3D ind() const { return impl()._ind(); }
   /// get the length from the point in the domain to the boundary in index
   /// space. It is in the range [0, 1]
-  BoutReal length(CELL_LOC loc) const {
-    return static_cast<const impl*>(this)->_length(loc);
-  }
+  BoutReal length(CELL_LOC loc) const { return impl()._length(loc); }
   /// Lower bound of how many points are between the first point in the domain
   /// and the boundary in the other direction.
-  signed char valid() const { return static_cast<const impl*>(this)->_valid(); }
+  signed char valid() const { return impl()._valid(); }
   /// Get the width of the boundary at the current point
-  int boundary_width() const { return static_cast<const impl*>(this)->_boundary_width(); }
+  int boundary_width() const { return impl()._boundary_width(); }
   /// Is this the lower boundary?
-  bool is_lower() const { return static_cast<const impl*>(this)->_is_lower(); }
+  bool is_lower() const { return impl()._is_lower(); }
 
   /*
    *         FIELD3D ACCESSORS
@@ -52,38 +54,28 @@ public:
   /// off = 1 is the last point in the domain
   /// off = 2 is the second to last point in the domain
   template <bool check = true>
-  BoutReal& getAt(Field3D& f, int off) const {
-    return static_cast<const impl*>(this)->template _getAt<check>(f, off);
+  BoutReal& getAt(Field3D& f, int offset) const {
+    return impl().template _getAt<check>(f, offset);
   }
   /// get the value at a given offset `off` of a field `f`.
   template <bool check = true>
-  BoutReal& getAt(const Field3D& f, int off) const {
-    return static_cast<const impl*>(this)->template _getAt<check>(f, off);
+  BoutReal getAt(const Field3D& f, int offset) const {
+    return impl().template _getAt<check>(f, offset);
   }
 
   /// Get the first point in the boundary
-  const BoutReal& next(const Field3D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 0);
-  }
+  const BoutReal& next(const Field3D& f) const { return impl()._getAt(f, 0); }
   /// Get the first point in the boundary
-  BoutReal& next(Field3D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 0);
-  }
+  BoutReal& next(Field3D& f) const { return impl()._getAt(f, 0); }
   /// Get the last point in the domain
-  const BoutReal& current(const Field3D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 1);
-  }
+  const BoutReal& current(const Field3D& f) const { return impl()._getAt(f, 1); }
   /// Get the last point in the domain
-  BoutReal& current(Field3D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 1);
-  }
+  BoutReal& current(Field3D& f) const { return impl()._getAt(f, 1); }
   /// Get the second to last point in the domain - this may not be valid and thus throw
-  const BoutReal& prev(const Field3D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 2);
-  }
+  const BoutReal& prev(const Field3D& f) const { return impl()._getAt(f, 2); }
   /// Get the offset from the last point in the domain
   /// For FA this is always ±1, for FCI this can be up to ±MYG, excluding 0
-  int offset() const { return static_cast<const impl*>(this)->_offset(); }
+  int offset() const { return impl()._offset(); }
   /*
    *         FIELD2D ACCESSORS
    */
@@ -94,35 +86,25 @@ public:
   /// off = 1 is the last point in the domain
   /// off = 2 is the second to last point in the domain
   template <bool check = true>
-  BoutReal& getAt(Field2D& f, int off) const {
-    return static_cast<const impl*>(this)->template _getAt<check>(f, off);
+  BoutReal& getAt(Field2D& f, int offset) const {
+    return impl().template _getAt<check>(f, offset);
   }
   /// get the value at a given offset `off` of a field `f`.
   template <bool check = true>
-  BoutReal& getAt(const Field2D& f, int off) const {
-    return static_cast<const impl*>(this)->template _getAt<check>(f, off);
+  BoutReal getAt(const Field2D& f, int offset) const {
+    return impl().template _getAt<check>(f, offset);
   }
 
   /// Get the first point in the boundary
-  const BoutReal& next(const Field2D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 0);
-  }
+  const BoutReal& next(const Field2D& f) const { return impl()._getAt(f, 0); }
   /// Get the first point in the boundary
-  BoutReal& next(Field2D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 0);
-  }
+  BoutReal& next(Field2D& f) const { return impl()._getAt(f, 0); }
   /// Get the last point in the domain
-  const BoutReal& current(const Field2D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 1);
-  }
+  const BoutReal& current(const Field2D& f) const { return impl()._getAt(f, 1); }
   /// Get the last point in the domain
-  BoutReal& current(Field2D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 1);
-  }
+  BoutReal& current(Field2D& f) const { return impl()._getAt(f, 1); }
   /// Get the second to last point in the domain - this may not be valid and thus throw
-  const BoutReal& prev(const Field2D& f) const {
-    return static_cast<const impl*>(this)->_getAt(f, 2);
-  }
+  const BoutReal& prev(const Field2D& f) const { return impl()._getAt(f, 2); }
 
   /*
    *         FUNCTIONS ACCESSORS
@@ -353,7 +335,7 @@ public:
 
 private:
   BoutReal small_value = 1e-4;
-  friend impl;
+  friend Impl;
 };
 
 namespace {

From 23d95be3f61e7e08837cd1222e44051cffe1f7b5 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 19 Aug 2026 16:58:59 +0100
Subject: [PATCH 1761/1827] Use concept to avoid passing `std::function`

---
 include/bout/boundary_region_iter.hxx | 68 ++++++++++++++-------------
 1 file changed, 36 insertions(+), 32 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 45afecda4a..dc6c3f6dd1 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -2,27 +2,39 @@
 
 #include <algorithm>
 #include <cmath>
+#include <concepts>
 #include <cstddef>
-#include <functional>
 #include <memory>
 #include <string>
 #include <type_traits>
 #include <vector>
 
-#include "bout/assert.hxx"
-#include "bout/boundary_common.hxx"
-#include "bout/bout_types.hxx"
-#include "bout/field_data.hxx"
-#include "bout/utils.hxx"
+#include <bout/assert.hxx>
+#include <bout/boundary_common.hxx>
+#include <bout/bout_types.hxx>
+#include <bout/boutexception.hxx>
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
+#include <bout/field_data.hxx>
 #include <bout/parallel_boundary_region.hxx>
 #include <bout/region.hxx>
 #include <bout/sys/parallel_stencils.hxx>
+#include <bout/utils.hxx>
 
 namespace bout {
 namespace boundary {
 
+/// Helper concept for `BoundaryRegionIterBase::getAt` function accessor overloads
+///
+/// This is a callable that takes two arguments:
+/// - `int yoffset`, the parallel slice offset
+/// - `Ind3D ind`, the index of the boundary point
+///
+/// and returns a `BoutReal`
+template <class F>
+concept function_accessor =
+    std::regular_invocable<F, int, Ind3D>
+    and std::is_same_v<std::invoke_result_t<F, int, Ind3D>, BoutReal>;
 template <typename Impl>
 class BoundaryRegionIterBase {
   BoundaryRegionIterBase() = default;
@@ -116,21 +128,20 @@ public:
   /// off = 1 is the last point in the domain
   /// off = 2 is the second to last point in the domain
   template <bool check = true>
-  BoutReal getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
-                 int off) const {
-    return static_cast<const impl*>(this)->template _getAt<check>(func, off);
+  BoutReal getAt(const function_accessor auto& func, int offset) const {
+    return impl().template _getAt<check>(func, offset);
   }
   /// Get the first point in the boundary
-  BoutReal next(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
-    return static_cast<const impl*>(this)->_getAt(func, 0);
+  BoutReal next(const function_accessor auto& func) const {
+    return impl()._getAt(func, 0);
   }
   /// Get the last point in the domain
-  BoutReal current(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
-    return static_cast<const impl*>(this)->_getAt(func, 1);
+  BoutReal current(const function_accessor auto& func) const {
+    return impl()._getAt(func, 1);
   }
   /// Get the second to last point in the domain - this may not be valid and thus throw
-  BoutReal prev(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
-    return static_cast<const impl*>(this)->_getAt(func, 2);
+  BoutReal prev(const function_accessor auto& func) const {
+    return impl()._getAt(func, 2);
   }
 
   /*
@@ -148,15 +159,13 @@ public:
     return current(f) * (1 + length(f.getLocation())) - prev(f) * length(f.getLocation());
   }
   /// Extrapolate a given function to the boundary
-  BoutReal
-  extrapolate_bounday_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
-                         [[maybe_unused]] CELL_LOC loc = CELL_CENTRE) const {
+  BoutReal extrapolate_bounday_o1(const function_accessor auto& func,
+                                  [[maybe_unused]] CELL_LOC loc = CELL_CENTRE) const {
     return current(func);
   }
   /// Extrapolate a given function to the boundary
-  BoutReal
-  extrapolate_boundary_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
-                          CELL_LOC loc = CELL_CENTRE) const {
+  BoutReal extrapolate_boundary_o2(const function_accessor auto& func,
+                                   CELL_LOC loc = CELL_CENTRE) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
       return extrapolate_boundary_o1(func);
@@ -169,9 +178,8 @@ public:
     return current(f) * (1 - length(f.getLocation())) + next(f) * length(f.getLocation());
   }
   /// Interpolate a field to the boundary, using the boundary values
-  BoutReal
-  interpolate_boundary_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& func,
-                          CELL_LOC loc = CELL_CENTRE) const {
+  BoutReal interpolate_boundary_o2(const function_accessor auto& func,
+                                   CELL_LOC loc = CELL_CENTRE) const {
     return current(func) * (1 - length(loc)) + next(func) * length(loc);
   }
   /// Extrapolate to the first boundary value freely
@@ -186,13 +194,11 @@ public:
   }
 
   /// Extrapolate to the first boundary value freely
-  BoutReal
-  extrapolate_next_o1(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+  BoutReal extrapolate_next_o1(const function_accessor auto& func) const {
     return current(func);
   }
   /// Extrapolate to the first boundary value freely
-  BoutReal
-  extrapolate_next_o2(const std::function<BoutReal(int yoffset, Ind3D ind)>& func) const {
+  BoutReal extrapolate_next_o2(const function_accessor auto& func) const {
     ASSERT3(valid() >= 0);
     if (valid() < 1) {
       return extrapolate_next_o1(func);
@@ -485,8 +491,7 @@ public:
     return f.ynext(_off)[_ind().yp(_off)];
   }
   template <bool check = true>
-  BoutReal _getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
-                  int off) const {
+  BoutReal _getAt(const function_accessor auto& f, int off) const {
     if constexpr (check) {
       ASSERT3(valid() > -off - 2);
     }
@@ -612,8 +617,7 @@ public:
     }
   }
   template <bool check = true>
-  BoutReal _getAt(const std::function<BoutReal(int yoffset, Ind3D ind)>& f,
-                  int off) const {
+  BoutReal _getAt(const function_accessor auto& f, int off) const {
     if constexpr (check) {
       ASSERT3(_valid() > -off - 2);
     }

From 6c8adabb674f360fb71d4b0b2657639157cce15c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 19 Aug 2026 17:03:31 +0100
Subject: [PATCH 1762/1827] Try to expand the documentation for the boundary
 regions classes

---
 include/bout/boundary_region_iter.hxx | 65 ++++++++++++++++++++-------
 1 file changed, 50 insertions(+), 15 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index dc6c3f6dd1..ebf8bed5c4 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -35,6 +35,11 @@ template <class F>
 concept function_accessor =
     std::regular_invocable<F, int, Ind3D>
     and std::is_same_v<std::invoke_result_t<F, int, Ind3D>, BoutReal>;
+
+/// Common base class for boundary region iterators
+///
+/// This uses CRTP: boundary region iterators should inherit from this,
+/// templated on themselves, and they must implement all methods that call `impl().`
 template <typename Impl>
 class BoundaryRegionIterBase {
   BoundaryRegionIterBase() = default;
@@ -60,11 +65,17 @@ public:
    *         FIELD3D ACCESSORS
    */
 
-  /// get the value at a given offset `off` of a field `f`.
-  /// off = -1 is the second point in the boundary
-  /// off = 0 is the first point in the boundary
-  /// off = 1 is the last point in the domain
-  /// off = 2 is the second to last point in the domain
+  /// Get the value at a given \p offset of a field \p f.
+  ///
+  /// `offset = -1` is the second point in the boundary
+  /// `offset = 0` is the first point in the boundary
+  /// `offset = 1` is the last point in the domain
+  /// `offset = 2` is the second to last point in the domain
+  ///
+  /// |---|---|---|--> interior points
+  /// -1  0 ^ 1   2
+  ///       |
+  ///    boundary
   template <bool check = true>
   BoutReal& getAt(Field3D& f, int offset) const {
     return impl().template _getAt<check>(f, offset);
@@ -92,11 +103,17 @@ public:
    *         FIELD2D ACCESSORS
    */
 
-  /// get the value at a given offset `off` of a field `f`.
-  /// off = -1 is the second point in the boundary
-  /// off = 0 is the first point in the boundary
-  /// off = 1 is the last point in the domain
-  /// off = 2 is the second to last point in the domain
+  /// Get the value at a given \p offset of a field \p f.
+  ///
+  /// `offset = -1` is the second point in the boundary
+  /// `offset = 0` is the first point in the boundary
+  /// `offset = 1` is the last point in the domain
+  /// `offset = 2` is the second to last point in the domain
+  ///
+  /// |---|---|---|--> interior points
+  /// -1  0 ^ 1   2
+  ///       |
+  ///    boundary
   template <bool check = true>
   BoutReal& getAt(Field2D& f, int offset) const {
     return impl().template _getAt<check>(f, offset);
@@ -122,11 +139,12 @@ public:
    *         FUNCTIONS ACCESSORS
    */
 
-  /// get the value at a given offset `off` of a field `f`.
-  /// off = -1 is the second point in the boundary
-  /// off = 0 is the first point in the boundary
-  /// off = 1 is the last point in the domain
-  /// off = 2 is the second to last point in the domain
+  /// Apply the function \p func at a given \p offset
+  ///
+  /// |---|---|---|--> interior points
+  /// -1  0 ^ 1   2
+  ///       |
+  ///    boundary
   template <bool check = true>
   BoutReal getAt(const function_accessor auto& func, int offset) const {
     return impl().template _getAt<check>(func, offset);
@@ -383,6 +401,11 @@ inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, BoundaryFreeExtrapolati
 }
 } // namespace
 
+/// An FCI-aware boundary region
+///
+/// Uses `BoundaryRegionIterFCI` as its iterator.
+///
+/// This can't use the legacy iteration methods (`first()`, `next()`, and so on)
 class BoundaryRegionFCI : public BoundaryRegionBase {
 public:
   BoundaryRegionFCI(const std::string& name, const BndryLoc& loc, int dir, Mesh* mesh)
@@ -436,6 +459,7 @@ private:
   }
 };
 
+/// Iterator over a `BoundaryRegionFCI`
 class BoundaryRegionIterFCI : public BoundaryRegionIterBase<BoundaryRegionIterFCI> {
 private:
   // TODO(dave) make non-const?
@@ -527,6 +551,11 @@ public:
   BoundaryRegionIterFCI& operator*() { return *this; }
 };
 
+/// Boundary region for field-aligned grids
+///
+/// FCI grids should use `BoundaryRegionFCI`
+///
+/// Uses `BoundaryRegionIterXY` as its iterator
 template <bool isXtemp>
 class BoundaryRegionXY : public BoundaryRegionBase {
 public:
@@ -557,6 +586,7 @@ private:
   signed char valid;
 };
 
+/// Iterator over a `BoundaryRegionXY`
 template <bool isX>
 class BoundaryRegionIterXY : public BoundaryRegionIterBase<BoundaryRegionIterXY<isX>> {
 private:
@@ -664,9 +694,14 @@ public:
   // No-op for compatibility
   BoundaryRegionIterXY& operator*() { return *this; }
 };
+
+/// Alias for boundary regions over X specifically
 using BoundaryRegionX = BoundaryRegionXY<true>;
+/// Alias for boundary regions over Y specifically
 using BoundaryRegionY = BoundaryRegionXY<false>;
+/// Alias for boundary region iterators over X specifically
 using BoundaryRegionIterX = BoundaryRegionIterXY<true>;
+/// Alias for boundary region iterators over Y specifically
 using BoundaryRegionIterY = BoundaryRegionIterXY<false>;
 
 inline std::shared_ptr<BoundaryRegionX>

From ca6dd1f0b989a2ac7067562d38f2182257777536 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 19 Aug 2026 17:07:17 +0100
Subject: [PATCH 1763/1827] Remove raw pointer from new boundary regions

---
 include/bout/boundary_region.hxx      | 14 +++++++++-----
 include/bout/boundary_region_iter.hxx |  8 ++++----
 src/mesh/boundary_region.cxx          |  4 ++--
 3 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/include/bout/boundary_region.hxx b/include/bout/boundary_region.hxx
index 739d06f11f..106d52f21c 100644
--- a/include/bout/boundary_region.hxx
+++ b/include/bout/boundary_region.hxx
@@ -1,13 +1,12 @@
-
-class BoundaryRegion;
-
 #ifndef BOUT_BNDRY_REGION_H
 #define BOUT_BNDRY_REGION_H
 
 #include <cstdint>
+#include <memory>
 #include <string>
 #include <utility>
 
+class BoundaryRegion;
 class Mesh;
 namespace bout {
 namespace globals {
@@ -42,16 +41,21 @@ constexpr BndryLoc BNDRY_INVALID = BndryLoc::invalid;
 /// Physical type of y boundary
 enum class YBndryType : std::int8_t { sheath, not_sheath, all };
 
+/// Base class for boundary regions
 class BoundaryRegionBase {
 public:
   BoundaryRegionBase() = delete;
+  BoundaryRegionBase(const BoundaryRegionBase&) = delete;
+  BoundaryRegionBase(BoundaryRegionBase&&) = delete;
+  BoundaryRegionBase& operator=(const BoundaryRegionBase&) = delete;
+  BoundaryRegionBase& operator=(BoundaryRegionBase&&) = delete;
   BoundaryRegionBase(std::string name, Mesh* passmesh = nullptr)
       : localmesh(passmesh ? passmesh : bout::globals::mesh), label(std::move(name)) {}
   BoundaryRegionBase(std::string name, BndryLoc loc, Mesh* passmesh = nullptr)
       : localmesh(passmesh ? passmesh : bout::globals::mesh), label(std::move(name)),
         location(loc) {}
 
-  virtual ~BoundaryRegionBase();
+  virtual ~BoundaryRegionBase() = default;
 
   virtual BoundaryRegion* getLegacyPointer();
   Mesh* localmesh; ///< Mesh does this boundary region belongs to
@@ -70,7 +74,7 @@ public:
   virtual bool
   isDone() = 0; ///< Returns true if outside domain. Can use this with nested nextX, nextY
 
-  BoundaryRegion* legacy{nullptr};
+  std::unique_ptr<BoundaryRegion> legacy{nullptr};
 };
 
 /// Describes a region of the boundary, and a means of iterating over it
diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index ebf8bed5c4..a0036d3a13 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -710,7 +710,7 @@ NewBoundaryRegionXIn(const std::string& name, int ymin, int ymax, Mesh* mesh) {
       name, -1, mesh,
       Region<Ind3D>(mesh->xstart, mesh->xstart, ymin, ymax, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
-  pointer->legacy = new ::BoundaryRegionXIn(name, ymin, ymax, mesh);
+  pointer->legacy = std::make_unique<::BoundaryRegionXIn>(name, ymin, ymax, mesh);
   return pointer;
 }
 
@@ -720,7 +720,7 @@ NewBoundaryRegionXOut(const std::string& name, int ymin, int ymax, Mesh* mesh) {
       name, 1, mesh,
       Region<Ind3D>(mesh->xend, mesh->xend, ymin, ymax, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
-  pointer->legacy = new ::BoundaryRegionXOut(name, ymin, ymax, mesh);
+  pointer->legacy = std::make_unique<::BoundaryRegionXOut>(name, ymin, ymax, mesh);
   return pointer;
 }
 
@@ -730,7 +730,7 @@ NewBoundaryRegionYUp(const std::string& name, int xmin, int xmax, Mesh* mesh) {
       name, 1, mesh,
       Region<Ind3D>(xmin, xmax, mesh->yend, mesh->yend, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
-  pointer->legacy = new ::BoundaryRegionYUp(name, xmin, xmax, mesh);
+  pointer->legacy = std::make_unique<::BoundaryRegionYUp>(name, xmin, xmax, mesh);
   return pointer;
 }
 
@@ -740,7 +740,7 @@ NewBoundaryRegionYDown(const std::string& name, int xmin, int xmax, Mesh* mesh)
       name, -1, mesh,
       Region<Ind3D>(xmin, xmax, mesh->ystart, mesh->ystart, mesh->zstart, mesh->zend,
                     mesh->LocalNy, mesh->LocalNz, mesh->maxregionblocksize));
-  pointer->legacy = new ::BoundaryRegionYDown(name, xmin, xmax, mesh);
+  pointer->legacy = std::make_unique<::BoundaryRegionYDown>(name, xmin, xmax, mesh);
   return pointer;
 }
 
diff --git a/src/mesh/boundary_region.cxx b/src/mesh/boundary_region.cxx
index 2dc64fc88f..e7c5151f5f 100644
--- a/src/mesh/boundary_region.cxx
+++ b/src/mesh/boundary_region.cxx
@@ -16,9 +16,9 @@ BoundaryRegion* BoundaryRegionBase::getLegacyPointer() {
   ASSERT3(legacy->location == location);
   ASSERT3(legacy->label == label);
   ASSERT3(legacy->localmesh == localmesh);
-  return legacy;
+  return legacy.get();
 }
-BoundaryRegionBase::~BoundaryRegionBase() { delete legacy; };
+
 BoundaryRegionXIn::BoundaryRegionXIn(std::string name, int ymin, int ymax, Mesh* passmesh)
     : BoundaryRegion(std::move(name), -1, 0, passmesh), ys(ymin), ye(ymax) {
   location = BNDRY_XIN;

From 999c444d6d8f8f4e06b0c972725041c275f3ffb0 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 19 Aug 2026 17:09:48 +0100
Subject: [PATCH 1764/1827] Fix some missing methods on the derived boundary
 iterators

---
 include/bout/boundary_region_iter.hxx | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index a0036d3a13..246badd1e0 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -11,6 +11,7 @@
 
 #include <bout/assert.hxx>
 #include <bout/boundary_common.hxx>
+#include <bout/boundary_region.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/field2d.hxx>
@@ -478,6 +479,8 @@ public:
   BoutReal s_z() const { return region->bndry_points[pos].intersection.s_z; };
   Mesh* localmesh() const { return region->localmesh; };
   int dir() const { return region->_dir; }
+  bool _is_lower() const { return region->_dir < 0; }
+
   template <bool check = true>
   BoutReal& _getAt(Field3D& f, int off) const {
     ASSERT3(f.hasParallelSlices());
@@ -572,7 +575,7 @@ public:
       location = dir == 1 ? BNDRY_YUP : BNDRY_YDOWN;
     }
   }
-  int dir() { return _dir; }
+  int dir() const { return _dir; }
   // legacy interface
   void first() override { throw BoutException("Legacy interface is not suppored"); }
   void next() override { throw BoutException("Legacy interface is not suppored"); }
@@ -598,6 +601,8 @@ public:
   BoundaryRegionIterXY(const BoundaryRegionXY<isX>* reg, bool isstart)
       : region(reg), pos(isstart ? 0 : reg->rgn.size()) {}
   int dir() const { return region->_dir; }
+  Ind3D ind() const { return _ind(); }
+
   template <bool check = true>
   BoutReal& _getAt(Field3D& f, int off) const {
     if constexpr (check) {

From 3d1f39b9d439a4a7b1525564b4661eadebbd14fe Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 19 Aug 2026 18:39:42 +0100
Subject: [PATCH 1765/1827] Move boundary condition kernels out of
 `BoundaryRegionIterBase`

---
 include/bout/boundary_region_iter.hxx      | 451 ++++++++++++---------
 include/bout/parallel_boundary_op.hxx      |  36 +-
 src/field/field3d.cxx                      |  12 +-
 tests/unit/include/bout/test_yboundary.cxx |  73 ++--
 4 files changed, 320 insertions(+), 252 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 246badd1e0..6287df2d24 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -37,10 +37,30 @@ concept function_accessor =
     std::regular_invocable<F, int, Ind3D>
     and std::is_same_v<std::invoke_result_t<F, int, Ind3D>, BoutReal>;
 
+/// Interface for boundary iterators
+template <class Iter>
+concept boundary_iterator = requires(Iter point, Field3D f) {
+  point.getAt(f, int{});
+  point.next(f);
+  point.current(f);
+  point.prev(f);
+
+  point.ind();
+  point.length(CELL_LOC{});
+  point.valid();
+  point.boundary_width();
+  point.is_lower();
+  point.offset();
+
+  point.smallValue();
+};
+
 /// Common base class for boundary region iterators
 ///
 /// This uses CRTP: boundary region iterators should inherit from this,
-/// templated on themselves, and they must implement all methods that call `impl().`
+/// templated on themselves, and they must implement all methods in
+/// `boundary_iterator`, (that is, those methods that call `impl().` in this
+/// class)
 template <typename Impl>
 class BoundaryRegionIterBase {
   BoundaryRegionIterBase() = default;
@@ -61,6 +81,9 @@ public:
   int boundary_width() const { return impl()._boundary_width(); }
   /// Is this the lower boundary?
   bool is_lower() const { return impl()._is_lower(); }
+  /// Get the offset from the last point in the domain
+  /// For FA this is always ±1, for FCI this can be up to ±MYG, excluding 0
+  int offset() const { return impl()._offset(); }
 
   /*
    *         FIELD3D ACCESSORS
@@ -97,9 +120,7 @@ public:
   BoutReal& current(Field3D& f) const { return impl()._getAt(f, 1); }
   /// Get the second to last point in the domain - this may not be valid and thus throw
   const BoutReal& prev(const Field3D& f) const { return impl()._getAt(f, 2); }
-  /// Get the offset from the last point in the domain
-  /// For FA this is always ±1, for FCI this can be up to ±MYG, excluding 0
-  int offset() const { return impl()._offset(); }
+
   /*
    *         FIELD2D ACCESSORS
    */
@@ -163,207 +184,20 @@ public:
     return impl()._getAt(func, 2);
   }
 
-  /*
-   *     INTERPOLATION and EXTRAPOLATION
-   */
-
-  // extrapolate a given field to the boundary
-  BoutReal extrapolate_boundary_o1(const Field3D& f) const { return current(f); }
-  // extrapolate a given field to the boundary
-  BoutReal extrapolate_boundary_o2(const Field3D& f) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_boundary_o1(f);
-    }
-    return current(f) * (1 + length(f.getLocation())) - prev(f) * length(f.getLocation());
-  }
-  /// Extrapolate a given function to the boundary
-  BoutReal extrapolate_bounday_o1(const function_accessor auto& func,
-                                  [[maybe_unused]] CELL_LOC loc = CELL_CENTRE) const {
-    return current(func);
-  }
-  /// Extrapolate a given function to the boundary
-  BoutReal extrapolate_boundary_o2(const function_accessor auto& func,
-                                   CELL_LOC loc = CELL_CENTRE) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_boundary_o1(func);
-    }
-    return current(func) * (1 + length(loc)) - prev(func) * length(loc);
-  }
-
-  /// Interpolate a field to the boundary, using the boundary values
-  BoutReal interpolate_boundary_o2(const Field3D& f) const {
-    return current(f) * (1 - length(f.getLocation())) + next(f) * length(f.getLocation());
-  }
-  /// Interpolate a field to the boundary, using the boundary values
-  BoutReal interpolate_boundary_o2(const function_accessor auto& func,
-                                   CELL_LOC loc = CELL_CENTRE) const {
-    return current(func) * (1 - length(loc)) + next(func) * length(loc);
-  }
-  /// Extrapolate to the first boundary value freely
-  BoutReal extrapolate_next_o1(const Field3D& f) const { return current(f); }
-  /// Extrapolate to the first boundary value freely
-  BoutReal extrapolate_next_o2(const Field3D& f) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_next_o1(f);
-    }
-    return current(f) * 2 - prev(f);
-  }
-
-  /// Extrapolate to the first boundary value freely
-  BoutReal extrapolate_next_o1(const function_accessor auto& func) const {
-    return current(func);
-  }
-  /// Extrapolate to the first boundary value freely
-  BoutReal extrapolate_next_o2(const function_accessor auto& func) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_next_o1(func);
-    }
-    return current(func) * 2 - prev(func);
-  }
-
-  /// extrapolate the gradient into the boundary
-  BoutReal extrapolate_grad_o1([[maybe_unused]] const Field3D& f) const { return 0; }
-  /// extrapolate the gradient into the boundary
-  BoutReal extrapolate_grad_o2(const Field3D& f) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return extrapolate_grad_o1(f);
-    }
-    return current(f) - next(f);
-  }
-
-  BoutReal extrapolate_boundary_free(const Field3D& f,
-                                     BoundaryFreeExtrapolation mode) const {
-    BoutReal fac = BoutNaN;
-    if (valid() > 0) {
-      fac = limitFreeScale(prev(f), current(f), mode);
-    } else {
-      fac = mode == BoundaryFreeExtrapolation::linear ? 0 : 1;
-    }
-    auto val = current(f);
-    BoutReal next = mode == BoundaryFreeExtrapolation::linear ? val + fac : val * fac;
-    return val * length(f.getLocation()) + next * (1 - length(f.getLocation()));
-  }
-
-  /*
-   *     APPLY BOUNDARY CONDITIONS
-   */
-
-  /// Apply a dirichlet boundary condition
-  void dirichlet_o1(Field3D& f, BoutReal value) const {
-    for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, -i) = value;
-    }
-  }
-
-  /// Apply a dirichlet boundary condition
-  void dirichlet_o2(Field3D& f, BoutReal value) const {
-    if (length(f.getLocation()) < small_value) {
-      return dirichlet_o1(f, value);
-    }
-    for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, -i) = parallel_stencil::dirichlet_o2(
-          i + 1, current(f), i + 1 - length(f.getLocation()), value);
-    }
-  }
-
-  /// Apply a dirichlet boundary condition
-  void dirichlet_o3(Field3D& f, BoutReal value) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return dirichlet_o2(f, value);
-    }
-    if (length(f.getLocation()) < small_value) {
-      for (int i = 0; i < boundary_width(); ++i) {
-        getAt(f, -i) = parallel_stencil::dirichlet_o2(
-            i + 2, prev(f), i + 1 - length(f.getLocation()), value);
-      }
-    } else {
-      for (int i = 0; i < boundary_width(); ++i) {
-        getAt(f, -i) = parallel_stencil::dirichlet_o3(
-            i + 2, prev(f), i + 1, current(f), i + 1 - length(f.getLocation()), value);
-      }
-    }
-  }
-
-  /// Ensure the value in the boundary is at least `value`
-  void limit_at_least(Field3D& f, BoutReal value) const {
-    for (int i = 0; i < boundary_width(); ++i) {
-      if (getAt(f, -i) < value) {
-        getAt(f, -i) = value;
-      }
-    }
-  }
-
-  /// Apply neumann boundary condition, where `value` is the gradient in index space
-
-  // neumann_o1 would give second order convergence, given an appropriate one-sided stencil.
-  // But in general we do not, and thus for normal C2 stencils, this is 1st order.
-  void neumann_o1(Field3D& f, BoutReal value) const {
-    for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, -i) = current(f) + value * (i + 1);
-    }
-  }
-
-  /// Apply neumann boundary condition, where `value` is the gradient in index space
-  void neumann_o2(Field3D& f, BoutReal value) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return neumann_o1(f, value);
-    }
-    for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, -i) = prev(f) + (2 + i) * value;
-    }
-  }
-
-  /// Apply neumann boundary condition, where `value` is the gradient in index space
-  void neumann_o3(Field3D& f, BoutReal value) const {
-    ASSERT3(valid() >= 0);
-    if (valid() < 1) {
-      return neumann_o2(f, value);
-    }
-    for (int i = 0; i < boundary_width(); ++i) {
-      getAt(f, -i) = parallel_stencil::neumann_o3(i + 1 - length(f.getLocation()), value,
-                                                  i + 1, current(f), 2, prev(f));
-    }
-  }
-
-  void set_free(Field3D& f, BoundaryFreeExtrapolation mode) const {
-    BoutReal fac = BoutNaN;
-    if (valid() > 0) {
-      fac = limitFreeScale(prev(f), current(f), mode);
-    } else {
-      fac = mode == BoundaryFreeExtrapolation::linear ? 0 : 1;
-    }
-    auto val = current(f);
-    if (mode == BoundaryFreeExtrapolation::linear) {
-      for (int i = 0; i < boundary_width(); ++i) {
-        val += fac;
-        getAt(f, -i) = val;
-      }
-    } else {
-      for (int i = 0; i < boundary_width(); ++i) {
-        val *= fac;
-        getAt(f, -i) = val;
-      }
-    }
-  }
   void setSmallValue(BoutReal val) {
     ASSERT2(val > 0);
     ASSERT2(val < 0.5);
     small_value = val;
   }
 
+  BoutReal smallValue() const { return small_value; }
+
 private:
   BoutReal small_value = 1e-4;
   friend Impl;
 };
 
-namespace {
+namespace details {
 /// Limited free gradient of log of a quantity
 /// This ensures that the guard cell values remain positive
 /// while also ensuring that the quantity never increases
@@ -400,7 +234,7 @@ inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, BoundaryFreeExtrapolati
 
   return fp;
 }
-} // namespace
+} // namespace details
 
 /// An FCI-aware boundary region
 ///
@@ -794,5 +628,232 @@ inline auto end(const BoundaryRegionXY<isX>& reg) {
   return BoundaryRegionIterXY<isX>(&reg, false);
 }
 
+/*
+ *     INTERPOLATION and EXTRAPOLATION
+ */
+
+/// Extrapolate a given field to the boundary
+template <boundary_iterator Iter>
+BoutReal extrapolate_boundary_o1(const Iter& point, const Field3D& f) {
+  return point.current(f);
+}
+
+/// Extrapolate a given field to the boundary
+template <boundary_iterator Iter>
+BoutReal extrapolate_boundary_o2(const Iter& point, const Field3D& f) {
+  ASSERT3(point.valid() >= 0);
+  if (point.valid() < 1) {
+    return extrapolate_boundary_o1(point, f);
+  }
+  return point.current(f) * (1 + point.length(f.getLocation()))
+         - point.prev(f) * point.length(f.getLocation());
+}
+
+/// Extrapolate a given function to the boundary
+template <boundary_iterator Iter>
+BoutReal extrapolate_bounday_o1(const Iter& point, const function_accessor auto& func,
+                                [[maybe_unused]] CELL_LOC loc = CELL_CENTRE) {
+  return point.current(func);
+}
+
+/// Extrapolate a given function to the boundary
+template <boundary_iterator Iter>
+BoutReal extrapolate_boundary_o2(const Iter& point, const function_accessor auto& func,
+                                 CELL_LOC loc = CELL_CENTRE) {
+  ASSERT3(point.valid() >= 0);
+  if (point.valid() < 1) {
+    return extrapolate_boundary_o1(point, func);
+  }
+  return point.current(func) * (1 + point.length(loc))
+         - point.prev(func) * point.length(loc);
+}
+
+/// Interpolate a field to the boundary, using the boundary values
+template <boundary_iterator Iter>
+BoutReal interpolate_boundary_o2(const Iter& point, const Field3D& f) {
+  return point.current(f) * (1 - point.length(f.getLocation()))
+         + point.next(f) * point.length(f.getLocation());
+}
+/// Interpolate a field to the boundary, using the boundary values
+template <boundary_iterator Iter>
+BoutReal interpolate_boundary_o2(const Iter& point, const function_accessor auto& func,
+                                 CELL_LOC loc = CELL_CENTRE) {
+  return point.current(func) * (1 - point.length(loc))
+         + point.next(func) * point.length(loc);
+}
+/// Extrapolate to the first boundary value freely
+template <boundary_iterator Iter>
+BoutReal extrapolate_next_o1(const Iter& point, const Field3D& f) {
+  return point.current(f);
+}
+/// Extrapolate to the first boundary value freely
+template <boundary_iterator Iter>
+BoutReal extrapolate_next_o2(const Iter& point, const Field3D& f) {
+  ASSERT3(point.valid() >= 0);
+  if (point.valid() < 1) {
+    return extrapolate_next_o1(point, f);
+  }
+  return point.current(f) * 2 - point.prev(f);
+}
+
+/// Extrapolate to the first boundary value freely
+template <boundary_iterator Iter>
+BoutReal extrapolate_next_o1(const Iter& point, const function_accessor auto& func) {
+  return point.current(func);
+}
+/// Extrapolate to the first boundary value freely
+template <boundary_iterator Iter>
+BoutReal extrapolate_next_o2(const Iter& point, const function_accessor auto& func) {
+  ASSERT3(point.valid() >= 0);
+  if (point.valid() < 1) {
+    return extrapolate_next_o1(func);
+  }
+  return point.current(func) * 2 - prev(func);
+}
+
+/// extrapolate the gradient into the boundary
+template <boundary_iterator Iter>
+BoutReal extrapolate_grad_o1([[maybe_unused]] const Iter& point,
+                             [[maybe_unused]] const Field3D& f) {
+  return 0;
+}
+/// extrapolate the gradient into the boundary
+template <boundary_iterator Iter>
+BoutReal extrapolate_grad_o2(const Iter& point, const Field3D& f) {
+  ASSERT3(point.valid() >= 0);
+  if (point.valid() < 1) {
+    return extrapolate_grad_o1(point, f);
+  }
+  return point.current(f) - point.next(f);
+}
+
+template <boundary_iterator Iter>
+BoutReal extrapolate_boundary_free(const Iter& point, const Field3D& f,
+                                   BoundaryFreeExtrapolation mode) {
+  BoutReal fac = BoutNaN;
+  if (point.valid() > 0) {
+    fac = limitFreeScale(point.prev(f), point.current(f), mode);
+  } else {
+    fac = mode == BoundaryFreeExtrapolation::linear ? 0 : 1;
+  }
+  const auto val = point.current(f);
+  const BoutReal next = mode == BoundaryFreeExtrapolation::linear ? val + fac : val * fac;
+  return val * point.length(f.getLocation()) + next * (1 - point.length(f.getLocation()));
+}
+
+/*
+ *     APPLY BOUNDARY CONDITIONS
+ */
+
+/// Apply a dirichlet boundary condition
+template <boundary_iterator Iter>
+void dirichlet_o1(const Iter& point, Field3D& f, BoutReal value) {
+  for (int i = 0; i < point.boundary_width(); ++i) {
+    point.getAt(f, -i) = value;
+  }
+}
+
+/// Apply a dirichlet boundary condition
+template <boundary_iterator Iter>
+void dirichlet_o2(const Iter& point, Field3D& f, BoutReal value) {
+  if (point.length(f.getLocation()) < point.smallValue()) {
+    return dirichlet_o1(point, f, value);
+  }
+  for (int i = 0; i < point.boundary_width(); ++i) {
+    point.getAt(f, -i) = parallel_stencil::dirichlet_o2(
+        i + 1, point.current(f), i + 1 - point.length(f.getLocation()), value);
+  }
+}
+
+/// Apply a dirichlet boundary condition
+template <boundary_iterator Iter>
+void dirichlet_o3(const Iter& point, Field3D& f, BoutReal value) {
+  ASSERT3(point.valid() >= 0);
+  if (point.valid() < 1) {
+    return dirichlet_o2(point, f, value);
+  }
+  if (point.length(f.getLocation()) < point.smallValue()) {
+    for (int i = 0; i < point.boundary_width(); ++i) {
+      point.getAt(f, -i) = parallel_stencil::dirichlet_o2(
+          i + 2, point.prev(f), i + 1 - point.length(f.getLocation()), value);
+    }
+  } else {
+    for (int i = 0; i < point.boundary_width(); ++i) {
+      point.getAt(f, -i) =
+          parallel_stencil::dirichlet_o3(i + 2, point.prev(f), i + 1, point.current(f),
+                                         i + 1 - point.length(f.getLocation()), value);
+    }
+  }
+}
+
+/// Ensure the value in the boundary is at least `value`
+template <boundary_iterator Iter>
+void limit_at_least(const Iter& point, Field3D& f, BoutReal value) {
+  for (int i = 0; i < point.boundary_width(); ++i) {
+    if (point.getAt(f, -i) < value) {
+      point.getAt(f, -i) = value;
+    }
+  }
+}
+
+/// Apply neumann boundary condition, where `value` is the gradient in index space
+
+// neumann_o1 would give second order convergence, given an appropriate one-sided stencil.
+// But in general we do not, and thus for normal C2 stencils, this is 1st order.
+template <boundary_iterator Iter>
+void neumann_o1(const Iter& point, Field3D& f, BoutReal value) {
+  for (int i = 0; i < point.boundary_width(); ++i) {
+    point.getAt(f, -i) = point.current(f) + value * (i + 1);
+  }
+}
+
+/// Apply neumann boundary condition, where `value` is the gradient in index space
+template <boundary_iterator Iter>
+void neumann_o2(const Iter& point, Field3D& f, BoutReal value) {
+  ASSERT3(point.valid() >= 0);
+  if (point.valid() < 1) {
+    return neumann_o1(point, f, value);
+  }
+  for (int i = 0; i < point.boundary_width(); ++i) {
+    point.getAt(f, -i) = point.prev(f) + (2 + i) * value;
+  }
+}
+
+/// Apply neumann boundary condition, where `value` is the gradient in index space
+template <boundary_iterator Iter>
+void neumann_o3(const Iter& point, Field3D& f, BoutReal value) {
+  ASSERT3(point.valid() >= 0);
+  if (point.valid() < 1) {
+    return neumann_o2(point, f, value);
+  }
+  for (int i = 0; i < point.boundary_width(); ++i) {
+    point.getAt(f, -i) =
+        parallel_stencil::neumann_o3(i + 1 - point.length(f.getLocation()), value, i + 1,
+                                     point.current(f), 2, point.prev(f));
+  }
+}
+
+template <boundary_iterator Iter>
+void set_free(const Iter& point, Field3D& f, BoundaryFreeExtrapolation mode) {
+  BoutReal fac = BoutNaN;
+  if (point.valid() > 0) {
+    fac = limitFreeScale(point.prev(f), point.current(f), mode);
+  } else {
+    fac = mode == BoundaryFreeExtrapolation::linear ? 0 : 1;
+  }
+  auto val = point.current(f);
+  if (mode == BoundaryFreeExtrapolation::linear) {
+    for (int i = 0; i < point.boundary_width(); ++i) {
+      val += fac;
+      point.getAt(f, -i) = val;
+    }
+  } else {
+    for (int i = 0; i < point.boundary_width(); ++i) {
+      val *= fac;
+      point.getAt(f, -i) = val;
+    }
+  }
+}
+
 } // namespace boundary
 } // namespace bout
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index d98aa7d4e8..6b56b4b2c4 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -251,27 +251,27 @@ public:
 class BoundaryOpPar_dirichlet_o1 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o1> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <class T>
-  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
-    pnt.dirichlet_o1(f, value);
+  template <bout::boundary::boundary_iterator Iter>
+  static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
+    dirichlet_o1(pnt, f, value);
   }
 };
 
 class BoundaryOpPar_dirichlet_o2 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o2> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <class T>
-  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
-    pnt.dirichlet_o2(f, value);
+  template <bout::boundary::boundary_iterator Iter>
+  static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
+    dirichlet_o2(pnt, f, value);
   }
 };
 
 class BoundaryOpPar_dirichlet_o3 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o3> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <class T>
-  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
-    pnt.dirichlet_o3(f, value);
+  template <bout::boundary::boundary_iterator Iter>
+  static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
+    dirichlet_o3(pnt, f, value);
   }
 };
 
@@ -279,9 +279,9 @@ class BoundaryOpPar_neumann_o1
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o1, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <class T>
-  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
-    pnt.neumann_o1(f, value);
+  template <bout::boundary::boundary_iterator Iter>
+  static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
+    neumann_o1(pnt, f, value);
   }
 };
 
@@ -289,9 +289,9 @@ class BoundaryOpPar_neumann_o2
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o2, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <class T>
-  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
-    pnt.neumann_o2(f, value);
+  template <bout::boundary::boundary_iterator Iter>
+  static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
+    neumann_o2(pnt, f, value);
   }
 };
 
@@ -299,9 +299,9 @@ class BoundaryOpPar_neumann_o3
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o3, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <class T>
-  static void apply_stencil(Field3D& f, T& pnt, BoutReal value) {
-    pnt.neumann_o3(f, value);
+  template <bout::boundary::boundary_iterator Iter>
+  static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
+    neumann_o3(pnt, f, value);
   }
 };
 
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 95ea1de05a..5d0fbbcc0c 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -31,6 +31,7 @@
 #include "bout/field2d.hxx"
 
 #include "bout/index_derivs_interface.hxx"
+#include "bout/yboundary_regions.hxx"
 #include <bout/boutcomm.hxx>
 #include <bout/globals.hxx>
 
@@ -513,9 +514,9 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices,
       for (auto& region : fieldmesh->getBoundariesPar()) {
         for (const auto& point : *region) {
           // Interpolate midpoint value in f3d
-          const BoutReal val = point.interpolate_boundary_o2(f3d);
+          const BoutReal val = interpolate_boundary_o2(point, f3d);
           // Set the same boundary value in this field
-          point.dirichlet_o1(*this, val);
+          dirichlet_o1(point, *this, val);
         }
       }
     }
@@ -526,9 +527,10 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices,
   // Loop over boundary regions
   for (const auto& newreg : fieldmesh->getBoundaries()) {
     if (newreg->isX) {
-      bout::boundary::iter_boundary(newreg, [&](auto& point) {
-        const BoutReal val = point.interpolate_boundary_o2(f3d);
-        point.dirichlet_o2(*this, val);
+      using namespace bout::boundary;
+      iter_boundary(newreg, [&](YBoundaryPoint auto& point) {
+        const BoutReal val = interpolate_boundary_o2(point, f3d);
+        dirichlet_o2(point, *this, val);
       });
       if (forceLegacy) {
         // get the old, potentially wrong behaviour
diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index 0255dd6de2..278ae90a8e 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -1,7 +1,11 @@
 #include "gtest/gtest.h"
 
-#include "bout/boutexception.hxx"
-#include "bout/output_bout_types.hxx"
+#include "bout/boundary_common.hxx"
+#include "bout/boundary_region.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/field3d.hxx"
+#include "bout/region.hxx"
+#include "bout/utils.hxx"
 #include "bout/yboundary_regions.hxx"
 
 #include "fake_mesh_fixture.hxx"
@@ -17,7 +21,7 @@ TEST_F(YBTest, dirichlet_o2_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) { point.dirichlet_o2(test, 2); });
+  sheath.iter([&](const YBoundaryPoint auto& point) { dirichlet_o2(point, test, 2); });
   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }
 
@@ -25,7 +29,7 @@ TEST_F(YBTest, neumann_o1_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) { point.neumann_o1(test, 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) { neumann_o1(point, test, 1); });
   EXPECT_TRUE(IsFieldEqual(test, 2.0, "RGN_YGUARDS"));
 }
 
@@ -33,7 +37,7 @@ TEST_F(YBTest, neumann_o2_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) { point.neumann_o2(test, 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) { neumann_o2(point, test, 1); });
   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }
 
@@ -41,7 +45,7 @@ TEST_F(YBTest, neumann_o3_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) { point.neumann_o3(test, 1); });
+  sheath.iter([&](const YBoundaryPoint auto& point) { neumann_o3(point, test, 1); });
   EXPECT_TRUE(IsFieldEqual(test, 0.0, "RGN_YGUARDS"));
 }
 
@@ -49,7 +53,7 @@ TEST_F(YBTest, bndry_size) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   int sum = 0;
-  sheath.iter([&](const YBoundaryPoint auto& point) { sum++; });
+  sheath.iter([&]([[maybe_unused]] const YBoundaryPoint auto& point) { sum++; });
   EXPECT_EQ(sum, 28);
 }
 
@@ -57,7 +61,7 @@ TEST_F(YBTest, interpolate_boundary_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0);
+    EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 1.0);
   });
 }
 
@@ -65,7 +69,7 @@ TEST_F(YBTest, interpolate_boundary_o2_const) {
   const Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.0);
+    EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 1.0);
   });
 }
 
@@ -73,7 +77,7 @@ TEST_F(YBTest, extrapolate_boundary_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    EXPECT_DOUBLE_EQ(point.extrapolate_boundary_o2(test), 1.0);
+    EXPECT_DOUBLE_EQ(extrapolate_boundary_o2(point, test), 1.0);
   });
 }
 
@@ -81,8 +85,8 @@ TEST_F(YBTest, dirichlet_o1) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    point.dirichlet_o1(test, 2.0);
-    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.5);
+    dirichlet_o1(point, test, 2.0);
+    EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 1.5);
   });
 }
 
@@ -90,8 +94,8 @@ TEST_F(YBTest, dirichlet_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    point.dirichlet_o2(test, 2.0);
-    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 2.0);
+    dirichlet_o2(point, test, 2.0);
+    EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 2.0);
   });
 }
 
@@ -99,24 +103,23 @@ TEST_F(YBTest, dirichlet_o3) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    point.dirichlet_o3(test, 2.0);
-    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 7. / 3.);
+    dirichlet_o3(point, test, 2.0);
+    EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 7. / 3.);
   });
 }
 
 TEST_F(YBTest, extrapolate_boundary_free) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2) + 1; }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
+  using namespace bout::boundary;
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    EXPECT_DOUBLE_EQ(point.extrapolate_boundary_free(
-                         test, bout::boundary::BoundaryFreeExtrapolation::limited),
-                     3);
-    EXPECT_DOUBLE_EQ(point.extrapolate_boundary_free(
-                         test, bout::boundary::BoundaryFreeExtrapolation::linear),
-                     3.5);
-    EXPECT_DOUBLE_EQ(point.extrapolate_boundary_free(
-                         test, bout::boundary::BoundaryFreeExtrapolation::exponential),
-                     5);
+    EXPECT_DOUBLE_EQ(
+        extrapolate_boundary_free(point, test, BoundaryFreeExtrapolation::limited), 3);
+    EXPECT_DOUBLE_EQ(
+        extrapolate_boundary_free(point, test, BoundaryFreeExtrapolation::linear), 3.5);
+    EXPECT_DOUBLE_EQ(
+        extrapolate_boundary_free(point, test, BoundaryFreeExtrapolation::exponential),
+        5);
   });
 }
 
@@ -124,8 +127,8 @@ TEST_F(YBTest, set_free) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2) + 1; }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    point.set_free(test, bout::boundary::BoundaryFreeExtrapolation::limited);
-    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 3);
+    set_free(point, test, bout::boundary::BoundaryFreeExtrapolation::limited);
+    EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 3);
   });
 }
 
@@ -133,7 +136,7 @@ TEST_F(YBTest, interpolate_boundary_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 2.5);
+    EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 2.5);
   });
 }
 
@@ -141,8 +144,8 @@ TEST_F(YBTest, limit_at_least) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    point.limit_at_least(test, 2.0);
-    EXPECT_DOUBLE_EQ(point.interpolate_boundary_o2(test), 1.5);
+    limit_at_least(point, test, 2.0);
+    EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 1.5);
   });
 }
 
@@ -150,7 +153,7 @@ TEST_F(YBTest, extrapolate_grad_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    EXPECT_DOUBLE_EQ(point.extrapolate_grad_o2(test), 1);
+    EXPECT_DOUBLE_EQ(extrapolate_grad_o2(point, test), 1);
   });
 }
 
@@ -158,7 +161,7 @@ TEST_F(YBTest, extrapolate_next_o1_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    EXPECT_DOUBLE_EQ(point.extrapolate_next_o1(test), 1);
+    EXPECT_DOUBLE_EQ(extrapolate_next_o1(point, test), 1);
   });
 }
 
@@ -166,7 +169,7 @@ TEST_F(YBTest, extrapolate_next_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const YBoundaryPoint auto& point) {
-    EXPECT_DOUBLE_EQ(point.extrapolate_next_o2(test), 2);
+    EXPECT_DOUBLE_EQ(extrapolate_next_o2(point, test), 2);
   });
 }
 
@@ -227,7 +230,9 @@ TEST_F(YBTest, getAt_square) {
 TEST_F(YBTest, getAt_func) {
   Field3D test = makeField<Field3D>([&](auto& i) { return i.y() - 2; }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  auto square = [&](int yo, Ind3D ind) -> double { return SQ(test[ind]); };
+  auto square = [&]([[maybe_unused]] int yo, Ind3D ind) -> BoutReal {
+    return SQ(test[ind]);
+  };
   sheath.iter([&](const YBoundaryPoint auto& point) {
     EXPECT_DOUBLE_EQ(point.getAt(square, 0), 4);
     EXPECT_DOUBLE_EQ(point.getAt(square, 1), 1);

From c5bf2c4b62e8e5bec92f3435193f9eacafbcfd1c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Fri, 21 Aug 2026 11:31:10 +0100
Subject: [PATCH 1766/1827] Remove duplicated function

Also in `boundary_common.hxx`
---
 include/bout/boundary_region_iter.hxx | 39 ---------------------------
 1 file changed, 39 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 6287df2d24..1c11fbb1e3 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -197,45 +197,6 @@ private:
   friend Impl;
 };
 
-namespace details {
-/// Limited free gradient of log of a quantity
-/// This ensures that the guard cell values remain positive
-/// while also ensuring that the quantity never increases
-///
-///  fm  fc | fp
-///         ^ boundary
-///
-/// exp( 2*log(fc) - log(fm) )
-inline BoutReal limitFreeScale(BoutReal fm, BoutReal fc, BoundaryFreeExtrapolation mode) {
-  if ((fm < fc) && (mode == BoundaryFreeExtrapolation::limited)) {
-    return fc; // Neumann rather than increasing into boundary
-  }
-  if (fm < 1e-10) {
-    return fc; // Low / no density condition
-  }
-
-  BoutReal fp = 0;
-  switch (mode) {
-  case BoundaryFreeExtrapolation::limited:
-  case BoundaryFreeExtrapolation::exponential:
-    fp = SQ(fc) / fm; // Exponential
-    break;
-  case BoundaryFreeExtrapolation::linear:
-    fp = (2.0 * fc) - fm; // Linear
-    break;
-  }
-
-#if CHECKLEVEL >= 2
-  if (!std::isfinite(fp)) {
-    throw BoutException("SheathBoundary limitFree {}: {}, {} -> {}",
-                        static_cast<int>(mode), fm, fc, fp);
-  }
-#endif
-
-  return fp;
-}
-} // namespace details
-
 /// An FCI-aware boundary region
 ///
 /// Uses `BoundaryRegionIterFCI` as its iterator.

From e27f32a2abce089b4548e16a9cd4cdb2635f4070 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 24 Aug 2026 09:58:46 +0100
Subject: [PATCH 1767/1827] Move boundary region iterators inside their
 container classes

This makes it much clearer that they are iterators, and also means the XY
iterator can inherit its parent's template argument.
---
 include/bout/boundary_region_iter.hxx | 424 ++++++++++++--------------
 include/bout/parallel_boundary_op.hxx |   6 +-
 include/bout/yboundary_regions.hxx    |   4 +-
 src/mesh/parallel_boundary_op.cxx     |   6 +-
 4 files changed, 205 insertions(+), 235 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 1c11fbb1e3..af10fd16b2 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -199,11 +199,103 @@ private:
 
 /// An FCI-aware boundary region
 ///
-/// Uses `BoundaryRegionIterFCI` as its iterator.
-///
 /// This can't use the legacy iteration methods (`first()`, `next()`, and so on)
 class BoundaryRegionFCI : public BoundaryRegionBase {
 public:
+  /// Iterator over a `BoundaryRegionFCI`
+  class Iterator : public BoundaryRegionIterBase<Iterator> {
+  private:
+    // TODO(dave) make non-const?
+    const BoundaryRegionFCI* region;
+    size_t pos{0};
+
+  public:
+    Iterator() = delete;
+    Iterator(const BoundaryRegionFCI* reg, bool isstart)
+        : region(reg), pos(isstart ? 0 : reg->bndry_points.size()) {}
+    void setValid(char valid) {
+      const_cast<BoundaryRegionFCI*>(region)->bndry_points[pos].valid = valid;
+    };
+    BoutReal s_x() const { return region->bndry_points[pos].intersection.s_x; };
+    BoutReal s_y() const { return region->bndry_points[pos].intersection.s_y; };
+    BoutReal s_z() const { return region->bndry_points[pos].intersection.s_z; };
+    Mesh* localmesh() const { return region->localmesh; };
+    int dir() const { return region->_dir; }
+    bool _is_lower() const { return region->_dir < 0; }
+
+    template <bool check = true>
+    BoutReal& _getAt(Field3D& f, int off) const {
+      ASSERT3(f.hasParallelSlices());
+      if constexpr (check) {
+        ASSERT3(_valid() > -off - 2);
+      }
+      auto _off = _offset() - (off * region->_dir);
+      return f.ynext(_off)[_ind().yp(_off)];
+    }
+    template <bool check = true>
+    const BoutReal& _getAt(const Field3D& f, int off) const {
+      ASSERT3(f.hasParallelSlices());
+      if constexpr (check) {
+        ASSERT3(_valid() > -off - 2);
+      }
+      auto _off = _offset() - (off * region->_dir);
+      return f.ynext(_off)[_ind().yp(_off)];
+    }
+    template <bool check = true>
+    BoutReal& _getAt(Field2D& f, int off) const {
+      ASSERT3(f.hasParallelSlices());
+      if constexpr (check) {
+        ASSERT3(_valid() > -off - 2);
+      }
+      auto _off = _offset() - (off * region->_dir);
+      return f.ynext(_off)[_ind().yp(_off)];
+    }
+    template <bool check = true>
+    const BoutReal& _getAt(const Field2D& f, int off) const {
+      ASSERT3(f.hasParallelSlices());
+      if constexpr (check) {
+        ASSERT3(_valid() > -off - 2);
+      }
+      auto _off = _offset() - (off * region->_dir);
+      return f.ynext(_off)[_ind().yp(_off)];
+    }
+    template <bool check = true>
+    BoutReal _getAt(const function_accessor auto& f, int off) const {
+      if constexpr (check) {
+        ASSERT3(valid() > -off - 2);
+      }
+      auto _off = _offset() + (off * region->_dir);
+      return f(_off, _ind().yp(_off));
+    }
+    signed char _offset() const { return region->bndry_points[pos].offset; }
+    signed char _valid() const { return region->bndry_points[pos].valid; }
+    Ind3D _ind() const { return region->bndry_points[pos].index; }
+    int _boundary_width() const {
+      return region->localmesh->ystart - region->bndry_points[pos].abs_offset + 1;
+    }
+    BoutReal _length([[maybe_unused]] CELL_LOC loc) const {
+      ASSERT3(loc == CELL_CENTRE);
+      return region->bndry_points[pos].length;
+    }
+
+    auto operator<=>(const Iterator& rhs) const {
+      ASSERT3(region == rhs.region);
+      return pos <=> rhs.pos;
+    }
+
+    bool operator==(Iterator lhs) const {
+      ASSERT3(region == lhs.region);
+      return pos == lhs.pos;
+    }
+
+    Iterator& operator++() {
+      ++pos;
+      return *this;
+    }
+
+    Iterator& operator*() { return *this; }
+  };
+
   BoundaryRegionFCI(const std::string& name, const BndryLoc& loc, int dir, Mesh* mesh)
       : BoundaryRegionBase(name, loc, mesh), _dir(dir), localmesh(mesh) {
     isParallel = true;
@@ -235,8 +327,11 @@ public:
   void next() override { throw BoutException("Legacy interface is not suppored"); }
   bool isDone() override { throw BoutException("Legacy interface is not suppored"); }
 
+  auto begin() const { return Iterator(this, true); }
+  auto end() const { return Iterator(this, false); }
+
 private:
-  friend class BoundaryRegionIterFCI;
+  friend class Iterator;
   int _dir;
   // Vector of points in the boundary
   bout::parallel_boundary_region::IndicesVec bndry_points;
@@ -255,108 +350,113 @@ private:
   }
 };
 
-/// Iterator over a `BoundaryRegionFCI`
-class BoundaryRegionIterFCI : public BoundaryRegionIterBase<BoundaryRegionIterFCI> {
-private:
-  // TODO(dave) make non-const?
-  const BoundaryRegionFCI* region;
-  size_t pos{0};
-
+/// Boundary region for field-aligned grids
+///
+/// FCI grids should use `BoundaryRegionFCI`
+///
+/// Template parameter `isXtemp` is `true` for boundaries in X, and `false` for boundaries in Y
+template <bool isXtemp>
+class BoundaryRegionXY : public BoundaryRegionBase {
 public:
-  BoundaryRegionIterFCI() = delete;
-  BoundaryRegionIterFCI(const BoundaryRegionFCI* reg, bool isstart)
-      : region(reg), pos(isstart ? 0 : reg->bndry_points.size()) {}
-  void setValid(char valid) {
-    const_cast<BoundaryRegionFCI*>(region)->bndry_points[pos].valid = valid;
-  };
-  BoutReal s_x() const { return region->bndry_points[pos].intersection.s_x; };
-  BoutReal s_y() const { return region->bndry_points[pos].intersection.s_y; };
-  BoutReal s_z() const { return region->bndry_points[pos].intersection.s_z; };
-  Mesh* localmesh() const { return region->localmesh; };
-  int dir() const { return region->_dir; }
-  bool _is_lower() const { return region->_dir < 0; }
+  /// Iterator over a `BoundaryRegionXY`
+  class Iterator : public BoundaryRegionIterBase<Iterator> {
+  private:
+    const BoundaryRegionXY<isXtemp>* region;
+    size_t pos{0};
+
+    /// Return the current index displaced by \p offset
+    Ind3D offsetInd(int offset) const {
+      if constexpr (isXtemp) {
+        return _ind().xp(offset);
+      } else {
+        return _ind().yp(offset);
+      }
+    }
 
-  template <bool check = true>
-  BoutReal& _getAt(Field3D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
-    if constexpr (check) {
-      ASSERT3(_valid() > -off - 2);
+  public:
+    Iterator() = delete;
+    Iterator(const BoundaryRegionXY<isXtemp>* reg, bool isstart)
+        : region(reg), pos(isstart ? 0 : reg->rgn.size()) {}
+    int dir() const { return region->_dir; }
+    Ind3D ind() const { return _ind(); }
+
+    template <bool check = true>
+    BoutReal& _getAt(Field3D& f, int off) const {
+      if constexpr (check) {
+        ASSERT3(_valid() > -off - 2);
+      }
+      auto _off = (1 - off) * region->_dir;
+      return f[offsetInd(_off)];
     }
-    auto _off = _offset() - (off * region->_dir);
-    return f.ynext(_off)[_ind().yp(_off)];
-  }
-  template <bool check = true>
-  const BoutReal& _getAt(const Field3D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
-    if constexpr (check) {
-      ASSERT3(_valid() > -off - 2);
+    template <bool check = true>
+    const BoutReal& _getAt(const Field3D& f, int off) const {
+      if constexpr (check) {
+        ASSERT3(_valid() > -off - 2);
+      }
+      auto _off = (1 - off) * region->_dir;
+      return f[offsetInd(_off)];
     }
-    auto _off = _offset() - (off * region->_dir);
-    return f.ynext(_off)[_ind().yp(_off)];
-  }
-  template <bool check = true>
-  BoutReal& _getAt(Field2D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
-    if constexpr (check) {
-      ASSERT3(_valid() > -off - 2);
+    template <bool check = true>
+    BoutReal& _getAt(Field2D& f, int off) const {
+      if constexpr (check) {
+        ASSERT3(_valid() > -off - 2);
+      }
+      auto _off = (1 - off) * region->_dir;
+      return f[offsetInd(_off)];
     }
-    auto _off = _offset() - (off * region->_dir);
-    return f.ynext(_off)[_ind().yp(_off)];
-  }
-  template <bool check = true>
-  const BoutReal& _getAt(const Field2D& f, int off) const {
-    ASSERT3(f.hasParallelSlices());
-    if constexpr (check) {
-      ASSERT3(_valid() > -off - 2);
+    template <bool check = true>
+    const BoutReal& _getAt(const Field2D& f, int off) const {
+      if constexpr (check) {
+        ASSERT3(_valid() > -off - 2);
+      }
+      auto _off = (1 - off) * region->_dir;
+      return f[offsetInd(_off)];
     }
-    auto _off = _offset() - (off * region->_dir);
-    return f.ynext(_off)[_ind().yp(_off)];
-  }
-  template <bool check = true>
-  BoutReal _getAt(const function_accessor auto& f, int off) const {
-    if constexpr (check) {
-      ASSERT3(valid() > -off - 2);
+    template <bool check = true>
+    BoutReal _getAt(const function_accessor auto& f, int off) const {
+      if constexpr (check) {
+        ASSERT3(_valid() > -off - 2);
+      }
+      auto _off = (1 - off) * region->_dir;
+      return f(0, offsetInd(_off));
+    }
+    signed char _offset() const { return region->_dir; }
+    signed char _valid() const { return region->valid; }
+    Ind3D _ind() const { return region->rgn[pos]; }
+    int _boundary_width() const {
+      if constexpr (isXtemp) {
+        return region->localmesh->xstart;
+      }
+      return region->localmesh->ystart;
+    }
+    BoutReal _length(CELL_LOC loc) const {
+      if (loc == CELL_XLOW) {
+        if (dir() == 1) {
+          return 1;
+        }
+        return 0;
+      }
+      return 0.5;
     }
-    auto _off = _offset() + (off * region->_dir);
-    return f(_off, _ind().yp(_off));
-  }
-  signed char _offset() const { return region->bndry_points[pos].offset; }
-  signed char _valid() const { return region->bndry_points[pos].valid; }
-  Ind3D _ind() const { return region->bndry_points[pos].index; }
-  int _boundary_width() const {
-    return region->localmesh->ystart - region->bndry_points[pos].abs_offset + 1;
-  }
-  BoutReal _length([[maybe_unused]] CELL_LOC loc) const {
-    ASSERT3(loc == CELL_CENTRE);
-    return region->bndry_points[pos].length;
-  }
 
-  auto operator<=>(const BoundaryRegionIterFCI& rhs) const {
-    ASSERT3(region == rhs.region);
-    return pos <=> rhs.pos;
-  }
+    auto operator<=>(const Iterator& rhs) const {
+      ASSERT3(region == rhs.region);
+      return pos <=> rhs.pos;
+    }
 
-  bool operator==(BoundaryRegionIterFCI lhs) const {
-    ASSERT3(region == lhs.region);
-    return pos == lhs.pos;
-  }
+    bool operator==(const Iterator& rhs) const {
+      ASSERT3(region == rhs.region);
+      return pos == rhs.pos;
+    }
 
-  BoundaryRegionIterFCI& operator++() {
-    ++pos;
-    return *this;
-  }
-  // No-op for compatibility
-  BoundaryRegionIterFCI& operator*() { return *this; }
-};
+    Iterator& operator++() {
+      ++pos;
+      return *this;
+    }
+
+    Iterator& operator*() { return *this; }
+  };
 
-/// Boundary region for field-aligned grids
-///
-/// FCI grids should use `BoundaryRegionFCI`
-///
-/// Uses `BoundaryRegionIterXY` as its iterator
-template <bool isXtemp>
-class BoundaryRegionXY : public BoundaryRegionBase {
-public:
   BoundaryRegionXY() = delete;
   BoundaryRegionXY(const std::string& name, int dir, Mesh* mesh, Region<Ind3D>&& rgn)
       : BoundaryRegionBase(name, mesh), _dir(dir),
@@ -376,133 +476,19 @@ public:
   void next() override { throw BoutException("Legacy interface is not suppored"); }
   bool isDone() override { throw BoutException("Legacy interface is not suppored"); }
 
+  auto begin() const { return Iterator(this, true); }
+  auto end() const { return Iterator(this, false); }
+
 private:
-  template <bool isIterX>
-  friend class BoundaryRegionIterXY;
   int _dir;
   std::vector<Ind3D> rgn;
   signed char valid;
 };
 
-/// Iterator over a `BoundaryRegionXY`
-template <bool isX>
-class BoundaryRegionIterXY : public BoundaryRegionIterBase<BoundaryRegionIterXY<isX>> {
-private:
-  const BoundaryRegionXY<isX>* region;
-  size_t pos{0};
-
-public:
-  BoundaryRegionIterXY() = delete;
-  BoundaryRegionIterXY(const BoundaryRegionXY<isX>* reg, bool isstart)
-      : region(reg), pos(isstart ? 0 : reg->rgn.size()) {}
-  int dir() const { return region->_dir; }
-  Ind3D ind() const { return _ind(); }
-
-  template <bool check = true>
-  BoutReal& _getAt(Field3D& f, int off) const {
-    if constexpr (check) {
-      ASSERT3(_valid() > -off - 2);
-    }
-    auto _off = (1 - off) * region->_dir;
-    if constexpr (isX) {
-      return f[_ind().xp(_off)];
-    } else {
-      return f[_ind().yp(_off)];
-    }
-  }
-  template <bool check = true>
-  const BoutReal& _getAt(const Field3D& f, int off) const {
-    if constexpr (check) {
-      ASSERT3(_valid() > -off - 2);
-    }
-    auto _off = (1 - off) * region->_dir;
-    if constexpr (isX) {
-      return f[_ind().xp(_off)];
-    } else {
-      return f[_ind().yp(_off)];
-    }
-  }
-  template <bool check = true>
-  BoutReal& _getAt(Field2D& f, int off) const {
-    if constexpr (check) {
-      ASSERT3(_valid() > -off - 2);
-    }
-    auto _off = (1 - off) * region->_dir;
-    if constexpr (isX) {
-      return f[_ind().xp(_off)];
-    } else {
-      return f[_ind().yp(_off)];
-    }
-  }
-  template <bool check = true>
-  const BoutReal& _getAt(const Field2D& f, int off) const {
-    if constexpr (check) {
-      ASSERT3(_valid() > -off - 2);
-    }
-    auto _off = (1 - off) * region->_dir;
-    if constexpr (isX) {
-      return f[_ind().xp(_off)];
-    } else {
-      return f[_ind().yp(_off)];
-    }
-  }
-  template <bool check = true>
-  BoutReal _getAt(const function_accessor auto& f, int off) const {
-    if constexpr (check) {
-      ASSERT3(_valid() > -off - 2);
-    }
-    auto _off = (1 - off) * region->_dir;
-    if constexpr (isX) {
-      return f(0, _ind().xp(_off));
-    } else {
-      return f(0, _ind().yp(_off));
-    }
-  }
-  signed char _offset() const { return region->_dir; }
-  signed char _valid() const { return region->valid; }
-  Ind3D _ind() const { return region->rgn[pos]; }
-  int _boundary_width() const {
-    if constexpr (isX) {
-      return region->localmesh->xstart;
-    }
-    return region->localmesh->ystart;
-  }
-  BoutReal _length(CELL_LOC loc) const {
-    if (loc == CELL_XLOW) {
-      if (dir() == 1) {
-        return 1;
-      }
-      return 0;
-    }
-    return 0.5;
-  }
-
-  auto operator<=>(const BoundaryRegionIterXY<isX>& rhs) const {
-    ASSERT3(region == rhs.region);
-    return pos <=> rhs.pos;
-  }
-
-  bool operator==(BoundaryRegionIterXY<isX> rhs) const {
-    ASSERT3(region == rhs.region);
-    return pos == rhs.pos;
-  }
-
-  BoundaryRegionIterXY& operator++() {
-    ++pos;
-    return *this;
-  }
-  // No-op for compatibility
-  BoundaryRegionIterXY& operator*() { return *this; }
-};
-
 /// Alias for boundary regions over X specifically
 using BoundaryRegionX = BoundaryRegionXY<true>;
 /// Alias for boundary regions over Y specifically
 using BoundaryRegionY = BoundaryRegionXY<false>;
-/// Alias for boundary region iterators over X specifically
-using BoundaryRegionIterX = BoundaryRegionIterXY<true>;
-/// Alias for boundary region iterators over Y specifically
-using BoundaryRegionIterY = BoundaryRegionIterXY<false>;
 
 inline std::shared_ptr<BoundaryRegionX>
 NewBoundaryRegionXIn(const std::string& name, int ymin, int ymax, Mesh* mesh) {
@@ -573,22 +559,6 @@ void iter_boundary(const Bndry& bndry, const Func& func) {
   }
 }
 
-inline auto begin(const BoundaryRegionFCI& reg) {
-  return BoundaryRegionIterFCI(&reg, true);
-}
-inline auto end(const BoundaryRegionFCI& reg) {
-  return BoundaryRegionIterFCI(&reg, false);
-}
-
-template <bool isX>
-inline auto begin(const BoundaryRegionXY<isX>& reg) {
-  return BoundaryRegionIterXY<isX>(&reg, true);
-}
-template <bool isX>
-inline auto end(const BoundaryRegionXY<isX>& reg) {
-  return BoundaryRegionIterXY<isX>(&reg, false);
-}
-
 /*
  *     INTERPOLATION and EXTRAPOLATION
  */
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index 6b56b4b2c4..c2b0dde90c 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -104,9 +104,9 @@ private:
   enum class ValueType { GEN, FIELD, REAL };
   const ValueType value_type{ValueType::REAL};
 
-  BoutReal getValue(const bout::boundary::BoundaryRegionIterFCI& bndry, BoutReal t);
-  BoutReal getValue(const bout::boundary::BoundaryRegionIterX& bndry, BoutReal t);
-  BoutReal getValue(const bout::boundary::BoundaryRegionIterY& bndry, BoutReal t);
+  BoutReal getValue(const bout::boundary::BoundaryRegionFCI::Iterator& bndry, BoutReal t);
+  BoutReal getValue(const bout::boundary::BoundaryRegionX::Iterator& bndry, BoutReal t);
+  BoutReal getValue(const bout::boundary::BoundaryRegionY::Iterator& bndry, BoutReal t);
 
   template <class T, bool isNeumann>
   friend class BoundaryOpParTemp;
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index afb1266cde..35dea88b71 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -41,8 +41,8 @@ public:
   /// The function must take a `const YBoundaryPoint auto& point` as its only argument.
   /// See also the documentation at ../../manual/sphinx/user_docs/boundary_options.rst
   template <class F>
-    requires std::regular_invocable<F&, const BoundaryRegionIterY&>
-             || std::regular_invocable<F&, const BoundaryRegionIterFCI&>
+    requires std::regular_invocable<F&, const BoundaryRegionY::Iterator&>
+             || std::regular_invocable<F&, const BoundaryRegionFCI::Iterator&>
   void iter(F func) {
     for (auto& region : boundary_regions) {
       for (auto& point : *region) {
diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx
index dc376e7e63..48a1743c4f 100644
--- a/src/mesh/parallel_boundary_op.cxx
+++ b/src/mesh/parallel_boundary_op.cxx
@@ -8,7 +8,7 @@
 #include "bout/mesh.hxx"
 #include "bout/output.hxx"
 
-BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterFCI& bndry,
+BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionFCI::Iterator& bndry,
                                  BoutReal t) {
   switch (value_type) {
   case ValueType::GEN:
@@ -24,7 +24,7 @@ BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterFCI& bn
   }
 }
 
-BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterX& bndry,
+BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionX::Iterator& bndry,
                                  [[maybe_unused]] BoutReal t) {
   switch (value_type) {
   case ValueType::FIELD:
@@ -37,7 +37,7 @@ BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterX& bndr
   }
 }
 
-BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionIterY& bndry,
+BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionY::Iterator& bndry,
                                  [[maybe_unused]] BoutReal t) {
   switch (value_type) {
   case ValueType::FIELD:

From 0c6c7d24f7ef00799c4021feac2fe79a5ce9934a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 24 Aug 2026 11:05:59 +0100
Subject: [PATCH 1768/1827] Apply some clang-tidy fixes

---
 include/bout/boundary_region_iter.hxx     |  4 ++--
 include/bout/parallel_boundary_region.hxx | 21 ++++++++-------------
 include/bout/yboundary_regions.hxx        |  2 +-
 3 files changed, 11 insertions(+), 16 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index af10fd16b2..1a2670e0b6 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -346,7 +346,7 @@ private:
   Ind3D xyz2ind(int x, int y, int z) const {
     const int ny = localmesh->LocalNy;
     const int nz = localmesh->LocalNz;
-    return Ind3D{((x * ny + y) * nz) + z, ny, nz};
+    return Ind3D{(((x * ny) + y) * nz) + z, ny, nz};
   }
 };
 
@@ -458,7 +458,7 @@ public:
   };
 
   BoundaryRegionXY() = delete;
-  BoundaryRegionXY(const std::string& name, int dir, Mesh* mesh, Region<Ind3D>&& rgn)
+  BoundaryRegionXY(const std::string& name, int dir, Mesh* mesh, const Region<Ind3D>& rgn)
       : BoundaryRegionBase(name, mesh), _dir(dir),
         valid(isXtemp ? mesh->xstart : mesh->ystart) {
     BOUT_FOR_SERIAL(i, rgn) { this->rgn.emplace_back(i); }
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
index 30c51c6c86..4881e42eda 100644
--- a/include/bout/parallel_boundary_region.hxx
+++ b/include/bout/parallel_boundary_region.hxx
@@ -1,25 +1,20 @@
 #ifndef BOUT_PAR_BNDRY_H
 #define BOUT_PAR_BNDRY_H
 
-#include "bout/assert.hxx"
-#include "bout/boundary_region.hxx"
-#include "bout/bout_enum_class.hxx"
-#include "bout/bout_types.hxx"
+#include <bout/assert.hxx>
+#include <bout/boundary_region.hxx>
+#include <bout/bout_types.hxx>
+#include <bout/field2d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/mesh.hxx>
+#include <bout/region.hxx>
+
 #include <algorithm>
 #include <cmath>
 #include <cstdlib>
-#include <functional>
 #include <string>
 #include <vector>
 
-#include "bout/build_defines.hxx"
-#include "bout/field2d.hxx"
-#include "bout/region.hxx"
-#include "bout/sys/parallel_stencils.hxx"
-#include "bout/utils.hxx"
-#include <bout/field3d.hxx>
-#include <bout/mesh.hxx>
-
 /**
  * Boundary region for parallel direction. This contains a vector of points that are
  * inside the boundary.
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 35dea88b71..252610064d 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -1,7 +1,7 @@
 #pragma once
 
+#include "bout/boundary_region.hxx"
 #include "bout/boundary_region_iter.hxx"
-
 #include "bout/boutexception.hxx"
 #include "bout/field_data.hxx"
 #include "bout/mask.hxx"

From 463fb0872debb240d135f6c3c95a3fb9855a1302 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 24 Aug 2026 11:51:45 +0100
Subject: [PATCH 1769/1827] Simplify implementation of FCI boundary iterator

By storing a couple more bits of information in `BoundaryRegionFCI::Iterator`,
we can avoid having to store a `const BoundaryRegionFCI*` meaning we don't need
`const_cast` any more, and can make things more regularly `const` correct.
---
 include/bout/boundary_region_iter.hxx      | 140 ++++++++++-----------
 include/bout/parallel_boundary_op.hxx      |  12 +-
 include/bout/yboundary_regions.hxx         |  22 +---
 src/field/field3d.cxx                      |   2 +-
 src/mesh/yboundary_regions.cxx             |   2 +-
 tests/unit/include/bout/test_yboundary.cxx |  54 ++++----
 6 files changed, 109 insertions(+), 123 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 1a2670e0b6..0bcb717e77 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -38,8 +38,13 @@ concept function_accessor =
     and std::is_same_v<std::invoke_result_t<F, int, Ind3D>, BoutReal>;
 
 /// Interface for boundary iterators
+///
+/// The function passed into `YBoundary::iter`, for example, operates over
+/// elements of types derived from `BoundaryRegionIterBase`, but because this
+/// uses CRTP they can be a bit difficult to name. Instead use `BoundaryIterator
+/// auto` as the parameter type.
 template <class Iter>
-concept boundary_iterator = requires(Iter point, Field3D f) {
+concept BoundaryIterator = requires(Iter point, Field3D f) {
   point.getAt(f, int{});
   point.next(f);
   point.current(f);
@@ -205,23 +210,24 @@ public:
   /// Iterator over a `BoundaryRegionFCI`
   class Iterator : public BoundaryRegionIterBase<Iterator> {
   private:
-    // TODO(dave) make non-const?
-    const BoundaryRegionFCI* region;
-    size_t pos{0};
+    parallel_boundary_region::Indices index;
+    Mesh* localmesh_m;
+    int _dir;
 
   public:
     Iterator() = delete;
-    Iterator(const BoundaryRegionFCI* reg, bool isstart)
-        : region(reg), pos(isstart ? 0 : reg->bndry_points.size()) {}
-    void setValid(char valid) {
-      const_cast<BoundaryRegionFCI*>(region)->bndry_points[pos].valid = valid;
-    };
-    BoutReal s_x() const { return region->bndry_points[pos].intersection.s_x; };
-    BoutReal s_y() const { return region->bndry_points[pos].intersection.s_y; };
-    BoutReal s_z() const { return region->bndry_points[pos].intersection.s_z; };
-    Mesh* localmesh() const { return region->localmesh; };
-    int dir() const { return region->_dir; }
-    bool _is_lower() const { return region->_dir < 0; }
+    Iterator(parallel_boundary_region::Indices index, const BoundaryRegionFCI& rgn)
+        : index(index), localmesh_m(rgn.localmesh), _dir(rgn._dir) {}
+
+    void setValid(char valid) { index.valid = valid; };
+
+    BoutReal s_x() const { return index.intersection.s_x; };
+    BoutReal s_y() const { return index.intersection.s_y; };
+    BoutReal s_z() const { return index.intersection.s_z; };
+
+    Mesh* localmesh() const { return localmesh_m; };
+    int dir() const { return _dir; }
+    bool _is_lower() const { return _dir < 0; }
 
     template <bool check = true>
     BoutReal& _getAt(Field3D& f, int off) const {
@@ -229,7 +235,7 @@ public:
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
-      auto _off = _offset() - (off * region->_dir);
+      auto _off = _offset() - (off * _dir);
       return f.ynext(_off)[_ind().yp(_off)];
     }
     template <bool check = true>
@@ -238,7 +244,7 @@ public:
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
-      auto _off = _offset() - (off * region->_dir);
+      auto _off = _offset() - (off * _dir);
       return f.ynext(_off)[_ind().yp(_off)];
     }
     template <bool check = true>
@@ -247,7 +253,7 @@ public:
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
-      auto _off = _offset() - (off * region->_dir);
+      auto _off = _offset() - (off * _dir);
       return f.ynext(_off)[_ind().yp(_off)];
     }
     template <bool check = true>
@@ -256,7 +262,7 @@ public:
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
-      auto _off = _offset() - (off * region->_dir);
+      auto _off = _offset() - (off * _dir);
       return f.ynext(_off)[_ind().yp(_off)];
     }
     template <bool check = true>
@@ -264,36 +270,23 @@ public:
       if constexpr (check) {
         ASSERT3(valid() > -off - 2);
       }
-      auto _off = _offset() + (off * region->_dir);
+      auto _off = _offset() + (off * _dir);
       return f(_off, _ind().yp(_off));
     }
-    signed char _offset() const { return region->bndry_points[pos].offset; }
-    signed char _valid() const { return region->bndry_points[pos].valid; }
-    Ind3D _ind() const { return region->bndry_points[pos].index; }
-    int _boundary_width() const {
-      return region->localmesh->ystart - region->bndry_points[pos].abs_offset + 1;
-    }
+    signed char _offset() const { return index.offset; }
+    signed char _valid() const { return index.valid; }
+    Ind3D _ind() const { return index.index; }
+    int _boundary_width() const { return localmesh_m->ystart - index.abs_offset + 1; }
     BoutReal _length([[maybe_unused]] CELL_LOC loc) const {
       ASSERT3(loc == CELL_CENTRE);
-      return region->bndry_points[pos].length;
-    }
-
-    auto operator<=>(const Iterator& rhs) const {
-      ASSERT3(region == rhs.region);
-      return pos <=> rhs.pos;
+      return index.length;
     }
 
-    bool operator==(Iterator lhs) const {
-      ASSERT3(region == lhs.region);
-      return pos == lhs.pos;
-    }
+    auto operator<=>(const Iterator& rhs) const { return _ind() <=> rhs._ind(); }
+    bool operator==(Iterator rhs) const { return _ind() == rhs._ind(); }
 
-    Iterator& operator++() {
-      ++pos;
-      return *this;
-    }
-
-    Iterator& operator*() { return *this; }
+    friend auto operator<=>(const Iterator& lhs, Ind3D ind) { return lhs._ind() <=> ind; }
+    friend bool operator==(Iterator lhs, Ind3D ind) { return lhs._ind() == ind; }
   };
 
   BoundaryRegionFCI(const std::string& name, const BndryLoc& loc, int dir, Mesh* mesh)
@@ -303,12 +296,13 @@ public:
   /// Add a point to the boundary
   void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
                  char valid, signed char offset) {
-    if (!bndry_points.empty() && bndry_points.back().index > ind) {
+    if (!bndry_points.empty() && bndry_points.back()._ind() > ind) {
       is_sorted = false;
     }
-    bndry_points.emplace_back(ind, bout::parallel_boundary_region::RealPoint{x, y, z},
-                              length, valid, offset,
-                              static_cast<unsigned char>(std::abs(offset)));
+    auto index = parallel_boundary_region::Indices{
+        ind,    bout::parallel_boundary_region::RealPoint{x, y, z}, length, valid,
+        offset, static_cast<unsigned char>(std::abs(offset))};
+    bndry_points.emplace_back(index, *this);
   }
   void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
                  BoutReal length, char valid, signed char offset) {
@@ -319,7 +313,7 @@ public:
     ensureSorted();
     const auto found =
         std::lower_bound(std::begin(bndry_points), std::end(bndry_points), ind);
-    return found != std::end(bndry_points) and found->index == ind;
+    return found != std::end(bndry_points) and found->_ind() == ind;
   }
   int dir() const { return _dir; }
   // legacy interface
@@ -327,21 +321,23 @@ public:
   void next() override { throw BoutException("Legacy interface is not suppored"); }
   bool isDone() override { throw BoutException("Legacy interface is not suppored"); }
 
-  auto begin() const { return Iterator(this, true); }
-  auto end() const { return Iterator(this, false); }
+  auto begin() const { return bndry_points.begin(); }
+  auto end() const { return bndry_points.end(); }
+  auto begin() { return bndry_points.begin(); }
+  auto end() { return bndry_points.end(); }
 
 private:
   friend class Iterator;
   int _dir;
   // Vector of points in the boundary
-  bout::parallel_boundary_region::IndicesVec bndry_points;
+  std::vector<Iterator> bndry_points;
   Mesh* localmesh;
   bool is_sorted{true};
   void ensureSorted() {
     if (is_sorted) {
       return;
     }
-    std::sort(std::begin(bndry_points), std::end(bndry_points));
+    std::ranges::sort(bndry_points);
   }
   Ind3D xyz2ind(int x, int y, int z) const {
     const int ny = localmesh->LocalNy;
@@ -564,13 +560,13 @@ void iter_boundary(const Bndry& bndry, const Func& func) {
  */
 
 /// Extrapolate a given field to the boundary
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_boundary_o1(const Iter& point, const Field3D& f) {
   return point.current(f);
 }
 
 /// Extrapolate a given field to the boundary
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_boundary_o2(const Iter& point, const Field3D& f) {
   ASSERT3(point.valid() >= 0);
   if (point.valid() < 1) {
@@ -581,14 +577,14 @@ BoutReal extrapolate_boundary_o2(const Iter& point, const Field3D& f) {
 }
 
 /// Extrapolate a given function to the boundary
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_bounday_o1(const Iter& point, const function_accessor auto& func,
                                 [[maybe_unused]] CELL_LOC loc = CELL_CENTRE) {
   return point.current(func);
 }
 
 /// Extrapolate a given function to the boundary
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_boundary_o2(const Iter& point, const function_accessor auto& func,
                                  CELL_LOC loc = CELL_CENTRE) {
   ASSERT3(point.valid() >= 0);
@@ -600,25 +596,25 @@ BoutReal extrapolate_boundary_o2(const Iter& point, const function_accessor auto
 }
 
 /// Interpolate a field to the boundary, using the boundary values
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal interpolate_boundary_o2(const Iter& point, const Field3D& f) {
   return point.current(f) * (1 - point.length(f.getLocation()))
          + point.next(f) * point.length(f.getLocation());
 }
 /// Interpolate a field to the boundary, using the boundary values
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal interpolate_boundary_o2(const Iter& point, const function_accessor auto& func,
                                  CELL_LOC loc = CELL_CENTRE) {
   return point.current(func) * (1 - point.length(loc))
          + point.next(func) * point.length(loc);
 }
 /// Extrapolate to the first boundary value freely
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_next_o1(const Iter& point, const Field3D& f) {
   return point.current(f);
 }
 /// Extrapolate to the first boundary value freely
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_next_o2(const Iter& point, const Field3D& f) {
   ASSERT3(point.valid() >= 0);
   if (point.valid() < 1) {
@@ -628,12 +624,12 @@ BoutReal extrapolate_next_o2(const Iter& point, const Field3D& f) {
 }
 
 /// Extrapolate to the first boundary value freely
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_next_o1(const Iter& point, const function_accessor auto& func) {
   return point.current(func);
 }
 /// Extrapolate to the first boundary value freely
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_next_o2(const Iter& point, const function_accessor auto& func) {
   ASSERT3(point.valid() >= 0);
   if (point.valid() < 1) {
@@ -643,13 +639,13 @@ BoutReal extrapolate_next_o2(const Iter& point, const function_accessor auto& fu
 }
 
 /// extrapolate the gradient into the boundary
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_grad_o1([[maybe_unused]] const Iter& point,
                              [[maybe_unused]] const Field3D& f) {
   return 0;
 }
 /// extrapolate the gradient into the boundary
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_grad_o2(const Iter& point, const Field3D& f) {
   ASSERT3(point.valid() >= 0);
   if (point.valid() < 1) {
@@ -658,7 +654,7 @@ BoutReal extrapolate_grad_o2(const Iter& point, const Field3D& f) {
   return point.current(f) - point.next(f);
 }
 
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 BoutReal extrapolate_boundary_free(const Iter& point, const Field3D& f,
                                    BoundaryFreeExtrapolation mode) {
   BoutReal fac = BoutNaN;
@@ -677,7 +673,7 @@ BoutReal extrapolate_boundary_free(const Iter& point, const Field3D& f,
  */
 
 /// Apply a dirichlet boundary condition
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 void dirichlet_o1(const Iter& point, Field3D& f, BoutReal value) {
   for (int i = 0; i < point.boundary_width(); ++i) {
     point.getAt(f, -i) = value;
@@ -685,7 +681,7 @@ void dirichlet_o1(const Iter& point, Field3D& f, BoutReal value) {
 }
 
 /// Apply a dirichlet boundary condition
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 void dirichlet_o2(const Iter& point, Field3D& f, BoutReal value) {
   if (point.length(f.getLocation()) < point.smallValue()) {
     return dirichlet_o1(point, f, value);
@@ -697,7 +693,7 @@ void dirichlet_o2(const Iter& point, Field3D& f, BoutReal value) {
 }
 
 /// Apply a dirichlet boundary condition
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 void dirichlet_o3(const Iter& point, Field3D& f, BoutReal value) {
   ASSERT3(point.valid() >= 0);
   if (point.valid() < 1) {
@@ -718,7 +714,7 @@ void dirichlet_o3(const Iter& point, Field3D& f, BoutReal value) {
 }
 
 /// Ensure the value in the boundary is at least `value`
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 void limit_at_least(const Iter& point, Field3D& f, BoutReal value) {
   for (int i = 0; i < point.boundary_width(); ++i) {
     if (point.getAt(f, -i) < value) {
@@ -731,7 +727,7 @@ void limit_at_least(const Iter& point, Field3D& f, BoutReal value) {
 
 // neumann_o1 would give second order convergence, given an appropriate one-sided stencil.
 // But in general we do not, and thus for normal C2 stencils, this is 1st order.
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 void neumann_o1(const Iter& point, Field3D& f, BoutReal value) {
   for (int i = 0; i < point.boundary_width(); ++i) {
     point.getAt(f, -i) = point.current(f) + value * (i + 1);
@@ -739,7 +735,7 @@ void neumann_o1(const Iter& point, Field3D& f, BoutReal value) {
 }
 
 /// Apply neumann boundary condition, where `value` is the gradient in index space
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 void neumann_o2(const Iter& point, Field3D& f, BoutReal value) {
   ASSERT3(point.valid() >= 0);
   if (point.valid() < 1) {
@@ -751,7 +747,7 @@ void neumann_o2(const Iter& point, Field3D& f, BoutReal value) {
 }
 
 /// Apply neumann boundary condition, where `value` is the gradient in index space
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 void neumann_o3(const Iter& point, Field3D& f, BoutReal value) {
   ASSERT3(point.valid() >= 0);
   if (point.valid() < 1) {
@@ -764,7 +760,7 @@ void neumann_o3(const Iter& point, Field3D& f, BoutReal value) {
   }
 }
 
-template <boundary_iterator Iter>
+template <BoundaryIterator Iter>
 void set_free(const Iter& point, Field3D& f, BoundaryFreeExtrapolation mode) {
   BoutReal fac = BoutNaN;
   if (point.valid() > 0) {
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index c2b0dde90c..928fd4ee28 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -251,7 +251,7 @@ public:
 class BoundaryOpPar_dirichlet_o1 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o1> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <bout::boundary::boundary_iterator Iter>
+  template <bout::boundary::BoundaryIterator Iter>
   static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
     dirichlet_o1(pnt, f, value);
   }
@@ -260,7 +260,7 @@ public:
 class BoundaryOpPar_dirichlet_o2 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o2> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <bout::boundary::boundary_iterator Iter>
+  template <bout::boundary::BoundaryIterator Iter>
   static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
     dirichlet_o2(pnt, f, value);
   }
@@ -269,7 +269,7 @@ public:
 class BoundaryOpPar_dirichlet_o3 : public BoundaryOpParTemp<BoundaryOpPar_dirichlet_o3> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <bout::boundary::boundary_iterator Iter>
+  template <bout::boundary::BoundaryIterator Iter>
   static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
     dirichlet_o3(pnt, f, value);
   }
@@ -279,7 +279,7 @@ class BoundaryOpPar_neumann_o1
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o1, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <bout::boundary::boundary_iterator Iter>
+  template <bout::boundary::BoundaryIterator Iter>
   static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
     neumann_o1(pnt, f, value);
   }
@@ -289,7 +289,7 @@ class BoundaryOpPar_neumann_o2
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o2, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <bout::boundary::boundary_iterator Iter>
+  template <bout::boundary::BoundaryIterator Iter>
   static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
     neumann_o2(pnt, f, value);
   }
@@ -299,7 +299,7 @@ class BoundaryOpPar_neumann_o3
     : public BoundaryOpParTemp<BoundaryOpPar_neumann_o3, true> {
 public:
   using BoundaryOpParTemp::BoundaryOpParTemp;
-  template <bout::boundary::boundary_iterator Iter>
+  template <bout::boundary::BoundaryIterator Iter>
   static void apply_stencil(Field3D& f, Iter& pnt, BoutReal value) {
     neumann_o3(pnt, f, value);
   }
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 252610064d..1912fb2290 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -15,15 +15,6 @@ class Options;
 
 namespace bout {
 namespace boundary {
-/// Helper concept for functions to pass into `YBoundary::iter`
-///
-/// The function passed into `YBoundary::iter` operates over elements of types
-/// derived from `BoundaryRegionIterBase`, but because this uses CRTP they can
-/// be a bit difficult to name. Instead use `YBoundaryPoint auto` as the
-/// parameter type.
-template <class T>
-concept YBoundaryPoint = std::derived_from<T, BoundaryRegionIterBase<T>>;
-
 /// This class allows to simplify iterating over y-boundaries.
 ///
 /// It makes it easier to write code for FieldAligned boundaries, but if a bit
@@ -31,26 +22,25 @@ concept YBoundaryPoint = std::derived_from<T, BoundaryRegionIterBase<T>>;
 ///
 /// An example how to replace old code is given here:
 /// ../../manual/sphinx/user_docs/boundary_options.rst
-
 class YBoundary {
 public:
   YBoundary(YBndryType type, Options* options_ptr, const Mesh& mesh);
 
   /// Iterate over the boundary.
   /// This function takes a lamda / templated function, that applies the boundary on the given point.
-  /// The function must take a `const YBoundaryPoint auto& point` as its only argument.
+  /// The function must take a `const BoundaryIterator auto& point` as its only argument.
   /// See also the documentation at ../../manual/sphinx/user_docs/boundary_options.rst
   template <class F>
     requires std::regular_invocable<F&, const BoundaryRegionY::Iterator&>
              || std::regular_invocable<F&, const BoundaryRegionFCI::Iterator&>
-  void iter(F func) {
-    for (auto& region : boundary_regions) {
-      for (auto& point : *region) {
+  void iter(F func) const {
+    for (const auto& region : boundary_regions) {
+      for (const auto& point : *region) {
         func(point);
       }
     }
-    for (auto& region : boundary_regions_par) {
-      for (auto& point : *region) {
+    for (const auto& region : boundary_regions_par) {
+      for (const auto& point : *region) {
         func(point);
       }
     }
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index 5d0fbbcc0c..cb5d5f44d3 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -528,7 +528,7 @@ void Field3D::setBoundaryTo(const Field3D& f3d, bool copyParallelSlices,
   for (const auto& newreg : fieldmesh->getBoundaries()) {
     if (newreg->isX) {
       using namespace bout::boundary;
-      iter_boundary(newreg, [&](YBoundaryPoint auto& point) {
+      iter_boundary(newreg, [&](BoundaryIterator auto& point) {
         const BoutReal val = interpolate_boundary_o2(point, f3d);
         dirichlet_o2(point, *this, val);
       });
diff --git a/src/mesh/yboundary_regions.cxx b/src/mesh/yboundary_regions.cxx
index 2e1f9ab734..743e58ccc9 100644
--- a/src/mesh/yboundary_regions.cxx
+++ b/src/mesh/yboundary_regions.cxx
@@ -61,7 +61,7 @@ YBoundary::YBoundary(YBndryType type, Options* options_ptr, const Mesh& mesh)
     }
   }
   // Cache boundary regions
-  iter([&](const YBoundaryPoint auto& point) {
+  iter([&](const BoundaryIterator auto& point) {
     if (point.dir() == 1) {
       _contains_high[point.ind()] = true;
     } else if (point.dir() == -1) {
diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index 278ae90a8e..9c2b2b40de 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -13,15 +13,15 @@
 
 using YBTest = FakeMeshFixture_tmpl<4, 5, 7>;
 
+using bout::boundary::BoundaryIterator;
 using bout::boundary::YBoundary;
-using bout::boundary::YBoundaryPoint;
 using bout::globals::mesh;
 
 TEST_F(YBTest, dirichlet_o2_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) { dirichlet_o2(point, test, 2); });
+  sheath.iter([&](const BoundaryIterator auto& point) { dirichlet_o2(point, test, 2); });
   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }
 
@@ -29,7 +29,7 @@ TEST_F(YBTest, neumann_o1_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) { neumann_o1(point, test, 1); });
+  sheath.iter([&](const BoundaryIterator auto& point) { neumann_o1(point, test, 1); });
   EXPECT_TRUE(IsFieldEqual(test, 2.0, "RGN_YGUARDS"));
 }
 
@@ -37,7 +37,7 @@ TEST_F(YBTest, neumann_o2_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) { neumann_o2(point, test, 1); });
+  sheath.iter([&](const BoundaryIterator auto& point) { neumann_o2(point, test, 1); });
   EXPECT_TRUE(IsFieldEqual(test, 3.0, "RGN_YGUARDS"));
 }
 
@@ -45,7 +45,7 @@ TEST_F(YBTest, neumann_o3_rgn) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) { neumann_o3(point, test, 1); });
+  sheath.iter([&](const BoundaryIterator auto& point) { neumann_o3(point, test, 1); });
   EXPECT_TRUE(IsFieldEqual(test, 0.0, "RGN_YGUARDS"));
 }
 
@@ -53,14 +53,14 @@ TEST_F(YBTest, bndry_size) {
   dynamic_cast<FakeMesh*>(mesh)->createBoundaries();
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   int sum = 0;
-  sheath.iter([&]([[maybe_unused]] const YBoundaryPoint auto& point) { sum++; });
+  sheath.iter([&]([[maybe_unused]] const BoundaryIterator auto& point) { sum++; });
   EXPECT_EQ(sum, 28);
 }
 
 TEST_F(YBTest, interpolate_boundary_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 1.0);
   });
 }
@@ -68,7 +68,7 @@ TEST_F(YBTest, interpolate_boundary_o2) {
 TEST_F(YBTest, interpolate_boundary_o2_const) {
   const Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 1.0);
   });
 }
@@ -76,7 +76,7 @@ TEST_F(YBTest, interpolate_boundary_o2_const) {
 TEST_F(YBTest, extrapolate_boundary_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(extrapolate_boundary_o2(point, test), 1.0);
   });
 }
@@ -84,7 +84,7 @@ TEST_F(YBTest, extrapolate_boundary_o2) {
 TEST_F(YBTest, dirichlet_o1) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     dirichlet_o1(point, test, 2.0);
     EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 1.5);
   });
@@ -93,7 +93,7 @@ TEST_F(YBTest, dirichlet_o1) {
 TEST_F(YBTest, dirichlet_o2) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     dirichlet_o2(point, test, 2.0);
     EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 2.0);
   });
@@ -102,7 +102,7 @@ TEST_F(YBTest, dirichlet_o2) {
 TEST_F(YBTest, dirichlet_o3) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     dirichlet_o3(point, test, 2.0);
     EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 7. / 3.);
   });
@@ -112,7 +112,7 @@ TEST_F(YBTest, extrapolate_boundary_free) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2) + 1; }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   using namespace bout::boundary;
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(
         extrapolate_boundary_free(point, test, BoundaryFreeExtrapolation::limited), 3);
     EXPECT_DOUBLE_EQ(
@@ -126,7 +126,7 @@ TEST_F(YBTest, extrapolate_boundary_free) {
 TEST_F(YBTest, set_free) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2) + 1; }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     set_free(point, test, bout::boundary::BoundaryFreeExtrapolation::limited);
     EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 3);
   });
@@ -135,7 +135,7 @@ TEST_F(YBTest, set_free) {
 TEST_F(YBTest, interpolate_boundary_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 2.5);
   });
 }
@@ -143,7 +143,7 @@ TEST_F(YBTest, interpolate_boundary_o2_square) {
 TEST_F(YBTest, limit_at_least) {
   Field3D test = 1.0;
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     limit_at_least(point, test, 2.0);
     EXPECT_DOUBLE_EQ(interpolate_boundary_o2(point, test), 1.5);
   });
@@ -152,7 +152,7 @@ TEST_F(YBTest, limit_at_least) {
 TEST_F(YBTest, extrapolate_grad_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(extrapolate_grad_o2(point, test), 1);
   });
 }
@@ -160,7 +160,7 @@ TEST_F(YBTest, extrapolate_grad_o2_square) {
 TEST_F(YBTest, extrapolate_next_o1_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(extrapolate_next_o1(point, test), 1);
   });
 }
@@ -168,7 +168,7 @@ TEST_F(YBTest, extrapolate_next_o1_square) {
 TEST_F(YBTest, extrapolate_next_o2_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(extrapolate_next_o2(point, test), 2);
   });
 }
@@ -177,13 +177,13 @@ TEST_F(YBTest, next_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter(
-      [&](const YBoundaryPoint auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
+      [&](const BoundaryIterator auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
 }
 
 TEST_F(YBTest, current_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(point.current(test), 1);
   });
 }
@@ -192,20 +192,20 @@ TEST_F(YBTest, prev_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter(
-      [&](const YBoundaryPoint auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
+      [&](const BoundaryIterator auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
 }
 
 TEST_F(YBTest, next_const) {
   const Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter(
-      [&](const YBoundaryPoint auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
+      [&](const BoundaryIterator auto& point) { EXPECT_DOUBLE_EQ(point.next(test), 4); });
 }
 
 TEST_F(YBTest, current_const) {
   const Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(point.current(test), 1);
   });
 }
@@ -214,13 +214,13 @@ TEST_F(YBTest, prev_const) {
   const Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter(
-      [&](const YBoundaryPoint auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
+      [&](const BoundaryIterator auto& point) { EXPECT_DOUBLE_EQ(point.prev(test), 0); });
 }
 
 TEST_F(YBTest, getAt_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(point.getAt(test, 0), 4);
     EXPECT_DOUBLE_EQ(point.getAt(test, 1), 1);
     EXPECT_DOUBLE_EQ(point.getAt(test, 2), 0);
@@ -233,7 +233,7 @@ TEST_F(YBTest, getAt_func) {
   auto square = [&]([[maybe_unused]] int yo, Ind3D ind) -> BoutReal {
     return SQ(test[ind]);
   };
-  sheath.iter([&](const YBoundaryPoint auto& point) {
+  sheath.iter([&](const BoundaryIterator auto& point) {
     EXPECT_DOUBLE_EQ(point.getAt(square, 0), 4);
     EXPECT_DOUBLE_EQ(point.getAt(square, 1), 1);
     EXPECT_DOUBLE_EQ(point.getAt(square, 2), 0);

From cb4d6206e290d04db2046d1581da0ead6c9cbfaf Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 24 Aug 2026 16:43:25 +0100
Subject: [PATCH 1770/1827] Reduce duplicated accessor code with templates

This could be simplified a little further using a concept instead of `requires`
---
 include/bout/boundary_region_iter.hxx | 161 ++++++++++----------------
 1 file changed, 61 insertions(+), 100 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 0bcb717e77..a8ecbe1ea7 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -20,6 +20,7 @@
 #include <bout/parallel_boundary_region.hxx>
 #include <bout/region.hxx>
 #include <bout/sys/parallel_stencils.hxx>
+#include <bout/traits.hxx>
 #include <bout/utils.hxx>
 
 namespace bout {
@@ -90,10 +91,6 @@ public:
   /// For FA this is always ±1, for FCI this can be up to ±MYG, excluding 0
   int offset() const { return impl()._offset(); }
 
-  /*
-   *         FIELD3D ACCESSORS
-   */
-
   /// Get the value at a given \p offset of a field \p f.
   ///
   /// `offset = -1` is the second point in the boundary
@@ -105,62 +102,48 @@ public:
   /// -1  0 ^ 1   2
   ///       |
   ///    boundary
-  template <bool check = true>
-  BoutReal& getAt(Field3D& f, int offset) const {
+  template <bool check = true, class T>
+    requires utils::is_Field_v<T>
+  const BoutReal& getAt(const T& f, int offset) const {
     return impl().template _getAt<check>(f, offset);
   }
-  /// get the value at a given offset `off` of a field `f`.
-  template <bool check = true>
-  BoutReal getAt(const Field3D& f, int offset) const {
-    return impl().template _getAt<check>(f, offset);
-  }
-
-  /// Get the first point in the boundary
-  const BoutReal& next(const Field3D& f) const { return impl()._getAt(f, 0); }
-  /// Get the first point in the boundary
-  BoutReal& next(Field3D& f) const { return impl()._getAt(f, 0); }
-  /// Get the last point in the domain
-  const BoutReal& current(const Field3D& f) const { return impl()._getAt(f, 1); }
-  /// Get the last point in the domain
-  BoutReal& current(Field3D& f) const { return impl()._getAt(f, 1); }
-  /// Get the second to last point in the domain - this may not be valid and thus throw
-  const BoutReal& prev(const Field3D& f) const { return impl()._getAt(f, 2); }
-
-  /*
-   *         FIELD2D ACCESSORS
-   */
 
-  /// Get the value at a given \p offset of a field \p f.
-  ///
-  /// `offset = -1` is the second point in the boundary
-  /// `offset = 0` is the first point in the boundary
-  /// `offset = 1` is the last point in the domain
-  /// `offset = 2` is the second to last point in the domain
-  ///
-  /// |---|---|---|--> interior points
-  /// -1  0 ^ 1   2
-  ///       |
-  ///    boundary
-  template <bool check = true>
-  BoutReal& getAt(Field2D& f, int offset) const {
-    return impl().template _getAt<check>(f, offset);
-  }
-  /// get the value at a given offset `off` of a field `f`.
-  template <bool check = true>
-  BoutReal getAt(const Field2D& f, int offset) const {
+  template <bool check = true, class T>
+    requires utils::is_Field_v<T>
+  BoutReal& getAt(T& f, int offset) const {
     return impl().template _getAt<check>(f, offset);
   }
 
   /// Get the first point in the boundary
-  const BoutReal& next(const Field2D& f) const { return impl()._getAt(f, 0); }
+  template <class T>
+    requires utils::is_Field_v<T>
+  const BoutReal& next(const T& f) const {
+    return getAt(f, 0);
+  }
   /// Get the first point in the boundary
-  BoutReal& next(Field2D& f) const { return impl()._getAt(f, 0); }
+  template <class T>
+    requires utils::is_Field_v<T>
+  BoutReal& next(T& f) const {
+    return getAt(f, 0);
+  }
   /// Get the last point in the domain
-  const BoutReal& current(const Field2D& f) const { return impl()._getAt(f, 1); }
+  template <class T>
+    requires utils::is_Field_v<T>
+  const BoutReal& current(const T& f) const {
+    return getAt(f, 1);
+  }
   /// Get the last point in the domain
-  BoutReal& current(Field2D& f) const { return impl()._getAt(f, 1); }
+  template <class T>
+    requires utils::is_Field_v<T>
+  BoutReal& current(T& f) const {
+    return getAt(f, 1);
+  }
   /// Get the second to last point in the domain - this may not be valid and thus throw
-  const BoutReal& prev(const Field2D& f) const { return impl()._getAt(f, 2); }
+  template <class T>
+    requires utils::is_Field_v<T>
+  const BoutReal& prev(const T& f) const {
+    return getAt(f, 2);
+  }
 
   /*
    *         FUNCTIONS ACCESSORS
@@ -177,17 +160,11 @@ public:
     return impl().template _getAt<check>(func, offset);
   }
   /// Get the first point in the boundary
-  BoutReal next(const function_accessor auto& func) const {
-    return impl()._getAt(func, 0);
-  }
+  BoutReal next(const function_accessor auto& func) const { return getAt(func, 0); }
   /// Get the last point in the domain
-  BoutReal current(const function_accessor auto& func) const {
-    return impl()._getAt(func, 1);
-  }
+  BoutReal current(const function_accessor auto& func) const { return getAt(func, 1); }
   /// Get the second to last point in the domain - this may not be valid and thus throw
-  BoutReal prev(const function_accessor auto& func) const {
-    return impl()._getAt(func, 2);
-  }
+  BoutReal prev(const function_accessor auto& func) const { return getAt(func, 2); }
 
   void setSmallValue(BoutReal val) {
     ASSERT2(val > 0);
@@ -229,8 +206,9 @@ public:
     int dir() const { return _dir; }
     bool _is_lower() const { return _dir < 0; }
 
-    template <bool check = true>
-    BoutReal& _getAt(Field3D& f, int off) const {
+    template <bool check = true, class T>
+      requires utils::is_Field_v<T>
+    const BoutReal& _getAt(const T& f, int off) const {
       ASSERT3(f.hasParallelSlices());
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
@@ -238,26 +216,10 @@ public:
       auto _off = _offset() - (off * _dir);
       return f.ynext(_off)[_ind().yp(_off)];
     }
-    template <bool check = true>
-    const BoutReal& _getAt(const Field3D& f, int off) const {
-      ASSERT3(f.hasParallelSlices());
-      if constexpr (check) {
-        ASSERT3(_valid() > -off - 2);
-      }
-      auto _off = _offset() - (off * _dir);
-      return f.ynext(_off)[_ind().yp(_off)];
-    }
-    template <bool check = true>
-    BoutReal& _getAt(Field2D& f, int off) const {
-      ASSERT3(f.hasParallelSlices());
-      if constexpr (check) {
-        ASSERT3(_valid() > -off - 2);
-      }
-      auto _off = _offset() - (off * _dir);
-      return f.ynext(_off)[_ind().yp(_off)];
-    }
-    template <bool check = true>
-    const BoutReal& _getAt(const Field2D& f, int off) const {
+
+    template <bool check = true, class T>
+      requires utils::is_Field_v<T>
+    BoutReal& _getAt(T& f, int off) const {
       ASSERT3(f.hasParallelSlices());
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
@@ -265,6 +227,7 @@ public:
       auto _off = _offset() - (off * _dir);
       return f.ynext(_off)[_ind().yp(_off)];
     }
+
     template <bool check = true>
     BoutReal _getAt(const function_accessor auto& f, int off) const {
       if constexpr (check) {
@@ -273,6 +236,7 @@ public:
       auto _off = _offset() + (off * _dir);
       return f(_off, _ind().yp(_off));
     }
+
     signed char _offset() const { return index.offset; }
     signed char _valid() const { return index.valid; }
     Ind3D _ind() const { return index.index; }
@@ -293,6 +257,7 @@ public:
       : BoundaryRegionBase(name, loc, mesh), _dir(dir), localmesh(mesh) {
     isParallel = true;
   };
+
   /// Add a point to the boundary
   void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
                  char valid, signed char offset) {
@@ -304,10 +269,14 @@ public:
         offset, static_cast<unsigned char>(std::abs(offset))};
     bndry_points.emplace_back(index, *this);
   }
+
+  /// Add a point to the boundary
   void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
                  BoutReal length, char valid, signed char offset) {
     add_point(xyz2ind(ix, iy, iz), x, y, z, length, valid, offset);
   }
+
+  /// Return `true` if the boundary contains a point at the given index
   bool contains(int ix, int iy, int iz) {
     const auto ind = xyz2ind(ix, iy, iz);
     ensureSorted();
@@ -315,7 +284,10 @@ public:
         std::lower_bound(std::begin(bndry_points), std::end(bndry_points), ind);
     return found != std::end(bndry_points) and found->_ind() == ind;
   }
+
+  /// The direction of the boundary
   int dir() const { return _dir; }
+
   // legacy interface
   void first() override { throw BoutException("Legacy interface is not suppored"); }
   void next() override { throw BoutException("Legacy interface is not suppored"); }
@@ -376,38 +348,26 @@ public:
     int dir() const { return region->_dir; }
     Ind3D ind() const { return _ind(); }
 
-    template <bool check = true>
-    BoutReal& _getAt(Field3D& f, int off) const {
+    template <bool check = true, class T>
+      requires utils::is_Field_v<T>
+    const BoutReal& _getAt(const T& f, int off) const {
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
       auto _off = (1 - off) * region->_dir;
       return f[offsetInd(_off)];
     }
-    template <bool check = true>
-    const BoutReal& _getAt(const Field3D& f, int off) const {
-      if constexpr (check) {
-        ASSERT3(_valid() > -off - 2);
-      }
-      auto _off = (1 - off) * region->_dir;
-      return f[offsetInd(_off)];
-    }
-    template <bool check = true>
-    BoutReal& _getAt(Field2D& f, int off) const {
-      if constexpr (check) {
-        ASSERT3(_valid() > -off - 2);
-      }
-      auto _off = (1 - off) * region->_dir;
-      return f[offsetInd(_off)];
-    }
-    template <bool check = true>
-    const BoutReal& _getAt(const Field2D& f, int off) const {
+
+    template <bool check = true, class T>
+      requires utils::is_Field_v<T>
+    BoutReal& _getAt(T& f, int off) const {
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
       auto _off = (1 - off) * region->_dir;
       return f[offsetInd(_off)];
     }
+
     template <bool check = true>
     BoutReal _getAt(const function_accessor auto& f, int off) const {
       if constexpr (check) {
@@ -416,6 +376,7 @@ public:
       auto _off = (1 - off) * region->_dir;
       return f(0, offsetInd(_off));
     }
+
     signed char _offset() const { return region->_dir; }
     signed char _valid() const { return region->valid; }
     Ind3D _ind() const { return region->rgn[pos]; }

From 13a1fed939cb5be5be00f73e904453a07f81c59c Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Mon, 24 Aug 2026 16:50:05 +0100
Subject: [PATCH 1771/1827] Use concept to simplify function

---
 include/bout/boundary_region_iter.hxx | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index a8ecbe1ea7..cd847bad5e 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -506,11 +506,9 @@ void iter_boundary(const std::shared_ptr<const BoundaryRegionBase>& bndrybase,
                       bndrybase->label);
 }
 
-template <class Bndry, class Func,
-          typename = std::enable_if_t<std::is_base_of<BoundaryRegionBase, Bndry>::value>>
+template <class Bndry, class Func>
+  requires std::derived_from<Bndry, BoundaryRegionBase>
 void iter_boundary(const Bndry& bndry, const Func& func) {
-  static_assert(std::is_base_of<BoundaryRegionBase, Bndry>::value,
-                "Bndry must derive from BoundaryRegionY");
   for (auto& point : bndry) {
     func(point);
   }

From 5917d08a30b0f87691369e935ce864dc4b8e2012 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 25 Aug 2026 12:10:33 +0100
Subject: [PATCH 1772/1827] Remove comparison operators between region points
 and `Ind3D`

Replaced with call to `binary_search` with a projection so that the comparison
is now between two `Ind3D`s naturally

Also add a unit test to check `contains` works
---
 include/bout/boundary_region_iter.hxx         |  9 ++---
 tests/unit/CMakeLists.txt                     |  1 +
 .../unit/include/bout/test_boundary_iter.cxx  | 35 +++++++++++++++++++
 3 files changed, 38 insertions(+), 7 deletions(-)
 create mode 100644 tests/unit/include/bout/test_boundary_iter.cxx

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index cd847bad5e..7bc0b6329e 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -248,9 +248,6 @@ public:
 
     auto operator<=>(const Iterator& rhs) const { return _ind() <=> rhs._ind(); }
     bool operator==(Iterator rhs) const { return _ind() == rhs._ind(); }
-
-    friend auto operator<=>(const Iterator& lhs, Ind3D ind) { return lhs._ind() <=> ind; }
-    friend bool operator==(Iterator lhs, Ind3D ind) { return lhs._ind() == ind; }
   };
 
   BoundaryRegionFCI(const std::string& name, const BndryLoc& loc, int dir, Mesh* mesh)
@@ -278,11 +275,9 @@ public:
 
   /// Return `true` if the boundary contains a point at the given index
   bool contains(int ix, int iy, int iz) {
-    const auto ind = xyz2ind(ix, iy, iz);
     ensureSorted();
-    const auto found =
-        std::lower_bound(std::begin(bndry_points), std::end(bndry_points), ind);
-    return found != std::end(bndry_points) and found->_ind() == ind;
+    return std::ranges::binary_search(bndry_points, xyz2ind(ix, iy, iz), {},
+                                      [](const auto& point) { return point._ind(); });
   }
 
   /// The direction of the boundary
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 951230abc2..4384440c74 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -69,6 +69,7 @@ set(serial_tests_source
     ./include/bout/test_array.cxx
     ./include/bout/test_assert.cxx
     ./include/bout/test_bout_enum_class.cxx
+    ./include/bout/test_boundary_iter.cxx
     ./include/bout/test_deriv_store.cxx
     ./include/bout/test_fv_ops.cxx
     ./include/bout/test_generic_factory.cxx
diff --git a/tests/unit/include/bout/test_boundary_iter.cxx b/tests/unit/include/bout/test_boundary_iter.cxx
new file mode 100644
index 0000000000..686e564f78
--- /dev/null
+++ b/tests/unit/include/bout/test_boundary_iter.cxx
@@ -0,0 +1,35 @@
+#include "gtest/gtest.h"
+
+#include "bout/boundary_region.hxx"
+#include "bout/boundary_region_iter.hxx"
+
+#include "fake_mesh_fixture.hxx"
+
+using BoundaryIteratorTest = FakeMeshFixture;
+
+using namespace bout::boundary;
+
+TEST_F(BoundaryIteratorTest, Contains) {
+  BoundaryRegionFCI bndry{"test", BndryLoc::yup, +1, bout::globals::mesh};
+
+  bndry.add_point(1, 0, 3, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(1, 1, 3, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(1, 2, 3, 0.0, 0.0, 0.0, 0.0, 0, 0);
+
+  ASSERT_TRUE(bndry.contains(1, 2, 3));
+  ASSERT_FALSE(bndry.contains(1, 3, 3));
+  ASSERT_FALSE(bndry.contains(3, 2, 1));
+}
+
+TEST_F(BoundaryIteratorTest, SetValid) {
+  BoundaryRegionFCI bndry{"test", BndryLoc::yup, +1, bout::globals::mesh};
+
+  bndry.add_point(1, 2, 3, 0.0, 0.0, 0.0, 0.0, 0, 0);
+
+  for (auto& point : bndry) {
+    point.setValid(6);
+  }
+
+  const auto first = *bndry.begin();
+  ASSERT_EQ(first.valid(), 6);
+}

From f63ff77461af60debb26f1afe3f158603941136a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 25 Aug 2026 12:55:58 +0100
Subject: [PATCH 1773/1827] Fix some clang-tidy issues

---
 include/bout/boundary_region_iter.hxx                | 1 -
 include/bout/coordinates.hxx                         | 3 ++-
 src/mesh/coordinates.cxx                             | 1 +
 src/mesh/yboundary_regions.cxx                       | 1 +
 tests/integrated/test-fci-boundary/get_par_bndry.cxx | 6 +++---
 tests/unit/include/bout/test_yboundary.cxx           | 1 +
 6 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 7bc0b6329e..48a378612d 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -21,7 +21,6 @@
 #include <bout/region.hxx>
 #include <bout/sys/parallel_stencils.hxx>
 #include <bout/traits.hxx>
-#include <bout/utils.hxx>
 
 namespace bout {
 namespace boundary {
diff --git a/include/bout/coordinates.hxx b/include/bout/coordinates.hxx
index d7526f9023..a090dcd959 100644
--- a/include/bout/coordinates.hxx
+++ b/include/bout/coordinates.hxx
@@ -26,8 +26,9 @@
 #ifndef BOUT_COORDINATES_H
 #define BOUT_COORDINATES_H
 
-#include "bout/assert.hxx"
 #include "bout/field_data.hxx"
+#include <bout/assert.hxx>
+#include <bout/boundary_region.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/build_defines.hxx>
 #include <bout/christoffel_symbols.hxx>
diff --git a/src/mesh/coordinates.cxx b/src/mesh/coordinates.cxx
index 4e61276457..bad8ebbd84 100644
--- a/src/mesh/coordinates.cxx
+++ b/src/mesh/coordinates.cxx
@@ -4,6 +4,7 @@
  * given the contravariant metric tensor terms
  **************************************************************************/
 
+#include "bout/boundary_region.hxx"
 #include "bout/christoffel_symbols.hxx"
 #include "bout/coordinates_accessor.hxx"
 #include "bout/field3d.hxx"
diff --git a/src/mesh/yboundary_regions.cxx b/src/mesh/yboundary_regions.cxx
index 743e58ccc9..12036a6466 100644
--- a/src/mesh/yboundary_regions.cxx
+++ b/src/mesh/yboundary_regions.cxx
@@ -1,5 +1,6 @@
 #include "bout/yboundary_regions.hxx"
 
+#include "bout/boundary_region.hxx"
 #include "bout/boundary_region_iter.hxx"
 #include "bout/field_data.hxx"
 #include "bout/options.hxx"
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 098ec2ea4a..45fadc03c1 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -25,11 +25,11 @@ int main(int argc, char** argv) {
     const auto boundary = static_cast<BoundaryParType>(i);
     const auto boundary_name = toString(boundary);
     mesh->communicate(fields[i]);
-    for (auto& bndry_par : mesh->getBoundariesPar(static_cast<BoundaryParType>(i))) {
-      output.write("{:s} region\n", toString(static_cast<BoundaryParType>(i)));
+    for (auto& bndry_par : mesh->getBoundariesPar(boundary)) {
+      output.write("{:s} region\n", boundary_name);
       for (const auto& pnt : *bndry_par) {
         fields[i][pnt.ind()] += 1;
-        output.write("{:s} increment\n", toString(static_cast<BoundaryParType>(i)));
+        output.write("{:s} increment\n", boundary_name);
       }
     }
     output.write("{:s} done\n", boundary_name);
diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index 9c2b2b40de..44d8be4f3b 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -2,6 +2,7 @@
 
 #include "bout/boundary_common.hxx"
 #include "bout/boundary_region.hxx"
+#include "bout/boundary_region_iter.hxx"
 #include "bout/bout_types.hxx"
 #include "bout/field3d.hxx"
 #include "bout/region.hxx"

From a0e5803293ab61afe6d8ddce68ca7b31ce0f0c86 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 25 Aug 2026 13:03:45 +0100
Subject: [PATCH 1774/1827] Rename `BoundaryRegionFCI` inner class

Now no longer an iterator, but really a single point
---
 include/bout/boundary_region_iter.hxx | 16 ++++++++--------
 include/bout/parallel_boundary_op.hxx |  2 +-
 include/bout/yboundary_regions.hxx    |  2 +-
 src/mesh/parallel_boundary_op.cxx     |  2 +-
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 48a378612d..b908cac2f9 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -183,16 +183,16 @@ private:
 /// This can't use the legacy iteration methods (`first()`, `next()`, and so on)
 class BoundaryRegionFCI : public BoundaryRegionBase {
 public:
-  /// Iterator over a `BoundaryRegionFCI`
-  class Iterator : public BoundaryRegionIterBase<Iterator> {
+  /// A single point in a `BoundaryRegionFCI`
+  class Point : public BoundaryRegionIterBase<Point> {
   private:
     parallel_boundary_region::Indices index;
     Mesh* localmesh_m;
     int _dir;
 
   public:
-    Iterator() = delete;
-    Iterator(parallel_boundary_region::Indices index, const BoundaryRegionFCI& rgn)
+    Point() = delete;
+    Point(parallel_boundary_region::Indices index, const BoundaryRegionFCI& rgn)
         : index(index), localmesh_m(rgn.localmesh), _dir(rgn._dir) {}
 
     void setValid(char valid) { index.valid = valid; };
@@ -245,8 +245,8 @@ public:
       return index.length;
     }
 
-    auto operator<=>(const Iterator& rhs) const { return _ind() <=> rhs._ind(); }
-    bool operator==(Iterator rhs) const { return _ind() == rhs._ind(); }
+    auto operator<=>(const Point& rhs) const { return _ind() <=> rhs._ind(); }
+    bool operator==(Point rhs) const { return _ind() == rhs._ind(); }
   };
 
   BoundaryRegionFCI(const std::string& name, const BndryLoc& loc, int dir, Mesh* mesh)
@@ -293,10 +293,10 @@ public:
   auto end() { return bndry_points.end(); }
 
 private:
-  friend class Iterator;
+  friend class Point;
   int _dir;
   // Vector of points in the boundary
-  std::vector<Iterator> bndry_points;
+  std::vector<Point> bndry_points;
   Mesh* localmesh;
   bool is_sorted{true};
   void ensureSorted() {
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index 928fd4ee28..d2edb89b08 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -104,7 +104,7 @@ private:
   enum class ValueType { GEN, FIELD, REAL };
   const ValueType value_type{ValueType::REAL};
 
-  BoutReal getValue(const bout::boundary::BoundaryRegionFCI::Iterator& bndry, BoutReal t);
+  BoutReal getValue(const bout::boundary::BoundaryRegionFCI::Point& bndry, BoutReal t);
   BoutReal getValue(const bout::boundary::BoundaryRegionX::Iterator& bndry, BoutReal t);
   BoutReal getValue(const bout::boundary::BoundaryRegionY::Iterator& bndry, BoutReal t);
 
diff --git a/include/bout/yboundary_regions.hxx b/include/bout/yboundary_regions.hxx
index 1912fb2290..91dcd529e0 100644
--- a/include/bout/yboundary_regions.hxx
+++ b/include/bout/yboundary_regions.hxx
@@ -32,7 +32,7 @@ public:
   /// See also the documentation at ../../manual/sphinx/user_docs/boundary_options.rst
   template <class F>
     requires std::regular_invocable<F&, const BoundaryRegionY::Iterator&>
-             || std::regular_invocable<F&, const BoundaryRegionFCI::Iterator&>
+             || std::regular_invocable<F&, const BoundaryRegionFCI::Point&>
   void iter(F func) const {
     for (const auto& region : boundary_regions) {
       for (const auto& point : *region) {
diff --git a/src/mesh/parallel_boundary_op.cxx b/src/mesh/parallel_boundary_op.cxx
index 48a1743c4f..713825aaf4 100644
--- a/src/mesh/parallel_boundary_op.cxx
+++ b/src/mesh/parallel_boundary_op.cxx
@@ -8,7 +8,7 @@
 #include "bout/mesh.hxx"
 #include "bout/output.hxx"
 
-BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionFCI::Iterator& bndry,
+BoutReal BoundaryOpPar::getValue(const bout::boundary::BoundaryRegionFCI::Point& bndry,
                                  BoutReal t) {
   switch (value_type) {
   case ValueType::GEN:

From 5dd7e5c60c699021e25f4ce75469b4d7a8bc73f5 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 25 Aug 2026 13:10:30 +0100
Subject: [PATCH 1775/1827] Rename `BoundaryRegionIterBase::getAt` -> `::at`

More in line with stdlib naming such as `std::vector::at`
---
 include/bout/boundary_region_iter.hxx      | 66 +++++++++++-----------
 tests/unit/include/bout/test_yboundary.cxx | 14 ++---
 2 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index b908cac2f9..02a09ac9fe 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -25,7 +25,7 @@
 namespace bout {
 namespace boundary {
 
-/// Helper concept for `BoundaryRegionIterBase::getAt` function accessor overloads
+/// Helper concept for `BoundaryRegionIterBase::at` function accessor overloads
 ///
 /// This is a callable that takes two arguments:
 /// - `int yoffset`, the parallel slice offset
@@ -45,7 +45,7 @@ concept function_accessor =
 /// auto` as the parameter type.
 template <class Iter>
 concept BoundaryIterator = requires(Iter point, Field3D f) {
-  point.getAt(f, int{});
+  point.at(f, int{});
   point.next(f);
   point.current(f);
   point.prev(f);
@@ -103,45 +103,45 @@ public:
   ///    boundary
   template <bool check = true, class T>
     requires utils::is_Field_v<T>
-  const BoutReal& getAt(const T& f, int offset) const {
-    return impl().template _getAt<check>(f, offset);
+  const BoutReal& at(const T& f, int offset) const {
+    return impl().template _at<check>(f, offset);
   }
 
   template <bool check = true, class T>
     requires utils::is_Field_v<T>
-  BoutReal& getAt(T& f, int offset) const {
-    return impl().template _getAt<check>(f, offset);
+  BoutReal& at(T& f, int offset) const {
+    return impl().template _at<check>(f, offset);
   }
 
   /// Get the first point in the boundary
   template <class T>
     requires utils::is_Field_v<T>
   const BoutReal& next(const T& f) const {
-    return getAt(f, 0);
+    return at(f, 0);
   }
   /// Get the first point in the boundary
   template <class T>
     requires utils::is_Field_v<T>
   BoutReal& next(T& f) const {
-    return getAt(f, 0);
+    return at(f, 0);
   }
   /// Get the last point in the domain
   template <class T>
     requires utils::is_Field_v<T>
   const BoutReal& current(const T& f) const {
-    return getAt(f, 1);
+    return at(f, 1);
   }
   /// Get the last point in the domain
   template <class T>
     requires utils::is_Field_v<T>
   BoutReal& current(T& f) const {
-    return getAt(f, 1);
+    return at(f, 1);
   }
   /// Get the second to last point in the domain - this may not be valid and thus throw
   template <class T>
     requires utils::is_Field_v<T>
   const BoutReal& prev(const T& f) const {
-    return getAt(f, 2);
+    return at(f, 2);
   }
 
   /*
@@ -155,15 +155,15 @@ public:
   ///       |
   ///    boundary
   template <bool check = true>
-  BoutReal getAt(const function_accessor auto& func, int offset) const {
-    return impl().template _getAt<check>(func, offset);
+  BoutReal at(const function_accessor auto& func, int offset) const {
+    return impl().template _at<check>(func, offset);
   }
   /// Get the first point in the boundary
-  BoutReal next(const function_accessor auto& func) const { return getAt(func, 0); }
+  BoutReal next(const function_accessor auto& func) const { return at(func, 0); }
   /// Get the last point in the domain
-  BoutReal current(const function_accessor auto& func) const { return getAt(func, 1); }
+  BoutReal current(const function_accessor auto& func) const { return at(func, 1); }
   /// Get the second to last point in the domain - this may not be valid and thus throw
-  BoutReal prev(const function_accessor auto& func) const { return getAt(func, 2); }
+  BoutReal prev(const function_accessor auto& func) const { return at(func, 2); }
 
   void setSmallValue(BoutReal val) {
     ASSERT2(val > 0);
@@ -207,7 +207,7 @@ public:
 
     template <bool check = true, class T>
       requires utils::is_Field_v<T>
-    const BoutReal& _getAt(const T& f, int off) const {
+    const BoutReal& _at(const T& f, int off) const {
       ASSERT3(f.hasParallelSlices());
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
@@ -218,7 +218,7 @@ public:
 
     template <bool check = true, class T>
       requires utils::is_Field_v<T>
-    BoutReal& _getAt(T& f, int off) const {
+    BoutReal& _at(T& f, int off) const {
       ASSERT3(f.hasParallelSlices());
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
@@ -228,7 +228,7 @@ public:
     }
 
     template <bool check = true>
-    BoutReal _getAt(const function_accessor auto& f, int off) const {
+    BoutReal _at(const function_accessor auto& f, int off) const {
       if constexpr (check) {
         ASSERT3(valid() > -off - 2);
       }
@@ -344,7 +344,7 @@ public:
 
     template <bool check = true, class T>
       requires utils::is_Field_v<T>
-    const BoutReal& _getAt(const T& f, int off) const {
+    const BoutReal& _at(const T& f, int off) const {
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
@@ -354,7 +354,7 @@ public:
 
     template <bool check = true, class T>
       requires utils::is_Field_v<T>
-    BoutReal& _getAt(T& f, int off) const {
+    BoutReal& _at(T& f, int off) const {
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
@@ -363,7 +363,7 @@ public:
     }
 
     template <bool check = true>
-    BoutReal _getAt(const function_accessor auto& f, int off) const {
+    BoutReal _at(const function_accessor auto& f, int off) const {
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
@@ -629,7 +629,7 @@ BoutReal extrapolate_boundary_free(const Iter& point, const Field3D& f,
 template <BoundaryIterator Iter>
 void dirichlet_o1(const Iter& point, Field3D& f, BoutReal value) {
   for (int i = 0; i < point.boundary_width(); ++i) {
-    point.getAt(f, -i) = value;
+    point.at(f, -i) = value;
   }
 }
 
@@ -640,7 +640,7 @@ void dirichlet_o2(const Iter& point, Field3D& f, BoutReal value) {
     return dirichlet_o1(point, f, value);
   }
   for (int i = 0; i < point.boundary_width(); ++i) {
-    point.getAt(f, -i) = parallel_stencil::dirichlet_o2(
+    point.at(f, -i) = parallel_stencil::dirichlet_o2(
         i + 1, point.current(f), i + 1 - point.length(f.getLocation()), value);
   }
 }
@@ -654,12 +654,12 @@ void dirichlet_o3(const Iter& point, Field3D& f, BoutReal value) {
   }
   if (point.length(f.getLocation()) < point.smallValue()) {
     for (int i = 0; i < point.boundary_width(); ++i) {
-      point.getAt(f, -i) = parallel_stencil::dirichlet_o2(
+      point.at(f, -i) = parallel_stencil::dirichlet_o2(
           i + 2, point.prev(f), i + 1 - point.length(f.getLocation()), value);
     }
   } else {
     for (int i = 0; i < point.boundary_width(); ++i) {
-      point.getAt(f, -i) =
+      point.at(f, -i) =
           parallel_stencil::dirichlet_o3(i + 2, point.prev(f), i + 1, point.current(f),
                                          i + 1 - point.length(f.getLocation()), value);
     }
@@ -670,8 +670,8 @@ void dirichlet_o3(const Iter& point, Field3D& f, BoutReal value) {
 template <BoundaryIterator Iter>
 void limit_at_least(const Iter& point, Field3D& f, BoutReal value) {
   for (int i = 0; i < point.boundary_width(); ++i) {
-    if (point.getAt(f, -i) < value) {
-      point.getAt(f, -i) = value;
+    if (point.at(f, -i) < value) {
+      point.at(f, -i) = value;
     }
   }
 }
@@ -683,7 +683,7 @@ void limit_at_least(const Iter& point, Field3D& f, BoutReal value) {
 template <BoundaryIterator Iter>
 void neumann_o1(const Iter& point, Field3D& f, BoutReal value) {
   for (int i = 0; i < point.boundary_width(); ++i) {
-    point.getAt(f, -i) = point.current(f) + value * (i + 1);
+    point.at(f, -i) = point.current(f) + value * (i + 1);
   }
 }
 
@@ -695,7 +695,7 @@ void neumann_o2(const Iter& point, Field3D& f, BoutReal value) {
     return neumann_o1(point, f, value);
   }
   for (int i = 0; i < point.boundary_width(); ++i) {
-    point.getAt(f, -i) = point.prev(f) + (2 + i) * value;
+    point.at(f, -i) = point.prev(f) + (2 + i) * value;
   }
 }
 
@@ -707,7 +707,7 @@ void neumann_o3(const Iter& point, Field3D& f, BoutReal value) {
     return neumann_o2(point, f, value);
   }
   for (int i = 0; i < point.boundary_width(); ++i) {
-    point.getAt(f, -i) =
+    point.at(f, -i) =
         parallel_stencil::neumann_o3(i + 1 - point.length(f.getLocation()), value, i + 1,
                                      point.current(f), 2, point.prev(f));
   }
@@ -725,12 +725,12 @@ void set_free(const Iter& point, Field3D& f, BoundaryFreeExtrapolation mode) {
   if (mode == BoundaryFreeExtrapolation::linear) {
     for (int i = 0; i < point.boundary_width(); ++i) {
       val += fac;
-      point.getAt(f, -i) = val;
+      point.at(f, -i) = val;
     }
   } else {
     for (int i = 0; i < point.boundary_width(); ++i) {
       val *= fac;
-      point.getAt(f, -i) = val;
+      point.at(f, -i) = val;
     }
   }
 }
diff --git a/tests/unit/include/bout/test_yboundary.cxx b/tests/unit/include/bout/test_yboundary.cxx
index 44d8be4f3b..34808dea30 100644
--- a/tests/unit/include/bout/test_yboundary.cxx
+++ b/tests/unit/include/bout/test_yboundary.cxx
@@ -222,21 +222,21 @@ TEST_F(YBTest, getAt_square) {
   Field3D test = makeField<Field3D>([&](auto& i) { return SQ(i.y() - 2); }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   sheath.iter([&](const BoundaryIterator auto& point) {
-    EXPECT_DOUBLE_EQ(point.getAt(test, 0), 4);
-    EXPECT_DOUBLE_EQ(point.getAt(test, 1), 1);
-    EXPECT_DOUBLE_EQ(point.getAt(test, 2), 0);
+    EXPECT_DOUBLE_EQ(point.at(test, 0), 4);
+    EXPECT_DOUBLE_EQ(point.at(test, 1), 1);
+    EXPECT_DOUBLE_EQ(point.at(test, 2), 0);
   });
 }
 
-TEST_F(YBTest, getAt_func) {
+TEST_F(YBTest, at_func) {
   Field3D test = makeField<Field3D>([&](auto& i) { return i.y() - 2; }, mesh);
   YBoundary sheath(YBndryType::all, nullptr, *mesh);
   auto square = [&]([[maybe_unused]] int yo, Ind3D ind) -> BoutReal {
     return SQ(test[ind]);
   };
   sheath.iter([&](const BoundaryIterator auto& point) {
-    EXPECT_DOUBLE_EQ(point.getAt(square, 0), 4);
-    EXPECT_DOUBLE_EQ(point.getAt(square, 1), 1);
-    EXPECT_DOUBLE_EQ(point.getAt(square, 2), 0);
+    EXPECT_DOUBLE_EQ(point.at(square, 0), 4);
+    EXPECT_DOUBLE_EQ(point.at(square, 1), 1);
+    EXPECT_DOUBLE_EQ(point.at(square, 2), 0);
   });
 }

From dd0d345def7fa6d54f625693390b2d5e2ae40700 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Tue, 25 Aug 2026 17:33:58 +0100
Subject: [PATCH 1776/1827] Ensure we're looking at the same FCI boundary in
 comparisons

---
 include/bout/boundary_region_iter.hxx | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 02a09ac9fe..0154bd75bf 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -245,8 +245,15 @@ public:
       return index.length;
     }
 
-    auto operator<=>(const Point& rhs) const { return _ind() <=> rhs._ind(); }
-    bool operator==(Point rhs) const { return _ind() == rhs._ind(); }
+    auto operator<=>(const Point& rhs) const {
+      // Ensure we're looking at the same boundary
+      ASSERT3(_dir == rhs._dir);
+      return _ind() <=> rhs._ind();
+    }
+    bool operator==(Point rhs) const {
+      ASSERT3(_dir == rhs._dir);
+      return _ind() == rhs._ind();
+    }
   };
 
   BoundaryRegionFCI(const std::string& name, const BndryLoc& loc, int dir, Mesh* mesh)

From 4641835c046a734367a1790a682b847f1f45602f Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 25 Aug 2026 10:46:35 -0700
Subject: [PATCH 1777/1827] Apply suggestions from code review

Co-authored-by: Peter Hill <zed.three@gmail.com>
Co-authored-by: Ben Dudson <dudson2@llnl.gov>
---
 include/bout/petsc_preconditioner.hxx | 2 +-
 include/bout/solver.hxx               | 2 +-
 src/solver/impls/cvode/cvode.cxx      | 5 ++++-
 src/solver/impls/cvode/cvode.hxx      | 2 +-
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/include/bout/petsc_preconditioner.hxx b/include/bout/petsc_preconditioner.hxx
index 877c52358d..98fb195952 100644
--- a/include/bout/petsc_preconditioner.hxx
+++ b/include/bout/petsc_preconditioner.hxx
@@ -13,7 +13,7 @@
 #include "bout/bout_enum_class.hxx"
 #include "bout/build_defines.hxx"
 
-BOUT_ENUM_CLASS(PetscMatrixExportFormat, binary, ascii);
+BOUT_ENUM_CLASS_NS(bout, PetscMatrixExportFormat, binary, ascii);
 
 #if BOUT_HAS_PETSC
 
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index ade7475206..c80833bd04 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -102,7 +102,7 @@ constexpr auto SOLVERRKGENERIC = "rkgeneric";
 enum class FieldCategories : std::uint8_t { VARS, DERIVS, MMS };
 enum class SOLVER_VAR_OP : std::uint8_t { LOAD, SET_ID, SAVE };
 
-BOUT_ENUM_CLASS(
+BOUT_ENUM_CLASS_NS(bout
     JacobianExportKind,
     system, ///< Jacobian of the full nonlinear system solved by the solver
     scaled, ///< Jacobian after solver-coordinate transforms such as variable scaling
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index d96be8df02..9527745aa9 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -37,6 +37,7 @@
 #include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
+#include "bout/build_config.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
@@ -45,6 +46,7 @@
 #include "bout/msg_stack.hxx"
 #include "bout/options.hxx"
 #include "bout/output.hxx"
+#include "bout/petsc_preconditioner.hxx"
 #include "bout/petsclib.hxx"
 #include "bout/region.hxx"
 #include "bout/solver.hxx"
@@ -52,6 +54,7 @@
 #include "bout/unused.hxx"
 
 #include "fmt/core.h"
+#include "fmt/format.h"
 
 #include <cvode/cvode.h>
 #include <cvode/cvode_bbdpre.h>
@@ -344,7 +347,7 @@ PetscErrorCode CvodeSolver::maybeExportOutputJacobian(BoutReal t) {
   save_vars(xdata);
   PetscCall(VecRestoreArray(x, &xdata));
 
-  PetscErrorCode ierr = saveDiagnosticJacobian(JacobianExportKind::rhs, x, t, 0.0);
+  const PetscErrorCode ierr = saveDiagnosticJacobian(JacobianExportKind::rhs, x, t, 0.0);
   PetscCall(VecDestroy(&x));
   PetscFunctionReturn(ierr);
 }
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index e17cda4624..b3093c8106 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -68,7 +68,7 @@ RegisterSolver<CvodeSolver> registersolvercvode("cvode");
 // Preconditioner selection for CVODE.
 // Note: String comparisons are case-insensitive so "Auto" avoids conflict with keyword
 BOUT_ENUM_CLASS(CvodePreconMethod, none, Auto, user, petsc, bbd);
-BOUT_ENUM_CLASS(CvodeJacobianExportTrigger,
+BOUT_ENUM_CLASS_NS(bout, CvodeJacobianExportTrigger,
                 output,      ///< Export once per solver output timestep
                 linear_setup ///< Export whenever CVODE rebuilds linear solver data
 );

From 987793618ac958b0e623ee686fea0b466be399ac Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 25 Aug 2026 11:45:31 -0700
Subject: [PATCH 1778/1827] Solvers: Namespace enums

---
 include/bout/petsc_preconditioner.hxx | 18 +++----
 include/bout/solver.hxx               | 18 ++-----
 src/solver/impls/cvode/cvode.cxx      | 69 ++++++++++++++-------------
 src/solver/impls/cvode/cvode.hxx      | 17 ++++---
 src/solver/impls/snes/snes.cxx        | 21 ++++----
 src/solver/impls/snes/snes.hxx        |  9 ++--
 src/solver/petsc_preconditioner.cxx   |  9 ++--
 7 files changed, 79 insertions(+), 82 deletions(-)

diff --git a/include/bout/petsc_preconditioner.hxx b/include/bout/petsc_preconditioner.hxx
index 98fb195952..36ece0b06e 100644
--- a/include/bout/petsc_preconditioner.hxx
+++ b/include/bout/petsc_preconditioner.hxx
@@ -84,13 +84,13 @@ public:
   /// writes the matrix itself in PETSc binary or ASCII format; companion metadata
   /// such as variable names and index mapping must be written separately by the
   /// calling solver.
-  static PetscErrorCode
-  saveMatrix(Mat matrix, const std::string& filename,
-             PetscMatrixExportFormat format = PetscMatrixExportFormat::binary);
+  static PetscErrorCode saveMatrix(
+      Mat matrix, const std::string& filename,
+      bout::PetscMatrixExportFormat format = bout::PetscMatrixExportFormat::binary);
   /// Save the internally owned coloring Jacobian matrix ``Jfd``.
-  PetscErrorCode
-  saveMatrix(const std::string& filename,
-             PetscMatrixExportFormat format = PetscMatrixExportFormat::binary) const;
+  PetscErrorCode saveMatrix(
+      const std::string& filename,
+      bout::PetscMatrixExportFormat format = bout::PetscMatrixExportFormat::binary) const;
 
   void reset();
 
@@ -105,9 +105,9 @@ private:
 // unconditionally in PETSc-enabled compilation units.
 class PetscPreconditioner {
 public:
-  void saveMatrix(
-      const std::string& UNUSED(filename),
-      PetscMatrixExportFormat UNUSED(format) = PetscMatrixExportFormat::binary) const {}
+  void saveMatrix(const std::string& UNUSED(filename),
+                  bout::PetscMatrixExportFormat UNUSED(format) =
+                      bout::PetscMatrixExportFormat::binary) const {}
   void reset() {}
 };
 
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index c80833bd04..388011d337 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -1,20 +1,10 @@
 /**************************************************************************
  * Base class for all solvers. Specifies required interface functions
  *
- * Changelog:
- *
- * 2009-08 Ben Dudson, Sean Farley
- *    * Major overhaul, and changed API. Trying to make consistent
- *      interface to PETSc and SUNDIALS solvers
- *
- * 2013-08 Ben Dudson
- *    * Added OO-style API, to allow multiple physics models to coexist
- *      For now both APIs are supported
- *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -102,8 +92,8 @@ constexpr auto SOLVERRKGENERIC = "rkgeneric";
 enum class FieldCategories : std::uint8_t { VARS, DERIVS, MMS };
 enum class SOLVER_VAR_OP : std::uint8_t { LOAD, SET_ID, SAVE };
 
-BOUT_ENUM_CLASS_NS(bout
-    JacobianExportKind,
+BOUT_ENUM_CLASS_NS(
+    bout, JacobianExportKind,
     system, ///< Jacobian of the full nonlinear system solved by the solver
     scaled, ///< Jacobian after solver-coordinate transforms such as variable scaling
     rhs     ///< Jacobian of the raw model RHS in physical variables
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 9527745aa9..20b498252b 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -71,10 +71,10 @@
 #include <string>
 #include <vector>
 
-BOUT_ENUM_CLASS(positivity_constraint, none, positive, non_negative, negative,
-                non_positive);
+BOUT_ENUM_CLASS_NS(bout, positivity_constraint, none, positive, non_negative, negative,
+                   non_positive);
 
-BOUT_ENUM_CLASS(linear_solver, gmres, fgmres, tfqmr, bcgs);
+BOUT_ENUM_CLASS_NS(bout, linear_solver, gmres, fgmres, tfqmr, bcgs);
 
 // NOLINTBEGIN(readability-identifier-length)
 namespace {
@@ -175,11 +175,11 @@ CvodeSolver::CvodeSolver(Options* opts)
       jacobian_export_kind((*options)["jacobian_export_kind"]
                                .doc("Which Jacobian to save for CVODE: system or rhs "
                                     "(scaled is not supported)")
-                               .withDefault(JacobianExportKind::system)),
+                               .withDefault(bout::JacobianExportKind::system)),
       jacobian_export_trigger(
           (*options)["jacobian_export_trigger"]
               .doc("When to save CVODE Jacobians: output or linear_setup")
-              .withDefault(CvodeJacobianExportTrigger::linear_setup)),
+              .withDefault(bout::CvodeJacobianExportTrigger::linear_setup)),
       jacobian_export_prefix(
           (*options)["jacobian_export_prefix"]
               .doc("Prefix for saved Jacobian matrix files and shared metadata JSON")
@@ -187,7 +187,7 @@ CvodeSolver::CvodeSolver(Options* opts)
       jacobian_export_format(
           (*options)["jacobian_export_format"]
               .doc("PETSc MatView format for saved Jacobians: binary or ascii")
-              .withDefault(PetscMatrixExportFormat::binary)),
+              .withDefault(bout::PetscMatrixExportFormat::binary)),
       suncontext(createSUNContext(BoutComm::get())) {
   has_constraints = false; // This solver doesn't have constraints
   canReset = true;
@@ -246,7 +246,7 @@ CvodeSolver::~CvodeSolver() {
 }
 
 #if BOUT_HAS_PETSC
-std::string CvodeSolver::getJacobianExportStem(JacobianExportKind kind) {
+std::string CvodeSolver::getJacobianExportStem(bout::JacobianExportKind kind) {
   const std::string datadir = Options::root()["datadir"];
   return fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix, toString(kind),
                      jacobian_export_counter++);
@@ -254,7 +254,8 @@ std::string CvodeSolver::getJacobianExportStem(JacobianExportKind kind) {
 
 std::string CvodeSolver::getJacobianMatrixFilename(const std::string& stem) const {
   return stem
-         + (jacobian_export_format == PetscMatrixExportFormat::binary ? ".dat" : ".txt");
+         + (jacobian_export_format == bout::PetscMatrixExportFormat::binary ? ".dat"
+                                                                            : ".txt");
 }
 
 PetscErrorCode CvodeSolver::exportMatrixAndMetadata(Mat jacobian,
@@ -272,9 +273,9 @@ PetscErrorCode CvodeSolver::exportMatrixAndMetadata(Mat jacobian,
   PetscFunctionReturn(PETSC_SUCCESS);
 }
 
-PetscErrorCode CvodeSolver::saveDiagnosticJacobian(JacobianExportKind kind, Vec x,
+PetscErrorCode CvodeSolver::saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x,
                                                    BoutReal t, BoutReal gamma) {
-  if (kind == JacobianExportKind::scaled) {
+  if (kind == bout::JacobianExportKind::scaled) {
     throw BoutException("solver:jacobian_export_kind=scaled is not supported for CVODE");
   }
 
@@ -286,7 +287,7 @@ PetscErrorCode CvodeSolver::saveDiagnosticJacobian(JacobianExportKind kind, Vec
   PetscCall(diagnostic_preconditioner.createJacobianPattern(
       index, *options, getLocalN(), n2Dvars(), n3Dvars(), BoutComm::get()));
 
-  if (kind == JacobianExportKind::rhs) {
+  if (kind == bout::JacobianExportKind::rhs) {
     PetscCall(diagnostic_preconditioner.updateColoring(CvodeSolver::petscFormRhsFunction,
                                                        this));
   } else {
@@ -296,7 +297,7 @@ PetscErrorCode CvodeSolver::saveDiagnosticJacobian(JacobianExportKind kind, Vec
 
   Vec diagnostic_f{nullptr};
   PetscCall(VecDuplicate(x, &diagnostic_f));
-  if (kind == JacobianExportKind::rhs) {
+  if (kind == bout::JacobianExportKind::rhs) {
     PetscCall(CvodeSolver::petscFormRhsFunction(nullptr, x, diagnostic_f, this));
   } else {
     PetscCall(CvodeSolver::petscFormFunction(nullptr, x, diagnostic_f, this));
@@ -318,11 +319,11 @@ PetscErrorCode CvodeSolver::saveDiagnosticJacobian(JacobianExportKind kind, Vec
 PetscErrorCode CvodeSolver::maybeExportJacobian(Mat system_jacobian, Vec x, BoutReal t,
                                                 BoutReal gamma) {
   if (!save_jacobian
-      or jacobian_export_trigger != CvodeJacobianExportTrigger::linear_setup) {
+      or jacobian_export_trigger != bout::CvodeJacobianExportTrigger::linear_setup) {
     PetscFunctionReturn(PETSC_SUCCESS);
   }
 
-  if (jacobian_export_kind == JacobianExportKind::system) {
+  if (jacobian_export_kind == bout::JacobianExportKind::system) {
     PetscCall(exportMatrixAndMetadata(system_jacobian,
                                       getJacobianExportStem(jacobian_export_kind)));
     PetscFunctionReturn(PETSC_SUCCESS);
@@ -332,7 +333,8 @@ PetscErrorCode CvodeSolver::maybeExportJacobian(Mat system_jacobian, Vec x, Bout
 }
 
 PetscErrorCode CvodeSolver::maybeExportOutputJacobian(BoutReal t) {
-  if (!save_jacobian or jacobian_export_trigger != CvodeJacobianExportTrigger::output) {
+  if (!save_jacobian
+      or jacobian_export_trigger != bout::CvodeJacobianExportTrigger::output) {
     PetscFunctionReturn(PETSC_SUCCESS);
   }
 
@@ -347,7 +349,8 @@ PetscErrorCode CvodeSolver::maybeExportOutputJacobian(BoutReal t) {
   save_vars(xdata);
   PetscCall(VecRestoreArray(x, &xdata));
 
-  const PetscErrorCode ierr = saveDiagnosticJacobian(JacobianExportKind::rhs, x, t, 0.0);
+  const PetscErrorCode ierr =
+      saveDiagnosticJacobian(bout::JacobianExportKind::rhs, x, t, 0.0);
   PetscCall(VecDestroy(&x));
   PetscFunctionReturn(ierr);
 }
@@ -526,22 +529,22 @@ int CvodeSolver::init() {
 #if !BOUT_HAS_PETSC
     throw BoutException("solver:save_jacobian for CVODE requires PETSc support.");
 #else
-    if (jacobian_export_kind == JacobianExportKind::scaled) {
+    if (jacobian_export_kind == bout::JacobianExportKind::scaled) {
       throw BoutException(
           "solver:jacobian_export_kind=scaled is not supported for CVODE because "
           "CVODE does not currently apply solver-coordinate scaling.");
     }
-    if (jacobian_export_kind == JacobianExportKind::system
-        and jacobian_export_trigger != CvodeJacobianExportTrigger::linear_setup) {
+    if (jacobian_export_kind == bout::JacobianExportKind::system
+        and jacobian_export_trigger != bout::CvodeJacobianExportTrigger::linear_setup) {
       throw BoutException("solver:jacobian_export_kind=system for CVODE requires "
                           "solver:jacobian_export_trigger=linear_setup.");
     }
-    if (jacobian_export_trigger == CvodeJacobianExportTrigger::output
-        and jacobian_export_kind != JacobianExportKind::rhs) {
+    if (jacobian_export_trigger == bout::CvodeJacobianExportTrigger::output
+        and jacobian_export_kind != bout::JacobianExportKind::rhs) {
       throw BoutException("solver:jacobian_export_trigger=output for CVODE currently "
                           "supports only solver:jacobian_export_kind=rhs.");
     }
-    if (jacobian_export_trigger == CvodeJacobianExportTrigger::linear_setup) {
+    if (jacobian_export_trigger == bout::CvodeJacobianExportTrigger::linear_setup) {
       if (func_iter) {
         throw BoutException("solver:jacobian_export_trigger=linear_setup for CVODE "
                             "requires Newton iteration (set solver:func_iter=false).");
@@ -587,18 +590,18 @@ int CvodeSolver::init() {
 
     switch ((*options)["linear_solver"]
                 .doc("Set linear solver type. Default is gmres.")
-                .withDefault(linear_solver::gmres)) {
-    case linear_solver::gmres:
+                .withDefault(bout::linear_solver::gmres)) {
+    case bout::linear_solver::gmres:
       sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl);
       break;
-    case linear_solver::fgmres:
+    case bout::linear_solver::fgmres:
       sun_solver = callWithSUNContext(SUNLinSol_SPFGMR, suncontext, uvec, prectype, maxl);
       break;
-    case linear_solver::tfqmr:
+    case bout::linear_solver::tfqmr:
       sun_solver =
           callWithSUNContext(SUNLinSol_SPTFQMR, suncontext, uvec, prectype, maxl);
       break;
-    case linear_solver::bcgs:
+    case bout::linear_solver::bcgs:
       sun_solver = callWithSUNContext(SUNLinSol_SPBCGS, suncontext, uvec, prectype, maxl);
       break;
     };
@@ -747,17 +750,17 @@ CvodeSolver::create_constraints(const std::vector<VarStr<FieldType>>& fields) {
                                             "positive, non_negative, negative, or "
                                             "non_positive.",
                                             f.name))
-                           .withDefault(positivity_constraint::none);
+                           .withDefault(bout::positivity_constraint::none);
                    switch (value) {
-                   case positivity_constraint::none:
+                   case bout::positivity_constraint::none:
                      return 0.0;
-                   case positivity_constraint::positive:
+                   case bout::positivity_constraint::positive:
                      return 2.0;
-                   case positivity_constraint::non_negative:
+                   case bout::positivity_constraint::non_negative:
                      return 1.0;
-                   case positivity_constraint::negative:
+                   case bout::positivity_constraint::negative:
                      return -2.0;
-                   case positivity_constraint::non_positive:
+                   case bout::positivity_constraint::non_positive:
                      return -1.0;
                    default:
                      throw BoutException("Incorrect value for "
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index b3093c8106..ae6cb5bb02 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -1,8 +1,6 @@
 /**************************************************************************
  * Interface to SUNDIALS CVODE
  *
- * NOTE: Only one solver can currently be compiled in
- *
  **************************************************************************
  * Copyright 2010 - 2026 BOUT++ contributors
  *
@@ -69,8 +67,8 @@ RegisterSolver<CvodeSolver> registersolvercvode("cvode");
 // Note: String comparisons are case-insensitive so "Auto" avoids conflict with keyword
 BOUT_ENUM_CLASS(CvodePreconMethod, none, Auto, user, petsc, bbd);
 BOUT_ENUM_CLASS_NS(bout, CvodeJacobianExportTrigger,
-                output,      ///< Export once per solver output timestep
-                linear_setup ///< Export whenever CVODE rebuilds linear solver data
+                   output,      ///< Export once per solver output timestep
+                   linear_setup ///< Export whenever CVODE rebuilds linear solver data
 );
 
 #if SUNDIALS_VERSION_AT_LEAST(6, 0, 0)
@@ -112,13 +110,13 @@ private:
                          N_Vector zvec, BoutReal gamma, BoutReal delta, int lr,
                          void* user_data);
   /// Construct the basename used for Jacobian outputs in ``datadir``.
-  std::string getJacobianExportStem(JacobianExportKind kind);
+  std::string getJacobianExportStem(bout::JacobianExportKind kind);
   /// Return the matrix filename including the extension for the selected format.
   std::string getJacobianMatrixFilename(const std::string& stem) const;
   /// Write one Jacobian matrix and the shared metadata JSON.
   PetscErrorCode exportMatrixAndMetadata(Mat jacobian, const std::string& stem);
   /// Build and save a diagnostic Jacobian of the requested kind.
-  PetscErrorCode saveDiagnosticJacobian(JacobianExportKind kind, Vec x, BoutReal t,
+  PetscErrorCode saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x, BoutReal t,
                                         BoutReal gamma);
   /// Save Jacobians during CVODE linear solver setup callbacks.
   PetscErrorCode maybeExportJacobian(Mat system_jacobian, Vec x, BoutReal t,
@@ -182,11 +180,12 @@ private:
   BoutReal cvode_nonlinear_convergence_coef;
   BoutReal cvode_linear_convergence_coef;
   bool save_jacobian; ///< Save PETSc Jacobian diagnostics to ``datadir``?
-  JacobianExportKind jacobian_export_kind; ///< Export ``system`` or ``rhs`` Jacobian
-  CvodeJacobianExportTrigger
+  bout::JacobianExportKind
+      jacobian_export_kind; ///< Export ``system`` or ``rhs`` Jacobian
+  bout::CvodeJacobianExportTrigger
       jacobian_export_trigger;        ///< Export on ``output`` or ``linear_setup``
   std::string jacobian_export_prefix; ///< Prefix for matrix files and ``*_metadata.json``
-  PetscMatrixExportFormat
+  bout::PetscMatrixExportFormat
       jacobian_export_format; ///< PETSc ``MatView`` format: binary or ascii
   int jacobian_export_counter{
       0}; ///< Running counter appended to successive Jacobian saves
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 275b1023da..5f59173a33 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -23,6 +23,7 @@
 #include <cmath>
 #include <cstddef>
 #include <fmt/format.h>
+#include <string>
 #include <vector>
 
 #include "petscerror.h"
@@ -383,7 +384,7 @@ SNESSolver::SNESSolver(Options* opts)
                         .withDefault<bool>(false)),
       jacobian_export_kind((*options)["jacobian_export_kind"]
                                .doc("Which Jacobian to save: system, scaled, or rhs")
-                               .withDefault(JacobianExportKind::system)),
+                               .withDefault(bout::JacobianExportKind::system)),
       jacobian_export_prefix(
           (*options)["jacobian_export_prefix"]
               .doc("Prefix for saved Jacobian matrix files and shared metadata JSON")
@@ -391,9 +392,9 @@ SNESSolver::SNESSolver(Options* opts)
       jacobian_export_format(
           (*options)["jacobian_export_format"]
               .doc("PETSc MatView format for saved Jacobians: binary or ascii")
-              .withDefault(PetscMatrixExportFormat::binary)) {}
+              .withDefault(bout::PetscMatrixExportFormat::binary)) {}
 
-std::string SNESSolver::getJacobianExportStem(JacobianExportKind kind) {
+std::string SNESSolver::getJacobianExportStem(bout::JacobianExportKind kind) {
   // The directory the output data is stored in
   const std::string datadir = Options::root()["datadir"];
   return fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix, toString(kind),
@@ -402,7 +403,8 @@ std::string SNESSolver::getJacobianExportStem(JacobianExportKind kind) {
 
 std::string SNESSolver::getJacobianMatrixFilename(const std::string& stem) const {
   return stem
-         + (jacobian_export_format == PetscMatrixExportFormat::binary ? ".dat" : ".txt");
+         + (jacobian_export_format == bout::PetscMatrixExportFormat::binary ? ".dat"
+                                                                            : ".txt");
 }
 
 PetscErrorCode SNESSolver::exportMatrixAndMetadata(Mat jacobian,
@@ -420,13 +422,14 @@ PetscErrorCode SNESSolver::exportMatrixAndMetadata(Mat jacobian,
   PetscFunctionReturn(PETSC_SUCCESS);
 }
 
-PetscErrorCode SNESSolver::saveDiagnosticJacobian(JacobianExportKind kind, Vec x_solver) {
+PetscErrorCode SNESSolver::saveDiagnosticJacobian(bout::JacobianExportKind kind,
+                                                  Vec x_solver) {
   PetscPreconditioner diagnostic_preconditioner;
   Field3D index = globalIndex(0);
   PetscCall(diagnostic_preconditioner.createJacobianPattern(
       index, *options, nlocal, n2Dvars(), n3Dvars(), BoutComm::get()));
 
-  if (kind == JacobianExportKind::rhs) {
+  if (kind == bout::JacobianExportKind::rhs) {
     PetscCall(diagnostic_preconditioner.updateColoring(FormRawFunctionForColoring, this));
   } else {
     PetscCall(
@@ -435,7 +438,7 @@ PetscErrorCode SNESSolver::saveDiagnosticJacobian(JacobianExportKind kind, Vec x
 
   Vec x_evaluate = x_solver;
   Vec physical_x{nullptr};
-  if (kind == JacobianExportKind::rhs) {
+  if (kind == bout::JacobianExportKind::rhs) {
     PetscCall(VecDuplicate(x_solver, &physical_x));
     PetscCall(toPhysicalState(x_solver, physical_x));
     x_evaluate = physical_x;
@@ -460,7 +463,7 @@ PetscErrorCode SNESSolver::maybeExportJacobian(Mat system_jacobian, Vec x_solver
     PetscFunctionReturn(PETSC_SUCCESS);
   }
 
-  if (jacobian_export_kind == JacobianExportKind::system) {
+  if (jacobian_export_kind == bout::JacobianExportKind::system) {
     PetscCall(exportMatrixAndMetadata(system_jacobian,
                                       getJacobianExportStem(jacobian_export_kind)));
     PetscFunctionReturn(PETSC_SUCCESS);
@@ -1245,7 +1248,7 @@ PetscErrorCode SNESSolver::updateResiduals(Vec x) {
 
   // Note: The ordering of quantities in the PETSc vectors
   // depends on the Solver::loop_vars function
-  Mesh* mesh = bout::globals::mesh;
+  const Mesh* mesh = bout::globals::mesh;
   int idx = 0; // Index into PETSc Vecs
 
   // Boundary cells
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 130d561116..9029f82a79 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -35,6 +35,7 @@
 
 class SNESSolver;
 
+#include <string>
 #include <vector>
 
 #include "mpi.h"
@@ -148,9 +149,9 @@ private:
   /// quantities are near zero then RTOL is used.
   PetscErrorCode rescale();
   /// Build and save a diagnostic Jacobian of the requested kind.
-  PetscErrorCode saveDiagnosticJacobian(JacobianExportKind kind, Vec x_solver);
+  PetscErrorCode saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x_solver);
   /// Construct the basename used for Jacobian outputs in ``datadir``.
-  std::string getJacobianExportStem(JacobianExportKind kind);
+  std::string getJacobianExportStem(bout::JacobianExportKind kind);
   /// Return the matrix filename including the extension for the selected format.
   std::string getJacobianMatrixFilename(const std::string& stem) const;
   /// Write the matrix and shared JSON metadata for one diagnostic Jacobian.
@@ -306,10 +307,10 @@ private:
   const BoutReal asinh_scale = 1e-5; // Scale below which asinh response becomes ~linear
 
   bool save_jacobian; ///< Save Jacobian diagnostics to ``datadir``?
-  JacobianExportKind
+  bout::JacobianExportKind
       jacobian_export_kind; ///< Export ``system``, ``scaled``, or ``rhs`` Jacobian
   std::string jacobian_export_prefix; ///< Prefix for matrix files and ``*_metadata.json``
-  PetscMatrixExportFormat
+  bout::PetscMatrixExportFormat
       jacobian_export_format; ///< PETSc ``MatView`` format: binary or ascii
   int jacobian_export_counter{
       0}; ///< Running counter appended to successive Jacobian saves
diff --git a/src/solver/petsc_preconditioner.cxx b/src/solver/petsc_preconditioner.cxx
index 063d85812e..d2df4c610e 100644
--- a/src/solver/petsc_preconditioner.cxx
+++ b/src/solver/petsc_preconditioner.cxx
@@ -74,13 +74,13 @@ void PetscPreconditioner::reset() {
 }
 
 PetscErrorCode PetscPreconditioner::saveMatrix(Mat matrix, const std::string& filename,
-                                               PetscMatrixExportFormat format) {
+                                               bout::PetscMatrixExportFormat format) {
   if (matrix == nullptr) {
     throw BoutException("Cannot save Jacobian matrix: matrix has not been created yet");
   }
 
   PetscViewer viewer{nullptr};
-  if (format == PetscMatrixExportFormat::binary) {
+  if (format == bout::PetscMatrixExportFormat::binary) {
     PetscCall(PetscViewerBinaryOpen(BoutComm::get(), filename.c_str(), FILE_MODE_WRITE,
                                     &viewer));
   } else {
@@ -93,8 +93,9 @@ PetscErrorCode PetscPreconditioner::saveMatrix(Mat matrix, const std::string& fi
   PetscFunctionReturn(PETSC_SUCCESS);
 }
 
-PetscErrorCode PetscPreconditioner::saveMatrix(const std::string& filename,
-                                               PetscMatrixExportFormat format) const {
+PetscErrorCode
+PetscPreconditioner::saveMatrix(const std::string& filename,
+                                bout::PetscMatrixExportFormat format) const {
   return saveMatrix(Jfd, filename, format);
 }
 

From 4c5e3d3f71209ea6b31fbf31eed09e0c8a0a23a9 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 25 Aug 2026 14:42:46 -0700
Subject: [PATCH 1779/1827] Solver: Reduce duplication between SNES & CVODE

Common Jacobian functions to do with choosing the name of the
output file are now merged.
---
 include/bout/petsc_preconditioner.hxx | 17 ++++++++++++
 include/bout/solver.hxx               | 12 ++++----
 src/solver/impls/cvode/cvode.cxx      | 34 +++++++----------------
 src/solver/impls/cvode/cvode.hxx      | 10 +------
 src/solver/impls/snes/snes.cxx        | 40 ++++++++-------------------
 src/solver/impls/snes/snes.hxx        | 10 +------
 src/solver/petsc_preconditioner.cxx   | 15 +++++++---
 src/solver/solver.cxx                 | 12 ++++++++
 8 files changed, 69 insertions(+), 81 deletions(-)

diff --git a/include/bout/petsc_preconditioner.hxx b/include/bout/petsc_preconditioner.hxx
index 36ece0b06e..58245b099a 100644
--- a/include/bout/petsc_preconditioner.hxx
+++ b/include/bout/petsc_preconditioner.hxx
@@ -15,6 +15,13 @@
 
 BOUT_ENUM_CLASS_NS(bout, PetscMatrixExportFormat, binary, ascii);
 
+BOUT_ENUM_CLASS_NS(
+    bout, JacobianExportKind,
+    system, ///< Jacobian of the full nonlinear system solved by the solver
+    scaled, ///< Jacobian after solver-coordinate transforms such as variable scaling
+    rhs     ///< Jacobian of the raw model RHS in physical variables
+);
+
 #if BOUT_HAS_PETSC
 
 #include "bout/petsc_interface.hxx"
@@ -92,11 +99,21 @@ public:
       const std::string& filename,
       bout::PetscMatrixExportFormat format = bout::PetscMatrixExportFormat::binary) const;
 
+  /// Return the matrix filename including the extension for the selected format.
+  static std::string getJacobianMatrixFilename(const std::string& jacobian_export_prefix,
+                                               bout::JacobianExportKind kind,
+                                               bout::PetscMatrixExportFormat format);
+
   void reset();
 
 private:
   Mat Jfd{nullptr};
   MatFDColoring fdcoloring{nullptr};
+
+  /// Running counter appended to successive Jacobian saves
+  /// This is shared between instances because diagnostic preconditioners
+  /// are created for each output.
+  static inline int jacobian_export_counter{0};
 };
 
 #else
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 388011d337..747e0536aa 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -92,13 +92,6 @@ constexpr auto SOLVERRKGENERIC = "rkgeneric";
 enum class FieldCategories : std::uint8_t { VARS, DERIVS, MMS };
 enum class SOLVER_VAR_OP : std::uint8_t { LOAD, SET_ID, SAVE };
 
-BOUT_ENUM_CLASS_NS(
-    bout, JacobianExportKind,
-    system, ///< Jacobian of the full nonlinear system solved by the solver
-    scaled, ///< Jacobian after solver-coordinate transforms such as variable scaling
-    rhs     ///< Jacobian of the raw model RHS in physical variables
-);
-
 /// A type to set where in the list monitors are added
 enum class MonitorPosition { BACK, FRONT };
 
@@ -653,6 +646,9 @@ protected:
   void writeJacobianMetadataJson(const std::string& filename,
                                  const std::string& solver_name) const;
 
+  /// Writes the Jacobian metadata on first call
+  void writeOnceJacobianMetadata(const std::string& solver_name);
+
   /// Maximum internal timestep
   BoutReal max_dt{-1.0};
 
@@ -718,6 +714,8 @@ private:
   bool save_repeat_run_id{false};
   /// Write ``jacobian_index_base`` to the dump files for Jacobian diagnostics.
   bool save_jacobian_index_base{false};
+  /// Has the Jacobian metadata file been written?
+  bool jacobian_metadata_written{false};
 
   /// Current iteration (output time-step) number
   int iteration{0};
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 20b498252b..70bc058c8f 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -246,30 +246,17 @@ CvodeSolver::~CvodeSolver() {
 }
 
 #if BOUT_HAS_PETSC
-std::string CvodeSolver::getJacobianExportStem(bout::JacobianExportKind kind) {
-  const std::string datadir = Options::root()["datadir"];
-  return fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix, toString(kind),
-                     jacobian_export_counter++);
-}
+PetscErrorCode CvodeSolver::exportMatrixAndMetadata(bout::JacobianExportKind kind,
 
-std::string CvodeSolver::getJacobianMatrixFilename(const std::string& stem) const {
-  return stem
-         + (jacobian_export_format == bout::PetscMatrixExportFormat::binary ? ".dat"
-                                                                            : ".txt");
-}
+                                                    Mat jacobian) {
 
-PetscErrorCode CvodeSolver::exportMatrixAndMetadata(Mat jacobian,
-                                                    const std::string& stem) {
-  if (!jacobian_metadata_written) {
-    const std::string datadir = Options::root()["datadir"];
-    const std::string metadata_filename = datadir + "/jacobian_metadata.json";
-    output.write("Jacobian metadata written to {}\n", metadata_filename);
-    writeJacobianMetadataJson(metadata_filename, "cvode");
-    jacobian_metadata_written = true;
-  }
+  Solver::writeOnceJacobianMetadata("cvode");
 
-  PetscCall(PetscPreconditioner::saveMatrix(jacobian, getJacobianMatrixFilename(stem),
-                                            jacobian_export_format));
+  PetscCall(PetscPreconditioner::saveMatrix(
+      jacobian,
+      PetscPreconditioner::getJacobianMatrixFilename(jacobian_export_prefix, kind,
+                                                     jacobian_export_format),
+      jacobian_export_format));
   PetscFunctionReturn(PETSC_SUCCESS);
 }
 
@@ -310,7 +297,7 @@ PetscErrorCode CvodeSolver::saveDiagnosticJacobian(bout::JacobianExportKind kind
                                x, nullptr));
   PetscCall(MatAssemblyBegin(diagnostic_jacobian, MAT_FINAL_ASSEMBLY));
   PetscCall(MatAssemblyEnd(diagnostic_jacobian, MAT_FINAL_ASSEMBLY));
-  PetscCall(exportMatrixAndMetadata(diagnostic_jacobian, getJacobianExportStem(kind)));
+  PetscCall(exportMatrixAndMetadata(kind, diagnostic_jacobian));
   PetscCall(VecDestroy(&diagnostic_f));
 
   PetscFunctionReturn(PETSC_SUCCESS);
@@ -324,8 +311,7 @@ PetscErrorCode CvodeSolver::maybeExportJacobian(Mat system_jacobian, Vec x, Bout
   }
 
   if (jacobian_export_kind == bout::JacobianExportKind::system) {
-    PetscCall(exportMatrixAndMetadata(system_jacobian,
-                                      getJacobianExportStem(jacobian_export_kind)));
+    PetscCall(exportMatrixAndMetadata(jacobian_export_kind, system_jacobian));
     PetscFunctionReturn(PETSC_SUCCESS);
   }
 
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index ae6cb5bb02..c855310188 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -109,12 +109,8 @@ private:
   static int petscPSolve(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec,
                          N_Vector zvec, BoutReal gamma, BoutReal delta, int lr,
                          void* user_data);
-  /// Construct the basename used for Jacobian outputs in ``datadir``.
-  std::string getJacobianExportStem(bout::JacobianExportKind kind);
-  /// Return the matrix filename including the extension for the selected format.
-  std::string getJacobianMatrixFilename(const std::string& stem) const;
   /// Write one Jacobian matrix and the shared metadata JSON.
-  PetscErrorCode exportMatrixAndMetadata(Mat jacobian, const std::string& stem);
+  PetscErrorCode exportMatrixAndMetadata(bout::JacobianExportKind kind, Mat jacobian);
   /// Build and save a diagnostic Jacobian of the requested kind.
   PetscErrorCode saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x, BoutReal t,
                                         BoutReal gamma);
@@ -187,10 +183,6 @@ private:
   std::string jacobian_export_prefix; ///< Prefix for matrix files and ``*_metadata.json``
   bout::PetscMatrixExportFormat
       jacobian_export_format; ///< PETSc ``MatView`` format: binary or ascii
-  int jacobian_export_counter{
-      0}; ///< Running counter appended to successive Jacobian saves
-  bool jacobian_metadata_written{
-      false}; ///< Has the shared metadata JSON already been written?
 
   // Diagnostics from CVODE
   int nsteps{0};
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index 5f59173a33..c08c4550ad 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -394,31 +394,15 @@ SNESSolver::SNESSolver(Options* opts)
               .doc("PETSc MatView format for saved Jacobians: binary or ascii")
               .withDefault(bout::PetscMatrixExportFormat::binary)) {}
 
-std::string SNESSolver::getJacobianExportStem(bout::JacobianExportKind kind) {
-  // The directory the output data is stored in
-  const std::string datadir = Options::root()["datadir"];
-  return fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix, toString(kind),
-                     jacobian_export_counter++);
-}
-
-std::string SNESSolver::getJacobianMatrixFilename(const std::string& stem) const {
-  return stem
-         + (jacobian_export_format == bout::PetscMatrixExportFormat::binary ? ".dat"
-                                                                            : ".txt");
-}
-
-PetscErrorCode SNESSolver::exportMatrixAndMetadata(Mat jacobian,
-                                                   const std::string& stem) {
-  if (!jacobian_metadata_written) {
-    const std::string datadir = Options::root()["datadir"];
-    const std::string metadata_filename = datadir + "/jacobian_metadata.json";
-    output.write("Jacobian metadata written to {}\n", metadata_filename);
-    writeJacobianMetadataJson(metadata_filename, "snes");
-    jacobian_metadata_written = true;
-  }
-
-  PetscCall(PetscPreconditioner::saveMatrix(jacobian, getJacobianMatrixFilename(stem),
-                                            jacobian_export_format));
+PetscErrorCode SNESSolver::exportMatrixAndMetadata(bout::JacobianExportKind kind,
+                                                   Mat jacobian) {
+  Solver::writeOnceJacobianMetadata("snes");
+
+  PetscCall(PetscPreconditioner::saveMatrix(
+      jacobian,
+      PetscPreconditioner::getJacobianMatrixFilename(jacobian_export_prefix, kind,
+                                                     jacobian_export_format),
+      jacobian_export_format));
   PetscFunctionReturn(PETSC_SUCCESS);
 }
 
@@ -449,7 +433,7 @@ PetscErrorCode SNESSolver::saveDiagnosticJacobian(bout::JacobianExportKind kind,
   PetscCall(SNESComputeJacobianDefaultColor(snes, x_evaluate, diagnostic_jacobian,
                                             diagnostic_jacobian,
                                             diagnostic_preconditioner.coloring()));
-  PetscCall(exportMatrixAndMetadata(diagnostic_jacobian, getJacobianExportStem(kind)));
+  PetscCall(exportMatrixAndMetadata(kind, diagnostic_jacobian));
 
   if (physical_x != nullptr) {
     PetscCall(VecDestroy(&physical_x));
@@ -464,8 +448,8 @@ PetscErrorCode SNESSolver::maybeExportJacobian(Mat system_jacobian, Vec x_solver
   }
 
   if (jacobian_export_kind == bout::JacobianExportKind::system) {
-    PetscCall(exportMatrixAndMetadata(system_jacobian,
-                                      getJacobianExportStem(jacobian_export_kind)));
+    PetscCall(exportMatrixAndMetadata(jacobian_export_kind, system_jacobian));
+
     PetscFunctionReturn(PETSC_SUCCESS);
   }
 
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 9029f82a79..9fa95988b0 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -150,12 +150,8 @@ private:
   PetscErrorCode rescale();
   /// Build and save a diagnostic Jacobian of the requested kind.
   PetscErrorCode saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x_solver);
-  /// Construct the basename used for Jacobian outputs in ``datadir``.
-  std::string getJacobianExportStem(bout::JacobianExportKind kind);
-  /// Return the matrix filename including the extension for the selected format.
-  std::string getJacobianMatrixFilename(const std::string& stem) const;
   /// Write the matrix and shared JSON metadata for one diagnostic Jacobian.
-  PetscErrorCode exportMatrixAndMetadata(Mat jacobian, const std::string& stem);
+  PetscErrorCode exportMatrixAndMetadata(bout::JacobianExportKind kind, Mat jacobian);
 
   BoutSnesOutput output_trigger; ///< Sets when outputs are written
 
@@ -312,10 +308,6 @@ private:
   std::string jacobian_export_prefix; ///< Prefix for matrix files and ``*_metadata.json``
   bout::PetscMatrixExportFormat
       jacobian_export_format; ///< PETSc ``MatView`` format: binary or ascii
-  int jacobian_export_counter{
-      0}; ///< Running counter appended to successive Jacobian saves
-  bool jacobian_metadata_written{
-      false}; ///< Has the shared metadata JSON already been written?
 
   std::vector<Field2D>
       resid_2d; ///< Storage for residuals of SNES solve, unpacked from snes_f
diff --git a/src/solver/petsc_preconditioner.cxx b/src/solver/petsc_preconditioner.cxx
index d2df4c610e..c7ecaced5f 100644
--- a/src/solver/petsc_preconditioner.cxx
+++ b/src/solver/petsc_preconditioner.cxx
@@ -21,6 +21,8 @@
 #include <utility>
 #include <vector>
 
+#include <fmt/format.h>
+
 namespace {
 class ColoringStencil {
 private:
@@ -93,10 +95,15 @@ PetscErrorCode PetscPreconditioner::saveMatrix(Mat matrix, const std::string& fi
   PetscFunctionReturn(PETSC_SUCCESS);
 }
 
-PetscErrorCode
-PetscPreconditioner::saveMatrix(const std::string& filename,
-                                bout::PetscMatrixExportFormat format) const {
-  return saveMatrix(Jfd, filename, format);
+std::string
+PetscPreconditioner::getJacobianMatrixFilename(const std::string& jacobian_export_prefix,
+                                               bout::JacobianExportKind kind,
+                                               bout::PetscMatrixExportFormat format) {
+  // The directory the output data is stored in
+  const std::string datadir = Options::root()["datadir"];
+  const std::string stem = fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix,
+                                       toString(kind), jacobian_export_counter++);
+  return stem + (format == bout::PetscMatrixExportFormat::binary ? ".dat" : ".txt");
 }
 
 PetscErrorCode PetscPreconditioner::createJacobianPattern(Field3D& index,
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 21943a14e5..5c4f779e14 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1345,6 +1345,18 @@ void Solver::writeJacobianMetadataJson(const std::string& filename,
             << "}\n";
 }
 
+void Solver::writeOnceJacobianMetadata(const std::string& solver_name) {
+  if (jacobian_metadata_written) {
+    return;
+  }
+
+  const std::string datadir = Options::root()["datadir"];
+  const std::string metadata_filename = datadir + "/jacobian_metadata.json";
+  output.write("Jacobian metadata written to {}\n", metadata_filename);
+  writeJacobianMetadataJson(metadata_filename, solver_name);
+  jacobian_metadata_written = true;
+}
+
 /**************************************************************************
  * Running user-supplied functions
  **************************************************************************/

From 64d91bc4a6a83be7643c893d906112652555bf1a Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 25 Aug 2026 15:53:57 -0700
Subject: [PATCH 1780/1827] Solver: Move more common functions into base class

Jacobian export settings common to both CVODE and SNES solvers,
now moved into Solver functions.
---
 include/bout/petsc_preconditioner.hxx |  10 ---
 include/bout/solver.hxx               |  16 ++++
 src/solver/impls/cvode/cvode.cxx      | 101 ++++++++++----------------
 src/solver/impls/cvode/cvode.hxx      |  16 ++--
 src/solver/impls/snes/snes.cxx        |  68 +++++++----------
 src/solver/impls/snes/snes.hxx        |   9 +--
 src/solver/petsc_preconditioner.cxx   |  11 ---
 src/solver/solver.cxx                 |  27 +++++++
 8 files changed, 116 insertions(+), 142 deletions(-)

diff --git a/include/bout/petsc_preconditioner.hxx b/include/bout/petsc_preconditioner.hxx
index 58245b099a..f413d28d3b 100644
--- a/include/bout/petsc_preconditioner.hxx
+++ b/include/bout/petsc_preconditioner.hxx
@@ -99,21 +99,11 @@ public:
       const std::string& filename,
       bout::PetscMatrixExportFormat format = bout::PetscMatrixExportFormat::binary) const;
 
-  /// Return the matrix filename including the extension for the selected format.
-  static std::string getJacobianMatrixFilename(const std::string& jacobian_export_prefix,
-                                               bout::JacobianExportKind kind,
-                                               bout::PetscMatrixExportFormat format);
-
   void reset();
 
 private:
   Mat Jfd{nullptr};
   MatFDColoring fdcoloring{nullptr};
-
-  /// Running counter appended to successive Jacobian saves
-  /// This is shared between instances because diagnostic preconditioners
-  /// are created for each output.
-  static inline int jacobian_export_counter{0};
 };
 
 #else
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 747e0536aa..7c670ad910 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -35,6 +35,7 @@
 #include "bout/mesh.hxx"
 #include "bout/monitor.hxx"
 #include "bout/options.hxx"
+#include "bout/petsc_preconditioner.hxx"
 #include "bout/region.hxx"
 
 #include <algorithm>
@@ -649,6 +650,10 @@ protected:
   /// Writes the Jacobian metadata on first call
   void writeOnceJacobianMetadata(const std::string& solver_name);
 
+#if BOUT_HAS_PETSC
+  void writeJacobianMatrix(bout::JacobianExportKind kind, Mat jacobian);
+#endif
+
   /// Maximum internal timestep
   BoutReal max_dt{-1.0};
 
@@ -716,6 +721,17 @@ private:
   bool save_jacobian_index_base{false};
   /// Has the Jacobian metadata file been written?
   bool jacobian_metadata_written{false};
+  /// Running counter appended to successive Jacobian saves
+  int jacobian_export_counter{0};
+  /// Prefix for matrix files and ``*_metadata.json``
+  std::string jacobian_export_prefix;
+  /// PETSc ``MatView`` format: binary or ascii
+  bout::PetscMatrixExportFormat jacobian_export_format;
+
+  /// Return the matrix filename including the extension for the selected format.
+  std::string getJacobianMatrixFilename(const std::string& jacobian_export_prefix,
+                                        bout::JacobianExportKind kind,
+                                        bout::PetscMatrixExportFormat format);
 
   /// Current iteration (output time-step) number
   int iteration{0};
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 70bc058c8f..2d572087ca 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -180,14 +180,6 @@ CvodeSolver::CvodeSolver(Options* opts)
           (*options)["jacobian_export_trigger"]
               .doc("When to save CVODE Jacobians: output or linear_setup")
               .withDefault(bout::CvodeJacobianExportTrigger::linear_setup)),
-      jacobian_export_prefix(
-          (*options)["jacobian_export_prefix"]
-              .doc("Prefix for saved Jacobian matrix files and shared metadata JSON")
-              .withDefault("jacobian")),
-      jacobian_export_format(
-          (*options)["jacobian_export_format"]
-              .doc("PETSc MatView format for saved Jacobians: binary or ascii")
-              .withDefault(bout::PetscMatrixExportFormat::binary)),
       suncontext(createSUNContext(BoutComm::get())) {
   has_constraints = false; // This solver doesn't have constraints
   canReset = true;
@@ -246,22 +238,16 @@ CvodeSolver::~CvodeSolver() {
 }
 
 #if BOUT_HAS_PETSC
-PetscErrorCode CvodeSolver::exportMatrixAndMetadata(bout::JacobianExportKind kind,
+void CvodeSolver::exportMatrixAndMetadata(bout::JacobianExportKind kind,
 
-                                                    Mat jacobian) {
+                                          Mat jacobian) {
 
   Solver::writeOnceJacobianMetadata("cvode");
-
-  PetscCall(PetscPreconditioner::saveMatrix(
-      jacobian,
-      PetscPreconditioner::getJacobianMatrixFilename(jacobian_export_prefix, kind,
-                                                     jacobian_export_format),
-      jacobian_export_format));
-  PetscFunctionReturn(PETSC_SUCCESS);
+  Solver::writeJacobianMatrix(kind, jacobian);
 }
 
-PetscErrorCode CvodeSolver::saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x,
-                                                   BoutReal t, BoutReal gamma) {
+void CvodeSolver::saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x, BoutReal t,
+                                         BoutReal gamma) {
   if (kind == bout::JacobianExportKind::scaled) {
     throw BoutException("solver:jacobian_export_kind=scaled is not supported for CVODE");
   }
@@ -271,74 +257,70 @@ PetscErrorCode CvodeSolver::saveDiagnosticJacobian(bout::JacobianExportKind kind
 
   PetscPreconditioner diagnostic_preconditioner;
   Field3D index = globalIndex(0);
-  PetscCall(diagnostic_preconditioner.createJacobianPattern(
+  BOUT_DO_PETSC(diagnostic_preconditioner.createJacobianPattern(
       index, *options, getLocalN(), n2Dvars(), n3Dvars(), BoutComm::get()));
 
   if (kind == bout::JacobianExportKind::rhs) {
-    PetscCall(diagnostic_preconditioner.updateColoring(CvodeSolver::petscFormRhsFunction,
-                                                       this));
+    BOUT_DO_PETSC(diagnostic_preconditioner.updateColoring(
+        CvodeSolver::petscFormRhsFunction, this));
   } else {
-    PetscCall(
+    BOUT_DO_PETSC(
         diagnostic_preconditioner.updateColoring(CvodeSolver::petscFormFunction, this));
   }
 
   Vec diagnostic_f{nullptr};
-  PetscCall(VecDuplicate(x, &diagnostic_f));
+  BOUT_DO_PETSC(VecDuplicate(x, &diagnostic_f));
   if (kind == bout::JacobianExportKind::rhs) {
-    PetscCall(CvodeSolver::petscFormRhsFunction(nullptr, x, diagnostic_f, this));
+    BOUT_DO_PETSC(CvodeSolver::petscFormRhsFunction(nullptr, x, diagnostic_f, this));
   } else {
-    PetscCall(CvodeSolver::petscFormFunction(nullptr, x, diagnostic_f, this));
+    BOUT_DO_PETSC(CvodeSolver::petscFormFunction(nullptr, x, diagnostic_f, this));
   }
-  PetscCall(MatFDColoringSetF(diagnostic_preconditioner.coloring(), diagnostic_f));
+  BOUT_DO_PETSC(MatFDColoringSetF(diagnostic_preconditioner.coloring(), diagnostic_f));
 
   Mat diagnostic_jacobian = diagnostic_preconditioner.jacobian();
-  PetscCall(MatZeroEntries(diagnostic_jacobian));
-  PetscCall(MatFDColoringApply(diagnostic_jacobian, diagnostic_preconditioner.coloring(),
-                               x, nullptr));
-  PetscCall(MatAssemblyBegin(diagnostic_jacobian, MAT_FINAL_ASSEMBLY));
-  PetscCall(MatAssemblyEnd(diagnostic_jacobian, MAT_FINAL_ASSEMBLY));
-  PetscCall(exportMatrixAndMetadata(kind, diagnostic_jacobian));
-  PetscCall(VecDestroy(&diagnostic_f));
-
-  PetscFunctionReturn(PETSC_SUCCESS);
+  BOUT_DO_PETSC(MatZeroEntries(diagnostic_jacobian));
+  BOUT_DO_PETSC(MatFDColoringApply(diagnostic_jacobian,
+                                   diagnostic_preconditioner.coloring(), x, nullptr));
+  BOUT_DO_PETSC(MatAssemblyBegin(diagnostic_jacobian, MAT_FINAL_ASSEMBLY));
+  BOUT_DO_PETSC(MatAssemblyEnd(diagnostic_jacobian, MAT_FINAL_ASSEMBLY));
+  exportMatrixAndMetadata(kind, diagnostic_jacobian);
+  BOUT_DO_PETSC(VecDestroy(&diagnostic_f));
 }
 
-PetscErrorCode CvodeSolver::maybeExportJacobian(Mat system_jacobian, Vec x, BoutReal t,
-                                                BoutReal gamma) {
+void CvodeSolver::maybeExportJacobian(Mat system_jacobian, Vec x, BoutReal t,
+                                      BoutReal gamma) {
   if (!save_jacobian
       or jacobian_export_trigger != bout::CvodeJacobianExportTrigger::linear_setup) {
-    PetscFunctionReturn(PETSC_SUCCESS);
+    return;
   }
 
   if (jacobian_export_kind == bout::JacobianExportKind::system) {
-    PetscCall(exportMatrixAndMetadata(jacobian_export_kind, system_jacobian));
-    PetscFunctionReturn(PETSC_SUCCESS);
+    exportMatrixAndMetadata(jacobian_export_kind, system_jacobian);
+    return;
   }
 
-  PetscFunctionReturn(saveDiagnosticJacobian(jacobian_export_kind, x, t, gamma));
+  saveDiagnosticJacobian(jacobian_export_kind, x, t, gamma);
 }
 
-PetscErrorCode CvodeSolver::maybeExportOutputJacobian(BoutReal t) {
+void CvodeSolver::maybeExportOutputJacobian(BoutReal t) {
   if (!save_jacobian
       or jacobian_export_trigger != bout::CvodeJacobianExportTrigger::output) {
-    PetscFunctionReturn(PETSC_SUCCESS);
+    return;
   }
 
   Vec x{nullptr};
-  PetscCall(VecCreate(BoutComm::get(), &x));
-  PetscCall(VecSetSizes(x, getLocalN(), PETSC_DETERMINE));
-  PetscCall(VecSetType(x, VECMPI));
-  PetscCall(VecSetUp(x));
+  BOUT_DO_PETSC(VecCreate(BoutComm::get(), &x));
+  BOUT_DO_PETSC(VecSetSizes(x, getLocalN(), PETSC_DETERMINE));
+  BOUT_DO_PETSC(VecSetType(x, VECMPI));
+  BOUT_DO_PETSC(VecSetUp(x));
 
   BoutReal* xdata = nullptr;
-  PetscCall(VecGetArray(x, &xdata));
+  BOUT_DO_PETSC(VecGetArray(x, &xdata));
   save_vars(xdata);
-  PetscCall(VecRestoreArray(x, &xdata));
+  BOUT_DO_PETSC(VecRestoreArray(x, &xdata));
 
-  const PetscErrorCode ierr =
-      saveDiagnosticJacobian(bout::JacobianExportKind::rhs, x, t, 0.0);
-  PetscCall(VecDestroy(&x));
-  PetscFunctionReturn(ierr);
+  saveDiagnosticJacobian(bout::JacobianExportKind::rhs, x, t, 0.0);
+  BOUT_DO_PETSC(VecDestroy(&x));
 }
 #endif
 
@@ -884,10 +866,7 @@ BoutReal CvodeSolver::run(BoutReal tout) {
   }
 
 #if BOUT_HAS_PETSC
-  const PetscErrorCode jacobian_export_error = maybeExportOutputJacobian(simtime);
-  if (jacobian_export_error != PETSC_SUCCESS) {
-    throw BoutException("Failed to export CVODE Jacobian diagnostics");
-  }
+  maybeExportOutputJacobian(simtime);
 #endif
 
   // Call rhs function to get extra variables at this time
@@ -1173,11 +1152,7 @@ int CvodeSolver::petscPSetup(BoutReal t, N_Vector yy, N_Vector UNUSED(yp),
     return 1;
   }
 
-  ierr = s->maybeExportJacobian(J, s->petsc_x, t, gamma);
-  if (ierr != 0) {
-    VecResetArray(s->petsc_x);
-    return 1;
-  }
+  s->maybeExportJacobian(J, s->petsc_x, t, gamma);
 
   ierr = KSPSetOperators(s->petsc_ksp, J, J);
   if (ierr == 0) {
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index c855310188..242ccf26ab 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -110,15 +110,14 @@ private:
                          N_Vector zvec, BoutReal gamma, BoutReal delta, int lr,
                          void* user_data);
   /// Write one Jacobian matrix and the shared metadata JSON.
-  PetscErrorCode exportMatrixAndMetadata(bout::JacobianExportKind kind, Mat jacobian);
+  void exportMatrixAndMetadata(bout::JacobianExportKind kind, Mat jacobian);
   /// Build and save a diagnostic Jacobian of the requested kind.
-  PetscErrorCode saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x, BoutReal t,
-                                        BoutReal gamma);
+  void saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x, BoutReal t,
+                              BoutReal gamma);
   /// Save Jacobians during CVODE linear solver setup callbacks.
-  PetscErrorCode maybeExportJacobian(Mat system_jacobian, Vec x, BoutReal t,
-                                     BoutReal gamma);
+  void maybeExportJacobian(Mat system_jacobian, Vec x, BoutReal t, BoutReal gamma);
   /// Save Jacobians once per solver output timestep.
-  PetscErrorCode maybeExportOutputJacobian(BoutReal t);
+  void maybeExportOutputJacobian(BoutReal t);
 #endif
 
   BoutReal hcur; //< Current internal timestep
@@ -179,10 +178,7 @@ private:
   bout::JacobianExportKind
       jacobian_export_kind; ///< Export ``system`` or ``rhs`` Jacobian
   bout::CvodeJacobianExportTrigger
-      jacobian_export_trigger;        ///< Export on ``output`` or ``linear_setup``
-  std::string jacobian_export_prefix; ///< Prefix for matrix files and ``*_metadata.json``
-  bout::PetscMatrixExportFormat
-      jacobian_export_format; ///< PETSc ``MatView`` format: binary or ascii
+      jacobian_export_trigger; ///< Export on ``output`` or ``linear_setup``
 
   // Diagnostics from CVODE
   int nsteps{0};
diff --git a/src/solver/impls/snes/snes.cxx b/src/solver/impls/snes/snes.cxx
index c08c4550ad..543bacb841 100644
--- a/src/solver/impls/snes/snes.cxx
+++ b/src/solver/impls/snes/snes.cxx
@@ -384,76 +384,58 @@ SNESSolver::SNESSolver(Options* opts)
                         .withDefault<bool>(false)),
       jacobian_export_kind((*options)["jacobian_export_kind"]
                                .doc("Which Jacobian to save: system, scaled, or rhs")
-                               .withDefault(bout::JacobianExportKind::system)),
-      jacobian_export_prefix(
-          (*options)["jacobian_export_prefix"]
-              .doc("Prefix for saved Jacobian matrix files and shared metadata JSON")
-              .withDefault("jacobian")),
-      jacobian_export_format(
-          (*options)["jacobian_export_format"]
-              .doc("PETSc MatView format for saved Jacobians: binary or ascii")
-              .withDefault(bout::PetscMatrixExportFormat::binary)) {}
-
-PetscErrorCode SNESSolver::exportMatrixAndMetadata(bout::JacobianExportKind kind,
-                                                   Mat jacobian) {
-  Solver::writeOnceJacobianMetadata("snes");
+                               .withDefault(bout::JacobianExportKind::system)) {}
 
-  PetscCall(PetscPreconditioner::saveMatrix(
-      jacobian,
-      PetscPreconditioner::getJacobianMatrixFilename(jacobian_export_prefix, kind,
-                                                     jacobian_export_format),
-      jacobian_export_format));
-  PetscFunctionReturn(PETSC_SUCCESS);
+void SNESSolver::exportMatrixAndMetadata(bout::JacobianExportKind kind, Mat jacobian) {
+  Solver::writeOnceJacobianMetadata("snes");
+  Solver::writeJacobianMatrix(kind, jacobian);
 }
 
-PetscErrorCode SNESSolver::saveDiagnosticJacobian(bout::JacobianExportKind kind,
-                                                  Vec x_solver) {
+void SNESSolver::saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x_solver) {
   PetscPreconditioner diagnostic_preconditioner;
   Field3D index = globalIndex(0);
-  PetscCall(diagnostic_preconditioner.createJacobianPattern(
+  BOUT_DO_PETSC(diagnostic_preconditioner.createJacobianPattern(
       index, *options, nlocal, n2Dvars(), n3Dvars(), BoutComm::get()));
 
   if (kind == bout::JacobianExportKind::rhs) {
-    PetscCall(diagnostic_preconditioner.updateColoring(FormRawFunctionForColoring, this));
+    BOUT_DO_PETSC(
+        diagnostic_preconditioner.updateColoring(FormRawFunctionForColoring, this));
   } else {
-    PetscCall(
+    BOUT_DO_PETSC(
         diagnostic_preconditioner.updateColoring(FormScaledFunctionForColoring, this));
   }
 
   Vec x_evaluate = x_solver;
   Vec physical_x{nullptr};
   if (kind == bout::JacobianExportKind::rhs) {
-    PetscCall(VecDuplicate(x_solver, &physical_x));
-    PetscCall(toPhysicalState(x_solver, physical_x));
+    BOUT_DO_PETSC(VecDuplicate(x_solver, &physical_x));
+    BOUT_DO_PETSC(toPhysicalState(x_solver, physical_x));
     x_evaluate = physical_x;
   }
 
   Mat diagnostic_jacobian = diagnostic_preconditioner.jacobian();
-  PetscCall(MatZeroEntries(diagnostic_jacobian));
-  PetscCall(SNESComputeJacobianDefaultColor(snes, x_evaluate, diagnostic_jacobian,
-                                            diagnostic_jacobian,
-                                            diagnostic_preconditioner.coloring()));
-  PetscCall(exportMatrixAndMetadata(kind, diagnostic_jacobian));
+  BOUT_DO_PETSC(MatZeroEntries(diagnostic_jacobian));
+  BOUT_DO_PETSC(SNESComputeJacobianDefaultColor(snes, x_evaluate, diagnostic_jacobian,
+                                                diagnostic_jacobian,
+                                                diagnostic_preconditioner.coloring()));
+  exportMatrixAndMetadata(kind, diagnostic_jacobian);
 
   if (physical_x != nullptr) {
-    PetscCall(VecDestroy(&physical_x));
+    BOUT_DO_PETSC(VecDestroy(&physical_x));
   }
-
-  PetscFunctionReturn(PETSC_SUCCESS);
 }
 
-PetscErrorCode SNESSolver::maybeExportJacobian(Mat system_jacobian, Vec x_solver) {
+void SNESSolver::maybeExportJacobian(Mat system_jacobian, Vec x_solver) {
   if (!save_jacobian) {
-    PetscFunctionReturn(PETSC_SUCCESS);
+    return;
   }
 
   if (jacobian_export_kind == bout::JacobianExportKind::system) {
-    PetscCall(exportMatrixAndMetadata(jacobian_export_kind, system_jacobian));
-
-    PetscFunctionReturn(PETSC_SUCCESS);
+    exportMatrixAndMetadata(jacobian_export_kind, system_jacobian);
+    return;
   }
 
-  PetscFunctionReturn(saveDiagnosticJacobian(jacobian_export_kind, x_solver));
+  saveDiagnosticJacobian(jacobian_export_kind, x_solver);
 }
 
 int SNESSolver::init() {
@@ -1768,7 +1750,8 @@ PetscErrorCode ComputeJacobianScaledColor(SNES snes, Vec x1, Mat Jac, Mat Jac_ne
 
   // Call the SNESSolver function
   PetscCall(fctx->scaleJacobian(Jac_new));
-  PetscFunctionReturn(fctx->maybeExportJacobian(Jac_new, x1));
+  fctx->maybeExportJacobian(Jac_new, x1);
+  PetscFunctionReturn(PETSC_SUCCESS);
 }
 
 PetscErrorCode ComputeJacobianDefaultMaybeExport(SNES snes, Vec x1, Mat Jac, Mat Jac_new,
@@ -1780,7 +1763,8 @@ PetscErrorCode ComputeJacobianDefaultMaybeExport(SNES snes, Vec x1, Mat Jac, Mat
     return err;
   }
 
-  PetscFunctionReturn(static_cast<SNESSolver*>(ctx)->maybeExportJacobian(Jac_new, x1));
+  static_cast<SNESSolver*>(ctx)->maybeExportJacobian(Jac_new, x1);
+  PetscFunctionReturn(PETSC_SUCCESS);
 }
 } // namespace
 
diff --git a/src/solver/impls/snes/snes.hxx b/src/solver/impls/snes/snes.hxx
index 9fa95988b0..ddb25b9975 100644
--- a/src/solver/impls/snes/snes.hxx
+++ b/src/solver/impls/snes/snes.hxx
@@ -135,7 +135,7 @@ public:
   ///
   /// ``system`` exports the Jacobian used directly by SNES. ``scaled`` and ``rhs``
   /// build throwaway coloring Jacobians for diagnostics only.
-  PetscErrorCode maybeExportJacobian(Mat system_jacobian, Vec x_solver);
+  void maybeExportJacobian(Mat system_jacobian, Vec x_solver);
 
   /// Save diagnostics to output
   void outputVars(Options& output_options, bool save_repeat = true) override;
@@ -149,9 +149,9 @@ private:
   /// quantities are near zero then RTOL is used.
   PetscErrorCode rescale();
   /// Build and save a diagnostic Jacobian of the requested kind.
-  PetscErrorCode saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x_solver);
+  void saveDiagnosticJacobian(bout::JacobianExportKind kind, Vec x_solver);
   /// Write the matrix and shared JSON metadata for one diagnostic Jacobian.
-  PetscErrorCode exportMatrixAndMetadata(bout::JacobianExportKind kind, Mat jacobian);
+  void exportMatrixAndMetadata(bout::JacobianExportKind kind, Mat jacobian);
 
   BoutSnesOutput output_trigger; ///< Sets when outputs are written
 
@@ -305,9 +305,6 @@ private:
   bool save_jacobian; ///< Save Jacobian diagnostics to ``datadir``?
   bout::JacobianExportKind
       jacobian_export_kind; ///< Export ``system``, ``scaled``, or ``rhs`` Jacobian
-  std::string jacobian_export_prefix; ///< Prefix for matrix files and ``*_metadata.json``
-  bout::PetscMatrixExportFormat
-      jacobian_export_format; ///< PETSc ``MatView`` format: binary or ascii
 
   std::vector<Field2D>
       resid_2d; ///< Storage for residuals of SNES solve, unpacked from snes_f
diff --git a/src/solver/petsc_preconditioner.cxx b/src/solver/petsc_preconditioner.cxx
index c7ecaced5f..dbec994c17 100644
--- a/src/solver/petsc_preconditioner.cxx
+++ b/src/solver/petsc_preconditioner.cxx
@@ -95,17 +95,6 @@ PetscErrorCode PetscPreconditioner::saveMatrix(Mat matrix, const std::string& fi
   PetscFunctionReturn(PETSC_SUCCESS);
 }
 
-std::string
-PetscPreconditioner::getJacobianMatrixFilename(const std::string& jacobian_export_prefix,
-                                               bout::JacobianExportKind kind,
-                                               bout::PetscMatrixExportFormat format) {
-  // The directory the output data is stored in
-  const std::string datadir = Options::root()["datadir"];
-  const std::string stem = fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix,
-                                       toString(kind), jacobian_export_counter++);
-  return stem + (format == bout::PetscMatrixExportFormat::binary ? ".dat" : ".txt");
-}
-
 PetscErrorCode PetscPreconditioner::createJacobianPattern(Field3D& index,
                                                           Options& options,
                                                           PetscInt nlocal, int n2d,
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 5c4f779e14..76216560d2 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -139,6 +139,13 @@ Solver::Solver(Options* opts)
               .doc("Write jacobian_index_base so saved PETSc Jacobians can be mapped "
                    "back to variables and cell indices in post-processing")
               .withDefault(false)),
+      jacobian_export_prefix((*options)["jacobian_export_prefix"]
+                                 .doc("Prefix for saved Jacobian matrix files")
+                                 .withDefault("jacobian")),
+      jacobian_export_format(
+          (*options)["jacobian_export_format"]
+              .doc("PETSc MatView format for saved Jacobians: binary or ascii")
+              .withDefault(bout::PetscMatrixExportFormat::binary)),
       is_nonsplit_model_diffusive(
           (*options)["is_nonsplit_model_diffusive"]
               .doc("If not a split operator, treat RHS as diffusive?")
@@ -1357,6 +1364,26 @@ void Solver::writeOnceJacobianMetadata(const std::string& solver_name) {
   jacobian_metadata_written = true;
 }
 
+#if BOUT_HAS_PETSC
+void Solver::writeJacobianMatrix(bout::JacobianExportKind kind, Mat jacobian) {
+  BOUT_DO_PETSC(PetscPreconditioner::saveMatrix(
+      jacobian,
+      getJacobianMatrixFilename(this->jacobian_export_prefix, kind,
+                                this->jacobian_export_format),
+      this->jacobian_export_format));
+}
+#endif
+
+std::string Solver::getJacobianMatrixFilename(const std::string& jacobian_export_prefix,
+                                              bout::JacobianExportKind kind,
+                                              bout::PetscMatrixExportFormat format) {
+  // The directory the output data is stored in
+  const std::string datadir = Options::root()["datadir"];
+  const std::string stem = fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix,
+                                       toString(kind), this->jacobian_export_counter++);
+  return stem + (format == bout::PetscMatrixExportFormat::binary ? ".dat" : ".txt");
+}
+
 /**************************************************************************
  * Running user-supplied functions
  **************************************************************************/

From 1ea20a603739e87cb0f146bef18fa6c3461183eb Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 25 Aug 2026 16:25:21 -0700
Subject: [PATCH 1781/1827] Solver::writeJacobianMetadataJson use
 fmt::format_to

Replace the iostream formatting with fmt::format.
---
 src/solver/solver.cxx | 55 ++++++++++++++++++++++++++-----------------
 1 file changed, 33 insertions(+), 22 deletions(-)

diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 76216560d2..8388759b74 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -52,6 +52,7 @@
 #include <cmath>
 #include <ctime>
 #include <fstream>
+#include <iterator>
 #include <memory>
 #include <numeric>
 #include <set>
@@ -1314,42 +1315,52 @@ void Solver::writeJacobianMetadataJson(const std::string& filename,
   }
 
   const auto metadata = getJacobianMetadata(solver_name);
-  std::ofstream json_file(filename);
-  if (!json_file.is_open()) {
+  std::ofstream output_file(filename);
+  if (!output_file.is_open()) {
     throw BoutException("Failed to open Jacobian metadata file '{}'", filename);
   }
 
+  std::string json_file;
+  json_file.reserve(512);
+
   auto write_variables = [&](const std::vector<JacobianVariableMetadata>& variables,
                              const char* name) {
-    json_file << "  \"" << name << "\": [\n";
+    fmt::format_to(std::back_inserter(json_file), "  \"{}\": [\n", name);
     for (std::size_t i = 0; i < variables.size(); ++i) {
       const auto& variable = variables[i];
-      json_file << "    {\"offset\": " << variable.offset << ", "
-                << "\"name\": \"" << jsonEscape(variable.name) << "\", "
-                << "\"location\": \"" << jsonEscape(variable.location) << "\", "
-                << "\"evolve_bndry\": " << (variable.evolve_bndry ? "true" : "false")
-                << ", "
-                << "\"constraint\": " << (variable.constraint ? "true" : "false") << ", "
-                << "\"description\": \"" << jsonEscape(variable.description) << "\"}";
+      fmt::format_to(
+          std::back_inserter(json_file),
+          "    {{\"offset\": {}, \"name\": \"{}\", \"location\": \"{}\", "
+          "\"evolve_bndry\": {}, \"constraint\": {}, \"description\": \"{}\"}}",
+          variable.offset, jsonEscape(variable.name), jsonEscape(variable.location),
+          variable.evolve_bndry ? "true" : "false",
+          variable.constraint ? "true" : "false", jsonEscape(variable.description));
       if (i + 1 != variables.size()) {
-        json_file << ",";
+        fmt::format_to(std::back_inserter(json_file), ",");
       }
-      json_file << "\n";
+      fmt::format_to(std::back_inserter(json_file), "\n");
     }
-    json_file << "  ]";
+    fmt::format_to(std::back_inserter(json_file), "  ]");
   };
 
-  json_file << "{\n"
-            << "  \"format_version\": " << metadata.format_version << ",\n"
-            << "  \"solver\": \"" << jsonEscape(metadata.solver_name) << "\",\n"
-            << "  \"n2d\": " << metadata.n2d << ",\n"
-            << "  \"n3d\": " << metadata.n3d << ",\n";
+  fmt::format_to(std::back_inserter(json_file),
+                 "{{\n"
+                 "  \"format_version\": {},\n"
+                 "  \"solver\": \"{}\",\n"
+                 "  \"n2d\": {},\n"
+                 "  \"n3d\": {},\n",
+                 metadata.format_version, jsonEscape(metadata.solver_name), metadata.n2d,
+                 metadata.n3d);
   write_variables(metadata.variables_2d, "variables_2d");
-  json_file << ",\n";
+  fmt::format_to(std::back_inserter(json_file), ",\n");
   write_variables(metadata.variables_3d, "variables_3d");
-  json_file << ",\n"
-            << "  \"ordering\": \"" << jsonEscape(metadata.ordering) << "\"\n"
-            << "}\n";
+  fmt::format_to(std::back_inserter(json_file),
+                 ",\n"
+                 "  \"ordering\": \"{}\"\n"
+                 "}}\n",
+                 jsonEscape(metadata.ordering));
+
+  output_file << json_file;
 }
 
 void Solver::writeOnceJacobianMetadata(const std::string& solver_name) {

From 6a486b7ea86581256491e690248233ff1ee0cd59 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 25 Aug 2026 16:42:27 -0700
Subject: [PATCH 1782/1827] PetscBinaryIO tidying and PETSc license

Copyright statement and BSD license as we're redistributing the code.

Tidying following @ZedThree comments: Remove python2 support,
shorten some code.

Rename short variables to pass Ruff check.
---
 .../jacobian_tools/PetscBinaryIO.py           | 127 +++++++++++-------
 1 file changed, 75 insertions(+), 52 deletions(-)

diff --git a/tests/integrated/jacobian_tools/PetscBinaryIO.py b/tests/integrated/jacobian_tools/PetscBinaryIO.py
index e3b329c11a..e5b484c4e1 100755
--- a/tests/integrated/jacobian_tools/PetscBinaryIO.py
+++ b/tests/integrated/jacobian_tools/PetscBinaryIO.py
@@ -35,15 +35,38 @@
 
 This module can also be used as a command line tool for converting matrices.
 Run with --help to see options.
+
+License
+=======
+Copyright (c) 1991-2021, UChicago Argonne, LLC and the PETSc Development Team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
 """
 
-import numpy as np
 import functools
+from contextlib import suppress
 
-try:
-    basestring  # Python-2 has basestring as a common parent of unicode and str
-except NameError:
-    basestring = str  # Python-3 is unicode through and through
+import numpy as np
 
 
 def update_wrapper_with_doc(wrapper, wrapped):
@@ -86,11 +109,8 @@ def decorated_f(self, *args, **kwargs):
         old_indices = self.indices
         old_complexscalars = self.complexscalars
 
-        try:
+        with suppress(KeyError):
             self.precision = kwargs.pop("precision")
-        except KeyError:
-            pass
-        else:
             changed = True
 
         try:
@@ -162,7 +182,7 @@ class MatSparse(tuple):
     _classid = 1211216
 
     def __repr__(self):
-        return "MatSparse: %s" % super(MatSparse, self).__repr__()
+        return f"MatSparse({repr(super())})"
 
 
 class IS(np.ndarray):
@@ -203,11 +223,8 @@ def __init__(self, precision=None, indices=None, complexscalars=None):
             defaultprecision, defaultindices, defaultcomplexscalars = (
                 petsc_conf.get_conf()
             )
-            if precision is None:
-                if defaultprecision is None:
-                    precision = "double"
-                else:
-                    precision = defaultprecision
+
+            precision = precision or defaultprecision or "double"
 
             if indices is None:
                 if defaultindices is None:
@@ -289,49 +306,58 @@ def writeVec(self, fh, vec):
     def readMatSparse(self, fh):
         """Reads a PETSc Mat, returning a sparse representation of the data. Must be called after readObjectType()
 
-        (M,N), (I,J,V) = readMatSparse(fid)
+        (M,N), (row_offsets,column_indices,nonzero_values) = readMatSparse(fid)
 
         Input:
           fid : file handle to open binary file.
         Output:
           M,N : matrix size
-          I,J : arrays of row and column for each nonzero
-          V: nonzero value
+          row_offsets,column_indices : arrays of row and column for each nonzero
+          nonzero_values: nonzero value
         """
 
         try:
             M, N, nz = np.fromfile(fh, dtype=self._inttype, count=3)
-            I = np.empty(M + 1, dtype=self._inttype)
-            I[0] = 0
+            row_offsets = np.empty(M + 1, dtype=self._inttype)
+            row_offsets[0] = 0
             rownz = np.fromfile(fh, dtype=self._inttype, count=M)
-            np.cumsum(rownz, out=I[1:])
-            assert I[-1] == nz
+            np.cumsum(rownz, out=row_offsets[1:])
+            assert row_offsets[-1] == nz
 
-            J = np.fromfile(fh, dtype=self._inttype, count=nz)
-            assert len(J) == nz
-            V = np.fromfile(fh, dtype=self._scalartype, count=nz)
-            assert len(V) == nz
+            column_indices = np.fromfile(fh, dtype=self._inttype, count=nz)
+            assert len(column_indices) == nz
+            nonzero_values = np.fromfile(fh, dtype=self._scalartype, count=nz)
+            assert len(nonzero_values) == nz
         except (AssertionError, MemoryError, IndexError):
             raise IOError("Inconsistent or invalid Mat data in file")
 
-        return MatSparse(((M, N), (I, J, V)))
+        return MatSparse(((M, N), (row_offsets, column_indices, nonzero_values)))
 
     @decorate_with_conf
     def writeMatSparse(self, fh, mat):
         """Writes a Mat into a PETSc binary file handle"""
 
-        ((M, N), (I, J, V)) = mat
-        metadata = np.array([MatSparse._classid, M, N, I[-1]], dtype=self._inttype)
-        rownz = I[1:] - I[:-1]
-
-        assert len(J.shape) == len(V.shape) == len(I.shape) == 1
-        assert len(J) == len(V) == I[-1] == rownz.sum()
+        ((M, N), (row_offsets, column_indices, nonzero_values)) = mat
+        metadata = np.array(
+            [MatSparse._classid, M, N, row_offsets[-1]], dtype=self._inttype
+        )
+        rownz = row_offsets[1:] - row_offsets[:-1]
+
+        assert (
+            len(column_indices.shape)
+            == len(nonzero_values.shape)
+            == len(row_offsets.shape)
+            == 1
+        )
+        assert (
+            len(column_indices) == len(nonzero_values) == row_offsets[-1] == rownz.sum()
+        )
         assert (rownz > -1).all()
 
         metadata.tofile(fh)
         rownz.astype(self._inttype).tofile(fh)
-        J.astype(self._inttype).tofile(fh)
-        V.astype(self._scalartype).tofile(fh)
+        column_indices.astype(self._inttype).tofile(fh)
+        nonzero_values.astype(self._scalartype).tofile(fh)
         return
 
     @decorate_with_conf
@@ -340,32 +366,32 @@ def readMatDense(self, fh):
 
         try:
             M, N, nz = np.fromfile(fh, dtype=self._inttype, count=3)
-            I = np.empty(M + 1, dtype=self._inttype)
-            I[0] = 0
+            row_offsets = np.empty(M + 1, dtype=self._inttype)
+            row_offsets[0] = 0
             rownz = np.fromfile(fh, dtype=self._inttype, count=M)
-            np.cumsum(rownz, out=I[1:])
-            assert I[-1] == nz
+            np.cumsum(rownz, out=row_offsets[1:])
+            assert row_offsets[-1] == nz
 
-            J = np.fromfile(fh, dtype=self._inttype, count=nz)
-            assert len(J) == nz
-            V = np.fromfile(fh, dtype=self._scalartype, count=nz)
-            assert len(V) == nz
+            column_indices = np.fromfile(fh, dtype=self._inttype, count=nz)
+            assert len(column_indices) == nz
+            nonzero_values = np.fromfile(fh, dtype=self._scalartype, count=nz)
+            assert len(nonzero_values) == nz
 
         except (AssertionError, MemoryError, IndexError):
             raise IOError("Inconsistent or invalid Mat data in file")
 
         mat = np.zeros((M, N), dtype=self._scalartype)
         for row in range(M):
-            rstart, rend = I[row : row + 2]
-            mat[row, J[rstart:rend]] = V[rstart:rend]
+            rstart, rend = row_offsets[row : row + 2]
+            mat[row, column_indices[rstart:rend]] = nonzero_values[rstart:rend]
         return mat.view(MatDense)
 
     @decorate_with_conf
     def readMatSciPy(self, fh):
         from scipy.sparse import csr_matrix
 
-        (M, N), (I, J, V) = self.readMatSparse(fh)
-        return csr_matrix((V, J, I), shape=(M, N))
+        (M, N), (row_offsets, column_indices, nonzero_values) = self.readMatSparse(fh)
+        return csr_matrix((nonzero_values, column_indices, row_offsets), shape=(M, N))
 
     @decorate_with_conf
     def writeMatSciPy(self, fh, mat):
@@ -374,10 +400,7 @@ def writeMatSciPy(self, fh, mat):
         if hasattr(mat, "tocsr"):
             mat = mat.tocsr()
         assert isinstance(mat, csr_matrix)
-        V = mat.data
         M, N = mat.shape
-        J = mat.indices
-        I = mat.indptr
         return self.writeMatSparse(fh, (mat.shape, (mat.indptr, mat.indices, mat.data)))
 
     @decorate_with_conf
@@ -457,7 +480,7 @@ def readBinaryFile(self, fid, mattype="sparse"):
 
         close = False
 
-        if isinstance(fid, basestring):
+        if isinstance(fid, str):
             fid = open(fid, "rb")
             close = True
 
@@ -496,7 +519,7 @@ def writeBinaryFile(self, fid, objects):
                     which must be of type Vec, IS, MatSparse, or MatSciPy.
         """
         close = False
-        if isinstance(fid, basestring):
+        if isinstance(fid, str):
             fid = open(fid, "wb")
             close = True
 

From 706a0ee81b0b572f71320ace3e054084f7154031 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 26 Aug 2026 09:18:55 +0100
Subject: [PATCH 1783/1827] Add unsorted boundary region iterator test

Co-authored-by: David Bold <dave@ipp.mpg.de>
---
 .../unit/include/bout/test_boundary_iter.cxx  | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/tests/unit/include/bout/test_boundary_iter.cxx b/tests/unit/include/bout/test_boundary_iter.cxx
index 686e564f78..526bdd4695 100644
--- a/tests/unit/include/bout/test_boundary_iter.cxx
+++ b/tests/unit/include/bout/test_boundary_iter.cxx
@@ -21,6 +21,26 @@ TEST_F(BoundaryIteratorTest, Contains) {
   ASSERT_FALSE(bndry.contains(3, 2, 1));
 }
 
+TEST_F(BoundaryIteratorTest, ContainsUnsorted) {
+  BoundaryRegionFCI bndry{"test", BndryLoc::yup, +1, bout::globals::mesh};
+
+  bndry.add_point(1, 0, 3, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(1, 1, 3, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(1, 2, 3, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(0, 1, 0, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(0, 1, 1, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(0, 1, 2, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(0, 1, 3, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(0, 0, 0, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(0, 0, 1, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(0, 0, 2, 0.0, 0.0, 0.0, 0.0, 0, 0);
+  bndry.add_point(0, 0, 3, 0.0, 0.0, 0.0, 0.0, 0, 0);
+
+  ASSERT_TRUE(bndry.contains(1, 2, 3));
+  ASSERT_FALSE(bndry.contains(1, 3, 3));
+  ASSERT_FALSE(bndry.contains(3, 2, 1));
+}
+
 TEST_F(BoundaryIteratorTest, SetValid) {
   BoundaryRegionFCI bndry{"test", BndryLoc::yup, +1, bout::globals::mesh};
 

From acdeec1894b4f61556e4b71c4990b59783ac254e Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 26 Aug 2026 11:27:53 +0100
Subject: [PATCH 1784/1827] Remove unused `BoundaryRegionPar`

Now entirely replaced with `BoundaryRegionFCI`
---
 CMakeLists.txt                                |   1 -
 examples/fci-wave/fci-wave.cxx                |   1 -
 include/bout/boundary_iterator.hxx            |   5 -
 include/bout/boundary_region_iter.hxx         |  88 ++++----
 include/bout/field_data.hxx                   |   6 +-
 include/bout/parallel_boundary_op.hxx         |   4 -
 include/bout/parallel_boundary_region.hxx     | 189 ------------------
 src/field/field3d.cxx                         |   3 +-
 src/field/field_data.cxx                      |   2 -
 src/mesh/boundary_factory.cxx                 |   2 -
 src/mesh/impls/bout/boutmesh.cxx              |   1 -
 src/mesh/parallel/fci.cxx                     |   2 -
 src/mesh/parallel/fci.hxx                     |   1 -
 src/mesh/parallel/shiftedmetric.cxx           |   3 -
 src/mesh/yboundary_regions.cxx                |   1 -
 .../test-fci-boundary/get_par_bndry.cxx       |   1 -
 16 files changed, 57 insertions(+), 253 deletions(-)
 delete mode 100644 include/bout/parallel_boundary_region.hxx

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c08b651317..6a260123e7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -180,7 +180,6 @@ set(BOUT_SOURCES
     ./include/bout/output.hxx
     ./include/bout/output_bout_types.hxx
     ./include/bout/parallel_boundary_op.hxx
-    ./include/bout/parallel_boundary_region.hxx
     ./include/bout/paralleltransform.hxx
     ./include/bout/petsc_interface.hxx
     ./include/bout/petsc_operators.hxx
diff --git a/examples/fci-wave/fci-wave.cxx b/examples/fci-wave/fci-wave.cxx
index fd3adbe2ab..8769b83470 100644
--- a/examples/fci-wave/fci-wave.cxx
+++ b/examples/fci-wave/fci-wave.cxx
@@ -1,4 +1,3 @@
-#include "bout/parallel_boundary_region.hxx"
 #include "bout/physicsmodel.hxx"
 
 #include <cmath>
diff --git a/include/bout/boundary_iterator.hxx b/include/bout/boundary_iterator.hxx
index b2d2b9fb99..8e5f37182e 100644
--- a/include/bout/boundary_iterator.hxx
+++ b/include/bout/boundary_iterator.hxx
@@ -1,16 +1,11 @@
 #pragma once
 
 #include "bout/assert.hxx"
-#include "bout/bout_types.hxx"
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/mesh.hxx"
-#include "bout/parallel_boundary_region.hxx"
 #include "bout/region.hxx"
-#include "bout/sys/parallel_stencils.hxx"
 #include "bout/sys/range.hxx"
-#include <algorithm>
-#include <functional>
 
 class BoundaryRegionIter {
 public:
diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 0154bd75bf..d85f5c364c 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -1,14 +1,5 @@
 #pragma once
 
-#include <algorithm>
-#include <cmath>
-#include <concepts>
-#include <cstddef>
-#include <memory>
-#include <string>
-#include <type_traits>
-#include <vector>
-
 #include <bout/assert.hxx>
 #include <bout/boundary_common.hxx>
 #include <bout/boundary_region.hxx>
@@ -17,11 +8,20 @@
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/field_data.hxx>
-#include <bout/parallel_boundary_region.hxx>
+#include <bout/mesh.hxx>
 #include <bout/region.hxx>
 #include <bout/sys/parallel_stencils.hxx>
 #include <bout/traits.hxx>
 
+#include <algorithm>
+#include <cmath>
+#include <concepts>
+#include <cstddef>
+#include <memory>
+#include <string>
+#include <type_traits>
+#include <vector>
+
 namespace bout {
 namespace boundary {
 
@@ -182,28 +182,50 @@ private:
 ///
 /// This can't use the legacy iteration methods (`first()`, `next()`, and so on)
 class BoundaryRegionFCI : public BoundaryRegionBase {
+  struct RealPoint {
+    BoutReal s_x;
+    BoutReal s_y;
+    BoutReal s_z;
+  };
+
 public:
   /// A single point in a `BoundaryRegionFCI`
   class Point : public BoundaryRegionIterBase<Point> {
   private:
-    parallel_boundary_region::Indices index;
+    /// Indices of the boundary point
+    Ind3D index;
+    /// Intersection with boundary in index space
+    RealPoint intersection;
+    /// Distance to intersection
+    BoutReal length_m;
+    /// How many points we can go in the opposite direction
+    signed char valid_m;
+    /// How many points we are away from the boundary
+    signed char offset_m;
+    unsigned char abs_offset_m;
+
     Mesh* localmesh_m;
-    int _dir;
+    /// Direction to the boundary. Positive values are in the sense of the
+    /// increasing coordinate
+    int dir_m;
 
   public:
     Point() = delete;
-    Point(parallel_boundary_region::Indices index, const BoundaryRegionFCI& rgn)
-        : index(index), localmesh_m(rgn.localmesh), _dir(rgn._dir) {}
+    Point(Ind3D index, RealPoint intersection, BoutReal length, signed char valid,
+          signed char offset, Mesh* mesh, int dir)
+        : index(index), intersection(intersection), length_m(length), valid_m(valid),
+          offset_m(offset), abs_offset_m(static_cast<unsigned char>(std::abs(offset))),
+          localmesh_m(mesh), dir_m(dir) {}
 
-    void setValid(char valid) { index.valid = valid; };
+    void setValid(char valid) { valid_m = valid; };
 
-    BoutReal s_x() const { return index.intersection.s_x; };
-    BoutReal s_y() const { return index.intersection.s_y; };
-    BoutReal s_z() const { return index.intersection.s_z; };
+    BoutReal s_x() const { return intersection.s_x; };
+    BoutReal s_y() const { return intersection.s_y; };
+    BoutReal s_z() const { return intersection.s_z; };
 
     Mesh* localmesh() const { return localmesh_m; };
-    int dir() const { return _dir; }
-    bool _is_lower() const { return _dir < 0; }
+    int dir() const { return dir_m; }
+    bool _is_lower() const { return dir_m < 0; }
 
     template <bool check = true, class T>
       requires utils::is_Field_v<T>
@@ -212,7 +234,7 @@ public:
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
-      auto _off = _offset() - (off * _dir);
+      auto _off = _offset() - (off * dir_m);
       return f.ynext(_off)[_ind().yp(_off)];
     }
 
@@ -223,7 +245,7 @@ public:
       if constexpr (check) {
         ASSERT3(_valid() > -off - 2);
       }
-      auto _off = _offset() - (off * _dir);
+      auto _off = _offset() - (off * dir_m);
       return f.ynext(_off)[_ind().yp(_off)];
     }
 
@@ -232,26 +254,26 @@ public:
       if constexpr (check) {
         ASSERT3(valid() > -off - 2);
       }
-      auto _off = _offset() + (off * _dir);
+      auto _off = _offset() + (off * dir_m);
       return f(_off, _ind().yp(_off));
     }
 
-    signed char _offset() const { return index.offset; }
-    signed char _valid() const { return index.valid; }
-    Ind3D _ind() const { return index.index; }
-    int _boundary_width() const { return localmesh_m->ystart - index.abs_offset + 1; }
+    signed char _offset() const { return offset_m; }
+    signed char _valid() const { return valid_m; }
+    Ind3D _ind() const { return index; }
+    int _boundary_width() const { return localmesh_m->ystart - abs_offset_m + 1; }
     BoutReal _length([[maybe_unused]] CELL_LOC loc) const {
       ASSERT3(loc == CELL_CENTRE);
-      return index.length;
+      return length_m;
     }
 
     auto operator<=>(const Point& rhs) const {
       // Ensure we're looking at the same boundary
-      ASSERT3(_dir == rhs._dir);
+      ASSERT3(dir_m == rhs.dir_m);
       return _ind() <=> rhs._ind();
     }
     bool operator==(Point rhs) const {
-      ASSERT3(_dir == rhs._dir);
+      ASSERT3(dir_m == rhs.dir_m);
       return _ind() == rhs._ind();
     }
   };
@@ -267,10 +289,8 @@ public:
     if (!bndry_points.empty() && bndry_points.back()._ind() > ind) {
       is_sorted = false;
     }
-    auto index = parallel_boundary_region::Indices{
-        ind,    bout::parallel_boundary_region::RealPoint{x, y, z}, length, valid,
-        offset, static_cast<unsigned char>(std::abs(offset))};
-    bndry_points.emplace_back(index, *this);
+    bndry_points.emplace_back(ind, RealPoint{x, y, z}, length, valid, offset, localmesh,
+                              _dir);
   }
 
   /// Add a point to the boundary
diff --git a/include/bout/field_data.hxx b/include/bout/field_data.hxx
index 20b6a517f9..c5e60011f1 100644
--- a/include/bout/field_data.hxx
+++ b/include/bout/field_data.hxx
@@ -30,7 +30,9 @@ class FieldData;
 #ifndef FIELD_DATA_H
 #define FIELD_DATA_H
 
+#include "bout/boundary_region.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/sys/expressionparser.hxx"
 #include "bout/unused.hxx"
 
 #include <cstdint>
@@ -47,12 +49,8 @@ class BoundaryRegionFCI;
 class Coordinates;
 class Mesh;
 
-#include "bout/boundary_region.hxx"
-class BoundaryRegionPar;
 enum class BndryLoc : std::int8_t;
 
-#include "bout/sys/expressionparser.hxx"
-
 /// Base class for both scalar and vector fields, holds common
 /// information about the grid, coordinates, and boundaries
 class FieldData {
diff --git a/include/bout/parallel_boundary_op.hxx b/include/bout/parallel_boundary_op.hxx
index d2edb89b08..6bd692f2a2 100644
--- a/include/bout/parallel_boundary_op.hxx
+++ b/include/bout/parallel_boundary_op.hxx
@@ -7,14 +7,10 @@
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_factory.hxx"
-#include "bout/parallel_boundary_region.hxx"
 #include "bout/sys/expressionparser.hxx"
 #include "bout/unused.hxx"
-#include "bout/utils.hxx"
 
-#include <map>
 #include <memory>
-#include <utility>
 
 //////////////////////////////////////////////////
 // Base class
diff --git a/include/bout/parallel_boundary_region.hxx b/include/bout/parallel_boundary_region.hxx
deleted file mode 100644
index 4881e42eda..0000000000
--- a/include/bout/parallel_boundary_region.hxx
+++ /dev/null
@@ -1,189 +0,0 @@
-#ifndef BOUT_PAR_BNDRY_H
-#define BOUT_PAR_BNDRY_H
-
-#include <bout/assert.hxx>
-#include <bout/boundary_region.hxx>
-#include <bout/bout_types.hxx>
-#include <bout/field2d.hxx>
-#include <bout/field3d.hxx>
-#include <bout/mesh.hxx>
-#include <bout/region.hxx>
-
-#include <algorithm>
-#include <cmath>
-#include <cstdlib>
-#include <string>
-#include <vector>
-
-/**
- * Boundary region for parallel direction. This contains a vector of points that are
- * inside the boundary.
- *
- */
-
-namespace bout {
-namespace parallel_boundary_region {
-
-struct RealPoint {
-  BoutReal s_x;
-  BoutReal s_y;
-  BoutReal s_z;
-};
-
-struct Indices {
-  // Indices of the boundary point
-  Ind3D index;
-  // Intersection with boundary in index space
-  RealPoint intersection;
-  // Distance to intersection
-  BoutReal length;
-  // Angle between field line and boundary
-  // BoutReal angle;
-  // How many points we can go in the opposite direction
-  signed char valid;
-  signed char offset;
-  unsigned char abs_offset;
-  Indices(Ind3D index, RealPoint intersection, BoutReal length, signed char valid,
-          signed char offset, unsigned char abs_offset)
-      : index(index), intersection(intersection), length(length), valid(valid),
-        offset(offset), abs_offset(abs_offset) {};
-
-  auto operator<=>(const Indices& rhs) const { return index <=> rhs.index; }
-  auto operator<=>(const Ind3D& rhs) const { return index <=> rhs; }
-};
-
-using IndicesVec = std::vector<Indices>;
-using IndicesIter = IndicesVec::iterator;
-using IndicesIterConst = IndicesVec::const_iterator;
-
-template <class IndicesVec, class IndicesIter>
-class BoundaryRegionParIterBase {
-
-public:
-  BoundaryRegionParIterBase(IndicesVec& bndry_points, IndicesIter bndry_position, int dir,
-                            Mesh* localmesh)
-      : bndry_points(bndry_points), bndry_position(bndry_position), _dir(dir),
-        localmesh(localmesh) {};
-
-  std::size_t size() { return this->bndry_points.size(); }
-
-  // getter
-  Ind3D ind() const { return bndry_position->index; }
-  BoutReal s_x() const { return bndry_position->intersection.s_x; }
-  BoutReal s_y() const { return bndry_position->intersection.s_y; }
-  BoutReal s_z() const { return bndry_position->intersection.s_z; }
-  BoutReal length([[maybe_unused]] CELL_LOC loc) const {
-    ASSERT3(loc == CELL_CENTRE);
-    return bndry_position->length;
-  }
-  signed char valid() const { return bndry_position->valid; }
-  signed char offset() const { return bndry_position->offset; }
-  unsigned char abs_offset() const { return bndry_position->abs_offset; }
-
-  // setter
-  void setValid(signed char valid) { bndry_position->valid = valid; }
-
-private:
-  const IndicesVec& bndry_points;
-  IndicesIter bndry_position;
-
-  constexpr static BoutReal small_value = 1e-2;
-  int _dir;
-
-public:
-  int dir() const { return _dir; }
-  Mesh* localmesh;
-};
-} // namespace parallel_boundary_region
-} // namespace bout
-using BoundaryRegionParIter = bout::parallel_boundary_region::BoundaryRegionParIterBase<
-    bout::parallel_boundary_region::IndicesVec,
-    bout::parallel_boundary_region::IndicesIter>;
-using BoundaryRegionParIterConst =
-    bout::parallel_boundary_region::BoundaryRegionParIterBase<
-        const bout::parallel_boundary_region::IndicesVec,
-        bout::parallel_boundary_region::IndicesIterConst>;
-
-class BoundaryRegionPar : public BoundaryRegionBase {
-public:
-  BoundaryRegionPar(const std::string& name, int dir, Mesh* passmesh)
-      : BoundaryRegionBase(name, passmesh), _dir(dir) {
-    ASSERT0(std::abs(dir) == 1);
-    BoundaryRegionBase::isParallel = true;
-  }
-  BoundaryRegionPar(const std::string& name, BndryLoc loc, int dir, Mesh* passmesh)
-      : BoundaryRegionBase(name, loc, passmesh), _dir(dir) {
-    BoundaryRegionBase::isParallel = true;
-    ASSERT0(std::abs(dir) == 1);
-  }
-
-  /// Add a point to the boundary
-  void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
-                 char valid, signed char offset) {
-    if (!bndry_points.empty() && bndry_points.back().index > ind) {
-      is_sorted = false;
-    }
-    bndry_points.emplace_back(ind, bout::parallel_boundary_region::RealPoint{x, y, z},
-                              length, valid, offset,
-                              static_cast<unsigned char>(std::abs(offset)));
-  }
-  void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
-                 BoutReal length, char valid, signed char offset) {
-    add_point(xyz2ind(ix, iy, iz, localmesh), x, y, z, length, valid, offset);
-  }
-
-  // final, so they can be inlined
-  void first() final { bndry_position = std::begin(bndry_points); }
-  void next() final { ++bndry_position; }
-  bool isDone() final { return (bndry_position == std::end(bndry_points)); }
-
-  bool contains(const BoundaryRegionPar& bndry) const {
-    ASSERT2(is_sorted);
-    return std::binary_search(std::begin(bndry_points), std::end(bndry_points),
-                              *bndry.bndry_position,
-                              [](const bout::parallel_boundary_region::Indices& i1,
-                                 const bout::parallel_boundary_region::Indices& i2) {
-                                return i1.index < i2.index;
-                              });
-  }
-
-  bool contains(const int ix, const int iy, const int iz) const {
-    const auto i2 = xyz2ind(ix, iy, iz, localmesh);
-    return std::ranges::any_of(bndry_points.begin(), bndry_points.end(),
-                               [&i2](auto i1) { return i1.index == i2; });
-  }
-
-  // setter
-  void setValid(char val) { bndry_position->valid = val; }
-
-  // BoundaryRegionParIterConst begin() const {
-  //   return BoundaryRegionParIterConst(bndry_points, bndry_points.begin(), dir);
-  // }
-  // BoundaryRegionParIterConst end() const {
-  //   return BoundaryRegionParIterConst(bndry_points, bndry_points.begin(), dir);
-  // }
-  BoundaryRegionParIter begin() {
-    return BoundaryRegionParIter(bndry_points, bndry_points.begin(), _dir, localmesh);
-  }
-  BoundaryRegionParIter end() {
-    return BoundaryRegionParIter(bndry_points, bndry_points.end(), _dir, localmesh);
-  }
-
-  int dir() const { return _dir; }
-
-private:
-  int _dir;
-  /// Vector of points in the boundary
-  bout::parallel_boundary_region::IndicesVec bndry_points;
-  /// Current position in the boundary points
-  bout::parallel_boundary_region::IndicesIter bndry_position;
-
-  static Ind3D xyz2ind(int x, int y, int z, Mesh* mesh) {
-    const int ny = mesh->LocalNy;
-    const int nz = mesh->LocalNz;
-    return Ind3D{(x * ny + y) * nz + z, ny, nz};
-  }
-  bool is_sorted{true};
-};
-
-#endif //  BOUT_PAR_BNDRY_H
diff --git a/src/field/field3d.cxx b/src/field/field3d.cxx
index cb5d5f44d3..70ba55368b 100644
--- a/src/field/field3d.cxx
+++ b/src/field/field3d.cxx
@@ -43,8 +43,6 @@
 #include <string>
 #include <utility>
 
-#include "bout/parallel_boundary_op.hxx"
-#include "bout/parallel_boundary_region.hxx"
 #include <bout/assert.hxx>
 #include <bout/boundary_factory.hxx>
 #include <bout/boundary_op.hxx>
@@ -57,6 +55,7 @@
 #include <bout/interpolation.hxx>
 #include <bout/mesh.hxx>
 #include <bout/output.hxx>
+#include <bout/parallel_boundary_op.hxx>
 #include <bout/region.hxx>
 #include <bout/utils.hxx>
 
diff --git a/src/field/field_data.cxx b/src/field/field_data.cxx
index 23865de974..a4df94a85b 100644
--- a/src/field/field_data.cxx
+++ b/src/field/field_data.cxx
@@ -1,7 +1,5 @@
 
 #include "bout/parallel_boundary_op.hxx"
-#include "bout/parallel_boundary_region.hxx"
-#include "bout/unused.hxx"
 #include <bout/boundary_factory.hxx>
 #include <bout/field_data.hxx>
 #include <bout/field_factory.hxx>
diff --git a/src/mesh/boundary_factory.cxx b/src/mesh/boundary_factory.cxx
index f0c41cf8a1..b745524fb4 100644
--- a/src/mesh/boundary_factory.cxx
+++ b/src/mesh/boundary_factory.cxx
@@ -1,6 +1,5 @@
 #include "bout/assert.hxx"
 #include "bout/parallel_boundary_op.hxx"
-#include "bout/parallel_boundary_region.hxx"
 #include <bout/boundary_factory.hxx>
 #include <bout/boundary_region_iter.hxx>
 #include <bout/boundary_standard.hxx>
@@ -10,7 +9,6 @@
 
 #include <array>
 #include <list>
-#include <map>
 #include <memory>
 #include <string>
 using std::list;
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 0e3c8bdcf3..347647b2cd 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -45,7 +45,6 @@
 #include <bout/msg_stack.hxx>
 #include <bout/options.hxx>
 #include <bout/output.hxx>
-#include <bout/parallel_boundary_region.hxx>
 #include <bout/region.hxx>
 #include <bout/sys/gettext.hxx>
 #include <bout/sys/range.hxx>
diff --git a/src/mesh/parallel/fci.cxx b/src/mesh/parallel/fci.cxx
index 72861eb68f..6b68a6635c 100644
--- a/src/mesh/parallel/fci.cxx
+++ b/src/mesh/parallel/fci.cxx
@@ -51,7 +51,6 @@
 #include "bout/msg_stack.hxx"
 #include "bout/options.hxx"
 #include "bout/parallel_boundary_op.hxx"
-#include "bout/parallel_boundary_region.hxx"
 #include "bout/paralleltransform.hxx"
 #include "bout/region.hxx"
 
@@ -59,7 +58,6 @@
 
 #include <array>
 #include <cmath>
-#include <cstddef>
 #include <cstdlib>
 #include <memory>
 #include <string>
diff --git a/src/mesh/parallel/fci.hxx b/src/mesh/parallel/fci.hxx
index f5d0642675..9fc89296dc 100644
--- a/src/mesh/parallel/fci.hxx
+++ b/src/mesh/parallel/fci.hxx
@@ -34,7 +34,6 @@
 #include <bout/boundary_region_iter.hxx>
 #include <bout/interpolation_xz.hxx>
 #include <bout/mask.hxx>
-#include <bout/parallel_boundary_region.hxx>
 #include <bout/paralleltransform.hxx>
 #include <bout/unused.hxx>
 
diff --git a/src/mesh/parallel/shiftedmetric.cxx b/src/mesh/parallel/shiftedmetric.cxx
index 705c48e944..972cb58330 100644
--- a/src/mesh/parallel/shiftedmetric.cxx
+++ b/src/mesh/parallel/shiftedmetric.cxx
@@ -6,7 +6,6 @@
  *
  */
 
-#include "bout/parallel_boundary_region.hxx"
 #include "bout/paralleltransform.hxx"
 #include <bout/boundary_region.hxx>
 #include <bout/constants.hxx>
@@ -15,8 +14,6 @@
 #include <bout/output.hxx>
 #include <bout/sys/timer.hxx>
 
-#include <cmath>
-
 #if BOUT_HAS_CUDA
 #include <bout/twiddle.hxx>
 #include <cuda_runtime.h>
diff --git a/src/mesh/yboundary_regions.cxx b/src/mesh/yboundary_regions.cxx
index 12036a6466..af186cf925 100644
--- a/src/mesh/yboundary_regions.cxx
+++ b/src/mesh/yboundary_regions.cxx
@@ -4,7 +4,6 @@
 #include "bout/boundary_region_iter.hxx"
 #include "bout/field_data.hxx"
 #include "bout/options.hxx"
-#include "bout/parallel_boundary_region.hxx"
 
 #include <memory>
 
diff --git a/tests/integrated/test-fci-boundary/get_par_bndry.cxx b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
index 45fadc03c1..fd3bc2889f 100644
--- a/tests/integrated/test-fci-boundary/get_par_bndry.cxx
+++ b/tests/integrated/test-fci-boundary/get_par_bndry.cxx
@@ -5,7 +5,6 @@
 #include "bout/options.hxx"
 #include "bout/options_io.hxx"
 #include "bout/output.hxx"
-#include "bout/parallel_boundary_region.hxx"
 #include "bout/yboundary_regions.hxx"
 
 #include <fmt/format.h>

From 1d19b72a31213da70bd186d013b0cfedad2fd464 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 26 Aug 2026 11:58:52 +0100
Subject: [PATCH 1785/1827] Fix FCI example

---
 examples/fci-wave/fci-wave.cxx | 72 ++++++++++++----------------------
 1 file changed, 25 insertions(+), 47 deletions(-)

diff --git a/examples/fci-wave/fci-wave.cxx b/examples/fci-wave/fci-wave.cxx
index 8769b83470..0ded45ebfd 100644
--- a/examples/fci-wave/fci-wave.cxx
+++ b/examples/fci-wave/fci-wave.cxx
@@ -1,4 +1,13 @@
-#include "bout/physicsmodel.hxx"
+#include <bout/boundary_region_iter.hxx>
+#include <bout/bout_types.hxx>
+#include <bout/coordinates.hxx>
+#include <bout/difops.hxx>
+#include <bout/field3d.hxx>
+#include <bout/options.hxx>
+#include <bout/output.hxx>
+#include <bout/physicsmodel.hxx>
+#include <bout/unused.hxx>
+#include <bout/yboundary_regions.hxx>
 
 #include <cmath>
 
@@ -19,35 +28,26 @@ class FCIwave : public PhysicsModel {
     Field3D f_B = f / Bxyz;
 
     f_B.splitParallelSlices();
-    mesh->getCoordinates()->getParallelTransform().integrateParallelSlices(f_B);
+    const Coordinates* coord = mesh->getCoordinates();
+    coord->getParallelTransform().integrateParallelSlices(f_B);
 
     // integrateParallelSlices replaces all yup/down points, so the boundary conditions
     // now need to be applied. If Bxyz has neumann parallel boundary conditions
     // then the boundary condition is simpler since f = 0 gives f_B=0 boundary condition.
 
-    /// Loop over the mesh boundary regions
-    for (const auto& reg : mesh->getBoundariesPar()) {
-      Field3D& f_B_next = f_B.ynext(reg->dir);
-      const Field3D& f_next = f.ynext(reg->dir);
-      const Field3D& B_next = Bxyz.ynext(reg->dir);
-
-      for (reg->first(); !reg->isDone(); reg->next()) {
-        f_B_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z()) =
-            f_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z())
-            / B_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z());
-      }
-    }
+    const auto ybndry = coord->getYBoundary();
+    ybndry.iter([&](const bout::boundary::BoundaryIterator auto& point) {
+      point.next(f_B) = point.next(f) / point.next(Bxyz);
+    });
 
     Field3D result;
     result.allocate();
 
-    Coordinates* coord = mesh->getCoordinates();
-
     for (auto i : result.getRegion(RGN_NOBNDRY)) {
       result[i] = Bxyz[i] * (f_B.yup()[i.yp()] - f_B.ydown()[i.ym()])
                   / (2. * coord->dy()[i] * sqrt(coord->g_22()[i]));
 
-      if (!finite(result[i])) {
+      if (!std::isfinite(result[i])) {
         output.write("[{:d},{:d},{:d}]: {:e}, {:e} -> {:e}\n", i.x(), i.y(), i.z(),
                      f_B.yup()[i.yp()], f_B.ydown()[i.ym()], result[i]);
       }
@@ -65,7 +65,7 @@ class FCIwave : public PhysicsModel {
     auto& options = Options::root()["fciwave"];
     div_integrate = options["div_integrate"].withDefault(true);
     log_density = options["log_density"].withDefault(false);
-    background = options["background"].withDefault(false);
+    background = options["background"].withDefault(0.0);
     log_background = log(background);
 
     // Neumann boundaries simplifies parallel derivatives
@@ -117,38 +117,16 @@ class FCIwave : public PhysicsModel {
     // between v, nv and momentum flux
 
     momflux.splitParallelSlices();
-    for (const auto& reg : mesh->getBoundariesPar()) {
+    const auto ybndry = mesh->getCoordinates()->getYBoundary();
+    ybndry.iter([&](const bout::boundary::BoundaryIterator auto& point) {
       // Using the values of density and velocity on the boundary
-      const Field3D& n_next = n.ynext(reg->dir);
-      const Field3D& v_next = v.ynext(reg->dir);
+      const BoutReal n_b = 0.5 * point.next(n) + point.current(n);
+      const BoutReal v_b = 0.5 * point.next(v) + point.current(v);
 
       // Set the momentum and momentum flux
-      Field3D& nv_next = nv.ynext(reg->dir);
-      Field3D& momflux_next = momflux.ynext(reg->dir);
-      momflux_next.allocate();
-
-      for (reg->first(); !reg->isDone(); reg->next()) {
-        // Density at the boundary
-        // Note: If evolving density, this should interpolate logn
-        // but neumann boundaries are used here anyway.
-        BoutReal n_b =
-            0.5
-            * (n_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z())
-               + n(reg->ind().x(), reg->ind().y(), reg->ind().z()));
-        // Velocity at the boundary
-        BoutReal v_b =
-            0.5
-            * (v_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z())
-               + v(reg->ind().x(), reg->ind().y(), reg->ind().z()));
-
-        nv_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z()) =
-            2. * n_b * v_b - nv(reg->ind().x(), reg->ind().y(), reg->ind().z());
-
-        momflux_next(reg->ind().x(), reg->ind().y() + reg->dir, reg->ind().z()) =
-            2. * n_b * v_b * v_b
-            - momflux(reg->ind().x(), reg->ind().y(), reg->ind().z());
-      }
-    }
+      point.next(nv) = 2. * n_b * v_b - point.current(nv);
+      point.next(momflux) = 2. * n_b * v_b * v_b - point.current(momflux);
+    });
 
     // Momentum
     ddt(nv) = -Div_par_integrate(momflux) - Grad_par(n) + Grad2_par2(nv);

From 5472277aa342620c417f6e188f82426cacedd27a Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 26 Aug 2026 13:21:51 +0100
Subject: [PATCH 1786/1827] Flip order of operands in single index `Delp2` to
 match `D2DX2`

Fixes #3455

The difference in order of the stencils for the single index `Delp2` and the
stencil used for `D2DX2` used in the full field `Delp2` can cause very small
differences in the results due to floating point maths not being commutative.

This can give sporadic failures in CI
---
 include/bout/single_index_ops.hxx | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/include/bout/single_index_ops.hxx b/include/bout/single_index_ops.hxx
index c29d1a471f..3f4686c514 100644
--- a/include/bout/single_index_ops.hxx
+++ b/include/bout/single_index_ops.hxx
@@ -5,7 +5,11 @@
 #ifndef SINGLE_INDEX_OPS_H
 #define SINGLE_INDEX_OPS_H
 
-#include "field_accessor.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/build_config.hxx"
+#include "bout/field_accessor.hxx"
+#include "bout/region.hxx"
+#include "bout/utils.hxx"
 
 // Ind3D: i.zp():
 BOUT_HOST_DEVICE inline int i_zp(const int id, const int nz) {
@@ -228,8 +232,8 @@ BOUT_HOST_DEVICE inline BoutReal Delp2(const FieldAccessor<location>& f, const i
   return (f.coords.G1(i) + f.coords.d1_dx(i) * f.coords.g11(i)) * (f[ixp] - f[ixm])
              / (2.0 * dx)                                            // DDX
          + f.coords.G3(i) * (f[izp] - f[izm]) / (2.0 * dz)           // DDZ
-         + f.coords.g11(i) * (f[ixp] - 2.0 * f[i] + f[ixm]) / SQ(dx) // D2DX2
-         + f.coords.g33(i) * (f[izp] - 2.0 * f[i] + f[izm]) / SQ(dz) // D2DZ2
+         + f.coords.g11(i) * (f[ixp] + f[ixm] - 2.0 * f[i]) / SQ(dx) // D2DX2
+         + f.coords.g33(i) * (f[izp] + f[izm] - 2.0 * f[i]) / SQ(dz) // D2DZ2
          + 2 * f.coords.g13(i) * ((f[izpxp] - f[izpxm]) - (f[izmxp] - f[izmxm]))
                / (4. * dz * dx); // D2DXDZ
 }

From 52e95ea0997a697420291d845cb31f74e0e401d3 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 26 Aug 2026 14:50:54 +0100
Subject: [PATCH 1787/1827] Reorder members for improved alignment

---
 include/bout/boundary_region_iter.hxx | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index d85f5c364c..1843a7d653 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -192,30 +192,29 @@ public:
   /// A single point in a `BoundaryRegionFCI`
   class Point : public BoundaryRegionIterBase<Point> {
   private:
-    /// Indices of the boundary point
+    /// Index of the first boundary point
     Ind3D index;
+    Mesh* localmesh_m;
     /// Intersection with boundary in index space
     RealPoint intersection;
     /// Distance to intersection
     BoutReal length_m;
+    /// Direction to the boundary. Positive values are in the sense of the
+    /// increasing coordinate
+    int dir_m;
     /// How many points we can go in the opposite direction
     signed char valid_m;
     /// How many points we are away from the boundary
     signed char offset_m;
     unsigned char abs_offset_m;
 
-    Mesh* localmesh_m;
-    /// Direction to the boundary. Positive values are in the sense of the
-    /// increasing coordinate
-    int dir_m;
-
   public:
     Point() = delete;
     Point(Ind3D index, RealPoint intersection, BoutReal length, signed char valid,
           signed char offset, Mesh* mesh, int dir)
-        : index(index), intersection(intersection), length_m(length), valid_m(valid),
-          offset_m(offset), abs_offset_m(static_cast<unsigned char>(std::abs(offset))),
-          localmesh_m(mesh), dir_m(dir) {}
+        : index(index), localmesh_m(mesh), intersection(intersection), length_m(length),
+          dir_m(dir), valid_m(valid), offset_m(offset),
+          abs_offset_m(static_cast<unsigned char>(std::abs(offset))) {}
 
     void setValid(char valid) { valid_m = valid; };
 

From c077f47de0af8192f63e45e10b5b51fab7f92b42 Mon Sep 17 00:00:00 2001
From: Peter Hill <peter.hill@york.ac.uk>
Date: Wed, 26 Aug 2026 14:52:10 +0100
Subject: [PATCH 1788/1827] Fix `BoundaryRegionXY::length` for staggered grids
 in Y

---
 include/bout/boundary_region_iter.hxx | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/include/bout/boundary_region_iter.hxx b/include/bout/boundary_region_iter.hxx
index 1843a7d653..d28f9d21d4 100644
--- a/include/bout/boundary_region_iter.hxx
+++ b/include/bout/boundary_region_iter.hxx
@@ -406,12 +406,11 @@ public:
       }
       return region->localmesh->ystart;
     }
+
     BoutReal _length(CELL_LOC loc) const {
-      if (loc == CELL_XLOW) {
-        if (dir() == 1) {
-          return 1;
-        }
-        return 0;
+      // Account for staggered grids
+      if ((isXtemp and loc == CELL_XLOW) or (not isXtemp and loc == CELL_YLOW)) {
+        return (dir() == 1) ? 1 : 0;
       }
       return 0.5;
     }

From 307074f2321da826d66c597cc03f6664b11b6fe5 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 27 Aug 2026 09:51:15 +0200
Subject: [PATCH 1789/1827] Update difops interface to take Field3DParallel

---
 include/bout/difops.hxx | 14 +++++++-------
 src/mesh/difops.cxx     | 15 +++++++--------
 2 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/include/bout/difops.hxx b/include/bout/difops.hxx
index 951ff5612f..0b3320c1f1 100644
--- a/include/bout/difops.hxx
+++ b/include/bout/difops.hxx
@@ -77,7 +77,7 @@ Field3D Grad_par(const Field3DParallel& var, CELL_LOC outloc = CELL_DEFAULT,
  * Combines the parallel and perpendicular calculation to include
  * grid-points at the corners.
  */
-Field3D Grad_parP(const Field3D& apar, const Field3D& f);
+Field3D Grad_parP(const Field3D& apar, const Field3DParallel& f);
 
 /*!
  * vpar times parallel derivative along unperturbed B-field (upwinding)
@@ -172,9 +172,9 @@ inline bout::FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc,
   return Grad2_par2(f, outloc, toString(method));
 }
 
-Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+Field3D Grad2_par2(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                    const std::string& method = "DEFAULT");
-inline Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc, DIFF_METHOD method) {
+inline Field3D Grad2_par2(const Field3DParallel& f, CELL_LOC outloc, DIFF_METHOD method) {
   return Grad2_par2(f, outloc, toString(method));
 }
 
@@ -257,7 +257,7 @@ Field3D Laplace_perp(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
  *
  */
 bout::FieldMetric Laplace_par(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT);
-Field3D Laplace_par(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT);
+Field3D Laplace_par(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT);
 
 /*!
  * Full Laplacian operator (par + perp)
@@ -265,7 +265,7 @@ Field3D Laplace_par(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT);
 bout::FieldMetric Laplace(const Field2D& f, CELL_LOC outloc = CELL_DEFAULT,
                           const std::string& dfdy_boundary_condition = "free_o3",
                           const std::string& dfdy_region = "");
-Field3D Laplace(const Field3D& f, CELL_LOC outloc = CELL_DEFAULT,
+Field3D Laplace(const Field3DParallel& f, CELL_LOC outloc = CELL_DEFAULT,
                 const std::string& dfdy_boundary_condition = "free_o3",
                 const std::string& dfdy_region = "");
 
@@ -292,11 +292,11 @@ bout::FieldMetric b0xGrad_dot_Grad(const Field2D& phi, const Field2D& A,
  * @param[in] A   The field being advected
  * @param[in] outloc  The cell location where the result is defined. By default the same as A.
  */
-Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field2D& A,
+Field3D b0xGrad_dot_Grad(const Field3DParallel& phi, const Field2D& A,
                          CELL_LOC outloc = CELL_DEFAULT);
 Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A,
                          CELL_LOC outloc = CELL_DEFAULT);
-Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A,
+Field3D b0xGrad_dot_Grad(const Field3DParallel& phi, const Field3D& A,
                          CELL_LOC outloc = CELL_DEFAULT);
 
 /*!
diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 7bd0c175e2..4defdae3f2 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -74,7 +74,7 @@ Field3D Grad_par(const Field3DParallel& var, CELL_LOC outloc, const std::string&
 * grid-points at the corners.
 *******************************************************************************/
 
-Field3D Grad_parP(const Field3D& apar, const Field3D& f) {
+Field3D Grad_parP(const Field3D& apar, const Field3DParallel& f) {
   ASSERT1_FIELDS_COMPATIBLE(apar, f);
   ASSERT1(f.hasParallelSlices());
 
@@ -301,7 +301,7 @@ bout::FieldMetric Grad2_par2(const Field2D& f, CELL_LOC outloc,
          + D2DY2(f, outloc, method) / coords.g_22();
 }
 
-Field3D Grad2_par2(const Field3D& f, CELL_LOC outloc, const std::string& method) {
+Field3D Grad2_par2(const Field3DParallel& f, CELL_LOC outloc, const std::string& method) {
   if (outloc == CELL_DEFAULT) {
     outloc = f.getLocation();
   }
@@ -713,11 +713,10 @@ bout::FieldMetric Laplace_par(const Field2D& f, CELL_LOC outloc) {
                / coords.J();
 }
 
-Field3D Laplace_par(const Field3D& f, CELL_LOC outloc) {
+Field3D Laplace_par(const Field3DParallel& f, CELL_LOC outloc) {
   const auto& coords = *f.getCoordinates(outloc);
   return D2DY2(f, outloc) / coords.g_22()
-         + DDY(coords.J().asField3DParallel() / coords.g_22(), outloc) * DDY(f, outloc)
-               / coords.J();
+         + DDY(coords.J() / coords.g_22(), outloc) * DDY(f, outloc) / coords.J();
 }
 
 /*******************************************************************************
@@ -737,7 +736,7 @@ bout::FieldMetric Laplace(const Field2D& f, CELL_LOC outloc,
                         dfdy_region);
 }
 
-Field3D Laplace(const Field3D& f, CELL_LOC outloc,
+Field3D Laplace(const Field3DParallel& f, CELL_LOC outloc,
                 const std::string& dfdy_boundary_condition,
                 const std::string& dfdy_region) {
   const auto& coords = *f.getCoordinates(outloc);
@@ -900,7 +899,7 @@ Field3D b0xGrad_dot_Grad(const Field2D& phi, const Field3D& A, CELL_LOC outloc)
   return result;
 }
 
-Field3D b0xGrad_dot_Grad(const Field3D& p, const Field2D& A, CELL_LOC outloc) {
+Field3D b0xGrad_dot_Grad(const Field3DParallel& p, const Field2D& A, CELL_LOC outloc) {
 
   if (outloc == CELL_DEFAULT) {
     outloc = A.getLocation();
@@ -934,7 +933,7 @@ Field3D b0xGrad_dot_Grad(const Field3D& p, const Field2D& A, CELL_LOC outloc) {
   return result;
 }
 
-Field3D b0xGrad_dot_Grad(const Field3D& phi, const Field3D& A, CELL_LOC outloc) {
+Field3D b0xGrad_dot_Grad(const Field3DParallel& phi, const Field3D& A, CELL_LOC outloc) {
 
   if (outloc == CELL_DEFAULT) {
     outloc = A.getLocation();

From da3008f1c3c507075b466247af403c29fe92d886 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 27 Aug 2026 09:51:57 +0200
Subject: [PATCH 1790/1827] Remove stale .asField3DParallel

This is not needed anymore
---
 src/mesh/g_values.cxx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/mesh/g_values.cxx b/src/mesh/g_values.cxx
index cf4713464e..3ed6b896ec 100644
--- a/src/mesh/g_values.cxx
+++ b/src/mesh/g_values.cxx
@@ -18,9 +18,9 @@ GValues::GValues(const Coordinates& coordinates) {
 
   auto* mesh = J.getMesh();
 
-  G1_m = (DDX(J * g11) + DDY(J.asField3DParallel() * g12) + DDZ(J * g13)) / J;
-  G2_m = (DDX(J * g12) + DDY(J.asField3DParallel() * g22) + DDZ(J * g23)) / J;
-  G3_m = (DDX(J * g13) + DDY(J.asField3DParallel() * g23) + DDZ(J * g33)) / J;
+  G1_m = (DDX(J * g11) + DDY(J * g12) + DDZ(J * g13)) / J;
+  G2_m = (DDX(J * g12) + DDY(J * g22) + DDZ(J * g23)) / J;
+  G3_m = (DDX(J * g13) + DDY(J * g23) + DDZ(J * g33)) / J;
 
   mesh->communicate_no_slices(G1_m, G2_m, G3_m);
 }

From 9876ba468e06ae94562ac32ec417188c7c6b8cdf Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 27 Aug 2026 09:52:52 +0200
Subject: [PATCH 1791/1827] Introduce `FieldMetricParallel`

This is a Field3DParallel for 3D metrics, and Field2D otherwise.
This allows simplify some code, that needs parallel slices
for 3D metrics, but is a field2d otherwise.
---
 include/bout/metric_tensor.hxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/bout/metric_tensor.hxx b/include/bout/metric_tensor.hxx
index 8ccaf23395..fa94d504a1 100644
--- a/include/bout/metric_tensor.hxx
+++ b/include/bout/metric_tensor.hxx
@@ -11,8 +11,10 @@
 namespace bout {
 #if BOUT_USE_METRIC_3D
 using FieldMetric = Field3D;
+using FieldMetricParallel = Field3DParallel;
 #else
 using FieldMetric = Field2D;
+using FieldMetricParallel = Field2D;
 #endif
 } // namespace bout
 

From 090da9a6a3964e0bc3e5bef66886c18628a93739 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 27 Aug 2026 09:53:08 +0200
Subject: [PATCH 1792/1827] Extend unit test

---
 tests/unit/field/test_field3d.cxx | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/tests/unit/field/test_field3d.cxx b/tests/unit/field/test_field3d.cxx
index 2be751a7c4..ec2c517628 100644
--- a/tests/unit/field/test_field3d.cxx
+++ b/tests/unit/field/test_field3d.cxx
@@ -2328,12 +2328,22 @@ TEST_F(Field3DTestFCI, MulField3DParallelPreservesParallelSlices) {
   EXPECT_FALSE(prod.hasParallelSlices());
   EXPECT_TRUE(IsFieldEqual(prod, 6.0));
 
-  const Field3DParallel prodpar = field.asField3DParallel() * rhs;
-  EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(prodpar)>, Field3DParallel>));
-  EXPECT_TRUE(prodpar.hasParallelSlices());
-  EXPECT_TRUE(IsFieldEqual(prodpar, 6.0));
-  EXPECT_TRUE(IsFieldEqual(prodpar.yup(), 12.0, "RGN_YPAR_+1"));
-  EXPECT_TRUE(IsFieldEqual(prodpar.ydown(), 20.0, "RGN_YPAR_-1"));
+  {
+    const Field3DParallel prodpar = field.asField3DParallel() * rhs;
+    EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(prodpar)>, Field3DParallel>));
+    EXPECT_TRUE(prodpar.hasParallelSlices());
+    EXPECT_TRUE(IsFieldEqual(prodpar, 6.0));
+    EXPECT_TRUE(IsFieldEqual(prodpar.yup(), 12.0, "RGN_YPAR_+1"));
+    EXPECT_TRUE(IsFieldEqual(prodpar.ydown(), 20.0, "RGN_YPAR_-1"));
+  }
+  {
+    const Field3DParallel prodpar = field * rhs;
+    EXPECT_TRUE((std::is_same_v<std::decay_t<decltype(prodpar)>, Field3DParallel>));
+    EXPECT_TRUE(prodpar.hasParallelSlices());
+    EXPECT_TRUE(IsFieldEqual(prodpar, 6.0));
+    EXPECT_TRUE(IsFieldEqual(prodpar.yup(), 12.0, "RGN_YPAR_+1"));
+    EXPECT_TRUE(IsFieldEqual(prodpar.ydown(), 20.0, "RGN_YPAR_-1"));
+  }
 }
 
 TEST_F(Field3DTestFCI, DivField3DParallelPreservesParallelSlices) {

From 502a650cbb42f23e6051cb3ef61e009747ce1a5d Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Thu, 27 Aug 2026 11:34:47 +0200
Subject: [PATCH 1793/1827] Add doc about `bout::FieldMetricParallel`

---
 manual/sphinx/user_docs/field_expressions.rst | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/manual/sphinx/user_docs/field_expressions.rst b/manual/sphinx/user_docs/field_expressions.rst
index 7c82d48884..90fc04881a 100644
--- a/manual/sphinx/user_docs/field_expressions.rst
+++ b/manual/sphinx/user_docs/field_expressions.rst
@@ -96,7 +96,7 @@ Several mixed-type combinations are supported directly:
 - `pow` follows the same mixed-rank pattern, so either operand can be
   `Field2D` or `Field3D` and the result is a `Field3D`
 - expressions involving metric components may return
-  `Coordinates::FieldMetric`, which is `Field2D` or `Field3D` depending
+  `bout::FieldMetric`, which is `Field2D` or `Field3D` depending
   on how BOUT++ was built
 
 In practice, this means code such as::
@@ -135,6 +135,9 @@ when working with `Field3DParallel` on FCI meshes:
   main field values
 - on FCI meshes, operands contributing to a `Field3DParallel`
   expression must have compatible parallel slices available
+- For metric components that should preserve parallel slices for FCI
+  `bout::FieldMetricParallel` acts like `Field3DParallel` for 3D metrics
+  and like `Field2D` otherwise.
 
 For example::
 

From f7537c16fab3c0817fa4f95520bac3c18ca32e96 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 28 Aug 2026 12:12:19 +0200
Subject: [PATCH 1794/1827] Honor bndry_flux for FCI for Div_par_K_Grad_par_mod

---
 src/mesh/difops.cxx | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/src/mesh/difops.cxx b/src/mesh/difops.cxx
index 7bd0c175e2..f70f349b2c 100644
--- a/src/mesh/difops.cxx
+++ b/src/mesh/difops.cxx
@@ -44,6 +44,7 @@
 #include <bout/solver.hxx>
 #include <bout/unused.hxx>
 #include <bout/utils.hxx>
+#include <bout/yboundary_regions.hxx>
 
 #include <cmath>
 #include <limits>
@@ -386,23 +387,32 @@ Field3D Div_par_K_Grad_par_mod_impl(const Field3DParallel& Kin,
     Field3D result{zeroFrom(fin)};
     flow_ylow = zeroFrom(fin);
 
+    const auto yboundary = coord->getYBoundary();
+
     BOUT_FOR(i, result.getRegion("RGN_NOBNDRY")) {
       const auto iyp = i.yp();
       const auto iym = i.ym();
 
       // Upper cell edge
-      const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]); // K at the upper boundary
-      const BoutReal gradient_up =
-          (f_up[iyp] - fin[i]) / (coord->dy()[i] * sqrt(coord->g_22_yhigh()[i]));
+      BoutReal flux_up = 0;
+      if (bndry_flux or not yboundary.contains<+1>(i)) {
+        const BoutReal c_up = 0.5 * (Kin[i] + K_up[iyp]); // K at the upper boundary
+
+        const BoutReal gradient_up =
+            (f_up[iyp] - fin[i]) / (coord->dy()[i] * sqrt(coord->g_22_yhigh()[i]));
 
-      const BoutReal flux_up = c_up * gradient_up * coord->cell_area_yhigh()[i];
+        flux_up = c_up * gradient_up * coord->cell_area_yhigh()[i];
+      }
 
       // Lower cell edge
-      const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]); // K at the lower boundary
-      const BoutReal gradient_down =
-          (fin[i] - f_down[iym]) / (coord->dy()[i] * sqrt(coord->g_22_ylow()[i]));
+      BoutReal flux_down = 0;
+      if (bndry_flux or not yboundary.contains<-1>(i)) {
+        const BoutReal c_down = 0.5 * (Kin[i] + K_down[iym]); // K at the lower boundary
+        const BoutReal gradient_down =
+            (fin[i] - f_down[iym]) / (coord->dy()[i] * sqrt(coord->g_22_ylow()[i]));
 
-      const BoutReal flux_down = c_down * gradient_down * coord->cell_area_ylow()[i];
+        flux_down = c_down * gradient_down * coord->cell_area_ylow()[i];
+      }
 
       // Add the fluxes
       result[i] = (flux_up - flux_down) / (coord->cell_volume()[i]);

From 1a71822b83a46268e2aa11c5234ec75537ac6227 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Fri, 28 Aug 2026 12:28:04 +0200
Subject: [PATCH 1795/1827] Honor bndry_flux for FCI for Div_par_K_Grad_par

---
 src/mesh/fv_ops.cxx | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/mesh/fv_ops.cxx b/src/mesh/fv_ops.cxx
index d00187fedc..afe8088523 100644
--- a/src/mesh/fv_ops.cxx
+++ b/src/mesh/fv_ops.cxx
@@ -12,6 +12,7 @@
 #include "bout/msg_stack.hxx"
 #include "bout/region.hxx"
 #include "bout/utils.hxx"
+#include <bout/yboundary_regions.hxx>
 
 namespace {
 template <class T>
@@ -211,8 +212,12 @@ Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin, bool bndry_fl
     const auto iyp = i.yp();
     const auto iym = i.ym();
 
-    if (bndry_flux || mesh->periodicY(i.x()) || !mesh->lastY(i.x())
-        || (i.y() != mesh->yend)) {
+    const auto yboundary = coord->getYBoundary();
+
+    if (bndry_flux
+        || (not K.isFci()
+            and (mesh->periodicY(i.x()) || !mesh->lastY(i.x()) || (i.y() != mesh->yend)))
+        or (K.isFci() and yboundary.contains<+1>(i))) {
 
       const BoutReal c = 0.5 * (K[i] + Kup[iyp]); // K at the upper boundary
       const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iyp]); // Jacobian at boundary
@@ -227,8 +232,11 @@ Field3D Div_par_K_Grad_par(const Field3D& Kin, const Field3D& fin, bool bndry_fl
     }
 
     // Calculate flux at lower surface
-    if (bndry_flux || mesh->periodicY(i.x()) || !mesh->firstY(i.x())
-        || (i.y() != mesh->ystart)) {
+    if (bndry_flux
+        || (not K.isFci()
+            and (mesh->periodicY(i.x()) || !mesh->firstY(i.x())
+                 || (i.y() != mesh->ystart)))
+        or (K.isFci() and yboundary.contains<-1>(i))) {
       const BoutReal c = 0.5 * (K[i] + Kdown[iym]); // K at the lower boundary
       const BoutReal J = 0.5 * (coord->J()[i] + coord->J()[iym]); // Jacobian at boundary
 

From d28d4dcb8497eec54fd5be75dc0f6c947d2fd021 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Wed, 2 Sep 2026 16:55:06 -0700
Subject: [PATCH 1796/1827] MeshFactory::create read mesh from data directory
 first

Tries to read the mesh from data directory first, falling back
to the previous behavior of reading relative to current directory.

Uses C++20 <filesystem> to manipulate paths and test existence.
---
 src/mesh/mesh.cxx | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index de17645e30..83325382ba 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -28,6 +28,7 @@
 
 #include <algorithm>
 #include <cstddef>
+#include <filesystem>
 #include <iterator>
 #include <memory>
 #include <optional>
@@ -37,6 +38,8 @@
 
 #include "impls/bout/boutmesh.hxx"
 
+namespace fs = std::filesystem;
+
 MeshFactory::ReturnType MeshFactory::create(Options* options,
                                             GridDataSource* source) const {
   return create(getType(options), options, source);
@@ -67,14 +70,22 @@ MeshFactory::ReturnType MeshFactory::create(const std::string& type, Options* op
             grid_name1, grid_name);
       }
     }
-    output << "\nGetting grid data from file " << grid_name << "\n";
 
-    // Create a grid file, using specified format if given
-    const auto grid_ext =
-        (*options)["format"].withDefault(Options::root()["format"].withDefault(""));
+    // Test whether the file is relative to the data directory
+    const auto datadir = fs::path(Options::root()["datadir"]);
+    const auto grid_path = fs::path(grid_name);
+    auto full_path = datadir / grid_path;
+
+    if (!fs::exists(full_path)) {
+      // Use the path relative to the current directory,
+      // typically where the executable was run from.
+      full_path = grid_path;
+    }
+
+    output << "\nGetting grid data from file " << full_path << "\n";
 
     // Create a grid file
-    source = static_cast<GridDataSource*>(new GridFile(grid_name));
+    source = static_cast<GridDataSource*>(new GridFile(full_path));
   } else {
     output << "\nGetting grid data from options\n";
     source = static_cast<GridDataSource*>(new GridFromOptions(options));

From fef8575e00ad430ddb3e9bf60053061984fc5da6 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Thu, 3 Sep 2026 17:20:06 -0700
Subject: [PATCH 1797/1827] MeshFactory: Throw on ambiguous grid file

If both data/file and ./file exist (and are different files),
throw an exception rather than picking one.

Document the new behavior and add unit tests.
---
 manual/sphinx/user_docs/bout_options.rst | 15 +++--
 src/mesh/mesh.cxx                        | 31 +++++++---
 tests/unit/mesh/test_mesh.cxx            | 72 ++++++++++++++++++++++++
 3 files changed, 105 insertions(+), 13 deletions(-)

diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst
index eb71de26e3..cb8fca8115 100644
--- a/manual/sphinx/user_docs/bout_options.rst
+++ b/manual/sphinx/user_docs/bout_options.rst
@@ -476,17 +476,22 @@ minimises ``abs(sqrt(NPES * (nx - 4) / ny) - NXPE)``).
 
 If you need to specify complex input values, e.g. numerical values
 from experiment, you may want to use a grid file. The grid file to use
-is specified relative to the root directory where the simulation is
-run (i.e. running “``ls ./data/BOUT.inp``” gives the options
-file). You can use the global option ``grid``, or ``mesh:file``:
+can be set with the global option ``grid``, or ``mesh:file``:
 
 .. code-block:: cfg
 
-    grid = "data/cbm18_8_y064_x260.nc"
+    grid = "cbm18_8_y064_x260.nc"
 
     # Alternatively:
     [mesh]
-    file = "data/cbm18_8_y064_x260.nc"
+    file = "cbm18_8_y064_x260.nc"
+
+Relative grid paths are first resolved relative to ``datadir``. If that
+file does not exist, BOUT++ falls back to resolving the path relative to
+the current working directory. If matching files exist in both places,
+BOUT++ throws an error rather than guessing which one to use. To avoid
+ambiguity entirely, use an explicit absolute path when the grid file is
+not inside ``datadir``.
 
 
 Communications
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 83325382ba..4e7f64de00 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -71,21 +71,36 @@ MeshFactory::ReturnType MeshFactory::create(const std::string& type, Options* op
       }
     }
 
-    // Test whether the file is relative to the data directory
-    const auto datadir = fs::path(Options::root()["datadir"]);
+    // Resolve mesh files relative to datadir first, then the current directory.
+    const auto datadir = fs::path(Options::root()["datadir"].withDefault("data"));
     const auto grid_path = fs::path(grid_name);
     auto full_path = datadir / grid_path;
 
-    if (!fs::exists(full_path)) {
-      // Use the path relative to the current directory,
-      // typically where the executable was run from.
-      full_path = grid_path;
+    const bool full_path_exists = fs::exists(full_path);
+    const bool grid_path_exists = fs::exists(grid_path);
+
+    if (full_path_exists and grid_path_exists and !fs::equivalent(full_path, grid_path)) {
+      throw BoutException(
+          "Ambiguous grid file path `{:s}`: found both `{:s}` (relative to "
+          "`datadir`) and `{:s}` (relative to the current working directory).\n"
+          "Please specify an explicit path.",
+          grid_name, full_path.string(), grid_path.string());
+    }
+
+    if (!full_path_exists and !grid_path_exists) {
+      throw BoutException(
+          "Could not find grid file `{:s}`.\n"
+          "Looked for `{:s}` (relative to `datadir`) and `{:s}` (relative to "
+          "the current working directory).",
+          grid_name, full_path.string(), grid_path.string());
     }
 
-    output << "\nGetting grid data from file " << full_path << "\n";
+    const auto resolved_path = full_path_exists ? full_path : grid_path;
+
+    output << "\nGetting grid data from file " << resolved_path << "\n";
 
     // Create a grid file
-    source = static_cast<GridDataSource*>(new GridFile(full_path));
+    source = static_cast<GridDataSource*>(new GridFile(resolved_path));
   } else {
     output << "\nGetting grid data from options\n";
     source = static_cast<GridDataSource*>(new GridFromOptions(options));
diff --git a/tests/unit/mesh/test_mesh.cxx b/tests/unit/mesh/test_mesh.cxx
index 8d64f1d0a3..6101c12b21 100644
--- a/tests/unit/mesh/test_mesh.cxx
+++ b/tests/unit/mesh/test_mesh.cxx
@@ -1,5 +1,8 @@
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
+
+#include <filesystem>
+#include <fstream>
 #include <vector>
 
 #include "bout/boutexception.hxx"
@@ -9,6 +12,7 @@
 
 #include "fake_mesh.hxx"
 #include "test_extras.hxx"
+#include "test_tmpfiles.hxx"
 
 /// Test fixture to make sure the global mesh is our fake one
 class MeshTest : public ::testing::Test {
@@ -22,6 +26,26 @@ class MeshTest : public ::testing::Test {
   WithQuietOutput quiet_warn{output_warn};
 };
 
+class MeshPathResolutionTest : public ::testing::Test {
+public:
+  void TearDown() override { Options::cleanup(); }
+};
+
+namespace {
+class ScopedCurrentPath {
+public:
+  explicit ScopedCurrentPath(const std::filesystem::path& path)
+      : previous_path(std::filesystem::current_path()) {
+    std::filesystem::current_path(path);
+  }
+
+  ~ScopedCurrentPath() { std::filesystem::current_path(previous_path); }
+
+private:
+  std::filesystem::path previous_path;
+};
+} // namespace
+
 TEST_F(MeshTest, CreateDefaultRegions) {
   EXPECT_NO_THROW(localmesh.createDefaultRegions());
   EXPECT_THROW(localmesh.createDefaultRegions(), BoutException);
@@ -268,6 +292,54 @@ TEST_F(MeshTest, GetField3DNoSource) {
   EXPECT_TRUE(IsFieldEqual(field3d_value, 0.0));
 }
 
+TEST_F(MeshPathResolutionTest, ThrowsIfGridFilePathIsAmbiguous) {
+  bout::testing::TempFile tempdir;
+  const auto base_path = std::filesystem::path(tempdir.string());
+  const auto datadir = base_path / "data";
+  const auto grid_name = "grid.nc";
+
+  std::filesystem::create_directories(datadir);
+  std::ofstream(datadir / grid_name).close();
+  std::ofstream(base_path / grid_name).close();
+
+  ScopedCurrentPath cwd(base_path);
+
+  auto& root = Options::root();
+  root["datadir"] = "data";
+  auto* mesh_options = root.getSection("mesh");
+  (*mesh_options)["file"] = grid_name;
+
+  try {
+    [[maybe_unused]] auto mesh = MeshFactory::getInstance().create(mesh_options);
+    FAIL() << "Expected BoutException";
+  } catch (const BoutException& e) {
+    EXPECT_THAT(std::string(e.what()), ::testing::HasSubstr("Ambiguous grid file path"));
+    EXPECT_THAT(std::string(e.what()), ::testing::HasSubstr("data/grid.nc"));
+    EXPECT_THAT(std::string(e.what()), ::testing::HasSubstr("grid.nc"));
+  }
+}
+
+TEST_F(MeshPathResolutionTest, ThrowsIfGridFileCannotBeFound) {
+  bout::testing::TempFile tempdir;
+  const auto base_path = std::filesystem::path(tempdir.string());
+
+  std::filesystem::create_directories(base_path);
+  ScopedCurrentPath cwd(base_path);
+
+  auto& root = Options::root();
+  root["datadir"] = "data";
+  auto* mesh_options = root.getSection("mesh");
+  (*mesh_options)["file"] = "missing-grid.nc";
+
+  try {
+    [[maybe_unused]] auto mesh = MeshFactory::getInstance().create(mesh_options);
+    FAIL() << "Expected BoutException";
+  } catch (const BoutException& e) {
+    EXPECT_THAT(std::string(e.what()), ::testing::HasSubstr("Could not find grid file"));
+    EXPECT_THAT(std::string(e.what()), ::testing::HasSubstr("missing-grid.nc"));
+  }
+}
+
 TEST_F(MeshTest, GetField3DNoSourceWithDefault) {
   WithQuietOutput warn{output_warn};
 

From 2ce90a7db4188b2acfed9e0bbde2af05af8aa12e Mon Sep 17 00:00:00 2001
From: maggul <mustafaaggul06@gmail.com>
Date: Thu, 3 Sep 2026 23:31:44 -0500
Subject: [PATCH 1798/1827] merge next-elimBE-new and MRI braches

---
 CMakeLists.txt                                |    2 +
 cmake/SetupBOUTThirdParty.cmake               |    2 +-
 include/bout/monitor.hxx                      |   14 +-
 include/bout/physicsmodel.hxx                 |   59 +-
 include/bout/solver.hxx                       |   35 +
 src/bout++.cxx                                |   64 +-
 src/physics/physicsmodel.cxx                  |   25 +-
 src/solver/impls/arkode/arkode.cxx            |  144 ++-
 src/solver/impls/arkode/arkode_mri.cxx        | 1081 +++++++++++++++++
 src/solver/impls/arkode/arkode_mri.hxx        |  196 +++
 src/solver/solver.cxx                         |  271 ++++-
 tests/integrated/CMakeLists.txt               |    1 +
 tests/integrated/test-kpr_mri/CMakeLists.txt  |    2 +
 tests/integrated/test-kpr_mri/README.md       |   37 +
 tests/integrated/test-kpr_mri/makefile        |    5 +
 tests/integrated/test-kpr_mri/runtest         |   23 +
 .../integrated/test-kpr_mri/test_kpr_mri.cxx  |  161 +++
 tests/integrated/test_suite                   |  366 ++++++
 18 files changed, 2446 insertions(+), 42 deletions(-)
 create mode 100644 src/solver/impls/arkode/arkode_mri.cxx
 create mode 100644 src/solver/impls/arkode/arkode_mri.hxx
 create mode 100644 tests/integrated/test-kpr_mri/CMakeLists.txt
 create mode 100644 tests/integrated/test-kpr_mri/README.md
 create mode 100644 tests/integrated/test-kpr_mri/makefile
 create mode 100755 tests/integrated/test-kpr_mri/runtest
 create mode 100644 tests/integrated/test-kpr_mri/test_kpr_mri.cxx
 create mode 100755 tests/integrated/test_suite

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6b1c4290db..3b180cf0e8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -325,6 +325,8 @@ set(BOUT_SOURCES
     ./src/solver/impls/adams_bashforth/adams_bashforth.hxx
     ./src/solver/impls/arkode/arkode.cxx
     ./src/solver/impls/arkode/arkode.hxx
+    ./src/solver/impls/arkode/arkode_mri.cxx
+    ./src/solver/impls/arkode/arkode_mri.hxx
     ./src/solver/impls/cvode/cvode.cxx
     ./src/solver/impls/cvode/cvode.hxx
     ./src/solver/impls/euler/euler.cxx
diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index f0c98548ea..c5e890d4c5 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -362,7 +362,7 @@ if(BOUT_USE_SUNDIALS)
     FetchContent_Declare(
       sundials
       GIT_REPOSITORY https://github.com/LLNL/sundials
-      GIT_TAG v7.2.1
+      GIT_TAG v7.9.0
     )
     # Note: These are settings for building SUNDIALS
     set(EXAMPLES_ENABLE_C
diff --git a/include/bout/monitor.hxx b/include/bout/monitor.hxx
index 359096e74f..991cbd65c5 100644
--- a/include/bout/monitor.hxx
+++ b/include/bout/monitor.hxx
@@ -86,10 +86,18 @@ public:
 
   /// number of RHS calls
   int ncalls = 0;
-  /// number of RHS calls for fast timescale
+  /// number of RHS calls for explicit timescale
   int ncalls_e = 0;
-  /// number of RHS calls for slow timescale
+  /// number of RHS calls for implicit timescale
   int ncalls_i = 0;
+  /// number of RHS calls for slow explicit timescale
+  int ncalls_se = 0;
+  /// number of RHS calls for slow implicit timescale
+  int ncalls_si = 0;
+  /// number of RHS calls for fast explicit timescale
+  int ncalls_fe = 0;
+  /// number of RHS calls for fast implicit timescale
+  int ncalls_fi = 0;
 
   /// wall time spent calculating RHS
   BoutReal wtime_rhs = 0;
@@ -122,7 +130,7 @@ public:
   /*!
    * Write job progress to screen
    */
-  void writeProgress(BoutReal simtime, bool output_split);
+  void writeProgress(BoutReal simtime, bool output_split, bool output_splitmri);
 };
 
 #endif // BOUT_MONITOR_H
diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index f9160f5709..e441734055 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -172,13 +172,26 @@ public:
    *
    * Returns a flag: 0 indicates success, non-zero an error flag
    */
+  int runRHS_se(BoutReal time, bool linear = false);
+  int runRHS_si(BoutReal time, bool linear = false);
+  int runRHS_fe(BoutReal time, bool linear = false);
+  int runRHS_fi(BoutReal time, bool linear = false);
+  int runRHS_s(BoutReal time, bool linear = false);
+  int runRHS_f(BoutReal time, bool linear = false);
   int runRHS(BoutReal time, bool linear = false);
 
   /*!
    * True if this model uses split operators
+   * RHS = convective + diffusive
    */
   bool splitOperator();
 
+  /*!
+   * True if this model uses Multi-Rate Integrator (MRI) split operators
+   * RHS =  rhs_se + rhs_si + rhs_fe + rhs_fi
+   */
+  bool splitOperatorMRI();
+
   /*!
    * Run the convective (usually explicit) part of the model
    *
@@ -200,7 +213,9 @@ public:
   /*!
    * True if a preconditioner has been defined
    */
-  bool hasPrecon();
+  bool hasPrecon() const { return (userprecon != nullptr); }
+  bool hasPreconFast() const { return (userprecon_f != nullptr); }
+  bool hasPreconSlow() const { return (userprecon_s != nullptr); }
 
   /*!
    * Run the preconditioner. The system state should be in the
@@ -211,7 +226,9 @@ public:
    *
    */
   int runPrecon(BoutReal t, BoutReal gamma, BoutReal delta);
-
+  int runPreconFast(BoutReal t, BoutReal gamma, BoutReal delta);
+  int runPreconSlow(BoutReal t, BoutReal gamma, BoutReal delta);
+  
   /*!
    * True if a Jacobian function has been defined
    */
@@ -270,6 +287,24 @@ protected:
    * which is set to true when the rhs() function can be
    * linearised. This is used in e.g. linear iterative solves.
    */
+  virtual int rhs_se(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_se(BoutReal t, bool UNUSED(linear)) { return rhs_se(t); }
+
+  virtual int rhs_si(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_si(BoutReal t, bool UNUSED(linear)) { return rhs_si(t); }
+
+  virtual int rhs_fe(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_fe(BoutReal t, bool UNUSED(linear)) { return rhs_fe(t); }
+
+  virtual int rhs_fi(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_fi(BoutReal t, bool UNUSED(linear)) { return rhs_fi(t); }
+
+  virtual int rhs_s(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_s(BoutReal t, bool UNUSED(linear)) { return rhs_s(t); }
+
+  virtual int rhs_f(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_f(BoutReal t, bool UNUSED(linear)) { return rhs_f(t); }
+
   virtual int rhs(BoutReal UNUSED(t)) { return 1; }
   virtual int rhs(BoutReal t, bool UNUSED(linear)) { return rhs(t); }
 
@@ -312,6 +347,9 @@ protected:
   /// Specify that this model is split into a convective and diffusive part
   void setSplitOperator(bool split = true) { splitop = split; }
 
+  /// Specify that this model is split into fast and slow parts
+  void setSplitOperatorMRI(bool split = true) { splitopmri = split; }
+
   /// Specify a preconditioner function
   void setPrecon(preconfunc pset) { userprecon = pset; }
   template <class Model>
@@ -319,6 +357,19 @@ protected:
     userprecon = static_cast<preconfunc>(preconditioner);
   }
 
+  /// Preconditioner for fast implicit RHS
+  void setPreconFast(preconfunc pset) { userprecon_f = pset; }
+  template <class Model>
+  void setPreconFast(ModelPreconFunc<Model> preconditioner) {
+    userprecon_f = static_cast<preconfunc>(preconditioner);
+  }
+  /// Preconditioner for slow implicit RHS
+  void setPreconSlow(preconfunc pset) { userprecon_s = pset; }
+  template <class Model>
+  void setPreconSlow(ModelPreconFunc<Model> preconditioner) {
+    userprecon_s = static_cast<preconfunc>(preconditioner);
+  }
+
   /// Specify a Jacobian-vector multiply function
   void setJacobian(jacobianfunc jset) { userjacobian = jset; }
   template <class Model>
@@ -397,8 +448,12 @@ private:
   bool restart_enabled{true};
   /// Split operator model?
   bool splitop{false};
+  /// MPI fast/slow split operator model?
+  bool splitopmri{false};
   /// Pointer to user-supplied preconditioner function
   preconfunc userprecon{nullptr};
+  preconfunc userprecon_f{nullptr};
+  preconfunc userprecon_s{nullptr};
   /// Pointer to user-supplied Jacobian-vector multiply function
   jacobianfunc userjacobian{nullptr};
   /// True if model already initialised
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 09ede6a32b..b4e4ec7967 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -93,6 +93,7 @@ constexpr auto SOLVEREULER = "euler";
 constexpr auto SOLVERRK3SSP = "rk3ssp";
 constexpr auto SOLVERPOWER = "power";
 constexpr auto SOLVERARKODE = "arkode";
+constexpr auto SOLVERARKODEMRI = "arkode_mri";
 constexpr auto SOLVERIMEXBDF2 = "imexbdf2";
 constexpr auto SOLVERSNES = "snes";
 constexpr auto SOLVERRKGENERIC = "rkgeneric";
@@ -317,9 +318,21 @@ public:
   /// Same but fur implicit timestep counter - for IMEX
   int resetRHSCounter_i();
 
+  /// Same but for slow explicit timestep counter - for MRI IMEX
+  int resetRHSCounter_se();
+  /// Same but for slow implicit timestep counter - for MRI IMEX
+  int resetRHSCounter_si();
+  /// Same but for fast explicit timestep counter - for MRI IMEX
+  int resetRHSCounter_fe();
+  /// Same but for fast implicit timestep counter - for MRI IMEX
+  int resetRHSCounter_fi();
+
   /// Test if this solver supports split operators (e.g. implicit/explicit)
   bool splitOperator();
 
+  /// Test if this solver supports split operators (e.g. implicit/explicit)
+  bool splitOperatorMRI();
+
   bool canReset{false};
 
   /// Add evolving variables to output (dump) file or restart file
@@ -550,11 +563,19 @@ protected:
   bool initialised{false};
   /// If calling user RHS for the first time
   bool first_rhs_call{true};
+  bool first_rhs_s_call{false};
+  bool first_rhs_f_call{false};
 
   /// Current simulation time
   BoutReal simtime{0.0};
 
   /// Run the user's RHS function
+  int run_rhs_se(BoutReal t, bool linear = false);
+  int run_rhs_si(BoutReal t, bool linear = false);
+  int run_rhs_fe(BoutReal t, bool linear = false);
+  int run_rhs_fi(BoutReal t, bool linear = false);
+  int run_rhs_s(BoutReal t, bool linear = false);
+  int run_rhs_f(BoutReal t, bool linear = false);
   int run_rhs(BoutReal t, bool linear = false);
   /// Calculate only the convective parts
   int run_convective(BoutReal t, bool linear = false);
@@ -589,8 +610,13 @@ protected:
 
   /// Do we have a user preconditioner?
   bool hasPreconditioner();
+  bool hasPreconditionerFast();
+  bool hasPreconditionerSlow();
+
   /// Run the user preconditioner
   int runPreconditioner(BoutReal time, BoutReal gamma, BoutReal delta);
+  int runPreconditionerFast(BoutReal time, BoutReal gamma, BoutReal delta);
+  int runPreconditionerSlow(BoutReal time, BoutReal gamma, BoutReal delta);
 
   /// Do we have a user Jacobian?
   bool hasJacobian();
@@ -681,6 +707,15 @@ private:
   int rhs_ncalls_e{0};
   /// Number of calls to the implicit (diffusive) RHS function
   int rhs_ncalls_i{0};
+  /// number of RHS calls for slow explicit timescale
+  int rhs_ncalls_se = 0;
+  /// number of RHS calls for slow implicit timescale
+  int rhs_ncalls_si = 0;
+  /// number of RHS calls for fast explicit timescale
+  int rhs_ncalls_fe = 0;
+  /// number of RHS calls for fast implicit timescale
+  int rhs_ncalls_fi = 0;
+
   /// Default sampling rate at which to call monitors - same as output to screen
   int default_monitor_period{1};
   /// timestep - shouldn't be changed after init is called.
diff --git a/src/bout++.cxx b/src/bout++.cxx
index 96d1efee86..5316d472e4 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -849,8 +849,12 @@ int BoutMonitor::call(Solver* solver, BoutReal t, [[maybe_unused]] int iter, int
   run_data.ncalls = solver->resetRHSCounter();
   run_data.ncalls_e = solver->resetRHSCounter_e();
   run_data.ncalls_i = solver->resetRHSCounter_i();
+  
+  run_data.ncalls_se = solver->resetRHSCounter_se();
+  run_data.ncalls_si = solver->resetRHSCounter_si();
+  run_data.ncalls_fe = solver->resetRHSCounter_fe();
+  run_data.ncalls_fi = solver->resetRHSCounter_fi();
 
-  const bool output_split = solver->splitOperator();
   run_data.wtime_rhs = Timer::resetTime("rhs");
   run_data.wtime_invert = Timer::resetTime("invert");
   // Time spent communicating (part of RHS)
@@ -872,16 +876,23 @@ int BoutMonitor::call(Solver* solver, BoutReal t, [[maybe_unused]] int iter, int
     first_time = false;
 
     // Print the column header for timing info
-    if (!output_split) {
-      output_progress.write(_("Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm "
-                              "   I/O   SOLVER\n\n"));
-    } else {
+    if (solver->splitOperator()) {
       output_progress.write(_("Sim Time  |  RHS_e evals  | RHS_I evals  | Wall Time |  "
                               "Calc    Inv   Comm    I/O   SOLVER\n\n"));
     }
+    else if (solver->splitOperatorMRI()) {
+      output_progress.write(_("Sim Time  |  RHS_se evals  | RHS_si evals  |  RHS_fe evals  |" 
+                              "RHS_fi evals  | Wall Time |  "
+                              "Calc    Inv   Comm    I/O   SOLVER\n\n"));
+    }
+    else
+    {
+      output_progress.write(_("Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm "
+                              "   I/O   SOLVER\n\n"));
+    }
   }
 
-  run_data.writeProgress(simtime, output_split);
+  run_data.writeProgress(simtime, solver->splitOperator(), solver->splitOperatorMRI());
 
   // This bit only to screen, not log file
 
@@ -905,7 +916,7 @@ int BoutMonitor::call(Solver* solver, BoutReal t, [[maybe_unused]] int iter, int
     BoutReal t_remain = mpi_start_time + wall_limit - bout::globals::mpi->MPI_Wtime();
     if (t_remain < run_data.wtime * 2) {
       // Less than 2 time-steps left
-      output_warn.write(_f("Only {:e} seconds ({:.2f} steps) left. Quitting\n"), t_remain,
+      output_warn.write(_("Only {:e} seconds ({:.2f} steps) left. Quitting\n"), t_remain,
                         t_remain / run_data.wtime);
       user_requested_exit = true;
     } else {
@@ -1011,6 +1022,10 @@ void RunMetrics::outputVars(Options& output_options) const {
   output_options["wtime"].assignRepeat(wtime, "t", true, "Output");
   output_options["ncalls"].assignRepeat(ncalls, "t", true, "Output");
   output_options["ncalls_e"].assignRepeat(ncalls_e, "t", true, "Output");
+  output_options["ncalls_se"].assignRepeat(ncalls_se, "t", true, "Output");
+  output_options["ncalls_si"].assignRepeat(ncalls_si, "t", true, "Output");
+  output_options["ncalls_fe"].assignRepeat(ncalls_fe, "t", true, "Output");
+  output_options["ncalls_fi"].assignRepeat(ncalls_fi, "t", true, "Output");
   output_options["ncalls_i"].assignRepeat(ncalls_i, "t", true, "Output");
   output_options["wtime_rhs"].assignRepeat(wtime_rhs, "t", true, "Output");
   output_options["wtime_invert"].assignRepeat(wtime_invert, "t", true, "Output");
@@ -1036,17 +1051,8 @@ void RunMetrics::calculateDerivedMetrics() {
   wtime_per_rhs_i = wtime / ncalls_i;
 }
 
-void RunMetrics::writeProgress(BoutReal simtime, bool output_split) {
-  if (!output_split) {
-    output_progress.write(
-        "{:.3e}      {:5d}       {:.2e}   {:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}\n",
-        simtime, ncalls, wtime, 100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime,
-        100. * wtime_invert / wtime,                    // Inversions
-        100. * wtime_comms / wtime,                     // Communications
-        100. * wtime_io / wtime,                        // I/O
-        100. * (wtime - wtime_io - wtime_rhs) / wtime); // Everything else
-
-  } else {
+void RunMetrics::writeProgress(BoutReal simtime, bool output_split, bool output_splitmri) {
+  if (output_split) {
     output_progress.write("{:.3e}      {:5d}            {:5d}       {:.2e}   {:5.1f}  "
                           "{:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}\n",
                           simtime, ncalls_e, ncalls_i, wtime,
@@ -1057,4 +1063,26 @@ void RunMetrics::writeProgress(BoutReal simtime, bool output_split) {
                           100. * (wtime - wtime_io - wtime_rhs)
                               / wtime); // Everything else
   }
+  else if (output_splitmri) {
+    output_progress.write("{:.3e}      {:8d}      {:8d}      {:8d}            {:8d}       {:.2e}   {:5.1f}  "
+                          "{:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}\n",
+                          simtime, ncalls_se, ncalls_si, ncalls_fe, ncalls_fi, wtime,
+                          100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime,
+                          100. * wtime_invert / wtime, // Inversions
+                          100. * wtime_comms / wtime,  // Communications
+                          100. * wtime_io / wtime,     // I/O
+                          100. * (wtime - wtime_io - wtime_rhs)
+                              / wtime); // Everything else
+  }
+  else
+  {
+    output_progress.write(
+        "{:.3e}      {:5d}       {:.2e}   {:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}\n",
+        simtime, ncalls, wtime, 100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime,
+        100. * wtime_invert / wtime,                    // Inversions
+        100. * wtime_comms / wtime,                     // Communications
+        100. * wtime_io / wtime,                        // I/O
+        100. * (wtime - wtime_io - wtime_rhs) / wtime); // Everything else
+
+  }
 }
diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx
index 6cdd78e351..b34980e0db 100644
--- a/src/physics/physicsmodel.cxx
+++ b/src/physics/physicsmodel.cxx
@@ -115,9 +115,16 @@ void PhysicsModel::initialise(Solver* s) {
   }
 }
 
-int PhysicsModel::runRHS(BoutReal time, bool linear) { return rhs(time, linear); }
+int PhysicsModel::runRHS_se(BoutReal time, bool linear) { return PhysicsModel::rhs_se(time, linear); }
+int PhysicsModel::runRHS_si(BoutReal time, bool linear) { return PhysicsModel::rhs_si(time, linear); }
+int PhysicsModel::runRHS_fe(BoutReal time, bool linear) { return PhysicsModel::rhs_fe(time, linear); }
+int PhysicsModel::runRHS_fi(BoutReal time, bool linear) { return PhysicsModel::rhs_fi(time, linear); }
+int PhysicsModel::runRHS_s(BoutReal time, bool linear) { return PhysicsModel::rhs_s(time, linear); }
+int PhysicsModel::runRHS_f(BoutReal time, bool linear) { return PhysicsModel::rhs_f(time, linear); }
+int PhysicsModel::runRHS(BoutReal time, bool linear) { return PhysicsModel::rhs(time, linear); }
 
 bool PhysicsModel::splitOperator() { return splitop; }
+bool PhysicsModel::splitOperatorMRI() { return splitopmri; }
 
 int PhysicsModel::runConvective(BoutReal time, bool linear) {
   return convective(time, linear);
@@ -128,6 +135,8 @@ int PhysicsModel::runDiffusive(BoutReal time, bool linear) {
 }
 
 bool PhysicsModel::hasPrecon() { return (userprecon != nullptr); }
+bool PhysicsModel::hasPreconFast() { return (userprecon_f != nullptr); }
+bool PhysicsModel::hasPreconSlow() { return (userprecon_s != nullptr); }
 
 int PhysicsModel::runPrecon(BoutReal t, BoutReal gamma, BoutReal delta) {
   if (!userprecon) {
@@ -136,6 +145,20 @@ int PhysicsModel::runPrecon(BoutReal t, BoutReal gamma, BoutReal delta) {
   return (*this.*userprecon)(t, gamma, delta);
 }
 
+int PhysicsModel::runPreconFast(BoutReal t, BoutReal gamma, BoutReal delta) {
+  if (!userprecon_f) {
+    return 1;
+  }
+  return (*this.*userprecon_f)(t, gamma, delta);
+}
+
+int PhysicsModel::runPreconSlow(BoutReal t, BoutReal gamma, BoutReal delta) {
+  if (!userprecon_s) {
+    return 1;
+  }
+  return (*this.*userprecon_s)(t, gamma, delta);
+}
+
 bool PhysicsModel::hasJacobian() { return (userjacobian != nullptr); }
 
 int PhysicsModel::runJacobian(BoutReal t) {
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 2035824054..870a39c801 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -125,6 +125,21 @@ ArkodeSolver::ArkodeSolver(Options* opts)
               .doc("Set timestep adaptivity function: pid, pi, i, explicit_gustafsson,  "
                    "implicit_gustafsson, imex_gustafsson.")
               .withDefault(AdapMethod::PID)),
+      small_nef((*options)["small_nef"]
+              .doc("Threshold for “multiple” successive error failures")
+              .withDefault(2)),
+      etamxf((*options)["etamxf"]
+              .doc("Maximum step size growth factor upon multiple successive failures")
+              .withDefault(0.3)),
+      eta_min((*options)["eta_min"]
+              .doc("Minimum value of step size growth factor upon a failure")
+              .withDefault(0.1)),
+      mx_growth((*options)["mx_growth"]
+              .doc("Maximum allowed growth factor in step size between consecutive steps")
+              .withDefault(20.0)),
+      error_bias((*options)["error_bias"]
+              .doc("Bias factor to slightly exaggerate the temporal error")
+              .withDefault(1.0)),
       abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
       reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-5)),
       use_vector_abstol((*options)["use_vector_abstol"]
@@ -157,6 +172,25 @@ ArkodeSolver::ArkodeSolver(Options* opts)
       nvector_type((*options)["nvector"]
                        .doc("N_Vector backend to use: sundials or manyvector")
                        .withDefault(NVectorType::Sundials)),
+      print_allstats((*options)["print_allstats"]
+                         .doc("Print all integrator stats at each evolve call")
+                         .withDefault(false)),
+      use_temporal_filtering((*options)["use_temporal_filtering"]
+                             .doc("Use temporal filtering of solution")
+                             .withDefault(false)),
+      temp_filtering(),
+      filtering_type((*options)["filtering_type"]
+                     .doc("Type of temporal filtering to perform: None, EMA, SRA")
+                     .withDefault(FilteringType::EMA)),
+      tau_mean((*options)["tau_mean"]
+                .doc("Interval over which means are calculated")
+                .withDefault(10.0)),
+      mean_start_time((*options)["mean_start_time"]
+                      .doc("Time at which averaging is allowed to start")
+                      .withDefault(0.0)),
+      lambda((*options)["lambda"]
+             .doc("Relaxation parameter for temporal filtering")
+             .withDefault(0.01)),
 #if ARKODE_OPTIMAL_PARAMS_SUPPORT
       optimize(
           (*options)["optimize"].doc("Use ARKode optimal parameters").withDefault(false)),
@@ -309,6 +343,11 @@ int ArkodeSolver::init() {
   if (ARKodeSetAdaptivityAdjustment(arkode_mem, 0) != ARK_SUCCESS) {
     throw BoutException("ARKodeSetAdaptivityAdjustment failed\n");
   }
+
+  if (SUNAdaptController_SetErrorBias(controller, error_bias)
+      != ARK_SUCCESS) {
+    throw BoutException("SUNAdaptController_SetErrorBias failed\n");
+  }
 #else
   int adap_method_int;
   // Could cast to underlying integer, but this is more explicit
@@ -492,6 +531,43 @@ int ArkodeSolver::init() {
     }
   }
 
+  // Enable temporal filtering if requested
+  if (use_temporal_filtering) {
+    if (filtering_type == FilteringType::None) {
+      filtering_type = FilteringType::EMA;
+      output.write("\tTemporal filtering type is None. Using EMA by default\n");
+    }
+    output.write("\tUsing temporal filtering of solution\n");
+    temp_filtering.reset_state();
+    temp_filtering.initialize(uvec);
+    temp_filtering.configure(filtering_type, tau_mean, mean_start_time);
+  }
+
+  // Specifies the threshold for “multiple” successive error failures 
+  // before the etamxf parameter from ARKodeSetMaxEFailGrowth() is applied.
+  if (ARKodeSetSmallNumEFails(arkode_mem, small_nef) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetSmallNumEFails failed\n");
+  }
+
+  // Specifies the maximum step size growth factor upon multiple 
+  // successive accuracy-based error failures in the solver.
+  if (ARKodeSetMaxEFailGrowth(arkode_mem, etamxf) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetMaxEFailGrowth failed\n");
+  }
+
+  // Specifies the minimum allowed reduction factor in step size 
+  // between step attempts, resulting from a temporal error failure 
+  // in the integration process.
+  if (ARKodeSetMinReduction(arkode_mem, eta_min) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetMinReduction failed\n");
+  }
+
+  // Specifies the maximum allowed growth factor in step size 
+  // between consecutive steps in the integration process.
+   if (ARKodeSetMaxGrowth(arkode_mem, mx_growth) != ARK_SUCCESS) {
+     throw BoutException("ARKodeSetMaxGrowth failed\n");
+  }
+
 #if ARKODE_OPTIMAL_PARAMS_SUPPORT
   if (optimize) {
     output.write("\tUsing ARKode inbuilt optimization\n");
@@ -576,9 +652,16 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   pre_ncalls = 0;
 
   int flag;
+  int mpi_rank;
   if (!monitor_timestep) {
     // Run in normal mode
     flag = ARKodeEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL);
+    if (flag != ARK_SUCCESS) {
+      output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n",
+                         simtime, flag);
+      return -1.0;
+    }
+    apply_temporal_filtering(simtime, uvec);
   } else {
     // Run in single step mode, to call timestep monitors
     BoutReal internal_time;
@@ -593,6 +676,7 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
                            internal_time, flag);
         return -1.0;
       }
+      apply_temporal_filtering(internal_time, uvec);
 
       // Call timestep monitor
       call_timestep_monitors(internal_time, internal_time - last_time);
@@ -600,6 +684,22 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
     // Get output at the desired time
     flag = ARKodeGetDky(arkode_mem, tout, 0, uvec);
     simtime = tout;
+    if (flag != ARK_SUCCESS) {
+      output_error.write("ERROR ARKodeGetDky failed at t = {:e}, flag = {:d}\n",
+                         simtime, flag);
+      return -1.0;
+    }
+  }
+
+  if (print_allstats) {
+    bout::globals::mpi->MPI_Comm_rank(BoutComm::get(), &mpi_rank);
+    if (mpi_rank == 0) {
+      flag = ARKodePrintAllStats(arkode_mem, stdout, SUN_OUTPUTFORMAT_TABLE);
+      if (flag != ARK_SUCCESS) {
+        output_error.write("ERROR ARKodePrintAllStats failed with the flag = {:d}\n", flag);
+            return -1.0;
+        }
+    }
   }
 
   // Copy variables
@@ -607,11 +707,6 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
   // run_diffusive(simtime);
-  if (flag != ARK_SUCCESS) {
-    output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n", simtime,
-                       flag);
-    return -1.0;
-  }
 
   return simtime;
 }
@@ -842,4 +937,43 @@ void ArkodeSolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolvec_
   }
 }
 
+void ArkodeSolver::apply_temporal_filtering(BoutReal internal_time,
+                                            N_Vector uvec)
+{
+  if (!use_temporal_filtering) {
+    return;
+  }
+
+  // Update the temporal filtering 
+  temp_filtering.update(internal_time, uvec);
+
+  // If no mean is available yet, do nothing
+  if (!temp_filtering.has_mean()) {
+    return;
+  }
+
+  int flag;
+    
+  // Get the current mean vector
+  N_Vector u_mean = temp_filtering.get_mean_vector();
+
+  // Apply the temporal filtering
+  // Gently relax the solution towards the mean
+  // Set u = (1 - lambda) * u + lambda * u_mean
+  N_VLinearSum(1.0 - lambda, uvec, lambda, u_mean, uvec);
+
+  // Reset ARKode with the new filtered state
+  flag = ARKodeReset(arkode_mem, internal_time, uvec);
+  if (flag != ARK_SUCCESS) {
+    throw BoutException("ARKodeReset failed in temporal filtering\n");
+  }
+
+  // For EMA: we keep averaging continuously (no reset).
+  // For SRA: enforce finite averaging windows of length tau_mean
+  // by restarting the averaging window when tau_mean_cur is equal to tau_mean
+  if (filtering_type == FilteringType::SRA && temp_filtering.window_full()) {
+    temp_filtering.restart_window(internal_time);
+  }
+}
+
 #endif
diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
new file mode 100644
index 0000000000..68a2b93896
--- /dev/null
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -0,0 +1,1081 @@
+/**************************************************************************
+ * Experimental interface to SUNDIALS ARKODE MRI solver
+ *
+ * NOTE: ARKODE is still in beta testing so use with cautious optimism
+ *
+ **************************************************************************
+ * Copyright 2010-2025 BOUT++ contributors
+ *
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#include "bout/build_defines.hxx"
+
+#if BOUT_HAS_ARKODE
+
+#include "arkode_mri.hxx"
+
+#if SUNDIALS_VERSION_AT_LEAST(7, 2, 0)
+
+#include "bout/assert.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/boutcomm.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/field2d.hxx"
+#include "bout/field3d.hxx"
+#include "bout/globals.hxx"
+#include "bout/mesh.hxx"
+#include "bout/mpi_wrapper.hxx"
+#include "bout/msg_stack.hxx"
+#include "bout/options.hxx"
+#include "bout/output.hxx"
+#include "bout/solver.hxx"
+#include "bout/sundials_backports.hxx"
+#include "bout/unused.hxx"
+
+#include <arkode/arkode.h>
+#include <arkode/arkode_arkstep.h>
+#include <arkode/arkode_bbdpre.h>
+#include <arkode/arkode_ls.h>
+
+#include <sundials/sundials_math.h>
+
+#include <algorithm>
+#include <iterator>
+#include <numeric>
+#include <vector>
+
+// NOLINTBEGIN(readability-identifier-length)
+namespace {
+int arkode_rhs_s_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_rhs_s_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_rhs_f_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_rhs_f_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_s_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_f_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+
+int arkode_s_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du,
+                   void* user_data);
+int arkode_f_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du,
+                   void* user_data);
+int arkode_s_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec,
+               BoutReal gamma, BoutReal delta, int lr, void* user_data);
+int arkode_f_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec,
+               BoutReal gamma, BoutReal delta, int lr, void* user_data);
+
+} // namespace
+// NOLINTEND(readability-identifier-length)
+
+ArkodeMRISolver::ArkodeMRISolver(Options* opts)
+    : Solver(opts), diagnose((*options)["diagnose"]
+                                 .doc("Print some additional diagnostics")
+                                 .withDefault(false)),
+      mxsteps((*options)["mxstep"]
+                  .doc("Maximum number of steps to take between outputs")
+                  .withDefault(500)),
+      // mxstepsize((*options)["mxstepsize"]
+      //             .doc("Maximum step size")
+      //             .withDefault(0.1)),
+      // inner_mxstepsize((*options)["inner_mxstepsize"]
+      //             .doc("Maximum step size")
+      //             .withDefault(0.1)),
+      treatment((*options)["treatment"]
+                    .doc("Use default capability (imex) or provide a specific treatment: "
+                         "implicit or explicit")
+                    .withDefault(MRI_Treatment::ImEx)),
+      inner_treatment((*options)["inner_treatment"]
+                    .doc("Use default capability (imex) or provide a specific inner_treatment: "
+                         "implicit or explicit")
+                    .withDefault(MRI_Treatment::ImEx)),
+      set_linear(
+          (*options)["set_linear"]
+              .doc("Use linear implicit solver (only evaluates jacobian inversion once)")
+              .withDefault(false)),
+      inner_set_linear(
+          (*options)["inner_set_linear"]
+              .doc("Use linear implicit solver (only evaluates jacobian inversion once)")
+              .withDefault(false)),
+      fixed_step((*options)["fixed_step"]
+                     .doc("Solve both fast and slow time scales using fixed time step sizes. NOTE: This is "
+                          "not recommended except for code comparison")
+                     .withDefault(false)),
+      order((*options)["order"].doc("Order of internal step").withDefault(3)),
+      abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
+      reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-10)),
+      use_vector_abstol((*options)["use_vector_abstol"]
+                            .doc("Use separate absolute tolerance for each field")
+                            .withDefault(false)),
+      use_precon((*options)["use_precon"]
+                     .doc("Use user-supplied preconditioner function")
+                     .withDefault(false)),
+      inner_use_precon((*options)["inner_use_precon"]
+                     .doc("Use user-supplied preconditioner function")
+                     .withDefault(false)),
+      maxl(
+          (*options)["maxl"].doc("Number of Krylov basis vectors to use").withDefault(0)),
+      inner_maxl(
+          (*options)["inner_maxl"].doc("Number of Krylov basis vectors to use").withDefault(0)),
+      rightprec((*options)["rightprec"]
+                    .doc("Use right preconditioning instead of left preconditioning")
+                    .withDefault(false)),
+      use_temporal_filtering((*options)["use_temporal_filtering"]
+                             .doc("Use temporal filtering of solution")
+                             .withDefault(false)),
+      temp_filtering(),
+      filtering_type((*options)["filtering_type"]
+                     .doc("Type of temporal filtering to perform: None, EMA, SRA")
+                     .withDefault(FilteringType::EMA)),
+      tau_mean((*options)["tau_mean"]
+                .doc("Interval over which means are calculated")
+                .withDefault(10.0)),
+      mean_start_time((*options)["mean_start_time"]
+                      .doc("Time at which averaging is allowed to start")
+                      .withDefault(0.0)),
+      lambda((*options)["lambda"]
+             .doc("Relaxation parameter for temporal filtering")
+             .withDefault(0.01)),
+      suncontext(createSUNContext(BoutComm::get())) {
+  has_constraints = false; // This solver doesn't have constraints
+
+  // Add diagnostics to output
+  add_int_diagnostic(nsteps, "arkode_nsteps", "Cumulative number of internal steps");
+  add_int_diagnostic(inner_nsteps, "arkode_inner_nsteps", "Cumulative number of inner internal steps");
+  add_int_diagnostic(nfe_evals, "arkode_nfe_evals",
+                     "No. of calls to fe (explicit portion of the right-hand-side "
+                     "function) function");
+  add_int_diagnostic(inner_nfe_evals, "arkode_inner_nfe_evals",
+                     "No. of calls to fe (explicit portion of the inner right-hand-side "
+                     "function) function");
+  add_int_diagnostic(nfi_evals, "arkode_nfi_evals",
+                     "No. of calls to fi (implicit portion of the right-hand-side "
+                     "function) function");
+  add_int_diagnostic(inner_nfi_evals, "arkode_inner_nfi_evals",
+                     "No. of calls to fi (implicit portion of inner the right-hand-side "
+                     "function) function");
+  add_int_diagnostic(nniters, "arkode_nniters", "No. of nonlinear solver iterations");
+  add_int_diagnostic(inner_nniters, "arkode_inner_nniters", "No. of inner nonlinear solver iterations");
+  add_int_diagnostic(npevals, "arkode_npevals", "No. of preconditioner evaluations");
+  add_int_diagnostic(inner_npevals, "arkode_inner_npevals", "No. of inner preconditioner evaluations");
+  add_int_diagnostic(nliters, "arkode_nliters", "No. of linear iterations");
+  add_int_diagnostic(inner_nliters, "arkode_inner_nliters", "No. of inner linear iterations");
+}
+
+ArkodeMRISolver::~ArkodeMRISolver() {
+  N_VDestroy(uvec);
+  ARKodeFree(&arkode_mem);
+  ARKodeFree(&inner_arkode_mem);
+  SUNLinSolFree(sun_solver);
+  SUNLinSolFree(inner_sun_solver);
+  SUNNonlinSolFree(nonlinear_solver);
+  SUNNonlinSolFree(inner_nonlinear_solver);
+  MRIStepInnerStepper_Free(&inner_stepper);
+}
+
+BoutReal ArkodeMRISolver::getCurrentTimestep() {
+  BoutReal hcur;
+  ARKodeGetCurrentStep(arkode_mem, &hcur);
+  return hcur;
+}
+
+/**************************************************************************
+ * Initialise
+ **************************************************************************/
+
+int ArkodeMRISolver::init() {
+  TRACE("Initialising ARKODE MRI solver");
+
+  Solver::init();
+
+  output.write("Initialising SUNDIALS' ARKODE MRI solver\n");
+
+  // Calculate number of variables (in generic_solver)
+  const int local_N = getLocalN();
+
+  // Get total problem size
+  int neq;
+  if (bout::globals::mpi->MPI_Allreduce(&local_N, &neq, 1, MPI_INT, MPI_SUM,
+                                        BoutComm::get())) {
+    throw BoutException("Allreduce localN -> GlobalN failed!\n");
+  }
+
+  output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3Dvars(),
+               n2Dvars(), neq, local_N);
+
+  // Allocate memory
+  uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
+  if (uvec == nullptr) {
+    throw BoutException("SUNDIALS memory allocation failed\n");
+  }
+
+  // Put the variables into uvec
+  save_vars(N_VGetArrayPointer(uvec));
+
+  switch (inner_treatment) {
+  case MRI_Treatment::ImEx:
+    inner_arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_f_explicit,
+                                    arkode_rhs_f_implicit, simtime, uvec);
+    output_info.write("\tUsing ARKODE ImEx inner solver \n");
+    break;
+  case MRI_Treatment::Explicit:
+    inner_arkode_mem =
+        callWithSUNContext(ARKStepCreate, suncontext, arkode_f_rhs, nullptr, simtime, uvec);
+    output_info.write("\tUsing ARKODE Explicit inner solver \n");
+    break;
+  case MRI_Treatment::Implicit:
+    inner_arkode_mem =
+        callWithSUNContext(ARKStepCreate, suncontext, nullptr, arkode_f_rhs, simtime, uvec);
+    output_info.write("\tUsing ARKODE Implicit inner solver \n");
+    break;
+  default:
+    throw BoutException("Invalid inner_treatment: {}\n", toString(inner_treatment));
+  }
+  if (inner_arkode_mem == nullptr) {
+    throw BoutException("ARKStepCreate failed\n");
+  }
+
+  // For callbacks, need pointer to solver object
+  if (ARKodeSetUserData(inner_arkode_mem, this) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetUserData failed\n");
+  }
+
+  if(inner_treatment != MRI_Treatment::Explicit)
+    if (ARKodeSetLinear(inner_arkode_mem, inner_set_linear) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSetLinear failed\n");
+    }
+
+  if (fixed_step) {
+    // If not given, default to adaptive timestepping
+    const BoutReal inner_fixed_timestep = (*options)["inner_timestep"].withDefault(1.0e-5);
+    if (ARKodeSetFixedStep(inner_arkode_mem, inner_fixed_timestep) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSetFixedStep failed\n");
+    }
+  }
+
+  if (ARKodeSetOrder(inner_arkode_mem, order) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetOrder failed\n");
+  }
+
+  if (ARKodeCreateMRIStepInnerStepper(inner_arkode_mem, &inner_stepper) != ARK_SUCCESS) {
+    throw BoutException("ARKodeCreateMRIStepInnerStepper failed\n");
+  }
+
+  // Initialize the slow integrator. Specify the explicit slow right-hand side
+  // function in y'=fe(t,y)+fi(t,y)+ff(t,y), the inital time T0, the
+  // initial dependent variable vector y, and the fast integrator.
+
+  switch (treatment) {
+  case MRI_Treatment::ImEx:
+    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, arkode_rhs_s_explicit, arkode_rhs_s_implicit,
+                                    simtime, uvec, inner_stepper);
+    output_info.write("\tUsing ARKODE-MRI ImEx solver \n");
+    break;
+  case MRI_Treatment::Explicit:
+    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, arkode_s_rhs, nullptr,
+                                    simtime, uvec, inner_stepper);
+    output_info.write("\tUsing ARKODE-MRI Explicit solver \n");
+    break;
+  case MRI_Treatment::Implicit:
+    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, nullptr, arkode_s_rhs,
+                                    simtime, uvec, inner_stepper);
+    output_info.write("\tUsing ARKODE-MRI Implicit solver \n");
+    break;
+  default:
+    throw BoutException("Invalid treatment: {}\n", toString(treatment));
+  }
+  if (arkode_mem == nullptr) {
+    throw BoutException("MRIStepCreate failed\n");
+  }
+
+  // For callbacks, need pointer to solver object
+  if (ARKodeSetUserData(arkode_mem, this) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetUserData failed\n");
+  }
+
+  if(treatment != MRI_Treatment::Explicit)
+    if (ARKodeSetLinear(arkode_mem, set_linear) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSetLinear failed\n");
+    }
+
+  if (fixed_step) {
+    // If not given, default to adaptive timestepping
+    const BoutReal fixed_timestep = (*options)["timestep"].withDefault(1.0e-4);
+    if (ARKodeSetFixedStep(arkode_mem, fixed_timestep) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSetFixedStep failed\n");
+    }
+  }
+
+  if (ARKodeSetOrder(arkode_mem, order) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetOrder failed\n");
+  }
+
+  if (use_vector_abstol) {
+    std::vector<BoutReal> f2dtols;
+    f2dtols.reserve(f2d.size());
+    std::transform(begin(f2d), end(f2d), std::back_inserter(f2dtols),
+                   [abstol = abstol](const VarStr<Field2D>& f2) {
+                     auto& f2_options = Options::root()[f2.name];
+                     const auto wrong_name = f2_options.isSet("abstol");
+                     if (wrong_name) {
+                       output_warn << "WARNING: Option 'abstol' for field " << f2.name
+                                   << " is deprecated. Please use 'atol' instead\n";
+                     }
+                     const std::string atol_name = wrong_name ? "abstol" : "atol";
+                     return f2_options[atol_name].withDefault(abstol);
+                   });
+
+    std::vector<BoutReal> f3dtols;
+    f3dtols.reserve(f3d.size());
+    std::transform(begin(f3d), end(f3d), std::back_inserter(f3dtols),
+                   [abstol = abstol](const VarStr<Field3D>& f3) {
+                     return Options::root()[f3.name]["atol"].withDefault(abstol);
+                   });
+
+    N_Vector abstolvec = N_VClone(uvec);
+    if (abstolvec == nullptr) {
+      throw BoutException("SUNDIALS memory allocation (abstol vector) failed\n");
+    }
+
+    set_abstol_values(N_VGetArrayPointer(abstolvec), f2dtols, f3dtols);
+
+    if (ARKodeSVtolerances(arkode_mem, reltol, abstolvec) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSVtolerances failed\n");
+    }
+    if (ARKodeSVtolerances(inner_arkode_mem, reltol, abstolvec) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSVtolerances failed\n");
+    }
+
+    N_VDestroy(abstolvec);
+  } else {
+    if (ARKodeSStolerances(arkode_mem, reltol, abstol) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSStolerances failed\n");
+    }
+    if (ARKodeSStolerances(inner_arkode_mem, reltol, abstol) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSStolerances failed\n");
+    }
+  }
+
+  if (ARKodeSetMaxNumSteps(arkode_mem, mxsteps) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetMaxNumSteps failed\n");
+  }
+  if (ARKodeSetMaxNumSteps(inner_arkode_mem, mxsteps) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetMaxNumSteps failed\n");
+  }
+
+  // if (ARKodeSetMaxStep(arkode_mem, mxstepsize) != ARK_SUCCESS) {
+  //   throw BoutException("ARKodeSetMaxStep failed\n");
+  // }
+  // if (ARKodeSetMaxStep(inner_arkode_mem, inner_mxstepsize) != ARK_SUCCESS) {
+  //   throw BoutException("ARKodeSetMaxStep failed\n");
+  // }
+
+  if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+    {
+      output.write("\tUsing Newton iteration for inner solver\n");
+
+      const auto prectype =
+          inner_use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE;
+      inner_sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, inner_maxl);
+      if (inner_sun_solver == nullptr) {
+        throw BoutException("Creating SUNDIALS inner linear solver failed\n");
+      }
+      if (ARKodeSetLinearSolver(inner_arkode_mem, inner_sun_solver, nullptr) != ARKLS_SUCCESS) {
+        throw BoutException("ARKodeSetLinearSolver failed for inner solver\n");
+      }
+
+      /// Set Preconditioner
+      if (inner_use_precon) {
+        if (hasPreconditionerFast()) {
+          output.write("\tUsing user-supplied preconditioner for inner (fast) solver\n");
+
+          if (ARKodeSetPreconditioner(inner_arkode_mem, nullptr, arkode_f_pre)
+              != ARKLS_SUCCESS) {
+            throw BoutException("ARKodeSetPreconditioner failed for inner solver\n");
+          }
+        } else {
+          output.write("\tUsing BBD preconditioner for inner (fast) solver\n");
+
+          /// Get options
+          // Compute band_width_default from actually added fields, to allow for multiple
+          // Mesh objects
+          //
+          // Previous implementation was equivalent to:
+          //   int MXSUB = mesh->xend - mesh->xstart + 1;
+          //   int band_width_default = n3Dvars()*(MXSUB+2);
+          const int band_width_default = std::accumulate(
+              begin(f3d), end(f3d), 0, [](int acc, const VarStr<Field3D>& fvar) {
+                Mesh* localmesh = fvar.var->getMesh();
+                return acc + localmesh->xend - localmesh->xstart + 3;
+              });
+
+          const auto inner_mudq = (*options)["inner_mudq"]
+                                .doc("Upper half-bandwidth to be used in the difference "
+                                     "quotient Jacobian approximation")
+                                .withDefault(band_width_default);
+          const auto inner_mldq = (*options)["inner_mldq"]
+                                .doc("Lower half-bandwidth to be used in the difference "
+                                     "quotient Jacobian approximation")
+                                .withDefault(band_width_default);
+          const auto inner_mukeep = (*options)["inner_mukeep"]
+                                  .doc("Upper half-bandwidth of the retained banded "
+                                       "approximate Jacobian block")
+                                  .withDefault(n3Dvars() + n2Dvars());
+          const auto inner_mlkeep = (*options)["mlkeep"]
+                                  .doc("Lower half-bandwidth of the retained banded "
+                                       "approximate Jacobian block")
+                                  .withDefault(n3Dvars() + n2Dvars());
+
+          if (ARKBBDPrecInit(inner_arkode_mem, local_N, inner_mudq, inner_mldq, inner_mukeep, inner_mlkeep, 0,
+                             arkode_f_bbd_rhs, nullptr)
+              != ARKLS_SUCCESS) {
+            throw BoutException("ARKBBDPrecInit failed for inner solver\n");
+          }
+        }
+      } else {
+        // Not using preconditioning
+        output.write("\tNo inner preconditioning\n");
+      }
+    }
+
+    /// Set Jacobian-vector multiplication function
+    output.write("\tUsing difference quotient approximation for Jacobian in the inner solver\n");
+  }
+
+  if (treatment == MRI_Treatment::ImEx or treatment == MRI_Treatment::Implicit) {
+    {
+      output.write("\tUsing Newton iteration\n");
+
+      const auto prectype =
+          use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE;
+      sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl);
+      if (sun_solver == nullptr) {
+        throw BoutException("Creating SUNDIALS linear solver failed\n");
+      }
+      if (ARKodeSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARKLS_SUCCESS) {
+        throw BoutException("ARKodeSetLinearSolver failed\n");
+      }
+
+      /// Set Preconditioner
+      if (use_precon) {
+        if (hasPreconditionerSlow()) {
+          output.write("\tUsing user-supplied preconditioner\n");
+
+          if (ARKodeSetPreconditioner(arkode_mem, nullptr, arkode_s_pre)
+              != ARKLS_SUCCESS) {
+            throw BoutException("ARKodeSetPreconditioner failed\n");
+          }
+        } else {
+          output.write("\tUsing BBD preconditioner\n");
+
+          /// Get options
+          // Compute band_width_default from actually added fields, to allow for multiple
+          // Mesh objects
+          //
+          // Previous implementation was equivalent to:
+          //   int MXSUB = mesh->xend - mesh->xstart + 1;
+          //   int band_width_default = n3Dvars()*(MXSUB+2);
+          const int band_width_default = std::accumulate(
+              begin(f3d), end(f3d), 0, [](int acc, const VarStr<Field3D>& fvar) {
+                Mesh* localmesh = fvar.var->getMesh();
+                return acc + localmesh->xend - localmesh->xstart + 3;
+              });
+
+          const auto mudq = (*options)["mudq"]
+                                .doc("Upper half-bandwidth to be used in the difference "
+                                     "quotient Jacobian approximation")
+                                .withDefault(band_width_default);
+          const auto mldq = (*options)["mldq"]
+                                .doc("Lower half-bandwidth to be used in the difference "
+                                     "quotient Jacobian approximation")
+                                .withDefault(band_width_default);
+          const auto mukeep = (*options)["mukeep"]
+                                  .doc("Upper half-bandwidth of the retained banded "
+                                       "approximate Jacobian block")
+                                  .withDefault(n3Dvars() + n2Dvars());
+          const auto mlkeep = (*options)["mlkeep"]
+                                  .doc("Lower half-bandwidth of the retained banded "
+                                       "approximate Jacobian block")
+                                  .withDefault(n3Dvars() + n2Dvars());
+
+          if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0,
+                             arkode_s_bbd_rhs, nullptr)
+              != ARKLS_SUCCESS) {
+            throw BoutException("ARKBBDPrecInit failed\n");
+          }
+        }
+      } else {
+        // Not using preconditioning
+        output.write("\tNo preconditioning\n");
+      }
+    }
+
+    /// Set Jacobian-vector multiplication function
+    output.write("\tUsing difference quotient approximation for Jacobian\n");
+  }
+
+  // Enable temporal filtering if requested
+  if (use_temporal_filtering) {
+    if (filtering_type == FilteringType::None) {
+      filtering_type = FilteringType::EMA;
+      output.write("\tTemporal filtering type is None. Using EMA by default\n");
+    }
+    output.write("\tUsing temporal filtering of solution\n");
+    temp_filtering.reset_state();
+    temp_filtering.initialize(uvec);
+    temp_filtering.configure(filtering_type, tau_mean, mean_start_time);
+  }
+
+  return 0;
+}
+
+/**************************************************************************
+ * Run - Advance time
+ **************************************************************************/
+
+int ArkodeMRISolver::run() {
+  TRACE("ArkodeMRISolver::run()");
+
+  if (!initialised) {
+    throw BoutException("ArkodeMRISolver not initialised\n");
+  }
+
+  for (int i = 0; i < getNumberOutputSteps(); i++) {
+
+    /// Run the solver for one output timestep
+    simtime = run(simtime + getOutputTimestep());
+
+    /// Check if the run succeeded
+    if (simtime < 0.0) {
+      // Step failed
+      output.write("Timestep failed. Aborting\n");
+
+      throw BoutException("ARKODE timestep failed\n");
+    }
+
+    // Get additional diagnostics
+    long int temp_long_int, temp_long_int2;
+    ARKodeGetNumSteps(arkode_mem, &temp_long_int);
+    nsteps = int(temp_long_int);
+    ARKodeGetNumRhsEvals(arkode_mem, 0, &temp_long_int);
+    ARKodeGetNumRhsEvals(arkode_mem, 1, &temp_long_int2);
+    nfe_evals = int(temp_long_int);
+    nfi_evals = int(temp_long_int2);
+    if (treatment == MRI_Treatment::ImEx or treatment == MRI_Treatment::Implicit) {
+      ARKodeGetNumNonlinSolvIters(arkode_mem, &temp_long_int);
+      nniters = int(temp_long_int);
+      ARKodeGetNumPrecEvals(arkode_mem, &temp_long_int);
+      npevals = int(temp_long_int);
+      ARKodeGetNumLinIters(arkode_mem, &temp_long_int);
+      nliters = int(temp_long_int);
+    }
+
+    ARKodeGetNumSteps(inner_arkode_mem, &temp_long_int);
+    inner_nsteps = int(temp_long_int);
+    ARKodeGetNumRhsEvals(inner_arkode_mem, 0, &temp_long_int);
+    ARKodeGetNumRhsEvals(inner_arkode_mem, 1, &temp_long_int2);
+    inner_nfe_evals = int(temp_long_int);
+    inner_nfi_evals = int(temp_long_int2);
+    if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+      ARKodeGetNumNonlinSolvIters(inner_arkode_mem, &temp_long_int);
+      inner_nniters = int(temp_long_int);
+      ARKodeGetNumPrecEvals(inner_arkode_mem, &temp_long_int);
+      inner_npevals = int(temp_long_int);
+      ARKodeGetNumLinIters(inner_arkode_mem, &temp_long_int);
+      inner_nliters = int(temp_long_int);
+    }
+
+    if (diagnose) {
+      output.write("\nARKODE: nsteps {:d}, nfe_evals {:d}, nfi_evals {:d}, nniters {:d}, "
+                   "npevals {:d}, nliters {:d}\n",
+                   nsteps, nfe_evals, nfi_evals, nniters, npevals, nliters);
+      if (treatment == MRI_Treatment::ImEx or treatment == MRI_Treatment::Implicit) {
+        output.write("    -> Newton iterations per step: {:e}\n",
+                     static_cast<BoutReal>(nniters) / static_cast<BoutReal>(nsteps));
+        output.write("    -> Linear iterations per Newton iteration: {:e}\n",
+                     static_cast<BoutReal>(nliters) / static_cast<BoutReal>(nniters));
+        output.write("    -> Preconditioner evaluations per Newton: {:e}\n",
+                     static_cast<BoutReal>(npevals) / static_cast<BoutReal>(nniters));
+      }
+
+      output.write("\nARKODE Inner: inner_nsteps {:d}, inner_nfe_evals {:d}, inner_nfi_evals {:d}, inner_nniters {:d}, "
+                   "inner_npevals {:d}, inner_nliters {:d}\n",
+                   inner_nsteps, inner_nfe_evals, inner_nfi_evals, inner_nniters, inner_npevals, inner_nliters);
+      if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+        output.write("    -> Inner Newton iterations per step: {:e}\n",
+                     static_cast<BoutReal>(inner_nniters) / static_cast<BoutReal>(inner_nsteps));
+        output.write("    -> Inner Linear iterations per Newton iteration: {:e}\n",
+                     static_cast<BoutReal>(inner_nliters) / static_cast<BoutReal>(inner_nniters));
+        output.write("    -> Inner Preconditioner evaluations per Newton: {:e}\n",
+                     static_cast<BoutReal>(inner_npevals) / static_cast<BoutReal>(inner_nniters));
+      }
+    }
+
+    if (call_monitors(simtime, i, getNumberOutputSteps())) {
+      // User signalled to quit
+      break;
+    }
+  }
+
+  return 0;
+}
+
+BoutReal ArkodeMRISolver::run(BoutReal tout) {
+  TRACE("Running solver: solver::run({:e})", tout);
+
+  bout::globals::mpi->MPI_Barrier(BoutComm::get());
+
+  pre_Wtime_s = 0.0;
+  pre_ncalls_s = 0;
+
+  int flag = ARKodeSetStopTime(arkode_mem, 1.0001*tout);
+  if (flag != ARK_SUCCESS) {
+    output_error.write("ERROR ARKodeSetStopTime failed at t = {:e}, flag = {:d}\n",
+      simtime, flag);
+    return -1.0;
+  }
+
+  flag = ARKodeSetStopTime(inner_arkode_mem, 1.0001*tout);
+  if (flag != ARK_SUCCESS) {
+    output_error.write("ERROR ARKodeSetStopTime failed at t = {:e}, flag = {:d}\n",
+      simtime, flag);
+    return -1.0;
+  }
+
+  if (!monitor_timestep) {
+    // Run in normal mode
+    flag = ARKodeEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL);
+    apply_temporal_filtering(simtime, uvec);
+  } else {
+    // Run in single step mode, to call timestep monitors
+    BoutReal internal_time;
+    ARKodeGetCurrentTime(arkode_mem, &internal_time);
+    while (internal_time < tout) {
+      // Run another step
+      const BoutReal last_time = internal_time;
+      flag = ARKodeEvolve(arkode_mem, tout, uvec, &internal_time, ARK_ONE_STEP);
+
+      if (flag != ARK_SUCCESS) {
+        output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n",
+                           internal_time, flag);
+        return -1.0;
+      }
+      apply_temporal_filtering(internal_time, uvec);
+
+      // Call timestep monitor
+      call_timestep_monitors(internal_time, internal_time - last_time);
+    }
+    // Update the current simulation time
+    simtime = tout;
+  }
+
+  // Copy variables
+  load_vars(N_VGetArrayPointer(uvec));
+  // Call rhs function to get extra variables at this time
+  run_rhs(simtime);
+  // run_diffusive(simtime);
+  if (flag != ARK_SUCCESS) {
+    output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n", simtime,
+                       flag);
+    return -1.0;
+  }
+
+  return simtime;
+}
+
+/**************************************************************************
+ * Explicit RHS function du = F^s_E(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_se(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_e({:e})", t);
+
+  // Load state from udata
+  load_vars(udata);
+
+  // Call RHS function
+  run_rhs_se(t);
+
+  // Save derivatives to dudata
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ *   Implicit RHS function du = F^s_I(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_si(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_si({:e})", t);
+
+  load_vars(udata);
+  // Call Implicit RHS function
+  run_rhs_si(t);
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ * Explicit RHS function du = F^f_E(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_fe(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_e({:e})", t);
+
+  // Load state from udata
+  load_vars(udata);
+
+  // Call RHS function
+  run_rhs_fe(t);
+
+  // Save derivatives to dudata
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ *   Implicit RHS function du = F^f_I(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_fi(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_si({:e})", t);
+
+  load_vars(udata);
+  // Call Implicit RHS function
+  run_rhs_fi(t);
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ * Slow RHS function du = F^s(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_s(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_e({:e})", t);
+
+  // Load state from udata
+  load_vars(udata);
+
+  // Call RHS function
+  run_rhs_s(t);
+
+  // Save derivatives to dudata
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ * Fast RHS function du = F^f(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_f(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_e({:e})", t);
+
+  // Load state from udata
+  load_vars(udata);
+
+  // Call RHS function
+  run_rhs_f(t);
+
+  // Save derivatives to dudata
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ * Preconditioner functions
+ **************************************************************************/
+
+void ArkodeMRISolver::pre_s(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata,
+                       BoutReal* rvec, BoutReal* zvec) {
+  TRACE("Running slow preconditioner: ArkodeMRISolver::pre_s({:e})", t);
+
+  const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
+
+  if (!hasPreconditionerSlow()) {
+    // Identity (but should never happen)
+    const auto length = N_VGetLocalLength_Parallel(uvec);
+    std::copy(rvec, rvec + length, zvec);
+    return;
+  }
+
+  // Load state from udata (as with res function)
+  load_vars(udata);
+
+  // Load vector to be inverted into F_vars
+  load_derivs(rvec);
+
+  runPreconditionerSlow(t, gamma, delta);
+
+  // Save the solution from F_vars
+  save_derivs(zvec);
+
+  pre_Wtime_s += bout::globals::mpi->MPI_Wtime() - tstart;
+  pre_ncalls_s++;
+}
+
+void ArkodeMRISolver::pre_f(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata,
+                       BoutReal* rvec, BoutReal* zvec) {
+  TRACE("Running fast preconditioner: ArkodeMRISolver::pre_f({:e})", t);
+
+  const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
+
+  if (!hasPreconditionerFast()) {
+    // Identity (but should never happen)
+    const auto length = N_VGetLocalLength_Parallel(uvec);
+    std::copy(rvec, rvec + length, zvec);
+    return;
+  }
+
+  // Load state from udata (as with res function)
+  load_vars(udata);
+
+  // Load vector to be inverted into F_vars
+  load_derivs(rvec);
+
+  runPreconditionerFast(t, gamma, delta);
+
+  // Save the solution from F_vars
+  save_derivs(zvec);
+
+  pre_Wtime_s += bout::globals::mpi->MPI_Wtime() - tstart;
+  pre_ncalls_s++;
+}
+
+/**************************************************************************
+ * ARKODE explicit RHS functions
+ **************************************************************************/
+
+// NOLINTBEGIN(readability-identifier-length)
+namespace {
+int arkode_rhs_s_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_se(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_rhs_s_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_si(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_rhs_f_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_fe(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_rhs_f_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_fi(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_s_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_s(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_f_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_f(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+/// RHS function for BBD preconditioner
+int arkode_s_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du,
+                   void* user_data) {
+  return arkode_rhs_s_implicit(t, u, du, user_data);
+}
+
+int arkode_f_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du,
+                   void* user_data) {
+  return arkode_rhs_f_implicit(t, u, du, user_data);
+}
+
+/// Preconditioner function
+int arkode_s_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec,
+               BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) {
+  BoutReal* udata = N_VGetArrayPointer(yy);
+  BoutReal* rdata = N_VGetArrayPointer(rvec);
+  BoutReal* zdata = N_VGetArrayPointer(zvec);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Run slow preconditioner
+  s->pre_s(t, gamma, delta, udata, rdata, zdata);
+
+  return 0;
+}
+
+int arkode_f_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec,
+               BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) {
+  BoutReal* udata = N_VGetArrayPointer(yy);
+  BoutReal* rdata = N_VGetArrayPointer(rvec);
+  BoutReal* zdata = N_VGetArrayPointer(zvec);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Run fast preconditioner
+  s->pre_f(t, gamma, delta, udata, rdata, zdata);
+
+  return 0;
+}
+
+} // namespace
+// NOLINTEND(readability-identifier-length)
+
+/**************************************************************************
+ * vector abstol functions
+ **************************************************************************/
+
+void ArkodeMRISolver::set_abstol_values(BoutReal* abstolvec_data,
+                                     std::vector<BoutReal>& f2dtols,
+                                     std::vector<BoutReal>& f3dtols) {
+  int p = 0; // Counter for location in abstolvec_data array
+
+  // All boundaries
+  for (const auto& i2d : bout::globals::mesh->getRegion2D("RGN_BNDRY")) {
+    loop_abstol_values_op(i2d, abstolvec_data, p, f2dtols, f3dtols, true);
+  }
+  // Bulk of points
+  for (const auto& i2d : bout::globals::mesh->getRegion2D("RGN_NOBNDRY")) {
+    loop_abstol_values_op(i2d, abstolvec_data, p, f2dtols, f3dtols, false);
+  }
+}
+
+void ArkodeMRISolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolvec_data,
+                                         int& p, std::vector<BoutReal>& f2dtols,
+                                         std::vector<BoutReal>& f3dtols, bool bndry) {
+  // Loop over 2D variables
+  for (std::vector<BoutReal>::size_type i = 0; i < f2dtols.size(); i++) {
+    if (bndry && !f2d[i].evolve_bndry) {
+      continue;
+    }
+    abstolvec_data[p] = f2dtols[i];
+    p++;
+  }
+
+  for (int jz = 0; jz < bout::globals::mesh->LocalNz; jz++) {
+    // Loop over 3D variables
+    for (std::vector<BoutReal>::size_type i = 0; i < f3dtols.size(); i++) {
+      if (bndry && !f3d[i].evolve_bndry) {
+        continue;
+      }
+      abstolvec_data[p] = f3dtols[i];
+      p++;
+    }
+  }
+}
+
+void ArkodeMRISolver::apply_temporal_filtering(BoutReal internal_time,
+                                               N_Vector uvec)
+{
+  if (!use_temporal_filtering) {
+    return;
+  }
+
+  // Update the temporal filtering 
+  temp_filtering.update(internal_time, uvec);
+
+  // If no mean is available yet, do nothing
+  if (!temp_filtering.has_mean()) {
+    return;
+  }
+
+  int flag;
+    
+  // Get the current mean vector
+  N_Vector u_mean = temp_filtering.get_mean_vector();
+
+  // Apply the temporal filtering
+  // Gently relax the solution towards the mean
+  // Set u = (1 - lambda) * u + lambda * u_mean
+  N_VLinearSum(1.0 - lambda, uvec, lambda, u_mean, uvec);
+
+  // Reset ARKode with the new filtered state
+  flag = ARKodeReset(arkode_mem, internal_time, uvec);
+  if (flag != ARK_SUCCESS) {
+    throw BoutException("ARKodeReset failed in temporal filtering\n");
+  }
+
+  // For EMA: we keep averaging continuously (no reset).
+  // For SRA: enforce finite averaging windows of length tau_mean
+  // by restarting the averaging window when tau_mean_cur is equal to tau_mean
+  if (filtering_type == FilteringType::SRA && temp_filtering.window_full()) {
+    temp_filtering.restart_window(internal_time);
+  }
+}
+
+#else
+#endif // SUNDIALS_VERSION CHECK
+#endif // BOUT_HAS_ARKODE
diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
new file mode 100644
index 0000000000..df9f956789
--- /dev/null
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -0,0 +1,196 @@
+/**************************************************************************
+ * Interface to ARKODE MRI solver
+ * NOTE: ARKODE is currently in beta testing so use with cautious optimism
+ *
+ * NOTE: Only one solver can currently be compiled in
+ *
+ **************************************************************************
+ * Copyright 2010-2025 BOUT++ contributors
+ *
+ * Contact: Ben Dudson, dudson2@llnl.gov
+ *
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#ifndef BOUT_ARKODE_MRI_SOLVER_H
+#define BOUT_ARKODE_MRI_SOLVER_H
+
+#include "bout/build_defines.hxx"
+#include "bout/solver.hxx"
+
+#if not BOUT_HAS_ARKODE
+
+namespace {
+RegisterUnavailableSolver
+    registerunavailablearkodemri("arkode_mri", "BOUT++ was not configured with ARKODE/SUNDIALS");
+}
+
+#else
+
+#include "bout/sundials_backports.hxx"
+#include "temporal_filtering.hxx"
+
+#if SUNDIALS_VERSION_LESS_THAN(7, 2, 0)
+
+namespace {
+RegisterUnavailableSolver
+    registerunavailablearkodemri("arkode_mri", "BOUT++ configured with ARKODE/SUNDIALS version less than 7.2.0");
+}
+
+#else // SUNDIALS_VERSION check
+
+#include "bout/bout_enum_class.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/region.hxx"
+#include <nvector/nvector_parallel.h>
+#include <arkode/arkode_mristep.h>
+#include <sundials/sundials_config.h>
+#include <vector>
+
+class ArkodeMRISolver;
+class Options;
+
+namespace {
+RegisterSolver<ArkodeMRISolver> registersolverarkodemri("arkode_mri");
+}
+
+// enum describing treatment of equations
+// Note: Capitalized because `explicit` is a C++ reserved keyword
+BOUT_ENUM_CLASS(MRI_Treatment, ImEx, Implicit, Explicit);
+
+class ArkodeMRISolver : public Solver {
+public:
+  explicit ArkodeMRISolver(Options* opts = nullptr);
+  ~ArkodeMRISolver();
+
+  // Get the current timestep
+  BoutReal getCurrentTimestep() override;
+
+  int init() override;
+
+  int run() override;
+  BoutReal run(BoutReal tout);
+
+  // These functions used internally (but need to be public)
+  void rhs_se(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_si(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_fe(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_fi(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_s(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_f(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void pre_s(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec,
+           BoutReal* zvec);
+  void pre_f(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec,
+           BoutReal* zvec);
+  void jac_s(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
+  void jac_f(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
+
+private:
+  bool diagnose{false}; //< Output additional diagnostics
+
+  N_Vector uvec{nullptr};    //< Values
+  void* arkode_mem{nullptr}; //< ARKODE internal memory block
+  void* inner_arkode_mem{nullptr}; //< ARKODE internal memory block
+  MRIStepInnerStepper inner_stepper{nullptr}; //< inner stepper
+
+  BoutReal pre_Wtime_s{0.0}; //< Time in preconditioner
+  BoutReal pre_Wtime_f{0.0}; //< Time in preconditioner
+  int pre_ncalls_s{0};       //< Number of calls to preconditioner
+  int pre_ncalls_f{0};       //< Number of calls to preconditioner
+
+  /// Maximum number of steps to take between outputs
+  int mxsteps;
+
+  // /// Maximum step sizes
+  // double mxstepsize;
+  // double inner_mxstepsize;
+
+  /// Integrator treatment enum: IMEX, Implicit or Explicit
+  MRI_Treatment treatment;
+  MRI_Treatment inner_treatment;
+  /// Use linear implicit solver (only evaluates jacobian inversion once)
+  bool set_linear;
+  bool inner_set_linear;
+  /// Solve both fast and slow portion in fixed timestep mode.
+  /// NOTE: This is not recommended except for code comparison
+  bool fixed_step;
+  /// Order of the internal step
+  int order;
+  /// Absolute tolerance
+  BoutReal abstol;
+  /// Relative tolerance
+  BoutReal reltol;
+  /// Use separate absolute tolerance for each field
+  bool use_vector_abstol;
+  /// Maximum timestep (only used if greater than zero)
+  bool use_precon;
+  bool inner_use_precon;
+  /// Number of Krylov basis vectors to use
+  int maxl;
+  int inner_maxl;
+  /// Use right preconditioning instead of left preconditioning
+  bool rightprec;
+  /// Temporal filtering of solution
+  /// - Whether to use temporal filtering
+  bool use_temporal_filtering{false};
+  /// Temporal filtering object
+  TemporalFiltering temp_filtering;
+  /// Type of temporal filtering to use
+  FilteringType filtering_type{FilteringType::None};
+  /// Interval over which means are calculated
+  /// - EMA: time scale of the exponential memory
+  /// - SRA: window length of each running-average block
+  BoutReal tau_mean{0.0};
+  /// Time at which averaging starts
+  BoutReal mean_start_time{0.0};
+  /// Relaxation/nudging parameter for temporal filtering
+  BoutReal lambda{0.0};
+
+  // Diagnostics from ARKODE MRI
+  int nsteps{0};
+  int nfe_evals{0};
+  int nfi_evals{0};
+  int nniters{0};
+  int npevals{0};
+  int nliters{0};
+  int inner_nsteps{0};
+  int inner_nfe_evals{0};
+  int inner_nfi_evals{0};
+  int inner_nniters{0};
+  int inner_npevals{0};
+  int inner_nliters{0};
+
+  void set_abstol_values(BoutReal* abstolvec_data, std::vector<BoutReal>& f2dtols,
+                         std::vector<BoutReal>& f3dtols);
+  void loop_abstol_values_op(Ind2D i2d, BoutReal* abstolvec_data, int& p,
+                             std::vector<BoutReal>& f2dtols,
+                             std::vector<BoutReal>& f3dtols, bool bndry);
+  void apply_temporal_filtering(BoutReal internal_time, N_Vector uvec);
+  /// SPGMR solver structure
+  SUNLinearSolver sun_solver{nullptr};
+  SUNLinearSolver inner_sun_solver{nullptr};
+  /// Solver for implicit stages
+  SUNNonlinearSolver nonlinear_solver{nullptr};
+  SUNNonlinearSolver inner_nonlinear_solver{nullptr};
+  /// Context for SUNDIALS memory allocations
+  sundials::Context suncontext;
+};
+
+#endif // SUNDIALS_VERSION CHECK
+#endif // BOUT_HAS_ARKODE
+#endif // BOUT_ARKODE_MRI_SOLVER_H
+
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 1f7b654427..5d826a0ef2 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -60,6 +60,7 @@
 // Implementations:
 #include "impls/adams_bashforth/adams_bashforth.hxx"
 #include "impls/arkode/arkode.hxx"
+#include "impls/arkode/arkode_mri.hxx"
 #include "impls/cvode/cvode.hxx"
 #include "impls/euler/euler.hxx"
 #include "impls/ida/ida.hxx"
@@ -961,7 +962,32 @@ int Solver::resetRHSCounter_e() {
   return t;
 }
 
+int Solver::resetRHSCounter_se() {
+  int t = rhs_ncalls_se;
+  rhs_ncalls_se = 0;
+  return t;
+}
+
+int Solver::resetRHSCounter_si() {
+  int t = rhs_ncalls_si;
+  rhs_ncalls_si = 0;
+  return t;
+}
+
+int Solver::resetRHSCounter_fe() {
+  int t = rhs_ncalls_fe;
+  rhs_ncalls_fe = 0;
+  return t;
+}
+
+int Solver::resetRHSCounter_fi() {
+  int t = rhs_ncalls_fi;
+  rhs_ncalls_fi = 0;
+  return t;
+}
+
 bool Solver::splitOperator() { return model->splitOperator(); }
+bool Solver::splitOperatorMRI() { return model->splitOperatorMRI(); }
 
 /////////////////////////////////////////////////////
 
@@ -1038,8 +1064,7 @@ void Solver::load_vars(BoutReal* udata) {
     f.var->setLocation(f.location);
   }
 
-  loop_vars(VarRange<FieldCategories::VARS, Field2D>(f2d),
-            VarRange<FieldCategories::VARS, Field3D>(f3d), udata, SOLVER_VAR_OP::LOAD);
+  loop_vars(udata, SOLVER_VAR_OP::LOAD_VARS);
 
   // Mark each vector as either co- or contra-variant
 
@@ -1061,8 +1086,7 @@ void Solver::load_derivs(BoutReal* udata) {
     f.F_var->setLocation(f.location);
   }
 
-  loop_vars(VarRange<FieldCategories::DERIVS, Field2D>(f2d),
-            VarRange<FieldCategories::DERIVS, Field3D>(f3d), udata, SOLVER_VAR_OP::LOAD);
+  loop_vars(udata, SOLVER_VAR_OP::LOAD_DERIVS);
 
   // Mark each vector as either co- or contra-variant
 
@@ -1078,13 +1102,13 @@ void Solver::load_derivs(BoutReal* udata) {
 void Solver::save_vars(BoutReal* udata) {
   for (const auto& f : f2d) {
     if (!f.var->isAllocated()) {
-      throw BoutException(_f("Variable '{:s}' not initialised"), f.name);
+      throw BoutException(_("Variable '{:s}' not initialised"), f.name);
     }
   }
 
   for (const auto& f : f3d) {
     if (!f.var->isAllocated()) {
-      throw BoutException(_f("Variable '{:s}' not initialised"), f.name);
+      throw BoutException(_("Variable '{:s}' not initialised"), f.name);
     }
   }
 
@@ -1211,6 +1235,170 @@ Field3D Solver::globalIndex(int localStart) {
  * Running user-supplied functions
  **************************************************************************/
 
+int Solver::run_rhs_se(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  pre_rhs(t);
+  status = model->runRHS_se(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_se++;
+  return status;
+}
+
+int Solver::run_rhs_si(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_s_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_s_call = false;
+  }
+
+  pre_rhs(t);
+  status = model->runRHS_si(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_si++;
+  return status;
+}
+
+int Solver::run_rhs_fe(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  pre_rhs(t);
+  status = model->runRHS_fe(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_fe++;
+  return status;
+}
+
+int Solver::run_rhs_fi(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_f_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_f_call = false;
+  }
+
+  pre_rhs(t);
+  status = model->runRHS_fi(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_fi++;
+  return status;
+}
+
+int Solver::run_rhs_s(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_call = false;
+  }
+
+  pre_rhs(t);
+
+  // Run both parts
+
+  int nv = getLocalN();
+  // Create two temporary arrays for system state
+  Array<BoutReal> tmp(nv);
+  Array<BoutReal> tmp2(nv);
+
+  save_vars(tmp.begin()); // Copy variables into tmp
+  pre_rhs(t);
+  status = model->runRHS_se(t, linear);
+  post_rhs(t); // Check variables, apply boundary conditions
+
+  load_vars(tmp.begin());   // Reset variables
+  save_derivs(tmp.begin()); // Save time derivatives
+  pre_rhs(t);
+  status = model->runRHS_si(t, linear);
+  post_rhs(t);
+  save_derivs(tmp2.begin()); // Save time derivatives
+  for (BoutReal *t = tmp.begin(), *t2 = tmp2.begin(); t != tmp.end(); ++t, ++t2) {
+    *t += *t2;
+  }
+  load_derivs(tmp.begin()); // Put back time-derivatives
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_se++;
+  rhs_ncalls_si++;
+  return status;
+}
+
+int Solver::run_rhs_f(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_call = false;
+  }
+
+  pre_rhs(t);
+
+  // Run both parts
+
+  int nv = getLocalN();
+  // Create two temporary arrays for system state
+  Array<BoutReal> tmp(nv);
+  Array<BoutReal> tmp2(nv);
+
+  save_vars(tmp.begin()); // Copy variables into tmp
+  pre_rhs(t);
+  status = model->runRHS_fe(t, linear);
+  post_rhs(t); // Check variables, apply boundary conditions
+
+  load_vars(tmp.begin());   // Reset variables
+  save_derivs(tmp.begin()); // Save time derivatives
+  pre_rhs(t);
+  status = model->runRHS_fi(t, linear);
+  post_rhs(t);
+  save_derivs(tmp2.begin()); // Save time derivatives
+  for (BoutReal *t = tmp.begin(), *t2 = tmp2.begin(); t != tmp.end(); ++t, ++t2) {
+    *t += *t2;
+  }
+  load_derivs(tmp.begin()); // Put back time-derivatives
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_fe++;
+  rhs_ncalls_fi++;
+  return status;
+}
+
 int Solver::run_rhs(BoutReal t, bool linear) {
   int status;
 
@@ -1222,7 +1410,53 @@ int Solver::run_rhs(BoutReal t, bool linear) {
     first_rhs_call = false;
   }
 
-  if (model->splitOperator()) {
+  if (model->splitOperatorMRI()) {
+    // Run all four parts
+
+    int nv = getLocalN();
+    // Create temporary arrays for system state
+    Array<BoutReal> tmp(nv);
+    Array<BoutReal> tmp2(nv);
+    Array<BoutReal> tmp3(nv);
+
+    save_vars(tmp.begin()); // Copy variables into tmp
+
+    pre_rhs(t);
+    status = model->runRHS_fe(t, linear);
+    post_rhs(t); // Check variables, apply boundary conditions
+    save_derivs(tmp2.begin()); // Save time derivatives
+
+    pre_rhs(t);
+    status = model->runRHS_fi(t, linear);
+    post_rhs(t);
+    save_derivs(tmp3.begin()); // Save time derivatives
+    for (BoutReal *t3 = tmp3.begin(), *t2 = tmp2.begin(); t3 != tmp3.end(); ++t3, ++t2) {
+        *t3 += *t2;
+    }
+
+    pre_rhs(t);
+    status = model->runRHS_se(t, linear);
+    post_rhs(t);
+    save_derivs(tmp2.begin()); // Save time derivatives
+    for (BoutReal *t3 = tmp3.begin(), *t2 = tmp2.begin(); t3 != tmp3.end(); ++t3, ++t2) {
+        *t3 += *t2;
+    }
+
+    pre_rhs(t);
+    status = model->runRHS_si(t, linear);
+    post_rhs(t);
+    save_derivs(tmp2.begin()); // Save time derivatives
+    for (BoutReal *t3 = tmp3.begin(), *t2 = tmp2.begin(); t3 != tmp3.end(); ++t3, ++t2) {
+        *t3 += *t2;
+    }
+    load_derivs(tmp3.begin()); // Put back time-derivatives
+
+    rhs_ncalls_fe++;
+    rhs_ncalls_fi++;
+    rhs_ncalls_se++;
+    rhs_ncalls_si++;
+
+  } else if (model->splitOperator()) {
     // Run both parts
 
     int nv = getLocalN();
@@ -1245,18 +1479,21 @@ int Solver::run_rhs(BoutReal t, bool linear) {
       *t += *t2;
     }
     load_derivs(tmp.begin()); // Put back time-derivatives
+    rhs_ncalls++;
+    rhs_ncalls_e++;
+    rhs_ncalls_i++;
   } else {
     pre_rhs(t);
     status = model->runRHS(t, linear);
     post_rhs(t);
+    rhs_ncalls++;
+    rhs_ncalls_e++;
+    rhs_ncalls_i++;
   }
 
   // If using Method of Manufactured Solutions
   add_mms_sources(t);
 
-  rhs_ncalls++;
-  rhs_ncalls_e++;
-  rhs_ncalls_i++;
   return status;
 }
 
@@ -1392,9 +1629,19 @@ bool Solver::varAdded(const std::string& name) {
 }
 
 bool Solver::hasPreconditioner() { return model->hasPrecon(); }
+bool Solver::hasPreconditionerFast() { return model->hasPreconFast(); }
+bool Solver::hasPreconditionerSlow() { return model->hasPreconSlow(); }
+
+int Solver::runPreconditioner(BoutReal time, BoutReal gamma, BoutReal delta) {
+  return model->runPrecon(time, gamma, delta);
+}
+
+int Solver::runPreconditionerFast(BoutReal time, BoutReal gamma, BoutReal delta) {
+  return model->runPreconFast(time, gamma, delta);
+}
 
-int Solver::runPreconditioner(BoutReal t, BoutReal gamma, BoutReal delta) {
-  return model->runPrecon(t, gamma, delta);
+int Solver::runPreconditionerSlow(BoutReal time, BoutReal gamma, BoutReal delta) {
+  return model->runPreconSlow(time, gamma, delta);
 }
 
 bool Solver::hasJacobian() { return model->hasJacobian(); }
diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt
index d87bd329f0..7f62fd7410 100644
--- a/tests/integrated/CMakeLists.txt
+++ b/tests/integrated/CMakeLists.txt
@@ -22,6 +22,7 @@ add_subdirectory(test-interpolate)
 add_subdirectory(test-interpolate-z)
 add_subdirectory(test-invertable-operator)
 add_subdirectory(test-invpar)
+add_subdirectory(test-kpr_mri)
 add_subdirectory(test-laplace)
 add_subdirectory(test-laplace-petsc3d)
 add_subdirectory(test-laplace-hypre3d)
diff --git a/tests/integrated/test-kpr_mri/CMakeLists.txt b/tests/integrated/test-kpr_mri/CMakeLists.txt
new file mode 100644
index 0000000000..45523803db
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/CMakeLists.txt
@@ -0,0 +1,2 @@
+bout_add_integrated_test(test_kpr_mri SOURCES test_kpr_mri.cxx
+REQUIRES BOUT_HAS_SUNDIALS)
diff --git a/tests/integrated/test-kpr_mri/README.md b/tests/integrated/test-kpr_mri/README.md
new file mode 100644
index 0000000000..2233782dd8
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/README.md
@@ -0,0 +1,37 @@
+test-kpr_mri
+===========
+
+ Multirate nonlinear Kvaerno-Prothero-Robinson ODE test problem:
+
+    [f]' = [ G  e ] [(-1+f^2-r)/(2f)] + [      r'(t)/(2f)        ]
+    [g]    [ e -1 ] [(-2+g^2-s)/(2g)]   [ s'(t)/(2*sqrt(2+s(t))) ]
+         = [ fs(t,f,g) ]
+           [ ff(t,f,g) ]
+
+ where r(t) = 0.5 * cos(t),  s(t) = cos(w * t),  0 < t < 5.
+
+ This problem has analytical solution given by
+    f(t) = sqrt(1+r(t)),  g(t) = sqrt(2+s(t)).
+
+ We use the parameters:
+   e = 0.5 (fast/slow coupling strength)
+   G = -100 (stiffness at slow time scale)
+   w = 100  (time-scale separation factor)
+
+ The stiffness of the slow time scale is essentially determined
+ by G, for |G| > 50 it is 'stiff' and ideally suited to a
+ multirate method that is implicit at the slow time scale.
+
+MRI implementations of the functions are as follows:
+
+The slow explicit RHS function:
+     [-0.5 * sin(t)/(2 * f)]
+     [          0          ]
+
+The slow implicit RHS function:
+      [G e] * [(-1 + f^2 - 0.5 * cos(t))/(2 * f) ]
+      [0 0]   [(-2 + g^2 - cos(w * t))/(2 * g)   ]
+
+The fast implicit RHS function:
+     [0  0] * [(-1 + f^2 - 0.5 * cos(t))/(2 * f)] + [         0                              ]
+     [e -1]   [(-2 + g^2 - cos(w * t))/(2 * g)  ]   [-w * sin(w * t)/(2 * sqrt(2 + cos(w*t)))]
diff --git a/tests/integrated/test-kpr_mri/makefile b/tests/integrated/test-kpr_mri/makefile
new file mode 100644
index 0000000000..84db76e5c3
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/makefile
@@ -0,0 +1,5 @@
+BOUT_TOP	= ../../..
+
+SOURCEC		= test_kpr_mri.cxx
+
+include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-kpr_mri/runtest b/tests/integrated/test-kpr_mri/runtest
new file mode 100755
index 0000000000..47f335dc94
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/runtest
@@ -0,0 +1,23 @@
+#!/usr/bin/env python3
+
+# requires: petsc
+
+from boututils.run_wrapper import shell_safe, launch_safe
+
+from sys import exit
+
+nthreads = 1
+nproc = 1
+
+print("Making solver test")
+shell_safe("make > make.log")
+
+print("Running solver test")
+status, out = launch_safe("./test_kpr_mri", nproc=nproc, mthread=nthreads, pipe=True)
+with open("run.log", "w") as f:
+    f.write(out)
+
+if status:
+    print(out)
+
+exit(status)
diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
new file mode 100644
index 0000000000..7741d9d24b
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
@@ -0,0 +1,161 @@
+#include "bout/sundials_backports.hxx"
+
+#if SUNDIALS_VERSION_AT_LEAST(7, 2, 0)
+
+#include "bout/physicsmodel.hxx"
+#include "bout/solver.hxx"
+
+#include <cmath>
+#include <memory>
+#include <string>
+#include <vector>
+
+// A simple phyics model with an analytical solution
+//
+class TestSolver : public PhysicsModel {
+public:
+  Field3D f, g;
+
+  BoutReal e  = 0.5;       /* fast/slow coupling strength */
+  BoutReal G  = -100.0;    /* stiffness at slow time scale */
+  BoutReal w  = 100.0;     /* time-scale separation factor */
+
+  int init(bool UNUSED(restarting)) override {
+    solver->add(f, "f");
+    solver->add(g, "g");
+
+    f = sqrt(3.0/2.0);
+    g = sqrt(3.0);
+
+    setSplitOperatorMRI();
+
+    return 0;
+  }
+
+  int rhs_se(BoutReal t) override {
+  /* fill in the slow explicit RHS function:
+     [-0.5*sin(t)/(2*f)]
+     [      0          ] */
+    ddt(f) = -0.5*sin(t)/(2.0*f(1,1,0));
+    ddt(g) = 0.0;
+
+    return 0;
+  }
+
+  int rhs_si(BoutReal t) override {
+    /* fill in the slow implicit RHS function:
+      [G e]*[(-1+f^2-0.5*cos(t))/(2*f)]
+      [0 0] [(-2+g^2-cos(w*t))/(2*g)  ]  */
+    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
+    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+    ddt(f) = G * tmp1 + e * tmp2;
+    ddt(g) = 0.0;
+
+    return 0;
+  }
+
+  int rhs_fe(BoutReal t) override {
+  /* fill in the fast explicit RHS function:
+     [0  0]*[(-1+f^2-0.5*cos(t))/(2*f)] + [         0                      ]
+     [e -1] [(-2+g^2-cos(w*t))/(2*g)  ]   [-w*sin(w*t)/(2*sqrt(2+cos(w*t)))] */
+    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
+    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+    ddt(f) = 0.0;
+    ddt(g) = e * tmp1 - tmp2 - w * sin(w*t) / (2.0 * sqrt(2.0 + cos(w * t)));
+
+    return 0;
+  }
+
+  int rhs_fi(BoutReal UNUSED(t)) override {
+
+    ddt(f) = 0.0;
+    ddt(g) = 0.0;
+
+    return 0;
+  }
+
+  BoutReal compute_error(BoutReal t)
+  {
+    /* Compute the error with the true solution:
+     f(t) = sqrt(0.5*cos(t) + 1.0)
+     g(t) = sqrt(cos(w*t) + 2.0) */
+    return sqrt( pow(sqrt(0.5*cos(t) + 1.0) - f(1,1,0), 2.0) +
+                 pow(sqrt(cos(w*t) + 2.0) - g(1,1,0), 2.0));
+  }
+
+  // Don't need any restarting, or options to control data paths
+  int postInit(bool) override { return 0; }
+};
+
+int main(int argc, char** argv) {
+  // Relative and Absolute tolerances
+  constexpr BoutReal rtol = 1.e-10;
+  constexpr BoutReal atol = 1.e-12;
+
+  // Our own output to stdout, as main library will only be writing to log files
+  Output output_test;
+
+  auto& root = Options::root();
+
+  root["mesh"]["MXG"] = 1;
+  root["mesh"]["MYG"] = 1;
+  root["mesh"]["nx"] = 3;
+  root["mesh"]["ny"] = 1;
+  root["mesh"]["nz"] = 1;
+
+  root["output"]["enabled"] = false;
+  root["restart_files"]["enabled"] = false;
+
+  Solver::setArgs(argc, argv);
+  BoutComm::setArgs(argc, argv);
+
+  bout::globals::mpi = new MpiWrapper();
+
+  bout::globals::mesh = Mesh::create();
+  bout::globals::mesh->load();
+
+  std::string sunsolver = "arkode_mri";
+  int nout = 100;
+  BoutReal timestep = 0.05;
+  BoutReal finaltime = nout*timestep;
+
+  // Global options
+  root["nout"] = nout;
+  root["timestep"] = timestep;
+  root[sunsolver]["rtol"] = rtol;
+  root[sunsolver]["atol"] = atol;
+
+  root[sunsolver]["use_temporal_filtering"] = true;
+  root[sunsolver]["tau_mean"] = 1.0;
+  root[sunsolver]["filtering_type"] = "ema";
+  root[sunsolver]["mean_start_time"] = 0.0;
+  root[sunsolver]["lambda"] = 10.0*rtol;
+
+  // Get specific options section for this solver. Can't just use default
+  // "solver" section, as we run into problems when solvers use the same
+  // name for an option with inconsistent defaults
+  auto options = Options::getRoot()->getSection(sunsolver);
+  auto solver = std::unique_ptr<Solver>{Solver::create(sunsolver, options)};
+
+  TestSolver model{};
+  solver->setModel(&model);
+
+  BoutMonitor bout_monitor{};
+  solver->addMonitor(&bout_monitor, Solver::BACK);
+
+  solver->solve();
+
+  BoutReal error = model.compute_error(finaltime);
+
+  std::cout << "error = " << error << std::endl;
+
+  return 0;
+}
+#else
+// ARKODE-MRI option for BOUT++
+// is not available with this configuration
+// do nothing for this test
+int main(int argc, char** argv) {
+  return 0;
+}
+#endif
\ No newline at end of file
diff --git a/tests/integrated/test_suite b/tests/integrated/test_suite
new file mode 100755
index 0000000000..307a8d84b3
--- /dev/null
+++ b/tests/integrated/test_suite
@@ -0,0 +1,366 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Run the test suite, report failures
+#
+# To set command for running parallel jobs, define environment variable
+# e.g. for bash
+# export MPIRUN="mpirun -np"
+# export MPIRUN="aprun -n"
+
+import os
+import sys
+import time
+import glob
+from boututils.run_wrapper import shell
+import threading
+import re
+import fcntl
+import select
+
+##################################################################
+
+import argparse
+
+parser = argparse.ArgumentParser(description="Run or build some tests.")
+parser.add_argument(
+    "-g",
+    "--get-list",
+    action="store_true",
+    help="Return a list of tests that would be run/build",
+)
+parser.add_argument(
+    "-m", "--make", action="store_true", help="Build the tests, rather then run them."
+)
+parser.add_argument(
+    "-a", "--all", action="store_true", dest="all_tests", help="Run all tests"
+)
+parser.add_argument(
+    "-b",
+    "--set-bool",
+    nargs="+",
+    metavar=("value1=False", "value2=True"),
+    help="Set a bool value for evaluating what scripts can be run.",
+)
+parser.add_argument(
+    "-l",
+    "--set-list",
+    nargs="+",
+    metavar=("test1", "test2"),
+    help="Set the tests that should be run.",
+)
+parser.add_argument(
+    "-j",
+    "--jobs",
+    nargs=1,
+    type=int,
+    dest="jobs",
+    help="Set the number of cores to use in parallel.",
+)
+
+args = parser.parse_args()
+
+##################################################################
+
+sys.path.append("..")
+from requirements import Requirements
+
+requirements = Requirements()
+
+if args.set_bool is not None:
+    lookup = {"false": False, "no": False, "true": True, "yes": True}
+    for setbool in args.set_bool:
+        k, v = setbool.split("=")
+        v = lookup[v.lower()]
+        requirements.add(k, v, override=True)
+
+try:
+    requirements.add("make", args.make)
+except RuntimeError:
+    raise RuntimeError(
+        "The make flag needs to be set by passing --make rather then --set-bool make=True"
+    )
+
+try:
+    requirements.add("all_tests", args.all_tests)
+except RuntimeError:
+    raise RuntimeError(
+        "The all-tests flag needs to be set by passing --all rather then --set-bool all_tests=True"
+    )
+
+##################################################################
+# Parallel stuff
+#
+# We can run in parallel. As some checks require several threads to
+# run, we take this into account when we schedule tests. Given a
+# certain amount of threads that we are told to use, we try to run
+# so many tests in parallel, that the total core count is not higher
+# than this number. If this isn't possible because some jobs require
+# more cores than we have threads, we run the remaining tests in
+# serial. The number of parallel threads is called cost of a test.
+#
+# The beginning of MAKEFLAGS has some flags that tell us what we are
+# supposed to be doing. Most of them we can ignore.
+# Check what we are supposed to be doing:
+if "MAKEFLAGS" in os.environ:
+    makeflags = os.environ["MAKEFLAGS"]
+    for token in makeflags:
+        if token == "n":
+            # Print recipies:
+            # We ignore this for now ...
+            sys.exit(0)
+        elif token == "q":
+            # Question mode:
+            # We are never up-to-date
+            sys.exit(1)
+        elif token in "ksBd":
+            # k - keep going
+            # s - silent
+            # B - always build (we do)
+            # d - debug
+            pass
+        elif token == " ":
+            break
+        elif token == "-":
+            # This is not from make
+            break
+        else:
+            # Not implemented
+            print("mode '%s' not implemented" % token)
+            # sys.exit(42)
+else:
+    makeflags = ""
+num_threads = 1
+if args.jobs:
+    num_threads = args.jobs[0]
+js_read = None
+# if we are running under make, we only have one thread (called job
+# in make terms) for sure, but might be able to run more threads
+# (depending what other jobs are currently running)
+# Additional jobs come in form of `tokens` that we need to give
+# back, if we are finished.
+# https://www.gnu.org/software/make/manual/html_node/POSIX-Jobserver.html
+if "--jobserver-auth=" in makeflags or "--jobserver-fds=" in makeflags:
+    try:
+        offset = makeflags.index("--jobserver-auth=")
+    except ValueError:
+        offset = makeflags.index("--jobserver-fds=")
+    file_desc = [int(i) for i in re.findall("\d+", makeflags[offset:])[0:2]]
+    js_read = file_desc[0]
+    js_write = file_desc[1]
+    js_tokens = b""
+
+
+class Test(threading.Thread):
+    def __init__(self, name, cmd, width, timeout):
+        threading.Thread.__init__(self)
+        self.name = name
+        self.cmd = cmd
+        self.width = width
+        self.local = threading.local()
+        self.cost = self._cost()
+        self.timeout = timeout
+
+    def run(self):
+        # Check requirements
+        self.local.req_met, self.local.req_expr = requirements.check(
+            self.name + "/runtest"
+        )
+        self.local.start_time = time.time()
+        if not self.local.req_met:
+            print(
+                "{:{width}}".format(self.name, width=self.width)
+                + "S - {0} => False".format(self.local.req_expr)
+            )
+            sys.stdout.flush()
+            self.status = 0
+        else:
+            # Run test, piping stdout so it is not sent to console
+            command = "cd {}; timeout {} {}".format(self.name, self.timeout, self.cmd)
+            self.status, self.output = shell(command, pipe=True)
+            print("{:{width}}".format(self.name, width=self.width), end="")
+            if self.status == 0:
+                # ✓ Passed
+                print("\u2713", end="")  # No newline
+            elif self.status == 124:
+                # 💤 timeout
+                print("\U0001f4a4", end="")  # No newline
+                self.output += "\n(It is likely that a timeout occured)"
+            else:
+                # ❌ Failed
+                print("\u274C", end="")  # No newline
+            print(" %7.3f s" % (time.time() - self.local.start_time), flush=True)
+
+    def _cost(self):
+        if self.cmd == "make":
+            return 1
+        with open(self.name + "/" + self.cmd, "r", encoding="utf8") as filein:
+            contents = filein.read()
+        # Find all lines starting with '#cores' or '#Cores:'
+        match = re.findall("^\s*\#\s?[Cc]ores:\s*?(\d+)", contents, re.MULTILINE)
+        if len(match) > 1:
+            raise RuntimeError(
+                "Found more then one match for core-count in " + self.name
+            )
+        if len(match) == 0:
+            # default; no mpi
+            return 1
+        c = int(match[0])
+        if c < 0:
+            raise RuntimeError(
+                "Core-count is %d and thus not positive in " % c + self.name
+            )
+        return c
+
+
+##################################################################
+
+if args.set_list is None:
+    # Get list of directories containing test cases
+    try:
+        # Requires python >= 3.5
+        tests = glob.iglob("**/runtest", recursive=True)
+    except TypeError:
+        # Fall back - check only a few folders ...
+        tests = glob.glob("*/runtest")
+        tests += glob.glob("*/*/runtest")
+        tests += glob.glob("*/*/*/runtest")
+        tests += glob.glob("*/*/*/*/runtest")
+
+    tests = [x.rsplit("/", 1)[0] for x in tests]
+
+else:
+    # Take the user provided list
+    tests = [x.rstrip("/") for x in args.set_list]
+
+
+if args.get_list:
+    for test in tests:
+        req_met, _ = requirements.check(test + "/runtest")
+        if req_met:
+            print(test)
+    sys.exit(0)
+
+
+# A function to get more threads from the job server
+def get_threads():
+    global js_read
+    if js_read:
+        global cost_remain, js_tokens, avail_threads, num_threads
+        try:
+            fl = fcntl.fcntl(js_read, fcntl.F_GETFL)
+        except OSError:
+            print("Warning - we are not part of the job pool 😭, running in serial")
+            js_read = None
+            return
+        isreadable, _, _ = select.select([js_read], [], [], 0)
+        if isreadable != []:
+            # Only set shortly to non-blocking, and only if we
+            # expect we can read. Old make uses blocking pipes, and
+            # assumes if it is non-blocking, a job is available.
+            fcntl.fcntl(js_read, fcntl.F_SETFL, fl | os.O_NONBLOCK)
+            new_token = os.read(js_read, cost_remain - avail_threads)
+            fcntl.fcntl(js_read, fcntl.F_SETFL, fl)
+            num_threads += len(new_token)
+            js_tokens += new_token
+            avail_threads += len(new_token)
+
+
+##################################################################
+# Run the actual test
+# Kill tests that take longer than 10 minutes (default)
+timeout = os.environ.get("BOUT_TEST_TIMEOUT", "10m" if not args.all_tests else "30m")
+command = "./runtest" if not args.make else "make"
+
+savepath = os.getcwd()  # Save current working directory
+failed = []
+
+start_time = time.time()
+
+test_type = "Making" if args.make else "Running"
+
+print(
+    "======= {} {} {} tests ========".format(
+        test_type, len(tests), savepath.split("/")[-1]
+    )
+)
+
+longest = max([len(s) for s in tests])
+avail_threads = num_threads
+tester = sorted(
+    [Test(t, command, longest + 1, timeout) for t in tests],
+    key=lambda x: x.cost,
+    reverse=True,
+)
+cost_remain = sum(x.cost for x in tester)
+get_threads()
+
+torun = [i for i in range(len(tests))]
+running = []
+
+while len(torun) + len(running):
+    if avail_threads:
+        # See whether we can start one
+        for i in torun[:]:
+            if tester[i].cost <= avail_threads:
+                torun.remove(i)
+                job = tester[i]
+                job.start()
+                running.append(job)
+                avail_threads -= job.cost
+                cost_remain -= job.cost
+        # if nothing is running, start the first
+        if running == []:
+            tostart = torun.pop(0)
+            job = tester[tostart]
+            job.start()
+            running.append(job)
+            avail_threads -= job.cost
+            cost_remain -= job.cost
+
+    # Are any jobs finished
+    for job in running:
+        job.join(0.1)
+        if not job.is_alive():
+            if job.status:
+                failed.append([job.name, job.output])
+            avail_threads += job.cost
+            running.remove(job)
+
+    # Try to get more jobs
+    if torun:
+        get_threads()
+    else:
+        # Free not-needed jobs
+        if avail_threads and js_read:
+            old_tokens = js_tokens[0:avail_threads]
+            js_tokens = js_tokens[avail_threads:]
+            os.write(js_write, old_tokens)
+            num_threads -= avail_threads
+            avail_threads = 0
+
+elapsed_time = time.time() - start_time
+
+print("\n")
+
+# Return remaining tokens
+if js_read is not None:
+    if js_tokens != "":
+        os.write(js_write, js_tokens)
+
+if failed:
+    print("======= FAILURES ========")
+    for test, output in failed:
+        # Note: need Unicode string in case output contains unicode
+        print("\n----- {0} -----\n{1}".format(test, output))
+
+    print(
+        "======= {0} failed in {1:.2f} seconds ========".format(
+            len(failed), elapsed_time
+        )
+    )
+
+    sys.exit(1)
+
+else:
+    print("======= All tests passed in {0:.2f} seconds =======".format(elapsed_time))

From 73faa54618b1606d849b081951abf0933fe73bab Mon Sep 17 00:00:00 2001
From: maggul <mustafaaggul06@gmail.com>
Date: Fri, 4 Sep 2026 01:00:12 -0500
Subject: [PATCH 1799/1827] missing f and py placeholder for now

---
 src/bout++.cxx                                | 2 +-
 tests/integrated/test-kpr_mri/test_kpr_mri.py | 8 ++++++++
 2 files changed, 9 insertions(+), 1 deletion(-)
 create mode 100644 tests/integrated/test-kpr_mri/test_kpr_mri.py

diff --git a/src/bout++.cxx b/src/bout++.cxx
index 5316d472e4..da7b95b24f 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -916,7 +916,7 @@ int BoutMonitor::call(Solver* solver, BoutReal t, [[maybe_unused]] int iter, int
     BoutReal t_remain = mpi_start_time + wall_limit - bout::globals::mpi->MPI_Wtime();
     if (t_remain < run_data.wtime * 2) {
       // Less than 2 time-steps left
-      output_warn.write(_("Only {:e} seconds ({:.2f} steps) left. Quitting\n"), t_remain,
+      output_warn.write(_f("Only {:e} seconds ({:.2f} steps) left. Quitting\n"), t_remain,
                         t_remain / run_data.wtime);
       user_requested_exit = true;
     } else {
diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.py b/tests/integrated/test-kpr_mri/test_kpr_mri.py
new file mode 100644
index 0000000000..90d8e37d0c
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.py
@@ -0,0 +1,8 @@
+#!/usr/bin/env python3
+
+#
+# Run the test, check it completed successfully
+# Place holder for now TODO: add a proper test for the KPR MRI module
+#
+def test_kpr_mri():
+    pass
\ No newline at end of file

From 7c4db2b1fb4f9983752829768554e5b4b8904cda Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 4 Sep 2026 07:55:40 -0700
Subject: [PATCH 1800/1827] Apply batched suggestions from code review

Improved documentation. No code changes.

[skip ci]

Co-authored-by: David Bold <dave@ipp.mpg.de>
---
 manual/sphinx/user_docs/bout_options.rst | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/manual/sphinx/user_docs/bout_options.rst b/manual/sphinx/user_docs/bout_options.rst
index cb8fca8115..3d25ac1a14 100644
--- a/manual/sphinx/user_docs/bout_options.rst
+++ b/manual/sphinx/user_docs/bout_options.rst
@@ -486,12 +486,9 @@ can be set with the global option ``grid``, or ``mesh:file``:
     [mesh]
     file = "cbm18_8_y064_x260.nc"
 
-Relative grid paths are first resolved relative to ``datadir``. If that
-file does not exist, BOUT++ falls back to resolving the path relative to
-the current working directory. If matching files exist in both places,
+Relative grid paths are resolved relative to ``datadir`` and the current working directory. If matching files exist in both places,
 BOUT++ throws an error rather than guessing which one to use. To avoid
-ambiguity entirely, use an explicit absolute path when the grid file is
-not inside ``datadir``.
+ambiguity, an explicit absolute path for the grid file can be used.
 
 
 Communications

From c5b645fc902e8a6ee1a6daeac72faa291157982c Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 4 Sep 2026 17:18:08 -0700
Subject: [PATCH 1801/1827] Document hypre_interface limitation

Corner equations are likely not handled correctly, but it probably
doesn't matter.
---
 manual/sphinx/developer_docs/code_layout.rst | 8 ++++++++
 manual/sphinx/user_docs/laplacian.rst        | 9 +++++++++
 2 files changed, 17 insertions(+)

diff --git a/manual/sphinx/developer_docs/code_layout.rst b/manual/sphinx/developer_docs/code_layout.rst
index 3c02602b44..90c4ed1822 100644
--- a/manual/sphinx/developer_docs/code_layout.rst
+++ b/manual/sphinx/developer_docs/code_layout.rst
@@ -97,6 +97,14 @@ The layout of the ``src/`` directory is as follows:
     variations, where some directions may be constant. See
     :ref:`sec-laplacian` for more details.
 
+    Known issue: ``src/invert/laplace/impls/hypre3d`` currently relies on
+    boundary elimination implemented in ``src/sys/hypre_interface.cxx``. That
+    elimination assumes each eliminated boundary row keeps only a single retained
+    neighbour. Corner rows where x- and y-boundary conditions both apply do not
+    satisfy that assumption, so ``LaplaceHypre3d`` does not preserve both corner
+    constraints exactly. Until the elimination is generalized, corner values from
+    ``LaplaceHypre3d`` should be treated as unreliable.
+
 - ``src/invert/parderiv``
 
   - Inversion of parallel derivatives, intended for use in
diff --git a/manual/sphinx/user_docs/laplacian.rst b/manual/sphinx/user_docs/laplacian.rst
index ade760d5c5..175abfe082 100644
--- a/manual/sphinx/user_docs/laplacian.rst
+++ b/manual/sphinx/user_docs/laplacian.rst
@@ -152,6 +152,15 @@ within the physics module using ``setGlobalFlags``,
     lap->setOuterBoundaryFlags(Outer_Flags_Value);
     lap->setFlags(Flags_Value);
 
+.. note::
+
+   Known issue: ``LaplaceHypre3d`` currently uses boundary-equation elimination in
+   its Hypre backend. At domain corners where an x-boundary and y-boundary
+   condition meet, the reduced system does not preserve both corner constraints
+   exactly. The returned corner values from ``LaplaceHypre3d`` should therefore be
+   treated as unreliable. This is usually acceptable because those corner values
+   are not normally used elsewhere in BOUT++ calculations.
+
 
 .. _tab-laplacesettings:
 .. table:: Laplacian inversion options

From 18c1197f54cb762a8141f20c88e58966edd8f384 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 4 Sep 2026 17:19:26 -0700
Subject: [PATCH 1802/1827] HypreMatrix: Simplify number of boundary rows

Calculation of boundary rows can just use the size of the container.
---
 include/bout/hypre_interface.hxx | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index da222b9d7b..76d60fefd6 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -931,9 +931,7 @@ public:
     if (elimBE) {
       HYPRE_Int* bi_array;
       HYPRE_Int* row_indexes;
-      // There must be an easier way to get nb
-      int nb = 0;
-      BOUT_FOR_SERIAL(i, index_converter->getRegionBndry()) { nb++; }
+      int nb = index_converter->getRegionBndry().size();
       HypreMalloc(bi_array, nb * sizeof(HYPRE_Int));
       nb = 0;
       BOUT_FOR_SERIAL(i, index_converter->getRegionBndry()) {

From f4d64c92c09884672e2735d9a8d59ee874f3f829 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 4 Sep 2026 17:21:33 -0700
Subject: [PATCH 1803/1827] HypreMatrix: Rename elimBE ->
 use_boundary_elimination

More descriptive flag. The API member function `setElimBE` is also
renamed to `setUseBoundaryElimination`
---
 include/bout/hypre_interface.hxx                  | 15 +++++++++------
 .../laplace/impls/hypre3d/hypre3d_laplace.cxx     |  2 +-
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index 76d60fefd6..3eb652c753 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -549,7 +549,8 @@ class HypreMatrix {
   std::vector<HYPRE_BigInt>* I;
   std::vector<std::vector<HYPRE_BigInt>>* J;
   std::vector<std::vector<HYPRE_Complex>>* V;
-  bool elimBE{false};
+  /// Enable reduction of boundary equations before assembling the Hypre matrix.
+  bool use_boundary_elimination{false};
   BoundaryEliminationPtr boundary_elimination;
   HypreLib hyprelib{};
 
@@ -575,7 +576,8 @@ public:
         initialised(other.initialised), yoffset(other.yoffset),
         parallel_transform(other.parallel_transform), assembled(other.assembled),
         num_rows(other.num_rows), I(other.I), J(other.J), V(other.V),
-        elimBE(other.elimBE), boundary_elimination(other.boundary_elimination) {
+        use_boundary_elimination(other.use_boundary_elimination),
+        boundary_elimination(other.boundary_elimination) {
     std::swap(hypre_matrix, other.hypre_matrix);
     std::swap(parallel_matrix, other.parallel_matrix);
   }
@@ -596,7 +598,7 @@ public:
     I = other.I;
     J = other.J;
     V = other.V;
-    elimBE = other.elimBE;
+    use_boundary_elimination = other.use_boundary_elimination;
     boundary_elimination = other.boundary_elimination;
     return *this;
   }
@@ -896,7 +898,8 @@ public:
     return Element(*this, global_row, global_column, positions, weights);
   }
 
-  void setElimBE() { elimBE = true; }
+  /// Enable elimination of boundary equations during matrix assembly.
+  void setUseBoundaryElimination() { use_boundary_elimination = true; }
 
   void assemble() {
     CALI_CXX_MARK_FUNCTION;
@@ -928,7 +931,7 @@ public:
     }
 
     // Eliminate boundary condition equations in hypre SetValues input arguments
-    if (elimBE) {
+    if (use_boundary_elimination) {
       HYPRE_Int* bi_array;
       HYPRE_Int* row_indexes;
       int nb = index_converter->getRegionBndry().size();
@@ -995,7 +998,7 @@ public:
     result.I = I; // We want the pointer to transfer so this works like a view
     result.J = J;
     result.V = V;
-    result.elimBE = elimBE;
+    result.use_boundary_elimination = use_boundary_elimination;
     result.boundary_elimination = boundary_elimination;
 
     return result;
diff --git a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
index 9138c5a647..fa555e6867 100644
--- a/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
+++ b/src/invert/laplace/impls/hypre3d/hypre3d_laplace.cxx
@@ -423,7 +423,7 @@ void LaplaceHypre3d::updateMatrix3D() {
     operator3D.ydown(ydown)(l, l.ym().zp()) += -C_d2f_dydz;
     operator3D.ydown(ydown)(l, l.ym().zm()) += C_d2f_dydz;
   }
-  operator3D.setElimBE();
+  operator3D.setUseBoundaryElimination();
   operator3D.assemble();
 
   if (print_matrix) {

From cf92081eb9d6cf8968680186208f2d01dfa9808e Mon Sep 17 00:00:00 2001
From: maggul <maggul@smu.edu>
Date: Fri, 25 Oct 2024 10:27:31 -0700
Subject: [PATCH 1804/1827] ARKODE_MRI interface

---
 include/bout/mesh.hxx              |  24 +++-
 include/bout/monitor.hxx           |  18 ++-
 include/bout/physicsmodel.hxx      |  34 +++++
 include/bout/solver.hxx            |  28 ++++
 src/bout++.cxx                     |  58 +++++---
 src/mesh/mesh.cxx                  |   4 +-
 src/physics/physicsmodel.cxx       |  29 +++-
 src/solver/impls/arkode/arkode.cxx |   5 +-
 src/solver/solver.cxx              | 212 ++++++++++++++++++++++++++++-
 tests/integrated/CMakeLists.txt    |   1 +
 10 files changed, 373 insertions(+), 40 deletions(-)

diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index dd7ccbfc0b..b001b8895f 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -47,19 +47,30 @@ class Mesh;
 #include "bout/array.hxx"
 #include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
-#include "bout/coordinates.hxx" // Coordinates class
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_data.hxx"
-#include "bout/fieldgroup.hxx"
-#include "bout/generic_factory.hxx"
-#include "bout/index_derivs_interface.hxx"
-#include "bout/mpi_wrapper.hxx"
 #include "bout/options.hxx"
-#include "bout/region.hxx"
+
+#include "bout/fieldgroup.hxx"
+
+class BoundaryRegion;
+class BoundaryRegionPar;
+
 #include "bout/sys/range.hxx" // RangeIterator
+
+#include <bout/griddata.hxx>
+
+#include "bout/coordinates.hxx" // Coordinates class
+
 #include "bout/unused.hxx"
 
+#include "bout/generic_factory.hxx"
+#include <bout/region.hxx>
+
+#include <bout/bout_enum_class.hxx>
+
+#include <list>
 #include <map>
 #include <memory>
 #include <optional>
@@ -72,7 +83,6 @@ namespace bout::boundary {
 class BoundaryRegionFCI;
 }
 class GridDataSource;
-
 class MeshFactory : public Factory<Mesh, MeshFactory, GridDataSource*, Options*> {
 public:
   static constexpr auto type_name = "Mesh";
diff --git a/include/bout/monitor.hxx b/include/bout/monitor.hxx
index 359096e74f..d1363e8009 100644
--- a/include/bout/monitor.hxx
+++ b/include/bout/monitor.hxx
@@ -33,7 +33,7 @@ class Monitor {
 public:
   /// A \p timestep_ of -1 defaults to the the frequency of the BOUT++
   /// output monitor
-  Monitor(BoutReal timestep_ = -1) : timestep(timestep_){};
+  Monitor(BoutReal timestep_ = -1) : timestep(timestep_) {};
 
   virtual ~Monitor() = default;
 
@@ -48,7 +48,7 @@ public:
   virtual int call(Solver* solver, BoutReal time, int iter, int nout) = 0;
 
   /// Callback function for when a clean shutdown is initiated
-  virtual void cleanup(){};
+  virtual void cleanup() {};
 
   virtual void outputVars([[maybe_unused]] Options& options,
                           [[maybe_unused]] const std::string& time_dimension) {}
@@ -86,10 +86,18 @@ public:
 
   /// number of RHS calls
   int ncalls = 0;
-  /// number of RHS calls for fast timescale
+  /// number of RHS calls for explicit timescale
   int ncalls_e = 0;
-  /// number of RHS calls for slow timescale
+  /// number of RHS calls for implicit timescale
   int ncalls_i = 0;
+  /// number of RHS calls for slow explicit timescale
+  int ncalls_se = 0;
+  /// number of RHS calls for slow implicit timescale
+  int ncalls_si = 0;
+  /// number of RHS calls for fast explicit timescale
+  int ncalls_fe = 0;
+  /// number of RHS calls for fast implicit timescale
+  int ncalls_fi = 0;
 
   /// wall time spent calculating RHS
   BoutReal wtime_rhs = 0;
@@ -122,7 +130,7 @@ public:
   /*!
    * Write job progress to screen
    */
-  void writeProgress(BoutReal simtime, bool output_split);
+  void writeProgress(BoutReal simtime, bool output_split, bool output_splitmri);
 };
 
 #endif // BOUT_MONITOR_H
diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index f9160f5709..282aff043a 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -172,6 +172,12 @@ public:
    *
    * Returns a flag: 0 indicates success, non-zero an error flag
    */
+  int runRHS_se(BoutReal time, bool linear = false);
+  int runRHS_si(BoutReal time, bool linear = false);
+  int runRHS_fe(BoutReal time, bool linear = false);
+  int runRHS_fi(BoutReal time, bool linear = false);
+  int runRHS_s(BoutReal time, bool linear = false);
+  int runRHS_f(BoutReal time, bool linear = false);
   int runRHS(BoutReal time, bool linear = false);
 
   /*!
@@ -179,6 +185,11 @@ public:
    */
   bool splitOperator();
 
+  /*!
+   * True if this model uses split operators
+   */
+  bool splitOperatorMRI();
+
   /*!
    * Run the convective (usually explicit) part of the model
    *
@@ -270,6 +281,24 @@ protected:
    * which is set to true when the rhs() function can be
    * linearised. This is used in e.g. linear iterative solves.
    */
+  virtual int rhs_se(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_se(BoutReal t, bool UNUSED(linear)) { return rhs_se(t); }
+
+  virtual int rhs_si(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_si(BoutReal t, bool UNUSED(linear)) { return rhs_si(t); }
+
+  virtual int rhs_fe(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_fe(BoutReal t, bool UNUSED(linear)) { return rhs_fe(t); }
+
+  virtual int rhs_fi(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_fi(BoutReal t, bool UNUSED(linear)) { return rhs_fi(t); }
+
+  virtual int rhs_s(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_s(BoutReal t, bool UNUSED(linear)) { return rhs_s(t); }
+
+  virtual int rhs_f(BoutReal UNUSED(t)) { return 1; }
+  virtual int rhs_f(BoutReal t, bool UNUSED(linear)) { return rhs_f(t); }
+
   virtual int rhs(BoutReal UNUSED(t)) { return 1; }
   virtual int rhs(BoutReal t, bool UNUSED(linear)) { return rhs(t); }
 
@@ -312,6 +341,9 @@ protected:
   /// Specify that this model is split into a convective and diffusive part
   void setSplitOperator(bool split = true) { splitop = split; }
 
+  /// Specify that this model is split into a convective and diffusive part
+  void setSplitOperatorMRI(bool split = true) { splitopmri = split; }
+
   /// Specify a preconditioner function
   void setPrecon(preconfunc pset) { userprecon = pset; }
   template <class Model>
@@ -397,6 +429,8 @@ private:
   bool restart_enabled{true};
   /// Split operator model?
   bool splitop{false};
+  /// Split operator model?
+  bool splitopmri{false};
   /// Pointer to user-supplied preconditioner function
   preconfunc userprecon{nullptr};
   /// Pointer to user-supplied Jacobian-vector multiply function
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 0d4b330ec6..120f89d217 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -94,6 +94,7 @@ constexpr auto SOLVEREULER = "euler";
 constexpr auto SOLVERRK3SSP = "rk3ssp";
 constexpr auto SOLVERPOWER = "power";
 constexpr auto SOLVERARKODE = "arkode";
+constexpr auto SOLVERARKODEMRI = "arkodemri";
 constexpr auto SOLVERIMEXBDF2 = "imexbdf2";
 constexpr auto SOLVERSNES = "snes";
 constexpr auto SOLVERRKGENERIC = "rkgeneric";
@@ -318,9 +319,21 @@ public:
   /// Same but fur implicit timestep counter - for IMEX
   int resetRHSCounter_i();
 
+  /// Same but for slow explicit timestep counter - for MRI IMEX
+  int resetRHSCounter_se();
+  /// Same but for slow implicit timestep counter - for MRI IMEX
+  int resetRHSCounter_si();
+  /// Same but for fast explicit timestep counter - for MRI IMEX
+  int resetRHSCounter_fe();
+  /// Same but for fast implicit timestep counter - for MRI IMEX
+  int resetRHSCounter_fi();
+
   /// Test if this solver supports split operators (e.g. implicit/explicit)
   bool splitOperator();
 
+  /// Test if this solver supports split operators (e.g. implicit/explicit)
+  bool splitOperatorMRI();
+
   bool canReset{false};
 
   /// Add evolving variables to output (dump) file or restart file
@@ -555,6 +568,12 @@ protected:
   BoutReal simtime{0.0};
 
   /// Run the user's RHS function
+  int run_rhs_se(BoutReal t, bool linear = false);
+  int run_rhs_si(BoutReal t, bool linear = false);
+  int run_rhs_fe(BoutReal t, bool linear = false);
+  int run_rhs_fi(BoutReal t, bool linear = false);
+  int run_rhs_s(BoutReal t, bool linear = false);
+  int run_rhs_f(BoutReal t, bool linear = false);
   int run_rhs(BoutReal t, bool linear = false);
   /// Calculate only the convective parts
   int run_convective(BoutReal t, bool linear = false);
@@ -681,6 +700,15 @@ private:
   int rhs_ncalls_e{0};
   /// Number of calls to the implicit (diffusive) RHS function
   int rhs_ncalls_i{0};
+  /// number of RHS calls for slow explicit timescale
+  int rhs_ncalls_se = 0;
+  /// number of RHS calls for slow implicit timescale
+  int rhs_ncalls_si = 0;
+  /// number of RHS calls for fast explicit timescale
+  int rhs_ncalls_fe = 0;
+  /// number of RHS calls for fast implicit timescale
+  int rhs_ncalls_fi = 0;
+
   /// Default sampling rate at which to call monitors - same as output to screen
   int default_monitor_period{1};
   /// timestep - shouldn't be changed after init is called.
diff --git a/src/bout++.cxx b/src/bout++.cxx
index 96d1efee86..478f3f1329 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -850,7 +850,11 @@ int BoutMonitor::call(Solver* solver, BoutReal t, [[maybe_unused]] int iter, int
   run_data.ncalls_e = solver->resetRHSCounter_e();
   run_data.ncalls_i = solver->resetRHSCounter_i();
 
-  const bool output_split = solver->splitOperator();
+  run_data.ncalls_se = solver->resetRHSCounter_se();
+  run_data.ncalls_si = solver->resetRHSCounter_si();
+  run_data.ncalls_fe = solver->resetRHSCounter_fe();
+  run_data.ncalls_fi = solver->resetRHSCounter_fi();
+
   run_data.wtime_rhs = Timer::resetTime("rhs");
   run_data.wtime_invert = Timer::resetTime("invert");
   // Time spent communicating (part of RHS)
@@ -872,16 +876,21 @@ int BoutMonitor::call(Solver* solver, BoutReal t, [[maybe_unused]] int iter, int
     first_time = false;
 
     // Print the column header for timing info
-    if (!output_split) {
-      output_progress.write(_("Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm "
-                              "   I/O   SOLVER\n\n"));
-    } else {
+    if (solver->splitOperator()) {
       output_progress.write(_("Sim Time  |  RHS_e evals  | RHS_I evals  | Wall Time |  "
                               "Calc    Inv   Comm    I/O   SOLVER\n\n"));
+    } else if (solver->splitOperatorMRI()) {
+      output_progress.write(
+          _("Sim Time  |  RHS_se evals  | RHS_si evals  |  RHS_fe evals  |"
+            "RHS_fi evals  | Wall Time |  "
+            "Calc    Inv   Comm    I/O   SOLVER\n\n"));
+    } else {
+      output_progress.write(_("Sim Time  |  RHS evals  | Wall Time |  Calc    Inv   Comm "
+                              "   I/O   SOLVER\n\n"));
     }
   }
 
-  run_data.writeProgress(simtime, output_split);
+  run_data.writeProgress(simtime, solver->splitOperator(), solver->splitOperatorMRI());
 
   // This bit only to screen, not log file
 
@@ -1011,6 +1020,10 @@ void RunMetrics::outputVars(Options& output_options) const {
   output_options["wtime"].assignRepeat(wtime, "t", true, "Output");
   output_options["ncalls"].assignRepeat(ncalls, "t", true, "Output");
   output_options["ncalls_e"].assignRepeat(ncalls_e, "t", true, "Output");
+  output_options["ncalls_se"].assignRepeat(ncalls_se, "t", true, "Output");
+  output_options["ncalls_si"].assignRepeat(ncalls_si, "t", true, "Output");
+  output_options["ncalls_fe"].assignRepeat(ncalls_fe, "t", true, "Output");
+  output_options["ncalls_fi"].assignRepeat(ncalls_fi, "t", true, "Output");
   output_options["ncalls_i"].assignRepeat(ncalls_i, "t", true, "Output");
   output_options["wtime_rhs"].assignRepeat(wtime_rhs, "t", true, "Output");
   output_options["wtime_invert"].assignRepeat(wtime_invert, "t", true, "Output");
@@ -1036,17 +1049,9 @@ void RunMetrics::calculateDerivedMetrics() {
   wtime_per_rhs_i = wtime / ncalls_i;
 }
 
-void RunMetrics::writeProgress(BoutReal simtime, bool output_split) {
-  if (!output_split) {
-    output_progress.write(
-        "{:.3e}      {:5d}       {:.2e}   {:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}\n",
-        simtime, ncalls, wtime, 100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime,
-        100. * wtime_invert / wtime,                    // Inversions
-        100. * wtime_comms / wtime,                     // Communications
-        100. * wtime_io / wtime,                        // I/O
-        100. * (wtime - wtime_io - wtime_rhs) / wtime); // Everything else
-
-  } else {
+void RunMetrics::writeProgress(BoutReal simtime, bool output_split,
+                               bool output_splitmri) {
+  if (output_split) {
     output_progress.write("{:.3e}      {:5d}            {:5d}       {:.2e}   {:5.1f}  "
                           "{:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}\n",
                           simtime, ncalls_e, ncalls_i, wtime,
@@ -1056,5 +1061,24 @@ void RunMetrics::writeProgress(BoutReal simtime, bool output_split) {
                           100. * wtime_io / wtime,     // I/O
                           100. * (wtime - wtime_io - wtime_rhs)
                               / wtime); // Everything else
+  } else if (output_splitmri) {
+    output_progress.write("{:.3e}      {:8d}      {:8d}      {:8d}            {:8d}      "
+                          " {:.2e}   {:5.1f}  "
+                          "{:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}\n",
+                          simtime, ncalls_se, ncalls_si, ncalls_fe, ncalls_fi, wtime,
+                          100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime,
+                          100. * wtime_invert / wtime, // Inversions
+                          100. * wtime_comms / wtime,  // Communications
+                          100. * wtime_io / wtime,     // I/O
+                          100. * (wtime - wtime_io - wtime_rhs)
+                              / wtime); // Everything else
+  } else {
+    output_progress.write(
+        "{:.3e}      {:5d}       {:.2e}   {:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}  {:5.1f}\n",
+        simtime, ncalls, wtime, 100. * (wtime_rhs - wtime_comms - wtime_invert) / wtime,
+        100. * wtime_invert / wtime,                    // Inversions
+        100. * wtime_comms / wtime,                     // Communications
+        100. * wtime_io / wtime,                        // I/O
+        100. * (wtime - wtime_io - wtime_rhs) / wtime); // Everything else
   }
 }
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index de17645e30..c55487fed6 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -12,7 +12,6 @@
 #include <bout/fieldgroup.hxx>
 #include <bout/generic_factory.hxx>
 #include <bout/globals.hxx>
-#include <bout/griddata.hxx>
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/openmpwrap.hxx>
@@ -35,6 +34,9 @@
 #include <utility>
 #include <vector>
 
+#include <bout/boutcomm.hxx>
+#include <bout/output.hxx>
+
 #include "impls/bout/boutmesh.hxx"
 
 MeshFactory::ReturnType MeshFactory::create(Options* options,
diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx
index 6cdd78e351..f2c1053ab1 100644
--- a/src/physics/physicsmodel.cxx
+++ b/src/physics/physicsmodel.cxx
@@ -2,15 +2,15 @@
  * Base class for Physics Models
  *
  * Changelog:
- * 
+ *
  * 2013-08 Ben Dudson <benjamin.dudson@york.ac.uk>
  *    * Initial version
- * 
+ *
  **************************************************************************
  * Copyright 2013 B.D.Dudson
  *
  * Contact: Ben Dudson, bd512@york.ac.uk
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -115,9 +115,30 @@ void PhysicsModel::initialise(Solver* s) {
   }
 }
 
-int PhysicsModel::runRHS(BoutReal time, bool linear) { return rhs(time, linear); }
+int PhysicsModel::runRHS_se(BoutReal time, bool linear) {
+  return PhysicsModel::rhs_se(time, linear);
+}
+int PhysicsModel::runRHS_si(BoutReal time, bool linear) {
+  return PhysicsModel::rhs_si(time, linear);
+}
+int PhysicsModel::runRHS_fe(BoutReal time, bool linear) {
+  return PhysicsModel::rhs_fe(time, linear);
+}
+int PhysicsModel::runRHS_fi(BoutReal time, bool linear) {
+  return PhysicsModel::rhs_fi(time, linear);
+}
+int PhysicsModel::runRHS_s(BoutReal time, bool linear) {
+  return PhysicsModel::rhs_s(time, linear);
+}
+int PhysicsModel::runRHS_f(BoutReal time, bool linear) {
+  return PhysicsModel::rhs_f(time, linear);
+}
+int PhysicsModel::runRHS(BoutReal time, bool linear) {
+  return PhysicsModel::rhs(time, linear);
+}
 
 bool PhysicsModel::splitOperator() { return splitop; }
+bool PhysicsModel::splitOperatorMRI() { return splitopmri; }
 
 int PhysicsModel::runConvective(BoutReal time, bool linear) {
   return convective(time, linear);
diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 2035824054..e39d65b976 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -335,9 +335,9 @@ int ArkodeSolver::init() {
     throw BoutException("Invalid adap_method\n");
   }
 
-  if (ARKStepSetAdaptivityMethod(arkode_mem, adap_method_int, 1, 1, nullptr)
+  if (ARKodeSetAdaptivityMethod(arkode_mem, adap_method_int, 1, 1, nullptr)
       != ARK_SUCCESS) {
-    throw BoutException("ARKStepSetAdaptivityMethod failed\n");
+    throw BoutException("ARKodeSetAdaptivityMethod failed\n");
   }
 #endif
 
@@ -528,6 +528,7 @@ int ArkodeSolver::run() {
 
     // Get additional diagnostics
     long int temp_long_int = 0;
+    long int temp_long_int = 0;
     ARKodeGetNumSteps(arkode_mem, &temp_long_int);
     nsteps = int(temp_long_int);
     ARKodeGetNumRhsEvals(arkode_mem, 0, &temp_long_int);
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 1f7b654427..a525cd4210 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -60,6 +60,7 @@
 // Implementations:
 #include "impls/adams_bashforth/adams_bashforth.hxx"
 #include "impls/arkode/arkode.hxx"
+#include "impls/arkode/arkode_mri.hxx"
 #include "impls/cvode/cvode.hxx"
 #include "impls/euler/euler.hxx"
 #include "impls/ida/ida.hxx"
@@ -961,7 +962,32 @@ int Solver::resetRHSCounter_e() {
   return t;
 }
 
+int Solver::resetRHSCounter_se() {
+  int t = rhs_ncalls_se;
+  rhs_ncalls_se = 0;
+  return t;
+}
+
+int Solver::resetRHSCounter_si() {
+  int t = rhs_ncalls_si;
+  rhs_ncalls_si = 0;
+  return t;
+}
+
+int Solver::resetRHSCounter_fe() {
+  int t = rhs_ncalls_fe;
+  rhs_ncalls_fe = 0;
+  return t;
+}
+
+int Solver::resetRHSCounter_fi() {
+  int t = rhs_ncalls_fi;
+  rhs_ncalls_fi = 0;
+  return t;
+}
+
 bool Solver::splitOperator() { return model->splitOperator(); }
+bool Solver::splitOperatorMRI() { return model->splitOperatorMRI(); }
 
 /////////////////////////////////////////////////////
 
@@ -1211,6 +1237,140 @@ Field3D Solver::globalIndex(int localStart) {
  * Running user-supplied functions
  **************************************************************************/
 
+int Solver::run_rhs_se(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_call = false;
+  }
+
+  pre_rhs(t);
+  status = model->runRHS_se(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_se++;
+  return status;
+}
+
+int Solver::run_rhs_si(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_call = false;
+  }
+
+  pre_rhs(t);
+  status = model->runRHS_si(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_si++;
+  return status;
+}
+
+int Solver::run_rhs_fe(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_call = false;
+  }
+
+  pre_rhs(t);
+  status = model->runRHS_fe(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_fe++;
+  return status;
+}
+
+int Solver::run_rhs_fi(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_call = false;
+  }
+
+  pre_rhs(t);
+  status = model->runRHS_fi(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_fi++;
+  return status;
+}
+
+int Solver::run_rhs_s(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_call = false;
+  }
+
+  pre_rhs(t);
+  status = model->runRHS_s(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_se++;
+  rhs_ncalls_si++;
+  return status;
+}
+
+int Solver::run_rhs_f(BoutReal t, bool linear) {
+  int status;
+
+  Timer timer("rhs");
+
+  if (first_rhs_call) {
+    // Ensure that nonlinear terms are calculated on first call
+    linear = false;
+    first_rhs_call = false;
+  }
+
+  pre_rhs(t);
+  status = model->runRHS_f(t, linear);
+  post_rhs(t);
+
+  // If using Method of Manufactured Solutions
+  add_mms_sources(t);
+
+  rhs_ncalls_fe++;
+  rhs_ncalls_fi++;
+  return status;
+}
+
 int Solver::run_rhs(BoutReal t, bool linear) {
   int status;
 
@@ -1222,7 +1382,48 @@ int Solver::run_rhs(BoutReal t, bool linear) {
     first_rhs_call = false;
   }
 
-  if (model->splitOperator()) {
+  // TO DO: Replace true with an appropriate boolean and check for efficiency
+  if (model->splitOperatorMRI()) {
+    // Run all four parts
+
+    int nv = getLocalN();
+    // Create temporary arrays for system state
+    Array<BoutReal> tmp(nv);
+    Array<BoutReal> tmp2(nv);
+    Array<BoutReal> tmp3(nv);
+
+    save_vars(tmp.begin()); // Copy variables into tmp
+
+    pre_rhs(t);
+    status = model->runRHS_fe(t, linear);
+    post_rhs(t);               // Check variables, apply boundary conditions
+    save_derivs(tmp2.begin()); // Save time derivatives
+
+    pre_rhs(t);
+    status = model->runRHS_fi(t, linear);
+    post_rhs(t);
+    save_derivs(tmp3.begin()); // Save time derivatives
+    for (BoutReal *t3 = tmp3.begin(), *t2 = tmp2.begin(); t3 != tmp3.end(); ++t3, ++t2) {
+      *t3 += *t2;
+    }
+
+    pre_rhs(t);
+    status = model->runRHS_se(t, linear);
+    post_rhs(t);
+    save_derivs(tmp2.begin()); // Save time derivatives
+    for (BoutReal *t3 = tmp3.begin(), *t2 = tmp2.begin(); t3 != tmp3.end(); ++t3, ++t2) {
+      *t3 += *t2;
+    }
+
+    pre_rhs(t);
+    status = model->runRHS_si(t, linear);
+    post_rhs(t);
+    save_derivs(tmp2.begin()); // Save time derivatives
+    for (BoutReal *t3 = tmp3.begin(), *t2 = tmp2.begin(); t3 != tmp3.end(); ++t3, ++t2) {
+      *t3 += *t2;
+    }
+    load_derivs(tmp3.begin()); // Put back time-derivatives
+  } else if (model->splitOperator()) {
     // Run both parts
 
     int nv = getLocalN();
@@ -1245,18 +1446,21 @@ int Solver::run_rhs(BoutReal t, bool linear) {
       *t += *t2;
     }
     load_derivs(tmp.begin()); // Put back time-derivatives
+    rhs_ncalls++;
+    rhs_ncalls_e++;
+    rhs_ncalls_i++;
   } else {
     pre_rhs(t);
     status = model->runRHS(t, linear);
     post_rhs(t);
+    rhs_ncalls++;
+    rhs_ncalls_e++;
+    rhs_ncalls_i++;
   }
 
   // If using Method of Manufactured Solutions
   add_mms_sources(t);
 
-  rhs_ncalls++;
-  rhs_ncalls_e++;
-  rhs_ncalls_i++;
   return status;
 }
 
diff --git a/tests/integrated/CMakeLists.txt b/tests/integrated/CMakeLists.txt
index d87bd329f0..7f62fd7410 100644
--- a/tests/integrated/CMakeLists.txt
+++ b/tests/integrated/CMakeLists.txt
@@ -22,6 +22,7 @@ add_subdirectory(test-interpolate)
 add_subdirectory(test-interpolate-z)
 add_subdirectory(test-invertable-operator)
 add_subdirectory(test-invpar)
+add_subdirectory(test-kpr_mri)
 add_subdirectory(test-laplace)
 add_subdirectory(test-laplace-petsc3d)
 add_subdirectory(test-laplace-hypre3d)

From 8110eeeb5dfef4e12fc3a26b3c815677616552af Mon Sep 17 00:00:00 2001
From: maggul <maggul@smu.edu>
Date: Fri, 25 Oct 2024 11:17:48 -0700
Subject: [PATCH 1805/1827] add missing files

---
 src/solver/impls/arkode/arkode_mri.cxx        | 1090 +++++++++++++++++
 src/solver/impls/arkode/arkode_mri.hxx        |  176 +++
 tests/integrated/test-kpr_mri/CMakeLists.txt  |    2 +
 tests/integrated/test-kpr_mri/README.md       |   37 +
 tests/integrated/test-kpr_mri/makefile        |    5 +
 tests/integrated/test-kpr_mri/runtest         |   23 +
 .../integrated/test-kpr_mri/test_kpr_mri.cxx  |  183 +++
 7 files changed, 1516 insertions(+)
 create mode 100644 src/solver/impls/arkode/arkode_mri.cxx
 create mode 100644 src/solver/impls/arkode/arkode_mri.hxx
 create mode 100644 tests/integrated/test-kpr_mri/CMakeLists.txt
 create mode 100644 tests/integrated/test-kpr_mri/README.md
 create mode 100644 tests/integrated/test-kpr_mri/makefile
 create mode 100755 tests/integrated/test-kpr_mri/runtest
 create mode 100644 tests/integrated/test-kpr_mri/test_kpr_mri.cxx

diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
new file mode 100644
index 0000000000..1fb9a79a24
--- /dev/null
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -0,0 +1,1090 @@
+/**************************************************************************
+ * Experimental interface to SUNDIALS ARKode MRI solver
+ *
+ * NOTE: ARKode is still in beta testing so use with cautious optimism
+ *
+ **************************************************************************
+ * Copyright 2010-2024 BOUT++ contributors
+ *
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#include "bout/build_config.hxx"
+
+#include "arkode_mri.hxx"
+
+#if BOUT_HAS_ARKODE
+
+#include "bout/bout_enum_class.hxx"
+#include "bout/boutcomm.hxx"
+#include "bout/boutexception.hxx"
+#include "bout/field3d.hxx"
+#include "bout/mesh.hxx"
+#include "bout/msg_stack.hxx"
+#include "bout/options.hxx"
+#include "bout/output.hxx"
+#include "bout/unused.hxx"
+#include "bout/utils.hxx"
+
+#include <arkode/arkode_arkstep.h>
+#include <arkode/arkode_bbdpre.h>
+#include <sundials/sundials_math.h>
+#include <sundials/sundials_types.h>
+
+#include <algorithm>
+#include <numeric>
+
+class Field2D;
+
+// NOLINTBEGIN(readability-identifier-length)
+namespace {
+int arkode_rhs_s_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_rhs_s_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_rhs_f_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_rhs_f_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_s_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+int arkode_f_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data);
+
+int arkode_s_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du,
+                   void* user_data);
+int arkode_f_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du,
+                   void* user_data);                   
+int arkode_s_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec,
+               BoutReal gamma, BoutReal delta, int lr, void* user_data);
+int arkode_f_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec,
+               BoutReal gamma, BoutReal delta, int lr, void* user_data);
+
+} // namespace
+// NOLINTEND(readability-identifier-length)
+
+ArkodeMRISolver::ArkodeMRISolver(Options* opts)
+    : Solver(opts), diagnose((*options)["diagnose"]
+                                 .doc("Print some additional diagnostics")
+                                 .withDefault(false)),
+      mxsteps((*options)["mxstep"]
+                  .doc("Maximum number of steps to take between outputs")
+                  .withDefault(500)),
+      treatment((*options)["treatment"]
+                    .doc("Use default capability (imex) or provide a specific treatment: "
+                         "implicit or explicit")
+                    .withDefault(MRI_Treatment::ImEx)),
+      inner_treatment((*options)["inner_treatment"]
+                    .doc("Use default capability (imex) or provide a specific inner_treatment: "
+                         "implicit or explicit")
+                    .withDefault(MRI_Treatment::ImEx)),
+      set_linear(
+          (*options)["set_linear"]
+              .doc("Use linear implicit solver (only evaluates jacobian inversion once)")
+              .withDefault(false)),
+      inner_set_linear(
+          (*options)["inner_set_linear"]
+              .doc("Use linear implicit solver (only evaluates jacobian inversion once)")
+              .withDefault(false)),
+      fixed_step((*options)["fixed_step"]
+                     .doc("Solve explicit portion in fixed timestep mode. NOTE: This is "
+                          "not recommended except for code comparison")
+                     .withDefault(false)),
+      order((*options)["order"].doc("Order of internal step").withDefault(4)),
+      adap_method(
+          (*options)["adap_method"]
+              .doc("Set timestep adaptivity function: pid, pi, i, explicit_gustafsson,  "
+                   "implicit_gustafsson, imex_gustafsson.")
+              .withDefault(MRI_AdapMethod::PID)),
+      abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
+      reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-5)),
+      use_vector_abstol((*options)["use_vector_abstol"]
+                            .doc("Use separate absolute tolerance for each field")
+                            .withDefault(false)),
+      use_precon((*options)["use_precon"]
+                     .doc("Use user-supplied preconditioner function")
+                     .withDefault(false)),
+      inner_use_precon((*options)["inner_use_precon"]
+                     .doc("Use user-supplied preconditioner function")
+                     .withDefault(false)),
+      maxl(
+          (*options)["maxl"].doc("Number of Krylov basis vectors to use").withDefault(0)),
+      inner_maxl(
+          (*options)["inner_maxl"].doc("Number of Krylov basis vectors to use").withDefault(0)),
+      rightprec((*options)["rightprec"]
+                    .doc("Use right preconditioning instead of left preconditioning")
+                    .withDefault(false)),
+      suncontext(createSUNContext(BoutComm::get())) {
+  has_constraints = false; // This solver doesn't have constraints
+
+  // Add diagnostics to output
+  add_int_diagnostic(nsteps, "arkode_nsteps", "Cumulative number of internal steps");
+  add_int_diagnostic(inner_nsteps, "arkode_inner_nsteps", "Cumulative number of inner internal steps");
+  add_int_diagnostic(nfe_evals, "arkode_nfe_evals",
+                     "No. of calls to fe (explicit portion of the right-hand-side "
+                     "function) function");
+  add_int_diagnostic(inner_nfe_evals, "arkode_inner_nfe_evals",
+                     "No. of calls to fe (explicit portion of the inner right-hand-side "
+                     "function) function");
+  add_int_diagnostic(nfi_evals, "arkode_nfi_evals",
+                     "No. of calls to fi (implicit portion of the right-hand-side "
+                     "function) function");
+  add_int_diagnostic(inner_nfi_evals, "arkode_inner_nfi_evals",
+                     "No. of calls to fi (implicit portion of inner the right-hand-side "
+                     "function) function");
+  add_int_diagnostic(nniters, "arkode_nniters", "No. of nonlinear solver iterations");
+  add_int_diagnostic(inner_nniters, "arkode_inner_nniters", "No. of inner nonlinear solver iterations");
+  add_int_diagnostic(npevals, "arkode_npevals", "No. of preconditioner evaluations");
+  add_int_diagnostic(inner_npevals, "arkode_inner_npevals", "No. of inner preconditioner evaluations");
+  add_int_diagnostic(nliters, "arkode_nliters", "No. of linear iterations");
+  add_int_diagnostic(inner_nliters, "arkode_inner_nliters", "No. of inner linear iterations");
+}
+
+ArkodeMRISolver::~ArkodeMRISolver() {
+  N_VDestroy(uvec);
+  ARKodeFree(&arkode_mem);
+  ARKodeFree(&inner_arkode_mem);
+  SUNLinSolFree(sun_solver);
+  SUNLinSolFree(inner_sun_solver);
+  SUNNonlinSolFree(nonlinear_solver);
+  SUNNonlinSolFree(inner_nonlinear_solver);
+  MRIStepInnerStepper_Free(&inner_stepper);
+
+  SUNAdaptController_Destroy(controller);
+  SUNAdaptController_Destroy(inner_controller);
+}
+
+/**************************************************************************
+ * Initialise
+ **************************************************************************/
+
+int ArkodeMRISolver::init() {
+  TRACE("Initialising ARKODE MRI solver");
+
+  Solver::init();
+
+  output.write("Initialising SUNDIALS' ARKODE MRI solver\n");
+
+  // Calculate number of variables (in generic_solver)
+  const int local_N = getLocalN();
+
+  // Get total problem size
+  int neq;
+  if (bout::globals::mpi->MPI_Allreduce(&local_N, &neq, 1, MPI_INT, MPI_SUM,
+                                        BoutComm::get())) {
+    throw BoutException("Allreduce localN -> GlobalN failed!\n");
+  }
+
+  output.write("\t3d fields = {:d}, 2d fields = {:d} neq={:d}, local_N={:d}\n", n3Dvars(),
+               n2Dvars(), neq, local_N);
+
+  // Allocate memory
+  uvec = callWithSUNContext(N_VNew_Parallel, suncontext, BoutComm::get(), local_N, neq);
+  if (uvec == nullptr) {
+    throw BoutException("SUNDIALS memory allocation failed\n");
+  }
+
+  // Put the variables into uvec
+  save_vars(N_VGetArrayPointer(uvec));
+
+  switch (inner_treatment) {
+  case MRI_Treatment::ImEx:
+    inner_arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_f_explicit,
+                                    arkode_rhs_f_implicit, simtime, uvec);
+    output_info.write("\tUsing ARKode ImEx inner solver \n");
+    break;
+  case MRI_Treatment::Explicit:
+    inner_arkode_mem =
+        callWithSUNContext(ARKStepCreate, suncontext, arkode_f_rhs, nullptr, simtime, uvec);
+    output_info.write("\tUsing ARKode Explicit inner solver \n");
+    break;
+  case MRI_Treatment::Implicit:
+    inner_arkode_mem =
+        callWithSUNContext(ARKStepCreate, suncontext, nullptr, arkode_f_rhs, simtime, uvec);
+    output_info.write("\tUsing ARKode Implicit inner solver \n");
+    break;
+  default:
+    throw BoutException("Invalid inner_treatment: {}\n", toString(inner_treatment));
+  }
+  if (inner_arkode_mem == nullptr) {
+    throw BoutException("ARKStepCreate failed\n");
+  }
+
+  // For callbacks, need pointer to solver object
+  if (ARKodeSetUserData(inner_arkode_mem, this) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetUserData failed\n");
+  }
+
+  if(inner_treatment != MRI_Treatment::Explicit)
+    if (ARKodeSetLinear(inner_arkode_mem, inner_set_linear) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSetLinear failed\n");
+    }
+
+  if (fixed_step) {
+    // If not given, default to adaptive timestepping
+    const BoutReal inner_fixed_timestep = (*options)["inner_timestep"];
+    if (ARKodeSetFixedStep(inner_arkode_mem, inner_fixed_timestep) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSetFixedStep failed\n");
+    }
+  }
+
+  if (ARKodeSetOrder(inner_arkode_mem, order) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetOrder failed\n");
+  }
+
+  if (ARKStepCreateMRIStepInnerStepper(inner_arkode_mem, &inner_stepper) != ARK_SUCCESS) {
+    throw BoutException("ARKStepCreateMRIStepInnerStepper failed\n");
+  }
+
+  // Initialize the slow integrator. Specify the explicit slow right-hand side
+  // function in y'=fe(t,y)+fi(t,y)+ff(t,y), the inital time T0, the
+  // initial dependent variable vector y, and the fast integrator.
+
+  switch (treatment) {
+  case MRI_Treatment::ImEx:
+    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, arkode_rhs_s_explicit, arkode_rhs_s_implicit, 
+                                    simtime, uvec, inner_stepper);
+    output_info.write("\tUsing ARKode ImEx solver \n");
+    break;
+  case MRI_Treatment::Explicit:
+    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, arkode_s_rhs, nullptr, 
+                                    simtime, uvec, inner_stepper);
+    output_info.write("\tUsing ARKode Explicit solver \n");
+    break;
+  case MRI_Treatment::Implicit:
+    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, nullptr, arkode_s_rhs,
+                                    simtime, uvec, inner_stepper);
+    output_info.write("\tUsing ARKode Implicit solver \n");
+    break;
+  default:
+    throw BoutException("Invalid treatment: {}\n", toString(treatment));
+  }
+  if (arkode_mem == nullptr) {
+    throw BoutException("MRIStepCreate failed\n");
+  }
+
+  // For callbacks, need pointer to solver object
+  if (ARKodeSetUserData(arkode_mem, this) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetUserData failed\n");
+  }
+
+  if(treatment != MRI_Treatment::Explicit)
+    if (ARKodeSetLinear(arkode_mem, set_linear) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSetLinear failed\n");
+    }
+
+  if (fixed_step) {
+    // If not given, default to adaptive timestepping
+    const BoutReal fixed_timestep = (*options)["timestep"];
+    if (ARKodeSetFixedStep(arkode_mem, fixed_timestep) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSetFixedStep failed\n");
+    }
+  }
+
+  if (ARKodeSetOrder(arkode_mem, order) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetOrder failed\n");
+  }
+
+  switch (adap_method) {
+  case MRI_AdapMethod::PID:
+    controller = SUNAdaptController_PID(suncontext);
+    inner_controller = SUNAdaptController_PID(suncontext);
+    break;
+  case MRI_AdapMethod::PI:
+    controller = SUNAdaptController_PI(suncontext);
+    inner_controller = SUNAdaptController_PI(suncontext);
+    break;
+  case MRI_AdapMethod::I:
+    controller = SUNAdaptController_I(suncontext);
+    inner_controller = SUNAdaptController_I(suncontext);
+    break;
+  case MRI_AdapMethod::Explicit_Gustafsson:
+    controller = SUNAdaptController_ExpGus(suncontext);
+    inner_controller = SUNAdaptController_ExpGus(suncontext);
+    break;
+  case MRI_AdapMethod::Implicit_Gustafsson:
+    controller = SUNAdaptController_ImpGus(suncontext);
+    inner_controller = SUNAdaptController_ImpGus(suncontext);
+    break;
+  case MRI_AdapMethod::ImEx_Gustafsson:
+    controller = SUNAdaptController_ImExGus(suncontext);
+    inner_controller = SUNAdaptController_ImExGus(suncontext);
+    break;
+  default:
+    throw BoutException("Invalid adap_method\n");
+  }
+
+  // if (ARKodeSetAdaptController(arkode_mem, controller) != ARK_SUCCESS) {
+  //   throw BoutException("ARKodeSetAdaptController failed\n");
+  // }
+
+  // if (ARKodeSetAdaptivityAdjustment(arkode_mem, 0) != ARK_SUCCESS) {
+  //   throw BoutException("ARKodeSetAdaptivityAdjustment failed\n");
+  // }
+
+  if (ARKodeSetFixedStep(arkode_mem, 0.001) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetAdaptController failed\n");
+  }
+
+  if (ARKodeSetAdaptController(inner_arkode_mem, controller) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetAdaptController failed\n");
+  }
+
+  if (ARKodeSetAdaptivityAdjustment(inner_arkode_mem, 0) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetAdaptivityAdjustment failed\n");
+  }
+
+  if (use_vector_abstol) {
+    std::vector<BoutReal> f2dtols;
+    f2dtols.reserve(f2d.size());
+    std::transform(begin(f2d), end(f2d), std::back_inserter(f2dtols),
+                   [abstol = abstol](const VarStr<Field2D>& f2) {
+                     auto& f2_options = Options::root()[f2.name];
+                     const auto wrong_name = f2_options.isSet("abstol");
+                     if (wrong_name) {
+                       output_warn << "WARNING: Option 'abstol' for field " << f2.name
+                                   << " is deprecated. Please use 'atol' instead\n";
+                     }
+                     const std::string atol_name = wrong_name ? "abstol" : "atol";
+                     return f2_options[atol_name].withDefault(abstol);
+                   });
+
+    std::vector<BoutReal> f3dtols;
+    f3dtols.reserve(f3d.size());
+    std::transform(begin(f3d), end(f3d), std::back_inserter(f3dtols),
+                   [abstol = abstol](const VarStr<Field3D>& f3) {
+                     return Options::root()[f3.name]["atol"].withDefault(abstol);
+                   });
+
+    N_Vector abstolvec = N_VClone(uvec);
+    if (abstolvec == nullptr) {
+      throw BoutException("SUNDIALS memory allocation (abstol vector) failed\n");
+    }
+
+    set_abstol_values(N_VGetArrayPointer(abstolvec), f2dtols, f3dtols);
+
+    if (ARKodeSVtolerances(arkode_mem, reltol, abstolvec) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSVtolerances failed\n");
+    }
+    if (ARKodeSVtolerances(inner_arkode_mem, reltol, abstolvec) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSVtolerances failed\n");
+    }
+
+    N_VDestroy(abstolvec);
+  } else {
+    if (ARKodeSStolerances(arkode_mem, reltol, abstol) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSStolerances failed\n");
+    }
+    if (ARKodeSStolerances(inner_arkode_mem, reltol, abstol) != ARK_SUCCESS) {
+      throw BoutException("ARKodeSStolerances failed\n");
+    }
+  }
+
+  if (ARKodeSetMaxNumSteps(arkode_mem, mxsteps) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetMaxNumSteps failed\n");
+  }
+  if (ARKodeSetMaxNumSteps(inner_arkode_mem, mxsteps) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetMaxNumSteps failed\n");
+  }
+
+  if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+    {
+      output.write("\tUsing Newton iteration for inner solver\n");
+
+      const auto prectype =
+          inner_use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE;
+      inner_sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, inner_maxl);
+      if (inner_sun_solver == nullptr) {
+        throw BoutException("Creating SUNDIALS inner linear solver failed\n");
+      }
+      if (ARKodeSetLinearSolver(inner_arkode_mem, inner_sun_solver, nullptr) != ARKLS_SUCCESS) {
+        throw BoutException("ARKodeSetLinearSolver failed for inner solver\n");
+      }
+
+      /// Set Preconditioner
+      if (inner_use_precon) {
+        if (hasPreconditioner()) {  // change to inner_hasPreconditioner when it is available
+          output.write("\tUsing user-supplied preconditioner for inner solver\n");
+
+          if (ARKodeSetPreconditioner(inner_arkode_mem, nullptr, arkode_f_pre)
+              != ARKLS_SUCCESS) {
+            throw BoutException("ARKodeSetPreconditioner failed for inner solver\n");
+          }
+        } else {
+          output.write("\tUsing BBD preconditioner for inner solver\n");
+
+          /// Get options
+          // Compute band_width_default from actually added fields, to allow for multiple
+          // Mesh objects
+          //
+          // Previous implementation was equivalent to:
+          //   int MXSUB = mesh->xend - mesh->xstart + 1;
+          //   int band_width_default = n3Dvars()*(MXSUB+2);
+          const int band_width_default = std::accumulate(
+              begin(f3d), end(f3d), 0, [](int acc, const VarStr<Field3D>& fvar) {
+                Mesh* localmesh = fvar.var->getMesh();
+                return acc + localmesh->xend - localmesh->xstart + 3;
+              });
+
+          const auto mudq = (*options)["mudq"]
+                                .doc("Upper half-bandwidth to be used in the difference "
+                                     "quotient Jacobian approximation")
+                                .withDefault(band_width_default);
+          const auto mldq = (*options)["mldq"]
+                                .doc("Lower half-bandwidth to be used in the difference "
+                                     "quotient Jacobian approximation")
+                                .withDefault(band_width_default);
+          const auto mukeep = (*options)["mukeep"]
+                                  .doc("Upper half-bandwidth of the retained banded "
+                                       "approximate Jacobian block")
+                                  .withDefault(n3Dvars() + n2Dvars());
+          const auto mlkeep = (*options)["mlkeep"]
+                                  .doc("Lower half-bandwidth of the retained banded "
+                                       "approximate Jacobian block")
+                                  .withDefault(n3Dvars() + n2Dvars());
+
+          if (ARKBBDPrecInit(inner_arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0,
+                             arkode_f_bbd_rhs, nullptr)
+              != ARKLS_SUCCESS) {
+            throw BoutException("ARKBBDPrecInit failed for inner solver\n");
+          }
+        }
+      } else {
+        // Not using preconditioning
+        output.write("\tNo inner preconditioning\n");
+      }
+    }
+
+    /// Set Jacobian-vector multiplication function
+    output.write("\tUsing difference quotient approximation for Jacobian in the inner solver\n");
+  }
+
+
+  if (treatment == MRI_Treatment::ImEx or treatment == MRI_Treatment::Implicit) {
+    {
+      output.write("\tUsing Newton iteration\n");
+
+      const auto prectype =
+          use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE;
+      sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, maxl);
+      if (sun_solver == nullptr) {
+        throw BoutException("Creating SUNDIALS linear solver failed\n");
+      }
+      if (ARKodeSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARKLS_SUCCESS) {
+        throw BoutException("ARKodeSetLinearSolver failed\n");
+      }
+
+      /// Set Preconditioner
+      if (use_precon) {
+        if (hasPreconditioner()) {
+          output.write("\tUsing user-supplied preconditioner\n");
+
+          if (ARKodeSetPreconditioner(arkode_mem, nullptr, arkode_s_pre)
+              != ARKLS_SUCCESS) {
+            throw BoutException("ARKodeSetPreconditioner failed\n");
+          }
+        } else {
+          output.write("\tUsing BBD preconditioner\n");
+
+          /// Get options
+          // Compute band_width_default from actually added fields, to allow for multiple
+          // Mesh objects
+          //
+          // Previous implementation was equivalent to:
+          //   int MXSUB = mesh->xend - mesh->xstart + 1;
+          //   int band_width_default = n3Dvars()*(MXSUB+2);
+          const int band_width_default = std::accumulate(
+              begin(f3d), end(f3d), 0, [](int acc, const VarStr<Field3D>& fvar) {
+                Mesh* localmesh = fvar.var->getMesh();
+                return acc + localmesh->xend - localmesh->xstart + 3;
+              });
+
+          const auto mudq = (*options)["mudq"]
+                                .doc("Upper half-bandwidth to be used in the difference "
+                                     "quotient Jacobian approximation")
+                                .withDefault(band_width_default);
+          const auto mldq = (*options)["mldq"]
+                                .doc("Lower half-bandwidth to be used in the difference "
+                                     "quotient Jacobian approximation")
+                                .withDefault(band_width_default);
+          const auto mukeep = (*options)["mukeep"]
+                                  .doc("Upper half-bandwidth of the retained banded "
+                                       "approximate Jacobian block")
+                                  .withDefault(n3Dvars() + n2Dvars());
+          const auto mlkeep = (*options)["mlkeep"]
+                                  .doc("Lower half-bandwidth of the retained banded "
+                                       "approximate Jacobian block")
+                                  .withDefault(n3Dvars() + n2Dvars());
+
+          if (ARKBBDPrecInit(arkode_mem, local_N, mudq, mldq, mukeep, mlkeep, 0,
+                             arkode_s_bbd_rhs, nullptr)
+              != ARKLS_SUCCESS) {
+            throw BoutException("ARKBBDPrecInit failed\n");
+          }
+        }
+      } else {
+        // Not using preconditioning
+        output.write("\tNo preconditioning\n");
+      }
+    }
+
+    /// Set Jacobian-vector multiplication function
+    output.write("\tUsing difference quotient approximation for Jacobian\n");
+  }
+
+  return 0;
+}
+
+/**************************************************************************
+ * Run - Advance time
+ **************************************************************************/
+
+int ArkodeMRISolver::run() {
+  TRACE("ArkodeMRISolver::run()");
+
+  if (!initialised) {
+    throw BoutException("ArkodeMRISolver not initialised\n");
+  }
+
+  for (int i = 0; i < getNumberOutputSteps(); i++) {
+
+    /// Run the solver for one output timestep
+    simtime = run(simtime + getOutputTimestep());
+
+    /// Check if the run succeeded
+    if (simtime < 0.0) {
+      // Step failed
+      output.write("Timestep failed. Aborting\n");
+
+      throw BoutException("ARKode timestep failed\n");
+    }
+
+    // Get additional diagnostics
+    long int temp_long_int, temp_long_int2;
+    ARKodeGetNumSteps(arkode_mem, &temp_long_int);
+    nsteps = int(temp_long_int);
+    MRIStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2); //Change after the release
+    nfe_evals = int(temp_long_int);
+    nfi_evals = int(temp_long_int2);
+    if (treatment == MRI_Treatment::ImEx or treatment == MRI_Treatment::Implicit) {
+      ARKodeGetNumNonlinSolvIters(arkode_mem, &temp_long_int);
+      nniters = int(temp_long_int);
+      ARKodeGetNumPrecEvals(arkode_mem, &temp_long_int);
+      npevals = int(temp_long_int);
+      ARKodeGetNumLinIters(arkode_mem, &temp_long_int);
+      nliters = int(temp_long_int);
+    }
+
+    ARKodeGetNumSteps(inner_arkode_mem, &temp_long_int);
+    inner_nsteps = int(temp_long_int);
+    ARKStepGetNumRhsEvals(inner_arkode_mem, &temp_long_int, &temp_long_int2); //Change after the release
+    inner_nfe_evals = int(temp_long_int);
+    inner_nfi_evals = int(temp_long_int2);
+    if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+      ARKodeGetNumNonlinSolvIters(inner_arkode_mem, &temp_long_int);
+      inner_nniters = int(temp_long_int);
+      ARKodeGetNumPrecEvals(inner_arkode_mem, &temp_long_int);
+      inner_npevals = int(temp_long_int);
+      ARKodeGetNumLinIters(inner_arkode_mem, &temp_long_int);
+      inner_nliters = int(temp_long_int);
+    }
+
+    if (diagnose) {
+      output.write("\nARKODE: nsteps {:d}, nfe_evals {:d}, nfi_evals {:d}, nniters {:d}, "
+                   "npevals {:d}, nliters {:d}\n",
+                   nsteps, nfe_evals, nfi_evals, nniters, npevals, nliters);
+      if (treatment == MRI_Treatment::ImEx or treatment == MRI_Treatment::Implicit) {
+        output.write("    -> Newton iterations per step: {:e}\n",
+                     static_cast<BoutReal>(nniters) / static_cast<BoutReal>(nsteps));
+        output.write("    -> Linear iterations per Newton iteration: {:e}\n",
+                     static_cast<BoutReal>(nliters) / static_cast<BoutReal>(nniters));
+        output.write("    -> Preconditioner evaluations per Newton: {:e}\n",
+                     static_cast<BoutReal>(npevals) / static_cast<BoutReal>(nniters));
+      }
+
+      output.write("\nARKODE Inner: inner_nsteps {:d}, inner_nfe_evals {:d}, inner_nfi_evals {:d}, inner_nniters {:d}, "
+                   "inner_npevals {:d}, inner_nliters {:d}\n",
+                   inner_nsteps, inner_nfe_evals, inner_nfi_evals, inner_nniters, inner_npevals, inner_nliters);
+      if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+        output.write("    -> Inner Newton iterations per step: {:e}\n",
+                     static_cast<BoutReal>(inner_nniters) / static_cast<BoutReal>(inner_nsteps));
+        output.write("    -> Inner Linear iterations per Newton iteration: {:e}\n",
+                     static_cast<BoutReal>(inner_nliters) / static_cast<BoutReal>(inner_nniters));
+        output.write("    -> Inner Preconditioner evaluations per Newton: {:e}\n",
+                     static_cast<BoutReal>(inner_npevals) / static_cast<BoutReal>(inner_nniters));
+      }
+    }
+
+    if (call_monitors(simtime, i, getNumberOutputSteps())) {
+      // User signalled to quit
+      break;
+    }
+  }
+
+  return 0;
+}
+
+BoutReal ArkodeMRISolver::run(BoutReal tout) {
+  TRACE("Running solver: solver::run({:e})", tout);
+
+  bout::globals::mpi->MPI_Barrier(BoutComm::get());
+
+  pre_Wtime_s = 0.0;
+  pre_ncalls_s = 0;
+
+  int flag;
+  if (!monitor_timestep) {
+    // Run in normal mode
+    flag = ARKodeEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL);
+  } else {
+    // Run in single step mode, to call timestep monitors
+    BoutReal internal_time;
+    ARKodeGetCurrentTime(arkode_mem, &internal_time);
+    while (internal_time < tout) {
+      // Run another step
+      const BoutReal last_time = internal_time;
+      flag = ARKodeEvolve(arkode_mem, tout, uvec, &internal_time, ARK_ONE_STEP);
+
+      if (flag != ARK_SUCCESS) {
+        output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n",
+                           internal_time, flag);
+        return -1.0;
+      }
+
+      // Call timestep monitor
+      call_timestep_monitors(internal_time, internal_time - last_time);
+    }
+    // Get output at the desired time
+    flag = ARKodeGetDky(arkode_mem, tout, 0, uvec);
+    simtime = tout;
+  }
+
+  // Copy variables
+  load_vars(N_VGetArrayPointer(uvec));
+  // Call rhs function to get extra variables at this time
+  run_rhs(simtime);
+  // run_diffusive(simtime);
+  if (flag != ARK_SUCCESS) {
+    output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n", simtime,
+                       flag);
+    return -1.0;
+  }
+
+  return simtime;
+}
+
+/**************************************************************************
+ * Explicit RHS function du = F^s_E(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_se(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_e({:e})", t);
+
+  // Load state from udata
+  load_vars(udata);
+
+  // Get the current timestep
+  // Note: ARKodeGetCurrentStep updated too late in older versions
+  ARKodeGetLastStep(arkode_mem, &hcur);
+
+  // Call RHS function
+  run_rhs_se(t);
+
+  // Save derivatives to dudata
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ *   Implicit RHS function du = F^s_I(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_si(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_si({:e})", t);
+
+  load_vars(udata);
+  ARKodeGetLastStep(arkode_mem, &hcur);
+  // Call Implicit RHS function
+  run_rhs_si(t);
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ * Explicit RHS function du = F^f_E(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_fe(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_e({:e})", t);
+
+  // Load state from udata
+  load_vars(udata);
+
+  // Get the current timestep
+  // Note: ARKodeGetCurrentStep updated too late in older versions
+  ARKodeGetLastStep(arkode_mem, &hcur);
+
+  // Call RHS function
+  run_rhs_fe(t);
+
+  // Save derivatives to dudata
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ *   Implicit RHS function du = F^f_I(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_fi(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_si({:e})", t);
+
+  load_vars(udata);
+  ARKodeGetLastStep(arkode_mem, &hcur);
+  // Call Implicit RHS function
+  run_rhs_fi(t);
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ * Slow RHS function du = F^s(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_s(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_e({:e})", t);
+
+  // Load state from udata
+  load_vars(udata);
+
+  // Get the current timestep
+  // Note: ARKodeGetCurrentStep updated too late in older versions
+  ARKodeGetLastStep(arkode_mem, &hcur);
+
+  // Call RHS function
+  // run_rhs_s(t);
+  run_rhs_s(t);
+
+  // Save derivatives to dudata
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ * Fast RHS function du = F^f(t, u)
+ **************************************************************************/
+
+void ArkodeMRISolver::rhs_f(BoutReal t, BoutReal* udata, BoutReal* dudata) {
+  TRACE("Running RHS: ArkodeMRISolver::rhs_e({:e})", t);
+
+  // Load state from udata
+  load_vars(udata);
+
+  // Get the current timestep
+  // Note: ARKodeGetCurrentStep updated too late in older versions
+  ARKodeGetLastStep(arkode_mem, &hcur);
+
+  // Call RHS function
+  // run_rhs_f(t);
+  run_rhs_f(t);
+
+  // Save derivatives to dudata
+  save_derivs(dudata);
+}
+
+/**************************************************************************
+ * Preconditioner functions
+ **************************************************************************/
+
+void ArkodeMRISolver::pre_s(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata,
+                       BoutReal* rvec, BoutReal* zvec) {
+  TRACE("Running preconditioner: ArkodeMRISolver::pre({:e})", t);
+
+  const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
+
+  if (!hasPreconditioner()) {
+    // Identity (but should never happen)
+    const auto length = N_VGetLocalLength_Parallel(uvec);
+    std::copy(rvec, rvec + length, zvec);
+    return;
+  }
+
+  // Load state from udata (as with res function)
+  load_vars(udata);
+
+  // Load vector to be inverted into F_vars
+  load_derivs(rvec);
+
+  runPreconditioner(t, gamma, delta);
+
+  // Save the solution from F_vars
+  save_derivs(zvec);
+
+  pre_Wtime_s += bout::globals::mpi->MPI_Wtime() - tstart;
+  pre_ncalls_s++;
+}
+
+void ArkodeMRISolver::pre_f(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata,
+                       BoutReal* rvec, BoutReal* zvec) {
+  TRACE("Running preconditioner: ArkodeMRISolver::pre({:e})", t);
+
+  const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
+
+  if (!hasPreconditioner()) {
+    // Identity (but should never happen)
+    const auto length = N_VGetLocalLength_Parallel(uvec);
+    std::copy(rvec, rvec + length, zvec);
+    return;
+  }
+
+  // Load state from udata (as with res function)
+  load_vars(udata);
+
+  // Load vector to be inverted into F_vars
+  load_derivs(rvec);
+
+  runPreconditioner(t, gamma, delta);
+
+  // Save the solution from F_vars
+  save_derivs(zvec);
+
+  pre_Wtime_s += bout::globals::mpi->MPI_Wtime() - tstart;
+  pre_ncalls_s++;
+}
+
+/**************************************************************************
+ * Jacobian-vector multiplication functions
+ **************************************************************************/
+
+void ArkodeMRISolver::jac_s(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata) {
+  TRACE("Running Jacobian: ArkodeMRISolver::jac({:e})", t);
+
+  if (not hasJacobian()) {
+    throw BoutException("No jacobian function supplied!\n");
+  }
+
+  // Load state from ydate
+  load_vars(ydata);
+
+  // Load vector to be multiplied into F_vars
+  load_derivs(vdata);
+
+  // Call function
+  runJacobian(t);
+
+  // Save Jv from vars
+  save_derivs(Jvdata);
+}
+
+void ArkodeMRISolver::jac_f(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata) {
+  TRACE("Running Jacobian: ArkodeMRISolver::jac({:e})", t);
+
+  if (not hasJacobian()) {
+    throw BoutException("No jacobian function supplied!\n");
+  }
+
+  // Load state from ydate
+  load_vars(ydata);
+
+  // Load vector to be multiplied into F_vars
+  load_derivs(vdata);
+
+  // Call function
+  runJacobian(t);
+
+  // Save Jv from vars
+  save_derivs(Jvdata);
+}
+
+/**************************************************************************
+ * ARKODE explicit RHS functions
+ **************************************************************************/
+
+// NOLINTBEGIN(readability-identifier-length)
+namespace {
+int arkode_rhs_s_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_se(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_rhs_s_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_si(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_rhs_f_explicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_fe(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_rhs_f_implicit(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_fi(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_s_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_s(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+int arkode_f_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
+
+  BoutReal* udata = N_VGetArrayPointer(u);
+  BoutReal* dudata = N_VGetArrayPointer(du);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate RHS function
+  try {
+    s->rhs_f(t, udata, dudata);
+  } catch (BoutRhsFail& error) {
+    return 1;
+  }
+  return 0;
+}
+
+/// RHS function for BBD preconditioner
+int arkode_s_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du,
+                   void* user_data) {
+  return arkode_rhs_s_implicit(t, u, du, user_data);
+}
+
+int arkode_f_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du,
+                   void* user_data) {
+  return arkode_rhs_f_implicit(t, u, du, user_data);
+}
+
+/// Preconditioner function
+int arkode_s_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec,
+               BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) {
+  BoutReal* udata = N_VGetArrayPointer(yy);
+  BoutReal* rdata = N_VGetArrayPointer(rvec);
+  BoutReal* zdata = N_VGetArrayPointer(zvec);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate residuals
+  s->pre_s(t, gamma, delta, udata, rdata, zdata);
+
+  return 0;
+}
+
+int arkode_f_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec,
+               BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) {
+  BoutReal* udata = N_VGetArrayPointer(yy);
+  BoutReal* rdata = N_VGetArrayPointer(rvec);
+  BoutReal* zdata = N_VGetArrayPointer(zvec);
+
+  auto* s = static_cast<ArkodeMRISolver*>(user_data);
+
+  // Calculate residuals
+  s->pre_f(t, gamma, delta, udata, rdata, zdata);
+
+  return 0;
+}
+
+} // namespace
+// NOLINTEND(readability-identifier-length)
+
+/**************************************************************************
+ * vector abstol functions
+ **************************************************************************/
+
+void ArkodeMRISolver::set_abstol_values(BoutReal* abstolvec_data,
+                                     std::vector<BoutReal>& f2dtols,
+                                     std::vector<BoutReal>& f3dtols) {
+  int p = 0; // Counter for location in abstolvec_data array
+
+  // All boundaries
+  for (const auto& i2d : bout::globals::mesh->getRegion2D("RGN_BNDRY")) {
+    loop_abstol_values_op(i2d, abstolvec_data, p, f2dtols, f3dtols, true);
+  }
+  // Bulk of points
+  for (const auto& i2d : bout::globals::mesh->getRegion2D("RGN_NOBNDRY")) {
+    loop_abstol_values_op(i2d, abstolvec_data, p, f2dtols, f3dtols, false);
+  }
+}
+
+void ArkodeMRISolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolvec_data,
+                                         int& p, std::vector<BoutReal>& f2dtols,
+                                         std::vector<BoutReal>& f3dtols, bool bndry) {
+  // Loop over 2D variables
+  for (std::vector<BoutReal>::size_type i = 0; i < f2dtols.size(); i++) {
+    if (bndry && !f2d[i].evolve_bndry) {
+      continue;
+    }
+    abstolvec_data[p] = f2dtols[i];
+    p++;
+  }
+
+  for (int jz = 0; jz < bout::globals::mesh->LocalNz; jz++) {
+    // Loop over 3D variables
+    for (std::vector<BoutReal>::size_type i = 0; i < f3dtols.size(); i++) {
+      if (bndry && !f3d[i].evolve_bndry) {
+        continue;
+      }
+      abstolvec_data[p] = f3dtols[i];
+      p++;
+    }
+  }
+}
+
+#endif
diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
new file mode 100644
index 0000000000..80c9c51ac8
--- /dev/null
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -0,0 +1,176 @@
+/**************************************************************************
+ * Interface to ARKODE MRI solver
+ * NOTE: ARKode is currently in beta testing so use with cautious optimism
+ *
+ * NOTE: Only one solver can currently be compiled in
+ *
+ **************************************************************************
+ * Copyright 2010-2024 BOUT++ contributors
+ *
+ * Contact: Ben Dudson, dudson2@llnl.gov
+ *
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#ifndef BOUT_ARKODE_MRI_SOLVER_H
+#define BOUT_ARKODE_MRI_SOLVER_H
+
+#include "bout/build_config.hxx"
+#include "bout/solver.hxx"
+
+#if not BOUT_HAS_ARKODE
+
+namespace {
+RegisterUnavailableSolver
+    registerunavailablearkodemri("arkode_mri", "BOUT++ was not configured with ARKODE/SUNDIALS");
+}
+
+#else
+
+#include "bout/bout_enum_class.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/sundials_backports.hxx"
+
+#include <nvector/nvector_parallel.h>
+#include <sundials/sundials_config.h>
+#include <arkode/arkode_mristep.h>
+
+#include <sundials/sundials_adaptcontroller.h>
+
+#include <vector>
+
+class ArkodeMRISolver;
+class Options;
+
+namespace {
+RegisterSolver<ArkodeMRISolver> registersolverarkodemri("arkode_mri");
+}
+
+// enum describing treatment of equations
+// Note: Capitalized because `explicit` is a C++ reserved keyword
+BOUT_ENUM_CLASS(MRI_Treatment, ImEx, Implicit, Explicit);
+
+// Adaptivity method
+BOUT_ENUM_CLASS(MRI_AdapMethod, PID, PI, I, Explicit_Gustafsson, Implicit_Gustafsson,
+                ImEx_Gustafsson);
+
+class ArkodeMRISolver : public Solver {
+public:
+  explicit ArkodeMRISolver(Options* opts = nullptr);
+  ~ArkodeMRISolver();
+
+  BoutReal getCurrentTimestep() override { return hcur; }
+
+  int init() override;
+
+  int run() override;
+  BoutReal run(BoutReal tout);
+
+  // These functions used internally (but need to be public)
+  void rhs_se(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_si(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_fe(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_fi(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_s(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void rhs_f(BoutReal t, BoutReal* udata, BoutReal* dudata);
+  void pre_s(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec,
+           BoutReal* zvec);
+  void pre_f(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec,
+           BoutReal* zvec);
+  void jac_s(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
+  void jac_f(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
+
+private:
+  BoutReal hcur; //< Current internal timestep
+
+  bool diagnose{false}; //< Output additional diagnostics
+
+  N_Vector uvec{nullptr};    //< Values
+  void* arkode_mem{nullptr}; //< ARKODE internal memory block
+  void* inner_arkode_mem{nullptr}; //< ARKODE internal memory block
+  MRIStepInnerStepper inner_stepper{nullptr}; //< inner stepper
+
+  BoutReal pre_Wtime_s{0.0}; //< Time in preconditioner
+  BoutReal pre_Wtime_f{0.0}; //< Time in preconditioner
+  int pre_ncalls_s{0};       //< Number of calls to preconditioner
+  int pre_ncalls_f{0};       //< Number of calls to preconditioner
+
+  /// Maximum number of steps to take between outputs
+  int mxsteps;
+  /// Integrator treatment enum: IMEX, Implicit or Explicit
+  MRI_Treatment treatment;
+  MRI_Treatment inner_treatment;
+  /// Use linear implicit solver (only evaluates jacobian inversion once)
+  bool set_linear;
+  bool inner_set_linear;
+  /// Solve explicit portion in fixed timestep mode. NOTE: This is not recommended except
+  /// for code comparison
+  bool fixed_step;
+  /// Order of the internal step
+  int order;
+  /// Timestep adaptivity function
+  MRI_AdapMethod adap_method;
+  /// Absolute tolerance
+  BoutReal abstol;
+  /// Relative tolerance
+  BoutReal reltol;
+  /// Use separate absolute tolerance for each field
+  bool use_vector_abstol;
+  /// Maximum timestep (only used if greater than zero)
+  bool use_precon;
+  bool inner_use_precon;
+  /// Number of Krylov basis vectors to use
+  int maxl;
+  int inner_maxl;
+  /// Use right preconditioning instead of left preconditioning
+  bool rightprec;
+
+  // Diagnostics from ARKODE MRI
+  int nsteps{0};
+  int nfe_evals{0};
+  int nfi_evals{0};
+  int nniters{0};
+  int npevals{0};
+  int nliters{0};
+  int inner_nsteps{0};
+  int inner_nfe_evals{0};
+  int inner_nfi_evals{0};
+  int inner_nniters{0};
+  int inner_npevals{0};
+  int inner_nliters{0};
+
+  void set_abstol_values(BoutReal* abstolvec_data, std::vector<BoutReal>& f2dtols,
+                         std::vector<BoutReal>& f3dtols);
+  void loop_abstol_values_op(Ind2D i2d, BoutReal* abstolvec_data, int& p,
+                             std::vector<BoutReal>& f2dtols,
+                             std::vector<BoutReal>& f3dtols, bool bndry);
+
+  /// SPGMR solver structure
+  SUNLinearSolver sun_solver{nullptr};
+  SUNLinearSolver inner_sun_solver{nullptr};
+  /// Solver for implicit stages
+  SUNNonlinearSolver nonlinear_solver{nullptr};
+  SUNNonlinearSolver inner_nonlinear_solver{nullptr};
+  /// Timestep controller
+  SUNAdaptController controller{nullptr};
+  SUNAdaptController inner_controller{nullptr};
+  /// Context for SUNDIALS memory allocations
+  sundials::Context suncontext;
+};
+
+#endif // BOUT_HAS_ARKODE
+#endif // BOUT_ARKODE_MRI_SOLVER_H
diff --git a/tests/integrated/test-kpr_mri/CMakeLists.txt b/tests/integrated/test-kpr_mri/CMakeLists.txt
new file mode 100644
index 0000000000..66a4474bb0
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/CMakeLists.txt
@@ -0,0 +1,2 @@
+bout_add_integrated_test(test_kpr_mri SOURCES test_kpr_mri.cxx 
+REQUIRES BOUT_HAS_SUNDIALS)
diff --git a/tests/integrated/test-kpr_mri/README.md b/tests/integrated/test-kpr_mri/README.md
new file mode 100644
index 0000000000..ffcef3ded9
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/README.md
@@ -0,0 +1,37 @@
+test-kpr_mri
+===========
+
+ Multirate nonlinear Kvaerno-Prothero-Robinson ODE test problem:
+
+    [f]' = [ G  e ] [(-1+f^2-r)/(2f)] + [      r'(t)/(2f)        ]
+    [g]    [ e -1 ] [(-2+g^2-s)/(2g)]   [ s'(t)/(2*sqrt(2+s(t))) ]
+         = [ fs(t,f,g) ]
+           [ ff(t,f,g) ]
+
+ where r(t) = 0.5 * cos(t),  s(t) = cos(w * t),  0 < t < 5.
+
+ This problem has analytical solution given by
+    f(t) = sqrt(1+r(t)),  g(t) = sqrt(2+s(t)).
+
+ We use the parameters:
+   e = 0.5 (fast/slow coupling strength) [default]
+   G = -100 (stiffness at slow time scale) [default]
+   w = 100  (time-scale separation factor) [default]
+
+ The stiffness of the slow time scale is essentially determined
+ by G, for |G| > 50 it is 'stiff' and ideally suited to a
+ multirate method that is implicit at the slow time scale.
+
+MRI implementations of the functions are as follows:
+
+The slow explicit RHS function:
+     [-0.5 * sin(t)/(2 * f)]
+     [          0          ]
+
+The slow implicit RHS function:
+      [G e] * [(-1 + f^2 - 0.5 * cos(t))/(2 * f) ]
+      [0 0]   [(-2 + g^2 - cos(w * t))/(2 * g)   ]
+
+The fast implicit RHS function:
+     [0  0] * [(-1 + f^2 - 0.5 * cos(t))/(2 * f)] + [         0                              ]
+     [e -1]   [(-2 + g^2 - cos(w * t))/(2 * g)  ]   [-w * sin(w * t)/(2 * sqrt(2 + cos(w*t)))]
diff --git a/tests/integrated/test-kpr_mri/makefile b/tests/integrated/test-kpr_mri/makefile
new file mode 100644
index 0000000000..84db76e5c3
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/makefile
@@ -0,0 +1,5 @@
+BOUT_TOP	= ../../..
+
+SOURCEC		= test_kpr_mri.cxx
+
+include $(BOUT_TOP)/make.config
diff --git a/tests/integrated/test-kpr_mri/runtest b/tests/integrated/test-kpr_mri/runtest
new file mode 100755
index 0000000000..47f335dc94
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/runtest
@@ -0,0 +1,23 @@
+#!/usr/bin/env python3
+
+# requires: petsc
+
+from boututils.run_wrapper import shell_safe, launch_safe
+
+from sys import exit
+
+nthreads = 1
+nproc = 1
+
+print("Making solver test")
+shell_safe("make > make.log")
+
+print("Running solver test")
+status, out = launch_safe("./test_kpr_mri", nproc=nproc, mthread=nthreads, pipe=True)
+with open("run.log", "w") as f:
+    f.write(out)
+
+if status:
+    print(out)
+
+exit(status)
diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
new file mode 100644
index 0000000000..c071f25ef2
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
@@ -0,0 +1,183 @@
+#include "bout/physicsmodel.hxx"
+#include "bout/solver.hxx"
+
+#include <cmath>
+#include <memory>
+#include <string>
+#include <vector>
+
+// A simple phyics model with a manufactured true solution
+//
+class TestSolver : public PhysicsModel {
+public:
+  Field3D f, g;
+
+  BoutReal e  = 0.5;       /* fast/slow coupling strength */
+  BoutReal G  = -100.0;    /* stiffness at slow time scale */
+  BoutReal w  = 100.0;     /* time-scale separation factor */
+
+  int init(bool UNUSED(restarting)) override {
+    solver->add(f, "f");
+    solver->add(g, "g");
+
+    f = sqrt(3.0/2.0);
+    g = sqrt(3.0);
+    
+    setSplitOperatorMRI();
+    
+    return 0;
+  }
+
+  int rhs_se(BoutReal t) override {
+  /* fill in the slow explicit RHS function:
+     [-0.5*sin(t)/(2*f)]
+     [      0          ] */
+    ddt(f) = -0.5*sin(t)/(2.0*f(1,1,0));
+    ddt(g) = 0.0;
+
+    return 0;
+  }
+
+  int rhs_si(BoutReal t) override {
+    /* fill in the slow implicit RHS function:
+      [G e]*[(-1+f^2-0.5*cos(t))/(2*f)]
+      [0 0] [(-2+g^2-cos(w*t))/(2*g)  ]  */
+    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
+    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+    ddt(f) = G * tmp1 + e * tmp2;
+    ddt(g) = 0.0;
+
+    return 0;
+  }
+
+  int rhs_fe(BoutReal UNUSED(t)) override {
+
+    ddt(f) = 0.0;
+    ddt(g) = 0.0;
+
+    return 0;
+  }
+
+  int rhs_fi(BoutReal t) override {
+  /* fill in the fast implicit RHS function:
+     [0  0]*[(-1+f^2-0.5*cos(t))/(2*f)] + [         0                      ]
+     [e -1] [(-2+g^2-cos(w*t))/(2*g)  ]   [-w*sin(w*t)/(2*sqrt(2+cos(w*t)))] */
+    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
+    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+    ddt(f) = 0.0;
+    ddt(g) = e * tmp1 - tmp2 - w * sin(w*t) / (2.0 * sqrt(2.0 + cos(w * t)));
+
+    return 0;
+  }
+
+  int rhs_s(BoutReal t) override {
+  /* fill in the RHS function:
+     [G e]*[(-1+f^2-0.5*cos(t))/(2*f)] + [-0.5*sin(t)/(2*f)]
+     [0 0] [(-2+g^2-cos(w*t))/(2*g)  ]   [      0          ] */
+    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
+    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+    ddt(f) = G * tmp1 + e * tmp2 - 0.5*sin(t) / (2.0 * f(1,1,0));
+    ddt(g) = 0.0;
+
+    return 0;
+  }
+
+  int rhs_f(BoutReal t) override {
+  /* fill in the RHS function:
+     [0  0]*[(-1+f^2-0.5*cos(t))/(2*f)] + [         0                      ]
+     [e -1] [(-2+g^2-cos(w*t))/(2*g)  ]   [-w*sin(w*t)/(2*sqrt(2+cos(w*t)))] */
+    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
+    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+    ddt(f) = 0.0;
+    ddt(g) = e * tmp1 - tmp2 - w * sin(w*t) / (2.0 * sqrt(2.0 + cos(w * t)));
+
+    return 0;
+  }
+
+  // int rhs(BoutReal t) override {
+  // /* fill in the RHS function:
+  //    [G  e]*[(-1+f^2-0.5*cos(t))/(2*f)] + [-0.5*sin(t)/(2*f)               ]
+  //    [e -1] [(-2+g^2-cos(w*t))/(2*g)  ]   [-w*sin(w*t)/(2*sqrt(2+cos(w*t)))] */
+  //   BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
+  //   BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+
+  //   ddt(f) = G * tmp1 + e * tmp2 - 0.5*sin(t) / (2.0 * f(1,1,0));
+  //   ddt(g) = e * tmp1 - tmp2 - w * sin(w*t) / (2.0 * sqrt(2.0 + cos(w * t)));
+
+  //   return 0;
+  // }
+
+  bool check_solution(BoutReal atol, BoutReal t) {
+    // Return true if correct solution
+    return ((std::abs(sqrt(0.5*cos(t) + 1.0) - f(1,1,0)) < atol) and (std::abs(sqrt(cos(w*t) + 2.0) - g(1,1,0)) < atol));
+  }
+
+  BoutReal compute_error(BoutReal t)
+  {
+    /* Compute the error with the true solution:
+     f(t) = sqrt(0.5*cos(t) + 1.0)
+     g(t) = sqrt(cos(w*t) + 2.0) */
+    return sqrt( pow(sqrt(0.5*cos(t) + 1.0) - f(1,1,0), 2.0) + 
+                 pow(sqrt(cos(w*t) + 2.0) - g(1,1,0), 2.0));
+  }
+
+  // Don't need any restarting, or options to control data paths
+  int postInit(bool) override { return 0; }
+};
+
+int main(int argc, char** argv) {
+  // Absolute tolerance for difference between the actual value and the
+  // expected value
+  constexpr BoutReal tolerance = 1.e-5;
+
+  // Our own output to stdout, as main library will only be writing to log files
+  Output output_test;
+
+  auto& root = Options::root();
+
+  root["mesh"]["MXG"] = 1;
+  root["mesh"]["MYG"] = 1;
+  root["mesh"]["nx"] = 3;
+  root["mesh"]["ny"] = 1;
+  root["mesh"]["nz"] = 1;
+
+  root["output"]["enabled"] = false;
+  root["restart_files"]["enabled"] = false;
+
+  Solver::setArgs(argc, argv);
+  BoutComm::setArgs(argc, argv);
+
+  bout::globals::mpi = new MpiWrapper();
+
+  bout::globals::mesh = Mesh::create();
+  bout::globals::mesh->load();
+
+  // Global options
+  root["nout"] = 100;
+  root["timestep"] = 0.05;
+
+  // Get specific options section for this solver. Can't just use default
+  // "solver" section, as we run into problems when solvers use the same
+  // name for an option with inconsistent defaults
+  auto options = Options::getRoot()->getSection("arkode_mri");
+  auto solver = std::unique_ptr<Solver>{Solver::create("arkode_mri", options)};
+  
+  TestSolver model{};
+  solver->setModel(&model);
+
+  BoutMonitor bout_monitor{};
+  solver->addMonitor(&bout_monitor, Solver::BACK);
+
+  solver->solve();
+
+  BoutReal error = model.compute_error(5.0);
+
+  std::cout << "error = " << error << std::endl;
+
+  if (model.check_solution(tolerance, 5.0)) {
+    output_test << " PASSED\n";
+    return 0;
+  }
+  output_test << " FAILED\n";
+  return 1;
+}

From 0ee723cef4033bf67139b0c104121482df079234 Mon Sep 17 00:00:00 2001
From: maggul <maggul@smu.edu>
Date: Fri, 25 Oct 2024 11:37:25 -0700
Subject: [PATCH 1806/1827] added treatment options

---
 tests/integrated/test-kpr_mri/test_kpr_mri.cxx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
index c071f25ef2..250f874fe6 100644
--- a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
@@ -24,7 +24,7 @@ class TestSolver : public PhysicsModel {
     g = sqrt(3.0);
     
     setSplitOperatorMRI();
-    
+
     return 0;
   }
 
@@ -155,6 +155,8 @@ int main(int argc, char** argv) {
   // Global options
   root["nout"] = 100;
   root["timestep"] = 0.05;
+  root["arkode_mri"]["treatment"] = "explicit";
+  root["arkode_mri"]["inner_treatment"] = "explicit";
 
   // Get specific options section for this solver. Can't just use default
   // "solver" section, as we run into problems when solvers use the same

From 6cd4c36781deffc52f459d6a1494add87750eb35 Mon Sep 17 00:00:00 2001
From: maggul <maggul@smu.edu>
Date: Mon, 18 Nov 2024 09:33:09 -0600
Subject: [PATCH 1807/1827] remove adaptivity

---
 src/solver/impls/arkode/arkode_mri.cxx | 55 +-------------------------
 src/solver/impls/arkode/arkode_mri.hxx | 11 ------
 2 files changed, 1 insertion(+), 65 deletions(-)

diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index 1fb9a79a24..e092f7be28 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -99,11 +99,6 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
                           "not recommended except for code comparison")
                      .withDefault(false)),
       order((*options)["order"].doc("Order of internal step").withDefault(4)),
-      adap_method(
-          (*options)["adap_method"]
-              .doc("Set timestep adaptivity function: pid, pi, i, explicit_gustafsson,  "
-                   "implicit_gustafsson, imex_gustafsson.")
-              .withDefault(MRI_AdapMethod::PID)),
       abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
       reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-5)),
       use_vector_abstol((*options)["use_vector_abstol"]
@@ -157,9 +152,6 @@ ArkodeMRISolver::~ArkodeMRISolver() {
   SUNNonlinSolFree(nonlinear_solver);
   SUNNonlinSolFree(inner_nonlinear_solver);
   MRIStepInnerStepper_Free(&inner_stepper);
-
-  SUNAdaptController_Destroy(controller);
-  SUNAdaptController_Destroy(inner_controller);
 }
 
 /**************************************************************************
@@ -293,53 +285,8 @@ int ArkodeMRISolver::init() {
     throw BoutException("ARKodeSetOrder failed\n");
   }
 
-  switch (adap_method) {
-  case MRI_AdapMethod::PID:
-    controller = SUNAdaptController_PID(suncontext);
-    inner_controller = SUNAdaptController_PID(suncontext);
-    break;
-  case MRI_AdapMethod::PI:
-    controller = SUNAdaptController_PI(suncontext);
-    inner_controller = SUNAdaptController_PI(suncontext);
-    break;
-  case MRI_AdapMethod::I:
-    controller = SUNAdaptController_I(suncontext);
-    inner_controller = SUNAdaptController_I(suncontext);
-    break;
-  case MRI_AdapMethod::Explicit_Gustafsson:
-    controller = SUNAdaptController_ExpGus(suncontext);
-    inner_controller = SUNAdaptController_ExpGus(suncontext);
-    break;
-  case MRI_AdapMethod::Implicit_Gustafsson:
-    controller = SUNAdaptController_ImpGus(suncontext);
-    inner_controller = SUNAdaptController_ImpGus(suncontext);
-    break;
-  case MRI_AdapMethod::ImEx_Gustafsson:
-    controller = SUNAdaptController_ImExGus(suncontext);
-    inner_controller = SUNAdaptController_ImExGus(suncontext);
-    break;
-  default:
-    throw BoutException("Invalid adap_method\n");
-  }
-
-  // if (ARKodeSetAdaptController(arkode_mem, controller) != ARK_SUCCESS) {
-  //   throw BoutException("ARKodeSetAdaptController failed\n");
-  // }
-
-  // if (ARKodeSetAdaptivityAdjustment(arkode_mem, 0) != ARK_SUCCESS) {
-  //   throw BoutException("ARKodeSetAdaptivityAdjustment failed\n");
-  // }
-
   if (ARKodeSetFixedStep(arkode_mem, 0.001) != ARK_SUCCESS) {
-    throw BoutException("ARKodeSetAdaptController failed\n");
-  }
-
-  if (ARKodeSetAdaptController(inner_arkode_mem, controller) != ARK_SUCCESS) {
-    throw BoutException("ARKodeSetAdaptController failed\n");
-  }
-
-  if (ARKodeSetAdaptivityAdjustment(inner_arkode_mem, 0) != ARK_SUCCESS) {
-    throw BoutException("ARKodeSetAdaptivityAdjustment failed\n");
+    throw BoutException("ARKodeSetFixedStep failed\n");
   }
 
   if (use_vector_abstol) {
diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
index 80c9c51ac8..9cd33c2df8 100644
--- a/src/solver/impls/arkode/arkode_mri.hxx
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -49,8 +49,6 @@ RegisterUnavailableSolver
 #include <sundials/sundials_config.h>
 #include <arkode/arkode_mristep.h>
 
-#include <sundials/sundials_adaptcontroller.h>
-
 #include <vector>
 
 class ArkodeMRISolver;
@@ -64,10 +62,6 @@ RegisterSolver<ArkodeMRISolver> registersolverarkodemri("arkode_mri");
 // Note: Capitalized because `explicit` is a C++ reserved keyword
 BOUT_ENUM_CLASS(MRI_Treatment, ImEx, Implicit, Explicit);
 
-// Adaptivity method
-BOUT_ENUM_CLASS(MRI_AdapMethod, PID, PI, I, Explicit_Gustafsson, Implicit_Gustafsson,
-                ImEx_Gustafsson);
-
 class ArkodeMRISolver : public Solver {
 public:
   explicit ArkodeMRISolver(Options* opts = nullptr);
@@ -122,8 +116,6 @@ private:
   bool fixed_step;
   /// Order of the internal step
   int order;
-  /// Timestep adaptivity function
-  MRI_AdapMethod adap_method;
   /// Absolute tolerance
   BoutReal abstol;
   /// Relative tolerance
@@ -165,9 +157,6 @@ private:
   /// Solver for implicit stages
   SUNNonlinearSolver nonlinear_solver{nullptr};
   SUNNonlinearSolver inner_nonlinear_solver{nullptr};
-  /// Timestep controller
-  SUNAdaptController controller{nullptr};
-  SUNAdaptController inner_controller{nullptr};
   /// Context for SUNDIALS memory allocations
   sundials::Context suncontext;
 };

From 153db72c9a527c2a24c4df2804cd7ce01443738e Mon Sep 17 00:00:00 2001
From: maggul <maggul@smu.edu>
Date: Thu, 9 Jan 2025 14:09:31 -0600
Subject: [PATCH 1808/1827] adaptive step and SUNDIALS release updates

---
 src/solver/impls/arkode/arkode_mri.cxx | 23 ++++++++++++-----------
 src/solver/impls/arkode/arkode_mri.hxx |  7 +++++--
 2 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index e092f7be28..e7227cdc41 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -95,12 +95,15 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
               .doc("Use linear implicit solver (only evaluates jacobian inversion once)")
               .withDefault(false)),
       fixed_step((*options)["fixed_step"]
-                     .doc("Solve explicit portion in fixed timestep mode. NOTE: This is "
+                     .doc("Solve both fast and slow time scales using fixed time step sizes. NOTE: This is "
                           "not recommended except for code comparison")
                      .withDefault(false)),
-      order((*options)["order"].doc("Order of internal step").withDefault(4)),
+      inner_timestep((*options)["inner_timestep"]
+                     .doc("Fixed step size to use for inner solver when running in fixed time step mode.")
+                     .withDefault(1.0e-4)),
+      order((*options)["order"].doc("Order of internal step").withDefault(3)),
       abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
-      reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-5)),
+      reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-10)),
       use_vector_abstol((*options)["use_vector_abstol"]
                             .doc("Use separate absolute tolerance for each field")
                             .withDefault(false)),
@@ -232,8 +235,8 @@ int ArkodeMRISolver::init() {
     throw BoutException("ARKodeSetOrder failed\n");
   }
 
-  if (ARKStepCreateMRIStepInnerStepper(inner_arkode_mem, &inner_stepper) != ARK_SUCCESS) {
-    throw BoutException("ARKStepCreateMRIStepInnerStepper failed\n");
+  if (ARKodeCreateMRIStepInnerStepper(inner_arkode_mem, &inner_stepper) != ARK_SUCCESS) {
+    throw BoutException("ARKodeCreateMRIStepInnerStepper failed\n");
   }
 
   // Initialize the slow integrator. Specify the explicit slow right-hand side
@@ -285,10 +288,6 @@ int ArkodeMRISolver::init() {
     throw BoutException("ARKodeSetOrder failed\n");
   }
 
-  if (ARKodeSetFixedStep(arkode_mem, 0.001) != ARK_SUCCESS) {
-    throw BoutException("ARKodeSetFixedStep failed\n");
-  }
-
   if (use_vector_abstol) {
     std::vector<BoutReal> f2dtols;
     f2dtols.reserve(f2d.size());
@@ -518,7 +517,8 @@ int ArkodeMRISolver::run() {
     long int temp_long_int, temp_long_int2;
     ARKodeGetNumSteps(arkode_mem, &temp_long_int);
     nsteps = int(temp_long_int);
-    MRIStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2); //Change after the release
+    ARKodeGetNumRhsEvals(arkode_mem, 0, &temp_long_int);
+    ARKodeGetNumRhsEvals(arkode_mem, 1, &temp_long_int2);
     nfe_evals = int(temp_long_int);
     nfi_evals = int(temp_long_int2);
     if (treatment == MRI_Treatment::ImEx or treatment == MRI_Treatment::Implicit) {
@@ -532,7 +532,8 @@ int ArkodeMRISolver::run() {
 
     ARKodeGetNumSteps(inner_arkode_mem, &temp_long_int);
     inner_nsteps = int(temp_long_int);
-    ARKStepGetNumRhsEvals(inner_arkode_mem, &temp_long_int, &temp_long_int2); //Change after the release
+    ARKodeGetNumRhsEvals(inner_arkode_mem, 0, &temp_long_int);
+    ARKodeGetNumRhsEvals(inner_arkode_mem, 1, &temp_long_int2);
     inner_nfe_evals = int(temp_long_int);
     inner_nfi_evals = int(temp_long_int2);
     if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
index 9cd33c2df8..3ced8af207 100644
--- a/src/solver/impls/arkode/arkode_mri.hxx
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -111,9 +111,12 @@ private:
   /// Use linear implicit solver (only evaluates jacobian inversion once)
   bool set_linear;
   bool inner_set_linear;
-  /// Solve explicit portion in fixed timestep mode. NOTE: This is not recommended except
-  /// for code comparison
+  /// Solve both fast and slow portion in fixed timestep mode.
+  /// NOTE: This is not recommended except for code comparison
   bool fixed_step;
+  /// Fixed step size to use for inner solver when running in fixed
+  /// time step mode.
+  BoutReal inner_timestep;
   /// Order of the internal step
   int order;
   /// Absolute tolerance

From 25c6305dbf4fe22b154cc124e39d1323967baa2d Mon Sep 17 00:00:00 2001
From: maggul <maggul@smu.edu>
Date: Fri, 7 Feb 2025 14:13:41 -0600
Subject: [PATCH 1809/1827] flag and test-kpr updates

---
 include/bout/solver.hxx                       |  2 ++
 src/solver/impls/arkode/arkode_mri.cxx        | 20 ++++++++++---------
 src/solver/solver.cxx                         |  8 ++++----
 tests/integrated/test-kpr_mri/CMakeLists.txt  |  2 +-
 .../integrated/test-kpr_mri/test_kpr_mri.cxx  | 10 ++++++++++
 5 files changed, 28 insertions(+), 14 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 120f89d217..840759d8ec 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -563,6 +563,8 @@ protected:
   bool initialised{false};
   /// If calling user RHS for the first time
   bool first_rhs_call{true};
+  bool first_rhs_s_call{false};
+  bool first_rhs_f_call{false};
 
   /// Current simulation time
   BoutReal simtime{0.0};
diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index e7227cdc41..f373a630f7 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -640,8 +640,8 @@ void ArkodeMRISolver::rhs_se(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   load_vars(udata);
 
   // Get the current timestep
-  // Note: ARKodeGetCurrentStep updated too late in older versions
-  ARKodeGetLastStep(arkode_mem, &hcur);
+  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
+  ARKodeGetCurrentStep(arkode_mem, &hcur);
 
   // Call RHS function
   run_rhs_se(t);
@@ -658,7 +658,8 @@ void ArkodeMRISolver::rhs_si(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   TRACE("Running RHS: ArkodeMRISolver::rhs_si({:e})", t);
 
   load_vars(udata);
-  ARKodeGetLastStep(arkode_mem, &hcur);
+  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
+  ARKodeGetCurrentStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs_si(t);
   save_derivs(dudata);
@@ -675,8 +676,8 @@ void ArkodeMRISolver::rhs_fe(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   load_vars(udata);
 
   // Get the current timestep
-  // Note: ARKodeGetCurrentStep updated too late in older versions
-  ARKodeGetLastStep(arkode_mem, &hcur);
+  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
+  ARKodeGetCurrentStep(arkode_mem, &hcur);
 
   // Call RHS function
   run_rhs_fe(t);
@@ -693,7 +694,8 @@ void ArkodeMRISolver::rhs_fi(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   TRACE("Running RHS: ArkodeMRISolver::rhs_si({:e})", t);
 
   load_vars(udata);
-  ARKodeGetLastStep(arkode_mem, &hcur);
+  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
+  ARKodeGetCurrentStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs_fi(t);
   save_derivs(dudata);
@@ -710,8 +712,8 @@ void ArkodeMRISolver::rhs_s(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   load_vars(udata);
 
   // Get the current timestep
-  // Note: ARKodeGetCurrentStep updated too late in older versions
-  ARKodeGetLastStep(arkode_mem, &hcur);
+  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
+  ARKodeGetCurrentStep(arkode_mem, &hcur);
 
   // Call RHS function
   // run_rhs_s(t);
@@ -733,7 +735,7 @@ void ArkodeMRISolver::rhs_f(BoutReal t, BoutReal* udata, BoutReal* dudata) {
 
   // Get the current timestep
   // Note: ARKodeGetCurrentStep updated too late in older versions
-  ARKodeGetLastStep(arkode_mem, &hcur);
+  ARKodeGetCurrentStep(arkode_mem, &hcur);
 
   // Call RHS function
   // run_rhs_f(t);
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index a525cd4210..860e5ac77c 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1264,10 +1264,10 @@ int Solver::run_rhs_si(BoutReal t, bool linear) {
 
   Timer timer("rhs");
 
-  if (first_rhs_call) {
+  if (first_rhs_s_call) {
     // Ensure that nonlinear terms are calculated on first call
     linear = false;
-    first_rhs_call = false;
+    first_rhs_s_call = false;
   }
 
   pre_rhs(t);
@@ -1308,10 +1308,10 @@ int Solver::run_rhs_fi(BoutReal t, bool linear) {
 
   Timer timer("rhs");
 
-  if (first_rhs_call) {
+  if (first_rhs_f_call) {
     // Ensure that nonlinear terms are calculated on first call
     linear = false;
-    first_rhs_call = false;
+    first_rhs_f_call = false;
   }
 
   pre_rhs(t);
diff --git a/tests/integrated/test-kpr_mri/CMakeLists.txt b/tests/integrated/test-kpr_mri/CMakeLists.txt
index 66a4474bb0..45523803db 100644
--- a/tests/integrated/test-kpr_mri/CMakeLists.txt
+++ b/tests/integrated/test-kpr_mri/CMakeLists.txt
@@ -1,2 +1,2 @@
-bout_add_integrated_test(test_kpr_mri SOURCES test_kpr_mri.cxx 
+bout_add_integrated_test(test_kpr_mri SOURCES test_kpr_mri.cxx
 REQUIRES BOUT_HAS_SUNDIALS)
diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
index 250f874fe6..6d4e6f805a 100644
--- a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
@@ -1,3 +1,5 @@
+#if SUNDIALS_VERSION_AT_LEAST(7, 2, 0)
+
 #include "bout/physicsmodel.hxx"
 #include "bout/solver.hxx"
 
@@ -183,3 +185,11 @@ int main(int argc, char** argv) {
   output_test << " FAILED\n";
   return 1;
 }
+#else
+// ARKODE-MRI option for BOUT++
+// is not available with this configuration
+// do nothing for this test
+int main(int argc, char** argv) {
+  return 0;
+}
+#endif
\ No newline at end of file

From 742e82ebf41c9e0184b49fc0bc5af5a8620971e1 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 7 Feb 2025 17:15:07 -0800
Subject: [PATCH 1810/1827] ARKode-MRI: Register unavailable if sundials
 version is too low

Provides an error message if arkode_mri solver is requested but
BOUT++ was built with a version of SUNDIALS lower than 7.2.0
---
 src/solver/impls/arkode/arkode_mri.hxx | 36 +++++++++++++++++++-------
 1 file changed, 26 insertions(+), 10 deletions(-)

diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
index 3ced8af207..e4216a4937 100644
--- a/src/solver/impls/arkode/arkode_mri.hxx
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -5,7 +5,7 @@
  * NOTE: Only one solver can currently be compiled in
  *
  **************************************************************************
- * Copyright 2010-2024 BOUT++ contributors
+ * Copyright 2010-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -36,18 +36,29 @@
 
 namespace {
 RegisterUnavailableSolver
-    registerunavailablearkodemri("arkode_mri", "BOUT++ was not configured with ARKODE/SUNDIALS");
+    registerunavailablearkodemri("arkode_mri",
+                                 "BOUT++ was not configured with ARKODE/SUNDIALS");
 }
 
 #else
 
-#include "bout/bout_enum_class.hxx"
-#include "bout/bout_types.hxx"
 #include "bout/sundials_backports.hxx"
 
+#if SUNDIALS_VERSION_LESS_THAN(7, 2, 0)
+
+namespace {
+RegisterUnavailableSolver registerunavailablearkodemri(
+    "arkode_mri", "BOUT++ configured with ARKODE/SUNDIALS version less than 7.2.0");
+}
+
+#else // SUNDIALS_VERSION check
+
+#include "bout/bout_enum_class.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/region.hxx"
+#include <arkode/arkode_mristep.h>
 #include <nvector/nvector_parallel.h>
 #include <sundials/sundials_config.h>
-#include <arkode/arkode_mristep.h>
 
 #include <vector>
 
@@ -82,9 +93,9 @@ public:
   void rhs_s(BoutReal t, BoutReal* udata, BoutReal* dudata);
   void rhs_f(BoutReal t, BoutReal* udata, BoutReal* dudata);
   void pre_s(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec,
-           BoutReal* zvec);
+             BoutReal* zvec);
   void pre_f(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata, BoutReal* rvec,
-           BoutReal* zvec);
+             BoutReal* zvec);
   void jac_s(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
   void jac_f(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
 
@@ -93,9 +104,9 @@ private:
 
   bool diagnose{false}; //< Output additional diagnostics
 
-  N_Vector uvec{nullptr};    //< Values
-  void* arkode_mem{nullptr}; //< ARKODE internal memory block
-  void* inner_arkode_mem{nullptr}; //< ARKODE internal memory block
+  N_Vector uvec{nullptr};                     //< Values
+  void* arkode_mem{nullptr};                  //< ARKODE internal memory block
+  void* inner_arkode_mem{nullptr};            //< ARKODE internal memory block
   MRIStepInnerStepper inner_stepper{nullptr}; //< inner stepper
 
   BoutReal pre_Wtime_s{0.0}; //< Time in preconditioner
@@ -164,5 +175,10 @@ private:
   sundials::Context suncontext;
 };
 
+<<<<<<< HEAD
+=======
+#endif // SUNDIALS_VERSION CHECK
+>>>>>>> 30c16d9141 (ARKode-MRI: Register unavailable if sundials version is too low)
+#endif // SUNDIALS_VERSION CHECK
 #endif // BOUT_HAS_ARKODE
 #endif // BOUT_ARKODE_MRI_SOLVER_H

From 1a6c0a0146e1c29d597a4bd89f5175cca2026251 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 7 Feb 2025 17:36:21 -0800
Subject: [PATCH 1811/1827] Add fast and slow preconditioner callbacks

PhysicsModel now has fast and slow preconditioners, and
these can be called by the Arkode MRI solver.
---
 include/bout/physicsmodel.hxx          |  40 +++++--
 include/bout/solver.hxx                |   5 +
 src/physics/physicsmodel.cxx           |  16 ++-
 src/solver/impls/arkode/arkode_mri.cxx | 157 ++++++++++++++-----------
 src/solver/solver.cxx                  |  23 +++-
 5 files changed, 154 insertions(+), 87 deletions(-)

diff --git a/include/bout/physicsmodel.hxx b/include/bout/physicsmodel.hxx
index 282aff043a..e8f79b313f 100644
--- a/include/bout/physicsmodel.hxx
+++ b/include/bout/physicsmodel.hxx
@@ -3,17 +3,10 @@
  *
  * @brief Base class for Physics Models
  *
- *
- *
- * Changelog:
- *
- * 2013-08 Ben Dudson <benjamin.dudson@york.ac.uk>
- *    * Initial version
- *
  **************************************************************************
- * Copyright 2013 B.D.Dudson
+ * Copyright 2013-2025 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -182,11 +175,13 @@ public:
 
   /*!
    * True if this model uses split operators
+   * RHS = convective + diffusive
    */
   bool splitOperator();
 
   /*!
-   * True if this model uses split operators
+   * True if this model uses Multi-Rate Integrator (MRI) split operators
+   * RHS =  rhs_se + rhs_si + rhs_fe + rhs_fi
    */
   bool splitOperatorMRI();
 
@@ -211,7 +206,9 @@ public:
   /*!
    * True if a preconditioner has been defined
    */
-  bool hasPrecon();
+  bool hasPrecon() const { return (userprecon != nullptr); }
+  bool hasPreconFast() const { return (userprecon_f != nullptr); }
+  bool hasPreconSlow() const { return (userprecon_s != nullptr); }
 
   /*!
    * Run the preconditioner. The system state should be in the
@@ -222,6 +219,8 @@ public:
    *
    */
   int runPrecon(BoutReal t, BoutReal gamma, BoutReal delta);
+  int runPreconFast(BoutReal t, BoutReal gamma, BoutReal delta);
+  int runPreconSlow(BoutReal t, BoutReal gamma, BoutReal delta);
 
   /*!
    * True if a Jacobian function has been defined
@@ -341,7 +340,7 @@ protected:
   /// Specify that this model is split into a convective and diffusive part
   void setSplitOperator(bool split = true) { splitop = split; }
 
-  /// Specify that this model is split into a convective and diffusive part
+  /// Specify that this model is split into fast and slow parts
   void setSplitOperatorMRI(bool split = true) { splitopmri = split; }
 
   /// Specify a preconditioner function
@@ -351,6 +350,19 @@ protected:
     userprecon = static_cast<preconfunc>(preconditioner);
   }
 
+  /// Preconditioner for fast implicit RHS
+  void setPreconFast(preconfunc pset) { userprecon_f = pset; }
+  template <class Model>
+  void setPreconFast(ModelPreconFunc<Model> preconditioner) {
+    userprecon_f = static_cast<preconfunc>(preconditioner);
+  }
+  /// Preconditioner for slow implicit RHS
+  void setPreconSlow(preconfunc pset) { userprecon_s = pset; }
+  template <class Model>
+  void setPreconSlow(ModelPreconFunc<Model> preconditioner) {
+    userprecon_s = static_cast<preconfunc>(preconditioner);
+  }
+
   /// Specify a Jacobian-vector multiply function
   void setJacobian(jacobianfunc jset) { userjacobian = jset; }
   template <class Model>
@@ -429,10 +441,12 @@ private:
   bool restart_enabled{true};
   /// Split operator model?
   bool splitop{false};
-  /// Split operator model?
+  /// MPI fast/slow split operator model?
   bool splitopmri{false};
   /// Pointer to user-supplied preconditioner function
   preconfunc userprecon{nullptr};
+  preconfunc userprecon_f{nullptr};
+  preconfunc userprecon_s{nullptr};
   /// Pointer to user-supplied Jacobian-vector multiply function
   jacobianfunc userjacobian{nullptr};
   /// True if model already initialised
diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index 840759d8ec..fffcf0fdda 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -610,8 +610,13 @@ protected:
 
   /// Do we have a user preconditioner?
   bool hasPreconditioner();
+  bool hasPreconditionerFast();
+  bool hasPreconditionerSlow();
+
   /// Run the user preconditioner
   int runPreconditioner(BoutReal time, BoutReal gamma, BoutReal delta);
+  int runPreconditionerFast(BoutReal time, BoutReal gamma, BoutReal delta);
+  int runPreconditionerSlow(BoutReal time, BoutReal gamma, BoutReal delta);
 
   /// Do we have a user Jacobian?
   bool hasJacobian();
diff --git a/src/physics/physicsmodel.cxx b/src/physics/physicsmodel.cxx
index f2c1053ab1..a30f65cb08 100644
--- a/src/physics/physicsmodel.cxx
+++ b/src/physics/physicsmodel.cxx
@@ -148,8 +148,6 @@ int PhysicsModel::runDiffusive(BoutReal time, bool linear) {
   return diffusive(time, linear);
 }
 
-bool PhysicsModel::hasPrecon() { return (userprecon != nullptr); }
-
 int PhysicsModel::runPrecon(BoutReal t, BoutReal gamma, BoutReal delta) {
   if (!userprecon) {
     return 1;
@@ -157,6 +155,20 @@ int PhysicsModel::runPrecon(BoutReal t, BoutReal gamma, BoutReal delta) {
   return (*this.*userprecon)(t, gamma, delta);
 }
 
+int PhysicsModel::runPreconFast(BoutReal t, BoutReal gamma, BoutReal delta) {
+  if (!userprecon_f) {
+    return 1;
+  }
+  return (*this.*userprecon_f)(t, gamma, delta);
+}
+
+int PhysicsModel::runPreconSlow(BoutReal t, BoutReal gamma, BoutReal delta) {
+  if (!userprecon_s) {
+    return 1;
+  }
+  return (*this.*userprecon_s)(t, gamma, delta);
+}
+
 bool PhysicsModel::hasJacobian() { return (userjacobian != nullptr); }
 
 int PhysicsModel::runJacobian(BoutReal t) {
diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index f373a630f7..25606a716a 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -4,7 +4,7 @@
  * NOTE: ARKode is still in beta testing so use with cautious optimism
  *
  **************************************************************************
- * Copyright 2010-2024 BOUT++ contributors
+ * Copyright 2010-2025 BOUT++ contributors
  *
  * This file is part of BOUT++.
  *
@@ -60,13 +60,13 @@ int arkode_s_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data);
 int arkode_f_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data);
 
 int arkode_s_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du,
-                   void* user_data);
+                     void* user_data);
 int arkode_f_bbd_rhs(sunindextype Nlocal, BoutReal t, N_Vector u, N_Vector du,
-                   void* user_data);                   
+                     void* user_data);
 int arkode_s_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec,
-               BoutReal gamma, BoutReal delta, int lr, void* user_data);
+                 BoutReal gamma, BoutReal delta, int lr, void* user_data);
 int arkode_f_pre(BoutReal t, N_Vector yy, N_Vector yp, N_Vector rvec, N_Vector zvec,
-               BoutReal gamma, BoutReal delta, int lr, void* user_data);
+                 BoutReal gamma, BoutReal delta, int lr, void* user_data);
 
 } // namespace
 // NOLINTEND(readability-identifier-length)
@@ -82,10 +82,11 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
                     .doc("Use default capability (imex) or provide a specific treatment: "
                          "implicit or explicit")
                     .withDefault(MRI_Treatment::ImEx)),
-      inner_treatment((*options)["inner_treatment"]
-                    .doc("Use default capability (imex) or provide a specific inner_treatment: "
-                         "implicit or explicit")
-                    .withDefault(MRI_Treatment::ImEx)),
+      inner_treatment(
+          (*options)["inner_treatment"]
+              .doc("Use default capability (imex) or provide a specific inner_treatment: "
+                   "implicit or explicit")
+              .withDefault(MRI_Treatment::ImEx)),
       set_linear(
           (*options)["set_linear"]
               .doc("Use linear implicit solver (only evaluates jacobian inversion once)")
@@ -95,12 +96,14 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
               .doc("Use linear implicit solver (only evaluates jacobian inversion once)")
               .withDefault(false)),
       fixed_step((*options)["fixed_step"]
-                     .doc("Solve both fast and slow time scales using fixed time step sizes. NOTE: This is "
+                     .doc("Solve both fast and slow time scales using fixed time step "
+                          "sizes. NOTE: This is "
                           "not recommended except for code comparison")
                      .withDefault(false)),
       inner_timestep((*options)["inner_timestep"]
-                     .doc("Fixed step size to use for inner solver when running in fixed time step mode.")
-                     .withDefault(1.0e-4)),
+                         .doc("Fixed step size to use for inner solver when running in "
+                              "fixed time step mode.")
+                         .withDefault(1.0e-4)),
       order((*options)["order"].doc("Order of internal step").withDefault(3)),
       abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
       reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-10)),
@@ -111,12 +114,13 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
                      .doc("Use user-supplied preconditioner function")
                      .withDefault(false)),
       inner_use_precon((*options)["inner_use_precon"]
-                     .doc("Use user-supplied preconditioner function")
-                     .withDefault(false)),
+                           .doc("Use user-supplied preconditioner function")
+                           .withDefault(false)),
       maxl(
           (*options)["maxl"].doc("Number of Krylov basis vectors to use").withDefault(0)),
-      inner_maxl(
-          (*options)["inner_maxl"].doc("Number of Krylov basis vectors to use").withDefault(0)),
+      inner_maxl((*options)["inner_maxl"]
+                     .doc("Number of Krylov basis vectors to use")
+                     .withDefault(0)),
       rightprec((*options)["rightprec"]
                     .doc("Use right preconditioning instead of left preconditioning")
                     .withDefault(false)),
@@ -125,7 +129,8 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
 
   // Add diagnostics to output
   add_int_diagnostic(nsteps, "arkode_nsteps", "Cumulative number of internal steps");
-  add_int_diagnostic(inner_nsteps, "arkode_inner_nsteps", "Cumulative number of inner internal steps");
+  add_int_diagnostic(inner_nsteps, "arkode_inner_nsteps",
+                     "Cumulative number of inner internal steps");
   add_int_diagnostic(nfe_evals, "arkode_nfe_evals",
                      "No. of calls to fe (explicit portion of the right-hand-side "
                      "function) function");
@@ -139,11 +144,14 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
                      "No. of calls to fi (implicit portion of inner the right-hand-side "
                      "function) function");
   add_int_diagnostic(nniters, "arkode_nniters", "No. of nonlinear solver iterations");
-  add_int_diagnostic(inner_nniters, "arkode_inner_nniters", "No. of inner nonlinear solver iterations");
+  add_int_diagnostic(inner_nniters, "arkode_inner_nniters",
+                     "No. of inner nonlinear solver iterations");
   add_int_diagnostic(npevals, "arkode_npevals", "No. of preconditioner evaluations");
-  add_int_diagnostic(inner_npevals, "arkode_inner_npevals", "No. of inner preconditioner evaluations");
+  add_int_diagnostic(inner_npevals, "arkode_inner_npevals",
+                     "No. of inner preconditioner evaluations");
   add_int_diagnostic(nliters, "arkode_nliters", "No. of linear iterations");
-  add_int_diagnostic(inner_nliters, "arkode_inner_nliters", "No. of inner linear iterations");
+  add_int_diagnostic(inner_nliters, "arkode_inner_nliters",
+                     "No. of inner linear iterations");
 }
 
 ArkodeMRISolver::~ArkodeMRISolver() {
@@ -192,18 +200,19 @@ int ArkodeMRISolver::init() {
 
   switch (inner_treatment) {
   case MRI_Treatment::ImEx:
-    inner_arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_f_explicit,
-                                    arkode_rhs_f_implicit, simtime, uvec);
+    inner_arkode_mem =
+        callWithSUNContext(ARKStepCreate, suncontext, arkode_rhs_f_explicit,
+                           arkode_rhs_f_implicit, simtime, uvec);
     output_info.write("\tUsing ARKode ImEx inner solver \n");
     break;
   case MRI_Treatment::Explicit:
-    inner_arkode_mem =
-        callWithSUNContext(ARKStepCreate, suncontext, arkode_f_rhs, nullptr, simtime, uvec);
+    inner_arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, arkode_f_rhs,
+                                          nullptr, simtime, uvec);
     output_info.write("\tUsing ARKode Explicit inner solver \n");
     break;
   case MRI_Treatment::Implicit:
-    inner_arkode_mem =
-        callWithSUNContext(ARKStepCreate, suncontext, nullptr, arkode_f_rhs, simtime, uvec);
+    inner_arkode_mem = callWithSUNContext(ARKStepCreate, suncontext, nullptr,
+                                          arkode_f_rhs, simtime, uvec);
     output_info.write("\tUsing ARKode Implicit inner solver \n");
     break;
   default:
@@ -218,7 +227,7 @@ int ArkodeMRISolver::init() {
     throw BoutException("ARKodeSetUserData failed\n");
   }
 
-  if(inner_treatment != MRI_Treatment::Explicit)
+  if (inner_treatment != MRI_Treatment::Explicit)
     if (ARKodeSetLinear(inner_arkode_mem, inner_set_linear) != ARK_SUCCESS) {
       throw BoutException("ARKodeSetLinear failed\n");
     }
@@ -245,12 +254,12 @@ int ArkodeMRISolver::init() {
 
   switch (treatment) {
   case MRI_Treatment::ImEx:
-    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, arkode_rhs_s_explicit, arkode_rhs_s_implicit, 
-                                    simtime, uvec, inner_stepper);
+    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, arkode_rhs_s_explicit,
+                                    arkode_rhs_s_implicit, simtime, uvec, inner_stepper);
     output_info.write("\tUsing ARKode ImEx solver \n");
     break;
   case MRI_Treatment::Explicit:
-    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, arkode_s_rhs, nullptr, 
+    arkode_mem = callWithSUNContext(MRIStepCreate, suncontext, arkode_s_rhs, nullptr,
                                     simtime, uvec, inner_stepper);
     output_info.write("\tUsing ARKode Explicit solver \n");
     break;
@@ -271,7 +280,7 @@ int ArkodeMRISolver::init() {
     throw BoutException("ARKodeSetUserData failed\n");
   }
 
-  if(treatment != MRI_Treatment::Explicit)
+  if (treatment != MRI_Treatment::Explicit)
     if (ARKodeSetLinear(arkode_mem, set_linear) != ARK_SUCCESS) {
       throw BoutException("ARKodeSetLinear failed\n");
     }
@@ -341,31 +350,34 @@ int ArkodeMRISolver::init() {
     throw BoutException("ARKodeSetMaxNumSteps failed\n");
   }
 
-  if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+  if (inner_treatment == MRI_Treatment::ImEx
+      or inner_treatment == MRI_Treatment::Implicit) {
     {
       output.write("\tUsing Newton iteration for inner solver\n");
 
       const auto prectype =
           inner_use_precon ? (rightprec ? SUN_PREC_RIGHT : SUN_PREC_LEFT) : SUN_PREC_NONE;
-      inner_sun_solver = callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, inner_maxl);
+      inner_sun_solver =
+          callWithSUNContext(SUNLinSol_SPGMR, suncontext, uvec, prectype, inner_maxl);
       if (inner_sun_solver == nullptr) {
         throw BoutException("Creating SUNDIALS inner linear solver failed\n");
       }
-      if (ARKodeSetLinearSolver(inner_arkode_mem, inner_sun_solver, nullptr) != ARKLS_SUCCESS) {
+      if (ARKodeSetLinearSolver(inner_arkode_mem, inner_sun_solver, nullptr)
+          != ARKLS_SUCCESS) {
         throw BoutException("ARKodeSetLinearSolver failed for inner solver\n");
       }
 
       /// Set Preconditioner
       if (inner_use_precon) {
-        if (hasPreconditioner()) {  // change to inner_hasPreconditioner when it is available
-          output.write("\tUsing user-supplied preconditioner for inner solver\n");
+        if (hasPreconditionerFast()) {
+          output.write("\tUsing user-supplied preconditioner for inner (fast) solver\n");
 
           if (ARKodeSetPreconditioner(inner_arkode_mem, nullptr, arkode_f_pre)
               != ARKLS_SUCCESS) {
             throw BoutException("ARKodeSetPreconditioner failed for inner solver\n");
           }
         } else {
-          output.write("\tUsing BBD preconditioner for inner solver\n");
+          output.write("\tUsing BBD preconditioner for inner (fast) solver\n");
 
           /// Get options
           // Compute band_width_default from actually added fields, to allow for multiple
@@ -410,10 +422,10 @@ int ArkodeMRISolver::init() {
     }
 
     /// Set Jacobian-vector multiplication function
-    output.write("\tUsing difference quotient approximation for Jacobian in the inner solver\n");
+    output.write(
+        "\tUsing difference quotient approximation for Jacobian in the inner solver\n");
   }
 
-
   if (treatment == MRI_Treatment::ImEx or treatment == MRI_Treatment::Implicit) {
     {
       output.write("\tUsing Newton iteration\n");
@@ -430,7 +442,7 @@ int ArkodeMRISolver::init() {
 
       /// Set Preconditioner
       if (use_precon) {
-        if (hasPreconditioner()) {
+        if (hasPreconditionerSlow()) {
           output.write("\tUsing user-supplied preconditioner\n");
 
           if (ARKodeSetPreconditioner(arkode_mem, nullptr, arkode_s_pre)
@@ -536,7 +548,8 @@ int ArkodeMRISolver::run() {
     ARKodeGetNumRhsEvals(inner_arkode_mem, 1, &temp_long_int2);
     inner_nfe_evals = int(temp_long_int);
     inner_nfi_evals = int(temp_long_int2);
-    if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+    if (inner_treatment == MRI_Treatment::ImEx
+        or inner_treatment == MRI_Treatment::Implicit) {
       ARKodeGetNumNonlinSolvIters(inner_arkode_mem, &temp_long_int);
       inner_nniters = int(temp_long_int);
       ARKodeGetNumPrecEvals(inner_arkode_mem, &temp_long_int);
@@ -558,16 +571,22 @@ int ArkodeMRISolver::run() {
                      static_cast<BoutReal>(npevals) / static_cast<BoutReal>(nniters));
       }
 
-      output.write("\nARKODE Inner: inner_nsteps {:d}, inner_nfe_evals {:d}, inner_nfi_evals {:d}, inner_nniters {:d}, "
+      output.write("\nARKODE Inner: inner_nsteps {:d}, inner_nfe_evals {:d}, "
+                   "inner_nfi_evals {:d}, inner_nniters {:d}, "
                    "inner_npevals {:d}, inner_nliters {:d}\n",
-                   inner_nsteps, inner_nfe_evals, inner_nfi_evals, inner_nniters, inner_npevals, inner_nliters);
-      if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+                   inner_nsteps, inner_nfe_evals, inner_nfi_evals, inner_nniters,
+                   inner_npevals, inner_nliters);
+      if (inner_treatment == MRI_Treatment::ImEx
+          or inner_treatment == MRI_Treatment::Implicit) {
         output.write("    -> Inner Newton iterations per step: {:e}\n",
-                     static_cast<BoutReal>(inner_nniters) / static_cast<BoutReal>(inner_nsteps));
+                     static_cast<BoutReal>(inner_nniters)
+                         / static_cast<BoutReal>(inner_nsteps));
         output.write("    -> Inner Linear iterations per Newton iteration: {:e}\n",
-                     static_cast<BoutReal>(inner_nliters) / static_cast<BoutReal>(inner_nniters));
+                     static_cast<BoutReal>(inner_nliters)
+                         / static_cast<BoutReal>(inner_nniters));
         output.write("    -> Inner Preconditioner evaluations per Newton: {:e}\n",
-                     static_cast<BoutReal>(inner_npevals) / static_cast<BoutReal>(inner_nniters));
+                     static_cast<BoutReal>(inner_npevals)
+                         / static_cast<BoutReal>(inner_nniters));
       }
     }
 
@@ -750,12 +769,12 @@ void ArkodeMRISolver::rhs_f(BoutReal t, BoutReal* udata, BoutReal* dudata) {
  **************************************************************************/
 
 void ArkodeMRISolver::pre_s(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata,
-                       BoutReal* rvec, BoutReal* zvec) {
+                            BoutReal* rvec, BoutReal* zvec) {
   TRACE("Running preconditioner: ArkodeMRISolver::pre({:e})", t);
 
   const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
 
-  if (!hasPreconditioner()) {
+  if (!hasPreconditionerSlow()) {
     // Identity (but should never happen)
     const auto length = N_VGetLocalLength_Parallel(uvec);
     std::copy(rvec, rvec + length, zvec);
@@ -768,7 +787,7 @@ void ArkodeMRISolver::pre_s(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal
   // Load vector to be inverted into F_vars
   load_derivs(rvec);
 
-  runPreconditioner(t, gamma, delta);
+  runPreconditionerSlow(t, gamma, delta);
 
   // Save the solution from F_vars
   save_derivs(zvec);
@@ -778,12 +797,12 @@ void ArkodeMRISolver::pre_s(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal
 }
 
 void ArkodeMRISolver::pre_f(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal* udata,
-                       BoutReal* rvec, BoutReal* zvec) {
+                            BoutReal* rvec, BoutReal* zvec) {
   TRACE("Running preconditioner: ArkodeMRISolver::pre({:e})", t);
 
   const BoutReal tstart = bout::globals::mpi->MPI_Wtime();
 
-  if (!hasPreconditioner()) {
+  if (!hasPreconditionerFast()) {
     // Identity (but should never happen)
     const auto length = N_VGetLocalLength_Parallel(uvec);
     std::copy(rvec, rvec + length, zvec);
@@ -796,7 +815,7 @@ void ArkodeMRISolver::pre_f(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal
   // Load vector to be inverted into F_vars
   load_derivs(rvec);
 
-  runPreconditioner(t, gamma, delta);
+  runPreconditionerFast(t, gamma, delta);
 
   // Save the solution from F_vars
   save_derivs(zvec);
@@ -809,7 +828,8 @@ void ArkodeMRISolver::pre_f(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal
  * Jacobian-vector multiplication functions
  **************************************************************************/
 
-void ArkodeMRISolver::jac_s(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata) {
+void ArkodeMRISolver::jac_s(BoutReal t, BoutReal* ydata, BoutReal* vdata,
+                            BoutReal* Jvdata) {
   TRACE("Running Jacobian: ArkodeMRISolver::jac({:e})", t);
 
   if (not hasJacobian()) {
@@ -829,7 +849,8 @@ void ArkodeMRISolver::jac_s(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutRe
   save_derivs(Jvdata);
 }
 
-void ArkodeMRISolver::jac_f(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata) {
+void ArkodeMRISolver::jac_f(BoutReal t, BoutReal* ydata, BoutReal* vdata,
+                            BoutReal* Jvdata) {
   TRACE("Running Jacobian: ArkodeMRISolver::jac({:e})", t);
 
   if (not hasJacobian()) {
@@ -953,18 +974,19 @@ int arkode_f_rhs(BoutReal t, N_Vector u, N_Vector du, void* user_data) {
 
 /// RHS function for BBD preconditioner
 int arkode_s_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du,
-                   void* user_data) {
+                     void* user_data) {
   return arkode_rhs_s_implicit(t, u, du, user_data);
 }
 
 int arkode_f_bbd_rhs(sunindextype UNUSED(Nlocal), BoutReal t, N_Vector u, N_Vector du,
-                   void* user_data) {
+                     void* user_data) {
   return arkode_rhs_f_implicit(t, u, du, user_data);
 }
 
 /// Preconditioner function
-int arkode_s_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec,
-               BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) {
+int arkode_s_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec,
+                 N_Vector zvec, BoutReal gamma, BoutReal delta, int UNUSED(lr),
+                 void* user_data) {
   BoutReal* udata = N_VGetArrayPointer(yy);
   BoutReal* rdata = N_VGetArrayPointer(rvec);
   BoutReal* zdata = N_VGetArrayPointer(zvec);
@@ -977,8 +999,9 @@ int arkode_s_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_
   return 0;
 }
 
-int arkode_f_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_Vector zvec,
-               BoutReal gamma, BoutReal delta, int UNUSED(lr), void* user_data) {
+int arkode_f_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec,
+                 N_Vector zvec, BoutReal gamma, BoutReal delta, int UNUSED(lr),
+                 void* user_data) {
   BoutReal* udata = N_VGetArrayPointer(yy);
   BoutReal* rdata = N_VGetArrayPointer(rvec);
   BoutReal* zdata = N_VGetArrayPointer(zvec);
@@ -999,8 +1022,8 @@ int arkode_f_pre(BoutReal t, N_Vector yy, N_Vector UNUSED(yp), N_Vector rvec, N_
  **************************************************************************/
 
 void ArkodeMRISolver::set_abstol_values(BoutReal* abstolvec_data,
-                                     std::vector<BoutReal>& f2dtols,
-                                     std::vector<BoutReal>& f3dtols) {
+                                        std::vector<BoutReal>& f2dtols,
+                                        std::vector<BoutReal>& f3dtols) {
   int p = 0; // Counter for location in abstolvec_data array
 
   // All boundaries
@@ -1014,8 +1037,8 @@ void ArkodeMRISolver::set_abstol_values(BoutReal* abstolvec_data,
 }
 
 void ArkodeMRISolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolvec_data,
-                                         int& p, std::vector<BoutReal>& f2dtols,
-                                         std::vector<BoutReal>& f3dtols, bool bndry) {
+                                            int& p, std::vector<BoutReal>& f2dtols,
+                                            std::vector<BoutReal>& f3dtols, bool bndry) {
   // Loop over 2D variables
   for (std::vector<BoutReal>::size_type i = 0; i < f2dtols.size(); i++) {
     if (bndry && !f2d[i].evolve_bndry) {
@@ -1037,4 +1060,6 @@ void ArkodeMRISolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolv
   }
 }
 
-#endif
+#else
+#endif // SUNDIALS_VERSION CHECK
+#endif // BOUT_HAS_ARKODE
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 860e5ac77c..3c4db0daa0 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1590,20 +1590,31 @@ void Solver::post_rhs(BoutReal UNUSED(t)) {
 #endif
 }
 
-bool Solver::varAdded(const std::string& name) {
-  return contains(f2d, name) || contains(f3d, name) || contains(v2d, name)
-         || contains(v3d, name);
+bool Solver::hasPreconditioner() { return model->hasPrecon(); }
+bool Solver::hasPreconditionerFast() { return model->hasPreconFast(); }
+bool Solver::hasPreconditionerSlow() { return model->hasPreconSlow(); }
+
+int Solver::runPreconditioner(BoutReal time, BoutReal gamma, BoutReal delta) {
+  return model->runPrecon(time, gamma, delta);
 }
 
-bool Solver::hasPreconditioner() { return model->hasPrecon(); }
+int Solver::runPreconditionerFast(BoutReal time, BoutReal gamma, BoutReal delta) {
+  return model->runPreconFast(time, gamma, delta);
+}
 
-int Solver::runPreconditioner(BoutReal t, BoutReal gamma, BoutReal delta) {
-  return model->runPrecon(t, gamma, delta);
+int Solver::runPreconditionerSlow(BoutReal time, BoutReal gamma, BoutReal delta) {
+  return model->runPreconSlow(time, gamma, delta);
 }
 
 bool Solver::hasJacobian() { return model->hasJacobian(); }
+
 int Solver::runJacobian(BoutReal time) { return model->runJacobian(time); }
 
+bool Solver::varAdded(const std::string& name) {
+  return contains(f2d, name) || contains(f3d, name) || contains(v2d, name)
+         || contains(v3d, name);
+}
+
 // Add source terms to time derivatives
 void Solver::add_mms_sources(BoutReal t) {
   if (!mms) {

From 1f83051b4cf195c54fcf0192538ed8c11edc9abc Mon Sep 17 00:00:00 2001
From: maggul <maggul@smu.edu>
Date: Fri, 7 Feb 2025 18:40:08 -0600
Subject: [PATCH 1812/1827] added required header file

---
 tests/integrated/test-kpr_mri/test_kpr_mri.cxx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
index 6d4e6f805a..b894ce0d6c 100644
--- a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
@@ -1,3 +1,5 @@
+#include "bout/sundials_backports.hxx"
+
 #if SUNDIALS_VERSION_AT_LEAST(7, 2, 0)
 
 #include "bout/physicsmodel.hxx"

From 595db6ff23e893c7f08f7305fa90c49204c0d32d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 7 Feb 2025 18:04:47 -0800
Subject: [PATCH 1813/1827] ARKode solver: Use ARKodeGetNumRhsEvals from v7.2.0

Previous use of ARKStepGetNumRhsEvals is deprecated from SUNDIALS
7.2.0, replaced by ARKodeGetNumRhsEvals

https://github.com/LLNL/sundials/blob/main/CHANGELOG.md#deprecation-notices
---
 src/solver/impls/arkode/arkode.cxx | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index e39d65b976..a492f5a3f4 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -528,13 +528,18 @@ int ArkodeSolver::run() {
 
     // Get additional diagnostics
     long int temp_long_int = 0;
-    long int temp_long_int = 0;
+    long int temp_long_int2 = 0;
     ARKodeGetNumSteps(arkode_mem, &temp_long_int);
     nsteps = int(temp_long_int);
-    ARKodeGetNumRhsEvals(arkode_mem, 0, &temp_long_int);
+#if SUNDIALS_VERSION_AT_LEAST(7, 2, 0)
+    ARKodeGetNumRhsEvals(arkode_mem, 0, &temp_long_int); // Explicit
+    ARKodeGetNumRhsEvals(arkode_mem, 1, &temp_long_int2); // Implicit
+#else
+    // This function was deprecated in 7.2.0
+    ARKStepGetNumRhsEvals(arkode_mem, &temp_long_int, &temp_long_int2);
+#endif
     nfe_evals = int(temp_long_int);
-    ARKodeGetNumRhsEvals(arkode_mem, 1, &temp_long_int);
-    nfi_evals = int(temp_long_int);
+    nfi_evals = int(temp_long_int2);
     if (treatment == Treatment::ImEx or treatment == Treatment::Implicit) {
       ARKodeGetNumNonlinSolvIters(arkode_mem, &temp_long_int);
       nniters = int(temp_long_int);

From 6f03a54e51facdd3991b06fbd033121bb08132db Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Fri, 7 Feb 2025 18:07:10 -0800
Subject: [PATCH 1814/1827] ARKode-MRI: Only call ARKodeGetCurrentStep if user
 requests it

Rather than calling `ARKodeGetCurrentStep` every rhs() call, only
call when the `getCurrentTimestep()` method is called.
---
 src/solver/impls/arkode/arkode_mri.cxx | 26 ++++++--------------------
 src/solver/impls/arkode/arkode_mri.hxx |  5 ++---
 2 files changed, 8 insertions(+), 23 deletions(-)

diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index 25606a716a..150e0c2ec3 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -165,6 +165,12 @@ ArkodeMRISolver::~ArkodeMRISolver() {
   MRIStepInnerStepper_Free(&inner_stepper);
 }
 
+BoutReal ArkodeMRISolver::getCurrentTimestep() {
+  BoutReal hcur;
+  ARKodeGetCurrentStep(arkode_mem, &hcur);
+  return hcur;
+}
+
 /**************************************************************************
  * Initialise
  **************************************************************************/
@@ -658,10 +664,6 @@ void ArkodeMRISolver::rhs_se(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   // Load state from udata
   load_vars(udata);
 
-  // Get the current timestep
-  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
-  ARKodeGetCurrentStep(arkode_mem, &hcur);
-
   // Call RHS function
   run_rhs_se(t);
 
@@ -677,8 +679,6 @@ void ArkodeMRISolver::rhs_si(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   TRACE("Running RHS: ArkodeMRISolver::rhs_si({:e})", t);
 
   load_vars(udata);
-  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
-  ARKodeGetCurrentStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs_si(t);
   save_derivs(dudata);
@@ -694,10 +694,6 @@ void ArkodeMRISolver::rhs_fe(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   // Load state from udata
   load_vars(udata);
 
-  // Get the current timestep
-  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
-  ARKodeGetCurrentStep(arkode_mem, &hcur);
-
   // Call RHS function
   run_rhs_fe(t);
 
@@ -713,8 +709,6 @@ void ArkodeMRISolver::rhs_fi(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   TRACE("Running RHS: ArkodeMRISolver::rhs_si({:e})", t);
 
   load_vars(udata);
-  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
-  ARKodeGetCurrentStep(arkode_mem, &hcur);
   // Call Implicit RHS function
   run_rhs_fi(t);
   save_derivs(dudata);
@@ -730,10 +724,6 @@ void ArkodeMRISolver::rhs_s(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   // Load state from udata
   load_vars(udata);
 
-  // Get the current timestep
-  // TO DO: Check to identify which time step is needed current/last, then correct accordingly
-  ARKodeGetCurrentStep(arkode_mem, &hcur);
-
   // Call RHS function
   // run_rhs_s(t);
   run_rhs_s(t);
@@ -752,10 +742,6 @@ void ArkodeMRISolver::rhs_f(BoutReal t, BoutReal* udata, BoutReal* dudata) {
   // Load state from udata
   load_vars(udata);
 
-  // Get the current timestep
-  // Note: ARKodeGetCurrentStep updated too late in older versions
-  ARKodeGetCurrentStep(arkode_mem, &hcur);
-
   // Call RHS function
   // run_rhs_f(t);
   run_rhs_f(t);
diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
index e4216a4937..be384f778a 100644
--- a/src/solver/impls/arkode/arkode_mri.hxx
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -78,7 +78,8 @@ public:
   explicit ArkodeMRISolver(Options* opts = nullptr);
   ~ArkodeMRISolver();
 
-  BoutReal getCurrentTimestep() override { return hcur; }
+  // Get the current timestep
+  BoutReal getCurrentTimestep() override;
 
   int init() override;
 
@@ -100,8 +101,6 @@ public:
   void jac_f(BoutReal t, BoutReal* ydata, BoutReal* vdata, BoutReal* Jvdata);
 
 private:
-  BoutReal hcur; //< Current internal timestep
-
   bool diagnose{false}; //< Output additional diagnostics
 
   N_Vector uvec{nullptr};                     //< Values

From 4bcc81356d2dad00c6e1038b6c3a9a1e2b0d0dc1 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 11 Feb 2025 16:36:49 -0800
Subject: [PATCH 1815/1827] Increment MRI rhs counts

When run_rhs is called (e.g. by CVODE), all rhs functions are
called (rhs_se, rhs_si, rhs_fe, rhs_fi), so all counters need to be
incremented.
---
 src/solver/solver.cxx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 3c4db0daa0..51a080eeea 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1423,6 +1423,10 @@ int Solver::run_rhs(BoutReal t, bool linear) {
       *t3 += *t2;
     }
     load_derivs(tmp3.begin()); // Put back time-derivatives
+    rhs_ncalls_fe++;
+    rhs_ncalls_fi++;
+    rhs_ncalls_se++;
+    rhs_ncalls_si++;
   } else if (model->splitOperator()) {
     // Run both parts
 

From 887ede316bb3e3aeb3a0295eda3ac6dbf55dc5ce Mon Sep 17 00:00:00 2001
From: maggul <maggul@smu.edu>
Date: Mon, 14 Apr 2025 02:06:10 -0500
Subject: [PATCH 1816/1827] run_rhs_f/s internally

---
 src/solver/impls/arkode/arkode_mri.cxx        |  8 +-
 src/solver/impls/arkode/arkode_mri.hxx        |  3 -
 src/solver/solver.cxx                         | 46 +++++++++++-
 .../integrated/test-kpr_mri/test_kpr_mri.cxx  | 74 +++++--------------
 4 files changed, 65 insertions(+), 66 deletions(-)

diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index 150e0c2ec3..b31e5e9033 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -100,10 +100,6 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
                           "sizes. NOTE: This is "
                           "not recommended except for code comparison")
                      .withDefault(false)),
-      inner_timestep((*options)["inner_timestep"]
-                         .doc("Fixed step size to use for inner solver when running in "
-                              "fixed time step mode.")
-                         .withDefault(1.0e-4)),
       order((*options)["order"].doc("Order of internal step").withDefault(3)),
       abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
       reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-10)),
@@ -240,7 +236,7 @@ int ArkodeMRISolver::init() {
 
   if (fixed_step) {
     // If not given, default to adaptive timestepping
-    const BoutReal inner_fixed_timestep = (*options)["inner_timestep"];
+    const BoutReal inner_fixed_timestep = (*options)["inner_timestep"].withDefault(1.0e-5);
     if (ARKodeSetFixedStep(inner_arkode_mem, inner_fixed_timestep) != ARK_SUCCESS) {
       throw BoutException("ARKodeSetFixedStep failed\n");
     }
@@ -293,7 +289,7 @@ int ArkodeMRISolver::init() {
 
   if (fixed_step) {
     // If not given, default to adaptive timestepping
-    const BoutReal fixed_timestep = (*options)["timestep"];
+    const BoutReal fixed_timestep = (*options)["timestep"].withDefault(1.0e-4);
     if (ARKodeSetFixedStep(arkode_mem, fixed_timestep) != ARK_SUCCESS) {
       throw BoutException("ARKodeSetFixedStep failed\n");
     }
diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
index be384f778a..17530324ce 100644
--- a/src/solver/impls/arkode/arkode_mri.hxx
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -124,9 +124,6 @@ private:
   /// Solve both fast and slow portion in fixed timestep mode.
   /// NOTE: This is not recommended except for code comparison
   bool fixed_step;
-  /// Fixed step size to use for inner solver when running in fixed
-  /// time step mode.
-  BoutReal inner_timestep;
   /// Order of the internal step
   int order;
   /// Absolute tolerance
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index 51a080eeea..c2f725384d 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1337,8 +1337,29 @@ int Solver::run_rhs_s(BoutReal t, bool linear) {
   }
 
   pre_rhs(t);
-  status = model->runRHS_s(t, linear);
+
+  // Run both parts
+
+  int nv = getLocalN();
+  // Create two temporary arrays for system state
+  Array<BoutReal> tmp(nv);
+  Array<BoutReal> tmp2(nv);
+
+  save_vars(tmp.begin()); // Copy variables into tmp
+  pre_rhs(t);
+  status = model->runRHS_se(t, linear);
+  post_rhs(t); // Check variables, apply boundary conditions
+
+  load_vars(tmp.begin());   // Reset variables
+  save_derivs(tmp.begin()); // Save time derivatives
+  pre_rhs(t);
+  status = model->runRHS_si(t, linear);
   post_rhs(t);
+  save_derivs(tmp2.begin()); // Save time derivatives
+  for (BoutReal *t = tmp.begin(), *t2 = tmp2.begin(); t != tmp.end(); ++t, ++t2) {
+    *t += *t2;
+  }
+  load_derivs(tmp.begin()); // Put back time-derivatives
 
   // If using Method of Manufactured Solutions
   add_mms_sources(t);
@@ -1360,8 +1381,29 @@ int Solver::run_rhs_f(BoutReal t, bool linear) {
   }
 
   pre_rhs(t);
-  status = model->runRHS_f(t, linear);
+
+  // Run both parts
+
+  int nv = getLocalN();
+  // Create two temporary arrays for system state
+  Array<BoutReal> tmp(nv);
+  Array<BoutReal> tmp2(nv);
+
+  save_vars(tmp.begin()); // Copy variables into tmp
+  pre_rhs(t);
+  status = model->runRHS_fe(t, linear);
+  post_rhs(t); // Check variables, apply boundary conditions
+
+  load_vars(tmp.begin());   // Reset variables
+  save_derivs(tmp.begin()); // Save time derivatives
+  pre_rhs(t);
+  status = model->runRHS_fi(t, linear);
   post_rhs(t);
+  save_derivs(tmp2.begin()); // Save time derivatives
+  for (BoutReal *t = tmp.begin(), *t2 = tmp2.begin(); t != tmp.end(); ++t, ++t2) {
+    *t += *t2;
+  }
+  load_derivs(tmp.begin()); // Put back time-derivatives
 
   // If using Method of Manufactured Solutions
   add_mms_sources(t);
diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
index b894ce0d6c..f5fdb78c23 100644
--- a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
@@ -74,48 +74,13 @@ class TestSolver : public PhysicsModel {
     return 0;
   }
 
-  int rhs_s(BoutReal t) override {
-  /* fill in the RHS function:
-     [G e]*[(-1+f^2-0.5*cos(t))/(2*f)] + [-0.5*sin(t)/(2*f)]
-     [0 0] [(-2+g^2-cos(w*t))/(2*g)  ]   [      0          ] */
-    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
-    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
-    ddt(f) = G * tmp1 + e * tmp2 - 0.5*sin(t) / (2.0 * f(1,1,0));
-    ddt(g) = 0.0;
-
-    return 0;
-  }
-
-  int rhs_f(BoutReal t) override {
-  /* fill in the RHS function:
-     [0  0]*[(-1+f^2-0.5*cos(t))/(2*f)] + [         0                      ]
-     [e -1] [(-2+g^2-cos(w*t))/(2*g)  ]   [-w*sin(w*t)/(2*sqrt(2+cos(w*t)))] */
-    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
-    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+  int rhs_fi(BoutReal UNUSED(t)) override {
     ddt(f) = 0.0;
-    ddt(g) = e * tmp1 - tmp2 - w * sin(w*t) / (2.0 * sqrt(2.0 + cos(w * t)));
+    ddt(g) = 0.0;
 
     return 0;
   }
 
-  // int rhs(BoutReal t) override {
-  // /* fill in the RHS function:
-  //    [G  e]*[(-1+f^2-0.5*cos(t))/(2*f)] + [-0.5*sin(t)/(2*f)               ]
-  //    [e -1] [(-2+g^2-cos(w*t))/(2*g)  ]   [-w*sin(w*t)/(2*sqrt(2+cos(w*t)))] */
-  //   BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
-  //   BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
-
-  //   ddt(f) = G * tmp1 + e * tmp2 - 0.5*sin(t) / (2.0 * f(1,1,0));
-  //   ddt(g) = e * tmp1 - tmp2 - w * sin(w*t) / (2.0 * sqrt(2.0 + cos(w * t)));
-
-  //   return 0;
-  // }
-
-  bool check_solution(BoutReal atol, BoutReal t) {
-    // Return true if correct solution
-    return ((std::abs(sqrt(0.5*cos(t) + 1.0) - f(1,1,0)) < atol) and (std::abs(sqrt(cos(w*t) + 2.0) - g(1,1,0)) < atol));
-  }
-
   BoutReal compute_error(BoutReal t)
   {
     /* Compute the error with the true solution:
@@ -130,9 +95,9 @@ class TestSolver : public PhysicsModel {
 };
 
 int main(int argc, char** argv) {
-  // Absolute tolerance for difference between the actual value and the
-  // expected value
-  constexpr BoutReal tolerance = 1.e-5;
+  // Relative and Absolute tolerances
+  constexpr BoutReal rtol = 1.e-10;
+  constexpr BoutReal atol = 1.e-12;
 
   // Our own output to stdout, as main library will only be writing to log files
   Output output_test;
@@ -156,18 +121,22 @@ int main(int argc, char** argv) {
   bout::globals::mesh = Mesh::create();
   bout::globals::mesh->load();
 
+  std::string sunsolver = "arkode_mri";
+  int nout = 100;
+  BoutReal timestep = 0.05;
+  BoutReal finaltime = nout*timestep;
+
   // Global options
-  root["nout"] = 100;
-  root["timestep"] = 0.05;
-  root["arkode_mri"]["treatment"] = "explicit";
-  root["arkode_mri"]["inner_treatment"] = "explicit";
+  root["nout"] = nout;
+  root["timestep"] = timestep;
+  root[sunsolver]["rtol"] = rtol;
+  root[sunsolver]["atol"] = atol;
 
   // Get specific options section for this solver. Can't just use default
   // "solver" section, as we run into problems when solvers use the same
   // name for an option with inconsistent defaults
-  auto options = Options::getRoot()->getSection("arkode_mri");
-  auto solver = std::unique_ptr<Solver>{Solver::create("arkode_mri", options)};
-  
+  auto options = Options::getRoot()->getSection(sunsolver);
+  auto solver = std::unique_ptr<Solver>{Solver::create(sunsolver, options)};
   TestSolver model{};
   solver->setModel(&model);
 
@@ -176,16 +145,11 @@ int main(int argc, char** argv) {
 
   solver->solve();
 
-  BoutReal error = model.compute_error(5.0);
+  BoutReal error = model.compute_error(finaltime);
 
   std::cout << "error = " << error << std::endl;
 
-  if (model.check_solution(tolerance, 5.0)) {
-    output_test << " PASSED\n";
-    return 0;
-  }
-  output_test << " FAILED\n";
-  return 1;
+  return 0;
 }
 #else
 // ARKODE-MRI option for BOUT++
@@ -194,4 +158,4 @@ int main(int argc, char** argv) {
 int main(int argc, char** argv) {
   return 0;
 }
-#endif
\ No newline at end of file
+#endif

From 0c406585f0c47d9f73013747dcfdc28bc5d392cf Mon Sep 17 00:00:00 2001
From: maggul <maggul@smu.edu>
Date: Mon, 21 Apr 2025 17:16:37 -0500
Subject: [PATCH 1817/1827] ARKodeSetStopTime before each evolve call

---
 src/solver/impls/arkode/arkode_mri.cxx | 31 +++++++++++++++++++++++---
 src/solver/impls/arkode/arkode_mri.hxx |  9 ++++----
 2 files changed, 33 insertions(+), 7 deletions(-)

diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index b31e5e9033..eb807e6740 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -78,6 +78,12 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
       mxsteps((*options)["mxstep"]
                   .doc("Maximum number of steps to take between outputs")
                   .withDefault(500)),
+      // mxstepsize((*options)["mxstepsize"]
+      //             .doc("Maximum step size")
+      //             .withDefault(0.1)),
+      // inner_mxstepsize((*options)["inner_mxstepsize"]
+      //             .doc("Maximum step size")
+      //             .withDefault(0.1)),
       treatment((*options)["treatment"]
                     .doc("Use default capability (imex) or provide a specific treatment: "
                          "implicit or explicit")
@@ -352,8 +358,14 @@ int ArkodeMRISolver::init() {
     throw BoutException("ARKodeSetMaxNumSteps failed\n");
   }
 
-  if (inner_treatment == MRI_Treatment::ImEx
-      or inner_treatment == MRI_Treatment::Implicit) {
+  // if (ARKodeSetMaxStep(arkode_mem, mxstepsize) != ARK_SUCCESS) {
+  //   throw BoutException("ARKodeSetMaxStep failed\n");
+  // }
+  // if (ARKodeSetMaxStep(inner_arkode_mem, inner_mxstepsize) != ARK_SUCCESS) {
+  //   throw BoutException("ARKodeSetMaxStep failed\n");
+  // }
+
+  if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
     {
       output.write("\tUsing Newton iteration for inner solver\n");
 
@@ -609,7 +621,20 @@ BoutReal ArkodeMRISolver::run(BoutReal tout) {
   pre_Wtime_s = 0.0;
   pre_ncalls_s = 0;
 
-  int flag;
+  int flag = ARKodeSetStopTime(arkode_mem, 1.0001*tout);
+  if (flag != ARK_SUCCESS) {
+    output_error.write("ERROR ARKodeSetStopTime failed at t = {:e}, flag = {:d}\n",
+      simtime, flag);
+    return -1.0;
+  }
+
+  flag = ARKodeSetStopTime(inner_arkode_mem, 1.0001*tout);
+  if (flag != ARK_SUCCESS) {
+    output_error.write("ERROR ARKodeSetStopTime failed at t = {:e}, flag = {:d}\n",
+      simtime, flag);
+    return -1.0;
+  }
+
   if (!monitor_timestep) {
     // Run in normal mode
     flag = ARKodeEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL);
diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
index 17530324ce..066d288b9c 100644
--- a/src/solver/impls/arkode/arkode_mri.hxx
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -115,6 +115,11 @@ private:
 
   /// Maximum number of steps to take between outputs
   int mxsteps;
+
+  // /// Maximum step sizes
+  // double mxstepsize;
+  // double inner_mxstepsize;
+
   /// Integrator treatment enum: IMEX, Implicit or Explicit
   MRI_Treatment treatment;
   MRI_Treatment inner_treatment;
@@ -171,10 +176,6 @@ private:
   sundials::Context suncontext;
 };
 
-<<<<<<< HEAD
-=======
-#endif // SUNDIALS_VERSION CHECK
->>>>>>> 30c16d9141 (ARKode-MRI: Register unavailable if sundials version is too low)
 #endif // SUNDIALS_VERSION CHECK
 #endif // BOUT_HAS_ARKODE
 #endif // BOUT_ARKODE_MRI_SOLVER_H

From 2a6368b6a4d67594aaa5bd0bc4b1e9a8f1b72c7e Mon Sep 17 00:00:00 2001
From: maggul <mustafaaggul06@gmail.com>
Date: Fri, 21 Nov 2025 23:15:41 -0600
Subject: [PATCH 1818/1827] continuous temporal filtering

---
 src/solver/impls/arkode/arkode.cxx            |  65 +++++++
 src/solver/impls/arkode/arkode.hxx            |  18 +-
 src/solver/impls/arkode/arkode_mri.cxx        |  65 +++++++
 src/solver/impls/arkode/arkode_mri.hxx        |  18 +-
 .../impls/arkode/temporal_filtering.hxx       | 176 ++++++++++++++++++
 src/solver/impls/cvode/cvode.cxx              |  65 +++++++
 src/solver/impls/cvode/cvode.hxx              |  18 +-
 .../integrated/test-kpr_mri/test_kpr_mri.cxx  |   6 +
 8 files changed, 428 insertions(+), 3 deletions(-)
 create mode 100644 src/solver/impls/arkode/temporal_filtering.hxx

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index a492f5a3f4..51b7f0829d 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -157,6 +157,22 @@ ArkodeSolver::ArkodeSolver(Options* opts)
       nvector_type((*options)["nvector"]
                        .doc("N_Vector backend to use: sundials or manyvector")
                        .withDefault(NVectorType::Sundials)),
+      use_temporal_filtering((*options)["use_temporal_filtering"]
+                             .doc("Use temporal filtering of solution")
+                             .withDefault(false)),
+      temp_filtering(),
+      filtering_type((*options)["filtering_type"]
+                     .doc("Type of temporal filtering to perform: None, EMA, SRA")
+                     .withDefault(FilteringType::None)),
+      tau_mean((*options)["tau_mean"]
+                .doc("Interval over which means are calculated")
+                .withDefault(10.0)),
+      mean_start_time((*options)["mean_start_time"]
+                      .doc("Time at which averaging is allowed to start")
+                      .withDefault(0.0)),
+      lambda((*options)["lambda"]
+             .doc("Relaxation parameter for temporal filtering")
+             .withDefault(0.01)),
 #if ARKODE_OPTIMAL_PARAMS_SUPPORT
       optimize(
           (*options)["optimize"].doc("Use ARKode optimal parameters").withDefault(false)),
@@ -492,6 +508,14 @@ int ArkodeSolver::init() {
     }
   }
 
+  // Enable temporal filtering if requested
+  if (use_temporal_filtering) {
+    output.write("\tUsing temporal filtering of solution\n");
+    temp_filtering.reset_state();
+    temp_filtering.initialize(uvec);
+    temp_filtering.configure(filtering_type, tau_mean, mean_start_time);
+  }
+
 #if ARKODE_OPTIMAL_PARAMS_SUPPORT
   if (optimize) {
     output.write("\tUsing ARKode inbuilt optimization\n");
@@ -585,6 +609,7 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   if (!monitor_timestep) {
     // Run in normal mode
     flag = ARKodeEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL);
+    apply_temporal_filtering(simtime, uvec);
   } else {
     // Run in single step mode, to call timestep monitors
     BoutReal internal_time;
@@ -599,6 +624,7 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
                            internal_time, flag);
         return -1.0;
       }
+      apply_temporal_filtering(internal_time, uvec);
 
       // Call timestep monitor
       call_timestep_monitors(internal_time, internal_time - last_time);
@@ -848,4 +874,43 @@ void ArkodeSolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolvec_
   }
 }
 
+void ArkodeSolver::apply_temporal_filtering(BoutReal internal_time,
+                                            N_Vector uvec)
+{
+  if (!use_temporal_filtering) {
+    return;
+  }
+
+  // Update the temporal filtering 
+  temp_filtering.update(internal_time, uvec);
+
+  // If no mean is available yet, do nothing
+  if (!temp_filtering.has_mean()) {
+    return;
+  }
+
+  int flag;
+    
+  // Get the current mean vector
+  N_Vector u_mean = temp_filtering.get_mean_vector();
+
+  // Apply the temporal filtering
+  // Gently relax the solution towards the mean
+  // Set u = (1 - lambda) * u + lambda * u_mean
+  N_VLinearSum(1.0 - lambda, uvec, lambda, u_mean, uvec);
+
+  // Reset ARKode with the new filtered state
+  flag = ARKodeReset(arkode_mem, internal_time, uvec);
+  if (flag != ARK_SUCCESS) {
+    throw BoutException("ARKodeReset failed in temporal filtering\n");
+  }
+
+  // For EMA: we keep averaging continuously (no reset).
+  // For SRA: enforce finite averaging windows of length tau_mean
+  // by restarting the averaging window when tau_mean_cur is equal to tau_mean
+  if (filtering_type == FilteringType::SRA && temp_filtering.window_full()) {
+    temp_filtering.restart_window(internal_time);
+  }
+}
+
 #endif
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index cc6b21c325..3ab3265220 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -44,6 +44,7 @@ RegisterUnavailableSolver
 #include "bout/bout_types.hxx"
 #include "bout/region.hxx"
 #include "bout/sundials_backports.hxx"
+#include "temporal_filtering.hxx"
 
 #include <nvector/nvector_parallel.h>
 #include <sundials/sundials_config.h>
@@ -182,6 +183,21 @@ private:
   bool use_jacobian;
   /// N_Vector backend to use
   NVectorType nvector_type;
+  /// Temporal filtering of solution
+  /// - Whether to use temporal filtering
+  bool use_temporal_filtering{false};
+  /// Temporal filtering object
+  TemporalFiltering temp_filtering;
+  /// Type of temporal filtering to use
+  FilteringType filtering_type{FilteringType::None};
+  /// Interval over which means are calculated
+  /// - EMA: time scale of the exponential memory
+  /// - SRA: window length of each running-average block
+  BoutReal tau_mean{0.0};
+  /// Time at which averaging starts
+  BoutReal mean_start_time{0.0};
+  /// Relaxation/nudging parameter for temporal filtering
+  BoutReal lambda{0.0};
 #if ARKODE_OPTIMAL_PARAMS_SUPPORT
   /// Use ARKode optimal parameters
   bool optimize;
@@ -204,7 +220,7 @@ private:
   SundialsNVectorInterface nvector_backend() {
     return SundialsNVectorInterface(*this, suncontext, nvector_type);
   }
-
+  void apply_temporal_filtering(BoutReal internal_time, N_Vector uvec);
   /// SPGMR solver structure
   SUNLinearSolver sun_solver{nullptr};
   /// Solver for implicit stages
diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index eb807e6740..4416af58d4 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -126,6 +126,22 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
       rightprec((*options)["rightprec"]
                     .doc("Use right preconditioning instead of left preconditioning")
                     .withDefault(false)),
+      use_temporal_filtering((*options)["use_temporal_filtering"]
+                             .doc("Use temporal filtering of solution")
+                             .withDefault(false)),
+      temp_filtering(),
+      filtering_type((*options)["filtering_type"]
+                     .doc("Type of temporal filtering to perform: None, EMA, SRA")
+                     .withDefault(FilteringType::None)),
+      tau_mean((*options)["tau_mean"]
+                .doc("Interval over which means are calculated")
+                .withDefault(10.0)),
+      mean_start_time((*options)["mean_start_time"]
+                      .doc("Time at which averaging is allowed to start")
+                      .withDefault(0.0)),
+      lambda((*options)["lambda"]
+             .doc("Relaxation parameter for temporal filtering")
+             .withDefault(0.01)),
       suncontext(createSUNContext(BoutComm::get())) {
   has_constraints = false; // This solver doesn't have constraints
 
@@ -512,6 +528,14 @@ int ArkodeMRISolver::init() {
     output.write("\tUsing difference quotient approximation for Jacobian\n");
   }
 
+  // Enable temporal filtering if requested
+  if (use_temporal_filtering) {
+    output.write("\tUsing temporal filtering of solution\n");
+    temp_filtering.reset_state();
+    temp_filtering.initialize(uvec);
+    temp_filtering.configure(filtering_type, tau_mean, mean_start_time);
+  }
+
   return 0;
 }
 
@@ -638,6 +662,7 @@ BoutReal ArkodeMRISolver::run(BoutReal tout) {
   if (!monitor_timestep) {
     // Run in normal mode
     flag = ARKodeEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL);
+    apply_temporal_filtering(simtime, uvec);
   } else {
     // Run in single step mode, to call timestep monitors
     BoutReal internal_time;
@@ -652,6 +677,7 @@ BoutReal ArkodeMRISolver::run(BoutReal tout) {
                            internal_time, flag);
         return -1.0;
       }
+      apply_temporal_filtering(internal_time, uvec);
 
       // Call timestep monitor
       call_timestep_monitors(internal_time, internal_time - last_time);
@@ -1067,6 +1093,45 @@ void ArkodeMRISolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolv
   }
 }
 
+void ArkodeMRISolver::apply_temporal_filtering(BoutReal internal_time,
+                                               N_Vector uvec)
+{
+  if (!use_temporal_filtering) {
+    return;
+  }
+
+  // Update the temporal filtering 
+  temp_filtering.update(internal_time, uvec);
+
+  // If no mean is available yet, do nothing
+  if (!temp_filtering.has_mean()) {
+    return;
+  }
+
+  int flag;
+    
+  // Get the current mean vector
+  N_Vector u_mean = temp_filtering.get_mean_vector();
+
+  // Apply the temporal filtering
+  // Gently relax the solution towards the mean
+  // Set u = (1 - lambda) * u + lambda * u_mean
+  N_VLinearSum(1.0 - lambda, uvec, lambda, u_mean, uvec);
+
+  // Reset ARKode with the new filtered state
+  flag = ARKodeReset(arkode_mem, internal_time, uvec);
+  if (flag != ARK_SUCCESS) {
+    throw BoutException("ARKodeReset failed in temporal filtering\n");
+  }
+
+  // For EMA: we keep averaging continuously (no reset).
+  // For SRA: enforce finite averaging windows of length tau_mean
+  // by restarting the averaging window when tau_mean_cur is equal to tau_mean
+  if (filtering_type == FilteringType::SRA && temp_filtering.window_full()) {
+    temp_filtering.restart_window(internal_time);
+  }
+}
+
 #else
 #endif // SUNDIALS_VERSION CHECK
 #endif // BOUT_HAS_ARKODE
diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
index 066d288b9c..d114114d62 100644
--- a/src/solver/impls/arkode/arkode_mri.hxx
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -43,6 +43,7 @@ RegisterUnavailableSolver
 #else
 
 #include "bout/sundials_backports.hxx"
+#include "temporal_filtering.hxx"
 
 #if SUNDIALS_VERSION_LESS_THAN(7, 2, 0)
 
@@ -145,6 +146,21 @@ private:
   int inner_maxl;
   /// Use right preconditioning instead of left preconditioning
   bool rightprec;
+  /// Temporal filtering of solution
+  /// - Whether to use temporal filtering
+  bool use_temporal_filtering{false};
+  /// Temporal filtering object
+  TemporalFiltering temp_filtering;
+  /// Type of temporal filtering to use
+  FilteringType filtering_type{FilteringType::None};
+  /// Interval over which means are calculated
+  /// - EMA: time scale of the exponential memory
+  /// - SRA: window length of each running-average block
+  BoutReal tau_mean{0.0};
+  /// Time at which averaging starts
+  BoutReal mean_start_time{0.0};
+  /// Relaxation/nudging parameter for temporal filtering
+  BoutReal lambda{0.0};
 
   // Diagnostics from ARKODE MRI
   int nsteps{0};
@@ -165,7 +181,7 @@ private:
   void loop_abstol_values_op(Ind2D i2d, BoutReal* abstolvec_data, int& p,
                              std::vector<BoutReal>& f2dtols,
                              std::vector<BoutReal>& f3dtols, bool bndry);
-
+  void apply_temporal_filtering(BoutReal internal_time, N_Vector uvec);
   /// SPGMR solver structure
   SUNLinearSolver sun_solver{nullptr};
   SUNLinearSolver inner_sun_solver{nullptr};
diff --git a/src/solver/impls/arkode/temporal_filtering.hxx b/src/solver/impls/arkode/temporal_filtering.hxx
new file mode 100644
index 0000000000..c608bb337f
--- /dev/null
+++ b/src/solver/impls/arkode/temporal_filtering.hxx
@@ -0,0 +1,176 @@
+/**************************************************************************
+ * SUNDIALS Temporal Filtering 
+ * NOTE: This is currently in beta testing so use with cautious optimism
+ *
+ **************************************************************************
+ * Copyright 2010-2025 BOUT++ contributors
+ *
+ * Contact: Ben Dudson, dudson2@llnl.gov
+ *
+ * This file is part of BOUT++.
+ *
+ * BOUT++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * BOUT++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with BOUT++.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **************************************************************************/
+
+#ifndef BOUT_TEMPORAL_FILTERING_H
+#define BOUT_TEMPORAL_FILTERING_H
+
+#include "bout/build_defines.hxx"
+#include "bout/sundials_backports.hxx"
+#include "bout/bout_enum_class.hxx"
+#include "bout/bout_types.hxx"
+#include "bout/region.hxx"
+#include <nvector/nvector_parallel.h>
+#include <sundials/sundials_nvector.h>
+#include <sundials/sundials_config.h>
+
+
+// Type of averaging to perform 
+// EMA = Exponential Moving Average
+// SRA = Simple Running Average
+BOUT_ENUM_CLASS(FilteringType, None, EMA, SRA);
+
+#define compare_float(a, b) (std::fabs((a) - (b)) < 1.0e-14)
+
+class TemporalFiltering {
+public:
+  TemporalFiltering() = default;
+
+  void initialize(N_Vector uvec) {
+    ASSERT1(uvec != nullptr);
+    if (!uvecmean) {
+      uvecmean = N_VClone(uvec);
+    }
+
+    // Initial mean = initial state
+    N_VScale(1.0, uvec, uvecmean);
+    reset_state();
+  }
+
+  void configure(FilteringType type,
+                 BoutReal tau_mean_in,
+                 BoutReal start_time_in) {
+    average_type    = type;
+    tau_mean        = tau_mean_in;
+    mean_start_time = start_time_in;
+
+    if (average_type != FilteringType::None && tau_mean <= 0.0) {
+      throw BoutException("TemporalFiltering: tau_mean must be > 0 when filtering is enabled\n");
+    }
+  }
+
+  void reset_state() {
+    prev_time    = 0.0;
+    tau_mean_cur = 0.0;
+    started      = false;
+  }
+
+  /// Update the internal mean based on current time and solution
+  void update(BoutReal time, N_Vector uvec) {
+    if (average_type == FilteringType::None || uvecmean == nullptr) {
+      return;
+    }
+
+    // Not yet time to start averaging
+    if (!started && compare_float(time, mean_start_time)) {
+      return;
+    }
+
+    // First step of this averaging
+    if (!started) {
+      N_VScale(1.0, uvec, uvecmean);
+      prev_time    = time;
+      tau_mean_cur = 0.0;
+      started      = true;
+      return;
+    }
+
+    BoutReal dt = time - prev_time;
+    if (compare_float(dt, 1.0e-15)) {
+      // just ignore if this ever happens
+      return;
+    }
+
+    tau_mean_cur += dt;
+
+    if (average_type == FilteringType::EMA) {
+      // Exponential moving average with timescale tau_mean
+      // alpha = dt / (tau_mean + dt)    (stable for dt << tau_mean)
+      // alpha = 1 - exp(-dt / tau_mean) (exact integration) -- not yet implemented
+      BoutReal alpha;
+      if(100.0*dt > tau_mean)
+        alpha = -expm1(-dt / tau_mean);
+      else
+        alpha = dt / (tau_mean + dt);
+
+      N_VLinearSum(1.0 - alpha, uvecmean, alpha, uvec, uvecmean);
+    } else if (average_type == FilteringType::SRA) {
+      // Simple running average over this window:
+      // u_mean_new = (T_old * u_mean_old + dt * u) / (T_old + dt)
+      BoutReal Told = tau_mean_cur - dt;
+      if (Told <= 0.0) {
+        // First effective dt in this window: mean = current state
+        N_VScale(1.0, uvec, uvecmean);
+      } else {
+        N_VLinearSum(Told / tau_mean_cur, uvecmean,
+                     dt   / tau_mean_cur, uvec,     uvecmean);
+      }
+    }
+
+    prev_time = time;
+  }
+
+  /// Do we have a usable mean?
+  bool has_mean() const {
+    return started && (uvecmean != nullptr);
+  }
+
+  /// For SRA: has this window reached at least tau_mean in duration?
+  bool window_full() const {
+    return (average_type == FilteringType::SRA) &&
+           (started && tau_mean_cur >= tau_mean);
+  }
+
+  /// Restart the averaging window (used only for SRA finite-memory behavior)
+  void restart_window(BoutReal current_time) {
+    started       = false;
+    tau_mean_cur  = 0.0;
+    mean_start_time = current_time; // next window starts from "now"
+  }
+
+  N_Vector get_mean_vector() const { return uvecmean; }
+
+  ~TemporalFiltering() {
+    if (uvecmean) {
+      N_VDestroy(uvecmean);
+    }
+  }
+
+private:
+  FilteringType average_type{FilteringType::None};
+  N_Vector uvecmean{nullptr};
+
+  BoutReal tau_mean{0.0};
+  BoutReal mean_start_time{0.0};
+  BoutReal prev_time{0.0};
+
+  /// Time accumulated in the current averaging window
+  BoutReal tau_mean_cur{0.0};
+
+  /// Has this averaging window been started at all?
+  bool started{false};
+};
+
+#endif // BOUT_TEMPORAL_FILTERING_H
\ No newline at end of file
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index d3441ad959..36115d2b1e 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -166,6 +166,23 @@ CvodeSolver::CvodeSolver(Options* opts)
               .doc("Factor by which the Krylov linear solver’s convergence test constant "
                    "is reduced from the nonlinear solver test constant.")
               .withDefault(0.05)),
+      use_temporal_filtering((*options)["use_temporal_filtering"]
+                             .doc("Use temporal filtering of solution")
+                             .withDefault(false)),
+      temp_filtering(),
+      filtering_type((*options)["filtering_type"]
+                     .doc("Type of temporal filtering to perform: None, EMA, SRA")
+                     .withDefault(FilteringType::None)),
+      tau_mean((*options)["tau_mean"]
+                .doc("Interval over which means are calculated")
+                .withDefault(10.0)),
+      mean_start_time((*options)["mean_start_time"]
+                      .doc("Time at which averaging is allowed to start")
+                      .withDefault(0.0)),
+      lambda((*options)["lambda"]
+             .doc("Relaxation parameter for temporal filtering")
+             .withDefault(0.01)),
+
       suncontext(createSUNContext(BoutComm::get())) {
   has_constraints = false; // This solver doesn't have constraints
   canReset = true;
@@ -555,6 +572,14 @@ int CvodeSolver::init() {
     throw BoutException("CVodeSetEpsLin failed\n");
   }
 
+  // Enable temporal filtering if requested
+  if (use_temporal_filtering) {
+    output.write("\tUsing temporal filtering of solution\n");
+    temp_filtering.reset_state();
+    temp_filtering.initialize(uvec);
+    temp_filtering.configure(filtering_type, tau_mean, mean_start_time);
+  }
+
   cvode_initialised = true;
 
   return 0;
@@ -694,6 +719,7 @@ BoutReal CvodeSolver::run(BoutReal tout) {
   if (!monitor_timestep) {
     // Run in normal mode
     flag = CVode(cvode_mem, tout, uvec, &simtime, CV_NORMAL);
+    apply_temporal_filtering(simtime, uvec);
   } else {
     // Run in single step mode, to call timestep monitors
     BoutReal internal_time;
@@ -707,6 +733,7 @@ BoutReal CvodeSolver::run(BoutReal tout) {
         throw BoutException("ERROR CVODE solve failed at t = {:e}, flag = {:d}\n",
                             internal_time, flag);
       }
+      apply_temporal_filtering(internal_time, uvec);
 
       // Call timestep monitor
       call_timestep_monitors(internal_time, internal_time - last_time);
@@ -1019,4 +1046,42 @@ void CvodeSolver::resetInternalFields() {
     throw BoutException("CVodeReInit failed\n");
   }
 }
+
+void CvodeSolver::apply_temporal_filtering(BoutReal internal_time,
+                                           N_Vector uvec) {
+  if (!use_temporal_filtering) {
+    return;
+  }
+
+  // Update the temporal filtering
+  temp_filtering.update(internal_time, uvec);
+
+  // If no mean is available yet, do nothing
+  if (!temp_filtering.has_mean()) {
+    return;
+  }
+
+  int flag;
+
+  // Get the current mean vector
+  N_Vector u_mean = temp_filtering.get_mean_vector();
+
+  // Apply the temporal filtering
+  // Gently relax the solution towards the mean
+  // Set u = (1 - lambda) * u + lambda * u_mean
+  N_VLinearSum(1.0 - lambda, uvec, lambda, u_mean, uvec);
+
+  // Reset CVODE with the new filtered state
+  flag = CVodeReInit(cvode_mem, internal_time, uvec);
+  if (flag != CV_SUCCESS) {
+    throw BoutException("CVodeReInit failed in temporal filtering\n");
+  }
+
+  // For EMA: we keep averaging continuously (no reset).
+  // For SRA: enforce finite averaging windows of length tau_mean
+  // by restarting the averaging window when tau_mean_cur is equal to tau_mean
+  if (filtering_type == FilteringType::SRA && temp_filtering.window_full()) {
+    temp_filtering.restart_window(internal_time);
+  }
+}
 #endif
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index c242e4128a..c7f5a03128 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -46,6 +46,7 @@ RegisterUnavailableSolver
 #include "bout/bout_types.hxx"
 #include "bout/region.hxx"
 #include "bout/sundials_backports.hxx"
+#include "../arkode/temporal_filtering.hxx"
 
 #if BOUT_HAS_PETSC
 #include "bout/petsc_preconditioner.hxx"
@@ -160,6 +161,21 @@ private:
   NVectorType nvector_type;
   BoutReal cvode_nonlinear_convergence_coef;
   BoutReal cvode_linear_convergence_coef;
+  /// Temporal filtering of solution
+  /// - Whether to use temporal filtering
+  bool use_temporal_filtering{false};
+  /// Temporal filtering object
+  TemporalFiltering temp_filtering;
+  /// Type of temporal filtering to use
+  FilteringType filtering_type{FilteringType::None};
+  /// Interval over which means are calculated
+  /// - EMA: time scale of the exponential memory
+  /// - SRA: window length of each running-average block
+  BoutReal tau_mean{0.0};
+  /// Time at which averaging starts
+  BoutReal mean_start_time{0.0};
+  /// Relaxation/nudging parameter for temporal filtering
+  BoutReal lambda{0.0};
 
   // Diagnostics from CVODE
   int nsteps{0};
@@ -181,7 +197,7 @@ private:
   SundialsNVectorInterface nvector_backend() {
     return SundialsNVectorInterface(*this, suncontext, nvector_type);
   }
-
+  void apply_temporal_filtering(BoutReal internal_time, N_Vector uvec);
   /// SPGMR solver structure
   SUNLinearSolver sun_solver{nullptr};
   /// Solver for functional iterations for Adams-Moulton
diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
index f5fdb78c23..2b5b91d927 100644
--- a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
@@ -132,6 +132,12 @@ int main(int argc, char** argv) {
   root[sunsolver]["rtol"] = rtol;
   root[sunsolver]["atol"] = atol;
 
+  root[sunsolver]["use_temporal_filtering"] = true;
+  root[sunsolver]["tau_mean"] = 1.0;
+  root[sunsolver]["filtering_type"] = "ema";
+  root[sunsolver]["mean_start_time"] = 0.0;
+  root[sunsolver]["lambda"] = 10.0*rtol;
+
   // Get specific options section for this solver. Can't just use default
   // "solver" section, as we run into problems when solvers use the same
   // name for an option with inconsistent defaults

From 146dd5e48cf8ab401247661f8d7cb77ade26a1a9 Mon Sep 17 00:00:00 2001
From: maggul <mustafaaggul06@gmail.com>
Date: Wed, 26 Nov 2025 19:55:55 -0600
Subject: [PATCH 1819/1827] bug fix

---
 src/solver/impls/arkode/temporal_filtering.hxx | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/solver/impls/arkode/temporal_filtering.hxx b/src/solver/impls/arkode/temporal_filtering.hxx
index c608bb337f..9935d48984 100644
--- a/src/solver/impls/arkode/temporal_filtering.hxx
+++ b/src/solver/impls/arkode/temporal_filtering.hxx
@@ -42,8 +42,6 @@
 // SRA = Simple Running Average
 BOUT_ENUM_CLASS(FilteringType, None, EMA, SRA);
 
-#define compare_float(a, b) (std::fabs((a) - (b)) < 1.0e-14)
-
 class TemporalFiltering {
 public:
   TemporalFiltering() = default;
@@ -84,7 +82,7 @@ public:
     }
 
     // Not yet time to start averaging
-    if (!started && compare_float(time, mean_start_time)) {
+    if (!started && (time + 1.0e-14 < mean_start_time)) {
       return;
     }
 
@@ -98,7 +96,7 @@ public:
     }
 
     BoutReal dt = time - prev_time;
-    if (compare_float(dt, 1.0e-15)) {
+    if (dt <= 1.0e-14) {
       // just ignore if this ever happens
       return;
     }

From d35eb2ab240310ef9639ac512daaaa5cac2f83d8 Mon Sep 17 00:00:00 2001
From: maggul <maggul@mtu.edu>
Date: Tue, 2 Jun 2026 18:53:12 -0500
Subject: [PATCH 1820/1827] print_allstats and new ARKODE functions

---
 src/solver/impls/arkode/arkode.cxx | 52 ++++++++++++++++++++++++++++++
 src/solver/impls/arkode/arkode.hxx | 10 ++++++
 2 files changed, 62 insertions(+)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 51b7f0829d..9e82b8ad8d 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -125,6 +125,18 @@ ArkodeSolver::ArkodeSolver(Options* opts)
               .doc("Set timestep adaptivity function: pid, pi, i, explicit_gustafsson,  "
                    "implicit_gustafsson, imex_gustafsson.")
               .withDefault(AdapMethod::PID)),
+      small_nef((*options)["small_nef"]
+              .doc("Threshold for “multiple” successive error failures")
+              .withDefault(2)),
+      etamxf((*options)["etamxf"]
+              .doc("Maximum step size growth factor upon multiple successive failures")
+              .withDefault(0.3)),
+      eta_min((*options)["eta_min"]
+              .doc("Minimum value of step size growth factor upon a failure")
+              .withDefault(0.1)),
+      mx_growth((*options)["mx_growth"]
+              .doc("Maximum allowed growth factor in step size between consecutive steps")
+              .withDefault(20.0)),
       abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
       reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-5)),
       use_vector_abstol((*options)["use_vector_abstol"]
@@ -157,6 +169,9 @@ ArkodeSolver::ArkodeSolver(Options* opts)
       nvector_type((*options)["nvector"]
                        .doc("N_Vector backend to use: sundials or manyvector")
                        .withDefault(NVectorType::Sundials)),
+      print_allstats((*options)["print_allstats"]
+                         .doc("Print all integrator stats at each evolve call")
+                         .withDefault(false)),
       use_temporal_filtering((*options)["use_temporal_filtering"]
                              .doc("Use temporal filtering of solution")
                              .withDefault(false)),
@@ -516,6 +531,31 @@ int ArkodeSolver::init() {
     temp_filtering.configure(filtering_type, tau_mean, mean_start_time);
   }
 
+  // Specifies the threshold for “multiple” successive error failures 
+  // before the etamxf parameter from ARKodeSetMaxEFailGrowth() is applied.
+  if (ARKodeSetSmallNumEFails(arkode_mem, small_nef) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetSmallNumEFails failed\n");
+  }
+
+  // Specifies the maximum step size growth factor upon multiple 
+  // successive accuracy-based error failures in the solver.
+  if (ARKodeSetMaxEFailGrowth(arkode_mem, etamxf) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetMaxEFailGrowth failed\n");
+  }
+
+  // Specifies the minimum allowed reduction factor in step size 
+  // between step attempts, resulting from a temporal error failure 
+  // in the integration process.
+  if (ARKodeSetMinReduction(arkode_mem, eta_min) != ARK_SUCCESS) {
+    throw BoutException("ARKodeSetMinReduction failed\n");
+  }
+
+  // Specifies the maximum allowed growth factor in step size 
+  // between consecutive steps in the integration process.
+   if (ARKodeSetMaxGrowth(arkode_mem, mx_growth) != ARK_SUCCESS) {
+     throw BoutException("ARKodeSetMaxGrowth failed\n");
+   }
+
 #if ARKODE_OPTIMAL_PARAMS_SUPPORT
   if (optimize) {
     output.write("\tUsing ARKode inbuilt optimization\n");
@@ -606,6 +646,7 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   pre_ncalls = 0;
 
   int flag;
+  int mpi_rank;
   if (!monitor_timestep) {
     // Run in normal mode
     flag = ARKodeEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL);
@@ -634,6 +675,17 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
     simtime = tout;
   }
 
+  if (print_allstats) {
+    bout::globals::mpi->MPI_Comm_rank(BoutComm::get(), &mpi_rank);
+    if (mpi_rank == 0) {
+      flag = ARKodePrintAllStats(arkode_mem, stdout, SUN_OUTPUTFORMAT_TABLE);
+      if (flag != ARK_SUCCESS) {
+        output_error.write("ERROR ARKodePrintAllStats failed with the flag = {:d}\n", flag);
+            return -1.0;
+        }
+    }
+  }
+
   // Copy variables
   backend.copy_state_from_vector(uvec);
   // Call rhs function to get extra variables at this time
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index 3ab3265220..ce3b4d6c0b 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -159,6 +159,14 @@ private:
   BoutReal cfl_frac;
   /// Timestep adaptivity function
   AdapMethod adap_method;
+  /// Threshold for “multiple” successive error failures
+  int small_nef;
+  /// Maximum step size growth factor upon multiple successive failures
+  BoutReal etamxf;
+  /// Minimum value of step size growth factor upon a failure
+  BoutReal eta_min;
+  /// Maximum allowed growth factor in step size between consecutive steps
+  BoutReal mx_growth;
   /// Absolute tolerance
   BoutReal abstol;
   /// Relative tolerance
@@ -183,6 +191,8 @@ private:
   bool use_jacobian;
   /// N_Vector backend to use
   NVectorType nvector_type;
+  /// ARKodePrintAllStats: print all available integrator statistics at the end of the run
+  bool print_allstats;
   /// Temporal filtering of solution
   /// - Whether to use temporal filtering
   bool use_temporal_filtering{false};

From 68d180112904dcab2901f4b944c057bab7559589 Mon Sep 17 00:00:00 2001
From: Mustafa Aggul <maggul@login35.chn.perlmutter.nersc.gov>
Date: Thu, 4 Jun 2026 11:09:33 -0700
Subject: [PATCH 1821/1827] added error_bias

---
 src/solver/impls/arkode/arkode.cxx | 8 ++++++++
 src/solver/impls/arkode/arkode.hxx | 2 ++
 2 files changed, 10 insertions(+)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 9e82b8ad8d..78aa9f4f96 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -137,6 +137,9 @@ ArkodeSolver::ArkodeSolver(Options* opts)
       mx_growth((*options)["mx_growth"]
               .doc("Maximum allowed growth factor in step size between consecutive steps")
               .withDefault(20.0)),
+      error_bias((*options)["error_bias"]
+              .doc("Bias factor to slightly exaggerate the temporal error")
+              .withDefault(1.0)),
       abstol((*options)["atol"].doc("Absolute tolerance").withDefault(1.0e-12)),
       reltol((*options)["rtol"].doc("Relative tolerance").withDefault(1.0e-5)),
       use_vector_abstol((*options)["use_vector_abstol"]
@@ -372,6 +375,11 @@ int ArkodeSolver::init() {
   }
 #endif
 
+  if (SUNAdaptController_SetErrorBias(controller, error_bias)
+      != ARK_SUCCESS) {
+    throw BoutException("SUNAdaptController_SetErrorBias failed\n");
+  }
+
   if (use_vector_abstol) {
     std::vector<BoutReal> f2dtols;
     f2dtols.reserve(f2d.size());
diff --git a/src/solver/impls/arkode/arkode.hxx b/src/solver/impls/arkode/arkode.hxx
index ce3b4d6c0b..d476a6c706 100644
--- a/src/solver/impls/arkode/arkode.hxx
+++ b/src/solver/impls/arkode/arkode.hxx
@@ -167,6 +167,8 @@ private:
   BoutReal eta_min;
   /// Maximum allowed growth factor in step size between consecutive steps
   BoutReal mx_growth;
+  /// Bias factor to slightly exaggerate the temporal error
+  BoutReal error_bias;
   /// Absolute tolerance
   BoutReal abstol;
   /// Relative tolerance

From b7e440e42a2f4bca7b49a34408a5c0bc13f30d94 Mon Sep 17 00:00:00 2001
From: maggul <maggul@mtu.edu>
Date: Thu, 4 Jun 2026 15:05:39 -0500
Subject: [PATCH 1822/1827] changed the default filtering_type to EMA

---
 src/solver/impls/arkode/arkode.cxx     | 6 +++++-
 src/solver/impls/arkode/arkode_mri.cxx | 6 +++++-
 src/solver/impls/cvode/cvode.cxx       | 6 +++++-
 3 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index 78aa9f4f96..d7dbc1d168 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -181,7 +181,7 @@ ArkodeSolver::ArkodeSolver(Options* opts)
       temp_filtering(),
       filtering_type((*options)["filtering_type"]
                      .doc("Type of temporal filtering to perform: None, EMA, SRA")
-                     .withDefault(FilteringType::None)),
+                     .withDefault(FilteringType::EMA)),
       tau_mean((*options)["tau_mean"]
                 .doc("Interval over which means are calculated")
                 .withDefault(10.0)),
@@ -533,6 +533,10 @@ int ArkodeSolver::init() {
 
   // Enable temporal filtering if requested
   if (use_temporal_filtering) {
+    if (filtering_type == FilteringType::None) {
+      filtering_type = FilteringType::EMA;
+      output.write("\tTemporal filtering type is None. Using EMA by default\n");
+    }
     output.write("\tUsing temporal filtering of solution\n");
     temp_filtering.reset_state();
     temp_filtering.initialize(uvec);
diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index 4416af58d4..74b75f8194 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -132,7 +132,7 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
       temp_filtering(),
       filtering_type((*options)["filtering_type"]
                      .doc("Type of temporal filtering to perform: None, EMA, SRA")
-                     .withDefault(FilteringType::None)),
+                     .withDefault(FilteringType::EMA)),
       tau_mean((*options)["tau_mean"]
                 .doc("Interval over which means are calculated")
                 .withDefault(10.0)),
@@ -530,6 +530,10 @@ int ArkodeMRISolver::init() {
 
   // Enable temporal filtering if requested
   if (use_temporal_filtering) {
+    if (filtering_type == FilteringType::None) {
+      filtering_type = FilteringType::EMA;
+      output.write("\tTemporal filtering type is None. Using EMA by default\n");
+    }
     output.write("\tUsing temporal filtering of solution\n");
     temp_filtering.reset_state();
     temp_filtering.initialize(uvec);
diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 36115d2b1e..5f813b0c41 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -172,7 +172,7 @@ CvodeSolver::CvodeSolver(Options* opts)
       temp_filtering(),
       filtering_type((*options)["filtering_type"]
                      .doc("Type of temporal filtering to perform: None, EMA, SRA")
-                     .withDefault(FilteringType::None)),
+                     .withDefault(FilteringType::EMA)),
       tau_mean((*options)["tau_mean"]
                 .doc("Interval over which means are calculated")
                 .withDefault(10.0)),
@@ -574,6 +574,10 @@ int CvodeSolver::init() {
 
   // Enable temporal filtering if requested
   if (use_temporal_filtering) {
+    if (filtering_type == FilteringType::None) {
+      filtering_type = FilteringType::EMA;
+      output.write("\tTemporal filtering type is None. Using EMA by default\n");
+    }
     output.write("\tUsing temporal filtering of solution\n");
     temp_filtering.reset_state();
     temp_filtering.initialize(uvec);

From fd8109d5b01f2e414fc28ffe814b735a0426836e Mon Sep 17 00:00:00 2001
From: maggul <mustafaaggul06@gmail.com>
Date: Thu, 18 Jun 2026 15:23:27 -0500
Subject: [PATCH 1823/1827] macro inconsistancy

---
 src/solver/impls/arkode/arkode.cxx | 27 ++++++++++++++++-----------
 1 file changed, 16 insertions(+), 11 deletions(-)

diff --git a/src/solver/impls/arkode/arkode.cxx b/src/solver/impls/arkode/arkode.cxx
index d7dbc1d168..0c30bbfbc0 100644
--- a/src/solver/impls/arkode/arkode.cxx
+++ b/src/solver/impls/arkode/arkode.cxx
@@ -50,7 +50,7 @@
 #include <arkode/arkode_arkstep.h>
 #include <arkode/arkode_bbdpre.h>
 #include <arkode/arkode_ls.h>
-#if SUNDIALS_CONTROLLER_SUPPORT
+#if ARKODE_CONTROLLER_SUPPORT
 #include <sunadaptcontroller/sunadaptcontroller_imexgus.h>
 #include <sunadaptcontroller/sunadaptcontroller_soderlind.h>
 #endif
@@ -343,6 +343,11 @@ int ArkodeSolver::init() {
   if (ARKodeSetAdaptivityAdjustment(arkode_mem, 0) != ARK_SUCCESS) {
     throw BoutException("ARKodeSetAdaptivityAdjustment failed\n");
   }
+
+  if (SUNAdaptController_SetErrorBias(controller, error_bias)
+      != ARK_SUCCESS) {
+    throw BoutException("SUNAdaptController_SetErrorBias failed\n");
+  }
 #else
   int adap_method_int;
   // Could cast to underlying integer, but this is more explicit
@@ -375,11 +380,6 @@ int ArkodeSolver::init() {
   }
 #endif
 
-  if (SUNAdaptController_SetErrorBias(controller, error_bias)
-      != ARK_SUCCESS) {
-    throw BoutException("SUNAdaptController_SetErrorBias failed\n");
-  }
-
   if (use_vector_abstol) {
     std::vector<BoutReal> f2dtols;
     f2dtols.reserve(f2d.size());
@@ -662,6 +662,11 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   if (!monitor_timestep) {
     // Run in normal mode
     flag = ARKodeEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL);
+    if (flag != ARK_SUCCESS) {
+      output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n",
+                         simtime, flag);
+      return -1.0;
+    }
     apply_temporal_filtering(simtime, uvec);
   } else {
     // Run in single step mode, to call timestep monitors
@@ -685,6 +690,11 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
     // Get output at the desired time
     flag = ARKodeGetDky(arkode_mem, tout, 0, uvec);
     simtime = tout;
+    if (flag != ARK_SUCCESS) {
+      output_error.write("ERROR ARKodeGetDky failed at t = {:e}, flag = {:d}\n",
+                         simtime, flag);
+      return -1.0;
+    }
   }
 
   if (print_allstats) {
@@ -703,11 +713,6 @@ BoutReal ArkodeSolver::run(BoutReal tout) {
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
   // run_diffusive(simtime);
-  if (flag != ARK_SUCCESS) {
-    output_error.write("ERROR ARKODE solve failed at t = {:e}, flag = {:d}\n", simtime,
-                       flag);
-    return -1.0;
-  }
 
   return simtime;
 }

From d5619e245297ba5f49f5ba24c85401783b7dd784 Mon Sep 17 00:00:00 2001
From: Mustafa Aggul <maggul@login26.chn.perlmutter.nersc.gov>
Date: Thu, 18 Jun 2026 14:30:04 -0700
Subject: [PATCH 1824/1827] print_allstats flag for CVODE

---
 src/solver/impls/cvode/cvode.cxx | 37 ++++++++++++++++++++++++++------
 src/solver/impls/cvode/cvode.hxx |  2 ++
 2 files changed, 32 insertions(+), 7 deletions(-)

diff --git a/src/solver/impls/cvode/cvode.cxx b/src/solver/impls/cvode/cvode.cxx
index 5f813b0c41..8979b1aa1b 100644
--- a/src/solver/impls/cvode/cvode.cxx
+++ b/src/solver/impls/cvode/cvode.cxx
@@ -166,6 +166,9 @@ CvodeSolver::CvodeSolver(Options* opts)
               .doc("Factor by which the Krylov linear solver’s convergence test constant "
                    "is reduced from the nonlinear solver test constant.")
               .withDefault(0.05)),
+      print_allstats((*options)["print_allstats"]
+                         .doc("Print all integrator stats at each evolve call")
+                         .withDefault(false)),
       use_temporal_filtering((*options)["use_temporal_filtering"]
                              .doc("Use temporal filtering of solution")
                              .withDefault(false)),
@@ -560,7 +563,9 @@ int CvodeSolver::init() {
 
 #if SUNDIALS_VERSION_MAJOR >= 6
   // Set the RHS function to be used in the nonlinear solver
-  CVodeSetNlsRhsFn(cvode_mem, cvode_nonlinear_rhs);
+  if (CVodeSetNlsRhsFn(cvode_mem, cvode_nonlinear_rhs) != CV_SUCCESS) {
+    throw BoutException("CVodeSetNlsRhsFn failed\n");
+  }
 #endif
 
   // Set internal tolerance factors
@@ -720,14 +725,23 @@ BoutReal CvodeSolver::run(BoutReal tout) {
   pre_ncalls = 0;
 
   int flag;
+  int mpi_rank;
   if (!monitor_timestep) {
     // Run in normal mode
     flag = CVode(cvode_mem, tout, uvec, &simtime, CV_NORMAL);
+    if (flag < 0) {
+      throw BoutException("ERROR CVODE solve failed at t = {:e}, flag = {:d}\n", simtime,
+                          flag);
+    }
     apply_temporal_filtering(simtime, uvec);
   } else {
     // Run in single step mode, to call timestep monitors
     BoutReal internal_time;
-    CVodeGetCurrentTime(cvode_mem, &internal_time);
+    flag = CVodeGetCurrentTime(cvode_mem, &internal_time);
+    if (flag != CV_SUCCESS) {
+      throw BoutException("ERROR CVodeGetCurrentTime failed with flag = {:d}\n", flag);
+    }
+
     while (internal_time < tout) {
       // Run another step
       const BoutReal last_time = internal_time;
@@ -744,20 +758,29 @@ BoutReal CvodeSolver::run(BoutReal tout) {
     }
     // Get output at the desired time
     flag = CVodeGetDky(cvode_mem, tout, 0, uvec);
+    if (flag != CV_SUCCESS) {
+      throw BoutException("ERROR CVodeGetDky failed at t = {:e}, flag = {:d}\n", tout,
+                          flag);
+    }
     simtime = tout;
   }
 
+  if (print_allstats) {
+    bout::globals::mpi->MPI_Comm_rank(BoutComm::get(), &mpi_rank);
+    if (mpi_rank == 0) {
+      flag = CVodePrintAllStats(cvode_mem, stdout, SUN_OUTPUTFORMAT_TABLE);
+      if (flag != CV_SUCCESS) {
+        throw BoutException("ERROR CVodePrintAllStats failed with flag = {:d}\n", flag);
+        }
+    }
+  }
+
   // Copy variables
   backend.copy_state_from_vector(uvec);
 
   // Call rhs function to get extra variables at this time
   run_rhs(simtime);
 
-  if (flag < 0) {
-    throw BoutException("ERROR CVODE solve failed at t = {:e}, flag = {:d}\n", simtime,
-                        flag);
-  }
-
   return simtime;
 }
 
diff --git a/src/solver/impls/cvode/cvode.hxx b/src/solver/impls/cvode/cvode.hxx
index c7f5a03128..406ddf0f64 100644
--- a/src/solver/impls/cvode/cvode.hxx
+++ b/src/solver/impls/cvode/cvode.hxx
@@ -161,6 +161,8 @@ private:
   NVectorType nvector_type;
   BoutReal cvode_nonlinear_convergence_coef;
   BoutReal cvode_linear_convergence_coef;
+  /// CVodePrintAllStats: print all available integrator statistics at the end of the run
+  bool print_allstats;
   /// Temporal filtering of solution
   /// - Whether to use temporal filtering
   bool use_temporal_filtering{false};

From 5361963a4edcca2f4f0b1e1ef4ebe5eb4be90467 Mon Sep 17 00:00:00 2001
From: maggul <mustafaaggul06@gmail.com>
Date: Fri, 4 Sep 2026 01:00:12 -0500
Subject: [PATCH 1825/1827] missing f and py placeholder for now

---
 tests/integrated/test-kpr_mri/test_kpr_mri.py | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 tests/integrated/test-kpr_mri/test_kpr_mri.py

diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.py b/tests/integrated/test-kpr_mri/test_kpr_mri.py
new file mode 100644
index 0000000000..90d8e37d0c
--- /dev/null
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.py
@@ -0,0 +1,8 @@
+#!/usr/bin/env python3
+
+#
+# Run the test, check it completed successfully
+# Place holder for now TODO: add a proper test for the KPR MRI module
+#
+def test_kpr_mri():
+    pass
\ No newline at end of file

From 0bd0b8f00ef0a9284187899fee86d2ca1bef48b7 Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 8 Sep 2026 10:32:16 -0700
Subject: [PATCH 1826/1827] Fix MRI integration follow-up issues

---
 include/bout/solver.hxx                       |  4 +-
 src/bout++.cxx                                | 28 +++---
 src/field/globalfield.cxx                     |  2 +
 src/solver/impls/arkode/arkode_mri.cxx        |  4 +-
 src/solver/solver.cxx                         | 89 ++++++++++++-------
 .../integrated/test-kpr_mri/test_kpr_mri.cxx  | 54 ++++++-----
 6 files changed, 106 insertions(+), 75 deletions(-)

diff --git a/include/bout/solver.hxx b/include/bout/solver.hxx
index fffcf0fdda..51983a948b 100644
--- a/include/bout/solver.hxx
+++ b/include/bout/solver.hxx
@@ -563,8 +563,8 @@ protected:
   bool initialised{false};
   /// If calling user RHS for the first time
   bool first_rhs_call{true};
-  bool first_rhs_s_call{false};
-  bool first_rhs_f_call{false};
+  bool first_rhs_s_call{true};
+  bool first_rhs_f_call{true};
 
   /// Current simulation time
   BoutReal simtime{0.0};
diff --git a/src/bout++.cxx b/src/bout++.cxx
index 478f3f1329..b8ea79a702 100644
--- a/src/bout++.cxx
+++ b/src/bout++.cxx
@@ -1035,18 +1035,24 @@ void RunMetrics::outputVars(Options& output_options) const {
 }
 
 void RunMetrics::calculateDerivedMetrics() {
-  // Terrible hack avoid divide-by-zero, needed because SLEPc solver
-  // doesn't call `run_rhs` which increments `ncalls`. Better fix is
-  // change `Solver::addMonitor` API to take a name so that we can
-  // replace `BoutMonitor` with a different implementation. Currently
-  // not possible because `Solver::removeMonitor` needs the pointer to
-  // the specific instance
-  if (ncalls == 0) {
-    return;
+  wtime_per_rhs = 0.0;
+  wtime_per_rhs_e = 0.0;
+  wtime_per_rhs_i = 0.0;
+
+  const auto total_ncalls =
+      (ncalls > 0) ? ncalls : (ncalls_se + ncalls_si + ncalls_fe + ncalls_fi);
+  const auto explicit_ncalls = (ncalls_e > 0) ? ncalls_e : (ncalls_se + ncalls_fe);
+  const auto implicit_ncalls = (ncalls_i > 0) ? ncalls_i : (ncalls_si + ncalls_fi);
+
+  if (total_ncalls > 0) {
+    wtime_per_rhs = wtime / total_ncalls;
+  }
+  if (explicit_ncalls > 0) {
+    wtime_per_rhs_e = wtime / explicit_ncalls;
+  }
+  if (implicit_ncalls > 0) {
+    wtime_per_rhs_i = wtime / implicit_ncalls;
   }
-  wtime_per_rhs = wtime / ncalls;
-  wtime_per_rhs_e = wtime / ncalls_e;
-  wtime_per_rhs_i = wtime / ncalls_i;
 }
 
 void RunMetrics::writeProgress(BoutReal simtime, bool output_split,
diff --git a/src/field/globalfield.cxx b/src/field/globalfield.cxx
index 6bd2fd4dbf..a8c8f3430f 100644
--- a/src/field/globalfield.cxx
+++ b/src/field/globalfield.cxx
@@ -2,6 +2,8 @@
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/globalfield.hxx>
+#include <bout/globals.hxx>
+#include <bout/mpi_wrapper.hxx>
 
 GlobalField::GlobalField(Mesh* m, int proc, int xsize, int ysize, int zsize)
     : mesh(m), data_on_proc(proc), nx(xsize), ny(ysize), nz(zsize) {
diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index 74b75f8194..9639275d3a 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -857,8 +857,8 @@ void ArkodeMRISolver::pre_f(BoutReal t, BoutReal gamma, BoutReal delta, BoutReal
   // Save the solution from F_vars
   save_derivs(zvec);
 
-  pre_Wtime_s += bout::globals::mpi->MPI_Wtime() - tstart;
-  pre_ncalls_s++;
+  pre_Wtime_f += bout::globals::mpi->MPI_Wtime() - tstart;
+  pre_ncalls_f++;
 }
 
 /**************************************************************************
diff --git a/src/solver/solver.cxx b/src/solver/solver.cxx
index c2f725384d..2e62d95527 100644
--- a/src/solver/solver.cxx
+++ b/src/solver/solver.cxx
@@ -1326,7 +1326,7 @@ int Solver::run_rhs_fi(BoutReal t, bool linear) {
 }
 
 int Solver::run_rhs_s(BoutReal t, bool linear) {
-  int status;
+  int status = 0;
 
   Timer timer("rhs");
 
@@ -1336,8 +1336,6 @@ int Solver::run_rhs_s(BoutReal t, bool linear) {
     first_rhs_call = false;
   }
 
-  pre_rhs(t);
-
   // Run both parts
 
   int nv = getLocalN();
@@ -1347,13 +1345,19 @@ int Solver::run_rhs_s(BoutReal t, bool linear) {
 
   save_vars(tmp.begin()); // Copy variables into tmp
   pre_rhs(t);
-  status = model->runRHS_se(t, linear);
+  auto part_status = model->runRHS_se(t, linear);
+  if (status == 0) {
+    status = part_status;
+  }
   post_rhs(t); // Check variables, apply boundary conditions
 
   load_vars(tmp.begin());   // Reset variables
   save_derivs(tmp.begin()); // Save time derivatives
   pre_rhs(t);
-  status = model->runRHS_si(t, linear);
+  part_status = model->runRHS_si(t, linear);
+  if (status == 0) {
+    status = part_status;
+  }
   post_rhs(t);
   save_derivs(tmp2.begin()); // Save time derivatives
   for (BoutReal *t = tmp.begin(), *t2 = tmp2.begin(); t != tmp.end(); ++t, ++t2) {
@@ -1370,7 +1374,7 @@ int Solver::run_rhs_s(BoutReal t, bool linear) {
 }
 
 int Solver::run_rhs_f(BoutReal t, bool linear) {
-  int status;
+  int status = 0;
 
   Timer timer("rhs");
 
@@ -1380,8 +1384,6 @@ int Solver::run_rhs_f(BoutReal t, bool linear) {
     first_rhs_call = false;
   }
 
-  pre_rhs(t);
-
   // Run both parts
 
   int nv = getLocalN();
@@ -1391,13 +1393,19 @@ int Solver::run_rhs_f(BoutReal t, bool linear) {
 
   save_vars(tmp.begin()); // Copy variables into tmp
   pre_rhs(t);
-  status = model->runRHS_fe(t, linear);
+  auto part_status = model->runRHS_fe(t, linear);
+  if (status == 0) {
+    status = part_status;
+  }
   post_rhs(t); // Check variables, apply boundary conditions
 
   load_vars(tmp.begin());   // Reset variables
   save_derivs(tmp.begin()); // Save time derivatives
   pre_rhs(t);
-  status = model->runRHS_fi(t, linear);
+  part_status = model->runRHS_fi(t, linear);
+  if (status == 0) {
+    status = part_status;
+  }
   post_rhs(t);
   save_derivs(tmp2.begin()); // Save time derivatives
   for (BoutReal *t = tmp.begin(), *t2 = tmp2.begin(); t != tmp.end(); ++t, ++t2) {
@@ -1414,7 +1422,7 @@ int Solver::run_rhs_f(BoutReal t, bool linear) {
 }
 
 int Solver::run_rhs(BoutReal t, bool linear) {
-  int status;
+  int status = 0;
 
   Timer timer("rhs");
 
@@ -1429,42 +1437,61 @@ int Solver::run_rhs(BoutReal t, bool linear) {
     // Run all four parts
 
     int nv = getLocalN();
-    // Create temporary arrays for system state
-    Array<BoutReal> tmp(nv);
-    Array<BoutReal> tmp2(nv);
-    Array<BoutReal> tmp3(nv);
+    // Reuse the same state for each MRI sub-RHS so each part sees the same input.
+    Array<BoutReal> state(nv);
+    Array<BoutReal> deriv_sum(nv);
+    Array<BoutReal> deriv_part(nv);
 
-    save_vars(tmp.begin()); // Copy variables into tmp
+    save_vars(state.begin()); // Copy variables into state
 
+    load_vars(state.begin());
     pre_rhs(t);
-    status = model->runRHS_fe(t, linear);
+    auto part_status = model->runRHS_fe(t, linear);
+    if (status == 0) {
+      status = part_status;
+    }
     post_rhs(t);               // Check variables, apply boundary conditions
-    save_derivs(tmp2.begin()); // Save time derivatives
+    save_derivs(deriv_sum.begin()); // Save time derivatives
 
+    load_vars(state.begin());
     pre_rhs(t);
-    status = model->runRHS_fi(t, linear);
+    part_status = model->runRHS_fi(t, linear);
+    if (status == 0) {
+      status = part_status;
+    }
     post_rhs(t);
-    save_derivs(tmp3.begin()); // Save time derivatives
-    for (BoutReal *t3 = tmp3.begin(), *t2 = tmp2.begin(); t3 != tmp3.end(); ++t3, ++t2) {
-      *t3 += *t2;
+    save_derivs(deriv_part.begin()); // Save time derivatives
+    for (BoutReal *sum = deriv_sum.begin(), *part = deriv_part.begin();
+         sum != deriv_sum.end(); ++sum, ++part) {
+      *sum += *part;
     }
 
+    load_vars(state.begin());
     pre_rhs(t);
-    status = model->runRHS_se(t, linear);
+    part_status = model->runRHS_se(t, linear);
+    if (status == 0) {
+      status = part_status;
+    }
     post_rhs(t);
-    save_derivs(tmp2.begin()); // Save time derivatives
-    for (BoutReal *t3 = tmp3.begin(), *t2 = tmp2.begin(); t3 != tmp3.end(); ++t3, ++t2) {
-      *t3 += *t2;
+    save_derivs(deriv_part.begin()); // Save time derivatives
+    for (BoutReal *sum = deriv_sum.begin(), *part = deriv_part.begin();
+         sum != deriv_sum.end(); ++sum, ++part) {
+      *sum += *part;
     }
 
+    load_vars(state.begin());
     pre_rhs(t);
-    status = model->runRHS_si(t, linear);
+    part_status = model->runRHS_si(t, linear);
+    if (status == 0) {
+      status = part_status;
+    }
     post_rhs(t);
-    save_derivs(tmp2.begin()); // Save time derivatives
-    for (BoutReal *t3 = tmp3.begin(), *t2 = tmp2.begin(); t3 != tmp3.end(); ++t3, ++t2) {
-      *t3 += *t2;
+    save_derivs(deriv_part.begin()); // Save time derivatives
+    for (BoutReal *sum = deriv_sum.begin(), *part = deriv_part.begin();
+         sum != deriv_sum.end(); ++sum, ++part) {
+      *sum += *part;
     }
-    load_derivs(tmp3.begin()); // Put back time-derivatives
+    load_derivs(deriv_sum.begin()); // Put back time-derivatives
     rhs_ncalls_fe++;
     rhs_ncalls_fi++;
     rhs_ncalls_se++;
diff --git a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
index 2b5b91d927..87670f71fe 100644
--- a/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
+++ b/tests/integrated/test-kpr_mri/test_kpr_mri.cxx
@@ -16,27 +16,27 @@ class TestSolver : public PhysicsModel {
 public:
   Field3D f, g;
 
-  BoutReal e  = 0.5;       /* fast/slow coupling strength */
-  BoutReal G  = -100.0;    /* stiffness at slow time scale */
-  BoutReal w  = 100.0;     /* time-scale separation factor */
+  BoutReal e = 0.5;    /* fast/slow coupling strength */
+  BoutReal G = -100.0; /* stiffness at slow time scale */
+  BoutReal w = 100.0;  /* time-scale separation factor */
 
   int init(bool UNUSED(restarting)) override {
     solver->add(f, "f");
     solver->add(g, "g");
 
-    f = sqrt(3.0/2.0);
+    f = sqrt(3.0 / 2.0);
     g = sqrt(3.0);
-    
+
     setSplitOperatorMRI();
 
     return 0;
   }
 
   int rhs_se(BoutReal t) override {
-  /* fill in the slow explicit RHS function:
-     [-0.5*sin(t)/(2*f)]
-     [      0          ] */
-    ddt(f) = -0.5*sin(t)/(2.0*f(1,1,0));
+    /* fill in the slow explicit RHS function:
+       [-0.5*sin(t)/(2*f)]
+       [      0          ] */
+    ddt(f) = -0.5 * sin(t) / (2.0 * f(1, 1, 0));
     ddt(g) = 0.0;
 
     return 0;
@@ -46,8 +46,10 @@ class TestSolver : public PhysicsModel {
     /* fill in the slow implicit RHS function:
       [G e]*[(-1+f^2-0.5*cos(t))/(2*f)]
       [0 0] [(-2+g^2-cos(w*t))/(2*g)  ]  */
-    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
-    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+    BoutReal tmp1 =
+        (-1.0 + f(1, 1, 0) * f(1, 1, 0) - 0.5 * cos(t)) / (2.0 * f(1, 1, 0));
+    BoutReal tmp2 =
+        (-2.0 + g(1, 1, 0) * g(1, 1, 0) - cos(w * t)) / (2.0 * g(1, 1, 0));
     ddt(f) = G * tmp1 + e * tmp2;
     ddt(g) = 0.0;
 
@@ -63,31 +65,25 @@ class TestSolver : public PhysicsModel {
   }
 
   int rhs_fi(BoutReal t) override {
-  /* fill in the fast implicit RHS function:
-     [0  0]*[(-1+f^2-0.5*cos(t))/(2*f)] + [         0                      ]
-     [e -1] [(-2+g^2-cos(w*t))/(2*g)  ]   [-w*sin(w*t)/(2*sqrt(2+cos(w*t)))] */
-    BoutReal tmp1 = (-1.0 + f(1,1,0) * f(1,1,0) - 0.5*cos(t)) / (2.0 * f(1,1,0));
-    BoutReal tmp2 = (-2.0 + g(1,1,0) * g(1,1,0) - cos(w*t)) / (2.0 * g(1,1,0));
+    /* fill in the fast implicit RHS function:
+       [0  0]*[(-1+f^2-0.5*cos(t))/(2*f)] + [         0                      ]
+       [e -1] [(-2+g^2-cos(w*t))/(2*g)  ]   [-w*sin(w*t)/(2*sqrt(2+cos(w*t)))] */
+    BoutReal tmp1 =
+        (-1.0 + f(1, 1, 0) * f(1, 1, 0) - 0.5 * cos(t)) / (2.0 * f(1, 1, 0));
+    BoutReal tmp2 =
+        (-2.0 + g(1, 1, 0) * g(1, 1, 0) - cos(w * t)) / (2.0 * g(1, 1, 0));
     ddt(f) = 0.0;
-    ddt(g) = e * tmp1 - tmp2 - w * sin(w*t) / (2.0 * sqrt(2.0 + cos(w * t)));
-
-    return 0;
-  }
-
-  int rhs_fi(BoutReal UNUSED(t)) override {
-    ddt(f) = 0.0;
-    ddt(g) = 0.0;
+    ddt(g) = e * tmp1 - tmp2 - w * sin(w * t) / (2.0 * sqrt(2.0 + cos(w * t)));
 
     return 0;
   }
 
-  BoutReal compute_error(BoutReal t)
-  {
+  BoutReal compute_error(BoutReal t) {
     /* Compute the error with the true solution:
      f(t) = sqrt(0.5*cos(t) + 1.0)
      g(t) = sqrt(cos(w*t) + 2.0) */
-    return sqrt( pow(sqrt(0.5*cos(t) + 1.0) - f(1,1,0), 2.0) + 
-                 pow(sqrt(cos(w*t) + 2.0) - g(1,1,0), 2.0));
+    return sqrt(pow(sqrt(0.5 * cos(t) + 1.0) - f(1, 1, 0), 2.0)
+                + pow(sqrt(cos(w * t) + 2.0) - g(1, 1, 0), 2.0));
   }
 
   // Don't need any restarting, or options to control data paths
@@ -124,7 +120,7 @@ int main(int argc, char** argv) {
   std::string sunsolver = "arkode_mri";
   int nout = 100;
   BoutReal timestep = 0.05;
-  BoutReal finaltime = nout*timestep;
+  BoutReal finaltime = nout * timestep;
 
   // Global options
   root["nout"] = nout;

From ad3ba2449399e08b9b867c8310df1a7f7f58ef8d Mon Sep 17 00:00:00 2001
From: Ben Dudson <dudson2@llnl.gov>
Date: Tue, 8 Sep 2026 20:22:07 -0700
Subject: [PATCH 1827/1827] Tidy and fix build

Fix many includes
---
 CMakeLists.txt                                |  2 +
 include/bout/globalindexer.hxx                |  7 +++
 include/bout/hypre_interface.hxx              |  2 -
 include/bout/mesh.hxx                         | 38 +++---------
 src/invert/parderiv/impls/cyclic/cyclic.cxx   | 12 +++-
 .../pardiv/impls/cyclic/pardiv_cyclic.cxx     |  6 +-
 src/mesh/impls/bout/boutmesh.cxx              |  1 +
 src/mesh/mesh.cxx                             |  6 +-
 src/mesh/surfaceiter.cxx                      |  1 +
 src/solver/impls/arkode/arkode_mri.cxx        | 62 +++++++++++--------
 src/solver/impls/arkode/arkode_mri.hxx        |  4 +-
 11 files changed, 73 insertions(+), 68 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 38fba02b97..0d74e9bf90 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -333,6 +333,8 @@ set(BOUT_SOURCES
     ./src/solver/impls/adams_bashforth/adams_bashforth.hxx
     ./src/solver/impls/arkode/arkode.cxx
     ./src/solver/impls/arkode/arkode.hxx
+    ./src/solver/impls/arkode/arkode_mri.cxx
+    ./src/solver/impls/arkode/arkode_mri.hxx
     ./src/solver/impls/cvode/cvode.cxx
     ./src/solver/impls/cvode/cvode.hxx
     ./src/solver/impls/euler/euler.cxx
diff --git a/include/bout/globalindexer.hxx b/include/bout/globalindexer.hxx
index bd4203a092..8fa9c309b5 100644
--- a/include/bout/globalindexer.hxx
+++ b/include/bout/globalindexer.hxx
@@ -1,14 +1,21 @@
 #ifndef BOUT_GLOBALINDEXER_H
 #define BOUT_GLOBALINDEXER_H
 
+#include <bout/array.hxx>
+#include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/mesh.hxx>
+#include <bout/mpi_wrapper.hxx>
 #include <bout/operatorstencil.hxx>
 #include <bout/paralleltransform.hxx>
 #include <bout/region.hxx>
 #include <bout/traits.hxx>
 
+#include <memory>
+#include <set>
+#include <vector>
+
 template <class T>
 class GlobalIndexer;
 
diff --git a/include/bout/hypre_interface.hxx b/include/bout/hypre_interface.hxx
index 3eb652c753..0f1617c5b3 100644
--- a/include/bout/hypre_interface.hxx
+++ b/include/bout/hypre_interface.hxx
@@ -704,7 +704,6 @@ public:
     void setValues(BoutReal value_) {
       CALI_CXX_MARK_FUNCTION;
 
-      TRACE("HypreMatrix setting values at ({}, {})", row, column);
       ASSERT3(!positions.empty());
       std::vector<HYPRE_Complex> values;
       std::transform(
@@ -719,7 +718,6 @@ public:
 
     void addValues(BoutReal value_) {
       CALI_CXX_MARK_FUNCTION;
-      TRACE("HypreMatrix setting values at ({}, {})", row, column);
       ASSERT3(!positions.empty());
       std::vector<HYPRE_Complex> values;
       std::transform(
diff --git a/include/bout/mesh.hxx b/include/bout/mesh.hxx
index b001b8895f..108f68c78e 100644
--- a/include/bout/mesh.hxx
+++ b/include/bout/mesh.hxx
@@ -4,20 +4,8 @@
  * Interface for mesh classes. Contains standard variables and useful
  * routines.
  *
- * Changelog
- * =========
- *
- * 2014-12 Ben Dudson <bd512@york.ac.uk>
- *     * Removing coordinate system into separate
- *       Coordinates class
- *     * Adding index derivative functions from derivs.cxx
- *
- * 2010-06 Ben Dudson, Sean Farley
- *     * Initial version, adapted from GridData class
- *     * Incorporates code from topology.cpp and Communicator
- *
  **************************************************************************
- * Copyright 2010-2025 BOUT++ contributors
+ * Copyright 2010-2026 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
  *
@@ -47,30 +35,19 @@ class Mesh;
 #include "bout/array.hxx"
 #include "bout/bout_enum_class.hxx"
 #include "bout/bout_types.hxx"
+#include "bout/coordinates.hxx" // Coordinates class
 #include "bout/field2d.hxx"
 #include "bout/field3d.hxx"
 #include "bout/field_data.hxx"
-#include "bout/options.hxx"
-
 #include "bout/fieldgroup.hxx"
-
-class BoundaryRegion;
-class BoundaryRegionPar;
-
+#include "bout/generic_factory.hxx"
+#include "bout/index_derivs_interface.hxx"
+#include "bout/mpi_wrapper.hxx"
+#include "bout/options.hxx"
+#include "bout/region.hxx"
 #include "bout/sys/range.hxx" // RangeIterator
-
-#include <bout/griddata.hxx>
-
-#include "bout/coordinates.hxx" // Coordinates class
-
 #include "bout/unused.hxx"
 
-#include "bout/generic_factory.hxx"
-#include <bout/region.hxx>
-
-#include <bout/bout_enum_class.hxx>
-
-#include <list>
 #include <map>
 #include <memory>
 #include <optional>
@@ -83,6 +60,7 @@ namespace bout::boundary {
 class BoundaryRegionFCI;
 }
 class GridDataSource;
+
 class MeshFactory : public Factory<Mesh, MeshFactory, GridDataSource*, Options*> {
 public:
   static constexpr auto type_name = "Mesh";
diff --git a/src/invert/parderiv/impls/cyclic/cyclic.cxx b/src/invert/parderiv/impls/cyclic/cyclic.cxx
index 6f432e3bcc..04b0cc4405 100644
--- a/src/invert/parderiv/impls/cyclic/cyclic.cxx
+++ b/src/invert/parderiv/impls/cyclic/cyclic.cxx
@@ -14,9 +14,9 @@
  *
  *
  **************************************************************************
- * Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+ * Copyright 2010 - 2026 BOUT++ contributors
  *
- * Contact: Ben Dudson, bd512@york.ac.uk
+ * Contact: Ben Dudson, dudson2@llnl.gov
  *
  * This file is part of BOUT++.
  *
@@ -40,12 +40,18 @@
 
 #if not BOUT_USE_METRIC_3D
 
+#include <bout/assert.hxx>
+#include <bout/bout_types.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
+#include <bout/coordinates.hxx>
 #include <bout/cyclic_reduction.hxx>
+#include <bout/dcomplex.hxx>
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
+#include <bout/field3d.hxx>
 #include <bout/globals.hxx>
+#include <bout/mpi_wrapper.hxx>
 #include <bout/surfaceiter.hxx>
 #include <bout/utils.hxx>
 
@@ -69,7 +75,7 @@ const Field3D InvertParCR::solve(const Field3D& f) {
 
   Field3D result = emptyFrom(f).setDirectionY(YDirectionType::Aligned);
 
-  Coordinates* coord = f.getCoordinates();
+  const Coordinates* coord = f.getCoordinates();
 
   Field3D alignedField = toFieldAligned(f, "RGN_NOBNDRY");
 
diff --git a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
index b5aee9d0a1..5a2036cddc 100644
--- a/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
+++ b/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx
@@ -40,12 +40,16 @@
 
 #if not BOUT_USE_METRIC_3D
 
+#include <bout/assert.hxx>
 #include <bout/boutexception.hxx>
 #include <bout/constants.hxx>
+#include <bout/coordinates.hxx>
 #include <bout/cyclic_reduction.hxx>
 #include <bout/derivs.hxx>
 #include <bout/fft.hxx>
+#include <bout/field3d.hxx>
 #include <bout/globals.hxx>
+#include <bout/mpi_wrapper.hxx>
 #include <bout/surfaceiter.hxx>
 #include <bout/utils.hxx>
 
@@ -65,7 +69,7 @@ Field3D InvertParDivCR::solve(const Field3D& f) {
 
   Field3D result = emptyFrom(f).setDirectionY(YDirectionType::Aligned);
 
-  Coordinates* coord = f.getCoordinates();
+  const Coordinates* coord = f.getCoordinates();
 
   Field3D alignedField = toFieldAligned(f, "RGN_NOBNDRY");
 
diff --git a/src/mesh/impls/bout/boutmesh.cxx b/src/mesh/impls/bout/boutmesh.cxx
index 347647b2cd..f3482f4d40 100644
--- a/src/mesh/impls/bout/boutmesh.cxx
+++ b/src/mesh/impls/bout/boutmesh.cxx
@@ -42,6 +42,7 @@
 #include <bout/fieldgroup.hxx>
 #include <bout/globals.hxx>
 #include <bout/griddata.hxx>
+#include <bout/mpi_wrapper.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/options.hxx>
 #include <bout/output.hxx>
diff --git a/src/mesh/mesh.cxx b/src/mesh/mesh.cxx
index 53f8709e79..2517040cd0 100644
--- a/src/mesh/mesh.cxx
+++ b/src/mesh/mesh.cxx
@@ -1,5 +1,5 @@
-#include "bout/assert.hxx"
 #include <bout/array.hxx>
+#include <bout/assert.hxx>
 #include <bout/bout_types.hxx>
 #include <bout/boutcomm.hxx>
 #include <bout/boutexception.hxx>
@@ -12,6 +12,7 @@
 #include <bout/fieldgroup.hxx>
 #include <bout/generic_factory.hxx>
 #include <bout/globals.hxx>
+#include <bout/griddata.hxx>
 #include <bout/mesh.hxx>
 #include <bout/msg_stack.hxx>
 #include <bout/openmpwrap.hxx>
@@ -35,9 +36,6 @@
 #include <utility>
 #include <vector>
 
-#include <bout/boutcomm.hxx>
-#include <bout/output.hxx>
-
 #include "impls/bout/boutmesh.hxx"
 
 namespace fs = std::filesystem;
diff --git a/src/mesh/surfaceiter.cxx b/src/mesh/surfaceiter.cxx
index d687ccd68e..a91b19d503 100644
--- a/src/mesh/surfaceiter.cxx
+++ b/src/mesh/surfaceiter.cxx
@@ -2,6 +2,7 @@
 #include <bout/surfaceiter.hxx>
 
 #include <bout/boutexception.hxx>
+#include <bout/mpi_wrapper.hxx>
 #include <bout/unused.hxx>
 
 int SurfaceIter::ySize() { return m->ySize(xpos); }
diff --git a/src/solver/impls/arkode/arkode_mri.cxx b/src/solver/impls/arkode/arkode_mri.cxx
index 9639275d3a..4029bb622d 100644
--- a/src/solver/impls/arkode/arkode_mri.cxx
+++ b/src/solver/impls/arkode/arkode_mri.cxx
@@ -23,30 +23,40 @@
  *
  **************************************************************************/
 
-#include "bout/build_config.hxx"
+#include "bout/build_defines.hxx"
 
 #include "arkode_mri.hxx"
 
 #if BOUT_HAS_ARKODE
+#include "bout/sundials_backports.hxx"
+#if SUNDIALS_VERSION_AT_LEAST(7, 2, 0)
 
-#include "bout/bout_enum_class.hxx"
+#include "temporal_filtering.hxx"
+
+#include "bout/bout_types.hxx"
 #include "bout/boutcomm.hxx"
 #include "bout/boutexception.hxx"
 #include "bout/field3d.hxx"
+#include "bout/globals.hxx"
 #include "bout/mesh.hxx"
 #include "bout/msg_stack.hxx"
 #include "bout/options.hxx"
 #include "bout/output.hxx"
+#include "bout/solver.hxx"
 #include "bout/unused.hxx"
-#include "bout/utils.hxx"
 
+#include <arkode/arkode.h>
 #include <arkode/arkode_arkstep.h>
 #include <arkode/arkode_bbdpre.h>
+#include <arkode/arkode_mristep.h>
 #include <sundials/sundials_math.h>
 #include <sundials/sundials_types.h>
 
 #include <algorithm>
+#include <iterator>
 #include <numeric>
+#include <string>
+#include <vector>
 
 class Field2D;
 
@@ -127,21 +137,20 @@ ArkodeMRISolver::ArkodeMRISolver(Options* opts)
                     .doc("Use right preconditioning instead of left preconditioning")
                     .withDefault(false)),
       use_temporal_filtering((*options)["use_temporal_filtering"]
-                             .doc("Use temporal filtering of solution")
-                             .withDefault(false)),
-      temp_filtering(),
+                                 .doc("Use temporal filtering of solution")
+                                 .withDefault(false)),
       filtering_type((*options)["filtering_type"]
-                     .doc("Type of temporal filtering to perform: None, EMA, SRA")
-                     .withDefault(FilteringType::EMA)),
+                         .doc("Type of temporal filtering to perform: None, EMA, SRA")
+                         .withDefault(FilteringType::EMA)),
       tau_mean((*options)["tau_mean"]
-                .doc("Interval over which means are calculated")
-                .withDefault(10.0)),
+                   .doc("Interval over which means are calculated")
+                   .withDefault(10.0)),
       mean_start_time((*options)["mean_start_time"]
-                      .doc("Time at which averaging is allowed to start")
-                      .withDefault(0.0)),
+                          .doc("Time at which averaging is allowed to start")
+                          .withDefault(0.0)),
       lambda((*options)["lambda"]
-             .doc("Relaxation parameter for temporal filtering")
-             .withDefault(0.01)),
+                 .doc("Relaxation parameter for temporal filtering")
+                 .withDefault(0.01)),
       suncontext(createSUNContext(BoutComm::get())) {
   has_constraints = false; // This solver doesn't have constraints
 
@@ -206,7 +215,8 @@ int ArkodeMRISolver::init() {
   // Get total problem size
   int neq;
   if (bout::globals::mpi->MPI_Allreduce(&local_N, &neq, 1, MPI_INT, MPI_SUM,
-                                        BoutComm::get())) {
+                                        BoutComm::get())
+      != 0) {
     throw BoutException("Allreduce localN -> GlobalN failed!\n");
   }
 
@@ -258,7 +268,8 @@ int ArkodeMRISolver::init() {
 
   if (fixed_step) {
     // If not given, default to adaptive timestepping
-    const BoutReal inner_fixed_timestep = (*options)["inner_timestep"].withDefault(1.0e-5);
+    const BoutReal inner_fixed_timestep =
+        (*options)["inner_timestep"].withDefault(1.0e-5);
     if (ARKodeSetFixedStep(inner_arkode_mem, inner_fixed_timestep) != ARK_SUCCESS) {
       throw BoutException("ARKodeSetFixedStep failed\n");
     }
@@ -381,7 +392,8 @@ int ArkodeMRISolver::init() {
   //   throw BoutException("ARKodeSetMaxStep failed\n");
   // }
 
-  if (inner_treatment == MRI_Treatment::ImEx or inner_treatment == MRI_Treatment::Implicit) {
+  if (inner_treatment == MRI_Treatment::ImEx
+      or inner_treatment == MRI_Treatment::Implicit) {
     {
       output.write("\tUsing Newton iteration for inner solver\n");
 
@@ -649,17 +661,17 @@ BoutReal ArkodeMRISolver::run(BoutReal tout) {
   pre_Wtime_s = 0.0;
   pre_ncalls_s = 0;
 
-  int flag = ARKodeSetStopTime(arkode_mem, 1.0001*tout);
+  int flag = ARKodeSetStopTime(arkode_mem, 1.0001 * tout);
   if (flag != ARK_SUCCESS) {
     output_error.write("ERROR ARKodeSetStopTime failed at t = {:e}, flag = {:d}\n",
-      simtime, flag);
+                       simtime, flag);
     return -1.0;
   }
 
-  flag = ARKodeSetStopTime(inner_arkode_mem, 1.0001*tout);
+  flag = ARKodeSetStopTime(inner_arkode_mem, 1.0001 * tout);
   if (flag != ARK_SUCCESS) {
     output_error.write("ERROR ARKodeSetStopTime failed at t = {:e}, flag = {:d}\n",
-      simtime, flag);
+                       simtime, flag);
     return -1.0;
   }
 
@@ -1097,14 +1109,12 @@ void ArkodeMRISolver::loop_abstol_values_op(Ind2D UNUSED(i2d), BoutReal* abstolv
   }
 }
 
-void ArkodeMRISolver::apply_temporal_filtering(BoutReal internal_time,
-                                               N_Vector uvec)
-{
+void ArkodeMRISolver::apply_temporal_filtering(BoutReal internal_time, N_Vector uvec) {
   if (!use_temporal_filtering) {
     return;
   }
 
-  // Update the temporal filtering 
+  // Update the temporal filtering
   temp_filtering.update(internal_time, uvec);
 
   // If no mean is available yet, do nothing
@@ -1113,7 +1123,7 @@ void ArkodeMRISolver::apply_temporal_filtering(BoutReal internal_time,
   }
 
   int flag;
-    
+
   // Get the current mean vector
   N_Vector u_mean = temp_filtering.get_mean_vector();
 
diff --git a/src/solver/impls/arkode/arkode_mri.hxx b/src/solver/impls/arkode/arkode_mri.hxx
index d114114d62..db8f81b005 100644
--- a/src/solver/impls/arkode/arkode_mri.hxx
+++ b/src/solver/impls/arkode/arkode_mri.hxx
@@ -29,7 +29,7 @@
 #ifndef BOUT_ARKODE_MRI_SOLVER_H
 #define BOUT_ARKODE_MRI_SOLVER_H
 
-#include "bout/build_config.hxx"
+#include "bout/build_defines.hxx"
 #include "bout/solver.hxx"
 
 #if not BOUT_HAS_ARKODE
@@ -42,8 +42,8 @@ RegisterUnavailableSolver
 
 #else
 
-#include "bout/sundials_backports.hxx"
 #include "temporal_filtering.hxx"
+#include "bout/sundials_backports.hxx"
 
 #if SUNDIALS_VERSION_LESS_THAN(7, 2, 0)